BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor
RpoD [Candidatus Liberibacter asiaticus str. psy62]
         (682 letters)

Database: nr 
           14,124,377 sequences; 4,842,793,630 total letters

Searching..................................................done


Results from round 1


>gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254039966|gb|ACT56762.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 682

 Score = 1397 bits (3616), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 682/682 (100%), Positives = 682/682 (100%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS
Sbjct: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP
Sbjct: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL
Sbjct: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD
Sbjct: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN
Sbjct: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA
Sbjct: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET
Sbjct: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG
Sbjct: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS
Sbjct: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP
Sbjct: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE
Sbjct: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKAIRKLKHPSRSKKLRSFLDG
Sbjct: 661 AKAIRKLKHPSRSKKLRSFLDG 682


>gi|315122849|ref|YP_004063338.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313496251|gb|ADR52850.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 683

 Score = 1094 bits (2830), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 549/687 (79%), Positives = 600/687 (87%), Gaps = 11/687 (1%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M  G+K+NRDSDSEHE+S+D+LVFDFSDDSWKKM+K A+QRGYVT+EELN   P +E S 
Sbjct: 1   MIKGRKKNRDSDSEHENSEDTLVFDFSDDSWKKMLKAAKQRGYVTVEELNTVFPSEEASV 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED-EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           EQ+E+T+AMLSNMGINVVD DDLED EEGSEDSLDL  S  N++V  QKRKD ADRSTDD
Sbjct: 61  EQIEETMAMLSNMGINVVDSDDLEDLEEGSEDSLDLTHSNGNTAVLSQKRKDLADRSTDD 120

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT
Sbjct: 121 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 180

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LLREIIDLEACIGP SK  FF G+E  S   +E+ + +++ D     E  I+S +K SK 
Sbjct: 181 LLREIIDLEACIGPGSKATFFQGSEADSCVNQEEGAPQEKAD----GEDGIKSVSKNSKV 236

Query: 240 DRSKV-----DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +   V     +S  EN + +E  LDEDEDDS HTLSAMEDQLRP+VM AL+EIAE Y++L
Sbjct: 237 ESDHVSSLSDNSAAENGDGEENGLDEDEDDSRHTLSAMEDQLRPQVMSALNEIAESYQKL 296

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
           R LQ+ +   Q DEK  VK + LK +LV+LVGSLSLNQSRIDLLVEQLYDISKRIM NEG
Sbjct: 297 RLLQE-STRRQNDEKYLVKYRELKGRLVELVGSLSLNQSRIDLLVEQLYDISKRIMKNEG 355

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
           ELLRLAQSYGIKRDVFL+R+QG ELDP W S AK F E +WKNFV CE+DSIL+IR++IK
Sbjct: 356 ELLRLAQSYGIKRDVFLDRYQGHELDPEWTSSAKGFSEKKWKNFVDCEMDSILRIRDDIK 415

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I+ ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI
Sbjct: 416 GIASETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 475

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA EKFDWCLGYKFSTY MWWVKQA+TRSIADQS TIRIPVHM + I+KVVR
Sbjct: 476 QEGNIGLMKAVEKFDWCLGYKFSTYGMWWVKQAVTRSIADQSRTIRIPVHMIETINKVVR 535

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           TARRMSN IKREPTP+EIAKKLAMP+E V+KVLKITKEPISLETPIGDEDTSHLGDFIED
Sbjct: 536 TARRMSNTIKREPTPDEIAKKLAMPLERVQKVLKITKEPISLETPIGDEDTSHLGDFIED 595

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNAVSP+DSAIQANLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE
Sbjct: 596 KNAVSPVDSAIQANLRENTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 655

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKAIRKLKHPSRSKKLRSFLD
Sbjct: 656 RIRQIEAKAIRKLKHPSRSKKLRSFLD 682


>gi|222149282|ref|YP_002550239.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
 gi|221736266|gb|ACM37229.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
          Length = 681

 Score =  838 bits (2166), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 437/704 (62%), Positives = 531/704 (75%), Gaps = 47/704 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKD 111
           EQ+EDT+AMLS+MGINVV+ +D ED         EE   +  +LA  A N++V   K+K+
Sbjct: 61  EQIEDTMAMLSDMGINVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKE 119

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
             DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR
Sbjct: 120 PTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWR 178

Query: 172 DELNDGTTLLREIIDLEACI-GPESKGG-FFHGTEGHSYQKREDSSQEKER------DDV 223
           DELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R      DD+
Sbjct: 179 DELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDI 238

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
               GD++   +  +D+                        S  +L+AME +LRP+VM  
Sbjct: 239 TNVGGDMQMPEEEEEDEDE----------------------SNLSLAAMEAELRPQVMET 276

Query: 284 LDEIAEVYRELRSLQDNAVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           LD IA+ Y++LR LQD  V       G        + K LK++L+  V SLSLNQ+RID 
Sbjct: 277 LDLIADTYKKLRKLQDQQVEARLACAGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDS 336

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK+
Sbjct: 337 LVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSVGNLAARGWKD 396

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F   E ++I +IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVI
Sbjct: 397 FAREENNTIREIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVI 456

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 457 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 516

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLE
Sbjct: 517 TIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLE 576

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMN
Sbjct: 577 TPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 636

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 TDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 680


>gi|325293528|ref|YP_004279392.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
 gi|325061381|gb|ADY65072.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
          Length = 684

 Score =  828 bits (2138), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 437/699 (62%), Positives = 530/699 (75%), Gaps = 34/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD----------LASSASNSSVFLQKRK 110
           EQ+EDT+AMLS+MGINV++ +D E+  G  +S D          LA S   +++   K+K
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDAEEAPGEAESDDSDNEESEGGELAPSG-GTALATAKKK 119

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           +  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIW
Sbjct: 120 EPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIW 178

Query: 171 RDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQETEG 228
           RDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R  ++   G
Sbjct: 179 RDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRR-LRAPSG 237

Query: 229 DIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
           D E    V  D       PPE  E D+         S  +L+AME +LRP+VM  LD IA
Sbjct: 238 D-EDVTDVGGDG-----LPPEEEEEDDDE-------SNLSLAAMEAELRPQVMETLDTIA 284

Query: 289 EVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           + Y++LR LQD       A  G        + K LK++L+  V SLSLNQ+R+D LVEQL
Sbjct: 285 DTYKKLRKLQDQQVEARLACTGTLSSGQERRYKDLKDQLITAVKSLSLNQNRVDSLVEQL 344

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           YDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F   E
Sbjct: 345 YDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSIANLAARGWKEFAREE 404

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKK
Sbjct: 405 SNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKK 464

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 465 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 524

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GD
Sbjct: 525 VHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGD 584

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL
Sbjct: 585 EEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 644

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 645 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 683


>gi|15889446|ref|NP_355127.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
 gi|20141718|sp|P33452|RPOD_AGRT5 RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15157308|gb|AAK87912.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
          Length = 684

 Score =  823 bits (2127), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 440/703 (62%), Positives = 530/703 (75%), Gaps = 42/703 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-------------GD-DLEDEEGSEDSLDLASSASNSSVFL 106
           EQ+EDT+AMLS+MGINV++             GD D E+ EG E    LA S   +++  
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDAEEAAPAEDDGDSDNEESEGGE----LAPSG-GTALAT 115

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA
Sbjct: 116 AKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQA 174

Query: 167 LIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQ 224
           LIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R  ++
Sbjct: 175 LIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRR-LR 233

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
              GD E    V  D       PPE  E D+         S  +L+AME +LRP+VM  L
Sbjct: 234 APTGD-EDVTDVGGDG-----LPPEEEEEDDDE-------SNLSLAAMEAELRPQVMETL 280

Query: 285 DEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           D IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ+RID L
Sbjct: 281 DTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSL 340

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           VEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F
Sbjct: 341 VEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEF 400

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS
Sbjct: 401 AREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVIS 460

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 461 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 520

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLET
Sbjct: 521 IRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLET 580

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNT
Sbjct: 581 PVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 640

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 641 DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 683


>gi|150397423|ref|YP_001327890.1| RNA polymerase sigma factor RpoD [Sinorhizobium medicae WSM419]
 gi|150028938|gb|ABR61055.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium medicae
           WSM419]
          Length = 684

 Score =  823 bits (2125), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 435/702 (61%), Positives = 530/702 (75%), Gaps = 40/702 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++D E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEADVEREGAPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLE--------------DEEGSEDSLDLASSASNSSVFL 106
           EQ+EDT++MLS+MGINV++ ++ E              + EG E      + AS +++  
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGGSDDDDSSDDAESEGGE-----LAPASGTALAT 115

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 116 SKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQA 174

Query: 167 LIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           LIIWRDELN+G TLLREIIDLE    GPE+K           +Q  E    E +R   +E
Sbjct: 175 LIIWRDELNEGQTLLREIIDLETTYSGPEAKAA-------PQFQSPEKI--EADRKAAEE 225

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            E   ++ A  + DD + V    + AE +E +    +D+S  +L+AME +LRP+VM  LD
Sbjct: 226 KEKVRKTRAAANDDDITNVGGEGQPAEEEEDD----DDESNLSLAAMEAELRPQVMETLD 281

Query: 286 EIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
            IAE Y++LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LV
Sbjct: 282 VIAETYKKLRKLQDQQVEARLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALV 341

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           EQLYDISKR+  NEG LLRLA+SYG+KR+ FLE++ G ELDP+W+    +     WK F 
Sbjct: 342 EQLYDISKRLTQNEGRLLRLAESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFA 401

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             E  +I  IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+
Sbjct: 402 RAENQTIRDIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISI 461

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TI
Sbjct: 462 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 521

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP
Sbjct: 522 RIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETP 581

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD
Sbjct: 582 VGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 641

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 642 HTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 683


>gi|209550278|ref|YP_002282195.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536034|gb|ACI55969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM2304]
          Length = 685

 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 439/709 (61%), Positives = 526/709 (74%), Gaps = 53/709 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     E+ EG E    LA S S ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGSDEESEGGE----LAPS-SGTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERD 221
           FQA+IIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQAIIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                       A+   DD + V     PPE  E DE         S  +L+AME +LRP
Sbjct: 234 -----------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRP 275

Query: 279 KVMCALDEIAEVYRELRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IAE Y++LR LQD  V      +G        + K LK++L+K V SLSLNQ
Sbjct: 276 QVMETLDTIAETYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELKDELIKAVKSLSLNQ 335

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +   
Sbjct: 336 NRIDALVEQLYDINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAA 395

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             WK F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEAN
Sbjct: 396 RGWKEFARGENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEAN 455

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 456 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 515

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KE
Sbjct: 516 ADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKE 575

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRF
Sbjct: 576 PISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 635

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 684


>gi|227822807|ref|YP_002826779.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
 gi|227341808|gb|ACP26026.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
          Length = 684

 Score =  822 bits (2122), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 435/697 (62%), Positives = 529/697 (75%), Gaps = 30/697 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++D E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEADVEREGTPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA---------SSASNSSVFLQKRKD 111
           EQ+EDT+AMLS+MGINV++ ++ E+  G +D              ++ S +++   K+K+
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEEAEEAAGGDDEDSSDDGESEGGELATVSGTALATGKKKE 120

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
             DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR
Sbjct: 121 PTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWR 179

Query: 172 DELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           DELN+G TLLREIIDLE    GPE+K           +Q  E    E +R   +E E   
Sbjct: 180 DELNEGQTLLREIIDLETTYSGPEAKAA-------PQFQSPEKI--EADRKAAEEKEKTR 230

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           +S    + DD + V    +  E +E +    +D+S  +L+AME +LRP+VM  LD IAE 
Sbjct: 231 KSRVAANDDDITNVGGEGQPVEEEEED----DDESNLSLAAMEAELRPQVMETLDIIAET 286

Query: 291 YRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           Y++LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LVEQLYD
Sbjct: 287 YKKLRKLQDQQVEARLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYD 346

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           ISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F   E  
Sbjct: 347 ISKRLMQNEGRLLRLAESYGVKRDSFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQ 406

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I  IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYT
Sbjct: 407 TIRDIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYT 466

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 467 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 526

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+
Sbjct: 527 MIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEE 586

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE
Sbjct: 587 DSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 646

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 647 VGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 683


>gi|222086540|ref|YP_002545074.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
 gi|221723988|gb|ACM27144.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
          Length = 687

 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 439/706 (62%), Positives = 526/706 (74%), Gaps = 45/706 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVERDGTSDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDE-----------------EGSEDSLDLASSASNSS 103
           EQ+EDT+AMLS+MGINV++ +D+E+                  EG E    LA S + S+
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDVEEAGAATSSDDDDSSDDDNGEGGE----LAPS-TGSA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIGGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGG-FFHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKARR 234

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +   GD         DD + V       E +E + DE     A    AME +LRP+VM
Sbjct: 235 G-RSPSGD---------DDITDVGGEGLPGEEEEEDEDESSLSLA----AMEAELRPQVM 280

Query: 282 CALDEIAEVYRELRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
             LD IAE Y++LR LQD  V      +G        + K LK++LVK V SLSLNQ+RI
Sbjct: 281 TTLDTIAETYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELKDELVKSVKSLSLNQNRI 340

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           D LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     W
Sbjct: 341 DALVEQLYDINKRLVQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGW 400

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRL
Sbjct: 401 KEFAKSENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRL 460

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 461 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 520

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPIS
Sbjct: 521 ARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPIS 580

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIG
Sbjct: 581 LETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 640

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 641 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 686


>gi|86358552|ref|YP_470444.1| RNA polymerase sigma factor RpoD [Rhizobium etli CFN 42]
 gi|86282654|gb|ABC91717.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 685

 Score =  821 bits (2120), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 441/709 (62%), Positives = 525/709 (74%), Gaps = 53/709 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     ED EG E    LA SA  ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGE----LAPSA-GTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                       A+   DD + V     PPE  E DE         S  +L+AME +LRP
Sbjct: 234 -----------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRP 275

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IAE Y++LR LQD       A  G        + K LK++L+K V SLSLNQ
Sbjct: 276 QVMETLDIIAETYKKLRKLQDQQVEQRLAATGTLSSAQERRYKELKDELIKAVKSLSLNQ 335

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +   
Sbjct: 336 NRIDALVEQLYDINKRLVQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAA 395

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             WK F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEAN
Sbjct: 396 RGWKEFAKAENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEAN 455

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 456 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 515

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KE
Sbjct: 516 ADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKE 575

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRF
Sbjct: 576 PISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 635

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 684


>gi|241205658|ref|YP_002976754.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859548|gb|ACS57215.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM1325]
          Length = 685

 Score =  819 bits (2116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 439/706 (62%), Positives = 528/706 (74%), Gaps = 47/706 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     E+ EG E    LA S S ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGSSDDDDAGSDEESEGGE----LAPS-SGTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LAAAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGG-FFHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKLAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                       A+   DD + V      AE +E +    ED+S  +L+AME +LRP+VM
Sbjct: 234 -----------RARSGDDDITDVGGEGLPAEEEEED----EDESNLSLAAMEAELRPQVM 278

Query: 282 CALDEIAEVYRELRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
             LD IAE Y++LR LQD  V      +G        + K LK++L+K V SLSLNQ+RI
Sbjct: 279 ETLDTIAETYKKLRKLQDQQVEQRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQNRI 338

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           D LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     W
Sbjct: 339 DALVEQLYDINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGW 398

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRL
Sbjct: 399 KEFARGENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRL 458

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 459 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 518

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPIS
Sbjct: 519 ARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPIS 578

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIG
Sbjct: 579 LETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 638

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 639 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 684


>gi|190892699|ref|YP_001979241.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190697978|gb|ACE92063.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|327189666|gb|EGE56814.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 685

 Score =  818 bits (2114), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 440/709 (62%), Positives = 525/709 (74%), Gaps = 53/709 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     ED EG E    LA S   ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGE----LAPSG-GTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                       A+   DD + V     PPE  E DE         S  +L+AME +LRP
Sbjct: 234 -----------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRP 275

Query: 279 KVMCALDEIAEVYRELRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IAE Y++LR LQD  V      +G        + K LK++L+K V SLSLNQ
Sbjct: 276 QVMETLDTIAETYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELKDELIKAVKSLSLNQ 335

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +   
Sbjct: 336 NRIDALVEQLYDINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAA 395

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             WK F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEAN
Sbjct: 396 RGWKEFAKGENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEAN 455

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 456 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 515

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KE
Sbjct: 516 ADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKE 575

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRF
Sbjct: 576 PISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 635

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 684


>gi|15966067|ref|NP_386420.1| RNA polymerase sigma factor RpoD [Sinorhizobium meliloti 1021]
 gi|307305622|ref|ZP_07585369.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
 gi|307317625|ref|ZP_07597064.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|7388096|sp|Q59753|RPOD_RHIME RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|1050336|gb|AAA88524.1| sigma factor [Sinorhizobium meliloti]
 gi|15075337|emb|CAC46893.1| RNA polymerase sigma factor transcription regulation protein
           [Sinorhizobium meliloti 1021]
 gi|306896783|gb|EFN27530.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|306902325|gb|EFN32921.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
          Length = 684

 Score =  818 bits (2112), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 433/702 (61%), Positives = 527/702 (75%), Gaps = 40/702 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++D E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEADVEREGAPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--------------EEGSEDSLDLASSASNSSVFL 106
           EQ+EDT++MLS+MGINV++ ++ E+               EG E      + AS +++  
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAAASDDDDGADEGESEGGE-----LAPASGTALAA 115

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 116 SKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQA 174

Query: 167 LIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           LIIWRDELN+G TLLREIIDLE    GPE+K           +Q  E    E +R   +E
Sbjct: 175 LIIWRDELNEGQTLLREIIDLETTYSGPEAKAA-------PQFQSPEKI--EADRKAAEE 225

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            E    +    + DD + V    +  E +E +    +D+S  +L+AME +LRP+VM  LD
Sbjct: 226 KEKVRRTRTAANDDDITNVGGEGQAPEEEEED----DDESNLSLAAMEAELRPQVMETLD 281

Query: 286 EIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
            IAE Y++LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LV
Sbjct: 282 VIAETYKKLRKLQDQQVEARLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALV 341

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           EQLYDISKR+  NEG LLRLA+SYG+KR+ FLE++ G ELDP+W+    +     WK F 
Sbjct: 342 EQLYDISKRLTQNEGRLLRLAESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFA 401

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             E  +I  IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+
Sbjct: 402 RAENQTIRDIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISI 461

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TI
Sbjct: 462 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 521

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP
Sbjct: 522 RIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETP 581

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD
Sbjct: 582 VGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 641

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 642 HTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 683


>gi|1765926|emb|CAA70052.1| RNA polymerase sigma-70 subunit [Rhizobium etli]
          Length = 685

 Score =  816 bits (2109), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 440/709 (62%), Positives = 523/709 (73%), Gaps = 53/709 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     ED EG E    LA SA  ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGE----LAPSA-GTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                       A+   DD + V     PPE  E DE         S  +L+AME +LRP
Sbjct: 234 -----------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRP 275

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IAE Y++LR LQD       A  G        + K LK++L+K V SLSLNQ
Sbjct: 276 QVMETLDIIAETYKKLRKLQDQQVEQRLAATGTLSSAQERRYKELKDELIKAVKSLSLNQ 335

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDI+KR++ NEG LLRLA+SY +KRD FLE+ QG ELDP+W+    +   
Sbjct: 336 NRIDALVEQLYDINKRLVQNEGRLLRLAESYAVKRDSFLEQDQGAELDPNWMKSIGNLAA 395

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             WK F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEAN
Sbjct: 396 RGWKEFAKAENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEAN 455

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 456 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 515

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KE
Sbjct: 516 ADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKE 575

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRF
Sbjct: 576 PISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 635

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 684


>gi|116253144|ref|YP_768982.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           viciae 3841]
 gi|115257792|emb|CAK08890.1| putative RNA polymerase sigma factor RpoD [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 685

 Score =  816 bits (2109), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 438/705 (62%), Positives = 526/705 (74%), Gaps = 45/705 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-------------GDDLEDEEGSEDSLDLASSASNSSVFLQ 107
           EQ+EDT++MLS+MGINV++              DD    +   +  +LA S S +++   
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGSSDDDDAGGDEESEGGELAPS-SGTALATA 119

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQAL
Sbjct: 120 KKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAL 178

Query: 168 IIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQE 225
           IIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R     
Sbjct: 179 IIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKLAEEKEKTR----- 233

Query: 226 TEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                   A+   DD + V     PPE  E DE         S  +L+AME +LRP+VM 
Sbjct: 234 -------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRPQVME 279

Query: 283 ALDEIAEVYRELRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
            LD IAE Y++LR LQD  V      +G        + K LK++L+K V SLSLNQ+RID
Sbjct: 280 TLDTIAETYKKLRKLQDQQVEQRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQNRID 339

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK
Sbjct: 340 ALVEQLYDINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWK 399

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F   E  +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLV
Sbjct: 400 EFARGENTTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLV 459

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 460 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 519

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISL
Sbjct: 520 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 579

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGM
Sbjct: 580 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGM 639

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 640 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 684


>gi|306844486|ref|ZP_07477075.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
 gi|306275097|gb|EFM56853.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
          Length = 672

 Score =  805 bits (2080), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 420/678 (61%), Positives = 519/678 (76%), Gaps = 42/678 (6%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDD--VQETEGDIESAAKVSKDDRSKVDSPPE 249
           PE+K        E    + R+D  Q + RDD  +    GD+        +D + +     
Sbjct: 199 PEAKQAPVIERVEEE--KPRDDRPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL----- 251

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---K 306
                             +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+    
Sbjct: 252 ------------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAAT 293

Query: 307 DEKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            E SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+
Sbjct: 294 GELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESF 353

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET IS
Sbjct: 354 GVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAIS 413

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 414 IGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 473

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I
Sbjct: 474 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEI 533

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+
Sbjct: 534 GREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDA 593

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 594 AIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 653

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 654 LRKLKHPSRSRKLRSFLD 671


>gi|225627926|ref|ZP_03785962.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|256160209|ref|ZP_05457903.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|256255415|ref|ZP_05460951.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|260169148|ref|ZP_05755959.1| RNA polymerase sigma factor RpoD [Brucella sp. F5/99]
 gi|261222619|ref|ZP_05936900.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|261758658|ref|ZP_06002367.1| RNA polymerase sigma factor [Brucella sp. F5/99]
 gi|265998584|ref|ZP_06111141.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|225617089|gb|EEH14135.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|260921203|gb|EEX87856.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|261738642|gb|EEY26638.1| RNA polymerase sigma factor [Brucella sp. F5/99]
 gi|262553208|gb|EEZ09042.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
          Length = 672

 Score =  804 bits (2077), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/676 (61%), Positives = 516/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKKLKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|225852960|ref|YP_002733193.1| RNA polymerase sigma factor RpoD [Brucella melitensis ATCC 23457]
 gi|256263561|ref|ZP_05466093.1| RNA polymerase sigma factor [Brucella melitensis bv. 2 str. 63/9]
 gi|225641325|gb|ACO01239.1| RNA polymerase sigma factor RpoD [Brucella melitensis ATCC 23457]
 gi|263093589|gb|EEZ17614.1| RNA polymerase sigma factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409500|gb|ADZ66565.1| RNA polymerase sigma factor RpoD [Brucella melitensis M28]
 gi|326539207|gb|ADZ87422.1| RNA polymerase sigma factor RpoD [Brucella melitensis M5-90]
          Length = 672

 Score =  804 bits (2076), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/676 (61%), Positives = 516/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNVLLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|17986815|ref|NP_539449.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           16M]
 gi|23502348|ref|NP_698475.1| RNA polymerase sigma factor RpoD [Brucella suis 1330]
 gi|82700292|ref|YP_414866.1| RNA polymerase sigma factor RpoD [Brucella melitensis biovar
           Abortus 2308]
 gi|161619426|ref|YP_001593313.1| RNA polymerase sigma factor RpoD [Brucella canis ATCC 23365]
 gi|189024598|ref|YP_001935366.1| RNA polymerase sigma factor RpoD [Brucella abortus S19]
 gi|237815873|ref|ZP_04594870.1| RNA polymerase sigma factor RpoD [Brucella abortus str. 2308 A]
 gi|254689668|ref|ZP_05152922.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|254694158|ref|ZP_05155986.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697811|ref|ZP_05159639.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254702196|ref|ZP_05164024.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|254714701|ref|ZP_05176512.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|254717762|ref|ZP_05179573.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|254730700|ref|ZP_05189278.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|256045103|ref|ZP_05448004.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114033|ref|ZP_05454810.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|256257919|ref|ZP_05463455.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|256369896|ref|YP_003107407.1| RNA polymerase sigma factor [Brucella microti CCM 4915]
 gi|260546908|ref|ZP_05822647.1| RNA polymerase sigma factor [Brucella abortus NCTC 8038]
 gi|260565297|ref|ZP_05835781.1| RNA polymerase sigma factor [Brucella melitensis bv. 1 str. 16M]
 gi|260566021|ref|ZP_05836491.1| RNA polymerase sigma factor [Brucella suis bv. 4 str. 40]
 gi|260755199|ref|ZP_05867547.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|260758418|ref|ZP_05870766.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|260762244|ref|ZP_05874587.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884215|ref|ZP_05895829.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|261214461|ref|ZP_05928742.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|261219607|ref|ZP_05933888.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|261322495|ref|ZP_05961692.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|261752768|ref|ZP_05996477.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|265991536|ref|ZP_06104093.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995374|ref|ZP_06107931.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|294852799|ref|ZP_06793472.1| RNA polymerase primary sigma factor [Brucella sp. NVSL 07-0026]
 gi|297248755|ref|ZP_06932473.1| RNA polymerase primary sigma factor [Brucella abortus bv. 5 str.
           B3196]
 gi|306843169|ref|ZP_07475787.1| RNA polymerase sigma factor RpoD [Brucella sp. BO2]
 gi|17982448|gb|AAL51713.1| RNA polymerase sigma factor rpod [Brucella melitensis bv. 1 str.
           16M]
 gi|23348329|gb|AAN30390.1| RNA polymerase sigma-70 factor [Brucella suis 1330]
 gi|82616393|emb|CAJ11454.1| Sigma-70 factor family:Sigma-70 factor, region 1.1:Sigma-70 region
           3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70,
           non-essent [Brucella melitensis biovar Abortus 2308]
 gi|161336237|gb|ABX62542.1| RNA polymerase sigma factor rpoD [Brucella canis ATCC 23365]
 gi|189020170|gb|ACD72892.1| RNA polymerase sigma factor [Brucella abortus S19]
 gi|237789171|gb|EEP63382.1| RNA polymerase sigma factor RpoD [Brucella abortus str. 2308 A]
 gi|256000059|gb|ACU48458.1| RNA polymerase sigma factor [Brucella microti CCM 4915]
 gi|260095958|gb|EEW79835.1| RNA polymerase sigma factor [Brucella abortus NCTC 8038]
 gi|260151365|gb|EEW86459.1| RNA polymerase sigma factor [Brucella melitensis bv. 1 str. 16M]
 gi|260155539|gb|EEW90619.1| RNA polymerase sigma factor [Brucella suis bv. 4 str. 40]
 gi|260668736|gb|EEX55676.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|260672676|gb|EEX59497.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675307|gb|EEX62128.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|260873743|gb|EEX80812.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|260916068|gb|EEX82929.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|260924696|gb|EEX91264.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|261295185|gb|EEX98681.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|261742521|gb|EEY30447.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|262766487|gb|EEZ12276.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|263002320|gb|EEZ14895.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|294821388|gb|EFG38387.1| RNA polymerase primary sigma factor [Brucella sp. NVSL 07-0026]
 gi|297175924|gb|EFH35271.1| RNA polymerase primary sigma factor [Brucella abortus bv. 5 str.
           B3196]
 gi|306286647|gb|EFM58210.1| RNA polymerase sigma factor RpoD [Brucella sp. BO2]
          Length = 672

 Score =  804 bits (2076), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/676 (61%), Positives = 516/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|256061534|ref|ZP_05451676.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 gi|261325543|ref|ZP_05964740.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 gi|261301523|gb|EEY05020.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
          Length = 672

 Score =  803 bits (2075), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/676 (61%), Positives = 516/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ L+EQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLIEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|39132|emb|CAA49185.1| vegetative sigma factor [Agrobacterium tumefaciens str. C58]
          Length = 684

 Score =  803 bits (2075), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 430/703 (61%), Positives = 524/703 (74%), Gaps = 42/703 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-------------GD-DLEDEEGSEDSLDLASSASNSSVFL 106
           EQ+EDT+AMLS+MGINV++             GD D E+ EG E    LA S   +++  
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDAEEAAPAEDDGDSDNEESEGGE----LAPSG-GTALAT 115

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            K+K+  DR TDDPVRMYLREMGS+ELLSREG+IAIAKRIEAGR  M++ LCESPLTFQA
Sbjct: 116 AKKKEPTDR-TDDPVRMYLREMGSVELLSREGQIAIAKRIEAGRETMISGLCESPLTFQA 174

Query: 167 LIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQ 224
           LIIWRDELN+GTTL+REIIDLE    GPE+K    F   E     ++    +EK R  ++
Sbjct: 175 LIIWRDELNEGTTLVREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRR-LR 233

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
              GD E    V  D       PPE  E D+         S  +L+AME +LRP+VM  L
Sbjct: 234 GPTGD-EDVTDVGGDG-----LPPEEEEEDDDE-------SNLSLAAMEAELRPQVMETL 280

Query: 285 DEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           D IA+ Y+ +R LQD       A  G        + K LK++L+  V SLSLNQ+RID L
Sbjct: 281 DTIADTYKNVRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSL 340

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           VEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F
Sbjct: 341 VEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEF 400

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS
Sbjct: 401 AREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVIS 460

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 461 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 520

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLET
Sbjct: 521 IRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLET 580

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+GDE+ SHLGDFIEDKNA+ P+D+AIQ  LRETTTRVLASLTP EERVLRM FGIGMNT
Sbjct: 581 PVGDEEDSHLGDFIEDKNALLPIDAAIQGFLRETTTRVLASLTPSEERVLRMPFGIGMNT 640

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVG+QF VTRERIRQIEAKA+R +KHPSRS+KLR+FLD
Sbjct: 641 DHTLEEVGQQFSVTRERIRQIEAKALRNVKHPSRSRKLRTFLD 683


>gi|254719520|ref|ZP_05181331.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|265984525|ref|ZP_06097260.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|306837542|ref|ZP_07470416.1| RNA polymerase sigma factor RpoD [Brucella sp. NF 2653]
 gi|264663117|gb|EEZ33378.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|306407378|gb|EFM63583.1| RNA polymerase sigma factor RpoD [Brucella sp. NF 2653]
          Length = 672

 Score =  803 bits (2074), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/676 (61%), Positives = 516/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E +SI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEANSISRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|62290370|ref|YP_222163.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 1 str.
           9-941]
 gi|254708148|ref|ZP_05169976.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 gi|261315652|ref|ZP_05954849.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 gi|62196502|gb|AAX74802.1| RpoD, RNA polymerase sigma-70 factor [Brucella abortus bv. 1 str.
           9-941]
 gi|261304678|gb|EEY08175.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
          Length = 672

 Score =  803 bits (2074), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/676 (61%), Positives = 516/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDCEEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|148559099|ref|YP_001259363.1| RNA polymerase sigma factor RpoD [Brucella ovis ATCC 25840]
 gi|148370356|gb|ABQ60335.1| RNA polymerase sigma-70 factor [Brucella ovis ATCC 25840]
          Length = 672

 Score =  802 bits (2072), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/676 (61%), Positives = 515/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KL MP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLTMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|163843732|ref|YP_001628136.1| RNA polymerase sigma factor RpoD [Brucella suis ATCC 23445]
 gi|163674455|gb|ABY38566.1| RNA polymerase sigma factor RpoD [Brucella suis ATCC 23445]
          Length = 666

 Score =  801 bits (2070), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/672 (61%), Positives = 514/672 (76%), Gaps = 36/672 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D+ ++  EEG++D  +       +      +K+  DR TDDPVRMYLREMGS+ELLSRE
Sbjct: 80  DDEQDNDREEGNDDEAE--EGGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVELLSRE 136

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESK 196
           GEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    GPE+K
Sbjct: 137 GEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAK 196

Query: 197 -GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E    +      + ++ DD+    GD+        +D + +           
Sbjct: 197 QAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL----------- 245

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDEKSSV 312
                       +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E SS 
Sbjct: 246 ------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGELSSS 293

Query: 313 ---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
              + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G++R+ 
Sbjct: 294 QERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGVRRED 353

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI EFR 
Sbjct: 354 FLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIGEFRR 413

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 414 IVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 473

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTP
Sbjct: 474 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTP 533

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANL
Sbjct: 534 EELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANL 593

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKH
Sbjct: 594 RDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 653

Query: 670 PSRSKKLRSFLD 681
           PSRS+KLRSFLD
Sbjct: 654 PSRSRKLRSFLD 665


>gi|254710518|ref|ZP_05172329.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|256032011|ref|ZP_05445625.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261318089|ref|ZP_05957286.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|265989123|ref|ZP_06101680.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261297312|gb|EEY00809.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|264661320|gb|EEZ31581.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
          Length = 672

 Score =  800 bits (2066), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/676 (61%), Positives = 515/676 (76%), Gaps = 38/676 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 416 EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 475

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 476 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 535

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S LGDFIEDKNA+ P+D+AI
Sbjct: 536 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSLLGDFIEDKNALLPIDAAI 595

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 596 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 655

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 656 KLKHPSRSRKLRSFLD 671


>gi|163761137|ref|ZP_02168214.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
 gi|162281688|gb|EDQ31982.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
          Length = 680

 Score =  799 bits (2064), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 424/687 (61%), Positives = 515/687 (74%), Gaps = 33/687 (4%)

Query: 10  DSDSEHE-DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           D+++E E    D  + D SDD+ KKMIK +++RGYVT++ELNA LP +EV+SEQ+ED ++
Sbjct: 11  DTENEREAGGPDGPLLDLSDDAVKKMIKTSKKRGYVTMDELNAVLPSEEVTSEQIEDILS 70

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ------KRKDSADRSTDDPVR 122
           MLS+MGINVV+ D+  +++ S+D     S     +          K+K+  DR TDDPVR
Sbjct: 71  MLSDMGINVVEEDEASEDKDSDDDSAETSEGGEVATAGGTAVAATKKKEPTDR-TDDPVR 129

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR+ELN+G TLLR
Sbjct: 130 MYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWREELNEGATLLR 189

Query: 183 EIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           EIIDLE    GPE+K    F   E     ++    +EK R            A K   DD
Sbjct: 190 EIIDLETTYSGPEAKAAPQFQSPEKIEADRKVAEEKEKAR------------AEKAKSDD 237

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            + V       E      D+D+D++  +L+AME +LRP+VM  LD IA+ Y++LR LQD 
Sbjct: 238 ITNV-----GGEGQYEEDDDDDDENNLSLAAMEAELRPQVMETLDTIADTYKKLRKLQDQ 292

Query: 301 ------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                 A  G        + K LKE L+  V SLSLNQ+RID LVEQLYDI+KR++ NEG
Sbjct: 293 QVEARLAATGTLSPAQERRYKELKEALITAVKSLSLNQNRIDSLVEQLYDINKRLVSNEG 352

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
            LLRLA+SYG+KRD FL ++ G ELDP+W+    +     WK+F   E  +I  +R EI+
Sbjct: 353 RLLRLAESYGVKRDDFLAQYSGAELDPNWMKSIANLSAKGWKDFAKSESTNIRDLRAEIQ 412

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 413 YLAQETGISISEFRRIVQMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 472

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 473 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 532

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIED
Sbjct: 533 TSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIED 592

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 593 KNAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 652

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 653 RIRQIEAKALRKLKHPSRSRKLRSFLD 679


>gi|239832356|ref|ZP_04680685.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
 gi|239824623|gb|EEQ96191.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
          Length = 672

 Score =  797 bits (2059), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/678 (62%), Positives = 515/678 (75%), Gaps = 42/678 (6%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GD----DLED--EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D    D ED  ++ SE+  DL  S   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREDNSDDDSEEGGDLVESGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRD+LND   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLNDSNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDD--VQETEGDIESAAKVSKDDRSKVDSPPE 249
           PE+K        E    + R+D  Q + RDD  +    GD+    +   +D + +     
Sbjct: 199 PEAKQAPVIERVEEE--KPRDDKPQRRSRDDDDITNVGGDMPVEEEEEDEDEANL----- 251

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---K 306
                             +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+    
Sbjct: 252 ------------------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEGRLAAT 293

Query: 307 DEKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            E SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+
Sbjct: 294 GELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESF 353

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G++R+ FL+ +QG ELDP WV          WK F A E  +I ++R+EI+ ++ ET IS
Sbjct: 354 GVRREEFLKEYQGHELDPKWVERVSTLSARGWKEFAAKEERTIDRLRSEIQMLATETAIS 413

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 414 IGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 473

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I
Sbjct: 474 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEI 533

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+
Sbjct: 534 GREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDA 593

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 594 AIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 653

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 654 LRKLKHPSRSRKLRSFLD 671


>gi|153009018|ref|YP_001370233.1| RNA polymerase sigma factor RpoD [Ochrobactrum anthropi ATCC 49188]
 gi|151560906|gb|ABS14404.1| RNA polymerase, sigma 70 subunit, RpoD [Ochrobactrum anthropi ATCC
           49188]
          Length = 671

 Score =  795 bits (2054), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/677 (61%), Positives = 515/677 (76%), Gaps = 41/677 (6%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLEDE------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ +++      + SE+  DL  S   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREENNDDDSEEGGDLVESGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRD+LND   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLNDSNILLREIIDLETTYAG 198

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDD--VQETEGDIESAAKVSKDDRSKVDSPPEN 250
           PE+K       E    +K  D   ++ RDD  +    GD+ +  +   +D + +      
Sbjct: 199 PEAKQAPV--IERVEEEKPRDDKPQRRRDDDDITNVGGDMPTEEEEEDEDEANL------ 250

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KD 307
                            +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     
Sbjct: 251 -----------------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEGRLAATG 293

Query: 308 EKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           E SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G
Sbjct: 294 ELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFG 353

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           ++R+ FL+ +QG ELDP WV          WK F A E  +I ++R+EI+ ++ ET ISI
Sbjct: 354 VRREEFLKEYQGHELDPKWVERVSTLSARGWKEFAAKEERAIDRLRSEIQMLATETAISI 413

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 414 GEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 473

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I 
Sbjct: 474 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIG 533

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+A
Sbjct: 534 REPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAA 593

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 594 IQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 653

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 654 RKLKHPSRSRKLRSFLD 670


>gi|319408880|emb|CBI82537.1| RNA polymerase sigma factor [Bartonella schoenbuchensis R1]
          Length = 667

 Score =  793 bits (2049), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 424/692 (61%), Positives = 522/692 (75%), Gaps = 44/692 (6%)

Query: 5   KKRNRDSDSEH-EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K + +DS +E  + S DS + DFSDD+ KKMIKLA++ GYVT++ELNA LP + V+SEQ+
Sbjct: 4   KAKQKDSVAETGQVSLDSPLLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSESVTSEQI 63

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSL-----DLASSASNSSVFLQKRKDSADRSTD 118
           EDT+AMLS MGINVVD +D  D E  E+ +     DL  + S S   + K  D+ DR TD
Sbjct: 64  EDTLAMLSEMGINVVDDEDEVDSEPYEEEITIEGGDLVEATSRSIATISK-CDTTDR-TD 121

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+ELN+  
Sbjct: 122 DPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELNEKR 181

Query: 179 TLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
            LLREIIDLE    GPE+K                  +   ER +V++ + ++  ++   
Sbjct: 182 ILLREIIDLEMTYAGPEAK-----------------QAPAIERSEVEKIKEEMPCSSMHD 224

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
            DD ++ D   E+ E DE NL         +L+AME++L P+VM  LD IAE Y +LR L
Sbjct: 225 VDDLAE-DIGVEDDEEDEVNL---------SLAAMENELCPQVMETLDFIAETYVKLRKL 274

Query: 298 QDNAVNG-----QKDEKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           QD  V       ++D  SS    KC  LK  LV+ V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 275 QDQHVESSLADCKEDALSSSQKKKCTQLKADLVQAVKSLSLNQNRIEALVEQLYDINKRL 334

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +H+EG+L RLA +YG+  + FL+ +QGRELD  W++Y    P   WK F   E   I  +
Sbjct: 335 VHSEGKLKRLANNYGVGHEDFLKEYQGRELDADWINYIATLPGSGWKEFSTREAKVIQSL 394

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI+S++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AK+YTNRGLQ
Sbjct: 395 RSEIQSLAQETAISIGEFRRIVTQVQKGEREATIAKKEMVEANLRLVISIAKRYTNRGLQ 454

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 455 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 514

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLG
Sbjct: 515 NKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLG 574

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 575 DFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 634

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 635 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 666


>gi|118591038|ref|ZP_01548438.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118436560|gb|EAV43201.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 662

 Score =  793 bits (2047), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/680 (61%), Positives = 514/680 (75%), Gaps = 36/680 (5%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  +  D  D  + D SD + KKMIK A++RGYVT +ELN  LP ++VSSE++EDT++M
Sbjct: 10  DTQEQSTDGPDGPLLDLSDAAVKKMIKAAKKRGYVTYDELNEVLPSEQVSSEKIEDTMSM 69

Query: 70  LSNMGINVVDGDDLEDEEGSE--DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           LS+MGINV+D D  E EEG E  D  DL + AS +++     K+ ADR TDDPVRMYLRE
Sbjct: 70  LSDMGINVIDSD--EAEEGPEEVDGGDLVA-ASTTALAKSTTKEPADR-TDDPVRMYLRE 125

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLR+IIDL
Sbjct: 126 MGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEAQVLLRDIIDL 185

Query: 188 EACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           EA   GP++K G                      DDV   EG+ E++   S+D  S+   
Sbjct: 186 EATYAGPDAKAGPAVAN-----------------DDVAPGEGNSENSGGASEDTESEDGE 228

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
              + ++DE        +S  +LSAME +L+P V+   D IA+ Y++LR LQD  V  + 
Sbjct: 229 GDGDDDDDEF-------ESNVSLSAMEAELKPGVLETFDNIADNYKKLRRLQDQLVENKL 281

Query: 307 DEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
             K+       + K LKE ++  V SLSLNQ+RID LV QLYDI+KR+M  EG LLRLA 
Sbjct: 282 ANKTLSPSQERRYKKLKEDIIVDVKSLSLNQNRIDALVAQLYDINKRLMGYEGRLLRLAD 341

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
           SY + R  FL+++QG ELDP+W+    +     WKNF+A E +++ ++R +I++++ ETG
Sbjct: 342 SYNVDRTDFLKQYQGAELDPNWLRKVANLSTRGWKNFIAKEKETVRELRQDIQTLATETG 401

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 402 LEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 461

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M +
Sbjct: 462 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLH 521

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+
Sbjct: 522 EIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPI 581

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 582 DAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 641

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+KLRSFLD
Sbjct: 642 KALRKLKHPSRSRKLRSFLD 661


>gi|110633818|ref|YP_674026.1| RNA polymerase sigma factor RpoD [Mesorhizobium sp. BNC1]
 gi|110284802|gb|ABG62861.1| RNA polymerase, sigma 38 subunit, RpoS [Chelativorans sp. BNC1]
          Length = 668

 Score =  792 bits (2046), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 425/678 (62%), Positives = 519/678 (76%), Gaps = 37/678 (5%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D  D  + D SDD+ KKMIKLA++RGYVT++ELNA LP  EVSSEQ+EDT+AMLS+MGIN
Sbjct: 14  DGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQIEDTMAMLSDMGIN 73

Query: 77  VVDGDDLEDEEGS-----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           VV+ ++  +E  +     E+S +LA + S  +V    +K+  DR TDDPVRMYLREMGS+
Sbjct: 74  VVEDEEAGEEAEADSAPEEESGELAETGS--AVATVAKKEPTDR-TDDPVRMYLREMGSV 130

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+ELNDG  LLREIIDLEA  
Sbjct: 131 ELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELNDGKILLREIIDLEATY 190

Query: 192 -GPESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            GPE K        E  +    E+    + RDD                DD + V     
Sbjct: 191 AGPEGKQAPVIARPEDVARPAPEEKLMRRARDD----------------DDITNV----- 229

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN---GQK 306
             E+     DE+ED++  +L+AME +L+P  M  LD IA+ Y +LR LQD  V    G  
Sbjct: 230 GGESRPEEDDEEEDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQDQEVESRLGDS 289

Query: 307 DEKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           D+ S+    + K LK++L+K V SLSLN  RI+ LVEQLYDI+KR++ NE +L RLA+SY
Sbjct: 290 DKLSAGQERRSKELKDELIKAVKSLSLNNQRIETLVEQLYDINKRLVQNELKLFRLAESY 349

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G++R+ FL+ +QG ELDP+W S     P+  W++FV  E D+I  +R+EI++++ ETGIS
Sbjct: 350 GVRREDFLKAYQGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSEIQNLAQETGIS 409

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 410 IGEFRRIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 469

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I
Sbjct: 470 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEI 529

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDK+A+ P+D+
Sbjct: 530 GREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKSAILPIDA 589

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 590 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 649

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 650 LRKLKHPSRSRKLRSFLD 667


>gi|13472238|ref|NP_103805.1| RNA polymerase sigma factor RpoD [Mesorhizobium loti MAFF303099]
 gi|14022983|dbj|BAB49591.1| RNA polymerase sigma subunit [Mesorhizobium loti MAFF303099]
          Length = 674

 Score =  791 bits (2043), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/679 (60%), Positives = 515/679 (75%), Gaps = 36/679 (5%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+SEQ+EDT+AMLS+MGINV
Sbjct: 16  ATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINV 75

Query: 78  VDGDDLEDE--------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           V+ D+  +E        +  ED+ +LA     +      +K+  DR TDDPVRMYLREMG
Sbjct: 76  VEDDEQGEEAEAGDTAADAEEDANELAEQTGTAVAATTTKKEPTDR-TDDPVRMYLREMG 134

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLREIIDLEA
Sbjct: 135 SVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELNESKILLREIIDLEA 194

Query: 190 CI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              GPE+K       +    ++ E++ + +E+              +  +DD   V +  
Sbjct: 195 TYAGPEAK-------QAPVVERIEEAPKAEEK-------------PRRGRDDEDDVTNVG 234

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
            +      + +EDED+++ +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 235 ADTRGIGDDDEEDEDEASLSLAAMEAELRPQVMETLDVIADTYKKLRKLQDQQVENRLAA 294

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR++ NEG+LLRLA+S
Sbjct: 295 AGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRLVQNEGKLLRLAES 354

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           YG++R+ FL+ +QG ELDP+W     +     WK F   E D+I  +R EI+ ++ ET I
Sbjct: 355 YGVRREEFLKEYQGSELDPNWTRAIGNLTSRGWKEFTKNEKDAIKDLRAEIQHLATETAI 414

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           SI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 415 SILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 474

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++
Sbjct: 475 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHE 534

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDK A+ P+D
Sbjct: 535 IGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKMAILPID 594

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 595 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 654

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 655 ALRKLKHPSRSRKLRSFLD 673


>gi|260464077|ref|ZP_05812272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
 gi|259030248|gb|EEW31529.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
          Length = 674

 Score =  791 bits (2042), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/683 (60%), Positives = 516/683 (75%), Gaps = 44/683 (6%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+SEQ+EDT+AMLS+MGINV
Sbjct: 16  ATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINV 75

Query: 78  VDGDDLEDE--------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           V+ D+  +E        +  ED+ +LA     +      +K+  DR TDDPVRMYLREMG
Sbjct: 76  VEDDEQGEEAEAGDTAADAEEDANELAEQTGTAVAATTTKKEPTDR-TDDPVRMYLREMG 134

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLREIIDLEA
Sbjct: 135 SVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELNESKILLREIIDLEA 194

Query: 190 CI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              GPE+K       +    ++ E++ + +E+              +  +D+   +    
Sbjct: 195 TYAGPEAK-------QAPVVERIEEAPKAEEK-------------PRRGRDEEEDIT--- 231

Query: 249 ENAENDERNLDEDEDD----SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---- 300
            N   D R L +D+++    ++ +L+AME +LRP+VM  LD IA+ Y++LR LQD     
Sbjct: 232 -NVGADTRGLTDDDEEDEDEASLSLAAMEAELRPQVMETLDVIADTYKKLRKLQDQQVEN 290

Query: 301 --AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
             A  G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR++ NEG+LLR
Sbjct: 291 RLAAAGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRLVQNEGKLLR 350

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           LA+SYG++R+ FL+ +QG ELDP+W     +     WK F   E D+I ++R EI+ ++ 
Sbjct: 351 LAESYGVRREEFLKEYQGSELDPNWTRAIGNLTSRGWKEFTKNEKDAIKELRAEIQHLAT 410

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 411 ETAISILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 470

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+
Sbjct: 471 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ 530

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDK A+
Sbjct: 531 MLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKMAI 590

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 591 LPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 650

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 651 IEAKALRKLKHPSRSRKLRSFLD 673


>gi|319782038|ref|YP_004141514.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167926|gb|ADV11464.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 673

 Score =  789 bits (2037), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/687 (60%), Positives = 512/687 (74%), Gaps = 53/687 (7%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+SEQ+EDT+AMLS+MGINV
Sbjct: 16  ATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINV 75

Query: 78  VDGDDLEDEEGSEDSL------------DLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           V+    +DE+G E               +LA     +      +K+  DR TDDPVRMYL
Sbjct: 76  VE----DDEQGEEPEAADTAADAEEDANELAEQTGTAVAATTTKKEPTDR-TDDPVRMYL 130

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLREII
Sbjct: 131 REMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELNESKILLREII 190

Query: 186 DLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           DLEA   GPE+K       +    ++ E              E  +E   + S+DD   +
Sbjct: 191 DLEATYAGPEAK-------QAPVVERVE--------------EAKVEDKPRRSRDDEDDI 229

Query: 245 DSPPENAENDERNLDEDEDD----SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                N   D R L +D+D+    ++ +L+AME +LRP+VM  LD IA+ Y++LR LQD 
Sbjct: 230 T----NVGADTRGLTDDDDEDEDEASLSLAAMEAELRPQVMETLDVIADTYKKLRKLQDQ 285

Query: 301 ------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                 A  G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR++ NEG
Sbjct: 286 QVENRLAAAGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRLVQNEG 345

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
           +LLRLA+SYG++R+ FL+ +QG ELDP+W     +     WK F   E D+I  +R EI+
Sbjct: 346 KLLRLAESYGVRREEFLKEYQGSELDPNWTRSIGNLTSRGWKEFTKNEKDAIKDLRAEIQ 405

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 406 NLATETAISILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 465

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 466 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 525

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIED
Sbjct: 526 TSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIED 585

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K A+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 586 KMAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 645

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 646 RIRQIEAKALRKLKHPSRSRKLRSFLD 672


>gi|328542886|ref|YP_004302995.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326412632|gb|ADZ69695.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 666

 Score =  785 bits (2026), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/673 (61%), Positives = 514/673 (76%), Gaps = 32/673 (4%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           +  D  + D SD + K+MIK A++RGYVT +ELN  LP ++VSSEQ+EDT++MLS+MGIN
Sbjct: 17  EGQDGPLLDLSDAAVKRMIKAAKKRGYVTYDELNEVLPSEQVSSEQIEDTMSMLSDMGIN 76

Query: 77  VVDGDDLEDE--EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           V+D D++++   +  +D  DL  S   +       ++  DR TDDPVRMYLREMGS+ELL
Sbjct: 77  VIDSDEVDEAAIDDGDDGSDLVPSGGTAVAKTTTTREPTDR-TDDPVRMYLREMGSVELL 135

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GP 193
           SREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  LLR+IIDLEA   GP
Sbjct: 136 SREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKVLLRDIIDLEATYAGP 195

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           ++K G               +  + E D+  ETE   + A   S DD  +       AE 
Sbjct: 196 DAKAG--------------PAGGDGEEDEEGETE---KRAPAASGDDSER------GAEG 232

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS--- 310
           +    +EDE ++  +LSAME +L+P+V+   D +A+ Y++LR LQD  V  +   ++   
Sbjct: 233 EGEEDEEDEFETNVSLSAMEAELKPQVLETFDRVADSYKKLRRLQDQLVENKLANRTLSP 292

Query: 311 --SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               + K LK+++V  V SLSLNQ+RID LVEQLYDI+KR+M  EG LLRLA S+G+ R 
Sbjct: 293 SQERRYKKLKDEIVVDVKSLSLNQNRIDALVEQLYDINKRLMGYEGRLLRLADSHGVDRT 352

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FL+++QG ELDP+W+    +     WKNFVA E D+I ++R EI++++ ETG+ I+EFR
Sbjct: 353 DFLKQYQGAELDPNWLRKVANLATRGWKNFVAKEKDTIRELRQEIQTLATETGLEITEFR 412

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 413 KIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 472

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPT
Sbjct: 473 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPT 532

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQ+N
Sbjct: 533 PEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAIQSN 592

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLK
Sbjct: 593 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+KLRSFLD
Sbjct: 653 HPSRSRKLRSFLD 665


>gi|254504180|ref|ZP_05116331.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
 gi|222440251|gb|EEE46930.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
          Length = 671

 Score =  781 bits (2017), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/682 (60%), Positives = 515/682 (75%), Gaps = 35/682 (5%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  +  D+ D  + D SD + KKMIK A++RGYVT +ELN  LP D+ SSE++ED ++M
Sbjct: 14  DNQEQGADNADGPLLDLSDAAVKKMIKAAKKRGYVTYDELNEVLPSDQNSSEKIEDIMSM 73

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            S+MGINV++ ++ ED     D  +L ++ S++       K+ ADR TDDPVRMYLREMG
Sbjct: 74  FSDMGINVIEAEEAEDAPEEVDGGELVAAKSSAVAKTTTGKEPADR-TDDPVRMYLREMG 132

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLR+IIDLEA
Sbjct: 133 SVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEAQVLLRDIIDLEA 192

Query: 190 CI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              GP++K G                    + DD  E+E   ES ++      ++ D P 
Sbjct: 193 TYAGPDAKAG-----------------PTGDNDDEPESENG-ESGSQ------NQTDGPS 228

Query: 249 ENAENDERNLDEDEDDSAH----TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           EN EN++   D ++DD       +LSAME +L+P+V+   D IA+ Y++LR LQD  V  
Sbjct: 229 ENTENEDSEGDGEDDDDEFESNVSLSAMEAELKPQVLETFDRIADDYKKLRRLQDQLVEN 288

Query: 305 QKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
           +   K+       + K LKE +V  V SLSLNQ+RID LV QLYDI+KR+M  EG LLRL
Sbjct: 289 KLANKTLSPSQERRYKKLKEDIVVDVKSLSLNQNRIDALVAQLYDINKRLMGYEGRLLRL 348

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A SY + R  FL+++QG ELDP+W+    +     WKNF+A E +++ ++R+EI++++ E
Sbjct: 349 ADSYNVDRQDFLKQYQGAELDPNWLRKVANLSTRGWKNFIAKEKENVRELRHEIQTLATE 408

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+ I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 409 TGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 468

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M
Sbjct: 469 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQM 528

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV 
Sbjct: 529 LHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVL 588

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 589 PIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 648

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 649 EAKALRKLKHPSRSRKLRSFLD 670


>gi|307944279|ref|ZP_07659620.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
 gi|307772625|gb|EFO31845.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
          Length = 669

 Score =  778 bits (2010), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/683 (60%), Positives = 509/683 (74%), Gaps = 49/683 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D  D  + D SD + KKMIK A++RG+VT +ELN  LP ++VSSE++ED ++MLS+MGIN
Sbjct: 17  DGPDGPLLDLSDAAVKKMIKAAKKRGFVTYDELNEVLPSEQVSSEKIEDIMSMLSDMGIN 76

Query: 77  VVDGDDLEDEEGSEDSLDLA--SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           V++ D  E EEG  D +D    ++   ++V     K+  DR TDDPVRMYLREMGS+ELL
Sbjct: 77  VIEAD--EAEEGGPDEVDGGELTTTKTTAVAKTTTKEPTDR-TDDPVRMYLREMGSVELL 133

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GP 193
           SREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  LLR+IIDLEA   GP
Sbjct: 134 SREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGNVLLRDIIDLEATYAGP 193

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           ++K G                      DD  + E         S +D ++  SP  +A N
Sbjct: 194 DAKAGPTGAN-----------------DDDPDGE---------SGNDNAEARSP--DAAN 225

Query: 254 DERNLDEDEDD----------SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            ER  D++  +          S  +LSAME +L+P+V+   D IA+ Y++LR LQD  V 
Sbjct: 226 SERGEDQEGAEGDDEDDDEFESNVSLSAMEAELKPQVLETFDNIADNYKKLRRLQDQLVE 285

Query: 304 GQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
            +   K+       + K LKE +V  V SLSLNQ+RID LV QLYDI+KR+M  EG LLR
Sbjct: 286 NKLANKTLSPSQERRYKKLKEDIVVDVKSLSLNQNRIDALVTQLYDINKRLMGYEGRLLR 345

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           LA SY + R  FL+++QG ELDP+W+    +     WKNF+A E +++ ++R EI++++ 
Sbjct: 346 LADSYNVDRSDFLKQYQGAELDPNWLRKVANLSSRGWKNFIAKEKETVRELRQEIQTLAT 405

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETG+ I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 406 ETGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 465

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+
Sbjct: 466 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ 525

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV
Sbjct: 526 MLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAV 585

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 586 LPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 645

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 646 IEAKALRKLKHPSRSRKLRSFLD 668


>gi|121601699|ref|YP_989245.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
 gi|120613876|gb|ABM44477.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
          Length = 666

 Score =  778 bits (2008), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/683 (60%), Positives = 504/683 (73%), Gaps = 53/683 (7%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           S D+   DFSDD+ KKMIKLA++ GYVT++ELNA LP DEV+SEQ+ED + M S MG+NV
Sbjct: 17  SLDNAPLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSDEVTSEQIEDILMMFSEMGVNV 76

Query: 78  VDGDDLEDEEGSEDSL-----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           VD +D  + E  E  +     DL  + S     + KR ++ DR TDDPVRMYLREMG++E
Sbjct: 77  VDDEDEIEAEHYEGEITVEGGDLVEATSREVATIPKR-EATDR-TDDPVRMYLREMGAVE 134

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI- 191
           LLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL +   LLREIIDLE    
Sbjct: 135 LLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELREQRILLREIIDLEMTYA 194

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           GPE+K       E    +K +  +   ++DDV     DI +                E+ 
Sbjct: 195 GPEAKQAPI--IERSEVEKIKKEASPSDKDDVDIIAEDIGA----------------EDD 236

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
           E+DE NL         + +AME++L P++M  L+ IAE Y +LR LQ+  V     E S 
Sbjct: 237 EDDEVNL---------SFAAMENELYPQIMETLNFIAETYVKLRKLQNQHV-----ESSL 282

Query: 312 VKCKV-------------LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
             CK              LK  L++ V SLSLNQ+RI+ LVEQLYDI+KR++HNEG+L R
Sbjct: 283 AACKASDLSSAQKKKSTQLKSDLIQAVKSLSLNQNRIEALVEQLYDINKRLVHNEGKLKR 342

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +A SYGI  + FL+ +QGRELD  WV+Y    P   WK F   EV+ I  +R+EI++++ 
Sbjct: 343 IANSYGIGHEDFLKEYQGRELDSDWVNYIATLPGSGWKEFSTREVEVIRNLRSEIQNLAQ 402

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 403 ETAISIGEFRRIVTQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 462

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+
Sbjct: 463 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ 522

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + ++I REPTPEE++ KL+MP+E V+KVLKI KEPISLETP+GDED SHLGDFIED+NA+
Sbjct: 523 ILHEIGREPTPEELSSKLSMPLEKVQKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNAL 582

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 583 LPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 642

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 643 IEAKALRKLKHPSRSRKLRSFLD 665


>gi|240850913|ref|YP_002972313.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
 gi|240268036|gb|ACS51624.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
          Length = 671

 Score =  775 bits (2002), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/694 (59%), Positives = 520/694 (74%), Gaps = 47/694 (6%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           K+  +++   + S D  + DFSDD+ KKMIKLA++ GYVT++ELNA LP DEV+SEQ+ED
Sbjct: 6   KQKDNAEVTSQASLDGPLLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSDEVTSEQIED 65

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSL-----DLASSASNSSVFLQKRKDSADRSTDDP 120
            +AM S MG+NVVD +D  + E  E+ +     DL  ++S++      +++  DR TDDP
Sbjct: 66  ILAMFSEMGVNVVDDEDEVESENYEEEVTVEGGDLVEASSHAIATTTNKREVTDR-TDDP 124

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDEL +   L
Sbjct: 125 VRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELKEQRIL 184

Query: 181 LREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LREIIDLE    GPE+K                  +   ER +V +TE +     K+S  
Sbjct: 185 LREIIDLETTYAGPEAK-----------------QAPVIERSEVNKTEEE-----KMSSG 222

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAH----TLSAMEDQLRPKVMCALDEIAEVYRELR 295
            R+  +S        ERN+++DE++       +L+AME++L P+VM  LD IA+ Y +LR
Sbjct: 223 IRNMGESA------GERNIEDDEEEDDDDVNLSLAAMENELCPQVMETLDFIAQTYVKLR 276

Query: 296 SLQDNAVNGQKDEK------SSVKCKV--LKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
            LQD  V     E+      SS K K   LK +L++ V SLSLNQ+RI+ LVEQLYDI+K
Sbjct: 277 KLQDQHVESSLAERKEGALTSSQKKKYIQLKGELIQAVKSLSLNQNRIEALVEQLYDINK 336

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           R++HNEG+L R+A SYGI  + FL+ +QGRELD  W++Y    P   W+ F   E   I 
Sbjct: 337 RLIHNEGKLKRIANSYGIGHEDFLKEYQGRELDADWMNYIAALPTPGWREFSMREAKEIQ 396

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           K+R+EI++++ ET ISI EFR IV  V+KGE E++IAKKEMVE+NLRLVIS+AKKYTNRG
Sbjct: 397 KLRSEIQNLAQETAISIGEFRRIVMQVQKGERESTIAKKEMVESNLRLVISIAKKYTNRG 456

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 457 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 516

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SH
Sbjct: 517 TINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSH 576

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 577 LGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQ 636

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 QFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670


>gi|49475878|ref|YP_033919.1| RNA polymerase sigma factor RpoD [Bartonella henselae str.
           Houston-1]
 gi|49238686|emb|CAF27936.1| RNA polymerase sigma factor rpod [Bartonella henselae str.
           Houston-1]
          Length = 667

 Score =  774 bits (1998), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/698 (59%), Positives = 514/698 (73%), Gaps = 49/698 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++   + S DS + DFSDD+ KKM+K+A++ GYVT++ELNA LPPDEV+S
Sbjct: 1   MATKVKQKDNTEVTTQASVDSPLLDFSDDAIKKMVKIAKKNGYVTMDELNAVLPPDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSE---DSLDLASSASNSSVFLQKRKDSADRST 117
           EQ+EDT+AM S MGINVVD +   +    E   +  DL  + SN+ V   KR +  DR T
Sbjct: 61  EQIEDTLAMFSEMGINVVDDEGEAENYEEEVRVEGGDLVEATSNALVTTAKR-ELTDR-T 118

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+EL + 
Sbjct: 119 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELKEQ 178

Query: 178 TTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
             LLREIIDLE    GPE+K                  +   ER +VQ+ + +  S+A  
Sbjct: 179 RILLREIIDLEMTYAGPEAK-----------------QAPVIERSEVQKVKEEKSSSAM- 220

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAH-----TLSAMEDQLRPKVMCALDEIAEVY 291
                        + EN  R++  +EDD        +L+AME++L P+VM  LD IAE Y
Sbjct: 221 ------------RDMENIARDIGVEEDDEEDDDVNLSLAAMENELCPQVMGTLDFIAETY 268

Query: 292 RELRSLQDNAVNGQKDEKSS--------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            +LR LQD  V     E+           KC  LK +LV+ V SLSLNQ+RI+ LVEQLY
Sbjct: 269 VKLRKLQDQHVESSLAERKEGALSPSQRKKCIQLKSELVQAVKSLSLNQNRIESLVEQLY 328

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++HNEG+L R+A +YG+  + FL+ +QGRELD  W++Y        WK F   E 
Sbjct: 329 DINKRLIHNEGKLKRIANNYGVGHEEFLKEYQGRELDADWINYIATLSGRGWKEFSKREA 388

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             I  +R+EI++++ ET ISI EFR IV+ V+KGE E++IAKKEMVEANLRLVIS+AKKY
Sbjct: 389 KEIKTLRSEIQNLAQETAISIGEFRRIVTQVQKGERESTIAKKEMVEANLRLVISIAKKY 448

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 449 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 508

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R++ ++I R+PTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDE
Sbjct: 509 HMIETINKIVRTSRQILHEIGRDPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDE 568

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D SHLGDFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 569 DDSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLE 628

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 629 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 666


>gi|49474476|ref|YP_032518.1| RNA polymerase sigma factor RpoD [Bartonella quintana str.
           Toulouse]
 gi|49239980|emb|CAF26393.1| RNA polymerase sigma factor rpod [Bartonella quintana str.
           Toulouse]
          Length = 670

 Score =  771 bits (1991), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/695 (59%), Positives = 517/695 (74%), Gaps = 40/695 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++ + + S DS + DFSDD+ KKM+KLA++ GYVT++ELNA LPPDEV+S
Sbjct: 1   MATKVKQKDNTEVKGQASVDSPLLDFSDDAIKKMVKLAKKNGYVTMDELNAVLPPDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL-----DLASSASNSSVFLQKRKDSADR 115
           EQ+EDT+AM S MGINVVD +D  + E  E+ +     DL     N+     KR +  DR
Sbjct: 61  EQIEDTLAMFSEMGINVVDDEDEGESEHYEEEVTVEGGDLVEVTRNAIATTTKR-EVTDR 119

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+EL 
Sbjct: 120 -TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELK 178

Query: 176 DGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           +   LLREIIDLE    GPE+K             +R +  + KE      T  D+E   
Sbjct: 179 EQRILLREIIDLEMTYAGPEAKQA--------PVIERSEIGKIKEEKSFSGTR-DMEE-- 227

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
            +++D    +    +  E+D+ NL         +L+AME++L P+VM  LD IAE Y +L
Sbjct: 228 NITRD----IGVEDDEEEDDDVNL---------SLAAMENELCPQVMETLDFIAEAYIKL 274

Query: 295 RSLQDNAVNGQKDEKS------SVKCKV--LKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           R LQD  V     E+       S K K   LK +L++ V SLSLNQ+RI+ LVEQLYDI+
Sbjct: 275 RKLQDQHVESSLAERKEGTLSLSQKKKYIQLKSELIQAVKSLSLNQNRIEALVEQLYDIN 334

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR++HNEG+L R+A +YG+  + FL+ +QGRELD  W++Y        WK F   EV  I
Sbjct: 335 KRLIHNEGKLKRIANNYGVSHEEFLKEYQGRELDADWINYIATLSGRGWKEFSMREVKEI 394

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +R+EI++++ ET ISI EFR IV+ V+KGE E++IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 395 QSLRSEIQNLAQETAISIGEFRRIVTQVQKGERESTIAKKEMVEANLRLVISIAKKYTNR 454

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 455 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 514

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED S
Sbjct: 515 ETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDS 574

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 575 HLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 634

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 635 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 669


>gi|182680201|ref|YP_001834347.1| RNA polymerase sigma factor RpoD [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182636084|gb|ACB96858.1| RNA polymerase, sigma 70 subunit, RpoD family [Beijerinckia indica
           subsp. indica ATCC 9039]
          Length = 685

 Score =  771 bits (1991), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/682 (60%), Positives = 508/682 (74%), Gaps = 37/682 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           DS + D SD + K+MIK+A++RG+VT  ELNA LP +EV+SEQ+ED +AML+ MGINVV+
Sbjct: 20  DSPLLDLSDAAVKRMIKVAKKRGFVTYSELNAVLPSEEVNSEQIEDILAMLNEMGINVVE 79

Query: 80  GDDLEDEEGSEDSL-------DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            ++ + EE  + +        DL   AS S     +  + +DR TDDPVRMYLREMGS+E
Sbjct: 80  SEEQDTEESEDSNEEEESEGGDLVE-ASQSKAVTTRSSEPSDR-TDDPVRMYLREMGSVE 137

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELND   LLR+IIDLEA   
Sbjct: 138 LLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNDSKVLLRDIIDLEAT-- 195

Query: 193 PESKGGFFHGTEGHSYQKRE-DSSQEKERDDVQETEGDIESAAKVSKDDRSK-------V 244
                  + G EG S  K + D++ E++ D+    E    S A ++   R +       +
Sbjct: 196 -------YAGPEGRSSPKLDLDATDEEDPDNPDAPEA--PSTAPLNPPGRLRPAREDGDI 246

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVN 303
           D PP     DE    ED+ +++ +LSAME +L+PKV+   D +A+ Y++LR LQD N  N
Sbjct: 247 DPPPMEEMFDE----EDDMENSVSLSAMEAELKPKVLETFDRVADAYKKLRRLQDQNVEN 302

Query: 304 GQKDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             K+E  +     K K LK+++V  V SLSLNQ+RI+ LVEQLYDI+KR++  E  LLRL
Sbjct: 303 KLKNETLTPAQERKYKTLKKEIVADVKSLSLNQNRIEALVEQLYDINKRLIGQETRLLRL 362

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A+ YG+ R+ FL  +Q  ELDP W+          WK+FVA   D+I  +  EI  ++ E
Sbjct: 363 AEGYGVAREDFLRNYQNSELDPKWLLRVSKLGSRGWKDFVAKAKDTIKDLLGEIHGLATE 422

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+ I EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 423 TGLEIQEFRKIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 482

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M
Sbjct: 483 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQM 542

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ 
Sbjct: 543 LHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAIL 602

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 603 PIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 662

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 663 EAKALRKLKHPSRSRKLRSFLD 684


>gi|158425267|ref|YP_001526559.1| RNA polymerase sigma factor RpoD [Azorhizobium caulinodans ORS 571]
 gi|158332156|dbj|BAF89641.1| sigma-70 [Azorhizobium caulinodans ORS 571]
          Length = 690

 Score =  768 bits (1984), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/682 (59%), Positives = 502/682 (73%), Gaps = 51/682 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D+ D  + D SD + +KMIK A++RGYVT E+LN  +P +EV+SEQ+EDT+AML++MGIN
Sbjct: 42  DAPDGPLLDLSDAAVRKMIKSAKRRGYVTYEQLNEVMPSEEVTSEQIEDTLAMLNDMGIN 101

Query: 77  VVDGDDLE-----------DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           V++ ++ E           DE    DS +LA  +  + V  + + +  +R TDDPVRMYL
Sbjct: 102 VIEAEEAEAEEASEEGETADEPEEVDSGELAEQSPRAVVRSETKSEPGER-TDDPVRMYL 160

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL +G  LLR+II
Sbjct: 161 REMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELTEGRVLLRDII 220

Query: 186 DLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           DLEA   GPE K G                            EG+   A +  +D     
Sbjct: 221 DLEATYAGPEGKAGPV-------------------------IEGETALAPEAGEDGLLND 255

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
            + P +        DED+ +++ +L+AME +++PKV+   + IA+ Y++LR LQD  V  
Sbjct: 256 SAAPGD--------DEDDMENSLSLAAMETEIKPKVLETFERIADNYKKLRRLQDQNVES 307

Query: 305 Q-KDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
           + K+E  S     K K LKE LV  + SLSLNQ+RID LVEQLY+I+KR++  EG LLRL
Sbjct: 308 KLKNETLSPAQERKAKKLKEDLVLDMKSLSLNQARIDSLVEQLYEINKRLVSLEGRLLRL 367

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A+SYG+ RD FL ++QG ELDP W+          WK FVA E D I  +R +I +++ E
Sbjct: 368 AESYGVARDDFLRQYQGYELDPKWLLRVSKLGSKGWKEFVAHEKDGIHTLRGDIHALATE 427

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T + I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 428 TALEIAEFRKIVQMVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 487

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M
Sbjct: 488 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQM 547

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV 
Sbjct: 548 LHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVL 607

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 608 PIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 667

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 668 EAKALRKLKHPSRSRKLRSFLD 689


>gi|163868737|ref|YP_001609951.1| RNA polymerase sigma factor RpoD [Bartonella tribocorum CIP 105476]
 gi|161018398|emb|CAK01956.1| RNA polymerase sigma factor [Bartonella tribocorum CIP 105476]
          Length = 671

 Score =  768 bits (1982), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/697 (59%), Positives = 516/697 (74%), Gaps = 43/697 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++   + S D  + DFSDD+ KKMIKLA++ GYVT++ELNA LP DEV+S
Sbjct: 1   MATKVKQKDNAEVTSQASLDGPLLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL-----DLASSASNSSVFLQKRKDSADR 115
           EQ+ED +AM S MG+NVVD ++  + E  E+ +     DL  ++S++      +++  DR
Sbjct: 61  EQIEDILAMFSEMGVNVVDDENEVESENYEEEITVEGGDLVEASSHAIATTTNKREVTDR 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDEL 
Sbjct: 121 -TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELK 179

Query: 176 DGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG-DIESA 233
           +   LLREIIDLE    GPE+K                  +   ER +V + +G DI S 
Sbjct: 180 EQRILLREIIDLETTYAGPEAK-----------------QAPVIERSEVDKIKGEDISSG 222

Query: 234 AK-VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            + + +D   +     +  ++D+ NL         +L+AME++L P+VM  LD IA+ Y 
Sbjct: 223 IRNIGEDIGERGIEEDDEEDDDDVNL---------SLAAMENELCPQVMETLDFIAQTYV 273

Query: 293 ELRSLQDNAVNGQKDEK------SSVKCKV--LKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           +LR LQD  V     E+      +S K K   LK +L++ V SLSLNQ+RI+ LVEQLYD
Sbjct: 274 KLRKLQDQHVESSLAERKEGALTASQKKKYIQLKGELIQAVKSLSLNQNRIEALVEQLYD 333

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           I+KR++HNEG+L R+A SYGI  D FL  +QGRELD  W++Y    P   WK F   E  
Sbjct: 334 INKRLIHNEGKLKRIANSYGIGHDDFLREYQGRELDADWMNYIATLPAPGWKEFSMREAK 393

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I K+R+EI++++  T ISI EFR IV  V+KGE E++IAKKEMVE+NLRLVIS+AKKYT
Sbjct: 394 EIQKLRSEIQNLAQATAISIGEFRRIVMQVQKGERESTIAKKEMVESNLRLVISIAKKYT 453

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 454 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 513

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED
Sbjct: 514 MIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDED 573

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEE
Sbjct: 574 DSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 633

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 634 VGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670


>gi|319405291|emb|CBI78905.1| RNA polymerase sigma factor [Bartonella sp. AR 15-3]
          Length = 669

 Score =  766 bits (1979), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 405/678 (59%), Positives = 508/678 (74%), Gaps = 41/678 (6%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           S D  + DFSDD+ KKMIKLA++ GYV ++ELNA L  +E++SEQ+ED +AM S MGI+V
Sbjct: 18  SSDGSLLDFSDDAIKKMIKLAQKNGYVMMDELNAALSAEEITSEQIEDILAMFSEMGISV 77

Query: 78  VDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +D +D  + E  E+ + +       A+N +V    +++ ADR TDDPVRMYLREMG++EL
Sbjct: 78  IDDEDEIEAEQYEEEITIEGGDLVEATNYAVATTSKREVADR-TDDPVRMYLREMGAVEL 136

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL +   LLREIIDLE    G
Sbjct: 137 LSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELQEQRILLREIIDLEMTYSG 196

Query: 193 PESKGG-FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K      G+E    ++   SS   + +D++E             D RS+ D   ++ 
Sbjct: 197 PEAKQAPIIDGSEVKKIKEETPSSSMHDVNDLKE-------------DIRSEDDDEEDDE 243

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG---QKDE 308
            N              +L+AME +L P+++  LD IAE Y +LR LQD  V      + E
Sbjct: 244 VN-------------LSLAAMEHELCPQIVETLDFIAETYVKLRKLQDQQVESSLSHRKE 290

Query: 309 K--SSVKCKV---LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           K  SS + K    LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR++H+EG+L RLA +Y
Sbjct: 291 KLLSSAQRKQYTQLKDALIQAVKSLSLNQNRIEALVEQLYDINKRLIHSEGKLKRLASNY 350

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           GI  + FL  +QGRELD  W++Y        WK F  CE  +I  +R+EI++++ ET IS
Sbjct: 351 GIGHEDFLREYQGRELDVDWINYITTLSGRGWKEFSTCEAKAIQSLRSEIQNLAQETAIS 410

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 411 ISEFRRIVTQVQKGEREANIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 470

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I
Sbjct: 471 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEI 530

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLGDFIED+NA+ P+D+
Sbjct: 531 GREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLGDFIEDRNALLPIDA 590

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANLR+TTTR+LASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 591 AIQANLRDTTTRILASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 650

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 651 LRKLKHPSRSRKLRSFLD 668


>gi|90418027|ref|ZP_01225939.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337699|gb|EAS51350.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 668

 Score =  766 bits (1977), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 401/676 (59%), Positives = 498/676 (73%), Gaps = 36/676 (5%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +E + D  + D SDD+ KKMIK A++RG+VT+++LN+ L  ++V+SEQ+ED +  L++MG
Sbjct: 19  NEGAPDGPLLDLSDDAVKKMIKAAKKRGFVTMDKLNSMLSAEDVTSEQIEDMMTNLNDMG 78

Query: 75  INVVDGDDLEDEEGSEDSLDLASS--ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           INVV+ D+  + E   +S +         + V    +K++ DR TDDPVRMYLREMGS+E
Sbjct: 79  INVVESDEEGENEEQSESSESTEVAETGRTQVATTTKKEAGDR-TDDPVRMYLREMGSVE 137

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI- 191
           LLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRDELN+G  +LREI+DLEA   
Sbjct: 138 LLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDELNEGNIMLREIVDLEATYA 197

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           GPE+K       EG                          S   VS        S    A
Sbjct: 198 GPEAKTPTPPAVEG--------------------------SNGSVSGVPNGPPHSTGARA 231

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQ 305
             +E + ++D+ ++  +L+AME ++RP+VM   D+IA+ YR LR LQD       A  G 
Sbjct: 232 PGEEEDEEDDDLENNLSLAAMEAEIRPQVMETFDQIADAYRRLRKLQDQQVENRLAAQGT 291

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                    K LKE+L+  V SLSLNQ+RID LV QLYDI+KR++ NEG LLRLA+S+G+
Sbjct: 292 LSPSQERSYKKLKEELITAVKSLSLNQNRIDALVAQLYDINKRLVGNEGRLLRLAESHGV 351

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           KRD FL  +QG ELDP+W  +  +     W  FV  E + I ++R EI++++ ETG+ I+
Sbjct: 352 KRDEFLNEYQGTELDPNWTRHIANLSGKGWLKFVQAEKEQIKRLRQEIQNLATETGLEIT 411

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 412 EFRRIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 471

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 472 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 531

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 532 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNAILPIDAAI 591

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 592 QGNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 651

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 652 KLKHPSRSRKLRSFLD 667


>gi|298292324|ref|YP_003694263.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
 gi|296928835|gb|ADH89644.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
          Length = 666

 Score =  765 bits (1976), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/687 (59%), Positives = 505/687 (73%), Gaps = 60/687 (8%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D+ DS + D SD   +KMIKLA++RGYVT +ELN  LP D+ +S+Q+ED  AML+ MGIN
Sbjct: 17  DTPDSPLLDLSDAGVRKMIKLAKKRGYVTYDELNEVLPSDQNTSDQIEDIYAMLNEMGIN 76

Query: 77  VVDGD----------------DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           VV+ +                D E+E G E    L  SA  + V  + + +  +R TDDP
Sbjct: 77  VVEAEEAEAEAEAEESGPEAADEEEESGGE----LTESAPRAVVRSETKSEPGER-TDDP 131

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL +G  L
Sbjct: 132 VRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVEGKVL 191

Query: 181 LREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LR+IIDLEA   GPE+K       EG S     +  +       + T G+      ++ D
Sbjct: 192 LRDIIDLEATYAGPEAKNSPI--VEGGSLAPEAEEER-------EPTLGET-----IASD 237

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                              D+D+ +++ +L+AME +++PKV+   D IA+ Y++LR LQD
Sbjct: 238 -------------------DDDDMENSLSLAAMEAEIKPKVLETFDNIADAYKKLRRLQD 278

Query: 300 NAVNGQ-KDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             V  + ++E  S     K K LK+ L+  V SLSLNQ+RID LVEQLYDI+KR++  EG
Sbjct: 279 QNVESKLRNESLSPSQDRKYKSLKDALIADVKSLSLNQARIDNLVEQLYDINKRLVSLEG 338

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
            L+RLA+S+G+ R+ FL+++QG ELDP W+   K+     WK FV  E+D+I  +R+EI 
Sbjct: 339 RLMRLAESFGVAREDFLKQYQGSELDPKWIIRVKNLTSRGWKGFVGQELDAIRDLRSEIH 398

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +++ ETG+ I EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 399 ALATETGLEIQEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 458

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 459 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 518

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIED
Sbjct: 519 TSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIED 578

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 579 KNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 639 RIRQIEAKALRKLKHPSRSRKLRSFLD 665


>gi|170744799|ref|YP_001773454.1| RNA polymerase sigma factor RpoD [Methylobacterium sp. 4-46]
 gi|168199073|gb|ACA21020.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium sp. 4-46]
          Length = 666

 Score =  764 bits (1972), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/693 (57%), Positives = 492/693 (70%), Gaps = 58/693 (8%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++++  E   D  + D +D S K+MIKLA++RGYVT +ELN  LP +E +SEQ+ED +  
Sbjct: 10  ETEAAPEQQTDGPLLDLTDASVKRMIKLAKKRGYVTYDELNEVLPQEEFTSEQIEDVLGQ 69

Query: 70  LSNMGINVVDGDDLEDEEGSE-------------DSLDLASSASNSSVFL--QKRKDSAD 114
           LS +G+NVV+ ++ +D +                +  ++A  A N    L  +  K+  D
Sbjct: 70  LSELGVNVVEAEEADDNQAEGAAAEGGGDDEEASEGTEVAEVAPNRPAVLRTETTKEPTD 129

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           R TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 130 R-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 188

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            DG  LLR+IIDLEA   GP+ + G                            EG++E+ 
Sbjct: 189 VDGRVLLRDIIDLEATYAGPDGRAG--------------------------PAEGEVEAE 222

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                      D P       E + DED+ ++  +LSAME +L+P+V+   D IAE YR+
Sbjct: 223 G----------DGPEGEVAAPEGDGDEDDLENNVSLSAMEAELKPRVLETFDAIAENYRK 272

Query: 294 LRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR +Q             +E  S +   LK ++V  V SLSLN +RI+ LVEQLYDI+KR
Sbjct: 273 LRQVQAQQAETRLQGAGANEGQSRQYAELKSRIVADVKSLSLNANRIEALVEQLYDINKR 332

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++  EG L+RLA+S+G+ RD FL  +QG+ELDPHWV          WKNF     D I  
Sbjct: 333 LISQEGRLMRLAESHGVARDEFLRHYQGQELDPHWVERVGKLGGKGWKNFTERGQDGIKT 392

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R +I S++ ETG+ I E+R IV MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 393 LREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGL 452

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 453 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 512

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 513 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 572

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 573 GDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 632

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 633 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665


>gi|27382460|ref|NP_773989.1| RNA polymerase sigma factor RpoD [Bradyrhizobium japonicum USDA
           110]
 gi|1742976|emb|CAA67902.1| primary sigma factor [Bradyrhizobium japonicum]
 gi|27355631|dbj|BAC52614.1| primary sigma factor [Bradyrhizobium japonicum USDA 110]
          Length = 719

 Score =  761 bits (1966), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 400/705 (56%), Positives = 505/705 (71%), Gaps = 30/705 (4%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K ++ +D+  +DS D  S + D SD + KKMIK A++RG+VT ++LN  LP D+ S EQ+
Sbjct: 15  KDDKAADAPEKDSQDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDQTSPEQI 74

Query: 64  EDTVAMLSNMGINVVDGDDLEDEE----GSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           ED ++MLS+MGINV + DD E EE    G ED  D            + +K      TDD
Sbjct: 75  EDIMSMLSDMGINVTEADDSEGEEDKDEGGEDETDNELVEVTQKAVTEVKKSEPGERTDD 134

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRDELN+G  
Sbjct: 135 PVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLSFQAIIIWRDELNEGKI 194

Query: 180 LLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQE------------KERDDVQET 226
            LR+IIDLEA   GPE+KGG      G    +  +++ E                     
Sbjct: 195 FLRDIIDLEATYAGPEAKGGMNTAMIGGPTGENGEATAEGGEAVAVTGAAPAHVAPPAAP 254

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED-DSAHTLSAMEDQLRPKVMCALD 285
                  A  +  + ++ +  P  A   E ++DED++ ++  +L+A+E +L+PKV+   D
Sbjct: 255 PAPTPFRAAPAAGNGAEAEKDPGEAAA-EADMDEDDEFENQMSLAAIEAELKPKVVEIFD 313

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKS---------SVKCKVLKEKLVKLVGSLSLNQSRID 336
           +IAE Y++LR LQ+  +  Q +  S           K + LK++++  V SL LNQ+RID
Sbjct: 314 KIAESYKKLRKLQEQDIQNQLESTSHGPSLSPHQERKYRKLKDEIIVEVKSLRLNQARID 373

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            LVEQLYDI+KR++ +EG L+RLA S+G+ R+ FL  + G ELDP W++         WK
Sbjct: 374 SLVEQLYDINKRLVSHEGRLMRLADSHGVAREDFLRNYTGSELDPRWLNRVSKLSAKGWK 433

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           NFV  E D I  +R+E+  ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLV
Sbjct: 434 NFVHHEKDRIKDLRHEVHQLAALTGLEIVEFRKIVHSVQKGEREARQAKKEMVEANLRLV 493

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 494 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 553

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SL
Sbjct: 554 RTIRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSL 613

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETP+GDE+ SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGM
Sbjct: 614 ETPVGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGM 673

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 674 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 718


>gi|319898528|ref|YP_004158621.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
 gi|319402492|emb|CBI76035.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
          Length = 669

 Score =  759 bits (1960), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/677 (60%), Positives = 509/677 (75%), Gaps = 39/677 (5%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           S D  + DFSDD+ KKMIKLA++ GYV ++ELNA L  DE +SEQ+EDT+AM S MGINV
Sbjct: 18  SSDGPLLDFSDDAIKKMIKLAKKNGYVIMDELNAALSADEFTSEQIEDTLAMFSEMGINV 77

Query: 78  VDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +D +D  + E  E+ + +       A+N +V    +++ ADR TDDPVRMYLREMG++EL
Sbjct: 78  IDDEDEIESEQYEEEIAIEGGDLVEATNYAVATTSKREVADR-TDDPVRMYLREMGAVEL 136

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL +   LLREIIDLE    G
Sbjct: 137 LSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELKEQRILLREIIDLEMTYAG 196

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           PE+K               E+S  +K +++       + S+ +   D    +    ++ +
Sbjct: 197 PEAKQAPII----------EESEVKKIKEET------LSSSMRDMDDIEEDIGGEDDDED 240

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG----QKDE 308
           +DE NL         +L+AME++L P+V+  LD IA+ Y +LR LQD  V      +K+E
Sbjct: 241 DDEVNL---------SLAAMENELCPQVVETLDFIADTYVKLRKLQDQQVESSLSYRKEE 291

Query: 309 K-SSVKCKV---LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
             SS + K    LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR++H+EG+L RLA +YG
Sbjct: 292 PLSSAQRKQYNQLKDDLIQAVKSLSLNQNRIEALVEQLYDINKRLIHSEGKLKRLASNYG 351

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I  + FL  +QGRELD  WV+Y        WK F  CE   I  +R+EI++++ ET ISI
Sbjct: 352 IGHEDFLREYQGRELDADWVNYIAALSGRGWKEFSTCEAKVIQNLRSEIQNLAQETAISI 411

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 412 GEFRRIVTQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 471

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I 
Sbjct: 472 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIG 531

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLGDFIED+NA+ P+D+A
Sbjct: 532 REPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLGDFIEDRNALLPIDAA 591

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 592 IQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 651

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 652 RKLKHPSRSRKLRSFLD 668


>gi|220927258|ref|YP_002502560.1| RNA polymerase sigma factor RpoD [Methylobacterium nodulans ORS
           2060]
 gi|219951865|gb|ACL62257.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium nodulans
           ORS 2060]
          Length = 665

 Score =  758 bits (1956), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 396/691 (57%), Positives = 489/691 (70%), Gaps = 55/691 (7%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++++  E   D  + D +D S K+MIKLA++RGYVT +ELN  LP +E +SEQ+ED +  
Sbjct: 10  ETEAAPEQQTDGPLLDLTDASVKRMIKLAKKRGYVTYDELNEVLPQEEFTSEQIEDVLGQ 69

Query: 70  LSNMGINVVDGDDLEDEEGSE------------DSLDLASSASNSSVFL--QKRKDSADR 115
           LS +G+NVV+ ++ +D +               +  ++A  A N    L  +  K+  DR
Sbjct: 70  LSELGVNVVEAEEADDNQAEGAGEGGAEDEEVSEGTEVAEVAQNRPAVLRTETTKEPTDR 129

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL 
Sbjct: 130 -TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELV 188

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           DG  LLR+IIDLEA          + G +G                             +
Sbjct: 189 DGRVLLRDIIDLEAT---------YAGPDGRGGPA---------------------EGEE 218

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
             + +  + + PP   E DE +L+ +      +LSAME +L+P+V+   D IAE YR+LR
Sbjct: 219 EGEGEAPEGEVPPPEGEGDEDDLENN-----VSLSAMEAELKPRVLETFDAIAENYRKLR 273

Query: 296 SLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           ++Q          G   E    +   LK ++V  V SLSLN +RI+ LVEQLYDI+KR++
Sbjct: 274 NVQAEQAETRLQGGGASEAQGRQYSELKSRIVADVKSLSLNANRIEALVEQLYDINKRLI 333

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             EG L+RLA+S+G+ RD FL  +QG ELDPHWV          WKNFV    D I  +R
Sbjct: 334 SQEGRLMRLAESHGVARDEFLRHYQGYELDPHWVERVGKLGGKGWKNFVERGADGIQSLR 393

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +I S++ ETG+ I E+R IV MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGLQF
Sbjct: 394 EQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQF 453

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 454 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 513

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGD
Sbjct: 514 KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 573

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 574 FIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 633

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 634 VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 664


>gi|114704974|ref|ZP_01437882.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
 gi|114539759|gb|EAU42879.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
          Length = 682

 Score =  757 bits (1955), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/694 (58%), Positives = 506/694 (72%), Gaps = 35/694 (5%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
           K++   +D   E + D  + D SDD+ KKMIK A++RG+VT+++LN+ L  D V+S+Q+E
Sbjct: 6   KEKEAPADERAEAATDGPLLDLSDDAVKKMIKAAKKRGFVTMDKLNSMLSSDGVTSDQVE 65

Query: 65  DTVAMLSNMGINVVDGDDLEDEEG-----------SEDSLDLASSASNSSVFLQKRKDSA 113
           D +AML++MGINVV+    +DEEG           S +S D+A +   + +   ++K S 
Sbjct: 66  DLMAMLNDMGINVVE----DDEEGEADNDNDNDDNSSNSTDVAETG-KTQIATTEKKSSG 120

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDE
Sbjct: 121 DR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDE 179

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           LN+G  LLR+I+DLEA          + G E  +       S+    +   +  G   SA
Sbjct: 180 LNEGNILLRDIVDLEAT---------YAGPEAKAPAAVAAPSEANGSEAGSDANGRTSSA 230

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
              + +     ++ P   E ++ + D++ + S   L+AME ++ P+VM   D IA+ Y  
Sbjct: 231 NGATAEQTRPGEARPIGTEEEDEDEDDENNLS---LAAMEAEILPQVMETFDLIADTYLR 287

Query: 294 LRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           LR LQD  V       G          + LKE L+  V  LSLNQ+RID LVEQLYDI+K
Sbjct: 288 LRKLQDQQVENRLQATGALSPSQEKSYRKLKEDLIAAVKGLSLNQNRIDALVEQLYDINK 347

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           R++ NEG+LLRL +S+G++RD FL  +QG ELDP+W     +     W +FV  +   I 
Sbjct: 348 RLVGNEGKLLRLGESHGVRRDEFLNEYQGSELDPNWTRRVANLSGKGWLDFVQKDKVKIQ 407

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           ++R EI++++ ETG+ I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 408 RLRGEIQNLATETGLEITEFRRIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRG 467

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 468 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 527

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SH
Sbjct: 528 TINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSH 587

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDKNAV P+D+AIQ NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 588 LGDFIEDKNAVLPIDAAIQGNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQ 647

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 648 QFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 681


>gi|92118365|ref|YP_578094.1| RNA polymerase sigma factor RpoD [Nitrobacter hamburgensis X14]
 gi|91801259|gb|ABE63634.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter hamburgensis
           X14]
          Length = 717

 Score =  756 bits (1953), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/703 (57%), Positives = 509/703 (72%), Gaps = 28/703 (3%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K ++ +D+  +D+ D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+
Sbjct: 15  KDDKAADAPEKDAADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQI 74

Query: 64  EDTVAMLSNMGINVVDGD--DLEDE--EGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           ED ++MLS+MGINV + D  D EDE  E +ED  D            + +K      TDD
Sbjct: 75  EDIMSMLSDMGINVSESDEADSEDENKEEAEDETDNELVEVTQKAVTEVKKSEPGERTDD 134

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  
Sbjct: 135 PVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKI 194

Query: 180 LLREIIDLEACI-GPESKG-------GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
            LR+IIDL+A   GP++K        G   G +G      + ++   E  D+  T     
Sbjct: 195 FLRDIIDLDATYAGPDAKNNMNPALLGAPTGPDGQPLPAGDAAAASGE-GDLGATVTAPP 253

Query: 232 SAAKVSKDDRSKVDSPPENAENDERN--------LDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +A       R+   +P    + DE++        ++ED+ D+  +L+A+E +L+PKV+  
Sbjct: 254 AAPPSPTPFRAVRGAPAGAGDRDEKDQTGAAEGEMEEDDFDNQMSLAAIEAELKPKVVET 313

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            D+IA+ Y++LR LQ+  ++ Q   ++       + + LK+++V  V SL LNQ+RID L
Sbjct: 314 FDKIADNYKKLRRLQEADISNQLQSETLSPNQERRYRKLKDEIVVEVKSLRLNQARIDSL 373

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           VEQLYDI+KR++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNF
Sbjct: 374 VEQLYDINKRLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPKWINRVSKLSAKGWKNF 433

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V  E D I ++R EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS
Sbjct: 434 VHHEKDRIKELRGEIQQLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVIS 493

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 494 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 553

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLET
Sbjct: 554 IRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLET 613

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNT
Sbjct: 614 PVGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 673

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 674 DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 716


>gi|319406862|emb|CBI80497.1| RNA polymerase sigma factor [Bartonella sp. 1-1C]
          Length = 669

 Score =  756 bits (1952), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/678 (59%), Positives = 501/678 (73%), Gaps = 41/678 (6%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           S D  + DFSDD+ KKM+KLA++ GYV ++ELNA L  +E +SEQ+ED +AM S MGI+V
Sbjct: 18  SSDGPLLDFSDDAIKKMMKLAKKNGYVLMDELNAALSSEEFTSEQIEDILAMFSEMGISV 77

Query: 78  VDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +D +D  + E  E+ + +       A+N +V    +++ ADR TDDPVRMYLREMG++EL
Sbjct: 78  IDDEDEIEAEQYEEEITVEGGDLVEATNYAVATTSKREVADR-TDDPVRMYLREMGAVEL 136

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL +   LLREIIDLE    G
Sbjct: 137 LSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELQEQRILLREIIDLEMTYSG 196

Query: 193 PESKGG-FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K       +E    ++   SS  ++ DD++E  G  +   +  + + S         
Sbjct: 197 PEAKQAPIIDESEVKKIKEETSSSNMRDMDDLEEEIGGEDDDEEDDEVNLS--------- 247

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG----QKD 307
                            L+AME +L P+V+  LD IAE Y +LR LQD  V      +K 
Sbjct: 248 -----------------LAAMEHELCPQVVDTLDFIAETYVKLRELQDQQVESSLSHRKA 290

Query: 308 EKSSVKCKV----LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           E  S + +     LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR++ +EG+L RLA +Y
Sbjct: 291 EPISSEQRKQYTELKDALIQAVKSLSLNQNRIEALVEQLYDINKRLIQSEGKLKRLASNY 350

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           GI  + FL  +QGRELD  WV+Y        WK F  CE   I  +RNEI++++ ET IS
Sbjct: 351 GIGHEDFLREYQGRELDADWVNYIATLSGRGWKEFSTCEAKVIQSLRNEIQNLAQETAIS 410

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 411 ISEFRRIVTQVQKGEREANIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 470

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I
Sbjct: 471 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEI 530

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLGDFIED+NA+ P+D+
Sbjct: 531 GREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLGDFIEDRNALLPIDA 590

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 591 AIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 650

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 651 LRKLKHPSRSRKLRSFLD 668


>gi|323137010|ref|ZP_08072090.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocystis sp. ATCC
           49242]
 gi|322397771|gb|EFY00293.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocystis sp. ATCC
           49242]
          Length = 670

 Score =  756 bits (1951), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/684 (59%), Positives = 501/684 (73%), Gaps = 51/684 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D+ D  + D +D + K+MIKLA++RG+VT  ELNA LP +EVSS+Q+ED  AMLS MGI 
Sbjct: 18  DTADGPLLDLNDAAVKRMIKLAKKRGFVTYAELNAVLPSEEVSSDQIEDVYAMLSEMGIT 77

Query: 77  VVDGDDLED-------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           V +GDD +D       EE   +  DL  S  +++V   +  + ADR TDDPVRMYLREMG
Sbjct: 78  VSEGDDPDDVEAEEQAEEEEGEGGDLVESPRSTAV-ATRTSEPADR-TDDPVRMYLREMG 135

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR+EL  G  LLR+IIDLEA
Sbjct: 136 SVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWREELEAGKVLLRDIIDLEA 195

Query: 190 CI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              GP+ K      T G                   ETEG++  A        +   +PP
Sbjct: 196 TYAGPDGKAA--GKTSG-------------------ETEGEMAPA--------TAPRTPP 226

Query: 249 EN------AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NA 301
                      +    +ED ++S  +LSAME +L+PKV+     +A+ Y++LR LQD N 
Sbjct: 227 AGLSEEAAPPEEAFEEEEDMENSV-SLSAMEAELKPKVLETFARVADAYKKLRRLQDQNV 285

Query: 302 VNGQKDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            N  K+E  +     K K +K+++V  V SLSLNQ+RI+ LVEQLYDI+KR++  E +LL
Sbjct: 286 ENKLKNETLTPAQERKYKTIKKEIVTDVKSLSLNQNRIEALVEQLYDINKRLIGYETKLL 345

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA S+G+ R+ F+++  G ELDP WV          WK FVA E D I  +R EI +++
Sbjct: 346 RLADSHGVAREDFIDKFHGSELDPKWVMRVAQLRSRGWKEFVAEEKDRIKDLRAEIHALA 405

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETG+ ISEFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 406 TETGLEISEFRKIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 465

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R
Sbjct: 466 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 525

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+++KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA
Sbjct: 526 QMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 585

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V P+++AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 586 VLPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 645

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 646 QIEAKALRKLKHPSRSRKLRSFLD 669


>gi|319403851|emb|CBI77437.1| RNA polymerase sigma factor [Bartonella rochalimae ATCC BAA-1498]
          Length = 669

 Score =  755 bits (1949), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/679 (59%), Positives = 500/679 (73%), Gaps = 43/679 (6%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           S D  + DFSDD+ KKM+KLA++  YV ++ELNA L  +E +SEQ+ED +AM S MGI+V
Sbjct: 18  SSDGSLLDFSDDAIKKMMKLAKKNSYVLMDELNAALSSEEFTSEQIEDILAMFSEMGISV 77

Query: 78  VDGDD-----LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           +D +D       +EE + +  DL   A+N +V    +++ ADR TDDPVRMYLREMG++E
Sbjct: 78  IDDEDEIESGQYEEEITVEGGDLVE-ATNYAVATTSKREVADR-TDDPVRMYLREMGAVE 135

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI- 191
           LLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL +   LLREIIDLE    
Sbjct: 136 LLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELQEQRILLREIIDLEMTYS 195

Query: 192 GPESKGG-FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           GPE+K       +E    ++   SS  ++ +D+ E  G  +   +  + + S        
Sbjct: 196 GPEAKQAPIIDESEVKKIKEETSSSSMRDMNDLGEEIGGEDDDEEDDEVNLS-------- 247

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG----QK 306
                             L+AME +L P+V+  LD IAE Y +LR LQD  V      +K
Sbjct: 248 ------------------LAAMEHELCPQVVETLDFIAETYVKLRELQDQQVESSLSHRK 289

Query: 307 DEKSSVKCKV----LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            E  S + +     LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR++ +EG+L RLA +
Sbjct: 290 AEPLSSEQRKQYTELKDALIQAVKSLSLNQNRIEALVEQLYDINKRLIQSEGKLKRLASN 349

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           YGI  + FL  +QGRELD  WV+Y        WK F  CE   I  +RNEI++++ ET I
Sbjct: 350 YGIGHEDFLREYQGRELDADWVNYIATLSGRGWKEFSTCEAKVIQSLRNEIQNLAQETAI 409

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           SISEFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 410 SISEFRRIVTQVQKGEREANIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 469

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++
Sbjct: 470 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHE 529

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLGDFIED+NA+ P+D
Sbjct: 530 IGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLGDFIEDRNALLPID 589

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 590 AAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 649

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 650 ALRKLKHPSRSRKLRSFLD 668


>gi|312113102|ref|YP_004010698.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
 gi|311218231|gb|ADP69599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
          Length = 697

 Score =  754 bits (1947), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/711 (56%), Positives = 511/711 (71%), Gaps = 45/711 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     +N D +++  +S DS V D  D + K++IK A+ RGYVT +E+N  +PP++VS 
Sbjct: 1   MATATTKNEDQETQASESTDSPVLDLLDAAVKRLIKTAKARGYVTYDEINEVMPPEDVSP 60

Query: 61  EQMEDTVAMLSNMGINVVDGDD--------LEDEEGSEDSLDLASSASNSSVFLQKRKDS 112
           +Q+ED + M S++GINVVD ++        L+DEE      D  ++ +N  V  Q+R   
Sbjct: 61  DQIEDIMTMFSDLGINVVDAEEVEEASAEHLDDEE------DDRAAPANLPV-KQERSTE 113

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+IIWRD
Sbjct: 114 VGERTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIGGLCESPLTFQAIIIWRD 173

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+G  LLR+IIDLEA       G F    EG   ++  D   + +   V      + +
Sbjct: 174 ELNEGKILLRDIIDLEATYS----GPFSRPEEGDGSEEEYDPEPQPQLQPVSGPRPVVTN 229

Query: 233 AAK----VSKDDRSKVDSPPEN-------AENDERNLDEDEDDSAHTLS--AMEDQLRPK 279
                  V+  + +   + PE         E  E   +ED+DD  ++LS  AME +L+PK
Sbjct: 230 GGGATNGVTGLNGANGHARPEGTDAVGPEGETAEFRGEEDDDDLENSLSLAAMEAELKPK 289

Query: 280 VMCALDEIAEVYRELRSLQD---------NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           V+   D IA  Y++LR LQD         +A++ Q++++S    + L++ +++ V SLSL
Sbjct: 290 VLETFDRIATEYKKLRKLQDQHVERKLADDALSPQQEKRS----RRLRDAVIQDVKSLSL 345

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
           N +RI+ LVEQLYDI+KR++  EG LLRLA  +G++RD FL  +QG ELDP+W+      
Sbjct: 346 NPARIESLVEQLYDINKRLIGYEGRLLRLADGFGVRRDEFLSYYQGSELDPNWIDRIGTL 405

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
               W+ FV  E   I +IR EI +++ ETG+ I+EFR IV +V+KGE EA  AKKEMVE
Sbjct: 406 KGKGWQKFVEKERQRIDEIRQEIYALATETGLDIAEFRRIVKIVQKGEREARQAKKEMVE 465

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 466 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 525

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KL+MP+E VRKVLKI 
Sbjct: 526 SIADQARTIRIPVHMIETINKIVRTSRQMMHEIGREPTPEELAEKLSMPLEKVRKVLKIA 585

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRM
Sbjct: 586 KEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRM 645

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 646 RFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 696


>gi|296445787|ref|ZP_06887740.1| RNA polymerase, sigma 70 subunit, RpoD [Methylosinus trichosporium
           OB3b]
 gi|296256767|gb|EFH03841.1| RNA polymerase, sigma 70 subunit, RpoD [Methylosinus trichosporium
           OB3b]
          Length = 669

 Score =  754 bits (1946), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/678 (58%), Positives = 503/678 (74%), Gaps = 40/678 (5%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           ++ D  + D +D + K+MIKLA++RG+VT  ELNA LP +EVSS+Q+ED  AML  MGI 
Sbjct: 18  ETADGPLLDLNDAAVKRMIKLAKKRGFVTYTELNAVLPSEEVSSDQIEDVYAMLQEMGIT 77

Query: 77  VVDGDDLEDEEGSEDSLDLASS-------ASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           V +GDD +D EG E   +  +        ++ ++    +  + ADR TDDPVRMYLREMG
Sbjct: 78  VSEGDDPDDAEGEEQQEEEEAETGGEVVESARATAVATRSSEPADR-TDDPVRMYLREMG 136

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR+EL  G  LLR+IIDLEA
Sbjct: 137 SVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWREELEAGKVLLRDIIDLEA 196

Query: 190 CI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              GPE K                ++     +DD+        + A   +   + +D P 
Sbjct: 197 TYAGPEGK----------------NAKPPAPQDDL--------APATAPRSPPAALDEPG 232

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKD 307
             AE  E   +ED+ +++ +LSAME +L+P+V+     +A+ Y++LR LQD N  N  K+
Sbjct: 233 APAE--ESFEEEDDLENSVSLSAMEAELKPRVLETFARVADAYKKLRRLQDQNVENKLKN 290

Query: 308 EKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           E  +     K K LK+++V  V SLSLNQ+RI+ LVEQLYDI+KR++  E +L  LA + 
Sbjct: 291 ETLTPAQERKYKQLKKEIVTDVKSLSLNQNRIEALVEQLYDINKRLVGYERKLFMLADAQ 350

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G++R+ F+++ QG ELDP W++         WK FVA E D I ++R EI +++ ETG+ 
Sbjct: 351 GVQREDFIDKFQGSELDPKWINRVSKLGSRGWKEFVANEKDRIRELRGEIHALATETGLE 410

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 411 IAEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 470

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I
Sbjct: 471 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEI 530

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+++KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+++
Sbjct: 531 GREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIEA 590

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 591 AIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 650

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 651 LRKLKHPSRSRKLRSFLD 668


>gi|75676624|ref|YP_319045.1| RNA polymerase sigma factor RpoD [Nitrobacter winogradskyi Nb-255]
 gi|74421494|gb|ABA05693.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter winogradskyi
           Nb-255]
          Length = 717

 Score =  753 bits (1943), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/707 (56%), Positives = 502/707 (71%), Gaps = 36/707 (5%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K ++ +D+  +D+ D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+
Sbjct: 15  KDDKAADAPEKDTADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQI 74

Query: 64  EDTVAMLSNMGINV-----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           ED ++MLS+MGINV      D +D   EE  E++ +     +  +V   K+ +  +R TD
Sbjct: 75  EDIMSMLSDMGINVSESEDADSEDENKEEADEETDNELVEVTQKAVTEVKKSEPGER-TD 133

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G 
Sbjct: 134 DPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGK 193

Query: 179 TLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LR+IIDLEA   GPE+K    +     +           +  D    EG  E+     
Sbjct: 194 IFLRDIIDLEATYAGPEAKSSM-NPALLGAPGGPGGQPLSADASDGASGEGGAEATVNAP 252

Query: 238 KDDRSKVDS------------------PPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
                                      P   AE +   ++ED+ D+  +L+A+E +L+PK
Sbjct: 253 PSAPPSPTPFRAARAAPAGAADREEKIPGAAAEGE---MEEDDFDNQMSLAAIEAELKPK 309

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSR 334
           V+   D+IA+ Y++LR LQ+  ++ Q   +S       + K LK++++  V SL LNQ+R
Sbjct: 310 VVETFDKIADSYKKLRRLQEADISNQLQNESLSPNQERRYKKLKDEIIVEVKSLRLNQAR 369

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           ID LVEQLYDI+KR++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         
Sbjct: 370 IDSLVEQLYDINKRLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKG 429

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           WKNFV  E D I ++R EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLR
Sbjct: 430 WKNFVHHEKDRIKELRGEIQQLAALTGLEIGEFRKIVQGVQKGEREARQAKKEMVEANLR 489

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIAD
Sbjct: 490 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 549

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+
Sbjct: 550 QARTIRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPL 609

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETP+GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGI
Sbjct: 610 SLETPVGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGI 669

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 670 GMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 716


>gi|115523078|ref|YP_779989.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisA53]
 gi|115517025|gb|ABJ05009.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           BisA53]
          Length = 704

 Score =  752 bits (1942), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/674 (58%), Positives = 492/674 (72%), Gaps = 12/674 (1%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS+MGINV + 
Sbjct: 31  SPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLSDMGINVSES 90

Query: 81  DDLEDEEGSEDSLDLASSASN-----SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           DD ++EE            ++     +    + +K      TDDPVRMYLREMG++ELLS
Sbjct: 91  DDTDNEEEETKEEADDEPDTDLVEVTAKAVTETKKSEPGERTDDPVRMYLREMGTVELLS 150

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPE 194
           REGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IIDLEA   GP+
Sbjct: 151 REGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIIDLEATYAGPD 210

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
           +K            +  ED                  + A       +  +   + AE+ 
Sbjct: 211 AKNNMNPALAAPEGETSEDPDAVAAPPAAPPQPTPFRAGAPRPAPAATPGEEGKDPAESA 270

Query: 255 -ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSV 312
            E ++D+DE ++  +L+A+E +L+PKV+   D+IAE Y++LR LQ+  ++ Q ++E  S 
Sbjct: 271 AEGDMDDDEFENQMSLAAIEAELKPKVVETFDKIAENYKKLRRLQEQDISNQLQNETLSP 330

Query: 313 ----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  EG LLRL  S+G+ R+
Sbjct: 331 AQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFEGRLLRLGDSHGVARE 390

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FL  +QG ELDP W++         WKNFV  E D I ++R EI+S++  TG+ I EFR
Sbjct: 391 DFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKELRQEIQSLAALTGLEIGEFR 450

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 451 KIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 510

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M N+I REPT
Sbjct: 511 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLNEIGREPT 570

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV P+D+AIQ+N
Sbjct: 571 PEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVLPIDAAIQSN 630

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLK
Sbjct: 631 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 690

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS+KLRSFLD 
Sbjct: 691 HPSRSRKLRSFLDN 704


>gi|85715949|ref|ZP_01046926.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85697147|gb|EAQ35028.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 716

 Score =  751 bits (1938), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/703 (57%), Positives = 512/703 (72%), Gaps = 29/703 (4%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K ++ +D+  +D  D  S + D SD + KKMIK A++RG+VT ++LN  LP +  S EQ+
Sbjct: 15  KDDKAADAPEKDIADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSETTSPEQI 74

Query: 64  EDTVAMLSNMGINV-----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           ED ++MLS+MGINV      D +D   EE  E++ +     +  +V   K+ +  +R TD
Sbjct: 75  EDIMSMLSDMGINVSESEDADSEDENKEEADEETDNELVEVTQKAVTEVKKSEPGER-TD 133

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G 
Sbjct: 134 DPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGK 193

Query: 179 TLLREIIDLEACI-GPESKG-----GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
             LR+IIDLEA   GPE+K      G   G +G      + S  +    DV  T     +
Sbjct: 194 IFLRDIIDLEATYAGPEAKSNQALLGSPAGPDGQPLSA-DASDADSGESDVGSTVTAPPA 252

Query: 233 AAKVSKDDRSKVDSPPENAENDERN---------LDEDEDDSAHTLSAMEDQLRPKVMCA 283
           A       R+   +P  +A+ D+++         ++ED+ D+  +L+A+E +L+PKV+  
Sbjct: 253 APPSPTPFRAARAAPAGSADPDDKDPGVAAAEGEMEEDDFDNQMSLAAIEAELKPKVVET 312

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            D+IA+ Y++LR LQ+  ++ Q   +S       + K LK++++  V SL LNQ+RID L
Sbjct: 313 FDKIADNYKKLRRLQEADISNQLQNESLSPNQERRYKKLKDEIIVEVKSLRLNQARIDSL 372

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           VEQLYDI+KR++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNF
Sbjct: 373 VEQLYDINKRLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNF 432

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V  E D I ++R EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS
Sbjct: 433 VHHEKDRIKELRGEIQQLAALTGLEIGEFRKIVQGVQKGEREARQAKKEMVEANLRLVIS 492

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 493 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 552

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLET
Sbjct: 553 IRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLET 612

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNT
Sbjct: 613 PVGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 672

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 673 DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 715


>gi|154245186|ref|YP_001416144.1| RNA polymerase sigma factor RpoD [Xanthobacter autotrophicus Py2]
 gi|154159271|gb|ABS66487.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthobacter autotrophicus
           Py2]
          Length = 666

 Score =  750 bits (1937), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 405/682 (59%), Positives = 497/682 (72%), Gaps = 50/682 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D+ D  + D SD + +KMIK A++RGYVT E+LN  +P +EV+SEQ+EDT+AML++MGIN
Sbjct: 17  DAPDGPLLDLSDAAVRKMIKNAKRRGYVTYEQLNEVMPSEEVTSEQIEDTLAMLNDMGIN 76

Query: 77  VVDGDDLEDEEGSEDSLDLAS-----------SASNSSVFLQKRKDSADRSTDDPVRMYL 125
           V++ ++ E EEG+E++                 A  +    + + + A+R TDDPVRMYL
Sbjct: 77  VIEAEEAEAEEGAEETETAEEPEEAEGGELAEPAPRAVARSETKSEPAER-TDDPVRMYL 135

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL +G  LLR+II
Sbjct: 136 REMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELTEGRVLLRDII 195

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           DLEA          + G EG +             +               + +D    D
Sbjct: 196 DLEAT---------YAGPEGKNPPAALGEEAALAPE---------------AGEDGLLGD 231

Query: 246 SP-PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           +P PE  ++D  N        + +L+AME +++PKV+   D IA  Y +LR LQD  V  
Sbjct: 232 APGPEGEDDDMEN--------SMSLAAMEAEIKPKVLETFDRIASSYTKLRRLQDQNVES 283

Query: 305 Q-KDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
           + K+E  S     K K LKE LV  V SLSLNQ+RID LVEQLY+I+KR++  EG LLRL
Sbjct: 284 KLKNETLSPAQERKAKKLKEDLVGDVKSLSLNQARIDALVEQLYEINKRLVGLEGRLLRL 343

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A SYG+ RD FL+ + G ELDP W+          WK FV  E D+I +IR +I +++ E
Sbjct: 344 ADSYGVTRDDFLKNYMGAELDPKWLLRVSKLGTKGWKGFVGHEKDTIHEIRGDIHALATE 403

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+ I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 404 TGLEIAEFRKIVQMVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 463

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M
Sbjct: 464 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQM 523

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ 
Sbjct: 524 LHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAIL 583

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 584 PIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 643

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 644 EAKALRKLKHPSRSRKLRSFLD 665


>gi|217977790|ref|YP_002361937.1| RNA polymerase sigma factor RpoD [Methylocella silvestris BL2]
 gi|217503166|gb|ACK50575.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocella silvestris
           BL2]
          Length = 683

 Score =  749 bits (1933), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/699 (58%), Positives = 511/699 (73%), Gaps = 35/699 (5%)

Query: 3   IGKKRNRDSDSEHE--DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           + KK N  +++E    ++ DS + D SD + K+MIK A++RG+VT  ELNA LP +EV+S
Sbjct: 1   MAKKDNEKTEAEGGVVETADSPLLDLSDAAVKRMIKAAKKRGFVTYAELNAVLPSEEVNS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL-------DLASSASNSSVFLQKRKDSA 113
           EQ+ED +AML+ MGINVV+ ++ E+ E  E +        DL  +++  +V + +  + A
Sbjct: 61  EQIEDILAMLNEMGINVVETEEQEEGEAEEAAEEEEAEGGDLVEASTVKAVTV-RSSEPA 119

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDE
Sbjct: 120 DR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDE 178

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK----REDSSQEKERDDVQETEGD 229
           LND   LLR+IIDLEA          + G +G +  K       +++             
Sbjct: 179 LNDSKVLLRDIIDLEAT---------YAGPDGRNTPKIDMTAPGAAEALAAQQAAPATAP 229

Query: 230 IESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
           +   A++       VD P PE+  ++E     D+ +++ +LSAME +L+PKV+   D +A
Sbjct: 230 LTPPARLRPAGEDGVDPPIPEDVFDEE-----DDMENSVSLSAMEAELKPKVLDTFDRVA 284

Query: 289 EVYRELRSLQD-NAVNGQKDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           + Y++LR LQD N  N  K+E  S     K K LK+++V  V SLSLN +RI+ LVEQLY
Sbjct: 285 DAYKKLRRLQDQNVENKLKNESLSPSQERKYKTLKKEVVTDVKSLSLNPNRIEALVEQLY 344

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++  E  LLRLA+  G+ R+ FL  +Q  ELDP W+          W++FVA   
Sbjct: 345 DINKRLIGLETRLLRLAEGSGVTREDFLRNYQNSELDPKWLLRVSKLGGRGWRDFVATAK 404

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D I  +  EI +++ ETG+ I EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKY
Sbjct: 405 DQIKDLLAEIHALATETGLEIQEFRKIVHMVQKGEREARQAKKEMVEANLRLVISIAKKY 464

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 465 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 524

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE
Sbjct: 525 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDE 584

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 585 EDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 644

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 645 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 683


>gi|90422490|ref|YP_530860.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisB18]
 gi|90104504|gb|ABD86541.1| sigma 70 (RpoD) [Rhodopseudomonas palustris BisB18]
          Length = 702

 Score =  747 bits (1929), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/683 (57%), Positives = 498/683 (72%), Gaps = 14/683 (2%)

Query: 12  DSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  +D+ D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++M
Sbjct: 20  DAPEKDAPDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSM 79

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSAS-----NSSVFLQKRKDSADRSTDDPVRMY 124
           LS+MGINV + DD + +E            +      +    + +K      TDDPVRMY
Sbjct: 80  LSDMGINVSEADDADSDEEDAKEEAEEEPDNELVEVTAKAVTETKKSEPGERTDDPVRMY 139

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+I
Sbjct: 140 LREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDI 199

Query: 185 IDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           IDLEA   GP++K    +          +  + +              +    +      
Sbjct: 200 IDLEATYAGPDAKNN-MNPALIAPPAAADGEAADGAEAVAAPPAAPPSATPFRAAPPPRP 258

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            D P E++E+ + + D+DE ++  +L+A+E +L+PKV+   D+IAE Y++LR LQ+  ++
Sbjct: 259 ADEPKESSESADGDADDDEFENQMSLAAIEAELKPKVVETFDKIAENYKKLRRLQEQDIS 318

Query: 304 GQ-KDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
            Q ++E  S     K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  EG LLR
Sbjct: 319 NQLQNETLSPAQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFEGRLLR 378

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           L  S+G+ R+ FL  +QG ELDP W++         WKNFVA E D I ++R EI+S++ 
Sbjct: 379 LGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVAHEKDRIKELRGEIQSLAA 438

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 439 LTGLEIGEFRKIVHGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 498

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+
Sbjct: 499 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ 558

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNA+
Sbjct: 559 MLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAI 618

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 619 LPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 678

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 679 IEAKALRKLKHPSRSRKLRSFLD 701


>gi|148257986|ref|YP_001242571.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. BTAi1]
 gi|146410159|gb|ABQ38665.1| RNA polymerase, sigma 70 subunit, RpoD [Bradyrhizobium sp. BTAi1]
          Length = 702

 Score =  744 bits (1920), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/705 (57%), Positives = 504/705 (71%), Gaps = 47/705 (6%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K ++ +D+  +DS D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+
Sbjct: 15  KDDKAADAPEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQI 74

Query: 64  EDTVAMLSNMGINVVD------------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
           ED ++MLS+MGINV +            GDD  D E  E         +  +V   K+ +
Sbjct: 75  EDIMSMLSDMGINVTEAEEADESEEKDDGDDETDNELVE--------ITQKAVTEVKKSE 126

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
             +R TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR
Sbjct: 127 PGER-TDDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWR 185

Query: 172 DELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           DELN+G   LR+IIDLEA   GPESKGG        + Q    ++ E E  D  E +  +
Sbjct: 186 DELNEGKIFLRDIIDLEATYAGPESKGGM-------NPQIAAPANGEGEAADGGEIQAAV 238

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQLRPKVM 281
              A   +    +  + P  A  +E++  E            ++  +L+A+E +L+PKV+
Sbjct: 239 APPAAPQQPTPFR--AAPNGAPVEEKDPGEAAAEADMDDDEFENQMSLAAIEAELKPKVV 296

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRID 336
              D+IA  Y++LR LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID
Sbjct: 297 ETFDKIASEYKKLRRLQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARID 356

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            LVEQLYDI+K+++  E  L+RLA S+G+ R+ FL  +QG ELDP W++         WK
Sbjct: 357 SLVEQLYDINKKLVSFESRLMRLADSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWK 416

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           NFV  E D I  +R E++S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLV
Sbjct: 417 NFVHYEKDRIKDLRQEVQSLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLV 476

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 477 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 536

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SL
Sbjct: 537 RTIRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSL 596

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETP+GDE+ SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGM
Sbjct: 597 ETPVGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGM 656

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 657 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 701


>gi|304391338|ref|ZP_07373282.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
 gi|303296694|gb|EFL91050.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
          Length = 692

 Score =  743 bits (1917), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/682 (58%), Positives = 503/682 (73%), Gaps = 31/682 (4%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D +DD  KKMIK A++RG+VT++ELNA +P DEVS +Q+EDT++MLS MGINVV+
Sbjct: 21  DRPLLDLNDDKVKKMIKAAKKRGFVTVDELNAVMPSDEVSPDQIEDTMSMLSEMGINVVE 80

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            ++ E+      +  +   A   +V    +K+  DR TDDPVRMYLREMGS+ELLSREGE
Sbjct: 81  EEESEEAPEEVSTEIV--EAGKKAVATVAKKEPTDR-TDDPVRMYLREMGSVELLSREGE 137

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKG- 197
           IAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL +   LLR+IIDLEA   GP++K  
Sbjct: 138 IAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELLEENILLRDIIDLEATYAGPDAKQN 197

Query: 198 -------------GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                            G+ G      E S +   R   ++   D E+A +  K   +  
Sbjct: 198 VPVNPNAPASVAEAVRQGSGG------EHSPEAIARRKAEKDGTDPEAAVEALKGPEAGD 251

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-- 302
           D+  EN    + + D+++D++A +L+AME +L+PKV+   D IA  Y++LR LQD  V  
Sbjct: 252 DTSSEN--KTDDDDDDEDDEAALSLAAMEAELKPKVLEIFDSIAGNYKKLRKLQDTYVEK 309

Query: 303 ---NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              N +       +   LKE++V  V SL LN +RI+ LVEQLYDI+KR++ +EG L+RL
Sbjct: 310 RMLNEKLSPSQEKRLVALKEEIVVSVKSLELNLNRIEALVEQLYDINKRLVQSEGRLMRL 369

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A+ +G+ R++FLE ++G ELDP+W+    +     WK F A E   I ++R +I+ +S E
Sbjct: 370 AEKHGVARELFLEEYRGAELDPNWIRRIANLGAKGWKEFCANEKPEIKELRADIQMLSHE 429

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+   EFR IV  V+KGE E+ IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 430 TGLDTGEFRRIVHQVQKGERESRIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 489

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M
Sbjct: 490 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQM 549

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE++ KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ 
Sbjct: 550 LHEIGREPTPEELSTKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAIL 609

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 610 PIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 669

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 670 EAKALRKLKHPSRSRKLRSFLD 691


>gi|209884282|ref|YP_002288139.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209872478|gb|ACI92274.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 708

 Score =  742 bits (1916), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/693 (57%), Positives = 498/693 (71%), Gaps = 17/693 (2%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K  + +++  +DS D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+
Sbjct: 15  KEQKAAETPEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQI 74

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS----NSSVFLQKRKDSADRSTDD 119
           ED +AMLS+MGINV + D+ ++EE  +D  D  +        S    + +K      TDD
Sbjct: 75  EDIMAMLSDMGINVSESDEADNEEEEKDEADDDTDNELVEVTSKAVTETKKSEPGERTDD 134

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  
Sbjct: 135 PVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKI 194

Query: 180 LLREIIDLEACI-GPESKGG----FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            LR+IIDLEA   GPE KGG       G  G   Q             V   +      A
Sbjct: 195 FLRDIIDLEATYAGPEGKGGVNTAMIAGPSGPDGQPTNAIVNGDGTVQVMPAQAAAAQTA 254

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDED-DSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
             +        +  ++A   E   DED++ ++  +L+A+E +L+P+V+   D+IA  Y++
Sbjct: 255 PQTATPFRPAPAAGDDASASEGEGDEDDEFENQMSLAAIEAELKPRVVETFDKIASEYKK 314

Query: 294 LRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLYDI+KR
Sbjct: 315 LRRLQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKR 374

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++  EG L RL  S+G+ R+ FL+ + G ELDP W++         WKNFVA E D I  
Sbjct: 375 LVSYEGRLFRLGDSHGVSREDFLKNYVGSELDPRWLNRVSKLSAKGWKNFVAHEKDKIKD 434

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+E++ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGL
Sbjct: 435 LRHEVQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGL 494

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 495 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 554

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHL
Sbjct: 555 INKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHL 614

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 615 GDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 674

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 675 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 707


>gi|192289891|ref|YP_001990496.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris TIE-1]
 gi|192283640|gb|ACF00021.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodopseudomonas
           palustris TIE-1]
          Length = 698

 Score =  741 bits (1914), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/675 (58%), Positives = 495/675 (73%), Gaps = 22/675 (3%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--- 77
           S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS+MGINV   
Sbjct: 31  SPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLSDMGINVSEA 90

Query: 78  --VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
              + ++ E +E +++ LD       +    + +K      TDDPVRMYLREMG++ELLS
Sbjct: 91  EDTEAEEEEAKEEADEELDNDLVEVTAKAVTETKKSEPGERTDDPVRMYLREMGTVELLS 150

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPE 194
           REGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IIDLEA   GPE
Sbjct: 151 REGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIIDLEATYAGPE 210

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            K     G  G      E+++ E +              +        +  + P  AE +
Sbjct: 211 GKNNI--GEPG------EEAAAEGDGGAPAHVAPPAAPPSATPFRPAQQRGAAPAEAEGE 262

Query: 255 ---ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKS 310
              E + D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+  +  Q ++E+ 
Sbjct: 263 GAPEGDGDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQDIANQLQNEQL 322

Query: 311 SV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
           S     K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  E  L+RLA S+G+ 
Sbjct: 323 SPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFESRLMRLADSHGVA 382

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           RD FL  +QG ELDP W++         WKNFV  E D I  +R E++S++  TG+ I E
Sbjct: 383 RDDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKDLRQEVQSMAALTGLEIGE 442

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 443 FRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 502

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M N+I RE
Sbjct: 503 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLNEIGRE 562

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV P+D+AIQ
Sbjct: 563 PTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVLPIDAAIQ 622

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RK
Sbjct: 623 SNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRK 682

Query: 667 LKHPSRSKKLRSFLD 681
           LKHPSRS+KLRSFLD
Sbjct: 683 LKHPSRSRKLRSFLD 697


>gi|86751238|ref|YP_487734.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris HaA2]
 gi|86574266|gb|ABD08823.1| sigma 70 (RpoD) [Rhodopseudomonas palustris HaA2]
          Length = 714

 Score =  741 bits (1912), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/694 (57%), Positives = 495/694 (71%), Gaps = 32/694 (4%)

Query: 16  EDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           +DS D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS+M
Sbjct: 24  KDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLSDM 83

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----RKDSADRSTDDPVRMYLREM 128
           GINV + ++ + E+            ++     QK     +K      TDDPVRMYLREM
Sbjct: 84  GINVSEAEESDSEDEDAKDEAEEEPDNDLVEVTQKAVTETKKSEPGERTDDPVRMYLREM 143

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IIDLE
Sbjct: 144 GTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIIDLE 203

Query: 189 ACI-GPESKGGFFHG-TEGHSYQKREDSSQEKERD----------DVQETEGDIESAAKV 236
           A   GP++K        EG      E++S E E D              T      A + 
Sbjct: 204 ATYAGPDAKANMNPAMAEGAG----EEASAEGEADAGAPAHVAPPAAPPTATPFRPAQQR 259

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           S    +            E ++D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR 
Sbjct: 260 SAPAAAPAAGEGGGEGAAEGDMDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRK 319

Query: 297 LQDNAVNGQKDEKSS---------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           LQ+  +  Q +  S           K K LK++++  V SL LNQ+RID LVEQLYDI+K
Sbjct: 320 LQEQDIANQLESASQGPSLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINK 379

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           +++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I 
Sbjct: 380 KLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHFEKDRIR 439

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           ++R EI+S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 440 ELRQEIQSMAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRG 499

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 500 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 559

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SH
Sbjct: 560 TINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSH 619

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 620 LGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQ 679

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 680 QFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 713


>gi|254470295|ref|ZP_05083699.1| sigma 70 [Pseudovibrio sp. JE062]
 gi|211960606|gb|EEA95802.1| sigma 70 [Pseudovibrio sp. JE062]
          Length = 701

 Score =  741 bits (1912), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/699 (56%), Positives = 499/699 (71%), Gaps = 50/699 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           +  D  + D S  + KKMIK A++RGY+T +ELN  LPPD+VSSEQ+EDT+++LS MGIN
Sbjct: 18  EGQDGPLLDLSVAAVKKMIKTAKKRGYITYDELNEVLPPDQVSSEQIEDTMSLLSEMGIN 77

Query: 77  VVDGDDLEDEE------GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           VV+ +D E+ +       + D  +L  ++S +       K+  DR TDDPVRMYLREMGS
Sbjct: 78  VVEAEDAEEGKEEEDAPAAVDGGELVVASSTAVTKTSTAKEPTDR-TDDPVRMYLREMGS 136

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+IIW +EL +G  LLR+IIDL+A 
Sbjct: 137 VELLSREGEIAIAKRIEAGREAMISGLCESPLTFQAIIIWGEELAEGKVLLRDIIDLDAT 196

Query: 191 I-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK-------------- 235
             GP   GG             +D   E+E    +  EG++  A +              
Sbjct: 197 YSGPGDAGG-----------PSDDDLSEQE----EAGEGEVPEAVRQKEKEEARKRKEEE 241

Query: 236 -------VSKDDRSKVDSPPENAENDERNLDEDEDDSAH-TLSAMEDQLRPKVMCALDEI 287
                   +    +      +  E  E   D+D++  A+ +LS ME +L+P V+   D+I
Sbjct: 242 ARKANGAAAPAPAADGAQGEQTGEGGESTDDDDDEYEANVSLSVMEAELKPMVVEIFDKI 301

Query: 288 AEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
            E Y++LR LQD  V  +   K+       + K LKE ++  V SL LN +RI+ LV+QL
Sbjct: 302 TEDYKKLRKLQDQLVENKLANKTLSPSQERRYKKLKEDIIAEVKSLHLNANRIETLVQQL 361

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           Y I+K +M  EG LLRLA S G+ R  F++ +QG ELDP+W+    +     WK FV  +
Sbjct: 362 YSINKMLMGYEGRLLRLADSNGVNRADFIKHYQGSELDPNWIRKVANLSGRGWKKFVTND 421

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            D I ++R EI+S++ ETG+ I+EFR +VSMV+KGE EA IAKKEMVEANLRLVIS+AKK
Sbjct: 422 GDMIRELRGEIQSLATETGLEITEFRTLVSMVQKGEREARIAKKEMVEANLRLVISIAKK 481

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 482 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 541

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+VRT+R+M ++I REPTPEE+++KL MP+E VRKVLKI KEPISLETPIGD
Sbjct: 542 VHMIETINKIVRTSRQMLHEIGREPTPEELSEKLQMPLEKVRKVLKIAKEPISLETPIGD 601

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL
Sbjct: 602 EEDSHLGDFIEDKNAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 661

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 662 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 700


>gi|91978433|ref|YP_571092.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris BisB5]
 gi|91684889|gb|ABE41191.1| RNA polymerase sigma factor RpoD-like [Rhodopseudomonas palustris
           BisB5]
          Length = 711

 Score =  740 bits (1910), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/690 (57%), Positives = 494/690 (71%), Gaps = 27/690 (3%)

Query: 16  EDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           +DS D  S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS+M
Sbjct: 24  KDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLSDM 83

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----RKDSADRSTDDPVRMYLREM 128
           GINV + ++ + E+            ++     QK     +K      TDDPVRMYLREM
Sbjct: 84  GINVSEAEESDSEDEESKDEAEEEPDNDLVEVTQKAVTETKKSEPGERTDDPVRMYLREM 143

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IIDLE
Sbjct: 144 GTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIIDLE 203

Query: 189 ACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           A   GP++K        G +    E++S E E              +        +  +P
Sbjct: 204 ATYAGPDAKNNMNPAMAGETG---EEASAEGEGGAPAHLAPPAAPPSATPFRPAQQRAAP 260

Query: 248 PE-------NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            +            E ++D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+ 
Sbjct: 261 SQAPAGEGGGEGAAEGDMDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQ 320

Query: 301 AVNGQKDEKSSV---------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            +  Q +  S           K K LK++++  V SL LNQ+RID LVEQLYDI+K+++ 
Sbjct: 321 DIANQLESASQGPSLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVS 380

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I ++R 
Sbjct: 381 FEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKELRQ 440

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           EI+S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 441 EIQSMAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFL 500

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 501 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 560

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDF
Sbjct: 561 IVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDF 620

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF V
Sbjct: 621 IEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 680

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 681 TRERIRQIEAKALRKLKHPSRSRKLRSFLD 710


>gi|39934363|ref|NP_946639.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           CGA009]
 gi|39648212|emb|CAE26731.1| RNA polymerase sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           CGA009]
          Length = 698

 Score =  740 bits (1910), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/672 (58%), Positives = 490/672 (72%), Gaps = 16/672 (2%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--- 77
           S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS+MGINV   
Sbjct: 31  SPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLSDMGINVSEA 90

Query: 78  --VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
              + ++ E +E +++ LD       +    + +K      TDDPVRMYLREMG++ELLS
Sbjct: 91  EDTEAEEEEAKEEADEELDNDLVEVTAKAVTETKKSEPGERTDDPVRMYLREMGTVELLS 150

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPE 194
           REGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IIDLEA   GPE
Sbjct: 151 REGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIIDLEATYAGPE 210

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            K       E  + +    +           +      A +     R    +  E     
Sbjct: 211 GKNNIGEPGEEAAAEGEGGAPAHVAPPAAPPSATPFRPAQQ-----RGAAPAEAEGEGAP 265

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSV- 312
           E + D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+  +  Q ++E+ S  
Sbjct: 266 EGDGDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQDIANQLQNEQLSPS 325

Query: 313 ---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
              K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  E  L+RLA S+G+ RD 
Sbjct: 326 QERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFESRLMRLADSHGVARDD 385

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL  +QG ELDP W++         WKNFV  E D I  +R E++S++  TG+ I EFR 
Sbjct: 386 FLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKDLRQEVQSMAALTGLEIGEFRK 445

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 446 IVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 505

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M N+I REPTP
Sbjct: 506 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLNEIGREPTP 565

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV P+D+AIQ+NL
Sbjct: 566 EELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVLPIDAAIQSNL 625

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKH
Sbjct: 626 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 685

Query: 670 PSRSKKLRSFLD 681
           PSRS+KLRSFLD
Sbjct: 686 PSRSRKLRSFLD 697


>gi|146338438|ref|YP_001203486.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. ORS278]
 gi|146191244|emb|CAL75249.1| sigma D (sigma 70) factor of RNA polymerase [Bradyrhizobium sp.
           ORS278]
          Length = 703

 Score =  739 bits (1907), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/697 (56%), Positives = 502/697 (72%), Gaps = 30/697 (4%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K ++ +D+  +D+ D  S + D SD + KKMIK A++RG+VT ++LN  LPPD  S EQ+
Sbjct: 15  KDDKAADAPEKDAADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPPDTTSPEQI 74

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDD 119
           ED ++MLS+MGINV + ++ ++ E  +D  D   +     +  +V   K+ +  +R TDD
Sbjct: 75  EDIMSMLSDMGINVTEAEETDEAEDKDDGDDETDNELVEITQKAVTEVKKSEPGER-TDD 133

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  
Sbjct: 134 PVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKI 193

Query: 180 LLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LR+IIDLEA   GPESKGG      G         +  +             +A   + 
Sbjct: 194 FLRDIIDLEATYAGPESKGGMNPQIAG--------PANGEAAAGEGGEIQAAVAAPPAAP 245

Query: 239 DDRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQLRPKVMCALDEIAE 289
              +   + P  A  +E++  E            ++  +L+A+E +L+PKV+   D+IA 
Sbjct: 246 QQATPFRAAPNGAPAEEKDPGEAAAEADMDDDEFENQMSLAAIEAELKPKVVETFDKIAS 305

Query: 290 VYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            Y++LR LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLYD
Sbjct: 306 EYKKLRRLQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYD 365

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           I+K+++  E  L+RLA S+G+ R+ FL  +QG ELDP W++         WKNFV  E D
Sbjct: 366 INKKLVSFESRLMRLADSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHYEKD 425

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I  +R E++S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYT
Sbjct: 426 RIKDLRQEVQSLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYT 485

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 486 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 545

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+
Sbjct: 546 MIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEE 605

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE
Sbjct: 606 DSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 665

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 666 VGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 702


>gi|316935466|ref|YP_004110448.1| RpoD subfamily RNA polymerase sigma 70 subunit [Rhodopseudomonas
           palustris DX-1]
 gi|315603180|gb|ADU45715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopseudomonas
           palustris DX-1]
          Length = 698

 Score =  736 bits (1900), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/673 (58%), Positives = 490/673 (72%), Gaps = 16/673 (2%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--- 77
           S + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS+MGINV   
Sbjct: 31  SPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLSDMGINVSEA 90

Query: 78  --VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
              + ++ E +E +++ LD       +    + +K      TDDPVRMYLREMG++ELLS
Sbjct: 91  EDTEAEEEEAKEEADEELDNDLVEVTAKAVTETKKSEPGERTDDPVRMYLREMGTVELLS 150

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPE 194
           REGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IIDLEA   GPE
Sbjct: 151 REGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIIDLEATYAGPE 210

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            K        G S ++     +      V        +        R    +  E     
Sbjct: 211 GKNNI-----GDSGEEAAAEGEGGAPAHVAPPAAPPSATPFRPAQQRGAAPAEGEGEGAP 265

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSV- 312
           E + D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+  +  Q ++E+ S  
Sbjct: 266 EGDGDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQDIANQLQNEQLSPS 325

Query: 313 ---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
              K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  E  L+RLA S+G+ RD 
Sbjct: 326 QERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFESRLMRLADSHGVARDD 385

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL  +QG ELDP W++         WKNFV  E D I  +R E++S++  TG+ I EFR 
Sbjct: 386 FLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKDLRQEVQSMAALTGLEIGEFRK 445

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 446 IVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 505

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M N+I REPTP
Sbjct: 506 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLNEIGREPTP 565

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV P+D+AIQ+NL
Sbjct: 566 EELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVLPIDAAIQSNL 625

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKH
Sbjct: 626 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 685

Query: 670 PSRSKKLRSFLDG 682
           PSRS+KLRSFLD 
Sbjct: 686 PSRSRKLRSFLDN 698


>gi|299131999|ref|ZP_07025194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
 gi|298592136|gb|EFI52336.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
          Length = 709

 Score =  733 bits (1893), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/698 (57%), Positives = 499/698 (71%), Gaps = 26/698 (3%)

Query: 6   KRNRDSDSEHEDSDD--SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K  + +++  +DS D  S + D SD + KKMIK A++RG+VT ++LN  LP D+ S EQ+
Sbjct: 15  KEAKAAETPEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDQTSPEQI 74

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS----NSSVFLQKRKDSADRSTDD 119
           ED +AMLS+MGINV + DD  DE+  +D  D  +        S    + +K      TDD
Sbjct: 75  EDIMAMLSDMGINVSEADDANDEDEEKDEADDDTDNELVEVTSKAVTETKKSEPGERTDD 134

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  
Sbjct: 135 PVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKI 194

Query: 180 LLREIIDLEACI-GPESKGG----FFHGTEGHSYQKR------EDSSQEKERDDVQETEG 228
            LR+IIDLEA   GPE K G       G  G   Q        + + Q          + 
Sbjct: 195 FLRDIIDLEATYAGPEGKNGVNPAMIAGPVGPDGQPTAAVVNGDGTVQVIAAQQAAPAQT 254

Query: 229 DIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
             ++A        +  D+     + DE    +DE ++  +L+A+E +L+P+V+   D+IA
Sbjct: 255 APQTATPFRPAPAAGDDAAAPEGDGDE----DDEFENQMSLAAIEAELKPRVVETFDKIA 310

Query: 289 EVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
             Y++LR LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLY
Sbjct: 311 SEYKKLRRLQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLY 370

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++  EG L RL  S+G+ R+ FL+ + G ELDP W++         WKNFVA E 
Sbjct: 371 DINKRLVSYEGRLFRLGDSHGVGREDFLKNYVGSELDPRWLNRVSKLAAKGWKNFVAHEK 430

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D I  +R+EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKY
Sbjct: 431 DKIKDLRHEIQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKY 490

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 491 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 550

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE
Sbjct: 551 HMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDE 610

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 611 EDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 670

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 671 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 708


>gi|300023333|ref|YP_003755944.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525154|gb|ADJ23623.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 666

 Score =  733 bits (1891), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/673 (57%), Positives = 488/673 (72%), Gaps = 43/673 (6%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           DS + D SD + K+++K A+ +GYVT+++LN+ LP +EVSS+Q+ED  A LS+MGI VV+
Sbjct: 25  DSPLLDLSDQAVKRLLKSAKAKGYVTLDQLNSVLPSEEVSSDQIEDLYATLSDMGITVVE 84

Query: 80  GDDLEDEEGSEDSLDL-----ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
            +D E+     +         A  A N+++   + K      TDDPVRMYLREMGS+ELL
Sbjct: 85  NEDGEEAAEGSEESGDEEEGRALVAQNNALVKSETKSEPAERTDDPVRMYLREMGSVELL 144

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GP 193
           SREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  LLR+IIDLEA   GP
Sbjct: 145 SREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKILLRDIIDLEATYEGP 204

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           E+K                   QE   +D  E E             +   +  P  A  
Sbjct: 205 EAK-----------------EVQEAASEDSPEPE-------------QPAANQRPSGAPE 234

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ--KDEKSS 311
            E + D+DE ++A +L+AME +L+PKV+   D+IA  Y++LR  QD  +  Q   D+ S 
Sbjct: 235 GEGD-DDDEFENAMSLAAMEAELKPKVLETFDQIAATYKKLRKQQDKKLEQQLVGDQGSR 293

Query: 312 VKCKV---LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
            + K    ++++++  V SLSLN +RI+ LVEQLY I+KR++  EG L+RLA SYG+ R 
Sbjct: 294 QQQKAYEKIRDEIIVDVKSLSLNNNRIESLVEQLYAINKRLIGLEGRLMRLADSYGVPRQ 353

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F++ + G ELD  W+       + +W  FV  E   ++ IR EI  ++ ETG+ I E+R
Sbjct: 354 HFIDEYYGNELDQTWLDRVAGNGK-KWGQFVKTERTQVVDIRTEIHQLATETGLEIPEYR 412

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 413 RIVKAVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 472

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPT
Sbjct: 473 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPT 532

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIED+NAV P+++AIQ+N
Sbjct: 533 PEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDRNAVLPIEAAIQSN 592

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLK
Sbjct: 593 LRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+KLRSFLD
Sbjct: 653 HPSRSRKLRSFLD 665


>gi|188579854|ref|YP_001923299.1| RNA polymerase sigma factor RpoD [Methylobacterium populi BJ001]
 gi|179343352|gb|ACB78764.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium populi
           BJ001]
          Length = 667

 Score =  727 bits (1877), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/693 (55%), Positives = 488/693 (70%), Gaps = 57/693 (8%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  +Q+ED +A 
Sbjct: 10  DADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDGDQIEDVLAQ 69

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLD-------------LASSASNSSVFLQK--RKDSAD 114
           L +MGI VV+ ++ E+      +               +A +A + +V +     ++  D
Sbjct: 70  LDDMGIRVVEAEESEETATEAKANGEAAEEEESAEGGEVAETAGSRAVAVATPTTREPTD 129

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           R TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 130 R-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 188

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            DG  LLR+IIDLEA   GP+++G                                   A
Sbjct: 189 VDGKVLLRDIIDLEATYAGPDARGA-----------------------------PQGGEA 219

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            +  + +      PPE  +      DED+ ++  +L+AME +++P+V+   D IA  YR+
Sbjct: 220 EEGEESEDGDGAVPPEGGD------DEDDMENNVSLAAMEAEIKPRVLETFDNIASNYRK 273

Query: 294 LRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ+      A  G      + K   LK+ +V  V SLSLN +RI+ LVEQLYDI+KR
Sbjct: 274 LRKLQNEETDLKAGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQLYDINKR 333

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV      +  
Sbjct: 334 LISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVERGGRQVAD 393

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 394 LREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGL 453

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 454 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 513

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 514 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 573

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 574 GDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 633

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 634 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 666


>gi|218528655|ref|YP_002419471.1| RNA polymerase sigma factor RpoD [Methylobacterium chloromethanicum
           CM4]
 gi|240137186|ref|YP_002961655.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
 gi|218520958|gb|ACK81543.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
           chloromethanicum CM4]
 gi|240007152|gb|ACS38378.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
          Length = 666

 Score =  726 bits (1873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/693 (55%), Positives = 493/693 (71%), Gaps = 58/693 (8%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  +Q+ED +A 
Sbjct: 10  DADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDGDQIEDVLAQ 69

Query: 70  LSNMGINVVD-------------GDDLEDEEGSEDSLDLASSASNSSVFLQK--RKDSAD 114
           L +MGI VV+               +  +EE S +  ++A ++   +V +     ++  D
Sbjct: 70  LDDMGIRVVEAEESEEAAPEAKANGEASEEEESTEGGEVAETSGTRAVAVATPTTREPTD 129

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           R TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 130 R-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 188

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            DG  LLR+IIDLEA   GP+++G                                 E+ 
Sbjct: 189 VDGKVLLRDIIDLEATYAGPDARGA------------------------------PQEAE 218

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           A+  + + ++   PPE A+      DED+ ++  +L+AME +++P+V+   D IA  YR+
Sbjct: 219 AEGEESEEAEGAVPPEGAD------DEDDMENNVSLAAMEAEIKPRVLETFDNIASNYRK 272

Query: 294 LRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ+         G      + K   LK+ +V  V SLSLN +RI+ LVEQLYDI+KR
Sbjct: 273 LRKLQNEETELKTGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQLYDINKR 332

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV      +  
Sbjct: 333 LISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVERGGRQVAD 392

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 393 LREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGL 452

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 453 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 512

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 513 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 572

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 573 GDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 632

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 633 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665


>gi|170747007|ref|YP_001753267.1| RNA polymerase sigma factor RpoD [Methylobacterium radiotolerans
           JCM 2831]
 gi|170653529|gb|ACB22584.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
           radiotolerans JCM 2831]
          Length = 659

 Score =  726 bits (1873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/688 (55%), Positives = 482/688 (70%), Gaps = 55/688 (7%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++D+  E   D  + D +D S K+M+KLA++RGYVT EE+N  LP  +   +Q+ED ++ 
Sbjct: 10  ETDAAPEQQTDGPLLDLTDASVKRMVKLAKKRGYVTYEEVNEVLPEGQSDPDQLEDVLSQ 69

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR----------KDSADRSTDD 119
           LS MGINVV+ ++ ++  G + +      A    V               K+  DR TDD
Sbjct: 70  LSEMGINVVEAEETDEAAGEKAADGEEEEAEGGEVAEVAPARAVAVATTTKEPTDR-TDD 128

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL +G  
Sbjct: 129 PVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVEGKV 188

Query: 180 LLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           LLR+IIDLEA   GP+ K                                   +A ++++
Sbjct: 189 LLRDIIDLEATYAGPDGK-----------------------------------NAPQLAE 213

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            + S+   PP   E  +   DED+ ++  +L+AME +++P+V+   D IA  YR+LR  Q
Sbjct: 214 GEESEDGEPPAPPEGGD---DEDDLENNVSLAAMEAEIKPRVLETFDAIAANYRKLRKFQ 270

Query: 299 -----DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
                  A   Q       K   LK+ +V  V SLSLN +RI+ LV QLY I+K+++ +E
Sbjct: 271 IEGTERKAAGEQNTPAQDQKQAELKDIVVADVKSLSLNNNRIEALVGQLYSINKQLIGHE 330

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           G L+R A+S+G+ RD FL  +QG ELDP+W+          WKN V      + ++R +I
Sbjct: 331 GRLMRFAESHGVARDEFLRHYQGYELDPNWMERVGTLGGKGWKNLVERGSKQVAELRAQI 390

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             ++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 391 LDLASETGLEIGEYRRIVNMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDL 450

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 451 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIV 510

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIE
Sbjct: 511 RTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 570

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 571 DKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTR 630

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 631 ERIRQIEAKALRKLKHPSRSRKLRSFLD 658


>gi|254559198|ref|YP_003066293.1| sigma D factor of RNA polymerase [Methylobacterium extorquens DM4]
 gi|254266476|emb|CAX22240.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens DM4]
          Length = 666

 Score =  724 bits (1869), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/693 (55%), Positives = 492/693 (70%), Gaps = 58/693 (8%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  +Q+ED +A 
Sbjct: 10  DADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDGDQIEDVLAQ 69

Query: 70  LSNMGINVVD-------------GDDLEDEEGSEDSLDLASSASNSSVFLQK--RKDSAD 114
           L +MGI VV+               +  +EE S +  ++A ++   +V +     ++  D
Sbjct: 70  LDDMGIRVVEAEESEEAAPEAKANGEASEEEESTEGGEVAETSGTRAVAVATPTTREPTD 129

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           R TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 130 R-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 188

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            DG  LLR+IIDLEA   GP+++G                                 E+ 
Sbjct: 189 VDGKVLLRDIIDLEATYAGPDARGA------------------------------PQEAE 218

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           A+  + + ++   PPE  +      DED+ ++  +L+AME +++P+V+   D IA  YR+
Sbjct: 219 AEGEESEEAEGAVPPEGGD------DEDDMENNVSLAAMEAEIKPRVLETFDNIASNYRK 272

Query: 294 LRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ+         G      + K   LK+ +V  V SLSLN +RI+ LVEQLYDI+KR
Sbjct: 273 LRKLQNEETELKTGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQLYDINKR 332

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV      +  
Sbjct: 333 LISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVERGGRQVAD 392

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 393 LREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGL 452

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 453 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 512

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 513 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 572

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 573 GDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 632

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 633 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665


>gi|163850052|ref|YP_001638095.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
 gi|163661657|gb|ABY29024.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
          Length = 718

 Score =  724 bits (1868), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/693 (55%), Positives = 492/693 (70%), Gaps = 58/693 (8%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  +Q+ED +A 
Sbjct: 62  DADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDGDQIEDVLAQ 121

Query: 70  LSNMGINVVD-------------GDDLEDEEGSEDSLDLASSASNSSVFLQK--RKDSAD 114
           L +MGI VV+               +  +EE S +  ++A ++   +V +     ++  D
Sbjct: 122 LDDMGIRVVEAEESEEAAPEAKANGEASEEEESTEGGEVAETSGTRAVAVATPTTREPTD 181

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           R TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 182 R-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 240

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            DG  LLR+IIDLEA   GP+++G                                 E+ 
Sbjct: 241 VDGKVLLRDIIDLEATYAGPDARGA------------------------------PQEAE 270

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           A+  + + ++   PPE  +      DED+ ++  +L+AME +++P+V+   D IA  YR+
Sbjct: 271 AEGEESEEAEGAVPPEGGD------DEDDMENNVSLAAMEAEIKPRVLETFDNIASNYRK 324

Query: 294 LRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ+         G      + K   LK+ +V  V SLSLN +RI+ LVEQLYDI+KR
Sbjct: 325 LRKLQNEETELKTGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQLYDINKR 384

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV      +  
Sbjct: 385 LISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVERGGRQVAD 444

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 445 LREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGL 504

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 505 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 564

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 565 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 624

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 625 GDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 684

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 685 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 717


>gi|154252764|ref|YP_001413588.1| RNA polymerase sigma factor RpoD [Parvibaculum lavamentivorans
           DS-1]
 gi|154156714|gb|ABS63931.1| RNA polymerase, sigma 70 subunit, RpoD [Parvibaculum
           lavamentivorans DS-1]
          Length = 656

 Score =  712 bits (1838), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/668 (58%), Positives = 476/668 (71%), Gaps = 38/668 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SD + KKMIK A+ RG+VT +ELN  LP +E SSEQ+EDT++MLS MGINVV+
Sbjct: 20  DGPLLDMSDAAVKKMIKAAKARGFVTYDELNKVLPSEEFSSEQIEDTLSMLSEMGINVVE 79

Query: 80  GDDLEDEEGSEDSLDLASSA-----SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
            D+ ED     D             +  +V       S+   TDDPVRMYLREMGS+ELL
Sbjct: 80  NDEAEDNAEGADGEADEDRDDEEAPTGKAVATTTTTSSSLDRTDDPVRMYLREMGSVELL 139

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GP 193
           SREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  LLR+IIDL+A   GP
Sbjct: 140 SREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELNEGKILLRDIIDLDATFAGP 199

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           ++K    H     + +       E+E  D    + +  S A +  + + KV    +    
Sbjct: 200 DAK-KVDHSQAALAGEAPPRIEPEEEEVDEDGEDDNSMSLAAMEAELKPKVLETFDTIAA 258

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           D + L +           ++DQ   KV  AL             Q  A++  +++K    
Sbjct: 259 DYKKLRK-----------LQDQ---KVELAL-------------QGEALSSAQEKK---- 287

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            + L   L++ V SLSLN +RI+ LVEQLY I+KR+M  EG LLRLA+S+GI RD FL++
Sbjct: 288 YQKLTSDLIEEVKSLSLNNNRIESLVEQLYAINKRLMGLEGRLLRLAESHGIPRDEFLKQ 347

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           + G ELDP+W+          W NF   E D +  +R EI++++ ETG+ I E+R IVS 
Sbjct: 348 YFGNELDPNWIRRVSRLKGKGWVNFTKDERDQVKDLRQEIQTLASETGLDIQEYRRIVSG 407

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 408 VQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 467

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A
Sbjct: 468 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELA 527

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQ+NLRETT
Sbjct: 528 EKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETT 587

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS
Sbjct: 588 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 647

Query: 674 KKLRSFLD 681
           +KLRSFLD
Sbjct: 648 RKLRSFLD 655


>gi|295690890|ref|YP_003594583.1| RNA polymerase sigma 70 factor subunit RpoD [Caulobacter segnis
           ATCC 21756]
 gi|295432793|gb|ADG11965.1| RNA polymerase, sigma 70 subunit, RpoD [Caulobacter segnis ATCC
           21756]
          Length = 652

 Score =  707 bits (1824), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/677 (56%), Positives = 479/677 (70%), Gaps = 38/677 (5%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++++      D  + D +D   KK IK A+ RGYVT++ELN  LP +EVS + +EDT+AM
Sbjct: 8   ETEAPEATGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAM 67

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MG+NVV+    E++    +  ++A+   N++V    +  + DR TDDPVRMYLREMG
Sbjct: 68  LSEMGVNVVE---AEEDAEGGEGGEVATRDENTTVITSDKPAAYDR-TDDPVRMYLREMG 123

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLRE+IDLE 
Sbjct: 124 SVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGSGRILLREVIDLE- 182

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                   G +    G + Q              ++ EG  E       DD +  ++ PE
Sbjct: 183 --------GTYAAINGVAAQP-----------AAEDEEGPAEPI-----DDEAG-EAKPE 217

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK--- 306
            AE ++ +  + +D +  T+SAME +LR  VM  LD IA  +   R LQD  V  +    
Sbjct: 218 GAEGEDDD--DFDDGAGPTVSAMEGELREGVMAILDAIASEFESFRKLQDKLVGSRLKGE 275

Query: 307 --DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
              E      + L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LLRLA SYG
Sbjct: 276 DLSEADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYG 335

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  FL+ + G EL+P W    K      W  FV  +  SI  IR EI +++ ETG+ I
Sbjct: 336 ISRAEFLKAYFGSELNPTWGEQVKAMGV-RWTKFVENDNSSISDIRQEIAALATETGVPI 394

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 395 DDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 454

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I 
Sbjct: 455 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIG 514

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+A
Sbjct: 515 REPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAA 574

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 575 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 634

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 635 RKLKHPSRSRKLRSFLD 651


>gi|159044804|ref|YP_001533598.1| RNA polymerase sigma factor RpoD [Dinoroseobacter shibae DFL 12]
 gi|157912564|gb|ABV93997.1| RNA polymerase sigma factor [Dinoroseobacter shibae DFL 12]
          Length = 664

 Score =  706 bits (1823), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/680 (55%), Positives = 474/680 (69%), Gaps = 56/680 (8%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + D S  + KKMI  AR RGY+T ++LN  LPPD+VSSEQ+ED ++MLS MGIN+++ D+
Sbjct: 19  MLDMSQAAVKKMIAEARTRGYITYDQLNQVLPPDQVSSEQIEDVMSMLSEMGINIIEEDE 78

Query: 83  LEDEEGSED-SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            ED +   + S  +  S+S+  V +          TDDPVRMYLREMGS+ELLSREGEIA
Sbjct: 79  AEDGDAPANASTQVVESSSSREVAVSTSSSETLDRTDDPVRMYLREMGSVELLSREGEIA 138

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA +G    G    
Sbjct: 139 IAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEATMG----GAM-- 192

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE-NDERNLDE 260
                              D+ +E+   +E AA          +SP   +E +DE  LD 
Sbjct: 193 -------------------DEDEESSSVVEMAA----------NSPAAPSEKSDEPELDA 223

Query: 261 DEDDSAHT-------------LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG--Q 305
           D +  A T             L+AME  L+PKV+  LD IA  Y +L  +QD  ++    
Sbjct: 224 DGNPIAKTDDEDDEDDQANMSLAAMEAALKPKVLETLDLIARDYAQLSEMQDLRISATLN 283

Query: 306 KDEKSSVK----CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
           +DE  SV+     + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  +++LA 
Sbjct: 284 EDESFSVEDESNYQKLRAEIVLLVNELHLHNNRIEALIDQLYGINRRIMAIDSSMVKLAD 343

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              I R  F+E ++G ELDP W+    + P   W+ F+      I ++R+++  +    G
Sbjct: 344 QARINRREFVEAYRGYELDPTWLERMAEKPGRGWQAFIERSTTKIEELRSDMAQVGTYVG 403

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I+EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 404 VDITEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 463

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M +
Sbjct: 464 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLH 523

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PL
Sbjct: 524 EIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPL 583

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 584 DSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 643

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+KLRSFLD
Sbjct: 644 KALRKLKHPSRSRKLRSFLD 663


>gi|167648221|ref|YP_001685884.1| RNA polymerase sigma factor RpoD [Caulobacter sp. K31]
 gi|167350651|gb|ABZ73386.1| RNA polymerase, sigma 70 subunit, RpoD [Caulobacter sp. K31]
          Length = 649

 Score =  706 bits (1822), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/670 (56%), Positives = 471/670 (70%), Gaps = 47/670 (7%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D +D   KK IK A+ RGYVT++ELN  LP +EV+SE +EDT+AMLS MG+NVV+
Sbjct: 18  DGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVTSEAIEDTLAMLSEMGVNVVE 77

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +  ED E SE   ++ +   N  V    +  + DR TDDPVRMYLREMGS+ELLSREGE
Sbjct: 78  AE--EDAETSEGG-EVVAREDNQQVITSDKPAAYDR-TDDPVRMYLREMGSVELLSREGE 133

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLRE+IDLE         G 
Sbjct: 134 IAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLREVIDLE---------GT 184

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
           +    G +     D    +  D  +E   + ++  +  +DD      P            
Sbjct: 185 YAAINGVAAAPAADDEPAEPSD--EEPGSEPKAEGEEDEDDFDDGAGP------------ 230

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ--------KDEKSS 311
                   T+SAME +LR  VM  LD IA  +   R LQD  V  +         D K+ 
Sbjct: 231 --------TVSAMEGELREGVMAILDAIASEFETFRKLQDKLVGSRLKGADLSDADRKA- 281

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
              + L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LLRLA SYGI R  FL
Sbjct: 282 --YEGLSNTIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYGISRSEFL 339

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           + + G EL+P+W+   K      W  FV  + +S+  IR EI +++ ETG+ I ++R IV
Sbjct: 340 KAYFGSELNPNWIDQVKAMGV-RWTKFVENDTNSVGDIRQEIAALATETGVPIDDYRRIV 398

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 399 QTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 458

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE
Sbjct: 459 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEE 518

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQ+NLRE
Sbjct: 519 LAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRE 578

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPS
Sbjct: 579 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 638

Query: 672 RSKKLRSFLD 681
           RS+KLRSFLD
Sbjct: 639 RSRKLRSFLD 648


>gi|149914287|ref|ZP_01902818.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
 gi|149811806|gb|EDM71639.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
          Length = 662

 Score =  705 bits (1820), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/682 (55%), Positives = 486/682 (71%), Gaps = 36/682 (5%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D + ED +  L  D S  + KKMI  AR++G++T ++LN  LPPD+VSSEQ+ED ++M
Sbjct: 6   NDDQKPEDQEAELSLDMSQAAVKKMIGEAREKGFITYDQLNKVLPPDQVSSEQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGIN+++  + + E+  + S  +A       + L   KD     TDDPVRMYLREMG
Sbjct: 66  LSEMGINIIE--EEDAEDEEQKSTAVAEIGRRGELALGSGKDEKLDRTDDPVRMYLREMG 123

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA
Sbjct: 124 SVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLGEDILLRDVIDLEA 183

Query: 190 CIGPESKGGFFHGTEGHSYQKRE----DSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
             G +       G +G +    E     ++   ER D  + E D          D + + 
Sbjct: 184 TFGTQ------MGEDGEAEAVVEAANVTTAPASERRDDGQPELDA---------DGNPIA 228

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
           S  ++ E+++ N+         +L+AME  L+P+V+  LD IA+ Y +L  +QD+ ++  
Sbjct: 229 SEDDDDEDEQANM---------SLAAMEAALKPRVLETLDRIADDYEKLSEMQDSRISAT 279

Query: 306 KDEKSSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +E  S   K       L+ ++V+LV SL L+ +RI+ L++QLY I++RIM  +G +++L
Sbjct: 280 LNEDGSFSAKQEQTYQTLRSEIVQLVNSLHLHNNRIEALIDQLYGINRRIMQIDGAMVKL 339

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A    I R  F++ ++GRELDP+W+    +     WK F+   +D + ++R ++  +   
Sbjct: 340 ADQARINRREFIDEYRGRELDPNWLDDMAEKDGRGWKMFMERSLDKVSELRADMAQVGQY 399

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+ ISEFR IV+ V+KGE EA +AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 400 VGLDISEFRRIVAQVQKGEKEARLAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 459

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M
Sbjct: 460 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQM 519

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN V 
Sbjct: 520 LHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNVVL 579

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PLDSAIQ NLRETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 580 PLDSAIQDNLRETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 639

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 640 EAKALRKLKHPSRSRKLRSFLD 661


>gi|197106036|ref|YP_002131413.1| RNA polymerase sigma factor RpoD [Phenylobacterium zucineum HLK1]
 gi|196479456|gb|ACG78984.1| RNA polymerase sigma factor RpoD [Phenylobacterium zucineum HLK1]
          Length = 638

 Score =  705 bits (1820), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 382/669 (57%), Positives = 464/669 (69%), Gaps = 55/669 (8%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D +D + KK IK A+ RGYVT++ELN  +P +EV+SE +EDT+AML+ MG+NVV+
Sbjct: 17  DGPLLDLTDAAVKKFIKQAKARGYVTMDELNKVMPSEEVTSEAIEDTLAMLNEMGVNVVE 76

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +  ED EG E       +    S  ++  K+ A   TDDPVRMYLREMGS+ELLSREGE
Sbjct: 77  SE--EDAEGGE------VAVREESAVVETTKEPAYDRTDDPVRMYLREMGSVELLSREGE 128

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLRE+IDLE   G +++G  
Sbjct: 129 IAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELEGGRILLREVIDLEQTYGGQNQGEA 188

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                     + E +  E E DD                                     
Sbjct: 189 PAEAAEAEEPEAEGAEGEGESDD------------------------------------- 211

Query: 260 EDEDDSAH-TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-----KDEKSSVK 313
            D DD A  T+SAME +LR  VM  LD IA  +   R LQ+  V  +       E     
Sbjct: 212 -DFDDGAGPTISAMEAELREGVMATLDAIAAEFESFRLLQEKLVAAKLKGEDLSEGDRKA 270

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            +     +V+ + +L LN +RI+ LVEQLY I+KR+M  EG LLRLA SYGI R  FL+ 
Sbjct: 271 YQAATGAIVQHLKTLKLNNNRIEALVEQLYAINKRLMVLEGRLLRLADSYGISRQEFLKA 330

Query: 374 HQGRELDPHWVSYAKDFPEG-EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           + G E+ P W    K  P G  W  F   +   I +IRNEI +++ ETG+ I ++R IV 
Sbjct: 331 YFGNEMRPDWTDMVK--PLGVRWTKFAENDASQIGEIRNEIAALAQETGVPIDDYRRIVQ 388

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 389 TVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 448

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+
Sbjct: 449 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEEL 508

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQ+NLRET
Sbjct: 509 AEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRET 568

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 569 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 628

Query: 673 SKKLRSFLD 681
           S+KLRSFLD
Sbjct: 629 SRKLRSFLD 637


>gi|16127277|ref|NP_421841.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1710678|sp|P52324|RPOD_CAUCR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1079588|gb|AAA82054.1| RNA polymerase principal sigma factor [Caulobacter crescentus CB15]
 gi|13424691|gb|AAK25009.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1585612|prf||2201399A sigma73 factor
          Length = 652

 Score =  703 bits (1815), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/679 (56%), Positives = 473/679 (69%), Gaps = 42/679 (6%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++++      D  + D +D   KK IK A+ RGYVT++ELN  LP +EVS + +EDT+AM
Sbjct: 8   ETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAM 67

Query: 70  LSNMGINVVDGDDLEDEE-GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           LS MG+NVV+ ++  +   G E    +A+   N++V    +  + DR TDDPVRMYLREM
Sbjct: 68  LSEMGVNVVEAEEDAENAEGGE----VATRDENTTVIASDKPAAYDR-TDDPVRMYLREM 122

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLRE+IDLE
Sbjct: 123 GSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLREVIDLE 182

Query: 189 ACIGPESKGGFFHGTEGHSYQ-KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                    G +    G + Q   ED     E  D +  E   E A    +DD      P
Sbjct: 183 ---------GTYAAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGP 233

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG--Q 305
                               T+SAME +LR  VM  LD IA  +   R LQD  V    +
Sbjct: 234 --------------------TVSAMEGELREGVMAILDAIASEFEAFRKLQDKLVGSRLK 273

Query: 306 KDEKSSVKCKV---LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            ++ S    K    L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LLRLA S
Sbjct: 274 GEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADS 333

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           YGI R  FL+ + G EL+P W    K      W  FV  +  S+  IR+EI +++ ETG+
Sbjct: 334 YGISRGEFLKAYFGSELNPTWSEQVKAMGV-RWTKFVENDSQSVTDIRSEIAALATETGV 392

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 393 PIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 452

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++
Sbjct: 453 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHE 512

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D
Sbjct: 513 IGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPID 572

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 573 AAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 632

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 633 ALRKLKHPSRSRKLRSFLD 651


>gi|221236078|ref|YP_002518515.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus NA1000]
 gi|220965251|gb|ACL96607.1| RNA polymerase sigma factor rpoD [Caulobacter crescentus NA1000]
          Length = 653

 Score =  703 bits (1814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/679 (56%), Positives = 473/679 (69%), Gaps = 42/679 (6%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++++      D  + D +D   KK IK A+ RGYVT++ELN  LP +EVS + +EDT+AM
Sbjct: 9   ETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAM 68

Query: 70  LSNMGINVVDGDDLEDEE-GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           LS MG+NVV+ ++  +   G E    +A+   N++V    +  + DR TDDPVRMYLREM
Sbjct: 69  LSEMGVNVVEAEEDAENAEGGE----VATRDENTTVIASDKPAAYDR-TDDPVRMYLREM 123

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLRE+IDLE
Sbjct: 124 GSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLREVIDLE 183

Query: 189 ACIGPESKGGFFHGTEGHSYQ-KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                    G +    G + Q   ED     E  D +  E   E A    +DD      P
Sbjct: 184 ---------GTYAAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGP 234

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG--Q 305
                               T+SAME +LR  VM  LD IA  +   R LQD  V    +
Sbjct: 235 --------------------TVSAMEGELREGVMAILDAIASEFEAFRKLQDKLVGSRLK 274

Query: 306 KDEKSSVKCKV---LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            ++ S    K    L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LLRLA S
Sbjct: 275 GEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADS 334

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           YGI R  FL+ + G EL+P W    K      W  FV  +  S+  IR+EI +++ ETG+
Sbjct: 335 YGISRGEFLKAYFGSELNPTWSEQVKAMGV-RWTKFVENDSQSVTDIRSEIAALATETGV 393

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 394 PIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 453

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++
Sbjct: 454 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHE 513

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D
Sbjct: 514 IGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPID 573

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 574 AAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 633

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 634 ALRKLKHPSRSRKLRSFLD 652


>gi|229526927|ref|ZP_04416329.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
 gi|229336054|gb|EEO01074.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
          Length = 547

 Score =  703 bits (1814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/571 (63%), Positives = 440/571 (77%), Gaps = 35/571 (6%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +RMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRD+LND   L
Sbjct: 1   MRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLNDSNIL 60

Query: 181 LREIIDLEACI-GPESK-GGFFHGTEGHSYQKREDSSQEKERDD--VQETEGDIESAAKV 236
           LREIIDLE    GPE+K        E    + R+D  Q + RDD  +    GD+    + 
Sbjct: 61  LREIIDLETTYAGPEAKQAPVIERVEEE--KPRDDKPQRRSRDDDDITNVGGDMPVEEEE 118

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             +D + +                       +L+AME +LRP+VM  LD IA+ Y++LR 
Sbjct: 119 EDEDEANL-----------------------SLAAMEAELRPQVMETLDLIADTYKKLRK 155

Query: 297 LQDNAVNGQ---KDEKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           LQD  V G+     E SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++
Sbjct: 156 LQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLV 215

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            NEG+LLRLA+S+G++R+ FL+ +QG ELDP WV          WK F A E  +I ++R
Sbjct: 216 QNEGKLLRLAESFGVRREEFLKEYQGHELDPKWVERVSTLSARGWKEFAAKEERTIDRLR 275

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +EI+ ++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 276 SEIQMLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQF 335

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 336 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 395

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGD
Sbjct: 396 KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGD 455

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 456 FIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 515

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 516 VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 546


>gi|163747450|ref|ZP_02154802.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
 gi|161379303|gb|EDQ03720.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
          Length = 671

 Score =  702 bits (1812), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/681 (54%), Positives = 490/681 (71%), Gaps = 31/681 (4%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           ++ + D++ +DSD     D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED 
Sbjct: 15  KDTNDDAKTDDSDSGHSLDMSQAAVKKMIGEAREKGYITYDQLNTVLPPDQVSSEQIEDV 74

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           ++MLS MGIN+++ ++ E+EE ++ S ++A++ SN  V L          TDDPVRMYLR
Sbjct: 75  MSMLSEMGINIIEDEEAEEEE-AKGSTEVATTESNRDVALSSGTSEKLDRTDDPVRMYLR 133

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++ID
Sbjct: 134 EMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVID 193

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           LEA  G +       G E  +      ++    + D  +TE D          D   + S
Sbjct: 194 LEATFGTQ------MGDEEETTPVVAPTATSDTKSDEGKTELDA---------DGHPISS 238

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
             ++ E+++ N+         +L+AME+ L+P+V+ ALD IA+ Y +L ++QD+ ++   
Sbjct: 239 DDDDDEDEQANM---------SLAAMEEALKPQVLEALDIIADDYEKLSAMQDSRISATL 289

Query: 307 DEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           +E  S         + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  +++LA
Sbjct: 290 NEDGSFTKDEEAMYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSAMVKLA 349

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               I R  F++ ++G ELDP+W+    +     W+ F+    + + ++RN++  +    
Sbjct: 350 DQARINRKEFVDNYRGYELDPNWMERMAEKSGRGWQMFIERSSEKVDELRNDMAQVGQYV 409

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 410 GLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 469

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M 
Sbjct: 470 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQML 529

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV P
Sbjct: 530 HEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLP 589

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 590 LDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 649

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKLKHPSRS+KLRSFLD
Sbjct: 650 AKALRKLKHPSRSRKLRSFLD 670


>gi|254476970|ref|ZP_05090356.1| Sigma-70, region 3 family [Ruegeria sp. R11]
 gi|214031213|gb|EEB72048.1| Sigma-70, region 3 family [Ruegeria sp. R11]
          Length = 661

 Score =  700 bits (1806), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/678 (55%), Positives = 485/678 (71%), Gaps = 33/678 (4%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DRKPDDQEPEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ ++ E+EE  + S DL ++ SN  V +   +      TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEDEEAEEEE-QKGSTDLVTTDSNREVAVAGAQTEKLDRTDDPVRMYLREMGSV 126

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 127 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 186

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA--KVSKDDRSKVDSPPE 249
           G                      +Q  E  DV E   D  + A  K +KD   ++D+   
Sbjct: 187 G----------------------NQMDEDGDVAEPVVDTSAVAANKPAKDTGPELDADGN 224

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
              +D+ + D+++  +  +L+AME  L+ KV+  L++I+  Y +L  +QD+ ++   +E 
Sbjct: 225 PIASDDDDDDDEQ--ANMSLAAMEAALKDKVLTTLEQISSDYSQLSEMQDSRISATLNED 282

Query: 310 SSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            S         + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA   
Sbjct: 283 GSFSDNDEQIYQSLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSSMVKLADQA 342

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            I R  F+E ++GRELDP+W++   + P   W+ F+    D + ++R ++  +    G+ 
Sbjct: 343 RINRREFVEAYRGRELDPNWLADMGEKPGRGWQMFIERSTDKVEELRADMAQVGQYVGLD 402

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 403 ISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 462

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 463 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 522

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDS
Sbjct: 523 GREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDS 582

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 583 AIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 642

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 643 LRKLKHPSRSRKLRSFLD 660


>gi|126727888|ref|ZP_01743716.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126702829|gb|EBA01934.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 661

 Score =  700 bits (1806), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/679 (56%), Positives = 479/679 (70%), Gaps = 31/679 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + DS+  D D+  + D S  + KKMI  AR +GY+T ++LNA LPP++VSSEQ+ED ++M
Sbjct: 6   NDDSKQNDQDNDGMTDTSQTAVKKMIAEARVKGYITYDQLNAVLPPEQVSSEQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGIN+++ ++ EDE  S D +   +      V     K+  DR TDDPVRMYLREMG
Sbjct: 66  LSEMGINIIEDEEAEDEVKSTDVV--TTDQERGLVLAGADKEKLDR-TDDPVRMYLREMG 122

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE 
Sbjct: 123 SVELLSREGEIAIAKRIEAGRKTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLET 182

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK-VSKDDRSKVDSPP 248
             G         G EG      ED           ET+   E+AA+ +  D     +   
Sbjct: 183 TFGNT------MGEEG------EDGVTAVPGAATAETKPSGETAAQELDADGNPISNDDD 230

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           ++ E+++ NL         +L+AME  L+P+V+  L+EIA+ Y EL  +QD  ++   +E
Sbjct: 231 DDDEDEQANL---------SLAAMEAVLKPRVLETLEEIADYYAELSDMQDVRISATLNE 281

Query: 309 KSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             S         + L+ K+V LV S+ L+ +RI+ L++QLY I++RIM  +  +++LA  
Sbjct: 282 SESYSSKEEDAYQALRTKIVDLVTSMHLHNNRIEALIDQLYGINRRIMQIDSSMVKLADQ 341

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F++ ++G ELDP W+    + P   W  F+    D + ++R E+  +    G+
Sbjct: 342 ARINRKEFIDAYRGHELDPTWLETIAELPGRGWAAFLERSADKVSELRTEMAQVGTYVGL 401

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 402 DISEFRRIVQQVQKGEKEARAAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 461

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 462 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 521

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+AKKL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 522 IGREPTPEELAKKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 581

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 582 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 641

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 642 ALRKLKHPSRSRKLRSFLD 660


>gi|260434101|ref|ZP_05788072.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417929|gb|EEX11188.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 662

 Score =  699 bits (1803), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/683 (55%), Positives = 487/683 (71%), Gaps = 35/683 (5%)

Query: 9   RDSDSEH--EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           +D++ E   +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED 
Sbjct: 4   KDTNEERKSDDQEQEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDV 63

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           ++MLS MGIN+++ ++ E+EE  + S DL ++ SN  V L   +      TDDPVRMYLR
Sbjct: 64  MSMLSEMGINIIEDEEAEEEE-QKGSTDLVTADSNREVALAGSQAEKLDRTDDPVRMYLR 122

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++ID
Sbjct: 123 EMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAISIWHDELLSEDILLRDVID 182

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE--SAAKVSKDDRSKV 244
           LEA  G                      +Q  E  DV+E   D     AAK +KD   ++
Sbjct: 183 LEATFG----------------------NQLDEDGDVEEPVVDTSKVQAAKPAKDTGPEL 220

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           D+      +D+ + ++++  +  +L+AME  L+ +V+  L+ I+  +  L  +QD+ ++ 
Sbjct: 221 DADGNPIASDDDDDEDEQ--ANMSLAAMEAALKDQVLTTLERISNDFAMLSEMQDSRISA 278

Query: 305 QKDEKSSVKC------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
             +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I+KR+M  +  +++
Sbjct: 279 TLNEDGSFSAEDEATYQKLRSEIVELVNGLHLHNNRIEALIDQLYGINKRVMALDSAMVK 338

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           LA    I R  F++ ++GRELDP+W+S     P   W+ F+    D + ++RN++  I  
Sbjct: 339 LADQARINRREFIDEYRGRELDPNWLSDMAQKPGRGWQMFIERSSDKVEELRNDMAQIGQ 398

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
             G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 399 YVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 458

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+
Sbjct: 459 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQ 518

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV
Sbjct: 519 MLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAV 578

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 579 LPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 638

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 639 IEAKALRKLKHPSRSRKLRSFLD 661


>gi|254464472|ref|ZP_05077883.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
 gi|206685380|gb|EDZ45862.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
          Length = 662

 Score =  698 bits (1801), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/678 (55%), Positives = 488/678 (71%), Gaps = 32/678 (4%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D D  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DRKPDDQDAEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ ++ E+EE ++ + DL ++     V L   +      TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEDEEAEEEE-NKGATDLVTTEGPREVALAGAQTEKLDRTDDPVRMYLREMGSV 126

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 127 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 186

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP--PE 249
           G +         +G       D S              +++AAK S+++  ++D+   P 
Sbjct: 187 GNQLD------EDGEDAAPVVDPSA-------------VQAAAKPSREEGPELDADGNPI 227

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV------N 303
           +A++DE   D+    +  +L+AME  L+ +V+  L+ I+  + EL  +QD+ +      +
Sbjct: 228 SADDDEDEDDQ----ANMSLAAMEAALKDRVLTTLERISTDFAELSEMQDSRISATLNED 283

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           G   E+  V+ + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA   
Sbjct: 284 GSFSEQDEVRYQSLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSSMVKLADQA 343

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            I R  F++ ++GRELDP+W+S   + P   W+ F+    D + ++R+++  +    G+ 
Sbjct: 344 RINRREFVDAYRGRELDPNWLSEMGEKPGRGWQMFIERSTDKVEELRSDMAQVGQYVGLD 403

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 404 ISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 463

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 464 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 523

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDS
Sbjct: 524 GREPTPEELADKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDS 583

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 584 AIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 643

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 644 LRKLKHPSRSRKLRSFLD 661


>gi|56696627|ref|YP_166988.1| RNA polymerase sigma factor RpoD [Ruegeria pomeroyi DSS-3]
 gi|56678364|gb|AAV95030.1| RNA polymerase sigma-70 factor RpoD [Ruegeria pomeroyi DSS-3]
          Length = 660

 Score =  698 bits (1801), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/679 (54%), Positives = 481/679 (70%), Gaps = 37/679 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + ED +D +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 9   DQKPEDQEDEVSLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 68

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ ++ E+EE  + S DL ++ SN  V L   +      TDDPVRMYLREMGS+
Sbjct: 69  EMGINIIEDEEAEEEE-QKGSTDLITTESNREVALAGAQAEKLDRTDDPVRMYLREMGSV 127

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 128 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 187

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G                          + DD  +      SA +  K  R   ++P  +A
Sbjct: 188 G-------------------------NQLDDEDDEPVVATSAVQAVKPQRE--ETPEYDA 220

Query: 252 END---ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           + +     + ++++D +  +L+AME  L+ KV+  L+ I+  Y +L  +QD+ ++   +E
Sbjct: 221 DGNPIVTEDDEDEDDQANMSLAAMEAALKDKVLITLERISSDYAQLSEMQDSRISATLNE 280

Query: 309 KSSVKC------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             S         + L+ ++V LV  L L+ +RI+ L++QLY I+KR+M  +  +++LA  
Sbjct: 281 DGSFSAHDEATYQSLRSEIVLLVNELHLHNNRIEALIDQLYGINKRVMSIDSSMVKLADQ 340

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F++ ++GRELDP+W++   + P   W+ F+    D + ++R ++  +    G+
Sbjct: 341 ARINRREFIDAYRGRELDPNWLAEMAEKPGRGWQMFIERSSDKVEELRADMAQVGQYVGL 400

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 401 DISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 460

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 461 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 520

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 521 IGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 580

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 581 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 640

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 641 ALRKLKHPSRSRKLRSFLD 659


>gi|259416365|ref|ZP_05740285.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
 gi|259347804|gb|EEW59581.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
          Length = 664

 Score =  697 bits (1799), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/679 (55%), Positives = 484/679 (71%), Gaps = 32/679 (4%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D D  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DRKPDDQDAEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ +D E+EE ++ + +L ++ SN  V +          TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEDEDAEEEE-NKGTTELVTTESNREVAVAGTGTEKLDRTDDPVRMYLREMGSV 126

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 127 ELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 186

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD---IESAAKVSKDDRSKVDSPP 248
           G                      +Q  E  DV E   D   +  AAK  KD   ++D+  
Sbjct: 187 G----------------------NQMDEEGDVAEPVVDPSAVSGAAKPEKDSGPELDADG 224

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
               N++ + D+D+D +  +L+AME  L+ +V+  L+ I+  +  L  +QD  ++   +E
Sbjct: 225 NPILNNDDDDDDDDDQANMSLAAMEAALKDRVLETLERISNDFVTLSEMQDLRISATLNE 284

Query: 309 KSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             S       + + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA  
Sbjct: 285 DGSFSKDDEARYQQLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSAMVKLADQ 344

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F+E ++GRELDP+W++   + P   W+ F+    D + ++R+++  +    G+
Sbjct: 345 ARINRKEFVEAYRGRELDPNWLAEMGEKPGRGWQMFIERSTDKVEELRSDMAQVGQYVGL 404

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 405 DISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 464

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 465 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 524

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 525 IGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 584

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 585 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 644

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 645 ALRKLKHPSRSRKLRSFLD 663


>gi|83941156|ref|ZP_00953618.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83955715|ref|ZP_00964295.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83840009|gb|EAP79185.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83846976|gb|EAP84851.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 660

 Score =  697 bits (1798), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/688 (54%), Positives = 486/688 (70%), Gaps = 41/688 (5%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K  N D+ S+ +D+  SL  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 3   AKDTNEDAKSDDQDAGHSL--DMSQAAVKKMIGEAREKGYITYDQLNTVLPPDQVSSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGINV++ ++ E+E+ ++   ++A++ SN  V L          TDDPVRM
Sbjct: 61  EDVMSMLSEMGINVIEDEEAEEED-AKGGTEIATTESNRDVALSSGTSEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD----IESAAKVSKD 239
           +IDLEA  G +                      E+E   V  T G      ES ++V  D
Sbjct: 180 VIDLEATFGTQM-------------------GDEEETTPVVPTAGTETKPAESTSEVDAD 220

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                +   +  ++++ N+         +L+AME  L+P+V+ ALD IA+ Y +L  +QD
Sbjct: 221 GNPISNDDDDEDDDEQANM---------SLAAMEAALKPQVLEALDIIADDYVKLSQIQD 271

Query: 300 NAVNGQKDEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           + ++   +E  +       + + ++ ++V LV  L L+ +RI+ L++QLY I++RIM  +
Sbjct: 272 SRISATLNEDGTFSKTDEEEYQRVRSEIVALVNDLHLHNNRIEALIDQLYGINRRIMQID 331

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
             +++LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++
Sbjct: 332 SAMVKLADQARINRKEFVDAYRGYELDPNWMERMAEKSGRGWQMFIERSSDKVDELRADM 391

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +    G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 392 AQVGQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDL 451

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 452 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 511

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIE
Sbjct: 512 RTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIE 571

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DKNAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 572 DKNAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTR 631

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 632 ERIRQIEAKALRKLKHPSRSRKLRSFLD 659


>gi|99081981|ref|YP_614135.1| RNA polymerase sigma factor RpoD [Ruegeria sp. TM1040]
 gi|99038261|gb|ABF64873.1| RNA polymerase, sigma 38 subunit, RpoS [Ruegeria sp. TM1040]
          Length = 664

 Score =  696 bits (1797), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/679 (55%), Positives = 483/679 (71%), Gaps = 32/679 (4%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D D  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DRKPDDQDAEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ ++ E+EE ++ + +L ++ SN  V +          TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEDEEAEEEE-NKGTTELVTTESNREVAVAGAATEKLDRTDDPVRMYLREMGSV 126

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 127 ELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 186

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD---IESAAKVSKDDRSKVDSPP 248
           G                      +Q  E  DV E   D   +  AAK  KD   ++D+  
Sbjct: 187 G----------------------NQMDEDGDVAEPVVDPSAVSGAAKPEKDSGPELDADG 224

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
               N++ + D+D+D +  +L+AME  L+ +V+  L+ I+  +  L  +QD  ++   +E
Sbjct: 225 NPILNNDDDDDDDDDQANMSLAAMEAALKDRVLETLERISSDFAMLSEMQDLRISATLNE 284

Query: 309 KSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             S       K + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA  
Sbjct: 285 DGSFSADDEAKYQQLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSAMVKLADQ 344

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F+E ++GRELDP+W+S   + P   W+ F+    + + ++R ++  +    G+
Sbjct: 345 ARINRKEFVEAYRGRELDPNWLSEMSEKPGRGWQMFIERSTEKVEELRADMAQVGQYVGL 404

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 405 DISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 464

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 465 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 524

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 525 IGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 584

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 585 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 644

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 645 ALRKLKHPSRSRKLRSFLD 663


>gi|254461643|ref|ZP_05075059.1| RNA polymerase sigma-70 factor RpoD [Rhodobacterales bacterium
           HTCC2083]
 gi|206678232|gb|EDZ42719.1| RNA polymerase sigma-70 factor RpoD [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 660

 Score =  696 bits (1796), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/678 (54%), Positives = 477/678 (70%), Gaps = 30/678 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D + +D D +   D S  + KKMI  AR+RG++T ++LNA LPPD+VSS+Q+ED ++M
Sbjct: 6   NDDRKSDDQDSAHTLDMSQTAVKKMIADARERGFITYDQLNAVLPPDQVSSDQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGI V + D+  +EE  + + DL ++ +N  V +          TDDPVRMYLREMG
Sbjct: 66  LSEMGIQVTEEDEDAEEE-DKGTTDLVAAGTNKEVAVSTAASEKLDRTDDPVRMYLREMG 124

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA
Sbjct: 125 SVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEA 184

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G                    D   E+E   V  T  +  +A K         D  P 
Sbjct: 185 TFG--------------------DQMGEEETTPVVPTAANSTTAPKAEGMAELDADGNPI 224

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE- 308
            +++D+ + DE  + S   L+AME  L+P+V+ +L+ IA +Y +L  +QD+ ++   +E 
Sbjct: 225 TSDDDDDDEDEQANMS---LAAMEAALKPQVLESLEVIAGLYEQLSQMQDSRISATLNED 281

Query: 309 -----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
                K     + L+ ++V LV  + L+ +RI+ L++QLY I++R+M  +  +++LA   
Sbjct: 282 DSFSDKQEANYQKLRSEIVVLVNEMHLHNNRIEALIDQLYGINRRVMSIDSSIVKLADQA 341

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            I R  F+E ++GRELDP+W+          W+ F+    D + ++R ++  +    G+ 
Sbjct: 342 RINRREFVEAYRGRELDPNWLEEMAGKAGRGWQMFIERSTDKVEELRADMAQVGQYVGLD 401

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 402 ISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 461

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 462 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 521

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDS
Sbjct: 522 GREPTPEELAAKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDS 581

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 582 AIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 641

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 642 LRKLKHPSRSRKLRSFLD 659


>gi|163738642|ref|ZP_02146056.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
 gi|161387970|gb|EDQ12325.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
          Length = 662

 Score =  696 bits (1796), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/679 (54%), Positives = 484/679 (71%), Gaps = 34/679 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DRKPDDQEPEISLDMSQTQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ ++ E+EE  + S +L ++ SN  V +          TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEDEEAEEEE-QKGSTELVTTESNREVAVAGAAAEKLDRTDDPVRMYLREMGSV 126

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 127 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 186

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G +                          +D + +E  ++++A  +    +K   P  +A
Sbjct: 187 GNQLD------------------------EDGEVSEPVVDTSAVAANKPAAKETGPELDA 222

Query: 252 END---ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           + +   + + D+++D +  +L+AME  L+ KV+  L++I+  Y +L  +QD+ ++   +E
Sbjct: 223 DGNPIAQDDDDDEDDQANMSLAAMEAALKDKVLTTLEQISSDYAQLSEMQDSRISATLNE 282

Query: 309 KSSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             S   +       L+ ++V LV  L L+ +RI+ L++QLY I++R+M  +  +++LA  
Sbjct: 283 DGSFSARDEQVYQSLRAEIVLLVNELHLHNNRIEALIDQLYGINRRVMSIDSSMVKLADQ 342

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F+E ++GRELDP+W+S   D P   W+ FV    D I ++R ++  +    G+
Sbjct: 343 ARINRREFVEAYRGRELDPNWLSDMGDKPGRGWQMFVERSTDKIEELRADMAQVGQYVGL 402

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 403 DISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 462

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 463 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 522

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 523 IGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 582

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 583 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 642

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 643 ALRKLKHPSRSRKLRSFLD 661


>gi|83594214|ref|YP_427966.1| RNA polymerase sigma factor RpoD [Rhodospirillum rubrum ATCC 11170]
 gi|83577128|gb|ABC23679.1| Sigma 70 (RpoD) [Rhodospirillum rubrum ATCC 11170]
          Length = 696

 Score =  696 bits (1795), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/704 (55%), Positives = 482/704 (68%), Gaps = 60/704 (8%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            E+  DS + D  + + KK++   + RGY+T +ELN  LPPD+VSSEQ+EDT+AMLS+MG
Sbjct: 15  QEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSSEQIEDTMAMLSDMG 74

Query: 75  INVVDGDDLEDEE------------GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           INVV     EDEE            G E+     ++  N S      +D   R TDDPVR
Sbjct: 75  INVV-----EDEEEGEASAAPPAEAGEEEPGREVAATGNVS------EDDIGR-TDDPVR 122

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +AL+ W D L DG  LLR
Sbjct: 123 MYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTIRALLQWHDALVDGRMLLR 182

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDS-------------SQEKERDDVQE--TE 227
           +IIDL+A  G  S  G     EG      EDS             +  KE D+ +E  T 
Sbjct: 183 DIIDLDATYG--SGAGPDVVAEGL-----EDSVVPLSPLALSPARALPKEADEAEEAVTP 235

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNL--DEDEDDSAH---TLSAMEDQLRPKVMC 282
           G  + +    + D +K    P +   DE      EDE D +    +L+AME +L P+V+ 
Sbjct: 236 GRDDDSEDEDEGDDAK----PADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLE 291

Query: 283 ALDEIAEVYRELRSLQDNAVNG-QKDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDL 337
             + IA  Y +L+  QD  +   QK E+       K   LK +LV L+  + LN +RI+ 
Sbjct: 292 TFEHIATTYGKLKKAQDQRIAALQKGEEPGAALERKYDKLKLELVGLMEDVHLNNARIEQ 351

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           LVEQL  ++K ++  EG+LLRLA+   I+RD FL+ + GRE+DP W       P   W++
Sbjct: 352 LVEQLNALNKGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWREDVAALPGKGWRD 411

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F     D I  IR  I  I+  + + I EFR IVS V+KGE EAS AKKEM+EANLRLVI
Sbjct: 412 FTTRFADEIKDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVI 471

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 472 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 531

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLE
Sbjct: 532 TIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLE 591

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGDE+ SHLGDFIEDKNAV PLD+AI +NLRET TRVLASLTPREERVLRMRFGIGMN
Sbjct: 592 TPIGDEEDSHLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREERVLRMRFGIGMN 651

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 652 TDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 695


>gi|254488657|ref|ZP_05101862.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
 gi|214045526|gb|EEB86164.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
          Length = 671

 Score =  695 bits (1794), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/684 (54%), Positives = 487/684 (71%), Gaps = 33/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K  N D+ S+ +++  SL  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 14  AKDTNEDTKSDDQEAGHSL--DMSQAAVKKMIGDAREKGYITYDQLNTVLPPDQVSSEQI 71

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN+++ +D E+EE ++   DL ++ SN  V L          TDDPVRM
Sbjct: 72  EDVMSMLSEMGINIIEDEDAEEEE-AKGGTDLTTTDSNRDVTLSSGTSEKLDRTDDPVRM 130

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 131 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRD 190

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G                      +Q  + D+       +      + +D S+
Sbjct: 191 VIDLEATFG----------------------TQMGDEDETTPVVPVVSGTEAKTNEDTSE 228

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           VD+      ND+ + ++++  +  +L+AME  L+P+V+ ALD IA+ Y +L  +QD+ ++
Sbjct: 229 VDADGNPIANDDDDDEDEQ--ANMSLAAMEAALKPQVLEALDIIADDYVKLSEIQDSRIS 286

Query: 304 GQKDEKSSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S   K       ++ ++V LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 287 ATLNEDGSFSKKDEEEYQKVRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSAMV 346

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R+++  + 
Sbjct: 347 KLADQARINRKEFVDNYRGYELDPNWMERMAEKSGRGWQMFIERSADKVEELRSDMAQVG 406

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 407 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 466

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 467 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 526

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 527 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 586

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 587 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 646

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 647 QIEAKALRKLKHPSRSRKLRSFLD 670


>gi|304322159|ref|YP_003855802.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303301061|gb|ADM10660.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 650

 Score =  695 bits (1794), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/675 (55%), Positives = 470/675 (69%), Gaps = 51/675 (7%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  V D +  S KKMI  A++RGYVT ++LNA LP  E +SEQ+ED +  LS+MGINV +
Sbjct: 13  DRPVLDLNLASVKKMIDAAKKRGYVTYDQLNAALPESEYTSEQIEDIMTKLSDMGINVTE 72

Query: 80  GDDLEDEEGSEDSLDLASSAS------NSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+   +  +++     + +S      +S+      K  +DR TDDPVRMYLREMG++EL
Sbjct: 73  DDEDGGDGDADEEGGEKAQSSAVVKKESSATVATNTKADSDR-TDDPVRMYLREMGAVEL 131

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-- 191
           LSREGEIAIAKRIEAGR  M+ +LCES LTF+A+ +WR+EL +G  LLR+IIDL+A    
Sbjct: 132 LSREGEIAIAKRIEAGRESMIRALCESSLTFEAITVWREELEEGRVLLRDIIDLDATYDG 191

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           GPESK          + Q+ ++    +  DD    EGD+                     
Sbjct: 192 GPESKPDMTKPEVAEAVQREQEERAAQGLDDEDIDEGDL--------------------- 230

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD----NAVNGQKD 307
                           +LSA E +LR  VM    EIAE +++LR LQD      ++G+  
Sbjct: 231 ----------------SLSAKEAELREGVMDTFSEIAEDFKKLRRLQDIQIEQQLSGEDL 274

Query: 308 EKSSVK-CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
             S +K  + L++ +V+ V S+ L+  RI+ LVEQLY+I++ +M  EG L+RLA SYG+ 
Sbjct: 275 SDSQLKRLRKLQKDIVERVRSVRLHNHRIEALVEQLYEINRSLMALEGRLVRLADSYGVN 334

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           R  FL  + G ELDP W+          W  F     D I+ +R  I  ++ ETG+++ +
Sbjct: 335 RQDFLTSYLGYELDPEWLDRVSAMDGRGWTQFTTKGRDQIVDLRENIGQLAQETGLTVKD 394

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR IV  V+KGE EA IAKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 395 FRRIVQTVQKGEREARIAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 454

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ N+I RE
Sbjct: 455 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILNEIGRE 514

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A KL+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQ
Sbjct: 515 PTPEELAAKLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQ 574

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RK
Sbjct: 575 SNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRK 634

Query: 667 LKHPSRSKKLRSFLD 681
           LKHPSRS+KLRSFLD
Sbjct: 635 LKHPSRSRKLRSFLD 649


>gi|302382122|ref|YP_003817945.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302192750|gb|ADL00322.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 652

 Score =  695 bits (1793), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/677 (56%), Positives = 474/677 (70%), Gaps = 33/677 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+    E + D  + D +D   KK IK A+ RGYVT+EELN  LP +EV+ + +EDT+AM
Sbjct: 3   DTQEAPEATTDGPLLDLTDAGVKKFIKQAKARGYVTMEELNKVLPSEEVTPDAIEDTLAM 62

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MG+NVV+ +    E+ +E +    +  + +SV     K + DR TDDPVRMYLREMG
Sbjct: 63  LSEMGVNVVEAE----EDAAESTGGELAEKAETSVTEGDAKPTYDR-TDDPVRMYLREMG 117

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M++ LCES LTF+A+++WRDEL +   LLRE+IDL+A
Sbjct: 118 SVELLSREGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWRDELANNRILLREVIDLDA 177

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G  +     H         +    + +      E E D                    
Sbjct: 178 TYGVLNPSSLPHNQPQPPIPGQPIPPKPEPEPGA-EAEAD-------------------- 216

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDE 308
            AE DE + ++ +D    ++SA+E +LR  VM  LD IA  +   R LQ+  V  + K E
Sbjct: 217 KAEQDEED-EDFDDGGGMSISALEAELRDGVMETLDAIAGDFDAFRKLQEKLVESRLKGE 275

Query: 309 KSSVKCK----VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           + S K +     L   +   + +L LN +RI+ LVEQLY I+KR++  EG LLRLA SYG
Sbjct: 276 ELSAKDRKAYDTLSAAISGRLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYG 335

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  FL+ +   ELDP W +  KD     W  F   E   I  IR+++ +++VE G+ I
Sbjct: 336 ISRPEFLKAYFTAELDPTWSTRVKDMGV-RWTKFSDNEATQIATIRHDVAAVAVEAGLPI 394

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 395 DDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 454

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I 
Sbjct: 455 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIG 514

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+A
Sbjct: 515 REPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAA 574

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 575 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 634

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 635 RKLKHPSRSRKLRSFLD 651


>gi|84687692|ref|ZP_01015565.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664275|gb|EAQ10766.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 670

 Score =  694 bits (1790), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/689 (53%), Positives = 490/689 (71%), Gaps = 33/689 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K  N D + + +D   + + D    + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 3   AKDANDDQNKDEQDDGSNPMGDMDQAAVKKMIAEAREKGYITYDQLNNVLPPDQVSSEQI 62

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGS-EDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ED ++MLS MGIN+++ ++ ED+    + S ++ +     +V +          TDDPVR
Sbjct: 63  EDVMSMLSEMGINIIEDEEAEDDNDDAKGSTEVVAKNQGGAVAVSSGDTEKLDRTDDPVR 122

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL +   LLR
Sbjct: 123 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLNEDILLR 182

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDL+A  G +       G +G             E +DV +  G+   AA  + + + 
Sbjct: 183 DVIDLDATFGRQ------MGEDG-------------EDEDVVQGLGE---AAATNTESQK 220

Query: 243 KVDSPPENAEND----ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           K D P  +A+ +    + + ++++D +  +L+AME  L+P+V+  L+ IA  Y +L  +Q
Sbjct: 221 KDDGPELDADGNPIAKDDDDEDEDDQANMSLAAMEAALKPRVLETLELIARDYTKLSEMQ 280

Query: 299 DNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           D  +      +G   +K+  + + L+ ++V LV  L L+ +RI+ LV+QLY I++RIM  
Sbjct: 281 DLRMSATLNEDGSFSDKAEAEYQKLRSEIVLLVNELHLHNNRIEALVDQLYGINRRIMSI 340

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
           +  +++LA    I R  F++ ++G ELDP+W+    + P   W+ F+    D + ++R +
Sbjct: 341 DSAMVKLADQARINRREFVDAYRGEELDPNWLERMAEKPGRGWQAFIERSSDKVAELRGD 400

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  +    G+ ISEFR IVS V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 401 MAQVGQYVGVDISEFRRIVSQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 460

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 461 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 520

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           VRT R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFI
Sbjct: 521 VRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFI 580

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDKNAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VT
Sbjct: 581 EDKNAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 640

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 641 RERIRQIEAKALRKLKHPSRSRKLRSFLD 669


>gi|89070863|ref|ZP_01158102.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89043551|gb|EAR49761.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 657

 Score =  693 bits (1789), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/683 (54%), Positives = 478/683 (69%), Gaps = 40/683 (5%)

Query: 9   RDSDSEHEDSDD-SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +D+D   ED  D ++  D S  + KKMI  AR+RGY+T ++LN+ LPPD+VSS+Q+ED +
Sbjct: 4   KDTDERKEDEQDGAMSLDMSQTAVKKMIADARERGYITYDQLNSVLPPDQVSSDQIEDVM 63

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +MLS MGI V + ++ E+ E    S DL ++  +  V +   +      TDDPVRMYLRE
Sbjct: 64  SMLSEMGIQVTEEEESEETE-ETKSTDLVTTGGSRDVAVSSGETEKLDRTDDPVRMYLRE 122

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL +   LLR++IDL
Sbjct: 123 MGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLNEDILLRDVIDL 182

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           EA  G +                              E EGD       + D   K + P
Sbjct: 183 EATFGNQL-----------------------------EEEGDTPVVEPGAADGAKKEEGP 213

Query: 248 PENAEND---ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
             +A+ +   + + ++++D +  +L+AME  L+P+V+  LD IA  +  L  +QD  ++ 
Sbjct: 214 ELDADGNPIAKDDDEDEDDAANMSLAAMEAALKPRVLETLDTIAADFGNLSEMQDARISA 273

Query: 305 QKDEKSSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           Q +E SS   K       L+ ++V+LV SL L+ +RI+ L++QLY I++RIM  +  +++
Sbjct: 274 QLNEDSSFTEKDEETYQKLRGEIVELVNSLHLHNNRIEALIDQLYGINRRIMSIDSSMVK 333

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           LA    I R  F++ ++G ELDP W+      P   W+ F+      + ++R E+  +  
Sbjct: 334 LADQARINRREFIDAYRGYELDPTWLDRMGQNPGRAWQAFIERSTGKVEELRAEMAQVGQ 393

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
             G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 394 YVGVDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 453

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+
Sbjct: 454 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQ 513

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV
Sbjct: 514 MLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAV 573

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 574 LPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 633

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 634 IEAKALRKLKHPSRSRKLRSFLD 656


>gi|163733984|ref|ZP_02141425.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
 gi|161392520|gb|EDQ16848.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
          Length = 660

 Score =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/686 (54%), Positives = 486/686 (70%), Gaps = 41/686 (5%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           ++ + D++ +D D     D S  + KKMI  AR++GY+T ++LN  LPPD+V+SEQ+ED 
Sbjct: 4   KDTNDDAKPDDQDAGHSLDMSQTAVKKMIAEAREKGYITYDQLNTVLPPDQVNSEQIEDV 63

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           ++MLS MGIN+++ +D E+EE ++ S +LA++     V L          TDDPVRMYLR
Sbjct: 64  MSMLSEMGINIIEDEDAEEEE-AKGSTELATTEGTREVTLGSGTSEKLDRTDDPVRMYLR 122

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+ IWRDEL     LLR++ID
Sbjct: 123 EMGSVELLSREGEIAIAKRIEAGRNTMISGLCESPLTFQAITIWRDELLSEDILLRDVID 182

Query: 187 LEACIGPE-----SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           LEA  G +     S G     TEG + QK E++S E + D                    
Sbjct: 183 LEATFGNQLDEDVSVGEPVVATEGAAPQK-EEASPELDADG------------------- 222

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
               +P  N ++D+ +   +      +L+AME  L+P+V+ ALD IA+ Y +L  +QD+ 
Sbjct: 223 ----NPIANDDDDDEDEQAN-----MSLAAMEAALKPQVLEALDIIADDYTKLSEMQDSR 273

Query: 302 VNGQKDEKSSVKC------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           ++   +E  S         + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  
Sbjct: 274 ISATLNEDGSFNAGDEALYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSA 333

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++  
Sbjct: 334 MVKLADQARINRREFVDEYRGYELDPNWMERMAEKSGRGWQMFIERSSDKVEELRTDMAQ 393

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 394 VGQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 453

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 454 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 513

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 514 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 573

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 574 NAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 633

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 634 IRQIEAKALRKLKHPSRSRKLRSFLD 659


>gi|254293486|ref|YP_003059509.1| RNA polymerase sigma factor RpoD [Hirschia baltica ATCC 49814]
 gi|254042017|gb|ACT58812.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hirschia baltica
           ATCC 49814]
          Length = 683

 Score =  692 bits (1787), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/689 (54%), Positives = 491/689 (71%), Gaps = 23/689 (3%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           + +  + E  ++ D  V D S+ S KK I   + RG++T +ELN  LP DEV+ +Q+ED 
Sbjct: 3   KTKADNEEVAENQDGPVLDLSNASVKKFIAAGKARGFITHDELNKVLPSDEVNPDQIEDV 62

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLD------LASSASNSSVFLQKRKDSADRSTDDP 120
           ++ LS MGINVVD D+  + +G E S D        + A +++     R D  DR TDDP
Sbjct: 63  MSALSEMGINVVDSDEEGEGDGDEASSDGENASGAVTKAKSTAAATGGRSDRYDR-TDDP 121

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+++WR EL D   L
Sbjct: 122 VRMYLREMGTVELLSREGEIAIAKRIEAGRDAMIRGLCESPLTFEAIMVWRQELEDERVL 181

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDLEA     + G   +     + +K E   +  E+ + +E     E    ++K  
Sbjct: 182 LRDIIDLEATYAAANGGVPDNSAAAVALEKGEPLEKTPEQLEAEEKAKQDE----IAKKK 237

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           R +   PPE    ++ + D+ +D  A ++SAME +LR  V   LD +A  ++  R LQ+ 
Sbjct: 238 RIEEGLPPEEEGKEDDDDDDFDDGGAMSMSAMEAELREGVTDILDNVASEFQAYRRLQEK 297

Query: 301 AVN--------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
            VN          KD +  VK   L++ +++ +  L LN +RI+ LVEQLY I+KR+M  
Sbjct: 298 LVNRHMEGKELSPKDSEEYVK---LQDDIIENLKKLHLNNARIETLVEQLYAINKRLMGL 354

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
           EG L+RLA ++G+ R  FL+ + G EL+P W +        +WK F+A E + + ++R+E
Sbjct: 355 EGGLMRLADAHGVPRKSFLDNYFGTELEPDWGTRV-SLISAKWKKFIAAETNKVEEMRSE 413

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I S++ E G+ I +FR IV+ V+KGE EA +AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 414 ISSLAQEMGVPIEDFRRIVATVQKGEREARVAKKEMVEANLRLVISIAKKYTNRGLQFLD 473

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 474 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 533

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           VRT R+M ++I REPTPEE+A+KL +P+E +RKVLKI KEPISLETPIGD++ S+LGDFI
Sbjct: 534 VRTQRQMLHEIGREPTPEELAEKLGLPLEKIRKVLKIAKEPISLETPIGDDEDSNLGDFI 593

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDK A+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VT
Sbjct: 594 EDKMALLPVDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 653

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 654 RERIRQIEAKALRKLKHPSRSRKLRSFLD 682


>gi|254511749|ref|ZP_05123816.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
 gi|221535460|gb|EEE38448.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
          Length = 662

 Score =  692 bits (1786), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/686 (55%), Positives = 485/686 (70%), Gaps = 35/686 (5%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K  N D  S+ ++ + SL  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 3   AKDTNEDRKSDEQEQEISL--DMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN+++ ++ E+EE ++ S DL ++     V L   +      TDDPVRM
Sbjct: 61  EDVMSMLSEMGINIIEDEEAEEEE-NKGSTDLVTTEGPREVALAGAQTEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES--AAKVSKDDR 241
           +IDLE   G                      +Q  E  DVQE   D  S  AAK  KD  
Sbjct: 180 VIDLETTFG----------------------NQLDEDGDVQEPVVDTSSVQAAKPEKDTG 217

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
            ++D+      +D+ + D+D+  +  +L+AME  L+ +V+  L+ I+  +  L  +QD+ 
Sbjct: 218 PELDADGNPIASDDDDDDDDQ--ANMSLAAMEAALKDQVLTTLERISNDFAMLSEMQDSR 275

Query: 302 V------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +      +G   EK     + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  
Sbjct: 276 ISATLNEDGSFSEKDEETYQKLRAEIVELVNGLHLHNNRIEALIDQLYGINRRIMSLDSS 335

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F++ ++GRELDP+W++   + P   W+ F+      + ++RN++  
Sbjct: 336 MVKLADQARINRREFIDAYRGRELDPNWLAEMAEKPGRGWQMFIERSTAKVEELRNDMAQ 395

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 396 VGQYVGLDIPEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 455

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 456 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 515

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 516 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 575

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 576 NAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 635

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 IRQIEAKALRKLKHPSRSRKLRSFLD 661


>gi|163742972|ref|ZP_02150355.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383655|gb|EDQ08041.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 662

 Score =  692 bits (1785), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/679 (54%), Positives = 484/679 (71%), Gaps = 34/679 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DRKPDDQEPEISLDMSQTQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ ++ E+EE  + S +L ++ SN  V +          TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEDEEAEEEE-QKGSTELVTTESNREVAVAGAAAEKLDRTDDPVRMYLREMGSV 126

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA  
Sbjct: 127 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEATF 186

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G +                          +D + +E  ++++A  +    +K   P  +A
Sbjct: 187 GNQLD------------------------EDGEVSEPVVDTSAVAANKPAAKETGPELDA 222

Query: 252 END---ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           + +   + + D+++D +  +L+AME  L+ KV+  L++I+  Y +L  +QD+ ++   +E
Sbjct: 223 DGNPIAQDDDDDEDDQANMSLAAMEAALKDKVLTTLEQISSDYAQLSEMQDSRISATLNE 282

Query: 309 KSSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             S   +       L+ ++V LV  L L+ +RI+ L++QLY I++R+M  +  +++LA  
Sbjct: 283 DGSFSARDEQVYQSLRSEIVLLVNELHLHNNRIEALIDQLYGINRRVMSIDSSMVKLADQ 342

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F+E ++GRELDP+W++   + P   W+ FV    + + ++R ++  +    G+
Sbjct: 343 ARINRREFVEAYRGRELDPNWLAEMGEKPGRGWQMFVERSTEKVEELRADMAQVGQYVGL 402

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 403 DISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 462

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 463 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 522

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 523 IGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 582

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 583 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 642

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+KLRSFLD
Sbjct: 643 ALRKLKHPSRSRKLRSFLD 661


>gi|310816221|ref|YP_003964185.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
 gi|308754956|gb|ADO42885.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
          Length = 658

 Score =  691 bits (1784), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/681 (54%), Positives = 480/681 (70%), Gaps = 35/681 (5%)

Query: 9   RDSDSEHEDSDDS-LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +DSD   ++  DS + FD S  + K+MI  AR+RGY+T ++LN+ LPPD+VSS+Q+ED +
Sbjct: 4   KDSDDVKDNEQDSDISFDMSQAAVKRMIADARERGYITYDQLNSVLPPDQVSSDQIEDVM 63

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +MLS MGI V D ++ E+      S ++A+  +          +  DR TDDPVRMYLRE
Sbjct: 64  SMLSEMGIQVTDEEETEEVADDGTSREVATVGARELTLAGPEVEKTDR-TDDPVRMYLRE 122

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTF A+ IWRDEL D   LLR++IDL
Sbjct: 123 MGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFNAITIWRDELMDEAVLLRDVIDL 182

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV-SKDDRSKVDS 246
           EA  G                      +Q  E DD    +    S  K+  +      D 
Sbjct: 183 EATFG----------------------NQMGEDDDAPVVDAAGGSEPKMRERGAELDADG 220

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
            P + ++D+ + D++    + +L+AME  LRP+V+ ALD IAE    L  LQ+  +  + 
Sbjct: 221 NPISRDDDDEDDDQN----SMSLAAMEATLRPRVLEALDTIAEQAMALEELQEARMRAKM 276

Query: 307 DEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           +E +        + +VL++K+V++V SL L+ +RID L++QLY I++RIM  +  +++LA
Sbjct: 277 EEGADFSVAEEGQYQVLRQKIVEVVNSLHLHSNRIDALIDQLYGINRRIMSIDSSMVKLA 336

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               I R  F++ ++G ELDP W+      P   W   +    + + ++R E+  +    
Sbjct: 337 DQARINRKEFIDEYRGSELDPSWLERMGQKPGRGWAMLIERSREKVEELRAEMAQVGQYV 396

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ I+EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 397 GVDINEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 456

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M 
Sbjct: 457 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQML 516

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ P
Sbjct: 517 HEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILP 576

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 577 LDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 636

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 AKALRKLKHPSRSRKLRSFLD 657


>gi|84515379|ref|ZP_01002741.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510662|gb|EAQ07117.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 659

 Score =  691 bits (1783), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/676 (54%), Positives = 475/676 (70%), Gaps = 31/676 (4%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D +  D D  +  D S  + K+MI  AR+RGY+T ++LNA LPP++VSS+Q+ED ++MLS
Sbjct: 8   DRKDNDQDGDISLDMSQAAVKRMIADARERGYITYDQLNAVLPPEQVSSDQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGI V + ++ E+ +      D+A+ + +  V +   +      TDDPVRMYLREMGS+
Sbjct: 68  EMGIQVTEEEESEESDDGAGGTDIATVSGSRDVTIGGAEAEKLDRTDDPVRMYLREMGSV 127

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE   
Sbjct: 128 ELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLETTF 187

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G +       G EG                   ET     S +   +D  S++D+     
Sbjct: 188 GNQ------LGEEGEV-----------------ETVVTAASVSDTKEDGGSELDADGNPI 224

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
             D+ + D+D+  +  +L+AME  L+P+V+  L+ IA  + +L  +QD  ++   +E SS
Sbjct: 225 SKDDDDDDDDQ--ANMSLAAMEAALKPRVLETLEIIARGFADLSDMQDARMSATLNEDSS 282

Query: 312 VKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
              K       L+ ++V LV SL L+ +RI+ L++QLY I++RIM  +  +++LA    I
Sbjct: 283 FSVKEEERYQTLRSEIVVLVNSLHLHNNRIEALIDQLYGINRRIMSIDSAMVKLADQARI 342

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  F++ ++GRELDP+W+    +     W+  V    D I ++RN++  +    G+ I+
Sbjct: 343 NRREFIDEYRGRELDPNWLEQMAEKSGRGWQALVEKSTDKIEELRNDMAQVGQYVGVDIT 402

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 403 EFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 462

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I R
Sbjct: 463 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGR 522

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSAI
Sbjct: 523 EPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSAI 582

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 583 QENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 642

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 643 KLKHPSRSRKLRSFLD 658


>gi|83951483|ref|ZP_00960215.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83836489|gb|EAP75786.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 660

 Score =  690 bits (1781), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/684 (53%), Positives = 474/684 (69%), Gaps = 42/684 (6%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D + +D D  +  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++M
Sbjct: 6   NDDQKPDDQDAEISLDLSQTAIKKMIAEAREKGYITYDQLNQALPPDQVSSEQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGIN+++    + EE  +    LA       V L   K+     TDDPVRMYLREMG
Sbjct: 66  LSEMGINIIE--AEDVEEEEQRVTALAEVGKRGEVTLGSGKEEKLDRTDDPVRMYLREMG 123

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLEA
Sbjct: 124 SVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLTEDILLRDVIDLEA 183

Query: 190 CIGPE------SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
             G +       +        G +  K+ +++QE + D                    + 
Sbjct: 184 TFGNQLGDDEDEEAPVVAANVGEAPGKKSETTQELDADG-------------------NP 224

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           + S  +  E+D+ N+         +L+AME  L+P+V+  LD IA  Y +L  +QD+ ++
Sbjct: 225 ISSDDDEDEDDQANM---------SLAAMEAALKPRVLETLDRIANDYEKLSEMQDSRIS 275

Query: 304 GQKDEKSSVKCKV------LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S   K       L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 276 ATLNEDGSFSAKQEATYQKLRSEIVELVNELHLHNNRIEALIDQLYGINQRIMSIDSAMV 335

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++GRELDP+W+          W+ F+    + + ++R ++  + 
Sbjct: 336 KLADQARINRREFIDAYRGRELDPNWLDDMASKSGRGWQMFMERSPEKVAELRADMAQVG 395

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 396 QYVGLDISEFRRIVGQVQKGEQEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 455

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 456 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 515

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 516 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 575

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 576 VLPLDSAIQDNLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 635

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 QIEAKALRKLKHPSRSRKLRSFLD 659


>gi|83859451|ref|ZP_00952972.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852898|gb|EAP90751.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 678

 Score =  690 bits (1781), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/698 (55%), Positives = 487/698 (69%), Gaps = 38/698 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M+     N ++ SE++D     + D +D + K MIK A++RGYVT +ELN  LP +E SS
Sbjct: 1   MSKAAAENAEATSENQDGP---LLDLTDQTVKAMIKTAKKRGYVTHDELNKVLPSEEFSS 57

Query: 61  EQMEDTVAMLSNMGINVVDGD-DLEDEEGSEDSLDLASSASNSSVFLQKRKD-------- 111
           EQ+ED +A LS MGI VVD + D+++E  S D  +       S+   +K K         
Sbjct: 58  EQIEDILAQLSEMGITVVDSEEDVDNEASSSDDEEDDEDEEKSTAVAKKAKSEVAAGQNT 117

Query: 112 -SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
            SA   TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+++W
Sbjct: 118 TSAQDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRNAMIRGLCESPLTFEAIMVW 177

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           RDEL +G  LLR+IIDL+A  G     G        S  + E    E + DD  E + D 
Sbjct: 178 RDELQEGQVLLRDIIDLDATYG-----GVREDATAVSDDEEEGEGDEAKADDA-EAKSDD 231

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           ES+     +          + E+D  N+         +L+AME +LR  VM  LD IA  
Sbjct: 232 ESSDSEDGEKSEGESDEDGDDEDDGANM---------SLAAMEAELRDGVMETLDAIATD 282

Query: 291 YRELRSLQDNAVNGQKD-----EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           +   R LQD  V+ +       +K       + E++V  + SL LN +RI+ LVEQL  I
Sbjct: 283 FDVFRQLQDRLVSSRLSGKHLSDKDQAAYDDVFERIVANLNSLHLNNARIEALVEQLDAI 342

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP--EGEWKNFVACEV 403
           +K++M  EG+LLR+A+++G+ R  FL+ +QG ELDP+W+   KD       W  FV  E 
Sbjct: 343 NKKLMGLEGKLLRMAEAHGVPRTDFLKSYQGHELDPNWL---KDMAGKSKAWGRFVEREE 399

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
               ++R +I +++ E+G+ I ++R IV+ V+KG  EA +AKKEMVEANLRLVIS+AKKY
Sbjct: 400 KEAGELREQIATLAQESGVPIDDYRRIVATVQKGAREARVAKKEMVEANLRLVISIAKKY 459

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 460 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 519

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KL+MP+E VRKV+KI KEPISLETPIGDE
Sbjct: 520 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLSMPLEKVRKVMKIAKEPISLETPIGDE 579

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNAV P+D+AI +NLRETTT VLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 580 EDSHLGDFIEDKNAVLPIDAAIHSNLRETTTLVLASLTPREERVLRMRFGIGMNTDHTLE 639

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 640 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 677


>gi|86137897|ref|ZP_01056473.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
 gi|85825489|gb|EAQ45688.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
          Length = 663

 Score =  690 bits (1780), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/678 (54%), Positives = 478/678 (70%), Gaps = 27/678 (3%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D + +D D  +  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++M
Sbjct: 6   NDDRKPDDQDAEISLDMSQAAVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGIN+++ +++E+EE  + S +L S+ S   V +          TDDPVRMYLREMG
Sbjct: 66  LSEMGINIIEDEEVEEEE-QKGSTELVSADSPREVAVAGAASEKLDRTDDPVRMYLREMG 124

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA
Sbjct: 125 TVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEA 184

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G +                    +    ++  QE + D            + + S  +
Sbjct: 185 TFGNQLDEDGEAEDPVVPVVPGAAPAAPAAKEQTQELDAD-----------GNPIASDDD 233

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           + E+++ N+         +L+AME  L+ +V+  L+ I+  + +L  +QD+ ++   +E 
Sbjct: 234 DDEDEQANM---------SLAAMEAALKDRVLTTLERISTDFSQLSEMQDSRISATLNED 284

Query: 310 SSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            S   K       L+ ++V+LV  L L+ +RID L++QLY I++R+M  +  +++LA   
Sbjct: 285 GSFSKKDEATYQSLRSEIVELVNGLHLHNNRIDALIDQLYGINRRVMQIDSSMVKLADQA 344

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            I R  F+E ++GRELDP+W+S   + P   W+ F+    D + ++R ++  +    G+ 
Sbjct: 345 RINRREFVEAYRGRELDPNWLSDMGEKPGRGWQMFIERSTDKVEELRADMAQVGQYVGLD 404

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 405 ISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 464

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 465 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 524

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDS
Sbjct: 525 GREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDS 584

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 585 AIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 644

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 645 LRKLKHPSRSRKLRSFLD 662


>gi|110679091|ref|YP_682098.1| RNA polymerase sigma factor RpoD [Roseobacter denitrificans OCh
           114]
 gi|109455207|gb|ABG31412.1| RNA polymerase sigma-70 factor RpoD [Roseobacter denitrificans OCh
           114]
          Length = 661

 Score =  690 bits (1780), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/686 (54%), Positives = 484/686 (70%), Gaps = 40/686 (5%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           ++ + D++ +D D     D S  + KKMI  AR++GY+T ++LN  LPPD+V+SEQ+ED 
Sbjct: 4   KDTNDDAKPDDQDAGHSLDMSQAAVKKMIAEAREKGYITYDQLNTVLPPDQVNSEQIEDV 63

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           ++MLS MGIN+++ +D E+EE ++ S ++A++     V L          TDDPVRMYLR
Sbjct: 64  MSMLSEMGINIIEDEDAEEEE-AKGSTEIATTEGTREVTLGSGTSEKLDRTDDPVRMYLR 122

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+ IWRDEL     LLR++ID
Sbjct: 123 EMGSVELLSREGEIAIAKRIEAGRNTMISGLCESPLTFQAITIWRDELLSEDILLRDVID 182

Query: 187 LEACIGPE-----SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           LEA  G +     S G      +G +  ++E+SS E + D                    
Sbjct: 183 LEATFGNQLDEDVSVGEPVVAADGATAPQKEESSPELDADG------------------- 223

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
               +P  N ++D+ +   +      +L+AME  L+P+V+ ALD IA  Y +L  +QD+ 
Sbjct: 224 ----NPIANDDDDDEDEQAN-----MSLAAMEAALKPQVLEALDIIASDYTKLSEMQDSR 274

Query: 302 V------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +      +G  DE      + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  
Sbjct: 275 ISATLNEDGSFDEGDEALYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSA 334

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++  
Sbjct: 335 MVKLADQARINRREFVDEYRGYELDPNWMERMTEKSGRGWQMFIERSSDKVEELRADMAQ 394

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 395 VGQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 454

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 455 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 514

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 515 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 574

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 575 NAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 634

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 635 IRQIEAKALRKLKHPSRSRKLRSFLD 660


>gi|260753821|ref|YP_003226714.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|258553184|gb|ACV76130.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 671

 Score =  688 bits (1776), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/676 (53%), Positives = 486/676 (71%), Gaps = 28/676 (4%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           ++ D+ + D ++ S +K I  A++RGYVT ++LN  LP D++SSEQ+ED ++ LS MGIN
Sbjct: 12  NAGDAPLIDLNETSIRKFITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGIN 71

Query: 77  VVDGDDLEDEEGSEDSLDL-----ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           +V+ +D   E+G ++  D          ++ +  +  +K+++DR TDDPVRMYLREMG++
Sbjct: 72  IVENED-SGEDGQQEEEDAAEELQGDGGTSPAPAITTKKETSDR-TDDPVRMYLREMGAV 129

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+  LCESP+TF  +I W + LN+GT  LREIIDL+A +
Sbjct: 130 ELLSREGEIAIAKRIEAGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAML 189

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                      T+G S  + E+   + + +  +   G   +  +   +D        EN 
Sbjct: 190 -----------TQGPSPDQFEEEGDDNDNEISERNAGP--TFKEDDDEDDDSEGELDENG 236

Query: 252 ENDER-NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-----AVNGQ 305
           +  +R N+DE ED++  +L+ ME+QL+P  +    +IA++YR+   LQ+        N +
Sbjct: 237 QRIQRENMDE-EDENTLSLAQMEEQLKPASLEKFAKIADLYRQFSVLQNARMRALGANEE 295

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
             E      + L+E+L   V S+  + +RI+ LVEQLY+ + R+    G++LRLA+ Y +
Sbjct: 296 FPEDQENAYQQLREELTAEVESVKFHNARIEFLVEQLYNYNSRLRTLNGQMLRLAERYKV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            RD FL  + G E++  WV       + +W NF   E +SI +IR+E+  I+  TG+++ 
Sbjct: 356 PRDSFLNAYLGNEMEEGWVERVSKI-DKKWANFTTSEAESIERIRSEVAEIAQVTGMTLK 414

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R IV+MV+KGE EA IAK EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 415 ELRRIVTMVQKGEREARIAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 474

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I R
Sbjct: 475 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQILHEIGR 534

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 535 EPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAI 594

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 595 QANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 654

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+K+RSFLD
Sbjct: 655 KLKHPSRSRKMRSFLD 670


>gi|209545152|ref|YP_002277381.1| RNA polymerase sigma factor RpoD [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209532829|gb|ACI52766.1| RNA polymerase, sigma 70 subunit, RpoD [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 650

 Score =  688 bits (1776), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/670 (53%), Positives = 471/670 (70%), Gaps = 46/670 (6%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           +D+ + D    + K++I   ++RGY+T +ELNA LP D++SSEQ+ED +A+LS MGI VV
Sbjct: 18  NDTTLLDTQSGAVKRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAVLSEMGIQVV 77

Query: 79  DGDDLEDEEGS-EDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSR 136
           + +D +D E + E+  + A +    +       D+     TDDPVRMYLREMGS+ELLSR
Sbjct: 78  ENEDNDDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTDDPVRMYLREMGSVELLSR 137

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L  G  LLR+I+DLEA       
Sbjct: 138 EGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEA------- 190

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                     +Q    + E+ A+  + +    D+ PE+ +    
Sbjct: 191 --------------------------MQSGGAEAEAGAEGGEQEDGSFDAAPESEDG--- 221

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-----NGQKDEKSS 311
              E+ D +  +LSA+E++L+P+++   +EI E+Y  L+ LQ   +       +  +KS 
Sbjct: 222 ---EEGDSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQSKRLETLTSGAEMSDKSE 278

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
              + L+E+LV  V  + L+ +RI++LV+ L +I +R+   EG +LRLA+S  + R+ FL
Sbjct: 279 KSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLEGRMLRLAESTKVSREDFL 338

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +++G ELDP W+      P   WKNFVA    S+L +R ++ S+S ETG+ + EFR + 
Sbjct: 339 IKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQVASLSQETGLPVGEFRRVY 398

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 399 ATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 458

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REP PEE
Sbjct: 459 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEE 518

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK AV PLD+AIQ NLRE
Sbjct: 519 LAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVIPLDAAIQTNLRE 578

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPS
Sbjct: 579 ATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPS 638

Query: 672 RSKKLRSFLD 681
           RS+KLRSFLD
Sbjct: 639 RSRKLRSFLD 648


>gi|56552519|ref|YP_163358.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241762241|ref|ZP_04760323.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|56544093|gb|AAV90247.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241373288|gb|EER62907.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
          Length = 671

 Score =  688 bits (1776), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/676 (53%), Positives = 486/676 (71%), Gaps = 28/676 (4%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           ++ D+ + D ++ S +K I  A++RGYVT ++LN  LP D++SSEQ+ED ++ LS MGIN
Sbjct: 12  NAGDAPLIDLNETSIRKFITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGIN 71

Query: 77  VVDGDDLEDEEGSEDSLDL-----ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           +V+ +D   E+G ++  D          ++ +  +  +K+++DR TDDPVRMYLREMG++
Sbjct: 72  IVENED-SGEDGQQEEEDAAEELQGDGGTSPAPAITTKKETSDR-TDDPVRMYLREMGAV 129

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+  LCESP+TF  +I W + LN+GT  LREIIDL+A +
Sbjct: 130 ELLSREGEIAIAKRIEAGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAML 189

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                      T+G S  + E+   + + +  +   G   +  +   +D        EN 
Sbjct: 190 -----------TQGPSPDQFEEDGDDNDNEISERNAGP--TFKEDDDEDDDSEGELDENG 236

Query: 252 ENDER-NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-----AVNGQ 305
           +  +R N+DE ED++  +L+ ME+QL+P  +    +IA++YR+   LQ+        N +
Sbjct: 237 QRIQRENMDE-EDENTLSLAQMEEQLKPASLEKFAKIADLYRQFSVLQNARMRALGANEE 295

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
             E      + L+E+L   V S+  + +RI+ LVEQLY+ + R+    G++LRLA+ Y +
Sbjct: 296 FPEDQENAYQQLREELTAEVESVKFHNARIEFLVEQLYNYNSRLRTLNGQMLRLAERYKV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            RD FL  + G E++  WV       + +W NF   E +SI +IR+E+  I+  TG+++ 
Sbjct: 356 PRDSFLNAYLGNEMEEGWVERVSKI-DKKWANFTTSEAESIERIRSEVAEIAQVTGMTLK 414

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R IV+MV+KGE EA IAK EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 415 ELRRIVTMVQKGEREARIAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 474

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I R
Sbjct: 475 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQILHEIGR 534

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 535 EPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAI 594

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 595 QANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 654

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+K+RSFLD
Sbjct: 655 KLKHPSRSRKMRSFLD 670


>gi|85705219|ref|ZP_01036318.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670092|gb|EAQ24954.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 661

 Score =  688 bits (1775), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/695 (53%), Positives = 478/695 (68%), Gaps = 60/695 (8%)

Query: 9   RDSDSEHED-SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +D+D +  D SD  +  D S  + K+MI  AR++G++T ++LN  LPPD+VSSEQ+ED +
Sbjct: 4   KDTDDQKPDESDTEVSLDMSQAAVKRMIAEAREKGFITYDQLNEVLPPDQVSSEQIEDVM 63

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +MLS MGIN+++ +D E+EEG   S  +A       + L   K+     TDDPVRMYLRE
Sbjct: 64  SMLSEMGINIIEAEDAEEEEGR--STAVAEIGRRGEITLGSGKEEKLDRTDDPVRMYLRE 121

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDL
Sbjct: 122 MGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLGEDILLRDVIDL 181

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           EA  G +                                 GD ++   V     + V S 
Sbjct: 182 EATFGTQL--------------------------------GDEDAEPVVGA---ANVTSA 206

Query: 248 PENAENDERNLDEDED--------------DSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           P N   D+   D D D               +  +L+AME  L+P+V+  LD IA+ Y +
Sbjct: 207 PGNLGRDDNEPDLDADGNPIHSDDDDEEDEQANMSLAAMEAALKPRVLETLDRIADDYAK 266

Query: 294 LRSLQDNAVNGQKDEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           L  +QD+ ++   +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I++
Sbjct: 267 LSEMQDSRISATLNEDGSFSREQEQTYQTLRSEIVELVNELHLHNNRIEALIDQLYGINR 326

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS-YAKDFPEGEWKNFVACEVDSI 406
           RIM  +  +++LA    I R  F++ ++GRELDP+W+   A+    G W+ F+    + +
Sbjct: 327 RIMQIDSAMVKLADQARINRSEFIDEYRGRELDPNWLDDMARKAGRG-WQMFIERSPEKV 385

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            ++R ++  +    G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 386 SELRADMAQVGQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNR 445

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 446 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 505

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S
Sbjct: 506 ETINKLVRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDS 565

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LGDFIEDKN + PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 566 QLGDFIEDKNVILPLDSAIQDNLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVG 625

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 626 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 660


>gi|114570679|ref|YP_757359.1| RNA polymerase sigma factor RpoD [Maricaulis maris MCS10]
 gi|114341141|gb|ABI66421.1| RNA polymerase, sigma 70 subunit, RpoD [Maricaulis maris MCS10]
          Length = 710

 Score =  688 bits (1775), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/724 (53%), Positives = 488/724 (67%), Gaps = 66/724 (9%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           ++ +++   E+SD  L  D +D S K M+K A++RGYVT +ELNA LP +E SSEQ+ED 
Sbjct: 3   KSAEANDATENSDGPL-LDLTDQSVKNMVKTAKKRGYVTHDELNAVLPSEEFSSEQIEDV 61

Query: 67  VAMLSNMGINVVDGDDL------EDEEGSEDSLDLASS---------------------- 98
           +A LS MGINVVD D        E  + ++ +   A++                      
Sbjct: 62  LAQLSEMGINVVDNDSDVDDDSAETPKPAKGAASAATTSSDDDEEDSDDEEESDSRAVAG 121

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           AS ++V       SADR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LC
Sbjct: 122 ASKTAVTGLNTPSSADR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRNAMIRGLC 180

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           ESPLTF+A+++WRDEL +G  LLR+IIDL+A  G            G   +  ED  +  
Sbjct: 181 ESPLTFEAIMVWRDELQEGQVLLRDIIDLDATYG------------GQQAEAAEDDDENA 228

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH----------- 267
             D   E E    +     K +    D   +  +  E++ D+DE+D              
Sbjct: 229 --DGTGEGETPTPAGGTTPKPESDDEDDGEDGEKKSEKSGDDDEEDGETSSSDDDDDDDE 286

Query: 268 -----TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KD--EKSSVKCKVL 317
                +LSAME +LR  VM  LD IA  +   R LQD  V  +   KD  ++S  K +  
Sbjct: 287 DGVSLSLSAMEAELRDGVMETLDSIATDFAAFRKLQDKLVAARIEGKDLTKQSREKYEGF 346

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           +  +V  + ++ LN +RI+ LVEQLY I+K  M  EG+LLR+A ++G+ R  F++ + G 
Sbjct: 347 QNAIVTNLNTMHLNNARIEALVEQLYAINKERMALEGKLLRMADAHGVPRAQFMDSYFGN 406

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           EL+P W +      +  W  F+  E     KIR+++  ++   G+ I + R IV  V+KG
Sbjct: 407 ELNPEWPTSMASTSKA-WARFIDREGVDAGKIRDDLADLTQRAGVPIEDLRRIVRTVQKG 465

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E EA +AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 466 EREARVAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 525

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLA
Sbjct: 526 TYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLA 585

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQANLRETTTRVL
Sbjct: 586 MPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAIQANLRETTTRVL 645

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLR
Sbjct: 646 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLR 705

Query: 678 SFLD 681
           SFLD
Sbjct: 706 SFLD 709


>gi|162149105|ref|YP_001603566.1| RNA polymerase sigma factor RpoD [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161787682|emb|CAP57278.1| RNA polymerase sigma factor rpoD (Sigma-A) [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 656

 Score =  687 bits (1774), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/670 (53%), Positives = 471/670 (70%), Gaps = 46/670 (6%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           +D+ + D    + K++I   ++RGY+T +ELNA LP D++SSEQ+ED +A+LS MGI VV
Sbjct: 24  NDTTLLDTQSGAVKRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAVLSEMGIQVV 83

Query: 79  DGDDLEDEEGS-EDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSR 136
           + +D +D E + E+  + A +    +       D+     TDDPVRMYLREMGS+ELLSR
Sbjct: 84  ENEDNDDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTDDPVRMYLREMGSVELLSR 143

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L  G  LLR+I+DLEA       
Sbjct: 144 EGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEA------- 196

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                     +Q    + E+ A+  + +    D+ PE+ +    
Sbjct: 197 --------------------------MQSGGAEAEAGAEGGEQEDGSFDAAPESEDG--- 227

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-----NGQKDEKSS 311
              E+ D +  +LSA+E++L+P+++   +EI E+Y  L+ LQ   +       +  +KS 
Sbjct: 228 ---EEGDSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQSKRLETLTSGAEMSDKSE 284

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
              + L+E+LV  V  + L+ +RI++LV+ L +I +R+   EG +LRLA+S  + R+ FL
Sbjct: 285 KSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLEGRMLRLAESTKVSREDFL 344

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +++G ELDP W+      P   WKNFVA    S+L +R ++ S+S ETG+ + EFR + 
Sbjct: 345 IKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQVASLSQETGLPVGEFRRVY 404

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 405 ATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 464

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REP PEE
Sbjct: 465 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEE 524

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK AV PLD+AIQ NLRE
Sbjct: 525 LAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVIPLDAAIQTNLRE 584

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPS
Sbjct: 585 ATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPS 644

Query: 672 RSKKLRSFLD 681
           RS+KLRSFLD
Sbjct: 645 RSRKLRSFLD 654


>gi|260576520|ref|ZP_05844509.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
 gi|259021243|gb|EEW24550.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
          Length = 668

 Score =  687 bits (1772), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/691 (53%), Positives = 476/691 (68%), Gaps = 50/691 (7%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D   + +++D SL  D S  + K+MI  AR+RGY+T ++LNA LPP++ SSEQ+ED ++M
Sbjct: 8   DGKPDEQEADTSL--DMSQAAVKRMIADARERGYITYDQLNAVLPPEQASSEQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGINV++ D++++    E + +L  ++++  + +      A   TDDPVRMYLREMG
Sbjct: 66  LSEMGINVIENDEIDE---GEPAGELVETSTSREIAVSGASAEALDRTDDPVRMYLREMG 122

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA
Sbjct: 123 SVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEA 182

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G    G                       DD     G +E+  +   D+   V +P  
Sbjct: 183 TFGRSLDG-----------------------DDDMVGPG-LETGIEAGLDE-VGVAAPRR 217

Query: 250 NAENDERNLDEDEDD-------------SAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           N   DE  LD D +              SA +L+AME  L+P+V+  L+ IA  Y  L  
Sbjct: 218 NGA-DEPELDADGNPISRADDDDEDDEASAMSLAAMEAALKPRVLETLEVIARDYATLAE 276

Query: 297 LQDNAVNGQKDEKSSVKC------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           +QD  ++   ++ S          + L+ ++V LV  L L+ +RI+ L++QLY I+++IM
Sbjct: 277 MQDRRMHATMNDASRFSANDEAIYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIM 336

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
                +++LA +  I R  F++ +QG ELDP W           W++ +    D + ++R
Sbjct: 337 AINSGMVKLADAARINRREFIDEYQGYELDPTWGDRMAAKAGRGWQSLMEKSRDKVEELR 396

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            ++  +    G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 397 ADMAQVGQYIGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQF 456

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 457 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 516

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGD
Sbjct: 517 KLVRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGD 576

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKNA+ PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 577 FIEDKNAILPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 636

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 667


>gi|126738765|ref|ZP_01754461.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
 gi|126719946|gb|EBA16653.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
          Length = 663

 Score =  687 bits (1772), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/678 (53%), Positives = 480/678 (70%), Gaps = 27/678 (3%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D + ED +  +  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++M
Sbjct: 6   NDDRKPEDQEAEISLDMSQAAVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGIN+++ +++E+EE ++ + DL ++     V L   +      TDDPVRMYLREMG
Sbjct: 66  LSEMGINIIEDEEVEEEE-NKGATDLVTTEGPREVALAGAQAEKLDRTDDPVRMYLREMG 124

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLE 
Sbjct: 125 SVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLET 184

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G +            +       + + E+D+  E + D            + + S  +
Sbjct: 185 TFGNQMDEDGEVDEPVVAPGAAAAPAAKSEKDEGPELDAD-----------GNPIASDDD 233

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           + E+++ N+         +L+AME  L+ +V+  L+ I+  + +L  +QD+ ++   +E 
Sbjct: 234 DDEDEQANM---------SLAAMEAALKDRVLVTLERISTDFAQLSEMQDSRISATLNED 284

Query: 310 SSVKCK------VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            S   +       L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA   
Sbjct: 285 GSFSSQDEKTYQSLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSNMVKLADQA 344

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            I R  F+E ++GRELDP+W+S   + P   W+ F+    + +  +R E+  +    G+ 
Sbjct: 345 RINRREFVEAYRGRELDPNWLSEMSEKPGRGWQMFIERSTEKVEDLRAEMAQVGQYVGLD 404

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 405 ISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 464

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 465 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 524

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDS
Sbjct: 525 GREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDS 584

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 585 AIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 644

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 645 LRKLKHPSRSRKLRSFLD 662


>gi|149202116|ref|ZP_01879089.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
 gi|149144214|gb|EDM32245.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
          Length = 661

 Score =  687 bits (1772), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/684 (54%), Positives = 483/684 (70%), Gaps = 45/684 (6%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + E+++  +  D S  + K+MI  AR++G++T ++LN  LPPD+VSSEQ+ED ++MLS
Sbjct: 8   DDKPEEAEAEVSLDMSQAAVKRMIAEAREKGFITYDQLNEVLPPDQVSSEQIEDVMSMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGIN+++ +D E+EEG   S  +A       + L   K+     TDDPVRMYLREMGS+
Sbjct: 68  EMGINIIEAEDAEEEEGR--STAVAEIGRRGEITLGSGKEEKLDRTDDPVRMYLREMGSV 125

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  
Sbjct: 126 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLGEDILLRDVIDLEATF 185

Query: 192 G-------PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           G        E   G  + T       R+DS            E D+++       D + +
Sbjct: 186 GTQLGDEDAEPVVGAANVTSAPGGMGRDDS------------EPDLDA-------DGNPI 226

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
            S  ++ ++++ N+         +L+AME  L+P+V+  LD IA  Y +L  +QD+ ++ 
Sbjct: 227 HSDDDDEDDEQANM---------SLAAMEAALKPRVLDTLDRIAADYAKLSEMQDSRISA 277

Query: 305 QKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
             +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +++
Sbjct: 278 TLNEDGSFSREQEATYQTLRSEIVELVNELHLHNNRIEALIDQLYGINRRIMQIDSAMVK 337

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           LA    I R  F+E ++GRELDP+W+   A+    G W+ F+    + + ++R ++  + 
Sbjct: 338 LADQARINRSEFIEEYRGRELDPNWLDDMARKAGRG-WQMFIERSPEKVAELRADMAQVG 396

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 397 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 456

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 457 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 516

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN 
Sbjct: 517 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNV 576

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 577 ILPLDSAIQDNLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 636

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 QIEAKALRKLKHPSRSRKLRSFLD 660


>gi|126730240|ref|ZP_01746051.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
 gi|126708973|gb|EBA08028.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
          Length = 667

 Score =  686 bits (1769), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/682 (54%), Positives = 484/682 (70%), Gaps = 31/682 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D++ ED ++ +  D S  + KKMI  AR+RGY+T ++LN  LPPD+VSS+Q+ED ++M
Sbjct: 6   NEDAKSEDQEEEISLDMSQAAVKKMIAEARERGYITYDQLNQVLPPDQVSSDQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEE-GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           LS MGI V + D+  +EE  ++ S DL  +     V L          TDDPVRMYLREM
Sbjct: 66  LSEMGIQVTEDDEESEEEDANKGSTDLVETKRGGEVALGSGTTEKLDRTDDPVRMYLREM 125

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW +EL     LLR++IDLE
Sbjct: 126 GSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHEELLSEDILLRDVIDLE 185

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                +       G +G   +   D+S       V+ + G+  +        + K D P 
Sbjct: 186 TTFSGQ------MGEDGELDEPVVDAS-------VETSNGEAGT--------QKKSDEPE 224

Query: 249 ENAEND--ERNLDEDEDDSAH-TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV--- 302
            +A+ +   R+ DED+D+ A+ +L+AME  L+P+V+  LD IA  Y +L  +QD+ +   
Sbjct: 225 YDADGNPISRDDDEDDDEQANMSLAAMETALKPRVLETLDRIARDYEQLAEMQDSRISAT 284

Query: 303 ---NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              +G  D       + L+ ++V+LV  L L+ +RI+ L++QLY I+KRIM  +  +++L
Sbjct: 285 LNEDGSFDSDDEATYQKLRGEIVELVNGLHLHNNRIEALIDQLYGINKRIMSIDSAMVKL 344

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R+++  +   
Sbjct: 345 ADQARINRREFVDEYRGHELDPNWLERMAEKSGRGWQMFIERSADKVEELRSDMAQVGQY 404

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 405 VGLDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 464

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M
Sbjct: 465 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQM 524

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ 
Sbjct: 525 LHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAIL 584

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 585 PLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 644

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 645 EAKALRKLKHPSRSRKLRSFLD 666


>gi|83309796|ref|YP_420060.1| RNA polymerase sigma factor RpoD [Magnetospirillum magneticum
           AMB-1]
 gi|82944637|dbj|BAE49501.1| DNA-directed RNA polymerase [Magnetospirillum magneticum AMB-1]
          Length = 679

 Score =  685 bits (1768), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/685 (55%), Positives = 486/685 (70%), Gaps = 18/685 (2%)

Query: 5   KKRNRDSDSEHED-SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K  N    SE++D + D  + D    + KKM+   ++RGYVT +ELNA +PP+EVSSEQ+
Sbjct: 4   KSTNTAEVSENQDEAMDGPLLDTLGVAVKKMVAKGKERGYVTYDELNAAMPPEEVSSEQI 63

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           EDT+AMLS +GINVV+ ++ ED        +   +   S       +D     TDDPVRM
Sbjct: 64  EDTMAMLSELGINVVESEEGEDNTPEAAEEETTETEGYSGAGNVDEEDLG--RTDDPVRM 121

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +A++ W D L +G  LLR+
Sbjct: 122 YLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTLRAVVDWHDALVEGKMLLRD 181

Query: 184 IIDLEACIG--PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           IIDL+A  G  PE +       EG   ++   +   + +      EG+ E   K   ++ 
Sbjct: 182 IIDLDATYGADPEPEELAEVEAEGVIVEEAAPAGAAEAK-----PEGEAEP--KAEGEEG 234

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN- 300
            K +      E +     E+ ++++ +L+AME +L P V+   + IA  + +L  +QD  
Sbjct: 235 EKEEGAEGEPEVEGEGEAEEGEENSISLAAMETELLPIVLETFEVIAATHHKLEKVQDQR 294

Query: 301 --AVNGQKDEKSSVKCKV--LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
             A+N  +    +++ K   LK +LV+L+  + LN +RI+ LVEQL  +++R+M  EG L
Sbjct: 295 LAALNKGEAVTPAMEKKYDKLKLELVRLMDGIHLNNARIEQLVEQLNGLNRRLMMQEGRL 354

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           LRLA+S  +KR  FL+ + G ELDP+W+       + +WK+F A        IR  I  I
Sbjct: 355 LRLAESCRVKRQDFLDAYYGSELDPNWIEQVTQRSK-QWKDFGARHGKDAADIRATIADI 413

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E G+ ISE+R IV  V++GE EAS AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 414 SAEAGLPISEYRRIVQTVQRGEREASRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQE 473

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+
Sbjct: 474 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTS 533

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL+MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKN
Sbjct: 534 RQMLHEIGREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKN 593

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLD+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 594 AVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 653

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 654 RQIEAKALRKLKHPSRSRKLRSFLD 678


>gi|255261823|ref|ZP_05341165.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
 gi|255104158|gb|EET46832.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
          Length = 658

 Score =  685 bits (1767), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/690 (54%), Positives = 476/690 (68%), Gaps = 44/690 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D  S++ D+D SL  D S  + KKMI  AR+RGY+T ++LN  LPP++VSSEQ
Sbjct: 1   MAAKDNDDRKSDNSDADISL--DMSQAAVKKMIGEARERGYITYDQLNQVLPPEQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN+++ +  ++E+  +   D+ ++  N  V +   +      TDDPVR
Sbjct: 59  IEDVMSMLSEMGINIIEEETEDEEQ--KGGTDVTTTGGNREVAVSSGETEKLDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLR 176

Query: 183 EIIDLEACIGP-----ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           ++IDLE   G      E +      T G +  K+E++         QE + D    AK  
Sbjct: 177 DVIDLETTFGDQMGEDEEEAPVVDTTAGAAAPKKEEA---------QELDADGNPIAKED 227

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
            DD  +                     +  +L+AME  L+P+V+  LD IA  + +L  +
Sbjct: 228 DDDEDE--------------------QANMSLAAMEAALKPRVLETLDLIANDFAKLSEM 267

Query: 298 QDNAVNGQKDEKSSVKCKV------LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           QD  ++   +E  S   K       L+ ++V+LV S+ L+ +RI+ L++QLY I++RIM 
Sbjct: 268 QDARISATLNEDESFSDKAEKSYQKLRSEIVELVNSMHLHNNRIEALIDQLYGINRRIMS 327

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            +  +++LA    I R  F++ ++G ELDP W+    + P   W+  +      I  +R 
Sbjct: 328 IDSSMVKLADQARINRREFIDAYRGHELDPTWLEQMGEKPGRGWQALIEKSTGKIEDLRA 387

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           ++  +    G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 388 DMAQVGQYIGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFL 447

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 448 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 507

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +VRT R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDF
Sbjct: 508 LVRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDF 567

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IEDKNAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF V
Sbjct: 568 IEDKNAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 627

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 628 TRERIRQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|126733203|ref|ZP_01748950.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
 gi|126716069|gb|EBA12933.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
          Length = 660

 Score =  684 bits (1764), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/664 (54%), Positives = 466/664 (70%), Gaps = 29/664 (4%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D S  + KKMI  AR+RGY+T ++LNA LPP++VSS+Q+ED ++MLS MGI V + ++ 
Sbjct: 19  LDMSQTAVKKMIADARERGYITYDQLNAVLPPEQVSSDQIEDVMSMLSEMGIQVTEEEES 78

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ E ++ +  +A+ A +  V L   +      TDDPVRMYLREMGS+ELLSREGEIAIA
Sbjct: 79  EETEENQGNTAVATVAGSREVTLGGAEAEKLDRTDDPVRMYLREMGSVELLSREGEIAIA 138

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE   G +       G 
Sbjct: 139 KRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLETTFGNQLGE---DGE 195

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E         +  E ++++ QE + D    AK   DD                       
Sbjct: 196 EETVVAAPAAAGTETKKEETQELDADGNPIAKDDDDDEED-------------------- 235

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV------KCKVL 317
            +  +L+AME  L+P+V+  L+ IA  +  L  +QD  ++   +E SS       K + L
Sbjct: 236 QANMSLAAMEAALKPRVLETLELIARDFAALSDMQDARMSATLNEDSSFSDKQEKKYQKL 295

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + ++V+LV SL L+ +RI+ L++QLY I++RIM  +  +++LA    I R  F+E ++GR
Sbjct: 296 RSEIVELVNSLHLHNNRIEALIDQLYGINRRIMSIDSSMVKLADQARINRREFIEAYRGR 355

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           ELDP+W+    +     W+  +      I ++R ++  +    G+ I+EFR IV  V+KG
Sbjct: 356 ELDPNWLDDMGEKSGRGWQMMIEKSTGKIEELRGDMAQVGQYVGVDITEFRRIVQQVQKG 415

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 416 EKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 475

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A+KL 
Sbjct: 476 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAEKLQ 535

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSAIQ NL+ETTTRVL
Sbjct: 536 MPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSAIQENLKETTTRVL 595

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLR
Sbjct: 596 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLR 655

Query: 678 SFLD 681
           SFLD
Sbjct: 656 SFLD 659


>gi|254441274|ref|ZP_05054767.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
 gi|198251352|gb|EDY75667.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
          Length = 655

 Score =  683 bits (1763), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/691 (54%), Positives = 475/691 (68%), Gaps = 58/691 (8%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           +D++ + +D+D SL  D S  + KKMI  AR+RG +T ++LNA LPPD+VSS+Q+ED ++
Sbjct: 4   KDTNVQRDDADHSL--DMSQAAVKKMIAEARERGTITYDQLNAVLPPDQVSSDQIEDVMS 61

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           ML+ MGI V + ++ E+ +    S +LA+ A    V L   +      TDDPVRMYLREM
Sbjct: 62  MLNEMGIQVTEEEESEEVDDDGTSKELATVAGGRDVVLGGAEAEKLDRTDDPVRMYLREM 121

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE
Sbjct: 122 GSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLE 181

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              G                   +  ++E E       E  + SA  V +    K D  P
Sbjct: 182 TTFG-------------------DQLAEETE-------ETAVVSAVSVGE----KSDEKP 211

Query: 249 ENAENDERNLDEDED------------DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           E        LD D +             +  +L+AME QL+P+V+  L+ IA+ + +L  
Sbjct: 212 E--------LDADGNPIANDDDDDEEEAANLSLAAMEAQLKPQVLDTLEVIAKGFAKLSD 263

Query: 297 LQDNAVNGQKDEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           +QD  ++   +E  S       K + L+ ++V+LV SL L+ +RI+ L++QLY I++RIM
Sbjct: 264 MQDLRMSATLNEDDSFSGKEEKKYQKLRSEIVQLVNSLHLHNNRIEALIDQLYGINRRIM 323

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             +  +++LA    I R  F++ ++GRELDP W+          W+  +      I ++R
Sbjct: 324 QIDSNMVKLADQSRINRREFIDAYRGRELDPSWLDEMGQKAGRGWQMLIERSTTKIEELR 383

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            E+  +    G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 384 AEMAQVGQYVGVDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQF 443

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 444 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 503

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT R+M ++I REPTPEE+A KL MP+E VRKV+KI KEPISLETPIGDE+ S LGD
Sbjct: 504 KLVRTGRQMLHEIGREPTPEELAAKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGD 563

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKNAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 564 FIEDKNAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 623

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS++LRSFLD
Sbjct: 624 VTRERIRQIEAKALRKLKHPSRSRRLRSFLD 654


>gi|114764808|ref|ZP_01443990.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114542694|gb|EAU45717.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 661

 Score =  682 bits (1761), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/681 (53%), Positives = 479/681 (70%), Gaps = 35/681 (5%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           + D++ E  DD+   D S  + KKMI  AR+RGY+T ++LN  LPPD+VSS+Q+ED ++M
Sbjct: 6   NDDAKPETQDDAHSLDMSQAAVKKMIAEARERGYITYDQLNQVLPPDQVSSDQIEDVMSM 65

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MGI V + D+  +E+ ++ S +L  ++    V L    +     TDDPVRMYLREMG
Sbjct: 66  LSEMGIQVTEEDEEAEEDANKGSTELVDASKGRDVALSSGANEKLDRTDDPVRMYLREMG 125

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW  EL +   LLR++IDLE 
Sbjct: 126 SVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHQELLEEEILLRDVIDLET 185

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G                      +Q  E   ++E   D    A  +  ++ K D P  
Sbjct: 186 TFG----------------------NQMDEEGGLEEPVVD----ATAATAEKPKKDEPEY 219

Query: 250 NAEND---ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
           +A+ +     + D+DE+ +  +L+AME  L+P+V+  L+ IA  Y +L ++QD  ++   
Sbjct: 220 DADGNPIARDDDDDDEEQANMSLAAMEAALKPRVLETLERIAGDYEQLAAMQDARISATL 279

Query: 307 DEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           +E  S       + + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +++LA
Sbjct: 280 NEDGSFSQADEAQYQQLRSEIVELVNGLHLHNNRIEALIDQLYGINRRIMSIDSSMVKLA 339

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               I R  F++ ++G ELDP+W+    + P   W+  +    D I  +R+++  +    
Sbjct: 340 DQARINRREFIDEYRGHELDPNWIERMSEKPGRGWQMLIERFEDKIEGLRSDMAQVGQYV 399

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 400 GLDISEFRRIVGQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 459

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M 
Sbjct: 460 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQML 519

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ P
Sbjct: 520 HEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILP 579

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 580 LDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 639

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKLKHPSRS+KLRSFLD
Sbjct: 640 AKALRKLKHPSRSRKLRSFLD 660


>gi|146276891|ref|YP_001167050.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555132|gb|ABP69745.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 667

 Score =  682 bits (1760), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/683 (54%), Positives = 477/683 (69%), Gaps = 37/683 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + ED D     D S  + K+MI  AR+RGY+T ++LN  LP D+VSSEQ+ED +AMLS
Sbjct: 8   DGKPEDQDAETSLDMSQAAVKRMIAEARERGYITYDQLNTVLPQDQVSSEQIEDVMAMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGINV++ ++ E+ E + + ++  S +   +V    + ++ DR TDDPVRMYLREMGS+
Sbjct: 68  EMGINVIENEEAEEGEPAGELVEQGSGSREIAV-AGTQGETLDR-TDDPVRMYLREMGSV 125

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  
Sbjct: 126 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEATF 185

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G                 +  D   + +  +++E E  + +AA      R+    P  +A
Sbjct: 186 G-----------------RSLDGDDDLDGPEIEEVE--VTAAAPSPAPRRTNASEPELDA 226

Query: 252 END----ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ--------- 298
           + +        DED++ SA +L+AME  L+P+V+  L+ IA  Y  L  +Q         
Sbjct: 227 DGNPISRAEEEDEDDEASAMSLAAMEAALKPRVLETLELIARDYATLAEMQTKRMSATLN 286

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           DN     +DE +  K   L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++
Sbjct: 287 DNIRFNPEDEAAYQK---LRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVK 343

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           LA +  I R  F+E +QG ELDP W           W+  +    D +  +R ++  +  
Sbjct: 344 LADAARINRREFIEEYQGYELDPTWAERMAQKSGRGWQTLMEKSRDKVEDLRGDMAQVGQ 403

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
             G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 404 YVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 463

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+
Sbjct: 464 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQ 523

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+
Sbjct: 524 MLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAI 583

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 584 LPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 643

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 644 IEAKALRKLKHPSRSRKLRSFLD 666


>gi|114771658|ref|ZP_01449062.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114547730|gb|EAU50620.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 656

 Score =  682 bits (1759), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/664 (55%), Positives = 476/664 (71%), Gaps = 34/664 (5%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D S  + KKMI +AR+RGY+T +ELN  +PPD+V+SEQ+ED ++MLS MGIN+++ D++E
Sbjct: 19  DMSQAAVKKMIAVARERGYITYDELNDVMPPDQVASEQIEDVMSMLSEMGINIIEADEVE 78

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE G  D   +A+ A   ++     K++ DR TDDPVRMYLREMGS+ELLSREGEIAIAK
Sbjct: 79  DE-GPTDVTVVANDAKEVTLAATG-KETLDR-TDDPVRMYLREMGSVELLSREGEIAIAK 135

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIEAGR  M+  LCESPLTFQA+ IWRDEL +   LLR++IDLE           F  T 
Sbjct: 136 RIEAGRKTMIEGLCESPLTFQAITIWRDELLEEEILLRDVIDLETT---------FSDTL 186

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                           DD     G +  A K S     ++D+      +DE   ++++D 
Sbjct: 187 D---------------DDEDPMVGPLTGAPKPSSSPAHELDADGNRLNDDEDEDEDEDDA 231

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE------KSSVKCKVLK 318
           +  +L+AME+ L+P V+  L +IA+ Y +L S+QD  ++   +E      KS    + L+
Sbjct: 232 ANISLAAMEETLKPDVLATLAKIAKDYNKLASMQDERISATINEDDTFSDKSEKSYQKLR 291

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
             LV+ V +L  + +RID L++QLY I+++IM  +  ++++A    I R  F+++++G+E
Sbjct: 292 NSLVEQVNALHFHNNRIDALIDQLYGINRKIMSIDSGMVKIADQSRINRREFVDKYRGQE 351

Query: 379 LDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           LDP W+    +  +G  WK F+    +   ++R ++  +    G+ I EFR IV+ V+KG
Sbjct: 352 LDPMWLDKIAENEDGRGWKTFIEKHREKAEELRADMAQVGHYVGVDIPEFRRIVNQVQKG 411

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 412 EKEARSAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 471

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A KL 
Sbjct: 472 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELASKLQ 531

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP++ VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PL+SAIQ NL+ETTTRVL
Sbjct: 532 MPLDKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLESAIQGNLKETTTRVL 591

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLR
Sbjct: 592 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLR 651

Query: 678 SFLD 681
           SFLD
Sbjct: 652 SFLD 655


>gi|148553355|ref|YP_001260937.1| RNA polymerase sigma factor RpoD [Sphingomonas wittichii RW1]
 gi|148498545|gb|ABQ66799.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingomonas wittichii RW1]
          Length = 674

 Score =  681 bits (1757), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/673 (53%), Positives = 487/673 (72%), Gaps = 26/673 (3%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D+ + D ++ S KK+I  A+++GY+T E+LN  LP D+++S+Q+ED ++ L+ MG+N+V+
Sbjct: 16  DAPLIDLNEGSLKKLIARAKRKGYITYEQLNEALPQDQMTSDQLEDVMSALNEMGVNIVE 75

Query: 80  GDDL-EDEEGSEDSLDLASSA----SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
            +D  EDE+  ED +D  + +    +  ++    +K++ DR TDDPVRMYLREMG++ELL
Sbjct: 76  NEDAGEDEQPEEDGIDEVAGSEEGDTGPALTTTAKKETVDR-TDDPVRMYLREMGAVELL 134

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           SREGEIAIAKRIEAGR  M+  LCESP+TF A+I W + LN+GT  LREI+DL+A +   
Sbjct: 135 SREGEIAIAKRIEAGRDTMILGLCESPITFNAIIEWSNALNEGTMQLREILDLDAML--- 191

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN- 253
           SKG      E       ED+  E       ET G      +  +++ S  +      E  
Sbjct: 192 SKGPTAEQVEN------EDADAEIS----AETAGPTFKEEEEPEEEASADEDEDSMTERR 241

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQKDEKSS 311
             R  ++D++D+  +L+ ME+QL+P  +     I ++Y+    +Q   V   G  D+  +
Sbjct: 242 APRPQEDDDEDNTLSLAQMEEQLKPMALERFAAITDLYKTFSQVQSARVAALGVGDDFPA 301

Query: 312 V---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               + + L+E+L   V S+  + ++I+ LV+QLY  ++R+    G++LRLA+ + + R 
Sbjct: 302 AEEERYQGLREQLTAEVESVQFHGAKIEYLVDQLYSFNRRLTTLGGQMLRLAERHKVPRR 361

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FLE +   E++  W+       + +W NF A E D++ +IRNEI  I+  TG+++SEFR
Sbjct: 362 DFLEAYVNHEMEDGWLDRVGRI-DKKWANFAANEADAVDRIRNEIGEIAQATGMALSEFR 420

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 421 RIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 480

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I REPT
Sbjct: 481 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQILHEIGREPT 540

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQ+N
Sbjct: 541 PEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQSN 600

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLK
Sbjct: 601 LKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 660

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+K+RSFLD
Sbjct: 661 HPSRSRKMRSFLD 673


>gi|144900406|emb|CAM77270.1| RNA polymerase sigma factor rpod [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 664

 Score =  680 bits (1755), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/673 (56%), Positives = 473/673 (70%), Gaps = 30/673 (4%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            E++ D  + D    + KKM+   R+RGYVT +ELNA LPPDEVSSEQ+EDT+AMLS MG
Sbjct: 15  QEENLDGPLLDALGVAVKKMVTRGRERGYVTYDELNAALPPDEVSSEQIEDTMAMLSEMG 74

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIEL 133
           INVV+ ++ ++    E   + A  +S +        D  D   TDDPVRMYLREMGS+EL
Sbjct: 75  INVVESEETDEAAAVETEEEEAEPSSGAGNV-----DEEDLGRTDDPVRMYLREMGSVEL 129

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           LSREGEIAIAKRIEAGR MM+  +CESPLT +A+I W D L +G  LLR+IIDL+A  G 
Sbjct: 130 LSREGEIAIAKRIEAGREMMIGGICESPLTIRAIIEWHDALQNGRMLLRDIIDLDATYGS 189

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
              G              E S +E E    +E      +  +   + R     P      
Sbjct: 190 GPGG--------------ELSEEEMEAGPAEEEPAAAPAEGEEGAEPR----DPNAPEGE 231

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN--AVNGQKDEKSS 311
            E   D + +D++ +L+AME QL P+V+   + IA  +  +  LQ +  A   + D  S+
Sbjct: 232 VEGEGDGEGEDNSISLAAMEAQLMPQVLETFEAIAANFLRMEKLQKDRMAALSKGDTVSA 291

Query: 312 V---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               K   LK ++V+L+  + LN +RI+ LV+ +  ++KR+M  EG LLRLA+S  +KR 
Sbjct: 292 ATEKKYDKLKAEMVRLMEDVHLNNARIEQLVDHMNGLNKRLMGFEGRLLRLAESCKVKRQ 351

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FL+ + G ELDP+W+          WK+F       +  IR +I  +S E G+ I+EFR
Sbjct: 352 DFLDSYFGSELDPNWLETVA-VKSKHWKDFSEKHRRDVGDIRTQIGVVSGEAGLPITEFR 410

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I+  V++GE EAS AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 411 RIIQTVQRGEREASKAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 470

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPT
Sbjct: 471 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPT 530

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A+KL+MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV PLD+AIQAN
Sbjct: 531 PEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPLDAAIQAN 590

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLK
Sbjct: 591 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 650

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+KLRSFLD
Sbjct: 651 HPSRSRKLRSFLD 663


>gi|84502758|ref|ZP_01000877.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84389153|gb|EAQ01951.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 663

 Score =  680 bits (1754), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/682 (53%), Positives = 474/682 (69%), Gaps = 30/682 (4%)

Query: 7   RNRDSDSEHEDSDDSLV-FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           ++ D D   +D  +  V  D S    KKMI  AR+RG++T ++LN  LP D+VSSEQ+ED
Sbjct: 4   KDTDEDQRQDDEQEQDVSLDLSQAQIKKMIAEARERGFITYDQLNQVLPQDQVSSEQIED 63

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            ++MLS MGIN+++ ++ E+EE    S  +  + SN  V L          TDDPVRMYL
Sbjct: 64  VMSMLSEMGINIIEDEEAEEEESK--STAVVETTSNREVALGSGSQEKLDRTDDPVRMYL 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++I
Sbjct: 122 REMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVI 181

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           DLE   G +       G E         ++        QE + + ++       D + + 
Sbjct: 182 DLETTFGDQ-----MEGDEDAPVVDPAQAAPAAPAAKPQEEQPEYDA-------DGNPIA 229

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
              +  E+++ N+         +L+AME  L+P+V+  LD IA  +  L  +QDN ++  
Sbjct: 230 KDEDEDEDEQANM---------SLAAMETALKPRVLETLDTIARDFAVLSEIQDNRISAT 280

Query: 306 KDEKSSVKC------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +++L
Sbjct: 281 LNEDDSFNASDEAEYQKLRAEIVELVNGLHLHNNRIEALIDQLYGINRRIMQIDSAMVKL 340

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A    I R  F+E ++G ELDP+W+    +     W+ F+    D +  +R+++  +   
Sbjct: 341 ADQARINRREFIEEYRGHELDPNWMERMSEKSGRGWQMFIDRFSDKVEDLRSDMAQVGQY 400

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 401 VGLDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 460

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M
Sbjct: 461 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQM 520

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ 
Sbjct: 521 LHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAIL 580

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 581 PLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 640

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+KLRSFLD
Sbjct: 641 EAKALRKLKHPSRSRKLRSFLD 662


>gi|103486468|ref|YP_616029.1| RNA polymerase sigma factor RpoD [Sphingopyxis alaskensis RB2256]
 gi|98976545|gb|ABF52696.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingopyxis alaskensis
           RB2256]
          Length = 669

 Score =  678 bits (1749), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/680 (52%), Positives = 486/680 (71%), Gaps = 25/680 (3%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +++E   D+ + D ++   KK+I   ++RGY+T +ELNA LP DE+SSEQ+ED ++ +S+
Sbjct: 3   TKNEADTDAPLIDLNEADVKKLIARGKKRGYLTYDELNAALPQDEMSSEQIEDIMSAISD 62

Query: 73  MGINVVDGDDLEDEEGSE---DSLDL-ASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           MGIN+V+ D+   EE  +   D +D+ A + S S+  ++K+K++ DR TDDPVRMYLREM
Sbjct: 63  MGINIVESDEDVQEEAEQEVDDEVDVSAGTGSVSNPAIEKKKETVDR-TDDPVRMYLREM 121

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF A+I W + LN+G   LREI+DLE
Sbjct: 122 GAVELLSREGEIAIAKRIEAGRDTMILGLCESPLTFNAIIEWSNALNNGDMQLREIVDLE 181

Query: 189 ACIG--PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           A +   P  +     G E     ++      K+ D+V+E     E AA    +D      
Sbjct: 182 AMLSKDPAPENLDEEGAEDGEISEKTAGVSFKDEDEVEE-----EPAADGDDED------ 230

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-- 304
             E       + D+D++D+  +L+AME+ L+P  +     I + ++  + LQ+  +    
Sbjct: 231 -GEGTSGKRESFDDDDEDNTLSLAAMEELLKPDALEKFANITKSFKAFQKLQEARLEALS 289

Query: 305 ---QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
              +    S  K   L+E+L   V S+  + ++I+ LV+QLY  ++R+    G++LRLA+
Sbjct: 290 SGEEFPAASEKKYHKLREELTAQVESVQFHGTKIEYLVDQLYSYNRRLTALGGQMLRLAE 349

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
            + + R  FL+ + GREL+ +W+       + +W  F   E  ++ +IR EI  I+   G
Sbjct: 350 RHKVPRKSFLDHYVGRELEENWLEEVAGI-DKKWAAFAENEAAAVDRIRVEISEIAQAAG 408

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S++EFR +V+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 409 MSLTEFRRVVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 468

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR +R+  +
Sbjct: 469 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRCSRQFLH 528

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNAV P+
Sbjct: 529 ESGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVIPV 588

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A+Q+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 589 DAAVQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 648

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+K+RSFLD
Sbjct: 649 KALRKLKHPSRSRKMRSFLD 668


>gi|254452739|ref|ZP_05066176.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
 gi|198267145|gb|EDY91415.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
          Length = 637

 Score =  678 bits (1749), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/664 (55%), Positives = 465/664 (70%), Gaps = 36/664 (5%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S  + KKMI  AR+RG +T ++LNA LPPD+VSS+Q+ED ++ML+ MGI V + ++ E+
Sbjct: 1   MSQAAVKKMIAEARERGTITYDQLNAVLPPDQVSSDQIEDVMSMLNEMGIQVTEEEESEE 60

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +    S +LA+ A    V L   +      TDDPVRMYLREMGS+ELLSREGEIAIAKR
Sbjct: 61  VDDDGTSKELATVAGRRDVILGGAEAEKLDRTDDPVRMYLREMGSVELLSREGEIAIAKR 120

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE   G             
Sbjct: 121 IEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLETTFG------------- 167

Query: 206 HSYQKREDSSQEKERDDVQETEGD--IESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                          D + E  G+  + SAA  ++    K D   +     + + D++E+
Sbjct: 168 ---------------DQLAEETGESAVVSAAPSAEKSEEKQDLDADGKPIAKDDDDDEEE 212

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV------KCKVL 317
            +  +L+AME QL+P+V+  L+ IA+ + +L  +QD+ ++   +E  S       K + L
Sbjct: 213 AANLSLAAMEAQLKPQVLDTLEVIAKGFAKLSDMQDSRMSATLNEDDSFSGKEEKKYQKL 272

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + ++V LV SL L+ +RID L++QLY I++RIM  +  +++LA    I R  F++ ++GR
Sbjct: 273 RSEVVALVVSLHLHNNRIDALIDQLYGINRRIMQIDSNMVKLADQSRINRREFVDAYRGR 332

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           ELDP W+          W+  +      I ++R E+  +    G+ ISEFR IV  V+KG
Sbjct: 333 ELDPTWLEEMGQKAGRGWQMLIERSTTKIEELRAEMAQVGQYVGVDISEFRRIVQQVQKG 392

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 393 EKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 452

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A KL 
Sbjct: 453 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAAKLQ 512

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSAIQ NL+ETTTRVL
Sbjct: 513 MPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRVL 572

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS++LR
Sbjct: 573 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRRLR 632

Query: 678 SFLD 681
           SFLD
Sbjct: 633 SFLD 636


>gi|288957899|ref|YP_003448240.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
 gi|288910207|dbj|BAI71696.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
          Length = 670

 Score =  676 bits (1744), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/671 (55%), Positives = 467/671 (69%), Gaps = 22/671 (3%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           E+S D  + D    + KKMI   ++RGYVT +ELNA LP D  SSEQ+EDT+AMLS MGI
Sbjct: 16  EESADGPLMDGMGLAVKKMIARGKERGYVTYDELNAALPQDSSSSEQIEDTMAMLSEMGI 75

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           N+V+ ++ + E   E + D    +S +        D     TDDPVRMYLREMGS+ELLS
Sbjct: 76  NIVESEEQDSENSGEGASDGEGRSSGNL------DDDDIGRTDDPVRMYLREMGSVELLS 129

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEIAIAKRIEAGR MM+ ++CESPLT +A++ W D L +G  LLR+IIDL+A  G   
Sbjct: 130 REGEIAIAKRIEAGREMMIGAICESPLTIRAILEWHDSLMEGKMLLRDIIDLDATYG--- 186

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                 G +G    +      E               A    + D  +   PP      E
Sbjct: 187 -----GGPDGEEMPEGLAEVVEAAGAAGPAGAAPAADAPADEEGDEPR---PPRAEGEGE 238

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDE----KS 310
              + +E ++A +LSAME  L+P+V+   + I   Y +L  L ++ +   Q+ E    ++
Sbjct: 239 EGEEGEEGENALSLSAMEAALKPQVIETFENIKATYDKLHKLHESRMAAMQRGEDLGKQT 298

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
             K   LK ++V+L+ ++ LN  RI+ LVEQLY +++++   EG LLR+A    +KR+ F
Sbjct: 299 DRKYDKLKTEMVELMNTVRLNNQRIEQLVEQLYGLNRKLTGFEGRLLRMATECRVKREDF 358

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L ++ G ELDP+W+   +      W  F       I K R  I +++ E  + I+EFR I
Sbjct: 359 LNQYFGHELDPNWLERIRGLNPKTWGKFAEKYDGDIRKTREAISNVAEEARLPINEFRRI 418

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS V+KGE EAS AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 419 VSTVQKGEKEASRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 478

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPE
Sbjct: 479 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPE 538

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A++L MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV PLD+AIQANLR
Sbjct: 539 ELAERLMMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPLDAAIQANLR 598

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHP
Sbjct: 599 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHP 658

Query: 671 SRSKKLRSFLD 681
           SRS+KLRSFLD
Sbjct: 659 SRSRKLRSFLD 669


>gi|294678570|ref|YP_003579185.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
 gi|1173126|sp|P46400|RPOD_RHOCA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|881516|gb|AAA70413.1| RpoD [Rhodobacter capsulatus SB 1003]
 gi|294477390|gb|ADE86778.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
          Length = 674

 Score =  676 bits (1743), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/678 (55%), Positives = 473/678 (69%), Gaps = 33/678 (4%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           +D+   FD S  + K+MI  A++RGY+TI++LNA +PP+ VS EQ+ED ++MLS MGINV
Sbjct: 15  ADEDASFDMSQAAVKRMIGEAKERGYITIDQLNAVMPPETVSGEQIEDVMSMLSEMGINV 74

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+    E EE     +    S S          ++ DR TDDPVRMYLREMGS+ELLSRE
Sbjct: 75  VE--GEEVEESEGGEVVETGSGSREIAVAGAAGETLDR-TDDPVRMYLREMGSVELLSRE 131

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  G    G
Sbjct: 132 GEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEEILLRDVIDLEATFGRSLDG 191

Query: 198 --GF--FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
             G     G EG             E  D++  EG   +A + + D+      P  +A+ 
Sbjct: 192 DEGMEGMEGIEGPVV----------EGLDLETAEGAAPAARRPASDE------PEYDADG 235

Query: 254 DE----RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           +        ++D+D S  +L+AME  L+PKV+  L+ IA  Y +L  +QD  ++   +E 
Sbjct: 236 NPISRIDEEEDDDDSSNMSLAAMEAALKPKVLETLELIARDYAKLAEMQDLRMSATLNED 295

Query: 310 SSVKC------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            +         + L+ ++V LV  L L+ +RI+ L++QLY I+++IM  +  +++LA + 
Sbjct: 296 GTFSVAEEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSIDSGMVKLADAA 355

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            I R  F++ ++G ELDP W+      P   W        D +  +R+E+  +    G+ 
Sbjct: 356 RINRREFIDEYRGYELDPTWMDRMSAKPARAWVTLFEKSRDKVEDLRHEMAQVGQYVGVD 415

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 416 ISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 475

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 476 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 535

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDS
Sbjct: 536 GREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDS 595

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 596 AIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 655

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 656 LRKLKHPSRSRKLRSFLD 673


>gi|332185826|ref|ZP_08387573.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
 gi|332014184|gb|EGI56242.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
          Length = 671

 Score =  675 bits (1742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/678 (52%), Positives = 481/678 (70%), Gaps = 42/678 (6%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + D ++ S KK+I  A++RGY+T ++LN  LP D++SS+Q+ED +A L+ MG+N+V+ ++
Sbjct: 16  LIDLNEASIKKLIARAKKRGYITYDQLNEALPQDQMSSDQLEDIMAALNEMGVNIVENEE 75

Query: 83  LEDEEGSED-------SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
             ++   E+       S+D  S +        K+K++ DR TDDPVRMYLREMG++ELLS
Sbjct: 76  QGEDGEGEEEADDAADSVDGDSDSGPQPE--AKKKETVDR-TDDPVRMYLREMGAVELLS 132

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI---- 191
           REGEIAIAKRIEAGR  M+  LCESP+TF A+I W   LN+GT  LREI+DL+A +    
Sbjct: 133 REGEIAIAKRIEAGRDTMILGLCESPITFNAIIDWSTALNEGTMQLREILDLDAMLSKDA 192

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           GPE+ G                   E E DD  E            +++  +     E+ 
Sbjct: 193 GPENLG-------------------EDEDDDNGEISAKNAGPQFKEEEEPEEPSVDDEDG 233

Query: 252 ENDERN---LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-----AVN 303
           E  ER     +++E+D+  +L+ ME+ L+P+ +     I  +Y++   +Q       A+ 
Sbjct: 234 EGGERRGPRAEDEEEDNTLSLAQMEETLKPQALEKFANITSIYKKFSKIQQQRLESMALG 293

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           G+       K   L+E+L   V S+  + ++I+ LV+QLY  ++R+    G++LRLA+ +
Sbjct: 294 GELSAADERKYHKLREELTAEVESVQFHNAKIEFLVDQLYAFNRRLTALGGQMLRLAERH 353

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + R  FL+R+ G ELD +W+   +   + +W NF + E  ++ +IR+EI  IS +TG++
Sbjct: 354 KVNRKDFLDRYLGHELDENWLDTVRGL-DKKWGNFASNEAATVDRIRSEIAEISQQTGMA 412

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ++EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 413 LTEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 472

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++ 
Sbjct: 473 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQ 532

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+
Sbjct: 533 GREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVIPVDA 592

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 593 AIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 652

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+K+RSFLD
Sbjct: 653 LRKLKHPSRSRKMRSFLD 670


>gi|260425299|ref|ZP_05779279.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
 gi|260423239|gb|EEX16489.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
          Length = 665

 Score =  675 bits (1742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/686 (53%), Positives = 480/686 (69%), Gaps = 38/686 (5%)

Query: 9   RDSDSEHEDS-DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +D+D    DS DD    D S  + KKMI  AR+RGY+T ++LN  LPPD+VSS+Q+ED +
Sbjct: 4   KDNDDAKPDSQDDGHSLDMSQAAVKKMIAEARERGYITYDQLNQVLPPDQVSSDQIEDVM 63

Query: 68  AMLSNMGINVVDGDDLEDEEG---SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           +MLS MGI V + D+  + +    ++ S +L  ++    V L   ++     TDDPVRMY
Sbjct: 64  SMLSEMGIQVTEDDEEGESDDDKDNKGSTELVDASRGRDVALSSGQNEKLDRTDDPVRMY 123

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW  EL +   LLR++
Sbjct: 124 LREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHQELLEEEILLRDV 183

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           IDLE   G                          + D+  + EG +      S  ++ + 
Sbjct: 184 IDLETTFG-------------------------NQMDEEGDLEGTVVDTGSGSVSEKPRR 218

Query: 245 DSPPENAEND--ERNLDEDEDDSAH-TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           D P  +A+ +   R  DED+D+ A+ +L+AME  L+P+V+  L+ I+  Y EL  +QD  
Sbjct: 219 DEPELDADGNPIAREDDEDDDEQANMSLAAMETALKPRVLETLERISRDYEELAEMQDAR 278

Query: 302 VNGQKDEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           ++   +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  
Sbjct: 279 ISATLNEDGSFSQSDEALYQKLRSEIVELVNGLHLHNNRIEALIDQLYGINRRIMSIDSS 338

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++  
Sbjct: 339 MVKLADQARINRREFVDEYRGNELDPNWMERMNEKSGRGWQMFIERFSDKVEELRADMAQ 398

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 399 VGQYVGLDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 458

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 459 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 518

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 519 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 578

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NA+ PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 579 NAILPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 638

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 639 IRQIEAKALRKLKHPSRSRKLRSFLD 664


>gi|77463967|ref|YP_353471.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126462810|ref|YP_001043924.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17029]
 gi|77388385|gb|ABA79570.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126104474|gb|ABN77152.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 668

 Score =  675 bits (1741), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/681 (54%), Positives = 475/681 (69%), Gaps = 32/681 (4%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + ED D     D S  + K+MI  AR+RGY+T ++LN  LP D+VSSEQ+ED +AMLS
Sbjct: 8   DGKPEDQDAETSLDMSQAAVKRMIAEARERGYITYDQLNTVLPQDQVSSEQIEDVMAMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGINV++ ++ E+ E + + ++  S +   +V    + ++ DR TDDPVRMYLREMGS+
Sbjct: 68  EMGINVIENEEAEEGEPAGELVEQGSGSREIAV-AGTQGETLDR-TDDPVRMYLREMGSV 125

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  
Sbjct: 126 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEA-- 183

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE-- 249
                      T G S     D   +    D      ++E AA  +   R    S PE  
Sbjct: 184 -----------TFGRSLDGDGDDEIDGPEID------EVEVAAAPAPAPRRSTSSEPELD 226

Query: 250 ---NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
              N  +     DED++ SA +L+AME  L+P+V+  L+ IA  Y +L  +Q+  ++   
Sbjct: 227 ADGNPISRAEEEDEDDEASAMSLAAMEAALKPRVLETLELIARDYGKLAEMQNRRMSATL 286

Query: 307 DE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           ++      +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA
Sbjct: 287 NDHIRFTTEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLA 346

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            +  I R  F++ +QG ELDP W           W+  +    D +  +R E+  +    
Sbjct: 347 DAARINRREFIDEYQGYELDPMWAERMAAKSGRGWQTLMEKSRDRVEDLRGEMAQVGQYV 406

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 407 GVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 466

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M 
Sbjct: 467 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQML 526

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ P
Sbjct: 527 HEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILP 586

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 587 LDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 646

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKLKHPSRS+KLRSFLD
Sbjct: 647 AKALRKLKHPSRSRKLRSFLD 667


>gi|89055941|ref|YP_511392.1| RNA polymerase sigma factor RpoD [Jannaschia sp. CCS1]
 gi|88865490|gb|ABD56367.1| RNA polymerase, sigma 70 subunit, RpoD [Jannaschia sp. CCS1]
          Length = 668

 Score =  672 bits (1734), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/686 (53%), Positives = 471/686 (68%), Gaps = 34/686 (4%)

Query: 9   RDSDSEHEDSDDS-LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +D+D   +D D++ +  D S  + KKMI  AR RGY+T ++LN  LPP++VSSEQ+ED +
Sbjct: 3   KDTDDRKQDGDETEMGLDMSQAAVKKMIAEARVRGYITYDQLNTVLPPEQVSSEQIEDVM 62

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +MLS MGIN+++ D+ E+ +       + +  S          +  DR TDDPVRMYLRE
Sbjct: 63  SMLSEMGINIIEDDEAEEGDDKPAGELVTTEGSREVAVAATETEKLDR-TDDPVRMYLRE 121

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL +   LLR++IDL
Sbjct: 122 MGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLEEDILLRDVIDL 181

Query: 188 EAC----IGPESKGGFFHGTEGHSYQKREDSSQEKERDDV--QETEGDIESAAKVSKDDR 241
           +      +G E+         G +      +   + + +   QE + D    AK   +D 
Sbjct: 182 DTTFGRTMGDENDTPVVPAGVGSTPPSATPAPPPEPKKEEPTQELDADGNPIAKDDDEDE 241

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
            +                     +  +L+AME  L+P+V+  LD+IA  Y  L  +QD+ 
Sbjct: 242 DE--------------------QANMSLAAMELALKPQVLATLDQIANDYIRLSEMQDSR 281

Query: 302 VNGQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           ++   +E  S       + + L+ ++V+LV  L L+ +RI+ LV+QLY I++RIM  +  
Sbjct: 282 ISATLNEDDSFSKAEEAEYQHLRSEIVELVNELHLHNNRIEALVDQLYGINRRIMSIDSS 341

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F+E ++ +ELDP W+          W+  +      I ++R ++  
Sbjct: 342 MVKLADQARINRREFIEEYRNQELDPTWMERMTQKSGRGWQALMERSSGKIEELRGDMAQ 401

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ I EFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 402 VGQYVGLDIPEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 461

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 462 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 521

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 522 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 581

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 582 NAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 641

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 642 IRQIEAKALRKLKHPSRSRKLRSFLD 667


>gi|326387391|ref|ZP_08209000.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208047|gb|EGD58855.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 667

 Score =  672 bits (1733), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/676 (53%), Positives = 485/676 (71%), Gaps = 28/676 (4%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           DS D+ + D +D S KK+I  A++RG +T +ELN  LP D++SSEQ+ED +A +S MG+N
Sbjct: 8   DSGDAPLIDLNDASIKKLIARAKRRGIITYDELNEALPQDQMSSEQIEDIMAAISEMGVN 67

Query: 77  VVDGDD--LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           +V+ D+  ++ EE   +  +   +  +    ++KRK++ +R TDDPVRMYLREMG++ELL
Sbjct: 68  IVESDEDAVDPEERDVEETEDTDTGMDDRPVVEKRKETIER-TDDPVRMYLREMGAVELL 126

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           SREGEIAIAKRIEAGR  M+  LCESP+TF A+I W + LN G   LREI+DL+A +  E
Sbjct: 127 SREGEIAIAKRIEAGRDTMIMGLCESPITFHAIIQWSEALNAGEMQLREILDLDAMLSKE 186

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERD-DVQE-TEG-DIESAAKVSKDDRSKVDSPPENA 251
            +               E+ S++ E D ++ E T G   +    + ++   + +      
Sbjct: 187 PQP--------------ENLSEDGEGDGEISEATAGPTFKEEEDIEEEASEEDEDDELRE 232

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD---NAVNGQKD- 307
               R  +EDE+D+  +L+ ME  L+P+ +    EI   +R    +Q    +A+    D 
Sbjct: 233 RRTPRPAEEDEEDNTLSLAQMEAALKPQALEKFAEITASFRAFERVQAERLDAIGLGIDF 292

Query: 308 --EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
             +K ++  K L+E+L   V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ + +
Sbjct: 293 PADKEALYHK-LREELTAHVESVQFHATKIEYLVDNLYTFNRRLTTLGGQMLRLAERHKV 351

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL+ + GRELD +W+  +    +  W  F A E D++ +IR+EI  I+  TG+S+S
Sbjct: 352 SRKDFLDGYLGRELDENWLQ-SMSGKDKRWGAFAANEADAVERIRSEISDIASATGMSLS 410

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 411 EFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 470

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++  R
Sbjct: 471 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGR 530

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 531 EPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAI 590

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 591 QSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 650

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+K+RSFLD
Sbjct: 651 KLKHPSRSRKMRSFLD 666


>gi|221639823|ref|YP_002526085.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides KD131]
 gi|332558839|ref|ZP_08413161.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
 gi|221160604|gb|ACM01584.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332276551|gb|EGJ21866.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
          Length = 668

 Score =  671 bits (1732), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/676 (54%), Positives = 473/676 (69%), Gaps = 22/676 (3%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + ED D     D S  + K+MI  AR+RGY+T ++LN  LP D+VSSEQ+ED +AMLS
Sbjct: 8   DGKPEDQDAETSLDMSQAAVKRMIAEARERGYITYDQLNTVLPQDQVSSEQIEDVMAMLS 67

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGINV++ ++ E+ E + + ++  S +   +V    + ++ DR TDDPVRMYLREMGS+
Sbjct: 68  EMGINVIENEEAEEGEPAGELVEQGSGSREIAV-AGTQGETLDR-TDDPVRMYLREMGSV 125

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  
Sbjct: 126 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEA-- 183

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                      T G S     D   +    D  E       A + S     ++D+   N 
Sbjct: 184 -----------TFGRSLDGDGDDEIDGPEIDEVEVAAAPAPAPRRSASSEPELDADG-NP 231

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE--- 308
            +     DED++ SA +L+AME  L+P+V+  L+ IA  Y +L  +Q+  ++   ++   
Sbjct: 232 ISRAEEEDEDDEASAMSLAAMEAALKPRVLETLELIARDYGKLAEMQNRRMSATLNDHIR 291

Query: 309 ---KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
              +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA +  I
Sbjct: 292 FTTEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLADAARI 351

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  F++ +QG ELDP W           W+  +    D +  +R E+  +    G+ IS
Sbjct: 352 NRREFIDEYQGYELDPMWAERMAAKSGRGWQTLMEKSRDRVEDLRGEMAQVGQYVGVDIS 411

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 412 EFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 471

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I R
Sbjct: 472 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGR 531

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSAI
Sbjct: 532 EPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSAI 591

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 592 QENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 651

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 652 KLKHPSRSRKLRSFLD 667


>gi|329114160|ref|ZP_08242922.1| RNA polymerase sigma factor RpoD [Acetobacter pomorum DM001]
 gi|326696236|gb|EGE47915.1| RNA polymerase sigma factor RpoD [Acetobacter pomorum DM001]
          Length = 672

 Score =  670 bits (1728), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/688 (52%), Positives = 473/688 (68%), Gaps = 51/688 (7%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +++  E   D+ + D    + KK+I   R+RG +T +ELNA LP D++SSEQ+ED +A+L
Sbjct: 17  TNAAQEQDGDTTLLDTRSSAVKKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVL 76

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----------RKDSADRSTDD 119
           S MGI VV+ +D ++EE         S  +++    +              +S  R TDD
Sbjct: 77  SEMGIQVVENEDNDNEEAEPKKAAAESEDADAEEEAETEAEAESPTGNVNAESVGR-TDD 135

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + + +   
Sbjct: 136 PVRMYLREMGTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEM 195

Query: 180 LLREIIDLEACIGPESKGGFF-HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           LLR+I+DLEA    +S G     G +G   +   DS  E+  +   E EGDIES      
Sbjct: 196 LLRDIVDLEAM---QSGGNPLEEGGDGTFNEAESDSDSEEAEEPETEGEGDIES------ 246

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
                                   + S  +LSA+E++L+P+++   DEI  +Y  LR LQ
Sbjct: 247 ------------------------EGSGLSLSALEEKLKPEILAHFDEIEPLYAALRKLQ 282

Query: 299 DN---AVNGQKDEKSSVK--CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
                A+   +D   + +     L+EKLV  V  + L+ +RI+ LV QL  + +++   E
Sbjct: 283 VQRIEALTSGEDVDGNFEENYVALREKLVGKVEQVHLHNNRIEDLVAQLKQMFQKLNMLE 342

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           G +LRLA+S  + R+ FL +++GRELDP W+          WKNFVA   ++++ +R+++
Sbjct: 343 GRMLRLAESCRVSREDFLLKYRGRELDPGWMDMVSALSGRSWKNFVAKHANTVVDLRDQV 402

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             ++ ETG+ I EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 403 AQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 462

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 463 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 522

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIE
Sbjct: 523 RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 582

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK A+ PLD+AIQ NLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 583 DKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 642

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 643 ERIRQIEAKALRKLKHPSRSRKLRSFLD 670


>gi|87200249|ref|YP_497506.1| RNA polymerase sigma factor RpoD [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87135930|gb|ABD26672.1| RNA polymerase, sigma 70 subunit, RpoD [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 667

 Score =  668 bits (1724), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/675 (53%), Positives = 479/675 (70%), Gaps = 26/675 (3%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           DS D+ + D +D S KK+I  A++RG +T +ELN  LP D++SSEQ+ED +A +S MG+N
Sbjct: 8   DSGDAPLIDLNDASIKKLIARAKRRGIITYDELNEALPQDQMSSEQIEDIMAAISEMGVN 67

Query: 77  VVDGDDLE---DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +V+ D+     +E   +D LD A +  +    + KRK++ +R TDDPVRMYLREMG++EL
Sbjct: 68  IVESDEDAVDPEERAQDDELDEAETVEDRPDVI-KRKETVER-TDDPVRMYLREMGAVEL 125

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           LSREGEIAIAKRIEAGR  M+  LCESP+TF A+I W + LN G   LREI+DL+A +  
Sbjct: 126 LSREGEIAIAKRIEAGRDTMIMGLCESPITFHAIIQWSEALNAGEMQLREILDLDAMLSK 185

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           E +            +   +  +E E +  + T G      +  +++ +  D   E  E 
Sbjct: 186 EPQP-----------ENLSEDGEEAEPEISEATAGPTFKEEEDIEEEETADDEDDELRER 234

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD---NAVNGQKDEKS 310
             R  +E+E+D+  +L+ ME QL+P  +    EI  ++R+   +Q    NA+    D  +
Sbjct: 235 RARPAEEEEEDNTLSLAQMEAQLKPAALERFAEITSLFRQFEKIQAERLNALGMGNDFPA 294

Query: 311 S--VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           +   + + L+E L   V S+  + S+I+ LV+ LY  ++R+    G++LRLA+ + + R 
Sbjct: 295 ARETQYQKLREDLTAQVESVQFHASKIEYLVDNLYAFNRRLTTLGGQMLRLAERHKVPRK 354

Query: 369 VFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            FL+ + GRELD  W+     +D     W  F A E   + +IR EI  I+  TG+S+ E
Sbjct: 355 DFLDMYVGRELDDGWLQGLAGRD---KRWAAFAANEATPVERIRAEISDIASATGMSLGE 411

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 412 FRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 471

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++  RE
Sbjct: 472 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGRE 531

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQ
Sbjct: 532 PTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQ 591

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           ANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RK
Sbjct: 592 ANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRK 651

Query: 667 LKHPSRSKKLRSFLD 681
           LKHPSRS+K+RSFLD
Sbjct: 652 LKHPSRSRKMRSFLD 666


>gi|94498543|ref|ZP_01305098.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
 gi|94421986|gb|EAT07032.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
          Length = 682

 Score =  667 bits (1722), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/696 (52%), Positives = 477/696 (68%), Gaps = 53/696 (7%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +E ED  D+ + D ++ S KK+I  A++RGY+T +ELN  LP D++SSEQ+ED +A L+ 
Sbjct: 12  AEGEDGGDAPLLDLNEASVKKLIARAKKRGYITYDELNDALPQDQMSSEQIEDIMAALNE 71

Query: 73  MGINVVDGDDLEDEEGSEDS------------LDLASSASNSSVFLQKRKDSADRSTDDP 120
           MG+N+V     E+EE SED              D +S      +  +K+K++ DR TDDP
Sbjct: 72  MGVNIV-----ENEEASEDGDEQREREDAEDAEDESSDDDGPKLVTEKKKETVDR-TDDP 125

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP TF A+I W   LN+G   
Sbjct: 126 VRMYLREMGAVELLSREGEIAIAKRIEAGRDTMIFGLCESPTTFNAIIEWSTALNNGEMQ 185

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI-ESAAKVSKD 239
           LREI+DL+A +                    +D + E   +  ++ +G+I E  A  S  
Sbjct: 186 LREILDLDAMLS-------------------KDPAPESLEEGAEDEDGEISEKTAGPSFK 226

Query: 240 DRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQLRPKVMCALDEIAEV 290
           +  + +    + + DE  L E            D+  +L+ ME+ L+P  +     I ++
Sbjct: 227 EEEEPEEESADGDEDEDGLTERRARRNEEEEEEDNTLSLAQMEETLKPMALEKFATITDI 286

Query: 291 YRELRSLQDNAVNGQKD-----EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           +R     Q+  +    +     +K+    + L+E L   V S+  +Q +I+ LV+QLY  
Sbjct: 287 FRNFSQAQEARMQAMANGDALSQKAEDDYQALRESLTAEVESVQFHQQKIEYLVDQLYAY 346

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
           ++R+    G++LRLA+ + + R  FL+R+   ELD  W+       + +W  F A E  S
Sbjct: 347 NRRLTALGGQMLRLAERHKVSRKDFLDRYVNHELDDGWLDKVSGL-DKKWTAFAAAEGRS 405

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           + +IRNEI  I+  TG+S+ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTN
Sbjct: 406 VDRIRNEIAEIAQATGMSLGEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTN 465

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 466 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 525

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+VRT+R+  ++  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ 
Sbjct: 526 IETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEED 585

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDKNA+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEV
Sbjct: 586 SHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+QF VTRERIRQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 646 GQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 681


>gi|58038783|ref|YP_190747.1| RNA polymerase sigma factor RpoD [Gluconobacter oxydans 621H]
 gi|58001197|gb|AAW60091.1| RNA polymerase sigma factor RpoD [Gluconobacter oxydans 621H]
          Length = 652

 Score =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 351/672 (52%), Positives = 458/672 (68%), Gaps = 40/672 (5%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            E   D+ + D    + K++I   R+RG++T +ELNA LP D++SSEQ+ED +A LS MG
Sbjct: 14  QEQEGDTTLLDTQSAAVKRLIAKGRERGHITFDELNAVLPQDQMSSEQIEDVMAALSEMG 73

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V++ +D ++ E   +                     A   TDDPVRMYLREMGS+ELL
Sbjct: 74  IQVIENEDQDEAEAPAEKEAEGDGEEAEGPQGGNVDAEAASRTDDPVRMYLREMGSVELL 133

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           SREGEIAIAKRIEAGR  M+  LCESPLT +A+I W + L DG  LLR+I+DLEA  G  
Sbjct: 134 SREGEIAIAKRIEAGRDEMIGGLCESPLTIRAIISWHERLKDGEMLLRDIVDLEASQGGG 193

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                  G EG    + +D+++++  +   +                             
Sbjct: 194 PDPEAVEGEEGDEASEEDDTAEDENEEGEGD----------------------------- 224

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKD--EK 309
                  ++ S  +LSA+E++L+P+++   + I  +Y +LR LQ     A+ G +D  +K
Sbjct: 225 ------QQEGSGLSLSALEEKLKPEILARFEAIEPLYHKLRKLQIKRIEALTGGEDHSDK 278

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
           S    + L+ +LV LV  + L+ +RI+ LV Q+    +++ + EG ++RLA+S  I RD 
Sbjct: 279 SEQTYEKLRHELVSLVEQVHLHNNRIEELVAQIKMQVQKLNNVEGRMMRLAESCKISRDD 338

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +++ RELDP W+      P   WKN     +D +  +R EI ++S ETG+ + EFR 
Sbjct: 339 FLIKYRSRELDPTWLDSISALPGKGWKNLTTKHMDQLRNLRGEIAALSHETGLPVGEFRR 398

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + + + +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 399 VYATISRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 458

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REP P
Sbjct: 459 YRRGYKFSTYATWWIRQAITRSIADQAKTIRIPVHMIETINKLVRTSRQMLHEIGREPAP 518

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK AV PLD+AIQ NL
Sbjct: 519 EELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVIPLDAAIQTNL 578

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKH
Sbjct: 579 REATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKH 638

Query: 670 PSRSKKLRSFLD 681
           PSRS+KLRSFLD
Sbjct: 639 PSRSRKLRSFLD 650


>gi|330993917|ref|ZP_08317847.1| RNA polymerase sigma factor rpoD [Gluconacetobacter sp. SXCC-1]
 gi|329758863|gb|EGG75377.1| RNA polymerase sigma factor rpoD [Gluconacetobacter sp. SXCC-1]
          Length = 659

 Score =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/694 (52%), Positives = 473/694 (68%), Gaps = 68/694 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+ S  +D+D +L+ D    + KK+I   ++RGY+T +ELNA LP D++SSEQ+ED +A 
Sbjct: 10  DTASGDQDNDTTLL-DTRSGAVKKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAA 68

Query: 70  LSNMGINVVDGDDLEDEEGSEDSL----DLASSASNSSVFLQKRKDSADRS-TDDPVRMY 124
           LS MG+ VV+ +D +D E +  +     D A   S S        D+     TDDPVRMY
Sbjct: 69  LSEMGMQVVENEDNDDTEAAATADTKGDDTAEEESESEEPAAGNVDTESLGRTDDPVRMY 128

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L  G  LLR+I
Sbjct: 129 LREMGSVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDI 188

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           +DLEA       GG                      D  +  EG+               
Sbjct: 189 VDLEAM----QSGG---------------------NDPAEAVEGE--------------- 208

Query: 245 DSPPENAENDERNLDEDEDDSAH-------TLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           D+  EN  N+    +E E +          +LSA+E++L+P+++    E+  +Y  L  +
Sbjct: 209 DAFAENDGNEAEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFKEVEALYEALHRV 268

Query: 298 QDNAVNGQKDEKSSVKCKV----------LKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           Q      ++ EK +    +          L+ +LV  V  + L+ +RI++LVE L +I +
Sbjct: 269 Q-----AERLEKFTAGSDISAEEESRYEQLRLELVGKVQQVHLHNARIEVLVEHLKEIFQ 323

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           R+   EG +LRLA+S  + RD FL +++GRELDP W+  A   P   WKNF+A   ++++
Sbjct: 324 RLNGLEGRMLRLAESTRVSRDDFLLKYRGRELDPGWMDMAAALPGKSWKNFIAKHGETVI 383

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           ++RN++  ++ ETG+ + EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRG
Sbjct: 384 RLRNQVADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRG 443

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 444 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 503

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SH
Sbjct: 504 TINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSH 563

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK AV PLD+AIQ NLRE TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 564 LGDFIEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQ 623

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 624 QFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|1519634|gb|AAC44891.1| sigma 70-type sigma factor SigA [Rhodobacter sphaeroides]
          Length = 666

 Score =  666 bits (1718), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/677 (54%), Positives = 471/677 (69%), Gaps = 26/677 (3%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + ED D     D S  + K+MI  A +RGY+T ++LN  LP D+VSSEQ+ED +AMLS
Sbjct: 8   DGKPEDQDAETSLDMSQAAVKRMIAEA-ERGYITYDQLNTVLPQDQVSSEQIEDVMAMLS 66

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            MGINV++ ++ E+ E + + ++  S +   +V    + ++ DR TDDPVRMYLREMGS+
Sbjct: 67  EMGINVIENEEAEEGEPAGELVEQGSGSREIAV-AGTQGETLDR-TDDPVRMYLREMGSV 124

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  
Sbjct: 125 ELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEATF 184

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G                   +D     E D+V+            S +     D  P + 
Sbjct: 185 GRSLD------------GDGDDEIDGPEIDEVEVAAARAAPRRSTSSEPELDADGNPISR 232

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE--- 308
             +E     D++ SA +L+AME  L+P+V+  L+ IA  Y +L  +Q+  ++   ++   
Sbjct: 233 AEEEDE---DDEASAMSLAAMEAALKPRVLETLELIARDYGKLAEMQNRRMSATLNDHIR 289

Query: 309 ---KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
              +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA +  I
Sbjct: 290 FTTEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLADAARI 349

Query: 366 KRDVFLERHQGRELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            R  F++ +QG ELDP W    A     G W+  +    D +  +R E+  +    G+ I
Sbjct: 350 NRREFIDEYQGYELDPMWAERMAAKVGRG-WQTLMEKSRDRVEDLRGEMAQVGQYVGVDI 408

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 409 SEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 468

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 469 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 528

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSA
Sbjct: 529 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSA 588

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER+RQIEAKA+
Sbjct: 589 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERLRQIEAKAL 648

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 649 RKLKHPSRSRKLRSFLD 665


>gi|296284010|ref|ZP_06862008.1| RNA polymerase sigma factor RpoD [Citromicrobium bathyomarinum
           JL354]
          Length = 667

 Score =  665 bits (1716), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/680 (53%), Positives = 483/680 (71%), Gaps = 25/680 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           S+++ ++++D+ + D ++ S KK+I  A++RGYVT +ELN  LP  E+SS+Q+ED  A +
Sbjct: 3   SEAKTKETEDAPLIDLNEASIKKLISKAKKRGYVTYDELNEALPQGEMSSDQIEDIQAAI 62

Query: 71  SNMGINVVDGDD---LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           S MG+ +V+ DD    E +E  E + D  +     S     +K + D  TDDPVRMYLRE
Sbjct: 63  SEMGVQIVESDDEVESEKDEVEEIAPDSGAKKDTKSAAAAPKK-TVDARTDDPVRMYLRE 121

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF A+I W D LN+G   LREI+DL
Sbjct: 122 MGAVELLSREGEIAIAKRIEAGRDTMIIGLCESPITFHAIIQWSDALNEGEMQLREILDL 181

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           +A +  E               K E+ +++   +  +ET G          DD +     
Sbjct: 182 DAMLSKEP-----------PVDKMEEENEDDSGEISEETAGPTIREDDDDDDDETAEGDE 230

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQ 305
             + E+  R+ D++ED++  +L+ ME  L+P  +     I +++++   LQ   V+  G+
Sbjct: 231 DGDGESKRRDDDDEEDNT-MSLAQMEAALKPDALERFARITDLFKKFEKLQAERVDVLGR 289

Query: 306 KDEKSSVKCKV---LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            D   + K K    L+E+L   V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ 
Sbjct: 290 GDAFPAAKEKKYEDLREQLTAEVESVQFHATKIEFLVDNLYAFNRRLTALGGQMLRLAER 349

Query: 363 YGIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
           + IKR  FL+ + G E+D  W+ S  KD    +W  F   E +SI +IR EI  I+ +TG
Sbjct: 350 HKIKRIDFLDAYLGNEMDDEWLTSRTKD---KKWAAFAEKEAESIERIRTEISDIASQTG 406

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 407 MALEEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 466

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  +
Sbjct: 467 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLH 526

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+
Sbjct: 527 EQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPV 586

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+AIQ+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 587 DAAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 646

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+K+RSFLD
Sbjct: 647 KALRKLKHPSRSRKMRSFLD 666


>gi|258542087|ref|YP_003187520.1| RNA polymerase sigma factor RpoD [Acetobacter pasteurianus IFO
           3283-01]
 gi|256633165|dbj|BAH99140.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-01]
 gi|256636222|dbj|BAI02191.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-03]
 gi|256639277|dbj|BAI05239.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-07]
 gi|256642331|dbj|BAI08286.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-22]
 gi|256645386|dbj|BAI11334.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-26]
 gi|256648441|dbj|BAI14382.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-32]
 gi|256651494|dbj|BAI17428.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-01-42C]
 gi|256654485|dbj|BAI20412.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-12]
          Length = 672

 Score =  661 bits (1706), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/691 (52%), Positives = 474/691 (68%), Gaps = 57/691 (8%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +++  E   D+ + D    + KK+I   R+RG +T +ELNA LP D++SSEQ+ED +A+L
Sbjct: 17  TNAAQEQDGDTTLLDTRSSAVKKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVL 76

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----------RKDSADRSTDD 119
           S MGI VV+ +D ++EE         S  +      +              +S  R TDD
Sbjct: 77  SEMGIQVVENEDNDNEEAEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGR-TDD 135

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + + +   
Sbjct: 136 PVRMYLREMGTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEM 195

Query: 180 LLREIIDLEACIGPESKGGFF-HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           LLR+I+DLEA    +S G     G +G   +   DS  E+  +   E EGDIES      
Sbjct: 196 LLRDIVDLEAM---QSGGNPLEEGGDGTFNEAESDSESEEAEEPEAEGEGDIES------ 246

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
                                   + S  +LSA+E++L+P+++   DEI  +Y ELR LQ
Sbjct: 247 ------------------------EGSGLSLSALEEKLKPEILAHFDEIEPLYAELRKLQ 282

Query: 299 DN---AVNGQKD-----EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
                A+   +D     E+S V    L+EKLV  V  + L+ +RI+ LV QL  + +++ 
Sbjct: 283 VQRIEALTSGEDVDGNFEESYV---ALREKLVGKVEQVHLHNNRIEDLVAQLKQMFQKLN 339

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             EG +LRLA+S  + R+ FL +++GRELDP W+          WKNFVA   ++++ +R
Sbjct: 340 MLEGRMLRLAESCRVSREDFLLKYRGRELDPGWMDMVSGLSGRSWKNFVAKHANTVVGLR 399

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++  ++ ETG+ I EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQF
Sbjct: 400 DQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEANLRLVISIAKKYTNRGLQF 459

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 460 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 519

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGD
Sbjct: 520 KLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 579

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK A+ PLD+AIQ NLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 580 FIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 639

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 640 VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670


>gi|1237088|emb|CAA92648.1| major sigma factor [Rhodobacter capsulatus]
          Length = 674

 Score =  661 bits (1705), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/674 (54%), Positives = 462/674 (68%), Gaps = 25/674 (3%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           +D+   FD S  + K+MI  A++RGY+TI++LNA +PP+ VS EQ+ED ++MLS MGINV
Sbjct: 15  ADEDASFDMSQAAVKRMIGEAKERGYITIDQLNAVMPPETVSGEQIEDVMSMLSEMGINV 74

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+    E EE     +    S S          ++ DR TDDPVRMYLREMGS+ELLSRE
Sbjct: 75  VE--GEEVEESEGGEVVETGSGSREIAVAGAAGETLDR-TDDPVRMYLREMGSVELLSRE 131

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA  G    G
Sbjct: 132 GEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEEILLRDVIDLEATFGRSLDG 191

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE-- 255
               G EG           E     V E      +        R   D P  +A+ +   
Sbjct: 192 D--EGLEG----------MEGIEGPVVEGLDLEAAEGAAPAARRPASDEPEYDADGNPIS 239

Query: 256 --RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
                ++D+D S  +L+AME  L+PKV+  L+ IA  Y +L  +QD  ++   +E  +  
Sbjct: 240 RIDEEEDDDDSSNMSLAAMEAALKPKVLETLELIARDYAKLAEMQDLRMSATLNEDGTFT 299

Query: 314 C------KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
                  + L+ ++V LV  L L+ +RI+ L++QLY I+++IM  +  +++LA +  I R
Sbjct: 300 VAEEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSIDSGMVKLADAARINR 359

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F++ ++G ELDP W+      P   W          +  +R+E+  +    G+ ISEF
Sbjct: 360 REFIDEYRGYELDPTWMDRMSAKPARAWVTLFEKSRHKVEDLRHEMAQVGQYVGVDISEF 419

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 420 RRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 479

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REP
Sbjct: 480 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREP 539

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+A+KL MP+E VRKV+KI KEPISLETPIG E+ S LGDFIEDKNA+ PLDSAIQ 
Sbjct: 540 TPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGHEEDSQLGDFIEDKNAILPLDSAIQE 599

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           NL+ETTTRVL SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKL
Sbjct: 600 NLKETTTRVLPSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 659

Query: 668 KHPSRSKKLRSFLD 681
           KHPSRS+KL SFLD
Sbjct: 660 KHPSRSRKLPSFLD 673


>gi|307295455|ref|ZP_07575291.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
 gi|306878494|gb|EFN09714.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
          Length = 681

 Score =  660 bits (1702), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/706 (51%), Positives = 481/706 (68%), Gaps = 53/706 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N     E +D+ D+ + D ++ S KK+I  A++RGY+T +ELN  LP D++SSEQ
Sbjct: 1   MASKANGKGAGEDQDTGDAPLLDLNEASIKKLIARAKKRGYITYDELNDALPQDQMSSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV------------FLQKRK 110
           +ED ++ L+ MG+N+V     E+EE  ED  D    + + S               +K+K
Sbjct: 61  IEDIMSALNEMGVNIV-----ENEEAGEDGDDQRDDSDDDSTDDSADDDGSPRPVAEKKK 115

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           ++ DR TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP TF A+I W
Sbjct: 116 ETVDR-TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPTTFNAIIEW 174

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
              LN+G   LREI+DL+A +                    +D + E   +  ++ +G+I
Sbjct: 175 STALNNGEMQLREILDLDAMLS-------------------KDPAPENLEEGAEDDDGEI 215

Query: 231 -ESAAKVSKDDRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQLRPKV 280
            E  A  S  +  + +    +A+ DE  L E            D+  +L+ ME+ L+P  
Sbjct: 216 SEKTAGPSFKEEEEPEEESADADEDEDGLTERRTRRVEEEEEEDNTLSLAQMEETLKPMA 275

Query: 281 MCALDEIAEVYRELRSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           +     I E++R   + Q++     A+     +K     + L+E+L   V S+  +Q +I
Sbjct: 276 LEKFATITEIFRTFSNAQESRMIAMAIGETLSQKDEDDYQELREQLTAEVESVQFHQQKI 335

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           + LV+QLY  ++R+    G++LRLA+ + + R  FL+R+   ELD  W+       + +W
Sbjct: 336 EYLVDQLYAYNRRLTALGGQMLRLAERHKVSRKDFLDRYVNHELDDGWLDRISGL-DKKW 394

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
             F A E  ++ +IR E+  I+  TG+S+SEFR IV+MV+KGE EA IAKKEMVEANLRL
Sbjct: 395 AAFAAAEGRAVERIRTEVSEIAQATGMSLSEFRRIVNMVQKGEREARIAKKEMVEANLRL 454

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 455 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 514

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+VRT+R+  ++  REPTPEE+A++L+MP+E VRKV+KI KEPIS
Sbjct: 515 ARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPIS 574

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIGDE+ SHLGDFIEDKNA+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIG
Sbjct: 575 LETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIG 634

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS K+RSFLD
Sbjct: 635 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSHKMRSFLD 680


>gi|294011419|ref|YP_003544879.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
 gi|292674749|dbj|BAI96267.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
          Length = 681

 Score =  658 bits (1698), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/701 (51%), Positives = 484/701 (69%), Gaps = 43/701 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N     E +D+ D+ + D ++ S KK+I  A++RGY+T +ELN  LP D++SSEQ
Sbjct: 1   MASKANGKGAGEDQDTGDAPLLDLNEASVKKLIARAKKRGYITYDELNDALPQDQMSSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV-------FLQKRKDSADR 115
           +ED ++ L+ MG+N+V+ ++  ++   +       SA +S+          +K+K++ DR
Sbjct: 61  IEDIMSALNEMGVNIVENEEAGEDGDDQRDDGDDDSADDSADDDGSPRPVTEKKKETVDR 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP TF A+I W   LN
Sbjct: 121 -TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPTTFNAIIEWSTALN 179

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI-ESAA 234
           +G   LREI+DL+A +                    +D + E   +  ++ +G+I E  A
Sbjct: 180 NGEMQLREILDLDAMLS-------------------KDPAPENLEEGAEDDDGEISEKTA 220

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDED---------DSAHTLSAMEDQLRPKVMCALD 285
             S  +  + +    + + DE  L E            D+  +L+ ME+ L+P  +    
Sbjct: 221 GPSFKEEEEPEEESADTDEDEDGLTERRARRMEEEEEEDNTLSLAQMEETLKPMALEKFA 280

Query: 286 EIAEVYRELRSLQDNAV----NGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
            I E++R     Q++ +    NG+   +K+    + L+E+L   V S+  +Q +I+ LV+
Sbjct: 281 TITEIFRTFSKAQESRMAAMANGETLSQKAEDDYQELREQLTAEVESVQFHQQKIEYLVD 340

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
           QLY  ++R+    G++LRLA+ + + R  FL+R+   ELD  W+       + +W  F A
Sbjct: 341 QLYAYNRRLTALGGQMLRLAERHKVSRKDFLDRYVNHELDDGWLDKVSGL-DKKWAAFAA 399

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E  ++ +IR E+  I+  TG+S+SEFR IV+MV+KGE EA IAKKEMVEANLRLVIS+A
Sbjct: 400 AEGRAVERIRVEVSEIAQATGMSLSEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIA 459

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 460 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 519

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+VRT+R+  ++  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPI
Sbjct: 520 IPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPI 579

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GDE+ SHLGDFIEDKNA+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDH
Sbjct: 580 GDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDH 639

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 640 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 680


>gi|148259873|ref|YP_001234000.1| RNA polymerase sigma factor RpoD [Acidiphilium cryptum JF-5]
 gi|326403199|ref|YP_004283280.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
 gi|146401554|gb|ABQ30081.1| RNA polymerase, sigma 70 subunit, RpoD [Acidiphilium cryptum JF-5]
 gi|325050060|dbj|BAJ80398.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
          Length = 638

 Score =  648 bits (1672), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 354/667 (53%), Positives = 463/667 (69%), Gaps = 53/667 (7%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D+   D    S K++I   ++RGY+T +ELNA LP ++ SSEQ+ED ++MLS MGI VV+
Sbjct: 19  DTATLDIQSASVKRLIARGKERGYITFDELNAVLPSEQNSSEQIEDVMSMLSEMGIQVVE 78

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G++ E+ E +  +     +A +         +S+   TDDPVRMYLREMG++ELLSREGE
Sbjct: 79  GEEGEEAETAGRAEKDEEAAEDEEAASGNISESSGSRTDDPVRMYLREMGTVELLSREGE 138

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR MM+  LCESPLTF+A+I W + L DG  LLR++IDLEA     ++GG 
Sbjct: 139 IAIAKRIEAGRDMMIGGLCESPLTFRAIISWHESLKDGKMLLRDVIDLEA-----TQGG- 192

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
             G  G +                                        P  A  +E   D
Sbjct: 193 --GDGGFN----------------------------------------PSAAVPEEPEED 210

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKD--EKSSVKC 314
           E+ + S  +LSA+E++L+P+V     E+ ++Y +   LQ     A+N  ++   +S    
Sbjct: 211 EEGESSGLSLSAVEEKLKPEVFETFTEVEKLYEKFMKLQHKRLEALNAGEEMASRSEKTY 270

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
           + L+++LV  V  +SL+ +RI+ LV QL ++++R+   EG++LRLA+   I RD FL+ +
Sbjct: 271 EKLRDELVAKVEQVSLHNNRIEELVIQLKELNQRLNGLEGQMLRLAEGCKITRDDFLDAY 330

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           +GRE+DP W+      P   WK FV      + ++R +I  I+ E  + I EFR + S V
Sbjct: 331 RGREMDPTWLDDVAKRPGKGWKVFVERYGTQVTELRAQIGRIAAEAQLPIEEFRRVYSTV 390

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 391 SRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 450

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+
Sbjct: 451 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAE 510

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ PLD+A+ ANLRE  T
Sbjct: 511 KLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPLDAAVHANLREAAT 570

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           RVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+
Sbjct: 571 RVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSR 630

Query: 675 KLRSFLD 681
           KLRSFL+
Sbjct: 631 KLRSFLE 637


>gi|119386779|ref|YP_917834.1| RNA polymerase sigma factor RpoD [Paracoccus denitrificans PD1222]
 gi|119377374|gb|ABL72138.1| RNA polymerase, sigma 70 subunit, RpoD [Paracoccus denitrificans
           PD1222]
          Length = 664

 Score =  647 bits (1670), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/665 (54%), Positives = 454/665 (68%), Gaps = 27/665 (4%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D S  + K+MI   R+RG++T ++LNA LPP++VSS+Q+ED ++MLS M I VV+ D+ 
Sbjct: 19  LDMSQAAVKRMIAEGRERGFITYDQLNAVLPPEQVSSDQIEDVMSMLSEMDIRVVESDEE 78

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            DE      L   +S S          +  DR TDDPVRMYLREMGS+ELLSREGEIAIA
Sbjct: 79  ADEAEPGGELATTASTSRELTVATTETEKLDR-TDDPVRMYLREMGSVELLSREGEIAIA 137

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIEAGR  M+A LCESPLTF+A+ +WR EL      L E I L   I  E+  G     
Sbjct: 138 KRIEAGRNTMIAGLCESPLTFKAITMWRQEL------LDEDILLRDVIDLETTFGRAMDE 191

Query: 204 EGHSYQKREDSSQEKERDDVQETEG-DIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
           +G             E ++V  TE     + A  +   R + +   +         +ED+
Sbjct: 192 DG-------------EEEEVLPTETRPAANTAGAAGTAREEEEFDADGNPMGREEDEEDD 238

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC------KV 316
           D    +L+AME  L+PKV+  L+ IA  Y EL  +QDN ++   +E  +         +V
Sbjct: 239 DGQNLSLAAMEASLKPKVLETLEAIARGYEELSHMQDNRMSATLNEDGTFSAAQESAYQV 298

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           L+  +V LV  L L+ +RI+ LV+Q+Y I++RI+  +  +++LA +  I R  F++ ++G
Sbjct: 299 LRSHIVALVNELHLHNNRIEALVDQIYGINRRIVTIDSNVVKLADAARINRREFIDAYRG 358

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            ELDP WV          W+         +  +R E+  +    G+ I EFR IVS V++
Sbjct: 359 SELDPTWVERMMQNKGRGWQALFEKSRPQVENLRAEMAMVGQHVGVDIEEFRRIVSQVQR 418

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE E+  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 419 GEKESRQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 478

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A+KL
Sbjct: 479 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAEKL 538

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSAIQ NL+ETTTRV
Sbjct: 539 QMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRV 598

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KL
Sbjct: 599 LASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKL 658

Query: 677 RSFLD 681
           RSFLD
Sbjct: 659 RSFLD 663


>gi|114797662|ref|YP_761566.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
 gi|114737836|gb|ABI75961.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
          Length = 666

 Score =  646 bits (1666), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/687 (52%), Positives = 475/687 (69%), Gaps = 38/687 (5%)

Query: 5   KKRNRDSDSEHED--SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           KK+N   D E ED    +S + DF+    KK++K A++RG++T +E+N  LP  ++SS+Q
Sbjct: 7   KKKNTAGDGEGEDDKETESGLVDFNATDVKKVLKRAQKRGFITHDEINQLLPDSDMSSDQ 66

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++ +S MGI VV+ ++  +E+G        +   +  V  +K        TDDPVR
Sbjct: 67  IEDVMSQISEMGIAVVETEEEAEEQGKA-----LTKIEDKKVVAKKGNARGSDRTDDPVR 121

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+++WRDE      L+ 
Sbjct: 122 MYLREMGAVELLSREGEIAIAKRIEAGRDAMIRGLCESPLTFEAMMVWRDE------LMN 175

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E I L   I  E+  G                ++    +     E   E AA V    RS
Sbjct: 176 ERILLRDLIDLEATYG----------------AENPPPEPKPVEERPPEPAAPVKGKKRS 219

Query: 243 KVDSPPENAEN---DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
             +     AE     ++  +E++D  A ++SAME +LR  V+  LDEIA+ +   R LQD
Sbjct: 220 AEEVDEVEAERMRQQQQEEEEEDDAVAMSMSAMEGELREGVLAKLDEIADAFSRFRKLQD 279

Query: 300 NA----VNGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                 + G+    K+  +   L  ++V  + ++ +N +RI+ LVEQLY I+K++M  EG
Sbjct: 280 RLLVRRIEGKDLTPKAQGEYDDLSLQIVDNLKTIHINNARIEALVEQLYAINKKLMGLEG 339

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
           +L+RLA ++G+ R  FL  + G EL+P W    ++    +WK  V  + + +  +R+EI 
Sbjct: 340 KLMRLADAHGVPRKEFLHNYIGSELEPDWAERVREIS-AKWKRLVDGKGEEVQVVRDEIS 398

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I+ E GI I +FR IV  V+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 399 EIAQEIGIPIDDFRRIVQTVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 458

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K++R
Sbjct: 459 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIIR 518

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T R+M ++I REPTPEE+A+KL +P+E +RKVLKI KEPISLETPIGD++ S+LGDFIED
Sbjct: 519 TQRQMLHEIGREPTPEELAEKLGLPLEKIRKVLKIAKEPISLETPIGDDEDSNLGDFIED 578

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K A+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 579 KMALLPVDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 639 RIRQIEAKALRKLKHPSRSRKLRSFLD 665


>gi|85373960|ref|YP_458022.1| RNA polymerase sigma factor RpoD [Erythrobacter litoralis HTCC2594]
 gi|84787043|gb|ABC63225.1| RNA polymerase sigma-70 factor [Erythrobacter litoralis HTCC2594]
          Length = 675

 Score =  631 bits (1628), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 348/680 (51%), Positives = 468/680 (68%), Gaps = 32/680 (4%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           ++D+ + D ++ S KKMI  A+++GYVT +ELN  LP  E+S +Q+ED    LS MG+ +
Sbjct: 11  AEDAPLIDLNEASIKKMITKAKRKGYVTYDELNEALPSGEMSPDQIEDIQTSLSEMGVQI 70

Query: 78  VDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           V+ D+  +         EE +  +       +       K+  + DR TDDPVRMYLREM
Sbjct: 71  VESDEEAEAEQEQANEVEEIAPGAAKDEKKDAKKPAAAVKKTTTGDR-TDDPVRMYLREM 129

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELLSREGEIAIAKRIEAGR  M+  LC+SP+TF A+I W + LN     LREI+DL+
Sbjct: 130 GAVELLSREGEIAIAKRIEAGRDTMIIGLCQSPITFHAIIQWSEALNAEEMQLREILDLD 189

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
           A +  E              +K E+ +++ +  ++ E E    +      D   +     
Sbjct: 190 AMLSKEPPA-----------EKLEEGAEDDDDGEISE-ENAGPTIVDDDDDTDDEDSDDE 237

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ----DNAVNG 304
           +  E   ++ D++++D+  +L+ ME  L+P  +     I  ++++   LQ    D    G
Sbjct: 238 DGEEGSSKSDDDEDEDNTMSLAQMEAALKPDAIERFARITSLFKKFEKLQLERVDTIARG 297

Query: 305 QKDEKSS-VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           +   K+   + + L E+L   V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ +
Sbjct: 298 EVLPKAKENRYEKLGEELTAEVESMQFHATKIEFLVDNLYAFNRRLTALGGQMLRLAERH 357

Query: 364 GIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
            IKR  FL+ + G ELD  ++     KD    +W  F   E D+I +IR EI  I+ +TG
Sbjct: 358 KIKRADFLQAYIGNELDEDFLKDRVKKD---KKWAAFADKEADAIDRIRTEIADIASQTG 414

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 415 MALPEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 474

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  +
Sbjct: 475 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLH 534

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+
Sbjct: 535 EQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPV 594

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 595 DAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 654

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+K+RSFLD
Sbjct: 655 KALRKLKHPSRSRKMRSFLD 674


>gi|85708548|ref|ZP_01039614.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85690082|gb|EAQ30085.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 674

 Score =  625 bits (1613), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 353/686 (51%), Positives = 470/686 (68%), Gaps = 30/686 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           S ++  D DD+ + D ++ S KK++  A+++GY+T +ELNA LP  E+S +Q+ED    L
Sbjct: 3   STAKAADKDDAPLIDLNEASVKKLMTKAKKKGYITYDELNAALPSGEMSPDQIEDIQTAL 62

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASN---------SSVFLQKRKDSADRSTDDPV 121
           S MG+ +V+ D+  + E  +++     S            ++     +K      TDDPV
Sbjct: 63  SEMGVQIVENDEEAEAEAEQEAEVEEMSVEGEAEKKKDTKAAAKPAAKKTGTGERTDDPV 122

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYLREMG++ELLSREGEIAIAKRIEAGR MM+  LCESP+TF A+I W + LN     L
Sbjct: 123 RMYLREMGAVELLSREGEIAIAKRIEAGRDMMIMGLCESPITFHAIIQWSEALNSEDMQL 182

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG-DIESAAKVSKDD 240
           REI+DL+A +  E               K E+ +++ + +  +ET G  I    +   D+
Sbjct: 183 REILDLDAMLSKEPPP-----------DKMEEENEDDDGEISEETAGPTIRDDDEDDSDE 231

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               +   E A   +   DE+E+D+  +L+ ME  L+P  +     I ++++    LQ  
Sbjct: 232 SEDGEDGEEGASKKD---DEEEEDNTLSLAQMEAALKPDAIERFARITKLFKTFEKLQAE 288

Query: 301 -----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                A   +  +    K + L E+L   V S+  + ++I+ LV+ LY  ++R+    G+
Sbjct: 289 RVETLAAGNEFPKAKENKYEKLSEELTAEVESVQFHATKIEFLVDNLYAFNRRLTALGGQ 348

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +LRLA+ + IKR  FL+ + G ELD  W++ A    + +W  F   E  +I +IR EI  
Sbjct: 349 MLRLAERHKIKRIDFLKSYVGNELDDSWIA-ANAKKDKKWAAFAEKEEAAIERIRTEITD 407

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I+ +TG+++ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 408 IAAQTGMALPEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 467

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 468 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 527

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+  ++  REPTPEE+A +L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 528 SRQFLHEEGREPTPEEMAARLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDK 587

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 588 NAVIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 647

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 648 IRQIEAKALRKLKHPSRSRKMRSFLD 673


>gi|329890710|ref|ZP_08269053.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
 gi|328846011|gb|EGF95575.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
          Length = 640

 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 350/667 (52%), Positives = 453/667 (67%), Gaps = 39/667 (5%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           E + D  + D +D   KK I+ A+ RGYVT+EELN  LP +EV+ +Q+ED +AMLS MG+
Sbjct: 11  ETNADGPLLDLTDAGVKKFIRQAKTRGYVTMEELNKVLPSEEVTPDQIEDILAMLSEMGV 70

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           NVV+ ++   E    D     ++A+ +SV     K + DR TDDPVRMYLREMG++ELLS
Sbjct: 71  NVVEAEEDAAEATGTD----VAAAAETSVAEAPAKAAYDR-TDDPVRMYLREMGTVELLS 125

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEIAIAKRIEAGR  M++ LCES LTF+A+++WR+EL +   LLRE+IDL+A  G  +
Sbjct: 126 REGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWREELANNRILLREVIDLDATYGILN 185

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                H     +    E     +E DD    +G   S + +  + R  V    +    D 
Sbjct: 186 PSSLPHNQPAPAQPTGEPDGDGEEDDDEDFDDGGAMSISALEAELRDGVMEVLDAIAVDF 245

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
               + +D        +E +L+ +V+ A D+  + Y  L +   + +   K   ++ + +
Sbjct: 246 GEFRKLQD------KLVEARLKGEVLTAKDQ--KTYEALTASISDRLKTMK--LNNARIE 295

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD-VFLERH 374
            L E+L  +   L   + R+  L +  Y IS+       E L+    +G + D  + ER 
Sbjct: 296 ALVEQLYAINKRLIGQEGRLLRLADG-YGISR------PEFLK--AYFGSEMDPTWAERI 346

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             +E+   W      F E E     A ++D+   IR +I +++ E G+ I ++R IV MV
Sbjct: 347 --KEMGVRWTK----FSENE-----AAQIDT---IRTQIAAVATEAGVPIDDYRRIVQMV 392

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 393 QKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 452

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I RE TPEE+A+
Sbjct: 453 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTQRQMLHEIGREATPEELAE 512

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +LAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTT
Sbjct: 513 RLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTT 572

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           RVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+
Sbjct: 573 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSR 632

Query: 675 KLRSFLD 681
           KLRSFLD
Sbjct: 633 KLRSFLD 639


>gi|262276866|ref|ZP_06054659.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
 gi|262223969|gb|EEY74428.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
          Length = 613

 Score =  561 bits (1445), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 314/663 (47%), Positives = 438/663 (66%), Gaps = 67/663 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           S++++++    RG++T EEL   L     + E ++  +  + +  I +V           
Sbjct: 8   SFERLVEKGLNRGFITYEELQKSLGKRNSNVESLDTALVHIFDQAITLV----------- 56

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++  D       S     K+  + +RS DDP+RMYLREMG +ELLSREGE AIAKRIE+G
Sbjct: 57  QNKSDFKVKKQESET--AKQTKTVERS-DDPIRMYLREMGGVELLSREGETAIAKRIESG 113

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
           R +M++SL ESP+T + +  W ++L +   L+R+IIDL+          F          
Sbjct: 114 RYVMISSLSESPITAKKIFDWEEKLINNEMLVRDIIDLDT--------NFI--------- 156

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA-ENDERNLDEDEDDSAHT 268
                      DD +  +   E + K +K+    +D+  E++ E+DE N+         +
Sbjct: 157 -----------DDEKLAKSIKEKSKKEAKEKNPNIDTESEDSNEDDEFNI---------S 196

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRS---------LQDNAVNGQKDEKSSVKCKVLKE 319
           L+++E +L+PK++ A   I + Y++L S         L++ A++  K +      K + E
Sbjct: 197 LASLEIELKPKILEAFSRITKNYKKLISYQRDKLECVLKNQALSDSKKKSYEKVKKEIME 256

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
           +L+K    L LNQ   + LV   Y  +K+I+  +GEL+R A  +GI RD F++ + G EL
Sbjct: 257 ELLK----LQLNQVTQEDLVALNYAENKKILSYDGELMRAANKHGISRDDFIKFYVGNEL 312

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +P++  +  +  E  W  F   E      +++++  +S   G+SIS+FR +V+ ++KGE 
Sbjct: 313 NPNFEKFLSE--EKSWLAFFTKEKKLFANLKDKLIELSDNIGMSISDFRILVNKIKKGER 370

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ IAKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 371 ESRIAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 430

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++  REPTPEE++KKLAMP
Sbjct: 431 ATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTQRQMMSEFGREPTPEELSKKLAMP 490

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E VRKVLKI KEP+SLETP+GDE+ S LGDFIED NA+ P+D+A+Q  L+ TTT+VLAS
Sbjct: 491 LEKVRKVLKIAKEPVSLETPVGDEEDSTLGDFIEDSNALIPVDAAVQTALKNTTTKVLAS 550

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS++L+SF
Sbjct: 551 LTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRQLKSF 610

Query: 680 LDG 682
           LD 
Sbjct: 611 LDN 613


>gi|330813718|ref|YP_004357957.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486813|gb|AEA81218.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 621

 Score =  560 bits (1442), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 319/660 (48%), Positives = 442/660 (66%), Gaps = 53/660 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           S++++++    RG++T EEL   L     + E +E +V  + +  I  V       ++  
Sbjct: 8   SFERLMEKGLSRGFITYEELQKSLGKRNANVESLEKSVLHIFDQAICFVK------KKSD 61

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                L S  S       K+  + DRS DDP+RMYLREMG +ELLSREGEIAIAKRIE+G
Sbjct: 62  FKVKKLESETS-------KQPKNQDRS-DDPIRMYLREMGGVELLSREGEIAIAKRIESG 113

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
           + +M++SL ESP+T + +  W + L +   L+R+IIDL+     + K       +    +
Sbjct: 114 KYVMVSSLSESPVTAKKIFEWEERLINNEMLVRDIIDLDTNFLDDDKLKKSIKEKKEKEE 173

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K +    +++ ++   T  DI             VD               D+D+   +L
Sbjct: 174 KLKKKESKEKGEETNTTTADI-------------VD---------------DDDEFNISL 205

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNA----VNGQK--DEKSSVKCKVLKEKLVK 323
           +++E +L+PK++   + I++ YR+L + Q+ +    ++ QK  D K     K+ KE + +
Sbjct: 206 ASLEIELKPKILKTFENISKNYRKLIAYQEESLQCILSSQKFSDSKKKNYEKIKKEIMEE 265

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           ++G L  NQ   + LV   Y+ +K+ ++ +G+L+R A  YGI RD F++ + G EL+P++
Sbjct: 266 MLG-LQFNQVTQEDLVALNYNENKKAINLDGDLMRAALKYGISRDDFIKFYVGNELNPNF 324

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKI-RNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
            S+     +  W  F   E   + KI R ++  +S   GISIS+F+ +V+ ++KGE E+ 
Sbjct: 325 ESFLSG--DKNWSKFFKNE-QKLFKISREKLTDLSKNIGISISDFKILVNKIKKGERESR 381

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 382 IAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 441

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++  REPTPEE++KKLAMP+E 
Sbjct: 442 WIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMMSEYGREPTPEELSKKLAMPLEK 501

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPISLETP+GDED S LGDFIED NA+ P+D+AIQ  L+ +TT+VLASLTP
Sbjct: 502 VRKVLKIAKEPISLETPVGDEDDSSLGDFIEDTNALIPVDAAIQTGLKNSTTKVLASLTP 561

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           REERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS++L+SFLD 
Sbjct: 562 REERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRQLKSFLDN 621


>gi|254455607|ref|ZP_05069036.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
 gi|207082609|gb|EDZ60035.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
          Length = 608

 Score =  555 bits (1429), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 308/662 (46%), Positives = 427/662 (64%), Gaps = 72/662 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           S+ +++     RG++T EELN  L    +S E        L+   I+++D          
Sbjct: 8   SFARLMGRGTHRGFITYEELNKSLGKRNLSDEN-------LAQAFIHILD---------- 50

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRS-----TDDPVRMYLREMGSIELLSREGEIAIAK 144
            +++ L    S+  V  +K   S +       +DDP+RMYLREMG +ELLSREGEIAIAK
Sbjct: 51  -ENITLVEKKSDFKVLRKKEGSSKEEGKTMEKSDDPIRMYLREMGGVELLSREGEIAIAK 109

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIEAG+ +M+ +L +SP+T Q    W D+L     L+REIID++                
Sbjct: 110 RIEAGKDVMLIALSQSPMTAQQFFEWNDQLQKDEILVREIIDIDT--------------- 154

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +Y + E +    ++ +  ETE                          DE + + DEDD
Sbjct: 155 --NYMEDETTGPSAKQKNAGETE-------------------------KDEGSGEGDEDD 187

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ----DNAVNGQKDEKSSVK-CKVLKE 319
              TL+AME +++PKV+  +  + + Y +L   Q    D  +N Q    +  K  + + +
Sbjct: 188 FNPTLAAMETEIKPKVLKTVSTLTKEYNKLIKYQKEKLDCILNSQNFSPAKEKGYQKIVD 247

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            +++ + SL L+ S ++ LV++ Y  +K+I+  EG LLRLA  + I R+ F++ + G E+
Sbjct: 248 DILENIKSLQLSPSVLEELVQKHYVENKKIISLEGNLLRLAMDHKIPRNEFIKFYIGNEI 307

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +P+   +        WK F +   +    IR  +  IS + GIS+++F+ +VS V+KGE 
Sbjct: 308 NPNLKKFLD--TNSIWKQFFSKNKEEFKNIRERLIEISHKLGISVTDFKKLVSRVQKGEK 365

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 366 ESRIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 425

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R + ++  RE TPEE+A+KL MP
Sbjct: 426 ATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTQRLILSEFGREATPEELAQKLRMP 485

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ VRKVLKI+KEP+SLE P+GDE+ S LGDFIED  A++PL+ AI++NL E TT++L++
Sbjct: 486 LDKVRKVLKISKEPVSLEKPVGDEEDSSLGDFIEDTKALAPLEQAIKSNLGEATTKILST 545

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREERVLRMRFG+GMNTDHTLEEVG QF VTRERIRQIEAKA+RKLKHPSRSK+L+SF
Sbjct: 546 LTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRSKQLKSF 605

Query: 680 LD 681
           L+
Sbjct: 606 LE 607


>gi|91762832|ref|ZP_01264797.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718634|gb|EAS85284.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 607

 Score =  553 bits (1424), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/665 (46%), Positives = 431/665 (64%), Gaps = 79/665 (11%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           S+ +++     RG++T +ELN  L    +S E +E          ++++D          
Sbjct: 8   SFARLMGRGTHRGFITFDELNKSLGKRNLSDENLEQAF-------MHILD---------- 50

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRS-----TDDPVRMYLREMGSIELLSREGEIAIAK 144
            +S+ L    S+  V  +K   S +       +DDP+RMYLREMG +ELLSREGEIAIAK
Sbjct: 51  -ESVALVEKKSDFKVLRKKENSSKEEGKTIEKSDDPIRMYLREMGGVELLSREGEIAIAK 109

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIEAG+ +M+ +L +SP+T Q  + W ++L     L+REIID++                
Sbjct: 110 RIEAGKDVMLIALAQSPITAQQFVEWDEKLQSDEILVREIIDIDT--------------- 154

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +Y + E++    ++ +  ET+                        +N+E N D+DE +
Sbjct: 155 --NYMEDENTGPSAKQRNSGETD------------------------KNEENNGDDDEFN 188

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK---- 320
              TL+AME +++PKV+  ++ + + Y +L   Q   ++   +   +V     KEK    
Sbjct: 189 P--TLAAMETEIKPKVLKTVNTLTKEYAKLIKYQKEKLDCILN---AVSFSAAKEKGHDK 243

Query: 321 ----LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
               +++ + SL L+ S ++ LV++ Y  +K+I+  EG LLRLA    I R+ F++ + G
Sbjct: 244 IVSDILENIKSLQLSPSVLEELVQKHYVENKKIVSLEGNLLRLAMDQKIPRNEFIKFYIG 303

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E++P+   +    P   WK F +   D    IR  +  IS + GIS+++++ IVS V+K
Sbjct: 304 NEINPNLKKFLDTNP--MWKQFFSKNKDEFKNIRERLIEISHKLGISVTDYKKIVSRVQK 361

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE E+ IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 362 GEKESRIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 421

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R + ++  RE TPEE+A+KL
Sbjct: 422 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTQRLILSEFGREATPEELAQKL 481

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP++ VRKVLKI+KEP+SLE P+GDE+ S LGDFIED  A++PL+ AI++NL E TT++
Sbjct: 482 RMPLDKVRKVLKISKEPVSLEKPVGDEEDSSLGDFIEDTKALAPLEQAIKSNLSEATTKI 541

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L++LTPREERVLRMRFG+GMNTDHTLEEVG QF VTRERIRQIEAKA+RKLKHPSRSK+L
Sbjct: 542 LSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRSKQL 601

Query: 677 RSFLD 681
           +SFL+
Sbjct: 602 KSFLE 606


>gi|71082746|ref|YP_265465.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71061859|gb|AAZ20862.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 595

 Score =  551 bits (1419), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 306/655 (46%), Positives = 426/655 (65%), Gaps = 79/655 (12%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            RG++T +ELN  L    +S E +E          ++++D           +S+ L    
Sbjct: 6   HRGFITFDELNKSLGKRNLSDENLEQAF-------MHILD-----------ESVALVEKK 47

Query: 100 SNSSVFLQKRKDSADRS-----TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           S+  V  +K   S +       +DDP+RMYLREMG +ELLSREGEIAIAKRIEAG+ +M+
Sbjct: 48  SDFKVLRKKENSSKEEGKTIEKSDDPIRMYLREMGGVELLSREGEIAIAKRIEAGKDVML 107

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            +L +SP+T Q  + W ++L     L+REIID++                  +Y + E++
Sbjct: 108 IALAQSPITAQQFVEWDEKLQSDEILVREIIDIDT-----------------NYMEDENT 150

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
               ++ +  ET+                        +N+E N D+DE +   TL+AME 
Sbjct: 151 GPSAKQRNSGETD------------------------KNEENNGDDDEFNP--TLAAMET 184

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK--------LVKLVG 326
           +++PKV+  ++ + + Y +L   Q   ++   +   +V     KEK        +++ + 
Sbjct: 185 EIKPKVLKTVNTLTKEYAKLIKYQKEKLDCILN---AVSFSAAKEKGHDKIVSDILENIK 241

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           SL L+ S ++ LV++ Y  +K+I+  EG LLRLA    I R+ F++ + G E++P+   +
Sbjct: 242 SLQLSPSVLEELVQKHYVENKKIVSLEGNLLRLAMDQKIPRNEFIKFYIGNEINPNLKKF 301

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
               P   WK F +   D    IR  +  IS + GIS+++++ IVS V+KGE E+ IAKK
Sbjct: 302 LDTNP--MWKQFFSKNKDEFKNIRERLIEISHKLGISVTDYKKIVSRVQKGEKESRIAKK 359

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 360 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 419

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+VRT R + ++  RE TPEE+A+KL MP++ VRKV
Sbjct: 420 AITRSIADQARTIRIPVHMIETINKIVRTQRLILSEFGREATPEELAQKLRMPLDKVRKV 479

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI+KEP+SLE P+GDE+ S LGDFIED  A++PL+ AI++NL E TT++L++LTPREER
Sbjct: 480 LKISKEPVSLEKPVGDEEDSSLGDFIEDTKALAPLEQAIKSNLSEATTKILSTLTPREER 539

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFG+GMNTDHTLEEVG QF VTRERIRQIEAKA+RKLKHPSRSK+L+SFL+
Sbjct: 540 VLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRSKQLKSFLE 594


>gi|254419911|ref|ZP_05033635.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
 gi|196186088|gb|EDX81064.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
          Length = 648

 Score =  538 bits (1386), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 275/420 (65%), Positives = 329/420 (78%), Gaps = 8/420 (1%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCKVLKEKLVKLVG 326
           ++SA+E +LR  VM  L+ IA  + E R LQD  V  + K E  S K     + L K + 
Sbjct: 230 SVSALEAELRDGVMEVLNLIAADFSEFRGLQDKLVQTRLKGEVLSAKDSKAYQTLTKSIS 289

Query: 327 ----SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
               ++ LN +RI+ LVEQLY I+KR++  EG LLRLA SYGI R  FL+ + G ELDP 
Sbjct: 290 DRLKTMKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYGISRPEFLKAYFGAELDPT 349

Query: 383 WVSYAKDFPEG-EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           W    K+  +G  W  F   E   I  IR ++ ++++E G+ I ++R IV  V+KGE EA
Sbjct: 350 WTERIKE--QGVRWTKFSDNEASQIATIRADVAAVALEAGLPIDDYRRIVQTVQKGEREA 407

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 408 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 467

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E
Sbjct: 468 WWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLE 527

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLT
Sbjct: 528 KVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLT 587

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 588 PREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 647


>gi|91204871|ref|YP_537226.1| RNA polymerase sigma factor RpoD [Rickettsia bellii RML369-C]
 gi|122426123|sp|Q1RKH7|RPOD_RICBR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|91068415|gb|ABE04137.1| RNA polymerase sigma factor [Rickettsia bellii RML369-C]
          Length = 641

 Score =  531 bits (1368), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 293/656 (44%), Positives = 419/656 (63%), Gaps = 67/656 (10%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--------DDLEDEEGSEDSL 93
           G VT  ++N  LP D  S E+++  +   S   ++++D         DD+E EEG + S 
Sbjct: 24  GSVTYNDINRALP-DGTSVEEIDKVMFRFSEAEVDILDTNEDDAIKIDDMEMEEGFKIST 82

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           ++     + +            +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  +
Sbjct: 83  NIDHEPEDETEEENIG------TTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTL 136

Query: 154 MASLCESPLTFQALIIWR-DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           +A+LC SP+       W  D +N+   LLR++IDLE+           H           
Sbjct: 137 IAALCRSPIAMDKFRKWYADLVNENNMLLRDLIDLES--------NMMHD---------- 178

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
                   D+  E+E D  S                 + E +E++ D D +++  ++S +
Sbjct: 179 --------DETSESEDDHNS-----------------DHEEEEQDHDHDHEENILSMSKV 213

Query: 273 EDQLRPKVMCALDEIAEVYREL-----RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           E Q+ P ++  + +IA +  EL     +S + +A  G K  ++S K     E L+  V  
Sbjct: 214 ETQILPNIIERMKKIAFICEELLIETKKSFEKSA--GPKILQNSKKYNDNLELLISEVSE 271

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           +  N  R + ++ ++Y I++ +++ E   L+LA+ YGI R  FL+ + G  ++  W    
Sbjct: 272 IHFNSKRTEEILSEMYRINRDLINKETAFLKLAEKYGITRQNFLDEYIGAVINAAWKEKM 331

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
               +  WK  +  E D I ++  E+ +I + TG+ +++F+ +V+ ++K E +   AKK+
Sbjct: 332 LKNKKAGWKELLTKESDYIDQMIAELSAIEINTGLLVNDFKKLVNAIQKSERQTLQAKKD 391

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 392 MIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 451

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPTP EIA +L+MP++ VRKV+
Sbjct: 452 ITRAIADQARTIRIPVHMIETINKIIRTSRQMLNELGYEPTPAEIAARLSMPIDKVRKVM 511

Query: 568 KITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           KI KEPISLE P+GD +D S+LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREER
Sbjct: 512 KIAKEPISLENPVGDGDDNSYLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREER 571

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 572 VLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 627


>gi|296116667|ref|ZP_06835277.1| RNA polymerase sigma factor RpoD [Gluconacetobacter hansenii ATCC
           23769]
 gi|295976879|gb|EFG83647.1| RNA polymerase sigma factor RpoD [Gluconacetobacter hansenii ATCC
           23769]
          Length = 659

 Score =  530 bits (1364), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 255/419 (60%), Positives = 330/419 (78%), Gaps = 5/419 (1%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-----NGQKDEKSSVKCKVLKEKLV 322
           +LSA+E++L+P+++   +E+  +Y  L  LQ   +      G+   ++    + L+ +LV
Sbjct: 239 SLSALEEKLKPEILEQFEEVEALYARLHELQATRLEKLTSGGEISAEAEAAYEQLRCELV 298

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
             V  + L+ +RI++LVE L  I +R+   EG +LRLA+S  + R+ FL +++GRELDP 
Sbjct: 299 GKVQQVHLHNTRIEVLVEHLKAIFQRLNGLEGRMLRLAESTKVSREDFLLKYRGRELDPG 358

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV      P   WKNFVA  +++++++R ++  ++ ETG+ + EFR + + V +GE +++
Sbjct: 359 WVDVVSALPGKAWKNFVAKHMETVIRLRGQVAELTQETGLPVGEFRRVYATVSRGERDSA 418

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 419 RAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 478

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REP PEE+A+KL MP+E 
Sbjct: 479 WIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEK 538

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK AV PLD+AIQ NLRE TTRVL+SLTP
Sbjct: 539 VRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVIPLDAAIQTNLREATTRVLSSLTP 598

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 599 REERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|157965030|ref|YP_001499854.1| RNA polymerase sigma factor RpoD [Rickettsia massiliae MTU5]
 gi|157844806|gb|ABV85307.1| RNA polymerase sigma factor [Rickettsia massiliae MTU5]
          Length = 633

 Score =  529 bits (1363), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 289/654 (44%), Positives = 417/654 (63%), Gaps = 76/654 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDDLEDEE-----GSEDSLDLAS 97
           VT +++N  LP ++  S  Q+E+ +   S+ GI++++ +  ED+E     G ++   L++
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGIDILESN--EDDEIKLDIGMDEEFKLST 84

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           +  N     +   +    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASL
Sbjct: 85  NVDNEP---EDEVEENIGATDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGHKTMTASL 141

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
           C SP+  +  I+W ++L +   LLR++IDLEA           H           D + E
Sbjct: 142 CRSPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETPE 182

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            + +   ETEG                               E+ +D+  ++S +E Q+ 
Sbjct: 183 NDEEHSSETEG-------------------------------EEHEDNHLSISRVETQIL 211

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK--------EKLVKLVGSLS 329
           P ++  + +I+ +  EL       +  +K  + S + KVL+        E L+  V  + 
Sbjct: 212 PNIIERMKKISFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNLELLINEVSEIH 265

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
            N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W      
Sbjct: 266 FNSKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLK 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +G WK  +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+
Sbjct: 326 NKKGAWKELMTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMI 385

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 386 EANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 445

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI
Sbjct: 446 RAIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKI 505

Query: 570 TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
            KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVL
Sbjct: 506 AKEPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVL 565

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 566 RMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 619


>gi|157826344|ref|YP_001494064.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
 gi|157800302|gb|ABV75556.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
          Length = 635

 Score =  528 bits (1361), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 289/653 (44%), Positives = 418/653 (64%), Gaps = 72/653 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP +E  S  Q+E+ +   S+ G+++++    DD++ + G ++   L+++ 
Sbjct: 27  VTYDDINKALPLNENPSIRQLEEAILKFSDAGVDILESNEDDDIKLDIGMDEEFKLSTNI 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC 
Sbjct: 87  DNEPEDEAEEENIG--TTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGRKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA I         H           D + E +
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEANI--------LH-----------DETPEND 185

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            +   ETEG                               E+ DD+  ++S +E Q+ P 
Sbjct: 186 EEHSSETEG-------------------------------EEHDDNHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---------EKLVKLVGSLSL 330
           ++  + +I+ +  EL       +  +K  + S + KVL+         E L+  V  +  
Sbjct: 215 IIERMKKISFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNNLELLLHEVSEIHF 268

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
           N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W       
Sbjct: 269 NSKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKN 328

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +  WK  +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+E
Sbjct: 329 KKVAWKELITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIE 388

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 389 ANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 448

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI 
Sbjct: 449 AIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIA 508

Query: 571 KEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           KEPISLE P+GD+ D   LGDFIEDKNA++P+D+AIQ+NLRE TTRVLA+LTPREERVLR
Sbjct: 509 KEPISLENPVGDDSDGGQLGDFIEDKNAIAPIDAAIQSNLREVTTRVLATLTPREERVLR 568

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 569 MRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 621


>gi|209965297|ref|YP_002298212.1| RNA polymerase sigma factor RpoD [Rhodospirillum centenum SW]
 gi|209958763|gb|ACI99399.1| DNA-directed RNA polymerase, sigma subunit RpoD [Rhodospirillum
           centenum SW]
          Length = 648

 Score =  528 bits (1360), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 268/419 (63%), Positives = 328/419 (78%), Gaps = 6/419 (1%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV----NGQKDEKSS-VKCKVLKEKLV 322
           +LSAME +L+PKV+     I E Y +L  +Q+  +     G++  K S  K   LK +L 
Sbjct: 230 SLSAMEAELKPKVIETFARIEETYEKLHKVQEQRLAVLQRGEELPKGSDKKYDKLKAELT 289

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            LV S+ LN +RI+ LVEQLY ++++++  EG+LLRLA    IKR+ FL  + G ELDP+
Sbjct: 290 DLVNSVRLNNARIEQLVEQLYGLNRKLLGYEGKLLRLATDCKIKREDFLHHYYGSELDPN 349

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+   +   +  W  F       + ++R  I  ++ +  + I EFR IVS V+KGE EAS
Sbjct: 350 WLERCRGLSKS-WGRFADKSSVEVGRVREAISEVADQVRLPIGEFRRIVSTVQKGEKEAS 408

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 409 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 468

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A++L MP+E 
Sbjct: 469 WIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAERLMMPLEK 528

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV PLD+AIQANLRETTTR+LA+LTP
Sbjct: 529 VRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPLDAAIQANLRETTTRILATLTP 588

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 589 REERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 647


>gi|157804249|ref|YP_001492798.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
 gi|157785512|gb|ABV74013.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
          Length = 635

 Score =  526 bits (1355), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 290/655 (44%), Positives = 414/655 (63%), Gaps = 76/655 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDDLEDEE-----GSEDSLDLAS 97
           VT +++N  LP ++  S  Q+E+ +   S+ GI++++ +  ED+E     G ++   L+ 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGIDILESN--EDDEIKLDIGMDEEFKLSI 84

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           +  N      + K+    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASL
Sbjct: 85  NVDNEPDDEVEEKNIG--TTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASL 142

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
           C SP+  +  I+W ++L +   LLR++IDLEA           H           D + E
Sbjct: 143 CRSPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETSE 183

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            + +   + EG                               E+ +D   ++S +E Q+ 
Sbjct: 184 NDEEHSSDNEG-------------------------------EEHEDHHLSMSRVETQIL 212

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---------EKLVKLVGSL 328
           P V+  + +IA +  EL       +  +K  + S + KVL+         E L+  V  +
Sbjct: 213 PNVIERMKKIAFICEEL------LIEAKKCYEKSFEPKVLQNSRKYNNNLELLINEVSEI 266

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
             N  + D ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W     
Sbjct: 267 HFNSKKTDEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKML 326

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              +  WK  +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M
Sbjct: 327 KNKKIAWKELITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDM 386

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 387 IEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 446

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+K
Sbjct: 447 TRAIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMK 506

Query: 569 ITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           I KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERV
Sbjct: 507 IAKEPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERV 566

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 567 LRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 621


>gi|67459749|ref|YP_247373.1| RNA polymerase sigma factor RpoD [Rickettsia felis URRWXCal2]
 gi|75535861|sp|Q4UJT1|RPOD_RICFE RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|67005282|gb|AAY62208.1| RNA polymerase sigma factor [Rickettsia felis URRWXCal2]
          Length = 635

 Score =  525 bits (1353), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 286/653 (43%), Positives = 418/653 (64%), Gaps = 72/653 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC+
Sbjct: 87  DNEPEDEVEEENIG--TTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCK 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H           D + E +
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETPEND 185

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            +   ETEG                               E+ +D+  ++S +E Q+ P 
Sbjct: 186 EEHSSETEG-------------------------------EEHEDNHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---------EKLVKLVGSLSL 330
           ++  + +I+ +  EL       +  +K  + S + KVL+         E L+  V  +  
Sbjct: 215 IIERMKKISFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNNLELLINEVSEIHF 268

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
           N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W       
Sbjct: 269 NSKRTEEILGKMYGINRDLINKEIAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKN 328

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +  WK  +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+E
Sbjct: 329 KKVAWKELITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIE 388

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 389 ANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 448

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI 
Sbjct: 449 AIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIA 508

Query: 571 KEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLR
Sbjct: 509 KEPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLR 568

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 569 MRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 621


>gi|34581080|ref|ZP_00142560.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|229587226|ref|YP_002845727.1| RNA polymerase sigma factor RpoD [Rickettsia africae ESF-5]
 gi|28262465|gb|EAA25969.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|228022276|gb|ACP53984.1| RNA polymerase sigma factor [Rickettsia africae ESF-5]
          Length = 634

 Score =  525 bits (1353), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 287/652 (44%), Positives = 418/652 (64%), Gaps = 71/652 (10%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC 
Sbjct: 87  DNEPEDEVEEENIG--TTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H           D + E +
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETPEND 185

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            ++  ETEG                               E+ +D+  ++S +E Q+ P 
Sbjct: 186 EENSSETEG-------------------------------EEHEDNHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK--------EKLVKLVGSLSLN 331
           V+  + +IA +  EL       +  +K  + S + KVL+        E L+  V  +  N
Sbjct: 215 VIERMKKIAFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNLELLINEVSEIHFN 268

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        
Sbjct: 269 SKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNK 328

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  WK  +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EA
Sbjct: 329 KVAWKELMTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEA 388

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+
Sbjct: 389 NLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRA 448

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI K
Sbjct: 449 IADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAK 508

Query: 572 EPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           EPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRM
Sbjct: 509 EPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRM 568

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 569 RFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 620


>gi|15893252|ref|NP_360966.1| RNA polymerase sigma factor RpoD [Rickettsia conorii str. Malish 7]
 gi|47606046|sp|Q92FZ8|RPOD_RICCN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|15620471|gb|AAL03867.1| RNA polymerase sigma factor [Rickettsia conorii str. Malish 7]
          Length = 634

 Score =  525 bits (1353), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 286/652 (43%), Positives = 419/652 (64%), Gaps = 71/652 (10%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M+ASLC 
Sbjct: 87  DNEPEDEVEEENIG--TTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMIASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H           D + E +
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETPEND 185

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            ++  ETEG                               E+ +D+  ++S +E Q+ P 
Sbjct: 186 EENSSETEG-------------------------------EEHEDNHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK--------EKLVKLVGSLSLN 331
           ++  + +IA +  EL       +  +K  + S + KVL+        E L+  V  +  N
Sbjct: 215 IIERMKKIAFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNLELLINEVSEIHFN 268

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        
Sbjct: 269 SKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNK 328

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  WK  +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EA
Sbjct: 329 KVAWKELMTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEA 388

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+
Sbjct: 389 NLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRA 448

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI K
Sbjct: 449 IADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAK 508

Query: 572 EPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           EPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRM
Sbjct: 509 EPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRM 568

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 569 RFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 620


>gi|157829159|ref|YP_001495401.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165933888|ref|YP_001650677.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str. Iowa]
 gi|157801640|gb|ABV76893.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165908975|gb|ABY73271.1| RNA polymerase sigma factor [Rickettsia rickettsii str. Iowa]
          Length = 634

 Score =  523 bits (1348), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 286/652 (43%), Positives = 417/652 (63%), Gaps = 71/652 (10%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC 
Sbjct: 87  DNEPEDEVEEENIG--TTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H           D + E +
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETPEND 185

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            +   ETEG                               E+ +D+  ++S +E Q+ P 
Sbjct: 186 EEHSSETEG-------------------------------EEHEDNHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK--------EKLVKLVGSLSLN 331
           ++  + +IA +  EL       +  +K  + S + KVL+        E L+  V  +  N
Sbjct: 215 IIERMKKIAFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNLELLINEVSEIHFN 268

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        
Sbjct: 269 SKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNK 328

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  WK  +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EA
Sbjct: 329 KVAWKELMTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEA 388

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+
Sbjct: 389 NLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRA 448

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI K
Sbjct: 449 IADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAK 508

Query: 572 EPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           EPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRM
Sbjct: 509 EPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRM 568

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 569 RFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 620


>gi|15604688|ref|NP_221206.1| RNA polymerase sigma factor RpoD [Rickettsia prowazekii str. Madrid
           E]
 gi|464670|sp|P33451|RPOD_RICPR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|434681|gb|AAB81404.1| major sigma factor of RNA polymerase [Rickettsia prowazekii]
 gi|3861383|emb|CAA15282.1| RNA POLYMERASE SIGMA FACTOR RPOD (rpoD) [Rickettsia prowazekii]
 gi|292572521|gb|ADE30436.1| RNA polymerase sigma factor [Rickettsia prowazekii Rp22]
          Length = 635

 Score =  523 bits (1348), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 287/653 (43%), Positives = 419/653 (64%), Gaps = 72/653 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N S    + ++    STDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC 
Sbjct: 87  DNESEDEVEEENIG--STDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H                  
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH------------------ 178

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            D+V E + +  S  +V                       E+ +D+  ++S +E Q+   
Sbjct: 179 -DEVHENDEEHNSETEV-----------------------EEHEDNHLSMSRVETQILHN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---------EKLVKLVGSLSL 330
           ++  + +I+ +  EL       +  +K  + S + KVL+         E L+  V  +  
Sbjct: 215 IIDRMKKISFICEEL------LIEAKKCYEESFEPKVLQNSKKYNNNLELLINEVSEIHF 268

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
           N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W       
Sbjct: 269 NSKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKN 328

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +  WK  +  E D I ++ NE+  I   TG+ +++F+ +V+ ++K E +   AKK+M+E
Sbjct: 329 KKVAWKELITKESDYIDQMINELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIE 388

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 389 ANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 448

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI 
Sbjct: 449 AIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIA 508

Query: 571 KEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLR
Sbjct: 509 KEPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLR 568

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF +G
Sbjct: 569 MRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRNG 621


>gi|117924113|ref|YP_864730.1| RpoD family RNA polymerase sigma factor [Magnetococcus sp. MC-1]
 gi|117607869|gb|ABK43324.1| RNA polymerase, sigma 70 subunit, RpoD [Magnetococcus sp. MC-1]
          Length = 683

 Score =  523 bits (1347), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 310/706 (43%), Positives = 420/706 (59%), Gaps = 66/706 (9%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D   ++  D   +  KK+I   ++RG++T +E+N  LP D  S+E MED V +L NMGI+
Sbjct: 2   DGKSNMAEDTKREDMKKLIARGKERGFLTYDEVNDVLPNDMTSAEDMEDVVGLLDNMGID 61

Query: 77  VVDGDDLEDEEGSE------------DSLD------------LASSASNSSVFLQKRKDS 112
           ++D    E EEG+             DSLD              S    S      R D 
Sbjct: 62  LIDD---EREEGARPKSRPAAGIGNLDSLDDDVDEEILGISDFDSEDDESDDEDGLRSDG 118

Query: 113 ADR-----STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           A        TDDPVRMYLREMGS+ELL+REGEIAIAKRIE G   ++A++C++P TF  +
Sbjct: 119 AIEDIDLGKTDDPVRMYLREMGSVELLTREGEIAIAKRIEEGCNEVIATICDAPSTFNEV 178

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           ++  + L  G   LRE++D+     P+ +G           +    +  + E  D  +  
Sbjct: 179 MMLAERLRAGEISLREVLDIST---PQDEGSEDEDLNNDDDEVEASTESDDEDVDEDDI- 234

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
             +    KV    R+ V  PP     +E     + D+          +L    +   DEI
Sbjct: 235 --VNGPVKV----RNPVPEPPPVKTEEEIAAQREADNEQFR------ELYEATLAIFDEI 282

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKCKVL-------KEKLVKLVGSLSLNQSRIDLLVE 340
                 L  L+D   +  +++     CK L       K ++V++V  +  +  + D LVE
Sbjct: 283 TRENEVLVELRDPLNDALQNDPEGETCKRLLAEYQAHKARIVEIVAGIKFSPKQRDRLVE 342

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF-- 398
           ++      +   E +++ +     +K+  F+E+  G E D  W+          WK    
Sbjct: 343 RIKSYVAAVRAQEQKIITIVTQCNVKKPEFIEQFTGNESDTTWIQNFAKTRSAPWKRLYE 402

Query: 399 ---VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              + CE   +      I+SI  E G ++++ +     +  GE  A+ AKKEMVEANLRL
Sbjct: 403 QSELICEAQLV------IRSIEEEAGQTVADLKKCNKKLMDGERRANQAKKEMVEANLRL 456

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+W  GYKFSTYA WW++QAITRSIADQ
Sbjct: 457 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEWRRGYKFSTYATWWIRQAITRSIADQ 516

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+VRT+R+M  ++ REPTPEEIA++++M +E VRKVLKI KEPIS
Sbjct: 517 ARTIRIPVHMIETINKLVRTSRQMVQEMGREPTPEEIAERMSMSLEKVRKVLKIAKEPIS 576

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETP+GDE+ SHLGDFIEDK+ +SP + AI +NLR+TT RVL +LT REE VLRMRFGIG
Sbjct: 577 LETPVGDEEDSHLGDFIEDKSMLSPSEHAIMSNLRDTTGRVLQTLTSREEHVLRMRFGIG 636

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+KLRSFL+
Sbjct: 637 LPTDHTLEEVGKQFNVTRERIRQIEAKALRKLRHPTRSRKLRSFLE 682


>gi|51474026|ref|YP_067783.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
 gi|81389911|sp|Q68VQ5|RPOD_RICTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|51460338|gb|AAU04301.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
          Length = 635

 Score =  522 bits (1345), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 287/653 (43%), Positives = 418/653 (64%), Gaps = 72/653 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGIDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N S    + ++    STDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC 
Sbjct: 87  DNESEDEVEEENIG--STDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H                  
Sbjct: 145 SPVAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH------------------ 178

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            D+V E + +  S  +V                       E+ +D+  ++S +E Q+   
Sbjct: 179 -DEVHENDEEHNSETEV-----------------------EEHEDNHLSMSRVETQILHN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---------EKLVKLVGSLSL 330
           ++  + +I+ +  EL       +  +K  + S   KVL+         E L+  V  +  
Sbjct: 215 IIDRMKKISFICEEL------LIEAKKCYEESFDPKVLQNSRKYNNNLELLIHEVSEIHF 268

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
           N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W       
Sbjct: 269 NSKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKN 328

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +  WK  +  E D I ++ NE+  I   TG+ +++F+ +V+ ++K E +   AKK+M+E
Sbjct: 329 KKVAWKELITKESDYIDQMINELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIE 388

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 389 ANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 448

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI 
Sbjct: 449 AIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIA 508

Query: 571 KEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLR
Sbjct: 509 KEPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLR 568

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF +G
Sbjct: 569 MRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRNG 621


>gi|238651104|ref|YP_002916962.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
 gi|238625202|gb|ACR47908.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
          Length = 634

 Score =  520 bits (1339), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 284/652 (43%), Positives = 415/652 (63%), Gaps = 71/652 (10%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N   P ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+++ 
Sbjct: 27  VTYDDINNAFPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC 
Sbjct: 87  DNEPEDEVEEENIG--TTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA           H           D + E +
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH-----------DETPEND 185

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            +   ETEG                               E+ +D+  ++S +E Q+ P 
Sbjct: 186 EEHSSETEG-------------------------------EEHEDNHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK--------EKLVKLVGSLSLN 331
           ++  + +IA +  EL       +  +K  + S + KVL+        E L+  V  +  N
Sbjct: 215 IIERMKKIAFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNLELLINEVSEIHFN 268

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        
Sbjct: 269 SKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNK 328

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  WK  +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EA
Sbjct: 329 KVAWKELMTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEA 388

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+
Sbjct: 389 NLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRA 448

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI K
Sbjct: 449 IADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAK 508

Query: 572 EPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           EPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE T RVLA+LTPREERVLRM
Sbjct: 509 EPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTIRVLATLTPREERVLRM 568

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 569 RFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 620


>gi|163796954|ref|ZP_02190910.1| RNA polymerase sigma factor rpoD [alpha proteobacterium BAL199]
 gi|159177701|gb|EDP62252.1| RNA polymerase sigma factor rpoD [alpha proteobacterium BAL199]
          Length = 639

 Score =  520 bits (1338), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 261/419 (62%), Positives = 325/419 (77%), Gaps = 6/419 (1%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQ----DNAVNGQKDEKSS-VKCKVLKEKLV 322
           +LSAME QL P+V+   D+IA+ Y ++  +Q    D    G++  +++  K + LK +L+
Sbjct: 221 SLSAMEQQLLPQVLETFDKIADTYGKMVRMQKRRFDKLKGGEELARTTERKYEKLKGELI 280

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           + + S+ L+ +RI+ LVEQLY +++R+   +  L + A   G+ R  F+E H G EL+P 
Sbjct: 281 EGMESVRLHNARIEALVEQLYTLNRRLSQVDIRLWKQADRVGVSRKSFMEEHFGNELEPD 340

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+       +  W+ F     + + + R  +  IS + G++I EFR IV  V+KGE EA 
Sbjct: 341 WLERVATV-DARWRKFAETAAEEVSEAREHLAMISADAGLTIGEFRRIVQTVQKGEREAG 399

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 400 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KL MP+E 
Sbjct: 460 WIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLVMPLEK 519

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV PLD+AI ANLRETTTRVLASLTP
Sbjct: 520 VRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAIHANLRETTTRVLASLTP 579

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 580 REERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 638



 Score =  179 bits (454), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 94/175 (53%), Positives = 125/175 (71%), Gaps = 8/175 (4%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D  + + K +IK  ++RG++T +E+NA LP +E+SSEQ+ED ++ L+ MG+NVV+
Sbjct: 24  DGPLMDNINQAVKNLIKKGKERGFLTYDEVNAALPQEEMSSEQIEDIMSALNEMGVNVVE 83

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +D  D+   ++  + A  A N S       D   R TDDPVRMYLREMGS+ELLSREGE
Sbjct: 84  NEDDGDQSAEKEDTE-AKLAGNVS------DDDVGR-TDDPVRMYLREMGSVELLSREGE 135

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           IAIAKRIEAGR MM+  +CESPLT +AL+ WRD+L +GT LLR+IIDLEA  G E
Sbjct: 136 IAIAKRIEAGREMMIGGICESPLTLRALVNWRDQLKEGTVLLRDIIDLEATYGAE 190


>gi|114328948|ref|YP_746105.1| RNA polymerase sigma factor RpoD [Granulibacter bethesdensis
           CGDNIH1]
 gi|114317122|gb|ABI63182.1| RNA polymerase sigma factor rpoD [Granulibacter bethesdensis
           CGDNIH1]
          Length = 654

 Score =  519 bits (1337), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 256/427 (59%), Positives = 330/427 (77%), Gaps = 5/427 (1%)

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ----DNAVNGQKDEKSSVKC- 314
           +D D    +LSA+E++L+P+ +   +EI  +Y++L  +Q    D+  +G++    S K  
Sbjct: 227 DDADGIGMSLSALEEKLKPETLQRFEEIEAIYKKLSKMQSKRLDSFTSGEEVTARSEKTY 286

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
           + ++++LV  V  + L+  R++ LV QL  +++R+   EG+LLRLA+S  + RD FLE+H
Sbjct: 287 EKMRDELVAKVSEVRLHNGRVEELVLQLKQLNQRLTGLEGQLLRLAESCKVPRDSFLEQH 346

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           +  EL+P+W+      P   WKNF A     + +IR  I  ++ + G+ I EF  +   V
Sbjct: 347 RNHELEPNWLERVSTLPGKAWKNFSARYPQEVGQIRGRIGEVAADAGLPIPEFLRVYKTV 406

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 407 NRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 466

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REP PEE+A+
Sbjct: 467 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPQPEELAE 526

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK A+ PLD+AIQANLRE TT
Sbjct: 527 KLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKAAIIPLDAAIQANLREATT 586

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           RVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+
Sbjct: 587 RVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSR 646

Query: 675 KLRSFLD 681
           KLRSFLD
Sbjct: 647 KLRSFLD 653


>gi|239948365|ref|ZP_04700118.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922641|gb|EER22665.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 635

 Score =  517 bits (1332), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 284/654 (43%), Positives = 411/654 (62%), Gaps = 74/654 (11%)

Query: 44  VTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSA 99
           VT +++N  LP ++  S  Q+E+ +   S+ G+++++    D+++ + G ++   L+ + 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSINV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC 
Sbjct: 87  DNEPEDEVEEENIG--TTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+T +  I+W ++L +   LLR++IDLEA           H                  
Sbjct: 145 SPITMRCFIVWYEDLVNEKMLLRDLIDLEA--------NMLH------------------ 178

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH-TLSAMEDQLRP 278
                                    D  PEN E    N + +E +  H ++  +E Q+ P
Sbjct: 179 -------------------------DETPENDEEHSSNTEGEEHEDNHLSMYRVETQILP 213

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---------EKLVKLVGSLS 329
            ++  + +I+ +  EL       +  +K  + S + KVL+         E L+  V  + 
Sbjct: 214 NIIERMKKISFICEEL------LIEAKKCYEKSFEPKVLQNSKKYNNNLELLINEVSEIH 267

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
            N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W      
Sbjct: 268 FNSKRTEEILGKMYGINRDLINKETTFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLK 327

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +  WK  +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+
Sbjct: 328 NKKVAWKELITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMI 387

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 388 EANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 447

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVHM + I+K++R +R+M N++  EPT  EIA +L+MP++ V KV+KI
Sbjct: 448 RAIADQARTIRIPVHMIETINKILRISRQMLNELGYEPTATEIANRLSMPLDKVCKVMKI 507

Query: 570 TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
            KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVL
Sbjct: 508 AKEPISLENPVGDDIDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVL 567

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF  G
Sbjct: 568 RMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRSG 621


>gi|296532787|ref|ZP_06895466.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
 gi|296266895|gb|EFH12841.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
          Length = 639

 Score =  508 bits (1309), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 251/422 (59%), Positives = 325/422 (77%), Gaps = 11/422 (2%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG--------QKDEKSSVKCKVLKE 319
           +LSA+E++L+P+ +   + I E+Y +L+ L    +           + EK+  K ++   
Sbjct: 220 SLSALEEKLKPEALATFEAIEELYGKLQKLSLKRMEAYTAGEEFASRTEKTYEKQRL--- 276

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
           +LV LV  + L+ +RI+ LV+QL  +++RI   EG++LRLA+   +KR+ FL+  +G E+
Sbjct: 277 ELVALVEKVQLHNNRIEELVDQLKGLNRRITSLEGQVLRLAEGSRVKREDFLQYWRGAEI 336

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           DP W       P+  WKNF+      + +IR ++ + +  TG+ + EF+ + + V +GE 
Sbjct: 337 DPAWFERISALPQKSWKNFIERSRQDVEQIRTQLSNTAALTGLPVDEFKRVYATVSRGER 396

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 397 DMTQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REP PEE+A+KL MP
Sbjct: 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPQPEELAEKLGMP 516

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK A+ PLD+AIQ+NLRE TTRVLAS
Sbjct: 517 LEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKAAIIPLDAAIQSNLREATTRVLAS 576

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSF
Sbjct: 577 LTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSF 636

Query: 680 LD 681
           LD
Sbjct: 637 LD 638



 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/180 (50%), Positives = 120/180 (66%), Gaps = 2/180 (1%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+    +++ +  + D    + KK+I   ++RGYVT +ELN  LP +EVSSE +EDT+AM
Sbjct: 10  DTVENRDEAVEGALLDILSAAVKKLIARGKERGYVTYDELNQALPSEEVSSELIEDTMAM 69

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLRE 127
           LS +GINVV+ ++ E+ EG+      A  A              +    TDDPVRMYLRE
Sbjct: 70  LSELGINVVEAEETEEAEGAAKPAAKAEGAEEDEEEEGGGNVDEESLGRTDDPVRMYLRE 129

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR MM+  LCESPLTFQA++ W + + +G  LLR++IDL
Sbjct: 130 MGSVELLSREGEIAIAKRIEAGRDMMIGGLCESPLTFQAILTWHNAVKEGRMLLRDVIDL 189


>gi|11993459|gb|AAG42748.1|AF299295_2 RNA polymerase sigma factor [Zymomonas mobilis]
          Length = 763

 Score =  500 bits (1287), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 299/676 (44%), Positives = 420/676 (62%), Gaps = 28/676 (4%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNM 73
           +++ D+ + D ++ S +K I   ++  YVT ++LN  LP D+    +++  +    ++  
Sbjct: 11  KNAGDAPLIDLNETSIRKFITQPKKTEYVTYDQLNEALPQDQDVFGTDRKYNVCPFVNGH 70

Query: 74  GI--NVVDGDD-LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
               N   G D  ++EE +   L       + S    +RK          V +  + + S
Sbjct: 71  QYRKNEDSGQDGQQEEENAAKKLQGQRWHFSGSGHYDQRKKHPTEQMIRCVCISAKWVRS 130

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
               SREGEIAIAKRIEAGR  M+  LCESP+TF  +I W + LN+GT  LREIIDL+A 
Sbjct: 131 -SFWSREGEIAIAKRIEAGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAM 189

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +           T+G S  + E+   + + +  +   G          DD        EN
Sbjct: 190 L-----------TQGPSPDQFEEDGDDNDNEISERNAGPTFKEDDDEDDDSEGELD--EN 236

Query: 251 AENDER-NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-----AVNG 304
            +  +R N+DE ED++  +L+ ME+QL+P  +    +IA++YR+   LQ+        N 
Sbjct: 237 GQRIQRENMDE-EDENTLSLAQMEEQLKPASLEKFAKIADLYRQFSVLQNARMRALGANE 295

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           +  E      + L+E+L   V S+  + +RI+ LVEQLY+ + R+    G++LRLA+ Y 
Sbjct: 296 EFPEDQENAYQQLREELTAEVESVKFHNARIEFLVEQLYNYNSRLRTLNGQMLRLAERYK 355

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + RD FL  + G E++  WV       + +  NF   E +SI +IR+E+  I+  TG+++
Sbjct: 356 VPRDSFLNAYLGNEMEEGWVERVFKNRQ-KMGNFTTSEAESIERIRSEVAEIAQVTGMTV 414

Query: 425 SEFRHIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
            E R IV+MV+KG   +  + K E ++     +  + K         L L +    GLMK
Sbjct: 415 KELRRIVTMVQKGRKRSPHSLKPEWLKPICVWLSLLPKNIPIAVCSSLXLFRXAISGLMK 474

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ ++I
Sbjct: 475 AVGKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQILHEI 534

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+
Sbjct: 535 GREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDA 594

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 595 AIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 654

Query: 664 IRKLKHPSRSKKLRSF 679
           +RKLKHPSRS+K+RSF
Sbjct: 655 LRKLKHPSRSRKMRSF 670


>gi|149184445|ref|ZP_01862763.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
 gi|148831765|gb|EDL50198.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
          Length = 668

 Score =  499 bits (1286), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 255/421 (60%), Positives = 320/421 (76%), Gaps = 10/421 (2%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQKDEKSSVKCK---VLKEKLV 322
           +L+ ME  L+P  +     I +++ +   LQ   V   G+ +     K K    L ++L 
Sbjct: 250 SLAQMEAALKPDAIERFARIKDLFGKFEKLQKERVEVLGRGEAFPPAKEKKYEALSDQLT 309

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
             V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ + +KR  FL+ + G ELD  
Sbjct: 310 AEVESVQFHATKIEFLVDNLYAFNRRLTALGGQMLRLAERHKVKRIDFLDAYIGNELDDS 369

Query: 383 WVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           W+     KD    +W  F   E D+I +IR EI  I+  TG+++ EFR IV+MV+KGE E
Sbjct: 370 WMDDRVKKD---KKWAAFAEKEADAIDRIRTEISDIASATGMALPEFRRIVNMVQKGERE 426

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 427 ARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 486

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+VR +R+  +   REPTPEE+A+KL+MP+
Sbjct: 487 TWWIRQAITRSIADQARTIRIPVHMIETINKLVRCSRQFLHDQGREPTPEEMAEKLSMPL 546

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+AIQANL+ET TRVLASL
Sbjct: 547 EKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASL 606

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+K+RSFL
Sbjct: 607 TPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFL 666

Query: 681 D 681
           D
Sbjct: 667 D 667


>gi|73666941|ref|YP_302957.1| RNA polymerase sigma factor rpoD [Ehrlichia canis str. Jake]
 gi|72394082|gb|AAZ68359.1| RNA polymerase, sigma 70 subunit, RpoD [Ehrlichia canis str. Jake]
          Length = 622

 Score =  499 bits (1285), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 288/663 (43%), Positives = 423/663 (63%), Gaps = 66/663 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-- 89
           K ++    ++G+VT  ++N       +S++ +++T++ML + GINV++  D EDE  S  
Sbjct: 12  KTLVSKGLKQGFVTFNDINDVFSDYVLSADNIDETISMLQDSGINVLEQSD-EDEANSIV 70

Query: 90  --------EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                    D  D++     S  F Q         TDDP+RMYL EM S+ELLSREGEI 
Sbjct: 71  EENRIKEDLDEDDVSDGGIKSWDFGQ---------TDDPIRMYLCEMSSVELLSREGEIE 121

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAK+I++ +  M+ SL ESP+  +  + WRD+L +   +LR++IDL+A    E    F  
Sbjct: 122 IAKKIKSEKVNMLRSLVESPVVLRTFMSWRDDLVNEQIMLRDLIDLDANYRYEFPEKFAD 181

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E         S  + ++D + E++ D +    +S+DD             DE N+  +
Sbjct: 182 ADEA--------SVLDYDKDLIDESDEDTD----ISEDD-------------DEENVSIN 216

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEI---AEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                 ++  ME+ L PKV+  LD +   AE   EL+      +N Q  EK   +   L 
Sbjct: 217 -----ASILEMENALLPKVVSILDSVIASAEKILELKKQYQGKIN-QDIEK---QYNDLH 267

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           + + +++  + L+ S +  + +Q+Y +SK I   E +++ LA+SYGI+R  FL+ +    
Sbjct: 268 DSIWEMIYQIKLSNSAVLSITQQIYSLSKSIAAEEAKIISLAESYGIQRKDFLDAYNTNS 327

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +        K     +W N +A E  +I+ + ++IK +S E   +++EF+ +V+ ++K E
Sbjct: 328 V------LQKKGTSPQWNNLLANEESNIVSMYSKIKLLSGEN--NLTEFKALVTKIQKHE 379

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A+ AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFST
Sbjct: 380 RAANQAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFST 439

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WWV+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M +++ REPT EE++ KL +
Sbjct: 440 YATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTLEELSAKLNI 499

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V+ +RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P D+A+ A+LRE TT+VL+
Sbjct: 500 NVDKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADLREITTKVLS 559

Query: 619 SLTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           +LTP+EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR
Sbjct: 560 TLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLR 619

Query: 678 SFL 680
            F 
Sbjct: 620 GFF 622


>gi|68171251|ref|ZP_00544654.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88657966|ref|YP_507558.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
 gi|67999333|gb|EAM85979.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88599423|gb|ABD44892.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 622

 Score =  498 bits (1281), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 290/664 (43%), Positives = 428/664 (64%), Gaps = 68/664 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-- 89
           + ++    ++G+VT  ++N       +SS+ +++T++ML + GINV++  D EDE  S  
Sbjct: 12  RTLVSKGLKQGFVTFNDINDVFSDYVLSSDNIDETISMLQDSGINVLEQSD-EDEANSII 70

Query: 90  -----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                +D +D     S++S+   K  D     TDDP+RMYL EM S+ELLSREGEI IAK
Sbjct: 71  EENRIKDEMD-EDDVSDTSI---KSWDFG--QTDDPIRMYLCEMSSVELLSREGEIEIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +I++ +  M+ SL ESP+  +  + WRD+L +   +LR++IDL+A               
Sbjct: 125 KIKSEKVNMLRSLVESPIVLRTFMSWRDDLVNEQIMLRDLIDLDA--------------- 169

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
            + Y+  E  S   + DD           A V   D+  +D P E+ +     + EDED+
Sbjct: 170 NYRYEFPEKFS---DTDD-----------ASVLGYDKDLMDEPDEDPD-----IPEDEDE 210

Query: 265 SAHTLSA----MEDQLRPKVMCALDEI---AEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
              +++A    ME+ L PKV+  LD +   AE   EL+      +N Q  EK   +   L
Sbjct: 211 ENISINASILEMENALLPKVVSILDSVIASAEKILELKKQYQGKIN-QDIEK---QYNDL 266

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            + + +++  + L+ S +  + +Q+Y +SK I   E +++ LA+SYGI+R  FL+ +   
Sbjct: 267 HDSIWEMIYQIKLSNSAVLSITQQIYSLSKSIAAEEAKIISLAESYGIQRKDFLDAYNTN 326

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            +        K     +W N +  E  +I+ + ++IK +S E   +++EF+ +V+ ++K 
Sbjct: 327 SV------LQKKGTSPQWDNMLLNEESNIVSMYSKIKLLSGEN--NLTEFKALVTKIQKH 378

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A+ AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFS
Sbjct: 379 ERAANQAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFS 438

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WWV+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M +++ REPT EE++ +L 
Sbjct: 439 TYATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTLEELSARLN 498

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ +RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P D+A+ A+LRE TT+VL
Sbjct: 499 INVDKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADLREITTKVL 558

Query: 618 ASLTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++LTP+EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KL
Sbjct: 559 STLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKL 618

Query: 677 RSFL 680
           R F 
Sbjct: 619 RGFF 622


>gi|294085800|ref|YP_003552560.1| sigma-70 factor RpoD [Candidatus Puniceispirillum marinum IMCC1322]
 gi|292665375|gb|ADE40476.1| Sigma 70 (RpoD) [Candidatus Puniceispirillum marinum IMCC1322]
          Length = 674

 Score =  496 bits (1278), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 256/419 (61%), Positives = 316/419 (75%), Gaps = 7/419 (1%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-AVNGQKDE----KSSVKCKVLKEKLV 322
           +L+AMED +R  VM   DEIA V++     QD   V   K E    KS V    LK KL 
Sbjct: 257 SLAAMEDAVRDDVMAMFDEIATVFKAFTKSQDRRLVRMSKGEALVPKSEVAHLELKIKLC 316

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+  +  N  RI+ L EQL+ +++ +   EG L+RLA   GI R   LE    RE+   
Sbjct: 317 ELMEGVIFNTGRIEALSEQLFTLNRHVTGIEGRLMRLAIDSGIPRAQVLEAWSWREVIEG 376

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W     DF    W+       + I +++++I+ +  +  ++I EFR ++  +++G+ EA+
Sbjct: 377 W--PGSDFSTKAWQKLDKNHSEEITELQDKIRLVVDDVSLAIPEFREVIQTIQRGQREAA 434

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 435 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 494

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KL+MP++ 
Sbjct: 495 WIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLSMPIDK 554

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV PLD+AI ANLRETTTRVLASLT 
Sbjct: 555 VRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAIHANLRETTTRVLASLTA 614

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFL+
Sbjct: 615 REERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLE 673


>gi|56416704|ref|YP_153778.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
 gi|56387936|gb|AAV86523.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
          Length = 632

 Score =  493 bits (1269), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 289/655 (44%), Positives = 408/655 (62%), Gaps = 67/655 (10%)

Query: 39  RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           +Q G +T ++++  L  D+V SSE +++T+++L + GI V+       E+  E+  D   
Sbjct: 32  KQGGVITFDDISDALSDDDVVSSESIDETISLLQDSGIGVL-------EQSDEEEADAVV 84

Query: 98  SASNSSVFLQKRKDSADRS---------TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S  N++      KD  D +         TDDP+RMYL EM S+ELLSREGEI IAKRI++
Sbjct: 85  SEENAA------KDEEDEAGMRSLDFGQTDDPIRMYLCEMSSVELLSREGEIEIAKRIKS 138

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
            +  M+ SL E+PL  +  + WRD+L +   +LR++IDL+A      +GG          
Sbjct: 139 EKINMLRSLIEAPLVLRTFMSWRDDLVNQQVMLRDLIDLDA----NYRGGAPRQEFEEGG 194

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           +  E    E    DV    GD                       +DE   DE ED SA  
Sbjct: 195 EYGEQEMAEPGDSDVG---GD---------------------GADDE---DEGEDSSAGN 227

Query: 269 LSA--MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            S   ME  L PKV+  LD   E   ++  ++    +  K +K +     L E + +LV 
Sbjct: 228 ASILEMESALLPKVISILDATIESAEKILEMKKQKRDSGKYDKKAYNA--LHENIWELVS 285

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            + L+   +  + +Q+Y++SK I   E  L+ L +SYG+ R  FLE +    +      +
Sbjct: 286 QMKLSDPAVLSVTQQIYNLSKAIAAEEAALMSLVESYGVDRKSFLEAYNNNTV------F 339

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            +     EWKN +  E  ++  I+N+++ +S E   S   F+ +V+ ++K E  A+ AK+
Sbjct: 340 EQANASPEWKNLLEKEKKTLTDIQNKVRLLSGED--SPGNFKALVAKIQKHERTANKAKQ 397

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WWV+Q
Sbjct: 398 EMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQ 457

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L M VE +RKV
Sbjct: 458 AITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSTRLGMNVEKIRKV 517

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+EER
Sbjct: 518 MKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPKEER 577

Query: 627 VLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 578 ILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 632


>gi|222475070|ref|YP_002563485.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
 gi|255003048|ref|ZP_05278012.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str. Puerto
           Rico]
 gi|255004170|ref|ZP_05278971.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Virginia]
 gi|222419206|gb|ACM49229.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
          Length = 646

 Score =  492 bits (1266), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 289/655 (44%), Positives = 408/655 (62%), Gaps = 67/655 (10%)

Query: 39  RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           +Q G +T ++++  L  D+V SSE +++T+++L + GI V+       E+  E+  D   
Sbjct: 46  KQGGVITFDDISDALSDDDVVSSESIDETISLLQDSGIGVL-------EQSDEEEADAVV 98

Query: 98  SASNSSVFLQKRKDSADRS---------TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S  N++      KD  D +         TDDP+RMYL EM S+ELLSREGEI IAKRI++
Sbjct: 99  SEENAA------KDEEDEAGMRSLDFGQTDDPIRMYLCEMSSVELLSREGEIEIAKRIKS 152

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
            +  M+ SL E+PL  +  + WRD+L +   +LR++IDL+A      +GG          
Sbjct: 153 EKINMLRSLIEAPLVLRTFMSWRDDLVNQQVMLRDLIDLDA----NYRGGAPRQEFEEGG 208

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           +  E    E    DV    GD                       +DE   DE ED SA  
Sbjct: 209 EYGEQEMAEPGDSDVG---GD---------------------GADDE---DEGEDSSAGN 241

Query: 269 LSA--MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            S   ME  L PKV+  LD   E   ++  ++    +  K +K +     L E + +LV 
Sbjct: 242 ASILEMESALLPKVISILDATIESAEKILEMKKQKRDSGKYDKKAYNA--LHENIWELVS 299

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            + L+   +  + +Q+Y++SK I   E  L+ L +SYG+ R  FLE +    +      +
Sbjct: 300 QMKLSDPAVLSVTQQIYNLSKAIAAEEAALMSLVESYGVDRKSFLEAYNNNTV------F 353

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            +     EWKN +  E  ++  I+N+++ +S E   S   F+ +V+ ++K E  A+ AK+
Sbjct: 354 EQANASPEWKNLLEKEKKTLTDIQNKVRLLSGED--SPGNFKALVAKIQKHERTANKAKQ 411

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WWV+Q
Sbjct: 412 EMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQ 471

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L M VE +RKV
Sbjct: 472 AITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSTRLGMNVEKIRKV 531

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+EER
Sbjct: 532 MKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPKEER 591

Query: 627 VLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 592 ILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 646


>gi|23013315|ref|ZP_00053224.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 333

 Score =  488 bits (1256), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 241/333 (72%), Positives = 280/333 (84%), Gaps = 1/333 (0%)

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           +M  EG LLRLA+S  +KR  FL+ + G ELDP+W+       + +WK+F A        
Sbjct: 1   MMMQEGRLLRLAESCRVKRQDFLDAYYGSELDPNWLEQVAQRSK-QWKDFAARHGKDAAD 59

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  I  IS E G+ ISE+R IV  V++GE E+S AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 60  IRATIAEISGEAGLPISEYRRIVQTVQRGERESSRAKKEMIEANLRLVISIAKKYTNRGL 119

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 120 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 179

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KL+MP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 180 INKLVRTSRQMLHEIGREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 239

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKNAV PLD+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 240 GDFIEDKNAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 299

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 300 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 332


>gi|88607510|ref|YP_505167.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
 gi|88598573|gb|ABD44043.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
          Length = 627

 Score =  487 bits (1253), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 286/659 (43%), Positives = 421/659 (63%), Gaps = 58/659 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           + K  +Q G VT ++LN  L  DEV +S+ +++T++ML + GI+V++           D 
Sbjct: 15  ITKGIKQGGIVTFDDLNDALSDDEVVTSDSIDETISMLQDSGISVLE---------QSDV 65

Query: 93  LDLASSASNSSVFLQKRKDSADRS-----TDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            D   + +  SV   +  +++ RS     TDDP+RMYL EM S+ELLSREGEI IAKRI+
Sbjct: 66  DDTDDTVTGESVVKDEEDEASIRSWDFGQTDDPIRMYLCEMSSVELLSREGEIEIAKRIK 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA---CIGPESKGGFFHGTE 204
           + +  M+  + E+PL  +  + WRD+L +   LLR++IDL+A   C  P+   GF  G +
Sbjct: 126 SEKVNMLRCMVEAPLVLRTFMSWRDDLVNQQVLLRDLIDLDANYRCGFPQP--GFGEG-D 182

Query: 205 GHSYQKREDSSQEKERDDV--QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
           G  Y           R DV     +GD++  + +  +     +S   NA           
Sbjct: 183 GEEYGV--------GRGDVVLPPDDGDVDPESSLDDEADEDDESSLGNA----------- 223

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                ++  ME  L PKV+  LD   E   ++  ++    +G + ++++     L + + 
Sbjct: 224 -----SILEMESALLPKVISILDSTIEAAEKILEMKKKKRDGGEYDENAYN--ELHDSIW 276

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           ++V  + L+ S +  + +Q+Y +SK I   E  L+ LA+SYG+ R  FL+ +    +   
Sbjct: 277 EMVSQMKLSDSAVASVTQQIYALSKSIAAEESSLISLAESYGVDRKSFLDAYNNNTI--- 333

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
               AK     EW+N +  E D++L+++N +K +S E       F+ +V+ ++K E  A+
Sbjct: 334 -AEQAK--TSFEWQNLLDKEGDTLLEMQNRVKLLSGED--CPGSFKALVAKIQKHERTAN 388

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA W
Sbjct: 389 RAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATW 448

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WV+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L + VE 
Sbjct: 449 WVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNINVEK 508

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP
Sbjct: 509 IRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTP 568

Query: 623 REERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +EER+LRMRFGIG +  DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 569 KEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 627


>gi|269958878|ref|YP_003328667.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
 gi|269848709|gb|ACZ49353.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
          Length = 649

 Score =  483 bits (1242), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 285/656 (43%), Positives = 411/656 (62%), Gaps = 69/656 (10%)

Query: 39  RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           +Q G +T ++++  L  D+V SSE +++T+++L + GI V+       E+  E+  D A 
Sbjct: 49  KQGGVITFDDISDALSDDDVVSSESIDETISLLQDSGIGVL-------EQSDEEEADAAV 101

Query: 98  SASNSSVFLQKRKDSADRS---------TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S  N++      KD  D S         TDDP+RMYL EM S+ELLSREGEI IAKRI++
Sbjct: 102 SEENAA------KDEEDESGMRSLDFGQTDDPIRMYLCEMSSVELLSREGEIEIAKRIKS 155

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
            +  M+ SL E+P+  +  + WRD+L +   +LR++IDL+A      +GG          
Sbjct: 156 EKVNMLRSLIEAPMVLRTFMSWRDDLVNQQVMLRDLIDLDA----NYRGGAPQQEFEEGE 211

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           +  E    + E  DV     D +   + +    +                         +
Sbjct: 212 EYGEREMADPEDSDVGHEGSDDDDEGEDASVGNA-------------------------S 246

Query: 269 LSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           +  ME  L PKV+  LD   E AE   E++  + ++  G+ DEK+  +   L E + +LV
Sbjct: 247 ILEMESALLPKVISILDATIESAEKILEMKKRKRDS--GKCDEKAYNE---LHENIWELV 301

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             + L+   +  + +Q+Y++SK I   E  L+ L +SYG+ R  FLE +    +      
Sbjct: 302 SQMKLSDPAVLSVTQQIYNLSKAIAAEEVALMSLVESYGVDRKSFLEAYNNNTV------ 355

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
           + +     EWKN +  E  ++  I+N+++ +S E   S   F+ +V+ ++K E  A+ AK
Sbjct: 356 FEQADASPEWKNLLEKEKKTLTDIQNKVRLLSGED--SPGSFKALVAKIQKHERTANKAK 413

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WWV+
Sbjct: 414 QEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVR 473

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L M VE +RK
Sbjct: 474 QAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLGMNVEKIRK 533

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V+KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+EE
Sbjct: 534 VMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPKEE 593

Query: 626 RVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 594 RILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 649


>gi|88810991|ref|ZP_01126247.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88791530|gb|EAR22641.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 609

 Score =  479 bits (1232), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 284/661 (42%), Positives = 397/661 (60%), Gaps = 75/661 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I   +++GY+T  E+N  LP D V  EQ+ED + M+++MGI+V       +     D
Sbjct: 11  RELIARGKEQGYLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGISV------HETAPDSD 64

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTD-------DPVRMYLREMGSIELLSREGEIAIAK 144
           +L L+ +A  +     +   +A  S D       DPVRMY+REMG++ELL+REGEI +AK
Sbjct: 65  TLLLSDAAVATDEDEAEEAAAALASVDAEFGRTTDPVRMYMREMGTVELLTREGEIELAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ +L   P + + L      +  G   L+EI+              F G E
Sbjct: 125 RIEEGLDQVLRALSAYPESARTLCSLHRHVEAGRLRLQEIL------------AGFRGLE 172

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                           D++      ++ +  +  DD                     ED+
Sbjct: 173 ----------------DELDGGADAVDVSVGIDGDD---------------------EDE 195

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-SVKCKVLKEKLVK 323
            + + +A +    P      ++  +++  +R L +  +   ++  S S +C+ L+E++  
Sbjct: 196 ESASNAAADSGPNP------EQAVQLFNRIRELHEALLIALQERGSGSEQCRELREEMGN 249

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
           L  S+ L    ID + E L    +RI   E E+ R+  +  G+ R  F+    GRE DP 
Sbjct: 250 LFLSMKLAPKVIDGMAENLRKAVERIRRAEREVTRICVKQAGMPRKEFITLFPGRETDPS 309

Query: 383 WVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           WV      D P   +   VA     +L+ +  + +I   TG+++SE + I   +  GE +
Sbjct: 310 WVDELIRADKP---YSEAVAERRQMLLEAQVGLAAIQEATGLAVSEVKEINRRMSIGEAK 366

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 367 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 426

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ RT+R+M  ++ REP P+E+A+++ MP 
Sbjct: 427 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRTSRQMLQEMGREPQPDELAERMEMPE 486

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED   +SP+DSA +  L+E+   VLA L
Sbjct: 487 DKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDAAVMSPVDSATREGLKESVREVLAGL 546

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFL
Sbjct: 547 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSESLRSFL 606

Query: 681 D 681
           D
Sbjct: 607 D 607


>gi|254362696|ref|ZP_04978782.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
 gi|153094317|gb|EDN75178.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
          Length = 623

 Score =  476 bits (1225), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 291/654 (44%), Positives = 400/654 (61%), Gaps = 57/654 (8%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSE 90
           I   R++GY+T+ E++  LP + V +EQ+ED + M+++MGI V+    D DDL   E   
Sbjct: 19  ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDADDLLLAENIA 78

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  D+   A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 79  DE-DVVEEATK---VLSTVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEGI 133

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +  ++ E P     L+    ++  G   L +++   A + P                 
Sbjct: 134 NEVQCAIAEYPEALSGLLACYAQVETGEMRLSDLVT--AFVDP----------------- 174

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             +  +E   +D++   G+          D    D P  + EN      EDE+  + + S
Sbjct: 175 --NILEEAPLEDIEAALGE----------DEESSDVPDVDDEN------EDENGDSSSDS 216

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLS 329
           + +  + P++        E +  LRS  +  +   QK  ++S K K   E L  +     
Sbjct: 217 SDDSSIDPELA------REKFEALRSQHEKVLLVIQKHGRTSKKSKEQIEILSHIFREFR 270

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSYAK 388
           L   + DLLV  +  + K++   E ++ R A  Y G+K+  FL+  QG EL   W+  A 
Sbjct: 271 LVPKQFDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQGHELSEAWIEKAI 330

Query: 389 DFPEGEWKNFVACEVDSI-LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           +  +       A  VD+I + I N ++++   +G++I++ R I   +  GE +A  AKKE
Sbjct: 331 NAKKNAAPKL-ANYVDNIRVNIAN-LQNLEQTSGLTIAQIREIGGRISNGELKARRAKKE 388

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 389 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 448

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVL
Sbjct: 449 ITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVL 508

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +V
Sbjct: 509 KIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEVLEGLTPREAKV 568

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 569 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|332288976|ref|YP_004419828.1| RNA polymerase sigma factor RpoD [Gallibacterium anatis UMN179]
 gi|330431872|gb|AEC16931.1| RNA polymerase sigma factor RpoD [Gallibacterium anatis UMN179]
          Length = 624

 Score =  473 bits (1218), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 292/662 (44%), Positives = 400/662 (60%), Gaps = 60/662 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---- 83
           K++I   +++GY+T  E+N  LP D V ++Q+ED + M+++MGI V+    D DDL    
Sbjct: 10  KQLIAQGKEQGYLTYAEVNDSLPEDLVDADQIEDIIQMINDMGIQVLESAPDADDLMLNE 69

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              DE+  E++  + SS            +S    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 70  NVTDEDAVEEATQVLSSV-----------ESEIGRTTDPVRMYMREMGSVELLTREGEID 118

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +  ++ E P     L+   D +  G   L ++I     + P +      
Sbjct: 119 IAKRIEEGINEVQCAVAEYPQALDHLLAQYDLVEKGEVRLSDLIT--GFVDPNAVD---- 172

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
            TE +S    +DS + ++ D++   + D     + S  + +       +A+ND  N   D
Sbjct: 173 -TEDYSKFMSDDSGEGEDDDNISSDDLDESDDDEDSDSESNN------SADNDSDN-SID 224

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
            + +    SA+++Q   K + A+D+                 G K  K  +        L
Sbjct: 225 PEMAREKFSALKEQ-HHKTVAAIDKYG--------------RGNKKAKDQINA------L 263

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELD 380
            ++     L   + D+LV  + D+ KRI   E ++ RLA  Y  + +  F +   G E +
Sbjct: 264 SEIFQQFRLVPKQFDILVLSMRDMMKRIRTQERQIQRLAVEYAKMPKGTFQKAFIGHETN 323

Query: 381 PHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
             W+  A     G+ W   +    D I +    +K I  E+G++I++ R I   + +GE 
Sbjct: 324 DAWIEKA--LAAGKNWSEKLKDYEDGIRQAIALLKVIEQESGLTITQIRQIGEKISQGEL 381

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 382 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 441

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP
Sbjct: 442 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMP 501

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 502 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLKVATHEVLEG 561

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 562 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 621

Query: 680 LD 681
           LD
Sbjct: 622 LD 623


>gi|322513554|ref|ZP_08066654.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinobacillus
           ureae ATCC 25976]
 gi|322120625|gb|EFX92519.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinobacillus
           ureae ATCC 25976]
          Length = 618

 Score =  473 bits (1218), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 286/656 (43%), Positives = 402/656 (61%), Gaps = 62/656 (9%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE      L 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDE------LM 68

Query: 95  LASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           LA + ++  V  +  K     +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  LAENIADEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              +  ++ E P     LI +  ++ +GT  L +++   A + P                
Sbjct: 129 INEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDP---------------- 170

Query: 210 KREDSSQEKERDDVQET--EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
              ++ +E   +D++    + D E+ A V  +   +      +  +D             
Sbjct: 171 ---NAQEEATVEDLEAVLDDEDAEAVADVDDESEEEGSDSSADTGDD------------- 214

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             ++++ +L  +   AL E  E     ++LQ    +G+  +KS  + + L +    +   
Sbjct: 215 --NSIDPELAREKFYALREQHE-----KALQAIQKHGRGHKKSREQIQALSD----IFRE 263

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L   + DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  
Sbjct: 264 FRLVPKQFDLLVESMQKMMKQVRAEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEK 323

Query: 387 AKDFPEGEWKNFVACEVDSI-LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
           A +  +G      A  VD I + I N ++ +   TG+++++ R I   +  GE +A  AK
Sbjct: 324 AINAKKGAAPKL-ANYVDQIRVNIAN-LQRMEQSTGLTVAQIREIGGRIANGELKARRAK 381

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 382 KEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 441

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RK
Sbjct: 442 QAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRK 501

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPREE
Sbjct: 502 VLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRIATNEVLEGLTPREE 561

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 617


>gi|167855425|ref|ZP_02478190.1| RNA polymerase sigma factor 70 [Haemophilus parasuis 29755]
 gi|219871370|ref|YP_002475745.1| RNA polymerase sigma factor RpoD [Haemophilus parasuis SH0165]
 gi|167853419|gb|EDS24668.1| RNA polymerase sigma factor 70 [Haemophilus parasuis 29755]
 gi|219691574|gb|ACL32797.1| RNA polymerase sigma factor RpoD [Haemophilus parasuis SH0165]
          Length = 621

 Score =  472 bits (1215), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 290/661 (43%), Positives = 402/661 (60%), Gaps = 70/661 (10%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL------ 83
           +I   R++GY+TI E++  LP + V ++Q+ED + M+++MGI V+    D DDL      
Sbjct: 17  LIAQGREQGYLTISEVHDHLPEELVDADQIEDIIQMINDMGIKVLETAPDADDLMLAGNI 76

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            DE+  E++  + S+            +S    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 77  ADEDVVEEATKVLSTV-----------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 125

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +   + E P     LI   D++ +GT  L +++   A + P +        
Sbjct: 126 KRIEEGINEVQCVIAEYPEALSELIARYDQVEEGTVRLSDLVT--AFVDPNA-------- 175

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                              V+ T  D   A    + +   V    + +E+ E + D  +D
Sbjct: 176 -------------------VESTPVDDLDADLDEESESDTVADIDDESEDGESSGDGGDD 216

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +S      ++ +L  +    L E     +  ++LQ    +G+  ++S  + + L +    
Sbjct: 217 NS------IDPELAREKFTLLKE-----QHQKALQAIQKHGRTSKRSRDQIQALSD---- 261

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPH 382
           +     L   + DLLVE +  + K++   E ++ R A  Y G+K+  F++  QG EL   
Sbjct: 262 IFREFRLVPKQFDLLVETMQKMMKQVRAEERQIQRYAVEYAGMKKTDFIKVFQGNELSEA 321

Query: 383 WVSYAKDFPEGEWKNFVACEVDSI-LKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           W+  A +  +G      A  VD+I + I N ++ +   TG++I++ R I   +  GE +A
Sbjct: 322 WIDKAINAKKGGVPKL-ANYVDNIRVNIAN-LQKLEETTGLTITQIREIGGRIADGELKA 379

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 380 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 439

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+K+ MP +
Sbjct: 440 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAEKMGMPED 499

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASL 620
            +RKVLKI KEPIS+ETP+GD+D SHLGDFIED +   PLDSA   +LR  T  VL   L
Sbjct: 500 KIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDSSLELPLDSATAESLRIATNAVLEEGL 559

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 560 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFL 619

Query: 681 D 681
           D
Sbjct: 620 D 620


>gi|258545971|ref|ZP_05706205.1| DNA-directed RNA polymerase, sigmasubunit [Cardiobacterium hominis
           ATCC 15826]
 gi|258518776|gb|EEV87635.1| DNA-directed RNA polymerase, sigmasubunit [Cardiobacterium hominis
           ATCC 15826]
          Length = 617

 Score =  470 bits (1209), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 288/676 (42%), Positives = 419/676 (61%), Gaps = 66/676 (9%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           SD E E  +    +D  D+  K+++   R++G++T EE++  LP   +  ++ ++ +A++
Sbjct: 2   SDFEQEPEE----YDVQDEV-KELLARGREQGFLTYEEIHEALPEHALEGDKYDEMIALI 56

Query: 71  SNMGINVVDGDDLEDEEG----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
             MGI+VV+      E+G    ++D  ++ S+A+ +   + +        T DPVRMY+R
Sbjct: 57  VEMGIDVVES---AQEDGGVIATDDEEEVPSAAALNEAEIGR--------TTDPVRMYMR 105

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG+++LL+REGEIAIAKRIEAG   +  +L E P    AL+    ++  G   L ++++
Sbjct: 106 EMGAVDLLTREGEIAIAKRIEAGLNTVQQTLAEFPFAVSALLEEFAKIEAGEGRLSDLVN 165

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                      G+     G  Y  +E+ +  +  DD +++E  I SA    +DD S   +
Sbjct: 166 -----------GY-----GDPYANKEEETLLESSDD-EDSETLI-SAGDDDEDDDSA--A 205

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
           P E A N++  L E ++   H L+A    +  K+M AL+            +  +++ +K
Sbjct: 206 PLEEAPNNQDALLEAKE-KLHELAA----IHKKLMTALN------------KGKSLDDKK 248

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGI 365
           ++K       L  ++ + + + S  Q  IDL+  QL   ++ I   E  L+RL  +  G+
Sbjct: 249 NQK-------LHGEIKEYIAAFSFPQKTIDLMEAQLNVAAEEIRDIERRLMRLVIERAGM 301

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R +F++   G E +P W+   +     ++   +   +  I   + +   I     +SI 
Sbjct: 302 PRKLFIQEFPGNETNPDWI-VGQSKQRRKYAEKLKGMITEIQVEQEKYLEIEKRYHMSIL 360

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I   +  G+ +A  AK+EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 361 QLKEIQKRLSMGKNQAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 420

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R +  K  R
Sbjct: 421 DKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRTLVQKNGR 480

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+ + MP E +RKVLKI KEPIS+ETPIGD++ SHLGDFIED N +SPL++A 
Sbjct: 481 EPTPEELAEAMDMPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNVMSPLEAAT 540

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L E T  VLASLTPREERVLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 541 TRGLSEATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALR 600

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HP+RS+ L+SFL+
Sbjct: 601 KLRHPNRSELLKSFLN 616


>gi|33151868|ref|NP_873221.1| RNA polymerase sigma factor RpoD [Haemophilus ducreyi 35000HP]
 gi|33148089|gb|AAP95610.1| RNA polymerase sigma factor [Haemophilus ducreyi 35000HP]
          Length = 613

 Score =  469 bits (1207), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 291/658 (44%), Positives = 398/658 (60%), Gaps = 65/658 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE      L
Sbjct: 10  LIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDE------L 63

Query: 94  DLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            LA + ++  V  +  K     +S    T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 64  MLAENIADEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEE 123

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   +  ++ E P     LI +  ++ +GT  L +++   A + P  +            
Sbjct: 124 GINEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPNIQA----------- 170

Query: 209 QKREDSSQEKERDDVQETEGDI-ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                       +DV E + D+ E A+ V  D   + +    +   D  N D++  D   
Sbjct: 171 -----------EEDVVELDSDLDEEASDVVADVDDENEDEESDGSAD--NTDDNSIDP-- 215

Query: 268 TLSAMEDQLRPKVMCALDEIA-EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLV 325
                             E+A E +  LR   + A+   QK  +S  K K   + L  + 
Sbjct: 216 ------------------ELAREKFYALREQHEKALQAIQKHGRSHKKSKQHIQALSDIF 257

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV 384
               L   + DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+
Sbjct: 258 REFRLVPKQFDLLVESMQRMMKQVRAEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWI 317

Query: 385 SYAKDFPEGEWKNFVACEVDSI-LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             A +  +G      A  V+ I + I N ++ +  +T +++++ R I   +  GE +A  
Sbjct: 318 DKAINARKGAAPKL-ANYVEQIRINISN-LQRMEQDTDLTVAQIREIGGRIASGELKARR 375

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKI 495

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD+D SHLGDFI+D+N   PLDSA   +LR  T  VL  LTPR
Sbjct: 496 RKVLKIAKEPISMETPIGDDD-SHLGDFIQDENLELPLDSATAESLRLATNEVLEGLTPR 554

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 612


>gi|297180868|gb|ADI17073.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured alpha proteobacterium HF0010_30A23]
          Length = 668

 Score =  468 bits (1204), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 244/419 (58%), Positives = 310/419 (73%), Gaps = 6/419 (1%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEK----LV 322
           +LSAME  LR  VM ALD IA  Y  L  +Q D     Q  E      +   E+    ++
Sbjct: 250 SLSAMEGILREDVMEALDVIAGAYGGLHKVQKDRMTLLQTGEDVPEDIEAAYEEGRDTVI 309

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           + +  + LN + ID LV+Q+  I+K I+ +E +L++L+    I RD F++ +   E+DP 
Sbjct: 310 RAMKLIRLNNNLIDQLVDQMKSINKAIIGHEIKLMKLSDRCKIPRDEFIDEYFENEIDPS 369

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+    +  +  WK           +IR +I  I  +  + +SEF+ IV  V+KGE +++
Sbjct: 370 WLERMAE-ADASWKMLYERYGSMAKEIREDIADIIHQVDLPVSEFKRIVEKVQKGERDSN 428

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 429 RAKAEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 488

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I RE TPEE+A +L MP+E 
Sbjct: 489 WIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREATPEELAARLGMPLEK 548

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKV+KI KEPISLETPIGDE+ SHLGDFI+D+NA+ P+++AI  NLRE+TTRVL+SLTP
Sbjct: 549 VRKVMKIAKEPISLETPIGDEEDSHLGDFIKDENAIIPVEAAINNNLRESTTRVLSSLTP 608

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 609 REERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 667


>gi|270158971|ref|ZP_06187627.1| RNA polymerase sigma factor RpoD [Legionella longbeachae D-4968]
 gi|289166186|ref|YP_003456324.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella longbeachae
           NSW150]
 gi|269987310|gb|EEZ93565.1| RNA polymerase sigma factor RpoD [Legionella longbeachae D-4968]
 gi|288859359|emb|CBJ13295.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella longbeachae
           NSW150]
          Length = 622

 Score =  468 bits (1203), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 286/661 (43%), Positives = 391/661 (59%), Gaps = 67/661 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    +DE     +
Sbjct: 15  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLN 73

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 74  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   +  N     L EII    D+E  I P S  G          
Sbjct: 133 VLKSLAHYPETVQLVLDDYERFNAQEIRLNEIISGFADVEDEIAPASSIGSML------- 185

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAH 267
               D  Q++E + +   E D +    + + D    D P PE A+               
Sbjct: 186 ----DEDQQQEEEILLSDEEDEDGEGGMVEVD----DGPNPEQAK--------------- 222

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                 D LR     A+  + E             +G+   K++   +++ E  +KL   
Sbjct: 223 ---IYFDDLRETYEAAIVALKE-------------HGRTHAKTTKALEIMSESFLKL--- 263

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS- 385
             L   ++D L      +   I  +E  ++RL  +   I R +F++   G+E D  W++ 
Sbjct: 264 -KLTSRQVDRLTRHFRQLRNHIREHERGIMRLCIEKARIPRKLFIDTFPGQETDLEWLNT 322

Query: 386 ----YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
               Y+K        N +    + IL+I++ + +  +E G+SISE + I   +  GE +A
Sbjct: 323 IIAKYSKKLD----MNRIQENTEEILRIQSRLVAFELEYGLSISEIKEINRKMSIGEAKA 378

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  +
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSED 498

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LT
Sbjct: 499 KIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLT 558

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+
Sbjct: 559 PREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLE 618

Query: 682 G 682
           G
Sbjct: 619 G 619


>gi|71899844|ref|ZP_00681993.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
 gi|71730361|gb|EAO32443.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
          Length = 623

 Score =  468 bits (1203), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 282/655 (43%), Positives = 397/655 (60%), Gaps = 56/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + L   E
Sbjct: 18  KQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLNE 77

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 78  GNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 137

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL+ + L+   +   +G   L E++            GF        
Sbjct: 138 EGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVV-----------VGF-------- 178

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                        +D+ E +  + SA  V+ +   +VD      E D+ ++  DED    
Sbjct: 179 -------------NDLIEEDNSVTSAVDVTDESIVEVD------EEDDDSVGNDED---- 215

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             + M      +V   ++ ++  Y + + L   A +G  + K+ +K +   E +  +  +
Sbjct: 216 --APMIGPDPAEVASRIESLSTEYAKFKKLY--AKHG-PEHKAVIKVR---EDVAAIFVT 267

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L+    DLLV+QL +    +  +E ++L LA +   + R  F+   +  + +  WV  
Sbjct: 268 FKLSLPLTDLLVQQLQNTVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNLEWVED 327

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    + +W + +    D I   +     +     +++++ + I  M+  GE +AS AKK
Sbjct: 328 AIKRKQ-KWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMMVYGEAKASKAKK 386

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA WW++Q
Sbjct: 387 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYATWWIRQ 446

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV
Sbjct: 447 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKV 506

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +
Sbjct: 507 MKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAK 566

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 567 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 621


>gi|254447663|ref|ZP_05061129.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium
           HTCC5015]
 gi|198263006|gb|EDY87285.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium
           HTCC5015]
          Length = 602

 Score =  468 bits (1203), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 284/666 (42%), Positives = 397/666 (59%), Gaps = 102/666 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------------ 79
           K +I   +++GY+T  E+N  LP + V  EQ+ED + M+++MGI V++            
Sbjct: 22  KLLIAKGKEQGYLTFAEVNDHLPNEIVDPEQVEDIIQMINDMGIKVLESAPDAEELLMME 81

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           GD   DE+  E    +A+ A+N S F +         T DPVRMY+REMG++ELL+REGE
Sbjct: 82  GDTSNDEDADEA---VANLANNDSDFGR---------TTDPVRMYMREMGTVELLTREGE 129

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I IAKRIE G   ++ +L   P    AL     E  DG      II+ E  I  +  GGF
Sbjct: 130 IEIAKRIEDGLRQVVTALSTYPHAVNALF----ETYDG------IIEREGRI-TDLIGGF 178

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                            + + D+VQ                       P   +N++   +
Sbjct: 179 I----------------DPDDDEVQN----------------------PNAPKNEDEEAE 200

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           ED       ++   +Q+R +   A  +   +Y             Q++ K+S       E
Sbjct: 201 EDTGPDLEEVAKHINQMRKQYEKATKKKDGIY-------------QREAKAS-------E 240

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL +L   L L+ + I+  ++ + D+  R+   E +++ +     G+ R  F++     E
Sbjct: 241 KLSELFMQLKLDNNFINREIQLVRDVVGRVRQLERDVMTICVHRCGMPRKTFIDSFPENE 300

Query: 379 LDPHWV---SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
            +P+WV   S +K F E      +A   + + +++  +  I  E+G+SIS+ + I   + 
Sbjct: 301 TNPNWVKDHSKSKKFGEK-----IAAHANDLNELQQHLIRIEQESGLSISDLKEINRKMS 355

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G+ +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 356 IGQAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 415

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A++
Sbjct: 416 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAER 475

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + VRKVLKI KEPIS+ETP+GD++ S LGDF++D NA SP+++A+   L E+T  
Sbjct: 476 MEMPEDKVRKVLKIAKEPISMETPVGDDEDSSLGDFLQDVNAESPIEAAVGEGLSESTRD 535

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +LA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  
Sbjct: 536 ILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDS 595

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 596 LRSFLD 601


>gi|71274854|ref|ZP_00651142.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Dixon]
 gi|71902125|ref|ZP_00684157.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
 gi|170729898|ref|YP_001775331.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa M12]
 gi|71164586|gb|EAO14300.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Dixon]
 gi|71728114|gb|EAO30313.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
 gi|167964691|gb|ACA11701.1| RNA polymerase sigma-70 factor [Xylella fastidiosa M12]
          Length = 623

 Score =  466 bits (1200), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 281/655 (42%), Positives = 398/655 (60%), Gaps = 56/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + L   E
Sbjct: 18  KQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLNE 77

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 78  GNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 137

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL+ + L+   +   +G   L E++            GF        
Sbjct: 138 EGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVV-----------VGF-------- 178

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                        +D+ E +  + S+  V+ +   +VD      E D+ ++  DED    
Sbjct: 179 -------------NDLIEDDNSVTSSVDVTDESIVEVD------EEDDDSVGNDED---- 215

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             + M      +V   ++ ++  Y + + L   A +G  + K+ +K +   E +  +  +
Sbjct: 216 --APMIGPDPAEVASRIESLSTEYAKFKKLY--AKHG-PEHKAVIKVR---EDMAAIFVT 267

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + +  WV  
Sbjct: 268 FKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNLEWVED 327

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    + +W + +    D I   +     +     +++++ + I  M+  GE +AS AKK
Sbjct: 328 AIKRKQ-KWSSALRDIKDQITAEQQSSIDLEKVNSLTLADIKEINRMMVYGEAKASKAKK 386

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA WW++Q
Sbjct: 387 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYATWWIRQ 446

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV
Sbjct: 447 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKV 506

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +
Sbjct: 507 MKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAK 566

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 567 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 621


>gi|32130003|sp|Q87DT7|RPOD_XYLFT RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|307579626|gb|ADN63595.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 618

 Score =  466 bits (1200), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 281/655 (42%), Positives = 398/655 (60%), Gaps = 56/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + L   E
Sbjct: 13  KQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLNE 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL+ + L+   +   +G   L E++            GF        
Sbjct: 133 EGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVV-----------VGF-------- 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                        +D+ E +  + S+  V+ +   +VD      E D+ ++  DED    
Sbjct: 174 -------------NDLIEEDNSVTSSVDVTDESIVEVD------EEDDDSVGNDED---- 210

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             + M      +V   ++ ++  Y + + L   A +G  + K+ +K +   E +  +  +
Sbjct: 211 --APMIGPDPAEVASRIESLSTEYAKFKKLY--AKHG-PEHKAVIKVR---EDVAAIFVT 262

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + +  WV  
Sbjct: 263 FKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNLEWVED 322

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    + +W + +    D I   +     +     +++++ + I  M+  GE +AS AKK
Sbjct: 323 AIKRKQ-KWSSALRDIKDQITAEQQASIDLEKVNSLTLADIKEINRMMVYGEAKASKAKK 381

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA WW++Q
Sbjct: 382 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYATWWIRQ 441

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV
Sbjct: 442 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKV 501

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +
Sbjct: 502 MKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAK 561

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 562 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|15837951|ref|NP_298639.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa 9a5c]
 gi|20140311|sp|Q9PDM9|RPOD_XYLFA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|9106350|gb|AAF84159.1|AE003967_3 RNA polymerase sigma-70 factor [Xylella fastidiosa 9a5c]
          Length = 618

 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 282/655 (43%), Positives = 399/655 (60%), Gaps = 56/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + L   E
Sbjct: 13  KQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLNE 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL+ + L+   +   +G   L E++            GF        
Sbjct: 133 EGLSEVQAALGVFPLSTELLLSEYELHKEGKRRLTEVV-----------VGF-------- 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                        +D+ E +  + S+  V+ +   +VD      E D+ ++  DED  A 
Sbjct: 174 -------------NDLIEEDNSVTSSVDVTDESIVEVD------EEDDDSVGNDED--AP 212

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+         +V   ++ ++  Y + + L   A +G  + K+ +K +   E +  +  +
Sbjct: 213 TIGPDP----AEVASRIESLSTEYAKFKKLY--AKHG-PEHKAVIKVR---EDVAAIFVT 262

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + +  WV  
Sbjct: 263 FKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNLEWVED 322

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    + +W + +    D I   +     +     +++++ + I  M+  GE +AS AKK
Sbjct: 323 AIKRKQ-KWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMMVYGEAKASKAKK 381

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA WW++Q
Sbjct: 382 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYATWWIRQ 441

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV
Sbjct: 442 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKV 501

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +
Sbjct: 502 MKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAK 561

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 562 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|28198503|ref|NP_778817.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa Temecula1]
 gi|182681181|ref|YP_001829341.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa M23]
 gi|28056587|gb|AAO28466.1| RNA polymerase sigma-70 factor [Xylella fastidiosa Temecula1]
 gi|182631291|gb|ACB92067.1| RNA polymerase, sigma 70 subunit, RpoD [Xylella fastidiosa M23]
          Length = 623

 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 281/655 (42%), Positives = 398/655 (60%), Gaps = 56/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + L   E
Sbjct: 18  KQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLNE 77

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 78  GNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 137

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL+ + L+   +   +G   L E++            GF        
Sbjct: 138 EGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVV-----------VGF-------- 178

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                        +D+ E +  + S+  V+ +   +VD      E D+ ++  DED    
Sbjct: 179 -------------NDLIEEDNSVTSSVDVTDESIVEVD------EEDDDSVGNDED---- 215

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             + M      +V   ++ ++  Y + + L   A +G  + K+ +K +   E +  +  +
Sbjct: 216 --APMIGPDPAEVASRIESLSTEYAKFKKLY--AKHG-PEHKAVIKVR---EDVAAIFVT 267

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + +  WV  
Sbjct: 268 FKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNLEWVED 327

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    + +W + +    D I   +     +     +++++ + I  M+  GE +AS AKK
Sbjct: 328 AIKRKQ-KWSSALRDIKDQITAEQQASIDLEKVNSLTLADIKEINRMMVYGEAKASKAKK 386

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA WW++Q
Sbjct: 387 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYATWWIRQ 446

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV
Sbjct: 447 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKV 506

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +
Sbjct: 507 MKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAK 566

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 567 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 621


>gi|238897855|ref|YP_002923534.1| RNA polymerase, sigma 70 (sigma D) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229465612|gb|ACQ67386.1| RNA polymerase, sigma 70 (sigma D) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 610

 Score =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 291/658 (44%), Positives = 387/658 (58%), Gaps = 66/658 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLIARGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEQAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + ++ D A  A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTGETHDDAVEAATQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +  G   L ++I+    + P  +     G   H 
Sbjct: 127 EGIHQVQCSVAEYPEAITYLLEQYDRVELGALRLSDLIN--GFVDPNIQENVLPGA-IHV 183

Query: 208 YQKREDSSQEKERD-DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  D+  + E D D  E E D            + +D  PE A+              
Sbjct: 184 GSELSDAEIDDEEDSDTSEVEDD------------NSID--PELAQQ------------- 216

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                              E+   Y   R+    A+  +     +   ++LK  L ++  
Sbjct: 217 ----------------KFSELRAQYESTRT----AIKQKGRHHLTTATEILK--LAEIFK 254

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV- 384
             SL   + D LV  +  +  R+   E  +L+L  +   + +  F+E     E +  W+ 
Sbjct: 255 QFSLVPKQFDYLVSSMRSMMDRVRVQERLILKLCVEQCKMPKKNFIELFLNNETNNSWLK 314

Query: 385 -SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            + A   P  E  N V  +V S ++   +++ I  ETG+SI + + I   +  GE +A  
Sbjct: 315 TALAMKKPWVEKLNDVLEDVQSNVQ---KLRQIEEETGLSIEQVKDINRRMAIGEAKARR 371

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP E +
Sbjct: 432 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPAPEELAERMLMPEEKI 491

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VLA LT R
Sbjct: 492 RKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRLATNDVLAGLTAR 551

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD
Sbjct: 552 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLKSFLD 609


>gi|23008120|ref|ZP_00049697.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 307

 Score =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 222/301 (73%), Positives = 260/301 (86%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           P+W++         WKNFV      +  +R +I +++ ETG+ I E+R IV+MV+KGE E
Sbjct: 6   PNWMTRVATLGGKGWKNFVERGGRQVADLREQILTLASETGLQIGEYRKIVAMVQKGERE 65

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 66  ARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 125

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+
Sbjct: 126 TWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPL 185

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASL
Sbjct: 186 EKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASL 245

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFL
Sbjct: 246 TPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 305

Query: 681 D 681
           D
Sbjct: 306 D 306


>gi|300112780|ref|YP_003759355.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299538717|gb|ADJ27034.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii
           C-113]
          Length = 602

 Score =  462 bits (1188), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 278/651 (42%), Positives = 385/651 (59%), Gaps = 68/651 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   + RGY++  E+N  LP + +  EQ+ED + M ++MGI+V +     D     D
Sbjct: 14  KLLIARGKDRGYLSYSEVNDHLPEEVIDPEQIEDIITMFNDMGISVHEDMAEADALAIMD 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +      A+  +       D     T DPVRMY+REMGS+ELL+REGEI+IAKRIE G  
Sbjct: 74  TAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAKRIEEGMR 133

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +  +L   P +   L+   +++  G   L ++I            GF            
Sbjct: 134 QVYTALSRFPGSVAELLRQYEKVEVGEIRLVDVI-----------SGF------------ 170

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
               QE E  D++E+  + E +                   + E N +E+ D+       
Sbjct: 171 ----QESEEADLKESAAEEEVSV------------------SSEGNAEEENDNG------ 202

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                       LD + E + +LR L +        + +    + L E  ++L     L+
Sbjct: 203 ----------LDLDRVQEYFAQLRKLYERC-QAADHKGNDGALEELSEYFLQLKLMPRLS 251

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
           Q     L+E L  +   I   E  ++++A  S  + R  FL   Q +E + +WV      
Sbjct: 252 QR----LIENLRRVVAEIRVLERSIMKIAVNSAQMPRKDFLSSFQKQETNLNWVE-KHIR 306

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +  + + +  + D+I K + ++ ++    G+SI++ + I   +  GE  A  AKKEMVE
Sbjct: 307 AKKHYSSVLRKQGDAIQKAQEKLIALEQRAGMSITQIKEINRSLSIGEARARRAKKEMVE 366

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 367 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 426

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP+E+A+++ MP + VRKVLKI 
Sbjct: 427 SIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAERVEMPKDKVRKVLKIA 486

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +EPIS+ETPIGD++ SHLGDF+ED   +SP DSAI + LRETT  +LA LTPRE +VLRM
Sbjct: 487 REPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQLILAGLTPREAKVLRM 546

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 547 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 597


>gi|213018850|ref|ZP_03334658.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995801|gb|EEB56441.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 632

 Score =  462 bits (1188), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 278/665 (41%), Positives = 410/665 (61%), Gaps = 68/665 (10%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED-- 91
           + K  R+ G++T +++N  L  +  S++ ++DT+A+L + GIN+++  + E+E  S +  
Sbjct: 18  VTKSIRKGGFITFDDINDKLSDENFSTDFIDDTIALLQDSGINILESSEDEEEAPSNNDG 77

Query: 92  -SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             LD   ++ N++  L +         DDPVR+YL++M S++LLSR  EI IAK+IE+ +
Sbjct: 78  NKLDDDETSLNTTTTLVQ--------NDDPVRIYLQDMSSVKLLSRADEIKIAKKIESEK 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             M+ ++ E+ + F+ +  WRD+L+ GT LLREII+L+A    +     F+  +      
Sbjct: 130 HNMLRAIIETSVAFKIIKTWRDDLSGGTFLLREIINLDAIYNSD-----FNMVD------ 178

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                +E E +DV++   D E                     NDE+  +E ED S+  L+
Sbjct: 179 ----KEESEAEDVRDCVNDEEKG-------------------NDEKG-NESEDISSANLN 214

Query: 271 A----MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                ME  L PKV+ ALDEI  +  E   L+ N+    KD   S + + L  ++  +  
Sbjct: 215 ISVLEMESDLLPKVITALDEIIALTNEALVLKKNS----KD--FSNELENLYNQIWSVAL 268

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR--------DVFLERHQGRE 378
            +  + + I  + ++LY+I++ I   E  L+  A+ Y I R        DV LE H+  E
Sbjct: 269 QIQFSDAAITRITQKLYEINRLITFEEANLITEARKYDIDRESFYNVYDDVLLE-HEFSE 327

Query: 379 LDPHWVSYAKDFPEGEWKN-FVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRK 436
           +    ++  +    GE KN F+    DS   I + + +I S   G  + EF+ ++  ++K
Sbjct: 328 ISFLKINENQSLFTGELKNKFLRFINDSYEYIASALSNIKSYVQGDRVQEFKKVIKRIQK 387

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKF
Sbjct: 388 HEQEVSQAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKF 447

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STY  WWVKQ+ITR+I +QS  +RIPVHM + I K+ +  R+M++++ REPT EE++ +L
Sbjct: 448 STYGTWWVKQSITRAIPEQSKVVRIPVHMVEIISKINKALRKMTHEMGREPTLEELSIEL 507

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           AMP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT V
Sbjct: 508 AMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSKPEDAAILADLRGITTNV 567

Query: 617 LASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           LA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR+KK
Sbjct: 568 LATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRAKK 627

Query: 676 LRSFL 680
           LR F 
Sbjct: 628 LRGFF 632


>gi|190571452|ref|YP_001975810.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357724|emb|CAQ55173.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 633

 Score =  462 bits (1188), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 278/663 (41%), Positives = 409/663 (61%), Gaps = 68/663 (10%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED---S 92
           K  R+ G++T +++N  L  +  S++ ++DT+A+L + GIN+++  + E+E  S +    
Sbjct: 21  KSIRKGGFITFDDINDKLSDENFSTDFIDDTIALLQDSGINILESSEDEEEAPSNNDGNK 80

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           LD   ++ N++  L +         DDPVR+YL++M S++LLSR  EI IAK+IE+ +  
Sbjct: 81  LDDDETSLNTTTTLVQ--------NDDPVRIYLQDMSSVKLLSRADEIKIAKKIESEKHN 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           M+ ++ E+ + F+ +  WRD+L+ GT LLREII+L+A    +     F+  +        
Sbjct: 133 MLRAIIETSVAFKIIKTWRDDLSGGTFLLREIINLDAIYNSD-----FNMVD-------- 179

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA- 271
              +E E +DV++   D E                     NDE+  +E ED S+  L+  
Sbjct: 180 --KEESEAEDVRDCVNDEEKG-------------------NDEKG-NESEDISSANLNIS 217

Query: 272 ---MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
              ME  L PKV+ ALDEI  +  E   L+ N+    KD   S + + L  ++  +   +
Sbjct: 218 VLEMESDLLPKVITALDEIIALTNEALVLKKNS----KD--FSNELENLYNQIWSVALQI 271

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR--------DVFLERHQGRELD 380
             + + I  + ++LY+I++ I   E  L+  A+ Y I R        DV LE H+  E+ 
Sbjct: 272 QFSDAAITRITQKLYEINRLITFEEANLITEARKYDIDRESFYNVYDDVLLE-HEFSEIS 330

Query: 381 PHWVSYAKDFPEGEWKN-FVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGE 438
              ++  +    GE KN F+    DS   I + + +I S   G  + EF+ ++  ++K E
Sbjct: 331 FLKINENQSLFTGELKNKFLRFINDSYEYIASALSNIKSYVQGDRVQEFKKVIKRIQKHE 390

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKFST
Sbjct: 391 QEVSQAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFST 450

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y  WWVKQ+ITR+I +QS  +RIPVHM + I K+ +  R+M++++ REPT EE++ +LAM
Sbjct: 451 YGTWWVKQSITRAIPEQSKVVRIPVHMVEIISKINKALRKMTHEMGREPTLEELSIELAM 510

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT VLA
Sbjct: 511 PLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSKPEDAAILADLRGITTNVLA 570

Query: 619 SLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           +LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR+KKLR
Sbjct: 571 TLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRAKKLR 630

Query: 678 SFL 680
            F 
Sbjct: 631 GFF 633


>gi|256823391|ref|YP_003147354.1| RNA polymerase sigma-70 subunit RpoD [Kangiella koreensis DSM
           16069]
 gi|256796930|gb|ACV27586.1| RNA polymerase, sigma 70 subunit, RpoD [Kangiella koreensis DSM
           16069]
          Length = 616

 Score =  461 bits (1187), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 286/667 (42%), Positives = 397/667 (59%), Gaps = 63/667 (9%)

Query: 26  FSDDSWKKMIKL----ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--- 78
            S++S +  +KL     +++GY+T  E+N  LPPD V  EQ+ED + M+++MGI V    
Sbjct: 1   MSENSQQSQLKLLIARGKEQGYLTYAEVNDHLPPDIVDPEQIEDIIRMINDMGIQVYETT 60

Query: 79  -DGDDL--EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            D D+L   DE  +++     ++A+ +SV      DS    T DPVRMY+REMGS+ELL+
Sbjct: 61  PDADELLMNDESVTDEEAAEEAAAALASV------DSEFGRTTDPVRMYMREMGSVELLT 114

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   ++ ++   P T + L+       +    L EI+          
Sbjct: 115 REGEIDIAKRIEEGIRQVLGAIANYPDTIRILLEEFALYQEEQVRLTEIVT--------- 165

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF  G E    Q+  +++Q             I ++A    D     D   ++ E  E
Sbjct: 166 --GFSDGEEAEFVQEESEAAQ-------------IAASASEELDSDDDADDDDDDEEETE 210

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            +   D +++A   + ++ Q   K + A+D+    +                 KS++K  
Sbjct: 211 VDTGPDPEEAAARFAELKKQY-DKTVKAVDKYGRTH-----------------KSTIKQL 252

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERH 374
              E + +L   L L     D LV  L      I   E  ++ L+ +   + R  F+   
Sbjct: 253 ---EAMKELFMQLRLAPRMFDFLVTNLRQKMDGIREQERYIMMLSVNGARMPRKTFISTF 309

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E DP W+       + ++   +A   + ILK + +++ I     +S+ E +     +
Sbjct: 310 SGSETDPSWIEQHVT-KKSKYSEPLAEHAEEILKAQRKLQIIEESCSLSVMEIKEANREM 368

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 369 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+
Sbjct: 429 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPQPEELAE 488

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D+A   +L+E T 
Sbjct: 489 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIDSPVDAATGESLKEVTD 548

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 549 EILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 608

Query: 675 KLRSFLD 681
           KLR++LD
Sbjct: 609 KLRTYLD 615


>gi|30248253|ref|NP_840323.1| RNA polymerase sigma factor RpoD [Nitrosomonas europaea ATCC 19718]
 gi|30180138|emb|CAD84140.1| DNA-dependent RNA polymerase sigma subunits (sigma70/32)
           [Nitrosomonas europaea ATCC 19718]
          Length = 751

 Score =  461 bits (1186), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 286/698 (40%), Positives = 407/698 (58%), Gaps = 84/698 (12%)

Query: 6   KRNRDSDSEHEDSD--DSLVFDFSDDS-------WKKMIKLARQRGYVTIEELNAFLPPD 56
           KRN+ + SE + +D  +S V   SD+         KK+I   ++RGY+T  E+N  LP D
Sbjct: 112 KRNKSTLSEKQITDLSESAVSVSSDNDIELRRMRLKKLIMQGKERGYLTYSEINDHLPDD 171

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK-----D 111
            + ++Q+E  ++M+++MGI+V   D+  D E    S D A++ ++  V  +        D
Sbjct: 172 MLDADQIESIISMINDMGISV--HDEAPDAEALLMS-DAATAVTDEDVVEEAEAALSSVD 228

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S    T DPVRMY+REMGS+ELL+RE EI IAKRIE G   M+ ++   P   + ++   
Sbjct: 229 SEFGRTTDPVRMYMREMGSVELLTRESEIEIAKRIEDGLRHMIQAISACPTIIENILELA 288

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
            ++ +G     E++D           GF                     DD  E  G   
Sbjct: 289 ADVENGRLRADELVD-----------GFLD-------------------DDTDEIMG--- 315

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDED----DSAHTLSAMEDQLRPKVMCALDEI 287
                               E  E +LD+D D    +     +A  D L+ K      E+
Sbjct: 316 -------------------KEMSEESLDQDFDSEDGEDEQVAAASADMLKMKA-----EV 351

Query: 288 AEVYRELRSLQDNA--VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            E +  +R   D    +  +KD +   K K L+EK+   + ++  +   ++ L +   DI
Sbjct: 352 LERFAVIRQTYDGMKKIINKKDGRQDKKYKQLQEKISTELMAMRFSAKMVEKLCDTQRDI 411

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEV 403
              I + E ++  L  +  G+ R+ F++   G E D  W+S   +   G+ +   +    
Sbjct: 412 VNDIRNCERKIAELCVTRAGMPRNYFIKAFPGNETDIDWIS--SEVESGQPYSQSLEHFR 469

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++++ + ++  +  + GI I E + I   +  GE +A  AK+EM EANLRLVIS+AKKY
Sbjct: 470 PAVMEQQQKMLELQKQAGIPIKELKEINRRMTTGEAKARRAKREMTEANLRLVISIAKKY 529

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 530 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 589

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ R +R++  +  +EP P  +A+K+ MP E +RK+LKI+KEPIS+ETPIGD+
Sbjct: 590 HMIETINKMNRISRQILQETGQEPEPAVLAEKMEMPEEKIRKILKISKEPISMETPIGDD 649

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIED + + P D+A+ A LR  T  VL SLTPRE +VLRMRFGI MNTDHTLE
Sbjct: 650 EDSHLGDFIEDASTMEPADAAVYAGLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLE 709

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVG+QF VTRERIRQIEAKA+RKL+HP+RS +LRSFLD
Sbjct: 710 EVGRQFDVTRERIRQIEAKALRKLRHPARSDRLRSFLD 747


>gi|52425815|ref|YP_088952.1| RNA polymerase sigma factor RpoD [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307867|gb|AAU38367.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 628

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 284/666 (42%), Positives = 404/666 (60%), Gaps = 72/666 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---- 83
           K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V+    D DDL    
Sbjct: 18  KLLIAQGKEQGYLTYAEVNDHLPEELVDTDQIEDIIQMINDMGIQVLESAPDADDLMLSE 77

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              DE+  E++  + SS            ++    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 78  TIADEDAVEEATQVLSSV-----------EAELGRTTDPVRMYMREMGSVELLTREGEID 126

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   + +++ E P     L+   +++ +G+  L ++I            GF  
Sbjct: 127 IAKRIEDGINEVQSAVAEYPEALDYLLKQYEQVEEGSVRLADLI-----------TGFVD 175

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                + +  E S  E+  DD    +GDI + A   +++  + D    + ++ + ++D +
Sbjct: 176 LNAEEASE--EISDLEEVLDD---EDGDIPADALNDEEEDEESDEGDTSTDDSDNSIDPE 230

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
              +    SA++DQ      C           +++L+     G+ D K   + +VL +  
Sbjct: 231 V--AREKFSALKDQ------C-----------VKTLEFIEKYGRTDNKVKEQIQVLSD-- 269

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELD 380
             +     L   + D LV  +  + K++   E ++ RLA  Y  + +D F +   G E  
Sbjct: 270 --IFTQFRLVPRQFDTLVLSMRSMMKQVRAEERQIQRLAVDYAKVPKDDFQKAFIGNETS 327

Query: 381 PHW----VSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVR 435
             W    +   K + E   +   A E+  SI++    ++ +  +T +++ + R I   + 
Sbjct: 328 EQWLESLLQSKKTYVEKLQQR--APEISKSIVR----LQQVETDTKLTVQQIRDIGERIA 381

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 382 QGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 441

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A++
Sbjct: 442 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAER 501

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  
Sbjct: 502 MGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHE 561

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 562 VLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSET 621

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 622 LRSFLD 627


>gi|114778492|ref|ZP_01453336.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114551217|gb|EAU53776.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 660

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 272/665 (40%), Positives = 402/665 (60%), Gaps = 56/665 (8%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL--------EDEEGS 89
            +Q G++T ++LN  LP   VS++++E  + + + MG+ VVD +          +D    
Sbjct: 21  GKQAGFITYDDLNKHLPGGLVSADRVEQLINVFTEMGVEVVDPERAPTGAYAMRKDRLRK 80

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           EDS   A ++   +V             DDPVRMYLREMG++ELL+REGEI IA+RIE G
Sbjct: 81  EDSALRADTSQLGTVI----------RIDDPVRMYLREMGTVELLTREGEIEIARRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIW-------RDE---LNDGTTLLREIIDLEACIGPESKGGF 199
           R  +  ++C  P TF+ +++        RDE   L +  +  R+IID++  +        
Sbjct: 131 RMQVHEAICLCPSTFREIMLLGERIIQIRDEAMELGEEPSF-RDIIDVDEKV-------- 181

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
            +      Y+ R   S+E + D+  ETE  ++   ++++  +++  +P            
Sbjct: 182 VNSAAIKEYENRMSRSEEDD-DEPVETEPKLD-GEQLTEAIKARTATP------------ 227

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK-VLK 318
            D      T+   E+QL  + +    E  +++ +   ++        D+   ++ + VL 
Sbjct: 228 -DGTPMQETVITKEEQLE-EALFHFGEAKKLHDDFIEVKKKLAKRPNDKALLLRSREVLD 285

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
             L++LV S+  +  ++D LV++  +  +++   E  +   A    + R +FLE     E
Sbjct: 286 AMLLELV-SIPFSPRQLDQLVQRFKNAVEKVRRFERSIRDYALEARMPRKLFLETFPVDE 344

Query: 379 LDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            +  W+    K   +  W   +      I + +  ++ +  ET + + E + +   +  G
Sbjct: 345 TNERWIDELMKQNKDAAWVTAIEEVTGKIKENQRRLRRVEQETEMGVVELKDVARKLTMG 404

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +   AK+EM+EANLRLVIS+AKKYTNRGL FLDLIQEGNIGLMKA EKF+W  GYKFS
Sbjct: 405 EAKMRQAKREMIEANLRLVISIAKKYTNRGLGFLDLIQEGNIGLMKAVEKFEWRRGYKFS 464

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K++R +R+++ +I REPTPEE+A+ L 
Sbjct: 465 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMMRVSRQIAQEIGREPTPEELAEHLE 524

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PVE V ++L++ KEP+SLETPIGD++ S LGDF+ED NA +PLDS I A L E T  VL
Sbjct: 525 LPVEKVLQILEVAKEPVSLETPIGDDEDSQLGDFVEDDNAENPLDSTIGAALAEATLEVL 584

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT RE++VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KL+
Sbjct: 585 ENLTDREQKVLRMRFGIGMNTDHTLEEVGKQFGVTRERIRQIEAKALRKLRHPSRSQKLK 644

Query: 678 SFLDG 682
           +F D 
Sbjct: 645 TFADA 649


>gi|296107953|ref|YP_003619654.1| RNA polymerase primary sigma factor [Legionella pneumophila 2300/99
           Alcoy]
 gi|295649855|gb|ADG25702.1| RNA polymerase primary sigma factor [Legionella pneumophila 2300/99
           Alcoy]
          Length = 621

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 386/660 (58%), Gaps = 66/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 15  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 73

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 74  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 133 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 190

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 191 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKVYFDELRE----- 229

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 230 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 262

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 263 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLSWLETI 322

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK          +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 323 ISKHAKKLD----LQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 378

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 379 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 438

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 439 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 498

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 499 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 558

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 559 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 618


>gi|54298252|ref|YP_124621.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
           str. Paris]
 gi|53752037|emb|CAH13463.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
           str. Paris]
          Length = 621

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 387/660 (58%), Gaps = 66/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 15  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 73

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 74  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 133 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 190

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 191 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKIYFDELRE----- 229

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 230 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 262

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 263 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLSWLETI 322

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK        + +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 323 ISKHAKKLD----LDRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 378

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 379 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 438

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 439 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 498

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 499 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 558

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 559 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 618


>gi|148359903|ref|YP_001251110.1| RNA polymerase sigma 70 factor RpoD [Legionella pneumophila str.
           Corby]
 gi|148281676|gb|ABQ55764.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila str.
           Corby]
          Length = 619

 Score =  459 bits (1182), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 386/660 (58%), Gaps = 66/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 13  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 71

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 72  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 130

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 131 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 188

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 189 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKVYFDELRE----- 227

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 228 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 260

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 261 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLSWLETI 320

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK          +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 321 ISKHAKKLD----LQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 376

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 377 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 436

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 437 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 496

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 497 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 556

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 557 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 616


>gi|54295203|ref|YP_127618.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
           str. Lens]
 gi|53755035|emb|CAH16523.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
           str. Lens]
          Length = 621

 Score =  459 bits (1181), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 386/660 (58%), Gaps = 66/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 15  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 73

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 74  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 133 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 190

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 191 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKIYFDELRE----- 229

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 230 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 262

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 263 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGWLETI 322

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK          +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 323 ISKHAKKLD----LQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 378

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 379 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 438

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 439 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 498

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 499 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 558

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 559 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 618


>gi|52842571|ref|YP_096370.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52629682|gb|AAU28423.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 623

 Score =  459 bits (1180), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 386/660 (58%), Gaps = 66/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 17  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 75

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 76  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 134

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 135 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 192

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 193 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKIYFDELRE----- 231

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 232 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 264

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 265 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGWLETI 324

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK          +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 325 ISKHAKKLD----LQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 380

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 381 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 440

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 441 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 500

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 501 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 560

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 561 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 620


>gi|307611207|emb|CBX00855.1| RNA polymerase sigma factor rpoD [Legionella pneumophila 130b]
          Length = 619

 Score =  459 bits (1180), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 386/660 (58%), Gaps = 66/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 13  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 71

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 72  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 130

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 131 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 188

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 189 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKIYFDELRE----- 227

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 228 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 260

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 261 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGWLETI 320

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK          +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 321 ISKHAKKLD----LQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 376

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 377 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 436

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 437 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 496

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 497 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 556

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 557 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 616


>gi|152995072|ref|YP_001339907.1| RNA polymerase sigma-70 subunit RpoD [Marinomonas sp. MWYL1]
 gi|150835996|gb|ABR69972.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas sp. MWYL1]
          Length = 612

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 292/670 (43%), Positives = 399/670 (59%), Gaps = 74/670 (11%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DG 80
           D      K++I   +++GY+T  E+N  LP D    EQ+E+ +AM+++MGI V     D 
Sbjct: 3   DTQQSRLKELISKGKEQGYLTYAEVNDHLPDDLSDPEQVEEIIAMINDMGITVSEVAPDK 62

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D L  EEG  D+ D A++   ++       D     T DPVRMY+REMG++ELL+R GEI
Sbjct: 63  DSLLMEEG--DATDEAAAEEAAAALAAVEGDIT--RTTDPVRMYMREMGTVELLTRAGEI 118

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           AIAKRIE G   +MA++   P     L+    ++ +    L +I             GF 
Sbjct: 119 AIAKRIEEGTREVMAAISYFPGAVDVLLDAYAKVQEEEGRLSDIF-----------SGFI 167

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
            G             +E   +DV   E  I+     S +D    D+  E  +N       
Sbjct: 168 DG-----------DGEEPVFEDVATEEPIIDEDTVDSDEDDDDSDTAEEETDN-----GP 211

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D +++A   + +      ++   L E+ E     R+ QD AV  +++E S      +   
Sbjct: 212 DPEETALRFNDI-----TRIYTELKELLET----RNRQDPAVQSKQEELS------ISFA 256

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
            +KLV  L       D LV+++    +++   E  ++++  +  G+ R  FL+R    E 
Sbjct: 257 PIKLVPKL------FDDLVDRVRSRMEKVREQERLIMQVCVRKSGMPRTEFLKRFPSNET 310

Query: 380 DPHWVS--------YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           +  W+         YA    E E +          ++ + +++++S ETG++I+E + I 
Sbjct: 311 NSDWLKEQIASGADYAATLEENEAE---------FMRSQRKLRAVSKETGLTIAELKEIN 361

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 362 RRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE
Sbjct: 422 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEE 481

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A SP+D A    LRE
Sbjct: 482 LAARMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDIATIEGLRE 541

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +TT VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPS
Sbjct: 542 STTMVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 601

Query: 672 RSKKLRSFLD 681
           RS+ LRSFLD
Sbjct: 602 RSEHLRSFLD 611


>gi|288941560|ref|YP_003443800.1| RNA polymerase sigma-70 subunit RpoD [Allochromatium vinosum DSM
           180]
 gi|288896932|gb|ADC62768.1| RNA polymerase, sigma 70 subunit, RpoD [Allochromatium vinosum DSM
           180]
          Length = 623

 Score =  457 bits (1175), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 291/663 (43%), Positives = 397/663 (59%), Gaps = 69/663 (10%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI-------NVVDGDDLEDE 86
           +I   +++GY+T  E+N  LPP  V ++Q+ED V M+++MGI       +VVD   L D 
Sbjct: 13  LIAKGKEQGYLTYTEVNDHLPPGIVETDQIEDIVRMINDMGIMVQETAPDVVD-HTLSDS 71

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             S+D    A++A+ +SV      DS    T DPVRMY+REMG++ELL+REGE+ IAKRI
Sbjct: 72  AVSDDEAAEAAAAALASV------DSEFGRTTDPVRMYMREMGTVELLTREGELQIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF-HGTEG 205
           E G   ++ +L   P + + LI   D ++     L ++I            GF    TE 
Sbjct: 126 EDGLNQVLNALSVYPRSIEKLIEIFDRVDREEARLTDVI-----------SGFNDEATET 174

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS----KVDSPPENAENDERNLDED 261
                 +  +  +   D  +T+ D+E+A   S DD      +VD+ P            D
Sbjct: 175 DETLATDVQAASETDADADKTDLDVEAADLDSDDDDDSATVEVDTGP------------D 222

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
            +D+A   + + ++ +  +  AL+E                 G+ DE+S    + + E  
Sbjct: 223 PEDAARRANLLRERYQ-TLKAALEEY----------------GRDDERSREAMQAVSEVF 265

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELD 380
           ++      L       L E L    +RI   E  ++ L  +  G+ R  F+E     E +
Sbjct: 266 LQ----FKLVSPVFQELAEILRATIERIRAQERAIMSLCVEQAGMGRKEFIETFPSNETN 321

Query: 381 PHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           P W+    A+  P       +A ++    + + +++ I  E  ++I E + +   +  GE
Sbjct: 322 PEWLDGLIARGRPFSVRLQELAPDIQ---RAQRKLQDIERENILTIGEIKEVNRKMSIGE 378

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 379 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 438

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A ++ M
Sbjct: 439 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAARMDM 498

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED   +SPLDSA    LRE T  +LA
Sbjct: 499 PEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPLDSATAEGLREATQNMLA 558

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS KLRS
Sbjct: 559 SLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKLRS 618

Query: 679 FLD 681
           FLD
Sbjct: 619 FLD 621


>gi|54307643|ref|YP_128663.1| RNA polymerase sigma factor RpoD [Photobacterium profundum SS9]
 gi|46912066|emb|CAG18861.1| putative DNA-directed RNA polymerase, sigmasubunit [Photobacterium
           profundum SS9]
          Length = 612

 Score =  457 bits (1175), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 285/661 (43%), Positives = 391/661 (59%), Gaps = 70/661 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD-LEDE 86
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D D+ +  E
Sbjct: 10  KLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEIMMTE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + ++D    A++ + SSV      +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 70  DNTDDDAIEAAAQALSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++      L +II            GF    E  
Sbjct: 124 EDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDII-----------SGFIDPNEEQ 172

Query: 207 SYQKREDS-SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
           +          E    D+ + + ++E+     +++ + +D  PE A      L    +  
Sbjct: 173 TAAPTATHIGSELSETDLADEDKNLETDDDDEEEEDTGID--PELAREKFLELRHSYEKM 230

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A  ++    +       A+ E++E++++ R                    ++ ++  KLV
Sbjct: 231 ALAINT-HGRHNATTEVAVGELSEIFKQFR--------------------LIPKQFDKLV 269

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV 384
            SL               D   ++  NE  ++R+   +  + +  F++   G E  P W+
Sbjct: 270 RSLR--------------DSMDKVRTNERLIMRMCIDNSKMPKKTFIKFFAGNESSPDWI 315

Query: 385 SYA----KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             A    K + E   KN+      S LK+R     +  ETG+SI   + I   +  GE +
Sbjct: 316 DEALNSGKPYAE-RLKNYEEDLRRSSLKLR----ILEKETGLSIERIKDISRRMSIGEAK 370

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 371 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 430

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP 
Sbjct: 431 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEELAERMQMPE 490

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA L
Sbjct: 491 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAATNDVLAGL 550

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFL
Sbjct: 551 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFL 610

Query: 681 D 681
           D
Sbjct: 611 D 611


>gi|269103529|ref|ZP_06156226.1| RNA polymerase sigma factor RpoD [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163427|gb|EEZ41923.1| RNA polymerase sigma factor RpoD [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 619

 Score =  456 bits (1174), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 286/656 (43%), Positives = 393/656 (59%), Gaps = 53/656 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLE-DE 86
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D D+L   E
Sbjct: 10  KLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADELMMTE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + +++    A++ + SSV      +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 70  DNADEDAIEAAAQALSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++      L +II     + P  +      T  H
Sbjct: 124 EDGINQVQCSVAEYPKAISQLLDMFDKVEADELRLTDIIS--GFVDPNEEET-AAPTATH 180

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              +  +S  E E  D+ E E + E        D + +D  PE A      L +  +  A
Sbjct: 181 IGSELSESDLEDEDRDLDEDEDEDEDGDSSDDSDDNNID--PEVAREKFTELRQSYEKMA 238

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +     +  P    A+DE++E++++ R                    ++ ++  KL+G
Sbjct: 239 LAIDT-HGRNHPTAELAVDELSEIFKQFR--------------------LVPKQFDKLIG 277

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS 385
           SL               D   R+  NE  ++R+   +  + +  F+    G E    W+ 
Sbjct: 278 SLR--------------DSMDRVRTNERLIMRMCVDNSKMPKKTFINLFAGNEASSEWID 323

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A +  +   +     E + + +   +++ +  ETG+SI   + I   +  GE +A  AK
Sbjct: 324 EALNSGKPYAERLKTYE-EELRRCSTKLRLLEEETGLSIERIKDISRRMSIGEAKARRAK 382

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 383 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 442

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 443 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 502

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A Q NLR  T  VLA LTPRE 
Sbjct: 503 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATQTNLRAATNEVLAGLTPREA 562

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 563 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 618


>gi|90411915|ref|ZP_01219923.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90327173|gb|EAS43545.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 612

 Score =  456 bits (1173), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 282/661 (42%), Positives = 390/661 (59%), Gaps = 70/661 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD--LED 85
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D D+  + +
Sbjct: 10  KLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEIMMTE 69

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +   ED+++ A+ A +S        +S    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 70  DNTDEDAIEAAAQALSSV-------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +  S+ E P     L+   D++      L +II            GF    E 
Sbjct: 123 IEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDII-----------SGFIDPNEE 171

Query: 206 HSYQKREDS-SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
            +          E    D+ + + ++E+     +++ + +D  PE A      L    + 
Sbjct: 172 QTAAPTATHIGSELSETDLADEDKNLETDEDDEEEEDTGID--PELAREKFLELRHSYEK 229

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            A  ++    +       A+ E++E++++ R                    ++ ++  KL
Sbjct: 230 MALAINT-HGRHNATTEVAVGELSEIFKQFR--------------------LIPKQFDKL 268

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW 383
           V SL               D   ++  NE  ++R+   +  + +  F++   G E  P W
Sbjct: 269 VRSLR--------------DSMDKVRTNERLIMRMCVDNSKMPKKTFIKFFAGNESSPDW 314

Query: 384 VSYAKDFPEGEWKNFVACEVD---SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           +  A +  +   +     E D   S LK+R     +  ETG+SI   + I   +  GE +
Sbjct: 315 IDEALNSGKPYAERLKIYEEDLRRSSLKLR----ILEKETGLSIERIKDISRRMSIGEAK 370

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 371 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 430

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP 
Sbjct: 431 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEELAERMQMPE 490

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA L
Sbjct: 491 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAATNDVLAGL 550

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFL
Sbjct: 551 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFL 610

Query: 681 D 681
           D
Sbjct: 611 D 611


>gi|319760203|ref|YP_004124141.1| RNA polymerase sigma factor [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318038917|gb|ADV33467.1| RNA polymerase sigma factor [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 620

 Score =  456 bits (1172), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 276/658 (41%), Positives = 389/658 (59%), Gaps = 57/658 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  L  D + S+Q+ + + M+++MGI V++     DE     
Sbjct: 10  KLLVTRGKEQGYLTFSEVNDHLSEDIIDSDQLHNIIQMMNDMGIQVMEEAPDSDEFLLTK 69

Query: 92  SLDLASS-----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + D   +     A+ ++V      D     T DPVRMY++EMG++ELL+REGEI IAKRI
Sbjct: 70  NCDTVVNNDEEDATEAAVQALSNTDPDLGRTTDPVRMYMKEMGAVELLTREGEIDIAKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+     +  G T L ++I            GF       
Sbjct: 130 EDGINQVQCSVAEYPEAITYLLEQYQRVETGETRLSDLI-----------TGFV------ 172

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D+     ++E+   +++ +   + S      +DE N + ++DD++
Sbjct: 173 ---------------DLDNFNQNVETIPNITQQNIHHLSSNILTVTDDEENTENEDDDNS 217

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                ++ +L  K   AL +  E  R     Q    NG+  +KSS   ++LK  L ++  
Sbjct: 218 -----IDPELARKKFIALRKQYETTR-----QTIKYNGRNHDKSS--SEILK--LSEIFK 263

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  RI  +E  +++L      + +  F++   G E +  W+ 
Sbjct: 264 QFRLVPKQFDYLVNNMRSMMDRIRFHERLIMKLCVDISKMPKKKFIDLFSGNETNKAWLI 323

Query: 386 YAKDFPEGEWKNF--VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            A     G  K    V  EV   +    ++  I  ETG++I + ++I   +  GE +A  
Sbjct: 324 QALSMNAGWAKKLDTVNAEVQQNIW---QLYQIEKETGLTIEQVKNINRRMSIGEAKARR 380

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EPTPEE++K++ +  + +
Sbjct: 441 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGCEPTPEELSKRMLISEDKI 500

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEP+S+ETPIGD++ SHLGDFIED N   PLDSA   NL+  T  VL+ LTPR
Sbjct: 501 RKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPLDSATSDNLKAATNDVLSGLTPR 560

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 EAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRSEILRSFLD 618


>gi|254281823|ref|ZP_04956791.1| RNA polymerase, sigma 70 subunit, RpoD family [gamma
           proteobacterium NOR51-B]
 gi|219678026|gb|EED34375.1| RNA polymerase, sigma 70 subunit, RpoD family [gamma
           proteobacterium NOR51-B]
          Length = 603

 Score =  455 bits (1171), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 287/657 (43%), Positives = 387/657 (58%), Gaps = 73/657 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D+L   E
Sbjct: 12  KALIAKGKEQGYLTYSEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELILTE 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  D      +A+ ++  L   ++ A R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 72  G--DRSADEIAAAEAAAALAAVENEAGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +MA++   P   + L    +E +  T   R++ D+   +G       +     H 
Sbjct: 129 EGIRELMAAMAHYPGVARRLT---EEYDLVTKEERKLADI--LVG-------YLDPADHV 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
              +E + Q               +AAK   DD    D+ P+  E  +R           
Sbjct: 177 PSAQEIAEQT--------------AAAKNKTDDDEAPDTGPDPIEAKKR----------- 211

Query: 268 TLSAMEDQLR--PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
             +A++ Q     KV+ A                       + + S K     +KL +L 
Sbjct: 212 -FTALKRQCTRTEKVLAA-----------------------ESRQSKKAIAEMDKLGELF 247

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV 384
               L     D LVE      + +   E E++R+  +   + R  F++  QG E D  WV
Sbjct: 248 KFFKLTPRVFDPLVEAPRTALQIVREQEREIMRIVVRECRMDRKDFIKSFQGSESDSRWV 307

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           S      + E    ++   D I +++  I ++  E G++++E + I   +  GE  A  A
Sbjct: 308 SRV--MRKKELGARISLHKDEIQRLQRRIGAVEDEIGLTVAEIKEINRRMSMGEARARRA 365

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 366 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 425

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VR
Sbjct: 426 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKVR 485

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ S LGDFIED    SP+DSA +  L E TT VLA LT RE
Sbjct: 486 KVLKIAKEPISMETPIGDDEDSSLGDFIEDVTIASPVDSATEEGLTEATTDVLAGLTARE 545

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 546 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 602


>gi|225630998|ref|YP_002727789.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
 gi|225592979|gb|ACN95998.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
          Length = 650

 Score =  454 bits (1169), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 271/660 (41%), Positives = 409/660 (61%), Gaps = 44/660 (6%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           K  ++ G++T +++N  L  +  SS+ ++D +++L + GINV+        E SED  D+
Sbjct: 20  KSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVL--------ESSEDEEDI 71

Query: 96  ASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            S++ +S +       +   +    DDPVR+YL++M S++LLSR  EI IAK+IE+ +  
Sbjct: 72  PSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEIAKKIESEKHN 131

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A           + ++ +   K E
Sbjct: 132 MLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAI----------YNSDFNVVPKEE 181

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
               E+  +DV+++E   E A   S D++   DS   + E D  N D    +   ++  M
Sbjct: 182 SEESEESAEDVEDSEDVSEDAEYCSDDEK---DSKKSDDEKDGNNEDISSVNLNVSILEM 238

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           E  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++  +   + L+ 
Sbjct: 239 ESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIWSIALQIKLSD 292

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQGRELDPHWVS 385
           + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+ +++    ++
Sbjct: 293 AAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHELKKISLLKIN 352

Query: 386 YAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +    GE KN    F+    + I    N IK    E   ++ EF+ ++  ++K E E 
Sbjct: 353 ENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQHIQED--NVQEFKELIKRIQKHEREV 410

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKFSTY  
Sbjct: 411 SEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGT 470

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ REPT EE++ +L MP+E
Sbjct: 471 WWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGREPTLEELSVELTMPLE 530

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT VLA+LT
Sbjct: 531 RIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRGITTNVLATLT 590

Query: 622 PREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           P+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR++KLR F 
Sbjct: 591 PKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRARKLRGFF 650


>gi|254497834|ref|ZP_05110600.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
 gi|254352912|gb|EET11681.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
          Length = 628

 Score =  454 bits (1169), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 279/656 (42%), Positives = 386/656 (58%), Gaps = 58/656 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    +DE     +
Sbjct: 22  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLN 80

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 81  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 139

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           ++ SL   P T Q +      L+D    + + I L   I      GF             
Sbjct: 140 VLKSLAHYPETVQLV------LDDYERFIAQEIRLNEII-----SGF------------A 176

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
           DS +E           +I S    S+ D   + +  E+ + +    + D+  +     A 
Sbjct: 177 DSDEE------MAPAANIGSMLDESQQDELILANDDEDEDGEGGIAEVDDGPNPEQAKAY 230

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
            D+LR     A+  + E             +G+   K++   + + +  +K    L L  
Sbjct: 231 FDELRECFNAAMVVLKE-------------HGRTHAKTNKSLEAMSDSFLK----LKLTS 273

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS-----Y 386
            ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W++     +
Sbjct: 274 RQVDRLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLEWLNNIIAKH 333

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           AK         +     + IL+I++ + S  VE G++I E + I   +  GE +A  AKK
Sbjct: 334 AKKLDMSRISEY----TEEILRIQSRLVSFEVEYGLTIGEIKDINRKMSIGEAKARRAKK 389

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 390 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 449

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + +RKV
Sbjct: 450 AITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDKIRKV 509

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTPRE +
Sbjct: 510 LKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTPREAK 569

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 570 VLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 625


>gi|1575485|gb|AAB09543.1| LprpoD [Legionella pneumophila]
          Length = 620

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 285/660 (43%), Positives = 386/660 (58%), Gaps = 67/660 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+I L +++GY+T  ++N  LP + V +E  +  ++ML  M I V +    EDE     +
Sbjct: 15  KVISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLN 73

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +       +++ L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 74  TEEVPDIEEAAMVLASVDKETGRTTD-PVRMYMREMGTVELLTREGEIRIAKRIEEGIYQ 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFHGTEGHSY 208
           ++ SL   P T Q ++   D        L EII    D++  I P +  G     E    
Sbjct: 133 VLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQ-- 190

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                          +E   D++   +  +   S VD  P N E  +   DE  +     
Sbjct: 191 ---------------EEILLDVDEEDEDGEGGISDVDDGP-NPEQAKIYFDELRE----- 229

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E     K M AL E                +G+ ++K+      + E  +KL    
Sbjct: 230 --AFE-----KAMKALKE----------------HGRTNKKTVELLDSMSESFLKL---- 262

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--- 384
            L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W+   
Sbjct: 263 KLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGWLETI 322

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              +AK          +    + IL++++++ S  +E G++ISE + I   +  G+ EA 
Sbjct: 323 ISKHAKKLD----LQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGD-EAR 377

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 378 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 437

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 438 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 497

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 498 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 557

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 558 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 617


>gi|225677095|ref|ZP_03788097.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225590854|gb|EEH12079.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 669

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 272/675 (40%), Positives = 417/675 (61%), Gaps = 56/675 (8%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           K  ++ G++T +++N  L  +  SS+ ++D +++L + GINV++   +EDEE      D+
Sbjct: 21  KSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVLES--IEDEE------DI 72

Query: 96  ASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            S++ +S +       +   +    DDPVR+YL++M S++LLSR  EI IAK+IE+ +  
Sbjct: 73  PSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEIAKKIESEKHN 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A           + ++ +   K E
Sbjct: 133 MLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAI----------YNSDFNVVPKEE 182

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRS------KVDSPPENAENDERNLDEDEDDSA 266
               E+  +DV+++E   E A   S D++       + DS   + E D +  D+++D + 
Sbjct: 183 SEESEESAEDVEDSEDVSEDAEYCSDDEKDSKKSDDEKDSKKSDDEKDSKKSDDEKDGNN 242

Query: 267 HTLSA---------MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
             +S+         ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L
Sbjct: 243 EDISSVNLNVSILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENL 296

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF------- 370
             ++  +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       
Sbjct: 297 YNQIWSIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDV 356

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISE 426
           L +H+ +++    ++  +    GE KN    F+    + I    N IK    E   ++ E
Sbjct: 357 LLKHELKKISLLKINENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQHIQED--NVQE 414

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F+ ++  ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +
Sbjct: 415 FKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVD 474

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ RE
Sbjct: 475 KFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGRE 534

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI 
Sbjct: 535 PTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAIL 594

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           A+LR  TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+R
Sbjct: 595 ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALR 654

Query: 666 KLKHPSRSKKLRSFL 680
           KLKHPSR++KLR F 
Sbjct: 655 KLKHPSRARKLRGFF 669


>gi|209696105|ref|YP_002264035.1| RNA polymerase sigma factor RpoD [Aliivibrio salmonicida LFI1238]
 gi|208010058|emb|CAQ80381.1| RNA polymerase sigma factor RpoD (sigma-70) [Aliivibrio salmonicida
           LFI1238]
          Length = 610

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 286/661 (43%), Positives = 383/661 (57%), Gaps = 72/661 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV    D DD+    
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDMS--L 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 68  NDDDAVTDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      L +II     + P   G          
Sbjct: 127 EGINEVQCSVAEFPGAISYLLEQFDKVQAEEIRLTDIIS--GFVDPNDDGS--------- 175

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK-VDSPPENAENDERNLDEDEDDSA 266
                 ++        + +E D+    K +KDD  + V   PE A      L      S 
Sbjct: 176 ------AAPTATHIGSELSESDLADEDKEAKDDEEEDVGIDPELALEKFTQLRT----SY 225

Query: 267 HTLS-AMEDQLR--PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           H +  A E+  R   K   A+ E+ +V+RE +                            
Sbjct: 226 HNMQLAFEEHGRDNGKAREAIGELTDVFREFK---------------------------- 257

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPH 382
                 L   + D LV ++     R+   E  ++R+   YG + +  F+    G E    
Sbjct: 258 ------LIPKQFDFLVREMRGSMDRVRTQERLIMRMCVEYGKMPKKSFIALFSGNEASDE 311

Query: 383 WVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           W +   A D P  E       ++   +K   +I SI  ETG+ +   + I   +  GE +
Sbjct: 312 WFNEILASDKPYVERLKRYEEDIRRSIK---KINSIVKETGLPVVNIKDISRRMSIGEAK 368

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 369 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 428

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP 
Sbjct: 429 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPE 488

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  VLA L
Sbjct: 489 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPVDSATSTSLKFATNDVLAGL 548

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 549 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 608

Query: 681 D 681
           D
Sbjct: 609 D 609


>gi|42521092|ref|NP_967007.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
 gi|42410833|gb|AAS14941.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
          Length = 642

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 270/660 (40%), Positives = 408/660 (61%), Gaps = 53/660 (8%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           K  ++ G++T +++N  L  +  SS+ ++D +++L + GINV+        E SED  D+
Sbjct: 21  KSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVL--------ESSEDEEDI 72

Query: 96  ASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            S++ +S +       +   +    DDPVR+YL++M S++LLSR  EI IAK+IE+G+  
Sbjct: 73  PSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEIAKKIESGKHN 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A           + ++ +   K E
Sbjct: 133 MLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDA----------MYNSDFNVVPKEE 182

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
               E+  +DV+++E D+   A+   DD           E D  N D    +   ++  M
Sbjct: 183 SEESEESAEDVEDSE-DVSEDAEYCSDD-----------EKDGNNEDISSVNLNVSILEM 230

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           E  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++  +   + L+ 
Sbjct: 231 ESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIWSIALQIKLSD 284

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQGRELDPHWVS 385
           + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+ +++    ++
Sbjct: 285 AAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHELKKISLLKIN 344

Query: 386 YAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +    GE KN    F+  + + I    N IK    E   ++ EF+ ++  ++K E E 
Sbjct: 345 ENQSSFTGELKNKFLRFIDDKSEHIASTLNGIKQHIQED--NVQEFKELIKRIQKHEREV 402

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKFSTY  
Sbjct: 403 SEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGT 462

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ REPT EE++ +L MP+E
Sbjct: 463 WWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGREPTLEELSVELTMPLE 522

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT VLA+LT
Sbjct: 523 RIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRGITTNVLATLT 582

Query: 622 PREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           P+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR++KLR F 
Sbjct: 583 PKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRARKLRGFF 642


>gi|120553592|ref|YP_957943.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei
           VT8]
 gi|120323441|gb|ABM17756.1| RNA polymerase, sigma 70 subunit, RpoD [Marinobacter aquaeolei VT8]
          Length = 618

 Score =  452 bits (1162), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 284/657 (43%), Positives = 386/657 (58%), Gaps = 61/657 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D L   E
Sbjct: 11  KDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTLLMTE 70

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  DS    ++A+ ++  L   +  A R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 71  G--DSTADEAAAAEAAAALAAVETDAGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +MA++   P T   +I   D + +    + +I+            GF    +   
Sbjct: 128 EGIRDVMAAVAHFPGTAGTVIQAYDRIIENEGRISDIVT-----------GFLDPDDAEP 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           +   ED+S E    D  +T  D +     S+DD      P E     E  L +++ D+A 
Sbjct: 177 FMG-EDTSTEDTSADDSDTSSDDDDDDTSSEDDNDNGPDPEETRLRFE--LLKEKLDAAE 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
              A   +   K   AL+E+ +V+                                    
Sbjct: 234 KALAKHGRGHKKTQEALNELGQVF----------------------------------AP 259

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS- 385
             L     D LV  +   +  +  NE  ++++  +   + R  F++   G E D  W   
Sbjct: 260 FKLANKAFDELVNVVRSTNDLVRENERAIMQICVRDCKMPRKDFIKWFPGNETDLEWAGE 319

Query: 386 -YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A   P   +   +   VD I++++  I+++  E  + +++ + I   V  GE +A  A
Sbjct: 320 IAATKKP---YAAAIGERVDEIVRLQKRIQNVQTEVDLDVADIKEINRRVSIGEAKARRA 376

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 377 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 436

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 437 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKIR 496

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED  A+SP+DSA    LRE T  VLA LT RE
Sbjct: 497 KVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSVLAGLTARE 556

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR F+D
Sbjct: 557 SKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFID 613


>gi|296932701|gb|ADH93504.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. In5]
          Length = 616

 Score =  451 bits (1160), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 277/651 (42%), Positives = 395/651 (60%), Gaps = 48/651 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D     D
Sbjct: 12  KELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L +++            G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAA 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           E       +  V+  +   +  A+ S DD  + +S P            D   +A    A
Sbjct: 180 EVPPPVDPK-AVKADDDTDDEEAEASTDDEEEAESGP------------DPVIAAQRFGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+ +     +  K+++   VL   L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKHG----RGNKAAIAELVL---LAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
             + + LVE++     R+   E  +++L  +   + R  FL +  G E+D  W S     
Sbjct: 266 PKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW-SDGLAR 324

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +G++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  AKKEMVE
Sbjct: 325 GKGKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEIKDINRRMSIGEAKARRAKKEMVE 384

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 385 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 444

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI 
Sbjct: 445 SIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIA 504

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRM
Sbjct: 505 KEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRM 564

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 565 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|3646419|emb|CAA07705.1| sigma-70 factor [Pseudomonas tolaasii]
          Length = 616

 Score =  451 bits (1160), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 283/653 (43%), Positives = 397/653 (60%), Gaps = 52/653 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D     D
Sbjct: 12  KELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   K    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVKTDIGRTTD-PVRMYMREMGTVELLTREGEIGIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEACIGPESKGGFFHGTEGHSYQK 210
            +M ++   P T   ++    E N  TT    + D L   I P+                
Sbjct: 131 EVMGAIAHFPGTVDRIL---SEYNRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDA 187

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
           +   + +   DD  E+ G          DD  +V+S P            D   +A    
Sbjct: 188 KAAKADDDSEDDDAESSG----------DDEDEVESGP------------DPIIAAQRFG 225

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A+ DQ+            E+ R  ++L+    +G+ ++++  +   L E    L   + L
Sbjct: 226 AVSDQM------------EITR--KALKK---HGRTNKQAIAELIALAE----LFMPIKL 264

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAK 388
              + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK
Sbjct: 265 VPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 324

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  AKKEM
Sbjct: 325 G--KAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRAKKEM 382

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 383 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 442

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLK
Sbjct: 443 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLK 502

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VL
Sbjct: 503 IAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVL 562

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 563 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|27904560|ref|NP_777686.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340403|sp|Q89B10|RPOD_BUCBP RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|27903957|gb|AAO26791.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
          Length = 609

 Score =  450 bits (1158), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 275/663 (41%), Positives = 393/663 (59%), Gaps = 77/663 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---- 83
           K ++   +++GY+T  E+N  L  + ++S+Q+ED + M+++MGI VV    D DDL    
Sbjct: 10  KLLVTYGKEQGYLTYSEINDHLSDNIINSDQIEDIIQMINDMGIQVVEKAPDSDDLILHE 69

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              + E  ED ++ A++   S+V      +S    T DPVRMY+REMG++ELL+REGEI 
Sbjct: 70  IKRNNETDEDIVE-ATAQVLSTV------ESELGRTTDPVRMYMREMGTVELLTREGEID 122

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +  S+ E P     L+   + +  G   L E+I     + P ++    H
Sbjct: 123 IAKRIEDGINQVQCSVAEYPEAITHLLEQYNRVELGELRLSELI--HGFVDPNAEA--VH 178

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
            +  +      +S +    D+ +E           + DD   VD  PE A      L   
Sbjct: 179 TSITNHINT--NSEEHHHNDNTEE-----------NNDDDHLVD--PELAREKFIALKNQ 223

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
              + + +   +++     +  ++ ++E++++ R                          
Sbjct: 224 YHITNYAIKT-KNRNHQDTLIEINNLSEIFKQFR-------------------------- 256

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELD 380
                   L   + D LV  +  + ++I   E  + +L   YG I +   L     ++ +
Sbjct: 257 --------LVPKQFDHLVINMRKMMQKIRIQERNIAKLCIEYGNIPKKALLNFFSLQKTN 308

Query: 381 PHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
             W    ++   P  +  N +  ++  ILK   +++ +  ETG++I + ++I   +  GE
Sbjct: 309 QIWSKIVQNIKKPWIDKFNTIKPDIQMILK---KLQKVEEETGLTIHQVKNINKRISLGE 365

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 366 AKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 425

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +I REPTPEE+++++ +
Sbjct: 426 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQEIGREPTPEELSERMLI 485

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIG++D SHLGDF+ED N   PLDSA  A+LR  T  VL+
Sbjct: 486 PEDKIRKVLKIAKEPISMETPIGEDDDSHLGDFLEDTNIELPLDSATSASLRSATKNVLS 545

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 546 GLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILRS 605

Query: 679 FLD 681
           FLD
Sbjct: 606 FLD 608


>gi|114330327|ref|YP_746549.1| RNA polymerase sigma factor RpoD [Nitrosomonas eutropha C91]
 gi|114307341|gb|ABI58584.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas eutropha C91]
          Length = 749

 Score =  449 bits (1156), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 274/662 (41%), Positives = 395/662 (59%), Gaps = 72/662 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK+I   ++RGY+T  E+N  LP D + ++Q+E  ++M+++MGI+V   D+  D E    
Sbjct: 144 KKLIMQGKERGYLTYSEINDHLPDDMLDADQIESIISMINDMGISV--HDEAPDAEALLM 201

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           S D A++ ++  V  +        DS    T DPVRMY+REMGS+ LL+RE EI IAKRI
Sbjct: 202 S-DTATAVADEDVAEETEAALSSVDSEFGRTTDPVRMYMREMGSVGLLTRESEIEIAKRI 260

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   M+ ++   P   + ++    ++  G     E++D           GF       
Sbjct: 261 EDGLRHMIQAISACPTIIENILGLAADVESGQLRADELVD-----------GFLD----- 304

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                         DD +E  G                   PE  E+ +++ D DE +  
Sbjct: 305 --------------DDTEEIIGK----------------GMPE--ESLDQDFDSDETEEE 332

Query: 267 HTLSAMEDQLRPK--VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
              SA  D L+ K  V+     I + Y +++ + D    G++D+K     K L+EK+   
Sbjct: 333 QIASANADMLKMKNEVLERFAMIRQTYDDMKKIIDKKGGGRQDKK----YKQLQEKISAE 388

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHN----EGELLRLAQSYG-IKRDVFLERHQGREL 379
           + ++  +      +VE+L D  + I+++    E ++  L      + R+ F++   G E 
Sbjct: 389 LMAMRFSAK----MVERLCDTQRAIVNDIRSCERKIAELCVVRAKMPRNHFIKAFPGNET 444

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W++   D  +  +   +     ++++ + ++ ++  + GI I E + I   +  GE 
Sbjct: 445 NIDWINSEVDANQ-PYSQSLEHYRPAVMEQQQKMLTLQEQAGIPIKELKEINRRMTTGEA 503

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 504 KARSAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 563

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  +EP P  +A+K+ M 
Sbjct: 564 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQEPEPAVLAEKMEMT 623

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED + + P D+AI A LR  T  VL S
Sbjct: 624 EEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVSTMEPADAAIYAGLRTVTKDVLDS 683

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HP+RS +LRSF
Sbjct: 684 LTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPARSDRLRSF 743

Query: 680 LD 681
           LD
Sbjct: 744 LD 745


>gi|149910043|ref|ZP_01898691.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149806911|gb|EDM66872.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 609

 Score =  449 bits (1155), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 281/656 (42%), Positives = 387/656 (58%), Gaps = 62/656 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 9   KLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQVEDIIQMINDMGIQVLETAPDADDLLMAE 68

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++      A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 69  NTTAPDDDAAEAAAAALASVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 128

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +  ++ E P    +L+   D+     + L +II     I P +       T   S   
Sbjct: 129 YAVQTAVAEYPEAINSLLAEYDKFLAEESRLSDIIT--GFIDPNADDVAPTATHIGSEVT 186

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
           ++ +  +   DD +E EG+             K   P E AE       E        L 
Sbjct: 187 KKQNESDSTDDDEEEEEGN-------------KGPDPEEAAE----KFAELRKHHTALLK 229

Query: 271 AMEDQL--RPKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKLV 325
            ++D     PK    ++ ++EV+R  R +    D  VN  +D    V+   ++E+LV   
Sbjct: 230 GIKDHGLDHPKTRLHVEMLSEVFRTFRLIPKQFDRIVNSMRDMMDHVR---VQERLV--- 283

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
                    I + VEQ                       + +  F+E   G E D  W  
Sbjct: 284 ---------IKMCVEQC---------------------KMPKAAFVEAFAGNETDFTWFE 313

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A+             + D + +  N++K +   TG++IS+ ++I   +  GE +A  AK
Sbjct: 314 KAQQSAAPYAPALQRIDFD-VRRCINKLKLVENTTGLTISQIKNINRRMSIGEAKARRAK 372

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 373 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 432

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + +RK
Sbjct: 433 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMMMPEDRIRK 492

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A + +L+  T  VLA LT RE 
Sbjct: 493 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLSLPVDAATKDSLKGATDDVLAGLTAREA 552

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 553 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 608


>gi|119473196|ref|ZP_01614893.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
 gi|119444560|gb|EAW25875.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
          Length = 614

 Score =  449 bits (1154), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 279/655 (42%), Positives = 381/655 (58%), Gaps = 55/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE   ++
Sbjct: 10  KLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  TTTDEDAAEAAAAALATVEKEIGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGIN 128

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +  S+ E P     L+   D+       L +II            GF    E  +    
Sbjct: 129 QVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------VGFIDPNEDEAPISA 177

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            +   E     + + + D + +     ++       PE A     NL +  + +  T  A
Sbjct: 178 TNIGSELSEKQLDDDDEDDDKSDDDEDEEEVDTGPDPEEARIHFENLRDLYNKARDTFEA 237

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
            + +  P    A+ EI E++R  + +    D  VN  ++    V+               
Sbjct: 238 -KGRSHPDSQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRV-------------- 282

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
              Q R  L+++Q   I+K                 + +  F++     E DP WV    
Sbjct: 283 ---QER--LIMKQAVQIAK-----------------LPKKAFVKHFANNETDPSWVDL-- 318

Query: 389 DFPEGEWKNFVACEVDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           +    E  +    EV   I++  N++  I   TG+SI   + I   +  GE +A  AKKE
Sbjct: 319 EISNNEKYSAKLEEVKPEIIRCINKLSIIEQTTGLSIERIKDINRRMSIGEAKARRAKKE 378

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 379 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 438

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVL
Sbjct: 439 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIRKVL 498

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE +V
Sbjct: 499 KIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAREAKV 558

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 559 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 613


>gi|163751572|ref|ZP_02158794.1| RNA polymerase sigma-70 factor [Shewanella benthica KT99]
 gi|161328580|gb|EDP99733.1| RNA polymerase sigma-70 factor [Shewanella benthica KT99]
          Length = 609

 Score =  448 bits (1153), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 290/661 (43%), Positives = 392/661 (59%), Gaps = 73/661 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +   D ++   SE
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMMSE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D   +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  DSTD-DDAAEEAAAALATVEAELGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + AS+ E P    A++   D        L +II     I P +       T   S   
Sbjct: 128 NTVQASVAEYPQAIAAILDQFDRYEAEEVRLSDIIS--GFIDPNADDIAPTATHVGS--- 182

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHTL 269
                      D+ ++E D +++     ++      P PE ++     L E  ++   TL
Sbjct: 183 -----------DLSQSELDKDNSKDDEDEEEEGPKGPDPEESKERFTQLREVHEN---TL 228

Query: 270 SAMEDQLR--PKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKL 324
             + D+ R  P+   AL EI E+++E R +    D  V G +     V+   ++E+L+  
Sbjct: 229 RIIADKGRGHPEATVALFEIGELFKEFRLMPKQFDRLVKGMRATMDKVR---VQERLI-- 283

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                     + L VEQ                       + +  F++ +   E    W 
Sbjct: 284 ----------MKLCVEQA---------------------KMPKKNFVKCYTADESSIAWF 312

Query: 385 SYAKDFPEGEWKNFVA----CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
               D      K +VA     E D + + R ++  I  ETG++I+  + I   +  GE +
Sbjct: 313 ----DAELASKKPYVAGLQMVETD-VRRCRFKLDIIEKETGLAIASIKDINRRMSIGEAK 367

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 368 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 427

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP 
Sbjct: 428 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPE 487

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA L
Sbjct: 488 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGL 547

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFL
Sbjct: 548 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFL 607

Query: 681 D 681
           D
Sbjct: 608 D 608


>gi|58584650|ref|YP_198223.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58418966|gb|AAW70981.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
          Length = 649

 Score =  448 bits (1152), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 265/666 (39%), Positives = 414/666 (62%), Gaps = 57/666 (8%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-----E 90
           K  ++ G++T +++N  L  + +SS+ ++DT+++L + GIN+++    EDEE +     +
Sbjct: 20  KSIKKGGFITFDDINDKLSDENLSSDFIDDTISLLQDSGINILESS--EDEEEAPSNSDD 77

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             LD   + SN++  L +         DDPVR+YL++M S++LLSR  EI IAK+IE+ +
Sbjct: 78  SKLDDDDALSNTTTTLVQ--------NDDPVRVYLQDMSSVKLLSRTDEIEIAKKIESEK 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             M+ ++ E+ +T + +  WRD+L+ G+ LLREIIDL+A                  Y  
Sbjct: 130 HNMLRAIIETSVTLKMIKAWRDDLSSGSLLLREIIDLDAI-----------------YNS 172

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDR----SKVDSPPENAENDERNLDEDEDDSA 266
             ++  ++E ++  E + D E+ ++ +KDD      ++DS   N E +  N D +  +  
Sbjct: 173 DFNAIPKEESEESIEDDKDSENVSEGTKDDEYCEDDEIDSKKGNDEKENSNEDINSANLN 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            ++  ME+ L PKV+ ALDEI        +L D A+  +KD    ++ + L +++  +V 
Sbjct: 233 VSILEMENDLLPKVIVALDEII-------TLADEALTLRKDPSGGLRYQNLYDQIWSIVL 285

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE-------RHQGREL 379
            + L+ + +  + ++LY+I++ IM  E  L+  A+ Y I R+ FL+       R++  E+
Sbjct: 286 QIKLSDTAVAKITQKLYNINRSIMLEEANLISEAKKYNIDRESFLKVYADVLLRYKLEEI 345

Query: 380 DPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
                S  +    GE KN    F+    + I    N IK    E   ++ EF+ ++   +
Sbjct: 346 SSLKSSENQFCFTGELKNKFVKFIDDNFEHIADTLNNIKQHIQED--NVQEFKELIKRTQ 403

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K E E S AK+ M++ANLRLV+S+AKKY+NRGL  LDLIQEGNIGLMKA +KFD+  GYK
Sbjct: 404 KHEREVSEAKQGMIKANLRLVVSIAKKYSNRGLALLDLIQEGNIGLMKAVDKFDYKRGYK 463

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R++++++ REPT EE++ +
Sbjct: 464 FSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKLTHEMGREPTLEELSME 523

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L MP+E +RKV+KI ++P+SL+ P G +D+S  GD IEDK    P D+AI  +LR  TT 
Sbjct: 524 LGMPLERIRKVMKIARDPVSLDAPTGKDDSSTFGDCIEDKRVSKPEDAAILTDLRCITTN 583

Query: 616 VLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +LA+LTP+EER++RMRFG+G +  +HTLEE+G  F VTRERIRQ+E+KA+RKLKHP R++
Sbjct: 584 LLATLTPKEERIIRMRFGLGKDCKEHTLEEIGCIFKVTRERIRQVESKALRKLKHPCRAR 643

Query: 675 KLRSFL 680
           KLR F 
Sbjct: 644 KLRGFF 649


>gi|82703177|ref|YP_412743.1| RNA polymerase sigma factor RpoD [Nitrosospira multiformis ATCC
           25196]
 gi|82411242|gb|ABB75351.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosospira multiformis
           ATCC 25196]
          Length = 707

 Score =  447 bits (1151), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 278/665 (41%), Positives = 400/665 (60%), Gaps = 80/665 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +I   ++RGY+T  E+N  LP D + +EQ+E+ ++M++++GI+V D   D E    SE
Sbjct: 105 KNLIVQGKERGYLTYAEINDHLPDDMLDAEQIENIISMINDVGISVYDEAPDAETLLMSE 164

Query: 91  DSLDLA-------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            +  +A       + A+ S+V      DS    T DPVRMY+REMGS+ELL+RE EI IA
Sbjct: 165 TAPTVADEDVVEEAEAALSTV------DSEFGRTTDPVRMYMREMGSVELLTRESEIEIA 218

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   M+ ++   P T   ++ + D ++     + E++D          G     T
Sbjct: 219 KRIEDGLKHMIQAISACPTTIAGILEFADRVSKDEMRVDELVD----------GLLDPST 268

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E    ++  D S E+E +   E E D+ + A               NA     NL + ++
Sbjct: 269 EEIISEEISDESLEQELNSDAEDE-DVTAVA---------------NA-----NLLKLKN 307

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL-V 322
           D+    +         V  A DE+ +V  +    + +     KD +  +  +++  +   
Sbjct: 308 DALERFAV--------VQKAYDEMQKVLEK----KGSGNKAYKDIQEQISSELMAIRFSA 355

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+V  L   Q     LV+++    ++IM    EL       G+ R+ F++   G E + +
Sbjct: 356 KMVERLCDTQR---ALVDEMRGYERKIM----ELC--VSKVGMSRNHFIKTFPGNESNLN 406

Query: 383 WV----SYAKDFPEG--EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           WV    +  K +      ++  +  +  ++L ++ ++       GI + E + I   +  
Sbjct: 407 WVDEEIALGKPYSAALERYRPEIVEQQQNLLALQKQV-------GIPLKELKEINRRMST 459

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 460 GEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 519

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  +EP P  +A+K+
Sbjct: 520 STYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQEPEPAVLAQKM 579

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++P D+A+ A+LR+ T  +
Sbjct: 580 EMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSATMAPADAAVYASLRDVTKDI 639

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++L
Sbjct: 640 LDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERL 699

Query: 677 RSFLD 681
           RSFLD
Sbjct: 700 RSFLD 704


>gi|33593188|ref|NP_880832.1| RNA polymerase sigma factor RpoD [Bordetella pertussis Tohama I]
 gi|33563563|emb|CAE42462.1| RNA polymerase sigma factor 70 [Bordetella pertussis Tohama I]
 gi|332382599|gb|AEE67446.1| RNA polymerase sigma factor RpoD [Bordetella pertussis CS]
          Length = 760

 Score =  447 bits (1151), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 266/678 (39%), Positives = 388/678 (57%), Gaps = 108/678 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------------ 79
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D            
Sbjct: 163 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 222

Query: 80  -------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
                   DD+EDE          + A+ ++V      DS    T DPVRMY+REMGS+E
Sbjct: 223 NAPVASNDDDVEDE----------AEAALTTV------DSDFGRTTDPVRMYMREMGSVE 266

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   M+ ++   P T   ++     + +G   + E++D    + 
Sbjct: 267 LLTREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD--GLVD 324

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           PE         +G  Y                       + A V+ D+            
Sbjct: 325 PE---------DGEEY-----------------------AGAGVTADE------------ 340

Query: 253 NDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                 DE +D  A  +S+ + + LR K +   DE+++ + ++R  Q     G K +   
Sbjct: 341 ------DEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMR--QSYEKEGYKSDAYL 392

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               +++ +L+ +  +  + +   D L   VE++  + + ++H            G+ R 
Sbjct: 393 KAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHT------CVDRAGMPRS 446

Query: 369 VFLERHQGRELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            FL+   G E +  WV    + A  + E      +  ++ ++ +++ ++  +     + +
Sbjct: 447 HFLKAFPGNETNLQWVLDEVAAAHAYSE-----TLERQIPAVQELQQKLIDLQTRVVLPL 501

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 502 KDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 561

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  
Sbjct: 562 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETG 621

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A
Sbjct: 622 AEPDPATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAA 681

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+
Sbjct: 682 LHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKAL 741

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HPSR+ KL+SFL+G
Sbjct: 742 RKLRHPSRADKLKSFLEG 759


>gi|114564160|ref|YP_751674.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella frigidimarina
           NCIMB 400]
 gi|114335453|gb|ABI72835.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella frigidimarina
           NCIMB 400]
          Length = 614

 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 281/654 (42%), Positives = 388/654 (59%), Gaps = 57/654 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + +S+ E P     ++   D+       L +II            GF +  +      
Sbjct: 131 NTVQSSVSEYPQAIAMILEQFDKYEAEELRLSDII-----------SGFINPDD------ 173

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                     DDV  T  ++ S    SK+D    D   ++ E +E N   D +++    +
Sbjct: 174 ----------DDVAPTATNVGSELADSKNDDDDDDDDDDDEEEEEGNKGPDPEEAKEKFT 223

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               QLR     +L  IAE  R              D   ++    +  +L K      L
Sbjct: 224 ----QLREAYEKSLGIIAEKGR--------------DHPEAIGSLFVIGELFK---EFRL 262

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKD 389
              + D LV+ + ++  R+   E  +++L   +  + +  F++   G E +  W +  K+
Sbjct: 263 VPKQFDRLVKSMRNMMDRVRIQERLVIKLCVEHAKMPKKNFIKAFTGNETNLDWFNKEKE 322

Query: 390 F--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
              P  E    +    D + +   ++ +I VET ++I+  + I   +  GE +A  AKKE
Sbjct: 323 STKPYAEGLRLIT---DDVTRCVTKLGAIEVETDLTIAGIKDINRRMSIGEAKARRAKKE 379

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 380 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 439

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVL
Sbjct: 440 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVL 499

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +V
Sbjct: 500 KIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAKV 559

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 560 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 613


>gi|33597397|ref|NP_885040.1| RNA polymerase sigma factor RpoD [Bordetella parapertussis 12822]
 gi|33573824|emb|CAE38132.1| RNA polymerase sigma factor 70 [Bordetella parapertussis]
          Length = 760

 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 266/678 (39%), Positives = 388/678 (57%), Gaps = 108/678 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------------ 79
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D            
Sbjct: 163 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 222

Query: 80  -------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
                   DD+EDE          + A+ ++V      DS    T DPVRMY+REMGS+E
Sbjct: 223 NAPVASNDDDVEDE----------AEAALTTV------DSDFGRTTDPVRMYMREMGSVE 266

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   M+ ++   P T   ++     + +G   + E++D    + 
Sbjct: 267 LLTREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD--GLVD 324

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           PE         +G  Y                       + A V+ D+            
Sbjct: 325 PE---------DGEEY-----------------------AGAGVTADE------------ 340

Query: 253 NDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                 DE +D  A  +S+ + + LR K +   DE+++ + ++R  Q     G K +   
Sbjct: 341 ------DEADDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMR--QSYEKEGYKSDAYL 392

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               +++ +L+ +  +  + +   D L   VE++  + + ++H            G+ R 
Sbjct: 393 KAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHT------CVDRAGMPRS 446

Query: 369 VFLERHQGRELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            FL+   G E +  WV    + A  + E      +  ++ ++ +++ ++  +     + +
Sbjct: 447 HFLKAFPGNETNLQWVLDEVAAAHAYSE-----TLERQIPAVQELQQKLIDLQTRVVLPL 501

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 502 KDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 561

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  
Sbjct: 562 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETG 621

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A
Sbjct: 622 AEPDPATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAA 681

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+
Sbjct: 682 LHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKAL 741

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HPSR+ KL+SFL+G
Sbjct: 742 RKLRHPSRADKLKSFLEG 759


>gi|163856346|ref|YP_001630644.1| RNA polymerase sigma factor RpoD [Bordetella petrii DSM 12804]
 gi|163260074|emb|CAP42375.1| RNA polymerase sigma-70 factor [Bordetella petrii]
          Length = 806

 Score =  447 bits (1149), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 266/666 (39%), Positives = 390/666 (58%), Gaps = 84/666 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI+V D   D E    SE
Sbjct: 209 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYDQAPDAETLLMSE 268

Query: 91  --------DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                   D ++  + A+ ++V      DS    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 269 NAPVASNDDDVEDEAEAALTTV------DSDFGRTTDPVRMYMREMGSVELLTREGEIEI 322

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++     + +G   + E++D    + PE        
Sbjct: 323 AKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD--GLVDPE-------- 372

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +G  Y                       + A V+ D+                  DE++
Sbjct: 373 -DGEEY-----------------------AGAGVAADE------------------DEND 390

Query: 263 DDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           D  A  +S+ + + LR K +   DE+ + + ++R  Q    +G K E      + +  +L
Sbjct: 391 DGPAGGMSSKQLEDLRVKALAKFDEVTKQFEKMR--QSYERDGYKSEAYIKAQEAILNEL 448

Query: 322 VKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           + +  +  + +   D L   VE++  + + ++H            G+ R  F++   G E
Sbjct: 449 MGIRFTAKMVEKLADTLRSQVEEVRQLERAVLHT------CVDRAGMPRSHFIKVFPGNE 502

Query: 379 LDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            +  WV    A   P   +   +  ++ ++ +++ ++  +     + + + + +   +  
Sbjct: 503 TNLDWVLQEVAAGHP---YAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMAT 559

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 560 GEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 619

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+
Sbjct: 620 STYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKM 679

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+    V
Sbjct: 680 DMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDVVKEV 739

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL
Sbjct: 740 LDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKL 799

Query: 677 RSFLDG 682
           +SFL+G
Sbjct: 800 KSFLEG 805


>gi|187478819|ref|YP_786843.1| RNA polymerase sigma factor RpoD [Bordetella avium 197N]
 gi|115423405|emb|CAJ49939.1| RNA polymerase sigma factor 70 [Bordetella avium 197N]
          Length = 726

 Score =  447 bits (1149), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 267/670 (39%), Positives = 389/670 (58%), Gaps = 92/670 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI+V D   D E    SE
Sbjct: 129 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYDQAPDAETLLMSE 188

Query: 91  --------DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                   D ++  + A+ ++V      DS    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 189 NAPVASNDDDVEDEAEAALTTV------DSDFGRTTDPVRMYMREMGSVELLTREGEIEI 242

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++     + +G   + E++D    + PE        
Sbjct: 243 AKRIEDGLKHMVMAISACPTTINEILAHATRVREGQNQIDEVVD--GLVDPE-------- 292

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +G  Y                       + A VS D+                  +E +
Sbjct: 293 -DGEEY-----------------------AGAGVSADE------------------EEGD 310

Query: 263 DDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRS-------LQDNAVNGQKDEKSSVKC 314
           D  A  +S+ + + LR K +   DE++  + ++R+         D  ++ Q+  ++ +  
Sbjct: 311 DGPAGGMSSKQLEDLRVKALAKFDEVSRQFDKMRNSYEKDGYRSDIYISAQETIQNELMG 370

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
                K+V+ +     NQ      VE++  + + ++H            G+ R  FL+  
Sbjct: 371 IRFTAKMVEKLADTLRNQ------VEEVRQLERAVLHT------CVDRAGMPRSHFLKVF 418

Query: 375 QGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
            G E +  WV    A   P  E    +  ++ ++ +++ ++  +     + + + + +  
Sbjct: 419 PGNETNLQWVVEEVAAGHPYAET---LERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 475

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 476 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 535

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +
Sbjct: 536 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 595

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+ 
Sbjct: 596 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 655

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR
Sbjct: 656 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 715

Query: 673 SKKLRSFLDG 682
           + KL+SFL+G
Sbjct: 716 ADKLKSFLEG 725


>gi|1905967|gb|AAC45085.1| RNA polymerase sigma 80 subunit [Bordetella pertussis 18323]
          Length = 733

 Score =  447 bits (1149), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 266/678 (39%), Positives = 388/678 (57%), Gaps = 108/678 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------------ 79
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D            
Sbjct: 136 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 195

Query: 80  -------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
                   DD+EDE          + A+ ++V      DS    T DPVRMY+REMGS+E
Sbjct: 196 NAPVASNDDDVEDE----------AEAALTTV------DSDFGRTTDPVRMYMREMGSVE 239

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   M+ ++   P T   ++     + +G   + E++D    + 
Sbjct: 240 LLTREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD--GLVD 297

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           PE         +G  Y                       + A V+ D+            
Sbjct: 298 PE---------DGEEY-----------------------AGAGVTADE------------ 313

Query: 253 NDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                 DE +D  A  +S+ + + LR K +   DE+++ + ++R  Q     G K +   
Sbjct: 314 ------DEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMR--QSYEKEGYKSDAYL 365

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               +++ +L+ +  +  + +   D L   VE++  + + ++H            G+ R 
Sbjct: 366 KAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHT------CVDRAGMPRS 419

Query: 369 VFLERHQGRELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            FL+   G E +  WV    + A  + E      +  ++ ++ +++ ++  +     + +
Sbjct: 420 HFLKAFPGNETNLQWVLDEVAAAHAYSE-----TLERQIPAVQELQQKLIDLQTRVVLPL 474

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 475 KDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 534

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  
Sbjct: 535 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETG 594

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A
Sbjct: 595 AEPDPATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAA 654

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+
Sbjct: 655 LHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKAL 714

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HPSR+ KL+SFL+G
Sbjct: 715 RKLRHPSRADKLKSFLEG 732


>gi|33519536|ref|NP_878368.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus]
 gi|33517199|emb|CAD83581.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus]
          Length = 617

 Score =  446 bits (1148), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 275/655 (41%), Positives = 376/655 (57%), Gaps = 54/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + S+Q+ + + M+++MGI V+    D DD    E
Sbjct: 10  KLLVTRGKEQGYLTFSEVNDHLPEDIIDSDQLNNIIQMMNDMGIQVMEEAPDSDDFLLTE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               S +    A+ ++V      D+    T DPVRMY++EMG++ELL+REGEI IAKRIE
Sbjct: 70  NCGTSNNDEEDATEAAVQALSHVDTDLGRTTDPVRMYMKEMGAVELLTREGEIDIAKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+     +  G   L +++            GF      H 
Sbjct: 130 DGIHQVQCSVAEYPEAITYLLEQYKRVKTGEVRLSDLV-----------TGFVELNLEH- 177

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                D+   K   D   T   I S   +  DD        EN END+ N + D + +  
Sbjct: 178 -----DTLSTKTIHDGYITPEIINSPIII--DDE-------ENTENDDDN-NVDPELARK 222

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             + ++ Q     +                     NG+   +S ++      KL ++   
Sbjct: 223 KFTDLQKQYEKTRITI-----------------KYNGRDHHQSLLEIL----KLSEVFKQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  RI   E  +++L      + +  F+    G E    W++ 
Sbjct: 262 FRLVPKQFDYLVNNMRSMMDRIRLQERLIMKLCVDVSQMPKKKFINLFSGNETSKDWLNK 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A       W   +      I +   ++  I  ETG++I + ++I   +  GE +A  AKK
Sbjct: 322 ALSL-NTSWSQKLHNVDSKIQQSLYQLHQIEKETGLTIEQIKNINKRMAIGEAKAKRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EPTPEE+A+++ M  + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRVSRQILQETGCEPTPEELAERMFMSEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEP+S+ETPIGD++ SHLGDFIED N   PLDSA   NLR  T  VL+ LTPRE +
Sbjct: 501 LKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPLDSATSDNLRAATNDVLSGLTPREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|33602137|ref|NP_889697.1| RNA polymerase sigma factor RpoD [Bordetella bronchiseptica RB50]
 gi|33576575|emb|CAE33653.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica RB50]
          Length = 722

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 266/678 (39%), Positives = 388/678 (57%), Gaps = 108/678 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------------ 79
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D            
Sbjct: 125 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 184

Query: 80  -------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
                   DD+EDE          + A+ ++V      DS    T DPVRMY+REMGS+E
Sbjct: 185 NAPVASNDDDVEDE----------AEAALTTV------DSDFGRTTDPVRMYMREMGSVE 228

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   M+ ++   P T   ++     + +G   + E++D    + 
Sbjct: 229 LLTREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD--GLVD 286

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           PE         +G  Y                       + A V+ D+            
Sbjct: 287 PE---------DGEEY-----------------------AGAGVTADE------------ 302

Query: 253 NDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                 DE +D  A  +S+ + + LR K +   DE+++ + ++R  Q     G K +   
Sbjct: 303 ------DEADDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMR--QSYEKEGYKSDAYL 354

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               +++ +L+ +  +  + +   D L   VE++  + + ++H            G+ R 
Sbjct: 355 KAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHT------CVDRAGMPRS 408

Query: 369 VFLERHQGRELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            FL+   G E +  WV    + A  + E      +  ++ ++ +++ ++  +     + +
Sbjct: 409 HFLKAFPGNETNLQWVLDEVAAAHAYSE-----TLERQIPAVQELQQKLIDLQTRVVLPL 463

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 464 KDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 523

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  
Sbjct: 524 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETG 583

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A
Sbjct: 584 AEPDPATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAA 643

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+
Sbjct: 644 LHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKAL 703

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HPSR+ KL+SFL+G
Sbjct: 704 RKLRHPSRADKLKSFLEG 721


>gi|120599857|ref|YP_964431.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146292207|ref|YP_001182631.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
           CN-32]
 gi|120559950|gb|ABM25877.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. W3-18-1]
 gi|145563897|gb|ABP74832.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
           CN-32]
          Length = 616

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 277/654 (42%), Positives = 385/654 (58%), Gaps = 55/654 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + +S+ E P     ++   D+       L +II            GF +  E      
Sbjct: 131 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEEDVAPT 179

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 E   +D+ + + + E      ++D +     PE A      L    +++   + 
Sbjct: 180 ATHIGSELSDEDLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALKIIE 239

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A + +  P+ + AL EI E+++E R                                  L
Sbjct: 240 A-KGREHPESVKALFEIGEIFKEFR----------------------------------L 264

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSY--A 387
              + D LV+ +  +  R+   E   ++L  +   + +  F++   G E +  W     A
Sbjct: 265 VPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFTGNETNLDWFHAEKA 324

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            + P  E    V    + +L+ R+++ ++  ETG++IS  + I   +  GE +A  AKKE
Sbjct: 325 SNKPYAEGLRMVE---EDVLRCRSKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKKE 381

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 382 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 441

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVL
Sbjct: 442 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVL 501

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +V
Sbjct: 502 KIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAKV 561

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 562 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|162452723|ref|YP_001615090.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
 gi|161163305|emb|CAN94610.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
          Length = 639

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 273/665 (41%), Positives = 385/665 (57%), Gaps = 100/665 (15%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD------- 82
           + +K+++  + +G++T +E+N  LP D V+ +Q++D V  L +  I +VDG         
Sbjct: 61  TLEKLVETGKSKGFLTYDEVNDALPAD-VAPDQLDDVVGALGDEDIEIVDGATQVKIAPK 119

Query: 83  -LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            + DEE  E  L +        V      D   +S +DPVRMYLR+MGS+ LL+REGE+ 
Sbjct: 120 RIADEEAGEKKLVVTPDREEEDV------DYYSKS-NDPVRMYLRKMGSVSLLTREGEVE 172

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   + A++ +SP+                  +REIIDL              
Sbjct: 173 IAKRIEIGEQKVNAAILDSPIA-----------------VREIIDL-------------- 201

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
              G   +K                              + +V    ++AEND++  DE+
Sbjct: 202 ---GEKLRKH-----------------------------KIRVKELIKDAENDDQEFDEE 229

Query: 262 EDDSAHTLSAMEDQLRPKVMCA--LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           E D    +  ++   R     A  L+E  EV  E+R  Q +           V+      
Sbjct: 230 EADR-RIIRLIDKVKRVDKKKAELLEERKEVKTEVRRKQID-----------VEVTQATA 277

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF---LERHQG 376
           +LV  +  + LN+  ID +V++L  +  ++   E     L +  G+ +      L + +G
Sbjct: 278 ELVTTLEEMRLNKRTIDKIVQKLKSLISKVEKAEAGATELERRTGLSKGELKRELIKVKG 337

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
                  ++   +    E  +F +    +I   +  +K +  E  I ++  R     +R+
Sbjct: 338 NRALEGRLAKKLNVQREELNDFES----TIKNAQKGLKKVEEELNIDVAAIRDTYENIRE 393

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE  A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 394 GERMAERAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKF 453

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +  REPTPEEIA+K+
Sbjct: 454 STYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEYGREPTPEEIAEKM 513

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ +SP ++ I  NL E T +V
Sbjct: 514 ELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSVISPAEAVINMNLAEQTRKV 573

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L
Sbjct: 574 LKTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKQL 633

Query: 677 RSFLD 681
           +SF+D
Sbjct: 634 KSFID 638


>gi|319425507|gb|ADV53581.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
           200]
          Length = 613

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 277/654 (42%), Positives = 385/654 (58%), Gaps = 55/654 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + +S+ E P     ++   D+       L +II            GF +  E      
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEEDVAPT 176

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 E   +D+ + + + E      ++D +     PE A      L    +++   + 
Sbjct: 177 ATHIGSELSDEDLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALKIIE 236

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A + +  P+ + AL EI E+++E R                                  L
Sbjct: 237 A-KGREHPESVKALFEIGEIFKEFR----------------------------------L 261

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSY--A 387
              + D LV+ +  +  R+   E   ++L  +   + +  F++   G E +  W     A
Sbjct: 262 VPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFTGNETNLDWFHAEKA 321

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            + P  E    V    + +L+ R+++ ++  ETG++IS  + I   +  GE +A  AKKE
Sbjct: 322 SNKPYAEGLRMVE---EDVLRCRSKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKKE 378

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 379 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 438

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVL
Sbjct: 439 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVL 498

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +V
Sbjct: 499 KIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAKV 558

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 559 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 612


>gi|331017645|gb|EGH97701.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 616

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 280/652 (42%), Positives = 392/652 (60%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L ++  L   I P+   G     E       
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDD--GIAPPAEVPPPVDP 186

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    E   DD +E+          S D+  +V+S P+     +R              A
Sbjct: 187 KAVKAEGADDDEEESAD--------SSDEEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAELV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W    AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +G++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           TKEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 TKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|71736970|ref|YP_272918.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557523|gb|AAZ36734.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 616

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 279/652 (42%), Positives = 395/652 (60%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   +      L++ T +  E   L   +      G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHI------LSEYTCVTSEGGRLSDVLS-----GYIDPDDGIAPPAE 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                + +    + T+ D E +A  S DD  +V+S P+     +R              A
Sbjct: 180 VPPPVDPKAVKAEGTDDDEEESADAS-DDEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAEMV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|257483092|ref|ZP_05637133.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289627702|ref|ZP_06460656.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289649021|ref|ZP_06480364.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298485287|ref|ZP_07003379.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298160137|gb|EFI01166.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320325995|gb|EFW82053.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320332070|gb|EFW88006.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330868477|gb|EGH03186.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330881700|gb|EGH15849.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891182|gb|EGH23843.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. mori
           str. 301020]
 gi|330985810|gb|EGH83913.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331011674|gb|EGH91730.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 616

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 276/652 (42%), Positives = 393/652 (60%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L +++            G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAE 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                + +    + T+ D E +A  S DD  +V+S P+     +R              A
Sbjct: 180 VPPPVDPKAVKAEGTDDDEEESADAS-DDEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAEMV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|149927883|ref|ZP_01916133.1| RNA polymerase sigma factor RpoD [Limnobacter sp. MED105]
 gi|149823322|gb|EDM82555.1| RNA polymerase sigma factor RpoD [Limnobacter sp. MED105]
          Length = 878

 Score =  445 bits (1144), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 280/702 (39%), Positives = 411/702 (58%), Gaps = 74/702 (10%)

Query: 1   MTIGKKRNRDS--------DSEHEDSDDSLV--FDFSDDSWKKMIKLARQRGYVTIEELN 50
           + I  KR R S        +S +  S ++ V   +   +  K +IK+ ++RGY+T  E+N
Sbjct: 230 LVIMPKRGRGSKAKDKALINSAYLSSANATVEELELRRNQLKTLIKMGKERGYLTFAEIN 289

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
             LP D    E +E  V+   +MGI V +     +     D+  + +SA ++    +   
Sbjct: 290 DHLPDDVTDGEVIEAMVSTFHDMGITVYEQAPDAEALLMNDNAPVGTSAEDAEEEAEAAL 349

Query: 111 DSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
            + D     T DPVRMY+REMG++ELL+REGEI IAKRIEAG   M+ ++   P   + +
Sbjct: 350 SNVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVQAISACPAIVEDV 409

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           +     + +G + + E++D           G                       D   TE
Sbjct: 410 VGLGQRIAEGLSTVDEVVD-----------GII---------------------DDSITE 437

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME----DQLRPKVMCA 283
             +E+AA             PE   +D+ N DE+E +   T S M     ++L+   +  
Sbjct: 438 EMVEAAA-------------PEETNDDDDNEDEEEGNDGGTTSGMSARQLEELKKNSLAV 484

Query: 284 LDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
             EI + + +L+ ++ D   N    +K+    + + E+ +K+  +    +    +L EQ+
Sbjct: 485 FAEIEKQFAKLKKVRADGGYNTPAYKKAK---EAIAEQFMKIRFTAKQVERLCSILREQV 541

Query: 343 YDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVA 400
             + K     E E+  +A    G+ R+ FL++ +G E++  WV +++       W    A
Sbjct: 542 DSVRK----IEREIYDIAVNRVGVPREQFLDKFRGHEVEAAWVDTFSAS--NAAWAETWA 595

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
             V +I +++ ++ +I     + +++ R I   +  GE  A +AK+EM+EANLRLVIS+A
Sbjct: 596 RNVPAINELQQKLVAIQDTVSLPLNDLRAINKQMVSGENRARLAKREMIEANLRLVISIA 655

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 656 KKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 715

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+ R +R++  +   EP P  +A+++ MP E +RK+LKI KEPIS+ETPI
Sbjct: 716 IPVHMIETINKMNRISRQILQETGIEPDPATLAERMEMPEEKIRKILKIAKEPISMETPI 775

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD+D SHLGDFIED + ++P D+A  ++LR  T  VL SLTPRE +VLRMRFGI M+TDH
Sbjct: 776 GDDDDSHLGDFIEDNHTLAPQDAAQYSSLRFVTKDVLDSLTPREAKVLRMRFGIEMSTDH 835

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 836 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 877


>gi|91788957|ref|YP_549909.1| sigma 70 (RpoD) [Polaromonas sp. JS666]
 gi|91698182|gb|ABE45011.1| RNA polymerase, sigma 70 subunit, RpoD [Polaromonas sp. JS666]
          Length = 784

 Score =  445 bits (1144), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 271/664 (40%), Positives = 385/664 (57%), Gaps = 79/664 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E++  LP   V +E +E  V ML++MG+ V         E + D
Sbjct: 184 KTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVVNMLNDMGVAVY--------EQAPD 235

Query: 92  SLDLASSASNSSVFLQKRK-----------DSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +  L  + +  +V  ++             DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 236 AETLLLNNTGPTVATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 295

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++ ESP T   ++   +E+ +G  ++  ++D           GF 
Sbjct: 296 EIAKRIEGGLMKMMEAISESPATIAEIMRLGEEIREGKIVISTVVD-----------GFS 344

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
           +  E   Y   ED  +  E DD     G                                
Sbjct: 345 NPNEADDYVAEEDFDEFDEEDDDDGKGG-------------------------------- 372

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-KVLKE 319
                +  L+   ++L+ + +   D+IA ++ ++    D    G     + VK  K L +
Sbjct: 373 -----SKALTKKLEELKKEALSRFDKIASLFEKVHKTYDKEGYGTP---TYVKAQKALSD 424

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L+ +  +    +   D+L  Q+ D+ K+    E EL R+  +  G+ ++ F++      
Sbjct: 425 ELMTVRFTAKTIEKLCDMLRGQVLDVRKK----ERELRRIIVEKCGMPQETFIKDFPPNL 480

Query: 379 LDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           L+  WV   K    G+ W   +A  +  I +++ ++  +     + + + + I   + +G
Sbjct: 481 LNLKWVE--KQVASGKPWSTVMARNIPPIQELQTKLAELQARVVVPLGQLKDINKRMNEG 538

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 539 ESNSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 598

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ 
Sbjct: 599 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQEFGFEPDASILAAKME 658

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +PL++A+QA LR+    +L
Sbjct: 659 IPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSANTAPLEAAMQAGLRDVVKDIL 718

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLR
Sbjct: 719 DSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLR 778

Query: 678 SFLD 681
           SF+D
Sbjct: 779 SFID 782


>gi|293604556|ref|ZP_06686961.1| DNA-directed RNA polymerase sigma subunit RpoD [Achromobacter
           piechaudii ATCC 43553]
 gi|292817137|gb|EFF76213.1| DNA-directed RNA polymerase sigma subunit RpoD [Achromobacter
           piechaudii ATCC 43553]
          Length = 770

 Score =  444 bits (1143), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 266/670 (39%), Positives = 386/670 (57%), Gaps = 92/670 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D   D E    SE
Sbjct: 173 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 232

Query: 91  --------DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                   D ++  + A+ ++V      DS    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 233 NAPVASNDDDVEDEAEAALTTV------DSDFGRTTDPVRMYMREMGSVELLTREGEIEI 286

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++     + +G   + E++D    + PE        
Sbjct: 287 AKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVD--GLVDPE-------- 336

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +G  Y                       + A V+ D+                  DE +
Sbjct: 337 -DGEEY-----------------------AGAGVTADE------------------DESD 354

Query: 263 DDSAHTLSAME-DQLRPKVMCALDEIAEVYRELR-------SLQDNAVNGQKDEKSSVKC 314
           D  A  +S+ + + LR K +   DE+ + + ++R          D  V  Q+  ++ +  
Sbjct: 355 DGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYKSDIYVRAQESIQNELMG 414

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
                K+V+ +     NQ      VE++  + + ++H            G+ R  F++  
Sbjct: 415 IRFTAKMVEKLADTLRNQ------VEEVRQLERAVLHT------CVDRAGMPRTHFIKVF 462

Query: 375 QGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
            G E +  WV    A   P   +   +  ++ ++ +++ ++  +     + + + + +  
Sbjct: 463 PGNETNLQWVVDEVAAGHP---YAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 519

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 520 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 579

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +
Sbjct: 580 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 639

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+ 
Sbjct: 640 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 699

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR
Sbjct: 700 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 759

Query: 673 SKKLRSFLDG 682
           + KL+SFL+G
Sbjct: 760 ADKLKSFLEG 769


>gi|317403353|gb|EFV83866.1| RNA polymerase sigma-70 factor [Achromobacter xylosoxidans C54]
          Length = 813

 Score =  444 bits (1143), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 269/670 (40%), Positives = 384/670 (57%), Gaps = 90/670 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D   D E    SE
Sbjct: 214 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 273

Query: 91  DSLDLASSASNSSVFLQKRK--------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +    A  ASN      + +        DS    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 274 N----APVASNDDDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEI 329

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++     + +G   + E++D    + PE        
Sbjct: 330 AKRIEDGLKHMVMAISACPTTINEILAHVLRVREGQAQIDEVVD--GLVDPE-------- 379

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +G  Y                       + A VS D+                  DE +
Sbjct: 380 -DGEEY-----------------------AGAGVSADE------------------DESD 397

Query: 263 DDSAHTLSAME-DQLRPKVMCALDEIAEVYRELR-------SLQDNAVNGQKDEKSSVKC 314
           D  A  +S+ + + LR K +   DE+ + + ++R          D  V  Q+  ++ +  
Sbjct: 398 DGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYKSDIYVRAQESIQNELMG 457

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
                K+V+ +     NQ      VE++  + + ++H            G+ R  F++  
Sbjct: 458 IRFTAKMVEKLADTLRNQ------VEEVRQLERAVLHT------CVDRAGMPRTHFIKVF 505

Query: 375 QGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
            G E +  WV    A   P  E    +  ++ ++ +++ ++  +     + + + + +  
Sbjct: 506 PGNETNLQWVVDEVAAGHPYAET---LERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 562

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 563 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 622

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +
Sbjct: 623 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 682

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+ 
Sbjct: 683 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 742

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR
Sbjct: 743 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 802

Query: 673 SKKLRSFLDG 682
           + KL+SFL+G
Sbjct: 803 ADKLKSFLEG 812


>gi|77359315|ref|YP_338890.1| RNA polymerase sigma factor [Pseudoalteromonas haloplanktis TAC125]
 gi|76874226|emb|CAI85447.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 615

 Score =  444 bits (1142), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 279/656 (42%), Positives = 384/656 (58%), Gaps = 56/656 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE   ++
Sbjct: 10  KLLILKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  TTTDEDAAEAAAAALATVEKEIGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGIN 128

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +  S+ E P     L+   D+       L +II            GF    E  +    
Sbjct: 129 QVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------VGFIDPNEDTAPISA 177

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLS 270
            +   E     + + + D + + +  +D+      P PE A     NL +  + +  T  
Sbjct: 178 TNIGSELSAKQLNDDDKDDDDSDEDDEDEEEVDTGPDPEEARVHFENLRDLYNKARETFE 237

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           A + +  P  + A+ EI E+++  + +    D  VN  ++    V+              
Sbjct: 238 A-KGRSHPDSLAAIFEIGELFKTFKLIPKQFDRMVNNMREMMDRVRV------------- 283

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
               Q R  L+++Q   I+K                 + +  F++     E D  WV   
Sbjct: 284 ----QER--LIMKQAVQIAK-----------------LPKKTFVKHFANNETDATWVDL- 319

Query: 388 KDFPEGEWKNFVACEVDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            +    E  +    EV   I++  N+++ I   TG++I   + I   +  GE +A  AKK
Sbjct: 320 -EIAANEKYSAKLEEVKPEIIRSLNKLRVIESSTGLNIERIKDINRRMSIGEAKARRAKK 378

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 379 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 438

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + VRKV
Sbjct: 439 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKVRKV 498

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE +
Sbjct: 499 LKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAREAK 558

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 559 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 614


>gi|237803341|ref|ZP_04590926.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331025322|gb|EGI05378.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 615

 Score =  444 bits (1142), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 279/653 (42%), Positives = 392/653 (60%), Gaps = 53/653 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L ++  L   I P+               K 
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPK- 187

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
              + + E DD +E   D       + D+  +V+S P+     +R              A
Sbjct: 188 ---AAKAEGDDEEEESAD-------ASDEEDEVESGPDPVIAQQR------------FGA 225

Query: 272 MEDQLRPKVMCALDEIAEVYRE-LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           + DQ+            E+ R+ L+ L        +D+K ++   V    L +L   + L
Sbjct: 226 VSDQM------------EITRKALKKLG-------RDDKHAIAEMV---ALAELFMPIKL 263

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAK 388
              + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK
Sbjct: 264 VPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 323

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              + ++   +A     I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEM
Sbjct: 324 G--KSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEM 381

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 382 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 441

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLK
Sbjct: 442 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLK 501

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VL
Sbjct: 502 IAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVL 561

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 562 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|332284638|ref|YP_004416549.1| RNA polymerase sigma factor RpoD [Pusillimonas sp. T7-7]
 gi|330428591|gb|AEC19925.1| RNA polymerase sigma factor RpoD [Pusillimonas sp. T7-7]
          Length = 749

 Score =  444 bits (1141), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 267/660 (40%), Positives = 381/660 (57%), Gaps = 73/660 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI+V D     D     D
Sbjct: 153 KVLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYDQAPDADALLMSD 212

Query: 92  SLDLASS---ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  +ASS     + +       DS    T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 213 NAPVASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 272

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   M+ ++   P T   ++ +   + DG   + E++D           G          
Sbjct: 273 GLKHMVMAIAACPTTVNEILQYIQRVRDGAAQIDEVVD-----------GLI-------- 313

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                           + EG+  + A VS D+                  DE+ED  A  
Sbjct: 314 ----------------DQEGEEYAGAGVSVDN------------------DENEDGPAGG 339

Query: 269 LSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           +S+ + + LR K +   + I+  + ++R+  +     Q  E +  +  +L E L+ +  +
Sbjct: 340 MSSKQLEHLRTKSLKKFENISVWFSKMRTAFERD-GYQAQEYAEAQEAILNE-LMGVRFT 397

Query: 328 LSLNQSRIDLLVEQLYDISK---RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
             + +   D L EQ+  + K    ++H            G+ R  F++   G E + +WV
Sbjct: 398 AKMVEKLADTLREQVAQVRKLERTVLHT------CVDRAGMPRAYFIKVFPGNETNLNWV 451

Query: 385 --SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
               A   P   +   +   + ++ +I+ ++  +     + + + + +   +  GE +A 
Sbjct: 452 LEEVAAGHP---YSETLERHIPAVQEIQQKLIDLQTSVVLPLKDLKDVNKRMATGEAKAR 508

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 509 KAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 568

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R  R++  +   EP P  +A+K+ MP + 
Sbjct: 569 WIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGAEPDPATLAQKMDMPEDK 628

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRK+LKI KEPIS+ETPIGD+D SHLGDFIED   +SP + A+  ++R+    VL SLTP
Sbjct: 629 VRKILKIAKEPISMETPIGDDDDSHLGDFIEDTGTLSPSEWALHGSMRDVVKEVLDSLTP 688

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+G
Sbjct: 689 REAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFLEG 748


>gi|311105374|ref|YP_003978227.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans A8]
 gi|310760063|gb|ADP15512.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans A8]
          Length = 750

 Score =  444 bits (1141), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 263/666 (39%), Positives = 389/666 (58%), Gaps = 84/666 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D   D E    SE
Sbjct: 153 KQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDAETLLMSE 212

Query: 91  --------DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                   D ++  + A+ ++V      DS    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 213 NAPVASNDDDVEDEAEAALTTV------DSDFGRTTDPVRMYMREMGSVELLTREGEIEI 266

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++     + +G   + E++D    + PE        
Sbjct: 267 AKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVD--GLVDPE-------- 316

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +G  Y                       + A V+ ++                  DE +
Sbjct: 317 -DGEEY-----------------------AGAGVTAEE------------------DEGD 334

Query: 263 DDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           D  A  +S+ + + LR K +   DE+ + + ++R   +   +G K +      + ++ +L
Sbjct: 335 DGPAGGMSSKQLEDLRVKALAKFDEVGKQFEKMRHSYEK--DGYKSDVYVRAQESIQNEL 392

Query: 322 VKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           + +  +  + +   D L   VE++  + + ++H            G+ R  F++   G E
Sbjct: 393 MGIRFTAKMVEKLADTLRQQVEEVRQLERAVLHT------CVDRAGMPRTHFIKVFPGNE 446

Query: 379 LDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            +  WV    A   P   +   +  ++ ++ +++ ++  +     + + + + +   +  
Sbjct: 447 TNMQWVVDEVAAGHP---YAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMAT 503

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 504 GEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 563

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+
Sbjct: 564 STYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKM 623

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+    V
Sbjct: 624 DMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDVVKEV 683

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL
Sbjct: 684 LDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKL 743

Query: 677 RSFLDG 682
           +SFL+G
Sbjct: 744 KSFLEG 749


>gi|28867765|ref|NP_790384.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213967690|ref|ZP_03395837.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382750|ref|ZP_07231168.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
           Max13]
 gi|302064027|ref|ZP_07255568.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
           K40]
 gi|302130708|ref|ZP_07256698.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|28851000|gb|AAO54079.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213927466|gb|EEB61014.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato T1]
 gi|330878419|gb|EGH12568.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 616

 Score =  444 bits (1141), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 279/652 (42%), Positives = 391/652 (59%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L ++  L   I P+   G     E       
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDD--GIAPPAEVPPPVDP 186

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    E   DD +E+          S D+  +V+S P+     +R              A
Sbjct: 187 KAVKAEGADDDEEESAD--------SSDEEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAELV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W    AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +G++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|332531768|ref|ZP_08407653.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038744|gb|EGI75186.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 616

 Score =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 280/655 (42%), Positives = 380/655 (58%), Gaps = 53/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE   ++
Sbjct: 10  KLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  TTTDEDAAEAAAAALATVEKEIGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGIN 128

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE-GHSYQK 210
            +  S+ E P     L+   D+       L +II     I P         T  G     
Sbjct: 129 QVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII--VGFIDPNEDTAPISATNIGSELSA 186

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
           ++    +K+  D  +++ + E       D        PE A     NL +  + +  T  
Sbjct: 187 KQLEDDDKDDKDDADSDDEDEEEIDTGPD--------PEEARIHFENLRDLYNKARDTFE 238

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           A + +  P+   A+ EI E++R  + +    D  VN  ++    V+              
Sbjct: 239 A-KGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRV------------- 284

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
               Q R  L+++Q   I+K                 + +  F++     E D  WV   
Sbjct: 285 ----QER--LIMKQAVQIAK-----------------LPKKTFVKHFANNETDASWVDLE 321

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
               E         + + I  I N++  I   TG+SI   + I   +  GE +A  AKKE
Sbjct: 322 ISGNEKYSAKLEEVKPEIIRSI-NKLSVIEQTTGLSIERIKDINRRMSIGEAKARRAKKE 380

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 381 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 440

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVL
Sbjct: 441 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIRKVL 500

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE +V
Sbjct: 501 KIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAREAKV 560

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 561 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 615


>gi|127511929|ref|YP_001093126.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637224|gb|ABO22867.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella loihica PV-4]
          Length = 616

 Score =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 274/654 (41%), Positives = 381/654 (58%), Gaps = 55/654 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D ++   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D  ++   ++       +     T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  DSTDEDAAEEAAAALATVEAELG--RTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + AS+ E P     ++   D        L +II            GF           
Sbjct: 131 NTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDII-----------SGFVDPNAEDMAPT 179

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 E   DD+ + + + +       ++ S     PE A      L E  + +   + 
Sbjct: 180 ATHIGSELSDDDLDDEDDEGDDEDDDGDEEDSPKGPDPEEARERFTQLREAHEKALKVIE 239

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
            ++ +  P+   AL +I E+++E R                                  L
Sbjct: 240 -LKGREHPEATAALFDIGEIFKEFR----------------------------------L 264

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS--YA 387
              + D LV+ + ++  ++   E  +++L  +   + +  F++ +   E    W +   A
Sbjct: 265 VPKQFDRLVKNMREMMDKVRIQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNEEIA 324

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
              P  E    VA +V    + R ++ +I  ETG++I+  + I   +  GE +A  AKKE
Sbjct: 325 AKKPYAEGLEMVAEDVQ---RCRAKLDAIENETGLAIAAIKDINRRMSIGEAKARRAKKE 381

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 382 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 441

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVL
Sbjct: 442 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKVL 501

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +V
Sbjct: 502 KIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAKV 561

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 562 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|330963831|gb|EGH64091.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 616

 Score =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 279/652 (42%), Positives = 391/652 (59%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L ++  L   I P+   G     E       
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDD--GIAPPAEVPPPVDP 186

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    E   DD +E+          S D+  +V+S P+     +R              A
Sbjct: 187 KAVKAEGADDDEEESAD--------SSDEEDEVESGPDPIIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAELV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W    AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +G++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|294139649|ref|YP_003555627.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
 gi|7388082|sp|O24744|RPOD_SHEVD RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1912047|dbj|BAA19475.1| RNA polymerase sigma factor [Shewanella violacea]
 gi|293326118|dbj|BAJ00849.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
          Length = 614

 Score =  443 bits (1139), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 283/655 (43%), Positives = 390/655 (59%), Gaps = 56/655 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +   D ++   +E
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMMTE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D   +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  DSTD-DDAAEEAAAALATVEAELGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + AS+ E P    +++   D        L +II     I P +       T   S   
Sbjct: 128 YTVQASVAEYPPAIASILDQFDRYEAEEVRLSDIIS--GFIDPNAADIAPTATHIGS--- 182

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             D SQ +   D  + +   +   +  +  +      P+  E+ ER   +  +   +TL 
Sbjct: 183 --DLSQSERDKDDSKDDSKDDDEDEEEEGPKG-----PDPEESKER-FTQLREVHENTLK 234

Query: 271 AMEDQLR--PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
            + D+ R  P+   AL EI E+++E R +        K+ ++++    ++E+L+      
Sbjct: 235 IIADKGRGHPEATVALFEIGELFKEFRLMPKQFDRLVKNMRATMDKVRVQERLI------ 288

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW--VSY 386
                 + L VEQ                       + +  F++ +   E    W     
Sbjct: 289 ------MKLCVEQA---------------------KMPKKNFVKGYTADESSIAWFDTEL 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A   P  E    +  +V    + R ++  I  ETG++I+  + I   +  GE +A  AKK
Sbjct: 322 ASKKPYAEGLKMIEPDVR---RCRFKLDIIEKETGLAIASIKDINRRMSIGEAKARRAKK 378

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 379 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 438

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 439 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 498

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 499 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGLTAREAK 558

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 559 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 613


>gi|71282406|ref|YP_270983.1| RNA polymerase sigma-70 factor [Colwellia psychrerythraea 34H]
 gi|71148146|gb|AAZ28619.1| RNA polymerase sigma-70 factor [Colwellia psychrerythraea 34H]
          Length = 616

 Score =  443 bits (1139), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 270/660 (40%), Positives = 379/660 (57%), Gaps = 63/660 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++GY+T  ++N  LP D + S+Q+ED V+M+++MGI V +          +D
Sbjct: 10  KDLITKGKEQGYLTFAQVNDHLPQDIIDSDQVEDIVSMINDMGIQVFEN------APDQD 63

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +L +A + ++        +     +S    T DPVRMY+REMG++ELL+R+GEI IAKRI
Sbjct: 64  TLMMAEANTDEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTRKGEIVIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D        L +II            GF       
Sbjct: 124 EEGIKEVQRSVSEYPPAINYLLDMWDNFEAEEVRLTDIII-----------GFLDPDAED 172

Query: 207 SYQKREDS--SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                  +    E  ++D+   + + +      +D+  +   P      ++  L  +  +
Sbjct: 173 DDVAAAATHVGSELSKEDLANEDSEKKEGDAEEEDEEEEDTGPDPELAREKFTLLREAHE 232

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A  +   + +       A+D +AEV++E R                            L
Sbjct: 233 NATKVVKKKGRGHKDAQEAIDAVAEVFKEFR----------------------------L 264

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
           +  L       D LV+ +  +  R+   E  +++   S G+ +  F++   G E    W 
Sbjct: 265 IPKL------FDKLVKNMRGMMDRLRVQERLIMKHCVSAGMPKTTFIKIFPGNETSKEWF 318

Query: 385 SY--AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
               A   P       +  +V+  +   N+I+    ET ++I   + I   +  GE +A 
Sbjct: 319 EAEKAAGNPYSTKLGDIEHDVERCIYKLNQIEE---ETHLNIHGIKDINRRMSIGEAKAR 375

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 376 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 435

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + 
Sbjct: 436 WIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELAERMVMPEDK 495

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED +   P+DSA   NL+  T  VLA LT 
Sbjct: 496 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGSGELPVDSATSENLKGATHEVLAGLTA 555

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++L+SFLDG
Sbjct: 556 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLKSFLDG 615


>gi|330898880|gb|EGH30299.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330980978|gb|EGH79081.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 616

 Score =  442 bits (1138), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 274/652 (42%), Positives = 392/652 (60%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L +++            G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAE 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                + +    +  + D E +A  S D+  +V+S P+     +R              A
Sbjct: 180 VPPPVDPKAAKAEGADDDEEESADAS-DEEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAEMV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|117921525|ref|YP_870717.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. ANA-3]
 gi|117613857|gb|ABK49311.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. ANA-3]
          Length = 619

 Score =  442 bits (1137), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 281/652 (43%), Positives = 393/652 (60%), Gaps = 48/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + +S+ E P     ++   D+       L +II     + P+ +      T   S   
Sbjct: 131 NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIIS--GFVNPDEEDLGPTATHIGSELS 188

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            ED   E + +D ++ +GD E     +K         PE A      L    +++   + 
Sbjct: 189 EEDLDDEDDDEDDEDEDGDGEGDDDGNK------GPDPEEARERFSQLRTAYENALKIID 242

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A + +  P+ + AL EI E+++E R                    ++ ++  +LV S+  
Sbjct: 243 A-KGREHPESIQALFEIGEIFKEFR--------------------LVPKQFDRLVKSM-- 279

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
            +S +D           R+   E  L++L  +   + +  F++   G E +  W    K+
Sbjct: 280 -RSMMD-----------RVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDWFDAEKN 327

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +   +     E D + + R+++ +I  ETG+ I+  + I   +  GE +A  AKKEMV
Sbjct: 328 STKPYAEGLRMVEED-VQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARRAKKEMV 386

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 387 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 446

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLKI
Sbjct: 447 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVLKI 506

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VLR
Sbjct: 507 AKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAKVLR 566

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 567 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 618


>gi|66047868|ref|YP_237709.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63258575|gb|AAY39671.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Pseudomonas syringae pv. syringae B728a]
          Length = 616

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 274/652 (42%), Positives = 392/652 (60%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L +++            G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAE 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                + +    +  + D E +A  S D+  +V+S P+     +R              A
Sbjct: 180 VPPPVDPKAVKAEGADDDEEESADAS-DEEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAEMV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|167622943|ref|YP_001673237.1| RNA polymerase sigma 70 subunit RpoD [Shewanella halifaxensis
           HAW-EB4]
 gi|167352965|gb|ABZ75578.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella halifaxensis
           HAW-EB4]
          Length = 615

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 283/656 (43%), Positives = 387/656 (58%), Gaps = 60/656 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D ++   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D   +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  DSTD-DDAAEEAAAALATVEAELGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + AS+ E P     ++   D        L +II     + P ++      T  H    
Sbjct: 131 NTVQASVAEYPQAIAMILEQFDRYEAEEVRLSDIIS--GFVDPNAED--VAPTATHVGSD 186

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             D   + E DD  + + D E       D        PE A+     L    +++   L 
Sbjct: 187 LSDDDLDDEDDDDDDDDDDEEEEGPKGPD--------PEEAKEKFTTLRVAHENA---LR 235

Query: 271 AMEDQLR--PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
            + D+ R  P+   AL EI E+++E R                                 
Sbjct: 236 IIADKGRGHPESTVALFEIGEIFKEFR--------------------------------- 262

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS-- 385
            L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   E    W +  
Sbjct: 263 -LMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNEE 321

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A   P  E    V+ +V    + R ++ +I  ETG++I   + I   +  GE +A  AK
Sbjct: 322 LASGKPYAEGLKVVSFDVQ---RCRAKLDAIETETGLAIGAIKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 614


>gi|254704732|ref|ZP_05166560.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 257

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 210/256 (82%), Positives = 239/256 (93%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 1   EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 60

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 61  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 120

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 121 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 180

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 181 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 240

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+KLRSFLD
Sbjct: 241 KLKHPSRSRKLRSFLD 256


>gi|257454210|ref|ZP_05619480.1| RNA polymerase sigma factor RpoD [Enhydrobacter aerosaccus SK60]
 gi|257448383|gb|EEV23356.1| RNA polymerase sigma factor RpoD [Enhydrobacter aerosaccus SK60]
          Length = 634

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 277/657 (42%), Positives = 396/657 (60%), Gaps = 43/657 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDS 92
           +I+L +++GY+T  E+N  LP     S+Q++D + ML+++GI + +   D +D   S+D+
Sbjct: 12  LIQLGKEQGYLTYAEINDQLPESVTESDQIDDIIQMLTDVGIKIFETAPDEDDIMLSDDA 71

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            D   +   ++  L   +    R+TD PVRMY+REMG+++LL+REGEIAIAKRIE G   
Sbjct: 72  DDDEIAVDEAAAVLASVESEPGRTTD-PVRMYMREMGTVDLLTREGEIAIAKRIEDGIRD 130

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEAC-IGPESKGGFFHGTEGHS 207
           +  ++   P T   LI    +  +G   + +II    D EA  + P +            
Sbjct: 131 VQHAMTFWPGTVAMLINEYRQTFEGEKKISDIITGFLDPEAADVIPLADDEEVEIALPII 190

Query: 208 YQKREDSSQEKERDDVQETEGDIESA-AKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             K +D + E E DD  E   +IE A  +VS+D           A+ +E          A
Sbjct: 191 KPKVKDDTAEDELDDEAENADEIEEADGEVSED-----------ADTEE----------A 229

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   E +LR       +E+ +++ +++ L         D  S V  K    +L     
Sbjct: 230 SGLDPEEVRLR------FEELEQLFTKVKDLL-----ATHDRDSEV-VKTAMNELANCFM 277

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              LN    D +++ + ++ + +  NE  +++L    G + +D F +     E +  W+ 
Sbjct: 278 LFKLNSRVSDNIMDMMREVYEDVRKNERHIMKLVIRRGKMPKDEFRKTFPHNETNLDWLP 337

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             +   +  + + +   +D +L+ +  I+      G+SI + + +   +  GE +A  AK
Sbjct: 338 -NRIAGKPAFADTLERVLDEVLQYQGRIQQHEQNLGMSIDQMKVVARNMSVGEAKARRAK 396

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 397 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 456

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRK
Sbjct: 457 QAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRK 516

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED +  SP+D A    L+E T  VLA+LT RE 
Sbjct: 517 VLKIAKEPISMETPIGDDEDSHLGDFIEDSSISSPVDEATAQGLKEATREVLANLTEREA 576

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VL+MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 577 KVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 633


>gi|330826139|ref|YP_004389442.1| RNA polymerase sigma-710 subunit RpoD [Alicycliphilus denitrificans
           K601]
 gi|329311511|gb|AEB85926.1| RNA polymerase, sigma 70 subunit, RpoD [Alicycliphilus
           denitrificans K601]
          Length = 802

 Score =  441 bits (1135), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 268/659 (40%), Positives = 379/659 (57%), Gaps = 69/659 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V     D + L    
Sbjct: 202 KKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNN 261

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +  +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 262 VAPTATTVEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 320

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 321 GGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPEEADD 369

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y   ED  +  E DD     G                                     + 
Sbjct: 370 YVAEEDFDEYDEEDDDDGKGG-------------------------------------SK 392

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE---KLVKL 324
            ++ + ++L+ + +   DE+  ++ ++  + D    G     S    KV  E   KL+ +
Sbjct: 393 AMTRLLEKLKTEALDRFDELRSLFEKMHKIYDKEGYG-----SPAYMKVQHEISAKLMTI 447

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHW 383
             +    +   D++  Q+ D+ K+    E EL R +    G+ ++ F++      L+  W
Sbjct: 448 RFTAKTIEKLCDMVRAQVDDVRKK----ERELRRIIVDKCGMPQETFIKEFPPNLLNLQW 503

Query: 384 VSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           V   K    G+ W   +   +  I +++  +  +     + ++E + I   + +GE  + 
Sbjct: 504 VE--KQAAAGKPWSAVMQRNIPPIQELQQHLIDLQSRVVVPLAELKAINKRMNQGEANSR 561

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 562 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 621

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 622 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 681

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTP
Sbjct: 682 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPIDAAMQAGLRDVVKDILDGLTP 741

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 742 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 800


>gi|323144090|ref|ZP_08078731.1| RNA polymerase sigma factor RpoD [Succinatimonas hippei YIT 12066]
 gi|322416132|gb|EFY06825.1| RNA polymerase sigma factor RpoD [Succinatimonas hippei YIT 12066]
          Length = 648

 Score =  441 bits (1134), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 279/675 (41%), Positives = 396/675 (58%), Gaps = 60/675 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL--- 83
           +K++I   +++GY+TIEE+N  +PPD +S +Q+   +    +MGINV     D DD+   
Sbjct: 10  FKQLIARGKEQGYLTIEEINDLIPPDIISGDQLSVFIQTFIDMGINVCETPPDPDDILLS 69

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +  + +E+ ++  ++  +S+V + +        T DPVRMY+REMG++ LL+R+ EI I+
Sbjct: 70  DSSQAAEEDVETVANQLDSTVDIGR--------TTDPVRMYMREMGNVSLLTRKDEIEIS 121

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +   + E PL  + L    DE                 + P+S+       
Sbjct: 122 KRIERGTNDVQMCIVEYPLAMEELFRRYDE----------------ALAPDSEIRLGDIV 165

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIES------AAKVSKDDRSKVDSPPENAENDERN 257
            G S   +E+ + +   DD  ETE DIE       +A+V  DD  +     EN    ++ 
Sbjct: 166 VGFSEPSKEEINIDI--DDSVETEEDIEKLIDEEESAEVQLDDVKE-----ENTGKAKKG 218

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDE--IAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                +D   +    ++    +     D   + + + ELR +Q   V     +K S   K
Sbjct: 219 KKSKVEDDPDSDEDEDEDSASQADSGPDPELVKQKFTELR-IQYEKVVAAHAKKGSAAVK 277

Query: 316 VLKEKLVKL---VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFL 371
             K++L KL     +  L    +D L+ +++D+  R+ + +  +  +A +  G+K D   
Sbjct: 278 KYKQELQKLSEMFSTFRLVPQVLDSLLRKMHDMMDRVKNQDHRIREVAVNICGMKLDELK 337

Query: 372 ERHQG--RELDPHWVSYAKDFPEGEWKNFVACEVDS---ILKIRNEIKSISVETGISISE 426
             +     E D  W   A        + +VA   D    I +  N +K +  E+GISI+ 
Sbjct: 338 AFYTDSEHESDMSWFDKAL----KSKRPYVARLKDYRPVIEECVNALKEVETESGISIAR 393

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R +   V  G+  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 394 LRDLSRRVMMGDAMAKKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 453

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE
Sbjct: 454 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEKGRE 513

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A+K+ +P + +RKV+KI KEPISLETP+GD+D SHLGDFIED + V P ++A  
Sbjct: 514 PTPEELAEKMGLPEDKIRKVMKIAKEPISLETPVGDDDDSHLGDFIEDSSIVVPAEAATS 573

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +L+     VL  + PRE +VLRMRFGIGM +DHTLEEVG+QF VTRERIRQIEAKA+RK
Sbjct: 574 ESLKNAINNVLDEMPPREAQVLRMRFGIGMPSDHTLEEVGRQFGVTRERIRQIEAKALRK 633

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP RS  LR FLD
Sbjct: 634 LRHPCRSAGLRGFLD 648


>gi|148284623|ref|YP_001248713.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
 gi|146740062|emb|CAM80186.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
          Length = 614

 Score =  441 bits (1134), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 248/594 (41%), Positives = 365/594 (61%), Gaps = 61/594 (10%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E+ + LAS+A+      ++  D    STD  VR YL++M +  LLSREGEI +AK++E G
Sbjct: 66  EEEVALASNATEGE--FEEDLDDNIYSTD-IVRAYLKDMSNTTLLSREGEIELAKQMEEG 122

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
           +  ++  +C  P   + LI W ++L     L+R +I+LE+ I                Y 
Sbjct: 123 KKTVIHFICHLPYVMKLLIQWYEDLVHSRILVRNLIELESNI----------------YD 166

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED +Q+       +++GD E           ++ + P                    L
Sbjct: 167 QPEDDNQQD-----YDSDGDCE-----------ELQNEP--------------------L 190

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS---SVKCKVLKEKLVKLVG 326
           + +E ++ PK++  +  ++++  +L  +  +     K   S   S K   L ++L+  V 
Sbjct: 191 TKVESEILPKILDKMQVVSDLATQLFEVAAHDFKLHKSSCSYQESKKFTELSKELIAAVS 250

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           ++  N+  I  ++ +LY ++K I+  E  LL+ A+ Y I R  FL ++       +W+  
Sbjct: 251 NIHFNKQSIKNILNKLYSVNKDIISKEINLLKAAEKYKISRHDFLFQYNS---GSNWLQK 307

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   + EW  F++ E D I    +    I     + +  F+ I+  ++ GE +  +AKK
Sbjct: 308 VKLLHQDEWNKFLSKEKDLIKSTIDCFGEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKK 367

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +MVE+N RLV+ VAK Y NRGL FLDLIQEGNIGLMKA +K+++ LGYKFST A WWV+Q
Sbjct: 368 KMVESNTRLVVHVAKPYVNRGLPFLDLIQEGNIGLMKAVDKYNYLLGYKFSTCATWWVRQ 427

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I+R++ADQ+ TIRIPVHM D I K+VR +++M N++  EPT  EIA+KL+MP++ V+KV
Sbjct: 428 SISRAVADQARTIRIPVHMADTISKIVRVSKQMHNELGYEPTASEIAEKLSMPIDKVKKV 487

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           ++I KEP+SLE PIG+ED S L DFIEDKNAV P++ AI+ +LRETTTR L++LT REER
Sbjct: 488 MRIAKEPVSLENPIGEEDGSCLSDFIEDKNAVLPIEEAIKFSLRETTTRALSTLTAREER 547

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VLR+RFGIG+ TD+TLEEVG +F VTRER+RQIEAKA+RKLKHP RSKKL+SFL
Sbjct: 548 VLRLRFGIGLPTDYTLEEVGGEFKVTRERVRQIEAKALRKLKHPVRSKKLKSFL 601


>gi|160900477|ref|YP_001566059.1| RNA polymerase sigma 70 subunit RpoD [Delftia acidovorans SPH-1]
 gi|160366061|gb|ABX37674.1| RNA polymerase, sigma 70 subunit, RpoD [Delftia acidovorans SPH-1]
          Length = 808

 Score =  441 bits (1134), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 271/657 (41%), Positives = 378/657 (57%), Gaps = 65/657 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V     D + L    
Sbjct: 208 KALIKLGKTRGYLTHSEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNN 267

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + +     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 268 TGQSATTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 326

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  E   
Sbjct: 327 GGLMDMMEAISASPATIAEILAMSEEIREGKVVISTIVD-----------GFVNANENDD 375

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y   ED  +  E DD     G   S A   K                   L+E ++++  
Sbjct: 376 YVAEEDFDEYDEEDDDDGKGG---SKALTKK-------------------LEELKNEALR 413

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
              AM +          D++ +VY +        +  QK          L E+L+ +  +
Sbjct: 414 RFDAMREN--------FDKMHKVYDKEGYGTPTYIKVQK---------ALTEELMTIRFT 456

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWV-- 384
               +   DL+  Q+ D+ K+    E EL + +    G+ ++ F+ +     L+  WV  
Sbjct: 457 AKTIEKLCDLVRAQVDDVRKK----ERELRKIIVDKCGMPQETFIAQFPPNLLNLQWVVQ 512

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A   P   W N +   +  + +++  +  +     + + E + I   +  GE  +  A
Sbjct: 513 QVAAGKP---WSNVLERNIPPVQELQQNLIDLQSRVVVPLDELKRINKRMNDGERASRDA 569

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 570 KKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 629

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +R
Sbjct: 630 RQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIR 689

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTPRE
Sbjct: 690 KIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPVDAAMQAGLRDVVKDILDGLTPRE 749

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 750 AKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 806


>gi|189183187|ref|YP_001936972.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
 gi|189179958|dbj|BAG39738.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
          Length = 615

 Score =  441 bits (1133), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 238/567 (41%), Positives = 352/567 (62%), Gaps = 58/567 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           + D VR YL++M +  LLSREGEI +AK++E G+  ++  +C  P   + LI W ++L  
Sbjct: 91  STDIVRAYLKDMSNTTLLSREGEIELAKQMEEGKKTVIHFICHLPYVMKLLIQWYEDLVH 150

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
              L+R +I+LE+ I                Y + ED +Q        +++GD E     
Sbjct: 151 SRILVRNLIELESNI----------------YDQPEDDNQHD-----YDSDGDCE----- 184

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
                 ++ + P                    L+ +E ++ PK++  +  ++++  +L  
Sbjct: 185 ------ELQNEP--------------------LTKVESEILPKILDKMQVVSDLATQLFE 218

Query: 297 LQDNAVNGQK---DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           +  +     K   + + S K   L ++L+  V ++  N+  I  ++ +LY ++K I+  E
Sbjct: 219 VAAHDFKLHKSSCNYQESKKFTELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKE 278

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
             LL+ A+ Y I R  FL ++       +W+   K   + EW  F++ E D I    +  
Sbjct: 279 INLLKAAEKYKISRHDFLFQYNS---GSNWLQKVKLLHQDEWNKFLSKEKDLIKSTIDYF 335

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             I     + +  F+ I+  ++ GE +  +AKK+MVE+N RLV+ VAK Y NRGL FLDL
Sbjct: 336 SEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDL 395

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +K+++ LGYKFST A WWV+Q+I+R++ADQ+ TIRIPVHM D I K+V
Sbjct: 396 IQEGNIGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMADTISKIV 455

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R +++M N++  EPT  EIA+KL+MP++ V+KV++I KEP+SLE PIG+ED S L DFIE
Sbjct: 456 RVSKQMHNELGYEPTASEIAEKLSMPIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIE 515

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DKNA+ P++ AI+ +LRETTTR L++LT REERVLR+RFGIG+ TD+TLEEVG +F VTR
Sbjct: 516 DKNAILPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTR 575

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQIEAKA+RKLKHP RSKKL+SFL
Sbjct: 576 ERVRQIEAKALRKLKHPVRSKKLKSFL 602


>gi|212633971|ref|YP_002310496.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
 gi|212555455|gb|ACJ27909.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
          Length = 612

 Score =  440 bits (1132), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 283/656 (43%), Positives = 385/656 (58%), Gaps = 63/656 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D ++   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D   +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  DSTD-DDAAEEAAAALATVEAELGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE-GHSYQ 209
             + AS+ E P     ++   D        L +II     I P ++      T  G    
Sbjct: 131 NTVQASVAEYPQAIAMILEQFDRFEAEEVRLSDIIS--GFIDPNAEDVAPTATHVGSELS 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHT 268
             E   ++ + DD  E EG                  P PE A+     L    + +   
Sbjct: 189 DEELDDEDDDEDDEDEEEGP---------------KGPDPEEAKEKFTTLRVAHERALEI 233

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
           +S ++ +  P+   AL EI E+++E R                                 
Sbjct: 234 IS-IKGRGHPESTVALFEIGEIFKEFR--------------------------------- 259

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS-- 385
            L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   E    W +  
Sbjct: 260 -LMPKQFDRLVKSMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNEE 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A   P  E    V  +V    + R ++ +I  ETG++I   + I   +  GE +A  AK
Sbjct: 319 LASGKPYAEGLKMVDYDVQ---RCRAKLDAIETETGLAIGAIKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 611


>gi|332528540|ref|ZP_08404528.1| RNA polymerase, sigma 70 subunit, rpod [Hylemonella gracilis ATCC
           19624]
 gi|332042051|gb|EGI78389.1| RNA polymerase, sigma 70 subunit, rpod [Hylemonella gracilis ATCC
           19624]
          Length = 784

 Score =  440 bits (1132), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 271/671 (40%), Positives = 380/671 (56%), Gaps = 83/671 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E++  LP     +E +E  VAMLS+MG+ V +      +    +
Sbjct: 174 KLLIKLGKTRGYLTHGEISDHLPDKLADAETLEVVVAMLSDMGVTVFE------QTPDAE 227

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L + ++A  ++   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 228 TLLINNTAPTAASEEEAEEEAEAAVSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 287

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   MM ++  SP T  AL+   +E+ +G  ++  ++D           GF + 
Sbjct: 288 AKRIEGGLMDMMEAISASPTTIAALLAMAEEIREGKVVISTVVD-----------GFVNA 336

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E   Y   ED  +  E DD     G                                  
Sbjct: 337 EESDDYVAEEDFDEYDEADDDDGKGG---------------------------------- 362

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-KVLKEKL 321
              +  L+   ++L+ + +   D I  ++ ++    D    G     + VK  K L ++L
Sbjct: 363 ---SKALTKKLEELKNQALERFDRIRSMFEKVHKAYDKEGYGTP---AYVKAQKALSDEL 416

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE-- 378
           + +  +    +   DL+  Q+ D+     H E EL R+     G  +D F+    GR+  
Sbjct: 417 MTIRFTAKTIEKLCDLVRGQVADVR----HKERELRRIIVDRCGYPQDQFVLEFGGRDKN 472

Query: 379 --------LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
                   LD  WV    +  +  W   ++  V  I  I+ ++  +     + + + + I
Sbjct: 473 GNPSKSHLLDLKWVEKQANAGK-PWSGIISRNVPPIQDIQQKLIDLQARVVVPLEQLKDI 531

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 532 NKRMNQGEAASRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 591

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP   
Sbjct: 592 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAS 651

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A+K+ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+++A+QA LR
Sbjct: 652 LLAQKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTANTAPVEAAMQAGLR 711

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +L  LTPRE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHP
Sbjct: 712 EVVKEILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHP 771

Query: 671 SRSKKLRSFLD 681
           SRS KLRSF D
Sbjct: 772 SRSDKLRSFTD 782


>gi|319762043|ref|YP_004125980.1| RNA polymerase sigma factor rpod [Alicycliphilus denitrificans BC]
 gi|317116604|gb|ADU99092.1| RNA polymerase sigma factor RpoD [Alicycliphilus denitrificans BC]
          Length = 802

 Score =  440 bits (1132), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 268/659 (40%), Positives = 378/659 (57%), Gaps = 69/659 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V     D + L    
Sbjct: 202 KKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNN 261

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +  +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 262 VAPTATTVEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 320

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 321 GGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPEEADD 369

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y   ED  +  E DD     G                                     + 
Sbjct: 370 YVAEEDFDEYDEEDDDDGKGG-------------------------------------SK 392

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE---KLVKL 324
            ++ + ++L+ + +   DE+  ++ ++  + D    G     S    KV  E   KL+ +
Sbjct: 393 AMTRLLEKLKTEALDRFDELRSLFEKMHKIYDKEGYG-----SPAYMKVQHEISAKLMTI 447

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHW 383
             +    +   D++  Q+ D+ K+    E EL R +    G+ ++ F +      L+  W
Sbjct: 448 RFTAKTIEKLCDMVRAQVDDVRKK----ERELRRIIVDKCGMPQETFSKEFPSNLLNLQW 503

Query: 384 VSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           V   K    G+ W   +   +  I +++  +  +     + ++E + I   + +GE  + 
Sbjct: 504 VE--KQAAAGKPWSAVMQRNIPPIQELQQHLIDLQSRVVVPLAELKAINKRMNQGEANSR 561

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 562 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 621

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 622 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 681

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTP
Sbjct: 682 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPIDAAMQAGLRDVVKDILDGLTP 741

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 742 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 800


>gi|330970856|gb|EGH70922.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 616

 Score =  440 bits (1132), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 273/652 (41%), Positives = 392/652 (60%), Gaps = 50/652 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L +++            G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAE 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                + +    +  + D E +A  S D+  +V+S P+     +R              A
Sbjct: 180 VPPPVDPKAVKAEGADDDEEESADAS-DEEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAEMV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 384 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 443

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI
Sbjct: 444 RSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKI 503

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLR
Sbjct: 504 AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLR 563

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNT+HTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 564 MRFGIDMNTNHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|157374211|ref|YP_001472811.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
           HAW-EB3]
 gi|157316585|gb|ABV35683.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
           HAW-EB3]
          Length = 612

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 278/666 (41%), Positives = 383/666 (57%), Gaps = 83/666 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +   D ++   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D  ++   ++       +     T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  DSTDEDAAEEAAAALATVEAELG--RTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + AS+ E P     ++   D        L +II            GF           
Sbjct: 131 NTVQASVAEYPQAISMILEQFDRYEAEEVRLSDII-----------SGFV---------- 169

Query: 211 REDSSQEKERDDVQETEGDI--------ESAAKVSKDDRSKVDSP----PENAENDERNL 258
                 +   DDV  T   +               +DD  + + P    PE A+     L
Sbjct: 170 ------DPNADDVAPTATHVGSELSDEELDDEDDEEDDDEEEEGPKGPDPEEAKERFTQL 223

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
            E  +++   + A++ +  P+   AL EI E+++E R                       
Sbjct: 224 REVHENTLKVI-ALKGRGHPESTLALFEIGELFKEFR----------------------- 259

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
                      L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   
Sbjct: 260 -----------LMPKQFDRLVKNMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSN 308

Query: 378 ELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W +   A   P  E    V  +V    + R ++ +I  ETG++I+  + I   + 
Sbjct: 309 ESSIEWFNEELASKKPYVEGLEMVDPDVR---RCRAKLDAIEKETGLAIASIKDINRRMS 365

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A++
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 485

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  
Sbjct: 486 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHE 545

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 546 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEI 605

Query: 676 LRSFLD 681
           L+SFLD
Sbjct: 606 LKSFLD 611


>gi|170725515|ref|YP_001759541.1| RNA polymerase sigma 70 subunit RpoD [Shewanella woodyi ATCC 51908]
 gi|169810862|gb|ACA85446.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella woodyi ATCC
           51908]
          Length = 611

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 282/656 (42%), Positives = 391/656 (59%), Gaps = 61/656 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +   D ++   SE
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEMMMSE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D   +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  DSTD-DDAAEEAAAALATVEAELGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             + AS+ E P     ++   D        L +II     + P ++      T  H   +
Sbjct: 128 NTVQASVAEYPQAIAMILEQYDRYEAEEIRLSDIIS--GFVDPNAED--VAPTATHVGSE 183

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             D   + E D+  E + D E   K            PE A+     L E  +++   ++
Sbjct: 184 LSDEDLDDEDDEDSEDDEDEEEGPK---------GPDPEEAKERFTQLREAHENTLRVIN 234

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
            ++ +  P+   AL EI E+++E R                                  L
Sbjct: 235 -LKGRGHPESTLALFEIGEIFKEFR----------------------------------L 259

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW----VS 385
              + D LV+ +  +  R+   E  +++L  +   + +  F++ +   E    W    ++
Sbjct: 260 MPKQFDRLVKSMRAMMDRVRVQERLIMKLCVEQAKMPKKNFVKGYTSDESSIAWFDEELA 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             K + EG        E D + + R ++ +I  ETG++I+  + I   +  GE +A  AK
Sbjct: 320 SKKPYVEG----LEMVEPD-VRRCRAKLDAIEKETGLAIAAIKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 610


>gi|149923522|ref|ZP_01911923.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149815591|gb|EDM75122.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 589

 Score =  439 bits (1130), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 261/654 (39%), Positives = 385/654 (58%), Gaps = 87/654 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           ++   +++G++T+ EL   LPPD +   ++++  +ML + G+ V                
Sbjct: 17  IVAFGKKKGHMTVAELRELLPPDVIDHGKLDEWKSMLESEGVKV---------------- 60

Query: 94  DLASSASNSS---VFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            LA S   S       +K KD +D S T+DPVRMYLR+MGS+ LL+REGE+ IAKRIE G
Sbjct: 61  -LAKSLEKSPKRKARTRKAKDESDTSRTNDPVRMYLRKMGSVSLLTREGEVEIAKRIEQG 119

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSY 208
              +   +  SP+    +    D++      +++++ +     GP+ K      ++    
Sbjct: 120 ELQVFEIVLASPVAVPYVQDMFDKIKRSQLRIKDVVTIATPNDGPQPK------SKAPVN 173

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           Q     + +K+ + V+    DIE          ++  +P + A+   + +++  DD    
Sbjct: 174 QDAAFENMQKQLEKVRRHHKDIEKLLA------AQAATPDKPAKERGKTVEQQVDDHQ-- 225

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
                       +  +D I E+Y     L    V+G  DE +S+      E++ +    L
Sbjct: 226 ------------IAIVDAIREMY-----LSRRPVDGMVDELNSIV-----ERVQRATQDL 263

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
           +  + R  + + +L  + + +  +E E  +L +  G+                    +  
Sbjct: 264 TTCERRAGMELSELRGLFRDVRLSEEEEFKLCRRLGL--------------------HPS 303

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +  E E +  +A +          I+ +  ETG+   +   + + + K   +A  AK E+
Sbjct: 304 ELHEIEARMKLATK---------RIRQVEQETGMDAPDLIELHTRLMKARRQADRAKAEL 354

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 355 VEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAI 414

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+ +P++ VRKVLK
Sbjct: 415 TRAIADQARTIRIPVHMIETINKLIRTSRSLVQELGREPTPEEIAEKMELPLDKVRKVLK 474

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPISLETPIG+E+ SHLGDFIEDKNAVSP +  I  NL + T RVLA+LTPREE+VL
Sbjct: 475 IAKEPISLETPIGEEEDSHLGDFIEDKNAVSPAEVVININLADQTRRVLATLTPREEKVL 534

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L++F++ 
Sbjct: 535 RMRFGIGETSDHTLEEVGQDFSVTRERIRQIEAKALRKLRHPSRSKRLKAFVES 588


>gi|295698766|ref|YP_003603421.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
 gi|291157279|gb|ADD79724.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
          Length = 629

 Score =  438 bits (1126), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 278/664 (41%), Positives = 392/664 (59%), Gaps = 60/664 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP D V S+Q+ED +  + +MGI V +      E   ED
Sbjct: 10  KVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTE------EVPDED 63

Query: 92  SLDLASSASNS--------SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L L    S++        +  L   +    R+TD P+RMY+REMG+IELL+REGEI IA
Sbjct: 64  ELILTDPTSSTDEETVEAATQVLSSVEQEIGRTTD-PIRMYMREMGTIELLTREGEIDIA 122

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +  S+ E P +   ++        G   L +II      G  S+  F    
Sbjct: 123 KRIEDGINQIQRSISEYPKSISYILKQYFLFESGEMKLSDII-----TGLSSEDTF---- 173

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
              S +  + +    + + +     +I S     KD     +S   N E++  ++D    
Sbjct: 174 --SSSKNVDKNFSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHID---- 227

Query: 264 DSAHTLSAMEDQLRPKVM-CALDEIAEVYREL-RSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                         PK+      E+   Y ++  SL++N +      KSS     +++ L
Sbjct: 228 --------------PKIARKKFLELQNQYEKVTHSLKENGI------KSSQSILDIQD-L 266

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE--RHQGRE 378
            ++     L   ++D L+  +    ++I   E  ++ ++ + Y I +  FL       +E
Sbjct: 267 CEIFKQFRLVPKQLDFLISDIRKTIEKIKIQEKLIINISFKEYKIPKKYFLNLFSENPKE 326

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            D   +  +  + + + K F   ++DS I++  NE+  I  +TGISIS+ + I   +  G
Sbjct: 327 YDLKELIVSNRYNKKDEKKF---KLDSTIVQALNELNEIEKDTGISISKIKEIGRKISIG 383

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 384 ETIARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 443

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+   +R++  +  REP+PEE+++++ 
Sbjct: 444 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNHISRQILQETGREPSPEELSERML 503

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P E +RKVLKI +EPIS+ETPIGD++ SHLGDFIED     PL+SA   +LR  T  VL
Sbjct: 504 IPEEKIRKVLKIAREPISMETPIGDDEDSHLGDFIEDTTLELPLESATSESLRSATNEVL 563

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + LT RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 564 SGLTTREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSELLR 623

Query: 678 SFLD 681
           SFLD
Sbjct: 624 SFLD 627


>gi|319792617|ref|YP_004154257.1| RNA polymerase, sigma 70 subunit, rpod [Variovorax paradoxus EPS]
 gi|315595080|gb|ADU36146.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus EPS]
          Length = 778

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 271/672 (40%), Positives = 384/672 (57%), Gaps = 85/672 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V +      +    +
Sbjct: 168 KTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLNDMGVAVYE------QTPDAE 221

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L ++A  ++   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 222 TLLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 281

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF + 
Sbjct: 282 AKRIEGGLMAMMEAISASPATIAEILRLANEIREGKVVISTIVD-----------GFSNP 330

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E   Y   ED  +  E DD     G                                  
Sbjct: 331 NEADDYVAEEDFDEFDEEDDDDGKGG---------------------------------- 356

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK-VLKEKL 321
              +  L+   ++L+   +   D IA ++ ++  + D    G     + VK +  L E+L
Sbjct: 357 ---SKALTKKLEELKRDALERFDRIAGMFEKVHKIYDKEGYGTP---AYVKAQEALSEEL 410

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE-- 378
           + +  +    +   DL+  Q+ D+ K+    E EL R+     G  +D F+    G +  
Sbjct: 411 MTIRFTAKTIEKLCDLVRTQVDDVRKK----ERELRRIIVDKCGFPQDEFIRDFSGYDKN 466

Query: 379 --------LDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
                   L+  WV   K    G+ W   +A  +  + +++  +  I     + +++ + 
Sbjct: 467 GNRIASNLLNLKWVE--KQAAAGKPWSAVLARNIPPVQELQQRLADIQSRVVVPLTQLKD 524

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 525 INKRMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 584

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP  
Sbjct: 585 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDA 644

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             +A K+ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED +  +P+++A+QA L
Sbjct: 645 GILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGL 704

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKH
Sbjct: 705 RDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKH 764

Query: 670 PSRSKKLRSFLD 681
           PSRS KLRSF+D
Sbjct: 765 PSRSDKLRSFID 776


>gi|88858406|ref|ZP_01133048.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
           tunicata D2]
 gi|88820023|gb|EAR29836.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
           tunicata D2]
          Length = 615

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 273/654 (41%), Positives = 380/654 (58%), Gaps = 54/654 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE   ++
Sbjct: 10  KLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVCESAPDADELMMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  TTTDEDAAEAAAAALATVDKEIGRTTD-PVRMYMREMGTVELLTREGEIQIAKRIEEGIN 128

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +  S+ E P     L+   D+       L +II            GFF   E       
Sbjct: 129 QVQISVAEYPEAITYLLEQWDKYEAEEIRLSDII-----------SGFFDSDEEQFPIAA 177

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLS 270
                +   + +++ + D++       ++      P PE A  +   L  D  + A  + 
Sbjct: 178 THIGSDLNDEQLKDEDVDLDDDDDDDSNEEEVDLGPDPELARENFEKL-RDLYNKARLIF 236

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             + +  P    A+ EI E++R  + +    D  VN  +D    V+              
Sbjct: 237 EEKGRSHPDAKEAITEIGELFRTFKLMPKQFDRMVNNMRDMMDRVRV------------- 283

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
               Q R  L+++Q   I+K                 + +  F++     E +  W+   
Sbjct: 284 ----QER--LIMKQACQIAK-----------------LPKKTFIKHFANNESNGEWLDIE 320

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            +  E        C  + I +  N+++++   TG+S+   + I   +  GE +A  AKKE
Sbjct: 321 INAGEKYSDKLAECRPE-IERSLNKLRNMEQTTGLSVERIKDINRRMSIGEAKARRAKKE 379

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 380 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 439

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVL
Sbjct: 440 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIRKVL 499

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +L+  T  VLA LT RE +V
Sbjct: 500 KIAKEPISMETPIGDDEDSHLGDFIEDSTIESPIDSATMESLKGATHEVLAGLTAREAKV 559

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD
Sbjct: 560 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLD 613


>gi|315127802|ref|YP_004069805.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315016316|gb|ADT69654.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 614

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 279/659 (42%), Positives = 382/659 (57%), Gaps = 63/659 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE   ++
Sbjct: 10  KLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  TTTDEDAAEAAAAALATVEKEIGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGIN 128

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF--HGTEGHSYQ 209
            +  S+ E P     L+   D+       L +II            GFF     E     
Sbjct: 129 QVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------SGFFDPDAEEAPPIA 177

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP--PENAENDERNLDEDEDDSAH 267
                S+  E+    + +   +       +D  +VD+   PE A     NL +    +  
Sbjct: 178 ATNIGSELSEK----QLDDSDDDDDDSDDEDEEEVDTGPDPEEARVHFENLRDLYTKARE 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQ---DNAVNGQKDEKSSVKCKVLKEKLVKL 324
           T    + +  P+   A+ EI E++R  + +    D  VN  ++    V+           
Sbjct: 234 TFDN-KGRSHPESQAAILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRV---------- 282

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                  Q R  L+++    +SK                 + +  F++     E D  W+
Sbjct: 283 -------QER--LIMKHAVQVSK-----------------LPKKTFVKHFANNETDTAWL 316

Query: 385 SYAKDFPEGEWKNFVACEVDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               +    E  +    EV   IL+  +++ S+   TG+SI   + I   +  GE +A  
Sbjct: 317 DI--EIAANEKHSAKLEEVKPEILRCISKLTSMEESTGLSIERIKDINRRMSIGEAKARR 374

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKI 494

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT R
Sbjct: 495 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAR 554

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 555 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 613


>gi|160872802|ref|ZP_02062934.1| RNA polymerase sigma factor RpoD (Sigma-70) [Rickettsiella grylli]
 gi|159121601|gb|EDP46939.1| RNA polymerase sigma factor RpoD (Sigma-70) [Rickettsiella grylli]
          Length = 642

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 279/682 (40%), Positives = 398/682 (58%), Gaps = 68/682 (9%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE-----QMEDTVAMLSNMGINVV 78
           F+      +++I   +++G+VT  E+N  L  D +S       Q+++ + ML+++GI V 
Sbjct: 3   FEQQQSRLRELITHGKKQGFVTYAEINDHLLEDIISEAEQEQLQLDEIILMLNDIGIPVY 62

Query: 79  D-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +   D+E    S    +     S+ +V +     +    T DPVRMY+REMG++ELL+RE
Sbjct: 63  EVPPDMETLLSSSIVNNAEEENSSENVTILGNITTELGRTTDPVRMYMREMGTVELLTRE 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALI--IWRDE-----LNDGTTLLREIIDLEAC 190
           GEI +AKRIE G   ++A+L + P+    ++    R E     LND   ++   +DLE  
Sbjct: 123 GEIKLAKRIEDGLQAILAALAQYPVNISHILNEYTRYEQQEIRLND---IISGFLDLEEL 179

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR--SKVDSPP 248
             P       + T   +  +R + S ++  D   +   D +S    + DD    ++D  P
Sbjct: 180 SIPLELPSGKNITSTETPDERFNRSDKRTDDKDNDEGDDAKSKISATDDDEGFGELDGGP 239

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-- 306
                        + + AHT  A                     EL++  +  +  QK  
Sbjct: 240 -------------DPELAHTRFA---------------------ELKAHYEAYIAAQKKW 265

Query: 307 --DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
              +K ++K  VL   L        L   ++D L   +  + ++I   E  ++RL  +  
Sbjct: 266 GRHDKKTIKQAVL---LADAFTKFKLIPRQLDKLTRNMRGLLEKIRLQERIIMRLCVNEA 322

Query: 365 -IKRDVFLERHQGRELDPHWVS---YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            + R +F+      E + +++    +AK       K  +A     I   +N++  +    
Sbjct: 323 KMPRLLFINTFPKNETNENFLKKHIHAKKSYSSRLKELLA----PITAAQNKLHELEKTI 378

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G++I+E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 379 GMTITEIKEINRQMSAGETKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 438

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++ 
Sbjct: 439 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQIL 498

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVS 599
               +EP+PE+++KK+ +P + +RK+LKI KEPIS+ETPIGDED  SHLGDFIED  A+S
Sbjct: 499 QATGKEPSPEDLSKKMGLPEDKIRKILKIAKEPISMETPIGDEDGDSHLGDFIEDAAALS 558

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+A    LRET  RVLASLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 559 PIDAATIEGLRETAQRVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 618

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HP+RS+ LRSFLD
Sbjct: 619 EAKALRKLRHPTRSEPLRSFLD 640


>gi|304415465|ref|ZP_07396113.1| RNA polymerase sigma 70 (sigma D) subunit [Candidatus Regiella
           insecticola LSR1]
 gi|304282694|gb|EFL91209.1| RNA polymerase sigma 70 (sigma D) subunit [Candidatus Regiella
           insecticola LSR1]
          Length = 612

 Score =  437 bits (1125), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 280/658 (42%), Positives = 382/658 (58%), Gaps = 64/658 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAVEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 127 EGINQVQCSVAEYPEAITYLLEQYDRVEAEEVRLSDLI-----------TGFV------- 168

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                D + ++  +D+  +       +++S ++   +DS  + A++D+ N     ++S  
Sbjct: 169 -----DLNAKENEEDITLSASATHIGSELSTEEL--IDSDGDTADSDDEN-----NNSID 216

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVG 326
            L A E                 + ELR   +N     +KD ++ +  K     L  +  
Sbjct: 217 PLLAREK----------------FSELREQYENTKKAIKKDGRNRLNAKNEILALSNIFK 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV- 384
              L   + D LV  +  + K+I   E  +++L  +   + + +FL      E D  W  
Sbjct: 261 LFRLVPKQFDYLVNNMRLMMKQIRAQERIIIKLCVEQCKMPKKIFLTLFTRHETDDKWFE 320

Query: 385 -SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            + + + P  E    VA +V      R ++  I  +TG+++ + + I   +  GE +A  
Sbjct: 321 EALSANKPWSEKLKEVAEDVGCC---RKKLIQIEEKTGLTVEQIKDINRRMSIGEAKARR 377

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R AR+M     +E           MP + +
Sbjct: 438 IRQAITRSIADQARTIRIPVHMIETINKLNRVARQML----QEXXXXXXXXXXXMPEDKI 493

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PL SA   +LR  T  VLA LTPR
Sbjct: 494 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLGSATSESLRSATHEVLAGLTPR 553

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 554 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|218674803|ref|ZP_03524472.1| RNA polymerase sigma factor RpoD [Rhizobium etli GR56]
          Length = 254

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 209/252 (82%), Positives = 235/252 (93%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 2   IVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTP
Sbjct: 62  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTP 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANL
Sbjct: 122 EELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANL 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKH
Sbjct: 182 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 241

Query: 670 PSRSKKLRSFLD 681
           PSRS+KLRSFLD
Sbjct: 242 PSRSRKLRSFLD 253


>gi|319944403|ref|ZP_08018677.1| DNA-directed RNA polymerase sigma subunit RpoD [Lautropia mirabilis
           ATCC 51599]
 gi|319742364|gb|EFV94777.1| DNA-directed RNA polymerase sigma subunit RpoD [Lautropia mirabilis
           ATCC 51599]
          Length = 785

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 262/664 (39%), Positives = 385/664 (57%), Gaps = 80/664 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---- 83
           +++IKL ++RG++T  E+N  LP      E ++  +   S+MGI+V     D D L    
Sbjct: 188 RQLIKLGKERGFLTYAEINDHLPEGLTEVEAIDQMIGTFSDMGISVYEQAPDTDSLLLND 247

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                S+D  +  + A+ SSV      DS    T DPVRMY+REMGS+ELL+REGEI IA
Sbjct: 248 RTVTSSDDDTEEEAEAALSSV------DSEFGRTTDPVRMYMREMGSVELLTREGEIVIA 301

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+IE G   MM ++   P T   ++   D++      + EI+D    + P++        
Sbjct: 302 KKIEEGLKDMMHAISACPTTIAEVLEQADKVRAAQLRVDEIVD--GLLDPDA-------- 351

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                            DD + + G                   P  ++ D    D+DE 
Sbjct: 352 -----------------DDEEMSFG-------------------PARSDGD----DDDEA 371

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             A   +A  ++L+ + +   D I   + ++R  Q    +G K        + ++ +L+ 
Sbjct: 372 SVAAMNNAKLEELKEEALSRFDSIGAAFEQMR--QALETDGYKSPAYLAAQESVQRQLMS 429

Query: 324 LVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  +  + +   D+L   V+++  + + I+             G+ R+ F++   G E +
Sbjct: 430 IRFTAKVVEKLCDMLRAQVDEVRTVERTILDI------CVNRVGMSREHFIKSFPGNETN 483

Query: 381 PHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
             WV    A + P   + + +A  +  I  ++ ++  + V   + + + + I   +  GE
Sbjct: 484 LAWVENELAGNPP---YADVLARSIPDIQDLQQKLIDLQVRVVLPLPDLKEINKRMAMGE 540

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA +KF++  G+KFST
Sbjct: 541 MKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEFRRGFKFST 600

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ M
Sbjct: 601 YATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGVEPDPATLAEKMDM 660

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+  ++RE    VL 
Sbjct: 661 PEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTTTLAPSDAALHDSMREVVKEVLD 720

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLTPRE +VLRMRFG+ M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+S
Sbjct: 721 SLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKS 780

Query: 679 FLDG 682
           FL+G
Sbjct: 781 FLEG 784


>gi|92113104|ref|YP_573032.1| sigma 70 (RpoD) [Chromohalobacter salexigens DSM 3043]
 gi|91796194|gb|ABE58333.1| RNA polymerase, sigma 70 subunit, RpoD [Chromohalobacter salexigens
           DSM 3043]
          Length = 614

 Score =  437 bits (1123), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 282/668 (42%), Positives = 377/668 (56%), Gaps = 83/668 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +++G++T  E+N  LP D    +Q+ED +AM+++MGI+VV+    ED     D
Sbjct: 11  KELIAQGKEQGFLTYAEVNDHLPEDIADPDQVEDIIAMINDMGISVVEEAPDEDTLMMSD 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                S+A  +   L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 71  QSADESAAEEAVAALAAVESDVGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGTR 129

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M+SL   P    +++   D   D     R        I P+       G  G +  + 
Sbjct: 130 EVMSSLAYLPGAVDSILSAYDATQDEEAPGRLSDLFSGFIDPD------EGIPGVAEAEV 183

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA--------ENDERNLDEDED 263
            +   E    D     GD+      ++++ +     PE A        E +ER     E+
Sbjct: 184 PEPEPEPSAAD-----GDVSEDDDEAEEEETGGGPDPEEARARFEQIREQNERAKAAIEE 238

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               +  A  +Q R         +AE++  +                    K++ +   +
Sbjct: 239 HGLGSKEASAEQAR---------LAELFSPI--------------------KLVPKHFER 269

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           LVG + ++       VEQ+    K IM          +   + R  F+    G E D  W
Sbjct: 270 LVGQVRIS-------VEQIRGQEKAIMQI------FVKQAKVPRKTFIGSFPGAESDLEW 316

Query: 384 VSYAKDFPEGEWKNFVACEV---DSILKIRNEI----KSISVETGISISEFRHIVSMVRK 436
           +             F+A      D +   R +I    + I  E  + +    HI  + R+
Sbjct: 317 LD-----------RFMAKHTKFADRLEPFRADIQRAQRKIGFEEEMVLLPVSHIKEVNRR 365

Query: 437 ---GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 366 LSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 425

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ 
Sbjct: 426 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELG 485

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L MP + VRKVLKI KEPIS+ETPIGD+D SHLGDFIED   + P+DSA    L E T
Sbjct: 486 ERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDSATGEGLIEAT 545

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 546 RNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 605

Query: 674 KKLRSFLD 681
           + LR+FLD
Sbjct: 606 EPLRTFLD 613


>gi|296112900|ref|YP_003626838.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|295920594|gb|ADG60945.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|326561129|gb|EGE11494.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 7169]
 gi|326564438|gb|EGE14665.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 103P14B1]
 gi|326564864|gb|EGE15069.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 46P47B1]
 gi|326567590|gb|EGE17705.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC1]
 gi|326569439|gb|EGE19499.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC8]
 gi|326571363|gb|EGE21378.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC7]
 gi|326575352|gb|EGE25280.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis CO72]
 gi|326576561|gb|EGE26468.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 101P30B1]
 gi|326577423|gb|EGE27307.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis O35E]
          Length = 626

 Score =  435 bits (1119), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 272/665 (40%), Positives = 385/665 (57%), Gaps = 60/665 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-----D 79
           D S      +I+L +++GY+T  E+N  LP     S+Q+ED + ML+++GI V      D
Sbjct: 12  DTSSSQLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDD 71

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D L  + GS+D +    +   ++  L   +    R+TD PVRMY+REMG+++LL+REGE
Sbjct: 72  DDILLSDTGSDDDI----ATDEAAAVLASVETEPGRTTD-PVRMYMREMGTVDLLTREGE 126

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I IAKRIE G   +   +   P T + ++    ++  G   + +I+            GF
Sbjct: 127 IGIAKRIEEGTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIV-----------SGF 175

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
            +G +G      E            E E D+ S     KDD          AE D     
Sbjct: 176 LNGDDGDFILNEE------------EIELDLGSPKTTDKDD----------AEED----- 208

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLK 318
             E D        +  L P      +E+   + E++ L D A     K  + S   KV  
Sbjct: 209 -GESDGTELDDTDDSSLDP------EEVRVRFEEIQRLYDVAQEALAKHGRGSEAVKVAY 261

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           ++L      + LN    D ++  + ++ + +  NE  +++L   +G +  D F +     
Sbjct: 262 DELANHFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEFKKTFPSN 321

Query: 378 ELDPHWVSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +  W+S+  K  P   +   +A     ++ ++ ++ +      + I + + +   +  
Sbjct: 322 ETNLEWLSHRIKGGPA--FAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVARQMAI 379

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKK+MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 380 GEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 439

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L
Sbjct: 440 STYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERL 499

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+++A    LRE T  V
Sbjct: 500 DMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLREATREV 559

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT RE +VL+MRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 560 LDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHL 619

Query: 677 RSFLD 681
           RSFL+
Sbjct: 620 RSFLE 624


>gi|262378901|ref|ZP_06072058.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
 gi|262300186|gb|EEY88098.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
          Length = 629

 Score =  435 bits (1118), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 276/653 (42%), Positives = 381/653 (58%), Gaps = 44/653 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +     D+   ED+ 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEDNA 73

Query: 94  DLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           + A   +           ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G   
Sbjct: 74  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           ++ S+   P   + ++    +  +G   L +I  L   + PES        E    ++ E
Sbjct: 134 VLHSIAYWPNAVEVVLKEYKDYQEGERRLADI--LSGYLDPESDEEIPEVIEDAVLEEDE 191

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLSA 271
           D +  K   +V+  + + E     S DD      P PE A+                   
Sbjct: 192 DETASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAK------------------- 232

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                         E+  V++E +S+       +K  + S + K   E L  +       
Sbjct: 233 ----------VRFTELETVWQETKSVI------EKHGRDSAEAKAALEALASVFMMFKFT 276

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV--SYAK 388
               D++ E +    ++I  +E E++R A   G + R  F     G+E +P W+    AK
Sbjct: 277 PRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDRTQFRTSFPGQESNPGWLDEQMAK 336

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P+   K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEM
Sbjct: 337 ASPD--IKGHLEKVRPDVLAFQQKIADIEKELGLNVIDIKDISKRMAIGEAKARRAKKEM 394

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 395 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 454

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 455 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 514

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 515 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSEGLKEATREVLENLTEREAKVL 574

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 575 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 627


>gi|294340365|emb|CAZ88746.1| RNA polymerase sigma factor rpoD (Sigma-70) [Thiomonas sp. 3As]
          Length = 778

 Score =  434 bits (1117), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 264/657 (40%), Positives = 376/657 (57%), Gaps = 64/657 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD-----LEDE 86
           K +IK+ + RG++T  E+N  +P +    E ME  V+ML+++GI V +        L ++
Sbjct: 177 KSLIKMGKTRGFLTYGEINDHIPDNLADPELMETIVSMLNDVGIAVYETTPDAQTLLLNQ 236

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   S +  +     +       DS    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 237 HGPTASSEEEAEEEAEAAL--SNVDSEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 294

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   MM ++  SP T   ++     ++ G   + E++D           G     E  
Sbjct: 295 EDGLRQMMLAISASPSTVAEILAMAARIHHGELPVDEVVD-----------GMVSDDESD 343

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD-SPPENAENDERNLDEDEDDS 265
            Y   ED                              VD S  E+ E       EDED  
Sbjct: 344 DYVAEED------------------------------VDYSLDESGE-------EDEDGG 366

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A   S   ++L+ K + A  ++ + + ++R   D   +G +        + +   L+++ 
Sbjct: 367 AGATSMKLEELKGKALEAFADVHDAFMKMRRAYDK--DGYRSASYLKAQEAISAALMEVR 424

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
            +    +   +LL  Q+ ++ +         +      G+ ++ F++   G +LD  WV 
Sbjct: 425 FTARTVEKLCNLLRAQVDEVRRYEREIRRYAV---DRCGMPQEEFIKSFPGHQLDLKWVD 481

Query: 386 YAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             K    G+ +   ++  V +I +++ ++  I     + + + + I + +  GE  A  A
Sbjct: 482 --KHVASGKPYSVILSRNVPAIKELQQKLIDIQTRVVVPLDDLKEINTQMSLGEQAAREA 539

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW+
Sbjct: 540 KREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWI 599

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+KV R +R+   +   EP    +A+K+ MP + VR
Sbjct: 600 RQAITRSIADQARTIRIPVHMIETINKVNRISRQHLQETGTEPDAAVLAEKMEMPEDKVR 659

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+LKI +EPIS+ETPIGD+D SHLGDFIED   ++P ++A+QA LR+    +L SLTPRE
Sbjct: 660 KILKIAREPISMETPIGDDDDSHLGDFIEDSGTLAPTEAAMQAGLRDVVKEILDSLTPRE 719

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI M  DHTLEEVGKQF VTRERIRQIEAKA+RKLKHP+RS KLRSFLD
Sbjct: 720 AKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPTRSDKLRSFLD 776


>gi|239814768|ref|YP_002943678.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus S110]
 gi|239801345|gb|ACS18412.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus S110]
          Length = 754

 Score =  434 bits (1117), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 266/671 (39%), Positives = 383/671 (57%), Gaps = 83/671 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V +      +    +
Sbjct: 144 KTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLNDMGVAVYE------QTPDAE 197

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L ++A  ++   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 198 TLLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 257

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   MM ++  SP T   ++    ++ +G  ++  ++D           GF + 
Sbjct: 258 AKRIEGGLMAMMEAISASPATIAEILRLAADIREGKVVISTVVD-----------GFSNP 306

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E   Y   ED  +  E DD     G                                  
Sbjct: 307 NEADDYVAEEDFDEFDEEDDDDGKGG---------------------------------- 332

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
              +  L+   ++L+   +   D IA ++ ++  + D    G    + + +   L ++L+
Sbjct: 333 ---SKALTKKLEELKRDALERFDRIASMFEKVHKIYDKEGYGTPAYEKAQQA--LSDELM 387

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE--- 378
            +  +    +   DL+  Q+ D+ K+    E EL R+     G  +D F+    G +   
Sbjct: 388 TIRFTAKTIEKLCDLVRTQVDDVRKK----ERELRRIIVDKCGFPQDEFIRDFSGYDKNG 443

Query: 379 -------LDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
                  L+  WV   K    G+ W   +A  +  + +++ ++  I     + +++ + I
Sbjct: 444 NRVPSNLLNQKWVE--KQAAAGKPWSAVLARNIPPVQELQQKLADIQSRVVVPLTQLKEI 501

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 502 NKRMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 561

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP   
Sbjct: 562 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAG 621

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A K+ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED +  +P+++A+QA LR
Sbjct: 622 ILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLR 681

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHP
Sbjct: 682 DVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHP 741

Query: 671 SRSKKLRSFLD 681
           SRS KLRSF+D
Sbjct: 742 SRSDKLRSFID 752


>gi|296136130|ref|YP_003643372.1| RNA polymerase, sigma 70 subunit, RpoD [Thiomonas intermedia K12]
 gi|295796252|gb|ADG31042.1| RNA polymerase, sigma 70 subunit, RpoD [Thiomonas intermedia K12]
          Length = 778

 Score =  434 bits (1117), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 264/657 (40%), Positives = 375/657 (57%), Gaps = 64/657 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD-----LEDE 86
           K +IK+ + RG++T  E+N  +P +    E ME  V+ML+++GI V +        L ++
Sbjct: 177 KSLIKMGKTRGFLTYGEINDHIPDNLADPELMETIVSMLNDVGIAVYETTPDAQTLLLNQ 236

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   S +  +     +       DS    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 237 HGPTASSEEEAEEEAEAAL--SNVDSEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 294

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   MM ++  SP T   ++     ++ G   + E++D           G     E  
Sbjct: 295 EDGLRQMMLAISASPSTVAEILAMAARIHHGELPVDEVVD-----------GMVSDDESD 343

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD-SPPENAENDERNLDEDEDDS 265
            Y   ED                              VD S  E+ E       EDED  
Sbjct: 344 DYVAEED------------------------------VDYSLDESGE-------EDEDGG 366

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A   S   ++L+ K + A  ++ + + ++R   D   +G +        + +   L+++ 
Sbjct: 367 AGATSMKLEELKGKALEAFADVHDAFMKMRRAYDK--DGYRSASYLKAQEAISAALMEVR 424

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
            +    +   +LL  Q+ ++ +         +      G+ ++ F++   G +LD  WV 
Sbjct: 425 FTARTVEKLCNLLRAQVDEVRRYEREIRRYAV---DRCGMPQEEFIKSFPGHQLDLKWVD 481

Query: 386 YAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             K    G+ +   ++  V +I +++  +  I     + + + + I + +  GE  A  A
Sbjct: 482 --KHVASGKPYSVILSRNVPAIKELQQRLIDIQTRVVVPLDDLKEINTQMSLGEQAAREA 539

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW+
Sbjct: 540 KREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWI 599

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+KV R +R+   +   EP    +A+K+ MP + VR
Sbjct: 600 RQAITRSIADQARTIRIPVHMIETINKVNRISRQHLQETGTEPDAAVLAEKMEMPEDKVR 659

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+LKI +EPIS+ETPIGD+D SHLGDFIED   ++P ++A+QA LR+    +L SLTPRE
Sbjct: 660 KILKIAREPISMETPIGDDDDSHLGDFIEDSGTLAPTEAAMQAGLRDVVKEILDSLTPRE 719

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI M  DHTLEEVGKQF VTRERIRQIEAKA+RKLKHP+RS KLRSFLD
Sbjct: 720 AKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPTRSDKLRSFLD 776


>gi|255318840|ref|ZP_05360066.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens
           SK82]
 gi|255304096|gb|EET83287.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens
           SK82]
          Length = 626

 Score =  434 bits (1117), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 276/653 (42%), Positives = 381/653 (58%), Gaps = 44/653 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +     D+   ED+ 
Sbjct: 11  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEDNA 70

Query: 94  DLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           + A   +           ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G   
Sbjct: 71  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           ++ S+   P   + ++    +  +G   L +I  L   + PES        E    ++ E
Sbjct: 131 VLHSIAYWPNAVEVVLKEYKDYQEGERRLADI--LSGYLDPESDEEIPEVIEDAVLEEDE 188

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLSA 271
           D +  K   +V+  + + E     S DD      P PE A+                   
Sbjct: 189 DETASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAK------------------- 229

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                         E+  V++E +S+       +K  + S + K   E L  +       
Sbjct: 230 ----------VRFTELETVWQETKSVI------EKHGRDSAEAKAALEALASVFMMFKFT 273

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV--SYAK 388
               D++ E +    ++I  +E E++R A   G + R  F     G+E +P W+    AK
Sbjct: 274 PRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDRTQFRTSFPGQESNPGWLDEQMAK 333

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P+   K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEM
Sbjct: 334 ASPD--IKGHLEKVRPDVLAFQQKIADIEKELGLNVIDIKDISKRMAIGEAKARRAKKEM 391

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 392 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 451

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 452 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 511

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 512 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSEGLKEATREVLENLTEREAKVL 571

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 572 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 624


>gi|303257749|ref|ZP_07343761.1| RNA polymerase sigma factor RpoD [Burkholderiales bacterium 1_1_47]
 gi|302859719|gb|EFL82798.1| RNA polymerase sigma factor RpoD [Burkholderiales bacterium 1_1_47]
          Length = 814

 Score =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 270/692 (39%), Positives = 402/692 (58%), Gaps = 79/692 (11%)

Query: 4   GKKRNRD---------SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP 54
           GK + RD         S + HE+ D     +      K +I++ ++RGY+T  E+N  +P
Sbjct: 185 GKGKARDKAMKEALNRSYAHHEEDDKETRLN----KLKALIRMGKERGYLTYSEVNDHMP 240

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS--SASNSSVFLQKRKDS 112
            + V  +Q++  ++ L+++GI V +     D+    DS+  AS  +A   +       DS
Sbjct: 241 ENIVDPDQIDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEEAEAALATVDS 300

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               T DPVRMY+REMGS+ELL+REGEI IAKRIE G   M+ ++   P T  A++   +
Sbjct: 301 EFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVHAISGCPTTIVAILEDAE 360

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ++ +GT  + +I+D           G   G                          D E+
Sbjct: 361 KVRNGTMQIDQIVD-----------GLVDGL-------------------------DEEA 384

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVY 291
           + +V++DD                   E  D  A  ++A + D+L+  V+  LD   E+Y
Sbjct: 385 SEQVAEDD-------------------ESTDIGASGMTAGQIDELKTVVLAKLDHCKELY 425

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           ++L+   +    G +          ++E+L+    SL    + ++ L   L    + +  
Sbjct: 426 QDLKHAYE--AEGYRSPAFIKAQDAIQEELL----SLRFTANTVERLCTMLKTQVEEVRK 479

Query: 352 NEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +  +  +   + R++FL+     E +  W S A    +  +   V  ++  I  ++
Sbjct: 480 YESRIYDIVVNRAKMPRELFLKEFLDNETNLAW-SQAIAESDKPYAIDVKRKLPEIQHLQ 538

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            ++++I     + + + + + + +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQF
Sbjct: 539 QQLQNIQNAVTLPLKDLKDVYNQMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQF 598

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 599 LDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 658

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R +R++  +   EP P E+A+K+ MP + +RK+LKI KEPIS+ETPIGD++ SHLGD
Sbjct: 659 KMNRISRQILQETGVEPDPAELAEKMDMPEDKIRKILKIAKEPISMETPIGDDEDSHLGD 718

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           F+ED   V+P ++A Q++L E T  VL SLTPRE +VLRMRFGI M+TDHTLEEVG+QF 
Sbjct: 719 FLEDFGTVAPAEAAQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFD 778

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VTRERIRQIEAKA+RKL+HPSRS KL+SF++G
Sbjct: 779 VTRERIRQIEAKALRKLRHPSRSDKLKSFMEG 810


>gi|331001176|ref|ZP_08324803.1| RNA polymerase sigma factor RpoD [Parasutterella excrementihominis
           YIT 11859]
 gi|329569108|gb|EGG50900.1| RNA polymerase sigma factor RpoD [Parasutterella excrementihominis
           YIT 11859]
          Length = 814

 Score =  434 bits (1115), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 270/692 (39%), Positives = 402/692 (58%), Gaps = 79/692 (11%)

Query: 4   GKKRNRD---------SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP 54
           GK + RD         S + HE+ D     +      K +I++ ++RGY+T  E+N  +P
Sbjct: 185 GKGKARDKAMKEALNRSYAHHEEDDKETRLN----KLKALIRMGKERGYLTYSEVNDHMP 240

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS--SASNSSVFLQKRKDS 112
            + V  +Q++  ++ L+++GI V +     D+    DS+  AS  +A   +       DS
Sbjct: 241 ENIVDPDQIDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEEAEAALATVDS 300

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               T DPVRMY+REMGS+ELL+REGEI IAKRIE G   M+ ++   P T  A++   +
Sbjct: 301 EFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVHAISGCPTTIVAILEDAE 360

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ++ +GT  + +I+D           G   G                          D E+
Sbjct: 361 KVRNGTMQIDQIVD-----------GLVDGL-------------------------DEEA 384

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVY 291
           + +V++DD                   E  D  A  ++A + D+L+  V+  LD   E+Y
Sbjct: 385 SEQVAEDD-------------------ESTDIGASGMTAGQIDELKTVVLAKLDHCKELY 425

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           ++L+   +    G +          ++E+L+    SL    + ++ L   L    + +  
Sbjct: 426 QDLKHAYE--AEGYRSPAFIKAQDAIQEELL----SLRFTANTVERLCTMLKTQVEEVRK 479

Query: 352 NEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +  +  +   + R++FL+     E +  W S A    +  +   V  ++  I  ++
Sbjct: 480 YESRIYDIVVNRAKMPRELFLKEFLDNETNLAW-SQAIAESDKPYAIDVKRKLPEIQHLQ 538

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            ++++I     + + + + + + +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQF
Sbjct: 539 QQLQNIQNAVTLPLKDLKDVYNQMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQF 598

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 599 LDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 658

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R +R++  +   EP P E+A+K+ MP + +RK+LKI KEPIS+ETPIGD++ SHLGD
Sbjct: 659 KMNRISRQILQETGVEPDPAELAEKMDMPEDKIRKILKIAKEPISMETPIGDDEDSHLGD 718

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           F+ED   V+P ++A Q++L E T  VL SLTPRE +VLRMRFGI M+TDHTLEEVG+QF 
Sbjct: 719 FLEDFGTVAPAEAAQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFD 778

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VTRERIRQIEAKA+RKL+HPSRS KL+SF++G
Sbjct: 779 VTRERIRQIEAKALRKLRHPSRSDKLKSFMEG 810


>gi|258593489|emb|CBE69828.1| RNA polymerase sigma factor rpoD (Sigma-80) [NC10 bacterium 'Dutch
           sediment']
          Length = 654

 Score =  433 bits (1114), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 271/681 (39%), Positives = 392/681 (57%), Gaps = 82/681 (12%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           G + N  S S  + +  ++V     +  K ++ L R++GY+T +E+N+FLP +  S +Q+
Sbjct: 52  GARSNAGSKSAKKPT--TVVSAALKEGIKPLVSLGRKKGYLTYDEVNSFLPEEVTSGDQI 109

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           +  + +   M I VVD  +      S         A      +     S+   TDDPVRM
Sbjct: 110 DKILNLFDEMDIEVVDEAERTKTTRSPAPQQEEEGAEVEPELI----PSSVGRTDDPVRM 165

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMG   LL+REGEI IAKRIE G   +  ++C      QA +  R+    G  LL E
Sbjct: 166 YLREMGKTPLLTREGEIQIAKRIEDGHKEVAEAVC------QAGVAVREITEIGERLLHE 219

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
                       K   +   E  S  + ++ S++KER+ + E    +E+     +D++ K
Sbjct: 220 ------------KARIY---ELLSLNEFDEISEQKERELLAEHTPTLEAL----RDEQVK 260

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +DS                             LR +    +  ++E +++ R L + A  
Sbjct: 261 IDS-----------------------------LRRRYQRGVGRLSERWQQ-RILDELAHR 290

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
                         K     L+  L +NQ  ID +V ++ ++ +RI   E EL  +A+ +
Sbjct: 291 --------------KAAQATLIRKLHVNQRVIDRVVARIRNLLERIEQGEQELREVARVH 336

Query: 364 GIKRD---VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            +  +   +     +G+      +         + K    CE  ++  I+ +I+ +  E 
Sbjct: 337 HLSMEDIRIIAGNGRGKTTAIRGILRRTGL---DRKGLDECE-HAVAAIQRKIRRVEEEA 392

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
             S  E R ++  +  GE +A +AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 393 DASGKELRSLLHAITTGERKAHLAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 452

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LM+A +KF++  GYKFSTYA WWV+QAITR+IADQ+ TIRIPVHM + I+K+ R +R + 
Sbjct: 453 LMRAVDKFEYQRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETINKLTRASRYLV 512

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  REPTPEEIA+K+ +PV+ VRKVLKI +EPISLETPIG+E+ SHLGDFIEDK  +SP
Sbjct: 513 QEFGREPTPEEIAQKIDLPVDKVRKVLKIAQEPISLETPIGEEEGSHLGDFIEDKGVISP 572

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +++ I  NL   T +VL +LT RE+++L++RFG+G   DHTLEEVG+QF VTRERIRQIE
Sbjct: 573 IEAVIGMNLSGQTEQVLETLTEREQKILKLRFGLGDGRDHTLEEVGQQFDVTRERIRQIE 632

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HP+RS+KL+SF++
Sbjct: 633 AKALRKLRHPTRSRKLKSFVE 653


>gi|89900350|ref|YP_522821.1| sigma 70 (RpoD) [Rhodoferax ferrireducens T118]
 gi|89345087|gb|ABD69290.1| sigma 70 (RpoD) [Rhodoferax ferrireducens T118]
          Length = 783

 Score =  431 bits (1109), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 263/672 (39%), Positives = 386/672 (57%), Gaps = 85/672 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E++  LP   V +E +E  ++ML++MG+ V +      +    +
Sbjct: 173 KALIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVISMLNDMGVAVYE------QTPDAE 226

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L ++ S ++   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 227 TLLLNNNVSTAATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 286

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   MM ++  SP T   ++   +++ +G  ++  I+D           GF + 
Sbjct: 287 AKRIEGGLMAMMEAISASPATIAEILRLSEDIREGKVVITTIVD-----------GFSNP 335

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E   Y   ED  +    DD     G                                  
Sbjct: 336 NEADDYVAEEDFDEFDAADDDDGKGG---------------------------------- 361

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-KVLKEKL 321
              +  L+   ++L+ + +   D + E++ ++ ++ +    G     S +K  K L E+L
Sbjct: 362 ---SKALTKKLEELKNEALSRFDRLRELFEKIHTIYNKEGYGTP---SYIKTQKALSEEL 415

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE-- 378
           + +  +    +   DL+  Q+ D+ K+    E EL R+     G  ++ F+    GR+  
Sbjct: 416 MSIRFTAKTIEKLCDLVRSQVDDVRKK----ERELRRIIVDKCGYPQENFIADFSGRDKH 471

Query: 379 --------LDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
                   L+  W+   K    G+ W   +A  +  +  ++ ++  +  +  + + + + 
Sbjct: 472 GNKVASQLLNLKWIE--KQAASGKHWGPIMARNIPPVQDLQQKLTDLQSKVVVPLDQLKD 529

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 530 INKRMNEGEYSSRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 589

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP  
Sbjct: 590 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDA 649

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             +A+++ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+++A+QA L
Sbjct: 650 SVLAERMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAANTAPMEAAMQAGL 709

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    +L SLTPRE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKH
Sbjct: 710 RDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKH 769

Query: 670 PSRSKKLRSFLD 681
           PSRS KLRSF D
Sbjct: 770 PSRSDKLRSFTD 781


>gi|241764884|ref|ZP_04762887.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax delafieldii 2AN]
 gi|241365587|gb|EER60323.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax delafieldii 2AN]
          Length = 788

 Score =  431 bits (1109), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 262/657 (39%), Positives = 378/657 (57%), Gaps = 65/657 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E++  LP   V +E +E  +  L+++G+ V     D + L   +
Sbjct: 188 KTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITD 247

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 248 NAPSGATEEEAEEAAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 306

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  E   
Sbjct: 307 GGLMAMMEAISASPATIAEILNMGEEIREGKVVISTIVD-----------GFSNPNEADD 355

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y   ED  +  E DD     G                                     + 
Sbjct: 356 YVAEEDFDEFDEADDDDGKGG-------------------------------------SK 378

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV-LKEKLVKLVG 326
            L+   ++L+ + +   D++ E++ ++  + D    G     + VK +  L E+L+ +  
Sbjct: 379 ALTKKLEELKKQALERFDKLRELFEKVHKVYDKEGYGTP---AYVKAQTALSEELMTIRF 435

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS 385
           +    +   D++  Q+ D+ K+    E EL R+     G+ ++ F++      L+  WV 
Sbjct: 436 TAKTIEKLCDMVRGQVDDVRKK----ERELRRIIVDKCGMPQETFIKDFPPNLLNLKWVE 491

Query: 386 YAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             K    G+ W   +A  +  I  ++ ++  +     + ++E + I   + +GE  +  A
Sbjct: 492 --KQAAAGKPWSAVMARNIPPIQDLQQKLADLQSRVVVPLAELKGINKRMNEGEATSRDA 549

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 550 KKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 609

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +R
Sbjct: 610 RQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIR 669

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K++KI KEPIS+ETPIGD+D SHLGDFIED    +P+++A+QA LR+    +L  LTPRE
Sbjct: 670 KIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTPRE 729

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 730 AKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 786


>gi|42521867|ref|NP_967247.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
 gi|39574397|emb|CAE77901.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
          Length = 609

 Score =  430 bits (1106), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 274/664 (41%), Positives = 383/664 (57%), Gaps = 100/664 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++ +KLA+++G +TIEE+N  LPP+ V+   ++  +  L   G+ + D  +   EE  E 
Sbjct: 31  QRFLKLAKEKGALTIEEINELLPPEIVAPSVLDSFMQGLEAGGVVISDLSESSKEEEGEG 90

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +      + +  +  +++ +S D   +DPVR+YLR+MGS+ LL+REGE+ IA+RIE G  
Sbjct: 91  AFLENVDSEDEEIDDEEKAESEDVKGNDPVRLYLRKMGSVSLLTREGEVEIARRIEKGER 150

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            ++ ++  SPL    +I     L++G   ++ I               F G E    Q  
Sbjct: 151 EIVRAILLSPLGTYEIIQLGKRLDEGRIKVKSI---------------FRGLEDEDTQ-- 193

Query: 212 EDSSQEKER-DDVQETEGDIESAAKVSKD-----DRSKVDSPPENAENDERNLDEDEDDS 265
                EKE  D + E  G +    K ++       + + ++P   A   E          
Sbjct: 194 ---YDEKEYIDKIHELIGRVTEYQKAAEKLFMTLRKEETNTPARQAAMKE---------- 240

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L AM D+L    M   +               +VN  +   + V  K   + LV  +
Sbjct: 241 ---LVAMNDKL----MANFE---------------SVNFNRKTINRVVIKF--KNLVNRI 276

Query: 326 GSLSLNQSRIDLLVEQLY--DIS------KRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           G+L   + RI   VE+ +  D++      K I  NE EL R+ +  G+    F       
Sbjct: 277 GTL---RRRIKDGVERTFSKDVTAMAERMKLIDANEKELTRMTRDTGLNYQKF------- 326

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                  SY     E E +                I  +  ET ++ +  +   + + KG
Sbjct: 327 ------KSYVLQAQEAEKR----------------ISRLDSETEMNHNWVKETYTAIWKG 364

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E EA  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 365 EREADAAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 424

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ REPTPEEIA K+ 
Sbjct: 425 TYATWWIRQAITRAIADQARTIRIPVHMIETINKLVRTSRYLIQELGREPTPEEIADKMD 484

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MPV+ VRKVLKI KEPISLETP+G+E+ SHLGDFIEDK  ++P ++ +  NL E T RVL
Sbjct: 485 MPVDKVRKVLKIAKEPISLETPVGEEEDSHLGDFIEDKKVINPAEAIVNLNLAEQTRRVL 544

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS KL+
Sbjct: 545 STLTPREEKVLRMRFGIGEESDHTLEEVGQDFNVTRERIRQIEAKALRKLRHPSRSNKLK 604

Query: 678 SFLD 681
           +F+D
Sbjct: 605 AFVD 608


>gi|171059243|ref|YP_001791592.1| RNA polymerase sigma-70 subunit RpoD [Leptothrix cholodnii SP-6]
 gi|170776688|gb|ACB34827.1| RNA polymerase, sigma 70 subunit, RpoD [Leptothrix cholodnii SP-6]
          Length = 754

 Score =  429 bits (1104), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 261/657 (39%), Positives = 379/657 (57%), Gaps = 65/657 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IK+ + RG++T +E+N  LP   V +E +E  V+ML++MGI V     D   L    
Sbjct: 154 KTLIKMGKTRGFLTHQEINDHLPEKLVEAEILEAIVSMLNDMGIAVYEQAPDAATLLIAG 213

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G   +     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 214 GGTTTSTEEEAEEAAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 272

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +++  GT  +  ++D           GF    E   
Sbjct: 273 GGLQAMMLAISASPATIAEVLEMANKIRAGTDPISSVVD-----------GFVAADEADD 321

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y   ED  +  E +D     G                                     + 
Sbjct: 322 YVAEEDFDEFDEEEDDDGNGG-------------------------------------SK 344

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            L+   ++L+ + +   D +   + ++R   D   +G K    +   + +  +L+ +  +
Sbjct: 345 ALTKKLEELKNQALVKFDALQLDFDKMRKAYDK--DGYKSPAYNKAQEAISGQLMTVRFT 402

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS- 385
           +   +   DLL  Q+ DI +     E EL ++     G+ ++ F++      L+  W   
Sbjct: 403 VKTIEKLCDLLRSQVDDIRR----FERELRKIVVDRCGMPQEYFIKSFPPNILNLEWAEN 458

Query: 386 -YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A + P   +   ++  + +I +++ ++  +  +  + I + + I   + +GE  +  A
Sbjct: 459 EIAANKP---YSAVMSRNLPAIQELQQKLTDLQTKAVVPIDDLKQINRRMNEGEASSREA 515

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 516 KREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 575

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A+K+ MP + +R
Sbjct: 576 RQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQEFGFEPDAPSLAEKMEMPEDKIR 635

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+++A+Q+ LR+    +L SLTPRE
Sbjct: 636 KIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPIEAAMQSGLRDVVRDILDSLTPRE 695

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKAIRKLKHPSRS KLR++LD
Sbjct: 696 AKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRSDKLRTYLD 752


>gi|212212053|ref|YP_002302989.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212010463|gb|ACJ17844.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
          Length = 698

 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 269/664 (40%), Positives = 365/664 (54%), Gaps = 87/664 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---EDE 86
           +++ A+ +GY+  E+L   LP D     QME  +  L+ MGI V     D D L   ED 
Sbjct: 103 LLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDADSLLLEEDT 162

Query: 87  EGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +  +D +  D+A   +  +             T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 163 QSDDDEINEDVAEVLATET------------RTTDPVRMYMREMGSVELLTREGEIVIAK 210

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P   +  I                                    
Sbjct: 211 RIEEGIRQVMGAVVQYPELIEKFI------------------------------------ 234

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                        KE D +  TEG +        D+     SP      D+     DEDD
Sbjct: 235 -------------KEYDTIVATEGRLSDLLIGFFDEEESTASPVAPEARDKEAETSDEDD 281

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLV 322
                S    +  P  +     + E+ ++L     NA+   G+K   +    K L E   
Sbjct: 282 GGEGGSDEFGESGPDPLITQQHMEEL-KKLYGRYQNAIKRYGKKAPATLKHQKALAE--- 337

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI-----KRDVFLERHQGR 377
            L  +  L+  + + L  QL    +R++       RL  SY +      R  F+      
Sbjct: 338 -LFSTFKLSIKQFNRLTGQL----RRMLRAARAQERLIMSYCVVKAKTPRKKFIASFPHN 392

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+   K+  + + K       + I + +  +  +  +  ++I E + I   V  G
Sbjct: 393 ETNMKWLEQYKNENKEQAKRLEKYSKE-IYRAQRNLAQLEEQNNLNIQEIKEINRRVAIG 451

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 452 EAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 511

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E TPEE+ +++ 
Sbjct: 512 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGRRMD 571

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D A  A L E T  +L
Sbjct: 572 MPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATREIL 631

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR++KL 
Sbjct: 632 STLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAEKLH 691

Query: 678 SFLD 681
           SF++
Sbjct: 692 SFIE 695


>gi|29654887|ref|NP_820579.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|161831165|ref|YP_001597431.1| RNA polymerase sigma factor RpoD [Coxiella burnetii RSA 331]
 gi|81628631|sp|Q83BB6|RPOD_COXBU RecName: Full=RNA polymerase sigma factor rpoD
 gi|29542156|gb|AAO91093.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|161763032|gb|ABX78674.1| RNA polymerase sigma factor RpoD [Coxiella burnetii RSA 331]
          Length = 698

 Score =  426 bits (1095), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 269/664 (40%), Positives = 365/664 (54%), Gaps = 87/664 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---EDE 86
           +++ A+ +GY+  E+L   LP D     QME  +  L+ MGI V     D D L   ED 
Sbjct: 103 LLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDADSLLLEEDT 162

Query: 87  EGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +  +D +  D+A   +  +             T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 163 QSDDDEINEDVAEVLATET------------RTTDPVRMYMREMGSVELLTREGEIVIAK 210

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P   +  I                                    
Sbjct: 211 RIEEGIRQVMGAVVQYPELIEKFI------------------------------------ 234

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                        KE D +  TEG +        D+     SP      D+     DEDD
Sbjct: 235 -------------KEYDTIVATEGRLSDLLIGFFDEEESTASPVAPEARDKEAETSDEDD 281

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLV 322
                S    +  P  +     + E+ ++L     NA+   G+K   +    K L E   
Sbjct: 282 GGEGGSDEFGESGPDPLITQQHMEEL-KKLYGRYQNAIKRYGKKAPATLKHQKALAE--- 337

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI-----KRDVFLERHQGR 377
            L  +  L+  + + L  QL    +R++       RL  SY +      R  F+      
Sbjct: 338 -LFSTFKLSIKQFNRLTGQL----RRMLRAARAQERLIMSYCVVKAKTPRKKFIASFPHN 392

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+   K+  + + K       + I + +  +  +  +  ++I E + I   V  G
Sbjct: 393 ETNMKWLEQYKNENKEQAKRLEKYSKE-IYRAQRNLAQLEEQNNLNIQEIKEINRRVAIG 451

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 452 EAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 511

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E TPEE+ +++ 
Sbjct: 512 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGRRMD 571

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D A  A L E T  +L
Sbjct: 572 MPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATREIL 631

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR++KL 
Sbjct: 632 STLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAEKLH 691

Query: 678 SFLD 681
           SF++
Sbjct: 692 SFIE 695


>gi|154705741|ref|YP_001423814.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355027|gb|ABS76489.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 698

 Score =  426 bits (1095), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 269/664 (40%), Positives = 365/664 (54%), Gaps = 87/664 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---EDE 86
           +++ A+ +GY+  E+L   LP D     QME  +  L+ MGI V     D D L   ED 
Sbjct: 103 LLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDADSLLLEEDT 162

Query: 87  EGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +  +D +  D+A   +  +             T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 163 QSDDDEINEDVAEVLATET------------RTTDPVRMYMREMGSVELLTREGEIVIAK 210

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P   +  I                                    
Sbjct: 211 RIEEGIRQVMGAVVQYPELIEKFI------------------------------------ 234

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                        KE D +  TEG +        D+     SP      D+     DEDD
Sbjct: 235 -------------KEYDTIVATEGRLSDLLIGFFDEEESTASPVAPEARDKEAETSDEDD 281

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLV 322
                S    +  P  +     + E+ ++L     NA+   G+K   +    K L E   
Sbjct: 282 GGEGGSDEFGESGPDPLITQQHMEEL-KKLYGRYQNAIKRYGKKAPATLKHQKALAE--- 337

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI-----KRDVFLERHQGR 377
            L  +  L+  + + L  QL    +R++       RL  SY +      R  F+      
Sbjct: 338 -LFSTFKLSIKQFNRLTGQL----RRMLRAARAQERLIMSYCVVKAKTPRKKFIASFPHN 392

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+   K+  + + K       + I + +  +  +  +  ++I E + I   V  G
Sbjct: 393 ETNMKWLEQYKNENKEQAKRLEKYSKE-IYRAQRNLAQLEEQNNLNIQEIKEINRRVAIG 451

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 452 EAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 511

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E TPEE+ +++ 
Sbjct: 512 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGRRMD 571

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D A  A L E T  +L
Sbjct: 572 MPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATREIL 631

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR++KL 
Sbjct: 632 STLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAEKLH 691

Query: 678 SFLD 681
           SF++
Sbjct: 692 SFIE 695


>gi|153208748|ref|ZP_01946986.1| RNA polymerase sigma factor RpoD [Coxiella burnetii 'MSU Goat
           Q177']
 gi|212219307|ref|YP_002306094.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120575780|gb|EAX32404.1| RNA polymerase sigma factor RpoD [Coxiella burnetii 'MSU Goat
           Q177']
 gi|212013569|gb|ACJ20949.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 698

 Score =  426 bits (1094), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 269/664 (40%), Positives = 365/664 (54%), Gaps = 87/664 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---EDE 86
           +++ A+ +GY+  E+L   LP D     QME  +  L+ MGI V     D D L   ED 
Sbjct: 103 LLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDADSLLLEEDT 162

Query: 87  EGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +  +D +  D+A   +  +             T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 163 QSDDDEINEDVAEVLATET------------RTTDPVRMYMREMGSVELLTREGEIVIAK 210

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P   +  I                                    
Sbjct: 211 RIEEGIRQVMGAVVQYPELIEKFI------------------------------------ 234

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                        KE D +  TEG +        D+     SP      D+     DEDD
Sbjct: 235 -------------KEYDTIVATEGRLSDLLIGFFDEEESTASPVAPEARDKEAETSDEDD 281

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLV 322
                S    +  P  +     + E+ ++L     NA+   G+K   +    K L E   
Sbjct: 282 GGEGGSDEFGESGPDPLITQQHMEEL-KKLYGRYQNAIKRYGKKAPATLKHQKALAE--- 337

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI-----KRDVFLERHQGR 377
            L  +  L+  + + L  QL    +R++       RL  SY +      R  F+      
Sbjct: 338 -LFSTFKLSIKQFNRLTGQL----RRMLRAARAQERLIMSYCVVKAKTPRKKFIASFPHN 392

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+   K+  + + K       + I + +  +  +  +  ++I E + I   V  G
Sbjct: 393 ETNMKWLEQYKNENKEQAKRLEKYSKE-IYRAQRNLAQLEEQNNLNIQEIKEINRRVAIG 451

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 452 EAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 511

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E TPEE+ +++ 
Sbjct: 512 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGRRID 571

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D A  A L E T  +L
Sbjct: 572 MPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATREIL 631

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR++KL 
Sbjct: 632 STLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAEKLH 691

Query: 678 SFLD 681
           SF++
Sbjct: 692 SFIE 695


>gi|261755428|ref|ZP_05999137.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261745181|gb|EEY33107.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 235

 Score =  411 bits (1056), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 194/234 (82%), Positives = 220/234 (94%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 1   MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVL
Sbjct: 61  ITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVL 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERV
Sbjct: 121 KIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 181 LRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 234


>gi|197120055|ref|YP_002140482.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
 gi|197089415|gb|ACH40686.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
          Length = 584

 Score =  409 bits (1052), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 214/414 (51%), Positives = 294/414 (71%), Gaps = 21/414 (5%)

Query: 279 KVMCALDEIAEV---YRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           KV+  +DEI E+     E++ + DN     K+ E    +   LK K+ + + SL L    
Sbjct: 181 KVLTIIDEIKEIDLRMNEIQGVLDNEKAAAKEREALGAEHAELKVKMAETLKSLRLKDRH 240

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           I+ + ++L ++S ++     E+  L +  G +R+ FL   +G          AK   E E
Sbjct: 241 IEKIAQRLKELSCKVDTVMQEITELEKESGAEREPFLAAFEG----------AKGGSEAE 290

Query: 395 WKNFVACEVDSILKIRNEIKS-------ISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           ++  +   ++   K+    +S       I  E+G   SE  + +  + +GE +A +AK E
Sbjct: 291 FQKKLNLTLEEGQKLEKRFRSSEARLKKIEQESGFKASELANALLAIEEGEHKAKLAKSE 350

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 351 LVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQA 410

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++A+P++ VRKVL
Sbjct: 411 ITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMALPLDKVRKVL 470

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+V
Sbjct: 471 KIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKV 530

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 531 LRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 584



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 54/143 (37%), Positives = 87/143 (60%), Gaps = 3/143 (2%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T EE+N  LPPD VSS+Q++D ++M  +M I +VD    +  
Sbjct: 5   SMDEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSDQIDDVMSMFGDMDIEIVDSA--QKV 62

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +  +  +DL     +     +   +      T DPVRMYLREMGS+ LL+REGE+ IAKR
Sbjct: 63  KIPKIKMDLEEEEEHEGSEEEVEFEPGTLGRTSDPVRMYLREMGSVSLLTREGEVEIAKR 122

Query: 146 IEAGRAMMMASLCESPLTFQALI 168
           IE G   + + +  +P+T + ++
Sbjct: 123 IEVGERDVASVILNTPITVREVV 145


>gi|253702377|ref|YP_003023566.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251777227|gb|ACT19808.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 584

 Score =  409 bits (1051), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 211/414 (50%), Positives = 294/414 (71%), Gaps = 21/414 (5%)

Query: 279 KVMCALDEIAEVYRELRSLQD----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           KV+  +DEI E+ + +  +Q       V  ++ E    +   LK K+ + + SL L    
Sbjct: 181 KVLTIIDEIKEIEQRMSEIQSALEAEKVAAKEREALGAEHAELKVKMAETLKSLRLKDRH 240

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           I+ + ++L ++S ++     E+  L +  G +R+ FL   +G          AK   E +
Sbjct: 241 IEKIAQRLKELSCKVDTVMQEIAELEKESGAEREPFLTAFEG----------AKGGSEAD 290

Query: 395 WKNFVACEVDSILKIRN-------EIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           ++  +   ++   K+         ++K I  E+G   SE  + +  + +GE +A +AK E
Sbjct: 291 FQKKLNMTLEEGQKLEKRFRSSEAKLKKIEQESGFKASELANALLAIEEGEHKAKLAKSE 350

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 351 LVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQA 410

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++A+P++ VRKVL
Sbjct: 411 ITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMALPLDKVRKVL 470

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+V
Sbjct: 471 KIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKV 530

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 531 LRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 584



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 54/143 (37%), Positives = 87/143 (60%), Gaps = 3/143 (2%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T EE+N  LPPD VSS+Q++D ++M  +M I +VD    +  
Sbjct: 5   SMDEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSDQIDDVMSMFGDMDIEIVDSA--QKV 62

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +  +  +DL     +     +   +      T DPVRMYLREMGS+ LL+REGE+ IAKR
Sbjct: 63  KIPKIKMDLEEEEEHEGSEEEVEFEPGTLGRTSDPVRMYLREMGSVSLLTREGEVEIAKR 122

Query: 146 IEAGRAMMMASLCESPLTFQALI 168
           IE G   + + +  +P+T + ++
Sbjct: 123 IEVGERDVASVILNTPITVREVV 145


>gi|114321663|ref|YP_743346.1| RNA polymerase, sigma 70 subunit, RpoD [Alkalilimnicola ehrlichii
           MLHE-1]
 gi|114228057|gb|ABI57856.1| RNA polymerase, sigma 70 subunit, RpoD [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 598

 Score =  406 bits (1043), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 209/373 (56%), Positives = 266/373 (71%), Gaps = 5/373 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
           S +C  L+E+L ++  +       ID LV+ L      +  NE  +L+     G+ R  F
Sbjct: 228 SPECAELREQLAEIFLTFKFPPKIIDQLVDGLRRDVNVLRRNERHILKACTKAGMPRKTF 287

Query: 371 LERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           +     RE DP W+    A   P   W   +A   D I + +  +     + G++I E +
Sbjct: 288 VRSFISRETDPGWLDEMLASKEP---WAQRLAEHEDDIRRAQQVLIDAERKVGMTIGEIK 344

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 345 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 404

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+
Sbjct: 405 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPS 464

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P+E+A+++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED NA+SP+DSA +  
Sbjct: 465 PDELAERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDINAMSPVDSATREG 524

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE+   VL+ LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 525 LRESVKGVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584

Query: 669 HPSRSKKLRSFLD 681
           HP+RS+ LRSFLD
Sbjct: 585 HPTRSEGLRSFLD 597



 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 56/155 (36%), Positives = 91/155 (58%), Gaps = 1/155 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++I   +++G++T  E+N  LP D V  EQ+ED + M+++MGINV +   D ++   S+
Sbjct: 10  KQLIAKGKEQGFLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGINVHEVAPDADELLLSD 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            ++      +  +       D+    T DPVRMY+REMG++ELL+REGEI +AKRIE G 
Sbjct: 70  AAVSTDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGTVELLTREGEIELAKRIEEGL 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             ++A+L   P     L+    ++ DG   L E++
Sbjct: 130 DQVLAALSAYPGAAAKLLDLYRKVQDGEMRLNELM 164


>gi|67810071|gb|AAY81984.1| RNase polymerase sigma factor [Wolbachia pipientis]
          Length = 571

 Score =  405 bits (1041), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 237/557 (42%), Positives = 349/557 (62%), Gaps = 33/557 (5%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            DDPVR+YL++M S++LLSR  EI IAK+IE+ +  M+ ++ E+ +T + + +WRD+L++
Sbjct: 36  NDDPVRIYLQDMSSVKLLSRADEIEIAKKIESEKHNMLRAIIETSVTLKVIKVWRDDLSN 95

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G  LLREIIDL+A           + ++ +   K E    E+  +DV+++E   E A   
Sbjct: 96  GALLLREIIDLDA----------IYNSDFNVVPKEESEESEESAEDVEDSEDVSEDAEYC 145

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           S D++   DS   + E D  N D    +   ++  ME  L PKV+ ALDEI  +  E   
Sbjct: 146 SDDEK---DSKKSDDEKDGNNEDISSVNLNVSILEMESDLLPKVIVALDEIITLTNEALI 202

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           L+ N+ N       S + + L  ++  +   + L+ + +  + ++LY I++ I   E  L
Sbjct: 203 LRKNSKNF------SNELENLYNQIWSIALQIKLSDAAVARITQELYKINRSITLEEANL 256

Query: 357 LRLAQSYGIKRDVF-------LERHQGRELDPHWVSYAKDFPEGEWKN----FVACEVDS 405
           +  A+ Y I R+ F       L +H+ +++    ++  +    GE KN    F+    + 
Sbjct: 257 IAEARKYDIDRESFYKVYDDVLLKHELKKISLLKINENQSSFTGELKNKFLRFIDDNSEH 316

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I    N IK    E   ++ EF+ ++  ++K E E S AK+EM++ANLRLV+S+AKKY+ 
Sbjct: 317 IASTLNGIKQHIQED--NVQEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSK 374

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLIQEGNIGLMKA +KFD+  GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM
Sbjct: 375 RGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHM 434

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I K+ R  R+M++++ REPT EE++ +L MP+E +RKV+KI ++P+SLE P G +D+
Sbjct: 435 VEIISKINRALRKMTHEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDDS 494

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEE 644
           S  GD IEDK    P D+AI A+LR  TT VLA+LTP+EER+LRMRFG+G +  +HTLEE
Sbjct: 495 STFGDCIEDKRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEE 554

Query: 645 VGKQFCVTRERIRQIEA 661
           VGK F VTRERIRQIEA
Sbjct: 555 VGKIFNVTRERIRQIEA 571


>gi|269468904|gb|EEZ80491.1| DNA-directed RNA polymerase, sigma subunit [uncultured SUP05
           cluster bacterium]
          Length = 603

 Score =  405 bits (1041), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 250/656 (38%), Positives = 370/656 (56%), Gaps = 67/656 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI----NVVDGDDLED 85
           + +K+I + +++GY+T  E+N  LP D ++ EQ+E  V +L  + I     V D D L  
Sbjct: 11  ALQKLIMIGKEQGYLTYAEINDILPEDLLTQEQVEPIVTILEELDIAVSDTVPDADTLVV 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G++      S+++ ++V      DS    T DPVRMY+REMG ++LL +  EI IAK 
Sbjct: 71  ESGAKAQ----STSAEAAVAALAALDSEFGRTTDPVRMYMREMGVVDLLEQSDEIRIAKE 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IEAG   +M S+   P            L +G   + ++I                G +G
Sbjct: 127 IEAGVFEIMKSITLYPAITGFFFKAHTRLEEGKCKMTDVI---------------IGYQG 171

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    ED +++K   D     G+ +   +  + +  +   P                D 
Sbjct: 172 DA----EDFAKKKAAFDA----GEFDDDEEYEEMEEMEYTGP----------------DE 207

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                  E  L+    C+     E Y+     + N  +G +D+K+    + L E L    
Sbjct: 208 GQVYGRFETVLK----CS-----EAYQ-----KTNEKHGFRDKKTIAARQQLSEGL---- 249

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             L L    +  ++E + D    +   E  +       G++R+ F +     E +  W+ 
Sbjct: 250 SDLRLAPKLVSTMMEVICDRVALVKKQEKTIQSACLYAGMEREQFFKLFNDNETNFDWLK 309

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   + +    +    D I   +  +     E  +++ E + +  + R+G+  A  AK
Sbjct: 310 GAK--LDKKVAEALKVSKDEIYYAQKNLLEFEEEMQLTVPELKALNKLYRRGDRRAKKAK 367

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            +M+EANLRLVIS+AKKY NRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW++
Sbjct: 368 SQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIR 427

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R  R++  K  RE TPEE+A ++ +P   + K
Sbjct: 428 QAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREATPEELAVEMELPEYKINK 487

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +LKI KEP+S+ETP+GD++ S++GDFIED N  SP++   + +L+ETT  +LA+L+PRE 
Sbjct: 488 ILKIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTRESLKETTGELLANLSPREA 547

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VL+MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+
Sbjct: 548 KVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLQSFLE 603


>gi|295698783|ref|YP_003603438.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
 gi|291157386|gb|ADD79831.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
          Length = 607

 Score =  404 bits (1039), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 262/644 (40%), Positives = 373/644 (57%), Gaps = 60/644 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP D V S+Q+ED +  + +MGI V +      E   ED
Sbjct: 10  KVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTE------EVPDED 63

Query: 92  SLDLASSASNS--------SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L L    S++        +  L   +    R+TD P+RMY+REMG+IELL+REGEI IA
Sbjct: 64  ELILTDPTSSTDEETVEAATQVLSSVEQEIGRTTD-PIRMYMREMGTIELLTREGEIDIA 122

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +  S+ E P +   ++        G   L +II      G  S+  F    
Sbjct: 123 KRIEDGINQIQRSISEYPKSISYILKQYFLFESGEMKLSDII-----TGLSSEDTF---- 173

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
              S +  + +    + + +     +I S     KD     +S   N E++  ++D    
Sbjct: 174 --SSSKNVDKNFSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHID---- 227

Query: 264 DSAHTLSAMEDQLRPKVM-CALDEIAEVYREL-RSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                         PK+      E+   Y ++  SL++N +      KSS     +++ L
Sbjct: 228 --------------PKIARKKFLELQNQYEKVTHSLKENGI------KSSQSILDIQD-L 266

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE--RHQGRE 378
            ++     L   ++D L+  +    ++I   E  ++ ++ + Y I +  FL       +E
Sbjct: 267 CEIFKQFRLVPKQLDFLISDIRKTIEKIKIQEKLIINISFKEYKIPKKYFLNLFSENPKE 326

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            D   +  +  + + + K F   ++DS I++  NE+  I  +TGISIS+ + I   +  G
Sbjct: 327 YDLKELIVSNRYNKKDEKKF---KLDSTIVQALNELNEIEKDTGISISKIKEIGRKISIG 383

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 384 ETIARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 443

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+   +R++  +  REP+PEE+++++ 
Sbjct: 444 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNHISRQILQETGREPSPEELSERML 503

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P E +RKVLKI +EPIS+ETPIGD++ SHLGDFIED     PL+SA   +LR  T  VL
Sbjct: 504 IPEEKIRKVLKIAREPISMETPIGDDEDSHLGDFIEDTTLELPLESATSESLRSATNEVL 563

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           + LT RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 564 SGLTTREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEA 607


>gi|261492895|ref|ZP_05989441.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. BOVINE]
 gi|261496755|ref|ZP_05993130.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261307594|gb|EEY08922.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261311436|gb|EEY12593.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. BOVINE]
          Length = 623

 Score =  404 bits (1037), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 216/382 (56%), Positives = 274/382 (71%), Gaps = 10/382 (2%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY- 363
           QK  ++S K K   E L  +     L   + DLLV  +  + K++   E ++ R A  Y 
Sbjct: 246 QKHGRTSKKSKEQIEILSHIFREFRLVSKQFDLLVASMQKLMKQVRTEERQIQRYAVEYA 305

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV---ACEVDSI-LKIRNEIKSISVE 419
           G+K+  FL+  QG EL   W+  A +      KN V   A  VD+I + I N ++++   
Sbjct: 306 GMKKADFLKAFQGHELSEAWIEKAINAK----KNAVPKLANYVDNIRVNIAN-LQNLEQT 360

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           +G++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 361 SGLTIAQIREIGGRISNGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 420

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 421 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQC 480

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFI+D++   
Sbjct: 481 LQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLEL 540

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PLDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 541 PLDSATAESLRMATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 600

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HPSRS+ LRSFLD
Sbjct: 601 EAKALRKLRHPSRSETLRSFLD 622



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 90/155 (58%), Gaps = 9/155 (5%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSE 90
           I   R++GY+T+ E++  LP + V +EQ+ED + M+++MGI V+    D DDL   E   
Sbjct: 19  ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDTDDLLLAENIA 78

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  D+   A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 79  DE-DVVEEATK---VLSTVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEGI 133

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  ++ E P     L+    ++  G   L +++
Sbjct: 134 NEVQCAIAEYPEALSGLLACYAQVETGEMRLSDLV 168


>gi|118602160|ref|YP_903375.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
 gi|118567099|gb|ABL01904.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 600

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 256/661 (38%), Positives = 377/661 (57%), Gaps = 80/661 (12%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD----GDDLED 85
           S +K+I   +++GY+T  E+N  LP D ++ EQ+E  V +L  + I V D     D L  
Sbjct: 11  SLQKLIMAGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDIAVSDIVPDADTLVV 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G++      S+++ +++      DS    T DPVRMY+REMG ++LL +E EI IAK 
Sbjct: 71  ESGAKAQ----STSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLEQEDEIRIAKE 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IEAG   +M  +   P+           L +G   + ++I     IG             
Sbjct: 127 IEAGVFEIMKGITLYPVITDFFFKAHTRLEEGKCKMTDVI-----IG------------- 168

Query: 206 HSYQKREDSSQEKERDDVQETEGDIES-AAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             YQ                  GD E  A K +  D  K D+            DE+ +D
Sbjct: 169 --YQ------------------GDTEDFAVKKAAFDAGKFDN------------DEEHED 196

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKV---LKEK 320
             +T                DE  +VY    ++   +    + +EK   + K    ++++
Sbjct: 197 MEYT--------------GPDE-NQVYNRFETISKCSKTYNETNEKLGFRHKKTIEMRQQ 241

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L + +  L L    ++ ++E + +  +++   E  +       G+ R  F E     E +
Sbjct: 242 LSQSLSDLRLAPKLVNTMIEVICNRVEQVKKQEKTIQNKCLDAGMNRLYFFESFSKNETN 301

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+S  K   + E K  +    D I   +  ++    E  ++I+E + +  M R+G+  
Sbjct: 302 FDWLSAIKLDEKTEEK--LKVSKDEIYYAQKNLQQFEEEMQLTITELKTLNKMYRRGDRR 359

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK +M+EANLRLVIS+AKKY NRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA
Sbjct: 360 AKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYA 419

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R  R++  K  RE +PEE+A ++ +P 
Sbjct: 420 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREASPEELATEMELPE 479

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             + K+LKI+KEP+S+ETP+GD++ S++GDFIED N  SP++   + +LRETT+ +L++L
Sbjct: 480 YKIIKILKISKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTKESLRETTSELLSNL 539

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE +VL+MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL
Sbjct: 540 SPREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLQSFL 599

Query: 681 D 681
           +
Sbjct: 600 E 600


>gi|255019635|ref|ZP_05291715.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus ATCC
           51756]
 gi|254970938|gb|EET28420.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus ATCC
           51756]
          Length = 625

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 202/357 (56%), Positives = 261/357 (73%), Gaps = 3/357 (0%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
           + LN  +IDL+ + L ++++ +   E EL+ L     G  R  F+  + G E D  WV  
Sbjct: 264 MKLNVRQIDLMADALRNLTEEVRLAERELMALCIDRAGFPRKEFVRSYPGHESDIAWVD- 322

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A+      +   +    D I+ +  ++  I    G+ I+E +    ++  GE +A  AKK
Sbjct: 323 AQIAAGRPYSPMMLVLRDEIVAVMTQLADIEERAGLPIAEIKEASRLMSIGEAKARRAKK 382

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 383 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 442

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A ++ MP + +RKV
Sbjct: 443 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAARMEMPEDKIRKV 502

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREE 625
           LKI KEPIS+ETPIGD++ SHLGDFIED+N  +P D+A+ A +RE    +L   LTPRE 
Sbjct: 503 LKIAKEPISMETPIGDDEDSHLGDFIEDRNVAAPTDAAVNAAIREVVEELLDTGLTPREA 562

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSF+DG
Sbjct: 563 KVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRSFVDG 619



 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 61/169 (36%), Positives = 92/169 (54%), Gaps = 9/169 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDD---LEDE 86
           K++I   +++GY+T  E+N  LP D    EQME+ + M+++MGI V +   DD   L D 
Sbjct: 11  KRLIARGKEQGYLTYREINDLLPEDVFDPEQMENVITMINDMGIEVFEEAPDDETLLMDN 70

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+       +  +          D     T DPVRMY+REMG++ELL+REGEI IA+RI
Sbjct: 71  EGNPIVAAQEAEEAAEEALAVVEADIG--RTSDPVRMYMREMGTVELLTREGEIEIARRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           E G   ++ ++   P T   L+    ++  G   L E++D  A I P +
Sbjct: 129 EDGLLQVLRAVSTCPTTIALLLEAAQKVEQGELRLDEVVD--AFIDPNA 175


>gi|322421611|ref|YP_004200834.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320127998|gb|ADW15558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 583

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 212/413 (51%), Positives = 293/413 (70%), Gaps = 20/413 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV----LKEKLVKLVGSLSLNQSR 334
           +V+  +DEI E+ + +  +Q  A+ G+   K S         LK K+ + + SL L    
Sbjct: 181 RVLGIIDEIKEMDQRMEQIQ-TALEGKVSAKESDALNSEHGELKVKMAETLKSLRLKDRH 239

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD----F 390
           I+ + ++L ++S ++     E+    +     +DVFL   +G +       ++K      
Sbjct: 240 IEKIAQRLKELSCKVDTVMQEVAEFEKETSTVKDVFLTAFEGLK-SASEADFSKKMHMTL 298

Query: 391 PEGEW--KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            EG+   K + + E +        +K I  E+G   SE  + +  + +GE +A +AK E+
Sbjct: 299 EEGQKLEKRYRSSEAN--------LKKIEQESGFKASELANALLAIEEGEHKAKLAKSEL 350

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 351 VEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAI 410

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++A+P++ VRKVLK
Sbjct: 411 TRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMALPLDKVRKVLK 470

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+VL
Sbjct: 471 IAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKVL 530

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 531 RMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 583


>gi|32034495|ref|ZP_00134667.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|126208939|ref|YP_001054164.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           L20]
 gi|307257544|ref|ZP_07539308.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|126097731|gb|ABN74559.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
 gi|306863980|gb|EFM95899.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 619

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 213/395 (53%), Positives = 275/395 (69%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E +  LR   + A+   QK  +S  K +   + L  +     L   + DLLVE +  + K
Sbjct: 225 EKFYALREQHEKALQAIQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMK 284

Query: 348 RIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           ++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  +G     +A  +D I
Sbjct: 285 QVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPK-LANYIDQI 343

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
               + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 344 RVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNR 403

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 404 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 463

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D S
Sbjct: 464 ETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 523

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVG
Sbjct: 524 HLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 583

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 584 KQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|295701329|ref|YP_003610330.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295441652|gb|ADG20819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 663

 Score =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 254/660 (38%), Positives = 371/660 (56%), Gaps = 58/660 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---------DD 82
           + +I+L ++RGY+T  E+N  LP +   +  +E  V+  ++MG+ V +          +D
Sbjct: 51  RALIQLGKERGYLTHAEINDHLPDNFAQTAAIETIVSTFNDMGVAVYEQAPSAEVLLMND 110

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                  +D  D  +  + SSV      DS    T DP RMY+REMG+  LL+R GEI I
Sbjct: 111 ATPATMLDDQADEEAEVALSSV------DSEFGRTTDPFRMYMREMGATGLLTRAGEIEI 164

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++  SP T  A+++   ++  G   + E++D           G    
Sbjct: 165 AKRIEGGLHEMVQAIAVSPATVSAILLSAKQIEAGELRIDELVD-----------GINAE 213

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
           TE          S E+   D  E E D E A   + DD    D   E++E ++R      
Sbjct: 214 TE----------SVEQSSTDFAE-EPDTEQA---TADDDGGGD---EHSEIEDR------ 250

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            D+A +  A   QL    +     + E++ ++   Q  A  G    K  V    L+E + 
Sbjct: 251 -DTARSNEARLKQLTSDSLVIFARVRELFEQISGSQ--AAQG----KGRVARADLREAIQ 303

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
           + +  +      ID L   +     ++   E  +L++A    G+ R+ F+E  QGRE D 
Sbjct: 304 RELAPIRFTARTIDRLCNAVQQQVAQVRAVERHILQIAVDRCGMPREKFVESFQGRETDL 363

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W S +      E+   +   + +I   + ++  I  + G+ + + + I   +   E + 
Sbjct: 364 AW-SESTAAASREYGAALERSLPAIQAEQRKLLDIETKVGLPLQQLKKINRQMMAAESKM 422

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTYA 
Sbjct: 423 LQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYAT 482

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WWV+QA+TRS+ADQ+ TIRIPVHM + I+K+ R +R +  +  RE  P  +A+++ +P E
Sbjct: 483 WWVRQAVTRSLADQARTIRIPVHMMESINKLNRISREILQQTGREAHPAVLAQRMEVPEE 542

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR +LKI ++P+SLETP+GDE  + L D IED  A SP D+A+QANLR      L +L+
Sbjct: 543 KVRAMLKIGRQPLSLETPVGDEADTTLSDVIEDPMATSPADAAVQANLRAAINTALDALS 602

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI   +D TLEE+GKQF +TRERIRQIE+KA+RKL HP+R+ KLR FLD
Sbjct: 603 PREAKVLRMRFGIDTASDCTLEELGKQFDLTRERIRQIESKAMRKLMHPNRTAKLRPFLD 662


>gi|165976903|ref|YP_001652496.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|303252483|ref|ZP_07338647.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307248518|ref|ZP_07530536.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307250749|ref|ZP_07532682.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307261955|ref|ZP_07543613.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|165877004|gb|ABY70052.1| RNA polymerase sigma factor [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|302648684|gb|EFL78876.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854994|gb|EFM87179.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306857217|gb|EFM89340.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306868366|gb|EFN00185.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 619

 Score =  402 bits (1033), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 213/395 (53%), Positives = 275/395 (69%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E +  LR   + A+   QK  +S  K +   + L  +     L   + DLLVE +  + K
Sbjct: 225 EKFYALREQHEKALQAIQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMK 284

Query: 348 RIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           ++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  +G     +A  +D I
Sbjct: 285 QVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPK-LANYIDQI 343

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
               + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 344 RVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNR 403

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 404 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 463

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D S
Sbjct: 464 ETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 523

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVG
Sbjct: 524 HLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 583

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 584 KQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|121997892|ref|YP_001002679.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
           SL1]
 gi|121589297|gb|ABM61877.1| RNA polymerase, sigma 70 subunit, RpoD [Halorhodospira halophila
           SL1]
          Length = 602

 Score =  402 bits (1033), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 213/398 (53%), Positives = 280/398 (70%), Gaps = 5/398 (1%)

Query: 287 IAEVYRELRSLQDNAVNGQKDEKS-SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           +AE++  LR+  +        E S S +   L+ +L ++  S+      +D + ++L   
Sbjct: 206 VAELFERLRAAYNEMQEVLATEGSASPRIAELRGELEEVFLSIKFTPKVVDAVADRLRGT 265

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWK-NFVACEV 403
              I   E E++ L    G + R  F++  Q RE DP W+       EGE +   +    
Sbjct: 266 VDTIRAREREIMNLCTREGRMARKEFVKSFQDRETDPTWLDDL--LAEGEERAERLQPHA 323

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           ++I K ++E+K I+ + G+S++E + I   +  GE +A  AKKEMVEANLRLVIS+AKKY
Sbjct: 324 EAIRKAQSELKEIADKNGLSVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKY 383

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 384 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 443

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + VRKVLKI KEPIS+ETPIGD+
Sbjct: 444 HMIETINKLNRVSRQMLQEMGREATPEELAERMEMPEDKVRKVLKIAKEPISMETPIGDD 503

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIED +  SP+DSA    LRE+   VL+ LTPRE +VLRMRFGI MNTDHTLE
Sbjct: 504 EDSHLGDFIEDTSVTSPVDSATSEGLRESVREVLSGLTPREAKVLRMRFGIDMNTDHTLE 563

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFL+
Sbjct: 564 EVGKQFDVTRERIRQIEAKALRKLRHPTRSDGLRSFLE 601



 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 58/158 (36%), Positives = 91/158 (57%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I   +++G++T  E+N  LP D V  +Q++D + M+++MGINV     D D+L    
Sbjct: 10  KQLIAKGKEQGFLTYAEVNDHLPDDIVDPDQIDDIIGMINDMGINVHETAPDSDELL--- 66

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +E ++      +  +       D+    T DPVRMY+REMGS+ELL+REGEI +AKRIE
Sbjct: 67  LAETTVATDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGSVELLTREGEIQLAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G    +A+L   P   + LI+  D   +G   L +I+
Sbjct: 127 DGLDRALAALSSYPEAARQLIMLYDRAQEGEARLTDIV 164


>gi|303250977|ref|ZP_07337166.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253124|ref|ZP_07535005.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302650194|gb|EFL80361.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859418|gb|EFM91450.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 619

 Score =  401 bits (1031), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 212/395 (53%), Positives = 273/395 (69%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E +  LR   + A+   QK  +S  K +   + L  +     L   + DLLVE +  + K
Sbjct: 225 EKFYALREQHEKALQAIQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMK 284

Query: 348 RIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           ++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  +G         +D I
Sbjct: 285 QVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLTNY-IDQI 343

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
               + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 344 RVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNR 403

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 404 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 463

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D S
Sbjct: 464 ETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 523

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVG
Sbjct: 524 HLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 583

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 584 KQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|261855081|ref|YP_003262364.1| RNA polymerase, sigma 70 subunit, RpoD [Halothiobacillus
           neapolitanus c2]
 gi|261835550|gb|ACX95317.1| RNA polymerase, sigma 70 subunit, RpoD [Halothiobacillus
           neapolitanus c2]
          Length = 608

 Score =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 205/377 (54%), Positives = 281/377 (74%), Gaps = 10/377 (2%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGI 365
           DE+S      L ++LV+L     LN +  + L+EQ+     RI   E +++  A    G+
Sbjct: 236 DERSPEYLASLADQLVQL----KLNPAFNEKLLEQIRQAIARIRLLEKQIMHQAVDKGGL 291

Query: 366 KRDVFLERHQGRELDPHWVSYA-KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           KR+ F+E  +  E D  WV  A K  P  ++   V  E++   +++  + +++ ++ +++
Sbjct: 292 KRETFIEAFRSNESDIGWVKVATKGKPTAKFSQ-VQPEIE---RLQKRLNTVARDSKLTV 347

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ R +  ++  GE +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 348 AQTREVHRLITLGEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 407

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 408 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 467

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           RE TPEE+A+++ +P + +RKVLKI KEPIS+ETPIG++D S+LGDFIED++A+SP+DSA
Sbjct: 468 REATPEELAERMDLPEDKIRKVLKIAKEPISMETPIGEDDDSNLGDFIEDQSAISPMDSA 527

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A+L E    +LASLTPRE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 528 TNASLSEIVREILASLTPREAKVLMMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKAL 587

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS++LRSF++
Sbjct: 588 RKLRHPSRSERLRSFIE 604



 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 59/160 (36%), Positives = 93/160 (58%), Gaps = 5/160 (3%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLED 85
           S K +I   R++GY+T  E++  LP   V ++Q+ED + M+  MGI+V     DGDDL  
Sbjct: 8   SIKSLIARGREQGYLTYAEISDHLPEALVDADQIEDIIGMIQEMGISVSEVAPDGDDLGL 67

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            + S  + D  ++    +V L  + D+    T DPVRMY+REMG+++LL+R+GEI IAKR
Sbjct: 68  ADESRAASDEDATEEAVAV-LASQVDAEFGRTTDPVRMYMREMGTVDLLNRQGEIEIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IE G   +  +L   P T + L+     +  G   ++++I
Sbjct: 127 IEEGLIDVTRALAFYPPTIETLLEHYARIEAGDLRMQDVI 166


>gi|21672345|ref|NP_660412.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|401010|sp|P32001|RPOD_BUCAP RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|144139|gb|AAA73234.1| sigma factor [Buchnera aphidicola]
 gi|21622948|gb|AAM67623.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 617

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 214/403 (53%), Positives = 279/403 (69%), Gaps = 19/403 (4%)

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLK-EKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E +RELR    N  N  K++  + +  +L+   L ++     L   + D LV  + ++  
Sbjct: 223 EKFRELRKQYTNTSNTIKNKNRNHQDSLLEIYNLSEIFKQFRLVPKQFDHLVNNMRNMMN 282

Query: 348 RIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV--------SYAKDFPEGEWKNF 398
           R+   E ++++L  +   I + +FL+   G+E D +W         S++K   E + K F
Sbjct: 283 RVRKQERKIMKLCIEECKIPKKIFLKIFSGKETDQNWFKKEQSSNQSWSKKLEEIKEKVF 342

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
            + +         ++K I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 343 SSMK---------KLKQIEKETGLTIEQVKDINKRMSIGEAKAKRAKKEMVEANLRLVIS 393

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 394 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 453

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +RKVLKI KEPIS+ET
Sbjct: 454 IRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMET 513

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ LT RE +VLRMRFGI MNT
Sbjct: 514 PIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNT 573

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 574 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 616



 Score =  107 bits (267), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 67/176 (38%), Positives = 101/176 (57%), Gaps = 9/176 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP + + SEQ++D + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTHGKEQGYLTYAEVNDHLPEEIIDSEQIDDIIQMINDMGIQVVEEAPDADDLILNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  INTDTDEDAVEAATQ--VLSSVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
            G   + +S+ E P     L+   D +  G   L +II     + P ++  F H T
Sbjct: 127 EGINQVQSSVSEYPEAITYLLEQYDRIKTGQIRLSDIIT--GFVDPNAEEIFSHST 180


>gi|307246390|ref|ZP_07528466.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307255376|ref|ZP_07537186.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307259826|ref|ZP_07541544.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306852723|gb|EFM84952.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306861685|gb|EFM93669.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306866124|gb|EFM97994.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 619

 Score =  398 bits (1023), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 212/395 (53%), Positives = 274/395 (69%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E +  LR   + A+   QK  +S  K +   + L  +     L   + DLLVE +  + K
Sbjct: 225 EKFYALREQHEKALQAIQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMK 284

Query: 348 RIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           ++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  +G     +A  +D I
Sbjct: 285 QVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPK-LANYIDQI 343

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
               + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 344 RVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNR 403

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 404 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 463

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D S
Sbjct: 464 ETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 523

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFI+D++   PLDSA   +LR  T  VL  LT RE +VLRMRFGI MNTDHTLEEVG
Sbjct: 524 HLGDFIQDESLELPLDSATAESLRLATNEVLEGLTLREAKVLRMRFGIDMNTDHTLEEVG 583

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 584 KQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|329898803|ref|ZP_08272472.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC3088]
 gi|328920738|gb|EGG28203.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC3088]
          Length = 600

 Score =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 212/400 (53%), Positives = 278/400 (69%), Gaps = 7/400 (1%)

Query: 286 EIAEVYRELRSLQDNA--VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E A+ ++ELR   +       +K  +S V  K L +KL ++     L     D L++   
Sbjct: 203 EAAKRFKELRKQWEKTEKALAEKGRQSKVTLKEL-DKLGEVFKFFKLTPRVFDPLLDMAR 261

Query: 344 DISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVS-YAKDFPEGEWKNFVAC 401
           D+ + +   E E++ +   +  + R  F++   G E +  W+    K  PE   K  +  
Sbjct: 262 DVLQEVRTQEREIMTICVRHCSVPRKAFIDSFVGNETNEAWLDDLIKKAPERAAK--LEA 319

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           + D++++++  I +   ++G+S+SE + I   +  GE  A  AKKEMVEANLRLVIS+AK
Sbjct: 320 DRDTLMRLQRRIIATEEKSGLSVSEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAK 379

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 380 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 439

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VRKVLKI KEPIS+ETPIG
Sbjct: 440 PVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIG 499

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED    SP+DSA    L+E TT VLA LT RE +VLRMRFGI MNTDHT
Sbjct: 500 DDEDSHLGDFIEDVTIASPVDSATGQGLQEATTEVLAGLTAREAKVLRMRFGIDMNTDHT 559

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 560 LEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 599



 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 55/134 (41%), Positives = 84/134 (62%), Gaps = 7/134 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D+L   E
Sbjct: 12  KSLIAKGKEQGYLTYSEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEEAPDADELLMTE 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G   + D+A++ + +++   + +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 72  GDSSADDIAAAEAAAALAAVETEAG---RTTDPVRMYMREMGTVELLTREGEIVIAKRIE 128

Query: 148 AGRAMMMASLCESP 161
            G   +MA+L   P
Sbjct: 129 EGIRELMAALAHYP 142


>gi|115375627|ref|ZP_01462884.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823184|ref|YP_003955542.1| RNA polymerase sigma factor rpod [Stigmatella aurantiaca DW4/3-1]
 gi|115367403|gb|EAU66381.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396256|gb|ADO73715.1| RNA polymerase sigma factor RpoD [Stigmatella aurantiaca DW4/3-1]
          Length = 706

 Score =  396 bits (1017), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 208/377 (55%), Positives = 274/377 (72%), Gaps = 25/377 (6%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           L+ K+++++  + LN+ ++D +V  L  + +R+   E EL          RD  LER  G
Sbjct: 342 LRTKMMEVLEEMRLNKKQVDRIVLNLKQLIERVDKAEEEL----------RD--LERRNG 389

Query: 377 ---RELDPHWVSYAKDFPEGEWK-----NFVACEVDSILK-IRN---EIKSISVETGISI 424
              +EL P  +  ++D P    K     NF   +++++ + +R    +IK +  E  + +
Sbjct: 390 VSMKELRPQ-LKESRDNPNTAKKLQKQLNFTPEQLEALDRDVRTAVRKIKRVEEEANLPV 448

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
              R     +R GE  A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 449 DALRRNYDAIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKA 508

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I 
Sbjct: 509 VDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEIG 568

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEEIA+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ 
Sbjct: 569 REPTPEEIAEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPADAV 628

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I  NL E T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+
Sbjct: 629 INMNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKAL 688

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRSK+LRSF++
Sbjct: 689 RKLRHPSRSKRLRSFVE 705



 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 87/155 (56%), Gaps = 1/155 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   R++G++T +E+N  LP D VSS+Q++D ++M  +  I +VD          + 
Sbjct: 107 KDLLAAGREKGFLTYDEVNDALPADIVSSDQIDDVMSMFGDNDIEIVDAQKAAQSNEIKP 166

Query: 92  SLDLAS-SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ +   S  ++        D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G 
Sbjct: 167 TVAVEEESKQDADADDDDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGE 226

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             ++ ++    +    ++   ++L  G   +R++I
Sbjct: 227 KEVLRAMLACRVAVADILDIGNKLKTGKLRVRDVI 261


>gi|220936192|ref|YP_002515091.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997502|gb|ACL74104.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 619

 Score =  395 bits (1016), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 211/400 (52%), Positives = 284/400 (71%), Gaps = 7/400 (1%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           +E  E + +LR++ + A+ G   +K + K + ++E++        L    +D L   L++
Sbjct: 222 EEARERFTKLRAMYEEAM-GFAAKKHTAKYRKVREEMASYFMEFKLLPRFVDQLTADLHE 280

Query: 345 ISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN--FVAC 401
           + +RI   E  ++ +      + R  F+      E +  W+       +G+ K+   +A 
Sbjct: 281 MVERIRMQERTVMDICVNRCNMPRKEFITAFPENETNLKWLDTQT---KGKSKHAKLLAE 337

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             D IL+I+ ++ +I  E+ ++ISE + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 338 HKDEILRIQKKLVAIEDESNLTISEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 397

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 398 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 457

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ RE TPEE+++++ MP + VRKVLKI KEPIS+ETPIG
Sbjct: 458 PVHMIETINKLNRISRQMLQEMGREATPEELSERMEMPEDKVRKVLKIAKEPISMETPIG 517

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED N +SP+++A +  L E T  VLASLTPRE +VLRMRFGI MNTDHT
Sbjct: 518 DDEDSHLGDFIEDVNVMSPIEAATREGLSEATRDVLASLTPREAKVLRMRFGIDMNTDHT 577

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 578 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEMLRSFLD 617



 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 58/161 (36%), Positives = 92/161 (57%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +++G++T  E+N  LP   V  EQ+ED +AM+++MGI V       ++    D
Sbjct: 11  KELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIAMINDMGIAV------HEQAPDSD 64

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTD-------DPVRMYLREMGSIELLSREGEIAIAK 144
           SL L+ S  ++     +   +A  S D       DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 65  SLILSDSTVSTDEDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGEIKIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   ++ +L   P +   L+   D++  G   L +++
Sbjct: 125 RIEDGLGQVLFALAHYPQSISTLLAEFDKVEAGEMKLTDLV 165


>gi|260222953|emb|CBA33035.1| RNA polymerase sigma factor rpoD [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 519

 Score =  395 bits (1015), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 236/574 (41%), Positives = 337/574 (58%), Gaps = 70/574 (12%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +RMY+REMG++ELL+REGEI IAKRIE G   MM ++  SP T   ++   +E+ +G  +
Sbjct: 1   MRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILRLGEEIREGKVV 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           +  I+D           GF +  E   Y   ED  +  E DD     G            
Sbjct: 61  ITTIVD-----------GFSNPNEADDYVAEEDFDEFDEADDDDGKGG------------ 97

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                                    +  L+   ++L+ + +   D++ E++ ++  + D 
Sbjct: 98  -------------------------SKALTKKLEELKKQALERFDKMRELFEKVHKVYDK 132

Query: 301 AVNGQKDEKSSVKC-KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              G     + VK  K L ++L+ +  +    +   D++  Q+ D+ K+    E EL R+
Sbjct: 133 EGYGTP---AYVKAQKALSDELMTIRFTAKAIEKLCDMVRAQVDDVRKK----ERELRRI 185

Query: 360 -AQSYGIKRDVFLERHQGRE----------LDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
                G  ++ F+    GR+          L+  W+   K    G+ W   +   +  + 
Sbjct: 186 IVDKCGYPQENFIADFSGRDKAGNKVASNLLNLKWIE--KQAASGKSWAAVMGRNIPPVQ 243

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++ ++  +  +  + + + + I   + +GE  +  AKKEM+EANLRLVIS+AKKYTNRG
Sbjct: 244 DLQQKLIDLQAQVVVPLDQLKDINKRMNEGEYASRAAKKEMIEANLRLVISIAKKYTNRG 303

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 304 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 363

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+   +   EP    +A+K+ +P + +RK++KI KEPIS+ETPIGD+D SH
Sbjct: 364 TINKMNRISRQHLQEFGFEPDASVLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSH 423

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED    +P+++A+QA LR+    +L SLTPRE +VLRMRFGI M +DHTLEEVGK
Sbjct: 424 LGDFIEDSANTAPMEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGK 483

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKLKHPSRS KLRSF D
Sbjct: 484 QFDVTRERIRQIEAKALRKLKHPSRSDKLRSFTD 517


>gi|257464575|ref|ZP_05628946.1| RNA polymerase sigma factor RpoD [Actinobacillus minor 202]
 gi|257450235|gb|EEV24278.1| RNA polymerase sigma factor RpoD [Actinobacillus minor 202]
          Length = 621

 Score =  395 bits (1015), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 207/381 (54%), Positives = 269/381 (70%), Gaps = 8/381 (2%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY- 363
           QK  ++  K +     L  +     L   + DLLV  +  + K++   E ++ R A  Y 
Sbjct: 244 QKHGRTHAKAREQINALSDIFREFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYA 303

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEG---EWKNFVACEVDSILKIRNEIKSISVET 420
           G+K+  FL+  Q  E    W+  A +  +G   +  N+V     +I+ ++N    +  ++
Sbjct: 304 GMKKADFLKAFQNNETTEAWIEKAINAKKGGAPKLANYVEKIRINIVNLQN----LEQQS 359

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 360 GLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 419

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 420 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCL 479

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFI+D++   P
Sbjct: 480 QEMGREATPEELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELP 539

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 540 LDSATAESLRIATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 599

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRS+ LRSFLD
Sbjct: 600 AKALRKLRHPSRSETLRSFLD 620



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/133 (38%), Positives = 80/133 (60%), Gaps = 11/133 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   R++GY+ + E++  LP + V +EQ+ED + M+++MGI V++     DE      L
Sbjct: 18  LIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDE------L 71

Query: 94  DLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            LA + ++  V  +  K     +S    T DPVRMY+REMG++ELL+RE EI I+KRIE 
Sbjct: 72  MLAENITDEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIEE 131

Query: 149 GRAMMMASLCESP 161
           G   +  ++ E P
Sbjct: 132 GINEVQCAVAEYP 144


>gi|240948851|ref|ZP_04753207.1| RNA polymerase sigma factor RpoD [Actinobacillus minor NM305]
 gi|240296666|gb|EER47277.1| RNA polymerase sigma factor RpoD [Actinobacillus minor NM305]
          Length = 621

 Score =  395 bits (1015), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 207/381 (54%), Positives = 269/381 (70%), Gaps = 8/381 (2%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY- 363
           QK  ++  K +     L  +     L   + DLLV  +  + K++   E ++ R A  Y 
Sbjct: 244 QKHGRTHAKAREQINALSDIFREFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYA 303

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEG---EWKNFVACEVDSILKIRNEIKSISVET 420
           G+K+  FL+  Q  E    W+  A +  +G   +  N+V     +I+ ++N    +  ++
Sbjct: 304 GMKKADFLKAFQNNETTEAWIEKAINAKKGGVPKLANYVEKIRINIVNLQN----LEQQS 359

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G++I++ R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 360 GLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 419

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 420 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCL 479

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFI+D++   P
Sbjct: 480 QEMGREATPEELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELP 539

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 540 LDSATAESLRIATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 599

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRS+ LRSFLD
Sbjct: 600 AKALRKLRHPSRSETLRSFLD 620



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/133 (38%), Positives = 80/133 (60%), Gaps = 11/133 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   R++GY+ + E++  LP + V +EQ+ED + M+++MGI V++     DE      L
Sbjct: 18  LIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDE------L 71

Query: 94  DLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            LA + ++  V  +  K     +S    T DPVRMY+REMG++ELL+RE EI I+KRIE 
Sbjct: 72  MLAENITDEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIEE 131

Query: 149 GRAMMMASLCESP 161
           G   +  ++ E P
Sbjct: 132 GINEVQCAVAEYP 144


>gi|118581452|ref|YP_902702.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118504162|gb|ABL00645.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter propionicus DSM
           2379]
          Length = 582

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 181/276 (65%), Positives = 233/276 (84%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +L    ++K I +E+G   SE    +  + +GEC+A IAK E++EANLRLV+S+AKKYTN
Sbjct: 307 LLSTARKLKKIELESGFKASELSAALQAIEEGECKARIAKSELIEANLRLVVSIAKKYTN 366

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 367 RGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM 426

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++RT+R++  +  REP PEEIA+++ +P++ VRKVLKI KEPISLETPIG+E+ 
Sbjct: 427 IETINKLIRTSRQLVQENGREPAPEEIAERMQLPLDKVRKVLKIAKEPISLETPIGEEED 486

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDK  +SP+++ I+ANL E T+RVL++LTPREE+VLRMRFGIG  +DHTLEEV
Sbjct: 487 SHLGDFIEDKAVISPIEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEV 546

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+ F VTRERIRQIEAKA+RKL+HPSRSKKL+SF++
Sbjct: 547 GQDFAVTRERIRQIEAKALRKLRHPSRSKKLKSFVE 582



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 53/146 (36%), Positives = 88/146 (60%), Gaps = 2/146 (1%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I L +++G++T EE+N  LPPD +++EQ++D + M  ++ I +VD         
Sbjct: 7   DGVKQLIDLGKEKGFLTFEEVNDILPPD-IATEQIDDVMGMFGDLDIEIVDSAQKVKIPK 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  ++    A   +  ++    S  R T DPVRMYLREMGS+ LL+REGE+ IAKRIE 
Sbjct: 66  MKLEMEEEEEAEGEAEEVEFEPGSIGR-TSDPVRMYLREMGSVSLLTREGEVEIAKRIED 124

Query: 149 GRAMMMASLCESPLTFQALIIWRDEL 174
           G   + + +  +P+T + ++   D+L
Sbjct: 125 GERDVASVILNTPITIKEVLQLGDKL 150


>gi|222053802|ref|YP_002536164.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221563091|gb|ACM19063.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 586

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 208/416 (50%), Positives = 290/416 (69%), Gaps = 23/416 (5%)

Query: 279 KVMCALDEIAEVYRELR----SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           +++  +DEI +  R +     +L+   +  ++ E    + +  K KL +L+ SL L    
Sbjct: 181 RLLATIDEIRDHDRRMEEIFLALEQTTLPAKEREALLAEQRDFKAKLAELLKSLRLKDRH 240

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           I+ + ++L ++S ++     E+  L +  G+            +L       AK  P+ E
Sbjct: 241 IEKISQRLKELSHKVDKMMHEIADLEKEAGV---------SSADLAAMLGKMAKG-PDEE 290

Query: 395 WKNF--VACEVDSILKIRNEIKS-------ISVETGISISEFRHIVSMVRKGECEASIAK 445
            K    +   ++ + K+    KS       I  E+G   SE    +  + +GE +A +AK
Sbjct: 291 KKVLKKLGISLEDVQKLEKRFKSAERKLKKIEQESGFKASELSTALQAIEEGEHKAKLAK 350

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 351 SELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIR 410

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++++P++ VRK
Sbjct: 411 QAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMSLPLDKVRK 470

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE
Sbjct: 471 VLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREE 530

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 531 KVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 586



 Score =  104 bits (260), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 58/147 (39%), Positives = 88/147 (59%), Gaps = 3/147 (2%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I L +++G++T EE+N  LPPD VSSEQ++D ++M  +M I +VD    +  + 
Sbjct: 7   DEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSEQIDDVMSMFGDMDIEIVDSA--QKVKI 64

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  LDL           +   +      T DPVRMYLREMGS+ LL+REGE+ IAKRIE
Sbjct: 65  PKVKLDLEDEEEMEGEQEEVEFEPGTLGRTSDPVRMYLREMGSVSLLTREGEVEIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDEL 174
            G   + + +  +P+T + +I   D+L
Sbjct: 125 VGERDVASVILNTPITVKEVISLGDKL 151


>gi|330448778|ref|ZP_08312425.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492969|dbj|GAA06922.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 616

 Score =  394 bits (1013), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 212/402 (52%), Positives = 273/402 (67%), Gaps = 17/402 (4%)

Query: 289 EVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E + ELR+  D        NG++D+++ +      E+L ++     L   + D LV  L 
Sbjct: 222 EKFLELRNAYDKMALAIDTNGRQDKQTEIAV----EELSEVFKQFRLIPKQFDRLVSSLR 277

Query: 344 DISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   ++  NE  ++R+   +  + +  F+    G E +  W+  A +  +   +     E
Sbjct: 278 DAMDKVRTNERLIMRMCVDNSKMPKKTFVTLFAGNEANQDWIDEALNSGKPYAERLKTYE 337

Query: 403 VD---SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
            D   S +K+R     +  ETG+SI   + I   +  GE +A  AKKEMVEANLRLVIS+
Sbjct: 338 EDLRRSAIKLR----MLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISI 393

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TI
Sbjct: 394 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 453

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETP
Sbjct: 454 RIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETP 513

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IGD++ SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +VLRMRFGI MNTD
Sbjct: 514 IGDDEDSHLGDFIEDTTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTD 573

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 574 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 615



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 59/142 (41%), Positives = 88/142 (61%), Gaps = 11/142 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLE-DE 86
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D D+L   E
Sbjct: 10  KLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADELMMTE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + +++    A++ + SSV      +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 70  DNADEDAIEAAAQALSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALI 168
           E G   +  S+ E P     L+
Sbjct: 124 EDGINQVQCSVAEYPSAIAHLL 145


>gi|254480921|ref|ZP_05094167.1| Sigma-70, non-essential region family [marine gamma proteobacterium
           HTCC2148]
 gi|214038716|gb|EEB79377.1| Sigma-70, non-essential region family [marine gamma proteobacterium
           HTCC2148]
          Length = 605

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 206/364 (56%), Positives = 261/364 (71%), Gaps = 3/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           EKL +L     L     D + +   +I   +   E E++R+A +  G+ R  F+   QG 
Sbjct: 243 EKLGELFKFFKLTPRVFDPISDTPRNILAAVRDQEREIMRIAIKVCGMPRKDFISTFQGS 302

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W+S  +   + ++   +  E + I +++  I++I  + G+ ISE + I   +  G
Sbjct: 303 ESDLKWLS--RQARKKDYGPKLNAEKEIIHRLQRRIQAIEGQCGLQISEIKEINRRMSMG 360

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 361 EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 420

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ 
Sbjct: 421 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMD 480

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA    L+E T  VL
Sbjct: 481 MPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTISSPVDSATGQGLQEATKDVL 540

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LR
Sbjct: 541 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLR 600

Query: 678 SFLD 681
           SFLD
Sbjct: 601 SFLD 604



 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 53/141 (37%), Positives = 88/141 (62%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D+L   E
Sbjct: 12  KALIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDMGIQVFEQAPDADELLMTE 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G   + D+A++ + +++   + +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 72  GDRSADDIAAAEAAAALAAVETEAG---RTTDPVRMYMREMGTVELLTREGEIVIAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   ++++L   P   ++++
Sbjct: 129 EGIRELLSALALYPGAVKSIL 149


>gi|77163592|ref|YP_342117.1| hypothetical protein Noc_0045 [Nitrosococcus oceani ATCC 19707]
 gi|254436143|ref|ZP_05049650.1| Sigma-70, non-essential region family [Nitrosococcus oceani AFC27]
 gi|76881906|gb|ABA56587.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
           19707]
 gi|207089254|gb|EDZ66526.1| Sigma-70, non-essential region family [Nitrosococcus oceani AFC27]
          Length = 602

 Score =  394 bits (1011), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 213/401 (53%), Positives = 283/401 (70%), Gaps = 11/401 (2%)

Query: 284 LDEIAEVYRELRSLQD--NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           LD + E + +LR L +   A + + ++++  +      +L KLV  LS        L+E 
Sbjct: 205 LDRVREQFTQLRELYERYQAADLKDNDRALAELSECFLQL-KLVPRLSQR------LIEN 257

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
           L  +   I   E  ++++A  S  + R  FL   Q +E + +WV       +  + + + 
Sbjct: 258 LRGVVAEIRVLERSIMKIAVNSAQMPRKDFLSSFQKQETNLNWVE-KHIRAKKHYSSVLR 316

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            + D+I K + ++  +    G+SI++ + I   +  GE  A  AKKEMVEANLRLVIS+A
Sbjct: 317 KQGDAIQKAQEKLIVLEQRAGMSITQIKEINRSLSIGEARARRAKKEMVEANLRLVISIA 376

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 377 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 436

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+ R +R+M  ++ REPTP+E+A+++ MP + VRKVLKI +EPIS+ETPI
Sbjct: 437 IPVHMIETINKLNRVSRQMLQEMGREPTPDELAERVEMPKDKVRKVLKIAREPISMETPI 496

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD++ SHLGDF+ED   +SP DSAI + LRETT  +LA LTPRE +VLRMRFGI MNTDH
Sbjct: 497 GDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQLILAGLTPREAKVLRMRFGIDMNTDH 556

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 557 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 597



 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 75/137 (54%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   + RGY++  E+N  LP D +  EQ+ED + M ++MGI+V +     D     D
Sbjct: 14  KLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEADALAIMD 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +       +  +       D     T DPVRMY+REMGS+ELL+REGEI+IAKRIE G  
Sbjct: 74  TAVADDEVAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAKRIEEGMR 133

Query: 152 MMMASLCESPLTFQALI 168
            +  +L   P +   L+
Sbjct: 134 QVYTALSRFPGSVAELL 150


>gi|198284073|ref|YP_002220394.1| RNA polymerase sigma-70 subunit RpoD [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|198248594|gb|ACH84187.1| RNA polymerase, sigma 70 subunit, RpoD [Acidithiobacillus
           ferrooxidans ATCC 53993]
          Length = 631

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 200/358 (55%), Positives = 260/358 (72%), Gaps = 5/358 (1%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
           + LN  +ID++ + L  +++ +   E EL+ L  +     R  F+  + G E D  W+  
Sbjct: 270 IKLNGRQIDVMTDALRGLTEEVRQCERELMELCIERARFPRKEFVRSYPGHEGDIGWID- 328

Query: 387 AKDFPEGEWKNFVACEV-DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            +    G   +    E  D I+ I   + +I    G+ I+E +    ++  GE +A  AK
Sbjct: 329 -QQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKRAGLPIAEIKEASRLMSIGEAKARRAK 387

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 388 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 447

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 448 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMEMPEDKIRK 507

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPRE 624
           VLKI KEPIS+ETPIGD++ SHLGDFIED+N  +P DSA+ A +RE    +L   LT RE
Sbjct: 508 VLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTAPADSAVNAAIREVVEELLDNGLTARE 567

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSF+DG
Sbjct: 568 AKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRSFVDG 625



 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 59/160 (36%), Positives = 88/160 (55%), Gaps = 7/160 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDD---LEDE 86
           K++I   +++GY+T  E+N  LP +    EQME+ ++M+++MGI V +   DD   L D 
Sbjct: 18  KRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDDDTLLMDG 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG        +  +          D     T DPVRMY+REMGS+ELL+REGEI IA+RI
Sbjct: 78  EGGTVVAAQEAEEAAEEALAVVEADIG--RTSDPVRMYMREMGSVELLTREGEIEIARRI 135

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E G   ++ ++   P T   L+     +  G T L E++D
Sbjct: 136 EDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVD 175


>gi|152656|gb|AAA26473.1| sigma factor [Stigmatella aurantiaca]
          Length = 706

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 207/377 (54%), Positives = 273/377 (72%), Gaps = 25/377 (6%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           L+ K+++++  + LN+ ++D +V  L  + +R+   E EL          RD  LER  G
Sbjct: 342 LRTKMMEVLEEMRLNKKQVDRIVLNLKQLIERVDKAEEEL----------RD--LERRNG 389

Query: 377 ---RELDPHWVSYAKDFPEGEWK-----NFVACEVDSILK-IRN---EIKSISVETGISI 424
              +EL P  +  ++D P    K     NF   +++++ + +R    +IK +  E  + +
Sbjct: 390 VSMKELRPQ-LKESRDNPNTAKKLQKQLNFTPEQLEALDRDVRTAVRKIKRVEEEANLPV 448

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
              R     +R GE  A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 449 DALRRNYDAIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKA 508

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I 
Sbjct: 509 VDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEIG 568

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEEIA+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ 
Sbjct: 569 REPTPEEIAEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPADAV 628

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I  NL   T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+
Sbjct: 629 INMNLAARTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKAL 688

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRSK+LRSF++
Sbjct: 689 RKLRHPSRSKRLRSFVE 705



 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 87/155 (56%), Gaps = 1/155 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   R++G++T +E+N  LP D VSS+Q++D ++M  +  I +VD          + 
Sbjct: 107 KDLLAAGREKGFLTYDEVNDALPADIVSSDQIDDVMSMFGDNDIEIVDAQKAAQSNEIKP 166

Query: 92  SLDLAS-SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ +   S  ++        D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G 
Sbjct: 167 TVAVEEESKQDADADDDDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGE 226

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             ++ ++    +    ++   ++L  G   +R++I
Sbjct: 227 KEVLRAMLACRVAVADILDIGNKLKTGKLRVRDVI 261


>gi|90580773|ref|ZP_01236576.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90438041|gb|EAS63229.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 616

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 213/398 (53%), Positives = 271/398 (68%), Gaps = 9/398 (2%)

Query: 289 EVYRELRSLQDN-AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR   D  A+  + + + +   +V  E+L ++     L   + D LV  L D   
Sbjct: 222 EKFLELRQAYDKMALAIETNGRQNATTEVAVEELSEVFKQFRLIPKQFDRLVSSLRDSMD 281

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD-- 404
           ++  NE  ++R+   +  + +  F+    G E    W+  A +  +   +   A E D  
Sbjct: 282 KVRTNERLIMRMCVDNSKMPKKTFVSLFAGNESSQDWIDEALNSGKPYAERLKAYEEDLR 341

Query: 405 -SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            S LK+R     +  ETG+SI   + I   +  GE +A  AKKEMVEANLRLVIS+AKKY
Sbjct: 342 RSSLKLR----MLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKY 397

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 398 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 457

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+
Sbjct: 458 HMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDD 517

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +VLRMRFGI MNTDHTLE
Sbjct: 518 EDSHLGDFIEDTTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLE 577

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 578 EVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 615



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/159 (39%), Positives = 95/159 (59%), Gaps = 11/159 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLE-DE 86
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D D+L   E
Sbjct: 10  KLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADELMMTE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + +++    A++ + SSV      +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 70  DNADEDAIEAAAQALSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G   +  S+ E P     L+   D++      L +II
Sbjct: 124 EDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDII 162


>gi|53802939|ref|YP_115383.1| RNA polymerase sigma-70 factor [Methylococcus capsulatus str. Bath]
 gi|53756700|gb|AAU90991.1| RNA polymerase sigma-70 factor [Methylococcus capsulatus str. Bath]
          Length = 599

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 199/345 (57%), Positives = 253/345 (73%), Gaps = 2/345 (0%)

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           L + L D   +I   E  L  +  + G + +  F+E   G E D  W+    D P   + 
Sbjct: 254 LTDTLRDTVAKIREQERALTDICVTKGKMPKAEFIESFSGSETDEGWLDRVCD-PAKPYA 312

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             +    + I +I+ ++  I  E  + I+  + I   V  GE +A +AK+EM+EANLRLV
Sbjct: 313 AAIKAHAEEIRRIQAKLAQIEKENRLDIALIKDIHRRVSAGENQARLAKREMIEANLRLV 372

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 373 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 432

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ REPTP+E+A ++ MP + VRKV+KI KEPIS+
Sbjct: 433 RTIRIPVHMIETINKLNRISRQMLQEMGREPTPDELAARMDMPEDKVRKVMKIAKEPISM 492

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD+D SHLGDFIED   +SP++ A  A+LRETT +VLA LT RE +VLRMRFGI M
Sbjct: 493 ETPIGDDDDSHLGDFIEDSRVLSPVEHATVASLRETTQQVLAGLTAREAKVLRMRFGIDM 552

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 553 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 597



 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/158 (36%), Positives = 94/158 (59%), Gaps = 5/158 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   + +GY+T  E+N  LP D V  EQMED + M+++MGI V + D  ++E+  +D
Sbjct: 11  KELIAKGKMQGYLTFSEVNDHLPSDIVDPEQMEDIICMINDMGIEVHE-DVPDNEDLIQD 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRS----TDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +  +A S  + +  +     S+  +    T DPVRMY+REMG++ELL+REGE++IAKRIE
Sbjct: 70  TAVVAESDEDEAAEVAAALASSVDTELGRTTDPVRMYMREMGTVELLTREGELSIAKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G  +    L   P   +  +   + +++G   L ++I
Sbjct: 130 EGLNIAANELVRFPAAMEHFLKAFETVDNGELRLSDLI 167


>gi|218665974|ref|YP_002426728.1| RNA polymerase sigma factor RpoD [Acidithiobacillus ferrooxidans
           ATCC 23270]
 gi|218518187|gb|ACK78773.1| RNA polymerase sigma factor RpoD [Acidithiobacillus ferrooxidans
           ATCC 23270]
          Length = 624

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 200/358 (55%), Positives = 260/358 (72%), Gaps = 5/358 (1%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
           + LN  +ID++ + L  +++ +   E EL+ L  +     R  F+  + G E D  W+  
Sbjct: 263 IKLNGRQIDVMTDALRGLTEEVRQCERELMELCIERARFPRKEFVRSYPGHEGDIGWID- 321

Query: 387 AKDFPEGEWKNFVACEV-DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            +    G   +    E  D I+ I   + +I    G+ I+E +    ++  GE +A  AK
Sbjct: 322 -QQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKRAGLPIAEIKEASRLMSIGEAKARRAK 380

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 381 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 440

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 441 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMEMPEDKIRK 500

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPRE 624
           VLKI KEPIS+ETPIGD++ SHLGDFIED+N  +P DSA+ A +RE    +L   LT RE
Sbjct: 501 VLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTAPADSAVNAAIREVVEELLDNGLTARE 560

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSF+DG
Sbjct: 561 AKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRSFVDG 618



 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/160 (36%), Positives = 88/160 (55%), Gaps = 7/160 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDD---LEDE 86
           K++I   +++GY+T  E+N  LP +    EQME+ ++M+++MGI V +   DD   L D 
Sbjct: 11  KRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDDDTLLMDG 70

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG        +  +          D     T DPVRMY+REMGS+ELL+REGEI IA+RI
Sbjct: 71  EGGTVVAAQEAEEAAEEALAVVEADIG--RTSDPVRMYMREMGSVELLTREGEIEIARRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E G   ++ ++   P T   L+     +  G T L E++D
Sbjct: 129 EDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVD 168


>gi|284008589|emb|CBA75169.1| RNA polymerase sigma-70 factor [Arsenophonus nasoniae]
          Length = 622

 Score =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 202/364 (55%), Positives = 263/364 (72%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           E+L ++     L   + D LV  + D+ +R+   E  +++L  +   + +  F+    G 
Sbjct: 259 EQLSEIFKQFRLIPKQFDYLVNNMRDMMERVRSQERLIMKLCIEQCKMPKKNFITLFSGN 318

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E + +W++ AK   +   +  V  E + I +   +++ I  ETG++I + + I   +  G
Sbjct: 319 ETNVNWLAAAKAMNKPWSEKLVEVE-EEIQRSLQKLQQIEEETGLTIEQVKDINRRMSIG 377

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 378 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 437

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ 
Sbjct: 438 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERML 497

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 498 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHEVL 557

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 558 AGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 617

Query: 678 SFLD 681
           SFLD
Sbjct: 618 SFLD 621



 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 17  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLILAE 76

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 77  TATDTDDDAVEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 133

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+     +  G T L +II
Sbjct: 134 DGINQVQCSVAEYPEAIAYLLDQYQRVEKGETRLSDII 171


>gi|268590608|ref|ZP_06124829.1| RNA polymerase sigma factor RpoD [Providencia rettgeri DSM 1131]
 gi|291314000|gb|EFE54453.1| RNA polymerase sigma factor RpoD [Providencia rettgeri DSM 1131]
          Length = 617

 Score =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 203/374 (54%), Positives = 263/374 (70%), Gaps = 2/374 (0%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKR 367
           +S  K     E+L ++     L   + D LV  + ++  R+   E  +++L  +   + +
Sbjct: 244 RSDAKTAAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPK 303

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F+    G E    W++ AK   +   +  +  E + IL+    ++ I  ETG++I + 
Sbjct: 304 KNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVE-EEILRCLQRLRQIEEETGLTIEQV 362

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 363 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 483 SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 542

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 543 SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 603 RHPSRSEVLRSFLD 616



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLILAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|254491243|ref|ZP_05104424.1| Sigma-70, non-essential region family [Methylophaga thiooxidans
           DMS010]
 gi|224463756|gb|EEF80024.1| Sigma-70, non-essential region family [Methylophaga thiooxydans
           DMS010]
          Length = 610

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 195/316 (61%), Positives = 244/316 (77%), Gaps = 2/316 (0%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +RD F++  QG E + +W        +  + + +    D ++  ++++  IS + G+SIS
Sbjct: 293 RRD-FIDSFQGNESNVNWAD-KHIRAKKHYSSTIKKHHDEVVAAQSKLAEISEDRGLSIS 350

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + I   +   E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 351 EIKEIARQMSISEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 410

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R AR+M  ++ R
Sbjct: 411 DKFEYQRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGR 470

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTP+E+A+++ MP + VRKVLKI+KEPIS+ETPIGD++ SHLGDF+ED N +SP DSAI
Sbjct: 471 EPTPDELAERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVISPSDSAI 530

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LRE T  VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 531 IEGLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 590

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRS +LRSFLD
Sbjct: 591 KLRHPSRSDQLRSFLD 606


>gi|183597880|ref|ZP_02959373.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
 gi|188022641|gb|EDU60681.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
          Length = 617

 Score =  391 bits (1005), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 202/364 (55%), Positives = 260/364 (71%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           E+L ++     L   + D LV  + ++  R+   E  +++L  +   + +  F+    G 
Sbjct: 254 EELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPKKNFITLFSGN 313

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E    W++ AK   +   +  V  E + IL+    ++ I  ETG++I + + I   +  G
Sbjct: 314 ETSETWLTAAKAMNKPWCEKLVEVE-EEILRCLQRLRQIEEETGLTIEQVKDINRRMSIG 372

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 373 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 432

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ 
Sbjct: 433 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMM 492

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 493 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATSESLRSATHEVL 552

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 553 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 612

Query: 678 SFLD 681
           SFLD
Sbjct: 613 SFLD 616



 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLILAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TTSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDHVEAGESRLSDLI 164


>gi|190575994|ref|YP_001973839.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
           K279a]
 gi|190013916|emb|CAQ47556.1| putative RNA polymerase sigma factor RpoD [Stenotrophomonas
           maltophilia K279a]
          Length = 617

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 210/396 (53%), Positives = 269/396 (67%), Gaps = 4/396 (1%)

Query: 289 EVYRELRSLQD--NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           EV   +++L D  NA      +        L+E++  +  +L L     D+L +QL D  
Sbjct: 221 EVAARMQALSDAFNAFKKAATKGDKKNLPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTM 280

Query: 347 KRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
             I  +E  +L LA     + R  F+   +G + +  WV  A    + +W + +    D 
Sbjct: 281 ASIKAHERRVLNLATVTARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSALREVKDQ 339

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I+  +     I   T + + E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 340 IIAEQQATIDIETLTQLDLEELKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTN 399

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 400 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 459

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD++ 
Sbjct: 460 IETINKLNRISRQMLQQYGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDED 519

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED N  SP+++    NL ET   VLA LTPRE +VLRMRFGI MNTDHTLEEV
Sbjct: 520 SHLGDFIEDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEV 579

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 580 GKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 615


>gi|90020363|ref|YP_526190.1| Fis family transcriptional regulator [Saccharophagus degradans
           2-40]
 gi|89949963|gb|ABD79978.1| RNA polymerase sigma factor RpoD-like protein [Saccharophagus
           degradans 2-40]
          Length = 613

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 202/364 (55%), Positives = 257/364 (70%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E L ++     L   + D + + +  I  R+   E E++RL    G + R  F++   G+
Sbjct: 250 EALGEIFKYFKLPPRQFDPIYQGIRQILTRVRAEEREIMRLCTRLGGMPRKTFMKEFPGQ 309

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W+  A      ++ + +    + I++ + ++K I  E+G+S+   + I   +  G
Sbjct: 310 ETDEDWIP-ATIGKGRDYSDSLKPYAEDIIRAQRKLKQIQEESGLSLGHIKEINRRMSIG 368

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 369 EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ 
Sbjct: 429 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 488

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA    L E T  VL
Sbjct: 489 MPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPVDSATIQGLTEATRSVL 548

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR
Sbjct: 549 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLR 608

Query: 678 SFLD 681
            FLD
Sbjct: 609 GFLD 612



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 87/141 (61%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K++I   R++GY+T +E+N  LP D    +Q+ED + M+++MGI V     D D+L   +
Sbjct: 12  KELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAPDADELLMTD 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  DS     +A+ ++  L   +  A R+T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 72  G--DSSADEIAAAEAAAALAAVETEAGRTT-DPVRMYMREMGTVELLTREGEIAIAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  ++   P   Q  +
Sbjct: 129 EGLRELNHAIALWPEAVQQYV 149


>gi|83648911|ref|YP_437346.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
 gi|83636954|gb|ABC32921.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
          Length = 639

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 206/385 (53%), Positives = 269/385 (69%), Gaps = 4/385 (1%)

Query: 300 NAVNGQKDE--KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           N +N   D+  ++S + +   +++ ++     L Q + D ++  +   +  +   E E+L
Sbjct: 255 NTLNAAIDKHGRASREAQECFDEVSRIFAPFKLAQKQFDEIINTIRVTNDSVRKYEREIL 314

Query: 358 RL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
            +  +   + R  F++   G E +  WV       E EW      + + I +++  I SI
Sbjct: 315 NICTRDCKMPRKNFIKMFPGNETNLEWVKGLGARSE-EWAKTAQTKEEEITRLQRRIVSI 373

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             E  + +++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 374 QNEVDLPVADIKEIHRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 433

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +
Sbjct: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 493

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R M  ++ RE TPEE+AKK+ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED +
Sbjct: 494 RHMLQEMGREATPEELAKKMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSH 553

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP+DSA    L+E+T RVLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERI
Sbjct: 554 AESPIDSATTEGLKESTRRVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERI 613

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKL+HPSRS  LRSF+D
Sbjct: 614 RQIEAKALRKLRHPSRSDHLRSFID 638


>gi|197121174|ref|YP_002133125.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
 gi|196171023|gb|ACG71996.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
          Length = 805

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 210/417 (50%), Positives = 287/417 (68%), Gaps = 26/417 (6%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-------EKLVKLVGSLSLNQ 332
           V+  +D I ++ R++  +++    G+K   S VK K LK        ++++ + ++ LN+
Sbjct: 399 VLKHIDRIRKLERDVAKVRETLQGGKK--LSEVKRKELKGEIRAIEAEMMENLEAIQLNK 456

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK-RDVFLERHQGRELDPHWVSYAKDFP 391
            +ID +V +L    KR+   E E     +  G+  +D+     + RE +      AK   
Sbjct: 457 KQIDRIVLRLKSFIKRVEEAEREFFDCERRTGVPVKDLRRLLRETREDEAERKKLAKKL- 515

Query: 392 EGEWKNFVACEVDSILKIRNEIKS-------ISVETGISISEFRHIVSMVRKGECEASIA 444
                    C +D + ++   ++S       +  E  + + E R    M+  GE +A  A
Sbjct: 516 --------RCALDEVEELDRTLRSAGRKILRVQEEAEVPVEELRRTYRMIGDGERKAERA 567

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 568 KTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWI 627

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+ +P++ VR
Sbjct: 628 RQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEIAEKMELPLDKVR 687

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E T +VLA+LTPRE
Sbjct: 688 KVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQTRKVLATLTPRE 747

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+SF++
Sbjct: 748 EKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKRLKSFVE 804


>gi|86157148|ref|YP_463933.1| sigma 70 (RpoD) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773659|gb|ABC80496.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 805

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 210/417 (50%), Positives = 287/417 (68%), Gaps = 26/417 (6%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-------EKLVKLVGSLSLNQ 332
           V+  +D I ++ R++  +++    G+K   S VK K LK        ++++ + ++ LN+
Sbjct: 399 VLKHIDRIRKLERDVAKVRETLQGGKK--LSEVKRKELKGEVRAIEAEMMENLEAIQLNK 456

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK-RDVFLERHQGRELDPHWVSYAKDFP 391
            +ID +V +L    KR+   E E     +  G+  +D+     + RE +      AK   
Sbjct: 457 KQIDRIVLRLKSFIKRVEEAEREFFDCERRTGVPVKDLRRLLRETREDEAERKKLAKKL- 515

Query: 392 EGEWKNFVACEVDSILKIRNEIKS-------ISVETGISISEFRHIVSMVRKGECEASIA 444
                    C +D + ++   ++S       +  E  + + E R    M+  GE +A  A
Sbjct: 516 --------RCALDEVEELDRTLRSAGRKILRVQEEAEVPVDELRRTYRMIGDGERKAERA 567

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 568 KTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWI 627

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+ +P++ VR
Sbjct: 628 RQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEIAEKMELPLDKVR 687

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E T +VLA+LTPRE
Sbjct: 688 KVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQTRKVLATLTPRE 747

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+SF++
Sbjct: 748 EKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKRLKSFVE 804


>gi|148266058|ref|YP_001232764.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146399558|gb|ABQ28191.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter uraniireducens
           Rf4]
          Length = 586

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 180/271 (66%), Positives = 232/271 (85%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            ++K I  E+G   +E    +  + +GE +A +AK E+VEANLRLV+S+AKKYTNRGLQF
Sbjct: 316 KKLKKIEQESGFQATELSTALLAIEEGERKAKLAKSELVEANLRLVVSIAKKYTNRGLQF 375

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+
Sbjct: 376 LDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN 435

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K++RT+R++  +I REP+PEEIA+++++P++ VRKVLKI KEPISLETPIG+E+ SHLGD
Sbjct: 436 KLIRTSRQLVQEIGREPSPEEIAERMSLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGD 495

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK  VSPL++ I+ANL E T+RVL++LTPREE+VLRMRFGIG  +DHTLEEVG+ F 
Sbjct: 496 FIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFE 555

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 556 VTRERIRQIEAKALRKLRHPSRAKKLKSFVE 586



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 57/146 (39%), Positives = 87/146 (59%), Gaps = 1/146 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I L +++G++T EE+N  LPPD VSSEQ++D ++M  +M I +VD         
Sbjct: 7   DEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSEQIDDVMSMFGDMDIEIVDSAQKVKIPK 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  L+           ++    +  R T DPVRMYLREMGS+ LL+REGE+ IAKRIE 
Sbjct: 67  VKLDLEDEEELEGEQEEVEFEPGTLGR-TSDPVRMYLREMGSVSLLTREGEVEIAKRIEV 125

Query: 149 GRAMMMASLCESPLTFQALIIWRDEL 174
           G   + + +  +P+T + +I   D+L
Sbjct: 126 GERDVASVILNTPITVKEVISLGDKL 151


>gi|78221616|ref|YP_383363.1| RNA polymerase sigma factor RpoD-like [Geobacter metallireducens
           GS-15]
 gi|78192871|gb|ABB30638.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter metallireducens
           GS-15]
          Length = 579

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 201/369 (54%), Positives = 269/369 (72%), Gaps = 16/369 (4%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           ++EK   LV SL L    I  + ++L ++S ++     E+  +    GI  +   E    
Sbjct: 223 IREKFADLVKSLRLKDRHITKIAQRLKELSGKVEAILTEIAAVETEAGINGERLKE---- 278

Query: 377 RELDPHWVSYAKDFPEGEWKNFV-ACEVDSILKIR---NEIKSISVETGISISEFRHIVS 432
                  V+   +  +G   N   A ++D   KIR    ++K +  E+G    E    + 
Sbjct: 279 ------IVAKGDEKAKGLKVNLEDAQKLDK--KIRAAEKKLKKLEHESGFKAQELSDALH 330

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE +A +AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 331 AIDRGEAKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 390

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEI
Sbjct: 391 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEI 450

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+++ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E 
Sbjct: 451 AERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQ 510

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T+RVL++LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 511 TSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSR 570

Query: 673 SKKLRSFLD 681
           +KKL+SF++
Sbjct: 571 AKKLKSFVE 579



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 53/149 (35%), Positives = 88/149 (59%), Gaps = 4/149 (2%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           SD+  ++++ + +++G++T +E+N  LPPD  S+EQ++D ++M   M I++VD    +  
Sbjct: 6   SDEVKQQLVDIGKEKGFLTYDEVNDVLPPD-FSTEQIDDVMSMFGEMDIDLVDSS--QKV 62

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +  +  LDL           +   +      T DPVRMYLREMGS+ LL+REGE+ IAKR
Sbjct: 63  KIPKMKLDLEEEEEMEGEQEEMEYEPGVLGRTSDPVRMYLREMGSVSLLTREGEVEIAKR 122

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDEL 174
           IE G   +   +  +P+T + +I   D+L
Sbjct: 123 IEEGERDIARVILTTPITVKEIIALGDKL 151


>gi|312883925|ref|ZP_07743642.1| RNA polymerase sigma factor RpoD [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309368383|gb|EFP95918.1| RNA polymerase sigma factor RpoD [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 618

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 205/374 (54%), Positives = 262/374 (70%), Gaps = 6/374 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S K ++  E ++ +     L   + D LVE+L    +R+   E  +++ +  YG + +  
Sbjct: 247 SPKAQIAHELVLDVFREFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMPKKS 306

Query: 370 FLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W+    A D P  E    +    D I +   ++K+I  ET +++   
Sbjct: 307 FITLFTGNESSDAWLDEILASDKPYAEK---IRRSEDDIRRSIAKLKTIEEETSLTVQSI 363

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 364 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 423

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 424 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 483

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 484 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAG 543

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 544 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 603

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 604 RHPSRSETLRSFLD 617



 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 88/139 (63%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +D++    +A  ++  L   ++   R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DDTITDEDAAEAAAAALSSVENEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              +  ++ E P T   ++
Sbjct: 129 INQVQNAVAEYPGTIPYIL 147


>gi|220915874|ref|YP_002491178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219953728|gb|ACL64112.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 802

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 210/417 (50%), Positives = 287/417 (68%), Gaps = 26/417 (6%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-------EKLVKLVGSLSLNQ 332
           V+  +D I ++ R++  +++    G+K   S VK K LK        ++++ + ++ LN+
Sbjct: 396 VLKHIDRIRKLERDVAKVRETLQGGKK--LSEVKRKELKGEIRAIEAEMMENLEAIQLNK 453

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK-RDVFLERHQGRELDPHWVSYAKDFP 391
            +ID +V +L    KR+   E E     +  G+  +D+     + RE +      AK   
Sbjct: 454 KQIDRIVLRLKSFIKRVEEAEREFFDCERRTGVPVKDLRRLLRETREDEAERKKLAKKL- 512

Query: 392 EGEWKNFVACEVDSILKIRNEIKS-------ISVETGISISEFRHIVSMVRKGECEASIA 444
                    C +D + ++   ++S       +  E  + + E R    M+  GE +A  A
Sbjct: 513 --------RCALDEVEELDRTLRSAGRKILRVQEEAEVPVEELRRTYRMIGDGERKAERA 564

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 565 KTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWI 624

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+ +P++ VR
Sbjct: 625 RQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEIAEKMELPLDKVR 684

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E T +VLA+LTPRE
Sbjct: 685 KVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQTRKVLATLTPRE 744

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+SF++
Sbjct: 745 EKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKRLKSFVE 801


>gi|254517369|ref|ZP_05129426.1| RNA polymerase sigma factor RpoD [gamma proteobacterium NOR5-3]
 gi|219674207|gb|EED30576.1| RNA polymerase sigma factor RpoD [gamma proteobacterium NOR5-3]
          Length = 607

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 212/426 (49%), Positives = 282/426 (66%), Gaps = 15/426 (3%)

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
           N+DED++DS      +E + R            + R+    +   +   + +K+++K   
Sbjct: 193 NVDEDDNDSPAGPDPVEAKKR---------FTALKRQFNKTEKILLEKGRQDKAAIKEM- 242

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
             EKL ++           D L ++       +   E E++RLA +   + R  F+   Q
Sbjct: 243 --EKLGEIFKFFKFTPKVFDPLNDEARSALAGVREQEREIMRLAVRRCQMPRKDFITSFQ 300

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G E +  W+S  +   + ++   +    + IL+ + +I  I   TG++++E + I   + 
Sbjct: 301 GNESNAKWLS--RHTRKKDYGPKLNAYKEEILRAQRQIGQIEAATGLTVTEIKEINRRMS 358

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 359 MGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 418

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ ++
Sbjct: 419 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 478

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+   SP+D+A    L E T  
Sbjct: 479 MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTINSPIDAATGQGLMEATKD 538

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  
Sbjct: 539 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDY 598

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 599 LRSFLD 604



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 60/143 (41%), Positives = 89/143 (62%), Gaps = 11/143 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL--ED 85
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D DDL   D
Sbjct: 12  KSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDADDLILTD 71

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +GS D +  A +A+  +      +  A R+TD PVRMY+REMG++ELL+REGEI IAKR
Sbjct: 72  GDGSADDIAAAEAAAALA----AVETEAGRTTD-PVRMYMREMGTVELLTREGEIVIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALI 168
           IE G   +MA+L   P   ++++
Sbjct: 127 IEEGIRELMAALAFYPGAVKSVL 149


>gi|116748652|ref|YP_845339.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697716|gb|ABK16904.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 599

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 220/482 (45%), Positives = 313/482 (64%), Gaps = 37/482 (7%)

Query: 227 EGDIESAAKVSKDDRSKVDSPPENA------ENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           EG++E A ++   +R   ++  E++       N +  L++D    +  L  ++D++  + 
Sbjct: 127 EGEVEIAKRIEAGEREIFNAIMESSIGIKEIMNLKHKLEDDNARVSDVLREVDDEITVEE 186

Query: 281 MCALDE-IAEVYRELRSLQDNAVNGQ---------KDEKSSVKCKVL--KEKLVKLVGSL 328
             A  E +  + RE++SL ++    Q         +DE+  +K +V   KE++V L+  L
Sbjct: 187 ETAQKERVVGILREVQSLDESNKILQTRLLSDSLTRDEEFVLKSQVQQNKEQIVSLLKGL 246

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
            L++  ID ++++L+     I  +E EL         +  + L     +EL P + +  +
Sbjct: 247 QLSKRHIDSIIDKLHLCLDVIERSEDEL---------RNCLLLSGKPLQELKPLYETAIE 297

Query: 389 DFPEG---------EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  +          E K+F+    +  ++ +  I+ + +E  +     R I+  V  G  
Sbjct: 298 DRGKARACADQVNMEEKDFLEL-ANKAIEAKQRIEELEIEAKMDSRSLRLILRRVEDGLI 356

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            A +AK E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 357 RAKLAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTY 416

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+  P
Sbjct: 417 ATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEIAEKMEFP 476

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK   SP+D+ I  NL E T + LA+
Sbjct: 477 VEKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKRVASPVDAVINLNLSEQTRKALAT 536

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREE+VLRMRFGIG   DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR K+L+SF
Sbjct: 537 LTPREEKVLRMRFGIGEKADHTLEEVGQDFAVTRERIRQIEAKALRKLRHPSRRKELKSF 596

Query: 680 LD 681
           ++
Sbjct: 597 IE 598



 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/162 (35%), Positives = 89/162 (54%), Gaps = 5/162 (3%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I + +++GY+T +E+N  LP D VS E+++D + +   M I +VD +       
Sbjct: 20  DDIKRLITVGKEKGYLTYDEVNEALPEDLVSPEKLDDMMMIFDEMDIEIVDSEQQVQVVR 79

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                D  S        LQ   D   R TD PV+MYLREMG + LL+REGE+ IAKRIEA
Sbjct: 80  ETSGADSDSLLEEEEDELQIEADVTSRVTD-PVKMYLREMGQVSLLTREGEVEIAKRIEA 138

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTT----LLREIID 186
           G   +  ++ ES +  + ++  + +L D       +LRE+ D
Sbjct: 139 GEREIFNAIMESSIGIKEIMNLKHKLEDDNARVSDVLREVDD 180


>gi|119504971|ref|ZP_01627048.1| putative transcriptional regulator, Fis family protein [marine
           gamma proteobacterium HTCC2080]
 gi|119459257|gb|EAW40355.1| putative transcriptional regulator, Fis family protein [marine
           gamma proteobacterium HTCC2080]
          Length = 606

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 208/368 (56%), Positives = 259/368 (70%), Gaps = 11/368 (2%)

Query: 319 EKLVKLVGSLSLNQSRIDLLV----EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +KL +L     L     D L+    E LY I K     E  ++R+A +   + R  F++ 
Sbjct: 244 DKLGELFKFFKLTPRVFDPLIDEPRESLYIIRK----QERAIMRIAVRECRMDRKEFIKS 299

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
             G E D  W+S      + +    +A   D I +++  I  +   TG+S++E + I   
Sbjct: 300 FSGSESDSRWISRVAR--KKDIGARLALHKDDIQRMQRRISEVEQATGLSVAEIKEINRR 357

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 358 MSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 417

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ 
Sbjct: 418 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 477

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA +  L E T
Sbjct: 478 ERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTISSPVDSATEEGLTEAT 537

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VLA LT RE +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS
Sbjct: 538 QDVLAGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 597

Query: 674 KKLRSFLD 681
             LRSFLD
Sbjct: 598 DYLRSFLD 605



 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 57/134 (42%), Positives = 84/134 (62%), Gaps = 7/134 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D+L   E
Sbjct: 12  KALIAKGKEQGYLTYAEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELILTE 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  D      +A+ ++  L   ++ A R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 72  G--DRSADEIAAAEAAAALAAVENEAGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 128

Query: 148 AGRAMMMASLCESP 161
            G   +MA++   P
Sbjct: 129 EGIRELMAAMAHYP 142


>gi|1938356|gb|AAC45155.1| RpoD [Xanthomonas campestris pv. campestris]
          Length = 622

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 205/356 (57%), Positives = 259/356 (72%), Gaps = 6/356 (1%)

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYA 387
           +LN    D LV QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A
Sbjct: 268 TLNVPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDA 327

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAK 445
               + +W + +    D I  +  +  SI +E    ++++E + I   +  GE +A  AK
Sbjct: 328 LKRKQ-KWSSALRDVKDQI--VSEQQGSIEMEKANYLTLAEIKDISRAMAYGEAKARKAK 384

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 385 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 444

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  REPTPEE+AK++ MP + +RK
Sbjct: 445 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREPTPEELAKEMDMPEDKIRK 504

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE 
Sbjct: 505 VMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREA 564

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 565 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 620



 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 87/142 (61%), Gaps = 4/142 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+ ++       D+    T DPVRMY+REMG++ELL+RE EIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEAAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREAEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALII 169
            G + + A+L   PL  +A  +
Sbjct: 133 EGLSQVQAALGTFPLVDRAAAV 154


>gi|254784701|ref|YP_003072129.1| RNA polymerase sigma factor RpoD [Teredinibacter turnerae T7901]
 gi|237686864|gb|ACR14128.1| RNA polymerase sigma factor RpoD [Teredinibacter turnerae T7901]
          Length = 619

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 212/413 (51%), Positives = 277/413 (67%), Gaps = 27/413 (6%)

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           D+LR +++ A D IA+             +G   +++ V  + L E    +     L   
Sbjct: 228 DELRVQLVAANDAIAK-------------HGLDSKETGVALEALGE----VFKFFKLAPR 270

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS----YAK 388
           + D +   + D+  RI   E E++RL  +  G+ R  F++   G E++  W+       +
Sbjct: 271 QFDPIYNYVRDVLARIRAEEKEIMRLCVRMAGMPRKTFVKEFPGNEINEDWIPEIIRKKR 330

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           D+ +    +    E D IL+ + +++ I  ETG+ ++  + I   +  GE  A  AKKEM
Sbjct: 331 DYSD----SLRPVEGD-ILRSQRKLQQIEEETGLELTAIKEINRRMSIGEARARRAKKEM 385

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 386 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 445

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VRKVLK
Sbjct: 446 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKVRKVLK 505

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED    SP++SA    L E T  VLA LT RE +VL
Sbjct: 506 IAKEPISMETPIGDDEDSHLGDFIEDTTITSPVESATSQGLMEATKAVLAGLTAREAKVL 565

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR FLD
Sbjct: 566 RMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFLD 618


>gi|261250212|ref|ZP_05942788.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
 gi|260939328|gb|EEX95314.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
          Length = 618

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 206/374 (55%), Positives = 260/374 (69%), Gaps = 6/374 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S K  +  E ++ +     L   + D LVE+L    +R+   E  +++    YG + +  
Sbjct: 247 SPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKATVEYGKMPKKS 306

Query: 370 FLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W+    A D P  E    V    D I +  +++K I  ET +++   
Sbjct: 307 FITLFTGNESTDAWLDEILASDKPYAEK---VRRSEDDIRRSISKLKIIEEETSLTVQNI 363

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 364 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 423

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 424 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 483

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 484 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAG 543

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 544 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 603

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 604 RHPSRSETLRSFLD 617



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 88/139 (63%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +D++    +A  ++  L   ++   R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DDTITDEDAAEAAAAALSSVENEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              +  ++ E P T   ++
Sbjct: 129 INQVQNAVAEYPGTIPYIL 147


>gi|295700891|ref|YP_003608784.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295440104|gb|ADG19273.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 665

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 244/662 (36%), Positives = 367/662 (55%), Gaps = 63/662 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           + +I+L +++GY+T  ++N  LP +  ++  ++  V+  S+MG+ V +     D E    
Sbjct: 54  RALIQLGKEQGYLTHAQINDHLPDNFTATAAIDSIVSAFSDMGVQVYE--QAPDAETLLL 111

Query: 89  --------SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                   S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEI
Sbjct: 112 NSNSPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEI 165

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           AIAKRIE G   M+ ++   PL   A++    ++ DG   + E++D     G   + G  
Sbjct: 166 AIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVD-----GLNEETG-- 218

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                 + ++ E +  + E D V         A + S D+    D P +++  DE  L  
Sbjct: 219 ------AAEEVESADADAEEDGV---------ADEDSDDEEEDDDGPADSSAADEARL-- 261

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                         QL    +    ++  +Y E+     NA + + D  S    +  +E+
Sbjct: 262 -------------KQLTSDCLEIFAQVGILYDEM-----NAAHTRGDVTSKGYLRA-REE 302

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGREL 379
           + + +  +      ID L   +     ++   E  +L++  S  G+ R+ F+E   G E 
Sbjct: 303 IQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVSKAGMPREKFIETFAGNEA 362

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W   A       +   +   + +I   + ++  I     + +   + I   +   E 
Sbjct: 363 DLGWTERAARTGASTYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRKMVAAES 422

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTY
Sbjct: 423 KMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTY 482

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +A+++ + 
Sbjct: 483 ATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAERMELS 542

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR +LKI K+P+SLETP+GD+  + LGD IED    SP D+A+QA+LR      L S
Sbjct: 543 EEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVSSPADAAMQADLRAAIDDALDS 602

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ +L+SF
Sbjct: 603 LSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLKSF 662

Query: 680 LD 681
           LD
Sbjct: 663 LD 664


>gi|294666254|ref|ZP_06731505.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292603963|gb|EFF47363.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 625

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 215/405 (53%), Positives = 277/405 (68%), Gaps = 12/405 (2%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 228 VATRMENLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 281

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 282 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 340

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +    D I  I  +  SI +E    +++ E + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 341 LRDVKDQI--ISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLV 398

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 399 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 458

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+
Sbjct: 459 RTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISM 518

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI M
Sbjct: 519 ETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDM 578

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 579 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|294625247|ref|ZP_06703887.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292600475|gb|EFF44572.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 621

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 215/405 (53%), Positives = 277/405 (68%), Gaps = 12/405 (2%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 224 VATRMENLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 277

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 278 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 336

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +    D I  I  +  SI +E    +++ E + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 337 LRDVKDQI--ISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLV 394

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 395 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 454

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+
Sbjct: 455 RTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISM 514

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI M
Sbjct: 515 ETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDM 574

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 575 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 619



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|21244512|ref|NP_644094.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|32130007|sp|Q8PG33|RPOD_XANAC RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|21110182|gb|AAM38630.1| RNA polymerase sigma-70 factor [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 625

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 215/405 (53%), Positives = 277/405 (68%), Gaps = 12/405 (2%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 228 VATRMENLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 281

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 282 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 340

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +    D I  I  +  SI +E    +++ E + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 341 LRDVKDQI--ISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLV 398

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 399 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 458

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+
Sbjct: 459 RTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISM 518

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI M
Sbjct: 519 ETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDM 578

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 579 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|89075585|ref|ZP_01161990.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048725|gb|EAR54297.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 616

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 207/395 (52%), Positives = 270/395 (68%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDN-AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR+  D  A+    + + +   ++  E+L ++     L   + D LV  L D   
Sbjct: 222 EKFLELRNAYDKMALAIDTNGRQNATTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDSMD 281

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           ++  NE  ++R+   +  + +  F+    G E    W+  A +  +   +     E D +
Sbjct: 282 KVRTNERLIMRMCVDNSKMPKKTFVSLFAGNESKQDWIDEALNSGKPYAERLKVYEED-L 340

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +   +++ +  ETG+SI   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 341 RRASIKLRMLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 400

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 401 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 460

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ S
Sbjct: 461 ETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDS 520

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED     P+D+A   NLR  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVG
Sbjct: 521 HLGDFIEDTTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVG 580

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 581 KQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 615



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/159 (39%), Positives = 95/159 (59%), Gaps = 11/159 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLE-DE 86
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D D+L   E
Sbjct: 10  KLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADELMMTE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + +++    A++ + SSV      +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 70  DNADEDAIEAAAQALSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G   +  S+ E P     L+   D++      L +II
Sbjct: 124 EDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDII 162


>gi|226946707|ref|YP_002801780.1| RNA polymerase sigma factor RpoD [Azotobacter vinelandii DJ]
 gi|226721634|gb|ACO80805.1| RNA polymerase sigma factor, sigma70; RpoD [Azotobacter vinelandii
           DJ]
          Length = 620

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 261/365 (71%), Gaps = 4/365 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  L   + L   + D LVEQ+ D   R+   E  +++L  +   + R  FL +  G 
Sbjct: 257 QALASLFMPIKLVPKQYDTLVEQVRDALTRVRAQERAIMQLCVRDARMPRADFLRQFPGN 316

Query: 378 ELDPHWVSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E D  WV   AK   + ++   +    D I + + ++  +  + G++I+E + I   +  
Sbjct: 317 ETDQDWVDLLAKG--KAKYAEALGNLADDIKQCQQKLIDLEQKVGLTIAEIKDINRQMSI 374

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 375 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 434

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 435 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 494

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E T  V
Sbjct: 495 DMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVATVESLKEATREV 554

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 555 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHL 614

Query: 677 RSFLD 681
           RSFLD
Sbjct: 615 RSFLD 619


>gi|289207448|ref|YP_003459514.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           K90mix]
 gi|288943079|gb|ADC70778.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           K90mix]
          Length = 629

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 205/401 (51%), Positives = 276/401 (68%), Gaps = 7/401 (1%)

Query: 285 DEIAEVYRELRSLQDNAVNG--QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           +E  E + +LR L   A     + D K+    +   E   K      L    +D L  +L
Sbjct: 232 EEARERFNKLRKLHAKAHKAFEKGDRKAYATAR---EATAKYFMEFKLVPRMVDQLTTKL 288

Query: 343 YDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           +    RI  +E  ++ LA +   + R  F++     E +  W+  A    +G++   +A 
Sbjct: 289 HGTIDRIRSHERRIMELAVNQAQMPRKSFIDSFPKNETNLDWIKQACK-AKGKYTTALAE 347

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             D I++++ ++  I  E  ++ISE + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 348 HEDEIVRLQKKLAEIEHEASLNISEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAK 407

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 408 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 467

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + +RKVLKI+KEPIS+ETPIG
Sbjct: 468 PVHMIETINKLNRVSRQMLQEMGREATPEELAERMEMPEDKIRKVLKISKEPISMETPIG 527

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED+   SP DSA + +L E T  +L++LTPRE +VLRMRFGI MNTDHT
Sbjct: 528 DDEDSHLGDFIEDEKVASPSDSAARESLSEATREILSTLTPREAKVLRMRFGIDMNTDHT 587

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVGKQF VTRERIRQIEAKA+RKL+HP+R++ LR++ D 
Sbjct: 588 LEEVGKQFDVTRERIRQIEAKALRKLRHPTRAELLRTYTDA 628


>gi|323493625|ref|ZP_08098746.1| RNA polymerase sigma factor RpoD [Vibrio brasiliensis LMG 20546]
 gi|323312148|gb|EGA65291.1| RNA polymerase sigma factor RpoD [Vibrio brasiliensis LMG 20546]
          Length = 617

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 205/374 (54%), Positives = 261/374 (69%), Gaps = 6/374 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S K ++  E ++ +     L   + D LVE+L    +R+   E  +++ +  YG + +  
Sbjct: 246 SPKAQIAHELVLDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMPKKS 305

Query: 370 FLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W+    A D P  E    +    D I +   ++K I  ET +++   
Sbjct: 306 FITLFTGNESSDAWLDEILASDKPYAEK---IRRSEDDIRRSIAKLKVIEEETSLTVQNI 362

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 363 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 483 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAT 542

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 543 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 603 RHPSRSETLRSFLD 616



 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 88/139 (63%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +D++    +A  ++  L   ++   R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DDTITDEDAAEAAAAALSSVENEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              +  ++ E P T   ++
Sbjct: 129 INQVQNAVAEYPGTIPYIL 147


>gi|319788464|ref|YP_004147939.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466976|gb|ADV28708.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 618

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 207/376 (55%), Positives = 263/376 (69%), Gaps = 7/376 (1%)

Query: 308 EKSSVKCKV-LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-I 365
           +K  +K +  + E+ V     L L     D+LV +L D+   I   E  +L LA +   +
Sbjct: 246 DKKVIKLRAEMAEQFVTFKLPLPLT----DVLVRKLRDVLTEIKDRERRVLHLATNVARM 301

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  F+   +G +++  WV       + +W + +    D I+  +    +I     + +S
Sbjct: 302 PRKDFIRAWEGNQVNLEWVDEVLKRKQ-KWSSALRDVKDQIIAEQQATIAIEQAMCLDLS 360

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + R I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 361 DIREIGRQLAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 420

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  R
Sbjct: 421 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGR 480

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           E TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+DS  
Sbjct: 481 EATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDSTT 540

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             NL ET   VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 541 NTNLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRS++LRSFLD
Sbjct: 601 KLRHPSRSEQLRSFLD 616



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 87/141 (61%), Gaps = 4/141 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K++I    ++GY+T  E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +
Sbjct: 12  KQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDVETLLLND 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       DS    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 72  GNTGNREIDDTAAEEAAAALTALDSEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 131

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   + A+L   P + +AL+
Sbjct: 132 EGLGQVQAALGSVPASVEALL 152


>gi|325924346|ref|ZP_08185890.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas gardneri ATCC
           19865]
 gi|325545211|gb|EGD16521.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas gardneri ATCC
           19865]
          Length = 625

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 214/405 (52%), Positives = 277/405 (68%), Gaps = 12/405 (2%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 228 VATRMENLANEYAKFKKIY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 281

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 282 TQLRGVVNGIKDHERKVLHLATAVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 340

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +    D I  +  +  SI +E    +++ E + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 341 LRDVKDQI--VSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLV 398

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 399 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 458

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+
Sbjct: 459 RTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISM 518

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI M
Sbjct: 519 ETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDM 578

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 579 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623


>gi|254522302|ref|ZP_05134357.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
 gi|219719893|gb|EED38418.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
          Length = 617

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 204/366 (55%), Positives = 259/366 (70%), Gaps = 2/366 (0%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQ 375
           L+E++  +  +L L     D+L +QL D    I  +E  +L LA     + R  F+   +
Sbjct: 251 LREEMSAVFVTLKLPLPLTDVLTKQLRDTMADIKSHERRVLNLATVTARMPRKDFIRSWE 310

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G + +  WV  A    + +W + +    D I+  +     I   T + + E + I   + 
Sbjct: 311 GNQTNLEWVEDALKRKQ-KWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRAMA 369

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 370 YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK+
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKE 489

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+++    NL ET   
Sbjct: 490 MDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRD 549

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++
Sbjct: 550 VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQ 609

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 610 LRSFLD 615


>gi|261344812|ref|ZP_05972456.1| RNA polymerase sigma factor RpoD [Providencia rustigianii DSM 4541]
 gi|282567259|gb|EFB72794.1| RNA polymerase sigma factor RpoD [Providencia rustigianii DSM 4541]
          Length = 616

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 202/374 (54%), Positives = 262/374 (70%), Gaps = 2/374 (0%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKR 367
           +S  K      +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +
Sbjct: 243 RSDAKTVAAINQLSDVFKEFRLVPKQFDYLVNNMREMMERVRQQERTIMKLCVEQCKMPK 302

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F+    G E    W++ AK   +   +  +  E D +L+    ++ I  ETG++I + 
Sbjct: 303 KNFITLFGGNETSETWLTAAKAMNKPWSEKLLDVEED-VLRCLQRLRQIEEETGLTIEQV 361

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 362 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 481

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 482 SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 541

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 542 SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 602 RHPSRSEVLRSFLD 615



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLILAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|289667862|ref|ZP_06488937.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 624

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 211/403 (52%), Positives = 275/403 (68%), Gaps = 8/403 (1%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 227 VATRMENLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 280

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 281 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 339

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D I+  +     +   + +++ E + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 340 LRDVKDQIISEQQGSMEMEKSSYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS 399

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 400 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 459

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ET
Sbjct: 460 IRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMET 519

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNT
Sbjct: 520 PIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNT 579

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 580 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|289664793|ref|ZP_06486374.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 624

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 211/403 (52%), Positives = 275/403 (68%), Gaps = 8/403 (1%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 227 VATRMENLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 280

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 281 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 339

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D I+  +     +   + +++ E + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 340 LRDVKDQIISEQQGSMEMEKSSYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS 399

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 400 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 459

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ET
Sbjct: 460 IRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMET 519

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNT
Sbjct: 520 PIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNT 579

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 580 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|166713725|ref|ZP_02244932.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 624

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 211/403 (52%), Positives = 275/403 (68%), Gaps = 8/403 (1%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 227 VATRMENLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 280

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 281 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 339

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D I+  +     +   + +++ E + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 340 LRDVKDQIISEQQGSMEMEKASYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS 399

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 400 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 459

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ET
Sbjct: 460 IRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMET 519

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNT
Sbjct: 520 PIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNT 579

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 580 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|108763751|ref|YP_633357.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|133312|sp|P17531|RPOD_MYXXA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-80
 gi|150118|gb|AAA25404.1| sigma factor (rpoD) [Myxococcus xanthus]
 gi|710343|gb|AAB60208.1| major sigma factor [Myxococcus xanthus]
 gi|108467631|gb|ABF92816.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|1586812|prf||2204381D sigma factor
          Length = 708

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 201/370 (54%), Positives = 267/370 (72%), Gaps = 3/370 (0%)

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK-RDVFLE 372
            K L+ K+++++  + LN+ ++D +V  L  + +R+   E EL  L + Y    +++  +
Sbjct: 341 IKDLRTKMMEVLEEMRLNKKQVDRIVINLKALIERVDKAEDELRDLERRYDCSMKELRPQ 400

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
             + RE +P+     +       +     + D    +R  IK +  E  + +   R    
Sbjct: 401 LKESRE-NPNIGKKLQKQLNLTPEQLEVLDRDVRTAVRK-IKKVEEEANLPVESLRRNYD 458

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +R GE  A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 459 AIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKR 518

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I REPTPEEI
Sbjct: 519 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEIGREPTPEEI 578

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E 
Sbjct: 579 AEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPADAVINMNLAEQ 638

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 639 TRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSR 698

Query: 673 SKKLRSFLDG 682
           SK+LRSF++ 
Sbjct: 699 SKRLRSFVES 708


>gi|315634867|ref|ZP_07890149.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           segnis ATCC 33393]
 gi|315476419|gb|EFU67169.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           segnis ATCC 33393]
          Length = 621

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 207/389 (53%), Positives = 267/389 (68%), Gaps = 8/389 (2%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
           ++L+  A +G+  +K+  + + L +    +     L   + D LV    D+ KR+ H E 
Sbjct: 238 KTLEIIAKHGRTGKKAKDEIQALSD----IFTQFRLVPKQFDTLVLSTRDMMKRVRHQER 293

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNE 412
            + RL   +  + +  F +   G E    W+   K    G+ W   +A   D + +    
Sbjct: 294 LIQRLVVDNAKMPKSSFQKSFIGHETSDVWL--VKALAAGKSWSEKLAQYEDELRQAIAH 351

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I  +T ++I + R I   + +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 352 LVQIEQDTNLTIGQIREIGERISQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 411

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 412 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 471

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R +R+M  ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFI
Sbjct: 472 NRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFI 531

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED     PLDSA   +L+  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VT
Sbjct: 532 EDSTLELPLDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 591

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 592 RERIRQIEAKALRKLRHPSRSETLRSFLD 620


>gi|254509368|ref|ZP_05121455.1| RNA polymerase sigma factor [Vibrio parahaemolyticus 16]
 gi|219547710|gb|EED24748.1| RNA polymerase sigma factor [Vibrio parahaemolyticus 16]
          Length = 620

 Score =  389 bits (999), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 204/374 (54%), Positives = 261/374 (69%), Gaps = 6/374 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S K  V  E ++ +     L   + D LV++L    +R+   E  +++ +  YG + +  
Sbjct: 249 SPKATVAHEMVIDVFKEFRLTPKQFDYLVDELRTSMERVRTQERLIMKASVEYGKMPKKS 308

Query: 370 FLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W+    A D P   + + +    D I +   ++K I  ET +++   
Sbjct: 309 FIALFSGNESSDAWLDEILASDKP---YADKIRRSEDDIRRSIAKLKIIEEETSLTVQNI 365

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 366 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 425

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 426 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 485

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 486 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAG 545

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 546 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 605

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 606 RHPSRSETLRSFLD 619



 Score = 90.5 bits (223), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 88/139 (63%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++++    +A  ++  L   ++   R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DETITDEDAAEAAAAALSSVENEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              +  ++ E P T   ++
Sbjct: 129 INQVQNAVAEYPGTIPYIL 147


>gi|188993312|ref|YP_001905322.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           campestris str. B100]
 gi|167735072|emb|CAP53284.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           campestris]
          Length = 624

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 214/405 (52%), Positives = 277/405 (68%), Gaps = 12/405 (2%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 227 VATRMENLANEYAKFKKIY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 280

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 281 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 339

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +    D I  +  +  SI +E    +++ E + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 340 LRDVKDQI--VSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLV 397

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 398 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 457

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+
Sbjct: 458 RTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISM 517

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI M
Sbjct: 518 ETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDM 577

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 578 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTELLLADYEAHKEGKKRLAEIV 170


>gi|78049468|ref|YP_365643.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325926137|ref|ZP_08187498.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas perforans
           91-118]
 gi|78037898|emb|CAJ25643.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325543482|gb|EGD14904.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas perforans
           91-118]
          Length = 625

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 206/367 (56%), Positives = 261/367 (71%), Gaps = 6/367 (1%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQG 376
           +E +  +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G
Sbjct: 260 REDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEG 319

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMV 434
            + +  WV  A    + +W + +    D I  I  +  SI +E    +++ E + I   +
Sbjct: 320 NQTNLEWVEDALKRKQ-KWSSALRDVKDQI--ISEQQGSIEMEKANYLTLGEIKEISRAM 376

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 377 AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 436

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK
Sbjct: 437 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 496

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET  
Sbjct: 497 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVR 556

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 557 DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 616

Query: 675 KLRSFLD 681
           +LRSFLD
Sbjct: 617 QLRSFLD 623



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|194367344|ref|YP_002029954.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
           R551-3]
 gi|194350148|gb|ACF53271.1| RNA polymerase, sigma 70 subunit, RpoD [Stenotrophomonas
           maltophilia R551-3]
          Length = 618

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 213/400 (53%), Positives = 275/400 (68%), Gaps = 12/400 (3%)

Query: 289 EVYRELRSLQDNAVNGQK------DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           EV   +++L D A N  K      D+KS +K   L+E++  +  +L L     D+L +QL
Sbjct: 222 EVAARMQALSD-AFNAFKKAVAKGDKKSLLK---LREEMSAVFVTLKLPLPLTDVLTKQL 277

Query: 343 YDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D    I  +E  +L LA     + R  F+   +G + +  WV  A    + +W + +  
Sbjct: 278 RDTMAGIKSHERRVLNLATVTARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSALRE 336

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             D I+  +     I   T + + + + +   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 337 VKDQIIAEQQATIDIEKLTQLDLDDLKELSRAMAYGEAKARKAKKEMVEANLRLVISIAK 396

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 397 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 456

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIG
Sbjct: 457 PVHMIETINKLNRISRQMLQQYGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIG 516

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED N  SP+++    NL ET   VLA LTPRE +VLRMRFGI MNTDHT
Sbjct: 517 DDEDSHLGDFIEDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHT 576

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 577 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|84622216|ref|YP_449588.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188574947|ref|YP_001911876.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|84366156|dbj|BAE67314.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188519399|gb|ACD57344.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 624

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 211/403 (52%), Positives = 274/403 (67%), Gaps = 8/403 (1%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   +  +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 227 VATRMQNLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 280

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 281 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 339

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D I+  +     +   + +++ E + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 340 LRDVKDQIISEQQGSMEMEKASYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS 399

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 400 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 459

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ET
Sbjct: 460 IRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMET 519

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNT
Sbjct: 520 PIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNT 579

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 580 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|325913856|ref|ZP_08176215.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325539931|gb|EGD11568.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 624

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 214/405 (52%), Positives = 277/405 (68%), Gaps = 12/405 (2%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 227 VATRMENLANEYAKFKKIY--AKNG-AEHKLVVKAR---EDIAAIFTTLKLPLPLTDALV 280

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 281 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 339

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +    D I  +  +  SI +E    +++ E + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 340 LRDVKDQI--VSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLV 397

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 398 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 457

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+
Sbjct: 458 RTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISM 517

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI M
Sbjct: 518 ETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDM 577

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 578 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 170


>gi|285019606|ref|YP_003377317.1| RNA polymerase sigma-70 factor, rpod protein [Xanthomonas
           albilineans GPE PC73]
 gi|283474824|emb|CBA17323.1| probable rna polymerase sigma-70 factor, rpod protein [Xanthomonas
           albilineans]
          Length = 620

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 202/366 (55%), Positives = 260/366 (71%), Gaps = 2/366 (0%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQ 375
           L+  + ++  +L L     D LV +L D   ++  +E  +L LA     + R  F+   +
Sbjct: 254 LRNDIAEVFVTLKLPLPLTDALVRKLRDAMAQVKEHERRVLHLATHVARMPRKDFIRSWE 313

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G + +  WV  A    + +W + +    D I+  +     +   T +S++E + I   + 
Sbjct: 314 GNQTNVVWVDDALKRKQ-KWSSALRDVKDQIIAEQEATVGVEQSTYLSLTELKEISRAMA 372

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 373 YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 432

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK+
Sbjct: 433 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKE 492

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+++    NL ET   
Sbjct: 493 MDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRD 552

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++
Sbjct: 553 VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQ 612

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 613 LRSFLD 618


>gi|21233164|ref|NP_639081.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770104|ref|YP_244866.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|32130006|sp|Q8P4H2|RPOD_XANCP RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|21115012|gb|AAM42993.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575436|gb|AAY50846.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           campestris str. 8004]
          Length = 624

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 205/367 (55%), Positives = 262/367 (71%), Gaps = 6/367 (1%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQG 376
           +E +  +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G
Sbjct: 259 REDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEG 318

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMV 434
            + +  WV  A    + +W + +    D I  +  +  SI +E    ++++E + I   +
Sbjct: 319 NQTNLEWVEDALKRKQ-KWSSALRDVKDQI--VSEQQGSIEMEKANYLTLAEIKDISRAM 375

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 376 AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 435

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK
Sbjct: 436 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 495

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET  
Sbjct: 496 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVR 555

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 556 DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 615

Query: 675 KLRSFLD 681
           +LRSFLD
Sbjct: 616 QLRSFLD 622



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 13  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 72

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 73  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 133 EGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIV 170


>gi|58580221|ref|YP_199237.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58424815|gb|AAW73852.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 629

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 211/403 (52%), Positives = 274/403 (67%), Gaps = 8/403 (1%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   +  +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 232 VATRMQNLANEYAKFKKVY--AKNG-AEHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 285

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 286 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 344

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D I+  +     +   + +++ E + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 345 LRDVKDQIISEQQGSMEMEKASYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS 404

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 405 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 464

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ET
Sbjct: 465 IRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMET 524

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNT
Sbjct: 525 PIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNT 584

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 585 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 627



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 95/158 (60%), Gaps = 4/158 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEE 87
           K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +
Sbjct: 18  KLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLND 77

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 78  GNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIE 137

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 138 EGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 175


>gi|78060207|ref|YP_366782.1| sigma 70 (RpoD) [Burkholderia sp. 383]
 gi|77964757|gb|ABB06138.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. 383]
          Length = 677

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 251/660 (38%), Positives = 362/660 (54%), Gaps = 61/660 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I L R+RGY+T  ++N  LP +   +  M+  V+  S+MG+ V     D + L   E
Sbjct: 68  RALIALGRERGYLTHADINDHLPDNFAQTAAMDTIVSTFSDMGVAVYEQAPDAEALLLTE 127

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  + A+ S+V      DS    T DPVRMY+REMG+ ELL+R GEI +
Sbjct: 128 AAPAVASDDQADEEAEAALSTV------DSEFGRTTDPVRMYMREMGASELLTRAGEIEV 181

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P     ++   D +  G   + E++D                
Sbjct: 182 AKRIEDGLQDMIQAIAACPSIVSTILADVDRIVAGELRIDELVD---------------- 225

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
             G S     D+ + +   + QE E ++ +A   S +D  + D+      N  R L+E  
Sbjct: 226 --GISV----DTDESEMTPESQEEEAEVLAADDDSDEDDVETDAGDSEKVNAAR-LEELT 278

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           +DS                  L   A V      L D  V G   E  S     ++  + 
Sbjct: 279 NDS------------------LVIFARVRALFEQLPDVPVTG---EARSAAAAQVRAAIQ 317

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
           + +  +      ID L E ++     +   E  +L +A    G+ RD F+E   G E D 
Sbjct: 318 RELAPIRFTAKTIDRLCEIVHGQVTEVRAIERSVLAIAVDRCGMPRDAFVESFPGHETDL 377

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W S      + ++   +     +I   + ++  I     + + + + I   +   E + 
Sbjct: 378 DWTSRTAATSQ-QFGAALERHQPAIQAAQQKLVDIESRVSLPLQQLKQINRQMSAAELKM 436

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+EM+EANLRLVIS+AKKY NRG+QFLDLIQEGNIGLMKA +KF++  G+KFSTYA 
Sbjct: 437 RQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYAT 496

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WWV+QA+TR++ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +AK++ M  E
Sbjct: 497 WWVRQAVTRALADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAKRMEMSEE 556

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR +LKI K+P+SLETP+GD+  + LGD IED +A SP ++AI AN+R      L  L+
Sbjct: 557 KVRSILKIAKQPVSLETPVGDDADATLGDMIEDVSASSPAEAAIHANMRAAIDEALNGLS 616

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFG+  N+DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ KLR FL+
Sbjct: 617 PREAKVLRMRFGLDTNSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADKLRPFLE 676


>gi|170719016|ref|YP_001784175.1| RNA polymerase sigma factor RpoD [Haemophilus somnus 2336]
 gi|168827145|gb|ACA32516.1| RNA polymerase, sigma 70 subunit, RpoD [Haemophilus somnus 2336]
          Length = 621

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 201/364 (55%), Positives = 253/364 (69%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           + L  +     L   + D LV  + D+ K +  +E ++ +L      + ++ F +   G 
Sbjct: 258 QALADIFTQFRLVPKQFDALVNYMRDMMKSVRQHERQIQKLVVDLAKMPKENFQKLFIGN 317

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E    W+          W   +     ++ +  N++  I  ET ++IS+ R I   V +G
Sbjct: 318 ESSEGWLDKLL-LARKPWSERLIQHESAVRQSINQLLKIEQETNLTISQIREICDKVAQG 376

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 377 ELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 436

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  K+ RE T EE+A+++ 
Sbjct: 437 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQKMGREATSEELAERMG 496

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 497 MPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLRAATHEVL 556

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 557 EGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLR 616

Query: 678 SFLD 681
           SFLD
Sbjct: 617 SFLD 620



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 92/164 (56%), Gaps = 21/164 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---- 83
           K +I   +++GY+T  E+N  LP D V ++Q+ED + M+++MGI V+    D DDL    
Sbjct: 10  KLLIARGKEQGYLTYAEVNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDADDLMLNE 69

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              DE+  E++  + SS            ++    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 70  NITDEDAVEEATQVLSSV-----------EAELGRTTDPVRMYMREMGSVELLTREGEID 118

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IAKRIE G   + +++   P     L+     + +G   L ++I
Sbjct: 119 IAKRIEEGINEVQSAVAAYPKALNYLLEQYTLVEEGGMRLADLI 162


>gi|145630289|ref|ZP_01786070.1| aspartate ammonia-lyase [Haemophilus influenzae R3021]
 gi|260582763|ref|ZP_05850550.1| aspartate ammonia-lyase [Haemophilus influenzae NT127]
 gi|144984024|gb|EDJ91461.1| aspartate ammonia-lyase [Haemophilus influenzae R3021]
 gi|260094213|gb|EEW78114.1| aspartate ammonia-lyase [Haemophilus influenzae NT127]
          Length = 629

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN-MGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L N  GI V+D     D+    
Sbjct: 17  EQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLS 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 77  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEGGI 135

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+   P     L+   D++  G   L ++I
Sbjct: 136 DEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI 170


>gi|304312382|ref|YP_003811980.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) [gamma
           proteobacterium HdN1]
 gi|301798115|emb|CBL46337.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) [gamma
           proteobacterium HdN1]
          Length = 627

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 207/386 (53%), Positives = 267/386 (69%), Gaps = 4/386 (1%)

Query: 300 NAVNGQKDEKS--SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           NA    ++EK   S      +E+L     +  L     + LV  + +  +R+  NE  ++
Sbjct: 239 NAAKTTREEKGRKSKPFTNAQEELANQFITFKLVPRLFEQLVGGVRETLERVRENERAIM 298

Query: 358 -RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
            R  +   + R  F+++  G E +  WV       +  +   V    D I+K++  +  +
Sbjct: 299 TRCIRIAKMPRKDFVKQFPGNETNIEWVDKIAG-GKTAYAERVGALKDDIIKLQQNLLGL 357

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                +SI+E + I   +  GE +A+ AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 358 ESTLSLSIAEIKEINRRISIGEAKAARAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +
Sbjct: 418 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVS 477

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M  ++ REPTPEE+ +++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED  
Sbjct: 478 RQMLQEMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 537

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP+D+A   +LRE T  VLASLT RE +VL MRFGI MNTDHTLEEVGKQF VTRERI
Sbjct: 538 MQSPVDAATAESLREATRDVLASLTAREAKVLAMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RQIEAKA+RKL+HPSRS+ LRSFLDG
Sbjct: 598 RQIEAKALRKLRHPSRSEHLRSFLDG 623



 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 56/135 (41%), Positives = 82/135 (60%), Gaps = 10/135 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +++G++T  ++N  LPPD    EQ+ED +AM+++MGI V      E   G+E 
Sbjct: 12  KQLIARGKEQGFLTFADVNDHLPPDITDPEQVEDIIAMINDMGIPV-----HEAAPGAEG 66

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            L   ++ SN     ++       D+    T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 67  LLRGGANPSNEDASDEESPANAVIDAEPGRTTDPVRMYMREMGSVELLTREGEIVIAKRI 126

Query: 147 EAGRAMMMASLCESP 161
           E G   +M++L   P
Sbjct: 127 EEGIREVMSALAFWP 141


>gi|260775520|ref|ZP_05884417.1| RNA polymerase sigma factor RpoD [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608701|gb|EEX34866.1| RNA polymerase sigma factor RpoD [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 617

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 204/374 (54%), Positives = 260/374 (69%), Gaps = 6/374 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S K  +  E ++ +     L   + D LVE+L    +R+   E  +++ +  YG + +  
Sbjct: 246 SPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMPKKS 305

Query: 370 FLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W+    + D P  E    +    D I +   ++K I  ET +++   
Sbjct: 306 FITLFTGNESSEAWLDEILSSDKPYAEK---IRRSEDDIRRSIMKLKVIEEETSLTVQNI 362

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 363 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 483 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATST 542

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 543 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 603 RHPSRSETLRSFLD 616



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 88/139 (63%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +D++    +A  ++  L   ++   R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DDTITDEDAAEAAAAALSSVENEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              +  ++ E P T   ++
Sbjct: 129 INQVQNAVAEYPGTIPYIL 147


>gi|37527834|ref|NP_931179.1| RNA polymerase sigma factor RpoD [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787270|emb|CAE16351.1| RNA polymerase sigma factor rpoD (Sigma-70) [Photorhabdus
           luminescens subsp. laumondii TTO1]
          Length = 614

 Score =  388 bits (996), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 200/363 (55%), Positives = 258/363 (71%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E +++++  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPKKNFITLFSGNE 311

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + AK   +   +  +  E D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 312 TSDIWFTAAKAMNKPWSEKLLEVE-DEVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 370

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 371 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 430

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 431 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 490

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 491 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 550

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 551 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610

Query: 679 FLD 681
           FLD
Sbjct: 611 FLD 613



 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TANDTDEDAVEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|113461378|ref|YP_719447.1| RNA polymerase sigma factor RpoD [Haemophilus somnus 129PT]
 gi|112823421|gb|ABI25510.1| RNA polymerase, sigma 70 subunit, RpoD [Haemophilus somnus 129PT]
          Length = 595

 Score =  388 bits (996), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 201/364 (55%), Positives = 253/364 (69%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           + L  +     L   + D LV  + D+ K +  +E ++ +L      + ++ F +   G 
Sbjct: 232 QALADIFTQFRLVPKQFDALVNYMRDMMKSVRQHERQIQKLVVDLAKMPKENFQKLFIGN 291

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E    W+          W   +     ++ +  N++  I  ET ++IS+ R I   V +G
Sbjct: 292 ESSEGWLDKLL-LARKPWSERLIQHESAVRQSINQLLKIEQETNLTISQIREICDKVAQG 350

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 351 ELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 410

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  K+ RE T EE+A+++ 
Sbjct: 411 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQKMGREATSEELAERMG 470

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 471 MPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLRAATHEVL 530

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 531 EGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLR 590

Query: 678 SFLD 681
           SFLD
Sbjct: 591 SFLD 594



 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 51/130 (39%), Positives = 74/130 (56%), Gaps = 21/130 (16%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL------EDEEGSEDSLDLASS 98
           +N  LP D V ++Q+ED + M+++MGI V+    D DDL       DE+  E++  + SS
Sbjct: 1   MNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDADDLMLNENITDEDAVEEATQVLSS 60

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                       ++    T DPVRMY+REMGS+ELL+REGEI IAKRIE G   + +++ 
Sbjct: 61  V-----------EAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEGINEVQSAVA 109

Query: 159 ESPLTFQALI 168
             P     L+
Sbjct: 110 AYPKALNYLL 119


>gi|68249130|ref|YP_248242.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae 86-028NP]
 gi|68057329|gb|AAX87582.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae 86-028NP]
          Length = 623

 Score =  388 bits (996), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 262 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITANGS 321

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 322 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 380

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 381 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 440

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 441 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 500

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 501 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 560

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 561 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 620

Query: 680 LD 681
           LD
Sbjct: 621 LD 622



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN-MGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L N  GI V+D     D+    
Sbjct: 17  EQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLS 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 77  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEGGI 135

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+   P     L+   D++  G   L ++I
Sbjct: 136 DEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI 170


>gi|323495834|ref|ZP_08100902.1| RNA polymerase sigma factor RpoD [Vibrio sinaloensis DSM 21326]
 gi|323319050|gb|EGA71993.1| RNA polymerase sigma factor RpoD [Vibrio sinaloensis DSM 21326]
          Length = 620

 Score =  388 bits (996), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/374 (54%), Positives = 261/374 (69%), Gaps = 6/374 (1%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S K ++  E ++ +     L   + D LV +L    +R+   E  +++ +  YG + +  
Sbjct: 249 SPKAQIAHELVLDVFKEFRLTPKQFDYLVNELRTSMERVRTQERLIMKASVEYGKMPKKS 308

Query: 370 FLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W+    A D P   + + +    D I +   ++K I  ET +++   
Sbjct: 309 FISLFSGNESSDAWLDEILASDKP---YADKIRRSEDDIRRSIMKLKMIEEETSLTVQSI 365

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 366 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 425

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 426 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 485

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 486 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAT 545

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 546 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 605

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 606 RHPSRSETLRSFLD 619



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KLLVLKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++++    +A  ++  L   ++   R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DETITDEDAAEAAAAALSSVENEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              +  ++ E P T   ++
Sbjct: 129 INQVQNAVAEYPGTIPYIL 147


>gi|148827724|ref|YP_001292477.1| DNA primase [Haemophilus influenzae PittGG]
 gi|148718966|gb|ABR00094.1| DNA primase [Haemophilus influenzae PittGG]
          Length = 629

 Score =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITANGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|290474860|ref|YP_003467740.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus bovienii
           SS-2004]
 gi|289174173|emb|CBJ80960.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus bovienii
           SS-2004]
          Length = 616

 Score =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 198/362 (54%), Positives = 258/362 (71%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E +++++  +   + +  F+    G E 
Sbjct: 255 LSEVFKQFRLIPKQFDYLVNNMRSMMDRVRLQERQIMKMCVELCKMPKKNFITLFSGNET 314

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W + AK      W + ++   D +++   +++ I  ETG++I + + I   +  GE 
Sbjct: 315 TDTWFTAAKAM-NKPWSDKLSEVEDDVMRSLQKLRQIEEETGLTIEQVKDINRRMSIGEA 373

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 374 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 433

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP
Sbjct: 434 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMP 493

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETP+GD+D SHLGDFIED     PLDSA   +LR  T  VLA 
Sbjct: 494 EDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAG 553

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 554 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 613

Query: 680 LD 681
           LD
Sbjct: 614 LD 615



 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGECRLSDLI 164


>gi|149376143|ref|ZP_01893908.1| sigma factor RpoD [Marinobacter algicola DG893]
 gi|149359548|gb|EDM48007.1| sigma factor RpoD [Marinobacter algicola DG893]
          Length = 616

 Score =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 198/365 (54%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L ++     L     D LV  +   +  +  NE  ++++  +   + R  F++   G E
Sbjct: 250 ELGQVFAPFKLGNKAFDELVNVVRSTNDLVRENERAIMKICVRECKMPRKDFIKSFPGNE 309

Query: 379 LDPHWVSYAKDFPEGE--WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   A+   +G+  +   +A  +D +++++  I +I  E  + +S+ + I   V  
Sbjct: 310 TSLDW---AEKMSKGKKPYAPLIAERIDEVVRLQKRIANIQTEVDLDVSDIKEINRRVSI 366

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 367 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 427 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A+SP+DSA    LRE T  V
Sbjct: 487 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L
Sbjct: 547 LSGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 606

Query: 677 RSFLD 681
           R F+D
Sbjct: 607 RGFID 611



 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 93/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D L   +
Sbjct: 11  KDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDADTLLMTD 70

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  DS    ++A+ ++  L   +  A R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 71  G--DSTADEAAAAEAAAALAAVESDAGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +MA++   P     +I   D + +    L +I+
Sbjct: 128 EGIRDVMAAVAHFPGITGTVIQAYDRIIENEGRLSDIV 165


>gi|212711167|ref|ZP_03319295.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
 gi|212686335|gb|EEB45863.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
          Length = 615

 Score =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 202/374 (54%), Positives = 261/374 (69%), Gaps = 2/374 (0%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKR 367
           +S  K     E+L ++     L   + D LV  + ++  R+   E  +++L  +   + +
Sbjct: 242 RSDAKTVAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPK 301

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F+    G E    W++ AK      W   +    + +L+    ++ I  ETG++I + 
Sbjct: 302 KNFITLFSGNETSETWLTAAKAM-NKPWSEKLLEVEEEVLRCLQRLRQIEEETGLTIEQV 360

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 361 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 420

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 421 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 480

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   
Sbjct: 481 SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 540

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 541 SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 600

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LRSFLD
Sbjct: 601 RHPSRSEVLRSFLD 614



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLILAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|145633515|ref|ZP_01789244.1| aspartate ammonia-lyase [Haemophilus influenzae 3655]
 gi|144985884|gb|EDJ92492.1| aspartate ammonia-lyase [Haemophilus influenzae 3655]
          Length = 628

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 267 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYEERQLQKILVDIAGMPKDDFEKIITTNGS 326

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 327 NSEWVTKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 385

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 386 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 445

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 446 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 505

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 506 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 565

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 566 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 625

Query: 680 LD 681
           LD
Sbjct: 626 LD 627



 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN-MGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L N  GI V+D     D+    
Sbjct: 17  EQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLS 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 77  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEEGI 135

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+   P     L+   D++  G   L ++I
Sbjct: 136 DEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI 170


>gi|16272477|ref|NP_438691.1| RNA polymerase sigma-70 factor [Haemophilus influenzae Rd KW20]
 gi|260580980|ref|ZP_05848803.1| transcription initiation factor sigma 70 [Haemophilus influenzae
           RdAW]
 gi|1173125|sp|P43766|RPOD_HAEIN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1573517|gb|AAC22190.1| RNA polymerase sigma-70 factor (rpoD) [Haemophilus influenzae Rd
           KW20]
 gi|260092339|gb|EEW76279.1| transcription initiation factor sigma 70 [Haemophilus influenzae
           RdAW]
          Length = 629

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|262392398|ref|YP_003284252.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
 gi|262335992|gb|ACY49787.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
          Length = 620

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 211/399 (52%), Positives = 268/399 (67%), Gaps = 11/399 (2%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N      +S K  V  E ++ +     L   + D LV +L   
Sbjct: 226 EKFNQLRSTYQNLQLAINEYG--YNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTA 283

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 284 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEK---IKRN 340

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 341 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKK 400

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 401 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 460

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD
Sbjct: 461 VHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGD 520

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 521 DEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 580

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 581 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619



 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 10  KSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 129 INQVQSSVAEYPGTIPYIL 147


>gi|145628917|ref|ZP_01784717.1| DNA primase [Haemophilus influenzae 22.1-21]
 gi|145635386|ref|ZP_01791088.1| aspartate ammonia-lyase [Haemophilus influenzae PittAA]
 gi|144979387|gb|EDJ89073.1| DNA primase [Haemophilus influenzae 22.1-21]
 gi|145267392|gb|EDK07394.1| aspartate ammonia-lyase [Haemophilus influenzae PittAA]
          Length = 623

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 262 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 321

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 322 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 380

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 381 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 440

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 441 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 500

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 501 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 560

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 561 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 620

Query: 680 LD 681
           LD
Sbjct: 621 LD 622



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN-MGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L N  GI V+D     D+    
Sbjct: 17  EQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLS 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 77  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEGGI 135

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+   P     L+   D++  G   L ++I
Sbjct: 136 DEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI 170


>gi|148825193|ref|YP_001289946.1| aspartate ammonia-lyase [Haemophilus influenzae PittEE]
 gi|148715353|gb|ABQ97563.1| aspartate ammonia-lyase [Haemophilus influenzae PittEE]
          Length = 645

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 284 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 343

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 344 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 402

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 403 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 462

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 463 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 522

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 523 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 582

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 583 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 642

Query: 680 LD 681
           LD
Sbjct: 643 LD 644



 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN-MGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L N  GI V+D     D+    
Sbjct: 39  EQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLS 98

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 99  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEGGI 157

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+   P     L+   D++  G   L ++I
Sbjct: 158 DEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI 192


>gi|262275021|ref|ZP_06052832.1| RNA polymerase sigma factor RpoD [Grimontia hollisae CIP 101886]
 gi|262221584|gb|EEY72898.1| RNA polymerase sigma factor RpoD [Grimontia hollisae CIP 101886]
          Length = 615

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 205/381 (53%), Positives = 264/381 (69%), Gaps = 10/381 (2%)

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           G+  E+++V    L E    +     L   + D LV ++ D   R+   E  ++RL    
Sbjct: 241 GRFHEQTTVAIAELSE----VFKQFRLVPKQFDRLVNEMRDTMDRVRTQERIIMRLCVDQ 296

Query: 364 G-IKRDVFLERHQGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
             + +  F++   G E    W+  + A D P  E    +    + + +   ++K +  ET
Sbjct: 297 AKMPKKTFVQLFAGNESSDAWLDKALASDKPYAER---LKQHEEDLRRCIQKLKIVEDET 353

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+S+   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 354 GLSVERVKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 413

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M 
Sbjct: 414 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 473

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P
Sbjct: 474 QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 533

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +DSA   NL+  T+ VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 534 MDSATMNNLKMATSEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 593

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRS+ LRSFLD
Sbjct: 594 AKALRKLRHPSRSEVLRSFLD 614



 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 58/154 (37%), Positives = 92/154 (59%), Gaps = 1/154 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE    +
Sbjct: 10  KLLVAKGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVETAPDADELMMSE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           ++    +   ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  TVADEDAVEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGIN 128

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            +  S+ E P +  +L+   D++      L +II
Sbjct: 129 QVQVSVAEYPGSISSLLDQFDKVEAEELRLTDII 162


>gi|145638551|ref|ZP_01794160.1| aspartate ammonia-lyase [Haemophilus influenzae PittII]
 gi|229844308|ref|ZP_04464448.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 6P18H1]
 gi|229846616|ref|ZP_04466724.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 7P49H1]
 gi|145272146|gb|EDK12054.1| aspartate ammonia-lyase [Haemophilus influenzae PittII]
 gi|229810709|gb|EEP46427.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 7P49H1]
 gi|229812557|gb|EEP48246.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 6P18H1]
 gi|309750056|gb|ADO80040.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2866]
 gi|309972316|gb|ADO95517.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2846]
          Length = 629

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|319775546|ref|YP_004138034.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           F3047]
 gi|317450137|emb|CBY86351.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           F3047]
          Length = 629

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|319897950|ref|YP_004136147.1| RNA polymerase, sigma 70 (sigma d) factor [Haemophilus influenzae
           F3031]
 gi|329122411|ref|ZP_08250998.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           aegyptius ATCC 11116]
 gi|317433456|emb|CBY81839.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           F3031]
 gi|327473693|gb|EGF19112.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           aegyptius ATCC 11116]
          Length = 629

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|301169248|emb|CBW28845.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           10810]
          Length = 629

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN-MGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L N  GI V+D     D+    
Sbjct: 17  EQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLS 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 77  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEGGI 135

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+   P     L+   D++  G   L ++I
Sbjct: 136 DEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI 170


>gi|189424079|ref|YP_001951256.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420338|gb|ACD94736.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 586

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 178/263 (67%), Positives = 226/263 (85%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E+G   +E    +  +R+GE +A IAK E++EANLRLV+S+AKKYTNRGLQFLDLIQEGN
Sbjct: 324 ESGFKATELSKAIRAIREGEHKARIAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGN 383

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R+
Sbjct: 384 IGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQ 443

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +  REP+PEEIA ++ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK  V
Sbjct: 444 LVQENGREPSPEEIADRMQLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVV 503

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +PL++ I+ANL E T+RVL++LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQ
Sbjct: 504 NPLEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQ 563

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSKKL+SF++
Sbjct: 564 IEAKALRKLRHPSRSKKLKSFVE 586



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 50/146 (34%), Positives = 85/146 (58%), Gaps = 1/146 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I + +++G++T +E+N  LPPD +++EQ++D + M  +M I +VD         
Sbjct: 7   DEVKQLIDIGKEKGFLTFDEVNDILPPD-IATEQIDDVMGMFGDMDIEIVDSAQKVKIPK 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  L+     +       + +  A   T DPVRMYLREMGS+ LL+REGE+ IAKRIE 
Sbjct: 66  IKIDLEEGEEEAEGEAEEVEFEPGAIGRTSDPVRMYLREMGSVSLLTREGEVEIAKRIED 125

Query: 149 GRAMMMASLCESPLTFQALIIWRDEL 174
           G   +   +  +P+T + ++   ++L
Sbjct: 126 GDREVAGIILNTPITVKEVLALGEKL 151


>gi|145637426|ref|ZP_01793085.1| aspartate ammonia-lyase [Haemophilus influenzae PittHH]
 gi|145269372|gb|EDK09316.1| aspartate ammonia-lyase [Haemophilus influenzae PittHH]
          Length = 629

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|77920269|ref|YP_358084.1| RNA polymerase, sigma(70) factor [Pelobacter carbinolicus DSM 2380]
 gi|77546352|gb|ABA89914.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter carbinolicus DSM
           2380]
          Length = 588

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 207/420 (49%), Positives = 297/420 (70%), Gaps = 28/420 (6%)

Query: 277 RPKVMCALDEIAEVYRELRSL-QDNAVNGQKDEKSSVKCKVLKEK--LVKLVGSLSLNQS 333
           R +++  +++I +   EL  L Q+ A  G + +++S++ ++ ++K  + +L+  + L   
Sbjct: 180 RTRILDLVEKIRQQNDELMVLCQELADCGDRQQRNSLRDQIAEKKASIGELMREIRLKDF 239

Query: 334 RIDLLVEQLYDISKRIMHNEGELL----RLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           ++D +V++L D+++++     E+      L Q +  IKR   L R +  + + H +S   
Sbjct: 240 QVDKIVDRLKDMAQQVKKGLSEVQACEEELKQPHKEIKR--LLRRMRKSDEEAHRISQDL 297

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKS-------ISVETGISISEFRHIVSMVRKGECEA 441
             P           +D++L +   +KS       +  E+G +  E    +  V KGE  A
Sbjct: 298 GVP-----------IDTLLSVEKRLKSAQRKFNRVEDESGFAPEELLGSLKEVMKGEWRA 346

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 347 KAAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 406

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  ++ REP PEEIA+++ +P+E
Sbjct: 407 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEMGREPVPEEIAERMELPLE 466

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR+VLKI KEPISLETPIG+E+ S LGDFIEDK  VSPL++ I+ NL + T+RVLASLT
Sbjct: 467 KVRRVLKIAKEPISLETPIGEEEDSSLGDFIEDKGVVSPLEAVIKGNLSDQTSRVLASLT 526

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+++L+SF++
Sbjct: 527 PREEKVLRMRFGIGEKSDHTLEEVGQDFAVTRERIRQIEAKALRKLRHPSRARRLKSFVE 586



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 51/137 (37%), Positives = 85/137 (62%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I + +++GY+T +E+N +LP   VSS+Q++D +++   M I VVD +       ++ 
Sbjct: 11  QQLIDMGKEKGYLTYDEVNDYLPESVVSSDQLDDVMSLFGEMDIEVVDSEQKVSVSKTQS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             D +SS S       + +      T DPVRMYLREMG + LL+REGE+ IAKRIE G A
Sbjct: 71  DSDDSSSDSGEEEEETEYEAGTLGRTSDPVRMYLREMGQVSLLTREGEVEIAKRIEEGEA 130

Query: 152 MMMASLCESPLTFQALI 168
           ++   + ++P+ F+ +I
Sbjct: 131 LVARVIMKTPIAFREVI 147


>gi|119773960|ref|YP_926700.1| RNA polymerase sigma-70 factor [Shewanella amazonensis SB2B]
 gi|119766460|gb|ABL99030.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella amazonensis
           SB2B]
          Length = 620

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 212/400 (53%), Positives = 280/400 (70%), Gaps = 13/400 (3%)

Query: 289 EVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+  DNA     V G+   +S+   + L E L ++     L   + D LV+ + 
Sbjct: 226 ERFAALRAAYDNALKVIEVKGRAHPEST---RALFE-LGEIFKEFRLVPKQFDRLVKSMR 281

Query: 344 DISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           ++  ++   E  +++L  +   + +  F++   G E D  W  + K+   G   +     
Sbjct: 282 EMMDKVRVQERLIMKLCVEQAKMPKKNFVKLFTGNETDLTW--FNKEIEAGRPYSADLKL 339

Query: 403 VDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           VD  + + R ++++I VETG+SI   + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 340 VDEDVQRCRAKLEAIEVETGLSIESIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 399

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 400 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 459

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ REP+PEE+A+++AMP + +RKVLKI KEPIS+ETPIG
Sbjct: 460 PVHMIETINKLNRISRQMLQEMGREPSPEELAERMAMPEDKIRKVLKIAKEPISMETPIG 519

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED     PLDSA   +L++ T  VLA LT RE +VLRMRFGI MNTDHT
Sbjct: 520 DDEDSHLGDFIEDTTLELPLDSATSESLKQATHEVLAGLTAREAKVLRMRFGIDMNTDHT 579

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 580 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 619



 Score = 94.4 bits (233), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 58/155 (37%), Positives = 89/155 (57%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D ++   SE
Sbjct: 13  KMLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEEAPDADEMMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             + +S+ E P     ++   D+       L +II
Sbjct: 131 NTVQSSVAEYPQAISMILEQFDQFEADAIRLSDII 165


>gi|311693206|gb|ADP96079.1| RNA polymerase, sigma 70 subunit, RpoD [marine bacterium HP15]
          Length = 615

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/383 (53%), Positives = 269/383 (70%), Gaps = 8/383 (2%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL- 359
           A +G+ D+K+    + L E L ++     L     D LV  +   +  +  NE  ++++ 
Sbjct: 233 AKHGRSDKKTQ---EALNE-LGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQIC 288

Query: 360 AQSYGIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
            +   + R  F++   G E +  W    AK   +  +   +A  +D +++++  I+++  
Sbjct: 289 VRECKMPRKDFIKSFPGNETNLDWADKIAKS--KKPYAAPLAERIDEVVRLQKRIQNVQT 346

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E  + +++ + I   V  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 347 EVDLDVADIKEINRRVSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 406

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 407 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 466

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ REPTPEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A+
Sbjct: 467 MLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQAL 526

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP+DSA    LRE T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 527 SPVDSATAEGLREATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQ 586

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRS  LR F+D
Sbjct: 587 IEAKALRKLRHPSRSDHLRGFID 609



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 63/152 (41%), Positives = 92/152 (60%), Gaps = 9/152 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D L   E
Sbjct: 11  KDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTLLMTE 70

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  DS    ++A+ ++  L   +  A R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 71  G--DSTADEAAAAEAAAALAAVETDAGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDEL--NDG 177
            G   +MA++   P T   +I   D +  N+G
Sbjct: 128 EGIRDVMAAVAHFPGTAGTVIQAYDRILENEG 159


>gi|28897178|ref|NP_796783.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153839257|ref|ZP_01991924.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ3810]
 gi|260361470|ref|ZP_05774529.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus K5030]
 gi|260878083|ref|ZP_05890438.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AN-5034]
 gi|260896978|ref|ZP_05905474.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio
           parahaemolyticus Peru-466]
 gi|260902497|ref|ZP_05910892.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ4037]
 gi|28805387|dbj|BAC58667.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus RIMD
           2210633]
 gi|149747222|gb|EDM58210.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ3810]
 gi|308088714|gb|EFO38409.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio
           parahaemolyticus Peru-466]
 gi|308089726|gb|EFO39421.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AN-5034]
 gi|308109810|gb|EFO47350.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ4037]
 gi|308110993|gb|EFO48533.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus K5030]
 gi|328471947|gb|EGF42824.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus 10329]
          Length = 620

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 211/399 (52%), Positives = 268/399 (67%), Gaps = 11/399 (2%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    +  S K  V  E ++ +     L   + D LV +L   
Sbjct: 226 EKFNQLRSTYQNLQLAINEYGYD--SPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTA 283

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 284 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSDAWLDEILASDKPYAEK---IKRN 340

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 341 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKK 400

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 401 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 460

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD
Sbjct: 461 VHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGD 520

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 521 DEDSHLGDFIEDTTLELPLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 580

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 581 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 129 INQVQSSVAEYPGTIPYIL 147


>gi|117618585|ref|YP_855378.1| RNA polymerase sigma factor RpoD [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559992|gb|ABK36940.1| RNA polymerase sigma factor RpoD [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 618

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 255/363 (70%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 256 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 315

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 316 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 374

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 375 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 434

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A ++ M
Sbjct: 435 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGM 494

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P D+A   +LR  T  VLA
Sbjct: 495 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLRNATREVLA 554

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 555 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 614

Query: 679 FLD 681
           FLD
Sbjct: 615 FLD 617


>gi|145640511|ref|ZP_01796095.1| DNA primase [Haemophilus influenzae R3021]
 gi|145275097|gb|EDK14959.1| DNA primase [Haemophilus influenzae 22.4-21]
          Length = 629

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/362 (56%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       
Sbjct: 268 LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRNQERQLQKILVDIAGMPKDDFEKIITTNGS 327

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE 
Sbjct: 328 NSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQ 386

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 387 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 446

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP
Sbjct: 447 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMP 506

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  
Sbjct: 507 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEG 566

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 567 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSF 626

Query: 680 LD 681
           LD
Sbjct: 627 LD 628


>gi|271499150|ref|YP_003332175.1| RNA polymerase sigma-70 subunit RpoD [Dickeya dadantii Ech586]
 gi|270342705|gb|ACZ75470.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya dadantii Ech586]
          Length = 611

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 201/363 (55%), Positives = 257/363 (70%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + DLLV  +  +  R+   E ++++L  +   + +  F+    G E
Sbjct: 249 KLSEVFKQFRLVPKQFDLLVNNMRSMMDRVRAQERQIMKLCVELCKMPKKNFVTLFTGNE 308

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W   A    +   +     E D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 309 TNSKWFEAAVSMGKPWCEKLREVE-DDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGE 367

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 368 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 428 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 487

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 488 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 547

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 548 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607

Query: 679 FLD 681
           FLD
Sbjct: 608 FLD 610



 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 96/155 (61%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+ E P     L+   D +  G + L ++I
Sbjct: 128 NQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 162


>gi|300724881|ref|YP_003714206.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297631423|emb|CBJ92120.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
          Length = 616

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 197/362 (54%), Positives = 257/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E +++++  +   + +  F+    G E 
Sbjct: 255 LSEVFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPKKNFITLFSGNET 314

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W + AK      W N +    + +++   +++ I  ETG++I + + I   +  GE 
Sbjct: 315 TDTWFTAAKAM-NKPWSNKLLEIEEEVMRSLQKLRQIEEETGLTIEQVKDINRRMSIGEA 373

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 374 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 433

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP
Sbjct: 434 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMP 493

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETP+GD++ SHLGDFIED     PLDSA   +LR  T  VLA 
Sbjct: 494 EDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAG 553

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 554 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 613

Query: 680 LD 681
           LD
Sbjct: 614 LD 615



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|91227144|ref|ZP_01261628.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|91188796|gb|EAS75083.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
          Length = 574

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 211/399 (52%), Positives = 268/399 (67%), Gaps = 11/399 (2%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N      +S K  V  E ++ +     L   + D LV +L   
Sbjct: 180 EKFNQLRSTYQNLQLAINEYG--YNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTA 237

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 238 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEK---IKRN 294

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 295 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKK 354

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 355 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 414

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD
Sbjct: 415 VHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGD 474

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 475 DEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 534

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 535 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 573



 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 39/52 (75%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 50  TTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 101


>gi|77461370|ref|YP_350877.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf0-1]
 gi|77385373|gb|ABA76886.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas fluorescens
           Pf0-1]
          Length = 615

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 198/355 (55%), Positives = 260/355 (73%), Gaps = 2/355 (0%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSY 386
           + L   + + LVE++     R+   E  +++L  +   + R  FL +  G E+D  W S 
Sbjct: 261 IKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW-SD 319

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    + ++   +A     I++ + ++ ++  ETG++I+E + I   +  GE +A  AKK
Sbjct: 320 ALAKGKSKYAEAIARVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRAKK 379

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 380 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 439

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKV
Sbjct: 440 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKV 499

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +
Sbjct: 500 LKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAK 559

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 560 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/136 (39%), Positives = 83/136 (61%), Gaps = 1/136 (0%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++IKL R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D+
Sbjct: 13  ELIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADA 72

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
               ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   
Sbjct: 73  DTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIRE 131

Query: 153 MMASLCESPLTFQALI 168
           +M+++   P T   ++
Sbjct: 132 VMSAIAHFPGTVDHIL 147


>gi|163802687|ref|ZP_02196578.1| RNA polymerase sigma factor RpoD [Vibrio sp. AND4]
 gi|159173575|gb|EDP58395.1| RNA polymerase sigma factor RpoD [Vibrio sp. AND4]
          Length = 620

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 210/403 (52%), Positives = 272/403 (67%), Gaps = 9/403 (2%)

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            AL++ +++    ++LQ  A+N    E  S K  +  E ++ +     L   + D LV +
Sbjct: 223 LALEKFSQLRNTYQNLQ-LAINEHGYE--SPKATLANELMLDVFREFRLTPKQFDHLVNE 279

Query: 342 LYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNF 398
           L     R+   E  +++    YG + +  F+    G E    W+    A D P  E    
Sbjct: 280 LRTAMDRVRTQERLIMKSTVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEK--- 336

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 337 IKRSEEDIRRSITKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVIS 396

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 397 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 456

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ET
Sbjct: 457 IRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMET 516

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNT
Sbjct: 517 PIGDDEDSHLGDFIEDTTLELPLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNT 576

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 577 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 129 INQVQSSVAEYPGTIPYIL 147


>gi|251791058|ref|YP_003005779.1| RNA polymerase sigma factor RpoD [Dickeya zeae Ech1591]
 gi|247539679|gb|ACT08300.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya zeae Ech1591]
          Length = 611

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 201/363 (55%), Positives = 257/363 (70%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + DLLV  +  +  R+   E ++++L  +   + +  F+    G E
Sbjct: 249 KLSEVFKQFRLVPKQFDLLVNNMRSMMDRVRTQERQIMKLCVELCKMPKKNFVTLFTGNE 308

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W   A    +   +     E D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 309 TNSKWFEAALSMGKPWCEKLREVE-DDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGE 367

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 368 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 428 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 487

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 488 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 547

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 548 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607

Query: 679 FLD 681
           FLD
Sbjct: 608 FLD 610



 Score = 97.4 bits (241), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 63/175 (36%), Positives = 102/175 (58%), Gaps = 13/175 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII----------DLEACIGPES 195
             +  S+ E P     L+   D +  G + L ++I          DL   + PE+
Sbjct: 128 NQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPNVAPEN 182


>gi|39546362|ref|NP_462126.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161616204|ref|YP_001590169.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167551873|ref|ZP_02345626.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|167990234|ref|ZP_02571334.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|168237909|ref|ZP_02662967.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|168243042|ref|ZP_02667974.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168262827|ref|ZP_02684800.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168463576|ref|ZP_02697493.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|194445988|ref|YP_002042478.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451693|ref|YP_002047209.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194472915|ref|ZP_03078899.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194736124|ref|YP_002116168.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197251872|ref|YP_002148141.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197264102|ref|ZP_03164176.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|198242489|ref|YP_002217192.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200389116|ref|ZP_03215728.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204928094|ref|ZP_03219294.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|207858469|ref|YP_002245120.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213425630|ref|ZP_03358380.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213586893|ref|ZP_03368719.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646106|ref|ZP_03376159.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213865054|ref|ZP_03387173.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|238910014|ref|ZP_04653851.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|61234163|sp|P0A2E3|RPOD_SALTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|61234169|sp|P0A2E4|RPOD_SALTI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|154406|gb|AAA27242.1| rpoD protein [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|161365568|gb|ABX69336.1| hypothetical protein SPAB_04007 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194404651|gb|ACF64873.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194409997|gb|ACF70216.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194459279|gb|EDX48118.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194711626|gb|ACF90847.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195633147|gb|EDX51561.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197215575|gb|ACH52972.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197242357|gb|EDY24977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197289083|gb|EDY28452.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|197937005|gb|ACH74338.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|199606214|gb|EDZ04759.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204322416|gb|EDZ07613.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205323318|gb|EDZ11157.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205331247|gb|EDZ18011.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205337819|gb|EDZ24583.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205348629|gb|EDZ35260.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|206710272|emb|CAR34630.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|301159764|emb|CBW19283.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312914239|dbj|BAJ38213.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321225894|gb|EFX50948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
          Length = 615

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 489

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 490 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 549

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 609

Query: 677 RSFLD 681
           RSFLD
Sbjct: 610 RSFLD 614



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|87119778|ref|ZP_01075675.1| RNA polymerase sigma factor [Marinomonas sp. MED121]
 gi|86165254|gb|EAQ66522.1| RNA polymerase sigma factor [Marinomonas sp. MED121]
          Length = 614

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 196/326 (60%), Positives = 241/326 (73%), Gaps = 17/326 (5%)

Query: 364 GIKRDVFLERHQGRELDPHW--------VSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           G+ R  FL+R    E +  W          YA    E E +          ++ + ++++
Sbjct: 297 GMPRTEFLKRFPNNETNIQWFPDQIASGAGYAAALQENEAE---------FMRSQRKLRN 347

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS +TG++I E + I   +  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 348 ISKDTGLTIVELKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 407

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R 
Sbjct: 408 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 467

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M  ++ RE TPEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED 
Sbjct: 468 SRQMLQEMGREATPEELAVRMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDD 527

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A SP+D+A    LRE TT VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRER
Sbjct: 528 GAESPIDTATIEGLREATTSVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 587

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 588 IRQIEAKALRKLRHPSRSEHLRSFLD 613


>gi|145300336|ref|YP_001143177.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853108|gb|ABO91429.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 616

 Score =  385 bits (990), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 199/378 (52%), Positives = 261/378 (69%), Gaps = 2/378 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 239 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 298

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 299 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 357

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 358 IAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P D+
Sbjct: 478 GREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADA 537

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 538 ATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSRS+ LRSFLD
Sbjct: 598 LRKLRHPSRSEVLRSFLD 615


>gi|330505280|ref|YP_004382149.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina NK-01]
 gi|328919566|gb|AEB60397.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina NK-01]
          Length = 615

 Score =  385 bits (990), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/364 (55%), Positives = 258/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV Q+ D   R+   E  +++L  +   + R  FL    G E+
Sbjct: 254 LAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRADFLRLFPGNEI 313

Query: 380 DPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           D  W   A D  +G+ K   A       I + + ++  +  E  +S++E + I   +  G
Sbjct: 314 DMDW---AADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKDINRRMSIG 370

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 371 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ 
Sbjct: 431 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 490

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL
Sbjct: 491 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVL 550

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LR
Sbjct: 551 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLR 610

Query: 678 SFLD 681
           SFLD
Sbjct: 611 SFLD 614


>gi|88704608|ref|ZP_01102321.1| RNA polymerase sigma factor rpoD [Congregibacter litoralis KT71]
 gi|88700929|gb|EAQ98035.1| RNA polymerase sigma factor rpoD [Congregibacter litoralis KT71]
          Length = 607

 Score =  385 bits (990), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 213/424 (50%), Positives = 277/424 (65%), Gaps = 16/424 (3%)

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           +DEDD+A T         P  + A      + R+    +       + +K+S+K     E
Sbjct: 195 DDEDDNAPT--------GPDPVEAKKRFTALKRQFNKTEKVLAEKGRQDKASIKEM---E 243

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           KL ++           D L ++       +   E E++R+  +   + R  F+   QG E
Sbjct: 244 KLGEIFKFFKFTPKVFDPLNDEARSALAGVREQEREIMRIVVRRCQMPRKEFITSFQGNE 303

Query: 379 LDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            +  W+S +A+    G   N      + I + + +I  I   TG++++E + I   +  G
Sbjct: 304 SNAKWLSRHARKKDYGPKLN---AHKEEIHRAQRQIGQIEEATGLTVTEIKEINRRMSMG 360

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 361 EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 420

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ 
Sbjct: 421 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 480

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+   SP+DSA    L+E T  VL
Sbjct: 481 MPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTIHSPIDSATGQGLQEATKDVL 540

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LR
Sbjct: 541 GGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLR 600

Query: 678 SFLD 681
           SFLD
Sbjct: 601 SFLD 604



 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 58/143 (40%), Positives = 87/143 (60%), Gaps = 11/143 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL--ED 85
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D DDL   D
Sbjct: 12  KSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDADDLILTD 71

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +GS D +  A +A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 72  GDGSADDIAAAEAAAALAA-----VETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALI 168
           IE G   +MA+L   P   ++++
Sbjct: 127 IEEGIRELMAALAFYPGAVKSVL 149


>gi|146309042|ref|YP_001189507.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina ymp]
 gi|145577243|gb|ABP86775.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas mendocina ymp]
          Length = 615

 Score =  385 bits (990), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/364 (55%), Positives = 258/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV Q+ D   R+   E  +++L  +   + R  FL    G E+
Sbjct: 254 LAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRADFLRLFPGNEI 313

Query: 380 DPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           D  W   A D  +G+ K   A       I + + ++  +  E  +S++E + I   +  G
Sbjct: 314 DMDW---AADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKDINRRMSIG 370

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 371 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ 
Sbjct: 431 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 490

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL
Sbjct: 491 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVL 550

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LR
Sbjct: 551 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLR 610

Query: 678 SFLD 681
           SFLD
Sbjct: 611 SFLD 614


>gi|253991033|ref|YP_003042389.1| RNA polymerase sigma factor RpoD [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782483|emb|CAQ85647.1| rna polymerase, sigma(70) factor; regulation of proteins induced a
           high temperatures (rna polymerase sigma 70 factor rpod)
           [Photorhabdus asymbiotica]
          Length = 651

 Score =  385 bits (990), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/363 (55%), Positives = 257/363 (70%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E +++++  +   + +  F+    G E
Sbjct: 289 KLSEIFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPKKNFITLFSGNE 348

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + AK   +   +  +  E + I +    ++ I  ETG++I + + I   +  GE
Sbjct: 349 TSDIWFTAAKAMNKPWSEKLLEVE-EEIQRSLQRLRQIEEETGLTIEQVKDINRRMSIGE 407

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 408 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 467

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 468 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 527

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 528 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 587

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 588 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 647

Query: 679 FLD 681
           FLD
Sbjct: 648 FLD 650



 Score =  101 bits (252), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 45  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 104

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 105 TTNDTDEDAVEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 161

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 162 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 199


>gi|62181728|ref|YP_218145.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62129361|gb|AAX67064.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|322716214|gb|EFZ07785.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 658

 Score =  385 bits (990), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 296 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 355

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 356 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 412

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 413 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 472

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 473 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 532

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 533 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 592

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 593 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 652

Query: 677 RSFLD 681
           RSFLD
Sbjct: 653 RSFLD 657



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|289827081|ref|ZP_06545870.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 615

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFIMLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 489

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 490 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 549

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 609

Query: 677 RSFLD 681
           RSFLD
Sbjct: 610 RSFLD 614



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|224585014|ref|YP_002638813.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|224469542|gb|ACN47372.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
          Length = 658

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 296 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 355

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 356 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 412

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 413 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 472

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 473 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 532

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 533 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 592

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 593 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 652

Query: 677 RSFLD 681
           RSFLD
Sbjct: 653 RSFLD 657



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|56415151|ref|YP_152226.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197364081|ref|YP_002143718.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|205358509|ref|ZP_02656872.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205359720|ref|ZP_02831723.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|16421768|gb|AAL22085.1| sigma D factor of RNA polymerase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56129408|gb|AAV78914.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095558|emb|CAR61123.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|205333914|gb|EDZ20678.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205343355|gb|EDZ30119.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|261248341|emb|CBG26178.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995406|gb|ACY90291.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|320087665|emb|CBY97429.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|323131572|gb|ADX19002.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326624968|gb|EGE31313.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332990077|gb|AEF09060.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 660

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 298 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 357

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 358 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 414

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 415 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 474

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 475 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 534

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 535 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 594

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 595 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 654

Query: 677 RSFLD 681
           RSFLD
Sbjct: 655 RSFLD 659



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|161506225|ref|YP_001573337.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160867572|gb|ABX24195.1| hypothetical protein SARI_04418 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 660

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 298 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 357

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 358 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 414

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 415 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 474

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 475 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 534

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 535 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 594

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 595 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 654

Query: 677 RSFLD 681
           RSFLD
Sbjct: 655 RSFLD 659



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|254229773|ref|ZP_04923181.1| sigma-70, non-essential region family [Vibrio sp. Ex25]
 gi|269968567|ref|ZP_06182570.1| RNA polymerase sigma factor [Vibrio alginolyticus 40B]
 gi|151937740|gb|EDN56590.1| sigma-70, non-essential region family [Vibrio sp. Ex25]
 gi|269826825|gb|EEZ81156.1| RNA polymerase sigma factor [Vibrio alginolyticus 40B]
          Length = 639

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 211/399 (52%), Positives = 268/399 (67%), Gaps = 11/399 (2%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N      +S K  V  E ++ +     L   + D LV +L   
Sbjct: 245 EKFNQLRSTYQNLQLAINEYG--YNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTA 302

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 303 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEK---IKRN 359

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 360 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKK 419

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 420 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD
Sbjct: 480 VHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGD 539

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 540 DEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 599

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 600 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 638



 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 29  KSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 88

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 89  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 147

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 148 INQVQSSVAEYPGTIPYIL 166


>gi|16761985|ref|NP_457602.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29143472|ref|NP_806814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|25288442|pir||AB0893 RNA polymerase sigma-70 factor [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16504288|emb|CAD07736.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139106|gb|AAO70674.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
          Length = 660

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 298 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 357

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 358 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 414

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 415 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 474

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 475 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 534

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 535 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 594

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 595 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 654

Query: 677 RSFLD 681
           RSFLD
Sbjct: 655 RSFLD 659



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|325576583|ref|ZP_08147301.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325161146|gb|EGC73261.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 629

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 206/377 (54%), Positives = 259/377 (68%), Gaps = 2/377 (0%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYG 364
           K  +S  + K    +L  +     L   + D+LV  + ++ KR+   E +L + L    G
Sbjct: 253 KHGRSGKRAKDQIAQLADIFKQFRLVPKQFDVLVLSMKNMIKRVRAEERQLQKVLVDIAG 312

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + +D F         +  WV+ A    +   K     E    L + N + +I   T ++I
Sbjct: 313 MPKDEFEALIVANGSNDTWVAKALKSTKAWAKRLPKYEERIRLSLDN-LANIEQHTNLTI 371

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + R I   V +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 372 QQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 431

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 432 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 491

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA
Sbjct: 492 REATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSA 551

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +L+  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 552 TAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 611

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS+ LRSFLD
Sbjct: 612 RKLRHPSRSETLRSFLD 628


>gi|291618943|ref|YP_003521685.1| RpoD [Pantoea ananatis LMG 20103]
 gi|291153973|gb|ADD78557.1| RpoD [Pantoea ananatis LMG 20103]
 gi|327395293|dbj|BAK12715.1| RNA polymerase sigma factor RpoD [Pantoea ananatis AJ13355]
          Length = 614

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/366 (54%), Positives = 258/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    G 
Sbjct: 251 QNLSDVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIEVCKMPKKNFITLFTGN 310

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   + A + P   W   +    D +++   ++  I  ETG++I + + I   + 
Sbjct: 311 ETNESWFKAALAMNKP---WSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQVKDINRRMS 367

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 487

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 488 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 547

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 607

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 608 LRSFLD 613



 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI 164


>gi|289676145|ref|ZP_06497035.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 438

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 213/427 (49%), Positives = 289/427 (67%), Gaps = 10/427 (2%)

Query: 259 DEDEDDSAHTLSAMEDQLR--PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
           D+DE++SA   S  ED++   P  + A      V  ++   +       +D+K ++   V
Sbjct: 17  DDDEEESADA-SDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMV 75

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQ 375
               L +L   + L   + + LVE++    +R+   E  +++L  +   + R  FL +  
Sbjct: 76  ---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFP 132

Query: 376 GRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E + I   +
Sbjct: 133 GNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRM 190

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 191 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 250

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +
Sbjct: 251 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 310

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T 
Sbjct: 311 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATR 370

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+
Sbjct: 371 EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 430

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 431 HLRSFLD 437


>gi|330831100|ref|YP_004394052.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806236|gb|AEB51435.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 618

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/378 (52%), Positives = 260/378 (68%), Gaps = 2/378 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 241 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 300

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 301 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 359

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 360 IAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 419

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++
Sbjct: 420 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 479

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P D+
Sbjct: 480 GREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADA 539

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 540 ATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 599

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSRS+ LRSFLD
Sbjct: 600 LRKLRHPSRSEVLRSFLD 617


>gi|146329704|ref|YP_001209965.1| RNA polymerase sigma-70 factor [Dichelobacter nodosus VCS1703A]
 gi|146233174|gb|ABQ14152.1| RNA polymerase sigma-70 factor [Dichelobacter nodosus VCS1703A]
          Length = 623

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/398 (51%), Positives = 274/398 (68%), Gaps = 7/398 (1%)

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           L E+++V+++L++  D    GQ    ++ K + L +++ +   + S  Q  +DL+  QL 
Sbjct: 230 LLELSQVFKKLKTALDK---GQS--LATKKNQKLHDEVKQYFVAFSFPQKTMDLMEAQLE 284

Query: 344 DISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +  + I   E  L+RL  +  G+ R  F+    G E D  WV         ++   +   
Sbjct: 285 EPMEMIHAIERRLMRLVIEKSGMPRKSFISDFPGHETDLEWVVKQSTL-RRKYAEKLKLM 343

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++ +   + +   +    G+SI + + I   +  G+  A  AK+EMVEANLRLVIS+AKK
Sbjct: 344 IEDVQAEQQKFLEVEKTYGMSIQQIKDIYRQLAVGKERAKRAKEEMVEANLRLVISIAKK 403

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 404 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIP 463

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R +  K  R+PTPEE++  + MP + +RKV KI KEPIS+ETPIGD
Sbjct: 464 VHMIETINKLNRISRMLQQKNGRDPTPEELSVAMDMPEDKIRKVWKIAKEPISMETPIGD 523

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDF+ED N +SPL++A    L E T  VLASLTPREERVLRMRFGI MNTDHTL
Sbjct: 524 DEDSHLGDFLEDSNVISPLEAATTRGLSEATNEVLASLTPREERVLRMRFGIDMNTDHTL 583

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EEVG+QF VTRERIRQIEAKA+RKL+HP+RS+ L+SFL
Sbjct: 584 EEVGRQFDVTRERIRQIEAKALRKLRHPNRSELLKSFL 621


>gi|89094383|ref|ZP_01167323.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081275|gb|EAR60507.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 616

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 196/345 (56%), Positives = 250/345 (72%), Gaps = 2/345 (0%)

Query: 338 LVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV Q+    + I + E  ++R+  Q   + R  F++   G E++  W +   +  E  + 
Sbjct: 271 LVNQVRSTIENIRNQERTIMRICTQRAKMPRKTFIKEFPGNEVNADWFNQVIESGES-YS 329

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             +   +  + + + ++    +ETGIS++E + +   +  GE  A  AKKEMVEANLRLV
Sbjct: 330 RAIKTNLIELKRAQKKLIQAEIETGISLAEIKEVNRRMSIGEARARRAKKEMVEANLRLV 389

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 390 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 449

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + VRKVLKI KEPIS+
Sbjct: 450 RTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMEMPEDKVRKVLKIAKEPISM 509

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ S LGDFIED    SP+DSA    LRE T  VLA LT RE +VLRMRFGI M
Sbjct: 510 ETPIGDDEDSSLGDFIEDTTISSPVDSATGEGLREATREVLAGLTVRESKVLRMRFGIEM 569

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR FLD
Sbjct: 570 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRGFLD 614



 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 51/138 (36%), Positives = 83/138 (60%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI+V +   D E    +E
Sbjct: 13  KELIARGKEQGYLTYSEVNDHLPQDIADPDQVEDIIRMINDMGISVSEEAPDAETLLMTE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                 +     +       D+    T DPVRMY+REMG++ELL+REGEI+IAKRIE G 
Sbjct: 73  GDSAEEADEEAVAALAAVESDAG--RTTDPVRMYMREMGTVELLTREGEISIAKRIEEGL 130

Query: 151 AMMMASLCESPLTFQALI 168
             +M+++   P T ++++
Sbjct: 131 REVMSAVACFPGTVESIL 148


>gi|94676896|ref|YP_589041.1| RNA polymerase, sigma 70 factor [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94220046|gb|ABF14205.1| RNA polymerase, sigma 70 factor [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 612

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 209/381 (54%), Positives = 266/381 (69%), Gaps = 10/381 (2%)

Query: 307 DEKSSVKCKVLKE--KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ--S 362
           D K     K ++E  KL ++     L   + D LV+ +  +  RI   E  +++L    S
Sbjct: 235 DTKGRSHAKAIEEILKLSEIFKQFHLAPKQFDYLVKNMRAVMDRIRLQERLVMKLCVDIS 294

Query: 363 YGIKRDVFLERHQGRELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
              K+D F++   G E    W   + A + P  E    V   V + L+   +++ I  ET
Sbjct: 295 KMPKKD-FIKLFAGNETSETWFKTALAMNQPWSEKLYNVDKNVHNSLQ---KLRQIEEET 350

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+SI + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 351 GLSIEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 410

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M 
Sbjct: 411 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 470

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +I REPTPEE+A+++ MP + +RKVLKI KEP+S+ETPIGD++ +HLGDFIED     P
Sbjct: 471 QEIGREPTPEELAERMFMPEDKIRKVLKIAKEPLSMETPIGDDEDTHLGDFIEDTTLELP 530

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           L+SA   +LR  T  +LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 531 LESATSESLRSATHEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFAVTRERIRQIE 590

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRS+ LRSFLD
Sbjct: 591 AKALRKLRHPSRSEVLRSFLD 611



 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 66/161 (40%), Positives = 95/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD-LEDE 86
           K ++   +++GY+T+ E+N  LP D V S+Q+ED + M+++MGI V+    D DD L DE
Sbjct: 10  KLLVTRGKEQGYLTVAEVNDLLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDILLDE 69

Query: 87  EGSEDSLDLASSASN--SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             S+   D   +A+   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  TNSDTDEDAVEAAAQVLSSV------ESEIVRTTDPVRMYMREMGTVELLTREGEINIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 124 RIEDGMTQVQCSVAEYPEAITYLLKQYDRVELGEARLSDLI 164


>gi|242240773|ref|YP_002988954.1| RNA polymerase sigma factor RpoD [Dickeya dadantii Ech703]
 gi|242132830|gb|ACS87132.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya dadantii Ech703]
          Length = 612

 Score =  385 bits (988), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 206/366 (56%), Positives = 259/366 (70%), Gaps = 8/366 (2%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + DLLV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 250 KLSEVFKQFRLVPKQFDLLVNSMRSMMDRVRTQERLIMKLCVEQCKMPKKNFMTMFTGNE 309

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVR 435
               W   + A   P  E    V  +V+ S+LK+    + I  ETG++I + + I   + 
Sbjct: 310 TSIKWFEAALAMGKPWSEKLREVTDDVERSLLKL----QQIEEETGLTIEQVKDINRRMS 365

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 485

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 486 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 545

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 546 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 605

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 606 LRSFLD 611



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 96/155 (61%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+ E P     L+   D +  G + L ++I
Sbjct: 128 NQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI 162


>gi|238918478|ref|YP_002931992.1| RNA polymerase sigma factor RpoD [Edwardsiella ictaluri 93-146]
 gi|238868046|gb|ACR67757.1| RNA polymerase sigma factor RpoD, putative [Edwardsiella ictaluri
           93-146]
          Length = 611

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 209/377 (55%), Positives = 265/377 (70%), Gaps = 8/377 (2%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA--QSYGIK 366
           +SS K +   + L ++     L   + D LV  + ++  R+   E  +++L   QS   K
Sbjct: 238 RSSGKAQEEIQNLSEIFKQFRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPK 297

Query: 367 RDVFLERHQGRELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           ++ F+    G E    W   + A   P GE    +  EV+  L+   ++  I  ETG++I
Sbjct: 298 KN-FITLFTGNETSITWFDAALAMGKPWGEKLKDMREEVERSLQ---KLHQIEEETGLTI 353

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 354 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 413

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 414 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 473

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA
Sbjct: 474 REPTPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 533

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 534 TSESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS+ LRSFLD
Sbjct: 594 RKLRHPSRSEVLRSFLD 610



 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 60/158 (37%), Positives = 90/158 (56%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               ++    +A  +   L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  ----NIADEDAAEAAVQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +      L ++I
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLI 162


>gi|322613615|gb|EFY10556.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621208|gb|EFY18066.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624271|gb|EFY21105.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627991|gb|EFY24780.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633109|gb|EFY29851.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636314|gb|EFY33022.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322643488|gb|EFY40050.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322644793|gb|EFY41328.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322648602|gb|EFY45049.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322653654|gb|EFY49980.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657762|gb|EFY54030.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663863|gb|EFY60062.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322669126|gb|EFY65277.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672881|gb|EFY68988.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322678129|gb|EFY74192.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681305|gb|EFY77338.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322687765|gb|EFY83732.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195577|gb|EFZ80754.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199742|gb|EFZ84832.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202510|gb|EFZ87550.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323208002|gb|EFZ92948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323212446|gb|EFZ97263.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215072|gb|EFZ99820.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222802|gb|EGA07167.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323224117|gb|EGA08410.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230441|gb|EGA14559.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235207|gb|EGA19293.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323239248|gb|EGA23298.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323244394|gb|EGA28400.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323247011|gb|EGA30977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323253507|gb|EGA37336.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323256187|gb|EGA39923.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262637|gb|EGA46193.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323267267|gb|EGA50751.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269331|gb|EGA52786.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 615

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVSEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 489

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 490 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 549

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 609

Query: 677 RSFLD 681
           RSFLD
Sbjct: 610 RSFLD 614



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|33340521|gb|AAQ14856.1| RpoD [Pseudomonas fluorescens]
          Length = 616

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 264/363 (72%), Gaps = 4/363 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + + LVE++    +R+   E  +++L  +   + R  F+ +  G E+
Sbjct: 255 LAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFVRQFPGNEV 314

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE
Sbjct: 315 DESWTDALAKG--KAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGE 372

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 373 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 432

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 433 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEM 492

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+
Sbjct: 493 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLS 552

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRS
Sbjct: 553 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRS 612

Query: 679 FLD 681
           FLD
Sbjct: 613 FLD 615



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 56/137 (40%), Positives = 85/137 (62%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D     D
Sbjct: 12  KELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|72383848|ref|YP_293202.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72123191|gb|AAZ65345.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 624

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 243/664 (36%), Positives = 360/664 (54%), Gaps = 69/664 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGD-----D 82
           + +I L R+RGY+T  ++N  LP +   +  ME  V+  S+MG+ V     D D     D
Sbjct: 15  RALIALGRERGYLTHADINDHLPDNFTQTAAMETIVSTFSDMGVTVYEQAPDADTLLLSD 74

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  + A+ S+V      DS    T DPVR+Y+REMG+ ELL+R GEI I
Sbjct: 75  TAPAGASDDQADEEAEAALSTV------DSEFGRTTDPVRLYMREMGASELLTRAGEIEI 128

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P     ++   D +  G   + E++               +G
Sbjct: 129 AKRIEGGLQGMIQAIAACPSVVSTMLADVDRIVAGELRIDELV---------------YG 173

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             DDV ++E      A  S D   + D+  ++   D  +++ D 
Sbjct: 174 IS----------------DDVNDSE-----IALASDDVHVEADASDDDPVGD--DVEPDA 210

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            DS    +A  +QL    + +L   A V      L D  V G+     S   + L+ K+ 
Sbjct: 211 GDSEKANAARLEQL---TLDSLAIFARVRALFEQLPDAPVTGKA---RSAAVEQLRSKIQ 264

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
             +  +      ID L   +++    +   E  +L +A    G+ R VF+E   G E D 
Sbjct: 265 SELAPIRFTAKTIDRLCASVHEQLTEVRAIERSILEIAVDRCGMPRKVFVESFPGNETDL 324

Query: 382 HWVS----YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            W S     ++ F     ++  A +       + ++  I  +  + + +F+ I   +   
Sbjct: 325 KWTSKMAATSRQFGAALKRHLPAIQAG-----QQKLIDIEAKVTLPLQQFKQINRQMSAA 379

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +   AK+E++EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFS
Sbjct: 380 ELKMRQAKRELIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFS 439

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WWV+QA+TR++ADQ+ TIR+PVHM + I+K+ R +R    +  RE  P  +A+++ 
Sbjct: 440 TYATWWVRQAVTRALADQARTIRVPVHMVEMINKLNRISRDFRQQTGREAHPAVLAERME 499

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  E VR +L+  ++P+SLETP+GD+  + LGD IED +A SP ++AI A++R      L
Sbjct: 500 MSEEKVRSILRSARQPVSLETPVGDDADATLGDMIEDVSASSPAEAAIHADMRAAIDEAL 559

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L+PRE +VLRMRFG+   +D TLEEV KQF VTRERIRQIE++A+RKL HPSR+ KLR
Sbjct: 560 DGLSPREAKVLRMRFGLDTTSDRTLEEVSKQFDVTRERIRQIESQAMRKLLHPSRADKLR 619

Query: 678 SFLD 681
            FL+
Sbjct: 620 PFLE 623


>gi|86148095|ref|ZP_01066395.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|218708434|ref|YP_002416055.1| RNA polymerase sigma factor RpoD [Vibrio splendidus LGP32]
 gi|85834082|gb|EAQ52240.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|218321453|emb|CAV17405.1| RNA polymerase sigma factor rpoD (Sigma-70) [Vibrio splendidus
           LGP32]
          Length = 614

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 212/404 (52%), Positives = 270/404 (66%), Gaps = 21/404 (5%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+++   ++++    +     L   + D LV +L 
Sbjct: 220 EKFTALRTSYQNRQLAINEYGHESPKATLATTMMQD----VFKEFRLTPKQFDYLVNELR 275

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
               R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 276 TSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 333

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            E D    IR  I+ + +   ET +++   + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 334 NEHD----IRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVI 389

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 390 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 449

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+E
Sbjct: 450 TIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISME 509

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LTPRE +VLRMRFGI MN
Sbjct: 510 TPIGDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMN 569

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 570 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 613



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 55/138 (39%), Positives = 86/138 (62%), Gaps = 1/138 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D   ++
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  ++   A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  DDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 129

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P T   ++
Sbjct: 130 NTVQLSVAEYPGTIPYIL 147


>gi|307129360|ref|YP_003881376.1| RNA polymerase sigma-70 (sigma D) factor [Dickeya dadantii 3937]
 gi|306526889|gb|ADM96819.1| RNA polymerase, sigma 70 (sigma D) factor [Dickeya dadantii 3937]
          Length = 611

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 201/363 (55%), Positives = 257/363 (70%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + DLLV  +  +  R+   E ++++L  +   + +  F+    G E
Sbjct: 249 KLSEVFKQFRLVPKQFDLLVNNMRAMMDRVRAQERQIMKLCVELCKMPKKNFVTLFTGNE 308

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W   A    +   +     E D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 309 TNRKWFDAALSMGKPWCEKLREVE-DDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGE 367

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 368 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 428 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 487

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 488 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 547

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 548 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607

Query: 679 FLD 681
           FLD
Sbjct: 608 FLD 610



 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 96/155 (61%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+ E P     L+   D +  G + L ++I
Sbjct: 128 NQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI 162


>gi|270263179|ref|ZP_06191449.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
 gi|270042867|gb|EFA15961.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
          Length = 648

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/363 (55%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 286 KLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFAGNE 345

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W   A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 346 TSNSWFEAALAMAKP-WSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 404

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 405 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 464

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 465 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 524

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 525 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 584

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 585 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 644

Query: 679 FLD 681
           FLD
Sbjct: 645 FLD 647



 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 96/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 46  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 105

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 106 NSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 159

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 160 RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 200


>gi|197335189|ref|YP_002157048.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
 gi|197316679|gb|ACH66126.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
          Length = 613

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 256/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRE 378
           +L  +     L   + D LV+++ D   R+   E  ++R+   YG + +  F+    G E
Sbjct: 251 ELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMPKKSFIALFTGNE 310

Query: 379 LDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W +   A D P  E       E D I +   ++ SI  ETG+ +   + I   +  
Sbjct: 311 SSDEWFNEIMASDKPYVE--RLQRYEED-IRRSIAKLDSIEKETGLPVENIKDISRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  V
Sbjct: 488 QMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPVDSATSTSLKFATNDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 93/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV    D DD+    
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDMS--L 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 68  NDDDAVTDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D++      L +II
Sbjct: 127 EGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDII 164


>gi|148979373|ref|ZP_01815479.1| RNA polymerase sigma factor RpoD [Vibrionales bacterium SWAT-3]
 gi|145961809|gb|EDK27102.1| RNA polymerase sigma factor RpoD [Vibrionales bacterium SWAT-3]
          Length = 614

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 209/401 (52%), Positives = 269/401 (67%), Gaps = 15/401 (3%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+ +   ++++    +     L   + D LV +L 
Sbjct: 220 EKFTALRTSYQNRQLAINEYGHESPKAMLATTMMQD----VFKEFRLTPKQFDYLVNELR 275

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
           +   R+   E  ++R    YG + +  F+    G E    W+    A D P  E    + 
Sbjct: 276 NSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEK---IK 332

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              + I +   ++  I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+A
Sbjct: 333 RHENDIRRSIQKLDMIEKETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIA 392

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 393 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 452

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPI
Sbjct: 453 IPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPI 512

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD++ SHLGDFIED     PLDSA   +LR  T  VLA LTPRE +VLRMRFGI MNTDH
Sbjct: 513 GDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDH 572

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 573 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 613



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 60/167 (35%), Positives = 97/167 (58%), Gaps = 3/167 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D   ++
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  ++   A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  DDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
             +  S+ E P T   ++   D +      L ++I+    + P+  G
Sbjct: 130 NTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLIN--GFVDPDDDG 174


>gi|84394590|ref|ZP_00993293.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84374781|gb|EAP91725.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 573

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 212/404 (52%), Positives = 270/404 (66%), Gaps = 21/404 (5%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+++   ++++    +     L   + D LV +L 
Sbjct: 179 EKFTALRTSYQNRQLAINEYGHESPKATLATTMMQD----VFKEFRLTPKQFDYLVNELR 234

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
               R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 235 TSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 292

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            E D    IR  I+ + +   ET +++   + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 293 NEHD----IRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVI 348

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 349 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 408

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+E
Sbjct: 409 TIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISME 468

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LTPRE +VLRMRFGI MN
Sbjct: 469 TPIGDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMN 528

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 529 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 572



 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 43/106 (40%), Positives = 65/106 (61%), Gaps = 1/106 (0%)

Query: 64  EDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ED + M+++MGI VV+   D +D   ++D  ++   A+ ++       +S    T DPVR
Sbjct: 1   EDIIQMINDMGIKVVETAPDADDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVR 60

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           MY+REMG++ELL+REGEI IAKRIE G   +  S+ E P T   ++
Sbjct: 61  MYMREMGTVELLTREGEIDIAKRIEDGINTVQLSVAEYPGTIPYIL 106


>gi|262199546|ref|YP_003270755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082893|gb|ACY18862.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 697

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/393 (51%), Positives = 266/393 (67%), Gaps = 17/393 (4%)

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           L D  +   K +K     +  KE + + +  L LN+S +D +V  L  I  ++   E E+
Sbjct: 313 LADRTLGEVKKKKYRDSIQANKEAMFEDLSELQLNKSVVDRMVANLKAIIVKLDRAETEI 372

Query: 357 LRLAQSYGIK--------RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
             +    G+         RD+     + R +   +     DF   E          +I  
Sbjct: 373 RAVENRLGMPAKEIRKTLRDMKASATKTRSVGKRFALTVDDFDAFEA---------AIKN 423

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
            + +IK +  E   S+ E R     +  GE  A  AK E+VEANLRLV+S+AKKYTNRGL
Sbjct: 424 AQKKIKVLEEECRSSVEELRQTFREMSDGERMAERAKSELVEANLRLVVSIAKKYTNRGL 483

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 484 QFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIET 543

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R +  ++ REPTPEEIA+++ +P++ VRKVLKI KEPISLETPIG+E+ SHL
Sbjct: 544 INKLVRTSRYLVQELGREPTPEEIAERMELPLDKVRKVLKIAKEPISLETPIGEEEDSHL 603

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+  SP D+ I  NL E T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ 
Sbjct: 604 GDFIEDKSVTSPSDAVISVNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQD 663

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L++F++
Sbjct: 664 FEVTRERIRQIEAKALRKLRHPSRSKRLKAFVE 696



 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 64/164 (39%), Positives = 91/164 (55%), Gaps = 14/164 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD----------GD 81
           KK+I+L R +G+VT +E+N  +P D +SSEQ++  ++ L   GI++VD           D
Sbjct: 114 KKLIELGRSKGFVTYDEVNDHMPEDVISSEQIDSWLSALGEEGIDIVDSAASARKKAPAD 173

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D +   G   SL+                 S  R T DPVRMYLR+MGS+ LL+REGE+ 
Sbjct: 174 DDDSSGGKVASLNDDKELEKEEEEEDY---SYSR-TSDPVRMYLRKMGSVSLLTREGEVE 229

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IAKRIE G   M+A++  S +  + LI    +L DG    +EII
Sbjct: 230 IAKRIEEGERRMLAAVLNSSVAVEELIDLGKQLADGKARAKEII 273


>gi|169794936|ref|YP_001712729.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter baumannii AYE]
 gi|184159289|ref|YP_001847628.1| DNA-directed RNA polymerase, sigma subunit [Acinetobacter baumannii
           ACICU]
 gi|213157659|ref|YP_002320457.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii
           AB0057]
 gi|215482482|ref|YP_002324668.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB307-0294]
 gi|239502295|ref|ZP_04661605.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB900]
 gi|260557301|ref|ZP_05829517.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii ATCC
           19606]
 gi|301346958|ref|ZP_07227699.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB056]
 gi|301513036|ref|ZP_07238273.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB058]
 gi|301596278|ref|ZP_07241286.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB059]
 gi|332854224|ref|ZP_08435244.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013150]
 gi|332866334|ref|ZP_08436939.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013113]
 gi|332872549|ref|ZP_08440518.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6014059]
 gi|169147863|emb|CAM85726.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter baumannii AYE]
 gi|183210883|gb|ACC58281.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii ACICU]
 gi|193078173|gb|ABO13119.2| sigma D (sigma 70) factor of RNA polymerase major sigma factor
           during exponential growth [Acinetobacter baumannii ATCC
           17978]
 gi|213056819|gb|ACJ41721.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii
           AB0057]
 gi|213988184|gb|ACJ58483.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB307-0294]
 gi|260409407|gb|EEX02709.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii ATCC
           19606]
 gi|322509200|gb|ADX04654.1| rpoD [Acinetobacter baumannii 1656-2]
 gi|323519229|gb|ADX93610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii TCDC-AB0715]
 gi|332728149|gb|EGJ59537.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013150]
 gi|332734682|gb|EGJ65786.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013113]
 gi|332739235|gb|EGJ70093.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6014059]
          Length = 628

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 201/379 (53%), Positives = 260/379 (68%), Gaps = 1/379 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           +K  ++S +     E L  +           D++ E +    ++I  NE E++R A   G
Sbjct: 249 EKHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRG 308

Query: 365 -IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + R+ F      +E +P W+         E K  +      +L  + +I  I  E G++
Sbjct: 309 RMDRNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLN 368

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           +SE + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 369 VSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 428

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++
Sbjct: 429 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 488

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+
Sbjct: 489 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDA 548

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A    L+E T  VL +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 549 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 608

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HPSRS+ LRSFL+ 
Sbjct: 609 LRKLRHPSRSEHLRSFLEN 627


>gi|169632612|ref|YP_001706348.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter baumannii SDF]
 gi|169151404|emb|CAP00133.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter baumannii]
          Length = 630

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 201/379 (53%), Positives = 260/379 (68%), Gaps = 1/379 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           +K  ++S +     E L  +           D++ E +    ++I  NE E++R A   G
Sbjct: 251 EKHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRG 310

Query: 365 -IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + R+ F      +E +P W+         E K  +      +L  + +I  I  E G++
Sbjct: 311 RMDRNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLN 370

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           +SE + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 371 VSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 430

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++
Sbjct: 431 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 490

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+
Sbjct: 491 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDA 550

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A    L+E T  VL +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 551 ATSKGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 610

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HPSRS+ LRSFL+ 
Sbjct: 611 LRKLRHPSRSEHLRSFLEN 629


>gi|283787203|ref|YP_003367068.1| RNA polymerase sigma-70 factor [Citrobacter rodentium ICC168]
 gi|282950657|emb|CBG90329.1| RNA polymerase sigma-70 factor [Citrobacter rodentium ICC168]
          Length = 614

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 311

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   ++  I  ETG++I + + I   +  
Sbjct: 312 TSETWFNAAIAMNKPWSEKLHDVADEVHRGLQ---KLHQIEEETGLTIEQVKDINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 489 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|94499953|ref|ZP_01306488.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
 gi|94427811|gb|EAT12786.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
          Length = 606

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 201/368 (54%), Positives = 258/368 (70%), Gaps = 10/368 (2%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           EKL +L   + L+    D LV    D    I   E +++ +  +   +KR  F++  QG 
Sbjct: 243 EKLAELFAPIKLSPKYFDDLVGTARDNLDFIRVQERQIMVICTRKAKMKRQEFIKSFQGN 302

Query: 378 ELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           E +  W+    +  KD+ +      +      + + + +I+ +    G+ IS+ + I   
Sbjct: 303 EGNDSWIDDLINAGKDYSQ-----IIENHGYDLKRAQKKIRQVKDRVGLEISDIKEINRR 357

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 358 VSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 417

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A
Sbjct: 418 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELA 477

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A +  L + T
Sbjct: 478 ERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNGHSPIDTATETGLTDAT 537

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 538 RSVLSGLTARESKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 597

Query: 674 KKLRSFLD 681
             LRSFLD
Sbjct: 598 DHLRSFLD 605



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 52/138 (37%), Positives = 83/138 (60%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++I   +++GY+T  ++N  LP D  + EQ+ED + M++++GI V +   D ++    E
Sbjct: 10  KELIAKGKEQGYLTYAQVNDHLPDDIATPEQVEDIIRMINDIGITVSEVAPDADELNMGE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            + D A+    ++       D     T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  VTTDEAAIEEAAAALAAVETDVG--RTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +MA+L   P   + ++
Sbjct: 128 REVMAALSYFPGAVRTVL 145


>gi|308050979|ref|YP_003914545.1| RNA polymerase, sigma 70 subunit, RpoD [Ferrimonas balearica DSM
           9799]
 gi|307633169|gb|ADN77471.1| RNA polymerase, sigma 70 subunit, RpoD [Ferrimonas balearica DSM
           9799]
          Length = 610

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 198/374 (52%), Positives = 264/374 (70%), Gaps = 2/374 (0%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKR 367
           + S++  +L  +L +L     L   + D+LV  +  +  R+   E  ++++  +   + +
Sbjct: 237 RDSLEAAMLITRLSELFKEFRLVPKQFDVLVNNMRSMMDRVRVQERLIMKMCVEQAKMPK 296

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             FL+   G E +  W+    D  +  +   +    + + +   ++  I  ETG+SI++ 
Sbjct: 297 KNFLKLFAGHESETAWLQAEIDAGKS-YSAALGEHQEELHRCIQKLAQIQEETGLSIAKI 355

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 356 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 415

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 416 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 475

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   
Sbjct: 476 TPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAQPVDSATAE 535

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 536 SLKAATAEVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 595

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ L+SFLD
Sbjct: 596 RHPSRSEILKSFLD 609


>gi|170723972|ref|YP_001751660.1| RNA polymerase sigma factor RpoD [Pseudomonas putida W619]
 gi|169761975|gb|ACA75291.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida W619]
          Length = 616

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/365 (54%), Positives = 260/365 (71%), Gaps = 4/365 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  L   + L   + D+LVE++ D   R+   E  +++L  +   + R  FL      
Sbjct: 253 QALADLFMPIKLVPKQFDVLVERVRDALARLRQQERAIMQLCVRDARMPRADFLRLFPSN 312

Query: 378 ELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E D  W    AK     +W   +  +  +I+  + ++  +  ETG++++E + I   +  
Sbjct: 313 ETDQTWSGDLAKR--NTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKDINRRMSI 370

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 490

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  V
Sbjct: 491 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 550

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ L
Sbjct: 551 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 610

Query: 677 RSFLD 681
           RSFLD
Sbjct: 611 RSFLD 615



 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     +
Sbjct: 12  KELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAE 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDYIL 147


>gi|283836397|ref|ZP_06356138.1| RNA polymerase sigma factor RpoD [Citrobacter youngae ATCC 29220]
 gi|291067770|gb|EFE05879.1| RNA polymerase sigma factor RpoD [Citrobacter youngae ATCC 29220]
          Length = 615

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/364 (54%), Positives = 256/364 (70%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           +KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G 
Sbjct: 252 QKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGN 311

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E    W + A    +  W   +    D + +   +++ I  ETG++I + + I   +  G
Sbjct: 312 ETSETWFNAAIAMNKP-WSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKDINRRMSIG 370

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 371 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 431 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 490

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 491 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVL 550

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 551 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 610

Query: 678 SFLD 681
           SFLD
Sbjct: 611 SFLD 614



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  TSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|332994458|gb|AEF04513.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 608

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 188/312 (60%), Positives = 240/312 (76%), Gaps = 1/312 (0%)

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E    W++ A       + + +A   + I +  +++  +  ETG+ I++ + 
Sbjct: 297 FIKAFAGNETSSAWLTKAIK-ANAAYSDALAVNKEEIERCISKMNQVEQETGLVIADIKD 355

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 356 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 415

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP
Sbjct: 416 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 475

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+++++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   + PLDSA   +L
Sbjct: 476 EELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSL 535

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+H
Sbjct: 536 KDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 595

Query: 670 PSRSKKLRSFLD 681
           PSRS++LRSFLD
Sbjct: 596 PSRSEQLRSFLD 607



 Score = 91.3 bits (225), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE   ++
Sbjct: 10  KLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDSDELLMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  ATADEDAAEAAAQALATVESEIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEDGIN 128

Query: 152 MMMASLCESPLTFQALI 168
            +  S+ E P     L+
Sbjct: 129 QVQCSVAEYPEAITYLL 145


>gi|205354126|ref|YP_002227927.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273907|emb|CAR38909.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
          Length = 615

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 489

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+E PIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 490 LMPEDKIRKVLKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 549

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 609

Query: 677 RSFLD 681
           RSFLD
Sbjct: 610 RSFLD 614



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|156932573|ref|YP_001436489.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156530827|gb|ABU75653.1| hypothetical protein ESA_00355 [Cronobacter sakazakii ATCC BAA-894]
          Length = 614

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  ++++  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKNFITLFTGNE 311

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA +V   L+   +++ I  ETG++I + + I   +  
Sbjct: 312 TSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQ---KLQQIEEETGLTIEQVKDINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 489 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 95/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|50119628|ref|YP_048795.1| RNA polymerase sigma factor RpoD [Pectobacterium atrosepticum
           SCRI1043]
 gi|49610154|emb|CAG73594.1| RNA polymerase sigma-70 factor [Pectobacterium atrosepticum
           SCRI1043]
          Length = 611

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/364 (56%), Positives = 257/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E 
Sbjct: 250 LSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTSNET 309

Query: 380 DPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           +  W + A     P  E  N VA +V   L+   ++K I  ETG++I + + I   +  G
Sbjct: 310 NNSWFAAAVAMGKPWSEKLNDVAEDVTRSLQ---KLKQIEEETGLTIEQVKDINRRMSIG 366

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 367 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 426

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 427 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 486

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 487 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 546

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 547 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 606

Query: 678 SFLD 681
           SFLD
Sbjct: 607 SFLD 610



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDADEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|324115354|gb|EGC09318.1| RNA polymerase sigma proteinRpoD [Escherichia fergusonii B253]
          Length = 613

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   ++  I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVADEVHRSLQ---KLHQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|237809411|ref|YP_002893851.1| RNA polymerase, sigma 70 subunit, RpoD [Tolumonas auensis DSM 9187]
 gi|237501672|gb|ACQ94265.1| RNA polymerase, sigma 70 subunit, RpoD [Tolumonas auensis DSM 9187]
          Length = 617

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 199/383 (51%), Positives = 263/383 (68%), Gaps = 4/383 (1%)

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
           +A+     +    K ++L+  L  +     L   + D LV  + ++ +R+   E  +LR 
Sbjct: 237 DAIKANGRDSDLAKVQILE--LANVFKEFRLVPKQFDRLVNSMREMMERVRVQERLILRY 294

Query: 360 AQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
              Y  + +  F+      E    W  +AK   +  W   +A   + + +   +++ +  
Sbjct: 295 CVEYAKMPKKNFVTAFTNNESSNGWFEFAKSSGK-PWSTALANMDEDVQRSIQKLQQVEQ 353

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETG+SI++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 354 ETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 413

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 414 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 473

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    
Sbjct: 474 MLQEMGREPNPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLA 533

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P D+A   +L+  T  VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 534 LPADAATSESLKAATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 593

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 594 IEAKALRKLRHPSRSEVLRSFLD 616


>gi|332163001|ref|YP_004299578.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318604173|emb|CBY25671.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325667231|gb|ADZ43875.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 612

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 207/394 (52%), Positives = 268/394 (68%), Gaps = 5/394 (1%)

Query: 291 YRELRSLQDNA-VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           + ELR   +NA +  +K+ +S         KL ++     L   + D LV  +  +  R+
Sbjct: 220 FSELREQYENARLEIKKNGRSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRV 279

Query: 350 MHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
              E  +++L  +   + +  F+      E    W  +A     G+ W   +    D + 
Sbjct: 280 RTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTW--FAAAIAMGKPWSEKLKDVSDDVQ 337

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 338 RSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 397

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 398 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 457

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 458 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 517

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 518 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 577

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 578 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|218550316|ref|YP_002384107.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ATCC
           35469]
 gi|218357857|emb|CAQ90501.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia fergusonii
           ATCC 35469]
 gi|325498620|gb|EGC96479.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ECD227]
          Length = 613

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   ++  I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVADEVHRSLQ---KLHQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|152978401|ref|YP_001344030.1| RNA polymerase sigma factor RpoD [Actinobacillus succinogenes 130Z]
 gi|150840124|gb|ABR74095.1| RNA polymerase, sigma 70 subunit, RpoD [Actinobacillus succinogenes
           130Z]
          Length = 623

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 209/398 (52%), Positives = 271/398 (68%), Gaps = 8/398 (2%)

Query: 289 EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E +  LR   D  +    K  + S K +   + L ++     L   + D+LV  +  + K
Sbjct: 228 EKFYALRDQHDKTIATIAKHGRGSAKAREQMKALSEIFTQFRLVPRQFDVLVIPMRKMMK 287

Query: 348 RIMHNEGELLRLAQSYG-IKRDVFLERHQ-GRELDPHWVS--YAKDFPEGEWKNFVACEV 403
           RI   E ++ R A  Y  + +D F++    G+E +  W++       P  E    +A   
Sbjct: 288 RIRAEERQIQRWAVDYARMPKDEFVKVFSTGKETNDAWLTKLLGGKKPYAEK---LAKYA 344

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D+I      ++++  E  ++I + R+I   + +GE +A  AKKEMVEANLRLVIS+AKKY
Sbjct: 345 DNIRASIARLQNLEQEAHLTIEQIRNIGDRISQGELKARRAKKEMVEANLRLVISIAKKY 404

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 405 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 464

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+
Sbjct: 465 HMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDD 524

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +VLRMRFGI MNTDHTLE
Sbjct: 525 DDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLE 584

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 585 EVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|88798840|ref|ZP_01114422.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778320|gb|EAR09513.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 614

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 191/321 (59%), Positives = 246/321 (76%), Gaps = 2/321 (0%)

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           ++  + R  F++   G E +  W++   + P+   + F   EV+ + + + ++++I   T
Sbjct: 295 RTLNMPRKAFIDAFVGHETEDEWLNELLENPKYADEAF-RYEVE-LRRAQRKLRNIQKNT 352

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GI+++E + I   +  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 353 GITLAEVKDIHRRISIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M 
Sbjct: 413 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REPTPEE+A+++ MP + +RKVLKI+KEPISLETPIGD++ S LGDFIED   + P
Sbjct: 473 QEMGREPTPEELAERMDMPEDKIRKVLKISKEPISLETPIGDDEDSSLGDFIEDNTMILP 532

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++SA    LR+ TT VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 533 VNSATSTGLRDATTEVLAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRS  LRSF+D
Sbjct: 593 AKALRKLRHPSRSDHLRSFID 613



 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 55/141 (39%), Positives = 85/141 (60%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K++I   +++GY+T  E+N  LP +  S +Q+ED +AM++++GI V     D D L   E
Sbjct: 12  KELIAKGKEQGYLTFAEVNDHLPEEINSPDQVEDIIAMINDIGIEVFEQAPDADQLLLSE 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S+ S D  ++   ++       D+    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 72  -SDQSTDEDATEEAAAALAAVETDTG--RTTDPVRMYMREMGTVELLTREGEIVIAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +M ++   P    ++I
Sbjct: 129 EGTREVMQAMAFYPGVIDSMI 149


>gi|59712861|ref|YP_205637.1| RNA polymerase sigma factor RpoD [Vibrio fischeri ES114]
 gi|59480962|gb|AAW86749.1| RNA polymerase, sigma-70 (sigma-D) factor [Vibrio fischeri ES114]
          Length = 613

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/366 (55%), Positives = 256/366 (69%), Gaps = 8/366 (2%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRE 378
           +L  +     L   + D LV+++ D   R+   E  ++R+   YG + +  F+    G E
Sbjct: 251 ELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMPKKSFIALFTGNE 310

Query: 379 LDPHWVS--YAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVR 435
               W +   A D P  E       ++  SI K+     SI  ETG+ +   + I   + 
Sbjct: 311 SSDEWFNEIMASDKPYVERLQRYEEDIRRSIAKL----DSIEKETGLPVENIKDISRRMS 366

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A++
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAER 486

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  
Sbjct: 487 MQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPVDSATSTSLKFATND 546

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 547 VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 606

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 607 LRSFLD 612



 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 63/170 (37%), Positives = 96/170 (56%), Gaps = 9/170 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV    D DD+    
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDMS--L 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 68  NDDDAVTDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            G   +  S+ E P     L+   D++      L +II     + P   G
Sbjct: 127 EGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIIS--GFVDPNDDG 174


>gi|326629245|gb|EGE35588.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 660

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 298 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 357

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 358 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 414

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 415 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 474

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 475 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 534

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+E PIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 535 LMPEDKIRKVLKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 594

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 595 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 654

Query: 677 RSFLD 681
           RSFLD
Sbjct: 655 RSFLD 659



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|167031434|ref|YP_001666665.1| RNA polymerase sigma factor RpoD [Pseudomonas putida GB-1]
 gi|166857922|gb|ABY96329.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida GB-1]
          Length = 616

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 199/365 (54%), Positives = 260/365 (71%), Gaps = 4/365 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  L   + L   + ++LVE++ D   R+   E  +++L  +   + R  FL      
Sbjct: 253 QALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSN 312

Query: 378 ELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E D  W    AK     +W   +  +  +I+  + ++  +  ETG++++E + I   +  
Sbjct: 313 ETDQTWSGDLAKR--NTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSI 370

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 490

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  V
Sbjct: 491 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 550

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ L
Sbjct: 551 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 610

Query: 677 RSFLD 681
           RSFLD
Sbjct: 611 RSFLD 615



 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     +
Sbjct: 12  KELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAE 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDYIL 147


>gi|123443868|ref|YP_001007839.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090829|emb|CAL13711.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 612

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 207/394 (52%), Positives = 268/394 (68%), Gaps = 5/394 (1%)

Query: 291 YRELRSLQDNA-VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           + ELR   +NA +  +K+ +S         KL ++     L   + D LV  +  +  R+
Sbjct: 220 FSELREQYENARLEIKKNGRSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRV 279

Query: 350 MHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
              E  +++L  +   + +  F+      E    W  +A     G+ W   +    D + 
Sbjct: 280 RTQERIIMKLCVEQCKMPKKNFVTLFTSNETSDTW--FAAAIAMGKPWSEKLKDVSDDVQ 337

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 338 RSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 397

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 398 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 457

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 458 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 517

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 518 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 577

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 578 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|27364091|ref|NP_759619.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus CMCP6]
 gi|320157475|ref|YP_004189854.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus MO6-24/O]
 gi|27360209|gb|AAO09146.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus CMCP6]
 gi|319932787|gb|ADV87651.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus MO6-24/O]
          Length = 624

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 208/403 (51%), Positives = 272/403 (67%), Gaps = 9/403 (2%)

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            AL++  ++    ++LQ  AVN    E  S +     E ++ +     L   + D LV +
Sbjct: 227 MALEKFTQLRNSYQNLQ-LAVNEHGRE--SAQTAQAHELMLDVFKEFRLTPKQFDHLVNE 283

Query: 342 LYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNF 398
           L     R+   E  +++ A     + +  F+    G E +  W+    A D P   +   
Sbjct: 284 LRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGNESNEEWLDQILASDKP---YVEK 340

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + I +   ++++I  ET +S++  + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 341 IKLHEEDIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVIS 400

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 401 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 460

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ET
Sbjct: 461 IRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMET 520

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNT
Sbjct: 521 PIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREAKVLRMRFGIDMNT 580

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 581 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 623



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 87/141 (61%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV    D DDL    
Sbjct: 10  KLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLA--L 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 68  SDETNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   + +S+ E P T   ++
Sbjct: 127 DGINQVQSSVAEYPGTIPYIL 147


>gi|238789198|ref|ZP_04632986.1| RNA polymerase sigma factor rpoD [Yersinia frederiksenii ATCC
           33641]
 gi|238722730|gb|EEQ14382.1| RNA polymerase sigma factor rpoD [Yersinia frederiksenii ATCC
           33641]
          Length = 612

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 207/394 (52%), Positives = 268/394 (68%), Gaps = 5/394 (1%)

Query: 291 YRELRSLQDNA-VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           + ELR   +NA +  +K+ +S         KL ++     L   + D LV  +  +  R+
Sbjct: 220 FSELREQYENARLEIKKNGRSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRV 279

Query: 350 MHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
              E  +++L  +   + +  F+      E    W  +A     G+ W   +    D + 
Sbjct: 280 RTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTW--FAAAIAMGKPWSEKLKDVSDDVQ 337

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 338 RSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 397

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 398 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 457

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 458 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 517

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 518 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 577

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 578 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|317049603|ref|YP_004117251.1| RNA polymerase,sigma 70 subunit,RpoD [Pantoea sp. At-9b]
 gi|316951220|gb|ADU70695.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. At-9b]
          Length = 614

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 200/366 (54%), Positives = 258/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L ++     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    G 
Sbjct: 251 QNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERIIMKLCVELCKMPKKNFITLFTGN 310

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W   + A + P   W   +    D +++   ++  I  ETG++I + + I   + 
Sbjct: 311 ETSESWFKAALAMNKP---WSEKLLEVQDDVMRCLQKLLQIEEETGLTIEQVKDINRRMS 367

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 487

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 488 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 547

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 607

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 608 LRSFLD 613



 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 94/155 (60%), Gaps = 1/155 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NSADTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+ E P     L+   D +  G + L ++I
Sbjct: 130 NQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI 164


>gi|1072030|gb|AAB60181.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 603

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 241 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 300

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 301 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 357

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 358 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 417

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 418 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 477

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 478 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 537

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 538 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 597

Query: 677 RSFLD 681
           RSFLD
Sbjct: 598 RSFLD 602



 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESQIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|91212497|ref|YP_542483.1| RNA polymerase sigma factor RpoD [Escherichia coli UTI89]
 gi|117625379|ref|YP_855524.1| RNA polymerase sigma factor RpoD [Escherichia coli APEC O1]
 gi|218560154|ref|YP_002393067.1| RNA polymerase sigma factor RpoD [Escherichia coli S88]
 gi|218691372|ref|YP_002399584.1| RNA polymerase sigma factor RpoD [Escherichia coli ED1a]
 gi|227887792|ref|ZP_04005597.1| RNA polymerase sigma factor RpoD [Escherichia coli 83972]
 gi|237706170|ref|ZP_04536651.1| RNA polymerase sigma factor RpoD [Escherichia sp. 3_2_53FAA]
 gi|300973231|ref|ZP_07172070.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 45-1]
 gi|301048094|ref|ZP_07195132.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 185-1]
 gi|306816579|ref|ZP_07450711.1| RNA polymerase sigma factor RpoD [Escherichia coli NC101]
 gi|331648869|ref|ZP_08349957.1| RNA polymerase sigma factor RpoD [Escherichia coli M605]
 gi|331659358|ref|ZP_08360300.1| RNA polymerase sigma factor RpoD (Sigma-70) [Escherichia coli
           TA206]
 gi|91074071|gb|ABE08952.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
           high temperatures [Escherichia coli UTI89]
 gi|115514503|gb|ABJ02578.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
           high temperatures [Escherichia coli APEC O1]
 gi|218366923|emb|CAR04694.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli S88]
 gi|218428936|emb|CAR09739.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli ED1a]
 gi|226899210|gb|EEH85469.1| RNA polymerase sigma factor RpoD [Escherichia sp. 3_2_53FAA]
 gi|227835188|gb|EEJ45654.1| RNA polymerase sigma factor RpoD [Escherichia coli 83972]
 gi|281180121|dbj|BAI56451.1| RNA polymerase sigma factor RpoD [Escherichia coli SE15]
 gi|294493374|gb|ADE92130.1| RNA polymerase sigma factor RpoD [Escherichia coli IHE3034]
 gi|300300014|gb|EFJ56399.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 185-1]
 gi|300410811|gb|EFJ94349.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 45-1]
 gi|305850144|gb|EFM50603.1| RNA polymerase sigma factor RpoD [Escherichia coli NC101]
 gi|307555174|gb|ADN47949.1| hypothetical protein ECABU_c34860 [Escherichia coli ABU 83972]
 gi|307625318|gb|ADN69622.1| RNA polymerase sigma factor RpoD [Escherichia coli UM146]
 gi|312947638|gb|ADR28465.1| RNA polymerase sigma factor RpoD [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315288818|gb|EFU48216.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 110-3]
 gi|315295035|gb|EFU54372.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 153-1]
 gi|315297744|gb|EFU57021.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 16-3]
 gi|320195230|gb|EFW69859.1| RNA polymerase sigma factor RpoD [Escherichia coli WV_060327]
 gi|323951399|gb|EGB47274.1| RNA polymerase sigma proteinRpoD [Escherichia coli H252]
 gi|323957772|gb|EGB53486.1| RNA polymerase sigma proteinRpoD [Escherichia coli H263]
 gi|324008872|gb|EGB78091.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 57-2]
 gi|330909133|gb|EGH37647.1| RNA polymerase sigma factor RpoD [Escherichia coli AA86]
 gi|331042616|gb|EGI14758.1| RNA polymerase sigma factor RpoD [Escherichia coli M605]
 gi|331053940|gb|EGI25969.1| RNA polymerase sigma factor RpoD (Sigma-70) [Escherichia coli
           TA206]
          Length = 613

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|269137812|ref|YP_003294512.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Edwardsiella tarda EIB202]
 gi|267983472|gb|ACY83301.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Edwardsiella tarda EIB202]
 gi|304557867|gb|ADM40531.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda FL6-60]
          Length = 611

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 208/377 (55%), Positives = 265/377 (70%), Gaps = 8/377 (2%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA--QSYGIK 366
           +SS K +   + L ++     L   + D LV  + ++  R+   E  +++L   QS   K
Sbjct: 238 RSSGKAQEEIQNLSEIFKQFRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPK 297

Query: 367 RDVFLERHQGRELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           ++ F+    G E    W   + A   P GE    +  +V+  L+   ++  I  ETG++I
Sbjct: 298 KN-FITLFTGNETSITWFDAALAMGKPWGEKLKDMREDVERSLQ---KLHQIEEETGLTI 353

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 354 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 413

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 414 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 473

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA
Sbjct: 474 REPTPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 533

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 534 TSESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS+ LRSFLD
Sbjct: 594 RKLRHPSRSEVLRSFLD 610



 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 60/158 (37%), Positives = 90/158 (56%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               ++    +A  +   L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  ----NIADEDAAEAAVQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +      L ++I
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLI 162


>gi|187733221|ref|YP_001881829.1| RNA polymerase sigma factor RpoD [Shigella boydii CDC 3083-94]
 gi|187430213|gb|ACD09487.1| RNA polymerase sigma factor RpoD [Shigella boydii CDC 3083-94]
          Length = 613

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|15803609|ref|NP_289642.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 EDL933]
 gi|15833204|ref|NP_311977.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           Sakai]
 gi|24114367|ref|NP_708877.1| RNA polymerase sigma factor RpoD [Shigella flexneri 2a str. 301]
 gi|74313602|ref|YP_312021.1| RNA polymerase sigma factor RpoD [Shigella sonnei Ss046]
 gi|82545322|ref|YP_409269.1| RNA polymerase sigma factor RpoD [Shigella boydii Sb227]
 gi|110643311|ref|YP_671041.1| RNA polymerase sigma factor RpoD [Escherichia coli 536]
 gi|110806954|ref|YP_690474.1| RNA polymerase sigma factor RpoD [Shigella flexneri 5 str. 8401]
 gi|157155497|ref|YP_001464528.1| RNA polymerase sigma factor RpoD [Escherichia coli E24377A]
 gi|168749343|ref|ZP_02774365.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4113]
 gi|168754040|ref|ZP_02779047.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4401]
 gi|168762022|ref|ZP_02787029.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4501]
 gi|168769477|ref|ZP_02794484.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4486]
 gi|168781203|ref|ZP_02806210.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4076]
 gi|168785943|ref|ZP_02810950.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC869]
 gi|168797660|ref|ZP_02822667.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC508]
 gi|170683578|ref|YP_001745339.1| RNA polymerase sigma factor RpoD [Escherichia coli SMS-3-5]
 gi|188493368|ref|ZP_03000638.1| RNA polymerase sigma factor RpoD [Escherichia coli 53638]
 gi|191166845|ref|ZP_03028670.1| RNA polymerase sigma factor RpoD [Escherichia coli B7A]
 gi|191172227|ref|ZP_03033770.1| RNA polymerase sigma factor RpoD [Escherichia coli F11]
 gi|193062048|ref|ZP_03043144.1| RNA polymerase sigma factor RpoD [Escherichia coli E22]
 gi|193067502|ref|ZP_03048470.1| RNA polymerase sigma factor RpoD [Escherichia coli E110019]
 gi|194427683|ref|ZP_03060230.1| RNA polymerase sigma factor RpoD [Escherichia coli B171]
 gi|194431653|ref|ZP_03063944.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae 1012]
 gi|195937213|ref|ZP_03082595.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4024]
 gi|208809700|ref|ZP_03252037.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813639|ref|ZP_03254968.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4045]
 gi|208820039|ref|ZP_03260359.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4042]
 gi|209399452|ref|YP_002272540.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920540|ref|YP_002294624.1| RNA polymerase sigma factor RpoD [Escherichia coli SE11]
 gi|215488398|ref|YP_002330829.1| RNA polymerase sigma factor RpoD [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217326836|ref|ZP_03442919.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           TW14588]
 gi|218555637|ref|YP_002388550.1| RNA polymerase sigma factor RpoD [Escherichia coli IAI1]
 gi|218696772|ref|YP_002404439.1| RNA polymerase sigma factor RpoD [Escherichia coli 55989]
 gi|218701838|ref|YP_002409467.1| RNA polymerase sigma factor RpoD [Escherichia coli IAI39]
 gi|218706692|ref|YP_002414211.1| RNA polymerase sigma factor RpoD [Escherichia coli UMN026]
 gi|254795019|ref|YP_003079856.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           TW14359]
 gi|256019017|ref|ZP_05432882.1| RNA polymerase sigma factor RpoD [Shigella sp. D9]
 gi|260845821|ref|YP_003223599.1| RNA polymerase, sigma 70 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260857197|ref|YP_003231088.1| RNA polymerase, sigma 70 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260869819|ref|YP_003236221.1| RNA polymerase, sigma 70 factor [Escherichia coli O111:H- str.
           11128]
 gi|261228080|ref|ZP_05942361.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261254936|ref|ZP_05947469.1| RNA polymerase, sigma 70 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284446|ref|YP_003501264.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
           CB9615]
 gi|293406680|ref|ZP_06650606.1| RNA polymerase sigma factor RpoD [Escherichia coli FVEC1412]
 gi|293412444|ref|ZP_06655167.1| RNA polymerase sigma factor rpoD [Escherichia coli B354]
 gi|293416506|ref|ZP_06659145.1| RNA polymerase primary sigma factor [Escherichia coli B185]
 gi|293449405|ref|ZP_06663826.1| RNA polymerase primary sigma factor [Escherichia coli B088]
 gi|298382421|ref|ZP_06992018.1| RNA polymerase sigma factor rpoD [Escherichia coli FVEC1302]
 gi|300818835|ref|ZP_07099041.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 107-1]
 gi|300821663|ref|ZP_07101809.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 119-7]
 gi|300901451|ref|ZP_07119536.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 198-1]
 gi|300917392|ref|ZP_07134058.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 115-1]
 gi|300923730|ref|ZP_07139755.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 182-1]
 gi|300937447|ref|ZP_07152273.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 21-1]
 gi|300977468|ref|ZP_07173931.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 200-1]
 gi|301021861|ref|ZP_07185824.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 69-1]
 gi|307310308|ref|ZP_07589956.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W]
 gi|309793633|ref|ZP_07688059.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 145-7]
 gi|312968589|ref|ZP_07782798.1| RNA polymerase sigma factor rpoD [Escherichia coli 2362-75]
 gi|331654667|ref|ZP_08355667.1| RNA polymerase sigma factor RpoD [Escherichia coli M718]
 gi|331664680|ref|ZP_08365586.1| RNA polymerase sigma factor RpoD [Escherichia coli TA143]
 gi|331669908|ref|ZP_08370753.1| RNA polymerase sigma factor RpoD [Escherichia coli TA271]
 gi|331679143|ref|ZP_08379815.1| RNA polymerase sigma factor RpoD [Escherichia coli H591]
 gi|331684720|ref|ZP_08385312.1| RNA polymerase sigma factor RpoD [Escherichia coli H299]
 gi|332280114|ref|ZP_08392527.1| RNA polymerase sigma 70 (sigma D) factor [Shigella sp. D9]
 gi|12517649|gb|AAG58201.1|AE005536_2 RNA polymerase, sigma(70) factor; regulation of proteins induced at
           high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|13363423|dbj|BAB37373.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli O157:H7 str.
           Sakai]
 gi|24053533|gb|AAN44584.1| sigmaD(70) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|73857079|gb|AAZ89786.1| RNA polymerase, sigma(70) factor [Shigella sonnei Ss046]
 gi|81246733|gb|ABB67441.1| RNA polymerase sigma(70) factor [Shigella boydii Sb227]
 gi|110344903|gb|ABG71140.1| RNA polymerase sigma factor RpoD [Escherichia coli 536]
 gi|110616502|gb|ABF05169.1| RpoD protein [Shigella flexneri 5 str. 8401]
 gi|157077527|gb|ABV17235.1| RNA polymerase sigma factor RpoD [Escherichia coli E24377A]
 gi|170521296|gb|ACB19474.1| RNA polymerase sigma factor RpoD [Escherichia coli SMS-3-5]
 gi|188016365|gb|EDU54487.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4113]
 gi|188488567|gb|EDU63670.1| RNA polymerase sigma factor RpoD [Escherichia coli 53638]
 gi|189000977|gb|EDU69963.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4076]
 gi|189358698|gb|EDU77117.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4401]
 gi|189361403|gb|EDU79822.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4486]
 gi|189367616|gb|EDU86032.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4501]
 gi|189374126|gb|EDU92542.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC869]
 gi|189379773|gb|EDU98189.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC508]
 gi|190903087|gb|EDV62811.1| RNA polymerase sigma factor RpoD [Escherichia coli B7A]
 gi|190907537|gb|EDV67133.1| RNA polymerase sigma factor RpoD [Escherichia coli F11]
 gi|192932268|gb|EDV84866.1| RNA polymerase sigma factor RpoD [Escherichia coli E22]
 gi|192959459|gb|EDV89894.1| RNA polymerase sigma factor RpoD [Escherichia coli E110019]
 gi|194414191|gb|EDX30466.1| RNA polymerase sigma factor RpoD [Escherichia coli B171]
 gi|194420009|gb|EDX36087.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae 1012]
 gi|195183229|dbj|BAG66772.1| RNA polymerase, sigma(70) factor [Escherichia coli O111:H-]
 gi|208729501|gb|EDZ79102.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4206]
 gi|208734916|gb|EDZ83603.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4045]
 gi|208740162|gb|EDZ87844.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4042]
 gi|209160852|gb|ACI38285.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4115]
 gi|209759228|gb|ACI77926.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759230|gb|ACI77927.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759232|gb|ACI77928.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759234|gb|ACI77929.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759236|gb|ACI77930.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209913799|dbj|BAG78873.1| RNA polymerase sigma factor RpoD [Escherichia coli SE11]
 gi|215266470|emb|CAS10908.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|217319203|gb|EEC27628.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353504|emb|CAU99623.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli 55989]
 gi|218362405|emb|CAR00029.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli IAI1]
 gi|218371824|emb|CAR19679.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli IAI39]
 gi|218433789|emb|CAR14706.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli UMN026]
 gi|254594419|gb|ACT73780.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257755846|dbj|BAI27348.1| RNA polymerase, sigma 70 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257760968|dbj|BAI32465.1| RNA polymerase, sigma 70 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257766175|dbj|BAI37670.1| RNA polymerase, sigma 70 factor [Escherichia coli O111:H- str.
           11128]
 gi|281602456|gb|ADA75440.1| putative DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Shigella flexneri 2002017]
 gi|284923096|emb|CBG36189.1| RNA polymerase sigma-70 factor [Escherichia coli 042]
 gi|290764319|gb|ADD58280.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
           CB9615]
 gi|291322495|gb|EFE61924.1| RNA polymerase primary sigma factor [Escherichia coli B088]
 gi|291426686|gb|EFE99718.1| RNA polymerase sigma factor RpoD [Escherichia coli FVEC1412]
 gi|291431862|gb|EFF04845.1| RNA polymerase primary sigma factor [Escherichia coli B185]
 gi|291469215|gb|EFF11706.1| RNA polymerase sigma factor rpoD [Escherichia coli B354]
 gi|298277561|gb|EFI19077.1| RNA polymerase sigma factor rpoD [Escherichia coli FVEC1302]
 gi|300308326|gb|EFJ62846.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 200-1]
 gi|300355153|gb|EFJ71023.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 198-1]
 gi|300397877|gb|EFJ81415.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 69-1]
 gi|300415349|gb|EFJ98659.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 115-1]
 gi|300420000|gb|EFK03311.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 182-1]
 gi|300457482|gb|EFK20975.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 21-1]
 gi|300525801|gb|EFK46870.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 119-7]
 gi|300528620|gb|EFK49682.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 107-1]
 gi|306909203|gb|EFN39698.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W]
 gi|308122590|gb|EFO59852.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 145-7]
 gi|312286807|gb|EFR14718.1| RNA polymerase sigma factor rpoD [Escherichia coli 2362-75]
 gi|313648184|gb|EFS12630.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2a str. 2457T]
 gi|315062375|gb|ADT76702.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli W]
 gi|320176471|gb|EFW51521.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae CDC 74-1112]
 gi|320179315|gb|EFW54273.1| RNA polymerase sigma factor RpoD [Shigella boydii ATCC 9905]
 gi|320182888|gb|EFW57762.1| RNA polymerase sigma factor RpoD [Shigella flexneri CDC 796-83]
 gi|320189419|gb|EFW64078.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC1212]
 gi|320201978|gb|EFW76553.1| RNA polymerase sigma factor RpoD [Escherichia coli EC4100B]
 gi|320640141|gb|EFX09713.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           G5101]
 gi|320645439|gb|EFX14448.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str.
           493-89]
 gi|320650750|gb|EFX19207.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str. H
           2687]
 gi|320656128|gb|EFX24040.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320661818|gb|EFX29226.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320666969|gb|EFX33945.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154524|gb|EFZ40724.1| RNA polymerase sigma factor rpoD [Escherichia coli EPECa14]
 gi|323163118|gb|EFZ48951.1| RNA polymerase sigma factor rpoD [Escherichia coli E128010]
 gi|323168088|gb|EFZ53775.1| RNA polymerase sigma factor rpoD [Shigella sonnei 53G]
 gi|323173687|gb|EFZ59316.1| RNA polymerase sigma factor rpoD [Escherichia coli LT-68]
 gi|323178773|gb|EFZ64349.1| RNA polymerase sigma factor rpoD [Escherichia coli 1180]
 gi|323183651|gb|EFZ69048.1| RNA polymerase sigma factor rpoD [Escherichia coli 1357]
 gi|323188489|gb|EFZ73774.1| RNA polymerase sigma factor rpoD [Escherichia coli RN587/1]
 gi|323377037|gb|ADX49305.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli KO11]
 gi|323946863|gb|EGB42881.1| RNA polymerase sigma protein RpoD [Escherichia coli H120]
 gi|323966596|gb|EGB62029.1| RNA polymerase sigma proteinRpoD [Escherichia coli M863]
 gi|323978859|gb|EGB73939.1| RNA polymerase sigma proteinRpoD [Escherichia coli TW10509]
 gi|324011983|gb|EGB81202.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 60-1]
 gi|324018214|gb|EGB87433.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 117-3]
 gi|324119675|gb|EGC13556.1| RNA polymerase sigma proteinRpoD [Escherichia coli E1167]
 gi|326337771|gb|EGD61605.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           1125]
 gi|326347336|gb|EGD71061.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           1044]
 gi|327251853|gb|EGE63539.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_7v]
 gi|331048049|gb|EGI20126.1| RNA polymerase sigma factor RpoD [Escherichia coli M718]
 gi|331058611|gb|EGI30592.1| RNA polymerase sigma factor RpoD [Escherichia coli TA143]
 gi|331062821|gb|EGI34735.1| RNA polymerase sigma factor RpoD [Escherichia coli TA271]
 gi|331073208|gb|EGI44531.1| RNA polymerase sigma factor RpoD [Escherichia coli H591]
 gi|331078335|gb|EGI49541.1| RNA polymerase sigma factor RpoD [Escherichia coli H299]
 gi|332086727|gb|EGI91867.1| RNA polymerase sigma factor rpoD [Shigella boydii 5216-82]
 gi|332086765|gb|EGI91902.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|332086940|gb|EGI92075.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|332092163|gb|EGI97241.1| RNA polymerase sigma factor rpoD [Shigella boydii 3594-74]
 gi|332102466|gb|EGJ05812.1| RNA polymerase sigma 70 (sigma D) factor [Shigella sp. D9]
 gi|332752740|gb|EGJ83125.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-671]
 gi|332753124|gb|EGJ83508.1| RNA polymerase sigma factor rpoD [Shigella flexneri 4343-70]
 gi|332754402|gb|EGJ84768.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2747-71]
 gi|332765316|gb|EGJ95540.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
           flexneri 2930-71]
 gi|332998670|gb|EGK18266.1| RNA polymerase sigma factor rpoD [Shigella flexneri VA-6]
 gi|332999827|gb|EGK19411.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-272]
 gi|332999919|gb|EGK19502.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-218]
 gi|333014798|gb|EGK34143.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-304]
 gi|333015695|gb|EGK35034.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-227]
          Length = 613

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|126642737|ref|YP_001085721.1| sigma D (sigma 70) factor of RNA polymerase major sigma factor
           during exponential growth [Acinetobacter baumannii ATCC
           17978]
          Length = 580

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 201/379 (53%), Positives = 260/379 (68%), Gaps = 1/379 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           +K  ++S +     E L  +           D++ E +    ++I  NE E++R A   G
Sbjct: 201 EKHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRG 260

Query: 365 -IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + R+ F      +E +P W+         E K  +      +L  + +I  I  E G++
Sbjct: 261 RMDRNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLN 320

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           +SE + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 321 VSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 380

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++
Sbjct: 381 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 440

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+
Sbjct: 441 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDA 500

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A    L+E T  VL +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 501 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 560

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HPSRS+ LRSFL+ 
Sbjct: 561 LRKLRHPSRSEHLRSFLEN 579


>gi|301325578|ref|ZP_07219046.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 78-1]
 gi|300847629|gb|EFK75389.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 78-1]
          Length = 613

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDPTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|157162543|ref|YP_001459861.1| RNA polymerase sigma factor RpoD [Escherichia coli HS]
 gi|170018681|ref|YP_001723635.1| RNA polymerase sigma factor RpoD [Escherichia coli ATCC 8739]
 gi|194439798|ref|ZP_03071864.1| RNA polymerase sigma factor RpoD [Escherichia coli 101-1]
 gi|253772097|ref|YP_003034928.1| RNA polymerase sigma factor RpoD [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038237|ref|ZP_04872295.1| RNA polymerase sigma factor RpoD [Escherichia sp. 1_1_43]
 gi|254163014|ref|YP_003046122.1| RNA polymerase sigma factor RpoD [Escherichia coli B str. REL606]
 gi|256024353|ref|ZP_05438218.1| RNA polymerase sigma factor RpoD [Escherichia sp. 4_1_40B]
 gi|300905790|ref|ZP_07123524.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 84-1]
 gi|300931954|ref|ZP_07147251.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 187-1]
 gi|300950721|ref|ZP_07164609.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 116-1]
 gi|300958456|ref|ZP_07170595.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 175-1]
 gi|301021226|ref|ZP_07185258.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 196-1]
 gi|301301890|ref|ZP_07208024.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 124-1]
 gi|301644765|ref|ZP_07244740.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 146-1]
 gi|307139755|ref|ZP_07499111.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|312972668|ref|ZP_07786841.1| RNA polymerase sigma factor rpoD [Escherichia coli 1827-70]
 gi|331643766|ref|ZP_08344897.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|157068223|gb|ABV07478.1| RNA polymerase sigma factor RpoD [Escherichia coli HS]
 gi|169753609|gb|ACA76308.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli ATCC 8739]
 gi|194421246|gb|EDX37267.1| RNA polymerase sigma factor RpoD [Escherichia coli 101-1]
 gi|226839861|gb|EEH71882.1| RNA polymerase sigma factor RpoD [Escherichia sp. 1_1_43]
 gi|242378617|emb|CAQ33404.1| RNA polymerase, sigma 70 (sigma D) factor, subunit of RNA
           polymerase sigma 70 [Escherichia coli BL21(DE3)]
 gi|253323141|gb|ACT27743.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974915|gb|ACT40586.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979071|gb|ACT44741.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|299881584|gb|EFI89795.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 196-1]
 gi|300314897|gb|EFJ64681.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 175-1]
 gi|300402389|gb|EFJ85927.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 84-1]
 gi|300449958|gb|EFK13578.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 116-1]
 gi|300460377|gb|EFK23870.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 187-1]
 gi|300842871|gb|EFK70631.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 124-1]
 gi|301076919|gb|EFK91725.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 146-1]
 gi|309703498|emb|CBJ02838.1| RNA polymerase sigma-70 factor [Escherichia coli ETEC H10407]
 gi|310332610|gb|EFP99823.1| RNA polymerase sigma factor rpoD [Escherichia coli 1827-70]
 gi|315256981|gb|EFU36949.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 85-1]
 gi|315617141|gb|EFU97750.1| RNA polymerase sigma factor rpoD [Escherichia coli 3431]
 gi|323935931|gb|EGB32226.1| RNA polymerase sigma protein RpoD [Escherichia coli E1520]
 gi|323941835|gb|EGB38014.1| RNA polymerase sigma proteinRpoD [Escherichia coli E482]
 gi|323960998|gb|EGB56615.1| RNA polymerase sigma proteinRpoD [Escherichia coli H489]
 gi|323971810|gb|EGB67035.1| RNA polymerase sigma proteinRpoD [Escherichia coli TA007]
 gi|331037237|gb|EGI09461.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|332345022|gb|AEE58356.1| RNA polymerase sigma factor protein RpoD [Escherichia coli UMNK88]
          Length = 613

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.0 bits (232), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|253686949|ref|YP_003016139.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251753527|gb|ACT11603.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 612

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/364 (55%), Positives = 257/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E 
Sbjct: 251 LSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNET 310

Query: 380 DPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           +  W + A     P  E  N V  +V   L+   +++ I  ETG++I + + I   +  G
Sbjct: 311 NSTWFAAAVAMGKPWSEKLNDVEEDVTRSLQ---KLQQIEEETGLTIEQVKDINRRMSIG 367

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 368 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 427

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 428 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 487

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 488 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 547

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 548 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 607

Query: 678 SFLD 681
           SFLD
Sbjct: 608 SFLD 611



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDADEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|227113748|ref|ZP_03827404.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 611

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/364 (55%), Positives = 257/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E 
Sbjct: 250 LSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNET 309

Query: 380 DPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           +  W + A     P  E  N V  +V   L+   +++ I  ETG++I + + I   +  G
Sbjct: 310 NSTWFAAAVAMGKPWSEKLNDVEEDVTRSLQ---KLQQIEEETGLTIEQVKDINRRMSIG 366

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 367 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 426

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 427 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 486

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 487 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 546

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 547 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 606

Query: 678 SFLD 681
           SFLD
Sbjct: 607 SFLD 610



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDADEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|331006388|ref|ZP_08329697.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC1989]
 gi|330419812|gb|EGG94169.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC1989]
          Length = 601

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 198/359 (55%), Positives = 252/359 (70%), Gaps = 2/359 (0%)

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
           ++    L   + D + ++   + + +   E  +L L  ++  + R  F++   G E DP 
Sbjct: 243 IIKFFKLPPRQFDPMYKKARGVLESVRREERRILSLCVRTAKMPRKTFIKEFPGNETDPT 302

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+    +       NF   + + IL+ + ++  I    GI +S  + I   +  GE  A 
Sbjct: 303 WIPGVIEKKRDYSANFEEVK-EEILRAQRKLDQIQNTVGIELSMIKEINRRMSIGEARAR 361

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 362 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 421

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP E 
Sbjct: 422 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEEK 481

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++SA    L E+T  VL+ LT 
Sbjct: 482 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTITSPVESATDVGLTESTRDVLSGLTA 541

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 542 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFLD 600



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 87/141 (61%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI----NVVDGDDLEDEE 87
           K +I   +++GY+T  ++N  LP D    +Q+ED + M+++MGI    N  D ++L   +
Sbjct: 11  KLLIARGKEQGYLTYADVNDHLPQDISDPDQVEDIIQMINDMGIRVYENAPDAEELLMTD 70

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  DS     +++ ++  L   +  A R+TD PVRMY+REMG++ELL+REGEIAIAKRIE
Sbjct: 71  G--DSSADEIASAEAAAALAAVETEAGRTTD-PVRMYMREMGTVELLTREGEIAIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +M +L   P   Q LI
Sbjct: 128 EGTRDLMHALACWPNVVQILI 148


>gi|266618720|pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
          Length = 613

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.0 bits (232), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|258623542|ref|ZP_05718543.1| RNA polymerase sigma factor [Vibrio mimicus VM573]
 gi|258623776|ref|ZP_05718733.1| RNA polymerase sigma factor [Vibrio mimicus VM603]
 gi|262172395|ref|ZP_06040073.1| RNA polymerase sigma factor RpoD [Vibrio mimicus MB-451]
 gi|258583899|gb|EEW08691.1| RNA polymerase sigma factor [Vibrio mimicus VM603]
 gi|258584204|gb|EEW08952.1| RNA polymerase sigma factor [Vibrio mimicus VM573]
 gi|261893471|gb|EEY39457.1| RNA polymerase sigma factor RpoD [Vibrio mimicus MB-451]
          Length = 625

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 213/405 (52%), Positives = 269/405 (66%), Gaps = 23/405 (5%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E SS+   + +E          L   + D LV
Sbjct: 231 EKFNELRGKFQNLQLAVNEFGRDSNQASEASSLVLDIFRE--------FRLTPKQFDHLV 282

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P   + 
Sbjct: 283 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP---YV 339

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             V  + D I +   +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 340 QKVREQEDDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLV 399

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 400 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 459

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+
Sbjct: 460 RTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISM 519

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI M
Sbjct: 520 ETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDM 579

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 580 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624


>gi|302185957|ref|ZP_07262630.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           642]
          Length = 616

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 262/363 (72%), Gaps = 4/363 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + + LVE++    +R+   E  +++L  +   + R  FL +  G E+
Sbjct: 255 LAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEV 314

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE
Sbjct: 315 DESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGE 372

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 373 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 432

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 433 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEM 492

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+
Sbjct: 493 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLS 552

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRS
Sbjct: 553 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRS 612

Query: 679 FLD 681
           FLD
Sbjct: 613 FLD 615



 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 82/137 (59%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|259907100|ref|YP_002647456.1| RNA polymerase sigma factor RpoD [Erwinia pyrifoliae Ep1/96]
 gi|224962722|emb|CAX54177.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia pyrifoliae
           Ep1/96]
 gi|283476901|emb|CAY72757.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia pyrifoliae DSM
           12163]
 gi|310766301|gb|ADP11251.1| RNA polymerase sigma factor RpoD [Erwinia sp. Ejp617]
          Length = 613

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/366 (55%), Positives = 260/366 (71%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G 
Sbjct: 250 QNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGN 309

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   + A + P  E  N V+ +V+  L+   +++ I  ETG++I + + I   + 
Sbjct: 310 ETNETWFKAALAMNKPWSEKLNDVSDDVNRGLQ---KLQQIEEETGLTIEQVKDINRRMS 366

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 486

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 487 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 546

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 547 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 606

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 607 LRSFLD 612



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|261820103|ref|YP_003258209.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae WPP163]
 gi|261604116|gb|ACX86602.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium wasabiae
           WPP163]
          Length = 611

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/364 (55%), Positives = 257/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E 
Sbjct: 250 LSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNET 309

Query: 380 DPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           +  W + A     P  E  N V  +V   L+   +++ I  ETG++I + + I   +  G
Sbjct: 310 NNSWFAAAVAMGKPWSEKLNDVEEDVTRSLQ---KLQQIEEETGLTIEQVKDINRRMSIG 366

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 367 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 426

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 427 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 486

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 487 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 546

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 547 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 606

Query: 678 SFLD 681
           SFLD
Sbjct: 607 SFLD 610



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDADEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|325273045|ref|ZP_08139355.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. TJI-51]
 gi|324101818|gb|EGB99354.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. TJI-51]
          Length = 616

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 199/365 (54%), Positives = 260/365 (71%), Gaps = 4/365 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  L   + L   + ++LVE++ D   R+   E  +++L  +   + R  FL      
Sbjct: 253 QALADLFMPIKLVPKQFEVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRMFPSN 312

Query: 378 ELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E D  W    AK     +W   +  +  +I+  + ++  +  ETG++++E + I   +  
Sbjct: 313 ETDQTWSGDLAKR--NTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSI 370

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 490

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  V
Sbjct: 491 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 550

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ L
Sbjct: 551 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 610

Query: 677 RSFLD 681
           RSFLD
Sbjct: 611 RSFLD 615



 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     +
Sbjct: 12  KELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAE 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDYIL 147


>gi|261342495|ref|ZP_05970353.1| RNA polymerase sigma factor RpoD [Enterobacter cancerogenus ATCC
           35316]
 gi|288315137|gb|EFC54075.1| RNA polymerase sigma factor RpoD [Enterobacter cancerogenus ATCC
           35316]
          Length = 614

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 206/397 (51%), Positives = 271/397 (68%), Gaps = 7/397 (1%)

Query: 289 EVYRELRS---LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + ELR+   L  + +  +    ++ + ++LK  L ++     L   + D LV  +  +
Sbjct: 220 EKFAELRTQYELARDTIKAKGRSHAAAQEQILK--LSEVFKQFRLVPKQFDYLVNSMRVM 277

Query: 346 SKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             R+   E  +++L  +   + +  F+    G E    W + A    +  W   +    D
Sbjct: 278 MDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKP-WSEKLHDVKD 336

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYT
Sbjct: 337 DVHRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 396

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 397 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 456

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++
Sbjct: 457 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 516

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEE
Sbjct: 517 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 576

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 577 VGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613



 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/141 (41%), Positives = 88/141 (62%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S ++ + A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TSNNTDEDAEEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 127 DGINQVQCSVAEYPEAITYLL 147


>gi|294634612|ref|ZP_06713146.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|291091942|gb|EFE24503.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
          Length = 613

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 209/377 (55%), Positives = 263/377 (69%), Gaps = 8/377 (2%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA--QSYGIK 366
           +SS K +     L ++     L   + D LV  +  +  R+   E  +++L   QS   K
Sbjct: 240 RSSAKAQEEILNLSEIFKQFRLVPKQFDYLVNNMRAMMDRVRGQERLIMKLCVEQSKMPK 299

Query: 367 RDVFLERHQGRELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           ++ F+    G E    W   + A   P GE    +  EV+  L+   ++  I  ETG++I
Sbjct: 300 KN-FITLFTGNETSITWFEAALAMGKPWGEKLKDMREEVERSLQ---KLHQIEEETGLTI 355

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 356 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 415

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 416 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 475

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA
Sbjct: 476 REPTPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 535

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 536 TSESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS+ LRSFLD
Sbjct: 596 RKLRHPSRSEVLRSFLD 612



 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 60/158 (37%), Positives = 90/158 (56%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               ++    +A  +   L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  ----NIADEDAAEAAVQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +      L ++I
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLI 162


>gi|260599325|ref|YP_003211896.1| RNA polymerase sigma factor RpoD [Cronobacter turicensis z3032]
 gi|260218502|emb|CBA33681.1| RNA polymerase sigma factor rpoD [Cronobacter turicensis z3032]
          Length = 614

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  ++++  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKMCVEQCKMPKKNFITLFTGNE 311

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA +V   L+   +++ I  ETG++I + + I   +  
Sbjct: 312 TSETWFNAAIAMNKPWSEKLHDVADDVHRSLQ---KLQQIEEETGLTIEQVKDINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 489 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 95/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|119474865|ref|ZP_01615218.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451068|gb|EAW32301.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 600

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 193/321 (60%), Positives = 239/321 (74%), Gaps = 2/321 (0%)

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           Q+   +RD F++  QG+E +  W+       E +    +    + IL+ + +I  I  +T
Sbjct: 281 QAKMTRRD-FVKSFQGQETNLDWIEQQIKAHE-DVAPVLEANKEEILRAQRKIAQIETQT 338

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G++I + + I   +  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 339 GLTILDIKEINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 398

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M 
Sbjct: 399 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 458

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REPTPEE+ +++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED     P
Sbjct: 459 QEMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIAQP 518

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +DSA    L+E T  VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 519 VDSATGQGLQEATKDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 578

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRS  LRSFLD
Sbjct: 579 AKALRKLRHPSRSDHLRSFLD 599



 Score = 91.7 bits (226), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/142 (40%), Positives = 85/142 (59%), Gaps = 10/142 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD-LEDE 86
           K +I   +++GY+T  E+N  LP D    +Q+ED + M++++GI V     D D+ L  E
Sbjct: 12  KTLIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDLGIQVFETAPDADEILLTE 71

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E S D +  A +A+  +    +        T DPVRMY+REMG++ELL+REGEIAIAKRI
Sbjct: 72  EDSTDDIAAAEAAAALAAVETEAG-----RTTDPVRMYMREMGTVELLTREGEIAIAKRI 126

Query: 147 EAGRAMMMASLCESPLTFQALI 168
           E G   +MA++   P   Q +I
Sbjct: 127 EEGIRDIMAAVAYYPGAVQDVI 148


>gi|153003633|ref|YP_001377958.1| RNA polymerase sigma-70 subunit RpoD [Anaeromyxobacter sp. Fw109-5]
 gi|152027206|gb|ABS24974.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter sp.
           Fw109-5]
          Length = 819

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 202/396 (51%), Positives = 275/396 (69%), Gaps = 21/396 (5%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +L    V+  K ++   + K ++ ++++ + ++ LN+ +ID +V +L    KR+   E E
Sbjct: 434 TLTTKKVSEPKRKELRSEIKTIEGEMMEHLEAIQLNKKQIDRIVLRLKGFIKRVEEAERE 493

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF---VACEVDSILKIRNE 412
           L    ++  +           REL        +D  EG  K     + C  + + ++   
Sbjct: 494 LADCERATSV---------PVRELRRLLREARED--EGARKKLGKKLGCSAEEVEELDRT 542

Query: 413 IKS-------ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           ++S       +  E  + + E R     +  GE +A  AK E+VEANLRLV+S+AKKYTN
Sbjct: 543 VRSAYRKMLRVQEEAEVPVDELRRTYRTISDGEHKAERAKTELVEANLRLVVSIAKKYTN 602

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 603 RGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM 662

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++RT+R +  ++ REPTPEEIA+K+ +P++ VRKVLKI KEPISLETPIG+E+ 
Sbjct: 663 IETINKLIRTSRYLVQELGREPTPEEIAEKMELPLDKVRKVLKIAKEPISLETPIGEEED 722

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDK+ VSP D+ I  NL E T +VLA+LTPREE+VLRMRFGIG  +DHTLEEV
Sbjct: 723 SHLGDFIEDKSLVSPSDAVINMNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEV 782

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+ F VTRERIRQIEAKA+RKL+HPSRSK+L+SF++
Sbjct: 783 GQDFEVTRERIRQIEAKALRKLRHPSRSKRLKSFVE 818


>gi|251793982|ref|YP_003008714.1| RNA polymerase sigma factor RpoD [Aggregatibacter aphrophilus
           NJ8700]
 gi|247535381|gb|ACS98627.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
           aphrophilus NJ8700]
          Length = 623

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 204/378 (53%), Positives = 261/378 (69%), Gaps = 2/378 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           +K  ++S K K   + L  +     L   + D+LV  + D+ KR+   E  + R+   + 
Sbjct: 246 EKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDMMKRVRAQERFIQRIVVDNA 305

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F +   G E    W+  A    +   +  V  E D    I N ++ I  +T ++
Sbjct: 306 KMPKSGFQKSFIGHETTDTWLIKALGADKAWSEKLVQYENDLRQAIANLVQ-IEQDTHLT 364

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I + R I   + +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 365 IQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 424

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++
Sbjct: 425 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 484

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            RE +PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDS
Sbjct: 485 GREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDS 544

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A   +L+  T  VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 545 ATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 604

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSRS+ LRSFLD
Sbjct: 605 LRKLRHPSRSETLRSFLD 622


>gi|227329605|ref|ZP_03833629.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 611

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/364 (55%), Positives = 257/364 (70%), Gaps = 6/364 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E 
Sbjct: 250 LSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNET 309

Query: 380 DPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           +  W + A     P  E  N V  +V   L+   +++ I  ETG++I + + I   +  G
Sbjct: 310 NNTWFAAAVAMGKPWSEKLNDVEEDVTRSLQ---KLQQIEEETGLTIEQVKDINRRMSIG 366

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 367 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 426

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 427 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 486

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 487 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 546

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 547 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 606

Query: 678 SFLD 681
           SFLD
Sbjct: 607 SFLD 610



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTNDADEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|238756616|ref|ZP_04617911.1| RNA polymerase sigma factor rpoD [Yersinia ruckeri ATCC 29473]
 gi|238705164|gb|EEP97586.1| RNA polymerase sigma factor rpoD [Yersinia ruckeri ATCC 29473]
          Length = 613

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 206/394 (52%), Positives = 268/394 (68%), Gaps = 5/394 (1%)

Query: 291 YRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           + +LR   +NA    +K+ +S +       KL ++     L   + D LV  +  +  R+
Sbjct: 221 FSDLREQYENARKEIKKNGRSHISAAAEILKLSEVFKQFRLVPKQFDYLVNNMRTMMDRV 280

Query: 350 MHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
              E  +++L  +   + +  F+      E    W  +A     G+ W   +    D + 
Sbjct: 281 RTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTW--FAAALAMGKPWSEKLKDVSDDVQ 338

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 339 RSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 398

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 399 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 458

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 459 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 518

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 519 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 578

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 579 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612



 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 92/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NT--NDTDDDAAEAAAQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|37678745|ref|NP_933354.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus YJ016]
 gi|37197486|dbj|BAC93325.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus YJ016]
          Length = 643

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 208/403 (51%), Positives = 272/403 (67%), Gaps = 9/403 (2%)

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            AL++  ++    ++LQ  AVN    E  S +     E ++ +     L   + D LV +
Sbjct: 246 MALEKFTQLRNSYQNLQ-LAVNEHGRE--SAQTAQAHELMLDVFKEFRLTPKQFDHLVNE 302

Query: 342 LYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNF 398
           L     R+   E  +++ A     + +  F+    G E +  W+    A D P   +   
Sbjct: 303 LRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGNESNEEWLDQILASDKP---YVEK 359

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + I +   ++++I  ET +S++  + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 360 IKLHEEDIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVIS 419

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 420 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 479

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ET
Sbjct: 480 IRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMET 539

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNT
Sbjct: 540 PIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREAKVLRMRFGIDMNT 599

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 600 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 642



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 88/141 (62%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV    D DDL   +
Sbjct: 29  KLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 88

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 89  --ETNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 145

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   + +S+ E P T   ++
Sbjct: 146 DGINQVQSSVAEYPGTIPYIL 166


>gi|238794325|ref|ZP_04637937.1| RNA polymerase sigma factor rpoD [Yersinia intermedia ATCC 29909]
 gi|238726319|gb|EEQ17861.1| RNA polymerase sigma factor rpoD [Yersinia intermedia ATCC 29909]
          Length = 612

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 206/394 (52%), Positives = 268/394 (68%), Gaps = 5/394 (1%)

Query: 291 YRELRSLQDNA-VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           + +LR   +NA +  +K+ +S         KL ++     L   + D LV  +  +  R+
Sbjct: 220 FSDLREQYENARMEIKKNGRSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRTMMDRV 279

Query: 350 MHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
              E  +++L  +   + +  F+      E    W  +A     G+ W   +    D + 
Sbjct: 280 RTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTW--FAAAIAMGKPWSEKLKDVSDDVQ 337

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 338 RSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 397

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 398 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 457

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 458 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 517

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 518 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 577

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 578 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 95/159 (59%), Gaps = 7/159 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            G   +  S+ E P     L+   D +  G   L ++I+
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIN 165


>gi|157148639|ref|YP_001455958.1| RNA polymerase sigma factor RpoD [Citrobacter koseri ATCC BAA-895]
 gi|157085844|gb|ABV15522.1| hypothetical protein CKO_04466 [Citrobacter koseri ATCC BAA-895]
          Length = 614

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 311

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V  +V   L+   +++ I  ETG++I + + I   +  
Sbjct: 312 TSETWFNAAIAMNKPWSEKLHDVTEDVQRSLQ---KLQQIEEETGLTIEQVKDINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 489 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTNNTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|311278024|ref|YP_003940255.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae SCF1]
 gi|308747219|gb|ADO46971.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae SCF1]
          Length = 614

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  + +R+   E  +++L  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNSMRTMMERVRIQERIIMKLCVEQCKMPKKNFITLFTGNE 311

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V  +V   L+   +++ I  ETG++I + + I   +  
Sbjct: 312 TSETWFNAAIAMNKPWSEKLHDVTEDVQRSLQ---KLQQIEEETGLTIEQVKDINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 489 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 94/155 (60%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+ E P     L+   D +      L ++I
Sbjct: 128 NQVQCSVAEYPEAITYLLEQYDRVEAAEARLSDLI 162


>gi|292486903|ref|YP_003529773.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
           CFBP1430]
 gi|292900702|ref|YP_003540071.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 gi|291200550|emb|CBJ47679.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 gi|291552320|emb|CBA19364.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
           CFBP1430]
 gi|312170973|emb|CBX79232.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora ATCC
           BAA-2158]
          Length = 614

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/366 (55%), Positives = 259/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G 
Sbjct: 251 QNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGN 310

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W   + A + P  E  N V+ +V+  L+   +++ I  ETG++I + + I   + 
Sbjct: 311 ETSETWFKAALAMNKPWSEKLNDVSEDVNRGLQ---KLQQIEEETGLTIEQVKDINRRMS 367

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 487

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 488 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 547

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 607

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 608 LRSFLD 613



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|293394293|ref|ZP_06638593.1| DNA-directed RNA polymerase sigma subunit RpoD [Serratia odorifera
           DSM 4582]
 gi|291423271|gb|EFE96500.1| DNA-directed RNA polymerase sigma subunit RpoD [Serratia odorifera
           DSM 4582]
          Length = 647

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 253/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL  +     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 285 KLSDVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFAGNE 344

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W   A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 345 TSDSWFEAALAMAKP-WSEKLKDVAEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 403

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 404 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 463

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 464 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 523

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 524 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 583

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 584 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 643

Query: 679 FLD 681
           FLD
Sbjct: 644 FLD 646



 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 96/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 46  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 105

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 106 NSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 159

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 160 RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 200


>gi|304409306|ref|ZP_07390926.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|307303664|ref|ZP_07583417.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|304351824|gb|EFM16222.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|306912562|gb|EFN42985.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|315266575|gb|ADT93428.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS678]
          Length = 611

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 197/353 (55%), Positives = 256/353 (72%), Gaps = 2/353 (0%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W +  K
Sbjct: 259 LVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGNETNLDWFNTEK 318

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              +   +     E D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKKEM
Sbjct: 319 ASTKPYAEGLRMVE-DDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKKEM 377

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 378 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 437

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLK
Sbjct: 438 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVLK 497

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VL
Sbjct: 498 IAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAKVL 557

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 558 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 610



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 89/155 (57%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             + +S+ E P     ++   D+       L +II
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII 162


>gi|15603106|ref|NP_246178.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|12721597|gb|AAK03325.1| RpoD [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 622

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 206/396 (52%), Positives = 268/396 (67%), Gaps = 5/396 (1%)

Query: 289 EVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + EL++    AV   +K  ++S K K   + L  +     L   + D LV  + ++ K
Sbjct: 228 EKFLELKTQHAKAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMK 287

Query: 348 RIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDS 405
            +   E  + ++      + ++ F +   G E    W+   K    G+ W   +A   + 
Sbjct: 288 SVRLQERSIQKIVVDKAKMPKEQFQKVFIGHENKDTWL--VKALSSGKTWSEKLAKHEEE 345

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I    + I  I  +T +++S+ R +   +  GE +A  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 346 IRYYIDNILEIERQTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTN 405

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 406 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 465

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D 
Sbjct: 466 IETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 525

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +VLRMRFGI MNTDHTLEEV
Sbjct: 526 SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 585

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 586 GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 621



 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 93/160 (58%), Gaps = 13/160 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP + V +EQ+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDADDLMLNE 69

Query: 88  --GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
               ED+++ A+   +S        ++    T DPVRMY+REMGS+ELL+REGEI IAKR
Sbjct: 70  TIADEDAVEEATQVLSSV-------EAEIGRTTDPVRMYMREMGSVELLTREGEIDIAKR 122

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IE G   + +++   P     L+     + +G   L ++I
Sbjct: 123 IEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLI 162


>gi|188532569|ref|YP_001906366.1| RNA polymerase sigma factor RpoD [Erwinia tasmaniensis Et1/99]
 gi|188027611|emb|CAO95461.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia tasmaniensis
           Et1/99]
          Length = 613

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/366 (55%), Positives = 259/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G 
Sbjct: 250 QNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERLIMKLCVELCKMPKKNFITLFTGN 309

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   + A + P  E  N V+ +V   L+   +++ I  ETG++I + + I   + 
Sbjct: 310 ETNETWFKAALAMNKPWSEKLNDVSEDVTRGLQ---KLQQIEEETGLTIEQVKDINRRMS 366

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 486

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 487 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 546

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 547 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 606

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 607 LRSFLD 612



 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAINYLLEQYDRVEAGEARLSDLI 164


>gi|71891846|ref|YP_277575.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|71795952|gb|AAZ40703.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 611

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 202/380 (53%), Positives = 262/380 (68%), Gaps = 6/380 (1%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQ 361
           NG+   KSS +      KL ++     L   + D LV  +  + +R+   E  +++L  +
Sbjct: 236 NGRNHIKSSKEIL----KLSEIFKQFRLVPKQFDYLVNNMRSMMERVRKQERLIMKLCVE 291

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+    G + +  W + A       W   +    + +    +++  I  ETG
Sbjct: 292 ISKMPKKNFIALFSGNQTNKTWFNTALSM-HTSWSEKLYKVDEDVQNSLSKLHQIEKETG 350

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 351 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 410

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  
Sbjct: 411 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQ 470

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +I  EPTPEE+A+++ M  + +RKVLKI KEPIS+ETP+GD++ SHLGDFIED N   PL
Sbjct: 471 EIGHEPTPEELAERMLMSEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTNHDLPL 530

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSA   NLR  T  +L+ LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEA
Sbjct: 531 DSATSDNLRTATHDILSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 590

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS+ LRSFLD
Sbjct: 591 KALRKLRHPSRSEILRSFLD 610



 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 60/158 (37%), Positives = 90/158 (56%), Gaps = 5/158 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE----E 87
           K ++ L +++GY+T  E+N  LP D V   Q+E+ + M+++MGI V++     DE    E
Sbjct: 10  KLLVTLGKEQGYLTFSEVNDHLPEDIVDPGQIENIIQMMNDMGIQVMEEAPNSDEFLLIE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  + D    A+ ++V      DS    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  HTHSTND-EEDATEAAVQALTNVDSELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+     +  G T L ++I
Sbjct: 129 DGINQVQCSVSEYPEAITYLLEQYKRVETGETRLSDLI 166


>gi|308188146|ref|YP_003932277.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pantoea vagans C9-1]
 gi|308058656|gb|ADO10828.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pantoea vagans C9-1]
          Length = 613

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/366 (54%), Positives = 257/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  +  + +R+   E  +++L  +   + +  F+    G 
Sbjct: 250 QNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPKKNFITLFTGN 309

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   + A + P   W   +    D +++   ++  +  ETG++I + + I   + 
Sbjct: 310 ETNESWFKAALAMNKP---WSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVKDINRRMS 366

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 486

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 487 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 546

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 547 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 606

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 607 LRSFLD 612



 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 96/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D++  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLI 164


>gi|317493716|ref|ZP_07952133.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918043|gb|EFV39385.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 610

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/365 (56%), Positives = 259/365 (70%), Gaps = 8/365 (2%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA--QSYGIKRDVFLERHQGRE 378
           L ++     L   + D LV  +  +  R+   E  +++L   QS   K++ F+    G E
Sbjct: 249 LSEVFKQFRLVPKQFDYLVNNMRQMMDRVRTQERLIMKLCVEQSKMPKKN-FITLFTGNE 307

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            +  W   + A   P GE    V  +V+  L+   ++  I  ETG++I + + I   +  
Sbjct: 308 TNTTWFDAALAMAKPWGEKLKDVREDVERSLQ---KLHQIEEETGLTIEQVKDINRRMSI 364

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 365 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 424

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 425 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 484

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 485 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATRDV 544

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 545 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 604

Query: 677 RSFLD 681
           RSFLD
Sbjct: 605 RSFLD 609



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 90/158 (56%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               ++    +A  +   L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  ----NIADEDAAEAAVQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +      L +II
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDII 162


>gi|237729995|ref|ZP_04560476.1| RNA polymerase sigma-70 factor [Citrobacter sp. 30_2]
 gi|226908601|gb|EEH94519.1| RNA polymerase sigma-70 factor [Citrobacter sp. 30_2]
          Length = 660

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 204/366 (55%), Positives = 260/366 (71%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           +KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G 
Sbjct: 297 QKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGN 356

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W   + A + P  E  + VA +V   L+   +++ I  ETG++I + + I   + 
Sbjct: 357 ETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQ---KLQQIEEETGLTIEQVKDINRRMS 413

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 414 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 473

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 474 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 533

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 534 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHD 593

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 594 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 653

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 654 LRSFLD 659



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 55  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 115 TSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 168

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 169 RIEDGINQVQCSVAEYPEAITYLL 192


>gi|217974326|ref|YP_002359077.1| RNA polymerase sigma 70 subunit RpoD [Shewanella baltica OS223]
 gi|217499461|gb|ACK47654.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS223]
          Length = 611

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 206/400 (51%), Positives = 276/400 (69%), Gaps = 5/400 (1%)

Query: 285 DEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           +E  E + +LR+  ++A+     K  +     K L E + ++     L   + D LV+ +
Sbjct: 213 EEARERFGQLRTAYESALKIIDAKGREHPESVKALFE-IGEIFKEFRLVPKQFDRLVKSM 271

Query: 343 YDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
             +  R+   E  +L+L  +   + +  F++   G E +  W +  K   +   +     
Sbjct: 272 RTMMDRVRVQERLVLKLCVEQAKMPKKNFVKFFTGNETNLDWFNTEKASTKPYAEGLRMV 331

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 332 E-DDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 390

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 391 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 450

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLKI KEPIS+ETPIG
Sbjct: 451 PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVLKIAKEPISMETPIG 510

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VLRMRFGI MNTDHT
Sbjct: 511 DDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHT 570

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 571 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 610



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 91/155 (58%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ D  ++   ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  DNTDEDAAEEAAAA--LATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             + +S+ E P     ++   D+       L +II
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII 162


>gi|304396867|ref|ZP_07378747.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
 gi|304355663|gb|EFM20030.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
          Length = 613

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/366 (54%), Positives = 257/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  +  + +R+   E  +++L  +   + +  F+    G 
Sbjct: 250 QNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPKKNFITLFTGN 309

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   + A + P   W   +    D +++   ++  +  ETG++I + + I   + 
Sbjct: 310 ETNESWFKAALAMNKP---WSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVKDINRRMS 366

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 486

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 487 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 546

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 547 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 606

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 607 LRSFLD 612



 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 96/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D++  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLI 164


>gi|262371919|ref|ZP_06065198.1| RNA polymerase sigma factor sigma-70 [Acinetobacter junii SH205]
 gi|262311944|gb|EEY93029.1| RNA polymerase sigma factor sigma-70 [Acinetobacter junii SH205]
          Length = 627

 Score =  382 bits (980), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 208/400 (52%), Positives = 267/400 (66%), Gaps = 3/400 (0%)

Query: 286 EIAEV-YRELRSL-QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E+A+V + EL S   D     +K  +SS + K   E L  +           D++ E + 
Sbjct: 227 EVAKVRFTELESAWNDTKAIIEKHGRSSEEAKAALESLAAVFMMFKFTPRLFDIISEMIR 286

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               +I  NE E++R A   G + R+ F      +E +P W+         E K  +   
Sbjct: 287 GTHDQIRANEREIMRYAVRRGRMDRNQFRTTFPEQESNPAWLDEQIAKAPAEIKPHLEKV 346

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
              +L  + +I  I  E  +++ E + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 347 RPDVLAFQQKIADIEKELDLNVKEIKDISKRMAVGEAKARRAKKEMVEANLRLVISIAKK 406

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 407 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 466

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD
Sbjct: 467 VHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGD 526

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+MRFGI M TDHTL
Sbjct: 527 DEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTL 586

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 587 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 626


>gi|82778397|ref|YP_404746.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae Sd197]
 gi|309785377|ref|ZP_07680008.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 1617]
 gi|81242545|gb|ABB63255.1| RNA polymerase, sigma(70) factor [Shigella dysenteriae Sd197]
 gi|308926497|gb|EFP71973.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 1617]
          Length = 613

 Score =  382 bits (980), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 257/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W + A     P  E  + V+ EV   L+   ++  I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAATAMNKPWSEKLHDVSEEVHRALQ---KLLQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|206576865|ref|YP_002236518.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae 342]
 gi|288933503|ref|YP_003437562.1| RNA polymerase, sigma 70 subunit, RpoD [Klebsiella variicola At-22]
 gi|290511438|ref|ZP_06550807.1| RNA polymerase primary sigma factor [Klebsiella sp. 1_1_55]
 gi|206565923|gb|ACI07699.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae 342]
 gi|288888232|gb|ADC56550.1| RNA polymerase, sigma 70 subunit, RpoD [Klebsiella variicola At-22]
 gi|289776431|gb|EFD84430.1| RNA polymerase primary sigma factor [Klebsiella sp. 1_1_55]
          Length = 613

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/397 (51%), Positives = 271/397 (68%), Gaps = 7/397 (1%)

Query: 289 EVYRELRS---LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + ELR+   L  + +  +    ++ + ++LK  L ++     L   + D LV  +  +
Sbjct: 219 EKFAELRTQYELTRDTIKAKGRSHAAAQEEILK--LSEVFKQFRLVPKQFDYLVNSMRSM 276

Query: 346 SKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             R+   E  +++L  +   + +  F+    G E    W + A    +  W   +    +
Sbjct: 277 MDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAVAMNKP-WSEKLLEVKE 335

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYT
Sbjct: 336 DVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 395

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 455

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++
Sbjct: 456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 515

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEE
Sbjct: 516 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 575

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 576 VGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612



 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 89/138 (64%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|152971991|ref|YP_001337100.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|330003818|ref|ZP_08304768.1| RNA polymerase sigma factor RpoD [Klebsiella sp. MS 92-3]
 gi|150956840|gb|ABR78870.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|328536802|gb|EGF63114.1| RNA polymerase sigma factor RpoD [Klebsiella sp. MS 92-3]
          Length = 613

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/397 (51%), Positives = 271/397 (68%), Gaps = 7/397 (1%)

Query: 289 EVYRELRS---LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + ELR+   L  + +  +    ++ + ++LK  L ++     L   + D LV  +  +
Sbjct: 219 EKFAELRTQYELTRDTIKAKGRSHAAAQEEILK--LSEVFKQFRLVPKQFDYLVNSMRSM 276

Query: 346 SKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             R+   E  +++L  +   + +  F+    G E    W + A    +  W   +    +
Sbjct: 277 MDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAVAMNKP-WSEKLLEVKE 335

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYT
Sbjct: 336 DVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 395

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 455

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++
Sbjct: 456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 515

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEE
Sbjct: 516 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 575

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 576 VGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612



 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 89/138 (64%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|114048481|ref|YP_739031.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-7]
 gi|113889923|gb|ABI43974.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-7]
          Length = 619

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 207/400 (51%), Positives = 275/400 (68%), Gaps = 5/400 (1%)

Query: 285 DEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           +E  E + +LR+  +NA+     K  +     K L E + ++     L   + D LV+ +
Sbjct: 221 EEARERFGQLRTAYENALKIIEAKGREHPESIKALFE-IGEIFKEFRLVPKQFDRLVKSM 279

Query: 343 YDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
             +  R+   E  L++L  +   + +  F++   G E +  W    K+  +   +     
Sbjct: 280 RSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDWFDAEKNSTKPYAEGLRMV 339

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E D + + R+++ +I  ETG+ I+  + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 340 EED-VQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 398

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 458

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLKI KEPIS+ETPIG
Sbjct: 459 PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVLKIAKEPISMETPIG 518

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VLRMRFGI MNTDHT
Sbjct: 519 DDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHT 578

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 579 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 618


>gi|85711761|ref|ZP_01042817.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina baltica
           OS145]
 gi|85694376|gb|EAQ32318.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina baltica
           OS145]
          Length = 611

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/377 (53%), Positives = 262/377 (69%), Gaps = 18/377 (4%)

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +V  +KL  L     L   + D LV+ +  + +R+   E  +++ A +  G+ +  F++
Sbjct: 243 ARVEIDKLSDLFKQFRLVPKQFDRLVQDMRAMMQRVRVQERLVMKAAVEQAGMPKRAFMK 302

Query: 373 RHQGRELDPHWVS--------YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
              G E    WV         YA    E         E++  +   NEI+    ETG++I
Sbjct: 303 AFAGNENSLAWVDEQISAGVDYATTLQEAR------VEIERCVTKLNEIEK---ETGLTI 353

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 354 AKVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 413

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 414 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 473

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP PEE+A+++AMP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA
Sbjct: 474 REPLPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSA 533

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +LR +   VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 534 TSESLRNSVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS++L+SFLD
Sbjct: 594 RKLRHPSRSEQLKSFLD 610



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 85/158 (53%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++G++T  E+N  LP + V S+Q+ED + M+++MGI V     D DDL   E
Sbjct: 10  KVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQIEDIIRMINDMGIRVFESAPDADDLMMSE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D      +A   +       D     T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  SAADEDAAEEAAQALATV-----DGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D        L EII
Sbjct: 125 DGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTEII 162


>gi|262042263|ref|ZP_06015428.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259040327|gb|EEW41433.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 611

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/397 (51%), Positives = 271/397 (68%), Gaps = 7/397 (1%)

Query: 289 EVYRELRS---LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + ELR+   L  + +  +    ++ + ++LK  L ++     L   + D LV  +  +
Sbjct: 217 EKFAELRTQYELTRDTIKAKGRSHAAAQEEILK--LSEVFKQFRLVPKQFDYLVNSMRSM 274

Query: 346 SKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             R+   E  +++L  +   + +  F+    G E    W + A    +  W   +    +
Sbjct: 275 MDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAVAMNKP-WSEKLLEVKE 333

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYT
Sbjct: 334 DVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 393

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 394 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 453

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++
Sbjct: 454 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 513

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEE
Sbjct: 514 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 573

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 574 VGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610



 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 89/138 (64%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|146313109|ref|YP_001178183.1| RNA polymerase sigma factor RpoD [Enterobacter sp. 638]
 gi|145319985|gb|ABP62132.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter sp. 638]
          Length = 631

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 208/395 (52%), Positives = 268/395 (67%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR+  + A +  K + +S    K   +KL  +     L   + D LV  +  +  
Sbjct: 237 EKFGELRTQYELARDTIKAKGRSHAAAKEEIQKLSDVFKQFRLVPKQFDYLVNSMRVMMD 296

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +++L  +   + +  F+    G E    W + A       W   +    D +
Sbjct: 297 RVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM-NKPWSEKLHDVSDDV 355

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 356 QRGLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 415

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 416 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 475

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ S
Sbjct: 476 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 535

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVG
Sbjct: 536 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 595

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 596 KQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 630



 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 95/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 29  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 88

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 89  NSNNTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 142

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +      L +II
Sbjct: 143 RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDII 183


>gi|297520936|ref|ZP_06939322.1| RNA polymerase sigma factor RpoD [Escherichia coli OP50]
          Length = 436

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 204/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 74  KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 133

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 134 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 190

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 191 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 250

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 251 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 310

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 311 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 370

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 371 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 430

Query: 677 RSFLD 681
           RSFLD
Sbjct: 431 RSFLD 435


>gi|157372533|ref|YP_001480522.1| RNA polymerase sigma factor RpoD [Serratia proteamaculans 568]
 gi|157324297|gb|ABV43394.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia proteamaculans
           568]
          Length = 647

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 285 KLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 344

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 345 TSDTWFAAALAMAKP-WSEKLKDVADDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 403

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 404 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 463

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 464 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 523

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 524 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 583

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 584 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 643

Query: 679 FLD 681
           FLD
Sbjct: 644 FLD 646



 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 46  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 105

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 106 NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 162

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 163 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 200


>gi|152999721|ref|YP_001365402.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS185]
 gi|160874340|ref|YP_001553656.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS195]
 gi|151364339|gb|ABS07339.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS185]
 gi|160859862|gb|ABX48396.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS195]
          Length = 627

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 197/353 (55%), Positives = 256/353 (72%), Gaps = 2/353 (0%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W +  K
Sbjct: 275 LVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGNETNLDWFNTEK 334

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              +   +     E D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKKEM
Sbjct: 335 ASTKPYAEGLRMVE-DDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKKEM 393

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 394 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 453

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLK
Sbjct: 454 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVLK 513

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VL
Sbjct: 514 IAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAKVL 573

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 574 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 626



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 89/155 (57%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 26  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 85

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 86  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 143

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             + +S+ E P     ++   D+       L +II
Sbjct: 144 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII 178


>gi|113971243|ref|YP_735036.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-4]
 gi|113885927|gb|ABI39979.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-4]
          Length = 619

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 207/400 (51%), Positives = 275/400 (68%), Gaps = 5/400 (1%)

Query: 285 DEIAEVYRELRSLQDNAVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           +E  E + +LR+  +NA+     K  +     K L E + ++     L   + D LV+ +
Sbjct: 221 EEARERFGQLRTAYENALKIIEAKGREHPESIKALFE-IGEIFKEFRLVPKQFDRLVKSM 279

Query: 343 YDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
             +  R+   E  L++L  +   + +  F++   G E +  W    K+  +   +     
Sbjct: 280 RSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDWFDAEKNSNKPYAEGLKMV 339

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E D + + R+++ +I  ETG+ I+  + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 340 EED-VQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 398

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 458

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLKI KEPIS+ETPIG
Sbjct: 459 PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKVLKIAKEPISMETPIG 518

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VLRMRFGI MNTDHT
Sbjct: 519 DDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHT 578

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 579 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 618


>gi|162420372|ref|YP_001604920.1| RNA polymerase sigma factor RpoD [Yersinia pestis Angola]
 gi|162353187|gb|ABX87135.1| RNA polymerase sigma factor RpoD [Yersinia pestis Angola]
          Length = 612

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 250 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 309

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 310 TSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 368

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 369 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 428

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 429 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 488

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   NLR  T  VLA
Sbjct: 489 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSENLRSATHDVLA 548

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 549 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608

Query: 679 FLD 681
           FLD
Sbjct: 609 FLD 611



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|50085952|ref|YP_047462.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter sp. ADP1]
 gi|49531928|emb|CAG69640.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter sp. ADP1]
          Length = 629

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 206/400 (51%), Positives = 266/400 (66%), Gaps = 3/400 (0%)

Query: 286 EIAEV-YRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           EIA+V + EL +   N     +K  ++S +     E L  +           D++ E + 
Sbjct: 229 EIAKVRFEELEAAWKNTKTVIEKHGRNSEEANAALESLATVFMMFKFTPRLFDIISEMIR 288

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
              + I  NE E++R A   G + R  F     G+E +P W+         E K ++   
Sbjct: 289 GTHENIRSNEREVMRYAVRRGRMDRTQFRTSFPGQESNPAWLEEQIAKAPNESKAYLEKV 348

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
              I   + +I  I  +  +++ E + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 349 RPDIQAFQQKIAEIEQDLNLNVREIKEIAKRMAVGEAKARRAKKEMVEANLRLVISIAKK 408

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 409 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 468

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD
Sbjct: 469 VHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGD 528

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+MRFGI M TDHTL
Sbjct: 529 DEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTL 588

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 589 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 628


>gi|238762467|ref|ZP_04623438.1| RNA polymerase sigma factor rpoD [Yersinia kristensenii ATCC 33638]
 gi|238699452|gb|EEP92198.1| RNA polymerase sigma factor rpoD [Yersinia kristensenii ATCC 33638]
          Length = 613

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/395 (51%), Positives = 266/395 (67%), Gaps = 7/395 (1%)

Query: 291 YRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           + ELR   +N   A+       +S   ++L   L ++     L   + D LV  +  +  
Sbjct: 221 FSELREQYENTRMAIKKNGRSHASAAAEILN--LSEVFKQFRLVPKQFDYLVNNMRAMMD 278

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +++L  +   + +  F+      E    W + A    +  W   +    D +
Sbjct: 279 RVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFAAAVAMGKP-WSEKLKDVSDDV 337

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 338 QRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 397

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 398 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 457

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ S
Sbjct: 458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVG
Sbjct: 518 HLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 577

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 578 KQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 95/159 (59%), Gaps = 7/159 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            G   +  S+ E P     L+   D +  G   L ++I+
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIN 165


>gi|221134905|ref|ZP_03561208.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola sp. HTCC2999]
          Length = 607

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 202/376 (53%), Positives = 266/376 (70%), Gaps = 6/376 (1%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR--LAQSYGIK 366
           +S+   K    KL  +     L   + D +V+ +  +  R+   E  +++  +AQ+   K
Sbjct: 234 RSNAAAKKQIAKLSDVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLIMKHCVAQAKMPK 293

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV-DSILKIRNEIKSISVETGISIS 425
           +D F++   G E    W  Y K     +    V     + I +  +++ ++  ETG+ I+
Sbjct: 294 KD-FIKAFAGNETSTDW--YYKILKTSKPYVLVLETFQEDIERSVSKMNAVEAETGLCIA 350

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 351 DIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 410

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ R
Sbjct: 411 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 470

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+++++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   + PLDSA 
Sbjct: 471 EPTPEELSERMIMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIIQPLDSAT 530

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             +L++ T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 531 GGSLKDATQDVLAGLTQREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 590

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRS++LRSFLD
Sbjct: 591 KLRHPSRSEQLRSFLD 606



 Score = 94.4 bits (233), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 57/141 (40%), Positives = 82/141 (58%), Gaps = 9/141 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V     D D+L   E
Sbjct: 9   KLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVFESAPDSDELLMAE 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D     ++A   +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  TTTDEEVAEAAAQALATV-----ESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIE 123

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 124 DGINQVQCSVAEYPEAITYLL 144


>gi|320539899|ref|ZP_08039558.1| putative RNA polymerase, sigma 70 (sigma D) factor [Serratia
           symbiotica str. Tucson]
 gi|320030085|gb|EFW12105.1| putative RNA polymerase, sigma 70 (sigma D) factor [Serratia
           symbiotica str. Tucson]
          Length = 607

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+  +E  +++L  +   + +  F+    G E
Sbjct: 245 KLSEVFKQFRLVPKQFDFLVNSMRAMMDRVHTHERTIMKLCVEQCKMPKKNFVTLFAGNE 304

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W   A+   +  W   +    + + +   ++  I  ETG++I + + I   +  GE
Sbjct: 305 TSDVWFEKAQAMTKP-WSEKLKDVAEDVQRSLQKLHQIEEETGLTIEQVKDINRRMSIGE 363

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 364 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 423

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ M
Sbjct: 424 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPMPEELAERMLM 483

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 484 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTFELPLDSATSESLRSATHDVLA 543

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 544 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 603

Query: 679 FLD 681
           FLD
Sbjct: 604 FLD 606



 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 63/169 (37%), Positives = 97/169 (57%), Gaps = 7/169 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII------DLEACIGP 193
             +  S+ E P     L+   D +  G   L ++I      D E  I P
Sbjct: 130 NQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPDAEEDIAP 178


>gi|238750950|ref|ZP_04612447.1| RNA polymerase sigma factor rpoD [Yersinia rohdei ATCC 43380]
 gi|238710864|gb|EEQ03085.1| RNA polymerase sigma factor rpoD [Yersinia rohdei ATCC 43380]
          Length = 612

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 200/364 (54%), Positives = 255/364 (70%), Gaps = 4/364 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 250 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 309

Query: 379 LDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
               W  +A     G+ W   +    D + +   +++ I  ETG++I + + I   +  G
Sbjct: 310 TSDTW--FAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIG 367

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 368 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 427

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 428 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 487

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 488 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 547

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 548 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 607

Query: 678 SFLD 681
           SFLD
Sbjct: 608 SFLD 611



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 EGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|85058229|ref|YP_453931.1| RNA polymerase sigma factor RpoD [Sodalis glossinidius str.
           'morsitans']
 gi|84778749|dbj|BAE73526.1| RNA polymerase sigma-70 factor RpoD [Sodalis glossinidius str.
           'morsitans']
          Length = 615

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/383 (53%), Positives = 263/383 (68%), Gaps = 10/383 (2%)

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-A 360
            NG+   KS+   ++L   L  +     L   + D LV  +  +  R+   E  +++L  
Sbjct: 239 TNGRSHAKSA--SEILN--LSDVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERLIMKLCV 294

Query: 361 QSYGIKRDVFLERHQGRELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +   + +  F+    G E    W   + A + P   W   +    D + +   +++ I  
Sbjct: 295 EISKMPKKNFVTLFAGNETSESWFKAALAMNKP---WSEKLHEVDDDVYRSLQKLRQIEE 351

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 352 ETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 411

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 412 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 471

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    
Sbjct: 472 MLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE 531

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 532 LPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 591

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 592 IEAKALRKLRHPSRSEVLRSFLD 614



 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTFAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TTSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|126173383|ref|YP_001049532.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125996588|gb|ABN60663.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS155]
          Length = 627

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/355 (56%), Positives = 256/355 (72%), Gaps = 6/355 (1%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSY-- 386
           L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W +   
Sbjct: 275 LVPKQFDRLVKSIRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGNETNLDWFNTEK 334

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A   P  E    V    D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 335 ASTKPYAEGLRMVE---DDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 391

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 392 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 451

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 452 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 511

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 512 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAK 571

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 572 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 626



 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 89/155 (57%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 26  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 85

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 86  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 143

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             + +S+ E P     ++   D+       L +II
Sbjct: 144 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII 178


>gi|302342714|ref|YP_003807243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
 gi|301639327|gb|ADK84649.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
          Length = 590

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 182/280 (65%), Positives = 228/280 (81%), Gaps = 1/280 (0%)

Query: 403 VDSILKI-RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           VD  L++ R  I+ + +E  +     R I+  V KG+  A  AK+E+VEANLRLV+S+AK
Sbjct: 310 VDESLRVARGRIREVEMECKMGAPSLRKILDRVGKGQTLAQDAKQELVEANLRLVVSIAK 369

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRI
Sbjct: 370 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRI 429

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K++RT+R +  +  REPTPEEIA+K+  P+E VRKVLKI KEPISLETPIG
Sbjct: 430 PVHMIETINKLIRTSRYLVQEFGREPTPEEIAEKMDFPLEKVRKVLKIAKEPISLETPIG 489

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E+ SHLGDFIEDK  ++P D+ I  NL E T +VLA+LTPREE+VLRMRFGIG  +DHT
Sbjct: 490 EEEDSHLGDFIEDKKVINPADAVISLNLCEQTRKVLATLTPREEKVLRMRFGIGQKSDHT 549

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL++F++
Sbjct: 550 LEEVGRDFDVTRERIRQIEAKALRKLRHPSRAKKLKAFIE 589



 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 53/172 (30%), Positives = 90/172 (52%), Gaps = 6/172 (3%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   R +G++T EE+N  L  +EV+S++M+D + +L  MGI +VD +     +  + S 
Sbjct: 14  LISKGRSKGFLTYEEINDALD-EEVTSDRMDDMLMVLDEMGIQLVDDEGSLKVKAQDSSF 72

Query: 94  DLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           +  +          + +   D     DPV+MYLREMG + LL+REGE+ IAKRIE G   
Sbjct: 73  EDEAEDEVVEAAEDEAEIPGDEGRVSDPVKMYLREMGQVSLLTREGEVEIAKRIEKGERQ 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFF 200
            + +L E  L    ++     L +    +R+++    D E+ +  E++   F
Sbjct: 133 CIDALLECSLCVAEILELGRRLENDELRIRDVVCDIDDEESFVQQETRKAEF 184


>gi|238760057|ref|ZP_04621208.1| RNA polymerase sigma factor rpoD [Yersinia aldovae ATCC 35236]
 gi|238701744|gb|EEP94310.1| RNA polymerase sigma factor rpoD [Yersinia aldovae ATCC 35236]
          Length = 611

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 206/396 (52%), Positives = 267/396 (67%), Gaps = 9/396 (2%)

Query: 291 YRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           + ELR   +N   A+       +S   ++L   L ++     L   + D LV  +  +  
Sbjct: 219 FSELRDQYENTRMAIKKNGRSHASAAAEILN--LSEVFKQFRLVPKQFDYLVNNMRAMMD 276

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDS 405
           R+   E  +++L  +   + +  F+      E    W  +A     G+ W   +    D 
Sbjct: 277 RVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTW--FAAAIAMGKPWSEKLKDVSDD 334

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 335 VQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 394

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 395 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 454

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ 
Sbjct: 455 IETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED 514

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEV
Sbjct: 515 SHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEV 574

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 575 GKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 95/159 (59%), Gaps = 7/159 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            G   +  S+ E P     L+   D +  G   L ++I+
Sbjct: 127 EGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIN 165


>gi|238896571|ref|YP_002921314.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae NTUH-K2044]
 gi|238548896|dbj|BAH65247.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 632

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/397 (51%), Positives = 270/397 (68%), Gaps = 7/397 (1%)

Query: 289 EVYRELRS---LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + ELR+   L  + +  +    ++ + ++LK  L ++     L   + D LV  +  +
Sbjct: 238 EKFAELRTQYELTRDTIKAKGRSHAAAQEEILK--LSEVFKQFRLVPKQFDYLVNSMRSM 295

Query: 346 SKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             R+   E  +++L  +   + +  F+    G E    W + A       W   +    +
Sbjct: 296 MDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAVAM-NKPWSEKLLEVKE 354

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYT
Sbjct: 355 DVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 414

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 415 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 474

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++
Sbjct: 475 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 534

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEE
Sbjct: 535 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 594

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 595 VGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 631



 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 89/138 (64%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 29  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 88

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 89  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 146

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 147 NQVQCSVAEYPEAITYLL 164


>gi|147756|gb|AAA24601.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 613

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.0 bits (232), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|328954514|ref|YP_004371848.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454838|gb|AEB10667.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 577

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/415 (49%), Positives = 288/415 (69%), Gaps = 8/415 (1%)

Query: 271 AMEDQLRP----KVMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
            +E  ++P    +V+  +  + ++ + L+S L    ++ +K  +   + +  ++++V+  
Sbjct: 162 GLEQGIQPDRLQQVIQGIYRLNDLIKRLQSCLASKTLSEEKRVQLQTRLERYRQRMVEQF 221

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
            SL L Q +++ ++ Q+ D S  +  ++ E+ R  Q  G+    F  RH  R+L    +S
Sbjct: 222 KSLKLPQHQLNRIIRQINDYSYAVRASQKEIDRCLQKIGLDAPEF--RHLCRKLQEKLLS 279

Query: 386 YAKDFPEGEWKNF-VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                 +GE     +A   +S    +  ++ I  ETG+S  +   I   V++G+ +AS A
Sbjct: 280 GISPELDGELSIVEIAQLAESWRGAQRRLQKIESETGLSAEKLLEIQKRVQRGDRQASRA 339

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKFSTYA WW+
Sbjct: 340 KSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYERGYKFSTYATWWI 399

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I REPTPEE+A+K+  P+E VR
Sbjct: 400 RQAITRAIADQARTIRIPVHMIETINKLLRTSRYLVQEIGREPTPEELAEKMEYPLEKVR 459

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPISLETPIG+E+ S+L DFIEDK   SP ++    NL E T +VL++LTPRE
Sbjct: 460 KVLKIAKEPISLETPIGEEEDSYLADFIEDKKISSPTEAVENLNLAEITRKVLSTLTPRE 519

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+V+R+RFGIG  TDHTLEEVGK+F VTRERIRQIEAKA+RKL+H SR K+L+SF
Sbjct: 520 EKVIRLRFGIGEKTDHTLEEVGKKFMVTRERIRQIEAKALRKLRHASRLKRLQSF 574



 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 40/51 (78%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           DDPV+MYLREMG++ LL+REGEI IAKRIE G   ++++L E+    +A++
Sbjct: 88  DDPVKMYLREMGTVSLLTREGEIEIAKRIEEGCKEIVSALLETKFGIRAIL 138


>gi|16130963|ref|NP_417539.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|89109837|ref|AP_003617.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|170082610|ref|YP_001731930.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238902178|ref|YP_002927974.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|1710680|sp|P00579|RPOD_ECOLI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|882590|gb|AAA89147.1| CG Site No. 231; alternate gene name alt [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1789448|gb|AAC76103.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|73671318|gb|AAZ80070.1| RpoD [Escherichia coli LW1655F+]
 gi|85675868|dbj|BAE77118.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|169890445|gb|ACB04152.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238863501|gb|ACR65499.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|260447898|gb|ACX38320.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli DH1]
 gi|315137660|dbj|BAJ44819.1| RNA polymerase sigma factor RpoD [Escherichia coli DH1]
          Length = 613

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 259/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|332307721|ref|YP_004435572.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175050|gb|AEE24304.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 613

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/377 (53%), Positives = 267/377 (70%), Gaps = 8/377 (2%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR--LAQSYGIK 366
           +S  K +   ++L ++     L   + D +V+ +  +  RI   E  +++  +A +   K
Sbjct: 240 RSHAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPK 299

Query: 367 RDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           +D F++   G E    W+    A D P  E       E++  +    ++ ++  ETG+ I
Sbjct: 300 KD-FIKAFSGNETSTDWLYELMASDAPYVEELKVHQEELERSI---GKMNAVEEETGLII 355

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 356 ADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 415

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 416 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 475

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+++++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   V PLDSA
Sbjct: 476 REPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQPLDSA 535

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +L+  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 536 TGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS++LRSFLD
Sbjct: 596 RKLRHPSRSEQLRSFLD 612



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 57/141 (40%), Positives = 83/141 (58%), Gaps = 9/141 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI----NVVDGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI    N  D D+L  +E
Sbjct: 10  KLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPDSDELLMQE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D     ++A   +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TTTDEEVAEAAAQALATV-----ESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 125 EGINQVQCSVAEYPEAITYLL 145


>gi|152984199|ref|YP_001346113.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PA7]
 gi|150959357|gb|ABR81382.1| sigma factor RpoD [Pseudomonas aeruginosa PA7]
          Length = 617

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 259/363 (71%), Gaps = 4/363 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++    + +   E  +++L  +   + R  FL      E 
Sbjct: 256 LAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHET 315

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  WV S  K  P+  +   +    D IL+ + ++ ++  E  ++++E + I   +  GE
Sbjct: 316 DEKWVDSVLKSKPK--YAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGE 373

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 374 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 433

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 434 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDM 493

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA
Sbjct: 494 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLA 553

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 554 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRS 613

Query: 679 FLD 681
           FLD
Sbjct: 614 FLD 616


>gi|296104731|ref|YP_003614877.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059190|gb|ADF63928.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 615

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V  +V   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVKEDVHRGLQ---KLQQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 489

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 490 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 549

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 609

Query: 677 RSFLD 681
           RSFLD
Sbjct: 610 RSFLD 614



 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/141 (41%), Positives = 88/141 (62%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S ++ + A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TSNNTDEDAEEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 127 DGINQVQCSVAEYPEAITYLL 147


>gi|262281266|ref|ZP_06059048.1| RNA polymerase sigma factor rpoD [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257497|gb|EEY76233.1| RNA polymerase sigma factor rpoD [Acinetobacter calcoaceticus
           RUH2202]
          Length = 627

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/365 (54%), Positives = 252/365 (69%), Gaps = 1/365 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E L  +           D++ E +    ++I  NE E++R A   G + R  F      +
Sbjct: 262 EALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREVMRYAVRRGRMDRTQFRTSFPKQ 321

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +P W+         E K  +      IL  + +I  I  E  +S++E + I   +  G
Sbjct: 322 ESNPAWLDEQIAKAPAEIKAHLEKVRPDILAFQQKIADIEKELNLSVAEIKDISKRMAIG 381

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 382 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 441

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L 
Sbjct: 442 TYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLE 501

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL
Sbjct: 502 MDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVL 561

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 562 ENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLR 621

Query: 678 SFLDG 682
           SFL+ 
Sbjct: 622 SFLEN 626


>gi|260767412|ref|ZP_05876349.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|260617524|gb|EEX42706.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|315181195|gb|ADT88109.1| RNA polymerase sigma factor RpoD [Vibrio furnissii NCTC 11218]
          Length = 628

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 207/403 (51%), Positives = 273/403 (67%), Gaps = 9/403 (2%)

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            AL +  E+  + ++LQ  A+N   +E S  K +   + ++ +     L   + D LV+ 
Sbjct: 231 LALQKFTELRNKFQNLQ-LAINEHGNESS--KAQQATDLVLDVFREFRLTPKQFDHLVDT 287

Query: 342 LYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNF 398
           L     R+   E  +++ + +   + +  F+    G E    W+    A D P   + + 
Sbjct: 288 LRTSMDRVRTQERLIMKSVVEVAKMPKKSFIAVFTGNESSEAWLDQVLASDKP---YVDK 344

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D I +   +++ I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 345 IRQYEDDIRRSIQKLQIIEQETSLTVERIKDISRRMSIGEAKARRAKKEMVEANLRLVIS 404

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 405 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 464

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ET
Sbjct: 465 IRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMET 524

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNT
Sbjct: 525 PIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNT 584

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 585 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 627


>gi|329298675|ref|ZP_08256011.1| RNA polymerase sigma factor RpoD [Plautia stali symbiont]
          Length = 610

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/362 (54%), Positives = 255/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    G E 
Sbjct: 249 LSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCVELCKMPKKNFITLFTGNET 308

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W   A    +   +     E D +++   ++  I  ETG++I + + I   +  GE 
Sbjct: 309 SESWFKTALAMNKPWSEKLQEVEKD-VMRSLQKLLQIEEETGLTIEQVKDINRRMSIGEA 367

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 368 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 427

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP
Sbjct: 428 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMP 487

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA 
Sbjct: 488 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAG 547

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 548 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 607

Query: 680 LD 681
           LD
Sbjct: 608 LD 609



 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 93/155 (60%), Gaps = 1/155 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   + +GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D   +E
Sbjct: 10  KLLVTRGKVQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLMLNE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NSTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 129

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  S+ E P     L+   D +  G + L ++I
Sbjct: 130 NQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI 164


>gi|15595773|ref|NP_249267.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAO1]
 gi|116054304|ref|YP_788749.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218889317|ref|YP_002438181.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa LESB58]
 gi|254243670|ref|ZP_04936992.1| sigma factor RpoD [Pseudomonas aeruginosa 2192]
 gi|296387081|ref|ZP_06876580.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAb1]
 gi|313111780|ref|ZP_07797573.1| sigma factor RpoD [Pseudomonas aeruginosa 39016]
 gi|133310|sp|P26480|RPOD_PSEAE RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|9946447|gb|AAG03965.1|AE004494_1 sigma factor RpoD [Pseudomonas aeruginosa PAO1]
 gi|216913|dbj|BAA14146.1| principal sigma factor [Pseudomonas aeruginosa]
 gi|30060254|gb|AAP13091.1| RpoD [Pseudomonas sp. M18]
 gi|115589525|gb|ABJ15540.1| sigma factor RpoD [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126197048|gb|EAZ61111.1| sigma factor RpoD [Pseudomonas aeruginosa 2192]
 gi|218769540|emb|CAW25300.1| sigma factor RpoD [Pseudomonas aeruginosa LESB58]
 gi|310884075|gb|EFQ42669.1| sigma factor RpoD [Pseudomonas aeruginosa 39016]
          Length = 617

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 259/363 (71%), Gaps = 4/363 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++    + +   E  +++L  +   + R  FL      E 
Sbjct: 256 LAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHET 315

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  WV S  K  P+  +   +    D IL+ + ++ ++  E  ++++E + I   +  GE
Sbjct: 316 DEKWVDSVLKSKPK--YAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGE 373

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 374 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 433

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 434 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDM 493

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA
Sbjct: 494 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLA 553

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 554 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRS 613

Query: 679 FLD 681
           FLD
Sbjct: 614 FLD 616


>gi|109897363|ref|YP_660618.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoalteromonas atlantica
           T6c]
 gi|109699644|gb|ABG39564.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoalteromonas atlantica
           T6c]
          Length = 613

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 204/377 (54%), Positives = 266/377 (70%), Gaps = 8/377 (2%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR--LAQSYGIK 366
           +S  K +   ++L ++     L   + D +V+ +  +  RI   E  +++  +A +   K
Sbjct: 240 RSHAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPK 299

Query: 367 RDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           +D F++   G E    W+    A D P  E       E++  +   N ++    ETG+ I
Sbjct: 300 KD-FIKAFSGNETSTDWLFEILASDAPYVEELKVHQEELERSIGKMNAVED---ETGLII 355

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 356 ADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 415

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 416 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 475

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+++++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   V PLDSA
Sbjct: 476 REPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQPLDSA 535

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +L+  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 536 TGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS++LRSFLD
Sbjct: 596 RKLRHPSRSEQLRSFLD 612



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 57/141 (40%), Positives = 83/141 (58%), Gaps = 9/141 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI----NVVDGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI    N  D D+L  +E
Sbjct: 10  KLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPDSDELLMQE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D     ++A   +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TTTDEEVAEAAAQALATV-----ESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 125 EGINQVQCSVAEYPEAITYLL 145


>gi|299768976|ref|YP_003731002.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
 gi|298699064|gb|ADI89629.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
          Length = 627

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 198/365 (54%), Positives = 252/365 (69%), Gaps = 1/365 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E L  +           D++ E +    ++I  NE E++R A   G + R  F      +
Sbjct: 262 EALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKQ 321

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +P W+         E K  +      +L  + +I  I  E  +S++E + I   +  G
Sbjct: 322 ESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIKDISKRMAIG 381

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 382 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 441

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L 
Sbjct: 442 TYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLE 501

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL
Sbjct: 502 MDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVL 561

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 562 ENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLR 621

Query: 678 SFLDG 682
           SFL+ 
Sbjct: 622 SFLEN 626


>gi|317050370|ref|YP_004111486.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
 gi|316945454|gb|ADU64930.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
          Length = 627

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 210/423 (49%), Positives = 286/423 (67%), Gaps = 22/423 (5%)

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           SAH  +    ++R  V   ++ I ++ ++L SL++    G+KD     K +   E +  +
Sbjct: 220 SAHVRAENATEMRDFV---INSICDIGQQLLSLREYKAKGKKD-----KYRKTLESMTAV 271

Query: 325 VGSLSLNQ---SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
           +  + L     SRI  ++++ Y  S+R      EL ++ +  G+ RD  L+   G E   
Sbjct: 272 ISEIRLTNETISRISNMIKEQYLESRR---AGSELAKIIKVTGLSRD-DLQYLCGEESSA 327

Query: 382 HWVSYAK---DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
             V  A+        +++  +    +SI  +R     I   TG+  +E   IV  VR+GE
Sbjct: 328 EHVESARAKTSLRAEDFERLLGKASESIASLRE----IEESTGVDANELMSIVQQVREGE 383

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E+  AK +++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 384 EESKAAKMQLIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 443

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ REPTPEEIA K+ +
Sbjct: 444 YATWWIRQAITRAIADQARTIRIPVHMIETINKLVRTSRNLVQELGREPTPEEIADKMDL 503

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE VRKVLKI KEPISLETPIG+E+ S LGDFIEDKN VSP ++ I  NL+E    VL 
Sbjct: 504 PVEKVRKVLKIAKEPISLETPIGEEEDSSLGDFIEDKNTVSPAEAVISFNLKEQVRSVLH 563

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L+ RE  VL++RFGI  ++DHTLEEVGK+F VTRERIRQIEAKA+RKL+HP+RSK LR+
Sbjct: 564 TLSAREAEVLKLRFGIDTDSDHTLEEVGKKFNVTRERIRQIEAKALRKLRHPTRSKILRT 623

Query: 679 FLD 681
           FL+
Sbjct: 624 FLE 626



 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 57/185 (30%), Positives = 98/185 (52%), Gaps = 25/185 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           + ++++ +++RG++T +ELN FLP +    + ++  +  L  +GI +V  + L   +G E
Sbjct: 11  FTQLMEKSKERGFITYDELNDFLPKETTDPDLIDSIIENLGRIGIRLVATNKLSKGKG-E 69

Query: 91  DSLDLASSASNSSVFLQKRK-----------------------DSADRSTDDPVRMYLRE 127
            S + A    +    L                           D++ R TDDPVR+YL+E
Sbjct: 70  SSDEFAVFLKDQPAVLDGDDIENDDEEESDEEESEESTLDLTPDTSFR-TDDPVRLYLKE 128

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ LL+REGE+ IAK+IEAG   +++SL   P   ++L    ++L  G   L++II L
Sbjct: 129 MGSVPLLTREGEVDIAKKIEAGYEKIISSLIAIPKAVESLQELAEKLEAGEIGLKDIIML 188

Query: 188 EACIG 192
           +  +G
Sbjct: 189 DDEVG 193


>gi|253997427|ref|YP_003049491.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera mobilis JLW8]
 gi|253984106|gb|ACT48964.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera mobilis JLW8]
          Length = 646

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/383 (51%), Positives = 270/383 (70%), Gaps = 10/383 (2%)

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-A 360
           V G +D    V   +L E LV+L  +   +  +++ L +Q+  + + +  +E ++L    
Sbjct: 267 VKGSQD---PVYLALLSEILVELT-AFRFSPKQVETLCDQVRGLVETVRGHERKVLDFCV 322

Query: 361 QSYGIKRDVFLERHQGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +  G+ R  F++   G E +  W+      D P   +   +A    SIL  +  I  +  
Sbjct: 323 EKAGMPRPYFIKSFPGNESNLAWLDDELKLDNP---YNEKLARFNHSILDQQQRIIDLET 379

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           + GIS  E + I   +  GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 380 KVGISAKELKEINKQMTTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 439

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 440 IGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 499

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A+K+ MP + +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   +
Sbjct: 500 ILQETGIEPDPALLAEKMEMPEDKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSTTL 559

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P+D+A+ A+LR+ T+ VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 560 APVDAAVYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQ 619

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HP+RS++LRSFL+
Sbjct: 620 IEAKALRKLRHPTRSERLRSFLE 642



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 58/159 (36%), Positives = 89/159 (55%), Gaps = 23/159 (14%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T  E+N  LP D   SEQ++  + M+++MGI V         E + D
Sbjct: 37  KSLIVLGKERGYLTYAEINDHLPDDVQGSEQIDGIIGMINDMGIQVY--------EETPD 88

Query: 92  SLDLASSASNSSVFLQKRKDSADRS----------TDDPVRMYLREMGSIELLSREGEIA 141
           +  L  S +  +V      + A+++          T DPVRMY+REMG+++LL+RE EI 
Sbjct: 89  AEALLMSDAPPAVTDDDAVEEAEQALATVDSEFGRTTDPVRMYMREMGTVDLLTRESEIE 148

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALI-----IWRDELN 175
           IA+RIE G   M+ ++   P T  AL+     + RDEL+
Sbjct: 149 IARRIEDGLKHMVQAIAACPTTIAALLEMVDKVERDELS 187


>gi|104779687|ref|YP_606185.1| RNA polymerase sigma factor RpoD [Pseudomonas entomophila L48]
 gi|95108674|emb|CAK13368.1| sigma D (sigma 70) factor of RNA polymerase [Pseudomonas
           entomophila L48]
          Length = 616

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/365 (54%), Positives = 258/365 (70%), Gaps = 4/365 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  L   + L   + D LVE++     R+   E  +++L  +   + R  FL      
Sbjct: 253 QALADLFMPIKLVPKQFDALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLFPSN 312

Query: 378 ELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E D  W    AK     +W   +  +  +I+  + ++  +  ETG++++E + I   +  
Sbjct: 313 ETDQTWSGDLAKR--NTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSI 370

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 490

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  V
Sbjct: 491 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 550

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ L
Sbjct: 551 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 610

Query: 677 RSFLD 681
           RSFLD
Sbjct: 611 RSFLD 615



 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     +
Sbjct: 12  KELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAE 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   +I
Sbjct: 131 EVMGAIAHFPGTVDYII 147


>gi|295097580|emb|CBK86670.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 614

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 257/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 252 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNE 311

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V  +V   L+   ++  I  ETG++I + + I   +  
Sbjct: 312 TSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQ---KLHQIEEETGLTIEQVKDINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 489 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/141 (41%), Positives = 88/141 (62%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S ++ + A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  TSNNTDEDAEEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 127 DGINQVQCSVAEYPEAITYLL 147


>gi|95928999|ref|ZP_01311744.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134900|gb|EAT16554.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
          Length = 583

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 178/269 (66%), Positives = 223/269 (82%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            K +  ETG S  E    +  V +GE  A  AK E+VEANLRLV+S+AKKYTNRGLQFLD
Sbjct: 313 FKRVEEETGFSPEELVDSLKEVHRGEWRAKAAKTELVEANLRLVVSIAKKYTNRGLQFLD 372

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+
Sbjct: 373 LIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKL 432

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +RT+R++  ++ REP PEEIA+++ +P+E VR+VLKI KEPISLETPIG+E+ S LGDFI
Sbjct: 433 IRTSRQLVQELGREPIPEEIAERMDLPLEKVRRVLKIAKEPISLETPIGEEEDSSLGDFI 492

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDK AVSPL++ I+ NL + T  VL++L+PREE+VLRMRFGIG  +DHTLEEVG+ F VT
Sbjct: 493 EDKGAVSPLEAVIKGNLSDQTAEVLSTLSPREEKVLRMRFGIGERSDHTLEEVGQDFNVT 552

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKL+HPSR+K+LRSF+D
Sbjct: 553 RERIRQIEAKALRKLRHPSRAKRLRSFVD 581



 Score =  107 bits (268), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 54/150 (36%), Positives = 91/150 (60%), Gaps = 4/150 (2%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           ++ ++++I+  +++GY+T +E+N  LP D VSS Q+ED + M   + I +VD +  E++ 
Sbjct: 7   EEEFQQLIETGKEKGYLTYDEVNDALPEDMVSSTQLEDVMTMFGELDIEIVDNETKEEKS 66

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + + D   S    + F    +      T DPVRMYLREMG + LL+REGE+ IAKRIE
Sbjct: 67  KGDSNDDEDDSKEEGNNF----EAGVIGRTSDPVRMYLREMGQVSLLTREGEVEIAKRIE 122

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDG 177
            G  ++   + ++P+  Q +I   D+L++G
Sbjct: 123 EGEGLITQVVLKTPIALQEVITLGDQLSEG 152


>gi|222034799|emb|CAP77541.1| RNA polymerase sigma factor rpoD [Escherichia coli LF82]
          Length = 613

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 203/365 (55%), Positives = 258/365 (70%), Gaps = 6/365 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIA Q+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIAVQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 RSFLD 681
           RSFLD
Sbjct: 608 RSFLD 612



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|107099562|ref|ZP_01363480.1| hypothetical protein PaerPA_01000575 [Pseudomonas aeruginosa PACS2]
          Length = 604

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 199/363 (54%), Positives = 259/363 (71%), Gaps = 4/363 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++    + +   E  +++L  +   + R  FL      E 
Sbjct: 243 LAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHET 302

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  WV S  K  P+  +   +    D IL+ + ++ ++  E  ++++E + I   +  GE
Sbjct: 303 DEKWVDSVLKSKPK--YAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGE 360

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 361 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 420

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 421 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDM 480

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA
Sbjct: 481 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLA 540

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 541 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRS 600

Query: 679 FLD 681
           FLD
Sbjct: 601 FLD 603


>gi|293610908|ref|ZP_06693207.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292826560|gb|EFF84926.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 628

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 196/349 (56%), Positives = 249/349 (71%), Gaps = 1/349 (0%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            D++ E +    ++I  NE E++R A   G + R  F      +E +P W+         
Sbjct: 279 FDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKQESNPAWLDEQIAKAPA 338

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E K  +      +L  + +I  I  E  +S++E + I   +  GE +A  AKKEMVEANL
Sbjct: 339 EIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAKKEMVEANL 398

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 399 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 458

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEP
Sbjct: 459 DQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEP 518

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL+MRFG
Sbjct: 519 ISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFG 578

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           I M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 579 IDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 627


>gi|260773557|ref|ZP_05882473.1| RNA polymerase sigma factor RpoD [Vibrio metschnikovii CIP 69.14]
 gi|260612696|gb|EEX37899.1| RNA polymerase sigma factor RpoD [Vibrio metschnikovii CIP 69.14]
          Length = 623

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 205/403 (50%), Positives = 273/403 (67%), Gaps = 9/403 (2%)

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            AL++  E+  + ++LQ  A+N   ++ S+ +     E ++ +     L   + D LV  
Sbjct: 226 LALEKFTELRNKYQNLQ-LAINEHGNDSSTTQQA--SELVLDIFREFRLTPKQFDHLVTT 282

Query: 342 LYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNF 398
           L +  +R+   E  +++ + +   + +  F+    G E    W+    A D P   +   
Sbjct: 283 LRNSMERVRTQERLIMKTVVEVAKMPKKSFIALFTGNESSEAWLDQVLATDKP---YVEK 339

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + I +   +++ I  ET + ++  + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 340 IRANEEMIRRSIQKLRIIEQETSLDVNRIKDISRRMSIGEAKARRAKKEMVEANLRLVIS 399

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 400 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 459

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ET
Sbjct: 460 IRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMET 519

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED     PLDSA   +LR  T   LA LTPRE +VLRMRFGI MNT
Sbjct: 520 PIGDDEDSHLGDFIEDTTLELPLDSATATSLRAATRDALAGLTPREAKVLRMRFGIDMNT 579

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 580 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DNTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 129 INQVQSAVAEYPGTIPYIL 147


>gi|238796946|ref|ZP_04640450.1| RNA polymerase sigma factor rpoD [Yersinia mollaretii ATCC 43969]
 gi|238719206|gb|EEQ11018.1| RNA polymerase sigma factor rpoD [Yersinia mollaretii ATCC 43969]
          Length = 634

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 204/395 (51%), Positives = 266/395 (67%), Gaps = 7/395 (1%)

Query: 291 YRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           + ELR   +N   A+       ++   ++L   L ++     L   + D LV  +  +  
Sbjct: 242 FSELREQYENTRMAIKKNGRSHATAAAEILN--LSEVFKQFRLVPKQFDYLVNNMRAMMD 299

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +++L  +   + +  F+      E    W + A    +  W   +    D +
Sbjct: 300 RVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFAAAVAMGKP-WSEKLKDVSDDV 358

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 359 QRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 418

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 419 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 478

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ S
Sbjct: 479 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 538

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVG
Sbjct: 539 HLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 598

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 599 KQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 633



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 95/159 (59%), Gaps = 7/159 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 32  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 91

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 92  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 148

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            G   +  S+ E P     L+   D +  G   L ++I+
Sbjct: 149 EGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIN 187


>gi|260548994|ref|ZP_05823216.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
 gi|260408162|gb|EEX01633.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
          Length = 628

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 200/379 (52%), Positives = 257/379 (67%), Gaps = 1/379 (0%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           +K  ++S +     E L  +           D++ E +    ++I  NE E++R A   G
Sbjct: 249 EKHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRG 308

Query: 365 -IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + R  F       E +P W+         E K  +      +L  + +I  I  E  +S
Sbjct: 309 RMDRTQFRTSFPKHESNPAWLDEQIAKAPAEIKVHLEKVRPDVLAFQQKIADIEKELNLS 368

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ++E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 369 VAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 428

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++
Sbjct: 429 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 488

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+
Sbjct: 489 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDA 548

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A    L+E T  VL +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 549 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 608

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HPSRS+ LRSFL+ 
Sbjct: 609 LRKLRHPSRSEHLRSFLEN 627


>gi|322831339|ref|YP_004211366.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
 gi|321166540|gb|ADW72239.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
          Length = 612

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 253/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL  +     L   + D LV  +  +  R+   E  ++++  +   + +  F+    G E
Sbjct: 250 KLSDVFKQFRLVPKQFDFLVNSMRSMMDRVRAQERLIMKVCVEQCKMPKKNFVNLFAGNE 309

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W   A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 310 TSDTWFDAALAMGKP-WSEKLKEVTEDVQRGLMKLRQIEEETGLTIEQVKDINRRMSIGE 368

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 369 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 428

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 429 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 488

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 489 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 548

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 549 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608

Query: 679 FLD 681
           FLD
Sbjct: 609 FLD 611



 Score = 99.0 bits (245), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 63/158 (39%), Positives = 93/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NRPDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEVRLSDLI 164


>gi|262401783|ref|ZP_06078349.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC586]
 gi|262352200|gb|EEZ01330.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC586]
          Length = 627

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 211/405 (52%), Positives = 268/405 (66%), Gaps = 23/405 (5%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 233 EKFNELRGKFQNLQLAVNEFGRDSNQASEASGLVLDIFRE--------FRLTPKQFDHLV 284

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P   + 
Sbjct: 285 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP---YV 341

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             V  + + I +   +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 342 QKVREQEEDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLV 401

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 402 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 461

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+
Sbjct: 462 RTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISM 521

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI M
Sbjct: 522 ETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDM 581

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 582 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 626


>gi|145597737|ref|YP_001161813.1| RNA polymerase sigma factor RpoD [Yersinia pestis Pestoides F]
 gi|145209433|gb|ABP38840.1| RNA polymerase sigma factor RpoD [Yersinia pestis Pestoides F]
          Length = 608

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 246 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 305

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 306 TSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 364

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 365 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 424

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 425 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 484

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 485 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLKLPLDSATSESLRSATHDVLA 544

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 545 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 604

Query: 679 FLD 681
           FLD
Sbjct: 605 FLD 607



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|110834924|ref|YP_693783.1| RNA polymerase sigma factor RpoD [Alcanivorax borkumensis SK2]
 gi|110648035|emb|CAL17511.1| RNA polymerase sigma factor RpoD [Alcanivorax borkumensis SK2]
          Length = 633

 Score =  379 bits (973), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 191/320 (59%), Positives = 239/320 (74%), Gaps = 1/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F++   G E +  W+       +G+   + ++   + + + + +I +I    G+
Sbjct: 312 GMDRKDFIKAFPGNETNMEWIDSQLKTKKGKAIADKLSVVKEDVQRAQRKISTIEDIIGL 371

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 372 PVADIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 431

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R  R+M  +
Sbjct: 432 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQMLQE 491

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REPTPEE+  +L MP + VRKVLKI KEPIS+ETPIGD++ S LGDFIED N  SP+D
Sbjct: 492 MGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNMESPVD 551

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SA    L E T  VLA+LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 552 SATSLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 611

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS+ LRSFLDG
Sbjct: 612 ALRKLRHPSRSEHLRSFLDG 631



 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 55/131 (41%), Positives = 80/131 (61%), Gaps = 7/131 (5%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSE 90
           I L +++GY+T  E+N  LP     ++Q+ED + M+++MGI VV    D D L  +E S 
Sbjct: 16  IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDE-SA 74

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D  ++   ++V      +     T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 75  DSTDEVAAEEAAAVLASVENEPG--RTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 132

Query: 151 AMMMASLCESP 161
             ++ +L   P
Sbjct: 133 REVLHALAFWP 143


>gi|51597716|ref|YP_071907.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           32953]
 gi|108809138|ref|YP_653054.1| RNA polymerase sigma factor RpoD [Yersinia pestis Antiqua]
 gi|108810668|ref|YP_646435.1| RNA polymerase sigma factor RpoD [Yersinia pestis Nepal516]
 gi|150260325|ref|ZP_01917053.1| RNA polymerase sigma factor RpoD [Yersinia pestis CA88-4125]
 gi|153950753|ref|YP_001399546.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           31758]
 gi|165924959|ref|ZP_02220791.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165937882|ref|ZP_02226443.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166008817|ref|ZP_02229715.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166212040|ref|ZP_02238075.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|167399605|ref|ZP_02305129.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167419320|ref|ZP_02311073.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167425120|ref|ZP_02316873.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|170022885|ref|YP_001719390.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis
           YPIII]
 gi|186896860|ref|YP_001873972.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis
           PB1/+]
 gi|218927836|ref|YP_002345711.1| RNA polymerase sigma factor RpoD [Yersinia pestis CO92]
 gi|229837321|ref|ZP_04457484.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Pestoides A]
 gi|229840533|ref|ZP_04460692.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229842919|ref|ZP_04463070.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229900861|ref|ZP_04515985.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Nepal516]
 gi|294502714|ref|YP_003566776.1| RNA polymerase sigma factor RpoD [Yersinia pestis Z176003]
 gi|51590998|emb|CAH22656.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           32953]
 gi|108774316|gb|ABG16835.1| RNA polymerase sigma factor RpoD [Yersinia pestis Nepal516]
 gi|108781051|gb|ABG15109.1| RNA polymerase sigma factor RpoD [Yersinia pestis Antiqua]
 gi|115346447|emb|CAL19320.1| RNA polymerase sigma factor RpoD [Yersinia pestis CO92]
 gi|149289733|gb|EDM39810.1| RNA polymerase sigma factor RpoD [Yersinia pestis CA88-4125]
 gi|152962248|gb|ABS49709.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           31758]
 gi|165914294|gb|EDR32910.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165923159|gb|EDR40310.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165992156|gb|EDR44457.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166206786|gb|EDR51266.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|166963314|gb|EDR59335.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167052109|gb|EDR63517.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167055883|gb|EDR65664.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|169749419|gb|ACA66937.1| RNA polymerase, sigma 70 subunit, RpoD [Yersinia pseudotuberculosis
           YPIII]
 gi|186699886|gb|ACC90515.1| RNA polymerase, sigma 70 subunit, RpoD [Yersinia pseudotuberculosis
           PB1/+]
 gi|229682200|gb|EEO78292.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Nepal516]
 gi|229689985|gb|EEO82043.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229696899|gb|EEO86946.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229705444|gb|EEO91454.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Pestoides A]
 gi|262360743|gb|ACY57464.1| RNA polymerase sigma factor RpoD [Yersinia pestis D106004]
 gi|294353173|gb|ADE63514.1| RNA polymerase sigma factor RpoD [Yersinia pestis Z176003]
 gi|320016798|gb|ADW00370.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 612

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 250 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 309

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 310 TSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 368

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 369 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 428

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 429 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 488

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 489 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 548

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 549 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608

Query: 679 FLD 681
           FLD
Sbjct: 609 FLD 611



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|23428541|gb|AAL11450.1| RNA polymerase sigma-70 subunit [Serratia plymuthica]
          Length = 612

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 197/363 (54%), Positives = 253/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 250 KLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFAGNE 309

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W   A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE
Sbjct: 310 TSDSWFEAALAMAKP-WSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 368

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLI++GNIGLMKA +KF++  GYKFST
Sbjct: 369 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIRKGNIGLMKAVDKFEYRRGYKFST 428

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 429 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 488

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 489 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 548

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF V RERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 549 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVIRERIRQIEAKALRKLRHPSRSEVLRS 608

Query: 679 FLD 681
           FLD
Sbjct: 609 FLD 611



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 96/161 (59%), Gaps = 13/161 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NSNSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 164


>gi|238782836|ref|ZP_04626865.1| RNA polymerase sigma factor rpoD [Yersinia bercovieri ATCC 43970]
 gi|238716259|gb|EEQ08242.1| RNA polymerase sigma factor rpoD [Yersinia bercovieri ATCC 43970]
          Length = 612

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/362 (54%), Positives = 253/362 (69%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E 
Sbjct: 251 LSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNET 310

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W + A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE 
Sbjct: 311 SDTWFAAAVAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEA 369

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 370 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 429

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP
Sbjct: 430 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMP 489

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA 
Sbjct: 490 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAG 549

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 550 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 609

Query: 680 LD 681
           LD
Sbjct: 610 LD 611



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 95/159 (59%), Gaps = 7/159 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            G   +  S+ E P     L+   D +  G   L ++I+
Sbjct: 127 EGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIN 165


>gi|15640541|ref|NP_230168.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121728933|ref|ZP_01681939.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V52]
 gi|153819447|ref|ZP_01972114.1| RNA polymerase sigma factor RpoD [Vibrio cholerae NCTC 8457]
 gi|153822185|ref|ZP_01974852.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|227080700|ref|YP_002809251.1| RNA polymerase sigma factor RpoD [Vibrio cholerae M66-2]
 gi|254291201|ref|ZP_04961997.1| RNA polymerase sigma factor RpoD [Vibrio cholerae AM-19226]
 gi|254850756|ref|ZP_05240106.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MO10]
 gi|255744255|ref|ZP_05418208.1| RNA polymerase sigma factor RpoD [Vibrio cholera CIRS 101]
 gi|9654945|gb|AAF93687.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121628781|gb|EAX61245.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V52]
 gi|126510018|gb|EAZ72612.1| RNA polymerase sigma factor RpoD [Vibrio cholerae NCTC 8457]
 gi|126520320|gb|EAZ77543.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|150422895|gb|EDN14846.1| RNA polymerase sigma factor RpoD [Vibrio cholerae AM-19226]
 gi|220897845|dbj|BAH11107.1| RNA polymerase sigma factor [Vibrio cholerae O1 biovar El tor]
 gi|227008588|gb|ACP04800.1| RNA polymerase sigma factor RpoD [Vibrio cholerae M66-2]
 gi|254846461|gb|EET24875.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MO10]
 gi|255738195|gb|EET93587.1| RNA polymerase sigma factor RpoD [Vibrio cholera CIRS 101]
          Length = 625

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 231 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 282

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 283 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 337

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 338 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 396

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 397 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 456

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 457 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 516

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 517 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 576

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 577 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 129 INQVQSAIAEYPGTIPYIL 147


>gi|153801472|ref|ZP_01956058.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-3]
 gi|124122963|gb|EAY41706.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-3]
          Length = 625

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 211/405 (52%), Positives = 268/405 (66%), Gaps = 23/405 (5%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 231 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 282

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P   + 
Sbjct: 283 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP---YA 339

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             V  + + I +   +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 340 AKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLV 399

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 400 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 459

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+
Sbjct: 460 RTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISM 519

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI M
Sbjct: 520 ETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDM 579

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 580 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 129 INQVQSAIAEYPGTIPYIL 147


>gi|261210089|ref|ZP_05924387.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC341]
 gi|260840854|gb|EEX67396.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC341]
          Length = 628

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 211/405 (52%), Positives = 268/405 (66%), Gaps = 23/405 (5%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 234 EKFNELRGKFQNLQLAVNEFGRDSNQASEASGLILDIFRE--------FRLTPKQFDHLV 285

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P   + 
Sbjct: 286 ETLRTSMDRVRTQERLVMKAVVEIAKMPKKSFIALFTGNESNEEWLDKVLASDKP---YV 342

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             V  + + I +   +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 343 QKVRDQEEDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLV 402

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 403 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 462

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+
Sbjct: 463 RTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISM 522

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI M
Sbjct: 523 ETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDM 582

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 583 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 627


>gi|254226294|ref|ZP_04919885.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V51]
 gi|125621156|gb|EAZ49499.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V51]
          Length = 625

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 231 EKFNELRGKFQNLQLAVNEFGRESHQASEASDLVLDIFRE--------FRLTPKQFDHLV 282

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 283 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 337

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 338 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 396

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 397 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 456

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 457 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 516

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 517 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 576

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 577 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 129 INQVQSAIAEYPGTIPYIL 147


>gi|121591668|ref|ZP_01678905.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 2740-80]
 gi|121546475|gb|EAX56696.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 2740-80]
          Length = 603

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 209 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 260

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 261 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 315

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 316 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 374

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 375 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 434

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 435 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 494

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 495 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 554

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 602



 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/123 (39%), Positives = 76/123 (61%), Gaps = 3/123 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGSEDSLDLASSASNSSVF 105
           E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     + ++    +A  ++  
Sbjct: 4   EVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAA 63

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
           L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T  
Sbjct: 64  LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIP 122

Query: 166 ALI 168
            ++
Sbjct: 123 YIL 125


>gi|22127411|ref|NP_670834.1| RNA polymerase sigma factor RpoD [Yersinia pestis KIM 10]
 gi|21960500|gb|AAM87085.1|AE013956_10 RNA polymerase, sigma(70) factor [Yersinia pestis KIM 10]
          Length = 632

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 254/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 270 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 329

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 330 TSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 388

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 389 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 448

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ M
Sbjct: 449 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 508

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 509 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 568

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 569 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 628

Query: 679 FLD 681
           FLD
Sbjct: 629 FLD 631



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 30  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 89

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 90  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 146

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 147 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 184


>gi|153214921|ref|ZP_01949704.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 1587]
 gi|262151177|ref|ZP_06028315.1| RNA polymerase sigma factor RpoD [Vibrio cholerae INDRE 91/1]
 gi|124114994|gb|EAY33814.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 1587]
 gi|262031008|gb|EEY49634.1| RNA polymerase sigma factor RpoD [Vibrio cholerae INDRE 91/1]
          Length = 595

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 201 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 252

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 253 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 307

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 308 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 366

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 367 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 426

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 427 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 486

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 487 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 546

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 547 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 594



 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/118 (38%), Positives = 73/118 (61%), Gaps = 3/118 (2%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
           +P + V SEQ+ED + M+++MGI VV+   D  +     + ++    +A  ++  L   +
Sbjct: 1   MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
               R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++
Sbjct: 61  SEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYIL 117


>gi|254237208|ref|ZP_04930531.1| sigma factor RpoD [Pseudomonas aeruginosa C3719]
 gi|126169139|gb|EAZ54650.1| sigma factor RpoD [Pseudomonas aeruginosa C3719]
          Length = 617

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/363 (54%), Positives = 258/363 (71%), Gaps = 4/363 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++    + +   E  +++L  +   + R  FL      E 
Sbjct: 256 LAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHET 315

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  WV S  K  P+  +   +    D IL+ + ++ ++  E  ++++E + I   +  GE
Sbjct: 316 DEKWVDSVLKSKPK--YAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGE 373

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 374 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 433

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+ +++ M
Sbjct: 434 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELGERMDM 493

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA
Sbjct: 494 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLA 553

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 554 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRS 613

Query: 679 FLD 681
           FLD
Sbjct: 614 FLD 616


>gi|153828433|ref|ZP_01981100.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
 gi|148876142|gb|EDL74277.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
          Length = 572

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 178 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 229

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 230 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 284

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 285 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 343

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 344 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 403

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 404 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 463

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 464 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 523

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 524 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 571


>gi|239996603|ref|ZP_04717127.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 382

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 188/312 (60%), Positives = 238/312 (76%), Gaps = 1/312 (0%)

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E    W+  A       +   +A   + I +  +++  +  ETG+ I++ + 
Sbjct: 71  FIKAFAGNETSNAWLHEAVK-SGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKD 129

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 130 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 189

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP
Sbjct: 190 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 249

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+++++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   + PLDSA   +L
Sbjct: 250 EELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSL 309

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+H
Sbjct: 310 KDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 369

Query: 670 PSRSKKLRSFLD 681
           PSRS++LRSFLD
Sbjct: 370 PSRSEQLRSFLD 381


>gi|262189558|ref|ZP_06047968.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CT 5369-93]
 gi|262034560|gb|EEY52890.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CT 5369-93]
          Length = 522

 Score =  378 bits (971), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 128 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 179

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 180 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 234

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 235 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 293

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 294 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 353

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 354 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 413

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 414 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 473

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 474 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 521



 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 32/44 (72%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYIL 44


>gi|24372864|ref|NP_716906.1| RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
 gi|24346976|gb|AAN54351.1|AE015572_6 RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
          Length = 616

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 199/355 (56%), Positives = 255/355 (71%), Gaps = 6/355 (1%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L   + D LV+ +  +  R+   E  L++L  +   + +  F++   G E +  W    K
Sbjct: 264 LVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDWFEAEK 323

Query: 389 --DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             + P  E    V  +V    + R+++ +I  ETG+ I+  + I   +  GE +A  AKK
Sbjct: 324 TSNKPYAEGLRMVEEDVQ---RCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615



 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 59/155 (38%), Positives = 89/155 (57%), Gaps = 3/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D +D   SE
Sbjct: 10  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMMSE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +    A+  +       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  D--NTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             + +S+ E P     ++   D+       L +II
Sbjct: 128 NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDII 162


>gi|229525180|ref|ZP_04414585.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
 gi|229338761|gb|EEO03778.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
          Length = 642

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 211/405 (52%), Positives = 268/405 (66%), Gaps = 23/405 (5%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 248 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 299

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P   + 
Sbjct: 300 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP---YV 356

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             V  + + I +   +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLV
Sbjct: 357 AKVRAQQEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLV 416

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 417 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 476

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+
Sbjct: 477 RTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISM 536

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI M
Sbjct: 537 ETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDM 596

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           NTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 597 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 641



 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 27  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 86

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 87  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 145

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 146 INQVQSAIAEYPGTIPYIL 164


>gi|226939395|ref|YP_002794468.1| RNA polymerase sigma factor RpoD [Laribacter hongkongensis HLHK9]
 gi|226714321|gb|ACO73459.1| RpoD [Laribacter hongkongensis HLHK9]
          Length = 649

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 190/350 (54%), Positives = 255/350 (72%), Gaps = 2/350 (0%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +++ L ++L  +   I  NE E+  +  Q   + RDVFL      E +  WV  A    +
Sbjct: 296 QVEALSDRLRSVVDDIRRNEREIQDICVQKCKMPRDVFLHTFVNNETNLEWVDAAMSLGK 355

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             + + +     +I + ++ + ++   + + I E + I   +  GE +A  AK+EM+EAN
Sbjct: 356 A-FASAIERYQHAIREKQSNLIALQDSSMLPIRELKEISRQMATGEAKARKAKREMIEAN 414

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 415 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 474

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R +R++  +   EP P E+A+++ MP + +RK++KI+KE
Sbjct: 475 ADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPAELARRMDMPEDKIRKIMKISKE 534

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PIS+ETPIGD+D SHLGDFIED   ++P D+A+ A+L+E T  VL SLTPRE +VLRMRF
Sbjct: 535 PISMETPIGDDDDSHLGDFIEDLATMAPSDAAMYASLKEATKEVLDSLTPREAKVLRMRF 594

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS++LRSFLD 
Sbjct: 595 GIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSERLRSFLDA 644



 Score = 95.5 bits (236), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/191 (33%), Positives = 104/191 (54%), Gaps = 19/191 (9%)

Query: 8   NRDSDSEHEDSDDSLVFDFSDDSWKKMIKL---ARQRGYVTIEELNAFLPPDEVSSEQME 64
           N +SD   E    +   D +++  K++ +L    ++RG++T  E+N  LP D + +EQ+E
Sbjct: 4   NSNSDKAAESKAQAAPLDNTEERRKRLKQLIVQGKERGFLTYAEINDSLPEDVLDAEQIE 63

Query: 65  DTVAMLSNMGINVVDG---------DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
             + M+++MGI V D           D       ED+++ A SA +S        DS   
Sbjct: 64  SIIGMITDMGIQVYDEAPDAEQLLMSDATPVVADEDAVEEAESALSSV-------DSEFG 116

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            T DPVRMY+REMG++ELL+REGEI IAKRIE G   M+ ++   P   + ++   +++ 
Sbjct: 117 RTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVQAISACPGIVKDVLDQIEKVE 176

Query: 176 DGTTLLREIID 186
           +    + E+ID
Sbjct: 177 NDELRIDEVID 187


>gi|119899516|ref|YP_934729.1| RNA polymerase sigma factor RpoD [Azoarcus sp. BH72]
 gi|119671929|emb|CAL95843.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 662

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 190/352 (53%), Positives = 255/352 (72%), Gaps = 10/352 (2%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW----VSYAKD 389
           I+ L + +  + +++  +E ++L+L     G+ R  F++   G+E    W    ++  K 
Sbjct: 313 IERLCDSVRHMVEQVRTHERQILQLCVDRAGMPRQHFIKVFPGQETSIDWLKDEIASGKS 372

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           + EG  +   A     +L+++ ++  +    GI + E + I   +  GE +   AK+EM 
Sbjct: 373 YAEGLMRIHPA-----VLEVQQKLIDLQDRIGIPLKELKDINRQMSTGEAKMRRAKREMT 427

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 428 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 487

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP E +RK++KI
Sbjct: 488 RSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAEKMEMPEEKIRKIMKI 547

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +KEPIS+ETPIGD+D SHLGDFIED   ++P ++A+ + LR+ T  VL SLTPRE +VLR
Sbjct: 548 SKEPISMETPIGDDDDSHLGDFIEDTATLAPAEAAMYSGLRDATAEVLDSLTPREAKVLR 607

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFLD
Sbjct: 608 MRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLD 659



 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 60/163 (36%), Positives = 90/163 (55%), Gaps = 13/163 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T  E++  LP D   +EQ+E  +A  +NMGI V D     +   +ED
Sbjct: 48  KTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIQVFD-----EAPAAED 102

Query: 92  SL---DLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L   ++A+S        +  +     DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 103 LLMSDNVATSVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 162

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIE G   M+ ++   P T   ++   D +      + E++D
Sbjct: 163 KRIEDGLKHMVQAISACPTTITEMLDTADRVARDEVRIDELVD 205


>gi|112702894|emb|CAL34114.1| RNA polymerase sigma factor rpoD [Cronobacter sakazakii]
          Length = 359

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 201/361 (55%), Positives = 256/361 (70%), Gaps = 6/361 (1%)

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  +  +  R+   E  ++++  +   + +  F+    G E    
Sbjct: 1   MFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKNFITLFTGNETSET 60

Query: 383 WV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           W   + A + P  E  + VA +V   L+   +++ I  ETG++I + + I   +  GE +
Sbjct: 61  WFNAAIAMNKPWSEKLHDVAEDVHRSLQ---KLQQIEEETGLTIEQVKDINRRMSIGEAK 117

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 118 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 177

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP 
Sbjct: 178 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPE 237

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA L
Sbjct: 238 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGL 297

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 298 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 357

Query: 681 D 681
           D
Sbjct: 358 D 358


>gi|294651232|ref|ZP_06728560.1| RNA polymerase sigma factor RpoD [Acinetobacter haemolyticus ATCC
           19194]
 gi|292822885|gb|EFF81760.1| RNA polymerase sigma factor RpoD [Acinetobacter haemolyticus ATCC
           19194]
          Length = 626

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 195/349 (55%), Positives = 247/349 (70%), Gaps = 1/349 (0%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            D++ E +     +I  NE E++R A   G + R  F      +E +P W+         
Sbjct: 277 FDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTFRTTFPEQESNPAWLDEQIAKAPA 336

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEMVEANL
Sbjct: 337 EIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDISKRMAVGEAKARRAKKEMVEANL 396

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 397 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 456

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEP
Sbjct: 457 DQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEP 516

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+MRFG
Sbjct: 517 ISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFG 576

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           I M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 577 IDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 625


>gi|262376664|ref|ZP_06069892.1| RNA polymerase sigma factor rpoD [Acinetobacter lwoffii SH145]
 gi|262308374|gb|EEY89509.1| RNA polymerase sigma factor rpoD [Acinetobacter lwoffii SH145]
          Length = 628

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 194/348 (55%), Positives = 246/348 (70%), Gaps = 1/348 (0%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            D++ E +     +I   E E++R A   G + R  F     G+E +P W+         
Sbjct: 279 FDIISEMIRGTHDQIRGAEREVMRYAVRRGRMDRTQFRTSFPGQESNPAWLDEQIAKTPA 338

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           + K ++      +L  + +I  I  E G+ +   + I   +  GE +A  AKKEMVEANL
Sbjct: 339 DQKAYLEKVRPDVLAFQQKIADIEKELGLDVKGIKDIAKRMAVGEAKARRAKKEMVEANL 398

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 399 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 458

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEP
Sbjct: 459 DQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEP 518

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+MRFG
Sbjct: 519 ISMETPIGDDEDSHLGDFIEDSNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFG 578

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 579 IDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 626


>gi|260912696|ref|ZP_05919182.1| DNA-directed RNA polymerase sigma subunit RpoD [Pasteurella
           dagmatis ATCC 43325]
 gi|260633074|gb|EEX51239.1| DNA-directed RNA polymerase sigma subunit RpoD [Pasteurella
           dagmatis ATCC 43325]
          Length = 623

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/378 (52%), Positives = 257/378 (67%), Gaps = 4/378 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG- 364
           K  ++S K K   + L  +     L   + D+LV  +  + K +   E  + ++      
Sbjct: 247 KHGRASKKSKDQIQALADVFTQFRLVPKQFDMLVNLMSGMMKSVRLQERNIQKIVVDKAK 306

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           + ++ F +   G E    W+   K    G+ W   +A     I    + I  I  +T ++
Sbjct: 307 MPKEQFQKVFIGHENQDTWL--VKALSAGKTWSEKLAKHEAEIRASIDNILEIERQTNLT 364

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + + R +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 365 VQQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 424

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++
Sbjct: 425 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 484

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            RE +PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDS
Sbjct: 485 GREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDS 544

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A   +L+  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 545 ATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 604

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSRS+ LRSFLD
Sbjct: 605 LRKLRHPSRSETLRSFLD 622


>gi|226951573|ref|ZP_03822037.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter sp. ATCC 27244]
 gi|226837676|gb|EEH70059.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter sp. ATCC 27244]
          Length = 626

 Score =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 195/349 (55%), Positives = 247/349 (70%), Gaps = 1/349 (0%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            D++ E +     +I  NE E++R A   G + R  F      +E +P W+         
Sbjct: 277 FDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTFRTTFPEQESNPAWLDEQIAKAPA 336

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEMVEANL
Sbjct: 337 EIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDISKRMAVGEAKARRAKKEMVEANL 396

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 397 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 456

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEP
Sbjct: 457 DQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEP 516

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+MRFG
Sbjct: 517 ISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFG 576

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           I M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 577 IDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 625


>gi|307824736|ref|ZP_07654959.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
 gi|307734094|gb|EFO04948.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
          Length = 602

 Score =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 182/267 (68%), Positives = 221/267 (82%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E G++IS  + I   +  GE +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 335 IEAEYGLTISGLKDINRRMSIGEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQ 394

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R 
Sbjct: 395 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 454

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R++  ++ RE TPEE+A+++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED 
Sbjct: 455 SRQILQELGREATPEELAERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDA 514

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
             +SP+++A  A LRE+T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRER
Sbjct: 515 KVLSPVEAATIAGLRESTQNVLAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRER 574

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           IRQIEAKA+RKL+HPSRS++LR FLDG
Sbjct: 575 IRQIEAKALRKLRHPSRSEQLRCFLDG 601



 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 54/144 (37%), Positives = 83/144 (57%), Gaps = 18/144 (12%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGS 89
           +I   + +GY+T  E+N  LP D V  EQ+ED + M+++MGI V     D D L  +  +
Sbjct: 13  LIAKGKVQGYLTYAEVNDHLPSDIVDPEQIEDIIGMINDMGIQVYEVAPDEDSLITDSAA 72

Query: 90  -----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                ED+ ++A+ AS  S F +         T DPVRMY+REMGS+ELL+R  E+ IAK
Sbjct: 73  VTTDDEDAEEVAALASVDSEFGR---------TTDPVRMYMREMGSVELLTRADELKIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G+  ++ ++  S +  +  +
Sbjct: 124 RIEEGQQQLVKAIARSCIVVEDFL 147


>gi|300718455|ref|YP_003743258.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia billingiae
           Eb661]
 gi|299064291|emb|CAX61411.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia billingiae
           Eb661]
          Length = 612

 Score =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 199/366 (54%), Positives = 253/366 (69%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  +     L   + D LV  +  +  R+   E  +++   +   + +  F+    G 
Sbjct: 249 QNLSDVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERLIMKFCVEICKMPKKNFITLFTGN 308

Query: 378 ELDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W   + A + P   W   +    D + +   ++  I  ETG++I + + I   + 
Sbjct: 309 ETSETWFKAALAMNKP---WSEKLKDVADDVQRGLMKLGQIEQETGLTIEQVKDINRRMS 365

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A++
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 485

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  
Sbjct: 486 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHD 545

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 546 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 605

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 606 LRSFLD 611



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/174 (39%), Positives = 100/174 (57%), Gaps = 13/174 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDLILNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ + A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSSDTDEDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII------DLEACIGPES 195
            G   +  S+ E P     L+   D +  G   L ++I      + EA I P +
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDMITGFVDPNAEAEIAPTA 180


>gi|157960786|ref|YP_001500820.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella pealeana ATCC
           700345]
 gi|157845786|gb|ABV86285.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella pealeana ATCC
           700345]
          Length = 616

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 207/407 (50%), Positives = 275/407 (67%), Gaps = 19/407 (4%)

Query: 285 DEIAEVYRELRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           +E  E +  LR   +NA+      G+   +S+V    + E    +     L   + D LV
Sbjct: 218 EEAKEKFTTLRLAHENALRIIADKGRGHPESTVALFEIGE----IFKEFRLMPKQFDRLV 273

Query: 340 EQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW----VSYAKDFPEGE 394
           + +  +  ++   E  +++L  +   + +  F++ +   E    W    ++  K + EG 
Sbjct: 274 KNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNDELASGKPYVEG- 332

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
                  E D + + R ++ +I VETG++I   + I   +  GE +A  AKKEMVEANLR
Sbjct: 333 ---LQMVEFD-VQRCRAKLDAIEVETGLAIGAIKDINRRMSIGEAKARRAKKEMVEANLR 388

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIAD
Sbjct: 389 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 448

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKVLKI KEPI
Sbjct: 449 QARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPI 508

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +VLRMRFGI
Sbjct: 509 SMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAKVLRMRFGI 568

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 569 DMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615



 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 58/131 (44%), Positives = 85/131 (64%), Gaps = 3/131 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   D ++   SE
Sbjct: 13  KLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMMSE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS D   +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 73  DSTD-DDAAEEAAAALATVEAELGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 151 AMMMASLCESP 161
             + AS+ E P
Sbjct: 131 NTVQASVAEYP 141


>gi|1710688|sp|P52327|RPOD_PSEPU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|762877|dbj|BAA06281.1| principal sigma factor [Pseudomonas putida]
 gi|1586519|prf||2204230A sigma factor
          Length = 614

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/365 (54%), Positives = 258/365 (70%), Gaps = 4/365 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           + L  L   + L   + ++LVE++ D   R+   E  +++L  +   + R  FL      
Sbjct: 251 QALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSN 310

Query: 378 ELDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E D  W    AK     +W   +  +  +I+  + ++  +  ETG++++E + I   +  
Sbjct: 311 ETDQTWSGDLAKR--NTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSI 368

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 488

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+  A   +L+E T  V
Sbjct: 489 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIYVATVESLKEATRDV 548

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA RKL+HP+RS+ L
Sbjct: 549 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAWRKLRHPTRSEHL 608

Query: 677 RSFLD 681
           RSFLD
Sbjct: 609 RSFLD 613



 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 60/154 (38%), Positives = 88/154 (57%), Gaps = 11/154 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +           D
Sbjct: 12  KELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFES------APDAD 65

Query: 92  SLDLASSASNSSVFLQKRKDSAD-----RSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +L LA + ++ +   +     A      R T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDIRRTTDPVRMYMREMGTVELLTREGEIEIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           E G   +M ++   P T   ++   D +N G  L
Sbjct: 126 EEGIREVMGAIAHFPGTVDYILGEYDRVNRGCRL 159


>gi|296532040|ref|ZP_06894819.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
 gi|296267655|gb|EFH13501.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
          Length = 640

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 192/414 (46%), Positives = 276/414 (66%), Gaps = 13/414 (3%)

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
           + ++++++P+V+ A     E +  LR+L             S   +  ++++V L G+L 
Sbjct: 236 ATLDEKMKPEVLAAFGAALEAHAALRALPVR----------SEAAQARRQEMVGLFGALR 285

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH-WVSYAK 388
           L  +R+D+LV ++ DI +R++  +G+ LRLA +  ++ +V L    G +      V  A+
Sbjct: 286 LRPARLDMLVGEVRDIQRRLLALDGKALRLAVAARVEHEVVLRLWDGSDAAVQALVEAAQ 345

Query: 389 DFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                  ++  A     D++ +IR  I  +   +G+  +E R + + V +GE +   AK+
Sbjct: 346 KVRSSAARHAQAVRDLRDTLPQIRAAIVMLEQSSGLPAAELRRVCAEVGRGERDMRKAKE 405

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+  ANLRLV+ +AK+Y NRGL F DLIQEGNIGLM+A +KFDW  G+KF+TYA WWV+Q
Sbjct: 406 ELTRANLRLVVHIAKRYRNRGLMFGDLIQEGNIGLMRAVDKFDWRRGFKFATYATWWVRQ 465

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRS+ADQ+ TIR+PVHM + + KV R +RR + K  REPTPEE+A +L M V+ VR V
Sbjct: 466 AITRSLADQARTIRVPVHMTETVGKVARMSRRFAQKAGREPTPEELAGELGMSVDKVRAV 525

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            ++ +EP+SLE PIG++D   LGDFIED+NAV P D+A ++ +R+ T R+L+ LTPREER
Sbjct: 526 QRLAREPVSLENPIGEDDDGRLGDFIEDENAVMPFDAASRSAMRDATMRILSDLTPREER 585

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LRMRFGIG   DHTLEEVGK F VTRERIRQIEAKA++KL+   R K LRSFL
Sbjct: 586 ILRMRFGIGGENDHTLEEVGKTFNVTRERIRQIEAKALKKLQVSKRGKSLRSFL 639



 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 41/72 (56%), Positives = 54/72 (75%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +DDPVRM+LREM   +LLSRE EIA+A+RIEAGR  M+A LCESP+TF  +  W+  L  
Sbjct: 137 SDDPVRMFLREMSGTDLLSREEEIALAQRIEAGRDAMLAGLCESPVTFTHIAAWKAALEQ 196

Query: 177 GTTLLREIIDLE 188
           G   LR++++LE
Sbjct: 197 GQMPLRDVVELE 208


>gi|15616680|ref|NP_239892.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681437|ref|YP_002467822.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|257471112|ref|ZP_05635111.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|11134512|sp|P57163|RPOD_BUCAI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|25288437|pir||B84936 RNA polymerase sigma factor rpoD [imported] - Buchnera sp.  (strain
           APS)
 gi|10038743|dbj|BAB12778.1| RNA polymerase sigma factor rpoD [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219624280|gb|ACL30435.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/362 (54%), Positives = 259/362 (71%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  + +R+   E  +++L  +   + +  F++    +++
Sbjct: 251 LSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKI 310

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W    ++  +   +N    + D  + ++  IK I  ETG++I + + I   +  GE 
Sbjct: 311 NYLWFIREQNTNQPWSENLKKVKEDVFISVKKLIK-IEEETGLTIEQVKDINKRMSIGEA 369

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 370 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 429

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P
Sbjct: 430 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIP 489

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ 
Sbjct: 490 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSG 549

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 550 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 609

Query: 680 LD 681
           LD
Sbjct: 610 LD 611



 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 93/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDLILNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  INTDTDEDAVEAATQ--VLSSVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L +II
Sbjct: 127 EGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDII 164


>gi|229507128|ref|ZP_04396634.1| RNA polymerase sigma factor RpoD [Vibrio cholerae BX 330286]
 gi|229509009|ref|ZP_04398497.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|229512571|ref|ZP_04402042.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TMA 21]
 gi|229519677|ref|ZP_04409120.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC9]
 gi|229520813|ref|ZP_04410235.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TM 11079-80]
 gi|229530331|ref|ZP_04419719.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 12129(1)]
 gi|229606193|ref|YP_002876841.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MJ-1236]
 gi|229332104|gb|EEN97592.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 12129(1)]
 gi|229342046|gb|EEO07042.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TM 11079-80]
 gi|229344366|gb|EEO09341.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC9]
 gi|229350464|gb|EEO15413.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TMA 21]
 gi|229353934|gb|EEO18868.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|229355873|gb|EEO20793.1| RNA polymerase sigma factor RpoD [Vibrio cholerae BX 330286]
 gi|229368848|gb|ACQ59271.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MJ-1236]
          Length = 642

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/408 (52%), Positives = 269/408 (65%), Gaps = 29/408 (7%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 248 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 299

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D P     
Sbjct: 300 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKP----- 354

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEANL
Sbjct: 355 -YVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 413

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 414 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 473

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEP
Sbjct: 474 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 533

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFG
Sbjct: 534 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 593

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 594 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 641



 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 27  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 86

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 87  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 145

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 146 INQVQSAIAEYPGTIPYIL 164


>gi|192362484|ref|YP_001981272.1| transcription initiation factor sigma 70 [Cellvibrio japonicus
           Ueda107]
 gi|190688649|gb|ACE86327.1| transcription initiation factor sigma 70 [Cellvibrio japonicus
           Ueda107]
          Length = 633

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 189/319 (59%), Positives = 238/319 (74%), Gaps = 5/319 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEG--EWKNFVACEVDSILKIRNEIKSISVETGI 422
           ++R  F++   G E +  W+    D  +G  E  + +   + ++   + ++  I  E+ +
Sbjct: 317 MQRKTFIKEFPGNETNADWLP---DLLKGKIEGADKLQVVLPNVQAEQQQLAQIEAESSL 373

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S++  + I   +  GE  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 374 SLASIKDINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 433

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +
Sbjct: 434 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQE 493

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REPTPEE+ +++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED   +SP++
Sbjct: 494 MGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIISPVE 553

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SA    L E T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 554 SATMEGLMEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 613

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKL+HPSRS  LRSFLD
Sbjct: 614 ALRKLRHPSRSDHLRSFLD 632



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 52/134 (38%), Positives = 83/134 (61%), Gaps = 7/134 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D L   +
Sbjct: 25  KELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIRVYETAPDADTLLMTD 84

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G   + ++A++ + +++   + +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 85  GDAAADEIAAAEAAAALVAVETETG---RTTDPVRMYMREMGTVELLTREGEIVIAKRIE 141

Query: 148 AGRAMMMASLCESP 161
            G   +M +L   P
Sbjct: 142 EGVRELMHALAYWP 155


>gi|311086952|gb|ADP67032.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/362 (54%), Positives = 259/362 (71%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  + +R+   E  +++L  +   + +  F++    +++
Sbjct: 251 LSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKI 310

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W    ++  +   +N    + D  + ++  IK I  ETG++I + + I   +  GE 
Sbjct: 311 NYLWFIREQNTNQPWSENLKKVKEDVFISVKKLIK-IEEETGLTIEQVKDINKRMSIGEA 369

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 370 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 429

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P
Sbjct: 430 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIP 489

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ 
Sbjct: 490 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSG 549

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 550 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 609

Query: 680 LD 681
           LD
Sbjct: 610 LD 611



 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 93/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDLILNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  INTDTDEDAVEAATQ--VLSSVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L +II
Sbjct: 127 EGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDII 164


>gi|311085799|gb|ADP65881.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086374|gb|ADP66455.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. TLW03
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/362 (54%), Positives = 259/362 (71%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  + +R+   E  +++L  +   + +  F++    +++
Sbjct: 251 LSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKI 310

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W    ++  +   +N    + D  + ++  IK I  ETG++I + + I   +  GE 
Sbjct: 311 NYLWFIREQNTNQPWSENLKKVKEDVFISVKKLIK-IEEETGLTIEQVKDINKRMSIGEA 369

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 370 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 429

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P
Sbjct: 430 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIP 489

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ 
Sbjct: 490 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSG 549

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 550 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 609

Query: 680 LD 681
           LD
Sbjct: 610 LD 611



 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 98/173 (56%), Gaps = 9/173 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDLILNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  INTDTDEDAVEAATQ--VLSSVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            G   +  S+ E P     L+   D +  G   L +II     + P ++  F 
Sbjct: 127 EGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIIT--GFVDPNAEEIFL 177


>gi|254429850|ref|ZP_05043557.1| Sigma-70, non-essential region family [Alcanivorax sp. DG881]
 gi|196196019|gb|EDX90978.1| Sigma-70, non-essential region family [Alcanivorax sp. DG881]
          Length = 633

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 191/320 (59%), Positives = 237/320 (74%), Gaps = 1/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F++   G E +  W+       +G+   + +    + + + + +I +I    G+
Sbjct: 312 GMDRKDFIKVFPGNETNMDWIDGQLKTKKGKAIADKLGAVKEDVQRAQRKIGTIEDIIGL 371

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 372 PVGDIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 431

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R  R+M  +
Sbjct: 432 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQMLQE 491

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REPTPEE+  +L MP + VRKVLKI KEPIS+ETPIGD++ S LGDFIED N  SP+D
Sbjct: 492 MGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNMESPVD 551

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SA    L E T  VLA+LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 552 SATSLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 611

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS+ LRSFLDG
Sbjct: 612 ALRKLRHPSRSEHLRSFLDG 631


>gi|90416498|ref|ZP_01224429.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
 gi|90331697|gb|EAS46925.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
          Length = 612

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 194/364 (53%), Positives = 258/364 (70%), Gaps = 2/364 (0%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E+L +L   L L   + D L+ ++    +R+   E +++RL    G + R  F++   G 
Sbjct: 249 EELAELFKYLKLTPRQFDPLIAKVRLAVERVRAEERKIMRLCIRLGKMPRKDFIKMFPGN 308

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W +      E  W   V+ +   IL+ + ++  +     ++I++ + I   +  G
Sbjct: 309 ESNMQWTAELAKSKES-WAERVSAQEVEILRSQRKLAQVEKLADMNIAQIKDINRRMTMG 367

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 368 EAMARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 427

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ 
Sbjct: 428 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPEELAERME 487

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIG+++ + +GD IED     PLD A + NL E+T  VL
Sbjct: 488 MPEDKIRKVLKIAKEPISMETPIGEDEDASIGDLIEDTTIALPLDEATKNNLTESTRGVL 547

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           +SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LR
Sbjct: 548 SSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDHLR 607

Query: 678 SFLD 681
           SF+D
Sbjct: 608 SFID 611



 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 60/163 (36%), Positives = 91/163 (55%), Gaps = 17/163 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V         E + D
Sbjct: 13  KDLIAKGREQRYLTYAEVNDHLPEDIADPEQVEDIIQMINDMGITVF--------ETAPD 64

Query: 92  SLDLASSASNSS---------VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +  L+S AS+++                +S    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 65  ADTLSSLASDNTPDEVAAAEAAAALASVESEQHRTTDPVRMYMREMGSVELLTREGEIEI 124

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           AKRIE G   +M+++ + P T   ++   +++  G   L +II
Sbjct: 125 AKRIEEGTRELMSAVADWPTTVATIVAEYEKVEAGEKKLTDII 167


>gi|219681993|ref|YP_002468377.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219621726|gb|ACL29882.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 198/362 (54%), Positives = 259/362 (71%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L ++     L   + D LV  +  + +R+   E  +++L  +   + +  F++    +++
Sbjct: 251 LSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKI 310

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W    ++  +   +N    + D  + ++  IK I  ETG++I + + I   +  GE 
Sbjct: 311 NYLWFIREQNTNQPWSENLKKVKEDVFVSVKKLIK-IEEETGLTIEQVKDINKRMSIGEA 369

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 370 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 429

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P
Sbjct: 430 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIP 489

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ 
Sbjct: 490 EDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSG 549

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 550 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 609

Query: 680 LD 681
           LD
Sbjct: 610 LD 611



 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 98/173 (56%), Gaps = 9/173 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV    D DDL   E
Sbjct: 10  KLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDLILNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ + A  A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  INTDTDEDAVEAATQ--VLSSVESELGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            G   +  S+ E P     L+   D +  G   L +II     + P ++  F 
Sbjct: 127 EGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIIT--GFVDPNAEEIFL 177


>gi|124515193|gb|EAY56704.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum rubarum]
          Length = 598

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 199/426 (46%), Positives = 291/426 (68%), Gaps = 45/426 (10%)

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK-------LVKLVGSLS 329
           R + +   D ++E++ +L ++ +   + QK+   + K K+L+E+       +V+L+  ++
Sbjct: 196 REQFVRQTDSLSELFLKLNAISEKWKDAQKN---TSKKKILREQAKKIKTEIVELIMEMN 252

Query: 330 LNQSRIDLLVEQLYDI--------------SKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
           L++ +++L++ QL+D+               +R+  N+ E+L+        +D   ER+Q
Sbjct: 253 LHRRQVELMIRQLHDVVSVLDESERTIDHSRRRLGANKEEILKAIALLKAGKDPG-ERYQ 311

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
               DP  +   K++         A E          +    V   +S SE R  +S++ 
Sbjct: 312 ----DPEKLELLKNYQ-------FALE---------RVHEAEVAALLSSSEIRDSLSLLE 351

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +   AK E+++ANLRLV+S+AK+YTNRGLQFLDLIQEGNIGLMKA +KF++  G+K
Sbjct: 352 AGEQKVREAKAELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFK 411

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT R +  ++ REP PEE+AK+
Sbjct: 412 FSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTTRHLVQELGREPLPEELAKE 471

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MPVE VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK ++SP+DSA++ +L     +
Sbjct: 472 MQMPVEKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKSISPIDSAVRYDLVRKIGK 531

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L+SLT REE+V+R+RFG+G +TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK 
Sbjct: 532 ALSSLTEREEKVIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKLRHPSRSKH 591

Query: 676 LRSFLD 681
           L+SF+D
Sbjct: 592 LKSFVD 597



 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 60/165 (36%), Positives = 100/165 (60%), Gaps = 9/165 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           K +I L ++RGY+T +ELN  LPP+ + S+Q+++ ++   +M I++VD +  E   G   
Sbjct: 11  KDLISLGKERGYLTYDELNNVLPPEAIGSDQLDNLMSYFGDMNIDIVDDESREAGYGEMD 70

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRS------TDDPVRMYLREMGSIELLSREGEIAI 142
           SE+    +   S   V  ++  +  D +       DDPVR+YL+EMG++ LL+REGEIAI
Sbjct: 71  SEEEEGFSDLESVRGVDSEEEDEGIDMTPGTLSRIDDPVRLYLKEMGAVPLLTREGEIAI 130

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           A+RIE G+  +   L   PLT ++++  R++   G   +REI+D+
Sbjct: 131 AQRIEEGQKEVSGILFGMPLTVRSILSLREKFQTGQIGIREIVDV 175


>gi|206603677|gb|EDZ40157.1| RNA polymerase, sigma 38 subunit, RpoS [Leptospirillum sp. Group II
           '5-way CG']
          Length = 598

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 201/425 (47%), Positives = 291/425 (68%), Gaps = 43/425 (10%)

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK-------LVKLVGSLS 329
           R + +   D ++E++ +L ++ +   + QK+   + K KVL+E+       +V+L+  ++
Sbjct: 196 REQFVRQTDSLSELFLKLNAISEKWKDAQKN---TSKKKVLREQAKKIKTEIVELIMEMN 252

Query: 330 LNQSRIDLLVEQLYDI------SKRIMHNEGELLRLAQSYGIKRDVFL-------ERHQG 376
           L++ +++L++ QL+D+      S+RI+ +    L   +   +K    L       ER+Q 
Sbjct: 253 LHRKQVELMIRQLHDVVSVLDESERIIDHSRRRLGANKEDILKAIALLKAGKDPGERYQ- 311

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
              DP  +   K++         A E          +    V   +S SE R  +S++  
Sbjct: 312 ---DPEKLELLKNYQ-------FALE---------RVHEAEVAALLSSSEIRDSLSLLEA 352

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +   AK E+++ANLRLV+S+AK+YTNRGLQFLDLIQEGNIGLMKA +KF++  G+KF
Sbjct: 353 GEQKVREAKAELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKF 412

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT R +  ++ REP PEE+AK++
Sbjct: 413 STYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTTRHLVQELGREPLPEELAKEM 472

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MPVE VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK ++SP+DSA++ +L     + 
Sbjct: 473 QMPVEKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKSISPIDSAVRYDLVRKIGKA 532

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+SLT REE+V+R+RFG+G +TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK L
Sbjct: 533 LSSLTEREEKVIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKLRHPSRSKHL 592

Query: 677 RSFLD 681
           +SF+D
Sbjct: 593 KSFVD 597



 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 60/165 (36%), Positives = 100/165 (60%), Gaps = 9/165 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           K +I L ++RGY+T +ELN  LPP+ + S+Q+++ ++   +M I++VD +  E   G   
Sbjct: 11  KDLISLGKERGYLTYDELNNVLPPEAIGSDQLDNLMSYFGDMNIDIVDDESREAGYGEMD 70

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRS------TDDPVRMYLREMGSIELLSREGEIAI 142
           SE+    +   S   V  ++  +  D +       DDPVR+YL+EMG++ LL+REGEIAI
Sbjct: 71  SEEEEGFSDLESVRGVDSEEEDEGIDMTPGTLSRIDDPVRLYLKEMGAVPLLTREGEIAI 130

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           A+RIE G+  +   L   PLT ++++  R++   G   +REI+D+
Sbjct: 131 AQRIEEGQKEVSGILFGMPLTVRSILSLREKFQTGQIGIREIVDV 175


>gi|325123225|gb|ADY82748.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 636

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 197/357 (55%), Positives = 252/357 (70%), Gaps = 9/357 (2%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVF---LERHQG-----RELDPHWVS 385
            D++ E +    ++I  NE E++R A   G + R  F     +H+      +E +P W+ 
Sbjct: 279 FDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKHESTSFPKQESNPAWLD 338

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                   E K  +      +L  + +I  I  E  +S++E + I   +  GE +A  AK
Sbjct: 339 EQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAK 398

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 399 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 458

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRK
Sbjct: 459 QAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRK 518

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE 
Sbjct: 519 VLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREA 578

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 579 KVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 635


>gi|297539657|ref|YP_003675426.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera sp. 301]
 gi|297259004|gb|ADI30849.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera sp. 301]
          Length = 645

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 194/367 (52%), Positives = 264/367 (71%), Gaps = 3/367 (0%)

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERH 374
           +L E LV+L  +   +  +++ L +Q+ D+ + I  +E ++L    +  G+ R  F++  
Sbjct: 277 LLSEILVELT-AFRFSPKQVEGLCDQVRDLVETIRSHERKVLDFCVEKSGMPRLHFIKSF 335

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E +  W++      +   +  +     SIL  +  +  +    GI I E + I   +
Sbjct: 336 PGNESNLGWLAEELKADKPYIEKLIRYN-HSILDQQQRLIDLEKNVGIPIKELKEINKQM 394

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G+
Sbjct: 395 TTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGF 454

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+
Sbjct: 455 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGVEPDPALLAE 514

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           K+ MP + +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++P+D+AI A+LR+ T+
Sbjct: 515 KMEMPEDKIRKILKISKEPISMETPIGDDEDSHLGDFIEDGQTLAPVDAAIYASLRDATS 574

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+
Sbjct: 575 EVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 634

Query: 675 KLRSFLD 681
           +LRSFL+
Sbjct: 635 RLRSFLE 641



 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 91/164 (55%), Gaps = 16/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---------GDD 82
           K +I L ++RGY+T  E+N  LP D  +SEQ++  + M+++MGI V +           D
Sbjct: 36  KSLIVLGKERGYLTYAEINDHLPDDVQNSEQIDGIIGMINDMGIQVYEEAPDAEVLLMSD 95

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                  ED+++ A  A  +        DS    T DPVRMY+REMG+++LL+RE EI I
Sbjct: 96  APPAVTDEDAVEEAEQALATV-------DSDFGRTTDPVRMYMREMGTVDLLTRESEIEI 148

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           A+RIE G   M+ ++   P T  AL+   D++ +    + +++D
Sbjct: 149 ARRIEDGLKHMVQAIAACPTTIAALLALVDKVENDELSVDDLVD 192


>gi|91794185|ref|YP_563836.1| RNA polymerase sigma factor RpoD-like protein [Shewanella
           denitrificans OS217]
 gi|91716187|gb|ABE56113.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella denitrificans
           OS217]
          Length = 617

 Score =  375 bits (964), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/362 (54%), Positives = 258/362 (71%), Gaps = 6/362 (1%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDP 381
           +L     L   + D LV+ +  +  R+   E  +L+L  +   + +  F++     E + 
Sbjct: 258 ELFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLILKLCVEQAKMPKKNFVKAFTSNETNL 317

Query: 382 HWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
            W +     + P  +    VA +V+   +  +++ +I +ET ++IS  + I   +  GE 
Sbjct: 318 DWFNKEMNSNKPYADALKAVAHDVN---RCSSKLTAIELETDLTISSIKDINRRMSIGEA 374

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 375 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 434

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP
Sbjct: 435 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMP 494

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA 
Sbjct: 495 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAG 554

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SF
Sbjct: 555 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSF 614

Query: 680 LD 681
           LD
Sbjct: 615 LD 616


>gi|45442721|ref|NP_994260.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus
           str. 91001]
 gi|45437587|gb|AAS63137.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus
           str. 91001]
          Length = 631

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/363 (54%), Positives = 253/363 (69%), Gaps = 2/363 (0%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 269 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 328

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 329 TSDTWFNAAVAMGK-PWSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 387

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 388 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 447

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+   +R+M  ++ REPTPEE+A+++ M
Sbjct: 448 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNGISRQMLQEMGREPTPEELAERMLM 507

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA
Sbjct: 508 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLA 567

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 568 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 627

Query: 679 FLD 681
           FLD
Sbjct: 628 FLD 630



 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 29  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 88

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 89  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 145

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 146 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 183


>gi|56461300|ref|YP_156581.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina loihiensis
           L2TR]
 gi|56180310|gb|AAV83032.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina loihiensis
           L2TR]
          Length = 609

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 201/384 (52%), Positives = 265/384 (69%), Gaps = 16/384 (4%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG- 364
           K  +     +V  +KL  L     L   + D LV+ +  + +R+   E  +++++   G 
Sbjct: 233 KHGRDGAGARVEIDKLSDLFKQFRLVPKQFDRLVKDMRAMMQRVRVQERIIMKISVEQGE 292

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK-------SIS 417
           + +  F++     E +  WV   K+   G      A   D++ ++R EI+        + 
Sbjct: 293 MPKRNFMKAFATHENNMAWVD--KEIDSG------ASYSDTLKEVRGEIERCVNKLVDVE 344

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 345 RETGLTIGKVKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 404

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R
Sbjct: 405 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 464

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   
Sbjct: 465 QMLQEMGREPLPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 524

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             P+DSA   +LR +   VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIR
Sbjct: 525 DLPIDSATSESLRNSVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 584

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRS++L+SFLD
Sbjct: 585 QIEAKALRKLRHPSRSEQLKSFLD 608



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 56/141 (39%), Positives = 80/141 (56%), Gaps = 9/141 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++G++T  E+N  LP + V S+Q+ED + M+++MGI V     D DDL   E
Sbjct: 10  KVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQVEDIIRMINDMGIRVFESAPDADDLMMAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D      +A   +       D     T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  SAADEDAAEEAAQALASV-----DGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P     L+
Sbjct: 125 EGINQVQCSVAEYPEAINFLL 145


>gi|99035119|ref|ZP_01314904.1| hypothetical protein Wendoof_01000264 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 502

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 227/527 (43%), Positives = 329/527 (62%), Gaps = 41/527 (7%)

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRD+L++G  LLREIIDL+A           + ++ +   K E    E+  +DV+++E  
Sbjct: 1   WRDDLSNGALLLREIIDLDAI----------YNSDFNVVPKEESEESEESAEDVEDSED- 49

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA----MEDQLRPKVMCALD 285
                 VS+D     D   ++ ++D+     +ED S+  L+     ME  L PKV+ ALD
Sbjct: 50  ------VSEDAEYCSDDKKDSKKSDDEKDGNNEDISSVNLNVSILEMESDLLPKVIVALD 103

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           EI  +  E   L+ N+ N       S + + L  ++  +   + L+ + +  + ++LY I
Sbjct: 104 EIITLTNEALILRKNSKN------FSNELENLYNQIWSIALQIKLSDAAVARITQELYKI 157

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVF-------LERHQGRELDPHWVSYAKDFPEGEWKN- 397
           ++ I   E  L+  A+ Y I R+ F       L +H+ +++    ++  +    GE KN 
Sbjct: 158 NRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHELKKISLLKINENQSSFTGELKNK 217

Query: 398 ---FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
              F+    + I    N IK    E   ++ EF+ ++  ++K E E S AK+EM++ANLR
Sbjct: 218 FLRFIDDNSEHIASTLNGIKQHIQED--NVQEFKELIKRIQKHEREVSEAKQEMIKANLR 275

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKFSTY  WWV+Q+ITR+I +
Sbjct: 276 LVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGTWWVRQSITRAIPE 335

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           QS  +RIPVHM + I K+ R  R+M++++ REPT EE++ +L MP+E +RKV+KI ++P+
Sbjct: 336 QSKVVRIPVHMVEIISKINRALRKMTHEMGREPTLEELSVELTMPLERIRKVMKIARDPV 395

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLE P G +D+S  GD IEDK    P D+AI A+LR  TT VLA+LTP+EER+LRMRFG+
Sbjct: 396 SLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGL 455

Query: 635 GMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR++KLR F 
Sbjct: 456 GKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRARKLRGFF 502


>gi|78486147|ref|YP_392072.1| sigma 70 (RpoD) [Thiomicrospira crunogena XCL-2]
 gi|78364433|gb|ABB42398.1| sigma 70 (RpoD) [Thiomicrospira crunogena XCL-2]
          Length = 594

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 203/411 (49%), Positives = 282/411 (68%), Gaps = 9/411 (2%)

Query: 273 EDQLRPKVMCA-LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           ED + P+ + A L ++A++  +  +L+    NG  D KS  K    + ++V L+ ++ L+
Sbjct: 191 EDGINPEELDAFLQKLAKLNAD--TLKAEEKNGYSDPKSVKK----RAEIVALLATVKLS 244

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
              ++ +++ +      I   E  ++  + +  G+ R  FL+   G E D   +   K+ 
Sbjct: 245 PVFVNRMIKGIKLRVSSIREQERNVVNAVMRQVGVPRPSFLKLFVGSETDYDVLDRLKEA 304

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
              +         D + + +  +  I     + I++++ I   + K E  A IAK+EM+E
Sbjct: 305 HPDKADALEEVRAD-VKRAQKRLAMIEKAEKMPINQYKTIYKDLSKAESIARIAKREMIE 363

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR
Sbjct: 364 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWWIRQAITR 423

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R  R++  K+ REPTPEE+A+++ MP + VRKV+KI 
Sbjct: 424 SIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEMPEDKVRKVMKIA 483

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETP+GD++ S LGDFIED N +SP DSA    + ET   +L++LTPRE +VLRM
Sbjct: 484 KEPISMETPVGDDEDSSLGDFIEDSNILSPQDSADLEGMGETVREMLSTLTPREAKVLRM 543

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFG+GMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+++L+SFLD
Sbjct: 544 RFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAERLKSFLD 594



 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/150 (34%), Positives = 85/150 (56%), Gaps = 13/150 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGS 89
           +I+ A+  GY+T  ++N  LP D++  +Q+   + +L + GI +     D D+L  +EG 
Sbjct: 13  LIERAKDLGYLTFSDVNDVLP-DDIEEDQLGQVLTILRDFGIQLFESAPDADELLTKEGE 71

Query: 90  --EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D+   A+  + + V      D+    T DPVRMY+REMGS+ELL+R+GE+ IAKRIE
Sbjct: 72  TFDDAAAEAAILALAEV------DAEFGRTTDPVRMYMREMGSVELLTRQGEVEIAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDG 177
            G   M+ ++ + P     L+     + DG
Sbjct: 126 YGIRDMLEAMAKYPQVAMELLASFSRIEDG 155


>gi|34499217|ref|NP_903432.1| RNA polymerase sigma factor RpoD [Chromobacterium violaceum ATCC
           12472]
 gi|34105068|gb|AAQ61424.1| RNA polymerase sigma factor RpoD [Chromobacterium violaceum ATCC
           12472]
          Length = 643

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 184/315 (58%), Positives = 240/315 (76%), Gaps = 1/315 (0%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           R  F++   G E +  WV    D  +  W   +     +I++ +  +  +  +  +SI  
Sbjct: 324 RAHFIKVFPGNETNLDWVENEIDSGKA-WSEALTRFKHAIIEKQTRLSDLQDKAMLSIKA 382

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 383 LKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 442

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE
Sbjct: 443 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQESGRE 502

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P P E+A+K+ MP E +RK++KI+KEPIS+ETPIGD+D SHLGDFIED+N ++P D+A+ 
Sbjct: 503 PDPAELAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQNNLAPSDAAMY 562

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           ++L++ T  VL +LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 563 SSLKDATKEVLDTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 622

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP+RS++LRSFLD
Sbjct: 623 LRHPTRSERLRSFLD 637



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 60/157 (38%), Positives = 86/157 (54%), Gaps = 21/157 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L ++RGY+T  E+N  LP D   +EQ+E+ V M++ +GI V        EE  + 
Sbjct: 29  RQLIALGKERGYLTYAEINDHLPEDVSDAEQIENIVTMIAGLGIQVC-------EEAPDA 81

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
              L S A+ S       +         DS    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 82  ETLLMSDATPSVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGSVELLTREGEIEI 141

Query: 143 AKRIEAGRAMMMASLCESPLTFQALI-----IWRDEL 174
           AKRIE G   M+ ++   P T   ++     + RDE+
Sbjct: 142 AKRIEDGLKYMIQAISACPGTIAEVLELMERVARDEI 178


>gi|301165749|emb|CBW25321.1| RNA polymerase sigma-70 factor [Bacteriovorax marinus SJ]
          Length = 582

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 200/409 (48%), Positives = 286/409 (69%), Gaps = 18/409 (4%)

Query: 286 EIAEVYRELRSLQDNA---VNGQKDEKSSVKCKVLKEK-----LVKLVGSLSLNQSRIDL 337
           +IA+V  E+ S+ DN    +N  ++E  ++K    +EK     +   +  L+ N+  I+ 
Sbjct: 177 DIAKVRDEIYSVCDNLETLLNRVENEDGTIKEYTQEEKKKMDTIALRLADLTFNRKIINS 236

Query: 338 LVEQL--YDISKRIMHNEGE-LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF--PE 392
            VE +  Y +  R ++ + E + +  +  G + D  +   +  E D      AKD    +
Sbjct: 237 FVEPVKKYYLQFRELYEQQERIFKFLEVEG-QDDYKVLYEKVLEDDAFKRRLAKDLYTTD 295

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            + +  +  + D I K+R     +S++ G+  ++   + +++ KGE +A +AK ++VEAN
Sbjct: 296 AKIEQLIRNQEDVIRKLRR----LSLDAGMEFTDIEDVYNIILKGETKADVAKSQLVEAN 351

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I
Sbjct: 352 LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAI 411

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+VRT+R++  ++ REPTPEEIA+++ +PV+ V+KV KI+KE
Sbjct: 412 ADQARTIRIPVHMIETINKMVRTSRQLIQELGREPTPEEIAERMELPVDKVKKVQKISKE 471

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ S LGDFIED   +SP D+ +   L E T  VL++LTPREE+VLRMRF
Sbjct: 472 PISLETPIGEEEDSSLGDFIEDDKIISPADAVMSVTLSEQTRSVLSTLTPREEKVLRMRF 531

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+K L+S++D
Sbjct: 532 GIGEKSDHTLEEVGQDFFVTRERIRQIEAKALRKLRHPSRAKMLKSYVD 580



 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 37/122 (30%), Positives = 66/122 (54%), Gaps = 5/122 (4%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           VF  S D  K +IK  + + ++T EE+N  +P   +  E +++ +  +  M I++ D   
Sbjct: 6   VFINSKDFSKLLIK-GKDQSFLTAEEINDAIPASIIEPEAIDEIMLKIQEMRIDIQD--- 61

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E  E  +D + L  +        ++ +     ++ DPV++YL+ MGS+ LL+REGE+ I
Sbjct: 62  -ETSEEEDDGIRLDGTEIIEETLSKEERAELKSASTDPVKLYLKRMGSVALLTREGEVVI 120

Query: 143 AK 144
           AK
Sbjct: 121 AK 122


>gi|91776674|ref|YP_546430.1| sigma 70 (RpoD) [Methylobacillus flagellatus KT]
 gi|91710661|gb|ABE50589.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacillus flagellatus
           KT]
          Length = 644

 Score =  374 bits (961), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 190/368 (51%), Positives = 263/368 (71%), Gaps = 6/368 (1%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQ 375
           L+  +++ + +   +  +++ L +++  + + I  +E +++    +  G+ R  F++   
Sbjct: 276 LQATIIEELMAFRFSAKQVEALCDRVRGMVEEIRSHERKIMDFCVEKAGMPRAHFIKSFP 335

Query: 376 GRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           G E +P W++   A + P  E        +D     + ++ +I    GI I E + I   
Sbjct: 336 GNEGNPEWLAAELAVNKPYVERLERFRHSIDDQ---QQQLLAIQERVGIPIRELKEINKQ 392

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +  GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 393 MSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 452

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A
Sbjct: 453 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLA 512

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +K+ MP + +RK+LKI+KEPIS+ETPIGD+D SHLGDFIED   ++P+D+A+ A+LR+ T
Sbjct: 513 EKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDVATLAPVDAAVYASLRDAT 572

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS
Sbjct: 573 KEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 632

Query: 674 KKLRSFLD 681
           ++LRSFL+
Sbjct: 633 ERLRSFLE 640



 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/164 (35%), Positives = 92/164 (56%), Gaps = 16/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---------GDD 82
           K +I L ++RGY+T  E+N  LP D   SEQ++  + M+++MGI V +           D
Sbjct: 33  KSLIILGKERGYLTYAEINDHLPDDVQDSEQIDSIIGMINDMGIQVYEEAPDAEALLMSD 92

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +      ED+++ A  A ++        DS    T DPVRMY+REMG+++LL+REGEI I
Sbjct: 93  VPAPVADEDAVEEAEQALSTV-------DSEFGRTTDPVRMYMREMGTVDLLTREGEIEI 145

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE G   M+ ++   P T   L+   D++  G   + +++D
Sbjct: 146 AKRIEDGLKHMVQAIAACPSTIAELLAMVDQVEKGELGVDDLVD 189


>gi|262364690|gb|ACY61247.1| RNA polymerase sigma factor RpoD [Yersinia pestis D182038]
          Length = 352

 Score =  374 bits (961), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 184/271 (67%), Positives = 221/271 (81%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 81  QKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 140

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 141 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 200

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGD
Sbjct: 201 KLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 260

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF 
Sbjct: 261 FIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 320

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 321 VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 351


>gi|32491217|ref|NP_871471.1| hypothetical protein WGLp468 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166424|dbj|BAC24614.1| rpoD [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 601

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/362 (54%), Positives = 255/362 (70%), Gaps = 2/362 (0%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGREL 379
           L  +     L   + D LV  +    ++I   E  ++R+  +   + +  F+    G E 
Sbjct: 240 LADIFKQFRLVPKQFDYLVFIIRSEIEKIRFYERRIMRICVNICKMPKKFFISLFSGNET 299

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W+  A    +  W   +      I  I N++K I + +GI+I + + I   +  GE 
Sbjct: 300 NDVWLKKALSL-DKPWSRKLYKLNKPICLILNKLKIIEINSGITIEQAKDINKRMSIGEA 358

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 359 KAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 418

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P
Sbjct: 419 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIP 478

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD++ SHLGDF+ED +   PLDSA   +LR  T  VL+ 
Sbjct: 479 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFLEDTSLDLPLDSATSESLRSATHDVLSG 538

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VL+MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 539 LTAREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILRSF 598

Query: 680 LD 681
           LD
Sbjct: 599 LD 600



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 58/155 (37%), Positives = 91/155 (58%), Gaps = 16/155 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N FLP + + S Q+ED + M+++MGI V+D      E  + +
Sbjct: 10  KLLVTRGKEQGYLTFSEVNDFLPENIIDSHQIEDIIQMINDMGIQVMD------EAPNSE 63

Query: 92  SLDLASSASNS-------SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +L L  S +NS       +  +    +S    T DPVRMY+REMGS++LL+REGEI +AK
Sbjct: 64  NLLLPDSNNNSDEDVAEAAAQVLSNVESEFGKTTDPVRMYMREMGSVQLLTREGEIDLAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           RIE G   +  ++ E P   +A+I   D+    TT
Sbjct: 124 RIEYGINQIQCAIVEYP---KAIIYLLDQYKKTTT 155


>gi|327479259|gb|AEA82569.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 4166]
          Length = 617

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 196/366 (53%), Positives = 258/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           E L  L   + L   + D LVE++ D   +I   E  +++L  +   + R  FL +    
Sbjct: 254 EALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQFPSN 313

Query: 378 ELDPHWVSYAKDFPEGE--WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   A+    G+  +   +    + I + + ++  +  +  ++I++ + I   + 
Sbjct: 314 ETNLDW---AEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRMS 370

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 371 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ ++
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 490

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  
Sbjct: 491 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATRE 550

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ 
Sbjct: 551 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 610

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 611 LRSFLD 616


>gi|153826548|ref|ZP_01979215.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
 gi|149739640|gb|EDM53854.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
          Length = 302

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 187/289 (64%), Positives = 227/289 (78%), Gaps = 3/289 (1%)

Query: 396 KNFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           K +VA   +   +IR  I+ + +   ET +S+   + I   +  GE +A  AKKEMVEAN
Sbjct: 13  KPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEAN 72

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 73  LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 132

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KE
Sbjct: 133 ADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKE 192

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRF
Sbjct: 193 PISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRF 252

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 253 GIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 301


>gi|307726543|ref|YP_003909756.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
 gi|307587068|gb|ADN60465.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
          Length = 803

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 466 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWAD--KIVSEGHSYSA 517

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 518 ILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 577

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 578 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 637

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 638 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 697

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 698 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 757

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 758 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 802



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 190 RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 249

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 250 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 309

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 310 GLKHMVMAISACPTTIADILAMAERVANEEVRIDELVD 347


>gi|296159636|ref|ZP_06842459.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295890080|gb|EFG69875.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 680

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 188/347 (54%), Positives = 245/347 (70%), Gaps = 13/347 (3%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W     D   GE   +
Sbjct: 343 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWA----DKIVGEGHAY 392

Query: 399 VACEVDSILKIRNE---IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            A    +I  IR +   +  +     + + + +     +  GE +A  AK+EM EANLRL
Sbjct: 393 SAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRL 452

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 453 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 512

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS
Sbjct: 513 ARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPIS 572

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI 
Sbjct: 573 METPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIE 632

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 633 MSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D       E   GF
Sbjct: 187 GLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGF 237


>gi|91777317|ref|YP_552525.1| RNA polymerase sigma factor RpoD [Burkholderia xenovorans LB400]
 gi|91689977|gb|ABE33175.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 680

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 188/347 (54%), Positives = 245/347 (70%), Gaps = 13/347 (3%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W     D   GE   +
Sbjct: 343 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWA----DKIVGEGHAY 392

Query: 399 VACEVDSILKIRNE---IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            A    +I  IR +   +  +     + + + +     +  GE +A  AK+EM EANLRL
Sbjct: 393 SAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRL 452

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 453 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 512

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS
Sbjct: 513 ARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPIS 572

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI 
Sbjct: 573 METPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIE 632

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 633 MSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D       E   GF
Sbjct: 187 GLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGF 237


>gi|146281106|ref|YP_001171259.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri A1501]
 gi|145569311|gb|ABP78417.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri A1501]
          Length = 569

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 196/366 (53%), Positives = 258/366 (70%), Gaps = 6/366 (1%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
           E L  L   + L   + D LVE++ D   +I   E  +++L  +   + R  FL +    
Sbjct: 206 EALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQFPSN 265

Query: 378 ELDPHWVSYAKDFPEGE--WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W   A+    G+  +   +    + I + + ++  +  +  ++I++ + I   + 
Sbjct: 266 ETNLDW---AEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRMS 322

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 323 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 382

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ ++
Sbjct: 383 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 442

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  
Sbjct: 443 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATRE 502

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ 
Sbjct: 503 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 562

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 563 LRSFLD 568


>gi|30064415|ref|NP_838586.1| RNA polymerase sigma factor RpoD [Shigella flexneri 2a str. 2457T]
 gi|30042672|gb|AAP18396.1| sigmaD(70) factor of RNA polymerase [Shigella flexneri 2a str.
           2457T]
          Length = 608

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 199/361 (55%), Positives = 255/361 (70%), Gaps = 6/361 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 251 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 367

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 677 R 677
           +
Sbjct: 608 Q 608



 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|148653373|ref|YP_001280466.1| RNA polymerase, sigma 70 subunit, RpoD [Psychrobacter sp. PRwf-1]
 gi|148572457|gb|ABQ94516.1| RNA polymerase, sigma 70 subunit, RpoD [Psychrobacter sp. PRwf-1]
          Length = 623

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 194/356 (54%), Positives = 256/356 (71%), Gaps = 4/356 (1%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS- 385
           L LN    D ++  ++D+   +   E +++RL    G + R  F +     E +  W++ 
Sbjct: 268 LKLNNRMADNVMAIMHDVYDDVRKQERQIMRLVIRRGKMPRSEFRKTFPSNETNVDWLTD 327

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             K  P+  + + +A  VD ++ ++  I+    +  + I+E + +   +  GE +A  AK
Sbjct: 328 RLKGNPK--FADSLAKVVDDVVVLQRRIRDHEDKLDMQITEMKEVARRMAIGEAKARRAK 385

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 386 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 445

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRK
Sbjct: 446 QAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRK 505

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED+   SP++ A  A L+E T  VL++LT RE 
Sbjct: 506 VLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDATSAGLQEATRDVLSNLTEREA 565

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 566 KVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 621



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 55/156 (35%), Positives = 91/156 (58%), Gaps = 8/156 (5%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGS 89
           +I++ +++GY+T  E+N  LP     S+Q+ED V ML+++GI +     D DD+   +G+
Sbjct: 16  LIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDADDILMNDGA 75

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D       A++ +  +    ++    T DPVRMY+REMG+++LL+REGEI IAKRIE G
Sbjct: 76  NDD----DMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              +  ++   P T Q ++   D +  G   L ++I
Sbjct: 132 IRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVI 167


>gi|224823888|ref|ZP_03696997.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
 gi|224604343|gb|EEG10517.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
          Length = 640

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 180/314 (57%), Positives = 241/314 (76%), Gaps = 3/314 (0%)

Query: 370 FLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           F++   G E++  WV    +   G+ W   +     +I++ + ++  +     +SI + +
Sbjct: 324 FIKYFPGNEINTDWVE--DEISSGKPWSEALTRFKYAIIEKQTKLAELQDRAMLSIKDLK 381

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I   +  GE +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 382 EINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 441

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 442 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGHEPD 501

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P E+A+++ MP + +RK++KI+KEPIS+ETPIGD+D SHLGDFIED+N ++P D+A+ ++
Sbjct: 502 PAELAERMEMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQNNLAPSDAAMYSS 561

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++ T  VL +LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 562 LKDATKEVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 621

Query: 669 HPSRSKKLRSFLDG 682
           HP+RS++LRSFLD 
Sbjct: 622 HPTRSERLRSFLDN 635



 Score = 97.4 bits (241), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 58/161 (36%), Positives = 88/161 (54%), Gaps = 14/161 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I L ++RGY+T  E+N  LP D   +EQ+E+ V M++ +GI V D      E    D+L
Sbjct: 31  LIALGKERGYLTYAEINDHLPEDVSDTEQIENIVTMITGLGIQVYD------EAPDADTL 84

Query: 94  DLASSASNSSVFLQKRK--------DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            ++ +    +      +        DS    T DPVRMY+REMGS+ELL+REGEI IAKR
Sbjct: 85  LMSDATPAVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGSVELLTREGEIEIAKR 144

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           IE G   M+ ++   P T   ++   + +  G   + E++D
Sbjct: 145 IEDGLKHMIEAISACPGTISEVLALLERVEAGDIRVDEVVD 185


>gi|209517800|ref|ZP_03266635.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
 gi|209501746|gb|EEA01767.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
          Length = 680

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWAD--KIVAEGHVYSA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D       E   GF
Sbjct: 187 GLKHMVMAISACPTTIADILAMAERVANDEVRIDELVDGLIDADAEDADGF 237


>gi|295700835|ref|YP_003608728.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295440048|gb|ADG19217.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 680

 Score =  372 bits (956), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWAD--KIVAEGHAYSA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D       E   GF
Sbjct: 187 GLKHMVMAISACPTTIADILAMAERVANDENRIDELVDGLIDADAEDADGF 237


>gi|187921407|ref|YP_001890439.1| RNA polymerase sigma factor RpoD [Burkholderia phytofirmans PsJN]
 gi|187719845|gb|ACD21068.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
           PsJN]
          Length = 681

 Score =  372 bits (955), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 188/347 (54%), Positives = 245/347 (70%), Gaps = 13/347 (3%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W     D   GE   +
Sbjct: 344 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWA----DKIVGEGHAY 393

Query: 399 VACEVDSILKIRNE---IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            A    +I  IR +   +  +     + + + +     +  GE +A  AK+EM EANLRL
Sbjct: 394 SAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRL 453

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 454 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 513

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS
Sbjct: 514 ARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPIS 573

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI 
Sbjct: 574 METPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIE 633

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 634 MSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 68  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 127

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 128 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 187

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D       E   GF
Sbjct: 188 GLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGF 238


>gi|121604510|ref|YP_981839.1| RpoD family RNA polymerase sigma factor [Polaromonas
           naphthalenivorans CJ2]
 gi|120593479|gb|ABM36918.1| RNA polymerase, sigma 70 subunit, RpoD [Polaromonas
           naphthalenivorans CJ2]
          Length = 736

 Score =  372 bits (955), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 192/348 (55%), Positives = 251/348 (72%), Gaps = 8/348 (2%)

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           DLL  Q+ D+ K+    E EL R+  +  G+ ++VF++      L+  WV   K    G+
Sbjct: 393 DLLRGQVLDVRKK----ERELRRIIVEKCGMPQEVFIKDFPPNLLNLKWVE--KQVAAGK 446

Query: 395 -WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W N +A  +  I +++ ++  +     + +   + I   + +GE  +  AKKEM+EANL
Sbjct: 447 PWSNVMARNIPPIQELQTKLGELQARVVVPLLHLKDINKRMNEGESNSRDAKKEMIEANL 506

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 507 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 566

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A+K+ +P E +RK++KI KEP
Sbjct: 567 DQARTIRIPVHMIETINKMNRLSRQHLQEFGFEPDASILAEKMEIPEEKIRKIMKIAKEP 626

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFIED    +PL++A+QA LR+    +L SLTPRE +VLRMRFG
Sbjct: 627 ISMETPIGDDDDSHLGDFIEDGANTAPLEAAMQAGLRDVVKDILDSLTPREAKVLRMRFG 686

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 687 IEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 734



 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 93/181 (51%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E++  LP   V +E +E  + ML++MG+ V     D + L    
Sbjct: 136 KTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVINMLNDMGVAVYEQAPDAETLLLNN 195

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 196 TGATVATEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 254

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++ ESP T   ++   D++ +G  ++  ++D           GF +  E   
Sbjct: 255 GGLMKMMEAISESPATIAEIMRLADDIREGKVVISTVVD-----------GFSNPNEADD 303

Query: 208 Y 208
           Y
Sbjct: 304 Y 304


>gi|323529251|ref|YP_004231403.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1001]
 gi|323386253|gb|ADX58343.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1001]
          Length = 680

 Score =  372 bits (954), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWAD--KIVAEGHSYSA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D       E   GF
Sbjct: 187 GLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDADAEDADGF 237


>gi|115358008|ref|YP_775146.1| RNA polymerase sigma factor RpoD [Burkholderia ambifaria AMMD]
 gi|115283296|gb|ABI88812.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           AMMD]
          Length = 805

 Score =  372 bits (954), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KITAEGHSYSA 519

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 520 VLARNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 579

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 580 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 639

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 640 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 699

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 700 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 759

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 760 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804


>gi|262369385|ref|ZP_06062713.1| DNA-directed RNA polymerase [Acinetobacter johnsonii SH046]
 gi|262315453|gb|EEY96492.1| DNA-directed RNA polymerase [Acinetobacter johnsonii SH046]
          Length = 628

 Score =  372 bits (954), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 204/408 (50%), Positives = 271/408 (66%), Gaps = 12/408 (2%)

Query: 278 PKVMCA-LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           P++  A  DE+   ++  R++       +K  +SS + +   E L  +           D
Sbjct: 227 PEIAKARFDELTAAWKNTRTII------EKHGRSSKEAEDALESLATVFMMFKFTPRLFD 280

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV--SYAKDFPEG 393
           ++ E +    ++I  +E E++R A   G + R  F     G+E +  W+    AK  P+ 
Sbjct: 281 IISEMIRGTHEQIRTSEREVMRYAVRRGRMDRTQFRTSFPGQESNFAWLDEQIAKASPDQ 340

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
             K ++      +L  + +I  I  +  + +   + I   +  GE +A  AKKEMVEANL
Sbjct: 341 --KGYLEKVRPDVLAFQQKIADIEKDLDLDVKGIKEISKRMAVGEAKARRAKKEMVEANL 398

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 399 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 458

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI KEP
Sbjct: 459 DQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEP 518

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+MRFG
Sbjct: 519 ISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFG 578

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 579 IDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 626


>gi|217969610|ref|YP_002354844.1| RNA polymerase sigma factor RpoD [Thauera sp. MZ1T]
 gi|217506937|gb|ACK53948.1| RNA polymerase, sigma 70 subunit, RpoD [Thauera sp. MZ1T]
          Length = 666

 Score =  372 bits (954), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 188/352 (53%), Positives = 257/352 (73%), Gaps = 10/352 (2%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW----VSYAKD 389
           I+ L + +  + +++  +E ++L+L     G+ R  F++   G+E++  W    ++  K+
Sbjct: 317 IEKLCDSVRHMVEQVRSHERQILQLCVDRAGMPRQHFIKVFPGQEVNLDWLKDEIAAGKN 376

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           + +G  +   A     +L+ + ++  +    GI + E + I   +  GE +   AK+EM 
Sbjct: 377 YADGLMRIHPA-----VLEEQQKLIDLQDRIGIPLKELKDINRQMSTGEAKMRRAKREMT 431

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 432 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 491

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R++  +  +EP P  +A+K+ MP E +RK++KI
Sbjct: 492 RSIADQARTIRIPVHMIETINKMNRISRQILQETGQEPDPATLAEKMEMPEEKIRKIMKI 551

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +KEPIS+ETPIGD+D SHLGDFIED   ++P ++A+ + LR+ T  VL SLT RE +VLR
Sbjct: 552 SKEPISMETPIGDDDDSHLGDFIEDTATLAPAEAAMYSGLRDATCEVLDSLTQREAKVLR 611

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFLD
Sbjct: 612 MRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLD 663


>gi|119944095|ref|YP_941775.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
 gi|119862699|gb|ABM02176.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
          Length = 617

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 193/326 (59%), Positives = 233/326 (71%), Gaps = 29/326 (8%)

Query: 370 FLERHQGRELDPHWVS--------YAKDFPEGE------WKNFVACEVDSILKIRNEIKS 415
           F++  +G E +P W+         YA    E E       +  +A EV S+L I N +K 
Sbjct: 306 FIKLFKGNETNPAWLEVILSNGTDYATRISEFEEDLRRCLRKMLAVEVQSVLTITN-MKG 364

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS    I              GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 365 ISRNMSI--------------GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 410

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R 
Sbjct: 411 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRV 470

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M  ++ REP PEE+A+++ MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED 
Sbjct: 471 SRQMLQEMGREPQPEELAERMMMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDT 530

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               P + A   +L+  T  VL  LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRER
Sbjct: 531 TIALPANCATSESLKNATNDVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 590

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 591 IRQIEAKALRKLRHPSRSEQLRSFLD 616



 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 59/141 (41%), Positives = 86/141 (60%), Gaps = 6/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K++I   +++G++T  E+N  LP D V SEQ+ED + M+ +MGI VV    D DD+    
Sbjct: 10  KELIIKGKEKGFLTYAEVNDHLPQDIVESEQIEDIIQMIGDMGIRVVETAPDADDMLI-- 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G++DS      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 68  GADDSETPDEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  ++ E P T   L+
Sbjct: 128 EGIKEVQTAVSEYPATISGLL 148


>gi|237748836|ref|ZP_04579316.1| RNA polymerase primary sigma factor [Oxalobacter formigenes OXCC13]
 gi|229380198|gb|EEO30289.1| RNA polymerase primary sigma factor [Oxalobacter formigenes OXCC13]
          Length = 819

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 182/320 (56%), Positives = 234/320 (73%), Gaps = 5/320 (1%)

Query: 364 GIKRDVFLERHQGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
           G+ R  F++   G E D  W+      D P   +   +   V  + +++ ++  I    G
Sbjct: 501 GVPRAHFIKTFPGNETDLTWIDEEVEADHP---YSAILERNVPMVKELQQKLVDIQNRIG 557

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +++ R I   +  GE  A  AKKEM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 558 MPLADLREINRKMVAGEMRARKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 617

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 618 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 677

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP P  +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P 
Sbjct: 678 ETGAEPDPATLAVKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPS 737

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A+ A++R     VL SLTPRE +VLRMRFG+ M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 738 DAALHASMRNVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEA 797

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS KL+SFL+
Sbjct: 798 KALRKLRHPSRSDKLKSFLE 817


>gi|78063051|ref|YP_372959.1| RNA polymerase sigma factor RpoD [Burkholderia sp. 383]
 gi|77970936|gb|ABB12315.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. 383]
          Length = 808

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 471 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWSE--KIMAEGHSYSA 522

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 523 VLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 582

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 583 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 642

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 643 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 702

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 703 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 762

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 763 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 807


>gi|161521349|ref|YP_001584776.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
           17616]
 gi|189352484|ref|YP_001948111.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
           17616]
 gi|160345399|gb|ABX18484.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia multivorans
           ATCC 17616]
 gi|189336506|dbj|BAG45575.1| RNA polymerase primary sigma factor [Burkholderia multivorans ATCC
           17616]
          Length = 804

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 467 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGNETDLDWAE--KIAAEGHSYSA 518

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 519 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 578

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 579 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 638

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 639 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 698

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 699 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 758

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 759 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 803



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 188 RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 247

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 248 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 307

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 308 GLRHMVMAISACPTTIADILAMAERVANDEIRVDELVD 345


>gi|116691983|ref|YP_837516.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia HI2424]
 gi|116649983|gb|ABK10623.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           HI2424]
          Length = 805

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KITAEGHPYSA 519

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 520 VLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 579

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 580 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 639

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 640 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 699

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 700 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 759

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 760 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804


>gi|172062815|ref|YP_001810466.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
 gi|171995332|gb|ACB66250.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
          Length = 805

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KIAAEGHSYSA 519

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 520 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 579

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 580 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 639

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 640 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 699

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 700 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 759

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 760 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804


>gi|134292973|ref|YP_001116709.1| RNA polymerase sigma factor RpoD [Burkholderia vietnamiensis G4]
 gi|134136130|gb|ABO57244.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia vietnamiensis
           G4]
          Length = 809

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 472 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KIAAEGHSYSA 523

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 524 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 583

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 584 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 643

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 644 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 703

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 704 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 763

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 764 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 808


>gi|221197050|ref|ZP_03570097.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD2M]
 gi|221203722|ref|ZP_03576740.1| sigma-70, non-essential region family [Burkholderia multivorans
           CGD2]
 gi|221175888|gb|EEE08317.1| sigma-70, non-essential region family [Burkholderia multivorans
           CGD2]
 gi|221183604|gb|EEE16004.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD2M]
          Length = 682

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 345 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGNETDLDWAE--KIAAEGHSYSA 396

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 397 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 456

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 457 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 516

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 517 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 576

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 577 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 636

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 637 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 66  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 125

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 126 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 185

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 186 GLRHMVMAISACPTTIADILAMAERVANDEIRVDELVD 223


>gi|126443442|ref|YP_001063518.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126222933|gb|ABN86438.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 736

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 399 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KIAAEGHSYGA 450

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 451 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 510

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 511 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 570

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 571 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 630

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 631 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 690

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 691 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 735



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 123 RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 182

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 183 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 242

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 243 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 280


>gi|118594360|ref|ZP_01551707.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440138|gb|EAV46765.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 654

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 197/410 (48%), Positives = 279/410 (68%), Gaps = 11/410 (2%)

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           L  +V+    +I   +++L  L++       +E    +  +LKE +     +   +   +
Sbjct: 251 LTKEVLSRFGKIKRAHKKLSELREQKKWTDDEEYKKHQDIILKELI-----NFRFSSKFV 305

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           ++L +++    K+I  +E  ++    +   + R  F++   G E +  W+   K+  + +
Sbjct: 306 EVLCDKVRTFVKQIRGHERAVMEFCVEESKMPRSHFIKSFPGNETNLKWL---KEEIKSD 362

Query: 395 WKNFVACEV--DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            K   + E    SIL  ++++ ++    GI I  F+ I   +  GE  A  AK+EM+EAN
Sbjct: 363 KKYVESLEKLKHSILDQQSKLIALEELAGIPIKNFKEINRHMTTGEARAKRAKREMIEAN 422

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 423 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 482

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R +R++     +EP P E+A+K+ MP E +RK+LKI+KE
Sbjct: 483 ADQARTIRIPVHMIETINKMNRISRQILQSTGQEPEPSELAEKMEMPEEKIRKILKISKE 542

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PIS+ETPIGD++ SHLGDFIED   ++P D+A+  +LR  T+ +L  LTPRE +VLRMRF
Sbjct: 543 PISMETPIGDDEDSHLGDFIEDVGTLTPDDAAVYGSLRSVTSEILEGLTPREAKVLRMRF 602

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS++L+SFL+G
Sbjct: 603 GIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSERLKSFLEG 652



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 55/133 (41%), Positives = 79/133 (59%), Gaps = 4/133 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVS-SEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
           K +I + ++RGY+T  E+N  LP DEVS SEQ+E  + ++++MGI V +   D E    S
Sbjct: 45  KALIIMGKERGYLTYAEINDHLP-DEVSESEQVEGIIGIINDMGIMVYEQAPDAESLLMS 103

Query: 90  EDSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +D   +    +           DS    T DPVRMY+REMG+++LL+REGEI IAKRIE 
Sbjct: 104 DDRAPVTDEEAAEEAEQALATVDSEFGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIED 163

Query: 149 GRAMMMASLCESP 161
           G   M+ ++   P
Sbjct: 164 GLRHMVQAISACP 176


>gi|76817579|ref|YP_335991.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710b]
 gi|76582052|gb|ABA51526.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710b]
          Length = 800

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 463 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 514

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 515 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 574

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 575 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 634

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 635 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 694

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 695 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 754

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 755 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 799



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 187 RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 246

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 247 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 306

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 307 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 344


>gi|167583913|ref|ZP_02376301.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ubonensis Bu]
          Length = 681

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 344 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYSA 395

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 396 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 455

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 456 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 515

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 516 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 575

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 576 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 635

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 636 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 65  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 124

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 125 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 184

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 185 GLRHMVMAISACPTTIADILAMAERVANEESRIDELVD 222


>gi|121597172|ref|YP_991115.1| RNA polymerase sigma factor RpoD [Burkholderia mallei SAVP1]
 gi|126456327|ref|YP_001076416.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|121224970|gb|ABM48501.1| RNA polymerase sigma factor RpoD [Burkholderia mallei SAVP1]
 gi|126230095|gb|ABN93508.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
          Length = 736

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 399 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 450

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 451 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 510

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 511 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 570

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 571 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 630

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 631 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 690

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 691 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 735



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 123 RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 182

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 183 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 242

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 243 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 280


>gi|170699447|ref|ZP_02890491.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           IOP40-10]
 gi|170135647|gb|EDT03931.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           IOP40-10]
          Length = 683

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 346 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KIAAEGHSYSA 397

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 398 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 457

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 458 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 517

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 518 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 577

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 578 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 637

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 638 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 682


>gi|170736023|ref|YP_001777283.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
 gi|169818211|gb|ACA92793.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
          Length = 683

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 346 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KITAEGHPYSA 397

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 398 VLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 457

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 458 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 517

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 518 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 577

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 578 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 637

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 638 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 682


>gi|83716798|ref|YP_438821.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|83650623|gb|ABC34687.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 800

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 463 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 514

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 515 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 574

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 575 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 634

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 635 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 694

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 695 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 754

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 755 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 799



 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 187 RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 246

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 247 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 306

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 307 GLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD 344


>gi|332974186|gb|EGK11120.1| DNA-directed RNA polymerase sigma subunit RpoD [Psychrobacter sp.
           1501(2011)]
          Length = 624

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 194/356 (54%), Positives = 255/356 (71%), Gaps = 4/356 (1%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS- 385
           L LN    D ++  ++D+   +   E +++RL    G + R  F +     E +  W++ 
Sbjct: 269 LKLNNRMSDNVMAIMHDVYDDVRKQERQIMRLVIRRGKMPRAEFRKTFPSNETNVDWLTD 328

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             K  P+  + + +A  VD ++ ++  I+    +  + I E + +   +  GE +A  AK
Sbjct: 329 RLKGNPK--FADSLAKVVDDVVVLQRRIRDHEDKLDMEIGEMKEVARRMAIGEAKARRAK 386

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 387 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 446

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRK
Sbjct: 447 QAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRK 506

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED+   SP++ A  A L+E T  VL++LT RE 
Sbjct: 507 VLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDATSAGLQEATRDVLSNLTEREA 566

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 567 KVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 622



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 55/156 (35%), Positives = 91/156 (58%), Gaps = 8/156 (5%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGS 89
           +I++ +++GY+T  E+N  LP     S+Q+ED V ML+++GI +     D DD+   +G+
Sbjct: 16  LIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDADDILMNDGA 75

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D       A++ +  +    ++    T DPVRMY+REMG+++LL+REGEI IAKRIE G
Sbjct: 76  NDD----EMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              +  ++   P T Q ++   D +  G   L ++I
Sbjct: 132 IRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVI 167


>gi|221212356|ref|ZP_03585333.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
 gi|221167455|gb|EED99924.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
          Length = 682

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 345 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGNETDLDWAE--KIAAEGHSYSA 396

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 397 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 456

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 457 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 516

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 517 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 576

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 577 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 636

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 637 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 66  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 125

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 126 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 185

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 186 GLRHMVMAISACPTTIADILAMAERVANDEIRVDELVD 223


>gi|325518128|gb|EGC97914.1| RNA polymerase sigma factor RpoD [Burkholderia sp. TJI49]
          Length = 682

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 345 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KIAAEGHSYSA 396

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 397 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 456

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 457 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 516

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 517 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 576

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 577 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 636

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 637 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 66  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 125

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 126 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 185

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 186 GLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD 223


>gi|94971322|ref|YP_593370.1| sigma 38, RpoS [Candidatus Koribacter versatilis Ellin345]
 gi|94553372|gb|ABF43296.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Koribacter
           versatilis Ellin345]
          Length = 574

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 170/274 (62%), Positives = 229/274 (83%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++ +++ +  E G+SI+E +     + +G+ +A  AKKE++EANLRLV+S+AKKYTNRGL
Sbjct: 298 LKGDLERMEQEAGVSIAELKRTQREIIQGDMDAEQAKKELIEANLRLVVSIAKKYTNRGL 357

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 358 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIET 417

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++RT+R++  ++ REP+ EEIAK++ +PV  VRKVLKI +EPISLETPIG+E+ SHL
Sbjct: 418 INKLIRTSRQLVQELGREPSSEEIAKRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHL 477

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++ VSP ++ I  NL++ T +VL +LT REE+V++MRFG+   ++HTLEEVG+ 
Sbjct: 478 GDFIEDRSMVSPAEAVINVNLKDQTAQVLRTLTAREEKVIKMRFGLEDGSEHTLEEVGQS 537

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKL+HPSRS+KLR+FLDG
Sbjct: 538 FAVTRERIRQIEAKALRKLRHPSRSRKLRAFLDG 571



 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 61/178 (34%), Positives = 97/178 (54%), Gaps = 29/178 (16%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG- 80
           +  D   D  KK+I   +++GY+T  E+N  +P D  S + ++D +  +   GI+V++G 
Sbjct: 1   MALDDKYDDIKKLIDTGKEKGYLTYSEVNDLIPHDVHSPDDLDDLLTTIGTQGIDVLEGP 60

Query: 81  -------------DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
                        DD+E  E  E  LDL   A      L+K        T+DPVRMYLRE
Sbjct: 61  GKLPSAAVLDKRYDDVEAGE-EEMELDLTPGA------LEK--------TNDPVRMYLRE 105

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           MG++ LL+REGE+ IAKRIE G+  ++ ++  SP+  + +I   ++L  G   ++EI+
Sbjct: 106 MGTVPLLTREGEVEIAKRIERGQLRVLKAISRSPIVIRDIIAIGEDLKRGVRSIKEIV 163


>gi|53716429|ref|YP_105146.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|53722776|ref|YP_111761.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei K96243]
 gi|67643221|ref|ZP_00441969.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|124381664|ref|YP_001025512.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10229]
 gi|126447609|ref|YP_001077577.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|134278673|ref|ZP_01765387.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167000270|ref|ZP_02266089.1| RNA polymerase sigma factor RpoD [Burkholderia mallei PRL-20]
 gi|167743532|ref|ZP_02416306.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|167820721|ref|ZP_02452401.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
 gi|167850557|ref|ZP_02476065.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|167899150|ref|ZP_02486551.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 7894]
 gi|167907493|ref|ZP_02494698.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei NCTC
           13177]
 gi|167915832|ref|ZP_02502923.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 112]
 gi|167923671|ref|ZP_02510762.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei BCC215]
 gi|217422551|ref|ZP_03454054.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|226195650|ref|ZP_03791237.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|237508723|ref|ZP_04521438.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           MSHR346]
 gi|242312268|ref|ZP_04811285.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254177429|ref|ZP_04884085.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254186160|ref|ZP_04892678.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|254194055|ref|ZP_04900487.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|254203084|ref|ZP_04909446.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208417|ref|ZP_04914766.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254265453|ref|ZP_04956318.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|254301213|ref|ZP_04968657.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|254359397|ref|ZP_04975669.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|52213190|emb|CAH39230.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei K96243]
 gi|52422399|gb|AAU45969.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|126240463|gb|ABO03575.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|134250457|gb|EBA50537.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|147746129|gb|EDK53207.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147751104|gb|EDK58172.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148028584|gb|EDK86544.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|157811356|gb|EDO88526.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157933846|gb|EDO89516.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|160698469|gb|EDP88439.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|169650806|gb|EDS83499.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|217394782|gb|EEC34801.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|225932135|gb|EEH28135.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|235000928|gb|EEP50352.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           MSHR346]
 gi|238524506|gb|EEP87939.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|242135507|gb|EES21910.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|243063759|gb|EES45945.1| RNA polymerase sigma factor RpoD [Burkholderia mallei PRL-20]
 gi|254216455|gb|EET05840.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|261826434|gb|ABM99450.2| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10229]
          Length = 680

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 187 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 224


>gi|167577173|ref|ZP_02370047.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
 gi|167615343|ref|ZP_02383978.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
          Length = 680

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 187 GLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD 224


>gi|238024932|ref|YP_002909164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
 gi|237879597|gb|ACR31929.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
          Length = 805

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/347 (53%), Positives = 244/347 (70%), Gaps = 13/347 (3%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W          E  ++
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLTWAEKVA----AESHSY 517

Query: 399 VACEVDSILKIRNE---IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            A  V +I  I  +   +  +     + + + +     +  GE +A  AK+EM EANLRL
Sbjct: 518 SAILVRNIPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRL 577

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 578 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 637

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS
Sbjct: 638 ARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPIS 697

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI 
Sbjct: 698 METPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIE 757

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 758 MSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804


>gi|186472768|ref|YP_001860110.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
 gi|184195100|gb|ACC73064.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
          Length = 685

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   E   +  
Sbjct: 348 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGNETDLEWAD--KIVSENHAYSA 399

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 400 ILSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 459

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 460 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 519

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 520 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 579

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 580 TPIGDDDDSHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 639

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 640 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 684



 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/177 (31%), Positives = 95/177 (53%), Gaps = 15/177 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +      +    +
Sbjct: 72  RALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIISTFNDMGVAVYE------QAPDAE 125

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L  +A N+S   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 126 TLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 185

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           AKRIE G   M+ ++   P T   ++   + + +    + E++D    +  E   GF
Sbjct: 186 AKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDVNAEDTDGF 242


>gi|107026824|ref|YP_624335.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia AU 1054]
 gi|105896198|gb|ABF79362.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia AU
           1054]
          Length = 805

 Score =  369 bits (948), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KITAEGHPYSA 519

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 520 VLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 579

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 580 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 639

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 640 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 699

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A  A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 700 TPIGDDDDSHLGDFIEDTNTVAPADAAPHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 759

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 760 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804


>gi|206562773|ref|YP_002233536.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia J2315]
 gi|198038813|emb|CAR54775.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia J2315]
          Length = 621

 Score =  369 bits (948), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 284 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGNETDLDWAE--KITAEGHSYSA 335

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 336 VLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 395

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 396 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 455

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 456 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 515

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 516 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 575

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 576 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 620


>gi|261400701|ref|ZP_05986826.1| RNA polymerase sigma factor RpoD [Neisseria lactamica ATCC 23970]
 gi|269209456|gb|EEZ75911.1| RNA polymerase sigma factor RpoD [Neisseria lactamica ATCC 23970]
          Length = 642

 Score =  369 bits (947), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 59/188 (31%), Positives = 103/188 (54%), Gaps = 17/188 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDTRPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|332704204|ref|ZP_08424292.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332554353|gb|EGJ51397.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 594

 Score =  369 bits (947), Expect = e-99,   Method: Compositional matrix adjust.
 Identities = 208/459 (45%), Positives = 297/459 (64%), Gaps = 38/459 (8%)

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP------KVMCALDEIAEVY 291
           KD R K+    +  E D+ +  EDE +    +  + D+++       K+   LD+ A + 
Sbjct: 160 KDSRIKLKDVVKTIEEDDPS--EDEMNQRQRVIFLLDEIKASFKKKRKIYTKLDQCATLD 217

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           R + SLQ   V+              KE++V+ +  + L ++ ID ++E + D  ++ MH
Sbjct: 218 RRVFSLQMEIVS-------------FKEEVVQKLREIKLEKTLIDRVIETVEDYVRQ-MH 263

Query: 352 N-----EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE---WKNFVACEV 403
           N        ++   ++    RD+F  R   R L+P   + A      E   +K  +A ++
Sbjct: 264 NCQRDLAAYIMSTGKTQSEIRDLF-RRVDDRTLNPLNAAEALGLTVEEFFSYKEMLAGKM 322

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           + +++++ +           +SE   ++  +R+G   AS AK+E++ ANLRLV+S+AKKY
Sbjct: 323 EILVRLQEKCCH-------QVSELEEVLWRIRRGNENASRAKRELIRANLRLVVSIAKKY 375

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 376 TNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPV 435

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K++RT+R +  ++ R+PTPEEIA+++  P+E V+KVLKI KEPISLETPIGDE
Sbjct: 436 HMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPIEKVKKVLKIAKEPISLETPIGDE 495

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIEDK AV+P +  +   L E   +VL+ LTPREE+VLR RFGIG  +DHTLE
Sbjct: 496 EDSSLGDFIEDKKAVAPAEEVVNTKLSEQIGKVLSDLTPREEQVLRKRFGIGEKSDHTLE 555

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ + 
Sbjct: 556 EVGKLFNVTRERIRQIEAKALRKLRHPVRSQILRSYYES 594



 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 94/165 (56%), Gaps = 16/165 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---------- 81
           K +I   +Q+G++T +ELN+ LP +  + EQ+E+ +++   + I +VD +          
Sbjct: 11  KTLIAQGKQKGFLTFKELNSALPSEVNNPEQIEEIISIFDQLEIAIVDSEKEGKKLQILS 70

Query: 82  -DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D E EE   D+  +   A N     +   D A RSTD PVRMYLREMGS+ LL REGE+
Sbjct: 71  ADSESEEVDVDAASVIEIAGND----EDAADYASRSTD-PVRMYLREMGSVPLLDREGEV 125

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            IAK+IE+G   ++ +L E P+  + L+    +L D    L++++
Sbjct: 126 VIAKKIESGELDVLYALVEVPVAVEELVQVGKDLKDSRIKLKDVV 170


>gi|113868683|ref|YP_727172.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha H16]
 gi|113527459|emb|CAJ93804.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia
           eutropha H16]
          Length = 827

 Score =  369 bits (947), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 179/319 (56%), Positives = 236/319 (73%), Gaps = 1/319 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G+ R  F+ R  G E +  WV       +G +   V   V ++ +++ ++  +     + 
Sbjct: 509 GMPRSEFVARFPGNETNLEWVHTIVADGKG-YSTIVERNVPAVHELQQKLIDLQSRVVLP 567

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 568 LKELKGVNRKMAEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 627

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  + 
Sbjct: 628 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 687

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++
Sbjct: 688 GNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEA 747

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 748 ALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 807

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HPSRS KL+SFL+G
Sbjct: 808 LRKLRHPSRSDKLKSFLEG 826



 Score = 98.2 bits (243), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 63/163 (38%), Positives = 93/163 (57%), Gaps = 13/163 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI V      E    +E 
Sbjct: 213 KALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIAV-----YEQAPDAET 267

Query: 92  SL--DLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L  D A SA++     ++ +      DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 268 LLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 327

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIEAG   M+ ++   P+T   ++   + + +    + E +D
Sbjct: 328 KRIEAGLKDMVMAISACPVTISEILAHAERVANDEIKIDEFVD 370


>gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma factor [Janthinobacterium sp.
           Marseille]
 gi|151280838|gb|ABR89248.1| RNA polymerase primary sigma factor [Janthinobacterium sp.
           Marseille]
          Length = 826

 Score =  369 bits (947), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 189/356 (53%), Positives = 252/356 (70%), Gaps = 18/356 (5%)

Query: 338 LVEQLYDISK----RIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +VE+L D  +     + H E ++L +A    G+ R  F++   G E +  WV       +
Sbjct: 477 VVEKLCDTLRGQVDEVRHIEKQILDVAVNRCGMPRGHFIKVFPGNETNLDWV-------D 529

Query: 393 GE------WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           GE      +   +A  V ++ +++ ++  +     + + + R I   +  GE +A  AK+
Sbjct: 530 GEVNGKHAYSVVLARNVPTVKELQQKLIDLQARVVLPLPDLRAINKKMAAGEMKARKAKR 589

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++Q
Sbjct: 590 EMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQ 649

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A K+ MP + +RK+
Sbjct: 650 AITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKI 709

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R     VL SLTPRE +
Sbjct: 710 MKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAK 769

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 770 VLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 825



 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 58/160 (36%), Positives = 87/160 (54%), Gaps = 7/160 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IK  ++RG++T  E+N  LP + +  E +E  +   ++MGI V +     D E    
Sbjct: 211 KTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMGIAVYE--QAPDAETLLL 268

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           S ++A+ AS+              DS    T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 269 SDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 328

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E G   M+ ++   P T   +I   + ++     + EI+D
Sbjct: 329 EDGLRDMIQAISACPTTIAEIIAAAERISKDEAKIDEIVD 368


>gi|4128212|gb|AAD03549.1| principal sigma factor [Burkholderia cepacia]
          Length = 621

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 284 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KIAAEGHSYSA 335

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 336 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 395

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 396 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 455

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 456 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 515

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 516 TPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 575

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 576 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 620


>gi|261377614|ref|ZP_05982187.1| RNA polymerase sigma factor RpoD [Neisseria cinerea ATCC 14685]
 gi|269146367|gb|EEZ72785.1| RNA polymerase sigma factor RpoD [Neisseria cinerea ATCC 14685]
          Length = 642

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 238/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  WV   ++  +G  W + +     +IL+ + E+ ++  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWVE--EEVAKGRVWSDALDRFRHAILEKQTELANMERETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNIAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 102/188 (54%), Gaps = 4/188 (2%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           RN++ + E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ 
Sbjct: 3   RNQNHE-EYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNI 61

Query: 67  VAMLSNMGINVVDGD-DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           V+M+S +GI V +   D ED   S+++      A   +       DS    T DPVRMY+
Sbjct: 62  VSMISGLGIQVTEHTPDAEDILLSDNAAVTDDDAVEEAEAALSNADSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILGLIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|254248772|ref|ZP_04942092.1| Sigma-70 region 1.1 [Burkholderia cenocepacia PC184]
 gi|124875273|gb|EAY65263.1| Sigma-70 region 1.1 [Burkholderia cenocepacia PC184]
          Length = 805

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 185/345 (53%), Positives = 246/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KITAEGHPYSA 519

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  V +I + +  +  +     + + + +     +  GE +A  AK+EM EA+LRLVI
Sbjct: 520 VLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEAHLRLVI 579

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 580 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 639

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 640 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 699

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 700 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 759

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 760 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804


>gi|240127996|ref|ZP_04740657.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-93-1035]
 gi|268686384|ref|ZP_06153246.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-93-1035]
 gi|268626668|gb|EEZ59068.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-93-1035]
          Length = 642

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 89/156 (57%), Gaps = 15/156 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENTLKNMVQAISACP 157


>gi|261363710|ref|ZP_05976593.1| RNA polymerase sigma factor RpoD [Neisseria mucosa ATCC 25996]
 gi|288568271|gb|EFC89831.1| RNA polymerase sigma factor RpoD [Neisseria mucosa ATCC 25996]
          Length = 649

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 183/319 (57%), Positives = 238/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  WV   ++  +G  W + +     +IL+ + E+ ++  ET IS
Sbjct: 328 MERDYFIQNFLPEITNLKWVE--EEVAKGRVWSDALDRFRHAILEKQTELANMEKETRIS 385

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 386 IEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 445

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 446 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQET 505

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 506 GEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 565

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 566 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 625

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 626 LRKLRHPTRSDRLRSFLDS 644



 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 55/184 (29%), Positives = 99/184 (53%), Gaps = 4/184 (2%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D +  L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S
Sbjct: 9   DYQEQDDNRPLTLEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMIS 68

Query: 72  NMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMG 129
            +GI V +   D ED   S+++  +    + +         DS    T DPVRMY+REMG
Sbjct: 69  GLGIQVTEQAPDAEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMG 128

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
            ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++  EA
Sbjct: 129 QVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVV--EA 186

Query: 190 CIGP 193
            I P
Sbjct: 187 IIDP 190


>gi|194098357|ref|YP_002001415.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae NCCP11945]
 gi|239998768|ref|ZP_04718692.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|240112698|ref|ZP_04727188.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae MS11]
 gi|240117739|ref|ZP_04731801.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID1]
 gi|254493553|ref|ZP_05106724.1| RNA polymerase sigma factor rpoD [Neisseria gonorrhoeae 1291]
 gi|268594613|ref|ZP_06128780.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|268598759|ref|ZP_06132926.1| RNA polymerase sigma factor [Neisseria gonorrhoeae MS11]
 gi|268603436|ref|ZP_06137603.1| sigma 70 domain-containing protein [Neisseria gonorrhoeae PID1]
 gi|193933647|gb|ACF29471.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512593|gb|EEH61938.1| RNA polymerase sigma factor rpoD [Neisseria gonorrhoeae 1291]
 gi|268548002|gb|EEZ43420.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|268582890|gb|EEZ47566.1| RNA polymerase sigma factor [Neisseria gonorrhoeae MS11]
 gi|268587567|gb|EEZ52243.1| sigma 70 domain-containing protein [Neisseria gonorrhoeae PID1]
 gi|317164060|gb|ADV07601.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 642

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 89/156 (57%), Gaps = 15/156 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACP 157


>gi|59801382|ref|YP_208094.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA 1090]
 gi|240014315|ref|ZP_04721228.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI18]
 gi|240016750|ref|ZP_04723290.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA6140]
 gi|240121878|ref|ZP_04734840.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID24-1]
 gi|240123293|ref|ZP_04736249.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID332]
 gi|240125543|ref|ZP_04738429.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-92-679]
 gi|268681916|ref|ZP_06148778.1| RNA polymerase sigma factor [Neisseria gonorrhoeae PID332]
 gi|268684130|ref|ZP_06150992.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-92-679]
 gi|293399243|ref|ZP_06643408.1| RNA polymerase primary sigma factor [Neisseria gonorrhoeae F62]
 gi|59718277|gb|AAW89682.1| putative RNA polymerase sigma factor [Neisseria gonorrhoeae FA
           1090]
 gi|268622200|gb|EEZ54600.1| RNA polymerase sigma factor [Neisseria gonorrhoeae PID332]
 gi|268624414|gb|EEZ56814.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-92-679]
 gi|291610657|gb|EFF39767.1| RNA polymerase primary sigma factor [Neisseria gonorrhoeae F62]
          Length = 642

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 89/156 (57%), Gaps = 15/156 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACP 157


>gi|330821204|ref|YP_004350066.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
 gi|327373199|gb|AEA64554.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
          Length = 805

 Score =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 183/344 (53%), Positives = 242/344 (70%), Gaps = 7/344 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W           +   
Sbjct: 468 VDEVRQVERQILHI------VVDKCGMPRSEFISRFPGSETDLAWAEKIATESHS-YSAI 520

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +   V +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVIS
Sbjct: 521 LQRNVPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 580

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 581 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 640

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+ET
Sbjct: 641 IRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMET 700

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+T
Sbjct: 701 PIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMST 760

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 761 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 84/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL + RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 191 RALIKLGKDRGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 250

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 251 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 310

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 311 GLRHMVMAISACPTTIADILAMAERVANDEIRIDELVD 348


>gi|240115443|ref|ZP_04729505.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID18]
 gi|260440745|ref|ZP_05794561.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 gi|268601118|ref|ZP_06135285.1| RNA polymerase, sigma 70 subunit [Neisseria gonorrhoeae PID18]
 gi|291044060|ref|ZP_06569776.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 gi|268585249|gb|EEZ49925.1| RNA polymerase, sigma 70 subunit [Neisseria gonorrhoeae PID18]
 gi|291012523|gb|EFE04512.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
          Length = 642

 Score =  368 bits (945), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 89/156 (57%), Gaps = 15/156 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACP 157


>gi|93005952|ref|YP_580389.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
 gi|92393630|gb|ABE74905.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
          Length = 648

 Score =  368 bits (945), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 196/375 (52%), Positives = 256/375 (68%), Gaps = 4/375 (1%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKR 367
           + S +     E+L      L LN    D ++  ++D+   +  +E +++RL    G + R
Sbjct: 274 RGSAQANEAYEQLASRFMMLKLNNRLSDQVMAIMHDVYDDVRKHERQIMRLVIRRGRMPR 333

Query: 368 DVFLERHQGRELDPHW-VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           + F +     E +  W +   K  P   +   +    D ++ ++  I+    +  + I +
Sbjct: 334 EEFRKTFPSNETNVDWLIERIKGKPA--FAATLEKVADDVILLQRAIRDYEHKLEMEIHD 391

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 392 MKDVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 451

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE
Sbjct: 452 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 511

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A  
Sbjct: 512 PTPEELGERLEMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTISSPVDDATA 571

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A LRE T  VL +LT RE RVL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 572 AGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 631

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFL+
Sbjct: 632 LRHPSRSEHLRSFLE 646


>gi|167566502|ref|ZP_02359418.1| RNA polymerase sigma factor RpoD [Burkholderia oklahomensis EO147]
 gi|167573583|ref|ZP_02366457.1| RNA polymerase sigma factor RpoD [Burkholderia oklahomensis C6786]
          Length = 681

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 184/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R    E D  W    K   EG  +  
Sbjct: 344 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPSNETDLDWAE--KIAAEGHSYSA 395

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 396 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 455

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 456 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 515

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 516 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 575

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 576 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 635

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 636 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 68  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 127

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 128 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 187

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 188 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 225


>gi|91777566|ref|YP_552774.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91690226|gb|ABE33424.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 665

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 243/664 (36%), Positives = 362/664 (54%), Gaps = 67/664 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V     D + L    
Sbjct: 54  RALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQAPDAETLLLNS 113

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEIAI
Sbjct: 114 NAPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEIAI 167

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   PL   A++    ++ DG   + E++D               G
Sbjct: 168 AKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVD---------------G 212

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +    EDS+  +   +V               +D      P +++  DE  L +  
Sbjct: 213 LNEDTIAAEEDSASAEASAEVD------ADTDGDEDEDSDDDVGPADSSAADEARLKQLT 266

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD--NAVNGQKDEKSSVKCKVLKEK 320
            D                 C      E++ ++  L D  NA + + D  S    +  +E+
Sbjct: 267 SD-----------------C-----LEIFAQVGMLSDQMNASHTRGDVTSKAYQRA-REE 303

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGREL 379
           + + +  +      ID L   +     ++   E  +L++  S  G+ R+ F+E   G E 
Sbjct: 304 IQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQIVVSKSGMPREKFIESFAGHEA 363

Query: 380 DPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           D  W   A     G      A E  + +I   + ++  I     + +   + I   +   
Sbjct: 364 DLGWTERAA---RGASAYGAALERHLPAIQSEQQKLIEIEATVSLPLKHLKEINRQMVAA 420

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFS
Sbjct: 421 ESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFS 480

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +A+++ 
Sbjct: 481 TYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPSVLAERME 540

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E VR +LKI K+P+S+ETP+GD+  + LGD IED  A SP D+A+QA+LR      L
Sbjct: 541 LSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAMQADLRAAIDDAL 600

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SL+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ +L+
Sbjct: 601 DSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLK 660

Query: 678 SFLD 681
           SFLD
Sbjct: 661 SFLD 664


>gi|254184931|ref|ZP_04891520.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184215523|gb|EDU12504.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 680

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 184/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAK +RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKTLRKLRHPSRSDKLKSFLEG 679



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 187 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 224


>gi|299135760|ref|ZP_07028944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
 gi|298601884|gb|EFI58038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
          Length = 573

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 170/273 (62%), Positives = 229/273 (83%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R +++ +  ++GIS+ + +     + +G+ +A  AK+E++EANLRLV+S+AKKYTNRGLQ
Sbjct: 297 RVDLQRVEADSGISLDDLKRTQREMIQGDMDAEKAKRELIEANLRLVVSIAKKYTNRGLQ 356

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I
Sbjct: 357 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETI 416

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K++RT+R++  ++ RE + EEIAK++ +PV  VRKVLKI +EPISLETPIG+E+ SHLG
Sbjct: 417 NKLIRTSRQLVQELGREASSEEIAKRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLG 476

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+ AVSP D+ I  NL+E T++VL +LTPREERV++MRFG+   ++HTLEEVG+ F
Sbjct: 477 DFIEDRMAVSPSDAVISVNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSF 536

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKL+HPSRS+KL++F+DG
Sbjct: 537 QVTRERIRQIEAKALRKLRHPSRSRKLKAFVDG 569



 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 95/164 (57%), Gaps = 4/164 (2%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD- 82
            D  ++   ++I   +++GY+T  E+N  LP D  S ++++D +  ++  GI V+ G+  
Sbjct: 5   LDKYEEDVDRIIDTGKEKGYLTYGEVNDLLPGDITSPDELDDLMTTINTQGIEVLSGEGR 64

Query: 83  -LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
               E  +EDS D  S      V L     + ++ T+DPVRMYLREMG++ LL+REGE+ 
Sbjct: 65  RAASERAAEDS-DNESGEEGDDVELDLSPGTLEK-TNDPVRMYLREMGTVPLLTREGEVE 122

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IAKRIE G+  +M ++  SP+  + +    ++L  G   ++E++
Sbjct: 123 IAKRIERGQLRVMKAISRSPIVIREITGLGEDLKRGVRNIKEVV 166


>gi|187929499|ref|YP_001899986.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12J]
 gi|187726389|gb|ACD27554.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12J]
          Length = 829

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 178/320 (55%), Positives = 237/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W+       +G+ +   V   V ++ +++ ++  +     +
Sbjct: 511 GMPRSDFVARFPGNETNLKWIETV--VADGKPYSTIVERNVPAVHELQQKLIDLQARVVL 568

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 569 PLTELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 628

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 629 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 688

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 689 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 748

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 749 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 808

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 809 ALRKLRHPSRSDKLKSFLEG 828



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/159 (36%), Positives = 87/159 (54%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V  E +E  VA L+++G+ V     D + L   +
Sbjct: 217 KALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLNDIGVAVYEQAPDAETLLLND 276

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 277 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 335

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 336 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 374


>gi|302036356|ref|YP_003796678.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
 gi|300604420|emb|CBK40752.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
          Length = 601

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 202/418 (48%), Positives = 282/418 (67%), Gaps = 16/418 (3%)

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNA----VNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
           ++LR K + +L+ + +V   L+ L D A     + +K +K   +   ++ ++V  + S++
Sbjct: 188 EELRVKTLDSLNAVRKVSASLKDLYDKARHVGADPEKQKKLRKQIDTVRGQVVDKMESVN 247

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           L+    D + +++ D++      E E+    +  G+  +       G EL        KD
Sbjct: 248 LHGVLKDRMTQRVRDLNLLFRQAEREVTSCQRRLGVGGEA------GAELLRRLCRTHKD 301

Query: 390 FPEGEWKNFVACEVDSILK-----IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASI 443
               + +  ++ EV   +K      +  I+ +  E   IS  E +  V  +   E +   
Sbjct: 302 LLAVKRRTSLSEEVLQDIKKHYQAAKGRIRQLETEEALISAEEIKDAVKHLDVAEEKVKR 361

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 362 GKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 421

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  K+ REPTPEEIA+++ +P++ V
Sbjct: 422 IRQAITRAIADQARTIRIPVHMIETINKLIRTSRHLVQKLGREPTPEEIAERMDLPLDKV 481

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RK+LKI +EPISLETPIG+E+ SHLGDFIEDK AVSPL++AI+ +L+      L +LTPR
Sbjct: 482 RKILKIAREPISLETPIGEEEDSHLGDFIEDKKAVSPLEAAIRYDLQRQINGALETLTPR 541

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR RFGIG  TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKLRSF++
Sbjct: 542 EEKVLRKRFGIGEATDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKKLRSFVE 599



 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 92/159 (57%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK+I L +++G++T ++LN+ LP D VSS+Q    + M   M I +V+  + E    + +
Sbjct: 11  KKLINLGKEKGFLTYDDLNSTLPADVVSSDQFSTIMTMFGEMDIEIVESAETERAPKAAE 70

Query: 92  SLDLASSASNSSVFLQKRKD-----SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +    +  S       K+      A   TDDPVR+YL+EMGS+ LLSREGEI IAKRI
Sbjct: 71  GEEAIEESEESEASEDNEKEIDLTPGALSRTDDPVRLYLKEMGSVALLSREGEIEIAKRI 130

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G+  +   +   P+T + ++  RD+L +G   +REI+
Sbjct: 131 EEGKKDIATVVYGLPMTLEFVLNLRDQLKNGKIDVREIV 169


>gi|241663618|ref|YP_002981978.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12D]
 gi|240865645|gb|ACS63306.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12D]
          Length = 821

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 178/320 (55%), Positives = 237/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W+       +G+ +   V   V ++ +++ ++  +     +
Sbjct: 503 GMPRSDFVARFPGNETNLKWIETV--VADGKPYSTIVERNVPAVHELQQKLIDLQARVVL 560

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 561 PLAELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 620

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 621 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 680

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 681 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 740

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 741 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 800

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 801 ALRKLRHPSRSDKLKSFLEG 820



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/159 (36%), Positives = 87/159 (54%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V  E +E  VA L+++G+ V     D + L   +
Sbjct: 209 KALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLNDIGVAVYEQAPDAETLLLND 268

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 269 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 327

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 328 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 366


>gi|309781724|ref|ZP_07676457.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_7_47FAA]
 gi|308919365|gb|EFP65029.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_7_47FAA]
          Length = 821

 Score =  368 bits (945), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 178/320 (55%), Positives = 237/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W+       +G+ +   V   V ++ +++ ++  +     +
Sbjct: 503 GMPRSDFVARFPGNETNLKWIETV--VADGKPYSTIVERNVPAVHELQQKLIDLQARVVL 560

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 561 PLTELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 620

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 621 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 680

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 681 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 740

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 741 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 800

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 801 ALRKLRHPSRSDKLKSFLEG 820



 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/159 (36%), Positives = 87/159 (54%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V  E +E  VA L+++G+ V     D + L   +
Sbjct: 209 KALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLNDIGVAVYEQAPDAETLLLND 268

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 269 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 327

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 328 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 366


>gi|225874024|ref|YP_002755483.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
 gi|83356350|gb|ABC16653.1| major sigma factor RpoD [Acidobacterium capsulatum]
 gi|225793569|gb|ACO33659.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
          Length = 597

 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 170/273 (62%), Positives = 228/273 (83%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           + +++ +  E G+SI++ +     + +G+ +A  AK+E++EANLRLV+S+AKKYTNRGLQ
Sbjct: 321 KTDLEKLEEEAGLSIADLKRTQREIIQGDMDAEQAKRELIEANLRLVVSIAKKYTNRGLQ 380

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I
Sbjct: 381 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETI 440

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K++RT+R++  ++ REPT EEIA+++ +PV  VRKVLKI +EPISLETPIG+E+ SHLG
Sbjct: 441 NKLIRTSRQLVQELGREPTSEEIARRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLG 500

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED  AVSP ++ I  NL+E T++VL +LTPREERV++MRFG+   ++HTLEEVG+ F
Sbjct: 501 DFIEDSQAVSPSEAVISVNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSF 560

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKL+HPSRS+KLR+F+D 
Sbjct: 561 QVTRERIRQIEAKALRKLRHPSRSRKLRAFVDN 593



 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 52/161 (32%), Positives = 92/161 (57%), Gaps = 8/161 (4%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D  ++  +K+I   +++GY+T  E+N  +P D  S E ++D +  +   GI++++G    
Sbjct: 43  DKYEEDLQKLIDAGKEKGYLTYNEVNDLIPGDMTSPEDLDDLMTTIGTQGIDILEGSPKL 102

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             +G +D          +   L+K        T+DPVRMYLREMG++ LL+REGE+ IAK
Sbjct: 103 GNDGFDDEDSDDVELDLTPGTLEK--------TNDPVRMYLREMGTVPLLTREGEVEIAK 154

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G+  +M ++  SP+  + +I   ++L  G   ++E++
Sbjct: 155 RIERGQLRVMKAVSRSPIVIREIIALGEDLRRGVRSVKEVV 195


>gi|167724581|ref|ZP_02407817.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 680

 Score =  367 bits (943), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 184/345 (53%), Positives = 245/345 (71%), Gaps = 9/345 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGSETDLDWAE--KVAAEGHSYGA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 455 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 514

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+E
Sbjct: 515 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISME 574

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTP E +VLRMRFGI M+
Sbjct: 575 TPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPSEAKVLRMRFGIEMS 634

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 635 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 187 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 224


>gi|90407543|ref|ZP_01215725.1| RNA polymerase sigma factor RpoD [Psychromonas sp. CNPT3]
 gi|90311353|gb|EAS39456.1| RNA polymerase sigma factor RpoD [Psychromonas sp. CNPT3]
          Length = 610

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 199/408 (48%), Positives = 269/408 (65%), Gaps = 8/408 (1%)

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           PK  C  +E AE + ELR L     +   K  ++  K +       +      L   + D
Sbjct: 206 PKGPCP-EESAEKFTELRRLNTIVEDMIAKHGRAHAKTRTAINAQAEFFQQFKLIPKQFD 264

Query: 337 LLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEG 393
            +V+ +      +   E  +L++  +   + +  F+   +G E +  W+   YA    E 
Sbjct: 265 RMVKTIRASMNMVRTQERLVLKICVEQNKMPKKAFISLFKGNETNKAWLDAIYAT---EK 321

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E+   +    + +++   ++  +  +T ++I   + I   +  GE +A  AKKEMVEANL
Sbjct: 322 EYAKRIKEFDEDLVRCIRKMALVETQTALTIINLKEISRKMSIGEAKARRAKKEMVEANL 381

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 382 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 441

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+M  ++ R+P P+E+A+++ MP + +RKVLKI KEP
Sbjct: 442 DQARTIRIPVHMIETINKLNRISRQMLQEMGRDPHPDELAERMMMPEDKIRKVLKIAKEP 501

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD++ SHLGDFIED     P+D A   +L+  T  VL  LT RE +VLRMRFG
Sbjct: 502 ISMETPIGDDEDSHLGDFIEDTTIALPVDCATSESLKNATNEVLEGLTAREAKVLRMRFG 561

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 562 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 609



 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 86/141 (60%), Gaps = 6/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K++I   +++G++T  E+N  LP D   +EQ+ED + M+ +MGI V     D D++   E
Sbjct: 10  KELIIKGKEKGFLTYAEVNDHLPQDIFEAEQIEDIIQMIGDMGIKVYETAPDADEISLGE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ D  +  + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  ESNDTADEDAVEAAAQV-LATVESEIGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   +  S+ E P T   L+
Sbjct: 128 EGIKEVQTSVSEYPGTITGLL 148


>gi|71065817|ref|YP_264544.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
 gi|71038802|gb|AAZ19110.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
          Length = 647

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 196/375 (52%), Positives = 256/375 (68%), Gaps = 4/375 (1%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKR 367
           + S +     E+L      L LN    D ++  ++D+   +  +E +++RL    G + R
Sbjct: 273 RGSAQANEAYEQLASRFMMLKLNNRLSDQVMAIMHDVYDDVRKHERQIMRLVIRRGRMPR 332

Query: 368 DVFLERHQGRELDPHW-VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           + F +     E +  W +   K  P   +   +    D ++ ++  I+    +  + I +
Sbjct: 333 EEFRKTFPSNETNVDWLIERIKGKPA--FAATLEKVTDDVILLQRAIRDYEHKLEMEIHD 390

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 391 MKDVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 450

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE
Sbjct: 451 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 510

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A  
Sbjct: 511 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTISSPVDDATA 570

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A LRE T  VL +LT RE RVL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 571 AGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 630

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFL+
Sbjct: 631 LRHPSRSEHLRSFLE 645


>gi|221068481|ref|ZP_03544586.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           KF-1]
 gi|220713504|gb|EED68872.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           KF-1]
          Length = 815

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 198/412 (48%), Positives = 273/412 (66%), Gaps = 14/412 (3%)

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           ++L+ + +   D + E++ ++  + D    G   E      K + E+L+ +  +    + 
Sbjct: 412 EELKNEALGRFDSMRELFDKMHKVYDK--EGYGTEAYMKVQKAITEELMTIRFTAKTIEK 469

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             DL+  Q+ D+ K+    E EL ++     G+ ++ F++      L+  WV   K    
Sbjct: 470 LCDLVRAQVDDVRKK----ERELRKIIVDKCGMPQEQFIKDFPPNLLNLDWV--IKQVAA 523

Query: 393 GEWKNFVAC---EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           G  KN+ A     +  + +++  +  +     + + E +HI   +  GE  +  AKKEM+
Sbjct: 524 G--KNYSAVLERNIPPVQELQQNLIDLQARVVVPLEELKHINKRMNSGERASRDAKKEMI 581

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 582 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 641

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI
Sbjct: 642 RSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKI 701

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTPRE +VLR
Sbjct: 702 AKEPISMETPIGDDDDSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLR 761

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 762 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 813



 Score =  102 bits (255), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 95/181 (52%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V     D + L    
Sbjct: 215 KMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNN 274

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + +     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 275 TGQSATTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 333

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 334 GGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVD-----------GFVNANENDD 382

Query: 208 Y 208
           Y
Sbjct: 383 Y 383


>gi|299066184|emb|CBJ37368.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CMR15]
          Length = 777

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 177/320 (55%), Positives = 238/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 459 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQARVVL 516

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 517 PLAELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 576

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 577 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 636

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 637 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 696

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 697 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 756

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 757 ALRKLRHPSRSDKLKSFLEG 776



 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 92/164 (56%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V +      +    +
Sbjct: 165 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYE------QAPDAE 218

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L  +A + +   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 219 TLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 278

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIEAG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 279 AKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 322


>gi|313668077|ref|YP_004048361.1| RNA polymerase sigma factor [Neisseria lactamica ST-640]
 gi|313005539|emb|CBN86975.1| RNA polymerase sigma factor [Neisseria lactamica 020-06]
          Length = 642

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 59/188 (31%), Positives = 103/188 (54%), Gaps = 17/188 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
 gi|300072989|gb|ADJ62388.1| RNA polymerase sigma-70 factor transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 850

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 178/318 (55%), Positives = 237/318 (74%), Gaps = 1/318 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  F++   G E++  WV   +     ++   ++  V +I +++ ++  +     + +
Sbjct: 533 MPRAHFIKVFPGNEVNLDWVD-GEVAANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPL 591

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + R I   +  GE +A +AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 592 QDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 651

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  
Sbjct: 652 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETG 711

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP P  +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A
Sbjct: 712 AEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAA 771

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + A++R     +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 772 LHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAL 831

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HPSRS KL+SFL+G
Sbjct: 832 RKLRHPSRSDKLKSFLEG 849



 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 59/158 (37%), Positives = 89/158 (56%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +IKL ++RG++T  E+N  LP + V  E +E  +   S+MGI+V +   D E    S+
Sbjct: 236 KTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMGISVYEHAPDAETLLLSD 295

Query: 91  DSLDLASSASNSSVFLQKRK--DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  ++AS     +         DS    T DPVRMY+REMGS+ELL+REGEI IAKRIE 
Sbjct: 296 NVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIED 355

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + ++     + EI+D
Sbjct: 356 GLKDMIQAISACPTTIAEILAAAERISKDEIKVDEIVD 393


>gi|194290318|ref|YP_002006225.1| RNA polymerase sigma factor rpod [Cupriavidus taiwanensis LMG
           19424]
 gi|193224153|emb|CAQ70162.1| RNA POLYMERASE SIGMA D (SIGMA-70) FACTOR TRANSCRIPTION REGULATOR
           PROTEIN [Cupriavidus taiwanensis LMG 19424]
          Length = 683

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 178/319 (55%), Positives = 236/319 (73%), Gaps = 1/319 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G+ R  F+ R  G E +  W+       +G +   V   V ++ +++ ++  +     + 
Sbjct: 365 GMPRADFVARFPGNETNLEWIHTVVADGKG-YSTIVERNVPAVHELQQKLIDLQARVVLP 423

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 424 LKELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 483

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  + 
Sbjct: 484 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 543

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++
Sbjct: 544 GNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEA 603

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 604 ALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 663

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HPSRS KL+SFL+G
Sbjct: 664 LRKLRHPSRSDKLKSFLEG 682



 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 63/163 (38%), Positives = 93/163 (57%), Gaps = 13/163 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI V      E    +E 
Sbjct: 69  KALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIAV-----YEQAPDAET 123

Query: 92  SL--DLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L  D A SA++     ++ +      DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 124 LLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 183

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIEAG   M+ ++   P+T   ++   + + +    + E +D
Sbjct: 184 KRIEAGLKDMVMAISACPVTISEILAHAERVANDEIKIDEFVD 226


>gi|300703499|ref|YP_003745101.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CFBP2957]
 gi|299071162|emb|CBJ42476.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CFBP2957]
          Length = 873

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 177/320 (55%), Positives = 238/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 555 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQSRVVL 612

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 613 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 672

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 673 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 732

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 733 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 792

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 793 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 852

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 853 ALRKLRHPSRSDKLKSFLEG 872



 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V     D + L   +
Sbjct: 262 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLND 321

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 322 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 380

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 381 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 419


>gi|240080942|ref|ZP_04725485.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 gi|268597061|ref|ZP_06131228.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 gi|268550849|gb|EEZ45868.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
          Length = 642

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 182/319 (57%), Positives = 236/319 (73%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D 
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADV 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 89/156 (57%), Gaps = 15/156 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACP 157


>gi|298369314|ref|ZP_06980632.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298283317|gb|EFI24804.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 648

 Score =  367 bits (942), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 186/318 (58%), Positives = 234/318 (73%), Gaps = 5/318 (1%)

Query: 367 RDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           RD F+        D +W+    AK   E  W   +     +IL+ + E+  +  ET ISI
Sbjct: 329 RDYFIRNFLPVITDLNWLENEIAK---ENAWSGALDRFRHAILEKQTELAEMEKETRISI 385

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 386 GELKDINKNMVISEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 445

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +  
Sbjct: 446 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETG 505

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A
Sbjct: 506 EEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDINNVAPADAA 565

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + ++L E T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 566 MYSSLHEVTKEVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 625

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HP+RS +LRSFLD 
Sbjct: 626 RKLRHPTRSDRLRSFLDS 643



 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 61/191 (31%), Positives = 107/191 (56%), Gaps = 20/191 (10%)

Query: 14  EHEDSDDS--LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           E+ D DD+  L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S
Sbjct: 7   EYHDQDDNRPLTVEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMIS 66

Query: 72  NMGINVV----DGDD--LEDEEGS---EDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            +GI V     D +D  L D   +   +D+++ A +A +S+       DS    T DPVR
Sbjct: 67  GLGIQVTEQAPDAEDILLSDNAATITDDDAVEEAEAALSSA-------DSEFGRTTDPVR 119

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    + 
Sbjct: 120 MYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSVAEILALIEQVRNDEIRVD 179

Query: 183 EIIDLEACIGP 193
           E++  EA I P
Sbjct: 180 EVV--EAIIDP 188


>gi|94311542|ref|YP_584752.1| RNA polymerase sigma factor RpoD [Cupriavidus metallidurans CH34]
 gi|93355394|gb|ABF09483.1| RNA polymerase sigma D factor (housekeeping sigma factor)
           [Cupriavidus metallidurans CH34]
          Length = 855

 Score =  367 bits (942), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 178/320 (55%), Positives = 236/320 (73%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W+ +   D     +   V   V ++ +++ ++  +     +
Sbjct: 537 GMPRADFVARFPGNETNLDWIQTIVAD--NKSYSTIVERNVPAVHELQQKLIDLQSRVVL 594

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 595 PLKELKDVNRKMSEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 654

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 655 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 714

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 715 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 774

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 775 AALDGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 834

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 835 ALRKLRHPSRSDKLKSFLEG 854



 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 63/163 (38%), Positives = 93/163 (57%), Gaps = 13/163 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI V      E    +E 
Sbjct: 241 KALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIAV-----YEQAPDAET 295

Query: 92  SL--DLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L  D A SA++     ++ +      DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 296 LLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 355

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIEAG   M+ ++   P+T   ++   + + +    + E +D
Sbjct: 356 KRIEAGLKDMVMAISACPVTISEILASAERVANEEIKIDEFVD 398


>gi|121595443|ref|YP_987339.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. JS42]
 gi|120607523|gb|ABM43263.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax sp. JS42]
          Length = 797

 Score =  367 bits (942), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 188/348 (54%), Positives = 246/348 (70%), Gaps = 8/348 (2%)

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           D++  Q+ D+ K     E EL R+     G+ ++ F++      L+  WV   K    G+
Sbjct: 454 DMVRAQVDDVRKM----ERELRRIIVDKCGMPQETFIKEFPANLLNLQWVE--KQAAAGK 507

Query: 395 -WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W   +   +  I +++ ++  +     + +SE + I   +  GE  +  AKKEM+EANL
Sbjct: 508 PWSAVMQRNIPPIQELQQKLIDLQARVVVPLSELKEINKRMNAGEASSRDAKKEMIEANL 567

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 568 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 627

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI KEP
Sbjct: 628 DQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEP 687

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTPRE +VLRMRFG
Sbjct: 688 ISMETPIGDDDDSHLGDFIEDSNNTAPVDAAMQAGLRDVVKDILDGLTPREAKVLRMRFG 747

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 748 IEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 795



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 64/181 (35%), Positives = 94/181 (51%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V     D + L    
Sbjct: 197 KKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNN 256

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +  +   +   L        R+TD PVRMY+REMG +ELL+REGEI IAKRIE
Sbjct: 257 VTPTATTVEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGKVELLTREGEIEIAKRIE 315

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 316 GGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPNEADD 364

Query: 208 Y 208
           Y
Sbjct: 365 Y 365


>gi|73540591|ref|YP_295111.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha JMP134]
 gi|72118004|gb|AAZ60267.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 783

 Score =  367 bits (942), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 180/321 (56%), Positives = 236/321 (73%), Gaps = 5/321 (1%)

Query: 364 GIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
           G+ R  F+ R  G E +  WV    A   P   +   V   V ++ +++ ++  +     
Sbjct: 465 GMPRSDFVARFPGNETNLDWVGTIVADGKP---YSTIVERNVPAVHELQQKLIDLQSRVV 521

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 522 LPLKELKGVNRKMAEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 581

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 582 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 641

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P 
Sbjct: 642 ETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPA 701

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 702 EAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEA 761

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           KA+RKL+HPSRS KL+SFL+G
Sbjct: 762 KALRKLRHPSRSDKLKSFLEG 782



 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 61/145 (42%), Positives = 86/145 (59%), Gaps = 13/145 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI V      E    +E 
Sbjct: 170 KALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIAV-----YEQAPDAET 224

Query: 92  SL--DLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L  D A SA++     ++ +      DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 225 LLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIVIA 284

Query: 144 KRIEAGRAMMMASLCESPLTFQALI 168
           KRIEAG   M+ ++   P+T   ++
Sbjct: 285 KRIEAGLKDMVMAISACPVTISEIL 309


>gi|17546934|ref|NP_520336.1| RNA polymerase sigma factor RpoD [Ralstonia solanacearum GMI1000]
 gi|17429234|emb|CAD15922.1| probable rna polymerase sigma d (sigma-70) factor transcription
           regulator protein [Ralstonia solanacearum GMI1000]
          Length = 755

 Score =  367 bits (942), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 177/320 (55%), Positives = 238/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 437 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQARVVL 494

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 495 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 554

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 555 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 614

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 615 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 674

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 675 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 734

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 735 ALRKLRHPSRSDKLKSFLEG 754



 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 92/164 (56%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V +      +    +
Sbjct: 142 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYE------QAPDAE 195

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L  +A + +   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 196 TLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 255

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIEAG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 256 AKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 299


>gi|121635207|ref|YP_975452.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis FAM18]
 gi|120866913|emb|CAM10672.1| RNA polymerase sigma factor [Neisseria meningitidis FAM18]
          Length = 658

 Score =  367 bits (942), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 337 MERDYFIQNFLPEITNLEWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 394

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 395 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 454

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 455 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 514

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 515 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 574

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 575 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 634

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 635 LRKLRHPTRSDRLRSFLDS 653



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/200 (31%), Positives = 109/200 (54%), Gaps = 20/200 (10%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           T+ K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++
Sbjct: 16  TMSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAD 72

Query: 62  QMEDTVAMLSNMGINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSA 113
           Q+++ V+M+S +GI V     D +D  L D      +D+++ A +A +S+       DS 
Sbjct: 73  QIDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSE 125

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   ++
Sbjct: 126 FGRTTDPVRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEK 185

Query: 174 LNDGTTLLREIIDLEACIGP 193
           +      + E++  EA I P
Sbjct: 186 IRKDEIRVDEVV--EAIIDP 203


>gi|264677331|ref|YP_003277237.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
 gi|262207843|gb|ACY31941.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
          Length = 815

 Score =  367 bits (942), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 198/412 (48%), Positives = 273/412 (66%), Gaps = 14/412 (3%)

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           ++L+ + +   D + E++ ++  + D    G   E      K + E+L+ +  +    + 
Sbjct: 412 EELKNEALGRFDSMRELFDKMHKVYDK--EGYGTEAYMKVQKAITEELMTIRFTAKTIEK 469

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             DL+  Q+ D+ K+    E EL ++     G+ ++ F++      L+  WV   K    
Sbjct: 470 LCDLVRAQVDDVRKK----ERELRKIIVDKCGMPQEQFIKDFPPNLLNLDWV--IKQVAA 523

Query: 393 GEWKNFVAC---EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           G  KN+ A     +  + +++  +  +     + + E +HI   +  GE  +  AKKEM+
Sbjct: 524 G--KNYSAVLERNIPPVQELQQNLIDLQARVVVPLEELKHINKRMNSGERASRDAKKEMI 581

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 582 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 641

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI
Sbjct: 642 RSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKI 701

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTPRE +VLR
Sbjct: 702 AKEPISMETPIGDDDDSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLR 761

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 762 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 813



 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 95/181 (52%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V     D + L    
Sbjct: 215 KMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNN 274

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + +     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 275 TGQSATTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 333

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 334 GGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVD-----------GFVNANENDD 382

Query: 208 Y 208
           Y
Sbjct: 383 Y 383


>gi|309378741|emb|CBX22691.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 642

 Score =  367 bits (942), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMERETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 59/188 (31%), Positives = 103/188 (54%), Gaps = 17/188 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDAHPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|325130608|gb|EGC53353.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           OX99.30304]
 gi|325142722|gb|EGC65100.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis 961-5945]
 gi|325198658|gb|ADY94114.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis G2136]
 gi|325201773|gb|ADY97227.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M01-240149]
 gi|325208475|gb|ADZ03927.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NZ-05/33]
          Length = 642

 Score =  367 bits (942), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLEWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 61/195 (31%), Positives = 108/195 (55%), Gaps = 18/195 (9%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           RN++ + E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ 
Sbjct: 3   RNQNHE-EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNI 61

Query: 67  VAMLSNMGINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           V+M+S +GI V     D +D  L D      +D+++ A +A +S+       DS    T 
Sbjct: 62  VSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTT 114

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++    
Sbjct: 115 DPVRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDE 174

Query: 179 TLLREIIDLEACIGP 193
             + E++  EA I P
Sbjct: 175 IRVDEVV--EAIIDP 187


>gi|299533869|ref|ZP_07047236.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni S44]
 gi|298718153|gb|EFI59143.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni S44]
          Length = 815

 Score =  367 bits (941), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 198/412 (48%), Positives = 273/412 (66%), Gaps = 14/412 (3%)

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           ++L+ + +   D + E++ ++  + D    G   E      K + E+L+ +  +    + 
Sbjct: 412 EELKNEALGRFDSMRELFDKMHKVYDK--EGYGTEAYMKVQKAITEELMTIRFTAKTIEK 469

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             DL+  Q+ D+ K+    E EL ++     G+ ++ F++      L+  WV   K    
Sbjct: 470 LCDLVRAQVDDVRKK----ERELRKIIVDKCGMPQEQFIKDFPPNLLNLDWV--IKQVAA 523

Query: 393 GEWKNFVAC---EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           G  KN+ A     +  + +++  +  +     + + E +HI   +  GE  +  AKKEM+
Sbjct: 524 G--KNYSAVLERNIPPVQELQQNLIDLQARVVVPLEELKHINKRMNSGERASRDAKKEMI 581

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 582 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 641

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI
Sbjct: 642 RSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKI 701

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTPRE +VLR
Sbjct: 702 AKEPISMETPIGDDDDSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLR 761

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 762 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 813



 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 95/181 (52%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V     D + L    
Sbjct: 215 KMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNN 274

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + +     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 275 TGQSATTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 333

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 334 GGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVD-----------GFVNANENDD 382

Query: 208 Y 208
           Y
Sbjct: 383 Y 383


>gi|161870399|ref|YP_001599571.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 053442]
 gi|218768518|ref|YP_002343030.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis Z2491]
 gi|254805303|ref|YP_003083524.1| RNA polymerase sigma factor [Neisseria meningitidis alpha14]
 gi|304387052|ref|ZP_07369304.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           meningitidis ATCC 13091]
 gi|121052526|emb|CAM08865.1| RNA polymerase sigma factor [Neisseria meningitidis Z2491]
 gi|161595952|gb|ABX73612.1| RNA polymerase primary sigma factor [Neisseria meningitidis 053442]
 gi|254668845|emb|CBA06900.1| RNA polymerase sigma factor [Neisseria meningitidis alpha14]
 gi|254669783|emb|CBA04064.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha153]
 gi|304338851|gb|EFM04953.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           meningitidis ATCC 13091]
 gi|308389681|gb|ADO32001.1| RNA polymerase sigma factor [Neisseria meningitidis alpha710]
 gi|319410767|emb|CBY91151.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
           WUE 2594]
 gi|325128589|gb|EGC51459.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis N1568]
 gi|325132679|gb|EGC55363.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M6190]
 gi|325134647|gb|EGC57287.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M13399]
 gi|325136570|gb|EGC59171.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M0579]
 gi|325138535|gb|EGC61098.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis ES14902]
 gi|325204514|gb|ADY99967.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M01-240355]
          Length = 642

 Score =  367 bits (941), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLEWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 59/188 (31%), Positives = 103/188 (54%), Gaps = 17/188 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|116620135|ref|YP_822291.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223297|gb|ABJ82006.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 563

 Score =  367 bits (941), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 191/382 (50%), Positives = 269/382 (70%), Gaps = 20/382 (5%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA--QSYGIK 366
           K +++C+   +KL+ +   +   Q R      QL+++++ I+     L R    QS  I+
Sbjct: 187 KKTLQCR---QKLMAIPRGMKPKQYR-----RQLWEVARLIVRT-ARLCRAVKFQSPVIR 237

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE-------IKSISVE 419
             +   R    EL P     AK   + + + + A   ++I  +R E       ++ +  +
Sbjct: 238 HLIDRLRSAVEELRPVENDLAKT--QRKLETWPAARAEAIKDLRKEQRSYGQKLQQMEEQ 295

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G S +E R  + ++ +   EA  AKKE++EANLRLV+S+AK+YTNRGLQFLDLIQEGNI
Sbjct: 296 YGASAAELRRTLEIITQAHQEAETAKKELIEANLRLVVSIAKRYTNRGLQFLDLIQEGNI 355

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WWV+QAITR+IADQ+ TIRIPVHM + I+K++RT+R+M
Sbjct: 356 GLMKAVDKFEYRRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETINKLIRTSRQM 415

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP+ EE+AK+L +PV  VRKVL++ +EPISLETPIG+E+ SHLGDFI D+N +S
Sbjct: 416 VQELGREPSNEELAKRLQLPVSKVRKVLRVAQEPISLETPIGEEEESHLGDFIVDQNGIS 475

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D+ I  NLRE T +VL +LTPREE++++MRFG+   ++HTLEEVG+ F VTRERIRQI
Sbjct: 476 PSDAVINLNLREQTAQVLKTLTPREEKIIKMRFGLEDGSEHTLEEVGQNFAVTRERIRQI 535

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HPSRS +LR+FL+
Sbjct: 536 EAKALRKLRHPSRSHRLRAFLE 557



 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 51/166 (30%), Positives = 90/166 (54%), Gaps = 8/166 (4%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +  D   D  ++++++ +++GYV  +E++  LP D      ++D +A L   GI ++   
Sbjct: 1   MALDDKYDGLQRLVQMGKEKGYVLYDEVSEVLPGDINGGNDLDDVLAGLDVAGIEIL--- 57

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                E  +D       +S   + L+          +DPVRMYLREMG++ LL+REGE+ 
Sbjct: 58  -----EEPKDFEKKIEESSEELIDLELPAGLGGEKINDPVRMYLREMGTVPLLTREGEVE 112

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           IA+RIE G+  ++ SL  +PL  Q +I   +E+ + T   R++I +
Sbjct: 113 IARRIERGQNTVLKSLFRAPLVVQEIIGMGEEVINDTLSARDVIQI 158


>gi|15677390|ref|NP_274545.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 gi|7226783|gb|AAF41893.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 gi|261392218|emb|CAX49733.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
           8013]
 gi|316985995|gb|EFV64932.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|325140674|gb|EGC63190.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis CU385]
 gi|325144806|gb|EGC67096.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M01-240013]
 gi|325199861|gb|ADY95316.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|325205715|gb|ADZ01168.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M04-240196]
          Length = 642

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLEWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.0 bits (214), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 61/195 (31%), Positives = 108/195 (55%), Gaps = 18/195 (9%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           RN++ + E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ 
Sbjct: 3   RNQNHE-EYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNI 61

Query: 67  VAMLSNMGINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           V+M+S +GI V     D +D  L D      +D+++ A +A +S+       DS    T 
Sbjct: 62  VSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTT 114

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++    
Sbjct: 115 DPVRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDE 174

Query: 179 TLLREIIDLEACIGP 193
             + E++  EA I P
Sbjct: 175 IRVDEVV--EAIIDP 187


>gi|254672481|emb|CBA05947.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha275]
          Length = 642

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLEWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 59/188 (31%), Positives = 103/188 (54%), Gaps = 17/188 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDTRPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|320105405|ref|YP_004180995.1| RpoD subfamily RNA polymerase sigma-70 factor [Terriglobus
           saanensis SP1PR4]
 gi|319923926|gb|ADV81001.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Terriglobus
           saanensis SP1PR4]
          Length = 567

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 184/341 (53%), Positives = 254/341 (74%), Gaps = 12/341 (3%)

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVF--LERHQGRELDPHWVSYAKDFPEGEWKNFVA-C 401
           I + + +  GE  RL        D    LER Q ++LD  + +   +  + E+K     C
Sbjct: 232 IVRELKYTNGEKKRLLDKVNKTVDAMRTLER-QIKQLDAKFEASKSEELKKEYKRQQKNC 290

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           +VD        +  + V+ G+++ + +     + +G+ +A  AK+E++EANLRLV+S+AK
Sbjct: 291 KVD--------LDRLEVDAGLTVEDLKRTQREMIQGDMDAEKAKRELIEANLRLVVSIAK 342

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRI
Sbjct: 343 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRI 402

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K++RT+R++  ++ RE + EEIA+++ +PV  VRKVLKI +EPISLETPIG
Sbjct: 403 PVHMIETINKLIRTSRQLVQELGREASSEEIARRMDIPVAKVRKVLKIAQEPISLETPIG 462

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E+ SHLGDFIED+ AVSP D+ I  NL+E T++VL +LTPREERV++MRFG+   ++HT
Sbjct: 463 EEEDSHLGDFIEDRMAVSPSDAVISVNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHT 522

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+ F VTRERIRQIEAKA+RKL+HPSRS+KL++F+DG
Sbjct: 523 LEEVGQSFQVTRERIRQIEAKALRKLRHPSRSRKLKAFVDG 563



 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 94/161 (58%), Gaps = 22/161 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD-------LED 85
           +++   +++GY+T  E+N  LP D  + + ++D +  ++  GI+V+ G+D        E+
Sbjct: 14  RIVDTGKEKGYLTYGEVNDLLPGDITTPDDLDDLLTTINTQGIDVLGGEDKFDARDKYEE 73

Query: 86  EEGSED-SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E S+D  LDL          L+K        T+DPVRMYLREMG++ LL+REGE+ IAK
Sbjct: 74  QEESDDVELDLTPGQ------LEK--------TNDPVRMYLREMGTVPLLTREGEVEIAK 119

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RIE G+  +M ++  S +  + ++   ++L  G   ++E++
Sbjct: 120 RIERGQLRVMKAISRSSIVIREIMGLGEDLKRGVRNVKEVV 160


>gi|225851205|ref|YP_002731439.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
 gi|225645895|gb|ACO04081.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
          Length = 577

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 205/449 (45%), Positives = 302/449 (67%), Gaps = 14/449 (3%)

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           AKV+ D R KV     N +++E + +++  D A  + A+      K +     +A +YRE
Sbjct: 137 AKVA-DGRMKVKDII-NIDSNEYDTEDESYDEAEVMDAITKDFIQKGLT----LAHMYRE 190

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           LR L+   +    D +   +      K+ + + SL++  +++D + ++L ++  ++   E
Sbjct: 191 LRDLEQAIIENPDDVELKKEFIEKHAKVNRFIKSLNIKFTKLDKIADELKELYMKLKRKE 250

Query: 354 GEL-LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD--FPEGEWKNFVACEVDSILKIR 410
            +L  R+ +   I  DV  +  +G   DP  +   ++  F  G ++  +  E    LK++
Sbjct: 251 KDLNKRIKRLQKIDPDV-EKLLKGDYDDPEILKKIEENGFSFGRFE-ILRTET---LKLQ 305

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            EI+ +    G   +EF H+++++++G  E +  K+++V++NLRLV+S+AKKYTNRGLQF
Sbjct: 306 EEIEELKEMIGTVPTEFDHVINIIQEGRKEVNETKQKIVQSNLRLVVSIAKKYTNRGLQF 365

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+
Sbjct: 366 LDLIQEGNIGLMKAVDKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN 425

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VR AR M  ++ REPTPEEIAKK+ MP E VRK+L+ ++EPISLETPIGD+D SHLGD
Sbjct: 426 KLVRVARSMVQELGREPTPEEIAKKVGMPPEKVRKILRTSQEPISLETPIGDDDESHLGD 485

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK  +SP    ++  LR+    VL++L+ REE+VLR RFG+  +T++TLE+VGK+F 
Sbjct: 486 FIEDKTVMSPEQHVLRQALRQQLEEVLSTLSEREEQVLRYRFGLEDDTEYTLEQVGKKFG 545

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           VTRERIRQIEAKA+RKL+HP R+K LR F
Sbjct: 546 VTRERIRQIEAKALRKLRHPHRAKYLRPF 574



 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 113/227 (49%), Gaps = 29/227 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  +K+I LA+++GYVT +EL+  +  D + S+++E  +  L+ + I+V++    E+  G
Sbjct: 6   DDVRKVIMLAKEKGYVTYKELSEIIDEDLLLSDELEQLIEYLNELNIDVIEEAKPEEFSG 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             D L +  S            D A   TDDPV++YL+EMG I LL+R+ EI +AK IE 
Sbjct: 66  ESDYLGINFS------------DDAWAKTDDPVKLYLKEMGKIPLLTRDEEIKLAKDIER 113

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL-------------EACIGPES 195
           GR  +   L  +    + L+    ++ DG   +++II++             EA +    
Sbjct: 114 GRKKVFRGLLRTSFLAERLLDEWAKVADGRMKVKDIINIDSNEYDTEDESYDEAEVMDAI 173

Query: 196 KGGFFHG--TEGHSYQKREDSSQE--KERDDVQETEGDIESAAKVSK 238
              F     T  H Y++  D  Q   +  DDV+  +  IE  AKV++
Sbjct: 174 TKDFIQKGLTLAHMYRELRDLEQAIIENPDDVELKKEFIEKHAKVNR 220


>gi|308270755|emb|CBX27365.1| RNA polymerase sigma factor rpoD [uncultured Desulfobacterium sp.]
          Length = 568

 Score =  367 bits (941), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 181/299 (60%), Positives = 227/299 (75%), Gaps = 14/299 (4%)

Query: 397 NFVACE-------VDSILKIRNEIKSISV-------ETGISISEFRHIVSMVRKGECEAS 442
           NF+ C         D IL I +EI   S        +        + ++S V +G   A 
Sbjct: 269 NFLKCARSSCKLGKDDILSIYDEINKYSSMIDENEKKIRTDCQALKKVMSSVAEGRLNAK 328

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK E+  ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 329 IAKSELTRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 388

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +  REP+PEEIA+K+ +P+E 
Sbjct: 389 WIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEQGREPSPEEIAEKMEIPLEK 448

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI +EPISLETPIG+E+ SHLGDFIEDK  + P D+AI  NL E T +VLA+LTP
Sbjct: 449 VRKVLKIAREPISLETPIGEEEDSHLGDFIEDKKFMLPSDAAINQNLAEQTRKVLATLTP 508

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLRMRFGIG   DHTLEEVG+ F VTRERIRQIEAKA+RKL+HP+RS+KL++F++
Sbjct: 509 REEKVLRMRFGIGERADHTLEEVGQDFQVTRERIRQIEAKALRKLRHPTRSRKLKNFIE 567



 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 77/141 (54%), Gaps = 20/141 (14%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG------DDLEDEE 87
           +I   +++GY+T ++LN  +  + +S +++++T  +L +  I ++D       DD   +E
Sbjct: 3   LISKGKKQGYITYDDLNEEMSDNIISIDKLDETFEVLDSNDIEIIDDNGKKADDDKTADE 62

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  +LA  A+N              +  DPV+MYL EM  + LLSREGE+ IAK+IE
Sbjct: 63  KKANQSELA--AANFG------------TVTDPVKMYLHEMSLVTLLSREGEVDIAKKIE 108

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   ++ ++  +P+  + +I
Sbjct: 109 DGEQEVLKAMVSTPIGMECII 129


>gi|171320298|ref|ZP_02909351.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171094445|gb|EDT39506.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 338

 Score =  366 bits (940), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 182/320 (56%), Positives = 235/320 (73%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E D  W    K   EG  +   ++  + +I + +  +  +     +
Sbjct: 20  GMPRSEFIARFPGSETDLDWAE--KIAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVL 77

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + + +     +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 78  PLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 137

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 138 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 197

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D
Sbjct: 198 TGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPAD 257

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+ A++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 258 AALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 317

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 318 ALRKLRHPSRSDKLKSFLEG 337


>gi|254469018|ref|ZP_05082424.1| sigma 70 [beta proteobacterium KB13]
 gi|207087828|gb|EDZ65111.1| sigma 70 [beta proteobacterium KB13]
          Length = 658

 Score =  366 bits (940), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 175/278 (62%), Positives = 223/278 (80%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SIL  + ++K +   +GI I  F+ I   + +GE  A  AK+EM+EANLRLVIS+AKKYT
Sbjct: 379 SILDQQAQLKELEDFSGIPIKNFKEINRQMTRGESRARRAKREMIEANLRLVISIAKKYT 438

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 439 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 498

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R++     +EP P  +A+K+ MP + +RK+LKI+KEPIS+ETPIGD++
Sbjct: 499 MIETINKMNRISRQILQATGQEPEPAVLAEKMEMPEDKIRKILKISKEPISMETPIGDDE 558

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED   ++P D+A+ ++LR  T  +L  LTPRE +VLRMRFGI MNTDHTLEE
Sbjct: 559 DSHLGDFIEDLGTLTPDDAAVYSSLRNVTNEILEGLTPREAKVLRMRFGIEMNTDHTLEE 618

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VGKQF VTRERIRQIEAKA+RKL+HP+RS +L+SFL+G
Sbjct: 619 VGKQFDVTRERIRQIEAKALRKLRHPTRSDRLKSFLEG 656



 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 57/172 (33%), Positives = 92/172 (53%), Gaps = 16/172 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVS-SEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +  K +I L ++RGY+T  E+N  LP DE+S ++Q+++ ++++ +MGI   D    E  +
Sbjct: 44  NQLKALIILGKERGYLTHAEINDHLP-DEISETDQVDEIISIIHDMGIRTYD----EAPD 98

Query: 88  GSEDSLDLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                +D A +        ++ +      DS    T DPVRMY+REMG + LL ++ EI 
Sbjct: 99  AENLLMDDAPAPVTDEEAAEEAEQALATVDSEFGRTTDPVRMYMREMGKVGLLDKKEEIE 158

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE----IIDLEA 189
           IAKRIE G   M+ ++   P     L+   D++  G   + E    +IDLEA
Sbjct: 159 IAKRIEDGLKHMVQAISACPGIIDDLMQMGDKVKAGELSVDEFVDGLIDLEA 210


>gi|251771800|gb|EES52375.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum
           ferrodiazotrophum]
          Length = 590

 Score =  366 bits (940), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 185/369 (50%), Positives = 264/369 (71%), Gaps = 12/369 (3%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           K K ++ ++V+++  + L Q +I++L+E+L D+  +    E  L +  +  G+  D  L 
Sbjct: 233 KVKKIRHEVVEVILEMHLQQRQINILIEKLRDVVGQFEETERTLDQCRRRIGLPVDEILA 292

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           +   +       +  K+     ++ F         K    I S+  ET +S SE +  + 
Sbjct: 293 KLSEKPKKSKLSAEKKEL----YEQFS--------KAHERILSLEAETFLSPSEAKESLQ 340

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE +   AK E+++ANLRLV+S+AK+YTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 341 QIIRGEEKVREAKSELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKR 400

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REP PEE+
Sbjct: 401 GFKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRHLVQELGREPLPEEL 460

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK++ MPV+ VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK  +SP+++A++ +L   
Sbjct: 461 AKEMQMPVDKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKTISPIEAAVRYDLVRK 520

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + L++LT REE+V+R+RFGIG  TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 521 IGQSLSTLTDREEKVIRLRFGIGELTDHTLEEVGQDFDVTRERIRQIEAKALRKLRHPSR 580

Query: 673 SKKLRSFLD 681
           S +L+SFLD
Sbjct: 581 SNQLKSFLD 589



 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 55/153 (35%), Positives = 89/153 (58%), Gaps = 9/153 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T +ELN  LP + V SE+M+  ++   +M I++V+ +    E    +
Sbjct: 11  KDLITLGKERGYLTYDELNHALPSETVDSEEMDSILSYFGDMNIDIVEDEADHVEFTEAE 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---------TDDPVRMYLREMGSIELLSREGEIAI 142
             +           L++  D+ D S         TDDPVR+YL+EMGS+ LL+REGEI I
Sbjct: 71  GEEEELFEEIEITALEEEADTEDLSDGIAAAGVRTDDPVRLYLKEMGSVPLLTREGEIKI 130

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           A+RIE G+  + + L   PL+ Q+++  RD++ 
Sbjct: 131 AQRIEEGKTEVFSFLFGVPLSIQSILGLRDKIQ 163


>gi|222111657|ref|YP_002553921.1| RNA polymerase sigma-70 subunit RpoD [Acidovorax ebreus TPSY]
 gi|221731101|gb|ACM33921.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax ebreus TPSY]
          Length = 801

 Score =  366 bits (940), Expect = 6e-99,   Method: Compositional matrix adjust.
 Identities = 187/348 (53%), Positives = 247/348 (70%), Gaps = 8/348 (2%)

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           D++  Q+ D+ K+    E EL R+     G+ ++ F++      L+  WV   K    G+
Sbjct: 458 DMVRAQVDDVRKK----ERELRRIIVDKCGMPQETFIKDFPANLLNLQWVE--KQAAAGK 511

Query: 395 -WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W   +   +  I +++ ++  +     + +SE + I   +  GE  +  AKKEM+EANL
Sbjct: 512 PWSAVMQRNIPPIQELQQKLMDLQARVVVPLSELKEINKRMNAGEASSRDAKKEMIEANL 571

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 572 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 631

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI KEP
Sbjct: 632 DQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEP 691

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFIED +  +P+D+A+QA LR+    +L  LTPRE +VLRMRFG
Sbjct: 692 ISMETPIGDDDDSHLGDFIEDSSNTAPVDAAMQAGLRDVVKDILDGLTPREAKVLRMRFG 751

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 752 IEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 799



 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 64/181 (35%), Positives = 95/181 (52%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V     D + L    
Sbjct: 201 KKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNN 260

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +  +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 261 VTPTATTVEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 319

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  E   
Sbjct: 320 GGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPNEADD 368

Query: 208 Y 208
           Y
Sbjct: 369 Y 369


>gi|322433717|ref|YP_004215929.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
 gi|321161444|gb|ADW67149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
          Length = 566

 Score =  366 bits (940), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 169/271 (62%), Positives = 227/271 (83%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +++ +  + GISI + +     + +G+ +A  AK+E++EANLRLV+S+AKKYTNRGLQFL
Sbjct: 292 DLERVEQDAGISIPDLKRTQREMIQGDMDAEKAKRELIEANLRLVVSIAKKYTNRGLQFL 351

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 352 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINK 411

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           ++RT+R++  ++ RE + EEIA+++ +PV  VRKVLKI +EPISLETPIG+E+ SHLGDF
Sbjct: 412 LIRTSRQLVQELGREASSEEIARRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLGDF 471

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IED+ AVSP D+ I  NL+E T++VL +LTPREERV++MRFG+   ++HTLEEVG+ F V
Sbjct: 472 IEDRMAVSPADAVISVNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQV 531

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RKL+HPSRS+KL++F+DG
Sbjct: 532 TRERIRQIEAKALRKLRHPSRSRKLKAFVDG 562



 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 90/157 (57%), Gaps = 15/157 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-----GDDLEDEEG 88
           ++++ +++GY+T  E+N  LP D  S + ++D +  ++  GI +       G D  + E 
Sbjct: 12  IVEVGKEKGYLTFGEVNDLLPGDITSPDDLDDLLTTINTQGIELGGDEDRRGRDKYEPEA 71

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E+S D+    S  ++            T+DPVRMYLREMG++ LL+REGE+ IAKRIE 
Sbjct: 72  GEESEDVELDLSPGTL----------EKTNDPVRMYLREMGTVPLLTREGEVEIAKRIER 121

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G+  +M ++  SP+  + ++   ++L  G   ++EI+
Sbjct: 122 GQIRVMKAISRSPIVIREIVALGEDLRRGVRNIKEIV 158


>gi|298529696|ref|ZP_07017099.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511132|gb|EFI35035.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 588

 Score =  366 bits (940), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 199/420 (47%), Positives = 283/420 (67%), Gaps = 25/420 (5%)

Query: 277 RPKVMCALDEIAEVYRELRSLQ---------DNAVNGQKDEKSSVKCKVL--KEKLVKLV 325
           R +V+  L+EI + Y++ RS+          D  V GQ+        K+L  K ++V+ +
Sbjct: 180 RERVIALLEEIKQCYKKRRSVYEKLNECARLDRRVYGQQK-------KILDYKYEIVEHL 232

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD---VFLERHQGRELDPH 382
             + L ++ ID ++E++ D  +++ + + +L     S G+ +D     L +   RE++P 
Sbjct: 233 KHIKLEKTLIDSIIERVNDYVRQMHNCQRDLSAYILSLGMSQDELHSLLNKLHNREINPV 292

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
             +        E  +F    +   ++I+  ++   +    ++ E   I+  + KG  EA 
Sbjct: 293 AAADQLGMTVDELFSFKEL-IYGKMEIQERLQQRCMH---NVHELEEILWRINKGNEEAL 348

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 349 RAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 408

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ R+P+PEEIA+++  P+E 
Sbjct: 409 WIRQAITRAIADQARTIRIPVHMIETINKLVRTSRYLVQELGRDPSPEEIAERMDYPLEK 468

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P D  + + L E  ++VLA LTP
Sbjct: 469 VKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPADEVVNSKLSEQISKVLAELTP 528

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           REE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  L+++ + 
Sbjct: 529 REEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSSSLKTYYES 588



 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 53/156 (33%), Positives = 94/156 (60%), Gaps = 4/156 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G++T +E+N  LP D  + EQ+E+ +++   + I +VDG     +  S  
Sbjct: 11  KALIAEGKKKGFLTFDEINKALPSDVTTPEQVEEIISIFDQLDIAIVDGK--AGKTISVS 68

Query: 92  SLDLASSASNSSVFLQKRKDSAD--RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S D  S A   ++ L + +D+A+    ++DPVR YLREMG++ LL R+GE+ IAK+IE+G
Sbjct: 69  SEDTNSLAETLALNLDRLEDTAEAVSRSNDPVRTYLREMGAVGLLDRDGEVVIAKKIESG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              ++ SL E P+  + LI   ++L      L++++
Sbjct: 129 EMEVLYSLVEVPVAIEELIQVGEDLKKEKIKLKDVV 164


>gi|1710686|sp|P52325|RPOD_NEIGO RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|808742|gb|AAA67115.1| sigma 70 [Neisseria gonorrhoeae]
          Length = 642

 Score =  366 bits (939), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 181/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W N +     +IL+ + E+  +  ET IS
Sbjct: 321 MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSNALDRFRHAILEKQTELADMEKETRIS 378

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E  ++ AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 379 IEELKEINKNMVSSEKVSAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 438

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 439 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 498

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 499 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADA 558

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 559 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 618

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 619 LRKLRHPTRSDRLRSFLDS 637



 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 89/156 (57%), Gaps = 15/156 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S +
Sbjct: 9   EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGL 68

Query: 74  GINVV----DGDD--LEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           GI V     D +D  L D      +D+++ A +A +S+       DS    T DPVRMY+
Sbjct: 69  GIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSA-------DSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACP 157


>gi|74318406|ref|YP_316146.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thiobacillus
           denitrificans ATCC 25259]
 gi|74057901|gb|AAZ98341.1| Carbamoyl-phosphate synthase L chain, ATP-binding [Thiobacillus
           denitrificans ATCC 25259]
          Length = 656

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 195/415 (46%), Positives = 277/415 (66%), Gaps = 24/415 (5%)

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           QL+ + +   D I + Y++    Q+  V         +K +    ++ +L+ ++  +  +
Sbjct: 252 QLKAEALAQFDYIRKAYKKA---QNAHVKYGLGSAQHMKAQA---EVTELLMAIRFSVRQ 305

Query: 335 IDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV--------S 385
           +D L EQ+    + +  +E +++       G+ R  F++   G E +  W+        +
Sbjct: 306 VDNLCEQIRSAVEEVRSHERKIMEFCVNRSGMPRAHFIKAFPGNETNLAWLDREIAAKKA 365

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
           Y     + +++  V    ++++ +++ +       G+ I   + I   +  GE +A  AK
Sbjct: 366 YCSTLSKVQYE--VKAHQEALIAMQDRV-------GLPIKNLKDINKQMSTGEAKARRAK 416

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 417 REMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 476

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A K+ MP + +RK
Sbjct: 477 QAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGIEPDPATLAIKMEMPEDKIRK 536

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++KI KEPIS+ETPIGD++ SHLGDFIED + +SP DSAI ANLR+ T  VL SLT RE 
Sbjct: 537 IMKIAKEPISMETPIGDDEDSHLGDFIEDASTLSPDDSAIYANLRDATREVLDSLTSREA 596

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+KL+SF+
Sbjct: 597 KVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEKLKSFV 651



 Score = 97.4 bits (241), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 58/163 (35%), Positives = 95/163 (58%), Gaps = 14/163 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RG++T  E+N  LP + + ++Q+E  ++M+++MGI V D      E    +
Sbjct: 56  KNLIILGKERGFLTYAEINDHLPDEVLDADQIEGVISMINDMGIQVYD------EAPDAE 109

Query: 92  SL---DLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +L   + A + ++  V  +  +     DS    T DPVRMY+REMGS++LL+REGEI IA
Sbjct: 110 TLLMQEAAPAVADEDVVAEAEQALTTVDSEFGRTTDPVRMYMREMGSVDLLTREGEIEIA 169

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIE G   M+ ++   PLT Q ++    ++      + E+ID
Sbjct: 170 KRIEEGLRHMVQAISSCPLTIQQILDMAAQVEKDELRIDELID 212


>gi|218780916|ref|YP_002432234.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
 gi|218762300|gb|ACL04766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
          Length = 595

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 179/299 (59%), Positives = 228/299 (76%), Gaps = 4/299 (1%)

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W     D  E + K    C    +++I+  I+   +    +    + + + +  G  +A 
Sbjct: 300 WAGECCDLEESQLK---VCYY-QVVEIQTSIRDRELALKANSLALKRVRACIWTGRGKAK 355

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 356 DAKAELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 415

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+  P+E 
Sbjct: 416 WIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEIAQKMEFPLEK 475

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+VLKI KEPISLETPIG+E+ SHLGDFIEDK  + P ++AI  NL E T +VLA+LTP
Sbjct: 476 VRRVLKIAKEPISLETPIGEEEDSHLGDFIEDKKFMLPSEAAISLNLAEQTRKVLATLTP 535

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLRMRFGIG   DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSRS+KL+SF+D
Sbjct: 536 REEKVLRMRFGIGEKADHTLEEVGKDFSVTRERIRQIEAKALRKLRHPSRSQKLKSFID 594



 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 57/154 (37%), Positives = 92/154 (59%), Gaps = 2/154 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I   +++GY+T +ELN  LP D VSS+Q++DT+ M   M I ++DG  +   + S+ 
Sbjct: 21  QELISKGKKQGYLTYDELNEALPEDMVSSDQIDDTLMMFDEMDIEILDGKKITVSDSSKM 80

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             D     S   V      D+   S  DPV++YLREMG + LLSR+GEI IAK+IE G  
Sbjct: 81  DDDSKDQDSEPEVPKPDLLDAGGSS--DPVKLYLREMGMVSLLSRDGEIEIAKKIEEGEQ 138

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            ++ +L E+ +  + LI  R E+ +G   L++++
Sbjct: 139 EVLKALLETTIGVEHLIDLRTEMAEGEVRLKDVL 172


>gi|156563504|dbj|BAF76047.1| Sigma70 [Ralstonia solanacearum]
          Length = 755

 Score =  365 bits (937), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 176/320 (55%), Positives = 237/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 437 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQARVVL 494

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 495 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 554

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 555 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 614

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 615 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 674

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SL PRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 675 AALHGSMRGVVKDVLDSLAPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 734

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 735 ALRKLRHPSRSDKLKSFLEG 754



 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 92/164 (56%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V +      +    +
Sbjct: 142 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYE------QAPDAE 195

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L  +A + +   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 196 TLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 255

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIEAG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 256 AKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 299


>gi|329906288|ref|ZP_08274384.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327547308|gb|EGF32147.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 827

 Score =  365 bits (937), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 187/346 (54%), Positives = 248/346 (71%), Gaps = 11/346 (3%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV--SYAKDFPEGEWK 396
           VE++  I ++I+       R+ +S+ IK  VF     G E +  WV    + + P   + 
Sbjct: 490 VEEVRHIERQILDVAVNKCRMPRSHFIK--VF----PGNETNLDWVDGEVSGNHP---YS 540

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             +   V ++ +++ ++  +     + + + R I   +  GE +A  AK+EM EANLRLV
Sbjct: 541 VILGRNVPTVKELQQKLLDLQSRVVLPLPDLRAINRRMAAGEMKARKAKREMTEANLRLV 600

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 601 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 660

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R++  +   EP P  +A K+ MP E +RK++KI KEPIS+
Sbjct: 661 RTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEEKIRKIMKIAKEPISM 720

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD+D SHLGDFIED N ++P D+A+ A++R     VL SLTPRE +VLRMRFGI M
Sbjct: 721 ETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEM 780

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS +L+SFL+G
Sbjct: 781 STDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDRLKSFLEG 826



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 89/160 (55%), Gaps = 7/160 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RG++T  E+N  LP + V  E +E  +   ++MGI V +     D E    
Sbjct: 211 KTLIKLGKDRGFLTYAEINDHLPENIVDPEAIEGIIGTFNDMGIAVYE--HAPDAESMLL 268

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + ++A+ AS+              DS    T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 269 TDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRI 328

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E G   M+ ++   P T   ++   + + +G T + EI+D
Sbjct: 329 EDGLKDMIQAISACPTTISEILAAAERITNGETKIDEIVD 368


>gi|297250830|ref|ZP_06934304.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
 gi|296837936|gb|EFH21874.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
          Length = 322

 Score =  365 bits (936), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 180/319 (56%), Positives = 237/319 (74%), Gaps = 3/319 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGIS 423
           ++RD F++       +  W+   ++  +G  W + +     +IL+ + E+  +  ET IS
Sbjct: 1   MERDYFIQNFLPEITNLQWIE--EEIAKGRVWSDALDRFRHAILEKQTELADMEKETRIS 58

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 59  IEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 118

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 119 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQET 178

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+
Sbjct: 179 GEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNIAPADA 238

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 239 AMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 298

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 299 LRKLRHPTRSDRLRSFLDS 317


>gi|120610093|ref|YP_969771.1| RpoD family RNA polymerase sigma factor [Acidovorax citrulli
           AAC00-1]
 gi|120588557|gb|ABM31997.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax citrulli
           AAC00-1]
          Length = 781

 Score =  365 bits (936), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 187/348 (53%), Positives = 247/348 (70%), Gaps = 8/348 (2%)

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           D++  Q+ D+ K+    E EL R+     G+ ++ F++      L+  WV   K    G+
Sbjct: 438 DMVRAQVDDVRKK----ERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVE--KQAAAGK 491

Query: 395 -WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W   +A  +  + +++  +  +     + +SE + I   + +GE  +  AKKEM+EANL
Sbjct: 492 PWSAVLARNIPPVQELQQRLMDLQSRVVVPLSELKDINKRMNEGESASRDAKKEMIEANL 551

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 552 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 611

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI KEP
Sbjct: 612 DQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEP 671

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFIED    +P+D+A+QA LR+    +L  LTPRE +VLRMRFG
Sbjct: 672 ISMETPIGDDDDSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFG 731

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 732 IEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 779



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 63/181 (34%), Positives = 94/181 (51%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V     D + L    
Sbjct: 181 KALITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLFQNN 240

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +  +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 241 VTPTATTVEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 299

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  E   
Sbjct: 300 GGLQAMMEAISASPATIAEILAMGEEIREGKVVISTIVD-----------GFSNPNEADD 348

Query: 208 Y 208
           Y
Sbjct: 349 Y 349


>gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA polymerase [Herminiimonas
           arsenicoxydans]
          Length = 858

 Score =  365 bits (936), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 180/324 (55%), Positives = 237/324 (73%), Gaps = 13/324 (4%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE------WKNFVACEVDSILKIRNEIKSISV 418
           + R+ F++   G E +  WV       +GE      +   +A  V ++ +++ ++  +  
Sbjct: 541 MPRNHFIKVFPGNETNLDWV-------DGEVEGNHPYSIVLARNVPAVKELQQKLIDLQA 593

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + + R I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 594 RVVLPLPDLRAINRKMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 653

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 654 IGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 713

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N +
Sbjct: 714 ILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTL 773

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D+A+ A++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQ
Sbjct: 774 APADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQ 833

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 834 IEAKALRKLRHPSRSDKLKSFLEG 857



 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 57/160 (35%), Positives = 87/160 (54%), Gaps = 7/160 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IK  ++RG++T  E+N  LP + +  E +E  +   ++MGI V +     D E    
Sbjct: 244 KTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMGIAVYE--QAPDAETLLL 301

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           S ++A+ AS+              DS    T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 302 SDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 361

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E G   M+ ++   P T   ++   + ++     + EI+D
Sbjct: 362 EDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIVD 401


>gi|326316262|ref|YP_004233934.1| RNA polymerase sigma-70 subunit RpoD [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323373098|gb|ADX45367.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 780

 Score =  365 bits (936), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 187/348 (53%), Positives = 247/348 (70%), Gaps = 8/348 (2%)

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           D++  Q+ D+ K+    E EL R+     G+ ++ F++      L+  WV   K    G+
Sbjct: 437 DMVRAQVDDVRKK----ERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVE--KQAAAGK 490

Query: 395 -WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W   +A  +  + +++  +  +     + +SE + I   + +GE  +  AKKEM+EANL
Sbjct: 491 PWSAVLARNIPPVQELQQRLMDLQSRVVVPLSELKDINKRMNEGESASRDAKKEMIEANL 550

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 551 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 610

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI KEP
Sbjct: 611 DQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEP 670

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFIED    +P+D+A+QA LR+    +L  LTPRE +VLRMRFG
Sbjct: 671 ISMETPIGDDDDSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFG 730

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 731 IEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 778



 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 63/181 (34%), Positives = 94/181 (51%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V     D + L    
Sbjct: 180 KALITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLFQNN 239

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +  +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 240 VTPTATTVEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 298

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  E   
Sbjct: 299 GGLQAMMEAISASPATIAEILAMGEEIREGKVVISTIVD-----------GFSNPNEADD 347

Query: 208 Y 208
           Y
Sbjct: 348 Y 348


>gi|193222233|emb|CAL60659.2| putative RNA polymerase sigma factor rpoD (Sigma-70) [Herminiimonas
           arsenicoxydans]
          Length = 800

 Score =  364 bits (934), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 180/324 (55%), Positives = 237/324 (73%), Gaps = 13/324 (4%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE------WKNFVACEVDSILKIRNEIKSISV 418
           + R+ F++   G E +  WV       +GE      +   +A  V ++ +++ ++  +  
Sbjct: 483 MPRNHFIKVFPGNETNLDWV-------DGEVEGNHPYSIVLARNVPAVKELQQKLIDLQA 535

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + + R I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 536 RVVLPLPDLRAINRKMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 595

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 596 IGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 655

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N +
Sbjct: 656 ILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTL 715

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D+A+ A++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQ
Sbjct: 716 APADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQ 775

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 776 IEAKALRKLRHPSRSDKLKSFLEG 799



 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 57/160 (35%), Positives = 87/160 (54%), Gaps = 7/160 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IK  ++RG++T  E+N  LP + +  E +E  +   ++MGI V +     D E    
Sbjct: 186 KTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMGIAVYE--QAPDAETLLL 243

Query: 92  SLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           S ++A+ AS+              DS    T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 244 SDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 303

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E G   M+ ++   P T   ++   + ++     + EI+D
Sbjct: 304 EDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIVD 343


>gi|325266676|ref|ZP_08133353.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella
           denitrificans ATCC 33394]
 gi|324982119|gb|EGC17754.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella
           denitrificans ATCC 33394]
          Length = 671

 Score =  364 bits (934), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 181/317 (57%), Positives = 235/317 (74%), Gaps = 3/317 (0%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISIS 425
           RD F+E       +  W+   ++  +   W   +A     IL+ + ++  +     ISI+
Sbjct: 353 RDYFIEHFMPNATNLAWLE--EEIGKNRVWSETLARFKHDILEKQAKMAELEAHARISIA 410

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + I   + K E E + AK++M++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 411 ELKEISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 470

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   
Sbjct: 471 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGE 530

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P ++A+
Sbjct: 531 EPDSAKLAELMDMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAPAEAAM 590

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 591 YSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 650

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+HP+RS KL+SFLD 
Sbjct: 651 KLRHPTRSDKLKSFLDS 667


>gi|254704733|ref|ZP_05166561.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261755429|ref|ZP_05999138.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261745182|gb|EEY33108.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 415

 Score =  363 bits (933), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 206/420 (49%), Positives = 277/420 (65%), Gaps = 38/420 (9%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+SEQ+EDT++MLS+MGINVV+
Sbjct: 20  DGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE 79

Query: 80  GDDLED--EEGSEDSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            D+ ++  EEG++D      DL  +   +      +K+  DR TDDPVRMYLREMGS+EL
Sbjct: 80  DDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDR-TDDPVRMYLREMGSVEL 138

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           LSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   LLREIIDLE    G
Sbjct: 139 LSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAG 198

Query: 193 PESK-GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           PE+K        E    +      + ++ DD+    GD+        +D + +       
Sbjct: 199 PEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANL------- 251

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ---KDE 308
                           +L+AME +LRP+VM  LD IA+ Y++LR LQD  V G+     E
Sbjct: 252 ----------------SLAAMEAELRPQVMETLDFIADTYKKLRKLQDQQVEGRLAATGE 295

Query: 309 KSSV---KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            SS    + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG+LLRLA+S+G+
Sbjct: 296 LSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEGKLLRLAESFGV 355

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           +R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI++++ ET ISI 
Sbjct: 356 RREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQNLATETAISIG 415


>gi|257092101|ref|YP_003165742.1| RNA polymerase sigma factor RpoD [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257044625|gb|ACV33813.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 648

 Score =  363 bits (933), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 182/312 (58%), Positives = 231/312 (74%)

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G EL+  WV          +   +     +I + + ++ ++    GI + E + 
Sbjct: 333 FIKVFPGNELNIDWVDVEIAAAGKTYGAVLLRNAPNIKEEQKKLLALQDRIGIPLRELKD 392

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 393 INKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 452

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E  P
Sbjct: 453 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEADP 512

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             +AKK+ MP E +RK+LKI+KEPIS+ETPIGD+D SHLGDFIED   ++P ++A+ ++L
Sbjct: 513 ATLAKKMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDHATLAPTEAALYSSL 572

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R  T  VL +LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+H
Sbjct: 573 RFITKDVLDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 632

Query: 670 PSRSKKLRSFLD 681
           PSRS KLRSFLD
Sbjct: 633 PSRSDKLRSFLD 644



 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 62/174 (35%), Positives = 96/174 (55%), Gaps = 18/174 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL ++RG++T  E+N  LP D V +EQ+E  +   ++MGI V D      E    +
Sbjct: 41  KTLIKLGKERGFLTYAEINDHLPDDVVDAEQIESIINTFNDMGIQVYD------EAPDAE 94

Query: 92  SLDLASSASNSSVFLQKRKDSADRS----------TDDPVRMYLREMGSIELLSREGEIA 141
           +L ++ +A  +       ++ A+++          T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 95  TLLMSDAAPAAGADDADVEEQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEIE 154

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           IAKRIE G   M+ ++   P T   ++   D +      + E+ID    I PE+
Sbjct: 155 IAKRIEDGLKHMIQAISACPTTIAEILNCADRIARDEMRIDELID--GLIDPET 206


>gi|325983602|ref|YP_004296004.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. AL212]
 gi|325533121|gb|ADZ27842.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. AL212]
          Length = 740

 Score =  363 bits (933), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 185/321 (57%), Positives = 241/321 (75%), Gaps = 13/321 (4%)

Query: 367 RDVFLERHQGRELDPHWVS----YAKDFPEG--EWKNFVACEVDSILKIRNEIKSISVET 420
           R+ F++   G E +  W++      K + +    +K  +  E  ++L +R++I       
Sbjct: 423 RNHFIKTFPGNETNLDWIAQEIKVGKPYSQALEHYKPAILEEQHNLLALRSKI------- 475

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GI I + + I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 476 GIPIKDLKEINRKMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 535

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++ 
Sbjct: 536 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQIL 595

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  +EP P  +A+K+ MP E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++P
Sbjct: 596 QETGQEPEPAVLAQKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDAATMAP 655

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+ A+LR  T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 656 ADAAVYASLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIE 715

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HP+RS++LRSFLD
Sbjct: 716 AKALRKLRHPARSERLRSFLD 736



 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 58/163 (35%), Positives = 91/163 (55%), Gaps = 14/163 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T  E+N  LP D + +EQ+E  ++M+++MGI+V       DE    +
Sbjct: 129 KILIGLGKERGYLTYAEINDHLPDDMLDAEQIEGIISMINDMGISV------HDEAPDVE 182

Query: 92  SLDLASSASNSSVFLQKRK--------DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +L ++ +A+  +      +        DS    T DPVRMY+REMGS+ LL+RE EI IA
Sbjct: 183 TLLMSDAATTVADEDVAEEAEAALSTVDSEFGRTTDPVRMYMREMGSVGLLTRESEIEIA 242

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIE G   M+ ++   P     +I    E+   T  + E++D
Sbjct: 243 KRIEGGLRHMIQAISACPPIIAKIIDLAVEVEKETMRIDEVVD 285


>gi|301064644|ref|ZP_07205038.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
 gi|300441264|gb|EFK05635.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
          Length = 590

 Score =  363 bits (932), Expect = 5e-98,   Method: Compositional matrix adjust.
 Identities = 173/273 (63%), Positives = 218/273 (79%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  I+ +   T ++  E +  +  V +   +AS AK E+++ANLRLV+S+AKKYTNRGL 
Sbjct: 317 RRVIRQVKERTNMTPRELKSELERVERSLEKASRAKSELIQANLRLVVSIAKKYTNRGLM 376

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I
Sbjct: 377 FLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETI 436

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K++RT+R +  +  REPT EEIA+K+  P++ VRKVLKI KEPISLETPIG+E+ SHLG
Sbjct: 437 NKLMRTSRYLVQEHGREPTSEEIAEKMEFPLDKVRKVLKIAKEPISLETPIGEEEDSHLG 496

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKN +SP D+ +   L E T +VL +LTPREE+VLRMRFGIG   DHTLEEVG+ F
Sbjct: 497 DFIEDKNILSPGDAVVNFGLAEQTRKVLTTLTPREEKVLRMRFGIGEKADHTLEEVGRDF 556

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKL+HPSRS+KL+SF+D 
Sbjct: 557 SVTRERIRQIEAKALRKLRHPSRSRKLKSFMDN 589


>gi|312795733|ref|YP_004028655.1| RNA polymerase sigma factor rpoD [Burkholderia rhizoxinica HKI 454]
 gi|312167508|emb|CBW74511.1| RNA polymerase sigma factor rpoD [Burkholderia rhizoxinica HKI 454]
          Length = 778

 Score =  363 bits (931), Expect = 6e-98,   Method: Compositional matrix adjust.
 Identities = 182/346 (52%), Positives = 244/346 (70%), Gaps = 11/346 (3%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           V+++  + ++I+H       +    G+ R  F+ R    E +  W     A+  P   + 
Sbjct: 441 VDEVRQVERQILHI------VVDKCGMPRAEFIARFPSNETNLDWAEQIVAEGHP---YS 491

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             +   + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLV
Sbjct: 492 AVLERNIPAIREQQQRLIDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLV 551

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+
Sbjct: 552 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 611

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+
Sbjct: 612 RTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISM 671

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M
Sbjct: 672 ETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEM 731

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 732 STDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 777



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 56/173 (32%), Positives = 93/173 (53%), Gaps = 7/173 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +   D E    ++
Sbjct: 165 RALIKLGKERGFLTYAEINDHLPDNFAETEAIESIISTFNDMGVAVYEQAPDAETLLLND 224

Query: 91  DSLDLASSASNSSVFLQKRK--DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++  ++S               DS    T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 225 NAPSVSSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 284

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP--ESKGGF 199
           G   M+ ++   P T   ++   + + +    + E++D    I P  E   GF
Sbjct: 285 GLKHMVQAISACPTTIADILAMAERVANDEIRVDELVD--GLIDPNAEDADGF 335


>gi|294787697|ref|ZP_06752941.1| RNA polymerase sigma factor RpoD [Simonsiella muelleri ATCC 29453]
 gi|294483990|gb|EFG31673.1| RNA polymerase sigma factor RpoD [Simonsiella muelleri ATCC 29453]
          Length = 652

 Score =  363 bits (931), Expect = 6e-98,   Method: Compositional matrix adjust.
 Identities = 175/277 (63%), Positives = 220/277 (79%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL+ + E+ ++     ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTN
Sbjct: 372 ILEKQTEMSNLEAHARISIEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTN 431

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 432 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 491

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ R +R+   +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD++ 
Sbjct: 492 IETINKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDED 551

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED N V+P D+A+ ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEV
Sbjct: 552 SHLGDFIEDANNVAPSDAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEV 611

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GKQF VTRERIRQIEAKA+RKL+HP+RS KL+SFLD 
Sbjct: 612 GKQFDVTRERIRQIEAKALRKLRHPTRSDKLKSFLDS 648



 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/189 (32%), Positives = 101/189 (53%), Gaps = 5/189 (2%)

Query: 8   NRDSDSEHEDSDD-SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           + DSD+E + SD+  L  +      +++I   ++RGY+T  E+N  LP D   +EQ+++ 
Sbjct: 10  DHDSDNEEQLSDNRPLTPEEQRARLRQLIIFGKERGYITYAEINDTLPDDMSDAEQIDNI 69

Query: 67  VAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMY 124
           V M+  +GI V +   D E    S++S  +A   + +       + DS    T DPVRMY
Sbjct: 70  VNMIQGLGIQVTEEAPDAETLLMSDNSAAVADEDAVAEAEAALSQADSEFGRTTDPVRMY 129

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG +ELL+R  EI IAK+IE     M+ ++   P +   ++   D++      + E+
Sbjct: 130 MREMGQVELLTRADEIIIAKKIENALKNMIQAISACPGSVGEILALIDQIKKDEIRVDEV 189

Query: 185 IDLEACIGP 193
           +  EA I P
Sbjct: 190 V--EAIIDP 196


>gi|71906166|ref|YP_283753.1| RNA polymerase sigma factor RpoD [Dechloromonas aromatica RCB]
 gi|71845787|gb|AAZ45283.1| RNA polymerase, sigma 70 subunit, RpoD [Dechloromonas aromatica
           RCB]
          Length = 657

 Score =  362 bits (930), Expect = 8e-98,   Method: Compositional matrix adjust.
 Identities = 182/320 (56%), Positives = 234/320 (73%), Gaps = 6/320 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK---SISVETG 421
           + R  F++   G E++  W   A        K +VA    +   I+ E K   ++    G
Sbjct: 337 MPRPHFIQSFPGNEINLDW---ADAEVAAAPKTYVAILTRNAPDIKEEQKKLLALQDRIG 393

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I + + + I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 394 IPLKDLKDINKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 453

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 454 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 513

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP P  +AKK+ MP + +RK++KI+KEPIS+ETPIGD+D SHLGDFIED   ++P 
Sbjct: 514 ETGAEPDPATLAKKMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDSGTLAPA 573

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A+ ++LR  T  +L +LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEA
Sbjct: 574 DAAMYSSLRGVTKEILDTLTTREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 633

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HP+RS KLRSF+D
Sbjct: 634 KALRKLRHPTRSDKLRSFVD 653



 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 60/145 (41%), Positives = 82/145 (56%), Gaps = 13/145 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL ++RGY+T  E+N  LP D V +E +E  ++  S M I V D     +   +ED
Sbjct: 50  KALIKLGKERGYLTYAEINDHLPDDVVDAESIEAIISTFSEMSIQVFD-----EAPAAED 104

Query: 92  SL---DLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L     A +A +  V  Q  +     DS    T DPVRMY+REMGS+ELL+REGEI IA
Sbjct: 105 LLMSDTAAVAADDEEVEAQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEIEIA 164

Query: 144 KRIEAGRAMMMASLCESPLTFQALI 168
           KRIE G   M+ ++   P T   ++
Sbjct: 165 KRIEEGLKHMIQAIAACPTTISDIL 189


>gi|294669659|ref|ZP_06734726.1| hypothetical protein NEIELOOT_01560 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308572|gb|EFE49815.1| hypothetical protein NEIELOOT_01560 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 496

 Score =  362 bits (929), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 176/288 (61%), Positives = 225/288 (78%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           W N +     +IL+ ++E+  +     ISI E + I   ++  E E + AK+EM++ANLR
Sbjct: 205 WANALERFQHAILEKQSELAEMEKTAQISIEELKEINKNMQSSERETARAKEEMIQANLR 264

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIAD
Sbjct: 265 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 324

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K+ R +R+   +   +P   ++A+ + MP + +RK++KI KEPI
Sbjct: 325 QARTIRIPVHMIETINKMNRISRQYLQETGEDPDSAKLAELMEMPEDKIRKIMKIAKEPI 384

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S+ETPIGD+D SHLGDFIED N V+P D+A+ ++LRE T  VL SLTPRE +VLRMRFGI
Sbjct: 385 SMETPIGDDDDSHLGDFIEDVNNVAPADAAMYSSLREVTADVLESLTPREAKVLRMRFGI 444

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS +L+SFLD 
Sbjct: 445 DMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDRLKSFLDS 492


>gi|258406014|ref|YP_003198756.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
 gi|257798241|gb|ACV69178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
          Length = 587

 Score =  362 bits (929), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 196/411 (47%), Positives = 279/411 (67%), Gaps = 26/411 (6%)

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           R  +   LDE A + + +R +Q+  ++              K ++V+++  + L ++ ID
Sbjct: 196 RVNIYYKLDECATLDKRVRGVQNKIID-------------YKHEVVQILRDIKLEKTLID 242

Query: 337 LLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
            ++E L+D  ++ MHN        +L + ++ G   ++F E  + REL+P   +      
Sbjct: 243 RVIETLHDYVRQ-MHNCRRDLSAYVLSVGKTRGEIEEIFAELDR-RELNPVIAADNLGMT 300

Query: 392 EGEWKNFVACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
             E  +F       +L  + EI + +  +   S+++   I+  + +G  +A  AK+E++ 
Sbjct: 301 VEELFSF-----KEMLAGKMEILQRLEEKCCHSVTDLEEILWRINRGNYDALRAKQELIR 355

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 356 SNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITR 415

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P PEEIA+++  PVE V+KVLKI 
Sbjct: 416 AIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPQPEEIAERMDYPVEKVKKVLKIA 475

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPISLETPIGDE+ S LGDFIEDK AV+P + A+ + L E  + VL+ LTPREE+VLR 
Sbjct: 476 KEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEAVNSKLAEQISTVLSELTPREEQVLRK 535

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 536 RFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQSLRSYYE 586



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/158 (31%), Positives = 84/158 (53%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G++T +ELN  LP +    EQ+E+ + +   + I +VD      + G   
Sbjct: 11  KTLIAEGKKKGFLTFDELNKALPNEVNQPEQIEEIITIFDQLDIAIVDA-----QTGKNL 65

Query: 92  SLDLASSASNSSVFLQKRKDSADRS----TDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    S  +S    +      +      + DPVRMYLREMG + LL REGE+ IAK+IE
Sbjct: 66  GMVAGDSGGDSEEEEELEITETEEVETTRSSDPVRMYLREMGIVPLLDREGEVEIAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   ++ +L E P+  + L+   D+L  GT  L++++
Sbjct: 126 DGELEVLYALIEVPVAVEELVGVGDDLQKGTIKLKDVV 163


>gi|83746506|ref|ZP_00943557.1| RpoD [Ralstonia solanacearum UW551]
 gi|83726837|gb|EAP73964.1| RpoD [Ralstonia solanacearum UW551]
          Length = 391

 Score =  362 bits (929), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 177/320 (55%), Positives = 238/320 (74%), Gaps = 3/320 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 73  GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQSRVVL 130

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 131 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 190

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 191 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 250

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 251 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 310

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 311 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 370

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RKL+HPSRS KL+SFL+G
Sbjct: 371 ALRKLRHPSRSDKLKSFLEG 390


>gi|218885598|ref|YP_002434919.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
 gi|218756552|gb|ACL07451.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 590

 Score =  362 bits (928), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 198/421 (47%), Positives = 284/421 (67%), Gaps = 17/421 (4%)

Query: 273 EDQL--RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK--SSVKCKVL--KEKLVKLVG 326
           ED++  R +V+  LDEI   Y++ R +     +    E+  ++++ ++L  KE +V  + 
Sbjct: 176 EDEMNQRSRVILLLDEIKHTYKKKRKVYAKLDDCCTLERRVTAIQKEILGFKEDIVNRLR 235

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQGRELDP 381
            + L ++ ID ++E + D  ++ MHN        +L   ++    +D+F    + RE++P
Sbjct: 236 DIKLEKTLIDRIIETVEDYVRQ-MHNCQRDLSAYILSTGKTQVEIQDIF-RMLEAREMNP 293

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              S A      E  +F    +  I +I N ++        ++++   ++  +++G   A
Sbjct: 294 VAASAALGMTVEELFSFKEMIIGKI-EILNRLQDKCCH---NVTDLEEVLWRIKRGNTHA 349

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P++
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPID 469

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    VLA LT
Sbjct: 470 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIASVLADLT 529

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 530 PREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQMLRSYYE 589

Query: 682 G 682
            
Sbjct: 590 S 590



 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 48/156 (30%), Positives = 86/156 (55%), Gaps = 2/156 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +  G++T +E+N  LP +  + EQ+E+ + +   + I +VD +    +     
Sbjct: 11  KSLIAKGKVSGFLTFDEVNKALPAEVNTPEQIEEIIGIFDQLEIAIVDTEKDGKKISVSP 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                  +    + L + ++SAD S+   DPVRMYLREMG++ LL R+GE+ IAK+IE G
Sbjct: 71  GESEEEPSGEPGLDLVEDEESADYSSRSTDPVRMYLREMGAVPLLDRDGEVQIAKKIELG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              ++ +L E P+  + LI   ++L      L++++
Sbjct: 131 EQDVLYALVEVPVAVEELINVGEDLKQNRIKLKDVV 166


>gi|26249652|ref|NP_755692.1| RpoD protein [Escherichia coli CFT073]
 gi|26110080|gb|AAN82266.1|AE016767_26 RpoD protein [Escherichia coli CFT073]
          Length = 246

 Score =  361 bits (927), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 176/244 (72%), Positives = 206/244 (84%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 2   KAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 61

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ 
Sbjct: 62  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 121

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL
Sbjct: 122 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVL 181

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 182 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 241

Query: 678 SFLD 681
           SFLD
Sbjct: 242 SFLD 245


>gi|116514979|ref|YP_802608.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256833|gb|ABJ90515.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 613

 Score =  361 bits (927), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 177/267 (66%), Positives = 217/267 (81%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  +T + I++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 346 IEKKTKLKITQIKDINKRIILGEEKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 405

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R 
Sbjct: 406 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 465

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M  +I REPTPEE+++K+ +  E +RKVLKI KEPIS+ETPIG++D +HLGDFIED 
Sbjct: 466 SRQMLQEIGREPTPEELSEKMLISEEKIRKVLKIAKEPISMETPIGEDDDTHLGDFIEDT 525

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           N   PL+SA   +L+  T  VL+ LT RE +VLRMRFGI MNTDHTLEEVG+QF VTRER
Sbjct: 526 NLELPLESATSESLKTITNDVLSGLTDREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRER 585

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           IRQIEAKA+RKL+HPSRS+ L+SFLD 
Sbjct: 586 IRQIEAKALRKLRHPSRSEILKSFLDN 612



 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/159 (33%), Positives = 90/159 (56%), Gaps = 9/159 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-----DE 86
           K ++   +++GY+T  E++  LP D V ++Q+++ + M+ ++GI +V+          +E
Sbjct: 10  KLLVSHGKEQGYLTYSEVHDHLPNDIVDADQIKNIIQMIKDLGIQIVEEVREIEELIINE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++   D   +A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 70  APTDTDEDTVEAATQ---VLSNVETEIGRTTD-PVRMYMREMGTVELLTREGEIGIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G   + +S+ E P +   L+     +  G   L E+I
Sbjct: 126 EEGINQVQSSVSEYPTSILYLLEQYHHVKLGNIKLSELI 164


>gi|224370025|ref|YP_002604189.1| RpoD [Desulfobacterium autotrophicum HRM2]
 gi|223692742|gb|ACN16025.1| RpoD [Desulfobacterium autotrophicum HRM2]
          Length = 618

 Score =  361 bits (926), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 168/257 (65%), Positives = 214/257 (83%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +  + I+  + KG   A  AK E+V ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 361 ATLKKIIKGIDKGRMVAKYAKSELVRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ 
Sbjct: 421 VDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEMG 480

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP+PEEIA+K+ +P++ VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK    P ++A
Sbjct: 481 KEPSPEEIAEKMEIPLDKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKFSLPSEAA 540

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I  NL E T +VLA+LTPREE+VLRMRFGIG   DHTLEEVG+ F VTRERIRQIEAKA+
Sbjct: 541 INLNLAEQTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFTVTRERIRQIEAKAL 600

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HP+RS+KL+SF++
Sbjct: 601 RKLRHPTRSRKLKSFIE 617



 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 48/159 (30%), Positives = 80/159 (50%), Gaps = 17/159 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S +  KK+I+  ++ G ++  E+N  +  +  SS+Q++D +     +GI+++D D  E  
Sbjct: 15  SKEVLKKLIERGKKEGSLSYAEINEAISENLKSSDQIDDIMVKFKQLGIDLIDTDKGEKP 74

Query: 87  EGSEDSLDLASSASNSSVFLQK--------------RKDSADR---STDDPVRMYLREMG 129
           +  +    + S+  N                     +  +AD    +  DPV+MYLREMG
Sbjct: 75  KKKKVKKVVKSARLNDGADDGDDDSEAPPGKKSKFGKATAADMEFGTVTDPVKMYLREMG 134

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            + LLSREGEI IAK+IE G   ++  L  SP+    L+
Sbjct: 135 MVTLLSREGEIEIAKKIEVGEREVLKGLLASPIAVDHLL 173


>gi|291614899|ref|YP_003525056.1| RNA polymerase, sigma 70 subunit, RpoD [Sideroxydans lithotrophicus
           ES-1]
 gi|291585011|gb|ADE12669.1| RNA polymerase, sigma 70 subunit, RpoD [Sideroxydans lithotrophicus
           ES-1]
          Length = 654

 Score =  360 bits (924), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 172/278 (61%), Positives = 222/278 (79%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I+  + ++ ++    GI I + + I   +  GE +A  AK++M+EANLRLVIS+AKKYT
Sbjct: 375 AIVDQQKKMLALQQRVGIPILDLKEINKQMTNGEAKARRAKRDMIEANLRLVISIAKKYT 434

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 435 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 494

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R++  +   E     +A K+ MP + +RK+LKI KEPIS+ETP+GD+D
Sbjct: 495 MIETINKMNRISRQILQETGMEADAATLAIKMEMPEDKIRKILKIAKEPISMETPVGDDD 554

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED N+++P+++A+  +LR  T  +L SLTPRE +VLRMRFGI MNTDHTLEE
Sbjct: 555 DSHLGDFIEDANSLAPIEAAVYDSLRNVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEE 614

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VGKQF VTRERIRQIEAKA+RKL+HPSRS+KL+SFLDG
Sbjct: 615 VGKQFDVTRERIRQIEAKALRKLRHPSRSEKLKSFLDG 652



 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 58/157 (36%), Positives = 86/157 (54%), Gaps = 3/157 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +I L ++RGY+T  E+N  LP D +  EQ+E  V+M+++MGI V D   D E    +E
Sbjct: 50  KALILLGKERGYLTFAEINDHLP-DMLEVEQVEGVVSMINDMGITVCDVAPDTESLVMNE 108

Query: 91  DSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            +  +A   +           DS    T DPVRMY+REMG + LL+R+ EI IAKRIE G
Sbjct: 109 TAPPVADEDAAEEAEAAISTVDSEFGRTTDPVRMYMREMGVVNLLTRQDEIEIAKRIEDG 168

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              M+ ++   P T   ++   D++      + E+ID
Sbjct: 169 LKHMIQAISACPATIAEILALADKVAKEELRIDELID 205


>gi|167829080|ref|ZP_02460551.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia pseudomallei
           9]
          Length = 285

 Score =  360 bits (924), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 170/246 (69%), Positives = 207/246 (84%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 39  GELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 98

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+
Sbjct: 99  STYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKM 158

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    V
Sbjct: 159 EMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDV 218

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL
Sbjct: 219 LDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKL 278

Query: 677 RSFLDG 682
           +SFL+G
Sbjct: 279 KSFLEG 284


>gi|256830224|ref|YP_003158952.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579400|gb|ACU90536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfomicrobium
           baculatum DSM 4028]
          Length = 588

 Score =  360 bits (923), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 198/423 (46%), Positives = 283/423 (66%), Gaps = 33/423 (7%)

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL---------KEKLVKLVGS 327
           R +V+  L+++  +YR+ + L         DE +++  +V          KE +V+ +  
Sbjct: 180 RERVIKLLEDVKNIYRKKKPLYTRL-----DECATLDKRVFGVQKKIMDYKEGVVQCLRD 234

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQS----YGIKRDVFLERHQGRE 378
           + L ++ ID ++E + D  ++ MHN        +L L +S    +GI      ++ + R 
Sbjct: 235 IKLEKTLIDRIIETVGDYVRQ-MHNCRRDLSAYILSLGKSQDEIFGI-----FKQLEERT 288

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           ++P   +        E  +F    V+  ++I  +++  ++     + +   I+  +RKG 
Sbjct: 289 INPVAAADQLGMTMEELFSFKEM-VNGKIEILGKLQENAMH---DVDQLEEILWRIRKGN 344

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 345 TDALDAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFST 404

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ R+P+PEEIA+++  
Sbjct: 405 YATWWIRQAITRAIADQARTIRIPVHMIETINKLVRTSRYLVQELGRDPSPEEIAERMDY 464

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P D  +   L E   +VL+
Sbjct: 465 PLEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPADEVVNTKLAEQIAQVLS 524

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS++LRS
Sbjct: 525 DLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQQLRS 584

Query: 679 FLD 681
           + +
Sbjct: 585 YYE 587



 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 52/159 (32%), Positives = 91/159 (57%), Gaps = 14/159 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++G++T +ELN  LP +  + EQ+E+ + +   + I++VD       E     +
Sbjct: 13  LIAEGKKKGFLTFDELNKALPSEVNTPEQIEEIIVIFDQLDIDIVD-------EKLSRGI 65

Query: 94  DLASSASNSSVFLQKRK-----DSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRI 146
           ++A          +K +     D AD S+  +DPVRMYLREMG++ LL R+GE+ IAK+I
Sbjct: 66  EIAEDDGEEPKEEEKLELAEDEDGADYSSRSNDPVRMYLREMGAVGLLDRDGEVYIAKKI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           EAG   +M +L E P+  + L+   ++L  G   L++++
Sbjct: 126 EAGELEVMYALVEVPVAVEELVRVGEDLKKGRMKLKDVV 164


>gi|121609019|ref|YP_996826.1| RpoD family RNA polymerase sigma factor [Verminephrobacter eiseniae
           EF01-2]
 gi|121553659|gb|ABM57808.1| RNA polymerase, sigma 70 subunit, RpoD family [Verminephrobacter
           eiseniae EF01-2]
          Length = 635

 Score =  360 bits (923), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 184/348 (52%), Positives = 248/348 (71%), Gaps = 8/348 (2%)

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           D++  Q+ D+ ++    E EL R+     G+ ++ F++      L+  WV   K    G+
Sbjct: 292 DMVRGQVDDVRRK----ERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVE--KQAAMGK 345

Query: 395 -WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W + +A  +  I  ++ ++  +     + ++E + I   + +GE  +  AKKEM+EANL
Sbjct: 346 PWSSIIARNIPPIQDLQQKLMDLQSRVVVPLTELKVINKRMNEGEATSRDAKKEMIEANL 405

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 406 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 465

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK++KI KEP
Sbjct: 466 DQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASLLAAKMEIPEDKIRKIMKIAKEP 525

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFIED +  +P+++A+QA LR+    +L  LTPRE +VLRMRFG
Sbjct: 526 ISMETPIGDDDDSHLGDFIEDASNTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFG 585

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 586 IEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 633



 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 92/181 (50%), Gaps = 16/181 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E++  LP   V +E +E  +  L+++G+ V     D + L   +
Sbjct: 35  KTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITD 94

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 95  NAPTGASEEEAEEAAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 153

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   MM ++  SP T   ++   +E+  G  ++  I+D           GF +  E   
Sbjct: 154 GGLMAMMEAISASPATIAEILNMGEEIRAGKVVISTIVD-----------GFSNPNEADD 202

Query: 208 Y 208
           Y
Sbjct: 203 Y 203


>gi|124267677|ref|YP_001021681.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Methylibium petroleiphilum PM1]
 gi|124260452|gb|ABM95446.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Methylibium petroleiphilum PM1]
          Length = 746

 Score =  359 bits (922), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 179/319 (56%), Positives = 234/319 (73%), Gaps = 3/319 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ +D F++      L+  W    K+    + +   +A  +  I  ++ ++  +     +
Sbjct: 428 GMPQDHFIKTFPPNSLNLKWAE--KEIAANKSYSAVMARNLPPIQDLQQKLIDLQSRAVV 485

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            I + + I   + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 486 PIDDLKLINKKMNQGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 545

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +
Sbjct: 546 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 605

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP    +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P++
Sbjct: 606 FGFEPDAPTLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPIE 665

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+QA LR+    +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 666 AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 725

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           AIRKLKHPSRS KLR++LD
Sbjct: 726 AIRKLKHPSRSDKLRTYLD 744



 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 66/188 (35%), Positives = 100/188 (53%), Gaps = 30/188 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IK+ + RG++T +E+N  LP   + +E +E  V+ML++MGI V         E + D
Sbjct: 146 KTLIKMGKTRGFLTHQEINDHLPEKLIEAEILEAIVSMLNDMGIAVY--------EQAPD 197

Query: 92  SLDL----ASSASNSSVFLQKRK-------DSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +  L     S+A+++    ++         DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 198 AATLLIAGGSTATSTDEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 257

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++ ESP T   +++  D++  G   + E +D           GF 
Sbjct: 258 EIAKRIEGGLQAMMLAISESPTTIAEILVLADKIRVGEMQISEAVD-----------GFV 306

Query: 201 HGTEGHSY 208
              E   Y
Sbjct: 307 SNEEADDY 314


>gi|332527902|ref|ZP_08403939.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Rubrivivax benzoatilyticus JA2]
 gi|332112479|gb|EGJ12272.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Rubrivivax benzoatilyticus JA2]
          Length = 734

 Score =  358 bits (918), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 177/319 (55%), Positives = 235/319 (73%), Gaps = 3/319 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ ++ F++      L+  W    K+   G+ +   +   + ++ +++ ++  +     +
Sbjct: 416 GMPQEQFIKTFPPNVLNLKWAE--KEAAAGKPYSAVLGRNLPAVQELQQKLIDLQGRAVV 473

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + + + I   +  GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 474 PLDDLKEINRHMNAGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 533

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +
Sbjct: 534 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 593

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP    +A+K+ +P + +RK++ I KEPIS+ETPIGD+D SHLGDFIED N V+P+D
Sbjct: 594 FGFEPDAPTLAEKMEIPEDKIRKIMMIAKEPISMETPIGDDDDSHLGDFIEDTNNVAPVD 653

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+QA LRE    +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 654 AAMQAGLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 713

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           AIRKLKHPSRS KLR++LD
Sbjct: 714 AIRKLKHPSRSDKLRTYLD 732



 Score =  105 bits (262), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 63/166 (37%), Positives = 93/166 (56%), Gaps = 19/166 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IK+ + RG++T +E+N  LP   V +E +E  V+ML++MGI V         E + D
Sbjct: 134 KTLIKMGKTRGFLTHQEINDHLPEKLVDNEILEAIVSMLNDMGIAVY--------EQAPD 185

Query: 92  SLDLASSASNSSVFLQKRK-----------DSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +  L  + SN++    +             DS    T DPVRMY+REMGS+ELL+REGEI
Sbjct: 186 AATLLINGSNTATATDEEAEEAAEAALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEI 245

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            IAKRIE G   MM ++  SP T   ++   D++  G   + E++D
Sbjct: 246 EIAKRIEGGLQAMMLAISASPTTIAEILAMADKIAAGEMQISEVVD 291


>gi|239906706|ref|YP_002953447.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
 gi|239796572|dbj|BAH75561.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
          Length = 588

 Score =  358 bits (918), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 197/441 (44%), Positives = 293/441 (66%), Gaps = 39/441 (8%)

Query: 261 DEDDSAHTLSAMEDQL--RPKVMCALDEIAEVYRELRSLQ---------DNAVNGQKDEK 309
           +EDD +      ED++  R +V+  L+E+   +R+ R +          D  V G + E 
Sbjct: 168 EEDDPS------EDEMNQRQRVIFLLEEVKTSFRKKRKVYSKFDQCACVDKRVAGIQKE- 220

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYG 364
                 V K+++V  +  + L ++ ID ++E + D  ++ MHN        +L + +S  
Sbjct: 221 ----IMVFKDEIVTRLRDIKLEKTLIDRIIEIVEDYVRQ-MHNCQRDLSAYILSVGKSQS 275

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE---WKNFVACEVDSILKIRNEIKSISVETG 421
             +++F +    RE++P   + +      E   +K  ++ +++ +++++++         
Sbjct: 276 EIQEMFAQ-LDAREINPMIAAESLGLTVEELFSFKEMLSAKMEILVRLQDKCCH------ 328

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
            ++ E   ++  +++G   A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 329 -NVHELEEVLWRIKRGNNAAQRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGL 387

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  
Sbjct: 388 MKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQ 447

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PTPEEIA+++  P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A++P 
Sbjct: 448 ELGRDPTPEEIAERMDYPLEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKALAPA 507

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  +   L E   +VL+ LTPREE+VLR RFG+G  +DHTLEEVGK F VTRERIRQIEA
Sbjct: 508 EEVVNTKLGEQIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEA 567

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           KA+RKL+HP RS+ LRS+ +G
Sbjct: 568 KALRKLRHPVRSQHLRSYYEG 588



 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 57/156 (36%), Positives = 95/156 (60%), Gaps = 4/156 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +Q+G++T +E+N  LP +  + EQ+E+ +A+   + IN+VD D  +D    E 
Sbjct: 11  KSLIIKGKQKGFLTFDEVNKALPSEVNNPEQLEEVIAIFDQLDINLVDTD--KDGRKIEV 68

Query: 92  SLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +      A ++ + L + +DS D S+   DPVRMYLREMG++ LL REGE+ IAK+IE G
Sbjct: 69  AAAEPDDAPDADLELTESEDSLDYSSRSTDPVRMYLREMGAVPLLDREGEVVIAKKIENG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              ++ +L E P+  + LI   ++L  G   L++++
Sbjct: 129 EMEVLYALVEVPVAVEELIQVGEDLKIGRIKLKDVV 164


>gi|283851053|ref|ZP_06368337.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
 gi|283573449|gb|EFC21425.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
          Length = 588

 Score =  357 bits (916), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 201/439 (45%), Positives = 287/439 (65%), Gaps = 35/439 (7%)

Query: 261 DEDDSAHTLSAMEDQL--RPKVMCALDEIAEVYRELRSLQ---------DNAVNGQKDEK 309
           +EDD +      ED++  R +V+  LDE+   +R+ R +          D  V G + E 
Sbjct: 168 EEDDPS------EDEMNQRQRVIFLLDEVKASFRKKRKIYSKLDQCACLDRRVAGIQKE- 220

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYG 364
                 V KE++V  +  + L ++ ID ++E + D  ++ MHN        +L + +S  
Sbjct: 221 ----IMVFKEEIVVRLRDIKLEKTLIDRIIEIVEDYVRQ-MHNCQRDLSAYILSVGKSQS 275

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI-KSISVETGIS 423
             +++F +    R+++P   + +      E  +F       +L  + EI   +  +    
Sbjct: 276 EIQEMFAQ-LDSRDINPVVAAESLGLTVEELFSF-----KEMLSAKMEILDRLQEKCCHH 329

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + E   ++  +++G   A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 330 VHELEEVLWRIKRGNTAAQRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMK 389

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++
Sbjct: 390 AVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEL 449

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            R+PTPEEIA+++  P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A++P + 
Sbjct: 450 GRDPTPEEIAERMDYPLEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKALAPAEE 509

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L E   +VL+ LTPREE+VLR RFG+G  +DHTLEEVGK F VTRERIRQIEAKA
Sbjct: 510 VVNTKLGEQIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKA 569

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP RS+ LRS+ +G
Sbjct: 570 LRKLRHPVRSQHLRSYYEG 588



 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/163 (36%), Positives = 92/163 (56%), Gaps = 18/163 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---------D 82
           K +I   +Q+G++T +E+N  LP +  + EQ+E+ +A+   + IN+VD D          
Sbjct: 11  KSLIVKGKQKGFLTFDEVNKALPSEVNNPEQLEEVIAIFDQLDINLVDTDKDGRKIEVAS 70

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E EE  +  L+L  S            D + RSTD PVRMYLREMG++ LL REGE+ I
Sbjct: 71  TEPEETPDADLELTESEDTL--------DYSSRSTD-PVRMYLREMGAVPLLDREGEVVI 121

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           AK+IE G   ++ +L E P+  + LI   ++L  G   L++++
Sbjct: 122 AKKIENGEMDVLYALVEVPVAVEELIQVGEDLKIGRIKLKDVV 164


>gi|303245332|ref|ZP_07331616.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
 gi|302493181|gb|EFL53043.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
          Length = 588

 Score =  357 bits (916), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 196/421 (46%), Positives = 278/421 (66%), Gaps = 27/421 (6%)

Query: 277 RPKVMCALDEIAEVYRELRSLQ---------DNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           R +V+  LDE+   +R+ R +          D  V G + E       V KE++V  +  
Sbjct: 180 RQRVIFLLDEVKVSFRKKRKIYSKLDQCACLDRRVAGIQKE-----IMVFKEEIVVRLRD 234

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           + L ++ ID ++E + D  ++ MHN        +L + +S    +++F +    RE++P 
Sbjct: 235 IKLEKTLIDRIIEIVEDYVRQ-MHNCQRDLSAYILSVGKSQSEIQELFAQ-LDAREVNPM 292

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEA 441
             + +      E  +F       +L  + EI   +  +    + +   ++  +++G   A
Sbjct: 293 VAAESLGLTVEELFSF-----KEMLTAKMEILDRLQEKCCHHVHDLEEVLWRIKRGNTAA 347

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 348 QRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 407

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P+E
Sbjct: 408 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPLE 467

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A++P +  +   L E   +VL+ LT
Sbjct: 468 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKALAPAEEVVNTKLGEQIGKVLSDLT 527

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFG+G  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 528 PREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQHLRSYYE 587

Query: 682 G 682
           G
Sbjct: 588 G 588



 Score =  103 bits (258), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 58/156 (37%), Positives = 96/156 (61%), Gaps = 4/156 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +Q+G++T +E+N  LP + +S EQ+E+ +A+   + IN+VD D  +D    E 
Sbjct: 11  KSLIVKGKQKGFLTFDEVNKALPSEVISPEQLEEVIAIFDQLDINLVDTD--KDGRKVEA 68

Query: 92  SLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S      A ++ + L + +D+ D S+   DPVRMYLREMG++ LL REGE+ IAK+IE G
Sbjct: 69  SSAEPDDAPDADLELTESEDTLDYSSRSTDPVRMYLREMGAVPLLDREGEVVIAKKIENG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              ++ +L E P+  + LI   ++L  G   L++++
Sbjct: 129 EMDVLYALVEVPVAVEELIQVGEDLKIGRIKLKDVV 164


>gi|317484461|ref|ZP_07943373.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
 gi|316924285|gb|EFV45459.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
          Length = 590

 Score =  357 bits (915), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 194/428 (45%), Positives = 284/428 (66%), Gaps = 31/428 (7%)

Query: 273 EDQL--RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV---------LKEKL 321
           ED++  R +V+  L+EI + +++ R      +  + DE  +++ +V          KE++
Sbjct: 176 EDEMNQRTRVILLLEEIRQTFKKKRK-----IYAKLDECCTLERRVTAIQKEIMAFKEEI 230

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK----RDVFLERHQGR 377
           V  +  + L ++ ID ++E + D  +++ + + +L     S G      +D+F  +   R
Sbjct: 231 VTRLRDIKLEKTLIDRIIETVEDYVRQMRNCQRDLSAYLLSTGKNQEEIKDLF-RKLDSR 289

Query: 378 ELDPHWVSYAKDFPEGE---WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           ++ P   +   +    E   +K  +  +++ + +++ +          ++S+   ++  +
Sbjct: 290 DISPVLAAKELNMSVDELFSYKEMILGKIEILQRLQEKCCH-------NVSDLEEVLWRI 342

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++G   A  AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 343 KRGNNAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGY 402

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA 
Sbjct: 403 KFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAD 462

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++  PV+ V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E   
Sbjct: 463 RMEYPVDKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIA 522

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VLA LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+
Sbjct: 523 SVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQ 582

Query: 675 KLRSFLDG 682
            LRSF D 
Sbjct: 583 VLRSFYDS 590



 Score = 84.7 bits (208), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 90/164 (54%), Gaps = 19/164 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD----GDDL---- 83
           K +I   ++ G++T EE+N  +P +  + EQ E+ + +   + I +VD    G  +    
Sbjct: 12  KSLIAKGKEMGFLTFEEVNKAVPLEMNTPEQFEEIIGIFDQLEIAIVDLEKDGKKIPVTS 71

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              D E SE+ L+L  +   +        D + RSTD PVRMYLREMG++ LL R+GE+ 
Sbjct: 72  AETDGEQSEERLELVDNEDAA--------DFSSRSTD-PVRMYLREMGAVPLLDRDGEVT 122

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IAK+IE G   ++ +L E P+  + LI   ++L      L++++
Sbjct: 123 IAKKIEQGEQDVLYALVEVPVAVEELINVGEDLKLNRIKLKDVV 166


>gi|319779662|ref|YP_004130575.1| RNA polymerase sigma factor RpoD [Taylorella equigenitalis MCE9]
 gi|317109686|gb|ADU92432.1| RNA polymerase sigma factor RpoD [Taylorella equigenitalis MCE9]
          Length = 840

 Score =  357 bits (915), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 183/351 (52%), Positives = 249/351 (70%), Gaps = 8/351 (2%)

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSY-----GIKRDVFLERHQGRELDPHWVS-YAKDFP 391
           +VE+L +I ++ +    EL +   S      G+ R+ F++   G E +  WV+   K  P
Sbjct: 491 MVEKLAEILRKQIERVRELEKAMISVCVDKVGMPREHFIDSFPGNETNLEWVNDELKKKP 550

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  +   +   +  I +I+ +   +  E  + I E + +   +  GE +A  AK EM+EA
Sbjct: 551 K--YAEKLERSIPDIHEIQQKFIDLEKEVILPIKELKDVNKRMVNGEAKAKKAKHEMIEA 608

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRS
Sbjct: 609 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 668

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+  IRIPVHM + I+K+ R  R++  +   EP    +A+K+ MP+E +RK+LKI+K
Sbjct: 669 IADQARIIRIPVHMIETINKINRITRQILQETGVEPDSAMLAEKMDMPIEKIRKILKISK 728

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           +PIS+ETPIGD+D SHLGDFIED + +SP ++A+Q ++ E    V+ SLT RE +VLRMR
Sbjct: 729 DPISMETPIGDDDDSHLGDFIEDTSTLSPEEAALQRSMSEVFDEVINSLTQREGKVLRMR 788

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FGIGM++D TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+ 
Sbjct: 789 FGIGMSSDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFLEN 839



 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 62/163 (38%), Positives = 87/163 (53%), Gaps = 14/163 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IK  +  GY+T  E+N  L  D V SE ME  V+ L +MGI V      E+   +ED
Sbjct: 245 RSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMVSTLESMGIPV-----YEEAPNAED 299

Query: 92  SLDLASSASNSSVFLQKRK--------DSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L LA  ++ +       +        DS    T DPVRMY+REMGS+ELL+R  EI IA
Sbjct: 300 -LILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYMREMGSVELLNRTKEIEIA 358

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           KRIE G   M+ ++  SP T   ++    ++ DG   + EI+D
Sbjct: 359 KRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEEIVD 401


>gi|94986960|ref|YP_594893.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731209|emb|CAJ54571.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 590

 Score =  356 bits (914), Expect = 6e-96,   Method: Compositional matrix adjust.
 Identities = 200/441 (45%), Positives = 289/441 (65%), Gaps = 39/441 (8%)

Query: 261 DEDDSAHTLSAMEDQL--RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV-- 316
           +EDD +      ED++  R +V+  L+EI +++++ R      V  + DE  +++ +V  
Sbjct: 170 EEDDPS------EDEMSQRNRVILLLEEIRQIFKKKRK-----VYLKLDECCTLERRVAG 218

Query: 317 -------LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYG 364
                   KE++V  +  + L ++ ID ++E + D  ++ MHN        LL   ++  
Sbjct: 219 IQKEILQFKEEIVTRLRDIKLEKTLIDRIIETVEDYVRQ-MHNCQRELSAYLLSTGKTQD 277

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE---WKNFVACEVDSILKIRNEIKSISVETG 421
             +D+F  +   REL P   +   +    E   +K  +  +++ + +++ +         
Sbjct: 278 EIKDLF-TKLDARELSPRDAALLLNMGVDELFSYKEMILGKIEILQRLQEKCCH------ 330

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
            ++ +   ++  +++G   A  AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 331 -NVVDLEEVLWRIKRGNNAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGL 389

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  
Sbjct: 390 MKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQ 449

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  R+PTPEEIA+++  P++ V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P 
Sbjct: 450 EFGRDPTPEEIAERMDYPLDKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPS 509

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  +   L E    VLA LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEA
Sbjct: 510 EEVVNTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEA 569

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           KA+RKL+HP RS+ LRSF D 
Sbjct: 570 KALRKLRHPVRSQVLRSFYDS 590



 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 53/157 (33%), Positives = 89/157 (56%), Gaps = 5/157 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +I   +  G+VT EE+N  +P D  + EQ E+ + +   + I +VD +  E ++ +  
Sbjct: 12  RTLIAKGKAAGFVTFEEVNKAVPIDMNTPEQFEEIIGIFDQLEIVIVDSEK-EGKKITVT 70

Query: 92  SLDLASSASNSSVFLQKRKDSAD---RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S +     S +   L   +D AD   RSTD PVRMYLREMG++ LL R+GE+ IAK++E 
Sbjct: 71  SPETDGDTSENCFDLVDTEDVADFSSRSTD-PVRMYLREMGAVPLLDRDGEVVIAKKVET 129

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G   ++ +L E P+  + LI   ++L      L++++
Sbjct: 130 GEQDVLYALVEVPVAVEELISVGEDLKLNRIKLKDVV 166


>gi|225848841|ref|YP_002729005.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644391|gb|ACN99441.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 586

 Score =  356 bits (913), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 196/450 (43%), Positives = 291/450 (64%), Gaps = 34/450 (7%)

Query: 250 NAENDERNLDEDEDDSAHTLSAME--DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           N E  E  +DE  D  +  L   E  D++    +    E+A++YR+L           + 
Sbjct: 153 NVEETEEKVDELSDGESLELENNENYDKITSDFIKKGLELAKLYRDL----------LEK 202

Query: 308 EKSSVKCKVLKEK---------LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           EK  ++ K L+ K         L K + SL++  +++D + ++L ++  ++  NE     
Sbjct: 203 EKIYLETKTLEAKREFVWQHAKLNKFIKSLNIKFTKLDKIADELKELYTKLRKNE----- 257

Query: 359 LAQSYGIKRDVFLERHQGREL--DPHWVSYAKDFPEGEWKNFVACEVDSI----LKIRNE 412
             + Y  +  +  + H   +L     +  Y +   + E   F     + +    L+++NE
Sbjct: 258 --KDYEKRIKIISKIHPDLDLMLSTEYEKYPEILKKLESNGFSYGRYEILRTETLRLKNE 315

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+ I  + G    EF H++ ++++G  E +  K+ +V+ANLRLV+S+AKKYTNRGLQFLD
Sbjct: 316 IEDIKAKIGTIPEEFDHVLDIIQQGRNEINNVKQILVKANLRLVVSIAKKYTNRGLQFLD 375

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +K+D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+
Sbjct: 376 LIQEGNIGLMKAVDKYDYKRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKL 435

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR M  ++ REPTPEEIAKK+ MP E V+K+L+ ++EPISLETPIG ++ +HLGDFI
Sbjct: 436 IRVARSMVQELGREPTPEEIAKKVGMPAEKVKKILRTSQEPISLETPIGTDEETHLGDFI 495

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDK+ +SP    ++  LR     VL++L+ REE+VLR RFG+  +T+HTLE+VGK+F VT
Sbjct: 496 EDKSVLSPEAHMLKNALRMQLDEVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVT 555

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RERIRQIEAKA+RKL+HP R+K L+ F++G
Sbjct: 556 RERIRQIEAKALRKLRHPHRAKYLKPFIEG 585



 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 49/163 (30%), Positives = 84/163 (51%), Gaps = 14/163 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D  + +I LAR++GYVT  E++ ++  +  SS E +E  +  L+ + I+V D + +++E+
Sbjct: 8   DDVRTLINLAREKGYVTYSEISTYVDEEFFSSDEHIESLIEYLNELNIDVRDDEKIKEED 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D + L               D      DDPV++YLREMG I LL RE EI  A  IE
Sbjct: 68  ---DDIYLGIDFD----------DDVWSKADDPVKLYLREMGKIPLLKREEEIKYAMEIE 114

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
            GR  +   L  +    + L+    ++ DG   +++++++E  
Sbjct: 115 RGRKKVFRGLLRTSFLTERLLDEWAKVVDGKLRVQDLLNVEET 157


>gi|303327390|ref|ZP_07357831.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
 gi|302862330|gb|EFL85263.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
          Length = 589

 Score =  356 bits (913), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 194/419 (46%), Positives = 277/419 (66%), Gaps = 13/419 (3%)

Query: 273 EDQL--RPKVMCALDEIAEVYRELRS----LQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           ED++  R +V+  LDEI +V+++ R     L D     ++   +  +    KE++V  + 
Sbjct: 175 EDEMNQRSRVILLLDEIKQVFKKKRKIYKKLDDCCTLERRVTATQKEIISFKEEIVTRLR 234

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG---IKRDVFLERHQGRELDPHW 383
            + L ++ ID ++E + D  +++ + + +L     S G   ++     +  + RE++P  
Sbjct: 235 DIKLEKTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGRTQVEIQTMFDGLEKREVNPTE 294

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            +        E  +F    +  I      +K +  +   ++ +   ++  +++G   A  
Sbjct: 295 AARDLKLSVDELFSFKEMIIGKI----EILKRLQEKCCHNVGDLEEVLWRIKRGNTAAMR 350

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 351 AKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 410

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  PVE V
Sbjct: 411 IRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYPVEKV 470

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  I   L E    VLA LTPR
Sbjct: 471 KKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVINTKLSEQLAAVLADLTPR 530

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ + 
Sbjct: 531 EEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQPLRSYYEN 589



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 90/164 (54%), Gaps = 19/164 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD--------- 82
           + +I   +  G++T EE+N  LP +  + EQ E+ + +   + I +VD +          
Sbjct: 11  QSLIAKGKGTGFLTFEEVNKALPVEMSTPEQFEEIIGIFEQLEIVIVDSEKDGKKISATA 70

Query: 83  -LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              D++ SED+LDL     ++        D + RSTD PVRMYLREMG++ LL R+GE+ 
Sbjct: 71  AETDDDVSEDTLDLTEDEESA--------DYSSRSTD-PVRMYLREMGAVPLLDRDGEVV 121

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IAK+IE G   ++ +L E P+  + LI   ++L      L++++
Sbjct: 122 IAKKIEMGEQDVLYALVEVPVAVEELINVGEDLRQNRVKLKDVV 165


>gi|46580198|ref|YP_011006.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120602415|ref|YP_966815.1| RpoD family RNA polymerase sigma factor [Desulfovibrio vulgaris
           DP4]
 gi|46449615|gb|AAS96265.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120562644|gb|ABM28388.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio vulgaris DP4]
 gi|311233814|gb|ADP86668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris RCH1]
          Length = 590

 Score =  355 bits (910), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 189/409 (46%), Positives = 270/409 (66%), Gaps = 26/409 (6%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           KV   LDE   + R + S+Q   +N              KE +V  +  + L ++ ID +
Sbjct: 201 KVYSKLDECCTLERRVASVQREIMN-------------YKEDIVSRLRDIKLEKTLIDRI 247

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKR---DVFLERHQGRELDPHWVSYAKDFPEGE- 394
           +E + D  +++ + + +L     S G  +          + RE+ P   S A +    E 
Sbjct: 248 IETVEDYVRQMHNCQRDLSAYILSTGKTQAEIQALFSGLEAREVSPVAASAALNMTVEEL 307

Query: 395 --WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             +K  +  +++ + +++++          ++++   ++  +++G   A  AK+E++ +N
Sbjct: 308 FSFKEMILGKIEILSRLQDKCCH-------NVNDLEEVLWRIKRGNSIAMRAKQELIRSN 360

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I
Sbjct: 361 LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI 420

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P++ V+KVLKI KE
Sbjct: 421 ADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPIDKVKKVLKIAKE 480

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    VLA LTPREE+VLR RF
Sbjct: 481 PISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLGEQIASVLADLTPREEQVLRKRF 540

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 541 GIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQTLRSYYE 589



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 91/165 (55%), Gaps = 20/165 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---------- 81
           K +I   +  G++T +E+N  LP +  + EQ+E+ + +   + I +VD +          
Sbjct: 11  KSLIAKGKVSGFLTFDEVNKALPAEVNTPEQIEEIIGIFDQLDIAIVDSEKDGKKISMSP 70

Query: 82  -DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            + E+E  SE  LDL+          ++  D + RSTD PVRMYLREMGS+ LL R+GE+
Sbjct: 71  GESEEEAPSEGGLDLSDD--------EETVDYSSRSTD-PVRMYLREMGSVPLLDRDGEV 121

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            IAK+IE G   ++ +L E P+  + L+   ++L      L++++
Sbjct: 122 VIAKKIEMGEQDVLYALVEVPVAVEELVNVGEDLKQNRIKLKDVV 166


>gi|291279867|ref|YP_003496702.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754569|dbj|BAI80946.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 598

 Score =  354 bits (908), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 164/261 (62%), Positives = 217/261 (83%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G + +E   I + + +GE EA  AK E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 338 GFTKNELEVIYNSLLEGEYEAEKAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIG 397

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA EKF++  GYKFSTYA WW++Q+ITR+IADQ+ TIRIPVHM + I+K++RT R++ 
Sbjct: 398 LMKAVEKFEYRRGYKFSTYATWWIRQSITRAIADQARTIRIPVHMIETINKMIRTIRQLQ 457

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ +EPTPEEIA+++ +PVE V+KVLKI KEP+SLETPIG+++ S LGDFIED++A +P
Sbjct: 458 IELGKEPTPEEIAERMDIPVEKVKKVLKIAKEPVSLETPIGEDEDSSLGDFIEDQSAKNP 517

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LD  +   L+E T  +L +LTPRE  VLR+RFGI  ++DHTLEEVG++F VTRERIRQIE
Sbjct: 518 LDEVVYEKLKEHTRAILDTLTPREASVLRLRFGIDCDSDHTLEEVGRRFNVTRERIRQIE 577

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HP+RS+ L++FL+
Sbjct: 578 AKALRKLRHPTRSRILKTFLE 598


>gi|78357095|ref|YP_388544.1| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
 gi|78219500|gb|ABB38849.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 589

 Score =  354 bits (908), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 195/425 (45%), Positives = 283/425 (66%), Gaps = 27/425 (6%)

Query: 273 EDQL--RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL---------KEKL 321
           ED++  R +V+  LDEI   +++ R      V  + DE  +++ +V          KE++
Sbjct: 175 EDEMNQRQRVILLLDEIQSTFKKKRK-----VYQRLDECCTLERRVYGIQKEIIAYKEEI 229

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQG 376
           V  +  + L ++ ID ++E + D  ++ MHN        +L   ++    R++F  +   
Sbjct: 230 VSRLRDIKLEKTLIDRIIETVEDYVRQ-MHNCQRDLSAYILSTGKTQTEMRELF-RQLDD 287

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           RE++P   + + +    E  +F    +   ++I N ++        ++++   ++  +++
Sbjct: 288 REINPVVAADSLNLTVEELFSFKEM-IMGKMEILNRLQEKCCH---NVTDLEEVLWRIKR 343

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G   A  AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 344 GNSHAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKF 403

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++
Sbjct: 404 STYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERM 463

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             P++ V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    V
Sbjct: 464 DYPIDKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIAAV 523

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LTPREE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ L
Sbjct: 524 LADLTPREEQVLRKRFGINEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQTL 583

Query: 677 RSFLD 681
           RS+ +
Sbjct: 584 RSYYE 588



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 52/159 (32%), Positives = 91/159 (57%), Gaps = 9/159 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +  G++T EE+N  LP +  + EQ+E+ + +   + I +VD +    ++G + 
Sbjct: 11  KTLIAKGKVAGFLTFEEVNKALPAEVNTPEQIEEIIGIFDQLDIAIVDSE----KDGKKI 66

Query: 92  SLDLASS---ASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRI 146
           S+  A +     +  + L    D AD S+   DPVRMYLREMG++ LL R+GE+ IAK+I
Sbjct: 67  SVSPAEADDEGGDGGLELTDEDDPADYSSRSTDPVRMYLREMGAVPLLDRDGEVNIAKKI 126

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G   ++ +L E P+  + LI   ++L +    L++++
Sbjct: 127 ETGEQDVLYALVEVPIAVEELISVGEDLKENRIKLKDVV 165


>gi|212702263|ref|ZP_03310391.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
 gi|212674326|gb|EEB34809.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
          Length = 589

 Score =  353 bits (907), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 197/422 (46%), Positives = 285/422 (67%), Gaps = 19/422 (4%)

Query: 273 EDQL--RPKVMCALDEIAEVYRELRSLQD--NAVNGQKDEKSSVKCKVL--KEKLVKLVG 326
           ED+L  R +V+  LDEI +++++ R +    +  N    + ++++ +++  KE++V  + 
Sbjct: 175 EDELNQRSRVILLLDEIKQIFKKKRKIYKKLDDCNTLDRKVTAIQKEIISYKEEIVTRLR 234

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQGRELDP 381
            + L ++ ID ++E + D  ++ MHN        +L   ++    +++F    Q R ++P
Sbjct: 235 DIKLEKTLIDRIIETVEDYVRQ-MHNCQRDLSAYILSTGRTQAEIQEMFTGLEQ-RTINP 292

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS-ISVETGISISEFRHIVSMVRKGECE 440
           +  +        E  +F    +  I     EI S +  +   ++++   ++  +++G   
Sbjct: 293 NDAARDLKLSVDELFSFKEMIIGKI-----EILSRLQEKCCHNVNDLEEVLWRIKRGNTA 347

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 348 AMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYA 407

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  PV
Sbjct: 408 TWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYPV 467

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  I   L E    VLA L
Sbjct: 468 EKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVINTKLSEQLAAVLADL 527

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ 
Sbjct: 528 TPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQPLRSYY 587

Query: 681 DG 682
           + 
Sbjct: 588 EN 589



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 51/156 (32%), Positives = 91/156 (58%), Gaps = 3/156 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +I   +  GY+T +E+N  LP +  + EQ E+ + +   + I +VD +  + ++ S  
Sbjct: 11  QSLIAKGKGMGYLTFDEVNKALPVEMNTPEQFEEIIGIFEQLEIAIVDSEK-DGKKISAT 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +    A + S+ L + ++SAD S+   DPVRMYLREMG++ LL R+GE+ IAK+IE G
Sbjct: 70  PTETDDDAMDGSLELAEDEESADYSSRSTDPVRMYLREMGAVPLLDRDGEVVIAKKIEMG 129

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              ++ +L E P+  + LI   ++L      L++++
Sbjct: 130 EQDVLYALVEVPVAVEELINVGEDLRQNRIKLKDVV 165


>gi|297181479|gb|ADI17666.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0130_23I23]
          Length = 602

 Score =  353 bits (907), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 168/237 (70%), Positives = 205/237 (86%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 364 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 423

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE++K+L +P + +
Sbjct: 424 IRQAITRSIADQARTIRIPVHMIETINKLNRLSRQMMQEIGREPTPEEMSKRLDIPEDKM 483

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI KEPIS+ETPIGD++ S+LGDF+ED +  SP+D A   +L+++T  +LASLT R
Sbjct: 484 RKVMKIAKEPISMETPIGDDEDSNLGDFLEDSSINSPIDDASIRSLKDSTDEILASLTAR 543

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +VLRMRFGIGMN DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFL
Sbjct: 544 EAKVLRMRFGIGMNNDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLKSFL 600



 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 52/146 (35%), Positives = 86/146 (58%), Gaps = 2/146 (1%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG-SED 91
           ++I+LA+ +GY+T  ++   LP     ++  E+ V +L +MGI V +    EDE    ED
Sbjct: 19  QLIQLAKDQGYLTHADITDTLPDGSTDADNFEEIVQVLKDMGIKVFEDTPDEDELMLGED 78

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                 +A ++   L + +  + R+TD PVRMY+REMGS++LL++ GEI IAKRIE+   
Sbjct: 79  EETDDVAAEDAVAALSQTEIESGRTTD-PVRMYMREMGSVDLLTKTGEIDIAKRIESAMK 137

Query: 152 MMMASLCESPLTFQALIIWRDELNDG 177
            ++A   E PL  + ++ + D +  G
Sbjct: 138 EVLALCAEYPLCIEYVLDFFDRIKIG 163


>gi|158522162|ref|YP_001530032.1| RpoD family RNA polymerase sigma factor [Desulfococcus oleovorans
           Hxd3]
 gi|158510988|gb|ABW67955.1| RNA polymerase, sigma 70 subunit, RpoD family [Desulfococcus
           oleovorans Hxd3]
          Length = 738

 Score =  353 bits (906), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 163/255 (63%), Positives = 208/255 (81%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R  +  +  G   A  +K E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGN+GLMKA +
Sbjct: 483 LRKTMKKIDDGYLRAKASKSELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNVGLMKAVD 542

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +   E
Sbjct: 543 KFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQERGYE 602

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+PEEIA+K+ +P+E VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK  + P ++A+ 
Sbjct: 603 PSPEEIAEKMEIPLEKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKFMIPSEAAVS 662

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            NL E T +VLA+LTPREE+VLRMRFGIG   DHTLEEVG+ F VTRERIRQIEAKA+RK
Sbjct: 663 MNLSEQTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFAVTRERIRQIEAKALRK 722

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP+RSK L+ F++
Sbjct: 723 LRHPTRSKMLKHFIE 737



 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 46/144 (31%), Positives = 82/144 (56%), Gaps = 6/144 (4%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++G +T EE+   +  +++ ++QM+D +  L ++ I+VV   D  D+ G ED  
Sbjct: 170 LIAKGKKQGELTYEEIAKAIEANDIPTDQMDDLLVHLDDLDISVVKKADQADDSG-EDGA 228

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
              +   +   +     DS   S  D V+MYLREMG + LLSREGE+ IAK+IEAG    
Sbjct: 229 KSTTRGDSPVTY-----DSDPGSVTDTVKMYLREMGLVTLLSREGEVEIAKKIEAGEQEA 283

Query: 154 MASLCESPLTFQALIIWRDELNDG 177
           +  + ++ +  +++I + D ++ G
Sbjct: 284 LRGMLDTAVGVESIIAYGDNIDVG 307


>gi|220904357|ref|YP_002479669.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219868656|gb|ACL48991.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 589

 Score =  353 bits (905), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 197/426 (46%), Positives = 280/426 (65%), Gaps = 27/426 (6%)

Query: 273 EDQL--RPKVMCALDEIAEVYR---------ELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           ED++  R +V+  LDEI + ++         ++ +  D  V   + E   + C   KE++
Sbjct: 175 EDEMNQRSRVILLLDEIKQTFKKKRKIYKKLDVCTCMDRRVTAVQKE---IIC--FKEEI 229

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQG 376
           V  +  + L ++ ID ++E + D  ++ MHN        +L   ++    + +F +  + 
Sbjct: 230 VTRLRDIKLEKTLIDRIIETVEDYVRQ-MHNCQRDLSAYILATGRTQAEIQAMF-DGLEQ 287

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           RE++P   +        E  +F    +  I +I N ++        ++++   ++  +++
Sbjct: 288 REINPMDAARDLKLSVDELFSFKEMIIGKI-EILNRLQEKCCH---NVTDLEEVLWRIKR 343

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G   A  AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 344 GNTAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKF 403

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++
Sbjct: 404 STYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERM 463

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             PVE V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  I   L E    V
Sbjct: 464 EYPVEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVINTKLSEQLAAV 523

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LTPREE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ L
Sbjct: 524 LADLTPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQPL 583

Query: 677 RSFLDG 682
           RS+ + 
Sbjct: 584 RSYYEN 589



 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 53/159 (33%), Positives = 94/159 (59%), Gaps = 9/159 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +I   +  G++T EE+N  LP +  + EQ E+ + +   + I +VD +    ++G + 
Sbjct: 11  QSLIAKGKGAGFLTFEEVNKALPVEMSTPEQFEEIIGIFEQLEIVIVDSE----KDGKKI 66

Query: 92  SLDLASS---ASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRI 146
           S   + S    ++SS+ L + +D+AD S+   DPVRMYLREMG++ LL R+GE+ IAK+I
Sbjct: 67  SATASESDEEITDSSLDLSEDEDTADYSSRSTDPVRMYLREMGAVPLLDRDGEVVIAKKI 126

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G   ++ +L E P+  + LI   ++L      L++++
Sbjct: 127 EMGEQDVLYALVEVPVAVEELINVGEDLRQNRIKLKDVV 165


>gi|242279084|ref|YP_002991213.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
 gi|242121978|gb|ACS79674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
          Length = 585

 Score =  352 bits (904), Expect = 9e-95,   Method: Compositional matrix adjust.
 Identities = 194/424 (45%), Positives = 283/424 (66%), Gaps = 23/424 (5%)

Query: 273 EDQL--RPKVMCALDEIAEVYRELR----SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           ED++  R +V+  LDE+ ++Y + R     L D A   +K  K   +    K ++V+ + 
Sbjct: 171 EDEMNQRQRVIFLLDEVKKLYDKKRDLYYKLDDCATLEKKVAKQQNEIVNYKTEIVERLR 230

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQGRELDP 381
            + + ++ ID ++E + D  ++ MHN        +L   ++    +D+F ++   RE++P
Sbjct: 231 DIKIEKTLIDQIIETVGDYVRQ-MHNCQRDLSAYILSTGKTQQEIKDLF-KQIDDREINP 288

Query: 382 HWVSYAKDFPEGE---WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
              S        E   +K  ++ +++ +++++++          ++ E   ++  ++ G 
Sbjct: 289 VAASDELGMTVDELFSFKEMISGKMEILVRLQDKCCH-------NVHELEEVLWRIKHGN 341

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 342 RSAMRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFST 401

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P+PEEIA+++  
Sbjct: 402 YATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPSPEEIAERMDY 461

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A +P +  +   L E    VL+
Sbjct: 462 PLEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAAAPAEEVVSTKLGEQIATVLS 521

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  LRS
Sbjct: 522 DLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSALLRS 581

Query: 679 FLDG 682
           + + 
Sbjct: 582 YYEN 585



 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 55/161 (34%), Positives = 92/161 (57%), Gaps = 13/161 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLED 85
           + K +I   +++G++T E+L   LP +   S+Q++D + +   + I +V    DG  + D
Sbjct: 9   AIKTLISEGKKQGFLTFEQLGKALPAEFNKSDQLDDVIKIFDQLNIAIVNTPEDGKKIMD 68

Query: 86  EE-GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               ++D +DL  S   S        D   RSTD PVRMYLREMG++ LL REGE+ IAK
Sbjct: 69  AGVDNDDDIDLTESEEESV-------DYVSRSTD-PVRMYLREMGAVGLLDREGEVVIAK 120

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +IE G   ++ +L E P+  + LI   ++L++    L++++
Sbjct: 121 KIENGEMDVLYALVEIPVAIEELISVGEDLDESRIKLKDVV 161


>gi|297180571|gb|ADI16783.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0010_11B23]
          Length = 605

 Score =  352 bits (904), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 167/237 (70%), Positives = 203/237 (85%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 367 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE++K+L +P + +
Sbjct: 427 IRQAITRSIADQARTIRIPVHMIETINKLNRLSRQMMQEIGREPTPEEMSKRLDIPEDKM 486

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI KEPIS+ETPIGD++ S+LGDF+ED +  SP+D A    L++ T  +LASLT R
Sbjct: 487 RKVMKIAKEPISMETPIGDDEDSNLGDFLEDTSINSPIDDASIRGLKDATDEILASLTAR 546

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +VLRMRFGIGMN DHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  L+SFL
Sbjct: 547 EAKVLRMRFGIGMNNDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDVLKSFL 603


>gi|317153216|ref|YP_004121264.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
 gi|316943467|gb|ADU62518.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
          Length = 581

 Score =  349 bits (896), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 198/427 (46%), Positives = 279/427 (65%), Gaps = 29/427 (6%)

Query: 273 EDQL--RPKVMCALDEIAE-------VYRELR--SLQDNAVNG-QKDEKSSVKCKVLKEK 320
           ED++  R +V+  LDE+ +       +Y +L   +  D  V G QKD        V K++
Sbjct: 167 EDEMNQRQRVIFLLDEVKKLFKKKRKIYEKLDYCAQTDKRVYGVQKD------ILVYKDE 220

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN-----EGELLRLAQSYGIKRDVFLERHQ 375
           +V  +  + L ++ ID ++E + D  ++ MHN        +L + Q+     ++F  +  
Sbjct: 221 VVTRLRDIKLEKTLIDRIIETVNDYVRQ-MHNCQRDLSAYVLSVGQTKAEIEELF-RQVD 278

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
            R ++P   +        E+ +F    +   L+I N ++        S+ +   ++  ++
Sbjct: 279 ARTVNPVVAADTLGLTVEEFFSFKEM-LAGKLEIMNRLQDKCCH---SVHDLEEVLWRIK 334

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G   A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 335 RGNLSAMRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYK 394

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P+PEEIA++
Sbjct: 395 FSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPSPEEIAER 454

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +  P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A +P +  +   L E    
Sbjct: 455 MDYPLEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKATAPAEEVVSTKLGEQIAS 514

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL+ LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  
Sbjct: 515 VLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSAL 574

Query: 676 LRSFLDG 682
           LRS+ + 
Sbjct: 575 LRSYFEN 581



 Score =  110 bits (274), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 65/155 (41%), Positives = 94/155 (60%), Gaps = 9/155 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD-DLEDEEGSE 90
           K +I   +QRG++T EEL+  LP D  + EQ+E+  A+   MGI +VD D D +  E  +
Sbjct: 11  KTLIAEGKQRGFLTYEELSKALPSDYNTPEQLEEIHAIFDQMGIALVDSDEDDKKLETDD 70

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             L+L     +S+       D A RSTD PVRMYLREMG++ LL REGE+ IAK+IE G 
Sbjct: 71  KELELTEKDDDSA-------DYASRSTD-PVRMYLREMGAVPLLDREGEVVIAKKIENGE 122

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             ++ SL E P+  + LI   ++L DG   L++++
Sbjct: 123 LEVLYSLIEVPVAVEELISVGEDLKDGRVKLKDVV 157


>gi|296161690|ref|ZP_06844493.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888004|gb|EFG67819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 628

 Score =  348 bits (893), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 224/660 (33%), Positives = 357/660 (54%), Gaps = 61/660 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD----GDDLEDEE 87
           + ++KL ++RG++T  E+   LP     ++ +E  V   +++GI V D    GD L   +
Sbjct: 19  RALMKLGKERGFLTHTEIVDHLPDCVAQADAIEGIVKAFNDVGIAVRDFAPTGDALLLGD 78

Query: 88  GSEDSL--DLAS--SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            ++ S   D+A   +A+  ++ + +   +AD     P+R YLREMG+  LL+REGEIA+A
Sbjct: 79  AAQQSAPDDVAEDETATALTIAISEPGPAAD-----PMRAYLREMGATPLLTREGEIAVA 133

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           +RIEA    M+  +   P T  A++   D +  G   + +++D           GF    
Sbjct: 134 RRIEACLREMLEVIALRPATVDAILARADRVAAGELDIDDLVD-----------GFL--- 179

Query: 204 EGHSYQKREDSSQEKERDD-VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                        E++ D+ +   +G     A  SK D    D  P NA           
Sbjct: 180 -------------EQQPDEMLPAMQGATAEGAAGSKVD----DGVPSNA----------- 211

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           +DSA  + A E ++  ++    + I    RE  +    AV G    +   +  ++   + 
Sbjct: 212 NDSAGAIEADEARI-ARLTAGCNAIFLQVREQLASWRAAVAGTTGRREDAQSTLVL--IA 268

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
             +G +  +   I  L   +    + I   E  +LRLA    G+ RD+F+E   G E DP
Sbjct: 269 STLGQIRFSARTIGELSADVRRAVEEIRGIERNVLRLAVNQGGMVRDMFVETFVGSETDP 328

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W++ A           + C   SI   + ++  I    G+S+ E + I   +   + E 
Sbjct: 329 EWLARAAAAAPACSAALMRC-APSIHGQQEKLAQIEAREGLSLQELKRISRKMNVADREL 387

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A++ M+EANLRLV+SVAKKY   G+  LDL+QEGNIGLMKA ++F++  G+KFSTYA 
Sbjct: 388 QDARRAMIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKFSTYAT 447

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q+++R+IAD   TIR+PVHM D +H+V R A  M  +  R+    E+A +L M  E
Sbjct: 448 WWIRQSVSRAIADYGRTIRVPVHMADAMHRVKRVAGEMRQETGRQARSSELAARLGMSEE 507

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR V ++T++P+SL+ PIG++  + LG+ +ED +A++PLD+ +QA+LR      L  LT
Sbjct: 508 KVRSVQRVTRQPVSLDVPIGEDADTTLGEMVEDPSALAPLDALLQADLRVAIDAALGVLT 567

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +V+++RFG+   ++HTLEE+G QF VTRER+RQI+ KA++KL+H      L+S+LD
Sbjct: 568 PREAKVIKLRFGVDAVSEHTLEELGDQFDVTRERVRQIQNKALQKLRHSDGISTLKSYLD 627


>gi|323697926|ref|ZP_08109838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           ND132]
 gi|323457858|gb|EGB13723.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans ND132]
          Length = 583

 Score =  347 bits (890), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 181/371 (48%), Positives = 255/371 (68%), Gaps = 13/371 (3%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ-- 375
           KE++V  +  + L ++ ID ++E + D  +++ + + +L     S G  +    E  Q  
Sbjct: 220 KEEIVTRLRDIKLEKTLIDRIIETVNDYVRQMHNCQRDLSAYVLSVGKTKAEIEELFQQV 279

Query: 376 -GRELDPHWVSYAKDFPEGEWKNF---VACEVDSILKIRNEIKSISVETGISISEFRHIV 431
             R ++P   S        E+ +F   +A +++ + +++++          S+ +   ++
Sbjct: 280 DARSINPVAASTQLGMTVEEFFSFKEMLAGKLEIMHRLQDKCCH-------SVHDLEEVL 332

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++ G   A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 333 WRIKSGNQTAMQAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQ 392

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P+PEE
Sbjct: 393 RGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPSPEE 452

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+++  P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A +P +  +   L E
Sbjct: 453 IAERMDYPLEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKATAPAEEVVSTKLSE 512

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL+ LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP 
Sbjct: 513 QIASVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPV 572

Query: 672 RSKKLRSFLDG 682
           RS  LRS+ + 
Sbjct: 573 RSALLRSYFEN 583



 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 60/156 (38%), Positives = 91/156 (58%), Gaps = 9/156 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G++T EEL+  LP D  S +Q+E+  A+   M I +VD DD + +   +D
Sbjct: 11  KALIAEGKKKGFLTYEELSKALPSDYNSPDQLEEIHAIFDQMDIALVDSDDSDKKLTDDD 70

Query: 92  SLDLASS--ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                    A + S       + A RSTD PVRMYLREMG++ LL REGE+ IAK+IE G
Sbjct: 71  DDKELEFDDADDDS------SEYASRSTD-PVRMYLREMGAVPLLDREGEVVIAKKIENG 123

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              ++ SL E P+  + LI   ++L DG   L++++
Sbjct: 124 EMDVLYSLVEVPVAVEELISVGEDLEDGRIKLKDVV 159


>gi|326566650|gb|EGE16791.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 585

 Score =  346 bits (888), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 229/613 (37%), Positives = 337/613 (54%), Gaps = 60/613 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-----D 79
           D S      +I+L +++GY+T  E+N  LP     S+Q+ED + ML+++GI V      D
Sbjct: 12  DTSSSQLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDD 71

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D L  + GS+D +    +   ++  L   +    R+TD PVRMY+REMG+++LL+REGE
Sbjct: 72  DDILLSDTGSDDDI----ATDEAAAVLASVETEPGRTTD-PVRMYMREMGTVDLLTREGE 126

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I IAKRIE G   +   +   P T + ++    ++  G   + +I+            GF
Sbjct: 127 IGIAKRIEEGTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIV-----------SGF 175

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
            +G +G      E            E E D+ S     KDD          AE D     
Sbjct: 176 LNGDDGDFILNEE------------EIELDLGSPKTTDKDD----------AEED----- 208

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLK 318
             E D        +  L P      +E+   + E++ L D A     K  + S   KV  
Sbjct: 209 -GESDGTELDDTDDSSLDP------EEVRVRFEEIQRLYDVAQEALAKHGRGSEAVKVAY 261

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           ++L      + LN    D ++  + ++ + +  NE  +++L   +G +  D F +     
Sbjct: 262 DELANHFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEFKKTFPSN 321

Query: 378 ELDPHWVSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +  W+S+  K  P   +   +A     ++ ++ ++ +      + I + + +   +  
Sbjct: 322 ETNVEWLSHRIKGGPA--FAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVARQMAI 379

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKK+MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 380 GEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 439

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L
Sbjct: 440 STYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERL 499

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+++A    LRE T  V
Sbjct: 500 DMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLREATREV 559

Query: 617 LASLTPREERVLR 629
           L +LT RE +VL+
Sbjct: 560 LDNLTEREAKVLK 572


>gi|145589878|ref|YP_001156475.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048284|gb|ABP34911.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 678

 Score =  343 bits (880), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 164/279 (58%), Positives = 216/279 (77%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V +I +++ ++  I     I + E + +   +  GE  A  AK+EM  ANLRLVIS+AKK
Sbjct: 398 VPAIQELQQKLIDIQTRVVIPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKK 457

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 458 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 517

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R++  +   EP    +A K+ +P + +RK++KI KEPIS+ETPIGD
Sbjct: 518 VHMIETINKMNRISRQILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPISMETPIGD 577

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N ++P ++A+  ++R+    VL SLTPRE +VLRMRFG+ M+TDHTL
Sbjct: 578 DEDSHLGDFIEDGNTLAPAEAALHDSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTL 637

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RK++HPSRS KL++FL+
Sbjct: 638 EEVGKQFDVTRERIRQIEAKALRKMRHPSRSDKLKTFLE 676



 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 89/159 (55%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IK+   +GY+T  E+N  +  +   ++ +E  +++L+++GI V     D + L   +
Sbjct: 68  KTLIKMGMSKGYLTHGEMNDVMSDELSDADALETLISLLNDIGITVYEQAPDAETLILSD 127

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +E +     +   +   L        R+TD PVRMY+REMG+++LL+REGEI IAK+IE
Sbjct: 128 NTEAAASEEEAEEKAEAALSTVDSEFGRTTD-PVRMYMREMGTVDLLTREGEIVIAKKIE 186

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ +L   P+T   ++   D++  G   + + +D
Sbjct: 187 AGLKDMVMALAACPVTIAEIMSNVDKIASGEMEIDQFVD 225


>gi|171464016|ref|YP_001798129.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|171193554|gb|ACB44515.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 900

 Score =  343 bits (879), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 163/279 (58%), Positives = 216/279 (77%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V +I +++ ++  I     I + E + +   +  GE  A  AK+EM  ANLRLVIS+AKK
Sbjct: 620 VPAIQELQQKLIDIQKNVVIPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKK 679

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 680 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 739

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R++  +   EP    +A K+ +P + +RK++KI KEP+S+ETPIGD
Sbjct: 740 VHMIETINKMNRISRQILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPVSMETPIGD 799

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N ++P ++A+  ++R+    VL SLTPRE +VLRMRFG+ M+TDHTL
Sbjct: 800 DEDSHLGDFIEDGNTLAPAEAALHNSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTL 859

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RK++HPSRS KL++FL+
Sbjct: 860 EEVGKQFDVTRERIRQIEAKALRKMRHPSRSDKLKTFLE 898



 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 55/157 (35%), Positives = 92/157 (58%), Gaps = 5/157 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVS-SEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
           K +IK+   +GY+T  E+N  +  DE+S ++ +E  +++L+++GI V +   D E    S
Sbjct: 297 KTLIKMGMSKGYLTQGEMNDVMS-DELSDADALETLISLLNDIGITVYEQAPDAETLILS 355

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++   AS     +       DS    T DPVRMY+REMG+++LL+REGEI IAK+IEAG
Sbjct: 356 DNTAAAASEEEAEAAL--STVDSEFGRTTDPVRMYMREMGTVDLLTREGEIVIAKKIEAG 413

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              M+ +L   P+T   ++   D++  G   + + +D
Sbjct: 414 LKDMVMALAACPVTIAEILSNVDKIASGEIEIDQFVD 450


>gi|148244277|ref|YP_001218971.1| DNA-directed RNA polymerase sigma-70 factor [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326104|dbj|BAF61247.1| DNA-directed RNA polymerase sigma-70 factor [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 603

 Score =  342 bits (877), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 180/364 (49%), Positives = 252/364 (69%), Gaps = 2/364 (0%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           +++L K +  L L    ++ ++E + +   ++   E  +  +    GI R  F E     
Sbjct: 242 RQQLSKGLSDLRLAPKLVNTMIEVICNRVSQVKEQEKIIKNICLDAGINRLHFFELFSNN 301

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E + +W+   K   E   KN    + D I   +  ++    E  ++I E + +  M R+G
Sbjct: 302 ETNFNWLDTVK-LDEKIEKNLKDSK-DKIYYAQKNLQQFEEEMQLTIVELKKLNKMYRRG 359

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  A  AK +M+EANLRLVIS+AKKY NRGLQFLDLIQEGN+GLMKA +KF++  GYKFS
Sbjct: 360 DRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 419

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R  R++  K  RE + EE+A ++ 
Sbjct: 420 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREASSEELATEME 479

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P   + K+LKI KEP+S+ETP+GD++ S++GDFIED N  SP++   + +LRETT  +L
Sbjct: 480 LPEYKIIKILKIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTKESLRETTGDLL 539

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L+PRE +VL+MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSR+ KL+
Sbjct: 540 SNLSPREAKVLKMRFGINMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLQ 599

Query: 678 SFLD 681
           SFL+
Sbjct: 600 SFLE 603



 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/160 (33%), Positives = 87/160 (54%), Gaps = 8/160 (5%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD----GDDLED 85
           + +K+I + +++GY+T  E+N  LP D ++ EQ+E  V +L  + I V D     D L  
Sbjct: 11  ALQKLIMVGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDITVSDTVPDADTLVV 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G++      S+++ +++      DS    T DPVRMY+REMG ++LL +E EI IAK 
Sbjct: 71  ESGAKAQ----STSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLEQEDEIRIAKE 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IEAG   +M S+   P+           L +G   + ++I
Sbjct: 127 IEAGVFEIMQSITLYPVITDFFFKAHTRLEEGKCKMTDVI 166


>gi|91779694|ref|YP_554902.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692354|gb|ABE35552.1| Sigma 70 (RpoD) [Burkholderia xenovorans LB400]
          Length = 628

 Score =  341 bits (875), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 219/660 (33%), Positives = 352/660 (53%), Gaps = 61/660 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD----GDDLEDEE 87
           + ++KL ++RG++T  E+   LP     ++ +E  V   +++GI V D    GD L   +
Sbjct: 19  RALMKLGKERGFLTHTEIVDHLPDCVAQADAIEGIVKAFNDVGIAVRDFAPTGDALLLGD 78

Query: 88  GSEDSL--DLAS--SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            ++ S   D+A   +A+  ++ + +   +AD     P+R YLREMG+  LL+REGEIA+A
Sbjct: 79  AAQQSAPDDVAEDETATALTIAISEPGPAAD-----PMRAYLREMGATPLLTREGEIAVA 133

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           +RIEA    M+  +   P T  A++   D +  G   + +++D           GF    
Sbjct: 134 RRIEACLREMLEVIALRPATVDAILSRADRVAAGELDIDDLVD-----------GFL--- 179

Query: 204 EGHSYQKREDSSQEKERDD-VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                        E++ D+ +   +G     A  SK D       P +A      ++ DE
Sbjct: 180 -------------EQQPDEMLPAMQGATAEGAAGSKAD----SGVPTSASESAGAIEADE 222

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
              A            ++    + I    RE  +    AV G+  ++   +  ++   + 
Sbjct: 223 ARIA------------RLTAGCNAIFSQVREQLASWRAAVAGRTGQREEAQSTLVL--IA 268

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
             +G +  +   I  L   +    + I   E  +LRLA    G+ RD+F+E   G E DP
Sbjct: 269 STLGQIRFSARTIGELSADVRRAVEEIRGIERNVLRLAVNQGGMARDMFVETFVGSETDP 328

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W++ A           + C   SI   + ++  I    G+S+ E + I   +   + E 
Sbjct: 329 EWLARAAAAAPACSAALMRC-APSIHSQQEKLAQIEAREGLSLQELKWISRKMNVADREL 387

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A++ M+EANLRLV+SVAKKY   G+  LDL+QEGNIGLMKA ++F++  G+KFSTYA 
Sbjct: 388 QDARRAMIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKFSTYAT 447

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q+++R+IAD   TIR+PVHM D +H+V R A  M  +  R     E+A +L M  E
Sbjct: 448 WWIRQSVSRAIADYGRTIRVPVHMADAMHRVKRVAGEMRQETGRPARSSELAARLGMSEE 507

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR V ++T++P+SL+ PIG+E  + LG+ +ED + ++PLD+ +QA+LR      L  LT
Sbjct: 508 KVRSVQRVTRQPVSLDVPIGEEADTTLGEMVEDSSTLAPLDALLQADLRVAIDAALGVLT 567

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +V+++RFG+   ++HTLEE+G QF VTRER+RQI+ KA++KL+H      L+++LD
Sbjct: 568 PREAKVIKLRFGVDAVSEHTLEELGDQFDVTRERVRQIQNKALQKLRHSDGISTLKNYLD 627


>gi|149921032|ref|ZP_01909492.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149818164|gb|EDM77620.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 547

 Score =  341 bits (874), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 161/269 (59%), Positives = 209/269 (77%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+ +  ETG+S      +   + K   E   AK E+VEANLRLV+S+AKKYTNRGLQFLD
Sbjct: 278 IRQVEQETGVSADNLVALYDSLTKARREREAAKAELVEANLRLVVSIAKKYTNRGLQFLD 337

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I+DQ+ TIR+PVHM + I+K+
Sbjct: 338 LIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAISDQARTIRVPVHMIESINKL 397

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +RT R++  +  REPT +EIA+K+ MPVE VR +L+I KEPISLETP+G++  S LGD I
Sbjct: 398 IRTTRQLVQEFGREPTHQEIAEKMNMPVEKVRSILRIAKEPISLETPLGEDGDSSLGDLI 457

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDKNA+ P    ++ +L + T R LASLTPREE++LR+RFGIG  +DHTLEEVG+ F VT
Sbjct: 458 EDKNALDPGSGVVERHLGDETRRALASLTPREEKILRLRFGIGEASDHTLEEVGRDFSVT 517

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+ KL+   R+K+LR F++
Sbjct: 518 RERIRQIEAKALSKLRKADRAKQLREFVE 546


>gi|9082209|gb|AAF82776.1|AF273254_1 RNA polymerase sigma factor [Coxiella burnetii]
          Length = 410

 Score =  340 bits (872), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 184/366 (50%), Positives = 242/366 (66%), Gaps = 10/366 (2%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI-----KRDVFLERHQ 375
           L +L  +  L+  + + L  QL    +R++       RL  SY +      R  F+    
Sbjct: 47  LAELFSTFKLSIKQFNRLTGQL----RRMLRAARAQERLIMSYCVVKAKTPRKKFIASFP 102

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             E +  W+   K+  + + K       + I + +  +  +  +  ++I E + I   V 
Sbjct: 103 HNETNMKWLEQYKNENKEQAKRLEKYSKE-IYRAQRNLAQLEEQNNLNIQEIKEINRRVA 161

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 162 IGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 221

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E TPEE+ ++
Sbjct: 222 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGRR 281

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D A  A L E T R
Sbjct: 282 MDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATRR 341

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
                 P   +VLRMRFGI MNTDHTLEEVG    VTRERIRQIEAKA+RKL+HPSR++K
Sbjct: 342 NFVYAYPARSQVLRMRFGIDMNTDHTLEEVGNNSDVTRERIRQIEAKALRKLRHPSRAEK 401

Query: 676 LRSFLD 681
           L SF++
Sbjct: 402 LHSFIE 407


>gi|193884351|dbj|BAG54997.1| Sigma70 [Ralstonia solanacearum]
          Length = 758

 Score =  340 bits (872), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 169/314 (53%), Positives = 227/314 (72%), Gaps = 3/314 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 437 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQARVVL 494

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 495 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 554

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 555 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 614

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EP P  +A+K+ MP + +RK+ KI KEPIS+ETPIGD+D SHLGDFIED N ++P +
Sbjct: 615 TGNEPDPATLAEKMEMPEDKIRKIRKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAE 674

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 675 AALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 734

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL    RS +L
Sbjct: 735 ALRKLCLLIRSGRL 748



 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 92/164 (56%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V +      +    +
Sbjct: 142 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYE------QAPDAE 195

Query: 92  SLDLASSASNSSVFLQKRK---------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +L L  +A + +   +  +         DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 196 TLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 255

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIEAG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 256 AKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 299


>gi|319941927|ref|ZP_08016248.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319804580|gb|EFW01450.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 917

 Score =  338 bits (866), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 160/263 (60%), Positives = 205/263 (77%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E+ ++++E       +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 651 ESHMTVAELLDTYKQMATGESKARNAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 710

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+++ R  R+
Sbjct: 711 VGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINRMNRITRQ 770

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
              +   EP    +A+ + MP + + K++KI KEPIS+ETPIGD+D SHLGDF+ED   V
Sbjct: 771 ELQETGVEPDSRRLAELMEMPEDKILKIMKIAKEPISMETPIGDDDDSHLGDFLEDTQTV 830

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++   A+L +T  +VL SL+PRE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQ
Sbjct: 831 APAEAVQNASLSDTVKQVLDSLSPREAKVLRMRFGIEMQSDHTLEEVGKQFDVTRERIRQ 890

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IE KA+RKL+HPSR+ KL+SFLD
Sbjct: 891 IETKALRKLRHPSRADKLKSFLD 913



 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 89/157 (56%), Gaps = 4/157 (2%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE---EGS 89
           K+I L ++RGYVT  E+N  +P   +  + +E  V +L N+ I V +    E++   +G 
Sbjct: 325 KLISLGKERGYVTYSEINDNIPNTLLDEDAIETIVNILGNLNIAVHEVAPDEEQLLIQGG 384

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            + +    + + +   L   +    R+TD PVR+Y+REMGS+ELLSR+ EI I+KRIE G
Sbjct: 385 AEGVSDEDAEAEAEAALSTVESEFGRTTD-PVRIYMREMGSVELLSRQDEIEISKRIEDG 443

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              M+ ++   P+T   ++   + +  G T + E++D
Sbjct: 444 LKHMVLAIARCPVTVHEILESAERIRSGETPIDEVVD 480


>gi|313673328|ref|YP_004051439.1| RNA polymerase, sigma 70 subunit, rpod [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312940084|gb|ADR19276.1| RNA polymerase, sigma 70 subunit, RpoD [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 601

 Score =  337 bits (865), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 169/303 (55%), Positives = 227/303 (74%), Gaps = 12/303 (3%)

Query: 389 DFPEGEWKNFVACEVDSILK--IRNEI---KSISVET-------GISISEFRHIVSMVRK 436
           D+   + K   ACEV  + +  I+N I   KSI ++        G S SE   +  M+  
Sbjct: 297 DYIHLDPKKLEACEVKHLSQRDIQNLIAKFKSIQLKAQKNIKLLGYSRSEVDLLHEMLTN 356

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
              +    K +++++NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 357 NMTKTERYKTKLIQSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYQRGYKF 416

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K+++ +R++   + REPTPEEIA+K+
Sbjct: 417 STYATWWIRQAITRAIADQARTIRIPVHMIETINKMMKISRQLQVDLGREPTPEEIAEKM 476

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +PVE V+KVL+I KEP+SLETPIG+++ S LGDFIEDK + +PLD  +   L E T ++
Sbjct: 477 DVPVEKVKKVLRIAKEPVSLETPIGEDEDSSLGDFIEDKKSKNPLDEVVYLKLSEHTKQI 536

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PRE  VLR+RFGI  ++DHTLEEVGK+F VTRERIRQIEAKA+RKL+HP+RS+ L
Sbjct: 537 LDTLSPREASVLRLRFGIDCSSDHTLEEVGKKFNVTRERIRQIEAKALRKLRHPTRSRIL 596

Query: 677 RSF 679
           ++F
Sbjct: 597 KTF 599



 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 74/279 (26%), Positives = 134/279 (48%), Gaps = 28/279 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD-------- 82
            K +I L +++G++T +E+N  +P D +  E +E+ +  L  + I+V+D  +        
Sbjct: 10  LKPLIALGKEKGFLTFDEINEMIPEDVLLPEILEEILVRLKQLKIDVIDNRNSAAPVIAA 69

Query: 83  --LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             +E+EE   D ++       S   +         S DDPV++YLREMG+I LLSRE E 
Sbjct: 70  PIIEEEEMELDDVE-------SEEIIMDENLEEGLSFDDPVKLYLREMGNIPLLSREEET 122

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            +AK IE G+  ++ +        +  +   +++ +G   L++++D E  I  E +    
Sbjct: 123 EVAKEIENGQREVIINTLSFIYAAEKFLTIVEDIKNGNFKLKDLVDFED-INVEDEIDID 181

Query: 201 HGTEGHSYQKREDSSQEKERDD----VQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
              E    ++ +D    K RD+    + +T   I  A K+ K  R+      E  E  ++
Sbjct: 182 EVDE-EELKRLKDERDLKIRDEYLSILDDTCLKISEAIKICKKIRTM--KKQERIEATKK 238

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCAL-DEIAEVYREL 294
            ++E  DD A  L  ++ ++   ++C L  EI+  Y EL
Sbjct: 239 QMNEILDDVARQL--LKIKVNYSLICNLAKEISTTYEEL 275


>gi|157826499|ref|YP_001495563.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801803|gb|ABV78526.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 514

 Score =  337 bits (864), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 199/539 (36%), Positives = 312/539 (57%), Gaps = 66/539 (12%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--------DDLEDEEGSEDSL 93
           G VT  ++N  LP D  S E+++  +   S   ++++D         DD+E EEG + S 
Sbjct: 24  GSVTYNDINRALP-DGTSVEEIDKVMFRFSEAEVDILDTNEDDAIKIDDIEMEEGFKIST 82

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           ++     + +            +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  +
Sbjct: 83  NIDHEPEDETEEENIG------TTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTL 136

Query: 154 MASLCESPLTFQALIIWR-DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           +A+LC SP+       W  D +N+   LLR++IDLE+           H           
Sbjct: 137 IAALCRSPIAMDKFRKWYADLVNENNMLLRDLIDLES--------NMMHD---------- 178

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
                   D+  E+E D  S                 + E +E++ D D +++  ++S +
Sbjct: 179 --------DETSESEDDHNS-----------------DHEEEEQDHDHDHEENILSMSKV 213

Query: 273 EDQLRPKVMCALDEIAEVYREL-----RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           E Q+ P ++  + +IA +  EL     +S + +A  G K  ++S K     E L+  V  
Sbjct: 214 ETQILPNIIERMKKIAFICEELLIETKKSFEKSA--GPKILQNSKKYNDNLELLISEVSE 271

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           +  N  R + ++ ++Y I++ +++ E   L+LA+ YGI R  FL+ + G  ++  W    
Sbjct: 272 IHFNSKRTEEILSEMYGINRDLINKETAFLKLAEKYGITRQNFLDEYIGAVINAAWKEKM 331

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
               +  WK  +  E D I ++  E+ +I + TG+ +++F+ +V+ ++K E +   AKK+
Sbjct: 332 LKNKKAGWKELLTKESDYIDQMIAELSAIEINTGLLVNDFKKLVNTIQKSERQTLQAKKD 391

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 392 MIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 451

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           ITR+IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPTP EIA +L+MP++ VRKV
Sbjct: 452 ITRAIADQARTIRIPVHMIETINKIIRTSRQMLNELGYEPTPAEIAARLSMPIDKVRKV 510


>gi|241896072|ref|ZP_04783368.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
 gi|241870672|gb|EER74423.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
          Length = 378

 Score =  335 bits (859), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 184/358 (51%), Positives = 232/358 (64%), Gaps = 23/358 (6%)

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           +V  +SLN  +ID L +Q+      ++   GE    A          LE  + + L    
Sbjct: 44  VVKPMSLNADQIDDLYDQIESAGISVVDENGEPTARA----------LENKKTK-LSAKE 92

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +  A D P G   N      D +     EI  +S+ TG         VS+  + E     
Sbjct: 93  LKQAADAPTGMKIN------DPVRMYLKEIGRVSLLTG------DEEVSLAERIEAGDET 140

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 141 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 200

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + REPTPEEI  ++ +  E V
Sbjct: 201 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRNLLQDLGREPTPEEIGAEMDVATEKV 260

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIED  AVSP DSA    L+E    VL +LT R
Sbjct: 261 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYQMLKEQLESVLDTLTDR 320

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+LR FLD
Sbjct: 321 EENVLRLRFGLEDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLRDFLD 378



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/116 (32%), Positives = 65/116 (56%), Gaps = 12/116 (10%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
           A + P  ++++Q++D    + + GI+VVD      E G   +  L +  +  S   ++ K
Sbjct: 43  AVVKPMSLNADQIDDLYDQIESAGISVVD------ENGEPTARALENKKTKLSA--KELK 94

Query: 111 DSADRST----DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +AD  T    +DPVRMYL+E+G + LL+ + E+++A+RIEAG       L E+ L
Sbjct: 95  QAADAPTGMKINDPVRMYLKEIGRVSLLTGDEEVSLAERIEAGDETAKQELAEANL 150


>gi|213162104|ref|ZP_03347814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 225

 Score =  335 bits (858), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 161/224 (71%), Positives = 189/224 (84%)

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 1   SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 60

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+E
Sbjct: 61  TIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISME 120

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MN
Sbjct: 121 TPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMN 180

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 181 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 224


>gi|325263837|ref|ZP_08130570.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030875|gb|EGB92157.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 369

 Score =  333 bits (855), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 155/238 (65%), Positives = 198/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 132 AKKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWW 191

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK+L MPVE V
Sbjct: 192 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAKELDMPVERV 251

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 252 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 311

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 312 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 369



 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 45/140 (32%), Positives = 74/140 (52%), Gaps = 12/140 (8%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
           D+  K+++ L +++   + ++E+N F    E+ +EQME     L +  I+V+    D DD
Sbjct: 9   DERLKELVVLGKKKKSILELQEINDFFNDMELDAEQMEKVFDHLESNNIDVLRISGDEDD 68

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++ E    D  ++     + SV      D    S +DPVRMYL+E+G + LLS E EI +
Sbjct: 69  VDVEVIITDEEEVDMENIDLSV-----PDGI--SIEDPVRMYLKEIGKVPLLSAEREIEL 121

Query: 143 AKRIEAGRAMMMASLCESPL 162
           A+R+E G       L E+ L
Sbjct: 122 AQRMEDGDEDAKKELAEANL 141


>gi|291287657|ref|YP_003504473.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290884817|gb|ADD68517.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 626

 Score =  333 bits (854), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 154/243 (63%), Positives = 201/243 (82%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE E   AK +++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 382 GENETEKAKSKLIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYKRGYKF 441

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K+++  R++   + REPTPEEI+ K+
Sbjct: 442 STYATWWIRQAITRAIADQARTIRIPVHMIETINKMMKITRQLQQDMGREPTPEEISSKM 501

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +PVE ++KV+KI KEP+SLETPIG+++ S LGDFIEDK+A +P +      L+E T ++
Sbjct: 502 DIPVEKIKKVMKIAKEPVSLETPIGEDEDSSLGDFIEDKSAKNPSEEVTYLKLKEHTKQI 561

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+ RE  VL++RFGI  ++DHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ L
Sbjct: 562 LETLSHREASVLKLRFGIECDSDHTLEEVGKQFNVTRERIRQIEAKALRKLRHPTRSRIL 621

Query: 677 RSF 679
           ++F
Sbjct: 622 KTF 624



 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 53/150 (35%), Positives = 92/150 (61%), Gaps = 6/150 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L +++G++T +E+N  LP D +S+E +++ + +L+ + I+V+D     D+ G   
Sbjct: 13  KSIIALGKEKGFLTFDEINENLPDDILSTELIDEIMMLLAQLKIDVIDSK--VDKPGLYS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           + D      + S  L++ ++S   STDDPVR+YL+EMG+I LL+RE EI +AK IE G+ 
Sbjct: 71  ADDDDDDEDSIS-LLKEVEESI--STDDPVRLYLKEMGNIALLNREEEIEVAKEIEEGQR 127

Query: 152 MMMASLCESPLTFQALI-IWRDELNDGTTL 180
            ++ ++   P T   ++ I R+  ND   L
Sbjct: 128 KVVRAVLLYPNTAMKIMDIARNIRNDSMRL 157


>gi|331701385|ref|YP_004398344.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
 gi|329128728|gb|AEB73281.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
          Length = 414

 Score =  332 bits (851), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 167/303 (55%), Positives = 218/303 (71%), Gaps = 4/303 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGE 438
           DP  +  AK   + E  +  A    + +KI + ++    E G +S+      +S+ ++ E
Sbjct: 115 DPRAIGAAKKVTKKELSDVSAP---TGVKINDPVRMYLKEIGRVSLLSADQEISLAKRIE 171

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFST
Sbjct: 172 AGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFST 231

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M
Sbjct: 232 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDM 291

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL 
Sbjct: 292 PTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLD 351

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ 
Sbjct: 352 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKD 411

Query: 679 FLD 681
           FLD
Sbjct: 412 FLD 414



 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 47/149 (31%), Positives = 73/149 (48%), Gaps = 11/149 (7%)

Query: 28  DDSWKK----MIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           D  +KK    ++K  +  G++T +EL   +  P  +S + ME  +  + + GI+VVD   
Sbjct: 53  DKPYKKEFDAIVKANKPIGHITYDELEKKIEKPYSLSEKDMEGLLESIEDSGISVVD--- 109

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
              E G  D   + ++   +   L           +DPVRMYL+E+G + LLS + EI++
Sbjct: 110 ---ENGDPDPRAIGAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADQEISL 166

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWR 171
           AKRIEAG       L E+ L     I  R
Sbjct: 167 AKRIEAGDEEAKQELAEANLRLVVSIAKR 195


>gi|116619924|ref|YP_822080.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223086|gb|ABJ81795.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 518

 Score =  331 bits (849), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 150/272 (55%), Positives = 215/272 (79%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++ EIK   +  G ++ E +H ++++R GE EA  AKK++VEANLRLV+SVAKKY NRGL
Sbjct: 244 LKREIKKREIAAGATLPELKHSLTVIRHGEAEAERAKKDLVEANLRLVVSVAKKYVNRGL 303

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGNIGLM+AA+KF++  GYKFSTYA WW++QAITR+IADQS TIRIPVHM + 
Sbjct: 304 HLLDLIQEGNIGLMRAADKFEYRRGYKFSTYATWWIRQAITRAIADQSRTIRIPVHMNES 363

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K +R  R +  ++ R PT +EI +++ +PVE V+K+  I+++P+SLETP+G +  S L
Sbjct: 364 MNKFLRATRELEKELGRTPTNDEIGRRMDIPVEKVQKLKTISRDPVSLETPVGRDGESAL 423

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD IED+   SP+D+ I++N+R+ T  +L +L+P+EE+V+RMRFGIG   +HTLEE+G++
Sbjct: 424 GDLIEDRWVGSPVDAVIESNVRDETAGILKTLSPKEEKVIRMRFGIGCEREHTLEEIGQE 483

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+R+L+ P R+++LR+ +
Sbjct: 484 FDVTRERIRQIEAKALRQLRAPERARRLRALM 515



 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 17/140 (12%)

Query: 53  LPPDEVS--SEQMEDTVAMLSN---MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ 107
           +P  EVS   +Q ED   +  N   +G++  D     D E + ++  L  +    S++  
Sbjct: 1   MPVGEVSLKVDQFEDQF-LAENPEALGLSFEDDPKFFDPEAAHEADFLHPAPVEESIY-- 57

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
                    TDDPVR+YLREMG++ LL+REGE+ +A+R+E G+  M  ++  S L  + +
Sbjct: 58  ---------TDDPVRVYLREMGAVPLLTREGEVDLARRMERGKLRMQKAISRSALVQRVV 108

Query: 168 IIWRDELNDGTTLLREIIDL 187
           +   D+L      +  ++DL
Sbjct: 109 VDVADQLKRANIEIESVVDL 128


>gi|332653408|ref|ZP_08419153.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
 gi|332518554|gb|EGJ48157.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
          Length = 446

 Score =  331 bits (849), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 199/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 209 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 268

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+KV+R +R++  ++  +P+PEEIA++++MPVE V
Sbjct: 269 IRQAITRAIADQARTIRIPVHMVETINKVIRVSRQLLQELGHDPSPEEIAEEMSMPVERV 328

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D++A  P ++A    L+E    VL++LTPR
Sbjct: 329 REILKIAQEPVSLETPIGEEEDSHLGDFIPDEDASEPAEAASFTLLKEQLVEVLSTLTPR 388

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VL++RFGI      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 389 EEKVLKLRFGIEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLN 446



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 63/117 (53%), Gaps = 2/117 (1%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I+  +++G ++  EL   L   ++ SEQM+    +L N+GI+ V G+D   E   +   
Sbjct: 59  LIERGKKKGNLSSTELMDVLEDMDLESEQMDKIYDVLENLGIDTV-GEDYIPELPDDAEP 117

Query: 94  DLASSASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            L +    S   +       D   TDDPVRMYL+E+G + LLS + EI +A+ + AG
Sbjct: 118 PLEAMEEISEEEMVDPNSMVDSFGTDDPVRMYLKEIGKVNLLSSDEEIELAQAMGAG 174


>gi|154502790|ref|ZP_02039850.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
 gi|153796673|gb|EDN79093.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
          Length = 371

 Score =  331 bits (848), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 154/238 (64%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 134 AKKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK+L MPVE V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAKELDMPVERV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 254 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 314 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 371



 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 38/124 (30%), Positives = 63/124 (50%), Gaps = 1/124 (0%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS 98
           +++  + I+E+N F    E+ +EQME     L    I+V+     +D +   D + +A  
Sbjct: 21  KKKSILEIQEINDFFADMELEAEQMEKVFEYLEANNIDVLRISSDDDLDVDMDVI-MAEE 79

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A +  +           S +DPVRMYL+E+G + LLS + EI +A+R+E G       L 
Sbjct: 80  ADDVDMENIDLSVPDGVSIEDPVRMYLKEIGKVPLLSADREIELAQRMEEGDEDAKKELA 139

Query: 159 ESPL 162
           E+ L
Sbjct: 140 EANL 143


>gi|317500513|ref|ZP_07958736.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089388|ref|ZP_08338287.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316898102|gb|EFV20150.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404756|gb|EGG84294.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 370

 Score =  331 bits (848), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 154/238 (64%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 133 AKKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK+L MPVE V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAKELDMPVERV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 253 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 41/136 (30%), Positives = 64/136 (47%), Gaps = 26/136 (19%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL------------EDE 86
           +++  + ++E+N F    E+S+EQME     L    I+V+                 E+E
Sbjct: 21  KKKSILDVQEINDFFADMELSAEQMEKVFEYLEGHNIDVLRITADTDDDVDIDNMIAEEE 80

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E   +++DL+     S               +DPVRMYL+E+G + LLS E EI +AKR+
Sbjct: 81  EVDMENIDLSVPEGVS--------------IEDPVRMYLKEIGKVPLLSAEREIELAKRM 126

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 127 EEGDEDAKKELAEANL 142


>gi|153816193|ref|ZP_01968861.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
 gi|145846528|gb|EDK23446.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
          Length = 383

 Score =  330 bits (845), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 154/238 (64%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 146 AKKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWW 205

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK+L MPVE V
Sbjct: 206 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAKELDMPVERV 265

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 266 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 325

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 326 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 383



 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 38/123 (30%), Positives = 60/123 (48%), Gaps = 26/123 (21%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL------------EDE 86
           +++  + ++E+N F    E+S+EQME     L    I+V+                 E+E
Sbjct: 34  KKKSILDVQEINDFFADMELSAEQMEKVFEYLEGHNIDVLRITADTDDDVDIDNMIAEEE 93

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E   +++DL+     S               +DPVRMYL+E+G + LLS E EI +AKR+
Sbjct: 94  EVDMENIDLSVPEGVS--------------IEDPVRMYLKEIGKVPLLSAEREIELAKRM 139

Query: 147 EAG 149
           E G
Sbjct: 140 EEG 142


>gi|332678201|gb|AEE87330.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida Fx1]
          Length = 577

 Score =  330 bits (845), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 182/369 (49%), Positives = 246/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK + +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYTKIVKELDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D    + EE  E  +  A
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTP-QIEEDDERKVSEA 75

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 76  NL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|332638574|ref|ZP_08417437.1| RNA polymerase sigma factor [Weissella cibaria KACC 11862]
          Length = 377

 Score =  329 bits (844), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 185/370 (50%), Positives = 238/370 (64%), Gaps = 26/370 (7%)

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
           +K   L++ LVK    + LN  +ID L E++      I+  +GE    A          L
Sbjct: 34  IKENALQDALVK---PMRLNADQIDELYEKIESAGISIVDEKGEPTARA----------L 80

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           E  + + L    +  A D P G   N      D +     EI  +S+ TG         V
Sbjct: 81  ENKKTK-LSEKELKQAADAPTGMKIN------DPVRMYLKEIGRVSLLTG------DEEV 127

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++  + E     AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+ 
Sbjct: 128 ALAERIEQGDDTAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYR 187

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + REPTPEE
Sbjct: 188 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRNLLQDLGREPTPEE 247

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           I  ++ +  + VR +LKI +EP+SLETPIG+ED SHLGDFIED  A+SP DSA    L+E
Sbjct: 248 IGAEMDIVTDKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAISPADSAAYQMLKE 307

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPS
Sbjct: 308 QLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 367

Query: 672 RSKKLRSFLD 681
           RSK+LR FLD
Sbjct: 368 RSKQLRDFLD 377



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 66/117 (56%), Gaps = 12/117 (10%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           +A + P  ++++Q+++    + + GI++VD      E+G   +  L +  +  S   ++ 
Sbjct: 41  DALVKPMRLNADQIDELYEKIESAGISIVD------EKGEPTARALENKKTKLSE--KEL 92

Query: 110 KDSADRST----DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           K +AD  T    +DPVRMYL+E+G + LL+ + E+A+A+RIE G       L E+ L
Sbjct: 93  KQAADAPTGMKINDPVRMYLKEIGRVSLLTGDEEVALAERIEQGDDTAKQELAEANL 149


>gi|134301933|ref|YP_001121902.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|254369360|ref|ZP_04985372.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
 gi|254372870|ref|ZP_04988359.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. novicida GA99-3549]
 gi|134049710|gb|ABO46781.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151570597|gb|EDN36251.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           novicida GA99-3549]
 gi|157122310|gb|EDO66450.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 577

 Score =  329 bits (844), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 182/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYTKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D    + EE  E  +  A
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTP-QIEEDDERKVSEA 75

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 76  NL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|118497505|ref|YP_898555.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           novicida U112]
 gi|195536199|ref|ZP_03079206.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208779304|ref|ZP_03246650.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
 gi|118423411|gb|ABK89801.1| RNA polymerase sigma-70 factor [Francisella novicida U112]
 gi|194372676|gb|EDX27387.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208745104|gb|EDZ91402.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
          Length = 577

 Score =  329 bits (844), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 182/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYTKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D    + EE  E  +  A
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTP-QIEEDDERKVSEA 75

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 76  NL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|157273328|gb|ABV27227.1| sigma 38 RpoS [Candidatus Chloracidobacterium thermophilum]
          Length = 549

 Score =  329 bits (844), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 155/245 (63%), Positives = 199/245 (81%), Gaps = 3/245 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           EA  A++EM+EANLRLV+S+AK Y NR  GLQF DLIQEGNIGLM+A EKFD+  GYKFS
Sbjct: 302 EAEKARREMIEANLRLVVSIAKNYINRSRGLQFSDLIQEGNIGLMRAVEKFDYRRGYKFS 361

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QA+TR+IADQ  TIR+PVHM + I+K+VRTAR M  ++ REPT EE+A++  
Sbjct: 362 TYATWWIRQAVTRAIADQGRTIRVPVHMVETINKIVRTARLMVQELGREPTHEELAQRTD 421

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PV  VR+ LKI +EPISLETPIGD+  S+LG FIED+N+++P +  +   LRE T  VL
Sbjct: 422 LPVAKVRQALKIAQEPISLETPIGDDGESNLGSFIEDRNSLNPAEMIVGKGLREATLEVL 481

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++LTPREE++L+MRFG+ G   + TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS+KL
Sbjct: 482 STLTPREEQILKMRFGLDGDGQERTLEEVGRYFHVTRERIRQIEAKALRKLRHPSRSRKL 541

Query: 677 RSFLD 681
           ++F D
Sbjct: 542 KTFYD 546



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
           +DRS D  + +YLREM ++ LL+RE E+ IAKRIE GR  +  +   S +  + L    +
Sbjct: 69  SDRSLD-AMTLYLREMSNVALLTREDEVNIAKRIERGRRRLYKAHSRSLIVAEQLEELAE 127

Query: 173 ELNDGTTLLREIID 186
           +L +    +R++ID
Sbjct: 128 QLKERKISIRQVID 141


>gi|254374325|ref|ZP_04989807.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
 gi|151572045|gb|EDN37699.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
          Length = 577

 Score =  329 bits (844), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 182/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYTKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKI 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D    + EE  E  +  A
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTP-QIEEDDERKVSEA 75

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 76  NL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|58698250|ref|ZP_00373169.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535222|gb|EAL59302.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 270

 Score =  329 bits (844), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 157/259 (60%), Positives = 206/259 (79%), Gaps = 1/259 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           ++ EF+ ++  ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLM
Sbjct: 12  NVQEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLM 71

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KFD+  GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M+++
Sbjct: 72  KAVDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHE 131

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REPT EE++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D
Sbjct: 132 MGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPED 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEA 661
           +AI A+LR  TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEA
Sbjct: 192 AAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEA 251

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKLKHPSR++KLR F 
Sbjct: 252 KALRKLKHPSRARKLRGFF 270


>gi|89256388|ref|YP_513750.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314834|ref|YP_763557.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502477|ref|YP_001428542.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167010407|ref|ZP_02275338.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367725|ref|ZP_04983746.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290953811|ref|ZP_06558432.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312822|ref|ZP_06803554.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144219|emb|CAJ79489.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129733|gb|ABI82920.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. holarctica OSU18]
 gi|134253536|gb|EBA52630.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156253080|gb|ABU61586.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 577

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 182/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYTKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMSKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D    + EE  E  +  A
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTP-QIEEDDERKVSEA 75

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 76  NL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|291550178|emb|CBL26440.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 373

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 136 AKKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK++ MPVE V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAKEMDMPVERV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 256 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 316 EQKVLRLRFGMNDGRARTLEEVGREFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 373



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 46/144 (31%), Positives = 73/144 (50%), Gaps = 18/144 (12%)

Query: 29  DSWKKMIKLARQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGD---- 81
           D  K ++ L +++  +  ++E+N F    E++++QME     L    I+V  + GD    
Sbjct: 10  DRLKDLVALGKKKKSILDVQEINDFFNDMELNADQMEKVFDYLEANNIDVLRISGDTPDE 69

Query: 82  ---DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
              DL+D   SE+  D+     + SV           S +DPVRMYL+E+G + LLS E 
Sbjct: 70  VDVDLDDIIISEED-DVDMENIDLSV-------PEGVSIEDPVRMYLKEIGKVPLLSAER 121

Query: 139 EIAIAKRIEAGRAMMMASLCESPL 162
           EI +A+R+E G       L E+ L
Sbjct: 122 EIELAQRMEEGDEEAKKELAEANL 145


>gi|28378605|ref|NP_785497.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum WCFS1]
 gi|300768133|ref|ZP_07078038.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308180761|ref|YP_003924889.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|28271441|emb|CAD64346.1| DNA-directed RNA polymerase, sigma factor 42 [Lactobacillus
           plantarum WCFS1]
 gi|300494197|gb|EFK29360.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308046252|gb|ADN98795.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 368

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 154/238 (64%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 131 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP E V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D+A    L+E    VL +LT R
Sbjct: 251 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADAAAYELLKEQLEGVLDTLTDR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 311 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 71/136 (52%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +IK  ++ G +  +EL +    P ++ +  ++  +  + + GI+VVD      E
Sbjct: 11  DKAVKALIKEYKKTGSIQYDELSDKLAAPYKLDASGIDKLLQKVEDAGISVVD------E 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G  D+  + S    S   L     ++    +DPVRMYL+E+G ++LL+ + E+A+A RI
Sbjct: 65  KGDPDARAVKSVKKVSKKELSDAGSASGIKINDPVRMYLKEIGRVDLLTADEEVALALRI 124

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 125 EQGDESAKQELAEANL 140


>gi|254556820|ref|YP_003063237.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
 gi|254045747|gb|ACT62540.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
          Length = 368

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 154/238 (64%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 131 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP E V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D+A    L+E    VL +LT R
Sbjct: 251 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADAAAYELLKEQLEGVLDTLTNR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 311 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 71/136 (52%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +IK  ++ G +  +EL +    P ++ +  ++  +  + + GI+VVD      E
Sbjct: 11  DKAVKALIKEYKKTGSIQYDELSDKLAAPYKLDASGIDKLLQKVEDAGISVVD------E 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G  D+  + S    S   L     ++    +DPVRMYL+E+G ++LL+ + E+A+A RI
Sbjct: 65  KGDPDARAVKSVKKVSKKELSDAGSASGIKINDPVRMYLKEIGRVDLLTADEEVALALRI 124

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 125 EQGDESAKQELAEANL 140


>gi|197301814|ref|ZP_03166884.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
 gi|197299254|gb|EDY33784.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
          Length = 372

 Score =  328 bits (842), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 135 AKKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK++ MPVE V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAKEMDMPVERV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 255 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 315 EQKVLRLRFGMNDGRARTLEEVGREFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 372



 Score = 45.8 bits (107), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS E EI +A+R+E G       L E+ L
Sbjct: 98  SIEDPVRMYLKEIGKVPLLSAEREIELAQRMEEGDEEAKKELAEANL 144


>gi|295110289|emb|CBL24242.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus obeum A2-162]
          Length = 376

 Score =  328 bits (842), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 139 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA+++ MPVE V
Sbjct: 199 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAEEMKMPVERV 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 259 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLIEVLGTLTER 318

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 319 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 376



 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 70/135 (51%), Gaps = 5/135 (3%)

Query: 33  KMIKLARQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDDLEDEEGS 89
           ++++LA+++  V   +E++ F     +  EQME  +  L   G++V  + G+D E     
Sbjct: 14  ELLELAKKKKNVLEYQEISDFFKDQPLEVEQMEKVLDFLEASGVDVLRISGNDEELILDV 73

Query: 90  EDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +D  D+        + L K   S     S +DPVRMYL+E+G + LL+ + EI +AKR+E
Sbjct: 74  DDDADIEKMDDEEEIELDKIDLSVPEGVSIEDPVRMYLKEIGKVSLLTADEEIELAKRME 133

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 134 QGDEEAKKRLAEANL 148


>gi|328465879|gb|EGF37062.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus MTCC
           5463]
          Length = 370

 Score =  328 bits (842), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 153/238 (64%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+CLG+KFSTYA WW
Sbjct: 133 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP   V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPTNKV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +LT R
Sbjct: 253 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+D
Sbjct: 313 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFMD 370



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 66/151 (43%), Gaps = 16/151 (10%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVERAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + L++ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 ---------DELNDGTTLLREIID-LEACIG 192
                    D + +G   L + +D  + C+G
Sbjct: 152 YVGRGMSFLDLIQEGNMGLMKAVDKFDYCLG 182


>gi|227510293|ref|ZP_03940342.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
 gi|227524444|ref|ZP_03954493.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227088403|gb|EEI23715.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227189945|gb|EEI70012.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
          Length = 389

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 165/303 (54%), Positives = 218/303 (71%), Gaps = 4/303 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGE 438
           DP  +  AK   + E  +  A    + +KI + ++    E G +S+      +++ ++ E
Sbjct: 90  DPRAIDAAKKVTKKELSDVSAP---TGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIE 146

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFST
Sbjct: 147 SGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFST 206

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M
Sbjct: 207 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDM 266

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL 
Sbjct: 267 PTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLD 326

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ 
Sbjct: 327 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKD 386

Query: 679 FLD 681
           FL+
Sbjct: 387 FLE 389



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 41/142 (28%), Positives = 71/142 (50%), Gaps = 7/142 (4%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + +++K  +  G++T +EL   +  P  +  ++ME+ +  + + GI+VVD      + G 
Sbjct: 35  FDQIVKDNKPIGHITYDELQKKIEEPFSLDKKEMEELLENIEDSGISVVD------DNGD 88

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D   + ++   +   L           +DPVRMYL+E+G + LLS + EI +AKRIE+G
Sbjct: 89  PDPRAIDAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIESG 148

Query: 150 RAMMMASLCESPLTFQALIIWR 171
                  L E+ L     I  R
Sbjct: 149 DEEAKQELAEANLRLVVSIAKR 170


>gi|187931644|ref|YP_001891628.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712553|gb|ACD30850.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 577

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 181/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LR+  +     R  F++ 
Sbjct: 216 KKLYTKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRVCVERSKTPRQEFIKV 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 45/136 (33%), Positives = 69/136 (50%), Gaps = 22/136 (16%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDL--EDEEG--SEDS 92
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D      ED+E   SED+
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEEDDERKVSEDN 76

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           LD                      T DP+RMY+REMG ++LL ++GE  IA RIE G   
Sbjct: 77  LD-----------------DLKGKTSDPIRMYMREMGIVDLLDKKGETDIAVRIEEGTTE 119

Query: 153 MMASLCESPLTFQALI 168
           + +++   P+  +  I
Sbjct: 120 VFSTILSYPIVIKTYI 135


>gi|260893571|ref|YP_003239668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
 gi|260865712|gb|ACX52818.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
          Length = 369

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW
Sbjct: 132 AKRRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWW 191

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REPTPEEIA+K+ +  E V
Sbjct: 192 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLVQELGREPTPEEIAEKMGISPEKV 251

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++K+ +EP+SLETPIG+E+ SHLGDFIED+ A +P + A  A LRE    VL SLTPR
Sbjct: 252 REIMKVAQEPVSLETPIGEEEDSHLGDFIEDQEAQAPAEEASYALLREQLNEVLQSLTPR 311

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL+HPSRSKKL+ +L+
Sbjct: 312 EQKVLRLRFGLDDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLE 369



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 42/140 (30%), Positives = 68/140 (48%), Gaps = 21/140 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-------DGDDLE 84
           +++I+  R+ G +T  E+   L   +++ EQ+++    L+  GI+VV       +G+  E
Sbjct: 18  EQLIEKGRKTGVLTYAEIMDDLQGMDLTPEQIDEIYERLAAEGIDVVPEAQDLGEGELKE 77

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +  G E+  +L                      DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 78  ERLGGEEETELGIPEGVE--------------IDDPVRMYLKEIGRIPLLTPEEEIELAK 123

Query: 145 RIEAGRAMMMASLCESPLTF 164
           R+E G       L E+ L  
Sbjct: 124 RMEQGDEEAKRRLIEANLRL 143


>gi|260101316|ref|ZP_05751553.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
 gi|260084901|gb|EEW69021.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
          Length = 370

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 153/238 (64%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+CLG+KFSTYA WW
Sbjct: 133 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP   V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPTNKV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +LT R
Sbjct: 253 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+D
Sbjct: 313 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFMD 370



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 66/151 (43%), Gaps = 16/151 (10%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVERAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + L++ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 ---------DELNDGTTLLREIID-LEACIG 192
                    D + +G   L + +D  + C+G
Sbjct: 152 YVGRGMSFLDLIQEGNMGLMKAVDKFDYCLG 182


>gi|116629751|ref|YP_814923.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri ATCC 33323]
 gi|238853400|ref|ZP_04643779.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282851794|ref|ZP_06261157.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300361838|ref|ZP_07058015.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311110607|ref|ZP_07712004.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
 gi|116095333|gb|ABJ60485.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus gasseri ATCC
           33323]
 gi|238833972|gb|EEQ26230.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282557036|gb|EFB62635.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300354457|gb|EFJ70328.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311065761|gb|EFQ46101.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
          Length = 373

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 175/365 (47%), Positives = 238/365 (65%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+   +L    +D LV++  D    I+  +GE  +LA                 
Sbjct: 35  KEFTAQLIKPYNLQGKAVDQLVQEFEDNGISIVDEKGEPSKLA----------------- 77

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRK 436
                 +   KD  + E K+  A    S +++ + ++    E G +S+      +++ ++
Sbjct: 78  ------LKKQKDVEKAELKDMSAP---SSVRMNDPVRMYLKEIGRVSLLNADQEIALAKR 128

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 129 IEAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 188

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 189 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 248

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 249 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 308

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 309 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 368

Query: 677 RSFLD 681
           + FLD
Sbjct: 369 KDFLD 373



 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 59/120 (49%), Gaps = 7/120 (5%)

Query: 44  VTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T +E  A  + P  +  + ++  V    + GI++VD      E+G    L L       
Sbjct: 32  ITEKEFTAQLIKPYNLQGKAVDQLVQEFEDNGISIVD------EKGEPSKLALKKQKDVE 85

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIEAG       L E+ L
Sbjct: 86  KAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIEAGDEEAKQELAEANL 145


>gi|326803636|ref|YP_004321454.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651510|gb|AEA01693.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 401

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 198/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E    +AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 150 VALAKRIEAGDPVAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDY 209

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR  R++  ++ REPTPE
Sbjct: 210 TKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLVRIQRQLLQELGREPTPE 269

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +P E VR ++KI++EP+SLETPIG+ED SHLGDFIED +A+ P +   Q  L+
Sbjct: 270 EIGAEMDLPTEKVRNIMKISQEPVSLETPIGEEDDSHLGDFIEDNDAMQPDEYTNQELLK 329

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLE+VG+QF VTRERIRQIEAKA+RKL+HP
Sbjct: 330 EQLNEVLDTLTDREENVLRLRFGLEDGQTKTLEQVGQQFGVTRERIRQIEAKALRKLRHP 389

Query: 671 SRSKKLRSFLD 681
           SR K+L+ FL+
Sbjct: 390 SRLKQLKDFLE 400



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 64/132 (48%), Gaps = 24/132 (18%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDD--------------LEDEEGSEDSLD------ 94
           P  ++ EQM+  +    + G+ VVD D                ED+E SE  +D      
Sbjct: 41  PYSLNDEQMDQLIEKFEDGGVAVVDEDGGPTNRQLQNEALKMQEDDEESEKDIDQILDEE 100

Query: 95  LASSASNSSVFLQKRKDSADRS----TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +   +        K ++  S    T+DPVRMYL+E+G ++LL+ + E+A+AKRIEAG 
Sbjct: 101 EKTKKKDKKDKKDTNKSASSTSSKVKTNDPVRMYLKEIGRVDLLTADEEVALAKRIEAGD 160

Query: 151 AMMMASLCESPL 162
            +    L E+ L
Sbjct: 161 PVAKQELAEANL 172


>gi|260583936|ref|ZP_05851684.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
 gi|260158562|gb|EEW93630.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
          Length = 374

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 161/274 (58%), Positives = 207/274 (75%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E  ++   +++G+ EA   K+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVPLLSADEEVNLALRIQQGDQEA---KQELAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLVRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGK 647
           GDFIED NA SP +    A L+E    VL  LT REE VLR+RFG+  N +  TLE+VG+
Sbjct: 281 GDFIEDDNATSPAEHTAYALLKEQLDEVLEQLTDREENVLRLRFGLDKNGEIRTLEQVGQ 340

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 341 VFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLD 374



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 66/125 (52%), Gaps = 10/125 (8%)

Query: 42  GYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS-SA 99
           G +  ++L+A +  P E+ +E M+  +    + G++VVD D      G   S  L+S SA
Sbjct: 27  GQILYDDLSAQIAIPYELDAEGMDKLIQQFEDAGVSVVDAD------GGPTSRQLSSESA 80

Query: 100 SNSSVFLQKRKD--SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
               V + + +   S++   +D VRMYL+E+G + LLS + E+ +A RI+ G       L
Sbjct: 81  KEPEVEMTEDETALSSNVKINDSVRMYLKEIGRVPLLSADEEVNLALRIQQGDQEAKQEL 140

Query: 158 CESPL 162
            E+ L
Sbjct: 141 AEANL 145


>gi|161507646|ref|YP_001577600.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus DPC
           4571]
 gi|160348635|gb|ABX27309.1| RNA polymerase sigma factor [Lactobacillus helveticus DPC 4571]
          Length = 356

 Score =  328 bits (840), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 153/238 (64%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+CLG+KFSTYA WW
Sbjct: 119 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKFSTYATWW 178

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP   V
Sbjct: 179 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPTNKV 238

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +LT R
Sbjct: 239 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETLTDR 298

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+D
Sbjct: 299 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFMD 356



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 66/151 (43%), Gaps = 16/151 (10%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 24  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVERAELKDMSA 77

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + L++ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 78  PSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 137

Query: 172 ---------DELNDGTTLLREIID-LEACIG 192
                    D + +G   L + +D  + C+G
Sbjct: 138 YVGRGMSFLDLIQEGNMGLMKAVDKFDYCLG 168


>gi|259046798|ref|ZP_05737199.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
 gi|259036566|gb|EEW37821.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
          Length = 374

 Score =  328 bits (840), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 161/274 (58%), Positives = 205/274 (74%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +++G+ EA   K+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVPLLSADEEVALALRIQEGDTEA---KQELAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMK  EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNMGLMKTVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLVRVQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGK 647
           GDFIED NA SP D    A L+E    VL  LT REE VLR+RFG+  N +  TLE+VG+
Sbjct: 281 GDFIEDDNATSPADHTAYALLKEQLDEVLEQLTDREENVLRLRFGLDKNGEIRTLEQVGQ 340

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 341 VFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLD 374



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 63/125 (50%), Gaps = 10/125 (8%)

Query: 42  GYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           G +  ++L+A +  P E+ +E M+  +    + G++VVD +      G   S  L+  + 
Sbjct: 27  GQILYDDLSAQIAIPFELDAEGMDKLIQKFEDAGVSVVDAN------GEPTSHQLSVESQ 80

Query: 101 NSSVFLQKRKDSADRST---DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
             +       D+A  S    +D VRMYL+E+G + LLS + E+A+A RI+ G       L
Sbjct: 81  REAEVGTVEDDTALSSNTKINDSVRMYLKEIGRVPLLSADEEVALALRIQEGDTEAKQEL 140

Query: 158 CESPL 162
            E+ L
Sbjct: 141 AEANL 145


>gi|227513300|ref|ZP_03943349.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
 gi|227083501|gb|EEI18813.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
          Length = 389

 Score =  328 bits (840), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 165/303 (54%), Positives = 218/303 (71%), Gaps = 4/303 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGE 438
           DP  +  AK   + E  +  A    + +KI + ++    E G +S+      +++ ++ E
Sbjct: 90  DPRAIDAAKKVTKKELSDVSAP---TGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIE 146

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFST
Sbjct: 147 SGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFST 206

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M
Sbjct: 207 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDM 266

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL 
Sbjct: 267 PTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLD 326

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ 
Sbjct: 327 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKD 386

Query: 679 FLD 681
           FL+
Sbjct: 387 FLE 389



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 41/142 (28%), Positives = 71/142 (50%), Gaps = 7/142 (4%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + +++K  +  G++T +EL   +  P  +  ++ME+ +  + + GI+VVD      + G 
Sbjct: 35  FDQIVKDNKPIGHITYDELQKKIEEPFSLDKKEMEELLENIEDSGISVVD------DNGD 88

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D   + ++   +   L           +DPVRMYL+E+G + LLS + EI +AKRIE+G
Sbjct: 89  PDPRAIDAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIESG 148

Query: 150 RAMMMASLCESPLTFQALIIWR 171
                  L E+ L     I  R
Sbjct: 149 DEEAKQELAEANLRLVVSIAKR 170


>gi|328676046|gb|AEB28721.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida 3523]
          Length = 577

 Score =  328 bits (840), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 181/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYSKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKI 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   ++  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSVE--WLE-----PLTKKYKFTENTIREINNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 66/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            ++RGY+T  ++   LP D     ++ E+  A+L + GI+V D       +  ED     
Sbjct: 17  GKERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYD----RTPQLEEDDERKV 72

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           S A+          D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 73  SEAN---------LDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|167758408|ref|ZP_02430535.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
 gi|167664305|gb|EDS08435.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
          Length = 371

 Score =  328 bits (840), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 134 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA +L MPVE V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAQLDMPVERV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 254 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 314 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 371



 Score = 47.0 bits (110), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 39/138 (28%), Positives = 70/138 (50%), Gaps = 6/138 (4%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  K+++ L +++   + ++E+N F    E+ +EQME     L +  I+V+    +  +
Sbjct: 9   EEKLKELVSLGKKKKSILELQEINDFFSDMELEAEQMERVFEHLESNNIDVLR---ISGD 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAK 144
           E  +        A    V ++K   S     S +DPVRMYL+E+G + LL+ E E+ +AK
Sbjct: 66  EDDDIDDVDIVIAEEDDVDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLTAEEEVDLAK 125

Query: 145 RIEAGRAMMMASLCESPL 162
           R+  G       L E+ L
Sbjct: 126 RMADGDEEAKKRLAEANL 143


>gi|225570457|ref|ZP_03779482.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
 gi|225160654|gb|EEG73273.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
          Length = 370

 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 133 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA +L MPVE V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAELDMPVERV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 253 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score = 44.3 bits (103), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 41/148 (27%), Positives = 71/148 (47%), Gaps = 27/148 (18%)

Query: 28  DDSWKKMIKLARQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDDL- 83
           ++  K+++ L +++  +  ++E+N F    E+ SEQME     L    I+V  + GDD  
Sbjct: 9   EEKLKELVSLGKKKKSILELQEINDFFSDMELESEQMERVFEHLEANNIDVLRISGDDDD 68

Query: 84  ---------EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
                    E++E   + +DL+     S               +DPVRMYL+E+G + LL
Sbjct: 69  IDDADIIISEEDEVDVEKIDLSVPDGIS--------------IEDPVRMYLKEIGKVPLL 114

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPL 162
           + + E+ +AKR+  G       L E+ L
Sbjct: 115 TADEEVDLAKRMADGDEEAKKRLAEANL 142


>gi|291546785|emb|CBL19893.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus sp. SR1/5]
          Length = 375

 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + +S  E   +   + KG+     AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGKVSLLSADEEIELAKRMEKGD---EAAKKRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA+++ MPV+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 223 INKLIRVSRQLLQELGREPTPEEIAEEMDMPVDRVREILKISQEPVSLETPIGEEEDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL++LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 283 GDFIQDDNVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGLDDGRARTLEEVGKE 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 343 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 375



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 70/134 (52%), Gaps = 4/134 (2%)

Query: 33  KMIKLARQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           ++++LA+++  V   +E++ F     +  +QME     L   G++V+   D+  DE   +
Sbjct: 14  ELLELAKKKKNVLEYQEISDFFKDSPLEVDQMEKVFDFLEASGVDVLRITDNSGDELLLD 73

Query: 91  DSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + +D+        V L K   S     S +DPVRMYL+E+G + LLS + EI +AKR+E 
Sbjct: 74  NDMDMDGMEDEEEVELDKIDLSVPEGVSIEDPVRMYLKEIGKVSLLSADEEIELAKRMEK 133

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 134 GDEAAKKRLAEANL 147


>gi|153853334|ref|ZP_01994743.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
 gi|149754120|gb|EDM64051.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
          Length = 369

 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 132 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWW 191

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA +L MPVE V
Sbjct: 192 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAELDMPVERV 251

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 252 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 311

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 312 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 369



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/128 (34%), Positives = 66/128 (51%), Gaps = 11/128 (8%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLD 94
           +++G + I+E+N F    E+ S+QME     L    ++V+    D DD+ DE    D  D
Sbjct: 21  KKKGILEIQEINDFFSDMELDSDQMEKVFDYLEANNVDVLRISNDDDDIPDEIVMSDEDD 80

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           +     + SV      D    S +DPVRMYL+E+G + LLS E E+ +AKR+  G     
Sbjct: 81  IDVEKIDLSV-----PDGI--SIEDPVRMYLKEIGKVPLLSAEEEVELAKRMADGDEEAK 133

Query: 155 ASLCESPL 162
             L E+ L
Sbjct: 134 KRLAEANL 141


>gi|226324578|ref|ZP_03800096.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
 gi|225207026|gb|EEG89380.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
          Length = 371

 Score =  327 bits (838), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 134 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYQKGFKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA +L MPV+ V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAELDMPVDRV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL++LT R
Sbjct: 254 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLSTLTER 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 314 EQKVLRLRFGMSDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 371



 Score = 45.4 bits (106), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 56/191 (29%), Positives = 82/191 (42%), Gaps = 27/191 (14%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-------- 79
           +  K ++ LA+++   + I+E+N      E+   QM+     L   GI+V+         
Sbjct: 10  EKLKNLVALAKKKKNILEIQEINDAFRDMELEPTQMDKVFEYLEANGIDVLQMNDDSNVD 69

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            DDLE     ED +D+     + SV      D    S +DPVRMYL+E+G + LLS E E
Sbjct: 70  DDDLEIMLSDEDEVDM--EKIDLSV-----PDGI--SIEDPVRMYLKEIGKVPLLSAEEE 120

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I +AKR+  G       L E+ L    + I +  +  G   L  I         E   G 
Sbjct: 121 IELAKRMADGDEEAKKRLAEANLRL-VVSIAKRYVGRGMLFLDLI--------QEGNLGL 171

Query: 200 FHGTEGHSYQK 210
               E   YQK
Sbjct: 172 IKAVEKFDYQK 182


>gi|166030947|ref|ZP_02233776.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
 gi|166029214|gb|EDR47971.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
          Length = 382

 Score =  327 bits (838), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 145 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA +L MPVE V
Sbjct: 205 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAELDMPVERV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A Q  L+E    VL +LT R
Sbjct: 265 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTER 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 325 EQKVLRLRFGMDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 382



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 72/139 (51%), Gaps = 8/139 (5%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLD 94
           + +  + ++E+N F    E+ +EQME     L    I+V+    DGD +E+ +  +DS D
Sbjct: 27  KNKSILELQEINDFFSDMELDAEQMEKVYEYLEANHIDVLRVSGDGDGIEELDDVDDS-D 85

Query: 95  LASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           +  +  +  V ++K   S     S +DPVRMYL+E+G + LLS + E+ +AKR+  G   
Sbjct: 86  IVLTDEDD-VDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSADEEVELAKRMAEGDED 144

Query: 153 MMASLCESPLTFQALIIWR 171
               L E+ L     I  R
Sbjct: 145 AKKRLAEANLRLVVSIAKR 163


>gi|42519241|ref|NP_965171.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|41583529|gb|AAS09137.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|329667249|gb|AEB93197.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii DPC 6026]
          Length = 372

 Score =  327 bits (838), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 175/365 (47%), Positives = 236/365 (64%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    L    +D LV++  D    I+   GE  +LA                 
Sbjct: 34  KEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVDENGEPSKLA----------------- 76

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRK 436
                 +   KD  + E K+  A    S +++ + ++    E G +S+      +++ ++
Sbjct: 77  ------LKKQKDVEKAELKDMSAP---SSVRMNDPVRMYLKEIGRVSLLNADQEIALAKR 127

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 128 IESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 187

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 188 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 247

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 248 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 307

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 308 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 367

Query: 677 RSFLD 681
           + FLD
Sbjct: 368 KDFLD 372



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 59/120 (49%), Gaps = 7/120 (5%)

Query: 44  VTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T +E  A  + P ++  + ++  V    + GI++VD      E G    L L       
Sbjct: 31  ITEKEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVD------ENGEPSKLALKKQKDVE 84

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 85  KAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGDEEAKQELAEANL 144


>gi|268319377|ref|YP_003293033.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
 gi|262397752|emb|CAX66766.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
          Length = 372

 Score =  327 bits (838), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 175/365 (47%), Positives = 236/365 (64%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    L    +D LV++  D    I+   GE  +LA                 
Sbjct: 34  KEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVDENGEPSKLA----------------- 76

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRK 436
                 +   KD  + E K+  A    S +++ + ++    E G +S+      +++ ++
Sbjct: 77  ------LKKQKDVEKAELKDMSAP---SSVRMNDPVRMYLKEIGRVSLLNADQEIALAKR 127

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 128 IESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 187

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 188 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 247

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 248 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 307

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 308 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 367

Query: 677 RSFLD 681
           + FLD
Sbjct: 368 KDFLD 372



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 59/120 (49%), Gaps = 7/120 (5%)

Query: 44  VTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T +E  A  + P ++  + ++  V    + GI++VD      E G    L L       
Sbjct: 31  ITEKEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVD------ENGEPSKLALKKQKDVE 84

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 85  KAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGDEEAKQELAEANL 144


>gi|56708122|ref|YP_170018.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670593|ref|YP_667150.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|224457213|ref|ZP_03665686.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370608|ref|ZP_04986613.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254874922|ref|ZP_05247632.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604614|emb|CAG45668.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320926|emb|CAL09051.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|151568851|gb|EDN34505.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254840921|gb|EET19357.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159323|gb|ADA78714.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 577

 Score =  327 bits (838), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 181/369 (49%), Positives = 245/369 (66%), Gaps = 10/369 (2%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK   +L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 216 KKLYTKIVKEFDNLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 275

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++   L+  W+      P  +   F    +  I  +  +I    +   + I E + +   
Sbjct: 276 YKVGSLE--WLE-----PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLE 328

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G
Sbjct: 329 ISRSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKG 388

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI 
Sbjct: 389 FKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEII 448

Query: 554 KKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +    M  E ++K+L I+  PIS+E+PIGD++ S +GDFIEDK+  SP+++A   NLRE 
Sbjct: 449 EHTPNMTKEKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKSNYSPIEAANLENLREA 508

Query: 613 TTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++ + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPS
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 672 RSKKLRSFL 680
           RS  L++FL
Sbjct: 569 RSAFLKTFL 577



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 14/132 (10%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA 96
            R+RGY+T  ++   LP D     ++ E+  A+L + GI+V D    + EE  E  +  A
Sbjct: 17  GRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTP-QIEEDDERKVSEA 75

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + ++
Sbjct: 76  NL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFST 123

Query: 157 LCESPLTFQALI 168
           +   P+  +  I
Sbjct: 124 ILSYPIVIKTYI 135


>gi|302670285|ref|YP_003830245.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
 gi|302394758|gb|ADL33663.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
          Length = 521

 Score =  327 bits (838), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 155/256 (60%), Positives = 202/256 (78%), Gaps = 5/256 (1%)

Query: 431 VSMVRKGECEASI-----AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +S  RK E  A I     AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 266 LSDARKKELNAIIYEGEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAV 325

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R
Sbjct: 326 EKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGR 385

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP PEE+AK++ MPVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A 
Sbjct: 386 EPLPEEVAKEMNMPVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAA 445

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT RE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+R
Sbjct: 446 FTLLKEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALR 505

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRS+KL+ +LD
Sbjct: 506 KLRHPSRSRKLKDYLD 521



 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 41/168 (24%), Positives = 83/168 (49%), Gaps = 34/168 (20%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSW----KKMIKLARQRGYVT-IEELNAFLPPD 56
           T G+K   D ++  ++S+D  + + + + +    K+++ LA+++  V    E++ F    
Sbjct: 97  TKGRKSKADKEAPSQNSEDGEIDEATRELFSQKVKEILALAKKKKNVLEYAEISDFFAEL 156

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLED---------------EEGSEDSLDLASSASN 101
            ++ EQ ++ + +L N GI+V+   + +                EE   +++DL+     
Sbjct: 157 NLNEEQFDNVLEVLENSGIDVLRVSEDDVDDIPDDDDMLLVDDDEEVDMENIDLSVPDGI 216

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S               +DPVRMYL+E+G + LL+ + EI +A+ +EAG
Sbjct: 217 S--------------IEDPVRMYLKEIGKVPLLTADQEIDLAQAMEAG 250


>gi|302871329|ref|YP_003839965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574188|gb|ADL41979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 417

 Score =  327 bits (837), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 180 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  REPTPEEIAK++ MPVE V
Sbjct: 240 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKV 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  + L+E    VL SL  R
Sbjct: 300 REILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNER 359

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 360 EKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 417



 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 48/140 (34%), Positives = 71/140 (50%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L + +G++T  E+   L   E+ + Q+E     L +MGI+VVD D + +EE  +D
Sbjct: 75  RELISLGQSKGFLTYSEIQEILDKVELDASQVESIYDTLESMGIDVVD-DRVSEEELLKD 133

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+                     + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 134 DLENLPEGI---------------AIDDPVRMYLKEIGKIPLLTPEEEIELAKRIEQGDE 178

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 179 EAKKRLAEANLRLVVSIAKR 198


>gi|312128161|ref|YP_003993035.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312134621|ref|YP_004001959.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|312792985|ref|YP_004025908.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|311774672|gb|ADQ04159.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311778180|gb|ADQ07666.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312180125|gb|ADQ40295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 417

 Score =  327 bits (837), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 194/437 (44%), Positives = 287/437 (65%), Gaps = 27/437 (6%)

Query: 249 ENAENDE-RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           +N EN+E +NL+ D++ +  T S  + ++  +++ +     +  +  +   +N   G+K 
Sbjct: 4   QNMENNEVKNLN-DQNINKETGSEQQQEVEKQLLASQKNENQEKQPAKKSTENKSEGKK- 61

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA---QSYG 364
             S  K  +++EK+ +L+   SL QS+  L   ++ +I  ++  +  ++  +    +S G
Sbjct: 62  -MSEEKKSLIREKVRELI---SLGQSKGFLTYSEIQEILDKVELDASQVENIYDTLESMG 117

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I  DV  +R    EL        ++ PEG     +A + D +     EI  I +   ++ 
Sbjct: 118 I--DVVDDRVSEEEL---LKDDLENLPEG-----IAID-DPVRMYLKEIGKIPL---LTP 163

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +   + +G+ EA   KK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA
Sbjct: 164 EEEIELAKRIEQGDEEA---KKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKA 220

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  
Sbjct: 221 VEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKG 280

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A
Sbjct: 281 REPTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAA 340

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             + L+E    VL SL  RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+
Sbjct: 341 AYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKAL 400

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRSKKL+ FL+
Sbjct: 401 RKLRHPSRSKKLKDFLE 417



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/140 (34%), Positives = 72/140 (51%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L + +G++T  E+   L   E+ + Q+E+    L +MGI+VVD D + +EE  +D
Sbjct: 75  RELISLGQSKGFLTYSEIQEILDKVELDASQVENIYDTLESMGIDVVD-DRVSEEELLKD 133

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+                     + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 134 DLENLPEGI---------------AIDDPVRMYLKEIGKIPLLTPEEEIELAKRIEQGDE 178

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 179 EAKKRLAEANLRLVVSIAKR 198


>gi|154498377|ref|ZP_02036755.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
 gi|150272688|gb|EDM99866.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
          Length = 441

 Score =  327 bits (837), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 152/248 (61%), Positives = 201/248 (81%), Gaps = 4/248 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+GE     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G
Sbjct: 198 IRRGEA----AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKG 253

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV+R +R++  ++  +P+PEEIA
Sbjct: 254 YKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVIRVSRQLLQELGHDPSPEEIA 313

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ MPV+ VR++LKI +EP+SLETPIG+E+ SHLGDFI D++A  P ++A    L+E  
Sbjct: 314 EEMNMPVDKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDEDASEPSEAASFTLLKEQL 373

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LTPREE+VL++RFGI      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 374 VDVLGTLTPREEKVLKLRFGIEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 433

Query: 674 KKLRSFLD 681
           KKL+ FL+
Sbjct: 434 KKLKDFLN 441



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/126 (31%), Positives = 65/126 (51%), Gaps = 16/126 (12%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--------DGDDLED 85
           +++ A+++G ++  EL   L   E+ SEQM+    +L N+GI  V        D D +  
Sbjct: 49  LVERAKKKGSLSTNELMDVLEGMELESEQMDKIYDVLENLGIETVSEYYLPELDADIMPP 108

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E  E+  +      N+ V      DS     DDPVRMYL+E+G + LL+ + E+ +A+ 
Sbjct: 109 MEELEEIPEEKIVDPNTLV------DSF--GIDDPVRMYLKEIGKVNLLNPDEEVQLAQD 160

Query: 146 IEAGRA 151
           + AG A
Sbjct: 161 MGAGDA 166


>gi|296133798|ref|YP_003641045.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola sp.
           JR]
 gi|296032376|gb|ADG83144.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola
           potens JR]
          Length = 366

 Score =  327 bits (837), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 203/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK+ + EANLRLV+S+AK+Y  RGL FLDLIQEGN+GL+KA EKFD+
Sbjct: 116 VELAKRMETGDEEAKRRLAEANLRLVVSIAKRYVGRGLLFLDLIQEGNLGLIKAVEKFDY 175

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 176 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPE 235

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +PV+ VR+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    LR
Sbjct: 236 EIAAEMDIPVDRVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFILLR 295

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 296 EQLEEVLETLTPREEKVLRLRFGLDDGRSRTLEEVGQEFGVTRERIRQIEAKALRKLRHP 355

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ FL+
Sbjct: 356 SRSKKLKDFLE 366



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 39/119 (32%), Positives = 67/119 (56%), Gaps = 6/119 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSE 90
           +++I+  ++RG +T  E+   L   +++ EQ+++    L+NMGI+VV +  DLE  +   
Sbjct: 12  QELIENGKKRGILTYTEIMNTLQNVDLNPEQIDEIYEKLANMGIDVVPEVPDLEPLDSEA 71

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              D   +     + +    D      DDPVRMYL+E+G + LL+ E E+ +AKR+E G
Sbjct: 72  IEADAEEAEIEVDLTV---PDGI--GIDDPVRMYLKEIGRVPLLTAEEEVELAKRMETG 125


>gi|222528719|ref|YP_002572601.1| RpoD subfamily RNA polymerase sigma-70 factor [Caldicellulosiruptor
           bescii DSM 6725]
 gi|222455566|gb|ACM59828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 417

 Score =  327 bits (837), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 180 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  REPTPEEIAK++ MPVE V
Sbjct: 240 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKV 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  + L+E    VL SL  R
Sbjct: 300 REILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNER 359

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 360 EKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 417



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/140 (34%), Positives = 72/140 (51%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L + +G++T  E+   L   E+ + Q+E+    L +MGI+VVD D + +EE  +D
Sbjct: 75  RELISLGQSKGFLTYSEIQEILDKVELDASQVENIYDTLESMGIDVVD-DRVSEEELLKD 133

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+                     + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 134 DLENLPEGI---------------AIDDPVRMYLKEIGKIPLLTPEEEIELAKRIEQGDE 178

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 179 EAKKRLAEANLRLVVSIAKR 198


>gi|294055048|ref|YP_003548706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614381|gb|ADE54536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 639

 Score =  326 bits (836), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 168/339 (49%), Positives = 233/339 (68%), Gaps = 7/339 (2%)

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC----EV 403
           R+   E EL  + + Y +K  +F +    ++L P ++   + + + E  + V      +V
Sbjct: 284 RMKKYEAELSGVLKKYCLKLKIFEDFL--KDLTPTYMELKELYDDLETADKVTARRRKQV 341

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D +  I   ++ I +E  I   E   I+  VR G  EA  AK EMVEANLRLVIS+AKKY
Sbjct: 342 D-VKAIERRLEEIKLEFKIESKELLDIIREVRIGTREAHKAKTEMVEANLRLVISIAKKY 400

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 401 TNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 460

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + ++KV++  +++  ++  EPT EE+A ++ +P+E V+ ++K+ ++PISL++P+GD 
Sbjct: 461 HMIETLNKVMQVQKQLLQELGHEPTAEEVADEMNLPIERVQSIMKMAQQPISLQSPVGDS 520

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D ++ GDFIEDK A +P D    + LRE  T VL SLT RE RVL +RFG+      TLE
Sbjct: 521 DDTNFGDFIEDKGAENPYDMTAYSLLREKITDVLDSLTERERRVLSLRFGLADGYSRTLE 580

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RK++HP+R ++L  F +G
Sbjct: 581 EVGRQFKVTRERIRQIEAKALRKMRHPTRIRQLHGFFEG 619



 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 76/132 (57%), Gaps = 11/132 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I++++++G++T +++N  LP    + E++E+ +++L N+ I V+D   +E         
Sbjct: 90  LIRMSKEQGFLTYKDINKGLPESVNNPEEIENVISILQNLEIEVLDDSQVE--------- 140

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
             A  A       ++ + S +   DDPVRMYL++MG + LL+RE E+AI+KRIE      
Sbjct: 141 --AYKARQEETEEKEVRTSQNDILDDPVRMYLKQMGQVPLLTREEEVAISKRIEKAELRA 198

Query: 154 MASLCESPLTFQ 165
             +L  + LT +
Sbjct: 199 QDALFSTALTLE 210


>gi|312876451|ref|ZP_07736435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796809|gb|EFR13154.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 419

 Score =  326 bits (836), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 182 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 241

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  REPTPEEIAK++ MPVE V
Sbjct: 242 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKV 301

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  + L+E    VL SL  R
Sbjct: 302 REILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNER 361

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 362 EKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 419



 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L + +G++T  E+   L   E+ + Q+E+    L +MGI++VD D + +EE  +D
Sbjct: 77  RELISLGQSKGFLTYSEIQEILDKVELDASQVENIYDTLESMGIDIVD-DRVSEEELLKD 135

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+                     + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 136 DLENLPEGI---------------AIDDPVRMYLKEIGKIPLLTPEEEIELAKRIEQGDE 180

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 181 EAKKRLAEANLRLVVSIAKR 200


>gi|153813734|ref|ZP_01966402.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
 gi|149830174|gb|EDM85267.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
          Length = 330

 Score =  326 bits (835), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 93  AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 152

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA+++ MPV+ V
Sbjct: 153 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAEEMKMPVDRV 212

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 213 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLIEVLGTLTER 272

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 273 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 330



 Score = 44.7 bits (104), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LL+ + EI +AKR+E G       L E+ L
Sbjct: 56  SIEDPVRMYLKEIGKVSLLTADEEIELAKRMEQGDEEAKKRLAEANL 102


>gi|303238871|ref|ZP_07325402.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593504|gb|EFL63221.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 359

 Score =  326 bits (835), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + KG+ E+   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 90  VRMYLKEIGKVPLLSADEEIQLAQKMEKGDSES---KRRLAEANLRLVVSIAKRYVGRGM 146

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 147 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 206

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ +EP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 207 INKLIRVSRQLLQELGKEPQPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 266

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 267 GDFIPDDDAPAPSEAAAFTLLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 326

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 327 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 359



 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 70/132 (53%), Gaps = 18/132 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---DLEDEEGSE 90
           +I   +Q+G +T +E+       E+  E +E     L NMGI++V GD   ++E+ + +E
Sbjct: 15  LIDKGKQKGMLTYKEIMDAFEEIEIEPEHIEKVYETLENMGIDIV-GDIEAEMEEIQLTE 73

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + LD++     S               DDPVRMYL+E+G + LLS + EI +A+++E G 
Sbjct: 74  EDLDISIPEGIS--------------IDDPVRMYLKEIGKVPLLSADEEIQLAQKMEKGD 119

Query: 151 AMMMASLCESPL 162
           +     L E+ L
Sbjct: 120 SESKRRLAEANL 131


>gi|295397565|ref|ZP_06807644.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
 gi|294974189|gb|EFG49937.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
          Length = 374

 Score =  326 bits (835), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 154/251 (61%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS+ ++ E    +AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 VSLAQRIEQGDPVAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDY 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + REPTPE
Sbjct: 184 HKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQDLGREPTPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +P E VR +LKI +EP+SLETPIG+ED SHLGDFIED +A SP D      L+
Sbjct: 244 EIGAEMDLPTEKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDHDATSPDDYTSAELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLE+VG+QF VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLNEVLDTLTDREENVLRLRFGLEDGQSKTLEQVGQQFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 36/51 (70%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           ++D   +DPVRMYL+E+G +ELL+ + E+++A+RIE G  +    L E+ L
Sbjct: 96  ASDVKINDPVRMYLKEIGRVELLTADEEVSLAQRIEQGDPVAKQELAEANL 146


>gi|146295919|ref|YP_001179690.1| RpoD family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409495|gb|ABP66499.1| RNA polymerase, sigma 70 subunit, RpoD [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 411

 Score =  326 bits (835), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 174 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 233

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  REPTPEEIAK++ MPVE V
Sbjct: 234 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKV 293

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  + L+E    VL SL  R
Sbjct: 294 REILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNER 353

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 354 EKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 411



 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 49/140 (35%), Positives = 72/140 (51%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L + +G++T  E+   L   E+ + Q+E+    L NMGI+VVD D + +EE  +D
Sbjct: 69  RELISLGQSKGFLTYSEIQEILDKVELDANQIENIYDTLENMGIDVVD-DRVSEEELLKD 127

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+                     + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 128 DLENLPEGI---------------AIDDPVRMYLKEIGKIPLLTPEEEIELAKRIEQGDE 172

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 173 EAKKRLAEANLRLVVSIAKR 192


>gi|281417615|ref|ZP_06248635.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
 gi|281409017|gb|EFB39275.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
          Length = 358

 Score =  326 bits (835), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 89  VRMYLKEIGKVPLLTAEEEIELAHRIEQGDAEA---KRRLAEANLRLVVSIAKRYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKLIRVSRQLLQELGREPHPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 266 GDFIPDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/133 (36%), Positives = 72/133 (54%), Gaps = 18/133 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---DLEDEEGS 89
           ++I+  +Q+G +T +E+       ++  EQ+E     L NMGI+VV GD   ++ED + +
Sbjct: 13  ELIEKGKQKGMLTYQEIMDAFEEVDIDPEQIEKIYETLENMGIDVV-GDIEAEMEDIQLT 71

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED LDL+     S               DDPVRMYL+E+G + LL+ E EI +A RIE G
Sbjct: 72  EDDLDLSIPEGIS--------------IDDPVRMYLKEIGKVPLLTAEEEIELAHRIEQG 117

Query: 150 RAMMMASLCESPL 162
            A     L E+ L
Sbjct: 118 DAEAKRRLAEANL 130


>gi|315029422|gb|EFT41354.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4000]
          Length = 368

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 165/306 (53%), Positives = 217/306 (70%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI + ++    E G    ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA   K+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 EGDQEA---KQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDNGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 10/132 (7%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            IK  + +G V  ++L N    P  + +E ME  +  + + GI+VVD    E+ + SE S
Sbjct: 16  FIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVD----ENGDPSEHS 71

Query: 93  LDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           L      +  +   Q    SA      +DPVRMYL+E+G ++LL+   E+ +A +IE G 
Sbjct: 72  LKKDEKEAEKA---QAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEEGD 128

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 129 QEAKQRLAEANL 140


>gi|227890104|ref|ZP_04007909.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
 gi|227849548|gb|EEJ59634.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
          Length = 372

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 173/360 (48%), Positives = 234/360 (65%), Gaps = 27/360 (7%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+   GE  +LA                      
Sbjct: 39  QLIKPYDLQGKAVDQLVQEFEDNGISIVDENGEPSKLA---------------------- 76

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEA 441
            +   KD  + E K+  A    S +++ + ++    E G +S+      +++ ++ E   
Sbjct: 77  -LKKQKDVEKAELKDMSAP---SSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGD 132

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA 
Sbjct: 133 EEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYAT 192

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP +
Sbjct: 193 WWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTD 252

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    VL +LT
Sbjct: 253 KVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLT 312

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 313 DREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 372



 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 54/111 (48%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 40  LIKPYDLQGKAVDQLVQEFEDNGISIVD------ENGEPSKLALKKQKDVEKAELKDMSA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 94  PSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGDEEAKQELAEANL 144


>gi|125973412|ref|YP_001037322.1| RNA polymerase sigma factor RpoD [Clostridium thermocellum ATCC
           27405]
 gi|125713637|gb|ABN52129.1| RNA polymerase, sigma 38 subunit, RpoS [Clostridium thermocellum
           ATCC 27405]
          Length = 358

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 89  VRMYLKEIGKVPLLTAEEEIELAHRIEQGDAEA---KRRLAEANLRLVVSIAKRYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKLIRVSRQLLQELGREPHPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 266 GDFIPDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score = 71.6 bits (174), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 49/133 (36%), Positives = 73/133 (54%), Gaps = 18/133 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---DLEDEEGS 89
           ++I+  +Q+G +T +E+       ++  EQ+E     L NMGI+VV GD   ++ED + +
Sbjct: 13  ELIEKGKQKGMLTYQEIMDAFEEVDIDPEQIEKIYETLENMGIDVV-GDIEAEMEDIQLT 71

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED+LDL+     S               DDPVRMYL+E+G + LL+ E EI +A RIE G
Sbjct: 72  EDNLDLSIPEGIS--------------IDDPVRMYLKEIGKVPLLTAEEEIELAHRIEQG 117

Query: 150 RAMMMASLCESPL 162
            A     L E+ L
Sbjct: 118 DAEAKRRLAEANL 130


>gi|323484375|ref|ZP_08089742.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692387|ref|ZP_08106623.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402369|gb|EGA94700.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503527|gb|EGB19353.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 372

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 202/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AKK + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EK+D+
Sbjct: 122 IELAKQMEMGNEYAKKRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKYDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I++++RT+R++  ++ REP PE
Sbjct: 182 SKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINRLIRTSRQLLQELGREPHPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+++ MPVE VR+++KI+++P+SLETPIG+E+ SHLGDFI+D +   PLD+A    L 
Sbjct: 242 EVAERMDMPVERVREIMKISQDPVSLETPIGEEEDSHLGDFIQDDHVQVPLDAATFTLLH 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLMEVLDTLTDREQKVLRLRFGLDDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 362 SRSKKLKDYLD 372



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + DDPVRMYL+E+G + LLS E EI +AK++E G       L E+ L
Sbjct: 98  NIDDPVRMYLKEIGKVPLLSPEEEIELAKQMEMGNEYAKKRLAEANL 144


>gi|227544906|ref|ZP_03974955.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300910067|ref|ZP_07127527.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
 gi|227185118|gb|EEI65189.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300892715|gb|EFK86075.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
          Length = 380

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 163/306 (53%), Positives = 217/306 (70%), Gaps = 10/306 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP  +   + F +   K+  A    + +KI + ++    E G    ++  E   +   + 
Sbjct: 81  DPRALKATEKFSQSAMKDTSAP---TGVKINDPVRMYLKEIGRVNLLTADEEVQLALRIE 137

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+    +AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 138 KGD---EVAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFK 194

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  +
Sbjct: 195 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAE 254

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP E VR +LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    +++    
Sbjct: 255 MDMPTEKVRNILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEMMKKQLEN 314

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 315 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 374

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 375 LKDFLE 380



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 71/136 (52%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  K+I+  +++  +  +EL   +  P E++++ +++ +  + + GI+VVD      E
Sbjct: 23  DTAVGKLIRNYKKQKQIEYDELTTKIAKPFELNADGIDNLLQNIEDAGISVVD------E 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G  D   L ++   S   ++          +DPVRMYL+E+G + LL+ + E+ +A RI
Sbjct: 77  NGDPDPRALKATEKFSQSAMKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVQLALRI 136

Query: 147 EAGRAMMMASLCESPL 162
           E G  +    L E+ L
Sbjct: 137 EKGDEVAKQELAEANL 152


>gi|253580849|ref|ZP_04858112.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847919|gb|EES75886.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 375

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 125 IELAKRMENGDEAAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 184

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 185 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPE 244

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ M VE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+
Sbjct: 245 EIAKEMDMSVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLK 304

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL++LT RE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 305 EQLVEVLSTLTDREQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 364

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ +LD
Sbjct: 365 SRSRKLKDYLD 375



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 44/147 (29%), Positives = 67/147 (45%), Gaps = 32/147 (21%)

Query: 34  MIKLARQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD---------- 82
           +++LA+++  V   +E+N F     +  EQME     L   G++V+   D          
Sbjct: 15  LLELAKKKKNVLEYQEINDFFKDQPLGVEQMEKVFDFLEASGVDVLRITDSNADDMILDD 74

Query: 83  -------LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
                  L++EE   D +DL+     S               +DPVRMYL+E+G + LLS
Sbjct: 75  DDADIDKLDEEEIELDKIDLSVPEGVS--------------IEDPVRMYLKEIGKVPLLS 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPL 162
            E EI +AKR+E G       L E+ L
Sbjct: 121 AEEEIELAKRMENGDEAAKKRLAEANL 147


>gi|312622967|ref|YP_004024580.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203434|gb|ADQ46761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 417

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 180 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  REPTPEEIAK++ MPVE V
Sbjct: 240 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKV 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  + L+E    VL SL  R
Sbjct: 300 REILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNER 359

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL++RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 360 EKKVLKLRFGLEDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 417



 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I L + +G++T  E+   L   E+ + Q+E+    L +MGI+VVD D + +EE  +D
Sbjct: 75  RELISLGQSKGFLTYSEIQEILDKVELDASQVENIYDTLESMGIDVVD-DRVSEEELLKD 133

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            ++                     + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 134 DIENLPEGI---------------AIDDPVRMYLKEIGKIPLLTPEEEIELAKRIEQGDE 178

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 179 EAKKRLAEANLRLVVSIAKR 198


>gi|148543974|ref|YP_001271344.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri DSM 20016]
 gi|184153369|ref|YP_001841710.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri JCM 1112]
 gi|227364887|ref|ZP_03848933.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|325682488|ref|ZP_08162005.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
 gi|148531008|gb|ABQ83007.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus reuteri DSM
           20016]
 gi|183224713|dbj|BAG25230.1| RNA polymerase sigma-43 factor RpoD [Lactobacillus reuteri JCM
           1112]
 gi|227070091|gb|EEI08468.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|324978327|gb|EGC15277.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
          Length = 380

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 163/306 (53%), Positives = 217/306 (70%), Gaps = 10/306 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP  +   + F +   K+  A    + +KI + ++    E G    ++  E   +   + 
Sbjct: 81  DPRALKATEKFSQSAMKDTSAP---TGVKINDPVRMYLKEIGRVNLLTADEEVQLALRIE 137

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+    +AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 138 KGD---EVAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFK 194

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  +
Sbjct: 195 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAE 254

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP E VR +LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    +++    
Sbjct: 255 MDMPTEKVRNILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEMMKKQLEN 314

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 315 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 374

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 375 LKDFLE 380



 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 71/136 (52%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  K+I+  +++  +  +EL   +  P E++++ +++ +  + + GI+VVD      E
Sbjct: 23  DTAVGKLIRNYKKQKQIEYDELTTKIAKPFELNADGIDNLLQNIEDAGISVVD------E 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G  D   L ++   S   ++          +DPVRMYL+E+G + LL+ + E+ +A RI
Sbjct: 77  NGDPDPRALKATEKFSQSAMKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVQLALRI 136

Query: 147 EAGRAMMMASLCESPL 162
           E G  +    L E+ L
Sbjct: 137 EKGDEVAKQELAEANL 152


>gi|29376087|ref|NP_815241.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis V583]
 gi|227518714|ref|ZP_03948763.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227553323|ref|ZP_03983372.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229545861|ref|ZP_04434586.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|229550053|ref|ZP_04438778.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|255975889|ref|ZP_05426475.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256619027|ref|ZP_05475873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256762453|ref|ZP_05503033.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256853088|ref|ZP_05558458.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256958944|ref|ZP_05563115.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256961963|ref|ZP_05566134.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256965161|ref|ZP_05569332.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|257078975|ref|ZP_05573336.1| sigma 42 [Enterococcus faecalis JH1]
 gi|257082587|ref|ZP_05576948.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|257085220|ref|ZP_05579581.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|257086781|ref|ZP_05581142.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|257089848|ref|ZP_05584209.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257416057|ref|ZP_05593051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis AR01/DG]
 gi|257419260|ref|ZP_05596254.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257422656|ref|ZP_05599646.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|293383032|ref|ZP_06628950.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|293389479|ref|ZP_06633936.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294779115|ref|ZP_06744526.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|300860473|ref|ZP_07106560.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|307271055|ref|ZP_07552338.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|307273262|ref|ZP_07554508.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|307274998|ref|ZP_07556161.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|307278111|ref|ZP_07559195.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|307289068|ref|ZP_07569024.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|307292033|ref|ZP_07571902.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|312900723|ref|ZP_07760020.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|312903270|ref|ZP_07762450.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|312907497|ref|ZP_07766488.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|312910115|ref|ZP_07768962.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|312951455|ref|ZP_07770352.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|30179886|sp|P52329|RPOD_ENTFA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|29343549|gb|AAO81311.1| RNA polymerase sigma-43 factor [Enterococcus faecalis V583]
 gi|227073834|gb|EEI11797.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227177552|gb|EEI58524.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229304757|gb|EEN70753.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|229309016|gb|EEN75003.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|255968761|gb|EET99383.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256598554|gb|EEU17730.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256683704|gb|EEU23399.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256711547|gb|EEU26585.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256949440|gb|EEU66072.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256952459|gb|EEU69091.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256955657|gb|EEU72289.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|256987005|gb|EEU74307.1| sigma 42 [Enterococcus faecalis JH1]
 gi|256990617|gb|EEU77919.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|256993250|gb|EEU80552.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|256994811|gb|EEU82113.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|256998660|gb|EEU85180.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257157885|gb|EEU87845.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ARO1/DG]
 gi|257161088|gb|EEU91048.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257164480|gb|EEU94440.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|291079697|gb|EFE17061.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|291081096|gb|EFE18059.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294453840|gb|EFG22231.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|295112959|emb|CBL31596.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Enterococcus sp. 7L76]
 gi|300849512|gb|EFK77262.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|306497031|gb|EFM66579.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|306499777|gb|EFM69138.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|306505508|gb|EFM74694.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|306508446|gb|EFM77553.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|306510247|gb|EFM79271.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|306512553|gb|EFM81202.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|310626525|gb|EFQ09808.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|310630611|gb|EFQ13894.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|310633146|gb|EFQ16429.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|311289388|gb|EFQ67944.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|311292204|gb|EFQ70760.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|315027303|gb|EFT39235.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2137]
 gi|315033932|gb|EFT45864.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0017]
 gi|315036941|gb|EFT48873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0027]
 gi|315144454|gb|EFT88470.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2141]
 gi|315147227|gb|EFT91243.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4244]
 gi|315150574|gb|EFT94590.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0012]
 gi|315152521|gb|EFT96537.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0031]
 gi|315155799|gb|EFT99815.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0043]
 gi|315158034|gb|EFU02051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0312]
 gi|315160483|gb|EFU04500.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0645]
 gi|315163977|gb|EFU07994.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1302]
 gi|315169073|gb|EFU13090.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1341]
 gi|315169690|gb|EFU13707.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1342]
 gi|315172348|gb|EFU16365.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1346]
 gi|315575904|gb|EFU88095.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309B]
 gi|315577570|gb|EFU89761.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0630]
 gi|315580556|gb|EFU92747.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309A]
 gi|327535095|gb|AEA93929.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis OG1RF]
 gi|329571347|gb|EGG53034.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1467]
          Length = 368

 Score =  325 bits (833), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 165/306 (53%), Positives = 217/306 (70%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI + ++    E G    ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA   K+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 EGDQEA---KQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 10/132 (7%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            IK  + +G V  ++L N    P  + +E ME  +  + + GI+VVD    E+ + SE S
Sbjct: 16  FIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVD----ENGDPSEHS 71

Query: 93  LDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           L      +  +   Q    SA      +DPVRMYL+E+G ++LL+   E+ +A +IE G 
Sbjct: 72  LKKDEKEAEKA---QAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEEGD 128

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 129 QEAKQRLAEANL 140


>gi|225575013|ref|ZP_03783623.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037764|gb|EEG48010.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
          Length = 374

 Score =  325 bits (833), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 137 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK++ M V+ V
Sbjct: 197 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAKEMEMSVDRV 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL++LT R
Sbjct: 257 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLVEVLSTLTDR 316

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 317 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 374



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/126 (33%), Positives = 63/126 (50%), Gaps = 2/126 (1%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS 98
           +++  +  +E+N F     + +EQ+E     L   GI+V+   D + +E      DL   
Sbjct: 21  KKKNVLEYQEINDFFKDTPLDTEQLEKVFDFLEASGIDVLRISDSDVDEALLLDEDLDKI 80

Query: 99  ASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           A    V L K   S     S +DPVRMYL+E+G + LL+ E EI +AKR+E G       
Sbjct: 81  AEEEDVELDKIDLSVPEGVSIEDPVRMYLKEIGKVNLLTAEEEIELAKRMEEGDEDAKKR 140

Query: 157 LCESPL 162
           L E+ L
Sbjct: 141 LAEANL 146


>gi|323480687|gb|ADX80126.1| RNA polymerase sigma factor rpoD (Sigma-42) [Enterococcus faecalis
           62]
          Length = 356

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 165/306 (53%), Positives = 217/306 (70%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI + ++    E G    ++ +E   +   + 
Sbjct: 54  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 113

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA   K+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 114 EGDQEA---KQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 170

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 171 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 230

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 231 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 290

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 291 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 350

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 351 LKDFLE 356



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 10/132 (7%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            IK  + +G V  ++L N    P  + +E ME  +  + + GI+VVD    E+ + SE S
Sbjct: 4   FIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVD----ENGDPSEHS 59

Query: 93  LDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           L      +  +   Q    SA      +DPVRMYL+E+G ++LL+   E+ +A +IE G 
Sbjct: 60  LKKDEKEAEKA---QAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEEGD 116

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 117 QEAKQRLAEANL 128


>gi|313903914|ref|ZP_07837294.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
 gi|313471063|gb|EFR66385.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
          Length = 373

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 199/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E    +AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 123 IELAKRMEEGDEVAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTPE
Sbjct: 183 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEYGREPTPE 242

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK + M VE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D+N   P D+A    L+
Sbjct: 243 EIAKNMNMSVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDENVPVPADAAAFTMLK 302

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L  RE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 303 EQLEEVLGTLAEREQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 362

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ +LD
Sbjct: 363 SRSRKLKDYLD 373



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 42/145 (28%), Positives = 76/145 (52%), Gaps = 8/145 (5%)

Query: 32  KKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K++I++A+++   + I E+  +     ++ +Q++  V+ L    I+V+    + D +G +
Sbjct: 13  KELIEVAKKKKNALEISEIADYFKELNLNDKQLKSVVSYLEEHDIDVLR---INDNDGPD 69

Query: 91  DSLDLASSAS--NSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           D + L S +   N    ++    S     S +DPVRMYL+E+G + LLS + EI +AKR+
Sbjct: 70  DEMLLISESDEDNEDNDMENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSADEEIELAKRM 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWR 171
           E G  +    L E+ L     I  R
Sbjct: 130 EEGDEVAKKRLAEANLRLVVSIAKR 154


>gi|116494985|ref|YP_806719.1| RNA polymerase sigma factor RpoD [Lactobacillus casei ATCC 334]
 gi|191638497|ref|YP_001987663.1| RNA polymerase sigma factor RpoD [Lactobacillus casei BL23]
 gi|227535009|ref|ZP_03965058.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|301066553|ref|YP_003788576.1| DNA-directed RNA polymerase sigma70/sigma32 subunit [Lactobacillus
           casei str. Zhang]
 gi|116105135|gb|ABJ70277.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei ATCC
           334]
 gi|190712799|emb|CAQ66805.1| RNA polymerase sigma factor [Lactobacillus casei BL23]
 gi|227187324|gb|EEI67391.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|300438960|gb|ADK18726.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus casei str. Zhang]
 gi|327382532|gb|AEA54008.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei LC2W]
 gi|327385729|gb|AEA57203.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei BD-II]
          Length = 422

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 162/278 (58%), Positives = 208/278 (74%), Gaps = 1/278 (0%)

Query: 405 SILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           S +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y
Sbjct: 145 SGVKINDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQEAKQRLAEANLRLVVSIAKRY 204

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 205 VGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 264

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+E
Sbjct: 265 HMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEE 324

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D SHLGDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLE
Sbjct: 325 DDSHLGDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLE 384

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 385 EVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 422



 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 70/136 (51%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      E
Sbjct: 65  DDAVKAVIKDYKKKKQITEDDLTDKLVKPFELKSGAIDDLMQKIEDNGIAIVD------E 118

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +I
Sbjct: 119 NGEPAAISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI 178

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 179 EQGDQEAKQRLAEANL 194


>gi|194467797|ref|ZP_03073783.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
 gi|194452650|gb|EDX41548.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
          Length = 380

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + KG+    +AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLTADEEVQLALRIEKGD---EVAKQELAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 71/136 (52%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  K+I+  +++  +  +EL   +  P E++++ +++ +  + + GI+VVD      E
Sbjct: 23  DTAVGKLIRNYKKQKQIEYDELTTKIAKPFELNADGIDNLLQNIEDAGISVVD------E 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G  D   L ++   S   ++          +DPVRMYL+E+G + LL+ + E+ +A RI
Sbjct: 77  NGDPDPRALKATEKLSQSAMKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVQLALRI 136

Query: 147 EAGRAMMMASLCESPL 162
           E G  +    L E+ L
Sbjct: 137 EKGDEVAKQELAEANL 152


>gi|255972833|ref|ZP_05423419.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
 gi|255963851|gb|EET96327.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
          Length = 368

 Score =  325 bits (833), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 165/306 (53%), Positives = 217/306 (70%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI + ++    E G    ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA   K+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 EGDQEA---KQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 67/132 (50%), Gaps = 10/132 (7%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            IK  + +G V  ++L N    P  + +E ME  +  + ++GI+VVD    E+ + SE S
Sbjct: 16  FIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDVGISVVD----ENGDPSEHS 71

Query: 93  LDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           L      +  +   Q    SA      +DPVRMYL+E+G ++LL+   E+ +A +IE G 
Sbjct: 72  LKKDEKEAEKA---QAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEEGD 128

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 129 QEAKQRLAEANL 140


>gi|256004390|ref|ZP_05429371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255991674|gb|EEU01775.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|316940353|gb|ADU74387.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 358

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 89  VRMYLKEIGKVPLLTAEEEIELAHRMEQGDAEA---KRRLAEANLRLVVSIAKRYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKLIRVSRQLLQELGREPHPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 266 GDFIPDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/133 (36%), Positives = 72/133 (54%), Gaps = 18/133 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---DLEDEEGS 89
           ++I+  +Q+G +T +E+       ++  EQ+E     L NMGI+VV GD   ++ED + +
Sbjct: 13  ELIEKGKQKGMLTYQEIMDAFEEVDIDPEQIEKIYETLENMGIDVV-GDIEAEMEDIQLT 71

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED LDL+     S               DDPVRMYL+E+G + LL+ E EI +A R+E G
Sbjct: 72  EDDLDLSIPEGIS--------------IDDPVRMYLKEIGKVPLLTAEEEIELAHRMEQG 117

Query: 150 RAMMMASLCESPL 162
            A     L E+ L
Sbjct: 118 DAEAKRRLAEANL 130


>gi|258539717|ref|YP_003174216.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus Lc 705]
 gi|257151393|emb|CAR90365.1| RNA polymerase sigma factor [Lactobacillus rhamnosus Lc 705]
          Length = 416

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 159/273 (58%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 147 VRMYLKEIGRVSLLTTDEEVALALKIEQGDQEA---KQRLAEANLRLVVSIAKRYVGRGM 203

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 204 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 263

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 264 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 323

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 324 GDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 383

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 384 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 416



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 70/136 (51%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      E
Sbjct: 59  DDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVD------E 112

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +I
Sbjct: 113 NGEPATISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTTDEEVALALKI 172

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 173 EQGDQEAKQRLAEANL 188


>gi|51891726|ref|YP_074417.1| RNA polymerase sigma factor RpoD [Symbiobacterium thermophilum IAM
           14863]
 gi|51855415|dbj|BAD39573.1| RNA polymerase major sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 388

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 153/248 (61%), Positives = 201/248 (81%), Gaps = 3/248 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + KG+ EA   K+++ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  G
Sbjct: 144 IEKGDEEA---KRKLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYRKG 200

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEEIA
Sbjct: 201 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVTRQLVQELGREPTPEEIA 260

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +PVE VR++ KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    L+E  
Sbjct: 261 AVMDIPVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFTLLKEQL 320

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL SLTPREE+VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 321 EEVLESLTPREEKVLRLRFGLDDGRARTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRS 380

Query: 674 KKLRSFLD 681
           KKL+ +L+
Sbjct: 381 KKLKDYLE 388



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 42/146 (28%), Positives = 69/146 (47%), Gaps = 16/146 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +++G ++ +E+   L   E+ +EQME     L+  GI +  GD+ ++ E   D
Sbjct: 16  KQLIAKGKRKGSLSYDEVADSLQELELDAEQMEAIFDTLTEAGIKL-QGDEPDEAEEPVD 74

Query: 92  ------SLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSR 136
                 +LD+                + +          + DDPVRMYL+E+G + LL+ 
Sbjct: 75  GDADVEALDVVEPPPVDDAEPDDDAAAGEDDDLSVPEGIAIDDPVRMYLKEIGRVPLLTA 134

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPL 162
           E EI  A+RIE G       L E+ L
Sbjct: 135 EEEIMYAERIEKGDEEAKRKLAEANL 160


>gi|270291312|ref|ZP_06197534.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304385062|ref|ZP_07367408.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
 gi|270280158|gb|EFA25994.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304329256|gb|EFL96476.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
          Length = 379

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 153/238 (64%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 142 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYQKGFKFSTYATWW 201

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ MP + V
Sbjct: 202 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPMPEEIGAEMDMPSDKV 261

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 262 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQLEGVLDTLTDR 321

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 322 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLD 379



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/153 (30%), Positives = 69/153 (45%), Gaps = 16/153 (10%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           ++ E ++D +  + + GI+VVD    E+ + SE +L    +   S   L   K  A    
Sbjct: 54  LTDEDVDDLIQRIEDAGISVVD----ENGDPSEKAL---KAQEISKEELDDTKAPAGVKI 106

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +DPVRMYL+E+G + LL+ + E+A+A RIE G       L E+ L     I  R  +  G
Sbjct: 107 NDPVRMYLKEIGRVSLLTADEEVALALRIEKGDERAKQELAEANLRLVVSIAKR-YVGRG 165

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
              L  I         E   G     E   YQK
Sbjct: 166 MQFLDLI--------QEGNMGLMKAVEKFDYQK 190


>gi|241668482|ref|ZP_04756060.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877016|ref|ZP_05249726.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843037|gb|EET21451.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 578

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 182/370 (49%), Positives = 251/370 (67%), Gaps = 12/370 (3%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK    L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 217 KKLYSKIVKEFECLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 276

Query: 374 HQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++   ++  W+ S  K +   ++ +    E+ ++ K  N+ +++ +   + I E + +  
Sbjct: 277 YEIGSIE--WLPSLTKKY---KFTDNTVKEIHNLTKQINQFQNLMM---MKIEELKKVNV 328

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + K E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  
Sbjct: 329 EISKSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRK 388

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI
Sbjct: 389 GFKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEI 448

Query: 553 AKKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            +    M  + ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE
Sbjct: 449 IEYTPNMTKDKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLRE 508

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               ++   LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHP
Sbjct: 509 AIKELIDTGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHP 568

Query: 671 SRSKKLRSFL 680
           SRS  L++FL
Sbjct: 569 SRSAFLKTFL 578



 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/133 (32%), Positives = 69/133 (51%), Gaps = 15/133 (11%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSE--QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
            ++RGY+T  ++   LP D VS +  + E+  A+L + GI+V D     DE+  E  +  
Sbjct: 17  GKERGYLTRADILDALPGD-VSEDPKKYEEIEAILIDAGIDVYDRTPELDEDDDERKVSE 75

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           A+             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + +
Sbjct: 76  ANL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFS 123

Query: 156 SLCESPLTFQALI 168
           ++   P+  +  I
Sbjct: 124 TILSYPIVVKTYI 136


>gi|199598416|ref|ZP_03211835.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|258508506|ref|YP_003171257.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
 gi|199590735|gb|EDY98822.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|257148433|emb|CAR87406.1| RNA polymerase sigma factor [Lactobacillus rhamnosus GG]
 gi|259649816|dbj|BAI41978.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
          Length = 416

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 159/273 (58%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 147 VRMYLKEIGRVSLLTADEEVALALKIEQGDQEA---KQRLAEANLRLVVSIAKRYVGRGM 203

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 204 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 263

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 264 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 323

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 324 GDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 383

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 384 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 416



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 70/136 (51%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      E
Sbjct: 59  DDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVD------E 112

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +I
Sbjct: 113 NGEPATISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI 172

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 173 EQGDQEAKQRLAEANL 188


>gi|227878689|ref|ZP_03996603.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256843283|ref|ZP_05548771.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256850360|ref|ZP_05555788.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|262046492|ref|ZP_06019454.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|293380134|ref|ZP_06626221.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295693058|ref|YP_003601668.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|312978174|ref|ZP_07789918.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
 gi|227861704|gb|EEJ69309.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256614703|gb|EEU19904.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256712757|gb|EEU27750.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|260573363|gb|EEX29921.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|290923304|gb|EFE00220.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295031164|emb|CBL50643.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|310894892|gb|EFQ43962.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
          Length = 370

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 120 IALAKRIESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 180 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 240 EIGAEMNMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   +VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEQVLETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS +LR F+D
Sbjct: 360 SRSNQLRDFMD 370



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 58/120 (48%), Gaps = 7/120 (5%)

Query: 44  VTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T E+  A  + P  +  + ++  V    + GI++VD      E G    L L       
Sbjct: 29  ITEEDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVE 82

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 83  KAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIESGDEEAKQELAEANL 142


>gi|160937106|ref|ZP_02084469.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440007|gb|EDP17755.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
          Length = 378

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 200/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +K E     A+K + E+NLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+
Sbjct: 127 VELAKKMELGDPEARKRLAESNLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDY 186

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VRT+R++  ++ REPT E
Sbjct: 187 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRTSRQLLQELGREPTTE 246

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA +L +PVE V +++K+++EP+SLETPIG+E+ SHLGDFI+D N + P D+A    L 
Sbjct: 247 EIAARLDLPVERVSEIMKMSQEPVSLETPIGEEEDSHLGDFIQDDNVLVPQDAAAFTLLH 306

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VLR+RFG+      TLEEVGKQF VTRERIRQIEAKA+RKL+HP
Sbjct: 307 EQLMEVLLTLTEREQKVLRLRFGLDDGRPRTLEEVGKQFNVTRERIRQIEAKALRKLRHP 366

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 367 SRSKKLKDYLD 377



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G I LL  E E+ +AK++E G       L ES L
Sbjct: 103 SLEDPVRMYLKEIGKIPLLGMEDEVELAKKMELGDPEARKRLAESNL 149


>gi|227904114|ref|ZP_04021919.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
 gi|227868133|gb|EEJ75554.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
          Length = 370

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 120 IALAKRIESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 180 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 240 EIGAEMNMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   +VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEQVLETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS +LR F+D
Sbjct: 360 SRSNQLRDFMD 370



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIESGDEEAKQELAEANL 142


>gi|167627930|ref|YP_001678430.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597931|gb|ABZ87929.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 578

 Score =  324 bits (831), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 182/370 (49%), Positives = 251/370 (67%), Gaps = 12/370 (3%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLER 373
           K L  K+VK    L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ 
Sbjct: 217 KKLYSKIVKEFECLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKV 276

Query: 374 HQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++   ++  W+ S  K +   ++ +    E+ ++ K  N+ +++ +   + I E + +  
Sbjct: 277 YEIGSIE--WLPSLTKKY---KFTDNTVKEIHNLTKQINQFQNLMM---MKIEELKKVNV 328

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + K E + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  
Sbjct: 329 EISKSEAKITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRK 388

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI
Sbjct: 389 GFKFSTYATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEI 448

Query: 553 AKKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            +    M  + ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE
Sbjct: 449 IEYTPNMTKDKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLRE 508

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               ++   LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHP
Sbjct: 509 AIKELIDTGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHP 568

Query: 671 SRSKKLRSFL 680
           SRS  L++FL
Sbjct: 569 SRSAFLKTFL 578



 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/133 (32%), Positives = 69/133 (51%), Gaps = 15/133 (11%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSE--QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
            ++RGY+T  ++   LP D VS +  + E+  A+L + GI+V D     DE+  E  +  
Sbjct: 17  GKERGYLTRADILDALPGD-VSEDPKKYEEIEAILIDAGIDVYDRTPELDEDDDERKVSE 75

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           A+             D     T DP+RMY+REMG ++LL ++GE  IA RIE G   + +
Sbjct: 76  ANL------------DDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEGTTEVFS 123

Query: 156 SLCESPLTFQALI 168
           ++   P+  +  I
Sbjct: 124 TILSYPIVVKTYI 136


>gi|83589488|ref|YP_429497.1| RNA polymerase sigma factor RpoD [Moorella thermoacetica ATCC
           39073]
 gi|83572402|gb|ABC18954.1| RNA polymerase, sigma 70 subunit, RpoD [Moorella thermoacetica ATCC
           39073]
          Length = 361

 Score =  324 bits (831), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 111 IELAKRMEAGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPE
Sbjct: 171 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +PVE VR++ KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    LR
Sbjct: 231 EIAHEMDIPVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDEDAQAPAEAASFMLLR 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL SLTPRE+RVLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 291 EQLEEVLNSLTPREKRVLRLRFGLDDGRARTLEEVGQEFGVTRERIRQIEAKALRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +L+
Sbjct: 351 SRSKKLKDYLE 361



 Score = 67.8 bits (164), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 68/124 (54%), Gaps = 20/124 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV------DGDDLED 85
           K++I+  + +G +T  E+   L   E+S EQ++D    L +MGI VV      +  + ED
Sbjct: 11  KELIEKGKSQGSLTYSEIMDALQGIELSPEQIDDIYEQLGHMGIEVVPEAAELEALEKED 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E  E  LDL S   N ++             DDPVRMYL+E+G + LL+ E EI +AKR
Sbjct: 71  SEAGETDLDL-SIPENVAI-------------DDPVRMYLKEIGRVPLLTPEEEIELAKR 116

Query: 146 IEAG 149
           +EAG
Sbjct: 117 MEAG 120


>gi|229552308|ref|ZP_04441033.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
 gi|229314290|gb|EEN80263.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
          Length = 416

 Score =  324 bits (831), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 159/273 (58%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 147 VRMYLKEIGRVSLLTADEEVALALKIEQGDQEA---KQRLAEANLRLVVSIAKRYVGRGM 203

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 204 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 263

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 264 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 323

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 324 GDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 383

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 384 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 416



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 70/136 (51%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      E
Sbjct: 59  DDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVD------E 112

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +I
Sbjct: 113 NGEPATISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI 172

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 173 EQGDQEAKQRLAEANL 188


>gi|769798|emb|CAA60113.1| sigma 42 [Enterococcus faecalis]
          Length = 368

 Score =  324 bits (831), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 165/306 (53%), Positives = 216/306 (70%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI + ++    E G    ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA   K+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 EGDQEA---KQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRMQRNLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 10/132 (7%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            IK  + +G V  ++L N    P  + +E ME  +  + + GI+VVD    E+ + SE S
Sbjct: 16  FIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVD----ENGDPSEHS 71

Query: 93  LDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           L      +  +   Q    SA      +DPVRMYL+E+G ++LL+   E+ +A +IE G 
Sbjct: 72  LKKDEKEAEKA---QAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEEGD 128

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 129 QEAKQRLAEANL 140


>gi|315038507|ref|YP_004032075.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325956923|ref|YP_004292335.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|312276640|gb|ADQ59280.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325333488|gb|ADZ07396.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|327183703|gb|AEA32150.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1118]
          Length = 370

 Score =  324 bits (831), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 120 IALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 180 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 240 EIGAEMNMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   +VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEQVLETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS +LR F+D
Sbjct: 360 SRSNQLRDFMD 370



 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIEAG       L E+ L
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIEAGDEEAKQELAEANL 142


>gi|239631415|ref|ZP_04674446.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|239525880|gb|EEQ64881.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
          Length = 352

 Score =  324 bits (831), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 162/278 (58%), Positives = 208/278 (74%), Gaps = 1/278 (0%)

Query: 405 SILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           S +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y
Sbjct: 75  SGVKINDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQEAKQRLAEANLRLVVSIAKRY 134

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 135 VGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 194

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+E
Sbjct: 195 HMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEE 254

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D SHLGDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLE
Sbjct: 255 DDSHLGDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLE 314

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 315 EVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 352



 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 66/130 (50%), Gaps = 7/130 (5%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           MIK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      E G   +
Sbjct: 1   MIKDYKKKKQITEDDLTDKLVKPFELKSGAIDDLMQKIEDNGIAIVD------ENGEPAA 54

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           + L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +IE G   
Sbjct: 55  ISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQE 114

Query: 153 MMASLCESPL 162
               L E+ L
Sbjct: 115 AKQRLAEANL 124


>gi|58337478|ref|YP_194063.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus NCFM]
 gi|58254795|gb|AAV43032.1| RNA polymerase sigma factor [Lactobacillus acidophilus NCFM]
          Length = 356

 Score =  324 bits (831), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 106 IALAKRIESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 165

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 166 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 225

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 226 EIGAEMNMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLK 285

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   +VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 286 EQLEQVLETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 345

Query: 671 SRSKKLRSFLD 681
           SRS +LR F+D
Sbjct: 346 SRSNQLRDFMD 356



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 24  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 77

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 78  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIESGDEEAKQELAEANL 128


>gi|167768032|ref|ZP_02440085.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|317498375|ref|ZP_07956670.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|167710361|gb|EDS20940.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|291561030|emb|CBL39830.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SSC/2]
 gi|316894269|gb|EFV16456.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 363

 Score =  324 bits (831), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 199/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 126 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA+++ +PVE V
Sbjct: 186 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAEEMDIPVERV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D+N   P D+A    L+E    VL +LT R
Sbjct: 246 REILKISQEPVSLETPIGEEEDSHLGDFIQDENVPVPADAAAFTLLKEQLDEVLGTLTER 305

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+  +   TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 306 EQKVLRLRFGLDDSRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 363



 Score = 44.7 bits (104), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS + EI +A+R+E G       L E+ L
Sbjct: 89  SIEDPVRMYLKEIGKVPLLSADEEIKLAQRMEEGDEAAKKKLAEANL 135


>gi|323466388|gb|ADX70075.1| RNA polymerase sigma factor [Lactobacillus helveticus H10]
          Length = 370

 Score =  324 bits (830), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW
Sbjct: 133 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP   V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPTNKV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +LT R
Sbjct: 253 RNILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+D
Sbjct: 313 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFMD 370



 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 52/111 (46%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE G       L E+ L
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIEEGDEEAKQELAEANL 142


>gi|116618341|ref|YP_818712.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|116097188|gb|ABJ62339.1| RNA polymerase, sigma 70 subunit, RpoD [Leuconostoc mesenteroides
           subsp. mesenteroides ATCC 8293]
          Length = 432

 Score =  324 bits (830), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 154/252 (61%), Positives = 195/252 (77%), Gaps = 3/252 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   +  G+ EA   K+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KFD
Sbjct: 180 IAKRIENGDVEA---KQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFD 236

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP P
Sbjct: 237 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLP 296

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  AVSP DSA    L
Sbjct: 297 EEIGAEMDLTADKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYEML 356

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+H
Sbjct: 357 REQLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRH 416

Query: 670 PSRSKKLRSFLD 681
           PSRSK+L+ F+D
Sbjct: 417 PSRSKQLKDFMD 428



 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 64/138 (46%), Gaps = 9/138 (6%)

Query: 28  DDSWKKMI---KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D + K +I   K A+Q  Y  + +  A   P  +  E +E  +  + + GI +VD    +
Sbjct: 69  DKATKALIAEYKAAKQITYAALSKRLA--EPFNLDEENIERLMEKVEDAGIAIVD----D 122

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           + + + + L    +        +  +  A    +DPVRMYL+E+G + LL    EI IAK
Sbjct: 123 NGDPAPEVLKAKQNKPTDQELAEAEETPAGIKINDPVRMYLKEIGRVNLLKGNEEIDIAK 182

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 183 RIENGDVEAKQELAEANL 200


>gi|266623970|ref|ZP_06116905.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288864209|gb|EFC96507.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 345

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 148/251 (58%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K E    +AK+++ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+
Sbjct: 94  IELAKKIELGDELAKEKLTEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDY 153

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VR +R++  ++ REP+PE
Sbjct: 154 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRVSRQLLQELGREPSPE 213

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A ++ MPVE VR+++K+++EP+SLETPIG+E+ SHLGDFI+D     P D+A    L 
Sbjct: 214 EVASRVDMPVERVREIMKVSQEPVSLETPIGEEEDSHLGDFIQDDQVAVPADAATFTMLH 273

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 274 EQLMEVLDTLTEREQKVLRLRFGLDDGRPRTLEEVGREFNVTRERIRQIEAKALRKLRHP 333

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 334 SRSKKLKDYLD 344



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 32/47 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS + EI +AK+IE G  +    L E+ L
Sbjct: 70  SVEDPVRMYLKEIGKVPLLSSDDEIELAKKIELGDELAKEKLTEANL 116


>gi|259503187|ref|ZP_05746089.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
 gi|259168844|gb|EEW53339.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
          Length = 380

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 159/288 (55%), Positives = 208/288 (72%), Gaps = 16/288 (5%)

Query: 410 RNEIKSISVETGISISE-----FRHI-----------VSMVRKGECEASIAKKEMVEANL 453
           +N +K  S  TG+ I++      + I           V +  + E    +AK+++ EANL
Sbjct: 93  QNAMKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVKLALRIEQGDEVAKQQLAEANL 152

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IA
Sbjct: 153 RLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIA 212

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ MP E VR +LKI +EP
Sbjct: 213 DQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEP 272

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLETPIG+ED SHLGDFIED++A SP D A    +++    VL +LT REE VLR+RFG
Sbjct: 273 VSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFG 332

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 333 LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 32/108 (29%), Positives = 57/108 (52%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P E+++E +++ +  + + GI+VVD +      G  D   L ++   S   ++       
Sbjct: 51  PYELNAEGIDNLLQNVEDAGISVVDAN------GDPDPRALKATEKLSQNAMKDTSAPTG 104

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L
Sbjct: 105 VKINDPVRMYLKEIGRVNLLTADEEVKLALRIEQGDEVAKQQLAEANL 152


>gi|227431669|ref|ZP_03913702.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352572|gb|EEJ42765.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 432

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 154/252 (61%), Positives = 195/252 (77%), Gaps = 3/252 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   +  G+ EA   K+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KFD
Sbjct: 180 IAKRIENGDVEA---KQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFD 236

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP P
Sbjct: 237 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLP 296

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  AVSP DSA    L
Sbjct: 297 EEIGAEIDLTADKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYEML 356

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+H
Sbjct: 357 REQLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRH 416

Query: 670 PSRSKKLRSFLD 681
           PSRSK+L+ F+D
Sbjct: 417 PSRSKQLKDFMD 428



 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 64/138 (46%), Gaps = 9/138 (6%)

Query: 28  DDSWKKMI---KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D + K +I   K A+Q  Y  + +  A   P  +  E +E  +  + + GI +VD    +
Sbjct: 69  DKATKALIAEYKAAKQITYAALSKRLA--EPFNLDEENIERLMEKVEDAGIAIVD----D 122

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           + + + + L    +        +  +  A    +DPVRMYL+E+G + LL    EI IAK
Sbjct: 123 NGDPAPEVLKAKQNKPTDQELAEAEETPAGIKINDPVRMYLKEIGRVNLLKGNEEIDIAK 182

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 183 RIENGDVEAKQELAEANL 200


>gi|313884259|ref|ZP_07818025.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620706|gb|EFR32129.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 376

 Score =  324 bits (830), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S+ ++ E    +AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 126 ISLAKRIEDGDELAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDY 185

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R +   + REPTPE
Sbjct: 186 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRNLLQDLGREPTPE 245

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +P E VR++LKI++EP+SLETPIG+ED SHLGDFIED+ A+SP      + LR
Sbjct: 246 EIGAEMDLPTEKVREILKISQEPVSLETPIGEEDDSHLGDFIEDEGAMSPESFTSSSLLR 305

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLE+VGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 306 EQLEDVLDTLTDREENVLRLRFGLDDGNIRTLEQVGKVFGVTRERIRQIEAKALRKLRHP 365

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 366 SRSKQLKDFLE 376



 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/152 (28%), Positives = 81/152 (53%), Gaps = 10/152 (6%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSN 72
           E++++ + L   + D + +++I   +  G +  +EL +    P ++ +E M+  +  + +
Sbjct: 4   ENKNTKNELTLSY-DQARQQLIAEKKLIGQIHYDELTDKIAGPYKLDAEAMDKLIQKVED 62

Query: 73  MGINVV--DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            GI VV  DG   + +      + + +S + +S    K K S      DPVRMYL+E+G 
Sbjct: 63  AGIAVVGDDGGPTKQQMVRAQEVKVDTSTTGNSATASKIKVS------DPVRMYLKEIGR 116

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           ++LLS + EI++AKRIE G  +    L E+ L
Sbjct: 117 VDLLSADAEISLAKRIEDGDELAKQELAEANL 148


>gi|312869100|ref|ZP_07729274.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
 gi|311095346|gb|EFQ53616.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
          Length = 380

 Score =  323 bits (829), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 158/288 (54%), Positives = 208/288 (72%), Gaps = 16/288 (5%)

Query: 410 RNEIKSISVETGISISE-----FRHI-----------VSMVRKGECEASIAKKEMVEANL 453
           +N +K  S  TG+ I++      + I           V +  + E    +AK+++ EANL
Sbjct: 93  QNAMKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVKLALRIEQGDEVAKQQLAEANL 152

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IA
Sbjct: 153 RLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIA 212

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ MP E +R +LKI +EP
Sbjct: 213 DQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKIRNILKIAQEP 272

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLETPIG+ED SHLGDFIED++A SP D A    +++    VL +LT REE VLR+RFG
Sbjct: 273 VSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFG 332

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 333 LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/108 (28%), Positives = 57/108 (52%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P E++++ +++ +  + + GI+VVD +      G  D   L ++   S   ++       
Sbjct: 51  PYELNADGIDNLLQNVEDAGISVVDAN------GDPDPRALKATEKLSQNAMKDTSAPTG 104

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L
Sbjct: 105 VKINDPVRMYLKEIGRVNLLTADEEVKLALRIEQGDEVAKQQLAEANL 152


>gi|291563082|emb|CBL41898.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SS3/4]
          Length = 374

 Score =  323 bits (829), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 200/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K E     AKK++ E+NLRLV+S+AK+Y  RG+Q LDLIQEGN+GL+KA EKFD+
Sbjct: 123 IELAKKIELGDEEAKKKLAESNLRLVVSIAKRYAGRGMQLLDLIQEGNLGLIKAVEKFDY 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VRT R++  K+ RE TPE
Sbjct: 183 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRTQRQLVQKLGREATPE 242

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK+L MPVE VR+++KI+++P+SLETPIG+E+ SHLGDFI+D N   P D+A    L 
Sbjct: 243 ELAKELDMPVERVREIMKISQDPVSLETPIGEEEDSHLGDFIQDNNVEVPADAATYTLLH 302

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL++LT RE++VLR+RFG+      TLEEVG+QF VTRERIRQIEAKA+RKL+HP
Sbjct: 303 EQLMDVLSTLTEREQKVLRLRFGLDDGRPRTLEEVGRQFNVTRERIRQIEAKALRKLRHP 362

Query: 671 SRSKKLRSFLD 681
           SRSK L+ +LD
Sbjct: 363 SRSKILKDYLD 373



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 30/47 (63%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
             DDPVRMYL+E+G + LLS + EI +AK+IE G       L ES L
Sbjct: 99  GVDDPVRMYLKEIGKVPLLSPDEEIELAKKIELGDEEAKKKLAESNL 145


>gi|172056869|ref|YP_001813329.1| RpoD family RNA polymerase sigma factor [Exiguobacterium sibiricum
           255-15]
 gi|171989390|gb|ACB60312.1| RNA polymerase, sigma 70 subunit, RpoD family [Exiguobacterium
           sibiricum 255-15]
          Length = 361

 Score =  323 bits (829), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 154/251 (61%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 111 VELAKRIEQNDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDY 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 171 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI+K++ +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A +P D+A    L+
Sbjct: 231 EISKEMEITPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATAPQDAAAYELLK 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 291 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FLD
Sbjct: 351 SRSKRLKDFLD 361



 Score = 44.7 bits (104), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 63/132 (47%), Gaps = 18/132 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSE 90
           ++I L  + G ++ +++   L   E + ++Q E+ + +L   GI V  DG   + EE   
Sbjct: 18  ELIALGHKNGELSHQKIEDKLSSFESMDAQQFEEFLQLLETEGIKVNNDGTGDDKEEADL 77

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + L +                      +DPVRMYL+E+G ++LL+ E E+ +AKRIE   
Sbjct: 78  NDLSVPPGVK----------------INDPVRMYLKEIGRVDLLNAEDEVELAKRIEQND 121

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 122 EEAKKRLAEANL 133


>gi|229824058|ref|ZP_04450127.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
 gi|229786412|gb|EEP22526.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
          Length = 379

 Score =  323 bits (829), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 154/239 (64%), Positives = 191/239 (79%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD   G+KFSTYA W
Sbjct: 141 IAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDHTKGFKFSTYATW 200

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + REPTPEEI  ++ +P E 
Sbjct: 201 WIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGREPTPEEIGAEMDLPTEK 260

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A+SP      A LRE    VL +LT 
Sbjct: 261 VREILKIAQEPVSLETPIGEEDDSHLGDFIEDEGAMSPEVFTSSALLREQLEDVLDTLTD 320

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLE+VGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 321 REENVLRLRFGLDDGNIRTLEQVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 379



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 69/137 (50%), Gaps = 9/137 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVV--DGDDLED 85
           ++ + +I   +  G V  +EL      P  + ++ ++  + ++ + G++VV  DG   + 
Sbjct: 21  EAVQALILAKKSEGQVHYDELTEKIASPYGLDADGIDTLIQIVEDNGVSVVGDDGGPTKQ 80

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +   E+    A  A+ S     K K S      DPVRMYL+E+G++ LLS E EI +A R
Sbjct: 81  QMVREEEQLQADLAAESKTATSKLKVS------DPVRMYLKEIGNVPLLSAEEEINLAVR 134

Query: 146 IEAGRAMMMASLCESPL 162
           I+ G  +    L E+ L
Sbjct: 135 IQGGDDIAKQELAEANL 151


>gi|300173322|ref|YP_003772488.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
 gi|299887701|emb|CBL91669.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
          Length = 432

 Score =  323 bits (829), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 154/253 (60%), Positives = 196/253 (77%), Gaps = 3/253 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +I   +  G+ EA   K+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KF
Sbjct: 179 NIAKRIEDGDIEA---KQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKF 235

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP 
Sbjct: 236 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPL 295

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  AVSP DSA    
Sbjct: 296 PEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYEM 355

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+
Sbjct: 356 LREQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415

Query: 669 HPSRSKKLRSFLD 681
           HPSRSK+L+ F+D
Sbjct: 416 HPSRSKQLKDFMD 428



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 42/145 (28%), Positives = 66/145 (45%), Gaps = 5/145 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +I   +    +T  +L   L  P  +  E +E  +  + + G+ +VD    E  
Sbjct: 69  DKAVKALIAEYKAAKAITYADLAKRLAEPFNLDGENIERLMEKVEDSGVAIVD----EKG 124

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E + + L    +  +     Q ++  A    +DPVRMYL+E+G + LL  + EI IAKRI
Sbjct: 125 EPAPEVLKAKQNKPSKEELDQAQETPAGIKINDPVRMYLKEIGRVNLLKGDEEINIAKRI 184

Query: 147 EAGRAMMMASLCESPLTFQALIIWR 171
           E G       L E+ L     I  R
Sbjct: 185 EDGDIEAKQELAEANLRLVVSIAKR 209


>gi|260886856|ref|ZP_05898119.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|330839344|ref|YP_004413924.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863455|gb|EEX77955.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|329747108|gb|AEC00465.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 375

 Score =  323 bits (829), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 150/251 (59%), Positives = 202/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     A+KE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 125 IALAKRMEAGDEEAQKELAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 184

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PE
Sbjct: 185 NKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQQLGREPSPE 244

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+ + + VE VR+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    L+
Sbjct: 245 EIAEAMEISVERVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFMLLK 304

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REERVLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 305 EQLEEVLDTLTEREERVLRLRFGLDDGRARTLEEVGQNFGVTRERIRQIEAKALRKLRHP 364

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ FLD
Sbjct: 365 SRSRKLKDFLD 375



 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 65/125 (52%), Gaps = 16/125 (12%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE----DEEGSEDSLDLAS 97
           G +T  EL   L   E++ ++++D     SN GI +VD  +      DE+ +E+ +D+  
Sbjct: 35  GVLTYGELMTALQEQELTPDEIDDLYETFSNKGIEIVDDSNRAQAEMDEDKAEEEVDIDL 94

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           S                 S DDPVRMYL+E+G + LLS + EIA+AKR+EAG       L
Sbjct: 95  SIPEGI------------SIDDPVRMYLKEIGRVPLLSADEEIALAKRMEAGDEEAQKEL 142

Query: 158 CESPL 162
            E+ L
Sbjct: 143 AEANL 147


>gi|227529171|ref|ZP_03959220.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350896|gb|EEJ41187.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
          Length = 380

 Score =  323 bits (828), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 158/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLSADEEVALALRIEQGDEEA---KQELAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 72/136 (52%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  K+I+  ++R ++  ++L   +  P E++++ +++ +  + + GI+VVD      E
Sbjct: 23  DTAVGKLIRTYKKRKHIKYDDLTELVAKPFELNADGIDNLLQNVEDSGISVVD------E 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G  D   L ++   S   ++          +DPVRMYL+E+G + LLS + E+A+A RI
Sbjct: 77  NGDPDPRALMATEKLSQKAMKDTSAPTGVKINDPVRMYLKEIGRVNLLSADEEVALALRI 136

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 137 EQGDEEAKQELAEANL 152


>gi|116492861|ref|YP_804596.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Pediococcus pentosaceus ATCC 25745]
 gi|116103011|gb|ABJ68154.1| RNA polymerase, sigma 70 subunit, RpoD [Pediococcus pentosaceus
           ATCC 25745]
          Length = 379

 Score =  323 bits (828), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 142 ARQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYQKGFKFSTYATWW 201

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ MP + V
Sbjct: 202 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPMPEEIGAEMDMPSDKV 261

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 262 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQLEGVLDTLTDR 321

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 322 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLD 379



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 68/153 (44%), Gaps = 16/153 (10%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           ++ E ++D +  + + GI+VVD    E+ + SE +L    +   S   L   K  A    
Sbjct: 54  LTDEDVDDLIQRIEDAGISVVD----ENGDPSEKAL---KAQEISKEELDDTKAPAGVKI 106

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +DPVRMYL+E+G + LL+ + E+ +A RIE G       L E+ L     I  R  +  G
Sbjct: 107 NDPVRMYLKEIGRVSLLTADQEVELALRIEKGDPRARQELAEANLRLVVSIAKR-YVGRG 165

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
              L  I         E   G     E   YQK
Sbjct: 166 MQFLDLI--------QEGNMGLMKAVEKFDYQK 190


>gi|257869538|ref|ZP_05649191.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
 gi|257803702|gb|EEV32524.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
          Length = 368

 Score =  323 bits (828), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 191/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 131 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ +P E V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT R
Sbjct: 251 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFGI      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 311 EENVLRLRFGIDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 70/139 (50%), Gaps = 12/139 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  + IK  + +G V  +EL N    P  + ++ M+  +  L + GI+VVD      E
Sbjct: 10  DKAVAEFIKENKPKGQVVYDELTNHLATPYSLDADAMDKLIQKLEDSGISVVD------E 63

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIA 143
            G      L S+    +   Q ++D +  +    +DPVRMYL+E+G + LL+ E E+A+A
Sbjct: 64  NGEPSVHSLKSNEKQQAT--QPQEDLSAPTGVKINDPVRMYLKEIGRVPLLTAEEEVALA 121

Query: 144 KRIEAGRAMMMASLCESPL 162
            +IE G       L E+ L
Sbjct: 122 LKIEEGDQEAKQRLAEANL 140


>gi|257867642|ref|ZP_05647295.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257873971|ref|ZP_05653624.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257876550|ref|ZP_05656203.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325571155|ref|ZP_08146727.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
 gi|257801725|gb|EEV30628.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257808135|gb|EEV36957.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257810716|gb|EEV39536.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325156240|gb|EGC68426.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
          Length = 368

 Score =  323 bits (828), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 191/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 131 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ +P E V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT R
Sbjct: 251 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFGI      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 311 EENVLRLRFGIDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 69/139 (49%), Gaps = 12/139 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  + I+  + +G V  +++ N    P  + ++ M+  +  L + GI+VVD      E
Sbjct: 10  DKAVAEYIRENKTKGQVVYDDITNRLATPYTLDADAMDKLIQKLEDSGISVVD------E 63

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIA 143
            G      L S+        Q ++D +  +    +DPVRMYL+E+G + LL+ E E+A+A
Sbjct: 64  NGEPSVHSLKSNEKRQET--QPQEDLSAPTGVKINDPVRMYLKEIGRVPLLTAEEEVALA 121

Query: 144 KRIEAGRAMMMASLCESPL 162
            +IE G       L E+ L
Sbjct: 122 LKIEEGDQEAKQRLAEANL 140


>gi|296112139|ref|YP_003622521.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
 gi|295833671|gb|ADG41552.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
          Length = 432

 Score =  323 bits (827), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 153/253 (60%), Positives = 196/253 (77%), Gaps = 3/253 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +I   +  G+ EA   K+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KF
Sbjct: 179 NIAKRIEDGDVEA---KQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKF 235

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP 
Sbjct: 236 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPL 295

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A+SP DSA    
Sbjct: 296 PEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAISPADSAAYEM 355

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+
Sbjct: 356 LREQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415

Query: 669 HPSRSKKLRSFLD 681
           HPSRSK+L+ F+D
Sbjct: 416 HPSRSKQLKDFMD 428



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 76/169 (44%), Gaps = 15/169 (8%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + KK     + E++ +  +L+ ++         K A+   YV + +  A   P  +  E 
Sbjct: 56  VAKKSGIIKNPEYDKAVKALIAEY---------KAAKAITYVALSQRLA--EPFNLDGEN 104

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E  +  + + G+ +VD    E  E + + L    +  +     Q ++  A    +DPVR
Sbjct: 105 IERLMEKIEDAGVAIVD----EKGEPAPEVLKAKQNKPSKEELEQAQETPAGIKINDPVR 160

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           MYL+E+G + LL  + EI IAKRIE G       L E+ L     I  R
Sbjct: 161 MYLKEIGRVNLLKGDEEINIAKRIEDGDVEAKQELAEANLRLVVSIAKR 209


>gi|291526136|emb|CBK91723.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale DSM
           17629]
 gi|291527130|emb|CBK92716.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale M104/1]
          Length = 418

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 181 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWW 240

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIAK++ MPVE V
Sbjct: 241 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAKEMNMPVERV 300

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 301 REILKISQEPVSLETPIGEEEDSHLGDFIKDDNVPVPADAAAFTLLKEQLEEVLGTLTER 360

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 361 EQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 418



 Score = 41.2 bits (95), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S +DPVRMYL+E+G + LLS + EI +A+ +E G
Sbjct: 106 SVEDPVRMYLKEIGKVPLLSADEEIELAQNMEDG 139


>gi|317122932|ref|YP_004102935.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
 gi|315592912|gb|ADU52208.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
          Length = 433

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 199/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++++ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KAAEKFD+  G+KFSTYA WW
Sbjct: 196 AKRKLIQANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAAEKFDYRKGFKFSTYATWW 255

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEEIAK++ +  E V
Sbjct: 256 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLVQELGREPTPEEIAKEMGIEPEKV 315

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED++A++P ++A Q  LRE    VL +LT R
Sbjct: 316 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDEDALAPAEAASQLLLREQLEDVLHTLTDR 375

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 376 EQKVLRLRFGLDDGRQRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 433



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 33/47 (70%), Gaps = 5/47 (10%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-----RAMMMASL 157
           + DDPVRMYL+E+G I LL+ E EI +AKRIE G     R ++ A+L
Sbjct: 159 ALDDPVRMYLKEIGRIPLLTPEQEIELAKRIEQGDEEAKRKLIQANL 205


>gi|238924709|ref|YP_002938225.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
 gi|238876384|gb|ACR76091.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
          Length = 434

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 197 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWW 256

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIAK++ MPVE V
Sbjct: 257 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAKEMNMPVERV 316

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 317 REILKISQEPVSLETPIGEEEDSHLGDFIKDDNVPVPADAAAFTLLKEQLEEVLGTLTER 376

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 377 EQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 434



 Score = 41.6 bits (96), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S +DPVRMYL+E+G + LLS + EI +A+ +E G
Sbjct: 122 SVEDPVRMYLKEIGKVPLLSADEEIELAQNMEDG 155


>gi|317473637|ref|ZP_07932926.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
 gi|316898927|gb|EFV20952.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
          Length = 364

 Score =  322 bits (826), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 198/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 127 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 186

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA+++ +PV+ V
Sbjct: 187 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAEEMDIPVDRV 246

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E  + VL +LT R
Sbjct: 247 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLSEVLGTLTER 306

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+  +   TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 307 EQKVLRLRFGLDDSRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 364



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 40/147 (27%), Positives = 73/147 (49%), Gaps = 16/147 (10%)

Query: 20  DSLVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           D  +  FS+     +++L ++ + ++   ++  +    +++S+ ME     L   G++V+
Sbjct: 2   DETMLQFSE-KLAGLVELGKKNKNFLEYAQIETYFKDFKLTSDMMEAIFDYLEQNGVDVL 60

Query: 79  ---DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
              +G+D ED E  E+  + A       V           S +DPVRMYL+E+G + LLS
Sbjct: 61  TIPEGEDDEDLEIKEEIEEEADLTIPDGV-----------SIEDPVRMYLKEIGKVPLLS 109

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPL 162
            + EI +A+R+E G       L E+ L
Sbjct: 110 ADEEIRLAQRMEEGDEEAKKKLAEANL 136


>gi|225377779|ref|ZP_03755000.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
 gi|225210363|gb|EEG92717.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
          Length = 426

 Score =  322 bits (825), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 189 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 248

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA ++ MPVE V
Sbjct: 249 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMNMPVERV 308

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 309 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLEEVLGTLTER 368

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 369 EQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 426



 Score = 46.6 bits (109), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 21/34 (61%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S +DPVRMYL+E+G + LLS E EI +AK +EAG
Sbjct: 114 SIEDPVRMYLKEIGKVPLLSAEEEIELAKNMEAG 147


>gi|167747159|ref|ZP_02419286.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
 gi|167654119|gb|EDR98248.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
          Length = 370

 Score =  322 bits (825), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 198/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 133 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA+++ +PV+ V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAEEMDIPVDRV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E  + VL +LT R
Sbjct: 253 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLSEVLGTLTER 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+  +   TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 313 EQKVLRLRFGLDDSRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 370



 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 41/149 (27%), Positives = 74/149 (49%), Gaps = 16/149 (10%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           S D  +  FS+     +++L ++ + ++   ++  +    +++S+ ME     L   G++
Sbjct: 6   SMDETMLQFSE-KLAGLVELGKKNKNFLEYAQIETYFKDFKLTSDMMEAIFDYLEQNGVD 64

Query: 77  VV---DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           V+   +G+D ED E  E+  + A       V           S +DPVRMYL+E+G + L
Sbjct: 65  VLTIPEGEDDEDLEIKEEIEEEADLTIPDGV-----------SIEDPVRMYLKEIGKVPL 113

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPL 162
           LS + EI +A+R+E G       L E+ L
Sbjct: 114 LSADEEIRLAQRMEEGDEEAKKKLAEANL 142


>gi|229916320|ref|YP_002884966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
 gi|229467749|gb|ACQ69521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
          Length = 364

 Score =  322 bits (825), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +G+ EA   KK + EANLRLV+S+AK+Y  RG+
Sbjct: 95  VRMYLKEIGRVDLLSAKDETELAKRIEQGDEEA---KKRLAEANLRLVVSIAKRYVGRGM 151

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 152 LFLDLIQEGNMGLIKAVEKFDYMKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 211

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIAK++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 212 INKLIRVQRQLLQDLGREPSPEEIAKEMELTPEKVREILKIAQEPVSLETPIGEEDDSHL 271

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 272 GDFIEDQDAMAPQDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 331

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 332 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 364



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 37/127 (29%), Positives = 62/127 (48%), Gaps = 8/127 (6%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           KL +++G V+++ +   L   EV S+ +++ +  L    I V         E + D+ + 
Sbjct: 18  KLGKKKGVVSMQAIQDRLSHFEVDSDFIDNFIEDLEAKDIRVT--------EDAADAEET 69

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
            +   +  V L           +DPVRMYL+E+G ++LLS + E  +AKRIE G      
Sbjct: 70  PAKKEDEEVDLNDLSVPPGIKINDPVRMYLKEIGRVDLLSAKDETELAKRIEQGDEEAKK 129

Query: 156 SLCESPL 162
            L E+ L
Sbjct: 130 RLAEANL 136


>gi|69249285|ref|ZP_00604924.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257877975|ref|ZP_05657628.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257881238|ref|ZP_05660891.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257884904|ref|ZP_05664557.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257889826|ref|ZP_05669479.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|258616539|ref|ZP_05714309.1| RNA polymerase sigma factor RpoD [Enterococcus faecium DO]
 gi|260559026|ref|ZP_05831212.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|261207559|ref|ZP_05922244.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289565071|ref|ZP_06445524.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|293556716|ref|ZP_06675279.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|293563374|ref|ZP_06677823.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|293568034|ref|ZP_06679372.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|294614871|ref|ZP_06694766.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|294618226|ref|ZP_06697809.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|314939477|ref|ZP_07846711.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|314941108|ref|ZP_07848006.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|314949892|ref|ZP_07853194.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
 gi|314951693|ref|ZP_07854736.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|314993960|ref|ZP_07859287.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|314996911|ref|ZP_07861912.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|68194219|gb|EAN08744.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257812203|gb|EEV40961.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257816896|gb|EEV44224.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257820742|gb|EEV47890.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257826186|gb|EEV52812.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|260074783|gb|EEW63099.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|260077942|gb|EEW65648.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289163078|gb|EFD10925.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|291589255|gb|EFF21065.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|291592333|gb|EFF23947.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|291595506|gb|EFF26816.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|291601048|gb|EFF31337.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|291604635|gb|EFF34120.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|313588970|gb|EFR67815.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|313591562|gb|EFR70407.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|313596157|gb|EFR75002.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|313600109|gb|EFR78952.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|313641279|gb|EFS05859.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|313643734|gb|EFS08314.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
          Length = 369

 Score =  322 bits (825), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 159/276 (57%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y  
Sbjct: 94  VKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVG 153

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 154 RGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 213

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 214 VETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDD 273

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 274 SHLGDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 333

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 334 GKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 58/115 (50%), Gaps = 9/115 (7%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N    P  +++++M+  +  + + GI+VVD       E  + S+    SA   +   +  
Sbjct: 34  NQLATPFTLNADEMDKLIQKIEDAGISVVD-------ENGDPSIHSLKSAEKKAEQAKTE 86

Query: 110 KDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
             SA      +DPVRMYL+E+G + LL+ E E+A+A +IE G       L E+ L
Sbjct: 87  DLSAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANL 141


>gi|227551146|ref|ZP_03981195.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257887737|ref|ZP_05667390.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257896230|ref|ZP_05675883.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257898868|ref|ZP_05678521.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|293379528|ref|ZP_06625670.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
 gi|293570226|ref|ZP_06681295.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|227179708|gb|EEI60680.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257823791|gb|EEV50723.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257832795|gb|EEV59216.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257836780|gb|EEV61854.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|291609633|gb|EFF38894.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|292641837|gb|EFF60005.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
          Length = 369

 Score =  322 bits (825), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 159/276 (57%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y  
Sbjct: 94  VKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVG 153

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 154 RGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 213

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 214 VETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDD 273

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 274 SHLGDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 333

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 334 GKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 58/115 (50%), Gaps = 9/115 (7%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N    P  +++++M+  +  + + GI+VVD       E  + S+    SA   +   +  
Sbjct: 34  NQLATPFTLNADEMDKLIQKIEDAGISVVD-------ENGDPSIHSLKSAEKKAEQAKTE 86

Query: 110 KDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
             SA      +DPVRMYL+E+G + LL+ E E+A+A +IE G       L E+ L
Sbjct: 87  DLSAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANL 141


>gi|332686632|ref|YP_004456406.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
 gi|332370641|dbj|BAK21597.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
          Length = 369

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 132 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 191

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ +P E V
Sbjct: 192 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKV 251

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP + A    L+E    VL +LT R
Sbjct: 252 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDR 311

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 312 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/130 (32%), Positives = 67/130 (51%), Gaps = 6/130 (4%)

Query: 34  MIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            IK  +Q+G V  ++L N    P  +S+ +ME  +  + + GI++VD    E  E SE S
Sbjct: 17  FIKENKQKGVVVYDDLANKLATPFTLSAGEMEKLIQQIEDNGISIVD----ETGEPSEHS 72

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           L      +  +  L+          +DPVRMYL+E+G ++LL+ E E+ +A +IE G   
Sbjct: 73  LKKDEKEAKKAE-LEDLSAPTGIKINDPVRMYLKEIGRVQLLTAEEEVELALKIEEGDQE 131

Query: 153 MMASLCESPL 162
               L E+ L
Sbjct: 132 AKQRLAEANL 141


>gi|294622679|ref|ZP_06701641.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
 gi|291597877|gb|EFF29007.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
          Length = 369

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 159/276 (57%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y  
Sbjct: 94  VKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVG 153

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 154 RGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 213

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 214 VETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDD 273

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 274 SHLGDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 333

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 334 GKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 58/115 (50%), Gaps = 9/115 (7%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N    P  +++++M+  +  + + GI+VVD       E  + S+    SA   +   +  
Sbjct: 34  NQLATPFTLNADEMDKLIQKIDDAGISVVD-------ENGDPSIHSLKSAEKKAEQAKTE 86

Query: 110 KDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
             SA      +DPVRMYL+E+G + LL+ E E+A+A +IE G       L E+ L
Sbjct: 87  DLSAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANL 141


>gi|326693497|ref|ZP_08230502.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc argentinum KCTC 3773]
          Length = 432

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 152/253 (60%), Positives = 196/253 (77%), Gaps = 3/253 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +I   +  G+ EA   K+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KF
Sbjct: 179 NIAKRIEAGDVEA---KQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKF 235

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP 
Sbjct: 236 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPL 295

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A+SP DSA    
Sbjct: 296 PEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAISPADSAAYEM 355

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+
Sbjct: 356 LRDQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415

Query: 669 HPSRSKKLRSFLD 681
           HPSRSK+L+ F+D
Sbjct: 416 HPSRSKQLKDFMD 428



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 68/147 (46%), Gaps = 9/147 (6%)

Query: 28  DDSWKKMI---KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D + K +I   K A++  Y T+ E  A   P  +  E +E  +  + + G+ +VD    E
Sbjct: 69  DKAVKALIAEYKPAKEVTYATLSERLA--EPFHLDGENIERLMEKVEDAGVAIVD----E 122

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             E + + L    +  +     Q     A    +DPVRMYL+E+G + LL  + EI IAK
Sbjct: 123 KGEPAPEVLQAKQNKPSKEELDQAEDTPAGIKINDPVRMYLKEIGRVNLLKGDEEINIAK 182

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWR 171
           RIEAG       L E+ L     I  R
Sbjct: 183 RIEAGDVEAKQELAEANLRLVVSIAKR 209


>gi|240147091|ref|ZP_04745692.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|257200737|gb|EEU99021.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|291536629|emb|CBL09741.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           M50/1]
          Length = 397

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 199/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 147 IELAKRMELGDQEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 206

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 207 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPE 266

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ MPVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+
Sbjct: 267 EIAAEMNMPVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLK 326

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL +RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 327 EQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHP 386

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ +L+
Sbjct: 387 SRSRKLKDYLE 397



 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L
Sbjct: 123 SIEDPVRMYLKEIGKVPLLSAEEEIELAKRMELGDQEAKKRLAEANL 169


>gi|325662013|ref|ZP_08150632.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331085863|ref|ZP_08334946.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471676|gb|EGC74895.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330406786|gb|EGG86291.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 370

 Score =  322 bits (824), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ E     AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 120 IELARRMEEGDEDAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 180 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L MPV+ VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A    L+
Sbjct: 240 EIAKELDMPVDRVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAATLLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL++LT RE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLDEVLSTLTDREQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS+KLR +LD
Sbjct: 360 SRSRKLRDYLD 370



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 64/131 (48%), Gaps = 27/131 (20%)

Query: 32  KKMIKLARQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL------- 83
           K++I L +++  +  ++E+N F    E+ SEQM+     L    I+V+   +        
Sbjct: 13  KELIALGKKKKSILELQEINDFFSDMELDSEQMDKVFEALEASNIDVLRIGEGDEDDDDI 72

Query: 84  -----EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                E++E   + +DL+     S               +DPVRMYL+E+G + LLS E 
Sbjct: 73  EIMLTEEDEVDMEKIDLSVPDGIS--------------IEDPVRMYLKEIGKVPLLSAEE 118

Query: 139 EIAIAKRIEAG 149
           EI +A+R+E G
Sbjct: 119 EIELARRMEEG 129


>gi|329766845|ref|ZP_08258374.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
 gi|328838571|gb|EGF88177.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
          Length = 361

 Score =  321 bits (823), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 151/244 (61%), Positives = 192/244 (78%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E   AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFS
Sbjct: 118 EAEKEQAKKDLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFS 177

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I++++R  R++   + REP PEEIAKK+ 
Sbjct: 178 TYATWWIRQAITRAIADQARTIRIPVHMVETINRLIRIQRQLLQDLGREPKPEEIAKKMN 237

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  E VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP++ A    L+E    +L
Sbjct: 238 MTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDAQSPVEHAANELLKEQLEEIL 297

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VL++RFG+     HTLEEVG  F VTRERIRQIEAKAIRKLKHPS+  KL+
Sbjct: 298 ETLTDREENVLKLRFGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSKLNKLK 357

Query: 678 SFLD 681
            F++
Sbjct: 358 GFME 361



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 49/89 (55%), Gaps = 3/89 (3%)

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-ASSASNSSVFLQKRKDS--ADRSTDDP 120
           E+ V  LS + I+    DD  +E  SED + + A+        L     S  A   T+DP
Sbjct: 28  EEIVDALSKLDISSEAMDDFYEELNSEDIILINANHVEEEEEELDLEDLSVPAGIRTNDP 87

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAG 149
           VRMYL+E+G + LLS+E E+ ++K IE G
Sbjct: 88  VRMYLKEIGKVPLLSKEKELELSKIIETG 116


>gi|291541030|emb|CBL14141.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           XB6B4]
          Length = 397

 Score =  321 bits (823), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 199/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 147 IELAKRMELGDQEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 206

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 207 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPE 266

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ MPVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+
Sbjct: 267 EIAAEMNMPVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLK 326

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL +RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 327 EQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHP 386

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ +L+
Sbjct: 387 SRSRKLKDYLE 397



 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L
Sbjct: 123 SIEDPVRMYLKEIGKVPLLSAEEEIELAKRMELGDQEAKKRLAEANL 169


>gi|331082069|ref|ZP_08331197.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330405664|gb|EGG85194.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 374

 Score =  321 bits (823), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 137 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA+++ M VE V
Sbjct: 197 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPHPEEIAEEMNMSVERV 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 257 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLVEVLGTLTER 316

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 317 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 374



 Score = 46.2 bits (108), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS E EI +A+R+E G       L E+ L
Sbjct: 100 SIEDPVRMYLKEIGKVPLLSAEEEITLAQRMEEGDESAKKRLAEANL 146


>gi|300813859|ref|ZP_07094164.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300512046|gb|EFK39241.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 361

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 200/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E   + AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 111 VEIAKRMENGDNSAKKELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDY 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P PE
Sbjct: 171 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLVQELGRDPLPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++++ VE VR++ KI +EP+SLETPIG+E+ SHLGDFI D+  +SP D+A    LR
Sbjct: 231 EIAKEMSIDVEKVREIQKIAQEPVSLETPIGEEEDSHLGDFIPDEEILSPQDAATFTLLR 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  + VL +LT RE++VL +RFG+      TLEEVGK+F VTRERIRQIEAKAIRKL+HP
Sbjct: 291 EQLSTVLETLTDREKKVLTLRFGLDDGRARTLEEVGKEFAVTRERIRQIEAKAIRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ FL+
Sbjct: 351 SRSKKLKDFLE 361



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 66/135 (48%), Gaps = 12/135 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D +   + K  +++G++T +E++  L    + S++++       N GI +     L DE 
Sbjct: 11  DTTINNLKKEGKEKGHLTYDEISFALEDIPMDSQEIDSIYKDFENDGIEL-----LNDER 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +   ++     + SV           S DDPVRMYL+E+G I LL+ + E+ IAKR+E
Sbjct: 66  DKDFKEEIDVEKEDLSV-------PKGISVDDPVRMYLKEIGKIPLLTGDEEVEIAKRME 118

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 119 NGDNSAKKELAEANL 133


>gi|104774139|ref|YP_619119.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423220|emb|CAI98048.1| RNA polymerase sigma factor RpoD (Sigma-A) [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC 11842]
          Length = 372

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 122 VALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 182 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +PV+ VR+ LK+ +EP+SLETPIG+ED SHLGDFIEDK+  SP   A    LR
Sbjct: 242 EIAAEMDLPVKKVREALKVAQEPVSLETPIGEEDDSHLGDFIEDKDTTSPEQHAASEMLR 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 DQLAEVLDTLTDREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRS KLR FL+
Sbjct: 362 SRSNKLRDFLE 372



 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E+G    L L    +     L     
Sbjct: 40  LIKPYKLEGKAVDQLVQEFEDNGISIVD------EDGKPSKLALTKQKNVEKAELNNMAA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                 +DPVRMYL+E+G   LL+ E E+A+AKRIEAG       L E+ L
Sbjct: 94  PTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRIEAGDEEAKQELAEANL 144


>gi|170017101|ref|YP_001728020.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
 gi|169803958|gb|ACA82576.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
          Length = 432

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 152/253 (60%), Positives = 196/253 (77%), Gaps = 3/253 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +I   +  G+ EA   K+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KF
Sbjct: 179 NIAKRIEDGDVEA---KQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKF 235

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP 
Sbjct: 236 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPL 295

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A+SP DSA    
Sbjct: 296 PEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAISPADSAAYEM 355

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+
Sbjct: 356 LRDQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415

Query: 669 HPSRSKKLRSFLD 681
           HPSRSK+L+ F+D
Sbjct: 416 HPSRSKQLKDFMD 428



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 54/117 (46%), Gaps = 4/117 (3%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  +  E +E  +  + + G+ +VD    E  E + + L    +  +     Q  +  A 
Sbjct: 97  PFNLDGENIERLMEKVEDAGVAIVD----EKGEPAPEVLQAKQNKPSKEELAQAEETPAG 152

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
              +DPVRMYL+E+G + LL  + EI IAKRIE G       L E+ L     I  R
Sbjct: 153 IKINDPVRMYLKEIGRVNLLKGDEEINIAKRIEDGDVEAKQELAEANLRLVVSIAKR 209


>gi|238916620|ref|YP_002930137.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
 gi|238871980|gb|ACR71690.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
          Length = 434

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EK+D+  G+KFSTYA WW
Sbjct: 197 AKKRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKYDYRKGFKFSTYATWW 256

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP+PEEIA+ + +PVE V
Sbjct: 257 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQELGREPSPEEIAENMDIPVERV 316

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A    L+E    VL +LT R
Sbjct: 317 REIQKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAASTLLKEQLVEVLGTLTER 376

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 377 EQKVLRLRFGMDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 434



 Score = 45.1 bits (105), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYL+E+G + LLS + EI  AKR+E G       L E+ L    + I +  +  G
Sbjct: 162 DDPVRMYLKEIGKVPLLSADEEIEYAKRMEEGDEEAKKRLAEANLRL-VVSIAKRYVGRG 220

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
              L  I         E   G     E + Y+K
Sbjct: 221 MQFLDLI--------QEGNLGLIKAVEKYDYRK 245


>gi|323340800|ref|ZP_08081052.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
 gi|323091923|gb|EFZ34543.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
          Length = 373

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E + +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLTAEEEKKLALRIEEGDEEA---KQRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R+M   + REP PEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQMLQDLGREPIPEEIGAEMNLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDHAATSPADHAAYELLKEQIESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 373



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/144 (32%), Positives = 74/144 (51%), Gaps = 9/144 (6%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + +++++  +Q G V   EL   + P +++SEQ+ D +A +   GI+VVD    E+ + +
Sbjct: 18  ALREVVQEFKQAGEVRYSELTKHVSPLDLTSEQINDLIADVEKRGISVVD----ENGDPT 73

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +SL+ A         L K   SA      +DPVRMYL+E+G + LL+ E E  +A RIE
Sbjct: 74  AESLNQAKEEEKE---LSKSDVSAPSGVKINDPVRMYLKEIGRVNLLTAEEEKKLALRIE 130

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G       L E+ L     I  R
Sbjct: 131 EGDEEAKQRLAEANLRLVVSIAKR 154


>gi|313903305|ref|ZP_07836697.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466393|gb|EFR61915.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
          Length = 432

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 199/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++++ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KAAEKFD+  G+KFSTYA WW
Sbjct: 195 AKRKLIQANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAAEKFDYRKGFKFSTYATWW 254

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEEIAK++ +  E V
Sbjct: 255 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLVQELGREPTPEEIAKEMGIEPEKV 314

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED++A++P ++A Q  LRE    VL +LT R
Sbjct: 315 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDEDALAPAEAASQLLLREQLEDVLHTLTDR 374

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 375 EQKVLRLRFGLDDGRQRTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 432



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 33/47 (70%), Gaps = 5/47 (10%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-----RAMMMASL 157
           + DDPVRMYL+E+G I LL+ E EI +AKRIE G     R ++ A+L
Sbjct: 158 ALDDPVRMYLKEIGRIPLLTPEQEIELAKRIEQGDEEAKRKLIQANL 204


>gi|301301338|ref|ZP_07207482.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851066|gb|EFK78806.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 372

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 135 AKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP PEEI  ++ MP E V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREPMPEEIGAEMDMPTEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT R
Sbjct: 255 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLESVLDTLTDR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 315 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 372



 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 63/114 (55%), Gaps = 10/114 (8%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++ ++QM+  +  + + GI+VVD    E+ E S  SL  A+  +  +   +  KD
Sbjct: 38  LVTPFKLDADQMDQLIGSIEDRGISVVD----ENGEPSAHSLKAATKEAEKA---ENDKD 90

Query: 112 SADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +  S    +DPVRMYL+E+G + LL+ + E+A+A +IE G       L E+ L
Sbjct: 91  VSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIEEGDQEAKQRLAEANL 144


>gi|283797719|ref|ZP_06346872.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291074616|gb|EFE11980.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|295092057|emb|CBK78164.1| RNA polymerase, sigma 70 subunit, RpoD [Clostridium cf.
           saccharolyticum K10]
          Length = 372

 Score =  321 bits (822), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 168/342 (49%), Positives = 237/342 (69%), Gaps = 12/342 (3%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           +QL  I   + +N+ ++L   +   I+ D+FLE     E D    +     PEG     V
Sbjct: 43  DQLDQIDDFLENNKVDVLTPEEDLDIEPDLFLEEEMTEEEDIDVDNLELSMPEG-----V 97

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           + E D +     EI  + + T          + + ++ E     AKK + EANLRLV+S+
Sbjct: 98  SIE-DPVRMYLKEIGKVPLLTP------EEEIDLAKRMEMGDESAKKRLAEANLRLVVSI 150

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RG+QFLDLIQEGN+GL+KA EK+D+  G+KFSTYA WW++QAITRSIADQ+ TI
Sbjct: 151 AKRYVGRGMQFLDLIQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTI 210

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I++++RT+R++  ++ REP+ EE+A+KL MPVE VR+++KI+++P+SLETP
Sbjct: 211 RIPVHMVETINRLIRTSRQLLQELGREPSAEELAEKLDMPVERVREIMKISQDPVSLETP 270

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+E+ SHLGDFI+D +   P+D+A    L E    VL +LT RE++VLR+RFG+     
Sbjct: 271 IGEEEDSHLGDFIQDDHVQVPVDAATYTLLHEQLMEVLDTLTDREQKVLRLRFGLDDGRP 330

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            TLEEVG++F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 331 RTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 372



 Score = 46.2 bits (108), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LL+ E EI +AKR+E G       L E+ L
Sbjct: 98  SIEDPVRMYLKEIGKVPLLTPEEEIDLAKRMEMGDESAKKRLAEANL 144


>gi|116514229|ref|YP_813135.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116093544|gb|ABJ58697.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
          Length = 372

 Score =  320 bits (821), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 122 VALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+    + R+P PE
Sbjct: 182 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQFLQDLGRDPEPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +PV+ VR+ LK+ +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 242 EIAAEMDLPVKKVREALKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 DQLAEVLDTLTDREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRS KLR FL+
Sbjct: 362 SRSNKLRDFLE 372



 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E+G    L L    +     L     
Sbjct: 40  LIKPYKLEGKAVDQLVQEFEDNGISIVD------EDGKPSKLALTKQKNVEKAELNNMAA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                 +DPVRMYL+E+G   LL+ E E+A+AKRIEAG       L E+ L
Sbjct: 94  PTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRIEAGDEEAKQELAEANL 144


>gi|256847131|ref|ZP_05552577.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
 gi|256715795|gb|EEU30770.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
          Length = 381

 Score =  320 bits (821), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 144 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 203

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ MP + V
Sbjct: 204 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDMPTKKV 263

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIED +A SP D A    +++    VL +LT R
Sbjct: 264 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDHDATSPADHAAYEMMKKQLENVLDTLTDR 323

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 324 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 381



 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 72/138 (52%), Gaps = 9/138 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D +  K+I+  ++   +  +EL+  L  P +++++ +++ +  + + GI+VVD      E
Sbjct: 22  DQAVGKLIRQYKKAKTIQYDELSKQLAAPFDLNADGLDNLMQNIEDAGISVVD------E 75

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAK 144
            G  D   L ++   S   +  R  SA      +DPVRMYL+E+G + LL+ + E+ +A 
Sbjct: 76  NGDPDPRALKATEKLSQKAVNDRDTSAPTGVKINDPVRMYLKEIGRVNLLTADQEVELAL 135

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 136 RIEKGDETAKQELAEANL 153


>gi|329910007|ref|ZP_08275189.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546317|gb|EGF31339.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 452

 Score =  320 bits (821), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 148/319 (46%), Positives = 224/319 (70%), Gaps = 1/319 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G+ R +F+    G E+D  W+       +  +   +A ++ +I +++  + ++    G+ 
Sbjct: 134 GMPRSLFIATFPGNEIDLGWIDLVVAGQQA-YCVTLARQIPAIKELQTRLVALQERVGLP 192

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + + R +   +  GE  A  AK++M EANLRLV+S+AKKY NRG+QFLDLIQEGNIGL+K
Sbjct: 193 LPQLRRVSKQMSTGELRARQAKRDMTEANLRLVVSIAKKYINRGMQFLDLIQEGNIGLLK 252

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QA++R+IADQ+ TIR+PVHM + ++K+ R ARR+  + 
Sbjct: 253 AVDKFEYRRGYKFSTYATWWIRQAVSRAIADQARTIRVPVHMLETVNKLNRIARRILQET 312

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E     +A  + +  + VR+++KI +EPIS+E+P+GD+  S LGDFI+D    +PL++
Sbjct: 313 GVEADLPTLALHMELTEQKVREIMKIAREPISMESPVGDDGDSQLGDFIQDSTTTAPLEA 372

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+ A++R     VL +L PRE ++LRMR+G+   +DHTLEEVGKQF VTRERIRQIE+KA
Sbjct: 373 AVDASMRTAIKEVLDALPPREAKILRMRYGLDTQSDHTLEEVGKQFEVTRERIRQIESKA 432

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           + KL+HPSR+ KL+ F++G
Sbjct: 433 LVKLRHPSRADKLKIFVEG 451


>gi|300214611|gb|ADJ79027.1| RNA polymerase sigma factor [Lactobacillus salivarius CECT 5713]
          Length = 372

 Score =  320 bits (821), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 135 AKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP PEEI  ++ MP E V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREPMPEEIGAEMDMPTEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT R
Sbjct: 255 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLESVLDTLTDR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 315 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 372



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 63/114 (55%), Gaps = 10/114 (8%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++ ++QM+  +  + + GI+VVD    E+ E S  SL  A+  +  +   +  KD
Sbjct: 38  LVTPFKLDADQMDQLIGSIEDRGISVVD----ENGEPSAHSLKAATKEAEKA---ENDKD 90

Query: 112 SADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +  S    +DPVRMYL+E+G + LL+ + E+A+A +IE G       L E+ L
Sbjct: 91  VSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIEEGDQEAKQRLAEANL 144


>gi|325125919|gb|ADY85249.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 372

 Score =  320 bits (821), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 198/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 122 VALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 182 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +PV+ VR++LKI +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+
Sbjct: 242 EIAAEMDLPVKKVREILKICQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L+ REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLAEVLDTLSDREEEVLRLRFGLDDGKSRTLEEVGQHFEVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRS +LR FLD
Sbjct: 362 SRSSQLRDFLD 372



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E+G    L L    +     L     
Sbjct: 40  LIKPYKLEDKAVDQLVQEFEDNGISIVD------EDGKPSKLALTKQKNVEKAELNNMAA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                 +DPVRMYL+E+G   LL+ E E+A+AKRIEAG       L E+ L
Sbjct: 94  PTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRIEAGDEEAKQELAEANL 144


>gi|254796694|ref|YP_003081530.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
 gi|254589929|gb|ACT69291.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
          Length = 620

 Score =  320 bits (821), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 238/678 (35%), Positives = 348/678 (51%), Gaps = 102/678 (15%)

Query: 32  KKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K +I    +RG+VT  EL ++F   D  +   +E+ ++ L   GI +++ D+ EDE   E
Sbjct: 14  KALITKGVKRGFVTYGELSDSFSDEDFENLNCIEEAISKLEESGIGILEKDE-EDELSEE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              +       + +            TDDPVR+YLREM  ++LLSR+ E+ IAK I A +
Sbjct: 73  VKEEDEEEDEAADIL---------GHTDDPVRLYLREMSYVKLLSRDDEVEIAKAIVAEK 123

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE-----SKGG-FFHGTE 204
              ++++   P   + ++    +L +GT  LRE+I+ ++ +  E     SKG   F G +
Sbjct: 124 FESLSAVLLFPSVMKGIVDLGTKLREGTISLREVIESDSGLKSELTEETSKGDDLFEGMD 183

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G   +  + S +E   + V E  G++E+    +                    LD+ ++ 
Sbjct: 184 GKPEEGNQMSDEEL-MEKVLEIFGELETIITSA--------------------LDKAKEG 222

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               +   E  L P+           YREL +L  N +N  K                  
Sbjct: 223 QMVKIVDGEVILDPE-----------YRELHTLAVNHLNQVK------------------ 253

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                LN   +    E     ++ I+  +  LL   +  G+ R V + + +   LD   +
Sbjct: 254 -----LNPKLLAEFFENTRKKNELILEKKKVLLTFLEERGLDRTVLI-KGKVHILDAGVL 307

Query: 385 SYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           S          K    C+   S+ +  + I+ +    G+       +   V      A+ 
Sbjct: 308 SEL-------LKKHNICDTHFSLEEFLSPIRELEKNEGMDYESISFLTRKVATHLDNANA 360

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  MVEANLRLVIS+AKKYTNRG+ F DLIQEGNIGLMKA +KFD   G+KFSTYA WW
Sbjct: 361 AKHRMVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFSTYATWW 420

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
            +QAITR+IAD    +R PVH+ +  +KV+RT RR+ N   REPT EEIA  L +  + V
Sbjct: 421 CRQAITRAIADCGSIVRKPVHIHETANKVMRTRRRLYNLNGREPTVEEIANLLKISPDKV 480

Query: 564 RKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +K LK+ ++PISLE+P+GD+  S   GDFIEDKNAVS +D  +  NLR+     LA L+P
Sbjct: 481 KKSLKVNQDPISLESPVGDDSNSGSFGDFIEDKNAVSQVDVVLSKNLRKVLDEALAMLSP 540

Query: 623 REERVLRMRFG------------------IGMN--TDHTLEEVGKQFCVTRERIRQIEAK 662
           REE++LR RFG                  I +N  T+ TLE+VG  + VTRERIRQIE+K
Sbjct: 541 REEKILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTNLTLEQVGILYNVTRERIRQIESK 600

Query: 663 AIRKLKHPSRSKKLRSFL 680
           ++RK++ PSRS KLR+FL
Sbjct: 601 SLRKMRSPSRSIKLRTFL 618


>gi|282882556|ref|ZP_06291177.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
 gi|281297698|gb|EFA90173.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
          Length = 361

 Score =  320 bits (820), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 199/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E   + AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 111 VEIAKRMENGDNSAKKELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDY 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P PE
Sbjct: 171 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLVQELGRDPLPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + VE VR++ KI +EP+SLETPIG+E+ SHLGDFI D+  +SP D+A    LR
Sbjct: 231 EIAKEMNIEVEKVREIQKIAQEPVSLETPIGEEEDSHLGDFIPDEEILSPQDAATFTLLR 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  + VL +LT RE++VL +RFG+      TLEEVGK+F VTRERIRQIEAKAIRKL+HP
Sbjct: 291 EQLSTVLETLTDREKKVLTLRFGLDDGRARTLEEVGKEFAVTRERIRQIEAKAIRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ FL+
Sbjct: 351 SRSKKLKDFLE 361



 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 68/137 (49%), Gaps = 16/137 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED-- 85
           D +   + K  +++G++T +E++  L    + S++++       N GI +++ D  +D  
Sbjct: 11  DTTINNLKKEGKEKGHLTYDEISFALEDIPMDSQEIDSIYKDFENDGIELLNDDRDKDYK 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +  DL+     S               DDPVRMYL+E+G I LL+ + E+ IAKR
Sbjct: 71  EEIDVEKEDLSVPKGIS--------------VDDPVRMYLKEIGKIPLLTGDEEVEIAKR 116

Query: 146 IEAGRAMMMASLCESPL 162
           +E G       L E+ L
Sbjct: 117 MENGDNSAKKELAEANL 133


>gi|218133123|ref|ZP_03461927.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991996|gb|EEC58000.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
          Length = 448

 Score =  320 bits (820), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +  G+ EA   K  + EANLRLV+S+AK+Y  RG+
Sbjct: 179 VRMYLKEIGKVPLLSAEEEIELAKRMENGDVEA---KNRLAEANLRLVVSIAKRYVGRGM 235

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 236 LFLDLIQEGNLGLIKAVDKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 295

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +PVE VR++ KI++EP+SLETPIG+E+ SHL
Sbjct: 296 INKLLRVSRQLLQELGREPTPEEIAKEMDIPVERVREIQKISQEPVSLETPIGEEEDSHL 355

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P + A    L+E    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 356 GDFIQDDNVPVPAEEAASTILKEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGRE 415

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR FLD
Sbjct: 416 FNVTRERIRQIEAKALRKLRHPSRSRKLRDFLD 448



 Score = 48.1 bits (113), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 56/110 (50%), Gaps = 13/110 (11%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG----SEDSLDLASSASNSSVFLQKRKDS 112
           E  ++++E     L    ++V   DD+E+EE      ED +D+     + SV        
Sbjct: 120 EFDADKVEKVFDFLEANNVDVKISDDVEEEEDIILDPEDDIDI--EKIDLSV-------P 170

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L
Sbjct: 171 EGVSIEDPVRMYLKEIGKVPLLSAEEEIELAKRMENGDVEAKNRLAEANL 220


>gi|328957491|ref|YP_004374877.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
 gi|328673815|gb|AEB29861.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
          Length = 373

 Score =  320 bits (820), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E   +   + +G+ EA   ++ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLTAAEEVELAIKIEEGDQEA---RQRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP ++A    L+E    VL +LT REE VLR+RFG+    + TLE+VGK 
Sbjct: 281 GDFIEDHDATSPAENAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRNRTLEDVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 373



 Score = 39.3 bits (90), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +DPVRMYL+E+G + LL+   E+ +A +IE G       L E+ L
Sbjct: 101 NDPVRMYLKEIGRVNLLTAAEEVELAIKIEEGDQEARQRLAEANL 145


>gi|227890913|ref|ZP_04008718.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
 gi|227867322|gb|EEJ74743.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
          Length = 372

 Score =  320 bits (820), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 135 AKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP PEEI  ++ MP E V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREPMPEEIGAEMDMPTEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT R
Sbjct: 255 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLESVLDTLTDR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 315 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 372



 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 64/114 (56%), Gaps = 10/114 (8%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P +++++QM+  +  + + GI+VVD    E+ E S  SL  A+  +  +   +  KD
Sbjct: 38  LVTPFKLNADQMDQLIGSIEDRGISVVD----ENGEPSAHSLKAATKEAEKA---ENDKD 90

Query: 112 SADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +  S    +DPVRMYL+E+G + LL+ + E+A+A +IE G       L E+ L
Sbjct: 91  VSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIEEGDQEAKQRLAEANL 144


>gi|90961886|ref|YP_535802.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius UCC118]
 gi|90821080|gb|ABD99719.1| RNA polymerase sigma factor [Lactobacillus salivarius UCC118]
          Length = 372

 Score =  320 bits (820), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 135 AKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP PEEI  ++ MP E V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREPMPEEIGAEMDMPTEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT R
Sbjct: 255 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLESVLDTLTDR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 315 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 372



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 60/111 (54%), Gaps = 4/111 (3%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++ ++QM+  +  + + GI+VVD    E+ E S  SL  A+  +  +   +    
Sbjct: 38  LVTPFKLDADQMDQLIGSIEDRGISVVD----ENGEPSAHSLKAAAKEAEKAENDKDVSA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + E+A+A +IE G       L E+ L
Sbjct: 94  PSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIEEGDQEAKQRLAEANL 144


>gi|331090835|ref|ZP_08339681.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399694|gb|EGG79356.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 370

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 133 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYEKGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA++L MPVE V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAEELDMPVERV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A    L+E    VL +LT R
Sbjct: 253 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAATLLKEQLGEVLNTLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score = 47.8 bits (112), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 43/130 (33%), Positives = 67/130 (51%), Gaps = 17/130 (13%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDD-- 82
           ++  K+++ L +++   + I+E+N      E+  EQME     L    I+V  ++GD   
Sbjct: 9   EEKLKELLALGKKKKNILEIQEINEIFADMELEPEQMEKVFEYLEGQNIDVLRINGDVDD 68

Query: 83  ---LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
              LE     ED +D+     + SV      D    S +DPVRMYL+E+G + LLS E E
Sbjct: 69  DDDLEVVITEEDEVDV--EKIDLSV-----PDGI--SIEDPVRMYLKEIGKVPLLSAEEE 119

Query: 140 IAIAKRIEAG 149
           I +AKR+  G
Sbjct: 120 IELAKRMAEG 129


>gi|302391478|ref|YP_003827298.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302203555|gb|ADL12233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 358

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +VEANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 121 AKRMLVEANLRLVVSIAKKYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+KV+R +R +  ++ REPTPEEIA+++ +  E V
Sbjct: 181 IRQAITRSIADQARTIRIPVHMVETINKVIRVSRHLLQELGREPTPEEIAEEMDLSEEKV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VLKI++EP+SLETPIG+E+ SHLGDFIED +A +P  +A    L+E    VL +L+ R
Sbjct: 241 REVLKISQEPVSLETPIGEEEDSHLGDFIEDDDAPAPSVAASHMMLQEQLDEVLDTLSDR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+RVL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 301 EKRVLELRFGVEDGRSRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/140 (31%), Positives = 73/140 (52%), Gaps = 14/140 (10%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           V +  ++  +K+I+   Q G +T +E+   L   E++ EQ++D     + + I VVD D+
Sbjct: 5   VRNIVEEKVEKLIEKGNQEGQITYKEVMDTLAKVELTPEQIDDIYQRFAELDIEVVDEDE 64

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E  + +E+ LDL+                     DDPVRMYL+E+G ++LL+ E E+ +
Sbjct: 65  DEVSKDTEEDLDLSVPDGVG--------------IDDPVRMYLKEIGKVDLLTAEEEVEL 110

Query: 143 AKRIEAGRAMMMASLCESPL 162
           AKR+E G       L E+ L
Sbjct: 111 AKRMEEGDMEAKRMLVEANL 130


>gi|256851182|ref|ZP_05556571.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260660606|ref|ZP_05861521.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|282934648|ref|ZP_06339891.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297206047|ref|ZP_06923442.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
 gi|256616244|gb|EEU21432.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260548328|gb|EEX24303.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|281301223|gb|EFA93524.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297149173|gb|EFH29471.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
          Length = 364

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KF++ LG+KFSTYA WW
Sbjct: 127 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFNYKLGFKFSTYATWW 186

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ M  + V
Sbjct: 187 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMGTDKV 246

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    VL +LT R
Sbjct: 247 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEEVLDTLTDR 306

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 307 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 364



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 65/136 (47%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D   K+++K  ++   +T  +     + P ++  + ++  V    + GI++VD +     
Sbjct: 7   DKKVKELVKEVKKSKEITETDFTEKLIKPYKLEGKAVDQLVQEFEDNGISIVDAN----- 61

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   +L L          L+     A    +DPVRMYL+E+G + LL+ + EIA+AKRI
Sbjct: 62  -GEPSNLALKKQKDVEKEELKDLSAPASVRMNDPVRMYLKEIGRVPLLNADEEIALAKRI 120

Query: 147 EAGRAMMMASLCESPL 162
           + G       L E+ L
Sbjct: 121 QDGDEEAKQELAEANL 136


>gi|260588574|ref|ZP_05854487.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
 gi|260541049|gb|EEX21618.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
          Length = 330

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 93  AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 152

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA+++ M VE V
Sbjct: 153 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPHPEEIAEEMNMSVERV 212

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT R
Sbjct: 213 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLVEVLGTLTER 272

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 273 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 330



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS E EI +A+R+E G       L E+ L
Sbjct: 56  SIEDPVRMYLKEIGKVPLLSAEEEITLAQRMEEGDESAKKRLAEANL 102


>gi|307721137|ref|YP_003892277.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
 gi|306979230|gb|ADN09265.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
          Length = 615

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 208/567 (36%), Positives = 321/567 (56%), Gaps = 57/567 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I LL++E EI I+K+IEAG ++++ ++C  P     ++ +++ L +
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKIEAGESIIIDAICSVPYLIDFILDYKEPLIN 162

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               ++E+         E +       +       E +   K++  V +     ++  K 
Sbjct: 163 RERRVKELFK-----SFEDEKDDGDDNDDSDDDSAEKTLSVKDKSRVDKVSTSFKALEKA 217

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            KD     +  PEN  ++   L E       T++  +  L+ K++  L   +++  EL  
Sbjct: 218 KKDWVKAAEKVPENLGDE---LSEGTVQYYLTVTFKKAVLKEKLL-DLGPTSKLINELVK 273

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
             + A+    DE    + K L+ KL     +L  N     +LVE++ D++K  + N    
Sbjct: 274 AMETALKS--DEGYDKELKRLEYKLPLFNATLKANHK---ILVEKIQDLTKEDIANMVPE 328

Query: 357 LRLAQSY-GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
             +  +Y  IK+ V     Q +E                 KN    E + +  I  +IK 
Sbjct: 329 ATMVSTYMEIKKLV-----QTKEAS---------------KNSFDMEPEKLADILEQIKR 368

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
                G +ISE                I+K +M ++NLRLV+S+AK+YTNRGL FLDLIQ
Sbjct: 369 -----GKNISE----------------ISKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQ 407

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ + 
Sbjct: 408 EGNIGLMKAVDKFEYQKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKI 467

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+   +  +EP  + IAK++ + VE V+ V+KITKEPISLE PIG ED    GDFIEDK
Sbjct: 468 MRKHLQENGKEPDVDTIAKEVGLSVEKVKNVIKITKEPISLEAPIGSEDDGRFGDFIEDK 527

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRE 654
            ++SP D+ ++ +LR    +VL  L  RE+ V+++RFGI  + +D TLEE+GK+  VTRE
Sbjct: 528 TSLSPSDAILKDDLRIQIEQVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELSVTRE 587

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           R+RQIE+ AI+KLKHP   +KL+++++
Sbjct: 588 RVRQIESSAIKKLKHPKVGRKLKNYIE 614


>gi|238854653|ref|ZP_04644983.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260664404|ref|ZP_05865256.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|282932956|ref|ZP_06338353.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|238832443|gb|EEQ24750.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260561469|gb|EEX27441.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|281302991|gb|EFA95196.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
          Length = 364

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA +KF++ LG+KFSTYA WW
Sbjct: 127 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFNYKLGFKFSTYATWW 186

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ M  + V
Sbjct: 187 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMGTDKV 246

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    VL +LT R
Sbjct: 247 RDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEEVLDTLTDR 306

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 307 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 364



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 36/136 (26%), Positives = 64/136 (47%), Gaps = 7/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D   K+++K  ++   +T  +     + P ++  + ++  V    + GI++VD +     
Sbjct: 7   DKKVKELVKEVKKSKEITETDFTEKLIKPYKLEGKAVDQLVQEFEDNGISIVDAN----- 61

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   +L L          L+     A    +DPVRMYL+E+G + LL+ + EI +AKRI
Sbjct: 62  -GDPSNLALKKQKDVEKEELKDLSAPASVRMNDPVRMYLKEIGRVPLLNADEEITLAKRI 120

Query: 147 EAGRAMMMASLCESPL 162
           + G       L E+ L
Sbjct: 121 QDGDEEAKQELAEANL 136


>gi|210615118|ref|ZP_03290449.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
 gi|210150426|gb|EEA81435.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
          Length = 370

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 133 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYQKGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA++L MPVE V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAEELDMPVERV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A    L+E    VL +LT R
Sbjct: 253 REILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAATLLKEQLGEVLDTLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 84/191 (43%), Gaps = 26/191 (13%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-------D 79
           ++  K ++ L +++   + I+E+N      E+ +EQME     L +  I+V+       D
Sbjct: 9   EEKLKNLVALGKKKKSILEIQEINEVFSDMELEAEQMEKIFEYLESQNIDVLRISPDTDD 68

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            DD+E     ED +D+     + SV      D    S +DPVRMYL+E+G + LLS E E
Sbjct: 69  ADDVEILLTDEDEVDM--EKIDLSV-----PDGI--SIEDPVRMYLKEIGKVPLLSAEEE 119

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I +AKR+  G       L E+ L     I  R  +  G   L  I         E   G 
Sbjct: 120 IELAKRMAEGDEDAKKRLAEANLRLVVSIAKR-YVGRGMLFLDLI--------QEGNLGL 170

Query: 200 FHGTEGHSYQK 210
               E   YQK
Sbjct: 171 IKAVEKFDYQK 181


>gi|315640587|ref|ZP_07895693.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
 gi|315483615|gb|EFU74105.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
          Length = 368

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVPLLTAAEEVELALKIEEGDQEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRIQRQLLQDLGREPTPEEIGAEMDLSTEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFGI      TLEEVGK 
Sbjct: 276 GDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/134 (30%), Positives = 67/134 (50%), Gaps = 10/134 (7%)

Query: 32  KKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K+ I+  +  G V  ++L N    P  + ++QM+  +  + + GI+VVD       E  E
Sbjct: 14  KEFIRKNKPNGQVVYDQLTNQLATPHNLDADQMDQLIQKIEDAGISVVD-------ENGE 66

Query: 91  DSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            S+    +AS     +Q+   SA      +DPVRMYL+E+G + LL+   E+ +A +IE 
Sbjct: 67  PSVHSLKNASKQEKTVQQEDLSAPTGVKINDPVRMYLKEIGRVPLLTAAEEVELALKIEE 126

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 127 GDQEAKQRLAEANL 140


>gi|163790450|ref|ZP_02184881.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
 gi|159874354|gb|EDP68427.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
          Length = 373

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E   +   + +G+ EA   ++ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLTAAEEVELAIKIEEGDQEA---RQRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP ++A    L+E    VL +LT REE VLR+RFG+    + TLE+VGK 
Sbjct: 281 GDFIEDHDATSPAENAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRNRTLEDVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 373



 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +DPVRMYL+E+G + LL+   E+ +A +IE G       L E+ L
Sbjct: 101 NDPVRMYLKEIGRVNLLTAAEEVELAIKIEEGDQEARQRLAEANL 145


>gi|317495391|ref|ZP_07953760.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
 gi|316914450|gb|EFV35927.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
          Length = 361

 Score =  320 bits (819), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 150/244 (61%), Positives = 192/244 (78%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E   AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFS
Sbjct: 118 ESEKEQAKKDLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFS 177

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I++++R  R++   + REP PEEIAKK+ 
Sbjct: 178 TYATWWIRQAITRAIADQARTIRIPVHMVETINRLIRVQRQLLQDLGREPKPEEIAKKMN 237

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP++ A    L+E    +L
Sbjct: 238 MTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDAQSPVEHAANELLKEQLEEIL 297

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VL++RFG+     HTLEEVG  F VTRERIRQIEAKAIRKLKHPS+  KL+
Sbjct: 298 ETLTDREENVLKLRFGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSKLNKLK 357

Query: 678 SFLD 681
            F++
Sbjct: 358 GFME 361



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 65/118 (55%), Gaps = 15/118 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++++  +++G +T EE+   L   ++SSE M+D    L+N  I +++ +         +
Sbjct: 14  KELLEKGKKQGELTQEEIIEALSKLDISSETMDDFYEELNNEDIILINEN--------HE 65

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +      + SV        A   T+DPVRMYL+E+G + LLS+E E+ ++K IE+G
Sbjct: 66  EEEEELDLEDLSV-------PAGIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIESG 116


>gi|322384625|ref|ZP_08058303.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150510|gb|EFX43991.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 371

 Score =  320 bits (819), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+A++Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 134 AKQRLAEANLRLVVSIARRYVGRGMLFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK++ +  + V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLLELGREPTPEEIAKEMELSTDKV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI++EP+SLETPIG+E+ S+LGDFIED++A++P D+A    L+E    VL +LT R
Sbjct: 254 REIMKISQEPVSLETPIGEENDSNLGDFIEDQDALAPADAASYELLKEQLEHVLDTLTER 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 314 EENVLRLRFGLEDGRSRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 371



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 24/147 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-- 89
           +++I+  +Q   +T +E+   L P +   EQ+++   +L+ +GI V +  D   E G+  
Sbjct: 23  EQLIESGKQHSSLTYKEIIEKLAPFDQEPEQIDEFFELLAELGIEVENETDDNPEPGNQT 82

Query: 90  -----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                ED L L + + N                 D VRMYL+E+G + LL+ + EI +AK
Sbjct: 83  KGSLDEDDLTLPAGSLN-----------------DSVRMYLKEIGRVHLLTADDEIELAK 125

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWR 171
           RI  G       L E+ L     I  R
Sbjct: 126 RIMEGDEEAKQRLAEANLRLVVSIARR 152


>gi|183220954|ref|YP_001838950.1| RNA polymerase sigma factor RpoD [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189911049|ref|YP_001962604.1| DNA-directed RNA polymerase sigma sigma70/sigma32 subunit
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167775725|gb|ABZ94026.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167779376|gb|ABZ97674.1| RNA polymerase sigma factor rpoD (Sigma-70) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 590

 Score =  320 bits (819), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 171/391 (43%), Positives = 251/391 (64%), Gaps = 23/391 (5%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSL-------SLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           +K  ++S K K LKEK+    G +        ++Q  I  + +++  +  R+   E   L
Sbjct: 209 RKYSENSKKFKELKEKIDLSTGKIDEAIRKIGVSQKEIQKISQKIKSMVFRVKEIEKHFL 268

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK----IRN-- 411
           ++   YG         H  RE+        K+    E +  + C++D + +    IRN  
Sbjct: 269 KIKAKYG---------HDVREIKALNRFIEKNENLDEIEKMMGCDIDEVREVIKDIRNNE 319

Query: 412 -EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +++ +  E G  + E +     + KGE E + AK+E+V ANLRLV+S+AK+Y NRG+ F
Sbjct: 320 RKLRRMEQEAGSPVGEIKDWGEKIIKGEREIAQAKRELVRANLRLVVSIAKRYANRGMHF 379

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGNIGL++A +KF++  GYKFSTYA WW++QAITR+I+DQ+ TIR+PVHM ++++
Sbjct: 380 FDLIQEGNIGLIRAVDKFEYKKGYKFSTYATWWIRQAITRAISDQARTIRVPVHMIEQVN 439

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           KV+R  R    +  R+P+ +EIA++L  PV+ V+ V  + +EPISLE P+G E+ S LGD
Sbjct: 440 KVIRETRLFVQEFGRDPSNDEIAERLGWPVQKVKAVKNVAREPISLEIPVGSEEDSELGD 499

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK  +SPL+SA  + L E   +VL +L  RE++V+RMRFG+      TLEEVG QF 
Sbjct: 500 FIEDKEVISPLNSAASSILSEQIRQVLQTLPAREQKVIRMRFGLDDGYAQTLEEVGYQFK 559

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+R+L+HPSRSKKL+ ++D
Sbjct: 560 VTRERIRQIEAKALRRLRHPSRSKKLKDYID 590



 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 75/137 (54%), Gaps = 3/137 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +K+I + +    V+ +E+N  LP   ++SE+++D   +L  MGI +V+    +  E S  
Sbjct: 11  QKIISIGKANREVSYDEINEILPDKILNSEKIDDVFTLLHEMGIEIVEEYSKKSLEESSS 70

Query: 92  SLDLASSASNSSVFL---QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                   +  +      +KR+ S   S++DP+R+YL+E+G + L+S E E+ +AKRIE 
Sbjct: 71  LTTTKEETTKETKEKPARKKRESSVSSSSEDPIRLYLKEIGKVSLISGETEVFLAKRIEK 130

Query: 149 GRAMMMASLCESPLTFQ 165
           G  ++  ++  S +  Q
Sbjct: 131 GEKIIEETILSSSILRQ 147


>gi|229543825|ref|ZP_04432884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
 gi|229324964|gb|EEN90640.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
          Length = 377

 Score =  320 bits (819), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVDLLSADEEIELAKRIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 QFLDLIQEGNMGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + REPTPEEIA+++ +  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVQRSLLQDLGREPTPEEIAEEMDISPDKVREIIKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/147 (29%), Positives = 75/147 (51%), Gaps = 18/147 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED------ 85
           +++++  ++RG++T + ++  L   +++S+QM++    L   GI+V D    ED      
Sbjct: 23  EQLVERGKKRGFLTYDTISEKLGHFDLTSDQMDEFYESLGEQGIDVTDDTSDEDAPSHLE 82

Query: 86  -EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            E+ +++  DL   +    V             +DPVRMYL+E+G ++LLS + EI +AK
Sbjct: 83  LEKENDEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSADEEIELAK 131

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWR 171
           RIE G       L E+ L     I  R
Sbjct: 132 RIEQGDEEAKRRLAEANLRLVVSIAKR 158


>gi|300812183|ref|ZP_07092625.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496819|gb|EFK31899.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 372

 Score =  320 bits (819), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 122 VALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LGYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 182 RLGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +PV+ VR++LKI +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+
Sbjct: 242 EIGAEMDLPVKKVREILKICQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L+ REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLAEVLDTLSDREEEVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRS +LR FLD
Sbjct: 362 SRSSQLRDFLD 372



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 55/120 (45%), Gaps = 6/120 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E G    L L    +     L     
Sbjct: 40  LIKPYKLEGKAVDQLVQEFEDNGISIVD------EGGKPSKLALTKQKNVEKAELNNMDA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                 +DPVRMYL+E+G + LL+ E E+A+AKRIEAG       L E+ L     I  R
Sbjct: 94  PTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRIEAGDEEAKQELAEANLRLVVSIAKR 153


>gi|121534199|ref|ZP_01666024.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
 gi|121307302|gb|EAX48219.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
          Length = 368

 Score =  320 bits (819), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 131 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTPEEIA+++ + VE V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEKGREPTPEEIAREMDISVERV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    L+E    VL +LTPR
Sbjct: 251 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFMLLKEQLEEVLETLTPR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 311 EEKVLRLRFGLDDGRARTLEEVGQYFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 368



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/121 (32%), Positives = 64/121 (52%), Gaps = 3/121 (2%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  E+   L  ++++ ++++D   + ++ GI +VD  ++ D E  ED       A+ 
Sbjct: 23  GVLTYSEIMDTLQGEDLTPDEIDDMYEVFNSKGIEIVD--EIPDVETLEDPDITEIEAAP 80

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
             V +         S DDPVRMYL+E+G + LL+ E EI +AKR+E G       L E+ 
Sbjct: 81  EEVDIDLSIPEGI-SIDDPVRMYLKEIGRVPLLTAEEEIQLAKRMEQGDEEAKRRLAEAN 139

Query: 162 L 162
           L
Sbjct: 140 L 140


>gi|167462413|ref|ZP_02327502.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 367

 Score =  319 bits (818), Expect = 8e-85,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+A++Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 130 AKQRLAEANLRLVVSIARRYVGRGMLFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWW 189

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK++ +  + V
Sbjct: 190 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLLELGREPTPEEIAKEMELSTDKV 249

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI++EP+SLETPIG+E+ S+LGDFIED++A++P D+A    L+E    VL +LT R
Sbjct: 250 REIMKISQEPVSLETPIGEENDSNLGDFIEDQDALAPADAASYELLKEQLEHVLDTLTER 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 310 EENVLRLRFGLEDGRSRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 367



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 24/147 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-- 89
           +++I+  +Q   +T +E+   L P +   EQ+++   +L+ +GI V +  D   E G+  
Sbjct: 19  EQLIESGKQHSSLTYKEIIEKLAPFDQEPEQIDEFFELLAELGIEVENETDDNPEPGNQT 78

Query: 90  -----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                ED L L + + N                 D VRMYL+E+G + LL+ + EI +AK
Sbjct: 79  KGSLDEDDLTLPAGSLN-----------------DSVRMYLKEIGRVHLLTADDEIELAK 121

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWR 171
           RI  G       L E+ L     I  R
Sbjct: 122 RIMEGDEEAKQRLAEANLRLVVSIARR 148


>gi|18202317|sp|P58290|RPOD_LACLC RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 364

 Score =  319 bits (818), Expect = 8e-85,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 93  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 152

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 153 QFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 212

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 213 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 272

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 273 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 332

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 333 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 364



 Score = 40.4 bits (93), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 34  IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 89

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 90  -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 121


>gi|312874241|ref|ZP_07734275.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
 gi|311090311|gb|EFQ48721.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
          Length = 382

 Score =  319 bits (818), Expect = 8e-85,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 194/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 132 IDLAKRIENNDDDAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 191

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 192 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 251

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ M  + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 252 EIGAEMDMSTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLK 311

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 312 EQLEEVLDTLTDREENVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 371

Query: 671 SRSKKLRSFLD 681
           SRS +L+ FLD
Sbjct: 372 SRSNQLKDFLD 382



 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 6/96 (6%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD D      G+  +L L          L     
Sbjct: 50  MVKPYQLEGKAIDQLVQEFEDNGISIVDND------GNPSNLSLKKQKDVEKAELNDMTA 103

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 104 PSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139


>gi|227892546|ref|ZP_04010351.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
 gi|227865667|gb|EEJ73088.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
          Length = 370

 Score =  319 bits (818), Expect = 8e-85,   Method: Compositional matrix adjust.
 Identities = 150/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 120 IALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+++  R++   + REPTPE
Sbjct: 180 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIKIQRQLLQDLGREPTPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +P   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 240 EIGAEMNVPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   +VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEQVLETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS +L+ F+D
Sbjct: 360 SRSNQLKDFMD 370



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 53/111 (47%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAIDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIEAG       L E+ L
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIEAGDEEAKQELAEANL 142


>gi|313123888|ref|YP_004034147.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280451|gb|ADQ61170.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 373

 Score =  319 bits (818), Expect = 8e-85,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + +S  E   +   +  G+ EA   K E+  ANLRLV+S+AK+Y  RG+
Sbjct: 104 VRQYLKRIGRVSLLSGDEEVQLAKRIEAGDQEA---KDELTSANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 SFLDLIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEIA ++ +PV+ VR+VLK+ +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+A SP   A    L++    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 281 GDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGLDDGNPRTLEEVGRV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS +LR FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSNQLRDFLE 373



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 7/98 (7%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD      ++G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVD------DKGEPSKLALAKQKNVEKAELEHLSA 95

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              R  +DPVR YL+ +G + LLS + E+ +AKRIEAG
Sbjct: 96  PGSR-MNDPVRQYLKRIGRVSLLSGDEEVQLAKRIEAG 132


>gi|259500591|ref|ZP_05743493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|302191282|ref|ZP_07267536.1| RNA polymerase sigma factor RpoD [Lactobacillus iners AB-1]
 gi|309805231|ref|ZP_07699283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|309807583|ref|ZP_07701535.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|312871770|ref|ZP_07731858.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|312875648|ref|ZP_07735649.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|325912054|ref|ZP_08174452.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
 gi|259167975|gb|EEW52470.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|308165465|gb|EFO67696.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|308169189|gb|EFO71255.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|311088902|gb|EFQ47345.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|311092712|gb|EFQ51068.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|325476004|gb|EGC79172.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
          Length = 382

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW
Sbjct: 145 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ M  + V
Sbjct: 205 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMSTDKV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    VL +LT R
Sbjct: 265 REILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDR 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 325 EENVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 6/96 (6%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD D      G+  +L L          L     
Sbjct: 50  MVKPYQLEGKAIDQLVQEFEDNGISIVDND------GNPSNLSLKKQKDVEKAELNDMTA 103

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 104 PSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139


>gi|300812189|ref|ZP_07092631.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496825|gb|EFK31905.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 373

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + +S  E   +   +  G+ EA   K E+  ANLRLV+S+AK+Y  RG+
Sbjct: 104 VRQYLKRIGRVSLLSGDEEVQLAKRIEAGDQEA---KDELTSANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 SFLDLIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEIA ++ +PV+ VR+VLK+ +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+A SP   A    L++    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 281 GDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGLDDGNPRTLEEVGRV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS +LR FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSNQLRDFLE 373



 Score = 48.1 bits (113), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 7/98 (7%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD      ++G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVD------DKGEPSKLALAKQKNVEKAELEHLSA 95

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              R  +DPVR YL+ +G + LLS + E+ +AKRIEAG
Sbjct: 96  PGSR-MNDPVRQYLKRIGRVSLLSGDEEVQLAKRIEAG 132


>gi|309810147|ref|ZP_07703992.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169419|gb|EFO71467.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
          Length = 382

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW
Sbjct: 145 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ M  + V
Sbjct: 205 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMSTDKV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    VL +LT R
Sbjct: 265 REILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDR 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 325 EENVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 46.2 bits (108), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 6/96 (6%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++    ++  V    + GI++VD D      G+  +L L          L     
Sbjct: 50  MVKPYQLEGRAIDQLVQEFEDNGISIVDND------GNPSNLSLKKQKDIEKAELNDMTA 103

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 104 PSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139


>gi|309803186|ref|ZP_07697283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|309806578|ref|ZP_07700575.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|312872984|ref|ZP_07733044.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315653573|ref|ZP_07906493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325912624|ref|ZP_08175007.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|329920166|ref|ZP_08276997.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
 gi|308164694|gb|EFO66944.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|308166998|gb|EFO69180.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|311091506|gb|EFQ49890.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315488935|gb|EFU78577.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325478045|gb|EGC81174.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|328936620|gb|EGG33064.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
          Length = 382

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW
Sbjct: 145 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ M  + V
Sbjct: 205 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMSTDKV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    VL +LT R
Sbjct: 265 REILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDR 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 325 EENVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 6/96 (6%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++    ++  V    + GI++VD D      G+  +L L          L     
Sbjct: 50  MVKPYQLEGRAIDQLVQEFEDNGISIVDND------GNPSNLSLKKQKDVEKAELNDMTA 103

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 104 PSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139


>gi|327473233|gb|EGF18653.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK408]
          Length = 370

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V KG+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEKGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 45.4 bits (106), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNTEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEKGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|15672535|ref|NP_266709.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281491019|ref|YP_003352999.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           KF147]
 gi|12723439|gb|AAK04651.1|AE006289_2 major RNA polymerase sigma factor [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281374777|gb|ADA64297.1| RNA polymerase sigma factor RpoD (Sigma-42) [Lactococcus lactis
           subsp. lactis KF147]
 gi|326406054|gb|ADZ63125.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           CV56]
          Length = 447

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 176 VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 235

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 236 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 295

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 296 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 355

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 356 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 415

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 416 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 447



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 117 IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 172

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 173 -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 204


>gi|403013|emb|CAA50594.1| major sigma factor [Lactococcus lactis]
          Length = 340

 Score =  319 bits (818), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 189 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 249 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 308

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 309 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 340



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 10  IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 65

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 66  -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 97


>gi|19862496|sp|Q04506|RPOD_LACLA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 386

 Score =  319 bits (818), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 115 VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 174

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 175 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 234

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 235 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 294

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 295 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 354

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 355 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 386



 Score = 40.4 bits (93), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 56  IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 111

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 112 -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 143


>gi|325686026|gb|EGD28084.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 372

 Score =  319 bits (818), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 150/251 (59%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 122 VALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LGYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 182 RLGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +PV+ VR++LK+ +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+
Sbjct: 242 EIGAEMDLPVKKVREILKLCQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L+ REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLAEVLDTLSDREEEVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRS +LR FLD
Sbjct: 362 SRSSQLRDFLD 372



 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 56/120 (46%), Gaps = 6/120 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E+G    L L    +     L     
Sbjct: 40  LIKPYKLEGKAVDQLVQEFEDNGISIVD------EDGKPSKLALTKQKNVEKAELNNMDA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                 +DPVRMYL+E+G + LL+ E E+A+AKRIEAG       L E+ L     I  R
Sbjct: 94  PTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRIEAGDEEAKQELAEANLRLVVSIAKR 153


>gi|216733|dbj|BAA01038.1| RNA polymerase sigma factor [Lactococcus lactis]
          Length = 340

 Score =  319 bits (818), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 189 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 249 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 308

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 309 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 340



 Score = 40.4 bits (93), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 10  IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 65

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 66  -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 97


>gi|257425686|ref|ZP_05602110.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257271380|gb|EEV03526.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
          Length = 368

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REP PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGREPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|239626722|ref|ZP_04669753.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516868|gb|EEQ56734.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 374

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 198/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +  E  +  A+K + E+NLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+
Sbjct: 123 IELAKSMELGSEDARKRLAESNLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDY 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VRT+R++  ++ REPT E
Sbjct: 183 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRTSRQLLQELGREPTTE 242

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA +  +PVE V +++K+ +EP+SLETPIG+E+ SHLGDFI+D N + P D+A    L 
Sbjct: 243 EIAARADLPVERVSEIMKMAQEPVSLETPIGEEEDSHLGDFIQDDNVMVPQDAAAFTLLH 302

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL++RFG+      TLEEVG+QF VTRERIRQIEAKA+RKL+HP
Sbjct: 303 EQLMEVLLTLTEREQKVLKLRFGLDDGRPRTLEEVGRQFNVTRERIRQIEAKALRKLRHP 362

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 363 SRSKKLKDYLD 373



 Score = 45.4 bits (106), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 30/47 (63%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G I LLS E EI +AK +E G       L ES L
Sbjct: 99  SLEDPVRMYLKEIGKIPLLSMEEEIELAKSMELGSEDARKRLAESNL 145


>gi|116511352|ref|YP_808568.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|125623388|ref|YP_001031871.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris MG1363]
 gi|116107006|gb|ABJ72146.1| RNA polymerase, sigma 70 subunit, RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|124492196|emb|CAL97125.1| RNA polymerase sigma factor rpoD (Sigma-42) [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070136|gb|ADJ59536.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris NZ9000]
          Length = 447

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 176 VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 235

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 236 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 295

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 296 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 355

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 356 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 415

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 416 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 447



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 117 IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 172

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 173 -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 204


>gi|242242833|ref|ZP_04797278.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
 gi|242233734|gb|EES36046.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
          Length = 368

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 155/276 (56%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + +K E    IAK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKKIEQGDEIAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    L++  I +V+  D  D +
Sbjct: 20  EDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQLNDNDITLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AK+IE
Sbjct: 80  DKINPNDLSAPPG--------------VKINDPVRMYLKEIGRVNLLSAQEEIELAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEIAKSRLAEANLRLVVSIAKR 149


>gi|242373866|ref|ZP_04819440.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
 gi|242348420|gb|EES40022.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
          Length = 368

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 155/276 (56%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + +K E    IAK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKKIEQGDEIAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    L++  I +V+  D  D +
Sbjct: 20  EDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQLNDNDITLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AK+IE
Sbjct: 80  EKLNPNDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEIAKSRLAEANLRLVVSIAKR 149


>gi|167630065|ref|YP_001680564.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
 gi|167592805|gb|ABZ84553.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
          Length = 371

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 134 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REP PEEIAK++ +PVE V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEYGREPMPEEIAKEMDIPVERV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    L+E    VL +LT R
Sbjct: 254 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFILLKEQLEEVLETLTAR 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 314 EMKVLRLRFGLDDGRSRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 371



 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/131 (34%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++G +T +E+   L   E++++Q++D    L NMGI+VV       E    +SL
Sbjct: 19  LIAKGKKKGVLTYQEIMDALQGVEMTADQVDDIYEQLGNMGIDVVP------ENTESESL 72

Query: 94  DLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           D A           +   S       DDPVRMYL+E+G + LLS E EI +AKR+E G  
Sbjct: 73  DKAEEPIIREEEEIEVDLSVPEGVGIDDPVRMYLKEIGRVPLLSAEEEIELAKRMEEGDE 132

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 133 AAKRRLAEANL 143


>gi|241889518|ref|ZP_04776817.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
 gi|241863825|gb|EER68208.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
          Length = 361

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 151/244 (61%), Positives = 191/244 (78%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E   AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFS
Sbjct: 118 EEEKEQAKKDLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFS 177

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I++++R  R++   + REP PEEIAKK+ 
Sbjct: 178 TYATWWIRQAITRAIADQARTIRIPVHMVETINRLIRIQRQLLQDLGREPKPEEIAKKMN 237

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  E VR++LKI +EP+SLETPIG+ED SHLGDFIEDK A SP++ A    L+E    +L
Sbjct: 238 MTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKEAQSPVEHAANELLKEQLEEIL 297

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VL++RFG+     HTLEEVG  F VTRERIRQIEAKAIRKLKHPS+  KL+
Sbjct: 298 ETLTDREENVLKLRFGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSKLNKLK 357

Query: 678 SFLD 681
            F++
Sbjct: 358 GFME 361



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 36/109 (33%), Positives = 58/109 (53%), Gaps = 14/109 (12%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           +G +T EE+   L   ++SSE M+D    L+N  I +++ +        E+  +      
Sbjct: 22  QGELTQEEIVDALSKLDISSEAMDDFYEELNNEDIILINAN-------HEEEEEEELDLE 74

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + SV        A   T+DPVRMYL+E+G + LLS+E E+ ++K IE G
Sbjct: 75  DLSV-------PAGIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIETG 116


>gi|313123889|ref|YP_004034148.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280452|gb|ADQ61171.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 372

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 150/251 (59%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 122 VALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LGYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 182 RLGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +PV  VR++LK+ +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+
Sbjct: 242 EIGAEMDLPVNKVREILKLCQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L+ REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLAEVLDTLSDREEEVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRS +LR FLD
Sbjct: 362 SRSSQLRDFLD 372



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 56/120 (46%), Gaps = 6/120 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E+G    L L    +     L     
Sbjct: 40  LIKPYKLEGKAVDQLVQEFEDNGISIVD------EDGKPSKLALTKQKNVEKAELNNMDA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                 +DPVRMYL+E+G + LL+ E E+A+AKRIEAG       L E+ L     I  R
Sbjct: 94  PTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRIEAGDEEAKQELAEANLRLVVSIAKR 153


>gi|325125918|gb|ADY85248.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 373

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + +S  E   +   +  G+ EA   K E+  ANLRLV+S+AK+Y  RG+
Sbjct: 104 VRQYLKRIGRVSLLSGDEEVQLAKRIGAGDQEA---KDELTNANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 SFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEIA ++ +PV+ VR+ LK+ +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREALKVAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+A SP   A    LR+    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 281 GDFIEDKDATSPEQHAASEMLRDQLAEVLDTLTDREENVLRLRFGLDDGNPRTLEEVGRV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS KLR FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSNKLRDFLE 373



 Score = 45.8 bits (107), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 7/100 (7%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           +  L P ++    ++  V    + GI++VD      ++G    L LA   +     L+  
Sbjct: 40  DCLLKPYQIEGRAVDQLVQEFEDNGISIVD------DKGEPSKLALAKQKNVEKAELEHL 93

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                R  +DPVR YL+ +G + LLS + E+ +AKRI AG
Sbjct: 94  SAPGSR-MNDPVRQYLKRIGRVSLLSGDEEVQLAKRIGAG 132


>gi|226311661|ref|YP_002771555.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226094609|dbj|BAH43051.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 376

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 107 VRMYLKEIGRVPLLSAEEEIKLAQRIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 164 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 223

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA+K+ +  E VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 224 INKLIRVSRQLLQELGREPMPEEIAEKMDLTPEKVREIMKIAQEPVSLETPIGEEDDSHL 283

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A+ P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 284 GDFIEDQDALEPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 343

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 344 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 376



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 43/142 (30%), Positives = 70/142 (49%), Gaps = 24/142 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV-----------VDG 80
           +++++L ++RG ++ +E+ A L   E  S+QM++    L + GI +           VD 
Sbjct: 20  EQLVELGKKRGALSYKEITARLAGFEQDSDQMDEFFEYLGDQGIEINNNENEDDDDEVDQ 79

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             ++DE+  E   D  S      +             +DPVRMYL+E+G + LLS E EI
Sbjct: 80  MIIKDEDNEEFDFDDLSVPPGIKI-------------NDPVRMYLKEIGRVPLLSAEEEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPL 162
            +A+RIE G       L E+ L
Sbjct: 127 KLAQRIEQGDEEAKRRLAEANL 148


>gi|160881641|ref|YP_001560609.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160430307|gb|ABX43870.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 372

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 135 AKKRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REP PEE+AK++ +PVE V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPFPEEVAKEMNIPVERV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A    L+E    VL +LT R
Sbjct: 255 REIQKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAFTLLKEQLMEVLGTLTDR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 315 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 372



 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 32/47 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           ST+DPVRMYL+E+G + LLS + EI +A+R+E G       L E+ L
Sbjct: 98  STEDPVRMYLKEIGKVPLLSADEEIVLAQRMEQGDKNAKKRLAEANL 144


>gi|154686781|ref|YP_001421942.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens FZB42]
 gi|154352632|gb|ABS74711.1| RpoD [Bacillus amyloliquefaciens FZB42]
          Length = 373

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 136 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 256 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 316 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 39/141 (27%), Positives = 69/141 (48%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDE 86
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++ + ++ ED 
Sbjct: 16  DQVKEQLTETGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELISENEETEDP 75

Query: 87  E-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                  +E+  DL   +    V             +DPVRMYL+E+G + LLS + EI 
Sbjct: 76  NIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVNLLSAKEEIT 124

Query: 142 IAKRIEAGRAMMMASLCESPL 162
            A++IE G       L E+ L
Sbjct: 125 YAQKIEEGDEESKRRLAEANL 145


>gi|314933733|ref|ZP_07841098.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
 gi|313653883|gb|EFS17640.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
          Length = 368

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + +K E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKKIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    L++  I +V+  D  D +
Sbjct: 20  EDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFEQLNDNDITLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AK+IE
Sbjct: 80  EKLNPNDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|223044379|ref|ZP_03614413.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
 gi|222442248|gb|EEE48359.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
          Length = 368

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + +K E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKKIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    L++  I +V+  D  D +
Sbjct: 20  EDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQLNDNDITLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AK+IE
Sbjct: 80  EKLNPNDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|52786447|ref|YP_092276.1| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|163119552|ref|YP_079858.2| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|319644974|ref|ZP_07999207.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
 gi|52348949|gb|AAU41583.1| SigA [Bacillus licheniformis ATCC 14580]
 gi|145903060|gb|AAU24220.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus
           licheniformis ATCC 14580]
 gi|317392783|gb|EFV73577.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
          Length = 373

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 136 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 256 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 316 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 76/158 (48%), Gaps = 20/158 (12%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++    F+   D   ++ +  ++RG +T EE+   +   ++ S+QM++    L
Sbjct: 2   ADKQAHETETEFTFEQVRD---QLTEAGKKRGVLTYEEIAERMSSFDIESDQMDEYYEFL 58

Query: 71  SNMGINVV-DGDDLEDEE-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
              G+ ++ + ++ ED        +E+  DL   +    V             +DPVRMY
Sbjct: 59  GEQGVELISENEETEDPNIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMY 107

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           L+E+G + LLS + EI  AK+IE G       L E+ L
Sbjct: 108 LKEIGRVNLLSAKEEIEYAKKIEEGDEESKRRLAEANL 145


>gi|310827637|ref|YP_003959994.1| RNA polymerase [Eubacterium limosum KIST612]
 gi|308739371|gb|ADO37031.1| RNA polymerase [Eubacterium limosum KIST612]
          Length = 395

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 148/237 (62%), Positives = 192/237 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 158 AKKELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTP EI K++    E V
Sbjct: 218 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPAEIGKEMGFSEEKV 277

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI ++P+SLETPIG+E+ SHLGDFIED NA +P ++A  A L+E    VL +LT R
Sbjct: 278 REIQKIAQDPVSLETPIGEEEDSHLGDFIEDDNAPAPSEAASYALLKEQLMEVLNTLTER 337

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L
Sbjct: 338 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYL 394



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 32/47 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVR+YL+E+G + LL+ E E+ IAKR+EAG       L E+ L
Sbjct: 121 SVNDPVRLYLKEIGKVPLLTAEQEMGIAKRMEAGDDEAKKELAEANL 167


>gi|88608313|ref|YP_506202.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600482|gb|ABD45950.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
          Length = 620

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 242/684 (35%), Positives = 351/684 (51%), Gaps = 114/684 (16%)

Query: 32  KKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K +I    +RG+VT  EL ++F   D  +   +E+ ++ L   GI +++ D+ EDE   E
Sbjct: 14  KALITKGVKRGFVTYGELSDSFSDEDFENLNCIEEAISKLEESGIGILEKDE-EDELSEE 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              +       + +            TDDPVR+YLREM  ++LLSR+ E+ IAK I A +
Sbjct: 73  VKEEDEEEDEAADIL---------GHTDDPVRLYLREMSYVKLLSRDDEVEIAKAIVAEK 123

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIID----LEACIGPESKGG--FFHGTE 204
              ++++   P   ++++    +L + T  LRE+I+    L++ +  E+  G   F G +
Sbjct: 124 FESLSAVLLFPSVLKSIVNLGTKLRECTISLREVIESDSGLKSELTEETGKGDDLFEGMD 183

Query: 205 G---HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
           G      Q  ++   EK  D   E E  I SA                        LD+ 
Sbjct: 184 GKPEEGNQMSDEELMEKVLDIFGELETIITSA------------------------LDKA 219

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           ++     +   E  L P+           YREL +L  N +N  K               
Sbjct: 220 KEGQMVKIVDGEVILDPE-----------YRELHTLAVNHLNQVK--------------- 253

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
                   LN   +    E     ++ I+  +  LL   + +G+ R V + + +   LD 
Sbjct: 254 --------LNPKLLAEFFENTRKKNELILEKKKVLLTFLEEHGLDRTVLI-KGKVHILDA 304

Query: 382 HWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             +S          K    C+   S+ +  + I+ +    G+   ++R I  + RK    
Sbjct: 305 VVLSEL-------LKEHNICDTHFSLEEFLSPIRELEKNEGM---DYRSISFLTRKVATH 354

Query: 441 ---ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              A+ AK  MVEANLRLVIS+AKKYTNRG+ F DLIQEGNIGLMKA +KFD   G+KFS
Sbjct: 355 LDNANAAKHRMVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFS 414

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW +QAITR+IAD    +R PVH+ +  +KV+RT RR+ N   REPT EEIA  L 
Sbjct: 415 TYATWWCRQAITRAIADCGSIVRKPVHIHETANKVMRTRRRLYNLNGREPTVEEIANLLK 474

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           +  + V+K LK+ ++PISLE+P+GD+  S   GDFIEDKNAVS +D  +  NLR+     
Sbjct: 475 ISPDKVKKSLKVNQDPISLESPVGDDSNSGSFGDFIEDKNAVSQVDVVLSKNLRKVLDEA 534

Query: 617 LASLTPREERVLRMRFG------------------IGMN--TDHTLEEVGKQFCVTRERI 656
           LA L+PREE++LR RFG                  I +N  T+ TLE+VG  + VTRERI
Sbjct: 535 LAMLSPREEKILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTNLTLEQVGILYNVTRERI 594

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQIE+K++RK++ PSRS KLR+FL
Sbjct: 595 RQIESKSLRKMRSPSRSIKLRTFL 618


>gi|295424882|ref|ZP_06817597.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
 gi|295065448|gb|EFG56341.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
          Length = 368

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 192/251 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 118 IALAKRIENGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 177

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 178 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 237

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK A SP   A    L+
Sbjct: 238 EIGAEMDMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKEATSPEQHASYEMLK 297

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 298 EQLEETLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 357

Query: 671 SRSKKLRSFLD 681
           SRS +L+ FLD
Sbjct: 358 SRSNQLKDFLD 368



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 52/111 (46%), Gaps = 6/111 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD +      G    L L          L+    
Sbjct: 36  LIEPYNLQGKAVDQLVQEFEDNGISIVDKN------GDPSKLALKKQKDIEKKELEDMSA 89

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE G       L E+ L
Sbjct: 90  PSSVRMNDPVRMYLKEIGRVPLLNADKEIALAKRIENGDEEAKQELAEANL 140


>gi|186472529|ref|YP_001859871.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
 gi|184194861|gb|ACC72825.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
          Length = 664

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 164/380 (43%), Positives = 240/380 (63%), Gaps = 10/380 (2%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGI 365
           D++ +     L+E + + +  +      ID L  ++     ++   E  +L++A     +
Sbjct: 288 DKRRATAIANLRESIQQELTPIRFTAKTIDRLCAEVQAQVAQVRAIERSILQIAVDRCDM 347

Query: 366 KRDVFLERHQGRELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
            R+ F+E   G E D  W     + +K +     ++  A + +     + ++  I     
Sbjct: 348 PRETFVESFPGNETDLDWTMRVAAKSKTYGPALERHLPAIQSE-----QQKLVDIEASIA 402

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + + + + I   +   E +   AK+EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGL
Sbjct: 403 LPLQQLKQINKQLGSAESKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGL 462

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  G+KFSTYA WWV+QAITR+IADQ+ TIR+PVHM + I+K+ R  R +  
Sbjct: 463 MKAVDKFEYRRGWKFSTYATWWVRQAITRAIADQARTIRVPVHMIESINKLNRIQREIVQ 522

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP P  +A+++ MP   +R +LKI K P SL++P+G++  + LGD IED +A SP 
Sbjct: 523 QTGQEPHPSVLAERMDMPEAKIRSILKIAKNPASLDSPVGEDADTTLGDMIEDTSATSPA 582

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A+ AN+R      L +LTPRE +VLRMR+GI   ++ TLEEVG+QF VTRERIRQIE 
Sbjct: 583 DAAVHANMRRAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIEG 642

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KAIRKL HPSR+ KLR FL+
Sbjct: 643 KAIRKLNHPSRADKLRPFLE 662


>gi|56421017|ref|YP_148335.1| RNA polymerase sigma factor RpoD [Geobacillus kaustophilus HTA426]
 gi|261417657|ref|YP_003251339.1| RNA polymerase sigma factor RpoD [Geobacillus sp. Y412MC61]
 gi|297529352|ref|YP_003670627.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|319767537|ref|YP_004133038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
 gi|56380859|dbj|BAD76767.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A)
           [Geobacillus kaustophilus HTA426]
 gi|261374114|gb|ACX76857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC61]
 gi|297252604|gb|ADI26050.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|317112403|gb|ADU94895.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
          Length = 375

 Score =  318 bits (816), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVPLLSAEEEIELAKRIEQGDEEA---KRRLTEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/136 (33%), Positives = 70/136 (51%), Gaps = 16/136 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-----DE 86
           +++ +L ++RG +T EE+   L   ++ S+QM++    L+  GI V+   DLE     D+
Sbjct: 23  EQLAELGKKRGILTYEEIAERLSGFDLDSDQMDEYYEYLAEQGIEVISESDLEADPDIDD 82

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E+  DL   +    V             +DPVRMYL+E+G + LLS E EI +AKRI
Sbjct: 83  LAKEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVPLLSAEEEIELAKRI 131

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 132 EQGDEEAKRRLTEANL 147


>gi|288555754|ref|YP_003427689.1| RNA polymerase sigma factor RpoD [Bacillus pseudofirmus OF4]
 gi|288546914|gb|ADC50797.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 372

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSAQEEIELAKRIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYEKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++     REPTPEE+A+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDFGREPTPEEVAEEMELTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQEALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 68/139 (48%), Gaps = 15/139 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD----L 83
           D   ++++++ ++RG +T  E+   L   +  S+QM++    L   G+ +++  D    L
Sbjct: 17  DQVKEQLVEVGKKRGVLTYTEITEKLAVFDQDSDQMDEFFEYLGEQGVEILNESDDVPNL 76

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +     E+  DL   +    +             +DPVRMYL+E+G + LLS + EI +A
Sbjct: 77  QQAAKEEEEFDLNDLSVPPGI-----------KINDPVRMYLKEIGRVPLLSAQEEIELA 125

Query: 144 KRIEAGRAMMMASLCESPL 162
           KRIE G       L E+ L
Sbjct: 126 KRIEQGDEEAKRRLAEANL 144


>gi|255282119|ref|ZP_05346674.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
 gi|255267438|gb|EET60643.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
          Length = 374

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/250 (60%), Positives = 196/250 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AKK ++EANLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 124 VELAKRVEAGDEEAKKRLIEANLRLVVSIAKKYVGRGMPFLDLIQEGNMGLMKAVDKFDY 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR IAD   TIR+PVHM + I+K +R  R +  ++ REPTPE
Sbjct: 184 AKGFKFSTYATWWIRQAITRGIADTGRTIRVPVHMVETINKTLRMTRTLLQELGREPTPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A++L +PV  VR+VLKI+++P+SL+TPIG+ED SHLGDFIED +A+SP DSA  + LR
Sbjct: 244 EVAERLNVPVSRVREVLKISRDPVSLDTPIGEEDDSHLGDFIEDDSALSPSDSAAFSMLR 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L SLT RE +V+++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EELGTALESLTDRERQVVQLRFGLIDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFL 680
           SRSK+L+ FL
Sbjct: 364 SRSKRLKDFL 373



 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 67/125 (53%), Gaps = 2/125 (1%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE-EGSEDSLDLASS 98
           ++  +T +E+N      ++S E+M+     L    I++V  D+ +D  E   D+ D    
Sbjct: 22  KKNMLTYKEVNDAFGSMQISEEKMDFVFEYLEKHNIDLVHEDNADDTTELLLDNDDDILL 81

Query: 99  ASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           +    V +    D  +  ST+DPVRMYL+E+G++ LL+ E E+ +AKR+EAG       L
Sbjct: 82  SDEEEVEIIDDADVLEGVSTEDPVRMYLKEIGNVPLLTTEEEVELAKRVEAGDEEAKKRL 141

Query: 158 CESPL 162
            E+ L
Sbjct: 142 IEANL 146


>gi|308174309|ref|YP_003921014.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|307607173|emb|CBI43544.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|328554255|gb|AEB24747.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens TA208]
 gi|328912652|gb|AEB64248.1| RNA polymerase sigma factor rpoD [Bacillus amyloliquefaciens LL3]
          Length = 373

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 136 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 256 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 316 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 42/158 (26%), Positives = 76/158 (48%), Gaps = 20/158 (12%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L  D   D   ++ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQTHETETELTLDQVKD---QLTETGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFL 58

Query: 71  SNMGINVV-DGDDLEDEE-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
              G+ ++ + ++ ED        +E+  DL   +    V             +DPVRMY
Sbjct: 59  GEQGVELISENEETEDPNIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMY 107

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           L+E+G + LLS + EI  A++IE G       L E+ L
Sbjct: 108 LKEIGRVNLLSAKEEITYAQKIEEGDEESKRRLAEANL 145


>gi|297584635|ref|YP_003700415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
 gi|297143092|gb|ADH99849.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
          Length = 371

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 209/276 (75%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G + +   +  V + ++ E +   AK+ + EANLRLV+S+AK+Y  
Sbjct: 96  IKINDPVRMYLKEIGRVPLLSAKEEVELAKRIEEDDEEAKRRLAEANLRLVVSIAKRYVG 155

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 156 RGMLFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 215

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEE++K++ +  + VR++LKI +EP+SLETPIG+ED 
Sbjct: 216 VETINKLIRVQRQLLQDLGREPTPEEVSKEMELTPDKVREILKIAQEPVSLETPIGEEDD 275

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 276 SHLGDFIEDQEALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 335

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 336 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 371



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 34/124 (27%), Positives = 65/124 (52%), Gaps = 16/124 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD----L 83
           D   +++++  ++RG +T  E+   L   +  S+QM++    L   G+++++  +    L
Sbjct: 17  DQVKEQLVEAGKKRGSLTYVEITEKLGAFDQDSDQMDEFFEHLGEQGVDIINESEAVPSL 76

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +  E  E++ DL   +    +             +DPVRMYL+E+G + LLS + E+ +A
Sbjct: 77  QQVE-KEEAFDLNDLSVPPGI-----------KINDPVRMYLKEIGRVPLLSAKEEVELA 124

Query: 144 KRIE 147
           KRIE
Sbjct: 125 KRIE 128


>gi|291484966|dbj|BAI86041.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto
           BEST195]
          Length = 371

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 157/276 (56%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  ++  +K E     +K+ + EANLRLV+S+AK+Y  
Sbjct: 96  VKINDPVRMYLKEIGRVNLLSAKEEIAYAKKIEEGDEESKRRLAEANLRLVVSIAKRYVG 155

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 156 RGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHM 215

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED 
Sbjct: 216 VETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDD 275

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 276 SHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 335

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 371



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 70/141 (49%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDE 86
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++ + ++ ED 
Sbjct: 14  DQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELISENEETEDP 73

Query: 87  E-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                  +E+  DL   +    V             +DPVRMYL+E+G + LLS + EIA
Sbjct: 74  NIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVNLLSAKEEIA 122

Query: 142 IAKRIEAGRAMMMASLCESPL 162
            AK+IE G       L E+ L
Sbjct: 123 YAKKIEEGDEESKRRLAEANL 143


>gi|311069121|ref|YP_003974044.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
 gi|310869638|gb|ADP33113.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
          Length = 373

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 136 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 256 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 316 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/158 (26%), Positives = 76/158 (48%), Gaps = 20/158 (12%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L  D   D   ++ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQTHETETELTIDQVKD---QLTEAGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFL 58

Query: 71  SNMGINVV-DGDDLEDEE-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
              G+ ++ + ++ ED        +E+  DL   +    V             +DPVRMY
Sbjct: 59  GEQGVELISENEETEDPNIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMY 107

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           L+E+G + LLS + EI  A++IE G       L E+ L
Sbjct: 108 LKEIGRVNLLSAKEEITYAQKIEEGDEESKRRLAEANL 145


>gi|221310444|ref|ZP_03592291.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314767|ref|ZP_03596572.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319690|ref|ZP_03600984.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323967|ref|ZP_03605261.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767573|ref|NP_390399.2| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296333322|ref|ZP_06875775.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305675173|ref|YP_003866845.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|321312003|ref|YP_004204290.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
 gi|251757327|sp|P06224|RPOD_BACSU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|225185201|emb|CAB14450.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. subtilis str. 168]
 gi|296149520|gb|EFG90416.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305413417|gb|ADM38536.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|320018277|gb|ADV93263.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
          Length = 371

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 134 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 254 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 314 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 371



 Score = 55.1 bits (131), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 40/141 (28%), Positives = 70/141 (49%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDE 86
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++ + ++ ED 
Sbjct: 14  DQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELISENEETEDP 73

Query: 87  E-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                  +E+  DL   +    V             +DPVRMYL+E+G + LLS + EIA
Sbjct: 74  NIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVNLLSAKEEIA 122

Query: 142 IAKRIEAGRAMMMASLCESPL 162
            A++IE G       L E+ L
Sbjct: 123 YAQKIEEGDEESKRRLAEANL 143


>gi|222151460|ref|YP_002560616.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
 gi|222120585|dbj|BAH17920.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
          Length = 366

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K  + EANLRLV+S+AK+Y  RG+
Sbjct: 97  VRMYLKEIGRVNLLSAEEEIELAKRIEQGDEEA---KARLAEANLRLVVSIAKRYVGRGM 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 154 LFLDLIQEGNMGLIKAVEKFDFTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 214 INKLIRVQRQLLQDLGRDPSPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHL 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 274 GDFIEDQDAQSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 334 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 366



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 70/130 (53%), Gaps = 14/130 (10%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I+  ++ G+++ EE+   L   E+ S+ M++    ++   I +++  D +D   ++D 
Sbjct: 23  QLIETGKKNGHLSHEEIADKLQNFEMDSDHMDEFFEAIAENDITLINEKDAQD---TDDK 79

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           ++L   ++   V             +DPVRMYL+E+G + LLS E EI +AKRIE G   
Sbjct: 80  INLNDLSAPPGV-----------KINDPVRMYLKEIGRVNLLSAEEEIELAKRIEQGDEE 128

Query: 153 MMASLCESPL 162
             A L E+ L
Sbjct: 129 AKARLAEANL 138


>gi|157693020|ref|YP_001487482.1| RNA polymerase sigma factor RpoD [Bacillus pumilus SAFR-032]
 gi|157681778|gb|ABV62922.1| DNA-directed RNA polymerase sigma subunit SigA [Bacillus pumilus
           SAFR-032]
          Length = 373

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 136 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 256 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 316 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/158 (27%), Positives = 77/158 (48%), Gaps = 20/158 (12%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L F+   D   K+ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQAHETETELTFEQVRD---KLTETGKKRGVLTYEEIAERMSSFEIESDQMDEYYEYL 58

Query: 71  SNMGINVV-DGDDLEDEE-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
              G+ ++ + ++ ED        +E+  DL   +    V             +DPVRMY
Sbjct: 59  GEQGVELISENEETEDPNVQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMY 107

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           L+E+G + LLS + EI  A++IE G       L E+ L
Sbjct: 108 LKEIGRVNLLSAKEEITYAQKIEEGDEESKRRLAEANL 145


>gi|15927141|ref|NP_374674.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus N315]
 gi|20178083|sp|Q99TT5|RPOD_STAAN RecName: Full=RNA polymerase sigma factor rpoD
 gi|13701359|dbj|BAB42653.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           N315]
          Length = 368

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR+VLKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREVLKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|323352412|ref|ZP_08087547.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|322121844|gb|EFX93585.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|325696737|gb|EGD38625.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK160]
 gi|328945882|gb|EGG40032.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1087]
          Length = 370

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNTEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|138896056|ref|YP_001126509.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196248949|ref|ZP_03147649.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
 gi|134267569|gb|ABO67764.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211825|gb|EDY06584.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
          Length = 375

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVPLLSAEEEIELAKRIEQGDEEA---KRRLTEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 47/143 (32%), Positives = 74/143 (51%), Gaps = 16/143 (11%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D  + + +++ +L ++RG +T EE+   L   ++ S+QM++    L++ GI V+   D+E
Sbjct: 16  DTLEQAKEQLAELGKKRGILTYEEIAERLSGFDLDSDQMDEYYEYLADQGIEVISESDIE 75

Query: 85  -----DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                DE   E+  DL   +    V             +DPVRMYL+E+G + LLS E E
Sbjct: 76  TDPDIDELVKEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVPLLSAEEE 124

Query: 140 IAIAKRIEAGRAMMMASLCESPL 162
           I +AKRIE G       L E+ L
Sbjct: 125 IELAKRIEQGDEEAKRRLTEANL 147


>gi|125717671|ref|YP_001034804.1| RNA polymerase sigma factor RpoD [Streptococcus sanguinis SK36]
 gi|125497588|gb|ABN44254.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32),
           putative [Streptococcus sanguinis SK36]
 gi|324990502|gb|EGC22438.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK353]
 gi|324995458|gb|EGC27370.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK678]
 gi|325688386|gb|EGD30405.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK72]
 gi|325690016|gb|EGD32020.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK115]
 gi|325693940|gb|EGD35858.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK150]
 gi|327461509|gb|EGF07840.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1]
 gi|327468857|gb|EGF14329.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK330]
 gi|327489365|gb|EGF21158.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1058]
 gi|332361594|gb|EGJ39398.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1056]
 gi|332363116|gb|EGJ40903.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK355]
 gi|332365901|gb|EGJ43657.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1059]
          Length = 370

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 48.1 bits (113), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|332362696|gb|EGJ40494.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK49]
          Length = 370

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|1519632|gb|AAC44890.1| sigma 70-type sigma factor SigA [Heliobacillus mobilis]
          Length = 333

 Score =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 96  AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REP PEEIAK++ +PV+ V
Sbjct: 156 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEFGREPNPEEIAKEMDIPVDRV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    L+E    VL +LT R
Sbjct: 216 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFILLKEQLEEVLETLTAR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ ++D
Sbjct: 276 EMKVLRLRFGLDDGRSRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYVD 333



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 53/98 (54%), Gaps = 12/98 (12%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           ++++Q++D    L NMGI+VV       E    +S++ A          ++ +   D S 
Sbjct: 1   MTADQVDDVYEQLGNMGIDVVS------EPAEAESMEKAEEPIIRESEEEEEEIEVDLSV 54

Query: 118 ------DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                 DDPVRMYL+E+G + LLS E EI +AKR+E G
Sbjct: 55  PEGVGIDDPVRMYLKEIGRVPLLSAEEEIELAKRMEDG 92


>gi|327458597|gb|EGF04945.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1057]
          Length = 370

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 46.2 bits (108), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +E+ +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQTGVATDDEINDQLVIPFTLDADGIENLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|70726356|ref|YP_253270.1| RNA polymerase sigma factor RpoD [Staphylococcus haemolyticus
           JCSC1435]
 gi|68447080|dbj|BAE04664.1| RNA polymerase sigma factor [Staphylococcus haemolyticus JCSC1435]
          Length = 368

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    IAK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 74/144 (51%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I   ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIDKGKKEGHLSHEEIAEKLQNFDMDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPNDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEIAKSRLAEANLRLVVSIAKR 149


>gi|1710683|sp|P52328|RPSD2_BACSP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|149623|gb|AAA25264.1| RNA polymerase sigma-subunit [Leptospira borgpetersenii]
          Length = 377

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD   G+KFSTYA WW
Sbjct: 140 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFSTYATWW 199

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA ++ + VE V
Sbjct: 200 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAAEMELSVEKV 259

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    VL +LT R
Sbjct: 260 REIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALTPADAAAYELLKEQLEDVLDTLTER 319

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 320 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 43/153 (28%), Positives = 72/153 (47%), Gaps = 14/153 (9%)

Query: 17  DSDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           D    L  +F+ D  K ++I+  ++R  +  +++   L P +   EQM++    L ++GI
Sbjct: 4   DQHTELETEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMDEFYEHLGDLGI 63

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS------TDDPVRMYLREMG 129
            VV+ +D       E+  +L     +            D S       +DPVRMYL+E+G
Sbjct: 64  EVVNEND-------EEVSNLRQGEDHDGNDNDDFNFDDDLSLPPGIKINDPVRMYLKEIG 116

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            + LLS + E+ +AKRI  G       L E+ L
Sbjct: 117 RVPLLSADDEVELAKRIMNGDEEAKRRLAEANL 149


>gi|324993240|gb|EGC25160.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK405]
          Length = 370

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQIGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|322385457|ref|ZP_08059101.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
 gi|321270195|gb|EFX53111.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
          Length = 370

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 65/131 (49%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +      +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G  
Sbjct: 71  ARVLNTEEEEVELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|20808174|ref|NP_623345.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516766|gb|AAM24949.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 372

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 153/238 (64%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 135 AKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ MP E V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEELAKEMGMPEEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL +LTPR
Sbjct: 255 REILKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAYTMLKEQLMDVLDTLTPR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 315 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 372



 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 82/160 (51%), Gaps = 16/160 (10%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +G+KR    + +   +++ L    + ++  ++I   ++ G +T  E+   L   +++ +Q
Sbjct: 1   MGRKRETHREGKSMSNNEEL----AREAINELINKGKKTGMLTYNEIMDSLEDIDLNPDQ 56

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E       +MGI +V GD+   EE SE+ L+L   +    V           S DDPVR
Sbjct: 57  IEKVYDTFEDMGIEIV-GDEPRQEEISEEDLNLDDLSLPEGV-----------SIDDPVR 104

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           MYL+E+G I LL+ E EI +AKRIE G       L E+ L
Sbjct: 105 MYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLIEANL 144


>gi|73662504|ref|YP_301285.1| RNA polymerase sigma factor RpoD [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
 gi|72495019|dbj|BAE18340.1| RNA polymerase sigma factor A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 368

 Score =  318 bits (814), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + +K E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLNAQEEIELAKKIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/144 (28%), Positives = 76/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   E+ S+QM++    L++  I++V+  D  D++
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFEMDSDQMDELFDQLTDNDISLVNEKDSSDKD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LL+ + EI +AK+IE
Sbjct: 80  SKLNPNDLSAPPG--------------VKINDPVRMYLKEIGRVNLLNAQEEIELAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|15924551|ref|NP_372085.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|21283242|ref|NP_646330.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49483810|ref|YP_041034.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|49486397|ref|YP_043618.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|57651954|ref|YP_186458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82751164|ref|YP_416905.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus RF122]
 gi|87162254|ref|YP_494216.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195369|ref|YP_500173.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|148268045|ref|YP_001246988.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394113|ref|YP_001316788.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|151221676|ref|YP_001332498.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|156979879|ref|YP_001442138.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|161509790|ref|YP_001575449.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221140019|ref|ZP_03564512.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253314932|ref|ZP_04838145.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253732214|ref|ZP_04866379.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733189|ref|ZP_04867354.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|255006347|ref|ZP_05144948.2| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257428347|ref|ZP_05604745.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257433672|ref|ZP_05610030.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257436586|ref|ZP_05612630.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257793637|ref|ZP_05642616.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|258411063|ref|ZP_05681343.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|258420133|ref|ZP_05683088.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|258423989|ref|ZP_05686871.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|258443599|ref|ZP_05691938.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|258448720|ref|ZP_05696832.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|258450610|ref|ZP_05698672.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|258453537|ref|ZP_05701515.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|262049137|ref|ZP_06022014.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262051223|ref|ZP_06023447.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|269203189|ref|YP_003282458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282893062|ref|ZP_06301296.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|282904143|ref|ZP_06312031.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282905970|ref|ZP_06313825.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282908880|ref|ZP_06316698.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282911199|ref|ZP_06319001.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282914368|ref|ZP_06322154.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282916831|ref|ZP_06324589.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282919337|ref|ZP_06327072.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282920110|ref|ZP_06327835.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282924662|ref|ZP_06332330.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282928194|ref|ZP_06335799.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|283770637|ref|ZP_06343529.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283958325|ref|ZP_06375776.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|284024620|ref|ZP_06379018.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 132]
 gi|293503442|ref|ZP_06667289.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|293510459|ref|ZP_06669165.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|293530999|ref|ZP_06671681.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|294848592|ref|ZP_06789338.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|295406684|ref|ZP_06816489.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295428139|ref|ZP_06820771.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296275817|ref|ZP_06858324.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297207720|ref|ZP_06924155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297245734|ref|ZP_06929599.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297590895|ref|ZP_06949533.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|300911801|ref|ZP_07129244.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|304380850|ref|ZP_07363510.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|60390420|sp|Q6G905|RPOD_STAAS RecName: Full=RNA polymerase sigma factor rpoD
 gi|60390434|sp|Q6GGD8|RPOD_STAAR RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393872|sp|P0A0I8|RPOD_STAAM RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393873|sp|P0A0I9|RPOD_STAAW RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393874|sp|P0A0J0|RPOD_STAA8 RecName: Full=RNA polymerase sigma factor rpoD
 gi|81694388|sp|Q5HFJ9|RPOD_STAAC RecName: Full=RNA polymerase sigma factor rpoD
 gi|153069|gb|AAB59090.1| sigma factor [Staphylococcus aureus]
 gi|14247332|dbj|BAB57723.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204682|dbj|BAB95378.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49241939|emb|CAG40633.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|49244840|emb|CAG43300.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57286140|gb|AAW38234.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82656695|emb|CAI81122.1| RNA polymerase sigma factor [Staphylococcus aureus RF122]
 gi|87128228|gb|ABD22742.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87202927|gb|ABD30737.1| RNA polymerase sigma factor, putative [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|147741114|gb|ABQ49412.1| RNA polymerase, sigma 70 subunit, RpoD family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946565|gb|ABR52501.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|150374476|dbj|BAF67736.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722014|dbj|BAF78431.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368599|gb|ABX29570.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|253724003|gb|EES92732.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728729|gb|EES97458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|257275188|gb|EEV06675.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257281765|gb|EEV11902.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257283937|gb|EEV14060.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257787609|gb|EEV25949.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|257840213|gb|EEV64677.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|257843844|gb|EEV68238.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|257845610|gb|EEV69642.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|257851005|gb|EEV74948.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|257857998|gb|EEV80887.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|257861768|gb|EEV84567.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|257864268|gb|EEV87018.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|259160860|gb|EEW45880.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|259162806|gb|EEW47371.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262075479|gb|ACY11452.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|269941051|emb|CBI49435.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282313497|gb|EFB43892.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282317147|gb|EFB47521.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282319318|gb|EFB49670.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282321549|gb|EFB51874.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282324894|gb|EFB55204.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282327144|gb|EFB57439.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282331262|gb|EFB60776.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282590001|gb|EFB95083.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|282594458|gb|EFB99443.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282595761|gb|EFC00725.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282764380|gb|EFC04506.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|283460784|gb|EFC07874.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283470839|emb|CAQ50050.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790474|gb|EFC29291.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|285817243|gb|ADC37730.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus 04-02981]
 gi|290920267|gb|EFD97333.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|291095108|gb|EFE25373.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|291466823|gb|EFF09343.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|294824618|gb|EFG41041.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|294968431|gb|EFG44455.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295128497|gb|EFG58131.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296887737|gb|EFH26635.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297177385|gb|EFH36637.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297575781|gb|EFH94497.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|298694843|gb|ADI98065.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300886047|gb|EFK81249.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|302333237|gb|ADL23430.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|302751392|gb|ADL65569.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304340577|gb|EFM06511.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312437970|gb|ADQ77041.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|312829949|emb|CBX34791.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315129839|gb|EFT85829.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|315195463|gb|EFU25850.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|315198744|gb|EFU29072.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140554|gb|EFW32408.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320144091|gb|EFW35860.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|323440459|gb|EGA98171.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O11]
 gi|323443233|gb|EGB00851.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O46]
 gi|329314237|gb|AEB88650.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus T0131]
 gi|329727416|gb|EGG63872.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329728458|gb|EGG64895.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 368

 Score =  318 bits (814), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 153/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|295399207|ref|ZP_06809189.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110191|ref|YP_003988507.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294978673|gb|EFG54269.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215292|gb|ADP73896.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 377

 Score =  318 bits (814), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSAEEEIELAKRIEQGDEEA---KRRLTEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 48/132 (36%), Positives = 71/132 (53%), Gaps = 5/132 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSE 90
           +++ +L ++RG +T EE+   L   ++ S+QM++    L++ GI V+   DLE D E   
Sbjct: 22  EQLTELGKKRGILTYEEIAERLSAFDLDSDQMDEFYEYLTDQGIEVISESDLESDLEHDP 81

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  DLA    +    L           +DPVRMYL+E+G + LLS E EI +AKRIE G 
Sbjct: 82  DIDDLAKEEFD----LNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRIEQGD 137

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 138 EEAKRRLTEANL 149


>gi|27468166|ref|NP_764803.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis ATCC
           12228]
 gi|57867102|ref|YP_188703.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis RP62A]
 gi|251810978|ref|ZP_04825451.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876013|ref|ZP_06284880.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|293366478|ref|ZP_06613155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|47606037|sp|Q8CP24|RPOD_STAES RecName: Full=RNA polymerase sigma factor rpoD
 gi|81674470|sp|Q5HNY7|RPOD_STAEQ RecName: Full=RNA polymerase sigma factor rpoD
 gi|27315712|gb|AAO04847.1|AE016748_81 RNA polymerase sigma factor [Staphylococcus epidermidis ATCC 12228]
 gi|57637760|gb|AAW54548.1| RNA polymerase sigma-70 factor [Staphylococcus epidermidis RP62A]
 gi|251805488|gb|EES58145.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281295038|gb|EFA87565.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|291319247|gb|EFE59616.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319400897|gb|EFV89116.1| RNA polymerase sigma factor rpoD [Staphylococcus epidermidis
           FRI909]
 gi|329725345|gb|EGG61828.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU144]
 gi|329735301|gb|EGG71593.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU045]
 gi|329737328|gb|EGG73582.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU028]
          Length = 368

 Score =  318 bits (814), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    IAK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 71/135 (52%), Gaps = 14/135 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    L++  I +V+  D  D +
Sbjct: 20  EDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQLNDNDITLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  DKINPNDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPL 162
            G  +  + L E+ L
Sbjct: 126 QGDEIAKSRLAEANL 140


>gi|182416400|ref|YP_001821466.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843614|gb|ACB77866.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 640

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 155/274 (56%), Positives = 203/274 (74%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +K I     I  +E   +V+  R    EA  AK EMVEANLRLVIS+AKKYTNRGL
Sbjct: 302 IQHRLKQIETIHRIDPAELLKVVTQTRVHVREAHQAKTEMVEANLRLVISIAKKYTNRGL 361

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 362 SFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 421

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++KV++  +++  +   EPTPEE+A ++ +PVE V++++K+ ++PISL++P+GD D +  
Sbjct: 422 LNKVMQVQKQLLQEYGHEPTPEEVADEMNLPVERVQQIMKMAQQPISLQSPVGDGDDTSF 481

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+A +P D    + LRE    VL SLT RE RVL +RFG+      TLEEVGKQ
Sbjct: 482 GDFIEDKSAENPYDMTAFSLLREKIIDVLDSLTERERRVLSLRFGLIDGYSRTLEEVGKQ 541

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RK++HP+R ++L  F D 
Sbjct: 542 FKVTRERIRQIEAKALRKMRHPTRIRQLHGFFDA 575



 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 54/184 (29%), Positives = 97/184 (52%), Gaps = 28/184 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  + +I+L++++GY+T +++N  LP    + E++++ +++L N+ I +++ D ++D +
Sbjct: 43  NDKIRHLIRLSKEQGYLTFDDINEALPESVENQEEIDNVLSILQNLEIEILEPDQVDDYK 102

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  +   S S+    L           DDPVRMYL++MG + LL+RE E+ I+KRIE
Sbjct: 103 QRMEEAEEEESRSSQHDIL-----------DDPVRMYLKQMGQVPLLTREQEVEISKRIE 151

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLL-------REIIDLEACIGPESKGGFF 200
                  A L      FQA II    +  G  L+       R +ID +     +S+  +F
Sbjct: 152 N------AELKAQEALFQATIIGNYIVTLGQKLIDRQERFDRVVIDKKI----DSRESYF 201

Query: 201 HGTE 204
            G E
Sbjct: 202 KGLE 205


>gi|91779751|ref|YP_554959.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692411|gb|ABE35609.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 647

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 156/336 (46%), Positives = 228/336 (67%), Gaps = 14/336 (4%)

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWV----SYAKDFPEGEWKNF--VACEVDS 405
           E E+ R+A +  G+ RD F+   +G E DP W     +  + F     +N   +  E + 
Sbjct: 317 EREIARIAVERCGVPRDTFIAHFRGNETDPAWARQLAAAGQPFSSVLERNLPAIGLEQEK 376

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +L ++  +        + + EFR +   +   E +   AK EM+EANLRLVIS+AK+YTN
Sbjct: 377 LLALQKRVV-------LPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTN 429

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL FLDLIQEGNIGLM+A +KF++  GYKFSTYA WW++QA++RSIADQ+ TIR+PVHM
Sbjct: 430 RGLLFLDLIQEGNIGLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPVHM 489

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + ++K+ R +R++  +   EP    +A+ + M  + VR +L+I KEP+SL+  +G+ D 
Sbjct: 490 IESLNKLKRISRKILQETGNEPDAALLAQLMEMQEQKVRAMLRIVKEPVSLDASVGENDD 549

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           + +GD IED  A+ P D+A+ A +R+  +  L +LTPRE ++LR+RFGI  + DHTLEE+
Sbjct: 550 TSIGDLIEDSAAILPDDAALHAGMRDAISEALMTLTPREAKILRLRFGIESSRDHTLEEL 609

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+QF +TRERIRQIE KA+RKL+HP+RS +L+SFLD
Sbjct: 610 GEQFELTRERIRQIEVKALRKLRHPARSARLKSFLD 645



 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 87/164 (53%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---------DD 82
           K +IKL  +RG+V   E++  LP      + +E+ V   S MGI V +          +D
Sbjct: 38  KALIKLGTERGFVIRGEISDCLPERLAQPDAIENVVRAFSEMGIAVFEQAPDAESMIMND 97

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 +++ ++  +  + SSV      D+    T DPVRMY+REMG+ ELL+R+GEIA+
Sbjct: 98  HPAAVATDEQIEEEAVTAISSV------DAEFGRTTDPVRMYMREMGTTELLTRQGEIAL 151

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           A+RIE GR  M+ ++   P T   ++   D +  G T + E +D
Sbjct: 152 AQRIEEGRNGMIRAISSCPATIAEILAIADGVACGETAIDEFVD 195


>gi|228476045|ref|ZP_04060753.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|314936318|ref|ZP_07843665.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
 gi|228269868|gb|EEK11348.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|313654937|gb|EFS18682.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
          Length = 368

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 153/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDMDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPNDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|258446806|ref|ZP_05694960.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
 gi|257854381|gb|EEV77330.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
          Length = 368

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 153/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|258437393|ref|ZP_05689377.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
 gi|257848598|gb|EEV72586.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
          Length = 368

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 153/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++++  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLINEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKR 149


>gi|23099399|ref|NP_692865.1| RNA polymerase sigma factor RpoD [Oceanobacillus iheyensis HTE831]
 gi|22777628|dbj|BAC13900.1| RNA polymerase sigma-43(-A) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 380

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S +E   + S + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLSAAEEIDLASSIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + REPTPEEI +++ +  + VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRVQRSLLQDLGREPTPEEIGEEMELGPDKVRDILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A+SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQEAISPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 380



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 63/130 (48%), Gaps = 8/130 (6%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           +++++ ++RG +  EE+   L   E+  EQM++    L   G++V+ G+       SED 
Sbjct: 31  RLLEIGKKRGSLAYEEVADGLSNFELEPEQMDEFYEYLEEQGVDVI-GE-------SEDD 82

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            ++   A      L           +DPVRMYL+E+G + LLS   EI +A  IE G   
Sbjct: 83  PEMQKIAKEEEFNLNDLSVPLGIKINDPVRMYLKEIGRVNLLSAAEEIDLASSIEEGDEE 142

Query: 153 MMASLCESPL 162
               L E+ L
Sbjct: 143 AKRRLAEANL 152


>gi|289550668|ref|YP_003471572.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315658163|ref|ZP_07911035.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
 gi|289180200|gb|ADC87445.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315496492|gb|EFU84815.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
          Length = 368

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 154/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    IAK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLNAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/144 (26%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++++  ++ G+++ EE+   +   ++ ++QM++    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLLEKGKKEGHLSHEEIAEKMQNFDMDTDQMDEFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 80  EKLNPNDLSAPPG--------------VKINDPVRMYLKEIGRVNLLNAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 126 QGDEIAKSRLAEANLRLVVSIAKR 149


>gi|260438482|ref|ZP_05792298.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
 gi|292809071|gb|EFF68276.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
          Length = 370

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 200/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 120 IELAKRMELGDEEAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+P+
Sbjct: 180 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPQ 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +PVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P ++A    L+
Sbjct: 240 EIADEMDIPVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPAEAAAFTLLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL++RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLNEVLGTLTEREQKVLKLRFGLEDGRARTLEEVGKVFNVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS+KLR +L+
Sbjct: 360 SRSRKLRDYLE 370



 Score = 45.8 bits (107), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS + EI +AKR+E G       L E+ L
Sbjct: 96  SIEDPVRMYLKEIGKVPLLSADEEIELAKRMELGDEEAKKKLAEANL 142


>gi|302386569|ref|YP_003822391.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197197|gb|ADL04768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 401

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K E     AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+
Sbjct: 150 IELAKKIELGDDDAKQRLTEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDY 209

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VR +R++  ++ REP PE
Sbjct: 210 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRVSRQLLQELGREPVPE 269

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA +  M V+ VR+++K+++EP+SLETPIG+E+ SHLGDFI+D+    P D+A    L 
Sbjct: 270 EIAARADMQVDRVREIMKVSQEPVSLETPIGEEEDSHLGDFIQDEQVAVPADAATFTMLH 329

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 330 EQLMEVLDTLTEREQKVLKLRFGLDDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHP 389

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 390 SRSKKLKDYLD 400



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 60/115 (52%), Gaps = 7/115 (6%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDDLEDEEGSEDSLDLA 96
           ++R  +  +E+  F   + + S++++     L N  ++V  + G+DLE +E   D     
Sbjct: 48  KKRNVLENQEILDFFVGENLDSDKLDQIFDFLENNKVDVLQIGGEDLELDE---DLFIEE 104

Query: 97  SSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                  + ++    S     S +DPVRMYL+E+G + LLS E EI +AK+IE G
Sbjct: 105 DIEDEEEIDMESIDLSVPEGISVEDPVRMYLKEIGKVPLLSSEDEIELAKKIELG 159


>gi|56963455|ref|YP_175186.1| RNA polymerase sigma factor RpoD [Bacillus clausii KSM-K16]
 gi|56909698|dbj|BAD64225.1| DNA-directed RNA polymerase major sigma-43 factor sigma-A [Bacillus
           clausii KSM-K16]
          Length = 373

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 163/305 (53%), Positives = 215/305 (70%), Gaps = 10/305 (3%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVRK 436
           P     AKD  E +  +     V   +KI + ++    E G    +S  E   +   + +
Sbjct: 75  PSLAQVAKDEEEFDLNDL---SVPPGIKINDPVRMYLKEIGRVPLLSAEEEIDLAKRIEQ 131

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA   KK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KF
Sbjct: 132 GDEEA---KKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYDKGFKF 188

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++     REPTPEE+ K++
Sbjct: 189 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDYGREPTPEEVGKEM 248

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    V
Sbjct: 249 DLSPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPSDAAAYELLKEQLEDV 308

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L
Sbjct: 309 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRL 368

Query: 677 RSFLD 681
           + FLD
Sbjct: 369 KDFLD 373



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 42/136 (30%), Positives = 67/136 (49%), Gaps = 8/136 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++  ++RG +T  E+   +   E  S+QM++    L   G+ +++       E
Sbjct: 17  DQVKEQLVETGKKRGTLTYAEITEKMAAFEQDSDQMDEFYEYLGEQGVELLN-------E 69

Query: 88  GSEDSLDLASSASNSSVF-LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +D   LA  A +   F L           +DPVRMYL+E+G + LLS E EI +AKRI
Sbjct: 70  SEDDVPSLAQVAKDEEEFDLNDLSVPPGIKINDPVRMYLKEIGRVPLLSAEEEIDLAKRI 129

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 130 EQGDEEAKKRLAEANL 145


>gi|322389216|ref|ZP_08062777.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
 gi|321144121|gb|EFX39538.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
          Length = 369

 Score =  317 bits (813), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 368



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 32/131 (24%), Positives = 63/131 (48%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N   + P  + ++ ++D +  + + GI++ D D          
Sbjct: 17  EFIRSHKKSGTATDDEINDQLVIPFTLDADGIDDLLQRIQDAGISITDKD-------GNP 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + ++     +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 70  SARVLTNEEEPELSDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILVEQGDL 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|296876770|ref|ZP_06900818.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
 gi|296432272|gb|EFH18071.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
          Length = 369

 Score =  317 bits (813), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 368



 Score = 44.3 bits (103), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 63/131 (48%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q G  T +E+N   + P  + ++ +ED +  + + GI++ D D          
Sbjct: 17  EFIRSHKQSGAATDDEINDKLVIPFTLDADGIEDLLQRIQDAGISITDKD-------GNP 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + ++     +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 70  SARVLNNEEEPELSDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILVEQGDL 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|257430984|ref|ZP_05607364.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
 gi|257278414|gb|EEV09050.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
          Length = 342

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 153/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 67  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 126

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 127 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 186

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 187 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 246

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 247 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 306

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 307 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 342



 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 69/128 (53%), Gaps = 14/128 (10%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           +K  +++G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +   +  D
Sbjct: 1   MKKVKKKGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNPSD 60

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           L++                    +DPVRMYL+E+G + LLS + EI +AKRIE G  +  
Sbjct: 61  LSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAK 106

Query: 155 ASLCESPL 162
           + L E+ L
Sbjct: 107 SRLAEANL 114


>gi|312867612|ref|ZP_07727818.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
 gi|311096675|gb|EFQ54913.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
          Length = 369

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 368



 Score = 42.7 bits (99), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 63/131 (48%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N   + P  + ++ +ED +  + + GI++ D D          
Sbjct: 17  EFIRSHKKSGTATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITDKD-------GNP 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + ++     +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 70  SARVLNNEEEPELSDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILVEQGDL 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|21910055|ref|NP_664323.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS315]
 gi|28896247|ref|NP_802597.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes SSI-1]
 gi|21904246|gb|AAM79126.1| putative RNA polymerase sigma 42 protein RpoD [Streptococcus
           pyogenes MGAS315]
 gi|28811498|dbj|BAC64430.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           SSI-1]
          Length = 369

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V KG+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAKGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 44.3 bits (103), Expect = 0.070,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFALDADQIDDLLERLTDGGISITD------KEGNPSSKYIVEELKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAKGDLMAKQRLAEANL 140


>gi|329769784|ref|ZP_08261185.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
 gi|328838146|gb|EGF87764.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
          Length = 362

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 150/244 (61%), Positives = 191/244 (78%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E   AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFS
Sbjct: 119 EEEKEQAKKDLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYEKGFKFS 178

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I++++R  R++   + REP PEEIAKK+ 
Sbjct: 179 TYATWWIRQAITRAIADQARTIRIPVHMVETINRLIRVQRQLLQDLGREPKPEEIAKKMN 238

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK A SP++ A    L+E    +L
Sbjct: 239 MTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKEAQSPVEHAANELLKEQLEEIL 298

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VL++RFG+     HTLEEVG  F VTRERIRQIEAKAIRKLKHPS+  KL+
Sbjct: 299 ETLTDREENVLKLRFGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSKLNKLK 358

Query: 678 SFLD 681
            F++
Sbjct: 359 GFME 362



 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 63/118 (53%), Gaps = 14/118 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K+ I+  +++G +T EE+   L   +VSSE ++D    L+   I +++ + +       +
Sbjct: 14  KEFIEKGKKQGELTQEEILDALSKLDVSSEAVDDFYEELNREDIILINANQV-------E 66

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +      + SV        A   T+DPVRMYL+E+G + LLS+E E+ ++K IE G
Sbjct: 67  EEEEELDLEDLSV-------PAGIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIENG 117


>gi|294501280|ref|YP_003564980.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|295706627|ref|YP_003599702.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
 gi|294351217|gb|ADE71546.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|294804286|gb|ADF41352.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
          Length = 377

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E  ++   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVDLLSAEEEINLAKRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVQRQLLQDLGREPSPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 69/139 (49%), Gaps = 3/139 (2%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++ ++ ++RG +T EE+   +   E+ S+QM++    L   G+ V+   +  D++   D 
Sbjct: 23  QLTEIGKKRGVLTYEEIAERMANFEIESDQMDEYYEYLGEQGVEVMSESEANDDDADPDI 82

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L+         L           +DPVRMYL+E+G ++LLS E EI +AKRIE G   
Sbjct: 83  QELSKEEEFD---LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEINLAKRIEEGDEE 139

Query: 153 MMASLCESPLTFQALIIWR 171
               L E+ L     I  R
Sbjct: 140 AKRRLAEANLRLVVSIAKR 158


>gi|319947289|ref|ZP_08021522.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
 gi|319746531|gb|EFV98791.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
          Length = 370

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAILVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 41.2 bits (95), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 65/131 (49%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N   + P  + ++ ++D +  + + GI++ D      +EG+  
Sbjct: 17  EFIRSHKKSGTATDDEINDQLVIPFTLDADGIDDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +      +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 71  ARVLNTEEEEPELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|239827752|ref|YP_002950376.1| RNA polymerase sigma factor RpoD [Geobacillus sp. WCH70]
 gi|239808045|gb|ACS25110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           WCH70]
          Length = 374

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVPLLSAEEEIELAKRIEQGDEEA---KRRLTEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQEATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 16/136 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE---- 87
           +++ +L ++RG +T EE+   L   ++ S+QM++    L++ GI V+   DL+ +     
Sbjct: 22  EQLTELGKKRGILTYEEIAERLSGFDLDSDQMDEFYEYLADQGIEVISESDLDADPDIDD 81

Query: 88  -GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E+  DL   +    V             +DPVRMYL+E+G + LLS E EI +AKRI
Sbjct: 82  LSKEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVPLLSAEEEIELAKRI 130

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 131 EQGDEEAKRRLTEANL 146


>gi|15674827|ref|NP_269001.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes M1 GAS]
 gi|50913963|ref|YP_059935.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10394]
 gi|71903245|ref|YP_280048.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS6180]
 gi|71910413|ref|YP_281963.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS5005]
 gi|94988285|ref|YP_596386.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS9429]
 gi|94990164|ref|YP_598264.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10270]
 gi|94992161|ref|YP_600260.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS2096]
 gi|94994083|ref|YP_602181.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10750]
 gi|139474032|ref|YP_001128748.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209559154|ref|YP_002285626.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|306827613|ref|ZP_07460893.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
 gi|13621959|gb|AAK33722.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes M1
           GAS]
 gi|50903037|gb|AAT86752.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10394]
 gi|71802340|gb|AAX71693.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS6180]
 gi|71853195|gb|AAZ51218.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS5005]
 gi|94541793|gb|ABF31842.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS9429]
 gi|94543672|gb|ABF33720.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10270]
 gi|94545669|gb|ABF35716.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS2096]
 gi|94547591|gb|ABF37637.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10750]
 gi|134272279|emb|CAM30532.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209540355|gb|ACI60931.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|304430176|gb|EFM33205.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
          Length = 369

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V KG+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAKGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 44.7 bits (104), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFALDADQIDDLLERLTDGGISITD------KEGNPSSKYIVEEPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAKGDLMAKQRLAEANL 140


>gi|19745866|ref|NP_607002.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS8232]
 gi|19748016|gb|AAL97501.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           MGAS8232]
          Length = 369

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V KG+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAKGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 44.7 bits (104), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFALDADQIDDLLERLTDGGISITD------KEGNPSSKYIVEEPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAKGDLMAKQRLAEANL 140


>gi|3062909|dbj|BAA25730.1| SigA [Bacillus sp.]
          Length = 372

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLTAEEEIELATRIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEE+A+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDVGREPSPEEVAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 70/139 (50%), Gaps = 15/139 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD----L 83
           D   +++++L ++RG +T  E+   L P +  S+QM++    L   G+ +++ ++    L
Sbjct: 17  DQVKEQLVELGKKRGVLTYAEITEKLAPYDQDSDQMDEFFEYLGEQGVEILNDNEEVPSL 76

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +  E  E+  DL   +    V             +DPVRMYL+E+G + LL+ E EI +A
Sbjct: 77  QQVEKEEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVPLLTAEEEIELA 125

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 126 TRIEQGDEEAKRRLAEANL 144


>gi|89895793|ref|YP_519280.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense Y51]
 gi|89335241|dbj|BAE84836.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 367

 Score =  317 bits (812), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 130 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYVKGFKFSTYATWW 189

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA ++ + VE V
Sbjct: 190 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAVQMDISVERV 249

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL +LTPR
Sbjct: 250 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPSEAASFILLKEQLEEVLETLTPR 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 310 EEKVLRLRFGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 367



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/142 (28%), Positives = 73/142 (51%), Gaps = 14/142 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D+ K++I+  +++G +T  E+   L   E+++EQ+++    +  MGI+++       E G
Sbjct: 4   DAVKELIQKGKKKGSLTYREIMDTLQGIELTAEQIDEVYEQIGRMGIDIIP------EAG 57

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADR--------STDDPVRMYLREMGSIELLSREGEI 140
             ++L+  +      V     ++  D           DDPVRMYL+E+G + LL+ E EI
Sbjct: 58  EVEALEKVTDEIPDDVDDPDVEEEVDVDLSIPEGVGIDDPVRMYLKEIGRVPLLTAEEEI 117

Query: 141 AIAKRIEAGRAMMMASLCESPL 162
            +AKR+E G       L E+ L
Sbjct: 118 ELAKRMEQGDESAKRRLAEANL 139


>gi|219670224|ref|YP_002460659.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense
           DCB-2]
 gi|219540484|gb|ACL22223.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfitobacterium hafniense DCB-2]
          Length = 372

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 135 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYVKGFKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIA ++ + VE V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAVQMDISVERV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL +LTPR
Sbjct: 255 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPSEAASFILLKEQLEEVLETLTPR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 315 EEKVLRLRFGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 372



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/142 (28%), Positives = 73/142 (51%), Gaps = 14/142 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D+ K++I+  +++G +T  E+   L   E+++EQ+++    +  MGI+++       E G
Sbjct: 9   DAVKELIQKGKKKGSLTYREIMDTLQGIELTAEQIDEVYEQIGRMGIDIIP------EAG 62

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADR--------STDDPVRMYLREMGSIELLSREGEI 140
             ++L+  +      V     ++  D           DDPVRMYL+E+G + LL+ E EI
Sbjct: 63  EVEALEKVTDEIPDDVDDPDVEEEVDVDLSIPEGVGIDDPVRMYLKEIGRVPLLTAEEEI 122

Query: 141 AIAKRIEAGRAMMMASLCESPL 162
            +AKR+E G       L E+ L
Sbjct: 123 ELAKRMEQGDESAKRRLAEANL 144


>gi|329733136|gb|EGG69473.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 314

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 153/276 (55%), Positives = 206/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 39  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 98

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 99  RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 158

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 159 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 218

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 219 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 278

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 279 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 314



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 32/45 (71%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +DPVRMYL+E+G + LLS + EI +AKRIE G  +  + L E+ L
Sbjct: 42  NDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANL 86


>gi|319892618|ref|YP_004149493.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162314|gb|ADV05857.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464344|gb|ADX76497.1| RNA polymerase sigma factor SigA [Staphylococcus pseudintermedius
           ED99]
          Length = 369

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 194/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E    +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 119 IELAKRIEQGDEVAKARLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDF 178

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 179 SKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPE 238

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+
Sbjct: 239 EIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLK 298

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 299 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 358

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ F+D
Sbjct: 359 SRSKRLKDFMD 369



 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 78/144 (54%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM++   M+++  I +++  D  D  
Sbjct: 21  EDVKKQLIEKGKKEGHLSHEEVADKLQNFDMDSDQMDEFFDMINDNDIQLINEKDSSD-- 78

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            ++D L+    ++   V             +DPVRMYL+E+G ++LLS + EI +AKRIE
Sbjct: 79  -TDDKLNPNDLSAPPGV-----------KINDPVRMYLKEIGRVDLLSAQEEIELAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  A L E+ L     I  R
Sbjct: 127 QGDEVAKARLAEANLRLVVSIAKR 150


>gi|184155321|ref|YP_001843661.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227514580|ref|ZP_03944629.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260662165|ref|ZP_05863061.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
 gi|183226665|dbj|BAG27181.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227086991|gb|EEI22303.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260553548|gb|EEX26440.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
          Length = 380

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 143 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 202

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M  + V
Sbjct: 203 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDMDTQKV 262

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LKI++EP+SLETPIG+ED SHLGDFIED +A SP D A    +++    VL +LT R
Sbjct: 263 RDILKISQEPVSLETPIGEEDDSHLGDFIEDHDATSPADHAAYEMMKKQLENVLDTLTDR 322

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 323 EENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 57/108 (52%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  ++++ M+  +  + + G++VVD      E G  D   L ++   SS  L+     + 
Sbjct: 51  PFGLNADGMDALLQNVEDAGVSVVD------ENGDPDLRALKATEKLSSKALKDTTAPSS 104

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ + E+A+A RIE G       L E+ L
Sbjct: 105 IKINDPVRMYLKEIGRVNLLTADEEVALALRIEKGDETAKQELAEANL 152


>gi|322373396|ref|ZP_08047932.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
 gi|321278438|gb|EFX55507.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
          Length = 369

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVENGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMGMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 41.2 bits (95), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++ ++D +  L++ GI++ D D      G+  S  +  +     +  ++   S  
Sbjct: 39  PFVLDADGIDDLLERLTDGGISITDKD------GNPSSKYVVEAPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  +E G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANL 140


>gi|212638699|ref|YP_002315219.1| RNA polymerase sigma factor RpoD [Anoxybacillus flavithermus WK1]
 gi|212560179|gb|ACJ33234.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Anoxybacillus flavithermus WK1]
          Length = 372

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSAEEEIELAKRIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDLGREPSPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 45/137 (32%), Positives = 68/137 (49%), Gaps = 15/137 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++++L ++RG +T EE+   L   ++ S+QM++    L+  GI VV         G  D
Sbjct: 17  EQLVELGKKRGVLTYEEIAERLSSFDLDSDQMDEYYEYLNEQGIEVV---------GESD 67

Query: 92  SLDLASSASNSSVFLQKRKDSADRST------DDPVRMYLREMGSIELLSREGEIAIAKR 145
             D      +      +  D  D S       +DPVRMYL+E+G + LLS E EI +AKR
Sbjct: 68  LDDTDLDDPDFDDLKDEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKR 127

Query: 146 IEAGRAMMMASLCESPL 162
           IE G       L E+ L
Sbjct: 128 IEQGDEEAKRRLAEANL 144


>gi|297617785|ref|YP_003702944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297145622|gb|ADI02379.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 361

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 124 AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLMKAVEKFDYRKGYKFSTYATWW 183

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +  K+ REPTP E+A+++ +PVE V
Sbjct: 184 IRQAITRAIADQARTIRIPVHMVETINKLSRIQRALLQKLGREPTPAEVAEEMDIPVERV 243

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++K+ +EP+SLETPIG+ED SHLGDFI D++A SP +SA    LRE    +L++LT R
Sbjct: 244 MEIMKVAQEPVSLETPIGEEDDSHLGDFITDEDAESPEESASFVLLREHLDGILSTLTDR 303

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +++
Sbjct: 304 EEKVLRLRFGLDDGRPRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYIE 361



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/134 (32%), Positives = 69/134 (51%), Gaps = 8/134 (5%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
            +++  +T +E++  L   ++ ++Q+ED    L  MGI V  GD  ++ E  E  ++   
Sbjct: 17  GKKKKNLTYDEISDDLQGIKLEADQIEDIYEHLQAMGIRV--GDSTDEFEVEETPVE-GE 73

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           +A    V + +  +      DDPVRMYL+E+G + LLS E EI +AKRIE G       L
Sbjct: 74  AAETEDVLVPEGVE-----IDDPVRMYLKEIGRVPLLSAEEEIELAKRIENGDEDAKRKL 128

Query: 158 CESPLTFQALIIWR 171
            E+ L     I  R
Sbjct: 129 VEANLRLVVSIAKR 142


>gi|444799|prf||1908232B RNA polymerase:SUBUNIT=sigma factor
          Length = 340

 Score =  317 bits (811), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 158/272 (58%), Positives = 200/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG 
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGN 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 189 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 249 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 308

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 309 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 340



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 50/103 (48%), Gaps = 26/103 (25%)

Query: 58  VSSEQMEDTVAMLSNMGINVVD-----------GDDLEDEEGSEDSLDLASSASNSSVFL 106
           +  + +ED    + + GI++VD            D++E EE S+ ++D     +N  +  
Sbjct: 10  IVDDALEDLFKQIQDAGISIVDKDGNPSPLALVTDEIEKEEVSDTAMD--EIVTNVRI-- 65

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      DDPVRMYL+E+G   L+S + E  +A+ I AG
Sbjct: 66  -----------DDPVRMYLKEIGRYPLISLDEETKLAEAIIAG 97


>gi|329117418|ref|ZP_08246135.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
 gi|326907823|gb|EGE54737.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
          Length = 369

 Score =  317 bits (811), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTGEEEKELAVAVDEGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 41.2 bits (95), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFVLDADQIDDLLERLTDGGISITD------KEGNPSSKYVVEEPKPEELTDEQLIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  ++ G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTGEEEKELAVAVDEGDLEAKQRLAEANL 140


>gi|15613939|ref|NP_242242.1| RNA polymerase sigma factor RpoD [Bacillus halodurans C-125]
 gi|12643264|sp|O66381|RPOD_BACHD RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|10173992|dbj|BAB05095.1| RNA polymerase major sigma factor [Bacillus halodurans C-125]
          Length = 372

 Score =  317 bits (811), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLTAEEEIELATRIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEE+A+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDLGREPSPEEVAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 70/139 (50%), Gaps = 15/139 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD----L 83
           D   +++++L ++RG +T  E+   L P +  S+QM++    L   G+ +++ ++    L
Sbjct: 17  DQVKEQLVELGKKRGVLTYAEITEKLAPYDQDSDQMDEFFEYLGEQGVEILNDNEEVPSL 76

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +  E  E+  DL   +    V             +DPVRMYL+E+G + LL+ E EI +A
Sbjct: 77  QQVEKEEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVPLLTAEEEIELA 125

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 126 TRIEQGDEEAKRRLAEANL 144


>gi|262282856|ref|ZP_06060623.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
 gi|262261108|gb|EEY79807.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
          Length = 370

 Score =  317 bits (811), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAILVEQGDTEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 43.9 bits (102), Expect = 0.094,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 65/131 (49%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G    +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKKTGTAIDDEINDKLIIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 71  ARVLHNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILVEQGDT 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|157151547|ref|YP_001450555.1| RNA polymerase sigma factor RpoD [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157076341|gb|ABV11024.1| RNA polymerase sigma factor [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 370

 Score =  317 bits (811), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAILVEQGDTEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 66/131 (50%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G V  +E+N   + P  + ++ +ED +  + + GI++ D      +EG+  
Sbjct: 17  EFIRNHKKAGTVIDDEINDKLIIPFTLDADGIEDLLQRIQDAGISITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  L +    + +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 71  ARVLHNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILVEQGDT 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|255525304|ref|ZP_05392244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296188172|ref|ZP_06856564.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
 gi|255510976|gb|EET87276.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296047298|gb|EFG86740.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
          Length = 361

 Score =  317 bits (811), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 202/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S+ ++ E    IAKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 111 ISLAQRIENGDQIAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 171 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+
Sbjct: 231 EVAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLK 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 291 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 351 SRSKKLKDYLD 361



 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/131 (33%), Positives = 71/131 (54%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I+  ++ G +T +E+   L   ++S EQ+E    +L +MGI V    D+++ E  E 
Sbjct: 19  KRLIEKGKKTGTLTYKEIMDELDEVDLSPEQIEKIYEVLESMGIEV--AGDIQEVEVDEK 76

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            LDL+     +               DDPVRMYL+E+G + LL+ E EI++A+RIE G  
Sbjct: 77  DLDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLAPEEEISLAQRIENGDQ 122

Query: 152 MMMASLCESPL 162
           +    L E+ L
Sbjct: 123 IAKKKLAEANL 133


>gi|315223009|ref|ZP_07864888.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319939161|ref|ZP_08013525.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
 gi|315187959|gb|EFU21695.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319812211|gb|EFW08477.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
          Length = 370

 Score =  317 bits (811), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAVLVEQGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 40.8 bits (94), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 64/131 (48%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N   + P  + ++ +ED +  + + GI + D      +EG+  
Sbjct: 17  EFIRNHKKTGTATDDEINDRLVIPFTLEADGIEDLLQRIQDAGIAITD------KEGNPS 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
              L +    + +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G  
Sbjct: 71  ERVLNTEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAVLVEQGDL 130

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 131 EAKQRLAEANL 141


>gi|152976724|ref|YP_001376241.1| RNA polymerase sigma factor RpoD [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152025476|gb|ABS23246.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus cytotoxicus
           NVH 391-98]
          Length = 373

 Score =  316 bits (810), Expect = 7e-84,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIQLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 70/139 (50%), Gaps = 23/139 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ SEQM++    L   GI++V  +D    EG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESEQMDEYYEYLGEQGIDLVGDND----EGPNN 77

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 78  HQITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIQLA 126

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 127 TRIEEGDEEAKRRLAEANL 145


>gi|317128328|ref|YP_004094610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315473276|gb|ADU29879.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 372

 Score =  316 bits (810), Expect = 7e-84,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S SE   +   +  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSASEEIDLAKKIEDGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEE++K++ +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDLGREPSPEEVSKEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQEALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 38/139 (27%), Positives = 68/139 (48%), Gaps = 15/139 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD----L 83
           D   +++++  ++RG +T  E+   L   +  S+QM++    L   G+ +++  +    L
Sbjct: 17  DQVKEQLLEAGKKRGVLTYAEITERLAVFDQDSDQMDEFFEFLGEQGVEILNETEGVPSL 76

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +  E  E+ +DL   +    +             +DPVRMYL+E+G + LLS   EI +A
Sbjct: 77  QQVEKEEEEIDLNDLSVPPGI-----------KINDPVRMYLKEIGRVPLLSASEEIDLA 125

Query: 144 KRIEAGRAMMMASLCESPL 162
           K+IE G       L E+ L
Sbjct: 126 KKIEDGDEEAKRRLAEANL 144


>gi|289548873|ref|YP_003473861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
 gi|289182490|gb|ADC89734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
          Length = 568

 Score =  316 bits (810), Expect = 7e-84,   Method: Compositional matrix adjust.
 Identities = 146/276 (52%), Positives = 207/276 (75%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           +  L +R E++ +  E GI   E   ++ ++++G  + + AK+ MV+ NLRLV+S+AKKY
Sbjct: 291 NEYLALRKEVEELRREMGILPEEIGRVIQIIKEGRTKVTQAKQVMVKCNLRLVVSIAKKY 350

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 351 VNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 410

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+ + +  ++++ ++ REPT EEIAK L +PV+  RKV+++ +EPISLETPIGD+
Sbjct: 411 HMIETINDITKAHKKLTQELGREPTAEEIAKYLGIPVDKARKVMRMAQEPISLETPIGDD 470

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + +HL DFIEDK+  SP +   +  LRE   +VL++L  +E  +L  R+G+   T++TLE
Sbjct: 471 EDAHLKDFIEDKSVPSPEEQVTRKLLREQLIKVLSTLGEKEREILMYRYGLVDGTEYTLE 530

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ++G+ F VTRERIRQIE KAIRKL+HP+RSK L+ F
Sbjct: 531 QIGRMFNVTRERIRQIETKAIRKLRHPARSKYLKDF 566



 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/156 (35%), Positives = 82/156 (52%), Gaps = 16/156 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK++ L  ++GYVT +ELN  L    + +E  E+ +  L   GI +V+     +E+  E 
Sbjct: 8   KKLMSLG-EKGYVTYDELNEALGDSLMDTELYEEIMDFLQERGIKLVE----SEEDREER 62

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
              L  SA +    LQ  KD       DPVR+Y+REMG I LL+RE EI  AK+IE GR 
Sbjct: 63  DEHLMVSADH---LLQSSKDG------DPVRLYMREMGKIPLLTREEEIKYAKQIEMGRK 113

Query: 152 MMMASLCESPLTF-QALIIWRDELNDGTTLLREIID 186
           +M   L  +     + L  W +  N G   +++I+D
Sbjct: 114 IMRRGLLRTSFLIDRVLKDWANVCN-GKLRVQDIVD 148


>gi|89100479|ref|ZP_01173341.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
 gi|89084822|gb|EAR63961.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
          Length = 374

 Score =  316 bits (810), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 155/276 (56%), Positives = 207/276 (75%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G + +   +  +S+ ++ E     AK+ + EANLRLV+S+AK+Y  
Sbjct: 99  VKINDPVRMYLKEIGRVDLLSAQEEISLAKRIEEGDEEAKRRLAEANLRLVVSIAKRYVG 158

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 159 RGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHM 218

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEEIA+ + +  + VR++LKI +EP+SLETPIG+ED 
Sbjct: 219 VETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPDKVREILKIAQEPVSLETPIGEEDD 278

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 279 SHLGDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 338

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 339 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 71/136 (52%), Gaps = 16/136 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDD----LEDE 86
           +++ ++ ++ G +  +++   L   E+ S+QM++    L + G+ +V D DD    +++ 
Sbjct: 22  EQLTEVGKKTGVLAYDDIAERLSNFELDSDQMDEFYEFLGDQGVELVGDNDDADPNVQEL 81

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E+  DL   +    V             +DPVRMYL+E+G ++LLS + EI++AKRI
Sbjct: 82  AKGEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAQEEISLAKRI 130

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 131 EEGDEEAKRRLAEANL 146


>gi|24379277|ref|NP_721232.1| RNA polymerase sigma factor RpoD [Streptococcus mutans UA159]
 gi|290580718|ref|YP_003485110.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
 gi|18202024|sp|O33662|RPOD_STRMU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|24377195|gb|AAN58538.1|AE014923_2 DNA-dependent RNA polymerase sigma subunit; major sigma factor
           (sigma 70/42) [Streptococcus mutans UA159]
 gi|2258087|dbj|BAA21507.1| sigma 42 protein [Streptococcus mutans]
 gi|254997617|dbj|BAH88218.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
          Length = 371

 Score =  316 bits (810), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGVVPLLTNEEEKELAIAVENGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 218 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 278 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSKQLRDFVE 370



 Score = 44.3 bits (103), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 31/108 (28%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P E+ +EQ++D +  L++ GI++ D       EG+  +           +  ++   S  
Sbjct: 41  PFELEAEQIDDLLERLTDGGISITD------REGNPSTKYAVEEIKPEELTDEELLGSNS 94

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +E G       L E+ L
Sbjct: 95  AKVNDPVRMYLKEIGVVPLLTNEEEKELAIAVENGDLEAKQRLAEANL 142


>gi|326791438|ref|YP_004309259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
 gi|326542202|gb|ADZ84061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
          Length = 363

 Score =  316 bits (810), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 126 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK++ MPV  V
Sbjct: 186 IRQAITRAIADQARTIRIPVHMVETINKLMRVSRQLLQELGRDPQPEEIAKRMDMPVSKV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI++EP+SLETPIG+E+ SHLGDFI D++   P ++A    L+E    VL +LT R
Sbjct: 246 REIMKISQEPVSLETPIGEEEDSHLGDFIPDEDIPVPAEAAAFTLLKEQLIEVLDTLTER 305

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 306 EQKVLRLRFGLDDGRARTLEEVGKEFSVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 363



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 66/131 (50%), Gaps = 16/131 (12%)

Query: 33  KMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++I +A+ ++G +  E++N      ++   ++E     L    I+V+   +L D E  + 
Sbjct: 20  QLINIAKDKKGMLDQEDINDVFSDMDLEPSKIEQIYEYLEAQNIDVIG--NLNDAEIDDV 77

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL++     S+             DDPVRMYL+E+G + LLS E EI +A+R++ G  
Sbjct: 78  DIDLSNLPDGISI-------------DDPVRMYLKEIGKVPLLSAEQEIILAQRMQDGDQ 124

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 125 EAKKKLAEANL 135


>gi|225163701|ref|ZP_03726004.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224801692|gb|EEG19985.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 631

 Score =  316 bits (810), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 156/277 (56%), Positives = 204/277 (73%), Gaps = 6/277 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGEC---EASIAKKEMVEANLRLVISVAKKYTN 465
           I   ++ I VE  I   E   ++ +VRK      EA  AK EMVEANLRLVIS+AKKYTN
Sbjct: 297 IHARLREIEVEQRI---EPAQLIEVVRKTNVHIREAHQAKTEMVEANLRLVISIAKKYTN 353

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 354 RGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 413

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + ++KV++  +++  +   EPTPEE+A ++ +PVE V++++K+ ++PISL++P+GD D 
Sbjct: 414 IETLNKVMQVQKQLLQEFGHEPTPEEVADEMNLPVERVQQIMKMAQQPISLQSPVGDGDD 473

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           +  GDFIEDK+A +P D    + LRE    VL SLT RE +VL +RFG+      TLEEV
Sbjct: 474 TSFGDFIEDKSAENPYDMTAYSLLREKIIDVLDSLTERERKVLSLRFGLVDGYSRTLEEV 533

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GKQF VTRERIRQIEAKA+RK++HP+R ++L  F D 
Sbjct: 534 GKQFKVTRERIRQIEAKALRKMRHPTRIRQLHGFFDA 570



 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 89/155 (57%), Gaps = 19/155 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED-E 86
           ++  + +I+L++++GY+T +++N  LP    + E++++ +++L N+ I +++ D +ED +
Sbjct: 38  NEKIRNLIRLSKEQGYLTFDDINEALPESVENQEEIDNVLSILQNLEIEILEPDQVEDYK 97

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E+  +  S  SN+ +             DDPVRMYL++MG + LL+RE E+ I+KRI
Sbjct: 98  QRQEEQEEEESRTSNNDIL------------DDPVRMYLKQMGQVPLLTREQEVEISKRI 145

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           E   +    +L      F+A I+ R     G  LL
Sbjct: 146 ETAESKAQEAL------FEASIVGRHIATLGAKLL 174


>gi|320547037|ref|ZP_08041336.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
 gi|320448322|gb|EFW89066.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
          Length = 369

 Score =  316 bits (809), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ +A   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSSEEEKELAVAVAAGDLQA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMSPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 43.9 bits (102), Expect = 0.086,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 39  PFSLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEEPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  + AG       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSSEEEKELAVAVAAGDLQAKQRLAEANL 140


>gi|171779914|ref|ZP_02920818.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281262|gb|EDT46697.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 369

 Score =  316 bits (809), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ +A   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSSEEEKELAVAVAAGDLQA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 42.7 bits (99), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   +  
Sbjct: 39  PFSLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEEPKPEELTDEELLGNNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  + AG       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSSEEEKELAVAVAAGDLQAKQRLAEANL 140


>gi|297544972|ref|YP_003677274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296842747|gb|ADH61263.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 357

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 120 AKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ MP E V
Sbjct: 180 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEELAKEMGMPEEKV 239

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL +LTPR
Sbjct: 240 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFTMLKEQLMDVLDTLTPR 299

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 300 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/138 (34%), Positives = 71/138 (51%), Gaps = 13/138 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S D+  ++I   ++ G +T  E+   L   +++ +Q+E       +MGI +V G++  
Sbjct: 5   ELSKDAITELINKGKKTGMLTYNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIV-GEEPR 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE +E+ LDL  S                 S DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 64  QEEINEEDLDLDLSLPEGI------------SIDDPVRMYLKEIGKIPLLTPEEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 112 RIEQGDEEAKKRLIEANL 129


>gi|300087894|ref|YP_003758416.1| RNA polymerase sigma 70 subunit RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299527627|gb|ADJ26095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 502

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 146/244 (59%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E+  A++ +++ANLRLV+SVAKK+  RG+  LDLIQEGNIGL++A EKFD+  G+KFS
Sbjct: 259 EIESGKAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFS 318

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++  +R MS K+ REPTP+EIA ++ 
Sbjct: 319 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRSMSQKLGREPTPDEIAAEME 378

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P E VR++ K+++ P+SLE+PIG+E+ SHLGDFIED+NA+ P D+A +  L+E    VL
Sbjct: 379 LPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALPPPDAASRQLLKEQIDNVL 438

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE RVL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP+RS+KL+
Sbjct: 439 DSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPTRSRKLK 498

Query: 678 SFLD 681
            +L+
Sbjct: 499 DYLE 502



 Score = 43.9 bits (102), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 26/34 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            DDPVRMYL E+G + LL+ E E  +AK++EAG+
Sbjct: 79  VDDPVRMYLHEIGRVPLLNAETEKMLAKKMEAGK 112


>gi|163781693|ref|ZP_02176693.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882913|gb|EDP76417.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
          Length = 571

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 148/277 (53%), Positives = 209/277 (75%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V   + ++ E++ +  E G+   E + ++ ++ +G  +   AK+ M+++NLRLV+S+AKK
Sbjct: 293 VSEYVSLKREVEKLRNEIGVIPEEIKRVMGIIEQGRKKVVKAKQVMIQSNLRLVVSIAKK 352

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y NRGL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW++QAITR+IADQ+ TIRIP
Sbjct: 353 YVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIP 412

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+++++ ++R+  ++ REPTPEEIAK L M  + VRKVL+  +EPISLETPIGD
Sbjct: 413 VHMIETINRIIKASKRLFQELGREPTPEEIAKHLGMTPDKVRKVLRSAQEPISLETPIGD 472

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ + L DFIEDK+  +P +   +  LRE   RVL +L+ +E  +LR R+G+   T++TL
Sbjct: 473 DEDTFLKDFIEDKSVPNPEEYVSRKLLREQLERVLETLSDKEREILRYRYGLVDGTEYTL 532

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+VGK F VTRERIRQIE+KAIRKL+HPSR+K L+ F
Sbjct: 533 EQVGKMFNVTRERIRQIESKAIRKLRHPSRAKYLKDF 569



 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 54/159 (33%), Positives = 91/159 (57%), Gaps = 11/159 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +S + ++++ +++G+VT +E+N  L  D VSS+  E+ +  L+N  I VV+ +  ED E 
Sbjct: 5   ESLRHLVEIGKEKGFVTYDEVNEVLEEDFVSSDSFEELIDTLANFNIQVVESE--EDYE- 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +DSLD    ++ S   + +          DPV++YL+EMG I LL+R+ EI  AK+IE 
Sbjct: 62  EKDSLDELVVSTESFTVMGR--------DGDPVKLYLKEMGKIPLLTRQQEIHYAKQIEI 113

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           GR +M   L  S    + L+    +L +G   + +I+DL
Sbjct: 114 GRKIMRRGLLRSSFLVEKLLQDWGKLCNGKLKIGDIMDL 152


>gi|57234646|ref|YP_181295.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
 gi|57225094|gb|AAW40151.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
          Length = 520

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 146/244 (59%), Positives = 200/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  A++ +++ANLRLV+SVAKK+  RG+  LDLIQEGNIGL++A EKFD+  G+KFS
Sbjct: 277 EIDAKRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFS 336

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++  +R++S K+ REPTP+EIA ++ 
Sbjct: 337 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEMD 396

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P E VR++ K+++ P+SLE+PIG+E+ SHLGDFIED+NA++P D+A +  L+E    VL
Sbjct: 397 LPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVL 456

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE RVL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+
Sbjct: 457 GSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLK 516

Query: 678 SFLD 681
            +L+
Sbjct: 517 DYLE 520



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            DDPVRMYL E+G + LLS E E  +AK++E G+
Sbjct: 97  VDDPVRMYLHEIGRVPLLSAEDEKTLAKKMEEGK 130


>gi|167037157|ref|YP_001664735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167039957|ref|YP_001662942.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter sp. X514]
 gi|256751255|ref|ZP_05492135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300915505|ref|ZP_07132817.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|307266219|ref|ZP_07547761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724719|ref|YP_003904470.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           sp. X513]
 gi|320115576|ref|YP_004185735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326390577|ref|ZP_08212133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
 gi|166854197|gb|ABY92606.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           sp. X514]
 gi|166855991|gb|ABY94399.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256749810|gb|EEU62834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300888457|gb|EFK83607.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|306918749|gb|EFN48981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581780|gb|ADN55179.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928667|gb|ADV79352.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325993402|gb|EGD51838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
          Length = 357

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 120 AKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ MP E V
Sbjct: 180 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEELAKEMGMPEEKV 239

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL +LTPR
Sbjct: 240 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFTMLKEQLMDVLDTLTPR 299

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 300 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 46/138 (33%), Positives = 71/138 (51%), Gaps = 13/138 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S ++  ++I   ++ G +T  E+   L   +++ +Q+E       +MGI +V G++  
Sbjct: 5   ELSKEAITELINKGKKTGMLTYNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIV-GEEPR 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE +E+ LDL  S                 S DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 64  QEEITEEDLDLDLSLPEGI------------SIDDPVRMYLKEIGKIPLLTPEEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 112 RIEQGDEEAKKRLIEANL 129


>gi|55823393|ref|YP_141834.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus
           CNRZ1066]
 gi|116628187|ref|YP_820806.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMD-9]
 gi|55739378|gb|AAV63019.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus CNRZ1066]
 gi|116101464|gb|ABJ66610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus thermophilus LMD-9]
 gi|312278801|gb|ADQ63458.1| RNA polymerase sigma factor [Streptococcus thermophilus ND03]
          Length = 369

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVENGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 41.2 bits (95), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++ ++D +  L++ GI++ D D      G+  S  +  +     +  ++   S  
Sbjct: 39  PFVLDADGIDDLLERLTDGGISITDKD------GNPSSKYVVEAPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  +E G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANL 140


>gi|312863004|ref|ZP_07723242.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
 gi|311100540|gb|EFQ58745.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
          Length = 369

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVENGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 41.2 bits (95), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++ ++D +  L++ GI++ D D      G+  S  +  +     +  ++   S  
Sbjct: 39  PFVLDADGIDDLLERLTDGGISITDKD------GNPSSKYVVEAPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  +E G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANL 140


>gi|40143|emb|CAA27538.1| unnamed protein product [Bacillus subtilis]
 gi|143454|gb|AAA22709.1| RNA polymerase sigma-43 factor [Bacillus subtilis]
 gi|1303833|dbj|BAA12489.1| RpoD [Bacillus subtilis]
          Length = 371

 Score =  316 bits (809), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 150/238 (63%), Positives = 188/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ + EANLRLV+S+AK+Y  RG+ FLDLI EGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 134 SKRRLAEANLRLVVSIAKRYVGRGMLFLDLIHEGNMGLMKAVEKFDYRKGYKFSTYATWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+ + +  E V
Sbjct: 194 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKV 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 254 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDR 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 314 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 371



 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 40/141 (28%), Positives = 70/141 (49%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDE 86
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++ + ++ ED 
Sbjct: 14  DQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELISENEETEDP 73

Query: 87  E-----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                  +E+  DL   +    V             +DPVRMYL+E+G + LLS + EIA
Sbjct: 74  NIQQLAKAEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVNLLSAKEEIA 122

Query: 142 IAKRIEAGRAMMMASLCESPL 162
            A++IE G       L E+ L
Sbjct: 123 YAQKIEEGDEESKRRLAEANL 143


>gi|239637627|ref|ZP_04678599.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|239596845|gb|EEQ79370.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|330686029|gb|EGG97652.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU121]
          Length = 367

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 150/251 (59%), Positives = 194/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E    IAK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 117 IELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDF 176

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PE
Sbjct: 177 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPE 236

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+
Sbjct: 237 EIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLK 296

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 297 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 356

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ F+D
Sbjct: 357 SRSKRLKDFMD 367



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 74/144 (51%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   E+ S+ M+D    L++  I +V+  D  D +
Sbjct: 19  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFEMDSDMMDDFFDQLNDNDITLVNEKDHSDTD 78

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G ++LLS + EI +AKRIE
Sbjct: 79  AKLNPNDLSAPPGVK--------------INDPVRMYLKEIGRVDLLSAQEEIELAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  + L E+ L     I  R
Sbjct: 125 QGDEIAKSRLAEANLRLVVSIAKR 148


>gi|228476995|ref|ZP_04061633.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322516348|ref|ZP_08069273.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
 gi|228251014|gb|EEK10185.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322125081|gb|EFX96474.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
          Length = 369

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVENGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 41.2 bits (95), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++ ++D +  L++ GI++ D D      G+  S  +  +     +  ++   S  
Sbjct: 39  PFVLDADGIDDLLERLTDGGISITDKD------GNPSSKYVVEAPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  +E G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANL 140


>gi|289578734|ref|YP_003477361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528447|gb|ADD02799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 357

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 120 AKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ MP E V
Sbjct: 180 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQELGREPTPEELAKEMGMPEEKV 239

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL +LTPR
Sbjct: 240 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFTMLKEQLMDVLDTLTPR 299

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 300 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/138 (34%), Positives = 71/138 (51%), Gaps = 13/138 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S D+  ++I   ++ G +T  E+   L   +++ +Q+E       +MGI +V G++  
Sbjct: 5   ELSKDAITELINKGKKTGMLTYNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIV-GEEPR 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE +E+ LDL  S                 S DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 64  QEEINEEDLDLDLSLPEGI------------SIDDPVRMYLKEIGKIPLLTPEEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 112 RIEQGDEEAKKRLIEANL 129


>gi|160947542|ref|ZP_02094709.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
 gi|158446676|gb|EDP23671.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
          Length = 382

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 152/260 (58%), Positives = 205/260 (78%), Gaps = 3/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +  G+ EA   KK++ E NLRLV+S+AK+Y  RG+QFLDLIQEGN+GL
Sbjct: 126 LSADEERILAENMEAGDIEA---KKKLAETNLRLVVSIAKRYVGRGMQFLDLIQEGNMGL 182

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA EKFD+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR  R++  
Sbjct: 183 MKAVEKFDFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLVRIERQLVQ 242

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REPT EEI++ + + V+ V ++ KI +EP+SLETPIG+ED SHLGDFIED+ A++P 
Sbjct: 243 ELGREPTNEEISEHMGIEVDKVNEIRKIAQEPVSLETPIGEEDDSHLGDFIEDETAIAPD 302

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++A  + L+E   +VL++L+ RE++VL +RFG+   T  TLEEVGK+F VTRERIRQIEA
Sbjct: 303 EAANFSMLKEQLNQVLSTLSDREKKVLELRFGLNDGTPRTLEEVGKEFEVTRERIRQIEA 362

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+KL+ FL+
Sbjct: 363 KALRKLKHPSRSQKLKDFLE 382



 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 67/125 (53%), Gaps = 4/125 (3%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSAS 100
           G+V  + L +    + +  + +E+  + L+   +  +D G++LED E  ED +DL     
Sbjct: 30  GFVNNKYLESLDLFNLIDIDDIEEIKSKLAENQVEFIDEGENLEDIEIVEDLIDLEDEKE 89

Query: 101 NSSVFLQKRKDSADR---STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           ++     K +D +D    + DDPV+MYL+E+G I LLS + E  +A+ +EAG       L
Sbjct: 90  DAEDEEIKLEDFSDLKGFNIDDPVKMYLKEIGKIPLLSADEERILAENMEAGDIEAKKKL 149

Query: 158 CESPL 162
            E+ L
Sbjct: 150 AETNL 154


>gi|291166412|gb|EFE28458.1| RNA polymerase sigma factor RpoD [Filifactor alocis ATCC 35896]
          Length = 372

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 203/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K +  + +AKK++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 122 IELAQKMDQGSELAKKKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REP PE
Sbjct: 182 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPRPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI+K + M VE +R++ KI++EP+SLETPIG+E+ SHLGDFI D +A++P ++A  + L+
Sbjct: 242 EISKVMDMSVEKIREIQKISQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYSLLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL++L  RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLEEVLSTLNEREQKVLKLRFGLEDGRTRTLEEVGKEFDVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +L+
Sbjct: 362 SRSKKLKDYLE 372



 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 72/138 (52%), Gaps = 15/138 (10%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---------DDLE 84
           +++  + +G +T  EL   L P  V+ + +E+    L+ +GI ++D          DD+E
Sbjct: 13  LLEKGKNKGTLTYMELAEILNPIAVNKDDIENIYETLNQLGIEIIDENTPKTHVNLDDIE 72

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           + E + D  DL  +     + + K       S DDPVRMYL+E+G I LLS E EI +A+
Sbjct: 73  EPEFT-DEKDLEETKVEEDLSVPK-----GISVDDPVRMYLKEIGKISLLSAEEEIELAQ 126

Query: 145 RIEAGRAMMMASLCESPL 162
           +++ G  +    L E+ L
Sbjct: 127 KMDQGSELAKKKLVEANL 144


>gi|55821465|ref|YP_139907.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMG
           18311]
 gi|55737450|gb|AAV61092.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus LMG 18311]
          Length = 369

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKKLAIAVENGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 41.6 bits (96), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++ ++D +  L++ GI++ D D      G+  S  +  +     +  ++   S  
Sbjct: 39  PFVLDADGIDDLLERLTDGGISITDKD------GNPSSKYVVEAPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LLS E E  +A  +E G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLSNEEEKKLAIAVENGDLEAKQRLAEANL 140


>gi|292491943|ref|YP_003527382.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580538|gb|ADE14995.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 578

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 161/373 (43%), Positives = 247/373 (66%), Gaps = 2/373 (0%)

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
           +S + + L+ +L +  G L L  +R+  L + + +  +++   E  L        G+ ++
Sbjct: 206 ASAQARELRGELAQEFGLLRLVPARLKQLAQPVQEWIRKVQTQEQVLKSCCIHQGGVSQE 265

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F +       +P WV       + E +  +  + ++I   +  +  + +E G+ ++E +
Sbjct: 266 DFWQSFSSNATNPQWVEDLLAVGQ-EDRQPLQAQAETIRAAQKVLTQVEIEVGLPLAELK 324

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +G+ +A  AK +MVEANLRLV+SVAKKY NRGL FLDLIQEGNIGLM+A +KF
Sbjct: 325 TVHRRLTRGQIQAQRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMRAVDKF 384

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR+I DQS TIRIPVH+ +K+ K+ R + ++  +  RE  
Sbjct: 385 DYRRGYKFSTYAHWWIRQAITRAIDDQSRTIRIPVHVMEKLSKLNRASYQLRQEKGREGR 444

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A++LA+  + +  + +I K+PISLETP+G ++ S LG+ +ED+   +P++ AI A 
Sbjct: 445 PEELAERLALSEQQIHHMHEIAKQPISLETPLGKDEDSQLGELMEDEQVPNPMEVAISAG 504

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+  T ++LA+LTPRE +V+ MRFGIGM+TDHTL EV +QF ++RERIRQIEA+A+ KL+
Sbjct: 505 LQAGTQQLLATLTPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQIEAQALSKLR 564

Query: 669 HPSRSKKLRSFLD 681
               SK LRSFL+
Sbjct: 565 RLGHSKALRSFLE 577



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 46/154 (29%), Positives = 75/154 (48%), Gaps = 8/154 (5%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           F+   +  K++I   + +G +T EEL  ++  +   S++ E  V        N+    DL
Sbjct: 3   FEMRQEELKRLILKGKAQGLLTEEELQEYIVQEVEDSDEAEAVV--------NLFHDQDL 54

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ +   D   L  + + S     +   S+D +  D V  Y+REMG+  LL+RE E+A+A
Sbjct: 55  EELDEKIDPALLLKNGTESEEETAEVVLSSDGAISDMVNTYMREMGAHALLAREEEVALA 114

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           K IEAG +    +L   P     L+ W DE + G
Sbjct: 115 KAIEAGLSQSTEALGSCPAIAAELLRWADEADAG 148


>gi|323127013|gb|ADX24310.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 369

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKVLAVAVAEGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFALDADQIDDLLERLTDGGISITD------KEGNPSSKYIVEEPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKVLAVAVAEGDLEAKQRLAEANL 140


>gi|322411497|gb|EFY02405.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 369

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKVLAVAVAEGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFALDADQIDDLLERLTDGGISITD------KEGNPSSKYIVEEPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKVLAVAVAEGDLEAKQRLAEANL 140


>gi|81428494|ref|YP_395494.1| RNA polymerase sigma factor RpoD [Lactobacillus sakei subsp. sakei
           23K]
 gi|78610136|emb|CAI55185.1| DNA-directed RNA polymerase sigma factor, sigma A (Primary sigma
           factor) [Lactobacillus sakei subsp. sakei 23K]
          Length = 369

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 159/286 (55%), Positives = 207/286 (72%), Gaps = 16/286 (5%)

Query: 412 EIKSISVETGISIS--------EFRHIVSMVRKGECEASI--------AKKEMVEANLRL 455
           E+K +S  TGI I+        E   +  +  + E + ++        AK+ + EANLRL
Sbjct: 84  ELKDMSAPTGIKINDPVRMYLKEIGRVSLLNAQQEVDLALRIEQGDQEAKQRLAEANLRL 143

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD   G+KFSTYA WW++QAITR+IADQ
Sbjct: 144 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQ 203

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ M  + VR++LKI +EP+S
Sbjct: 204 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMNTDKVREILKIAQEPVS 263

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+ED SHLGDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+ 
Sbjct: 264 LETPIGEEDDSHLGDFIEDQDATSPEEHASYELLKEQLESVLDTLTDREENVLRLRFGLD 323

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 324 DGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 71/139 (51%), Gaps = 14/139 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +IK  + +  +T +EL A  + P  + ++++ + +  + + GI +VD       
Sbjct: 13  DTAVKALIKEYKPKKEITNDELVAKIVKPFALEADEINELMQQVEDHGIGIVD------- 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIA 143
              ED    A++     V  ++ KD +  +    +DPVRMYL+E+G + LL+ + E+ +A
Sbjct: 66  ---EDGNPSAATLKKEKVSAKELKDMSAPTGIKINDPVRMYLKEIGRVSLLNAQQEVDLA 122

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 123 LRIEQGDQEAKQRLAEANL 141


>gi|325686025|gb|EGD28083.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 373

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + +S  E   +   +  G+ EA   K E+  ANLRLV+S+AK+Y  RG+
Sbjct: 104 VRQYLKRIGRVSLLSGDEEVQLAKRIEAGDQEA---KDELTSANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA  KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 SFLDLIQEGNMGLMKAVGKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEIA ++ +PV+ VR+VLK+ +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+A SP   A    L++    VL +LT  EE VLR+RFG+      TLEEVG+ 
Sbjct: 281 GDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDSEENVLRLRFGLDDGNPRTLEEVGRV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS +LR FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSNQLRDFLE 373



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 7/98 (7%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD      ++G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVD------DKGEPSKLALAKQKNVEKAELEHLSA 95

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              R  +DPVR YL+ +G + LLS + E+ +AKRIEAG
Sbjct: 96  PGSR-MNDPVRQYLKRIGRVSLLSGDEEVQLAKRIEAG 132


>gi|146319082|ref|YP_001198794.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05ZYH33]
 gi|146321288|ref|YP_001200999.1| RNA polymerase sigma factor RpoD [Streptococcus suis 98HAH33]
 gi|223932503|ref|ZP_03624504.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|253752138|ref|YP_003025279.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|253753963|ref|YP_003027104.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|253755898|ref|YP_003029038.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|330833083|ref|YP_004401908.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
 gi|145689888|gb|ABP90394.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 05ZYH33]
 gi|145692094|gb|ABP92599.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 98HAH33]
 gi|223898774|gb|EEF65134.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|251816427|emb|CAZ52060.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|251818362|emb|CAZ56188.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|251820209|emb|CAR46610.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|292558723|gb|ADE31724.1| RNA polymerase sigma factor rpoD [Streptococcus suis GZ1]
 gi|319758521|gb|ADV70463.1| RNA polymerase sigma factor RpoD [Streptococcus suis JS14]
 gi|329307306|gb|AEB81722.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
          Length = 372

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGVVPLLTNEEEQELALAVEAGDPEA---KQRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLVREQRNLLQELGQDPTPEQIAERMDMTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 279 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 339 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 371



 Score = 44.3 bits (103), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 66/131 (50%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +++G  T +E+N   + P  + ++ ++D +  + + GI++VD      +EG+  
Sbjct: 20  EFIRNHKKQGSATDDEINDQLVIPFTLDADGIDDLLQRIQDAGISIVD------KEGNPS 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  +           ++   S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 74  ARAMQVEEEPELS-DEELLGSTSAKVNDPVRMYLKEIGVVPLLTNEEEQELALAVEAGDP 132

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 133 EAKQRLAEANL 143


>gi|270307915|ref|YP_003329973.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
 gi|270153807|gb|ACZ61645.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
          Length = 520

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 146/244 (59%), Positives = 200/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  A++ +++ANLRLV+SVAKK+  RG+  LDLIQEGNIGL++A EKFD+  G+KFS
Sbjct: 277 EIDAKRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFS 336

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++  +R++S K+ REPTP+EIA ++ 
Sbjct: 337 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIALEMD 396

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P E VR++ K+++ P+SLE+PIG+E+ SHLGDFIED+NA++P D+A +  L+E    VL
Sbjct: 397 LPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVL 456

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE RVL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+
Sbjct: 457 GSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLK 516

Query: 678 SFLD 681
            +L+
Sbjct: 517 DYLE 520



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            DDPVRMYL E+G + LLS E E  +AK++E G+
Sbjct: 97  VDDPVRMYLHEIGRVPLLSAEDEKTLAKKMEEGK 130


>gi|73748391|ref|YP_307630.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|147669171|ref|YP_001213989.1| RpoD family RNA polymerase sigma factor [Dehalococcoides sp. BAV1]
 gi|289432439|ref|YP_003462312.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
 gi|73660107|emb|CAI82714.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|146270119|gb|ABQ17111.1| RNA polymerase, sigma 70 subunit, RpoD family [Dehalococcoides sp.
           BAV1]
 gi|288946159|gb|ADC73856.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
          Length = 520

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 146/244 (59%), Positives = 200/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  A++ +++ANLRLV+SVAKK+  RG+  LDLIQEGNIGL++A EKFD+  G+KFS
Sbjct: 277 EIDAKRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFS 336

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++  +R++S K+ REPTP+EIA ++ 
Sbjct: 337 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIALEMD 396

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P E VR++ K+++ P+SLE+PIG+E+ SHLGDFIED+NA++P D+A +  L+E    VL
Sbjct: 397 LPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVL 456

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE RVL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+
Sbjct: 457 GSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLK 516

Query: 678 SFLD 681
            +L+
Sbjct: 517 DYLE 520



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            DDPVRMYL E+G + LLS E E  +AK++E G+
Sbjct: 97  VDDPVRMYLHEIGRVPLLSAEDEKTLAKKMEEGK 130


>gi|225868705|ref|YP_002744653.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701981|emb|CAW99541.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
          Length = 369

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKVLAVAVAAGDMEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 65/131 (49%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+    + P  + ++Q++D +  L++ GI++ D      +EG+  
Sbjct: 16  EFIRHHKKEGTATDDEVTEKLVIPFTLDADQIDDLLERLTDGGISITD------KEGNPS 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG  
Sbjct: 70  SKYVVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKVLAVAVAAGDM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|222152854|ref|YP_002562031.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
 gi|222113667|emb|CAR41594.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
          Length = 369

 Score =  315 bits (808), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ +A   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKELAIAVAAGDVDA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 45.1 bits (105), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 31/108 (28%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P E+ ++Q++D +  L++ GI++ D D      GS  S  +        +  ++   S  
Sbjct: 39  PFELDADQIDDLLERLTDGGISITDKD------GSPSSKYIVEEPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ + E  +A  + AG       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSDEEKELAIAVAAGDVDAKQRLAEANL 140


>gi|302024138|ref|ZP_07249349.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05HAS68]
          Length = 372

 Score =  315 bits (807), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGVVPLLTNEEEQELALAVEAGDPEA---KQRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLVREQRNLLQELGQDPTPEQIAERMDMTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 279 GDFIEDEIIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 339 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 371



 Score = 44.3 bits (103), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 66/131 (50%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +++G  T +E+N   + P  + ++ ++D +  + + GI++VD      +EG+  
Sbjct: 20  EFIRNHKKQGSATDDEINDQLVIPFTLDADGIDDLLQRIQDAGISIVD------KEGNPS 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +  +           ++   S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 74  ARAMQVEEEPELS-DEELLGSTSAKVNDPVRMYLKEIGVVPLLTNEEEQELALAVEAGDP 132

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 133 EAKQRLAEANL 143


>gi|195977963|ref|YP_002123207.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|195974668|gb|ACG62194.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 369

 Score =  315 bits (807), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKVLAVAVAAGDMEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 43.5 bits (101), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 65/131 (49%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+    + P  + ++Q++D +  L++ GI++ D      +EG+  
Sbjct: 16  EFIRHHKKEGTATDDEVTEKLVIPFTLDADQIDDLLERLTDGGISITD------KEGNPS 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG  
Sbjct: 70  SKYVVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKVLAVAVAAGDM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|254445278|ref|ZP_05058754.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
 gi|198259586|gb|EDY83894.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
          Length = 576

 Score =  315 bits (807), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 149/253 (58%), Positives = 197/253 (77%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++ VR+    A  AK EMVEANLRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF+
Sbjct: 302 LIAEVRRHLKAAHKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 361

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + ++KV++  +++  +   EPTP
Sbjct: 362 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQLLQEYGHEPTP 421

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+++A+PVE V+ ++K+ ++PISL++P+GD D ++ GDFIEDK+A +P D    + L
Sbjct: 422 EEVAEEMALPVERVQTIMKMAQQPISLQSPVGDGDDTNFGDFIEDKSAENPYDQTAFSLL 481

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE    VL SLT RE RVL +RFG+      TLEEVGKQF VTRERIRQIEAKA+RK++H
Sbjct: 482 REKIIDVLDSLTERERRVLSLRFGLVDGYSRTLEEVGKQFKVTRERIRQIEAKALRKMRH 541

Query: 670 PSRSKKLRSFLDG 682
           P+R ++L  F + 
Sbjct: 542 PTRIRQLHGFFEN 554



 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 34/116 (29%), Positives = 72/116 (62%), Gaps = 11/116 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +I+ ++++GY+T  ++N  LP    S + +++ +++L N+ I+++D +++++ +  ++
Sbjct: 25  RYLIRQSKEQGYLTHGDINEALPEGIDSQDDIDNVISILQNLEIDILDPEEVDNFKAKQE 84

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +   + +N    L           DDPVRMYL++MG + LL+RE E+ I+KRIE
Sbjct: 85  EAEEEQTKANQHDIL-----------DDPVRMYLKQMGQVPLLTREQEVEISKRIE 129


>gi|78044024|ref|YP_359316.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996139|gb|ABB15038.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 370

 Score =  315 bits (807), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 133 AKRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R +  ++ REPTPEEIAK++ +  + V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISEDKV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDF+ED +A +P++ A    LRE    VL +LT R
Sbjct: 253 REIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTER 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 313 EQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 370



 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 45/145 (31%), Positives = 71/145 (48%), Gaps = 15/145 (10%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++   ++++  ++RG +T  +L   L   +++SEQ+++    L+N GI VV       
Sbjct: 5   MQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVP------ 58

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADR--------STDDPVRMYLREMGSIELLSRE 137
            E  E  LD  +S  +   F     D  D         + DDPVRMYL+E+G + LL+ E
Sbjct: 59  -EIPELELDSINSLDDDVDFKPSDIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPE 117

Query: 138 GEIAIAKRIEAGRAMMMASLCESPL 162
            EI +AKR E G       L E+ L
Sbjct: 118 EEIELAKRKEEGDEEAKRKLAEANL 142


>gi|225870339|ref|YP_002746286.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
 gi|225699743|emb|CAW93506.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
          Length = 369

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKVLAVAVAAGDMEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 65/131 (49%), Gaps = 7/131 (5%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+    + P  + ++Q++D +  L++ GI++ D      +EG+  
Sbjct: 16  EFIRHHKKEGTATDDEVTEKLVIPFTLDADQIDDLLERLTDGGISITD------KEGNPS 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG  
Sbjct: 70  SKYVVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKVLAVAVAAGDM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|222097738|ref|YP_002531795.1| RNA polymerase sigma factor rpod [Bacillus cereus Q1]
 gi|221241796|gb|ACM14506.1| RNA polymerase sigma-43 factor [Bacillus cereus Q1]
          Length = 375

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAGEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 73/147 (49%), Gaps = 19/147 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE----- 86
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V GD+  DE     
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLV-GDNDNDEGPNNR 80

Query: 87  --EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               SE+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A 
Sbjct: 81  QIAKSEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLAT 129

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWR 171
           RIE G       L E+ L     I  R
Sbjct: 130 RIEEGDEEAKRRLAEANLRLVVSIAKR 156


>gi|148380889|ref|YP_001255430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           3502]
 gi|153931224|ref|YP_001385198.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|153937635|ref|YP_001388667.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|153940633|ref|YP_001392215.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|168179368|ref|ZP_02614032.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|168181623|ref|ZP_02616287.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|170757237|ref|YP_001782571.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|170761654|ref|YP_001788251.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|187778482|ref|ZP_02994955.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226950364|ref|YP_002805455.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|237796391|ref|YP_002863943.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|148290373|emb|CAL84500.1| RNA polymerase sigma factor (sigma-43) [Clostridium botulinum A
           str. ATCC 3502]
 gi|152927268|gb|ABS32768.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|152933549|gb|ABS39048.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|152936529|gb|ABS42027.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|169122449|gb|ACA46285.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|169408643|gb|ACA57054.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|182669799|gb|EDT81775.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|182675034|gb|EDT86995.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|187772107|gb|EDU35909.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226843729|gb|ACO86395.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|229260977|gb|ACQ52010.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|295320212|gb|ADG00590.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           230613]
 gi|322807253|emb|CBZ04827.1| RNA polymerase sigma factor RpoD [Clostridium botulinum H04402 065]
          Length = 361

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E    +AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 111 IELAQRIEAGDMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 171 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+
Sbjct: 231 EVAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLK 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 291 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 351 SRSKKLKDYLD 361



 Score = 60.8 bits (146), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 41/131 (31%), Positives = 70/131 (53%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I   ++ G ++ +E+   L   ++S EQ+E    +L +MG+ V    D+ D +  E+
Sbjct: 19  RRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESMGVEVTG--DMNDIDVKEE 76

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL+     +               DDPVRMYL+E+G + LL+ E EI +A+RIEAG  
Sbjct: 77  DIDLSVPEGIA--------------IDDPVRMYLKEIGKVALLTSEEEIELAQRIEAGDM 122

Query: 152 MMMASLCESPL 162
           +    L E+ L
Sbjct: 123 VAKKKLAEANL 133


>gi|288905580|ref|YP_003430802.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|306831670|ref|ZP_07464827.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978609|ref|YP_004288325.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288732306|emb|CBI13876.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|304426095|gb|EFM29210.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178537|emb|CBZ48581.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 369

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ +A   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAAGDLQA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 39  PFSLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEEPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  + AG       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAAGDLQAKQRLAEANL 140


>gi|300854008|ref|YP_003778992.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434123|gb|ADK13890.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 354

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 202/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S+ ++ E    IAKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 104 ISLAKRIEEGDQIAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 163

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REP PE
Sbjct: 164 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQELGREPHPE 223

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+
Sbjct: 224 EVAQIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLK 283

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 284 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 343

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 344 SRSKKLKDYLD 354



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 48/131 (36%), Positives = 71/131 (54%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK+I+  ++ G +T +E+   L   ++S EQ+E     L +MGI V  GD+ E E  +E 
Sbjct: 12  KKIIEKGKKNGTLTYKEIMDELEEVDLSPEQIEKIYEALESMGIEVT-GDEHETE-SNEK 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +LDL+     +               DDPVRMYL+E+G + LL  E EI++AKRIE G  
Sbjct: 70  NLDLSVPDGIA--------------IDDPVRMYLKEIGKVPLLLPEEEISLAKRIEEGDQ 115

Query: 152 MMMASLCESPL 162
           +    L E+ L
Sbjct: 116 IAKKKLAEANL 126


>gi|42783418|ref|NP_980665.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 10987]
 gi|47567855|ref|ZP_00238563.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217961783|ref|YP_002340353.1| RNA polymerase sigma factor RpoD [Bacillus cereus AH187]
 gi|228916924|ref|ZP_04080486.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228987542|ref|ZP_04147661.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229141030|ref|ZP_04269573.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|229157906|ref|ZP_04285980.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|229163237|ref|ZP_04291192.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|229198419|ref|ZP_04325125.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|301055785|ref|YP_003793996.1| RNA polymerase sigma factor [Bacillus anthracis CI]
 gi|42739347|gb|AAS43273.1| RNA polymerase sigma-43 factor [Bacillus cereus ATCC 10987]
 gi|47555532|gb|EAL13875.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217066780|gb|ACJ81030.1| RNA polymerase sigma-43 factor [Bacillus cereus AH187]
 gi|228585119|gb|EEK43231.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|228620300|gb|EEK77171.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|228625565|gb|EEK82318.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|228642463|gb|EEK98751.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|228772274|gb|EEM20721.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228842748|gb|EEM87834.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|300377954|gb|ADK06858.1| RNA polymerase sigma factor [Bacillus cereus biovar anthracis str.
           CI]
 gi|324328197|gb|ADY23457.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 375

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 72/139 (51%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D  ++EG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND--NDEGPNN 79

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                SE+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 80  RQIAKSEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 128

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 129 TRIEEGDEEAKRRLAEANL 147


>gi|306833811|ref|ZP_07466936.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
 gi|304424005|gb|EFM27146.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
          Length = 369

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ +A   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVATGDLQA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 42.0 bits (97), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 39  PFSLDADQIDDLLERLTDGGISITD------KEGNPSTKYIVEEPKPEELTDEELLGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVATGDLQAKQRLAEANL 140


>gi|1173127|sp|P43344|RPOD_SERMA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
          Length = 215

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 152/214 (71%), Positives = 179/214 (83%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 1   LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 61  TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 121 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREXKVLRMRFGIDMNTDHTLEEVGK 180

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 181 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 214


>gi|30022370|ref|NP_834001.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 14579]
 gi|218232261|ref|YP_002369099.1| RNA polymerase sigma factor RpoD [Bacillus cereus B4264]
 gi|228923044|ref|ZP_04086337.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228960557|ref|ZP_04122206.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229048011|ref|ZP_04193587.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|229111765|ref|ZP_04241313.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|229129569|ref|ZP_04258539.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|229146877|ref|ZP_04275242.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|229152492|ref|ZP_04280684.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|296504786|ref|YP_003666486.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
 gi|29897928|gb|AAP11202.1| RNA polymerase sigma factor rpoD [Bacillus cereus ATCC 14579]
 gi|218160218|gb|ACK60210.1| RNA polymerase sigma-43 factor [Bacillus cereus B4264]
 gi|228631100|gb|EEK87737.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|228636705|gb|EEK93170.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|228653886|gb|EEL09754.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|228671759|gb|EEL27055.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|228723468|gb|EEL74837.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|228799157|gb|EEM46125.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228836677|gb|EEM82025.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296325838|gb|ADH08766.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
          Length = 375

 Score =  315 bits (807), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 72/139 (51%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D  +EEG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND--NEEGPNN 79

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 80  RQISKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 128

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 129 TRIEEGDEEAKRRLAEANL 147


>gi|167755652|ref|ZP_02427779.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|237734400|ref|ZP_04564881.1| RNA polymerase sigma factor rpoD [Mollicutes bacterium D7]
 gi|167704591|gb|EDS19170.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|229382630|gb|EEO32721.1| RNA polymerase sigma factor rpoD [Coprobacillus sp. D7]
          Length = 417

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 151/239 (63%), Positives = 190/239 (79%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 178 AKKELAAANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWW 237

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++  ++ REP+ EEIA+K+  M  E 
Sbjct: 238 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLIQELGREPSAEEIAEKMDGMTPEK 297

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI+ EP+SLETPIG+ED SHLGDFIED+ A+SP D A    L++    VL  LT 
Sbjct: 298 VREIQKISLEPVSLETPIGEEDDSHLGDFIEDEGAMSPDDYAANELLKDELNEVLLELTD 357

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHPSRSK+L+ FLD
Sbjct: 358 REEKVLRLRFGLDDGRTRTLEEVGKEFSVTRERIRQIEAKALRKLKHPSRSKRLKDFLD 416



 Score = 40.8 bits (94), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 26/32 (81%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +DPV+MYL+E+G +ELL+ + EI +AK+I  G
Sbjct: 143 NDPVKMYLKEIGRVELLTHDEEIDLAKKILEG 174


>gi|224476669|ref|YP_002634275.1| RNA polymerase sigma factor RpoD [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421276|emb|CAL28090.1| RNA polymerase sigma factor SigA [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 369

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 152/276 (55%), Positives = 204/276 (73%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G + +   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 94  VKINDPVRMYLKEIGRVDLLNAQEEIELAKRIEQGDEVAKARLAEANLRLVVSIAKRYVG 153

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 154 RGMLFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 213

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 214 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDD 273

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+   SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 274 SHLGDFIEDQEVQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 333

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 334 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 369



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/144 (28%), Positives = 75/144 (52%), Gaps = 14/144 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K+++   ++ G+++ EE+   L   ++ S+QM++    +++  IN+V+  D  D +
Sbjct: 21  EDVKKQLLDKGKKEGHLSHEEIAEKLQNFDMDSDQMDEFFDQINDNDINLVNEKDSSDTD 80

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G ++LL+ + EI +AKRIE
Sbjct: 81  EKLNPHDLSAPPGVK--------------INDPVRMYLKEIGRVDLLNAQEEIELAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G  +  A L E+ L     I  R
Sbjct: 127 QGDEVAKARLAEANLRLVVSIAKR 150


>gi|302389497|ref|YP_003825318.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
 gi|302200125|gb|ADL07695.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
          Length = 367

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 163/306 (53%), Positives = 221/306 (72%), Gaps = 11/306 (3%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILK--------IRNEIKSISVETGISISEFRHIVSMVR 435
           ++ A D PE   +     E+D  +         +R  +K I     ++  E   +   + 
Sbjct: 65  INDADDIPESLLEEISEVELDLSIPEGVAIDDPVRMYLKEIGKIPLLTPEEEIELAKRIE 124

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ EA   K+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYK
Sbjct: 125 KGDKEA---KRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYK 181

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+PTPEEIA++
Sbjct: 182 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPTPEEIAEE 241

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +PVE VR+++KI +EP+SLETPIG+E+ SHLGDFI D+ A +P D+A    LRE    
Sbjct: 242 MELPVEKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDEEAQAPADAAAYRLLREQLED 301

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LTPREE+VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKK
Sbjct: 302 VLETLTPREEKVLRLRFGLDDGKPRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSKK 361

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 362 LKDFLE 367



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/136 (33%), Positives = 72/136 (52%), Gaps = 19/136 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPP-DEVSSEQMEDTVAMLSNMGINVV-DGDDLED---E 86
           K++I+  ++ G +T +E+   L   +++ +EQ++       +MGI ++ D DD+ +   E
Sbjct: 18  KELIEKGKKTGVLTYKEIMETLGDIEDLDAEQIDKIYESFEDMGIEIINDADDIPESLLE 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E SE  LDL+     +               DDPVRMYL+E+G I LL+ E EI +AKRI
Sbjct: 78  EISEVELDLSIPEGVA--------------IDDPVRMYLKEIGKIPLLTPEEEIELAKRI 123

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 124 EKGDKEAKRRLAEANL 139


>gi|16800559|ref|NP_470827.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116872885|ref|YP_849666.1| RNA polymerase sigma factor RpoD [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|217964400|ref|YP_002350078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290894216|ref|ZP_06557185.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|20140102|sp|Q92BQ6|RPOD_LISIN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|16413964|emb|CAC96722.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116741763|emb|CAK20887.1| RNA polymerase sigma factor RpoD (Sigma-A) [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217333670|gb|ACK39464.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290556213|gb|EFD89758.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|307571035|emb|CAR84214.1| RNA polymerase sigma factor [Listeria monocytogenes L99]
 gi|313623755|gb|EFR93895.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL J1-023]
          Length = 374

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EET--ESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|251782161|ref|YP_002996463.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390790|dbj|BAH81249.1| RNA polymerase sigma factor [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 369

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E +     V +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKVFAVAVAEGDLEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 41.2 bits (95), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 52/108 (48%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +        +  ++   S  
Sbjct: 39  PFALDADQIDDLLERLTDGGISITD------KEGNPSSKYIVEEPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E   A  +  G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTSEEEKVFAVAVAEGDLEAKQRLAEANL 140


>gi|206971344|ref|ZP_03232295.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218899458|ref|YP_002447869.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228902815|ref|ZP_04066960.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|228910126|ref|ZP_04073946.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228941457|ref|ZP_04104008.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954576|ref|ZP_04116601.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228967357|ref|ZP_04128392.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974388|ref|ZP_04134957.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980981|ref|ZP_04141284.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|229071795|ref|ZP_04205010.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|229081552|ref|ZP_04214050.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|229180570|ref|ZP_04307912.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|229192502|ref|ZP_04319465.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|206734116|gb|EDZ51287.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218541635|gb|ACK94029.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228591079|gb|EEK48935.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|228602994|gb|EEK60473.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|228701757|gb|EEL54245.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|228711390|gb|EEL63350.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228778772|gb|EEM27036.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228785438|gb|EEM33448.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792392|gb|EEM39959.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228805233|gb|EEM51827.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818238|gb|EEM64312.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228849643|gb|EEM94477.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228856824|gb|EEN01339.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|326942074|gb|AEA17970.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 375

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 72/139 (51%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D  +EEG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND--NEEGPNN 79

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 80  RQITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 128

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 129 TRIEEGDEEAKRRLAEANL 147


>gi|313618909|gb|EFR90770.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL S4-378]
          Length = 374

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEVGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 69/137 (50%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EET--ESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IE G       L E+ L
Sbjct: 130 IEVGDIEAKGRLAEANL 146


>gi|229174966|ref|ZP_04302486.1| RNA polymerase sigma factor [Bacillus cereus MM3]
 gi|228608634|gb|EEK65936.1| RNA polymerase sigma factor [Bacillus cereus MM3]
          Length = 375

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 72/139 (51%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D  ++EG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND--NDEGPNN 79

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 80  RQITKAEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 128

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 129 TRIEEGDEEAKRRLAEANL 147


>gi|289434736|ref|YP_003464608.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|289170980|emb|CBH27522.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|313633237|gb|EFS00106.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL N1-067]
          Length = 374

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 69/137 (50%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G + LL+ + EIA+AKR
Sbjct: 83  EE--TESFDLTDLSVPPGV-----------KINDPVRMYLKEIGRVNLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|313890499|ref|ZP_07824127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332523157|ref|ZP_08399409.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
 gi|313121016|gb|EFR44127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332314421|gb|EGJ27406.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 369

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+ +A   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTGEEEKELAIAVAEGDVDA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 39  PFVLDADQIDDLLERLTDGGISITD------KEGNPSTKYIVEEPKPEELTDEQLIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G       L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTGEEEKELAIAVAEGDVDAKQRLAEANL 140


>gi|313608766|gb|EFR84582.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-208]
          Length = 374

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EE--TESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|255026189|ref|ZP_05298175.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-003]
          Length = 361

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 111 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 170

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 171 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 230

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 231 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 290

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 291 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 350

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 351 SRSKQLKDFLE 361



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 10  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 69

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 70  EE--TESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 116

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 117 IEAGDIEAKGRLAEANL 133


>gi|229098765|ref|ZP_04229703.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
 gi|229104924|ref|ZP_04235581.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|229117789|ref|ZP_04247154.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228665652|gb|EEL21129.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228678498|gb|EEL32718.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|228684609|gb|EEL38549.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
          Length = 375

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 72/139 (51%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ ++ ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D  +EEG   
Sbjct: 22  EQLTEVGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND--NEEGPNN 79

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 80  RQITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 128

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 129 TRIEEGDEEAKRRLAEANL 147


>gi|163942050|ref|YP_001646934.1| RNA polymerase sigma factor RpoD [Bacillus weihenstephanensis
           KBAB4]
 gi|229013514|ref|ZP_04170648.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
 gi|229019517|ref|ZP_04176334.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|229025758|ref|ZP_04182158.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|229061987|ref|ZP_04199313.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|229135118|ref|ZP_04263920.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|229169042|ref|ZP_04296758.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|163864247|gb|ABY45306.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614451|gb|EEK71560.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|228648347|gb|EEL04380.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|228717296|gb|EEL68969.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|228735541|gb|EEL86136.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|228741773|gb|EEL91956.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|228747751|gb|EEL97620.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
          Length = 375

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 71/138 (51%), Gaps = 19/138 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE----- 86
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V GD+  DE     
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLV-GDNDNDEGPNNR 80

Query: 87  --EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A 
Sbjct: 81  QITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLAT 129

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 130 RIEEGDEEAKRRLAEANL 147


>gi|330955107|gb|EGH55367.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae Cit 7]
          Length = 216

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/215 (69%), Positives = 180/215 (83%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 1   GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ S
Sbjct: 61  ETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDS 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRMRFGI MNTDHTLEEVG
Sbjct: 121 HLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVG 180

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 181 KQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 215


>gi|228993035|ref|ZP_04152958.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
 gi|228999085|ref|ZP_04158667.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|229006633|ref|ZP_04164267.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228754494|gb|EEM03905.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228760702|gb|EEM09666.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|228766683|gb|EEM15323.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
          Length = 373

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 17/136 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V GD+ E       
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLV-GDNDEGPNNHQI 80

Query: 89  --SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A RI
Sbjct: 81  TKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLATRI 129

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 130 EEGDEEAKRRLAEANL 145


>gi|134300301|ref|YP_001113797.1| RNA polymerase sigma factor RpoD [Desulfotomaculum reducens MI-1]
 gi|134053001|gb|ABO50972.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfotomaculum reducens
           MI-1]
          Length = 367

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +GE EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 98  VRMYLKEIGRVPLLSPEEEVDLAKRMEQGEEEA---KRRLAEANLRLVVSIAKRYVGRGM 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 155 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIAK++ +  E VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 215 INKLIRVSRQLLQELGREPSPEEIAKEMDISGEKVREILKIAQEPVSLETPIGEEEDSHL 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A +P + A    LRE    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 275 GDFIEDADARAPAEEASFTLLREQLDEVLKTLTDREQKVLRLRFGLDDGRARTLEEVGQK 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAK +RKL+HPSRSKKL+ +LD
Sbjct: 335 FGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLD 367



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/138 (35%), Positives = 74/138 (53%), Gaps = 16/138 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K++I+  ++RG +T  E+   L   E+S +Q++D    +S MGI VV    DLE      
Sbjct: 11  KELIEKGKKRGVLTYNEIMDTLQGTELSPDQIDDIYEKISAMGIEVVPLASDLE------ 64

Query: 91  DSLDLASSASNSSVFLQKRKDSADRST------DDPVRMYLREMGSIELLSREGEIAIAK 144
             L++  S  NS+   ++ +   D S       DDPVRMYL+E+G + LLS E E+ +AK
Sbjct: 65  -PLEVDDSVENSTE--EEVEVEVDLSIPEGIGIDDPVRMYLKEIGRVPLLSPEEEVDLAK 121

Query: 145 RIEAGRAMMMASLCESPL 162
           R+E G       L E+ L
Sbjct: 122 RMEQGEEEAKRRLAEANL 139


>gi|16803494|ref|NP_464979.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46907682|ref|YP_014071.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092744|ref|ZP_00230530.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|47095405|ref|ZP_00233015.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499695|ref|ZP_03668044.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Finland
           1988]
 gi|224501605|ref|ZP_03669912.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-561]
 gi|226224055|ref|YP_002758162.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Clip81459]
 gi|254824487|ref|ZP_05229488.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|254827742|ref|ZP_05232429.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|254829787|ref|ZP_05234442.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 10403S]
 gi|254852080|ref|ZP_05241428.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|254898380|ref|ZP_05258304.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes J0161]
 gi|254912128|ref|ZP_05262140.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|254932639|ref|ZP_05265998.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|254936456|ref|ZP_05268153.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|254994146|ref|ZP_05276336.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-064]
 gi|255029176|ref|ZP_05301127.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes LO28]
 gi|255522085|ref|ZP_05389322.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J1-175]
 gi|284801841|ref|YP_003413706.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284994983|ref|YP_003416751.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|315282349|ref|ZP_07870778.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|1710684|sp|P52331|RPOD_LISMO RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|664756|gb|AAC43306.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes]
 gi|16410883|emb|CAC99532.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46880950|gb|AAT04248.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47016226|gb|EAL07149.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47018932|gb|EAL09679.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|225876517|emb|CAS05226.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. CLIP 80459]
 gi|258600121|gb|EEW13446.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|258605378|gb|EEW17986.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|258609048|gb|EEW21656.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|284057403|gb|ADB68344.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284060450|gb|ADB71389.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|293584198|gb|EFF96230.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|293590099|gb|EFF98433.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|293593725|gb|EFG01486.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|313614010|gb|EFR87725.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|328465497|gb|EGF36726.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 1816]
 gi|332311895|gb|EGJ24990.1| RNA polymerase sigma factor rpoD [Listeria monocytogenes str. Scott
           A]
 gi|1093602|prf||2104269C RNA polymerase:SUBUNIT=sigma
          Length = 374

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EE--TESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|311031650|ref|ZP_07709740.1| RNA polymerase sigma factor RpoD [Bacillus sp. m3-13]
          Length = 374

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLSAEEEISLANRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+ + +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRQLLQDLGREPSPEEIAEDMDLTPDKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 67/131 (51%), Gaps = 6/131 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++ ++ ++RG +T EE+   +   E+ S+QM++    L   G+ ++       E GS+D
Sbjct: 22  EQLTEVGKKRGVLTYEEIAEKMAGFEIESDQMDEYYEYLGEQGVEIIG------EAGSDD 75

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             +    A      L           +DPVRMYL+E+G ++LLS E EI++A RIE G  
Sbjct: 76  DPNTQQLAKEEEFDLNDLTVPPGVKINDPVRMYLKEIGRVDLLSAEEEISLANRIEEGDE 135

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 136 EAKRRLAEANL 146


>gi|30264362|ref|NP_846739.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Ames]
 gi|47529811|ref|YP_021160.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187190|ref|YP_030442.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Sterne]
 gi|49481307|ref|YP_038350.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141207|ref|YP_085621.1| RNA polymerase sigma factor RpoD [Bacillus cereus E33L]
 gi|65321666|ref|ZP_00394625.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bacillus anthracis str. A2012]
 gi|118479464|ref|YP_896615.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872043|ref|ZP_02216683.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167634513|ref|ZP_02392833.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|167638663|ref|ZP_02396939.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|170687516|ref|ZP_02878733.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|170707362|ref|ZP_02897816.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|196046412|ref|ZP_03113638.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218905429|ref|YP_002453263.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225866273|ref|YP_002751651.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228929335|ref|ZP_04092360.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935612|ref|ZP_04098427.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948006|ref|ZP_04110292.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229093361|ref|ZP_04224468.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|229123831|ref|ZP_04253025.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|229186532|ref|ZP_04313694.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|229601154|ref|YP_002868581.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
 gi|254684050|ref|ZP_05147910.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str.
           CNEVA-9066]
 gi|254736399|ref|ZP_05194105.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741437|ref|ZP_05199124.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Kruger B]
 gi|254757799|ref|ZP_05209826.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Australia
           94]
 gi|30259020|gb|AAP28225.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Ames]
 gi|47504959|gb|AAT33635.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181117|gb|AAT56493.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Sterne]
 gi|49332863|gb|AAT63509.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974676|gb|AAU16226.1| RNA polymerase sigma-43 factor [Bacillus cereus E33L]
 gi|118418689|gb|ABK87108.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis str. Al
           Hakam]
 gi|164712174|gb|EDR17711.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167513511|gb|EDR88881.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|167529965|gb|EDR92700.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|170127606|gb|EDS96479.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|170668711|gb|EDT19457.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|196022882|gb|EDX61563.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218536133|gb|ACK88531.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225787167|gb|ACO27384.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228596963|gb|EEK54621.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|228659652|gb|EEL15298.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|228690017|gb|EEL43818.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|228811696|gb|EEM58031.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824052|gb|EEM69869.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830349|gb|EEM75961.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229265562|gb|ACQ47199.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
          Length = 373

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 70/139 (50%), Gaps = 23/139 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D    EG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND----EGPNN 77

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 78  HQITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 126

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 127 TRIEEGDEEAKRRLAEANL 145


>gi|312143990|ref|YP_003995436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311904641|gb|ADQ15082.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 360

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 198/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK+++VEANLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 110 VMLAKRMEQGDEWAKQQLVEANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLMKAVEKFDY 169

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+K++R +R++  +  REP PE
Sbjct: 170 TKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVETINKLIRVSRQLLQEKGREPKPE 229

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +  E VR+++KI +EP+SLETPIG+E+ SHLGDFIED+++ +P  +A    L+
Sbjct: 230 EIGEEMDISAEKVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDEDSPAPASAASYILLK 289

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+RVL +RFGI      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 290 EQLDGVLDTLTEREKRVLELRFGIEDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHP 349

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +L+
Sbjct: 350 SRSKKLKDYLE 360



 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 15/135 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  + +I   ++ G +T EE+   L   ++ SE +E    + +   IN+V+    +DEE 
Sbjct: 12  DEVQALISRGKKEGELTYEEIMDALEDIDLDSEDIEQIYDLFNEKNINIVNEKLQQDEEE 71

Query: 89  SEDS-LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +DS LDL+                     DDPVRMYL+E+G ++LL+ + E+ +AKR+E
Sbjct: 72  EDDSGLDLSVPKGVG--------------IDDPVRMYLKEIGKVDLLTADEEVMLAKRME 117

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 118 QGDEWAKQQLVEANL 132


>gi|227817068|ref|YP_002817077.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
 gi|227007300|gb|ACP17043.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
          Length = 373

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 17/136 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V GD+ E       
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLV-GDNDEGPNNHQI 80

Query: 89  --SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A RI
Sbjct: 81  TKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLATRI 129

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 130 EEGDEEAKRRLAEANL 145


>gi|205374117|ref|ZP_03226917.1| RNA polymerase sigma factor RpoD [Bacillus coahuilensis m4-4]
          Length = 337

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/266 (58%), Positives = 202/266 (75%), Gaps = 9/266 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +S E  IS++E       + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+ FLDLIQ
Sbjct: 81  LSAEEEISLAE------RIEQGDEEA---KRRLAEANLRLVVSIAKRYVGRGMLFLDLIQ 131

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R 
Sbjct: 132 EGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRV 191

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R++   + REP+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED 
Sbjct: 192 QRQLLQDLGREPSPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDS 251

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRER
Sbjct: 252 EAQSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRER 311

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 312 IRQIEAKALRKLRHPSRSKRLKDFLE 337



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 56/112 (50%), Gaps = 17/112 (15%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE------DSLDLASSASNSSVFLQKRK 110
           ++ S+Q+++    L   GI +V  +D + +  +E      +  DL   +    V      
Sbjct: 9   DLDSDQIDEYFEQLGEQGIEIVHENDSDSDPNAEQLNKNEEEFDLNDLSVPPGV------ 62

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                  +DPVRMYL+E+G ++LLS E EI++A+RIE G       L E+ L
Sbjct: 63  -----KINDPVRMYLKEIGRVDLLSAEEEISLAERIEQGDEEAKRRLAEANL 109


>gi|225412271|ref|ZP_03761460.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
 gi|225042189|gb|EEG52435.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
          Length = 376

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 191/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K + E+NLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 138 AAKRLAESNLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 197

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+++VRT+R++  ++ REPT EEIA +  M VE V
Sbjct: 198 IRQAITRSIADQARTIRIPVHMVENINRLVRTSRQLLQELGREPTTEEIAARAEMSVERV 257

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L E    VL +LT R
Sbjct: 258 SEILKMSQEPVSLETPIGEEEDSHLGDFIQDDNVTVPQDAATYTLLHEQLMEVLTTLTER 317

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 318 EQKVLRLRFGLDDGRPRTLEEVGREFKVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 375



 Score = 43.9 bits (102), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 29/47 (61%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S  DPVRMYL+E+G I LL  E EI +A+++E G       L ES L
Sbjct: 101 SLQDPVRMYLKEIGKIPLLDMEAEIRLARQMEEGDREAAKRLAESNL 147


>gi|300765597|ref|ZP_07075576.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
 gi|300513698|gb|EFK40766.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
          Length = 374

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 363

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 364 SRSKQLKDFLE 374



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 69/137 (50%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +    I V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAEIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EET--ESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|229086862|ref|ZP_04219022.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
 gi|228696437|gb|EEL49262.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
          Length = 373

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 70/139 (50%), Gaps = 23/139 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D    EG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND----EGPNR 77

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 78  HQITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 126

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 127 TRIEEGDEEAKRRLAEANL 145


>gi|169830688|ref|YP_001716670.1| RNA polymerase sigma factor RpoD [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637532|gb|ACA59038.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 360

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 199/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS+ R+ E     AK+ ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 110 VSLARRMEAGDDEAKRRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 169

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 170 KKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRISRQLLQELGREPLPE 229

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ +  + VR++ KI +EP+SLETPIG+E+ SHLGDFIED++A +P + A    LR
Sbjct: 230 EIAREMDISEDKVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDQDAQAPAEEASFTLLR 289

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+RVLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL+HP
Sbjct: 290 EQLDDVLKTLTEREQRVLRLRFGLDDGRARTLEEVGQEFGVTRERIRQIEAKTLRKLRHP 349

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 350 SRSKKLKDYLD 360



 Score = 56.6 bits (135), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/117 (32%), Positives = 65/117 (55%), Gaps = 10/117 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSEDS 92
           +++  +QRG +T  E+   L   E++ +Q++D    L+  GI VV +G DL     + + 
Sbjct: 12  LVEKGKQRGTLTYNEVMDSLQGFELTPDQIDDVYERLAGEGIEVVPEGPDL----AALEE 67

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                    + + + +  D      DDPVRMYL+E+G I LL+ E E+++A+R+EAG
Sbjct: 68  ETREEDVEEAEIAIPEGVD-----IDDPVRMYLKEIGRIPLLTPEEEVSLARRMEAG 119


>gi|315303191|ref|ZP_07873849.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
 gi|313628434|gb|EFR96909.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
          Length = 386

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 136 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 195

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 196 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 255

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 256 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 315

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 316 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 375

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 376 SRSKQLKDFLE 386



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 35  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 94

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 95  EE--TESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 141

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 142 IEAGDIEAKGRLAEANL 158


>gi|1943995|dbj|BAA19494.1| sigA=sigma70 [Staphylococcus aureus]
          Length = 368

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 152/276 (55%), Positives = 205/276 (74%), Gaps = 1/276 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +++   +  + + ++ E    +AK  + EANLRLV+S+AK+Y  
Sbjct: 93  VKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVG 152

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IA Q+ TIRIPVHM
Sbjct: 153 RGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIAHQARTIRIPVHM 212

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 213 VETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDD 272

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEV
Sbjct: 273 SHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEV 332

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GK F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 333 GKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 43/143 (30%), Positives = 74/143 (51%), Gaps = 14/143 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D + 
Sbjct: 21  DVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDE 80

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE 
Sbjct: 81  KLNPSDLSAPPGVK--------------INDPVRMYLKEIGRVNLLSAQEEIELAKRIEQ 126

Query: 149 GRAMMMASLCESPLTFQALIIWR 171
           G  +  + L E+ L     I  R
Sbjct: 127 GDEVAKSRLAEANLRLVVSIAKR 149


>gi|254721884|ref|ZP_05183673.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. A1055]
          Length = 373

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGI 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 17/136 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V GD+ E       
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLV-GDNDEGPNNHQI 80

Query: 89  --SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A RI
Sbjct: 81  TKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLATRI 129

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 130 EEGDEEAKRRLAEANL 145


>gi|225026959|ref|ZP_03716151.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
 gi|224955724|gb|EEG36933.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
          Length = 422

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRL +S+AK+Y+ RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 184 AKKKLSEANLRLTVSIAKRYSGRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 243

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+ITR+IADQ+ TIRIPVHM + +++V RT+RR+  +  REPTPEEIA+ + +PVE V
Sbjct: 244 IRQSITRAIADQARTIRIPVHMVETMNRVNRTSRRLLQEYGREPTPEEIAEAMNLPVERV 303

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ KI++EP+SLETPIG+E+ SHLGDFI+D++   P D A    LRE   +V+ +L+ R
Sbjct: 304 LEISKISQEPVSLETPIGEEEDSHLGDFIQDEHIPVPADEAAHTLLREQLEKVMDTLSER 363

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL +RFG+     HTLEEVG++F VTRERIRQIEAKA+RKL+HP+RS+KLR FL+
Sbjct: 364 EQKVLALRFGLEDGKPHTLEEVGREFQVTRERIRQIEAKALRKLRHPTRSRKLRDFLE 421



 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 74/156 (47%), Gaps = 23/156 (14%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV-----VDGDDLEDEEGSEDSL 93
           +Q+  V ++E+        ++  Q+E  +A L    I+V     ++ DD+ED+ G  DSL
Sbjct: 47  KQKNVVELQEIRDVFQNSPLTQAQLERIIAYLEEQKIDVLTMPDINADDIEDDVGEIDSL 106

Query: 94  D-------------LASSASNSSVFLQKRKDSADRSTD-----DPVRMYLREMGSIELLS 135
           +             +  +A     + +  ++S +  T+     DPVRMYL+E+G I LLS
Sbjct: 107 NDMDVFQKPDRIGNVQVTAEIEKGYEKTAEESENSFTERGNAEDPVRMYLKEIGRIPLLS 166

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            E EI +AKR+E G       L E+ L     I  R
Sbjct: 167 SEEEIELAKRMEEGDEEAKKKLSEANLRLTVSIAKR 202


>gi|229031941|ref|ZP_04187928.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
 gi|228729405|gb|EEL80395.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
          Length = 375

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIEDGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 72/139 (51%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D  +EEG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND--NEEGPNN 79

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 80  RQISKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 128

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 129 TRIEDGDEEAKRRLAEANL 147


>gi|299822900|ref|ZP_07054786.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
 gi|299816429|gb|EFI83667.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
          Length = 389

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 150/251 (59%), Positives = 194/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 139 VALAKRIETGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 198

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 199 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 258

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+
Sbjct: 259 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLK 318

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 319 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHP 378

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 379 SRSKQLKDFLE 389



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 69/138 (50%), Gaps = 22/138 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD---------LE 84
           +I+  ++ G +T +++ A L P  + S+QM++ +  L+  GI V D  D         L 
Sbjct: 37  LIETGKKSGTLTYDKVAAQLAPFTLDSDQMDEFLVHLTQNGIEVTDDVDEDEDPDEKELI 96

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE  E  LDL   +    V             +DPVRMYL+E+G + LL+ + E+A+AK
Sbjct: 97  KEETEE--LDLTDMSVPPGV-----------KINDPVRMYLKEIGRVNLLTADEEVALAK 143

Query: 145 RIEAGRAMMMASLCESPL 162
           RIE G       L E+ L
Sbjct: 144 RIETGDIEAKGRLAEANL 161


>gi|270487764|ref|ZP_06204838.1| sigma-70, region 4 [Yersinia pestis KIM D27]
 gi|270336268|gb|EFA47045.1| sigma-70, region 4 [Yersinia pestis KIM D27]
          Length = 215

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 151/214 (70%), Positives = 179/214 (83%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 1   MQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 61  TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 121 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 180

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 181 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 214


>gi|319651585|ref|ZP_08005712.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396652|gb|EFV77363.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 374

 Score =  314 bits (804), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLSAEEEIALANRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPDKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 68/135 (50%), Gaps = 16/135 (11%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE----- 87
           +++++ ++ G +  +++   L   EV S QM++    L + G+ +V  ++ ED       
Sbjct: 23  QLVEIGKKTGVLAYDDIAERLSQFEVDSHQMDEFYEFLGDQGVELVGDNENEDPNVQELA 82

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EIA+A RIE
Sbjct: 83  KNEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIALANRIE 131

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 132 EGDEEAKRRLAEANL 146


>gi|220932077|ref|YP_002508985.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
 gi|219993387|gb|ACL69990.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
          Length = 358

 Score =  314 bits (804), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 152/238 (63%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+VEANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 121 AKRELVEANLRLVVSIAKKYVGRGMSFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTPEEI +++ MP E V
Sbjct: 181 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEKGREPTPEEIGEEMGMPAEKV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFIED++A +P  +A    LRE    VL +LT R
Sbjct: 241 REILKIAQEPVSLETPIGEEEDSHLGDFIEDEDAPAPASAASFTLLREQLDDVLDTLTDR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+RVL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 301 EKRVLELRFGLEDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 358



 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 47/131 (35%), Positives = 70/131 (53%), Gaps = 14/131 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++IK  ++ GY+T EE+   L   E+SSE +E    + + M I+VVD  D  D++  +D
Sbjct: 14  KELIKKGKEEGYLTYEEIMDSLEEIELSSEDIEKIYELFNEMNIDVVDDVDEVDDDKGDD 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+L+                     DDPVRMYL+E+G + LL+ E E+ +AKRIE G  
Sbjct: 74  DLELSIPEGV--------------GIDDPVRMYLKEIGKVPLLTAEEEVDLAKRIEQGDE 119

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 120 QAKRELVEANL 130


>gi|224542125|ref|ZP_03682664.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524962|gb|EEF94067.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
          Length = 418

 Score =  314 bits (804), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 151/239 (63%), Positives = 189/239 (79%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 179 AKKELAAANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWW 238

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++  ++ REPT EEIA+K+  M    
Sbjct: 239 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQELGREPTAEEIAEKMDGMTPAK 298

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI+ EP+SLETPIG+ED SHLGDFIED+ A+SP D A    L++    VL  LT 
Sbjct: 299 VREIQKISLEPVSLETPIGEEDDSHLGDFIEDEGAMSPDDYASNELLKDELNEVLLELTD 358

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHPSRSK+L+ FLD
Sbjct: 359 REEKVLRLRFGLDDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPSRSKRLKDFLD 417



 Score = 45.1 bits (105), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 73/159 (45%), Gaps = 42/159 (26%)

Query: 32  KKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---------- 80
           K +I  A+ +G  +T ++L+AF    ++  E  E+ +  ++   I + DG          
Sbjct: 18  KMLISAAKAKGNRLTQDDLDAFQSRYDLDDEAYENLIDAINENHIEIEDGLDALEIDDDD 77

Query: 81  ------DDLEDEEGSE------------------DSLDLASSASNSSVFLQKRKD----- 111
                 DDL+D EG E                  + LD+    +N  ++ Q   D     
Sbjct: 78  FMAGGADDLDDLEGLEVDTDDDTGDDDIANLDFGNDLDMDFGDTNK-MYNQSDDDDDMNQ 136

Query: 112 -SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++   +DPV+MYL+E+G ++LL+ E EI +AKRI  G
Sbjct: 137 LGSNVKINDPVKMYLKEIGRVDLLTHEQEIELAKRILEG 175


>gi|187736115|ref|YP_001878227.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
 gi|187426167|gb|ACD05446.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
          Length = 688

 Score =  314 bits (804), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 152/248 (61%), Positives = 194/248 (78%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK   EA  AK EMVEANLRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  G
Sbjct: 437 LRKWLREARRAKDEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRG 496

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K++R  +++  +  REPTPEEIA
Sbjct: 497 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLMRVQKQLVQEYGREPTPEEIA 556

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ +PVE VR VLK+ ++PISL+ P+GD D +  GDFIEDK A +P++ A  + L+E  
Sbjct: 557 EEIHLPVERVRSVLKMAQQPISLQAPVGDSDDTSFGDFIEDKAAENPMEEASFSFLKEKI 616

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LT RE  V+  RFG+   +  TLEEVG+QF VTRERIRQIEAKA+RKL+HP+R 
Sbjct: 617 KDVLDTLTDREREVIEQRFGLRDGSPRTLEEVGRQFSVTRERIRQIEAKALRKLRHPTRI 676

Query: 674 KKLRSFLD 681
            K++ FL+
Sbjct: 677 SKIKGFLE 684



 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 41/116 (35%), Positives = 71/116 (61%), Gaps = 7/116 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++IKLA+++GY+T +++N  LP D V  +  E  +  L +M  +++D  D++      D
Sbjct: 162 RELIKLAKEQGYLTFDDINDSLPNDIVDQQDYEAIMDRLRSMAFDIIDASDVD---SYTD 218

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++   +    L+ + D      DDPVRMYL++MG + LL+RE E+AI+KRIE
Sbjct: 219 RTRISTEEEDEEEKLEAKMDI----LDDPVRMYLKQMGQVSLLTREEEVAISKRIE 270


>gi|298246437|ref|ZP_06970243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553918|gb|EFH87783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 422

 Score =  314 bits (804), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 147/243 (60%), Positives = 192/243 (79%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   A+K + EANLRLV+SVAKKY  RG+  LDLIQEGNIGL++A EKFD+  G+KFST
Sbjct: 180 SEGEEAQKRLTEANLRLVVSVAKKYIGRGMNLLDLIQEGNIGLIRAVEKFDYNKGFKFST 239

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I++++R +RR+   + REPT EEIA ++ +
Sbjct: 240 YATWWIRQAITRAIADQARTIRIPVHMVETINRLIRISRRLLQDLGREPTSEEIAAQMEI 299

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E VR+++K+++EP+SLETPIG+ED SHLGDFIED  A++P D+A    L+E    VL 
Sbjct: 300 SAEKVREIIKVSQEPVSLETPIGEEDDSHLGDFIEDHTALAPADAASHQLLKEQVEDVLD 359

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLT RE +VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ 
Sbjct: 360 SLTERERKVLQLRFGLDDGRSRTLEEVGKEFHVTRERIRQIEAKALRKLRHPSRSRKLKD 419

Query: 679 FLD 681
           +LD
Sbjct: 420 YLD 422



 Score = 43.9 bits (102), Expect = 0.091,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S DDPVRMYLRE+G + LL+   EI +A+ +E G+A
Sbjct: 132 SLDDPVRMYLREIGRVPLLTAHEEIRLAQLMERGKA 167


>gi|77406972|ref|ZP_00783989.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
 gi|77174413|gb|EAO77265.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
          Length = 369

 Score =  314 bits (804), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELAVAVAEGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 368



 Score = 43.9 bits (102), Expect = 0.083,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 55/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +     +  +  ++   S  
Sbjct: 39  PFVLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEGPKSEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEGDLMAKQRLAEANL 140


>gi|22537572|ref|NP_688423.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae 2603V/R]
 gi|25011538|ref|NP_735933.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae NEM316]
 gi|76788342|ref|YP_330069.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77409561|ref|ZP_00786243.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
 gi|77412516|ref|ZP_00788814.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77414847|ref|ZP_00790961.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|22534455|gb|AAN00296.1|AE014257_3 RNA polymerase sigma-70 factor [Streptococcus agalactiae 2603V/R]
 gi|24413077|emb|CAD47155.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           NEM316]
 gi|76563399|gb|ABA45983.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77159097|gb|EAO70294.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|77161430|gb|EAO72443.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77171826|gb|EAO75013.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
          Length = 369

 Score =  314 bits (804), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELAVAVAEGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 368



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 39  PFVLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEGPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEGDLMAKQRLAEANL 140


>gi|168187756|ref|ZP_02622391.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
 gi|169294399|gb|EDS76532.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
          Length = 368

 Score =  313 bits (803), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 200/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 118 VDLAQRIEAGEMYAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 177

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 178 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPE 237

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+
Sbjct: 238 EIAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLK 297

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 298 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 357

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 358 SRSKKLKDYLD 368



 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/131 (33%), Positives = 69/131 (52%), Gaps = 15/131 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G +T +E+   L   E+S EQ+E    +L +M I V+ GD  + E   E+
Sbjct: 25  KSLIDKGKKKGSLTYKEIMDELDNVELSPEQIEKVYGVLESMDIEVI-GDMKDMESEEEE 83

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL+     S               DDPVRMYL+E+G + LL+ + E+ +A+RIEAG  
Sbjct: 84  EIDLSVPEGIS--------------IDDPVRMYLKEIGKVPLLTPDEEVDLAQRIEAGEM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 YAKKKLAEANL 140


>gi|322387734|ref|ZP_08061343.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
 gi|321141601|gb|EFX37097.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
          Length = 369

 Score =  313 bits (803), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDVEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  +  +EPTPE+IA+K+ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQEYGQEPTPEQIAEKMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 43.9 bits (102), Expect = 0.098,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 64/131 (48%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N  L  P  +  E +E+ +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKKTGTATDDEINNVLVIPFALDVEGIENLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SERVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDV 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|289167835|ref|YP_003446104.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
 gi|288907402|emb|CBJ22239.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
          Length = 369

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  +  +EPTPE+IA+K+ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQEYGQEPTPEQIAEKMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKQKGTATDDEINASLVLPFTLDADGIEDLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDI 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|319745370|gb|EFV97681.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           agalactiae ATCC 13813]
          Length = 380

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 110 VRMYLKEIGVVPLLTNEEEKELAVAVAEGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 166

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 167 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 226

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 227 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 286

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 287 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 346

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 347 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 379



 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 50  PFVLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEGPKPEELTDEELIGSNS 103

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 104 AKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEGDLMAKQRLAEANL 151


>gi|167772125|ref|ZP_02444178.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
 gi|167665923|gb|EDS10053.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
          Length = 361

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD   G+KFSTYA WW
Sbjct: 124 ARKRLSEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDHTKGFKFSTYATWW 183

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+KV + +  + +K   EPT EEI+ +L MPV+ V
Sbjct: 184 IRQAITRAIADQARTIRIPVHMVETINKVKKVSSLLLHKNGHEPTAEEISAELDMPVDKV 243

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++++ +EP+SLETPIG+E+ SHLGDFI D++A +P  +A    LRE  + VL +LTPR
Sbjct: 244 REIMRVAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPDTAASHTLLREQLSEVLQTLTPR 303

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 304 EEKVLRLRFGLEDGRSRTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 361



 Score = 41.2 bits (95), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 32/124 (25%), Positives = 63/124 (50%), Gaps = 20/124 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG------DDLED 85
           K++++  + +G +T +E++  L   +   EQ++    +L    I +++       +D +D
Sbjct: 11  KELLESGKAKGKLTTKEISDALEELDYDVEQVDKMYDLLEQNNIEIIEDMVTPVEEDFKD 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
             G    LD+A +A   ++             DDPV++YL+E+G + LLS + EI +A R
Sbjct: 71  L-GKGTDLDVALAAEGINI-------------DDPVKVYLKEIGRVPLLSADEEIDLAVR 116

Query: 146 IEAG 149
           +  G
Sbjct: 117 MAQG 120


>gi|323703334|ref|ZP_08114984.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531697|gb|EGB21586.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 367

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 130 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 189

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK++ +  + V
Sbjct: 190 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAKEMNISGDKV 249

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED +A +P + A    LRE    VL +LT R
Sbjct: 250 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDADARAPAEEASFTLLREQLDEVLKTLTDR 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL+HPSRSKKL+ +LD
Sbjct: 310 EQKVLRLRFGLDDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLD 367



 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 75/141 (53%), Gaps = 7/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSE 90
           K+MI+  ++RG +T  E+   L   E+++EQ++D    L+ MGI VV +  DLE  E  +
Sbjct: 14  KEMIEKGKKRGSLTYGEIMDSLQGAELTAEQIDDIYEQLAAMGIEVVPEVTDLEPLE-VD 72

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ D  +      + + +         DDPVRMYL+E+G + LLS E E+ +AKR+E G 
Sbjct: 73  DAADTPTEDVEIDLSIPE-----GIGIDDPVRMYLKEIGRVPLLSPEEEVELAKRMEQGD 127

Query: 151 AMMMASLCESPLTFQALIIWR 171
                 L E+ L     I  R
Sbjct: 128 EEAKRRLAEANLRLVVSIAKR 148


>gi|261367093|ref|ZP_05979976.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
 gi|282571217|gb|EFB76752.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
          Length = 364

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 148/248 (59%), Positives = 196/248 (79%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E   AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD   G
Sbjct: 117 IQAGGPEGEKAKQRLSEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDHTKG 176

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV + + ++ ++   +P+ EEIA
Sbjct: 177 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVKKVSSQLLHEYGHDPSAEEIA 236

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L M V+ VR+++++ +EP+SLETPIG+E+ SHLGDFI D +A  P ++A Q  L+E  
Sbjct: 237 ERLDMSVDKVREIMRVAQEPVSLETPIGEEEDSHLGDFIPDDDAPVPAEAASQTLLKEQL 296

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 297 ADVLKTLTPREEKVLRLRFGLEDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 356

Query: 674 KKLRSFLD 681
           KKLR FLD
Sbjct: 357 KKLRDFLD 364



 Score = 40.4 bits (93), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + DDPV++YL+E+G + LL+ E EI +A +I+AG
Sbjct: 87  TIDDPVKVYLKEIGRVPLLTPEEEIDLALKIQAG 120


>gi|253682266|ref|ZP_04863063.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
 gi|253561978|gb|EES91430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
          Length = 368

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 153/251 (60%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S+ ++ E     AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 118 ISLAQRIEDGDMYAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 177

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 178 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPE 237

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+
Sbjct: 238 EIAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLK 297

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 298 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 357

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 358 SRSKKLKDYLD 368



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 70/131 (53%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G +T +E+   L   E++ EQ+E    +L +M I V+   D+++ E  E+
Sbjct: 26  KNLIDKGKKKGNLTYKEIMDELDNVELTPEQIEKVYGVLESMDIEVIG--DMKEIETEEE 83

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL+     S               DDPVRMYL+E+G + LLS + EI++A+RIE G  
Sbjct: 84  EIDLSIPEGIS--------------IDDPVRMYLKEIGKVPLLSPDEEISLAQRIEDGDM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 YAKKKLAEANL 140


>gi|322379076|ref|ZP_08053479.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
 gi|322379940|ref|ZP_08054217.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321147638|gb|EFX42261.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321148568|gb|EFX43065.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
          Length = 634

 Score =  313 bits (802), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 197/576 (34%), Positives = 321/576 (55%), Gaps = 74/576 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I LLS+E E+ ++K+I+ G  +++ ++C  P     +  +++ L +
Sbjct: 119 SDSPVRMYLREMGEIPLLSKEEEVYLSKQIKLGENIILDAICSVPYLIDFIYNYKEALIN 178

Query: 177 GTTLLREII---DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
               ++E+    D E  +  + +      +E     + + +S +K++  V+E     ++ 
Sbjct: 179 RERRVKELFRNFDNEGSMAKKDEDVEIEDSEEEDTPEIKRNSSDKDKKRVEEVLESFKAL 238

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            K  K+    +++P          ++E ED   H L+                       
Sbjct: 239 NKAKKEWLKLLNTP----------VEEQEDPLLHALTL---------------------- 266

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
                            + KC+VLKEKL  L  +  L    I+ LV+ +    K     E
Sbjct: 267 -----------------AYKCRVLKEKLYDLGPTSKL----INELVKAMETSLKSDDGFE 305

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD-SILKIRNE 412
            EL RL     +  +  +E H+         +  K+      +  +A   + +++ +  E
Sbjct: 306 KELKRLEYKLSLFNESLIENHK---------NILKNITTMSREEIIAMMPEATMIGVYME 356

Query: 413 IKSI-----SVETGISI--SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IK +     + + G ++  S+ + I+S +++G+  +  AK +M  +NLRLV+S+AK+YT+
Sbjct: 357 IKKLFQTKEASKDGFNLEPSKLKEILSQIKRGKLISDRAKNKMARSNLRLVVSIAKRYTS 416

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL FLDLIQEGNIGLMKA +KF+    YKFSTYA WW+KQAI+R+IADQ+ TIRIP+HM
Sbjct: 417 RGLPFLDLIQEGNIGLMKAVDKFEHEKNYKFSTYATWWIKQAISRAIADQARTIRIPIHM 476

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            D I+++ +  R+   +  +EP  + +AK++ +P++ VR V+KITKEPISLE+P+G++D 
Sbjct: 477 IDTINRINKVMRKYMQENGKEPDLDLVAKEVGLPLDKVRNVIKITKEPISLESPVGNDDD 536

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEE 644
              GDF+EDKN V  ++  ++ +L+     VL  L  RE+ V+RMRFG+  + +D TLEE
Sbjct: 537 GKFGDFVEDKNVVGSMEHIMREDLKAQIDGVLDQLNEREKSVIRMRFGLLEDESDRTLEE 596

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +GK+  VTRER+RQIE+ AI+KL+ P   + LRS+L
Sbjct: 597 IGKELNVTRERVRQIESSAIKKLRSPQYGRLLRSYL 632


>gi|323490072|ref|ZP_08095293.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
 gi|323396368|gb|EGA89193.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
          Length = 384

 Score =  313 bits (802), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +   E   +  ++ +G+ EA   KK + EANLRLV+S+AK+Y  RG+
Sbjct: 115 VRMYLKEIGRVDLLKAEEEVRLAKLIEQGDEEA---KKRLAEANLRLVVSIAKRYVGRGM 171

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 172 LFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 231

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 232 INKLIRVQRQLLQDLGRDPSPEEIGEEMDLLPEKVREILKIAQEPVSLETPIGEEDDSHL 291

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 292 GDFIEDSDAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 351

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 352 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 384



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 68/144 (47%), Gaps = 6/144 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +++ K++I+  ++ G +  E++   L   E+ S+ +E+ +  L   GI      +LE + 
Sbjct: 28  EEAKKQLIEAGKKTGELNYEQIADKLAIFEMESDAVEEFIDQLEGHGI------ELERKS 81

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E+ LD     +     L           +DPVRMYL+E+G ++LL  E E+ +AK IE
Sbjct: 82  DDEEHLDRLMKPTEDKFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLKAEEEVRLAKLIE 141

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
            G       L E+ L     I  R
Sbjct: 142 QGDEEAKKRLAEANLRLVVSIAKR 165


>gi|293376344|ref|ZP_06622581.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325843397|ref|ZP_08167955.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645033|gb|EFF63106.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489319|gb|EGC91693.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 456

 Score =  313 bits (802), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 146/242 (60%), Positives = 195/242 (80%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   AKK +VEANLRLV+S+AK++  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTY
Sbjct: 214 EGEYAKKRLVEANLRLVVSIAKRHVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTY 273

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP PEEI++K+ + 
Sbjct: 274 ATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQELGREPLPEEISEKMGIA 333

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR++LKI++EP+SLE+P+G+ED SHLGDFI D +A+SP + A    L++    VL +
Sbjct: 334 PEKVREILKISQEPVSLESPVGEEDDSHLGDFIPDADALSPSEFASNEMLKKELDDVLET 393

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT REERVLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS++L+ F
Sbjct: 394 LTDREERVLRLRFGLEDGRTRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSRRLKDF 453

Query: 680 LD 681
           ++
Sbjct: 454 ME 455



 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/140 (29%), Positives = 75/140 (53%), Gaps = 23/140 (16%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD---------- 82
           ++IKL ++RGY+T +E+N      ++  E +   + +  + GI++V  +           
Sbjct: 17  QLIKLGKKRGYLTYDEINNSFEQVQLDPEMISSFLDLYDSEGISIVKSEKIVETPEVGET 76

Query: 83  --------LEDEEGSEDSLDL-ASSASNSSVFLQKRKDSADRST----DDPVRMYLREMG 129
                   L D +  ED  ++ A+ ++   V L+++ D  + ++    +DPVRMYL+E+G
Sbjct: 77  EEEDTVLLLPDFDADEDEDNIPANFSTEDEVDLEEKFDEFEFTSQFKINDPVRMYLKEIG 136

Query: 130 SIELLSREGEIAIAKRIEAG 149
            +ELLS + EI  AK+IE G
Sbjct: 137 RVELLSSQEEINFAKKIERG 156


>gi|299144149|ref|ZP_07037229.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518634|gb|EFI42373.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 383

 Score =  313 bits (802), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 146 AKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVEKFDYTKGFKFSTYATWW 205

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P PEEI K++ + VE V
Sbjct: 206 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLVQELGRDPLPEEIGKEMNLEVEKV 265

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI +EP+SLETPIG+E+ SHLGDFI D   +SP D+A    L+E    VL +LT R
Sbjct: 266 REIQKIAQEPVSLETPIGEEEDSHLGDFIPDDEILSPSDAATFTLLKEQLEDVLQTLTDR 325

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 326 EKKVLTLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 383



 Score = 47.8 bits (112), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S DDPVRMYL+E+G I LL+ + EI IA+R+E G       L E+ L
Sbjct: 109 SVDDPVRMYLKEIGKIPLLTGDEEIDIAQRMEVGDEDAKQELAEANL 155


>gi|229828460|ref|ZP_04454529.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
 gi|229793054|gb|EEP29168.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
          Length = 614

 Score =  313 bits (802), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 143/238 (60%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 377 AKQKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 436

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA+++    + V
Sbjct: 437 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAREMETTPDRV 496

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI+D+NA  P ++A    L+E    VL +LT R
Sbjct: 497 REILKISQEPVSLETPIGEEEDSHLGDFIQDENAPVPAEAATFTLLKEQLNEVLDTLTER 556

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 557 ERKVLILRFGLEDGRGRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 614



 Score = 45.1 bits (105), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 11/74 (14%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYL+E+G + LL+ E E+ +A+++E G   + A         + + I R+E+  G
Sbjct: 302 DDPVRMYLKEIGKVHLLTAEEEVDLAQKMEKG---LKAD--------EQIEILREEIRSG 350

Query: 178 TTLLREIIDLEACI 191
                ++++LEA I
Sbjct: 351 DLSEEDMMNLEAQI 364


>gi|110798581|ref|YP_696687.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
 gi|15186722|dbj|BAB62883.1| RNA polymerase major sigma factor [Clostridium perfringens]
 gi|110673228|gb|ABG82215.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
          Length = 366

 Score =  313 bits (801), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 203/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K E  ++ AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 116 IELAKKIEEGSNYAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 175

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PE
Sbjct: 176 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLVQELGRDPLPE 235

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K++ MPV+ VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+
Sbjct: 236 ELSKQMDMPVDKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTMLK 295

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 296 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 355

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 356 SRSKKLKDYLD 366



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 46/131 (35%), Positives = 69/131 (52%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   ++ G +T +E+   L   E++ EQ+E    +L +MGI V+     E EE  E+
Sbjct: 24  KRLIDKGKKSGSLTYKEIMDELDEIELNPEQIEKIYEVLESMGIEVISEI--EQEEEEEE 81

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            LDL+     +               DDPVRMYL+E+G ++LLS E EI +AK+IE G  
Sbjct: 82  ELDLSVPEGIA--------------IDDPVRMYLKEIGKVQLLSSEDEIELAKKIEEGSN 127

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 128 YAKKKLAEANL 138


>gi|255659373|ref|ZP_05404782.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
 gi|260848459|gb|EEX68466.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
          Length = 373

 Score =  313 bits (801), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 203/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 123 VALAKRMEAGDEEAQKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 183 NKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQQLGREPTPE 242

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + V+ VR+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P D+A    L+
Sbjct: 243 EIAKEMEIGVDRVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPADAASFMLLK 302

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 303 EQLEDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGQNFGVTRERIRQIEAKALRKLRHP 362

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ FLD
Sbjct: 363 SRSRKLKDFLD 373



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 33/47 (70%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S DDPVRMYL+E+G + LL+ E E+A+AKR+EAG       L E+ L
Sbjct: 99  SIDDPVRMYLKEIGRVPLLTAEEEVALAKRMEAGDEEAQKRLAEANL 145


>gi|110803528|ref|YP_699284.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169343561|ref|ZP_02864560.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170763881|ref|ZP_02634334.2| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170764050|ref|ZP_02630759.2| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170764227|ref|ZP_02638581.2| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|182420445|ref|ZP_02641259.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182624422|ref|ZP_02952206.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|110684029|gb|ABG87399.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169298121|gb|EDS80211.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170663661|gb|EDT16344.1| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170713105|gb|EDT25287.1| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715649|gb|EDT27831.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|177910425|gb|EDT72802.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|182382279|gb|EDT79758.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 366

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 203/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K E  ++ AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 116 IELAKKIEEGSNYAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 175

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PE
Sbjct: 176 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLVQELGRDPLPE 235

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K++ MPV+ VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+
Sbjct: 236 ELSKQMDMPVDKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTMLK 295

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 296 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 355

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 356 SRSKKLKDYLD 366



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 46/131 (35%), Positives = 68/131 (51%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   ++ G +T +E+   L   E++ EQ+E    +L +MGI V+     E EE  E+
Sbjct: 24  KRLIDKGKKSGSLTYKEIMDELDEIELNPEQIEKIYEVLESMGIEVISEI--EQEEEEEE 81

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            LDL+     +               DDPVRMYL+E+G + LLS E EI +AK+IE G  
Sbjct: 82  ELDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLSSEDEIELAKKIEEGSN 127

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 128 YAKKKLAEANL 138


>gi|18310989|ref|NP_562923.1| RNA polymerase sigma factor RpoD [Clostridium perfringens str. 13]
 gi|18145671|dbj|BAB81713.1| transcription initiation factor sigma A [Clostridium perfringens
           str. 13]
          Length = 373

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 203/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K E  ++ AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 123 IELAKKIEEGSNYAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PE
Sbjct: 183 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLVQELGRDPLPE 242

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K++ MPV+ VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+
Sbjct: 243 ELSKQMDMPVDKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTMLK 302

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 303 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 362

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 363 SRSKKLKDYLD 373



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 46/131 (35%), Positives = 70/131 (53%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   ++ G +T +E+   L   E++ EQ+E    +L +MGI V+   ++E EE  E+
Sbjct: 31  KRLIDKGKKSGSLTYKEIMDELDEIELNPEQIEKIYEVLESMGIEVIS--EIEQEEEEEE 88

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            LDL+     +               DDPVRMYL+E+G + LLS E EI +AK+IE G  
Sbjct: 89  ELDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLSSEDEIELAKKIEEGSN 134

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 135 YAKKKLAEANL 145


>gi|118444745|ref|YP_878546.1| RNA polymerase sigma factor RpoD [Clostridium novyi NT]
 gi|118135201|gb|ABK62245.1| RNA polymerase sigma-70 factor [Clostridium novyi NT]
          Length = 368

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 131 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK + MPV+ V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEIAKIMEMPVDKV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTPR
Sbjct: 251 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 311 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 368



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 45/131 (34%), Positives = 69/131 (52%), Gaps = 15/131 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G +T +E+   L   E+S EQ+E   A+L +M I V+ GD  + E   E+
Sbjct: 25  KSLIDKGKKKGSLTYKEIMDELDNVELSPEQIEKVYAVLESMDIEVI-GDMKDMETEEEE 83

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL+     S               DDPVRMYL+E+G + LL+ + EI +A+RIE G  
Sbjct: 84  EIDLSVPEGIS--------------IDDPVRMYLKEIGKVPLLTPDEEIDLAQRIEEGEM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 YAKKKLAEANL 140


>gi|319935434|ref|ZP_08009871.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809650|gb|EFW06063.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 422

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 160/285 (56%), Positives = 209/285 (73%), Gaps = 8/285 (2%)

Query: 402 EVDSILKIRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           ++ S +KI + +K    E G    +S  E   +   + +G+ EA   KK++  ANLRLV+
Sbjct: 140 QLGSNVKINDPVKMYLKEIGRVELLSHDEEIDLAKRILEGDEEA---KKKLAAANLRLVV 196

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 197 SIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQAR 256

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISL 576
           TIRIPVHM + I+K+ R  R++  ++ REP  EEIA+K+  M  E VR++ KI+ EP+SL
Sbjct: 257 TIRIPVHMVETINKLTRVQRQLIQELGREPLAEEIAEKMDGMTPEKVREIQKISLEPVSL 316

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIG+ED SHLGDFIED+ A+SP D A    L++    VL  LT REE+VLR+RFG+  
Sbjct: 317 ETPIGEEDDSHLGDFIEDEGAMSPDDYAANELLKDELNEVLLELTDREEKVLRLRFGLDD 376

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               TLEEVGK+F VTRERIRQIEAKA+RKLKHPSRSK+L+ FLD
Sbjct: 377 GRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPSRSKRLKDFLD 421



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 68/150 (45%), Gaps = 42/150 (28%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----------------DDLED 85
           G ++ ++L+AFL   ++  E  E+ +  +++ GI + DG                 DL+D
Sbjct: 30  GTLSQDDLDAFLTKYDLDDESAEELLQFITDSGIVIEDGLDALELDDEELLKGVGTDLDD 89

Query: 86  EEGSED----------------SLDLAS-----SASNSSVFLQKRKDSADR-----STDD 119
            EG ED                 LD        +   ++++     D  ++       +D
Sbjct: 90  LEGLEDLGALEGLDDALGEDVPDLDFVGDFDMMTGDTANMYTHNDDDDENQLGSNVKIND 149

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           PV+MYL+E+G +ELLS + EI +AKRI  G
Sbjct: 150 PVKMYLKEIGRVELLSHDEEIDLAKRILEG 179


>gi|331269992|ref|YP_004396484.1| RpoD family RNA polymerase sigma-70 subunit [Clostridium botulinum
           BKT015925]
 gi|329126542|gb|AEB76487.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           botulinum BKT015925]
          Length = 368

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 151/238 (63%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 131 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK + MPV+ V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEIAKIMEMPVDKV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTPR
Sbjct: 251 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 311 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 368



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 64/131 (48%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++G +T +E+   L   E++ EQ+E    +L +M I VV         G   
Sbjct: 26  KNLIDKGKKKGNLTYKEIMDELDNVELTPEQIEKVYGVLESMDIEVV---------GDIK 76

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            ++      + SV           S DDPVRMYL+E+G + LLS + EI +A+RIE G  
Sbjct: 77  EIETEEEEIDLSV-------PEGISIDDPVRMYLKEIGKVPLLSPDEEINLAQRIEDGDM 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 YAKKKLAEANL 140


>gi|288818771|ref|YP_003433119.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|288788171|dbj|BAI69918.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|308752357|gb|ADO45840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 570

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 145/273 (53%), Positives = 205/273 (75%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L +  E+K +  E G+   E   ++ ++++G  + + AK+ MV+ NLRLV+S+AKKY NR
Sbjct: 296 LTLEREVKELRKELGVLPEELDRVMHIIKEGRTKVTKAKQVMVKCNLRLVVSIAKKYVNR 355

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM 
Sbjct: 356 GLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMI 415

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+ + +  +++  ++ REP PEEIAK L + VE  RKV++ ++EPISLETPIGD++ +
Sbjct: 416 ETINDITKAHKKLFQELGREPFPEEIAKYLGISVEKARKVMRTSQEPISLETPIGDDEET 475

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HL DFIEDK+ +SP +   +  LRE   +VL++L  +E+ +L  R+G+   T++TLE++G
Sbjct: 476 HLKDFIEDKSVLSPEEQVSRKLLREQLIKVLSTLGEKEKEILMYRYGLVDGTEYTLEQIG 535

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           K F VTRERIRQIE KAIRKL+HP+R+K L+ F
Sbjct: 536 KMFNVTRERIRQIETKAIRKLRHPARAKYLKDF 568



 Score = 70.9 bits (172), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 49/137 (35%), Positives = 75/137 (54%), Gaps = 12/137 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S D+ KK+++L  ++GYVT +E+N  L  D V SE  E+ +  L   G+ +++ +++ +
Sbjct: 2   LSKDNIKKLMELG-EKGYVTYDEINEALGEDVVDSEAYEEIMDFLQERGVRIIESEEITE 60

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E    D      + S  ++ L  R         DPV++YLREMG I LLSRE EI  AK+
Sbjct: 61  ELEHGDEF----TVSTENLLLTAR-------DGDPVKLYLREMGRIPLLSREEEIMYAKQ 109

Query: 146 IEAGRAMMMASLCESPL 162
           IE GR +M   L  +  
Sbjct: 110 IEMGRKIMRRGLLRTSF 126


>gi|75761907|ref|ZP_00741832.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490615|gb|EAO53906.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 268

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 31  AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEI +++ +  E V
Sbjct: 91  IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A    L+E    VL +LT R
Sbjct: 151 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDR 210

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 211 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 268


>gi|307706485|ref|ZP_07643293.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
 gi|307708623|ref|ZP_07645087.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307615372|gb|EFN94581.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307618125|gb|EFN97284.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
          Length = 369

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDI 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|313888947|ref|ZP_07822607.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845120|gb|EFR32521.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 362

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 148/251 (58%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E    +AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 112 VEIAKRMEEGDELAKKELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDY 171

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P PE
Sbjct: 172 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLVQDLGRDPLPE 231

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ + VE VR++ KI +EP+SLETPIG+E+ SHLGDFI D   +SP D+A    L+
Sbjct: 232 EIAAEMNLDVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIPDDEILSPQDAATFTLLK 291

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 292 EQLNTVLETLTDREKKVLTLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHP 351

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +L+
Sbjct: 352 SRSKKLKDYLE 362



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 32/47 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + DDPVRMYL+E+G I LL+ E E+ IAKR+E G  +    L E+ L
Sbjct: 88  TVDDPVRMYLKEIGKISLLTAEEEVEIAKRMEEGDELAKKELAEANL 134


>gi|270292885|ref|ZP_06199096.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|306825379|ref|ZP_07458719.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315613017|ref|ZP_07887928.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|322374450|ref|ZP_08048964.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|331266528|ref|YP_004326158.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
 gi|270278864|gb|EFA24710.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|304432317|gb|EFM35293.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315315127|gb|EFU63168.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|321279950|gb|EFX56989.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|326683200|emb|CBZ00818.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
          Length = 369

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 45.1 bits (105), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 65/130 (50%), Gaps = 8/130 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            I+  ++ G  T +E+N+ L  P  + ++ +ED +  + + GI++ D       EG+  S
Sbjct: 18  FIRNHKKTGTATDDEINSSLVIPFTLDADGIEDLLQRIQDAGISITDN------EGNP-S 70

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
             + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG   
Sbjct: 71  ARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDIE 130

Query: 153 MMASLCESPL 162
               L E+ L
Sbjct: 131 AKQRLAEANL 140


>gi|322376488|ref|ZP_08050981.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
 gi|321282295|gb|EFX59302.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
          Length = 369

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q+G  T +E+NA  + P  + ++ +ED +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKQKGTATDDEINASLVVPFTLDADGIEDLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDI 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|325290508|ref|YP_004266689.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965909|gb|ADY56688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 392

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 146/251 (58%), Positives = 198/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +  E    +AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 142 IELAKSMEAGDEMAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDF 201

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+PTPE
Sbjct: 202 RKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVNRQLLQELGRDPTPE 261

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E AK + +P E VR+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+
Sbjct: 262 ETAKVMDIPEERVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPSEAASFLLLK 321

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 322 EQLEEVLETLTSREEKVLRLRFGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLRHP 381

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 382 SRSKKLKDYLD 392



 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 48/144 (33%), Positives = 73/144 (50%), Gaps = 12/144 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I+L + +G +T +E+   L   ++S EQ+E+    +S +GI+V+D    E  EG  D +
Sbjct: 36  LIELGKTKGNLTYDEIANALQKIDLSEEQIEEVYDQISTLGIDVID----EHSEGETDIV 91

Query: 94  ------DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                  LA   S  +       +      DDPVRMYL+E+G + LL+ E EI +AK +E
Sbjct: 92  IDKETEKLAEEISEETDIDLSIPEGV--GIDDPVRMYLKEIGRVPLLTAEEEIELAKSME 149

Query: 148 AGRAMMMASLCESPLTFQALIIWR 171
           AG  M    L E+ L     I  R
Sbjct: 150 AGDEMAKRRLAEANLRLVVSIAKR 173


>gi|169829158|ref|YP_001699316.1| RNA polymerase sigma factor rpoD [Lysinibacillus sphaericus C3-41]
 gi|168993646|gb|ACA41186.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Lysinibacillus sphaericus C3-41]
          Length = 375

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 188/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 138 ARKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWW 197

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEI +++ +  E V
Sbjct: 198 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKV 257

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED  A SP D A    L+E    VL +LT R
Sbjct: 258 REILKIAQEPVSLETPIGEEDDSHLGDFIEDSEAQSPSDHAAYELLKEQLEDVLDTLTDR 317

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 318 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/141 (29%), Positives = 74/141 (52%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGINVVDGDDLEDE 86
           DD+ K + + A+  G ++++E++  L P E+ +E++      L  +  I ++  ++ E+E
Sbjct: 18  DDAKKFLQEKAKTEGEISMKEISEKLTPYELENEEIFHFAEDLEKHKDIQIIGKEEFEEE 77

Query: 87  -----EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                E +E++ DL   +    V             +DPVRMYL+E+G ++LLS E EI 
Sbjct: 78  SLMKEEANEETFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEQEIK 126

Query: 142 IAKRIEAGRAMMMASLCESPL 162
           +A+RIE G       L E+ L
Sbjct: 127 LAERIEQGDEEARKRLAEANL 147


>gi|307705133|ref|ZP_07642010.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
 gi|307621329|gb|EFO00389.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
          Length = 369

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q+G  T +E+NA  + P  + ++ +ED +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKQKGTATDDEINASLVVPFTLDADGIEDLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDI 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|296161119|ref|ZP_06843929.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888642|gb|EFG68450.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 705

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 223/322 (69%), Gaps = 9/322 (2%)

Query: 364 GIKRDVFLERHQGRELDPHW----VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           G+ RD F+   +G E    W    V+  + F     +N  A +++     + ++ ++   
Sbjct: 387 GVPRDTFVAHFRGNETHLAWARQLVAAGQPFSSVLERNLPAIDLE-----QEKLLALQQR 441

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             + + EFR +   +   E +   AK EM+EANLRLVIS+AK+YTNRGL FLDLIQEGNI
Sbjct: 442 VVLPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNRGLLFLDLIQEGNI 501

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLM+A +KF++  GYKFSTYA WW++QA++RSIADQ+ TIR+PVHM + ++K+ R +R++
Sbjct: 502 GLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPVHMIESLNKLKRISRQI 561

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP    +A+++ M  + VR +L+I +EP+SL+  +G+ D + +GD IED  A+ 
Sbjct: 562 LQETGSEPDAALLAQRMEMQEQKVRAMLRIVREPVSLDASVGENDDTSIGDLIEDSTAIL 621

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D+A+ A++R+  +  L +LTPRE ++LR+RFGI    DHTLEE+G+QF +TRERIRQI
Sbjct: 622 PDDAALHASMRDAISEALMTLTPREAKILRLRFGIESGRDHTLEELGEQFELTRERIRQI 681

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E KA+RKL+HP+RS++L+SFLD
Sbjct: 682 EVKALRKLRHPARSERLKSFLD 703



 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 58/174 (33%), Positives = 92/174 (52%), Gaps = 16/174 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD------LED 85
           + +IKL  +RG+V   E++  LP      + +E+ +   S MGI V +         L D
Sbjct: 97  RALIKLGTERGFVIRGEISDCLPERLAQPDAIENVIRAFSEMGIAVFEQAPDAESMILHD 156

Query: 86  EEG--SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                ++D ++  +  + SSV      D+    T DPVRMY+REMG+ ELL+R+GEIA+A
Sbjct: 157 RAAVSADDQIEEEAVTAISSV------DAEFGRTTDPVRMYMREMGTTELLTRQGEIALA 210

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           +RIE GR  M+ ++   P T   ++   D +  G T + E++D    I P + G
Sbjct: 211 RRIEEGRNGMIRAISSCPATIAEILAIADGVACGETAIDELVD--GLIDPAATG 262


>gi|293365255|ref|ZP_06611972.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|306829363|ref|ZP_07462553.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
 gi|291316705|gb|EFE57141.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|304428449|gb|EFM31539.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
          Length = 369

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 45.4 bits (106), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 65/130 (50%), Gaps = 8/130 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
            I+  ++ G  T +E+N+ L  P  + ++ +ED +  + + GI++ D       EG+  S
Sbjct: 18  FIRNHKKTGTATDDEINSSLVIPFTLDADGIEDLLQRIQDAGISITDN------EGNP-S 70

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
             + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG   
Sbjct: 71  ARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDIE 130

Query: 153 MMASLCESPL 162
               L E+ L
Sbjct: 131 AKQRLAEANL 140


>gi|307709167|ref|ZP_07645626.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
 gi|307620113|gb|EFN99230.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
          Length = 369

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  +Q+G  T +E+NA  + P  + ++ +ED +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKQKGTATDDEINASLVVPFTLDADGIEDLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDI 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|299535819|ref|ZP_07049140.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
 gi|298729019|gb|EFI69573.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
          Length = 375

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 188/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 138 ARKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWW 197

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEI +++ +  E V
Sbjct: 198 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKV 257

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED  A SP D A    L+E    VL +LT R
Sbjct: 258 REILKIAQEPVSLETPIGEEDDSHLGDFIEDSEAQSPSDHAAYELLKEQLEDVLDTLTDR 317

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 318 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/141 (30%), Positives = 75/141 (53%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGINVVDGDDLEDE 86
           DD+ K + + A+  G ++++E++  L P E+ +E++      L  +  I ++  ++ E+E
Sbjct: 18  DDAKKFLQEKAKTEGEISMKEISEKLTPYELENEEIFHFAEDLEKHKDIQIIGKEEFEEE 77

Query: 87  -----EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                E +E++ DL   +    V             +DPVRMYL+E+G ++LLS E EIA
Sbjct: 78  SLMKEEANEETFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEQEIA 126

Query: 142 IAKRIEAGRAMMMASLCESPL 162
           +A+RIE G       L E+ L
Sbjct: 127 LAERIEQGDEEARKRLAEANL 147


>gi|196034883|ref|ZP_03102290.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
 gi|195992422|gb|EDX56383.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
          Length = 373

 Score =  312 bits (799), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+E  SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEGDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 17/136 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V GD+ E       
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLV-GDNDEGPNNHQI 80

Query: 89  --SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A RI
Sbjct: 81  TKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLATRI 129

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 130 EEGDEEAKRRLAEANL 145


>gi|118586868|ref|ZP_01544302.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
 gi|71466858|emb|CAH41003.1| rpoD protein [Oenococcus oeni]
 gi|118432700|gb|EAV39432.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
          Length = 458

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 166/361 (45%), Positives = 231/361 (63%), Gaps = 24/361 (6%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+    +LN  +ID L+E++ D    I+  +G      +S   K +           +P 
Sbjct: 119 KMAKPFALNADQIDKLIEKVEDAGISIVDEDGNPSE--KSLKTKSN-----------NPS 165

Query: 383 W--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +S A   P+G   N      D +     EI  +S+   ++  +   I   + KG  +
Sbjct: 166 QEELSQASSAPKGVKIN------DPVRMYLKEIGRVSL---LNADQEVAIAKRIEKGGSD 216

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A++E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA
Sbjct: 217 GERARQELAEANLRLVVSIAKRYVGRGMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYA 276

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P PEEI  ++ +  
Sbjct: 277 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRTLIQDLGRDPMPEEIGAEMELTA 336

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + VR++ KI +EP+SLETPIG+ED SHLGDFIED    SP++S     L++    VL +L
Sbjct: 337 DKVREIQKIAQEPVSLETPIGEEDDSHLGDFIEDNEGESPIESTSDQMLKDQLEEVLGTL 396

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+
Sbjct: 397 TEREENVLRLRFGLEDGKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFM 456

Query: 681 D 681
           +
Sbjct: 457 E 457



 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 66/121 (54%), Gaps = 5/121 (4%)

Query: 30  SWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           S K  IK  ++ G V  ++L N    P  ++++Q++  +  + + GI++VD    ED   
Sbjct: 97  SLKAFIKKNKKSGQVVYDDLENKMAKPFALNADQIDKLIEKVEDAGISIVD----EDGNP 152

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           SE SL   S+  +     Q          +DPVRMYL+E+G + LL+ + E+AIAKRIE 
Sbjct: 153 SEKSLKTKSNNPSQEELSQASSAPKGVKINDPVRMYLKEIGRVSLLNADQEVAIAKRIEK 212

Query: 149 G 149
           G
Sbjct: 213 G 213


>gi|168491966|ref|ZP_02716109.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183573791|gb|EDT94319.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
          Length = 369

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    +L +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 68/138 (49%), Gaps = 22/138 (15%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDD------LED 85
           + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +       L +
Sbjct: 17  EFIRNHKQKGIATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNEGNPSARVLSN 76

Query: 86  EEGSEDS-LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           EE  E S  DL  S S                 +DPVRMYL+E+G + LL+ E E  +A 
Sbjct: 77  EEEPELSDEDLIGSTSAK--------------VNDPVRMYLKEIGVVPLLTNEEEKELAL 122

Query: 145 RIEAGRAMMMASLCESPL 162
            +EAG       L E+ L
Sbjct: 123 AVEAGDIEAKQRLAEANL 140


>gi|160893000|ref|ZP_02073788.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
 gi|156865083|gb|EDO58514.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
          Length = 377

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 146/237 (61%), Positives = 191/237 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 140 AKQKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 199

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA  + +PVE V
Sbjct: 200 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEIADVMDIPVERV 259

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI++EP+SLETPIG+E+ SHLGDFI D N   P D+A    L+E    VL +LT R
Sbjct: 260 REILKISQEPVSLETPIGEEEDSHLGDFIPDDNMPVPADAAAFTLLKEQLVEVLDTLTER 319

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR ++
Sbjct: 320 EKKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLRDYI 376



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L
Sbjct: 103 SIEDPVRMYLKEIGKVPLLSAEEEIELAKRMEEGDEQAKQKLAEANL 149


>gi|15900942|ref|NP_345546.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae TIGR4]
 gi|15903023|ref|NP_358573.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae R6]
 gi|111657922|ref|ZP_01408632.1| hypothetical protein SpneT_02000898 [Streptococcus pneumoniae
           TIGR4]
 gi|116516638|ref|YP_816435.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae D39]
 gi|148985044|ref|ZP_01818287.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|148989116|ref|ZP_01820506.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|148994179|ref|ZP_01823494.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|148998339|ref|ZP_01825781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|149003984|ref|ZP_01828792.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|149006254|ref|ZP_01829966.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|149013172|ref|ZP_01833989.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|149019675|ref|ZP_01834994.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168483147|ref|ZP_02708099.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|168487460|ref|ZP_02711968.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|168488915|ref|ZP_02713114.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|168494506|ref|ZP_02718649.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|168576202|ref|ZP_02722096.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|169833634|ref|YP_001694498.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182684177|ref|YP_001835924.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|221231817|ref|YP_002510969.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225854569|ref|YP_002736081.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae JJA]
 gi|225856717|ref|YP_002738228.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae P1031]
 gi|225858886|ref|YP_002740396.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 70585]
 gi|225861039|ref|YP_002742548.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|237650028|ref|ZP_04524280.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974]
 gi|237821736|ref|ZP_04597581.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298230104|ref|ZP_06963785.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298255542|ref|ZP_06979128.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|298502915|ref|YP_003724855.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|303256088|ref|ZP_07342108.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|303260611|ref|ZP_07346576.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|303263023|ref|ZP_07348956.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|303264870|ref|ZP_07350786.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|303266910|ref|ZP_07352787.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|303269116|ref|ZP_07354896.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|307067745|ref|YP_003876711.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|307127396|ref|YP_003879427.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|61234224|sp|P0A4I9|RPOD_STRPN RecName: Full=RNA polymerase sigma factor rpoD
 gi|61234230|sp|P0A4J0|RPOD_STRR6 RecName: Full=RNA polymerase sigma factor rpoD
 gi|2108331|emb|CAA72252.1| rpoD [Streptococcus pneumoniae]
 gi|14972548|gb|AAK75186.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae TIGR4]
 gi|15458593|gb|AAK99783.1| RNA polymerase sigmA FACTOR 70 [Streptococcus pneumoniae R6]
 gi|116077214|gb|ABJ54934.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae D39]
 gi|147755736|gb|EDK62781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|147758043|gb|EDK65049.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|147762031|gb|EDK68993.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|147763023|gb|EDK69967.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|147922742|gb|EDK73859.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|147925339|gb|EDK76417.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|147927422|gb|EDK78452.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|147931050|gb|EDK82030.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168996136|gb|ACA36748.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043392|gb|EDT51438.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629511|gb|ACB90459.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|183569691|gb|EDT90219.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|183572434|gb|EDT92962.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|183575600|gb|EDT96128.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|183577989|gb|EDT98517.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|220674277|emb|CAR68818.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225720127|gb|ACO15981.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae 70585]
 gi|225722225|gb|ACO18078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae JJA]
 gi|225725305|gb|ACO21157.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae P1031]
 gi|225728137|gb|ACO23988.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238510|gb|ADI69641.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|301794192|emb|CBW36610.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV104]
 gi|301800046|emb|CBW32640.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae OXC141]
 gi|301802035|emb|CBW34765.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV200]
 gi|302596935|gb|EFL64061.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|302635850|gb|EFL66352.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|302638261|gb|EFL68731.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|302641365|gb|EFL71732.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|302643543|gb|EFL73813.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|302645558|gb|EFL75789.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|306409282|gb|ADM84709.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|306484458|gb|ADM91327.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|327389372|gb|EGE87717.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA04375]
 gi|332073431|gb|EGI83910.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17570]
 gi|332075028|gb|EGI85499.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17545]
 gi|332075404|gb|EGI85873.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41301]
 gi|332200548|gb|EGJ14620.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41317]
 gi|332201555|gb|EGJ15625.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47368]
 gi|332202930|gb|EGJ16998.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47901]
          Length = 369

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    +L +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 68/138 (49%), Gaps = 22/138 (15%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDD------LED 85
           + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +       L +
Sbjct: 17  EFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNEGNPSARVLSN 76

Query: 86  EEGSEDS-LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           EE  E S  DL  S S                 +DPVRMYL+E+G + LL+ E E  +A 
Sbjct: 77  EEEPELSDEDLIGSTSAK--------------VNDPVRMYLKEIGVVPLLTNEEEKELAL 122

Query: 145 RIEAGRAMMMASLCESPL 162
            +EAG       L E+ L
Sbjct: 123 AVEAGDIEAKQRLAEANL 140


>gi|307703796|ref|ZP_07640737.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
 gi|307622631|gb|EFO01627.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
          Length = 318

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 48  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 104

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 105 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 164

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 165 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 224

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 225 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 284

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 285 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 317



 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S     +DPVRMYL+E+G + LL+ E E  +A  +EAG       L E+ L
Sbjct: 39  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDIEAKQRLAEANL 89


>gi|309800318|ref|ZP_07694490.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
 gi|308116065|gb|EFO53569.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
          Length = 369

 Score =  311 bits (798), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 45.4 bits (106), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 65/131 (49%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N A + P  +  E +E+ +  + + GI++ D       EG+  
Sbjct: 17  EFIRNHKKTGTATDDEINNALVIPFTLDVEGIENLLQRIQDAGISITDN------EGNP- 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 70  SARVLSTEEEPELTDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDI 129

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 130 EAKQRLAEANL 140


>gi|315924365|ref|ZP_07920587.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622244|gb|EFV02203.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 396

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 145/237 (61%), Positives = 190/237 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 159 AKKELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWW 218

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTP EI K++    + V
Sbjct: 219 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEYGREPTPAEIGKEMGFSEDKV 278

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI ++P+SLETPIG+E+ SHLGDFI D  A +P ++A  A L+E    VL++LT R
Sbjct: 279 REIQKIAQDPVSLETPIGEEEDSHLGDFIPDDEAPAPSEAASYALLKEQLIDVLSTLTDR 338

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L
Sbjct: 339 EEKVLRLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDYL 395



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 70/135 (51%), Gaps = 13/135 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD-DLEDEEGSEDS 92
           +I+  +Q+G +  E++   L   +  S++++     L    I +   D D+ D       
Sbjct: 41  LIERGKQKGILNSEDIEHALSEKDFDSDEIDAVYLYLQKQNIRLTFKDMDMTD------- 93

Query: 93  LDLASSASNSSV----FLQKRKD-SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           LD AS A   S+       K++D + + + +DPVR+YL+E+G + LL+ + E+AIAKR+ 
Sbjct: 94  LDDASIAELRSIEKDEKTNKKEDLTENVNVNDPVRLYLKEIGRVSLLTADEEMAIAKRMA 153

Query: 148 AGRAMMMASLCESPL 162
           AG       L E+ L
Sbjct: 154 AGDEDAKKELAEANL 168


>gi|169824520|ref|YP_001692131.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302380672|ref|ZP_07269137.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|303233690|ref|ZP_07320344.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
 gi|167831325|dbj|BAG08241.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302311615|gb|EFK93631.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|302495124|gb|EFL54876.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
          Length = 388

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E  +  AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 138 VQLAQEMENGSKRAKKKLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDY 197

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VR  R++   + R+PT E
Sbjct: 198 TRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRIERQLLQDLGRDPTNE 257

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + VE VR+V KI +EP+SLETPIG+E+ SHLGDFIED  A++P ++A    LR
Sbjct: 258 EIAKEMGIEVEKVREVRKIAQEPVSLETPIGEEEDSHLGDFIEDDTAIAPDEAANFTMLR 317

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +L +L  RE +VL +RFG+   T  TLEEVGK F VTRERIRQIEAKA+RKLKHP
Sbjct: 318 EELEGILNTLNERERKVLALRFGLVDGTPRTLEEVGKDFDVTRERIRQIEAKALRKLKHP 377

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ FL+
Sbjct: 378 SRSQKLKDFLE 388



 Score = 43.5 bits (101), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 30/47 (63%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + DDPV+MYL+E+G I LLS + E+ +A+ +E G       L E+ L
Sbjct: 114 NVDDPVKMYLKEIGKIPLLSADEEVQLAQEMENGSKRAKKKLAEANL 160


>gi|291520418|emb|CBK75639.1| RNA polymerase, sigma 70 subunit, RpoD [Butyrivibrio fibrisolvens
           16/4]
          Length = 376

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 148/251 (58%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +K E     AK ++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 125 VELAQKMEDGDQEAKNKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLMKAVEKFDY 184

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTPE
Sbjct: 185 HKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEYGREPTPE 244

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  + + V+ V ++LKI++EP+SLETPIG+E+ SHLGDF+ D+N   P ++A    L+
Sbjct: 245 EIAAAMGITVDRVHEILKISQEPVSLETPIGEEEDSHLGDFLPDENVPVPAEAATFTLLK 304

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+RVL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 305 EQLHEVLDTLTEREQRVLILRFGLEDGKARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 364

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ +LD
Sbjct: 365 SRSRKLKDYLD 375



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 9/136 (6%)

Query: 28  DDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    ++IK+A+ Q+  +   E++ FL   ++ ++QME  +  L   GI      D+   
Sbjct: 20  DSKIAELIKIAKSQKNILEDYEISEFLKDYKIDAKQMERILTYLDKKGI------DVNFS 73

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G  D+L LAS   +         DS   S +DPVRMYL+E+G + LLS E E+ +A+++
Sbjct: 74  SGPSDALLLASDDEDLEDIDMSVPDSV--SIEDPVRMYLKEIGKVPLLSAEEEVELAQKM 131

Query: 147 EAGRAMMMASLCESPL 162
           E G       L E+ L
Sbjct: 132 EDGDQEAKNKLAEANL 147


>gi|312865945|ref|ZP_07726166.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
 gi|311098349|gb|EFQ56572.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
          Length = 338

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 150/273 (54%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I +   ++  E + +     +G+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 68  VRMYLKEIGIVPLLTNEEEKELAIAAAEGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 124

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 125 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 184

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 185 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 244

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 245 GDFIEDEVIENPVDYTTRIVLREQLNEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 304

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 305 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 337



 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +  +     +  ++   S  
Sbjct: 8   PFVLDADQIDDLLERLTDGGISITD------KEGNPSSKYVVEAPKPEELTDEELLGSNS 61

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A     G  M    L E+ L
Sbjct: 62  AKVNDPVRMYLKEIGIVPLLTNEEEKELAIAAAEGDLMAKQRLAEANL 109


>gi|153953576|ref|YP_001394341.1| hypothetical protein CKL_0942 [Clostridium kluyveri DSM 555]
 gi|219854198|ref|YP_002471320.1| hypothetical protein CKR_0855 [Clostridium kluyveri NBRC 12016]
 gi|146346457|gb|EDK32993.1| RpoD2 [Clostridium kluyveri DSM 555]
 gi|219567922|dbj|BAH05906.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 354

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 152/251 (60%), Positives = 201/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S+ +K E    IAKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 104 MSLAKKIEEGDQIAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 163

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP  E
Sbjct: 164 RKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPHAE 223

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+
Sbjct: 224 EVAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLK 283

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 284 EQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHP 343

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 344 SRSKKLKDYLD 354



 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 71/131 (54%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK+I+  ++ G +T +E+   L   ++S +Q+E    +L +MGI V    D+ + E +E 
Sbjct: 12  KKLIEKGKKNGTLTYKEIMDELQEVDLSPQQIEKIYEVLESMGIEV--NGDMNELELNEK 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +LDL+     +               DDPVRMYL+E+G + LL  E E+++AK+IE G  
Sbjct: 70  NLDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLLPEEEMSLAKKIEEGDQ 115

Query: 152 MMMASLCESPL 162
           +    L E+ L
Sbjct: 116 IAKKKLAEANL 126


>gi|322391830|ref|ZP_08065295.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
 gi|321145310|gb|EFX40706.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
          Length = 381

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGVVPLLTNEEEKELALAVEAGDVEA---KQRLAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 288 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 348 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 380



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 63/131 (48%), Gaps = 8/131 (6%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + I+  ++ G  T +E+N  L  P  +  E +E+ +  + + GI + D       EG+  
Sbjct: 29  EFIRNHKKTGTATDDEINNVLVIPFALDVEGIENLLQRIQDAGIAITDN------EGNP- 81

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +EAG  
Sbjct: 82  SERVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDV 141

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 142 EAKQRLAEANL 152


>gi|24214932|ref|NP_712413.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45657567|ref|YP_001653.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|26399555|sp|P59117|RPOD_LEPIN RecName: Full=RNA polymerase sigma factor rpoD
 gi|47605974|sp|P61540|RPOD_LEPIC RecName: Full=RNA polymerase sigma factor rpoD
 gi|24195965|gb|AAN49431.1|AE011394_5 RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45600806|gb|AAS70290.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 585

 Score =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 175/405 (43%), Positives = 257/405 (63%), Gaps = 29/405 (7%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKL-------VKLVGSLSLNQSRIDLLVEQLYDISK 347
           + LQ+     +K  ++S K K  KEK+          +  L ++Q  I  + +++  +  
Sbjct: 193 KVLQEAVSKIRKYSETSKKYKEFKEKIDASTEIIHNAIRELGVSQKEIQKISQKIKSMVF 252

Query: 348 RIMHNEGELLRLAQSYGIK-RDV-----FLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           RI   +   L++   YG   RD+     F+E+++  +LD   V    +  E         
Sbjct: 253 RIKEIDRHFLKIKAQYGQDVRDIKAFNRFIEKNE--KLDDIEVKMGVNIDE--------- 301

Query: 402 EVDSILK-IRN---EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            V  ++K IRN   +++ +  E G ++ E +     + KGE E S AKKE+V+ANLRLV+
Sbjct: 302 -VREVIKDIRNNERKLRRMEQEAGSTVQEIKDWGEKIIKGEREISQAKKELVKANLRLVV 360

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y NRG+ F DLIQEGNIGL+KA +KF++  GYKFSTYA WW++QAITR+I+DQ+ 
Sbjct: 361 SIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWWIRQAITRAISDQAR 420

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM ++++KV+R  R    +  R+P  EEIA++L  PV+ V+ V  + +EPISLE
Sbjct: 421 TIRVPVHMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLGWPVQKVKMVKNVAREPISLE 480

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+G E+ S LGDFI D    +P+++A  + L E   +VL +L  RE++V+RMRFG+   
Sbjct: 481 IPVGSEEDSELGDFIPDTEVETPVNAAASSILAEQIRQVLHTLPAREQKVIRMRFGLDDG 540

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEEVG QF VTRERIRQIEAKA+R+L+HPSRSKKL+ ++DG
Sbjct: 541 YPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSRSKKLKDYIDG 585


>gi|229825188|ref|ZP_04451257.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
 gi|229790560|gb|EEP26674.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
          Length = 372

 Score =  311 bits (797), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 142/238 (59%), Positives = 191/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K++ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 135 ARKKLTEANLRLVVSIAKRYLGRGMQFLDLIQEGNMGLIKAVEKFDYTKGYKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+ITR+IADQ+ TIRIPVHM + I+K++R  R+++  + REP PEEI K+L M  E V
Sbjct: 195 IKQSITRAIADQARTIRIPVHMVETINKLIRAQRQLTQTLGREPQPEEIGKELNMEPEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++KI +EP+S ETPIG+E+ SH+GDFI D + ++P+++A  A L+E    VL SLT R
Sbjct: 255 RSIMKIAQEPVSFETPIGEEEDSHIGDFIPDDSNMAPVEAATHAILKEQLEEVLDSLTER 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E RV+++RFG+      TLEEVGK+F VTRERIRQIE+KA+RKL+ PSRS+KL+ +L+
Sbjct: 315 EARVIKLRFGLEDGRTRTLEEVGKEFNVTRERIRQIESKALRKLRQPSRSRKLKDYLE 372



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 45/146 (30%), Positives = 78/146 (53%), Gaps = 9/146 (6%)

Query: 32  KKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K+++K A+++ G +  E++ A     E+S +++E     L   GI+V+  D+L+D +  E
Sbjct: 11  KELVKDAKEKKGVLEAEDVKAVFAGREISEDELEKCYRYLERQGIDVLIIDELDDVD--E 68

Query: 91  DSLDLASSASNSSVFLQKRKDSA-----DRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           D + L S+  N  +  +K +++        ST+DPVRMYL+E+G + LL  + EI +AK 
Sbjct: 69  DKI-LISTEDNDEIEREKIEETEITVPEGISTEDPVRMYLKEIGKVPLLDMDEEIKLAKS 127

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR 171
           +  G       L E+ L     I  R
Sbjct: 128 MAEGDDEARKKLTEANLRLVVSIAKR 153


>gi|258516189|ref|YP_003192411.1| RNA polymerase sigma factor RpoD [Desulfotomaculum acetoxidans DSM
           771]
 gi|257779894|gb|ACV63788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 359

 Score =  311 bits (797), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 109 VELAKRMEMGEEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDY 168

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PE
Sbjct: 169 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPMPE 228

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ +  + VR+++KI +EP+SLETPIG+E+ SHLGDFIED +A +P + A    LR
Sbjct: 229 EIAKEMNITEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDHDARAPAEEASFTLLR 288

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL+HP
Sbjct: 289 EQLDDVLKTLTDREQKVLRLRFGLDDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHP 348

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +LD
Sbjct: 349 SRSKKLKDYLD 359



 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 69/134 (51%), Gaps = 10/134 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           ++ + +++  +++GY+T  E+   L   E++ +Q++D    LS MGI+++  +   DE  
Sbjct: 8   ENIRSLVEKGKKQGYLTYHEIMDVLQTTELTPDQIDDVYEQLSGMGIDLLATEPEMDEAA 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +   D+    S                 DDPVRMYL+E+G + LLS E E+ +AKR+E 
Sbjct: 68  VKPDEDVEVDLSVPEGI----------GIDDPVRMYLKEIGRVPLLSSEEEVELAKRMEM 117

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 118 GEEEAKRRLAEANL 131


>gi|147677242|ref|YP_001211457.1| RNA polymerase sigma factor RpoD [Pelotomaculum thermopropionicum
           SI]
 gi|146273339|dbj|BAF59088.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
          Length = 363

 Score =  311 bits (796), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + KG+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 94  VRMYLKEIGRVPLLTPEEEVELAKRMEKGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 150

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 151 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 210

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++  ++ R+P+PEEIAK++ +  + VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 211 INKLVRVQRQLLQELGRDPSPEEIAKEMNITEDKVREILKIAQEPVSLETPIGEEEDSHL 270

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A +P + A    LRE    VL +LT RE+RVLR+RFG+      TLEEVG++
Sbjct: 271 GDFIEDHEARAPAEEASFTLLREQLDEVLKTLTEREQRVLRLRFGLDDGRARTLEEVGQK 330

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAK +RKL+HPSRSKKL+ +LD
Sbjct: 331 FGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLD 363



 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 47/147 (31%), Positives = 75/147 (51%), Gaps = 6/147 (4%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D  +D  +++I+  ++RG +T  E+   L   +++ EQ++D    L+ +GI VV   ++ 
Sbjct: 4   DEKNDGVRELIEKGKKRGVLTYNEIMDSLQGTDLTPEQIDDIYEKLAGLGIEVVP--EIP 61

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D E   DS  L +      V L   +       DDPVRMYL+E+G + LL+ E E+ +AK
Sbjct: 62  DIE-PLDSSALENPPDEVEVDLSIPEGVG---IDDPVRMYLKEIGRVPLLTPEEEVELAK 117

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWR 171
           R+E G       L E+ L     I  R
Sbjct: 118 RMEKGDEEAKRRLAEANLRLVVSIAKR 144


>gi|126652263|ref|ZP_01724442.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
 gi|126590995|gb|EAZ85107.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
          Length = 375

 Score =  311 bits (796), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 188/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 138 ARKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWW 197

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEI +++ +  E V
Sbjct: 198 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKV 257

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED  A SP D A    L+E    V+ +LT R
Sbjct: 258 REILKIAQEPVSLETPIGEEDDSHLGDFIEDSEAQSPSDHAAYELLKEQLEDVIDTLTDR 317

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 318 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/141 (30%), Positives = 75/141 (53%), Gaps = 17/141 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGINVVDGDDLEDE 86
           DD+ K + + A+  G ++++E++  L P E+ +E++      L  +  I ++  ++ E+E
Sbjct: 18  DDAKKFLQEKAKTEGEISMKEISEKLTPYELENEEIFHFAEDLEKHKDIQIIGKEEFEEE 77

Query: 87  -----EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                E +E++ DL   +    V             +DPVRMYL+E+G ++LLS E EIA
Sbjct: 78  SLMKEEANEETFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEQEIA 126

Query: 142 IAKRIEAGRAMMMASLCESPL 162
           +A+RIE G       L E+ L
Sbjct: 127 LAERIEQGDEEARKRLAEANL 147


>gi|47679387|gb|AAT36674.1| DNA-directed RNA polymerase sigma A subunit [Oenococcus oeni PSU-1]
          Length = 465

 Score =  311 bits (796), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 165/361 (45%), Positives = 231/361 (63%), Gaps = 24/361 (6%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+    +LN  +ID L+E++ D    I+  +G      +S   K +           +P 
Sbjct: 126 KMAKPFALNADQIDKLIEKVEDAGISIVDEDGNPSE--KSLKTKSN-----------NPS 172

Query: 383 W--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +S A   P+G   N      D +     EI  +S+   ++  +   I   + KG  +
Sbjct: 173 QEELSQASSAPKGVKIN------DPVRMYLKEIGRVSL---LNADQEVAIAKRIEKGGSD 223

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A++E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA
Sbjct: 224 GERARQELAEANLRLVVSIAKRYVGRGMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYA 283

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P PEEI  ++ +  
Sbjct: 284 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRTLIQDLGRDPMPEEIGAEMELTA 343

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + VR++ KI +EP+SLETPIG+E+ SHLGDFIED    SP++S     L++    VL +L
Sbjct: 344 DKVREIQKIAQEPVSLETPIGEENDSHLGDFIEDNEGESPIESTSDQMLKDQLEEVLGTL 403

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+
Sbjct: 404 TEREENVLRLRFGLEDGKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFM 463

Query: 681 D 681
           +
Sbjct: 464 E 464



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 66/121 (54%), Gaps = 5/121 (4%)

Query: 30  SWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           S K  IK  ++ G V  ++L N    P  ++++Q++  +  + + GI++VD    ED   
Sbjct: 104 SLKAFIKKNKKSGQVVYDDLENKMAKPFALNADQIDKLIEKVEDAGISIVD----EDGNP 159

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           SE SL   S+  +     Q          +DPVRMYL+E+G + LL+ + E+AIAKRIE 
Sbjct: 160 SEKSLKTKSNNPSQEELSQASSAPKGVKINDPVRMYLKEIGRVSLLNADQEVAIAKRIEK 219

Query: 149 G 149
           G
Sbjct: 220 G 220


>gi|85860024|ref|YP_462226.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
 gi|85723115|gb|ABC78058.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
          Length = 580

 Score =  310 bits (795), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 187/434 (43%), Positives = 276/434 (63%), Gaps = 35/434 (8%)

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIA-------EVYRELRSLQDNAVNGQKDEKSSV 312
           EDED         ED  R +V+  LD++A       ++ ++LR+ +D + +G+K  K  +
Sbjct: 164 EDEDGYVE-----EDSQRERVIKLLDKVAMLDGKNDQILQKLRA-KDLSEDGRKALK--I 215

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + +  K+ ++KL   +   + +ID LV  +      +   E E+ +  +  G+       
Sbjct: 216 QMEKNKKAIIKLCRKVRFGKKQIDKLVANIKRYLAELEKAEDEIQKCKEETGLSLTQI-- 273

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVAC--------EVDSILKIRN-EIKSISVETGIS 423
                       S  K +P+ E                V+++++  N ++K+I+ ETG S
Sbjct: 274 --------EKACSRLKKYPQDEAAILAEYGITMEKLKSVEAMIREANRKLKNITKETGYS 325

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ++ F+ I+  +  GE +A  AK+++VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 326 VTAFKKILFNIEHGEKKAEEAKRKLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMK 385

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++
Sbjct: 386 AVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEL 445

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REP+P+EIA K+  P+E VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK  +SP ++
Sbjct: 446 GREPSPDEIANKMEYPLEKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKKIMSPSEA 505

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I  +L E T ++L++LTPREE+VLRMRFGI    ++  EE+ +Q     E    IE  A
Sbjct: 506 TISMDLAEQTRKILSTLTPREEKVLRMRFGISERIEYGEEEL-EQGEEEGEFPGPIETGA 564

Query: 664 IRKLKHPSRSKKLR 677
            RKL++PSR + ++
Sbjct: 565 YRKLRNPSRRRTVK 578



 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 89/173 (51%), Gaps = 26/173 (15%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---GD 81
           +   + +KK+I L  ++G++T +++N FLP D  SS+Q++D + +     I+++D   G+
Sbjct: 4   NIQSEEFKKLISLGEEKGFLTYDDVNDFLPSDITSSDQIDDIIMLFGEKNIDIIDTEKGE 63

Query: 82  DL-------EDEEGSEDSL-DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            L       E E   E  L D+ S A                 T DPV+MYLREMG + L
Sbjct: 64  KLLVKSPVEERETAKEGELIDMMSVAGK---------------TGDPVKMYLREMGYVSL 108

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           LSR+GE+ IAK IE G    M ++     + + ++   ++L      ++ +ID
Sbjct: 109 LSRDGEVEIAKIIEEGAQEAMGAVFGVTASVKEVVDIGNKLKSDEIRIKNVID 161


>gi|116491026|ref|YP_810570.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290890507|ref|ZP_06553582.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
 gi|116091751|gb|ABJ56905.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290479903|gb|EFD88552.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
          Length = 458

 Score =  310 bits (795), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 165/361 (45%), Positives = 231/361 (63%), Gaps = 24/361 (6%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+    +LN  +ID L+E++ D    I+  +G      +S   K +           +P 
Sbjct: 119 KMAKPFALNADQIDKLIEKVEDAGISIVDEDGNPSE--KSLKTKSN-----------NPS 165

Query: 383 W--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +S A   P+G   N      D +     EI  +S+   ++  +   I   + KG  +
Sbjct: 166 QEELSQASSAPKGVKIN------DPVRMYLKEIGRVSL---LNADQEVAIAKRIEKGGSD 216

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A++E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA
Sbjct: 217 GERARQELAEANLRLVVSIAKRYVGRGMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYA 276

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P PEEI  ++ +  
Sbjct: 277 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRTLIQDLGRDPMPEEIGAEMELTA 336

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + VR++ KI +EP+SLETPIG+E+ SHLGDFIED    SP++S     L++    VL +L
Sbjct: 337 DKVREIQKIAQEPVSLETPIGEENDSHLGDFIEDNEGESPIESTSDQMLKDQLEEVLGTL 396

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+
Sbjct: 397 TEREENVLRLRFGLEDGKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFM 456

Query: 681 D 681
           +
Sbjct: 457 E 457



 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 66/121 (54%), Gaps = 5/121 (4%)

Query: 30  SWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           S K  IK  ++ G V  ++L N    P  ++++Q++  +  + + GI++VD    ED   
Sbjct: 97  SLKAFIKKNKKSGQVVYDDLENKMAKPFALNADQIDKLIEKVEDAGISIVD----EDGNP 152

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           SE SL   S+  +     Q          +DPVRMYL+E+G + LL+ + E+AIAKRIE 
Sbjct: 153 SEKSLKTKSNNPSQEELSQASSAPKGVKINDPVRMYLKEIGRVSLLNADQEVAIAKRIEK 212

Query: 149 G 149
           G
Sbjct: 213 G 213


>gi|297588502|ref|ZP_06947145.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
 gi|297573875|gb|EFH92596.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
          Length = 389

 Score =  310 bits (794), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E  +  AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 139 VKLAQEMENGSKRAKKKLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDY 198

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++VR  R++   + R+PT E
Sbjct: 199 TRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLVRIERQLLQDLGRDPTNE 258

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + VE VR+V KI +EP+SLETPIG+E+ SHLGDFIED  A++P ++A    LR
Sbjct: 259 EIAKEMGIEVEKVREVRKIAQEPVSLETPIGEEEDSHLGDFIEDDTAIAPDEAANFTMLR 318

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +L +L  RE +VL +RFG+   T  TLEEVGK F VTRERIRQIEAKA+RKLKHP
Sbjct: 319 EELEGILNTLNERERKVLALRFGLVDGTPRTLEEVGKDFDVTRERIRQIEAKALRKLKHP 378

Query: 671 SRSKKLRSFLD 681
           SRS+KL+ FL+
Sbjct: 379 SRSQKLKDFLE 389



 Score = 44.3 bits (103), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 30/47 (63%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + DDPV+MYL+E+G I LLS E E+ +A+ +E G       L E+ L
Sbjct: 115 NVDDPVKMYLKEIGKIPLLSAEEEVKLAQEMENGSKRAKKKLAEANL 161


>gi|312880428|ref|ZP_07740228.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
 gi|310783719|gb|EFQ24117.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
          Length = 387

 Score =  310 bits (794), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +  E   + +K ++VEANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EKFD+
Sbjct: 137 VELAKGVEAGHAPSKAKLVEANLRLVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEKFDY 196

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPT E
Sbjct: 197 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLVQRLGREPTAE 256

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +P E V ++ +I +EP+SLETPIG+E+ S LGDF+EDK+  SP ++A    LR
Sbjct: 257 EIAGEMEIPAERVEEIQRIAQEPVSLETPIGEEEDSQLGDFLEDKDLPSPEEAAASQILR 316

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +L  LT RE  VLR+RFG+     HTLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 317 EQLEEMLEDLTDREREVLRLRFGLEDGHPHTLEEVGRRFGVTRERIRQIEAKALRKLRHP 376

Query: 671 SRSKKLRSFLD 681
           SRSKKLR FL+
Sbjct: 377 SRSKKLRDFLE 387



 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 77/134 (57%), Gaps = 7/134 (5%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D+ ++++   R++G+VT E++   LP + +S++ +++    L  +GI V++     +E  
Sbjct: 33  DNVRELLHEGREKGFVTYEDIEKHLPKEVLSADVLDNLYFNLMELGIEVMEEAKTREETP 92

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +++ L  A+       + ++  +  D    DPVRMYLRE+G I LL+ E E+ +AK +EA
Sbjct: 93  ADEPLPQAT-------YQEEMGELEDLPLSDPVRMYLREIGKIPLLTPEEEVELAKGVEA 145

Query: 149 GRAMMMASLCESPL 162
           G A   A L E+ L
Sbjct: 146 GHAPSKAKLVEANL 159


>gi|327440913|dbj|BAK17278.1| DNA-directed RNA polymerase, sigma subunit [Solibacillus silvestris
           StLB046]
          Length = 375

 Score =  310 bits (793), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 187/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD   G+KFSTYA WW
Sbjct: 138 ARKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHRKGFKFSTYATWW 197

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEI +++ +  E V
Sbjct: 198 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKV 257

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED  A SP D A    L+E    VL +LT R
Sbjct: 258 REILKIAQEPVSLETPIGEEDDSHLGDFIEDSEAQSPSDHAAYELLKEQLEDVLDTLTDR 317

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 318 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 77/151 (50%), Gaps = 17/151 (11%)

Query: 18  SDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           S D++V   S +  KK ++  A+Q G ++++E++  L   E+ +E++ +    +    + 
Sbjct: 8   SKDTVVNGVSLEQVKKQLLAKAKQVGEMSMKEISDTLAFFELENEEIFNFADEIEKNDVT 67

Query: 77  VVDGDD-----LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           V   ++     L  +E SE++ DL   +    V             +DPVRMYL+E+G +
Sbjct: 68  VEGKEEFEEEALSKQESSEEAFDLNDLSVPPGV-----------KINDPVRMYLKEIGRV 116

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +LLS + EI +A+RIE G       L E+ L
Sbjct: 117 DLLSADQEIRLAERIEQGDEEARKRLAEANL 147


>gi|304317433|ref|YP_003852578.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778935|gb|ADL69494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 357

 Score =  310 bits (793), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 157/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + KG+ EA   KK + EANLRLV+S+AK+Y  RG+
Sbjct: 88  VRMYLKEIGKIPLLSPDEEIELAKRIEKGDEEA---KKRLTEANLRLVVSIAKRYVGRGM 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 145 QFLDLIQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 204

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P PEEIAK++ M V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 205 INKLIRVSRQLLQELGRDPLPEEIAKEMDMSVDKVREIMKIAQEPVSLETPIGEEEDSHL 264

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 265 GDFIPDEDAPAPAEAAAFTMLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 324

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 325 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 44/134 (32%), Positives = 67/134 (50%), Gaps = 12/134 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +S K++I   ++ G +T  E+   L   ++ +EQ+E        +GI +V  +  ++E  
Sbjct: 8   NSIKELIDKGKKNGMLTYNEIMNSLEDIDMDAEQIEKVYDTFEKLGIEIVGEEPQQEELI 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E+ LDL  S                 + DDPVRMYL+E+G I LLS + EI +AKRIE 
Sbjct: 68  PEEDLDLDLSIPEGI------------NIDDPVRMYLKEIGKIPLLSPDEEIELAKRIEK 115

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 116 GDEEAKKRLTEANL 129


>gi|150390747|ref|YP_001320796.1| RpoD family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950609|gb|ABR49137.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           metalliredigens QYMF]
          Length = 372

 Score =  310 bits (793), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 202/251 (80%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +  + E    +AKK++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 122 IDLATRMEAGDELAKKKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REP PE
Sbjct: 182 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEFGREPKPE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ +P E VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A  + L+
Sbjct: 242 EIAKEMDLPEEKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFSLLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPRE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLIEVLDTLTPREQKVLRLRFGLDDGRARTLEEVGKKFDVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ +L+
Sbjct: 362 SRSKKLKDYLE 372



 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 46/143 (32%), Positives = 73/143 (51%), Gaps = 9/143 (6%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +S KK+I+  ++RG +T  E+   L   E+  EQ+E+     + +GI++V GD   
Sbjct: 6   NMKKESIKKLIEKGKKRGIITYAEIVHALEDIELDKEQIEEIYEHFATLGIDIV-GDKEA 64

Query: 85  DEEGSEDSLDL-----ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           D+    D  +L      + A N    +   K       DDPVRMYL+E+G + LL+   E
Sbjct: 65  DDVDDVDEAELEDEEEVTVAENIEADINMLKGVI---IDDPVRMYLKEIGKVPLLTGPEE 121

Query: 140 IAIAKRIEAGRAMMMASLCESPL 162
           I +A R+EAG  +    L E+ L
Sbjct: 122 IDLATRMEAGDELAKKKLVEANL 144


>gi|116328273|ref|YP_797993.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116330997|ref|YP_800715.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
 gi|116121017|gb|ABJ79060.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116124686|gb|ABJ75957.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
          Length = 585

 Score =  310 bits (793), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 151/285 (52%), Positives = 209/285 (73%), Gaps = 4/285 (1%)

Query: 402 EVDSILK-IRN---EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           EV  ++K IRN   +++ +  E G ++ E +     + KGE E S AKKE+V+ANLRLV+
Sbjct: 301 EVREVIKDIRNNERKLRRMEQEAGSTVQEIKDWGEKIIKGEREISQAKKELVKANLRLVV 360

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y NRG+ F DLIQEGNIGL+KA +KF++  GYKFSTYA WW++QAITR+I+DQ+ 
Sbjct: 361 SIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWWIRQAITRAISDQAR 420

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM ++++KV+R  R    +  R+P  EEIA++L  PV+ V+ V  + +EPISLE
Sbjct: 421 TIRVPVHMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLGWPVQKVKMVKNVAREPISLE 480

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+G E+ S LGDFI D    +P+++A  + L E   +VL +L  RE++V+RMRFG+   
Sbjct: 481 IPVGSEEDSELGDFIPDTEVETPVNTAASSILAEQIRQVLHTLPAREQKVIRMRFGLDDG 540

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEEVG QF VTRERIRQIEAKA+R+L+HPSRSKKL+ ++DG
Sbjct: 541 YPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSRSKKLKDYIDG 585



 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 82/135 (60%), Gaps = 11/135 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +K+I L +  G V+ +++N  LP   ++SE+++D   +L  MGI +V       EE + +
Sbjct: 11  QKIISLGKANGEVSYDDINEILPDKILNSEKIDDFFTLLHEMGIEIV-------EEYTRN 63

Query: 92  SLDLASS--ASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +L+ AS+    + S   +K+K+S+  ++   DP+++YLRE+G + L+S E E+ +AKRIE
Sbjct: 64  TLEPASTLVPKDDSKPARKKKESSASASGSEDPIKLYLREIGKVSLISGETEVFLAKRIE 123

Query: 148 AGRAMMMASLCESPL 162
            G  ++  ++  S +
Sbjct: 124 KGEKIIEETILSSSI 138


>gi|194397936|ref|YP_002037704.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
 gi|194357603|gb|ACF56051.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
          Length = 369

 Score =  309 bits (792), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 151/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V  G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVEAGDIEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    +L +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RK + PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKXRQPSRSKPLRDFIE 368



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 68/138 (49%), Gaps = 22/138 (15%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDD------LED 85
           + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +       L +
Sbjct: 17  EFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNEGNPSARVLSN 76

Query: 86  EEGSEDS-LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           EE  E S  DL  S S                 +DPVRMYL+E+G + LL+ E E  +A 
Sbjct: 77  EEEPELSDEDLIGSTSAK--------------VNDPVRMYLKEIGVVPLLTNEEEKELAL 122

Query: 145 RIEAGRAMMMASLCESPL 162
            +EAG       L E+ L
Sbjct: 123 AVEAGDIEAKQRLAEANL 140


>gi|28211633|ref|NP_782577.1| RNA polymerase sigma factor RpoD [Clostridium tetani E88]
 gi|28204075|gb|AAO36514.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 366

 Score =  309 bits (792), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 198/238 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 129 ARKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 188

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK++ + V+ V
Sbjct: 189 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAKEMEISVDRV 248

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A    L+E    VL +LTPR
Sbjct: 249 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPAEAAAFTMLKEQLINVLDTLTPR 308

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 309 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 366



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 62/133 (46%), Gaps = 19/133 (14%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   ++ G +T +E+   L   E++ EQ+E     L +M I+V              
Sbjct: 23  KNLIDKGKKSGSLTYKEIMDELEEIELTPEQIEKVYEALESMNIDV-------------- 68

Query: 92  SLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              L +         ++   S     S DDPVRMYL+E+G + LL+ E E+ +A+RIEAG
Sbjct: 69  ---LGADEIKKEEEEEEIDISVPEGISIDDPVRMYLKEIGKVPLLTSEEEVDLAQRIEAG 125

Query: 150 RAMMMASLCESPL 162
                  L E+ L
Sbjct: 126 ELKARKKLAEANL 138


>gi|289450258|ref|YP_003475183.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184805|gb|ADC91230.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 353

 Score =  309 bits (791), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 148/273 (54%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E + +   +++G  EA   K  + EANLRLV+S+AK+Y  RG+
Sbjct: 84  VRMYLKEIGKVPLLNAEEEKDLARAMKEGSQEA---KDRLCEANLRLVVSIAKRYVGRGM 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 141 QFLDLIQEGNLGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 200

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REP  EE+A+++ +  E VR++ KI++EP+SLE PIG+E+ SHL
Sbjct: 201 INKLIRVQRQLLQELGREPEVEELAQEMGISPEKVREIQKISQEPVSLEKPIGEEEDSHL 260

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A SP D A    L+E    +L+ LTPREE+VLR+RFG+      TLEEVG++
Sbjct: 261 GDFIPDDDAPSPADQAAFTLLKEQLLEILSGLTPREEKVLRLRFGLDDGRSRTLEEVGRE 320

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RK++HPSRSKKL+ +LD
Sbjct: 321 FNVTRERIRQIEAKALRKMRHPSRSKKLKDYLD 353



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 111 DSAD-RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           DS+D  + DDPVRMYL+E+G + LL+ E E  +A+ ++ G       LCE+ L     I 
Sbjct: 73  DSSDVMNVDDPVRMYLKEIGKVPLLNAEEEKDLARAMKEGSQEAKDRLCEANLRLVVSIA 132

Query: 170 WR 171
            R
Sbjct: 133 KR 134


>gi|94263094|ref|ZP_01286913.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456637|gb|EAT06745.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 540

 Score =  309 bits (791), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 148/261 (56%), Positives = 192/261 (73%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+       I + + +G+  +  AK  +V+ANLRLV+SVAKKY  RGLQ LDLIQEGNIG
Sbjct: 279 GLDQEGLAEIQAGIARGQEVSQEAKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNIG 338

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA EKF++  GYKFSTYA WW++QA+TR+IADQ  TIRIPVHM D I+++++ A+   
Sbjct: 339 LMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQGRTIRIPVHMIDTINRMLKGAKEFQ 398

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  REPTP+E+A+ L + V  V+ VLKI KEP+SL+TP+G+ + S L DFIED  A SP
Sbjct: 399 RQHGREPTPDEMAQHLGVEVAKVKSVLKIAKEPLSLDTPVGNSNDSFLADFIEDTEAASP 458

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            ++ I  NL+    RVL +L+PREE VLR+RFG+    D TLEEVG+ F VTRERIRQIE
Sbjct: 459 DEATIYENLQSNLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQIE 518

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA++KLKHP+R  +L SF D
Sbjct: 519 AKALKKLKHPARRNQLSSFYD 539



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 42/67 (62%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPV++YL+EMGS+ LLS E EIA+A+ IEAG  ++  +L  +P     L    D++  G 
Sbjct: 98  DPVKVYLQEMGSVPLLSTEEEIAVAREIEAGELLIQQALLTAPPAIAYLSKLIDKVMAGN 157

Query: 179 TLLREII 185
             L +++
Sbjct: 158 RQLSDLL 164


>gi|312195623|ref|YP_004015684.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226959|gb|ADP79814.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 418

 Score =  309 bits (791), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 148/266 (55%), Positives = 204/266 (76%), Gaps = 4/266 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ E G+     R +V + R GE    IAK  +VEANLRLV+S+A++Y  RG+ FLDLIQ
Sbjct: 157 LAAENGLVGDLRRELVWVERDGE----IAKSRLVEANLRLVVSIARRYVGRGMLFLDLIQ 212

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R 
Sbjct: 213 EGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRI 272

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R++   + REPTPEEIAK++ +  + VR++ K+ +EPISLETPIG+E+ SHLGDFIED 
Sbjct: 273 QRQLLQDLGREPTPEEIAKEMDLTPDKVREIQKVAQEPISLETPIGEEEDSHLGDFIEDS 332

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +AV P+D+A    L+E    VL +L+ RE++V+++RFG+      TLEEVG++F VTRER
Sbjct: 333 DAVVPVDAASFLLLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRER 392

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 393 IRQIESKTLSKLRHPSRSQKLRDYLE 418



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 28/38 (73%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +ADR + D VR YL ++G + LL+ E E+ +AKR+EAG
Sbjct: 113 AADRMSHDSVRQYLSQIGRVRLLTAEEEVDLAKRVEAG 150


>gi|220927994|ref|YP_002504903.1| RNA polymerase sigma factor RpoD [Clostridium cellulolyticum H10]
 gi|219998322|gb|ACL74923.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulolyticum H10]
          Length = 359

 Score =  309 bits (791), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 197/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 122 AKRRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYRRGFKFSTYATWW 181

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP P+EIAK++ M V+ V
Sbjct: 182 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPDEIAKEIGMSVDKV 241

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI++EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E    VL +LTPR
Sbjct: 242 REIMKISQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTLLKEQLIDVLDTLTPR 301

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 302 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 359



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 64/131 (48%), Gaps = 12/131 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +Q+G +T +E+       E+  E +E     L  MG++V+   D E EE    
Sbjct: 13  KELIDRGKQKGMLTYKEIMDAFEEIELEPEHIEKIYETLETMGVDVIGDIDSEMEE---- 68

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            + L     + SV           S DDPVRMYL+E+G + LL+ + EI +A R+E G  
Sbjct: 69  -IQLTDEELDISV-------PEGVSIDDPVRMYLKEIGKVPLLTADEEIDLAHRMENGDI 120

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 121 EAKRRLAEANL 131


>gi|15606649|ref|NP_214029.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
 gi|2983864|gb|AAC07417.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
          Length = 575

 Score =  308 bits (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 166/409 (40%), Positives = 261/409 (63%), Gaps = 32/409 (7%)

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E+A+ YR L  +++  +    +E S  K      ++ K++  + +  ++ + + E     
Sbjct: 182 ELAKAYRNLLDVREEYIKNPSEE-SRKKYLYAHARMNKIIKEMKIKYAKFERVTE----- 235

Query: 346 SKRIMHNEGELLRLAQSYGIKR---DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
                    E++++ + Y  KR   +  + + +    DP +  +A++F   E    +  E
Sbjct: 236 ---------EIIKIYKEYARKRKDLNARIRKLKALYKDPDY--FAQNFLTDENLQKIVQE 284

Query: 403 ----VDSILKIRNEIKSIS-----VETGISI---SEFRHIVSMVRKGECEASIAKKEMVE 450
                + +L + NE  S+      ++  I +    E   ++ ++ +G  +   AK+ M++
Sbjct: 285 KNIPTEKVLNLINEYNSLKREVQRIQNLIGVFPEEELPKVMKIIEQGRKKVVQAKQVMIQ 344

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW++QAITR
Sbjct: 345 SNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITR 404

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+K+++ ++++  +  REPTPEEIA+ L +PVE V+KV+K +
Sbjct: 405 AIADQARTIRIPVHMIETINKIIKASKKLFQENGREPTPEEIAEYLDIPVEKVKKVMKFS 464

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +EPISLETPIGD+D + L DFIEDK+  +P +   +  LRE   +VL++L+ +E  +L  
Sbjct: 465 QEPISLETPIGDDDDTFLKDFIEDKSIPNPEEQVTRKLLREQLQKVLSTLSEKEREILMY 524

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+G+   T++TLE+VGK F VTRERIRQIE KA+RKL+HP+R+K L+ F
Sbjct: 525 RYGLVDGTEYTLEQVGKMFNVTRERIRQIENKALRKLRHPARAKYLKDF 573



 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 52/159 (32%), Positives = 87/159 (54%), Gaps = 7/159 (4%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +S K +I++ +++GYVT +E+N  L  D  SSE  E+ + +L  M I VV+  +  +EE 
Sbjct: 5   ESVKALIEMGKEKGYVTYDEINEVLEEDVTSSELFEELIDILHRMNIQVVESKEEYEEES 64

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E   +      + S+       ++     DPV++YLREMG I LL RE EI  A++IE 
Sbjct: 65  EETQEEEEEVVVSGSL-------TSSSRDGDPVKLYLREMGKIPLLKREEEIYYARQIEI 117

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           GR +M   L  +    + ++    +L +G   ++E++DL
Sbjct: 118 GRKIMRRGLMRTSFLVEKILDDWAKLCNGKLKIQEVMDL 156


>gi|218962087|ref|YP_001741862.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730744|emb|CAO81656.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
          Length = 579

 Score =  308 bits (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 153/284 (53%), Positives = 212/284 (74%), Gaps = 4/284 (1%)

Query: 403 VDSILKIRN---EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           V+++ KI+N   +I+ + +ET ++ ++   ++  + + E     A+ EM+EAN+RLVIS+
Sbjct: 292 VETLRKIKNARRKIRRVELETKMTGNKLIFLLREIDRAERNKERAQNEMIEANVRLVISI 351

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK Y NRGL+FLDLIQEGN GLM+A EK+D+  GYKFSTYA WW++QAITR+IADQ+ TI
Sbjct: 352 AKHYNNRGLEFLDLIQEGNTGLMRAVEKYDYRKGYKFSTYATWWIRQAITRAIADQARTI 411

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+ RT+RR+  K+ REP PEEI++ L +PVE ++ ++ I+KEP+SL+ P
Sbjct: 412 RIPVHMIESINKINRTSRRLMQKLGREPYPEEISEVLDIPVEKIKNIMSISKEPVSLDKP 471

Query: 580 IG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           IG D + S LGDFIED+  +SP   A ++ L++    VL +LTPREERV+R+RFGI    
Sbjct: 472 IGHDSEDSILGDFIEDRTIISPERLAERSLLKKQVDEVLKTLTPREERVIRLRFGIDDGY 531

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             TLEEVG  F VTRERIRQIE KA++KL+HPSR+  L+ FLD 
Sbjct: 532 HRTLEEVGNIFQVTRERIRQIEDKALKKLRHPSRAAILQQFLDN 575



 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 49/137 (35%), Positives = 77/137 (56%), Gaps = 12/137 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           ++  KK+++L ++ GY+T +++N  LPP     ++++D +  LS  GI ++D    E E+
Sbjct: 5   NECLKKLVELGKESGYITFKQINEILPPSPFFLDKVDDIIFDLSQDGIEIID----ETEK 60

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               S       S +  F  KR        DDPVRMYLREMG + LL REGE+ +AK+IE
Sbjct: 61  RITKSGAAIRKPSTAKKFKSKR------YYDDPVRMYLREMGRVPLLDREGEVRVAKKIE 114

Query: 148 AGRAMMMASL--CESPL 162
             + M+  ++  C S L
Sbjct: 115 TYQKMINQNVFKCGSTL 131


>gi|225026302|ref|ZP_03715494.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
 gi|224956366|gb|EEG37575.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
          Length = 367

 Score =  308 bits (789), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 143/238 (60%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K+++EANLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA EKFD+  G KFSTY+ WW
Sbjct: 130 ARKQLIEANLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVEKFDYKKGNKFSTYSTWW 189

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR IAD + TIR+PVHM + I+K +RT+R +  ++ REPT EEIAKK+ MPV  +
Sbjct: 190 IRQAITRGIADTAKTIRVPVHMVETINKTLRTSRMLLQELGREPTNEEIAKKMNMPVAKI 249

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK +++P+SL+TPIG+E+ S LGDFIED++ +SP+DSA  + L+E     +ASLT R
Sbjct: 250 DEILKTSRDPVSLDTPIGEEEDSQLGDFIEDESLLSPVDSASFSMLKEELEEAMASLTER 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ FL+
Sbjct: 310 ERNVIKLRFGLDDGKTRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDFLE 367



 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 48/189 (25%), Positives = 81/189 (42%), Gaps = 22/189 (11%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           FS+   K + +  + +  +  +E+N      E++ E+ E  +      G++V++     +
Sbjct: 8   FSNIMEKLLKQAHKNKNVLEYKEINDAFKNIELTPEKFEWILDYFEKQGVDVLNT----N 63

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSAD----RSTDDPVRMYLREMGSIELLSREGEIA 141
           EE   D   +        +      D AD     S +DPVRMYL+E+G+I LL+ E E+ 
Sbjct: 64  EEDDGDDNFIDDDTEEVEII-----DDADILEGVSLEDPVRMYLKEIGNIPLLTAEEEVF 118

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           +A+RIE G       L E+ L    + I +  +  G + L  I         E   G   
Sbjct: 119 LAQRIEKGDEQARKQLIEANLRL-VVSIAKKYVGRGMSFLDLI--------QEGNMGLMK 169

Query: 202 GTEGHSYQK 210
             E   Y+K
Sbjct: 170 AVEKFDYKK 178


>gi|304439790|ref|ZP_07399688.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371777|gb|EFM25385.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 370

 Score =  308 bits (789), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 148/252 (58%), Positives = 198/252 (78%), Gaps = 3/252 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   + KG+ EA+   +E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD
Sbjct: 122 IAKRMEKGDREAA---RELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFD 178

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+P
Sbjct: 179 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSP 238

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEIA+++ + VE VR++ KI +EP+SLETPIG+E+ SHLGDFI D+   SP D+A    L
Sbjct: 239 EEIAEEMNIDVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIPDEEIQSPQDAATFTLL 298

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE    VL +LT RE++VL +RFG+    + TLEEVGK+F VTRERIRQIEAKA+RKL+H
Sbjct: 299 REQLGDVLDTLTDREKKVLTLRFGLEDGRNRTLEEVGKEFDVTRERIRQIEAKALRKLRH 358

Query: 670 PSRSKKLRSFLD 681
           PSRS+KL+ +L+
Sbjct: 359 PSRSRKLKDYLE 370



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 49/149 (32%), Positives = 78/149 (52%), Gaps = 12/149 (8%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           + ED D S+  D   DS   ++K  +++G +T EE+   L    + S++++         
Sbjct: 6   DFEDEDQSMSKDSIVDS---LMKTGKKKGNLTYEEIVDALDEIPMESDEIDSLYKEFEKK 62

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           GI ++D +  +DE+  +D +DL  S  + SV           S DDPVRMYL+E+G I L
Sbjct: 63  GIELLDEEIGDDEDDDDDKIDL--SKEDLSV-------PKGISVDDPVRMYLKEIGKIPL 113

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPL 162
           L+ + E+ IAKR+E G       L E+ L
Sbjct: 114 LTADEEVVIAKRMEKGDREAARELAEANL 142


>gi|94266972|ref|ZP_01290621.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93452327|gb|EAT02958.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 353

 Score =  308 bits (789), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 147/252 (58%), Positives = 190/252 (75%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I + + +G+  +  AK  +V+ANLRLV+SVAKKY  RGLQ LDLIQEGNIGLMKA EKF+
Sbjct: 101 IQAGIARGQEVSQEAKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNIGLMKAVEKFE 160

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QA+TR+IADQ  TIRIPVHM D I+++++ A+    +  REPTP
Sbjct: 161 YRRGYKFSTYATWWIRQAVTRAIADQGRTIRIPVHMIDTINRMLKGAKEFQRQHGREPTP 220

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +E+A+ L + V  V+ VLKI KEP+SL+TP+G+ + S L DFIED  A SP ++ I  NL
Sbjct: 221 DEMAQHLGVEVAKVKSVLKIAKEPLSLDTPVGNSNDSFLADFIEDTEAASPDEATIYENL 280

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    RVL +L+PREE VLR+RFG+    D TLEEVG+ F VTRERIRQIEAKA++KLKH
Sbjct: 281 QSNLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQIEAKALKKLKH 340

Query: 670 PSRSKKLRSFLD 681
           P+R  +L SF D
Sbjct: 341 PARRNQLSSFYD 352


>gi|210620870|ref|ZP_03292287.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
 gi|210155082|gb|EEA86088.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
          Length = 388

 Score =  308 bits (789), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 145/239 (60%), Positives = 194/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA W
Sbjct: 150 LAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYEKGFKFSTYATW 209

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+  PEEIAK++ + VE 
Sbjct: 210 WIRQAITRAIADQARTIRIPVHMVETINKLMRVSRQLLQELGRDAKPEEIAKEMDLSVEK 269

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A +P  SA  + L+E    VL SL  
Sbjct: 270 VREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPDISAAYSLLKEQIDEVLGSLNE 329

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 330 REQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 388



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 44/150 (29%), Positives = 66/150 (44%), Gaps = 12/150 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE----GS 89
           +I   ++ G +T EE+       E++ EQM++    L ++GI +VD    ++      G+
Sbjct: 20  LILKGKKNGSLTFEEIGDAFETVEMNKEQMDNLYDTLQSVGIELVDEKSKKNNATFAVGN 79

Query: 90  EDSLDLASSASNSSVFLQKRKDS--------ADRSTDDPVRMYLREMGSIELLSREGEIA 141
            D +         S    K  DS           S DDPVRMYL+E+G I LL    E+ 
Sbjct: 80  NDDMGFDHIDDPDSDDDDKDGDSEALDLSLPKGISIDDPVRMYLKEIGKIPLLKPHEEVE 139

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            AKR+  G  +    L E+ L     I  R
Sbjct: 140 YAKRMHEGDELAKQRLVEANLRLVVSIAKR 169


>gi|269792833|ref|YP_003317737.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100468|gb|ACZ19455.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 387

 Score =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++VEANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 150 AKEKLVEANLRLVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEKFDYRKGYKFSTYATWW 209

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R +  ++ REP+ EEIA+++ + V+ V
Sbjct: 210 IRQAITRAIADQARTIRIPVHMVETINKLIRISRVLVQRLGREPSAEEIAQEMGVTVDRV 269

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ KI +EP+SLETPIG+E+ S LGDF+EDK+  SP ++A    LRE    +L  LT R
Sbjct: 270 EEIQKIAQEPVSLETPIGEEEDSQLGDFLEDKDLPSPDEAAANQILREQLEEMLEDLTDR 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ VLR+RFG+     HTLEEVG++F VTRERIRQIEAKA+RKL+HPSRSK+LR FLD
Sbjct: 330 EKEVLRLRFGLEDGHSHTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSKRLRDFLD 387



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 46/133 (34%), Positives = 69/133 (51%), Gaps = 18/133 (13%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------GDDLEDEEGSED 91
           AR++G+VT +++   LP + +S++ +++    L  +GI+VVD      GD +      E+
Sbjct: 41  AREKGFVTYDDIEKHLPKELLSADVLDNLYYNLMELGIDVVDETKAQRGDSI-----GEE 95

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L   S A +         D  D    DPVRMYLRE+G I LLS E E+ +AK +EAG  
Sbjct: 96  VLPQISPADDLG-------DLEDLPLSDPVRMYLREIGRIPLLSPEEEVELAKGVEAGDK 148

Query: 152 MMMASLCESPLTF 164
                L E+ L  
Sbjct: 149 RAKEKLVEANLRL 161


>gi|188585841|ref|YP_001917386.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350528|gb|ACB84798.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 360

 Score =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ EANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 123 AKRKLAEANLRLVVSIAKKYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 182

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA+++ M  + V
Sbjct: 183 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLVQELGREPLPEEIAEQMDMSEDKV 242

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+ED SHLGDFIED++A  P D+A    L+     VL SLTPR
Sbjct: 243 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDAKPPADAAAFELLKGQLEEVLDSLTPR 302

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP RSK+L+ +LD
Sbjct: 303 EQKVLRLRFGLDDGKTRTLEEVGKHFGVTRERIRQIEAKALRKLRHPMRSKRLKDYLD 360



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 44/132 (33%), Positives = 70/132 (53%), Gaps = 19/132 (14%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---DLEDEEGSE 90
           ++K+ ++RG++T +E+   L   ++SS+Q+++   +L+  GI+VVD     D +D   +E
Sbjct: 17  LLKVGKERGFLTYKEIMDQLSEFQLSSDQIDEFYEVLTQAGIDVVDAIGEVDPDDPTKAE 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             L L      S                DPVRMYL+E+G I LLS + EI +AK+IE G 
Sbjct: 77  LDLSLPEGVEVS----------------DPVRMYLKEIGKIPLLSPDDEIELAKKIEEGD 120

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 121 EGAKRKLAEANL 132


>gi|225174152|ref|ZP_03728151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169937|gb|EEG78732.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 372

 Score =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+ + EANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 122 IALAKRMEAGDEEAKRRLAEANLRLVVSIAKKYVGRGMLFLDLIQEGNLGLIKAVEKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP P+
Sbjct: 182 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLVQELGREPAPD 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  + +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED++  +P ++A    L+
Sbjct: 242 EIAHVMNISEERVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDVQAPAEAAAFELLK 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LTPRE++VL +RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLDDVLETLTPREKKVLTLRFGLEDGRSRTLEEVGQVFGVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
            RSK+L+ +L+
Sbjct: 362 MRSKRLKDYLE 372



 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 75/131 (57%), Gaps = 4/131 (3%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSED 91
           ++++  ++RG +T +E+   L   ++S+E++++    LS +G++VVD   +LE  +  E+
Sbjct: 17  ELVQRGKKRGLLTYKEIIEPLQEMDLSAEEIDEFYDHLSRLGVDVVDDVAELETLDVDEE 76

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           ++          + L   +       +DPVRMYL+E+G I LLS + EIA+AKR+EAG  
Sbjct: 77  TIKEEEDTPEEEIDLTVPEGIG---VNDPVRMYLKEIGKIPLLSSDEEIALAKRMEAGDE 133

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 134 EAKRRLAEANL 144


>gi|227499199|ref|ZP_03929334.1| RNA polymerase [Acidaminococcus sp. D21]
 gi|226904646|gb|EEH90564.1| RNA polymerase [Acidaminococcus sp. D21]
          Length = 582

 Score =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 191/239 (79%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 344 AKKALSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYATWW 403

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REPTPEEIA+++ +PVE V
Sbjct: 404 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQELGREPTPEEIAQEMDVPVERV 463

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++ KI +EP+SLETPIG+E+ SHLGDFIED+ A SP ++A    L+E   +VL   L+P
Sbjct: 464 REIQKIAQEPVSLETPIGEEEDSHLGDFIEDQEAPSPAEAASYTLLQEQLGKVLQEHLSP 523

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE RVL +RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+ P RSK L+ FL+
Sbjct: 524 RERRVLELRFGLLDGRTRTLEEVGQYFGVTRERIRQIEAKALRKLRSPKRSKPLKEFLE 582



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 38/109 (34%), Positives = 55/109 (50%), Gaps = 10/109 (9%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA---SSASNSSVFLQKRKDS 112
           D +S ++M++  + L+   I VVD    E+E  + D  +L    S  SN SV        
Sbjct: 93  DSISVDEMDEIYSKLAEKNIEVVDDHAEEEEPENMDDEELTIEESELSNLSV-------P 145

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
                DDPVRMYL+E+G + LLS   EI +AKR + G    +    +SP
Sbjct: 146 EGVIVDDPVRMYLKEIGRVPLLSGNDEIKLAKRTDKGNQAAVILDGQSP 194


>gi|288916958|ref|ZP_06411330.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288351667|gb|EFC85872.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score =  308 bits (788), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 142/244 (58%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 149 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 208

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 209 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 268

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 269 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 328

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR
Sbjct: 329 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLR 388

Query: 678 SFLD 681
            +L+
Sbjct: 389 DYLE 392



 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 66/121 (54%), Gaps = 10/121 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K +I   ++ G++T E++   +   E+  EQ E  + +L++ GI V+       E G
Sbjct: 13  DEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAETVLQVLNDEGIEVL-------EAG 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E++ D A   +      ++    A   T DPVRMYL+E+G + LL+ E E+ +AKRIEA
Sbjct: 66  GENA-DEADLLARRRREEEELALKA--PTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEA 122

Query: 149 G 149
           G
Sbjct: 123 G 123


>gi|163815580|ref|ZP_02206953.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
 gi|158449217|gb|EDP26212.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
          Length = 399

 Score =  307 bits (787), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 141/250 (56%), Positives = 196/250 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     AKK++ E+NLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 148 IELAKRMEAGDEAAKKKLAESNLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 207

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV R +R +  K+ REP PE
Sbjct: 208 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVTRVSRDLLQKLGREPLPE 267

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+ + + +P E V++++KI +EP+SLETPIG+E+ SHLGDFI+D++  +P+++  Q  L 
Sbjct: 268 EVGEVMGLPKERVQEIMKIAQEPVSLETPIGEEEDSHLGDFIQDESIPTPVEATNQTLLH 327

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    V+++LT RE+RV+++RFG       TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 328 EQLDDVVSTLTEREQRVIKLRFGWDDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHP 387

Query: 671 SRSKKLRSFL 680
           +RS+KL+ FL
Sbjct: 388 NRSRKLKDFL 397



 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/100 (33%), Positives = 52/100 (52%), Gaps = 1/100 (1%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           M+     L   G++++   D ++EE + D   +A       +      D +  +T DPV+
Sbjct: 72  MQKIFNFLEQNGVDILQITDTDEEEPALDEDVIAEGEEVEKIDFTDTGDISS-TTQDPVK 130

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           MYL+++G + LLS E EI +AKR+EAG       L ES L
Sbjct: 131 MYLKDIGKVPLLSAEEEIELAKRMEAGDEAAKKKLAESNL 170


>gi|158313963|ref|YP_001506471.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158109368|gb|ABW11565.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 409

 Score =  307 bits (787), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 142/244 (58%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 285

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 286 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 345

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR
Sbjct: 346 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLR 405

Query: 678 SFLD 681
            +L+
Sbjct: 406 DYLE 409



 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 66/121 (54%), Gaps = 10/121 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K +I   ++ G++T E++   +   E+  EQ E  + +L++ GI V+       E G
Sbjct: 30  DEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAETVLQVLNDEGIEVL-------EAG 82

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E++ D A   +      ++    A   T DPVRMYL+E+G + LL+ E E+ +AKRIEA
Sbjct: 83  GENA-DEADLLARRRREEEELALKA--PTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEA 139

Query: 149 G 149
           G
Sbjct: 140 G 140


>gi|86739990|ref|YP_480390.1| sigma 38 [Frankia sp. CcI3]
 gi|86566852|gb|ABD10661.1| RNA polymerase, sigma 70 subunit, RpoD [Frankia sp. CcI3]
          Length = 409

 Score =  307 bits (787), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 142/244 (58%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 285

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 286 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 345

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR
Sbjct: 346 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLR 405

Query: 678 SFLD 681
            +L+
Sbjct: 406 DYLE 409



 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 40/121 (33%), Positives = 64/121 (52%), Gaps = 10/121 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K +I   ++ G++T E++   +   E+  EQ E  + +L++ GI V+        E 
Sbjct: 30  DEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAETVLQVLNDEGIEVL--------EA 81

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +S D A   +      ++    A   T DPVRMYL+E+G + LL+ E E+ +AKRIEA
Sbjct: 82  GGESPDEADLLARRRREEEELALKA--PTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEA 139

Query: 149 G 149
           G
Sbjct: 140 G 140


>gi|111221463|ref|YP_712257.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
 gi|111148995|emb|CAJ60675.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
          Length = 409

 Score =  307 bits (787), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 142/244 (58%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 285

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 286 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 345

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR
Sbjct: 346 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLR 405

Query: 678 SFLD 681
            +L+
Sbjct: 406 DYLE 409



 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 65/121 (53%), Gaps = 10/121 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K +I   ++ G++T E++   +   E+  EQ E  + +L++ GI V+       E G
Sbjct: 30  DEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAETVLQVLNDEGIEVL-------EAG 82

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E+  D A   +      ++    A   T DPVRMYL+E+G + LL+ E E+ +AKRIEA
Sbjct: 83  GENP-DEADLLARRRREEEELALKA--PTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEA 139

Query: 149 G 149
           G
Sbjct: 140 G 140


>gi|323704675|ref|ZP_08116253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323536137|gb|EGB25910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 357

 Score =  307 bits (786), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 156/273 (57%), Positives = 210/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + KG+ EA   KK + EANLRLV+S+AK+Y  RG+
Sbjct: 88  VRMYLKEIGKIPLLSPDEEIELAKRIEKGDEEA---KKRLTEANLRLVVSIAKRYVGRGM 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 145 LFLDLIQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 204

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P PEEIAK++ M V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 205 INKLIRVSRQLLQELGRDPLPEEIAKEMDMSVDKVREIMKIAQEPVSLETPIGEEEDSHL 264

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 265 GDFIPDEDAPAPAEAAAFTMLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 324

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 325 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 67/134 (50%), Gaps = 12/134 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +S K++I   ++ G +T  E+   L   ++ ++Q+E        +GI +V  +  +DE  
Sbjct: 8   NSIKELIDKGKKNGMLTYNEIMNSLEDIDMDADQIEKVYDTFEKLGIEIVGEEPQQDELI 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E+ LDL  +                 + DDPVRMYL+E+G I LLS + EI +AKRIE 
Sbjct: 68  PEEDLDLDLTIPEGI------------NIDDPVRMYLKEIGKIPLLSPDEEIELAKRIEK 115

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 116 GDEEAKKRLTEANL 129


>gi|289642669|ref|ZP_06474809.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507499|gb|EFD28458.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 392

 Score =  307 bits (786), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 141/244 (57%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 149 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 208

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QA+TR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 209 TYATWWIRQAVTRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 268

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 269 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 328

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR
Sbjct: 329 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLR 388

Query: 678 SFLD 681
            +L+
Sbjct: 389 DYLE 392



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/123 (30%), Positives = 64/123 (52%), Gaps = 14/123 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDDLEDE 86
           D  K +I   ++ G++T E++   L   E+  EQ +  + +L++ GI +++  G+D E+ 
Sbjct: 13  DEVKDLITRGKEIGFLTTEDVTVALQAAELPPEQTDAVLQVLNDEGIEILEAGGEDAEEN 72

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +            +  +             T DPVRMYL+E+G + LL+ E E+ +AKRI
Sbjct: 73  DLLARRRREEEELALKA------------PTSDPVRMYLKEIGKVPLLTAEEEVDLAKRI 120

Query: 147 EAG 149
           EAG
Sbjct: 121 EAG 123


>gi|269836760|ref|YP_003318988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786023|gb|ACZ38166.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 538

 Score =  307 bits (786), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 144/239 (60%), Positives = 192/239 (80%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IA+K++ EANLRLV+SVAKKY  RG+  LDL+QEGN+GL++A EKF    G+KFSTYA W
Sbjct: 300 IARKKLTEANLRLVVSVAKKYGGRGMSMLDLVQEGNLGLIRAVEKFQHHKGFKFSTYATW 359

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM ++I++++RT+RR+  ++ REPT EEIA ++ +P + 
Sbjct: 360 WIRQAITRAIADQARTIRIPVHMVEQINRLIRTSRRLQQELGREPTSEEIAAEMGLPPDK 419

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++LKI++EP+SLE PIG+E+ S+LGDFIED  A++P D+A    L+E    VL SL  
Sbjct: 420 VREILKISQEPVSLEMPIGEEEDSNLGDFIEDSKALAPSDAASLKLLKEQVDDVLGSLGD 479

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE RVL +RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKLR +L+
Sbjct: 480 RERRVLELRFGLDDGRTRTLEEVGREFGVTRERIRQIEAKALRKLRHPSRSKKLRDYLE 538



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 72/120 (60%), Gaps = 8/120 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I+ AR++GY++ EEL A +      +  ++   + L+ M + V+D       E + D
Sbjct: 43  RRIIERAREQGYLSAEEL-ADVASAPGGAAAVDAITSQLAEMNVPVLD-----PAEDAPD 96

Query: 92  SLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             D+A+  +++ +F  +  D   +  S DDPVR+YLRE+G ++LL+ E E+A+A+ +E G
Sbjct: 97  LPDVAAVEADNDLFSTELSDVDLSGVSLDDPVRIYLREIGRVQLLTGEQEVALAQAMERG 156


>gi|40353297|gb|AAR84412.1| essential primary sigma 70 factor [Frankia sp. EaI-12]
          Length = 409

 Score =  307 bits (786), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 142/244 (58%), Positives = 198/244 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 285

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 286 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 345

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR
Sbjct: 346 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLR 405

Query: 678 SFLD 681
            +L+
Sbjct: 406 DYLE 409



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 68/125 (54%), Gaps = 18/125 (14%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K +I   ++ G++T E++   +   E+  EQ E  + +L++ GI V+       E G
Sbjct: 30  DEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAETVLQVLNDEGIEVL-------EAG 82

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRS----TDDPVRMYLREMGSIELLSREGEIAIAK 144
            E+       A    +  ++R++  + +    T +PVRMYL+E+G + LL+ E ++ +AK
Sbjct: 83  GEN-------ADEPDLLARRRREKEELALKAPTSEPVRMYLKEIGKVPLLTAEEQVDLAK 135

Query: 145 RIEAG 149
           RIEAG
Sbjct: 136 RIEAG 140


>gi|289523410|ref|ZP_06440264.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503102|gb|EFD24266.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 412

 Score =  307 bits (786), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 142/234 (60%), Positives = 185/234 (79%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++EANLRLV+S+AKKY  RGL FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QA
Sbjct: 179 LIEANLRLVVSIAKKYIGRGLSFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQA 238

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPT EEIA+ L +P E V  + 
Sbjct: 239 ITRAIADQARTIRIPVHMVETINKLIRVSRQLVQQLGREPTIEEIAQSLGLPPEKVEDIQ 298

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           +I +EP+SLETPIG+E+ S LGDF+EDK + +P D+     LRE    +L  LT RE  V
Sbjct: 299 RIAQEPVSLETPIGEEEDSQLGDFLEDKESPNPEDATAGQLLREQLEEMLGELTEREREV 358

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LR+RFG+     HTLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSK+LR +L+
Sbjct: 359 LRLRFGLEDGHAHTLEEVGKRFNVTRERIRQIEAKALRKLRHPSRSKRLRDYLE 412



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 76/135 (56%), Gaps = 10/135 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVS-SEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           ++ +++++  RQ+G++T ++L  +LP + +S ++ M++  + L  +GI+V + D L+   
Sbjct: 59  ENIRELLQEGRQKGFITYDDLEKYLPQEALSEADIMDNVYSNLLELGIDVKEEDKLQ--- 115

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                 ++        V L++  D    S  DPVRMYLRE+G I LL+ E E+ +AKR+E
Sbjct: 116 ------EIRQGELLPQVSLEELSDIESVSISDPVRMYLREIGKISLLTPEEEVELAKRVE 169

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 170 EGEEEAKKKLIEANL 184


>gi|167463432|ref|ZP_02328521.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 375

 Score =  306 bits (785), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 151/251 (60%), Positives = 198/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD 
Sbjct: 125 VELAKRIEQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDH 184

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 185 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPE 244

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ +  + VR+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+
Sbjct: 245 EIAKEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLK 304

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 305 EQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 364

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 365 SRSKRLKDFLE 375



 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/135 (34%), Positives = 74/135 (54%), Gaps = 13/135 (9%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE----- 87
           ++I+L ++R  +T +E+   L P +  +EQ++D    LS MGI+V  G++ +D+E     
Sbjct: 21  QLIELGKKRSSLTYKEIMDRLAPYDQDAEQIDDFFEHLSEMGIDV--GNENDDDEDNIRP 78

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+ D+ D   +  +        K       +DPVRMYL+E+G + LLS E E+ +AKRIE
Sbjct: 79  GNTDNEDEDFNFEDDLTLPPGIK------INDPVRMYLKEIGRVPLLSAEDEVELAKRIE 132

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 133 QGDEEAKRRLTEANL 147


>gi|315645989|ref|ZP_07899110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315278750|gb|EFU42064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 376

 Score =  306 bits (785), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 139 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA ++ + VE V
Sbjct: 199 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMELSVEKV 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    VL +LT R
Sbjct: 259 REIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTER 318

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 319 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 376



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 47/147 (31%), Positives = 76/147 (51%), Gaps = 3/147 (2%)

Query: 17  DSDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           D    L  +F+ D  K ++I+  ++R  ++ +++   L P +  +EQME+    L+++GI
Sbjct: 4   DQHTELETEFTLDQVKDQLIEQGKKRSVLSYKDIMEKLSPFDQDTEQMEEFYEQLADLGI 63

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           +VV+ +D  DE     S D  S  +    F            +DPVRMYL+E+G + LLS
Sbjct: 64  DVVNEND--DEGTHRQSEDSESRENEDFGFDDDLSLPPGIKINDPVRMYLKEIGRVPLLS 121

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPL 162
            + EI +A RIE G       L E+ L
Sbjct: 122 ADDEIELANRIEQGDEEAKRRLAEANL 148


>gi|306820486|ref|ZP_07454120.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551472|gb|EFM39429.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 538

 Score =  306 bits (785), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 154/286 (53%), Positives = 211/286 (73%), Gaps = 9/286 (3%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           KN V   V   LK   +I+ ++VE    +SE      MV+  E     AK ++VEANLRL
Sbjct: 262 KNNVDDPVRMYLKEIGKIQLLTVEEEHRLSEL-----MVKGDEY----AKMKIVEANLRL 312

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ
Sbjct: 313 VVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQ 372

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++  ++ R+P PEEIA+++ M  + +R+++KI +EP+S
Sbjct: 373 ARTIRIPVHMVETINKLIRINRQLVQELGRDPRPEEIAEQMGMSQDKIREIMKIAQEPVS 432

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFI D +A +P ++A  + LRE   +VL +LT RE RVL++RFG+ 
Sbjct: 433 LETPIGEEEDSHLGDFIPDDDAQAPSEAAAYSLLREQIEQVLCTLTDRERRVLKLRFGLD 492

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVGK+F VTRERIRQIEAKA+RKL+ P +S KL+ +LD
Sbjct: 493 DGRPRTLEEVGKEFDVTRERIRQIEAKALRKLRGPKKSNKLKDYLD 538



 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 42/170 (24%), Positives = 78/170 (45%), Gaps = 24/170 (14%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           S ++D +D L     + + + +I+  R+ GY+  + +   +   ++  E++ED     ++
Sbjct: 163 SVYDDKEDILSVMEYEKAVQGLIEKGRRDGYIDYDTIMNTVDNYDIGKEKIEDMYDRFAS 222

Query: 73  MGINVVDGDDL-----------EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            GI+++D  D            +  EG  D L L  S + ++V             DDPV
Sbjct: 223 FGIDIIDDMDKDTPHDEAKGGEQKSEGDFDLLSLELSLTKNNV-------------DDPV 269

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           RMYL+E+G I+LL+ E E  +++ +  G       + E+ L     I  R
Sbjct: 270 RMYLKEIGKIQLLTVEEEHRLSELMVKGDEYAKMKIVEANLRLVVSIAKR 319


>gi|150015739|ref|YP_001307993.1| RNA polymerase sigma factor RpoD [Clostridium beijerinckii NCIMB
           8052]
 gi|149902204|gb|ABR33037.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 376

 Score =  306 bits (785), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 139 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEI+K + +PV+ V
Sbjct: 199 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPFPEEISKVMELPVDKV 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTPR
Sbjct: 259 REIQKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPR 318

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 319 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 376



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 66/131 (50%), Gaps = 17/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   ++ G +T +E+   +   ++S EQ+E    +L   G+ ++   ++ D E +E+
Sbjct: 35  KELIDKGKKNGSLTYKEIMEAMDHIDLSPEQIEKIYEVLEMTGVEIIG--EIADTE-TEE 91

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL+     +               DDPVRMYL+E+G + LLS E EI  AK IE G  
Sbjct: 92  EIDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLSSEQEITYAKEIEEGNQ 137

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 138 KAKKKLAEANL 148


>gi|160915039|ref|ZP_02077252.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
 gi|158432838|gb|EDP11127.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
          Length = 398

 Score =  306 bits (785), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 148/239 (61%), Positives = 188/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK+++ ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 158 AKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++   + R+PT EEIA K+  +  E 
Sbjct: 218 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPTAEEIAAKMENISPEK 277

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  EP+SLETPIG+ED SHLGDFIEDK A+SP + A    L++    VL  LT 
Sbjct: 278 VREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTE 337

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 338 REEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 396



 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 33/51 (64%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           AS+     Q   +S+    +DPV+MYL+E+G +ELL  + E  IA+RI+AG
Sbjct: 104 ASDIEHLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAG 154


>gi|261405623|ref|YP_003241864.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329925852|ref|ZP_08280581.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261282086|gb|ACX64057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328939598|gb|EGG35946.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 377

 Score =  306 bits (785), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 140 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWW 199

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA ++ + VE V
Sbjct: 200 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMELSVEKV 259

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    VL +LT R
Sbjct: 260 REIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTER 319

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 320 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 60.5 bits (145), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 48/148 (32%), Positives = 77/148 (52%), Gaps = 5/148 (3%)

Query: 17  DSDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           D    L  +F+ D  K ++I+  ++R  ++ +++   L P +  +EQME+    L+++GI
Sbjct: 5   DQHTELETEFTLDQVKDQLIEQGKKRSVLSYKDIMEKLSPFDQDTEQMEEFYEQLADLGI 64

Query: 76  NVVDGDDLEDEEGSE-DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           +VV+ +D   EEG    S D  S  +    F            +DPVRMYL+E+G + LL
Sbjct: 65  DVVNEND---EEGPHRQSGDSESHDNEDFGFDDDLSLPPGIKINDPVRMYLKEIGRVPLL 121

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPL 162
           S + EI +A RIE G       L E+ L
Sbjct: 122 SADDEIELANRIEQGDEEAKRRLAEANL 149


>gi|282891123|ref|ZP_06299627.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498940|gb|EFB41255.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 546

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 151/291 (51%), Positives = 212/291 (72%), Gaps = 3/291 (1%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P  E   + A ++++    + ++K   +  G S+ +F+  V M+++   ++  AK+EMVE
Sbjct: 254 PRAERNKYAAAKLNAA---KRKLKKRELAAGRSLEDFKKDVRMLQRWMDKSQEAKREMVE 310

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR
Sbjct: 311 SNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTR 370

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIPVHM + I+KV+R A+++  +  REP+PEE+A +L +  E VR++ KI 
Sbjct: 371 AIADQARTIRIPVHMIETINKVLRGAKKLMMETGREPSPEELANELGITAERVREIYKIA 430

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           + PISL+  +GD   S  GDF+ED  A SP ++   + L++    VLA+LT RE +VL  
Sbjct: 431 QHPISLQAEVGDGGESQFGDFLEDTGADSPAEATGYSILKDKMNEVLATLTDRERKVLIQ 490

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFG+      TLEEVG +F VTRERIRQIEAKA+RK++HP+RSK+L++FLD
Sbjct: 491 RFGLLDGKPKTLEEVGVEFNVTRERIRQIEAKALRKMRHPTRSKQLKAFLD 541



 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/117 (35%), Positives = 67/117 (57%), Gaps = 10/117 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           ++ LA+++GY+T EE+N  LP    +++Q++  +  LS M + V++       +   +  
Sbjct: 21  LVSLAKEQGYITYEEINEILPMTFDNADQIDQVLIFLSGMDVQVLN-------QAEVERQ 73

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                 +     L KR +    S DDPVRMYL+EMGS+ LLSRE E+ I+KRIE  +
Sbjct: 74  KEKKKEAKEMEGLPKRSEG---SPDDPVRMYLKEMGSVPLLSREEEVEISKRIEKAQ 127


>gi|308069922|ref|YP_003871527.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|310643031|ref|YP_003947789.1| RNA polymerase sigma factor rpod [Paenibacillus polymyxa SC2]
 gi|305859201|gb|ADM70989.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|309247981|gb|ADO57548.1| RNA polymerase sigma factor rpoD [Paenibacillus polymyxa SC2]
          Length = 377

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 140 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYEKGFKFSTYATWW 199

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEE+A ++ + VE V
Sbjct: 200 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEVAAEMELSVEKV 259

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    VL +LT R
Sbjct: 260 REIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTER 319

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 320 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/152 (26%), Positives = 75/152 (49%), Gaps = 4/152 (2%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + +  L  D   D   ++I+L ++   +  +++   L P +   EQM++    L
Sbjct: 2   ANDQHTELETELTLDQVKD---QLIELGKKSSSLNYKDIMEKLSPFDQDPEQMDEFYEQL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            ++GI VV+ +D E     ++  D  ++  +   F            +DPVRMYL+E+G 
Sbjct: 59  GDLGIEVVNDNDEEVTRLRQND-DPENNDGDDFNFDDDLSLPPGIKINDPVRMYLKEIGR 117

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + LLS + E+ +AKRI  G       L E+ L
Sbjct: 118 VPLLSADDEVELAKRINNGDEEAKRRLAEANL 149


>gi|293375429|ref|ZP_06621710.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325844412|ref|ZP_08168139.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645982|gb|EFF64011.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489086|gb|EGC91470.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 464

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 145/242 (59%), Positives = 192/242 (79%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA  AKK +VE+NLRLV+S+A+++  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTY
Sbjct: 222 EAEYAKKRLVESNLRLVVSIARRHIGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTY 281

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP PEEIA+K+ + 
Sbjct: 282 ATWWIRQAITRAIADQARTIRIPVHMIETINKLVRIQRQLVQELGREPLPEEIAEKMEIT 341

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E  R++LKI++EPISLE+P+GDE  S LGDFI D +A+SP D      L++    VL +
Sbjct: 342 PEKAREILKISQEPISLESPVGDEADSSLGDFIPDADALSPSDFTSNEMLKKELAEVLET 401

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT REERVLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS++L+ F
Sbjct: 402 LTDREERVLRLRFGLEDGHTRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSRRLKDF 461

Query: 680 LD 681
           ++
Sbjct: 462 ME 463



 Score = 43.9 bits (102), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 35/148 (23%), Positives = 63/148 (42%), Gaps = 31/148 (20%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+IKL ++RGY+T +E+N      ++  E +   + +  +  I++V    + +    +  
Sbjct: 17  KLIKLGKKRGYLTYDEINNSFAEVQLDPEMISSFLDLYESEQIDIVKAKKVVETPKVKKE 76

Query: 93  LDLASSASNSSV----------------------FLQKRKD---------SADRSTDDPV 121
           +       N+                        F  + +D         ++     DPV
Sbjct: 77  VKETPKVQNTEEEQTTTEEADFEENEEEENIPADFKIEEEDEEPFDAFEITSQLKLSDPV 136

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAG 149
            MYL+E+G +ELLS + EI  AK+IE G
Sbjct: 137 HMYLKEIGRVELLSSQEEIKFAKKIERG 164


>gi|149194280|ref|ZP_01871377.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
 gi|149135455|gb|EDM23934.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
          Length = 604

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 195/573 (34%), Positives = 319/573 (55%), Gaps = 71/573 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I LL ++ E+ I +RI+ G  +++ ++C  P     ++ +++ L +
Sbjct: 96  SDSPVRMYLREMGHIPLLDKDEEVEIFRRIQLGEEIILDAICSIPFLIDLVLKYKEPLLN 155

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD---DVQETEGDIESA 233
               ++E+                 G +      RE    E  ++     +E E  I+  
Sbjct: 156 RERRVKELFKNFVDEEEVEDEDTKEGKKNKKISLREKRINELFKNLEKAKKEWEKVIDEY 215

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI---AEV 290
            ++ KD      S PE             D+  H +  +  + + KV  AL+E+   +++
Sbjct: 216 DRILKDT-----SMPE-------------DERLHKILQLTFK-KKKVKDALNELGYTSKL 256

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
             E+    + A+ G KD +  +K +                + R+ L  EQL ++ K I+
Sbjct: 257 INEIVKTVETALKGDKDFEKELKKR----------------EYRLPLFNEQLRNLHKEIL 300

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
               EL         K D+                 A   PE    N V  ++  +++ +
Sbjct: 301 SKITEL--------SKEDI-----------------AAMVPEHTMVN-VYMDIKKLVEAK 334

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
              +++    G+   +   I+  +++G+   + AK++M  ANLRLV+S+AKKYTNRGL F
Sbjct: 335 KASENM---FGMDPKKLEVILEQLKRGKKIVTEAKEKMARANLRLVVSIAKKYTNRGLPF 391

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+IADQ+ T+RIP+HM + I+
Sbjct: 392 LDLIQEGNIGLMKAIDKFEFEKGYKFSTYATWWIRQAISRAIADQARTVRIPIHMIENIN 451

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++ +  R+   +  +EP+ E IAK++ MPVE ++++LKI+KEPISLE P+G+E+    GD
Sbjct: 452 QINKIIRKYVQEEGKEPSLEVIAKEMKMPVEKIKQILKISKEPISLEAPVGEEEDGKFGD 511

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQF 649
           FIEDK+  +P D  +  +LR+    +L +L  RE+ V++MRFG+  + ++ TLEE+GK  
Sbjct: 512 FIEDKSFSNPYDEVVLEDLRKHIDEILENLNEREKAVIKMRFGLMPDKSERTLEEIGKAL 571

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRER+RQIE+ AI+KL+HP+  K L+++++ 
Sbjct: 572 NVTRERVRQIESSAIKKLRHPNIGKLLKNYIES 604


>gi|182418305|ref|ZP_02949600.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237666788|ref|ZP_04526773.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182377687|gb|EDT75231.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237657987|gb|EEP55542.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 369

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 132 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWW 191

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEI+K + +PV+ V
Sbjct: 192 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPFPEEISKVMDLPVDKV 251

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTPR
Sbjct: 252 REIQKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPR 311

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 312 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 369



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 65/132 (49%), Gaps = 18/132 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSE 90
           K+++   ++ G +T +E+   +   ++  EQ+E     L  M I ++ + ++  D   +E
Sbjct: 27  KELLDKGKKNGSLTYKEIMEAMDHIDLGPEQIEKIYEALEMMNIEIIGEANETAD---AE 83

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +DL+     +               DDPVRMYL+E+G + LLS E EI  A++IE G 
Sbjct: 84  EEIDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLSSEQEIEYAQQIEEGN 129

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 130 QRAKKKLAEANL 141


>gi|160878392|ref|YP_001557360.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427058|gb|ABX40621.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 371

 Score =  306 bits (784), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 144/271 (53%), Positives = 205/271 (75%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +S++E    + + +K E   ++AK+ + E+NLRLV+S+AK+Y  RGL
Sbjct: 101 VKQYLKEIGSYPLLSVAEE---IELAKKIEAGDNMAKQILAESNLRLVVSIAKRYVGRGL 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAITRSIADQS TIRIPVHM + 
Sbjct: 158 SFLDLIQEGNLGLIKAVDKFDYNKGYKFSTYATWWIRQAITRSIADQSRTIRIPVHMSEV 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K  R +R +  ++ REP+ +E+A  + +P+E VR++LK++ +PISL+TPIG+ED SHL
Sbjct: 218 INKTYRVSRNLLQELGREPSEQELADAMNLPIEKVREILKVSADPISLDTPIGEEDDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D   + P D+A  A L++  +++L +LT RE+RVL +RFG+      TLEEVGK+
Sbjct: 278 GDFIKDDTIMGPEDAASYAVLQDQISKLLDTLTEREQRVLILRFGLQDGRSRTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIEAKA+RKL+HPSR++ L+ +
Sbjct: 338 FNVTRERIRQIEAKALRKLRHPSRARMLKGY 368



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 46/134 (34%), Positives = 69/134 (51%), Gaps = 7/134 (5%)

Query: 32  KKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K++I  A   +G + ++++N F     ++  Q++     L    I V++  D EDE   +
Sbjct: 13  KELIAFANDNKGVIEVDKVNDFFKELNLNVRQIDKIYEYLEANNIVVLNPTD-EDEPNED 71

Query: 91  DSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             L+L     +S +       SA  ST  DDPV+ YL+E+GS  LLS   EI +AK+IEA
Sbjct: 72  ALLELED---DSDMIGDTEDLSAMTSTISDDPVKQYLKEIGSYPLLSVAEEIELAKKIEA 128

Query: 149 GRAMMMASLCESPL 162
           G  M    L ES L
Sbjct: 129 GDNMAKQILAESNL 142


>gi|188587782|ref|YP_001920276.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251778486|ref|ZP_04821406.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188498063|gb|ACD51199.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243082801|gb|EES48691.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 374

 Score =  306 bits (784), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 194/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA W
Sbjct: 136 VAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATW 195

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEI+K + +PV+ 
Sbjct: 196 WIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPFPEEISKVMELPVDK 255

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTP
Sbjct: 256 VREIQKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTP 315

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 316 REEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 374



 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/131 (33%), Positives = 64/131 (48%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   ++ G +T +E+   +   ++S EQ+E    +L  MGI V+ G    D    E+
Sbjct: 32  KGLIDKGKKNGSLTYKEIMDEIDHIDLSPEQIEKIYEVLEMMGIEVIGGAT--DAPEVEE 89

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL      +               DDPVRMYL+E+G + LLS E EI  AKRIE G  
Sbjct: 90  EIDLTVLEGIA--------------IDDPVRMYLKEIGKVPLLSSEQEIDYAKRIEEGDP 135

Query: 152 MMMASLCESPL 162
           +    L E+ L
Sbjct: 136 VAKKKLAEANL 146


>gi|312196071|ref|YP_004016132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311227407|gb|ADP80262.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score =  306 bits (783), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 140/239 (58%), Positives = 194/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 155 VAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 214

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEIAK++ +  + 
Sbjct: 215 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIAKEMDLTPDK 274

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++LK+ +EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ 
Sbjct: 275 VREILKVAQEPVSLETPIGEEEDSHLGDFIEDSDAVVPVDAASFLLLQEQLDSVLHTLSD 334

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 335 REKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 393



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 66/122 (54%), Gaps = 18/122 (14%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   ++ G++T +++   +   E+  EQ E  + +L++ GI V+D            
Sbjct: 18  KDLITRGKEAGFLTTDDITVAIQAAELPQEQAEQVLTLLNDEGIEVLDPR---------- 67

Query: 92  SLDLASSASNSSVFLQKRKD----SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               A SA  S +  ++R++    +A   T DPVRMYL+E+G + LL+   E+ +AKRIE
Sbjct: 68  ----ADSAETSDLLARRRREEEALNAKAPTSDPVRMYLKEIGKVPLLTAAEEVDLAKRIE 123

Query: 148 AG 149
           AG
Sbjct: 124 AG 125


>gi|322383680|ref|ZP_08057431.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151892|gb|EFX44835.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 354

 Score =  306 bits (783), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD   GYKFSTYA WW
Sbjct: 117 AKRRLTEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWW 176

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPEEIAK++ +  + V
Sbjct: 177 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAKEMELSTDKV 236

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    VL +LT R
Sbjct: 237 REIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTER 296

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 297 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 354



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 73/134 (54%), Gaps = 13/134 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE-----G 88
           MI+L ++R  +T +E+   L P +  +EQ++D    LS MGI+V  G++ +D+E     G
Sbjct: 1   MIELGKKRSSLTYKEIMDRLAPYDQDAEQIDDFFEHLSEMGIDV--GNENDDDEDNIRPG 58

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D+ D   +  +        K       +DPVRMYL+E+G + LLS E E+ +AKRIE 
Sbjct: 59  NTDNEDEDFNFEDDLTLPPGIK------INDPVRMYLKEIGRVPLLSAEDEVELAKRIEQ 112

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 113 GDEEAKRRLTEANL 126


>gi|326204489|ref|ZP_08194346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985282|gb|EGD46121.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 359

 Score =  306 bits (783), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 122 AKRRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYRRGFKFSTYATWW 181

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP P+EIAK++ M V+ V
Sbjct: 182 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPDEIAKEIGMSVDKV 241

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI++EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E    VL +LT R
Sbjct: 242 REIMKISQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTLLKEQLIDVLDTLTAR 301

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 302 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 359



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 69/134 (51%), Gaps = 18/134 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---DLEDEEG 88
           K++I   +Q+G +T +E+       E+  E +E     L  MG++VV GD   ++E+ + 
Sbjct: 13  KELIDRGKQKGMLTYKEIIDAFEEIELEPEHIEKIYETLETMGVDVV-GDMEAEMEEIQL 71

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +++ LD++     S               DDPVRMYL+E+G + LLS + EI +A R+E 
Sbjct: 72  TDEELDISIPEGIS--------------IDDPVRMYLKEIGKVPLLSADEEIDLAHRMEN 117

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 118 GDIEAKRRLAEANL 131


>gi|260655747|ref|ZP_05861216.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
 gi|260629363|gb|EEX47557.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
          Length = 969

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 146/260 (56%), Positives = 198/260 (76%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ +    V++ ++ E     AK E++ ANLRLV+S+AKKY  RG+QFLDLIQEGN+GL
Sbjct: 710 VSLLDAAEEVALAKRVEAGDETAKDEIINANLRLVVSIAKKYIGRGMQFLDLIQEGNLGL 769

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  
Sbjct: 770 IRAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKMVRISRQLVQ 829

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K+ REP+ EEIA ++ +  E V ++ +I++ P+SLETPIG+E+ S LGDFIED++  SP 
Sbjct: 830 KLGREPSDEEIAAEMKIEPERVEEIKRISQMPVSLETPIGEEEDSQLGDFIEDRSLPSPE 889

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D A    L+E    +L +L+ RE  VLR RFG+     +TLEEVG++F VTRERIRQIEA
Sbjct: 890 DVAADNLLQEQIEEMLNALSDREREVLRYRFGLEDGRSYTLEEVGRRFGVTRERIRQIEA 949

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRSKKLR FLD
Sbjct: 950 KALRKLRHPSRSKKLRDFLD 969



 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/152 (28%), Positives = 76/152 (50%), Gaps = 12/152 (7%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSW-KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           D +S   D +D+ +   S   W +++  + + +G+VT +++   +P D  +S+ +E  + 
Sbjct: 577 DEESGEADDEDAALARQSRMKWVRELYTVGKDKGFVTNQDIEETVPADAWNSDVLEFVIE 636

Query: 69  MLSNMGINVVD------GD-----DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
            L N+G+++VD      GD               + D  S   N   + ++     D   
Sbjct: 637 NLMNLGVDLVDSTGSAAGDVTAGQAAARALAESKNSDADSDEDNDPGYGEELGKMEDVPL 696

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            DPVRMYLR++G + LL    E+A+AKR+EAG
Sbjct: 697 SDPVRMYLRDIGKVSLLDAAEEVALAKRVEAG 728


>gi|229825330|ref|ZP_04451399.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
 gi|229790702|gb|EEP26816.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
          Length = 409

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 142/236 (60%), Positives = 186/236 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   + E+NLRLV+S+AKKY  RGL FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW
Sbjct: 171 ATDRLTESNLRLVVSIAKKYVGRGLSFLDLIQEGNLGLIKAVDKFDYSKGYKFSTYATWW 230

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIRIPVHM + I+K  R +R +  ++ REPT EEIAK++ +PVE V
Sbjct: 231 IRQAITRSIADQSRTIRIPVHMSEVINKAYRISRSLLQELGREPTEEEIAKEMNLPVEKV 290

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI+ +PISL+TPIG+ED SHLGDFI+D   + P D+A    L++   ++L +L+ R
Sbjct: 291 REIMKISADPISLDTPIGEEDDSHLGDFIKDDTIMGPEDAAAYTMLQDQIQKLLTTLSER 350

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+RVL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP+R++ LR F
Sbjct: 351 EQRVLILRFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLRHPNRARMLRGF 406



 Score = 41.6 bits (96), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +DDPV++YL+E+G+  LLS + E+ +AK+I  G       L ES L
Sbjct: 135 SDDPVKIYLKEIGNYPLLSMDEEVELAKKIAEGDQYATDRLTESNL 180


>gi|291533682|emb|CBL06795.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Megamonas hypermegale
           ART12/1]
          Length = 329

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 150/266 (56%), Positives = 201/266 (75%), Gaps = 3/266 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +  G+ EA   +K + EANLRLV+S+AK+Y  RG+
Sbjct: 66  VRMYLKEIGRVPLLSADEEIKLAKRMEDGDLEA---QKRLAEANLRLVVSIAKRYVGRGM 122

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 123 LFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 182

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++   + REP+PEEIAK++ + V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 183 INKLIRVSRQLLQSLGREPSPEEIAKEMDVSVDRVREIMKIAQEPVSLETPIGEEEDSHL 242

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A +P ++A    L+E    VL +LT REE+VLR+RFG+      TLEEVG+ 
Sbjct: 243 GDFIEDHDAPAPAEAASFVLLKEQLEDVLDTLTEREEKVLRLRFGLDDGRARTLEEVGQN 302

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
           F VTRERIRQIEAKA+RKL+HPSRSK
Sbjct: 303 FGVTRERIRQIEAKALRKLRHPSRSK 328



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 13/111 (11%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
           + PDE+  +++ DT    +  GI+++D G+D+    G +D  +L     +  + L   + 
Sbjct: 9   MSPDEI--DELYDT---FTKRGIDIIDNGNDI----GPDDDSNLKDDEDDIDIDLSIPEG 59

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
               + DDPVRMYL+E+G + LLS + EI +AKR+E G       L E+ L
Sbjct: 60  I---NIDDPVRMYLKEIGRVPLLSADEEIKLAKRMEDGDLEAQKRLAEANL 107


>gi|187934045|ref|YP_001885115.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722198|gb|ACD23419.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
          Length = 374

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 194/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA W
Sbjct: 136 VAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATW 195

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEI+K + +PV+ 
Sbjct: 196 WIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPFPEEISKVMELPVDK 255

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTP
Sbjct: 256 VREIQKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTP 315

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 316 REEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 374



 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 44/131 (33%), Positives = 64/131 (48%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   ++ G +T +E+   +   ++S EQ+E    +L  MGI V+ G    D    E+
Sbjct: 32  KGLIDKGKKNGSLTYKEIMDEIDHIDLSPEQIEKIYEVLEMMGIEVIGGAT--DAPEVEE 89

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +DL      +               DDPVRMYL+E+G + LLS E EI  AKRIE G  
Sbjct: 90  EIDLTVLEGIA--------------IDDPVRMYLKEIGKVPLLSSEQEIDYAKRIEEGDP 135

Query: 152 MMMASLCESPL 162
           +    L E+ L
Sbjct: 136 VAKKKLAEANL 146


>gi|297570260|ref|YP_003691604.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296926175|gb|ADH86985.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 555

 Score =  305 bits (782), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 146/263 (55%), Positives = 194/263 (73%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           + G+   E   +++ +  GE  +  AK  +V++NLRLV+SVAKKY  RGLQ LDL+QEGN
Sbjct: 291 QYGLDRQELSALLAQISLGEEISREAKNRLVQSNLRLVVSVAKKYAGRGLQLLDLVQEGN 350

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ  TIRIPVHM D I+++++ A+ 
Sbjct: 351 IGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQGRTIRIPVHMIDTINRMLKGAKE 410

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
              +  REPTPEE+A+ L + +  V+ +LKI KEP+SL+TP+G  + S L DFIED ++ 
Sbjct: 411 YQRQHGREPTPEEMAEHLGVDIAKVKSILKIAKEPLSLDTPVGSGEDSFLSDFIEDADST 470

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP ++ I  +L++   RVL +LTPREE VLR+RFGI   TD TLEEVG+ F VTRERIRQ
Sbjct: 471 SPDEATIYDSLQDNLARVLKTLTPREEMVLRLRFGIDTATDLTLEEVGENFSVTRERIRQ 530

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA++KLKHP+R   L  F D
Sbjct: 531 IEAKALKKLKHPTRKSILSPFYD 553



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 40/67 (59%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPV++YL+EMG++ LLS E E+A+AK IE G   +  +L  +P     L     ++  G 
Sbjct: 108 DPVKVYLQEMGAVALLSSEEEVAVAKEIERGERTIQDALVIAPPALAYLDEIAKKIQHGN 167

Query: 179 TLLREII 185
            +L +I+
Sbjct: 168 RMLSDIV 174


>gi|315185629|gb|EFU19397.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta thermophila DSM
           6578]
          Length = 568

 Score =  305 bits (781), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 145/269 (53%), Positives = 198/269 (73%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+  +E   +I +   +   + +G      AK ++++ANLRLV+S+AKKYTNRGL F D
Sbjct: 299 LKAFEIEFEATIPQILEMSKEIARGHHLMKTAKDKLIQANLRLVVSIAKKYTNRGLHFFD 358

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV
Sbjct: 359 LVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKV 418

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R AR++   + REPT EEIA +L  P+  V+ V  + +EPISLE+PIG+E+ S +GDFI
Sbjct: 419 QREARQLMQVLGREPTDEEIADRLGWPLSRVKSVKNVAREPISLESPIGEEEDSSVGDFI 478

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDK AV+P      A L++    VLA+L PRE+ VL+MRFG+      TLEEVG  F VT
Sbjct: 479 EDKTAVNPSHQTAYALLQQQIKDVLATLPPREQEVLKMRFGLEDGYSLTLEEVGLYFNVT 538

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+R+L+HP RS++L+ +L+
Sbjct: 539 RERIRQIEAKALRRLRHPKRSRRLKDYLE 567



 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 81/134 (60%), Gaps = 17/134 (12%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVS--SEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           S +K+I+  +++G +T ++L+ FLP +E+S   E++++ +A+L    I VV+ DD    E
Sbjct: 4   SVQKLIEYGKRKGILTYDDLSDFLP-EEISDSEEKIQEVLAVLEEAHIQVVEEDD---SE 59

Query: 88  GSEDSLDLASSASNSS-VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           G E      S A N   V + +R+ S    TDDP+R+YLRE+G   LL+ E E++++K++
Sbjct: 60  GGE------SKAKNRRRVVITEREGS----TDDPIRLYLREIGRENLLTAEEEVSLSKQM 109

Query: 147 EAGRAMMMASLCES 160
           E G  ++   L  S
Sbjct: 110 EEGENIIKEVLKHS 123


>gi|169334166|ref|ZP_02861359.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258883|gb|EDS72849.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
          Length = 403

 Score =  305 bits (781), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 150/272 (55%), Positives = 199/272 (73%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +  G+ EA   +K++ EANLRLV+S+AK+Y NRG+
Sbjct: 135 VRMYLKEIGKVDLLSAEEELDLAQKIESGDVEA---RKKLCEANLRLVVSIAKRYVNRGM 191

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 192 SFLDLIQEGNLGLLKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 251

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R +   + R+P   EIAK++ +P E VR ++KI+++P+SLETPIG+E+ SHL
Sbjct: 252 INKLKRVQRMLIQDLGRDPNSHEIAKEMGLPEEKVRDIMKISQDPVSLETPIGEEEDSHL 311

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +AV+P ++A    LR     VL +LT RE +VL +RFG+      TLEEVG  
Sbjct: 312 GDFIPDDDAVAPEEAASYMLLRTQLFEVLKTLTDREAKVLILRFGLEDGRPRTLEEVGDI 371

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           FCVTRERIRQIEAKA+RKL+HP+RSKKLR FL
Sbjct: 372 FCVTRERIRQIEAKALRKLRHPTRSKKLRDFL 403



 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 33/93 (35%), Positives = 46/93 (49%), Gaps = 9/93 (9%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +DPVRMYL+E+G ++LLS E E+ +A++IE+G       LCE+ L     I  R  +N G
Sbjct: 132 NDPVRMYLKEIGKVDLLSAEEELDLAQKIESGDVEARKKLCEANLRLVVSIAKR-YVNRG 190

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            + L  I         E   G     E   Y K
Sbjct: 191 MSFLDLI--------QEGNLGLLKAVEKFDYTK 215


>gi|171914125|ref|ZP_02929595.1| RNA polymerase sigma factor RpoD [Verrucomicrobium spinosum DSM
           4136]
          Length = 576

 Score =  305 bits (781), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 148/273 (54%), Positives = 203/273 (74%), Gaps = 1/273 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++   +   ++  E+R +V+   +   E++ AK EMVEANLRLVIS+AKKYTNRGL
Sbjct: 301 VQKALEDFELHAWVTPEEYRRLVAETIQWSKESTKAKTEMVEANLRLVISIAKKYTNRGL 360

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLM+A EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM D 
Sbjct: 361 SFLDLIQEGNMGLMRAVEKFEYKRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIDT 420

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SH 587
           I+K++R  +++  ++ R+PTP+EIA+++ +PVE V  VL+++++P+SL+T +GD D  + 
Sbjct: 421 INKLLRVQKQLVQELGRDPTPDEIAEEIHLPVERVNAVLRMSQQPVSLQTKVGDSDGDTE 480

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            GDFIED  +VSP++      LR+    VL SLT RE  VL  RFG+   +  TLEEVG+
Sbjct: 481 FGDFIEDNTSVSPMELTAMNLLRDKLKDVLDSLTDRERAVLEQRFGLVDGSGRTLEEVGR 540

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           QF VTRERIRQIEAKA+RKL+HP+R +KL  F 
Sbjct: 541 QFHVTRERIRQIEAKALRKLRHPTRIRKLGGFF 573



 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/187 (28%), Positives = 97/187 (51%), Gaps = 8/187 (4%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I+LA+++ Y+T ++ N  LP   V+ E M++ +  L ++ I V++   ++  +      
Sbjct: 53  LIRLAKEQDYLTFDDFNESLPNGFVTPELMDEILIRLRSLEIEVIEPTQVDRVKTKR--- 109

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
             A+ A +    +++R+D      DDPVRMYL++MG++ LL+R+ EI I+KRIE   + +
Sbjct: 110 --ATVAEDEDTVVEEREDGQLDMLDDPVRMYLKQMGAVPLLTRDQEIGISKRIEKAESHL 167

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
            A L          +   D L  GT    +++ L+  I  E +  +F        Q R+D
Sbjct: 168 QACLQNIGFIATEYLHLGDALASGTERFDKLV-LDRQI--EDRDSYFKKLRQVCDQVRDD 224

Query: 214 SSQEKER 220
            S+  E+
Sbjct: 225 ISKANEQ 231


>gi|293400669|ref|ZP_06644814.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305695|gb|EFE46939.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 396

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 188/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK+++ ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 156 AKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 215

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++   + R+P+ EEIA K+  +  E 
Sbjct: 216 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMENISPEK 275

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  EP+SLETPIG+ED SHLGDFIEDK A+SP + A    L++    VL  LT 
Sbjct: 276 VREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTE 335

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 336 REEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394



 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 30/43 (69%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           Q   +S+    +DPV+MYL+E+G +ELL  + E  IA+RI+AG
Sbjct: 110 QSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAG 152


>gi|291531112|emb|CBK96697.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 358

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 121 ARKRLSEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I KV + + ++ ++   EPTP+EIA +L + V+ V
Sbjct: 181 IRQAITRSIADQARTIRIPVHMVETITKVKKVSSQLLHENGHEPTPQEIADRLGITVDRV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++L+I+++P+SLETPIG+E+ SHLGDFI D++A +P ++A +  L+E  + +L +LTPR
Sbjct: 241 REILRISQDPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAASRTLLKEQLSEILGTLTPR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 301 EEKVLRLRFGLEDGRPRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 358



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 65/141 (46%), Gaps = 15/141 (10%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----D 81
            +D    ++I   +Q G +T +E+   L   +  ++++        +  I +VD     +
Sbjct: 1   MADSKINELINHGKQSGKLTTKEITDVLEELDFDADEINKLYDDFESSNIEIVDDFSADE 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           DL+      DS D  SS S+  +           + DDPV++YL+E+G + LL+ E EI 
Sbjct: 61  DLDSALDFTDSDDFESSLSSEGI-----------AIDDPVKIYLKEIGRVPLLTAEEEIE 109

Query: 142 IAKRIEAGRAMMMASLCESPL 162
           +A R+  G       L E+ L
Sbjct: 110 LATRMAQGDKYARKRLSEANL 130


>gi|167750934|ref|ZP_02423061.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|167656113|gb|EDS00243.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|291557421|emb|CBL34538.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 358

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 121 ARKRLSEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I KV + + ++ ++   EPTP+EIA +L + V+ V
Sbjct: 181 IRQAITRSIADQARTIRIPVHMVETITKVKKVSSQLLHENGHEPTPQEIADRLGITVDRV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++L+I+++P+SLETPIG+E+ SHLGDFI D++A +P ++A +  L+E  + +L +LTPR
Sbjct: 241 REILRISQDPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAASRTLLKEQLSEILGTLTPR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 301 EEKVLRLRFGLEDGRPRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 358



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 65/141 (46%), Gaps = 15/141 (10%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----D 81
            +D    ++I   +Q G +T +E+   L   +  ++++        +  I +VD     +
Sbjct: 1   MADSKINELINHGKQNGKLTTKEITDVLEELDFDADEINKLYDDFESSNIEIVDDFSADE 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           DL+      DS D  SS S+  +           + DDPV++YL+E+G + LL+ E EI 
Sbjct: 61  DLDSALDFTDSDDFESSLSSEGI-----------AIDDPVKIYLKEIGRVPLLTAEEEIE 109

Query: 142 IAKRIEAGRAMMMASLCESPL 162
           +A R+  G       L E+ L
Sbjct: 110 LATRMAQGDKYARKRLSEANL 130


>gi|309775524|ref|ZP_07670524.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916618|gb|EFP62358.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 397

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 188/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK+++ ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 157 AKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 216

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++   + R+P+ EEIA K+  +  E 
Sbjct: 217 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMENISPEK 276

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  EP+SLETPIG+ED SHLGDFIEDK A+SP + A    L++    VL  LT 
Sbjct: 277 VREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTE 336

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 337 REEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 395



 Score = 40.4 bits (93), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 29/43 (67%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           Q   +S+    +DPV+MYL+E+G +ELL  + E  IA+RI+ G
Sbjct: 111 QSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIAQRIQDG 153


>gi|307718768|ref|YP_003874300.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532493|gb|ADN02027.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 580

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 144/269 (53%), Positives = 198/269 (73%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+  +E   +I +   +   + +G      AK ++++ANLRLV+S+AKKYTNRGL F D
Sbjct: 311 LKAFEIEFEATIPQILEMSKEIARGHHLMKTAKDKLIQANLRLVVSIAKKYTNRGLHFFD 370

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV
Sbjct: 371 LVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKV 430

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R AR++   + REPT EEIA +L  P+  V+ V  + +EPISLE+PIG+E+ S +GDFI
Sbjct: 431 QREARQLMQVLGREPTDEEIADRLGWPLSRVKSVKNVAREPISLESPIGEEEDSSVGDFI 490

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDK A++P      A L++    VLA+L PRE+ VL+MRFG+      TLEEVG  F VT
Sbjct: 491 EDKTAINPSHQTAYALLQQQIKDVLATLPPREQEVLKMRFGLEDGYSLTLEEVGLYFNVT 550

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+R+L+HP RS++L+ +L+
Sbjct: 551 RERIRQIEAKALRRLRHPKRSRRLKDYLE 579



 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 81/134 (60%), Gaps = 17/134 (12%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVS--SEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           S +K+I+  +++G +T ++L+ FLP +E+S   E++++ +A+L    I VV+ DD    E
Sbjct: 16  SVQKLIEYGKRKGILTYDDLSDFLP-EEISDSEEKIQEVLAVLEEAHIQVVEEDD---SE 71

Query: 88  GSEDSLDLASSASNSS-VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           G E      S A N   V + +R+ S    TDDP+R+YLRE+G   LL+ E E++++K++
Sbjct: 72  GGE------SKAKNRRRVVITEREGS----TDDPIRLYLREIGRENLLTAEEEVSLSKQM 121

Query: 147 EAGRAMMMASLCES 160
           E G  ++   L  S
Sbjct: 122 EEGETIIKEVLKHS 135


>gi|309388945|gb|ADO76825.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 364

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK+++V+ANLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 114 VELAKRMEQGEEWAKQQLVQANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLMKAVDKFDY 173

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+K++R +R++  +  REP  E
Sbjct: 174 TKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVETINKLIRVSRQLLQEKGREPKDE 233

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ +  E VR+++KI+++P+SLETPIG+E+ SHLGDFIED ++ +P  +A    L+
Sbjct: 234 EIGAEMDISAEKVREIMKISQDPVSLETPIGEEEDSHLGDFIEDVDSPAPASAASYILLK 293

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+RVL +RFGI      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 294 EQLNDVLDTLTDREKRVLELRFGIEDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHP 353

Query: 671 SRSKKLRSFLD 681
           SRSKK++ +L+
Sbjct: 354 SRSKKIKDYLN 364



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/131 (31%), Positives = 67/131 (51%), Gaps = 9/131 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK++   ++ G +T E++   L   ++ SE +E    + S M I VV+       +  + 
Sbjct: 15  KKLVSRGKKEGELTYEDIMDALEDIDLDSEDIEKIYEIFSEMNIEVVNS------KLEDS 68

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             D      NS + L   K +   S DDPVRMYL+E+G ++LL+ E E+ +AKR+E G  
Sbjct: 69  EEDDDEDDQNSGLDLSIPKSA---SIDDPVRMYLKEIGKVDLLTAEEEVELAKRMEQGEE 125

Query: 152 MMMASLCESPL 162
                L ++ L
Sbjct: 126 WAKQQLVQANL 136


>gi|313897367|ref|ZP_07830910.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
 gi|312957737|gb|EFR39362.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
          Length = 398

 Score =  304 bits (779), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 188/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK+++ ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 158 AKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++   + R+P+ EEIA K+  +  E 
Sbjct: 218 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMENISPEK 277

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  EP+SLETPIG+ED SHLGDFIEDK A+SP + A    L++    VL  LT 
Sbjct: 278 VREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTE 337

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 338 REEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 396



 Score = 43.5 bits (101), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 30/43 (69%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           Q   +S+    +DPV+MYL+E+G +ELL  + E  IA+RI+AG
Sbjct: 112 QSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAG 154


>gi|223985702|ref|ZP_03635749.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
 gi|223962313|gb|EEF66778.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
          Length = 408

 Score =  304 bits (779), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 188/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ +NLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 168 AKRILISSNLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 227

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++   + REPT EEIA+K+  +  + 
Sbjct: 228 IRQAITRAIADQARTIRIPVHMVETINKLTRVQRQLVQDLGREPTAEEIAEKMENITPDK 287

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  EP+SLETPIG+ED SHLGDFIEDK+A+SP   A    L++    VL  LT 
Sbjct: 288 VREIQKIALEPVSLETPIGEEDDSHLGDFIEDKDAMSPDQYANNQLLKDEINNVLQGLTE 347

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+LR F+D
Sbjct: 348 REEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLRDFVD 406



 Score = 44.7 bits (104), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 11/71 (15%)

Query: 80  GDDLEDE-EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           G+D ++E E  E  +DL+ + S+S               +DPV+MYL+E+G + LL+ E 
Sbjct: 104 GEDFDEEVEDVEVPIDLSETYSSSPYV----------RINDPVKMYLKEIGRVPLLNPED 153

Query: 139 EIAIAKRIEAG 149
           E  IA+RI+AG
Sbjct: 154 EPEIARRIQAG 164


>gi|254519856|ref|ZP_05131912.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
 gi|226913605|gb|EEH98806.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
          Length = 370

 Score =  304 bits (779), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 133 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEI+K + +PV+ V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPFPEEISKVMDLPVDKV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A    L+E    VL +LTPR
Sbjct: 253 REIQKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPAEAAAFTMLKEQLINVLDTLTPR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 313 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 370



 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/159 (32%), Positives = 79/159 (49%), Gaps = 27/159 (16%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           GKK N D +S+      ++V        K ++   ++ G +T +E+   +   ++S EQ+
Sbjct: 11  GKKENEDKNSKM-----TIV--------KNLLDKGKKSGTLTYKEIMDEVEHIDLSPEQI 57

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           E    +L +MGI V+ GD  E +E  E+ LDL  +                 + DDPVRM
Sbjct: 58  EKIYEVLESMGIEVI-GDPNEADE-VEEELDLDLTIPEGI------------AIDDPVRM 103

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           YL+E+G + LLS E EI +A RIE G       L E+ L
Sbjct: 104 YLKEIGKVPLLSSEEEIELANRIEQGDQRAKKKLAEANL 142


>gi|164688099|ref|ZP_02212127.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
 gi|164602512|gb|EDQ95977.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
          Length = 385

 Score =  304 bits (778), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 145/239 (60%), Positives = 197/239 (82%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA W
Sbjct: 147 IAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYERGFKFSTYATW 206

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK++ M  E 
Sbjct: 207 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAKEMDMSEEK 266

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+++KI ++P+SLETPIG+E+ SHLGDFI D++A++P ++A  + L++    VL SL  
Sbjct: 267 VREIMKIAQDPVSLETPIGEEEDSHLGDFIPDEDALAPAEAAAYSLLKDQIEEVLGSLNE 326

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 327 REQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 385



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 72/156 (46%), Gaps = 14/156 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEG 88
           + K +I   +++G +T+ E+       E+  +Q+E+    L N+GI ++ D     D + 
Sbjct: 11  TAKTLIDKGKKQGSLTLSEIMEAFSETELDKDQVENLYETLGNLGIEIIEDKTQKADVDF 70

Query: 89  SEDSLDLASSASNSSVF---LQKRKD-SADR---------STDDPVRMYLREMGSIELLS 135
           S++  DL        V    L+K  D   D+         S DDPVRMYL+E+G I LL 
Sbjct: 71  SDNDNDLIVDKDFDGVSDDELKKEDDIEMDKIDLSLPKGISIDDPVRMYLKEIGKIPLLK 130

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
              EI  AKR+  G  +    L E+ L     I  R
Sbjct: 131 PHEEIEYAKRMLEGDEIAKQRLVEANLRLVVSIAKR 166


>gi|257066626|ref|YP_003152882.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256798506|gb|ACV29161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 602

 Score =  304 bits (778), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 143/247 (57%), Positives = 194/247 (78%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+    +  AKK++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G
Sbjct: 356 LRRAVLNSKRAKKKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRG 415

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA
Sbjct: 416 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIA 475

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ + VE V+++ KI++EP+SLETPIG+ED SHLGDFIED +A+ P ++A    LRE  
Sbjct: 476 EQMGLEVEKVQEIRKISQEPVSLETPIGEEDDSHLGDFIEDDSAIDPGEAANYTMLREQL 535

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL+ L  RE+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S
Sbjct: 536 NDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKS 595

Query: 674 KKLRSFL 680
           + L+ FL
Sbjct: 596 ELLKDFL 602



 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            DDPV+MYL+E+G ++LL+   EI +A+R+E G
Sbjct: 115 VDDPVKMYLKEIGKVDLLTATEEIILARRMEMG 147


>gi|323342093|ref|ZP_08082326.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464518|gb|EFY09711.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 459

 Score =  304 bits (778), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 187/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 219 ARRILISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 278

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +   + REPT EEIA ++  +  E 
Sbjct: 279 IRQAITRAIADQARTIRIPVHMVETINKLTRIQRSLVQTLGREPTAEEIAAEMENITPEK 338

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  +P+SLETPIG+ED SHLGDFIEDK+A+SP + A    L+E    VL  LT 
Sbjct: 339 VREIQKIALDPVSLETPIGEEDDSHLGDFIEDKDALSPDEYANNQLLKEEIKMVLEGLTE 398

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+LR F+D
Sbjct: 399 REEKVLRLRFGLEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLRDFVD 457



 Score = 38.1 bits (87), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 40/72 (55%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VD D + DE   ++  D + +  + S +  +   +     +DPV+MYL+E+G + LL  +
Sbjct: 79  VDDDFISDEAEEDEIFDDSLNKVDLSSYENELTSANMVRINDPVKMYLKEIGRVNLLDAK 138

Query: 138 GEIAIAKRIEAG 149
            E  IA+R++ G
Sbjct: 139 DEPEIARRLQEG 150


>gi|269215371|ref|ZP_06159225.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
 gi|269131227|gb|EEZ62301.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
          Length = 383

 Score =  304 bits (778), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 138/238 (57%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 145 AKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+PTPEEI +K+ +  E V
Sbjct: 205 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQDLNRDPTPEEIGEKMGLSAERV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED +AV P D+A  + L+E  ++VL  L  R
Sbjct: 265 REIQKISQEPVSLETPIGEEEDSQLGDFIEDDSAVVPPDAASFSMLQEQLSKVLDGLAER 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+     HTLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 325 ERKVISLRFGLEDGHPHTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 382



 Score = 45.4 bits (106), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 36/99 (36%), Positives = 50/99 (50%), Gaps = 27/99 (27%)

Query: 80  GDDLEDEEGSEDSLDLA-------------SSASNSSVFLQK---------RKDSADRS- 116
           GDDL  E+G +   +L+              +AS S + L K         R+ S+D S 
Sbjct: 14  GDDLAAEDGKDVDANLSDEELLEGIPENELKAASTSEINLPKLSSSRASKVRRRSSDGSS 73

Query: 117 ----TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
               T DPVRMYL+E+G + LL+   EI +A +IEAG A
Sbjct: 74  AVMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVA 112


>gi|257791063|ref|YP_003181669.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|317488219|ref|ZP_07946788.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325830757|ref|ZP_08164141.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
 gi|257474960|gb|ACV55280.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|316912661|gb|EFV34201.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325487164|gb|EGC89607.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
          Length = 409

 Score =  303 bits (777), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 138/238 (57%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 171 AKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 230

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP+PEEI K++ +P E V
Sbjct: 231 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGREPSPEEIGKEMGLPAERV 290

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV P D+A  + L+E  ++VL  L  R
Sbjct: 291 REIQKISQEPVSLETPIGEEEDSQLGDFIEDDAAVVPPDAASFSMLQEQLSKVLDGLAER 350

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 351 ERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 408



 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 33/49 (67%), Gaps = 4/49 (8%)

Query: 109 RKDSADRS----TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           RK +AD S    T DPVRMYL+E+G + LL+   EI +A +IEAG A M
Sbjct: 92  RKRNADASVTMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVAAM 140


>gi|251796255|ref|YP_003010986.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
 gi|247543881|gb|ACT00900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
          Length = 376

 Score =  303 bits (777), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 149/251 (59%), Positives = 197/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD 
Sbjct: 126 IELARRIENGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDH 185

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPTPE
Sbjct: 186 QKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPTPE 245

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +  + VR+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+
Sbjct: 246 EIAAEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLK 305

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 306 EQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 365

Query: 671 SRSKKLRSFLD 681
           SRSK+L+ FL+
Sbjct: 366 SRSKRLKDFLE 376



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 69/134 (51%), Gaps = 8/134 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++I+  ++R  +T +E+   L P +   EQ+++    L ++GI V++  D ED     D
Sbjct: 20  EQLIEQGKKRASLTYKEIMEKLSPFDQDPEQIDEFFEQLDDLGIEVLNERD-EDR----D 74

Query: 92  SLDLASSASNSSVFLQKRKDSA---DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            L+    +   S       D A       +DPVRMYL+E+G + LLS + EI +A+RIE 
Sbjct: 75  PLNRGEDSERESDDFNFDDDLALPPGIKINDPVRMYLKEIGRVPLLSADDEIELARRIEN 134

Query: 149 GRAMMMASLCESPL 162
           G       L E+ L
Sbjct: 135 GDEEAKRRLAEANL 148


>gi|304403970|ref|ZP_07385632.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
 gi|304346948|gb|EFM12780.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
          Length = 377

 Score =  303 bits (777), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 154/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + KG+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSADDEVELAKRIEKGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA ++ +  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVSRQLLQELGREPAPEEIAAEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 66/130 (50%), Gaps = 1/130 (0%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I+  ++R  +T +E+   L P +   EQ+++    L ++GI VV+ +D E     +D 
Sbjct: 21  QLIEHGKKRSSLTYKEIMEKLAPFDQDPEQIDEFFEQLDDLGIEVVNEND-ESPISRDDH 79

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                  ++   F            +DPVRMYL+E+G + LLS + E+ +AKRIE G   
Sbjct: 80  DRDRDQENDEFNFDDDLALPPGIKINDPVRMYLKEIGRVPLLSADDEVELAKRIEKGDEE 139

Query: 153 MMASLCESPL 162
               L E+ L
Sbjct: 140 AKRRLAEANL 149


>gi|284049111|ref|YP_003399450.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283953332|gb|ADB48135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 589

 Score =  303 bits (777), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 147/239 (61%), Positives = 189/239 (79%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 351 AKKCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYATWW 410

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REPTPEEIAK++ + VE V
Sbjct: 411 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQELGREPTPEEIAKEMDVSVERV 470

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++ KI +EP+SLETPIG+E+ SHLGDFIED+ A SP D+A    L+E   +VL   L+ 
Sbjct: 471 REIQKIAQEPVSLETPIGEEEDSHLGDFIEDQEAPSPADAASYTLLQEQLGKVLQEHLSA 530

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE RVL +RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+ P RSK L+ FL+
Sbjct: 531 RERRVLELRFGLMDGRTRTLEEVGQYFGVTRERIRQIEAKALRKLRSPKRSKPLKEFLE 589



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/116 (37%), Positives = 61/116 (52%), Gaps = 13/116 (11%)

Query: 39  RQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS---EDSLD 94
           +  G +T +E+   L   D VS ++M+   + L+   I VVD D  EDEE     ED L 
Sbjct: 81  KNHGVLTYKEIQDRLQNEDTVSVDEMDAIYSKLAEKNIEVVD-DGAEDEEPETIDEDELK 139

Query: 95  L-ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +  S  +N SV             DDPVRMYL+E+G + LL+ + EI +AKR + G
Sbjct: 140 VDESELANLSV-------PEGVIVDDPVRMYLKEIGRVPLLAGDDEIKLAKRADKG 188


>gi|292670109|ref|ZP_06603535.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648297|gb|EFF66269.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 382

 Score =  303 bits (777), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 142/251 (56%), Positives = 189/251 (75%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ E     A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 131 IELARRMEAGDESARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 190

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K +R +R++   + R+PT E
Sbjct: 191 SKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKYIRISRQLLQDLGRDPTAE 250

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK++ +    VR+++KI +EP+SLETPIG+E+ SHLGDFIED+ A+ P D+A    L+
Sbjct: 251 EVAKEMGLSTLRVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDEAALDPADAASVMLLK 310

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  T VL +L PRE  VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 311 EQITEVLQTLAPREAEVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHP 370

Query: 671 SRSKKLRSFLD 681
            R +KL+   D
Sbjct: 371 VRLRKLQGNFD 381



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 28/34 (82%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + DDPVRMYL+E+G + LL+ + EI +A+R+EAG
Sbjct: 107 AVDDPVRMYLKEIGRVPLLTADEEIELARRMEAG 140


>gi|332799075|ref|YP_004460574.1| RpoD subfamily RNA polymerase sigma-70 [Tepidanaerobacter sp. Re1]
 gi|332696810|gb|AEE91267.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tepidanaerobacter
           sp. Re1]
          Length = 374

 Score =  303 bits (777), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 137 AKRRLAEANLRLVVSIAKKYVGRGMLFLDLIQEGNLGLMKAVEKFDYKKGYKFSTYATWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEIA+++ +PVE V
Sbjct: 197 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQELGRDPLPEEIAEEMELPVEKV 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SL TPIG+E+ S LGDFI D  A++P D+A    L+E    VL +LTPR
Sbjct: 257 REIMKIAQEPVSLATPIGEEEDSFLGDFIPDDEALAPADAAAYLLLKEQLEDVLETLTPR 316

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 317 EEKVLRLRFGLDDGRPRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 39/132 (29%), Positives = 66/132 (50%), Gaps = 14/132 (10%)

Query: 34  MIKLARQRGYVTIEE-LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           +I+  ++ G ++  E ++A    +++ +EQ++        MGI V+D           D 
Sbjct: 26  LIEKGKKNGVLSYGEIMDALEDIEDLDTEQIDKIYESFEEMGIEVLD-----------DG 74

Query: 93  LDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            ++    +   V  ++   SA    + DDPVRMYL+E+G + LLS E EI ++KRIE G 
Sbjct: 75  EEIPEEETLEEVPTEEIDLSAPEGVAIDDPVRMYLKEIGKVPLLSAEEEIMLSKRIEEGD 134

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 135 KEAKRRLAEANL 146


>gi|297622151|ref|YP_003710288.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
 gi|297377452|gb|ADI39282.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
          Length = 555

 Score =  303 bits (777), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 146/261 (55%), Positives = 198/261 (75%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G S+ E++  V M+++   ++  AK+EMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+G
Sbjct: 290 GRSLEEYKKDVRMLQRWMDKSQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMG 349

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++ 
Sbjct: 350 LMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKLM 409

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  REPTPEE+A +L +  E +R++ KI + PISL+  +GD   S  GDF+ED  A SP
Sbjct: 410 METGREPTPEELANELGLSAERIREIYKIAQHPISLQAEVGDGGESQFGDFLEDTGADSP 469

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            ++   + L++    VL +LT RE +VL  RFG+      TLEEVG +F VTRERIRQIE
Sbjct: 470 AEATGYSILKDKMNEVLLTLTDRERKVLIQRFGLNDGKPKTLEEVGVEFNVTRERIRQIE 529

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RK++HP+RSK+L++FLD
Sbjct: 530 AKALRKMRHPTRSKQLKAFLD 550



 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 66/117 (56%), Gaps = 10/117 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           ++ +A+ +G++T EE+N  LP    +++Q++  +  LS M + +++       +   +  
Sbjct: 22  LVAIAKDQGFITYEEINDVLPMTIDTADQIDQILIFLSGMDVQILN-------QSEVERQ 74

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                 +     L +R +    + DDPVRMYL+EMGS+ LL+RE E+ I+KRIE  +
Sbjct: 75  KEKKKEAKELEGLPRRVEG---TPDDPVRMYLKEMGSVPLLTREEEVEISKRIEKAQ 128


>gi|332297995|ref|YP_004439917.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181098|gb|AEE16786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 599

 Score =  303 bits (776), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 149/276 (53%), Positives = 197/276 (71%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I KI  +++ +  E    +SE   +   + +G      AK  ++ ANLRLV+S+AKKYTN
Sbjct: 324 IQKIDRKLRRLEYEFENDVSEILSMAKEIDRGRRMMKEAKNRLINANLRLVVSIAKKYTN 383

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQF DL+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM
Sbjct: 384 RGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHM 443

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            ++I+KVVR +R++  +  REPT EEIA +L  PV  V++V  + +EPISLETPIG+E+ 
Sbjct: 444 IEQINKVVRESRQLMQRFGREPTDEEIAAQLGWPVNRVKQVKSVAREPISLETPIGEEED 503

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDFIEDK   +P        L++    +LA+L PRE+ VL+MRFG+      TLEEV
Sbjct: 504 SLLGDFIEDKEVENPAAKTAYTMLQDHLRSILATLPPREQEVLKMRFGLDDGFSLTLEEV 563

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G  F VTRERIRQIEAKA+R+L+HP RS  LR ++D
Sbjct: 564 GLYFNVTRERIRQIEAKALRRLRHPRRSGGLRDYID 599



 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 71/138 (51%), Gaps = 16/138 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL---- 83
           D +  K+++  + +  VT +ELN +LPP+ +++++ME+ + +L    + + + D L    
Sbjct: 5   DPAITKLLEYGKTKHSVTWDELNEYLPPEILNTDKMENVLMLLEKNHVQIEEEDTLDDAD 64

Query: 84  ----------EDEEGSEDSLDLASSASNSSVFLQKR--KDSADRSTDDPVRMYLREMGSI 131
                        + + D  D     +      +KR   +  D S DDPVR+YLRE+G  
Sbjct: 65  ASADDASADDASADDASDDDDSTEEETKPEEPERKRLVYNDKDSSGDDPVRLYLREIGKE 124

Query: 132 ELLSREGEIAIAKRIEAG 149
            LL+ E E+ ++K++E G
Sbjct: 125 HLLTAEQEVFLSKKMEDG 142


>gi|283769573|ref|ZP_06342469.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
 gi|283103841|gb|EFC05227.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
          Length = 413

 Score =  303 bits (776), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 154/283 (54%), Positives = 204/283 (72%), Gaps = 7/283 (2%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A   DS+     EI  + +   +  SE   I   + +G+ EA   +  ++ +NLRLV+S+
Sbjct: 136 ATSGDSVKMYLKEIGRVPL---LKASEEIEIAKKIEQGDEEA---RNVLISSNLRLVVSI 189

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TI
Sbjct: 190 AKKYVGRGMQFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTI 249

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLET 578
           RIPVHM + I+K+ R  R +  ++ REPTPEEI+  L  +  + VR++ KI  +P+SLET
Sbjct: 250 RIPVHMVETINKLTRVERSLVQELSREPTPEEISACLEGISADKVREIKKIALDPVSLET 309

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+ED SHLGDFIEDK+A+SP   A    L++    VL+ LT REE+VLR+RFG+    
Sbjct: 310 PIGEEDDSHLGDFIEDKDALSPDQYASNQLLKDEINDVLSGLTEREEKVLRLRFGLYDGR 369

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG++F VTRERIRQIEAKA+RKLKHP+RSK+L+ F D
Sbjct: 370 TRTLEEVGREFNVTRERIRQIEAKALRKLKHPNRSKRLKDFFD 412



 Score = 37.4 bits (85), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 24/34 (70%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++ D V+MYL+E+G + LL    EI IAK+IE G
Sbjct: 137 TSGDSVKMYLKEIGRVPLLKASEEIEIAKKIEQG 170


>gi|169351085|ref|ZP_02868023.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
 gi|169292147|gb|EDS74280.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
          Length = 415

 Score =  303 bits (775), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 145/231 (62%), Positives = 182/231 (78%), Gaps = 1/231 (0%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+
Sbjct: 184 NLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRA 243

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKIT 570
           IADQ+ TIRIPVHM + I+K+ R  R +  ++ REPT EEIA+++  M  E VR++ KI+
Sbjct: 244 IADQARTIRIPVHMVETINKLTRIQRLLIQELGREPTAEEIAERIDGMTPEKVREIQKIS 303

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            EP+SLETPIG+ED SHLGDFIED+  +SP D A    L++    VL  LT REE+VLR+
Sbjct: 304 LEPVSLETPIGEEDDSHLGDFIEDEGVMSPDDYAANELLKDELNEVLLELTDREEKVLRL 363

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHPSRSK+L+ FLD
Sbjct: 364 RFGLDDGRTRTLEEVGKEFSVTRERIRQIEAKALRKLKHPSRSKRLKDFLD 414



 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D+L +   A ++   + K +  ++   +DPV+MYL+E+G +ELLS + EI +AK+I  
Sbjct: 113 TSDTLHMYQVA-DADAEMDKNQLGSNVKINDPVKMYLKEIGRVELLSHDDEIKLAKKILE 171

Query: 149 G 149
           G
Sbjct: 172 G 172


>gi|255655465|ref|ZP_05400874.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-23m63]
 gi|296451458|ref|ZP_06893195.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296880193|ref|ZP_06904159.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
 gi|296259725|gb|EFH06583.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296428782|gb|EFH14663.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
          Length = 388

 Score =  303 bits (775), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 146/239 (61%), Positives = 195/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA W
Sbjct: 150 IAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATW 209

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK++ M  + 
Sbjct: 210 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAKEMEMTEDK 269

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A +P ++A  + L+E    VL SL  
Sbjct: 270 VREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAYSLLKEQIEDVLGSLND 329

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 330 REQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 388



 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 42/148 (28%), Positives = 72/148 (48%), Gaps = 16/148 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV------------ 77
           + K +I+  +++G +T+ E+       E+  +Q+E+    L N+GI +            
Sbjct: 14  TAKTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKADIDF 73

Query: 78  -VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELL 134
            V  DDL      ED+ +  S   +S++ ++    S  +  S DDPVRMYL+E+G I LL
Sbjct: 74  SVADDDLSIGHLDEDA-EAISHEDSSAIEIETVDLSLPKGISIDDPVRMYLKEIGKIPLL 132

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPL 162
               E+  A+R+  G  +    L E+ L
Sbjct: 133 KPHEEVEFARRMHEGDEIAKQRLVEANL 160


>gi|254975009|ref|ZP_05271481.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-66c26]
 gi|255092397|ref|ZP_05321875.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile CIP
           107932]
 gi|255100481|ref|ZP_05329458.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-63q42]
 gi|255306421|ref|ZP_05350592.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile ATCC
           43255]
 gi|255314137|ref|ZP_05355720.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-76w55]
 gi|255516815|ref|ZP_05384491.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-97b34]
 gi|255649917|ref|ZP_05396819.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-37x79]
 gi|260683071|ref|YP_003214356.1| RNA polymerase factor sigma-43 [Clostridium difficile CD196]
 gi|260686669|ref|YP_003217802.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
 gi|306520001|ref|ZP_07406348.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-32g58]
 gi|260209234|emb|CBA62522.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           CD196]
 gi|260212685|emb|CBE03759.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
          Length = 388

 Score =  303 bits (775), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 146/239 (61%), Positives = 195/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA W
Sbjct: 150 IAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATW 209

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK++ M  + 
Sbjct: 210 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAKEMEMTEDK 269

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A +P ++A  + L+E    VL SL  
Sbjct: 270 VREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAYSLLKEQIEDVLGSLND 329

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 330 REQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 388



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/150 (30%), Positives = 71/150 (47%), Gaps = 20/150 (13%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV------------ 77
           + K +I+  +++G +T+ E+       E+  +Q+E+    L N+GI +            
Sbjct: 14  TAKTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKADIDF 73

Query: 78  -VDGDDLE----DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            V  DDL     DE+    S D +S+    +V L   K     S DDPVRMYL+E+G I 
Sbjct: 74  SVADDDLSIGHLDEDAEAISHDDSSAIEIETVDLSLPKGI---SIDDPVRMYLKEIGKIP 130

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           LL    E+  A+R+  G  +    L E+ L
Sbjct: 131 LLKPHEEVEFARRMHEGDEIAKQRLVEANL 160


>gi|320530862|ref|ZP_08031899.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136896|gb|EFW28841.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 381

 Score =  303 bits (775), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 141/248 (56%), Positives = 190/248 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + R+ E   + A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 130 VELARRMEAGDASARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 189

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+VR +R +  ++ R+ T E
Sbjct: 190 SKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKLVRVSRSLLQELGRDATAE 249

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + V  VR+++KI +EP+SLETP+G+E+ SHLGDFIED+ A+ P D+A    L+
Sbjct: 250 EIAKEMGLSVVRVREIMKIAQEPVSLETPVGEEEDSHLGDFIEDEAALDPADAASMMLLK 309

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  + VL +L PRE  VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 310 EQISEVLKTLAPREAEVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHP 369

Query: 671 SRSKKLRS 678
            R +KL+ 
Sbjct: 370 VRLRKLQG 377



 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/127 (33%), Positives = 67/127 (52%), Gaps = 10/127 (7%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  EL   L   ++S ++M+D        G+ +VD  D+E    +ED+  LA+  ++
Sbjct: 30  GTLTFSELIEELEKSDMSPDEMDDLYGRFQEFGVEIVDDTDME-AMAAEDAESLAADDAD 88

Query: 102 SSVFLQKRKDSADRST------DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                Q+     D S       DDPVRMYL+E+G + LL+ E E+ +A+R+EAG A    
Sbjct: 89  ME---QEEAVEIDLSVPEGVALDDPVRMYLKEIGRVPLLTAEEEVELARRMEAGDASARH 145

Query: 156 SLCESPL 162
            L E+ L
Sbjct: 146 RLEEANL 152


>gi|196229539|ref|ZP_03128404.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196226771|gb|EDY21276.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 671

 Score =  303 bits (775), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 151/271 (55%), Positives = 198/271 (73%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           ++K   + T +S  EF+     ++    +A  AK EMVEANLRLVIS+AKKYTNRGL FL
Sbjct: 398 KLKDQQMRTWLSPEEFQEEYKELKVWLKKALKAKTEMVEANLRLVISIAKKYTNRGLSFL 457

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 458 DLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 517

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           ++R  +++     REPTPEE+A ++ +PVE VR VLK+ ++PISL++P+G+ D +  GDF
Sbjct: 518 LMRVQKQLVQDYGREPTPEEVADEIQLPVERVRAVLKMAQQPISLQSPVGESDDTSFGDF 577

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IEDK A +  D      L+E    VL +LT RE +VL  RFG+      TLEEVG+QF V
Sbjct: 578 IEDKGAENLSDMTAIVLLKEKIKDVLETLTERERQVLEQRFGLVDGYSRTLEEVGRQFKV 637

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RK++HP+R ++L  FL+ 
Sbjct: 638 TRERIRQIEAKALRKMRHPTRIRQLEGFLEA 668



 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/116 (35%), Positives = 68/116 (58%), Gaps = 8/116 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++IKLA+++GY+T ++LN  LP +    ++ME  +  L +M I +++  D+       D
Sbjct: 136 RELIKLAKEQGYLTFDDLNEALPDNVNDPDEMETIMNRLRSMEIEIIEASDV-------D 188

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                  A +     +K +   D   DDPVRMYL++MG + LL+RE E+ I+KRIE
Sbjct: 189 RFKDGKKADDQEEEEEKPEAKLD-ILDDPVRMYLKQMGQVPLLTREQEVEISKRIE 243


>gi|126699059|ref|YP_001087956.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile 630]
 gi|115250496|emb|CAJ68320.1| RNA polymerase sigma factor SigA1 (sigma-43) [Clostridium
           difficile]
          Length = 390

 Score =  303 bits (775), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 146/239 (61%), Positives = 195/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA W
Sbjct: 152 IAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATW 211

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK++ M  + 
Sbjct: 212 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAKEMEMTEDK 271

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A +P ++A  + L+E    VL SL  
Sbjct: 272 VREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAYSLLKEQIEDVLGSLND 331

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 332 REQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 390



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/150 (30%), Positives = 71/150 (47%), Gaps = 20/150 (13%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV------------ 77
           + K +I+  +++G +T+ E+       E+  +Q+E+    L N+GI +            
Sbjct: 16  TAKTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKADIDF 75

Query: 78  -VDGDDLE----DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            V  DDL     DE+    S D +S+    +V L   K     S DDPVRMYL+E+G I 
Sbjct: 76  SVADDDLSIGHLDEDAEAISHDDSSAIEIETVDLSLPKGI---SIDDPVRMYLKEIGKIP 132

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           LL    E+  A+R+  G  +    L E+ L
Sbjct: 133 LLKPHEEVEFARRMHEGDEIAKQRLVEANL 162


>gi|158320313|ref|YP_001512820.1| RpoD family RNA polymerase sigma factor [Alkaliphilus oremlandii
           OhILAs]
 gi|158140512|gb|ABW18824.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           oremlandii OhILAs]
          Length = 372

 Score =  303 bits (775), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 135 AKKRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGFKFSTYATWW 194

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIA ++ +  E V
Sbjct: 195 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAAEMDLSEEKV 254

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A  + L+E    VL +LTPR
Sbjct: 255 REILKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFSLLKEQLVEVLDTLTPR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 315 EQKVLRLRFGLDDGRARTLEEVGKKFDVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 372



 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 47/151 (31%), Positives = 77/151 (50%), Gaps = 15/151 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD------- 81
           ++ K +I+  ++RG +T  E+   L   ++  EQ+++     S+MGI++V GD       
Sbjct: 10  ETVKNLIEKGKKRGMITYSEVMDALEDVDLDKEQIDEIYDHFSSMGIDIV-GDKRDMVED 68

Query: 82  -DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D+ DE   E  ++      + +  L+        + DDPVRMYL+E+G + LLS E EI
Sbjct: 69  LDMMDESVLEPEVEAEEIIEDDASLLK------GVNIDDPVRMYLKEIGKVPLLSAEEEI 122

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +AKR++AG       L E+ L     I  R
Sbjct: 123 ELAKRMDAGDEEAKKRLVEANLRLVVSIAKR 153


>gi|325478784|gb|EGC81895.1| RNA polymerase sigma factor RpoD [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 604

 Score =  303 bits (775), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 141/237 (59%), Positives = 189/237 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW
Sbjct: 368 AKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 427

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA+++ + VE V
Sbjct: 428 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKV 487

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++ KI++EP+SLETPIG+ED SHLGDFIED  A+ P ++A    LRE    VL+ L  R
Sbjct: 488 QEIRKISQEPVSLETPIGEEDDSHLGDFIEDDTAIDPGEAANYTMLREQLNDVLSCLGAR 547

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 548 EKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 604



 Score = 44.3 bits (103), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 36/122 (29%), Positives = 59/122 (48%), Gaps = 12/122 (9%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD--LEDEEGSED------ 91
           Q G +T  ++  F    E+  +  +  +  + ++GI +V+  +  LEDEE +ED      
Sbjct: 28  QDGLITYSQIYTFENFKEMEDDSKKFVINQVLSLGIEIVEKSETVLEDEEVTEDMKDDLS 87

Query: 92  ---SLDLASSASNSSVFLQKRKD-SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               L+           L K  D       DDPV+MYL+E+G + LL+   EI +A+R+E
Sbjct: 88  DDEDLEEEIEEDEVEEDLNKNVDIMVGVKVDDPVKMYLKEIGKVSLLTATEEIILARRME 147

Query: 148 AG 149
            G
Sbjct: 148 MG 149


>gi|313897024|ref|ZP_07830571.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974471|gb|EFR39939.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 381

 Score =  303 bits (775), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 141/248 (56%), Positives = 190/248 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + R+ E   + A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 130 VELARRMEAGDASARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 189

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+VR +R +  ++ R+ T E
Sbjct: 190 SKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKLVRVSRSLLQELGRDATAE 249

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + V  VR+++KI +EP+SLETP+G+E+ SHLGDFIED+ A+ P D+A    L+
Sbjct: 250 EIAKEMGLSVVRVREIMKIAQEPVSLETPVGEEEDSHLGDFIEDEAALDPADAASMMLLK 309

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  + VL +L PRE  VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 310 EQISEVLKTLAPREAEVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHP 369

Query: 671 SRSKKLRS 678
            R +KL+ 
Sbjct: 370 VRLRKLQG 377



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 43/127 (33%), Positives = 67/127 (52%), Gaps = 10/127 (7%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  EL   L   ++S ++M+D        G+ +VD  D+E    +ED+  LA+  ++
Sbjct: 30  GTLTFSELIEELEKSDMSPDEMDDLYGRFREFGVEIVDDTDME-AMAAEDAESLAADDAD 88

Query: 102 SSVFLQKRKDSADRST------DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                Q+     D S       DDPVRMYL+E+G + LL+ E E+ +A+R+EAG A    
Sbjct: 89  ME---QEEAVEIDLSVPEGVALDDPVRMYLKEIGRVPLLTAEEEVELARRMEAGDASARH 145

Query: 156 SLCESPL 162
            L E+ L
Sbjct: 146 RLEEANL 152


>gi|317132028|ref|YP_004091342.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470007|gb|ADU26611.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 372

 Score =  302 bits (774), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 149/247 (60%), Positives = 196/247 (79%), Gaps = 1/247 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R GE + + A+K + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GY
Sbjct: 127 RMGEGDVA-ARKRLSEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGY 185

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KVVR  R++  ++ R+P  EEIA+
Sbjct: 186 KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVVRVERQLLQELGRQPQAEEIAE 245

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            + M V+ VR+++K+ +EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E   
Sbjct: 246 LMGMSVDKVREIMKVAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAASHTLLKEQLG 305

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL +LT RE +VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSK
Sbjct: 306 DVLKTLTQREAKVLRLRFGLDDGRPRTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 365

Query: 675 KLRSFLD 681
           KL+ FLD
Sbjct: 366 KLKDFLD 372



 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/146 (28%), Positives = 70/146 (47%), Gaps = 23/146 (15%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD------ 82
           D   ++I+  + +G +T+ E+   L   +  +EQ E     L +  I+V+D  +      
Sbjct: 10  DRIAELIETGKTKGNLTMTEITDALEEIDFDAEQTEKLYEALEHHNIDVLDDQEEPTPEE 69

Query: 83  ------LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
                  + EE S+ ++DL SS S   +           + DDPV++YL+E+G + LLS 
Sbjct: 70  LEGDLEEDAEEASKPNVDLESSLSAEGI-----------AIDDPVKVYLKEIGRVPLLSG 118

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPL 162
           E EI +AKR+  G       L E+ L
Sbjct: 119 EEEIELAKRMGEGDVAARKRLSEANL 144


>gi|160935059|ref|ZP_02082445.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
 gi|156866512|gb|EDO59884.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
          Length = 365

 Score =  302 bits (774), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 152/248 (61%), Positives = 197/248 (79%), Gaps = 1/248 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E + S AKK + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  G
Sbjct: 119 IRISEGDES-AKKRLSEANLRLVVSIAKRYLGRGMQFLDLIQEGNLGLIKAVEKFDYTKG 177

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV + + ++ +    EPT +EIA
Sbjct: 178 YKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVKKVSSQLLHTNGHEPTADEIA 237

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L MPV+ VR+++++ +EP+SLETPIG+E+ SHLGDFI D +A +P D+A    L+E  
Sbjct: 238 LELDMPVDKVREIMRVAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPADAASHILLKEQL 297

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 298 AEVLDTLTPREEKVLRLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 357

Query: 674 KKLRSFLD 681
           KKL+ FLD
Sbjct: 358 KKLKDFLD 365



 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 35/125 (28%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           A+ +G ++ +E+   +   +   EQ+E     L  MG+ +V+  D E+    + + DL  
Sbjct: 19  AKAKGQLSNKEILDAIGELDFEPEQLEKFYDTLEAMGVEIVE--DFEEIPLDDINFDLVP 76

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
              + +    +       + DDPV++YL+E+G + LLS E EI +A RI  G       L
Sbjct: 77  DDEDDA----EVPAVESVAIDDPVKVYLKEIGRVPLLSPEEEIDLAIRISEGDESAKKRL 132

Query: 158 CESPL 162
            E+ L
Sbjct: 133 SEANL 137


>gi|302874342|ref|YP_003842975.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
 gi|307689391|ref|ZP_07631837.1| RNA polymerase sigma factor RpoD [Clostridium cellulovorans 743B]
 gi|302577199|gb|ADL51211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
          Length = 363

 Score =  302 bits (774), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 126 AKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEE+A+K+ MPV+ V
Sbjct: 186 IRQAITRAIADQARTIRIPVHMVETINKLLRITRQLVQELGRDPLPEELAEKMEMPVDKV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ KI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E    VL +LTPR
Sbjct: 246 IEIRKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTMLKEQLINVLDTLTPR 305

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 306 EEKVLRLRFGLDDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 363



 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 47/131 (35%), Positives = 70/131 (53%), Gaps = 16/131 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I+  ++ G +T  E+   L   E+S EQ+E    +L ++GI V+   D++D E +ED
Sbjct: 21  KSLIETGKKTGSLTYTEIIDELENIELSPEQIEKIYEVLESVGIEVIG--DMKDIEVTED 78

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             DL+     +               DDPVRMYL+E+G + LLS E EI +A+RIEAG  
Sbjct: 79  EFDLSVPEGIA--------------IDDPVRMYLKEIGKVPLLSPETEIELAERIEAGDP 124

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 125 AAKKKLAEANL 135


>gi|302338588|ref|YP_003803794.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635773|gb|ADK81200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 612

 Score =  302 bits (773), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 170/374 (45%), Positives = 238/374 (63%), Gaps = 19/374 (5%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + +L  L+  L ++Q  I    E+  D +KRI+H + E  R+ +  G+     L R+ GR
Sbjct: 249 RHELFSLIEELDIHQEEIVGFSEKFSDTAKRILHYQREQERIERRLGVTSSKEL-RNMGR 307

Query: 378 ELDPHWVSYAKDFPEGEWK--NFVACEVDSIL-KIR----NE--IKSISVETGISISEFR 428
            L           PE   K    +    D I  KIR    NE  ++SI +E   +I    
Sbjct: 308 GLA---------IPERRRKIEEELQLSSDQIKEKIRQIQVNEKHLQSIELEFEDAIDSIL 358

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                +  G+     AK  +++ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF
Sbjct: 359 ERSKEISHGQVMMKNAKDRLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKF 418

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KVVR +R++   + R+PT
Sbjct: 419 EYSKGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVVRESRQLMQILGRDPT 478

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A++L   V  V+ V  + +EPISLETPIG+E+ S LGDFIEDK+  +P +      
Sbjct: 479 DEEVAERLGWTVLRVKSVKNVAREPISLETPIGEEEDSLLGDFIEDKDIENPANQTAFTL 538

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    V+ +L PRE+ VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R+L+
Sbjct: 539 LQEQLQEVMKTLPPREQEVLKMRFGLDDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLR 598

Query: 669 HPSRSKKLRSFLDG 682
           HP RS++L+ ++D 
Sbjct: 599 HPKRSRRLKDYIDN 612



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 85/172 (49%), Gaps = 32/172 (18%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD------- 79
           +D S  K+++ A+++  +T +E+N FLP   V+SE++E+ +A+L    I++ D       
Sbjct: 6   ADKSVAKLLEYAKEKKRITYDEVNDFLPDSIVNSEKIEEVIALLEEHNISLDDEQDKNDD 65

Query: 80  -----------------------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
                                  GD  E  + S + + L  S   +   +   KD++  +
Sbjct: 66  MPDDDGELDDDFVDLDDDDDDSDGDMDEKGDTSLEDIPLKRSPDRTRRVVYNDKDAS--A 123

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            DDP+R+YLRE+G   LL+ E E+ ++K++E G A++   + ES +    L 
Sbjct: 124 VDDPIRLYLREIGKESLLTAEQEVELSKQMEHGEAIIKRVVKESGMIIPQLF 175


>gi|195953901|ref|YP_002122191.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195933513|gb|ACG58213.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 578

 Score =  302 bits (773), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 143/273 (52%), Positives = 201/273 (73%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L ++ EI+ I    G+   E   I++++ +G      +K  MV++NLRLV+S+AKKY NR
Sbjct: 303 LALQREIEDIERRLGVLPEELNKIINIIEQGRKRVKESKDMMVKSNLRLVVSIAKKYINR 362

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW+KQAITR+IADQ+ TIRIPVHM 
Sbjct: 363 GLHFLDLIQEGNMGLMKAVDKYDYKKGFKFSTYATWWIKQAITRAIADQAKTIRIPVHMI 422

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ + ++++  +  REP+PEEIAK L M  E VRK+LK  +EPISLETPIGD++ +
Sbjct: 423 ETINKISKVSKKLFQEYGREPSPEEIAKALNMSPEKVRKILKSIQEPISLETPIGDDEDT 482

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HL DFIED +  +P ++  +  LRE   +++ +L+ +E  V+  RFG+    +HTLE+VG
Sbjct: 483 HLKDFIEDSSISNPEEATARRLLREQIEKIINTLSDKEREVIMYRFGLVDGIEHTLEQVG 542

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             F +TRERIRQIE+KAIRK++HPSR+K L+ F
Sbjct: 543 TMFNLTRERIRQIESKAIRKIRHPSRAKYLKDF 575



 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/162 (30%), Positives = 85/162 (52%), Gaps = 17/162 (10%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-------DE 86
           ++++ +++GYVT +++N ++  D V S+++E    +LS  GI +++ D+ E       D 
Sbjct: 10  LLEIGKEKGYVTYDDINEYVSEDLVESDELESLFDILSEKGIQILE-DEAEAAIHHETDN 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  E+  ++  SAS            AD   +D VR YL+EMG I LL R  EI  AK I
Sbjct: 69  EILEEDDEMIVSASIVE---------ADLKNNDSVRYYLKEMGKIALLGRADEIEHAKYI 119

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           E GR  +   L  +      ++ +  ++ DG    +EI+D++
Sbjct: 120 EMGRKQLRRGLLRTSFLVDMVLRYWAKVCDGKMRSQEILDMQ 161


>gi|328948111|ref|YP_004365448.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328448435|gb|AEB14151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 655

 Score =  302 bits (773), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 148/277 (53%), Positives = 198/277 (71%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I KI  +++ +  +   S+ E   +   + +G  +   AK  ++ ANLRLV+S+AKKYTN
Sbjct: 379 IQKIDRKLRELEYDFENSVDEILEMKKEIERGRLQLEQAKNRLINANLRLVVSIAKKYTN 438

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQ  DLIQEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM
Sbjct: 439 RGLQLFDLIQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHM 498

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            ++I+KVVR +R++  K  REPT EEIA +L+ P+  V++V  + +EPISLETPIG+E+ 
Sbjct: 499 IEQINKVVRESRQLMQKYGREPTDEEIAAQLSWPLARVKQVKNVAREPISLETPIGEEED 558

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDFIEDK   +P +      L+E    VL++L  RE+ VL+MRFG+      TLEEV
Sbjct: 559 SSLGDFIEDKEIENPANQTAYTLLQEQLRSVLSTLPQREQEVLKMRFGLDDGYSLTLEEV 618

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G  F VTRERIRQIEAKA+R+L+HP RS  LR ++D 
Sbjct: 619 GLYFNVTRERIRQIEAKALRRLRHPRRSNGLRDYIDS 655



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 76/131 (58%), Gaps = 5/131 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL--ED 85
           D + KK++  A  +  ++ +E+   L P+ V+S +ME+ + +L+   I V++ D L  ++
Sbjct: 71  DPNVKKLLDYACSKQIISWDEITEILTPEFVNSPKMEEVLQLLTKNNIQVMEEDSLLDDE 130

Query: 86  EEGSEDSLDLASSASNSSVFLQKRK---DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           E   ED     S + + S F +K +   +  +   DDP+R+YLRE+G   LL+ E E+ +
Sbjct: 131 ENEEEDDEGALSDSEDDSKFDEKHRLVSNDKEYGVDDPIRLYLREIGKENLLTAEQEVIL 190

Query: 143 AKRIEAGRAMM 153
           +K++E G+ ++
Sbjct: 191 SKQMEDGQNII 201


>gi|253576089|ref|ZP_04853421.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251844432|gb|EES72448.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 374

 Score =  302 bits (773), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 148/238 (62%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD   G+KFSTYA WW
Sbjct: 137 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHKKGFKFSTYATWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA ++ + VE V
Sbjct: 197 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPAPEEIAAEMDLSVEKV 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E    VL +LT R
Sbjct: 257 REIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTER 316

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 317 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score = 43.9 bits (102), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 30/45 (66%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +DPVRMYL+E+G + LLS + E+ +AKRIE G       L E+ L
Sbjct: 102 NDPVRMYLKEIGRVPLLSADDEMELAKRIENGDEEAKRRLAEANL 146


>gi|227499774|ref|ZP_03929874.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227218160|gb|EEI83426.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 606

 Score =  301 bits (772), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 141/237 (59%), Positives = 189/237 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW
Sbjct: 370 AKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 429

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA+++ + V+ V
Sbjct: 430 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVDKV 489

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++ KI++EP+SLETPIG+ED SHLGDFIED  AV P ++A    LRE    VL+ L  R
Sbjct: 490 QEIRKISQEPVSLETPIGEEDDSHLGDFIEDDTAVDPGEAANYTMLREQLNDVLSCLGAR 549

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 550 EKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 606



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 25/33 (75%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            DDPV+MYL+E+G + LL+   EI +A+R+E G
Sbjct: 119 VDDPVKMYLKEIGKVSLLTATEEIILARRMEMG 151


>gi|297379310|gb|ADI34197.1| RNA polymerase sigma factor RpoD [Helicobacter pylori v225d]
          Length = 677

 Score =  301 bits (771), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 192/575 (33%), Positives = 320/575 (55%), Gaps = 72/575 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L +
Sbjct: 162 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALIN 221

Query: 177 GTTLLREII-----DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
               ++E+      D E  +    K       E    ++R+    EK+R  V++ +   +
Sbjct: 222 RERRVKELFRSFDDDDENSVSDSKKDD--DSEEYEENEERKKVVSEKDRKRVEKVQESFK 279

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS-AMEDQLRPKVMCALDEIAEV 290
           +  K  K+    +++P          +DE ED+    L+ A + Q     +  L+  +++
Sbjct: 280 ALDKAKKEWLKALEAP----------VDEKEDELVRLLTLAYKRQTLKDRLYDLEPTSKL 329

Query: 291 YREL-RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             EL ++++    +G   EK   + K L+ KL     +L  N  +I   +  + +++K  
Sbjct: 330 INELVKTMETTLKSGDGFEK---ELKRLEYKLPLFNDTLIANHKKI---LANITNMTKED 383

Query: 350 MHNEGELLRLAQSYGIKRDVFLERH---QGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +  +     +   Y   + +FL +    +G +LDP+                        
Sbjct: 384 IIAQVPEATMVSVYMDLKKLFLTKEASEEGFDLDPN------------------------ 419

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
                              + + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+R
Sbjct: 420 -------------------KLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSR 460

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM 
Sbjct: 461 GLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMI 520

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D  
Sbjct: 521 DTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDG 580

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEV 645
             GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+
Sbjct: 581 KFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEI 640

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 641 GKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 675


>gi|325849230|ref|ZP_08170681.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325480230|gb|EGC83297.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 612

 Score =  301 bits (771), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 142/250 (56%), Positives = 196/250 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + +   +A+ AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+
Sbjct: 363 VKRLNRAIFDANRAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDY 422

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ E
Sbjct: 423 NRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNE 482

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ + VE V+++ KI +EP+SLETPIG+E+ SHLGDFIED  A++P D+A  + LR
Sbjct: 483 EIAEQMGIEVEKVQEIRKIAQEPVSLETPIGEEEDSHLGDFIEDDTAINPDDAANYSMLR 542

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    VL+ L  RE+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P
Sbjct: 543 DQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSP 602

Query: 671 SRSKKLRSFL 680
           ++S+ L+ FL
Sbjct: 603 NKSELLKDFL 612



 Score = 42.0 bits (97), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DDPV+MYL+E+G ++LL    EI +AK++E G
Sbjct: 126 DDPVKMYLKEIGKVKLLDAHEEIFLAKKMELG 157


>gi|308061382|gb|ADO03270.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Cuz20]
          Length = 672

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 192/575 (33%), Positives = 319/575 (55%), Gaps = 72/575 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L +
Sbjct: 157 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALIN 216

Query: 177 GTTLLREII-----DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
               ++E+      D E  +    K       E    ++R+    EK+R  V++ +   +
Sbjct: 217 RERRVKELFRSFDDDDENSVSDSKKDD--DSEEYEENEERKKVVSEKDRKRVEKVQESFK 274

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS-AMEDQLRPKVMCALDEIAEV 290
           +  K  K+    +++P          +DE ED+    L+ A + Q     +  L+  +++
Sbjct: 275 ALDKAKKEWLKALEAP----------VDEKEDELVRLLTLAYKRQTLKDRLYDLEPTSKL 324

Query: 291 YREL-RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             EL ++++    +G   EK   + K L+ KL     +L  N  +I   +  +  ++K  
Sbjct: 325 INELVKTMETTLKSGDGFEK---ELKRLEYKLPLFNDTLIANHKKI---LANITSMTKED 378

Query: 350 MHNEGELLRLAQSYGIKRDVFLERH---QGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +  +     +   Y   + +FL +    +G +LDP+                        
Sbjct: 379 IIAQVPEATMVSVYMDLKKLFLTKEASEEGFDLDPN------------------------ 414

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
                              + + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+R
Sbjct: 415 -------------------KLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSR 455

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM 
Sbjct: 456 GLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMI 515

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D  
Sbjct: 516 DTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDG 575

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEV 645
             GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+
Sbjct: 576 KFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEI 635

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 636 GKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 670


>gi|77165531|ref|YP_344056.1| hypothetical protein Noc_2066 [Nitrosococcus oceani ATCC 19707]
 gi|76883845|gb|ABA58526.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
           19707]
          Length = 579

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 143/266 (53%), Positives = 201/266 (75%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           + VE G+ + E + I   + + + +A  AK +MVEANLRLV+SVAKKY NRGL FLDLIQ
Sbjct: 313 VEVEAGLPLDELKAIHQRLVRSQFQAQRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQ 372

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KFD+  GYKFSTYA WW++QAITR+I DQS TIRIPVH+ +K+ K+ R 
Sbjct: 373 EGNIGLMKAVDKFDYHRGYKFSTYAHWWIRQAITRAIDDQSRTIRIPVHVMEKLSKLNRA 432

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           + ++  +  RE  PEE+A++LA+  + + ++ +I K+PISLETP+G ++ S LG+ +ED+
Sbjct: 433 SYQLRQEKGREGRPEELAERLALSEQQIHRMHEIAKQPISLETPLGKDEDSQLGELMEDE 492

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              +P++ AI A L+    ++LA+L+PRE +V+ MRFGIGM+TDHTL EV +QF ++RER
Sbjct: 493 QVPNPMEVAITAGLQTGAQQLLAALSPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRER 552

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEA+A+ KL+    SK LR+FL+
Sbjct: 553 IRQIEAQALGKLRRLGHSKALRNFLE 578



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 43/163 (26%), Positives = 77/163 (47%), Gaps = 7/163 (4%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           F+   +  K++I   + +G +T EEL  ++  +   S++ E    +  +       G D 
Sbjct: 3   FEMRQEELKRLILKGKAQGLLTEEELQDYIIQEVEDSDEAETMAHLFHHH-----QGLD- 56

Query: 84  EDEEGSEDSLDLASSASNS-SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           E  E  + +L L +S+    +  L   +  +  +  D V  Y+REMG+  LL+RE EI +
Sbjct: 57  EFNEALDSTLLLKNSSEEEIAETLPTLEGESTGAVSDMVYAYMREMGAHALLTREEEITL 116

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           AK IE G +    +L   P     L+ W +E+  G   L++ +
Sbjct: 117 AKAIETGLSQSTEALGNCPAAVAELVRWAEEVATGKGRLKDWL 159


>gi|310659059|ref|YP_003936780.1| RNA polymerase sigma factor rpod [Clostridium sticklandii DSM 519]
 gi|308825837|emb|CBH21875.1| RNA polymerase sigma factor RpoD [Clostridium sticklandii]
          Length = 376

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 145/239 (60%), Positives = 195/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAKK++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA W
Sbjct: 138 IAKKKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGFKFSTYATW 197

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  +  R+P PEE+AK++ MP E 
Sbjct: 198 WIRQAITRAIADQARTIRIPVHMVETINKLIRVHRQLLQEYGRDPKPEELAKEMDMPEEK 257

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +R+++KI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A  + L+E    VL +L  
Sbjct: 258 IREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAYSLLKEQLEDVLCTLNE 317

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 318 REQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 376



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 72/136 (52%), Gaps = 6/136 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE---G 88
           K +I   ++ G +T E++   L   E+  EQ+E+     + +GI+++D ++++D+     
Sbjct: 14  KSLIDKGKKDGSLTYEQIGEALSEMELDKEQIENIYDTFAQLGIDILD-ENIKDDTVIFN 72

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            E + +  +   +      K   S  +  S DDPVRMYL+E+G I LLS E EI +A+++
Sbjct: 73  KEFNKNPDAETEDEDEDASKLDLSIPKGVSIDDPVRMYLKEIGKIPLLSAEEEIDLAEKM 132

Query: 147 EAGRAMMMASLCESPL 162
             G  +    L E+ L
Sbjct: 133 GYGDEIAKKKLVEANL 148


>gi|256545301|ref|ZP_05472665.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
 gi|256398982|gb|EEU12595.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
          Length = 614

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 142/250 (56%), Positives = 196/250 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + +   +A+ AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+
Sbjct: 365 VKRLNRAIFDANRAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDY 424

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ E
Sbjct: 425 NRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNE 484

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ + VE V+++ KI +EP+SLETPIG+E+ SHLGDFIED  A++P D+A  + LR
Sbjct: 485 EIAEQMGIEVEKVQEIRKIAQEPVSLETPIGEEEDSHLGDFIEDDTAINPDDAANYSMLR 544

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    VL+ L  RE+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P
Sbjct: 545 DQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSP 604

Query: 671 SRSKKLRSFL 680
           ++S+ L+ FL
Sbjct: 605 NKSELLKDFL 614



 Score = 42.0 bits (97), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DDPV+MYL+E+G ++LL    EI +AK++E G
Sbjct: 128 DDPVKMYLKEIGKVKLLDAHEEIFLAKKMELG 159


>gi|212697198|ref|ZP_03305326.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675973|gb|EEB35580.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 617

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 142/250 (56%), Positives = 196/250 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + +   +A+ AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+
Sbjct: 368 VKRLNRAIFDANRAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDY 427

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ E
Sbjct: 428 NRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNE 487

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ + VE V+++ KI +EP+SLETPIG+E+ SHLGDFIED  A++P D+A  + LR
Sbjct: 488 EIAEQMGIEVEKVQEIRKIAQEPVSLETPIGEEEDSHLGDFIEDDTAINPDDAANYSMLR 547

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    VL+ L  RE+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P
Sbjct: 548 DQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSP 607

Query: 671 SRSKKLRSFL 680
           ++S+ L+ FL
Sbjct: 608 NKSELLKDFL 617



 Score = 41.6 bits (96), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DDPV+MYL+E+G ++LL    EI +AK++E G
Sbjct: 131 DDPVKMYLKEIGKVKLLDAHEEIFLAKKMELG 162


>gi|254434698|ref|ZP_05048206.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|207091031|gb|EDZ68302.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 595

 Score =  301 bits (770), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 143/266 (53%), Positives = 201/266 (75%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           + VE G+ + E + I   + + + +A  AK +MVEANLRLV+SVAKKY NRGL FLDLIQ
Sbjct: 329 VEVEAGLPLDELKAIHQRLVRSQFQAQRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQ 388

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KFD+  GYKFSTYA WW++QAITR+I DQS TIRIPVH+ +K+ K+ R 
Sbjct: 389 EGNIGLMKAVDKFDYHRGYKFSTYAHWWIRQAITRAIDDQSRTIRIPVHVMEKLSKLNRA 448

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           + ++  +  RE  PEE+A++LA+  + + ++ +I K+PISLETP+G ++ S LG+ +ED+
Sbjct: 449 SYQLRQEKGREGRPEELAERLALSEQQIHRMHEIAKQPISLETPLGKDEDSQLGELMEDE 508

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              +P++ AI A L+    ++LA+L+PRE +V+ MRFGIGM+TDHTL EV +QF ++RER
Sbjct: 509 QVPNPMEVAITAGLQTGAQQLLAALSPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRER 568

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEA+A+ KL+    SK LR+FL+
Sbjct: 569 IRQIEAQALGKLRRLGHSKALRNFLE 594



 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 79/166 (47%), Gaps = 7/166 (4%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           S+ F+   +  K++I   + +G +T EEL  ++  +   S++ E    +  +       G
Sbjct: 16  SMDFEMRQEELKRLILKGKAQGLLTEEELQDYIIQEVEDSDEAETMAHLFHHH-----QG 70

Query: 81  DDLEDEEGSEDSLDLASSASNS-SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D E  E  + +L L +S+    +  L   +  +  +  D V  Y+REMG+  LL+RE E
Sbjct: 71  LD-EFNEALDSTLLLKNSSEEEIAETLPTLEGESTGAVSDMVYAYMREMGAHALLTREEE 129

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           I +AK IE G +    +L   P     L+ W +E+  G   L++ +
Sbjct: 130 ITLAKAIETGLSQSTEALGNCPAAVAELVRWAEEVATGKGRLKDWL 175


>gi|308182264|ref|YP_003926391.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
 gi|308064449|gb|ADO06341.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
          Length = 682

 Score =  301 bits (770), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 193/575 (33%), Positives = 320/575 (55%), Gaps = 72/575 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L +
Sbjct: 167 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALIN 226

Query: 177 GTTLLREII-----DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
               ++E+      D E  +    K       E +  +KR  +  EK+R  V++ +   +
Sbjct: 227 RERRVKELFRSFDDDDENSVSDSKKDDDSEEDEENEERKR--AVSEKDRKRVEKVQESFK 284

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS-AMEDQLRPKVMCALDEIAEV 290
           +  K  K+    +++P          +DE ED+    L+ A + Q     +  L+  +++
Sbjct: 285 ALDKAKKEWLKALEAP----------VDEKEDELVRLLTLAYKRQTLKDRLYDLEPTSKL 334

Query: 291 YREL-RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             EL ++++    +G   EK     K L+ KL     +L  N  +I   +  + +++K  
Sbjct: 335 INELVKTMETTLKSGDGFEKE---LKRLEYKLPLFNDTLIANHKKI---LANITNMTKED 388

Query: 350 MHNEGELLRLAQSYGIKRDVFLERH---QGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +  +     +   Y   + +FL +    +G +LDP+                        
Sbjct: 389 IIAQVPEATMVSVYMDLKKLFLTKEASEEGFDLDPN------------------------ 424

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
                              + + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+R
Sbjct: 425 -------------------KLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSR 465

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM 
Sbjct: 466 GLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMI 525

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D  
Sbjct: 526 DTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDG 585

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEV 645
             GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+
Sbjct: 586 KFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEI 645

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 646 GKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 680


>gi|46445811|ref|YP_007176.1| RNA polymerase sigma factor [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399452|emb|CAF22901.1| probable transcription initiation factor sigma 70 [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 554

 Score =  301 bits (770), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 146/262 (55%), Positives = 199/262 (75%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G S+ +F+  V M+++   ++  AK+EMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+
Sbjct: 288 AGRSLDDFKKDVKMLQRWMDKSQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNM 347

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++
Sbjct: 348 GLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKL 407

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  REP+PEE+AK+L +  E VR++ KI + PISL+  +GD   S  GDF+ED  A S
Sbjct: 408 MMETGREPSPEELAKELGITAERVREIYKIAQHPISLQAEVGDGGESQFGDFLEDTGADS 467

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++   + L++    VL++L+ RE +VL  RFG+      TLEEVG +F VTRERIRQI
Sbjct: 468 PAEATGYSILKDKMGEVLSTLSDRERKVLIQRFGLLDGKPKTLEEVGVEFNVTRERIRQI 527

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RK++HP RSK+L++FLD
Sbjct: 528 EAKALRKMRHPIRSKQLKAFLD 549



 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ +++ +G++T EE+N  LP    S++Q++  +  LS M I V++  +++  +E  +++
Sbjct: 21  LVAISKDQGFITYEEINEILPMSFDSADQIDQILIFLSGMDIQVLNQSEVDRQKERKKEA 80

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L S    S           + S DDPVRMYL+EMGS+ LLSRE E+ I+KRIE  +  
Sbjct: 81  KELESMPKRS-----------EGSPDDPVRMYLKEMGSVPLLSREEEVEISKRIEKAQVQ 129

Query: 153 M 153
           +
Sbjct: 130 I 130


>gi|332295554|ref|YP_004437477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
 gi|332178657|gb|AEE14346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
          Length = 356

 Score =  300 bits (768), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 141/237 (59%), Positives = 188/237 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ EANLRLV+S+AKKYT RGL FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 119 AKKKLAEANLRLVVSIAKKYTKRGLLFLDLIQEGNMGLLRAVEKFDYRKGYKFSTYATWW 178

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IADQ+ TIRIPVHM + I+K  +T R +S ++ R+PT EEIA+K+ + VE +
Sbjct: 179 IRQAVTRAIADQARTIRIPVHMVETINKYKKTVRNLSQQLSRKPTDEEIAEKMEVNVEKI 238

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +I++EPIS+ETPIG ++ SHLGDFI D++  SP+++     L+E    V+  L PR
Sbjct: 239 HEIKRISQEPISIETPIGKDEDSHLGDFIADESISSPMEAVTYRLLKEDLEEVIKDLQPR 298

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KLR +L
Sbjct: 299 ERDVVRLRFGLVDGHARTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSRKLRDYL 355


>gi|320527310|ref|ZP_08028495.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
 gi|320132334|gb|EFW24879.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
          Length = 468

 Score =  300 bits (768), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 142/239 (59%), Positives = 187/239 (78%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++ +NLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 229 ARNILISSNLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 288

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEG 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++  ++ R+P+ EEI++++  +  E 
Sbjct: 289 IRQAITRAIADQARTIRIPVHMVETINKLTRVQRQLVQELGRDPSAEEISQRMEGISPEK 348

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  EP+SLETPIG+ED SHLGDFIEDK A+SP   A    L++    VL+ LT 
Sbjct: 349 VREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDQYASNQLLKDEINSVLSGLTE 408

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKLKHPSRSK+L+ F D
Sbjct: 409 REEKVLRLRFGLYDGRTRTLEEVGREFSVTRERIRQIEAKALRKLKHPSRSKRLKDFFD 467



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 38/149 (25%), Positives = 64/149 (42%), Gaps = 47/149 (31%)

Query: 37  LARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE------ 90
           +A++ G +  +++ A L   ++S + M++     +   I +V+ DD+E+   +E      
Sbjct: 88  IAKKSGSIAQKDIMASLEHLDMSDDDMDELWDWFNTENIQIVEDDDIEELTATEDDDLDL 147

Query: 91  ------------------------------DSLDLASSASNSSVFLQKRKDSADRSTDDP 120
                                         + LDL S +S  +V L           +DP
Sbjct: 148 LDDDVDNEEDENVDDKDHDLDEDDEEKPLSNLLDLTSFSSGGNVQL-----------NDP 196

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAG 149
           V+MYL+E+G + LL  E E  IAKRIE G
Sbjct: 197 VKMYLKEIGRVPLLKPEDEPEIAKRIEEG 225


>gi|206889536|ref|YP_002248786.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741474|gb|ACI20531.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 479

 Score =  300 bits (767), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 141/269 (52%), Positives = 194/269 (72%), Gaps = 1/269 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I  EIK I  E+G+ I E ++I   + K +C     K E++  NLRLV+++AK Y  RGL
Sbjct: 201 IHAEIKKIENESGLKIDELKNIWQKIYKAKCLVEDTKNELITRNLRLVVNIAKNYVGRGL 260

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGNIGLMKA +KF +  G+KFSTYA WW++QAITR++ DQ+ TIR+PVHM + 
Sbjct: 261 PLLDLIEEGNIGLMKAVDKFKYEKGFKFSTYATWWIRQAITRALIDQTKTIRVPVHMMEF 320

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            ++V + +R ++ ++ REP  EEIA+KL +PV  V +V +  ++PI L+TPIGDEDT  L
Sbjct: 321 YNRVTKASRELTQQLGREPNNEEIAEKLGVPVRKVEEVFRAIQDPIGLQTPIGDEDT-EL 379

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DFI DK + SP+  A +  L E   R+L +LTP+EE+V++MRFGIG + DHTLEEVG+ 
Sbjct: 380 EDFIGDKTSPSPVSEAERTELSEHIQRILKTLTPKEEKVIKMRFGIGEDRDHTLEEVGRY 439

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             +TRER+RQIE KA+RKLKHPSR + L+
Sbjct: 440 LSITRERVRQIETKALRKLKHPSRMRLLK 468



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 38/155 (24%), Positives = 80/155 (51%), Gaps = 19/155 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D +++++ L ++RG +T +E+N  LP +  S E++ED + +LS+MG+ VVD         
Sbjct: 5   DIFEEIVNLGKKRGKLTYDEINEALPSEYYSPEEIEDLIDVLSDMGVRVVD--------- 55

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                             ++ +   +   +D V+ Y   MG I +L++E E+ +AK+++ 
Sbjct: 56  ---------EDEEEVFLEEEEEIEEEEHVEDLVQAYFNSMGDIPILTKEEEVELAKKLQE 106

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           G++++  ++    L +Q ++   ++  D  TL  E
Sbjct: 107 GKSIIKETVMGLSL-YQKILEEINKEEDSETLTEE 140


>gi|295098975|emb|CBK88064.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium cylindroides
           T2-87]
          Length = 368

 Score =  300 bits (767), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 148/263 (56%), Positives = 195/263 (74%), Gaps = 5/263 (1%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E  + I E + + S+V  GE     AK+ ++ +NLRLV+S+AKKY  RG+ FLDLIQEGN
Sbjct: 108 EPDLDIEERKKLASVVADGEE----AKQVLISSNLRLVVSIAKKYVGRGMLFLDLIQEGN 163

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            GL+KA EKFD+  G+KFSTYA WW++Q+ITR+IADQ+ TIRIPVHM + I+K+ R  R+
Sbjct: 164 CGLIKAVEKFDYTKGFKFSTYATWWIRQSITRAIADQARTIRIPVHMVETINKLTRIQRQ 223

Query: 539 MSNKIKREPTPEEIAKKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +   + R+P PEEIA+K+  +  + VR++ KI  +P+SLETPIG+ED SHLGDFIEDK  
Sbjct: 224 LVQDLGRDPLPEEIAEKMENITADKVREIQKIALDPVSLETPIGEEDDSHLGDFIEDKET 283

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +SP D      L++    VL  LT REE+VLR+RFG+      TLEEVGK+F VTRERIR
Sbjct: 284 LSPDDYTNNQLLKDEINNVLQGLTEREEKVLRLRFGLMDGRTRTLEEVGKEFNVTRERIR 343

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QIEAKA+RKLKHP+RSK+L+ F+
Sbjct: 344 QIEAKALRKLKHPNRSKRLKDFV 366



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 44/80 (55%)

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           +M   V+D  D + +   +D++D  S     S   Q   +++    +DPV+MYL+E+G I
Sbjct: 22  DMEEEVIDDVDEDLDSRIDDAVDENSIEDEISQLEQTFANASHTKINDPVKMYLKEIGQI 81

Query: 132 ELLSREGEIAIAKRIEAGRA 151
            LL  + E  IAKRI+ G A
Sbjct: 82  PLLDPKEEPIIAKRIQDGEA 101


>gi|109948008|ref|YP_665236.1| RNA polymerase sigma factor RpoD [Helicobacter acinonychis str.
           Sheeba]
 gi|109715229|emb|CAK00237.1| RNA polymerase sigma-70 factor [Helicobacter acinonychis str.
           Sheeba]
          Length = 659

 Score =  300 bits (767), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 191/575 (33%), Positives = 322/575 (56%), Gaps = 72/575 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVR+YLREMG+I+LL +E EI ++K+I  G  +++ ++C  P     +  ++D L +
Sbjct: 144 SDSPVRVYLREMGNIDLLKKEEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALIN 203

Query: 177 GTTLLREII-----DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
               ++E+      D E  +    K       E +  +K+  S + K+R  V++ +   +
Sbjct: 204 RERRVKELFRSFDDDDENSVSDSKKDDDNEEDEENEERKKVVSERNKKR--VEKVQESFK 261

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS-AMEDQLRPKVMCALDEIAEV 290
           +  K  K+    +++P          +DE ED+    L+ A + Q     +  L+  +++
Sbjct: 262 ALDKAKKEWLKALEAP----------IDEKEDELVRLLTLAHKRQTLKDRLYDLEPTSKL 311

Query: 291 YREL-RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             EL ++++    +G   EK   + K L+ KL     +L  N  +I   +  + +++K  
Sbjct: 312 INELVKTMETTLKSGDGFEK---ELKRLEYKLPLFNDTLIANHQKI---LSNITNMTKED 365

Query: 350 MHNEGELLRLAQSYGIKRDVFLERH---QGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +  +     +   Y   + +FL +    +G +LDP+                        
Sbjct: 366 IIAQVPETTMVSVYMDLKKLFLTKEASEEGFDLDPN------------------------ 401

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
                              + + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+R
Sbjct: 402 -------------------KLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSR 442

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGNIGLMKA +KF++  G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM 
Sbjct: 443 GLPFLDLIQEGNIGLMKAVDKFEYEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMI 502

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D  
Sbjct: 503 DTINRINKVMRKHMQENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDG 562

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEV 645
             GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+
Sbjct: 563 KFGDFVEDKNIVSSIDHIMREDLKVQIEGVLDQLNEREKAVIRMRFGLLDDESDRTLEEI 622

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 623 GKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 657


>gi|218288616|ref|ZP_03492893.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258511944|ref|YP_003185378.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|218241273|gb|EED08448.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257478670|gb|ACV58989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 368

 Score =  299 bits (766), Expect = 8e-79,   Method: Compositional matrix adjust.
 Identities = 155/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVPLLSAQEEIELAKRIEQGDEEA---KQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA ++ +  E VR++ KI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVSRQLLQELGREPTPEEIAAEMDLTPEKVREIQKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIPDDEAPAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 368



 Score = 54.3 bits (129), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 45/152 (29%), Positives = 79/152 (51%), Gaps = 15/152 (9%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ E  D D  +      ++ +++I+L +++G +T EE++  L   ++ ++ M+D    L
Sbjct: 4   TNDEIRDEDQGITLQ---EAKQQLIELGKKQGSLTYEEISDRLSSFDMDADAMDDFFEQL 60

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           + +GI+VV+     DEEG  +  D      +    ++           DPVRMYL+E+G 
Sbjct: 61  AELGIDVVNE---RDEEGGREDDDYDLDDLSVPPGVK---------ISDPVRMYLKEIGR 108

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + LLS + EI +AKRIE G       L E+ L
Sbjct: 109 VPLLSAQEEIELAKRIEQGDEEAKQRLAEANL 140


>gi|256827331|ref|YP_003151290.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
 gi|256583474|gb|ACU94608.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
          Length = 422

 Score =  299 bits (766), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 138/238 (57%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 184 AKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 243

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REPTPEEIA+++ +  + V
Sbjct: 244 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGREPTPEEIAEEMDLTPDRV 303

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV P D+A  + L+E  T+VL  L  R
Sbjct: 304 REIQKISQEPVSLETPIGEEEDSQLGDFIEDDAAVVPPDAASFSMLQEQLTKVLDGLAER 363

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 364 ERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 421



 Score = 42.4 bits (98), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 25/33 (75%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G + LL+   EI +A +IEAG
Sbjct: 116 TGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAG 148


>gi|156740279|ref|YP_001430408.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231607|gb|ABU56390.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 541

 Score =  299 bits (765), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 145/267 (54%), Positives = 195/267 (73%), Gaps = 8/267 (2%)

Query: 423 SISEFRHIVSMVRKGEC--------EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           S+ E +H+ + VR            +   A++++ +ANLRLV+SVAKKY  RGLQ LDLI
Sbjct: 275 SVEEVQHMCADVRDQLWRDWNLAIEQGKTAREDLTQANLRLVVSVAKKYIGRGLQLLDLI 334

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I++++R
Sbjct: 335 QEGNVGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLMR 394

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
            +RRM  ++ REPT EE+++ L +PV+ VR + K + EP+SLETP+G E+ S LGDFIED
Sbjct: 395 ESRRMLQELGREPTDEELSRALGIPVDKVRSIRKTSLEPVSLETPVGQEEDSQLGDFIED 454

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
              ++P D+A    LRE   +VL  LT RE RVL++RFG+      TLEEVGK+F VTRE
Sbjct: 455 SKVLAPSDAASHQMLREQVEQVLNQLTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRE 514

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE KA+RKL+HP   KKLR +L+
Sbjct: 515 RIRQIEVKALRKLRHPRLGKKLRDYLE 541



 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 36/128 (28%), Positives = 60/128 (46%), Gaps = 25/128 (19%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-----GDDLE 84
           S   ++ + +QRG+VT  E+   L   +  S+++ +    L + GI   D     G +++
Sbjct: 38  SLSDLLAIGKQRGFVTEGEIAQLLAGSDADSDRLAEIQQALQSAGIATRDEMIAGGAEID 97

Query: 85  ---DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              +EEG  D L +   + N                 D VRMYLRE+G + LL+   E  
Sbjct: 98  VHFEEEGDLDDLSVEGISIN-----------------DTVRMYLREIGRVPLLTARQETL 140

Query: 142 IAKRIEAG 149
           +A++IE G
Sbjct: 141 LAQKIEIG 148


>gi|257063660|ref|YP_003143332.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256791313|gb|ACV21983.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 394

 Score =  299 bits (765), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 190/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 156 AKDQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 215

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P+PEEI +K+ +  E V
Sbjct: 216 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGRDPSPEEIGEKMGLSAERV 275

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ K+++EP+SLETPIG+E+ S LGDFIED +A+ P+D+A  A ++E  ++VL +L  R
Sbjct: 276 REIQKLSQEPVSLETPIGEEEDSQLGDFIEDDSAIVPVDAASFAMMQEQLSKVLDTLGER 335

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+  RFG+     HTLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 336 ERNVVIKRFGLEDGQPHTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 393



 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 26/35 (74%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           T DPVRMYL+E+G + LL+   E+ +A +IEAG A
Sbjct: 89  TGDPVRMYLKEIGKVPLLTPSEEVDLAMKIEAGVA 123


>gi|148654464|ref|YP_001274669.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566574|gb|ABQ88719.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 541

 Score =  298 bits (764), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 140/242 (57%), Positives = 186/242 (76%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   A++++ +ANLRLV+SVAKKY  RGLQ LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 300 QGKTAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVEKFDYRKGFKFSTY 359

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I++++R +RRM  ++ REPT EE+++ L +P
Sbjct: 360 ATWWIRQAITRAIADQARTIRIPVHMVETINRLMRESRRMLQELGREPTDEELSRALGIP 419

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ VR + K + EP+SLETP+G E+ S LGDFIED   ++P D+A    LRE   +VL  
Sbjct: 420 VDKVRSIRKTSLEPVSLETPVGQEEDSQLGDFIEDSKVLAPSDAASHQMLREQVEQVLNQ 479

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE RVL++RFG+      TLEEVGK+F VTRERIRQIE KA+RKL+HP   KKLR +
Sbjct: 480 LTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQIEVKALRKLRHPRLGKKLRDY 539

Query: 680 LD 681
           L+
Sbjct: 540 LE 541



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 61/128 (47%), Gaps = 25/128 (19%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-----GDDLE 84
           S   ++ + +QRG+VT  E+   L   +  S+++ +    L   GI   D     G +++
Sbjct: 38  SLSDLLAIGKQRGFVTEGEIAQLLANSDADSDRLAEIQQALQAAGIATRDEMITGGAEID 97

Query: 85  ---DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              +EEG  D L++   + N                 D VRMYLRE+G + LL+   EI 
Sbjct: 98  IPFEEEGDFDDLNVEGISVN-----------------DTVRMYLREIGRVPLLNARQEIL 140

Query: 142 IAKRIEAG 149
           +A++IE G
Sbjct: 141 LAQKIEIG 148


>gi|330836587|ref|YP_004411228.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
 gi|329748490|gb|AEC01846.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
          Length = 685

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 206/579 (35%), Positives = 312/579 (53%), Gaps = 90/579 (15%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL-------T 163
           + +D + DDP+R+YLR++G   LL+ E E  +A+++E G  +M   + +S +        
Sbjct: 188 EKSDSTIDDPIRLYLRDIGKESLLTAEQERELAQKMEEGSGIMRDVILKSGMMVTCFGDI 247

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
           FQ + +  DE +  +  L    DL+  I  + +   F+                  +D +
Sbjct: 248 FQKMTLKIDEADPESLPLMTSKDLKDLISEQKRYAQFY------------------KDGL 289

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           ++ +G +++   + K+   K+D+  ++   DE NL +        LS +E  L+P+ + A
Sbjct: 290 KDIQGAMKAYLALKKE---KIDTSGDSIFTDE-NLVKKRHALMKKLSLIE--LQPEEITA 343

Query: 284 LDE-IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
             E   +  R++ SLQ          KSS++ ++       +  +  L Q   DL+    
Sbjct: 344 FTEKFMDAERKISSLQAK--------KSSLEAQL------GVSSTRELRQMGRDLVTP-- 387

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL-DPHWVSYAKDFPEGEWKNFVAC 401
              +KR++        L + + +  DV  E+ +  +L +        DF E         
Sbjct: 388 ---AKRVL--------LEEKFAMSADVIKEKIRDIQLTEKKLHEIESDFEEN-------- 428

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               IL+   EIK                     +G    + AK  + +ANLRLV+S+AK
Sbjct: 429 -TQVILEHAKEIK---------------------RGRIMMTAAKDRLTQANLRLVVSIAK 466

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGL F DL+QEGNIGL+KA EKF++   +KFSTYA WW++QAITR+I+DQ  TIR+
Sbjct: 467 KYTNRGLPFNDLVQEGNIGLIKAVEKFEFRKNFKFSTYATWWIRQAITRAISDQGRTIRV 526

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM ++I+KV +    +   + R PT EEIAKKL  P E V+ V  + +EPISLETP+G
Sbjct: 527 PVHMIEQINKVKKEENALIQSLGRNPTDEEIAKKLGWPEEKVKGVKNVAREPISLETPVG 586

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E+ S L DFIEDK+A +P        L+E   + LA+L PRE+ VL+MRFG+      T
Sbjct: 587 EEEDSLLSDFIEDKDAENPASQTSYMLLQEQLQKELATLPPREKDVLKMRFGLDDGFALT 646

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           LEEVG  F VTRERIRQIEAK++R+++HP RS+KLR FL
Sbjct: 647 LEEVGLSFKVTRERIRQIEAKSLRRMRHPKRSRKLRDFL 685


>gi|189219555|ref|YP_001940196.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186413|gb|ACD83598.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 623

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 167/380 (43%), Positives = 240/380 (63%), Gaps = 24/380 (6%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYD----------ISKRIMHNEGELLRLAQSYGIKRDV 369
           KL +L+  L L   ++D L  QL D          + K +   +G L ++ + +  K+ V
Sbjct: 245 KLPELIERLELLIEKVDSLYSQLLDCPEKSKERKSLEKELQRQKGCLEKIYEKFYFKQKV 304

Query: 370 FLERHQGRELDPHWVSYAKDFP--EGEWKNFVACEVD------SILKIRNEIKSISVETG 421
             +  Q  E      SY ++    E   +NF   E D      ++  + ++++ +  +  
Sbjct: 305 IEDFVQTSE------SYYREIISLEQNLENFEKEEADPQEREKNLKAVHSKLRELEKQIQ 358

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +  F+     +++   EA  AK EMVEANLRLVIS+AKKY+NRGL FLDLIQEGN+GL
Sbjct: 359 LPLPVFKEKHQELKQWLNEAIKAKSEMVEANLRLVISIAKKYSNRGLSFLDLIQEGNMGL 418

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K++R  +++  
Sbjct: 419 MKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLMRVQKQLIQ 478

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REPTPEEIA +  M V+ +R ++K+ + PISL+  +G+ + +  GDFIEDK A +P 
Sbjct: 479 ELGREPTPEEIADETQMSVDRIRTIIKMAQHPISLQAQVGESEDTTFGDFIEDKAAENPS 538

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +    + LRE    VL +LT RE  V+  RFG+      TLEEVGKQF VTRERIRQIEA
Sbjct: 539 EMTGYSLLREKIKDVLGTLTERERTVIEQRFGLLDGYPRTLEEVGKQFRVTRERIRQIEA 598

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RK++HP+R + L+ FL+
Sbjct: 599 KALRKMRHPTRLRHLKGFLE 618



 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 46/140 (32%), Positives = 74/140 (52%), Gaps = 32/140 (22%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL----- 83
           +  + +IKLA+++GY+T +++N  LP    +SE++E     L  + I+++D  D+     
Sbjct: 85  EKLRTLIKLAKEQGYLTYDDINEALPESVNNSEEIEAVYDFLRTLEIDIIDSSDVDNAKA 144

Query: 84  ------EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
                 E+ EG E  LD+                      DDPVRMYL++MG + LL+RE
Sbjct: 145 VTALDAEEIEGKESKLDI---------------------VDDPVRMYLKQMGQVPLLTRE 183

Query: 138 GEIAIAKRIEAGRAMMMASL 157
            E+ I+KRIE   AM+ + L
Sbjct: 184 QEVEISKRIEQSEAMVKSCL 203


>gi|307243281|ref|ZP_07525452.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
 gi|306493409|gb|EFM65391.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
          Length = 384

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 145/239 (60%), Positives = 195/239 (81%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA W
Sbjct: 146 FAKQKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATW 205

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P P+EIAK++ M  E 
Sbjct: 206 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPDEIAKEMNMTEEK 265

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+++KI ++P+SLETPIG+E+ SHLGDFI D++A +P ++A  + L+E    VL +L  
Sbjct: 266 VREIMKIAQDPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAYSLLKEQIEDVLNTLND 325

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE+ VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR FLD
Sbjct: 326 REQNVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDFLD 384



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 40/145 (27%), Positives = 68/145 (46%), Gaps = 12/145 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE-- 86
           ++ KK+ +  ++ G VT+ ++      +++     E+    L N+GI VVD  +++ +  
Sbjct: 13  EAQKKLFEKGKKDGTVTLIDIMEAFQDNDMDKGVAENLYETLGNLGIEVVDDKEVKADID 72

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSRE 137
               D LD+ +         +   +S+D          S DDPVRMYL+E+G I LL   
Sbjct: 73  LSKPDDLDIQAIDEEEDK-EEIVAESSDPVEIAVPKGISIDDPVRMYLKEIGKIPLLKPH 131

Query: 138 GEIAIAKRIEAGRAMMMASLCESPL 162
            E+  AKR+  G       L E+ L
Sbjct: 132 EEVEYAKRMAEGDEFAKQKLVEANL 156


>gi|312898762|ref|ZP_07758151.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
 gi|310620193|gb|EFQ03764.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
          Length = 437

 Score =  298 bits (764), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 139/240 (57%), Positives = 188/240 (78%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            +IAKK++ +ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA
Sbjct: 198 GNIAKKKLTDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYA 257

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++     REP PEEIA+K+ +PV
Sbjct: 258 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEKMGVPV 317

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VR+++KI +EP+SLETPIG+E+ SHLGDFIED+ A++P D+A    L+E    V + L
Sbjct: 318 ERVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDQEAIAPDDAASFILLKEQIEDVFSCL 377

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VL +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  + +K++ FL
Sbjct: 378 TDRERKVLYLRFGLKDGRPRTLEEVGQHFNVTRERIRQIEGKALSKLRNWGKREKIKDFL 437



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/115 (32%), Positives = 65/115 (56%), Gaps = 4/115 (3%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSEDSLDLA 96
            +Q+G ++  E+   +   ++++++M+      ++ G++V+ + + L + E   D  D  
Sbjct: 76  GKQQGSLSYSEIMNAMGDCDMTADEMDRMYEHFTDNGVDVLGESEQLNENESLNDDADDD 135

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S     +V L   +     + DDPVRMYL+E+G + LLS E EI +AKRIEAG A
Sbjct: 136 SENETVNVNLSVPEGV---NIDDPVRMYLKEIGRVPLLSAEEEITLAKRIEAGSA 187


>gi|227486750|ref|ZP_03917066.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227235220|gb|EEI85235.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 601

 Score =  298 bits (763), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/237 (59%), Positives = 185/237 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW
Sbjct: 365 AKEKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 424

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA  + + VE V
Sbjct: 425 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIADIMGIEVEKV 484

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ KI +EP+SLETPIG+ED SHLGDFIED  A+ P ++A    LRE    VL+ L  R
Sbjct: 485 SEIRKIAQEPVSLETPIGEEDDSHLGDFIEDDTAIDPGEAANYTMLREQLNDVLSCLGAR 544

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+RVL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 545 EKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 601



 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 26/32 (81%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DDPV+MYL+E+G ++LL+   EI +A+R+E G
Sbjct: 115 DDPVKMYLKEIGKVDLLTATEEIILARRMETG 146


>gi|328915181|gb|AEB56014.1| transcription initiation factor sigma 70 [Chlamydophila psittaci
           6BC]
          Length = 561

 Score =  298 bits (763), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/289 (51%), Positives = 205/289 (70%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E   F A ++D+    +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+N
Sbjct: 259 AERNKFAAAKLDAA---KRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESN 315

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 316 LRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 375

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + 
Sbjct: 376 ADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQH 435

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  +G+   S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RF
Sbjct: 436 PISLQAEVGEGGESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRF 495

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 496 GLLDGKPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 544



 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E  +E  +++
Sbjct: 16  LVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQKERKKEA 75

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 76  KELEGLAKRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 124

Query: 153 M 153
           +
Sbjct: 125 I 125


>gi|62185569|ref|YP_220354.1| RNA polymerase sigma factor [Chlamydophila abortus S26/3]
 gi|62148636|emb|CAH64409.1| major sigma factor [Chlamydophila abortus S26/3]
          Length = 571

 Score =  298 bits (763), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/289 (51%), Positives = 205/289 (70%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E   F A ++D+    +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+N
Sbjct: 269 AERNKFAAAKLDAA---KRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESN 325

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 326 LRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 385

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + 
Sbjct: 386 ADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQH 445

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  +G+   S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RF
Sbjct: 446 PISLQAEVGEGGESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRF 505

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 506 GLLDGKPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E  +E  +++
Sbjct: 26  LVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|253573701|ref|ZP_04851044.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
 gi|251847229|gb|EES75234.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
          Length = 325

 Score =  298 bits (763), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 144/238 (60%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+A++Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 88  AKRRLAEANLRLVVSIARRYVGRGMVFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +I REPTPEEIAK++ +  + V
Sbjct: 148 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEIGREPTPEEIAKEMDLTPDKV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ S+LGDFIED +A +P ++A    L+E    VL +LT R
Sbjct: 208 REIMKIAQEPVSLETPIGEENDSNLGDFIEDHDAPAPAEAAAYELLKEQLEEVLDTLTER 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 268 EENVLRLRFGMDDGRTRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSKRLKDFME 325



 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 30/45 (66%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           DDPVRMYL+E+G + LLS E EI +A+RIE G       L E+ L
Sbjct: 53  DDPVRMYLKEIGRVPLLSAEEEIELAQRIENGDEEAKRRLAEANL 97


>gi|329943340|ref|ZP_08292114.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
 gi|332287916|ref|YP_004422817.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313848489|emb|CBY17493.1| major sigma factor [Chlamydophila psittaci RD1]
 gi|325507028|gb|ADZ18666.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328814887|gb|EGF84877.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
          Length = 571

 Score =  298 bits (763), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/289 (51%), Positives = 205/289 (70%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E   F A ++D+    +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+N
Sbjct: 269 AERNKFAAAKLDAA---KRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESN 325

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 326 LRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 385

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + 
Sbjct: 386 ADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQH 445

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  +G+   S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RF
Sbjct: 446 PISLQAEVGEGGESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRF 505

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 506 GLLDGKPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E  +E  +++
Sbjct: 26  LVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|89897819|ref|YP_514929.1| RNA polymerase sigma factor [Chlamydophila felis Fe/C-56]
 gi|89331191|dbj|BAE80784.1| DNA-directed RNA polymerase sigma 70 [Chlamydophila felis Fe/C-56]
          Length = 570

 Score =  298 bits (762), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/289 (51%), Positives = 205/289 (70%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E   F A ++D+    +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+N
Sbjct: 267 AERNKFAAAKLDAA---KRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESN 323

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 324 LRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 383

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + 
Sbjct: 384 ADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQH 443

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  +G+   S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RF
Sbjct: 444 PISLQAEVGEGGESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRF 503

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 504 GLLDGKPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 552



 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E  +E  +++
Sbjct: 24  LVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLAGMDIQVLNQADVERQKERKKEA 83

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 84  KELEGLARRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 132

Query: 153 M 153
           +
Sbjct: 133 I 133


>gi|255994475|ref|ZP_05427610.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
 gi|255993188|gb|EEU03277.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
          Length = 447

 Score =  298 bits (762), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 149/288 (51%), Positives = 204/288 (70%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E +  +A +V   L  +NEI+          + ++  + ++ + + + + A  ++ EANL
Sbjct: 160 EEEKILATQVKHALAKQNEIRERLERLKEGSATYKKEMKLLDEYKQDYNKAMHQLCEANL 219

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK + +RG+ FLDLIQEGN+GLMKA +KFD    +KFSTYA WW++QAITR+IA
Sbjct: 220 RLVVSIAKNHKDRGMHFLDLIQEGNLGLMKAVDKFDVDRNFKFSTYATWWIRQAITRAIA 279

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + IHK+ R +R +  ++ REP PEEIAK++ +  E VR +L+I++EP
Sbjct: 280 DQARTIRIPVHMVETIHKLTRISRTLLQELGREPKPEEIAKEMDITTEKVRDILRISQEP 339

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLE PIG+E+ SHLGDFI D    SPLD A  + LR+    VL +L  RE  VL++RFG
Sbjct: 340 VSLEKPIGEEEDSHLGDFIPDTEVPSPLDVAFSSMLRDELLEVLNTLGERERNVLKLRFG 399

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +      TLEEVGKQF VTRERIRQIE+KAIRKLKHP+ SKKLR ++D
Sbjct: 400 LVDGKQRTLEEVGKQFDVTRERIRQIESKAIRKLKHPNMSKKLRDYID 447



 Score = 38.1 bits (87), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           DDPV+MYL+E+G + LL+RE E  +A +++   A
Sbjct: 141 DDPVKMYLKEIGQVPLLTREEEKILATQVKHALA 174


>gi|304437691|ref|ZP_07397643.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369324|gb|EFM22997.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 370

 Score =  298 bits (762), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 120 VALAQRMEAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ R+P PE
Sbjct: 180 SKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRISRQLLQELGRDPRPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + V  V +++KI +EP+SLETPIG+E+ SHLGDFIED+ A +P ++A    LR
Sbjct: 240 EIAKEMGISVARVHEIMKIAQEPVSLETPIGEEEDSHLGDFIEDEAAPAPAEAASFMLLR 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+ VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRSK LR FL+
Sbjct: 360 SRSKVLRDFLE 370



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/34 (61%), Positives = 29/34 (85%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S DDPVRMYL+E+G + LL+ E E+A+A+R+EAG
Sbjct: 96  SLDDPVRMYLKEIGHVPLLTAEEEVALAQRMEAG 129


>gi|238927758|ref|ZP_04659518.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
 gi|238884474|gb|EEQ48112.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
          Length = 383

 Score =  298 bits (762), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 147/251 (58%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 133 VALAQRMEAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 192

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ R+P PE
Sbjct: 193 SKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRISRQLLQELGRDPHPE 252

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK++ + V  V +++KI +EP+SLETPIG+E+ SHLGDFIED+ A +P ++A    LR
Sbjct: 253 EIAKEMGITVARVHEIMKIAQEPVSLETPIGEEEDSHLGDFIEDEAAPAPAEAASFMLLR 312

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+ VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 313 EQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHP 372

Query: 671 SRSKKLRSFLD 681
           SRSK LR FL+
Sbjct: 373 SRSKVLRDFLE 383



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 60/108 (55%), Gaps = 7/108 (6%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  E+   L   ++S ++M+D     S+ G+ +VD  D+  +E +ED          
Sbjct: 42  GSLTFGEIIDALQKQDMSPDEMDDMYQRFSDEGVEIVD--DVATDERAEDEKPEKEEEVE 99

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             + + +       S DDPVRMYL+E+G + LL+ E E+A+A+R+EAG
Sbjct: 100 IDLTVPE-----GISLDDPVRMYLKEIGHVPLLTAEEEVALAQRMEAG 142


>gi|300113721|ref|YP_003760296.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299539658|gb|ADJ27975.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii
           C-113]
          Length = 578

 Score =  298 bits (762), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 142/266 (53%), Positives = 200/266 (75%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +  E G+ ++E + I   + + + +A  AK +MVEANLRLV+SVAKKY NRGL FLDLIQ
Sbjct: 312 VEAEAGLPLAELKVIHQRLVQSQFQAQRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQ 371

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KFD+  GYKFSTYA WW++QAITR+I DQS TIRIPVH+ +K+ K+ R 
Sbjct: 372 EGNIGLMKAVDKFDYHRGYKFSTYAHWWIRQAITRAIDDQSRTIRIPVHVMEKLSKLNRA 431

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           + ++  +  RE  PEE+A++L +  + + ++ +I K+PISLETP+G ++ S LG+ +ED+
Sbjct: 432 SYQLRQEKGREGRPEELAERLDLSEQQIHRMHEIAKQPISLETPLGKDEDSQLGELMEDE 491

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              +P++ AI A L+    R+LA+L+PRE +V+ MRFGIGM+TDHTL EV +QF ++RER
Sbjct: 492 QVPNPMEVAITAGLQTGAQRLLAALSPREAQVVAMRFGIGMDTDHTLGEVARQFDLSRER 551

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEA+A+ KL+    SK LR+FL+
Sbjct: 552 IRQIEAQALGKLRRLGHSKALRNFLE 577



 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 43/161 (26%), Positives = 73/161 (45%), Gaps = 8/161 (4%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           F+   +  K++I   + +G +T EEL  ++  +   S++ E    +  + G++  D    
Sbjct: 3   FEVRQEELKRLILKGKAQGLLTEEELQEYIIQEVEDSDEAETMANLFHHQGLDEFD---- 58

Query: 84  EDEEGSEDSLDLASSASNS-SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
              E  + +L L   A    +  +   +     +  D V  Y+REMGS  LL+RE EI +
Sbjct: 59  ---ETLDSTLLLKHGAEEEIAEAVPSLEGEGTGTVSDMVYAYMREMGSHALLTREEEITL 115

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           AK IE G      +L   P     L+ W DE+  G   L++
Sbjct: 116 AKAIETGLNQSTEALGGCPAAVAELLRWTDEVAAGKGRLKD 156


>gi|29840756|ref|NP_829862.1| RNA polymerase sigma factor [Chlamydophila caviae GPIC]
 gi|29835106|gb|AAP05740.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 572

 Score =  298 bits (762), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 150/289 (51%), Positives = 205/289 (70%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E   F A ++D+    +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+N
Sbjct: 269 AERNKFAAAKLDAA---KRRLHKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESN 325

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 326 LRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 385

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + 
Sbjct: 386 ADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQH 445

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  +G+   S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RF
Sbjct: 446 PISLQAEVGEGGESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRF 505

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 506 GLLDGKPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E  +E  +++
Sbjct: 26  LVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|520418|gb|AAA50747.1| major sigma factor [Chlamydophila psittaci]
          Length = 571

 Score =  298 bits (762), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 150/289 (51%), Positives = 205/289 (70%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E   F A ++D+    +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+N
Sbjct: 269 AERNKFAAAKLDAA---KRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESN 325

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 326 LRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 385

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + 
Sbjct: 386 ADQARTIRIPVHMIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQH 445

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  +G+   S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RF
Sbjct: 446 PISLQAEVGEGGESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRF 505

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 506 GLLDGKPKTLEEVGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E  +E  +++
Sbjct: 26  LVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|15644718|ref|NP_206888.1| RNA polymerase sigma factor RpoD [Helicobacter pylori 26695]
 gi|2500785|sp|P55993|RPOD_HELPY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2313167|gb|AAD07156.1| RNA polymerase sigma-70 factor (rpoD) [Helicobacter pylori 26695]
          Length = 671

 Score =  297 bits (761), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 193/575 (33%), Positives = 323/575 (56%), Gaps = 72/575 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L +
Sbjct: 156 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALIN 215

Query: 177 GTTLLREII-----DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
               ++E+      D E  +    K       E +  +K+  S ++K+R  V++ +   +
Sbjct: 216 RERRVKELFRSFDDDDENSVSDSKKDEDNEEDEENEERKKVVSEKDKKR--VEKVQESFK 273

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS-AMEDQLRPKVMCALDEIAEV 290
           +  K  K+    +++P          +DE ED+   +L+ A + Q     +  L+  +++
Sbjct: 274 ALDKAKKEWLKALEAP----------IDEREDELVRSLTLAYKRQTLKDRLYDLEPTSKL 323

Query: 291 YREL-RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             EL ++++    +G   EK   + K L+ KL     +L  N  +I   +  + +++K  
Sbjct: 324 INELVKTMETTLKSGDGFEK---ELKRLEYKLPLFNDTLIANHKKI---LANITNMTKED 377

Query: 350 MHNEGELLRLAQSYGIKRDVFLER---HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +  +     +   Y   + +FL +    +G +L P                         
Sbjct: 378 IIAQVPEATMVSVYMDLKKLFLTKEASEEGFDLAP------------------------- 412

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
               N++K I              +  +++G+  +  AK +M ++NLRLV+S+AK++T+R
Sbjct: 413 ----NKLKEI--------------LEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSR 454

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM 
Sbjct: 455 GLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMI 514

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D  
Sbjct: 515 DTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDG 574

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEV 645
             GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+
Sbjct: 575 KFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEI 634

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 635 GKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 669


>gi|257784627|ref|YP_003179844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
 gi|257473134|gb|ACV51253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
          Length = 455

 Score =  297 bits (761), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 186/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 217 AKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 276

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++     R+PTPEEI  ++ M  + V
Sbjct: 277 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDFGRDPTPEEIGSEMGMSPDRV 336

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV+P D+A  + LRE   +VL SL  R
Sbjct: 337 REIQKISQEPVSLETPIGEEEDSQLGDFIEDSTAVAPPDAASDSMLREQLEQVLDSLADR 396

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V++ RFG+      TLEEVGK+F VTRERIRQIE+K + KL+HPSRS +L+ +++
Sbjct: 397 ERKVIKFRFGLEDGHPRTLEEVGKEFGVTRERIRQIESKTLAKLRHPSRSGRLKDYME 454



 Score = 44.3 bits (103), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 27/35 (77%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           T DPVRMYL+E+G ++LL+   E+ +A +IEAG A
Sbjct: 150 TGDPVRMYLKEIGKVDLLTASEEVHLAMKIEAGTA 184


>gi|320530863|ref|ZP_08031900.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136897|gb|EFW28842.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 370

 Score =  297 bits (760), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 133 ARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ R+P PEEIAK++ + V  V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLVRISRQLLQELGRDPRPEEIAKEMGISVARV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++KI +EP+SLETPIG+E+ SHLGDFIED+ A +P ++A    LRE    VL +LT R
Sbjct: 253 HEIMKIAQEPVSLETPIGEEEDSHLGDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 313 EKNVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 370



 Score = 43.9 bits (102), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  EL   L   ++S ++M+D     ++ G+++VD      E  + D       A  
Sbjct: 28  GSLTYGELIDALQKQDMSPDEMDDMYQRFTDEGVDIVD------EASAADEPAPEEPAEK 81

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                         S DDPVRMYL+E+G + LL+ E E+ +A+ +EAG
Sbjct: 82  EEEVEIDLSIPEGVSLDDPVRMYLKEIGHVPLLTAEEEVELAQLMEAG 129


>gi|313897089|ref|ZP_07830636.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974536|gb|EFR40004.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 370

 Score =  297 bits (760), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 189/238 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 133 ARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ R+P PEEIAK++ + V  V
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLVRISRQLLQELGRDPRPEEIAKEMGISVARV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++KI +EP+SLETPIG+E+ SHLGDFIED+ A +P ++A    LRE    VL +LT R
Sbjct: 253 HEIMKIAQEPVSLETPIGEEEDSHLGDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDR 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 313 EKNVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 370



 Score = 43.9 bits (102), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 6/108 (5%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  EL   L   ++S ++M+D     ++ G+++VD      E  + D       A  
Sbjct: 28  GSLTYGELIDALQKQDMSPDEMDDMYQRFADEGVDIVD------EASAADEPAPEEPAEK 81

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                         S DDPVRMYL+E+G + LL+ E E+ +A+ +EAG
Sbjct: 82  EEEVEIDLSIPEGVSLDDPVRMYLKEIGHVPLLTAEEEVELAQLMEAG 129


>gi|295695448|ref|YP_003588686.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
 gi|295411050|gb|ADG05542.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
          Length = 379

 Score =  297 bits (760), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA  A   +++ANLRLV+S+AK+Y  RG+
Sbjct: 110 VRMYLKEIGRVPLLSAEEEIELAKRIEQGDEEAKAA---LIKANLRLVVSIAKRYVGRGM 166

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 167 LFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 226

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+PTPEEIA+++ M  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 227 INKLIRVSRQLLQELGRDPTPEEIAEEMDMSPDKVREIMKIAQEPVSLETPIGEEDDSHL 286

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 287 GDFIPDDDALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 346

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 347 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 379



 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/131 (34%), Positives = 71/131 (54%), Gaps = 1/131 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++++  R+RG +T  E+   L P E   +QM++    LS  GI V++ ++ ED    ED
Sbjct: 22  QQLVETGRKRGALTYHEIMDRLAPFEQDPDQMDEFFDYLSEQGIEVLNENE-EDLVLEED 80

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +   A    +    L+          +DPVRMYL+E+G + LLS E EI +AKRIE G  
Sbjct: 81  NEHPAEEEDHEEYDLEDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRIEQGDE 140

Query: 152 MMMASLCESPL 162
              A+L ++ L
Sbjct: 141 EAKAALIKANL 151


>gi|315651467|ref|ZP_07904490.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
 gi|315486287|gb|EFU76646.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
          Length = 389

 Score =  297 bits (760), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 187/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K+M E+NLRLV+S+AK+Y  RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 152 ARKQMAESNLRLVVSIAKRYMGRGMQFLDLIQEGNLGLLRAVEKFDYQKGFKFSTYATWW 211

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+++++  R++  +  REP P+E+AK + +PV  V
Sbjct: 212 IRQAITRSIADQARTIRIPVHMVETINRLIKIQRKLVQEFGREPRPDEVAKVMGIPVSKV 271

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++    EP+S+ETPIGDED SHLGDF++D NA  P++ A+   L +    V+ SLT R
Sbjct: 272 REIMSFALEPVSMETPIGDEDDSHLGDFLQDSNAKIPVNFAMDVLLHDQLMEVIKSLTER 331

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++V+ +RFG+      TLEEVGK F +TRERIRQIEAK++RKL++PS+ ++L+ FL+
Sbjct: 332 EQKVILLRFGLEDGKPRTLEEVGKVFGITRERIRQIEAKSLRKLRNPSKVRRLKDFLE 389


>gi|296269171|ref|YP_003651803.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091958|gb|ADG87910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 367

 Score =  297 bits (760), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 192/238 (80%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 131 AKQRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + REPTPEEIAK++ +PVE V
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLHQDLGREPTPEEIAKEMDLPVERV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +I +EP+SL++PIG+ED S LGDFIED +AV PL++A    L++    +L++L+ R
Sbjct: 251 VEIQRIAQEPVSLQSPIGEED-SDLGDFIEDADAVVPLEAAAFILLQDHLDDILSTLSER 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+R++++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HP+R++ LR +LD
Sbjct: 310 EQRIIQLRFGLADGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPTRAQVLRDYLD 367



 Score = 45.1 bits (105), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 36/121 (29%), Positives = 57/121 (47%), Gaps = 19/121 (15%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS 98
           R RG V I+++       E S + ++  V ML++  + V+  +D +     E+  D  + 
Sbjct: 9   RTRGGVAIDDVAVAADRTEPSDDALDRVVQMLADEDLEVLAAEDEDPIRFDEEDFDSGAP 68

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                             T+D VR+YLRE+G + LL+ E E+ +AK IEAG       LC
Sbjct: 69  ------------------TNDLVRIYLREIGKVPLLTAEEEVELAKAIEAG-LFAEDKLC 109

Query: 159 E 159
           E
Sbjct: 110 E 110


>gi|292670108|ref|ZP_06603534.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648296|gb|EFF66268.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 370

 Score =  297 bits (760), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 195/251 (77%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ ++ E     A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 120 VALAQRMEAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ R+P PE
Sbjct: 180 SKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRISRQLLQELGRDPHPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+++ + V  V +++KI +EP+SLETPIG+E+ SHLGDFIED+ A +P ++A    LR
Sbjct: 240 EVAREMGISVARVHEIMKIAQEPVSLETPIGEEEDSHLGDFIEDEAAPAPAEAASFMLLR 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE+ VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRSK LR FL+
Sbjct: 360 SRSKVLRDFLE 370



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 56/108 (51%), Gaps = 6/108 (5%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G +T  EL   L   ++S ++M+D     S+ G+ +VD        G     + A     
Sbjct: 28  GTLTYGELIDALQKQDMSPDEMDDMYQRFSDEGVEIVDD---AATAGEPAEEEPAEKEEE 84

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             + L   +     S DDPVRMYL+E+G + LL+ E E+A+A+R+EAG
Sbjct: 85  VEIDLSVPEGV---SLDDPVRMYLKEIGHVPLLTAEEEVALAQRMEAG 129


>gi|323142246|ref|ZP_08077080.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
 gi|322413309|gb|EFY04194.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
          Length = 546

 Score =  297 bits (760), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 146/238 (61%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW
Sbjct: 309 AKQCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYNKGFKFSTYATWW 368

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK++   V+ V
Sbjct: 369 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEIAKEMDTSVDRV 428

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED +A +P D+A    LRE    VL +LT R
Sbjct: 429 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDHDAPAPADAASFTLLREQLEEVLETLTIR 488

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+RVL +RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 489 EKRVLELRFGLEDGRSRTLEEVGQHFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 546



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/100 (33%), Positives = 57/100 (57%), Gaps = 10/100 (10%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE-----GSEDSLDLASSASNSSVFLQKRK 110
           ++++ E +E    +++  G+ +VD D+  DE+     G+++  D  SS+      L+   
Sbjct: 51  EDITPEDVEHIYEVITRKGLELVDDDNASDEDILPLVGNDEDNDEPSSSE-----LENMS 105

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                S DDPVRMYL+E+G + LL  E E+ +AKR++ GR
Sbjct: 106 VPEGISIDDPVRMYLKEIGRVPLLIGEDEVKLAKRMDKGR 145


>gi|114567027|ref|YP_754181.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|114337962|gb|ABI68810.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 358

 Score =  296 bits (758), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 191/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW
Sbjct: 121 AKRQLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLMKAVEKFDYRKGYKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E+A+++ + V+ V
Sbjct: 181 IRQAITRAIADQARTIRIPVHMVETINKLSRVQRSLLQILGREPTPAEVAEEMDIAVDRV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++K+ +EP+SLETPIG+ED SHLGDFI D+ A SP +SA    LRE    +L +LT R
Sbjct: 241 IEIMKVAQEPVSLETPIGEEDDSHLGDFITDEEAESPEESASFVLLREHLDGILNTLTER 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKL+ +++
Sbjct: 301 EEKVLRLRFGLDDGRPRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYIE 358



 Score = 44.3 bits (103), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 54/116 (46%), Gaps = 16/116 (13%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           EEL +F     + ++Q++D    L ++GI +          G+E   +L     +     
Sbjct: 31  EELQSF----NLEADQIDDIFEHLQSLGITI----------GTEQDAELDEENESIETEE 76

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
               D  +   DDPVRMYL+E+G + LL    EI +A+RIE G       L E+ L
Sbjct: 77  VVIPDGIE--IDDPVRMYLKEIGRVPLLIAAQEIDLAQRIEEGDEEAKRQLVEANL 130


>gi|289423762|ref|ZP_06425557.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
 gi|289155801|gb|EFD04471.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
          Length = 385

 Score =  296 bits (758), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 143/238 (60%), Positives = 195/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 148 SKQKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWW 207

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK + M  + V
Sbjct: 208 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAKVMNMSEDKV 267

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI ++P+SLETPIG+E+ SHLGDFI D++A +P ++A  + L+E    VL +L  R
Sbjct: 268 REIMKIAQDPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAYSLLKEQIEEVLNTLNDR 327

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 328 EQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 385



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 51/115 (44%), Gaps = 23/115 (20%)

Query: 64  EDTVAMLSNMGINVVDG------------DDLE----DEEGSEDSLDLASSASNSSVFLQ 107
           E+    L N+GI V++             DDL+    DEE SED+    +  +  +V   
Sbjct: 50  ENLYETLGNLGIEVINDKEFKADINLNEPDDLDIKSIDEESSEDTETAETETAEIAV--- 106

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                   S DDPVRMYL+E+G I LL    E+  A+ +  G       L E+ L
Sbjct: 107 ----PKGISIDDPVRMYLKEIGKIPLLKPHEEVEFARLMSEGDERSKQKLVEANL 157


>gi|282856776|ref|ZP_06266037.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
 gi|282585399|gb|EFB90706.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
          Length = 642

 Score =  296 bits (758), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 144/254 (56%), Positives = 193/254 (75%), Gaps = 3/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   V  G+ EA   K+++++ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EK
Sbjct: 392 RELAIKVEAGDAEA---KQQIIDANLRLVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEK 448

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  K+ REP
Sbjct: 449 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKMVRISRQLVQKLGREP 508

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           + EEIA ++ +    V ++ +I + P+SLETPIG+E+ S LGDFIED+N  SP D+A   
Sbjct: 509 SDEEIAHEMEIESGRVEEIRRIAQLPVSLETPIGEEEDSQLGDFIEDRNMPSPEDAAAGN 568

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L E    +L +L+ RE  VLR RFG+     +TLEEVG++F VTRERIRQIEAKA+RKL
Sbjct: 569 LLHEQIEEMLDALSDREREVLRYRFGLEDGRSYTLEEVGRRFGVTRERIRQIEAKALRKL 628

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKLR FL+
Sbjct: 629 RHPSRSKKLRDFLE 642



 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 47/147 (31%), Positives = 72/147 (48%), Gaps = 29/147 (19%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-------------- 79
           +I   R+ GYVT +++  ++P D  SSE +++    L+ +GI V+D              
Sbjct: 257 LIVQGRKNGYVTHKDIEKYIPADYWSSEILDNVFINLTELGIQVLDDSAQVSSKDGSSAK 316

Query: 80  -----------GDDLE--DEEGSEDSL-DLASSASNSSV-FLQKRKDSADRSTDDPVRMY 124
                       D+ E  D  G +DS  D ASS  + +  + ++     D    DPVRMY
Sbjct: 317 SKRPSRSRTKISDERESPDVPGDDDSASDFASSGGDEAPGYGEELGRMEDVPLSDPVRMY 376

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRA 151
           LRE+G + LLS E E  +A ++EAG A
Sbjct: 377 LREIGKVPLLSGEKERELAIKVEAGDA 403


>gi|15835519|ref|NP_297278.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270285702|ref|ZP_06195096.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270289710|ref|ZP_06196012.1| RNA polymerase sigma factor [Chlamydia muridarum Weiss]
 gi|301337097|ref|ZP_07225299.1| RNA polymerase sigma factor [Chlamydia muridarum MopnTet14]
 gi|7388084|sp|P56835|RPOD_CHLMU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|7190932|gb|AAF39698.1| RNA polymerase sigma factor RpoD [Chlamydia muridarum Nigg]
          Length = 571

 Score =  296 bits (758), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 194/264 (73%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDSGESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 81.3 bits (199), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LPP   S EQ++  +  L+ M + V++  D+E  +E  +++
Sbjct: 26  LVTLAKDQGFITYEEINEILPPSFDSPEQIDQVLIFLAGMDVQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  S           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRS-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|268610742|ref|ZP_06144469.1| RNA polymerase sigma factor RpoD [Ruminococcus flavefaciens FD-1]
          Length = 360

 Score =  296 bits (758), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 143/238 (60%), Positives = 192/238 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AKKY  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 123 AKKRLSEANLRLVVSIAKKYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWW 182

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I KV + + ++ ++   +P+PEEIA KL MPV+ V
Sbjct: 183 IRQAITRAIADQARTIRIPVHMVETITKVKKVSSQLLHENGHDPSPEEIADKLNMPVDKV 242

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++++ ++P+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E    VL++LT R
Sbjct: 243 REIMRVAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAASHTLLKEQLNEVLSTLTDR 302

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VL++RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKK++ FLD
Sbjct: 303 EAKVLKLRFGLEDGKSRTLEEVGQRFDVTRERIRQIEAKALRKLRHPSRSKKVKDFLD 360



 Score = 41.2 bits (95), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 30/47 (63%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + DDPV++YL+E+G + LL+ E EI +A+R+  G       L E+ L
Sbjct: 86  AIDDPVKIYLKEIGRVPLLTTEEEIELAQRMAKGDRYAKKRLSEANL 132


>gi|328955627|ref|YP_004372960.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
 gi|328455951|gb|AEB07145.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
          Length = 442

 Score =  296 bits (758), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 204 AKQALISANLRLVVSIAKRYVGRGMHFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYATWW 263

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+PTPEEI  ++ M  + V
Sbjct: 264 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQELGRDPTPEEIGAEMEMSADRV 323

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV P D+A  + LRE   +VL SL  R
Sbjct: 324 REIQKISQEPVSLETPIGEEEDSQLGDFIEDAQAVVPPDAASFSMLREQLVQVLDSLADR 383

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+      TLEEVG+ F VTRERIRQIE+K + KL+HPSRS KL+ +++
Sbjct: 384 ERKVIELRFGLNDGHPRTLEEVGRDFGVTRERIRQIESKTLAKLRHPSRSSKLKDYIE 441



 Score = 42.7 bits (99), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+   E+ +A +IEAG
Sbjct: 137 TGDPVRMYLKEIGKVDLLTAADEVDLAMKIEAG 169


>gi|291542495|emb|CBL15605.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 367

 Score =  296 bits (757), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 142/238 (59%), Positives = 193/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 129 AKQRLSEANLRLVVSIAKRYLGRGMQFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWW 188

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+KV +   ++ ++   EP+ +EIA ++ MPV+ V
Sbjct: 189 IRQAITRAIADQARTIRIPVHMVETINKVKKVQSQLLHQNGHEPSADEIAAEIDMPVDKV 248

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++++ +EP+SLETPIG+E+ SHLGDFI D +A +P D+A    LRE  + VL++LTPR
Sbjct: 249 REIMRVAQEPVSLETPIGEEEDSHLGDFIPDNDAPAPADAASHTMLREQLSDVLSTLTPR 308

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 309 EAKVLKLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 366



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 68/132 (51%), Gaps = 6/132 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSE 90
           +++++L +Q+G +T +++   +   +   EQ+E     L+ +GI +V D  D++      
Sbjct: 12  RELVELGKQKGQLTNQDILDAIGEIDFDPEQLEKLYDSLAQLGIEIVEDSGDIKI----- 66

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D +DL            +  ++   S DDPV++YL+E+G + LLS + EI +A RI  G 
Sbjct: 67  DDIDLGFDEGKDGDSHAQIAETGSVSVDDPVKVYLKEIGRVPLLSSDEEINLAIRIADGD 126

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 127 VAAKQRLSEANL 138


>gi|288574624|ref|ZP_06392981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570365|gb|EFC91922.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  296 bits (757), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 142/250 (56%), Positives = 189/250 (75%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK +++EANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EKFD+
Sbjct: 131 VELAKRVEMGDDEAKSQLIEANLRLVVSIAKKYMGRGMLFLDLIQEGNLGLIRAVEKFDY 190

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV+R +R +   + REPT E
Sbjct: 191 SRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVMRASRNLVQSLGREPTDE 250

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +    V ++ K+ +EPISLE+P+G+ED S LGDFIEDK+ +SP DS     LR
Sbjct: 251 EIAAEMGIEPAKVVQIRKVAQEPISLESPVGEEDDSELGDFIEDKDMISPDDSTSMEFLR 310

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    VL  LT RE++VLR+RFG      +TLE+VG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 311 DQLDDVLEGLTDREKQVLRLRFGFDDGQCYTLEDVGRRFGVTRERIRQIEAKALRKLRHP 370

Query: 671 SRSKKLRSFL 680
           SRS  LR ++
Sbjct: 371 SRSVTLRDYM 380



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/141 (27%), Positives = 69/141 (48%), Gaps = 10/141 (7%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +V D   D  K ++   + +G+VT E++   + P  ++   +E     L  +GI++    
Sbjct: 23  IVLDQYLDKIKDILLEGQSKGFVTKEDIKRHMTPQTLNEVLLEKIYDNLRALGIDI---- 78

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                +G +D  +      +S +   +   S      DPVRMYLRE+G+I LL++  E+ 
Sbjct: 79  -----QGIDDEDEKKGDDPSSRI-SGESVSSDSGGGGDPVRMYLREIGTIPLLNQPQEVE 132

Query: 142 IAKRIEAGRAMMMASLCESPL 162
           +AKR+E G     + L E+ L
Sbjct: 133 LAKRVEMGDDEAKSQLIEANL 153


>gi|162447798|ref|YP_001620930.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
 gi|161985905|gb|ABX81554.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
          Length = 419

 Score =  296 bits (757), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 142/261 (54%), Positives = 196/261 (75%), Gaps = 4/261 (1%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E  +S  + + +   +RKG      AK+++VEAN RLV+S+AKKYT RGL FLDLIQEGN
Sbjct: 158 EVDLSDEDVQSLEDTIRKGHY----AKEKLVEANYRLVVSIAKKYTQRGLLFLDLIQEGN 213

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLM+A +KFD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K++R  R+
Sbjct: 214 MGLMRAVDKFDYEKGFKFSTYATWWIRQAITRAVADQARTIRIPVHMVETINKMIRIQRQ 273

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  ++ R+ T EEIA+K+ +  E V+ + +I KEPISLE P+G+E+ S LGDFI D NA+
Sbjct: 274 LVQELGRDATIEEIAEKMDITPEKVQNIQRIAKEPISLEAPVGEEEDSSLGDFISDPNAL 333

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D  +Q  +++T   VL +LT REE+VLR+R+G+     HTLEEVG++F VTRERIRQ
Sbjct: 334 NPHDYMMQEMVKKTLDEVLETLTDREEKVLRLRYGLLDGKTHTLEEVGREFGVTRERIRQ 393

Query: 659 IEAKAIRKLKHPSRSKKLRSF 679
           IEAKA+RKL+ P R  KL+ F
Sbjct: 394 IEAKALRKLRSPQRQNKLKEF 414


>gi|16752284|ref|NP_445653.1| RNA polymerase sigma factor [Chlamydophila pneumoniae AR39]
 gi|7190028|gb|AAF38883.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
          Length = 591

 Score =  296 bits (757), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 196/264 (74%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 310 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 369

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 370 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 429

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED   
Sbjct: 430 KLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGSESSFGDFLEDTAV 489

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 490 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIR 549

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 550 QIEAKALRKMRHPIRSKQLRAFLD 573



 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 73/127 (57%), Gaps = 10/127 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S    ++++ LA+++G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E +
Sbjct: 38  SQKKLEELVALAKEQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQIDVERQ 97

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  +               L +R +    + DDPVRMYL+EMG++ LL+RE E+ I+KRI
Sbjct: 98  KEKKKEAKELEG-------LARRTEG---TPDDPVRMYLKEMGTVPLLTREEEVEISKRI 147

Query: 147 EAGRAMM 153
           E  +  +
Sbjct: 148 EKAQVQI 154


>gi|221195781|ref|ZP_03568834.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
 gi|221184255|gb|EEE16649.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
          Length = 455

 Score =  296 bits (757), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 186/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 217 AKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 276

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+PTPEEI  ++ M  + V
Sbjct: 277 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPTPEEIGAEMGMSPDRV 336

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  A++P D+A  + LRE   +VL  L  R
Sbjct: 337 REIQKISQEPVSLETPIGEEEDSQLGDFIEDSTAIAPPDAASDSMLREQLEQVLDGLADR 396

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V++ RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS +L+ +++
Sbjct: 397 ERKVIKFRFGLEDGRPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSRLKDYME 454



 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+   E+ +A +IEAG
Sbjct: 150 TGDPVRMYLKEIGKVDLLTASEEVNLAMKIEAG 182


>gi|218673095|ref|ZP_03522764.1| RNA polymerase sigma factor RpoD [Rhizobium etli GR56]
          Length = 355

 Score =  296 bits (757), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 190/379 (50%), Positives = 241/379 (63%), Gaps = 51/379 (13%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     ED EG E    LA S   ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGSDDDDAGGDEDSEGGE----LAPSG-GTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K       +  S +K E  +  K  +D
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKA----APQFQSPEKIE--ADRKAAED 228

Query: 223 VQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
           +++T       A+   DD + V     PPE  E DE         S  +L+AME +LRP+
Sbjct: 229 IEKTR-----RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRPQ 276

Query: 280 VMCALDEIAEVYRELRSLQDNAV------NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           VM  LD IAE Y++LR LQD  V      +G        + K LK++L+K V SLSLNQ+
Sbjct: 277 VMETLDTIAETYKKLRKLQDQQVEQRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQN 336

Query: 334 RIDLLVEQLYDISKRIMHN 352
           RID LVEQLYDI+KR++ N
Sbjct: 337 RIDALVEQLYDINKRLVSN 355


>gi|144616|gb|AAA23168.1| sigma-A protein (sigA) [Chlamydia muridarum]
          Length = 571

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/264 (54%), Positives = 195/264 (73%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AK+EMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKQEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDSGESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++   +VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEATGYSMLKDKMKKVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LPP   S EQ++  +  L+ M + V++  D+E  +E  +++
Sbjct: 26  LVTLAKDQGFITYEEINEILPPSFDSPEQIDQVLIFLAGMDVQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  S           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRS-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|15618665|ref|NP_224951.1| RNA polymerase sigma factor [Chlamydophila pneumoniae CWL029]
 gi|15836289|ref|NP_300813.1| RNA polymerase sigma factor [Chlamydophila pneumoniae J138]
 gi|33242115|ref|NP_877056.1| RNA polymerase sigma factor [Chlamydophila pneumoniae TW-183]
 gi|6831651|sp|Q9Z7F0|RPOD_CHLPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|4377063|gb|AAD18894.1| RNA Polymerase Sigma-66 [Chlamydophila pneumoniae CWL029]
 gi|8979129|dbj|BAA98964.1| RNA polymerase sigma-66 [Chlamydophila pneumoniae J138]
 gi|33236625|gb|AAP98713.1| sigma factor 70 [Chlamydophila pneumoniae TW-183]
          Length = 572

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 196/264 (74%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGSESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 73/127 (57%), Gaps = 10/127 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S    ++++ LA+++G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E +
Sbjct: 19  SQKKLEELVALAKEQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQIDVERQ 78

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  +               L +R +    + DDPVRMYL+EMG++ LL+RE E+ I+KRI
Sbjct: 79  KEKKKEAKELEG-------LARRTEG---TPDDPVRMYLKEMGTVPLLTREEEVEISKRI 128

Query: 147 EAGRAMM 153
           E  +  +
Sbjct: 129 EKAQVQI 135


>gi|269302545|gb|ACZ32645.1| RNA polymerase sigma factor RpoD [Chlamydophila pneumoniae LPCoLN]
          Length = 570

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 196/264 (74%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 289 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 348

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 349 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 408

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED   
Sbjct: 409 KLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESSFGDFLEDTAV 468

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 469 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIR 528

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 529 QIEAKALRKMRHPIRSKQLRAFLD 552



 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 73/127 (57%), Gaps = 10/127 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S    ++++ LA+++G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E +
Sbjct: 17  SQKKLEELVALAKEQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQIDVERQ 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  +               L +R +    + DDPVRMYL+EMG++ LL+RE E+ I+KRI
Sbjct: 77  KEKKKEAKELEG-------LARRTEG---TPDDPVRMYLKEMGTVPLLTREEEVEISKRI 126

Query: 147 EAGRAMM 153
           E  +  +
Sbjct: 127 EKAQVQI 133


>gi|152993293|ref|YP_001359014.1| RNA polymerase sigma factor RpoD [Sulfurovum sp. NBC37-1]
 gi|151425154|dbj|BAF72657.1| RNA polymerase sigma 70 factor [Sulfurovum sp. NBC37-1]
          Length = 612

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 138/264 (52%), Positives = 198/264 (75%), Gaps = 3/264 (1%)

Query: 421 GISISE--FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           G  +SE   + I+  +R+G+ ++ +AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGN
Sbjct: 348 GFDLSEEKLQAILEQIRQGKAKSEVAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGN 407

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+
Sbjct: 408 IGLMKAVDKFEYEKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRK 467

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
              +  +EP  E IAK++ + V+ V+ V+KITKEP+SLETP+GDED    GDFIEDK  +
Sbjct: 468 HLQETGKEPDLETIAKEVGLTVDKVKNVIKITKEPVSLETPVGDEDDGRFGDFIEDKTTL 527

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIR 657
           SP D+ ++ +L      VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+R
Sbjct: 528 SPTDAVLKDDLNNQIDEVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVR 587

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIE+ AI+KLKHP   +KL+++++
Sbjct: 588 QIESSAIKKLKHPKVGRKLKNYIE 611



 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 40/58 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E E+ ++KRIE G  +++ ++C  P     ++ +++ L
Sbjct: 101 SDSPVRMYLREMGKIPLLTKEEEVDLSKRIEEGEDIIIDAICSVPYLIGYILNYKEPL 158


>gi|210633964|ref|ZP_03297935.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
 gi|210159008|gb|EEA89979.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
          Length = 445

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 206 AKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYATWW 265

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ M  + V
Sbjct: 266 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMDMSADRV 325

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV P D+A  + L+E  T+VL  L  R
Sbjct: 326 REIQKISQEPVSLETPIGEEEDSQLGDFIEDAQAVVPADAASFSMLQEQLTQVLDGLAER 385

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 386 ERKVIELRFGLVDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 443



 Score = 44.3 bits (103), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 39/159 (24%), Positives = 67/159 (42%), Gaps = 37/159 (23%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD----- 82
           D + +K++ L  + G VT +E+   L   +V+  Q+      L + G+ +V  ++     
Sbjct: 13  DTTIEKLLNLGSKAGSVTEDEIQIVLKDVDVTDAQLTSIYQFLRDRGVEIVSANEDDESE 72

Query: 83  --------------LEDEEGSEDSLDLASSASNSSVFLQKRKDSA--------------D 114
                           DE   +  L +A  A       + +K +               D
Sbjct: 73  LVVDDDDRDAMDDLDGDESDEDHDLKMAKQADAEMASTKSKKKARTVRTTRSRSRTRGID 132

Query: 115 RST----DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            ST     DPVRMYL+E+G ++LL+   E+ +A +IEAG
Sbjct: 133 ASTVMLTGDPVRMYLKEIGKVDLLTAAEEVDLAMKIEAG 171


>gi|257457793|ref|ZP_05622954.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257444843|gb|EEV19925.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 607

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 146/256 (57%), Positives = 190/256 (74%), Gaps = 7/256 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E RH  +M++K       AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA 
Sbjct: 358 EIRHGHAMLKK-------AKDKLINANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAV 410

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++  K  R
Sbjct: 411 EKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLMQKFGR 470

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPT EEIA +L   VE V++V  + +EPISLETPIG+E+ S LGDFIEDK+  +P +   
Sbjct: 471 EPTDEEIAVQLGWNVERVKQVKNVAREPISLETPIGEEEDSSLGDFIEDKDVENPSNLTE 530

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL+ L  RE+ VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R
Sbjct: 531 YILLQEQLRSVLSCLPLREQEVLKMRFGLDEGYALTLEEVGLYFNVTRERIRQIEAKALR 590

Query: 666 KLKHPSRSKKLRSFLD 681
           +L+HP +S KL+ +LD
Sbjct: 591 RLRHPKQSTKLKDYLD 606



 Score = 47.0 bits (110), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 75/160 (46%), Gaps = 22/160 (13%)

Query: 23  VFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDG 80
           + D S+D    K+I  A++   +T +EL+  LP    SSE  M++ + +L    I V+D 
Sbjct: 1   MIDISEDPIIIKLIAHAKEHKTLTWDELSDLLPEKMTSSETVMDEILDLLEQEQIQVIDD 60

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--------------------TDDP 120
              E+++   D LD     +   +F +   +S +                       DDP
Sbjct: 61  AVEENDDVFADELDEVELEAEEQLFEEAELESGNEPEFSKPEDTHKKLLNNDREAIVDDP 120

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           +++YLR++G   LL+ E E+ ++K +E G  ++  ++  S
Sbjct: 121 IKLYLRDIGKENLLTAEQEVILSKAMEDGENIIKNAIKNS 160


>gi|261407775|ref|YP_003244016.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329927238|ref|ZP_08281536.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261284238|gb|ACX66209.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328938638|gb|EGG35021.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 316

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+A++Y  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 79  AKRRLAEANLRLVVSIARRYAGRGMQFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+VR +R++  ++ REPTPEEI K++ +  E V
Sbjct: 139 IRQAITRSIADQARTIRIPVHMVETINKLVRVSRQLLQELGREPTPEEIGKEMDISPEKV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ K+++EP+SLETP+G+E  S+LGDFIED++A++P D+A    L+E    VL +LT R
Sbjct: 199 REIQKVSQEPVSLETPVGEESDSNLGDFIEDQDALAPADAAAFELLKEQLEEVLDTLTER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 259 EENVLRLRFGLEDGRTRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 316



 Score = 42.4 bits (98), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 29/44 (65%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           DPVRMYL+E+G + LLS + E+ ++KRIE G       L E+ L
Sbjct: 45  DPVRMYLKEIGRVPLLSADEEVELSKRIEEGDEEAKRRLAEANL 88


>gi|315647917|ref|ZP_07901018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315276563|gb|EFU39906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 316

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 145/238 (60%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ + EANLRLV+S+A++Y  RG+QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 79  AKRRLAEANLRLVVSIARRYAGRGMQFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+VR +R++  ++ REPTPEEI K++ +  E V
Sbjct: 139 IRQAITRSIADQARTIRIPVHMVETINKLVRVSRQLLQELGREPTPEEIGKEMDITPEKV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ K+++EP+SLETP+G+E  S+LGDFIED++A++P D+A    L+E    VL +LT R
Sbjct: 199 REIQKVSQEPVSLETPVGEESDSNLGDFIEDQDALAPADAAAFELLKEQLEEVLDTLTER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 259 EENVLRLRFGLEDGRTRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 316



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 29/44 (65%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           DPVRMYL+E+G + LLS + E+ ++KRIE G       L E+ L
Sbjct: 45  DPVRMYLKEIGRVPLLSADEEVELSKRIEEGDEEAKRRLAEANL 88


>gi|332975851|gb|EGK12729.1| DNA-directed RNA polymerase sigma subunit SigA [Desmospora sp.
           8437]
          Length = 372

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 152/273 (55%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSAEEEVELAKRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA+++ +  E VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVSRQLLQELGREPSPEEIAEEMDLSPEKVREIMKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P D+A    L+E    VL +L+ REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIPDDDAQAPADAAAYELLKEQLKDVLDTLSDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 10/132 (7%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++  L ++RG +T +E+   +   +   +Q+++    L+  GI V++ DD        + 
Sbjct: 21  RLTDLGKKRGVLTYKEITEKMSVFDQEPQQVDEFFEALNEQGIEVLNEDD--------EP 72

Query: 93  LDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ +      +  L +   S       +DPVRMYL+E+G + LLS E E+ +AKRIE G 
Sbjct: 73  MEFSDEEEEENDELLEDDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEVELAKRIEEGD 132

Query: 151 AMMMASLCESPL 162
                 L E+ L
Sbjct: 133 EEAKRRLAEANL 144


>gi|291543225|emb|CBL16334.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus sp. 18P13]
          Length = 360

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 144/240 (60%), Positives = 192/240 (80%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AKK + EANLRLV+S+AKKY  RG+QFLDLIQEGN+GL+KA +KFD+  G+KFSTYA 
Sbjct: 121 SYAKKRLSEANLRLVVSIAKKYVGRGMQFLDLIQEGNLGLIKAVDKFDYTKGFKFSTYAT 180

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I KV +   ++ ++   EPT +EIA++L MPVE
Sbjct: 181 WWIRQAITRAIADQARTIRIPVHMVETITKVKKIISQLLHETGHEPTADEIAERLEMPVE 240

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR++++I ++P+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E    VL++LT
Sbjct: 241 KVREIMRIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAASLILLKEQLNEVLSTLT 300

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VL++RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKK++ FLD
Sbjct: 301 EREAKVLKLRFGLEDGRSRTLEEVGREFEVTRERIRQIEAKALRKLRHPSRSKKVKDFLD 360



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 68/139 (48%), Gaps = 15/139 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----DDL 83
           ++S   +I+ A+  G ++  ELN      ++ +EQ++       N  I +V+      DL
Sbjct: 5   NESIDALIERAKASGKLSTRELNDAFERFDLDAEQIDSFYETCINNNIEIVEDFMPDTDL 64

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +    S+ S DL  + S   +           + DDPV++YL+E+G + LLS E EI +A
Sbjct: 65  KLGLDSDLSDDLEMALSTEGI-----------AIDDPVKIYLKEIGRVPLLSAEEEIELA 113

Query: 144 KRIEAGRAMMMASLCESPL 162
           +R+  G +     L E+ L
Sbjct: 114 QRMSKGDSYAKKRLSEANL 132


>gi|271963879|ref|YP_003338075.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270507054|gb|ACZ85332.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 392

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 138/268 (51%), Positives = 203/268 (75%), Gaps = 8/268 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  SV + ++  EF+ +V        + + AK+ ++EANLRLV+S+AK+Y  RG+ FLDL
Sbjct: 133 KLTSVVSRLAFPEFKELV-------WQGTRAKQRLIEANLRLVVSIAKRYVGRGMLFLDL 185

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+V
Sbjct: 186 IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 245

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++   + REP PEEIA ++ +P++ V ++ +I +EP+SL++PIG+ED S LGDFIE
Sbjct: 246 RVQRQLHQDLGREPAPEEIALEMDLPIDRVIEIQRIAQEPVSLQSPIGEED-SDLGDFIE 304

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +AV P+++A    L++    +LA+L+ RE+R++++RFG+      TLEEVG++F VTR
Sbjct: 305 DADAVVPMEAAAFIMLQDQLDDILATLSDREQRIIQLRFGLADGHPRTLEEVGREFGVTR 364

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIE+K + KL+HP+R++ LR +LD
Sbjct: 365 ERIRQIESKTLAKLRHPTRAQMLRDYLD 392



 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 63/123 (51%), Gaps = 17/123 (13%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D    ++   R+RG VT++++ A L   E+ S+ +E  V ML+  G+ V++    E+E
Sbjct: 22  SVDQVADLVAKGRERGSVTVDDVAAALDKSELPSDALERVVRMLAEHGVEVLEPQG-EEE 80

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D  D+   A  S                D VR+YLRE+G + LL+ E E+ +AK I
Sbjct: 81  TTRSDEEDVGKRAPTS----------------DLVRIYLREIGRVPLLTAEEEVELAKSI 124

Query: 147 EAG 149
           EAG
Sbjct: 125 EAG 127


>gi|254302832|ref|ZP_04970190.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148323024|gb|EDK88274.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 418

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 152/306 (49%), Positives = 210/306 (68%), Gaps = 10/306 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSM 433
           E +P ++   +D  E E  N     + +  K+   IK    E G    ++  E       
Sbjct: 116 EFNPEYI---EDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKR 172

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
             +G+ EAS   K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  G
Sbjct: 173 AYEGDEEAS---KKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 229

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A
Sbjct: 230 YKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILA 289

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L M VE ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE  
Sbjct: 290 ERLGMEVEKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREEL 349

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR 
Sbjct: 350 DAVLKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRK 409

Query: 674 KKLRSF 679
           KKL  F
Sbjct: 410 KKLEDF 415



 Score = 45.8 bits (107), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ + EI  A
Sbjct: 127 EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHDEEIEYA 170

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KR   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 171 KRAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 227

Query: 204 EGHSY 208
           +G+ +
Sbjct: 228 KGYKF 232


>gi|139436983|ref|ZP_01771143.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
 gi|133776630|gb|EBA40450.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
          Length = 454

 Score =  295 bits (755), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 186/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 216 AKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYQKGFKFSTYATWW 275

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ M  + V
Sbjct: 276 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMDMSADRV 335

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  A+ P D+A  + L+E  T+VL SL  R
Sbjct: 336 REIQKISQEPVSLETPIGEEEDSQLGDFIEDSQAIVPPDAASFSMLQEQLTQVLDSLADR 395

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +++
Sbjct: 396 ERKVIELRFGLVDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYIE 453



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+   E+ +A +IEAG
Sbjct: 149 TGDPVRMYLKEIGKVDLLTASEEVDLAMKIEAG 181


>gi|159896548|ref|YP_001542795.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889587|gb|ABX02667.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 400

 Score =  295 bits (754), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 138/238 (57%), Positives = 183/238 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  ANLRLV+SVAKKY  RGL  LDLIQEGN+GL++A EKF++  G+KFSTYA WW
Sbjct: 163 AREHLTTANLRLVVSVAKKYIGRGLSLLDLIQEGNVGLIRAVEKFNYTKGFKFSTYATWW 222

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I++++RTARR++ +  REP+ EE+A+ L + VE V
Sbjct: 223 IRQAITRAIADQARTIRIPVHMVETINRMMRTARRLTQENGREPSDEELAQALDLTVEKV 282

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K + EP+SLETP+G E+ S LGDF+ D+   +P D+A    LRE   +VL  LT R
Sbjct: 283 RSIRKTSMEPVSLETPVGQEEDSQLGDFLPDEKLEAPSDAASHQMLREQVAQVLDQLTER 342

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+RVL++RFG+   T  TLEEVGK+F VTRERIRQIE KA+RKL+HP   KKLR +L+
Sbjct: 343 EKRVLKLRFGLEDGTQRTLEEVGKEFGVTRERIRQIEVKALRKLRHPRFGKKLRDYLE 400



 Score = 44.7 bits (104), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 39/137 (28%), Positives = 64/137 (46%), Gaps = 20/137 (14%)

Query: 19  DDSLVFDFSDD-----SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           D  L  D +DD     +   ++   ++RGYVT  E+   +       +Q+E+    L   
Sbjct: 9   DSELAGDETDDFPALRTLSDLLATGKKRGYVTPGEIQQIIDSQRDEDKQLEEIRDTLQKA 68

Query: 74  GINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            I V + GDD ++   SE+     +  SN  +           S +D VR+YLRE+G + 
Sbjct: 69  NIRVEETGDDDDEITVSENP---EADFSNEGI-----------SVNDTVRLYLREIGLVP 114

Query: 133 LLSREGEIAIAKRIEAG 149
           LL  E E+ +A+ +E G
Sbjct: 115 LLKGEQEVELARAMEDG 131


>gi|229815176|ref|ZP_04445512.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
 gi|229809186|gb|EEP44952.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
          Length = 448

 Score =  295 bits (754), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 209 AKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYATWW 268

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ M  + V
Sbjct: 269 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMDMSADRV 328

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV P D+A  + L+E  T+VL  L  R
Sbjct: 329 REIQKISQEPVSLETPIGEEEDSQLGDFIEDAQAVVPADAASFSMLQEQLTQVLDGLAER 388

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+ +RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 389 ERKVIELRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 446



 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+   E+ +A +IEAG
Sbjct: 142 TGDPVRMYLKEIGKVDLLTAAEEVDLAMKIEAG 174


>gi|237804965|ref|YP_002889119.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273265|emb|CAX10180.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
          Length = 571

 Score =  295 bits (754), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 194/264 (73%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E  +E  +++
Sbjct: 26  LVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  S           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRS-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|315638945|ref|ZP_07894116.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
 gi|315480974|gb|EFU71607.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
          Length = 657

 Score =  295 bits (754), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 137/259 (52%), Positives = 197/259 (76%), Gaps = 1/259 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S  + I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA
Sbjct: 397 SRLKEILEQIKRGKKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKA 456

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  
Sbjct: 457 VDKFEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKNG 516

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP   +IAK++ + V+ V++V+KITKEPISLE PIG ED    GDF+EDKN++SP+D+ 
Sbjct: 517 KEPDVNDIAKEVGLSVDKVKQVIKITKEPISLEAPIGSEDDGKFGDFVEDKNSLSPMDNI 576

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+E    VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 577 LKDDLKEQIDEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSA 636

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           I+KLKHP   +KL+++++G
Sbjct: 637 IKKLKHPKVGRKLKNYIEG 655


>gi|15605346|ref|NP_220132.1| RNA polymerase sigma factor [Chlamydia trachomatis D/UW-3/CX]
 gi|76789354|ref|YP_328440.1| RNA polymerase sigma factor [Chlamydia trachomatis A/HAR-13]
 gi|166154830|ref|YP_001654948.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|166155705|ref|YP_001653960.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|255311437|ref|ZP_05354007.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276]
 gi|255317738|ref|ZP_05358984.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276s]
 gi|255348997|ref|ZP_05381004.1| RNA polymerase sigma factor [Chlamydia trachomatis 70]
 gi|255503536|ref|ZP_05381926.1| RNA polymerase sigma factor [Chlamydia trachomatis 70s]
 gi|255507214|ref|ZP_05382853.1| RNA polymerase sigma factor [Chlamydia trachomatis D(s)2923]
 gi|301336109|ref|ZP_07224353.1| RNA polymerase sigma factor [Chlamydia trachomatis L2tet1]
 gi|1710679|sp|P18333|RPOD_CHLTR RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|144609|gb|AAA23165.1| RNA polymerase sigma-subunit [Chlamydia trachomatis]
 gi|3329060|gb|AAC68218.1| RNA Polymerase Sigma-66 [Chlamydia trachomatis D/UW-3/CX]
 gi|76167884|gb|AAX50892.1| RpoD [Chlamydia trachomatis A/HAR-13]
 gi|165930818|emb|CAP04316.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931693|emb|CAP07270.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|289525658|emb|CBJ15139.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296435222|gb|ADH17400.1| RNA polymerase sigma factor [Chlamydia trachomatis E/150]
 gi|296436151|gb|ADH18325.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9768]
 gi|296438011|gb|ADH20172.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11074]
 gi|296438941|gb|ADH21094.1| RNA polymerase sigma factor [Chlamydia trachomatis E/11023]
 gi|297140513|gb|ADH97271.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9301]
 gi|297748745|gb|ADI51291.1| RpoD [Chlamydia trachomatis D-EC]
 gi|297749625|gb|ADI52303.1| RpoD [Chlamydia trachomatis D-LC]
          Length = 571

 Score =  295 bits (754), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 194/264 (73%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E  +E  +++
Sbjct: 26  LVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  S           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRS-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|296437079|gb|ADH19249.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11222]
          Length = 571

 Score =  295 bits (754), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 194/264 (73%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E  +E  +++
Sbjct: 26  LVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  S           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRS-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|256027745|ref|ZP_05441579.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260494274|ref|ZP_05814405.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289765702|ref|ZP_06525080.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260198420|gb|EEW95936.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289717257|gb|EFD81269.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
          Length = 416

 Score =  294 bits (753), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 150/298 (50%), Positives = 206/298 (69%), Gaps = 7/298 (2%)

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVRKGECEA 441
           Y +D  E E  N     + +  K+   IK    E G    ++  E         +G+ EA
Sbjct: 119 YIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYEGDEEA 178

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S   K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA 
Sbjct: 179 S---KKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYAT 235

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L M V+
Sbjct: 236 WWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERLGMEVD 295

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    VL +L+
Sbjct: 296 KIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAVLKTLS 355

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 356 PREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKLEDF 413



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ + EI  A
Sbjct: 125 EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHDEEIEYA 168

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KR   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 169 KRAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 225

Query: 204 EGHSY 208
           +G+ +
Sbjct: 226 KGYKF 230


>gi|331001843|ref|ZP_08325365.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412817|gb|EGG92200.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 389

 Score =  294 bits (753), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 186/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K M E+NLRLV+S+AK+Y  RG+Q LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 152 AAKRMAESNLRLVVSIAKRYMGRGMQLLDLIQEGNLGLLRAVEKFDYKKGFKFSTYATWW 211

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+++++T R++   + REP+PEE+AK++ + V  V
Sbjct: 212 IRQAITRSIADQARTIRIPVHMVETINRLIKTQRKLVQILGREPSPEEVAKEMNISVPKV 271

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++    EP+S+ETPIGDED SHLGDF++D NA  P++ A+   L +    V+  LT R
Sbjct: 272 REIMSFALEPVSMETPIGDEDDSHLGDFLQDYNAKVPVNFAMDVLLHDQLMDVIKLLTER 331

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++V+ +RFG+      TLEEVGK F +TRERIRQIEAK++RKL++PS+SK+LR FL+
Sbjct: 332 EQKVILLRFGLEDGKPRTLEEVGKVFGITRERIRQIEAKSLRKLRNPSKSKRLRDFLE 389



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 43/136 (31%), Positives = 58/136 (42%), Gaps = 19/136 (13%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DGD  +DE   ED  DL     N    L    D    S +DP++MYL+E+G I LL+ + 
Sbjct: 80  DGD-FDDEFNEEDIKDLRDIDLN---VLDDLNDYV--SIEDPIKMYLKEIGKIPLLNVDD 133

Query: 139 EIAIAKRI----EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           E+ +AK+I    E+ R      + ES L     I  R  +  G  LL  I         E
Sbjct: 134 EMDLAKKISDPDESIRKEAAKRMAESNLRLVVSIAKR-YMGRGMQLLDLI--------QE 184

Query: 195 SKGGFFHGTEGHSYQK 210
              G     E   Y+K
Sbjct: 185 GNLGLLRAVEKFDYKK 200


>gi|313113550|ref|ZP_07799138.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310624065|gb|EFQ07432.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 377

 Score =  294 bits (753), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 142/249 (57%), Positives = 191/249 (76%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R  +     A++++ EANLRLV+SVAK+Y  RGL FLDLIQEGN+GLMKAAEKF+   
Sbjct: 128 LARAAQAGDEDARRKLSEANLRLVVSVAKRYAGRGLPFLDLIQEGNLGLMKAAEKFEPER 187

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++Q+ITR+IADQ  TIRIPVH+ + I++V +    +  K  REPT EEI
Sbjct: 188 GFKFSTYATWWIRQSITRAIADQGRTIRIPVHLVESINRVKKMTGDLLRKNGREPTAEEI 247

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L M  + VR++L++ ++PISLETP+G+E+ +HL DFI+D++A  P+D A +  LR  
Sbjct: 248 AVQLDMEPDRVRELLQLAQDPISLETPVGEEEDAHLEDFIQDEDAGVPVDEAGRQLLRRE 307

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL SLTPREERV+ +RFG+     HTLEE+GK+F VTRER+RQIEAKA+RKL+HPSR
Sbjct: 308 LFSVLKSLTPREERVIALRFGLEDGRAHTLEELGKEFNVTRERVRQIEAKALRKLRHPSR 367

Query: 673 SKKLRSFLD 681
           +K+LR +LD
Sbjct: 368 AKRLRDYLD 376


>gi|237744142|ref|ZP_04574623.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
 gi|229431371|gb|EEO41583.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
          Length = 417

 Score =  294 bits (753), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 150/298 (50%), Positives = 206/298 (69%), Gaps = 7/298 (2%)

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVRKGECEA 441
           Y +D  E E  N     + +  K+   IK    E G    ++  E         +G+ EA
Sbjct: 120 YIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYEGDEEA 179

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S   K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA 
Sbjct: 180 S---KKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYAT 236

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L M V+
Sbjct: 237 WWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERLGMEVD 296

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    VL +L+
Sbjct: 297 KIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAVLKTLS 356

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 357 PREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKLEDF 414



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ + EI  A
Sbjct: 126 EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHDEEIEYA 169

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KR   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 170 KRAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 226

Query: 204 EGHSY 208
           +G+ +
Sbjct: 227 KGYKF 231


>gi|257438255|ref|ZP_05614010.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199332|gb|EEU97616.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 359

 Score =  294 bits (752), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 142/251 (56%), Positives = 192/251 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R  +   + A++++ EANLRLV+SVAK+Y  RGL FLDLIQEGN+GLMKAAEKF+ 
Sbjct: 108 LELARAAQAGDADARRKLSEANLRLVVSVAKRYAGRGLPFLDLIQEGNLGLMKAAEKFEP 167

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q+ITR+IADQ   IRIPVH+ + I++V +TA  +  K  REPT E
Sbjct: 168 DRGFRFSTYATWWIRQSITRAIADQGRVIRIPVHLVESINRVKKTAGELLRKNGREPTAE 227

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA +L M  + VR++L++ ++PISLETP+G+E+ +HL DFI+D+ A  P+D A +  LR
Sbjct: 228 EIAVRLDMEPDRVRELLQLAQDPISLETPVGEEEDAHLEDFIQDEEAGVPVDEAGRELLR 287

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL SLTPREERVL +RFG+      TLEE+GK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 288 RELANVLKSLTPREERVLTLRFGLEDGQARTLEELGKEFNVTRERIRQIEAKALRKLRHP 347

Query: 671 SRSKKLRSFLD 681
           SR+K+LR +L+
Sbjct: 348 SRAKRLRDYLE 358



 Score = 38.1 bits (87), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           + DDPV+ YL+E+G + LL+ E E+ +A+  +AG A     L E+ L  
Sbjct: 84  ALDDPVKAYLKEIGRVPLLTMEQELELARAAQAGDADARRKLSEANLRL 132


>gi|256845590|ref|ZP_05551048.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294785121|ref|ZP_06750409.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
 gi|256719149|gb|EEU32704.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294486835|gb|EFG34197.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
          Length = 418

 Score =  294 bits (752), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 151/306 (49%), Positives = 210/306 (68%), Gaps = 10/306 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSM 433
           E +P ++   +D  E E  N     + +  K+   IK    E G    ++  E       
Sbjct: 116 EFNPEYI---EDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKK 172

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
             +G+ EAS   K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  G
Sbjct: 173 AYEGDEEAS---KKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 229

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A
Sbjct: 230 YKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILA 289

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE  
Sbjct: 290 ERLGMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREEL 349

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR 
Sbjct: 350 DAVLKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRK 409

Query: 674 KKLRSF 679
           KKL  F
Sbjct: 410 KKLEDF 415



 Score = 44.7 bits (104), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ + EI  A
Sbjct: 127 EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHDEEIEYA 170

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 171 KKAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 227

Query: 204 EGHSY 208
           +G+ +
Sbjct: 228 KGYKF 232


>gi|218282286|ref|ZP_03488585.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
 gi|218216721|gb|EEC90259.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
          Length = 409

 Score =  294 bits (752), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 141/238 (59%), Positives = 184/238 (77%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ +NLRLV+S+AKKY  RG+ FLDLIQEGN GL+KA EKFD+  G+KFSTYA WW
Sbjct: 171 AKQTLISSNLRLVVSIAKKYVGRGMLFLDLIQEGNCGLIKAVEKFDYTKGFKFSTYATWW 230

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++Q+ITR+IADQ+ TIRIPVHM + I+K+ R  R++   + R+P PEEIA+K+  +  E 
Sbjct: 231 IRQSITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPMPEEIAEKMENISAEK 290

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI  +P+SLETPIG+ED SHLGDFIEDK+ +SP D      L++    VL  LT 
Sbjct: 291 VREIQKIALDPVSLETPIGEEDDSHLGDFIEDKDTLSPDDYTNNQLLKDEINAVLQGLTE 350

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLK+P+R K+LR F+
Sbjct: 351 REEKVLRLRFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKNPNRCKRLRDFV 408


>gi|237803044|ref|YP_002888238.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|231274278|emb|CAX11073.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
          Length = 571

 Score =  294 bits (752), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 146/264 (55%), Positives = 193/264 (73%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 291 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 350

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 351 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 410

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED   
Sbjct: 411 KLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTAV 470

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP +    + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 471 ESPAEVTGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIR 530

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 531 QIEAKALRKMRHPIRSKQLRAFLD 554



 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 73/121 (60%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E  +E  +++
Sbjct: 26  LVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQKERKKEA 85

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  S           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 86  KELEGLAKRS-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 134

Query: 153 M 153
           +
Sbjct: 135 I 135


>gi|291522892|emb|CBK81185.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 366

 Score =  293 bits (751), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 137/250 (54%), Positives = 189/250 (75%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK  ++EANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 115 VELSKRAEAGDQKAKDRIIEANLRLVVSIAKKYVGRGIPFLDLIQEGNMGLIKAVEKFDY 174

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++Q+ITR IAD+  TIR+PVHM + I+K +R +R +  ++ REPT E
Sbjct: 175 AKGFKFSTYATWWIRQSITRGIADKGKTIRVPVHMVETINKTLRMSRNLLQELGREPTSE 234

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L    + V + L+I+++P+S+++PIG+E+ S LGDFIED+N +SP DSA    L+
Sbjct: 235 EIAERLGTTKQKVEEALEISRDPVSMDSPIGEEEDSSLGDFIEDENMLSPSDSADYQMLK 294

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     L +LT RE +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 295 KELVNALDTLTDRERKVIELRFGLIDGQARTLEEVGKEFKVTRERIRQIEAKALRKLRHP 354

Query: 671 SRSKKLRSFL 680
           SRS+KL+ FL
Sbjct: 355 SRSRKLKDFL 364



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 21/34 (61%), Positives = 29/34 (85%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S +DPVRMYL+E+GS++LLS E E+ ++KR EAG
Sbjct: 91  SLEDPVRMYLKEIGSVKLLSPEEEVELSKRAEAG 124


>gi|330444010|ref|YP_004376996.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
 gi|328807120|gb|AEB41293.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
          Length = 562

 Score =  293 bits (751), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 145/264 (54%), Positives = 196/264 (74%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEG
Sbjct: 281 VAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEG 340

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+
Sbjct: 341 NMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAK 400

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  +EP+PEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED   
Sbjct: 401 KLMMETGKEPSPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESAFGDFLEDTAV 460

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIR
Sbjct: 461 ESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIR 520

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RK++HP RSK+LR+FLD
Sbjct: 521 QIEAKALRKMRHPIRSKQLRAFLD 544



 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 72/121 (59%), Gaps = 12/121 (9%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           ++ LA+++G++T EE+N  LP    S EQ++  +  L+ M I +++  D+E  +E  ++ 
Sbjct: 16  LVSLAKEQGFITYEEINEILPMSFDSPEQIDQVLIFLAGMDIQILNQIDVERQKERKKEV 75

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L   A  +           + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE  +  
Sbjct: 76  KELEGLAKRT-----------EGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIEKAQVQ 124

Query: 153 M 153
           +
Sbjct: 125 I 125


>gi|51244645|ref|YP_064529.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50875682|emb|CAG35522.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 534

 Score =  293 bits (751), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 143/262 (54%), Positives = 196/262 (74%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E+G S+     ++  V +G   +  AK+ +V ANLRLVISV+K++ NRGLQF DLIQEGN
Sbjct: 271 ESGSSLQSLNELLKEVEEGRFISKEAKEALVRANLRLVISVSKRFVNRGLQFSDLIQEGN 330

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA EKFD+  G+KFSTYA WW++Q+ITR IADQ  TIR+PVHM + I++++R ++ 
Sbjct: 331 IGLMKAVEKFDYRRGFKFSTYATWWIRQSITRGIADQGRTIRLPVHMIETINRMLRVSKD 390

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
              +  REP+ EE+A +L   V+ V+  LKI K+ ISL+TP+GD+  ++LGDFI DKN +
Sbjct: 391 FYLEEHREPSVEEVAGQLGTEVDKVKSALKIAKDAISLDTPVGDDGETYLGDFIVDKNCL 450

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P   A+ A+L+E  ++VL+SL+PREE+VL+MR+GI    ++TLEEVG+ F VTRERIRQ
Sbjct: 451 GPDGFAMVASLKECLSQVLSSLSPREEKVLKMRYGILEKREYTLEEVGRCFNVTRERIRQ 510

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEA+AI KLKHPSR   L+ F+
Sbjct: 511 IEAQAISKLKHPSRCGDLKVFM 532



 Score = 37.7 bits (86), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 35/61 (57%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           +RK     +  D + +Y+REMGS++LL  + E  +A+ IE G+  +  ++ +S L    L
Sbjct: 67  QRKQGDSTAAADSMNIYMREMGSLKLLKYDDERKLAQTIEKGKKQVQFAVLQSTLAMPIL 126

Query: 168 I 168
           +
Sbjct: 127 L 127


>gi|296327931|ref|ZP_06870466.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296154887|gb|EFG95669.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 418

 Score =  293 bits (751), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 148/303 (48%), Positives = 207/303 (68%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRK 436
           E +P ++   +D  E E  N     + +  K+   IK    E G + +      +   +K
Sbjct: 116 EFNPEYI---EDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYAKK 172

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 173 AYEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 232

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 233 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 292

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 293 GMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 352

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 353 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 412

Query: 677 RSF 679
             F
Sbjct: 413 EDF 415



 Score = 45.8 bits (107), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ E EI  A
Sbjct: 127 EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHEEEIDYA 170

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 171 KKAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 227

Query: 204 EGHSY 208
           +G+ +
Sbjct: 228 KGYKF 232


>gi|254750874|ref|ZP_05202913.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Vollum]
          Length = 359

 Score =  293 bits (750), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 146/259 (56%), Positives = 191/259 (73%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKL 667
           F VTRERIRQIEAKA+RKL
Sbjct: 341 FGVTRERIRQIEAKALRKL 359



 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 44/139 (31%), Positives = 70/139 (50%), Gaps = 23/139 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG--- 88
           +++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++V  +D    EG   
Sbjct: 22  EQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDLVGDND----EGPNN 77

Query: 89  -----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  DL   +    V             +DPVRMYL+E+G ++LLS E EI +A
Sbjct: 78  HQITKTEEEFDLNDLSVPPGV-----------KINDPVRMYLKEIGRVDLLSAEEEIRLA 126

Query: 144 KRIEAGRAMMMASLCESPL 162
            RIE G       L E+ L
Sbjct: 127 TRIEEGDEEAKRRLAEANL 145


>gi|260890619|ref|ZP_05901882.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260859664|gb|EEX74164.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 392

 Score =  293 bits (749), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 140/246 (56%), Positives = 187/246 (76%), Gaps = 3/246 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V  GE EA   K++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGN+GLMKA EKF++  G
Sbjct: 148 VLNGEEEA---KQKLIESNLRLVVSIAKKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKG 204

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R +  +  +EPT EE+A
Sbjct: 205 FKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIILQETGKEPTAEELA 264

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +KL +PVE V+ +L++ ++PISLETP+G E+ S LGDF+ED    +P D+  +  L+E  
Sbjct: 265 EKLELPVEKVKSILEMNQDPISLETPVGSEEDSELGDFVEDDKFANPYDATTRVLLKEQL 324

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L  REE VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR 
Sbjct: 325 DEVLKTLNEREEMVLRYRYGLDDGSQKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRR 384

Query: 674 KKLRSF 679
           KKL  +
Sbjct: 385 KKLEDY 390



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 91/207 (43%), Gaps = 38/207 (18%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-------- 80
           +S    IK AR++  V+ EE+N+ L     S+E+++  +  L++ G+ +VD         
Sbjct: 10  NSLANFIKQAREQKVVSYEEINSVLSIG-FSTEKIDQLIKKLTDDGVQIVDTAREKEDLL 68

Query: 81  ---DDLE--------DEEGSEDSLDLASSASNSSV--FLQ----KRKDSADRSTDDPVRM 123
              D +E        D E S D   + S   +S V   LQ    K  +S D   D+P++M
Sbjct: 69  KVPDSIEAIEKMEISDFEDSHDEF-VESEIDDSEVDKLLQTDLLKMAESMD--VDEPIKM 125

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLRE+G I LLS E EI  A+R+  G       L ES L    + I +   N G  +L  
Sbjct: 126 YLREIGQIPLLSYEEEIDYAQRVLNGEEEAKQKLIESNLRL-VVSIAKKHTNRGLKMLDL 184

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQK 210
           I         E   G     E   Y+K
Sbjct: 185 I--------QEGNMGLMKAVEKFEYEK 203


>gi|325473907|gb|EGC77095.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           F0402]
          Length = 619

 Score =  293 bits (749), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 148/290 (51%), Positives = 201/290 (69%), Gaps = 4/290 (1%)

Query: 397 NFVACEVDSILK----IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           N  A EV  I      +  +I+ I  +   ++ E   + S ++ G+     AK +++ AN
Sbjct: 330 NISANEVKDIYTQIQVLTRKIRKIEYDFEATVDEVIDLTSEIKNGQRMLKNAKDKLINAN 389

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKY NRGLQF DL+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI
Sbjct: 390 LRLVVSIAKKYINRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSI 449

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           +DQ+ TIR+PVHM ++I+KV R +R++  K+ REP  +EIA +L   +E V++V  + +E
Sbjct: 450 SDQARTIRVPVHMIEQINKVNRESRQLMQKLGREPNDDEIALQLGWSIEKVKQVKNVARE 509

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ + LGD IEDK   +P +      L+E    VL+SL  RE+ VL+MRF
Sbjct: 510 PISLETPIGEEEDTLLGDLIEDKGVENPSNRTELTLLQEQLEMVLSSLPEREQEVLKMRF 569

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI      TLEEVG  F VTRERIRQIEAK +R+L+HP RS+KL+ +LD 
Sbjct: 570 GIEGGYPLTLEEVGLYFDVTRERIRQIEAKGLRRLRHPKRSRKLKDYLDN 619



 Score = 38.5 bits (88), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 32/44 (72%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + S +   DDP+++YL+E+G  +LL+ + E++++K +E G A++
Sbjct: 122 RTSHEAGVDDPIKLYLQEIGKEDLLTADEEVSLSKSMEDGEAII 165


>gi|303233350|ref|ZP_07320019.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
 gi|302480479|gb|EFL43570.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
          Length = 441

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 185/237 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +  ANLRL +S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 203 AKQALTSANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 262

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P+PEEI K++ M  + +
Sbjct: 263 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGRDPSPEEIGKEMNMSPDKI 322

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV+P D+A  + LRE   +VL SL  R
Sbjct: 323 REIQKISQEPVSLETPIGEEEDSSLGDFIEDSTAVAPPDAASDSMLREQLNQVLDSLADR 382

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V++ RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS +L+ ++
Sbjct: 383 ERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSARLKDYV 439



 Score = 44.3 bits (103), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 27/33 (81%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+ + E+ +A +IEAG
Sbjct: 136 TGDPVRMYLKEIGKVDLLTADDEVHLAMKIEAG 168


>gi|160945279|ref|ZP_02092505.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443010|gb|EDP20015.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|295105509|emb|CBL03053.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 360

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 142/234 (60%), Positives = 185/234 (79%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + EANLRLV+SVAK+Y  RGL FLDLIQEGN+GLMKAAEKF+   G+KFSTYA WW++Q+
Sbjct: 126 LSEANLRLVVSVAKRYAGRGLPFLDLIQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQS 185

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ  TIRIPVH+ + I++V +TA  + +K  REPT EEIA  L M  + VR++L
Sbjct: 186 ITRAIADQGRTIRIPVHLVESINRVKKTAGDLLHKNGREPTVEEIAAALDMEPDKVRELL 245

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++++EPISLETP+G+E+ +HL DFI+D++A  P+D A +  LR     VL SLTPREERV
Sbjct: 246 QLSQEPISLETPVGEEEDAHLEDFIQDEDAGVPVDEAGRQLLRRELLHVLKSLTPREERV 305

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + +RFG+      TLEE+GK+F VTRER+RQIEAKA+RKL+HPSR+K LR +LD
Sbjct: 306 ITLRFGLEDGRARTLEELGKEFNVTRERVRQIEAKALRKLRHPSRAKLLRDYLD 359


>gi|290967746|ref|ZP_06559301.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
 gi|290782262|gb|EFD94835.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
          Length = 423

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 137/237 (57%), Positives = 187/237 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++ +ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW
Sbjct: 187 AKKKLTDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVDKFDYSKGYKFSTYATWW 246

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  R+P PEEIA+K+ +PVE V
Sbjct: 247 IRQAITRAIADQARTIRIPVHMVETINKLIRISRQLIQEKGRDPLPEEIAEKMEIPVERV 306

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFIED+ AV+P D+A    L+E    V + LT R
Sbjct: 307 REIMKIAQEPVSLETPIGEEEDSHLGDFIEDQEAVAPDDAASFILLKEQIEEVFSCLTDR 366

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +VL +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  + +K++ FL
Sbjct: 367 ERKVLYLRFGLKDGRPRTLEEVGQYFNVTRERIRQIEGKALGKLRNWGKREKIKDFL 423



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 67/120 (55%), Gaps = 9/120 (7%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++++L +++G +T  E+   +  DE+++EQ++      ++ GI+++       EE + + 
Sbjct: 58  QLLRLGQKQGSLTYTEIMNVMEEDELTTEQIDKMYETFADKGIDIIG------EESNGNE 111

Query: 93  LDLASSASNSSVFLQKRKDSA---DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D  S   N  V   +  D +     + DDPVRMYL+E+G + LLS + EI +AK IE G
Sbjct: 112 HDEISDTENEHVPDLRTVDLSVPEGINIDDPVRMYLKEIGRVPLLSADEEITLAKAIEKG 171


>gi|319789700|ref|YP_004151333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114202|gb|ADU96692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 563

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 177/437 (40%), Positives = 264/437 (60%), Gaps = 16/437 (3%)

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           N E   R++    DD A      E Q R K    +++I E+  E   LQ      +++  
Sbjct: 137 NGEIKVRDIMRSPDDFAE---GGESQRRKKFFSIVEQIKELLPEFNRLQKQYYRNKRN-- 191

Query: 310 SSVKCKVLKE--KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA---QSYG 364
           + VK   LK   K+  L+  L L+ S  + L + +Y+  K +  +E  L +L+      G
Sbjct: 192 AEVKRAYLKTWAKINGLLRQLPLSYSIYERLADDIYNKYKLLKKSERSLQKLSGKLSFLG 251

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           +  +    R    E+       A  +   E +  V   +D+    R+ ++S+ +    + 
Sbjct: 252 LPIEEICHRLDDDEIREKID--ASRYTTREIRKMVKKYLDTKETYRSVLESLDMPRN-AF 308

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +   +K   EA   K+ +V +NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA
Sbjct: 309 YELAEKIYFYKKDSQEA---KQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKA 365

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV++ +R+M  ++ 
Sbjct: 366 VDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKVIKISRQMFQEMG 425

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP PEEIA++L MP   VR +L++ +EP+SLETPIGD++ S LG+FIED  +  P    
Sbjct: 426 REPKPEEIAERLKMPASKVRSILQLAQEPVSLETPIGDDEDSTLGNFIEDTKSPIPEQEV 485

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I+ +L+E  +++L+ L+ RE  VL++RFG+    +HTLE+VGK+  VTRERIRQIE+KA+
Sbjct: 486 IKKDLQEKVSQLLSQLSEREALVLKLRFGLDGYPEHTLEQVGKELKVTRERIRQIESKAL 545

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL++   +  L  FL+
Sbjct: 546 RKLRNSGLNIDLSIFLE 562



 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 87/156 (55%), Gaps = 14/156 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           +++++I L +++GY+T +EL   L  + ++ E +E+ +  L    I ++       +EG 
Sbjct: 5   NFEEIIALGKEKGYITFDELMEHLDEEVLTPELIEELITQLDEYDIQIIP------KEG- 57

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED +DL      S + +    D+  RS DDP+R+YLREM  I LL R  EI++AKR+E G
Sbjct: 58  EDHVDL------SKLQITIAPDTIPRS-DDPIRLYLREMSGISLLKRHEEISLAKRVELG 110

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           R  ++  L ++      ++   + + +G   +R+I+
Sbjct: 111 RKALVRYLLKTSAVLNYVLEAEERIRNGEIKVRDIM 146


>gi|257126628|ref|YP_003164742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
 gi|257050567|gb|ACV39751.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
          Length = 392

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 136/236 (57%), Positives = 183/236 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW
Sbjct: 155 AKQKLIESNLRLVVSIAKKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWW 214

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + +R +  +  +EPT EE+A+KL +PVE V
Sbjct: 215 IRQAITRAIADQGRTIRIPVHMIETINKIKKESRIILQETGKEPTAEELAEKLELPVEKV 274

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L++ ++PISLETP+G E+ S LGDF+ED    +P D+  +  L+E    VL +L  R
Sbjct: 275 KSILEMNQDPISLETPVGSEEDSELGDFVEDDKFANPYDATTRILLKEQLDEVLKTLNER 334

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  +
Sbjct: 335 EEMVLRYRYGLDDGSQKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRKKLEDY 390



 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 93/206 (45%), Gaps = 36/206 (17%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD------- 81
           +S    IK AR++  V+ EE+N+ L     S+E++E  +  L++ G+ +VD         
Sbjct: 10  NSLANFIKQAREQKVVSYEEINSVLSIG-FSTEKIEQLIKKLTDDGVQIVDTKKEKEDLL 68

Query: 82  -------DLEDEEGS--EDSLD--LASSASNSSV--FLQ----KRKDSADRSTDDPVRMY 124
                  D+E  E S  ED+ D  + S   +S V   LQ    K  +S D   D+P++MY
Sbjct: 69  KVPETLADIEKMEISDFEDTHDEFVESEIDDSEVDKLLQTDLLKMAESMD--VDEPIKMY 126

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LRE+G I LLS E EI  A+R+  G       L ES L    + I +   N G  +L  I
Sbjct: 127 LREIGQIPLLSYEEEIDYAQRVLDGEEEAKQKLIESNLRL-VVSIAKKHTNRGLKMLDLI 185

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQK 210
                    E   G     E   Y+K
Sbjct: 186 --------QEGNMGLMKAVEKFEYEK 203


>gi|34763652|ref|ZP_00144580.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|237742311|ref|ZP_04572792.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
 gi|27886661|gb|EAA23826.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|229429959|gb|EEO40171.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
          Length = 340

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/306 (49%), Positives = 210/306 (68%), Gaps = 10/306 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIVSM 433
           E +P ++   +D  E E  N     + +  K+   IK    E G    ++  E       
Sbjct: 38  EFNPEYI---EDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKK 94

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
             +G+ EAS   K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  G
Sbjct: 95  AYEGDEEAS---KKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 151

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A
Sbjct: 152 YKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILA 211

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE  
Sbjct: 212 ERLGMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREEL 271

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR 
Sbjct: 272 DAVLKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRK 331

Query: 674 KKLRSF 679
           KKL  F
Sbjct: 332 KKLEDF 337



 Score = 44.7 bits (104), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ + EI  A
Sbjct: 49  EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHDEEIEYA 92

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 93  KKAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 149

Query: 204 EGHSY 208
           +G+ +
Sbjct: 150 KGYKF 154


>gi|320355021|ref|YP_004196360.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320123523|gb|ADW19069.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 533

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 142/260 (54%), Positives = 189/260 (72%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GIS   F  +   +  G   A  AK+ +V ANLRLVISV+KK+ NRG+Q  DLIQEGNIG
Sbjct: 272 GISWPAFIEVQQEIEIGRETARQAKETLVRANLRLVISVSKKFMNRGMQLPDLIQEGNIG 331

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA EK+D+  GYKFSTYA WW++QA+TR IADQ  TIR+PVHM + I++++R ++   
Sbjct: 332 LMKAVEKYDYKRGYKFSTYATWWIRQAVTRGIADQGRTIRLPVHMIETINRMLRFSKDFQ 391

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
               REPTPEE+AK+L   VE V+  LK  K+ ISL+ P+ DE+ + L DFIED     P
Sbjct: 392 RIESREPTPEEMAKQLGTDVEKVQVALKTAKDAISLDAPVNDEEDTLLSDFIEDHAHPDP 451

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            + +I  +L+    +V+ SLTPREE+VLRMR+GI +  DHTLEEVG+ F VTRERIRQIE
Sbjct: 452 QEHSITESLKRCLCKVMGSLTPREEKVLRMRYGIEIGCDHTLEEVGQCFAVTRERIRQIE 511

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           A+A++KL+HP+RS+ L++F+
Sbjct: 512 AQALKKLRHPARSQDLQAFI 531



 Score = 38.9 bits (89), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 112 SADR----STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           S DR    S+ DP+ +YLREMG+  LL  E E+ +A+ +E G   + +++    L   AL
Sbjct: 58  SGDRRGMGSSIDPMNIYLREMGNQRLLKHEEEMELARMVEEGETRIQSAVLRLTLGITAL 117

Query: 168 IIWRDELNDGTTLLREII 185
               + L  G   +  +I
Sbjct: 118 NDLAENLLRGNVRINSVI 135


>gi|294782673|ref|ZP_06747999.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
 gi|294481314|gb|EFG29089.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
          Length = 500

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 153/308 (49%), Positives = 210/308 (68%), Gaps = 10/308 (3%)

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG----ISISEFRHIV 431
           G E +P    Y +D  E E  N     + +  K+   IK    E G    ++  E     
Sbjct: 196 GDEFNP---DYIEDINEEELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYA 252

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
               +G+ EAS   ++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++ 
Sbjct: 253 KKAYEGDEEAS---QKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYT 309

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE 
Sbjct: 310 KGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEI 369

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L M VE ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE
Sbjct: 370 LAERLGMEVEKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILRE 429

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPS
Sbjct: 430 ELDGVLKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPS 489

Query: 672 RSKKLRSF 679
           R KKL  F
Sbjct: 490 RKKKLEDF 497



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 44/91 (48%), Gaps = 3/91 (3%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           D+P++MYLRE+G + LL+ + EI  AK+   G       L ES L    + I +   N G
Sbjct: 227 DEPIKMYLREIGQVPLLTHDEEIEYAKKAYEGDEEASQKLIESNLRL-VVSIAKKHTNRG 285

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
             LL  I   E  IG       F  T+G+ +
Sbjct: 286 LKLLDLI--QEGNIGLMKAVEKFEYTKGYKF 314


>gi|262038195|ref|ZP_06011589.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747776|gb|EEY35221.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 393

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 138/246 (56%), Positives = 189/246 (76%), Gaps = 3/246 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V KG+ EA   K++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGN+GLMKA EKF++  G
Sbjct: 149 VLKGDEEA---KQKLIESNLRLVVSIAKKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKG 205

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R +  +  +EPT EE++
Sbjct: 206 FKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIILQETGKEPTAEELS 265

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           KKL +PV+ V+ +L++ ++PISLETP+G E+ S LGDF+ED   ++P D+  +  L+E  
Sbjct: 266 KKLEIPVDKVKNILEMNQDPISLETPVGSEEDSELGDFVEDDKFLNPYDATTRVLLKEQL 325

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L +L  REE VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR 
Sbjct: 326 DEILKTLNEREEMVLRYRYGLDDGSQKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRR 385

Query: 674 KKLRSF 679
           KKL  +
Sbjct: 386 KKLEDY 391



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 91/203 (44%), Gaps = 39/203 (19%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-------------- 79
           ++K A++   V+ EE+N+ L     S+++++  +  L + G+N+VD              
Sbjct: 15  LMKQAKEEKIVSYEEINSILSVG-FSTQKIDQLIKKLQDDGVNIVDTLKDKQELLKVNKI 73

Query: 80  -GDDLE-----DEEGSEDSLDLASSASNSSV--FLQ----KRKDSADRSTDDPVRMYLRE 127
             +DLE     D + SED   + +   +S V   LQ    K  +S D   D+P++MYLRE
Sbjct: 74  LSEDLEKVEVVDFDDSEDEF-VENEIDDSEVDKLLQTDLLKMAESMD--VDEPIKMYLRE 130

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           +G I LLS E EI  A+R+  G       L ES L    + I +   N G  +L  I   
Sbjct: 131 IGQIPLLSYEEEIDYAQRVLKGDEEAKQKLIESNLRL-VVSIAKKHTNRGLKMLDLI--- 186

Query: 188 EACIGPESKGGFFHGTEGHSYQK 210
                 E   G     E   Y+K
Sbjct: 187 -----QEGNMGLMKAVEKFEYEK 204


>gi|320537364|ref|ZP_08037319.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
 gi|320145829|gb|EFW37490.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
          Length = 604

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 145/277 (52%), Positives = 196/277 (70%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I KI   ++ I  +   +I +   +   + +G      AK +++ ANLRLV+S+AKKYTN
Sbjct: 328 IQKITRRLRKIEYDFENNIDDIIVMAREIHRGHTMLKKAKDKLINANLRLVVSIAKKYTN 387

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL F DL+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM
Sbjct: 388 RGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHM 447

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            ++I+KV R +R++  K+ R+PT EEIA +L   VE V++V  + +EPISLETPIG+E+ 
Sbjct: 448 IEQINKVARESRQLLQKLGRDPTDEEIATQLCWTVEKVKQVKNVAREPISLETPIGEEED 507

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDFI D    +P +   +  LRE    VL++L  RE  VL+MRFG+  +   TLEEV
Sbjct: 508 SSLGDFIPDTEIENPSNVTEKILLREEVQSVLSTLPSREHEVLKMRFGLDGDYSQTLEEV 567

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G  F VTRERIRQIEAKA+R+L+HP  S++L+ FLD 
Sbjct: 568 GLYFDVTRERIRQIEAKALRRLRHPRHSRRLKDFLDN 604



 Score = 43.9 bits (102), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 32/136 (23%), Positives = 69/136 (50%), Gaps = 13/136 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA-MLSNMGINVVDGDDLEDE--- 86
           + +++  A+++  +T +E+  FLP     SE + D +A  L+   I ++  ++ E+E   
Sbjct: 10  FTELLVYAKEKKSITWDEIYKFLPDGMAVSEDLMDEIAEFLTQKKIYILSNNEDENEIDF 69

Query: 87  -------EGSEDSLDLASSASNSSVFLQKR--KDSADRSTDDPVRMYLREMGSIELLSRE 137
                  +   +  +    +       QKR   ++ D   DDP+++YLR++G   LL+ +
Sbjct: 70  DQNEEELDYESEEFENEDESGEEKEETQKRLLVNTKDSLIDDPIKLYLRDIGQERLLTAK 129

Query: 138 GEIAIAKRIEAGRAMM 153
            E+ ++KR+E G  ++
Sbjct: 130 QEVILSKRMEDGENII 145


>gi|308233952|ref|ZP_07664689.1| RNA polymerase, sigma 70 subunit, RpoD [Atopobium vaginae DSM
           15829]
 gi|328943964|ref|ZP_08241429.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
 gi|327491933|gb|EGF23707.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
          Length = 441

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 182/237 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +  ANLRL +S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 203 AKQALTSANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 262

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  + +   + REPTPEEI +++ M  + V
Sbjct: 263 IRQAITRAIADQARTIRIPVHMVETINKLVRVQKELLQDLGREPTPEEIGEQMKMSADRV 322

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED  AV+P D+A  + LRE   +VL  L  R
Sbjct: 323 REIQKISQEPVSLETPIGEEEDSSLGDFIEDSTAVAPPDAASDSMLREQLNQVLDGLADR 382

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V++ RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS +L+ ++
Sbjct: 383 ERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSGRLKDYI 439



 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+   E+ +A +I+AG
Sbjct: 136 TGDPVRMYLKEIGKVDLLNASEEVHLAMKIQAG 168


>gi|325677627|ref|ZP_08157279.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
 gi|324110595|gb|EGC04759.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
          Length = 366

 Score =  292 bits (747), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 143/242 (59%), Positives = 194/242 (80%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +AS A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTY
Sbjct: 125 DASKARKRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLIKAVEKFDYKKGFKFSTY 184

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I KV + + ++ +K   +P+PEEIA+ L M 
Sbjct: 185 ATWWIRQAITRAIADQARTIRIPVHMVETITKVKKASSQLLHKNGHDPSPEEIAEDLDMS 244

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE VR++++I ++P+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E   +VL++
Sbjct: 245 VEKVREIMRIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAASLVLLKEQIDQVLST 304

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT REE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP+RS K+R +
Sbjct: 305 LTEREEKVLRLRFGLEDGRSRTLEEVGQEFKVTRERIRQIEAKALRKLRHPNRSNKVRDY 364

Query: 680 LD 681
           LD
Sbjct: 365 LD 366



 Score = 38.1 bits (87), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 57/119 (47%), Gaps = 23/119 (19%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---------DGDDLE 84
           +++  +Q G +T +E+   L       +QM+      S + I ++         D ++ E
Sbjct: 11  LLEHGKQTGKLTTKEITDALEKLNFDVDQMDGVYEKCSELNIEIIDDVVVDDTLDFNNPE 70

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           D+   ED +D++ S    ++             DDPV++YL+E+G + LL+ E EI +A
Sbjct: 71  DDLEQED-VDISLSTDGIAI-------------DDPVKIYLKEIGRVPLLTSEEEIQLA 115


>gi|319957164|ref|YP_004168427.1| RNA polymerase, sigma 70 subunit, rpod [Nitratifractor salsuginis
           DSM 16511]
 gi|319419568|gb|ADV46678.1| RNA polymerase, sigma 70 subunit, RpoD [Nitratifractor salsuginis
           DSM 16511]
          Length = 618

 Score =  292 bits (747), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 134/253 (52%), Positives = 193/253 (76%), Gaps = 1/253 (0%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+  +R G+ ++  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF+
Sbjct: 365 ILEQIRIGKAKSEKAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFE 424

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  
Sbjct: 425 YQKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKHLQETGKEPDL 484

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E IA+++ + V+ V+ V+KITKEP+SLETP+GDED    GDFIEDKN++SP ++ +  +L
Sbjct: 485 ETIAEEVGLSVDKVKNVIKITKEPVSLETPVGDEDDGRFGDFIEDKNSISPTEAVLNDDL 544

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLK
Sbjct: 545 NQQIDEVLGQLNEREQAVIRMRFGLLEDMSDRTLEEIGKELNVTRERVRQIESSAIKKLK 604

Query: 669 HPSRSKKLRSFLD 681
           HP   +KL+++++
Sbjct: 605 HPKVGRKLKNYIE 617


>gi|42526854|ref|NP_971952.1| RNA polymerase sigma factor RpoD [Treponema denticola ATCC 35405]
 gi|41817169|gb|AAS11863.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
          Length = 619

 Score =  292 bits (747), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 148/290 (51%), Positives = 201/290 (69%), Gaps = 4/290 (1%)

Query: 397 NFVACEVDSILK----IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           N  A EV  I      +  +I+ I  +   ++ E   + S ++ G+     AK +++ AN
Sbjct: 330 NISANEVKDIYTQIQVLTRKIRKIEYDFEATVDEVIDLTSEIKNGQRMLKNAKDKLINAN 389

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKY NRGLQF DL+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI
Sbjct: 390 LRLVVSIAKKYINRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSI 449

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           +DQ+ TIR+PVHM ++I+KV R +R++  K+ REP  +EIA +L   +E V++V  + +E
Sbjct: 450 SDQARTIRVPVHMIEQINKVNRESRQLMQKLGREPNDDEIALQLGWSIEKVKQVKNVARE 509

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ + LGD IEDK   +P +      L+E    VL+SL  RE+ VL+MRF
Sbjct: 510 PISLETPIGEEEDTLLGDLIEDKGVENPSNRTELTLLQEQLEMVLSSLPEREQEVLKMRF 569

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI      TLEEVG  F VTRERIRQIEAK +R+L+HP RS+KL+ +LD 
Sbjct: 570 GIEGGYPLTLEEVGLYFDVTRERIRQIEAKGLRRLRHPKRSRKLKDYLDN 619



 Score = 38.1 bits (87), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 32/44 (72%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + S +   DDP+++YL+E+G  +LL+ + E++++K +E G A++
Sbjct: 122 RTSHEAGVDDPIKLYLQEIGKEDLLTADEEVSLSKSMEDGEAII 165


>gi|262068176|ref|ZP_06027788.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
 gi|291378119|gb|EFE85637.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
          Length = 502

 Score =  292 bits (747), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 139/243 (57%), Positives = 188/243 (77%), Gaps = 3/243 (1%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EAS   ++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 260 GDEEAS---QKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 316

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 317 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 376

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M VE ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 377 GMEVEKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDGV 436

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 437 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 496

Query: 677 RSF 679
             F
Sbjct: 497 EDF 499



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 3/92 (3%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            D+P++MYLRE+G + LL+ + EI  AK+   G       L ES L    + I +   N 
Sbjct: 228 VDEPIKMYLREIGQVPLLTHDEEIEYAKKAYEGDEEASQKLIESNLRL-VVSIAKKHTNR 286

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G  LL  I   E  IG       F  T+G+ +
Sbjct: 287 GLKLLDLI--QEGNIGLMKAVEKFEYTKGYKF 316


>gi|302335781|ref|YP_003800988.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
 gi|301319621|gb|ADK68108.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
          Length = 453

 Score =  292 bits (747), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 186/238 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ ANLRL +S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 215 AKQALISANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 274

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ +  + V
Sbjct: 275 IRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMGISADRV 334

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI++EP+SLETPIG+E+ S LGDFIED +AV+P ++A  + LRE   +VL SL  R
Sbjct: 335 REIQKISQEPVSLETPIGEEEDSSLGDFIEDSSAVAPPEAASDSMLREQLEQVLDSLADR 394

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V++ RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS +L+ +++
Sbjct: 395 ERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSGRLKDYME 452



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVRMYL+E+G ++LL+   E+ +A +IEAG
Sbjct: 148 TGDPVRMYLKEIGKVDLLTASEEVHLAMKIEAG 180


>gi|19704653|ref|NP_604215.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714957|gb|AAL95514.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 331

 Score =  291 bits (746), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 148/303 (48%), Positives = 207/303 (68%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRK 436
           E +P ++   +D  E E  N     + +  K+   IK    E G + +      +   +K
Sbjct: 29  EFNPEYI---EDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYAKK 85

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 86  AYEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 145

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 146 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 205

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 206 GMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 265

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 266 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 325

Query: 677 RSF 679
             F
Sbjct: 326 EDF 328



 Score = 45.8 bits (107), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 55/125 (44%), Gaps = 19/125 (15%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE  +E  L+L +SA                  D+P++MYLRE+G + LL+ E EI  A
Sbjct: 40  EDELSNEKLLNLGNSAK----------------VDEPIKMYLREIGQVPLLTHEEEIDYA 83

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+   G       L ES L    + I +   N G  LL  I   E  IG       F  T
Sbjct: 84  KKAYEGDEEASKKLIESNLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKFEYT 140

Query: 204 EGHSY 208
           +G+ +
Sbjct: 141 KGYKF 145


>gi|168335371|ref|ZP_02693465.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Epulopiscium
           sp. 'N.t. morphotype B']
          Length = 364

 Score =  291 bits (746), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 139/251 (55%), Positives = 199/251 (79%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++ E     A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 114 IKLAKRMESGDEEARKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 173

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PE
Sbjct: 174 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLMRIQRQLLQELGRDPQPE 233

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ + V  VR+++KI++EP++LETPIG+E+ ++LGDF+ D++A +P ++A    L+
Sbjct: 234 EIAREMELSVNKVREIMKISQEPVALETPIGEEEDTNLGDFLADEDAPAPAEAAAFTLLK 293

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT RE++VL++RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 294 EQLIEVLDTLTDREQKVLKLRFGLDDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHP 353

Query: 671 SRSKKLRSFLD 681
           SRSKKLR +L+
Sbjct: 354 SRSKKLRDYLE 364



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 57/114 (50%), Gaps = 16/114 (14%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           +AFL   E+   ++E     L    I+++ +  ++E+E  +ED +D       S      
Sbjct: 38  DAFLDL-ELEPTKIEQVYEFLEAQSIDIIGEISNIENENLNEDIIDFTLPEGVS------ 90

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                    DDPVRMYL+E+G + LLS + EI +AKR+E+G       L E+ L
Sbjct: 91  --------IDDPVRMYLKEIGKVPLLSADDEIKLAKRMESGDEEARKRLAEANL 136


>gi|223936990|ref|ZP_03628898.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894271|gb|EEF60724.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 614

 Score =  291 bits (745), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 138/243 (56%), Positives = 184/243 (75%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK EM EANLRLVIS+ KKYTNRGL FLD+IQEGN+GLMK  EKF++  GYKFST
Sbjct: 367 AKAHQAKTEMAEANLRLVISIGKKYTNRGLAFLDIIQEGNMGLMKGVEKFEYRRGYKFST 426

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I K++R  +++  +  RE TPEEIA ++ +
Sbjct: 427 YATWWIRQAITRAIADQARTIRIPVHMIEIIGKLMRAQKQLLQEFGREATPEEIADEMQI 486

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V+ +LK+ ++PIS++  +GD D +  GDFIEDK+A +P D    + L++    VLA
Sbjct: 487 SVERVKSILKMAQQPISMQASVGDSDDATFGDFIEDKSAENPSDMTSYSLLKDKLNDVLA 546

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT RE R++ +RFG+      TLEEVGKQ+ VTRERIRQIEAKA+RKL+HP+R + L+ 
Sbjct: 547 TLTERERRIVELRFGLVDGYARTLEEVGKQYKVTRERIRQIEAKALRKLRHPTRVRHLKG 606

Query: 679 FLD 681
           FL+
Sbjct: 607 FLE 609



 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/127 (33%), Positives = 67/127 (52%), Gaps = 35/127 (27%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL-------- 83
           K+++ LA+++G++T +++N  LP   V+ + ++     L+N+ I +VD  ++        
Sbjct: 83  KELVLLAKEQGHLTYDDINDALPDTVVTPDDLDQVYTKLNNLEIEIVDAAEVDRVKQPEA 142

Query: 84  ---EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
              EDE+G  D LD                        DPVRMYLR+MG + LL+RE E+
Sbjct: 143 EEQEDEKGRLDILD------------------------DPVRMYLRQMGKVPLLTREQEV 178

Query: 141 AIAKRIE 147
           AI KRIE
Sbjct: 179 AICKRIE 185


>gi|295101750|emb|CBK99295.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 359

 Score =  291 bits (744), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 139/238 (58%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ + EANLRLV+SVAK+Y  RGL FLDLIQEGN+GLMKAAEKF+   G+KFSTYA WW
Sbjct: 121 ARRRLSEANLRLVVSVAKRYAGRGLPFLDLIQEGNLGLMKAAEKFEPDRGFKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+ITR+IADQ  TIRIPVH+ + I++V +TA  +  +  REPT EEIA +L M    V
Sbjct: 181 IRQSITRAIADQGRTIRIPVHLVESINRVKKTAGELLRRTGREPTAEEIAAQLDMEPARV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++++ ++PISLETP+G+E+ +HL DFI+D  A  P D A +  LR     VL SLTPR
Sbjct: 241 RELIQLAQDPISLETPVGEEEDAHLEDFIQDDEAGVPADEAGRQLLRRELMNVLKSLTPR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EERV+ +RFG+      TLEE+G++F VTRER+RQIEAKA+RKL+HPSR+K+LR +LD
Sbjct: 301 EERVIALRFGLEDGRARTLEELGREFNVTRERVRQIEAKALRKLRHPSRAKRLRDYLD 358


>gi|288574317|ref|ZP_06392674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570058|gb|EFC91615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  291 bits (744), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 140/251 (55%), Positives = 193/251 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E    +AK+++++ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EKFD+
Sbjct: 131 VELAKRVEDGDQVAKQKIIDANLRLVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEKFDY 190

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REPT E
Sbjct: 191 RKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKMVRVSRQLVQRMGREPTDE 250

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI++ + +    V ++ +I + P+SLETPIG+E+ S LGDFIED++  SP D+A    L 
Sbjct: 251 EISEAMEIESTKVEEIRRIAQLPVSLETPIGEEEDSQLGDFIEDRDMPSPEDAASCNLLH 310

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +L +L+ RE  VLR RFG+     +TLEEVG++F VTRERIRQIEAKA+RKL+HP
Sbjct: 311 EQIEDMLDALSDREREVLRYRFGLEDGRSYTLEEVGRRFGVTRERIRQIEAKALRKLRHP 370

Query: 671 SRSKKLRSFLD 681
           SRSKKLR FL+
Sbjct: 371 SRSKKLRDFLE 381



 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 42/119 (35%), Positives = 68/119 (57%), Gaps = 6/119 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSE 90
           +++I   R+ GYVT +++  F+P +  S++ +E+    L  +GI V+ DGD     + SE
Sbjct: 27  RQLIMQGRKNGYVTQKDIEKFIPIEFWSTDVLENVFDNLMELGIEVIEDGDPRLKSDKSE 86

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                ASS+    V++ +     D    DPVRMYLRE+G ++LL    E+ +AKR+E G
Sbjct: 87  -----ASSSDEEHVYVDELGKLDDIPLTDPVRMYLREIGKVDLLDASEEVELAKRVEDG 140


>gi|294790965|ref|ZP_06756123.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
 gi|294458862|gb|EFG27215.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
          Length = 588

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 349 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 408

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 409 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 468

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E  T+VL +L+PR
Sbjct: 469 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFTQVLETLSPR 528

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 529 EAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 586



 Score = 38.5 bits (88), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 30/42 (71%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+     +T DPV+ YL+++G + LL+ + E+ +++RIEAG
Sbjct: 275 KRRVVTTGATADPVKDYLKQIGRVNLLNAQQEVDLSERIEAG 316


>gi|317056182|ref|YP_004104649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Ruminococcus albus
           7]
 gi|315448451|gb|ADU22015.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ruminococcus
           albus 7]
          Length = 366

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 143/242 (59%), Positives = 194/242 (80%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA  A+K + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTY
Sbjct: 125 EAVKARKRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLIKAVEKFDYKKGFKFSTY 184

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I KV + + ++ +K   +P+PEEIA++L M 
Sbjct: 185 ATWWIRQAITRAIADQARTIRIPVHMVETITKVKKVSSQLLHKNGHDPSPEEIAEELDMS 244

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE VR++++I ++P+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E   +VL++
Sbjct: 245 VERVREIMRIAQDPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAASLVLLKEQIDQVLST 304

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT REE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+HP+RS K+R +
Sbjct: 305 LTEREEKVLRLRFGLQDGRSRTLEEVGQEFKVTRERIRQIEAKALRKLRHPNRSNKVRDY 364

Query: 680 LD 681
           LD
Sbjct: 365 LD 366


>gi|327398426|ref|YP_004339295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
 gi|327181055|gb|AEA33236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
          Length = 491

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 141/234 (60%), Positives = 188/234 (80%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M++ANLRLV+S+AKK+ NRGL FLDLIQEGNIGLMK+ +KFD+  G+KFSTYA WW++Q+
Sbjct: 258 MIKANLRLVVSIAKKHLNRGLSFLDLIQEGNIGLMKSVDKFDYKKGFKFSTYATWWIRQS 317

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I+R+IADQ+ TIRIPVHM + I+K+VR ++ +  +  +EPT +E+A+ L M  E ++ ++
Sbjct: 318 ISRAIADQARTIRIPVHMIETINKIVRASKLLIQENGKEPTAQELAEYLGMDEEKIKSII 377

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPISLETPIGD++ +HL DFIED  + SPLD  I++NL+E    VL++LT RE +V
Sbjct: 378 KIAKEPISLETPIGDDNDTHLEDFIEDTKSESPLDYVIKSNLKEKVEEVLSTLTDRERKV 437

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           L MR+GIG   DHTLEEVGK   VTRER+RQIEAKA+RKL+HP RS+ L SF++
Sbjct: 438 LMMRYGIGDGFDHTLEEVGKVLGVTRERVRQIEAKALRKLRHPKRSRVLASFVE 491



 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 87/160 (54%), Gaps = 18/160 (11%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + +DD+ ++++   +++GYVT +E+N  LP + +S ++++D +    ++ I++VD D + 
Sbjct: 4   NLNDDAIRRILSEGKKKGYVTYDEINDILP-EGISVDEIDDIIRQCDDLDIDIVDTDKVS 62

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            E+  E+          S++                 RMYLREMG+I LLSRE EI IAK
Sbjct: 63  SEKNIEEFELEEDEEVGSAI-----------------RMYLREMGNIPLLSREEEIEIAK 105

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +IE  +  +   L E P T +A+   R ++ +G   ++ I
Sbjct: 106 KIEEHKNNLTRKLIEMPFTCEAIEELRQKIIEGEEKVKNI 145


>gi|15894582|ref|NP_347931.1| RNA polymerase sigma factor RpoD [Clostridium acetobutylicum ATCC
           824]
 gi|464686|sp|P33656|RPOD_CLOAB RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15024230|gb|AAK79271.1|AE007642_3 RNA polymerase sigma factor RPOD [Clostridium acetobutylicum ATCC
           824]
 gi|312373|emb|CAA80625.1| major vegetative sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|325508714|gb|ADZ20350.1| major vegetative sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 378

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 149/238 (62%), Positives = 196/238 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 141 ARKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDFKKGFKFSTYATWW 200

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIAK + MPV+ V
Sbjct: 201 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEIAKIMDMPVDKV 260

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P D+A    L+E   ++L +LTPR
Sbjct: 261 REIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPADAAAFRMLKEQLLKILNTLTPR 320

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 321 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 378



 Score = 57.0 bits (136), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 44/140 (31%), Positives = 69/140 (49%), Gaps = 16/140 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   ++ G +T +E+   L   ++  EQ+E    +L ++G++VV   D+ + E  E+
Sbjct: 36  KNLIDKGKKSGSLTYKEIMDELQEVDLGPEQIEKIYEVLESVGVDVVG--DMHEIEVEEE 93

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            LDL      +               DDPVRMYL+E+G + LLS E EI +A+RI+ G  
Sbjct: 94  DLDLTIPEGIA--------------IDDPVRMYLKEIGKVPLLSPEEEIDLAQRIKNGDR 139

Query: 152 MMMASLCESPLTFQALIIWR 171
                L E+ L     I  R
Sbjct: 140 SARKKLAEANLRLVVSIAKR 159


>gi|311064624|ref|YP_003971349.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
 gi|310866943|gb|ADP36312.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
          Length = 506

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 268 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 327

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 328 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 387

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 388 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 447

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 448 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 505



 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 195 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 236


>gi|224283384|ref|ZP_03646706.1| RNA polymerase sigma factor [Bifidobacterium bifidum NCIMB 41171]
          Length = 506

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 268 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 327

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 328 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 387

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 388 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 447

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 448 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 505



 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 195 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 236


>gi|303229406|ref|ZP_07316196.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
 gi|303230872|ref|ZP_07317619.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514632|gb|EFL56627.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302515942|gb|EFL57894.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 388

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 137/237 (57%), Positives = 184/237 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++V+ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW
Sbjct: 152 AKKKLVDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWW 211

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++     REPTPEEIA+ + +  E V
Sbjct: 212 IRQAITRAIADQARTIRIPVHMVETINKLIRISRQLLQDKGREPTPEEIAEGMGITAERV 271

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI +EP+SLETPIG+E+ SHLGDFIED++AV+P D+A    L+E    V   LT R
Sbjct: 272 REIQKIAQEPVSLETPIGEEEDSHLGDFIEDQDAVAPDDAASYILLQEQIEDVFTCLTDR 331

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++VL +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 332 EQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 388



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/126 (34%), Positives = 72/126 (57%), Gaps = 14/126 (11%)

Query: 33  KMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-- 89
           ++++  R+ G +T  E+ +A     E+++EQ++D     + + I VV   + +D++ +  
Sbjct: 16  QLLEKGRKSGVLTQSEISDALHEQSELTAEQLDDIYVTFNKLNIEVVPDVEDDDKDDAIE 75

Query: 90  ----EDSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIA 143
                D+   A+S  N S+ L     S D S   DDPVRMYL+E+G + LLS + EI +A
Sbjct: 76  PDDDVDNDRDAASEKNISIDL-----SVDASVNIDDPVRMYLKEIGRVPLLSADEEIVLA 130

Query: 144 KRIEAG 149
           K+IEAG
Sbjct: 131 KQIEAG 136


>gi|269798255|ref|YP_003312155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282850493|ref|ZP_06259872.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294792116|ref|ZP_06757264.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
 gi|294793987|ref|ZP_06759124.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|269094884|gb|ACZ24875.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282579986|gb|EFB85390.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294455557|gb|EFG23929.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|294457346|gb|EFG25708.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
          Length = 386

 Score =  290 bits (743), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 136/237 (57%), Positives = 184/237 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK++V+ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW
Sbjct: 150 AKKKLVDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWW 209

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++     REP PEEIA+ + + VE V
Sbjct: 210 IRQAITRAIADQARTIRIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERV 269

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ KI +EP+SLETPIG+E+ SHLGDFIED++A++P D+A    L+E    V   LT R
Sbjct: 270 REIQKIAQEPVSLETPIGEEEDSHLGDFIEDQDAIAPDDAASYILLQEQIEDVFTCLTDR 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++VL +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 330 EQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 386



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 69/125 (55%), Gaps = 14/125 (11%)

Query: 33  KMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGDDLEDE-- 86
           ++++  R+ G +T  E+ +A     E+++EQ++D    L  + + +V   D DD +    
Sbjct: 16  QLLEKGRKSGVLTQSEISDALHEQTEITAEQLDDIYTTLGKLNVEIVADIDADDTDSHTI 75

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLSREGEIAIAK 144
           E  ED  D  SS    S+ L     S D     DDPVRMYL+E+G + LLS + EI +AK
Sbjct: 76  ETDEDE-DEVSSEKKISIDL-----SVDSGVNIDDPVRMYLKEIGRVPLLSADEEIVLAK 129

Query: 145 RIEAG 149
           +IEAG
Sbjct: 130 QIEAG 134


>gi|57168867|ref|ZP_00367997.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|305431982|ref|ZP_07401149.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
 gi|57019703|gb|EAL56389.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|304445066|gb|EFM37712.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
          Length = 621

 Score =  290 bits (743), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 135/257 (52%), Positives = 194/257 (75%), Gaps = 1/257 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +
Sbjct: 363 LKEILEQIKRGKKISDEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVD 422

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +E
Sbjct: 423 KFEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKE 482

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P    IAK++ + V+ V++V+KITKEPISLE PIG ED    GDF+ED+N++SP+D  ++
Sbjct: 483 PDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPIGSEDDGKFGDFVEDRNSLSPMDHILK 542

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            +L+E    VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+
Sbjct: 543 DDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIK 602

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHP   +KL+++++G
Sbjct: 603 KLKHPKVGRKLKNYIEG 619


>gi|257467207|ref|ZP_05631518.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315918337|ref|ZP_07914577.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313692212|gb|EFS29047.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 352

 Score =  290 bits (742), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 146/280 (52%), Positives = 198/280 (70%), Gaps = 1/280 (0%)

Query: 401 CEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
            E+ + +K+   IK    E G I +   +  + + +K       A K ++EANLRLV+S+
Sbjct: 70  AELSNGMKVDEPIKMYLREIGQIPLLTHKEELELAKKALEGDEFANKRLIEANLRLVVSI 129

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TI
Sbjct: 130 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 189

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP
Sbjct: 190 RIPVHMIETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETP 249

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G E+ S LGDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   + 
Sbjct: 250 VGSEEDSELGDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSP 309

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 310 KTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 349



 Score = 42.0 bits (97), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            D+P++MYLRE+G I LL+ + E+ +AK+   G       L E+ L    + I +   N 
Sbjct: 78  VDEPIKMYLREIGQIPLLTHKEELELAKKALEGDEFANKRLIEANLRL-VVSIAKKHTNR 136

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G  LL  I   E  IG       F  T+G+ +
Sbjct: 137 GLKLLDLI--QEGNIGLMKAVEKFEYTKGYKF 166


>gi|257453204|ref|ZP_05618503.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|317059738|ref|ZP_07924223.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|313685414|gb|EFS22249.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
          Length = 436

 Score =  290 bits (742), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 146/280 (52%), Positives = 198/280 (70%), Gaps = 1/280 (0%)

Query: 401 CEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
            E+ + +K+   IK    E G I +   +  + + +K       A K ++EANLRLV+S+
Sbjct: 154 AELSNGMKVDEPIKMYLREIGQIPLLTHKEELELAKKALEGDEFANKRLIEANLRLVVSI 213

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TI
Sbjct: 214 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 273

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP
Sbjct: 274 RIPVHMIETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETP 333

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G E+ S LGDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   + 
Sbjct: 334 VGSEEDSELGDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSP 393

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 394 KTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 433



 Score = 42.4 bits (98), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            D+P++MYLRE+G I LL+ + E+ +AK+   G       L E+ L    + I +   N 
Sbjct: 162 VDEPIKMYLREIGQIPLLTHKEELELAKKALEGDEFANKRLIEANLRL-VVSIAKKHTNR 220

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G  LL  I   E  IG       F  T+G+ +
Sbjct: 221 GLKLLDLI--QEGNIGLMKAVEKFEYTKGYKF 250


>gi|310287737|ref|YP_003938995.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
 gi|309251673|gb|ADO53421.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
          Length = 506

 Score =  290 bits (742), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 268 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 327

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 328 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 387

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 388 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 447

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 448 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 505



 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 195 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 236


>gi|283783165|ref|YP_003373919.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
 gi|283441732|gb|ADB14198.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
          Length = 489

 Score =  290 bits (742), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 251 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 310

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 311 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 370

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L PR
Sbjct: 371 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLAPR 430

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 431 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 488



 Score = 40.8 bits (94), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 178 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 219


>gi|213691851|ref|YP_002322437.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|213523312|gb|ACJ52059.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|320457946|dbj|BAJ68567.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 464

 Score =  290 bits (742), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 226 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 285

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 286 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 345

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 346 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 405

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 406 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 463



 Score = 40.4 bits (93), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 153 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 194


>gi|313140538|ref|ZP_07802731.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
 gi|313133048|gb|EFR50665.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
          Length = 500

 Score =  290 bits (742), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 262 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 321

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 322 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 381

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 382 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 441

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 442 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 499



 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 189 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 230


>gi|296454312|ref|YP_003661455.1| RpoD family RNA polymerase sigma-70 factor [Bifidobacterium longum
           subsp. longum JDM301]
 gi|296183743|gb|ADH00625.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. longum JDM301]
          Length = 474

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 236 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 295

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 296 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 355

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 356 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 415

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 416 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 473



 Score = 40.4 bits (93), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 163 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 204


>gi|291457726|ref|ZP_06597116.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
 gi|291380779|gb|EFE88297.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
          Length = 472

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 234 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 293

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 294 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 353

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 354 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 413

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 414 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 471



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 161 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 202


>gi|297243591|ref|ZP_06927522.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
 gi|296888342|gb|EFH27083.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
          Length = 489

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 251 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 310

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 311 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 370

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L PR
Sbjct: 371 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLAPR 430

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 431 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 488



 Score = 40.8 bits (94), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 178 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 219


>gi|227547666|ref|ZP_03977715.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
 gi|227211921|gb|EEI79817.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
          Length = 464

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 226 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 285

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 286 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 345

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 346 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 405

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 406 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 463



 Score = 40.4 bits (93), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 153 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 194


>gi|23465986|ref|NP_696589.1| RNA polymerase sigma factor [Bifidobacterium longum NCC2705]
 gi|46191322|ref|ZP_00206768.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bifidobacterium longum DJO10A]
 gi|189439160|ref|YP_001954241.1| RNA polymerase sigma factor [Bifidobacterium longum DJO10A]
 gi|312132592|ref|YP_003999931.1| rpod [Bifidobacterium longum subsp. longum BBMN68]
 gi|317482450|ref|ZP_07941467.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689398|ref|YP_004209132.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691364|ref|YP_004220934.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|23326702|gb|AAN25225.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           longum NCC2705]
 gi|189427595|gb|ACD97743.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium longum
           DJO10A]
 gi|311773536|gb|ADQ03024.1| RpoD [Bifidobacterium longum subsp. longum BBMN68]
 gi|316916110|gb|EFV37515.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456220|dbj|BAJ66842.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|320460734|dbj|BAJ71354.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 474

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 236 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 295

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 296 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 355

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 356 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 415

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 416 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 473



 Score = 40.4 bits (93), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 163 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 204


>gi|239621277|ref|ZP_04664308.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|239515738|gb|EEQ55605.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
          Length = 488

 Score =  290 bits (741), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 250 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 309

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 310 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 369

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 370 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 429

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 430 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 487



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 177 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 218


>gi|221633686|ref|YP_002522912.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
 gi|221156620|gb|ACM05747.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
          Length = 509

 Score =  290 bits (741), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 135/253 (53%), Positives = 192/253 (75%), Gaps = 4/253 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + R GE     A++++ EANLRLV+S+AK+YT RGL  LDLIQEGN+GLM+A +KF
Sbjct: 261 HWQRLRRDGEA----ARRKLTEANLRLVVSIAKRYTGRGLTLLDLIQEGNLGLMRAVDKF 316

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
               G+KFSTYA WW++QAITR++AD + TIR+PVH+ + +++V R AR+++ ++ REPT
Sbjct: 317 QTHKGFKFSTYATWWIRQAITRALADHARTIRLPVHLVETLNRVSRVARQLTQELGREPT 376

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A  + MP++ +R++L+  ++P+SLE P+G E+ S LGDF+ED+ AV+PLD+A  + 
Sbjct: 377 TSELAAAVNMPLDRLRELLQAAQDPVSLEAPVGQEEESTLGDFLEDERAVAPLDAAALSL 436

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    +LA+LT RE RVL MRFG+     +TLEEVG+ F VTRER+RQIEAKA+RKL+
Sbjct: 437 LREQVQSLLATLTERERRVLAMRFGLEDGQTYTLEEVGRAFGVTRERVRQIEAKALRKLR 496

Query: 669 HPSRSKKLRSFLD 681
           HP R++ LR FL+
Sbjct: 497 HPQRARALRDFLE 509



 Score = 41.2 bits (95), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 36/142 (25%), Positives = 64/142 (45%), Gaps = 19/142 (13%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           KR+R+  +    S D  V   +D     ++  AR  G +T E+  A +  D +  +  E 
Sbjct: 11  KRSREVVTRANGSVDLPVLAGAD----AILATARLHGRLTREQWLALI--DTLGPDAAET 64

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            +A L   G+ V   + LE +               S  +  +++   D   +DPVR+YL
Sbjct: 65  ALAELQAEGVPVAIEEALEPD-------------GTSRSWEPEKEADPDLLVEDPVRLYL 111

Query: 126 REMGSIELLSREGEIAIAKRIE 147
            E+G + LL+ E E+ + + +E
Sbjct: 112 AEIGRVPLLTAEQEVELGRAVE 133


>gi|237740231|ref|ZP_04570712.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
 gi|229422248|gb|EEO37295.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
          Length = 269

 Score =  290 bits (741), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 136/236 (57%), Positives = 184/236 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW
Sbjct: 31  ASQKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L M VE +
Sbjct: 91  IRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERLGMEVEKI 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    VL +L+PR
Sbjct: 151 KAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDGVLKTLSPR 210

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 211 EEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKLEDF 266


>gi|257464031|ref|ZP_05628416.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 436

 Score =  290 bits (741), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 145/274 (52%), Positives = 195/274 (71%), Gaps = 1/274 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +K+   IK    E G I +   +  + + +K       A K ++EANLRLV+S+AKK+TN
Sbjct: 160 MKVDEPIKMYLREIGQIPLLTHKEELELAKKALEGDEFANKRLIEANLRLVVSIAKKHTN 219

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM
Sbjct: 220 RGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHM 279

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ 
Sbjct: 280 IETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGSEED 339

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEV
Sbjct: 340 SELGDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEV 399

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 400 GKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 433



 Score = 44.3 bits (103), Expect = 0.078,   Method: Compositional matrix adjust.
 Identities = 38/128 (29%), Positives = 58/128 (45%), Gaps = 3/128 (2%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +DL D+E   D+ DL           +  + S     D+P++MYLRE+G I LL+ + E+
Sbjct: 126 EDLLDKEEDFDASDLEELPEEELSNEELAELSNGMKVDEPIKMYLREIGQIPLLTHKEEL 185

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            +AK+   G       L E+ L    + I +   N G  LL  I   E  IG       F
Sbjct: 186 ELAKKALEGDEFANKRLIEANLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKF 242

Query: 201 HGTEGHSY 208
             T+G+ +
Sbjct: 243 EYTKGYKF 250


>gi|317061552|ref|ZP_07926037.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
 gi|313687228|gb|EFS24063.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 363

 Score =  289 bits (740), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 145/274 (52%), Positives = 195/274 (71%), Gaps = 1/274 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +K+   IK    E G I +   +  + + +K       A K ++EANLRLV+S+AKK+TN
Sbjct: 87  MKVDEPIKMYLREIGQIPLLTHKEELELAKKALEGDEFANKRLIEANLRLVVSIAKKHTN 146

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM
Sbjct: 147 RGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHM 206

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ 
Sbjct: 207 IETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGSEED 266

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEV
Sbjct: 267 SELGDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEV 326

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 327 GKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 360



 Score = 43.9 bits (102), Expect = 0.087,   Method: Compositional matrix adjust.
 Identities = 38/128 (29%), Positives = 58/128 (45%), Gaps = 3/128 (2%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +DL D+E   D+ DL           +  + S     D+P++MYLRE+G I LL+ + E+
Sbjct: 53  EDLLDKEEDFDASDLEELPEEELSNEELAELSNGMKVDEPIKMYLREIGQIPLLTHKEEL 112

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            +AK+   G       L E+ L    + I +   N G  LL  I   E  IG       F
Sbjct: 113 ELAKKALEGDEFANKRLIEANLRL-VVSIAKKHTNRGLKLLDLI--QEGNIGLMKAVEKF 169

Query: 201 HGTEGHSY 208
             T+G+ +
Sbjct: 170 EYTKGYKF 177


>gi|269127406|ref|YP_003300776.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312364|gb|ACY98738.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 385

 Score =  289 bits (740), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 132/242 (54%), Positives = 189/242 (78%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E + AK+ ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 145 EGARAKQRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTY 204

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + REPTP EI  ++ +P
Sbjct: 205 ATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLHQDLGREPTPAEIGAEMGLP 264

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V ++ +I +EP+SL++PIG+ED S LGDFIED +AV PL++A    L++    +L +
Sbjct: 265 AERVVEIQRIAQEPVSLQSPIGEED-SDLGDFIEDADAVVPLEAAAFILLQDQLEDILCT 323

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE+R++++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSR++ LR +
Sbjct: 324 LSEREQRIIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRAQMLREY 383

Query: 680 LD 681
           L+
Sbjct: 384 LE 385



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 58/123 (47%), Gaps = 16/123 (13%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D    ++   R+ G VT++++ A +   E+ ++ +E  V  L+  G+ V++      E
Sbjct: 12  SVDQVADLVVRGREHGGVTVDDVAAAIDRSELPADSLERVVLALAEQGVEVLESPGETGE 71

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D  DL      S                D VR+YLRE+G + LL+ E E+ +AK I
Sbjct: 72  LSRADEDDLGKRVPTS----------------DLVRIYLREIGRVPLLTAEEEVELAKTI 115

Query: 147 EAG 149
           EAG
Sbjct: 116 EAG 118


>gi|298253932|ref|ZP_06977519.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
 gi|297532075|gb|EFH71050.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
          Length = 489

 Score =  289 bits (740), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 251 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 310

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 311 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 370

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L PR
Sbjct: 371 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLAPR 430

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 431 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 488



 Score = 40.8 bits (94), Expect = 0.78,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 178 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 219


>gi|304437692|ref|ZP_07397644.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369325|gb|EFM22998.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 381

 Score =  289 bits (740), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 142/252 (56%), Positives = 190/252 (75%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + R+ E     A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 130 VDLARRMEAGDETARHRLEEANLRLVVSIAKRYVGRGMMFLDLIQEGNLGLLKAVEKFDY 189

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K +R +R++  ++ R+PTPE
Sbjct: 190 SKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKYIRVSRQLLQELGRDPTPE 249

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ + V  VR+++KI++EP+SLETPIG+E+ +HL DFIED+ A  P D+A    L+
Sbjct: 250 EIAHRMGLSVARVREIMKISQEPVSLETPIGEEEDTHLSDFIEDEAAPDPADAASMLLLK 309

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  + VL +L PRE  VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 310 EQISEVLTTLAPREAEVLRLRFGLVDGRSRTLEEVGQNFGVTRERIRQIEAKALRKLRHP 369

Query: 671 SRSKKLRSFLDG 682
            R +KL+   D 
Sbjct: 370 VRLRKLQGNFDA 381



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 57/123 (46%), Gaps = 29/123 (23%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL---------------EDE 86
           G +T  EL   L  D V+ + M+       + GI ++D  D+               +DE
Sbjct: 31  GTLTCSELMDALAQDSVTPDAMDALYQRCMDEGIEIIDDADVGAEDDAADFADDLEDKDE 90

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++  +DL+     +               DDPVRMYL+E+G + LL+ E E+ +A+R+
Sbjct: 91  TDADVDIDLSVPEGVA--------------LDDPVRMYLKEIGRVPLLTAEEEVDLARRM 136

Query: 147 EAG 149
           EAG
Sbjct: 137 EAG 139


>gi|15639484|ref|NP_218934.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025724|ref|YP_001933496.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum SS14]
 gi|6094131|sp|O83506|RPOD_TREPA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|3322782|gb|AAC65480.1| RNA polymerase sigma-70 factor (rpoD) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018299|gb|ACD70917.1| RNA polymerase sigma-70 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 611

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 141/255 (55%), Positives = 189/255 (74%), Gaps = 3/255 (1%)

Query: 430 IVSMVR---KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM R   +G      AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA E
Sbjct: 356 ILSMARAIHRGHVMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVE 415

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++  K  RE
Sbjct: 416 KFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLLQKFGRE 475

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+ EEIA++L   VE V++V  + +EPISLETPIG+E+ S LGDF+ D +  +P     +
Sbjct: 476 PSDEEIAQQLCWTVEKVKQVKSVAREPISLETPIGEEEDSSLGDFVPDADVENPSRVTER 535

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    +L++L  RE  VLRMRFG+  +   TLEEVG  F VTRERIRQIEAKA+++
Sbjct: 536 VLLKEEVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKR 595

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP  S++L+ FLD
Sbjct: 596 LRHPRHSRRLKDFLD 610



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 74/156 (47%), Gaps = 28/156 (17%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINV-------------- 77
           ++++ AR++  +T +E+   L    V +E++  D + ML    I V              
Sbjct: 12  RLLEYAREKKAITHDEVENILAHYGVETEELLHDVLDMLEQENIKVFSSEEEELEDEVFA 71

Query: 78  -VDGDDLEDEEGS--------EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            + G   +D +GS         D L  +S  +  ++    R    + + DDPV++YLR++
Sbjct: 72  GLKGPAADDGDGSFPLSTERVRDKLCDSSRGARQNLLSNAR----NIALDDPVKLYLRDI 127

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           G  +LL+ E E+ ++KR+E G  ++   + +S L  
Sbjct: 128 GQEKLLTAEQEVMLSKRMEEGEGIIKDIITQSGLLL 163


>gi|291059871|gb|ADD72606.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 610

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 141/255 (55%), Positives = 189/255 (74%), Gaps = 3/255 (1%)

Query: 430 IVSMVR---KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM R   +G      AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA E
Sbjct: 355 ILSMARAIHRGHVMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVE 414

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++  K  RE
Sbjct: 415 KFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLLQKFGRE 474

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+ EEIA++L   VE V++V  + +EPISLETPIG+E+ S LGDF+ D +  +P     +
Sbjct: 475 PSDEEIAQQLCWTVEKVKQVKSVAREPISLETPIGEEEDSSLGDFVPDADVENPSRVTER 534

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    +L++L  RE  VLRMRFG+  +   TLEEVG  F VTRERIRQIEAKA+++
Sbjct: 535 VLLKEEVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKR 594

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP  S++L+ FLD
Sbjct: 595 LRHPRHSRRLKDFLD 609



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 74/156 (47%), Gaps = 28/156 (17%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINV-------------- 77
           ++++ AR++  +T +E+   L    V +E++  D + ML    I V              
Sbjct: 11  RLLEYAREKKAITHDEVENILAHYGVETEELLHDVLDMLEQENIKVFSSEEEELEDEVFA 70

Query: 78  -VDGDDLEDEEGS--------EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            + G   +D +GS         D L  +S  +  ++    R    + + DDPV++YLR++
Sbjct: 71  GLKGPAADDGDGSFPLSTERVRDKLCDSSRGARQNLLSNAR----NIALDDPVKLYLRDI 126

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           G  +LL+ E E+ ++KR+E G  ++   + +S L  
Sbjct: 127 GQEKLLTAEQEVMLSKRMEEGEGIIKDIITQSGLLL 162


>gi|212715646|ref|ZP_03323774.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
 gi|212661013|gb|EEB21588.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
          Length = 448

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 210 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 269

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 270 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 329

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 330 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLSPR 389

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 390 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 447



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 137 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 178


>gi|229817449|ref|ZP_04447731.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
 gi|229785238|gb|EEP21352.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
          Length = 482

 Score =  288 bits (738), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 244 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 303

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 304 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 363

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L++   +VL +L+PR
Sbjct: 364 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQDQFKQVLETLSPR 423

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 424 ESGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 481



 Score = 38.9 bits (89), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 30/42 (71%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 171 KRRVVTAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 212


>gi|308234847|ref|ZP_07665584.1| RNA polymerase sigma factor [Gardnerella vaginalis ATCC 14018]
 gi|311114490|ref|YP_003985711.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
 gi|310945984|gb|ADP38688.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
          Length = 434

 Score =  288 bits (738), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 196 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 255

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 256 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 315

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 316 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLSPR 375

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 376 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 433



 Score = 40.8 bits (94), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 123 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 164


>gi|309801431|ref|ZP_07695558.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
 gi|308221946|gb|EFO78231.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
          Length = 461

 Score =  288 bits (738), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 223 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 282

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 283 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 342

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 343 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 402

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 403 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 460



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 150 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 191


>gi|171742642|ref|ZP_02918449.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
 gi|171278256|gb|EDT45917.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
          Length = 461

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 223 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 282

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 283 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 342

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 343 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 402

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 403 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 460



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 150 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 191


>gi|154509177|ref|ZP_02044819.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798811|gb|EDN81231.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
          Length = 561

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 324 AKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 383

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 384 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTAEKV 443

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 444 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSER 503

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+G     TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 504 EAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 561



 Score = 40.8 bits (94), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A+RIEAG
Sbjct: 259 ATADPVKDYLKQIGKVSLLNAEQEVDLARRIEAG 292


>gi|119026029|ref|YP_909874.1| RNA polymerase sigma factor [Bifidobacterium adolescentis ATCC
           15703]
 gi|118765613|dbj|BAF39792.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 479

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 241 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 300

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 301 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 360

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 361 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 420

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 421 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 478



 Score = 40.4 bits (93), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 168 KRRVIAAGATADPVKDYLKQIGRVNLLNAEQEVDLSERIEAG 209


>gi|154488794|ref|ZP_02029643.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
 gi|154082931|gb|EDN81976.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
          Length = 478

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 240 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 299

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 300 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 359

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 360 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 419

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 420 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 477



 Score = 40.4 bits (93), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 167 KRRVIAAGATADPVKDYLKQIGRVNLLNAEQEVDLSERIEAG 208


>gi|320096194|ref|ZP_08027783.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319976875|gb|EFW08629.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 543

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 306 AKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 365

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 366 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 425

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 426 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSER 485

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+G     TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 486 EAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 543



 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +A+RIEAG
Sbjct: 241 ATADPVKDYLKQIGKVSLLNAAQEVDLARRIEAG 274


>gi|306822519|ref|ZP_07455897.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
 gi|304554064|gb|EFM41973.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
          Length = 472

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 234 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 293

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 294 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 353

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 354 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 413

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 414 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 471



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 161 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 202


>gi|315604554|ref|ZP_07879617.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315313566|gb|EFU61620.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 516

 Score =  287 bits (735), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 279 AKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 338

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 339 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTAEKV 398

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 399 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSER 458

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+G     TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 459 EAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 516



 Score = 40.8 bits (94), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A+RIEAG
Sbjct: 214 ATADPVKDYLKQIGKVSLLNAEQEVDLARRIEAG 247


>gi|225351336|ref|ZP_03742359.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157680|gb|EEG70963.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 472

 Score =  287 bits (735), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 234 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 293

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 294 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 353

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 354 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLSPR 413

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 414 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 471



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 161 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 202


>gi|283456279|ref|YP_003360843.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
 gi|283102913|gb|ADB10019.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
          Length = 328

 Score =  287 bits (735), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 90  AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 150 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 210 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 270 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 327



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 17  KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 58


>gi|293189827|ref|ZP_06608541.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
 gi|292821242|gb|EFF80187.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
          Length = 561

 Score =  287 bits (735), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 324 AKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 383

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 384 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTAEKV 443

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 444 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSER 503

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+G     TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 504 EAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 561



 Score = 40.8 bits (94), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A+RIEAG
Sbjct: 259 ATADPVKDYLKQIGKVSLLNAEQEVDLARRIEAG 292


>gi|152990473|ref|YP_001356195.1| RNA polymerase sigma factor RpoD [Nitratiruptor sp. SB155-2]
 gi|151422334|dbj|BAF69838.1| RNA polymerase sigma 70 factor [Nitratiruptor sp. SB155-2]
          Length = 608

 Score =  287 bits (735), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 132/253 (52%), Positives = 194/253 (76%), Gaps = 1/253 (0%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF+
Sbjct: 355 ILEQIKRGKKISEEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFE 414

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  
Sbjct: 415 YKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIVRKHLQETGKEPDV 474

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E IA+++ MPVE V+ V+KITKEP+SLE PIG+E+    GDFIEDKNA +PL+  ++ ++
Sbjct: 475 ETIAEEVGMPVEKVKNVIKITKEPVSLEAPIGNEEDGKFGDFIEDKNAPNPLEVIMKEDM 534

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     +L +L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLK
Sbjct: 535 KSKIEEILENLNEREKAVVRMRFGLMPDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 594

Query: 669 HPSRSKKLRSFLD 681
           HP   +K++++++
Sbjct: 595 HPKVGRKIKNYIE 607


>gi|224418172|ref|ZP_03656178.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253827499|ref|ZP_04870384.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313141707|ref|ZP_07803900.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253510905|gb|EES89564.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313130738|gb|EFR48355.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
          Length = 616

 Score =  287 bits (734), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 161/381 (42%), Positives = 245/381 (64%), Gaps = 28/381 (7%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG---ELLRLAQSYGIKRDV 369
           K + LKEKL+ L G  S       L+ E +  +   I  +EG   EL RL     +  D+
Sbjct: 251 KKQFLKEKLLDL-GPTS------KLITELVKAMENTIKSDEGFDRELKRLEYRLPLFNDI 303

Query: 370 FLERHQG-----RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG--- 421
            L  H+       E++   +  A   PE       A  V + ++I+   ++     G   
Sbjct: 304 LLANHKKILDNITEMNKSDIIAA--VPE-------ATMVSTYMEIKKLFQTKLASEGSFD 354

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   + + I+  +++G+  A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGL
Sbjct: 355 LEPEKLKQILEQIKRGKDIADRAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 414

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   
Sbjct: 415 MKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKYLQ 474

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  ++IA+++ +PV+ V+ V+KITKEPISLE PIG+ +    GDF+EDK +V P+
Sbjct: 475 EEGKEPDIDKIAEEVGLPVDKVKNVIKITKEPISLEAPIGNGEDGKFGDFVEDKGSVGPM 534

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIE 660
           +S ++ +L+E    VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE
Sbjct: 535 ESILKEDLKEQIDDVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIE 594

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           + AI+KLKHP   +KL+++++
Sbjct: 595 SSAIKKLKHPKVGRKLKNYIE 615



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 45/70 (64%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           F+++R+      +D PVRMYLREMG I LL+RE E+ ++K IE G  +++ ++C  P   
Sbjct: 89  FMKERELLEWSRSDSPVRMYLREMGQIPLLTREDEVELSKNIELGENIILDAICSVPYLI 148

Query: 165 QALIIWRDEL 174
             ++ +++ L
Sbjct: 149 DFILDYKEAL 158


>gi|183601374|ref|ZP_02962744.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683429|ref|YP_002469812.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191127|ref|YP_002968521.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           Bl-04]
 gi|241196533|ref|YP_002970088.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           DSM 10140]
 gi|183218980|gb|EDT89621.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219621079|gb|ACL29236.1| principal sigma factor RpoD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249519|gb|ACS46459.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240251087|gb|ACS48026.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|295794116|gb|ADG33651.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 488

 Score =  287 bits (734), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 250 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 309

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 310 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 369

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PR
Sbjct: 370 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFRQVLETLSPR 429

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 430 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 487



 Score = 39.3 bits (90), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 43/92 (46%), Gaps = 30/92 (32%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           V S+  ED  A+L+N G+N                               KR+     +T
Sbjct: 157 VVSDNDEDDEALLANPGVN------------------------------PKRRVVTTGAT 186

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 187 ADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 218


>gi|237751866|ref|ZP_04582346.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376742|gb|EEO26833.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 615

 Score =  287 bits (734), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 159/376 (42%), Positives = 245/376 (65%), Gaps = 22/376 (5%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           K + LKEKL+ L  +  L    I+ LV+ + +  K     + EL RL     +  D+ LE
Sbjct: 253 KKQFLKEKLLDLGPTSKL----INELVKAMENTIKSDEGFDKELKRLEYRLPLFNDMLLE 308

Query: 373 RHQG-----RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG---ISI 424
            H+       E++   ++ A   PE       A  V + ++I+   ++ +   G   +  
Sbjct: 309 NHKKILENITEMNKTEITAA--VPE-------ATMVSTYMEIKKLFQTKAASEGSFDLEP 359

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + + I+  +++G+  A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA
Sbjct: 360 EKLKQILEQIKRGKDIADKAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKA 419

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GY+FSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  
Sbjct: 420 VDKFEYKKGYRFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKCLQEEG 479

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E+IA+++ +P++ V+ V+KITKEPISLE PIG+ +    GDF+EDK+AV P+D  
Sbjct: 480 KEPDLEKIAEEVGLPLDKVKNVIKITKEPISLEAPIGNGEDGKFGDFVEDKSAVGPMDHI 539

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 540 LKEDLKSQIDDVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 599

Query: 664 IRKLKHPSRSKKLRSF 679
           I+KLKHP   +KL+++
Sbjct: 600 IKKLKHPKVGRKLKNY 615


>gi|269121540|ref|YP_003309717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
 gi|268615418|gb|ACZ09786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
          Length = 387

 Score =  286 bits (733), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 135/236 (57%), Positives = 184/236 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW
Sbjct: 150 AKQKLIESNLRLVVSIAKKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWW 209

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + +R +  +  +E T EE+AKKL +PV+ V
Sbjct: 210 IRQAITRAIADQGRTIRIPVHMIETINKIKKESRIILQETGKEATAEELAKKLEIPVDKV 269

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L++ ++PISLETP+G E+ S LGDF+ED   ++P D+  +  L+E    VL +L+ R
Sbjct: 270 KSILEMNQDPISLETPVGSEEDSELGDFVEDDKFLNPYDATTRVLLKEQLDGVLKTLSER 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  +
Sbjct: 330 EEMVLRYRYGLDDGSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRKKLEDY 385



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/199 (24%), Positives = 86/199 (43%), Gaps = 27/199 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-----DDL 83
           D   +++K A++ G ++ EE+N  +P D    E+++  +  + + GI++VD      D +
Sbjct: 10  DKLLELVKQAKEDGVISYEEINGVIPED-FPVEKIDQLIRGIEDKGISIVDTLVEKKDYM 68

Query: 84  EDEEGSEDS------------LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           E     + +             ++  +  N  +     K +     D+P++MYLRE+G I
Sbjct: 69  ESNSTKKSAKIPEIEEEEFNEEEIDETEVNELLHTDLIKLAEIMDVDEPIKMYLREIGQI 128

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+ E EIA+A+++          L ES L    + I +   N G  +L  I       
Sbjct: 129 PLLTYEEEIALAQKVLENDEEAKQKLIESNLRL-VVSIAKKHTNRGLKMLDLI------- 180

Query: 192 GPESKGGFFHGTEGHSYQK 210
             E   G     E   Y+K
Sbjct: 181 -QEGNMGLMKAVEKFEYEK 198


>gi|289178873|gb|ADC86119.1| HrdB [Bifidobacterium animalis subsp. lactis BB-12]
          Length = 522

 Score =  286 bits (733), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 284 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 343

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 344 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 403

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PR
Sbjct: 404 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFRQVLETLSPR 463

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 464 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 521



 Score = 39.3 bits (90), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 30/42 (71%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 211 KRRVVTTGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 252


>gi|237736224|ref|ZP_04566705.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
 gi|229421777|gb|EEO36824.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
          Length = 351

 Score =  286 bits (733), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 137/236 (58%), Positives = 181/236 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++EANLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW
Sbjct: 114 ASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWW 173

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + AR    +  ++ TPE +A++L M VE V
Sbjct: 174 IRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKV 233

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + + ++ ++PISLETP+G E+ S LGDF+ED   ++P +   ++ LRE    VL SL+ R
Sbjct: 234 KAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSR 293

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE+VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 294 EEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 349



 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S D   D+P++MYLRE+G I LLS + E+  AKR   G       L E+ L    + I +
Sbjct: 73  SGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRL-VVSIAK 131

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              N G  LL  I   E  IG       F  T+G+ +
Sbjct: 132 KHTNRGLKLLDLI--QEGNIGLMKAVEKFEYTKGYKF 166


>gi|23295779|gb|AAN12882.1| principal sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis]
          Length = 508

 Score =  286 bits (733), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 270 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 329

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 330 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 389

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PR
Sbjct: 390 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFRQVLETLSPR 449

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 450 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 507



 Score = 39.3 bits (90), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 43/92 (46%), Gaps = 30/92 (32%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           V S+  ED  A+L+N G+N                               KR+     +T
Sbjct: 177 VVSDNDEDDEALLANPGVN------------------------------PKRRVVTTGAT 206

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 207 ADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 238


>gi|325971191|ref|YP_004247382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
 gi|324026429|gb|ADY13188.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
          Length = 685

 Score =  286 bits (733), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 137/247 (55%), Positives = 182/247 (73%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G+     AK  ++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF++  G
Sbjct: 439 IKYGQKMMKDAKDRLIRANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKG 498

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KVVR +R +   + REPT EE+A
Sbjct: 499 FKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVVRESRMLMQSLGREPTDEEVA 558

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +KL      V+ V  + +EPISLETP+G+E+ S L DFIEDK   +P      + L+E  
Sbjct: 559 EKLGWTESKVKAVKNVAREPISLETPVGEEEDSLLSDFIEDKEVENPATQTAYSLLQEQL 618

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VLA+L  RE+ VL+MRFG+      TLEEVG  F +TRERIRQIEAKA+R+L+HP RS
Sbjct: 619 KDVLATLPAREQEVLKMRFGLEDGYSLTLEEVGLYFELTRERIRQIEAKALRRLRHPKRS 678

Query: 674 KKLRSFL 680
           +KL+ F+
Sbjct: 679 RKLKDFI 685



 Score = 45.4 bits (106), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 34/50 (68%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           D +D S DDP+R+YLRE+G   LL+ + E+ ++K++E G  ++   + ES
Sbjct: 193 DKSDSSGDDPIRLYLREIGKENLLTADQEVELSKKMEDGALIIKEVIQES 242


>gi|315226631|ref|ZP_07868419.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
 gi|315120763|gb|EFT83895.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
          Length = 690

 Score =  286 bits (732), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 451 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 510

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 511 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 570

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PR
Sbjct: 571 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFKQVLETLSPR 630

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPSRS+ L+ FLD
Sbjct: 631 EAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHPSRSQTLQDFLD 688



 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCESPLTFQALIIWRDE 173
           +T DPV+ YL+++G + LL+ + E+ +++RIEAG     ++ +     +TFQ     +  
Sbjct: 385 ATSDPVKDYLKQIGRVNLLNAQQEVDLSERIEAGLYAQHLLDTTPADQMTFQRKRELKWA 444

Query: 174 LNDG 177
            NDG
Sbjct: 445 ANDG 448


>gi|291522137|emb|CBK80430.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 365

 Score =  286 bits (731), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 179/238 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+M EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EK+D+  GYKFSTYA WW
Sbjct: 127 AAKKMAEANLRLVVSIAKRYVGRGMQFLDLIQEGNVGLIKAIEKYDYTKGYKFSTYATWW 186

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + ++K+ +  R ++ ++ REP+ EEIA+ + M V  V
Sbjct: 187 IRQAITRSIADQARTIRIPVHMVETMNKLTKVQRSLTQELGREPSVEEIAENVHMDVNRV 246

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LK+ +E +SLETP+G E+ SHL DFIED +   P D A    L++    VL  L  R
Sbjct: 247 REILKLVQETVSLETPVGSEEESHLADFIEDDHTPLPSDEAAFGQLKDDIRSVLDKLNER 306

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++VLRMRFG+    +HTLEEVG++  VTRERIRQIEAKA+RKL+   +S  L  +L+
Sbjct: 307 EQKVLRMRFGLDDGKEHTLEEVGQELHVTRERIRQIEAKALRKLRQSGKSAGLEGYLN 364



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 39/138 (28%), Positives = 68/138 (49%), Gaps = 15/138 (10%)

Query: 29  DSWKKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE- 86
           D  K+++  A++R   +T + ++ F     ++ EQME     L + GI V   +D  D  
Sbjct: 10  DKLKELVPFAKEREQELTSDMISDFFGHMPLTEEQMEKIYDYLESNGIFVDRSNDEPDRR 69

Query: 87  --EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             + +E+ +D    +    +            TDDPVRMYL+E+G+I LL+ E E+ +AK
Sbjct: 70  MLDEAEEEIDPNDISVPEGI-----------RTDDPVRMYLKEIGNIPLLTPEEEVELAK 118

Query: 145 RIEAGRAMMMASLCESPL 162
            ++ G       + E+ L
Sbjct: 119 EMKEGSKQAAKKMAEANL 136


>gi|159901184|ref|YP_001547431.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159894223|gb|ABX07303.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 375

 Score =  286 bits (731), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 132/243 (54%), Positives = 185/243 (76%), Gaps = 1/243 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+  A++ +++ANLRLV+S+AKKY  RG+ FLDLIQEGNIGLM+A EKFD+  G+KFSTY
Sbjct: 133 ESEAARQHLIQANLRLVVSIAKKYVGRGMSFLDLIQEGNIGLMRATEKFDYHKGFKFSTY 192

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSI+D S TIR+PVH+ + I++V RTA ++   ++REP+ EEI + L +P
Sbjct: 193 ATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALEREPSAEEIGEALGLP 252

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + VR+VL++ ++P+SLETP+G+E  S LGDFIED  +  PLD A +  LRE    VL  
Sbjct: 253 ADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATEHLLREQLDEVLCK 312

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS-RSKKLRS 678
           L  RE R++ +R+G+      TLEEVG++F +TRERIRQIEAK +RKL+HP+   +KLR+
Sbjct: 313 LDERERRIIELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKLRHPAFGGRKLRA 372

Query: 679 FLD 681
           +L+
Sbjct: 373 YLE 375



 Score = 46.2 bits (108), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 59/117 (50%), Gaps = 9/117 (7%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           ARQ  Y+T +++   LPP + ++   ++         I ++       EE    ++ L S
Sbjct: 4   ARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPIL-------EEPPTAAVHLRS 56

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-RAMM 153
              +    L++       S DDPVRMYLRE+G + LL+   E  +AK++E G RAM+
Sbjct: 57  RDVDDD-DLERSLIREGVSLDDPVRMYLREIGQVHLLTAHEETMLAKQLERGERAMI 112


>gi|238927759|ref|ZP_04659519.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
 gi|238884475|gb|EEQ48113.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
          Length = 382

 Score =  286 bits (731), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 141/251 (56%), Positives = 189/251 (75%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + R+ E     A+  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+
Sbjct: 131 VELARRMEAGDEAARHRLEEANLRLVVSIAKRYAGRGMMFLDLIQEGNLGLLKAVEKFDY 190

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K +R +R++  ++ R+PTPE
Sbjct: 191 SKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKYIRISRQLLQELGRDPTPE 250

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ + V  VR+++KI++EP+SLETPIG+E+ + L DFIED+ A  P D+A    L+
Sbjct: 251 EIAHRMGLSVARVREIMKISQEPVSLETPIGEEEDTRLSDFIEDEAAPDPADAASMLLLK 310

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  + VL +L PRE  VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 311 EQISEVLTTLAPREAEVLRLRFGLVDGRSRTLEEVGQNFGVTRERIRQIEAKALRKLRHP 370

Query: 671 SRSKKLRSFLD 681
            R +KL+   D
Sbjct: 371 VRLRKLQGNFD 381



 Score = 46.2 bits (108), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 35/113 (30%), Positives = 56/113 (49%), Gaps = 8/113 (7%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----A 96
           G +T  EL   L  + V+ + M++         I +VD  D+  +E   D  D+      
Sbjct: 31  GTLTCSELMEALVQEGVTPDAMDELYQHCMEENIEIVDDADVGADEELSDFTDIEDKDET 90

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            +  +    L   +  A    DDPVRMYL+E+G + LL+ E E+ +A+R+EAG
Sbjct: 91  DADVDVDTVLSVPEGVA---LDDPVRMYLKEIGRVPLLTAEEEVELARRMEAG 140


>gi|332980900|ref|YP_004462341.1| RNA polymerase sigma-70 subunit RpoD [Mahella australiensis 50-1
           BON]
 gi|332698578|gb|AEE95519.1| RNA polymerase, sigma 70 subunit, RpoD [Mahella australiensis 50-1
           BON]
          Length = 356

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 194/238 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 119 AKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWW 178

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REP PEE+A+++ + V+ V
Sbjct: 179 IRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLMQELGREPAPEEVAEEMGISVDKV 238

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++KI +EP+SLETPIG+E+ SHLGDFI D +A +P ++A    L+E    VL +LTPR
Sbjct: 239 RDIMKIAQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFTLLKEQLMDVLDTLTPR 298

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 299 EEKVLRLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 356



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 68/131 (51%), Gaps = 14/131 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I+  + +G +T +E+   L   ++  +Q++     L  +GI+V++ + +E E+   +
Sbjct: 12  KQLIETGKSKGVLTYKEIMDMLEDVDIDPDQIDKLYDTLETLGIDVIE-EPIEHEDNVVE 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             DL +                  + DDPVRMYL+E+G I LLS + EI +AKRIE G  
Sbjct: 71  E-DLEAGLPEGV------------NIDDPVRMYLKEIGKIPLLSSDEEIELAKRIEQGDE 117

Query: 152 MMMASLCESPL 162
                L E+ L
Sbjct: 118 EAKKRLAEANL 128


>gi|257470878|ref|ZP_05634968.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|317065080|ref|ZP_07929565.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690756|gb|EFS27591.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 418

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 136/236 (57%), Positives = 180/236 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++EANLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW
Sbjct: 181 ASKQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYSKGYKFSTYATWW 240

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + AR    +  ++ TPE + ++L M V+ V
Sbjct: 241 IRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLGERLGMEVDKV 300

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + + ++ ++PISLETP+G E+ S LGDF+ED   ++P +   ++ LRE    VL +L+ R
Sbjct: 301 KAIQEMNQDPISLETPVGSEEDSELGDFVEDHKMLNPYELTNRSLLREQLNGVLNTLSSR 360

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EERVLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 361 EERVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 416



 Score = 45.4 bits (106), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S D   D+P++MYLRE+G I LLS + E+  AKR   G       L E+ L    + I +
Sbjct: 140 SGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDDWASKQLIEANLRL-VVSIAK 198

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              N G  LL  I   E  IG       F  ++G+ +
Sbjct: 199 KHTNRGLKLLDLI--QEGNIGLMKAVEKFEYSKGYKF 233


>gi|157164653|ref|YP_001467098.1| RNA polymerase sigma factor RpoD [Campylobacter concisus 13826]
 gi|112799942|gb|EAT97286.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter concisus 13826]
          Length = 617

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 132/259 (50%), Positives = 195/259 (75%), Gaps = 1/259 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +  + I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA
Sbjct: 359 ARLKEILEQIKRGKKISDEAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKA 418

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  
Sbjct: 419 VDKFEYRKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKINRKYLQEEG 478

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP    IAK++ + V+ V++V+KITKEPISLE PI +E+    GDF+EDK ++SP+D  
Sbjct: 479 KEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPIANEEDGKFGDFVEDKTSLSPIDQI 538

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++++LRE    VL+ L  RE+ V+ MRFG+  + +D TLEE+GK   VTRER+RQIE+ A
Sbjct: 539 LKSDLREQIDDVLSQLNEREKAVISMRFGLLEDESDRTLEEIGKALNVTRERVRQIESSA 598

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           I+KLKHP   +KL+++++G
Sbjct: 599 IKKLKHPKVGRKLKNYIEG 617


>gi|158316157|ref|YP_001508665.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158111562|gb|ABW13759.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 400

 Score =  285 bits (730), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 130/243 (53%), Positives = 185/243 (76%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+  LDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 157 EQDGQIAKRKLVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTKGYKFS 216

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QA+TR+IADQ  TIRIPVHM + I+KV R  R++   + REP+PEEIA ++ 
Sbjct: 217 TYATWWIRQAVTRAIADQGRTIRIPVHMVETINKVTRIQRQLLQDLGREPSPEEIATQVD 276

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +    V ++LK+ + P++LETPIG+E  S LGDFIED +A+ P ++A    L+E    VL
Sbjct: 277 LAPHRVEEILKVGQTPVALETPIGEEQDSQLGDFIEDNDAIVPFEAASFVLLQEQIDSVL 336

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE++V+++RFG+      TLE+VG++F VTRERIRQIE++ + KL HP+RS++LR
Sbjct: 337 HTLSEREKKVIQLRFGLTDGQPRTLEQVGREFGVTRERIRQIESRTLAKLSHPARSQRLR 396

Query: 678 SFL 680
            +L
Sbjct: 397 DYL 399



 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 45/145 (31%), Positives = 71/145 (48%), Gaps = 30/145 (20%)

Query: 15  HED---SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           HED   +D S   + +++  + +I   ++ G+VT +++ A L   E+  E  +  + +L+
Sbjct: 8   HEDAPPTDLSAPDEAAEEKIRSLIARGKENGFVTPDDIAAALLAAELPPESSDVVLRLLA 67

Query: 72  NMGINVVD--GDDLED-----EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
             GI V+D  G D  D      EG E +L    S                    DPVRMY
Sbjct: 68  EDGIEVLDEVGGDASDMPSRRREGEELALTTPPS--------------------DPVRMY 107

Query: 125 LREMGSIELLSREGEIAIAKRIEAG 149
           L+ +G + LL+ E E+ +AKRIEAG
Sbjct: 108 LKAIGRVRLLTAEEEVDLAKRIEAG 132


>gi|253581343|ref|ZP_04858569.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836707|gb|EES65241.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 414

 Score =  285 bits (729), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 136/236 (57%), Positives = 180/236 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++EANLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW
Sbjct: 177 ASKQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYSKGYKFSTYATWW 236

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + AR    +  ++ TPE + ++L M V+ V
Sbjct: 237 IRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLGERLGMEVDKV 296

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + + ++ ++PISLETP+G E+ S LGDF+ED   ++P +   ++ LRE    VL +L+ R
Sbjct: 297 KAIQEMNQDPISLETPVGSEEDSELGDFVEDHKMLNPYELTNRSLLREQLNGVLNTLSSR 356

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EERVLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 357 EERVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 412



 Score = 45.8 bits (107), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S D   D+P++MYLRE+G I LLS + E+  AKR   G       L E+ L    + I +
Sbjct: 136 SGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASKQLIEANLRL-VVSIAK 194

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              N G  LL  I   E  IG       F  ++G+ +
Sbjct: 195 KHTNRGLKLLDLI--QEGNIGLMKAVEKFEYSKGYKF 229


>gi|270283843|ref|ZP_05965086.2| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
 gi|270277549|gb|EFA23403.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
          Length = 485

 Score =  285 bits (729), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 247 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 306

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 307 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 366

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++     GD IED +A++P D+   + L+E   +VL +L+PR
Sbjct: 367 QEVQKYGREPISLHTPLGEDGDPEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPR 426

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 427 EAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 484



 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 30/42 (71%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG
Sbjct: 174 KRRVVTTGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAG 215


>gi|269837239|ref|YP_003319467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786502|gb|ACZ38645.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 390

 Score =  285 bits (728), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 180/238 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +++ANLRLV+SVAKKY  RGL FLDLIQEGNIGLMKA +KFD+  G+KFSTYA WW
Sbjct: 153 ARAHLIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATDKFDYKRGFKFSTYATWW 212

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+I+DQS TIR+PVH+ + I++V +T++R+    +REPT EE+A+ + +P E V
Sbjct: 213 IRQAITRAISDQSRTIRLPVHVGETINRVKKTSQRLQQIFEREPTFEEVARAMDIPEEKV 272

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL  ++ P+SLE P+G E  + LGDFIED     PL+ A Q  L+   +  L+ LT R
Sbjct: 273 RQVLDASRHPVSLEAPVGQEGDAFLGDFIEDDTMPPPLELASQELLKHQISDALSKLTER 332

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E R++ +RFG+      TLEEVG++F +TRERIRQIEAKA+RKL+HP+ S +LR +LD
Sbjct: 333 ERRIIILRFGLEDGQFRTLEEVGREFGITRERIRQIEAKALRKLRHPTYSHRLRGYLD 390



 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 67/120 (55%), Gaps = 4/120 (3%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   + RGY+  +E+ A  P  E + E +++  + L   GI V+D +   +  G+  SL
Sbjct: 5   LIARGKDRGYLLSDEIIAAFPNAEENVESLDEFYSTLVEQGIEVLDQEPT-NGNGTTASL 63

Query: 94  D--LASSASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               AS  + +S  +  R+D AD  S  D VR+YL+E+G   LL+ E E+ +AKR+E G+
Sbjct: 64  SERTASQPAPASPTIDTRQDVADAVSVSDSVRLYLQEIGETSLLTMEEEVWLAKRMERGK 123


>gi|34558185|ref|NP_908000.1| RNA polymerase sigma factor RpoD [Wolinella succinogenes DSM 1740]
 gi|34483904|emb|CAE10900.1| RNA POLYMERASE SIGMA FACTOR [Wolinella succinogenes]
          Length = 620

 Score =  285 bits (728), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 161/383 (42%), Positives = 248/383 (64%), Gaps = 28/383 (7%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG---ELLRLAQSYGIKR 367
           + K + LKE+L+ L G  S       L+ E +  +   + ++EG   EL RL     +  
Sbjct: 253 AYKKQTLKERLLDL-GPTS------KLINELVKAMENTLRNDEGFDRELKRLEYKLPLFN 305

Query: 368 DVFLERHQG-----RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN--EIKSISVET 420
           +  LE HQ       E+  + ++ A   PE       A  V + ++I+   + K  S E+
Sbjct: 306 ETLLENHQKILENITEMSKNDIASA--VPE-------ATMVSTYMEIKKLFQTKQASEES 356

Query: 421 -GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             +   + + I+  +++G+  A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNI
Sbjct: 357 FDLEPEKLKEILEQIKRGKDIADKAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNI 416

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+ 
Sbjct: 417 GLMKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKY 476

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  +EP  E I++++ +PV+ V+ V+KITKEPISLE PIG ++    GDF+EDK++V 
Sbjct: 477 LQEEGKEPDVETISEEVGLPVDKVKNVIKITKEPISLEAPIGSDEDGKFGDFVEDKSSVG 536

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQ 658
           P+D  ++ +L+     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQ
Sbjct: 537 PMDHILKEDLKTQIDEVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQ 596

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IE+ AI+KLKHP   +KL+++++
Sbjct: 597 IESSAIKKLKHPKVGRKLKNYIE 619



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 45/70 (64%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           F+++R+      +D PVRMYLREMG I LL+++ EI ++K IE G  +++ ++C  P   
Sbjct: 90  FMKERELLEWSRSDSPVRMYLREMGQIPLLTKDEEIELSKNIELGENIILDAICSVPYLI 149

Query: 165 QALIIWRDEL 174
             ++ +++ L
Sbjct: 150 DFILDYKEAL 159


>gi|218515736|ref|ZP_03512576.1| RNA polymerase sigma factor RpoD [Rhizobium etli 8C-3]
          Length = 191

 Score =  285 bits (728), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 141/192 (73%), Positives = 161/192 (83%), Gaps = 5/192 (2%)

Query: 493 GYKFSTYAMWWVK---QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           GYK   YA WW+      + R         R  VHM + I+K+VRT+R+M ++I REPTP
Sbjct: 1   GYKVLDYATWWMPSGDHPLDRRTRPARSAFR--VHMIETINKIVRTSRQMLHEIGREPTP 58

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANL
Sbjct: 59  EELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANL 118

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKH
Sbjct: 119 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 178

Query: 670 PSRSKKLRSFLD 681
           PSRS+KLRSFLD
Sbjct: 179 PSRSRKLRSFLD 190


>gi|242310656|ref|ZP_04809811.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
 gi|239523054|gb|EEQ62920.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
          Length = 615

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 132/256 (51%), Positives = 195/256 (76%), Gaps = 1/256 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I+  +++G+  A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +
Sbjct: 359 LKQILEQIKRGKDIADRAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVD 418

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +E
Sbjct: 419 KFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKYLQEEGKE 478

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P  E+IA+++ +PV+ V+ V+KITKEPISLE PIG+ +    GDF+EDK ++ P+DS ++
Sbjct: 479 PDIEKIAEEVGLPVDKVKNVIKITKEPISLEAPIGNGEDGKFGDFVEDKASLGPMDSILK 538

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            +L+     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+
Sbjct: 539 EDLKAQIDDVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIK 598

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHP   +KL+++++
Sbjct: 599 KLKHPKVGRKLKNYIE 614



 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 45/70 (64%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           F+++R+      +D PVRMYLREMG I LL+RE E+ ++K IE G  +++ ++C  P   
Sbjct: 89  FMKERELLEWSRSDSPVRMYLREMGQIPLLTREDEVELSKNIELGENIILDAICSVPYLI 148

Query: 165 QALIIWRDEL 174
             ++ +++ L
Sbjct: 149 DFILDYKEAL 158


>gi|294786990|ref|ZP_06752244.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
 gi|294485823|gb|EFG33457.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
          Length = 403

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 184/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW
Sbjct: 164 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 223

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V
Sbjct: 224 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 283

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PR
Sbjct: 284 QEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFKQVLETLSPR 343

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V++MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPSRS+ L+ FLD
Sbjct: 344 EAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHPSRSQTLQDFLD 401



 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 37/60 (61%), Gaps = 2/60 (3%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCESPLTFQ 165
           KR+     +T DPV+ YL+++G + LL+ + E+ +++RIEAG     ++ +     +TFQ
Sbjct: 90  KRRILTTGATSDPVKDYLKQIGRVNLLNAQQEVDLSERIEAGLYAQHLLDTTPADQMTFQ 149


>gi|91203809|emb|CAJ71462.1| strongly similar to transcription initiation factor sigma RpoD
           [Candidatus Kuenenia stuttgartiensis]
          Length = 551

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 135/239 (56%), Positives = 182/239 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++  ANLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  GYKFSTYA WW
Sbjct: 308 AKRKLSGANLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWW 367

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + + K+   ++++     REPT EEIA+++ + V   
Sbjct: 368 IRQAITRSIADQARTIRIPVHMIETMSKIRNISKKLLQDKGREPTIEEIAREVKISVPEA 427

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VLKI++  ISL+ P+G+ + S  GDFIED+ A SP+ +A Q  L++    VL +LT R
Sbjct: 428 RRVLKISRHQISLDRPVGESEDSSFGDFIEDEKAESPVAAATQEMLKDKIESVLETLTYR 487

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  ++++R+GIG    +TLEEVGK F VTRER+RQIEAKA+RKL+HP RS+KL  FLDG
Sbjct: 488 EREIIKLRYGIGDGYTYTLEEVGKIFKVTRERVRQIEAKAVRKLQHPIRSRKLEGFLDG 546



 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 82/147 (55%), Gaps = 4/147 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPD-EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K + +  +++GY+T EELN  LP D E+   +++D + ML  +GI+++D  D+E  E  +
Sbjct: 9   KLLTQKGKEKGYLTYEELNDMLPDDAEIPPGKIDDILMMLDELGIDLIDEADIEGREVVD 68

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                 +   + S F      +     DDPVRMYL +MG I LL+R+ EI +AK+IE  R
Sbjct: 69  SE---EAEHYSESEFGFGEVSTVTEKIDDPVRMYLTQMGEIPLLTRDEEIMLAKKIEITR 125

Query: 151 AMMMASLCESPLTFQALIIWRDELNDG 177
              +  +  S L+ Q  +   +++N+G
Sbjct: 126 RGFLKKVLHSDLSLQTCLKIVEDVNNG 152


>gi|226327187|ref|ZP_03802705.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
 gi|225204405|gb|EEG86759.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
          Length = 201

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 137/200 (68%), Positives = 165/200 (82%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 60

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REP+PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PL
Sbjct: 61  EMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL 120

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEA
Sbjct: 121 DSATSESLRSATHEVLAGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 180

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS+ LRSFLD
Sbjct: 181 KALRKLRHPSRSEVLRSFLD 200


>gi|313893234|ref|ZP_07826811.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313442587|gb|EFR61002.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 386

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 133/232 (57%), Positives = 179/232 (77%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V+ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAI
Sbjct: 155 VDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAI 214

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++R +R++     REP PEEIA+ + + VE VR++ K
Sbjct: 215 TRAIADQARTIRIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERVREIQK 274

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I +EP+SLETPIG+E+ SHLGDFIED++A++P D+A    L+E    V   LT RE++VL
Sbjct: 275 IAQEPVSLETPIGEEEDSHLGDFIEDQDAIAPDDAASYILLQEQIEDVFTCLTDREQQVL 334

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 335 ILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 386



 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/125 (34%), Positives = 72/125 (57%), Gaps = 8/125 (6%)

Query: 32  KKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           +++++  R+ G +T  E+ +A     E+++EQ++D    L  + I VV   D++ E+  E
Sbjct: 15  EQLLEKGRKTGVLTQSEISDALHEQAEITAEQLDDIYTTLGKLNIEVVA--DIDAEDVDE 72

Query: 91  DSL----DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + +    D     S  S+ +    DS   + DDPVRMYL+E+G + LLS + EI +AK+I
Sbjct: 73  NPIVPEEDAEEVVSEKSISIDLSVDSG-VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQI 131

Query: 147 EAGRA 151
           EAG A
Sbjct: 132 EAGAA 136


>gi|157364824|ref|YP_001471591.1| RpoD family RNA polymerase sigma factor [Thermotoga lettingae TMO]
 gi|157315428|gb|ABV34527.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga lettingae
           TMO]
          Length = 400

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 184/248 (74%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK++++E+NLRLV+S+AK+Y  RGL FLDLIQEGNIGL+KA EKFDW  
Sbjct: 146 LARRAQIGNKRAKEKLIESNLRLVVSIAKRYIGRGLPFLDLIQEGNIGLLKAVEKFDWKK 205

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R    K   +P+ EE+
Sbjct: 206 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLNRITREYYQKHGEQPSLEEL 265

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  PV+ V ++L+ +KE +SLE P+G+++ S +GDF+ D+N  SP   A++  +RE 
Sbjct: 266 AKLMDKPVDKVEEILQASKETVSLEAPVGEDEDSTVGDFVADENITSPKKEAMRMLMREE 325

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L PRE  VL+MR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 326 LEKVLKTLNPREAMVLKMRYGLLDGKAKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 385

Query: 673 SKKLRSFL 680
           SK L+S +
Sbjct: 386 SKYLKSLI 393



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 65/133 (48%), Gaps = 8/133 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + +IK  +++G++T ++++   PPD     +  +E     L    IN+      +D E  
Sbjct: 40  RNLIKTGKKKGFITYDDIDKAFPPDYDGFDTSLIEHIYEELEKNKINI------QDTEPI 93

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E+ +D    +   S+  +  +   + +  DP++MYLRE+G I LL+   E  +A+R + G
Sbjct: 94  EEIIDEDVESEIPSLLEEGPEIYDNVALKDPIKMYLREIGKIPLLTPSQERELARRAQIG 153

Query: 150 RAMMMASLCESPL 162
                  L ES L
Sbjct: 154 NKRAKEKLIESNL 166


>gi|224438138|ref|ZP_03659073.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313144578|ref|ZP_07806771.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313129609|gb|EFR47226.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
          Length = 623

 Score =  284 bits (726), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 129/257 (50%), Positives = 194/257 (75%), Gaps = 1/257 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I+  +++G+  +  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA 
Sbjct: 366 KLKEILEQIKRGKSISDKAKAKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAV 425

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  G+KFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +
Sbjct: 426 DKFEYKKGFKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRIHKIMRKHIQETGK 485

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  E IAK++ +P++ V+ V+KITKEP+SL+ PIG +D    GDF+EDK++V P+D  +
Sbjct: 486 EPDIEYIAKEVGLPIDKVKNVIKITKEPVSLDAPIGSDDDGKFGDFVEDKSSVGPMDYIL 545

Query: 606 QANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ AI
Sbjct: 546 KEDLKVQIDDVLEQLNDREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAI 605

Query: 665 RKLKHPSRSKKLRSFLD 681
           +KLKHP   +KL+++++
Sbjct: 606 KKLKHPKVGRKLKNYIE 622



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E E++++K IE G   ++ ++C  P     +  ++D L
Sbjct: 111 SDSPVRMYLREMGQIPLLTKEEEVSLSKNIELGENTILDAICSVPYLIDFIYDYKDAL 168


>gi|221632805|ref|YP_002522027.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
 gi|221156346|gb|ACM05473.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
          Length = 369

 Score =  284 bits (726), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 140/272 (51%), Positives = 194/272 (71%), Gaps = 2/272 (0%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R +I  + +E G   SE   +  +  K + E   A+  +++ANLRLV+SVAKKY  RGL 
Sbjct: 100 RGKIAKVRLERGDYKSEDERLALVADKEDGER--ARAHLIQANLRLVVSVAKKYVGRGLS 157

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA EKFD+  GYKFSTYA WW++QAITR+I+DQS TIR+PVH+ + I
Sbjct: 158 FLDLIQEGNIGLMKATEKFDYKRGYKFSTYATWWIRQAITRAISDQSRTIRLPVHVGETI 217

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +++ + + R+   ++REPT  E+A+ L MP E +R++L+  + P+SLE PIG +  + LG
Sbjct: 218 NRIKKISHRLQQILEREPTQLEVARALDMPEEKIRQILEAARLPVSLEAPIGQDGDAFLG 277

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+   +PL+ A Q  LR+     L+ LT RE R++ +R+G+      TLEEVG++F
Sbjct: 278 DFIEDETQPAPLEIASQQLLRQQLEEALSRLTERERRIIILRYGLEDGQFRTLEEVGREF 337

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +TRERIRQIEAKA+RKL+HPS S+ LR +LD
Sbjct: 338 GITRERIRQIEAKALRKLRHPSCSRFLRGYLD 369



 Score = 37.7 bits (86), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 29/43 (67%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +R D    ST D VR+YL+E+G   LL+ + E+ +A+RIE G+
Sbjct: 60  ERFDDDGLSTSDTVRLYLQEIGETALLTPQEEVWLAQRIERGK 102


>gi|227495524|ref|ZP_03925840.1| sigma factor [Actinomyces coleocanis DSM 15436]
 gi|226831071|gb|EEH63454.1| sigma factor [Actinomyces coleocanis DSM 15436]
          Length = 505

 Score =  284 bits (726), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 180/242 (74%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  ++K  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 264 DGQLSKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 323

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M 
Sbjct: 324 ATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMT 383

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E   +VL +
Sbjct: 384 PEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPTDAVSFTLLQEQLHKVLDT 443

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+G     TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 444 LSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 503

Query: 680 LD 681
           LD
Sbjct: 504 LD 505



 Score = 39.3 bits (90), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +A+RIEAG
Sbjct: 203 ATTDPVKDYLKQIGKVSLLTAADEVDLARRIEAG 236


>gi|238018971|ref|ZP_04599397.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
 gi|237864455|gb|EEP65745.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
          Length = 387

 Score =  283 bits (725), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 133/232 (57%), Positives = 179/232 (77%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V+ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAI
Sbjct: 156 VDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAI 215

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++R +R++     REP PEEIA+ + + VE VR++ K
Sbjct: 216 TRAIADQARTIRIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERVREIQK 275

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I +EP+SLETPIG+E+ SHLGDFIED++A++P D+A    L+E    V   LT RE++VL
Sbjct: 276 IAQEPVSLETPIGEEEDSHLGDFIEDQDAIAPDDAASYILLQEQIEDVFTCLTDREQQVL 335

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 336 ILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 387



 Score = 56.6 bits (135), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/124 (32%), Positives = 71/124 (57%), Gaps = 5/124 (4%)

Query: 32  KKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGDDLEDEE 87
           +++++  R+ G +T  E+ +A     ++++EQ++D       + I VV   DG+D +   
Sbjct: 15  EQLLEKGRKTGVLTQSEISDALHEQTDLTAEQLDDIYTTFGKLNIEVVADIDGEDADANP 74

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  D   ++S  ++ +    DS   + DDPVRMYL+E+G + LLS + EI +AK+IE
Sbjct: 75  IEPEEEDEEDTSSEKNISIDLSVDSG-VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIE 133

Query: 148 AGRA 151
           AG A
Sbjct: 134 AGAA 137


>gi|310777992|ref|YP_003966325.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747315|gb|ADO81977.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 408

 Score =  283 bits (725), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 136/236 (57%), Positives = 179/236 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++VEANLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW
Sbjct: 171 ATQQLVEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWW 230

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ TPE +A++L M  E +
Sbjct: 231 IRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDATPEVLAERLGMESEKI 290

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L++ ++PISLETP+G E+ S LGDF+ED   +SP +   +  L+E    VL SL+ R
Sbjct: 291 KAILEMNQDPISLETPVGSEEDSELGDFVEDNKMLSPYEQTNRNLLKEQLDDVLQSLSER 350

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE+VLR R+G+      TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 351 EEKVLRFRYGLDDGCPRTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 406



 Score = 41.6 bits (96), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 31/97 (31%), Positives = 45/97 (46%), Gaps = 3/97 (3%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S+    D+P++MYLRE+G + LL+ + EI  AK    G       L E+ L    + I +
Sbjct: 130 SSGVDVDEPIKMYLREIGQVPLLTHKQEIEHAKNSAEGDEWATQQLVEANLRL-VVSIAK 188

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              N G  LL  I   E  IG       F  T+G+ +
Sbjct: 189 KHTNRGLKLLDLI--QEGNIGLMKAVEKFEYTKGYKF 223


>gi|294102609|ref|YP_003554467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
 gi|293617589|gb|ADE57743.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
          Length = 377

 Score =  283 bits (725), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 141/251 (56%), Positives = 192/251 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     AK+++++ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EKFD+
Sbjct: 127 VELAKRVEAGEEEAKQQIIDANLRLVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEKFDY 186

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIR+PVHM + I+K+VR +R++  K+ REPT E
Sbjct: 187 RKGFKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKMVRVSRQLVQKLGREPTDE 246

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ +    V ++ +I + P+SLETPIG+E+ S LGDFIED++  SP ++A    L 
Sbjct: 247 EIAAEMEIEPSKVEEIRRIAQLPVSLETPIGEEEDSQLGDFIEDRDLPSPEEAAASHLLH 306

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +L +L+ RE  VL+ RFG+     +TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 307 EQIDEMLEALSEREREVLQYRFGLEDGRSYTLEEVGKRFGVTRERIRQIEAKALRKLRHP 366

Query: 671 SRSKKLRSFLD 681
           SRSKKLR FLD
Sbjct: 367 SRSKKLRDFLD 377



 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/116 (34%), Positives = 65/116 (56%), Gaps = 6/116 (5%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I+  + +G+VT +++  F+P +  S++ +ED V+ L  MGI V +      EEG E + 
Sbjct: 27  LIQEGQTKGFVTQKDIEKFIPVEFWSADVLEDVVSNLMEMGIEVTE------EEGKERAQ 80

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            +A   + +     +     D    DPVRMYLRE+G + LL    E+ +AKR+EAG
Sbjct: 81  HIAEEEALAQPADGEIGKLDDIPLTDPVRMYLREIGKVPLLEPAQEVELAKRVEAG 136


>gi|254457867|ref|ZP_05071294.1| sigma 28 [Campylobacterales bacterium GD 1]
 gi|207085260|gb|EDZ62545.1| sigma 28 [Campylobacterales bacterium GD 1]
          Length = 623

 Score =  283 bits (725), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 134/253 (52%), Positives = 194/253 (76%), Gaps = 1/253 (0%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+  +++G+  + I+K +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF+
Sbjct: 370 ILEQIKRGKNISEISKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFE 429

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  
Sbjct: 430 YQKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKHLQEHGKEPDV 489

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E IA ++ + VE V+ V+KITKEPISLE PIG+ED    GDFIEDK+++SP D+ ++ +L
Sbjct: 490 EVIALEVGLSVEKVKNVIKITKEPISLEAPIGNEDDGRFGDFIEDKSSISPSDAILKDDL 549

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R     VL  L  RE+ V+++RFGI  + +D TLEE+G++  VTRER+RQIE+ AI+KLK
Sbjct: 550 RVQIEGVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGRELNVTRERVRQIESSAIKKLK 609

Query: 669 HPSRSKKLRSFLD 681
           HP   +KL+S+++
Sbjct: 610 HPKVGRKLKSYIE 622



 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 42/58 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E EI I+K+IE G ++++ ++C  P   + ++ +R+ L
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKIEGGESIIIDAICSVPYLIRFILDYREPL 160


>gi|149175263|ref|ZP_01853885.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148845872|gb|EDL60213.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 561

 Score =  283 bits (725), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 151/368 (41%), Positives = 232/368 (63%), Gaps = 41/368 (11%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + K+  L+  LSL   R+ + +++L  IS+R+   E ++                    R
Sbjct: 209 RRKMATLIEELSLRTQRLQIGMKRLEQISQRMTELEDQI--------------------R 248

Query: 378 ELDPHWVSYAKD---FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           ++    +  +KD     E E ++ VA  +++   +R  IK+                  V
Sbjct: 249 DMSDMRIKNSKDDRANLERELQDLVAMTMETPETLRERIKA------------------V 290

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++   +   A +E+   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  GY
Sbjct: 291 KQRYLDYETAMRELSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGY 350

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQ+ TIRIPVHM + + K+ + ++++  +  REPT EE A+
Sbjct: 351 KFSTYATWWIRQAITRAIADQARTIRIPVHMIETMSKLRKVSKQLLQENGREPTLEETAE 410

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
              + +E  R+VLKI++ PISL+ P+G+ + S+ GDFIED ++ SP+++A Q  L++   
Sbjct: 411 VAGISLEETRRVLKISRHPISLDRPVGESEDSYFGDFIEDSDSDSPVNTASQEMLKDKID 470

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL +LT RE  ++++RFG+G    +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RSK
Sbjct: 471 HVLKTLTYREREIIKLRFGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSK 530

Query: 675 KLRSFLDG 682
           +L+ F++G
Sbjct: 531 QLQGFIEG 538



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 72/133 (54%), Gaps = 12/133 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D    ++I+  +++GY+T ++++A+LP + ++ E++++ +     + I  ++ D + D+ 
Sbjct: 5   DARLNELIENGKKQGYLTYDQVSAYLPDEALNPEKLDNLL-----LTIEEIELDIIPDQI 59

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    +     S +S       D   R  DDPVRMYL +MG I LL+R+ EI +AK+IE
Sbjct: 60  ITILQPEKPKGRSRTS-------DDLSRRIDDPVRMYLTQMGEIPLLTRDEEIRLAKKIE 112

Query: 148 AGRAMMMASLCES 160
             R      L  S
Sbjct: 113 ITRRRFRRELLSS 125


>gi|32266044|ref|NP_860076.1| RNA polymerase sigma factor RpoD [Helicobacter hepaticus ATCC
           51449]
 gi|32262093|gb|AAP77142.1| RNA polymerase sigma 70 factor [Helicobacter hepaticus ATCC 51449]
          Length = 623

 Score =  283 bits (724), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 165/417 (39%), Positives = 264/417 (63%), Gaps = 27/417 (6%)

Query: 279 KVMCALDEIAEVYRE-LRSLQDNAVNGQKDEKSSV-----KCKVLKEKLVKLVGSLSLNQ 332
           KVM +   + +  +E L+ L+   V G+ DE + +     K  +LK KL+ L  +  L  
Sbjct: 219 KVMESFKALDKAKKEWLKVLETPIVEGE-DELAHILLLSHKKHILKMKLLDLGPTSKL-- 275

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD--- 389
             I  LV+ + +  K     E EL RL     +  D+ +E HQ  ++  +  + ++D   
Sbjct: 276 --IGELVKAMENTLKSGDGFERELKRLEYKLPLFNDMLVENHQ--KILANITTMSRDEIA 331

Query: 390 --FPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS--EFRHIVSMVRKGECEASIAK 445
              PE    + V  E+  + + +      + E G ++   + + I+  +++G+  +  AK
Sbjct: 332 AMVPETTMVS-VYVELKKLFQTKE-----ASEGGFNLEPEKLKEILEQIKRGKSISDKAK 385

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++
Sbjct: 386 AKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGFKFSTYATWWIR 445

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  + IAK++ +P++ V+ 
Sbjct: 446 QAISRAIADQARTIRIPIHMIETINRIHKIMRKHVQETGKEPDIDFIAKEVGLPIDKVKN 505

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V+KITKEP+SL+ PIG +D    GDF+EDK++V P+D  ++ +L+     VL  L  RE+
Sbjct: 506 VIKITKEPVSLDAPIGSDDDGKFGDFVEDKSSVGPMDYILKEDLKVQIDEVLEQLNDREK 565

Query: 626 RVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++
Sbjct: 566 AVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIE 622



 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E EI+++K+IE G   ++ ++C  P     +  ++D L
Sbjct: 111 SDSPVRMYLREMGQISLLTKEEEISLSKKIELGENTILDAICSVPYLIDFIYDYKDAL 168


>gi|225018167|ref|ZP_03707359.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
 gi|224949164|gb|EEG30373.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
          Length = 372

 Score =  283 bits (724), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 146/251 (58%), Positives = 196/251 (78%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + +K       A+K + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+
Sbjct: 122 IDLAQKMSAGDPYARKRLSEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDY 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV + + ++ +K   E + E
Sbjct: 182 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVKKVSSQLLHKNGHEASAE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L MPV+ VR+++++++EP+SLETPIG+E+ SHL DFI D +A +P ++A    LR
Sbjct: 242 EIAEELDMPVDKVREIMRVSQEPVSLETPIGEEEDSHLSDFIPDDDAPAPAEAASHTLLR 301

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HP
Sbjct: 302 EQLGDVLGTLTEREEKVLRLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHP 361

Query: 671 SRSKKLRSFLD 681
           SRSKKL+ FLD
Sbjct: 362 SRSKKLKDFLD 372



 Score = 41.6 bits (96), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 31/47 (65%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + DDPV++YL+E+G + LL+ E EI +A+++ AG       L E+ L
Sbjct: 98  NIDDPVKVYLKEIGKVPLLTAEEEIDLAQKMSAGDPYARKRLSEANL 144


>gi|304389369|ref|ZP_07371334.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|304327487|gb|EFL94720.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
          Length = 564

 Score =  283 bits (724), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 135/256 (52%), Positives = 187/256 (73%), Gaps = 4/256 (1%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + R +  +V+ G+    +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL++A 
Sbjct: 313 QIRELHYVVQDGQ----MAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAV 368

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + R
Sbjct: 369 EKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGR 428

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+  
Sbjct: 429 EPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVS 488

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEAK + 
Sbjct: 489 FMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMS 548

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HP+RS+ LR +L+
Sbjct: 549 KLRHPARSQSLRDYLN 564



 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 10/74 (13%)

Query: 86  EEGSEDS-LDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLS 135
           E+ S+D+ L   + +S S+ +    KD AD          +T DPV+ YL+++G + LL+
Sbjct: 222 EDKSKDTKLGSKAKSSTSAEYTLSEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLN 281

Query: 136 REGEIAIAKRIEAG 149
            E E+ ++KRIEAG
Sbjct: 282 AEQEVDLSKRIEAG 295


>gi|255322395|ref|ZP_05363541.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
 gi|255300768|gb|EET80039.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
          Length = 627

 Score =  283 bits (724), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 130/257 (50%), Positives = 193/257 (75%), Gaps = 1/257 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +
Sbjct: 371 LKEILEQIKRGKKISDEAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVD 430

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +E
Sbjct: 431 KFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKINRKYLQEEGKE 490

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P    IA ++ +  + +++V+KITKEPISLE PIG+ED    GDF+ED++++SP+D  ++
Sbjct: 491 PDINVIAAEVGLSADKIKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRSSLSPMDHILK 550

Query: 607 ANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            +L+E    VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ AI+
Sbjct: 551 NDLKEQIDEVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIK 610

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHP   +KL+++++G
Sbjct: 611 KLKHPKVGRKLKNYIEG 627


>gi|296120487|ref|YP_003628265.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
 gi|296012827|gb|ADG66066.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
          Length = 550

 Score =  283 bits (724), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 130/239 (54%), Positives = 183/239 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  GYKFSTYA WW
Sbjct: 305 AMRDLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWW 364

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + + K+ + A+++  ++ REPT EE A+   + +E  
Sbjct: 365 IRQAITRAIADQARTIRIPVHMIETMSKLRKVAKKLLQEMGREPTLEETAEAAGVSLEET 424

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V+KI++ PISL+ P+G+ + S+ GDFIED N  SP+ +A Q  L++    VL +LT R
Sbjct: 425 RRVMKISRHPISLDRPVGESEDSYFGDFIEDDNTESPVMAATQEMLKDKIDNVLKTLTYR 484

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  ++++R+G+G    +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RSK+L+ FLDG
Sbjct: 485 EREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSKQLKGFLDG 543



 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 77/152 (50%), Gaps = 9/152 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D    ++I   +++G++T  ++N +LP + ++ E++++ +  +   G+ +V     +D+ 
Sbjct: 5   DQGLHELIVRGKKQGFLTYSQINDYLPDEAMNPEKLDELLGSIWEEGLKIVT----DDQV 60

Query: 88  GS--EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           G   E+     + A N    + + K    +  DDPVRMYL +MG I LL+RE EI++AK 
Sbjct: 61  GMIVEEKKKPRTRAKNGKEVVVEEKS---KKIDDPVRMYLTQMGEIPLLTREKEISLAKT 117

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           IE  R      L E     +       ++N G
Sbjct: 118 IEVTRNQFREELLECDYALKMAFDTLSKVNSG 149


>gi|298346920|ref|YP_003719607.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
 gi|298236981|gb|ADI68113.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
          Length = 563

 Score =  283 bits (723), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 135/256 (52%), Positives = 187/256 (73%), Gaps = 4/256 (1%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + R +  +V+ G+    +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL++A 
Sbjct: 312 QIRELHYVVQDGQ----MAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAV 367

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + R
Sbjct: 368 EKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGR 427

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+  
Sbjct: 428 EPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVS 487

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEAK + 
Sbjct: 488 FMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMS 547

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HP+RS+ LR +L+
Sbjct: 548 KLRHPARSQSLRDYLN 563



 Score = 42.7 bits (99), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 9/62 (14%)

Query: 97  SSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           + +S S+ +    KD AD          +T DPV+ YL+++G + LL+ E E+ ++KRIE
Sbjct: 233 AKSSTSAEYTLSEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIE 292

Query: 148 AG 149
           AG
Sbjct: 293 AG 294


>gi|315656627|ref|ZP_07909514.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|315492582|gb|EFU82186.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 564

 Score =  283 bits (723), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 135/256 (52%), Positives = 187/256 (73%), Gaps = 4/256 (1%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + R +  +V+ G+    +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL++A 
Sbjct: 313 QIRELHYVVQDGQ----MAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAV 368

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + R
Sbjct: 369 EKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGR 428

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+  
Sbjct: 429 EPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVS 488

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEAK + 
Sbjct: 489 FMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMS 548

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HP+RS+ LR +L+
Sbjct: 549 KLRHPARSQSLRDYLN 564



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 9/62 (14%)

Query: 97  SSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           + +S S+ +    KD AD          +T DPV+ YL+++G + LL+ E E+ ++KRIE
Sbjct: 234 AKSSTSAEYTLSEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIE 293

Query: 148 AG 149
           AG
Sbjct: 294 AG 295


>gi|157737257|ref|YP_001489940.1| RNA polymerase sigma factor RpoD [Arcobacter butzleri RM4018]
 gi|157699111|gb|ABV67271.1| RNA polymerase sigma 70 factor [Arcobacter butzleri RM4018]
          Length = 626

 Score =  283 bits (723), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 128/258 (49%), Positives = 195/258 (75%), Gaps = 1/258 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +++G+     +K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA 
Sbjct: 369 ELKAVLEQIKRGKQITDTSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAV 428

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +
Sbjct: 429 DKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKGVQENGK 488

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  EEIAK++ +PV+ V++V+KITKEP+SLE PIG ++    GDF+ D+ A +P+D+ +
Sbjct: 489 EPDIEEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDEDGKFGDFVPDEKAPTPIDNIM 548

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + +L+    ++L+ L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI
Sbjct: 549 KEDLQGQIDQILSQLNEREQAVIRMRFGLMEDASDRTLEEIGKELNVTRERVRQIESSAI 608

Query: 665 RKLKHPSRSKKLRSFLDG 682
           +KLKHP   K L+++++ 
Sbjct: 609 KKLKHPKVGKNLKNYVES 626



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 40/58 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E E+ I+K+IE G  +++ ++C  P     ++ +R+ L
Sbjct: 101 SDSPVRMYLREMGQIPLLTKEEEVEISKKIETGEDIILDAICYVPYLIDFILEYREPL 158


>gi|268680166|ref|YP_003304597.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
 gi|268618197|gb|ACZ12562.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
          Length = 617

 Score =  283 bits (723), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 131/257 (50%), Positives = 193/257 (75%), Gaps = 1/257 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I+  +++G+  A  +K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +
Sbjct: 361 LKEILEQIKRGKKIADESKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVD 420

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +E
Sbjct: 421 KFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKHLQEEGKE 480

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P  E IA ++ +  + V+ V+KITKEPISLE PIG+ED    GDF+EDK +++PL+  ++
Sbjct: 481 PDIETIALEVGLSADKVKNVIKITKEPISLEAPIGNEDDGKFGDFVEDKTSIAPLEHILK 540

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           ++L+E    VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+
Sbjct: 541 SDLKEQIDDVLDQLNDREKAVIRMRFGLMHDESDRTLEEIGKELNVTRERVRQIESSAIK 600

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHP   +KL+++++ 
Sbjct: 601 KLKHPKVGRKLKNYIES 617


>gi|315655467|ref|ZP_07908366.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
 gi|315490122|gb|EFU79748.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
          Length = 553

 Score =  283 bits (723), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 135/260 (51%), Positives = 189/260 (72%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  + R +  +V+ G+    +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL
Sbjct: 298 MTPKQIRELHYVVQDGQ----MAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGL 353

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M  
Sbjct: 354 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 413

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P 
Sbjct: 414 DLGREPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPA 473

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEA
Sbjct: 474 DAVSFMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEA 533

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HP+RS+ LR +L+
Sbjct: 534 KTMSKLRHPARSQSLRDYLN 553



 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 9/59 (15%)

Query: 100 SNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S S+ +    KD AD          +T DPV+ YL+++G + LL+ E E+ ++KRIEAG
Sbjct: 226 STSAEYTLSEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAG 284


>gi|315636974|ref|ZP_07892198.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
 gi|315478804|gb|EFU69513.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
          Length = 626

 Score =  283 bits (723), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 128/258 (49%), Positives = 195/258 (75%), Gaps = 1/258 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +++G+     +K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA 
Sbjct: 369 ELKAVLEQIKRGKQITDTSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAV 428

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +
Sbjct: 429 DKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKGVQENGK 488

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  EEIAK++ +PV+ V++V+KITKEP+SLE PIG ++    GDF+ D+ A +P+D+ +
Sbjct: 489 EPDIEEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDEDGKFGDFVPDEKAPTPIDNIM 548

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + +L+    ++L+ L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI
Sbjct: 549 KEDLQGQIDQILSQLNEREQAVIRMRFGLMEDASDRTLEEIGKELNVTRERVRQIESSAI 608

Query: 665 RKLKHPSRSKKLRSFLDG 682
           +KLKHP   K L+++++ 
Sbjct: 609 KKLKHPKVGKNLKNYVES 626



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 40/58 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E E+ I+K+IE G  +++ ++C  P     ++ +R+ L
Sbjct: 101 SDSPVRMYLREMGQIPLLTKEEEVEISKKIETGEDIILDAICYVPYLIDFILEYREPL 158


>gi|297625160|ref|YP_003706594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
 gi|297166340|gb|ADI16051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
          Length = 446

 Score =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 144/259 (55%), Positives = 186/259 (71%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R +  +V  GE    +A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 192 EQRALKRIVEDGE----MARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 247

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   YKFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 248 EKFEYRRRYKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSR 307

Query: 546 EPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EP+ EE+A+ +      E V +V K+++EP+SLETPIGDE  S  GDFI D N  SP+D 
Sbjct: 308 EPSYEEVAEAMGPGWSAEKVEEVFKVSQEPVSLETPIGDEKDSFYGDFIPDDNVESPVDQ 367

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A +  L E   + L  LT RE  VL+ R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 368 ASKTLLSEELEKALDKLTERESMVLKFRKGLVDGREHTLEEVGAHFGVTRERIRQIENKA 427

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FLD
Sbjct: 428 LRKLKYHESRTRKLRDFLD 446



 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 67/139 (48%), Gaps = 21/139 (15%)

Query: 32  KKMIKLARQRGYVTIEELN-AFLPPDEVSSE-----QMEDTVAMLSNMGINVVDGDDLED 85
           +++++ A + G V  EE+  A    +E  +E       +D + +L   G+ + D    ED
Sbjct: 40  QRLLEAATRDGSVNTEEMTTALTAANEALAEGDTEISFDDLMKVLEARGVEIADL--AED 97

Query: 86  EEGSEDSLD----LASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIE 132
           E   ED  D    L          ++ R++   R         ST+DPVR YL E+G + 
Sbjct: 98  EVLDEDEFDEVDALGDLDEPEDELVRDREEIEARAEAMAGSRLSTNDPVRQYLHEIGRVS 157

Query: 133 LLSREGEIAIAKRIEAGRA 151
           LL+ E EI++A+RIE G A
Sbjct: 158 LLTLEEEISLARRIEEGEA 176


>gi|320449783|ref|YP_004201879.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
 gi|320149952|gb|ADW21330.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
          Length = 494

 Score =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 144/259 (55%), Positives = 189/259 (72%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 240 ELKRYLHLAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 295

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR +  ++ R
Sbjct: 296 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARSLQQELGR 355

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EPT EEIA+ +    +   V + LKI +EP+SLETPIGDE  S  GDFI D+N  SP+D+
Sbjct: 356 EPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVDA 415

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 416 AAQSLLAEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 475

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FLD
Sbjct: 476 LRKLKYHESRTRKLRDFLD 494


>gi|154148465|ref|YP_001406295.1| RNA polymerase sigma factor RpoD [Campylobacter hominis ATCC
           BAA-381]
 gi|153804474|gb|ABS51481.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter hominis ATCC BAA-381]
          Length = 624

 Score =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 129/257 (50%), Positives = 190/257 (73%), Gaps = 1/257 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +
Sbjct: 368 LKQILEQIKRGKKISDEAKSLMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVD 427

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +E
Sbjct: 428 KFEYRKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKINRKYVQENGKE 487

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P    +AK++ + ++ +++V+KITKEPISLE P+G+ED    GDF+EDK  +SP+D  ++
Sbjct: 488 PDITILAKEVGLSIDKIKQVIKITKEPISLEAPVGNEDDGKFGDFVEDKGTISPIDQILK 547

Query: 607 ANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            +L+E   +VL  L  RE  V+RMRFG +   +D TLEE+GK+  VTRER+RQIEA AI+
Sbjct: 548 NDLKEQIDKVLDQLNERERAVIRMRFGLLDDESDRTLEEIGKELSVTRERVRQIEASAIK 607

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHP   + L+ +++ 
Sbjct: 608 KLKHPKVGRDLKKYIES 624



 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/146 (28%), Positives = 72/146 (49%), Gaps = 14/146 (9%)

Query: 40  QRGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           Q+ YVT E L  F    P     +++ED   +  N  I ++   ++   +  ED   +  
Sbjct: 19  QKNYVTFERLIKFFDKAPTSTQVKKIED---LAKNFKIKLISSAEIAKIKNIEDLKRIKE 75

Query: 98  SASNSSVFLQKRKD---SADRS------TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +   L+K  D   ++D        +D PVRMYLREMG+++LL +E EI I+K+IE 
Sbjct: 76  REKKAKSELEKNDDFDIASDNELLEWSRSDSPVRMYLREMGAVDLLKKEEEIEISKKIEL 135

Query: 149 GRAMMMASLCESPLTFQALIIWRDEL 174
           G  +++ + C  P     ++ + + L
Sbjct: 136 GEDIIIDAFCSVPFLIDFILAYEEPL 161


>gi|295394756|ref|ZP_06804971.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294972352|gb|EFG48212.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 473

 Score =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 136/239 (56%), Positives = 177/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA W
Sbjct: 235 IAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 294

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E 
Sbjct: 295 WIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPER 354

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +V K  +EPISL TP+G++  S  GD IED  AV P DS     L+E    VL +L+ 
Sbjct: 355 VVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADSVSFTLLQEQLHSVLDTLSE 414

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 415 REAGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAKLRHPSRSQVLRDYLD 473



 Score = 40.0 bits (92), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 172 ATADPVKDYLKQIGKVALLNAAEEVDLAKRIEAG 205


>gi|78777303|ref|YP_393618.1| RNA polymerase sigma factor RpoD [Sulfurimonas denitrificans DSM
           1251]
 gi|78497843|gb|ABB44383.1| sigma 28 (Flagella/Sporulation) [Sulfurimonas denitrificans DSM
           1251]
          Length = 623

 Score =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 134/253 (52%), Positives = 192/253 (75%), Gaps = 1/253 (0%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+  +++G+  + I+K +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF+
Sbjct: 370 ILEQIKRGKNISEISKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFE 429

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  
Sbjct: 430 YQKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKHLQEHGKEPDV 489

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E IA ++ + VE V+ V+KITKEPISLE PIG ED    GDFIEDK ++SP D+ ++ +L
Sbjct: 490 EVIALEVGLSVEKVKNVIKITKEPISLEAPIGSEDDGRFGDFIEDKTSLSPSDAILKDDL 549

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R     VL  L  RE+ V+++RFGI  + +D TLEE+GK+  VTRER+RQIE+ AI+KLK
Sbjct: 550 RVQIESVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 609

Query: 669 HPSRSKKLRSFLD 681
           HP   +KL+++++
Sbjct: 610 HPKVGRKLKNYIE 622



 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 41/58 (70%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E EI I+K+IE G ++++ ++C  P     ++ +R+ L
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKIEGGESIIIDAICSVPYLIDFILDYREPL 160


>gi|313680173|ref|YP_004057912.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Oceanithermus
           profundus DSM 14977]
 gi|313152888|gb|ADR36739.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oceanithermus
           profundus DSM 14977]
          Length = 484

 Score =  282 bits (721), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 161/354 (45%), Positives = 224/354 (63%), Gaps = 32/354 (9%)

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE------RHQGRELDPHWVSYAKDF 390
           L +E+  D+++R+   E  + RLA+  G++ D+  +      RH GR   PH   Y  + 
Sbjct: 154 LTLEEEIDLARRVEEGEAAVERLAEFTGLEADLIKKVIRAQVRHGGR--VPHIPGYEAE- 210

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
                      + D+I  +   ++++           +  + + R GE    IA++ ++E
Sbjct: 211 ---------RVDEDTIQAVDARLRALP-------KPQKRYLHIARDGE----IARQHLIE 250

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW++QAI R
Sbjct: 251 ANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTYATWWIRQAINR 310

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLK 568
           +IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T  EIA  +      + V +  K
Sbjct: 311 AIADQARTIRIPVHMVETINKLTRTARQLQQELGREATYAEIADAMGPGWDAKKVEETFK 370

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I +EP+SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E   + L+ L+ RE  VL
Sbjct: 371 IAQEPVSLETPIGDEKDSFYGDFIPDEHLASPVDSAAQSLLSEELEKALSKLSEREAMVL 430

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           ++R G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 431 KLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 484



 Score = 43.9 bits (102), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 20/38 (52%), Positives = 27/38 (71%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           ST DPVR YL E+G + LL+ E EI +A+R+E G A +
Sbjct: 136 STSDPVRQYLHEIGQVPLLTLEEEIDLARRVEEGEAAV 173


>gi|256390959|ref|YP_003112523.1| RNA polymerase sigma factor [Catenulispora acidiphila DSM 44928]
 gi|256357185|gb|ACU70682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 559

 Score =  281 bits (720), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 322 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 381

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 382 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 441

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 442 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 501

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 502 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 559



 Score = 42.0 bits (97), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 258 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 291


>gi|297566693|ref|YP_003685665.1| RpoD subfamily RNA polymerase sigma-70 subunit [Meiothermus
           silvanus DSM 9946]
 gi|296851142|gb|ADH64157.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus
           silvanus DSM 9946]
          Length = 483

 Score =  281 bits (720), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 146/258 (56%), Positives = 189/258 (73%), Gaps = 10/258 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH+  + R GE    +A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EK
Sbjct: 232 RHL-HIARDGE----LARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEK 286

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++   YKFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR+M  ++ REP
Sbjct: 287 FEYKRRYKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQMQQELGREP 346

Query: 548 TPEEIAKKLAMP---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           T EEI++ +  P    + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+DSA
Sbjct: 347 TYEEISEAMG-PGWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDSA 405

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            Q+ L E   + L  L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA+
Sbjct: 406 AQSMLSEELEKALGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL 465

Query: 665 RKLK-HPSRSKKLRSFLD 681
           RKLK H SR++KLR FLD
Sbjct: 466 RKLKYHESRTRKLRDFLD 483



 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 8/84 (9%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA----MMMASLCESPLTFQALIIWR 171
           ST DPVR YL E+G + LL+ E EI +A+R+E G A    +   +  E+ L  Q L   R
Sbjct: 136 STSDPVRQYLHEIGQVPLLTLEEEIDLARRVEDGVASAQFLAQETGLETDLIRQVL---R 192

Query: 172 DELNDGTTLLREIIDLEACIGPES 195
            ++  G   + ++  +E  + PE+
Sbjct: 193 AQVQGGAR-IHQVPGMEVKLDPET 215


>gi|170691127|ref|ZP_02882293.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
 gi|170144376|gb|EDT12538.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
          Length = 202

 Score =  281 bits (720), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 132/201 (65%), Positives = 166/201 (82%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 60

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P 
Sbjct: 61  ETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPA 120

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A+ A++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 121 DAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEA 180

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           KA+RKL+HPSRS KL+SFL+G
Sbjct: 181 KALRKLRHPSRSDKLKSFLEG 201


>gi|148658692|ref|YP_001278897.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148570802|gb|ABQ92947.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 401

 Score =  281 bits (720), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 132/242 (54%), Positives = 178/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A++ +++ANLRLV+S+AKKY  RG+  LDLIQEGNIGLM+A EKFD+  GYKFSTY
Sbjct: 160 EGQAARERLIQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRKGYKFSTY 219

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR IADQS TIR+PVH+ + I++V+R + R+     R+PTP+EIA +L +P
Sbjct: 220 ATWWIRQAITRVIADQSRTIRLPVHVGETINRVMRASNRIQQTTGRDPTPDEIALELGIP 279

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE VR+VL+  ++ ISLETPIG E  + L DFIED   V+P+DSA    LRE     L  
Sbjct: 280 VEKVRRVLEAARQTISLETPIGTEGDTVLADFIEDGKGVTPMDSASHHILREQIDSALEK 339

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE R++++R+G+      TLEEVG++F +TRERIRQIEA+ +RKL+HP   + LR +
Sbjct: 340 LPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLRKLRHPHYGRGLRGY 399

Query: 680 LD 681
           L+
Sbjct: 400 LE 401



 Score = 41.6 bits (96), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             DDPVR+YLRE+G + LL+ + EI +A+++E G
Sbjct: 101 GVDDPVRVYLREIGRVNLLTAQEEIMLAQQVERG 134


>gi|308177806|ref|YP_003917212.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
 gi|307745269|emb|CBT76241.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
          Length = 403

 Score =  281 bits (720), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 135/242 (55%), Positives = 178/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  IAK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 162 DGKIAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTY 221

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M 
Sbjct: 222 ATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMT 281

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +
Sbjct: 282 PEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDT 341

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 342 LSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 401

Query: 680 LD 681
           LD
Sbjct: 402 LD 403



 Score = 42.0 bits (97), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 42/82 (51%), Gaps = 9/82 (10%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR-------STDDPVRMYLRE 127
           +   D DD  D E S DS D  S   +    L    D A +       +T DPV+ YL++
Sbjct: 55  VASTDADD--DAEPSTDSKDSKSEDDSKGFTLSSGDDDAPQQQVMVAGATADPVKDYLKQ 112

Query: 128 MGSIELLSREGEIAIAKRIEAG 149
           +G + LL+ E E+ +A RIEAG
Sbjct: 113 IGKVALLNAEQEVDLALRIEAG 134


>gi|325295045|ref|YP_004281559.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065493|gb|ADY73500.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 563

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 185/238 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V +NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 325 AKQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 384

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+KV++ +R+M  +  REP PEEIA++L MP   V
Sbjct: 385 IRQAITRAIADQARTIRIPVHMIETINKVIKASRQMFLEKGREPRPEEIAERLRMPASKV 444

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++++ +EP+SLETPIGD++ S LG+FIED  +  P    I+ +L+E  +++L++L+ R
Sbjct: 445 RSIIQLAQEPVSLETPIGDDEDSTLGNFIEDSKSPIPEHEVIKKDLQEKVSQLLSTLSER 504

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  VL++RFG+    +HTLE+VG++  VTRERIRQIE+KA+RKLK+      L  FL+
Sbjct: 505 EALVLKLRFGLDGYPEHTLEQVGRELKVTRERIRQIESKALRKLKNCGLDIDLSIFLE 562



 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 49/156 (31%), Positives = 88/156 (56%), Gaps = 14/156 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           +++++I L R +GY+T +EL   L  + ++ E +E+ +  L    I+++       +EG 
Sbjct: 5   NFEEIIALGRDKGYITFDELMEHLDEEVLTPELIEELITQLDEFDIHIIP------KEG- 57

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED +DL      S + +    D+  RS DDP+R+YLREM  I LL R  EIA+AKR+E G
Sbjct: 58  EDHVDL------SKLQITIAPDTMPRS-DDPIRLYLREMSGISLLKRHEEIALAKRVELG 110

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           R  ++  L ++      ++   +++ +G   +R+I+
Sbjct: 111 RKALLRYLLKTNAVLDYILNVEEKIKNGELKVRDIM 146


>gi|282854019|ref|ZP_06263356.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|282583472|gb|EFB88852.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|314922986|gb|EFS86817.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL001PA1]
 gi|314966763|gb|EFT10862.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA2]
 gi|314981097|gb|EFT25191.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA3]
 gi|315091922|gb|EFT63898.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA4]
 gi|315093321|gb|EFT65297.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL060PA1]
 gi|327327588|gb|EGE69364.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL103PA1]
          Length = 510

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 269 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 328

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 329 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMT 388

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 389 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 448

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 449 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 508

Query: 680 LD 681
           LD
Sbjct: 509 LD 510



 Score = 38.9 bits (89), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 208 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 241


>gi|328907303|gb|EGG27069.1| RNA polymerase sigma factor RpoD [Propionibacterium sp. P08]
          Length = 506

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 265 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 324

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 325 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMT 384

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 385 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 444

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 445 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 504

Query: 680 LD 681
           LD
Sbjct: 505 LD 506



 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 204 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 237


>gi|50842515|ref|YP_055742.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|289425323|ref|ZP_06427100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289427207|ref|ZP_06428923.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|295130592|ref|YP_003581255.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|50840117|gb|AAT82784.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           KPA171202]
 gi|289154301|gb|EFD02989.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289159676|gb|EFD07864.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|291377120|gb|ADE00975.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|332675432|gb|AEE72248.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           266]
          Length = 506

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 265 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 324

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 325 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMT 384

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 385 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 444

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 445 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 504

Query: 680 LD 681
           LD
Sbjct: 505 LD 506



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 204 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 237


>gi|315078017|gb|EFT50068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA2]
          Length = 511

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 270 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 329

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 330 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMT 389

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 390 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 449

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 450 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 509

Query: 680 LD 681
           LD
Sbjct: 510 LD 511



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 209 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 242


>gi|314960003|gb|EFT04105.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA2]
          Length = 511

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 270 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 329

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 330 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMT 389

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 390 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 449

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 450 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 509

Query: 680 LD 681
           LD
Sbjct: 510 LD 511



 Score = 38.9 bits (89), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 209 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 242


>gi|315103424|gb|EFT75400.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA2]
          Length = 510

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 269 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 328

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 329 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMT 388

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 389 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 448

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 449 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 508

Query: 680 LD 681
           LD
Sbjct: 509 LD 510



 Score = 38.9 bits (89), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 208 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 241


>gi|313838731|gb|EFS76445.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL086PA1]
          Length = 511

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 270 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 329

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 330 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMT 389

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 390 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 449

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 450 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 509

Query: 680 LD 681
           LD
Sbjct: 510 LD 511



 Score = 38.9 bits (89), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 209 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 242


>gi|313812944|gb|EFS50658.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA1]
          Length = 511

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 270 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 329

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 330 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMT 389

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 390 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 449

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 450 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 509

Query: 680 LD 681
           LD
Sbjct: 510 LD 511



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 209 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 242


>gi|313764456|gb|EFS35820.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA1]
 gi|313772162|gb|EFS38128.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL074PA1]
 gi|313792142|gb|EFS40243.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA1]
 gi|313801905|gb|EFS43139.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA2]
 gi|313807517|gb|EFS46004.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA2]
 gi|313815995|gb|EFS53709.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA1]
 gi|313818559|gb|EFS56273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA2]
 gi|313820326|gb|EFS58040.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA1]
 gi|313822867|gb|EFS60581.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA2]
 gi|313825201|gb|EFS62915.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA1]
 gi|313827777|gb|EFS65491.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA2]
 gi|313830354|gb|EFS68068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL007PA1]
 gi|313833727|gb|EFS71441.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL056PA1]
 gi|314915449|gb|EFS79280.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA4]
 gi|314918269|gb|EFS82100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA1]
 gi|314920081|gb|EFS83912.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA3]
 gi|314925214|gb|EFS89045.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA3]
 gi|314931603|gb|EFS95434.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL067PA1]
 gi|314955756|gb|EFT00156.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA1]
 gi|314958170|gb|EFT02273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA1]
 gi|314962801|gb|EFT06901.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA1]
 gi|314967832|gb|EFT11931.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA1]
 gi|314973358|gb|EFT17454.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA1]
 gi|314976037|gb|EFT20132.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL045PA1]
 gi|314978425|gb|EFT22519.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA2]
 gi|314983942|gb|EFT28034.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA1]
 gi|314988126|gb|EFT32217.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA2]
 gi|314989931|gb|EFT34022.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA3]
 gi|315080641|gb|EFT52617.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL078PA1]
 gi|315084314|gb|EFT56290.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA2]
 gi|315085657|gb|EFT57633.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA3]
 gi|315088921|gb|EFT60897.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA1]
 gi|315095903|gb|EFT67879.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL038PA1]
 gi|315098534|gb|EFT70510.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA2]
 gi|315101108|gb|EFT73084.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA1]
 gi|315105654|gb|EFT77630.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA1]
 gi|315108328|gb|EFT80304.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA2]
 gi|327326185|gb|EGE67975.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA2]
 gi|327330255|gb|EGE72004.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL097PA1]
 gi|327331940|gb|EGE73677.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA3]
 gi|327443141|gb|EGE89795.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA2]
 gi|327445925|gb|EGE92579.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA2]
 gi|327448095|gb|EGE94749.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA1]
 gi|327450784|gb|EGE97438.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA3]
 gi|327453139|gb|EGE99793.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL092PA1]
 gi|327453872|gb|EGF00527.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL083PA2]
 gi|328753472|gb|EGF67088.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL020PA1]
 gi|328754202|gb|EGF67818.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA1]
 gi|328754546|gb|EGF68162.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA2]
 gi|328760854|gb|EGF74420.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL099PA1]
          Length = 511

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 270 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 329

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 330 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMT 389

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 390 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 449

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 450 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 509

Query: 680 LD 681
           LD
Sbjct: 510 LD 511



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 209 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 242


>gi|239626174|ref|ZP_04669205.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47_FAA]
 gi|239520404|gb|EEQ60270.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47FAA]
          Length = 409

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 143/280 (51%), Positives = 197/280 (70%), Gaps = 6/280 (2%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            D I +   EI SIS+ T    ++        RK E +A  A +++VEANLRLV+S+AK+
Sbjct: 136 ADPIREYLKEIGSISLLTPEEETDLAR-----RKSEGDAE-AGRQLVEANLRLVVSIAKR 189

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YT RG+ FLDL+QEGN+GLMKA EKFD+  GY+ STYA WWVKQ+ITRS+ADQS TIR+P
Sbjct: 190 YTGRGMGFLDLVQEGNLGLMKAVEKFDYSKGYRLSTYATWWVKQSITRSLADQSRTIRLP 249

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + ++K+ R  R +S ++ REP+ EEIA+++ MP + V ++++ + + +SLETP+GD
Sbjct: 250 VHMVEAVNKIRRAQRSLSVRLGREPSTEEIAEEVGMPEKRVTELIQASGDTVSLETPVGD 309

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ S+LGDF+ D    S  D A    LRE    +L  L PRE  V+ +RFG+      TL
Sbjct: 310 EEGSNLGDFVADDANASTEDKAESFLLREEIDAMLQGLNPREREVIILRFGLETGHPLTL 369

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EEVG++F VTRERIRQIE  A+RKL++PS+S+K+R FL G
Sbjct: 370 EEVGRRFNVTRERIRQIETAALRKLRNPSKSRKIRDFLPG 409



 Score = 41.6 bits (96), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 32/47 (68%), Gaps = 5/47 (10%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKR-----IEAGRAMMMASL 157
           ST DP+R YL+E+GSI LL+ E E  +A+R      EAGR ++ A+L
Sbjct: 134 STADPIREYLKEIGSISLLTPEEETDLARRKSEGDAEAGRQLVEANL 180


>gi|297626466|ref|YP_003688229.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922231|emb|CBL56801.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 509

 Score =  281 bits (718), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 331

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 332 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 391

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 392 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVNFTLLQEQLHDVLDTLSER 451

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 452 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 509



 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 207 ATADPVKDYLKQIGKVALLNAAQEVDLAKRIEAG 240


>gi|291277050|ref|YP_003516822.1| RNA polymerase sigma-70 factor [Helicobacter mustelae 12198]
 gi|290964244|emb|CBG40093.1| RNA polymerase sigma factor (sigma-70) [Helicobacter mustelae
           12198]
          Length = 614

 Score =  281 bits (718), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 130/256 (50%), Positives = 191/256 (74%), Gaps = 1/256 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I+  +++G+  +  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +
Sbjct: 358 LKEILEQIKRGKIISDKAKNKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVD 417

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+   +KFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +E
Sbjct: 418 KFDYKRNFKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRIHKIMRKYIQETGKE 477

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P  E IA+K+ + V+ V+ V+KITKEP+SLE PIG ++    GDF+EDKN+ + +D  ++
Sbjct: 478 PDVEIIAEKVGLSVDKVKHVIKITKEPVSLEAPIGSDEDGKFGDFVEDKNSTNTMDQIMK 537

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            +LR     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+
Sbjct: 538 EDLRAQIFEVLDQLNEREQAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIK 597

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHP   +KLR++++
Sbjct: 598 KLKHPKVGRKLRNYIE 613



 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 46/70 (65%), Gaps = 1/70 (1%)

Query: 106 LQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           L K +D  + S +D PVRMYLREMG IELL++E E+ ++++I+ G  +++ ++C  P   
Sbjct: 90  LMKERDLLEWSRSDSPVRMYLREMGQIELLTKEDEVELSRQIKLGENIILDAICSVPYLI 149

Query: 165 QALIIWRDEL 174
             +  +R+ L
Sbjct: 150 DFIYDYREAL 159


>gi|313837136|gb|EFS74850.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA2]
 gi|314927842|gb|EFS91673.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL044PA1]
 gi|314971907|gb|EFT16005.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA3]
          Length = 370

 Score =  281 bits (718), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 134/242 (55%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 129 DGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 188

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M 
Sbjct: 189 ATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMT 248

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +
Sbjct: 249 AEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDT 308

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +
Sbjct: 309 LSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDY 368

Query: 680 LD 681
           LD
Sbjct: 369 LD 370



 Score = 38.5 bits (88), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 68  ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 101


>gi|309812669|ref|ZP_07706413.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
 gi|308433364|gb|EFP57252.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
          Length = 550

 Score =  281 bits (718), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 313 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 372

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 373 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 432

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 433 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 492

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 493 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 550



 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 249 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 282


>gi|154173683|ref|YP_001408074.1| RNA polymerase sigma factor RpoD [Campylobacter curvus 525.92]
 gi|112802903|gb|EAU00247.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter curvus 525.92]
          Length = 614

 Score =  281 bits (718), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 131/259 (50%), Positives = 195/259 (75%), Gaps = 1/259 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +  + I+  +++G+  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA
Sbjct: 356 ARLKEILEQIKRGKKISDEAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKA 415

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  
Sbjct: 416 VDKFEYRKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKINRKYLQEEG 475

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP    IAK++ + V+ V++V+KITKEPISLE PI +E+    GDF+EDK+++SP++  
Sbjct: 476 KEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPIANEEDGKFGDFVEDKSSLSPIEQI 535

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +LRE    VL+ L  RE+ V+ MRFG+  + +D TLEE+GK   VTRER+RQIE+ A
Sbjct: 536 LKGDLREQIDDVLSQLNDREKAVICMRFGLLEDESDRTLEEIGKALNVTRERVRQIESSA 595

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           I+KLKHP   +KL+++++G
Sbjct: 596 IKKLKHPKVGRKLKNYIEG 614



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ E+ I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQISLLTKDEEVEISKKIELGEDIIIDAFCSVPFLIDFILDYKEPL 159


>gi|257068601|ref|YP_003154856.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
 gi|256559419|gb|ACU85266.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
          Length = 433

 Score =  281 bits (718), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 196 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYAKGYKFSTYATWW 255

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 256 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 315

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 316 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 375

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 376 EAGVVSMRFGLEDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 433



 Score = 38.1 bits (87), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +A+RIEAG
Sbjct: 126 ATADPVKDYLKQIGKVALLNAAQEVELAERIEAG 159


>gi|291295726|ref|YP_003507124.1| RNA polymerase sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
 gi|290470685|gb|ADD28104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
          Length = 507

 Score =  280 bits (717), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 162/349 (46%), Positives = 220/349 (63%), Gaps = 23/349 (6%)

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           L +E+  D+++R+        RLA+  G+  D  L RH  R              + +  
Sbjct: 178 LTLEEEIDLARRVEEGVAAAQRLAEETGL--DAELIRHVLRS-------------QVQGS 222

Query: 397 NFVACEVDSILKIRNE-IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           + VA    + L+I  E I ++         E +  + + R GE    I ++ ++EANLRL
Sbjct: 223 SRVASIPGTDLRIDPETIAAVDARLRALPREVKRYLHIARDGE----ICRQHLIEANLRL 278

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AKKYT RGL FLDLIQEGN GL++A EKF++   +KFSTYA WW++QAI R+IADQ
Sbjct: 279 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEFKRRFKFSTYATWWIRQAINRAIADQ 338

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--VEGVRKVLKITKEP 573
           + TIRIPVHM + I+K+ RTAR+M  ++ REP+ EEIA  +      + V +  KI +EP
Sbjct: 339 ARTIRIPVHMVETINKLTRTARQMQQELGREPSYEEIADAMGPGWDAKKVEETFKIAQEP 398

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E   + L  L+ RE  VL++R G
Sbjct: 399 VSLETPIGDEKDSFYGDFIPDEHMASPVDSAAQSMLSEELEKALGKLSEREAMVLKLRKG 458

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           +    +HTLEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 459 LIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 507



 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 26/36 (72%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           ST DPVR YL E+G + LL+ E EI +A+R+E G A
Sbjct: 160 STSDPVRQYLHEIGQVPLLTLEEEIDLARRVEEGVA 195


>gi|332670669|ref|YP_004453677.1| RpoD subfamily RNA polymerase sigma-70 subunit [Cellulomonas fimi
           ATCC 484]
 gi|332339707|gb|AEE46290.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas fimi
           ATCC 484]
          Length = 538

 Score =  280 bits (717), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 301 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 360

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 361 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 420

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 421 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHQVLDTLSER 480

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 481 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 538



 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 237 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 270


>gi|256832655|ref|YP_003161382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686186|gb|ACV09079.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 504

 Score =  280 bits (717), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 267 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 326

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 327 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 386

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 387 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHQVLDTLSER 446

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 447 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 504



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 202 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 235


>gi|317124635|ref|YP_004098747.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
 gi|315588723|gb|ADU48020.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
          Length = 587

 Score =  280 bits (717), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 350 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 409

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 410 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 469

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 470 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 529

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 530 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 587



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 12/81 (14%)

Query: 81  DDLEDEEGSEDS---LDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREM 128
           D  E  +G +D+    D A+ A + S F+ +  D  D          +T DPV+ YL+++
Sbjct: 239 DVAESADGDDDAAPVTDKAAEAEDESGFVIRDDDEDDAPAQQVVTAGATADPVKDYLKQI 298

Query: 129 GSIELLSREGEIAIAKRIEAG 149
           G + LL+ E E+ +AKRIEAG
Sbjct: 299 GKVALLNAEQEVELAKRIEAG 319


>gi|269956779|ref|YP_003326568.1| RpoD subfamily RNA polymerase sigma-70 subunit [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269305460|gb|ACZ31010.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 549

 Score =  280 bits (717), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 312 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 371

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 372 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 431

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 432 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHQVLDTLSER 491

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 492 EAGVVSMRFGLQDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 549



 Score = 42.0 bits (97), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 239 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 272


>gi|302522320|ref|ZP_07274662.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302431215|gb|EFL03031.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 514

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 277 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 336

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 337 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 396

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 397 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 456

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 457 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 514



 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 209 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 246


>gi|297191610|ref|ZP_06909008.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297151002|gb|EFH30922.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 516

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 279 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 338

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 339 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 398

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 399 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 458

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 459 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 516



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 215 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 248


>gi|300871651|ref|YP_003786524.1| RNA polymerase sigma-70 factor RpoD [Brachyspira pilosicoli
           95/1000]
 gi|300689352|gb|ADK32023.1| RNA polymerase sigma factor rpoD (Sigma-70) [Brachyspira pilosicoli
           95/1000]
          Length = 568

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 166/382 (43%), Positives = 231/382 (60%), Gaps = 32/382 (8%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           +KE +VKL+  + LN+  ID + E+L     RI   E    +L + YG            
Sbjct: 203 IKENIVKLLSKVKLNRMEIDRIAEKLKFYLHRINQIEEYFEKLKKRYG------------ 250

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH------- 429
           +E+   + +Y  +   G  K +    VD        IK+  V T    S+ R        
Sbjct: 251 KEISD-FENYYNEIESGNKKIYTRL-VDEFNITPEAIKA--VLTSFHNSQVRMADIYDEV 306

Query: 430 ------IVSMVRKGEC---EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
                 +V  VRK +    + + AK  +V+ANLRLVIS+AKKYTNRGL F DL+QEGNIG
Sbjct: 307 RTDKETLVEWVRKIDSSRRKIAQAKDHIVKANLRLVISIAKKYTNRGLHFFDLVQEGNIG 366

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA +KF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R  R+  
Sbjct: 367 LIKAVDKFEYKKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRVLRQYM 426

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  REP+ +EIA+ L+ P   V+ V  + K+P+SL  PIGDE+ + LG+ IEDK   SP
Sbjct: 427 QQYGREPSIQEIARALSWPESRVKSVRNVAKDPVSLNAPIGDEEDTILGELIEDKEFESP 486

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +      LR+    +L +L  RE++V+RMR+G+    +HTLEEVG  F VTRERIRQIE
Sbjct: 487 QNITTFKILRKHIDSLLDNLPEREQKVIRMRYGLDDGYNHTLEEVGYVFKVTRERIRQIE 546

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKAIR+L+  S+ K+L+ FLD 
Sbjct: 547 AKAIRRLRATSKKKELKEFLDS 568



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 35/154 (22%), Positives = 79/154 (51%), Gaps = 11/154 (7%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEEGSEDS 92
           M++      Y+T +E+NA +  D + ++ M+    +L+   I +V D  + E    +++ 
Sbjct: 1   MLEKGNANKYLTFKEINAAI--DNMDTDVMDILFQLLNARKIVIVEDKREFESLSKNQNK 58

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           +D A+       F+       +   DDP+R+YL+E+G ++LL+ + E+  +K+IE G + 
Sbjct: 59  IDDAAR------FIHVEDKVGN--NDDPIRLYLKEIGKVDLLTHDDEVEYSKKIELGESE 110

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           + + +  + L    ++     ++ G   + EI++
Sbjct: 111 IESIILNTHLVVGEVLNTIKCVHSGKVSIHEILE 144


>gi|283781338|ref|YP_003372093.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283439791|gb|ADB18233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 524

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 136/271 (50%), Positives = 192/271 (70%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +E++SI V T  + +  +  V M+++   +   AK+E+ E NLRLV+S+AKKY NRGL F
Sbjct: 254 SELRSILVATQETPASMQKRVDMLKRVYTDYQQAKRELSEGNLRLVVSIAKKYRNRGLSF 313

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN GLM+A +KF++  G+KF TYA WW++QAITR++ADQS TIRIPVHM + + 
Sbjct: 314 LDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQSRTIRIPVHMVETMS 373

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           +V   +R++  ++ REPT EE A+K    V+  R+VL +++ PISL+ P+G+ + SH GD
Sbjct: 374 RVRNVSRQLLQELGREPTLEETARKAKTTVDEARRVLAMSRYPISLDRPVGNSEDSHFGD 433

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            + D  A SP   A Q  LR    +VL +L+ RE  ++++R+G+G    +TLEEVG  F 
Sbjct: 434 LLPDGTAESPATGASQEMLRTRINKVLKTLSYREREIIKLRYGLGDGYSYTLEEVGHIFK 493

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+ PSRS++L  FLD
Sbjct: 494 VTRERIRQIEAKAVRKLQQPSRSQELVGFLD 524



 Score = 48.9 bits (115), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 29/49 (59%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
           +DDPVRMYL +MG I LL+R  EI +AK+IE  R      L E     Q
Sbjct: 71  SDDPVRMYLTQMGEIPLLTRAQEIYLAKKIEVTRRRFRTKLLECDYVIQ 119


>gi|318059566|ref|ZP_07978289.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075441|ref|ZP_07982773.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 446

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 209 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 268

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 269 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 328

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 329 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 388

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 389 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 446



 Score = 42.4 bits (98), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 141 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 178


>gi|333024008|ref|ZP_08452072.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
 gi|332743860|gb|EGJ74301.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
          Length = 493

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 256 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 315

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 316 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 375

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 376 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 435

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 436 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 493



 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 188 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 225


>gi|313682108|ref|YP_004059846.1| RNA polymerase, sigma 70 subunit, rpod [Sulfuricurvum kujiense DSM
           16994]
 gi|313154968|gb|ADR33646.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfuricurvum kujiense DSM
           16994]
          Length = 620

 Score =  280 bits (716), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 132/253 (52%), Positives = 193/253 (76%), Gaps = 1/253 (0%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+  +++G+  + ++K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF+
Sbjct: 367 ILEQIKRGKNISEVSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFE 426

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  
Sbjct: 427 YQKGYKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKHLQEHGKEPDV 486

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E IA+++ + VE V+ V+KITKEPISLE PIG+E+    GDFIEDK ++SP D+ ++ +L
Sbjct: 487 ETIAEEVGLSVEKVKNVIKITKEPISLEAPIGNEEDGRFGDFIEDKMSLSPSDAILKDDL 546

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     VL  L  RE+ V++MRFGI  + +D TLEE+GK+  VTRER+RQIE+ AI+KLK
Sbjct: 547 KVQIESVLEQLNEREKAVIKMRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 606

Query: 669 HPSRSKKLRSFLD 681
           HP   +KL+++++
Sbjct: 607 HPKVGRKLKNYIE 619



 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 40/58 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL++E E+ I+KR+E G  +++ ++C  P     ++ ++D L
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEVEISKRMEMGEGIIIDAICSVPYLIDFILDYKDPL 160


>gi|254386999|ref|ZP_05002279.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194345824|gb|EDX26790.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 520

 Score =  280 bits (716), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 283 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 342

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 343 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 402

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 403 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 462

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 463 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 520



 Score = 42.4 bits (98), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 15/86 (17%)

Query: 79  DGDDLEDEEGSEDSLDLASSA---------SNSSVFLQKRKDSADR------STDDPVRM 123
           D D+  DEE +ED+   A +          S   V      D+  +      +T DPV+ 
Sbjct: 167 DADEAGDEESAEDAPGAAKAEGDEEEEGGESKGFVISDDEDDAPAQQVAVAGATADPVKD 226

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG 149
           YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 227 YLKQIGKVPLLNAEQEVELAKRIEAG 252


>gi|254391058|ref|ZP_05006266.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
 gi|197704753|gb|EDY50565.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
          Length = 514

 Score =  280 bits (716), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 277 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 336

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 337 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 396

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 397 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 456

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 457 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 514



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 213 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 246


>gi|295836123|ref|ZP_06823056.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295825874|gb|EDY42152.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 493

 Score =  280 bits (716), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 256 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 315

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 316 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 375

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 376 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 435

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 436 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 493



 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 188 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 225


>gi|222100016|ref|YP_002534584.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
 gi|221572406|gb|ACM23218.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
          Length = 392

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 182/248 (73%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK++++ +NLRLV+S+AK+Y  RGL F DLIQEGNIGL+KA EKFDW  
Sbjct: 137 LARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDWRK 196

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R    K   EP+ EE+
Sbjct: 197 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLNRLRREYYQKYGEEPSVEEL 256

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  P E ++++L+  KE ISLE+PIG+++ S + DF+ D++  SP   A++  +RE 
Sbjct: 257 AKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSIEDFVADESVPSPKKEAMRMLMREE 316

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 317 LEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 376

Query: 673 SKKLRSFL 680
           SK L+S L
Sbjct: 377 SKYLKSLL 384



 Score = 44.3 bits (103), Expect = 0.072,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 64/120 (53%), Gaps = 9/120 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           KK+I   +++GY+T E+++   PP+  E  +  +E     L   GIN+V+ D  E+ E S
Sbjct: 32  KKLINQGKKKGYITYEDIDKAFPPNYEEFDTNLIEKIYEELEKHGINIVESDSEEETETS 91

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            + L+      +  +      D+++    D ++MYL+E+G I LL+   E  +A+R + G
Sbjct: 92  TEELEELLEKESPEIH-----DASN--VRDSIKMYLKEIGKIPLLTPAQERELARRAQMG 144


>gi|239928504|ref|ZP_04685457.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 490

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 253 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 312

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 313 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 372

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 373 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 432

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 433 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 490



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 48/84 (57%), Gaps = 14/84 (16%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD---------SADRSTDDPVRMYL 125
           + +VD + LED + +E+        + S+ F+   +D         +A  +T DPV+ YL
Sbjct: 144 VELVDDEVLEDTKVAEEP-----EGAESAGFVLSDEDEDDAPAQQVAAAGATADPVKDYL 198

Query: 126 REMGSIELLSREGEIAIAKRIEAG 149
           +++G + LL+ E E+ +AKRIEAG
Sbjct: 199 KQIGKVPLLNAEQEVELAKRIEAG 222


>gi|294631847|ref|ZP_06710407.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292835180|gb|EFF93529.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 515

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 278 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 338 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 397

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 398 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 457

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 458 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 515



 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 210 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 247


>gi|260906542|ref|ZP_05914864.1| RNA polymerase principal sigma factor [Brevibacterium linens BL2]
          Length = 473

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 135/239 (56%), Positives = 177/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA W
Sbjct: 235 IAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 294

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP+PEE+AK+L M  E 
Sbjct: 295 WIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPSPEELAKELDMTPER 354

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +V K  +EPISL TP+G++  S  GD IED  AV P DS     L+E    VL +L+ 
Sbjct: 355 VVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPSDSVSFTLLQEQLHSVLDTLSE 414

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 415 REAGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAKLRHPSRSQVLRDYLD 473



 Score = 39.3 bits (90), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 172 ATADPVKDYLKQIGKVALLNAAEEVDLAKRIEAG 205


>gi|29828986|ref|NP_823620.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29606091|dbj|BAC70155.1| RNA polymerase major sigma factor, sigma-70 family [Streptomyces
           avermitilis MA-4680]
          Length = 512

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 275 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 334

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 335 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 394

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 395 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 454

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 455 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 512



 Score = 42.4 bits (98), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 207 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 244


>gi|326443878|ref|ZP_08218612.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 537

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 300 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 359

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 360 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 419

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 420 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 479

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 480 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 537



 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 236 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 269


>gi|239917829|ref|YP_002957387.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
 gi|281413678|ref|ZP_06245420.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family protein [Micrococcus
           luteus NCTC 2665]
 gi|239839036|gb|ACS30833.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
          Length = 497

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 260 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 319

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 320 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 379

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 380 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 439

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 440 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 497



 Score = 39.7 bits (91), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A RIEAG
Sbjct: 196 ATADPVKDYLKQIGKVALLNAEQEVDLAMRIEAG 229


>gi|116333403|ref|YP_794930.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
 gi|116098750|gb|ABJ63899.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
          Length = 368

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 140/259 (54%), Positives = 182/259 (70%), Gaps = 16/259 (6%)

Query: 410 RNEIKSISVETGISISE-----FRHI-----------VSMVRKGECEASIAKKEMVEANL 453
           + E+K  S  TG+ I++      + I           V++  + E     AK+E+ EANL
Sbjct: 87  KKELKDASTTTGVKINDPVRMYLKEIGRVNLLTADEEVALALRIENGEEAAKQELAEANL 146

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IA
Sbjct: 147 RLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIA 206

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP
Sbjct: 207 DQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEP 266

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL +LT REE VLR+RFG
Sbjct: 267 VSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLDTLTDREENVLRLRFG 326

Query: 634 IGMNTDHTLEEVGKQFCVT 652
           +      TLEEVGK F VT
Sbjct: 327 LDDGRTRTLEEVGKVFGVT 345



 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 42/148 (28%), Positives = 79/148 (53%), Gaps = 9/148 (6%)

Query: 18  SDDSLVFD--FSDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMG 74
           + D  +FD    + + + +IK  ++ G++T ++L +    P  + ++QM+  +  +S+ G
Sbjct: 5   TTDQPMFDQKAYNKTVRALIKDTKKAGHITYDDLTDKVATPYTLDAKQMDKLLETISDAG 64

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I+VVD       +G  D+  + +  + S   L+    +     +DPVRMYL+E+G + LL
Sbjct: 65  ISVVDA------KGEPDARAVKAQKAVSKKELKDASTTTGVKINDPVRMYLKEIGRVNLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPL 162
           + + E+A+A RIE G       L E+ L
Sbjct: 119 TADEEVALALRIENGEEAAKQELAEANL 146


>gi|291436829|ref|ZP_06576219.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
 gi|291339724|gb|EFE66680.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
          Length = 509

 Score =  280 bits (716), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 331

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 332 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 391

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 392 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 451

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 452 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 509



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 48/84 (57%), Gaps = 14/84 (16%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD---------SADRSTDDPVRMYL 125
           + +VD + LED + +E+        + S+ F+   +D         +A  +T DPV+ YL
Sbjct: 163 VELVDDEVLEDTKVAEEP-----EGAESAGFVLSDEDEDDAPAQQVAAAGATADPVKDYL 217

Query: 126 REMGSIELLSREGEIAIAKRIEAG 149
           +++G + LL+ E E+ +AKRIEAG
Sbjct: 218 KQIGKVPLLNAEQEVELAKRIEAG 241


>gi|294815528|ref|ZP_06774171.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294328127|gb|EFG09770.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 529

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 292 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 351

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 352 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 411

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 412 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 471

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 472 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 529



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 228 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 261


>gi|1582791|prf||2119302A sigma factor
          Length = 445

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 208 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 267

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 268 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 327

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 328 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 387

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 388 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 445



 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 144 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 177


>gi|289706929|ref|ZP_06503266.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
 gi|289556364|gb|EFD49718.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
          Length = 509

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 331

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 332 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 391

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 392 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 451

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 452 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 509



 Score = 39.7 bits (91), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A RIEAG
Sbjct: 208 ATADPVKDYLKQIGKVALLNAEQEVDLAMRIEAG 241


>gi|291454591|ref|ZP_06593981.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
 gi|581664|emb|CAA53564.1| sigma factor (RNA polymerase subunit) [Streptomyces griseus]
 gi|291357540|gb|EFE84442.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
          Length = 510

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 273 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 332

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 333 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 392

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 393 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 452

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 453 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 510



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 205 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 242


>gi|302537370|ref|ZP_07289712.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
 gi|302446265|gb|EFL18081.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
          Length = 526

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 289 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 348

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 349 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 408

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 409 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 468

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 469 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 526



 Score = 42.0 bits (97), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 225 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 258


>gi|296129901|ref|YP_003637151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296021716|gb|ADG74952.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 495

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 258 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 317

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 318 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 377

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 378 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHQVLDTLSER 437

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 438 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 495



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 193 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 226


>gi|296270363|ref|YP_003652995.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296093150|gb|ADG89102.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 555

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 318 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 377

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A++L M  E V
Sbjct: 378 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKV 437

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 438 IEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 497

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 498 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 555



 Score = 40.4 bits (93), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 25/31 (80%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 256 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 286


>gi|182435494|ref|YP_001823213.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776131|ref|ZP_08235396.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|11132962|sp|P77951|HRDB_STRGR RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|1617256|gb|AAB16905.1| principal sigma factor [Streptomyces griseus]
 gi|178464010|dbj|BAG18530.1| RNA polymerase principal sigma factor hrdB [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656464|gb|EGE41310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 514

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 277 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 336

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 337 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 396

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 397 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 456

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 457 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 514



 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 213 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 246


>gi|21224164|ref|NP_629943.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289768642|ref|ZP_06528020.1| transcription initiation factor sigma [Streptomyces lividans TK24]
 gi|12644145|sp|P18183|HRDB_STRCO RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|3036885|emb|CAA18518.1| major vegetative sigma factor [Streptomyces coelicolor A3(2)]
 gi|289698841|gb|EFD66270.1| transcription initiation factor sigma [Streptomyces lividans TK24]
          Length = 511

 Score =  280 bits (715), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 334 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 393

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 394 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 453

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 454 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 511



 Score = 42.7 bits (99), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 14/83 (16%)

Query: 79  DGDDLEDE------------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           DG+ LEDE            EG+E++  + S         Q+   +A  +T DPV+ YL+
Sbjct: 163 DGELLEDEATEEPKAATEEPEGTENAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLK 220

Query: 127 EMGSIELLSREGEIAIAKRIEAG 149
           ++G + LL+ E E+ +AKRIEAG
Sbjct: 221 QIGKVPLLNAEQEVELAKRIEAG 243


>gi|282862331|ref|ZP_06271393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282562670|gb|EFB68210.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 515

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 278 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 338 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 397

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 398 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 457

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 458 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 515



 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 214 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 247


>gi|239991260|ref|ZP_04711924.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 515

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 278 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 338 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 397

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 398 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 457

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 458 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 515



 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 214 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 247


>gi|307325028|ref|ZP_07604232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889174|gb|EFN20156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 502

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 265 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 324

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 325 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 384

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 385 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 444

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 445 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 502



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 197 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 234


>gi|48745|emb|CAA37175.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 442

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 205 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 264

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 265 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 324

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 325 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 384

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 385 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 442



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 14/83 (16%)

Query: 79  DGDDLEDE------------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           DG+ LEDE            EG+E++  + S         Q+   +A  +T DPV+ YL+
Sbjct: 94  DGELLEDEATEEPKAATEEPEGTENAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLK 151

Query: 127 EMGSIELLSREGEIAIAKRIEAG 149
           ++G + LL+ E E+ +AKRIEAG
Sbjct: 152 QIGKVPLLNAEQEVELAKRIEAG 174


>gi|159899067|ref|YP_001545314.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159892106|gb|ABX05186.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 386

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 149 ARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWW 208

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V RT+ ++   ++REPTPEEIA+ + +    V
Sbjct: 209 IRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHKLQQTMQREPTPEEIAEAMGITASKV 268

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P+D+A    LRE    VL  L  R
Sbjct: 269 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRVSTPVDAAAMTMLREQIEEVLQKLPER 328

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 329 ERKIIQLRYGLKDGRYRTLEEVGLEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 386



 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 63/120 (52%), Gaps = 5/120 (4%)

Query: 33  KMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K+++LA + +  +  E++ + LP  E + E +E     +   GI VVD D+  +    + 
Sbjct: 4   KLLELAAKNQNRIKREDILSVLPEPETNIEALESLYEQIEEAGIEVVDADEAPNVADLDL 63

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            LDL S             D +D + DDPVRMYL+E+G + LL+   E+ +AK++E   A
Sbjct: 64  DLDLDSDHDLDGAL----PDLSDIALDDPVRMYLQEIGQVPLLTAAEEVDLAKKMEVAHA 119


>gi|288923254|ref|ZP_06417393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288345398|gb|EFC79788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 400

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 130/271 (47%), Positives = 194/271 (71%), Gaps = 8/271 (2%)

Query: 418 VETGISISE----FRHIVSMVRKG----ECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +E G+  SE     R I   +R+     E +  IAK+++VEANLRLV+S+AK+Y  RG+ 
Sbjct: 129 IEAGLFASEKLAATRKISPQLRQDLQAVEQDGQIAKRKLVEANLRLVVSIAKRYVGRGML 188

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QA+TR++ADQ  TIRIPVHM + +
Sbjct: 189 LLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAVTRALADQGRTIRIPVHMAETV 248

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +KV R  R++  ++ REP+PEEI  ++ +    V ++LKI + P++LETPIG E  S LG
Sbjct: 249 NKVTRIQRQLLQELGREPSPEEIGTQIDLTAHKVEEILKIAQTPVALETPIGAEQDSQLG 308

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED +A++P ++A    L++    VL +L  RE++V+++RFG+      TLE++G++F
Sbjct: 309 DFIEDDDAIAPFEAASSVLLQKHIESVLHTLPAREKKVIQLRFGLTDGQPRTLEQIGREF 368

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            + +ERIRQIE++ + KL HP+RS++LR +L
Sbjct: 369 GIPQERIRQIESRTLAKLSHPARSQRLRDYL 399



 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/119 (31%), Positives = 61/119 (51%), Gaps = 17/119 (14%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDDLEDEEGSE 90
           + I   ++ G+VT E++   L   E+  E  +  + +L++ GI V+D   DD+ D  G  
Sbjct: 29  EFITRGKENGFVTPEDVATALLDAELPPENSDAVLRLLADDGIEVLDEIDDDVPDPPGRR 88

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              +  +SA  +S               DPVRMYL+ +G + LL+   E+ +AKRIEAG
Sbjct: 89  RGPEEHASAMPTS---------------DPVRMYLKTIGRVRLLTAAEEVDLAKRIEAG 132


>gi|256784755|ref|ZP_05523186.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 492

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 255 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 314

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 315 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 374

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 375 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 434

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 435 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 492



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 14/83 (16%)

Query: 79  DGDDLEDE------------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           DG+ LEDE            EG+E++  + S         Q+   +A  +T DPV+ YL+
Sbjct: 144 DGELLEDEATEEPKAATEEPEGTENAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLK 201

Query: 127 EMGSIELLSREGEIAIAKRIEAG 149
           ++G + LL+ E E+ +AKRIEAG
Sbjct: 202 QIGKVPLLNAEQEVELAKRIEAG 224


>gi|50726933|gb|AAT81163.1| principal sigma factor [Streptomyces ansochromogenes]
          Length = 440

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 203 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 262

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 263 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 322

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 323 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQPDSVLDTLSER 382

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 383 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 440



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 135 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 172


>gi|218295160|ref|ZP_03495996.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
 gi|218244363|gb|EED10888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
          Length = 439

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 142/259 (54%), Positives = 190/259 (73%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 185 ELKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 240

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 241 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGR 300

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EP+ EEIA+ +    +   V + LKI +EP+SLETPIGDE  S  GDFI D+N  SP+++
Sbjct: 301 EPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEA 360

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 361 AAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 420

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FLD
Sbjct: 421 LRKLKYHESRTRKLRDFLD 439



 Score = 41.2 bits (95), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 25/34 (73%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ST DPVR YL E+G + LL+ E EI +A+++E G
Sbjct: 92  STSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG 125


>gi|153306|gb|AAA26763.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450078|prf||1920369B RNA polymerase:SUBUNIT=sigma
          Length = 525

 Score =  280 bits (715), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 288 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 347

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 348 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 407

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 408 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 467

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 468 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 525



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 224 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 257


>gi|239982743|ref|ZP_04705267.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 491

 Score =  280 bits (715), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 254 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 313

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 314 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 373

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 374 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 433

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 434 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 491



 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 186 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 223


>gi|311898773|dbj|BAJ31181.1| putative RNA polymerase major sigma factor [Kitasatospora setae
           KM-6054]
          Length = 541

 Score =  279 bits (714), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 304 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 363

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 364 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 423

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 424 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 483

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 484 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 541



 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 240 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 273


>gi|224372659|ref|YP_002607031.1| RNA polymerase sigma factor RpoD [Nautilia profundicola AmH]
 gi|223588464|gb|ACM92200.1| rna polymerase sigma factor [Nautilia profundicola AmH]
          Length = 604

 Score =  279 bits (714), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 129/263 (49%), Positives = 194/263 (73%), Gaps = 1/263 (0%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+   +   I+  +++G+   + AK++M  ANLRLV+S+AKKYTNRGL FLDLIQEGNIG
Sbjct: 342 GMEPEKLEVILEQLKRGKKITTEAKEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIG 401

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAI+R+IADQ+ T+RIP+HM + I+++ +  R+  
Sbjct: 402 LMKAIDKFEFEKGYKFSTYATWWIRQAISRAIADQARTVRIPIHMIENINQINKIVRKYV 461

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  +EP+ E IAK++ MP+E V+++LKI+KEP+SLE P+G+E+    GDFIEDK   +P
Sbjct: 462 QEEGKEPSLEVIAKEMKMPIEKVKQILKISKEPVSLEAPVGEEEDGKFGDFIEDKTFTNP 521

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQI 659
            +  +  +LR+    +L  L  RE  V++MRFG+  + ++ TLEE+GK   VTRER+RQI
Sbjct: 522 YEEVVNEDLRKHIEEILEQLNERERAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQI 581

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           E+ AI+KL+HP+  K L+++++ 
Sbjct: 582 ESSAIKKLRHPNIGKFLKNYIES 604



 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 38/58 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL ++ EI I +RI+ G  +++ ++C  P     ++ +++ L
Sbjct: 96  SDSPVRMYLREMGHIPLLDKDEEIEIFRRIQLGEEIILDAICSIPFLIDLVLKYKEPL 153


>gi|320008126|gb|ADW02976.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 515

 Score =  279 bits (714), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 278 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 338 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 397

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 398 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 457

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 458 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 515



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 214 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 247


>gi|290956933|ref|YP_003488115.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
 gi|260646459|emb|CBG69556.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
          Length = 516

 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 279 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 338

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 339 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 398

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 399 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 458

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 459 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 516



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 211 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 248


>gi|329940007|ref|ZP_08289289.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329300833|gb|EGG44729.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 512

 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 275 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 334

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 335 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 394

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 395 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 454

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 455 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 512



 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 207 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 244


>gi|302554625|ref|ZP_07306967.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472243|gb|EFL35336.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 513

 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 276 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 335

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 336 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 395

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 396 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 455

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 456 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 513



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 208 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 245


>gi|256825489|ref|YP_003149449.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
 gi|256688882|gb|ACV06684.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
          Length = 594

 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 357 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 416

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 417 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 476

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 477 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPSDAVSFTLLQEQLHSVLDTLSER 536

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 537 EAGVVSMRFGLADGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 594



 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T D V+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 293 ATADAVKDYLKQIGKVALLNAEQEVDLAKRIEAG 326


>gi|134098380|ref|YP_001104041.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006918|ref|ZP_06564891.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133911003|emb|CAM01116.1| RNA polymerase major sigma factor [Saccharopolyspora erythraea NRRL
           2338]
          Length = 467

 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/249 (54%), Positives = 183/249 (73%), Gaps = 4/249 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  
Sbjct: 223 IVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTK 278

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+
Sbjct: 279 GYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEEL 338

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++ 
Sbjct: 339 AKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQ 398

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSR
Sbjct: 399 LQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSR 458

Query: 673 SKKLRSFLD 681
           S+ LR +LD
Sbjct: 459 SQVLRDYLD 467



 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE+G  DS D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +A
Sbjct: 131 EDEDGKADS-DFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELA 189

Query: 144 KRIEAG 149
           KRIEAG
Sbjct: 190 KRIEAG 195


>gi|297156708|gb|ADI06420.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 515

 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 278 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 338 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 397

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 398 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 457

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 458 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 515



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 210 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 247


>gi|297202863|ref|ZP_06920260.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297148238|gb|EDY59236.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 512

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 275 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 334

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 335 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 394

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 395 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 454

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 455 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 512



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 211 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 244


>gi|237751154|ref|ZP_04581634.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
 gi|229373599|gb|EEO23990.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
          Length = 632

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 134/258 (51%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I+  +++G+  +  AK +M  +NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA 
Sbjct: 375 KLKEILEQIKRGKRISDTAKTKMSRSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAV 434

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++   YKFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+K+    R+ + +   
Sbjct: 435 DKFEYRKQYKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINKIKNLMRKHAQEKGE 494

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           E   E IA ++ + V+ V+ V+KITKEPISLE PIG++D    GDF+EDK+ +S +D  +
Sbjct: 495 ELDVESIANQVGLSVDKVKNVIKITKEPISLEAPIGNDDDGKFGDFVEDKSTMSSMDIML 554

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + +LRE    VL  L  RE+ V++MRFG+  + +D TLEE+GK   VTRER+RQIE+ AI
Sbjct: 555 KEDLREQIDNVLDQLNEREKAVIKMRFGLLEDESDRTLEEIGKALNVTRERVRQIESSAI 614

Query: 665 RKLKHPSRSKKLRSFLDG 682
           +KLKHP   ++LR +L G
Sbjct: 615 KKLKHPRIGRQLRQYLGG 632



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 38/58 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LLS+E EI ++K +E G  +++ ++C  P     +  ++D L
Sbjct: 107 SDSPVRMYLREMGQIPLLSKEEEINLSKDMEKGEDIIIDAICSVPYLIDFIYDYKDAL 164


>gi|271968332|ref|YP_003342528.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270511507|gb|ACZ89785.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 561

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 324 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 383

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A++L M  E V
Sbjct: 384 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKV 443

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G+E  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 444 VEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHSVLDTLSER 503

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 504 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 561



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 255 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 292


>gi|328885546|emb|CCA58785.1| RNA polymerase sigma factor RpoD [Streptomyces venezuelae ATCC
           10712]
          Length = 567

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 330 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 389

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 390 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 449

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 450 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 509

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 510 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 567



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 266 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 299


>gi|302542036|ref|ZP_07294378.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302459654|gb|EFL22747.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 502

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 265 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 324

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 325 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 384

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 385 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 444

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 445 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 502



 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 197 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 234


>gi|72162538|ref|YP_290195.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71916270|gb|AAZ56172.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thermobifida
           fusca YX]
          Length = 616

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 379 AKKHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 438

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 439 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 498

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P ++     L+E    VL +L+ R
Sbjct: 499 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIQPGEAVSFTLLQEQLHSVLDTLSER 558

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 559 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 616



 Score = 42.4 bits (98), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 314 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 347


>gi|72161271|ref|YP_288928.1| sigma-70 factor [Thermobifida fusca YX]
 gi|71915003|gb|AAZ54905.1| sigma-70 factor [Thermobifida fusca YX]
          Length = 388

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 132/254 (51%), Positives = 194/254 (76%), Gaps = 5/254 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +VR+G+    +AK+ ++E+NLRLV+SVAK+Y  RGL  LDLIQEGN+GL++A E
Sbjct: 139 FEDLNELVREGK----LAKRRLIESNLRLVVSVAKRYLGRGLALLDLIQEGNLGLIRAVE 194

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + I+++ RT RR+  ++ RE
Sbjct: 195 KFDYTRGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVESINRLARTRRRLHQELGRE 254

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E++++L +  + V ++ ++++EPISL TPIG+ED++  GDFIED +AV P+++A  
Sbjct: 255 PTLHELSRELNVDHDRVVEIHRVSQEPISLHTPIGEEDSA-FGDFIEDTDAVPPVEAAAF 313

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++   +VL  L+ RE+RV+ +RFG+     HTLEEVG++F VTRERIRQIE+K + K
Sbjct: 314 VMLQDQLAQVLGGLSEREQRVITLRFGLEDGKPHTLEEVGRKFGVTRERIRQIESKTLAK 373

Query: 667 LKHPSRSKKLRSFL 680
           L+ PSR++ LR +L
Sbjct: 374 LRQPSRARILRDYL 387


>gi|88856913|ref|ZP_01131565.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88813881|gb|EAR23751.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 454

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 217 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 276

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE++++L M  E V
Sbjct: 277 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 336

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L++    +L SL+ R
Sbjct: 337 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDTEAVVPADAVGFTMLQKQLESLLDSLSER 396

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 397 EAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 454



 Score = 37.4 bits (85), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +A RIEAG
Sbjct: 151 ATADPVKDYLKQIGKVALLNAAQEVELAMRIEAG 184


>gi|229820409|ref|YP_002881935.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
 gi|229566322|gb|ACQ80173.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
          Length = 499

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 262 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 321

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 322 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 381

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 382 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSER 441

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 442 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 499



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 198 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 231


>gi|119717187|ref|YP_924152.1| RNA polymerase sigma factor [Nocardioides sp. JS614]
 gi|119537848|gb|ABL82465.1| RNA polymerase, sigma 70 subunit, RpoD [Nocardioides sp. JS614]
          Length = 495

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 258 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 317

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 318 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 377

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 378 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHAVLDTLSER 437

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 438 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 495



 Score = 41.6 bits (96), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 194 ATADPVKDYLKQIGKVPLLNAEMEVELAKRIEAG 227


>gi|156740438|ref|YP_001430567.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231766|gb|ABU56549.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 405

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 132/242 (54%), Positives = 178/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A++ +++ANLRLV+S+AKKY  RG+  LDLIQEGNIGLM+A EKFD+  GYKFSTY
Sbjct: 164 EGQAARERLIQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRKGYKFSTY 223

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR IADQS TIR+PVH+ + I++V+RT+ R+     R+PTP+EIA +L +P
Sbjct: 224 ATWWIRQAITRVIADQSRTIRLPVHVGETINRVMRTSNRIQQTTGRDPTPDEIALELGIP 283

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE VR+VL+  ++ ISLETPIG E  S L DFIED    +P++SA    LRE     L  
Sbjct: 284 VEKVRRVLEAARQTISLETPIGPEGDSVLADFIEDGKGATPMESASSHILREQIDSALEK 343

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE R++++R+G+      TLEEVG++F +TRERIRQIEA+ +RKL+HP   + LR +
Sbjct: 344 LPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLRKLRHPHYGRGLRGY 403

Query: 680 LD 681
           L+
Sbjct: 404 LE 405



 Score = 41.6 bits (96), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             DDPVR+YLRE+G + LL+ + EI +A+++E G
Sbjct: 105 GVDDPVRVYLREIGRVNLLTAQEEIMLAQQVERG 138


>gi|269794902|ref|YP_003314357.1| RNA polymerase sigma-70 subunit RpoD [Sanguibacter keddieii DSM
           10542]
 gi|269097087|gb|ACZ21523.1| RNA polymerase, sigma 70 subunit, RpoD [Sanguibacter keddieii DSM
           10542]
          Length = 516

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 279 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 338

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 339 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 398

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 399 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHQVLDTLSER 458

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 459 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 516



 Score = 41.6 bits (96), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 214 ATADPVKDYLKQIGKVALLNAEQEVDLAKRIEAG 247


>gi|94984583|ref|YP_603947.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94554864|gb|ABF44778.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 532

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 140/245 (57%), Positives = 185/245 (75%), Gaps = 3/245 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTY
Sbjct: 288 DGAAARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTY 347

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ REPT EEIA+ +   
Sbjct: 348 ATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREPTYEEIAEAMGPG 407

Query: 560 VEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+D+A +  L E   + L
Sbjct: 408 WDAAKVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVDNAAKTLLSEELEKAL 467

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKL 676
           + LT RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KL
Sbjct: 468 SKLTEREALVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLKYHESRTRKL 527

Query: 677 RSFLD 681
           R FLD
Sbjct: 528 RDFLD 532



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++DPVR YL E+G + LL+ E EIA+A+RIE G
Sbjct: 228 SNDPVRQYLHEIGRVPLLTLEEEIALARRIEEG 260


>gi|328950970|ref|YP_004368305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451294|gb|AEB12195.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
          Length = 477

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 141/257 (54%), Positives = 187/257 (72%), Gaps = 7/257 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + + R GE    +A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EK
Sbjct: 225 KRYLHLARDGE----LARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEK 280

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++   YKFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  +  REP
Sbjct: 281 FEYKRRYKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQEKGREP 340

Query: 548 TPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + EEIA+ +    +   V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+D+A 
Sbjct: 341 SYEEIAEAMGPGWDAKRVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDAAA 400

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA+R
Sbjct: 401 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALR 460

Query: 666 KLK-HPSRSKKLRSFLD 681
           KLK H SR++KLR FLD
Sbjct: 461 KLKYHESRTRKLRDFLD 477



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 34/98 (34%), Positives = 49/98 (50%), Gaps = 9/98 (9%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
           D+   E  E+ + +L   GI+V+     EDEE  E  L+     S     +  R      
Sbjct: 79  DDAFEESYEEVIDLLEGEGIDVLS----EDEELEEPILEGEDDLSEDEPAIATRV----- 129

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           S  DPVR YL E+G + LL+ E EI +A+R+E G A +
Sbjct: 130 SISDPVRQYLHEIGQVPLLTLEEEIDLARRVEEGEAAI 167


>gi|281412780|ref|YP_003346859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
 gi|281373883|gb|ADA67445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 407

 Score =  278 bits (711), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 181/248 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK++++ +NLRLV+S+AK+Y  RGL F DLIQEGNIGL+KA EKFDW  
Sbjct: 152 LARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDWRK 211

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R    K   EP+ EE+
Sbjct: 212 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLNRLRREYYQKHGEEPSIEEL 271

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  P E ++++L+  KE ISLE+PIG+++ S + DF+ D +  SP   A++  +RE 
Sbjct: 272 AKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSIEDFVADDSIASPKKEAMRMLMREE 331

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 332 LEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 391

Query: 673 SKKLRSFL 680
           SK L+S L
Sbjct: 392 SKYLKSLL 399



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 63/120 (52%), Gaps = 6/120 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           KK+I L +++GY+T E+++   PPD  +  +  +E     L   GIN+V+ +  E+E  +
Sbjct: 44  KKLISLGKKKGYITYEDIDKAFPPDFEDFDTNLIERIHEELEKHGINIVENEPEEEEISA 103

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S D             +  DS++    D ++MYL+E+G I LL+   E  +A+R + G
Sbjct: 104 --SSDEQELEELLERESPEIHDSSN--VRDSIKMYLKEIGKIPLLTPAQERELARRAQMG 159


>gi|55980501|ref|YP_143798.1| RNA polymerase pricipal sigma factor RpoD [Thermus thermophilus
           HB8]
 gi|209447478|pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447484|pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|55771914|dbj|BAD70355.1| RNA polymerase pricipal sigma factor (RpoD) [Thermus thermophilus
           HB8]
          Length = 423

 Score =  278 bits (711), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 143/259 (55%), Positives = 190/259 (73%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 169 EHKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 224

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 225 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGR 284

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EPT EEIA+ +    +   V + LKI +EP+SLETPIGDE  S  GDFI D++  SP+D+
Sbjct: 285 EPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDA 344

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 345 ATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKA 404

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FLD
Sbjct: 405 LRKLKYHESRTRKLRDFLD 423


>gi|46198472|ref|YP_004139.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
 gi|21730342|pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730348|pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|49259060|pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259066|pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|78101162|pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101168|pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101224|pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101230|pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101236|pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101242|pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101248|pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101254|pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101260|pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101266|pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101762|pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101768|pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|83754377|pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754383|pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|210061069|pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061075|pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|4239959|dbj|BAA74758.1| principal sigma factor [Thermus thermophilus]
 gi|46196094|gb|AAS80512.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
          Length = 423

 Score =  278 bits (711), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 143/259 (55%), Positives = 190/259 (73%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 169 EHKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 224

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 225 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGR 284

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EPT EEIA+ +    +   V + LKI +EP+SLETPIGDE  S  GDFI D++  SP+D+
Sbjct: 285 EPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDA 344

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 345 ATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKA 404

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FLD
Sbjct: 405 LRKLKYHESRTRKLRDFLD 423


>gi|326332703|ref|ZP_08198965.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
 gi|325949484|gb|EGD41562.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
          Length = 530

 Score =  278 bits (711), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 293 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 352

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 353 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 412

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 413 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHAVLDTLSER 472

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 473 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 530



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 229 ATADPVKDYLKQIGKVPLLNAEMEVELAKRIEAG 262


>gi|148270473|ref|YP_001244933.1| RpoD family RNA polymerase sigma factor [Thermotoga petrophila
           RKU-1]
 gi|170289132|ref|YP_001739370.1| RpoD family RNA polymerase sigma factor [Thermotoga sp. RQ2]
 gi|147736017|gb|ABQ47357.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga
           petrophila RKU-1]
 gi|170176635|gb|ACB09687.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga sp. RQ2]
          Length = 407

 Score =  278 bits (711), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 181/248 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK++++ +NLRLV+S+AK+Y  RGL F DLIQEGNIGL+KA EKFDW  
Sbjct: 152 LARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDWRK 211

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R    K   EP+ EE+
Sbjct: 212 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLNRLRREYYQKHGEEPSIEEL 271

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  P E ++++L+  KE ISLE+PIG+++ S + DF+ D +  SP   A++  +RE 
Sbjct: 272 AKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSIEDFVADDSIASPKKEAMRMLMREE 331

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 332 LEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 391

Query: 673 SKKLRSFL 680
           SK L+S L
Sbjct: 392 SKYLKSLL 399



 Score = 45.4 bits (106), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 61/120 (50%), Gaps = 6/120 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           KK+I L +++GY+T E+++   PPD  +  +  +E     L   GIN+V+ +  E+E   
Sbjct: 44  KKLISLGKKKGYITYEDIDKAFPPDFEDFDTNLIERIHEELEKHGINIVESESEEEEMSV 103

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
               D             +  DS++    D ++MYL+E+G I LL+   E  +A+R + G
Sbjct: 104 PG--DEQELEELLERESPEIHDSSN--VRDSIKMYLKEIGKIPLLTPAQERELARRAQMG 159


>gi|5030433|gb|AAC44889.2| sigma 70-type sigma factor SigA [Thermotoga maritima]
          Length = 407

 Score =  278 bits (711), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 181/248 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK++++ +NLRLV+S+AK+Y  RGL F DLIQEGNIGL+KA EKFDW  
Sbjct: 152 LARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDWRK 211

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R    K   EP+ EE+
Sbjct: 212 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLNRLRREYYQKHGEEPSIEEL 271

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  P E ++++L+  KE ISLE+PIG+++ S + DF+ D +  SP   A++  +RE 
Sbjct: 272 AKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSIEDFVADDSIASPKKEAMRMLMREE 331

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 332 LEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 391

Query: 673 SKKLRSFL 680
           SK L+S L
Sbjct: 392 SKYLKSLL 399



 Score = 46.2 bits (108), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 62/120 (51%), Gaps = 6/120 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           KK+I L +++GY+T E+++   PPD     +  +E     L   GIN+V+ +  E+E  +
Sbjct: 44  KKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIVENEPEEEEISA 103

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S D             +  DS++    D ++MYL+E+G I LL+   E  +A+R + G
Sbjct: 104 --SSDEQELEELLEKESPEIHDSSN--VRDSIKMYLKEIGKIPLLTPAQERELARRAQMG 159


>gi|331696864|ref|YP_004333103.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951553|gb|AEA25250.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 461

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 139/267 (52%), Positives = 192/267 (71%), Gaps = 6/267 (2%)

Query: 417 SVETGISISE--FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++E+G  +S    R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLI
Sbjct: 199 AIESGEKVSPQLRRDLRWIVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLI 254

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R
Sbjct: 255 QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGR 314

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R +   + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED
Sbjct: 315 IQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIED 374

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             AV  +D+     L++    VLA+L+ RE  V+R+RFG+      TL+E+G+ + VTRE
Sbjct: 375 SEAVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRE 434

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 435 RIRQIESKTMSKLRHPSRSQVLRDYLD 461



 Score = 44.7 bits (104), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 142 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 189


>gi|302557983|ref|ZP_07310325.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302475601|gb|EFL38694.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 509

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 331

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 332 ICQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 391

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 392 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 451

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 452 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 509



 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 29/38 (76%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 204 AAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 241


>gi|15644200|ref|NP_229250.1| RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
 gi|6831649|sp|P77994|RPOD_THEMA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|4982015|gb|AAD36519.1|AE001796_11 RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
          Length = 399

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 181/248 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK++++ +NLRLV+S+AK+Y  RGL F DLIQEGNIGL+KA EKFDW  
Sbjct: 144 LARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDWRK 203

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R    K   EP+ EE+
Sbjct: 204 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLNRLRREYYQKHGEEPSIEEL 263

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  P E ++++L+  KE ISLE+PIG+++ S + DF+ D +  SP   A++  +RE 
Sbjct: 264 AKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSIEDFVADDSIASPKKEAMRMLMREE 323

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 324 LEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 383

Query: 673 SKKLRSFL 680
           SK L+S L
Sbjct: 384 SKYLKSLL 391



 Score = 46.2 bits (108), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 62/120 (51%), Gaps = 6/120 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           KK+I L +++GY+T E+++   PPD     +  +E     L   GIN+V+ +  E+E  +
Sbjct: 36  KKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIVENEPEEEEISA 95

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S D             +  DS++    D ++MYL+E+G I LL+   E  +A+R + G
Sbjct: 96  --SSDEQELEELLEKESPEIHDSSN--VRDSIKMYLKEIGKIPLLTPAQERELARRAQMG 151


>gi|302537866|ref|ZP_07290208.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302446761|gb|EFL18577.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 481

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 244 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATWW 303

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQS TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 304 IRQAITRAMADQSRTIRIPVHMVEIINKLARVQRQMLQDLGREPTPEELGKELDMTPEKV 363

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E    +L +L+ R
Sbjct: 364 IEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTFLQEQLQSILGTLSER 423

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MR+G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 424 EAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 481



 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+ +G + LL+ E E+ +AKRIEAG
Sbjct: 180 ATADPVKDYLKLIGKVPLLNAEQEVELAKRIEAG 213


>gi|152965499|ref|YP_001361283.1| RNA polymerase sigma factor [Kineococcus radiotolerans SRS30216]
 gi|151360016|gb|ABS03019.1| RNA polymerase, sigma 70 subunit, RpoD family [Kineococcus
           radiotolerans SRS30216]
          Length = 502

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 135/238 (56%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 265 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 324

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 325 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 384

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 385 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 444

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 445 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 502



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 201 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 234


>gi|320334918|ref|YP_004171629.1| RpoD subfamily RNA polymerase sigma-70 factor [Deinococcus
           maricopensis DSM 21211]
 gi|319756207|gb|ADV67964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           maricopensis DSM 21211]
          Length = 525

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 139/245 (56%), Positives = 185/245 (75%), Gaps = 3/245 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTY
Sbjct: 281 DGAAARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTY 340

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ REPT EEIA+ +   
Sbjct: 341 ATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREPTYEEIAEAMGPG 400

Query: 560 VEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+++A +  L E   + L
Sbjct: 401 WDAAKVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVENAAKTLLSEELEKAL 460

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKL 676
           + LT RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KL
Sbjct: 461 SKLTEREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLKYHESRTRKL 520

Query: 677 RSFLD 681
           R FLD
Sbjct: 521 RDFLD 525



 Score = 42.0 bits (97), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++DPVR YL E+G + LL+ E EI++A+RIE G
Sbjct: 222 SNDPVRQYLHEIGRVPLLTLEEEISLARRIEEG 254


>gi|320104559|ref|YP_004180150.1| RNA polymerase sigma-70 subunit RpoD [Isosphaera pallida ATCC
           43644]
 gi|319751841|gb|ADV63601.1| RNA polymerase, sigma 70 subunit, RpoD [Isosphaera pallida ATCC
           43644]
          Length = 592

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 181/238 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K++W  G+KFSTYA WW
Sbjct: 351 AKRKLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEWRRGFKFSTYATWW 410

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + + K+    +++  +  REPT EE A+   + +E  
Sbjct: 411 IRQAITRAIADQARTIRIPVHMIETMSKLRNVNKKLLQEKGREPTIEETARAANISIEET 470

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V+KI++ PISL+ P+G+ + S+ GDFIED  A +P++SA Q  L++   +VL +LT R
Sbjct: 471 RRVMKISRHPISLDRPVGESEDSYFGDFIEDTTAENPINSATQEMLKDKIDQVLKTLTYR 530

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  ++++R+G+G    +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RS++L  FL+
Sbjct: 531 EREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSRQLEGFLE 588



 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 74/168 (44%), Gaps = 41/168 (24%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGD- 81
            D  D+  K ++ L +++G++T+ ++N  LP D  S  ++++     L  +G+ V+  D 
Sbjct: 1   MDMLDEGLKALLDLGKRQGFLTMSQINEVLPDDAGSQPDRLDALFNTLEELGVEVLQRDE 60

Query: 82  ----------------------------------DLEDEEGSEDSLDLASSASNSSVFLQ 107
                                             D E +   +  LDL    S+  + L 
Sbjct: 61  EADGRIAPGDDLDDESDDLMADPEDLAAVHDHELDPESDADGDPGLDLEEPGSDLDLDLD 120

Query: 108 KRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                   D   R  DDPVRMYL +MG I LL+RE EI++A+RIE+ R
Sbjct: 121 GDLAVEDLDDMSRRIDDPVRMYLTQMGEIPLLTREQEISLAERIESTR 168


>gi|21466021|pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|11527292|gb|AAG36964.1|AF291720_1 sigma factor SigA [Thermus aquaticus]
          Length = 438

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 141/259 (54%), Positives = 190/259 (73%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 184 ELKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 239

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 240 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGR 299

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EP+ EEIA+ +    +   V + LKI +EP+SLETPIGDE  S  GDFI D+N  SP+++
Sbjct: 300 EPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEA 359

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 360 AAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 419

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FL+
Sbjct: 420 LRKLKYHESRTRKLRDFLE 438



 Score = 41.2 bits (95), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 25/34 (73%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ST DPVR YL E+G + LL+ E EI +A+++E G
Sbjct: 91  STSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG 124


>gi|153309|gb|AAA26764.1| principal sigma-like factor [Streptomyces aureofaciens]
          Length = 528

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATWW 350

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQS TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 351 IRQAITRAMADQSRTIRIPVHMVEIINKLARVQRQMLQDLGREPTPEELGKELDMTPEKV 410

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E    +L +L+ R
Sbjct: 411 IEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTFLQEQLQSILGTLSER 470

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MR+G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 471 EAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSRSQVLRGYLD 528



 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+ +G + LL+ E E+ +AKRIEAG
Sbjct: 227 ATADPVKDYLKLIGKVPLLNAEQEVELAKRIEAG 260


>gi|297559739|ref|YP_003678713.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844187|gb|ADH66207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 364

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 128/237 (54%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 126 AKRSLIEANLRLVVSIAKRYMGRGLLLLDLVQEGNLGLIRAVEKFDYGKGFKFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+KVVR   ++  ++ REP+ EEI+       + V
Sbjct: 186 IRQAITRAIADQARTIRIPVHMVETINKVVRVQHQLHQQLGREPSVEEISSAAGFVGQRV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +I +EP+SL++PIG+E+ S  GDFIED +AV+P+++A    L+E    +L  L+ R
Sbjct: 246 VEIQRIAREPVSLQSPIGEEE-SDFGDFIEDSDAVAPVEAAAFTVLQEQLGAILGGLSDR 304

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E R++R+RFG+     HTLEEVG++F VTRERIRQIEAK + KL+HPSR+  LR F+
Sbjct: 305 ERRIIRLRFGMADGHPHTLEEVGREFGVTRERIRQIEAKTLAKLRHPSRAGSLRDFI 361



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 60/125 (48%), Gaps = 21/125 (16%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           M++L    G V+  E+ + L   +   + ++  VA L+ +G+ V   +D     GSED  
Sbjct: 1   MVRLLPDTGPVSRGEVASALERLDAPPDYLDQAVAHLARIGVEVAGPED----TGSEDPG 56

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
            +A              D   RS  D VR+YLRE+G + LLS E E+ +AK +E G   +
Sbjct: 57  PVA--------------DGGRRSGSDLVRLYLREIGRVPLLSAEQEVELAKAVEVG---L 99

Query: 154 MASLC 158
            A  C
Sbjct: 100 YAQHC 104


>gi|269125851|ref|YP_003299221.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268310809|gb|ACY97183.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 559

 Score =  278 bits (710), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 322 AKAHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 381

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 382 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 441

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 442 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHSVLDTLSER 501

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 502 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 559



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 257 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 290


>gi|284031355|ref|YP_003381286.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810648|gb|ADB32487.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 442

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 205 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 264

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 265 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 324

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P ++     L+E    VL +L+ R
Sbjct: 325 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPAEAVSFTLLQEQLHAVLDTLSER 384

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 385 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 442



 Score = 42.0 bits (97), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 140 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 173


>gi|258645217|ref|ZP_05732686.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
 gi|260402567|gb|EEW96114.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
          Length = 388

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 144/271 (53%), Positives = 191/271 (70%), Gaps = 12/271 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECE---------ASIAKKEMVEANLRLVISVAKK 462
           EI +I + TG   S+   +  +V KG  +         A  AKK + +ANLRLV+S+AKK
Sbjct: 117 EIGAIKLLTG---SQEIELAKLVEKGSFDDATGRDKMAADEAKKALSDANLRLVVSIAKK 173

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  RGLQFLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIR+P
Sbjct: 174 YLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRVP 233

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R++  +  RE T EE+AK + + V  +R+V KI ++PISLETPIG+
Sbjct: 234 VHMVETINKLNRISRQLLQEKGREATNEELAKAMGVSVAKIREVKKIAQDPISLETPIGE 293

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED  A++P D+A    LRE    +L  LT RE +VL +RFG+      TL
Sbjct: 294 KEDSHLGDFIEDHEAIAPDDAAGSILLREQIDELLRELTDRERQVLELRFGLKDGRPRTL 353

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EEVGK F VTRERIRQIE KA+ KLK  ++S
Sbjct: 354 EEVGKYFDVTRERIRQIEGKALTKLKKSAKS 384



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + DDPV+MYL+E+G+I+LL+   EI +AK +E G
Sbjct: 106 NIDDPVKMYLKEIGAIKLLTGSQEIELAKLVEKG 139


>gi|328954372|ref|YP_004371706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454696|gb|AEB10525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 436

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 128/256 (50%), Positives = 186/256 (72%), Gaps = 1/256 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +   +R+ E E   A+ EM++ANLRLV+S+AKKY +RGL F DLIQEGN+GLMKA 
Sbjct: 182 EIKQLAKKIREKENEVVRARDEMIKANLRLVVSIAKKYLHRGLSFSDLIQEGNLGLMKAV 241

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            ++D+  GY+ ST+A WW++Q ITR+I D++ TIRIPVH+++  ++  R    +  ++ R
Sbjct: 242 TRYDYTTGYRLSTFASWWIRQTITRAIYDKTRTIRIPVHLQEIRNRCYRAFYDLLKELGR 301

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  +EIA++  +P + +  V  ++ EPISLETP+GDE    LGDFI +  A+SP DS I
Sbjct: 302 EPLLKEIAERSGVPEDKILVVTNLSDEPISLETPVGDEG-DRLGDFIRNDQAISPFDSII 360

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            + L E T  +L++LTPREE++++MRFGIG   +HTLEE+G++F V+RERIRQIE KA++
Sbjct: 361 SSELSEKTDAILSTLTPREEKIMKMRFGIGAEVEHTLEEIGREFKVSRERIRQIEKKALK 420

Query: 666 KLKHPSRSKKLRSFLD 681
           +LKHP+R   L  FL+
Sbjct: 421 RLKHPTRKATLEDFLE 436


>gi|148272828|ref|YP_001222389.1| RNA polymerase sigma factor [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830758|emb|CAN01698.1| RNA polymerase principal sigma factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 492

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 255 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 314

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE++++L M  E V
Sbjct: 315 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 374

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L++    +L SL+ R
Sbjct: 375 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDTEAVVPADAVGFTMLQKQLESLLDSLSER 434

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 435 EAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 492


>gi|15807631|ref|NP_294640.1| RNA polymerase sigma-A factor [Deinococcus radiodurans R1]
          Length = 360

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 139/245 (56%), Positives = 183/245 (74%), Gaps = 3/245 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTY
Sbjct: 116 DGAAARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTY 175

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T EEIA+ +   
Sbjct: 176 ATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREATHEEIAEAMGPG 235

Query: 560 VEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+D+A +  L E   + L
Sbjct: 236 WDAAKVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVDNAAKTLLSEELEKAL 295

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKL 676
             LT RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KL
Sbjct: 296 GKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLKYHESRTRKL 355

Query: 677 RSFLD 681
           R FLD
Sbjct: 356 RDFLD 360



 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++DPVR YL E+G + LL+ E EIA+A+RIE G
Sbjct: 57  SNDPVRQYLHEIGRVSLLTLEEEIALARRIEEG 89


>gi|21466008|pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466014|pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
          Length = 332

 Score =  277 bits (709), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 141/259 (54%), Positives = 190/259 (73%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 78  ELKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 133

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 134 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGR 193

Query: 546 EPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EP+ EEIA+ +      + V + LKI +EP+SLETPIGDE  S  GDFI D+N  SP+++
Sbjct: 194 EPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEA 253

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 254 AAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 313

Query: 664 IRKLK-HPSRSKKLRSFLD 681
           +RKLK H SR++KLR FL+
Sbjct: 314 LRKLKYHESRTRKLRDFLE 332



 Score = 39.3 bits (90), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 24/33 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVR YL E+G + LL+ E EI +A+++E G
Sbjct: 1   TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG 33


>gi|254382161|ref|ZP_04997522.1| sigma factor [Streptomyces sp. Mg1]
 gi|194341067|gb|EDX22033.1| sigma factor [Streptomyces sp. Mg1]
          Length = 416

 Score =  277 bits (708), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 179 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATWW 238

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQS TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 239 IRQAITRAMADQSRTIRIPVHMVEIINKLARVQRQMLQDLGREPTPEELGKELDMTPEKV 298

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E    +L +L+ R
Sbjct: 299 IEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTFLQEQLQSILGTLSER 358

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MR+G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 359 EAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 416



 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+ +G + LL+ E E+ +AKRIEAG
Sbjct: 115 ATADPVKDYLKLIGKVPLLNAEQEVELAKRIEAG 148


>gi|37522141|ref|NP_925518.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35213141|dbj|BAC90513.1| principal RNA polymerase sigma factor [Gloeobacter violaceus PCC
           7421]
          Length = 400

 Score =  277 bits (708), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 139/277 (50%), Positives = 196/277 (70%), Gaps = 8/277 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D + +   E++  +   GI+  +FR  ++  R+       AK +MV++NLRLV+S+AKKY
Sbjct: 131 DQVTESEQELRRWAEAAGIAYEQFRDRIAYGRR-------AKDKMVQSNLRLVVSIAKKY 183

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 184 MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 243

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 244 HLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 303

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 304 EDSRLGDFIE-ADGETPEDKVAKNLLREDLEAVLNTLSPRERDVLRLRYGLDDGRMKTLE 362

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 363 EIGQLFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 399


>gi|184201082|ref|YP_001855289.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
 gi|183581312|dbj|BAG29783.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
          Length = 572

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 335 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 394

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 395 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMTPEKV 454

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 455 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 514

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 515 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 572



 Score = 38.9 bits (89), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A RIEAG
Sbjct: 270 ATADPVKDYLKQIGKVALLNAEQEVDLALRIEAG 303


>gi|323359909|ref|YP_004226305.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323276280|dbj|BAJ76425.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 436

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 199 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 258

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE++++L M  E V
Sbjct: 259 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 318

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+     +L SL+ R
Sbjct: 319 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDTEAVVPADAVGFTMLQRQLESLLDSLSER 378

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 379 EAGVIRMRFGLGDGQPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 436



 Score = 37.4 bits (85), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +A RIEAG
Sbjct: 133 ATADPVKDYLKQIGKVPLLNAAEEVELAMRIEAG 166


>gi|324997280|ref|ZP_08118392.1| RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 469

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 136/254 (53%), Positives = 185/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 220 RDLRWIVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 275

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 276 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 335

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 336 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 395

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    VLA+L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 396 LLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 455

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 456 RHPSRSQVLRDYLD 469



 Score = 45.4 bits (106), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 34/58 (58%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 140 SADFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 197


>gi|297562250|ref|YP_003681224.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296846698|gb|ADH68718.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 571

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 334 AKKHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 393

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A++L M  E V
Sbjct: 394 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKV 453

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P ++     L+E    VL +L+ R
Sbjct: 454 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIQPGEAVSFTLLQEQLHSVLDTLSER 513

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 514 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 571



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 28/37 (75%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 266 AAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 302


>gi|84495969|ref|ZP_00994823.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
 gi|84382737|gb|EAP98618.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
          Length = 546

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 309 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 368

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 369 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAIELDMTPEKV 428

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 429 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 488

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 489 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQALRDYLD 546



 Score = 42.0 bits (97), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 245 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 278


>gi|50954703|ref|YP_061991.1| RNA polymerase sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50951185|gb|AAT88886.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 440

 Score =  277 bits (708), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 203 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 262

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE++K+L M  E V
Sbjct: 263 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSKELDMTPEKV 322

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L++    +L SL+ R
Sbjct: 323 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDIEAVVPADAVGFTMLQKQLESLLDSLSER 382

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 383 EAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 440


>gi|296127158|ref|YP_003634410.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296018974|gb|ADG72211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 587

 Score =  277 bits (708), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 161/371 (43%), Positives = 223/371 (60%), Gaps = 10/371 (2%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           +KE +VKL+  + LN+  ID + E+L     RI   E    +L + Y  +   F   ++ 
Sbjct: 222 VKENIVKLLTKVRLNRMEIDRIAEKLKFYLHRINQIEEYFEKLKKRYYKEISDFENYYKE 281

Query: 377 RELDPH--WVSYAKDF---PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            E      ++    +F   PE      +   + S  K +  +  I  E  I        V
Sbjct: 282 IESGNKDIYIRLVDEFNITPEA-----IEAVITSFHKAQVRMADIYDEVRIDKETLVEWV 336

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     + + AK  +V+ANLRLVI++AKKY NRGL F DL+QEGNIGL+KA +KF++ 
Sbjct: 337 RKIDSARRKIAQAKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYK 396

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R  R+   +  REP+ +E
Sbjct: 397 KGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVQRVLRQYMQQHGREPSIQE 456

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IAK L  P   V+ V  + K+P+SL  PIGDE+ + LG+ IEDK   SP +      LR+
Sbjct: 457 IAKALGWPESRVKSVRNVAKDPVSLNAPIGDEEDTILGELIEDKEFESPQNITTFKILRK 516

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L SL  RE++V+RMRFG+     HTLEEVG  F VTRERIRQIEAKAIR+L+  S
Sbjct: 517 QIDSILDSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAIRRLRAQS 576

Query: 672 RSKKLRSFLDG 682
           + K+L+ FLD 
Sbjct: 577 KKKELKDFLDS 587



 Score = 47.0 bits (110), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 33/161 (20%), Positives = 82/161 (50%), Gaps = 11/161 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLED 85
           +++  +K+++      Y+T +E+N  +  D + ++ M+    +L+   I +V D  + E 
Sbjct: 13  NNEKIRKLLEKGNANKYLTFKEINGAI--DNMDTDVMDILFQLLNARKIVIVEDKREFES 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +++ +D      +++ F+       +   DDP+R+YL+E+G + LL+ + E+  +K+
Sbjct: 71  LSKNQNKID------DTAKFIHVEDKVGN--NDDPIRLYLKEIGKVSLLTHDDEVDYSKK 122

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           IE+G + +   +  + L    ++     +  G   + EI++
Sbjct: 123 IESGESEIENIILNTHLVVGEVLNTIKNVQTGKVSIHEILE 163


>gi|289642419|ref|ZP_06474565.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507764|gb|EFD28717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 425

 Score =  276 bits (707), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 130/254 (51%), Positives = 185/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G      AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EK
Sbjct: 176 RDLQTLVRDGHA----AKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEK 231

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REP
Sbjct: 232 FDYAKGYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREP 291

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A   
Sbjct: 292 TDEELALELDMPIEQVVELRRYAQDTVSLETAVGDDGDSVLGDFIEDADATSPADAASYG 351

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +++    VL SLTPRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L
Sbjct: 352 AMQDEIEGVLNSLTPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLREL 411

Query: 668 KHPSRSKKLRSFLD 681
           + P+ + +LR FLD
Sbjct: 412 RKPAVAGRLREFLD 425



 Score = 41.2 bits (95), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 27/41 (65%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           R  S    T D VRMYLRE+G + LL+   E+ ++KR+EAG
Sbjct: 117 RATSEHAGTADLVRMYLREIGKVPLLNAAQEVELSKRVEAG 157


>gi|119961685|ref|YP_947521.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
 gi|119948544|gb|ABM07455.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
          Length = 437

 Score =  276 bits (707), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 200 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 259

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 260 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDMTPEKV 319

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 320 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 379

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 380 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 437



 Score = 41.2 bits (95), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 9/76 (11%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-------RSTDDPVRMYLREMGSIEL 133
           DD+ED  G+  + D A+ + +  V+     D A         +T DPV+ YL+++G + L
Sbjct: 95  DDVED--GATATKDKAAPSGSGFVYSDADDDDAPVQQVMSAGATADPVKDYLKQIGKVAL 152

Query: 134 LSREGEIAIAKRIEAG 149
           L+ E E+ +A RIEAG
Sbjct: 153 LNAEQEVDLALRIEAG 168


>gi|163841160|ref|YP_001625565.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
 gi|1808669|emb|CAA71796.1| RNA polymerase [Renibacterium salmoninarum]
 gi|162954636|gb|ABY24151.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
          Length = 462

 Score =  276 bits (707), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 225 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNMGLIRAVEKFDYTKGFKFSTYATWW 284

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 285 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDMTPEKV 344

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 345 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 404

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 405 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 462



 Score = 39.3 bits (90), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A RIEAG
Sbjct: 160 ATADPVKDYLKQIGKVALLNAEQEVDLALRIEAG 193


>gi|237785650|ref|YP_002906355.1| RNA polymerase sigma factor [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237758562|gb|ACR17812.1| RNA polymerase sigma factor A [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 621

 Score =  276 bits (707), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 135/262 (51%), Positives = 187/262 (71%), Gaps = 4/262 (1%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T +S ++ R + S+   G      AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+
Sbjct: 364 TKLSPAQSRDLRSIAHDGRK----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNL 419

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKFD+  GYKFSTYA WW++QAITRS+ADQ+ TIRIPVHM + I+K+ R  R +
Sbjct: 420 GLIRAVEKFDYTKGYKFSTYATWWIRQAITRSMADQARTIRIPVHMVEVINKLGRIQREL 479

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              + REPTPEE+A+++ +  + V ++ +  +EPISL+  IGDE  S LGDFIED  AV 
Sbjct: 480 LQDLSREPTPEELAREMDITEDKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVV 539

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D+     L++    VL +LT RE  V+R+RFG+      TL+E+G+ + VTRERIRQI
Sbjct: 540 AVDAVSFTLLQDQLQDVLKTLTEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQI 599

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E+K + KL+HPSRS+ LR +LD
Sbjct: 600 ESKTMSKLRHPSRSQVLRDYLD 621



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++A+RIEAG
Sbjct: 302 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAQRIEAG 349


>gi|87307035|ref|ZP_01089181.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
 gi|87290408|gb|EAQ82296.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
          Length = 519

 Score =  276 bits (706), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 158/391 (40%), Positives = 230/391 (58%), Gaps = 37/391 (9%)

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           YR+ R     + +  +  ++ V+    + + VKLV  L L   RI+  +  L D SKRI 
Sbjct: 166 YRDYRIATSKSRSESQRAEAWVRLGRRRRRSVKLVEELGLRTQRIESKIGTLEDFSKRID 225

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             +  +    ++ G         H+    D  W++        E++N +    ++   +R
Sbjct: 226 ELKVRIDEHKKAKG---------HESERAD--WIA--------EYRNILVATQETPTSLR 266

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  + V      SE++               AK+E+ E NLRLV+S+AKKY NRGL F
Sbjct: 267 RRVNQLKV----IYSEYQQ--------------AKRELSEGNLRLVVSIAKKYRNRGLSF 308

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN GLM+A +KF++  G+KF TYA WW++QAITR++ADQS TIRIPVHM + + 
Sbjct: 309 LDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQSRTIRIPVHMVETMS 368

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           +V   AR++  +  REPT EE A++    VE  R+VL +++ PISL+ P+G+ + S  GD
Sbjct: 369 RVRNVARQLLQEKGREPTLEETARRAGTTVEEARRVLAMSRYPISLDRPVGNSEDSQFGD 428

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            + D  A SP   A Q  LR   +RVL +L+ RE  ++++R+G+G    +TLEEVG  F 
Sbjct: 429 LLPDGEAESPAIGAAQEMLRTRISRVLKTLSYREREIIKLRYGLGDGYSYTLEEVGHIFK 488

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+ PSRS++L  FLD
Sbjct: 489 VTRERIRQIEAKAVRKLQQPSRSQELVGFLD 519



 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 37/67 (55%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D  +  +DDPVRMYL +MG I LL+R+ EI +A++IE  RA     L E     Q  I  
Sbjct: 60  DDGETWSDDPVRMYLTQMGEIPLLTRQEEIFLARKIELTRAKFRGMLLECDYVIQDAIKV 119

Query: 171 RDELNDG 177
              + DG
Sbjct: 120 LRRVQDG 126


>gi|227503480|ref|ZP_03933529.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
 gi|227075983|gb|EEI13946.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
          Length = 493

 Score =  276 bits (706), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 135/260 (51%), Positives = 186/260 (71%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R + S+ R G      AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL
Sbjct: 238 LSPMEKRDLRSIARDGRK----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 293

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  
Sbjct: 294 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQ 353

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +
Sbjct: 354 DLGREPTPQELAKEMDITEEKVMEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAV 413

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+
Sbjct: 414 DAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIES 473

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HPSRS+ LR +LD
Sbjct: 474 KTMSKLRHPSRSQVLRDYLD 493



 Score = 46.2 bits (108), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 168 SVALRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 215


>gi|256375646|ref|YP_003099306.1| RNA polymerase sigma factor [Actinosynnema mirum DSM 43827]
 gi|255919949|gb|ACU35460.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 435

 Score =  276 bits (706), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 136/254 (53%), Positives = 185/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 186 RDLRWIVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 241

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 242 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 301

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 302 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 361

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    VLA+L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 362 LLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 421

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 422 RHPSRSQVLRDYLD 435



 Score = 44.7 bits (104), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 116 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 163


>gi|22298160|ref|NP_681407.1| RNA polymerase sigma factor RpoD [Thermosynechococcus elongatus
           BP-1]
 gi|22294339|dbj|BAC08169.1| principal RNA polymerase sigma factor [Thermosynechococcus
           elongatus BP-1]
          Length = 418

 Score =  276 bits (706), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 138/262 (52%), Positives = 192/262 (73%), Gaps = 8/262 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E G+++  FRH + + RK       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 164 ELGMTVPAFRHRLFVGRK-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 216

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 217 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKL 276

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 277 LSQEMGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGE 335

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D   +  LRE    VL +L+PRE  VL++R+G+      TLEE+G+ F VTRERIRQ
Sbjct: 336 TPEDQVSKHLLREDLETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTRERIRQ 395

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 396 IEAKALRKLRHPNRNSVLKEYI 417



 Score = 42.4 bits (98), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 52/88 (59%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           ++  +ED VA+LS+ G++ V+ ++ E E+  E S DL    +      ++ +      T+
Sbjct: 43  ATAPLEDEVALLSDYGLDAVEIEEEESEDFEEVSDDLDGKPTKGRASRRRTQVKKKHYTE 102

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRI 146
           D +R+YL+E+G I LL  + EI +A++I
Sbjct: 103 DSIRLYLQEIGRIRLLRADEEIELARKI 130


>gi|309791233|ref|ZP_07685765.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308226795|gb|EFO80491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 391

 Score =  276 bits (706), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 128/243 (52%), Positives = 177/243 (72%), Gaps = 3/243 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE+   ++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFST
Sbjct: 152 CES---RQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFST 208

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQS TIR+PVHM + I +V RT+ ++   ++REPTPEEIA+ + +
Sbjct: 209 YATWWIRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHKLQQSMQREPTPEEIAEAMGI 268

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               VR+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  A LRE    VL 
Sbjct: 269 SAGKVRRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPSEAAAAAMLREQIEEVLQ 328

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR 
Sbjct: 329 KLPERERKIIQLRYGLKDGRYRTLEEVGVEFGITRERIRQIEAVALRKLRHPHLGKKLRG 388

Query: 679 FLD 681
           +LD
Sbjct: 389 YLD 391



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 63/118 (53%), Gaps = 11/118 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++++++AR RGY+T  ++    P  E+   +++   A +   G+ VV           E 
Sbjct: 17  ERLLEIARARGYLTYNDILEAFPQPELHVAEVDQLYATMQAEGLKVV-----------ES 65

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + +L +        L +  D  D + DDPVRMYL+E+G + LL+ E E+ +AK +EAG
Sbjct: 66  AAELEAPHPADEDTLTELPDLTDIAFDDPVRMYLQEIGQVPLLTAEKEVELAKSMEAG 123


>gi|227875511|ref|ZP_03993651.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269977243|ref|ZP_06184216.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|306818820|ref|ZP_07452542.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
 gi|227843847|gb|EEJ54016.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269934546|gb|EEZ91107.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|304648506|gb|EFM45809.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
          Length = 614

 Score =  276 bits (706), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 377 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 436

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L M  E V
Sbjct: 437 IRQAITRAMADQARTIRVPVHMVEVINKLARVQRQMLQDLGREPTPDELARELDMTPEKV 496

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   RVL +L+ R
Sbjct: 497 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFVMLQEQLQRVLDTLSER 556

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MR+G+      TL+++G ++ VTRERIRQIE+K + KL+HP+RS+ LR +L+
Sbjct: 557 EAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMSKLRHPARSQSLRDYLN 614



 Score = 44.3 bits (103), Expect = 0.078,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIE 132
           D+ED+             S ++ F+   KD  D          +T DPV+ YL+++G + 
Sbjct: 269 DIEDDTADYSGDSKHKKGSKTAEFVISEKDETDEPAQKVTVAGATSDPVKDYLKQIGKVA 328

Query: 133 LLSREGEIAIAKRIEAG 149
           LL+ E E+ +AKRIEAG
Sbjct: 329 LLNAEQEVNLAKRIEAG 345


>gi|300741779|ref|ZP_07071800.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
 gi|300380964|gb|EFJ77526.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
          Length = 468

 Score =  276 bits (706), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 231 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWW 290

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 291 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMAPEKV 350

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 351 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 410

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 411 EAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 468



 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ + E+ +A RIEAG
Sbjct: 167 ATADPVKDYLKQIGKVSLLNAQQEVDLAMRIEAG 200


>gi|306836272|ref|ZP_07469254.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
 gi|304567864|gb|EFM43447.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
          Length = 492

 Score =  276 bits (706), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 135/260 (51%), Positives = 186/260 (71%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R + S+ R G      AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL
Sbjct: 237 LSPMEKRDLRSIARDGRK----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 292

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  
Sbjct: 293 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQ 352

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +
Sbjct: 353 DLGREPTPQELAKEMDITEEKVMEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAV 412

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+
Sbjct: 413 DAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIES 472

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HPSRS+ LR +LD
Sbjct: 473 KTMSKLRHPSRSQVLRDYLD 492



 Score = 46.2 bits (108), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 167 SVALRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 214


>gi|296393381|ref|YP_003658265.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180528|gb|ADG97434.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 441

 Score =  276 bits (706), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 204 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 263

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+ +++ +P E V
Sbjct: 264 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELGREMDIPPEKV 323

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 324 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQAVLETLSER 383

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 384 EAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 441



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 34/58 (58%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S D       S    Q RK++   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 112 SGDFVWDEDESEALRQARKNAELTASADSVRAYLKQIGKVALLNAEQEVELAKRIEAG 169


>gi|312195044|ref|YP_004015105.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226380|gb|ADP79235.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 424

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 128/249 (51%), Positives = 183/249 (73%), Gaps = 4/249 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR GE     AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  
Sbjct: 180 LVRDGEA----AKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAK 235

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+
Sbjct: 236 GYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEEL 295

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++ 
Sbjct: 296 ALELDMPLEQVVELRRYAQDTVSLETTVGDDGDSVLGDFIEDSDATSPADAASYGAMQDE 355

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL +L+PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ 
Sbjct: 356 IDHVLGNLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAV 415

Query: 673 SKKLRSFLD 681
           + +LR FLD
Sbjct: 416 AGRLREFLD 424



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 41/117 (35%), Positives = 59/117 (50%), Gaps = 14/117 (11%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I   R  G V+  EL   L   +V  E +   VA L   G+ VV     E+E+G+E  
Sbjct: 54  ELIARGRDSGEVSRSELREALESADVGVELLPALVARLVAAGVEVV-----EEEDGAE-- 106

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                SA+ S      R  +    T D VRMYLRE+G + LL+   E+ ++KR+EAG
Sbjct: 107 ----RSAAPSET---GRVTAEHAGTADLVRMYLREIGRVPLLNAAQEVELSKRVEAG 156


>gi|87311289|ref|ZP_01093411.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87286029|gb|EAQ77941.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 567

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 133/274 (48%), Positives = 193/274 (70%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R E++ + + T  S    R      R+   E    K+E+   NLRLV+S+AKKY NRGL
Sbjct: 290 LRQELRDLMILTLESPRGLRQRCERYRRQFDEYEKVKRELSSGNLRLVVSIAKKYRNRGL 349

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN GLM+A +K+++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM D 
Sbjct: 350 SFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIDV 409

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K+    +R+  +++REPT +EIA++  + +E VR+V+ I ++P+SL+ PIG+ + S  
Sbjct: 410 LSKLRNVQKRLLQELRREPTMDEIARRAEIDLEEVRRVMDIGRQPVSLDRPIGESEDSSF 469

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+FIED +  +P+ SA    LR+    +L +LT RE  ++++R+G+G    +TLEEVG+ 
Sbjct: 470 GEFIEDSHEETPIRSASNQILRDRIQGLLKTLTYREREIIKLRYGLGDGYTYTLEEVGRI 529

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRER+RQIEAKA+RKL+HP RS++L  FL G
Sbjct: 530 FKVTRERVRQIEAKAVRKLQHPVRSQQLEGFLAG 563



 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/148 (29%), Positives = 74/148 (50%), Gaps = 23/148 (15%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +  D     +++  + +GY+T +E+N +LP +  S E+++  +  L   GI +V      
Sbjct: 12  ELCDQDLIALMERGKTQGYLTYDEVNNYLPDEASSPEKLDKLLTELEQKGIELVTS---- 67

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSAD--------------RSTDDPVRMYLREMGS 130
                ED  D A ++   S   Q+ +++ D              ++ DDP+RMYL +M S
Sbjct: 68  ---APEDDFDDAPTSRAPSA--QEFREAIDDEEGTDTFVPEEISKANDDPIRMYLSQMAS 122

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLC 158
           I LL+R+ EIA+AK+IE  R     S+ 
Sbjct: 123 IPLLTRDQEIALAKKIEITRKQFRRSVL 150


>gi|307700837|ref|ZP_07637862.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
 gi|307613832|gb|EFN93076.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
          Length = 614

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 377 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 436

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L M  E V
Sbjct: 437 IRQAITRAMADQARTIRVPVHMVEVINKLARVQRQMLQDLGREPTPDELARELDMTPEKV 496

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   RVL +L+ R
Sbjct: 497 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFVMLQEQLQRVLDTLSER 556

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MR+G+      TL+++G ++ VTRERIRQIE+K + KL+HP+RS+ LR +L+
Sbjct: 557 EAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMSKLRHPARSQSLRDYLN 614



 Score = 44.3 bits (103), Expect = 0.072,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIE 132
           D+ED+             S ++ F+   KD  D          +T DPV+ YL+++G + 
Sbjct: 269 DIEDDTADYSGDSKHKKGSKTAEFVISEKDETDEPAQKVTVAGATSDPVKDYLKQIGKVA 328

Query: 133 LLSREGEIAIAKRIEAG 149
           LL+ E E+ +AKRIEAG
Sbjct: 329 LLNAEQEVNLAKRIEAG 345


>gi|311111671|ref|YP_003982893.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
 gi|310943165|gb|ADP39459.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
          Length = 468

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 231 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWW 290

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 291 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMAPEKV 350

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 351 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 410

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 411 EAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 468



 Score = 38.5 bits (88), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ + E+ +A RIEAG
Sbjct: 167 ATADPVKDYLKQIGKVSLLNAQQEVDLAMRIEAG 200


>gi|160941150|ref|ZP_02088487.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435711|gb|EDP13478.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
          Length = 406

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 142/277 (51%), Positives = 193/277 (69%), Gaps = 6/277 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D I +   EI SI++ T    S+        RK E +    +K +VEANLRLV+S+AK+Y
Sbjct: 135 DPIREYLKEIGSIALLTPEEESDLAR-----RKSEGDVEAGRK-LVEANLRLVVSIAKRY 188

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T RG+ FLDL+QEGN+GLMKA EKFD+  GY+ STYA WWVKQ+ITRS+ADQS TIR+PV
Sbjct: 189 TGRGMSFLDLVQEGNLGLMKAVEKFDYAKGYRLSTYATWWVKQSITRSLADQSRTIRLPV 248

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + ++K+ R  R +S K+ REP+ EE+A+++ M  + V ++++ + + +SLETP+GDE
Sbjct: 249 HMVEAVNKIRRAQRSLSVKLGREPSMEEVAEEVNMSGKRVAELIQASGDTVSLETPVGDE 308

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S+LGDF+ D    S  D A    LRE    +L  L PRE  V+ +RFG+      TLE
Sbjct: 309 EGSNLGDFVADDANASTEDKAESFLLREEIDSMLQGLNPREREVIILRFGLETGHPLTLE 368

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EVGK+F VTRERIRQIE  A+RKL++PS+SKK+R FL
Sbjct: 369 EVGKRFNVTRERIRQIETAALRKLRNPSKSKKIRDFL 405



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 33/47 (70%), Gaps = 5/47 (10%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKR-----IEAGRAMMMASL 157
           ST DP+R YL+E+GSI LL+ E E  +A+R     +EAGR ++ A+L
Sbjct: 132 STADPIREYLKEIGSIALLTPEEESDLARRKSEGDVEAGRKLVEANL 178


>gi|255327076|ref|ZP_05368152.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
 gi|255296293|gb|EET75634.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
          Length = 457

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 220 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWW 279

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 280 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMTPEKV 339

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 340 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 399

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 400 EAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 457



 Score = 38.5 bits (88), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ + E+ +A RIEAG
Sbjct: 156 ATADPVKDYLKQIGKVSLLNAQQEVDLAMRIEAG 189


>gi|325962990|ref|YP_004240896.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469077|gb|ADX72762.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 437

 Score =  276 bits (705), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 200 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 259

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 260 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDMTPEKV 319

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 320 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 379

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 380 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 437



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 7/80 (8%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-------RSTDDPVRMYLREMG 129
           +++G D  +E+   D +  A+ +    V+     D A         +T DPV+ YL+++G
Sbjct: 89  ILEGPDAVEEDAEADPVKGAAGSGKGFVYSDADDDDAPVQQVMSAGATADPVKDYLKQIG 148

Query: 130 SIELLSREGEIAIAKRIEAG 149
            + LL+ E E+ +A RIEAG
Sbjct: 149 KVALLNAEQEVDLALRIEAG 168


>gi|116670178|ref|YP_831111.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116610287|gb|ABK03011.1| RNA polymerase, sigma 70 subunit, RpoD [Arthrobacter sp. FB24]
          Length = 441

 Score =  275 bits (704), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 204 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 263

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 264 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDMTPEKV 323

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 324 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 383

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 384 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 441



 Score = 39.3 bits (90), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A RIEAG
Sbjct: 139 ATADPVKDYLKQIGKVALLNAEQEVDLALRIEAG 172


>gi|148654372|ref|YP_001274577.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566482|gb|ABQ88627.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 402

 Score =  275 bits (704), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 126/238 (52%), Positives = 174/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 165 ARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWW 224

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V RT+ ++   ++REPTPEEIA  + +    V
Sbjct: 225 IRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHKLQQTMQREPTPEEIADAMGISSTKV 284

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE    VL  L  R
Sbjct: 285 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASMLREQLEEVLQKLPER 344

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 345 ERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 402



 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 47/168 (27%), Positives = 79/168 (47%), Gaps = 16/168 (9%)

Query: 23  VFDFSDDSWKK----MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           + + +  +W +    ++++ R RG++T  E+   LP  E     ++   A L   GI VV
Sbjct: 14  IVEQTQQAWAQTLEYLLEIGRTRGFLTYNEILEALPQPEHHIADVDQLYASLQAEGIRVV 73

Query: 79  DGDDLEDEEGSEDSLDLASSASNSS-VFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
                      E  LD+  + S      L    D  D + DDPVRMYL+E+G + LLS E
Sbjct: 74  -----------ETPLDIHDNGSTGDDELLADMPDLTDVALDDPVRMYLQEIGQVPLLSAE 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            E+ +AK +EAG     A   E   ++Q  +++  ++  G    + +I
Sbjct: 123 QEVMLAKAMEAGHRARRALEREEYSSWQERVMYEQQVAQGNEARQHLI 170


>gi|225619915|ref|YP_002721172.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225214734|gb|ACN83468.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 587

 Score =  275 bits (704), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 160/371 (43%), Positives = 224/371 (60%), Gaps = 10/371 (2%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           +K+ +VKL+  + LN+  ID + E+L     RI   E    +L + Y  +   F   ++ 
Sbjct: 222 VKDSIVKLLSKVRLNRMEIDRIAEKLKFYLHRINQIEEYFEKLKKRYYKEISDFENYYKE 281

Query: 377 RELDPH--WVSYAKDF---PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            E      ++    +F   PE      +   + S  K +  +  I  E  I        V
Sbjct: 282 IESGNKDIYIRLVDEFNITPEA-----IEAVITSFHKAQVRMADIYDEVRIDKETLVEWV 336

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     + + AK  +V+ANLRLVI++AKKY NRGL F DL+QEGNIGL+KA +KF++ 
Sbjct: 337 RKIDSSRRKIAQAKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYK 396

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R  R+   +  REP+ +E
Sbjct: 397 KGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVQRVLRQYMQQHGREPSIQE 456

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IAK L+ P   V+ V  + K+P+SL  PIGDE+ + LG+ IEDK   SP +      LR+
Sbjct: 457 IAKALSWPESRVKSVRNVAKDPVSLNAPIGDEEDTILGELIEDKEFESPQNITTFKILRK 516

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L SL  RE++V+RMRFG+     HTLEEVG  F VTRERIRQIEAKAIR+L+  S
Sbjct: 517 QIDSILDSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAIRRLRAQS 576

Query: 672 RSKKLRSFLDG 682
           + K+L+ FLD 
Sbjct: 577 KKKELKDFLDS 587



 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 34/161 (21%), Positives = 81/161 (50%), Gaps = 11/161 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLED 85
           +++  +K+++      Y+T +E+N  +  D + ++ M+    +L+   I +V D  + E 
Sbjct: 13  NNEKIRKLLEKGNTNKYLTFKEINGAI--DNMDTDVMDILFQLLAARKIVIVEDKREFES 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +++ +D A+       F+       +   DDP+R+YL+E+G + LL+ + E+  +K+
Sbjct: 71  LSKNQNKIDDAAK------FIHVEDKVGN--NDDPIRLYLKEIGKVSLLTHDDEVDYSKK 122

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           IE+G + +   +  + L    ++     +  G   + EI++
Sbjct: 123 IESGESEIENIILNTHLVVGEVLNTIKNVQIGKVSIHEILE 163


>gi|317506483|ref|ZP_07964284.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
 gi|316255244|gb|EFV14513.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
          Length = 452

 Score =  275 bits (704), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 215 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 274

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+ +++ +P E V
Sbjct: 275 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELGREMDIPPEKV 334

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 335 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQAVLETLSER 394

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 395 EAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 452



 Score = 43.9 bits (102), Expect = 0.083,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 38/66 (57%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ++EE    + D       S    Q RK++   ++ D VR YL+++G + LL+ E E+ +A
Sbjct: 115 DEEEPERTAGDFVWDEDESEALRQARKNAELTASADSVRAYLKQIGKVALLNAEQEVELA 174

Query: 144 KRIEAG 149
           KRIEAG
Sbjct: 175 KRIEAG 180


>gi|283457795|ref|YP_003362387.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
 gi|283133802|dbj|BAI64567.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
          Length = 460

 Score =  275 bits (704), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 223 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWW 282

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+ K+L M  E V
Sbjct: 283 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMTPEKV 342

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 343 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 402

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 403 EAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 460



 Score = 40.8 bits (94), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ + E+ +AKRIEAG
Sbjct: 159 ATADPVKDYLKQIGKVSLLNAQQEVDLAKRIEAG 192


>gi|225388546|ref|ZP_03758270.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
 gi|225045391|gb|EEG55637.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
          Length = 381

 Score =  275 bits (703), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 129/246 (52%), Positives = 184/246 (74%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK E + + AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GY
Sbjct: 137 RKAEGDEA-AKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGY 195

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K STYA WW++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A+
Sbjct: 196 KLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELAE 255

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L M  + V ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE   
Sbjct: 256 ALDMTEDKVMEIMQIAREPASLETPIGEEDDSNLGDFVADNNVVTPEGNVESVMLREHID 315

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +L  L  RE +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK
Sbjct: 316 ALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375

Query: 675 KLRSFL 680
           ++R FL
Sbjct: 376 RIRDFL 381



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 70/151 (46%), Gaps = 16/151 (10%)

Query: 28  DDSWKKMIKLAR----QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD- 82
           DD  KK+ KL      +   +   E+N F   D +S EQM+   + L N  I+VV   D 
Sbjct: 4   DDFLKKLEKLVELAKGKHNTLDAGEINDFFAGDSLSPEQMDHIYSYLENRNIDVVPELDE 63

Query: 83  -LEDEEGSEDSLDLASSASNSSVFLQKRK------DSADR----STDDPVRMYLREMGSI 131
            +  EE +           +   F++  +      D+ D      T+DPVRMYL+E+G++
Sbjct: 64  KMLSEESALLDDLDLDLDLDDDSFMKDTEEEEIDLDAVDLLEGIGTEDPVRMYLKEIGTV 123

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
            LL+ + E+ +A+R   G       L E+ L
Sbjct: 124 PLLTADEELQLAQRKAEGDEAAKERLIEANL 154


>gi|302525743|ref|ZP_07278085.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434638|gb|EFL06454.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 476

 Score =  275 bits (703), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 135/254 (53%), Positives = 184/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 227 RDLKWIVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 282

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 283 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 342

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 343 TPEELAKEMDISPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 402

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 403 LLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 462

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 463 RHPSRSQVLRDYLD 476



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 36/61 (59%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S D+ D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEA
Sbjct: 144 SSDNPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEA 203

Query: 149 G 149
           G
Sbjct: 204 G 204


>gi|170782020|ref|YP_001710352.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156588|emb|CAQ01739.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 355

 Score =  275 bits (703), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 118 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 177

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE++++L M  E V
Sbjct: 178 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 237

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L++    +L SL+ R
Sbjct: 238 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDTEAVVPADAVGFTMLQKQLESLLDSLSER 297

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 298 EAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 355


>gi|220912379|ref|YP_002487688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219859257|gb|ACL39599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 433

 Score =  275 bits (703), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 196 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 255

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 256 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDMTPEKV 315

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 316 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSER 375

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 376 EAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 433



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +A RIEAG
Sbjct: 131 ATADPVKDYLKQIGKVALLNAEQEVDLALRIEAG 164


>gi|325283594|ref|YP_004256135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
 gi|324315403|gb|ADY26518.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
          Length = 487

 Score =  275 bits (703), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 138/245 (56%), Positives = 182/245 (74%), Gaps = 3/245 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTY
Sbjct: 243 DGAAARQGLIEANLRLVVSIAKKYTGRGLNFLDLIQEGNQGLIRAVEKFEYRRRYKFSTY 302

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE  PEEIA+ +   
Sbjct: 303 ATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREALPEEIAEAMGPG 362

Query: 560 VEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   V +V K+++EP+SLETPIGDE  S  GDFI D N  SP+D+A +  L E   + L
Sbjct: 363 WDANKVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDDNLDSPVDNAAKTLLSEELEKAL 422

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKL 676
             LT RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KL
Sbjct: 423 GKLTEREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLKYHESRTRKL 482

Query: 677 RSFLD 681
           R FL+
Sbjct: 483 RDFLE 487



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++DPVR YL E+G + LL+ E EIA+A+RIE G
Sbjct: 183 SNDPVRQYLHEIGRVPLLTLEEEIALARRIEDG 215


>gi|296139587|ref|YP_003646830.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027721|gb|ADG78491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 483

 Score =  275 bits (703), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 246 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 305

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 306 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 365

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 366 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 425

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 426 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 483



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 30/71 (42%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 82  DLEDEEGSED---SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D ED+E SE    S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 141 DAEDDEPSEQDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 200

Query: 139 EIAIAKRIEAG 149
           E+ +AKRIEAG
Sbjct: 201 EVELAKRIEAG 211


>gi|108805110|ref|YP_645047.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766353|gb|ABG05235.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 366

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 149/313 (47%), Positives = 211/313 (67%), Gaps = 16/313 (5%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +V  ER  GRE          D P  +  + VA   DSI     EI  + + T     E 
Sbjct: 69  EVTPERAAGRE---------GDNPASQLAHAVATG-DSIRMYLAEIGRVPLLT--HADEI 116

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   + +G C+ S  K ++VEANLRLV+S+AKKY NRG+ FLDLIQEGNIGL++AAEK
Sbjct: 117 R-LAKAISRG-CKRS--KDKLVEANLRLVVSIAKKYRNRGVSFLDLIQEGNIGLIRAAEK 172

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IAD+  TIRIPVHM +K++K  RT RRM+  + REP
Sbjct: 173 FDYRKGFKFSTYATWWIRQAITRAIADKGRTIRIPVHMVEKVNKYHRTQRRMTQALGREP 232

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++L +PVE V ++ +I++  ISLETP+GD+++S LGDF+ED +AV+P D+  ++
Sbjct: 233 TDEEVAEELGVPVEEVLRLQEISQRSISLETPVGDDESSSLGDFLEDASAVTPTDAVSES 292

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+      L  L  RE +++ MRFG+  +   TLEEVG++F +TRER+RQI+ K +  L
Sbjct: 293 LLKLHLREALDELPERERQIIEMRFGMKDDRPRTLEEVGREFDITRERVRQIQMKTLNLL 352

Query: 668 KHPSRSKKLRSFL 680
           +   R++ LR +L
Sbjct: 353 REQRRTQNLREYL 365



 Score = 39.7 bits (91), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 77/182 (42%), Gaps = 15/182 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++   R +G+++ E++   +   ++S ++ E+  A L    I +VD    E E  
Sbjct: 11  DRAYELLSKGRSQGFLSAEDVADLVREGDLSPDEAEELYATLEEEDITLVDE---ELEGA 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +E + + A+     +   Q     A   T D +RMYL E+G + LL+   EI +AK I  
Sbjct: 68  AEVTPERAAGREGDNPASQLAHAVA---TGDSIRMYLAEIGRVPLLTHADEIRLAKAISR 124

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G       L E+ L    + I +   N G + L  I         E   G     E   Y
Sbjct: 125 GCKRSKDKLVEANLRL-VVSIAKKYRNRGVSFLDLI--------QEGNIGLIRAAEKFDY 175

Query: 209 QK 210
           +K
Sbjct: 176 RK 177


>gi|87307232|ref|ZP_01089377.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87289972|gb|EAQ81861.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 507

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 150/365 (41%), Positives = 220/365 (60%), Gaps = 35/365 (9%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + K V+L+  L+L  ++I  L+ +L +IS+R+    G++   A   G+ R          
Sbjct: 166 RAKAVRLIEELNLRTNKISALLPKLREISERMDTLLGQIDE-ATKAGVSRT--------- 215

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                          G+  N +  E+  ++K+  E  ++     + ISEF+         
Sbjct: 216 ---------------GQTVNELRTELRYLMKVTLESPTMLRRRLLRISEFQE-------- 252

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             E   AK+ +   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +KF++  GYKFS
Sbjct: 253 --EYDAAKRLLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEYQRGYKFS 310

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQS TIR+PVHM D + KV    R +  ++ R+PT EE+A++  
Sbjct: 311 TYATWWIRQAITRAIADQSRTIRVPVHMIDTMGKVRAVTRDLLQELGRDPTAEEVAERAG 370

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + ++  R +LK+ + P+SL+ P+GD D S  G+F+ED     PL    Q  L++    VL
Sbjct: 371 LSIDDARVILKMNRNPLSLDQPVGDHDDSFFGEFLEDHRDEDPLYETHQQALKDRLCEVL 430

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L  RE  ++R+R+G+     +TLEEVGK F VTRER+RQIE+KA+RKL+ P RS+ L 
Sbjct: 431 EALNHREREIIRLRYGLTDGYSYTLEEVGKIFSVTRERVRQIESKAVRKLQQPYRSRGLA 490

Query: 678 SFLDG 682
           SFL+G
Sbjct: 491 SFLEG 495



 Score = 46.6 bits (109), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 54/122 (44%), Gaps = 5/122 (4%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           +  D DD E +  +    D A    +  +F      S D   DDP+RMYL +MG I +LS
Sbjct: 3   HAFDNDDFEQDPAARFPADAAEEQED--MF---EDPSDDSQIDDPIRMYLMQMGEIPMLS 57

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           R+ E+  A++IE  R     +   +    +  +   +++ DG   L   +++      E 
Sbjct: 58  RQEEVDAARQIEFWRTRFRHAFISNDFILEQSVQLLEQVRDGKLRLDRTVEVSVTNAKEK 117

Query: 196 KG 197
           K 
Sbjct: 118 KN 119


>gi|325068636|ref|ZP_08127309.1| RNA polymerase, sigma 70 subunit, RpoD [Actinomyces oris K20]
          Length = 542

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 305 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 364

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 365 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKV 424

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 425 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSER 484

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 485 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 542



 Score = 41.6 bits (96), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 240 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 273


>gi|226366217|ref|YP_002784000.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226244707|dbj|BAH55055.1| RNA polymerase sigma factor SigA [Rhodococcus opacus B4]
 gi|254553058|dbj|BAH85841.1| RNA polymerase sigma A factor [Rhodococcus opacus]
          Length = 457

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 220 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 279

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 280 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 339

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 340 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 399

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 400 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 457



 Score = 45.1 bits (105), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 34/58 (58%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 128 SGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 185


>gi|300867798|ref|ZP_07112441.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
 gi|300334215|emb|CBN57613.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
          Length = 391

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 137/261 (52%), Positives = 189/261 (72%), Gaps = 8/261 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+ +  FRH + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++
Sbjct: 138 VGMPLPAFRHRLHLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSL 190

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +
Sbjct: 191 GLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLL 250

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +
Sbjct: 251 SQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGET 309

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQI
Sbjct: 310 PEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQI 369

Query: 660 EAKAIRKLKHPSRSKKLRSFL 680
           EAKA+RKL+HP+R+  L+ ++
Sbjct: 370 EAKALRKLRHPNRNSILKEYI 390



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 39/68 (57%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +GDD ED   ++   D A S S  +   ++ +      T+D +R+YL+E+G I LL  + 
Sbjct: 41  EGDDREDFLDAQPEEDDAKSGSKVAKARRRAQAKKKHYTEDSIRLYLQEIGRIRLLRADE 100

Query: 139 EIAIAKRI 146
           EI +A++I
Sbjct: 101 EIELARKI 108


>gi|325107209|ref|YP_004268277.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967477|gb|ADY58255.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 590

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 125/238 (52%), Positives = 181/238 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+   NLRLV+S+AKKY NRG+ FLDLIQEGN GLM+A +K+++  GYKFSTYA WW
Sbjct: 343 AMRELSGGNLRLVVSIAKKYRNRGMNFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWW 402

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + + K+ +  + +  ++ REPT EE+A+   + +E  
Sbjct: 403 IRQAITRAIADQARTIRIPVHMIETMSKLRKVGKDLVQELGREPTIEEMAEAAEVSLEEA 462

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V+KI+++PISL+ PIG+ + S+ GDFIED +  SP+ +A Q  L++    VL +LT R
Sbjct: 463 RRVMKISRQPISLDRPIGEGEDSYFGDFIEDHSTDSPVSTATQEMLKDKIDHVLKTLTYR 522

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  ++++R+G+G    +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RS +L+ F++
Sbjct: 523 EREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSHQLKGFIE 580



 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/191 (28%), Positives = 96/191 (50%), Gaps = 22/191 (11%)

Query: 24  FDFS--------DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           F+FS        DD+ +++IK  +++G++T  ++N +LP ++V+ E+++  +  L  +G+
Sbjct: 20  FEFSRSIFVHQLDDNLQQLIKQGQKQGFLTFSQVNEYLPDEDVNPEKLDTLLLSLEELGM 79

Query: 76  NVVDGDDLE------DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            +V    +       D E ++      S +   +  L +  D   R  DDPVR+YL +MG
Sbjct: 80  EIVSEKHVSKKKVQLDAEAAQRKKKKPSKSEKRNGELAEDDDEGSRRIDDPVRIYLTQMG 139

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI-----IWRDELNDGTTL---L 181
            I LL+R+ EI +AK+IE  R      L  +    ++ I     + R EL    T+   L
Sbjct: 140 EIPLLTRDEEITLAKKIEVTRKRFRRQLLSNDCAMRSAIETLAKVHRGELPFDRTIKVSL 199

Query: 182 REIIDLEACIG 192
            E ++ E  IG
Sbjct: 200 TESVEKEQVIG 210


>gi|313892356|ref|ZP_07825948.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|313119215|gb|EFR42415.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
          Length = 393

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 143/298 (47%), Positives = 193/298 (64%), Gaps = 9/298 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE- 438
           D  W    KD+ + E  ++   + +    +R  ++       +S  E   +   + KG+ 
Sbjct: 87  DKDWEKQEKDWTKVENNDYAVTQGNVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKGKM 146

Query: 439 --------CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
                     A  AKKEM  ANLRLV+S+AKKY  RG+ FLDLIQEGNIGL+KA +KFD+
Sbjct: 147 LDATEEDKLRAEDAKKEMANANLRLVVSIAKKYPGRGMPFLDLIQEGNIGLLKAVDKFDY 206

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+K+ R  R+   +  RE + E
Sbjct: 207 KKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVETINKMNRIGRKFLQEFGREASNE 266

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK++ + VE +R+  K  ++PISLETPIG+++ SHLGDFIED+   SP + A     R
Sbjct: 267 ELAKEMGISVEKIREAKKAAQDPISLETPIGEKEDSHLGDFIEDQKTSSPEEEAAATMRR 326

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   ++L  LT RE+ VL +RFG+   T  TLEEVGK F VTRERIRQIE KA++KL+
Sbjct: 327 EQIYKLLNELTEREKGVLALRFGMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKLR 384



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 19/34 (55%), Positives = 26/34 (76%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           DPVR+YLRE G+  LLS E E+ +AK+IE G+ +
Sbjct: 114 DPVRLYLRECGATPLLSAEEEMTLAKQIEKGKML 147


>gi|257056422|ref|YP_003134254.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
 gi|256586294|gb|ACU97427.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
          Length = 439

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 134/254 (52%), Positives = 184/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 190 RDLKWIVRDGER----AKSHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 245

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 246 FDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 305

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 306 TPEELAKEMDISPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 365

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 366 LLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 425

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 426 RHPSRSQVLRDYLD 439



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 40/74 (54%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V +  D  DEE   +  D       S    Q RKD+   ++ D VR YL+++G + LL+
Sbjct: 94  TVTEDTDESDEESDANDPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLN 153

Query: 136 REGEIAIAKRIEAG 149
            E E+ +AKRIEAG
Sbjct: 154 AEEEVELAKRIEAG 167


>gi|320531403|ref|ZP_08032370.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320136375|gb|EFW28356.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 537

 Score =  275 bits (702), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 300 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 359

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 360 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKV 419

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 420 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSER 479

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 480 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 537



 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 235 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 268


>gi|117928637|ref|YP_873188.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649100|gb|ABK53202.1| RNA polymerase, sigma 70 subunit, RpoD [Acidothermus cellulolyticus
           11B]
          Length = 495

 Score =  275 bits (702), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 258 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 317

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + R+PTPEE+A +L M  E V
Sbjct: 318 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGRDPTPEELAVELDMTPEKV 377

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 378 MEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPSDAVSFTLLQEQLHSVLETLSER 437

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 438 EAGVVSMRFGLTDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 495



 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 194 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 227


>gi|300784507|ref|YP_003764798.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
 gi|299794021|gb|ADJ44396.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
          Length = 467

 Score =  275 bits (702), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 135/254 (53%), Positives = 184/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 218 RDLKWIVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 273

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 274 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 333

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 334 TPEELAKEMDISPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 393

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 394 LLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 453

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 454 RHPSRSQVLRDYLD 467



 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 35/59 (59%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D+ D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 137 DNPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 195


>gi|283795510|ref|ZP_06344663.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291077175|gb|EFE14539.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
          Length = 377

 Score =  275 bits (702), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 129/246 (52%), Positives = 183/246 (74%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK E + S AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GY
Sbjct: 133 RKAEGDVS-AKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGY 191

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K STYA WW++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E++ 
Sbjct: 192 KLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVAELSA 251

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L M  + V ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE   
Sbjct: 252 ALDMSEDKVMEIMQIAREPASLETPIGEEDDSNLGDFVADGNVVTPEGNVESVMLREHID 311

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +L  L  RE +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK
Sbjct: 312 ALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 371

Query: 675 KLRSFL 680
           ++R FL
Sbjct: 372 RIRDFL 377



 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/142 (30%), Positives = 74/142 (52%), Gaps = 15/142 (10%)

Query: 32  KKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           +K++ LA+ ++  + I E+N F   D +S+EQME   + L    I+V+   ++ DE  + 
Sbjct: 13  RKLVDLAKTKQNALDIAEINDFFAADNLSTEQMEQIYSYLEQNNIDVIP--EVIDE--TS 68

Query: 91  DSLDLASSASNSSVFLQKRK------DSADR----STDDPVRMYLREMGSIELLSREGEI 140
            + +L         F++  +      D+ D      T+DPVRMYL+E+G++ LLS E E+
Sbjct: 69  LNDELLLLDDVDDDFMKNGEEEDIDLDAIDLLEGIGTEDPVRMYLKEIGTVPLLSAEEEL 128

Query: 141 AIAKRIEAGRAMMMASLCESPL 162
            +AKR   G       L E+ L
Sbjct: 129 RLAKRKAEGDVSAKERLIEANL 150


>gi|329946883|ref|ZP_08294295.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328526694|gb|EGF53707.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 543

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 306 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 365

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 366 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKV 425

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 426 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSER 485

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 486 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 543



 Score = 41.6 bits (96), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 241 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 274


>gi|168704760|ref|ZP_02737037.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 556

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 128/258 (49%), Positives = 188/258 (72%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +  R  V ++++   E   AK+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A
Sbjct: 293 ASLRRRVGIMKQRFAEYEQAKRDLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRA 352

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +K++   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + + K+   ++++  ++ 
Sbjct: 353 VDKYEHRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIETMSKLRNVSKQLLQELG 412

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPT +E A    +  E  ++VLKI+++PISL+ P+G+ + S+ GDFIED +  SP+++A
Sbjct: 413 REPTVQETADAAKISYEECKRVLKISRQPISLDRPVGESEDSYFGDFIEDNSVESPVNAA 472

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L++    VL +LT RE  ++++R+G+G    +TLEEVG+ F VTRER+RQIEAKA+
Sbjct: 473 TNEMLKDKIEGVLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAV 532

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HP RS++L  FLDG
Sbjct: 533 RKLQHPVRSRQLEGFLDG 550



 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 79/145 (54%), Gaps = 5/145 (3%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPP--DEVS-SEQMEDTVAMLSNMGINVVDGDDL 83
           +D+  K +++  +Q G +T +E+N  LP   D V  S+++E  + +L   GI+V+D DD 
Sbjct: 5   NDEVLKALVERGKQVGSLTYDEVNTALPEGRDGVPESDRLEHVLEILDANGISVIDEDDG 64

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E    +  + D A +   +  +  +  D   R  DDPVRMYL +MG IELL+R+ E+++A
Sbjct: 65  EAVADAPVAADAAVADPEAPSY--EDSDGDGRHIDDPVRMYLTQMGQIELLNRKQEVSLA 122

Query: 144 KRIEAGRAMMMASLCESPLTFQALI 168
            +IE  R      + E     + ++
Sbjct: 123 MKIELTRRRFRRKVLECDYAMRQVV 147


>gi|309389374|gb|ADO77254.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 310

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 133/253 (52%), Positives = 189/253 (74%), Gaps = 2/253 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ E     A++++ EANLRLV+S+AKKY  +G+ FLDLIQEGN GLMKA EKFD+
Sbjct: 57  VELAKRIEQGDQRAREQLTEANLRLVVSIAKKYIGQGMSFLDLIQEGNKGLMKAVEKFDY 116

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++Q+ITR++ADQ+ TIRIPVHM + ++K+ R  +R+   ++REPT E
Sbjct: 117 TKGYKFSTYATWWIRQSITRALADQARTIRIPVHMVETMNKLRRIEKRLKKDLEREPTLE 176

Query: 551 EIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EI +++ M  E V ++  L + ++P SL+TPIG+E  SHL DFIED++A +P   A    
Sbjct: 177 EIGEEMNMEPEKVLEIQKLAMNQQPTSLDTPIGEEKDSHLKDFIEDQDAPAPEMLASSEL 236

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++    VL +LT RE+R++++RFG+      TL+EVG QF VTRERIRQI+AKA+RKL+
Sbjct: 237 LKDQLETVLDTLTDREKRIIKLRFGLEDGRQRTLKEVGSQFGVTRERIRQIQAKALRKLR 296

Query: 669 HPSRSKKLRSFLD 681
           HP+RSK+LR +L+
Sbjct: 297 HPTRSKELRGYLN 309



 Score = 46.2 bits (108), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DD VR+YL+EMG ++LL +E E+ +AKRIE G       L E+ L    + I +  +  G
Sbjct: 35  DDSVRVYLKEMGKVDLLDKEEEVELAKRIEQGDQRAREQLTEANLRL-VVSIAKKYIGQG 93

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            + L  I         E   G     E   Y K
Sbjct: 94  MSFLDLI--------QEGNKGLMKAVEKFDYTK 118


>gi|329121328|ref|ZP_08249954.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|327469737|gb|EGF15203.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 396

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 143/298 (47%), Positives = 193/298 (64%), Gaps = 9/298 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE- 438
           D  W    KD+ + E  ++   + +    +R  ++       +S  E   +   + KG+ 
Sbjct: 90  DKDWEKQEKDWTKVENNDYAVTQGNVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKGKM 149

Query: 439 --------CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
                     A  AKKEM  ANLRLV+S+AKKY  RG+ FLDLIQEGNIGL+KA +KFD+
Sbjct: 150 LDATEEDKLRAEDAKKEMANANLRLVVSIAKKYPGRGMPFLDLIQEGNIGLLKAVDKFDY 209

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+K+ R  R+   +  RE + E
Sbjct: 210 KKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVETINKMNRIGRKFLQEFGREASNE 269

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK++ + VE +R+  K  ++PISLETPIG+++ SHLGDFIED+   SP + A     R
Sbjct: 270 ELAKEMGISVEKIREAKKAAQDPISLETPIGEKEDSHLGDFIEDQKTSSPEEEAAATMRR 329

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   ++L  LT RE+ VL +RFG+   T  TLEEVGK F VTRERIRQIE KA++KL+
Sbjct: 330 EQIYKLLNELTEREKGVLALRFGMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKLR 387



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 27/37 (72%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           +  DPVR+YLRE G+  LLS E E+ +AK+IE G+ +
Sbjct: 114 NVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKGKML 150


>gi|311742667|ref|ZP_07716476.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
 gi|311314295|gb|EFQ84203.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
          Length = 464

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 227 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 286

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTP+E+AK+L M  E V
Sbjct: 287 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAKELDMTPEKV 346

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 347 VEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHAVLDTLSER 406

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 407 ESGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 464



 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 163 ATADPVKDYLKQIGKVSLLTAGEEVELAKRIEAG 196


>gi|158334991|ref|YP_001516163.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158305232|gb|ABW26849.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 371

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 136/269 (50%), Positives = 195/269 (72%), Gaps = 8/269 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +++  ++E  + ++ FRH +   R+       AK +MV++NLRLV+S+AKKY NRGL F 
Sbjct: 110 QLQEWALEVDMPLNRFRHRLHAGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQ 162

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I +
Sbjct: 163 DLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISR 222

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDF
Sbjct: 223 IKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDF 282

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE  +  +P D   ++ LRE    VL +L+PRE  VL++R+G+      TLEE+G+ F V
Sbjct: 283 IES-DGETPEDQVSKSLLREDLETVLDTLSPRERDVLKLRYGLDDGRMKTLEEIGQIFNV 341

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 342 TRERIRQIEAKALRKLRHPNRNSVLKEYI 370


>gi|326384438|ref|ZP_08206118.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196783|gb|EGD53977.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 466

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 134/260 (51%), Positives = 188/260 (72%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+++ R +  + R G    + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL
Sbjct: 211 LSVAQRRDLSWISRDG----NRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 266

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  
Sbjct: 267 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQ 326

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +
Sbjct: 327 DLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAV 386

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+
Sbjct: 387 DAVSFTLLQDQLQDVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIES 446

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HPSRS+ LR +LD
Sbjct: 447 KTMSKLRHPSRSQVLRDYLD 466



 Score = 44.7 bits (104), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 147 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 194


>gi|226306303|ref|YP_002766263.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
 gi|226185420|dbj|BAH33524.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
          Length = 452

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 215 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 274

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 275 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 334

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 335 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 394

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 395 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 452



 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 37/66 (56%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +A
Sbjct: 115 EPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELA 174

Query: 144 KRIEAG 149
           KRIEAG
Sbjct: 175 KRIEAG 180


>gi|118465794|ref|YP_882772.1| RNA polymerase sigma factor [Mycobacterium avium 104]
 gi|254776035|ref|ZP_05217551.1| RNA polymerase sigma factor [Mycobacterium avium subsp. avium ATCC
           25291]
 gi|118167081|gb|ABK67978.1| sigma factor MysA [Mycobacterium avium 104]
          Length = 496

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 259 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 318

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 319 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 378

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 379 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 438

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 439 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 496



 Score = 45.1 bits (105), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M+ + E
Sbjct: 177 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMSEMAE 236


>gi|284990384|ref|YP_003408938.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284063629|gb|ADB74567.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 429

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 134/254 (52%), Positives = 185/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 180 RDLNWIVRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 235

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 236 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 295

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  + V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 296 TPEELAKEMDITPDKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 355

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +++  T VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 356 LMQDQLTSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 415

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 416 RHPSRSQVLRDYLD 429



 Score = 44.3 bits (103), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 110 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVDLAKRIEAG 157


>gi|111023781|ref|YP_706753.1| RNA polymerase sigma factor [Rhodococcus jostii RHA1]
 gi|110823311|gb|ABG98595.1| sigma factor, sigma 70 type, probable group 1 (principle sigma
           factor) [Rhodococcus jostii RHA1]
          Length = 457

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 220 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 279

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 280 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 339

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 340 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 399

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 400 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 457



 Score = 45.1 bits (105), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 34/58 (58%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 128 SGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 185


>gi|229491308|ref|ZP_04385134.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|229321847|gb|EEN87642.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 430

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 193 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 252

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 253 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 312

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 313 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 372

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 373 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 430



 Score = 45.1 bits (105), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 37/66 (56%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +A
Sbjct: 93  EPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELA 152

Query: 144 KRIEAG 149
           KRIEAG
Sbjct: 153 KRIEAG 158


>gi|227495998|ref|ZP_03926309.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
 gi|226834486|gb|EEH66869.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
          Length = 541

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 304 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 363

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 364 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKV 423

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 424 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSER 483

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 484 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 541



 Score = 39.3 bits (90), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 239 ATADPVKDYLKQIGKVALLNAAEEVELAKRIEAG 272


>gi|255325126|ref|ZP_05366232.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311739588|ref|ZP_07713423.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|255297691|gb|EET77002.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311305404|gb|EFQ81472.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 490

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 135/260 (51%), Positives = 186/260 (71%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R + S+ R G      AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL
Sbjct: 235 LSPMEKRDLRSIARDGRK----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 290

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  
Sbjct: 291 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQ 350

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +
Sbjct: 351 DLGREPTPQELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAV 410

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+
Sbjct: 411 DAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIES 470

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HPSRS+ LR +LD
Sbjct: 471 KTMSKLRHPSRSQVLRDYLD 490



 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 165 SAALRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 212


>gi|86742187|ref|YP_482587.1| sigma 38 [Frankia sp. CcI3]
 gi|86569049|gb|ABD12858.1| sigma 38 [Frankia sp. CcI3]
          Length = 422

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 127/254 (50%), Positives = 183/254 (72%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +V+ G      AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EK
Sbjct: 173 RDLGLLVKDGHA----AKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEK 228

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REP
Sbjct: 229 FDYAKGYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREP 288

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A   
Sbjct: 289 TDEELALELDMPIEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYG 348

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +++    VL  L+PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L
Sbjct: 349 AMQDEIENVLGGLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLREL 408

Query: 668 KHPSRSKKLRSFLD 681
           + P+ + +LR FLD
Sbjct: 409 RKPAVAGRLREFLD 422



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 70/131 (53%), Gaps = 19/131 (14%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           DD+   D S  +  ++I   R+ G ++  EL   L   ++  E +   +A L+ +GI ++
Sbjct: 43  DDTDELDVS--AVAEVIARGREAGEISRSELRDVLESADIGIELLPALIARLNAVGIELL 100

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D     +EE S+D    A++AS S+        +    T D VRMYLRE+G + LL+   
Sbjct: 101 D-----EEEASDD----ATAASRST--------AEHAGTADLVRMYLREIGKVPLLNAAQ 143

Query: 139 EIAIAKRIEAG 149
           E+ ++KR+EAG
Sbjct: 144 EVELSKRVEAG 154


>gi|219847900|ref|YP_002462333.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542159|gb|ACL23897.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 381

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 173/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 144 ARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYATWW 203

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V RT+ R+   ++REPTPEEIA  + +    V
Sbjct: 204 IRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHRLQQTMQREPTPEEIADAMGISAGKV 263

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE    VL  L  R
Sbjct: 264 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASLLREQLEEVLMKLPER 323

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 324 ERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 381



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 43/125 (34%), Positives = 65/125 (52%), Gaps = 21/125 (16%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV------DG-DDLE 84
           ++++  AR RGY+T  ++ A  P  E    +++   AML   GI VV      DG  D E
Sbjct: 3   EQLLAAARVRGYITHADILATFPNPEHDIAEIDQLYAMLQAEGIRVVESSDELDGPTDFE 62

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            E   + ++DL               D  + + DDPVRMYL+E+G + LL+ E E+ +AK
Sbjct: 63  PETDHDLTVDL--------------PDLGEIAFDDPVRMYLQEIGQVPLLTAEQEVELAK 108

Query: 145 RIEAG 149
            +EAG
Sbjct: 109 AMEAG 113


>gi|308232215|ref|ZP_07415319.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308373480|ref|ZP_07667590.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
 gi|308214639|gb|EFO74038.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308337452|gb|EFP26303.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
          Length = 413

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 176 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 235

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 236 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 295

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 296 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 355

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 356 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 413



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-- 149
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG  
Sbjct: 84  SGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLY 143

Query: 150 RAMMMASLCE 159
              +M  L E
Sbjct: 144 ATQLMTELSE 153


>gi|302386858|ref|YP_003822680.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197486|gb|ADL05057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 380

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 126/237 (53%), Positives = 179/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GYK STYA WW
Sbjct: 144 AKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWW 203

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A+ L M  + V
Sbjct: 204 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVSELAEALDMSEDKV 263

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE    +L  L  R
Sbjct: 264 MEIMQIAREPASLETPIGEEDDSNLGDFVADNNVVTPEGNVESVMLREHIDALLGDLKER 323

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 324 ERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 380



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 68/129 (52%), Gaps = 12/129 (9%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDE 86
           D   K+++LA+ +   + + E+N F   +E+++EQM+     L N G++V+   DD    
Sbjct: 8   DKLGKLVELAKTKHNALDVTEINNFFMGEELTTEQMDQIYTYLENRGVDVIPVIDDSVLT 67

Query: 87  EGSEDSLDLASSASNSSVFLQKRK------DSADR----STDDPVRMYLREMGSIELLSR 136
           +    S DL         F++         D+ D      T+DPVRMYL+E+G++ LL+ 
Sbjct: 68  DDVLLSDDLLLDDDLDDSFIKDVDEEDIDLDAIDLLEGIGTEDPVRMYLKEIGTVPLLNA 127

Query: 137 EGEIAIAKR 145
           E E+ +AKR
Sbjct: 128 EEELRLAKR 136


>gi|262202178|ref|YP_003273386.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
 gi|262085525|gb|ACY21493.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
          Length = 489

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 252 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 311

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 312 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 371

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 372 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 431

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 432 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 489



 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 170 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 217


>gi|54025729|ref|YP_119971.1| RNA polymerase sigma factor [Nocardia farcinica IFM 10152]
 gi|54017237|dbj|BAD58607.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 454

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 217 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 276

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 277 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 336

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 337 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 396

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 397 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 454



 Score = 45.1 bits (105), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 34/58 (58%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 125 SGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 182


>gi|160941160|ref|ZP_02088497.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435721|gb|EDP13488.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
          Length = 381

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 126/238 (52%), Positives = 179/238 (75%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GYK STYA W
Sbjct: 144 FAKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATW 203

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A+ L M  + 
Sbjct: 204 WIRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELAEALDMTEDK 263

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE    +L  L  
Sbjct: 264 VMEIMQIAREPASLETPIGEEDDSNLGDFVADNNVVTPEGNVESVMLREHIDALLGDLKE 323

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 324 RERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 45.8 bits (107), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 74/153 (48%), Gaps = 20/153 (13%)

Query: 28  DDSWKKMIKLAR----QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           DD  KK+ KL      +   +   E+N F   D +S EQM+   + L    I+VV    L
Sbjct: 4   DDFLKKLEKLVEHAKTKHNTLDAGEINDFFTGDNLSPEQMDQIYSYLEGRNIDVVPV--L 61

Query: 84  EDEEGSEDSLDLASSASNSSV----FLQKRK------DSADR----STDDPVRMYLREMG 129
           ++   +ED++ L     +  +    F++  +      D+ D      T+DPVRMYL+E+G
Sbjct: 62  DEAMLTEDTVLLDDIDLDLDLDDDSFIKDAEEEEIDLDAVDLLEGIGTEDPVRMYLKEIG 121

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           ++ LL+ + E+ +A+R   G       L E+ L
Sbjct: 122 TVPLLTADEELDLAQRKADGDEFAKERLIEANL 154


>gi|239626154|ref|ZP_04669185.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239520384|gb|EEQ60250.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 381

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 126/237 (53%), Positives = 179/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GYK STYA WW
Sbjct: 145 AKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A+ L M  + V
Sbjct: 205 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELAEALDMTEDKV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE    +L  L  R
Sbjct: 265 MEIMQIAREPASLETPIGEEDDSNLGDFVADNNVVTPEGNVESVMLREHIDALLGDLKER 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 325 ERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 45/153 (29%), Positives = 75/153 (49%), Gaps = 20/153 (13%)

Query: 28  DDSWKKMIKLAR----QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           DD  KK+ KL      +   +   E+N F   D +S EQM+   + L N  I+VV    L
Sbjct: 4   DDFLKKLEKLVEHAKSKHNTLDAGEINDFFTGDNLSPEQMDQIYSYLENRNIDVVPV--L 61

Query: 84  EDEEGSEDSLDLASSASNSSV----FLQKRK------DSADR----STDDPVRMYLREMG 129
           ++   +ED++ L     +  +    F++  +      D+ D      T+DPVRMYL+E+G
Sbjct: 62  DEAMLTEDTVLLDDIDLDLDLDDDSFIKDAEEEEIDLDAVDLLEGIGTEDPVRMYLKEIG 121

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           ++ LL+ + E+ +A+R   G       L E+ L
Sbjct: 122 TVPLLTADEELNLAQRKADGDDYAKERLIEANL 154


>gi|120403451|ref|YP_953280.1| RNA polymerase sigma factor [Mycobacterium vanbaalenii PYR-1]
 gi|119956269|gb|ABM13274.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 478

 Score =  274 bits (700), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 241 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 300

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 301 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 360

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 361 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 420

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 421 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 478



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 46/86 (53%), Gaps = 5/86 (5%)

Query: 79  DGDD---LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           DGDD    E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+
Sbjct: 133 DGDDDGVAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLN 192

Query: 136 REGEIAIAKRIEAG--RAMMMASLCE 159
            E E+ +AKRIEAG     +MA L +
Sbjct: 193 AEEEVELAKRIEAGLYATQLMAELAD 218


>gi|254821650|ref|ZP_05226651.1| RNA polymerase sigma factor [Mycobacterium intracellulare ATCC
           13950]
          Length = 488

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 251 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 310

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 311 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 370

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 371 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 430

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 431 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 488



 Score = 45.1 bits (105), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 169 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 216


>gi|331003577|ref|ZP_08327074.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412418|gb|EGG91809.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 409

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 125/237 (52%), Positives = 179/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  G+K STYA WW
Sbjct: 172 AKQRLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGFKLSTYATWW 231

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A +L M  E V
Sbjct: 232 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELANELGMTEEKV 291

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++I +EP SLETPIG+ED S+LGDF+ D N ++P  +     LRE    +L  L  R
Sbjct: 292 MEIMQIAREPASLETPIGEEDDSNLGDFVADANVLTPEGNVESVMLREHIDTLLGDLKER 351

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 352 ERQVIVLRFGLEDGHPRTLEEVGKEFKVTRERIRQIEAKALRKLRNPVRSKRIRDFL 408



 Score = 42.0 bits (97), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 38/142 (26%), Positives = 64/142 (45%), Gaps = 34/142 (23%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---------------------- 81
           ++I E+N F    E+++E +E   + L N GI + +                        
Sbjct: 51  LSIGEINDFFADTELNTESIEQIYSYLENKGIEINEDSVDDMNIDIDNIDNITDEDSLLL 110

Query: 82  -DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D E ++ SE+ +DL++      V            T+DPVRMYL+E+G++ LL+   E+
Sbjct: 111 DDDEFDKDSEEDIDLSAIDLLEGV-----------GTEDPVRMYLKEIGTVPLLTANEEL 159

Query: 141 AIAKRIEAGRAMMMASLCESPL 162
            +AKR + G       L E+ L
Sbjct: 160 ELAKRKQDGDEYAKQRLIEANL 181


>gi|315652381|ref|ZP_07905370.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
 gi|315485355|gb|EFU75748.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
          Length = 410

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 125/237 (52%), Positives = 178/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  G+K STYA WW
Sbjct: 173 AKQRLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGFKLSTYATWW 232

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A  L M  E V
Sbjct: 233 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELANALDMTEEKV 292

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++I +EP SLETPIG+ED S+LGDF+ D N ++P  +     LRE    +L  L  R
Sbjct: 293 MEIMQIAREPASLETPIGEEDDSNLGDFVADSNVLTPEGNVESVMLREHIDTLLGDLKER 352

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 353 ERQVIVLRFGLEDGHPRTLEEVGKEFKVTRERIRQIEAKALRKLRNPVRSKRIRDFL 409



 Score = 45.1 bits (105), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 66/152 (43%), Gaps = 35/152 (23%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD---------------------- 81
           + I E+N F    E++S+ +E   + L N GI + +                        
Sbjct: 51  LNIGEINDFFAGIELNSDSIEQIYSYLENKGIEINENSSDDLNIDIDNIDNITDEDSLLL 110

Query: 82  DLEDE--EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           D EDE  + SE+ +DL++      V            T+DPVRMYL+E+G++ LL+   E
Sbjct: 111 DDEDEFDKDSEEDIDLSAIDLLEGV-----------GTEDPVRMYLKEIGTVPLLTANEE 159

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           + +AKR + G       L E+ L     I  R
Sbjct: 160 LELAKRKQDGDEYAKQRLIEANLRLVVSIAKR 191


>gi|226356403|ref|YP_002786143.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226318393|gb|ACO46389.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 547

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 138/241 (57%), Positives = 182/241 (75%), Gaps = 3/241 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW
Sbjct: 307 ARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWW 366

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           ++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T EEIA+ +    +  
Sbjct: 367 IRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREATHEEIAEAMGPGWDAA 426

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+++A +  L E   + L+ LT
Sbjct: 427 KVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVENAAKTLLSEELEKALSKLT 486

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFL 680
            RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KLR FL
Sbjct: 487 EREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLKYHESRTRKLRDFL 546

Query: 681 D 681
           D
Sbjct: 547 D 547



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 26/33 (78%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++DPVR YL E+G + LL+ E EIA+A+RIE G
Sbjct: 244 SNDPVRQYLHEIGRVSLLTLEEEIALARRIEEG 276


>gi|118469122|ref|YP_887090.1| RNA polymerase sigma factor [Mycobacterium smegmatis str. MC2 155]
 gi|555680|gb|AAA85642.1| sigma factor MysA [Mycobacterium smegmatis]
 gi|118170409|gb|ABK71305.1| sigma factor MysA [Mycobacterium smegmatis str. MC2 155]
          Length = 466

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 229 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 288

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 289 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 348

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 349 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 408

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 409 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 466



 Score = 46.2 bits (108), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 80  GDDLEDEEGSED--SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            DD  DE   +D  S D       S    Q RKD+   ++ D VR YL+++G + LL+ E
Sbjct: 123 ADDDIDEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAE 182

Query: 138 GEIAIAKRIEAG 149
            E+ +AKRIEAG
Sbjct: 183 EEVELAKRIEAG 194


>gi|18477828|emb|CAC83737.1| RNA polymerase sigma 70 [Rhodococcus fascians]
          Length = 474

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 136/267 (50%), Positives = 190/267 (71%), Gaps = 6/267 (2%)

Query: 417 SVETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           S E G  + +++ R +  + R G    + AK  ++EANLRLV+S+AK+YT RG+ FLDLI
Sbjct: 212 SAEKGEKLPVAQRRDMTWICRDG----NRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLI 267

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R
Sbjct: 268 QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGR 327

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R +   + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED
Sbjct: 328 IQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIED 387

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             AV  +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRE
Sbjct: 388 SEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRE 447

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 448 RIRQIESKTMSKLRHPSRSQVLRDYLD 474



 Score = 45.8 bits (107), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 47/89 (52%), Gaps = 9/89 (10%)

Query: 70  LSNMGINVVDG-------DDLEDEEGSED--SLDLASSASNSSVFLQKRKDSADRSTDDP 120
           L+    +VV+G       +D   E  +ED  S D       S    Q RKD+   ++ D 
Sbjct: 114 LAAAANDVVEGRRRRQPEEDATSEPTAEDKASGDFVWDEEESEALRQARKDAELTASADS 173

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAG 149
           VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 174 VRAYLKQIGKVALLNAEEEVELAKRIEAG 202


>gi|283779933|ref|YP_003370688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438386|gb|ADB16828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 545

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 150/365 (41%), Positives = 212/365 (58%), Gaps = 36/365 (9%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + K V+LV  ++L  +R+  L ++L DI  R+                       R Q R
Sbjct: 202 RNKCVRLVEEMNLRNNRLQPLFDKLSDILGRMK--------------------TLRSQIR 241

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E + H VS       G     +  E+  +++I  E  +      +  +E+R         
Sbjct: 242 EANIHGVS------GGRTAQQLRKELVHLMRITLETPATLKRRIVRTNEYRE-------- 287

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK+ +   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +KF++  GYKFS
Sbjct: 288 --NYDAAKRVLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEYARGYKFS 345

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQS TIR+PVHM D + KV    R++  ++ REPTPEE+A+   
Sbjct: 346 TYATWWIRQAITRAIADQSRTIRVPVHMIDTMSKVRAVTRQLVQELGREPTPEEVARVAG 405

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + ++  R VLK+ ++P+SL+ P+GD D S+ G+F+ D     PL    Q  L+      +
Sbjct: 406 LTLDDARCVLKMARQPLSLDQPVGDHDDSYFGEFLADHREEDPLYDTHQQALKHQIEEAM 465

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L  RE  +LR+R+G+     +TLEEVGK F VTRER+RQIE KA+RKL+ P R++ L 
Sbjct: 466 QGLNYREREILRLRYGLTDGYAYTLEEVGKIFSVTRERVRQIETKAVRKLQQPYRNRSLT 525

Query: 678 SFLDG 682
           SFLDG
Sbjct: 526 SFLDG 530



 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 30/81 (37%), Positives = 41/81 (50%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           +TDDPVRMYL +MG I LL+R  EI  A+ IEA R     S+  +    Q  +   + + 
Sbjct: 74  ATDDPVRMYLMQMGQIPLLNRTQEIDSARTIEATRLKFRHSMLATDYVLQGAVELLERVR 133

Query: 176 DGTTLLREIIDLEACIGPESK 196
           DG   L   I++      E K
Sbjct: 134 DGQLRLDRTIEVSVTNTSEKK 154


>gi|297571337|ref|YP_003697111.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
 gi|296931684|gb|ADH92492.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 510

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 273 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDYAKGYKFSTYATWW 332

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT EE+A +L M  E V
Sbjct: 333 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTVEELAHELDMTEEKV 392

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 393 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVGFTLLQEQLHQVLDTLSER 452

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 453 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 510



 Score = 43.9 bits (102), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 9/62 (14%)

Query: 97  SSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           ++A  S  F+ +  D  D          +T DPV+ YL+++G + LL+ E E+ +AKRIE
Sbjct: 181 TTAKRSGAFIVRDSDDTDEPVQRVHVAGATADPVKDYLKQIGKVALLNAEEEVELAKRIE 240

Query: 148 AG 149
           AG
Sbjct: 241 AG 242


>gi|240169695|ref|ZP_04748354.1| RNA polymerase sigma factor [Mycobacterium kansasii ATCC 12478]
          Length = 518

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 281 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 340

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 341 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 400

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 401 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 460

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 461 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 518



 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +MA + E
Sbjct: 199 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAE 258


>gi|158313089|ref|YP_001505597.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108494|gb|ABW10691.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 423

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 124/243 (51%), Positives = 178/243 (73%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFST
Sbjct: 181 TDGQAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFST 240

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L M
Sbjct: 241 YATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDM 300

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL 
Sbjct: 301 PIEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIDNVLG 360

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR 
Sbjct: 361 ALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLRE 420

Query: 679 FLD 681
           FLD
Sbjct: 421 FLD 423



 Score = 45.1 bits (105), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 59/117 (50%), Gaps = 15/117 (12%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I   R+ G ++  EL   L   ++  E +   ++ L   GI++V        E  E+ 
Sbjct: 54  ELIARGRETGELSRSELREALEAADIGVELLPALISRLGAAGIDLV--------EEEEER 105

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +   + A+  +V      D A   T D VRMYLRE+G + LL+   E+ ++KR+EAG
Sbjct: 106 VTPGAPAAGRTV-----ADHA--GTADLVRMYLREIGKVPLLNAAQEVELSKRVEAG 155


>gi|296117756|ref|ZP_06836340.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969487|gb|EFG82728.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
          Length = 471

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 234 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 293

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 294 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 353

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 354 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSER 413

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 414 EAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 471



 Score = 45.8 bits (107), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++A+RIEAG
Sbjct: 146 SATLRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAERIEAG 193


>gi|163848612|ref|YP_001636656.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526547|ref|YP_002571018.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163669901|gb|ABY36267.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450426|gb|ACM54692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 381

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 173/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 144 ARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYATWW 203

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V RT+ R+   ++REPTPEEIA  + +    V
Sbjct: 204 IRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHRLQQTMQREPTPEEIADAMGISAGKV 263

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE    VL  L  R
Sbjct: 264 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASLLREQLEEVLMKLPER 323

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 324 ERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 381



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 56/111 (50%), Gaps = 7/111 (6%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++++  AR RGY+T  ++ A  P  E    +++   AML   GI V++  D  D  G  D
Sbjct: 3   EQLLAAARVRGYITHADILATFPNPEHDIAEIDQLYAMLQAEGIKVIESSDELD--GPTD 60

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                      +  +    D  D + DDPVRMYL+E+G + LL+ E E+ +
Sbjct: 61  F-----EPDPDADLIADLPDLGDIAFDDPVRMYLQEIGQVPLLTAEQEVEL 106


>gi|319949012|ref|ZP_08023109.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
 gi|319437300|gb|EFV92323.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
          Length = 460

 Score =  273 bits (699), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 223 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 282

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 283 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 342

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 343 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLRSVLDTLSER 402

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 403 EAGVVRLRFGLTDGLPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 460



 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-- 149
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG  
Sbjct: 131 SGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLY 190

Query: 150 RAMMMASLCE 159
               MA + E
Sbjct: 191 ATWYMAQVTE 200


>gi|282899714|ref|ZP_06307678.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195593|gb|EFA70526.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 390

 Score =  273 bits (699), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 137/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +  FR+ + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 139 LPLPTFRYRLHVGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 191

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 192 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 251

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 252 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPE 310

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   ++ LRE   RVL SL PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 311 DQVSKSLLREDLERVLDSLGPRERDVLRLRYGLDNGRMKTLEEIGQIFNVTRERIRQIEA 370

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 371 KALRKLRHPNRNSVLKEYI 389


>gi|119512308|ref|ZP_01631394.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119463021|gb|EAW43972.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 391

 Score =  273 bits (699), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 137/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I +  FR+ + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 140 IPLPAFRYRLHIGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 192

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 193 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 252

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 253 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPE 311

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 312 DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEA 371

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 372 KALRKLRHPNRNSVLKEYI 390


>gi|17232755|ref|NP_489303.1| RNA polymerase sigma factor RpoD [Nostoc sp. PCC 7120]
 gi|75907632|ref|YP_321928.1| RNA polymerase sigma factor RpoD [Anabaena variabilis ATCC 29413]
 gi|133465|sp|P26683|RPOD_ANASP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|142108|gb|AAA22043.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134402|dbj|BAB76962.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|75701357|gb|ABA21033.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 390

 Score =  273 bits (698), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 136/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +  FR+ + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 139 LPLPAFRYRLHIGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 191

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 192 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 251

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 252 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPE 310

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 311 DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEA 370

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 371 KALRKLRHPNRNSVLKEYI 389


>gi|296171852|ref|ZP_06852951.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
 gi|295893936|gb|EFG73705.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
          Length = 503

 Score =  273 bits (698), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 266 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 325

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 326 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 385

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 386 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 445

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 446 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 503



 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +MA + E
Sbjct: 184 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAE 243


>gi|308183886|ref|YP_003928019.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
 gi|308059806|gb|ADO01702.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
          Length = 679

 Score =  273 bits (698), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 418 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 477

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 478 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 537

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 538 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 597

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 598 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 657

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 658 SSAIKKLRSPQYGRILRNYL 677


>gi|13195265|gb|AAK15630.1|AF326348_2 RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 467

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 230 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 289

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 290 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 349

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 350 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSER 409

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 410 EAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 467



 Score = 45.8 bits (107), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++A+RIEAG
Sbjct: 142 SATLRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAERIEAG 189


>gi|227504950|ref|ZP_03934999.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
 gi|227198459|gb|EEI78507.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
          Length = 465

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 144/298 (48%), Positives = 199/298 (66%), Gaps = 10/298 (3%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           VS AK    G +  +    +D + K R E    +    +S  E R + S+ R G      
Sbjct: 178 VSLAKRIEAGLYAQY---RMDEMEKARAEGDKAA---KLSPMEKRDLRSIARDGRK---- 227

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 228 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 287

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E+AK++ +  E V
Sbjct: 288 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPIELAKEMDITEEKV 347

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 348 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSER 407

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 408 EAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 465



 Score = 45.8 bits (107), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 32/43 (74%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 145 QARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 187


>gi|15827492|ref|NP_301755.1| RNA polymerase sigma factor [Mycobacterium leprae TN]
 gi|221229969|ref|YP_002503385.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
 gi|699190|gb|AAA62955.1| rpoT [Mycobacterium leprae]
 gi|4587111|dbj|BAA76621.1| RpoT [Mycobacterium leprae]
 gi|13093042|emb|CAC31403.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933076|emb|CAR71117.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 574

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 134/262 (51%), Positives = 188/262 (71%), Gaps = 4/262 (1%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T +  ++ R ++ + R G+     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+
Sbjct: 317 TKLPTAQRRDMMWICRDGDR----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNL 372

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +
Sbjct: 373 GLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQREL 432

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV 
Sbjct: 433 LQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVV 492

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQI
Sbjct: 493 AVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQI 552

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E+K + KL+HPSRS+ LR +LD
Sbjct: 553 ESKTMSKLRHPSRSQVLRDYLD 574



 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 34/102 (33%), Positives = 51/102 (50%), Gaps = 2/102 (1%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +E  E T A  ++      D + +E  E  + S D       S    Q RKD+   ++ D
Sbjct: 213 TEDGEATAATKTDEASTDDDEEIVEPTEKDKASGDFVWDEDESEALRQARKDAELTASAD 272

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
            VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 273 SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 314


>gi|323484891|ref|ZP_08090246.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323693741|ref|ZP_08107938.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323401772|gb|EGA94115.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323502192|gb|EGB18057.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 374

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 128/246 (52%), Positives = 184/246 (74%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK E + + AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GY
Sbjct: 130 RKAEGDDN-AKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGY 188

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K STYA WW++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+++
Sbjct: 189 KLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVAELSE 248

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L M  + V ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE   
Sbjct: 249 ALEMSEDKVMEIMQIAREPASLETPIGEEDDSNLGDFVADSNVVTPEGNVESVMLREHID 308

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +L  L  RE +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK
Sbjct: 309 ALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 368

Query: 675 KLRSFL 680
           ++R FL
Sbjct: 369 RIRDFL 374



 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/130 (31%), Positives = 70/130 (53%), Gaps = 12/130 (9%)

Query: 29  DSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +  K+++ LA+ ++  + I E+N F   D +S+EQME   + L N  I+++   ++ DE 
Sbjct: 8   EKLKRLVDLAKTKQNALDITEINNFFAGDNLSTEQMEQIYSYLENSNIDIIP--EVIDE- 64

Query: 88  GSEDSLDLASSASNSSVFLQKRK----DSADR----STDDPVRMYLREMGSIELLSREGE 139
                 D          FL++ +    D+ D      T+DPVRMYL+E+G++ LLS + E
Sbjct: 65  TILAEDDALLLDDADDDFLKEEEEIDLDAIDLLEGIGTEDPVRMYLKEIGTVPLLSADEE 124

Query: 140 IAIAKRIEAG 149
           + +AKR   G
Sbjct: 125 LRLAKRKAEG 134


>gi|227549126|ref|ZP_03979175.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078794|gb|EEI16757.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 520

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 283 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 342

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 343 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 402

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 403 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSER 462

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 463 EAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 520



 Score = 46.2 bits (108), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL  E E+++AKRIEAG
Sbjct: 195 SAALRQARKDAQLTASADSVRAYLKQIGKVALLDAELEVSLAKRIEAG 242


>gi|254424926|ref|ZP_05038644.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196192415|gb|EDX87379.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 404

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 168 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 227

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 228 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKL 287

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL++L+PR
Sbjct: 288 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPEDEVSKSLLREDLESVLSTLSPR 346

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 347 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 403


>gi|189485247|ref|YP_001956188.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
 gi|170287206|dbj|BAG13727.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
          Length = 573

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 155/398 (38%), Positives = 241/398 (60%), Gaps = 22/398 (5%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
           + L+  +++ +  E+   K K  + ++V L+  L+LNQ +I  L+ ++  I++++   + 
Sbjct: 187 KKLKLKSISCKDKEQYKEKVKEFRSEIVSLIVELNLNQDKIRRLINKIKTIAQKLNEIKE 246

Query: 355 ELLRLAQSYG--------IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
            L R  + Y         + +   L +    E         KD  E          V ++
Sbjct: 247 GLRRFERKYKNSFSKVQVLFKSCNLGKISSAEFKKSTGLSMKDVAED------IANVKTL 300

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM--VEANLRLVISVAKKYT 464
           L     +K  +++ G  I+    I +  R  E E  I + +M  +EAN RLV+S+AKK+ 
Sbjct: 301 L-----VKQTNLKDGFVITPEEMIETDRRIRELEYVIHRDKMKLIEANFRLVVSIAKKHV 355

Query: 465 N-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
               L+  DLIQEGN+GL KA EKF+W  G+KFSTYA WW++Q+I R+IADQ+ TIRIPV
Sbjct: 356 GISNLELSDLIQEGNLGLSKAVEKFEWKRGFKFSTYATWWIRQSINRAIADQARTIRIPV 415

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM++ I K+ ++ +     + REPT +E +K L +  + +R++LK+ +EP+SL  P+G+E
Sbjct: 416 HMKELISKLTKSKKECQQNMGREPTIQEYSKILKLSCDRIRRILKMMQEPVSLAMPVGEE 475

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S L DFIED+N+ +P+    Q  L+    +VLA+L PRE  ++R+R+GIG+    TLE
Sbjct: 476 EDSRLEDFIEDQNSPNPVVKTQQYRLQLELEKVLATLAPREAEIIRLRYGIGIGYPSTLE 535

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGK+F +TRER+RQIEAKAIRKLK+P R+K LR +LD
Sbjct: 536 EVGKKFGITRERVRQIEAKAIRKLKYPRRNKSLREYLD 573



 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/142 (24%), Positives = 70/142 (49%), Gaps = 10/142 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D +K +I   +++GY+T E ++  LP   + +E+++     L N+GI V+D  +   ++ 
Sbjct: 5   DLFKGLIDTGKEQGYLTYEAISKNLPQRSMIAEEIDGFFVTLDNLGIKVLDNREYRSDKV 64

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +   ++          +++   + +    +PVRMYL EM  + LL R  E+ + K I  
Sbjct: 65  KKSRGEV----------VERSMKTVNEEDINPVRMYLSEMAKVPLLERNMELKLVKSIRE 114

Query: 149 GRAMMMASLCESPLTFQALIIW 170
               + + + ESPL  + +  W
Sbjct: 115 NEDRLKSIVLESPLIIKEIRNW 136


>gi|156744261|ref|YP_001434390.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156235589|gb|ABU60372.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 399

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 125/238 (52%), Positives = 173/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 162 ARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWW 221

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V R + ++   ++REPTPEEIA  + +    V
Sbjct: 222 IRQAITRAIADQSRTIRLPVHMGEAISQVKRASHKLQQMMQREPTPEEIADAMGISSTKV 281

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE    VL  L  R
Sbjct: 282 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASMLREQLEEVLQKLPER 341

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 342 ERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 399



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/168 (28%), Positives = 80/168 (47%), Gaps = 16/168 (9%)

Query: 23  VFDFSDDSWKK----MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           + + +  +W +    ++ + R RG++T  E+   LP  E     ++   A L   GI VV
Sbjct: 11  IVEQTRQAWAQTLEYLLDIGRTRGFLTYNEILEALPQPEYHVADVDQLYASLQAEGIRVV 70

Query: 79  DGDDLEDEEGSEDSLDLA-SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
                      E  LD++   A      L +  D  D + DDPVRMYL+E+G + LLS E
Sbjct: 71  -----------ETPLDMSDHGAVGDDELLAEMPDLTDVALDDPVRMYLQEIGQVPLLSAE 119

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            E+ +AK +EAG     A  CE   ++Q  +++  ++  G    + +I
Sbjct: 120 QEVMLAKAMEAGHRARRALECEEYSSWQERMMYEQQVAQGNEARQHLI 167


>gi|16332132|ref|NP_442860.1| RNA polymerase sigma factor RpoD [Synechocystis sp. PCC 6803]
 gi|47717353|sp|P74565|RPOD_SYNY3 RecName: Full=RNA polymerase sigma factor rpoD
 gi|1653761|dbj|BAA18672.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 425

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA+K+ M +E +
Sbjct: 249 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKL 308

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 309 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPR 367

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 368 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 424


>gi|32476381|ref|NP_869375.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|32446926|emb|CAD78832.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|327539012|gb|EGF25646.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica WH47]
          Length = 519

 Score =  273 bits (698), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 138/278 (49%), Positives = 192/278 (69%), Gaps = 3/278 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           + +L  R +I +   ET  S+   R+ V M+     +   AK+E+ E NLRLV+S+AKKY
Sbjct: 245 EQLLHERRQILTACQETPTSL---RNRVKMLGSVYSDYQQAKRELSEGNLRLVVSIAKKY 301

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL FLDLIQEGN GLM+A +KF++  G+KF TYA WW++QAITR++ADQS TIRIPV
Sbjct: 302 RNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQSRTIRIPV 361

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + + +V   AR++  ++ REP+ EE A++  + +E  R+VL +++ PISL+ P+G+ 
Sbjct: 362 HMVETMSRVRNVARQLLQELGREPSIEETARRADVTIEEARRVLTMSRFPISLDRPVGNS 421

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S  GD + D  A SP   A Q  LR+  T VL SL+ RE  ++++R+G+G    +TLE
Sbjct: 422 EDSQFGDLLPDGTAESPQIGATQEMLRQRITGVLKSLSYREREIIKLRYGLGDGYSYTLE 481

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVG  F VTRERIRQIEAKA+RKL+ PSRS+ L  FLD
Sbjct: 482 EVGHIFKVTRERIRQIEAKAVRKLQQPSRSQDLVGFLD 519



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 32/50 (64%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           D ++  +DDPVRMYL +MG I LL+R  EI +AKRIE  R      L E+
Sbjct: 60  DESETWSDDPVRMYLTQMGEIPLLTRRQEIELAKRIEETRRRFRTKLLEN 109


>gi|227833276|ref|YP_002834983.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184260|ref|ZP_06043681.1| RNA polymerase sigma factor [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454292|gb|ACP33045.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
          Length = 485

 Score =  273 bits (698), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 143/298 (47%), Positives = 199/298 (66%), Gaps = 10/298 (3%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           VS AK    G +  +    +D + K R E    +    +S  E R + ++ R G      
Sbjct: 198 VSLAKRIEAGLYAQY---RMDEMEKARAEGDKAA---KLSPMEKRDMRAIARDGRK---- 247

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 248 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 307

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E+AK++ +  E V
Sbjct: 308 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPLELAKEMDITEEKV 367

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 368 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSER 427

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 428 EAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 485



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 160 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 207


>gi|2267165|gb|AAC64856.1| sigma 80 [Helicobacter pylori]
          Length = 685

 Score =  273 bits (698), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 424 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 483

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 484 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 543

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 544 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 603

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 604 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 663

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 664 SSAIKKLRSPQYGRILRNYL 683


>gi|220906934|ref|YP_002482245.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863545|gb|ACL43884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 378

 Score =  273 bits (698), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 136/262 (51%), Positives = 189/262 (72%), Gaps = 8/262 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E  + +  FRH + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 124 EVDMPLQSFRHRLHIGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 176

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 177 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKL 236

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 237 LSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGE 295

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D   +  LRE    VL +L+PRE  VL++R+G+      TLEE+G+ F VTRERIRQ
Sbjct: 296 TPEDQVSKNLLREDLETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTRERIRQ 355

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 356 IEAKALRKLRHPNRNSVLKEYI 377


>gi|169630092|ref|YP_001703741.1| RNA polymerase sigma factor [Mycobacterium abscessus ATCC 19977]
 gi|169242059|emb|CAM63087.1| Probable RNA polymerase sigma factor RpoD (Sigma-A) [Mycobacterium
           abscessus]
          Length = 467

 Score =  273 bits (698), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 230 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 289

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 290 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 349

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 350 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 409

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 410 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 467



 Score = 47.8 bits (112), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 29/70 (41%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           GDD E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E
Sbjct: 127 GDD-EPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEE 185

Query: 140 IAIAKRIEAG 149
           + +AKRIEAG
Sbjct: 186 VELAKRIEAG 195


>gi|4587113|dbj|BAA76622.1| RpoT [Mycobacterium leprae]
          Length = 576

 Score =  273 bits (698), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 134/262 (51%), Positives = 188/262 (71%), Gaps = 4/262 (1%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T +  ++ R ++ + R G+     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+
Sbjct: 319 TKLPTAQRRDMMWICRDGDR----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNL 374

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +
Sbjct: 375 GLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQREL 434

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV 
Sbjct: 435 LQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVV 494

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQI
Sbjct: 495 AVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQI 554

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E+K + KL+HPSRS+ LR +LD
Sbjct: 555 ESKTMSKLRHPSRSQVLRDYLD 576



 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 34/102 (33%), Positives = 51/102 (50%), Gaps = 2/102 (1%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +E  E T A  ++      D + +E  E  + S D       S    Q RKD+   ++ D
Sbjct: 215 TEDGEATAATKTDEASTDDDEEIVEPTEKDKASGDFVWDEDESEALRQARKDAELTASAD 274

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
            VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 275 SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 316


>gi|282896628|ref|ZP_06304643.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281198498|gb|EFA73384.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 390

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 137/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +  FR+ + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 139 LPLPTFRYRLHVGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 191

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 192 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 251

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 252 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPE 310

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   ++ LRE   RVL SL PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 311 DQVSKSLLREDLERVLDSLGPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEA 370

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 371 KALRKLRHPNRNSVLKEYI 389


>gi|172040581|ref|YP_001800295.1| RNA polymerase sigma factor [Corynebacterium urealyticum DSM 7109]
 gi|171851885|emb|CAQ04861.1| RNA polymerase sigma factor A [Corynebacterium urealyticum DSM
           7109]
          Length = 545

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 308 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 367

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ + V+ V
Sbjct: 368 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAREMDITVDKV 427

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 428 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSER 487

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 488 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 545



 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 35/48 (72%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q R+D+A  ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 226 SAALRQARRDAALTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 273


>gi|317008763|gb|ADU79343.1| RNA polymerase sigma factor RpoD [Helicobacter pylori India7]
          Length = 676

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 415 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 474

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 475 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 534

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 535 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 594

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 595 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 654

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 655 SSAIKKLRSPQYGRILRNYL 674



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 161 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 218


>gi|145224520|ref|YP_001135198.1| RNA polymerase sigma factor [Mycobacterium gilvum PYR-GCK]
 gi|315444851|ref|YP_004077730.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
 gi|145217006|gb|ABP46410.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
 gi|315263154|gb|ADT99895.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
          Length = 488

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 251 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 310

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 311 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 370

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 371 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 430

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 431 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 488



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 3/84 (3%)

Query: 79  DGDDL-EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           D D L E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E
Sbjct: 145 DDDSLPEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAE 204

Query: 138 GEIAIAKRIEAGR--AMMMASLCE 159
            E+ +AKRIEAG     +MA   E
Sbjct: 205 EEVELAKRIEAGLYCTQLMAEFAE 228


>gi|312139434|ref|YP_004006770.1| sigma-70 factor siga [Rhodococcus equi 103S]
 gi|325672677|ref|ZP_08152373.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|311888773|emb|CBH48085.1| sigma-70 factor SigA [Rhodococcus equi 103S]
 gi|325556554|gb|EGD26220.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 459

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 222 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 281

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 282 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 341

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 342 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 401

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 402 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 459



 Score = 45.1 bits (105), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 140 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 187


>gi|68536164|ref|YP_250869.1| RNA polymerase sigma factor [Corynebacterium jeikeium K411]
 gi|68263763|emb|CAI37251.1| RNA polymerase sigma factor A [Corynebacterium jeikeium K411]
          Length = 544

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 307 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKGYKFSTYATWW 366

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ + V+ V
Sbjct: 367 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAREMDITVDKV 426

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 427 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSER 486

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 487 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 544



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 225 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 272


>gi|266625476|ref|ZP_06118411.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288862622|gb|EFC94920.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 381

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 126/237 (53%), Positives = 178/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GYK STYA WW
Sbjct: 145 AKERLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+  E+A  L M  + V
Sbjct: 205 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELADALDMSEDKV 264

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE    +L  L  R
Sbjct: 265 MEIMQIAREPASLETPIGEEDDSNLGDFVADNNVVTPEGNVESVMLREHIDALLGDLKER 324

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 325 ERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 64/126 (50%), Gaps = 13/126 (10%)

Query: 33  KMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGDDLEDEEG 88
           K+++L + +   + + E+N F   D ++ EQM+   + L N G++V+   D   L D+  
Sbjct: 12  KLVELGKTKHNALDVTEINNFFMGDSLTPEQMDQIYSYLENRGVDVIPVIDDSILADDVL 71

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSIELLSREGE 139
             D   L     + S      ++  D           T+DPVRMYL+E+G++ LLS + E
Sbjct: 72  LSDDALLLDDDLDDSFIKGADEEDIDLDAIDLLEGIGTEDPVRMYLKEIGTVPLLSADEE 131

Query: 140 IAIAKR 145
           + +AKR
Sbjct: 132 LRLAKR 137


>gi|317013514|gb|ADU80950.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Gambia94/24]
          Length = 681

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 420 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 479

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 480 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 539

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 540 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 599

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 600 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 659

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 660 SSAIKKLRSPQYGRILRNYL 679



 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 166 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 223


>gi|269219424|ref|ZP_06163278.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211120|gb|EEZ77460.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 592

 Score =  273 bits (697), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 132/238 (55%), Positives = 175/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 355 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDFTKGFKFSTYATWW 414

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT  E+AK+L M  E V
Sbjct: 415 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTTIELAKELDMTEEKV 474

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ R
Sbjct: 475 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVGFTLLQEQLRQVLDTLSER 534

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 535 EAGVVAMRFGLTDGQTKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 592



 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 13/83 (15%)

Query: 80  GDDLEDEEGSED----SLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLR 126
           G+D +D++G+E     +L   +  ++   F  K  D +D          +T DPV+ YL+
Sbjct: 239 GEDSDDKDGTERPRGRNLTEDAIPASKGAFTMKDSDESDEPAVRVHVAGATADPVKDYLK 298

Query: 127 EMGSIELLSREGEIAIAKRIEAG 149
           ++G + LL+ E E+ +A+RIEAG
Sbjct: 299 QIGKVPLLNAEEEVELARRIEAG 321


>gi|25991936|gb|AAN76995.1|AF481769_1 primary sigma 70 transcriptional factor [Frankia sp. ACN14a]
          Length = 385

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 124/238 (52%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 148 AKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWW 207

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP+E V
Sbjct: 208 IRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQV 267

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL  L PR
Sbjct: 268 VELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGGLNPR 327

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR FLD
Sbjct: 328 EREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLREFLD 385



 Score = 40.4 bits (93), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 19/131 (14%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           DD    D S  +  ++I   R+ G ++  EL   L   ++  E +   +A LS  G+ ++
Sbjct: 6   DDGDELDVS--AVAEVIARGREAGEISRSELRDALESADIGLELLPALIAKLSAAGVELL 63

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                                +   V    R  +    T D VRMYLRE+G + LL+   
Sbjct: 64  -----------------EEEETTDDVTAATRSTAEHAGTADLVRMYLREIGKVPLLNAAQ 106

Query: 139 EIAIAKRIEAG 149
           E+ ++KR+EAG
Sbjct: 107 EVELSKRVEAG 117


>gi|108562514|ref|YP_626830.1| RNA polymerase sigma factor RpoD [Helicobacter pylori HPAG1]
 gi|107836287|gb|ABF84156.1| RNA polymerase sigma-80 factor [Helicobacter pylori HPAG1]
          Length = 692

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 434 NKLKEILEQIKRGKLISDRAKNKMAQSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 493

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 494 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETG 553

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 554 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 613

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 614 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 673

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 674 IKKLRSPQYGRILRNYL 690


>gi|15611152|ref|NP_222803.1| RNA polymerase sigma factor RpoD [Helicobacter pylori J99]
 gi|11387124|sp|Q9ZMY3|RPOD_HELPJ RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|4154591|gb|AAD05665.1| RNA POLYMERASE SIGMA FACTOR (SIGMA-70) [Helicobacter pylori J99]
          Length = 681

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 420 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 479

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 480 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 539

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 540 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 599

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 600 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 659

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 660 SSAIKKLRSPQYGRILRNYL 679



 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 166 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 223


>gi|186686393|ref|YP_001869589.1| RNA polymerase sigma factor RpoD [Nostoc punctiforme PCC 73102]
 gi|8118663|gb|AAF73062.1|AF265349_1 primary vegetative sigma factor [Nostoc punctiforme]
 gi|186468845|gb|ACC84646.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 389

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 136/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +  FR+ + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 138 LPLPAFRYRLHVGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 190

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 191 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 250

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 251 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPE 309

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 310 DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEA 369

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 370 KALRKLRHPNRNSVLKEYI 388


>gi|300781032|ref|ZP_07090886.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
 gi|300532739|gb|EFK53800.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
          Length = 536

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 299 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 358

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 359 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 418

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 419 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSER 478

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 479 EAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 536



 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL  E E+++AKRIEAG
Sbjct: 211 SAALRQARKDAQLTASADSVRAYLKQIGKVALLDAEQEVSLAKRIEAG 258


>gi|225388598|ref|ZP_03758322.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
 gi|225045346|gb|EEG55592.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
          Length = 405

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/272 (50%), Positives = 188/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  +K I     ++  E   +     +G+ EA    K +VEANLRLV+S+AK+YT RG+
Sbjct: 136 IREYLKEIGAIALLTPEEEAGLAKRCAEGDEEAG---KRLVEANLRLVVSIAKRYTGRGM 192

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGNIGLMKA EKFD+  GY+ STYA WWVKQAITR++ADQ+ TIR+PVHM + 
Sbjct: 193 SFLDLVQEGNIGLMKAVEKFDYEKGYRLSTYATWWVKQAITRALADQARTIRLPVHMVEA 252

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ RT R +S ++ R+P+  E+A+ + M  + V ++++ + + +SLETP+GDED S L
Sbjct: 253 VNKIRRTQRDLSVQLGRDPSNRELAEAVGMTEKRVEELIQTSGDTVSLETPVGDEDGSSL 312

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D    S  D A    LRE    +L  L  RE +V+++RFG+      TLEEVG+Q
Sbjct: 313 GDFVADNAGDSTEDQAENVLLREEIDSMLQGLNERERQVIKLRFGLENGRPLTLEEVGRQ 372

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE  A+RKL++P RSKK+R FL
Sbjct: 373 FNVTRERIRQIETAALRKLRNPVRSKKVRDFL 404



 Score = 41.6 bits (96), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 32/47 (68%), Gaps = 5/47 (10%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRI-----EAGRAMMMASL 157
           ST DP+R YL+E+G+I LL+ E E  +AKR      EAG+ ++ A+L
Sbjct: 131 STGDPIREYLKEIGAIALLTPEEEAGLAKRCAEGDEEAGKRLVEANL 177


>gi|288920765|ref|ZP_06415065.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288347841|gb|EFC82118.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 425

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 124/243 (51%), Positives = 178/243 (73%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFST
Sbjct: 183 TDGQAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFST 242

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L M
Sbjct: 243 YATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELAFELDM 302

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL 
Sbjct: 303 PIEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIDNVLG 362

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR 
Sbjct: 363 ALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLRE 422

Query: 679 FLD 681
           FLD
Sbjct: 423 FLD 425



 Score = 41.2 bits (95), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 33/117 (28%), Positives = 58/117 (49%), Gaps = 13/117 (11%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I   R+ G ++  EL   L   ++  E +   +A L   GI++V           E+ 
Sbjct: 54  ELIARGRETGELSRAELREALEAADIGVELLPALIARLGAAGIDLV-----------EEE 102

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            +   + + ++   +   D A   T D VRMYLRE+G + LL+   E+ ++KR+EAG
Sbjct: 103 EESERAPAGATTPGRTVADHA--GTADLVRMYLREIGKVPLLNAAQEVELSKRVEAG 157


>gi|260578861|ref|ZP_05846767.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
 gi|258603008|gb|EEW16279.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
          Length = 552

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 315 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKGYKFSTYATWW 374

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ + V+ V
Sbjct: 375 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAREMDITVDKV 434

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 435 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSER 494

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 495 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 552



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 233 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 280


>gi|269793869|ref|YP_003313324.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
 gi|269096054|gb|ACZ20490.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
          Length = 342

 Score =  273 bits (697), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 173/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +VEANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 105 AKSHLVEANLRLVVSIAKKYTGRGLLFLDLIQEGNTGLIRAVEKFDYAKGFKFSTYATWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQ+ TIRIPVHM + I+KV R  R+M   + REPTPEE+A +L M  E V
Sbjct: 165 IRQAITRGMADQARTIRIPVHMVEVINKVSRAQRQMLQDLGREPTPEELALELDMTPEKV 224

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G+E  S  GD IED  AV P D+   + L++    +L +L+ R
Sbjct: 225 LEVQKHGREPISLHTPLGEEGGSEFGDLIEDTEAVVPADAVNFSFLQQQIHGILDTLSER 284

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 285 EAGVITMRYGLTDGLPKTLDQIGHVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 342



 Score = 41.6 bits (96), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 24/48 (50%), Positives = 31/48 (64%), Gaps = 2/48 (4%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           A  +T DPV+ YL+ +G + LL+ E EI IA RIEAG  M+ A   ES
Sbjct: 38  AAGATADPVKDYLKIIGRVPLLNAEQEIEIAMRIEAG--MLAAHYLES 83


>gi|317010368|gb|ADU84115.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SouthAfrica7]
          Length = 685

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 427 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 486

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 487 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKYMQENG 546

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 547 KEPDLELVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 606

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 607 MREDLKAQIDGVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 666

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 667 IKKLRSPQYGRILRNYL 683


>gi|308371101|ref|ZP_07423832.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308379284|ref|ZP_07485758.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308405944|ref|ZP_07494511.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|308329814|gb|EFP18665.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308357496|gb|EFP46347.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308365045|gb|EFP53896.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|323718698|gb|EGB27860.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CDC1551A]
          Length = 530

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 293 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 352

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 353 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 412

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 413 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 472

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 473 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 530



 Score = 45.4 bits (106), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 211 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 270


>gi|1072017|gb|AAA81640.1| sigma factor [Mycobacterium bovis]
 gi|1072019|gb|AAA81641.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 410

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 411 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 470

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 471 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|15609840|ref|NP_217219.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Rv]
 gi|15842241|ref|NP_337278.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CDC1551]
 gi|31793875|ref|NP_856368.1| RNA polymerase sigma factor [Mycobacterium bovis AF2122/97]
 gi|121638578|ref|YP_978802.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148662544|ref|YP_001284067.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148823893|ref|YP_001288647.1| RNA polymerase sigma factor [Mycobacterium tuberculosis F11]
 gi|167970074|ref|ZP_02552351.1| RNA polymerase sigma factor RpoD [Mycobacterium tuberculosis H37Ra]
 gi|218754439|ref|ZP_03533235.1| RNA polymerase sigma factor [Mycobacterium tuberculosis GM 1503]
 gi|224991070|ref|YP_002645759.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253798215|ref|YP_003031216.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|254551759|ref|ZP_05142206.1| RNA polymerase sigma factor [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260187720|ref|ZP_05765194.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CPHL_A]
 gi|289448358|ref|ZP_06438102.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289553511|ref|ZP_06442721.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289762874|ref|ZP_06522252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|294994205|ref|ZP_06799896.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 210]
 gi|297635311|ref|ZP_06953091.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN 4207]
 gi|297732307|ref|ZP_06961425.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN R506]
 gi|306780885|ref|ZP_07419222.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|306790106|ref|ZP_07428428.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|306798608|ref|ZP_07436910.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|306804467|ref|ZP_07441135.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|306807495|ref|ZP_07444163.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|306968762|ref|ZP_07481423.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|307080806|ref|ZP_07489976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|313659640|ref|ZP_07816520.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN V2475]
 gi|61234251|sp|P0A602|RPOD_MYCTU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|61234258|sp|P0A603|RPOD_MYCBO RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1072023|gb|AAA81643.1| sigma factor [Mycobacterium bovis]
 gi|1072025|gb|AAA81644.1| sigma factor [Mycobacterium tuberculosis str. Erdman]
 gi|1171102|gb|AAA86043.1| sigma factor MysA [Mycobacterium tuberculosis H37Rv]
 gi|2181994|emb|CAB09463.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium
           tuberculosis H37Rv]
 gi|13882532|gb|AAK47092.1| RNA polymerase principal sigma factor SigA [Mycobacterium
           tuberculosis CDC1551]
 gi|31619469|emb|CAD94907.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium bovis
           AF2122/97]
 gi|121494226|emb|CAL72704.1| RNA polymerase sigma factor sigA [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148506696|gb|ABQ74505.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148722420|gb|ABR07045.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis F11]
 gi|224774185|dbj|BAH26991.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253319718|gb|ACT24321.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|289421316|gb|EFD18517.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289438143|gb|EFD20636.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289710380|gb|EFD74396.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|308326286|gb|EFP15137.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|308333457|gb|EFP22308.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|308341125|gb|EFP29976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|308346090|gb|EFP34941.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|308348951|gb|EFP37802.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|308353649|gb|EFP42500.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|308361450|gb|EFP50301.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|326904319|gb|EGE51252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis W-148]
 gi|328457987|gb|AEB03410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           4207]
          Length = 528

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 410

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 411 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 470

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 471 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 45.4 bits (106), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|41408918|ref|NP_961754.1| RNA polymerase sigma factor [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397277|gb|AAS05137.1| SigA [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 509

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 331

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +     REPTPEE+AK++ +  E V
Sbjct: 332 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDPGREPTPEELAKEMDITPEKV 391

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 392 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 451

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 452 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 509



 Score = 45.4 bits (106), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 31/88 (35%), Positives = 46/88 (52%), Gaps = 4/88 (4%)

Query: 76  NVVDGDD--LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            V D DD   E  E  + S D       S    Q R+D+   ++ D VR YL+++G + L
Sbjct: 162 TVADEDDEIAEPSEKDKASGDFVWDEDESEALRQARRDAELTASADSVRAYLKQIGKVAL 221

Query: 134 LSREGEIAIAKRIEAG--RAMMMASLCE 159
           L+ E E+ +AKRIEAG     +M+ + E
Sbjct: 222 LNAEEEVELAKRIEAGLYATQLMSEMAE 249


>gi|317011933|gb|ADU82541.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Lithuania75]
          Length = 680

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 422 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 481

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 482 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 541

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 542 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 601

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 602 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 661

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 662 IKKLRSPQYGRILRNYL 678


>gi|289570879|ref|ZP_06451106.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
 gi|289544633|gb|EFD48281.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
          Length = 528

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 410

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 411 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 470

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 471 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|217032875|ref|ZP_03438353.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298736968|ref|YP_003729498.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
 gi|216945415|gb|EEC24081.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298356162|emb|CBI67034.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
          Length = 679

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 418 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 477

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 478 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 537

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 538 ENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 597

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 598 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 657

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 658 SSAIKKLRSPQYGRILRNYL 677



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 164 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 221


>gi|307636779|gb|ADN79229.1| RNA polymerase sigma factor [Helicobacter pylori 908]
 gi|325995367|gb|ADZ50772.1| RNA polymerase sigma factor [Helicobacter pylori 2018]
 gi|325996964|gb|ADZ49172.1| RNA polymerase sigma factor [Helicobacter pylori 2017]
          Length = 681

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 420 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 479

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 480 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 539

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 540 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 599

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 600 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 659

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 660 SSAIKKLRSPQYGRILRNYL 679



 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 166 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 223


>gi|300933014|ref|ZP_07148270.1| RNA polymerase sigma factor [Corynebacterium resistens DSM 45100]
          Length = 571

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 129/248 (52%), Positives = 183/248 (73%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+ E +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G
Sbjct: 324 LREIERDGRRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKG 383

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP+PEE+A
Sbjct: 384 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPSPEELA 443

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ + V+ V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++  
Sbjct: 444 REMDITVDKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQL 503

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS
Sbjct: 504 QDVLHTLSDREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 563

Query: 674 KKLRSFLD 681
           + LR +LD
Sbjct: 564 QVLRDYLD 571



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 252 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 299


>gi|111225055|ref|YP_715849.1| alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
 gi|111152587|emb|CAJ64329.1| Alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
          Length = 373

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 124/238 (52%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 136 AKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP+E V
Sbjct: 196 IRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL  L PR
Sbjct: 256 VELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGGLNPR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR FLD
Sbjct: 316 EREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLREFLD 373



 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 52/117 (44%), Gaps = 17/117 (14%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I   R+ G ++  EL   L   ++  E +   +A LS  G+ ++              
Sbjct: 6   EVIARGREAGEISRSELRDALESADIGLELLPALIAKLSAAGVELL-------------- 51

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                  +   V    R  +    T D VRMYLRE+G + LL+   E+ ++KR+EAG
Sbjct: 52  ---EEEETTDDVTAATRSTAEHAGTADLVRMYLREIGKVPLLNAAQEVELSKRVEAG 105


>gi|254778811|ref|YP_003056916.1| RNA polymerase sigma factor RpoD [Helicobacter pylori B38]
 gi|254000722|emb|CAX28640.1| RNA polymerase sigma factor rpoD (Sigma-70) [Helicobacter pylori
           B38]
          Length = 679

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 418 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 477

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 478 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 537

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 538 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 597

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 598 DHIMREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 657

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 658 SSAIKKLRSPQYGRILRNYL 677



 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 164 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 221


>gi|219558712|ref|ZP_03537788.1| RNA polymerase sigma factor [Mycobacterium tuberculosis T17]
          Length = 530

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 293 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 352

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 353 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 412

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 413 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 472

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 473 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 530



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 211 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 270


>gi|81299460|ref|YP_399668.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 7942]
 gi|93141306|sp|P38023|RPOD1_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD1
 gi|81168341|gb|ABB56681.1| Sigma-70 factor [Synechococcus elongatus PCC 7942]
          Length = 399

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 223 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 282

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL++L+PR
Sbjct: 283 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPR 341

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 342 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 398


>gi|227872476|ref|ZP_03990816.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
 gi|227841677|gb|EEJ51967.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
          Length = 385

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 126/237 (53%), Positives = 180/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD   G+K STYA WW
Sbjct: 148 AKQRLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDPEKGFKLSTYATWW 207

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+ +E+A+ L M  E V
Sbjct: 208 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVKELAEHLDMTEEKV 267

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++++I +EP SLETPIG+ED S+LGDF+ D N +SP  +     LRE    +L  L  R
Sbjct: 268 QEIMQIAREPASLETPIGEEDDSNLGDFVADTNVLSPEGNVESVMLREHIDTLLGDLKER 327

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 328 ERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 384



 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 65/129 (50%), Gaps = 15/129 (11%)

Query: 58  VSSEQMEDTVAMLSNMGINV---VDGDDLE--DEEGSEDSLDLASSASNSSVFLQKRK-- 110
           ++ EQME  + +L N GI +   +D D L+  +++G +   D      +   F+++ +  
Sbjct: 38  LNEEQMEQVLLLLENKGIEINPILDEDALKTIEKDGDKAEPDALLPLEDDDDFVKEEEGE 97

Query: 111 ----DSADR----STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
               D+ D      T+DPVRMYL+E+G++ LL+ E E A+A + + G       L E+ L
Sbjct: 98  EIDLDAVDLLEGIGTEDPVRMYLKEIGTVPLLTAEEEYALAMKKQEGDEYAKQRLIEANL 157

Query: 163 TFQALIIWR 171
                I  R
Sbjct: 158 RLVVSIAKR 166


>gi|239931428|ref|ZP_04688381.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 430

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/239 (53%), Positives = 180/239 (75%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 192 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 251

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +  REPTPEE+A  L +P E 
Sbjct: 252 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGREPTPEEVAAHLDLPPER 311

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 312 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 371

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 372 RERKVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 430


>gi|210134292|ref|YP_002300731.1| RNA polymerase sigma factor RpoD [Helicobacter pylori P12]
 gi|210132260|gb|ACJ07251.1| RNA polymerase sigma-80 factor [Helicobacter pylori P12]
          Length = 680

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 419 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 478

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 479 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 538

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 539 ENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 598

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 599 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 658

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 659 SSAIKKLRSPQYGRILRNYL 678


>gi|332707223|ref|ZP_08427276.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
 gi|332353957|gb|EGJ33444.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
          Length = 373

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 136/264 (51%), Positives = 191/264 (72%), Gaps = 8/264 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           + E  + +  FR+ + + R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQE
Sbjct: 117 ATEVDMELPAFRYRLHVGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQE 169

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T 
Sbjct: 170 GSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTT 229

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +
Sbjct: 230 KLLSQEMGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-AD 288

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERI
Sbjct: 289 GETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERI 348

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 349 RQIEAKALRKLRHPNRNSILKEYI 372


>gi|298491609|ref|YP_003721786.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298233527|gb|ADI64663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 390

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 136/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +  FR+ + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 139 LPLPTFRYRLHVGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 191

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 192 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 251

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 252 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPE 310

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 311 DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEA 370

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 371 KALRKLRHPNRNSVLKEYI 389


>gi|118618666|ref|YP_906998.1| RNA polymerase sigma factor [Mycobacterium ulcerans Agy99]
 gi|118570776|gb|ABL05527.1| RNA polymerase sigma factor SigA [Mycobacterium ulcerans Agy99]
          Length = 501

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 264 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 323

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 324 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 383

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 384 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 443

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 444 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 501



 Score = 45.8 bits (107), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +A
Sbjct: 164 EPSEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELA 223

Query: 144 KRIEAG--RAMMMASLCE 159
           KRIEAG     +MA L +
Sbjct: 224 KRIEAGLYATQLMAELTD 241


>gi|261838959|gb|ACX98724.1| sigma 70 (RpoD) [Helicobacter pylori 52]
          Length = 685

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 427 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 486

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 487 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 546

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 547 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 606

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 607 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 666

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 667 IKKLRSPQYGRILRNYL 683


>gi|213964575|ref|ZP_03392775.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
 gi|213952768|gb|EEB64150.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
          Length = 520

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 133/260 (51%), Positives = 187/260 (71%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+ ++ R +  + R G+     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL
Sbjct: 265 IAYAQKRDLREISRDGQR----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 320

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  
Sbjct: 321 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQ 380

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +
Sbjct: 381 DLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAV 440

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+
Sbjct: 441 DAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIES 500

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HPSRS+ LR +L+
Sbjct: 501 KTMSKLRHPSRSQVLRDYLE 520



 Score = 48.1 bits (113), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 35/48 (72%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+A  ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 201 SARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAG 248


>gi|29832222|ref|NP_826856.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29609340|dbj|BAC73391.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 389

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 126/239 (52%), Positives = 179/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 151 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 210

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +P E 
Sbjct: 211 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLDLPGER 270

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 271 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDATSPVESAAFLLLREHLDAVLSTLGE 330

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 331 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 389


>gi|56750888|ref|YP_171589.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 6301]
 gi|56685847|dbj|BAD79069.1| principal RNA polymerase sigma factor RpoD1 [Synechococcus
           elongatus PCC 6301]
          Length = 399

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 223 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 282

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL++L+PR
Sbjct: 283 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPR 341

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 342 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 398


>gi|317179895|dbj|BAJ57681.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F32]
          Length = 671

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 413 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 472

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 473 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 532

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 533 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 592

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 593 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 652

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 653 IKKLRSPQYGRILRNYL 669


>gi|208434051|ref|YP_002265717.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
 gi|208431980|gb|ACI26851.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
          Length = 682

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 421 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 480

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 481 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 540

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 541 ENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 600

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE
Sbjct: 601 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 660

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 661 SSAIKKLRSPQYGRILRNYL 680



 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 40/58 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D+PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 167 SDNPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 224


>gi|317179521|dbj|BAJ57309.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F30]
          Length = 666

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 408 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 467

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 468 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 527

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 528 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 587

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 588 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 647

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 648 IKKLRSPQYGRILRNYL 664


>gi|183982025|ref|YP_001850316.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
 gi|183175351|gb|ACC40461.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
          Length = 501

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 264 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 323

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 324 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 383

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 384 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 443

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 444 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 501



 Score = 45.8 bits (107), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +MA L +
Sbjct: 182 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELTD 241


>gi|217140|dbj|BAA01749.1| principal sigma factor [Synechococcus elongatus PCC 7942]
          Length = 384

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 148 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 207

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 208 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 267

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL++L+PR
Sbjct: 268 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPR 326

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 327 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 383


>gi|302551232|ref|ZP_07303574.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302468850|gb|EFL31943.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 438

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 126/239 (52%), Positives = 179/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 200 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 259

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +P E 
Sbjct: 260 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLELPPER 319

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 320 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 379

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 380 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 438


>gi|1072021|gb|AAA81642.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 410

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 411 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 470

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL HPSRS+ LR +LD
Sbjct: 471 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLHHPSRSQVLRDYLD 528



 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|126434760|ref|YP_001070451.1| RNA polymerase sigma factor [Mycobacterium sp. JLS]
 gi|126234560|gb|ABN97960.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 480

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 243 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 302

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 303 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 362

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 363 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 422

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 423 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 480



 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 84  EDEEGSEDS------LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           EDEE +E S       D       S    Q RKD+   ++ D VR YL+++G + LL+ E
Sbjct: 137 EDEEIAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAE 196

Query: 138 GEIAIAKRIEAG 149
            E+ +AKRIEAG
Sbjct: 197 EEVELAKRIEAG 208


>gi|308062951|gb|ADO04838.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Sat464]
          Length = 666

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 408 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 467

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 468 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 527

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 528 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 587

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 588 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 647

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 648 IKKLRSPQYGRILRNYL 664


>gi|108799152|ref|YP_639349.1| RNA polymerase sigma factor [Mycobacterium sp. MCS]
 gi|119868267|ref|YP_938219.1| RNA polymerase sigma factor [Mycobacterium sp. KMS]
 gi|108769571|gb|ABG08293.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694356|gb|ABL91429.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
          Length = 480

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 243 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 302

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 303 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 362

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 363 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSER 422

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 423 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 480



 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 84  EDEEGSEDS------LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           EDEE +E S       D       S    Q RKD+   ++ D VR YL+++G + LL+ E
Sbjct: 137 EDEEIAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAE 196

Query: 138 GEIAIAKRIEAG 149
            E+ +AKRIEAG
Sbjct: 197 EEVELAKRIEAG 208


>gi|2522316|gb|AAB81010.1| RNA polymerase principal sigma factor RpoD [Helicobacter pylori]
          Length = 680

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 126/260 (48%), Positives = 193/260 (74%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 419 LAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 478

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 479 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 538

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 539 ETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 598

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG +   ++ TLEE+GK+  VTRER+RQIE
Sbjct: 599 DHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESERTLEEIGKELNVTRERVRQIE 658

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 659 SSAIKKLRSPQYGRILRNYL 678



 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 222


>gi|291439801|ref|ZP_06579191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342696|gb|EFE69652.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 390

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/239 (53%), Positives = 180/239 (75%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 152 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 211

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +  REPTPEE+A  L +P E 
Sbjct: 212 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGREPTPEEVAAHLDLPPER 271

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 272 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 331

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 332 RERKVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 390


>gi|196234461|ref|ZP_03133287.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
 gi|196221517|gb|EDY16061.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
          Length = 479

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 131/267 (49%), Positives = 190/267 (71%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++++  E  ++ SE    +  +++ + +A  A+ EMVE NLRLV+S+A++Y NRG  FLD
Sbjct: 211 MRNLQAEMWLNPSELNVELQEMKRWQRKALEARTEMVECNLRLVVSIAREYQNRGQPFLD 270

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLM+A E+F++  GYKF+T A WW++QAI+RSIA+Q+ TIRIP HM D + K+
Sbjct: 271 LIQEGNIGLMRAVERFEYRRGYKFATCATWWIRQAISRSIANQARTIRIPTHMIDLLAKL 330

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R  R+M+ +  R+PT E++A +L +P+  VR +LK+ +EPIS+ TP+G+E  S LGDFI
Sbjct: 331 IRVQRQMTQESGRDPTAEDLAGELHLPLRRVRALLKMAEEPISIHTPVGEEGGSRLGDFI 390

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED +   P   A  A LRE    VL +LT RE  +L  RFG+    + TLEE+G+ F VT
Sbjct: 391 EDHSVEDPSKQAAVAMLREKINAVLHTLTEREREILEQRFGLIDGRERTLEEIGRHFKVT 450

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSF 679
           RER+RQIEAKA+RK++HP R ++L+  
Sbjct: 451 RERVRQIEAKALRKMRHPERRRQLQGL 477


>gi|261837545|gb|ACX97311.1| transcription initiation factor sigma-80 [Helicobacter pylori 51]
          Length = 684

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 426 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 485

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 486 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 545

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 546 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 605

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 606 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 665

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 666 IKKLRSPQYGRILRNYL 682


>gi|315586085|gb|ADU40466.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           35A]
          Length = 680

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 422 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 481

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 482 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 541

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 542 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 601

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 602 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 661

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 662 IKKLRSPQYGRILRNYL 678


>gi|332672929|gb|AEE69746.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           83]
          Length = 674

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 416 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 475

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 476 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 535

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 536 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 595

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 596 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 655

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 656 IKKLRSPQYGRILRNYL 672


>gi|172035791|ref|YP_001802292.1| RNA polymerase sigma factor RpoD [Cyanothece sp. ATCC 51142]
 gi|171697245|gb|ACB50226.1| group 1 sigma-70 RNA polymerase sigma factor A [Cyanothece sp. ATCC
           51142]
          Length = 416

 Score =  271 bits (693), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/267 (51%), Positives = 192/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K+  +E+   + +F+  + + RK       AK +MV +NLRLV+S+AKKY NRGL F DL
Sbjct: 157 KTWKLESKAYLPKFKRRLYLGRK-------AKDKMVHSNLRLVVSIAKKYMNRGLSFQDL 209

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 210 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 269

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 270 KTTKLLSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 329

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 330 -ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 388

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 389 ERIRQIEAKALRKLRHPNRNSILKEYI 415


>gi|217034615|ref|ZP_03440022.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
 gi|216942910|gb|EEC22397.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
          Length = 671

 Score =  271 bits (693), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 413 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 472

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 473 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 532

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 533 KEPDLEVVAEEVRLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 592

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 593 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 652

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 653 IKKLRSPQYGRILRNYL 669


>gi|217077377|ref|YP_002335095.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
 gi|217037232|gb|ACJ75754.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
          Length = 371

 Score =  271 bits (693), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 131/245 (53%), Positives = 177/245 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     AK+++VE+NLRLV+S+AK+Y  +GL FLDLIQEGN+GL+KA EKFDW  
Sbjct: 118 LARRAQLGDERAKQKLVESNLRLVVSIAKRYVGKGLSFLDLIQEGNVGLLKAVEKFDWKK 177

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + I+KV +  R    +   E   EE+
Sbjct: 178 GYKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKVQKIMREYYQEHGTEIPIEEL 237

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK +  PVE V ++L+  KE  SLE P+G++D S +GDFI D+   SP   A++  +RE 
Sbjct: 238 AKLIGKPVEKVEEILQAAKETTSLEAPVGEDDDSTVGDFIADETIASPKKEAMRMLIREE 297

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +VL +L  RE+ VL+MR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSR
Sbjct: 298 VDKVLETLNDREKLVLKMRYGLIDGKAKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 357

Query: 673 SKKLR 677
           S+ L+
Sbjct: 358 SRYLK 362



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 38/148 (25%), Positives = 70/148 (47%), Gaps = 27/148 (18%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D  D   +K+I + +++G+VT E+++   PP++                     DG+ LE
Sbjct: 8   DSLDSKIEKLIAIGKEKGFVTYEDIDKMFPPEKADE-----------------FDGNVLE 50

Query: 85  D--EEGSEDSLDLASSASNSSV-------FLQKRKDSADR-STDDPVRMYLREMGSIELL 134
              EE  ++++ +    +N  +       FL++     D  +T D ++MYL+++G I LL
Sbjct: 51  KVYEELEKNNVAITEETTNDGIEDVTLEDFLEESPKFYDNMATKDLIKMYLKDIGKIPLL 110

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPL 162
           S+  E  +A+R + G       L ES L
Sbjct: 111 SQSMERELARRAQLGDERAKQKLVESNL 138


>gi|188526895|ref|YP_001909582.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
 gi|188143135|gb|ACD47552.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
          Length = 661

 Score =  271 bits (693), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 403 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 462

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 463 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 522

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 523 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 582

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 583 MREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 642

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 643 IKKLRSPQYGRILRNYL 659


>gi|5921146|dbj|BAA84590.1| RNA polymerase sigma 70 [Helicobacter pylori]
          Length = 675

 Score =  271 bits (693), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 126/257 (49%), Positives = 190/257 (73%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 417 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 476

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 477 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 536

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN  S +D  
Sbjct: 537 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIASSIDHI 596

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 597 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 656

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 657 IKKLRSPQYGRILRNYL 673


>gi|284928680|ref|YP_003421202.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
 gi|284809139|gb|ADB94844.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
          Length = 420

 Score =  271 bits (692), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 141/284 (49%), Positives = 199/284 (70%), Gaps = 12/284 (4%)

Query: 401 CEVDSILKIRNEIKSIS----VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            EV S+L+ +  I ++     +E    + +F+  + + RK       AK +MV +NLRLV
Sbjct: 144 SEVTSLLQEKKTISNLEKIWELEQKSYLPKFKRRLYLGRK-------AKDKMVHSNLRLV 196

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS
Sbjct: 197 VSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQS 256

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+PVH+ + I ++ +T + +S +++R+PT EEIA ++ M +E +R + K  + PISL
Sbjct: 257 RTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISL 316

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+  
Sbjct: 317 ETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLENVLDTLSPRERDVLRLRYGLDD 375

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 376 GRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 419



 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIELLS 135
           +D D  E    S +S+       N  +   +R+D++ +   T+D +R+YL+E+G I LL 
Sbjct: 21  IDEDINETSSDSINSITTEPDGKNRKISASRRRDTSKKKPYTEDSIRVYLQEIGRIRLLR 80

Query: 136 REGEIAIAKRI 146
            E EI +A++I
Sbjct: 81  AEEEIELARKI 91


>gi|126659035|ref|ZP_01730176.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
 gi|126619692|gb|EAZ90420.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
          Length = 416

 Score =  271 bits (692), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/267 (51%), Positives = 192/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K+  +E+   + +F+  + + RK       AK +MV +NLRLV+S+AKKY NRGL F DL
Sbjct: 157 KTWKLESKAYLPKFKRRLYLGRK-------AKDKMVHSNLRLVVSIAKKYMNRGLSFQDL 209

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 210 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 269

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 270 KTTKLLSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 329

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 330 -ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 388

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 389 ERIRQIEAKALRKLRHPNRNSILKEYI 415



 Score = 37.4 bits (85), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIELLSREGEIA 141
           ED + S + +  A       +   +R+D   +   T+D +R+YL+E+G I LL  E EI 
Sbjct: 23  EDPDTSTNDIAEADGKKTRKITASRRRDPGKKKPYTEDSIRVYLQEIGRIRLLRAEEEIE 82

Query: 142 IAKRI 146
           +A++I
Sbjct: 83  LARKI 87


>gi|119489756|ref|ZP_01622514.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454330|gb|EAW35480.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 391

 Score =  271 bits (692), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 136/259 (52%), Positives = 189/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ EFR  + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 140 MALPEFRRRLYLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 192

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 193 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQ 252

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 253 EMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPE 311

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 312 DQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEA 371

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 372 KALRKLRHPNRNSILKEYI 390


>gi|317181391|dbj|BAJ59175.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F57]
          Length = 665

 Score =  271 bits (692), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 191/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 407 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 466

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 467 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 526

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 527 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 586

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 587 MREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 646

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 647 IKKLRSPQYGRILRNYL 663


>gi|254389040|ref|ZP_05004270.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441042|ref|ZP_08215776.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702757|gb|EDY48569.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
          Length = 385

 Score =  271 bits (692), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 180/239 (75%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 147 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFSTYATW 206

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A +L +P E 
Sbjct: 207 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQEQGSEPTPEEVAAQLDLPPER 266

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+E+   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 267 VSEVLRLAQEPVSLHAPVGEEEDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 326

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 327 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 385



 Score = 37.4 bits (85), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 7/62 (11%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+E+S     SA  +      R +S+  S+D   R YLRE+G I LL+   E+ +A+R+E
Sbjct: 62  GAEESAPRPGSARTA------RSESSGPSSDL-FRQYLREIGRIPLLTAAEEVELARRVE 114

Query: 148 AG 149
           AG
Sbjct: 115 AG 116


>gi|239616750|ref|YP_002940072.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
 gi|239505581|gb|ACR79068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
          Length = 405

 Score =  270 bits (691), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 140/285 (49%), Positives = 196/285 (68%), Gaps = 7/285 (2%)

Query: 400 ACEVDSILKIRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           A E+   + +++ IK    E G    ++ S+ R +    +KG+ +A   ++E++ ANLRL
Sbjct: 115 APEMYDNISLKDPIKMYLKEIGKIPLLTPSKERELARRAQKGDKKA---REELITANLRL 171

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RGL FLDLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ
Sbjct: 172 VVSIAKRYIGRGLSFLDLIQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQ 231

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+PVHM + I+KV +  R    +    PT EE+ K      E + ++L  +KE +S
Sbjct: 232 ARTIRVPVHMVETINKVNKVIREHLQEHGEYPTVEELGKLTGKTPEKIEEILAASKETVS 291

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LE+PI  ++ S +GDF+ D++   P ++AI+  LRE    VL +L+PRE  VL+MR+G+ 
Sbjct: 292 LESPISGDEESTMGDFVHDESIEKPEEAAIKMLLREQIDEVLDTLSPREAMVLKMRYGLL 351

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                TLEEVG+ F VTRERIRQIE KA+RKL+HPSRSK+L++ L
Sbjct: 352 DGKTKTLEEVGQFFNVTRERIRQIEVKALRKLRHPSRSKQLKALL 396



 Score = 43.9 bits (102), Expect = 0.100,   Method: Compositional matrix adjust.
 Identities = 31/110 (28%), Positives = 54/110 (49%), Gaps = 7/110 (6%)

Query: 43  YVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           Y+T E+++   PPD     S  +E     L    + +++ +  ED+E S       + A 
Sbjct: 51  YITYEDIDNAFPPDYEGFDSSLVEVIYEELEKNKVRILEKEPTEDQEESGQE----NPAE 106

Query: 101 NSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +    L+   +  D  S  DP++MYL+E+G I LL+   E  +A+R + G
Sbjct: 107 DIETLLESAPEMYDNISLKDPIKMYLKEIGKIPLLTPSKERELARRAQKG 156


>gi|113478384|ref|YP_724445.1| RNA polymerase sigma factor RpoD [Trichodesmium erythraeum IMS101]
 gi|110169432|gb|ABG53972.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 386

 Score =  270 bits (691), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 150 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 209

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA  + M +E +
Sbjct: 210 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATSMEMTIEKL 269

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL SL+PR
Sbjct: 270 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPEDEVSKNLLREDLESVLNSLSPR 328

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 329 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 385



 Score = 37.7 bits (86), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 48/96 (50%), Gaps = 6/96 (6%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE--DEEGSEDSLDLASSASNSSVFLQKRK 110
           + P   SSE  + T     N  + ++ GD  E  D +  ED L     A + +    K+K
Sbjct: 12  IQPQLESSELFQPTPTRQVNDELEILIGDREEYIDAQSDEDDLKSGKVAKSRTRTAGKKK 71

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                 T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 72  ----HYTEDSIRLYLQEIGRIRLLRADEEIELARKI 103


>gi|166368188|ref|YP_001660461.1| RNA polymerase sigma factor RpoD [Microcystis aeruginosa NIES-843]
 gi|166090561|dbj|BAG05269.1| principal RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 416

 Score =  270 bits (691), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 180 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA K+ M +E +
Sbjct: 240 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKL 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 300 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPR 358

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 359 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415


>gi|169883526|gb|ACA97858.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 416

 Score =  270 bits (691), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 180 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA K+ M +E +
Sbjct: 240 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKL 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 300 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPR 358

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 359 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415


>gi|1710685|sp|P52322|RPOD_MICAE RecName: Full=RNA polymerase sigma factor rpoD1
 gi|786173|dbj|BAA08853.1| sigma factor [Microcystis aeruginosa]
 gi|1783286|dbj|BAA12850.1| principal sigma factor [Microcystis aeruginosa]
          Length = 416

 Score =  270 bits (691), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 180 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA K+ M +E +
Sbjct: 240 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKL 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 300 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPR 358

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 359 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415


>gi|159026614|emb|CAO86546.1| rpoD1 [Microcystis aeruginosa PCC 7806]
          Length = 416

 Score =  270 bits (691), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 180 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA K+ M +E +
Sbjct: 240 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKL 299

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 300 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPR 358

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 359 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415


>gi|38233991|ref|NP_939758.1| RNA polymerase sigma factor [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200253|emb|CAE49937.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 502

 Score =  270 bits (690), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 265 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 324

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 325 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 384

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 385 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSER 444

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 445 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 502



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 177 SAALRQARKDAELSASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 224


>gi|259507416|ref|ZP_05750316.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
 gi|259164981|gb|EEW49535.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
          Length = 381

 Score =  270 bits (690), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 144 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 203

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 204 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 263

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 264 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 323

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 324 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 381



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 55/105 (52%), Gaps = 18/105 (17%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--DGDDLEDEEGSEDSLDLASSASNSSV 104
           EE  AF+P DE+   + +D VA L          DG  + DE+              S+ 
Sbjct: 15  EEDPAFIPGDEL---EQDDEVAPLGEEEEEEEEDDGSSVWDED-------------ESAT 58

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 59  LRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 103


>gi|254416030|ref|ZP_05029786.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177205|gb|EDX72213.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 380

 Score =  270 bits (690), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 136/262 (51%), Positives = 189/262 (72%), Gaps = 8/262 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E  + +  FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 126 EVEMELPAFRQRLFLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 178

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 179 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKI 238

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 239 LSQELGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGE 297

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQ
Sbjct: 298 TPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQ 357

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 358 IEAKALRKLRHPNRNSILKEYI 379


>gi|258653895|ref|YP_003203051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258557120|gb|ACV80062.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 448

 Score =  270 bits (690), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 211 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 270

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  + V
Sbjct: 271 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPDKV 330

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 331 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQAVLQTLSER 390

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 391 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 448



 Score = 44.3 bits (103), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 129 SEALKQARKDAELTASADSVRAYLKQIGKVALLNAEEEVDLAKRIEAG 176


>gi|209523577|ref|ZP_03272131.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495982|gb|EDZ96283.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 387

 Score =  270 bits (690), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 151 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 210

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 211 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 270

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 271 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPEDQVSKNLLREDLESVLDTLSPR 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 330 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 386


>gi|307152414|ref|YP_003887798.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982642|gb|ADN14523.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 377

 Score =  270 bits (690), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 136/267 (50%), Positives = 192/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  + + G+ +  F+  + + R+       AK +MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 118 KEWAQQVGMELPAFQRRLYLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDL 170

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 171 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 230

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 231 KTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 290

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 291 -ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 349

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 350 ERIRQIEAKALRKLRHPNRNSILKEYI 376


>gi|218438948|ref|YP_002377277.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171676|gb|ACK70409.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 376

 Score =  270 bits (689), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 135/262 (51%), Positives = 190/262 (72%), Gaps = 8/262 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           + G+ +  F+  + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 122 QVGMELPAFQRRLYLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 174

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 175 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKI 234

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 235 LSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGE 293

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQ
Sbjct: 294 TPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQ 353

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 354 IEAKALRKLRHPNRNSILKEYI 375


>gi|300858628|ref|YP_003783611.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686082|gb|ADK29004.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206337|gb|ADL10679.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis C231]
 gi|302330894|gb|ADL21088.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276579|gb|ADO26478.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis I19]
          Length = 517

 Score =  270 bits (689), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 280 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 339

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 340 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 399

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 400 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSER 459

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 460 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 517



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 192 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 239


>gi|154484558|ref|ZP_02027006.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
 gi|149734406|gb|EDM50323.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
          Length = 429

 Score =  270 bits (689), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 125/240 (52%), Positives = 179/240 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK++++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD+  GYK STYA W
Sbjct: 190 VAKEKLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATW 249

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q++TR++AD + TIR+PVHM + I+++ +  R+++ ++  EP+ +E+A  L M  E 
Sbjct: 250 WIRQSVTRALADHARTIRVPVHMVETINRMSKMQRKLTLELGYEPSTKELATALDMTEEK 309

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++++I +EP SLETPIG+ED S+LGDF+ D N V+P  +     LRE    +L  L  
Sbjct: 310 VLEIMQIAREPASLETPIGEEDDSNLGDFVADNNTVTPEANIESVMLREHIDVLLQDLKD 369

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE  V+ +RFG+      TLEEVGK F VTRERIRQIEAKA+RKL++P RSKK++ FL+ 
Sbjct: 370 REREVIILRFGLRDGHPRTLEEVGKIFNVTRERIRQIEAKALRKLRNPVRSKKIKDFLNN 429



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 48/183 (26%), Positives = 78/183 (42%), Gaps = 45/183 (24%)

Query: 34  MIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-------------- 78
           +I+LA ++   +TI E+  F   D+++ +Q  D V  L+   IN+               
Sbjct: 27  LIELAHKKEDRLTINEVQDFFKDDDLTEKQKTDVVTELTGKKINITMEVDVNEPKAPKAD 86

Query: 79  -------DGDDLEDEEGSEDSL------DLASSASNSSVFLQKRK-------------DS 112
                  D D  ED E + D +      D+A  A++    L+                D+
Sbjct: 87  SAKSDDADNDFPEDGEATVDLVAEPTDEDIAMVAADEGDLLEPTDENFENDEEETVEFDA 146

Query: 113 ADR----STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            D      T+DPVRMYL+E+G++ LL+ + E+ +AKR   G  +    L E+ L     I
Sbjct: 147 VDLLEGVGTEDPVRMYLKEIGTVPLLTADEELELAKRKTEGDIVAKEKLIEANLRLVVSI 206

Query: 169 IWR 171
             R
Sbjct: 207 AKR 209


>gi|23308878|ref|NP_601117.2| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|21324681|dbj|BAB99304.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigA)
           [Corynebacterium glutamicum ATCC 13032]
          Length = 498

 Score =  270 bits (689), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 261 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 320

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 321 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 380

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 381 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 440

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 441 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 498



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 173 SATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 220


>gi|317176909|dbj|BAJ54698.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F16]
          Length = 671

 Score =  270 bits (689), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 126/257 (49%), Positives = 190/257 (73%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 413 NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 472

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 473 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 532

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+ KEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 533 KEPDLEVVAEEVGLSLDKVKNVIKVAKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDRI 592

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 593 MREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 652

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 653 IKKLRSPQYGRILRNYL 669


>gi|12958492|gb|AAK09321.1|AF320817_2 sigma factor SigA [[Brevibacterium] flavum]
          Length = 498

 Score =  270 bits (689), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 261 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 320

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 321 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 380

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 381 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 440

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 441 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 498



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 173 SATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 220


>gi|28210583|ref|NP_781527.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
 gi|28203021|gb|AAO35464.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 282

 Score =  270 bits (689), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 126/239 (52%), Positives = 187/239 (78%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E++++NLRLV+S+AKKY  RGL FLDL+QEGN+GLMKA +K+D+  GY+FSTYA WW
Sbjct: 45  AKSELIKSNLRLVVSIAKKYIGRGLSFLDLVQEGNLGLMKAVDKYDYKKGYRFSTYATWW 104

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+TRSIADQS TIRIPVHM + I K++RT +++  ++ REPT EEIA+   + +E +
Sbjct: 105 IKQAVTRSIADQSRTIRIPVHMNEVISKMIRTKKKLEQELDREPTEEEIAETAEISIEKI 164

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++  ++++P+SLETP+G+ + + L +FI D   + P D   +  L +T + VL++L+PR
Sbjct: 165 KRIYNVSQDPVSLETPVGENEDTILQNFISDDRYL-PEDKVTEQMLGDTLSNVLSTLSPR 223

Query: 624 EERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EER++R+R+G +G     TLEE+G++F +TRERIRQIEA+AIRKL+HP+R KKL+ + +
Sbjct: 224 EERIVRLRYGLVGDGESRTLEEIGREFNLTRERIRQIEARAIRKLRHPTRIKKLQGYFE 282



 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           S  +  DD + MYL+E+G  +LL+ E EI +AKRIE G     + L +S L
Sbjct: 4   SNAKVVDDYINMYLKEIGQSDLLTAEEEIDLAKRIEKGDERAKSELIKSNL 54


>gi|207093142|ref|ZP_03240929.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 319

 Score =  270 bits (689), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 127/257 (49%), Positives = 192/257 (74%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA
Sbjct: 61  NKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKA 120

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  
Sbjct: 121 VDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENG 180

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  
Sbjct: 181 KEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHI 240

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKA 663
           ++ +L+     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ A
Sbjct: 241 MREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSA 300

Query: 664 IRKLKHPSRSKKLRSFL 680
           I+KL+ P   + LR++L
Sbjct: 301 IKKLRSPQYGRILRNYL 317


>gi|284052417|ref|ZP_06382627.1| RNA polymerase sigma factor RpoD [Arthrospira platensis str.
           Paraca]
 gi|291570496|dbj|BAI92768.1| principal RNA polymerase sigma factor SigA [Arthrospira platensis
           NIES-39]
          Length = 387

 Score =  270 bits (689), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 151 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 210

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 211 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 270

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 271 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPEDQVSKNLLREDLESVLDTLSPR 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 330 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 386


>gi|257438148|ref|ZP_05613903.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199479|gb|EEU97763.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 461

 Score =  270 bits (689), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 130/239 (54%), Positives = 179/239 (74%), Gaps = 4/239 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+KAAEKFD   G++FSTYA WW
Sbjct: 224 ARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGFRFSTYATWW 283

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +   EPTPEE+AK + M VE V
Sbjct: 284 IRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGHEPTPEELAKAMDMSVERV 343

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  +A +A + +   + L SLTPR
Sbjct: 344 REIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGKAADRAMVAQQINQALKSLTPR 403

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAKAIRKL     S+K  + L+G
Sbjct: 404 EEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRKL----HSRKCLALLNG 458



 Score = 44.7 bits (104), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 14/70 (20%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           GD+ ED+   E+  DL              K + D   DDPV+ YL+++G I LLS E E
Sbjct: 79  GDENEDDPAEENPADL--------------KAAMDELLDDPVKNYLKQIGQIPLLSAEQE 124

Query: 140 IAIAKRIEAG 149
           + ++KRI AG
Sbjct: 125 VDLSKRIHAG 134


>gi|72383665|ref|YP_293020.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL2A]
 gi|72003515|gb|AAZ59317.1| sigma-70 factor [Prochlorococcus marinus str. NATL2A]
          Length = 420

 Score =  270 bits (689), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 137/268 (51%), Positives = 192/268 (71%), Gaps = 8/268 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K  +V   + ++ FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F D
Sbjct: 158 VKEWAVLADMPLARFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQD 210

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++
Sbjct: 211 LIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRI 270

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +T + +S +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFI
Sbjct: 271 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI 330

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E  +  +P     +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VT
Sbjct: 331 E-ADIENPEQDVAKTLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVT 389

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 390 RERIRQIEAKALRKLRHPNRNGVLKEYI 417


>gi|145295815|ref|YP_001138636.1| RNA polymerase sigma factor [Corynebacterium glutamicum R]
 gi|140845735|dbj|BAF54734.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 494

 Score =  269 bits (688), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 257 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 316

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 317 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 376

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 377 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 436

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 437 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 494



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 169 SATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 216


>gi|297569039|ref|YP_003690383.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296924954|gb|ADH85764.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 445

 Score =  269 bits (688), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 121/239 (50%), Positives = 184/239 (76%), Gaps = 1/239 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  M++ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+A  +FD+  G KFSTYA W
Sbjct: 208 VAKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASW 267

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+I D++ TIR+PVH  +   +  +    +  ++ REPTP EI++K  +P+E 
Sbjct: 268 WIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGREPTPAEISEKTGLPMEK 327

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  + + ++EPISLETP+GD+D++ LGDF+E++ +VSP ++     L E  T +L++L+P
Sbjct: 328 ILAIFEASREPISLETPVGDDDST-LGDFLENQESVSPYEAVKGNQLAERVTTILSTLSP 386

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+++R+RFGIG + ++TLEE+GK+F V+RERIRQIE KA+ +L+H SR +KL++FLD
Sbjct: 387 REEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRREKLKNFLD 445


>gi|284046806|ref|YP_003397146.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951027|gb|ADB53771.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 380

 Score =  269 bits (688), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 133/273 (48%), Positives = 189/273 (69%), Gaps = 3/273 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  +R  ++SI     ++  +  H+   + +G+  A   K++M+EANLRLV+S+AK Y 
Sbjct: 108 SLDSLRLYLRSIGRVNLLTAEQEVHLAQRIERGDMRA---KQQMIEANLRLVVSIAKGYL 164

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            RGL FLDLIQEG++GL++A EKFD   G+KFSTYA WW++QA+TR+IAD+  TIRIPVH
Sbjct: 165 GRGLTFLDLIQEGSLGLIRAVEKFDHRRGFKFSTYATWWIRQAVTRAIADKGRTIRIPVH 224

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M +K++KVV   R++   + REPTPEEIA +L   V  VR +L++ ++P+SLE PIG+E+
Sbjct: 225 MVEKLNKVVHVERQLVQSLGREPTPEEIAAELECTVREVRDILRMAQQPVSLEKPIGEEE 284

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDF+ED+ A SP + A +   R+   R L +L  RE  V+ MRFG+G     TLEE
Sbjct: 285 ESELGDFVEDQTAESPFELASENLRRDNVRRALQALPQREREVIEMRFGLGGGRPRTLEE 344

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           VG+ F VTRERIRQIE   ++KL+    +++LR
Sbjct: 345 VGRAFNVTRERIRQIENHTLKKLEALPEAQRLR 377



 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 46/161 (28%), Positives = 80/161 (49%), Gaps = 16/161 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           + ++++I   ++RGY+T EE+   L   EV+ EQ+++  A L   GI+VV+ D       
Sbjct: 19  EEFRQLIAEGQERGYLTFEEIATTLEEVEVTKEQVQELHAHLEEHGIDVVEAD------- 71

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADR--------STDDPVRMYLREMGSIELLSREGEI 140
            + ++  A +A       ++   SA R         + D +R+YLR +G + LL+ E E+
Sbjct: 72  GKPAVSAAGAAEGERPDTRRSSGSAKRPEIDLTVEPSLDSLRLYLRSIGRVNLLTAEQEV 131

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
            +A+RIE G       + E+ L    + I +  L  G T L
Sbjct: 132 HLAQRIERGDMRAKQQMIEANLRL-VVSIAKGYLGRGLTFL 171


>gi|124025264|ref|YP_001014380.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL1A]
 gi|123960332|gb|ABM75115.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. NATL1A]
          Length = 420

 Score =  269 bits (688), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 137/268 (51%), Positives = 192/268 (71%), Gaps = 8/268 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K  +V   + ++ FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F D
Sbjct: 158 VKEWAVLADMPLTRFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQD 210

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++
Sbjct: 211 LIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRI 270

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +T + +S +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFI
Sbjct: 271 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI 330

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E  +  +P     +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VT
Sbjct: 331 E-ADIENPEQDVAKTLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVT 389

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 390 RERIRQIEAKALRKLRHPNRNGVLKEYI 417


>gi|294812504|ref|ZP_06771147.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325103|gb|EFG06746.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 436

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 180/239 (75%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 198 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFSTYATW 257

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A +L +P E 
Sbjct: 258 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQEQGSEPTPEEVAAQLDLPPER 317

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+E+   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 318 VSEVLRLAQEPVSLHAPVGEEEDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 377

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 378 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 436



 Score = 37.7 bits (86), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 7/62 (11%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+E+S     SA  +      R +S+  S+D   R YLRE+G I LL+   E+ +A+R+E
Sbjct: 113 GAEESAPRPGSARTA------RSESSGPSSDL-FRQYLREIGRIPLLTAAEEVELARRVE 165

Query: 148 AG 149
           AG
Sbjct: 166 AG 167


>gi|62390750|ref|YP_226152.1| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|41326088|emb|CAF20251.1| RNA POLYMERASE SIGMA 70 FACTOR [Corynebacterium glutamicum ATCC
           13032]
          Length = 494

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 257 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 316

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 317 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 376

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 377 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 436

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 437 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 494



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 169 SATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 216


>gi|320161271|ref|YP_004174495.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319995124|dbj|BAJ63895.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 409

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 125/237 (52%), Positives = 179/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ AN RLVISVAKKY  RG+ FLDLIQEGNIGL++A +KFD+  G+KFSTYA WW
Sbjct: 171 AREHLITANSRLVISVAKKYMGRGVPFLDLIQEGNIGLIRATKKFDYRRGHKFSTYATWW 230

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IADQ  TIR+PVHM D+I+K++R   +++ ++ REP+ EE+A+ L +P   V
Sbjct: 231 IRQAVTRAIADQGRTIRVPVHMGDQINKLLRVQHQLTQRLGREPSVEELAEALDVPPRKV 290

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             ++++ + P+SLETP  DE+ S LGDFIED+ A  P D+A    LR+    VL +L PR
Sbjct: 291 ENMIQVARRPLSLETPTDDEEDSVLGDFIEDEEAPPPDDTATYNLLRQHLEEVLNTLPPR 350

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E R+L++R+G+     +TLEEVG++  VTRER+RQIEA+A+ +L+HPS  +KLR +L
Sbjct: 351 EVRILQLRYGLLDGQAYTLEEVGRKMGVTRERVRQIEAQALSRLRHPSIRRKLRDYL 407



 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/124 (33%), Positives = 67/124 (54%), Gaps = 11/124 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I L RQ+ YVTI+++  F P  E   EQ+E+  A L + GI       LEDE   E +
Sbjct: 24  RLIDLGRQKSYVTIDDILHFFPEAEQDVEQLEEAFAALMSAGIPY-----LEDEIVEEPA 78

Query: 93  LDLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            +   +    +V  +  +      D A+  TDD + +YL+E+  + LL+ E E+ +A+RI
Sbjct: 79  EEELEAHEEGAVEEEGEEKSLALDDLANIDTDDTIGLYLKEVSRVPLLTAEEEVELAQRI 138

Query: 147 EAGR 150
           E GR
Sbjct: 139 ERGR 142


>gi|159903037|ref|YP_001550381.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9211]
 gi|159888213|gb|ABX08427.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9211]
          Length = 425

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 189 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 249 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 308

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +    LD A +  LRE    VLA+L+PR
Sbjct: 309 RFIAKSAQLPISLETPIGKEEDSRLGDFIESDSENPELDVA-KTLLREDLEGVLATLSPR 367

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 368 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 424


>gi|67921267|ref|ZP_00514786.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67857384|gb|EAM52624.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 414

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 141/289 (48%), Positives = 202/289 (69%), Gaps = 9/289 (3%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           E +W + VA E++    I +  K+   ++   + +F+  + + R+       AK +MV +
Sbjct: 134 EPKWSDIVA-ELNKAEIISDLEKTWKQQSKAYLPKFKRRLYLGRR-------AKDKMVHS 185

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+
Sbjct: 186 NLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRA 245

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA ++ M +E +R + K  +
Sbjct: 246 IADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQ 305

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R
Sbjct: 306 LPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLR 364

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 365 YGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 413


>gi|169838629|ref|ZP_02871817.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 323

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 130/241 (53%), Positives = 182/241 (75%), Gaps = 3/241 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M EAN+RLV+S+AK+Y+ RGL FLDLIQEGN GL++A EKFD   G+KFSTYA WW
Sbjct: 83  AKDKMAEANMRLVVSIAKRYSGRGLDFLDLIQEGNTGLLRAVEKFDPDKGFKFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+  IRIPVHM + I+K++RT RRM+ ++ REPT EE++K+L M  + +
Sbjct: 143 IRQAITRAIADQARVIRIPVHMVETINKLLRTQRRMTQELNREPTIEELSKELDMEPDKI 202

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             V+KI ++  SL+  +   GDE+ S LGDFIED++  +P +SA    L+E    +L+SL
Sbjct: 203 EYVMKIKQDIHSLDAGVGRDGDEEDSVLGDFIEDEDTATPEESASSQLLKEQVQGILSSL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE+++++MRFG+     HTLEEVG++F VTRERIRQIEAKA+ KL+    +KKL  +L
Sbjct: 263 SDREQKIIKMRFGLENGKSHTLEEVGQEFAVTRERIRQIEAKALAKLRKHKDAKKLHEYL 322

Query: 681 D 681
           +
Sbjct: 323 N 323



 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D  +DD VR+YLRE+G I LLS E E+ +A R+  G
Sbjct: 44  DDVSDDSVRLYLREIGKIPLLSAEEEMELAHRVVQG 79


>gi|25028360|ref|NP_738414.1| RNA polymerase sigma factor [Corynebacterium efficiens YS-314]
 gi|23493645|dbj|BAC18614.1| sigma factor SigA [Corynebacterium efficiens YS-314]
          Length = 506

 Score =  269 bits (688), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 178/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 269 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 328

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 329 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 388

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 389 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 448

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 449 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 506



 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 55/105 (52%), Gaps = 18/105 (17%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--DGDDLEDEEGSEDSLDLASSASNSSV 104
           EE  AF+P DE+   + +D VA L          DG  + DE+              S+ 
Sbjct: 140 EEDPAFIPGDEL---EQDDEVAPLGEEEEEEEEDDGSSVWDED-------------ESAT 183

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 184 LRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 228


>gi|319441597|ref|ZP_07990753.1| RNA polymerase sigma factor [Corynebacterium variabile DSM 44702]
          Length = 536

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 299 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 358

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  + V
Sbjct: 359 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEDKV 418

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 419 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSER 478

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 479 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 536



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 217 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 264


>gi|295102137|emb|CBK99682.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 461

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 130/239 (54%), Positives = 179/239 (74%), Gaps = 4/239 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+KAAEKFD   G++FSTYA WW
Sbjct: 224 ARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGFRFSTYATWW 283

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +   EPTPEE+AK + M VE V
Sbjct: 284 IRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGHEPTPEELAKAMDMSVERV 343

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  +A +A + +   + L SLTPR
Sbjct: 344 REIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGKAADRAMVAQQINQALKSLTPR 403

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAKAIRKL     S+K  + L+G
Sbjct: 404 EEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRKL----HSRKCLALLNG 458



 Score = 42.7 bits (99), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 20/40 (50%), Positives = 28/40 (70%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           K + D   DDPV+ YL+++G I LLS E E+ ++KRI AG
Sbjct: 95  KAAMDELLDDPVKNYLKQIGQIPLLSAEQEVDLSKRIHAG 134


>gi|291458966|ref|ZP_06598356.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418220|gb|EFE91939.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 388

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 124/237 (52%), Positives = 180/237 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD   G+K STYA WW
Sbjct: 151 AKQRLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDPEKGFKLSTYATWW 210

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP+ +E+A+ L M  + V
Sbjct: 211 IRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVKELAEHLDMSEDKV 270

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++++I +EP SLETPIG+ED S+LGDF+ D N ++P  +     LRE    +L  L  R
Sbjct: 271 QEIMQIAREPASLETPIGEEDDSNLGDFVADANVLTPESNVEAVMLREHIDSLLGDLKER 330

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 331 ERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 387



 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 41/128 (32%), Positives = 62/128 (48%), Gaps = 14/128 (10%)

Query: 58  VSSEQMEDTVAMLSNMGIN---VVDGDDLEDEEG--SEDSLDLASSASNSSVFLQKRKDS 112
           +S EQM++ V ++ N  I    VVD   ++D E   ++ S D      +   FL++  + 
Sbjct: 42  LSEEQMDNVVRLIENRKIEINPVVDEAAIKDLEAGKAKASPDDELLPLDDESFLKEESEE 101

Query: 113 ADR---------STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            D           T+DPVRMYL+E+G++ LLS E E A+A R + G       L E+ L 
Sbjct: 102 IDLDAVDLLEGIGTEDPVRMYLKEIGTVSLLSAEEEYALAIRKQQGDEAAKQRLIEANLR 161

Query: 164 FQALIIWR 171
               I  R
Sbjct: 162 LVVSIAKR 169


>gi|227542254|ref|ZP_03972303.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227182083|gb|EEI63055.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 603

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 366 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 425

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 426 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 485

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 486 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLKTLSER 545

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 546 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 603



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 279 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 326


>gi|28572422|ref|NP_789202.1| RNA polymerase sigma factor [Tropheryma whipplei TW08/27]
 gi|28410553|emb|CAD66939.1| RNA polymerase principal sigma factor hrdb [Tropheryma whipplei
           TW08/27]
          Length = 387

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 137/253 (54%), Positives = 186/253 (73%), Gaps = 4/253 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR G+     AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EK
Sbjct: 138 RELRWVVRDGQR----AKDHLLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEK 193

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R++   + REP
Sbjct: 194 FDYVKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLSRVQRQLLQDLGREP 253

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP+E+ ++L MP E V +V K  +EPISL TP+GDE  S  GD IED +AV+P D+   +
Sbjct: 254 TPDELGRELDMPPERVVEVQKYGREPISLHTPLGDEGDSEFGDLIEDVDAVAPDDAVGFS 313

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    +L SL+ RE  V+RMRFG+  +   TL+ VG+ F VTRERIRQIEAK + KL
Sbjct: 314 MLQQQLRLLLDSLSEREAGVIRMRFGLDYDMPKTLDYVGEYFDVTRERIRQIEAKTMAKL 373

Query: 668 KHPSRSKKLRSFL 680
           +HPSRS+ LR +L
Sbjct: 374 RHPSRSQCLRDYL 386



 Score = 41.6 bits (96), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 28/34 (82%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ + E+++AKRIEAG
Sbjct: 86  ATADPVKDYLKQIGKVSLLTADEEVSLAKRIEAG 119


>gi|227488750|ref|ZP_03919066.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227091172|gb|EEI26484.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
          Length = 599

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 362 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 421

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V
Sbjct: 422 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKV 481

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 482 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLKTLSER 541

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 542 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 599



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 275 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 322


>gi|119953489|ref|YP_945698.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
 gi|119862260|gb|AAX18028.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
          Length = 630

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 128/255 (50%), Positives = 186/255 (72%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 373 IISMSEEILKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 432

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 433 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 492

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P      
Sbjct: 493 PTDEELSSRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSF 552

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    VL +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 553 VVLQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 612

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 613 LKNPKKTQKLKDYLE 627



 Score = 43.1 bits (100), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 39/156 (25%), Positives = 74/156 (47%), Gaps = 35/156 (22%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---------DGDD------------ 82
           +T E+L+ FL  D +  + ++    +L N GI++V         D D+            
Sbjct: 33  ITFEDLSTFLSGDMLDPDNIDYIYGVLENEGISLVNEKMESDICDIDEFDEADKLDSQCM 92

Query: 83  -LEDEEGSEDSLDLASSASNSSVFLQKRKDSA--------DRSTDDPVRMYLREMGSIEL 133
            L+D   S+D +D      +  V  ++   S         D +++DP+R+YL+E+G   L
Sbjct: 93  MLDDSIQSDDEIDDKLDEFDDEVLDKEDFSSGYIKSGLLKDSNSEDPIRLYLKEIGKEFL 152

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           L+   E+ +AK++++G      S+ E+ L  + L+I
Sbjct: 153 LTGNQEVELAKQMDSGE-----SIIENILKNEGLVI 183


>gi|291459241|ref|ZP_06598631.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418495|gb|EFE92214.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 398

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 131/273 (47%), Positives = 188/273 (68%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E + +    ++G+    +A++ +VEANLRLV+S+AK+YT RG+
Sbjct: 127 VRFYLKEIGTIPLLSPEEEKELARRSKEGD---PLARQRLVEANLRLVVSIAKRYTGRGM 183

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGN+GLMK  EKF+   G+K STYA WW++Q ITR++ADQS TIR+PVHM + 
Sbjct: 184 SILDLIQEGNLGLMKGVEKFEPDKGFKLSTYATWWIRQGITRALADQSRTIRVPVHMVES 243

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV RT RR++ ++  EP+P+E+A  L M  E ++++L ++K+P SLETP+GDE+ S+L
Sbjct: 244 INKVTRTQRRLTLELGYEPSPKELAASLNMTEEKLKEILDVSKQPTSLETPVGDEEDSNL 303

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+ D+  +SP  +A    LRE   ++L +L  RE  VL  RFG+     HTLEEVG+ 
Sbjct: 304 SDFVADEKMISPEQNAANVMLREEIDKLLENLKDRERDVLIHRFGLHGEESHTLEEVGQM 363

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRER+RQIEAKA++K+  P     L  FL+
Sbjct: 364 FGVTRERVRQIEAKALKKISLPKYKNALAGFLE 396



 Score = 43.5 bits (101), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 32/55 (58%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           TDDPVR YL+E+G+I LLS E E  +A+R + G  +    L E+ L     I  R
Sbjct: 123 TDDPVRFYLKEIGTIPLLSPEEEKELARRSKEGDPLARQRLVEANLRLVVSIAKR 177


>gi|254232809|ref|ZP_04926136.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
 gi|124601868|gb|EAY60878.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
          Length = 528

 Score =  269 bits (687), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+ L++A EKFD+  GYKFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLRLIRAVEKFDYTKGYKFSTYATWW 350

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 410

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 411 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSER 470

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 471 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 45.4 bits (106), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|94263318|ref|ZP_01287133.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456273|gb|EAT06403.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 442

 Score =  268 bits (686), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 120/239 (50%), Positives = 184/239 (76%), Gaps = 1/239 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  M++ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+A  +FD+  G KFSTYA W
Sbjct: 205 VAKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASW 264

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+I D++ TIR+PVH  +   +  +    +  ++ REPTP EI++K  +P+E 
Sbjct: 265 WIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGREPTPVEISEKTGLPMEK 324

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  + + ++EPISLETP+GD+D++ LGDF+E++ ++SP ++     L E  T +L++L+P
Sbjct: 325 ILAIFEASREPISLETPVGDDDST-LGDFLENQESISPYEAVKGNQLAERVTTILSTLSP 383

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+++R+RFGIG + ++TLEE+GK+F V+RERIRQIE KA+ +L+H SR +KL++FLD
Sbjct: 384 REEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRREKLKNFLD 442


>gi|313112817|ref|ZP_07798464.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624887|gb|EFQ08195.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 458

 Score =  268 bits (686), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 131/239 (54%), Positives = 178/239 (74%), Gaps = 4/239 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+KAAEKFD   G++FSTYA WW
Sbjct: 221 ARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGFRFSTYATWW 280

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +   EPTPEE+AK + M VE V
Sbjct: 281 IRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGHEPTPEELAKAMDMSVERV 340

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  +A +A + +     L SLTPR
Sbjct: 341 REIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGKAADRAMVAQQINLALKSLTPR 400

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAKAIRKL     S+K  S L+G
Sbjct: 401 EEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRKL----HSRKCLSLLNG 455



 Score = 42.0 bits (97), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           K + D   DDPV+ YL+++G I LLS E E+ +++RI AG
Sbjct: 92  KAAMDELLDDPVKNYLKQIGQIPLLSAEQEVELSRRIHAG 131


>gi|297199501|ref|ZP_06916898.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297147415|gb|EDY56986.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 428

 Score =  268 bits (686), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 190 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 249

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E 
Sbjct: 250 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLDLAPER 309

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 310 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 369

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 370 RERKVVQLRYGLADGRARTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 428


>gi|295103972|emb|CBL01516.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 457

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 160/368 (43%), Positives = 230/368 (62%), Gaps = 27/368 (7%)

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS----YGIKRDVFLERHQGR 377
           +K +G + L      L  EQ  ++S+RI H   E   + Q+    YG     +++++  R
Sbjct: 107 LKQIGQIPL------LSAEQEVELSRRI-HAGAEAAHILQADRQKYGAPE--YIKKNSAR 157

Query: 378 ---ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E D +  SY +D  E   K+    E  +  +   E    +VE G    E R  +   
Sbjct: 158 FSFEEDENSRSYTEDLDEDGEKSAEDAEEKADEEKAME----AVENGPLSEERRQELLKT 213

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+KAAEKFD   G+
Sbjct: 214 RR---DGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGF 270

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +   EPTPEE+AK
Sbjct: 271 RFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGHEPTPEELAK 330

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  +A +A + +   
Sbjct: 331 AMDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGKAADRAMVAQQIN 390

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAKAIRKL     S+
Sbjct: 391 LALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRKL----HSR 446

Query: 675 KLRSFLDG 682
           K  + L+G
Sbjct: 447 KCLTLLNG 454



 Score = 42.0 bits (97), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           K + D   DDPV+ YL+++G I LLS E E+ +++RI AG
Sbjct: 92  KAAMDELLDDPVKNYLKQIGQIPLLSAEQEVELSRRIHAG 131


>gi|33239946|ref|NP_874888.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33237472|gb|AAP99540.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 438

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 132/236 (55%), Positives = 179/236 (75%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW+
Sbjct: 203 KEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWI 262

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +R
Sbjct: 263 RQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKLR 322

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            + K  + PISLETPIG E+ S LGDFIE  +    LD A +  LRE    VLA+L+PRE
Sbjct: 323 FIAKSAQLPISLETPIGKEEDSRLGDFIESDSENPELDVA-KTLLREDLEGVLATLSPRE 381

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 382 RDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 437


>gi|307324812|ref|ZP_07604018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889694|gb|EFN20674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 414

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 176 VAKRRLIEANLRLVVSVAKRYIGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 235

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E 
Sbjct: 236 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLDLLPER 295

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 296 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 355

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 356 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 414


>gi|307298746|ref|ZP_07578549.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
 gi|306915911|gb|EFN46295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
          Length = 416

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/277 (50%), Positives = 189/277 (68%), Gaps = 6/277 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D I     EI  IS+   ++ S  R +    +KGE +A   K+E++ ANLRLV+S+AK+Y
Sbjct: 137 DPIKMYLKEIGKISL---LTPSRERELARRAQKGEPKA---KEELITANLRLVVSIAKRY 190

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RGL FLDLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIR+PV
Sbjct: 191 IGRGLTFLDLIQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPV 250

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ +  R         PT EE+        E + ++L  +KE +SLE+PI  +
Sbjct: 251 HMVETINKLNKVIREHLQDHGEYPTIEELGNLTGKTPEKIEEILAASKETVSLESPISGD 310

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S +GDFI D +   P ++A++  LRE   ++L +L+PRE  VL+MR+G+      TLE
Sbjct: 311 EESTMGDFIHDDSMEQPEEAAMKMLLREQIDQILDTLSPREAMVLKMRYGLLDGKTKTLE 370

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EVG+ F VTRERIRQIE KA+RKL+HPSRSK+L++ L
Sbjct: 371 EVGQFFNVTRERIRQIEVKALRKLRHPSRSKQLKALL 407



 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 43/157 (27%), Positives = 71/157 (45%), Gaps = 9/157 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVVDGDDLED 85
           D   KK+++  +++G+VT E++++  PPD     S  +E          IN+V     E 
Sbjct: 48  DKRIKKLLRQGKKKGFVTYEDIDSAFPPDYEGFDSSLVESIYEEFEKNKINIV-----EK 102

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAK 144
           E   +D    + S+      L+   +  D  S  DP++MYL+E+G I LL+   E  +A+
Sbjct: 103 EPVEDDDDIESESSEELVSILETTPEMYDNISLKDPIKMYLKEIGKISLLTPSRERELAR 162

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           R + G       L  + L     I  R  +  G T L
Sbjct: 163 RAQKGEPKAKEELITANLRLVVSIAKR-YIGRGLTFL 198


>gi|187918567|ref|YP_001884130.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
 gi|119861415|gb|AAX17210.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
          Length = 630

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 128/255 (50%), Positives = 186/255 (72%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 373 IISMSEEILKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 432

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 433 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 492

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P      
Sbjct: 493 PTDEELSARLGWDLKKVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSF 552

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    VL +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 553 VVLQDQIRSVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 612

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 613 LKNPKKTQKLKDYLE 627


>gi|219685543|ref|ZP_03540360.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
 gi|219672942|gb|EED29964.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
          Length = 631

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628



 Score = 37.4 bits (85), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 50/99 (50%), Gaps = 20/99 (20%)

Query: 79  DGDDLE--------DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           DG+D++        DEE      DL S    S+          D  ++DP+++YL+E+G 
Sbjct: 98  DGEDIDINGKLDDCDEEDISVKDDLGSGYIKSNAL-------KDSHSEDPIKLYLKEIGK 150

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
             LL+   E+ +AK++++G      S+ E+ L  + L+I
Sbjct: 151 EFLLTGNQEVELAKQMDSGE-----SIIENILKNEGLVI 184


>gi|219684458|ref|ZP_03539402.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
 gi|219672447|gb|EED29500.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
          Length = 631

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|315453594|ref|YP_004073864.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
 gi|315132646|emb|CBY83274.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
          Length = 621

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 125/256 (48%), Positives = 187/256 (73%), Gaps = 1/256 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I+  +++G+  +  AK +M  +NLRLV+S+AK+YT+RGL FLDLIQEGNIGLMKA 
Sbjct: 364 KLKEILEQIKRGKLISDKAKNKMARSNLRLVVSIAKRYTSRGLPFLDLIQEGNIGLMKAV 423

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF+    Y+FSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +
Sbjct: 424 DKFEHEKNYRFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKYMQENGK 483

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  + +AK++ +P++ V+ V+KITKEPISLE+P+G++D    GDF+E+   V  +D  +
Sbjct: 484 EPDLDLVAKEVGLPLDKVKNVIKITKEPISLESPVGNDDDGKFGDFVENDKVVGSMDHIM 543

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + +L+     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI
Sbjct: 544 REDLKTQIDGVLDQLNEREKSVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAI 603

Query: 665 RKLKHPSRSKKLRSFL 680
           +KL+ P   + LRS+L
Sbjct: 604 KKLRSPQYGRLLRSYL 619



 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 46/70 (65%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           F+++++ +    +D PVRMYLREMG I LLS+E E+ ++K+I+ G  +++ ++C  P   
Sbjct: 97  FIKEKELTEWSRSDSPVRMYLREMGEIPLLSKEEEVELSKQIKLGENIILDAICSVPYLI 156

Query: 165 QALIIWRDEL 174
             +  ++D L
Sbjct: 157 DFIYGYKDAL 166


>gi|302545597|ref|ZP_07297939.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463215|gb|EFL26308.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 443

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 205 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 264

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E 
Sbjct: 265 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAIHLDLTPER 324

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 325 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 384

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 385 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 443


>gi|160942567|ref|ZP_02089814.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446151|gb|EDP23154.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
          Length = 457

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 160/368 (43%), Positives = 230/368 (62%), Gaps = 27/368 (7%)

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS----YGIKRDVFLERHQGR 377
           +K +G + L      L  EQ  ++S+RI H   E   + Q+    YG     +++++  R
Sbjct: 107 LKQIGQIPL------LSAEQEVELSRRI-HAGAEAAHILQADRQKYGAPE--YIKKNSAR 157

Query: 378 ---ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E D +  SY +D  E   K+    E  +  +   E    +VE G    E R  +   
Sbjct: 158 FSFEEDENSRSYTEDLDEDGEKSAEDAEEKADEEKAME----AVENGPLSEERRQELLKT 213

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+KAAEKFD   G+
Sbjct: 214 RR---DGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGF 270

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +   EPTPEE+AK
Sbjct: 271 RFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGHEPTPEELAK 330

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  +A +A + +   
Sbjct: 331 AMDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGKAADRAMVAQQIN 390

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAKAIRKL     S+
Sbjct: 391 LALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRKL----HSR 446

Query: 675 KLRSFLDG 682
           K  + L+G
Sbjct: 447 KCLTLLNG 454



 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           K + D   DDPV+ YL+++G I LLS E E+ +++RI AG
Sbjct: 92  KAAMDELLDDPVKNYLKQIGQIPLLSAEQEVELSRRIHAG 131


>gi|150020921|ref|YP_001306275.1| RpoD family RNA polymerase sigma factor [Thermosipho melanesiensis
           BI429]
 gi|149793442|gb|ABR30890.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosipho
           melanesiensis BI429]
          Length = 370

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 128/234 (54%), Positives = 174/234 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++VE+NLRLV+S+AK+Y  +GL FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW
Sbjct: 128 AKQKLVESNLRLVVSIAKRYVGKGLSFLDLIQEGNVGLLKAVEKFDWKKGYKFSTYATWW 187

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIR+PVHM + I+KV +  R    +   E   EE+AK +  PVE V
Sbjct: 188 IRQAITRAIADQARTIRVPVHMVETINKVQKIMRDYYQQHGTEIPIEELAKIIGKPVEKV 247

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L+  KE  SLE P+G+++ S +GDF+ D++  SP   A++  +RE   +VL +L  R
Sbjct: 248 EEILQAAKETTSLEAPVGEDEDSTVGDFVADESIASPKKEAMRMLIREEVEKVLETLNDR 307

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           E+ VL+MR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSRS+ L+
Sbjct: 308 EKLVLKMRYGLIDGKSKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSRYLK 361



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 36/140 (25%), Positives = 69/140 (49%), Gaps = 27/140 (19%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED--EEGSE 90
           K+IK+ +++G+VT ++++  LPP+++                    DG+ LE   EE  +
Sbjct: 15  KLIKVGKEKGFVTYDDIDKMLPPEKIDD-----------------FDGNILEKVYEELEK 57

Query: 91  DSLDLASSASNSSV-------FLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAI 142
           +++ +  +     +       FL++     D  +T D ++MYL+++G I LLS+  E  +
Sbjct: 58  NNILITENNPQEQIEDVSLEDFLEESPRFYDNMATKDLIKMYLKDIGKIPLLSQSMEREL 117

Query: 143 AKRIEAGRAMMMASLCESPL 162
           A+R + G       L ES L
Sbjct: 118 ARRAQQGDERAKQKLVESNL 137


>gi|283780465|ref|YP_003371220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438918|gb|ADB17360.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 544

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 131/269 (48%), Positives = 187/269 (69%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+  + +ET  S    R     +++   E   AK+++   NLRLV+S+AKKY NRGL FL
Sbjct: 271 ELHHLMMETLESPRSLRARCVAMQRQYIEYEAAKRQLSSGNLRLVVSIAKKYRNRGLSFL 330

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN GLM+A +K+++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM D + K
Sbjct: 331 DLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIDVLSK 390

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    +++  ++ REPT EE+   + +P+E V++VL I + P+SL+ P+GD + S  G+F
Sbjct: 391 LRNVQKKLLQELGREPTTEEVTALVDLPLEEVKRVLDIGRHPVSLDRPVGDSEDSSFGEF 450

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IED  + +P+  A    LRE    +L +LT RE  ++R+R+G+     +TLEEVG+ F V
Sbjct: 451 IEDTASDNPVLCATNGILRERIDGLLKTLTWREREIIRLRYGLCDGYTYTLEEVGRIFKV 510

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQIEAKA+RKL+HP RSK+L  FL
Sbjct: 511 TRERVRQIEAKAVRKLQHPVRSKQLEGFL 539



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 69/119 (57%), Gaps = 7/119 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K+++     +GY+T E++N +LP  +V+ E++++ +  L + GI +VD   +E  +    
Sbjct: 9   KELVAKGNTQGYLTYEDVNNYLPDQDVNPEKLDNLLVALEHAGIELVDQPPVEPGKPR-- 66

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              L     + +V L  + + + +   DP+R+YL +M  I LLSR+ EI++AK+IE  R
Sbjct: 67  ---LFVPRESDAVPL--KPEESKKLNSDPIRLYLSQMAEIPLLSRQEEISLAKKIEVTR 120


>gi|51598964|ref|YP_073152.1| RNA polymerase sigma factor RpoD [Borrelia garinii PBi]
 gi|51573535|gb|AAU07560.1| RNA polymerase sigma-70 factor [Borrelia garinii PBi]
          Length = 631

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|187250727|ref|YP_001875209.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
 gi|186970887|gb|ACC97872.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
          Length = 571

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 155/401 (38%), Positives = 247/401 (61%), Gaps = 15/401 (3%)

Query: 286 EIAEVYRELR--SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           EI E+ ++LR  S+ D  +N     K +   +  ++++V  +  L+LNQ++I  L  ++ 
Sbjct: 180 EITELMKKLREPSISDKMLN-----KYTEALEKKQKEVVDSIIKLNLNQNKIKRLTNRIK 234

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDV---FLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
            +++RI  +  +L R  + +G   +V   F +  +G+ +    +     F   E    + 
Sbjct: 235 SLAQRIAESRNDLNRFDEYFGQYAEVKKLFTQASKGK-ISKAELKKKTRFTYEE----LE 289

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
             +++I  IR+  + +     +S  EF      +   E      K ++++ANLRLV+S+A
Sbjct: 290 TAINNIDMIRSRHEKLINTLPMSEKEFLAFNDRIVFFEDMILQDKLKLIKANLRLVVSIA 349

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KK+ N  L+  DLIQEG +GLMKA EKF++  G+KFSTYA WW++Q+I R+IADQ+ TIR
Sbjct: 350 KKHVNSNLELSDLIQEGGLGLMKAVEKFEYKRGFKFSTYATWWIRQSINRAIADQANTIR 409

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM++ + K+ +   +   +  REP+ E+ +K L + +E V+ VLKI ++PISL TP+
Sbjct: 410 IPVHMKELVSKLTKVTNKFRQEHGREPSLEDYSKSLRLSMEKVKGVLKIMQDPISLSTPV 469

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+++ S+L DFIEDK   +P  +A     ++  + VL +L+ RE +++R+RFGI      
Sbjct: 470 GEDEDSNLEDFIEDKAGANPTVTASDFLRKQEVSEVLNTLSEREAKIIRLRFGIDSGYPR 529

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVGK F VTRER+RQIEAKAIRKL+HPSR+K L+ + D
Sbjct: 530 TLEEVGKMFNVTRERVRQIEAKAIRKLRHPSRTKMLKDYSD 570



 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 40/154 (25%), Positives = 84/154 (54%), Gaps = 14/154 (9%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + + ++ ++K ++++ ++ G++T++E+N  L    +S+E ++  +  L ++GI VVD   
Sbjct: 1   MVNVANKAFKDLVEVGKENGFLTLDEINRSLTSSSMSAEDIDGLMGTLEDLGIQVVDRKK 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            +       S+ +A   + +  F+      A+    + +RMYL EMG + LLSR+ EI +
Sbjct: 61  YK-------SVAMAEKEAYTEEFM------ANPDISNSIRMYLSEMGKVPLLSRDEEITL 107

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           A+ +      +   + ESP+T + +  W +EL D
Sbjct: 108 ARNVREREKELRKLVLESPITMREICNW-EELVD 140


>gi|111115542|ref|YP_710160.1| RNA polymerase sigma factor RpoD [Borrelia afzelii PKo]
 gi|110890816|gb|ABH01984.1| RNA polymerase sigma-70 factor [Borrelia afzelii PKo]
          Length = 631

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628



 Score = 41.6 bits (96), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 12/85 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEEG     DL S    S+V         D  ++DP+++YL+E+G   LL+   E+ +AK
Sbjct: 112 DEEGISIKDDLGSGYIKSNVL-------KDSHSEDPIKLYLKEIGKEFLLTGNQEVELAK 164

Query: 145 RIEAGRAMMMASLCESPLTFQALII 169
           ++++G      S+ E+ L  + L+I
Sbjct: 165 QMDSG-----ESIIENILKNEGLVI 184


>gi|1588486|prf||2208419B RNA polymerase sigma factor
          Length = 391

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 135/260 (51%), Positives = 189/260 (72%), Gaps = 8/260 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ + +FR  +   R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++G
Sbjct: 139 GMPLKDFRRRLFHGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 191

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S
Sbjct: 192 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILS 251

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ R+PT EEIA+++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P
Sbjct: 252 QELGRKPTEEEIAERMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETP 310

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D   ++ LRE    VL +L+ RE  VLR+R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 311 EDQVSKSLLREDLENVLDTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 370

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           AKA+RKL+HP+R+  L+ ++
Sbjct: 371 AKALRKLRHPNRNSILKEYI 390


>gi|224534471|ref|ZP_03675047.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
 gi|224514148|gb|EEF84466.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
          Length = 631

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628



 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 12/85 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEEG     DL S    S+V         D  ++DP+++YL+E+G   LL+   E+ +AK
Sbjct: 112 DEEGISVKDDLGSGYIKSNVL-------KDSHSEDPIKLYLKEIGKEFLLTGNQEVELAK 164

Query: 145 RIEAGRAMMMASLCESPLTFQALII 169
           ++++G      S+ E+ L  + L+I
Sbjct: 165 QMDSGE-----SIIENILKNEGLVI 184


>gi|218245044|ref|YP_002370415.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257058068|ref|YP_003135956.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218165522|gb|ACK64259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256588234|gb|ACU99120.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 379

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV +NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 143 AKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 202

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA ++ M +E +
Sbjct: 203 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATRMEMTIEKL 262

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 263 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGENPEDEVSKNLLREDLENVLDTLSPR 321

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 322 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 378


>gi|216263390|ref|ZP_03435385.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
 gi|215980234|gb|EEC21055.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
          Length = 631

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628



 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 12/85 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEEG     DL S    S+V         D  ++DP+++YL+E+G   LL+   E+ +AK
Sbjct: 112 DEEGISIKDDLGSGYIKSNVL-------KDSHSEDPIKLYLKEIGKEFLLTGNQEVELAK 164

Query: 145 RIEAGRAMMMASLCESPLTFQALII 169
           ++++G      S+ E+ L  + L+I
Sbjct: 165 QMDSG-----ESIIENILKNEGLVI 184


>gi|194477302|ref|YP_002049481.1| RNA polymerase sigma factor [Paulinella chromatophora]
 gi|171192309|gb|ACB43271.1| RNA polymerase sigma factor [Paulinella chromatophora]
          Length = 460

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 136/259 (52%), Positives = 188/259 (72%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ +FR  + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL
Sbjct: 209 MSLIKFRRRLMLGRR-------AKAKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGL 261

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S 
Sbjct: 262 IRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQ 321

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P 
Sbjct: 322 EFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPE 380

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
               +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEA
Sbjct: 381 QDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEA 440

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA+RKL+HP+R+  L+ ++
Sbjct: 441 KALRKLRHPNRNGVLKEYI 459


>gi|170078618|ref|YP_001735256.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
 gi|558881|gb|AAB41506.1| SigA [Synechococcus sp. PCC 7002]
 gi|169886287|gb|ACB00001.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
          Length = 375

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 135/260 (51%), Positives = 189/260 (72%), Gaps = 8/260 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ + +FR  +   R+       AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++G
Sbjct: 123 GMPLKDFRRRLFHGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 175

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S
Sbjct: 176 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILS 235

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ R+PT EEIA+++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P
Sbjct: 236 QELGRKPTEEEIAERMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETP 294

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D   ++ LRE    VL +L+ RE  VLR+R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 295 EDQVSKSLLREDLENVLDTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 354

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           AKA+RKL+HP+R+  L+ ++
Sbjct: 355 AKALRKLRHPNRNSILKEYI 374


>gi|154249128|ref|YP_001409953.1| RpoD family RNA polymerase sigma factor [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153064|gb|ABS60296.1| RNA polymerase, sigma 70 subunit, RpoD family [Fervidobacterium
           nodosum Rt17-B1]
          Length = 372

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 126/234 (53%), Positives = 176/234 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E++ +NLRLV+S+AK+Y  +GL FLDLIQEG++GL+KA EKFDW  GYKFSTYA WW
Sbjct: 130 AKEELIISNLRLVVSMAKRYLGKGLSFLDLIQEGSLGLIKAVEKFDWSKGYKFSTYATWW 189

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIR+PVHM + I+K+ +  R    +   EP+ E IA+++  PV+ +
Sbjct: 190 IRQAITRAIADQARTIRVPVHMVETINKIQKIKREYVQEHGEEPSIEYIAEQVGKPVDKI 249

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L+   E +SLETP+ +ED S +GDFI D++  SP   AI+  +RE   ++L +L  R
Sbjct: 250 EEILQAAPETLSLETPVNEEDDSSMGDFIADESIGSPKKEAIRTLMREEIDKLLETLNDR 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           E++VL+MR+G+      TLEEVG+ F VTRERIRQIE KA+RKL+HPSRS+ LR
Sbjct: 310 EKKVLKMRYGLYNGKPMTLEEVGQFFGVTRERIRQIEVKALRKLRHPSRSRYLR 363



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 59/121 (48%), Gaps = 16/121 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPP---DEVSSEQMEDTVAMLSNMGINVVDGDDLED-EEG 88
           K+++L +++GY+T ++++   PP   D + S  ++     L    I + D  DL + EE 
Sbjct: 18  KLVELGKRKGYITYDDIDRTFPPGDADSLDSNFLDMVYETLEKNKIEIRDTTDLMNIEEE 77

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  L  +    NS+               D ++MYLR++G I LL+   E  +A+R + 
Sbjct: 78  VKAYLSESPEIFNST------------EPKDLIKMYLRDIGKIRLLTPSEEKRLAQRAQM 125

Query: 149 G 149
           G
Sbjct: 126 G 126


>gi|28493466|ref|NP_787627.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
 gi|28476507|gb|AAO44596.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
          Length = 387

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 137/253 (54%), Positives = 186/253 (73%), Gaps = 4/253 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +VR G+     AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EK
Sbjct: 138 RELRWVVRDGQR----AKDHLLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEK 193

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R++   + REP
Sbjct: 194 FDYVKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLSRVQRQLLQDLGREP 253

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP+E+ ++L MP E V +V K  +EPISL TP+GDE  S  GD IED +AV+P D+   +
Sbjct: 254 TPDELGRELDMPPERVVEVQKYGREPISLHTPLGDEGDSEFGDLIEDVDAVAPDDAVGFS 313

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    +L SL+ RE  V+RMRFG+  +   TL+ VG+ F VTRERIRQIEAK + KL
Sbjct: 314 MLQQQLRLLLDSLSEREAGVIRMRFGLDDDMPKTLDYVGEYFDVTRERIRQIEAKTMAKL 373

Query: 668 KHPSRSKKLRSFL 680
           +HPSRS+ LR +L
Sbjct: 374 RHPSRSQCLRDYL 386



 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 28/34 (82%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ + E+++AKRIEAG
Sbjct: 86  ATADPVKDYLKQIGKVSLLTADEEVSLAKRIEAG 119


>gi|302560773|ref|ZP_07313115.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302478391|gb|EFL41484.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 404

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 166 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 225

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP E+A  L +P E 
Sbjct: 226 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPGEVAAHLDLPPER 285

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 286 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 345

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 346 RERKVVQLRYGLVDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 404


>gi|224532358|ref|ZP_03672988.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
 gi|224512665|gb|EEF83036.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
          Length = 631

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|596248|gb|AAC44104.1| primary sigma factor [Borrelia burgdorferi]
          Length = 543

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 286 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 345

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 346 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 405

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 406 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 465

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 466 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 525

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 526 LKNPKKTQKLKDYLE 540



 Score = 37.4 bits (85), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 36/56 (64%), Gaps = 5/56 (8%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           D  ++DP+++YL+E+G   LL+   E+ +AK++++G      S+ E+ L  + L+I
Sbjct: 46  DSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQMDSG-----ESIIENILKNEGLVI 96


>gi|224531865|ref|ZP_03672497.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
 gi|224511330|gb|EEF81736.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628



 Score = 37.7 bits (86), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 52/94 (55%), Gaps = 15/94 (15%)

Query: 78  VDG--DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           +DG  DD ++E+ S    DL S    S+V         D  ++DP+++YL+E+G   LL+
Sbjct: 104 IDGKLDDCDEEDISVKD-DLGSGYIKSNVL-------KDSHSEDPIKLYLKEIGKEFLLT 155

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
              E+ +AK++++G  ++     E+ L  + L+I
Sbjct: 156 GNQEVELAKQMDSGEGII-----ENILKNEGLVI 184


>gi|218249968|ref|YP_002375211.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
 gi|218165156|gb|ACK75217.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|297194519|ref|ZP_06911917.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152294|gb|EFH31643.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 366

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 128 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 187

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E 
Sbjct: 188 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVATHLELTSER 247

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 248 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLDAVLSTLGE 307

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 308 RERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 366


>gi|195941530|ref|ZP_03086912.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 80a]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|86607034|ref|YP_475797.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
 gi|86555576|gb|ABD00534.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
          Length = 404

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 129/237 (54%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 168 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 227

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +  +++S ++ R PT EEIA ++ + +E +
Sbjct: 228 IRQAITRAIADQSRTIRLPVHLYETISRIKKVTKQLSQELGRRPTEEEIATRMEITIEKL 287

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE +   +P +   +  LRE    VL +LTPR
Sbjct: 288 RFIAKSAQLPISLETPIGKEEDSRLGDFIESEGE-TPEERVAKVLLREDLESVLETLTPR 346

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 347 ERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 403


>gi|15595057|ref|NP_212846.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi B31]
 gi|216264471|ref|ZP_03436463.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221217929|ref|ZP_03589396.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225548954|ref|ZP_03769931.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|225549892|ref|ZP_03770853.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|226320452|ref|ZP_03796018.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|226321409|ref|ZP_03796936.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|3915854|sp|P52323|RPOD_BORBU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2688647|gb|AAC67061.1| RNA polymerase sigma-70 factor (rpoD) [Borrelia burgdorferi B31]
 gi|215980944|gb|EEC21751.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221192235|gb|EEE18455.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225369351|gb|EEG98803.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|225370557|gb|EEG99993.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|226233205|gb|EEH31957.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|226234094|gb|EEH32809.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|312148540|gb|ADQ31199.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           JD1]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|223889384|ref|ZP_03623970.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
 gi|223885070|gb|EEF56174.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|312149387|gb|ADQ29458.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           N40]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628


>gi|254525463|ref|ZP_05137515.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
 gi|221536887|gb|EEE39340.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
          Length = 393

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 157 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 216

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 217 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 276

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 277 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 335

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 336 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 392


>gi|225551881|ref|ZP_03772824.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
 gi|225371676|gb|EEH01103.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
          Length = 631

 Score =  267 bits (683), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 187/255 (73%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 374 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 433

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 434 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 493

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 494 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 553

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 554 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 613

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 614 LKNPKKTQKLKDYLE 628



 Score = 38.5 bits (88), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 12/85 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEE      DL S    S+V         D  ++DP+++YL+E+G   LL+   E+ +AK
Sbjct: 112 DEEDISVKDDLGSGYIKSNVL-------KDSHSEDPIKLYLKEIGKEFLLTGNQEVELAK 164

Query: 145 RIEAGRAMMMASLCESPLTFQALII 169
           ++++G      S+ E+ L  + L+I
Sbjct: 165 QMDSGE-----SIIENILKNEGLVI 184


>gi|78778882|ref|YP_396994.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9312]
 gi|78712381|gb|ABB49558.1| Sigma-70 factor [Prochlorococcus marinus str. MIT 9312]
          Length = 393

 Score =  267 bits (682), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 157 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 216

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 217 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 276

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 277 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 335

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 336 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 392


>gi|297160766|gb|ADI10478.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 453

 Score =  267 bits (682), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 125/239 (52%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 215 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 274

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E 
Sbjct: 275 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAHHLDLLPER 334

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 335 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 394

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 395 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 453



 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 27/41 (65%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           R +++   + D  R YLRE+G I LLS   E+ +A+R+EAG
Sbjct: 145 RAETSSGPSSDLFRQYLREIGRIPLLSAAEEVELARRVEAG 185


>gi|305681425|ref|ZP_07404232.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
 gi|305659630|gb|EFM49130.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
          Length = 608

 Score =  267 bits (682), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 126/238 (52%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 371 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 430

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E++K++ +  + V
Sbjct: 431 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPYELSKEMDITEDKV 490

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 491 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSER 550

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 551 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 608



 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 283 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 330


>gi|271966792|ref|YP_003340988.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270509967|gb|ACZ88245.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 331

 Score =  267 bits (682), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 126/237 (53%), Positives = 173/237 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK++T RG+ F DLIQEGN+GL++AAEKFD+  G+KFSTYA WW
Sbjct: 94  AKNHLLEANLRLVVSIAKRHTGRGMAFADLIQEGNLGLIRAAEKFDYTKGFKFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+TR++ADQ  TIRIPVHM + I+KV R  R+M   + REP+P+E+A +L M VE +
Sbjct: 154 IKQAVTRALADQGRTIRIPVHMVEVINKVARVQRQMMVTLGREPSPQELAVELDMTVEKI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G E  +  GD IED  A+ P ++     L+     VL +L+ R
Sbjct: 214 TEVQKYGREPISLHTPLGAEGDAEFGDVIEDSEAILPEEAVTFILLQRQLHAVLEALSER 273

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+RFG+      TL+E+GK F VTRERIRQIE+K + KL+HP+R++ LR +L
Sbjct: 274 EAGVMRLRFGLADGQPKTLDEIGKVFGVTRERIRQIESKTMSKLRHPARARALRDYL 330


>gi|33863540|ref|NP_895100.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9313]
 gi|33640989|emb|CAE21447.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9313]
          Length = 461

 Score =  267 bits (682), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 225 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 284

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 285 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 344

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 345 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DTENPEQDVAKNLLREDLEGVLATLSPR 403

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 404 ERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIRQIEAKALRKLRHPNRNGVLKEYI 460


>gi|203284607|ref|YP_002222347.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
 gi|201084050|gb|ACH93641.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
          Length = 630

 Score =  267 bits (682), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 128/255 (50%), Positives = 186/255 (72%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 373 IISMSEEILKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 432

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 433 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 492

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P      
Sbjct: 493 PTDEELSIRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSF 552

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    VL +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 553 VVLQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 612

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 613 LKNPKKTQKLKDYLE 627



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 39/160 (24%), Positives = 71/160 (44%), Gaps = 43/160 (26%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---GDDLEDEEGSEDSLDLASSAS 100
           +T E+L+ FL  D +  + ++    +L N GI +++   G D+ D     D LD AS   
Sbjct: 33  ITFEDLSTFLSGDMLEPDNIDCIYGILENEGIGLINEKIGSDICDV----DELDEASKLD 88

Query: 101 NSSVFLQ-------------------------------KRKDSADRSTDDPVRMYLREMG 129
           +  + L                                K     D +++DP+R+YL+E+G
Sbjct: 89  SQCMMLDDAIQVDDELDDKLDDFDDEVLDKEDYNSGYIKSGLLKDSNSEDPIRLYLKEIG 148

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
              LL+   E+ +AK++++G      S+ E+ L  + L+I
Sbjct: 149 KEFLLTGNQEVELAKQMDSG-----ESIIENILKNEGLVI 183


>gi|318041167|ref|ZP_07973123.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0101]
          Length = 464

 Score =  267 bits (682), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 228 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 287

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 288 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKL 347

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 348 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 406

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 407 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 463


>gi|124022438|ref|YP_001016745.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9303]
 gi|123962724|gb|ABM77480.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
          Length = 444

 Score =  267 bits (682), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 208 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 267

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 268 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 327

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 328 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DTENPEQDVAKNLLREDLEGVLATLSPR 386

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 387 ERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIRQIEAKALRKLRHPNRNGVLKEYI 443


>gi|1149588|emb|CAA89984.1| SigA sigma factor [Corynebacterium glutamicum]
          Length = 497

 Score =  266 bits (681), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 126/238 (52%), Positives = 177/238 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 260 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 319

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E++K++ +  E V
Sbjct: 320 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQELSKEMDISEEKV 379

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 380 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLETLSER 439

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + K +HPSRS+ LR +LD
Sbjct: 440 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKRRHPSRSQVLRDYLD 497



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 172 SATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 219


>gi|312200424|ref|YP_004020485.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311231760|gb|ADP84615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 403

 Score =  266 bits (681), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 119/244 (48%), Positives = 184/244 (75%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  +A +++VEANLRLV+S+AK+Y  RG+ FLD++QEGN+GL++A EKFD+  GYKFS
Sbjct: 160 ERDGQVAARQLVEANLRLVVSIAKRYAGRGMLFLDVVQEGNLGLIRAVEKFDYTKGYKFS 219

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WWV+QAITR++ADQS T+R+PVH+ + ++++VR  R +  ++ RE T EE+A  L 
Sbjct: 220 TYATWWVRQAITRALADQSRTVRLPVHLVELLNQLVRLRRELLMELGREATREELATALG 279

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +    V ++ +I++EP+SL++P+GD+  + LGD IED  A+ P+++A+ +      + VL
Sbjct: 280 VTANRVDELQRISREPVSLDSPVGDDADTELGDLIEDTAAIEPVEAAMVSVRAAQLSAVL 339

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L  RE RV+++RFG+     HTLEE+G++F +TRERIRQIE + + KL+HP+RS+ LR
Sbjct: 340 RALPDRERRVIQLRFGLADGQVHTLEEIGREFGLTRERIRQIEQRTLAKLRHPARSEALR 399

Query: 678 SFLD 681
           S+L+
Sbjct: 400 SYLE 403



 Score = 44.7 bits (104), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 20/31 (64%), Positives = 24/31 (77%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DPVRMYL  +G   LL+ EGE+ +AKRIEAG
Sbjct: 104 DPVRMYLASIGKTPLLTAEGEVDLAKRIEAG 134


>gi|33861053|ref|NP_892614.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|33639785|emb|CAE18955.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus subsp. pastoris str. CCMP1986]
          Length = 396

 Score =  266 bits (681), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 160 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 219

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 220 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 279

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 280 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 338

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 339 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 395


>gi|78185245|ref|YP_377680.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9902]
 gi|78169539|gb|ABB26636.1| Sigma-70 factor [Synechococcus sp. CC9902]
          Length = 451

 Score =  266 bits (681), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 215 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 274

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 275 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 334

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 335 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 393

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 394 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 450


>gi|33866315|ref|NP_897874.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8102]
 gi|33639290|emb|CAE08298.1| Putative principal RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
          Length = 471

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 235 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 294

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 295 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 354

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 355 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 413

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 414 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 470


>gi|317969651|ref|ZP_07971041.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0205]
          Length = 470

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 234 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 293

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 294 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKL 353

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 354 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 412

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 413 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 469


>gi|225021265|ref|ZP_03710457.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945998|gb|EEG27207.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 617

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 126/238 (52%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 380 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 439

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E++K++ +  + V
Sbjct: 440 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPYELSKEMDITEDKV 499

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ R
Sbjct: 500 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSER 559

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 560 EAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 617



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG
Sbjct: 292 SAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAG 339


>gi|78212231|ref|YP_381010.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9605]
 gi|78196690|gb|ABB34455.1| Sigma-70 factor [Synechococcus sp. CC9605]
          Length = 435

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 199 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 258

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 259 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 318

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 319 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 377

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 378 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 434


>gi|88807657|ref|ZP_01123169.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
 gi|88788871|gb|EAR20026.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
          Length = 447

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 211 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 270

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 271 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 330

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 331 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 389

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 390 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 446


>gi|123965795|ref|YP_001010876.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9515]
 gi|123200161|gb|ABM71769.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9515]
          Length = 397

 Score =  266 bits (681), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 161 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 220

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 221 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 280

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 281 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 339

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 340 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 396


>gi|260435157|ref|ZP_05789127.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260413031|gb|EEX06327.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 458

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 222 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 281

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 282 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 341

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 342 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 400

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 401 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 457


>gi|116072877|ref|ZP_01470142.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
 gi|116064403|gb|EAU70164.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
          Length = 451

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 215 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 274

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 275 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 334

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 335 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 393

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 394 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 450


>gi|87302644|ref|ZP_01085461.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87282988|gb|EAQ74945.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 469

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 233 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 292

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 293 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 352

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 353 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 411

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 412 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 468


>gi|157412913|ref|YP_001483779.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9215]
 gi|157387488|gb|ABV50193.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9215]
          Length = 393

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 157 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 216

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 217 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 276

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 277 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 335

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 336 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 392


>gi|40353313|gb|AAR84420.1| essential primary sigma 70 factor [Frankia sp. ACN1ag]
          Length = 255

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 123/216 (56%), Positives = 173/216 (80%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 40  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 99

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 100 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 160 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEXLDSVL 219

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +L+ RE++V+++RFG+      TLEEVG++F VTR
Sbjct: 220 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|40353309|gb|AAR84418.1| essential primary sigma 70 factor [Frankia sp. D11]
 gi|40353317|gb|AAR84422.1| essential primary sigma 70 factor [Frankia sp. HR2714]
 gi|40353319|gb|AAR84423.1| essential primary sigma 70 factor [Frankia sp. Flec]
          Length = 255

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 123/216 (56%), Positives = 173/216 (80%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 40  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 99

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 100 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 160 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 219

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +L+ RE++V+++RFG+      TLEEVG++F VTR
Sbjct: 220 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|149178485|ref|ZP_01857074.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148842698|gb|EDL57072.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 588

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 124/239 (51%), Positives = 172/239 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+  EK+++  GYKFSTYA WW
Sbjct: 320 AKQQLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATWW 379

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++AD + TIRIPVHM   I  +   + ++  +  REPT EE+A  + + VE  
Sbjct: 380 IRQAITRAVADHARTIRIPVHMFQSISTLKARSEQIRQETGREPTMEELADSVGLGVEET 439

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++K  K PISL+TP+G+ + S  GDF+ED +  SP D+A++  L++    VL SLT R
Sbjct: 440 ERIMKTWKHPISLDTPVGESEDSSFGDFLEDGHESSPADAAMREMLKDKIEHVLKSLTYR 499

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  ++R+R+G+G    +TLEE G+ F VTRERIRQIE+KA+RKL+H +RS  LR F+D 
Sbjct: 500 EREIIRLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALRKLQHQTRSAHLRGFVDA 558



 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 79/155 (50%), Gaps = 18/155 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDDLED 85
           D +   + + A ++G++T ++++ FLP +      +E  V  L   G++++D    D++D
Sbjct: 5   DANLNLLFQEAEKQGFLTFQQVHTFLPDEGGDPSLIEYIVVGLEERGLDLIDDPNADIDD 64

Query: 86  EEGSEDSLDLASSASNSSVFLQKR------------KDSADRSTDDPVRMYLREMGSIEL 133
           EE +  S+D  SSA+  S   Q              +     S+ DP+RMYL +MG+I L
Sbjct: 65  EEVA--SVD--SSANTHSDVAQGADEDSDDASSSIVEPETSLSSRDPIRMYLSQMGNIPL 120

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           LSR  EI +AK+IE  R     ++ ES    +  I
Sbjct: 121 LSRSREIFLAKKIEITRKRFRRTVLESDFALKIAI 155


>gi|290960625|ref|YP_003491807.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
 gi|260650151|emb|CBG73267.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
          Length = 387

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 124/239 (51%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 149 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 208

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E 
Sbjct: 209 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPDEVAAHLDLAPER 268

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 269 VSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 328

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 329 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 387


>gi|123968088|ref|YP_001008946.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           AS9601]
 gi|123198198|gb|ABM69839.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. AS9601]
          Length = 394

 Score =  266 bits (680), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 158 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 218 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 277

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 278 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 336

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 337 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 393


>gi|126695861|ref|YP_001090747.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9301]
 gi|126542904|gb|ABO17146.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9301]
          Length = 394

 Score =  266 bits (680), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 158 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +
Sbjct: 218 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKL 277

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 278 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVSKTLLREDLEGVLATLSPR 336

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+GI      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 337 ERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 393


>gi|254430902|ref|ZP_05044605.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
 gi|197625355|gb|EDY37914.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
          Length = 503

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 267 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 326

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 327 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKL 386

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 387 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 445

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 446 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 502


>gi|203288141|ref|YP_002223156.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
 gi|201085361|gb|ACH94935.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
          Length = 630

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 128/255 (50%), Positives = 186/255 (72%), Gaps = 3/255 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 373 IISMSEEILKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 432

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 433 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQILGKD 492

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P      
Sbjct: 493 PTDEELSIRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSF 552

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    VL +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 553 VILQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIESKALRR 612

Query: 667 LKHPSRSKKLRSFLD 681
           LK+P +++KL+ +L+
Sbjct: 613 LKNPKKTQKLKDYLE 627



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 39/160 (24%), Positives = 71/160 (44%), Gaps = 43/160 (26%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---GDDLEDEEGSEDSLDLASSAS 100
           +T E+L+ FL  D +  + ++    +L N GI +++   G D+ D     D LD AS   
Sbjct: 33  ITFEDLSTFLSGDMLEPDNIDCIYGILENEGIGLINEKIGSDICDV----DELDEASKLD 88

Query: 101 NSSVFLQ-------------------------------KRKDSADRSTDDPVRMYLREMG 129
           +  + L                                K     D +++DP+R+YL+E+G
Sbjct: 89  SQCMMLDDAIQVDDELDDKLDDFDDEVLDKEDYNSGYIKSGLLKDSNSEDPIRLYLKEIG 148

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
              LL+   E+ +AK++++G      S+ E+ L  + L+I
Sbjct: 149 KEFLLTGNQEVELAKQMDSG-----ESIIENILKNEGLVI 183


>gi|269925486|ref|YP_003322109.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789146|gb|ACZ41287.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 338

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 122/242 (50%), Positives = 179/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A++ ++EANLRLV+SVAKK+ NRGL  LDLI+EGNIGLM+A +KFD+  G+KFSTY
Sbjct: 97  EGERARRHLIEANLRLVVSVAKKHMNRGLSLLDLIEEGNIGLMRATDKFDYRKGFKFSTY 156

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QA+TR+IADQ+ TIR+PVH+ + ++ + + +R++S ++ REPT EE+A+ + M 
Sbjct: 157 ATWWIRQAVTRAIADQARTIRLPVHITETMNHLYKASRKLSQELGREPTCEELAEYMGMN 216

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR +++ ++ P+SLE P+G +  S LG FI D    +P+D AI   L+   ++VL S
Sbjct: 217 PEKVRLIMRASRHPLSLEGPVGTDGDSSLGQFIPDSTTETPVDLAIGEVLKRELSKVLNS 276

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT +E +V+ +R+G+  ++ HTLEEVG +  VTRER+RQIEAKA+ KL+ P +   LR F
Sbjct: 277 LTEKERKVMVLRYGLEGSSPHTLEEVGHRLGVTRERVRQIEAKALEKLRKPGKLNHLRDF 336

Query: 680 LD 681
           LD
Sbjct: 337 LD 338



 Score = 41.6 bits (96), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 30/43 (69%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           K+++      DD VRMYLRE+G + LL+ E E+ +AK++E G+
Sbjct: 30  KQEEDLSEDLDDSVRMYLREIGLVPLLTAEQEVELAKKMERGK 72


>gi|256396128|ref|YP_003117692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256362354|gb|ACU75851.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 390

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 123/242 (50%), Positives = 179/242 (73%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK+ ++EANLRLV+S+AK+Y  RG+  LDL+QEGN+GL++A EKFD+  GYKFST
Sbjct: 148 LEGQAAKRRLIEANLRLVVSIAKRYLGRGMSILDLVQEGNLGLIRAVEKFDYTRGYKFST 207

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + +++VVR  RR+  +   EPTP++IA+ L +
Sbjct: 208 YATWWIRQAMSRALADQARTIRVPVHVVELMNRVVRLQRRLLQENGVEPTPDDIAEVLGV 267

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V +VL++ +EP+SL  P+G+ED   LGD IED +AVSP DS     LRE    +L+
Sbjct: 268 AVERVVEVLRLAQEPVSLHAPVGEEDDVALGDLIEDADAVSPADSVAVVMLREHLDALLS 327

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+RV+++R+G+     HTLEE+G+ F VTRERIRQIEAK + KL+  + + +L  
Sbjct: 328 TLGEREKRVVQLRYGLTDGQPHTLEEIGRTFGVTRERIRQIEAKTLAKLRGHTYADQLLD 387

Query: 679 FL 680
           +L
Sbjct: 388 YL 389


>gi|320160330|ref|YP_004173554.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319994183|dbj|BAJ62954.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 543

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 129/266 (48%), Positives = 178/266 (66%), Gaps = 29/266 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A  KFD   GYKFSTYA WW
Sbjct: 278 ANQTLIRANLRLVVSIAKRYLGRGVSFLDLIQEGNLGLLRAVNKFDPTRGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA---------- 553
           ++Q+I+R IA+Q+ TIRIPVH+ + I +++R  R +  ++ REPT EE+A          
Sbjct: 338 IRQSISRYIAEQARTIRIPVHLFESITRLLRVQRTLIQQLGREPTAEELALEAGFLSDED 397

Query: 554 -------------------KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
                              ++       V++VL+  +EP+SLE P+GDED+S LGDFIED
Sbjct: 398 AQAIRKARAEGKSIDPELMRRWNFATSKVQRVLQSAEEPVSLERPVGDEDSSQLGDFIED 457

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A+ P+D+A +  LRE     L+ L+ RE +VL +RFG+    DHTLEEV + F VTRE
Sbjct: 458 DEALEPMDAAAREMLREQVQNALSILSERERQVLELRFGLIDGKDHTLEEVSRYFNVTRE 517

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RIRQIEAKA+RKL+HP+RS+ LR +L
Sbjct: 518 RIRQIEAKALRKLRHPTRSRHLREYL 543



 Score = 41.6 bits (96), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 26/36 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           ++DPVR+YL+E+G I LL  + E  +A RIEA R +
Sbjct: 92  SEDPVRLYLKEIGQINLLDADSEFRLAARIEAWRHL 127


>gi|113954073|ref|YP_731235.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
 gi|113881424|gb|ABI46382.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
          Length = 440

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 204 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 263

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 264 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 323

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 324 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 382

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 383 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 439


>gi|87123878|ref|ZP_01079728.1| Sigma-70 factor [Synechococcus sp. RS9917]
 gi|86168447|gb|EAQ69704.1| Sigma-70 factor [Synechococcus sp. RS9917]
          Length = 456

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 220 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 279

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 280 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 339

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 340 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 398

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 399 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 455


>gi|330466485|ref|YP_004404228.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
 gi|328809456|gb|AEB43628.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
          Length = 535

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 134/254 (52%), Positives = 186/254 (73%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R ++ + R GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 286 RDLLWISRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 341

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 342 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 401

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 402 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 461

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 462 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 521

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 522 RHPSRSQVLRDYLD 535



 Score = 43.9 bits (102), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q R+D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 216 SEALKQARRDAELTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAG 263


>gi|148238947|ref|YP_001224334.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 7803]
 gi|147847486|emb|CAK23037.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. WH 7803]
          Length = 450

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 214 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 273

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 274 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 333

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 334 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 392

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 393 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 449


>gi|159037077|ref|YP_001536330.1| RNA polymerase sigma factor [Salinispora arenicola CNS-205]
 gi|157915912|gb|ABV97339.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 532

 Score =  265 bits (678), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/254 (52%), Positives = 186/254 (73%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R ++ + R GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 283 RDLMWISRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 338

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 339 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 398

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 399 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 458

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 459 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 518

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 519 RHPSRSQVLRDYLD 532



 Score = 44.3 bits (103), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q R+D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 213 SEALKQARRDAELTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAG 260


>gi|325106737|ref|YP_004267805.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967005|gb|ADY57783.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 575

 Score =  265 bits (677), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 123/239 (51%), Positives = 172/239 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+  EK+++  GYKFSTYA WW
Sbjct: 316 AKQKLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATWW 375

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++AD + TIRIPVHM   I  +   A ++  +  REPT EE+A  + M VE  
Sbjct: 376 IRQAITRAVADHARTIRIPVHMFQSISTLKAKAEQIRQETGREPTMEELAAAIDMSVEET 435

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++K  K P+SL+TP+G+ + S  GDF++D +  +P D+A+Q  LR+    VL SLT R
Sbjct: 436 ERIMKTWKHPVSLDTPVGESEDSSFGDFLQDDSENTPADTAMQQMLRDKINHVLKSLTYR 495

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  ++++R+G+G    +TLEE G+ F VTRERIRQIE+KA+RKL+H +RS  L+ F+D 
Sbjct: 496 EREIIKLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALRKLQHQTRSNHLKGFVDA 554



 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 28/172 (16%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-- 79
           +V  FS+ S + ++K A + G ++ + ++ FLP +      ++  V  L  + I++ D  
Sbjct: 1   MVTRFSE-SIQPLMKSALKAGRLSYQSMDEFLPDEGGDPTLIDQIVLALDQLEIDMYDDP 59

Query: 80  --------------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
                            +E+E+ SED    A     + V           S+ DP+RMYL
Sbjct: 60  SGRIQKIPEKIGLPNQPIEEEDASEDDAVPAVVGPETPV-----------SSRDPIRMYL 108

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            +MG+I LL+R  EI +AK+IE  R     +  ES  T   ++   +++N G
Sbjct: 109 SQMGNIPLLTRADEIYLAKQIEVTRKRFRRTAMESDFTLAIVVDMFEKVNTG 160


>gi|21220928|ref|NP_626707.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289771799|ref|ZP_06531177.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
 gi|19856645|sp|P18182|HRDA_STRCO RecName: Full=RNA polymerase principal sigma factor hrdA
 gi|6759560|emb|CAB69753.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701998|gb|EFD69427.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
          Length = 396

 Score =  265 bits (677), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 123/239 (51%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 158 LAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 217

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E 
Sbjct: 218 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDLAPER 277

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL++L  
Sbjct: 278 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGE 337

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 338 RERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLRDHAYADQLRGYLD 396


>gi|311895920|dbj|BAJ28328.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 389

 Score =  265 bits (677), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 127/239 (53%), Positives = 175/239 (73%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK+ ++EANLRLV+SVAK+Y  RGL  LDLIQEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 151 IAKRRLIEANLRLVVSVAKRYVGRGLTLLDLIQEGNVGLIRAVEKFDYARGYKFSTYATW 210

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++V+R  R +  +   EPT  E+   L +P E 
Sbjct: 211 WIRQAMSRALADQARTIRVPVHVVELINRVLRVQRGLLQERGVEPTAAEVGAVLQLPPER 270

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+VLK+ +EP+SL TP+G+ED   LGD IED +A SP +SA    LRE    VLA+L  
Sbjct: 271 VREVLKLAQEPVSLHTPVGEEDDVALGDLIEDADAASPPESAAFLLLREHLEAVLATLGE 330

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+  + + +LR +LD
Sbjct: 331 RERQVVQLRYGLDDGRPRTLEEIGHLFGVTRERIRQIEAKTLGKLRDHAFADQLRGYLD 389


>gi|327539652|gb|EGF26260.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 567

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 126/281 (44%), Positives = 193/281 (68%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A   D    +R E++ + + T  S +   + ++ VR+   +    K+E+   NLRLV+S+
Sbjct: 283 AMSRDEAADLRQELRELMLVTQESPTSLHNRMAKVRRHFDQYEATKRELSAGNLRLVVSI 342

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY NRGL FLDLIQEGN GLM+A +K+++  G+KFSTYA WW++QAITR+IADQ+ TI
Sbjct: 343 AKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTI 402

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM D + K+ +  +R++  ++REPT E+IA+   +P+E VR+V+ I + P+SL+ P
Sbjct: 403 RIPVHMIDVLSKLRQAQKRLTQTLRREPTYEDIAEATDVPIEEVRRVMDIGRHPVSLDRP 462

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G+ + S  G+F++D    +P+  A    LR     +L +LT RE  ++R+R+G+     
Sbjct: 463 VGEGEDSSFGEFVQDSETDNPVRIAASGMLRNKIDELLKTLTFREREIIRLRYGLVDGYS 522

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +TLEE G+ F VTRER+RQIEAKA+ K++ PSR+++L S+L
Sbjct: 523 YTLEECGRIFKVTRERVRQIEAKAVAKMQSPSRAERLSSYL 563



 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 82/165 (49%), Gaps = 31/165 (18%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG------- 80
           D    ++I    + G++T +E+NA+LP ++V+ E++   +  L N GI +++        
Sbjct: 5   DQDLSQLIARGTKDGFLTYDEVNAYLPDEDVNPEKLNSLLLALENRGIQLIEASEKKARD 64

Query: 81  ----------------DDLEDEEGSEDSL-DLASSASNSSVFLQKRKDSADRSTDDPVRM 123
                           D   DEE  E  L + A+S S SS  + K       +++DP+RM
Sbjct: 65  AAARRPSPNVRGLRSVDMTADEESPEQILANEAASQSFSSADMPK-------ASEDPIRM 117

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           YL +M  I LLSRE EIA+AK+IE  R     SL E+    +A +
Sbjct: 118 YLSQMAEIPLLSREEEIALAKKIEITRKQYRRSLLETDYALRATV 162


>gi|164688461|ref|ZP_02212489.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
 gi|164602874|gb|EDQ96339.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
          Length = 306

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 129/242 (53%), Positives = 179/242 (73%), Gaps = 1/242 (0%)

Query: 439 CEA-SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           CE   +AKK +VE+NLRLV+S+A+KY  + +  LDLIQEG +GL++AAEKFD+  G+KFS
Sbjct: 60  CEGDEVAKKILVESNLRLVVSIARKYARKEMAMLDLIQEGTLGLIRAAEKFDYTKGFKFS 119

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW+KQ ITR+IADQS TIR+PVHM +KI+KV   + +++ ++ REP PEEIAK++ 
Sbjct: 120 TYATWWIKQGITRAIADQSRTIRVPVHMVEKINKVSTISSQLAKELGREPKPEEIAKRMH 179

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PVE V +V++I++ P S+E+ IG ED + L   I DK A SP +   ++ L++    VL
Sbjct: 180 VPVEKVVQVIRISQRPQSIESTIGQEDDTELEQVIPDKEAHSPEEIVTRSLLKDQIEYVL 239

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L+ RE+ V+++RFG+G     TLEEVG+ F VTRER RQIE KA+RKL HPSRS KL 
Sbjct: 240 DTLSEREKGVIKLRFGLGDGEKKTLEEVGRAFNVTRERARQIEKKALRKLAHPSRSNKLL 299

Query: 678 SF 679
            +
Sbjct: 300 DY 301



 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 47/96 (48%), Gaps = 24/96 (25%)

Query: 69  MLSN--MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           ML+N  +GIN V   D+  E  S + ++L                      DD +++YL+
Sbjct: 2   MLNNNSIGINKVKESDISLEGNSNNLVNL----------------------DDSMKIYLK 39

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           E+G I LLSR+ E+ IAKRI  G  +    L ES L
Sbjct: 40  EIGKIPLLSRQEELDIAKRICEGDEVAKKILVESNL 75


>gi|256787912|ref|ZP_05526343.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
          Length = 365

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 123/239 (51%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 127 LAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 186

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E 
Sbjct: 187 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDLAPER 246

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL++L  
Sbjct: 247 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGE 306

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 307 RERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLRDHAYADQLRGYLD 365


>gi|145594022|ref|YP_001158319.1| RNA polymerase sigma factor [Salinispora tropica CNB-440]
 gi|145303359|gb|ABP53941.1| RNA polymerase sigma factor RpoD [Salinispora tropica CNB-440]
          Length = 542

 Score =  265 bits (676), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 179/238 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 305 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 364

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 365 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 424

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   + L++   +VL +L+ R
Sbjct: 425 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQTLSER 484

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 485 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 542



 Score = 43.9 bits (102), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q R+D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 223 SEALKQARRDAELTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAG 270


>gi|32474203|ref|NP_867197.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32444741|emb|CAD74742.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 567

 Score =  265 bits (676), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 126/281 (44%), Positives = 193/281 (68%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A   D    +R E++ + + T  S +   + ++ VR+   +    K+E+   NLRLV+S+
Sbjct: 283 AMSRDEAADLRQELRELMLVTQESPTSLHNRMAKVRRHFDQYEATKRELSAGNLRLVVSI 342

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY NRGL FLDLIQEGN GLM+A +K+++  G+KFSTYA WW++QAITR+IADQ+ TI
Sbjct: 343 AKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTI 402

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM D + K+ +  +R++  ++REPT E+IA+   +P+E VR+V+ I + P+SL+ P
Sbjct: 403 RIPVHMIDVLSKLRQAQKRLTQTLRREPTYEDIAEATDVPIEEVRRVMDIGRHPVSLDRP 462

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G+ + S  G+F++D    +P+  A    LR     +L +LT RE  ++R+R+G+     
Sbjct: 463 VGEGEDSSFGEFVQDSETDNPVRIAASGMLRNKIDELLKTLTFREREIIRLRYGLVDGYS 522

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +TLEE G+ F VTRER+RQIEAKA+ K++ PSR+++L S+L
Sbjct: 523 YTLEECGRIFKVTRERVRQIEAKAVAKMQSPSRAERLSSYL 563



 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 82/165 (49%), Gaps = 31/165 (18%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG------- 80
           D    ++I    + G++T +E+NA+LP ++V+ E++   +  L N GI +++        
Sbjct: 5   DQDLSQLIARGTKDGFLTYDEVNAYLPDEDVNPEKLNSLLLALENRGIQLIEASEKKARD 64

Query: 81  ----------------DDLEDEEGSEDSL-DLASSASNSSVFLQKRKDSADRSTDDPVRM 123
                           D   DEE  E  L + A+S S SS  + K       +++DP+RM
Sbjct: 65  AAARRPSPNVRGLRSVDMTADEESPEQILANEAASQSFSSADMPK-------ASEDPIRM 117

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           YL +M  I LLSRE EIA+AK+IE  R     SL E+    +A +
Sbjct: 118 YLSQMAEIPLLSREEEIALAKKIEITRKQYRRSLLETDYALRATV 162


>gi|238063497|ref|ZP_04608206.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
 gi|237885308|gb|EEP74136.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
          Length = 534

 Score =  265 bits (676), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 179/238 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 297 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 356

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V
Sbjct: 357 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKV 416

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   + L++   +VL +L+ R
Sbjct: 417 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQTLSER 476

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 477 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 534



 Score = 43.9 bits (102), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q R+D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 215 SEALKQARRDAELTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAG 262


>gi|86609652|ref|YP_478414.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558194|gb|ABD03151.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 403

 Score =  265 bits (676), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 129/237 (54%), Positives = 178/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 167 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 226

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +  + +S ++ R+PT EEIA ++ + +E +
Sbjct: 227 IRQAITRAIADQSRTIRLPVHLYETISRIKKVTKLLSQELGRKPTEEEIATRMEITIEKL 286

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +LT R
Sbjct: 287 RFIAKSAQLPISLETPIGKEEDSRLGDFIES-DGETPEDRVAKVLLREDLESVLETLTAR 345

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 346 ERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 402


>gi|116075287|ref|ZP_01472547.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
 gi|116067484|gb|EAU73238.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
          Length = 479

 Score =  264 bits (675), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 243 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 302

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 303 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 362

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 363 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPR 421

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 422 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 478


>gi|302534283|ref|ZP_07286625.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443178|gb|EFL14994.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 361

 Score =  264 bits (675), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 123/239 (51%), Positives = 177/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 123 MAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 182

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E 
Sbjct: 183 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTAEEVAAHLELTPER 242

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 243 VLEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPMESAAFFLLREHLEAVLSTLGE 302

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 303 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 361


>gi|313891780|ref|ZP_07825385.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|329121139|ref|ZP_08249770.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|313119774|gb|EFR42961.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|327471301|gb|EGF16755.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 374

 Score =  264 bits (675), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 128/223 (57%), Positives = 168/223 (75%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A  AKK + +ANLRLV+S+AKKY  RGLQFLDLIQEGN+GL+KA +KFD+  GYKFST
Sbjct: 138 INADKAKKALSDANLRLVVSIAKKYLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGYKFST 197

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q+ITR+IADQ+ TIR+PVHM + I+K+ R +R++  +  REPT  EIAK + +
Sbjct: 198 YATWWIRQSITRAIADQARTIRVPVHMVETINKLNRISRQLLQEKGREPTEYEIAKAMDV 257

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V  VR+V KI ++PISLETPIG+++ SHLGDFIED++A++P D+     L+E    +L 
Sbjct: 258 SVGKVREVKKIAQDPISLETPIGEKEDSHLGDFIEDQDAIAPDDATDSILLKEQIEELLT 317

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +LT RE +VL +RFG+      TLEEVG  F VTRERIRQIE 
Sbjct: 318 NLTDRERQVLELRFGLKDGRPRTLEEVGNNFDVTRERIRQIEG 360



 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 57/111 (51%), Gaps = 14/111 (12%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV---VDGDDLEDEEGSEDSLDLASS 98
           G ++ + +N F+  + +  E ++   A L   GI+V   V GD  ED E +   L     
Sbjct: 28  GMISGDIVNDFVNENHIDIEGLDLLNAALHEHGIDVYMNVPGD--EDSEENNKPLKKIQP 85

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  V          +  DDPV+MYL+E+G+++LL+ E E+ +AK +E G
Sbjct: 86  KPSKRV---------SQGIDDPVKMYLKEIGTVDLLTAEEEVTLAKAVEKG 127


>gi|302866088|ref|YP_003834725.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
 gi|302568947|gb|ADL45149.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
          Length = 551

 Score =  264 bits (675), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 134/254 (52%), Positives = 186/254 (73%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R ++ + R GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 302 RDLMWISRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 357

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 358 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 417

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 418 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 477

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 478 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 537

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 538 RHPSRSQVLRDYLD 551



 Score = 43.9 bits (102), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q R+D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 232 SEALKQARRDAELTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAG 279


>gi|315502644|ref|YP_004081531.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|315409263|gb|ADU07380.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 551

 Score =  264 bits (674), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 134/254 (52%), Positives = 186/254 (73%), Gaps = 4/254 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R ++ + R GE     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 302 RDLMWISRDGER----AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 357

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 358 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 417

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 418 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 477

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 478 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 537

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 538 RHPSRSQVLRDYLD 551



 Score = 43.9 bits (102), Expect = 0.086,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S    Q R+D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 232 SEALKQARRDAELTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAG 279


>gi|260424772|ref|ZP_05733235.2| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
 gi|260403136|gb|EEW96683.1| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
          Length = 394

 Score =  263 bits (673), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 129/221 (58%), Positives = 163/221 (73%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ AKKEM  ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA
Sbjct: 158 AAEAKKEMANANLRLVVSIAKKYPGRGMPFLDLIQEGNMGLLKAVDKFDYTKGYKFSTYA 217

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIR+PVHM + I+K+ R  R    +  RE T EE+AK++   V
Sbjct: 218 TWWIRQAITRSIADQARTIRVPVHMVETINKMNRVGRHFLQEHGREATNEELAKEMETSV 277

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +R+  K  ++PISLETPIG+++ SHLGDFIED+   SP D A     RE   ++L +L
Sbjct: 278 EKIREAKKAAQDPISLETPIGEKEDSHLGDFIEDQKTASPEDEAAATMRREQIHQLLETL 337

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           T RE+ V+ +R+GI   T  TLEEVGK F VTRERIRQIE 
Sbjct: 338 TEREKGVIALRYGIDDGTQRTLEEVGKYFGVTRERIRQIEG 378



 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 60/121 (49%), Gaps = 12/121 (9%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DG-DDLEDEEGSEDSLDLAS 97
           G +  +++  F     ++S+Q++     L   G+ ++   DG D+  D E  E+  D   
Sbjct: 26  GNIKYDDILLFTKEKSLTSKQLDSVFKALHEGGVEIIYEEDGKDEFRDGESEEEFEDELL 85

Query: 98  SASNSSVFLQKR---KDSADRSTD-----DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              ++   + ++   K   D S D     DPVR+YLRE G+  LL+ E E+ +A+ IE G
Sbjct: 86  EDGDAEADVDEKEWEKGDGDISADPAGITDPVRLYLRECGTTPLLTSEQEMKLAQTIEIG 145

Query: 150 R 150
           +
Sbjct: 146 K 146


>gi|40353315|gb|AAR84421.1| essential primary sigma 70 factor [Frankia sp. HRX401a]
          Length = 255

 Score =  263 bits (673), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 122/216 (56%), Positives = 172/216 (79%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FL LIQEGN+GL++A EKFD+  GYKFS
Sbjct: 40  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLHLIQEGNLGLIRAVEKFDYTKGYKFS 99

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 100 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 160 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 219

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +L+ RE++V+++RFG+      TLEEVG++F VTR
Sbjct: 220 HTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|226355184|ref|YP_002784924.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226317174|gb|ACO45170.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 399

 Score =  263 bits (672), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 137/257 (53%), Positives = 178/257 (69%), Gaps = 7/257 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH+  +V  GE     AKK + EANLRLV+S+AKKY NRGL  LDLIQEGN GL++A EK
Sbjct: 147 RHLQRLVEDGEA----AKKSLTEANLRLVVSIAKKYANRGLNLLDLIQEGNQGLIRAVEK 202

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QA+TR+IAD+S TIR+PVHM + I+K+ R +R++  ++ REP
Sbjct: 203 FEYRRGYKFSTYATWWIRQALTRAIADKSRTIRVPVHMVETINKLSRISRQLEMELSREP 262

Query: 548 TPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             EE+A+ +      E V    K+  EPISLETPIGDE  S  GDF+ D+   SP+ +A 
Sbjct: 263 LAEEMAEAMGPGWDAEKVTDTQKVGHEPISLETPIGDEGDSFYGDFLPDERFGSPVQNAS 322

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q  L E   R L+SL  RE  VL++R G     +HTLEEVG+   VTRER+RQIE+KA+R
Sbjct: 323 QTLLSEALERALSSLGEREALVLKLRNGFVDGREHTLEEVGQLLSVTRERVRQIESKALR 382

Query: 666 KLKH-PSRSKKLRSFLD 681
           KLK+  S +  LR FLD
Sbjct: 383 KLKYGESLNAGLRDFLD 399



 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 38/74 (51%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VD + L+D  G E  LD A   +       +   SAD    D +R YL E+G IELLS  
Sbjct: 57  VDPEVLDDGLGLEADLDSAPVDATKDAEELEIHISADAYQGDSLRQYLHEIGQIELLSAV 116

Query: 138 GEIAIAKRIEAGRA 151
            E+ +A+R E G A
Sbjct: 117 EEMDLARRYEEGEA 130


>gi|294629207|ref|ZP_06707767.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292832540|gb|EFF90889.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 386

 Score =  263 bits (672), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 123/239 (51%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 148 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 207

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP E+A +L +  + 
Sbjct: 208 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPAEVAAQLDLTPDR 267

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 268 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGE 327

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 328 RERKVVQLRYGLMDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 386


>gi|224533326|ref|ZP_03673920.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
 gi|224513491|gb|EEF83848.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
          Length = 255

 Score =  263 bits (672), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 124/248 (50%), Positives = 183/248 (73%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++  G
Sbjct: 5   IAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE++
Sbjct: 65  FKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELS 124

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L++  
Sbjct: 125 DRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQI 184

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P ++
Sbjct: 185 RAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKT 244

Query: 674 KKLRSFLD 681
           +KL+ +L+
Sbjct: 245 QKLKDYLE 252


>gi|257892237|ref|ZP_05671890.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
 gi|257828616|gb|EEV55223.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
          Length = 332

 Score =  263 bits (671), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 130/239 (54%), Positives = 172/239 (71%), Gaps = 1/239 (0%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y  
Sbjct: 94  VKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVG 153

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 154 RGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 213

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED 
Sbjct: 214 VETINKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDD 273

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           SHLGDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEE
Sbjct: 274 SHLGDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEE 332



 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 58/115 (50%), Gaps = 9/115 (7%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N    P  +++++M+  +  + + GI+VVD       E  + S+    SA   +   +  
Sbjct: 34  NQLATPFTLNADEMDKLIQKIEDAGISVVD-------ENGDPSIHSLKSAEKKAEQAKTE 86

Query: 110 KDSADRST--DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
             SA      +DPVRMYL+E+G + LL+ E E+A+A +IE G       L E+ L
Sbjct: 87  DLSAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALALKIEEGDQEAKQRLAEANL 141


>gi|213026208|ref|ZP_03340655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 445

 Score =  262 bits (670), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 141/278 (50%), Positives = 190/278 (68%), Gaps = 6/278 (2%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 163 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 222

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 223 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 279

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 280 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 339

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 340 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 399

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED
Sbjct: 400 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIED 437



 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 37/52 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+
Sbjct: 6   TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLL 57


>gi|271962349|ref|YP_003336545.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270505524|gb|ACZ83802.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 324

 Score =  262 bits (669), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 128/237 (54%), Positives = 171/237 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   VEANLRLV+S+AK++  RG+  LDLIQEGN+GL++A EKFD  LG+KFSTYA WW
Sbjct: 87  AKDRFVEANLRLVVSIAKRHAGRGVPLLDLIQEGNLGLIRAVEKFDHRLGFKFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ T+R+PVHM + I+KV R  R++   + REPTPEEIA +L +  E V
Sbjct: 147 IKQAITRAMADQARTVRVPVHMVEMINKVARVERQLLCDLGREPTPEEIAAELDLTPEKV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++    +EPISL TP+GDE  S LGD IED  AV+P  +     L+E    +LA+LT R
Sbjct: 207 TEIKGHGREPISLHTPLGDEGDSELGDLIEDAEAVTPEAAVAFTLLQEQVRALLATLTGR 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+ MRFG       TL+E+G+ + +TRERIRQIE+K + +L+HPSRS+ LR +L
Sbjct: 267 EAGVISMRFGFADGRPWTLDEIGRVYGLTRERIRQIESKTMSRLRHPSRSQPLRDYL 323



 Score = 38.1 bits (87), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 25/34 (73%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPVR YLR++  I LL+   E+ +A+R+EAG
Sbjct: 24  ATADPVRDYLRQIARIPLLTAGQEVELARRVEAG 57


>gi|148241988|ref|YP_001227145.1| RNA polymerase sigma factor RpoD [Synechococcus sp. RCC307]
 gi|147850298|emb|CAK27792.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. RCC307]
          Length = 401

 Score =  262 bits (669), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 131/237 (55%), Positives = 178/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 165 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 224

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +
Sbjct: 225 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 284

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PR
Sbjct: 285 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPDQDVAKNLLREDLEGVLATLSPR 343

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+ KL+HP+R+  L+ ++
Sbjct: 344 ERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALLKLRHPNRNGVLKEYI 400


>gi|269926188|ref|YP_003322811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789848|gb|ACZ41989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 463

 Score =  262 bits (669), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 125/248 (50%), Positives = 180/248 (72%), Gaps = 3/248 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VRK   E   AK +++EAN RLV+S+AKKY  RGL  LDLIQEGNIGLM+AA+KFD+  G
Sbjct: 218 VRK---EGEGAKCKLIEANTRLVVSIAKKYLGRGLSLLDLIQEGNIGLMRAADKFDYTRG 274

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QA+TR+IADQS TIR+PVH+ + + K+ +T++++  ++  EPT E+++
Sbjct: 275 YKFSTYATWWIRQAVTRAIADQSRTIRLPVHVCETVSKIHKTSQKLQQELGHEPTIEQLS 334

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L MP++ V ++ + +K P+SLE PIG++  S LGDF+ED + ++P+  A    LRE  
Sbjct: 335 SELGMPMKKVVQIQQASKFPVSLEAPIGEDGDSMLGDFLEDVHVLNPVQKAANDILREQI 394

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L P+E +VL +RFG+      TLEEVG +F +TRER+RQIE  A+R+L+     
Sbjct: 395 NSVLQNLPPKERKVLELRFGLVDGKCRTLEEVGNEFAITRERVRQIECTALRRLRENHLI 454

Query: 674 KKLRSFLD 681
           K+LR FL+
Sbjct: 455 KQLRDFLE 462



 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 36/57 (63%), Gaps = 3/57 (5%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM---MMASLCESPLTFQALIIWR 171
           D+PV+MYLRE+G + LL+ E E+ +A++IE  R +    +     + +T  AL I++
Sbjct: 69  DEPVQMYLREIGKVPLLTAEQEVILARKIELSRRLDEYWLQQHTNADVTLVALKIYK 125


>gi|254382896|ref|ZP_04998252.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
 gi|194341797|gb|EDX22763.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
          Length = 362

 Score =  261 bits (668), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 123/239 (51%), Positives = 177/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 124 MAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 183

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E 
Sbjct: 184 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTVEEVAVHLELTPER 243

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 244 VLEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFFLLREHLEAVLSTLGE 303

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 304 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 362



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 5/48 (10%)

Query: 107 QKRKDSADRSTD-----DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           Q+RK +AD  +      D  R YLRE+G I LL+   E+ +A+R+EAG
Sbjct: 47  QQRKRTADSGSGSGPSADLFRQYLREIGRIPLLTAAEEVELARRVEAG 94


>gi|239979292|ref|ZP_04701816.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 357

 Score =  261 bits (668), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 121/238 (50%), Positives = 174/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+SVAK+YT RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 120 AKGRLIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVRT R +  +  REP  EE+ ++L +  E V
Sbjct: 180 IRQAMSRALADQARTIRVPVHVVELINRVVRTQRALLQEAGREPAAEEVGERLGLSAEKV 239

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++  EPISL  P+G ED   LGD IED +A SP +SA    LR+    VLA+L  R
Sbjct: 240 EEVLRLAHEPISLHAPVGGEDDVFLGDLIEDADAASPAESAALLLLRQHLDAVLATLGDR 299

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G       TLEE+G+ F VTRER+RQIE+K +R+L+  + + +LR +L+
Sbjct: 300 ERQVVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLREHTAAGQLRGYLE 357



 Score = 37.7 bits (86), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLC 158
           + A  +  D  R YLRE+G I LLS   E+ +A+R+EAG   A  +A  C
Sbjct: 52  EQAGAAAPDLFRQYLREIGRIPLLSAADEVELARRVEAGVFAAAKLAGGC 101


>gi|581612|emb|CAA37172.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 396

 Score =  261 bits (667), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 122/239 (51%), Positives = 177/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 158 LAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 217

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E 
Sbjct: 218 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDLAPER 277

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL++L  
Sbjct: 278 VGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGE 337

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+   VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 338 RERKVVQLRYGLADGRPRTLEEIGRLGGVTRERIRQIESKTLSKLRDHAYADQLRGYLD 396


>gi|320353903|ref|YP_004195242.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320122405|gb|ADW17951.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 439

 Score =  261 bits (667), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 122/239 (51%), Positives = 177/239 (74%), Gaps = 1/239 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK  M+ ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+A  +FD+  G KFSTYA W
Sbjct: 202 FAKDSMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYKKGNKFSTYASW 261

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+I D++ TIR+PVH  +   +  +    +  ++ REPTP EI+K   +P++ 
Sbjct: 262 WIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGREPTPVEISKMTDLPMDK 321

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  +L+ ++EPISLETP+GD+D++ LGDF+E++ + SP D+     L    T VL++LT 
Sbjct: 322 ILAILEASREPISLETPVGDDDST-LGDFLENQESESPYDAVQNRELAHRVTEVLSTLTD 380

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+++R+RFGIG   ++TLEE+GK+F V+RERIRQIE KA+ +L+H SR +KLR FLD
Sbjct: 381 REEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRREKLRFFLD 439


>gi|327539483|gb|EGF26098.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 562

 Score =  261 bits (667), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 122/239 (51%), Positives = 171/239 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +KF+   GYKFSTYA WW
Sbjct: 312 AKRVLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWW 371

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM D ++K+ +  R +  +  REPT EE++K+  + ++  
Sbjct: 372 IRQAITRAIADQSRTIRVPVHMIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDT 431

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LK++++P+SL+ P+GD D S  G+F++D     PL    +  L+      + +L  R
Sbjct: 432 RVILKMSRQPLSLDQPVGDHDDSVFGEFLQDHRDDDPLVETNREALKHQIDLAMETLNYR 491

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  +LR+R+G+     +TLEEVG+ F VTRER+RQIE+KA+RKL+ P R+K L SFLDG
Sbjct: 492 EREILRLRYGLADGYTYTLEEVGRIFQVTRERVRQIESKAVRKLQQPYRAKSLVSFLDG 550



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 52/106 (49%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S ++ S A+     + +R +     T+DPVRMYL +MG I LL+R+ E+A A++IEA R 
Sbjct: 70  SEEIESGAAGDEDVVSRRDEFPTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQIEATRE 129

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
                +  +    QA +    ++ D    L   I++      E K 
Sbjct: 130 RYRHCMMATDFMLQAALKLLQQVRDKQLRLDRTIEVSVTNAAEKKA 175


>gi|32474487|ref|NP_867481.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32445025|emb|CAD75027.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 568

 Score =  261 bits (667), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 122/239 (51%), Positives = 171/239 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +KF+   GYKFSTYA WW
Sbjct: 318 AKRVLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWW 377

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM D ++K+ +  R +  +  REPT EE++K+  + ++  
Sbjct: 378 IRQAITRAIADQSRTIRVPVHMIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDT 437

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +LK++++P+SL+ P+GD D S  G+F++D     PL    +  L+      + +L  R
Sbjct: 438 RVILKMSRQPLSLDQPVGDHDDSVFGEFLQDHRDDDPLVETNREALKHQIDLAMETLNYR 497

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  +LR+R+G+     +TLEEVG+ F VTRER+RQIE+KA+RKL+ P R+K L SFLDG
Sbjct: 498 EREILRLRYGLADGYTYTLEEVGRIFQVTRERVRQIESKAVRKLQQPYRAKSLVSFLDG 556



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 52/106 (49%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S ++ S A+     + +R +     T+DPVRMYL +MG I LL+R+ E+A A++IEA R 
Sbjct: 76  SEEIESGAAGDEDVVSRRDEFPTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQIEATRE 135

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
                +  +    QA +    ++ D    L   I++      E K 
Sbjct: 136 RYRHCMMATDFMLQAALKLLQQVRDKQLRLDRTIEVSVTNAAEKKA 181


>gi|320010942|gb|ADW05792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 358

 Score =  261 bits (666), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 122/239 (51%), Positives = 177/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 120 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 179

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EP PEE+A +L +  E 
Sbjct: 180 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPAPEEVAAQLDLTPER 239

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED    GD IED +A SP+++A    LRE    VL++L  
Sbjct: 240 VSEVLRLAQEPVSLHAPVGEEDDVAFGDLIEDGDAASPVETAAFLLLREHLEVVLSTLGE 299

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 300 RERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLDKLRGHAFADQLRGYLD 358



 Score = 39.3 bits (90), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + R DS    T D  R YLRE+G I LLS   E+ +A+R+EAG
Sbjct: 49  RSRPDSGG-PTSDLFRQYLREIGRIPLLSAADEVELARRVEAG 90


>gi|1519636|gb|AAB07551.1| SigA [Chloroflexus aurantiacus J-10-fl]
          Length = 343

 Score =  260 bits (665), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 122/236 (51%), Positives = 169/236 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 106 ARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYATWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V RT+ R+   ++R+ TPEEIA  + +    V
Sbjct: 166 IRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHRLQQTMQRDATPEEIADAMGISAGKV 225

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P ++   + LRE    VL  L  R
Sbjct: 226 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAPAASLLREQLEEVLMKLPER 285

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR+ 
Sbjct: 286 ERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHPHLGKKLRAI 341



 Score = 37.7 bits (86), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           ML   GI V++  D  D   ++   D        +  +    D  D + DDPVRMYL+E+
Sbjct: 1   MLQAEGIKVIESSDELDGRPTDFEPD------PDADLIADLPDLGDIAFDDPVRMYLQEI 54

Query: 129 GSIELLSREGEIAI 142
           G + LL+ E E+ +
Sbjct: 55  GQVPLLTAEQEVEL 68


>gi|291451171|ref|ZP_06590561.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291354120|gb|EFE81022.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 397

 Score =  260 bits (665), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 121/238 (50%), Positives = 174/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+SVAK+YT RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 160 AKGRLIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 219

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVRT R +  +  REP  EE+ ++L +  E V
Sbjct: 220 IRQAMSRALADQARTIRVPVHVVELINRVVRTQRALLQEAGREPAAEEVGERLGLSAEKV 279

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++  EPISL  P+G ED   LGD IED +A SP +SA    LR+    VLA+L  R
Sbjct: 280 EEVLRLAHEPISLHAPVGGEDDVFLGDLIEDADAASPAESAALLLLRQHLDAVLATLGDR 339

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G       TLEE+G+ F VTRER+RQIE+K +R+L+  + + +LR +L+
Sbjct: 340 ERQVVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLREHTAAGQLRGYLE 397



 Score = 37.7 bits (86), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLC 158
           + A  +  D  R YLRE+G I LLS   E+ +A+R+EAG   A  +A  C
Sbjct: 92  EQAGAAAPDLFRQYLREIGRIPLLSAADEVELARRVEAGVFAAAKLAGGC 141


>gi|291301996|ref|YP_003513274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571216|gb|ADD44181.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 559

 Score =  260 bits (664), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ ANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 322 AKNHLLAANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 381

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP PEE+AK++ +  E V
Sbjct: 382 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPAPEELAKEMDISPEKV 441

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   + L+    +VL +L+ R
Sbjct: 442 LEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQGQLQQVLQTLSER 501

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 502 EAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 559



 Score = 45.1 bits (105), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 39/66 (59%), Gaps = 3/66 (4%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ED EGS D  D      +S    Q RKD+   ++ D VR YL+++G + LL+   E+ +A
Sbjct: 225 EDGEGS-DGFDWDDE--DSEALKQARKDAEMTASADSVRAYLKQIGKVPLLNAAQEVELA 281

Query: 144 KRIEAG 149
           KRIEAG
Sbjct: 282 KRIEAG 287


>gi|328882302|emb|CCA55541.1| RNA polymerase principal sigma factor HrdA [Streptomyces venezuelae
           ATCC 10712]
          Length = 336

 Score =  260 bits (664), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 122/239 (51%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK++++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 98  IAKRKLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 157

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++V+R  RRM  +   EPT EE+A +L +  E 
Sbjct: 158 WIRQAMSRALADQARTIRVPVHVVELINRVIRVQRRMLQERGYEPTAEEVAAQLDLAPER 217

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+E+   LGD IED +A SP++SA    LR     VL++L  
Sbjct: 218 VGEVLRLAQEPVSLHAPVGEEEDVALGDLIEDGDAASPVESAAFLLLRRHLEDVLSTLGE 277

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 278 RERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLGKLRDHAYADQLRGYLD 336


>gi|85057387|ref|YP_456303.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789492|gb|ABC65224.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 465

 Score =  260 bits (664), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 127/247 (51%), Positives = 179/247 (72%), Gaps = 11/247 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK  +VE+N RLV+S+AK+Y  RG+ FLDLIQEGN+GLM+A +KFD+  G+KFSTY
Sbjct: 218 QARRAKDILVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQKGFKFSTY 277

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVH+ + I+K+    R+++ K+K++PT EE+A K+ + 
Sbjct: 278 ATWWIRQAITRAIADQARTIRIPVHIVETINKMALCTRKLTQKLKKKPTVEELADKMNIS 337

Query: 560 VEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            E +R +  I K+PISLE P    +ED + LGDFI D N +SP +      ++E T ++L
Sbjct: 338 AEKIRSIQYIEKKPISLEAPARENEEDETSLGDFISDPNILSPHEYM----MKEVTQKLL 393

Query: 618 -----ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
                 +LT REE+VL+MR+G+     HTLEEVG  F VTRERIRQIE+KA+R+L+ P++
Sbjct: 394 DEVLENTLTEREEKVLKMRYGLLDGKTHTLEEVGTLFGVTRERIRQIESKALRRLRTPAK 453

Query: 673 SKKLRSF 679
             KL+S 
Sbjct: 454 QSKLKSL 460


>gi|39939114|ref|NP_950880.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|39722223|dbj|BAD04713.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 460

 Score =  260 bits (664), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 127/247 (51%), Positives = 179/247 (72%), Gaps = 11/247 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK  +VE+N RLV+S+AK+Y  RG+ FLDLIQEGN+GLM+A +KFD+  G+KFSTY
Sbjct: 213 QARRAKDILVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQKGFKFSTY 272

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVH+ + I+K+    R+++ K+K++PT EE+A K+ + 
Sbjct: 273 ATWWIRQAITRAIADQARTIRIPVHIVETINKMALCTRKLTQKLKKKPTVEELADKMNIS 332

Query: 560 VEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            E +R +  I K+PISLE P    +ED + LGDFI D N +SP +      ++E T ++L
Sbjct: 333 AEKIRSIQYIEKKPISLEAPARENEEDETSLGDFISDPNILSPHEYM----MKEVTQKLL 388

Query: 618 -----ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
                 +LT REE+VL+MR+G+     HTLEEVG  F VTRERIRQIE+KA+R+L+ P++
Sbjct: 389 DEVLENTLTDREEKVLKMRYGLLDGKTHTLEEVGTLFGVTRERIRQIESKALRRLRTPAK 448

Query: 673 SKKLRSF 679
             KL+S 
Sbjct: 449 QSKLKSL 455


>gi|329934715|ref|ZP_08284756.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
 gi|329305537|gb|EGG49393.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
          Length = 363

 Score =  259 bits (663), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 121/239 (50%), Positives = 178/239 (74%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 125 MAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 184

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EP+ EE+A +L +  E 
Sbjct: 185 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPSAEEVAAQLDLSPER 244

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+E+   LGD IED +A SP++SA    LRE    VL++L  
Sbjct: 245 VGEVLRLAQEPVSLHAPVGEEEDVALGDLIEDGDATSPVESAAFLLLREHLDAVLSTLGE 304

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +L+
Sbjct: 305 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAYADQLRGYLE 363


>gi|297163178|gb|ADI12890.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 336

 Score =  259 bits (663), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 122/238 (51%), Positives = 169/238 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +VEANLRLV+SVAK+YT RGL FLDLIQEGN GL++AAEKFD+  G+KFSTYA WW
Sbjct: 98  AKTHLVEANLRLVVSVAKRYTGRGLAFLDLIQEGNTGLIRAAEKFDYAKGFKFSTYATWW 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA++R++ADQS TIR+PVH  + I+++ R  R +      EPTPE++A+K  +PV  +
Sbjct: 158 IKQAVSRALADQSRTIRVPVHTVELINRIARVRRELILDTGAEPTPEQVAEKAEVPVGRL 217

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++   TKEP+SL   + DE  S  GD I D +  SP D    + L++    +LA +TPR
Sbjct: 218 AELDGYTKEPVSLHVALSDEGDSEFGDLIVDSDTPSPWDMVTFSLLQQALRTLLAEMTPR 277

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  ++ +R+G+      TLEE+G+ + VTRERIRQIE++ + KL+HPSRS+ LR +LD
Sbjct: 278 EAGIISLRYGLFGGRARTLEEIGQVYGVTRERIRQIESRTMSKLRHPSRSQALRDYLD 335



 Score = 38.5 bits (88), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +E E G E+  DL ++  +    L    D+   STD PV+ YL+ +  + LL+ E E+ +
Sbjct: 5   VETESGLENPADLPAAEDDEPTALL---DTPVGSTD-PVKDYLKLIARVRLLTAEQEVDL 60

Query: 143 AKRIEAG 149
           AKRIEAG
Sbjct: 61  AKRIEAG 67


>gi|240142885|ref|YP_002967398.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
 gi|240012832|gb|ACS44057.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
          Length = 531

 Score =  259 bits (663), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 122/269 (45%), Positives = 182/269 (67%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  +++  G S+  FR +   VR    +   A+  +V +NLRLV SVAKKYTNR L  LD
Sbjct: 260 VDEVAIPFGGSVRRFRLVQREVRAAHGDLRKARDTLVTSNLRLVFSVAKKYTNRPLPILD 319

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEGNIGLM+A EKFD+  G+KFSTYA+WW+KQ+I+RSIAD   TIR+PVH+ +K  K+
Sbjct: 320 LVQEGNIGLMRAIEKFDYRRGWKFSTYAIWWIKQSISRSIADHGRTIRLPVHLHEKAAKI 379

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            RTA R+  ++ R P+P E+A+ L + V  V +++ +++E +SL+ P+G++     GD +
Sbjct: 380 DRTAARLRAELGRPPSPPELAQALDIDVRQVERLMNMSRETVSLDLPVGEDGDVRFGDLV 439

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED+ A  P+  A  A L++  +  +  L  RE+ ++RMRFGIG     TLEE+G+ F ++
Sbjct: 440 EDEKAPDPVGLADLAKLKDAVSDAVGDLPEREQTIIRMRFGIGYADQMTLEEIGQHFRIS 499

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQ+E+KAI++L+ P     LR FLD
Sbjct: 500 RERVRQVESKAIQRLRSPEIGAYLRKFLD 528



 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 32/63 (50%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           +  D +  Y RE+G   +L+RE E+A+AKR+EA R  + AS        +    WR  + 
Sbjct: 55  AVPDALSFYAREIGRHRVLTREEEVALAKRVEAARLSLFASFVALGSMARFAAEWRSAVV 114

Query: 176 DGT 178
            G 
Sbjct: 115 SGA 117


>gi|156742920|ref|YP_001433049.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234248|gb|ABU59031.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 348

 Score =  259 bits (663), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 119/243 (48%), Positives = 171/243 (70%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A  A++ +++ANLRLV+S+AKKY  RGL  LDLIQEGNIGLM+A EKFD+  G +FST
Sbjct: 106 AAAQEARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDYHKGNRFST 165

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA+TR+IA+Q  TIR+PVHM + + +V RTA R++  ++R+PTPEEIA  L  
Sbjct: 166 YATWWIRQAVTRAIAEQGRTIRLPVHMSESVGQVKRTADRLAQALERQPTPEEIATALGQ 225

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E + +VL+ ++ P+SLETP+G++    LGDF++D    +P+++A Q  LR      L 
Sbjct: 226 PTERIERVLEASRRPVSLETPVGEDGEHTLGDFLQDSELPTPVEAASQQLLRRDLAAALD 285

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE R++ +R+G+      TLEEVG+   +TRER RQIEA+A+R+L+ P     LR 
Sbjct: 286 RLNERERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALRRLRAPDVGLHLRD 345

Query: 679 FLD 681
           +L+
Sbjct: 346 YLE 348


>gi|289578595|ref|YP_003477222.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528308|gb|ADD02660.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 273

 Score =  258 bits (659), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 120/238 (50%), Positives = 177/238 (74%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK  +E+NLRLV+S+AK Y  +G+ F DLIQEGN+GL+KA E+FD+  GYKFSTYA WW
Sbjct: 36  AKKRFIESNLRLVVSIAKGYVGKGISFPDLIQEGNLGLLKAVERFDYRKGYKFSTYATWW 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ ITR+IADQ+ TIRIPVHM + ++K+++  ++   K+ REP+ EEIA+++ +  +  
Sbjct: 96  IKQTITRAIADQARTIRIPVHMVESVNKLLKIQKQFLQKLGREPSIEEIAEEMNISEKKA 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L+I +  +SLE P+G+++   LGD I DK AV P++      L+E    VL++L PR
Sbjct: 156 KVLLEIVQGIVSLEEPVGEDENGKLGDIIADKEAVDPVEELESMLLKEQVDEVLSTLAPR 215

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQF-CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EE+VLR+RFG+      TLEEVGK+   ++RER+RQIE KA+++L+HP+RS++L+ FL
Sbjct: 216 EEKVLRLRFGLDDGKIRTLEEVGKELGGISRERVRQIETKALKRLRHPNRSRRLKEFL 273


>gi|269123266|ref|YP_003305843.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
 gi|268314592|gb|ACZ00966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
          Length = 379

 Score =  257 bits (657), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 124/221 (56%), Positives = 169/221 (76%), Gaps = 1/221 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF+   G+KFSTYA WW
Sbjct: 141 AKQQLMESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFESDKGFKFSTYATWW 200

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  +EPT + +A+ + MPVE V
Sbjct: 201 IRQAITRAIADQGRTIRIPVHMIETINKIKKASRIHLQETGKEPTDDYLAEIVEMPVEKV 260

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTP 622
           + +L++ ++PISLETP+G ED S LGDF+ED   ++P ++ +++ L+E    VL   L  
Sbjct: 261 KNILEMNQDPISLETPVGSEDDSELGDFVEDDKFLNPHEATVRSVLKEKLNDVLRKELNE 320

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           REE+VLR+R+G+      TLEEVGK F VTRERIRQIE KA
Sbjct: 321 REEQVLRLRYGLDDGAPKTLEEVGKIFDVTRERIRQIEVKA 361



 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 85/188 (45%), Gaps = 15/188 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG------DD 82
           +S   +IK+A++   ++ EE+N  +  +  S +++E T   L  + + +V+         
Sbjct: 10  ESLSNLIKIAKEEKIISREEINKLMK-NNFSQDKIEATFFKLQELNVEIVNKIADKNKSK 68

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIELLSREGEI 140
            E E   ++ L++          L +   +   S+D  +P++MYLRE+G I LL  E E 
Sbjct: 69  KEIERNKKEELEINIDEKEVEALLNEDLTTVSESSDVDEPIKMYLREIGQIPLLKSEEEF 128

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-----LEACIGPES 195
            +A+RI  G       L ES L    + I +   N G  LL  I +     ++A    ES
Sbjct: 129 ELARRIGEGDERAKQQLMESNLRL-VVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFES 187

Query: 196 KGGFFHGT 203
             GF   T
Sbjct: 188 DKGFKFST 195


>gi|163847594|ref|YP_001635638.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222525449|ref|YP_002569920.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163668883|gb|ABY35249.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449328|gb|ACM53594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 345

 Score =  257 bits (657), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 123/266 (46%), Positives = 181/266 (68%), Gaps = 4/266 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++  T ++  E   ++  V++GE     A++ +++ANLRLV+S+AKKY  RGL  LDLIQ
Sbjct: 84  LATATDLTPRERYELLQAVQQGEE----ARRHLIQANLRLVVSIAKKYVGRGLALLDLIQ 139

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLM+A EKFD+  G +FSTYA WW++QA+TR+IA+Q  TIR+PVHM + + +V R 
Sbjct: 140 EGNIGLMRAVEKFDYHKGNRFSTYATWWIRQAVTRAIAEQGRTIRLPVHMSESVGQVKRI 199

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           A R++  ++R+PT EEIA  L  PVE ++++L+  + P+SLETP+GDE    LGDF+ D+
Sbjct: 200 AERLAQSLERQPTAEEIAMALGQPVERIQRILEAARRPVSLETPVGDEGEHTLGDFLTDE 259

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              +P + A Q  LR      L  L  RE R++ +R+G+      TLEEVG+   +TRER
Sbjct: 260 ELPTPGEMAAQKLLRRDLCAALDRLNDRERRIIDLRYGLVDGRRRTLEEVGRVLGMTRER 319

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RQIEA+A+R+L+ P   + LR +L+
Sbjct: 320 ARQIEAEALRRLRSPEVGQHLRDYLE 345


>gi|330946209|gb|EGH47399.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 230

 Score =  257 bits (656), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 128/226 (56%), Positives = 169/226 (74%), Gaps = 3/226 (1%)

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 4   FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 61

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 62  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 121

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPT
Sbjct: 122 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 181

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           PEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED
Sbjct: 182 PEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIED 227


>gi|162605994|ref|XP_001713512.1| RNA-polymerase sigma factor [Guillardia theta]
 gi|13794432|gb|AAK39807.1|AF165818_15 RNA-polymerase sigma factor [Guillardia theta]
          Length = 460

 Score =  256 bits (655), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 134/258 (51%), Positives = 181/258 (70%), Gaps = 9/258 (3%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + +FR I+   R+       AK+ MV ANLRLV+S+AK+Y NRG+   DLIQEG++GL++
Sbjct: 175 VRKFRSILHNARR-------AKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIR 227

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD   G+KFSTYA WWVKQA+TR+IAD S TIR+PVH+ D I  + +T R ++ +I
Sbjct: 228 AAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVHLYDTISAIRKTTRNLNIEI 287

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLD 602
            R PT EEIAK++ M VE +R VL+  +  +SLE P+  D+DTS L DFIE  +  SP +
Sbjct: 288 GRSPTEEEIAKRMDMSVEKLRNVLQSAQPTLSLERPLKNDDDTSQLSDFIE-ADQESPEE 346

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              ++ LR+    V+ SL+PRE  V+RMR+G+      TLEE+G+ F VTRER+RQIEAK
Sbjct: 347 HVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERVRQIEAK 406

Query: 663 AIRKLKHPSRSKKLRSFL 680
           AIRKL+ P RS  LR ++
Sbjct: 407 AIRKLRQPYRSSILRDYV 424


>gi|159037062|ref|YP_001536315.1| RNA polymerase sigma factor SigB [Salinispora arenicola CNS-205]
 gi|157915897|gb|ABV97324.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 328

 Score =  256 bits (655), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 120/242 (49%), Positives = 179/242 (73%), Gaps = 1/242 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFST
Sbjct: 85  VEGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFST 144

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQS TIRIPVHM ++++++VRT R +S  + REPT  E+A+ L +
Sbjct: 145 YATWWIRQAITRAMADQSRTIRIPVHMVEQVNRMVRTRRDLSVSLGREPTVTEVARALDV 204

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV-SPLDSAIQANLRETTTRVL 617
           P   + +++   +EP+SL+  +G++  S LGDF+   NA  +P ++A +  LR+    VL
Sbjct: 205 PEVQIIELISYDREPVSLDQAVGEDGESPLGDFVAVVNATAAPDNTAERGELRQEVRGVL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   +RKL+ P R+++L 
Sbjct: 265 ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLRKLRAPERAQRLA 324

Query: 678 SF 679
           ++
Sbjct: 325 AY 326


>gi|37520903|ref|NP_924280.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35211898|dbj|BAC89275.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 350

 Score =  256 bits (654), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 125/275 (45%), Positives = 194/275 (70%), Gaps = 7/275 (2%)

Query: 410 RNEIKSISVETGISISEF--RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           R++ ++++ E+ +  +    +   ++VR+GE     AK  +V+ANLRLV+SVAKKY  RG
Sbjct: 77  RSKFQAVAAESWLESANLTPQQWSTIVREGER----AKAHLVKANLRLVVSVAKKYQGRG 132

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  LDLIQEG +GL++AAEKFD+  G+KFSTYA WW++Q ITR+IA Q+ TIR+PVH+ +
Sbjct: 133 LHLLDLIQEGTLGLIRAAEKFDYTRGFKFSTYATWWIRQGITRAIAMQARTIRLPVHIVE 192

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K++++ +  R++S ++ R P+ +EIA+ + M  + +R V K  + P+SLETP+G E+ + 
Sbjct: 193 KVNRIKKATRQLSQQLGRSPSEDEIAQAVEMDADQLRFVRKAIQLPVSLETPVGREEDTA 252

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD I+ K    P    ++  + +    +L +LTPRE  VLR+R+G+      TL+EVG+
Sbjct: 253 LGDLIQAKGN-EPEHGVVRDLMNQDLESLLQTLTPRERDVLRLRYGLIDGRSRTLDEVGQ 311

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           QF +TRERIRQIEA+A+RKL+HP R +++R +L+G
Sbjct: 312 QFGLTRERIRQIEARALRKLRHPQRLQRVREYLEG 346


>gi|51246355|ref|YP_066239.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50877392|emb|CAG37232.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 447

 Score =  256 bits (654), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 118/239 (49%), Positives = 176/239 (73%), Gaps = 1/239 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  M+ ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+A  +FD+  G KFSTYA W
Sbjct: 210 VAKDTMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASW 269

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+I D++ TIR+PVH  +   +  +    +  ++ REPTP EI+K   +P++ 
Sbjct: 270 WIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYALFKELGREPTPLEISKTTNLPMDK 329

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  +L+ ++EPISLETP+GD+D S LGDF+E++ + SP ++     L    T +L++L+ 
Sbjct: 330 ILSILEASREPISLETPVGDDD-STLGDFLENQESQSPYEAVQNRELSGRVTEILSTLSD 388

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+++R+RFGIG   ++TLEE+GK+F V+RERIRQIE KA+ +L+H SR  KL+ F+D
Sbjct: 389 REEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRRDKLKFFVD 447


>gi|153304|gb|AAA26762.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450077|prf||1920369A RNA polymerase:SUBUNIT=sigma
          Length = 393

 Score =  256 bits (654), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 121/239 (50%), Positives = 175/239 (73%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 155 MAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 214

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E 
Sbjct: 215 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTAEEVAVHLELTPER 274

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA      E    VL++L  
Sbjct: 275 VLEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFFLRCEHLEAVLSTLGE 334

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 335 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 393


>gi|148823899|ref|YP_001288653.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis F11]
 gi|253798208|ref|YP_003031209.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308232219|ref|ZP_07415326.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308369834|ref|ZP_07419229.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308371106|ref|ZP_07423839.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308372374|ref|ZP_07428435.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308373485|ref|ZP_07432499.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308374669|ref|ZP_07436917.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308375503|ref|ZP_07444157.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308377104|ref|ZP_07441142.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308378072|ref|ZP_07481430.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308379289|ref|ZP_07485765.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308380449|ref|ZP_07489983.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
 gi|148722426|gb|ABR07051.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis F11]
 gi|253319711|gb|ACT24314.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308214646|gb|EFO74045.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308326293|gb|EFP15144.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308329821|gb|EFP18672.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308333464|gb|EFP22315.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308337459|gb|EFP26310.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308341132|gb|EFP29983.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308346083|gb|EFP34934.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308348958|gb|EFP37809.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308353656|gb|EFP42507.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308357503|gb|EFP46354.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308361457|gb|EFP50308.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
          Length = 345

 Score =  256 bits (653), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 121/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 96  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 151

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 152 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 211

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 212 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 270

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 271 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 330

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 331 LRHGERADRLRSY 343


>gi|282861771|ref|ZP_06270835.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282563587|gb|EFB69125.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 355

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 118/243 (48%), Positives = 177/243 (72%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  +A++ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFST
Sbjct: 113 VQGRMAERRLIEANLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFST 172

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EP+ EE+A +L +
Sbjct: 173 YATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGHEPSAEEVAAQLDL 232

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  +L++ +EP+SL  P+G+ED    GD IED +A SP++SA    LRE    VL+
Sbjct: 233 TPERVETILRLAQEPVSLHAPVGEEDDVAFGDLIEDGDAPSPVESAAFLLLREHLEAVLS 292

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR 
Sbjct: 293 TLGERERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLARLRDHAFADQLRG 352

Query: 679 FLD 681
           +LD
Sbjct: 353 YLD 355


>gi|167970067|ref|ZP_02552344.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215404675|ref|ZP_03416856.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           02_1987]
 gi|215428138|ref|ZP_03426057.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T92]
 gi|215431649|ref|ZP_03429568.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           EAS054]
 gi|218754446|ref|ZP_03533242.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis GM
           1503]
 gi|219558719|ref|ZP_03537795.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T17]
 gi|254551766|ref|ZP_05142213.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260187727|ref|ZP_05765201.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|260201835|ref|ZP_05769326.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T46]
 gi|260206019|ref|ZP_05773510.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis K85]
 gi|289746512|ref|ZP_06505890.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|294994199|ref|ZP_06799890.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis 210]
 gi|297635318|ref|ZP_06953098.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           4207]
 gi|297732314|ref|ZP_06961432.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           R506]
 gi|289687040|gb|EFD54528.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|323718704|gb|EGB27866.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CDC1551A]
 gi|328457981|gb|AEB03404.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           4207]
          Length = 333

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 121/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 84  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 139

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 140 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 199

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 200 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 258

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 259 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 318

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 319 LRHGERADRLRSY 331


>gi|160902263|ref|YP_001567844.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359907|gb|ABX31521.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 414

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 128/237 (54%), Positives = 174/237 (73%), Gaps = 2/237 (0%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V+ANLRLVIS+AK+YT RGL FLDLIQEGNIGL++A EKFDW  G+KFSTYA WWV+Q
Sbjct: 171 ELVKANLRLVISIAKRYTGRGLTFLDLIQEGNIGLIRAVEKFDWKRGFKFSTYATWWVRQ 230

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVH+ + I+++    R+   +    P+ E++A+ L  P+E + ++
Sbjct: 231 AITRAIADQARTIRIPVHLVESINRMNIVIRKHLQETGEYPSTEKLAELLDKPLEKMDEI 290

Query: 567 LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           L  TKE IS++ PI   D++ +++GDF+ED  A  P + A++  L+E   +VL SL P+E
Sbjct: 291 LLATKEIISVDAPISGSDDEEAYIGDFLEDSEADQPEEIAVRMILKEEIEKVLESLRPKE 350

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             VL+MR+G+      TLEEVG  F VTRERIRQIE KA+RKL+HPSRS +L+   D
Sbjct: 351 ATVLKMRYGLLDGKMKTLEEVGNFFNVTRERIRQIEVKALRKLRHPSRSLQLKEISD 407


>gi|15609847|ref|NP_217226.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Rv]
 gi|15842248|ref|NP_337285.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CDC1551]
 gi|31793882|ref|NP_856375.1| RNA polymerase sigma factor SigB [Mycobacterium bovis AF2122/97]
 gi|121638585|ref|YP_978809.1| RNA polymerase sigma factor SigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148662551|ref|YP_001284074.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215412516|ref|ZP_03421250.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           94_M4241A]
 gi|215446963|ref|ZP_03433715.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|224991077|ref|YP_002645766.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|254365367|ref|ZP_04981412.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289444252|ref|ZP_06433996.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289448365|ref|ZP_06438109.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289570886|ref|ZP_06451113.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289575408|ref|ZP_06455635.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289751363|ref|ZP_06510741.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289754812|ref|ZP_06514190.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289758838|ref|ZP_06518216.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|289762881|ref|ZP_06522259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|298526180|ref|ZP_07013589.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|307085405|ref|ZP_07494518.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|313659647|ref|ZP_07816527.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           V2475]
 gi|1171103|gb|AAA86044.1| sigma factor MysB [Mycobacterium tuberculosis H37Rv]
 gi|2182001|emb|CAB09470.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium tuberculosis H37Rv]
 gi|13882539|gb|AAK47099.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis CDC1551]
 gi|31619476|emb|CAD94914.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium bovis AF2122/97]
 gi|121494233|emb|CAL72711.1| RNA polymerase sigma factor sigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|134150880|gb|EBA42925.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148506703|gb|ABQ74512.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|224774192|dbj|BAH26998.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|289417171|gb|EFD14411.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289421323|gb|EFD18524.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289539839|gb|EFD44417.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289544640|gb|EFD48288.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289691950|gb|EFD59379.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289695399|gb|EFD62828.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289710387|gb|EFD74403.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|289714402|gb|EFD78414.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|298495974|gb|EFI31268.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|308365051|gb|EFP53902.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|326904326|gb|EGE51259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis W-148]
          Length = 323

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 121/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 74  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 129

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 130 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 189

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 190 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 248

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 249 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 308

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 309 LRHGERADRLRSY 321


>gi|240169688|ref|ZP_04748347.1| RNA polymerase sigma factor SigB [Mycobacterium kansasii ATCC
           12478]
          Length = 319

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 185/253 (73%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RELAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PV+ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 186 TDEELAEESGIPVDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 244

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 245 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCK 304

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 305 LRHGERADRLRSY 317


>gi|289553505|ref|ZP_06442715.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
 gi|289438137|gb|EFD20630.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
          Length = 338

 Score =  255 bits (652), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 121/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 89  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 144

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 145 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 204

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 205 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 263

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 264 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 323

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 324 LRHGERADRLRSY 336


>gi|296171822|ref|ZP_06852936.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295893958|gb|EFG73726.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 329

 Score =  255 bits (652), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G+     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 80  RDLEAVVRDGQA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 136 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 196 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 254

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 255 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 314

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 315 LRHGERADRLRSY 327


>gi|315444860|ref|YP_004077739.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263163|gb|ADT99904.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 319

 Score =  255 bits (652), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 183/252 (72%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 246 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 305

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 306 RNGDRADRLRSY 317


>gi|1657704|gb|AAC44535.1| sigma factor MytB [Mycobacterium tuberculosis]
          Length = 345

 Score =  255 bits (652), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 121/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 96  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 151

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 152 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 211

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 212 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 270

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 271 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 330

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 331 LRHGERADRLRSY 343


>gi|133468|sp|P27785|RPOD_STRAU RecName: Full=RNA polymerase sigma factor rpoD
          Length = 317

 Score =  255 bits (652), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 121/239 (50%), Positives = 175/239 (73%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 79  MAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATW 138

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E 
Sbjct: 139 WIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTAEEVAVHLELTPER 198

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA      E    VL++L  
Sbjct: 199 VLEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFFLRCEHLEAVLSTLGE 258

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 259 RERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 317


>gi|145224529|ref|YP_001135207.1| RNA polymerase sigma factor SigB [Mycobacterium gilvum PYR-GCK]
 gi|145217015|gb|ABP46419.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
          Length = 329

 Score =  255 bits (651), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 183/252 (72%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 80  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 136 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 196 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 255

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 256 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 315

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 316 RNGDRADRLRSY 327


>gi|239940961|ref|ZP_04692898.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 15998]
 gi|239987439|ref|ZP_04708103.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 11379]
          Length = 363

 Score =  255 bits (651), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 120/238 (50%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 126 AKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+IA +L +  E V
Sbjct: 186 IRQAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIAVELDLTPERV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++ +EP+SL  P+G+ED    GD IED +A SP++SA    LR+    VL++L  R
Sbjct: 246 TEVLRLAQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGER 305

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR +LD
Sbjct: 306 ERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDHAFADQLRGYLD 363



 Score = 37.7 bits (86), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + R DS    T D  R YLRE+G I LL+   E+ +A+R+EAG
Sbjct: 54  RNRADSGG-PTSDLFRQYLREIGRIPLLTAAEEVELARRVEAG 95


>gi|291444398|ref|ZP_06583788.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
 gi|291347345|gb|EFE74249.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
          Length = 395

 Score =  255 bits (651), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 120/238 (50%), Positives = 176/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 158 AKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+IA +L +  E V
Sbjct: 218 IRQAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIAVELDLTPERV 277

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++ +EP+SL  P+G+ED    GD IED +A SP++SA    LR+    VL++L  R
Sbjct: 278 TEVLRLAQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGER 337

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR +LD
Sbjct: 338 ERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDHAFADQLRGYLD 395



 Score = 37.7 bits (86), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + R DS    T D  R YLRE+G I LL+   E+ +A+R+EAG
Sbjct: 86  RNRADSGG-PTSDLFRQYLREIGRIPLLTAAEEVELARRVEAG 127


>gi|296121158|ref|YP_003628936.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013498|gb|ADG66737.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 577

 Score =  254 bits (650), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 120/238 (50%), Positives = 172/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+  EK+++  GYKFSTYA WW
Sbjct: 298 SKQQLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEFRRGYKFSTYATWW 357

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++AD + TIRIPVHM   I  +   + ++  +  REPT EE+A  + M VE  
Sbjct: 358 IRQAITRAVADHARTIRIPVHMFQSISTLKNKSEQIRQETGREPTIEELALAVDMSVEDT 417

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++K  K P+SL+TPIG+ + S  GDF+ED +  +P D+A++  LR+    VL SLT R
Sbjct: 418 ERIMKTWKHPMSLDTPIGESEDSSFGDFLEDSHESTPADNALREMLRDKIDIVLRSLTYR 477

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  ++R+R+G+G    +TLEE G+ F VTRERIRQIE+KA++KL+H +R+  L+ F++
Sbjct: 478 EREIIRLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALKKLQHHTRAHHLQGFVE 535



 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 39/145 (26%), Positives = 71/145 (48%), Gaps = 13/145 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D S  + ++++     RG++T  E++ ++P +      +++ +  L   G++ V+ +  
Sbjct: 1   MDQSQLALRELLNQGASRGFLTYAEIDRYIPDEGGDPALVDELIMALEAAGLDAVEPEGG 60

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            D   S   L++    SNSS             + DP+RMYL +MG I LL+RE EI +A
Sbjct: 61  IDPLQSLPPLEMLEPESNSS-------------SRDPIRMYLSQMGHIPLLTREREIYLA 107

Query: 144 KRIEAGRAMMMASLCESPLTFQALI 168
           K+IE  R      + ES    + ++
Sbjct: 108 KQIEMTRRWFRRRMLESDFAIRIVV 132


>gi|309790481|ref|ZP_07685041.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227468|gb|EFO81136.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 346

 Score =  254 bits (650), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 124/266 (46%), Positives = 180/266 (67%), Gaps = 4/266 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ E  +S ++ R++   V +G    + A++ +++ANLRLV+S+AKKY  RGL  LDLIQ
Sbjct: 85  LATEDQLSGTQRRNLEHEVERG----NDARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQ 140

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLM+A EKFD   G +FSTYA WW++QA+TRSIA+Q  TIR+PVHM + + +V RT
Sbjct: 141 EGNIGLMRAVEKFDHRKGNRFSTYATWWIRQAVTRSIAEQGRTIRLPVHMSESVSQVKRT 200

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           + R+S  ++R+P+ EEIA  L  P E + +VL+  + P+SLETP+GDE    LGDF+ D 
Sbjct: 201 SERLSQSLERQPSAEEIAIALGQPTERIERVLEAARRPVSLETPVGDEGEHTLGDFLPDD 260

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +  +P D A    LR+     L  L  RE R++ +R+G+      TLEEVG+   +TRER
Sbjct: 261 DLPTPGDFASAQLLRQDLCAALDHLNERERRIIDLRYGLLDGRRRTLEEVGRTLGMTRER 320

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RQIEA+A+R+L+ P   + LR +L+
Sbjct: 321 ARQIEAEALRRLRSPDVGQHLRDYLE 346


>gi|182438860|ref|YP_001826579.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326779516|ref|ZP_08238781.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178467376|dbj|BAG21896.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326659849|gb|EGE44695.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 363

 Score =  254 bits (650), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 120/238 (50%), Positives = 174/238 (73%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 126 AKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+IA  L +  E V
Sbjct: 186 IRQAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIAVDLDLTPERV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L++ +EP+SL  P+G+ED    GD IED +A SP++SA    LRE    VL++L  R
Sbjct: 246 TDILRLAQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGER 305

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR +LD
Sbjct: 306 ERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDHAFADQLRGYLD 363



 Score = 38.5 bits (88), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + R DS   +T D  R YLRE+G I LL+   E+ +A+R+EAG
Sbjct: 54  RNRADSGG-ATSDLFRQYLREIGRIPLLTAAEEVELARRVEAG 95


>gi|117928920|ref|YP_873471.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649383|gb|ABK53485.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
          Length = 413

 Score =  254 bits (650), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 116/233 (49%), Positives = 170/233 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLV+SVAK+Y+NRG+ FLD+IQEGN+GL++A EKFD+  GYKFSTYAMWW
Sbjct: 176 AKAHMLEANLRLVVSVAKRYSNRGMAFLDVIQEGNLGLIRAVEKFDYTKGYKFSTYAMWW 235

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIR+PVH+ ++++K+ R  R +  +  REPT EE+A +L    E +
Sbjct: 236 IRQAITRALADQARTIRLPVHVVEQLNKLTRLQRELHQQFGREPTAEELAAELDRTPEQI 295

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L+  ++P+SL+ P+GD++ + LGD IED  A +  D+     + +T  R LA L PR
Sbjct: 296 EEMLRNARQPVSLDNPVGDDEDTLLGDLIEDMEAPAASDALEYQAMIDTVHRALAGLDPR 355

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E RV+ +RFG+     HTL+E+G+   +TRER+RQIE +A+ KL+ P+    L
Sbjct: 356 EARVIALRFGLVGGRPHTLDEIGRDVGLTRERVRQIEREALAKLRDPNSPDSL 408



 Score = 38.1 bits (87), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 21/31 (67%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DPVR YL E+G   LL    E+ +AKRIEAG
Sbjct: 114 DPVRNYLNEIGRTPLLDAAQEVELAKRIEAG 144


>gi|219849486|ref|YP_002463919.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543745|gb|ACL25483.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 345

 Score =  254 bits (649), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 124/268 (46%), Positives = 182/268 (67%), Gaps = 4/268 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++  T ++  E   ++  V++GE     A++ +++ANLRLV+S+AKKY  RGL  LDL
Sbjct: 82  QRLATATDLTPRERCELLKAVQEGEE----ARRHLIQANLRLVVSIAKKYVGRGLSLLDL 137

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLM+A EKFD   G +FSTYA WW++QA+TR++A+Q  TIR+PVHM + + +V 
Sbjct: 138 IQEGNIGLMRAVEKFDHHKGNRFSTYATWWIRQAVTRALAEQGRTIRLPVHMSESVAQVK 197

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R A R++  ++R+PTPEEIA  L  PVE ++++L+  + P+SLETP+GDE    LGDFI 
Sbjct: 198 RIADRLAQSLERQPTPEEIAMALGQPVERIQRILEAARCPVSLETPVGDEGEHTLGDFIT 257

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D+   +P + A Q  L       L  L+ RE R++ +R+G+      TLEEVG+   +TR
Sbjct: 258 DEELPAPGEIAAQKLLHRDLCAALNQLSDRERRIIDLRYGLLDGRRRTLEEVGRVLGMTR 317

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ER RQIEA+A+R+L+ P   + LR +LD
Sbjct: 318 ERARQIEAEALRRLRSPEIGQHLRDYLD 345


>gi|218515956|ref|ZP_03512796.1| RNA polymerase sigma factor RpoD [Rhizobium etli 8C-3]
          Length = 321

 Score =  254 bits (649), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 162/324 (50%), Positives = 200/324 (61%), Gaps = 47/324 (14%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     ED EG E    LA S   ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGE----LAPSG-GTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                       A+   DD + V     PPE  E DE         S  +L+AME +LRP
Sbjct: 234 -----------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRP 275

Query: 279 KVMCALDEIAEVYRELRSLQDNAV 302
           +VM  LD IAE Y++LR LQD  V
Sbjct: 276 QVMETLDTIAETYKKLRKLQDQQV 299


>gi|120403441|ref|YP_953270.1| RNA polymerase sigma factor SigB [Mycobacterium vanbaalenii PYR-1]
 gi|119956259|gb|ABM13264.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 329

 Score =  254 bits (649), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 182/252 (72%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 80  RDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 136 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 196 TDEELAAESGIPVEKITDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 255

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 256 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 315

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 316 RNGERADRLRSY 327


>gi|116749951|ref|YP_846638.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116699015|gb|ABK18203.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 433

 Score =  254 bits (649), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 122/238 (51%), Positives = 173/238 (72%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EMV+ANLRLV+S+AK+Y  RG+ F DLIQEGN+GL+KA  +FD   G +FSTYA WW
Sbjct: 197 AKQEMVKANLRLVLSIAKRYRGRGMSFDDLIQEGNLGLLKAVGRFDHTKGNRFSTYATWW 256

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+Q+I R I D++ TIR+PVH  +  +   +    +  ++ REP+P+EIA++  +P++ V
Sbjct: 257 VRQSIIRGIYDKTRTIRLPVHFIELKNLFFKVFYELLKELGREPSPQEIAERAKLPLDKV 316

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + VL +  +PISLETPIG ED   LGDFIED+ A SP++      L E T  +L+SL PR
Sbjct: 317 QMVLTLAAQPISLETPIG-EDEQRLGDFIEDERAASPMEECSDRELAEITRSLLSSLQPR 375

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE++LR+RFGI      TLE++GK F V++ERIRQIE KA+RKL++P+R   L++F++
Sbjct: 376 EEKILRLRFGIDGQPAETLEKIGKTFKVSKERIRQIEKKALRKLRNPNRQSCLKTFME 433


>gi|118472772|ref|YP_887083.1| RNA polymerase sigma factor SigB [Mycobacterium smegmatis str. MC2
           155]
 gi|118174059|gb|ABK74955.1| sigma factor SigB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score =  254 bits (648), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 183/252 (72%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLQAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGTDEEAPLGDFIEDSEAMSAENAVISE 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 246 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 305

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 306 RNGERADRLRSY 317


>gi|160331013|ref|XP_001712214.1| rpoD [Hemiselmis andersenii]
 gi|159765661|gb|ABW97889.1| rpoD [Hemiselmis andersenii]
          Length = 485

 Score =  254 bits (648), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 133/258 (51%), Positives = 180/258 (69%), Gaps = 9/258 (3%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + +FR I+   R+       AK+ MV ANLRLV+S+AK+Y NRG+   DLIQEG++GL++
Sbjct: 192 VKKFRAILHNARR-------AKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIR 244

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD   G+KFSTYA WWVKQA+TR+IAD S TIR+PVH+ D I  + +T R ++ +I
Sbjct: 245 AAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVHLYDTISAIRKTTRTLNIEI 304

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLD 602
            R PT EEIA+K+ M VE +R VL+  +  +SLE P+  D+D S L DFIE  +  SP +
Sbjct: 305 GRSPTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLKNDDDASQLSDFIE-ADQESPEE 363

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              ++ LR+    V+ SL+PRE  V+RMR+G+      TLEE+G+ F VTRER+RQIEAK
Sbjct: 364 HVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERVRQIEAK 423

Query: 663 AIRKLKHPSRSKKLRSFL 680
           AIRKL+ P RS  LR ++
Sbjct: 424 AIRKLRQPYRSSILRDYV 441


>gi|108799144|ref|YP_639341.1| RNA polymerase sigma factor SigB [Mycobacterium sp. MCS]
 gi|119868259|ref|YP_938211.1| RNA polymerase sigma factor SigB [Mycobacterium sp. KMS]
 gi|126434752|ref|YP_001070443.1| RNA polymerase sigma factor SigB [Mycobacterium sp. JLS]
 gi|108769563|gb|ABG08285.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694348|gb|ABL91421.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
 gi|126234552|gb|ABN97952.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 319

 Score =  253 bits (647), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 118/255 (46%), Positives = 183/255 (71%), Gaps = 4/255 (1%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S  R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A
Sbjct: 67  SRKRDLAAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRA 122

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + 
Sbjct: 123 MEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLG 182

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           RE T EE+A++  +P E +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ 
Sbjct: 183 REATDEELAEESGIPAEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAV 242

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I   L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + +
Sbjct: 243 ISELLHTDIRHVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVM 302

Query: 665 RKLKHPSRSKKLRSF 679
            KL++  R+ +LRS+
Sbjct: 303 AKLRNGERADRLRSY 317


>gi|284931435|gb|ADC31373.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. F]
          Length = 646

 Score =  253 bits (647), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 121/241 (50%), Positives = 178/241 (73%), Gaps = 7/241 (2%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V +NLRLV S+AKKY NRGL F+DLIQEG+IGLMKA  KF++ LG KFSTYA WW++Q
Sbjct: 400 QLVTSNLRLVTSIAKKYLNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQ 459

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG---- 562
           AITR+IADQ+ T+RIPVHM + I+K+++T R ++ ++ R+PT EE+ + +   V G    
Sbjct: 460 AITRAIADQARTVRIPVHMVETINKLIKTERMLTQQLGRDPTLEELTEAMGGQVNGFTPK 519

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SL 620
            V  + K+ +EP+SL+ PIG ++ S   DF++D++ + P +   +  + E    +   +L
Sbjct: 520 KVADIKKLNQEPVSLDKPIGHDEESQFVDFVKDRDILKPDEYTEKLIVTEHINELFVNTL 579

Query: 621 TPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           T +EE+++RMR+G+   +   TLEEVG++F VTRERIRQIE+KA+RKLKHPS++ +LRSF
Sbjct: 580 TKKEEQIIRMRYGLHPWHQQMTLEEVGQKFNVTRERIRQIESKALRKLKHPSKNARLRSF 639

Query: 680 L 680
           L
Sbjct: 640 L 640


>gi|19910022|dbj|BAB87262.1| RNA polymerase sigma factor [Guillardia theta]
          Length = 490

 Score =  253 bits (647), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 133/258 (51%), Positives = 180/258 (69%), Gaps = 9/258 (3%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + +FR I+   R+       AK+ MV ANLRLV+S+AK+Y NRG+   DLIQEG++GL++
Sbjct: 192 VKKFRSILHNARR-------AKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIR 244

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD   G+KFSTYA WWVKQA+TR+IAD S TIR+PVH+ D I  + +T R ++ +I
Sbjct: 245 AAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVHLYDTISAIRKTTRTLNIEI 304

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLD 602
            R PT EEIA+K+ M VE +R VL+  +  +SLE P+  D+D S L DFIE  +  SP +
Sbjct: 305 GRSPTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLKNDDDASQLSDFIE-ADQESPEE 363

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              ++ LR+    V+ SL+PRE  V+RMR+G+      TLEE+G+ F VTRER+RQIEAK
Sbjct: 364 HVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERVRQIEAK 423

Query: 663 AIRKLKHPSRSKKLRSFL 680
           AIRKL+ P RS  LR ++
Sbjct: 424 AIRKLRQPYRSSILRDYV 441


>gi|183982017|ref|YP_001850308.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
 gi|183175343|gb|ACC40453.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
          Length = 333

 Score =  253 bits (647), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G    + A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 84  RELAAVVRDG----AEARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 139

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 140 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 199

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 200 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 258

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 259 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCK 318

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 319 LRHGERADRLRSY 331



 Score = 38.1 bits (87), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D VR+YL  +G   LL+ EGE+ +AKRIEAG
Sbjct: 35  DLVRVYLNGIGKTALLNAEGEVELAKRIEAG 65


>gi|239931595|ref|ZP_04688548.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291439967|ref|ZP_06579357.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
 gi|291342862|gb|EFE69818.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
          Length = 335

 Score =  253 bits (646), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 118/237 (49%), Positives = 166/237 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + EANLRLV+SVAK+YT RGLQF+DLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 96  AKNHLTEANLRLVVSVAKRYTGRGLQFMDLIQEGNAGLIRAVEKFDYTKGFKFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ ITR++ADQS TIRIPVH  + I++V R  R +      EPTPE++A++ ++ VE +
Sbjct: 156 IKQGITRAMADQSRTIRIPVHAVEVINRVARVRRELIRATGTEPTPEDVAERASISVEKL 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++    +EP+SL+ P+ +E     GD I D ++ SP +     +L+     VLA L+PR
Sbjct: 216 AELDAYAREPVSLDLPLSEEGGGEFGDLIVDSDSPSPWEVVAFGHLQRAVRSVLADLSPR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++ +R+G+      TLEE+G+ + VTRERIRQIE+K + KL+HP+RS  LR +L
Sbjct: 276 EAGIISLRYGLFGERPRTLEEIGQVYGVTRERIRQIESKTMSKLRHPARSHALRDYL 332


>gi|1553023|gb|AAC45103.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  253 bits (646), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|1553011|gb|AAC45097.1| primary sigma factor [Borrelia afzelii]
          Length = 450

 Score =  253 bits (646), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|239934546|emb|CAR94587.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 296

 Score =  253 bits (646), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 152/317 (47%), Positives = 204/317 (64%), Gaps = 30/317 (9%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+IIWRD LND   LLREIIDLE 
Sbjct: 1   TVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQAIIIWRDALNDSQILLREIIDLET 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV--DSP 247
                     + G E       E   +EK         G+  S ++   DD + V  D+P
Sbjct: 61  T---------YAGPEAKQAPVIERVEEEKP------AAGNDRSRSRRDDDDITNVGGDTP 105

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            E+        D+++D++  +L+AME +LRP+VM  LD IA+ YR+LR LQD  V  +  
Sbjct: 106 VEDD-------DDEDDEANLSLAAMEAELRPQVMETLDVIADTYRKLRKLQDQQVENRLA 158

Query: 308 EKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
              S+      + K LK++L+K V SLSLNQ+RI+ LV QLYDI+KR++ NEG LLRLA+
Sbjct: 159 ASGSLSPSQERRYKELKDQLIKAVKSLSLNQNRIEALVAQLYDINKRLVQNEGRLLRLAE 218

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
           SYG++R+ FL+ +QG ELDP+W+    +     WK F   E D+I  +R EI++++ ET 
Sbjct: 219 SYGVRREDFLKEYQGNELDPNWLKAVSNLTTRGWKEFTKNEKDTIKNLRTEIQNMAQETA 278

Query: 422 ISISEFRHIVSMVRKGE 438
           ISISEFR IV+ V+KGE
Sbjct: 279 ISISEFRRIVNQVQKGE 295


>gi|1553025|gb|AAC45104.1| primary sigma factor [Borrelia garinii]
 gi|1553031|gb|AAC45107.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  253 bits (646), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|1553027|gb|AAC45105.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  253 bits (646), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|256377300|ref|YP_003100960.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255921603|gb|ACU37114.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 349

 Score =  253 bits (646), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 121/238 (50%), Positives = 172/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT +G+  LD+IQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 112 AKDHLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFSTYATWW 171

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQS TIR+PVHM + + K+ R  R + ++  RE T EE+A +L +  E V
Sbjct: 172 IRQAITRALADQSRTIRLPVHMVEVVTKLARVERDLLHRNGREATAEEVAVELDVTPEKV 231

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  + P+SL+  IG E  + +GD I D+NAV+PL++   A L      VL +LTPR
Sbjct: 232 VELRQHARTPVSLDQTIGAEADTSIGDLIADENAVAPLEAVSSALLSADLRAVLDTLTPR 291

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMR+G      HTLEEVG+ + VTRERIRQIE++ + KL+HP+RS+ L  +LD
Sbjct: 292 EAGVVRMRYGFPDGVLHTLEEVGRVYGVTRERIRQIESRTMAKLQHPARSRGLEGYLD 349


>gi|1553019|gb|AAC45101.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  253 bits (646), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|1553029|gb|AAC45106.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  253 bits (645), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|1553013|gb|AAC45098.1| primary sigma factor [Borrelia afzelii]
 gi|1553015|gb|AAC45099.1| primary sigma factor [Borrelia afzelii]
 gi|1553021|gb|AAC45102.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  253 bits (645), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|294660419|ref|NP_853171.2| RNA polymerase sigma factor RpoD [Mycoplasma gallisepticum str.
           R(low)]
 gi|284812078|gb|AAP56739.2| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(low)]
 gi|284930653|gb|ADC30592.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(high)]
          Length = 643

 Score =  253 bits (645), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 121/241 (50%), Positives = 179/241 (74%), Gaps = 7/241 (2%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V +NLRLV S+AKKY NRGL F+DLIQEG+IGLMKA  KF++ LG KFSTYA WW++Q
Sbjct: 397 QLVTSNLRLVTSIAKKYLNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQ 456

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG---- 562
           AITR+IADQ+ T+RIPVHM + I+K+++T R ++ ++ R+PT EE+ + +   V G    
Sbjct: 457 AITRAIADQARTVRIPVHMVETINKLIKTERMLTQQLGRDPTLEELTEAMGGQVNGFTPK 516

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASL 620
            V  + K+ +EP+SL+ PIG ++ S   DF++D++ + P +   +  + E    + + +L
Sbjct: 517 KVADIKKLNQEPVSLDKPIGHDEESQFVDFVKDRDILKPDEYTEKLIVTEHINELFINTL 576

Query: 621 TPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           T +EE+++RMR+G+   +   TLEEVG++F VTRERIRQIE+KA+RKLKHPS++ +LRSF
Sbjct: 577 TKKEEQIIRMRYGLHPWHQQMTLEEVGQKFNVTRERIRQIESKALRKLKHPSKNARLRSF 636

Query: 680 L 680
           L
Sbjct: 637 L 637


>gi|1553033|gb|AAC45108.1| primary sigma factor [Borrelia japonica]
          Length = 450

 Score =  253 bits (645), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|1553017|gb|AAC45100.1| primary sigma factor [Borrelia burgdorferi 297]
          Length = 450

 Score =  252 bits (644), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 175/241 (72%), Gaps = 3/241 (1%)

Query: 430 IVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           I+SM   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA E
Sbjct: 210 IISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVE 269

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++
Sbjct: 270 KFEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKD 329

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +    
Sbjct: 330 PTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSF 389

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+
Sbjct: 390 VVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRR 449

Query: 667 L 667
           L
Sbjct: 450 L 450


>gi|262202171|ref|YP_003273379.1| sigma-70 family RNA polymerase sigma factor [Gordonia bronchialis
           DSM 43247]
 gi|262085518|gb|ACY21486.1| RNA polymerase sigma factor, sigma-70 family [Gordonia bronchialis
           DSM 43247]
          Length = 337

 Score =  251 bits (642), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 119/259 (45%), Positives = 187/259 (72%), Gaps = 6/259 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S ++ R +  +VR+GE     A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 82  LSAAKKRDLAIVVREGEA----ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 137

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 138 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 197

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T EE+A +  +P E +  +L  +++P+SL+ P+G ++ + LGDFIED  A S  
Sbjct: 198 QLGREATDEELANESGIPAEKIADLLDHSRDPVSLDMPVGSDEEAPLGDFIEDAEATSA- 256

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +SA+ A L  T  R VLA+L  RE++V+RMR+G+      TL+++G+ F ++RER+RQIE
Sbjct: 257 ESAVIAGLMHTDVRAVLATLDEREQQVIRMRYGLDDGQPRTLDQIGRMFGLSRERVRQIE 316

Query: 661 AKAIRKLKHPSRSKKLRSF 679
            + + KL+   R+++LR++
Sbjct: 317 REVMGKLRQGDRAERLRAY 335


>gi|330466466|ref|YP_004404209.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
 gi|328809437|gb|AEB43609.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
          Length = 335

 Score =  251 bits (642), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 117/240 (48%), Positives = 175/240 (72%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 94  EGQAAKNHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 153

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR++ADQ+ TIRIPVHM ++++++VR  R +S  + REP+  EIA+ L +P
Sbjct: 154 ATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRARRELSVSLGREPSVAEIARALDVP 213

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              V +++   +EP+SL+  +G++  S LGDF+   +  S +D A +  LR   + VLA+
Sbjct: 214 EFQVIELISYDREPVSLDQTVGEDGESALGDFVAAVDPSSMVDDADRGELRNEVSIVLAT 273

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL+ P R+++L ++
Sbjct: 274 LSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRAPERAQRLEAY 333


>gi|21449377|gb|AAM54109.1|AF453501_35 RNA polymerase sigma factor [Actinosynnema pretiosum subsp.
           auranticum]
          Length = 348

 Score =  251 bits (640), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 120/238 (50%), Positives = 172/238 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT +G+  LD+IQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 111 AKDHLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFSTYATWW 170

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQS TIR+PVHM + + K+ R  R + ++  RE T EE+A +L +  E V
Sbjct: 171 IRQAITRALADQSRTIRLPVHMVEVVTKLARIERDLLHRNGREATAEEVAVELDVTPEKV 230

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ +  + P+SL+  IG E  + +GD I D+NAV+PL++   A L      VL +LTPR
Sbjct: 231 VELRQHARTPVSLDQTIGAEADTSIGDLIADENAVAPLEAVSSALLSADLRAVLETLTPR 290

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+RMR+G      HTL+EVG+ + VTRERIRQIE++ + KL+HP+RS+ L  +LD
Sbjct: 291 EAGVVRMRYGFPDGVLHTLDEVGRVYGVTRERIRQIESRTMAKLQHPARSRGLEGYLD 348


>gi|328474970|gb|EGF45764.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 346

 Score =  251 bits (640), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 117/204 (57%), Positives = 157/204 (76%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+
Sbjct: 124 IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDF 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P+PE
Sbjct: 184 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGRDPSPE 243

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+
Sbjct: 244 EIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLK 303

Query: 611 ETTTRVLASLTPREERVLRMRFGI 634
           E    VL +LT REE VLR+RFG+
Sbjct: 304 EQLEDVLDTLTDREENVLRLRFGL 327



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EE--TESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|118463509|ref|YP_882780.1| RNA polymerase sigma factor SigB [Mycobacterium avium 104]
 gi|254776043|ref|ZP_05217559.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|118164796|gb|ABK65693.1| sigma factor SigB [Mycobacterium avium 104]
          Length = 319

 Score =  251 bits (640), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 119/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G+     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLEAVVRDGQA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 186 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 244

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 245 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 304

Query: 667 LKHPSRSKKLRSF 679
           L++  R+ +LRS+
Sbjct: 305 LRNGERADRLRSY 317


>gi|145594010|ref|YP_001158307.1| RNA polymerase sigma factor SigB [Salinispora tropica CNB-440]
 gi|145303347|gb|ABP53929.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 332

 Score =  251 bits (640), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 116/242 (47%), Positives = 175/242 (72%), Gaps = 1/242 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFST
Sbjct: 89  AEGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFST 148

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM ++++++VRT R +S  + REPT  E+A+ L +
Sbjct: 149 YATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRTRRELSVSLGREPTVAEVARTLDI 208

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVL 617
           P   V +++   +EP+SL+  +G++  S LGDF+   ++ +  D  +    LR+    VL
Sbjct: 209 PEIQVIELISYDREPVSLDQTVGEDGESPLGDFVAAVDSTAGTDDTVSGGELRQEMCGVL 268

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL+ P R+++L 
Sbjct: 269 ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLHKLRAPERAQRLE 328

Query: 678 SF 679
           ++
Sbjct: 329 AY 330


>gi|254821657|ref|ZP_05226658.1| RNA polymerase sigma factor SigB [Mycobacterium intracellulare ATCC
           13950]
          Length = 319

 Score =  251 bits (640), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 120/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G+     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLEAVVRDGKA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PV+ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 186 TDEELAAESGIPVDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 244

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 245 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 304

Query: 667 LKHPSRSKKLRSF 679
           L++  R+ +LRS+
Sbjct: 305 LRNGERADRLRSY 317


>gi|41408924|ref|NP_961760.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397283|gb|AAS05143.1| SigB [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 332

 Score =  250 bits (639), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 119/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G+     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 83  RDLEAVVRDGQA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 138

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 139 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 198

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A
Sbjct: 199 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIA 257

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 258 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSK 317

Query: 667 LKHPSRSKKLRSF 679
           L++  R+ +LRS+
Sbjct: 318 LRNGERADRLRSY 330


>gi|148657222|ref|YP_001277427.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569332|gb|ABQ91477.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 349

 Score =  250 bits (639), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 115/238 (48%), Positives = 167/238 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+S+AKKY  RGL  LDLIQEGNIGLM+A EKFD   G +FSTYA WW
Sbjct: 112 ARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHRKGNRFSTYATWW 171

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IA+Q  TIR+PVHM + + +V R A R++  ++R+PTPEEIA  L  P E +
Sbjct: 172 IRQAVTRAIAEQGRTIRLPVHMSESVGQVKRAADRLAQVLERQPTPEEIATALGQPTERI 231

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL+ ++ P+SLE P+G++    LGDF++D +  +P+++A    LR      L  L  R
Sbjct: 232 ERVLEASRRPVSLEMPVGEDGEHTLGDFLQDSDLPTPVEAASHQLLRRDLAAALDRLNER 291

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E R++ +R+G+      TLEEVG+   +TRER RQIEA+A+R+L+ P     LR +L+
Sbjct: 292 ERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALRRLRAPDVGLHLRDYLE 349


>gi|94985446|ref|YP_604810.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94555727|gb|ABF45641.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 403

 Score =  250 bits (638), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 124/245 (50%), Positives = 171/245 (69%), Gaps = 3/245 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + AK+ ++EANLRLV+S+AK+YTNRGL  LDLIQEGN GL++A EKF++  GYKFSTY
Sbjct: 159 DGAAAKQALIEANLRLVVSIAKRYTNRGLGLLDLIQEGNQGLIRAVEKFEYRRGYKFSTY 218

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q++TR+IAD+S TIR+PVHM + I+++ R  R++  ++ REP P EIA+ +   
Sbjct: 219 ATWWIRQSLTRAIADKSRTIRVPVHMVETINRLSRMTRQLEMELSREPLPAEIAEAMGPG 278

Query: 560 VEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   V +  K+  EP+SLE PIG+E  S  GDF+ D    SP+ +A QA L E   R  
Sbjct: 279 WDAAKVEETQKVGWEPMSLEMPIGEEGDSTYGDFLPDDRFASPIQNASQALLSEALERAF 338

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP-SRSKKL 676
            +L  RE  VLR+R G     +HTLEEVG+   VTRER+RQIE KA+RKLK+    ++ L
Sbjct: 339 GTLNEREALVLRLRHGFVDGHEHTLEEVGQLLSVTRERVRQIENKALRKLKYQEGLTRGL 398

Query: 677 RSFLD 681
           R FL+
Sbjct: 399 RDFLE 403


>gi|298247391|ref|ZP_06971196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297550050|gb|EFH83916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 385

 Score =  249 bits (637), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 115/241 (47%), Positives = 169/241 (70%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A+  + EANLRLV+S+A+KY  RG+   DLIQEGN GLM A EKFD+  G+KFSTYA
Sbjct: 145 AQNARDRLTEANLRLVVSIARKYMGRGMALADLIQEGNAGLMLAVEKFDYTRGFKFSTYA 204

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAI R+IA+Q+ TIR+PVH  + ++++ RT+ ++  ++ REP+ EEIA+++ + V
Sbjct: 205 TWWIRQAINRAIANQARTIRLPVHFHEAVNRLHRTSSQLFQELGREPSAEEIAERMHISV 264

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V  +L+  K+PISLE+P+GD+  S LGDF+ED+   SP D   +  LRE    VL  L
Sbjct: 265 DTVYDILEAGKQPISLESPVGDDGDSSLGDFVEDQVTASPADITTRNILREQIAHVLDEL 324

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE  +++  FG     +HTL E+G+   ++RER+RQIEAKA+RKL+    S++L+ FL
Sbjct: 325 NERERHIIQYHFGFLDGKEHTLAEIGENLHLSRERVRQIEAKALRKLRQSYSSRQLKDFL 384

Query: 681 D 681
           +
Sbjct: 385 N 385


>gi|118618673|ref|YP_907005.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
 gi|118570783|gb|ABL05534.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
          Length = 323

 Score =  249 bits (637), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 120/253 (47%), Positives = 184/253 (72%), Gaps = 6/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G    + A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 74  RELAAVVRDG----AEARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 129

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +   + RE 
Sbjct: 130 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREIHQNLGREA 189

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++A+ A
Sbjct: 190 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA-ENAVIA 248

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  T  R VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + K
Sbjct: 249 ELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCK 308

Query: 667 LKHPSRSKKLRSF 679
           L+H  R+ +LRS+
Sbjct: 309 LRHGERADRLRSY 321



 Score = 38.1 bits (87), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D VR+YL  +G   LL+ EGE+ +AKRIEAG
Sbjct: 25  DLVRVYLNGIGKTALLNAEGEVELAKRIEAG 55


>gi|169630111|ref|YP_001703760.1| RNA polymerase sigma factor SigB [Mycobacterium abscessus ATCC
           19977]
 gi|169242078|emb|CAM63106.1| RNA polymerase sigma factor [Mycobacterium abscessus]
          Length = 323

 Score =  249 bits (637), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 112/240 (46%), Positives = 177/240 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E + A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 82  EGNAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 141

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE + EE+A++  +P
Sbjct: 142 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQRLGREASDEELAEESGIP 201

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE +  +L  +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I   L      VLA+
Sbjct: 202 VEKIGDLLDHSRDPVSLDMPVGTDEEAPLGDFIEDTEAMSAENAVIAELLHSDVRSVLAT 261

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE + + KL+H  R+++LRS+
Sbjct: 262 LDEREQQVIRLRYGLDDGQARTLDQIGKLFGLSRERVRQIEREVMAKLRHGDRAERLRSY 321


>gi|163849112|ref|YP_001637156.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222527085|ref|YP_002571556.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670401|gb|ABY36767.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222450964|gb|ACM55230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 398

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/238 (49%), Positives = 170/238 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++M  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD+  GYKFSTYA WW
Sbjct: 159 ARQQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWW 218

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA++R++ADQS  +R+PVH+ + ++++    R+++  + REPT  E+A  L M  E +
Sbjct: 219 IKQALSRALADQSRLVRLPVHLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEKL 278

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ +  ++P+SL TP+G+E  S L DFI D +A+   D+A    LR+  T  L  L+ R
Sbjct: 279 RELRRTAQDPVSLATPVGEEADSTLADFIPDPHALDADDAAASGMLRQQITAALDQLSER 338

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E RVL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 339 ERRVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 396



 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/122 (33%), Positives = 68/122 (55%), Gaps = 15/122 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDD--LEDEEG 88
           + +I   RQ+G+VT E++   +P PDE S E ++   A L+  G+ V +GD+  L+DE  
Sbjct: 21  QALIAQGRQQGFVTFEDIQRLVPNPDE-SIELIDSIYAALAEAGVPVQEGDETALDDE-- 77

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                     +S +++ L    + +D    D VR+YLRE+G + LL+ E E  +A+ IE 
Sbjct: 78  ---------PSSPATMDLDLDDELSDALLSDSVRLYLREIGQVPLLTAEQEKRLAQLIEQ 128

Query: 149 GR 150
           G+
Sbjct: 129 GQ 130


>gi|94313583|ref|YP_586792.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
 gi|93357435|gb|ABF11523.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
          Length = 617

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 130/319 (40%), Positives = 212/319 (66%), Gaps = 2/319 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           GI R+ FL+   G E+D  W  + A +   G     V   +  I  I+ E++ +     +
Sbjct: 298 GIAREQFLQTFPGHEIDLGWSEALAAERISGAADALVRA-IPEIQAIQREMRVLENRAAM 356

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S+ + +++   V K    A  A+ EM+ +NLRLV+S AKKY +RG+  LDLIQEGN+GLM
Sbjct: 357 SLGDLKNLGQRVAKARARAQAARDEMIRSNLRLVVSNAKKYLHRGMPLLDLIQEGNLGLM 416

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +A ++FD+  GYKFSTYA WW++Q ITR+IAD+  TIRIP+H+ + + KV R +R + ++
Sbjct: 417 RAVDRFDYRRGYKFSTYATWWIRQGITRAIADKGPTIRIPIHLVEVVGKVNRASRELFHE 476

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
               P PE +A +L++ V+ V+ +L + KEP+SLE  +G+   + L D + D+ + SP +
Sbjct: 477 TGEAPAPEALAARLSLSVKKVKAILDLVKEPLSLEMSVGESGDALLWDTLTDECSASPDE 536

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SA++ +LR+     LA+L PRE ++++MR+G+   TD+TLEE+G+Q+ ++RER+RQ+E +
Sbjct: 537 SAMRVSLRKDLDEALATLKPREAKIVKMRYGVDAGTDYTLEEIGQQYGLSRERVRQLERQ 596

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKL++P R+ +L++  D
Sbjct: 597 ALRKLRNPDRAPRLQAHRD 615



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/162 (29%), Positives = 83/162 (51%), Gaps = 10/162 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE-- 86
           +S   ++ L  +RG++T  E++  LP  +    Q      +L  +G+ +V+   L +E  
Sbjct: 7   ESLVALVALGSERGFLTHGEISDALPDSDFGQIQR-----VLEELGVQIVE-RTLANEPI 60

Query: 87  --EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             E   D+L +  +    +     + D  +  T DPV++YLRE+G+I LL+RE E+AIA+
Sbjct: 61  RLEEHADALVVDEAVIEEAAAAVMQADGREARTTDPVQLYLREIGTIPLLTREDEVAIAR 120

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           R E     M+A +   PL    L+   DE+  G   + ++ID
Sbjct: 121 RHEIAVTEMVAEMVSCPLVVYELLTMADEIERGEMAVDDLID 162


>gi|91200070|emb|CAJ73113.1| similar to transcription initiation factor sigma 70 [Candidatus
           Kuenenia stuttgartiensis]
          Length = 491

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/272 (45%), Positives = 180/272 (66%), Gaps = 3/272 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           NEI+++     +   E + I+  +     E  +A+K   E NLRLV+S+AKKY  RG+ F
Sbjct: 220 NEIEAL---FAMPAKELKKIIFSINSIYNEYVMARKRFSEGNLRLVVSIAKKYRKRGMAF 276

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGN GLM+A +K+D+ +G+KFSTYA WW+KQAI R+  ++  TIRIPVHM D I+
Sbjct: 277 HDLIQEGNTGLMRAVDKYDYRMGFKFSTYATWWIKQAIIRATEEKVRTIRIPVHMMDVIN 336

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K    A+        +   E IA+    P+  + ++L+IT +PISLETPIG +  +   D
Sbjct: 337 KSTYVAKAGQGSSAEKIQLEAIARDTNTPLPEIYRLLQITSQPISLETPIGSDGETMFED 396

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FI+DK   +P+  A ++ L+E   +VL +L+ RE  ++++RFGI     H+LEE+GK+F 
Sbjct: 397 FIQDKKIDAPIFLAQRSLLKEQIQKVLDTLSYREREIIKLRFGISDGYTHSLEEIGKRFN 456

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +TRERIRQIEA A+RKL+HP RS+KL  FL+G
Sbjct: 457 ITRERIRQIEAIALRKLQHPVRSRKLEGFLEG 488


>gi|284046131|ref|YP_003396471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950352|gb|ADB53096.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 367

 Score =  249 bits (635), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/234 (50%), Positives = 170/234 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MVE+NLRLV+S+AK Y N+GL FLDLIQEG +GL++AAEKFD+  G+KFSTYA WW
Sbjct: 131 AKQKMVESNLRLVVSIAKNYRNQGLPFLDLIQEGTLGLVRAAEKFDYRKGFKFSTYATWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R++AD++ TIRIPVH+ +K++K+ R  R++  ++ REPT EEIA    +  E V
Sbjct: 191 IRQAIARALADKARTIRIPVHVVEKLNKIGRAERKLVTELGREPTAEEIADVTGIDPEEV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             + +  + P+SLE P+GDE+ S  G FI D+ A SP + A +   +E     L +L+ R
Sbjct: 251 DSIKRSAQAPVSLEKPVGDEEESEFGQFIADERAESPYERAAEILTKEALREALENLSYR 310

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           E RVL +R+G+G     TL+EVG+ F VTRERIRQIE ++++KL+  + ++KLR
Sbjct: 311 ERRVLELRYGLGGEHPRTLDEVGRTFNVTRERIRQIENQSLKKLQSLAEAQKLR 364


>gi|111023771|ref|YP_706743.1| RNA polymerase sigma factor SigB [Rhodococcus jostii RHA1]
 gi|110823301|gb|ABG98585.1| sigma factor, sigma 70 type, group 2 (proven non-essential)
           [Rhodococcus jostii RHA1]
          Length = 323

 Score =  249 bits (635), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 116/264 (43%), Positives = 189/264 (71%), Gaps = 6/264 (2%)

Query: 418 VETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +ETG  +S ++ R + ++VR+G+     A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 62  LETGKRLSPAKKRDLATVVREGQS----ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 117

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 118 EGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 177

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIED 
Sbjct: 178 KRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDS 237

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK F ++RER
Sbjct: 238 EATSAENAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRER 297

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R+++LRS+
Sbjct: 298 VRQIEREVMGKLRQGDRAERLRSY 321


>gi|134098366|ref|YP_001104027.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006932|ref|ZP_06564905.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|133910989|emb|CAM01102.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 324

 Score =  249 bits (635), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 116/248 (46%), Positives = 177/248 (71%), Gaps = 4/248 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++VR G     +AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 79  AVVRDG----VLAKNHLMEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYT 134

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  K+ RE T EE
Sbjct: 135 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKIARIKRDLHQKLGREATDEE 194

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +  + VE V  +L  +++P+SL+ P+G E+ + LGDFIED  +    ++ I   L++
Sbjct: 195 LANEAGLTVEKVADLLDHSRDPVSLDMPVGAEEDAPLGDFIEDAESADAENAVISGFLQD 254

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              RVL++L  RE+ V+RMR+G+      TL+++GK F ++RER+RQIE + + KL+   
Sbjct: 255 DLRRVLSTLEEREQAVIRMRYGLDDGQPRTLDQIGKAFGLSRERVRQIEREVMSKLRQGD 314

Query: 672 RSKKLRSF 679
           R+ KLR++
Sbjct: 315 RADKLRAY 322


>gi|54025745|ref|YP_119987.1| RNA polymerase sigma factor SigB [Nocardia farcinica IFM 10152]
 gi|54017253|dbj|BAD58623.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 322

 Score =  249 bits (635), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 115/258 (44%), Positives = 182/258 (70%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S ++ + +  +VR G+     A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 67  LSAAKKKDLAMIVRDGQA----ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 122

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 123 IRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 182

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T EE+A +  +PVE +  +L  +++P+SL+ P+G+++ + LGDFIED  A S  
Sbjct: 183 QLGREATDEELAAESGIPVEKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDSEATSAE 242

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            + I   L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE 
Sbjct: 243 SAVIAGLLHHDVRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIER 302

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL+   R+ +LR++
Sbjct: 303 EVMAKLRKGERADRLRAY 320


>gi|226366207|ref|YP_002783990.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|226244697|dbj|BAH55045.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|254553060|dbj|BAH85842.1| RNA polymerase sigma B factor [Rhodococcus opacus]
          Length = 323

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 116/264 (43%), Positives = 189/264 (71%), Gaps = 6/264 (2%)

Query: 418 VETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +ETG  +S ++ R + ++VR+G+     A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 62  LETGKRLSPAKKRDLATVVREGQS----ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 117

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 118 EGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 177

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIED 
Sbjct: 178 KRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDS 237

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK F ++RER
Sbjct: 238 EATSAENAVIAGLLHSDVRTVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRER 297

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R+++LRS+
Sbjct: 298 VRQIEREVMGKLRQGDRAERLRSY 321


>gi|251733349|emb|CAR82424.1| RNA polymerase sigma factor [Sinorhizobium americanum]
 gi|251733415|emb|CAR82457.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733417|emb|CAR82458.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733419|emb|CAR82459.1| RNA polymerase sigma factor [Sinorhizobium terangae]
          Length = 202

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 145/178 (81%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYSGAELDPNWMKSISNLAGKGWKEFAKAENQTIRDIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|302866072|ref|YP_003834709.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315502628|ref|YP_004081515.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302568931|gb|ADL45133.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315409247|gb|ADU07364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 328

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 117/242 (48%), Positives = 171/242 (70%), Gaps = 1/242 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFST
Sbjct: 85  AEGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFST 144

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM ++++++VR  R +S  + REPT  E+A  L +
Sbjct: 145 YATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRVRRELSVTLGREPTVSEVATALEI 204

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVL 617
           P   V +++   +EP+SL+  +G++  S LGDF+   +    P D+A    LR     VL
Sbjct: 205 PEFQVIELISYDREPVSLDQAVGEDGESALGDFVAAVDPRTEPGDAATNGELRNEVRIVL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL+ P R+ +L 
Sbjct: 265 ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRDPERANRLE 324

Query: 678 SF 679
           ++
Sbjct: 325 AY 326


>gi|251733355|emb|CAR82427.1| RNA polymerase sigma factor [Rhizobium galegae]
          Length = 202

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 122/190 (64%), Positives = 147/190 (77%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+  V SLSLNQ+R+D LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  AATGTLSSAQERRYKELKDELITAVKSLSLNQNRVDSLVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++QG ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYQGAELDPNWMKSIANLAARGWKEFARAENTTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDW 490
           LMKA +KF++
Sbjct: 191 LMKAVDKFEY 200


>gi|251733379|emb|CAR82439.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733381|emb|CAR82440.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733383|emb|CAR82441.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733385|emb|CAR82442.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733421|emb|CAR82460.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
 gi|251733423|emb|CAR82461.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
          Length = 202

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 145/178 (81%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|251733367|emb|CAR82433.1| RNA polymerase sigma factor [Agrobacterium vitis]
          Length = 202

 Score =  248 bits (633), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 148/178 (83%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+  V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++QG ELDP+W+    +     WK+F   E ++I +IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYQGAELDPNWMKSVGNLAARGWKDFAREENNTIREIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|269926941|ref|YP_003323564.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269790601|gb|ACZ42742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 596

 Score =  248 bits (633), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 120/231 (51%), Positives = 165/231 (71%), Gaps = 1/231 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + K   E  IA+K ++EANLRLV+S+AKKYT RG+  LDLIQEGNIGL+KA EKF    G
Sbjct: 245 ITKWIAEGDIARKRLIEANLRLVVSIAKKYTGRGITLLDLIQEGNIGLIKAVEKFRHQKG 304

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ +  RR++ ++ REPT +EIA
Sbjct: 305 YKFSTYATWWIRQAITRAIADQARTIRIPVHMGEAINKIAQARRRLTQELGREPTEQEIA 364

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L +PVE +R+V KI++EPISLE P+G+E+ + LGDFI+D  A +P+D+A Q+ LR+  
Sbjct: 365 NYLGIPVEKIREVQKISQEPISLENPVGEEEDTSLGDFIQDHKAPAPMDAASQSLLRDQI 424

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +VL  L+ RE  VL MRFG+         EV     V+  ++ Q E++ +
Sbjct: 425 DQVLKHLSERERGVLLMRFGLDCEP-RPYREVAHILAVSPNQVMQAESRVL 474



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 46/76 (60%)

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I   LRE    V+  +   E  ++R RFG+ +    TLEEVG+ F VTRERIRQIE+KA+
Sbjct: 520 IDQKLREALASVMLHVPAPERDMMRFRFGLDIGQPRTLEEVGRAFGVTRERIRQIESKAL 579

Query: 665 RKLKHPSRSKKLRSFL 680
           RKL+     ++L   L
Sbjct: 580 RKLRRDVFRRQLEDLL 595



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 14/77 (18%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           N  D  DLE EE  +D  DL              +D    + DDP+R+YLRE+G   LLS
Sbjct: 44  NDADYVDLEIEESLQDPEDL--------------EDLEGTNLDDPIRLYLREIGKENLLS 89

Query: 136 REGEIAIAKRIEAGRAM 152
           +E EI +A++ E G  +
Sbjct: 90  QEQEIELARKNERGNYL 106


>gi|251733409|emb|CAR82454.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733411|emb|CAR82455.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733413|emb|CAR82456.1| RNA polymerase sigma factor [Sinorhizobium saheli]
          Length = 202

 Score =  247 bits (631), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 120/178 (67%), Positives = 145/178 (81%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA+SYG+KR+ FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLMQNEGRLLRLAESYGVKREAFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|324999213|ref|ZP_08120325.1| RNA polymerase sigma factor SigB [Pseudonocardia sp. P1]
          Length = 380

 Score =  247 bits (631), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 115/252 (45%), Positives = 179/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR G    ++AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 131 RDLRAVVRDG----ALAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEK 186

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQ+ TIR+PVH+ ++++K+ R  R M  +  REP
Sbjct: 187 FDYTKGFKFSTYATWWIRQAITRGMADQARTIRLPVHLVEQVNKLARIKRDMHQRQGREP 246

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +  E+A++  +P   +  +L   ++P+SL+ P+G E+ + LGDFIED  A    ++ I +
Sbjct: 247 SEAELAQESGIPEHKISDLLDHARDPVSLDMPVGSEEEAPLGDFIEDAEATDAENTVISS 306

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L +   RVLA+L  RE++V+RMRFG+      TL+++G+ F ++RER+RQIE + + KL
Sbjct: 307 LLSDDLRRVLATLEDREQKVIRMRFGLDDGQPRTLDQIGRAFTLSRERVRQIEREVMAKL 366

Query: 668 KHPSRSKKLRSF 679
           +   R+ KLR++
Sbjct: 367 RVGERADKLRAY 378


>gi|226306291|ref|YP_002766251.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229491301|ref|ZP_04385127.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|226185408|dbj|BAH33512.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229321840|gb|EEN87635.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 323

 Score =  247 bits (630), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 112/258 (43%), Positives = 185/258 (71%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++++ R + ++VR+G+     A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 68  LTVAKKRDLATIVREGQS----ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 123

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 124 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 183

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIED  A S  
Sbjct: 184 QLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDSEATSAE 243

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ I   L      VL +L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE 
Sbjct: 244 NAVIAGLLHSDVRSVLGTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIER 303

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL+   R++KLRS+
Sbjct: 304 EVMGKLRVGDRAEKLRSY 321


>gi|168012500|ref|XP_001758940.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
 gi|12697780|dbj|BAB21618.1| PpSIG2 [Physcomitrella patens]
 gi|14669832|dbj|BAB62008.1| PpSIG2 [Physcomitrella patens]
 gi|162690077|gb|EDQ76446.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
          Length = 579

 Score =  247 bits (630), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 129/290 (44%), Positives = 188/290 (64%), Gaps = 14/290 (4%)

Query: 402 EVDSILKIRNEIKSISVETG--ISISEFRHIVSM--------VRKGECEASIAKKEMVEA 451
           ++  +LK+ N   ++  E G   +I E+   V M        ++KG      AK +MV +
Sbjct: 288 QIQDLLKLENIKSNLEREIGRNATIGEWSRAVGMEQNAFEARLKKGR----FAKDKMVNS 343

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK Y  RG+   DLIQEG++GL++ AEKFD   G+KFSTYA WW++QA+TRS
Sbjct: 344 NLRLVVSIAKNYQGRGMTLQDLIQEGSMGLVRGAEKFDPTKGFKFSTYAHWWIRQAVTRS 403

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQS TIR+P+H+ + I ++ +  R +  +  RE   EE+A+ + + VE ++ V+K  K
Sbjct: 404 IADQSRTIRLPIHLYEVISRINKAKRMLVQEHGREARNEEVAELVGLTVEKLKSVVKSAK 463

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            P S+E PIG +  + LG+ + D +  SP D+ ++  +R+    VL +L PRE  VLR+R
Sbjct: 464 APGSMERPIGKDGDTTLGELVADTDVDSPEDAIVKQLMRQDIEGVLRTLNPREREVLRLR 523

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TLEE+G+ F VTRERIRQIEAKA+RKL+ PSR+  LR +LD
Sbjct: 524 FGLDDGRSKTLEEIGQIFKVTRERIRQIEAKAMRKLRQPSRNSILREYLD 573


>gi|251733405|emb|CAR82452.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733407|emb|CAR82453.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733425|emb|CAR82462.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733427|emb|CAR82463.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733429|emb|CAR82464.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733431|emb|CAR82465.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733433|emb|CAR82466.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733435|emb|CAR82467.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733437|emb|CAR82468.1| RNA polymerase sigma factor [Ensifer adhaerens]
          Length = 202

 Score =  247 bits (630), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 120/178 (67%), Positives = 145/178 (81%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+R+D LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRVDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYSGAELDPNWMKSISNLAGKGWKEFAKSENQTIRDIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|555686|gb|AAA85644.1| sigma factor MysB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score =  246 bits (629), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 115/246 (46%), Positives = 178/246 (72%), Gaps = 4/246 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLQAVVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGTDEEAPLGDFIEDSEAMSAENAVISE 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 246 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 305

Query: 668 KHPSRS 673
           ++  R+
Sbjct: 306 RNGERA 311


>gi|251733361|emb|CAR82430.1| RNA polymerase sigma factor [Agrobacterium tumefaciens]
          Length = 202

 Score =  246 bits (629), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 146/178 (82%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+  V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E ++I +IR EI+++S ETGISI+EFR IVS
Sbjct: 83  QYHGAELDPNWMKSIANLAARGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|226357433|ref|YP_002787172.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226319423|gb|ACO47418.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 363

 Score =  246 bits (629), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 127/259 (49%), Positives = 177/259 (68%), Gaps = 7/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R +   V  GE     AK++++EANLRLV+S+AKKY NRG+  LDLIQEGN GL++ A
Sbjct: 108 ERRRLQRTVEDGEH----AKQQLIEANLRLVVSIAKKYANRGMGLLDLIQEGNQGLIRGA 163

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++  G+KFSTYA WW++QA+ R+IADQ+  IRIPVHM + I+K+ RT R++  ++ R
Sbjct: 164 EKFEYRRGFKFSTYATWWIRQAVNRAIADQARNIRIPVHMVETINKLNRTTRQLQMELSR 223

Query: 546 EPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EP+  E A+ +    + V+  + L++T++ ISL TP+GDE  S + DF+ D    SPL  
Sbjct: 224 EPSHAETAEAMGPGWDEVKVEETLRLTRDTISLATPVGDEGDSSIADFLPDDRRESPLSR 283

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                + E   R LA+L PRE  V+R+R G+    +HTLEEVGK F VTRERIRQIE KA
Sbjct: 284 VSSVLMSEALDRTLATLEPREALVIRLRNGLEDGREHTLEEVGKHFGVTRERIRQIENKA 343

Query: 664 IRKLKH-PSRSKKLRSFLD 681
           +RK+K+  S+   LR +L+
Sbjct: 344 LRKIKYEQSKRGSLRDYLE 362



 Score = 39.3 bits (90), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++DPVR YL E+G + LL+   EI +A+R+EAG+
Sbjct: 59  SNDPVRQYLHEIGRVPLLTVTEEIDLARRMEAGQ 92


>gi|312139424|ref|YP_004006760.1| sigma-70 factor sigb [Rhodococcus equi 103S]
 gi|325672687|ref|ZP_08152383.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
 gi|311888763|emb|CBH48075.1| sigma-70 factor SigB [Rhodococcus equi 103S]
 gi|325556564|gb|EGD26230.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
          Length = 322

 Score =  246 bits (629), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 112/258 (43%), Positives = 184/258 (71%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ R + ++VR GE     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 67  LTAAKKRDLATIVRDGEA----ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 122

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 123 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 182

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T EE++++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIED  A S  
Sbjct: 183 QLGREATDEELSQESGIPEHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDSEATSAE 242

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE 
Sbjct: 243 NAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIER 302

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL+   R+ +LR++
Sbjct: 303 EVMGKLRQGERADRLRAY 320


>gi|50365086|ref|YP_053511.1| RNA polymerase sigma factor [Mesoplasma florum L1]
 gi|50363642|gb|AAT75627.1| RNA polymerase sigma factor [Mesoplasma florum L1]
          Length = 471

 Score =  246 bits (629), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 132/295 (44%), Positives = 179/295 (60%), Gaps = 60/295 (20%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ +NL+LVISVA+K+ NRGL F DLI+EGNIGL+KA +KFD+  G+KFSTYA WW++QA
Sbjct: 177 LITSNLKLVISVARKHLNRGLDFADLIEEGNIGLIKAVDKFDYEKGFKFSTYATWWIRQA 236

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVEGVRK 565
           ITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP+ +E+A+++   M  E V +
Sbjct: 237 ITRAIADQARTIRIPVHMVETINKLSRIERQLTQELGREPSSKEVAERMGGDMTAEKVVE 296

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + KI  EP+SLE P GDED +H GDF+EDK+ +SP D   +  LRE   +V   +  REE
Sbjct: 297 IKKIAVEPVSLEKPFGDEDDTHFGDFVEDKDMISPTDFTEKEILREVIDKVFEDMPAREE 356

Query: 626 RVLRMRFGI-------------------------GMN---------------------TD 639
           +V+RMR+GI                          +N                      D
Sbjct: 357 KVIRMRYGIVPTKVRTLIRLAEECNDETAGELAKAINKLDIHLETPVEKIRTVDSKIIQD 416

Query: 640 HTL--------EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
           H L        EEVGK+  VTRERIRQIEAK IRKLK P+ + K    L+ F  G
Sbjct: 417 HLLKYEASKTLEEVGKELNVTRERIRQIEAKTIRKLKQPANANKSGKVLKEFYKG 471


>gi|320159820|ref|YP_004173044.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319993673|dbj|BAJ62444.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 396

 Score =  246 bits (628), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 128/256 (50%), Positives = 182/256 (71%), Gaps = 6/256 (2%)

Query: 431 VSMVRKGECEASI-----AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +S  R+GE EA I     A++ +++AN RLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA 
Sbjct: 141 LSPQRRGELEAQIQDGESAREHLIKANTRLVVSIAKRYIGRGVPFLDLIQEGNLGLMKAV 200

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK+++  G++FSTYA WW++Q ITRSIADQ  TIR+PVHM D+I ++ RT   M  K+ R
Sbjct: 201 EKYEYQRGFRFSTYATWWIRQTITRSIADQGRTIRVPVHMVDRIRRLYRTTHEMEQKLGR 260

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSA 604
            PT EE+A  + +    V  +++++  P+SLE+PI  DE+ S LG FIED+   SP+ + 
Sbjct: 261 TPTNEELADAIGIKASKVDWMMRVSWLPLSLESPINEDEEDSELGQFIEDQVTPSPMQTT 320

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               LRE    VL +L  RE R+LR+RFG+     +TLEEVG++F +TRERIRQIE KA+
Sbjct: 321 YSNLLREKIQEVLDTLPAREARILRLRFGLENGRTYTLEEVGQKFGLTRERIRQIENKAL 380

Query: 665 RKLKHPSRSKKLRSFL 680
           R+L+HP R+++L+ +L
Sbjct: 381 RRLRHPRRARQLKDYL 396



 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 5/120 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +++ A  +GY+T E+L    P      E+ E  +  L   G+++ D ++ E     ED
Sbjct: 15  KMLLEKADVQGYLTTEDLMEAYPNVGEDHERFEAILLALRRHGVDIYDTEENEYPFPDED 74

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                        F     D    S+DD V +YL+EM  + LLS E E+ +AKRIE GRA
Sbjct: 75  IDGAFIEEDPVQTF-----DLNRISSDDTVGLYLKEMSRVPLLSSEEEVELAKRIERGRA 129


>gi|1519642|gb|AAB07554.1| SigD [Chloroflexus aurantiacus J-10-fl]
          Length = 398

 Score =  246 bits (628), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 118/238 (49%), Positives = 167/238 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ EM  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD+  GYKFSTYA WW
Sbjct: 159 ARHEMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWW 218

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA++R++ADQS  +R+PVH+ + ++++    R+++  + REPT  E+A  L M  E +
Sbjct: 219 IKQALSRALADQSRLVRLPVHLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEKL 278

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             V +  ++P+SL TP+G+E  S L DFI D +A+   D+A    +R+  T  L  L+ R
Sbjct: 279 ATVRRTAQDPVSLATPVGEEANSTLADFIPDPHALDADDAAASGIVRQQITAALDQLSER 338

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E RVL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 339 ERRVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 396



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/122 (33%), Positives = 68/122 (55%), Gaps = 15/122 (12%)

Query: 32  KKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDD--LEDEEG 88
           + +I   RQ+G+VT E++   +P PDE S E ++   A L+  G+ V +GD+  L+DE  
Sbjct: 21  QALIAQGRQQGFVTFEDIQRLVPNPDE-SIELIDSIYAALAEAGVPVQEGDETALDDE-- 77

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                     +S +++ L    + +D    D VR+YLRE+G + LL+ E E  +A+ IE 
Sbjct: 78  ---------PSSPATMDLDLDDELSDALLSDSVRLYLREIGQVPLLTAEQEKRLAQLIEQ 128

Query: 149 GR 150
           G+
Sbjct: 129 GQ 130


>gi|257056437|ref|YP_003134269.1| RNA polymerase sigma factor SigB [Saccharomonospora viridis DSM
           43017]
 gi|256586309|gb|ACU97442.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 342

 Score =  246 bits (628), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 115/247 (46%), Positives = 175/247 (70%), Gaps = 4/247 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR GE     AK  +++ANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  
Sbjct: 98  VVRDGEE----AKNHLLQANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTK 153

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR +ADQ  TIR+PVH+ ++++K+ R  R +  ++ RE T EE+
Sbjct: 154 GFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQVNKLARIKRDLHQRLGREATHEEL 213

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +  +  + V  +L   ++P+SL+ P+G ++ + LGDFIED  A +  +S I   L++ 
Sbjct: 214 AAESGIAEKKVADLLDHARDPVSLDMPVGADEDAPLGDFIEDSEAANAENSVISTLLQDD 273

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RVLA+L  REE V+R+R+G+      TL+++GK F ++RER+RQIE + + KL+H  R
Sbjct: 274 LRRVLATLDDREEHVIRLRYGLDDGQPRTLDQIGKHFSLSRERVRQIEREVMAKLRHGER 333

Query: 673 SKKLRSF 679
           + KLR++
Sbjct: 334 ADKLRAY 340


>gi|219847152|ref|YP_002461585.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219541411|gb|ACL23149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 398

 Score =  246 bits (628), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 117/238 (49%), Positives = 168/238 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++M  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD   GYKFSTYA WW
Sbjct: 159 ARQKMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHTKGYKFSTYATWW 218

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA++R++ADQS  +R+PVH+ + ++++    R+++  + REPT  E+A  L M  E +
Sbjct: 219 IKQALSRALADQSRLVRLPVHLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEKL 278

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ +  ++P+SL TP+G+E  S L DFI D +A+   D+A    LR+     L  L+ R
Sbjct: 279 RELRRTAQDPVSLATPVGEEADSTLADFIPDPHALDADDAAASGMLRQQIAAALDQLSER 338

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E RVL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 339 ERRVLELRYGLADGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 396



 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/120 (35%), Positives = 64/120 (53%), Gaps = 9/120 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +I   RQ+G+VT E++   +P  E S EQ++   A L+  G+ V DGD  E   G E 
Sbjct: 21  QALIAQGRQQGFVTFEDIQRLVPNLEESVEQIDSIYAALAEAGVPVHDGD--EPVSGDE- 77

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                 S + S   L    + +D    D VR+YLRE+G + LL+ E E  +A+ IE G+A
Sbjct: 78  ------SLTPSVTDLDLDDELSDALLSDSVRLYLREIGQVPLLTAEQEKQLAQMIERGQA 131


>gi|300784474|ref|YP_003764765.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
 gi|299793988|gb|ADJ44363.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
          Length = 343

 Score =  246 bits (628), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 114/264 (43%), Positives = 183/264 (69%), Gaps = 6/264 (2%)

Query: 418 VETGISISEFRH--IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++TG +++  R   + ++VR G     +AK  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 82  LDTGENLTTKRRTELAALVRDGH----VAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 137

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQ  TIR+PVH+ ++++K+ R 
Sbjct: 138 EGNLGLIRAVEKFDYSKGFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQVNKLARI 197

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ R+ T EE+A +  +P   +  +L  +++P+SL+ P+G E+ + LGDFIED 
Sbjct: 198 KRDLHQQLGRDATHEELAAESGIPAHKISDLLDHSRDPVSLDMPVGTEEDAPLGDFIEDS 257

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A     + I   L++   RVLA+L  RE+ V+R+R+G+      TL+++GK F ++RER
Sbjct: 258 EATDAESAVISGLLQDDLRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSRER 317

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R+ +LR++
Sbjct: 318 VRQIEREVMSKLRQGERADRLRAY 341


>gi|251733363|emb|CAR82431.1| RNA polymerase sigma factor [Agrobacterium rhizogenes]
 gi|251733369|emb|CAR82434.1| RNA polymerase sigma factor [Rhizobium tropici]
 gi|251733371|emb|CAR82435.1| RNA polymerase sigma factor [Rhizobium tropici]
          Length = 202

 Score =  246 bits (627), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 145/178 (81%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++LVK V SLSLNQ+RID LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDELVKSVKSLSLNQNRIDALVEQLYDINKRLVQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++QG ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISISEFR IV 
Sbjct: 83  QYQGAELDPNWMKSIGNLAARGWKEFAKSENTTIRDIRQEIQNLATETGISISEFRRIVH 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|238063483|ref|ZP_04608192.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237885294|gb|EEP74122.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 334

 Score =  246 bits (627), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 114/242 (47%), Positives = 174/242 (71%), Gaps = 1/242 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 91  AEGRTAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM ++++++VR  R ++  + REPT  E+A+ + +
Sbjct: 151 YATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRARRELAVTLGREPTVAEVARAMDV 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL 617
           P   V +++   +EP+SL+  +G++  S LGDF+   + A  P  +A+   LR     VL
Sbjct: 211 PEFQVIELISYDREPVSLDQAVGEDGESALGDFVAAVDPAAEPGATAVDGELRNEVRIVL 270

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL+ P R+++L 
Sbjct: 271 ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRAPERAQRLE 330

Query: 678 SF 679
           ++
Sbjct: 331 AY 332


>gi|108803721|ref|YP_643658.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764964|gb|ABG03846.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 365

 Score =  245 bits (626), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 121/238 (50%), Positives = 167/238 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +  ANLRLV+S+AKKY  RG+  LDLIQEGNIGLM+A EKFD+  GYKFSTYA WW
Sbjct: 128 AKAHLTRANLRLVVSIAKKYAGRGVSLLDLIQEGNIGLMRAVEKFDYRKGYKFSTYATWW 187

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IAD+  TIR+PVHM +KI+K  R  R +++++ R+PT EE+A+++ + VE V
Sbjct: 188 IRQAVTRAIADKGRTIRVPVHMVEKINKYYRVQRTLASELNRDPTDEEVAREMGVEVEEV 247

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ ++++  ISLETP+G++ +S LGDFI D+ + SP D A  + L+      L  L  R
Sbjct: 248 ERIRQVSRRSISLETPVGEDHSSELGDFIADEESESPHDLAKSSLLKARMREALNGLPER 307

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  VL  RFG+      TLEEVG++F VTRERIRQI+  A+ K+K    +  LR  LD
Sbjct: 308 ERMVLEYRFGLTGGQPKTLEEVGERFDVTRERIRQIQLTALAKIKSSPHAASLRDLLD 365



 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 66/150 (44%), Gaps = 8/150 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++ +  ++ G +   E+   L   ++S+E+++    +L   G+ +VD   L +    E+
Sbjct: 14  RELFEAGQEAGVLESGEVLDLLQEVDLSTEEIQQVYGLLREQGVEIVDSGFLSESPEEEE 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                              D   R T D V+MYL E+G   LLS+  E+ +AKRIE G  
Sbjct: 74  EDVQVVEEVLEG-------DLKSRYTGDAVQMYLDEIGKTPLLSKAQEVYLAKRIERGDR 126

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLL 181
              A L  + L    + I +     G +LL
Sbjct: 127 RAKAHLTRANLRL-VVSIAKKYAGRGVSLL 155


>gi|269837876|ref|YP_003320104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269787139|gb|ACZ39282.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 341

 Score =  245 bits (626), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 117/258 (45%), Positives = 175/258 (67%), Gaps = 3/258 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  ++ I+    ++  E   +   + +G+ EA    +  V +NLRLV+S+AK+Y  RGL
Sbjct: 72  IRLYLRDIAQAPLLTAEEEVELAKRIEEGDVEAL---QRFVRSNLRLVVSIAKRYVGRGL 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGN+GL++A +K+DW  GY+FSTYA WW++QAITR+IADQ  TIR+PVHM D 
Sbjct: 129 SLLDLIQEGNLGLIRAVQKYDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPVHMIDS 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I +  RT  +++ ++ R P  EE+A+ +++P E V + ++  +  ISLE PIG+++   L
Sbjct: 189 ITRYRRTVMQLTQELGRPPRAEEVAEAMSVPPEKVEQFIRAAQRTISLEKPIGEDEEGTL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I D+ A SP + A++  L+     VL  LTPRE  VL++RFG+G  + HTL EVG+Q
Sbjct: 249 ADLIADEVARSPEEEAVETLLQRDVAEVLEELTPRERLVLQLRFGLGNGSPHTLSEVGQQ 308

Query: 649 FCVTRERIRQIEAKAIRK 666
             ++RER+RQIE++A+RK
Sbjct: 309 LDISRERVRQIESEALRK 326



 Score = 38.1 bits (87), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/31 (51%), Positives = 23/31 (74%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           DP+R+YLR++    LL+ E E+ +AKRIE G
Sbjct: 70  DPIRLYLRDIAQAPLLTAEEEVELAKRIEEG 100


>gi|302525710|ref|ZP_07278052.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434605|gb|EFL06421.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 317

 Score =  245 bits (626), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 111/248 (44%), Positives = 175/248 (70%), Gaps = 4/248 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++VR G     +AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 72  ALVRDGH----VAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYS 127

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQ  TIR+PVH+ ++++K+ R  R +  ++ R+ T EE
Sbjct: 128 KGFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQVNKLARIRRDLHQQLGRDATHEE 187

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ +  +PV  +  +L  +++P+SL+ P+G E+ + LGDFIED  A     + I   L++
Sbjct: 188 LSAESGIPVHKISDLLDQSRDPVSLDMPVGTEEDAPLGDFIEDSEATDAESAVISGLLQD 247

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              RVLA+L  RE+ V+R+R+G+      TL+++GK F ++RER+RQIE + + KL+   
Sbjct: 248 DLRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSRERVRQIEREVMAKLRQGE 307

Query: 672 RSKKLRSF 679
           R+ +LR++
Sbjct: 308 RADRLRAY 315


>gi|251733373|emb|CAR82436.1| RNA polymerase sigma factor [Sinorhizobium arboris LMG 14919]
 gi|251733375|emb|CAR82437.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733377|emb|CAR82438.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733393|emb|CAR82446.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733395|emb|CAR82447.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733397|emb|CAR82448.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733399|emb|CAR82449.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733401|emb|CAR82450.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733403|emb|CAR82451.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
          Length = 202

 Score =  245 bits (625), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 119/178 (66%), Positives = 144/178 (80%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+  NEG LLRLA+SYG+KR+ FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLTQNEGRLLRLAESYGVKREAFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|298244164|ref|ZP_06967970.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551645|gb|EFH85510.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 316

 Score =  245 bits (625), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/281 (44%), Positives = 185/281 (65%), Gaps = 6/281 (2%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            + DS+     EI  I + + +S S    +      GE EA   +  ++EANLRLV+S+A
Sbjct: 42  AQSDSLRLYLREISRIPLLSAVSES---RLAERAENGEKEA---RNHLIEANLRLVVSIA 95

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  +GL   DLI EGNIGL++A  KFD+  G++FSTYA WW+KQAITR+I + +  +R
Sbjct: 96  KKYVGQGLSLEDLIGEGNIGLIRAVTKFDYRKGFRFSTYATWWIKQAITRAILEGTRVVR 155

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PV++ +++ +V RT R++  ++ REPTPE I ++L M  E V ++L   ++  SL+ P+
Sbjct: 156 LPVYIMEEVMRVKRTTRQLYQELGREPTPEIIGERLGMTAERVSELLIWAEKVFSLDAPL 215

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            +E+ + LGD IED     P++   Q  LRE   +VL  LT RE +V+ +RFG+  + DH
Sbjct: 216 SEEEENTLGDIIEDVRERGPMEITDQQLLREEIRKVLGQLTVRERQVIELRFGLIDDHDH 275

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVGK+  VTRER+RQIE +AIRKL+HP  S+ L+ +LD
Sbjct: 276 TLEEVGKKLKVTRERVRQIEERAIRKLRHPQASRILKDYLD 316


>gi|301320481|gb|ADK69124.1| putative RNA polymerase sigma factor RpoD [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 506

 Score =  244 bits (623), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 181/299 (60%), Gaps = 60/299 (20%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E+NL+LVISVA+K+ NRGL F DLI+EGNIGLMKA +KF++  G+KFSTYA WW
Sbjct: 207 GRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWW 266

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP  +EIA ++   + G 
Sbjct: 267 IRQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNADEIANRVGEGITGD 326

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V ++ K++ EP+SLE P GDED +H GDF+EDK+ VSP +   +  L+E   +V   + 
Sbjct: 327 KVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMP 386

Query: 622 PREERVLRMRFGI------------------------------GMNTDHTLEEV------ 645
           PREE+V+RMR+GI                               ++ D  +E+V      
Sbjct: 387 PREEKVIRMRYGIVPTRLRTLLRLTQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNQ 446

Query: 646 ------------------GKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                             GK+  VTRERIRQIEAK IRKLK PS + K    L+ F  G
Sbjct: 447 IINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|197294657|ref|YP_001799198.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853984|emb|CAM11947.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 476

 Score =  244 bits (623), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 127/281 (45%), Positives = 190/281 (67%), Gaps = 21/281 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           + K RN+      E  +S  E + + S +     +A+ AK  +VE+N RLV+S+AK+Y  
Sbjct: 207 LTKFRNQ------EIDLSDQEVKQLESQI----IQANQAKDVLVESNYRLVVSIAKRYIG 256

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG+ FLDLIQEGN+GLM+A +KFD+  G + STYA +WV Q +TR+IADQ+ TIRIPVH+
Sbjct: 257 RGVLFLDLIQEGNMGLMRAVDKFDYQKGLRLSTYATYWVIQGVTRAIADQARTIRIPVHI 316

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--E 583
            + I+K+    R+++ ++K++PT EE+A+K+ +P + +R +  I K+PISLE P  +  E
Sbjct: 317 VETINKMSLCTRKLTQELKKKPTIEELAEKMNIPADKLRSIQYIEKKPISLEVPPAENKE 376

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-----ASLTPREERVLRMRFGIGMNT 638
           D + LGDFI D N +SP +      ++E T ++L      +LT REE+VL+MR+G     
Sbjct: 377 DETSLGDFISDPNVLSPHEYM----MKEVTQKLLDEVLENTLTEREEKVLKMRYGFLDGK 432

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            +TLEE+G  F VTRERIRQIE+KA+R+L+ P++  KL+S 
Sbjct: 433 VYTLEEIGNLFGVTRERIRQIESKALRRLRTPAKQSKLKSL 473


>gi|15827487|ref|NP_301750.1| RNA polymerase sigma factor SigB [Mycobacterium leprae TN]
 gi|221229964|ref|YP_002503380.1| RNA polymerase sigma factor SigB [Mycobacterium leprae Br4923]
 gi|699187|gb|AAA62952.1| u1764a [Mycobacterium leprae]
 gi|13093037|emb|CAC31395.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933071|emb|CAR71109.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 319

 Score =  244 bits (623), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 115/233 (49%), Positives = 173/233 (74%), Gaps = 2/233 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QA
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A +  +P+E +  +L
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEELAAESGIPIEKINDLL 205

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREER 626
           + +++P+SL+ P+G E+ + LGDFIED  A+S  ++A+ A L  T  R VLA+L  RE +
Sbjct: 206 EHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-ENAVIAELLHTDIRSVLATLDEREHQ 264

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           V+R+RFG+      TL+++GK F ++RER+RQIE   + KL++  R+ +LRS+
Sbjct: 265 VIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCKLRNGERADRLRSY 317


>gi|251733359|emb|CAR82429.1| RNA polymerase sigma factor [Rhizobium leguminosarum]
          Length = 202

 Score =  244 bits (623), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 120/178 (67%), Positives = 145/178 (81%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+RID LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRIDALVEQLYDINKRLVSNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++QG ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISISEFR IV 
Sbjct: 83  QYQGAELDPNWMKSIGNLAARGWKEFARGENTTIRDIRQEIQNLATETGISISEFRRIVH 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|251733387|emb|CAR82443.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733389|emb|CAR82444.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733391|emb|CAR82445.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
          Length = 202

 Score =  244 bits (623), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 118/178 (66%), Positives = 144/178 (80%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+  NEG LLRLA+SYG++R+ FLE
Sbjct: 23  RYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLTQNEGRLLRLAESYGVRREAFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|18477825|emb|CAC83730.1| sigma factor [Rhodococcus fascians]
          Length = 323

 Score =  244 bits (622), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 115/258 (44%), Positives = 181/258 (70%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  + R++  +VR G    S A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 68  LSAVKKRNLAIIVRDG----SAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 123

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 124 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 183

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T EE++ +  + VE +  +L  +++P+SL+ P+G ++ + LGDFIED  A S  
Sbjct: 184 QLGREATDEELSSESGIAVEKIADLLDHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAE 243

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ I   L      VL +L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE 
Sbjct: 244 NAVIAGLLHSDVRVVLGTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIER 303

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL+   R++KLRS+
Sbjct: 304 EVMVKLRQGDRAEKLRSY 321


>gi|42561001|ref|NP_975452.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492498|emb|CAE77094.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
          Length = 522

 Score =  244 bits (622), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 181/299 (60%), Gaps = 60/299 (20%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E+NL+LVISVA+K+ NRGL F DLI+EGNIGLMKA +KF++  G+KFSTYA WW
Sbjct: 223 GRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWW 282

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP  +EIA ++   + G 
Sbjct: 283 IRQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNADEIANRVGEGITGD 342

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V ++ K++ EP+SLE P GDED +H GDF+EDK+ VSP +   +  L+E   +V   + 
Sbjct: 343 KVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPNEYTEKKILKEVMDKVFEDMP 402

Query: 622 PREERVLRMRFGI------------------------------GMNTDHTLEEV------ 645
           PREE+V+RMR+GI                               ++ D  +E+V      
Sbjct: 403 PREEKVIRMRYGIVPTRLRTLLRLTQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNQ 462

Query: 646 ------------------GKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                             GK+  VTRERIRQIEAK IRKLK PS + K    L+ F  G
Sbjct: 463 IINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 521


>gi|331703466|ref|YP_004400153.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802021|emb|CBW54175.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 506

 Score =  244 bits (622), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 181/299 (60%), Gaps = 60/299 (20%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E+NL+LVISVA+K+ NRGL F DLI+EGNIGLMKA +KF++  G+KFSTYA WW
Sbjct: 207 GRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWW 266

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP  +EIA ++   + G 
Sbjct: 267 IRQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNADEIANRVGEGITGD 326

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V ++ K++ EP+SLE P GDED +H GDF+EDK+ VSP +   +  L+E   +V   + 
Sbjct: 327 KVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMP 386

Query: 622 PREERVLRMRFGI------------------------------GMNTDHTLEEV------ 645
           PREE+V+RMR+GI                               ++ D  +E+V      
Sbjct: 387 PREEKVIRMRYGIVPTRLRTLLRLAQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQ 446

Query: 646 ------------------GKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                             GK+  VTRERIRQIEAK IRKLK PS + K    L+ F  G
Sbjct: 447 IINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|256383860|gb|ACU78430.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384691|gb|ACU79260.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455677|gb|ADH21912.1| RNA polymerase sigma-A factor [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 506

 Score =  244 bits (622), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 181/299 (60%), Gaps = 60/299 (20%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E+NL+LVISVA+K+ NRGL F DLI+EGNIGLMKA +KF++  G+KFSTYA WW
Sbjct: 207 GRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWW 266

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP  +EIA ++   + G 
Sbjct: 267 IRQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNADEIANRVGEGITGD 326

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V ++ K++ EP+SLE P GDED +H GDF+EDK+ VSP +   +  L+E   +V   + 
Sbjct: 327 KVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMP 386

Query: 622 PREERVLRMRFGI------------------------------GMNTDHTLEEV------ 645
           PREE+V+RMR+GI                               ++ D  +E+V      
Sbjct: 387 PREEKVIRMRYGIVPTRLRTLLRLAQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQ 446

Query: 646 ------------------GKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                             GK+  VTRERIRQIEAK IRKLK PS + K    L+ F  G
Sbjct: 447 IINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|305681000|ref|ZP_07403807.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
 gi|305659205|gb|EFM48705.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
          Length = 365

 Score =  244 bits (622), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 113/241 (46%), Positives = 176/241 (73%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 124 EGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 183

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE+A++  + 
Sbjct: 184 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEELAEESGID 243

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    +SA+ A+LR +  R V+ 
Sbjct: 244 ESKIELLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEAADA-ESAVVASLRHSDIRDVIG 302

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+RMR+G+      TL+++G+QF ++RER+RQIE + +RKL+   R++KLR 
Sbjct: 303 TLEDREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMRKLRDGQRAEKLRE 362

Query: 679 F 679
           +
Sbjct: 363 Y 363



 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 52/97 (53%), Gaps = 8/97 (8%)

Query: 75  INVVDGDD----LEDEEGSEDSLDLASSASNSSVFL---QKRKDSADRSTDDPVRMYLRE 127
           ++VV GD+    ++D+ G++D LD     S   + +    +R  + D  + D VR+YL  
Sbjct: 15  LDVVMGDEPTDLVDDDPGADDILDPTDEESAFDLAVDRGSRRGQNNDNPSADLVRVYLNG 74

Query: 128 MGSIELLSREGEIAIAKRIEAG-RAMMMASLCESPLT 163
           +G   LL+ E E+ +A+ IE G  A  + +  + PLT
Sbjct: 75  IGKTALLTAEDEVHLAQTIEVGLYAEYLLTDSDEPLT 111


>gi|167745452|ref|ZP_02417579.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|317472996|ref|ZP_07932299.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|167655173|gb|EDR99302.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|316899541|gb|EFV21552.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 347

 Score =  243 bits (621), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 116/250 (46%), Positives = 178/250 (71%), Gaps = 1/250 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++ E  +  AK +M+ +NLRLV+SVAK+Y    G+  LDLIQEGNIGLMKA +KFD+ 
Sbjct: 97  LAKEIEAGSQSAKDKMINSNLRLVVSVAKRYAAGSGMALLDLIQEGNIGLMKAVDKFDYR 156

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYAMWW++Q++TR+IADQ+ TIRIPVHM++K+ KV   AR+   +  REP  +E
Sbjct: 157 RGYKFSTYAMWWIRQSVTRAIADQARTIRIPVHMKEKMGKVSGAARKFLEENGREPNADE 216

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ + +  + + +++++  + +SL++P+G+E+ + L +F+ D++      +A Q  L E
Sbjct: 217 LAELMEISRDQMDEIMRLYSDTVSLDSPVGEEEDAMLMNFVADESMPEQYQTAEQGILSE 276

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L+ LT RE+ +LR+RFG   N   TLEEVG+++ VTRERIRQIE KA+RKLK   
Sbjct: 277 QINEILSELTEREQTILRLRFGFVENRIWTLEEVGREYHVTRERIRQIEGKALRKLKMKK 336

Query: 672 RSKKLRSFLD 681
            +K LR++++
Sbjct: 337 ETKSLRAYIE 346


>gi|225021249|ref|ZP_03710441.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945982|gb|EEG27191.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 391

 Score =  243 bits (621), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 113/241 (46%), Positives = 176/241 (73%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 150 EGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 209

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE+A++  + 
Sbjct: 210 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEELAEESGID 269

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    +SA+ A+LR +  R V+ 
Sbjct: 270 ESKIELLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEAADA-ESAVVASLRHSDIRDVIG 328

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+RMR+G+      TL+++G+QF ++RER+RQIE + +RKL+   R++KLR 
Sbjct: 329 TLEDREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMRKLRDGQRAEKLRE 388

Query: 679 F 679
           +
Sbjct: 389 Y 389



 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 52/97 (53%), Gaps = 8/97 (8%)

Query: 75  INVVDGDD----LEDEEGSEDSLDLASSASNSSVFL---QKRKDSADRSTDDPVRMYLRE 127
           ++VV GD+    ++D+ G++D LD     S   + +    +R  + D  + D VR+YL  
Sbjct: 41  LDVVMGDEPTDLVDDDPGADDILDPTDEESAFDLAVDRGSRRGQNNDNPSADLVRVYLNG 100

Query: 128 MGSIELLSREGEIAIAKRIEAG-RAMMMASLCESPLT 163
           +G   LL+ E E+ +A+ IE G  A  + +  + PLT
Sbjct: 101 IGKTALLTAEDEVHLAQTIEVGLYAEYLLTDSDEPLT 137


>gi|206895369|ref|YP_002247042.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206737986|gb|ACI17064.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 360

 Score =  243 bits (621), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 121/250 (48%), Positives = 172/250 (68%), Gaps = 1/250 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + ++ E   + A++E+++ NLRLVIS+AKKYTN+GL F++LIQEGNIGL+KA EKFDW  
Sbjct: 109 LAQRIEKNDAAAREELIKRNLRLVISIAKKYTNKGLSFMELIQEGNIGLIKAVEKFDWRK 168

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW+KQAITR++ADQS  IR PVHM +  H+  +    + N++ REPT +E+
Sbjct: 169 GYKFSTYATWWIKQAITRALADQSRLIRRPVHMVEAYHQFQKKLNELYNQLGREPTVQEL 228

Query: 553 AKKLAMPVEGVRKVLKITK-EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A+ L    + V  + +++  EP SL+  IGD+D S + DF+ D    +      +   R 
Sbjct: 229 AEALGFSEDKVLALKQMSNPEPQSLDATIGDQDDSRVQDFVPDTGEGAADKYFWEEERRR 288

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL++L  RE  ++ MR+G+    +HTLEEVG  F +TRER+RQIE KA+RKL+HP+
Sbjct: 289 VLEEVLSTLNKREREIIEMRYGLVDGVEHTLEEVGASFNITRERVRQIETKALRKLRHPT 348

Query: 672 RSKKLRSFLD 681
           R +KLR +LD
Sbjct: 349 RIRKLREYLD 358


>gi|269925789|ref|YP_003322412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789449|gb|ACZ41590.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 363

 Score =  243 bits (621), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 123/279 (44%), Positives = 189/279 (67%), Gaps = 8/279 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D++     EI S+ +   ++  E   +   + KG+ EA    +  V ANLRLV+S+AK+Y
Sbjct: 90  DAVKIYLREIGSVPL---LTPKEEVELAKRIEKGDTEAL---QRFVLANLRLVVSIAKRY 143

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RGL  LDLIQEGNIGLM+A +KFDW  G++FSTYA WW++QAITR+I D+S  IR+P 
Sbjct: 144 VGRGLPLLDLIQEGNIGLMRAVQKFDWRKGHRFSTYATWWIRQAITRAIGDKSREIRLPA 203

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ ++++++ R  +++S  + REPTPEEIA+K     E VR++L   ++P+SL+TP+G+E
Sbjct: 204 HINEELNRINRIRQQLSQTVNREPTPEEIAEKAGTSPERVRELLGYLQQPVSLDTPVGEE 263

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTL 642
             S LG+F+ D  A +P + A    L+    RVL   LTPRE+RVL++R+G+G    ++L
Sbjct: 264 ADSTLGEFVPDVRA-NPEEEATDEVLKTEMDRVLDEVLTPREKRVLQLRYGLGDGHTYSL 322

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+VG++  VTRER+RQ+E +A+ KL+     +KL  +++
Sbjct: 323 EKVGRELGVTRERVRQLEKQALEKLRRGPAIRKLAEYME 361



 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/122 (29%), Positives = 62/122 (50%), Gaps = 11/122 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +++ K++I L + +G+VT  ++   +P  E + +        L   GI V+  +  E E 
Sbjct: 10  EEAIKRLITLGKSKGHVTERDVFELVPEAEDNIDCFNQVSDALIREGIEVLPEETTEAEA 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G E+ LD       +  +L            D V++YLRE+GS+ LL+ + E+ +AKRIE
Sbjct: 70  GPEEDLDQTLEELENDGYLT-----------DAVKIYLREIGSVPLLTPKEEVELAKRIE 118

Query: 148 AG 149
            G
Sbjct: 119 KG 120


>gi|269126637|ref|YP_003300007.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311595|gb|ACY97969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 444

 Score =  243 bits (621), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 113/236 (47%), Positives = 168/236 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLV+SVAKKY++RGL  LD++QEGN+GL++A EKFD+  G+KFSTYAMWW
Sbjct: 207 AKSHMLEANLRLVVSVAKKYSDRGLSLLDVVQEGNLGLIRAVEKFDYTKGFKFSTYAMWW 266

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  AD + TIR+PVH+ + + K+ R  R M  ++ REPTPEE+A +L      V
Sbjct: 267 IRQAIQRGFADSARTIRLPVHVLEMLSKLSRVERDMHQRLGREPTPEELAAELDKSPAQV 326

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++L+ +++PISL++ IG++  + +GD IED ++    +   +  + +   R L+ L+PR
Sbjct: 327 RELLRTSRQPISLDSTIGEDGETRIGDLIEDIDSPEASEMVDRQLMADQLRRSLSILSPR 386

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE ++ MRFG+   T  TL+E+GK   +TRERIRQ+E +++ KL+HPS +  L  F
Sbjct: 387 EEMIMSMRFGLYDGTPRTLDEIGKHLGLTRERIRQLEKESLSKLRHPSNATPLLDF 442


>gi|317506478|ref|ZP_07964279.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
 gi|316255239|gb|EFV14508.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
          Length = 348

 Score =  243 bits (621), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 112/264 (42%), Positives = 183/264 (69%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I+   G++    R + ++VR G      A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 87  INTSEGLTPQRRRELKAVVRDGRA----ARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQ 142

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 143 EGNLGLIRAMEKFDYSKGFKFSTYATWWIRQAITRGVADQSRTIRLPVHLVEQVNKLSRI 202

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T EE++++  +P   +  +L  +++P+SL+ P+G ++ + LGDFIED 
Sbjct: 203 KRELHQQLGREATSEELSRETGIPEHRIADLLDHSRDPVSLDMPVGADEEAPLGDFIEDS 262

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              S  ++ I   L      VLA+L+  E++V+R+R+G+      TL+++GK F ++RER
Sbjct: 263 EGASAENAVIAGFLHRDVRSVLATLSDSEQQVIRLRYGLDDGQPRTLDQIGKIFSLSRER 322

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL++  R+++LRS+
Sbjct: 323 VRQIEREVMVKLRNGDRAERLRSY 346


>gi|221633247|ref|YP_002522472.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
 gi|221156052|gb|ACM05179.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
          Length = 340

 Score =  243 bits (620), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 114/241 (47%), Positives = 169/241 (70%), Gaps = 3/241 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA    +  V +NLRLV+S+AK+Y  RGL  LDLIQEGNIGLM+A EKFDW  G
Sbjct: 95  IKEGDTEA---LQRFVRSNLRLVVSIAKRYVGRGLSLLDLIQEGNIGLMRAVEKFDWRRG 151

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y+FSTYA WW++QAITR+IADQ  TIR+PVHM D I +  RT  +++ ++ R+PTPEEIA
Sbjct: 152 YRFSTYATWWIRQAITRAIADQGRTIRLPVHMTDSITRYHRTTTQLAQELGRQPTPEEIA 211

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + +++  E + ++++  +  +SL+ P+ +ED + LGD I D+ A SP + A ++ +R   
Sbjct: 212 EAMSVQPEKIAQIVRAAQRAVSLDQPLSEEDETSLGDLIADELAQSPEELAEESLMRRDI 271

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L  LTPRE  VL++R+G+      TL EVG    ++RER+RQIE +A+RKL+  +R 
Sbjct: 272 AEILEMLTPRERLVLQLRYGLSDGEPRTLAEVGDLLGISRERVRQIENEALRKLRRIARE 331

Query: 674 K 674
           +
Sbjct: 332 R 332


>gi|302035824|ref|YP_003796146.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
 gi|300603888|emb|CBK40220.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
          Length = 419

 Score =  243 bits (620), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 118/245 (48%), Positives = 166/245 (67%), Gaps = 1/245 (0%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E    +S ++        AK E+V  NLRLV++VAK YT RGL  LDL+QEGNIGLMKAA
Sbjct: 166 ELDAALSQLKASRITLETAKDELVRCNLRLVVNVAKHYTGRGLTLLDLVQEGNIGLMKAA 225

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           E++    G+KFSTYA WW++Q ITRS+ADQS TIRIPVH  +  ++++R +RR+  ++ R
Sbjct: 226 ERYQHRKGFKFSTYATWWIRQGITRSLADQSRTIRIPVHQTEASNRILRASRRLVQQLGR 285

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P  EE+A  + M  + + + ++  +EP++LE  +GD  T  LG+ + D+ AV P     
Sbjct: 286 QPRLEEVASTMRMRPDRLHETIQAFQEPVALEHRVGDGGT-ELGELLPDQQAVPPDAHVN 344

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L     R+L +LTPRE+ V+R+RFGIG +   TLE+VG+   VTRERIRQIEAKA++
Sbjct: 345 RTELTREMDRILGTLTPREQTVIRLRFGIGEDQARTLEQVGQHLSVTRERIRQIEAKALK 404

Query: 666 KLKHP 670
           KLK P
Sbjct: 405 KLKTP 409


>gi|156742838|ref|YP_001432967.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234166|gb|ABU58949.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 351

 Score =  243 bits (619), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 116/243 (47%), Positives = 167/243 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  A++ +++ANLRLV+SVAKKY    L F+DL+QEGNIGLM+A EKFD   G +FST
Sbjct: 109 VQAEEARRRLIQANLRLVVSVAKKYIGGPLSFMDLVQEGNIGLMRAVEKFDASKGNRFST 168

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+QS  IR+PVH+ D I +V R ARR+   ++REPT +EIA+ + M
Sbjct: 169 YATWWIRQAITRAIAEQSRLIRLPVHLSDVIAQVRRVARRLEQSLEREPTIKEIAEAVGM 228

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P   V+ +L+ + +PISLE PI ++    +G+ + D  A +P++ A Q  L+    + L 
Sbjct: 229 PERKVKMLLQASAQPISLEQPITNDGEGQIGELLADDGADAPMEIATQHMLQRDLEQALM 288

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE  VLR+R+G+      TLEE+G  F +TRER RQIEA A+R L+ P  S +L++
Sbjct: 289 DLPDRERAVLRLRYGLTDGRRRTLEEIGSAFGITRERTRQIEADALRLLRRPGVSARLQA 348

Query: 679 FLD 681
           +L+
Sbjct: 349 YLE 351



 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 7/56 (12%)

Query: 102 SSVFLQ-------KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           S VF Q        ++ S+  + DD  +MYLRE+G + LLS   E+A+A  I AGR
Sbjct: 29  SDVFWQTDFADVVAQRASSGETLDDSTQMYLREIGQVSLLSAAEEVALANDISAGR 84


>gi|163848723|ref|YP_001636767.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526666|ref|YP_002571137.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670012|gb|ABY36378.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450545|gb|ACM54811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 360

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 111/238 (46%), Positives = 166/238 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+SVAKKY    + F+DL+QEGNIGLM+A EKFD+  G +FSTYA WW
Sbjct: 123 ARRRLIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWW 182

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IA+QS  IR+PVH+ + I  + R   R+  +++REPT EE+A  L M V  V
Sbjct: 183 IRQAVTRAIAEQSRLIRLPVHLSESIVHLRRAIYRLEQELEREPTAEELAHALNMSVRKV 242

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++++ + +PISLE P+ +E    + + + D+   SP++ A Q  L    T  L  L  R
Sbjct: 243 KRLIRASTQPISLEQPLNNEQEGRVSETLADETVASPMEIAEQKMLHAELTAALNELPER 302

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E ++L++R+G+      TLEEVG  F +TRER RQIEA+A+R+L+HPS  ++L S+LD
Sbjct: 303 ERKILQLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHPSVGQRLHSYLD 360


>gi|313665390|ref|YP_004047261.1| RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
 gi|312949647|gb|ADR24243.1| putative RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
          Length = 498

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 133/302 (44%), Positives = 182/302 (60%), Gaps = 66/302 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E+NL+LVISVA+K+ NRGL F DLI+EGNIGLMKA +KF++  G+KFSTYA WW
Sbjct: 199 GRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWW 258

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP  EEIA ++    EG+
Sbjct: 259 IRQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNAEEIANRVG---EGI 315

Query: 564 R--KVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              KV++I K   EP+SLE P GDED +H GDF+EDK+ VSP +   +  L+E   +V  
Sbjct: 316 TSDKVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPNEYTEKEILKEVMDKVFE 375

Query: 619 SLTPREERVLRMRFGI------------------------------GMNTDHTLEEV--- 645
            + PREE+V+RMR+GI                               ++ D  +E+V   
Sbjct: 376 DMPPREEKVIRMRYGIVPTRLRTLLRLAQECNDSSAKELKQAIEELDIHLDTPIEKVRKF 435

Query: 646 ---------------------GKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFL 680
                                GK+  VTRERIRQIEAK IRKLK PS + K    L+ F 
Sbjct: 436 NNEIINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSLNNKSGKTLKEFY 495

Query: 681 DG 682
            G
Sbjct: 496 KG 497


>gi|72161811|ref|YP_289468.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915543|gb|AAZ55445.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 438

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 111/236 (47%), Positives = 167/236 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLV+SVAKKY++RG+  LD++QEGN+GL++A EKFD+  GYKFSTYAMWW
Sbjct: 201 AKAHMLEANLRLVVSVAKKYSDRGMPLLDVVQEGNLGLIRAVEKFDYAKGYKFSTYAMWW 260

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  AD + TIR+PVH+ + + K+ R  R M   + REPTP+E+A++L      +
Sbjct: 261 IRQAIQRGFADSARTIRLPVHVLELLSKLSRLERDMHQTLGREPTPDELAQELGKTPAQI 320

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L+IT++PISL++ IG++  + +GD IED +A    +   +  + +   R L  L PR
Sbjct: 321 EELLRITRQPISLDSTIGEDGETRIGDLIEDVDASEASEVVDRQLMADQLRRALDDLEPR 380

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E  ++ +RFG+      TL+E+GK   +TRERIRQ+E +++ KL+HPSR+++L  F
Sbjct: 381 EATIMSLRFGLFDGRPRTLDEIGKHLGLTRERIRQLEKQSLSKLRHPSRARQLLDF 436



 Score = 44.3 bits (103), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 35/141 (24%), Positives = 64/141 (45%), Gaps = 24/141 (17%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I   R RG+V++ EL        ++  +    +  LS+ G+ + + +D   + G +D+
Sbjct: 24  ELIARGRARGHVSLSELRTAFSEAGITPAEGRSLLRELSDTGVRIANNEDTPVDPGDDDT 83

Query: 93  LD--LASSASNSSVFLQ--------KRKDSADRSTDDP--------------VRMYLREM 128
           L+  L +++  S             +   +   +TD P              V  YL+ +
Sbjct: 84  LEAVLETTSKGSGRRRSAKKRSRKKQPAQAGAETTDAPEADLDDHSPALGDSVHTYLKAI 143

Query: 129 GSIELLSREGEIAIAKRIEAG 149
           G  ELL+ E E+ +AKRIEAG
Sbjct: 144 GRRELLTAEQEVELAKRIEAG 164


>gi|302344687|ref|YP_003809216.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301641300|gb|ADK86622.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 363

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 117/242 (48%), Positives = 166/242 (68%), Gaps = 1/242 (0%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +V  + +   E   A  EMVEANLRL +S+AKKYT RGL F DLIQEGNIGLMKA  ++
Sbjct: 111 QLVRDINRARREVEAAVSEMVEANLRLAVSIAKKYTFRGLSFADLIQEGNIGLMKAVNRY 170

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GY+FST+A WW++Q I+R+I DQ+ TIRIP+H+ +   K  R    +  ++ REPT
Sbjct: 171 DYRTGYRFSTFASWWIRQTISRAIYDQARTIRIPIHLLELRSKYFRVYYGLLKELGREPT 230

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P+E+A+K+ +  + V++++ +T +  SLETP+G ED   LGDFIE+K+A  P     +  
Sbjct: 231 PKEVAEKVGITEDKVKEIINLTLDSTSLETPVG-EDGDELGDFIENKDAEDPFSMVGETE 289

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +       L SL  RE R+L MRFG+G   +HTLEEVG+ F ++RER+RQIE KA+++L+
Sbjct: 290 MHGHLEAALDSLDGRERRILEMRFGLGDEDEHTLEEVGQVFGLSRERVRQIEKKALQRLR 349

Query: 669 HP 670
           HP
Sbjct: 350 HP 351


>gi|305644360|gb|ADM53781.1| RNA polymerase sigma factor [Aeromonas hydrophila]
 gi|305644362|gb|ADM53782.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 115/176 (65%), Positives = 139/176 (78%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     
Sbjct: 61  LQEMGREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAL 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P D+A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRER
Sbjct: 121 PADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 176


>gi|318058872|ref|ZP_07977595.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|333027299|ref|ZP_08455363.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
 gi|332747151|gb|EGJ77592.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
          Length = 338

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 119/238 (50%), Positives = 171/238 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 101 AKRRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 160

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVR  R +  +   EP+  E+A  L +  E V
Sbjct: 161 IRQAMSRALADQARTIRVPVHVVELINRVVRVQRGLLQERGHEPSHAEVAALLGLTKERV 220

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++ +EP+SL TP+G ED   LGD IED +A SP +SA    LR     VL++L  R
Sbjct: 221 GEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVLSTLGER 280

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+  + + +LR +LD
Sbjct: 281 ERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHAFADQLRGYLD 338


>gi|251733365|emb|CAR82432.1| RNA polymerase sigma factor [Agrobacterium rubi]
          Length = 202

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 119/178 (66%), Positives = 146/178 (82%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+  V SLSLNQ+R+D LVEQLYDISKR+M NEG+LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDQLITAVKSLSLNQNRVDSLVEQLYDISKRLMQNEGKLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E ++I  IR EI++++ ETGISI+EFR IVS
Sbjct: 83  QYHGAELDPNWMKSIANLAAKGWKEFAREENNTIRDIRLEIQNLAQETGISIAEFRRIVS 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|303279757|ref|XP_003059171.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459007|gb|EEH56303.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 587

 Score =  242 bits (617), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 118/237 (49%), Positives = 169/237 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M++ANLRLV+S+AK+Y N+ + F DLIQEG +GL++ AEKFD+  GYKFSTYA WW
Sbjct: 333 AKNQMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKFDFKRGYKFSTYAHWW 392

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TRSI+DQS TIR+PVH+ + I ++ +  R++  K  R+PT EEIA+ + M VE +
Sbjct: 393 IRQAVTRSISDQSRTIRLPVHLFEIISRMSKVERQLVMKYGRDPTTEEIAEVMDMTVEKI 452

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++ K +  PISL   + D+D+  + + + D +A  P D+  +  L+E    VL +L+PR
Sbjct: 453 NQIQKASLVPISLSQSVNDDDSRTVEETLVDDHAEHPDDATGKVLLKEDLENVLNTLSPR 512

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKL+ PSR+  LR +L
Sbjct: 513 ERDVLRLRYGMDDGRVKTLEEIGNVFSVTRERIRQIEAKALRKLRQPSRNGILREYL 569


>gi|83319868|ref|YP_424476.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|83283754|gb|ABC01686.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 505

 Score =  242 bits (617), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 133/302 (44%), Positives = 181/302 (59%), Gaps = 66/302 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E+NL+LVISVA+K+ NRGL F DLI+EGNIGLMKA +KF++  G+KFSTYA WW
Sbjct: 207 GRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWW 266

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + QAITR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP  EEIA ++    EG+
Sbjct: 267 ISQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNAEEIANRVG---EGI 323

Query: 564 R--KVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              KV++I K   EP+SLE P GDED +H GDF+EDK+ VSP +   +  L+E   +V  
Sbjct: 324 TSDKVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPSEYTEKEILKEVMDKVFE 383

Query: 619 SLTPREERVLRMRFGI------------------------------GMNTDHTLEEV--- 645
            + PREE+V+RMR+GI                               ++ D  +E+V   
Sbjct: 384 DMPPREEKVIRMRYGIVPTRLRTLLRLAQECNDTNAKELKQAIEELDIHLDTPIEKVRKF 443

Query: 646 ---------------------GKQFCVTRERIRQIEAKAIRKLKHPSRSKK----LRSFL 680
                                GK+  VTRERIRQIEAK IRKLK PS + K    L+ F 
Sbjct: 444 NNEIINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFY 503

Query: 681 DG 682
            G
Sbjct: 504 KG 505


>gi|256375630|ref|YP_003099290.1| RNA polymerase sigma factor SigB [Actinosynnema mirum DSM 43827]
 gi|255919933|gb|ACU35444.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 330

 Score =  242 bits (617), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 111/236 (47%), Positives = 168/236 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 93  AKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 152

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQ  TIR+PVH+ ++++K+ R  R +  ++ RE T EE+A +  +    V
Sbjct: 153 IRQAITRGMADQGRTIRLPVHLVEQVNKLARIKRDLHQQLGREATNEELAAESGLSPTKV 212

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L   ++P+SL+ P+G E+ + LGDFIED +A     + I   L++   RVLA+L  R
Sbjct: 213 SDLLDHARDPVSLDMPVGAEEDAPLGDFIEDSDATDAESAVISGLLQDDLRRVLATLEQR 272

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+ V+R+R+G+      TL+++GKQF ++RER+RQIE + + KL+   R+ KLR++
Sbjct: 273 EQAVIRLRYGLEDGQPRTLDQIGKQFGLSRERVRQIEREVMSKLRQGERAAKLRAY 328


>gi|256371066|ref|YP_003108890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256007650|gb|ACU53217.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 337

 Score =  241 bits (616), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 117/250 (46%), Positives = 165/250 (66%), Gaps = 4/250 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR+GE     AK+  ++ANLRLV+S+AK+Y   GL  LDLIQEGN+GL+ A EKFDW  
Sbjct: 92  LVRQGEE----AKRAFIQANLRLVVSIAKRYQASGLPLLDLIQEGNMGLIHAVEKFDWRK 147

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR IA+   TIR+PVH  D + +V R   ++  ++ R PT  E+
Sbjct: 148 GFKFSTYATWWIRQAITRGIANTGRTIRLPVHAGDSLSRVQRAQVQLEVRLGRAPTVREL 207

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A ++ +P + + + L+   EP+SL  P+ D+  + LGD +ED  + +P D A +  L   
Sbjct: 208 AAEVDLPYDKLVEALRFRAEPVSLSEPLRDDGDAELGDVVEDSQSATPFDVAAEHLLPSE 267

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +R+LA L  RE  +LR+R+G+      TLEEVG+ F +TRERIRQIEA+A+ KL+HPS 
Sbjct: 268 VSRLLAPLDGREREILRLRYGLDRGEPRTLEEVGEYFHLTRERIRQIEARAMSKLRHPSA 327

Query: 673 SKKLRSFLDG 682
               R  L G
Sbjct: 328 DIGARDLLTG 337


>gi|318080032|ref|ZP_07987364.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 340

 Score =  241 bits (616), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 119/238 (50%), Positives = 171/238 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 103 AKRRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 162

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVR  R +  +   EP+  E+A  L +  E V
Sbjct: 163 IRQAMSRALADQARTIRVPVHVVELINRVVRVQRGLLQERGHEPSHAEVAALLGLTKERV 222

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++ +EP+SL TP+G ED   LGD IED +A SP +SA    LR     VL++L  R
Sbjct: 223 GEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVLSTLGER 282

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+  + + +LR +LD
Sbjct: 283 ERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHAFADQLRGYLD 340


>gi|309791990|ref|ZP_07686468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225984|gb|EFO79734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 396

 Score =  241 bits (616), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 115/238 (48%), Positives = 170/238 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++M  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD   G+KFSTYA WW
Sbjct: 157 ARQQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHDKGFKFSTYATWW 216

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA++R++ADQS  +R+PVH+ + ++++    R+++ ++ REP   E+A +L+M  E +
Sbjct: 217 IKQALSRALADQSRLVRLPVHLGETLNRIQAARRQLTQRLGREPYDSELADELSMSQEKL 276

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ +  ++P+SL TP+G+E  S L DFI D +A+   D+A    LR+     L  LT R
Sbjct: 277 RELRRTAQDPVSLATPVGEEADSTLADFIPDPHALDADDAAASGMLRQQIATALDQLTER 336

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 337 ERKVLELRYGLTDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 394



 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 42/120 (35%), Positives = 63/120 (52%), Gaps = 16/120 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD---LEDEEGSE 90
           +I L RQRG+VT EE+ A +P  E + + ++   A L+   I V D  D   LE+E  S 
Sbjct: 22  LIALGRQRGFVTFEEIQALVPNPEEAIDAIDSLYATLAEASIPVRDSADDATLEEETIST 81

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +DL    S++ +              D VR+YLRE+G + LL+ E E  +A+ IE G+
Sbjct: 82  VVIDLDEGLSDALL-------------GDSVRLYLREIGQVPLLTAEQEKRLAQTIERGQ 128


>gi|298244288|ref|ZP_06968094.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551769|gb|EFH85634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 334

 Score =  241 bits (616), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 110/236 (46%), Positives = 166/236 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++EANLRLV+S+AK+Y+N+GL  LDLIQEGNIGLM+A +KFD+  G++FSTYA WW
Sbjct: 96  ARQRLIEANLRLVVSIAKRYSNQGLPLLDLIQEGNIGLMRATQKFDYKRGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI+R+IA+ S +I IPVH+ + I+K+ R  RR+  +   EP PE++A +L +P E V
Sbjct: 156 IRQAISRAIAEHSRSIHIPVHVVELIYKIKRITRRLYQEQGVEPLPEQVAAELGLPRERV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L ++++PISL+ P+ D++  HL D +ED +    +D   Q   RE   + +  L PR
Sbjct: 216 VELLNVSEQPISLDAPMADDEEYHLSDMLEDTSMAPTIDVVSQQLQREHIEQAMTVLNPR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E  ++ MR+G+      +L+EV   F +TRERIRQIE KA+RKL++P R + LR  
Sbjct: 276 ERTIIEMRYGLKDGHSLSLDEVSVLFHLTRERIRQIEVKALRKLRYPERYEGLRDL 331


>gi|149183340|ref|ZP_01861778.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
 gi|148848937|gb|EDL63149.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
          Length = 330

 Score =  241 bits (615), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 119/221 (53%), Positives = 161/221 (72%), Gaps = 3/221 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + + +G+ EA   K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 113 VRMYLKEIGRVDLLSAQEEISLANRIEEGDEEA---KRRLAEANLRLVVSIAKRYVGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 170 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 230 INKLIRVQRQLLQDLGREPSPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           GDFIED  A SP + A    L+E    VL +LT REE VLR
Sbjct: 290 GDFIEDAEAQSPSEHAAYELLKEQLEDVLDTLTDREENVLR 330



 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 72/135 (53%), Gaps = 4/135 (2%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++L ++RG +T E++   L   E+ S+ M++    L   G+ +++    E+EE
Sbjct: 24  DQVKEQLMELGKKRGVLTYEDIAEKLANFELESDTMDEFYEQLGEQGVEIIN----ENEE 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + ++   + A +    L           +DPVRMYL+E+G ++LLS + EI++A RIE
Sbjct: 80  DDDPNIQQLNKADDEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAQEEISLANRIE 139

Query: 148 AGRAMMMASLCESPL 162
            G       L E+ L
Sbjct: 140 EGDEEAKRRLAEANL 154


>gi|271965471|ref|YP_003339667.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270508646|gb|ACZ86924.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 452

 Score =  241 bits (615), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 111/233 (47%), Positives = 166/233 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLV+SVAKKYT+RG+  LD++QEGN+GL++A EKFD+  GYKFSTYAMWW
Sbjct: 215 AKDHMLEANLRLVVSVAKKYTDRGMALLDVVQEGNLGLIRAVEKFDYTKGYKFSTYAMWW 274

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  AD + TIR+PVH+ + + K+ R  R M  ++ REPTPEE+A +L    + +
Sbjct: 275 IRQAIQRGFADSARTIRLPVHVLEMLSKLSRVERDMHQRLGREPTPEELAVELDKTPDQI 334

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L+ +++PISL   IG++  + +GD IED ++    +   +  L E    VL +L+PR
Sbjct: 335 EELLRTSRQPISLNATIGEDGETTIGDLIEDVDSPEASEVVDRQLLGEQLRGVLGNLSPR 394

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E +++ +RFG+     HTL+E+GK   +TRERIRQ+E +++ KL+HPS ++ L
Sbjct: 395 EAKIMALRFGLVDGKPHTLDEIGKHLGLTRERIRQLEKESLSKLRHPSNTRPL 447


>gi|206889845|ref|YP_002248858.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741783|gb|ACI20840.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 427

 Score =  241 bits (614), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 130/290 (44%), Positives = 189/290 (65%), Gaps = 7/290 (2%)

Query: 394 EWKNFVACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           E  N    E+D   K R EI   +++   TG++  EF      ++K   E + AK +M+E
Sbjct: 139 ELTNMFVEELD---KFRREIIKGENLQPITGMTNEEFLDHFMTIKKIFNEFTEAKNKMIE 195

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NL+LV+S+AKKYT RGL   DLIQEGNIGLMKA EKF++  G+KFSTY+ WW++Q+I R
Sbjct: 196 SNLKLVVSIAKKYTGRGLNLEDLIQEGNIGLMKAVEKFEYKKGFKFSTYSTWWIRQSINR 255

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IA+ S TIRIPVH+ D I K+ +  R +    + EP  EEI+  L +P + +   L I+
Sbjct: 256 AIAEHSKTIRIPVHVIDNICKINKIYRELYQNSENEPDIEEISLNLNIPSDKIADFLAIS 315

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEP+S++  + D+D S L +FIED N+ +P + A+  +L+    +V + L+ RE+ +L  
Sbjct: 316 KEPVSIDMSLRDDD-SLLKEFIEDMNSPNPYEEALHDDLKHLIEKVFSLLSKREKEILMR 374

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+GI      +L+EVGK+F V+RERIRQIE +A+RKLK   R K LR F+
Sbjct: 375 RYGINEEKPKSLDEVGKEFSVSRERIRQIELRAMRKLKRLCRLKWLREFI 424


>gi|37522577|ref|NP_925954.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35213578|dbj|BAC90949.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 305

 Score =  241 bits (614), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 113/250 (45%), Positives = 172/250 (68%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +  ++  G  EA  AK+ +V ANLRLV+S+AKKY NRG+ FLDLIQEG IGLM+AAEKFD
Sbjct: 53  LAQVIATGGSEAEAAKRRLVRANLRLVVSIAKKYLNRGVPFLDLIQEGAIGLMRAAEKFD 112

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++Q ITR+IA QS T+R+PVHM +K+++V R  R+++ ++ R+PT 
Sbjct: 113 FERGFKFSTYAYWWIRQGITRAIASQSRTVRLPVHMVEKLNQVKRVRRQLTQELARKPTK 172

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            E+A+ L + ++ + ++L   +  +SL   +G E+ + L   IED + +SP +      L
Sbjct: 173 PEMAEALELDIDKLDEILDAGRRTLSLHVKVGKEEDTELLQLIEDSDTISPSEVLDHNLL 232

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E    +L  LTPRE  ++ +RFG+     +TL ++G+ + ++RER+RQI+AKA+RKL+H
Sbjct: 233 VEQIESLLHLLTPRERDIIELRFGLADGNSYTLADIGEMYNLSRERVRQIQAKAMRKLRH 292

Query: 670 PSRSKKLRSF 679
           P R   LR +
Sbjct: 293 PRRQVLLRDW 302


>gi|295839080|ref|ZP_06826013.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295827312|gb|EDY44634.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 360

 Score =  241 bits (614), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 119/238 (50%), Positives = 169/238 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 123 AKRRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 182

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++R++ADQ+ TIR+PVH+ + I++VVR  R +  +   EP   E+A  L +  E V
Sbjct: 183 IRQAMSRALADQARTIRVPVHVVELINRVVRARRTLLQERGHEPCDAEVAAVLGLTPERV 242

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +VL++ +EP+SL TP+G ED   LGD IED +A SP +SA    LR     VL++L  R
Sbjct: 243 GEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVLSTLGER 302

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+    + +LR +LD
Sbjct: 303 ERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHVFADQLRGYLD 360


>gi|269925873|ref|YP_003322496.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789533|gb|ACZ41674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 326

 Score =  241 bits (614), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 115/238 (48%), Positives = 169/238 (71%), Gaps = 2/238 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++ M+E NLRLV+S+A++Y  RGL   DLI+EGN+GLM+AA+KFD+  GY+FSTYA W
Sbjct: 90  MARRRMIECNLRLVVSIARRYAGRGLPLSDLIEEGNLGLMRAADKFDYRRGYRFSTYATW 149

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QA+TR++A QS  +R+PVH+ + +H + + + R+S ++ REPT EEIA +L +  E 
Sbjct: 150 WIRQAVTRALASQSRVVRLPVHVTELMHNITKVSHRLSQELGREPTSEEIAAELNITPER 209

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+V+K ++ P+SLE P G++    + + IED N  SP D   +  LRE    +L  LT 
Sbjct: 210 VREVVKASQYPMSLEQPYGEDGDGTVEEIIEDPNIESPADQVSRDILREQILALLDDLTD 269

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +VL +R+G+  N  +TLEEVGK   VTRERIRQIE +A+ KL+    ++ LRSF+
Sbjct: 270 RERQVLDLRYGLTGNHSYTLEEVGKVLGVTRERIRQIEKEALSKLR--PHAESLRSFM 325


>gi|326384463|ref|ZP_08206143.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326196808|gb|EGD54002.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 332

 Score =  240 bits (613), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 113/248 (45%), Positives = 180/248 (72%), Gaps = 6/248 (2%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR+GE     A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  
Sbjct: 88  LVREGEQ----ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYAK 143

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAI+R +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE T EE+
Sbjct: 144 GYKFSTYATWWIRQAISRGMADQSRTIRLPVHLVEQVNKLARIRRELHQQLGREATDEEL 203

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +  +P E +  ++  +++P+SL+ P+G+++ + LGDFIED  A S  ++ + ANL  +
Sbjct: 204 ALESGIPAEKIADLMDHSRDPVSLDMPVGNDEEAPLGDFIEDAEATSA-ETVVIANLLHS 262

Query: 613 TTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             R VL++L  RE +V+ MR+G+      TL+++G+ F ++RER+RQIE + + KL+   
Sbjct: 263 DIRSVLSTLDEREMQVITMRYGLDDGQPRTLDQIGRAFGLSRERVRQIEREVMGKLRQGD 322

Query: 672 RSKKLRSF 679
           R++KLR++
Sbjct: 323 RAEKLRAY 330


>gi|164687939|ref|ZP_02211967.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
 gi|164602352|gb|EDQ95817.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
          Length = 294

 Score =  240 bits (613), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 125/251 (49%), Positives = 170/251 (67%), Gaps = 2/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +K   E   AK++ + AN RLV+S+AKKY    +  LDLIQ GNIGL+KA EK+D+
Sbjct: 43  VELAKKVNEEIPEAKEDFINANYRLVVSIAKKYRKENVDILDLIQAGNIGLIKAVEKYDY 102

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW+KQ+ITR I D   TIRIPVH+  +I+ V R  + +SN ++REP+ E
Sbjct: 103 TKGYKFSTYATWWIKQSITRYIDDCENTIRIPVHLHQRINFVKRKKQELSNVLQREPSLE 162

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP--LDSAIQAN 608
           E+A    M V+ V ++LK  K  +SL+TPI +++ S L +FI      S   +    Q N
Sbjct: 163 ELADICDMDVDKVIEILKRDKNVVSLDTPIKEDEDSSLVEFIPSDANFSDVVMHEVEQHN 222

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    +L  L+ +E++VLRMRFG+  +   TLEE+GK F VTRERIRQIEAKAIRKL+
Sbjct: 223 LKEKINELLTGLSEQEQKVLRMRFGLDDDDPKTLEEIGKVFGVTRERIRQIEAKAIRKLR 282

Query: 669 HPSRSKKLRSF 679
           HPSR  +L++F
Sbjct: 283 HPSRLNQLKNF 293


>gi|300868700|ref|ZP_07113311.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
 gi|300333261|emb|CBN58503.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
          Length = 462

 Score =  240 bits (613), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 116/243 (47%), Positives = 169/243 (69%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FST
Sbjct: 217 TEGIQAKDHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFST 276

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R  + E+IA +L M
Sbjct: 277 YAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTASIEDIAAELGM 336

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               VR+VL      +SLET +G+E  + LGD ++D ++VSP +  ++  L     ++LA
Sbjct: 337 TAPQVREVLLRVPRSVSLETKVGNEKDTELGDLLDDADSVSPEELLMREALHRDLQQLLA 396

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE  V+ MRFG+G    ++L E+G+   ++RER+RQIEAKA++KL+ P R  ++R 
Sbjct: 397 DLTSRERDVILMRFGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRVRD 456

Query: 679 FLD 681
           +L+
Sbjct: 457 YLE 459



 Score = 39.3 bits (90), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 27/96 (28%), Positives = 52/96 (54%), Gaps = 7/96 (7%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED-EEGSEDSLDLASSASNSSVFLQKRKD 111
           +PP    +E   D      ++  +VV+GD  +  E+  ED +++    +       K  +
Sbjct: 43  MPPTSFYAEAEYDEQLQGHSLQPDVVEGDAEQAVEDLQEDEIEVLDGDTA------KFNN 96

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +A R T D VR+YL+E+G + LL R+ E++ A++++
Sbjct: 97  TASRRTTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQ 132


>gi|296269678|ref|YP_003652310.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296092465|gb|ADG88417.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 478

 Score =  240 bits (613), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 110/233 (47%), Positives = 170/233 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLV+SVAKKYT+RG+  LD++QEGN+GL++A EKFD+  GYKFSTYAMWW
Sbjct: 241 AKDHMLEANLRLVVSVAKKYTDRGMSLLDVVQEGNLGLIRAVEKFDYTKGYKFSTYAMWW 300

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  AD + TIR+PVH+ + + K+ R  R M  ++ REPTPEE+A +L    + +
Sbjct: 301 IRQAIQRGFADSARTIRLPVHVLEMLSKLSRVERDMHQRLGREPTPEELAVELDKTPDQI 360

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L+ +++PISL++ IG++  + +GD IED +++   +   +  L E    +L +L+PR
Sbjct: 361 EELLRTSRQPISLDSTIGEDGETCIGDLIEDVDSLEASEIVDRQLLAEQLKGMLDNLSPR 420

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E +++ +RFG+     HTL+E+GK+  +TRERIRQ+E +++ KL+HPS ++ L
Sbjct: 421 EAKIMSLRFGLVDGKPHTLDEIGKRLGLTRERIRQLEKESLSKLRHPSNARPL 473


>gi|331696792|ref|YP_004333031.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951481|gb|AEA25178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 348

 Score =  240 bits (613), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 109/236 (46%), Positives = 170/236 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 111 ARNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYAKGFKFSTYATWW 170

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQ+ TIR+PVH+ ++++K+ R  R M  ++ RE T  E+A++  +P E +
Sbjct: 171 IRQAITRGMADQARTIRLPVHLVEQVNKLARIKRDMHQRLGREATHAELAEESGLPEEKI 230

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L   ++P+SL+ P+G E+ + LGDFIED  A    ++ I   L +   RVLA+L  R
Sbjct: 231 ADLLDHARDPVSLDMPVGSEEEAPLGDFIEDAEAADAENTVISHLLHDDLRRVLATLDER 290

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+ V+RMR+G+      TL+++G++F ++RER+RQIE + + KL+   R+ +LR++
Sbjct: 291 EQNVIRMRYGLDDGQPCTLDQIGRRFGLSRERVRQIEREVMAKLRVGERADRLRAY 346


>gi|38233998|ref|NP_939765.1| RNA polymerase sigma factor SigB [Corynebacterium diphtheriae NCTC
           13129]
 gi|38605711|sp|P33118|RPSB_CORDI RecName: Full=RNA polymerase sigma factor sigB
 gi|38200260|emb|CAE49944.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 329

 Score =  240 bits (613), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 112/241 (46%), Positives = 177/241 (73%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 88  EGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTY 147

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE+A++  + 
Sbjct: 148 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEELAEESGIE 207

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    +SA+ A+LR +  R VL 
Sbjct: 208 ESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-ESAVVASLRHSDIRTVLD 266

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+R+R+G+      TL+++G+QF ++RER+RQIE + + KL+  +R++KLR+
Sbjct: 267 TLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMSKLRDGARAEKLRA 326

Query: 679 F 679
           +
Sbjct: 327 Y 327


>gi|86606677|ref|YP_475440.1| RNA polymerase sigma factor SigC [Synechococcus sp. JA-3-3Ab]
 gi|86555219|gb|ABD00177.1| RNA polymerase sigma-70 factor family [Synechococcus sp. JA-3-3Ab]
          Length = 364

 Score =  240 bits (612), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 128/313 (40%), Positives = 189/313 (60%), Gaps = 35/313 (11%)

Query: 371 LERHQGRELD-PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           L++  GRE     W + A  +PE  W N    ++  I +I                    
Sbjct: 84  LQKELGREPTLAEWAARANQYPE--WANLTPEKLQQIQRI-------------------- 121

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
                         AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD
Sbjct: 122 -----------GKRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFD 170

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R PT 
Sbjct: 171 PKKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKLSQEKGRTPTI 230

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E+IA +L M V  VR++L      +SLET +G +  + LGD +E  + +SP ++ ++  L
Sbjct: 231 EDIASELEMTVPQVRELLVRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEETMMREAL 289

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                ++LA LT RE  V+RMRFG+G    ++L E+G+   ++RER+RQIEAKA++KL+ 
Sbjct: 290 HRDLQQLLADLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQ 349

Query: 670 PSRSKKLRSFLDG 682
           P R  ++R +L+ 
Sbjct: 350 PKRRNRVRDYLEA 362



 Score = 37.7 bits (86), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 29/37 (78%), Gaps = 1/37 (2%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           + A RSTD  VR+YL+E+G + LL R+ E+A+A+R++
Sbjct: 37  EPARRSTD-LVRLYLQEIGRVPLLGRDEEVALAQRVQ 72


>gi|296393377|ref|YP_003658261.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180524|gb|ADG97430.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 377

 Score =  240 bits (612), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 109/252 (43%), Positives = 177/252 (70%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++ R G+     A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 128 RELKTVARDGQA----ARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQEGNLGLIRAMEK 183

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE 
Sbjct: 184 FDYAKGFKFSTYATWWIRQAITRGVADQSRTIRLPVHLVEQVNKLSRIKRELHQQLGREA 243

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE++++  +P   +  +L  +++P+SL+ P+G ++ + LGDFIED    S  ++ I  
Sbjct: 244 TSEELSRETGIPEHRIADLLDHSRDPVSLDMPVGADEEAPLGDFIEDSEGASAENAVIAG 303

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L   E++V+R+R+G+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 304 FLHRDVRTVLATLNEVEQQVIRLRYGLDDGQPRTLDQIGKVFSLSRERVRQIEREVMVKL 363

Query: 668 KHPSRSKKLRSF 679
           ++  R+++LRS+
Sbjct: 364 RNGDRAERLRSY 375


>gi|40353301|gb|AAR84414.1| essential primary sigma 70 factor [Frankia sp. ORS020607]
 gi|40353303|gb|AAR84415.1| essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|40353305|gb|AAR84416.1| essential primary sigma 70 factor [Frankia sp. CeD]
          Length = 217

 Score =  239 bits (611), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 110/192 (57%), Positives = 156/192 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 26  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 85

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 86  TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 145

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 146 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 205

Query: 618 ASLTPREERVLR 629
            +L+ RE++V++
Sbjct: 206 HTLSDREKKVIQ 217


>gi|213964561|ref|ZP_03392761.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
 gi|213952754|gb|EEB64136.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
          Length = 329

 Score =  239 bits (610), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 110/241 (45%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YTNRG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 88  EGKAARAHLLEANLRLVVSLAKRYTNRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 147

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE T EE+A++  +P
Sbjct: 148 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKISRIKRELYQQLGREATNEELAEESGIP 207

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    + A+ A+LR    R VL+
Sbjct: 208 EAKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDSEATDA-EEAVVASLRHHDVRKVLS 266

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+++R+G+      TL+++G+ F ++RER+RQIE + + KL+   R+ KLR 
Sbjct: 267 TLEIREQEVIKLRYGLDDGLPRTLDQIGRHFGLSRERVRQIEREVMSKLREGDRADKLRE 326

Query: 679 F 679
           +
Sbjct: 327 Y 327


>gi|296139548|ref|YP_003646791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027682|gb|ADG78452.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 330

 Score =  239 bits (610), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 112/258 (43%), Positives = 181/258 (70%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S+ R +  +VR G+     A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 75  LSASKKRDLAFIVRDGQA----ARQHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 130

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 131 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIRRELHQ 190

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T  E+A +  +P E +  ++  +++P+SL+ P+G ++ + LGDFIED  A S  
Sbjct: 191 QLGREATDAELAAESGIPAEKIADLMDHSRDPVSLDMPVGSDEEAPLGDFIEDAEAASAE 250

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            + I   +      VLA+L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE 
Sbjct: 251 SAVISTLMHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIER 310

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL++  R+ +LR++
Sbjct: 311 EVMSKLRNGERADRLRAY 328


>gi|40353311|gb|AAR84419.1| essential primary sigma 70 factor [Frankia sp. ACN14a]
          Length = 214

 Score =  239 bits (610), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 110/192 (57%), Positives = 156/192 (81%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 23  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 82

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ 
Sbjct: 83  TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMD 142

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 143 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 202

Query: 618 ASLTPREERVLR 629
            +L+ RE++V++
Sbjct: 203 HTLSDREKKVIQ 214


>gi|237785656|ref|YP_002906361.1| RNA polymerase sigma factor SigB [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237758568|gb|ACR17818.1| RNA polymerase sigma factor B [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 326

 Score =  239 bits (610), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 113/237 (47%), Positives = 173/237 (72%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 90  ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  +    +
Sbjct: 150 IRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIDESKI 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
             +LK +++P+SL+ P+G ++ + LGDFIED  A    + A+ A+LR +  R VLA+L  
Sbjct: 210 DLLLKQSRDPVSLDMPVGTDEEAPLGDFIEDSEATDA-EEAVVASLRHSDIRTVLATLEK 268

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           RE+ V+R+RFG+      TL+++G++F ++RER+RQIE + + KL+   R+ KLRS+
Sbjct: 269 REQDVIRLRFGLDDGVPRTLDQIGREFGLSRERVRQIEREVMAKLRKGERADKLRSY 325


>gi|305644358|gb|ADM53780.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  239 bits (610), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 138/176 (78%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     
Sbjct: 61  LQEMGREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAL 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P D+A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VT ER
Sbjct: 121 PADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTVER 176


>gi|300858635|ref|YP_003783618.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686089|gb|ADK29011.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206344|gb|ADL10686.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis C231]
 gi|302330901|gb|ADL21095.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276586|gb|ADO26485.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis I19]
          Length = 329

 Score =  239 bits (609), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 112/237 (47%), Positives = 174/237 (73%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 92  ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  +    +
Sbjct: 152 IRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIDESKI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
             +L+ +++P+SL+ P+G ++ + LGDFIED  A    +SA+ A+LR +  R VL +L  
Sbjct: 212 EILLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-ESAVVASLRHSDIRSVLDTLER 270

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           RE+ V+RMR+G+      TL+++G+QF ++RER+RQIE + + KL+  +R+ KLR++
Sbjct: 271 REQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMTKLRDGARADKLRAY 327


>gi|219847826|ref|YP_002462259.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542085|gb|ACL23823.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 361

 Score =  239 bits (609), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 109/238 (45%), Positives = 165/238 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+SVAKKY    + F+DL+QEGNIGLM+A EKFD+  G +FSTYA WW
Sbjct: 124 ARRRLIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWW 183

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IA+QS  IR+PVH+ + I  + R   R+  +++REPTPEE+A  L M +  V
Sbjct: 184 IRQAVTRAIAEQSRLIRLPVHLSESIVHLRRAIYRLEQELEREPTPEELAHALNMSLRKV 243

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L+ + +PISLE P+  +    + + + D+ A SP++ A Q  L+      L  L  R
Sbjct: 244 KRLLRASTQPISLEQPLNADQEGRVSETLADETAASPMEIAEQNMLQAELNAALNELPER 303

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E ++L++R+G+      TLEEVG  F +TRER RQIEA+A+R+L+HPS   +L  +L+
Sbjct: 304 ERKILQLRYGLLDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHPSVGNRLFGYLE 361


>gi|159896899|ref|YP_001543146.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889938|gb|ABX03018.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 391

 Score =  239 bits (609), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 109/238 (45%), Positives = 167/238 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            ++++ +ANLRLV+SVAKKY    + F+DLIQEGNIGLM+A EKFD+  G +FSTYA WW
Sbjct: 154 GRRKLTQANLRLVVSVAKKYIGNHMSFMDLIQEGNIGLMRAVEKFDYRKGNRFSTYATWW 213

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IA+QS TIR+PVH+ + I ++ R A ++   ++RE TP+E+A  L + +  V
Sbjct: 214 IRQAVTRAIAEQSRTIRLPVHLSESIAQMRRVAYQLEQALQREATPDELADALGVSLRKV 273

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L  + +P+SLE PIG E    +G+F+ D    +PL+ A +  L++     L+ L  R
Sbjct: 274 KRMLNASVQPVSLEQPIGKEGQGRVGEFLADDTDEAPLEQATRMMLQDELADALSQLPDR 333

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E ++L +R+G+      TLEEVG +F +TRER RQIEA+A+R L+ P+  + LR++LD
Sbjct: 334 ERQILLLRYGLADGKRRTLEEVGAEFGITRERTRQIEAEAMRHLRQPNVGQHLRAYLD 391



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 34/47 (72%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           V L+++K     + +D V+MYLRE+G +ELL+ E EI +AK+IE GR
Sbjct: 78  VNLRRKKTLYSEAVEDSVQMYLREIGEVELLTAEEEITLAKQIETGR 124


>gi|251733357|emb|CAR82428.1| RNA polymerase sigma factor [Rhizobium giardinii]
          Length = 202

 Score =  238 bits (608), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 117/178 (65%), Positives = 142/178 (79%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+  V SLSLNQ+R+D LVEQLYDI+KR++ NEG LLRLA+SYG+KRD FLE
Sbjct: 23  RYKELKDELITAVKSLSLNQNRVDSLVEQLYDINKRLVQNEGRLLRLAESYGVKRDSFLE 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           ++ G ELDP+W+    +     WK F   E   I  IR EI++++ ETGISISEFR IV 
Sbjct: 83  QYSGAELDPNWMKSIANLAAKGWKEFAKNENTMIRNIRAEIQNLATETGISISEFRRIVH 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|305644356|gb|ADM53779.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  238 bits (608), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 114/176 (64%), Positives = 138/176 (78%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     
Sbjct: 61  LQEMGREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAL 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P D+A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VT ER
Sbjct: 121 PADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTWER 176


>gi|297561520|ref|YP_003680494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845968|gb|ADH67988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 468

 Score =  238 bits (608), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 109/236 (46%), Positives = 165/236 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLV+SVAKKY++RG+  LD++QEGN+GL++A EKFD+  G+KFSTYAMWW
Sbjct: 231 AKSHMLEANLRLVVSVAKKYSDRGMSLLDVVQEGNLGLIRAVEKFDYTKGFKFSTYAMWW 290

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  AD + TIR+PVH+ + + KV R  R M   + REPTPEE+  +L      +
Sbjct: 291 IRQAIQRGFADSARTIRLPVHVLELLSKVSRLERDMHQALGREPTPEELGLELDKTPAQI 350

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++T++PISL++ IG++  + +GD IED +A    +   +  + +     L+ L PR
Sbjct: 351 EELLRVTRQPISLDSTIGEDGETRIGDLIEDVDASEASEVVDRQLMADQLRNALSDLEPR 410

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E  ++ +RFG+      TL+E+GK   +TRERIRQ+E +++ KL+HPSR+++L  F
Sbjct: 411 EATIMSLRFGLMDGRPRTLDEIGKHLGLTRERIRQLEKQSLSKLRHPSRAQQLLDF 466


>gi|68536171|ref|YP_250876.1| RNA polymerase sigma factor SigB [Corynebacterium jeikeium K411]
 gi|260578869|ref|ZP_05846775.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
 gi|68263770|emb|CAI37258.1| RNA polymerase sigma factor B [Corynebacterium jeikeium K411]
 gi|258603016|gb|EEW16287.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
          Length = 343

 Score =  238 bits (606), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 109/241 (45%), Positives = 175/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 102 EGKAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 161

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE++++  + 
Sbjct: 162 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEELSEESGIE 221

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +LK +++P+SL+ P+G ++ + LGDFIED +A    ++A+ A+LR +  R VL 
Sbjct: 222 ESKIEMLLKQSRDPVSLDMPVGSDEEAPLGDFIEDSDATDA-ETAVVASLRHSDVRAVLG 280

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+++R+G+      TL+++G++F ++RER+RQIE + + KL+   R+ KLR 
Sbjct: 281 TLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREGDRADKLRE 340

Query: 679 F 679
           +
Sbjct: 341 Y 341


>gi|300933022|ref|ZP_07148278.1| RNA polymerase sigma factor SigB [Corynebacterium resistens DSM
           45100]
          Length = 337

 Score =  238 bits (606), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 110/241 (45%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 96  EGKAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 155

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  + 
Sbjct: 156 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIE 215

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +LK +++P+SL+ P+G ++ + LGDFIED +A    ++A+ A+LR +  R VL 
Sbjct: 216 ESKIELLLKQSRDPVSLDMPVGSDEEAPLGDFIEDSDATDA-EAAVVASLRHSDVRAVLG 274

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+++R+G+      TL+++G++F ++RER+RQIE + + KL+   R+ KLR 
Sbjct: 275 TLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREGHRADKLRE 334

Query: 679 F 679
           +
Sbjct: 335 Y 335


>gi|308804840|ref|XP_003079732.1| SigA (ISS) [Ostreococcus tauri]
 gi|116058189|emb|CAL53378.1| SigA (ISS) [Ostreococcus tauri]
          Length = 525

 Score =  237 bits (605), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 120/251 (47%), Positives = 170/251 (67%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS +R+   +   AK EM++ANLRLV+S+AKKY N  + F DLIQEG +GL++ AEKFD+
Sbjct: 264 VSALRQRLHDGKAAKNEMIQANLRLVVSIAKKYANTNMSFQDLIQEGCVGLIRGAEKFDF 323

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QA+TRSI+DQS TIR+PVH+ + I ++ +  ++ +    R PT E
Sbjct: 324 QRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVHLFEIISRISKMEQKFALYNGRPPTLE 383

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANL 609
           EIA ++ M VE + ++ K  + P+SL   +G E+    + D + D NA  P   + ++ L
Sbjct: 384 EIASEMEMSVEKITQIKKAAQAPVSLAQTMGGENKGRTIEDTLIDANAEGPEKVSGKSLL 443

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E    VL +L PRE  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKLK 
Sbjct: 444 KEDLENVLNTLNPRERDVLRLRYGLDDGRVKTLEEIGTVFSVTRERIRQIEAKALRKLKQ 503

Query: 670 PSRSKKLRSFL 680
           PSR++ L+ + 
Sbjct: 504 PSRNQVLQEYF 514


>gi|319941926|ref|ZP_08016247.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
 gi|319804579|gb|EFW01449.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
          Length = 779

 Score =  237 bits (605), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 116/259 (44%), Positives = 172/259 (66%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +SE R +   ++  +     AK +M+EANLRLVIS+AK Y NRGL   DLIQEGN+GL
Sbjct: 519 LKLSEQRELGRAMKLAQTNLMQAKAKMIEANLRLVISIAKGYVNRGLAMTDLIQEGNLGL 578

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WWV+Q++TR++AD   TIRIPVHM +  +K+ R  ++   
Sbjct: 579 MKAVDKFEYRRGYKFSTYATWWVRQSVTRAVADFGNTIRIPVHMTESYNKLRRQKQKFLQ 638

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  R+PT +E+A+   +P++ V  + +  +   S++ PIGDE+ +   DF+       P 
Sbjct: 639 QHGRQPTEQELAELADLPLQKVNLLTQAMRGVESIDAPIGDEEDATKLDFVRGNERDDPG 698

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +    ++ +   + L  L PRE +VLR+R+GIG N DHTLEEVG+   +TRER+RQIE+
Sbjct: 699 VAFQDRSMIDCIQKSLNELNPREAQVLRLRYGIGTNQDHTLEEVGRTLGLTRERVRQIES 758

Query: 662 KAIRKLKHPSRSKKLRSFL 680
            AIRKL+ P  +++LR +L
Sbjct: 759 AAIRKLRTPDFTERLRDYL 777



 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 86/162 (53%), Gaps = 6/162 (3%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDE- 86
           + + ++++L R RG+VT+ ++N +LP   + +SE +++    L  +GI V +    ED+ 
Sbjct: 185 NGYGELVRLGRSRGWVTLADINDYLPESALRTSENLQEVTEQLGRLGIQVFEAPPDEDDI 244

Query: 87  --EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
              G            +++V L   +      + DP+R YLR +GS +LL+R GEI +AK
Sbjct: 245 LINGMGGDNSDDIDEDDAAVMLTPEESVG--LSKDPLRAYLRGVGSHKLLTRAGEIEVAK 302

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            IE     ++A++ E P+  + ++   + L D  T +  ++D
Sbjct: 303 SIEQFTIKLVATIVEYPIAVEEILRLGEALKDENTAVDTVVD 344


>gi|1519638|gb|AAB07552.1| SigB [Chloroflexus aurantiacus J-10-fl]
          Length = 346

 Score =  237 bits (604), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 110/233 (47%), Positives = 162/233 (69%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ANLRLV+SVAKKY    + F+DL+QEGNIGLM+A EKFD+  G +FSTYA WW++QA+
Sbjct: 114 IQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWIRQAV 173

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IA+QS  IR+PVH+ + I  + R   R+  +++REPT EE+A  L M V  V+++++
Sbjct: 174 TRAIAEQSRLIRLPVHLSESIVHLRRAIYRLEQELEREPTAEELAHALNMSVRKVKRLIR 233

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
            + +PISLE P+ +E    + + + D+   SP++ A Q  L    T  L  L  RE ++L
Sbjct: 234 ASTQPISLEQPLNNEQEGRVSETLADETVASPMEIAEQKMLHAELTAALNELPERERKIL 293

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++R+G+      TLEEVG  F +TRER RQIEA+A+R+L+HPS  ++L S+LD
Sbjct: 294 QLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHPSVGQRLHSYLD 346


>gi|145295824|ref|YP_001138645.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum R]
 gi|12958494|gb|AAK09322.1|AF320818_1 sigma factor SigB [[Brevibacterium] flavum]
 gi|140845744|dbj|BAF54743.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 331

 Score =  237 bits (604), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 109/237 (45%), Positives = 173/237 (72%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 94  ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  +    +
Sbjct: 154 IRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIEESKI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
             +L+ +++P+SL+ P+G ++ + LGDFIED  A    +SA+ A++R +  R VL +L P
Sbjct: 214 EMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-ESAVVASMRHSDIRAVLNTLEP 272

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+   R+ +LR +
Sbjct: 273 REQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMSKLRDGERASRLREY 329


>gi|319441590|ref|ZP_07990746.1| RNA polymerase sigma factor SigB [Corynebacterium variabile DSM
           44702]
          Length = 397

 Score =  237 bits (604), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 114/265 (43%), Positives = 186/265 (70%), Gaps = 8/265 (3%)

Query: 418 VETG--ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +ETG  ++ +  R +  + R+G      A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 136 LETGEKLTRARKRDLKILAREGRA----ARTHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 191

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 192 EGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRI 251

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R M   + RE T EE+A++  +    +  +LK +++P+SL+ P+G ++ + LGDFIED 
Sbjct: 252 KREMYQHLGREATNEELAEESGIDESKIETLLKQSRDPVSLDMPVGSDEEAPLGDFIEDS 311

Query: 596 NAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++    ++A+ A+LR +  R VL +L  RE+ V+++R+G+      TL+++G+ F ++RE
Sbjct: 312 DSTDA-EAAVVASLRHSDVRAVLDTLEEREQDVIKLRYGLDDGMPRTLDQIGRSFGLSRE 370

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE + + KL+   R++KLR +
Sbjct: 371 RVRQIEREVMAKLREGERAEKLREY 395


>gi|40353307|gb|AAR84417.1| essential primary sigma 70 factor [Frankia sp. ARgP5ag]
          Length = 217

 Score =  237 bits (604), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 109/192 (56%), Positives = 155/192 (80%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFS
Sbjct: 26  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 85

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PE IAK++ 
Sbjct: 86  TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEVIAKEMD 145

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL
Sbjct: 146 LTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVL 205

Query: 618 ASLTPREERVLR 629
            +L+ RE++V++
Sbjct: 206 HTLSDREKKVIQ 217


>gi|207723755|ref|YP_002254153.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206588959|emb|CAQ35921.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
          Length = 773

 Score =  237 bits (604), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 113/229 (49%), Positives = 162/229 (70%), Gaps = 3/229 (1%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 498 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQSRVVL 555

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 556 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 615

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 616 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 675

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
              EP P  +A+K+ MP + +RK++KI KEPIS++TPIGD+D SHLGDF
Sbjct: 676 TGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMKTPIGDDDDSHLGDF 724



 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V     D + L   +
Sbjct: 205 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLND 264

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 265 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 323

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 324 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 362


>gi|257064907|ref|YP_003144579.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256792560|gb|ACV23230.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 314

 Score =  236 bits (603), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 116/239 (48%), Positives = 172/239 (71%), Gaps = 4/239 (1%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R ++ + R G+     AK ++V ANLRLV+S+AKKY  RGL  LDL+QEGN+GL++A 
Sbjct: 66  ECRKLLRVQRAGQE----AKDKLVAANLRLVVSIAKKYRGRGLPLLDLVQEGNLGLIRAV 121

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+K STYA WW++QA+TR+IAD++ TIR+PVH+   ++KVVR    ++++++R
Sbjct: 122 EKFDYTKGFKLSTYATWWIRQAVTRAIADKARTIRLPVHVVGLMNKVVRVQHELADELER 181

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P+P EIA +L +  + V ++LK+  EP+SLETP+GD+ TS +GDFIED+N+    D+A 
Sbjct: 182 DPSPAEIADRLGISEQCVVELLKLGSEPLSLETPVGDDKTSEIGDFIEDRNSEDAFDAAA 241

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +A LR+     L+ L  RE +++ +RFGI      TL ++G Q  VTRERIRQIE+K +
Sbjct: 242 EAMLRDDVASALSRLPERERKIIELRFGIVDGEPRTLAQIGDQLGVTRERIRQIESKTL 300


>gi|37523928|ref|NP_927305.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35214934|dbj|BAC92300.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 344

 Score =  236 bits (603), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 112/239 (46%), Positives = 167/239 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++ ANLRLV+S+AKKY  R + FLDLIQEGNIGLM+A EKFD   GY+FSTYA WW
Sbjct: 106 AQRKLINANLRLVVSIAKKYIGRNVPFLDLIQEGNIGLMRATEKFDPEKGYRFSTYATWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+ITR+IA+Q+ TIR+P+HM +K+ KV R  R  + ++ R P+ +E+A +LA+ V+ +
Sbjct: 166 IRQSITRAIANQARTIRLPIHMVEKVRKVRREMRMATLELGRRPSEDELASRLAIKVKKL 225

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + +++++P+SL+ P+G E    LG+ IED  A  P D  +Q  L       +  L P 
Sbjct: 226 RTIQEVSRQPVSLDMPVGSEGDISLGEMIEDGTAERPFDELVQKALASELYAAMNVLKPV 285

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  VL +RFG+      TL EVG++F +TRERIRQIE++A+RKL+   R + L+ ++ G
Sbjct: 286 EREVLALRFGLKGEEGLTLREVGERFDLTRERIRQIESEALRKLRRSKRKQILQQYVGG 344


>gi|154506043|ref|ZP_02042781.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
 gi|153793542|gb|EDN75962.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
          Length = 297

 Score =  236 bits (603), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 111/225 (49%), Positives = 161/225 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++M EANLRLV++VAK Y  +G+QF+DLIQEGNIGLM+A EKFD+  G KFSTYA+WW
Sbjct: 66  ARRKMEEANLRLVVAVAKHYAGKGMQFMDLIQEGNIGLMRAVEKFDYTKGSKFSTYAVWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K+AI R++  QS  IR+PV +   ++K+ +T R+M   + RE   EEIAK+L M  E V
Sbjct: 126 IKEAILRALDSQSREIRVPVRVAQNMNKISKTERKMEQTLGREVAAEEIAKELHMTTEEV 185

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++    K P+SLETP+GDE+ S+L DFIED    +P ++      +E    +L++LT +
Sbjct: 186 ERMQSYIKNPVSLETPVGDEENSNLEDFIEDTQEPTPEEAVAALVQKEEVQEMLSTLTEK 245

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+++LR+R+G+     HTLEE G+   VTRERIRQ+E++A+ KL+
Sbjct: 246 EQKILRLRYGLEDGNVHTLEETGQILGVTRERIRQLESRALEKLR 290


>gi|86610159|ref|YP_478921.1| RNA polymerase sigma factor SigC [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558701|gb|ABD03658.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 366

 Score =  236 bits (602), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 189/315 (60%), Gaps = 39/315 (12%)

Query: 371 LERHQGRELDP---HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           L++  GR  DP    WV+ A  +PE  W      ++  I +I                  
Sbjct: 86  LQKELGR--DPTLAEWVAKANQYPE--WAQLTPEKLQQIQRI------------------ 123

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
                           AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EK
Sbjct: 124 -------------GKRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEK 170

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R P
Sbjct: 171 FDPKKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKLSQEKGRTP 230

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E+IA +L M    VR++L      +SLET +G +  + LGD +E  + +SP ++ ++ 
Sbjct: 231 TIEDIASELEMTPPQVRELLVRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEETMMRE 289

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L     ++L+ LT RE  V+RMRFG+G    ++L E+G+   ++RER+RQIEAKA++KL
Sbjct: 290 ALHRDLQQLLSDLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVRQIEAKALQKL 349

Query: 668 KHPSRSKKLRSFLDG 682
           + P R  ++R +L+ 
Sbjct: 350 RQPKRRNRVRDYLEA 364


>gi|193216688|ref|YP_001999930.1| RNA polymerase sigma factor [Mycoplasma arthritidis 158L3-1]
 gi|193002011|gb|ACF07226.1| RNA polymerase sigma-70 factor [Mycoplasma arthritidis 158L3-1]
          Length = 513

 Score =  236 bits (601), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 112/245 (45%), Positives = 167/245 (68%), Gaps = 9/245 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V+ NLRLVI+ AK+Y NRGL F+DLI EGN G+MKA  K+D+  G+KFSTYA WW
Sbjct: 260 ARDMLVKRNLRLVINNAKRYKNRGLSFIDLISEGNSGIMKAVSKYDYKKGFKFSTYATWW 319

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVE 561
           ++QAITR++ADQ+ TIR+PVHM + I+K+++  R +  +    PT EEIAKK       E
Sbjct: 320 IRQAITRAVADQARTIRVPVHMVETINKILKIERELQQEFGYPPTDEEIAKKFGGDFTAE 379

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASL 620
            VR + KI  +PISL+  IG E+ S   DF++D++ +SP D A Q  L      ++ +SL
Sbjct: 380 KVRYIRKINIDPISLDKNIGKEENSSFSDFVKDESVISPNDFASQQELAVILNEMINSSL 439

Query: 621 TPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            P ++ ++R R+G+G +        HTL+E+ K+  +++E++R++EAK +RKLKHP + K
Sbjct: 440 DPEDQALIRKRYGVGQDPSGVPYRPHTLDELAKELNISKEKVRKLEAKILRKLKHPQKRK 499

Query: 675 KLRSF 679
           KL+ F
Sbjct: 500 KLKEF 504


>gi|227833285|ref|YP_002834992.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184270|ref|ZP_06043691.1| RNA polymerase sigma factor SigB [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454301|gb|ACP33054.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
          Length = 331

 Score =  236 bits (601), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 108/241 (44%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 90  EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 149

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  + 
Sbjct: 150 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELAEESGIE 209

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R V+ 
Sbjct: 210 ESKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDA-ETAVVASMRHSDIRSVIG 268

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SL  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+  +R+ +LR 
Sbjct: 269 SLEEREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMAKLREGNRADRLRE 328

Query: 679 F 679
           +
Sbjct: 329 Y 329


>gi|284991968|ref|YP_003410522.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284065213|gb|ADB76151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 327

 Score =  236 bits (601), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 114/242 (47%), Positives = 173/242 (71%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK+ ++EANLRLV+SVAK+YT  G+ FLDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 85  ADGKAAKRHLLEANLRLVVSVAKRYTGHGMTFLDLIQEGNVGLIRAVEKFDYTKGFKFST 144

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++AD   TIR+PVH+ ++++KVVRT RR+  +++REPT EE+  +L M
Sbjct: 145 YATWWIRQAITRAMADSGRTIRLPVHLAEQVNKVVRTRRRIHQELEREPTAEELGLELDM 204

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E + ++L+ +++ +SL+  +G ++ S LGDFIED +A    D+     ++     VL+
Sbjct: 205 TPERITELLEYSRDLVSLDQTVGADEESRLGDFIEDADAAVAEDAVAFQMMKGDVRNVLS 264

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE  V+ +RFG+      TLE++GKQF ++RER+RQIE + + KL+ P R+  LR 
Sbjct: 265 TLEERERDVVVLRFGLDGGQPRTLEQIGKQFGLSRERVRQIERETMAKLRDPQRADALRD 324

Query: 679 FL 680
           +L
Sbjct: 325 YL 326


>gi|227504896|ref|ZP_03934945.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
 gi|227198489|gb|EEI78537.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
          Length = 337

 Score =  235 bits (600), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 112/259 (43%), Positives = 184/259 (71%), Gaps = 6/259 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+ +E R +  +VR+G+     A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 82  ITRAEKRDLKILVREGKK----ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 137

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  
Sbjct: 138 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQ 197

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + RE T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    
Sbjct: 198 SLGREATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDA- 256

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++A+ A +R +  R V+ +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE
Sbjct: 257 ETAVVAAMRHSDIRGVIETLEEREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIE 316

Query: 661 AKAIRKLKHPSRSKKLRSF 679
            + + KL+  +R+ +LR +
Sbjct: 317 REVMAKLRDGNRADRLREY 335


>gi|19553123|ref|NP_601125.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|62390759|ref|YP_226161.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|1149591|emb|CAA89988.1| SigB sigma factor [Corynebacterium glutamicum]
 gi|21324689|dbj|BAB99312.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigB)
           [Corynebacterium glutamicum ATCC 13032]
 gi|41326097|emb|CAF20260.1| RNA POLYMERASE SIGMA FACTOR [Corynebacterium glutamicum ATCC 13032]
          Length = 331

 Score =  235 bits (600), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 108/237 (45%), Positives = 173/237 (72%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 94  ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQS TIR+PVH+ ++++K+ R  R +   + RE T EE+A++  +    +
Sbjct: 154 IRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKRELYQHLGREATNEELAEESGIEESKI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
             +L+ +++P+SL+ P+G ++ + LGDFIED  A    +SA+ A++R +  R VL +L P
Sbjct: 214 EMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-ESAVVASMRHSDIRAVLNTLEP 272

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+   R+ +LR +
Sbjct: 273 REQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMSKLRDGERASRLREY 329


>gi|168009564|ref|XP_001757475.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691169|gb|EDQ77532.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 591

 Score =  235 bits (600), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 115/242 (47%), Positives = 164/242 (67%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   +K +MV +NLRLV+S+ K Y  RG+   DLIQEG++GL++ AEKFD   G+KFSTY
Sbjct: 346 EGRYSKDKMVNSNLRLVVSIVKNYQGRGMTLPDLIQEGSMGLIRGAEKFDPDKGFKFSTY 405

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QA+TR+IADQS  IR+P+H+ + I ++ +  + +  +  R+P  EE+A+ + M 
Sbjct: 406 AHWWIRQAVTRAIADQSRIIRLPIHLYEVISRINKAKKMLIQEHGRQPRDEEVAELVGMS 465

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE ++ ++K  K P S++  IG E    +G+ I DK+  SP D  I+  L++    VL +
Sbjct: 466 VEKLKFIVKSAKTPSSMDRLIGKEKDQSIGEMIADKDVESPEDDLIRQVLKQDVDGVLCT 525

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L PRE  VLR+RFG+      TLEE+G  F VTRERIRQIEAKA+RKL+ PSR+  LR +
Sbjct: 526 LNPREREVLRLRFGLDDGQSRTLEEIGTLFKVTRERIRQIEAKAMRKLRQPSRNGVLREY 585

Query: 680 LD 681
           LD
Sbjct: 586 LD 587


>gi|148657263|ref|YP_001277468.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569373|gb|ABQ91518.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 345

 Score =  235 bits (600), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 112/243 (46%), Positives = 165/243 (67%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  A++ +++ANLRLV+S+AKKY    L F+DL+QEGNIGLM+A EKFD   G +FST
Sbjct: 103 MQAEEARRRLIQANLRLVVSIAKKYIGGPLSFMDLVQEGNIGLMRAVEKFDAGKGNRFST 162

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+QS  IR+PVH+ D I ++ R ARR+   ++REPT EEIA  + M
Sbjct: 163 YATWWIRQAITRAIAEQSRLIRLPVHLSDVIAQLRRVARRLEQSLEREPTVEEIAAAIDM 222

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P   V+ +L+ + +PISLE PI  +    + + + D +A +P++ A +  L+    + L 
Sbjct: 223 PEHKVKLLLQASAQPISLEQPITSDGEGQISELLADDDADAPMEIATRRMLQHDLAQALM 282

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE  VL++R+G+      TLEEVG  F +TRER RQIEA A+R+L+ P    +L++
Sbjct: 283 ELPDRERAVLQLRYGLTDGRRRTLEEVGSAFGITRERTRQIEADALRQLRRPGIGARLQA 342

Query: 679 FLD 681
           +L+
Sbjct: 343 YLE 345



 Score = 40.8 bits (94), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 79  DGDDLEDEEGSE--DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           D   +ED+ G+E  DS  L   +      L +++ S   + DD  +MYLRE+G + LLS 
Sbjct: 10  DQHRVEDDPGAEEIDSFWLTDISD-----LDEKRLSRSETIDDSTQMYLREIGQVSLLSA 64

Query: 137 EGEIAIAKRIEAGR 150
           E EI +A  I AGR
Sbjct: 65  EEEITLANDIRAGR 78


>gi|284122199|ref|ZP_06386842.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283829365|gb|EFC33758.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 414

 Score =  235 bits (599), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 117/233 (50%), Positives = 162/233 (69%), Gaps = 1/233 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V+ NLRLV+ +AK++T RG+ FLDLIQEGNIGLM+AAE+F +  G+KFSTYA WW
Sbjct: 179 AKEGLVQHNLRLVVDIAKRFTGRGMGFLDLIQEGNIGLMRAAERFQYRKGFKFSTYATWW 238

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+Q I R++ADQS TIR+PVH  +   ++++ + R++ K+ REP+ EEIA  LA+  E V
Sbjct: 239 VRQGILRAVADQSRTIRVPVHTTEAWQRMIKISHRLAQKLGREPSNEEIALALAVKPERV 298

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +   +   EPIS + P  D +T  LGD + D +A  P +   +  +R    R+L  LTPR
Sbjct: 299 QHTTQAFLEPISFDQPNADGET-FLGDCLPDDHASPPDEHLQEEQMRSQLHRLLRVLTPR 357

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           EE+V+R+RFGIG     TLEEVGK   VTRERIRQIE  A++KL+ P+   +L
Sbjct: 358 EEQVIRLRFGIGNGQSRTLEEVGKLLNVTRERIRQIEVLAMKKLREPTVKAQL 410


>gi|332709863|ref|ZP_08429819.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
 gi|332351234|gb|EGJ30818.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
          Length = 417

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 116/245 (47%), Positives = 169/245 (68%), Gaps = 1/245 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E   AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FS
Sbjct: 172 QAEGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFS 231

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R  T ++IA +L 
Sbjct: 232 TYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQERGRTATIDDIAVELE 291

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M    VR+VL      +SLE  +G E  + LGD +E +   SP +  ++  L+    ++L
Sbjct: 292 MTAAQVREVLLRVPRSVSLEIKVGKERDTELGDLLETEE-TSPEEVLMREALQRDLQQLL 350

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE  V+RMRFG+G N  ++L E+G+   ++RER+RQIEAKA++KL+ P R  ++R
Sbjct: 351 ADLTNRERDVIRMRFGLGDNQPYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRVR 410

Query: 678 SFLDG 682
            +L+ 
Sbjct: 411 DYLEA 415


>gi|309790033|ref|ZP_07684607.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227888|gb|EFO81542.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 358

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 103/238 (43%), Positives = 166/238 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+SVAKKY N  + F+DL+QEGNIGLM+A EKFD   G +FSTYA WW
Sbjct: 121 ARRRLIQANLRLVVSVAKKYINSPMAFMDLVQEGNIGLMRAVEKFDHTKGNRFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++RSIA+QS  IR+PVH+ + + ++ R   ++  + +REPT +EIA  + + +  V
Sbjct: 181 IRQAVSRSIAEQSRVIRLPVHLSESLVQMRRAIYKLEQQFEREPTAQEIAHSMGLSLRKV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L+ + +P+SLE P+ +E    +G+ + D+N  +P+D A Q    +     L  L  R
Sbjct: 241 KRLLQASAQPVSLEQPLNNEQEGRVGEVLADENVETPMDLATQKMFHQELYAALNDLPDR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E ++L++R+G+      TLEEVG  F +TRER RQIEA+A+R+L+ P   ++L+++L+
Sbjct: 301 ERKILQLRYGLFDGQRRTLEEVGMAFGITRERTRQIEAEAMRRLRQPQVGQRLQAYLE 358


>gi|158335266|ref|YP_001516438.1| RNA polymerase sigma factor SigC [Acaryochloris marina MBIC11017]
 gi|158305507|gb|ABW27124.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 111/239 (46%), Positives = 169/239 (70%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 184 AKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWW 243

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S    R  + E+IA+++ M  E +
Sbjct: 244 IRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKLSQSKGRTASIEDIAQEMDMTPEQI 303

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++L      +SLE  +G +  + LGD +E  + +SP +  ++ +L++   ++LA LTPR
Sbjct: 304 RELLVRVPRSVSLEIKVGKDKDTELGDLLETDD-ISPEELIMRESLQQELKQLLADLTPR 362

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  V+ MRFG+     H+L ++GK   ++RER+RQIE+KA++KL+ P R  ++R FL+ 
Sbjct: 363 ERDVITMRFGLNDGKTHSLAQIGKSLDLSRERVRQIESKALQKLRQPKRRNRIRDFLEA 421


>gi|220907205|ref|YP_002482516.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863816|gb|ACL44155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 455

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 120/285 (42%), Positives = 186/285 (65%), Gaps = 10/285 (3%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             VA ++ ++L    +  + ++  G+ + E   I       + E   AK+ M++ANLRLV
Sbjct: 178 GVVAGQLKTLLAEGKQAWATAI--GMMVGELDQI-------QKEGVRAKEHMIQANLRLV 228

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA QS
Sbjct: 229 VSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQS 288

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+PVH+ +K++K+ +  R++S +    P+ E+IA +L M V  VR++L      +SL
Sbjct: 289 RTIRLPVHITEKLNKIKKAQRKISQEKGHTPSIEDIATELEMTVPQVRELLVRVPRSVSL 348

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ET +G +  + LGD +E  + +SP +  ++ +L     ++LA LT RE  V+ MRFG+G 
Sbjct: 349 ETKVGKDKDTELGDLLETDD-LSPEEMMMRESLHRELEKLLADLTSRERDVISMRFGLGD 407

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              ++L ++G+   ++RER+RQIEAKA++KL+ P R  ++R +LD
Sbjct: 408 GHAYSLADIGRALDLSRERVRQIEAKALQKLRQPKRRNRVRDYLD 452


>gi|25028367|ref|NP_738421.1| RNA polymerase sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259507424|ref|ZP_05750324.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
 gi|23493652|dbj|BAC18621.1| sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259164989|gb|EEW49543.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
          Length = 333

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 109/241 (45%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 92  EGKKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 151

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  + 
Sbjct: 152 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIE 211

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R VL+
Sbjct: 212 ESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-ETAVVASMRHSDIRSVLS 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+   R+ KLR 
Sbjct: 271 TLEQREQDVIRLRYGLEDGVPRTLDQIGRRFGLSRERVRQIEREVMSKLRDGERAAKLRE 330

Query: 679 F 679
           +
Sbjct: 331 Y 331


>gi|313123887|ref|YP_004034146.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280450|gb|ADQ61169.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 378

 Score =  234 bits (598), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 116/246 (47%), Positives = 170/246 (69%), Gaps = 5/246 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKF 488
           V + ++ E    +AK E+  ANLRLV+S+AK+Y   N  +  LDLIQEGNIGLMKA +KF
Sbjct: 123 VEVAKRIENGDELAKDELAAANLRLVVSIAKRYAKHNGKMGILDLIQEGNIGLMKAVDKF 182

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ   IRIPVH+ + I+K+ R  R +   + R+  
Sbjct: 183 DYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVVESINKMNRIQRILQQDLDRDAK 242

Query: 549 PEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PEE+A ++  P++ V++++ + K  E  SL+ P+G+E  S LGD +ED  A++P +    
Sbjct: 243 PEELAAEMNEPLQKVQEIITVAKNQETDSLDKPVGEEGDSQLGDLLEDNKAINPEEYTAS 302

Query: 607 ANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L++  + ++   LT RE +VL++RFG+  +  HTLEEVG+   VTRER+RQIEAKA++
Sbjct: 303 EMLKDQLSSMMGEFLTDREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQIEAKAVK 362

Query: 666 KLKHPS 671
           KLKH S
Sbjct: 363 KLKHHS 368



 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 1/90 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VRMYL+E+G + LLSR+ E+ +AKRIE G  +    L  + L     I  R   ++G 
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRIENGDELAKDELAAANLRLVVSIAKRYAKHNGK 161

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSY 208
             + ++I  E  IG       F  ++G  +
Sbjct: 162 MGILDLIQ-EGNIGLMKAVDKFDYSKGFKF 190


>gi|119773417|ref|YP_926157.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
 gi|119765917|gb|ABL98487.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
          Length = 969

 Score =  234 bits (597), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 142/362 (39%), Positives = 224/362 (61%), Gaps = 24/362 (6%)

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKR---DVFLERHQGRELDPH 382
           S+ L +  +++L++ LY+   ++   + EL+ L  +   + R   +   E+  GREL   
Sbjct: 617 SIVLTEDALNILIKALYESIDKVSDIKTELVNLYTREIKLPRKTAESVAEQKMGREL--- 673

Query: 383 WVSYAK-DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            +S  K ++P  E K  +     +I +++ ++++I+ +TGI +   + I S ++K + + 
Sbjct: 674 -ISQLKTEYPLCEDK--LERHAGAINRLQAQMQNINQKTGIDLYSLQDIGSKIKKLQRDI 730

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A+ EM+  NLRLV+SVA KY  RGL+  DL+QEGNIGLMKA EKFD   G+KFSTYA 
Sbjct: 731 SAARDEMITFNLRLVLSVANKYLGRGLELADLVQEGNIGLMKAVEKFDHRKGFKFSTYAT 790

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-- 559
           WW++QAITR+IADQ+  IRIPVH+ + ++K++  ++ +++K  R P   E++  L+MP  
Sbjct: 791 WWIRQAITRAIADQARIIRIPVHVNESLNKLISASKVLTHKFGRGPKISELSLILSMPET 850

Query: 560 -VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE ++++L +  EP++        +  H  +   D  A+SP +  I  +       +L 
Sbjct: 851 KVENLKQILVM--EPVA--------EADHNTNGYVDWAAMSPEEEIIDDDRDTNIKDLLK 900

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT +E++VL +RFGI   T+ TLEEVG+QF VTRERIRQIEAK+++KL H SRS  L  
Sbjct: 901 GLTDKEKKVLELRFGINAATELTLEEVGQQFDVTRERIRQIEAKSLKKLAHTSRSSHLAI 960

Query: 679 FL 680
           F 
Sbjct: 961 FF 962


>gi|296117743|ref|ZP_06836327.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969474|gb|EFG82715.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 334

 Score =  234 bits (597), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 107/241 (44%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 93  EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 152

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  + 
Sbjct: 153 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELAEESGIE 212

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R V+ 
Sbjct: 213 ENKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEATDA-ETAVVASMRHSDIRDVIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+  +R+ +LR 
Sbjct: 272 TLEQREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMAKLRDGNRADRLRE 331

Query: 679 F 679
           +
Sbjct: 332 Y 332


>gi|328480117|gb|EGF49090.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus MTCC
           5462]
          Length = 206

 Score =  234 bits (597), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 113/199 (56%), Positives = 150/199 (75%), Gaps = 1/199 (0%)

Query: 405 SILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           S +KI + ++    E G +S+      V++  K E     AK+ + EANLRLV+S+AK+Y
Sbjct: 8   SGVKINDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQEAKQRLAEANLRLVVSIAKRY 67

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 68  VGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 127

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+E
Sbjct: 128 HMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEE 187

Query: 584 DTSHLGDFIEDKNAVSPLD 602
           D SHLGDFIED++A SP D
Sbjct: 188 DDSHLGDFIEDQDATSPED 206



 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 30/45 (66%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +DPVRMYL+E+G + LL+ + E+A+A +IE G       L E+ L
Sbjct: 13  NDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQEAKQRLAEANL 57


>gi|160902123|ref|YP_001567704.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359767|gb|ABX31381.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 418

 Score =  234 bits (596), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 131/296 (44%), Positives = 191/296 (64%), Gaps = 10/296 (3%)

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           F + E K +    +   +KI   +K IS    +S S  R +    +KG+ +A   + E++
Sbjct: 128 FSDTELKMYDNISLGDPIKIY--LKEISKVELLSPSRERQLARRAQKGDQKA---RDELI 182

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +ANLRLVIS+AK+YT RGL FLDLIQEGNIGL+KA +KFDW  G+KFSTYA WW++QAIT
Sbjct: 183 KANLRLVISIAKRYTGRGLTFLDLIQEGNIGLIKAVDKFDWRKGFKFSTYATWWIRQAIT 242

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVH+ + I+++ +  R    +    P+ +E+A+ L  P + + ++L  
Sbjct: 243 RAIADQARTIRIPVHLVETINRMNKVIREYLQENGDYPSAQELAEILDKPEDKINEILMS 302

Query: 570 TKEPISLETPI----GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            K+ +SL +PI    GD++ S  GDFI      +P + A +  ++E    VL +L  +E 
Sbjct: 303 AKDVLSLNSPISSGNGDDEESETGDFIS-TEETTPEEEAQKMIMKERLEEVLDTLNSKEA 361

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VL+MR+G       TLEEVG+ F VTRERIRQIE KA+RKL+HP+R  +L+  ++
Sbjct: 362 LVLKMRYGFLDGKQKTLEEVGQFFNVTRERIRQIETKALRKLRHPNRVAQLKDIVE 417


>gi|86608944|ref|YP_477706.1| sigma-70 family RNA polymerase sigma factor [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557486|gb|ABD02443.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 320

 Score =  234 bits (596), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 111/251 (44%), Positives = 171/251 (68%), Gaps = 3/251 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ +G      AK+E+V ANLRLV+S+AKKY NRG+ FLDLIQEG IGL++AAEKF++  
Sbjct: 67  LIAEGGAAGERAKRELVRANLRLVVSIAKKYLNRGVPFLDLIQEGTIGLIRAAEKFEYER 126

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR++A+Q   +RIPVHM +K+++V R  R ++  + R PT  EI
Sbjct: 127 GYKFSTYAYWWIRQGITRAVANQGRLVRIPVHMVEKLNQVKRIRRELTETLNRRPTQAEI 186

Query: 553 AKKLAMP---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A+ L +    ++ +  +L+  ++ +SL TP+G E+   L   IED N+++P        L
Sbjct: 187 AEALEISPDKLDALLTLLEAGRQTLSLHTPVGKEEDRELMQLIEDANSLTPESQMDLHLL 246

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 +L  L+PRE+ +L++R+G+     HTL E+G+ F ++RER+RQI+A+A+RKL+H
Sbjct: 247 SAQLEEMLEQLSPREQEILKLRYGLKDGHLHTLSEIGQLFGLSRERVRQIQARAMRKLRH 306

Query: 670 PSRSKKLRSFL 680
           P R + L  ++
Sbjct: 307 PRRQEILADWM 317


>gi|254416308|ref|ZP_05030062.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196176990|gb|EDX72000.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 416

 Score =  233 bits (595), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 117/245 (47%), Positives = 168/245 (68%), Gaps = 1/245 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E   AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FS
Sbjct: 171 QAEGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFS 230

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R  T E+IAK+L 
Sbjct: 231 TYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEQGRTATIEDIAKELE 290

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M    VR+VL      +SLE  +G E  + LGD +E +   SP D  ++  L+    ++L
Sbjct: 291 MDAPQVREVLMRVPRSVSLEIKVGKEKDTELGDLLETEE-TSPEDVLMREALQRDLQQLL 349

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE  V+ MRFG+G    ++L E+G+   ++RER+RQIEAKA++KL+ P R  ++R
Sbjct: 350 ADLTSRERDVICMRFGLGDGHPYSLAEIGRALELSRERVRQIEAKALQKLRQPKRRNRVR 409

Query: 678 SFLDG 682
            +L+ 
Sbjct: 410 DYLEA 414



 Score = 37.4 bits (85), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 28/36 (77%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           SA+R T D VR+YL+E+G + LL R+ E++ A++++
Sbjct: 53  SANRRTTDLVRLYLQEIGRVRLLRRDEEVSEAQKVQ 88


>gi|164415557|gb|ABY53195.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415559|gb|ABY53196.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415561|gb|ABY53197.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415563|gb|ABY53198.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415565|gb|ABY53199.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415567|gb|ABY53200.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415569|gb|ABY53201.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415571|gb|ABY53202.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415573|gb|ABY53203.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415575|gb|ABY53204.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415577|gb|ABY53205.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415579|gb|ABY53206.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415581|gb|ABY53207.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415583|gb|ABY53208.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415585|gb|ABY53209.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415587|gb|ABY53210.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415589|gb|ABY53211.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415591|gb|ABY53212.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415593|gb|ABY53213.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 166

 Score =  233 bits (594), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 112/164 (68%), Positives = 135/164 (82%)

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+K+ KEPIS+E
Sbjct: 1   TIRIPVHMMETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKVAKEPISME 60

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MN
Sbjct: 61  TPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMN 120

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 164


>gi|300812193|ref|ZP_07092635.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496829|gb|EFK31909.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 378

 Score =  233 bits (594), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 114/233 (48%), Positives = 164/233 (70%), Gaps = 5/233 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           AK E+  ANLRLV+S+AK+Y   N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA 
Sbjct: 136 AKDELAAANLRLVVSIAKRYAKHNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYAT 195

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR++ADQ   IRIPVH+ + I+K+ R  R +   + R+  PEE+A ++  P++
Sbjct: 196 WWIRQAITRALADQDRMIRIPVHVVESINKMNRIQRTLQQDLDRDAKPEELAAEMNEPLQ 255

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V++++ + K  E  SL+ P+G+E  S LGD +ED  A++P +      L++  + ++  
Sbjct: 256 KVQEIITVAKNQETDSLDKPVGEEGDSQLGDLLEDNKAINPEEYTASEMLKDQLSIMMGE 315

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            LT RE +VL++RFG+  +  HTLEEVG+   VTRER+RQIEAKA++KLKH S
Sbjct: 316 FLTDREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQIEAKAVKKLKHHS 368



 Score = 44.7 bits (104), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VRMYL+E+G + LLSR+ E+ +AKRIE G       L  + L     I  R   ++G 
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRIENGDESAKDELAAANLRLVVSIAKRYAKHNGK 161

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSY 208
             + ++I  E  IG       F  ++G  +
Sbjct: 162 MGILDLIQ-EGNIGLMKAVDKFDYSKGFKF 190


>gi|254423226|ref|ZP_05036944.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190715|gb|EDX85679.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 431

 Score =  233 bits (593), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 115/261 (44%), Positives = 177/261 (67%), Gaps = 8/261 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+S+ E   I       + E + AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +G
Sbjct: 176 GMSVEEIVEI-------QNEGTRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLG 228

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L +A EKFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S
Sbjct: 229 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKIS 288

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
               R    E+IAK+L M V  +R+VL      +SL+T +G +  + LGD +E ++ +SP
Sbjct: 289 QTQGRTAKAEDIAKELDMTVAQIREVLLKVPRSVSLDTKVGKDRDTELGDLLETED-ISP 347

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D  ++ +L+    ++L  LT RE+ V+ +RFG+     ++L E+G+   ++RER+RQIE
Sbjct: 348 EDRLMRESLKRELHQLLTDLTTREQEVITLRFGLDDGVPYSLAEIGRTLELSRERVRQIE 407

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           +KA++KL+ P R  ++R +L+
Sbjct: 408 SKALQKLRQPKRRNRVRDYLE 428


>gi|298242664|ref|ZP_06966471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297555718|gb|EFH89582.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 394

 Score =  233 bits (593), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 106/236 (44%), Positives = 165/236 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K +VEANLRLV+S+AK+Y N+G+  LDLIQEGN+GL++A +KFD   G++FSTYA WW
Sbjct: 158 AQKRLVEANLRLVVSIAKRYNNQGISLLDLIQEGNLGLIRAVQKFDPQRGFRFSTYATWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI+R++A+ + TI +PVH+ + I+K+ R  R++   + R+P PEEIA+ + +  E V
Sbjct: 218 IRQAISRAVAEHTRTIHVPVHVVELIYKMKRITRQLYQDLGRDPFPEEIAQAINLTKERV 277

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++  I + PISL+ P+ +++  HL D +ED +A +P +      LR+  +R L +L+ R
Sbjct: 278 VELQSIAEAPISLDAPLIEDEQYHLADMLEDTHAAAPAEVVTHQVLRDHISRALETLSQR 337

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E +V+ +R+G+     HTLEE+   F +TRERIRQIE KA+R L+HP +   L  +
Sbjct: 338 ERQVIELRYGLYDGYCHTLEELSAYFKLTRERIRQIEVKALRTLRHPIQIHMLHDY 393



 Score = 41.2 bits (95), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 52/114 (45%), Gaps = 9/114 (7%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNS---SVFLQKRKDS-----ADRSTDDPVRMYLRE 127
           + +DGD   +E G         +A N     VF ++ +++     +DR  D+ +R YL E
Sbjct: 73  SFLDGDSSNEESGGPTRRRRGKAAQNEMQDDVFFEEEEEAETEGESDREVDNAIRQYLAE 132

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           +G   LL+ E E+ IA R+  G       L E+ L     I  R   N G +LL
Sbjct: 133 IGRFPLLTSEQELTIAWRVANGDMEAQKRLVEANLRLVVSIAKRYN-NQGISLL 185


>gi|110004382|emb|CAK98720.1| probable rna polymerase sigma-a factor protein [Spiroplasma citri]
          Length = 445

 Score =  233 bits (593), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 128/303 (42%), Positives = 182/303 (60%), Gaps = 60/303 (19%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    + +++ +NL+LV+SVA+K+ NRGL F DLI+EGNIGLMKA +KFD+  G+KFSTY
Sbjct: 143 EIRFGRDKLITSNLKLVVSVARKHLNRGLDFSDLIEEGNIGLMKAVDKFDYKRGFKFSTY 202

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--A 557
           A WW++QA TR+IADQ+ TIRIPVHM + I+K+ R  R+++ ++ REP+  EIA+K+   
Sbjct: 203 ATWWIRQATTRAIADQARTIRIPVHMVETINKLTRIERQLTQELGREPSYNEIAEKMGQG 262

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  E VR++ +++ EP+SLE PIGDED +H GDF++DK+  +P +   + +LRE    V 
Sbjct: 263 MVGEKVREIKRLSIEPVSLEKPIGDEDDTHFGDFVDDKDIFTPDEYTEKESLREVIDEVF 322

Query: 618 AS-LTPREERVLRMRFG------------------------------IGMNTDHTLEEV- 645
              L+ REE+V+RMRFG                              + ++ D  +E+V 
Sbjct: 323 HEILSAREEKVIRMRFGLLPTKLRTVLRLAKECEDETFPELVQTVKALDIHYDTPIEKVQ 382

Query: 646 -----------------------GKQFCVTRERIRQIEAKAIRKLK---HPSRSKKLRSF 679
                                  GK+F VTRERIRQIEAK IRK K     S++K L+ F
Sbjct: 383 SQKHALIDKHLSKYDSPKTLEEVGKEFKVTRERIRQIEAKTIRKFKPNQANSKAKVLKDF 442

Query: 680 LDG 682
             G
Sbjct: 443 FKG 445


>gi|255076341|ref|XP_002501845.1| predicted protein [Micromonas sp. RCC299]
 gi|226517109|gb|ACO63103.1| predicted protein [Micromonas sp. RCC299]
          Length = 595

 Score =  232 bits (591), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/240 (48%), Positives = 163/240 (67%), Gaps = 3/240 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M++ANLRLV+S+AK+Y N+ + F DLIQEG +GL++ AEKFD+  GYKFSTYA WW
Sbjct: 345 AKNAMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKFDFKRGYKFSTYAHWW 404

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TRSI+DQS TIR+PVH+ + I ++ +  R+M  K+ R+PT EE+A  + M VE +
Sbjct: 405 IRQAVTRSISDQSRTIRLPVHLFEIISRMSKVERQMVLKLGRDPTHEELADAMEMTVEKI 464

Query: 564 RKVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +++ K +  PISL   + +   ED   + D + D     P     +  L+E    VL +L
Sbjct: 465 KQIKKASLVPISLSQTVNNSNGEDKRTVEDTLIDDYTEHPEGETGKVLLKEDLENVLNTL 524

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKL+ PSR+  LR +L
Sbjct: 525 NPRERDVLRLRYGLDDGRVKTLEEIGNVFSVTRERIRQIEAKALRKLRQPSRNGILREYL 584



 Score = 37.4 bits (85), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E GS    + AS+A +       RK++  +   D ++ YL+++G++ LL+   E+ +AKR
Sbjct: 237 EPGSAQEANEASAAESRRNRRIARKNADTKKQTDSMKTYLKDIGTVSLLTGAEEVELAKR 296

Query: 146 IEAGRAMMMASLCE 159
           I+    M + S+CE
Sbjct: 297 IQ--DLMYLNSVCE 308


>gi|251733351|emb|CAR82425.1| RNA polymerase sigma factor [Mesorhizobium loti]
          Length = 202

 Score =  232 bits (591), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 112/178 (62%), Positives = 143/178 (80%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR++ NEG+LLRLA+SYG++R+ FL+
Sbjct: 23  RLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRLVQNEGKLLRLAESYGVRREEFLK 82

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
            +QG ELDP+W     +     WK F   E D+I  +R EI++++ ET ISI EFR IV+
Sbjct: 83  EYQGSELDPNWTRAIGNLTSRGWKEFTKNEKDAIKDLRAEIQNLATETAISILEFRKIVN 142

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 143 QVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|298245985|ref|ZP_06969791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553466|gb|EFH87331.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 417

 Score =  231 bits (590), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/281 (41%), Positives = 184/281 (65%), Gaps = 9/281 (3%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A E D+++    EI  + +     I+  R I  + ++ E     A K+ + ANLRLV+S+
Sbjct: 144 AGESDAVMTYLREIGRVPM-----ITHEREI-ELAQRIESGDRDAMKQFILANLRLVVSI 197

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RGL  LDLIQEGNIGL++A +++DW  G++FST+A WW++QAI+R++AD+  TI
Sbjct: 198 AKRYVGRGLTLLDLIQEGNIGLIRAVQRYDWRRGHRFSTHATWWIRQAISRAVADKGRTI 257

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLKITKEPISLET 578
           R+PV++   ++++ R  +R+  ++ REP+ +E+A+   + PV  + ++      P+SLE 
Sbjct: 258 RLPVYVNTALNRIRRERQRLLQELGREPSEQELAEATGLDPVRMI-ELQAAPGAPVSLEL 316

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMN 637
           P+G++D   LGD + D  + SP D A    L++   RVL S LTPRE+ VL++RFG+G  
Sbjct: 317 PVGEDDDQELGDVLPDTESASPEDLATTQTLKDEVQRVLESVLTPREQLVLQLRFGLGNG 376

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             H LE+VG++  +TRER+RQIEA A+ KL+ P   ++LR 
Sbjct: 377 QAHPLEQVGRELGITRERVRQIEAGALAKLRQPPVLERLRG 417



 Score = 37.7 bits (86), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 26/39 (66%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + AD    D V  YLRE+G + +++ E EI +A+RIE+G
Sbjct: 140 NGADAGESDAVMTYLREIGRVPMITHEREIELAQRIESG 178


>gi|227503471|ref|ZP_03933520.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|306836281|ref|ZP_07469263.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
 gi|227075974|gb|EEI13937.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|304567873|gb|EFM43456.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
          Length = 337

 Score =  231 bits (590), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 106/241 (43%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 96  EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 155

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE++++  + 
Sbjct: 156 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELSEESGID 215

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R V+ 
Sbjct: 216 ENKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDA-ETAVVASMRHSDIRGVID 274

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+  +R+ +LR 
Sbjct: 275 TLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMAKLRDGNRADRLRE 334

Query: 679 F 679
           +
Sbjct: 335 Y 335


>gi|227549119|ref|ZP_03979168.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078816|gb|EEI16779.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 331

 Score =  231 bits (590), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 103/236 (43%), Positives = 166/236 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 94  ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + REPT EE++ +  +    +
Sbjct: 154 IRQAITRGMADQSRTIRLPVHLVEQVNKLSRIRREMYQSLGREPTNEELSDESGIEESKI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L+ +++P+SL+ P+G ++ + LGDFIED  A    D+ + +   +    ++  L  R
Sbjct: 214 EMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEATDAEDAVVSSLRHDDIQDIIGGLEQR 273

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+ V+R+R+G+      TL+++G+QF ++RER+RQIE + + KL+   R+ +LR +
Sbjct: 274 EQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMAKLRVGERADRLRDY 329


>gi|291550766|emb|CBL27028.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 280

 Score =  231 bits (590), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 128/290 (44%), Positives = 188/290 (64%), Gaps = 17/290 (5%)

Query: 389 DFPEGEWKNFVACEVDSILKIR-NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           + PEG        EV   LKI  NEI  I +   +S  E R +      G+ +A   +++
Sbjct: 6   NLPEG-------TEVTEPLKIYLNEIGQIPL---LSEEEERDLGCKSASGDEDA---RRK 52

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + E NLRLV+S+AK YT RG+  +DLIQEGNIGLM AAEK+D+    +FSTYA WW+K+A
Sbjct: 53  LEEGNLRLVVSLAKHYTGRGITLMDLIQEGNIGLMHAAEKYDYTKENRFSTYASWWIKEA 112

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEGVRKV 566
           + R+I  QS  IR+PVH+ + + KV + ++ +  K  RE TPEEIA+++     E V+++
Sbjct: 113 MQRAIDQQSREIRVPVHVAENMKKVQKISKDLQQKFGREATPEEIAEEMKDKSPEFVKEI 172

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L   + P+SLETP+G++  ++LGD +EDK+A +P D+  Q   +E    +L SL  RE +
Sbjct: 173 LSYLQNPVSLETPVGEDGENNLGDMVEDKDATTPEDAMNQLVQKEEVQELLESLNDRERQ 232

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           V+R+RFG+     HTLEE+G +  VTRER+RQIEA+A+ KL+  S++ KL
Sbjct: 233 VIRLRFGLEDGKTHTLEEIGDELNVTRERVRQIEARAMEKLR--SKATKL 280


>gi|311739612|ref|ZP_07713447.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305428|gb|EFQ81496.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 337

 Score =  231 bits (590), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 106/241 (43%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 96  EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 155

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE++++  + 
Sbjct: 156 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELSEESGID 215

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R V+ 
Sbjct: 216 ENKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDA-ETAVVASMRHSDIRGVID 274

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+  +R+ +LR 
Sbjct: 275 TLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMAKLRDGNRADRLRE 334

Query: 679 F 679
           +
Sbjct: 335 Y 335


>gi|227488742|ref|ZP_03919058.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227542262|ref|ZP_03972311.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227091164|gb|EEI26476.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227182091|gb|EEI63063.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 327

 Score =  231 bits (589), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 108/241 (44%), Positives = 173/241 (71%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  M+EANLRLV+S+AK+Y+ RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 86  EGDKARNHMLEANLRLVVSLAKRYSGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 145

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  +  RE T EE+A++  + 
Sbjct: 146 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQFGREVTNEELAEESGID 205

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  + + +++P+SL+ P+G ++ + LGDFIED  A    + A+  +LR +  R V+ 
Sbjct: 206 ENKIEMLFRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-EEAVVVSLRHSDIRAVID 264

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+RMR+G+      TL+++G+++ ++RER+RQIE + + KL+  SR++KLR+
Sbjct: 265 TLEGREQDVIRMRYGLDDGVPRTLDQIGRRYGLSRERVRQIEREVMAKLREGSRAEKLRA 324

Query: 679 F 679
           +
Sbjct: 325 Y 325


>gi|325686024|gb|EGD28082.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 378

 Score =  231 bits (588), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 114/233 (48%), Positives = 163/233 (69%), Gaps = 5/233 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           AK E+  ANLRLV+S+AK+Y   N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA 
Sbjct: 136 AKDELAAANLRLVVSIAKRYAKHNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYAT 195

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR++ADQ   IRIPVH+ + I+K+ R  R +   + R+  PEE+A ++  P++
Sbjct: 196 WWIRQAITRALADQDRMIRIPVHVVESINKMNRIQRILQQDLDRDAKPEELAAEMNEPLQ 255

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V++++ + K  E  SL+ P+G+E  S LGD +ED  A +P +      L++  + ++  
Sbjct: 256 KVQEIITVAKNQETDSLDKPVGEEGDSQLGDLLEDNKATNPEEYTAFEMLKDQLSSMMGE 315

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            LT RE +VL++RFG+  +  HTLEEVG+   VTRER+RQIEAKA++KLKH S
Sbjct: 316 FLTNREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQIEAKAVKKLKHHS 368



 Score = 44.7 bits (104), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VRMYL+E+G + LLSR+ E+ +AKRIE G       L  + L     I  R   ++G 
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRIENGDESAKDELAAANLRLVVSIAKRYAKHNGK 161

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSY 208
             + ++I  E  IG       F  ++G  +
Sbjct: 162 MGILDLIQ-EGNIGLMKAVDKFDYSKGFKF 190


>gi|86607249|ref|YP_476012.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
 gi|86555791|gb|ABD00749.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
          Length = 361

 Score =  231 bits (588), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 117/254 (46%), Positives = 167/254 (65%), Gaps = 9/254 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I +S  R   S +R+GE     A+++++ ANLRLV+SVAKKY NRG+ FLDLIQEGN+GL
Sbjct: 109 IPVSTLR---SRIRQGEQ----AQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNMGL 161

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKF+   G++FSTYA WW++Q ITR IA+Q+ TIR+PVHM DK+  + RT R +  
Sbjct: 162 IRATEKFNAERGFRFSTYAHWWIRQGITRCIANQARTIRLPVHMVDKVRLLKRTNRELMK 221

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              R PT  E+A+ L + V+ +R + +    P+SL+ P+G E  S LGD + D+    P 
Sbjct: 222 ARGRRPTEAELAEALGIKVKKLRMIQQAAALPLSLDVPVGQEGESRLGDLLPDERQEQPF 281

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  +  +LR+     + +L P E +VL +R+G+      TL EVG  F +TRERIRQIE 
Sbjct: 282 EEILVQSLRQDVRSAMQALKPIERQVLELRYGLDGQRARTLREVGDHFNLTRERIRQIER 341

Query: 662 KAIRKLK--HPSRS 673
            A+RKL+  HPSR+
Sbjct: 342 DALRKLRLGHPSRA 355


>gi|255325135|ref|ZP_05366241.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
 gi|255297700|gb|EET77011.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
          Length = 365

 Score =  230 bits (587), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 106/241 (43%), Positives = 174/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 124 EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 183

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE++++  + 
Sbjct: 184 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELSEESGID 243

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
              +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R V+ 
Sbjct: 244 ENKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDA-ETAVVASMRHSDIRGVID 302

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+  +R+ +LR 
Sbjct: 303 TLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMAKLRDGNRADRLRE 362

Query: 679 F 679
           +
Sbjct: 363 Y 363


>gi|330040254|ref|XP_003239821.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
 gi|327206746|gb|AEA38923.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
          Length = 414

 Score =  230 bits (587), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 117/231 (50%), Positives = 166/231 (71%), Gaps = 2/231 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+ ANLRLV+S+AK+Y+NRG+   DL+QEG++GL++A EKFD   G+KFSTYA WW
Sbjct: 159 AKERMIAANLRLVVSIAKRYSNRGMSLQDLVQEGSLGLIRATEKFDSEKGFKFSTYATWW 218

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+++R+IAD S TIR+PVH+ D +  + +T R ++ ++ R PT EEIA K+ + V+ +
Sbjct: 219 IKQSVSRAIADHSRTIRLPVHLYDTLSAIKKTTRILTIELGRSPTEEEIACKMDVTVDKL 278

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           R VL+  +  +SLE PI  D DT+ L DFIE  +  SP +   ++ LR+    V+ SL+ 
Sbjct: 279 RSVLQSAQPTLSLEKPIKNDGDTAQLSDFIE-ADQESPDEHVEKSMLRDDLRDVINSLSL 337

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           RE  V+RMR+G+      TLEE+G+ F VTRER+RQIEAKAIRKL+ P RS
Sbjct: 338 RERDVIRMRYGLDDGKIRTLEEIGQIFSVTRERVRQIEAKAIRKLRQPYRS 388


>gi|170076898|ref|YP_001733536.1| group 2 sigma factor [Synechococcus sp. PCC 7002]
 gi|169884567|gb|ACA98280.1| Group 2 sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score =  230 bits (586), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 116/273 (42%), Positives = 181/273 (66%), Gaps = 8/273 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR   +  + + G+S+ E   I+    K       AK+ M++ANLRLV+SVAKKY NRGL
Sbjct: 131 IRQGKQRWAEQVGLSVKELDSILKAGAK-------AKEHMIQANLRLVVSVAKKYQNRGL 183

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEG +GL +A +KFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K
Sbjct: 184 ELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK 243

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +  R++S      P+ +++A+ L M  E VR+VL+     +SLE  +G +  + L
Sbjct: 244 LNKIKKAQRQISQTQGCTPSLDDVAQALEMTPEQVREVLQKVPRSVSLEIRVGKDRDTEL 303

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD +E ++A SP ++ ++ +L+     +L  LT RE  V+++R+G+G    ++L E+G+ 
Sbjct: 304 GDLLETQDA-SPEENLVRESLQRDLHNLLTELTDREREVIQLRYGLGDGKTYSLAEIGRM 362

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             ++RER+RQIEAKA++KL+ P R   +R +LD
Sbjct: 363 LELSRERVRQIEAKALQKLRQPKRRNIMRDYLD 395


>gi|37523331|ref|NP_926708.1| RNA polymerase sigma factor SigC [Gloeobacter violaceus PCC 7421]
 gi|35214335|dbj|BAC91703.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 362

 Score =  229 bits (585), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 116/242 (47%), Positives = 169/242 (69%), Gaps = 3/242 (1%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            S AKK+M+EANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA
Sbjct: 120 GSRAKKKMIEANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYA 179

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q ITR+IA QS TIR+PVH+ +K++++ +T R++S  + R PT  EIA++L M  
Sbjct: 180 YWWIRQGITRAIATQSRTIRLPVHITEKLNRIKKTQRKLSQNLGRTPTISEIAEELEMEP 239

Query: 561 EGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             VR+++      +SLET +G D+DT      + +   VSP +SA+Q +LR     +L  
Sbjct: 240 AHVRELMSRVPRSVSLETRVGKDKDTEL--GELLEAEEVSPEESAVQESLRRDVKELLDD 297

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE  V+ MR+G+     ++L E+G+   ++RER+RQIE+KA++KL+ P R  K+R +
Sbjct: 298 LTLRERDVITMRYGLLDGRTYSLSEIGRALDLSRERVRQIESKALQKLRQPRRRAKVRDY 357

Query: 680 LD 681
           L+
Sbjct: 358 LE 359


>gi|319948428|ref|ZP_08022566.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
 gi|319437910|gb|EFV92892.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
          Length = 322

 Score =  229 bits (585), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 109/241 (45%), Positives = 172/241 (71%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 80  AEGEAARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFST 139

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE T EE+A++  +
Sbjct: 140 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATLEELAEESGI 199

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P   + ++L  +++P+SL+ P+G ++ + LGDFIED  A S  ++ +   +      VLA
Sbjct: 200 PAHKIEELLDHSRDPVSLDMPVGADEEAPLGDFIEDAEATSAENTVVSNVMHSDVRAVLA 259

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE++V+ +RFG+      TL+++GK+F ++RER+RQIE + + KL+   R+ KLRS
Sbjct: 260 TLEEREQQVITLRFGLDDGQPRTLDQIGKRFGLSRERVRQIEREVMAKLREGRRADKLRS 319

Query: 679 F 679
           +
Sbjct: 320 Y 320


>gi|213616352|ref|ZP_03372178.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 508

 Score =  229 bits (585), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 126/259 (48%), Positives = 172/259 (66%), Gaps = 6/259 (2%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 489

Query: 557 AMPVEGVRKVLKITKEPIS 575
            MP + +RKVLKI KEPIS
Sbjct: 490 LMPEDKIRKVLKIAKEPIS 508



 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147


>gi|258653916|ref|YP_003203072.1| RNA polymerase sigma factor SigB [Nakamurella multipartita DSM
           44233]
 gi|258557141|gb|ACV80083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 334

 Score =  229 bits (584), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 103/236 (43%), Positives = 165/236 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++ ANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 97  ARNHLLVANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI+R +ADQ  TIR+PVH+ ++++K+ R  R +  ++ R+ T  E+A +  +P E +
Sbjct: 157 IRQAISRGMADQGRTIRLPVHLVEQVNKLSRLKRELHQQLGRDATLAELAHESGIPEEKI 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L   ++P+SL+ P+G ++ + LGDFIED  + S   + +   + +   RVL +L  R
Sbjct: 217 ADLLDHARDPVSLDMPVGSDEEAPLGDFIEDSESTSAEAAVVAGFMHDDINRVLRTLDDR 276

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+ V+R+R+G+      TL+E+G+ F ++RER+RQIE  ++ KL+   RS+ LRS+
Sbjct: 277 EQTVVRLRYGLDDGRPRTLDEIGRHFGISRERVRQIERDSMAKLRVGDRSEVLRSY 332


>gi|330862244|emb|CBX72405.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 553

 Score =  228 bits (582), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 129/290 (44%), Positives = 183/290 (63%), Gaps = 5/290 (1%)

Query: 291 YRELRSLQDNA-VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           + ELR   +NA +  +K+ +S         KL ++     L   + D LV  +  +  R+
Sbjct: 263 FSELREQYENARLEIKKNGRSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRV 322

Query: 350 MHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSIL 407
              E  +++L  +   + +  F+      E    W  +A     G+ W   +    D + 
Sbjct: 323 RTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTW--FAAAIAMGKPWSEKLKDVSDDVQ 380

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 381 RSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 440

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 441 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 500

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+E
Sbjct: 501 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISME 550



 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 53  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 112

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 113 NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 169

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 170 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI 207


>gi|145347899|ref|XP_001418397.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578626|gb|ABO96690.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 344

 Score =  228 bits (582), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 116/238 (48%), Positives = 161/238 (67%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM++ANLRLV+S+AKKY N  + F DLIQEG +GL++ AEKFD+  GYKFSTYA WW
Sbjct: 91  AKNEMIQANLRLVVSIAKKYANSNMSFQDLIQEGCVGLIRGAEKFDFQRGYKFSTYAHWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TRSI+DQS TIR+PVH+ + I ++ +  ++ +    R PT EEIA ++ M  E +
Sbjct: 151 IRQAVTRSISDQSRTIRLPVHLFEIISRISKMEQKFALHNGRNPTTEEIAAEMDMSAEKI 210

Query: 564 RKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            ++ K  + P+SL +T  GD     + D + D  A  P   + ++ L+E    VL +L P
Sbjct: 211 TQIKKAAQAPVSLAQTMGGDNKGRTVEDTLVDVTAEGPEKVSGKSLLKEDLENVLNTLNP 270

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKLK PSR+  L+ + 
Sbjct: 271 RERDVLRLRYGLDDGRVKTLEEIGTVFSVTRERIRQIEAKALRKLKQPSRNSILQEYF 328


>gi|26665386|dbj|BAC44904.1| principal sigma factor [Fischerella major NIES-592]
          Length = 203

 Score =  228 bits (581), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 112/204 (54%), Positives = 152/204 (74%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R ++K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIVK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIES-DGETPEDQVSKNLLREDLEKVLDSLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|86608149|ref|YP_476911.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556691|gb|ABD01648.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 361

 Score =  228 bits (581), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 115/259 (44%), Positives = 168/259 (64%), Gaps = 7/259 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           IS+S  R   S +R+GE     A+++++ ANLRLV+SVAKKY NRG+ FLDLIQEGNIGL
Sbjct: 109 ISVSTLR---SRIRQGEQ----AQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNIGL 161

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKF+   G++FSTYA WW++Q ITR IA+Q+ TIR+PVHM DK+  + RT R +  
Sbjct: 162 IRATEKFNAERGFRFSTYAHWWIRQGITRCIANQARTIRLPVHMVDKVRLLKRTNRELMK 221

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              R PT  E+A+ L + V+ +R + +    P+SL+ P+G E  S LGD ++D+    P 
Sbjct: 222 LQGRRPTEAELAEALGIKVKKLRMIQQAAALPLSLDVPVGQEGESRLGDLLQDERQEQPF 281

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +  ++++     + +L P E +VL +R+G+      TL EVG  F +TRERIRQIE 
Sbjct: 282 QGILVQSMQQDVRSAMQTLKPIERQVLELRYGLDGQQARTLREVGDHFNLTRERIRQIER 341

Query: 662 KAIRKLKHPSRSKKLRSFL 680
            A+RKL+    S+ L  ++
Sbjct: 342 DALRKLRVGYSSRALAQYI 360


>gi|56752254|ref|YP_172955.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 6301]
 gi|81300658|ref|YP_400866.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 7942]
 gi|56687213|dbj|BAD80435.1| group2 RNA polymerase sigma factor RpoD5 [Synechococcus elongatus
           PCC 6301]
 gi|81169539|gb|ABB57879.1| group2 RNA polymerase sigma factor SigC [Synechococcus elongatus
           PCC 7942]
          Length = 398

 Score =  228 bits (580), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 114/242 (47%), Positives = 165/242 (68%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   AK  M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTY
Sbjct: 155 EGQRAKDHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTY 214

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q ITR+IA QS TIR+PVH+ +K++++ +  R+++    R    EEIA++L M 
Sbjct: 215 AYWWIRQGITRAIATQSRTIRLPVHVTEKLNRIKKAQRKIAQTKGRTANLEEIAQELEMT 274

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + VR+VL    + ISLET +G E  + LGD +E  +  +P +   Q +L     R+L  
Sbjct: 275 PDQVREVLLRVPKSISLETRVGKEKDTELGDLLETTD-FTPEERLTQESLSNDLQRLLLE 333

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE  V+RMRFG+     ++L E+G+   ++RER+RQIEAKA++KL+HP R  ++R +
Sbjct: 334 LNHRERDVIRMRFGLRDGQIYSLAEIGQVLDLSRERVRQIEAKALQKLRHPRRRNQIRDY 393

Query: 680 LD 681
           L+
Sbjct: 394 LE 395


>gi|297170837|gb|ADI21856.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured verrucomicrobium HF0130_25O04]
          Length = 303

 Score =  228 bits (580), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 109/256 (42%), Positives = 175/256 (68%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ IS    +++ E   + S ++ G+ +A   ++ M+ ANLRLV+ +AK+Y+N GL  LD
Sbjct: 13  LRQISTVPLLTVEEEIELASRIKNGDEKA---RETMITANLRLVVKIAKEYSNIGLSLLD 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIGLMKA E+FD   G K STY  WW+KQAI R++A+QS TIR+PVHM D++ ++
Sbjct: 70  LINEGNIGLMKAVERFDPSKGGKLSTYGAWWIKQAIKRALANQSKTIRLPVHMVDRVTQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            RT+ +++ K+ REPT EE+A ++ +PV  +  +  ++++P SL++P+G+ D S LG+ +
Sbjct: 130 RRTSVQLAEKLGREPTDEELAAEMNLPVARITLLKSVSRKPASLDSPLGENDGSTLGEMV 189

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+ + +P +     +L      VLA L PRE  ++R+RFG+      TLEEVG++  VT
Sbjct: 190 ADEKSANPYEHLQSKSLVGDVNSVLAQLEPREADIIRLRFGLEGLEPLTLEEVGEKIGVT 249

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ++ +A+R+L+
Sbjct: 250 RERVRQLQEQALRQLR 265


>gi|26554290|ref|NP_758224.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
 gi|26454299|dbj|BAC44628.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
          Length = 427

 Score =  227 bits (579), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 115/243 (47%), Positives = 169/243 (69%), Gaps = 7/243 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +++ +NLRLV S+AKKY NRGL   DL+QEG++GLMKA  KFD+ LG KFSTYA WW
Sbjct: 179 AINQLMTSNLRLVTSIAKKYLNRGLDLEDLLQEGSLGLMKAITKFDYKLGNKFSTYATWW 238

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           ++QAITR+IADQ+ TIRIPVHM + I+K+ +  R++  +  R+PTPEE+A  +     G 
Sbjct: 239 IRQAITRAIADQARTIRIPVHMVETINKLSKAERQLMQEYGRDPTPEELADAMDGTAAGF 298

Query: 563 -VRKVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             +K+L I K   +P+SL+ P+G ++ S   DF++D + ++P     +  + E    +L 
Sbjct: 299 TAKKILNIKKLNIDPVSLDKPVGKDEESKFVDFVKDDDNLNPEQFTEKELMGEHIDDILK 358

Query: 619 S-LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  +EE ++RMR+G+   +   TLEEVG+++ +TRER+RQIEAKA+RK+KHPS+S  L
Sbjct: 359 KFLQEKEEDIIRMRYGLPPYSHPMTLEEVGEKYGITRERVRQIEAKALRKIKHPSKSGIL 418

Query: 677 RSF 679
           + F
Sbjct: 419 KGF 421


>gi|126699102|ref|YP_001087999.1| RNA polymerase sigma factor rpoD [Clostridium difficile 630]
 gi|115250539|emb|CAJ68363.1| RNA polymerase sigma factor SigA2 (sigma-43) [Clostridium
           difficile]
          Length = 296

 Score =  227 bits (579), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 117/243 (48%), Positives = 167/243 (68%), Gaps = 6/243 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +S+AK++ + +N RLV+S+AK+Y    +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA
Sbjct: 55  SSVAKEKFINSNYRLVVSIAKRYKRDSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYA 114

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQ+ITR I D   TIRIP+H+  +I+ V +  + + N + REPT +EIA    + V
Sbjct: 115 TWWIKQSITRYIDDCENTIRIPIHLHQRINFVKKKKQELLNVLLREPTIDEIADACGLEV 174

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIED----KNAVSPLDSAIQANLRETTTRV 616
           + V ++L+  K  +SL+TP+ +++ S L +FI      K+ V  +    Q NL+E    +
Sbjct: 175 DKVLELLRRDKNVVSLDTPLKEDEDSSLVEFIPSDADFKDVV--IHEVEQHNLKEKIEEL 232

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  +E++VLRMRFGI  +   TLE++GK F VTRERIRQIEAKAIRKL+HPS+ K+L
Sbjct: 233 LTGLGEQEQQVLRMRFGIDDDDPKTLEQIGKVFGVTRERIRQIEAKAIRKLRHPSKLKQL 292

Query: 677 RSF 679
           + F
Sbjct: 293 KHF 295


>gi|254975054|ref|ZP_05271526.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-66c26]
 gi|255092443|ref|ZP_05321921.1| RNA polymerase sigma factor rpoD [Clostridium difficile CIP 107932]
 gi|255100524|ref|ZP_05329501.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-63q42]
 gi|255308764|ref|ZP_05352935.1| RNA polymerase sigma factor rpoD [Clostridium difficile ATCC 43255]
 gi|255314181|ref|ZP_05355764.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-76w55]
 gi|255516860|ref|ZP_05384536.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-97b34]
 gi|255649961|ref|ZP_05396863.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-37x79]
 gi|306520043|ref|ZP_07406390.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-32g58]
          Length = 294

 Score =  227 bits (579), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 117/243 (48%), Positives = 167/243 (68%), Gaps = 6/243 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +S+AK++ + +N RLV+S+AK+Y    +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA
Sbjct: 53  SSVAKEKFINSNYRLVVSIAKRYKRDSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYA 112

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQ+ITR I D   TIRIP+H+  +I+ V +  + + N + REPT +EIA    + V
Sbjct: 113 TWWIKQSITRYIDDCENTIRIPIHLHQRINFVKKKKQELLNVLLREPTIDEIADACGLEV 172

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIED----KNAVSPLDSAIQANLRETTTRV 616
           + V ++L+  K  +SL+TP+ +++ S L +FI      K+ V  +    Q NL+E    +
Sbjct: 173 DKVLELLRRDKNVVSLDTPLKEDEDSSLVEFIPSDADFKDVV--IHEVEQHNLKEKIEEL 230

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  +E++VLRMRFGI  +   TLE++GK F VTRERIRQIEAKAIRKL+HPS+ K+L
Sbjct: 231 LTGLGEQEQQVLRMRFGIDDDDPKTLEQIGKVFGVTRERIRQIEAKAIRKLRHPSKLKQL 290

Query: 677 RSF 679
           + F
Sbjct: 291 KHF 293


>gi|260683114|ref|YP_003214399.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260686712|ref|YP_003217845.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
 gi|260209277|emb|CBA62619.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260212728|emb|CBE03837.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
          Length = 301

 Score =  227 bits (579), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 117/243 (48%), Positives = 167/243 (68%), Gaps = 6/243 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +S+AK++ + +N RLV+S+AK+Y    +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA
Sbjct: 60  SSVAKEKFINSNYRLVVSIAKRYKRDSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYA 119

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQ+ITR I D   TIRIP+H+  +I+ V +  + + N + REPT +EIA    + V
Sbjct: 120 TWWIKQSITRYIDDCENTIRIPIHLHQRINFVKKKKQELLNVLLREPTIDEIADACGLEV 179

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIED----KNAVSPLDSAIQANLRETTTRV 616
           + V ++L+  K  +SL+TP+ +++ S L +FI      K+ V  +    Q NL+E    +
Sbjct: 180 DKVLELLRRDKNVVSLDTPLKEDEDSSLVEFIPSDADFKDVV--IHEVEQHNLKEKIEEL 237

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  +E++VLRMRFGI  +   TLE++GK F VTRERIRQIEAKAIRKL+HPS+ K+L
Sbjct: 238 LTGLGEQEQQVLRMRFGIDDDDPKTLEQIGKVFGVTRERIRQIEAKAIRKLRHPSKLKQL 297

Query: 677 RSF 679
           + F
Sbjct: 298 KHF 300


>gi|160902085|ref|YP_001567666.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359729|gb|ABX31343.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 424

 Score =  227 bits (579), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 115/252 (45%), Positives = 168/252 (66%), Gaps = 5/252 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ +     A++E+++ANLRLVIS+AK+Y   GL FLDLIQEGNIGLMKA  KFDW  
Sbjct: 171 LARRAQMGDKRAREELIKANLRLVISIAKRYVGHGLGFLDLIQEGNIGLMKAVAKFDWKK 230

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTY+ WW++QAITR+IADQ  T+RIPVH+ + I+++ R   +   +    P  EE+
Sbjct: 231 GYKFSTYSYWWIRQAITRAIADQGRTVRIPVHLVETINRMNRVVNKYIQENGEVPDLEEL 290

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQAN 608
           +  +  PV+ +++VL   K   SL  PI +    E  S + DFI D ++ +P +   +  
Sbjct: 291 SVLMDKPVDKMKEVLISAKNIFSLNAPISNDVDAEGESEVLDFI-DSDSPTPDEEGRKMI 349

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R+    ++ +L+P+E  +L+MR+G       TLEEVG+ F VTRERIRQIE+K+IRKLK
Sbjct: 350 IRQKMEMIIDTLSPKEAMILKMRYGFVDGKQKTLEEVGEFFNVTRERIRQIESKSIRKLK 409

Query: 669 HPSRSKKLRSFL 680
           HP+R K + + +
Sbjct: 410 HPARKKMIENII 421


>gi|26665382|dbj|BAC44902.1| principal sigma factor [Anabaena planctonica TAC421]
          Length = 203

 Score =  227 bits (579), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 112/204 (54%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE +   +P D   +  LRE   +VL SL PRE  VL
Sbjct: 121 SAQSPISLETPIGKEEDSRLGDFIESEGE-TPEDQVSKNLLREDLEKVLDSLGPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|23978369|dbj|BAC21149.1| principal sigma factor [Pseudanabaena sp. PCC 7403]
          Length = 203

 Score =  227 bits (578), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 111/204 (54%), Positives = 151/204 (74%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIES-DGETPDDQVAKSLLREDLESVLGTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|291566491|dbj|BAI88763.1| group 2 RNA polymerase sigma factor SigC [Arthrospira platensis
           NIES-39]
          Length = 385

 Score =  227 bits (578), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 115/271 (42%), Positives = 182/271 (67%), Gaps = 2/271 (0%)

Query: 412 EIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           E+K I  E     +E  ++ V  +++ + E   AK  M++ANLRLV+SVAKKY NRGL+ 
Sbjct: 113 ELKQIMAEGKRCWAELANLSVEELKQVQREGIQAKDHMIKANLRLVVSVAKKYQNRGLEL 172

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q ITR+IA QS TIR+PVH+ +K++
Sbjct: 173 LDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQGITRAIATQSRTIRLPVHITEKLN 232

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ +  R++S +  R  T ++IA +L M  + +R+VL      +SLET +G +  + LGD
Sbjct: 233 KIKKAQRKISQEKSRTATIDDIATELKMTPDQIREVLLRVPRSVSLETKVGTDKDTELGD 292

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E + + +P +  ++ +L      +LA L+ +E  V++MR+G+G    ++L E+G+   
Sbjct: 293 LLETEES-TPEELLMRESLYRELQHILADLSGKERAVIQMRYGLGDGHPYSLAEIGRALD 351

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++RER+RQIEAKA++KL+ P R  ++R +LD
Sbjct: 352 LSRERVRQIEAKALQKLRQPKRRNRVRDYLD 382


>gi|9837536|gb|AAG00589.1|AF288784_1 SigC [Synechococcus elongatus PCC 7942]
          Length = 398

 Score =  227 bits (578), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 114/242 (47%), Positives = 164/242 (67%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   AK  M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTY
Sbjct: 155 EGQRAKDHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTY 214

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q ITR+IA QS TIR+PVH+ +K+ ++ +  R+++    R    EEIA++L M 
Sbjct: 215 AYWWIRQGITRAIATQSRTIRLPVHVTEKLTRIKKAQRKIAQTKGRTANLEEIAQELEMT 274

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + VR+VL    + ISLET +G E  + LGD +E  +  +P +   Q +L     R+L  
Sbjct: 275 PDQVREVLLRVPKSISLETRVGKEKDTELGDLLETTD-FTPEERLTQESLSNDLQRLLLE 333

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE  V+RMRFG+     ++L E+G+   ++RER+RQIEAKA++KL+HP R  ++R +
Sbjct: 334 LNHRERDVIRMRFGLRDGQIYSLAEIGQVLDLSRERVRQIEAKALQKLRHPRRRNQIRDY 393

Query: 680 LD 681
           L+
Sbjct: 394 LE 395


>gi|218661052|ref|ZP_03516982.1| RNA polymerase sigma factor RpoD [Rhizobium etli IE4771]
          Length = 276

 Score =  226 bits (577), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 148/301 (49%), Positives = 184/301 (61%), Gaps = 47/301 (15%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVD-----------------GDDLEDEEGSEDSLDLASSASNSS 103
           EQ+EDT++MLS+MGINV++                     ED EG E    LA S   ++
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGE----LAPSG-GTA 115

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLT
Sbjct: 116 LATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLT 174

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERD 221
           FQALIIWRDELN+GTTLLREIIDLE    GPE+K    F   E     ++    +EK R 
Sbjct: 175 FQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR- 233

Query: 222 DVQETEGDIESAAKVSKDDRSKVDS---PPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                       A+   DD + V     PPE  E DE         S  +L+AME +LRP
Sbjct: 234 -----------RARSGDDDITDVGGEGLPPEEEEEDEDE-------SNLSLAAMEAELRP 275

Query: 279 K 279
           +
Sbjct: 276 Q 276


>gi|47459124|ref|YP_015986.1| RNA polymerase sigma factor [Mycoplasma mobile 163K]
 gi|47458453|gb|AAT27775.1| DNA-directed RNA polymerase sigma factor [Mycoplasma mobile 163K]
          Length = 488

 Score =  226 bits (577), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 109/241 (45%), Positives = 163/241 (67%), Gaps = 9/241 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++  NLRLVI+ AKKY NRGL F+DLI EGN GL+KAA K+D+  G+KFSTYA WWV+QA
Sbjct: 243 LIHHNLRLVINNAKKYKNRGLSFIDLISEGNAGLIKAATKYDYRRGFKFSTYATWWVRQA 302

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVEGVRK 565
           ITR++ADQ+  +R+PVHM + I+K+++  R +  ++   PT ++IA+K       E V+ 
Sbjct: 303 ITRAVADQARIVRVPVHMVETINKIIKIERELHQELGVPPTDKQIAEKYGNNFTAEKVQY 362

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + KI  +PISL+  IG +D S   DF++D++ VSPL+ A Q  L    T +L       E
Sbjct: 363 IRKINIDPISLDKSIGKDDDSSFSDFVKDESVVSPLEFASQNELSGILTDILEKHLDEAE 422

Query: 626 R-VLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           R +++ RFGIG++ D      H+LEE+  +  +++E++R +E+K +RKLKHP + KKL+ 
Sbjct: 423 RDLIKKRFGIGVDKDGNRISSHSLEELAAELQISKEKVRSLESKILRKLKHPQKRKKLKE 482

Query: 679 F 679
           F
Sbjct: 483 F 483


>gi|255655509|ref|ZP_05400918.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-23m63]
          Length = 294

 Score =  226 bits (577), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 116/243 (47%), Positives = 167/243 (68%), Gaps = 6/243 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +S+AK++ + +N RLV+S+AK+Y    +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA
Sbjct: 53  SSVAKEKFINSNYRLVVSIAKRYKRDSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYA 112

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQ+ITR I D   TIRIP+H+  +I+ V +  + + N + REPT +EIA    + V
Sbjct: 113 TWWIKQSITRYIDDCENTIRIPIHLHQRINFVKKKKQELLNVLLREPTIDEIADACGLEV 172

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIED----KNAVSPLDSAIQANLRETTTRV 616
           + V ++L+  K  +SL+TP+ +++ S L +FI      K+ V  +    Q NL+E    +
Sbjct: 173 DKVLELLRRDKNVVSLDTPLKEDEDSSLVEFIPSDADFKDVV--MHEVEQHNLKEKIEEL 230

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  +E++VLRMRFGI  +   TLE++G+ F VTRERIRQIEAKAIRKL+HPS+ K+L
Sbjct: 231 LTGLGEQEQQVLRMRFGIDDDDPKTLEQIGRVFGVTRERIRQIEAKAIRKLRHPSKLKQL 290

Query: 677 RSF 679
           + F
Sbjct: 291 KHF 293


>gi|172040574|ref|YP_001800288.1| RNA polymerase sigma factor SigB [Corynebacterium urealyticum DSM
           7109]
 gi|171851878|emb|CAQ04854.1| RNA polymerase sigma factor B [Corynebacterium urealyticum DSM
           7109]
          Length = 340

 Score =  226 bits (576), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 112/241 (46%), Positives = 175/241 (72%), Gaps = 2/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 99  EGKAARTHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYKKGFKFSTY 158

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  +P
Sbjct: 159 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATYEELAEESGIP 218

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
            + +  ++K +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A+LR +  R VLA
Sbjct: 219 EDRIEMLMKQSRDPVSLDMPVGTDEEAPLGDFIEDSEAED-AEAAVVASLRHSDIRSVLA 277

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE+ V+ +R+G+      TL+++G+QF ++RER+RQIE + + KL+   R+ KLR 
Sbjct: 278 TLEQREQDVITLRYGLDDGLPRTLDQIGRQFGLSRERVRQIEREVMAKLREGQRADKLRE 337

Query: 679 F 679
           +
Sbjct: 338 Y 338


>gi|254421571|ref|ZP_05035289.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196189060|gb|EDX84024.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 390

 Score =  226 bits (576), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 105/225 (46%), Positives = 159/225 (70%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K++M+EANLRLV++VAKKY  R L+FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 154 SKRKMIEANLRLVVAVAKKYQKRNLEFLDLIQEGTLGLERGVEKFDPMKGYKFSTYAYWW 213

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ R  R +S K+ R P   EI ++L +  + V
Sbjct: 214 IRQAITRAIAQQARTIRLPIHITEKLNKIKRVQRELSQKLGRSPNAAEIGQELELEPKQV 273

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  IGD   + L D +ED  A SP D  +Q +LR    R+L+ LT +
Sbjct: 274 REYLSIARQPISLDVRIGDNQDTELQDLLEDDGA-SPEDYTVQQSLRSDIFRMLSELTSQ 332

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ V+ +RFG+      +L +VG++  ++RER+RQ+E +A++ L+
Sbjct: 333 QQEVINLRFGLADGNPLSLAKVGQRMGISRERVRQLEQQALKHLR 377


>gi|218439766|ref|YP_002378095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172494|gb|ACK71227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 418

 Score =  226 bits (576), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 121/290 (41%), Positives = 178/290 (61%), Gaps = 9/290 (3%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVE-TGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           +W +     V  + +I NE K       G+ + E   I    +K   EA   K  M++AN
Sbjct: 135 KWADAAEVSVFEVKQILNEGKRHWANLAGLKVQELEQI----QKAGIEA---KNHMIKAN 187

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+SVAK+Y NRGL+ LDLIQEG +GL +A EKFD   GY+FSTYA WW++Q ITR+I
Sbjct: 188 LRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAI 247

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A QS  IR+PVH+ +K++K+ +  R+M+    R PT EE+A ++ M    +R+VL     
Sbjct: 248 ATQSRIIRLPVHITEKLNKIKKAQRKMAQIKGRTPTMEELAVEVDMTAPQIREVLMRVPR 307

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SLE  +G E  + L D +E   A SP +S +   LR+    +LA LT RE  V++MR+
Sbjct: 308 SVSLEIKVGKEKDTELVDLLETTEA-SPEESLVNETLRQDLQNLLADLTTREREVIQMRY 366

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G      ++L ++G+   ++RER+RQIEAKAI+KL+ P R  ++R + + 
Sbjct: 367 GFKDGKCYSLADIGRALQLSRERVRQIEAKAIQKLRQPKRRNQIRDYFEA 416


>gi|296451502|ref|ZP_06893237.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296880149|ref|ZP_06904116.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
 gi|296259567|gb|EFH06427.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296428874|gb|EFH14754.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
          Length = 301

 Score =  226 bits (576), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 116/243 (47%), Positives = 167/243 (68%), Gaps = 6/243 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +S+AK++ + +N RLV+S+AK+Y    +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA
Sbjct: 60  SSVAKEKFINSNYRLVVSIAKRYKRDSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYA 119

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQ+ITR I D   TIRIP+H+  +I+ V +  + + N + REPT +EIA    + V
Sbjct: 120 TWWIKQSITRYIDDCENTIRIPIHLHQRINFVKKKKQELLNVLLREPTIDEIADACGLEV 179

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIED----KNAVSPLDSAIQANLRETTTRV 616
           + V ++L+  K  +SL+TP+ +++ S L +FI      K+ V  +    Q NL+E    +
Sbjct: 180 DKVLELLRRDKNVVSLDTPLKEDEDSSLVEFIPSDADFKDVV--MHEVEQHNLKEKIEEL 237

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  +E++VLRMRFGI  +   TLE++G+ F VTRERIRQIEAKAIRKL+HPS+ K+L
Sbjct: 238 LTGLGEQEQQVLRMRFGIDDDDPKTLEQIGRVFGVTRERIRQIEAKAIRKLRHPSKLKQL 297

Query: 677 RSF 679
           + F
Sbjct: 298 KHF 300


>gi|168009782|ref|XP_001757584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691278|gb|EDQ77641.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 583

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 121/273 (44%), Positives = 175/273 (64%), Gaps = 15/273 (5%)

Query: 408 KIRNEI-KSISVETGISISEFRHIVSM--------VRKGECEASIAKKEMVEANLRLVIS 458
           KIR E+ + I  E   ++SE+   VS+        V++G      AK ++V +NLRLV+S
Sbjct: 304 KIRAELQRDIGREP--TLSEWSQAVSLDQTSLELRVKEGRS----AKDKLVNSNLRLVVS 357

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           + K Y  RG+   DLIQEG++GL++ AEKFD  +GYKFSTYA WW++QA+TR+IADQS  
Sbjct: 358 IVKNYQGRGMTLPDLIQEGSLGLIRGAEKFDPEMGYKFSTYATWWIRQAVTRAIADQSRI 417

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVH+ + I ++ +    +S ++ R+P  EE+A  + M VE +  ++K  + P S++ 
Sbjct: 418 IRLPVHIYEVISRINKAKMTISQELGRQPRDEEVAAMVGMSVEKLLFIVKSARPPTSMDR 477

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG +    LG+ + DK   SP D  +   L++    VL SL P E  VLR+RFG+    
Sbjct: 478 PIGKDGEQSLGEMVADKGVGSPEDDIMTQVLKQDIEDVLRSLNPMEREVLRLRFGLSGAQ 537

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TL+++G  F VTRERIRQIEAKA+RKL+HPS
Sbjct: 538 SMTLKDLGIIFKVTRERIRQIEAKALRKLRHPS 570


>gi|153814577|ref|ZP_01967245.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|317501262|ref|ZP_07959466.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089991|ref|ZP_08338881.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848071|gb|EDK24989.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|316897329|gb|EFV19396.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330402905|gb|EGG82471.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 273

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 108/226 (47%), Positives = 155/226 (68%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E NLRLV+S+AK YT RGL  +DLIQEGNIGLM AAEK+D+    +FSTYA WW
Sbjct: 44  ARARLEEGNLRLVVSIAKHYTGRGLPLMDLIQEGNIGLMHAAEKYDYTKDNRFSTYASWW 103

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           +K+AITR+I  QS  IR+PVH+ + I +V + A+ +  +  RE  P EIAKKL     E 
Sbjct: 104 IKEAITRAIDQQSREIRVPVHVAENIKRVQKAAKELQQEFGREAEPGEIAKKLGDRTEEE 163

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V+ +L   + P+SLETP+G++    LGDF+ED++  +P D+      +E    +L +L  
Sbjct: 164 VKNILSYIRNPVSLETPVGEDGEDSLGDFVEDRSETTPEDAMDVLVRKEEVQELLETLND 223

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ V+ +RFG+G +  +TLEE+G+   +TRER+RQIE+KA+ KL+
Sbjct: 224 REKEVISLRFGLGKDRTYTLEEIGESLGITRERVRQIESKAMEKLR 269


>gi|81300366|ref|YP_400574.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
 gi|81169247|gb|ABB57587.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
          Length = 310

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 107/234 (45%), Positives = 165/234 (70%), Gaps = 1/234 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+FLDLIQEG +GL +A EKFD   GYKFSTYA WW
Sbjct: 75  AKERMIKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYAFWW 134

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++ ++ +  R +++++ R P+ +EIA+ + +P+  +
Sbjct: 135 IRQSMTRAIACQSRTIRLPVHLTERLSQIRKVTRELAHELGRLPSRQEIAEAVQLPLNDL 194

Query: 564 RKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+ +++  SL+ P+  ED  S LG+ I D N   P+D    A  RE     L  LTP
Sbjct: 195 ETILRQSRQCTSLDAPVSGEDGKSFLGELIADPNGNEPMDIMENAMQREQLDAWLEHLTP 254

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +E +VL +RFG+G    HTL E+G+   V+RER+RQ+E KA+RKL++ ++  ++
Sbjct: 255 QERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKLRNLTKRSRI 308


>gi|56750024|ref|YP_170725.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
 gi|56684983|dbj|BAD78205.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
          Length = 316

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 107/234 (45%), Positives = 165/234 (70%), Gaps = 1/234 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+FLDLIQEG +GL +A EKFD   GYKFSTYA WW
Sbjct: 81  AKERMIKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYAFWW 140

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++ ++ +  R +++++ R P+ +EIA+ + +P+  +
Sbjct: 141 IRQSMTRAIACQSRTIRLPVHLTERLSQIRKVTRELAHELGRLPSRQEIAEAVQLPLNDL 200

Query: 564 RKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+ +++  SL+ P+  ED  S LG+ I D N   P+D    A  RE     L  LTP
Sbjct: 201 ETILRQSRQCTSLDAPVSGEDGKSFLGELIADPNGNEPMDIMENAMQREQLDAWLEHLTP 260

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +E +VL +RFG+G    HTL E+G+   V+RER+RQ+E KA+RKL++ ++  ++
Sbjct: 261 QERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKLRNLTKRSRI 314


>gi|40353299|gb|AAR84413.1| alternative primary sigma 70 factor [Frankia sp. ORS020607]
          Length = 220

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 152/207 (73%), Gaps = 4/207 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +V+ G      AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EK
Sbjct: 11  RDLGLLVKDGHA----AKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEK 66

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REP
Sbjct: 67  FDYAKGYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREP 126

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A   
Sbjct: 127 TDEELALELDMPIEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYG 186

Query: 608 NLRETTTRVLASLTPREERVLRMRFGI 634
            +++    VL  L+PRE  V+R+RFG+
Sbjct: 187 AMQDEIENVLGGLSPREREVMRLRFGL 213


>gi|209525810|ref|ZP_03274346.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209493783|gb|EDZ94102.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 407

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 117/288 (40%), Positives = 183/288 (63%), Gaps = 9/288 (3%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVE-TGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           W       V  + +I  E K    E   +S+ E + +       + E   AK  M++ANL
Sbjct: 125 WAAAGGVNVAQLKQIMAEGKRCWAELANLSVEELKQV-------QREGLQAKDHMIKANL 177

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q ITR+IA
Sbjct: 178 RLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQGITRAIA 237

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            QS TIR+PVH+ +K++K+ +  R++S +  R  T ++IA +L M  + +R+VL      
Sbjct: 238 TQSRTIRLPVHITEKLNKIKKAQRKISQEKSRTATIDDIATELKMTPDQIREVLLRVPRS 297

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLET +G +  + LGD +E + + +P +  ++ +L      +LA L+ +E  V++MR+G
Sbjct: 298 VSLETKVGTDKDTELGDLLETEES-TPEELLMRESLYRELQNLLADLSGKERAVIQMRYG 356

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +G    ++L E+G+   ++RER+RQIEAKA++KL+ P R  ++R +LD
Sbjct: 357 LGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRVRDYLD 404


>gi|168703618|ref|ZP_02735895.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 521

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 113/276 (40%), Positives = 169/276 (61%), Gaps = 2/276 (0%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           ++  +++       ++  E   +V ++RK        +KE+ EANLRLV+S+AK Y NRG
Sbjct: 244 RLGRQLRDAECRACMTADELAALVRVLRKRRLAYQAVRKELAEANLRLVVSIAKNYRNRG 303

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLIQEGN GLM+A +K++W L +KF TYA WWV+Q ITR++ D + T+R+P H   
Sbjct: 304 LPFSDLIQEGNRGLMRAVDKYEWRLEFKFGTYATWWVRQGITRALHDNARTVRVPCHQIS 363

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            + ++ +    ++    REPT EE+A+ L +  E  R +  + + P+SL   +G +    
Sbjct: 364 LLSRMEKLRGELTVATGREPTSEELAEALGVKPEEARSLRIVGRHPVSLNDSVGGDGERA 423

Query: 588 LGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           L DF+ D + +SP    + AN L+E    VL SL PRE  V+ +RFG+   T  TL+EV 
Sbjct: 424 LEDFLSDTH-ISPPGEHVDANLLKERIGEVLKSLAPREREVIELRFGLKDGTPKTLDEVA 482

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           KQ+ +TRERIRQIEA+ + KL+ P+RS +L  F D 
Sbjct: 483 KQYGITRERIRQIEARGLLKLRQPTRSCRLEEFADA 518



 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 30/44 (68%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           DD + +YLR+MGSI LL+RE E+A+AKR+E  R    A+    P
Sbjct: 68  DDALGLYLRQMGSIPLLNREKELALAKRLEHHRNRFRAAALLCP 111


>gi|189916717|gb|ACE62869.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 108/159 (67%), Positives = 131/159 (82%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM++ I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD
Sbjct: 1   VHMKETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGD 60

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 61  DEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTL 120

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 159


>gi|1769598|gb|AAB39998.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 115/273 (42%), Positives = 178/273 (65%), Gaps = 8/273 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR   +  + + G+S+ E   I+    K       AK+ M++ANLRLV+SVAKKY NRGL
Sbjct: 131 IRQGKQRWAEQVGLSVKELDSILKAGAK-------AKEHMIQANLRLVVSVAKKYQNRGL 183

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEG +GL +A +KFD   GY+FSTYA WW++Q ITR    QS TIR+PVH+ +K
Sbjct: 184 ELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWWIRQGITRGDRTQSRTIRLPVHVTEK 243

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +  R++S      P+ +++A+ L M  E VR+VL+     +SLE  +G +  + L
Sbjct: 244 LNKIKKAQRQISQTQGCTPSLDDVAQALEMTPEQVREVLQKVPRSVSLEIRVGKDRDTEL 303

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD +E ++A SP ++ ++ +L+     +L  LT RE  V+++R+G+G    ++L E+G+ 
Sbjct: 304 GDLLETQDA-SPEENLVRESLQRDLHNLLTELTDREREVIQLRYGLGDGKTYSLAEIGRM 362

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+RER+RQIEAKA++KL+ P R   +R +LD
Sbjct: 363 LDVSRERVRQIEAKALQKLRQPKRRNIMRDYLD 395


>gi|23978337|dbj|BAC21138.1| principal sigma factor [Pseudanabaena sp. PCC 7367]
          Length = 203

 Score =  224 bits (572), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 110/204 (53%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIES-DGETPDDQVAKNLLREDLENVLGTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           ++R+G+      TLEE+G+ F VT
Sbjct: 180 KLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|170076992|ref|YP_001733630.1| group II sigma-70 type sigma factor [Synechococcus sp. PCC 7002]
 gi|1769590|gb|AAB95227.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169884661|gb|ACA98374.1| Group II sigma-70 type sigma factor (RpoD family) [Synechococcus
           sp. PCC 7002]
          Length = 365

 Score =  224 bits (572), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 109/260 (41%), Positives = 178/260 (68%), Gaps = 5/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +   + + S + KG     +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL
Sbjct: 109 LGLETVKQLNSALYKGR----VAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGL 164

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +AAEKFD   GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  
Sbjct: 165 NRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRTLKQ 224

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            ++R PT  E+A++L +  + + ++L++ ++ +SL   +G  + + L D +ED     P 
Sbjct: 225 TLQRNPTEAELAQELDITADQLHQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDGLQLPE 284

Query: 602 DSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +   +A +R+    VL   LT RE+ V+ +R+G+     HTLEEVG  F ++RER+RQI+
Sbjct: 285 ERMSEAMMRQELWDVLGDVLTDREKEVIALRYGLSSEQPHTLEEVGGMFNLSRERVRQIQ 344

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           +KA+RKL+ P  +++L+S+L
Sbjct: 345 SKAMRKLRRPQVARRLKSWL 364


>gi|194246700|ref|YP_002004339.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
 gi|193807057|emb|CAP18493.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
          Length = 419

 Score =  224 bits (572), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 123/259 (47%), Positives = 176/259 (67%), Gaps = 8/259 (3%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ISE   I+ +  K       AK  +VEAN RLV+S+AK+Y  RGL+FLDLIQEGN GLM+
Sbjct: 163 ISELNDILKISNK-------AKHRLVEANYRLVVSIAKRYIRRGLEFLDLIQEGNRGLMR 215

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF+   G K STYA +W+ Q I R++ADQ+  IR+PVH+ D+I+ +     ++  K+
Sbjct: 216 AIEKFNIDKGCKLSTYATFWIVQKILRAVADQARIIRLPVHIVDRINIISMAKSKLRLKL 275

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPT EE+++ + +  + +R +  I K+PISLE  +G++D S LG+FI D +++SP D 
Sbjct: 276 HREPTIEELSEFINISEKKLRIIEIIKKKPISLEARVGEKDDSSLGEFISDPDSLSPHDY 335

Query: 604 AIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            +Q  ++ T   +L  +LT REE++LRMR+G+     HTLEEVG  F VTRERIRQIEAK
Sbjct: 336 MLQEIMKNTLNEILEDTLTDREEKILRMRYGLSNGKVHTLEEVGNVFGVTRERIRQIEAK 395

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A R+L+ P+R  KL++  +
Sbjct: 396 AFRRLRTPARQNKLKTLYN 414


>gi|22298374|ref|NP_681621.1| RNA polymerase sigma factor [Thermosynechococcus elongatus BP-1]
 gi|22294553|dbj|BAC08383.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 309

 Score =  224 bits (572), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 108/251 (43%), Positives = 175/251 (69%), Gaps = 7/251 (2%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +++++GE     AK++M+EANLRLV+SVAKKY  R L+ LDL+QEG +GL +  EKFD
Sbjct: 64  LCNILKRGER----AKQKMIEANLRLVVSVAKKYQKRNLELLDLVQEGTLGLERGVEKFD 119

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+ RT R ++ K+ R  TP
Sbjct: 120 PTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKRTQRELAQKLGRSATP 179

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            E+AK L +  E +R+ L + ++P+SL+  +GD   + LG+ +ED +++SP       +L
Sbjct: 180 AEVAKALELEPEQIREYLTLARQPVSLDLRVGDNQDTELGELLED-DSLSPEQFTTVESL 238

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     LA LTP++ +VL +R+G+G   + +L +VG+Q  ++RER+RQ+E +A+  L+ 
Sbjct: 239 RDDVNLWLAELTPQQRQVLTLRYGLGDGQELSLAKVGEQLNLSRERVRQLERQALDHLRR 298

Query: 670 PSRSKKLRSFL 680
             R +++  +L
Sbjct: 299 --RRQQMYEYL 307


>gi|23978365|dbj|BAC21147.1| principal sigma factor [Leptolyngbya sp. PCC 7375]
          Length = 203

 Score =  224 bits (572), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 110/204 (53%), Positives = 151/204 (74%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL++L+P E  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIES-DGETPEDEVSKSLLREDLEGVLSTLSPSERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|197302434|ref|ZP_03167489.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
 gi|197298332|gb|EDY32877.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
          Length = 283

 Score =  224 bits (571), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 105/227 (46%), Positives = 161/227 (70%), Gaps = 1/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ + E NLRLV+S+AK YT RG+  +DLIQEGNIGLM+A EK+D+    +FSTYA WW
Sbjct: 53  ARRRLEEGNLRLVVSIAKHYTGRGIPLMDLIQEGNIGLMRAVEKYDFTKENRFSTYASWW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           +K+AI R+I  QS  IR+PVH+ + + KV R ++ +   + RE TPEEIA+KL     E 
Sbjct: 113 IKEAIQRAIDQQSREIRVPVHVAEAMKKVQRISKELQQSLGREATPEEIAEKLGDKSTED 172

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V+ +L   + P+SLETP+G++  ++LGD +EDK + +P ++      +E  + +L +L  
Sbjct: 173 VKNILSYLQNPVSLETPVGEDGENNLGDMVEDKASPTPEEAMNLLVQKEEVSELLNALND 232

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE++V+R+R+G+     HTLEE+G++  VTRER+RQIE++A+ KL++
Sbjct: 233 REKQVIRLRYGLEDGKTHTLEEIGEELKVTRERVRQIESRAMEKLRN 279


>gi|148358826|ref|YP_001250033.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|296106871|ref|YP_003618571.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
 gi|148280599|gb|ABQ54687.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|295648772|gb|ADG24619.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
          Length = 341

 Score =  224 bits (571), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 105/240 (43%), Positives = 170/240 (70%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H  ++  KG+ EA   +K+M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GLMK+ EKF
Sbjct: 91  HYATLALKGDMEA---RKKMIESNLRLVVKIARRYLNRGLPLLDLIEEGNLGLMKSVEKF 147

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP+
Sbjct: 148 DPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEPS 207

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA+ +  P+E V+K+L +  +  S++TPIG ++T  L D I D+N+++P +     N
Sbjct: 208 PEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDTIADENSLNPAELLTNEN 267

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+    +L  LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L+
Sbjct: 268 LRQHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTLR 327


>gi|5771430|gb|AAD51396.1|AF117715_5 stationary phase specific sigma factor homolog [Legionella
           pneumophila]
          Length = 341

 Score =  224 bits (571), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 105/240 (43%), Positives = 170/240 (70%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H  ++  KG+ EA   +K+M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GLMK+ EKF
Sbjct: 91  HYATLALKGDMEA---RKKMIESNLRLVVKIARRYLNRGLPLLDLIEEGNLGLMKSVEKF 147

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP+
Sbjct: 148 DPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEPS 207

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA+ +  P+E V+K+L +  +  S++TPIG ++T  L D I D+N+++P +     N
Sbjct: 208 PEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDTIADENSLNPAELLTNEN 267

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+    +L  LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L+
Sbjct: 268 LRQHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTLR 327


>gi|54294183|ref|YP_126598.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|54297202|ref|YP_123571.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53750987|emb|CAH12398.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53754015|emb|CAH15486.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|307609996|emb|CBW99528.1| RNA polymerase sigma factor RpoS [Legionella pneumophila 130b]
          Length = 341

 Score =  224 bits (571), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 105/240 (43%), Positives = 170/240 (70%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H  ++  KG+ EA   +K+M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GLMK+ EKF
Sbjct: 91  HYATLALKGDMEA---RKKMIESNLRLVVKIARRYLNRGLPLLDLIEEGNLGLMKSVEKF 147

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP+
Sbjct: 148 DPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEPS 207

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA+ +  P+E V+K+L +  +  S++TPIG ++T  L D I D+N+++P +     N
Sbjct: 208 PEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDTIADENSLNPAELLTNEN 267

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+    +L  LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L+
Sbjct: 268 LRQHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTLR 327


>gi|330961077|gb|EGH61337.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 167

 Score =  224 bits (570), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 109/164 (66%), Positives = 134/164 (81%)

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI KEPIS+E
Sbjct: 3   TIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISME 62

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRMRFGI MN
Sbjct: 63  TPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMN 122

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 123 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 166


>gi|254421657|ref|ZP_05035375.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
 gi|196189146|gb|EDX84110.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
          Length = 467

 Score =  224 bits (570), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 107/257 (41%), Positives = 175/257 (68%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           + F +    +R+   +A  AK+ M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A
Sbjct: 210 TAFGYTEGQLRQKLRQARAAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRA 269

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           AEKFD   GYKFSTYA WW++Q ITR+IA+ + TIR+P+H+ +K++K+ +  R +  +++
Sbjct: 270 AEKFDPDKGYKFSTYAYWWIRQGITRTIANDARTIRLPIHIVEKLNKLKKAQRELRKELQ 329

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R PT  E+A  L M  E +R + ++ ++ +SL   +G  + + L + +ED N++SP    
Sbjct: 330 RTPTEVEVAAALEMTPEQLRTLQQVQRKSLSLNHRVGKGEDTELMELLEDGNSLSPESQI 389

Query: 605 IQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            ++ +R+  + VL   LT RE+ ++ +R+G+     HTLEEVG  F ++RER+RQI+ KA
Sbjct: 390 SESMMRQEISDVLTEVLTEREKEIIALRYGLTTGETHTLEEVGGIFQLSRERVRQIQTKA 449

Query: 664 IRKLKHPSRSKKLRSFL 680
           +RKL+ P  + +L+++L
Sbjct: 450 MRKLRRPQVAARLKNWL 466


>gi|23978350|dbj|BAC21142.1| principal sigma factor [Xenococcus sp. PCC 7307]
          Length = 203

 Score =  224 bits (570), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/204 (54%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKSLLREDLESVLDTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|282897491|ref|ZP_06305492.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281197586|gb|EFA72481.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 429

 Score =  224 bits (570), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 167/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 190 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 249

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E++A +L M    V
Sbjct: 250 IRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLALELDMTPNQV 309

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLET +G +  + LG+ +E  + ++P ++ ++ +L++    +L+ LT R
Sbjct: 310 REVLLRVPRSVSLETKVGKDKDTELGELLE-TDTITPEETLMRESLQKDIHHLLSDLTTR 368

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P R   +R +L+
Sbjct: 369 EREVILMRFGLADGHSYSLAEIGRALELSRERVRQIESKALQKLRQPKRRNLVRDYLE 426


>gi|52841515|ref|YP_095314.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52628626|gb|AAU27367.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 359

 Score =  224 bits (570), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 105/240 (43%), Positives = 170/240 (70%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H  ++  KG+ EA   +K+M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GLMK+ EKF
Sbjct: 109 HYATLALKGDMEA---RKKMIESNLRLVVKIARRYLNRGLPLLDLIEEGNLGLMKSVEKF 165

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP+
Sbjct: 166 DPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEPS 225

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA+ +  P+E V+K+L +  +  S++TPIG ++T  L D I D+N+++P +     N
Sbjct: 226 PEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDTIADENSLNPAELLTNEN 285

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+    +L  LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L+
Sbjct: 286 LRQHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTLR 345


>gi|23978335|dbj|BAC21137.1| principal sigma factor [Phormidium sp. IAM M-99]
          Length = 203

 Score =  223 bits (569), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 110/204 (53%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++N RLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VLA+L+PRE+ VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIES-DGETPEDQVSKNLLREDLEGVLATLSPREKDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+ +G+      TLEE+G+ F VT
Sbjct: 180 RLHYGLDDGRMKTLEEIGQIFNVT 203


>gi|302867958|ref|YP_003836595.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|302570817|gb|ADL47019.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 314

 Score =  223 bits (569), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 112/235 (47%), Positives = 162/235 (68%), Gaps = 3/235 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  M+EANLRLV+SVAK+Y   G L  LDLIQEG IGLM+A EKFD   G KFSTYA W
Sbjct: 76  ARHHMIEANLRLVVSVAKRYALAGRLPLLDLIQEGTIGLMRAVEKFDHRRGLKFSTYATW 135

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W+KQAI R++ DQS TIR+P H+ + +++V RT R ++ ++ REPTP E+A ++ +P E 
Sbjct: 136 WIKQAIGRALTDQSRTIRLPAHLVEVLNRVNRTRRTLAGELDREPTPAEVAARVEVPAEK 195

Query: 563 VRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           V  +L+  +EP+SL TP+ G   T+ LGD + D+ A  P    + +  R     VL +L+
Sbjct: 196 VELLLRHDREPVSLHTPVAGAAGTTELGDLLPDE-APGPAGVVVSSWRRRYLDEVLGTLS 254

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            RE  V+  R+G+  +   TL+E+G +  +TRER+RQIE++A+RKL+HP+R++ L
Sbjct: 255 EREAAVICQRYGLDDDRPSTLDEIGTRIGLTRERVRQIESQALRKLRHPTRARVL 309


>gi|282900041|ref|ZP_06308000.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195073|gb|EFA70011.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 432

 Score =  223 bits (569), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 167/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 193 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 252

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E++A +L M    V
Sbjct: 253 IRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLALELDMTPNQV 312

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLET +G +  + LG+ +E  + ++P ++ ++ +L++    +L+ LT R
Sbjct: 313 REVLLRVPRSVSLETKVGKDKDTELGELLE-TDTITPEETLMRESLQKDIHHLLSDLTTR 371

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P R   +R +L+
Sbjct: 372 EREVILMRFGLADGHSYSLAEIGRALELSRERVRQIESKALQKLRQPKRRNLVRDYLE 429


>gi|16331222|ref|NP_441950.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1001398|dbj|BAA10020.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 345

 Score =  223 bits (569), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 102/225 (45%), Positives = 161/225 (71%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 109 AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 168

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q  TIR+P+H+ +K++K+ +T R +S ++ R  TP E+AK L +    +
Sbjct: 169 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKTQRELSQQLGRSATPAEVAKALEIDPSQI 228

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L ++++PISL+  +GD   + L + +ED+  VSP     Q ++R+    +LA LTP+
Sbjct: 229 REYLSLSRQPISLDVRVGDNQDTELSELLEDE-GVSPDAYITQESMRQDLQNLLAELTPQ 287

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL MRFG+    + +L ++G+   ++RER+RQ+E +A+ +LK
Sbjct: 288 QQAVLTMRFGLNDGQELSLAKIGQHLNISRERVRQLENQALAQLK 332


>gi|171322946|ref|ZP_02911628.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171091683|gb|EDT37240.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 498

 Score =  223 bits (569), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 105/237 (44%), Positives = 153/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D+  G++FSTYA WW
Sbjct: 261 ARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 320

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +     TP E+A  +  PV+ V
Sbjct: 321 IRQAITHALADLGRTIRVPTHTVDALNKLSRLARAHRQRAGTAATPAELAVHMGEPVDKV 380

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++ I KEP+S + P+  E      D   D    SP D+A  A LR T T V+  L PR
Sbjct: 381 RDLMAIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAAGAAQLRRTITAVIDRLPPR 440

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+ P     LRSF+
Sbjct: 441 EAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRAPDTLGLLRSFI 497



 Score = 43.9 bits (102), Expect = 0.094,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 51/111 (45%), Gaps = 13/111 (11%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL----NDGTTLLRE 183
           MG+  LL+R+ E A A+RIE GRA   A LC  P    AL+  R E+    +  +T +  
Sbjct: 1   MGTTPLLTRDDEFAYAQRIERGRAASAAVLCGDPDALDALVSIRIEIAQCRSAASTYVIF 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           + D     GP       H   G S      ++ E  RDD  +    IE++A
Sbjct: 61  LDD-----GPRDNTTADHAEAGTS----ATAAGEPARDDDTQANTQIEASA 102


>gi|23978340|dbj|BAC21139.1| principal sigma factor [Stanieria cyanosphaera str. PCC 7437]
          Length = 203

 Score =  223 bits (569), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 110/204 (53%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+P E  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKSLLREDLENVLDTLSPSERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|254422659|ref|ZP_05036377.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190148|gb|EDX85112.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 298

 Score =  223 bits (568), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 113/262 (43%), Positives = 173/262 (66%), Gaps = 10/262 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GIS +E   IV+    GE     AK  MVEANLRLV+SVAKKY  R +  LDLIQEG IG
Sbjct: 47  GISEAELAAIVT---AGEQ----AKHRMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIG 99

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           + +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R+ +
Sbjct: 100 MQRGVEKFDPSKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQFT 159

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  R PT  EIA+     ++ VR+ L  +++P+SL+  +GD   + LGD +ED +  +P
Sbjct: 160 QQHGRTPTASEIAQATGFTIKQVREYLDRSRQPLSLDLKVGDNQDTQLGDLLED-DGQTP 218

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D A  ++L+    R++A LTP++++V+ +RFG+    + TL ++G    ++RER+RQIE
Sbjct: 219 DDYATASSLKSDLKRIMADLTPQQQQVIALRFGLEDGKNMTLAKIGAMLDISRERVRQIE 278

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
            +A+ KL+   R   +R +L G
Sbjct: 279 REALTKLR--KRQSDMREYLAG 298


>gi|189916711|gb|ACE62866.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916713|gb|ACE62867.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916715|gb|ACE62868.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 108/159 (67%), Positives = 130/159 (81%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD
Sbjct: 1   VHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGD 60

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 61  DEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTL 120

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 159


>gi|307152078|ref|YP_003887462.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982306|gb|ADN14187.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 328

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 108/268 (40%), Positives = 186/268 (69%), Gaps = 6/268 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVA 460
           ++L+ ++E+ +I +E   S++E+ + V M    + +   +   AK++M+EANLRLV+++A
Sbjct: 50  TLLEKKDEL-AIQLEREPSLTEWANHVQMSEEELNRAIQQGKRAKRKMIEANLRLVVAIA 108

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA Q+ TIR
Sbjct: 109 KKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIR 168

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +T R +S ++ R  TP EIAK L +  + +R+ L ++++PISL+  +
Sbjct: 169 LPIHITEKLNKIKKTQRELSQQLGRSATPSEIAKALDLEPDQIREFLSMSRQPISLDVRV 228

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD   + L + +ED+  +SP +   Q  +R+    +LA LTP++  VL +RFG+    + 
Sbjct: 229 GDNQDTELSELLEDE-GISPDNYITQELMRQDLQDLLAELTPQQREVLSLRFGLQDGKEL 287

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L ++G++  ++RER+RQ+E +A+ +L+
Sbjct: 288 SLAKIGQRMNISRERVRQLEHQALSQLR 315


>gi|3249733|gb|AAC26669.1| RNA polymerase sigma-like factor [Streptomyces peucetius]
          Length = 162

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 107/162 (66%), Positives = 131/162 (80%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 1   YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEM 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+
Sbjct: 61  PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLS 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 121 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 162


>gi|298490007|ref|YP_003720184.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231925|gb|ADI63061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 417

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 108/238 (45%), Positives = 167/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 178 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 237

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA  S TIR+PVH+ +K++K+ +  R++S +  R PT E++A +L M    V
Sbjct: 238 IRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTLEDLAIELDMTPTQV 297

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLET +G +  + LG+ +E  ++++P +  ++ +L++    +LA LT R
Sbjct: 298 REVLLRVPRSVSLETKVGKDKDTELGELLE-TDSITPEEMLMRESLQKDLHHLLADLTSR 356

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P R   +R +L+
Sbjct: 357 ERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNLIRDYLE 414


>gi|23978360|dbj|BAC21145.1| principal sigma factor [Pleurocapsa sp. PCC 7314]
          Length = 203

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 111/204 (54%), Positives = 149/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V +NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKSLLREDLESVLDTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|189916709|gb|ACE62865.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 107/159 (67%), Positives = 130/159 (81%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+K+ KEPIS+ETPIGD
Sbjct: 1   VHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKVAKEPISMETPIGD 60

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 61  DEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTL 120

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 159


>gi|269114989|ref|YP_003302752.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis]
 gi|268322614|emb|CAX37349.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis ATCC 23114]
          Length = 538

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 108/248 (43%), Positives = 162/248 (65%), Gaps = 9/248 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V+ NLRLVI+ AK+Y NRGL F+DLI EGN G+MKA  K+D+  G+KFSTYA WW
Sbjct: 285 ARDMLVKRNLRLVINNAKRYKNRGLNFIDLISEGNAGIMKAVSKYDYTKGFKFSTYATWW 344

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVE 561
           ++QAITR++ADQ+ T+R+PVHM + I+K+++  R +  +    PT EEIAKK       E
Sbjct: 345 IRQAITRAVADQARTVRVPVHMVETINKILKIERELQQENGYPPTDEEIAKKYGGDFTAE 404

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASL 620
            VR + KI  +PISL+  IG E+ S   DF++D++ +SP   A    L      ++   L
Sbjct: 405 KVRYIRKINIDPISLDKNIGKEENSSFSDFVKDESVISPTSYASHEELSVIINEMIEEGL 464

Query: 621 TPREER-VLRMRFGI-----GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + + +R ++R RFGI          HTL+E+ K+  +++E++RQ+E K +RKLKHP + +
Sbjct: 465 SDQADRDLIRKRFGINDLKGNKYKPHTLDELSKELGISKEKVRQLETKVLRKLKHPQKRR 524

Query: 675 KLRSFLDG 682
           KL+ F + 
Sbjct: 525 KLKEFFNS 532


>gi|12045103|ref|NP_072914.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|255660251|ref|ZP_05405660.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|1350862|sp|P47491|RPOD_MYCGE RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1045940|gb|AAC71469.1| RNA polymerase sigma factor RpoD [Mycoplasma genitalium G37]
 gi|166078711|gb|ABY79329.1| RNA polymerase sigma factor RpoD [synthetic Mycoplasma genitalium
           JCVI-1.0]
          Length = 497

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 114/245 (46%), Positives = 172/245 (70%), Gaps = 8/245 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V +NLRLV+S+AKK+  RGL F DLIQEGN+GL+KA  KF+W LG KFSTYA WW
Sbjct: 246 AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWW 305

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           +KQAITR+IADQ+ T+RIPVHM + I+++ +  R +  ++ REPT EE+A+K+    EG 
Sbjct: 306 IKQAITRAIADQARTVRIPVHMVETINRLAKAERALYQELGREPTDEELAEKMGGQAEGF 365

Query: 563 -VRKVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLD-SAIQANLRETTTRVL 617
            V+K+ +I +   +P+SL+  +G ++ S  GDF++D +A +P + +  ++N  +    + 
Sbjct: 366 NVKKIAEIKRLSLDPVSLDKTVGHDEESQFGDFVKDTDAQTPDEFTESRSNSEKIDELLN 425

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +L+ +EE ++RMR G+   N   TL+EVG++  + RE+IRQIE KAIRKL+H  R+  +
Sbjct: 426 NNLSEQEELIVRMRIGMPPYNEPKTLDEVGQKILIPREKIRQIENKAIRKLRHAVRNNPI 485

Query: 677 R-SFL 680
             SFL
Sbjct: 486 SMSFL 490


>gi|170700559|ref|ZP_02891561.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170134549|gb|EDT02875.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 519

 Score =  222 bits (566), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 107/255 (41%), Positives = 164/255 (64%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +  G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 266 RALGAALSDGQQKVRDGTRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEK 325

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 326 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRA 385

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +P   +R VL +  EP+SL+TP+ D +T  L D IED+ + SP +     
Sbjct: 386 TPAELAAESGLPEGKLRAVLALPAEPLSLDTPLPDAETG-LVDLIEDQASASPFERLADT 444

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  T +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 445 RMRECVTSLLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 504

Query: 668 KHPSRSKKLRSFLDG 682
           +  + ++   SFLD 
Sbjct: 505 RTAAEAEGAESFLDA 519



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 41/148 (27%), Positives = 74/148 (50%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TLRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PAAPAPFAGAAPVDVDRDALDEGRALLGDLARGTSASTDPLALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALI 168
            +A+ IE GR  ++ +L   P    AL+
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALL 154


>gi|308189916|ref|YP_003922847.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
 gi|307624658|gb|ADN68963.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
          Length = 489

 Score =  222 bits (566), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/269 (42%), Positives = 175/269 (65%), Gaps = 10/269 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I E + +   + KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G+
Sbjct: 220 LTIEEEKKLAQEMEKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGI 279

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA  K++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  
Sbjct: 280 VKAVSKYNVSKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQ 339

Query: 542 KIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++  EPT E IA++       E VR + KI  +PISL+  IG E+ S   DF++D++ V+
Sbjct: 340 ELGYEPTDEMIAERYGNGYDAEKVRYIRKINIDPISLDKQIGKENDSSFSDFVKDESVVN 399

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRM-RFGIGMNTD------HTLEEVGKQFCVT 652
           P+D A Q  L ET   +L      +ER+L   RFG+G++ +      H+LE++ ++  V+
Sbjct: 400 PVDYASQEELVETLNSILEKSLDDDERILICKRFGVGVDENGNKYPIHSLEKLAEERNVS 459

Query: 653 RERIRQIEAKAIRKLKHPSR-SKKLRSFL 680
           +ERIRQIE K +RKLK  +R  + L+ F+
Sbjct: 460 KERIRQIENKILRKLKSSTRKGRHLKDFI 488


>gi|171920395|ref|ZP_02931720.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|183508771|ref|ZP_02958238.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701631|ref|ZP_02971335.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
 gi|171902833|gb|EDT49122.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|182675710|gb|EDT87615.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186700864|gb|EDU19146.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
          Length = 448

 Score =  222 bits (566), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 163/252 (64%), Gaps = 14/252 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           I K ++  +N+RLV S+AKKY NRGL   DLIQEG+ GL+KA +KFD   G+KFSTYA W
Sbjct: 192 IGKNQLYTSNMRLVTSIAKKYLNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATW 251

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL------ 556
           W++Q+ITR+IADQ+  IRIPVHM + I+K+ +  R +  ++ R+PT EEIA+ +      
Sbjct: 252 WIRQSITRAIADQARQIRIPVHMVETINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQA 311

Query: 557 ------AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
                  +  + V ++ K+  +P+SL+  IG ++ S   DFI D   +SP     +  L 
Sbjct: 312 KNQKEQLITAQKVVEIKKLNVDPVSLDKQIGHDEESQFSDFISDDEIISPEKYTEKKALN 371

Query: 611 ETTTRVLAS-LTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    +    L   E+RV++MR+G +     +TLEEVG+   VTRER RQIE+KAIRKLK
Sbjct: 372 DQINEMFEKVLNDNEQRVIKMRYGLLPFERPYTLEEVGEYLGVTRERARQIESKAIRKLK 431

Query: 669 HPSRSKKLRSFL 680
           HPS++ KLRSF+
Sbjct: 432 HPSKTAKLRSFI 443


>gi|171920947|ref|ZP_02932089.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|185178923|ref|ZP_02964687.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188024158|ref|ZP_02996885.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188518597|ref|ZP_03004049.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|188524519|ref|ZP_03004514.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195868018|ref|ZP_03080013.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198273631|ref|ZP_03206166.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209554143|ref|YP_002284749.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225550349|ref|ZP_03771298.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
 gi|225551084|ref|ZP_03772030.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|171903184|gb|EDT49473.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|184209186|gb|EDU06229.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188018789|gb|EDU56829.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188997798|gb|EDU66895.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|195659715|gb|EDX53095.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195660310|gb|EDX53572.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198249659|gb|EDY74440.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209541644|gb|ACI59873.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225378899|gb|EEH01264.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|225379503|gb|EEH01865.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
          Length = 448

 Score =  222 bits (566), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 163/252 (64%), Gaps = 14/252 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           I K ++  +N+RLV S+AKKY NRGL   DLIQEG+ GL+KA +KFD   G+KFSTYA W
Sbjct: 192 IGKNQLYTSNMRLVTSIAKKYLNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATW 251

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL------ 556
           W++Q+ITR+IADQ+  IRIPVHM + I+K+ +  R +  ++ R+PT EEIA+ +      
Sbjct: 252 WIRQSITRAIADQARQIRIPVHMVETINKLTKAERSLIQELGRDPTAEEIAQAMNKASQA 311

Query: 557 ------AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
                  +  + V ++ K+  +P+SL+  IG ++ S   DFI D   +SP     +  L 
Sbjct: 312 KNQKEQLITAQKVVEIKKLNVDPVSLDKQIGHDEESQFSDFISDDEIISPEKYTEKKALN 371

Query: 611 ETTTRVLAS-LTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    +    L   E+RV++MR+G +     +TLEEVG+   VTRER RQIE+KAIRKLK
Sbjct: 372 DQINEMFEKVLNDNEQRVIKMRYGLLPFERPYTLEEVGEHLGVTRERARQIESKAIRKLK 431

Query: 669 HPSRSKKLRSFL 680
           HPS++ KLRSF+
Sbjct: 432 HPSKTAKLRSFI 443


>gi|115358293|ref|YP_775431.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
 gi|115283581|gb|ABI89097.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 516

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 107/255 (41%), Positives = 164/255 (64%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +  G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 263 RALGAALSDGQQKVRDGTRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEK 322

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 323 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRA 382

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +P   +R VL +  EP+SL+TP+ D +T  L D IED+ + SP +     
Sbjct: 383 TPAELAAESGLPEGKLRAVLALPAEPLSLDTPLPDAETG-LVDLIEDQASASPFERLADT 441

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  T +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 442 RMRECVTSLLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 501

Query: 668 KHPSRSKKLRSFLDG 682
           +  + ++   SFLD 
Sbjct: 502 RTAAEAEGAESFLDA 516



 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 41/148 (27%), Positives = 74/148 (50%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TLRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PASPAPFAGAAPVDVDRDALDEGRALLGDLARGTSASTDPLALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALI 168
            +A+ IE GR  ++ +L   P    AL+
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALL 154


>gi|119512139|ref|ZP_01631231.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
 gi|119463229|gb|EAW44174.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
          Length = 442

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 108/238 (45%), Positives = 166/238 (69%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 203 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 262

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E++A +L M    V
Sbjct: 263 IRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLAIELEMTPTQV 322

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLET +G +  + LG+ +E  + V+P +  ++ +L++    +LA LT R
Sbjct: 323 REVLLKVPRSVSLETKVGKDKDTELGELLE-TDCVTPEEMLMRESLQKDLHSLLADLTSR 381

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P R   +R +L+
Sbjct: 382 ERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNLIRDYLE 439


>gi|319777141|ref|YP_004136792.1| putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
 gi|238810060|dbj|BAH69850.1| hypothetical protein [Mycoplasma fermentans PG18]
 gi|318038216|gb|ADV34415.1| Putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
          Length = 489

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/269 (42%), Positives = 175/269 (65%), Gaps = 10/269 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I E + +   + KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G+
Sbjct: 220 LTIEEEKKLAQEMEKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGI 279

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA  K++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  
Sbjct: 280 VKAVSKYNVSKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQ 339

Query: 542 KIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++  EPT E IA++       E VR + KI  +PISL+  IG E+ S   DF++D++ V+
Sbjct: 340 ELGYEPTDEMIAERYGNGYDAEKVRYIRKINIDPISLDKQIGKENDSSFSDFVKDESVVN 399

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRM-RFGIGMNTD------HTLEEVGKQFCVT 652
           P+D A Q  L ET   +L      +ER+L   RFG+G++ +      H+LE++ ++  V+
Sbjct: 400 PVDYASQEELVETLNSILEKSLDDDERILICKRFGVGVDENGNKYPIHSLEKLAEERNVS 459

Query: 653 RERIRQIEAKAIRKLKHPSR-SKKLRSFL 680
           +ERIRQIE K +RKLK  +R  + L+ F+
Sbjct: 460 KERIRQIENKILRKLKSSTRKGRHLKDFI 488


>gi|13357909|ref|NP_078183.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|170762330|ref|YP_001752432.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|11357048|pir||E82901 RNA polymerase sigma factor UU349 [imported] - Ureaplasma
           urealyticum
 gi|6899329|gb|AAF30758.1|AE002132_2 RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|168827907|gb|ACA33169.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
          Length = 448

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 163/252 (64%), Gaps = 14/252 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           I K ++  +N+RLV S+AKKY NRGL   DLIQEG+ GL+KA +KFD   G+KFSTYA W
Sbjct: 192 IGKNQLYTSNMRLVTSIAKKYLNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATW 251

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL------ 556
           W++Q+ITR+IADQ+  IRIPVHM + I+K+ +  R +  ++ R+PT EEIA+ +      
Sbjct: 252 WIRQSITRAIADQARQIRIPVHMVETINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQA 311

Query: 557 ------AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
                  +  + V ++ K+  +P+SL+  IG ++ S   DFI D   +SP     +  L 
Sbjct: 312 KNQKEQLITAQKVVEIKKLNVDPVSLDKQIGHDEESQFSDFISDDEIISPEKYTEKKALN 371

Query: 611 ETTTRVLAS-LTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    +    L   E+RV++MR+G +     +TLEEVG+   VTRER RQIE+KAIRKLK
Sbjct: 372 DQINEMFEKVLNDNEQRVIKMRYGLLPFERPYTLEEVGEYLGVTRERARQIESKAIRKLK 431

Query: 669 HPSRSKKLRSFL 680
           HPS++ KLRSF+
Sbjct: 432 HPSKTAKLRSFI 443


>gi|170782897|ref|YP_001711231.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
 gi|169157467|emb|CAQ02657.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
          Length = 347

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 112/239 (46%), Positives = 157/239 (65%), Gaps = 5/239 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V ANLRLV+S+AK+YT RGL FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 110 AKQHLVNANLRLVVSIAKRYTGRGLPFLDLIQEGNMGLVRAVEKFDYQAGFKFSTYASWW 169

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+ITR +AD S TIRIPVH  + I+++    R + +++ R+P+ EEIA++   PV  V
Sbjct: 170 IKQSITRGMADTSRTIRIPVHTVEHINRINAVQRELGDELGRDPSMEEIARESDTPVTKV 229

Query: 564 RKVLKITKEPISLETPI----GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R +L   +EP+SL+  +    GD DT  + D IED +   P+D   Q  +    TR++  
Sbjct: 230 RYLLDRAQEPMSLQVLVGGSGGDGDT-EMADLIEDADVTQPIDVVTQQLMAAHVTRLIDG 288

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  R+  V+RMRFG+      +L  V +Q  VTRER+RQIE K + KL+ P     +R 
Sbjct: 289 LAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVTRERVRQIEKKVLAKLRIPELEMYIRG 347


>gi|88809466|ref|ZP_01124974.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786685|gb|EAR17844.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 376

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 128/357 (35%), Positives = 212/357 (59%), Gaps = 22/357 (6%)

Query: 334 RIDLLV-EQLYDISKRIMHNEGELLR---LAQSYGIKRDVF-LERHQGRELD--PHWVSY 386
           R+DLL  E+   +S+++   E  L++   L+      R +  LE  Q RE +   HW + 
Sbjct: 31  RVDLLTSEEEVTLSRQVQQRERLLVQERDLSTRIAAIRVLLDLEELQQREANHISHWPTR 90

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAK 445
                  EW       +  + ++ NE  ++ + E+G+   E +  +   R+       A+
Sbjct: 91  Q------EWARAAELPLSELNRLLNEGYTLWAKESGLDTKELQQRLREGRR-------AR 137

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++
Sbjct: 138 DRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIR 197

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q ITR+IA QS TIR+PVH+ +K++++ R  + ++++  R  +  ++AK+L +  E VR+
Sbjct: 198 QGITRAIATQSRTIRLPVHITEKLNRIKRVQQEIASEKGRLASVSDLAKELGVSEETVRQ 257

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            L      +SLET +G +  + LGD +ED +A +P  +  + +L +    +L  L+PRE 
Sbjct: 258 TLARVPRSVSLETRVGKDQDTQLGDLLEDGHA-TPEQTLTRDSLHDDLEHLLEELSPREA 316

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            V+R RFG+  +T  TL E+G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 317 EVIRSRFGLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQPQRRSKVRDYIQG 373


>gi|332708935|ref|ZP_08428906.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352477|gb|EGJ32046.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 333

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 108/256 (42%), Positives = 170/256 (66%), Gaps = 10/256 (3%)

Query: 432 SMVRKGECE-------ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S V K E E        + AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL + 
Sbjct: 79  SYVNKSEAELKKAIDQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERG 138

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD   GYKFSTYA WW++QAITR+IA Q+  IR+P+H+ +K++K+ +  R +S  + 
Sbjct: 139 VEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARAIRLPIHITEKLNKIKKVQRELSQTLG 198

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R  TP EIAK+L +    +R+ L I ++PISL+  +GD   + L + +ED + ++P++  
Sbjct: 199 RNATPTEIAKELDLEPAQIREYLSIARQPISLDVRVGDNQDTELSELLED-DGLTPVNYT 257

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            Q +LR+    +LA LTP++  VL +RFG+    + +L +VGK+  ++RER+RQ+E +A+
Sbjct: 258 TQESLRQDLNLLLAELTPQQREVLALRFGLEDGKELSLAKVGKRLNLSRERVRQLEHQAL 317

Query: 665 RKLKHPSRSKKLRSFL 680
            +L+   R    R ++
Sbjct: 318 AQLRR--RHANFREYI 331


>gi|116514228|ref|YP_813134.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
 gi|116093543|gb|ABJ58696.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
          Length = 378

 Score =  222 bits (565), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 111/233 (47%), Positives = 159/233 (68%), Gaps = 5/233 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           AK E+  ANLRLV+S+AK+Y   N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA 
Sbjct: 136 AKDELAAANLRLVVSIAKRYAKHNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYAT 195

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR++ADQ   IRIPVH+ + I+K+ R  R +   + R   PEE+A ++  P++
Sbjct: 196 WWIRQAITRALADQDRMIRIPVHVVESINKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQ 255

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V++++ + K  E  SL+  +G+E  S LGD +ED  A++P +      L++  + ++  
Sbjct: 256 KVQEIITVAKNQETDSLDKSVGEEGDSQLGDLLEDNKAINPEEYTAFEMLKDQLSGMMGE 315

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            LT RE +VL++RFG+     HTLEEVG+   VTRER+RQIE KA++KLK  S
Sbjct: 316 FLTDREAKVLKLRFGLENYEPHTLEEVGRSLGVTRERVRQIEDKAVKKLKQHS 368



 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 52/113 (46%), Gaps = 14/113 (12%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           A+S+ N  V+             D VRMYL+E+G + LLSR+ E+ +AKRI+ G      
Sbjct: 92  AASSDNDQVY-------------DSVRMYLKEIGKVPLLSRDEEVEVAKRIKNGDESAKD 138

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
            L  + L     I  R   ++G   + ++I  E  IG       F  ++G  +
Sbjct: 139 ELAAANLRLVVSIAKRYAKHNGKMGILDLIQ-EGNIGLMKAVDKFDYSKGFKF 190


>gi|218248849|ref|YP_002374220.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257061911|ref|YP_003139799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218169327|gb|ACK68064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256592077|gb|ACV02964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 417

 Score =  221 bits (564), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 109/238 (45%), Positives = 167/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M++ANLRLV+SVAKKY +RGL+ LDLIQEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 178 AKEQMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWW 237

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+I+ QS  IR+PVH+ +K++K+ R  R++S +  R+ T EE++K+L M  E +
Sbjct: 238 IRQGITRAISTQSRIIRLPVHITEKLNKIKRAQRKLSQEKGRKATIEEMSKELDMSAEQI 297

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLE  +G E  + L D +E +   SP +S I  +LR+    +L  LT R
Sbjct: 298 REVLLRIPRSVSLEVKVGKEKDTELVDLLETE-CQSPEESLISESLRKDLQVLLEDLTER 356

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ V+++R+G    T ++L ++G+   ++RER+RQIEAKA++KL+ P R  ++R + +
Sbjct: 357 EQDVIKLRYGFEDGTCYSLADIGRVLELSRERVRQIEAKALQKLRQPRRRNQIRDYFE 414


>gi|104774138|ref|YP_619118.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423219|emb|CAI98047.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125917|gb|ADY85247.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 378

 Score =  221 bits (564), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 111/233 (47%), Positives = 159/233 (68%), Gaps = 5/233 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           AK E+  ANLRLV+S+AK+Y   N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA 
Sbjct: 136 AKDELAAANLRLVVSIAKRYAKHNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYAT 195

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR++ADQ   IRIPVH+ + I+K+ R  R +   + R   PEE+A ++  P++
Sbjct: 196 WWIRQAITRALADQDRMIRIPVHVVESINKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQ 255

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V++++ + K  E  SL+  +G+E  S LGD +ED  A++P +      L++  + ++  
Sbjct: 256 KVQEIITVAKNQETDSLDKSVGEEGDSQLGDLLEDNKAINPEEYTAFEMLKDQLSGMMGE 315

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            LT RE +VL++RFG+     HTLEEVG+   VTRER+RQIE KA++KLK  S
Sbjct: 316 FLTDREAKVLKLRFGLENYEPHTLEEVGRSLGVTRERVRQIEDKAVKKLKQHS 368



 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 52/113 (46%), Gaps = 14/113 (12%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           A+S+ N  V+             D VRMYL+E+G + LLSR+ E+ +AKRI+ G      
Sbjct: 92  AASSDNDQVY-------------DSVRMYLKEIGKVPLLSRDEEVEVAKRIKNGDESAKD 138

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
            L  + L     I  R   ++G   + ++I  E  IG       F  ++G  +
Sbjct: 139 ELAAANLRLVVSIAKRYAKHNGKMGILDLIQ-EGNIGLMKAVDKFDYSKGFKF 190


>gi|189218244|ref|YP_001938886.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189185102|gb|ACD82287.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 287

 Score =  221 bits (564), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 110/236 (46%), Positives = 163/236 (69%), Gaps = 4/236 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA   +++M++ANLRLV+ +A  Y N GL   DLI EGNIGLMKA ++FD   G
Sbjct: 33  IQQGDQEA---RRQMIQANLRLVVKIAHDYANSGLPLPDLISEGNIGLMKAVDRFDPSKG 89

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K STYA WW+KQ+I R++A+QS TIR+PVH+ DKI K+ R A ++S  + R+PT EE+A
Sbjct: 90  GKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDKIAKMRRVAMQLSEILGRDPTDEELA 149

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           ++L M    V ++  I   P SL+  +G +ED + LG+ ++D++A SP  S +  NL+ T
Sbjct: 150 EELGMSTTKVAELRTIAIRPASLDATVGEEEDGTALGELVKDESAASPDQSVLDQNLKNT 209

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +L  L  RE ++L +RFG+  N   TLEE+GK+F VTRERIRQ++  A+RK++
Sbjct: 210 IMELLPKLDERERKILSLRFGLEGNEQMTLEEIGKEFHVTRERIRQLQNIALRKIR 265



 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 5/47 (10%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-----RAMMMASL 157
           + D  +++YLRE+  I LL++E E+ +AKRI+ G     R M+ A+L
Sbjct: 3   NNDSALKLYLREISQIPLLTKEKEVELAKRIQQGDQEARRQMIQANL 49


>gi|172063054|ref|YP_001810705.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171995571|gb|ACB66489.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 520

 Score =  221 bits (564), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 105/237 (44%), Positives = 157/237 (66%), Gaps = 1/237 (0%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA WW++
Sbjct: 285 RAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIR 344

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +P   +R 
Sbjct: 345 QAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLPEGKLRA 404

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL +  EP+SL+TP+ D +T  L D IED+ + SP +      +RE  T +L S+TP E 
Sbjct: 405 VLALPAEPLSLDTPLPDAETG-LVDLIEDQASASPFERLADTRMRECVTSLLRSVTPAEA 463

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++   SFLD 
Sbjct: 464 DVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTAAEAEGAESFLDA 520



 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 41/148 (27%), Positives = 74/148 (50%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TLRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PAAPAPFAGAAPVDVDRDALDEGRALLGDLARGTSASTDPLALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALI 168
            +A+ IE GR  ++ +L   P    AL+
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALL 154


>gi|186681474|ref|YP_001864670.1| RNA polymerase sigma factor SigC [Nostoc punctiforme PCC 73102]
 gi|186463926|gb|ACC79727.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 416

 Score =  221 bits (564), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 107/239 (44%), Positives = 165/239 (69%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 177 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 236

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E++A +L M    V
Sbjct: 237 IRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLATELEMTPTQV 296

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLET +G +  + LG+ +E  + V+P +  ++ +L+     +L+ LT R
Sbjct: 297 REVLLRVPRSVSLETKVGKDKDTELGELLE-TDCVTPEEMLMRESLQRDLHHLLSDLTSR 355

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P R   +R +L+ 
Sbjct: 356 ERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNLIRDYLES 414


>gi|81300555|ref|YP_400763.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
 gi|123556657|sp|Q31ME3|RPOD2_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD2
 gi|81169436|gb|ABB57776.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score =  221 bits (563), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 164/229 (71%), Gaps = 1/229 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 85  AKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYKFSTYAYWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S ++ R  T  E+A+ L +P+E V
Sbjct: 145 IRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATASELAEVLELPLEQV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ +++ ++P+SL+  +GD   + L + +ED+ + SP D   Q +LR     ++A LTP+
Sbjct: 205 REYIQMNRQPVSLDVKVGDSQDTELQELLEDEQS-SPSDYVEQESLRRDLRNLMAELTPQ 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           ++ V+ +R+G+      +L +VG++  ++RER+R++E +A+  L+  SR
Sbjct: 264 QQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRRRSR 312


>gi|2385506|dbj|BAA22190.1| RpoD2 protein [Synechococcus elongatus PCC 7942]
          Length = 320

 Score =  221 bits (563), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 164/229 (71%), Gaps = 1/229 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 85  AKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYKFSTYAYWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S ++ R  T  E+A+ L +P+E V
Sbjct: 145 IRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATASELAEVLELPLEQV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ +++ ++P+SL+  +GD   + L + +ED+ + SP D   Q +LR     ++A LTP+
Sbjct: 205 REYIQMNRQPVSLDVKVGDSQDTELQELLEDEQS-SPSDYVEQESLRRDLRNLMAELTPQ 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           ++ V+ +R+G+      +L +VG++  ++RER+R++E +A+  L+  SR
Sbjct: 264 QQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRRRSR 312


>gi|56750962|ref|YP_171663.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81299380|ref|YP_399588.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
 gi|123769297|sp|Q31QR8|RPOD4_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD4
 gi|56685921|dbj|BAD79143.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81168261|gb|ABB56601.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
          Length = 311

 Score =  221 bits (563), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 106/226 (46%), Positives = 163/226 (72%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M++ANLRLV+SVAKKY N+GL+ LDLIQEG++GL +A EKFD  LGYKFSTYA WW
Sbjct: 74  AKTKMLKANLRLVVSVAKKYQNQGLELLDLIQEGSLGLERAVEKFDPALGYKFSTYAYWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+I + + TIR+P+H+ +KI ++ +  R +++++KR P+  EIA+ L +P++ V
Sbjct: 134 IRQSMTRAIDNHARTIRLPIHVSEKISRIKKMTRELTHQLKRLPSRAEIAEALKLPLQDV 193

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L  +    SL+    GD+  S LGD I D  ++ P+D+  +    E  +  LA LT 
Sbjct: 194 EMLLSQSTPCTSLDAQARGDDGRSFLGDLIPDPKSLEPMDAMDRHIQHEQISTWLAHLTE 253

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++VL++RFG+     HTL E+G++  V+RERIRQ+EA+A++KL+
Sbjct: 254 REQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVEARALQKLR 299


>gi|75907387|ref|YP_321683.1| RNA polymerase sigma factor SigC [Anabaena variabilis ATCC 29413]
 gi|75701112|gb|ABA20788.1| RNA polymerase, sigma subunit, RpsC/SigC [Anabaena variabilis ATCC
           29413]
          Length = 416

 Score =  221 bits (563), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 109/251 (43%), Positives = 170/251 (67%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + K + +   +K+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD 
Sbjct: 164 VEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDP 223

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E
Sbjct: 224 TKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLE 283

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +  ++ +L+
Sbjct: 284 DLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDGVTPEEMLMRESLQ 342

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P
Sbjct: 343 RDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQP 402

Query: 671 SRSKKLRSFLD 681
            R   +R +L+
Sbjct: 403 KRRNLIRDYLE 413


>gi|17229184|ref|NP_485732.1| RNA polymerase sigma factor SigC [Nostoc sp. PCC 7120]
 gi|20141790|sp|Q03066|RPSC_ANASP RecName: Full=RNA polymerase sigma-C factor
 gi|17135512|dbj|BAB78058.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score =  221 bits (563), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 109/251 (43%), Positives = 170/251 (67%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + K + +   +K+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD 
Sbjct: 164 VEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDP 223

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E
Sbjct: 224 TKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLE 283

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +  ++ +L+
Sbjct: 284 DLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDGVTPEEMLMRESLQ 342

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P
Sbjct: 343 RDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQP 402

Query: 671 SRSKKLRSFLD 681
            R   +R +L+
Sbjct: 403 KRRNLIRDYLE 413


>gi|58696753|ref|ZP_00372293.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
 gi|58537061|gb|EAL60191.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
          Length = 183

 Score =  221 bits (563), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 108/183 (59%), Positives = 144/183 (78%), Gaps = 1/183 (0%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
            A+ WV+Q+ITR+I +QS  +RIP+HM + I K+ R  R+M++++ REPT EE++ +L M
Sbjct: 1   MALGWVRQSITRAIPEQSKVVRIPLHMVEIISKINRALRKMTHEMGREPTLEELSVELTM 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT VLA
Sbjct: 61  PLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRGITTNVLA 120

Query: 619 SLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           +LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR++KLR
Sbjct: 121 TLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRARKLR 180

Query: 678 SFL 680
            F 
Sbjct: 181 GFF 183


>gi|254496518|ref|ZP_05109389.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
 gi|254354257|gb|EET12921.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
          Length = 342

 Score =  221 bits (562), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 106/256 (41%), Positives = 172/256 (67%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H  ++  KG+     A+K+M+E+NLRLV+ ++++Y NRGL  LD
Sbjct: 76  LSEIGFSPLLSAEEEVHYATLALKGDV---AARKKMIESNLRLVVKISRRYLNRGLPLLD 132

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GLMK+ EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 133 LIEEGNLGLMKSVEKFDPNRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 192

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR+++ K+  EP+PEEIA+ +  P+E V+K+L +  +  S++TPIG ++   L D I
Sbjct: 193 LRAARQLTQKLDHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDENKSLLDTI 252

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+N+V+P +     NLR     +L  LT  +++V+  RFG+      TLE+VGK+  +T
Sbjct: 253 ADENSVNPAELLTNENLRLHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLT 312

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ +A++ L+
Sbjct: 313 RERVRQIQVEALKTLR 328


>gi|142114|gb|AAA22047.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score =  221 bits (562), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 109/251 (43%), Positives = 170/251 (67%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + K + +   +K+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD 
Sbjct: 164 VEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDP 223

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R PT E
Sbjct: 224 TKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLE 283

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +  ++ +L+
Sbjct: 284 DLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDGVTPEEMLMRESLQ 342

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL+ P
Sbjct: 343 RDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQP 402

Query: 671 SRSKKLRSFLD 681
            R   +R +L+
Sbjct: 403 KRRNLIRDYLE 413


>gi|186681941|ref|YP_001865137.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186464393|gb|ACC80194.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 339

 Score =  221 bits (562), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 166/237 (70%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M++ANLRLV++VAKKY +R L+F+DLIQEG +GL +  +KFD  LGYKFSTYA WW
Sbjct: 104 AKQKMIQANLRLVVAVAKKYQHRNLEFMDLIQEGTLGLERGVDKFDPALGYKFSTYAYWW 163

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA Q  TIR+P+H+ +K++K+ R  R +S ++ R PT  EIA  L++    V
Sbjct: 164 IRQGITRAIAQQGRTIRLPIHVFEKLNKIKRVQRELSQQLGRVPTTAEIANALSLTPSQV 223

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + ++P SLE  +G++  + L D +ED +  SP D A++ +L +    +LA L+P+
Sbjct: 224 RECLYLARQPFSLEARVGEQQDTELQDILED-DGPSPEDYAVEESLHQDLQDLLAKLSPQ 282

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  +L +RFG+    + +L ++G +  ++RER+RQIE KA+  L+   + +++RS+L
Sbjct: 283 QREILTLRFGLTDGYELSLAQIGDRMGISRERVRQIEQKALSLLRR--QKEQVRSYL 337



 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 49/92 (53%), Gaps = 14/92 (15%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE------AGRAMMMASLCESPLTF 164
           D   R+TDD VR YL+E+G ++LL+RE E+  A++++      A +  +   L   P T 
Sbjct: 22  DKKPRATDDIVRSYLQEIGRVDLLTREQEVIFAQQVQLMMNLLAAKEELAVKLDHEP-TL 80

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           Q    W D +  G     E+++L+   G ++K
Sbjct: 81  QE---WADRVELGA----EVLELQLSQGHQAK 105


>gi|282895449|ref|ZP_06303586.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199482|gb|EFA74345.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 327

 Score =  221 bits (562), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 157/225 (69%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  +GYKFSTYA WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K+ R P+P EIAK+L +    +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIAKELELEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  +GD   + L + +ED + +SP     Q  LR     +LA LTP+
Sbjct: 212 REYLNIARQPISLDVRVGDNQDTELQEMLED-DGLSPEHYTTQEFLRHDLNNLLAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+ +RFG+    + +L +VG +  ++RER+RQ+E +A+  L+
Sbjct: 271 QREVVTLRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQALTHLR 315


>gi|56752354|ref|YP_173055.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
 gi|56687313|dbj|BAD80535.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
          Length = 320

 Score =  221 bits (562), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 164/229 (71%), Gaps = 1/229 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 85  AKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGFEKFDPSKGYKFSTYAYWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S ++ R  T  E+A+ L +P+E V
Sbjct: 145 IRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATASELAEVLELPLEQV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ +++ ++P+SL+  +GD   + L + +ED+ + SP D   Q +LR     ++A LTP+
Sbjct: 205 REYIQMNRQPVSLDVKVGDSQDTELQELLEDEQS-SPSDYVEQESLRRDLRNLMAELTPQ 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           ++ V+ +R+G+      +L +VG++  ++RER+R++E +A+  L+  SR
Sbjct: 264 QQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRRRSR 312


>gi|220907092|ref|YP_002482403.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7425]
 gi|219863703|gb|ACL44042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 318

 Score =  220 bits (561), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 111/249 (44%), Positives = 171/249 (68%), Gaps = 6/249 (2%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T   +SE   +  +V +GE    +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG I
Sbjct: 64  TAAKLSEA-ELQGVVNRGE----LAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTI 118

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R++
Sbjct: 119 GMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQL 178

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           S ++ R  T  E+A++L +  + VR+ L+ +++P+SL+  +GD   + LG+ +ED  A S
Sbjct: 179 SQQLGRAATIGELAQELELTPKQVREYLERSRQPLSLDVRVGDNQDTELGELLED-TAAS 237

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D   QA+LR    R++A LTP++ +VL +RFG+      TL +VG    ++RER+RQI
Sbjct: 238 PEDFTSQASLRADLDRLMADLTPQQRQVLSLRFGLEDGQPLTLAKVGDMLNISRERVRQI 297

Query: 660 EAKAIRKLK 668
           E +A+ KL+
Sbjct: 298 EREALSKLR 306


>gi|172035560|ref|YP_001802061.1| RNA polymerase sigma factor [Cyanothece sp. ATCC 51142]
 gi|171697014|gb|ACB49995.1| group 2 sigma-70 RNA polymerase sigma factor B [Cyanothece sp. ATCC
           51142]
          Length = 328

 Score =  220 bits (561), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 102/225 (45%), Positives = 161/225 (71%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ +T R +S  + R  TP EIA++L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQTLGRSATPAEIAQELEIEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  +GD   + L + +ED+  VSP     Q  LR+  + ++A LTP+
Sbjct: 212 REFLSIARQPISLDVRVGDNQDTELSELLEDQ-GVSPDIYITQELLRQDLSNLMAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+    + +L ++GK+  ++RER+RQ+E +A+ +L+
Sbjct: 271 QRTVLTLRFGLEDGKELSLAKIGKRLNISRERVRQLEHQALAQLR 315


>gi|134293382|ref|YP_001117118.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
 gi|134136539|gb|ABO57653.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 518

 Score =  220 bits (561), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 105/255 (41%), Positives = 166/255 (65%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +R G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 265 RALGAALRDGQQKLGDGTRAMLEANLRLVLSIARKYVNRGVDLPDLVQDGCLGLMRAIEK 324

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 325 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQSQRVQRHALRFRQRHGRRA 384

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A    +  + +R +L +  EP+SL+TP+ D +T  L D IED+ + SP +     
Sbjct: 385 TPAELAADTGLAEDKLRALLALPAEPLSLDTPLPDAETG-LVDLIEDQTSASPFERLANT 443

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  + +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 444 RMRECVSSLLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 503

Query: 668 KHPSRSKKLRSFLDG 682
           +  ++++  +SFLD 
Sbjct: 504 RTAAQAEGAQSFLDA 518



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/149 (30%), Positives = 76/149 (51%), Gaps = 2/149 (1%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++  A ++GY+T  +L   LPPD  S++ +E   A L+++GI+V+D 
Sbjct: 7   TLRADTPLDPIIQLLARAGEQGYLTHADLVDALPPDSDSADALEVVRAALADIGIDVLDE 66

Query: 81  DDLEDEEGSEDSLDL-ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                       +D+   +   S   L      A  STD P+ +Y+R + ++ LL RE E
Sbjct: 67  PAAPAPFVGTTPVDVDRDTLDESRALLGDLARGASASTD-PMALYMRRIHAVPLLKREDE 125

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALI 168
           I +A+ IE GR  ++ +L   P    AL+
Sbjct: 126 IVLAREIETGRHQILHALAGYPPAVDALL 154


>gi|158337052|ref|YP_001518227.1| RNA polymerase sigma factor SigD [Acaryochloris marina MBIC11017]
 gi|158307293|gb|ABW28910.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  220 bits (561), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 106/235 (45%), Positives = 164/235 (69%), Gaps = 1/235 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K   E   AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD   G
Sbjct: 73  LQKALHEGEAAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKG 132

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +T R++S K+ R  T  E+A
Sbjct: 133 YRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKTQRQLSQKLGRAATISELA 192

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L +  + VR+ L+  ++P+SL+  +GD   + LG+ IED +  SP +  +QA+LR   
Sbjct: 193 TSLDLTTKQVREYLERARQPLSLDVRVGDNQDTELGELIEDPSE-SPENFTLQASLRGDL 251

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R++A LT ++++VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+
Sbjct: 252 ERLMADLTDQQQQVLHLRFGLDDGQPLTLAKIGDRLSISRERVRQIEREALSKLR 306


>gi|126661338|ref|ZP_01732404.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126617371|gb|EAZ88174.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 328

 Score =  220 bits (561), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 102/225 (45%), Positives = 161/225 (71%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ +T R +S  + R  TP EIA++L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQSLGRSATPAEIAQELEIEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  +GD   + L + +ED+  VSP     Q  LR+  + ++A LTP+
Sbjct: 212 REFLSIARQPISLDVRVGDNQDTELSELLEDQ-GVSPDIYITQELLRQDLSNLMAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+    + +L ++GK+  ++RER+RQ+E +A+ +L+
Sbjct: 271 QRTVLTLRFGLEDGKELSLAKIGKRLNISRERVRQLEHQALAQLR 315


>gi|254253854|ref|ZP_04947171.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898499|gb|EAY70342.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 547

 Score =  220 bits (560), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 104/236 (44%), Positives = 159/236 (67%), Gaps = 1/236 (0%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA WW++
Sbjct: 312 RAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCVGLMRAIEKFEYRRGFKFSTYATWWIR 371

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +  + +R 
Sbjct: 372 QAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLDEDKLRA 431

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L +  EP+SL+TP+ D DT  L D IED+ + SP +    A +RE  T +L S+TP E 
Sbjct: 432 ILALPAEPVSLDTPLPDTDTG-LVDTIEDQASASPFERLADARMRECVTSLLRSVTPTEA 490

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  ++FLD
Sbjct: 491 DVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTVAEAEGAQTFLD 546



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/140 (30%), Positives = 74/140 (52%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++ LA ++GY+T  +L   LPP+  S++ +E   A L+++GI V+D         
Sbjct: 50  DPIIQLLALAGEQGYLTHADLVDALPPESDSADALEVVRAALADIGIAVLDEPPAPVPFT 109

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +D+   A +    L         ++ DP+ +Y+R M ++ LL+RE EIA+A+ IE 
Sbjct: 110 GAAPVDVDRDALDEGRALLGELARGASASTDPLALYMRRMHAVPLLTREDEIALAREIET 169

Query: 149 GRAMMMASLCESPLTFQALI 168
           GR  ++ +L   P    AL+
Sbjct: 170 GRHQVLHALAGCPAAVDALL 189


>gi|182415180|ref|YP_001820246.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177842394|gb|ACB76646.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 353

 Score =  220 bits (560), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 113/248 (45%), Positives = 166/248 (66%), Gaps = 4/248 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I E   +   +RKG+     A+  M++ANLRLV+ +A  Y + GL  LDLI EGNIGL
Sbjct: 64  LTIDEEISLAKRIRKGD---KAARDHMIKANLRLVVKIAMDYKDFGLPLLDLISEGNIGL 120

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ DKI K+ RTA  ++ 
Sbjct: 121 IKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDKISKMRRTAMALTE 180

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSP 600
           ++ REPT EE+A +L +P   V  +  ++  P SL+ P+G+E D++  G+ + D NAVSP
Sbjct: 181 ELGREPTDEELAIELQIPTSKVAHLKSVSVRPASLDAPVGEEGDSATFGEIVGDDNAVSP 240

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +   + NL      ++ASL  RE  ++R+RFG+    + TLEEVG++F VTRERIRQ+E
Sbjct: 241 FEGLREKNLNSDLHAMVASLDEREAEIIRLRFGLDGKDELTLEEVGRRFHVTRERIRQLE 300

Query: 661 AKAIRKLK 668
             A+ K++
Sbjct: 301 YLALSKMR 308


>gi|26665384|dbj|BAC44903.1| principal sigma factor [Gloeobacter violaceus PCC 8105]
          Length = 203

 Score =  220 bits (560), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 109/204 (53%), Positives = 148/204 (72%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+A KY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIALKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDF E  +  +P D   +  LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFSE-ADGETPEDKVAKNLLREDLEAVLNTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQLFNVT 203


>gi|282900289|ref|ZP_06308240.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281194794|gb|EFA69740.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 327

 Score =  220 bits (560), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 157/225 (69%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  +GYKFSTYA WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K+ R P+P EIAK+L +    +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIAKELELEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  +GD   + L + +ED + +SP     Q  LR     +LA LTP+
Sbjct: 212 REYLNIARQPISLDVRVGDNQDTELQEMLED-HGLSPEHYTTQEFLRHDLNNLLAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+ +RFG+    + +L +VG +  ++RER+RQ+E +A+  L+
Sbjct: 271 QREVVILRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQALTHLR 315


>gi|67924587|ref|ZP_00518002.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853561|gb|EAM48905.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 328

 Score =  220 bits (560), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 103/225 (45%), Positives = 160/225 (71%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S  + R  TP EIA++L +    +
Sbjct: 152 IRQAITRAIAQQSRTIRLPIHITEKLNKIKKTQRELSQTLGRSATPSEIAQELEIEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  +GD   + L + +ED+  VSP     Q  LR+    ++A LTP+
Sbjct: 212 REFLSIARQPISLDVRVGDNQDTELSELLEDQ-GVSPDLYITQELLRQDLRNLMAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+    + +L ++GK+  ++RER+RQ+E +A+ +L+
Sbjct: 271 QRTVLTLRFGLEDGKELSLAKIGKRMNISRERVRQLEHQALAQLR 315


>gi|270157097|ref|ZP_06185754.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|289164492|ref|YP_003454630.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
 gi|269989122|gb|EEZ95376.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|288857665|emb|CBJ11508.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
          Length = 341

 Score =  219 bits (559), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 106/256 (41%), Positives = 172/256 (67%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H  ++  KG+     A+K+M+E+NLRLV+ ++++Y NRGL  LD
Sbjct: 75  LSEIGFSPLLSAEEEVHYATLALKGDV---AARKKMIESNLRLVVKISRRYLNRGLPLLD 131

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GLMK+ EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 132 LIEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 191

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR+++ K+  EP+PEEIA+ +  P+E V+K+L +  +  S++TPIG ++   L D I
Sbjct: 192 LRAARQLTQKLDHEPSPEEIAEMVDKPLEDVQKLLGLNDKVTSVDTPIGFDENKSLLDTI 251

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+N+V+P +     NLR     +L  LT  +++V+  RFG+      TLE+VGK+  +T
Sbjct: 252 PDENSVNPAELLTNENLRLHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLT 311

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ +A++ L+
Sbjct: 312 RERVRQIQVEALKTLR 327


>gi|218439771|ref|YP_002378100.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7424]
 gi|218172499|gb|ACK71232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 328

 Score =  219 bits (557), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 162/225 (72%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ +T R +S ++ R  TP EIAK L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQQLGRSATPAEIAKALDLEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L ++++PISL+  +GD   + L + +ED+  +SP +   Q  +R+    +LA LTP+
Sbjct: 212 REFLSMSRQPISLDVRVGDNQDTELSELLEDE-GISPDNYITQELMRQDLHDLLAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+    + +L ++G++  ++RER+RQ+E +A+ +L+
Sbjct: 271 QREVLSLRFGLQDGKELSLAKIGQRMNISRERVRQLEHQALSQLR 315


>gi|26665380|dbj|BAC44901.1| principal sigma factor [Chlorogloeopsis fritschii PCC 6912]
          Length = 198

 Score =  219 bits (557), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/199 (54%), Positives = 146/199 (73%), Gaps = 1/199 (0%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           +V+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IAD
Sbjct: 1   MVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIAD 60

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           QS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PI
Sbjct: 61  QSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI 120

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETPIG E+ S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+
Sbjct: 121 SLETPIGKEEDSRLGDFIES-DGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGL 179

Query: 635 GMNTDHTLEEVGKQFCVTR 653
                 TLEE+G+ F VTR
Sbjct: 180 DDGRMKTLEEIGQIFNVTR 198


>gi|221212711|ref|ZP_03585688.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
 gi|221167810|gb|EEE00280.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
          Length = 522

 Score =  219 bits (557), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 109/255 (42%), Positives = 167/255 (65%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +V+ +  G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G IGLM+A EK
Sbjct: 269 RALVAALNDGQQKVRDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEK 328

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QAI R++AD++ TIR+PVH+ D+  +V R A R   +  R+P
Sbjct: 329 FEYRRGFKFSTYATWWIRQAIARAVADRARTIRVPVHVGDQHQRVRRQALRFRQRTGRQP 388

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +  + +R +L +  EP+SL+TP+ D DT  L D IED+ + SP +     
Sbjct: 389 TPAELAAETGLAEDKLRAILALPAEPVSLDTPLPDADTG-LVDLIEDETSASPFEQLAGT 447

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE    +L S+TP E  VLR RFG+G     T + + K   ++RER+RQIE +A+  L
Sbjct: 448 RMRECVRSLLRSVTPTEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEKRALAAL 507

Query: 668 KHPSRSKKLRSFLDG 682
           +  + ++   +FLD 
Sbjct: 508 RTAAEAEGAHAFLDA 522



 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/155 (31%), Positives = 76/155 (49%), Gaps = 30/155 (19%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----------- 77
           D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V           
Sbjct: 15  DPIIQLLALASEQGYLTHADLVDALPPESDSPDALDVVRAALADIGITVLDEPAAPPPFA 74

Query: 78  ----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
               VD D    EEG     DLA  AS S+               DP+ +Y+R M ++ L
Sbjct: 75  AAPAVDVDRDALEEGRALLGDLARGASAST---------------DPLALYMRRMHAVPL 119

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           L+RE EIA+A+ +E GR  M+ +L   P    AL+
Sbjct: 120 LTREDEIALARELETGRHQMLHALAGCPPAVDALL 154


>gi|148271746|ref|YP_001221307.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147829676|emb|CAN00592.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 347

 Score =  219 bits (557), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 111/239 (46%), Positives = 156/239 (65%), Gaps = 5/239 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V ANLRLV+S+AK+YT RGL FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 110 AKQHLVNANLRLVVSIAKRYTGRGLPFLDLIQEGNMGLVRAVEKFDYQAGFKFSTYASWW 169

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+ITR +AD S TIRIPVH  + I+++    R ++ ++ R+P+ EEIA++   PV  V
Sbjct: 170 IKQSITRGMADTSRTIRIPVHTVEHINRINAVQRELAVELGRDPSMEEIARESDTPVTKV 229

Query: 564 RKVLKITKEPISLETPI----GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R +L   +EP+SL+  +    GD DT  + D IED +   P+D   Q  +     R++  
Sbjct: 230 RYLLDRAQEPMSLQVLVGGSGGDGDT-EMADLIEDADVTQPIDVVTQQLMAAHVMRLIDG 288

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  R+  V+RMRFG+      +L  V +Q  VTRER+RQIE K + KL+ P     +R 
Sbjct: 289 LAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVTRERVRQIEKKVLAKLRIPELETYIRG 347


>gi|23978372|dbj|BAC21150.1| principal sigma factor [Synechococcus sp. PCC 7001]
          Length = 203

 Score =  219 bits (557), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/204 (53%), Positives = 147/204 (72%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++  RLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSKFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFDVT 203


>gi|113477482|ref|YP_723543.1| RNA polymerase sigma factor SigD [Trichodesmium erythraeum IMS101]
 gi|110168530|gb|ABG53070.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 319

 Score =  219 bits (557), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 108/247 (43%), Positives = 170/247 (68%), Gaps = 8/247 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE + I+   R+GE     AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+
Sbjct: 69  LSKSELQRII---REGER----AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGM 121

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R+++ 
Sbjct: 122 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKVQRQLTQ 181

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R  T  EIA++L +  + +R+ L+  + P+SL+  +GD   + LGD +ED  A SP 
Sbjct: 182 QLGRSATTGEIAEELGLTPKQIRECLERARLPLSLDLRVGDNQDTELGDLLEDTGA-SPE 240

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D A+Q+++R     ++  LTP++++VL +RFG+      TL ++G    ++RER+RQIE 
Sbjct: 241 DYALQSSMRTDLESIMVDLTPQQKQVLALRFGLEDGQTMTLSKIGAHLNISRERVRQIER 300

Query: 662 KAIRKLK 668
           +A+ KL+
Sbjct: 301 EALSKLR 307


>gi|23978293|dbj|BAC21127.1| principal sigma factor [Arthrospira platensis]
          Length = 203

 Score =  218 bits (556), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/204 (53%), Positives = 148/204 (72%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEK D   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PV + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVLLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIES-DGETPEDQVSKNLLREDLESVLDTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|300781025|ref|ZP_07090879.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
 gi|300532732|gb|EFK53793.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
          Length = 330

 Score =  218 bits (556), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 102/236 (43%), Positives = 166/236 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 93  ARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWW 152

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + REP+ EE+A++  +    +
Sbjct: 153 IRQAITRGMADQSRTIRLPVHLVEQVNKLSRIRREMYQSLGREPSNEELAEESGIDESKI 212

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L+ +++P+SL+ P+G ++ + LGDFIED  A    D+ +     +    ++  L  R
Sbjct: 213 EMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEAADAEDAVVSVLRHDDIHDIINGLEQR 272

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+   R+ +LR +
Sbjct: 273 EQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMSKLRVGERADRLRDY 328


>gi|126660028|ref|ZP_01731150.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
 gi|126618706|gb|EAZ89453.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
          Length = 418

 Score =  218 bits (556), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/239 (45%), Positives = 160/239 (66%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM++ANLRLV+SVAKKY +RGL+ LDLIQEG +GL KA EKFD   GY+FSTYA WW
Sbjct: 179 AKDEMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAYWW 238

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS  IR+PVH+ +K++K+ +  R++S    R  T EEI K+L M    V
Sbjct: 239 IRQGITRAIATQSRIIRLPVHITEKLNKIKQVQRKISQAKGRSATLEEIGKELNMSSTQV 298

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R VL      +SLE  +G E  + L D +E ++ +SP ++    +LR     +L  LT R
Sbjct: 299 RDVLMKIPRSVSLEIKVGKEKDTELVDLLESED-ISPEENLAIESLRRDIGILLEDLTER 357

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E+ V+++R+G      ++L ++G+   ++RER+RQIEAKA++KL+ P R  ++R + + 
Sbjct: 358 EQEVIKLRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQKLRQPRRRNQIRDYFES 416


>gi|145596092|ref|YP_001160389.1| RpoD family RNA polymerase sigma factor [Salinispora tropica
           CNB-440]
 gi|145305429|gb|ABP56011.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora tropica
           CNB-440]
          Length = 332

 Score =  218 bits (556), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 101/261 (38%), Positives = 174/261 (66%), Gaps = 7/261 (2%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G+  +E + +V        E + AK   + ANLRLV+S+A++Y   G+  LDLIQEG
Sbjct: 77  VPAGVEKAELQRLV-------AEGARAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEG 129

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N GL++A EKFD+  G+KFSTYA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR
Sbjct: 130 NTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVAR 189

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +++ ++  +P PE+IA  L + VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A
Sbjct: 190 QLTRELGSDPEPEQIATALGVTVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDA 249

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP D  +    R+    +L+ L  R   ++R R+G+    +H+L EV  +F ++RERIR
Sbjct: 250 PSPEDIVLTGLERQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIR 309

Query: 658 QIEAKAIRKLKHPSRSKKLRS 678
           Q+E +A+ +L+  +R++ L++
Sbjct: 310 QLEIQALGRLRELARAEGLQA 330


>gi|302391919|ref|YP_003827739.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
 gi|302203996|gb|ADL12674.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
          Length = 273

 Score =  218 bits (556), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/241 (45%), Positives = 172/241 (71%), Gaps = 3/241 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+KE++E NLRLV+S+AKKY  +G++F D+IQEGN+GLMKA +KFD   GY+FSTYA WW
Sbjct: 34  ARKELIEHNLRLVVSIAKKYRGKGMEFEDMIQEGNLGLMKAIDKFDPDKGYRFSTYATWW 93

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+ITR++  ++ TIR+PVH+ +K  KV +   ++ N++ REPT EEI+++  +  E V
Sbjct: 94  IRQSITRALP-EAKTIRVPVHVWEKTTKVFKAKEKLYNQLNREPTFEEISEETGIDSEKV 152

Query: 564 RKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +++++I+ +    SL   +GD++ + LG+ I D +   P+    +  L+E    VL  LT
Sbjct: 153 KEIIRISSDQNLASLNNLVGDDENTELGELIADDDVEEPMTDLNRQFLQEDLEEVLEELT 212

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE  ++R+RFG+  N   TL+EV  +F ++RERIRQI+ KA+R+L+HPSRSK L++++ 
Sbjct: 213 DREAEIIRLRFGLKDNWPKTLQEVADRFKLSRERIRQIQEKALRRLRHPSRSKALKAYIA 272

Query: 682 G 682
           G
Sbjct: 273 G 273


>gi|307152083|ref|YP_003887467.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982311|gb|ADN14192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 418

 Score =  218 bits (555), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 105/239 (43%), Positives = 161/239 (67%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M++ANLRLV+SVAK+Y NRGL+ LDLIQEG +GL +A +KFD   GY+FSTYA WW
Sbjct: 179 AKEQMIKANLRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWW 238

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS  IR+PVH+ +K++K+ +  R+++      P+ EE++++L M    +
Sbjct: 239 IRQGITRAIATQSRIIRLPVHITEKLNKIKKAQRKIAQLKGATPSIEELSQELEMSPPQI 298

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLE  +G E  + L D +E   A SP D+     LR+    +LA LT R
Sbjct: 299 REVLMRVPRSVSLEIKVGKEKDTELIDLLETTEA-SPEDNIANEALRQDLHNLLADLTTR 357

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  V+++R+G      ++L ++G+   ++RER+RQIEAKAI+KL+ P R  ++R + + 
Sbjct: 358 EREVIQLRYGFKDGKSYSLADIGRTLQLSRERVRQIEAKAIQKLRQPKRRNQIRDYFEA 416


>gi|298241844|ref|ZP_06965651.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297554898|gb|EFH88762.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 366

 Score =  218 bits (555), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 103/246 (41%), Positives = 165/246 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + ++     +IA++++VE+NLRLVIS+A++YT+ G+  +DLIQEGN+GLM+AAEKFD 
Sbjct: 117 IDLAQRAAAGDTIARRKLVESNLRLVISIARRYTSTGVPLIDLIQEGNLGLMRAAEKFDH 176

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA WW++QA++R+  +QS  I +P H+  ++ KV R + ++S +   +P PE
Sbjct: 177 QRGCHFGTYATWWIRQAVSRAAGEQSRMIHLPEHVSTRLRKVRRISAQLSQENGLDPMPE 236

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +IA+     V+ V+ +L + ++P+SL+TP+ DE    LGD +ED    +P ++A +  L 
Sbjct: 237 QIAEACHFEVDEVKNLLGVIEQPVSLDTPVDDETRYSLGDTLEDDTTPAPAETASRHLLG 296

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   R LA LTPRE  V+ +R+GIG     TL EVGK+  ++RER+RQ+E  A+ KL+  
Sbjct: 297 EELHRALAVLTPRERSVVMLRYGIGDGRSRTLLEVGKELGISRERVRQLEVVALMKLRSV 356

Query: 671 SRSKKL 676
           + ++ L
Sbjct: 357 TNAQAL 362


>gi|16331621|ref|NP_442349.1| RNA polymerase sigma factor SigC [Synechocystis sp. PCC 6803]
 gi|2500787|sp|Q59996|RPSC_SYNY3 RecName: Full=Probable RNA polymerase sigma-C factor
 gi|1001684|dbj|BAA10419.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 404

 Score =  218 bits (555), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 161/247 (65%), Gaps = 8/247 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+++ E  +I       E +   AK  M++ANLRLV+SVAKKY NRGL+ LDLIQEG +G
Sbjct: 149 GLTVEELENI-------EKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLG 201

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L +A EKFD   GY+FSTY+ WW++Q ITR+IA QS  IR+PVH+ +K++K+ R  R++S
Sbjct: 202 LERAVEKFDPTKGYRFSTYSYWWIRQGITRAIATQSRMIRLPVHITEKLNKIKRAQRKIS 261

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +    P  +E+A++L M  E VR+VL      +SLE  +G +  + L D +E  +  SP
Sbjct: 262 QEKGHTPKIDEVAEELGMTPEQVREVLTQVPRSVSLELKVGQDKDTELMDLLE-TDTQSP 320

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D  ++  L+     +L  LTPRE+ V+ +RFG      H+L E+G+   ++RER+RQIE
Sbjct: 321 EDELMREALQNDMQEILLDLTPREQEVIALRFGFQDGVAHSLSEIGRILNLSRERVRQIE 380

Query: 661 AKAIRKL 667
           AKA++KL
Sbjct: 381 AKALQKL 387


>gi|220907004|ref|YP_002482315.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7425]
 gi|219863615|gb|ACL43954.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 327

 Score =  218 bits (555), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 107/249 (42%), Positives = 168/249 (67%), Gaps = 7/249 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + VR+G+     AK++M+EANLRLV+SVAKKY  R L+ LDLIQEG +GL +  EKFD  
Sbjct: 84  TAVRRGQR----AKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGTLGLERGVEKFDPT 139

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA Q+ T+R+P+H+ +K++K+ +  R +S ++ R  TP E
Sbjct: 140 RGYKFSTYAYWWIRQAITRAIAQQARTVRLPIHITEKLNKIKKAQRVLSQRLGRSATPAE 199

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA++L +    +R+ L + ++P+SL+  +GD   + L D +ED ++ SP        LR+
Sbjct: 200 IAQELELEPSQIREYLTLARQPVSLDLRVGDNQDTELRDLLED-DSPSPEQYTTGEALRD 258

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +LA LTP++  VL +RFG+    + +L +VG+Q  ++RER+RQ+E +A+  L+   
Sbjct: 259 DVNHLLAELTPQQREVLTLRFGLEDGKELSLAKVGEQLSLSRERVRQLERQALDHLRR-- 316

Query: 672 RSKKLRSFL 680
           R  ++R +L
Sbjct: 317 RKLQVREYL 325


>gi|166364164|ref|YP_001656437.1| RNA polymerase sigma factor [Microcystis aeruginosa NIES-843]
 gi|166086537|dbj|BAG01245.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 328

 Score =  218 bits (555), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 159/225 (70%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ RT R ++ K+ R  TP EIA +L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKRTQRELAQKLGRSATPAEIALELELEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + ++PISL+  +GD   + L + +ED + VSP     Q  LR+    +LA LTP+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLED-SGVSPDTFITQELLRQDLANLLAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+ +RFG+    + +L ++G++  ++RER+RQ+E +A+  L+
Sbjct: 271 QREVITLRFGLTDGKELSLAKIGQRMNISRERVRQLEHQALAHLR 315


>gi|119487601|ref|ZP_01621211.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
 gi|119455770|gb|EAW36906.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
          Length = 404

 Score =  218 bits (554), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 109/244 (44%), Positives = 164/244 (67%), Gaps = 1/244 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E   AK  M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FS
Sbjct: 159 QTEGIKAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFS 218

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TY+ WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R  T ++IA +L 
Sbjct: 219 TYSYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRIATIDDIAAELE 278

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M    VR+VL      +SLET +G  D       + +    SP D  ++ +L     ++L
Sbjct: 279 MTPAQVREVLLKVPRSVSLETKVGS-DKDTELGELLETEEASPEDQLMRESLHRDLQQLL 337

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A L+ RE  V++MR+G+G    ++L E+G++  ++RER+RQIEAKA++KL+ P R  ++R
Sbjct: 338 ADLSDRERDVIQMRYGLGNGHTYSLAEIGRELELSRERVRQIEAKALQKLRQPKRRNRVR 397

Query: 678 SFLD 681
            +L+
Sbjct: 398 DYLE 401



 Score = 42.4 bits (98), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           DLED       LDL S         QK K++ +R T D VR+YL+E+G + LL R+ E+A
Sbjct: 13  DLEDLSKQPSDLDLESMEEIDPA--QKTKNNNNRRTTDLVRVYLQEIGRVRLLGRDEEVA 70

Query: 142 IAKRIE 147
            A++++
Sbjct: 71  EAQKVQ 76


>gi|22297808|ref|NP_681055.1| RNA polymerase sigma factor SigD [Thermosynechococcus elongatus
           BP-1]
 gi|22293985|dbj|BAC07817.1| group2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 315

 Score =  218 bits (554), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 107/240 (44%), Positives = 165/240 (68%), Gaps = 6/240 (2%)

Query: 434 VRKGECEASI-----AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           + +GE E  I     AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKF
Sbjct: 65  ISEGELETIIENGERAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKF 124

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R++S ++ R  T
Sbjct: 125 DPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQRLGRAAT 184

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A +L +    VR+ L+  ++P+SL+  +GD   + LG+ +ED +++SP + A Q+ 
Sbjct: 185 INELAAELELTPAQVREYLERARQPLSLDVRVGDNQDTELGELLED-SSISPEEFATQSL 243

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR    R++A LTP++  VL +RFG+      TL +VG+   ++RER+RQIE +A+ KL+
Sbjct: 244 LRSDLERLMAELTPQQRHVLSLRFGLENGQPLTLAKVGELLNISRERVRQIEREALSKLR 303


>gi|291302005|ref|YP_003513283.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571225|gb|ADD44190.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 323

 Score =  218 bits (554), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 107/252 (42%), Positives = 164/252 (65%), Gaps = 10/252 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+   E   AK  +++ANLRLV+S+AK+Y  RG+  LDLIQEGN+GL++A EKFD+  G
Sbjct: 76  LRQIVAEGRRAKSMLLKANLRLVVSIAKRYVGRGVALLDLIQEGNLGLIRAVEKFDYTKG 135

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR++ADQ+ TIR+P H  ++I+++ +  R ++ +  REP  EEIA
Sbjct: 136 FKFSTYATWWIRQAITRAMADQARTIRVPAHTAEQINRIAKIRRELTAEQGREPRHEEIA 195

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN----- 608
           +++ +    V ++L   ++PISL+ P+ D+  + L D +       P+D A + N     
Sbjct: 196 ERMGLEPYRVLELLSYDRDPISLDQPVSDDRQTPLSDLV-----ARPVDPAAEPNPANAQ 250

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+   R L  L  RE  VLR RFGI      TLEEVG++  ++RER+RQ+E  ++ KL+
Sbjct: 251 LRQELERALTDLPARERAVLRARFGIDDGRQRTLEEVGEELGLSRERVRQLEKLSLNKLR 310

Query: 669 HPSRSKKLRSFL 680
            P  ++ L  +L
Sbjct: 311 EPGMARALAEYL 322


>gi|282900303|ref|ZP_06308254.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
 gi|281194808|gb|EFA69754.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
          Length = 399

 Score =  218 bits (554), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 108/242 (44%), Positives = 171/242 (70%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTY
Sbjct: 157 QGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTY 216

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K  R PT  E+A+ L M 
Sbjct: 217 AYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKFARNPTEVEMAEFLEMT 276

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ +R++ ++ ++ +SL   +G E+ + L D +ED++  SP     +  +R+    VL  
Sbjct: 277 VQQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNQSPEAKMNENMMRQEIWEVLGD 336

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ 
Sbjct: 337 VLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKG 396

Query: 679 FL 680
           +L
Sbjct: 397 WL 398


>gi|160937287|ref|ZP_02084649.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
 gi|158439851|gb|EDP17600.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
          Length = 298

 Score =  218 bits (554), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 116/244 (47%), Positives = 163/244 (66%), Gaps = 11/244 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A+++M+ +NLRLVI+ AKKY    + L  LDLIQEGN+GL+KA EK++  LG++FSTYA 
Sbjct: 61  ARQKMISSNLRLVINQAKKYVTYTQSLTLLDLIQEGNLGLIKAVEKYNPELGFRFSTYAS 120

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP---TPEEIAKKLAM 558
           WW+KQAITR+I+     IR+PVH  + I KV    +R +++I ++    TPE++      
Sbjct: 121 WWIKQAITRAISVLDKAIRLPVHFCEDIQKV----KRATHEIMQQNDIVTPEKLKDITGF 176

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               + K+L      ISLETP+G+E T  LGDF+ED    S  + A++  ++   +R + 
Sbjct: 177 SEGKIEKILMNMNHTISLETPVGEEAT--LGDFVEDTLTPSIEEQAMENAMQREISRQME 234

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L PRE+ +L +RFG+     HTLEEVGKQ  VTRERIRQIE KA+RKL+HP+RS+ LR 
Sbjct: 235 CLRPREQTILALRFGLNGQNPHTLEEVGKQMGVTRERIRQIEMKALRKLRHPNRSRYLRE 294

Query: 679 FLDG 682
           F+ G
Sbjct: 295 FILG 298


>gi|22298042|ref|NP_681289.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
 gi|22294220|dbj|BAC08051.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 375

 Score =  217 bits (553), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 106/262 (40%), Positives = 178/262 (67%), Gaps = 8/262 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             I++SE +HI       E +   AK ++++ANLRLV+++AKKY + G++FLDLIQEG++
Sbjct: 119 ANITLSELQHI-------ERQGQRAKNQLLQANLRLVVNIAKKYQHHGVEFLDLIQEGSL 171

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL +A EKFD   G++FSTYA WW++Q+ITR++A QS TIR+P+HM +K++K+ R  RR+
Sbjct: 172 GLERAVEKFDPTKGFRFSTYAYWWIRQSITRAVASQSRTIRLPIHMVEKLNKIKRAQRRL 231

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           + +    P+  +IA++L + V  VR+VL    + ++LE  +G +  + L + IE   A +
Sbjct: 232 AAQRGAMPSLADIAQELNLEVSQVRQVLMAVPKSVALEQRVGSDQETELQELIESP-APT 290

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +  ++ +LR T  ++L+ L+PRE +V+ +R+G+G      L EV     ++RERIRQI
Sbjct: 291 PDEVIMRESLRTTLKQLLSDLSPRERQVMELRYGLGEQPALELAEVAVLLGLSRERIRQI 350

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E +A++KL+ P R ++++ +L+
Sbjct: 351 EHRALQKLRQPQRRREIQDYLE 372


>gi|311897949|dbj|BAJ30357.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 323

 Score =  217 bits (553), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 111/248 (44%), Positives = 157/248 (63%), Gaps = 7/248 (2%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+S  E R I         +A  AK   + +NLRLV++VA++Y   GL  LDLIQEGN G
Sbjct: 72  GVSTEELRAIAE-------DAERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAG 124

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++A EKFD+  G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ +  R  +
Sbjct: 125 LVRAVEKFDYSKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRKVQREKA 184

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REP P EIA +L    + V+ VL   ++P+SL   + DE  +  GD +ED  AVSP
Sbjct: 185 KELGREPDPAEIAAELDTTEQRVKDVLDWARDPVSLNMAVDDEGETQFGDLVEDTGAVSP 244

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+ +    RE    ++  L  R   ++R R+G+    + TL EVGKQ  +TRERIRQIE
Sbjct: 245 EDAVMVMLRREELDGLIGRLDDRTASIIRSRYGMEDGRERTLTEVGKQHGLTRERIRQIE 304

Query: 661 AKAIRKLK 668
             A+ +LK
Sbjct: 305 KHALAELK 312


>gi|298490639|ref|YP_003720816.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298232557|gb|ADI63693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 327

 Score =  217 bits (553), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 101/235 (42%), Positives = 161/235 (68%), Gaps = 1/235 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VKQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K+ R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED+   SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVRVGDNQDTELQEMLEDEGP-SPEYYTTQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +LA LTP++  VL +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+
Sbjct: 261 NNLLAELTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQALAHLR 315


>gi|88858314|ref|ZP_01132956.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
 gi|88819931|gb|EAR29744.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
          Length = 339

 Score =  217 bits (553), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 108/231 (46%), Positives = 161/231 (69%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 97  CEAS--RKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 154

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+KL  
Sbjct: 155 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAEKLDR 214

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           PVE V K+L++ ++  S++TPIG +    L D + D+    P +S IQ  ++RE     L
Sbjct: 215 PVEDVTKMLRLNEKITSVDTPIGGDSEKALLDILADEKGGGP-ESCIQDEDIRENIVHWL 273

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE+VGK+  +TRER+RQI+ +A+R+LK
Sbjct: 274 EELNAKQREVLARRFGLLGYEPSTLEDVGKEIGLTRERVRQIQVEALRRLK 324


>gi|48743|emb|CAA37174.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 332

 Score =  217 bits (553), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 109/233 (46%), Positives = 152/233 (65%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTY
Sbjct: 92  ESERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTY 151

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P EIA +L   
Sbjct: 152 ATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEIAAELGST 211

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  
Sbjct: 212 PERVHDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L PR   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 LDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|159027100|emb|CAO89285.1| rpoD [Microcystis aeruginosa PCC 7806]
          Length = 328

 Score =  217 bits (553), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 159/225 (70%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ RT R ++ K+ R  TP EIA +L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKRTQRELAQKLGRSATPAEIALELDLEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + ++PISL+  +GD   + L + +ED + VSP     Q  LR+    +LA LTP+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLED-SGVSPDTFITQELLRQDLANLLAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+ +RFG+    + +L ++G++  ++RER+RQ+E +A+  L+
Sbjct: 271 QREVITLRFGLTDGKELSLAKIGQRMNISRERVRQLEHQALAHLR 315


>gi|221196694|ref|ZP_03569741.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
 gi|221203363|ref|ZP_03576382.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221177297|gb|EEE09725.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221183248|gb|EEE15648.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
          Length = 524

 Score =  217 bits (553), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 163/246 (66%), Gaps = 1/246 (0%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G IGLM+A EKF++  G+KF
Sbjct: 280 GQQKVRDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKF 339

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI R++AD++ TIR+PVH+ D+  +V R A R   +  R+PTP E+A + 
Sbjct: 340 STYATWWIRQAIARAVADRARTIRVPVHVGDQHQRVRRQALRFRQRTGRQPTPAELAAET 399

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  + +R +L +  EP+SL+TP+ D DT  L D IED+ + SP +    A +RE    +
Sbjct: 400 GLAEDKLRAILALPAEPVSLDTPLPDADTG-LVDLIEDETSASPFEQLAGARMRECVRSL 458

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L S+TP E  VLR RFG+G     T + + K   ++RER+RQIE +A+  L+  + ++  
Sbjct: 459 LRSVTPAEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEKRALAALRTAAEAEGA 518

Query: 677 RSFLDG 682
            +FLD 
Sbjct: 519 HAFLDA 524



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/140 (29%), Positives = 74/140 (52%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D         
Sbjct: 15  DPIIQLLALASEQGYLTHADLVDALPPESDSPDALDVVRAALADIGITVLDEPAAPPPFA 74

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  ++D+   A      L         ++ DP+ +Y+R M ++ LL+RE EIA+A+ +E 
Sbjct: 75  AAPAVDVDRDALEEGRALLGDLARGASASTDPLALYMRRMHAVPLLTREDEIALARELET 134

Query: 149 GRAMMMASLCESPLTFQALI 168
           GR  M+ +L   P    AL+
Sbjct: 135 GRHQMLHALAGCPPAVDALL 154


>gi|13508091|ref|NP_110040.1| RNA polymerase sigma factor [Mycoplasma pneumoniae M129]
 gi|2500786|sp|P78022|RPOD_MYCPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1674175|gb|AAB96132.1| Sigma-70 Factor Family [Mycoplasma pneumoniae M129]
 gi|301633308|gb|ADK86862.1| RNA polymerase sigma factor RpoD [Mycoplasma pneumoniae FH]
          Length = 499

 Score =  217 bits (553), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 112/247 (45%), Positives = 169/247 (68%), Gaps = 8/247 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V +NLRLV+S+AKK+  RGL F DLIQEGN+GL+KA  KF+W LG KFSTYA WW
Sbjct: 248 AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWW 307

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
           +KQAITR+IADQ+ T+RIPVHM + I+++ +  R ++ ++ REPT EE+A+K+    EG 
Sbjct: 308 IKQAITRAIADQARTVRIPVHMVETINRLAKAERALNQELGREPTAEELAEKMGGQAEGF 367

Query: 563 -VRKVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLD-SAIQANLRETTTRVL 617
            V+K+ +I +   +P+SL+  +G ++ S  GDF+ D +A  P + +  ++N  +    + 
Sbjct: 368 TVKKIAEIKRLSLDPVSLDKTVGHDEESQFGDFVRDTDAQMPDEFTESRSNYEKIDELLN 427

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L+ +EE ++RMR G+   N   TL+EV ++  + RE+IRQIE KAIRKL+   R+  +
Sbjct: 428 NCLSEQEELIVRMRIGMPPYNETKTLDEVSQKIKIPREKIRQIETKAIRKLRQAVRNNHM 487

Query: 677 R-SFLDG 682
             SF+ G
Sbjct: 488 SLSFMRG 494


>gi|158335492|ref|YP_001516664.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158305733|gb|ABW27350.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 327

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 106/237 (44%), Positives = 159/237 (67%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+SVAKKY  R L+ LDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ +  R +S K+ R  TP EIA+ L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKAQRELSQKLGRSATPAEIAEALELEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L I ++PISL+  +GD   + L D +ED +  SP        LR+   ++L  LTP+
Sbjct: 212 RDYLTIARQPISLDLRVGDNQDTELRDLLED-DGQSPEQFTTTEALRDDVNQLLKELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  VL +RFG+    + +L +VG+Q  ++RER+RQ+E +A+  L+   R  ++R ++
Sbjct: 271 QRDVLMLRFGLNNGKELSLAKVGQQLSLSRERVRQLERQALDYLRR--RKGEVREYI 325


>gi|6463986|dbj|BAA86958.1| group 2 sigma factor RpoD4 [Synechococcus sp. PCC 7942]
          Length = 311

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 105/226 (46%), Positives = 162/226 (71%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M++ANLRLV+SVAKK  N+GL+ LDLIQEG++GL +A EKFD  LGYKFSTYA WW
Sbjct: 74  AKTKMLKANLRLVVSVAKKCQNQGLELLDLIQEGSLGLERAVEKFDPALGYKFSTYAYWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+I + + TIR+P+H+ +KI ++ +  R +++++KR P+  EIA+ L +P++ V
Sbjct: 134 IRQSMTRAIDNHARTIRLPIHVSEKISRIKKMTRELTHQLKRLPSRAEIAEALKLPLQDV 193

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L  +    SL+    GD+  S LGD I D  ++ P+D+  +    E  +  LA LT 
Sbjct: 194 EMLLSQSTPCTSLDAQARGDDGRSFLGDLIPDPKSLEPMDAMDRHIQHEQISTWLAHLTE 253

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++VL++RFG+     HTL E+G++  V+RERIRQ+EA+A++KL+
Sbjct: 254 REQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVEARALQKLR 299


>gi|21221637|ref|NP_627416.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|256787171|ref|ZP_05525602.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
 gi|289771070|ref|ZP_06530448.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
 gi|19856654|sp|P18249|HRDD_STRCO RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|7799522|emb|CAB90986.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701269|gb|EFD68698.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
          Length = 332

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 109/233 (46%), Positives = 152/233 (65%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTY
Sbjct: 92  ESERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTY 151

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P EIA +L   
Sbjct: 152 ATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEIAAELGST 211

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  
Sbjct: 212 PERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L PR   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 LDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|319953761|ref|YP_004165028.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319422421|gb|ADV49530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 116/285 (40%), Positives = 185/285 (64%), Gaps = 6/285 (2%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K     E  S+ K   EI  + +   I+  E   +   ++KG+ +A++ K  + +ANLR 
Sbjct: 8   KQVTNRETASLDKYLQEIGKVDL---ITADEEVELAQRIKKGD-QAALEK--LTKANLRF 61

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+Q
Sbjct: 62  VVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQ 121

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S  +R+P++    I+K+ +T   +    +R+P+PEEIAK+L M VE V++ LK +   +S
Sbjct: 122 SRIVRLPLNKIGSINKINKTFAFLEQAHERQPSPEEIAKELDMTVEDVKQSLKNSGRHVS 181

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++ P+ D + S+L D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+ 
Sbjct: 182 MDAPLIDGEDSNLYDVLRSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLA 241

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 242 GQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|254415890|ref|ZP_05029647.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177317|gb|EDX72324.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 352

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 102/249 (40%), Positives = 169/249 (67%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S ++K   + + AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  
Sbjct: 105 SALKKIINQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPT 164

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA Q+  IR+P+H+ +K++K+ +  R +S ++ R  TP E
Sbjct: 165 RGYKFSTYAYWWIRQAITRAIAQQARAIRLPIHITEKLNKIKKVQRELSQRLGRNATPTE 224

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           I ++L +    +R+ L I ++P+SL+  +GD   + L D +ED +  +P+    Q +LR+
Sbjct: 225 IGQELELEPAQIREYLSIARQPVSLDVRVGDNQDTELSDLLED-SGPTPVHYTTQESLRQ 283

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +LA LTP++  VL +RFG+    + +L +VG++  ++RER+RQ+E +A+ +L+   
Sbjct: 284 DLDNLLAELTPQQREVLALRFGLEDGNELSLAKVGQRLNLSRERVRQLEHQALAQLRR-- 341

Query: 672 RSKKLRSFL 680
           R   +R ++
Sbjct: 342 RHATVREYI 350


>gi|77359643|ref|YP_339218.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874554|emb|CAI85775.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 324

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 105/230 (45%), Positives = 157/230 (68%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 79  CEAS--RKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA  L  
Sbjct: 137 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAACLDK 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ ++  S++ PIG E+ + L D I D N V P       ++ +     L 
Sbjct: 197 PVEDVTKMLRLNEKIASVDMPIGGENDTALLDIIADDNNVGPEGEVQNNDMNKHIVDWLG 256

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L P++  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+R+LK
Sbjct: 257 ELNPKQREVLARRFGLLGYEPSTLEDVGREIGLTRERVRQIQVEALRRLK 306


>gi|72080402|ref|YP_287460.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 7448]
          Length = 489

 Score =  217 bits (552), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 230 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 289

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 290 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 349

Query: 550 EEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 350 EEISERLGGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 407

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 408 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 465

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 466 RQIEAKILKKLRTPHRRLSLRDF 488


>gi|167579340|ref|ZP_02372214.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
          Length = 482

 Score =  217 bits (552), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 102/246 (41%), Positives = 161/246 (65%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF++  G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKVADRIERRSGARASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+  Q  + +  T +
Sbjct: 355 GLSAERLRAVLMLPREPRSLNAPLGDDDQAEFGDIVEDASTPSLFDALAQGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQTLRITADACNA 474

Query: 677 RSFLDG 682
           R FLD 
Sbjct: 475 RDFLDA 480



 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 29/42 (69%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 109 DPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAET 150


>gi|83720670|ref|YP_440648.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|167617444|ref|ZP_02386075.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
 gi|83654495|gb|ABC38558.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 483

 Score =  217 bits (552), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 102/246 (41%), Positives = 161/246 (65%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF++  G+KF
Sbjct: 236 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKF 295

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 296 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKVADRIERRSGARASLAELSEAT 355

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+  Q  + +  T +
Sbjct: 356 GLSAERLRAVLMLPREPRSLNAPLGDDDQAEFGDIVEDASTPSLFDALAQGQMCDVVTSL 415

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +   
Sbjct: 416 LKTMSAQEADILRRRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQTLRITADACNA 475

Query: 677 RSFLDG 682
           R FLD 
Sbjct: 476 RDFLDA 481



 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 29/42 (69%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 110 DPLALFVRRMHAVPLLTHAQEIALATEIEAGREQVLQALAET 151


>gi|76799605|ref|ZP_00781725.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
 gi|76585040|gb|EAO61678.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
          Length = 278

 Score =  217 bits (552), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 100/183 (54%), Positives = 141/183 (77%), Gaps = 3/183 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V +G+    +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELAVAVAEGDL---MAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDF 591
           GDF
Sbjct: 276 GDF 278



 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 54/108 (50%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  +  +        +  ++   S  
Sbjct: 39  PFVLDADQIDDLLERLTDGGISITD------KEGNPSTKYVVEGPKPEELTDEELIGSNS 92

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ E E  +A  +  G  M    L E+ L
Sbjct: 93  AKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEGDLMAKQRLAEANL 140


>gi|315127432|ref|YP_004069435.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
 gi|315015946|gb|ADT69284.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
          Length = 323

 Score =  216 bits (551), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 105/230 (45%), Positives = 157/230 (68%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 78  CEAS--RKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 135

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+ L  
Sbjct: 136 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAESLDR 195

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ ++  S++ PIG E+ S L D I D+  V P       ++       L 
Sbjct: 196 PVEDVTKMLRLNEKIASVDMPIGSENDSALLDVIADEKNVGPEGEVQNNDMNTHIIDWLG 255

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L P++  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+R+LK
Sbjct: 256 ELNPKQREVLARRFGLLGYEPSTLEDVGREIGLTRERVRQIQVEALRRLK 305


>gi|144575263|gb|AAZ53437.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           7448]
          Length = 676

 Score =  216 bits (551), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 417 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 476

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 477 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 536

Query: 550 EEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 537 EEISERLGGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 594

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 595 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 652

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 653 RQIEAKILKKLRTPHRRLSLRDF 675


>gi|161936260|ref|YP_115577.2| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 489

 Score =  216 bits (551), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 230 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 289

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 290 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 349

Query: 550 EEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 350 EEISERLGGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 407

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 408 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 465

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 466 RQIEAKILKKLRTPHRRLSLRDF 488


>gi|148377531|ref|YP_001256407.1| RNA polymerase sigma factor [Mycoplasma agalactiae PG2]
 gi|148291577|emb|CAL58963.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae PG2]
          Length = 509

 Score =  216 bits (551), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 111/256 (43%), Positives = 168/256 (65%), Gaps = 10/256 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG  +   A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K++   G+K
Sbjct: 254 KGGFKGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIIKAVQKYNVNKGFK 313

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR++ADQS T+R+PVHM + I+K+ +  R +  +   +PT EEIA++
Sbjct: 314 FSTYATWWIRQAITRAVADQSRTVRVPVHMVETINKITKIERELQQENGVDPTDEEIAQR 373

Query: 556 LA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                  E VR + KI  +PISL+  IG E+ S   DF++D++ V+P+D A    L ET 
Sbjct: 374 YGNDFTAEKVRHIRKINIDPISLDKQIGKENDSSFSDFVKDESVVNPVDYASHEELVETL 433

Query: 614 TRVLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +L  +L   E  ++  R+G+G + +       +LEE+  +  V++ERIRQIE K +RK
Sbjct: 434 NAILKDTLDADEYELICKRYGVGFDNNGEKYKVFSLEELALERNVSKERIRQIENKILRK 493

Query: 667 LK-HPSRSKKLRSFLD 681
           LK  P RS+ L+ F++
Sbjct: 494 LKSSPERSRYLKVFME 509


>gi|71893415|ref|YP_278861.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae J]
          Length = 489

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 230 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 289

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 290 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 349

Query: 550 EEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 350 EEISERLDGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 407

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 408 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 465

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 466 RQIEAKILKKLRTPHRRLSLRDF 488


>gi|291566702|dbj|BAI88974.1| group 2 RNA polymerase sigma factor SigB [Arthrospira platensis
           NIES-39]
          Length = 334

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 112/265 (42%), Positives = 172/265 (64%), Gaps = 12/265 (4%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S + G+S SE   I++  R+       AK++M+EANLRLV+S+AKKY  R ++FLDLIQE
Sbjct: 79  SAKAGLSESEMTDIINRGRR-------AKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQE 131

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL +  EKFD   GYKFSTYA WW++QAITR+IA  S TIR+P+H+ +K++K+ R  
Sbjct: 132 GTLGLERGVEKFDPMRGYKFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEKLNKIKRVQ 191

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R +  +  R  TP EIAK L +    +R  L  ++ P+SL+  +GD   + L D +ED++
Sbjct: 192 RELFQQYGRNATPTEIAKALDLEPSQIRDYLLASRHPVSLDLRVGDNQDTELQDLLEDES 251

Query: 597 AVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           A +  DS + Q  LR+    ++A LTP++  VL +R+G+    + +L +VG Q  ++RER
Sbjct: 252 ASA--DSYVTQQLLRQDLKDMMADLTPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRER 309

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           +RQ+E +A+  L+   R  ++R +L
Sbjct: 310 VRQLENQALNHLRR--RKAQVREYL 332


>gi|53987186|gb|AAV27387.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 676

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 417 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 476

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 477 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 536

Query: 550 EEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 537 EEISERLGGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 594

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 595 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 652

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 653 RQIEAKILKKLRTPHRRLSLRDF 675


>gi|186680839|ref|YP_001864035.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186463291|gb|ACC79092.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 378

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 113/275 (41%), Positives = 189/275 (68%), Gaps = 6/275 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           LK+  E   + + + + ++E + + S + +G     +AK++M+ +NLRLV+S+AK+Y NR
Sbjct: 108 LKLGQEPTKLEIASELEMTE-KQLESRLYQG----RVAKRKMIRSNLRLVVSIAKRYLNR 162

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+ FLDLIQEG +GL +A EKFD   GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ 
Sbjct: 163 GVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIV 222

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +K++K+ +  R +  K+ R PT  E+A+ L + V+ +R++ ++ ++ +SL   +G E+ +
Sbjct: 223 EKLNKLKKAQRELKQKLCRNPTEGEMAEALDISVQQLRQLQQLRRQALSLNHRVGKEEDT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            L D +ED++ +SP     +  +R+    VL   LTPRE+ V+ +R+G+  +   TLEEV
Sbjct: 283 ELMDLLEDEDNLSPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEV 342

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G  F ++RER+RQI++KA+RKL+ P  +K+L+ +L
Sbjct: 343 GNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKGWL 377


>gi|167561013|ref|ZP_02353929.1| RNA polymerase sigma factor [Burkholderia oklahomensis EO147]
          Length = 476

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 100/246 (40%), Positives = 164/246 (66%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +GE   S A  +M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A +KF++  G+K
Sbjct: 228 EGEARISAATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFK 287

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++ 
Sbjct: 288 FSTYATWWIRQAISRAVADRARTIRLPVHVGDQARRVRKIADRIKQRSGMRASLAELSEA 347

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             +  E +R VL++ +EP SL TP+GD+D +  GD +ED +  S  D+   A +R+    
Sbjct: 348 TELSTERLRAVLELPREPRSLNTPLGDDDQAEFGDLVEDASTPSLFDALAGAQMRDVVAS 407

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L +++ +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +  
Sbjct: 408 LLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKRALQTLRVTAEACN 467

Query: 676 LRSFLD 681
              FLD
Sbjct: 468 AHDFLD 473


>gi|312601028|gb|ADQ90283.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 168]
          Length = 676

 Score =  216 bits (551), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 417 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 476

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 477 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 536

Query: 550 EEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 537 EEISERLGGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 594

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 595 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 652

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 653 RQIEAKILKKLRTPHRRLSLRDF 675


>gi|226328647|ref|ZP_03804165.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
 gi|225203380|gb|EEG85734.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
          Length = 327

 Score =  216 bits (550), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 102/233 (43%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ ++++YTNRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 87  SRQRMIESNLRLVVKISRRYTNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA+ L  PVE V
Sbjct: 147 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSVEEIAESLDKPVEDV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D+N   P  +    NL+E   + L  L P+
Sbjct: 207 SKMLRLNERITSVDTPIGGDSDKALLDIISDENEEGPEATIQNNNLKENIIKWLFELNPK 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+LK   +S+ L
Sbjct: 267 QREVLARRFGLLGYEAETLEDVGREIGLTRERVRQIQVEGLRRLKDILQSQGL 319


>gi|167568274|ref|ZP_02361148.1| RNA polymerase sigma factor [Burkholderia oklahomensis C6786]
          Length = 483

 Score =  216 bits (550), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 100/246 (40%), Positives = 164/246 (66%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +GE   S A  +M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A +KF++  G+K
Sbjct: 235 EGEARISAATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFK 294

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++ 
Sbjct: 295 FSTYATWWIRQAISRAVADRARTIRLPVHVGDQARRVRKIADRIKQRSGMRASLAELSEA 354

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             +  E +R VL++ +EP SL TP+GD+D +  GD +ED +  S  D+   A +R+    
Sbjct: 355 TELSTERLRAVLELPREPRSLNTPLGDDDQAEFGDLVEDASTPSLFDALAGAQMRDVVAS 414

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L +++ +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +  
Sbjct: 415 LLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKRALQTLRVTAEACN 474

Query: 676 LRSFLD 681
              FLD
Sbjct: 475 AHDFLD 480


>gi|261210105|ref|ZP_05924403.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
 gi|260840870|gb|EEX67412.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
          Length = 336

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 157/226 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 316


>gi|113477826|ref|YP_723887.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110168874|gb|ABG53414.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 384

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 110/267 (41%), Positives = 174/267 (65%), Gaps = 8/267 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++V  G + S+  H     R  +C    AK+ M+ +NLRLV+S+AK+Y NRG+ FLDLIQ
Sbjct: 123 VAVAAGFTESQLDH-----RLHQCRT--AKRRMISSNLRLVVSIAKRYLNRGVPFLDLIQ 175

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG +GL +AAEKFD   GYKFSTYA WW++Q ITR+IA+Q  TIR+PVH+ ++I+K+ R 
Sbjct: 176 EGALGLNRAAEKFDPDKGYKFSTYAYWWIRQGITRTIANQGRTIRLPVHVVEQINKLRRV 235

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +   + R P   EIA++L + +  +R + +I ++ +SL   +G ++ + L DF+ED 
Sbjct: 236 YRDLRRSLNRIPNDTEIAQELEISLPQLRNLQQIRRKTLSLNHRLGTDENTELLDFLEDN 295

Query: 596 NAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
              +P        +R+    VL   L+ RE+ V+ +R+G+     HTL+EV +   ++RE
Sbjct: 296 ENSTPEAQMNDMMMRQDILEVLNHVLSNREQDVISLRYGLITGEPHTLDEVSRMINLSRE 355

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           R+RQI+AKA+RKL+ P  +++L+ +L+
Sbjct: 356 RVRQIQAKAMRKLRRPQVAERLKGWLN 382


>gi|144227447|gb|AAZ44150.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           J]
          Length = 676

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 168/263 (63%), Gaps = 20/263 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +K + +  I KK    +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D
Sbjct: 417 LAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYD 476

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT 
Sbjct: 477 YTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTA 536

Query: 550 EEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEI+++L      + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI  
Sbjct: 537 EEISERLDGEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAI-- 594

Query: 608 NLRETTTRVL-----ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
             RE   +VL     ++L   E   ++ R+G+G N +      H+ EE+     VT+ER+
Sbjct: 595 --REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERV 652

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++KL+ P R   LR F
Sbjct: 653 RQIEAKILKKLRTPHRRLSLRDF 675


>gi|172065170|ref|YP_001815882.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171997412|gb|ACB68329.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 621

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 150/237 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D+  G++FSTYA WW
Sbjct: 384 ARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 443

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +     TP E+A  +  PV+ V
Sbjct: 444 IRQAITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKV 503

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++ I KEP+S + P+  E      D   D    SP D+A    LR T   V+  L PR
Sbjct: 504 RDLMAIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAAGATQLRRTIAAVIDRLPPR 563

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LRSF+
Sbjct: 564 EAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRASDTLGLLRSFI 620



 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 52/144 (36%), Positives = 73/144 (50%), Gaps = 4/144 (2%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I     RG+VT  ++   LP D+ +   ++   A+L  +GI V D  D       E   
Sbjct: 28  LIATGLSRGFVTHGDIIDGLPDDDANDSGIDAVAAVLDELGIAVCDSADTASGWTLERYF 87

Query: 94  DLASSA---SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             A  A   ++ +  L      A R+TD PVR+YLREMG+  LL+R+ E A A+RIE GR
Sbjct: 88  RPAPPARAWADGAGTLAAADLLAPRTTD-PVRLYLREMGTTPLLTRDEEFAYARRIERGR 146

Query: 151 AMMMASLCESPLTFQALIIWRDEL 174
           A   A LC  P    AL+  R E+
Sbjct: 147 AASAAVLCGDPDALDALVSIRVEI 170


>gi|258623793|ref|ZP_05718750.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
 gi|258583916|gb|EEW08708.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
          Length = 336

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 157/226 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 316


>gi|258623525|ref|ZP_05718526.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|262172378|ref|ZP_06040056.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
 gi|258584187|gb|EEW08935.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|261893454|gb|EEY39440.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
          Length = 336

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 157/226 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 316


>gi|262164038|ref|ZP_06031777.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
 gi|262027566|gb|EEY46232.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
          Length = 336

 Score =  216 bits (550), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 157/226 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 316


>gi|291298947|ref|YP_003510225.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290568167|gb|ADD41132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 330

 Score =  216 bits (549), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 159/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++ ++ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 80  AKEQFIKANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYQRGFKFSTYATWW 139

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI+R+IA Q  T+R+PVH+ + ++++  TAR+++ ++  +P PE+IA  L + VE V
Sbjct: 140 IRQAISRAIAQQERTVRLPVHLVEDVNRMRNTARQLTRELGADPEPEQIANALGVTVERV 199

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++ +++ +SL+TPIGD+  ++LGD + D +  +P D  I    RE    +L  L  R
Sbjct: 200 NELIRWSQDTVSLDTPIGDDGDTNLGDLVADSDEPTPEDVVIAGMERERIDMMLGHLDER 259

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +++ R+G+    +H+L EV  +F ++RERIRQ+E +A+ +LK
Sbjct: 260 SAGIVKARYGLEDGREHSLTEVAHRFALSRERIRQLEIQALARLK 304


>gi|212711364|ref|ZP_03319492.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
 gi|212686093|gb|EEB45621.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
          Length = 328

 Score =  216 bits (549), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 97/225 (43%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+PEEIA++L  PVE V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPSPEEIAERLDKPVEDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TPI  +    L + + D N   P ++    NL+E   + L  L P+
Sbjct: 208 SRMLRLNERITSVDTPIAGDSEKSLLEVLSDDNESGPENTIQDNNLKENIVKWLYELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 268 QREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLRRLK 312


>gi|118581147|ref|YP_902397.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118503857|gb|ABL00340.1| RNA polymerase, sigma 70 subunit, RpoD family [Pelobacter
           propionicus DSM 2379]
          Length = 323

 Score =  216 bits (549), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 111/279 (39%), Positives = 174/279 (62%), Gaps = 5/279 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           D  E E    V    D  +KI   ++ I     ++  + + +   + KG+     A+ +M
Sbjct: 43  DHAEAELPPAVLETFDDAIKIY--LRDIQRTPLLTAEQEKEVARQIEKGDM---AARNKM 97

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F+     +FSTYA WW++QAI
Sbjct: 98  IESNLRLVVKIAKRYINRGLPFLDLIEEGNLGLIKAVERFNLAKECRFSTYATWWIRQAI 157

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R++ +QS TIR+PVH+ D I+++ +  RR+S  ++REP   EIA+++ + +  VR+++ 
Sbjct: 158 DRALVNQSRTIRLPVHVSDDINRMAKVTRRLSQTLQREPHAHEIAEEMNVKLAYVRRLMT 217

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S+ETPIGD     L D IED + V+P D     +  E  +     L+  E+++L
Sbjct: 218 LLRRTCSMETPIGDGSDYFLIDTIEDTSMVAPSDLLENIDRYEQISEHFKELSESEQKIL 277

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL
Sbjct: 278 ALRFGLDDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKL 316


>gi|171322339|ref|ZP_02911166.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171092333|gb|EDT37699.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 234

 Score =  216 bits (549), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/235 (44%), Positives = 155/235 (65%), Gaps = 1/235 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA WW++QA
Sbjct: 1   MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+  +  +P   +R VL
Sbjct: 61  VARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELIAETGLPEGKLRAVL 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +  EP+SL+TP+ D +T  L D IED+ + SP +      +RE  T +L S+TP E  V
Sbjct: 121 ALPAEPLSLDTPLPDAETG-LVDLIEDQASASPFEHLADTRMRECVTSLLRSVTPAEADV 179

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++   SFLD 
Sbjct: 180 LRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTVAEAEGAESFLDA 234


>gi|119513754|ref|ZP_01632741.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
 gi|119461595|gb|EAW42645.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
          Length = 327

 Score =  216 bits (549), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K  R PTP EIA +L +    +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKFGRSPTPTEIAHELELEPMQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + ++P+SL+  +GD   + L + +ED+   SP     Q  LR+    +LA LTP+
Sbjct: 212 REYLNMARQPVSLDVKVGDNQDTELQEMLEDEGP-SPEYYTTQEFLRQDLNNLLAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +VL +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+
Sbjct: 271 QRQVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQALAHLR 315


>gi|170704115|ref|ZP_02894732.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170130976|gb|EDS99686.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 575

 Score =  216 bits (549), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 151/237 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D+  G++FSTYA WW
Sbjct: 338 ARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 397

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +     TP E+A  +  PV+ V
Sbjct: 398 IRQAITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKV 457

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++ I KEP+S + P+  E      D   D +  SP D+A    LR T   V+  L PR
Sbjct: 458 RDLMAIVKEPVSADVPVSPEGDMTFADVAADTSTPSPEDAAGATQLRRTIAAVIDRLPPR 517

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LRSF+
Sbjct: 518 EAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRASDALGLLRSFI 574



 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 63/125 (50%), Gaps = 4/125 (3%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA---SNSSVFLQKR 109
           +P D+ +   ++   A+L  +GI V D  D       E        A   ++ +  L   
Sbjct: 1   MPDDDANDSGVDAVAAVLGELGIAVCDSADTASGWTLERYFRPTPPARAWADGAGTLVAA 60

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
              A R+TD PVR+YLREMG+  LL+R+ E A A+RIE GRA   A LC  P    AL+ 
Sbjct: 61  DLLAPRTTD-PVRLYLREMGTTPLLTRDEEFAYARRIERGRAASAAVLCGDPDALDALVS 119

Query: 170 WRDEL 174
            R E+
Sbjct: 120 IRVEI 124


>gi|75907421|ref|YP_321717.1| sigma 28 (flagella/sporulation) [Anabaena variabilis ATCC 29413]
 gi|75701146|gb|ABA20822.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 378

 Score =  216 bits (549), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 106/242 (43%), Positives = 171/242 (70%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTY
Sbjct: 136 QGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTY 195

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K  R P+  E+A+ L + 
Sbjct: 196 AYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKFSRNPSEAEMAEALEIS 255

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V  +R++ ++ ++ +SL   +G E+ + L D +ED++ +SP     +  +R+    VL  
Sbjct: 256 VPQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQEIWEVLGD 315

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ 
Sbjct: 316 VLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKG 375

Query: 679 FL 680
           +L
Sbjct: 376 WL 377


>gi|186684216|ref|YP_001867412.1| RNA polymerase sigma factor [Nostoc punctiforme PCC 73102]
 gi|186466668|gb|ACC82469.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 327

 Score =  216 bits (549), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 101/235 (42%), Positives = 160/235 (68%), Gaps = 1/235 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VQQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++  + R PTP EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQTLGRSPTPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED +  SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVKVGDNQDTELQEMLED-SGPSPEYYTNQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +LA LTP++  VL +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+
Sbjct: 261 NNLLAELTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQALAHLR 315


>gi|17231741|ref|NP_488289.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|8489803|gb|AAF75759.1|AF262218_1 group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|17133384|dbj|BAB75948.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
          Length = 390

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 106/242 (43%), Positives = 171/242 (70%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTY
Sbjct: 148 QGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTY 207

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K  R P+  E+A+ L + 
Sbjct: 208 AYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKFSRNPSEAEMAEALEIS 267

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V  +R++ ++ ++ +SL   +G E+ + L D +ED++ +SP     +  +R+    VL  
Sbjct: 268 VPQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQEIWEVLGD 327

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ 
Sbjct: 328 VLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKG 387

Query: 679 FL 680
           +L
Sbjct: 388 WL 389


>gi|172036788|ref|YP_001803289.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
 gi|171698242|gb|ACB51223.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
          Length = 420

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/239 (44%), Positives = 160/239 (66%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K EM++ANLRLV+SVAKKY +RGL+ LDLIQEG +GL KA EKFD   GY+FSTYA WW
Sbjct: 181 SKDEMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAYWW 240

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS  IR+PVH+ +K++K+ +  R++S    R  T EEI K+L M    V
Sbjct: 241 IRQGITRAIATQSRIIRLPVHVTEKLNKIKQVQRQISQAKGRNATLEEIGKELNMTPTQV 300

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V       +SLE  +G E  + L D +E ++ +SP ++    +LR     +L  LT R
Sbjct: 301 REVFMKIPRSVSLEIKVGKEKDTELVDLLESED-ISPEENLAIESLRRDIGILLEDLTER 359

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E+ V+++R+G      ++L ++G+   ++RER+RQIEAKA++KL+ P R  ++R + + 
Sbjct: 360 EQEVIKLRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQKLRQPRRRNQIRDYFES 418


>gi|254527154|ref|ZP_05139206.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538578|gb|EEE41031.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 313

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L+ L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|161521004|ref|YP_001584431.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|189352818|ref|YP_001948445.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
 gi|160345054|gb|ABX18139.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
 gi|189336840|dbj|BAG45909.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 525

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 106/239 (44%), Positives = 159/239 (66%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + M+EANLRLV+S+A+KY NRG+   DL+Q+G IGLM+A EKF++  G+KFSTYA WW
Sbjct: 288 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYATWW 347

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R++AD++ TIR+PVH+ D+  +V R A R   +  R+PTP E+A +  +  + +
Sbjct: 348 IRQAIARAVADRARTIRVPVHVGDQHQRVRRQALRFRQRTGRQPTPAELAAETGLAEDKL 407

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +L +  EP+SL+TP+ D DT  L D IED+ + SP +      +RE    +L S+TP 
Sbjct: 408 RAILALPAEPVSLDTPLPDADTG-LVDLIEDETSASPFEQLAGTRMRECVRSLLRSVTPT 466

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  VLR RFG+G     T + + K   ++RER+RQIE +A+  L+  + ++   +FLD 
Sbjct: 467 EADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEKRALAALRTAAEAEGAHAFLDA 525



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 77/157 (49%), Gaps = 34/157 (21%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----------- 77
           D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V           
Sbjct: 15  DPIIQLLALASEQGYLTHADLVDALPPESDSPDALDVVRAALADIGITVLDEPAAPPPFA 74

Query: 78  ------VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
                 VD D LE  EG     DLA  AS S+               DP+ +Y+R M ++
Sbjct: 75  AAPAVDVDRDTLE--EGRALLGDLARGASAST---------------DPLALYMRRMHAV 117

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            LL+RE EIA+A+ +E GR  M+ +L   P    AL+
Sbjct: 118 PLLTREDEIALARELETGRHQMLHALAGCPPAVDALL 154


>gi|318042101|ref|ZP_07974057.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 309

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 106/230 (46%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 74  SKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+ +EIA+ + MP++ +
Sbjct: 134 IRQSMTRAIACQSRTIRLPVHLSERLTAIRKVSLDLAHKLGAMPSRKEIAEAMDMPIDEL 193

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D + V PLD   +    E   R L+ LT 
Sbjct: 194 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADNSHVEPLDQVERGMHHEQLGRWLSHLTE 253

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E +VL +RFG+     HTL E+G+   V+RER+RQ+E KA+RKL+H +R
Sbjct: 254 QERQVLELRFGLEGEERHTLAEIGRMLDVSRERVRQVELKALRKLRHLTR 303


>gi|157413850|ref|YP_001484716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388425|gb|ABV51130.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 313

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L+ L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|123969020|ref|YP_001009878.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199130|gb|ABM70771.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 313

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L+ L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|126696812|ref|YP_001091698.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126543855|gb|ABO18097.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 313

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L+ L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|115360900|ref|YP_778037.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
 gi|115286228|gb|ABI91703.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
          Length = 617

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 150/237 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D   G++FSTYA WW
Sbjct: 380 AKAGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDHRRGFRFSTYATWW 439

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +     TP E+A  +  PV+ V
Sbjct: 440 IRQAITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKV 499

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ I KEP+S + P+  E      D   D    SP D+A    LR T   V+  L PR
Sbjct: 500 RELMAIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAAGATQLRRTIAAVIDRLPPR 559

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LRSF+
Sbjct: 560 EAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRASDTLGLLRSFV 616



 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 64/197 (32%), Positives = 86/197 (43%), Gaps = 9/197 (4%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I     RG+VT  ++   LP D+ +   ++   A+L  +GI V D  D       E   
Sbjct: 28  LIATGLSRGFVTRGDIIDGLPDDDANDSGVDAVAAVLGELGIAVSDSADTASGWTLERYF 87

Query: 94  DLASSAS--NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             A  A             D     T DPVR+YLREMG+  LL+R+ E A A+RIE GRA
Sbjct: 88  RPAPPARAWADGAGALAAADLLAPRTTDPVRLYLREMGTTPLLTRDEEFAYARRIERGRA 147

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFFHGTEGHSYQK 210
              A LC  P    AL+  R E+    T     +I L+   GP       H   G S   
Sbjct: 148 ASAAVLCGDPDALDALVSIRVEIAQCRTAASTYVIFLDD--GPRDDTSADHAEAGTSAT- 204

Query: 211 REDSSQEKERDDVQETE 227
              ++ E  RDD  +TE
Sbjct: 205 ---ATGEPARDDDTQTE 218


>gi|159039487|ref|YP_001538740.1| RpoD family RNA polymerase sigma factor [Salinispora arenicola
           CNS-205]
 gi|157918322|gb|ABV99749.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 329

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 100/261 (38%), Positives = 173/261 (66%), Gaps = 7/261 (2%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           V  G+  +E + +V        E   AK   + ANLRLV+S+A++Y   G+  LDLIQEG
Sbjct: 75  VPAGVERAELQRLV-------AEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEG 127

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N GL++A EKFD+  G+KFSTYA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR
Sbjct: 128 NTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVAR 187

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +++ ++  +P PE+IA  L + VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A
Sbjct: 188 QLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDA 247

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP +  +    R+    +L+ L  R   ++R R+G+    +H+L EV  +F ++RERIR
Sbjct: 248 PSPEEIVLTGLERQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIR 307

Query: 658 QIEAKAIRKLKHPSRSKKLRS 678
           Q+E +A+ +L+  +R++ L++
Sbjct: 308 QLEIQALGRLRELARAEGLQA 328


>gi|33861845|ref|NP_893406.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33640213|emb|CAE19748.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 313

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLATIRKISRELAHKLGAMPSRIEIAEAMEIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L+ L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|238060708|ref|ZP_04605417.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
 gi|237882519|gb|EEP71347.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
          Length = 331

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 97/240 (40%), Positives = 164/240 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  AEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+IA  L +
Sbjct: 151 YATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNAARQLTRELGSDPEPEQIAAALGV 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP D  +    R+    +L 
Sbjct: 211 TVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEDIVLTGLERQRIEGLLN 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +R++ L++
Sbjct: 271 HLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQA 330


>gi|257061333|ref|YP_003139221.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8802]
 gi|256591499|gb|ACV02386.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 328

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 157/225 (69%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ +T R +S K+ R  TP EIA  L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAAVLEIEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + ++PISL+  +GD   + L + +ED  A SP     Q  LR+    ++  LTP+
Sbjct: 212 RECLSMARQPISLDVRVGDNQDTELSELLEDHEA-SPDQYITQELLRQDLKNLMEELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+    + +L ++GK+  ++RER+RQ+E +A+ +L+
Sbjct: 271 QRSVLILRFGLEDGKELSLAKIGKKLNISRERVRQLEHQALAQLR 315


>gi|229520830|ref|ZP_04410252.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
 gi|229342063|gb|EEO07059.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
          Length = 335

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  VRTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYVRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|209527735|ref|ZP_03276230.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209491813|gb|EDZ92173.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 332

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 110/264 (41%), Positives = 169/264 (64%), Gaps = 10/264 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S + G+S SE   I++  R+       AK++M+EANLRLV+S+AKKY  R ++FLDLIQE
Sbjct: 77  SAKAGLSESEMTEIMNRGRR-------AKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQE 129

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL +  EKFD   GYKFSTYA WW++QAITR+IA  S TIR+P+H+ +K++K+ R  
Sbjct: 130 GTLGLERGVEKFDPMRGYKFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEKLNKIKRVQ 189

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R +  +  R  TP EIAK L +    +R  L  ++ P+SL+  +GD   + L D +ED++
Sbjct: 190 RELFQQYGRNATPTEIAKALDLEPSQIRDYLLASRHPVSLDLRVGDNQDTELQDLLEDES 249

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A S  +   Q  LR+    ++A LTP++  VL +R+G+    + +L +VG    ++RER+
Sbjct: 250 A-SADNYVTQQLLRQDLKDLMADLTPQQREVLTLRYGLNDGKEMSLSKVGVHMNISRERV 308

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQ+E +A+  L+   R  ++R +L
Sbjct: 309 RQLENQALNHLRR--RKAQVREYL 330


>gi|298490014|ref|YP_003720191.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231932|gb|ADI63068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 332

 Score =  215 bits (547), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 104/230 (45%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E  IAK+ MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  AEGEIAKRRMVEANLRLVVSVAKKYIKRNIDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S K+ R PT  E+A +L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQKLGRAPTAIELADELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               VR+ L+  + P+SL+  +GD   + LG+ +ED  A +P D  IQ++L     R++ 
Sbjct: 212 TPRQVRECLEKARLPLSLDLRLGDNYDTELGEMLEDTGA-TPEDFVIQSSLSSDIERLMK 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+++ V+++RFG+      TL ++G+   ++RER+RQIE +A+ KL+
Sbjct: 271 ELTPQQKEVIKLRFGLIDGQALTLSKIGEILNISRERVRQIEREALTKLR 320


>gi|123966683|ref|YP_001011764.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201049|gb|ABM72657.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 313

 Score =  215 bits (547), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLATIRKVSRELAHKLGAMPSRIEIAEAMEIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L  L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLTHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|218247332|ref|YP_002372703.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8801]
 gi|218167810|gb|ACK66547.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 328

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 157/225 (69%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ +T R +S K+ R  TP EIA  L +    +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAAVLEIEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + ++PISL+  +GD   + L + +ED  A SP     Q  LR+    ++  LTP+
Sbjct: 212 RECLSMARQPISLDVRVGDNQDTELSELLEDHEA-SPDQYITQELLRQDLKNLMEELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+    + +L ++GK+  ++RER+RQ+E +A+ +L+
Sbjct: 271 QRSVLILRFGLEDGKELSLAKIGKKLNISRERVRQLEHQALAQLR 315


>gi|119509984|ref|ZP_01629125.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119512944|ref|ZP_01632006.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119462397|gb|EAW43372.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119465308|gb|EAW46204.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
          Length = 389

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 106/242 (43%), Positives = 172/242 (71%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTY
Sbjct: 147 QGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTY 206

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K+ R P   E+A+ L + 
Sbjct: 207 AYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKLCRNPNEAEMAEALEIS 266

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ +R++ ++ ++ +SL   +G E+ + L D +ED++ +SP     +  +R+    VL  
Sbjct: 267 VQQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQEIWEVLGD 326

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ 
Sbjct: 327 VLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKG 386

Query: 679 FL 680
           +L
Sbjct: 387 WL 388


>gi|291320189|ref|YP_003515450.1| DNA directed RNA polymerase sigma factor [Mycoplasma agalactiae]
 gi|290752521|emb|CBH40493.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae]
          Length = 509

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 111/256 (43%), Positives = 166/256 (64%), Gaps = 10/256 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K++   G+K
Sbjct: 254 KGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIIKAVQKYNVNKGFK 313

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR++ADQS T+R+PVHM + I+K+ +  R +  +   +PT EEIA++
Sbjct: 314 FSTYATWWIRQAITRAVADQSRTVRVPVHMVETINKITKIERELQQENGVDPTDEEIAQR 373

Query: 556 LA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                  E VR + KI   PISL+  IG E+ S   DF++D++ V+P+D A    L ET 
Sbjct: 374 YGNDFTAEKVRHIRKINIGPISLDKQIGKENDSSFSDFVKDESVVNPVDYASHEELVETL 433

Query: 614 TRVLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +L  +L   E  ++  R+G+G + +       +LEE+  +  V++ERIRQIE K +RK
Sbjct: 434 NAILKDTLDADEYELICKRYGVGFDNNGEKYKVFSLEELALERNVSKERIRQIENKILRK 493

Query: 667 LK-HPSRSKKLRSFLD 681
           LK  P RS+ L+ F++
Sbjct: 494 LKSSPERSRYLKVFME 509


>gi|298492420|ref|YP_003722597.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298234338|gb|ADI65474.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 389

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 105/242 (43%), Positives = 171/242 (70%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTY
Sbjct: 147 QGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTY 206

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K+ R P+  E+A  L + 
Sbjct: 207 AYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKLARNPSEAEMATALEIS 266

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ +R++ ++ ++ +SL   +G E+ + L D +ED++  SP     +  +R+    VL  
Sbjct: 267 IQQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNQSPEAKMNENMMRQEIWEVLGD 326

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ 
Sbjct: 327 VLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKG 386

Query: 679 FL 680
           +L
Sbjct: 387 WL 388


>gi|239981636|ref|ZP_04704160.1| RNA polymerase principal sigma factor hrdD [Streptomyces albus
           J1074]
 gi|291453499|ref|ZP_06592889.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|17366575|sp|Q59914|HRDD_STRGR RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|510454|emb|CAA56305.1| sigma factor [Streptomyces griseus]
 gi|291356448|gb|EFE83350.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 332

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 149/230 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  AEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L+ 
Sbjct: 151 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNRENGRDPEPAEIAAELSS 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 211 TPERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 271 QLDDRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 320


>gi|171909626|ref|ZP_02925096.1| RNA polymerase sigma factor [Verrucomicrobium spinosum DSM 4136]
          Length = 298

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 107/241 (44%), Positives = 158/241 (65%), Gaps = 3/241 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG+ EA   +  M+ ANLRLV+ +A+ Y N GL  LDLI EGNIGLMKA E+FD   G
Sbjct: 35  IKKGDPEA---RSHMIRANLRLVVKIAQDYANYGLPLLDLISEGNIGLMKAVERFDPNKG 91

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K STYA WW+KQ+I R++A+QS TIR+PVHM DKI K+ R A  MS ++ REPT +E++
Sbjct: 92  GKLSTYAAWWIKQSIKRALANQSKTIRLPVHMVDKISKMRRVAMAMSEELGREPTDDELS 151

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ +    + ++   +  P SL+ PI ++D++  G+ + D+NA +P D     N+    
Sbjct: 152 EEIGIDRGKLSQLKVASMRPASLDAPISEDDSTEFGEIVGDENAQTPFDLLSHKNMHSQL 211

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L  L  RE +++  RFG+      TLEEVG++F VTRERIRQ++  A+RKL+   + 
Sbjct: 212 DGLLTVLDERERKIIDARFGLNGQKARTLEEVGQEFGVTRERIRQLQNIALRKLRRALQK 271

Query: 674 K 674
           K
Sbjct: 272 K 272


>gi|298250072|ref|ZP_06973876.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297548076|gb|EFH81943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 319

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 106/259 (40%), Positives = 169/259 (65%), Gaps = 1/259 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           +I + R +    R  + EA  AK++++EANLRLV+ +A+KY   G+  +DLIQEGN+GLM
Sbjct: 60  NIRKQRGLSRSARLDDNEAQEAKRQLIEANLRLVMHIARKYRGFGVDLMDLIQEGNLGLM 119

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A +KFD+  GY+FSTYA WW++Q ITR++++Q+  IR+P++  ++I ++ R  R+M   
Sbjct: 120 HAVDKFDYKKGYRFSTYATWWIRQYITRALSEQAHMIRVPLYKIEEIKRLGRVKRKMQQG 179

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDFIEDKNAVSPL 601
              EPT EE+A ++ + V  V  +L   +E ISL+ P  G +D   L + +ED    SP 
Sbjct: 180 ETGEPTLEELAVQMEISVPEVIALLSTNQETISLDMPRKGGDDEISLSEVLEDDPIYSPE 239

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +   L+E    +L  LTPRE++VL++RFG+  N +H+L E GK+  ++ E +RQ+E 
Sbjct: 240 RVVLTQTLQEQVQDILNCLTPREKKVLQLRFGLNGNGEHSLTETGKKMGLSHEAVRQMEF 299

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           +A++KL HP R ++L+ FL
Sbjct: 300 RALKKLGHPCRDRRLQDFL 318


>gi|78185087|ref|YP_377522.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|116072338|ref|ZP_01469605.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|78169381|gb|ABB26478.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
 gi|116064860|gb|EAU70619.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 313

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 109/230 (47%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P   EIA+ + +PVE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPNRLEIAEAMDIPVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +A  PLD   Q    E   R L+ L+ 
Sbjct: 198 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSADEPLDIVEQRIHHEQLGRWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VLR+RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQNVLRLRFGLEGNERHTLAEIGRMMEVSRERVRQVELKALRKLRNLTR 307


>gi|78779769|ref|YP_397881.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713268|gb|ABB50445.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 313

 Score =  214 bits (546), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +R +++K+   P+  EIA+ + + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLAAIRKVSRELAHKLGAMPSRIEIAEAMDIDVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL+      SL+ P+ GD+  S LGD I D N   PLD   Q   +E   + L+ L+ 
Sbjct: 198 DSVLRQALSTSSLDAPVNGDDGRSFLGDLIADSNTEEPLDKVEQKMHQEQLGKWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTR 307


>gi|332140079|ref|YP_004425817.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|332143123|ref|YP_004428861.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550101|gb|AEA96819.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327553145|gb|AEA99863.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 330

 Score =  214 bits (545), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 103/230 (44%), Positives = 156/230 (67%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+ +NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 85  CEAS--RKRMIVSNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 142

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +R +R +S K+  EPT EEIA  L  
Sbjct: 143 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRASRELSQKLDHEPTAEEIAAALDK 202

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++TPIG E+   L D I D+   SP +S   ++++      L 
Sbjct: 203 PVEDVTKMLRLNERITSVDTPIGGENDKALLDIIADEKEFSPEESLQDSDIKSNIITWLE 262

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L P++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+L+
Sbjct: 263 ELNPKQREVLARRFGLMGYEPSTLEDVGAEIGLTRERVRQIQVEALRRLR 312


>gi|113954655|ref|YP_729975.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882006|gb|ABI46964.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 313

 Score =  214 bits (545), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 110/241 (45%), Positives = 164/241 (68%), Gaps = 5/241 (2%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+R G+     AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   
Sbjct: 71  MIRVGQR----AKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTR 126

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EI
Sbjct: 127 GYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRLEI 186

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ L MPVE +  +L+      SL+ P+  ED  S LGD I D +A  PLD   Q    E
Sbjct: 187 SEALDMPVEELDSLLRQALTTSSLDAPVNGEDGRSFLGDLIADSSAEEPLDKVEQRIHHE 246

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              R L+ L+ +E+ VL +RFG+  N  HTL ++G+   V+RER+RQ+E K++RKL++ +
Sbjct: 247 QLGRWLSHLSEQEQHVLTLRFGLNGNERHTLAQIGRLLDVSRERVRQVELKSLRKLRNLT 306

Query: 672 R 672
           R
Sbjct: 307 R 307


>gi|330469769|ref|YP_004407512.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328812740|gb|AEB46912.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 333

 Score =  214 bits (545), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 97/240 (40%), Positives = 164/240 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+  GYKFST
Sbjct: 93  AEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGYKFST 152

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+IA  L +
Sbjct: 153 YATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIAAALGV 212

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP +  +    R+    +L 
Sbjct: 213 TVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLN 272

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +R++ L++
Sbjct: 273 HLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQA 332


>gi|78222633|ref|YP_384380.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78193888|gb|ABB31655.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter metallireducens
           GS-15]
          Length = 326

 Score =  214 bits (545), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 107/260 (41%), Positives = 172/260 (66%), Gaps = 3/260 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I   T ++  E + + S + KG+     A+ +M+E+NLRLV+ +AK+Y NRGL
Sbjct: 58  IKLYLREIQRTTLLTADEEKVLASRIAKGD---KAARDKMIESNLRLVVKIAKRYINRGL 114

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D 
Sbjct: 115 PFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDD 174

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+++  R + N+  REPT +E+A ++ +    +R+++ + K+  S+E P+G+     L
Sbjct: 175 INKMLKITRELVNRFNREPTVKEVATEMNVNSAYIRRLMVLLKKTYSIERPMGENSDYFL 234

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D IED ++VSP       N  E  ++  ASL+  E+++L +RFG+      TL+ +G+ 
Sbjct: 235 IDTIEDTSSVSPAVLLEDLNKYEIVSKWFASLSENEQKILTLRFGLEDKEPQTLDTIGRS 294

Query: 649 FCVTRERIRQIEAKAIRKLK 668
           F VTRERIRQIEAK++ KL+
Sbjct: 295 FGVTRERIRQIEAKSLEKLR 314


>gi|253988173|ref|YP_003039529.1| RNA polymerase sigma factor RpoS [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779623|emb|CAQ82784.1| rna polymerase sigma factor (sigma-38) [Photorhabdus asymbiotica]
          Length = 332

 Score =  214 bits (545), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 96/234 (41%), Positives = 165/234 (70%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++ M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA W
Sbjct: 91  LARRRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 150

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+PEEIA++L  PV+ 
Sbjct: 151 WIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSPEEIAEQLDKPVDD 210

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +  IS++TPI  +    L D + D+N   P  +  + +++++  + L  L  
Sbjct: 211 VSRMLRLNERIISVDTPISSDSDKALLDVLSDENETGPEGTTQEDDMKKSIVKWLFELNS 270

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++  VL  RFG+      TLE+VGK+  +TRER+RQI+ + +R+LK   +++ L
Sbjct: 271 KQREVLARRFGLLGYEAETLEDVGKEIGLTRERVRQIQVEGLRRLKDIMQTQGL 324


>gi|56267933|gb|AAV85439.1| RpoS [Listonella anguillarum]
 gi|56267935|gb|AAV85440.1| RpoS [Listonella anguillarum]
 gi|167987243|gb|ACA13292.1| RpoS [Listonella anguillarum]
 gi|222101826|gb|ACM44037.1| RNA polymerase sigma factor [Listonella anguillarum]
          Length = 333

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 102/226 (45%), Positives = 155/226 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  ARKRMIESNLRLVVKISRRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PVE V
Sbjct: 150 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAFQLDKPVEDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    ++RE+    L  L P+
Sbjct: 210 SKMLRLNERISSVDTPIGGDGDKALLDIIPDTNNSDPEISTQDDDIRESLLNWLDELNPK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 270 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 315


>gi|162450883|ref|YP_001613250.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161161465|emb|CAN92770.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 463

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 154/234 (65%), Gaps = 1/234 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V ANLRLV + A++  +RG+  LDLIQEGN+GL++AAEKFD+  GY+FSTYAMWW+KQA+
Sbjct: 231 VRANLRLVAAAARQLRHRGVPLLDLIQEGNLGLIRAAEKFDYRRGYRFSTYAMWWIKQAL 290

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +R++  Q   IR+PVH+ +   + ++  R +  +  RE  PEE+A++  + +E ++ + +
Sbjct: 291 SRALLYQGQVIRVPVHIAETRRRALQARRELEQEHAREAAPEEVAERSGLSMEKLQALRE 350

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +   P+ L+ P+GD+D +  GDF   + A +P +  +   L    + +L SLTPRE  VL
Sbjct: 351 MALPPVYLDAPVGDDDGARQGDFFASEGA-APDELLVHRRLHAQVSALLESLTPRERDVL 409

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           R+RFG+     HTL E+G  F V+RER+RQIE  A+ KL+  SR + L + L G
Sbjct: 410 RLRFGLDGGQPHTLAEIGGMFSVSRERVRQIEESALSKLRTLSRRQALETPLGG 463


>gi|313678638|ref|YP_004056378.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
 gi|312950821|gb|ADR25416.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
          Length = 509

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 110/256 (42%), Positives = 167/256 (65%), Gaps = 10/256 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K++   G+K
Sbjct: 254 KGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIIKAVQKYNVNKGFK 313

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR++ADQS T+R+PVHM + I+K+ +  R +  +   +PT EEIA++
Sbjct: 314 FSTYATWWIRQAITRAVADQSRTVRVPVHMVETINKITKIERELQQENGVDPTDEEIAQR 373

Query: 556 LA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                  E VR + KI  +PISL+  IG E+ S   DF++D++ V+P++ A    L ET 
Sbjct: 374 YGNDFTAEKVRHIRKINIDPISLDKQIGKENDSSFSDFVKDESVVNPVEYASHEELVETL 433

Query: 614 TRVLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +L  +L   E  ++  R+G+G + +       +LEE+  +  V++ERIRQIE K +RK
Sbjct: 434 NTILKDTLDADEYELICKRYGVGFDNNGEKYKVFSLEELALERNVSKERIRQIENKILRK 493

Query: 667 LK-HPSRSKKLRSFLD 681
           LK  P RS+ L+ F++
Sbjct: 494 LKSSPERSRYLKVFME 509


>gi|260902364|ref|ZP_05910759.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
 gi|308110564|gb|EFO48104.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
          Length = 329

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 146 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 206 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 266 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 310


>gi|260878982|ref|ZP_05891337.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|260895455|ref|ZP_05903951.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|157674653|gb|ABV60415.1| RpoS [Vibrio parahaemolyticus]
 gi|308088215|gb|EFO37910.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|308090442|gb|EFO40137.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|328474140|gb|EGF44945.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 10329]
          Length = 329

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 146 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 206 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 266 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 310


>gi|197286082|ref|YP_002151954.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227356592|ref|ZP_03840979.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
 gi|194683569|emb|CAR44440.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227163348|gb|EEI48275.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
          Length = 329

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ ++++YTNRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRQRMIESNLRLVVKISRRYTNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA+ L  PV+ V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSVEEIAQTLDKPVDDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D+N   P  +    NL+E   + L  L P+
Sbjct: 208 SKMLRLNERISSVDTPIGGDSDKALLDIISDENEEGPEATIQNNNLKENIVKWLFELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+LK
Sbjct: 268 QREVLARRFGLLGYEAETLEDVGREIGLTRERVRQIQVEGLRRLK 312


>gi|12958587|gb|AAK09363.1|AF321124_1 RpoS [Vibrio harveyi]
          Length = 327

 Score =  214 bits (544), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 84  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 143

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 144 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 203

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 204 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 264 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 308


>gi|196232822|ref|ZP_03131672.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196223021|gb|EDY17541.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 296

 Score =  214 bits (544), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 106/245 (43%), Positives = 161/245 (65%), Gaps = 3/245 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + + ++KG+     A+  M+ +NLRLV+ +A  Y N GL  LDLI EGNIGLMKA E+FD
Sbjct: 34  LAAKIKKGD---KAARSLMIRSNLRLVVKIAHDYANLGLPLLDLISEGNIGLMKAVERFD 90

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G K STYA WW+KQ+I R++A+QS TIR+PVH+ DKI K+ R A +MS ++ REPT 
Sbjct: 91  PAKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDKISKMRRVALQMSEELGREPTD 150

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +E+A+++ +    + ++  ++  P SL+ PI D+D++  G+ + D  A++P +     NL
Sbjct: 151 DELAEEVGLSSGKISQLKTVSIRPASLDAPISDDDSTEFGEIVGDLEALTPFERLRDKNL 210

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    +L  L  RE++++  RFG+      TLEEVGK+F VTRERIRQ++  A+ KL+ 
Sbjct: 211 RDEVGDLLEVLDEREKKIIFSRFGLDGGKAKTLEEVGKKFGVTRERIRQLQNIALMKLRR 270

Query: 670 PSRSK 674
             + K
Sbjct: 271 ALQKK 275


>gi|153214922|ref|ZP_01949705.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|153826929|ref|ZP_01979596.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|153829928|ref|ZP_01982595.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|229530348|ref|ZP_04419736.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|254226840|ref|ZP_04920411.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|254291219|ref|ZP_04962015.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|262190768|ref|ZP_06048995.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
 gi|124114995|gb|EAY33815.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|125620637|gb|EAZ49000.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|148874616|gb|EDL72751.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|149739232|gb|EDM53500.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|150422913|gb|EDN14864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|229332121|gb|EEN97609.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|262033353|gb|EEY51864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
          Length = 335

 Score =  214 bits (544), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|163846411|ref|YP_001634455.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222524178|ref|YP_002568649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163667700|gb|ABY34066.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222448057|gb|ACM52323.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 313

 Score =  214 bits (544), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 98/260 (37%), Positives = 169/260 (65%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + ++E + +++ V  GE     A+ +++ +NLRLV+S+A++Y   GL  LDLIQEG++GL
Sbjct: 56  LPLAEKQRLIAQVNAGEQ----ARAQLINSNLRLVVSIARRYQGHGLSLLDLIQEGSVGL 111

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M+A +KFD   G KFSTYA +W++Q+I R+IAD S T+R+PVH+ +++ ++ R  + +S 
Sbjct: 112 MRAVDKFDASRGLKFSTYATYWIRQSIGRAIADHSRTVRLPVHLGERLSRLSRLRQELSQ 171

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REPT EE+A+   + VE V +  +    P SL+ P  ++    L + + D    +P 
Sbjct: 172 QLDREPTLEELAQAAGLSVEQVERAEQAGLAPTSLDEPHTEDGGGALAEILTDPLQPTPF 231

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   ++ L+      L  L+PRE  +LR+R+G+     HTLE++G++  +TRER+RQ+E 
Sbjct: 232 DEVSESMLQADVQHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEH 291

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           +A+RKL+ PS   +L+ +++
Sbjct: 292 EALRKLRDPSLHPQLQGYVN 311


>gi|153802558|ref|ZP_01957144.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
 gi|124121921|gb|EAY40664.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
          Length = 335

 Score =  214 bits (544), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|37524720|ref|NP_928064.1| RNA polymerase sigma factor RpoS [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784145|emb|CAE13014.1| RNA polymerase sigma factor (sigma-38) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 332

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 96/234 (41%), Positives = 165/234 (70%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++ M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA W
Sbjct: 91  LARQRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 150

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+PEEIA++L  PV+ 
Sbjct: 151 WIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSPEEIAEQLDKPVDD 210

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +  IS++TPI  +    L D + D+N   P  +  + +++++  + L  L  
Sbjct: 211 VSRMLRLNERIISVDTPISGDSDKALLDVLSDENETGPEGTTQEDDMKKSIVKWLFELNS 270

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++  VL  RFG+      TLE+VGK+  +TRER+RQI+ + +R+LK   +++ L
Sbjct: 271 KQREVLARRFGLLGYEAETLEDVGKEIGLTRERVRQIQVEGLRRLKDIMQTQGL 324


>gi|147674644|ref|YP_001216035.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262169845|ref|ZP_06037535.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
 gi|146316527|gb|ABQ21066.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|227012360|gb|ACP08570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262021579|gb|EEY40290.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
          Length = 335

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|229512804|ref|ZP_04402271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|229350053|gb|EEO15006.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|327483355|gb|AEA77762.1| RNA polymerase sigma factor RpoS [Vibrio cholerae LMA3894-4]
          Length = 335

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|15640556|ref|NP_230185.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590676|ref|ZP_01678009.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121728563|ref|ZP_01681585.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|153819103|ref|ZP_01971770.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|153823615|ref|ZP_01976282.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227080717|ref|YP_002809268.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229507145|ref|ZP_04396651.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229508992|ref|ZP_04398480.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229519660|ref|ZP_04409103.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229606176|ref|YP_002876824.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254850774|ref|ZP_05240124.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255744238|ref|ZP_05418191.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262149032|ref|ZP_06028176.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
 gi|6094129|sp|O51804|RPOS_VIBCH RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38 factor
 gi|2897902|gb|AAC38175.1| sigma S [Vibrio cholerae]
 gi|9654961|gb|AAF93702.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121547462|gb|EAX57570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121629175|gb|EAX61616.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|126510335|gb|EAZ72929.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|126518864|gb|EAZ76087.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227008605|gb|ACP04817.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229344349|gb|EEO09324.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229353917|gb|EEO18851.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229355890|gb|EEO20810.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229368831|gb|ACQ59254.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254846479|gb|EET24893.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255738178|gb|EET93570.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262031177|gb|EEY49797.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
          Length = 335

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|158969744|gb|ABW86844.1| RpoS [Vibrio alginolyticus]
          Length = 330

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 87  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 147 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 207 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 267 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 311


>gi|254230502|ref|ZP_04923875.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262393289|ref|YP_003285143.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|151936974|gb|EDN55859.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262336883|gb|ACY50678.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
          Length = 328

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 145 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 205 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 265 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 309


>gi|91227834|ref|ZP_01262007.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269965239|ref|ZP_06179373.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
 gi|91188344|gb|EAS74640.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269830225|gb|EEZ84452.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
          Length = 328

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 145 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 205 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 265 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 309


>gi|148240795|ref|YP_001226182.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849334|emb|CAK24885.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 376

 Score =  213 bits (543), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 101/235 (42%), Positives = 159/235 (67%), Gaps = 1/235 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q 
Sbjct: 140 MIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQG 199

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IA QS TIR+PVH+ +K++++ R  + ++++  R  +  ++AK+L +  + VR+ L
Sbjct: 200 ITRAIATQSRTIRLPVHITEKLNRIKRVQQEIASEQGRLASVSDLAKELGVSEDTVRQTL 259

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                 +SLET +G +  + LGD +ED +A +P  +  +  L +    +L  L PRE  V
Sbjct: 260 ARVPRSVSLETRVGKDQDTQLGDLLEDGHA-TPEQTLTRDALHDDLEHLLDELNPREAEV 318

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +R RFG+  +T  TL E+G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 319 IRSRFGLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQPQRRSKVRDYIQG 373


>gi|145284374|gb|ABP51953.1| RpoS [Vibrio alginolyticus]
          Length = 328

 Score =  213 bits (543), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 145 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 205 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 265 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 309


>gi|27364956|ref|NP_760484.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|320155343|ref|YP_004187722.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
 gi|27361102|gb|AAO10011.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|319930655|gb|ADV85519.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
          Length = 330

 Score =  213 bits (543), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 87  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV+ V
Sbjct: 147 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVDDV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    ++R +    L  L P+
Sbjct: 207 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDEDMRVSLIHWLEELNPK 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 267 QKEVLARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLR 311


>gi|148240072|ref|YP_001225459.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147848611|emb|CAK24162.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 313

 Score =  213 bits (543), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 159/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + MPVE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRLEIAEAMDMPVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +   PLD   Q    E   R ++ L+ 
Sbjct: 198 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLEEPLDRVEQRMHHEQLGRWMSHLSD 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL +RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLRNLTR 307


>gi|37680992|ref|NP_935601.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
 gi|37199742|dbj|BAC95572.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
          Length = 330

 Score =  213 bits (543), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 87  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV+ V
Sbjct: 147 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVDDV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    ++R +    L  L P+
Sbjct: 207 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDEDMRVSLIHWLEELNPK 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 267 QKEVLARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLR 311


>gi|239995277|ref|ZP_04715801.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii ATCC
           27126]
          Length = 330

 Score =  213 bits (543), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 103/230 (44%), Positives = 156/230 (67%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+ +NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 85  CEAS--RKRMIVSNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 142

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +R +R +S K+  EPT EEIA  L  
Sbjct: 143 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRASRELSQKLDHEPTAEEIALALDK 202

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++TPIG E+   L D I D+   SP +S   ++++      L 
Sbjct: 203 PVEDVTKMLRLNERITSVDTPIGGENDKALLDIIADEKEFSPEESLQDSDIKSNIVTWLE 262

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L P++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+L+
Sbjct: 263 ELNPKQREVLARRFGLMGYEPSTLEDVGAEIGLTRERVRQIQVEALRRLR 312


>gi|153835750|ref|ZP_01988417.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156975773|ref|YP_001446680.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
 gi|148867581|gb|EDL66895.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156527367|gb|ABU72453.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
          Length = 328

 Score =  213 bits (543), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 145 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 205 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 265 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 309


>gi|329941264|ref|ZP_08290543.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
 gi|329299795|gb|EGG43694.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
          Length = 332

 Score =  213 bits (543), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 150/230 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L    E V
Sbjct: 156 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEIAAELGSNAERV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 216 TDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGRLDQR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 276 TASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|225159269|ref|ZP_03725570.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224802166|gb|EEG20437.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 373

 Score =  213 bits (542), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 107/236 (45%), Positives = 159/236 (67%), Gaps = 4/236 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+     A+  M+ ANLRLV+ +A  Y + GL  LDLI EGNIGL+KA E+FD   G
Sbjct: 86  IRRGD---KAARDHMISANLRLVVKIAMDYKDFGLPLLDLISEGNIGLVKAVERFDPRKG 142

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K STYA WW+KQ+I R++A+QS TIR+PVH+ DKI ++ RTA  ++ ++ REP+ EEIA
Sbjct: 143 GKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDKIARMRRTAMALTEQLGREPSDEEIA 202

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            +L +P   V  +  ++  P SL+ P+G D D+S  G+ + D+NAVSP +S  + +    
Sbjct: 203 MELQIPTSKVAHLKSVSVRPASLDAPVGEDGDSSTFGELVGDENAVSPFESLKERSRNAD 262

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++ SL PRE  ++R RFG+    + TLEEVG++F VTRER+RQ++  A+ K++
Sbjct: 263 LKEMVDSLEPREAEIIRYRFGLDGRDELTLEEVGQKFKVTRERVRQLQNLALSKMR 318


>gi|302392313|ref|YP_003828133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302204390|gb|ADL13068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 275

 Score =  213 bits (542), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 109/253 (43%), Positives = 169/253 (66%), Gaps = 2/253 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S+ RK +   S AK +++  NLRLV+S+A K+  +GL   DL+QEGNIGL+ A EKFD 
Sbjct: 23  ISLARKAQAGDSEAKDKLIRHNLRLVVSIANKHQGKGLDLQDLVQEGNIGLITAVEKFDP 82

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW+KQ +TR+IA+Q  TIRIPVH+  K +K+ +    +  ++ REPT E
Sbjct: 83  DKGYRFSTYASWWIKQRVTRAIANQGKTIRIPVHVWQKTNKIFKVKDDLQTELGREPTAE 142

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++  + +E +++V+++  +    SL   +GD+  + LG  +   +A  P++   Q  
Sbjct: 143 EIAEETDISLEKIKEVMRVITDQNLASLNQFVGDDRDTELGQLVPSGSADDPVEGTSQQL 202

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    +L  L+ RE  V+R+RFG+  +   TL+EVG++  VTRERIRQI+ KA+ +LK
Sbjct: 203 LKEDLEELLTELSDREAEVIRLRFGLRDSRPRTLKEVGEELGVTRERIRQIQLKALNRLK 262

Query: 669 HPSRSKKLRSFLD 681
           HP+R K+L+ +L+
Sbjct: 263 HPTRIKQLKGYLE 275


>gi|186685842|ref|YP_001869038.1| RNA polymerase sigma factor SigD [Nostoc punctiforme PCC 73102]
 gi|186468294|gb|ACC84095.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score =  213 bits (542), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 102/230 (44%), Positives = 162/230 (70%), Gaps = 1/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  IAK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  ADGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S K+ R PT  E+A++L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQKLGRAPTAGELAQELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR+ L+  + P+SL+  +GD   + LG+ +ED  A SP +  +Q++L     R++ 
Sbjct: 212 TPKQVREYLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEEFVMQSSLSYDLDRLMG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP++  V+ +RFG+      TL ++G+   ++RER+RQIE +A+ KL+
Sbjct: 271 DLTPQQREVITLRFGLTDGQALTLAKIGEILNISRERVRQIEREALTKLR 320


>gi|88809137|ref|ZP_01124646.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88787079|gb|EAR18237.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 313

 Score =  213 bits (542), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 159/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + MPVE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLTSIRKVSLDLAHKLGAMPSRLEIAEAMDMPVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +   PLD   Q    E   R ++ L+ 
Sbjct: 198 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLEEPLDRVEQRIHHEQLGRWMSHLSD 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL +RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLRNLTR 307


>gi|282895663|ref|ZP_06303788.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199357|gb|EFA74222.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 396

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 107/242 (44%), Positives = 170/242 (70%), Gaps = 1/242 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTY
Sbjct: 154 QGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTY 213

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K  R PT  E+A+ L M 
Sbjct: 214 AYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKFARNPTEAEMAEFLEMT 273

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ +R++ ++ ++ +SL   +G E+ + L D +ED++  SP     +  +R+    VL  
Sbjct: 274 VQQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNQSPEAKMNENMMRQEIWEVLGD 333

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ 
Sbjct: 334 VLTSREKDVISLRYGLTTSEPCTLEEVGNIFNLSRERVRQIQSKAMRKLRRPHIAKRLKG 393

Query: 679 FL 680
           +L
Sbjct: 394 WL 395


>gi|223936758|ref|ZP_03628668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894609|gb|EEF61060.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 352

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 105/239 (43%), Positives = 161/239 (67%), Gaps = 3/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + + ++KG+ +A   ++ M++ANLRLV+ +A+ Y   GL  LDLI EGNIGLMKA E+FD
Sbjct: 106 LAARIKKGDKKA---RELMIKANLRLVVKIARDYEGIGLPLLDLISEGNIGLMKAVERFD 162

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G K STY  WW+KQ+I R++A+QS TIR+PVH+ DKI K+ RTA ++   + REP+ 
Sbjct: 163 PAKGGKLSTYGSWWIKQSIKRALANQSKTIRLPVHLVDKISKMRRTALKLQEILGREPSD 222

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A +L +    V ++      P SL+ PIGDED+++  + ++D+NA +P +   +  +
Sbjct: 223 EELADELNISAMRVSQMRTAAIRPASLDAPIGDEDSNNFAEVVQDENADTPYEQLEEKTV 282

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    ++ +L PRE  +LR RFG+      TLEEVG++F VTRER+RQI+  A++KL+
Sbjct: 283 TKMLQELVKTLDPREATILRARFGLDGGNQKTLEEVGQKFGVTRERVRQIQNIALKKLR 341


>gi|261345855|ref|ZP_05973499.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
 gi|282566345|gb|EFB71880.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
          Length = 328

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+PEEIA++L  PVE V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPSPEEIAEQLDKPVEDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TPI  +    L + + D N   P ++    +L+E   + L  L P+
Sbjct: 208 SRMLRLNERITSVDTPIAGDSEKSLLEVLSDDNDSGPENTIQDNDLKENIVKWLYELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 268 QREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLRRLK 312


>gi|75908126|ref|YP_322422.1| RNA polymerase sigma factor [Anabaena variabilis ATCC 29413]
 gi|75701851|gb|ABA21527.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 327

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 99/235 (42%), Positives = 160/235 (68%), Gaps = 1/235 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VKQTVTQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++  + R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQTLGRSPSPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED+   SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVKVGDNQDTELQEMLEDEGP-SPEYYTTQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +LA LTP++  V+ +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+
Sbjct: 261 NTLLAELTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQALAHLR 315



 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 25/37 (67%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           D+  + T D VR YLRE+G + LL+RE EI   K+++
Sbjct: 10  DTNTKFTADMVRTYLREIGRVPLLTREQEIVYGKQVQ 46


>gi|163802977|ref|ZP_02196864.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
 gi|159173267|gb|EDP58095.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
          Length = 328

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 156/226 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 145 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 205 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLILWLEELNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 265 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLRE 310


>gi|302869477|ref|YP_003838114.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315504060|ref|YP_004082947.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302572336|gb|ADL48538.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315410679|gb|ADU08796.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 333

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 164/240 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 93  AEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFST 152

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+IA  L +
Sbjct: 153 YATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGV 212

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP +  +    R+    +L 
Sbjct: 213 TVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLN 272

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +R++ L++
Sbjct: 273 HLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQA 332


>gi|28200488|gb|AAO31615.1| RNA polymerase subunit sigma factor S [Vibrio vulnificus]
          Length = 343

 Score =  213 bits (542), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 87  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV+ V
Sbjct: 147 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVDDV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    ++R +    L  L P+
Sbjct: 207 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDEDMRVSLIHWLEELNPK 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 267 QKEVLARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLR 311


>gi|332532870|ref|ZP_08408743.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332037716|gb|EGI74167.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 324

 Score =  213 bits (542), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/230 (44%), Positives = 156/230 (67%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 79  CEAS--RKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT +EIA  L  
Sbjct: 137 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTADEIAACLDR 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++ PIG E+ S L D I D+ +  P       ++ +     L 
Sbjct: 197 PVEDVTKMLRLNERIASVDMPIGGENDSVLLDIIPDEKSAGPEGEVQNNDINKHIVDWLG 256

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L P++  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+R+LK
Sbjct: 257 ELNPKQREVLARRFGLLGYEPSTLEDVGREIGLTRERVRQIQVEALRRLK 306


>gi|302552062|ref|ZP_07304404.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302469680|gb|EFL32773.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 332

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 108/235 (45%), Positives = 152/235 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  ADAERAKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L  
Sbjct: 151 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPTEIAAELGS 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 211 TPERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 271 RLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|17231292|ref|NP_487840.1| RNA polymerase sigma factor [Nostoc sp. PCC 7120]
 gi|8489801|gb|AAF75758.1|AF262217_2 group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
 gi|17132934|dbj|BAB75499.1| group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
          Length = 327

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 99/235 (42%), Positives = 160/235 (68%), Gaps = 1/235 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VKQTVTQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++  + R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQTLGRSPSPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED +  SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVKVGDNQDTELQEMLED-DGPSPEYYTTQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +LA LTP++  V+ +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+
Sbjct: 261 NTLLAELTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQALAHLR 315



 Score = 38.5 bits (88), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 25/37 (67%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           D+  + T D VR YLRE+G + LL+RE EI   K+++
Sbjct: 10  DTNTKFTADMVRTYLREIGRVPLLTREQEIVYGKQVQ 46


>gi|317969130|ref|ZP_07970520.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0205]
          Length = 309

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 105/230 (45%), Positives = 161/230 (70%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 74  SKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+ +EIA+++ MP++ +
Sbjct: 134 IRQSMTRAIACQSRTIRLPVHLSERLTAIRKVSLELAHKLGAMPSRKEIAEEMDMPLDEL 193

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D++   PLD   +   +E   R L  LT 
Sbjct: 194 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADQSNSEPLDQVERGIHQEQLGRWLTHLTD 253

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E +VL +RFG+     HTL E+G+   V+RER+RQ+E KA+RKL+H +R
Sbjct: 254 QERQVLELRFGLEGEERHTLAEIGRMLEVSRERVRQVELKALRKLRHLTR 303


>gi|218247827|ref|YP_002373198.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8801]
 gi|257060853|ref|YP_003138741.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8802]
 gi|218168305|gb|ACK67042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256591019|gb|ACV01906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 318

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 109/253 (43%), Positives = 167/253 (66%), Gaps = 7/253 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + + S +  GE     AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EK
Sbjct: 71  KELRSAIEAGEA----AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEK 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R++S +  R  
Sbjct: 127 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQEKGRAA 186

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T  E+A++L +    VR+ L+  ++P+SL+  +GD   + LGD +ED    SP D A  +
Sbjct: 187 TIAELAEELELTPRQVREYLERARQPLSLDLRVGDNQDTELGDLLED-TGQSPEDYATHS 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+    R++  LTP+++ VL +RFG+      TL ++G    ++RER+RQIE +A+ KL
Sbjct: 246 SLQLDLDRLMEELTPQQKEVLALRFGLSDGKPLTLAKIGSILNISRERVRQIEREALAKL 305

Query: 668 KHPSRSKKLRSFL 680
           +   R   +R +L
Sbjct: 306 R--KRKANIREYL 316



 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 33/49 (67%), Gaps = 2/49 (4%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           +  +S+ DPVR YLRE+G + LL+ E EI  AKR++  R + + +L ES
Sbjct: 2   NVSKSSPDPVRAYLREIGRVPLLTHEEEILYAKRVQ--RFVALETLKES 48


>gi|119493081|ref|ZP_01624006.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
 gi|119452826|gb|EAW34001.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
          Length = 331

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 105/266 (39%), Positives = 177/266 (66%), Gaps = 8/266 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++  TG+S +E  H          +  IAK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQ
Sbjct: 72  LATATGLSEAELNHQFQ-------QGIIAKQKMISSNLRLVVSIAKRYLNRGVPFLDLIQ 124

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG +GL +A EKFD   GYKFSTYA WW++Q ITR+IA+Q  T+R+PVH+ ++++K+   
Sbjct: 125 EGALGLNRATEKFDPDKGYKFSTYAYWWIRQGITRTIANQGRTVRLPVHVVEQLNKLQGI 184

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            + +   ++R+PT +E+A+ L++  + +R + ++ ++ +SL   +G E+ S L D +ED 
Sbjct: 185 HQDLRRSLRRKPTEDELAEALSISPQQLRLLEQVRRKSLSLNHRVGSEENSELMDLLEDY 244

Query: 596 NAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            ++SP     +  +R+    VL S L  RE+ +L +R+G+     +TL+EV     ++RE
Sbjct: 245 ESLSPESQINELMMRQELLEVLRSVLNEREQDILSLRYGLTTGVPYTLDEVSGMCSLSRE 304

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+RQI+AKA+RKL+ P  +++L+ ++
Sbjct: 305 RVRQIQAKAMRKLRRPQVAERLKGWI 330


>gi|88798286|ref|ZP_01113872.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
 gi|88779062|gb|EAR10251.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
          Length = 344

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/256 (40%), Positives = 165/256 (64%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  +   + RKGE      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 76  LNEIGFSPLLSPEEEVYFARLARKGE---PAGRKRMIESNLRLVVKIARRYLNRGLTLLD 132

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 133 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 192

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EPTPE+IA+ L  PVE V+K+L + +   S++TPIG      L + I
Sbjct: 193 LRAARELAQKLDHEPTPEDIAQLLEKPVEDVKKMLALNERVTSIDTPIGPSSEKSLLETI 252

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D  A  P D+    +L+ +  R L  L+ ++  V+  RFG+      TLE+VG++  +T
Sbjct: 253 SDDRASDPSDTLQDDDLKASIDRWLDELSEKQREVVARRFGLRGYETSTLEDVGREIGLT 312

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ +++R+L+
Sbjct: 313 RERVRQIQVESLRRLR 328


>gi|260361829|ref|ZP_05774845.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
 gi|308114475|gb|EFO52015.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
          Length = 329

 Score =  213 bits (541), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMFESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 146 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 206 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 266 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 310


>gi|166363676|ref|YP_001655949.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166086049|dbj|BAG00757.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 414

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 106/262 (40%), Positives = 169/262 (64%), Gaps = 8/262 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ + E   I+++        + AK++M++ANLRLV+SVAKKY NRGL+ LDLIQEG +G
Sbjct: 159 GLEVGELEEIIAL-------GTRAKEQMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLG 211

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L +A +KFD   GY+FSTYA WW++Q +TR+IA +S  IR+PVH+ +K++++ +  R++S
Sbjct: 212 LERAVKKFDPTKGYRFSTYAYWWIRQGMTRAIATKSQIIRLPVHITEKLNRIKKAQRKIS 271

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
               R  T EEIA++LA+  E VR++L      +SLE  +G E  + L D +E + AVS 
Sbjct: 272 QMRGRTATVEEIAQELALTPEAVRELLMTVPRSVSLEIKVGKEKDTELLDLLEIE-AVSS 330

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +  +  +L+     +LA LT RE  V+ +R+G      H+L ++G+   ++RER+RQIE
Sbjct: 331 ENHFVYESLQRDIRELLADLTAREREVIELRYGFLDGKSHSLADIGRTLELSRERVRQIE 390

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
            KA++KL+      ++R + + 
Sbjct: 391 LKALQKLRQSQLHNQIRDYFEA 412



 Score = 37.0 bits (84), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 50/104 (48%), Gaps = 27/104 (25%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G DLED        DL SS           K  ++ +T D VR+YL+++G + LL R+ E
Sbjct: 36  GSDLED--------DLVSSPE---------KSYSNGTTTDLVRLYLQDIGRVPLLKRDEE 78

Query: 140 IAIAKRIEAGRAMMMASLCESPL--------TFQALIIWRDELN 175
           +  A++++  R + +  LC + +         F  LI  RD+L 
Sbjct: 79  VEQAQQVQ--RHLSLLKLCAAAVKQGDAQVQQFVKLIEVRDQLT 120


>gi|162455526|ref|YP_001617893.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161166108|emb|CAN97413.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 715

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 159/238 (66%), Gaps = 8/238 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           AK   V+ANLRLV+S+A++Y NRG L  +DLIQEGNIGLMKA E+FD   GY+FSTYA W
Sbjct: 484 AKNRFVKANLRLVVSIARRY-NRGRLPLIDLIQEGNIGLMKAVERFDHSRGYRFSTYASW 542

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++ AI+R++AD+   +RIPVHM D  ++V R  + +  +   EPT EE+ K+  +P E 
Sbjct: 543 WIRHAISRALADKGRAVRIPVHMLDTYNRVARATQAIIARTGHEPTIEELEKETGVPREK 602

Query: 563 VRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + KV     E P SL+ P+GDED     DF++++NA+SP D        +   R+L +LT
Sbjct: 603 LDKVKDFYAETPFSLDRPVGDEDGRKFIDFLQEENALSPFDHLANRKWSDEVRRLLTTLT 662

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           P E R++R RFG+    + TL+E+G ++ ++RERIRQ++ +A+ K++     K++R +
Sbjct: 663 PIESRIIRWRFGLDDEDELTLKEIGDKYNLSRERIRQLQEQALGKIR-----KQMRDY 715


>gi|189424151|ref|YP_001951328.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420410|gb|ACD94808.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 320

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 105/243 (43%), Positives = 160/243 (65%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R+ E     A+ +M+EANLRLV+ +AK+Y NRGL FLDLI+EGN+GLMKA E+F    
Sbjct: 78  LARRVEQGDKAARNQMIEANLRLVVKIAKRYLNRGLPFLDLIEEGNLGLMKAVERFSLEK 137

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA WW++Q+I R++ +QS TIR+PVH+ D I ++++ +R++S ++ REP+ +E+
Sbjct: 138 ECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDISRMLKVSRQLSQELHREPSVQEL 197

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + +    +RK++ + +   S++ PIG+ +   L D IED NAVSP D     +  E 
Sbjct: 198 ADAMQIKPLHIRKLMILLRRTCSMDVPIGEGNDFFLVDTIEDTNAVSPADLLENIDRYEL 257

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
                  L+  E  +L +RFG+      TL+ +G+ F VTRERIRQIEAK++ KLK  ++
Sbjct: 258 IAEHFDQLSENERTILGLRFGLDDRDPQTLDTIGQSFGVTRERIRQIEAKSLEKLKALAK 317

Query: 673 SKK 675
           S K
Sbjct: 318 SSK 320


>gi|111018672|ref|YP_701644.1| sigma factor, sigma 70 type, group 2 [Rhodococcus jostii RHA1]
 gi|110818202|gb|ABG93486.1| sigma factor, sigma 70 type, probable group 2 [Rhodococcus jostii
           RHA1]
          Length = 520

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 113/265 (42%), Positives = 173/265 (65%), Gaps = 8/265 (3%)

Query: 419 ETGISISEFRH--IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           + G  +S+ RH  +  + R G+     AK+  +EANLRLV+S+A++Y  RGL  LDL+QE
Sbjct: 260 DAGEKLSDQRHRDLHRVCRDGQH----AKRRFLEANLRLVVSIARRYQGRGLDLLDLVQE 315

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQS  IRIPVHM ++I ++ +  
Sbjct: 316 GNLGLIRAVEKFDYKTGFKFSTYATWWIRQAITRALADQSRVIRIPVHMVEQIDQLGKER 375

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            R++ +  REPTP E+A  L   +E +  + K  +  +SL+  +  ++  H G   ED  
Sbjct: 376 ARLTKETGREPTPSELATALDTTIEHIGDLEKYDQRVLSLD--VLTDNAEHDGLDFEDDL 433

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV   + A +    ET   VL+ L+ R+ +V+R+R+G+  +  +TL+E+GK + VTRERI
Sbjct: 434 AVVAEEVAERRRFYETLESVLSPLSERDAQVIRLRYGLTGSDPYTLDEIGKIYGVTRERI 493

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIE+K ++ +K  S +  LR F D
Sbjct: 494 RQIESKLLKAMKEESVADILRPFYD 518


>gi|170078438|ref|YP_001735076.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169886107|gb|ACA99820.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 318

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 158/225 (70%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW
Sbjct: 83  AKQKMVEANLRLVVSVAKKYIKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++    R  +  E+A +L +  + V
Sbjct: 143 IRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQANGRSASIPELADELGLTTKQV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L+ +++P+SL+  +GD + + L + +ED + ++P D A  A L+    R+L  LT +
Sbjct: 203 RDYLEKSRQPLSLDLRVGDNNDTELIELLED-DGLTPDDYATHAALKRDLARMLNDLTAQ 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL +RFG+   T HTL ++G+   ++RER+RQIE +A+ KL+
Sbjct: 262 QQEVLTLRFGLRDGTPHTLAKIGEHLSISRERVRQIEREALAKLR 306


>gi|148264661|ref|YP_001231367.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146398161|gb|ABQ26794.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter uraniireducens
           Rf4]
          Length = 336

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/247 (41%), Positives = 165/247 (66%), Gaps = 3/247 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + + + + KGE     A+ +M+E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL
Sbjct: 76  LTADEEKELAARIDKGE---KAARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGL 132

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D I+K++R  R +  
Sbjct: 133 IKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDINKMLRITRELVQ 192

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K+ REP+ +E+A  + +    +R+++ + K+  S+E P+G+ +   L D IED + VSP 
Sbjct: 193 KVNREPSIKEVATAMDVNSAYIRRLMVLLKKTYSIERPMGENNDYFLIDTIEDTSTVSPA 252

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +     N  E  ++   +L+  E+R+L +RFG+      TL+ +G+ F VTRERIRQIEA
Sbjct: 253 ELLEDVNRYEMVSKWFETLSDSEKRILTLRFGLDDKDPQTLDTIGRSFGVTRERIRQIEA 312

Query: 662 KAIRKLK 668
           K++ KL+
Sbjct: 313 KSLEKLR 319


>gi|300868245|ref|ZP_07112876.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
 gi|300333769|emb|CBN58060.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
          Length = 319

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/225 (45%), Positives = 155/225 (68%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW
Sbjct: 84  AKRMMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 143

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA++  TIR+P+H+ +K++K+ +  R ++ K+ R  T  E+A +L +  + +
Sbjct: 144 IRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRYLAQKLGRAATANELAAELELTPKQI 203

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+  + P+SL+  +GD   + LGD +ED  A SP D A+QA+LR     ++A LT +
Sbjct: 204 REYLERARLPLSLDLRVGDNQDTELGDLLEDTGA-SPEDFALQASLRADLEMLMADLTQQ 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+
Sbjct: 263 QREVLALRFGLEDGQTLTLSKIGDRLNISRERVRQIEREALTKLR 307


>gi|126453822|ref|YP_001064420.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|167736534|ref|ZP_02409308.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|217424965|ref|ZP_03456461.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242317344|ref|ZP_04816360.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254188239|ref|ZP_04894751.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|254295684|ref|ZP_04963141.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|126227464|gb|ABN91004.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|157805995|gb|EDO83165.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157935919|gb|EDO91589.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|217391985|gb|EEC32011.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242140583|gb|EES26985.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
          Length = 482

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|167916992|ref|ZP_02504083.1| RNA polymerase sigma factor [Burkholderia pseudomallei BCC215]
          Length = 482

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|134284106|ref|ZP_01770800.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167900733|ref|ZP_02487938.1| RNA polymerase sigma factor [Burkholderia pseudomallei NCTC 13177]
 gi|167908960|ref|ZP_02496051.1| RNA polymerase sigma factor [Burkholderia pseudomallei 112]
 gi|226194652|ref|ZP_03790247.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|134244558|gb|EBA44662.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|225933353|gb|EEH29345.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
          Length = 482

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.4 bits (93), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|297159879|gb|ADI09591.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           bingchenggensis BCW-1]
          Length = 333

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 107/234 (45%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E + AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 92  AEGARAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA +L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEHSEIAAELGS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 TTERVSDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++ R+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 RLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 325


>gi|53717743|ref|YP_106729.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52208157|emb|CAH34087.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
          Length = 482

 Score =  212 bits (540), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVNASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|124024644|ref|YP_001018951.1| type II alternative RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
 gi|123964930|gb|ABM79686.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9303]
          Length = 376

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 124/349 (35%), Positives = 198/349 (56%), Gaps = 10/349 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP-E 392
           R++LL  +      R++     LL+  +     ++   E  +  EL     +++  +P +
Sbjct: 31  RVELLTHEEEVTLARLVQRREALLKQERQLASSQEAIKELQRLEELQQREANHSCHWPTK 90

Query: 393 GEWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  KI    K+    TG+   E +  +   R+       AK +M++A
Sbjct: 91  QEWAMAAGLTLAELQDKIETGYKTWGALTGLDPLELKRSLRAGRR-------AKDQMIQA 143

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 144 NLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPARGFRFSTYAYWWIRQGITRA 203

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+P+H+ +K++++ R  + +++   R  +  ++AK L +  E VR  L    
Sbjct: 204 IATQSRTIRLPMHITEKLNRIKRVQQEIASNQGRLASIADLAKALGLSEETVRLTLMRVP 263

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             ISLET IG E  S LGD +ED NA +P +   +  L      +L  L+ RE  V+R R
Sbjct: 264 RSISLETRIGQEQDSQLGDLLEDSNA-TPEEKLTRDQLHNDLEILLDELSNREATVIRRR 322

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           FG+  +T  TL ++G+   ++RER+RQIE+ A+ KL+ P R  K+R ++
Sbjct: 323 FGLEDDTPQTLTQIGEAMHLSRERVRQIESHALLKLRQPQRRCKVRDYI 371



 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 5/59 (8%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + SS   +   L +R  S D     PVR+YL+++G +ELL+ E E+ +A+ ++   A++
Sbjct: 1   MKSSPQQTKTSLVRRSGSTD-----PVRLYLQDIGRVELLTHEEEVTLARLVQRREALL 54


>gi|330723944|gb|AEC46314.1| RNA polymerase sigma factor [Mycoplasma hyorhinis MCLD]
          Length = 524

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 109/265 (41%), Positives = 166/265 (62%), Gaps = 17/265 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++   ++ G      A+  ++  NLRLVI+ AK+Y NRGL F+DLI EGN G++KA +K+
Sbjct: 264 NLAKQIKNGGRAGKRARHTLINRNLRLVINNAKRYKNRGLTFIDLISEGNQGILKAVDKY 323

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT
Sbjct: 324 DYTKGYKFSTYATWWIRQAITRAVADQARIIRIPVHMVETINKINKIERELQQEYGVTPT 383

Query: 549 PEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E+IA+ +      E VR   KI  +PISL+  IG E+ S   DFI+D++ +SP+D +  
Sbjct: 384 DEQIAEVMGGDFTAEKVRYTKKINIDPISLDKAIGKEEYSSFSDFIKDESVISPIDYS-- 441

Query: 607 ANLRETTTRVLASLTP----REERVLRM-RFGIGMNTD------HTLEEVGKQFCVTRER 655
              RE  T++L  +       +E+V  M R+G G + +      H+ +E+ K+  VT+ER
Sbjct: 442 --EREEKTKILKQMIENNLDNDEKVFIMKRYGFGTDPNGEQYRIHSFDELAKERGVTKER 499

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIE+K ++KL+HP +  K R  +
Sbjct: 500 IRQIESKILKKLRHPQKKWKQRDLI 524


>gi|260436706|ref|ZP_05790676.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260414580|gb|EEX07876.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 377

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 159/239 (66%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW
Sbjct: 137 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + V
Sbjct: 197 IRQGITRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTV 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L      +SL+T +G E  + LGD IED +A +P  +     L      +L  LT R
Sbjct: 257 RQTLARVPRSVSLDTRVGREQDTQLGDLIEDGHA-TPEQTLTHDELHNDLEDLLDELTSR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  VLR RFG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 316 EAAVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQRRSKVRDYIQG 374


>gi|298248273|ref|ZP_06972078.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
 gi|297550932|gb|EFH84798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
          Length = 1341

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 107/229 (46%), Positives = 161/229 (70%), Gaps = 1/229 (0%)

Query: 440  EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +  IA+++++E NLRLVISVAKKY   G Q  DLIQEGN+GL++A EKFD   GY+FSTY
Sbjct: 1100 QGKIAREKLIEHNLRLVISVAKKYARVGRQLEDLIQEGNLGLIRACEKFDTDKGYRFSTY 1159

Query: 500  AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            A WW++QAITRS+A+QS TIR+PV++ +K+H++ R  R +  ++ REPT EE+AK   + 
Sbjct: 1160 ATWWIRQAITRSLAEQSRTIRLPVYLVEKLHQLHRGQRDLELQLGREPTLEELAKHQNLD 1219

Query: 560  VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            ++ V++ L + ++ +SL+ PIG E  + LG+ IE   +  P ++      +E  ++++ +
Sbjct: 1220 IDKVQEYLVLRQQILSLDAPIGAEQETTLGEMIEQPRS-DPQENINNYADKEAVSQLMQN 1278

Query: 620  LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LT R+ RV+ +RFG+     H LEE+G    VTRER+RQIE KA+R+LK
Sbjct: 1279 LTERQRRVISLRFGLEDGKIHKLEEIGSMLNVTRERVRQIEEKALRQLK 1327


>gi|167843756|ref|ZP_02469264.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|254197157|ref|ZP_04903580.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|169653899|gb|EDS86592.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
          Length = 482

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|262401766|ref|ZP_06078332.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
 gi|262352183|gb|EEZ01313.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
          Length = 336

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 98/225 (43%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    +  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLGWMDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|4105839|gb|AAD02575.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 589

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 114/269 (42%), Positives = 167/269 (62%), Gaps = 11/269 (4%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           ++ET +S+SE R  +   R+       AK  MV ANLRLVI  AK++ NRG+ F DL+QE
Sbjct: 311 AMETNMSVSELRGKLIKGRR-------AKNRMVAANLRLVICFAKRFRNRGVAFQDLVQE 363

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G+IGL++  EK+D   G++FSTYA WW++Q I +++ + S   R+PVH+ + I ++ R +
Sbjct: 364 GSIGLIRGVEKYDANRGFRFSTYASWWIRQGIHKALLECSKMFRLPVHVNEMIKEIRRCS 423

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS----HLGDFI 592
             + N + REPT  EIA K+ MP E V  +L+  +  +SLE P+   D+S     LGD +
Sbjct: 424 YELMNILGREPTKLEIAMKVGMPEEKVIFLLQRAQTALSLEMPLRGSDSSLESRTLGDVV 483

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
               + SP DSA   +LR    R L+ L  RE  V+RMRFG+      +L EVG  FCVT
Sbjct: 484 SSTASPSPEDSAFGTSLRYDLERALSQLDFREREVIRMRFGLDDGRTKSLGEVGSLFCVT 543

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQIE +A+RKL+ P  +  L+ +++
Sbjct: 544 RERVRQIETRALRKLRDPRCNIFLKEYME 572


>gi|2618586|dbj|BAA23365.1| sigma factor [Vibrio cholerae]
          Length = 335

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 98/225 (43%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTY  WW
Sbjct: 91  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYTTWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 151 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+    L  L P+
Sbjct: 211 TKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 315


>gi|328883104|emb|CCA56343.1| RNA polymerase principal sigma factor HrdD [Streptomyces venezuelae
           ATCC 10712]
          Length = 333

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 107/225 (47%), Positives = 148/225 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   +++NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 97  AKDLFIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P EIA +L    E V
Sbjct: 157 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEIAAELDTKPERV 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 217 VDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIDKLDHR 276

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++RMR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK
Sbjct: 277 TASIIRMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELK 321


>gi|162448460|ref|YP_001610827.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159042|emb|CAN90347.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 446

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 167/247 (67%), Gaps = 1/247 (0%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G    + AK E+V+ANLRL +++A+++   G+  LDL+QEGN+GL++AA+KF++  G++
Sbjct: 201 RGRRAVAQAKSELVQANLRLAVAIAREHQRFGVPLLDLVQEGNLGLIRAADKFEYRRGHR 260

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F TYA WW+KQAI R+I +Q   +R+PVH+     +VVR  R +  +  REP+ EEIA++
Sbjct: 261 FGTYAAWWIKQAIKRTILNQGKPVRMPVHLTAIRSQVVRARRDLVQERGREPSVEEIAER 320

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             + VE VR + ++  EP+SL+ P+G+E  +  GD + +    +P D   +  L E T  
Sbjct: 321 SGLTVEKVRVISELALEPLSLDAPVGEEGDTRYGDLLANDEP-TPADMLARRRLIEQTRE 379

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L SL PRE  +LR RFG+  N D TLEE+G+ F +TRERIRQIEAK + KL+  SR ++
Sbjct: 380 LLDSLQPRERELLRRRFGLDGNEDETLEEIGQSFSLTRERIRQIEAKLLEKLRTRSRQRE 439

Query: 676 LRSFLDG 682
           L S+L+G
Sbjct: 440 LGSYLEG 446



 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +Y R +   + L+REGE+AI +RIEAG      +   SP+  + L    +++  G   LR
Sbjct: 50  LYFRALAGSQPLTREGEVAIGRRIEAGALACFEAWVRSPVALRELASTAEDVQVGALSLR 109

Query: 183 EII 185
           +++
Sbjct: 110 DLL 112


>gi|237810316|ref|YP_002894767.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
 gi|237504080|gb|ACQ96398.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
          Length = 482

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|254182275|ref|ZP_04888872.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184212813|gb|EDU09856.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 482

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|304373196|ref|YP_003856405.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
 gi|304309387|gb|ADM21867.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
          Length = 524

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 109/265 (41%), Positives = 166/265 (62%), Gaps = 17/265 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++   ++ G      A+  ++  NLRLVI+ AK+Y NRGL F+DLI EGN G++KA +K+
Sbjct: 264 NLAKQIKNGGRAGKRARHTLINRNLRLVINNAKRYKNRGLTFIDLISEGNQGILKAVDKY 323

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT
Sbjct: 324 DYTKGYKFSTYATWWIRQAITRAVADQARIIRIPVHMVETINKINKIERELQQEYGVTPT 383

Query: 549 PEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E+IA+ +      E VR   KI  +PISL+  IG E+ S   DFI+D++ +SP+D +  
Sbjct: 384 DEQIAEVMGGDFTAEKVRYTKKINIDPISLDKAIGKEEDSSFSDFIKDESVISPIDYS-- 441

Query: 607 ANLRETTTRVLASLTP----REERVLRM-RFGIGMNTD------HTLEEVGKQFCVTRER 655
              RE  T++L  +       +E+V  M R+G G + +      H+ +E+ K+  VT+ER
Sbjct: 442 --EREEKTKILKQMIENNLDNDEKVFIMKRYGFGTDPNGEQYRIHSFDELAKERGVTKER 499

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIE+K ++KL+HP +  K R  +
Sbjct: 500 IRQIESKILKKLRHPQKKWKQRDLI 524


>gi|76812098|ref|YP_331741.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254261622|ref|ZP_04952676.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|76581551|gb|ABA51026.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254220311|gb|EET09695.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
          Length = 482

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|282899735|ref|ZP_06307698.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195350|gb|EFA70284.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 332

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 159/229 (69%), Gaps = 1/229 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  IAK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FSTY
Sbjct: 93  QGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPSKGYRFSTY 152

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R +S  + R P+  E+A++L + 
Sbjct: 153 AYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRYLSQTLGRSPSIAELAQELEIT 212

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + VR  L+  + P+SL+  +GD   + LG+ +ED  A SP D  IQ++L     R++  
Sbjct: 213 PKQVRDCLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEDYVIQSSLSSELDRMMTH 271

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LTP++  V+++RFG+      TL  +G+   ++RER+RQIE +A+ +L+
Sbjct: 272 LTPQQREVIKLRFGLVDGQSMTLARIGEVLNISRERVRQIEREALTRLR 320


>gi|167834949|ref|ZP_02461832.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 301

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 98/246 (39%), Positives = 161/246 (65%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+K+ +RGL   DL+QEGN+GL++A EKF++  G+KF
Sbjct: 54  GEARISAATARMAEANLRLVLSIARKHASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKF 113

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D++ +V + A R+  +     +  E++   
Sbjct: 114 STYATWWIRQAISRAIADRARTIRVPVHVGDEVRRVRKVADRIERRSGARASLAELSAAT 173

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +PVE +R +L + +EP SL  P+G++D +  GD +ED +  S  D+     + +  T +
Sbjct: 174 GLPVERLRAMLMLPREPRSLNAPLGNDDQAEFGDLVEDASTPSLFDALAHGQMCDVVTSL 233

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  Q  V+RE++R+IE +A++ L+  + +   
Sbjct: 234 LKTMSAQEADILRRRFGIGGDEPWSYEQIAAQTGVSREQVRRIEKRALQTLRVTAEACNA 293

Query: 677 RSFLDG 682
             FLD 
Sbjct: 294 HDFLDA 299


>gi|325285575|ref|YP_004261365.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324321029|gb|ADY28494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 104/250 (41%), Positives = 170/250 (68%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQVALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R+P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQAHERKPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M +E V++ LK +   +S++ P+ D + S+L D +    + +P    +  +LR
Sbjct: 157 EIAKELDMTIEDVKQSLKNSGRHVSMDAPLIDGEDSNLYDVLRSGESPNPDRELLIESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLAEQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|268591356|ref|ZP_06125577.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
 gi|291313333|gb|EFE53786.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
          Length = 328

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 95/225 (42%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+PEEIA++L  PVE V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPSPEEIAEQLDKPVEDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TPI  +    L + + D N   P ++    +L+E   + L  L P+
Sbjct: 208 SRMLRLNERITSVDTPIAGDSEKSLLEVLSDDNDSGPENTIQDNDLKENIVKWLYELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLEEVG++  +TRER+RQI+ + +++LK
Sbjct: 268 QREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLKRLK 312


>gi|294055548|ref|YP_003549206.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614881|gb|ADE55036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 342

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 150/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+ +A  Y N GL  +DLI EGNIGL+KA E+FD   G K STYA WW
Sbjct: 79  ARDHMISANLRLVVKIAHDYNNFGLPLMDLISEGNIGLVKAVERFDPSKGGKLSTYAAWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I R++A+QS TIR+PVH+ DKI  + +    +++++ REPT EEIA  + MPV  V
Sbjct: 139 IKQSIKRALANQSKTIRLPVHLVDKIAYMRKITAELADELDREPTDEEIAYTMGMPVNKV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +  ++  P SL+ P+G++  +  G+ + D+N  +PL++  + +L      ++A L  R
Sbjct: 199 AHLKSVSVRPSSLDAPVGEDGDTSFGELVGDENQATPLENLQEKSLSNDMHSMIALLDQR 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  ++R+RFG+      TLEEVG+QF +TRER+RQI+  AI K++
Sbjct: 259 EAEIIRLRFGLDGEHPLTLEEVGEQFKITRERVRQIQNIAIHKMR 303


>gi|260767191|ref|ZP_05876133.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|260617799|gb|EEX42976.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|315181178|gb|ADT88092.1| RNA polymerase sigma factor RpoS [Vibrio furnissii NCTC 11218]
          Length = 329

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 156/226 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 146 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAVELDKPVDDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    ++R++    L  L P+
Sbjct: 206 SKMLRLNERISSVDTPIGGDGDKALLDIIPDINNSDPEVSTQDDDIRDSLVAWLDELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 266 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 311


>gi|260063687|ref|YP_003196767.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88783132|gb|EAR14305.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 104/237 (43%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ EEIAK+L M VE V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQAHERVPSAEEIAKELDMTVEDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ LK +   +S++ P+ D + S+L D +    + +P    +  +LR    R L +LTPR
Sbjct: 170 KQSLKNSGRHVSMDAPLIDGEDSNLYDVLRSGESPNPDKELLHESLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVIRLYFGLAGQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|78062752|ref|YP_372660.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
 gi|77970637|gb|ABB12016.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 511

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 105/246 (42%), Positives = 162/246 (65%), Gaps = 1/246 (0%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G++GLM+A EKF++  G+KF
Sbjct: 267 GQQKVRDATRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGSLGLMRAIEKFEYRRGFKF 326

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR++AD++ TIR+PVH+ D+  +V R A R   +  R  TP E+A + 
Sbjct: 327 STYATWWIRQAITRAVADRARTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAET 386

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  + +R VL +  EP+SL+ P+ D DT  L + IED+ + SP +      +RE    +
Sbjct: 387 GLDEDKLRAVLALPAEPVSLDAPLPDADTG-LVELIEDQASASPFEQLADTRMRECVRSL 445

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  
Sbjct: 446 LRSVTPAEADVLRRRFGLGGTEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENA 505

Query: 677 RSFLDG 682
           +SFLD 
Sbjct: 506 QSFLDA 511



 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/140 (28%), Positives = 73/140 (52%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D         
Sbjct: 15  DPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDEPAAPAPFA 74

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +D+   A +    +         ++ DP+ +Y+R M ++ LL+REGEI +A+ IE 
Sbjct: 75  GSAPVDVDRDALDEGRAMLGDLARGTGASTDPLALYMRRMQAVPLLTREGEIVLAREIET 134

Query: 149 GRAMMMASLCESPLTFQALI 168
           GR  ++ +L   P    AL+
Sbjct: 135 GRHQILHALAGYPAAVDALL 154


>gi|89901840|ref|YP_524311.1| sigma 28 [Rhodoferax ferrireducens T118]
 gi|89346577|gb|ABD70780.1| sigma 28 [Rhodoferax ferrireducens T118]
          Length = 726

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 112/241 (46%), Positives = 152/241 (63%), Gaps = 6/241 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +MV ANL+LV+ +AKKY   G    DL+QEGNIGL+KA +++DW  G+K STYA WW
Sbjct: 371 ARDQMVIANLKLVLFIAKKYLYSGQPLDDLLQEGNIGLIKAVDRYDWRRGFKLSTYATWW 430

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R +AD+S TIR+PVH+  K  ++   A  +     R PT EEIAKK+ MP   V
Sbjct: 431 IRQQVGRYVADKSKTIRLPVHVYVKTQQIAHAAHAIELATGRMPTIEEIAKKMEMPASKV 490

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLT 621
             +     EP+    PI D D   L       N V+  P+D    + L  +  R LA+L 
Sbjct: 491 APLALAIPEPL----PIHDVDVDSLIAIDAQDNYVARDPMDIVSDSQLIGSIDRFLATLK 546

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           P++E+VLR+RFGIG +   TLEE+G +  VTRERIRQIEAKAI  LKHP+R ++L   L+
Sbjct: 547 PKDEQVLRLRFGIGAHEAMTLEEIGTRLEVTRERIRQIEAKAICHLKHPARLERLLRDLN 606

Query: 682 G 682
           G
Sbjct: 607 G 607


>gi|183600216|ref|ZP_02961709.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
 gi|188022512|gb|EDU60552.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
          Length = 328

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+ EEIA++L  PVE V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPSAEEIAEQLDKPVEDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TPI  +    L + + D+N   P  +    NL+E   + L  L P+
Sbjct: 208 SRMLRLNERITSVDTPIAGDSEKSLLEVLSDENESGPEHTIQDNNLKENIVKWLFELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 268 QREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLRRLK 312


>gi|302560146|ref|ZP_07312488.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302477764|gb|EFL40857.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 332

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 106/229 (46%), Positives = 149/229 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P E+A +L    E V
Sbjct: 156 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEVAAELGSTPERV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 216 VDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGRLDQR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 276 TASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|297200336|ref|ZP_06917733.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|197709451|gb|EDY53485.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 332

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 107/234 (45%), Positives = 152/234 (64%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTY
Sbjct: 92  ESERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTY 151

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L   
Sbjct: 152 ATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEIAAELGSN 211

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E    ++  
Sbjct: 212 AERVVDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 272 LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|116073370|ref|ZP_01470632.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068675|gb|EAU74427.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 313

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 106/230 (46%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + MP+E +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRLEIAEAMDMPLEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D ++  PL    Q+   E   R L+ L+ 
Sbjct: 198 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADNSSDEPLAKVEQSIHHEQLGRWLSHLSD 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL +RFG+  N  HTL E+G+   V+RERIRQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLNLRFGLNGNERHTLAEIGRLLEVSRERIRQVELKALRKLRNLTR 307


>gi|19910026|dbj|BAB87264.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 427

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 111/243 (45%), Positives = 164/243 (67%), Gaps = 7/243 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +V++NLR V+S+AKKY N+  +   DLIQEG+IGLMKAAE+FD   G+KF TYA W
Sbjct: 178 ARARLVQSNLRWVVSIAKKYANKHTMPLQDLIQEGSIGLMKAAERFDLDKGFKFLTYATW 237

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAI RS+ DQ  TIR+PVH+ D ++ + +T +++++++ R PTPEE+A +L +PV  
Sbjct: 238 WIRQAIFRSLQDQGRTIRLPVHVHDSLYLIKKTRQQLASRLGRIPTPEELADELNIPVSR 297

Query: 563 VRKVLKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + +    PISLE+PI  E +S     +LGDFIE +  + P +   +  LRE    VL
Sbjct: 298 LAFITQAASLPISLESPISSETSSTKARNNLGDFIESE-CLQPDEQLERTMLREDLENVL 356

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L  RE  ++RMR+G+   +  TL+E+G+   +TRERIRQIE  A+RKLK P R   L 
Sbjct: 357 ATLKARERDIIRMRYGLVDGSPKTLDEIGEIVGLTRERIRQIEQSAMRKLKAPYRKAILC 416

Query: 678 SFL 680
            ++
Sbjct: 417 DYI 419


>gi|159026170|emb|CAO88820.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 318

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 104/238 (43%), Positives = 164/238 (68%), Gaps = 3/238 (1%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA W
Sbjct: 82  FAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYW 141

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++    R  T  E+A++L +  + 
Sbjct: 142 WIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQDKGRAATIAELAEELDLTPKQ 201

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR  L+ +++P+SL+  +GD   + LG+ +ED   +SP D    ++L+    +++A LTP
Sbjct: 202 VRDYLERSRQPLSLDLKVGDNQDTELGELLED-TGLSPEDYTAHSSLQVDLEKLMADLTP 260

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +++ V+ +RFG+      TL ++G +  ++RER+RQIE +AI KL+   R  K+R +L
Sbjct: 261 QQKEVICLRFGLDNGQPLTLAKIGVRLNISRERVRQIEREAIAKLR--KRKAKIREYL 316



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 2/46 (4%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++  DPVR YLRE+G + LLS E EI  AK+++  R + +  + ES
Sbjct: 5   KNPTDPVRAYLREIGRVPLLSHEEEILYAKQVQ--RLIFLEKIKES 48


>gi|72382695|ref|YP_292050.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|124026414|ref|YP_001015529.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|72002545|gb|AAZ58347.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|123961482|gb|ABM76265.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 313

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 105/230 (45%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + + +E +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLATIRKVSLDLAHKLGAMPSRIEIAEAMEIELEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ GDE  S LGD I D +   PLD   Q   +E   R L+ L+ 
Sbjct: 198 DSILRQALTTSSLDAPVNGDEGRSFLGDLIADGSGEEPLDKVEQKIHQEQLGRWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ V+R+RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVIRLRFGLEGNERHTLAEIGRLLQVSRERVRQVELKALRKLRNLTR 307


>gi|254388870|ref|ZP_05004102.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294813166|ref|ZP_06771809.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441537|ref|ZP_08216271.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|197702589|gb|EDY48401.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294325765|gb|EFG07408.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
          Length = 333

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 106/234 (45%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + +NLRLV++VA++Y   GL  LDL+QEGN GL++A EKFD+  G+KFST
Sbjct: 92  AEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLVQEGNAGLVRAVEKFDYSKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA++L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREKGREPEAAEIAQELGS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D   +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 TPERVTDVLDWARDPVSLNMAVDDAGETQFGDLLEDTSAVSPEQSVLTLLRSEGLDDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   ++RMR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 KLDQRTASIIRMRYGIMDGRERTLTEVGKEHGLTRERIRQIEKHALLELKRMAR 325


>gi|87125501|ref|ZP_01081346.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86166801|gb|EAQ68063.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 312

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 110/245 (44%), Positives = 166/245 (67%), Gaps = 5/245 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   M+R G+     AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKF
Sbjct: 67  HDRRMIRVGKR----AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKF 122

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+
Sbjct: 123 DPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPS 182

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             EIA+ + MP++ +  +L+      SL+ P+ G+E  S LGD I D +   PLD   Q+
Sbjct: 183 RVEIAEAMDMPLDELDALLRQALTTSSLDAPVNGEEGRSFLGDLIADTSHDEPLDKVEQS 242

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E   R L+ L+ +E+ VL +RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL
Sbjct: 243 IHHEQLGRWLSHLSEQEQYVLGLRFGLNGNERHTLAEIGRLMEVSRERVRQVELKALRKL 302

Query: 668 KHPSR 672
           ++ +R
Sbjct: 303 RNLTR 307


>gi|239930706|ref|ZP_04687659.1| RNA polymerase principal sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291439071|ref|ZP_06578461.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341966|gb|EFE68922.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 332

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 106/233 (45%), Positives = 151/233 (64%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTY
Sbjct: 92  DAERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTY 151

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P E+A +L   
Sbjct: 152 ATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEVAAELGST 211

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  
Sbjct: 212 PERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|78185801|ref|YP_378235.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78170095|gb|ABB27192.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 377

 Score =  211 bits (537), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 119/352 (33%), Positives = 201/352 (57%), Gaps = 10/352 (2%)

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP- 391
            R+DLL  +      R++     LL+  +          E H+  EL     ++   +P 
Sbjct: 31  GRVDLLTSEEEVTLARLVQRRETLLKQQRELSDTNQAIGELHRLEELQRREANHHSHWPT 90

Query: 392 EGEWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           + EW    A  +  +  +I    ++ + +  I   E +  +   R+       AK  M++
Sbjct: 91  KQEWARAAALTLQELQNRIDAGYEAWAEKAAIDAKELKLSLRNGRR-------AKDHMIQ 143

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q +TR
Sbjct: 144 ANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGMTR 203

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + VR+ L+  
Sbjct: 204 AIATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTVRQTLERV 263

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
              +SL++ +G +  + LGD IED  A +P ++     L      +L  LTPRE  VLR 
Sbjct: 264 PRSVSLDSRVGKDQDTQLGDLIEDGKA-TPEETLTHDELHNDLEGLLDELTPREASVLRR 322

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P +  K+R ++ G
Sbjct: 323 RFGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQKRSKIRDYIQG 374


>gi|90416198|ref|ZP_01224130.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90331923|gb|EAS47137.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 306

 Score =  211 bits (537), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 102/233 (43%), Positives = 158/233 (67%), Gaps = 1/233 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL+ LDLI+EGNIGLM+A EKFD  LGY+FSTYA WW
Sbjct: 63  ARKRMIESNLRLVVKIARRYVNRGLELLDLIEEGNIGLMRAVEKFDPELGYRFSTYATWW 122

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R + +Q+ TIR+PVH+  +++  VR +R+++ ++   PTPEEIA+++  PVE V
Sbjct: 123 IRQTIERGLMNQTRTIRLPVHIVKELNVYVRASRKLAQRLDHTPTPEEIAEEVDKPVEDV 182

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+  +++   S++ P+ + + S L + I  + A SP       NL E   + LA L  +
Sbjct: 183 LKIFSLSERISSIDIPVAENEKS-LIETISAEGASSPERQVEGENLSEVLNKWLAQLPEK 241

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+  + + TLE+VG++  +TRER+RQI+  A+R+L+   R   L
Sbjct: 242 QREVLVRRFGLLHHQEETLEQVGREIGLTRERVRQIQVDALRRLRDVLRKHGL 294


>gi|87301096|ref|ZP_01083937.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87284064|gb|EAQ76017.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 308

 Score =  211 bits (537), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 105/226 (46%), Positives = 158/226 (69%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 73  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 132

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  V R +  +++K+   P+  EIA+ +A+P++ +
Sbjct: 133 IRQSMTRAIACQSRTIRLPVHLSERLSAVRRVSLELAHKLGAMPSRSEIAEAMAIPIQEL 192

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+ +    SL+ P+ G+E  S LGD I D +   PLD   +    E   R L+ L+ 
Sbjct: 193 DGLLRQSLTTSSLDAPVNGEEGRSFLGDLIADSSHDEPLDQVERGMHHEQLERWLSYLSE 252

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E +VL +RFG+  +  HTL E+G+   V+RER+RQ+E KA+RKL+
Sbjct: 253 QERQVLDLRFGLDGHERHTLAEIGRLLDVSRERVRQVELKALRKLR 298


>gi|323495851|ref|ZP_08100919.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
 gi|323319067|gb|EGA72010.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
          Length = 331

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV+ V
Sbjct: 148 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATKLDKPVDDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 208 SKMLRLNERISSVDTPIGGDGEKALLDIIPDVNNSDPEVSTQDDDIKNSLIHWLDELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 268 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 312


>gi|302336705|ref|YP_003801911.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301633890|gb|ADK79317.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 322

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 155/238 (65%), Gaps = 2/238 (0%)

Query: 433 MVRKGECEASIAKKE--MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + RK   EA + K    M+ +NLRLV+S+AKKY +RGL FLDLI EGNIGL++A E+FD+
Sbjct: 73  LFRKRTIEAVLRKSRDRMITSNLRLVVSIAKKYQHRGLSFLDLIDEGNIGLIEAVERFDY 132

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTY  WW++Q++ +++AD+  TIRIP+H+ + I K+    + ++ ++ R+P+  
Sbjct: 133 TKRCKFSTYGTWWIQQSVIKALADKGRTIRIPIHVLNIIRKLFSVTKHLTQELGRDPSSA 192

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  + +PVE V  +L+ + E  SL+  + DE+ + L D +   + + P +S     L+
Sbjct: 193 EIAAYMDLPVERVESILQYSGETASLDVTVDDENITSLSDLVFSDDYIEPFESVFHVTLK 252

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    +L  L+ RE+ ++++RFG+   T  TLEE+G    +TRER+RQI+ KAI KL+
Sbjct: 253 DLLDTILGQLSEREQTIIKLRFGLADRTPLTLEEIGSILGITRERVRQIQNKAIEKLR 310


>gi|225011103|ref|ZP_03701566.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
 gi|225004737|gb|EEG42696.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
          Length = 287

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 168/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +   ++A + +  ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDAVALERLTTANLRFVVSVAKQYQNQGLTLPDLINEGNVGLVKAAKRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++QAI +++A+Q+  +R+P++    I+K+ +    +    +R P+PE
Sbjct: 97  TRGFKFISYAVWWIRQAILQALAEQARIVRLPLNKIGSINKINKAFSYLEQAHQRPPSPE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M V  V++ LK +   +S++ P+ D + S L D ++  ++  P  + IQ++L 
Sbjct: 157 EIAKELEMTVSDVKQSLKNSGRHVSMDAPLIDGENSSLYDVLDYGDSPRPDQALIQSSLH 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              TR L +L+PRE  V+++ +GIG     TL E+G  F +TRER+RQI  KAIRKL+H 
Sbjct: 217 TEITRALDTLSPREADVIKLFYGIGEQPPMTLAEIGLTFDLTRERVRQIREKAIRKLRHS 276

Query: 671 SRSKKLRSFL 680
           S++K L+++L
Sbjct: 277 SKNKLLKTYL 286


>gi|113474616|ref|YP_720677.1| RNA polymerase sigma factor [Trichodesmium erythraeum IMS101]
 gi|110165664|gb|ABG50204.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 336

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 160/237 (67%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 101 AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 160

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q+ TIR+P+H+ +K++K+ R  R +   + R PTP EIA+ L +    +
Sbjct: 161 IRQAITRAIAQQARTIRLPIHITEKLNKIKRVQRELIQSLGRSPTPSEIAQALELEPSQI 220

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L + + PISL+  +GD   + L + +ED+ + SP D      LR+    +LA L+ +
Sbjct: 221 REYLLMARHPISLDLRVGDNQDTELQELLEDETS-SPDDYITGELLRQDINTLLAELSEQ 279

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RVL +RFG+    + +L +VG +  ++RER+RQ+E +A+  L+   R  K+R ++
Sbjct: 280 QRRVLVLRFGLEDGKEMSLAKVGDKLQLSRERVRQLEHQALAFLRR--RQAKVREYV 334


>gi|119489578|ref|ZP_01622338.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454490|gb|EAW35638.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 319

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/249 (41%), Positives = 164/249 (65%), Gaps = 8/249 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+S+ E +  +        +   AK++MVEANLRLV+SVAKKY  R +  LDLIQEG I
Sbjct: 67  AGVSLKELKQALE-------DGQTAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTI 119

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R +
Sbjct: 120 GMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRSL 179

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           +  + R  T  E+A +L +  + +R+ L+  + P+SL+  +GD   + LGD +ED  A S
Sbjct: 180 AQDLGRAATIAELADELDLNPKQIREYLERARLPLSLDLRVGDNQDTELGDLLEDDGA-S 238

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D A+Q+++R     ++A LT ++ +VL +RFG+      TL ++G +  ++RER+RQI
Sbjct: 239 PEDYALQSSMRSDLEVLMADLTDQQRQVLALRFGLENGQTMTLAKIGDRLNISRERVRQI 298

Query: 660 EAKAIRKLK 668
           E +A+ KL+
Sbjct: 299 EREALTKLR 307


>gi|78212423|ref|YP_381202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196882|gb|ABB34647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 312

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 77  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 136

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + +P++ +
Sbjct: 137 IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRVEIAEAMDIPLDEL 196

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +   PLD   Q    E   R L+ L+ 
Sbjct: 197 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLDEPLDIVEQRIHHEQLGRWLSHLSE 256

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VLRMRFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 257 QEQHVLRMRFGLEGNERHTLAEIGRLMEVSRERVRQVELKALRKLRNLTR 306


>gi|300865041|ref|ZP_07109868.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
 gi|300336978|emb|CBN55018.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
          Length = 334

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/264 (39%), Positives = 173/264 (65%), Gaps = 10/264 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +++  +S +E + ++   R+       AK++M+EANLRLV+++AKKY  R ++FLDLIQE
Sbjct: 79  ALQVQLSEAELKRLMHQGRR-------AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 131

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL +  EKFD   GYKFSTYA WW++QAITR+IA  + TIR+P+H+ +K++K+ +  
Sbjct: 132 GTLGLERGVEKFDPMRGYKFSTYAYWWIRQAITRAIAQHARTIRLPIHITEKLNKIKKVQ 191

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R ++ ++ R PTP EI   L +    +R+ L + + P+SL+  +GD   + L + +ED++
Sbjct: 192 RELAQQLGRSPTPAEIGSALELHPSQIREYLLMARHPVSLDLRVGDNQDTELQELLEDES 251

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP D      LR+    ++A LTP++  VL +RFG+    + +L +VG++  ++RER+
Sbjct: 252 A-SPDDYITGELLRQDLNNLMAELTPQQRDVLSLRFGLEDGHEMSLAKVGERLKLSRERV 310

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQ+E +A+  L+   R  ++R +L
Sbjct: 311 RQLEHQALAHLRR--RQAQVREYL 332


>gi|282865528|ref|ZP_06274579.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282559572|gb|EFB65123.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 333

 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 108/236 (45%), Positives = 151/236 (63%), Gaps = 5/236 (2%)

Query: 438 ECEASIAKKE-----MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           E EA +A+ E      + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  
Sbjct: 86  ELEALVAEGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAK 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EI
Sbjct: 146 GFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEI 205

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L    E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E 
Sbjct: 206 AAELGSNTERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLRSEE 265

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++  L  R   ++RMR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 266 LEDLIGKLDNRTASIIRMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 321


>gi|294629875|ref|ZP_06708435.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292833208|gb|EFF91557.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 332

 Score =  211 bits (536), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 106/229 (46%), Positives = 149/229 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L    E V
Sbjct: 156 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNRENGRDPEPAEIAAELGSTPERV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 216 ADVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSEELDDLIGRLDQR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 276 TASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|172038507|ref|YP_001805008.1| RNA polymerase sigma factor SigD [Cyanothece sp. ATCC 51142]
 gi|171699961|gb|ACB52942.1| group 2 sigma-70 RNA polymerase sigma factor D [Cyanothece sp. ATCC
           51142]
          Length = 318

 Score =  211 bits (536), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 109/247 (44%), Positives = 167/247 (67%), Gaps = 8/247 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  EFR   S+V  GE     AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+
Sbjct: 68  LSKREFR---SIVESGEA----AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R +S 
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRELSQ 180

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  R  T  E+A++L +  + VR+ L+  ++P+SL+  +GD   + LGD +ED +  SP 
Sbjct: 181 QKGRAATVTELAEELDLTPKQVREYLERARQPLSLDLRVGDNQDTELGDLLED-DGQSPE 239

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D A  ++L+    R++  LT +++ V+ +RFG+      TL ++G +  ++RER+RQIE 
Sbjct: 240 DFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNISRERVRQIER 299

Query: 662 KAIRKLK 668
           +A+ KL+
Sbjct: 300 EALSKLR 306



 Score = 39.7 bits (91), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 24/33 (72%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +S  DPVR YL+E+G + LL+ E EI  AKR++
Sbjct: 5   KSNPDPVRAYLKEIGRVPLLTHEEEILYAKRVQ 37


>gi|148978207|ref|ZP_01814737.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
 gi|145962629|gb|EDK27905.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
          Length = 326

 Score =  211 bits (536), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 155/226 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV  V
Sbjct: 143 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIASKLDKPVGDV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S   ++++ +    L  L P+
Sbjct: 203 SKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDSDIKNSLIFWLDELNPK 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 263 QKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEGLRRLRE 308


>gi|289746505|ref|ZP_06505883.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687033|gb|EFD54521.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
          Length = 216

 Score =  211 bits (536), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 103/202 (50%), Positives = 143/202 (70%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G  ++ EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +
Sbjct: 15  GADRSVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQREL 74

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV 
Sbjct: 75  LQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVV 134

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQI
Sbjct: 135 AVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQI 194

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E+K + KL+HPSRS+ LR +LD
Sbjct: 195 ESKTMSKLRHPSRSQVLRDYLD 216


>gi|86146341|ref|ZP_01064665.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
 gi|85835820|gb|EAQ53954.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
          Length = 326

 Score =  211 bits (536), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 155/226 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV  V
Sbjct: 143 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIASKLDKPVGDV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S   ++++ +    L  L P+
Sbjct: 203 SKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDSDIKNSLIFWLDELNPK 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 263 QKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEGLRRLRE 308


>gi|308048570|ref|YP_003912136.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
 gi|307630760|gb|ADN75062.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
          Length = 328

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 101/238 (42%), Positives = 160/238 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+ + + + ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 75  VYYARRAQRDCAKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDP 134

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++ +  EPT E
Sbjct: 135 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHTLDHEPTAE 194

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA KL  PVE V ++LK+ ++  S++TPIG +    L D I D + V P   A   ++ 
Sbjct: 195 EIAMKLDKPVEDVSRMLKLNEKISSVDTPIGGDSDKALLDVIADDDRVCPEVQAQDDDIN 254

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  R L  L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+R+L+
Sbjct: 255 GSVVRWLGELNSKQREVLARRFGLLGYEPSTLEDVGREIGLTRERVRQIQVEALRRLR 312


>gi|78214100|ref|YP_382879.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78198559|gb|ABB36324.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 377

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 158/237 (66%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW
Sbjct: 137 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + V
Sbjct: 197 IRQGITRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTV 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L      +SL+T +G E  + LGD IED +A +P  +     L      +L  LT R
Sbjct: 257 RQTLARVPRSVSLDTRVGREQDTQLGDLIEDGHA-TPEQTLTHDELHNDLEHLLDELTSR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR RFG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P R  K+R ++
Sbjct: 316 EAAVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQRRSKIRDYI 372


>gi|153840560|ref|ZP_01993227.1| RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149745777|gb|EDM56907.1| RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 415

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 31  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ T R+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 91  IRQTIERALMNQTRTTRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 151 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 210

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 211 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 255


>gi|33864481|ref|NP_896041.1| putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641261|emb|CAE22391.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
          Length = 376

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 123/349 (35%), Positives = 197/349 (56%), Gaps = 10/349 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP-E 392
           R++LL  +      R++     LL+  +     ++   E  +  EL     +++  +P +
Sbjct: 31  RVELLTNEEEVTLARLVQRREALLKQERKLASNQEAIKELQRLEELQQREANHSCHWPTK 90

Query: 393 GEWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  KI    K+    TG+   E +  +   R+       AK +M++A
Sbjct: 91  QEWAMAAGLTLAELQEKIETGYKTWGALTGLDPLELKRSLRAGRR-------AKDQMIQA 143

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 144 NLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRA 203

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+P+H+ +K++++ R  + +++   R  +  ++AK L +  E VR  L    
Sbjct: 204 IATQSRTIRLPMHITEKLNRIKRVQQEIASSQGRLASIADLAKALGLSEETVRLTLMRVP 263

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             ISLET IG E  + LGD +ED NA +P +   +  L      +L  L+ RE  V+R R
Sbjct: 264 RSISLETRIGQEQDTQLGDLLEDSNA-TPEEKLTRNQLHNDLEILLDELSNREATVIRRR 322

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           FG+  +T  TL ++G+   ++RER+RQIE  A+ KL+ P R  K+R ++
Sbjct: 323 FGLEDDTPQTLTQIGEAMHLSRERVRQIETHALLKLRQPQRRCKVRDYI 371



 Score = 37.7 bits (86), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 28/37 (75%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + DPVR+YL+++G +ELL+ E E+ +A+ ++   A++
Sbjct: 18  STDPVRLYLQDIGRVELLTNEEEVTLARLVQRREALL 54


>gi|293363636|ref|ZP_06610388.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
 gi|292552792|gb|EFF41550.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
          Length = 492

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 108/264 (40%), Positives = 171/264 (64%), Gaps = 11/264 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +   + KG      A+ +++  NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K
Sbjct: 227 KQLAKQMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRGLTFIDLISEGNAGILKAVQK 286

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           ++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  ++  EP
Sbjct: 287 YNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQELGHEP 346

Query: 548 TPEEIAKKLAMPV--EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           T  +IA +       E VR + KI  +PISL+  IG E+ S   DF++D N ++P+D A 
Sbjct: 347 TDSQIANRFGNDYTEEKVRYIRKINVDPISLDKQIGKENDSSFSDFVKDDNILNPVDYAS 406

Query: 606 QANLRETTTRVL-ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQ-FCVTRERIR 657
           Q  L E    ++  SL   E  ++  R+G+G++++      H+L+E+ ++   V++ERIR
Sbjct: 407 QEQLSELLIDLIDKSLEKDERELICKRYGVGVDSNGEKYRVHSLDELARERGGVSKERIR 466

Query: 658 QIEAKAIRKLKHPSRS-KKLRSFL 680
           QIE K +RKLK+ S++ + L+ F+
Sbjct: 467 QIENKILRKLKNSSKNGRHLKDFI 490


>gi|332994558|gb|AEF04613.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas sp. SN2]
          Length = 330

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 101/230 (43%), Positives = 155/230 (67%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+ +NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 85  CEAS--RKRMIVSNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 142

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPT EEIA  L  
Sbjct: 143 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTAEEIALALDK 202

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++TPIG E+   L D + D+    P ++   ++++      L 
Sbjct: 203 PVEDVTKMLRLNERITSVDTPIGGENDKALLDILADEKEFGPEENLQDSDIKSNIVGWLE 262

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L P++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+L+
Sbjct: 263 ELNPKQREVLARRFGLMGYEPSTLEDVGAEIGLTRERVRQIQVEALRRLR 312


>gi|148242803|ref|YP_001227960.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851113|emb|CAK28607.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 309

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 108/230 (46%), Positives = 158/230 (68%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 74  SKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  V +    +++K+   P+  EIA +L M +E +
Sbjct: 134 IRQSMTRAIACQSRTIRLPVHLSERLATVRKATMDLAHKLGAMPSRREIATELGMGLEEL 193

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ PI G+E  S LG+ I D     PLD+  +    E   R L+ LT 
Sbjct: 194 DGLLRQALTTSSLDAPISGEEGRSFLGELIADPRNEEPLDAVERRMHHEQLGRWLSYLTA 253

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E++VL MRFG+G    HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 254 QEKQVLEMRFGLGGEQRHTLAEIGRLMEVSRERVRQVELKALRKLRNLTR 303


>gi|302543058|ref|ZP_07295400.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460676|gb|EFL23769.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           himastatinicus ATCC 53653]
          Length = 333

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 107/234 (45%), Positives = 150/234 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E + AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 92  AEGARAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA++L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEHMEIAEELGS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 TPERVSDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++ R+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 RLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 325


>gi|29830237|ref|NP_824871.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607348|dbj|BAC71406.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 331

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 107/230 (46%), Positives = 150/230 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   +++NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 95  AKDVFIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P EIA +L      V
Sbjct: 155 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEIAAELDSNPARV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 215 TDVLDWARDPVSLNMHVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGRLDQR 274

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 275 TASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 324


>gi|218245053|ref|YP_002370424.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|218165531|gb|ACK64268.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 375

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 107/238 (44%), Positives = 172/238 (72%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 137 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A++L M    +
Sbjct: 197 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQKLQRNPNEKELAQELEMTPPQL 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +  LR   + VL+  LT 
Sbjct: 257 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEEQMNEGMLRNEISAVLSDVLTE 316

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 317 REKDVISLRYGLSTSQPHTLEEVGGMFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 374


>gi|167813607|ref|ZP_02445287.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
          Length = 302

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 55  GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 114

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 115 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 174

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 175 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 235 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 294

Query: 677 RSFLD 681
             FLD
Sbjct: 295 HDFLD 299


>gi|225011624|ref|ZP_03702062.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
 gi|225004127|gb|EEG42099.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
          Length = 287

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 104/250 (41%), Positives = 169/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    IA +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQIALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKTYAFLEQAHERAPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M +  V++ LK +   +S++ P+ + + S+L D +    + +P    +  +LR
Sbjct: 157 EIAKELDMTINDVKESLKNSGRHVSMDAPLVEGEDSNLYDVLNSGESPNPDRVLLHESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVVRLYFGLGDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286



 Score = 38.1 bits (87), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL+E+G ++L++ E E+ +A+RI+AG  + +  L ++ L F  + + +   N G TL
Sbjct: 21  YLQEIGKVDLITAEEEVELAQRIKAGDQIALEKLTKANLRF-VVSVAKQYQNQGLTL 76


>gi|163787530|ref|ZP_02181977.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159877418|gb|EDP71475.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 169/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    IA +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQIALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQSHERPPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M +  V++ +K +   +S++ P+ + + S+L D +    + +P    +  +LR
Sbjct: 157 EIAKELDMTINDVKESMKNSGRHVSMDAPLVEGEDSNLYDVLRSGESPNPDRDLLHESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLGNQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|332878128|ref|ZP_08445857.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332683866|gb|EGJ56734.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 287

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 104/237 (43%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIA++L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQANERVPSAEEIARELDMSVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   IS++ P+ + + S+L D I    + +P    I A+LR    R L +LTPR
Sbjct: 170 KESMKNSGRHISMDAPLVEGEDSNLYDVIRSNESPNPDKELILASLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVIRLYFGLGDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|126441635|ref|YP_001057174.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126221128|gb|ABN84634.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 482

 Score =  210 bits (534), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IA+++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIAERARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.4 bits (93), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|257058077|ref|YP_003135965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|256588243|gb|ACU99129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 375

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 107/238 (44%), Positives = 172/238 (72%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 137 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A++L M    +
Sbjct: 197 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQKLQRNPNEKELAQELEMTPPQL 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +  LR   + VL+  LT 
Sbjct: 257 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEEQMNEGMLRNEISAVLSDVLTE 316

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 317 REKDVISLRYGLSTSQPHTLEEVGGMFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 374


>gi|332292552|ref|YP_004431161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|332170638|gb|AEE19893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 287

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 164/237 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SV+K+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVSKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+PEEIAK+L M +  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQANERPPSPEEIAKELDMSINDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ LK +   IS++ P+ + + S+L D +    + +P    +  +L+    R L +LTPR
Sbjct: 170 KESLKNSGRHISMDAPLVEGEDSNLYDVLNSGESPNPDRELLHESLKTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLGDQQPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|218710550|ref|YP_002418171.1| RNA polymerase sigma factor RpoS [Vibrio splendidus LGP32]
 gi|218323569|emb|CAV19793.1| RNA polymerase sigma factor rpoS (Sigma-38 factor) [Vibrio
           splendidus LGP32]
          Length = 335

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 155/226 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV  V
Sbjct: 152 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIASKLDKPVGDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S   ++++ +    L  L P+
Sbjct: 212 SKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDSDIKNSLIFWLDELNPK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 272 QKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEGLRRLRE 317


>gi|53724654|ref|YP_101962.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|121599433|ref|YP_994127.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|167001162|ref|ZP_02266961.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
 gi|238561900|ref|ZP_00441190.2| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|254176911|ref|ZP_04883568.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254203640|ref|ZP_04910000.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208616|ref|ZP_04914964.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254360328|ref|ZP_04976598.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|52428077|gb|AAU48670.1| RNA polymerase sigma factor RpoD, putative [Burkholderia mallei
           ATCC 23344]
 gi|121228243|gb|ABM50761.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|147745152|gb|EDK52232.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147750492|gb|EDK57561.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148029568|gb|EDK87473.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|160697952|gb|EDP87922.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|238523583|gb|EEP87020.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|243062992|gb|EES45178.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
          Length = 482

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IA+++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIAERARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.4 bits (93), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|149197281|ref|ZP_01874333.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139827|gb|EDM28228.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 404

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 99/229 (43%), Positives = 150/229 (65%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVE NLRLVIS+A+KY+N    FLDLIQEGNIGL+ A EK+D   GY FSTYA WW++QA
Sbjct: 172 MVEGNLRLVISIARKYSNSQEGFLDLIQEGNIGLVSAVEKYDASFGYTFSTYATWWIRQA 231

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ++R+  +   T+++P ++  K++K+ RT R +  K  RE T +E+++ + +    +R + 
Sbjct: 232 VSRARTELVRTMKLPANIMVKVNKIYRTERELFQKFGREATIDEVSEAVELSPAKIRSLK 291

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ ++PISL+T + +E T  LGD + + + V P     Q  L E+   +L  L  RE+ +
Sbjct: 292 RMCQQPISLQTTVSEEHTGELGDIVSNDDDVLPDAEVEQKQLHESLVAMLDILNEREQEI 351

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LRMRFG+     HTLE +  +F ++RERIRQIE  A++KL+ P+  K L
Sbjct: 352 LRMRFGLADGEYHTLENIANEFGISRERIRQIETSALKKLRRPTAVKCL 400


>gi|113953359|ref|YP_732042.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
 gi|113880710|gb|ABI45668.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
          Length = 376

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 122/356 (34%), Positives = 210/356 (58%), Gaps = 24/356 (6%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYG-----IKRDVFLERHQGRELD--PHWVSY 386
           R+DLL  +   +  R++     L R  + +      I+R + LE  Q RE +   HW + 
Sbjct: 31  RVDLLTAEDEVVLSRLVQQYERLKREERQFAEDHPAIERLLCLEELQLREANHLSHWPT- 89

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI--SEFRHIVSMVRKGECEASIA 444
                  EW       +  +    N+  +   ET  ++  ++ R +   +R+G      A
Sbjct: 90  -----RQEWARAAEMPLQEL----NKGLTQGYETWANLISTDSRELQLRLRRGRK----A 136

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  M++ANLRLV++VAKKY +RG++ LDL+QEG +GL +A EKFD   G++FSTY+ WW+
Sbjct: 137 RDRMIQANLRLVVAVAKKYQHRGMELLDLVQEGTLGLERAVEKFDSTRGFRFSTYSYWWI 196

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q ITR+IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L++  + VR
Sbjct: 197 RQGITRAIATQSRTIRLPVHITEKLNRIKRVQQEIASNEGRTASMTDLARELSVSEDTVR 256

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L      +SLET +G +  + LG+ +ED++A +P  +  + +L +    +L  LTPRE
Sbjct: 257 QTLARVPRSVSLETKVGRDQDTQLGELLEDEHA-TPEQTLTRDSLHDDLEHLLNELTPRE 315

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             V+R RFG+  +T  TL ++G+   ++RER+RQIE +A+ KL+ P R  K+R ++
Sbjct: 316 ATVIRCRFGLEDDTPRTLAQIGEDMNLSRERVRQIETRALLKLRQPQRRNKVRDYI 371


>gi|85712119|ref|ZP_01043172.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
 gi|85694109|gb|EAQ32054.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
          Length = 333

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 100/233 (42%), Positives = 158/233 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  ARKRMIESNLRLVVKIARRYCNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EPT E+IA  L  PVE +
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELAHKLDHEPTAEDIAASLNKPVEDI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG ++   L D + D+    P       +L+E  T  L +L P+
Sbjct: 212 TKMLRLNERVTSVDTPIGGDNDKALLDILTDEADDGPEGVLQDGDLKERITEWLDALNPK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++ VL  RFG+      TLE+VG +  +TRER+RQI+ +A+RKL+   R + L
Sbjct: 272 QKEVLARRFGLLGYEPSTLEDVGHEIGLTRERVRQIQVEALRKLRDFLRQQGL 324


>gi|124386302|ref|YP_001028216.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126449023|ref|YP_001081831.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126450673|ref|YP_001081854.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|124294322|gb|ABN03591.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126241893|gb|ABO04986.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126243543|gb|ABO06636.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
          Length = 482

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 235 GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 294

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IA+++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 295 STYATWWIRQAISRAIAERARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 354

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 355 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 414

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 415 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 474

Query: 677 RSFLD 681
             FLD
Sbjct: 475 HDFLD 479



 Score = 40.4 bits (93), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|167822153|ref|ZP_02453624.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 9]
          Length = 299

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 52  GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 111

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 112 STYATWWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 171

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 172 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 231

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 232 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 291

Query: 677 RSFLD 681
             FLD
Sbjct: 292 HDFLD 296


>gi|153839213|ref|ZP_01991880.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149747278|gb|EDM58264.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 31  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ T R+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 91  IRQTIERALMNQTRTTRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 151 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 210

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 211 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 255


>gi|84390122|ref|ZP_00991384.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
 gi|84376776|gb|EAP93651.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
          Length = 326

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 155/226 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV  V
Sbjct: 143 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIASKLDKPVGDV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S   ++++ +    L  L P+
Sbjct: 203 SKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDSDIKNSLIFWLDELNPK 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 263 QKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEGLRRLRE 308


>gi|290959686|ref|YP_003490868.1| sigma factor HrdD [Streptomyces scabiei 87.22]
 gi|260649212|emb|CBG72326.1| sigma factor HrdD [Streptomyces scabiei 87.22]
          Length = 332

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 107/240 (44%), Positives = 153/240 (63%), Gaps = 5/240 (2%)

Query: 438 ECEASIAKKE-----MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           E EA +A  E      + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  
Sbjct: 85  ELEALVADSERAKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRK 144

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EI
Sbjct: 145 GFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEI 204

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L    + V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E 
Sbjct: 205 AAELGSNADRVTDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVLTLLRSEE 264

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              ++  L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 265 LDDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|149190125|ref|ZP_01868401.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
 gi|148836014|gb|EDL52975.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
          Length = 325

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 154/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 82  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA+KL  PV  V
Sbjct: 142 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAQKLDKPVSDV 201

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D     P  S    +++ +    L  L P+
Sbjct: 202 SKMLRLNERISSVDTPIGGDGEKALLDIIPDSTHSDPEVSTQDDDIKSSLIHWLDELNPK 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 262 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 306


>gi|307151291|ref|YP_003886675.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306981519|gb|ADN13400.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 318

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 104/247 (42%), Positives = 165/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+       AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD   G
Sbjct: 73  LRRTMAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKG 132

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++ K  R  T  E+A
Sbjct: 133 YRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQKQGRAATISELA 192

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L +    VR+ L+  ++P+SL+  +GD   + LG+ +ED    SP D A  ++L+   
Sbjct: 193 QELELTPRQVREYLERARQPLSLDLRVGDNQDTELGELLED-TGTSPEDYATHSSLQLDL 251

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            ++++ LTP++  VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+   R 
Sbjct: 252 EKLMSDLTPQQREVLALRFGLVDGQPLTLAKIGVRLNISRERVRQIEREALSKLR--KRK 309

Query: 674 KKLRSFL 680
             ++ +L
Sbjct: 310 ANIKEYL 316



 Score = 42.0 bits (97), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 6/54 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM------MMASLCESPL 162
           ++  DPVR YLRE+G + LL+ E EI +AKR++   A+      +  +L   PL
Sbjct: 5   KNPTDPVRAYLREIGRVPLLTHEEEIVLAKRVQRSMALQEIKDTLTKNLSREPL 58


>gi|17231302|ref|NP_487850.1| RNA polymerase sigma factor SigD [Nostoc sp. PCC 7120]
 gi|8489797|gb|AAF75755.1|AF262216_2 group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
 gi|17132944|dbj|BAB75509.1| group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
          Length = 332

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 101/230 (43%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  IAK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  ADGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S ++ R PT  E+A +L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQRLGRAPTAGELANELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR+ L+  + P+SL+  +GD   + LG+ +ED  A SP D  +Q++L      ++ 
Sbjct: 212 TPKQVREYLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEDFVMQSSLSNDLEVLME 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+++ V+ +RFG+      TL  +G+   ++RER+RQIE +A+ KL+
Sbjct: 271 QLTPQQKEVITLRFGLIDGQALTLARIGEILNISRERVRQIEREALTKLR 320


>gi|107026582|ref|YP_624093.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116692228|ref|YP_837761.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|105895956|gb|ABF79120.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116650228|gb|ABK10868.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
          Length = 514

 Score =  210 bits (534), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 105/246 (42%), Positives = 161/246 (65%), Gaps = 1/246 (0%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KF
Sbjct: 270 GQQKVRDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKF 329

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A + 
Sbjct: 330 STYATWWIRQAIARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAET 389

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  + +R VL +  EP+SL+TP+ D DT  L + IED+ + SP +      +R+    +
Sbjct: 390 GLAEDKLRAVLALPAEPVSLDTPLPDADTG-LVELIEDQASASPFEQLADTRMRDCVRSL 448

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  
Sbjct: 449 LRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENA 508

Query: 677 RSFLDG 682
           +SFLD 
Sbjct: 509 QSFLDA 514



 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 39/140 (27%), Positives = 75/140 (53%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++ LA ++GY+T  +L   LPP+  SS+ ++   A L+++GI V+D   +     
Sbjct: 15  DPIIQLLALAGEQGYLTHADLVDALPPESDSSDALDVVRAALADIGIAVLDEPAVPAPFA 74

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +++   A +    +         ++ DP+ +Y+R M ++ LL+REGEI +A+ IE 
Sbjct: 75  GAAPVEVDRDALDEGRAMLGDLARGTSASTDPLALYMRRMHAVPLLTREGEIVLAREIET 134

Query: 149 GRAMMMASLCESPLTFQALI 168
           GR  ++ ++   P    AL+
Sbjct: 135 GRHQVLHAIAGYPPAVDALL 154


>gi|305664513|ref|YP_003860800.1| putative sigma factor A [Maribacter sp. HTCC2170]
 gi|88708530|gb|EAR00766.1| putative sigma factor A [Maribacter sp. HTCC2170]
          Length = 287

 Score =  210 bits (534), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 105/250 (42%), Positives = 168/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    IA +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQIALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQAHERMPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M VE V++ LK +   +S++ P+   + S+L D +    + +P    +  +LR
Sbjct: 157 EIAKELDMTVEDVKQSLKNSGRHVSMDAPLIAGEDSNLYDVLRSGESPNPDRELLHESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLAGQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|113474981|ref|YP_721042.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166029|gb|ABG50569.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 496

 Score =  210 bits (534), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 110/238 (46%), Positives = 159/238 (66%), Gaps = 4/238 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV ANLRLV SVAK+Y NRGL F DLIQEG IGL++A EKFD   GYKFSTY +WW
Sbjct: 261 AKNQMVTANLRLVTSVAKRYQNRGLDFQDLIQEGVIGLLRATEKFDHTKGYKFSTYGIWW 320

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP-TPEEIAKKLAMPVEG 562
           ++QAITR+I D S  +R+PV++ + I ++ +  +++S  I+  P T EE+A ++ M  E 
Sbjct: 321 IRQAITRAICDYSRIVRLPVYLYETISQIKKIVKQIS--IECSPLTAEEVATRMEMTTEK 378

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           ++ +++  +E +SL+ PI   +     + I+  N  +P     +  L+E    VL +LT 
Sbjct: 379 LQFIIECAQETLSLDYPINKGENIIYKEMIKF-NGETPTKYVFENCLQEDVESVLKTLTE 437

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  VL+MRFG+    + TL+E+G  F +TRERIRQIEAKA+RKL+ P R+  LR ++
Sbjct: 438 RERNVLQMRFGLDDGQEKTLKEIGDTFNLTRERIRQIEAKALRKLEDPKRNHILREYI 495


>gi|228472793|ref|ZP_04057551.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
 gi|228275844|gb|EEK14610.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
          Length = 287

 Score =  210 bits (534), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 104/250 (41%), Positives = 168/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    IA + + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDKIALERLTKANLRFVVSVAKQYQNQGLTLPDLINEGNMGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQTHERVPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M V  V++ +K +   IS++ P+ + + S+L D +    + +P    +  +L+
Sbjct: 157 EIAKELDMSVNDVKESMKNSGRHISMDAPLVEGEDSNLYDVLRSGESPNPDKELMHESLK 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+G N   TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLGENYPMTLEEIGETFELTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|167717486|ref|ZP_02400722.1| RNA polymerase sigma factor [Burkholderia pseudomallei DM98]
          Length = 294

 Score =  210 bits (534), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 159/245 (64%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE   S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KF
Sbjct: 47  GEARISAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKF 106

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++  
Sbjct: 107 STYATWWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEAT 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P E +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +
Sbjct: 167 GLPAERLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSL 226

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +++ +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +   
Sbjct: 227 LKTMSAQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNA 286

Query: 677 RSFLD 681
             FLD
Sbjct: 287 HDFLD 291


>gi|254386169|ref|ZP_05001481.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194345026|gb|EDX25992.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 325

 Score =  210 bits (534), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 105/234 (44%), Positives = 150/234 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK+  + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 84  AEGERAKEVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 143

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 144 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHTEIAAELDT 203

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + V  VL   ++P+SL   + D+  +  GD +ED +A+SP  S +     E    +L 
Sbjct: 204 TAKRVGDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAISPEQSVLSLLRSEELEDLLG 263

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 264 KLDQRTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 317


>gi|154706690|ref|YP_001423754.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355976|gb|ABS77438.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 352

 Score =  209 bits (533), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 100/240 (41%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   V KG+ +A   +K+M+EANLRLV+ +A+ Y NRGL FLDLI+EGN+GLM A EKFD
Sbjct: 102 IARRVHKGDPKA---RKQMIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLMSAVEKFD 158

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WW++Q I R+I +QS T+R+P+H+  +++  +RTA++++ ++  E TP
Sbjct: 159 PERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHVIKELNVYLRTAKKLTQEVDHEATP 218

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E++A  +  PV+ +R+++ +     S++ PI ++    L D + D N + P       +L
Sbjct: 219 EDVAHLIDKPVQEIRRIMDLAPSATSIDVPISEDGQKSLVDTLADDNNIDPARLIQNVDL 278

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   R LA L  R   V+ +RFG+  N   TLE VGK   +TRER+RQI+  A+++L+H
Sbjct: 279 QDHIERWLAQLDERHREVVILRFGLHENEKGTLEAVGKAVGLTRERVRQIQIDALQQLRH 338


>gi|254509205|ref|ZP_05121302.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
 gi|219547863|gb|EED24891.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
          Length = 331

 Score =  209 bits (533), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 148 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 208 SKMLRLNERISSVDTPIGGDGEKALLDIIPDVNNSDPEVSTQDDDIKSSLVHWLDELNPK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 268 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 312


>gi|332518972|ref|ZP_08395439.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
 gi|332044820|gb|EGI81013.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
          Length = 287

 Score =  209 bits (533), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 169/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQVALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQAHERPPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M +  V++ +K +   +S++ P+ + + S+L D +    + +P    +  +LR
Sbjct: 157 EIAKELDMTINDVKESMKNSGRHVSMDAPLVEGEDSNLYDVLNSGESPNPDRELLHESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLGNQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|330446961|ref|ZP_08310612.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491152|dbj|GAA05109.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 333

 Score =  209 bits (533), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 156/226 (69%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 90  VARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATW 149

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA++L  PV+ 
Sbjct: 150 WIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAQQLEKPVDD 209

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +   S++ PIG +    L D I D+   SP  S    +++ +    L  L P
Sbjct: 210 VNRMLRLNERVSSVDNPIGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNP 269

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 KQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRRLR 315


>gi|251733353|emb|CAR82426.1| RNA polymerase sigma factor [Bradyrhizobium japonicum]
          Length = 205

 Score =  209 bits (533), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 105/178 (58%), Positives = 133/178 (74%)

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           K + LK++++  V SL LNQ+RID LVEQLYDI+KR++ +EG L+RLA S+G+ R+ FL 
Sbjct: 26  KYRKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKRLVSHEGRLMRLADSHGVAREDFLR 85

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
            + G ELDP W++         WKNFV  E D I  +R+E+  ++  TG+ I EFR IV 
Sbjct: 86  NYTGSELDPRWLNRVSKLSAKGWKNFVHIEKDRIKDLRHEVHQLAALTGLEIVEFRKIVH 145

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 146 SVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 203


>gi|163754266|ref|ZP_02161389.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
 gi|161326480|gb|EDP97806.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
          Length = 287

 Score =  209 bits (533), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 169/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    IA +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQIALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKTFAYLEQSHERIPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M V  V++ +K +   +S++ P+ + + S+L D +    + +P    +  +L+
Sbjct: 157 EIAKELDMTVNDVKESMKNSGRHVSMDAPLVEGEDSNLYDVLNSGESPNPDKELLHESLK 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLGNQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|124023660|ref|YP_001017967.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123963946|gb|ABM78702.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 313

 Score =  209 bits (533), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 165/245 (67%), Gaps = 5/245 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   M+R G      AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKF
Sbjct: 67  HQRRMIRIGRR----AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKF 122

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+
Sbjct: 123 DPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPS 182

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             EIA+ + +PV+ +  +L+      SL+ P+ G+E  S LGD I D +   PLD   Q 
Sbjct: 183 RSEIAEAMDIPVDELDSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLGEPLDKVEQR 242

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E   R L+ L+ +E+ VL++RFG+  +  HTL E+G+   V+RER+RQ+E KA+RKL
Sbjct: 243 IHHEQLGRWLSHLSEQEQHVLKLRFGLETHDRHTLAEIGRLMEVSRERVRQVELKALRKL 302

Query: 668 KHPSR 672
           ++ +R
Sbjct: 303 RNLTR 307


>gi|222056415|ref|YP_002538777.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221565704|gb|ACM21676.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 358

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +M+E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW
Sbjct: 117 ARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWW 176

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +QS TIR+PVH+ D I+K++R  R +  KI REP+ +E+A  + +    +
Sbjct: 177 IRQSIERALVNQSRTIRLPVHVSDDINKMLRITRELLQKINREPSIKEVATAMEVNSAYI 236

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+ +   L D IED + VSP +     N  E  ++   +L+  
Sbjct: 237 RRLMVLLKKTYSIERPMGENNDYFLIDTIEDTSTVSPAELLEDVNRYEMVSKWFDTLSDN 296

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+++L +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL+
Sbjct: 297 EKKILTLRFGLDDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLR 341


>gi|90580346|ref|ZP_01236153.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
 gi|90438648|gb|EAS63832.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
          Length = 337

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 156/226 (69%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 94  VARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATW 153

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA++L  PV+ 
Sbjct: 154 WIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAQQLEKPVDD 213

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +   S++ PIG +    L D I D+   SP  S    +++ +    L  L P
Sbjct: 214 VNRMLRLNERVSSVDNPIGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNP 273

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 274 KQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRRLR 319


>gi|75908113|ref|YP_322409.1| RNA polymerase sigma factor SigD [Anabaena variabilis ATCC 29413]
 gi|75701838|gb|ABA21514.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 332

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 100/230 (43%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  ADGEVAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S ++ R PT  E+A +L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQRLGRAPTAGELANELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR+ L+  + P+SL+  +GD   + LG+ +ED  A SP D  +Q++L      ++ 
Sbjct: 212 TPKQVREYLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEDFVMQSSLSNDLEVLME 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+++ V+ +RFG+      TL  +G+   ++RER+RQIE +A+ KL+
Sbjct: 271 QLTPQQKEVITLRFGLIDGQALTLARIGEILNISRERVRQIEREALTKLR 320


>gi|22124745|ref|NP_668168.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM 10]
 gi|45440189|ref|NP_991728.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108808779|ref|YP_652695.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|108810903|ref|YP_646670.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|145600262|ref|YP_001164338.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|153997601|ref|ZP_02022701.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162420853|ref|YP_001605522.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165925871|ref|ZP_02221703.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165936700|ref|ZP_02225267.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166010016|ref|ZP_02230914.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166212931|ref|ZP_02238966.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|167398742|ref|ZP_02304266.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167421704|ref|ZP_02313457.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167423190|ref|ZP_02314943.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|218930373|ref|YP_002348248.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|229838982|ref|ZP_04459141.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229896462|ref|ZP_04511630.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|229899549|ref|ZP_04514690.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229901116|ref|ZP_04516239.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|270489294|ref|ZP_06206368.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294505063|ref|YP_003569125.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957564|gb|AAM84419.1|AE013686_2 RNA polymerase, sigma S (sigma38) factor [Yersinia pestis KIM 10]
 gi|45435045|gb|AAS60605.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108774551|gb|ABG17070.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|108780692|gb|ABG14750.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|115348984|emb|CAL21944.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|145211958|gb|ABP41365.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|149289238|gb|EDM39318.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162353668|gb|ABX87616.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165915349|gb|EDR33959.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165922483|gb|EDR39660.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165990923|gb|EDR43224.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166205718|gb|EDR50198.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|166960623|gb|EDR56644.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167051246|gb|EDR62654.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167057360|gb|EDR67106.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|224483372|gb|ACN50513.1| RpoS [Yersinia pestis]
 gi|229681841|gb|EEO77934.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|229687041|gb|EEO79116.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695348|gb|EEO85395.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229700536|gb|EEO88567.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|262363123|gb|ACY59844.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367053|gb|ACY63610.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337798|gb|EFA48575.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294355522|gb|ADE65863.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320016550|gb|ADW00122.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 332

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|153207564|ref|ZP_01946247.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161829847|ref|YP_001597499.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918356|ref|ZP_02218442.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212211994|ref|YP_002302930.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212218001|ref|YP_002304788.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120576532|gb|EAX33156.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161761714|gb|ABX77356.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918006|gb|EDR36610.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212010404|gb|ACJ17785.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212012263|gb|ACJ19643.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 352

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 100/240 (41%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   V KG+ +A   +K+M+EANLRLV+ +A+ Y NRGL FLDLI+EGN+GLM A EKFD
Sbjct: 102 IARRVHKGDPKA---RKQMIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLMTAVEKFD 158

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WW++Q I R+I +QS T+R+P+H+  +++  +RTA++++ ++  E TP
Sbjct: 159 PERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHVIKELNVYLRTAKKLTQEVDHEATP 218

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E++A  +  PV+ +R+++ +     S++ PI ++    L D + D N + P       +L
Sbjct: 219 EDVAHLIDKPVQEIRRIMDLAPSATSIDVPISEDGQKSLVDTLADDNNIDPARLIQNVDL 278

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   R LA L  R   V+ +RFG+  N   TLE VGK   +TRER+RQI+  A+++L+H
Sbjct: 279 QDHIERWLAQLDERHREVVILRFGLHENEKGTLEAVGKAVGLTRERVRQIQIDALQQLRH 338


>gi|86132636|ref|ZP_01051229.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
 gi|85816878|gb|EAQ38063.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
          Length = 287

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 166/237 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SV+K+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEQLTKANLRFVVSVSKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+PEEIAK+L M ++ V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQANERPPSPEEIAKELDMTIKDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ LK +   IS++ P+ + + S+L D +    + +P  + +  +L+    R L +LTPR
Sbjct: 170 KESLKNSGRHISMDAPLVEGEDSNLYDVLNSGESPNPDRALLHESLKTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     +LEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLGDQRPMSLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|87123422|ref|ZP_01079273.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86169142|gb|EAQ70398.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 376

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 104/239 (43%), Positives = 156/239 (65%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV++VAKKY  RGL+ LDL+QEG +GL +A EKFD   G++FSTYA WW
Sbjct: 136 ARDRMIAANLRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS TIR+PVH+ +K++++ R  + ++++  R  T  ++A+KL +  E V
Sbjct: 196 IRQGITRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASQEGRIATLTDLAQKLGLSEETV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L      +SLE  +G E  + LGD +ED  A +P     +  L      +L  LT R
Sbjct: 256 RLTLMRVPRSVSLELRVGKEQDTQLGDLLEDGKA-TPEQELTRDALHHDLEHLLDELTDR 314

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  V+R+RFG+  +T  TL ++G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 315 EAAVIRLRFGLDNDTPCTLAQIGETMALSRERVRQIETRALLKLRQPQRRCKVRDYIQG 373


>gi|95930284|ref|ZP_01313022.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95133747|gb|EAT15408.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 296

 Score =  209 bits (533), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 101/251 (40%), Positives = 166/251 (66%), Gaps = 3/251 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R + + V  G+ +A   + +M+E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL
Sbjct: 42  LTAEEERALATKVEAGDEQA---RAKMIESNLRLVVKIAKRYMNRGLPFLDLIEEGNMGL 98

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D ++++++  + +  
Sbjct: 99  IKAVERFQVAKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDNVNRMLKATKEVLK 158

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K+  EP+  +IA+ +  PVE VR++ ++ K+  S+E P+GD D   L D +ED + ++P 
Sbjct: 159 KLNHEPSEAQIAEAMGAPVEEVRRLQQLVKKTYSIEHPLGDNDNYSLMDTLEDSSVINPA 218

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +     +  +   + L+SL   E  +L +RFG+      TL+ +GK++ VTRERIRQIEA
Sbjct: 219 ELLENQDQYDFVNKWLSSLKENERDILMLRFGLNDCEPETLDTIGKRYGVTRERIRQIEA 278

Query: 662 KAIRKLKHPSR 672
           K++ KL+   R
Sbjct: 279 KSLDKLRRMMR 289


>gi|89075068|ref|ZP_01161509.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
 gi|89049155|gb|EAR54720.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
          Length = 337

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 156/226 (69%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 94  VARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATW 153

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA++L  PV+ 
Sbjct: 154 WIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAQQLEKPVDD 213

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +   S++ PIG +    L D I D+   SP  S    +++ +    L  L P
Sbjct: 214 VNRMLRLNERVSSVDNPIGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNP 273

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 274 KQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRRLR 319


>gi|170735771|ref|YP_001777031.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169817959|gb|ACA92541.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 511

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 106/246 (43%), Positives = 160/246 (65%), Gaps = 1/246 (0%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KF
Sbjct: 267 GQQKVRDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKF 326

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A + 
Sbjct: 327 STYATWWIRQAIARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAET 386

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +    +R VL +  EP+SL+TP+ D DT  L + IED+ + SP +      +RE    +
Sbjct: 387 GLDEGKLRAVLALPAEPVSLDTPLPDADTG-LVELIEDQASASPFEQLADTRMRECVRAL 445

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  
Sbjct: 446 LRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENA 505

Query: 677 RSFLDG 682
           +SFLD 
Sbjct: 506 QSFLDA 511



 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 37/140 (26%), Positives = 73/140 (52%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D   +     
Sbjct: 15  DPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDEPAVPAPFA 74

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +++   A +    +         ++ DP+ +Y+R M ++ LL+REGEI +A+ IE 
Sbjct: 75  GAAPVEVDRDALDEGRAMLGDLARGTSASTDPLALYMRRMHAVPLLTREGEIVLAREIET 134

Query: 149 GRAMMMASLCESPLTFQALI 168
           GR  ++ ++   P     L+
Sbjct: 135 GRHQVLHAIAGYPPAVDVLL 154


>gi|1350861|sp|P47765|RPOS_YEREN RecName: Full=RNA polymerase sigma factor rpoS
 gi|687583|gb|AAC43391.1| RpoS [Yersinia enterocolitica]
          Length = 331

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 211 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 271 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 323


>gi|260775503|ref|ZP_05884400.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608684|gb|EEX34849.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 327

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 84  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 143

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 144 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDV 203

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 204 SKMLRLNERISSVDTPIGGDGEKALLDIIPDVNNSDPEVSTQDDDIKSSLIHWLDELNPK 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 264 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 308


>gi|238754524|ref|ZP_04615879.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
 gi|238707353|gb|EEP99715.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|291515538|emb|CBK64748.1| RNA polymerase sigma factor, sigma-70 family [Alistipes shahii WAL
           8301]
          Length = 286

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 176/268 (65%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   ++KG+ EA    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGKEELITVEEEVELAQRIKKGDQEAL---EKLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   R   + +R P+PEE+A +L +P E V   L++    +S++ P  D + + L D +
Sbjct: 139 NKAFARFEQEHERTPSPEELATELELPKEKVTDTLRVAGRHVSVDAPFADGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + ++ +     I  +L     R L +LT RE  +++  FGIG  ++ TLEE+G++F +T
Sbjct: 199 VNPDSPNADRGLINESLSTEVDRALETLTERERDIIKYFFGIG-TSEMTLEEIGEKFDLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+H SRSK L+S+L
Sbjct: 258 RERVRQIKEKAIRRLRHSSRSKLLKSYL 285


>gi|260434805|ref|ZP_05788775.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260412679|gb|EEX05975.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 312

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 106/230 (46%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 77  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 136

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + +P++ +
Sbjct: 137 IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRVEIAEAMDIPLDEL 196

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +   PL+   Q    E   R L+ L+ 
Sbjct: 197 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLDEPLEIVEQRIHHEQLGRWLSHLSE 256

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VLRMRFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 257 QEQHVLRMRFGLEGNERHTLAEIGRLMEVSRERVRQVELKALRKLRNLTR 306


>gi|238786006|ref|ZP_04629967.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
 gi|238713067|gb|EEQ05118.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|238758207|ref|ZP_04619386.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
 gi|238703537|gb|EEP96075.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|309792450|ref|ZP_07686915.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225522|gb|EFO79285.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 311

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 92/238 (38%), Positives = 157/238 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++ +NLRLV+S+A++Y   GL  LDLIQEG++GLM+A +KFD   G KFSTYA +W
Sbjct: 74  ARAQLINSNLRLVVSIARRYQGHGLSLLDLIQEGSLGLMRAVDKFDPSRGLKFSTYATYW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++ R+IAD   T+R+PVH+ +++ ++ R  +R++ ++ R+PTPEE+A +L +  + V
Sbjct: 134 IRQSVGRAIADHGRTVRLPVHLGERLSRLARARQRLTQRLDRDPTPEEVADELGITTDQV 193

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +  +    P SL+    D+ T  L + I D    +PLD      LR+     ++ LT R
Sbjct: 194 TRAEQAALTPASLDETHSDDGTGALAEVISDPLEPTPLDHVAHGLLRDDLCEAMSHLTQR 253

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  +L +R+G+   T  TLE++G++  +TRER+RQ+E++A+RKL+ P   ++L  + +
Sbjct: 254 ERSILNLRYGLEGETALTLEQIGQRLSLTRERVRQLESEALRKLRDPHLGRRLHGYFE 311


>gi|238761664|ref|ZP_04622639.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
 gi|238700178|gb|EEP92920.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDRPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 324


>gi|269925235|ref|YP_003321858.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269788895|gb|ACZ41036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 344

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 158/247 (63%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K   E   A+ +++E NLRLV+S+A++Y   G+   DLI+EGN+GLM+AAEKFDW  G
Sbjct: 97  LKKAVEEGKAARHKLIEHNLRLVVSIARRYVGHGMPLADLIEEGNLGLMRAAEKFDWRRG 156

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++QA+TR +A+   TIR+PVH+ + + K+ R  +R+S ++ REPT +E+A
Sbjct: 157 FRFSTYATWWIRQAVTRGLAEGGRTIRLPVHVGEALTKIGRETQRLSLELGREPTNQELA 216

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   +  E + +    ++ P+SLE P+G++  ++LG+ +ED  A +P   A    L E  
Sbjct: 217 EATGLSPERIDEYKNASRLPLSLEAPLGEDGETNLGEVLEDTEAANPEHIADHTMLGEDI 276

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L  R+  ++ MR+G+      TLE  G++  VTRER RQIE +A+ +L+     
Sbjct: 277 KRALERLNERQRAIIIMRYGLYGGQPMTLEAAGRKLGVTRERARQIEQEALNRLRQSDAK 336

Query: 674 KKLRSFL 680
           + L S +
Sbjct: 337 QFLASHV 343


>gi|16330303|ref|NP_441031.1| RNA polymerase sigma factor SigD [Synechocystis sp. PCC 6803]
 gi|1652792|dbj|BAA17711.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 318

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 105/242 (43%), Positives = 161/242 (66%), Gaps = 5/242 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R +   +++GE     AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  E
Sbjct: 70  IRELEKAIKEGER----AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVE 125

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R++S +  R 
Sbjct: 126 KFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQEKGRA 185

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            +  E+A+ L +  + VR+ L+ ++ P+SL+  +GD   + LGD +ED   + P D A  
Sbjct: 186 ASIAELAEHLELTPKQVREYLERSRHPLSLDLRVGDNQDTELGDLLEDDGPL-PEDFATY 244

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A+L+     ++A LTP++  VL +RFG+      TL  +G    ++RER+RQIE +A+ K
Sbjct: 245 ASLQLDLDSLMAELTPQQREVLILRFGLNDGQPLTLASIGSMLSISRERVRQIEREALNK 304

Query: 667 LK 668
           L+
Sbjct: 305 LR 306


>gi|313159603|gb|EFR58965.1| putative RNA polymerase sigma factor RpoD [Alistipes sp. HGB5]
          Length = 286

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 176/268 (65%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   ++KG+ EA    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGKEELITVEEEVELAQRIKKGDQEAL---EKLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   R   + +R P+PEE+A +L +P E V   L++    +S++ P  D + + L D +
Sbjct: 139 NKAFARFEQEHERTPSPEELATELELPKEKVTDTLRVAGRHVSVDAPFADGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + ++ +     I  +L     R L +LT RE  +++  FGIG  ++ TLEE+G++F +T
Sbjct: 199 VNPDSPNADRGLINESLSTEVDRALETLTDRERDIIKYFFGIG-TSEMTLEEIGEKFDLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+H SRSK L+S+L
Sbjct: 258 RERVRQIKEKAIRRLRHSSRSKLLKSYL 285


>gi|51595126|ref|YP_069317.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           32953]
 gi|153948385|ref|YP_001402250.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|170025640|ref|YP_001722145.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           YPIII]
 gi|186894139|ref|YP_001871251.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588408|emb|CAH20016.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Yersinia pseudotuberculosis IP
           32953]
 gi|152959880|gb|ABS47341.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|169752174|gb|ACA69692.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis YPIII]
 gi|186697165|gb|ACC87794.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis PB1/+]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|238791265|ref|ZP_04634904.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
 gi|238729398|gb|EEQ20913.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|318040801|ref|ZP_07972757.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CB0101]
          Length = 381

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 103/281 (36%), Positives = 181/281 (64%), Gaps = 9/281 (3%)

Query: 401 CEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           C V  +  +IR + ++ +  + +S++E +  +   R+       A+  M++ANLRLV++V
Sbjct: 99  CTVSELREQIRQKQQAWAEHSNLSVAELKQALHHGRR-------ARDRMIQANLRLVVAV 151

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY  RG++ LDL+QEG +GL +A EK+D   G++FSTYA WW++Q ITR+IA QS TI
Sbjct: 152 AKKYQQRGMELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAYWWIRQGITRAIATQSRTI 211

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVH+ +K++++ +  R+++ +  R  +  ++A++L +  E VR  L      +SL+T 
Sbjct: 212 RLPVHVTEKLNRIKKAQRQIATEHGRLASVSDLARELGLSEEVVRLTLMRVPRSVSLDTR 271

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G E  + LGD +ED +A +P     + +L +    +L  LT RE  V+R+R+G+  +T 
Sbjct: 272 VGREQDTQLGDLLEDSHA-TPEQELTRESLHDDLESLLEELTAREAAVIRLRYGLEDDTP 330

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TL ++G+   ++RER+RQIE++A+ KL+ P R  +++ ++
Sbjct: 331 QTLSQIGEDLHLSRERVRQIESRALLKLRQPQRRCRVQDYM 371


>gi|238797130|ref|ZP_04640632.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
 gi|238718977|gb|EEQ10791.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
          Length = 332

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|54310169|ref|YP_131189.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
 gi|46914610|emb|CAG21387.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
          Length = 342

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 96/226 (42%), Positives = 155/226 (68%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IA+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 98  IARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATW 157

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA KL  PV+ 
Sbjct: 158 WIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIALKLEKPVDD 217

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +   S++ PIG +    L D I D+   SP  S    +++ +    L  L P
Sbjct: 218 VNRMLRLNERVSSVDNPIGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNP 277

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 278 KQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRRLR 323


>gi|206563110|ref|YP_002233873.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
 gi|198039150|emb|CAR55114.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 508

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 105/246 (42%), Positives = 161/246 (65%), Gaps = 1/246 (0%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KF
Sbjct: 264 GQQKVRDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKF 323

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A + 
Sbjct: 324 STYATWWIRQAIARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAET 383

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  + +R VL +  EP+SL+TP+ D DT  L + IED+ + SP +      +R+    +
Sbjct: 384 GLAEDKLRAVLALPAEPVSLDTPLPDADTG-LVELIEDQASASPFEQLADTRMRDCVRSL 442

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  
Sbjct: 443 LRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENA 502

Query: 677 RSFLDG 682
           +SFLD 
Sbjct: 503 QSFLDA 508



 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 74/140 (52%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D   +     
Sbjct: 15  DPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDEPAVPAPFA 74

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +++   A +    +         ++ DP+ +Y+R M ++ LL+REGEI +A+ IE 
Sbjct: 75  GAAPVEVDRDALDEGRAMLGDLARGTSASTDPLALYMRRMHAVPLLTREGEIVLAREIET 134

Query: 149 GRAMMMASLCESPLTFQALI 168
           GR  ++ ++   P    AL+
Sbjct: 135 GRHQVLHAIAGYPPAVDALL 154


>gi|295838256|ref|ZP_06825189.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|197698235|gb|EDY45168.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 341

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 105/225 (46%), Positives = 146/225 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 105 AKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L    E V
Sbjct: 165 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGSTPERV 224

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 225 SDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAVSPEQSVMTLLRSEELDELIGRLDER 284

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 285 TASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 329


>gi|323493642|ref|ZP_08098763.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
 gi|323312165|gb|EGA65308.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
          Length = 326

 Score =  209 bits (531), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 143 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 203 SKMLRLNERISSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDDDIKNSLIHWLDELNPK 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 263 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 307


>gi|215404668|ref|ZP_03416849.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|298526173|ref|ZP_07013582.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
 gi|298495967|gb|EFI31261.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
          Length = 197

 Score =  209 bits (531), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 102/196 (52%), Positives = 140/196 (71%)

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + R
Sbjct: 2   EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGR 61

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+  
Sbjct: 62  EPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVS 121

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + 
Sbjct: 122 FTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMS 181

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRS+ LR +LD
Sbjct: 182 KLRHPSRSQVLRDYLD 197


>gi|123441128|ref|YP_001005116.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332160357|ref|YP_004296934.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122088089|emb|CAL10877.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318604409|emb|CBY25907.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664587|gb|ADZ41231.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859888|emb|CBX70219.1| RNA polymerase sigma factor rpoS [Yersinia enterocolitica W22703]
          Length = 332

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 324


>gi|134291946|ref|YP_001115715.1| RpoD family RNA polymerase sigma factor [Burkholderia vietnamiensis
           G4]
 gi|134135135|gb|ABO59460.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           vietnamiensis G4]
          Length = 628

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 100/237 (42%), Positives = 152/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW
Sbjct: 391 ARMGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWW 450

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D I+K+ R AR    +     TP E+A ++  P++ V
Sbjct: 451 IRQAITHALADLGRTIRVPTHTVDAINKLTRIAREHRQRSGAAATPHELAVQMGEPLDKV 510

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++ I KEP+S + P+  E      D   D +  SP D+A  A LR+T   ++  L  R
Sbjct: 511 RDLMSIVKEPMSADAPVSPEGEMTFVDVAPDVSTPSPEDAAGAAQLRDTIAAMIGRLPAR 570

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LR+F+
Sbjct: 571 EATVLRLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRASDGLDVLRAFI 627



 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 75/152 (49%), Gaps = 11/152 (7%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I     RG+VT  ++   LP D+     ++ T AML  +GI V DG        +  +L
Sbjct: 33  LISTGLTRGFVTHGDIIDALPDDDAHQGGVDATAAMLRELGIAVSDG-----AHAAGWTL 87

Query: 94  DLASSASNSS------VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           D     + S+             + +   T DPVR+YLREMG   LL+R+ EI  A+RIE
Sbjct: 88  DRYFQPTPSARAWAEGAGALAAAELSAPRTTDPVRLYLREMGMTPLLTRDEEIMHAQRIE 147

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
            GRA  +A LC  P    AL+  R E+ +G T
Sbjct: 148 RGRAASVAVLCGDPQALDALVAMRIEIAEGRT 179


>gi|261250229|ref|ZP_05942805.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
 gi|260939345|gb|EEX95331.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
          Length = 323

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 80  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 139

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 140 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDV 199

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 200 SKMLRLNERISSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDDDIKSSLIHWLDELNPK 259

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 260 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 304


>gi|302519838|ref|ZP_07272180.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302428733|gb|EFL00549.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 341

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 105/225 (46%), Positives = 146/225 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 105 AKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L    E V
Sbjct: 165 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGSTPERV 224

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 225 SDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAVSPEQSVMTLLRSEELDELIGRLDER 284

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 285 TASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 329


>gi|317493947|ref|ZP_07952364.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918274|gb|EFV39616.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 328

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 162/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV  V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDRPVTDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 208 SRMLRLNERITSVDTPLGGDSEKALLDILTDENESGPEDTTQSDDMKQSIVKWLFELNAK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 268 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 320


>gi|213963182|ref|ZP_03391440.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
 gi|213954266|gb|EEB65590.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
          Length = 287

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 104/237 (43%), Positives = 162/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIA++L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQANERVPSAEEIARELDMSVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K     IS++ P+ + + S+L D I    + +P  S I  +LR    R L +LTPR
Sbjct: 170 KESMKNAGRHISMDAPLVEGEDSNLYDVIRSNESPNPDKSLILDSLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVIRLYFGLGDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|269960386|ref|ZP_06174759.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
 gi|269834813|gb|EEZ88899.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
          Length = 255

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 101/231 (43%), Positives = 157/231 (67%), Gaps = 1/231 (0%)

Query: 439 CEA-SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           C A  +  K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 6   CVAMKLLDKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 65

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L 
Sbjct: 66  TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLD 125

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PVE V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L
Sbjct: 126 IPVEDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWL 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 186 EELNPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLR 236


>gi|33862619|ref|NP_894179.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33634535|emb|CAE20521.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 313

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 165/245 (67%), Gaps = 5/245 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   M+R G      AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKF
Sbjct: 67  HQRRMIRIGRR----AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKF 122

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+
Sbjct: 123 DPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAIPS 182

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             EIA+ + +PV+ +  +L+      SL+ P+ G+E  S LGD I D +   PLD   Q 
Sbjct: 183 RSEIAEAMDIPVDELDSLLRQALTTSSLDAPVNGEERRSFLGDLIADSSLGEPLDKVEQR 242

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E   R L+ L+ +E+ VL++RFG+  +  HTL E+G+   V+RER+RQ+E KA+RKL
Sbjct: 243 IHHEQLGRWLSHLSEQEQHVLKLRFGLETHDRHTLAEIGRLMEVSRERVRQVELKALRKL 302

Query: 668 KHPSR 672
           ++ +R
Sbjct: 303 RNLTR 307


>gi|312883942|ref|ZP_07743659.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309368400|gb|EFP95935.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 325

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 99/226 (43%), Positives = 155/226 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 82  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 142 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIALQLDKPVDDV 201

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 202 SKMLRLNERISSVDTPIGGDGEKALLDIIPDVNNSDPEVSTQDDDIKSSLIDWLDELNPK 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 262 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 307


>gi|119511025|ref|ZP_01630145.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119464276|gb|EAW45193.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 332

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 99/230 (43%), Positives = 162/230 (70%), Gaps = 1/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  ADGETAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S ++ R P+  E+A++L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQQLGRAPSAAELAQELDL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR+ L+  + P+SL+  +GD   + LG+ +ED  A SP +  +Q++L     R++ 
Sbjct: 212 TPKQVREYLERARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEEFVMQSSLSYDLERLME 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+++ V+++RFG+      TL ++G    ++RER+RQIE +A+ KL+
Sbjct: 271 ELTPQQKEVIKLRFGLLDGQALTLAKIGDILNISRERVRQIEREALTKLR 320


>gi|86141299|ref|ZP_01059845.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85831858|gb|EAQ50313.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 287

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 162/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+PEEIAK+L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQANERPPSPEEIAKELDMTVNEV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ LK     +S++ P+ + + S+L D +    + +P    +  +L     R L +LTPR
Sbjct: 170 KESLKNAGRHVSMDAPLIEGEDSNLYDVLRSGESPNPDRELLSESLSTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLGHQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|167754493|ref|ZP_02426620.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
 gi|167659118|gb|EDS03248.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
          Length = 286

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 176/268 (65%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   ++KG+ EA    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGKEELITVEEEVELAQRIKKGDQEAL---EKLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   R   + +R P+PEE+A +L +P E V   L++    +S++ P  D + + L D +
Sbjct: 139 NKAFARFEQEHERTPSPEELANELELPKEKVTDTLRVAGRHVSVDAPFADGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + ++ +     I  +L     R L +LT RE  +++  FGIG  ++ TLEE+G++F +T
Sbjct: 199 VNPDSPNADRGLINESLSTEVDRALETLTERERDIIKYFFGIGC-SEMTLEEIGEKFDLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+H SRSK L+S+L
Sbjct: 258 RERVRQIKEKAIRRLRHSSRSKLLKSYL 285


>gi|1405331|dbj|BAA11832.1| chloroplast RNA polymerase sigma subunit [Cyanidium caldarium]
          Length = 591

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 108/242 (44%), Positives = 162/242 (66%), Gaps = 10/242 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+S+AK+Y+NRG+   DLIQEG+IGL++  EKFD   G++FSTYA WW
Sbjct: 352 AKERMVTANLRLVVSIAKRYSNRGVALQDLIQEGSIGLIRGVEKFDAERGFRFSTYATWW 411

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+ITR+I+D S +IR+PVH+ D I  + +  + +  ++ R P+ EEI + + +     
Sbjct: 412 IRQSITRAISDSSRSIRLPVHVHDTISLIRKQTKALQVELGRPPSEEEICESVGIDRAKY 471

Query: 564 RKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQA----NLRETTTRVLA 618
           R V++ ++  +SLETP+   D  H LG+ +     ++P + A +      LRE+  +VL 
Sbjct: 472 RLVMECSRNIVSLETPLRSGDDVHFLGESL-----IAPEERAEENCSRDTLRESIEKVLH 526

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+ RE  V+RMRFG+      TLEEVG +F VTRERIRQIE+KA++KL+ P+ +  L  
Sbjct: 527 CLSTREREVIRMRFGLTDGRPRTLEEVGSRFNVTRERIRQIESKALKKLRTPAENNFLDE 586

Query: 679 FL 680
           +L
Sbjct: 587 YL 588


>gi|219849586|ref|YP_002464019.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543845|gb|ACL25583.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 314

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 100/279 (35%), Positives = 173/279 (62%), Gaps = 4/279 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             +I + R   + ++ E  +  +E + + + V  GE     A+ +++ +NLRLV+S+A++
Sbjct: 37  AQTIAQGRRAAERLTNEPSLHSTEKKRLAAQVAAGEQ----ARAQLINSNLRLVVSIARR 92

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL  LDLIQEG+IGLM+A +KFD   G KFSTYA +W++Q+I R+IAD S T+R+P
Sbjct: 93  YQGHGLTLLDLIQEGSIGLMRAVDKFDAGRGLKFSTYATYWIRQSIGRAIADHSRTVRLP 152

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VH+ +++ ++ R  + ++ ++ REPT EE+A    + VE V +  +    P SL+    +
Sbjct: 153 VHLGERLSRLARLRQELAQQLDREPTLEELANAAGLSVEQVERAEQAGLAPTSLDEAHTE 212

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +    L + + D    +P D   +  L+      L+ L+PRE  +LR+R+G+     HTL
Sbjct: 213 DGGGALSEILTDPLQPTPFDEVSEGMLQADVQAALSQLSPRERNILRLRYGLDGEPMHTL 272

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++G++  +TRER+RQ+E +A+RKL+ PS   +L+ +++
Sbjct: 273 EQIGQRLRLTRERVRQLEYEALRKLRDPSLYPQLQGYVN 311


>gi|14994233|gb|AAK73284.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 144

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 100/137 (72%), Positives = 116/137 (84%)

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+ 
Sbjct: 6   REATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTT 65

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              NL ET   VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 66  TNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 125

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS++LRSFLD
Sbjct: 126 RKLRHPSRSEQLRSFLD 142


>gi|90020900|ref|YP_526727.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
 gi|89950500|gb|ABD80515.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
          Length = 333

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/230 (42%), Positives = 158/230 (68%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 89  CEAS--RKRMIESNLRLVVKIARRYVNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 146

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EP+PEEIA  L  
Sbjct: 147 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPSPEEIATLLEK 206

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E V ++L + +   S++ PIG      + D + D++   P++   +++L ++    L 
Sbjct: 207 PLEDVERMLALNERVTSMDVPIGPSSEKTVVDTVADQDVSDPVELLQESDLSQSLDGWLD 266

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ ++  V+  RFG+  +   TLEEVGK+  +TRER+RQI+ +A+R+L+
Sbjct: 267 ELSEKQREVVARRFGLRGHETSTLEEVGKEIGLTRERVRQIQVEALRRLR 316


>gi|302535003|ref|ZP_07287345.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443898|gb|EFL15714.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 325

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/234 (45%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK+  + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 84  AEGERAKEVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 143

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA  L  
Sbjct: 144 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRIQREFNRENGRDPEHAEIAAALDS 203

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + V  VL   ++P+SL   + DE  +  GD +ED +A+SP  S +     E    +L 
Sbjct: 204 TEKRVGDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAISPEQSVLSLLRSEELEDLLG 263

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 264 KLDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAR 317


>gi|148243538|ref|YP_001228695.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851848|emb|CAK29342.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 370

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/238 (41%), Positives = 164/238 (68%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV++VAKKY +RG++ LDL+QEG +GL +  EK+D   G++FSTYA WW
Sbjct: 131 AKERMIQANLRLVVAVAKKYQHRGMELLDLVQEGTLGLERGVEKYDPTRGFRFSTYAYWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS TIR+PVH+ +K++++ +  R +++++ R  T ++++++L +  E V
Sbjct: 191 IRQGITRAIATQSRTIRLPVHITEKLNRIKKAQRDIASRLGRTATLKDLSQELQLSEEVV 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L      +SL+T +G +  + LGD +ED    +P     +  L +    +L  L+ R
Sbjct: 251 RQTLMRVPRSVSLDTRVGRDMDTELGDLLED-GMPTPEQRLTREKLHDDLLVLLNELSGR 309

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E RV+R+RFG+  +T  TL E+GK   ++RER+RQIE++A+ KL+ P R  ++R +++
Sbjct: 310 EARVIRLRFGLDDDTPQTLAEIGKTLDLSRERVRQIESRALHKLRLPERRGRVRDYME 367


>gi|17158751|ref|NP_478262.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|464687|sp|Q03065|RPSB_ANASP RecName: Full=RNA polymerase sigma-B factor
 gi|424021|pir||B47017 probable transcription initiation factor sigma SigB - Anabaena sp
 gi|142112|gb|AAA22046.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134700|dbj|BAB77258.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
          Length = 332

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 156/229 (68%), Gaps = 1/229 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  IAK++M++ANLRLV+S+AKKY  R L+FLDLIQEG +GL +  EKFD  LGYKFSTY
Sbjct: 93  QGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYKFSTY 152

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q ITR+IA QS TIR+P+HM DK++K+    R +S K+       EIA+ L + 
Sbjct: 153 AYWWIRQGITRAIAQQSRTIRLPIHMADKLNKIKCVQRELSQKLGYIAGVTEIAQALNLE 212

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              +R+ L++ ++P+SL+  IG E  + L D ++D + +SP   A +  L +    +LA 
Sbjct: 213 PSQIREYLQLVRQPVSLDMRIGFEQDTQLQDLLKD-DGMSPERYAERELLYQDIHNLLAK 271

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LTP+++ VL +RFG+    + TL ++ ++  ++RER+RQ+E +A+  L+
Sbjct: 272 LTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERVRQVEKQALTLLR 320


>gi|166367266|ref|YP_001659539.1| RNA polymerase sigma factor SigD [Microcystis aeruginosa NIES-843]
 gi|166089639|dbj|BAG04347.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 318

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 103/238 (43%), Positives = 163/238 (68%), Gaps = 3/238 (1%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA W
Sbjct: 82  FAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYW 141

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++    R  T  E+A++L +  + 
Sbjct: 142 WIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQDKGRAATIAELAEELDLTPKQ 201

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR  L+ +++P+SL+  +GD   + LG+ +ED   +SP D    ++L+    +++A LTP
Sbjct: 202 VRDYLERSRQPLSLDLKVGDNQDTELGELLED-TGLSPEDYTAYSSLQVDLEKLMADLTP 260

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +++ V+ +RFG+      TL ++G +  ++RER+RQIE +AI KL+   R   +R +L
Sbjct: 261 QQKEVICLRFGLDNGQPLTLAKIGVRLNISRERVRQIEREAIAKLRK--RKGNIREYL 316



 Score = 38.1 bits (87), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 2/46 (4%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++  DPVR YLRE+G + LL+ E EI  AK+++  R + +  + ES
Sbjct: 5   KNPTDPVRAYLREIGRVPLLTHEEEILYAKQVQ--RLIFLEKIKES 48


>gi|238750591|ref|ZP_04612091.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
 gi|238711239|gb|EEQ03457.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
          Length = 332

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 159/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 316


>gi|11133042|sp|Q60012|HRDD_STRVF RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|1407711|gb|AAB03580.1| sigma factor [Streptomyces viridifaciens]
          Length = 332

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 104/229 (45%), Positives = 148/229 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P E+A +L    E V
Sbjct: 156 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEVAAELGSTPERV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + D   +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 216 IDVLDWARDPVSLNMAVDDAGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGRLDQR 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 276 TASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|333030005|ref|ZP_08458066.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
 gi|332740602|gb|EGJ71084.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
          Length = 286

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 180/271 (66%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   ++KG+    +A +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIKKGD---RVALEKLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+P+E+A +L MPV+ V   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFAKFEQEYERRPSPQELADELEMPVDKVTDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L E   R L++L  RE+++++M FGIG   + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLSEEIDRALSTLEDREKQIIKMFFGIGCQ-EMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQNNRSKLLKSYL 285


>gi|33240812|ref|NP_875754.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238341|gb|AAQ00407.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 313

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 104/230 (45%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P   EIA+++ + VE +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLATIRKVSLDLAHKLGAMPNRLEIAEEMDIEVEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ GD+  S LGD I D +   PLD   Q+  +E   R L  L+ 
Sbjct: 198 DSILRQALTTSSLDAPVNGDDGRSFLGDLIADSSVEEPLDKVEQSIHQEQLGRWLTHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E K++RKL++ +R
Sbjct: 258 QEQHVLKLRFGLEGNDRHTLAEIGRLLEVSRERVRQVELKSLRKLRNLTR 307


>gi|329960773|ref|ZP_08299079.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
 gi|328532374|gb|EGF59175.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
          Length = 286

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 108/269 (40%), Positives = 178/269 (66%), Gaps = 6/269 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    IA +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RIALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D + ++   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F +
Sbjct: 199 VNDDSPMAD-RSLVNESLAREIDRALSTLTEREKEIIQMFFGIGQQ-EMTLEEIGDKFGL 256

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 257 TRERVRQIKEKAIRRLRQSNRSKLLKSYL 285


>gi|186683480|ref|YP_001866676.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186465932|gb|ACC81733.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 100/237 (42%), Positives = 160/237 (67%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M++ANLRLV+S+AKKY    L FLDLIQEG++GL +  EKFD   GYKFSTY  WW
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQRHNLDFLDLIQEGSLGLERGVEKFDPTKGYKFSTYGYWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+Q  TIR+P+H+ +K++K+ R  R ++ K+ R PT  +IA++L++  + +
Sbjct: 157 IRQAITRAIAEQGRTIRLPIHITEKLNKIKRIQRELTQKLGRTPTAVDIAEELSLDPKQI 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L + ++P+SLE  +G +    L D +ED N +SP   A    L++    +L+ L P+
Sbjct: 217 RDYLLLARQPVSLELRVGSDKDIELQDMLED-NGLSPELYADHKFLQQNIQNLLSKLNPQ 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + ++L  RFG+    + +L E+G++  ++RER+RQIE +A+  L+      K+ S+L
Sbjct: 276 QRQILTFRFGLTDGNELSLAEIGQRMGISRERVRQIEQQALGSLRR--HKDKIHSYL 330


>gi|189467039|ref|ZP_03015824.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224535443|ref|ZP_03675982.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319901765|ref|YP_004161493.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
 gi|189435303|gb|EDV04288.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224522909|gb|EEF92014.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319416796|gb|ADV43907.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
          Length = 286

 Score =  208 bits (529), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 108/269 (40%), Positives = 178/269 (66%), Gaps = 6/269 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    IA +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RIALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D + ++   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F +
Sbjct: 199 VNDDSPMAD-RSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQQ-EMTLEEIGDKFGL 256

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 257 TRERVRQIKEKAIRRLRQSNRSKLLKSYL 285


>gi|254495200|ref|ZP_05108124.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
 gi|85819552|gb|EAQ40709.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
          Length = 287

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 164/237 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+PEEIAKKL M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAFLEQENERPPSPEEIAKKLDMTVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    +  +LR    R L +LTPR
Sbjct: 170 KESMKNSGRHVSMDAPLIEGEDSNLYDVLNSGESPNPDRVLLHESLRIEINRALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+++ FG+G +   TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L ++L
Sbjct: 230 EADVVKLYFGLGEHQPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILMTYL 286


>gi|90412104|ref|ZP_01220111.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
 gi|90327082|gb|EAS43461.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
          Length = 334

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 95/226 (42%), Positives = 155/226 (68%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IA+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 90  IARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATW 149

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA +L  PV+ 
Sbjct: 150 WIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIALQLEKPVDD 209

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V ++L++ +   S++ PIG +    L D I D+   SP  S    +++ +    L  L P
Sbjct: 210 VNRMLRLNERVSSVDNPIGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNP 269

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 KQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRRLR 315


>gi|318056947|ref|ZP_07975670.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|318078687|ref|ZP_07986019.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actF]
          Length = 307

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 105/225 (46%), Positives = 146/225 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 71  AKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 130

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L    E V
Sbjct: 131 IRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGSTPERV 190

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R
Sbjct: 191 SDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAVSPEQSVMTLLRSEELDELIGRLDER 250

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 251 TASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 295


>gi|29654959|ref|NP_820651.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|81788312|sp|Q9KI19|RPOS_COXBU RecName: Full=RNA polymerase sigma factor rpoS
 gi|7340285|gb|AAF61172.1|AF244357_1 stress response sigma factor RpoS [Coxiella burnetii]
 gi|29542228|gb|AAO91165.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
          Length = 352

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   V KG+ +A   +K+M+EANLRLV+ +A+ Y NRGL FLDLI+EGN+GL+ A EKFD
Sbjct: 102 IARRVHKGDPKA---RKQMIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLLTAVEKFD 158

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WW++Q I R+I +QS T+R+P+H+  +++  +RTA++++ ++  E TP
Sbjct: 159 PERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHVIKELNVYLRTAKKLTQEVDHEATP 218

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E++A  +  PV+ +R+++ +     S++ PI ++    L D + D N + P       +L
Sbjct: 219 EDVAHLIDKPVQEIRRIMDLAPSATSIDVPISEDGQKSLVDTLADDNNIDPARLIQNVDL 278

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   R LA L  R   V+ +RFG+  N   TLE VGK   +TRER+RQI+  A+++L+H
Sbjct: 279 QDHIERWLAQLDERHREVVILRFGLHENEKGTLEAVGKAVGLTRERVRQIQIDALQQLRH 338


>gi|307324239|ref|ZP_07603447.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889970|gb|EFN20948.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 334

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 104/225 (46%), Positives = 146/225 (64%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW++QA
Sbjct: 102 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYATWWIRQA 161

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA +L   +E V  VL
Sbjct: 162 ITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEHAEIAVELGSTMERVSDVL 221

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
              ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R   +
Sbjct: 222 DWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIGRLDDRTASI 281

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           ++ R+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 282 IKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 326


>gi|218440063|ref|YP_002378392.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172791|gb|ACK71524.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 372

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 173/238 (72%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 134 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  ++ R PT +E+A+ L +  E +
Sbjct: 194 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRVLKQQLHRNPTEKELAQALEVDAENL 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +A +R+  + VL   LT 
Sbjct: 254 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDEDLQLPEEKMNEAMMRQDISAVLTDVLTE 313

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 314 REKDVIALRYGLSTSQPYTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 371


>gi|110638185|ref|YP_678394.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
 gi|110280866|gb|ABG59052.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
          Length = 287

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 100/247 (40%), Positives = 167/247 (67%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G
Sbjct: 43  IREGD---QLALEKLTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +T   +  K +REP+P+E+A
Sbjct: 100 FKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGSLNKISKTFSELEQKYEREPSPDELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L +    V   LKI+   +S++ P    + + L D +E+ +  +P  S +  +LR   
Sbjct: 160 EVLEVSTAEVVDTLKISGRHVSMDAPFVQGEENSLLDVLENSSESAPDSSLMNDSLRREV 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L++LT RE  V+ + FG+      TLEE+G++F +TRER+RQI+ KAIR+L+H SRS
Sbjct: 220 QRALSTLTQREADVISLYFGLNGEHSMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRS 279

Query: 674 KKLRSFL 680
           K L+ +L
Sbjct: 280 KALKPYL 286


>gi|124006216|ref|ZP_01691051.1| RpoD [Microscilla marina ATCC 23134]
 gi|123988140|gb|EAY27798.1| RpoD [Microscilla marina ATCC 23134]
          Length = 287

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 100/247 (40%), Positives = 168/247 (68%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G
Sbjct: 43  IREGD---QVALEKLTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +T   +  K +REP+P+E+A
Sbjct: 100 FKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGSLNKISKTFSELEQKYEREPSPDELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L +    V   LKI+   +S++ P    + + L D +E+++ V P    +  +LR+  
Sbjct: 160 EVLDVTTSEVVDTLKISGRHVSMDAPFVQGEENSLLDVLENESEVKPDSELMNDSLRKEV 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L++LT RE  V+ + FG+      TLEE+G++F +TRER+RQI+ KAIR+L+H SRS
Sbjct: 220 QRALSTLTQREADVITLYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRS 279

Query: 674 KKLRSFL 680
           K L+ +L
Sbjct: 280 KALKPYL 286


>gi|218441429|ref|YP_002379758.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7424]
 gi|218174157|gb|ACK72890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 318

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 101/225 (44%), Positives = 156/225 (69%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA WW
Sbjct: 83  AKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA++S TIR+P+H+ +K++K+ +  R++S    R  T  E+A++L +    V
Sbjct: 143 IRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQAKGRAATISELAEELELTPRQV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L+  ++P+SL+  +GD   + LG+ +ED    SP D A  ++L+    ++++ LTP+
Sbjct: 203 RDYLERARQPLSLDLKVGDNQDTELGELLED-TGTSPEDYATHSSLQVDLEKLMSDLTPQ 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+
Sbjct: 262 QKEVLALRFGLVDGQPLTLAKIGVRLNISRERVRQIEREALSKLR 306



 Score = 41.2 bits (95), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 27/38 (71%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           ++  DPVR YLRE+G + LL+ E EI +AKR++   A+
Sbjct: 5   KNPTDPVRAYLREIGRVPLLTHEEEIVLAKRVQRFMAL 42


>gi|33866155|ref|NP_897714.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639130|emb|CAE08136.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 313

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 105/230 (45%), Positives = 160/230 (69%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + +P++ +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRVEIAEAMDIPLDEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +   PLD   Q    E   R L+ L+ 
Sbjct: 198 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLDEPLDIVEQRIHHEQLGRWLSHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R
Sbjct: 258 QEQHVLKLRFGLEGNERHTLAEIGRLMDVSRERVRQVELKALRKLRNLTR 307


>gi|119468990|ref|ZP_01612015.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
 gi|119447642|gb|EAW28909.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
          Length = 324

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 102/230 (44%), Positives = 155/230 (67%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS  +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 79  CEAS--RKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+ L  
Sbjct: 137 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAECLDK 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ ++  S++ PIG E+ S L D + D+    P        + +     L 
Sbjct: 197 PVEDVTKMLRLNEKIASVDMPIGGENDSVLLDILPDEKGNGPEGEVQDTEINKHIVDWLG 256

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+R+LK
Sbjct: 257 ELNLKQREVLARRFGLLGYEPSTLEDVGREIGLTRERVRQIQVEALRRLK 306


>gi|39996625|ref|NP_952576.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|39983506|gb|AAR34899.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|298505638|gb|ADI84361.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           sulfurreducens KN400]
          Length = 328

 Score =  208 bits (529), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 154/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +M+E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW
Sbjct: 92  ARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +QS TIR+PVH+ D I+K+++  R +  ++ REP+ +E+A ++ +    V
Sbjct: 152 IRQSIERALVNQSRTIRLPVHVSDDINKMLKITRELVQRLNREPSVKEVATEMKVNSAYV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+     L D IED + VSP       N  E  ++  ASL+  
Sbjct: 212 RRLMVLLKKTYSIERPMGENSDYFLIDTIEDTSTVSPAVLLEDLNKYEIVSKWFASLSEN 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ +L +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL+
Sbjct: 272 EQTILTLRFGLEDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKLR 316


>gi|320010254|gb|ADW05104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 333

 Score =  207 bits (528), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 106/236 (44%), Positives = 151/236 (63%), Gaps = 5/236 (2%)

Query: 438 ECEASIAKKE-----MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           E EA +A+ E      + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  
Sbjct: 86  ELEALVAESERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAK 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EI
Sbjct: 146 GFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHTEI 205

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L    E V  VL   ++P+SL   + D+  +  GD +ED +A+SP  S +     E 
Sbjct: 206 AAELDTNAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAISPEQSVMTLLRSEE 265

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++  L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 266 LEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 321


>gi|326335966|ref|ZP_08202143.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325691930|gb|EGD33892.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 287

 Score =  207 bits (528), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 168/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    +A + + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDKVALERLTKANLRFVVSVAKQYQNQGLTLPDLINEGNMGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQTHERIPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L M V  V++ +K +   IS++ P+ + + S+L D +    + +P    +  +L+
Sbjct: 157 EIARELDMSVSDVKESMKNSGRHISMDAPLVEGEDSNLYDVLRSGESPNPDKELMHESLK 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  V+R+ FG+G N   TLEE+G+ F +TRER+RQI+ KAIR+LKH 
Sbjct: 217 TEIERALETLTPREADVIRLYFGLGENYPMTLEEIGETFELTRERVRQIKEKAIRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286


>gi|253573078|ref|ZP_04850470.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
 gi|251837335|gb|EES65434.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
          Length = 286

 Score =  207 bits (528), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 178/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLAREIDRALSTLTEREKEIIQMFFGIGQQ-EMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285


>gi|223937956|ref|ZP_03629855.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223893357|gb|EEF59819.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 353

 Score =  207 bits (528), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 100/235 (42%), Positives = 158/235 (67%), Gaps = 3/235 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG+ +A   +++M++ANLRLV+ +A++Y + G+  LDLI EGN+GLMKA E+FD   G
Sbjct: 109 IKKGDKKA---REQMIKANLRLVVKIAREYEDYGMPLLDLINEGNMGLMKAVERFDPAKG 165

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K STY+ WW+KQ+I R++A+QS TIR+PVH+ DK+  + + + ++   + REPT EE+ 
Sbjct: 166 AKLSTYSAWWIKQSIKRALANQSKTIRLPVHVVDKLFHMRQASVKLQEVLGREPTDEELG 225

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L    + V ++      P SLE P+GD++TS + D + D+ A +P +   +       
Sbjct: 226 DELGFSAQKVAQLRTAAIRPASLEAPLGDDETSRIADVVRDETADTPYEQLEEKTNTSML 285

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++A+L PRE  +LR RFG+  + + TLEEVG++F VTRERIRQI+  A+ KL+
Sbjct: 286 RELVATLDPREAEILRYRFGLDGDPERTLEEVGQKFGVTRERIRQIQNVALNKLR 340


>gi|294634769|ref|ZP_06713298.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
 gi|291091828|gb|EFE24389.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
          Length = 328

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 89  SRKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 148

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV  V
Sbjct: 149 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLEKPVHDV 208

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D     +++++  + L  L  +
Sbjct: 209 SRMLRLNERITSVDTPLGGDSEKALLDILTDENESGPEDCTQNDDMKQSIVKWLFELNAK 268

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 269 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 313


>gi|315185771|gb|EFU19537.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 338

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 96/235 (40%), Positives = 150/235 (63%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  M+ ANLRLV+S+AKKY +RGL  LDLI EGNIGL++A E+FD+  G +FSTY  WW+
Sbjct: 103 KNRMITANLRLVVSIAKKYQHRGLSLLDLIDEGNIGLIEAVERFDYTKGCRFSTYGTWWI 162

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAI +S+AD+S  IRIP+HM + I  V   ++ ++ ++ R+PT EE+++   +P   V 
Sbjct: 163 RQAIVKSLADKSRVIRIPIHMLNTIKNVFMLSKELAQELGRDPTEEELSRYTGLPDRRVA 222

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +++++++E  SL+  + +E+ + LGD + D     P +      LR+     L+ L+ RE
Sbjct: 223 EIMQVSQETASLDITVDEENMTTLGDLVSDDEDQGPFEKVFHRYLRDVLLEALSDLSERE 282

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             V+ +RFG+      TLEE GK   +TRER+RQI+ KA+ KL+     +  R +
Sbjct: 283 RNVISLRFGLNGEGPLTLEETGKLLGITRERVRQIQEKALAKLREMGFIRDFRHY 337


>gi|269140216|ref|YP_003296917.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|228204742|gb|ACP74149.1| RNA polymerase sigma factor [Edwardsiella tarda]
 gi|267985877|gb|ACY85706.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|304560047|gb|ADM42711.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda FL6-60]
          Length = 328

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 89  SRKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 148

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV  V
Sbjct: 149 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAERLEKPVHDV 208

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D     +++++  + L  L  +
Sbjct: 209 SRMLRLNERITSVDTPLGGDSEKALLDILTDENESGPEDCTQNDDMKQSIVKWLFELNAK 268

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 269 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 313


>gi|239942002|ref|ZP_04693939.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 15998]
 gi|239988467|ref|ZP_04709131.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 11379]
          Length = 308

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 107/239 (44%), Positives = 152/239 (63%), Gaps = 5/239 (2%)

Query: 435 RKGECEASIAKKE-----MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++ E EA +A  E      + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD
Sbjct: 58  KREELEALVADGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFD 117

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P  
Sbjct: 118 YAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEH 177

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA +L    E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +    
Sbjct: 178 AEIAAELDSNAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLR 237

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E    ++  L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 238 SEELEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 296


>gi|291445451|ref|ZP_06584841.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348398|gb|EFE75302.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 333

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 107/239 (44%), Positives = 152/239 (63%), Gaps = 5/239 (2%)

Query: 435 RKGECEASIAKKE-----MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++ E EA +A  E      + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD
Sbjct: 83  KREELEALVADGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFD 142

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P  
Sbjct: 143 YAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEH 202

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA +L    E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +    
Sbjct: 203 AEIAAELDSNAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLR 262

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E    ++  L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 263 SEELEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 321


>gi|29346721|ref|NP_810224.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|153808302|ref|ZP_01960970.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|160882661|ref|ZP_02063664.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|160891864|ref|ZP_02072867.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167762326|ref|ZP_02434453.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|218130148|ref|ZP_03458952.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|237712837|ref|ZP_04543318.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|237718434|ref|ZP_04548915.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|255693898|ref|ZP_05417573.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|260173882|ref|ZP_05760294.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides sp. D2]
 gi|262408807|ref|ZP_06085352.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270296469|ref|ZP_06202669.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|293371428|ref|ZP_06617859.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|294648199|ref|ZP_06725739.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294810777|ref|ZP_06769425.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298484065|ref|ZP_07002233.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|299149080|ref|ZP_07042142.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|315922146|ref|ZP_07918386.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|317476641|ref|ZP_07935886.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|317480344|ref|ZP_07939445.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|329955895|ref|ZP_08296698.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
 gi|29338618|gb|AAO76418.1| RNA polymerase sigma factor rpoD (Sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|149129205|gb|EDM20421.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|156111976|gb|EDO13721.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|156858342|gb|EDO51773.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167699969|gb|EDS16548.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|217987652|gb|EEC53980.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|229447165|gb|EEO52956.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|229452367|gb|EEO58158.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|260620263|gb|EEX43134.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|262353018|gb|EEZ02113.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270273873|gb|EFA19735.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|292633625|gb|EFF52183.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|292636474|gb|EFF54952.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294442110|gb|EFG10929.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298269746|gb|EFI11339.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|298513841|gb|EFI37728.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|313696021|gb|EFS32856.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|316903519|gb|EFV25372.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|316907237|gb|EFV28946.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|328525275|gb|EGF52325.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
          Length = 286

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 178/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQQ-EMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285


>gi|120434745|ref|YP_860432.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
 gi|117576895|emb|CAL65364.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
          Length = 287

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ EEIAK+L M +  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQSHERPPSAEEIAKELDMTINDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    +  +LR    R L +LTPR
Sbjct: 170 KESMKNSGRHVSMDAPLVEGEDSNLYDVLRSGESPNPDKELLHESLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVIRLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|166078602|gb|ABY81278.1| alternative sigma factor S [Listonella anguillarum]
          Length = 332

 Score =  207 bits (528), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 101/226 (44%), Positives = 154/226 (68%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  ARKRMIESNLRLVVKISRRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  P E V
Sbjct: 150 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAFQLDKP-EDV 208

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    ++RE+    L  L P+
Sbjct: 209 SKMLRLNERISSVDTPIGGDGDKALLDIIPDTNNSDPEISTQDDDIRESLLNWLDELNPK 268

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+ 
Sbjct: 269 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRE 314


>gi|332708973|ref|ZP_08428943.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352162|gb|EGJ31732.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 373

 Score =  207 bits (527), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 105/239 (43%), Positives = 171/239 (71%), Gaps = 1/239 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +AAEKFD   GYKFSTYA W
Sbjct: 134 VAKRKMIRSNLRLVVSIAKRYINRGVPFLDLIQEGALGLNRAAEKFDPDKGYKFSTYAYW 193

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P   E+A+ L + +  
Sbjct: 194 WIRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRELKQKLQRNPNELELAQALEISLSH 253

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LT 621
           +R++L++ +  +SL   +G  + + L D +ED +   P D   ++ +R+    VL+  LT
Sbjct: 254 LRQLLELRRRSLSLNHRVGKGEDTELMDLLEDNDLRLPEDKMNESMMRQEIWEVLSDVLT 313

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI++KA+RKL+ P  +++LR +L
Sbjct: 314 EREKDVISLRYGLASSEPYTLEEVGGMFNLSRERVRQIQSKAMRKLRRPQVARRLRDWL 372


>gi|182438069|ref|YP_001825788.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326778714|ref|ZP_08237979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178466585|dbj|BAG21105.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326659047|gb|EGE43893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 333

 Score =  207 bits (527), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 107/236 (45%), Positives = 151/236 (63%), Gaps = 5/236 (2%)

Query: 438 ECEASIAKKE-----MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           E EA +A+ E      + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  
Sbjct: 86  ELEALVAEGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAK 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EI
Sbjct: 146 GFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEI 205

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L    E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E 
Sbjct: 206 AAELDSNAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLRSEE 265

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++  L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK
Sbjct: 266 LEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELK 321


>gi|322420057|ref|YP_004199280.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320126444|gb|ADW14004.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 330

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 100/225 (44%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ +NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW
Sbjct: 89  ARDRMIVSNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWW 148

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +QS TIR+PVH+ D I+K++R  R +  K+ REPT +E+A  L + V  V
Sbjct: 149 IRQSIERALVNQSRTIRLPVHVSDDINKMLRVTRELVQKMNREPTIKEVADTLEVNVTYV 208

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+ +   L D IED + +SP       N  E  ++   +L+  
Sbjct: 209 RRLMVLLKKTYSIERPMGENNDYFLIDTIEDTSTISPAVLLEDLNKYELVSKWFETLSDA 268

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+++L +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL+
Sbjct: 269 EKKILTLRFGLEDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLR 313


>gi|295132793|ref|YP_003583469.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294980808|gb|ADF51273.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 287

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ EEIAK+L M +  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKTFAFLEQSHERPPSAEEIAKELDMTINDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    +  +LR    R L +LTPR
Sbjct: 170 KESMKNSGRHVSMDAPLVEGEDSNLYDVLRSGESPNPDKDLLHESLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVIRLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|116071891|ref|ZP_01469159.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116065514|gb|EAU71272.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 355

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 99/239 (41%), Positives = 160/239 (66%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW
Sbjct: 115 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 174

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + V
Sbjct: 175 IRQGMTRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTV 234

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+     +SL++ +G +  + LGD IED  A +P ++     L      +L  LT R
Sbjct: 235 RQTLERVPRSVSLDSRVGKDQDTQLGDLIEDGKA-TPEETLTHDELHNDLEGLLDELTTR 293

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  VLR RFG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P +  K+R ++ G
Sbjct: 294 EAAVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQKRSKIRDYIQG 352


>gi|153311|gb|AAA26765.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450079|prf||1920369C RNA polymerase:SUBUNIT=sigma
          Length = 325

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 105/234 (44%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK+  + +NLRLV++V ++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 84  AEGERAKEVFIRSNLRLVVAVVRRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 143

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 144 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNRENGRDPEHAEIAAELDS 203

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + V  VL   ++P+SL   + DE  +  GD +ED +A+SP  S +     E    +L 
Sbjct: 204 TEKRVGDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAISPEQSVLSLLRSEELEDLLG 263

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 264 KLDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAR 317


>gi|284009102|emb|CBA76093.1| RNA polymerase sigma factor RpoS [Arsenophonus nasoniae]
          Length = 329

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 97/224 (43%), Positives = 156/224 (69%), Gaps = 2/224 (0%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 91  QRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWWIR 150

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA++L  PV+ V +
Sbjct: 151 QTIERAIMNQTRTIRLPIHIVKELNVYLRIARELAQKLDHEPSAEEIAERLDKPVDDVSR 210

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPRE 624
           +L++ +   S++TPIG +    L D + D N   P +  IQA N++E+  + L  L  ++
Sbjct: 211 MLRLNERISSVDTPIGGDSDKALLDVLSDDNDSGP-EGTIQANNMKESIVKWLFELNAKQ 269

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 270 REVLARRFGLLGYESETLEEVGREIGLTRERVRQIQVEGLRRLK 313


>gi|291286384|ref|YP_003503200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290883544|gb|ADD67244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 322

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 97/234 (41%), Positives = 154/234 (65%), Gaps = 1/234 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ M++ NLRLV+S+AKKY NRG+  +DL++EGNIGL+KA EKFD+  G+KFSTYA WW
Sbjct: 83  SKETMIKCNLRLVVSIAKKYINRGMNLVDLVEEGNIGLLKAVEKFDYTKGFKFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R+I +Q   +RIPVHM + I KV++T   +  K+ REPT  E++    MP+  +
Sbjct: 143 IRQAIERAIINQCRMVRIPVHMSENISKVMKTQNELQQKLGREPTIHELSTACKMPLSTL 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +KV    K+  SL+ P+G +++S L +FI +D+  + P       + +E   + L  L+ 
Sbjct: 203 KKVFDAIKQDTSLDMPVGGDESSTLHEFIADDEKYLDPYLKIENTSKKEIIFKWLTFLSD 262

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            E+ ++  R+G+  N   TLE +G    +TRER+RQIE + + K+++   +KK+
Sbjct: 263 NEKTIIIRRYGLTGNDPETLESIGNDLGITRERVRQIEKRVLSKMRNLLATKKI 316


>gi|116074180|ref|ZP_01471442.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116069485|gb|EAU75237.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 364

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 117/320 (36%), Positives = 188/320 (58%), Gaps = 15/320 (4%)

Query: 365 IKRDVFLERHQGRELDP--HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           I+R + LE+ Q RE +   HW +      + EW        + +  +  E     + +  
Sbjct: 55  IQRLLELEQLQQREANHVCHWPT------KKEWAEAAGLTQEQLTTVLRE--GYGIWSDH 106

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S  E + +   +R+G      A+  M++ANLRLV++VAKKY  RGL+ LDL+QEG +GL 
Sbjct: 107 SALESKELQKRLREGRR----ARDRMIQANLRLVVTVAKKYQQRGLELLDLVQEGTLGLE 162

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +A EKFD   G++FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++++ +  + ++  
Sbjct: 163 RAVEKFDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEKLNRIKKVQQEIATN 222

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R  +  ++++ L +  E VR  L      +SLET +G +  + LGD +ED +A +P  
Sbjct: 223 EGRIASISDLSRALGISEETVRLTLMRVPRSVSLETRVGKDQDTQLGDLLEDCHA-TPEQ 281

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  + +L      +L  LT RE  V+R RFG+  +T  TL E+G+   ++RER+RQIE +
Sbjct: 282 TLTKNSLHSDLEELLGELTAREAEVIRRRFGLEDDTPLTLAEIGETMGLSRERVRQIETR 341

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+ KL+ P R  K+R ++ G
Sbjct: 342 ALLKLRQPQRRSKVRDYILG 361


>gi|15828925|ref|NP_326285.1| RNA polymerase sigma factor [Mycoplasma pulmonis UAB CTIP]
 gi|14089868|emb|CAC13627.1| DNA-DIRECTED RNA POLYMERASE SIGMA FACTOR (SIGMA-A) [Mycoplasma
           pulmonis]
          Length = 461

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 110/270 (40%), Positives = 175/270 (64%), Gaps = 9/270 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ++ +E + +   ++KG  +  IAK +++  NLRLVI+ AKKY NRGL F+DLI EGN 
Sbjct: 190 TLLTAAEEKQLAIDMKKGGLKGKIAKDKLINRNLRLVINNAKKYKNRGLSFIDLISEGNA 249

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G++KA +KFD   G+KFSTYA WW++Q+ITR++ADQ+ TIRIPVHM + I+K+++  R +
Sbjct: 250 GIIKAVQKFDESKGFKFSTYATWWIRQSITRAVADQARTIRIPVHMVETINKIIKIEREL 309

Query: 540 SNKIKREPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
             ++   PT E+IA++     +   VR + K+  +PISL+  +G E+ S   DF++D++ 
Sbjct: 310 QQELGVNPTDEQIAERYGNDYDAKKVRYIRKMNIDPISLDKTVGKENDSFFSDFVKDESV 369

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRM-RFGIGMNTD------HTLEEVGKQFC 650
           +SP+D A + +L E    +L      EERVL M R+GIG + +      HT +++  +  
Sbjct: 370 ISPIDHAAKEDLNEHLLELLNEQLTEEERVLIMKRYGIGEDENGVPYQVHTFDQLATEKN 429

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++E+IRQ E K +R+LK   + K L+ +L
Sbjct: 430 TSKEKIRQWENKILRRLKATKKRKILKEYL 459


>gi|33866957|ref|NP_898516.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639558|emb|CAE08942.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 467

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 105/257 (40%), Positives = 162/257 (63%), Gaps = 5/257 (1%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R + + +R G      AK  M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A 
Sbjct: 213 EARELKTALRNGR----RAKDHMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAV 268

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD   G++FSTYA WW++Q +TR+IA QS TIR+PVH+ +K++++ R  + ++    R
Sbjct: 269 EKFDPTRGFRFSTYAYWWIRQGMTRAIATQSRTIRLPVHVTEKLNRIKRAQQEIATNEGR 328

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             +  ++A+ L +  + VR+ L      +SL+T +G +  + LGD IED  A +P  +  
Sbjct: 329 IASIADLARALKLSEDTVRQTLARVPRSVSLDTRVGRDQDTQLGDLIEDGKA-TPEQTLT 387

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L      +L  LT RE  VLR RFG+  +T  TL ++G+   ++RER+RQIE +A+ 
Sbjct: 388 HDELHNDLEHLLDELTSREAAVLRRRFGLEDDTPQTLAQIGEALKLSRERVRQIETRALL 447

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+ P R  K+R ++ G
Sbjct: 448 KLRQPQRRSKVRDYIQG 464



 Score = 37.4 bits (85), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 46/86 (53%), Gaps = 7/86 (8%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR-------KDSADRSTDDPVRMYLRE 127
           +N  D + ++    ++D        SN S  L ++       +D   RST D +R+YL++
Sbjct: 60  VNRADPEGIQRFCRTDDGCGEPCRQSNCSTPLPRQPRRTGETRDRRSRSTTDLLRLYLQD 119

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMM 153
           +G ++LL+ E E+ +A+ ++   A++
Sbjct: 120 IGRVDLLTNEEEVTLARLVQRREALL 145


>gi|295087657|emb|CBK69180.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
          Length = 286

 Score =  207 bits (527), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 178/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELAVELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQQ-EMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285


>gi|294155544|ref|YP_003559928.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
 gi|291599870|gb|ADE19366.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
          Length = 490

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 111/266 (41%), Positives = 174/266 (65%), Gaps = 11/266 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R +  ++ KG      A+ +++  NLRLVI+ AKKY NRGL F+DLI EGN G++KA 
Sbjct: 223 EERRLAKLMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRGLTFIDLISEGNAGILKAV 282

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +K++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  ++  
Sbjct: 283 QKYNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQELGH 342

Query: 546 EPTPEEIAKKLAMPV--EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EPT  +IA +       E VR + KI  +PISL+  IG E+ S   DF++D + ++P+D 
Sbjct: 343 EPTDAQIANRFGNEYTEEKVRYIRKINIDPISLDKQIGKENDSSFSDFVKDDSVMTPVDF 402

Query: 604 AIQANLRETTTRVLASLTPREER-VLRMRFGIGMNTD------HTLEEVGKQ-FCVTRER 655
           A Q  L E    ++     R+ER ++  RFG+G++++      H+L+E+ K+   V++ER
Sbjct: 403 ASQEQLSELLLELINKSLERDERELICKRFGVGVDSEGNKYRVHSLDELAKERGGVSKER 462

Query: 656 IRQIEAKAIRKLKHPSRS-KKLRSFL 680
           +RQIE K +RKLK+ S++ + LR F+
Sbjct: 463 VRQIENKILRKLKNSSKNGRHLRDFI 488


>gi|53714034|ref|YP_100026.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|60682231|ref|YP_212375.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|253564677|ref|ZP_04842133.1| RpoD [Bacteroides sp. 3_2_5]
 gi|255010339|ref|ZP_05282465.1| putative sigma factor A [Bacteroides fragilis 3_1_12]
 gi|265766346|ref|ZP_06094387.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|313148138|ref|ZP_07810331.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
 gi|52216899|dbj|BAD49492.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|57471281|gb|AAW50926.1| RpoD [Bacteroides fragilis]
 gi|60493665|emb|CAH08454.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|251946142|gb|EES86519.1| RpoD [Bacteroides sp. 3_2_5]
 gi|263254014|gb|EEZ25479.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|301163709|emb|CBW23263.1| putative sigma factor A [Bacteroides fragilis 638R]
 gi|313136905|gb|EFR54265.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
          Length = 286

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 178/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELAGELDIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQQ-EMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285


>gi|159903877|ref|YP_001551221.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889053|gb|ABX09267.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 313

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 102/230 (44%), Positives = 158/230 (68%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  E+A+ + +  E +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSERLATIRKISSDLAHKLGAMPSRAELAEAMEIDAEEL 197

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ GD+  S LGD I D +   PLD   Q   +E   R L  L+ 
Sbjct: 198 DSILRQALTTSSLDAPVNGDDGRSFLGDLIADSSLEEPLDKVEQRIHQEQLGRWLTHLSE 257

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E+ VL++RFG+  N  HTL E+G+   V+RER+RQ+E K++RKL++ +R
Sbjct: 258 QEQHVLKLRFGLEGNERHTLAEIGRLLQVSRERVRQVELKSLRKLRNLTR 307


>gi|310766652|gb|ADP11602.1| RNA polymerase sigma factor RpoS [Erwinia sp. Ejp617]
          Length = 330

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAQKLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 322


>gi|2624188|emb|CAA05499.1| rpoS gene [Kluyvera cryocrescens]
          Length = 345

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 105 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 165 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 224

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 225 SRMLRLNERITSVDTPLGGDSEKALLDILADENENGPEDTTQDDDMKQSIVKWLFELNAK 284

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 285 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 337


>gi|298209056|ref|YP_003717235.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
 gi|83848983|gb|EAP86852.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
          Length = 287

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 100/237 (42%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SV+K+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVSKQYQNQGLTLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R PTPEEIA++L M +  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQSNQRPPTPEEIAQELEMTISEV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ LK +   +S++ P+ D + S+L D ++   + +P    +  +L+    R L +LTPR
Sbjct: 170 KESLKNSGRHLSMDAPLVDGEDSNLYDVLKFGESPNPEKDLLVESLQTEIDRALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KA R+LKH SRSK L+++L
Sbjct: 230 EADVIRLYFGLGQQQPLTLEEIGETFELTRERVRQIKEKATRRLKHTSRSKILKTYL 286


>gi|289808389|ref|ZP_06539018.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 148

 Score =  207 bits (526), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 102/146 (69%), Positives = 120/146 (82%)

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED 
Sbjct: 2   SRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDT 61

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRER
Sbjct: 62  TLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 121

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 122 IRQIEAKALRKLRHPSRSEVLRSFLD 147


>gi|313674339|ref|YP_004052335.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Marivirga
           tractuosa DSM 4126]
 gi|312941037|gb|ADR20227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marivirga
           tractuosa DSM 4126]
          Length = 287

 Score =  207 bits (526), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 98/238 (41%), Positives = 161/238 (67%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+W
Sbjct: 49  LALEKLTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVW 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I +++A+QS  +R+P++    ++K+ +T   +  K +REP+P+E+A+ L +    
Sbjct: 109 WIRQSILQALAEQSRIVRLPLNRVGSLNKISKTFSTLEQKFEREPSPDELAEVLEVTSNE 168

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V   +KI+   +S++ P    + + L D +E+    SP D  +  +LR    R L++LT 
Sbjct: 169 VVDTMKISGRHVSMDAPFVQGEENSLLDVLENDGEESPDDELMNDSLRREVQRALSTLTQ 228

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  V+ + FG+      TLEE+G++F +TRER+RQI+ KAIR+L+H SRSK L+ +L
Sbjct: 229 READVITLYFGLNGEHSMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRSKALKPYL 286


>gi|56459854|ref|YP_155135.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
 gi|56178864|gb|AAV81586.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
          Length = 322

 Score =  207 bits (526), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 98/233 (42%), Positives = 156/233 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E+NLRLV+ +A++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 81  ARRRMIESNLRLVVKIARRYSNRGLPLLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 140

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EPT E+IAK L  PV  +
Sbjct: 141 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELAHKLDHEPTAEDIAKSLNKPVGDI 200

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG ++   L D + D     P       NL+   T  L SL  +
Sbjct: 201 TKMLRLNERIGSVDTPIGGDNDKALLDILTDDADTGPEGVLQDENLKGNITEWLQSLNQK 260

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+RKL+   + + L
Sbjct: 261 QREVLARRFGLMGYEPSTLEDVGREIGLTRERVRQIQVEALRKLRDSLKQQGL 313


>gi|282896368|ref|ZP_06304389.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
 gi|281198656|gb|EFA73536.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
          Length = 332

 Score =  207 bits (526), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 99/230 (43%), Positives = 158/230 (68%), Gaps = 1/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  IAK++MVEANLRL++SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  AQGEIAKRKMVEANLRLLVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPSKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R +S  + R P+  E+A++L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRDLSQTLGRSPSIAELAQELEI 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR  L+  + P+SL+  +GD   + LG+ +ED  A SP D  IQ++L     R++ 
Sbjct: 212 TPKQVRDCLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEDYVIQSSLSSELERMMT 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LT ++  V+++RFG+      TL  +G+   ++RER+RQIE +A+ +L+
Sbjct: 271 HLTTQQREVIKLRFGLVDGQSMTLARIGEVLNISRERVRQIEREALTRLR 320


>gi|127512145|ref|YP_001093342.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637440|gb|ABO23083.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella loihica
           PV-4]
          Length = 324

 Score =  207 bits (526), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 100/231 (43%), Positives = 159/231 (68%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 81  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 138

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA++L +
Sbjct: 139 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEQLDL 198

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           P   V K+LK+ +   S++TP+G ++   L D + D + V P D  +Q  ++ ++  R L
Sbjct: 199 PSSDVSKMLKLNERITSVDTPLGGDNDKALLDVLADDDCVGP-DYKVQDDDMSKSVVRWL 257

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++L+
Sbjct: 258 DELNSKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLR 308


>gi|167469361|ref|ZP_02334065.1| RNA polymerase sigma factor RpoS [Yersinia pestis FV-1]
          Length = 277

 Score =  206 bits (525), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 163/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 37  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 97  IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 157 SRMLRLNERITSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 216

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 217 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 269


>gi|120553862|ref|YP_958213.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei
           VT8]
 gi|120323711|gb|ABM18026.1| RNA polymerase, sigma 38 subunit, RpoS [Marinobacter aquaeolei VT8]
          Length = 332

 Score =  206 bits (525), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 99/241 (41%), Positives = 158/241 (65%), Gaps = 3/241 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +   + RKGE      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 81  YFARLARKGE---ESGRKRMIESNLRLVVKIARRYVNRGLTLLDLIEEGNLGLIRAVEKF 137

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPT
Sbjct: 138 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNLYLRAARELTQKLDHEPT 197

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA+ +  PV+ V+++L + +   S++TPIG      L D + D+ A  P D     N
Sbjct: 198 AEEIARMVDKPVDDVKRMLGLNERVASMDTPIGAGSDKSLMDTVADEGASDPADLLQDNN 257

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     + +  L+ +++ VL  RFG+      TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 258 MCSCLEKWIDQLSDKQQEVLSRRFGLRGYPISTLEEVGQEIGLTRERVRQIQVEALRRLR 317

Query: 669 H 669
            
Sbjct: 318 E 318


>gi|67922139|ref|ZP_00515654.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856039|gb|EAM51283.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 318

 Score =  206 bits (525), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 104/241 (43%), Positives = 164/241 (68%), Gaps = 5/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +   S+V  GE     AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EK
Sbjct: 71  KEFCSVVEAGEA----AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEK 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R +S +  R  
Sbjct: 127 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRELSQQKGRAA 186

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T  E+A++L +  + VR  L+ +++P+SL+  +GD   + LGD +ED+   SP D A  +
Sbjct: 187 TISELAEELDLTPKQVRDYLERSRQPLSLDLRVGDNQDTELGDLLEDEGQ-SPEDFATHS 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+    +++  LT ++++V+ +RFG+      TL ++G +  ++RER+RQIE +A+ KL
Sbjct: 246 SLQFDLEKLMEDLTIQQKQVIALRFGLMDGQPLTLAKIGSRLNISRERVRQIEREALSKL 305

Query: 668 K 668
           +
Sbjct: 306 R 306



 Score = 40.4 bits (93), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 24/33 (72%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +S  DPVR YL+E+G + LLS E EI  AKR++
Sbjct: 5   KSNPDPVRAYLKEIGRVPLLSHEEEILYAKRVQ 37


>gi|254432880|ref|ZP_05046583.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
 gi|197627333|gb|EDY39892.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
          Length = 331

 Score =  206 bits (525), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 103/230 (44%), Positives = 157/230 (68%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 96  SKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + MP++ +
Sbjct: 156 IRQSMTRAIACQSRTIRLPVHLSERLSAIRKVSLDLAHKLGAMPSRHEIAEAMDMPLDEL 215

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ GDE  S LGD I D +   PLD   +    E     +  L+ 
Sbjct: 216 DGLLRQALTTSSLDAPVNGDEGRSFLGDLIADSSEEEPLDRVERGLNHEQLDHWMNHLSE 275

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +E  VL++RFG+     HTL E+G+Q  V+RER+RQ+E KA+RKL++ +R
Sbjct: 276 QERHVLQLRFGLEGRDRHTLAEIGRQLDVSRERVRQVELKALRKLRNLTR 325


>gi|242238323|ref|YP_002986504.1| RNA polymerase sigma factor RpoS [Dickeya dadantii Ech703]
 gi|242130380|gb|ACS84682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech703]
          Length = 330

 Score =  206 bits (525), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAERLDRPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSDKALLDILADEKDNGPEDTTQNNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|292487251|ref|YP_003530123.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
 gi|292900377|ref|YP_003539746.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|3183703|emb|CAA10959.1| RpoS [Erwinia amylovora]
 gi|291200225|emb|CBJ47353.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|291552670|emb|CBA19715.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
          Length = 330

 Score =  206 bits (525), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEKLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 322


>gi|311747140|ref|ZP_07720925.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
 gi|126578848|gb|EAZ83012.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
          Length = 287

 Score =  206 bits (525), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 99/247 (40%), Positives = 166/247 (67%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G
Sbjct: 43  IREGD---QLALEKLTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +T   +  + +REP+PEE+A
Sbjct: 100 FKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGSLNKISKTFSELEQRFEREPSPEELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L +    V   +KI+   +S++ P    + + L D +E+     P D  +  +LR+  
Sbjct: 160 EVLEVTANEVVDTMKISGRHVSMDAPFVQGEENSLLDVLENDGDEKPDDGLMNDSLRKEV 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L++LT RE  V+ + FG+      TLEE+G++F +TRER+RQI+ KAIR+L+H SRS
Sbjct: 220 QRALSTLTQREADVITLYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRS 279

Query: 674 KKLRSFL 680
           K L+ +L
Sbjct: 280 KTLKPYL 286


>gi|126659335|ref|ZP_01730471.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
 gi|126619417|gb|EAZ90150.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
          Length = 318

 Score =  206 bits (525), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 104/241 (43%), Positives = 164/241 (68%), Gaps = 5/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + + S++  GE     AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EK
Sbjct: 71  KELQSIIEIGEA----AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEK 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R +S +  R  
Sbjct: 127 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRELSQQKGRAA 186

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T  E+A++L +  + VR+ L+  ++P+SL+  +GD   + LGD +ED +  SP D A  +
Sbjct: 187 TVVELAEELDLTPKQVREYLERARQPLSLDLRVGDNQDTELGDLLED-DGQSPEDFATHS 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+    R++  LT +++ V+ +RFG+      TL ++G +  ++RER+RQIE +A+ KL
Sbjct: 246 SLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNISRERVRQIEREALSKL 305

Query: 668 K 668
           +
Sbjct: 306 R 306



 Score = 39.7 bits (91), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 24/33 (72%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +S  DPVR YL+E+G + LL+ E EI  AKR++
Sbjct: 5   KSNPDPVRAYLKEIGRVPLLTHEEEILYAKRVQ 37


>gi|312171353|emb|CBX79612.1| RNA polymerase sigma factor rpoS [Erwinia amylovora ATCC BAA-2158]
          Length = 330

 Score =  206 bits (525), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEKLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|297614550|gb|ADI48581.1| putative DNA-directed RNA polymerase sigma 38 subunit [uncultured
           bacterium fss6]
          Length = 322

 Score =  206 bits (525), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 101/256 (39%), Positives = 166/256 (64%), Gaps = 4/256 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  H   + RKG+ +A   +  M+E+NLRLV+ +A++YTNRGL  LDL++EGN+GL
Sbjct: 61  LSAEEEVHFSRLARKGDAKA---RARMIESNLRLVVKIARRYTNRGLALLDLVEEGNLGL 117

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++
Sbjct: 118 IRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNSYLRAARELAH 177

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSP 600
            +  EPT E+IA+KL + V  V ++L++ +   S++TP+G  D    L D + D N   P
Sbjct: 178 TLDHEPTAEDIAEKLDVSVADVSRMLRLNERVTSVDTPMGGSDNDKTLVDMLTDDNDYGP 237

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                + ++R+     L +L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+
Sbjct: 238 EGDMQEEDVRDHIMTWLENLNEKQREVLARRFGLLGYEPATLEDVGREIGLTRERVRQIQ 297

Query: 661 AKAIRKLKHPSRSKKL 676
            +A+R+L+   R + L
Sbjct: 298 VEALRRLRDMLRQQGL 313


>gi|45128589|gb|AAS55058.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  206 bits (524), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 121/277 (43%), Positives = 167/277 (60%), Gaps = 11/277 (3%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    +  S K  V  E ++ +     L   + D LV +L   
Sbjct: 218 EKFNQLRSTYQNLQLAINEYGYD--SPKATVANEMMLDVFKEFRLTPKQXDHLVNELRTA 275

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 276 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGXESSDAWLDEILASDXPYAEK---IKRN 332

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 333 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKK 392

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 393 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 452

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           VHM + I+K+ R +R+M  ++ REP PEE+A+++ MP
Sbjct: 453 VHMIETINKLNRISRQMLQEMGREPLPEELAERMQMP 489



 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 53/131 (40%), Positives = 80/131 (61%), Gaps = 3/131 (2%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
           ++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D  ++    
Sbjct: 10  EQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALNDDTNITDED 69

Query: 100 SNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   + +S+
Sbjct: 70  AAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEGINQVQSSV 128

Query: 158 CESPLTFQALI 168
            E P T   ++
Sbjct: 129 AEYPGTIPYIL 139


>gi|188534815|ref|YP_001908612.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
 gi|188029857|emb|CAO97741.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
          Length = 330

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEKLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 322


>gi|305666839|ref|YP_003863126.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
 gi|88709063|gb|EAR01297.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
          Length = 287

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 103/247 (41%), Positives = 164/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R G+    +A +++  ANLR V+SVAK+Y N+GL+  DLI EGN+GL+KAA++FD   G
Sbjct: 43  IRAGD---QVALEKLTTANLRFVVSVAKQYQNQGLKLPDLINEGNLGLVKAAKRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +    +R P+ EEIA
Sbjct: 100 FKFISYAVWWIRQSILQALAEQSRVVRLPLNKIGSINKIKKTFSYLEQAHERPPSAEEIA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L M V  V++ LK T   +S++ P+   + S+L D +    +  P    +Q +L    
Sbjct: 160 KELEMTVTEVKQSLKNTGRHVSMDAPLRQGEDSNLYDVLRSGESPRPDKILLQQSLNTEI 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L +L+PRE  V+++ +GIG     TL E+G+ F +TRER+RQI  KAIRKL+H SRS
Sbjct: 220 NRALETLSPREADVVKLYYGIGDQQSMTLAEIGQTFDLTRERVRQIREKAIRKLRHNSRS 279

Query: 674 KKLRSFL 680
           K L+++L
Sbjct: 280 KLLKTYL 286


>gi|157961021|ref|YP_001501055.1| RpoD family RNA polymerase sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846021|gb|ABV86520.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella pealeana
           ATCC 700345]
          Length = 322

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 101/231 (43%), Positives = 157/231 (67%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 79  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA KL +
Sbjct: 137 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIADKLDL 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           P   V ++LK+ +   S++TP+G E    L D + D + V P D  +Q  ++ ++  + L
Sbjct: 197 PSADVSRMLKLNERITSVDTPLGGESDKALLDVLADDDNVGP-DYKVQDEDMSKSVVKWL 255

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 256 DELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 306


>gi|189461487|ref|ZP_03010272.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198275894|ref|ZP_03208425.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
 gi|189431821|gb|EDV00806.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198271523|gb|EDY95793.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
          Length = 286

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 110/271 (40%), Positives = 177/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    IA +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RIALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGI    + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLSREIDRALSTLTEREKDIIQMFFGIN-TQEMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 285


>gi|325280261|ref|YP_004252803.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312070|gb|ADY32623.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 286

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 107/269 (39%), Positives = 176/269 (65%), Gaps = 6/269 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+ +A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGKEDLITVEEEVELAQRIRKGDQKAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   R   + +R P+PEE+A  L +P E V   L+++   IS++ P +  ED S L   
Sbjct: 139 NKAFSRFEQENERRPSPEELADSLDLPAEKVADTLRVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D + ++   + I  +L     R L++LT RE  ++++ FGI    + TLEE+G++F +
Sbjct: 199 VNDDSPIAD-RTLINESLSTEVERALSTLTERERDIIKLFFGINTQ-EMTLEEIGEKFGL 256

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI+ KAIR+L+H SRSK L+++L
Sbjct: 257 TRERVRQIKEKAIRRLRHSSRSKLLKTYL 285


>gi|170731361|ref|YP_001763308.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
 gi|169814603|gb|ACA89186.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 857

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 103/232 (44%), Positives = 152/232 (65%), Gaps = 6/232 (2%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++ M  ANL+LV  +AKKY   G    DL QEGNIGL+KA E+FDW  G+KFSTYA W
Sbjct: 514 LARERMAVANLKLVFHLAKKYRYSGEPLDDLAQEGNIGLLKAVERFDWRRGFKFSTYATW 573

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R +AD+  T+R+PVH+ +K  ++ R  + + ++  R P   EIA +L M V+ 
Sbjct: 574 WIRQQIGRHLADKCRTVRVPVHVHEKAQRLSRETQALESETGRAPELHEIAARLNMAVQK 633

Query: 563 VRKVLKITKEPISL-ETPIGDEDTSHL-GDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           V ++ ++  EP+ + E PI +     +  DF+    +  P+D   ++ L ET  ++L++L
Sbjct: 634 VAELQRLAPEPLPIHELPIDELIAVEVRSDFV----SPDPMDIVSKSELLETIDKLLSTL 689

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            P+EE+ LR+RFGIG+    TLEE+G Q+ VTRER+RQIE  A+R LKHP R
Sbjct: 690 KPKEEQTLRLRFGIGVEEALTLEEIGCQYGVTRERVRQIEVAALRNLKHPRR 741


>gi|271501815|ref|YP_003334841.1| RpoD subfamily RNA polymerase sigma-70 subunit [Dickeya dadantii
           Ech586]
 gi|270345370|gb|ACZ78135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech586]
          Length = 330

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|253700182|ref|YP_003021371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775032|gb|ACT17613.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 333

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ +NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW
Sbjct: 88  ARDRMIVSNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +QS TIR+PVH+ D I+K++R  R +  K+ REPT +E+A  L + +  V
Sbjct: 148 IRQSIERALVNQSRTIRLPVHVSDDINKMLRVTRELVQKMNREPTIKEVADTLEVNITYV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+ +   L D IED + +SP       N  E  ++   +L+  
Sbjct: 208 RRLMVLLKKTYSIERPMGENNDYFLIDTIEDTSTISPAVLLEDLNKYELVSKWFETLSDA 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+++L +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL+
Sbjct: 268 EKKILTLRFGLDDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLR 312


>gi|254424042|ref|ZP_05037760.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196191531|gb|EDX86495.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 319

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 102/232 (43%), Positives = 155/232 (66%), Gaps = 1/232 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ +NLRLV+S+AKKY    L  +DLIQEG++GL +  EKFD   GY+FSTYA WW
Sbjct: 83  AKDKMMRSNLRLVVSIAKKYRGSKLDMMDLIQEGSLGLCRGVEKFDPLKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IAD   TIR+P+H+ +K+ K+ +  R +S ++ R  T  E+A+K+++P E V
Sbjct: 143 IRQAITRAIADTGRTIRLPIHINEKLSKIRKAQREVSLELGRPATVSEVAEKVSLPAEKV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ + ++ P+SL   IG E  + LG  +E  ++ SP + A Q  L+    ++LA LT R
Sbjct: 203 RELQRQSRLPLSLNMRIGSEQNTELGALLES-DSQSPEEYATQNLLKRDIGQLLARLTER 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++ V+ MRFG+      TL ++G    ++RER+RQIE KA+R L+H  R  K
Sbjct: 262 QKDVISMRFGLDDGKKKTLAQIGHDLDISRERVRQIERKALRTLRHTGRGLK 313


>gi|317968274|ref|ZP_07969664.1| putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 382

 Score =  206 bits (524), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 100/259 (38%), Positives = 169/259 (65%), Gaps = 8/259 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +SI+E +  +   R+       A+  M++ANLRLV++VAKKY  RG++ LDL+QEG +GL
Sbjct: 121 LSIAELKQALHQGRR-------ARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGL 173

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +A EK+D   G++FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++++ +  R++++
Sbjct: 174 ERAVEKYDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEKLNRIKKAQRQIAS 233

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  R  +  ++AK+L +  E +R  L      +SL+T +G +  + LGD +ED +A +P 
Sbjct: 234 EHGRLASVADLAKELGLSEEVIRLTLMRVPRSVSLDTRVGRDQDTELGDLLEDGHA-TPE 292

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +  +  L +    +L  L+ RE  V+R+RFG+  +T  TL ++G+   ++RER+RQIE 
Sbjct: 293 QALTKTQLHDDLEALLEELSGREAEVIRLRFGLENDTPQTLSQIGEDLHLSRERVRQIET 352

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           +A+ KL+ P R  ++  +L
Sbjct: 353 RALLKLRQPQRRCRVHDYL 371


>gi|238921111|ref|YP_002934626.1| RNA polymerase sigma factor RpoS [Edwardsiella ictaluri 93-146]
 gi|238870680|gb|ACR70391.1| RNA polymerase sigma factor RpoS, putative [Edwardsiella ictaluri
           93-146]
          Length = 328

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 89  SRKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 148

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA++L  PV  V
Sbjct: 149 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAEEIAERLEKPVHDV 208

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D     +++++    L  L  +
Sbjct: 209 SRMLRLNERITSVDTPLGGDSEKALLDILTDENESGPEDCTQNDDMKQSIVNWLFELNAK 268

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 269 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 313


>gi|119492598|ref|ZP_01623816.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119453067|gb|EAW34237.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 333

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 156/237 (65%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 98  AKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFSTYAYWW 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IA    TIR+P+H+ +K++K+ R  R +  K  R PTP EIA+ L +    +
Sbjct: 158 VRQAITRAIAQNGRTIRLPIHITEKLNKIKRVQRDLVQKYGRNPTPTEIAEALELEPSQI 217

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L  ++ PISL+  +GD   + L + +ED+ A S  +      LR+    ++  LTP+
Sbjct: 218 REYLLASRHPISLDLRVGDNQDTELQELLEDETA-SADNYVTHELLRQDLKSLIDELTPQ 276

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  V+ +R+G+    + +L +VG +  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 277 QREVILLRYGLEDGKELSLSKVGARMSISRERVRQLENQALNHLRR--RKSQVREYL 331


>gi|146299193|ref|YP_001193784.1| RpoD family RNA polymerase sigma factor [Flavobacterium johnsoniae
           UW101]
 gi|57471283|gb|AAW50927.1| RpoD [Flavobacterium johnsoniae]
 gi|146153611|gb|ABQ04465.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacterium
           johnsoniae UW101]
          Length = 287

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 162/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIAK+L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYALLEQSNERPPSAEEIAKELDMTVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    I  +LR    R L +LTPR
Sbjct: 170 KESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPNPDRELIHESLRTEIERSLETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|307153454|ref|YP_003888838.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306983682|gb|ADN15563.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 372

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 106/239 (44%), Positives = 172/239 (71%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 134 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 193

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  ++ R PT +E+A+ L +  E +
Sbjct: 194 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRVLKQQLHRNPTEQELAQALEIDCEHL 253

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED+    P +   +A +R+    VL   LT 
Sbjct: 254 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDEELQLPEEKMNEAMMRQDIAAVLTDVLTE 313

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L+
Sbjct: 314 REKDVIALRYGLITSQPYTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWLN 372


>gi|152971625|ref|YP_001336734.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580660|ref|YP_002236889.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|262041489|ref|ZP_06014687.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288933843|ref|YP_003437902.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|330008320|ref|ZP_08306195.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
 gi|150956474|gb|ABR78504.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569718|gb|ACI11494.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|259041148|gb|EEW42221.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288888572|gb|ADC56890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|328535178|gb|EGF61679.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
          Length = 330

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|307132339|ref|YP_003884355.1| RNA polymerase sigma-S (sigma 38) factor [Dickeya dadantii 3937]
 gi|306529868|gb|ADM99798.1| RNA polymerase, sigma S (sigma 38) factor [Dickeya dadantii 3937]
          Length = 330

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|126667564|ref|ZP_01738534.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
 gi|126627990|gb|EAZ98617.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
          Length = 333

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +   + RKGE      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 82  YFARLARKGE---ESGRKRMIESNLRLVVKIARRYVNRGLTLLDLIEEGNLGLIRAVEKF 138

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R I +Q+ TIR+P+H+  +++  +R AR ++ ++  EPT
Sbjct: 139 DPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHVVKELNLYLRAARELTQQLDHEPT 198

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA+K+  PV+ V+++L + +   S++TPIG      L D + D+ A  P D     N
Sbjct: 199 AEEIARKVDKPVKDVKRMLGLNERVASMDTPIGAGGEKSLLDTVADEGASDPADVLQDNN 258

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     + +  L+ +++ VL  RFG+      TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 259 ISVCLQQWIDQLSEKQQEVLARRFGLRGYPVSTLEEVGQEIGLTRERVRQIQVEALRRLR 318


>gi|157369077|ref|YP_001477066.1| RNA polymerase sigma factor RpoS [Serratia proteamaculans 568]
 gi|157320841|gb|ABV39938.1| RNA polymerase, sigma 70 subunit, RpoD family [Serratia
           proteamaculans 568]
          Length = 332

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 316


>gi|209524631|ref|ZP_03273179.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495089|gb|EDZ95396.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 331

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/247 (40%), Positives = 166/247 (67%), Gaps = 8/247 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+++ +HI+        +  +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+
Sbjct: 81  LSVAQLQHILH-------QGQLAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGM 133

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R+++ 
Sbjct: 134 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLAQ 193

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R  T  E+A +L +  + +R+ L+ ++ P+SL+  +GD   + L D +ED  + SP 
Sbjct: 194 QLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLDLRVGDNQDTELVDLLED-TSNSPE 252

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             A+ ++LR     ++  LT ++ +VL +RFG+      TL ++G +  ++RER+RQIE 
Sbjct: 253 QFALNSSLRSDLESLMTDLTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRERVRQIER 312

Query: 662 KAIRKLK 668
           +A+ KL+
Sbjct: 313 EALTKLR 319


>gi|149917806|ref|ZP_01906301.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
 gi|149821326|gb|EDM80728.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
          Length = 431

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 98/243 (40%), Positives = 159/243 (65%), Gaps = 1/243 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           +   V+ VR+   +   AK + V+ANLRLV+S+A+++ +  +   DLIQEGNIGLMKA +
Sbjct: 180 YAEYVANVRRSSRKLRSAKNKFVKANLRLVVSIARRFNHGRMPLQDLIQEGNIGLMKAVD 239

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD+  G++FSTY  WW++ AI+R+IAD+   +R+PVHM D  HKV +  R +  K+ RE
Sbjct: 240 RFDYRKGFRFSTYGSWWIRHAISRAIADKGRQVRLPVHMIDAYHKVNKARRELEAKLGRE 299

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           PT EE+A+   + +  + ++   +   PISL+ P+ D D   +GDF+ED+NA  P +   
Sbjct: 300 PTREELAQHTGIALAKIERMGTMLVDNPISLDKPVSDADGRKMGDFLEDENAEDPGEGLE 359

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L E   R+++ L P E  ++R RFG+  + + TL+E+G Q+ ++RERIRQ++ +A+ 
Sbjct: 360 ADALNEQVKRLVSKLRPIEADIIRKRFGLIDDEELTLKEIGGQYSLSRERIRQLQEQALG 419

Query: 666 KLK 668
           K++
Sbjct: 420 KIR 422


>gi|251788478|ref|YP_003003199.1| RNA polymerase sigma factor RpoS [Dickeya zeae Ech1591]
 gi|247537099|gb|ACT05720.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya zeae
           Ech1591]
          Length = 330

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|270264030|ref|ZP_06192298.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
 gi|270042223|gb|EFA15319.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
          Length = 332

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 316


>gi|23428544|gb|AAL11451.1| RNA polymerase sigma-38 subunit [Serratia plymuthica]
          Length = 331

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 211 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 315


>gi|284051429|ref|ZP_06381639.1| RNA polymerase sigma factor SigD [Arthrospira platensis str.
           Paraca]
          Length = 319

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/248 (39%), Positives = 165/248 (66%), Gaps = 8/248 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S+++ +HI+        +  +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG
Sbjct: 68  NLSVAQLQHILH-------QGQLAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIG 120

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           + +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R+++
Sbjct: 121 MQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLA 180

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ R  T  E+A +L +  + +R+ L+ ++ P+SL+  +GD   + L D +ED    SP
Sbjct: 181 QQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLDLRVGDNQDTELVDLLEDTTN-SP 239

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
              A+ ++LR     ++  LT ++ +VL +RFG+      TL ++G +  ++RER+RQIE
Sbjct: 240 EQFALNSSLRSDLESLMTDLTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRERVRQIE 299

Query: 661 AKAIRKLK 668
            +A+ KL+
Sbjct: 300 REALTKLR 307


>gi|256819198|ref|YP_003140477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
 gi|256580781|gb|ACU91916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
          Length = 287

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 161/237 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIA++L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQANERVPSAEEIARELDMSVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K     IS++ P+ + + S+L D I    + +P  S I  +LR    R L +LTPR
Sbjct: 170 KESMKNAGRHISMDAPLVEGEDSNLYDVIRSNESPNPDKSLILDSLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLSDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|300718097|ref|YP_003742900.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
 gi|299063933|emb|CAX61053.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
          Length = 330

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 162/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA++L  PVE V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELTHKLDHEPSAEEIAEQLDKPVEDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 322


>gi|304413872|ref|ZP_07395289.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304283592|gb|EFL91987.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 332

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 95/246 (38%), Positives = 163/246 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+  C    +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 79  VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDP 138

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ E
Sbjct: 139 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAE 198

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S+++P+G +    L D + D +   P D+    +++
Sbjct: 199 EIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSEKALLDILSDDSENGPEDTTQNDDMK 258

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +  + L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ + +R+L+  
Sbjct: 259 HSIVKWLFELNAKQREVLARRFGLLGYEAATLENVGKEIGLTRERVRQIQVEGLRRLREI 318

Query: 671 SRSKKL 676
            +++ L
Sbjct: 319 LQTQGL 324


>gi|284036901|ref|YP_003386831.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
 gi|283816194|gb|ADB38032.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
          Length = 287

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 100/247 (40%), Positives = 164/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    ++ + + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G
Sbjct: 43  IREGD---QLSLERLTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +T   +  K +REP+PEE+A
Sbjct: 100 FKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGSLNKISKTFSDLEQKFEREPSPEELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L +    V   LKI+   +S++ P    + + L D +E+     P    I  +LR+  
Sbjct: 160 AVLEISAAEVVDTLKISGRHVSMDAPFVQGEENSLLDVLENDGEDKPDSGLINDSLRKEV 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L++LT RE  V+ + FG+      TLEE+G++F +TRER+RQI+ KAIR+L+H SRS
Sbjct: 220 QRALSTLTQREADVITLYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRS 279

Query: 674 KKLRSFL 680
           K L+++L
Sbjct: 280 KALKTYL 286


>gi|254413477|ref|ZP_05027247.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196179584|gb|EDX74578.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 331

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 104/249 (41%), Positives = 165/249 (66%), Gaps = 7/249 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S +R G+     AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD  
Sbjct: 87  SCIRAGQT----AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPT 142

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R++S  + R  T  E
Sbjct: 143 KGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQTLGRAATISE 202

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L +  + VR+ L+  ++P+SL+  +GD   + LG+ +ED +  SP D A  + ++ 
Sbjct: 203 LATELDLTPKQVREYLEKARQPLSLDLRVGDNQDTELGELLED-SGPSPEDFATYSAMQV 261

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +++A LT ++  VL +RFG+      TL ++G Q  ++RER+RQIE +A+ KL+   
Sbjct: 262 DLEKLMADLTEQQREVLMLRFGLVDGQPMTLAKIGDQLKISRERVRQIEREALSKLRK-- 319

Query: 672 RSKKLRSFL 680
           R   +R ++
Sbjct: 320 RQADMREYI 328


>gi|441116|gb|AAA61628.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|1090521|prf||2019251A RNA polymerase sigma factor
          Length = 330

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|1769596|gb|AAB39997.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 317

 Score =  206 bits (523), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 103/237 (43%), Positives = 158/237 (66%), Gaps = 4/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW
Sbjct: 83  AKQKMVEANLRLVVSVAKKYIKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+QS TIR+P+H+ +K++K+ +  R+++    R  +  E+A +L +  + V
Sbjct: 143 IRQAITRAIAEQSRTIRLPIHITEKLNKIKKAQRQLAQANGRSASIPELADELGLTTKQV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L+ +++P+SL+  +GD + + L +  +D     P D A  A L+    R+L  LT +
Sbjct: 203 RDYLEKSRQPLSLDLRVGDNNDTELIELEDDGEL--PDDYATHAALKRDLARMLNDLTAQ 260

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++ VL +RFG+   T HTL ++G+   ++RER+RQIE  ++ KL+   R  KL  +L
Sbjct: 261 QQEVLTLRFGLRDGTPHTLAKIGEHLNISRERVRQIEHGSLAKLRKQKR--KLGEYL 315


>gi|146312853|ref|YP_001177927.1| RNA polymerase sigma factor RpoS [Enterobacter sp. 638]
 gi|145319729|gb|ABP61876.1| RNA polymerase, sigma 38 subunit, RpoS [Enterobacter sp. 638]
          Length = 330

 Score =  206 bits (523), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|157374437|ref|YP_001473037.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
           HAW-EB3]
 gi|157316811|gb|ABV35909.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
           HAW-EB3]
          Length = 323

 Score =  206 bits (523), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 100/239 (41%), Positives = 161/239 (67%), Gaps = 2/239 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK       ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 70  VYFSRKALKGCGKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDP 129

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT E
Sbjct: 130 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAE 189

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           EIA+KL +P   V ++LK+ +   S++TP+G ++   L D + D ++V P D  +Q  ++
Sbjct: 190 EIAEKLDLPSADVSRMLKLNERITSVDTPLGGDNDKALLDVLADDDSVGP-DYKVQDEDM 248

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  + L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 249 SKSVVKWLDELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 307


>gi|6010728|gb|AAF01230.1|AF184099_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  206 bits (523), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|325297456|ref|YP_004257373.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
 gi|324317009|gb|ADY34900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
          Length = 286

 Score =  206 bits (523), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 177/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+     A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RAALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+Q+  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQARIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELDIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLSREIDRALSTLTDREKEIIQMFFGIG-TQEMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 285


>gi|308187918|ref|YP_003932049.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
 gi|308058428|gb|ADO10600.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
          Length = 330

 Score =  206 bits (523), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 162/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 322


>gi|197119058|ref|YP_002139485.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
 gi|197088418|gb|ACH39689.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
          Length = 333

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ +NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW
Sbjct: 88  ARDRMIVSNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +QS TIR+PVH+ D I+K++R  R +  K+ REP+ +E+A  L + V  V
Sbjct: 148 IRQSIERALVNQSRTIRLPVHVSDDINKMLRVTRELVQKMNREPSIKEVADTLEVNVTYV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+ +   L D IED + +SP       N  E  ++   +L+  
Sbjct: 208 RRLMVLLKKTYSIERPMGENNDYFLIDTIEDTSTISPAVLLEDLNKYELVSKWFETLSDA 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+++L +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL+
Sbjct: 268 EKKILTLRFGLDDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLR 312


>gi|291565943|dbj|BAI88215.1| group 2 RNA polymerase sigma factor SigD [Arthrospira platensis
           NIES-39]
          Length = 331

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 99/247 (40%), Positives = 165/247 (66%), Gaps = 8/247 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+++ +HI+        +  +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+
Sbjct: 81  LSVAQLQHILH-------QGQLAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGM 133

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R+++ 
Sbjct: 134 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLAQ 193

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ R  T  E+A +L +  + +R+ L+ ++ P+SL+  +GD   + L D +ED    SP 
Sbjct: 194 QLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLDLRVGDNQDTELVDLLEDTTN-SPE 252

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             A+ ++LR     ++  LT ++ +VL +RFG+      TL ++G +  ++RER+RQIE 
Sbjct: 253 QFALNSSLRSDLESLMTDLTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRERVRQIER 312

Query: 662 KAIRKLK 668
           +A+ KL+
Sbjct: 313 EALTKLR 319


>gi|119944449|ref|YP_942129.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
 gi|119863053|gb|ABM02530.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
          Length = 322

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 95/226 (42%), Positives = 154/226 (68%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +++K M+E+NLRLV+ ++++Y NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 81  VSRKRMIESNLRLVVKISRRYNNRGLSLLDLVEEGNLGLIRAVEKFDPEKGFRFSTYATW 140

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  K++  +RTAR +++ +  EPT EEIA+ L +  + 
Sbjct: 141 WIRQTIERAIMNQTRTIRLPIHIVKKLNVYLRTARELTHTLTHEPTAEEIAEVLGVSAKE 200

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V K+LK+ +   S++ PIG+     L D I D+   SP +   +A+++    + L  L P
Sbjct: 201 VSKILKLNERISSVDIPIGNNSDKELLDIIPDRKEASPENELQEADMKLRIVKWLEDLNP 260

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A++ L+
Sbjct: 261 KQREVLARRFGLLGYEAATLENVGKEIGLTRERVRQIQVEALKYLR 306


>gi|311278284|ref|YP_003940515.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
 gi|308747479|gb|ADO47231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|205353865|ref|YP_002227666.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273646|emb|CAR38635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|326628975|gb|EGE35318.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|16330349|ref|NP_441077.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1652838|dbj|BAA17757.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 369

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 108/238 (45%), Positives = 166/238 (69%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 132 AKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPDKGYKFSTYAYWW 191

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  ++KR P   E+A  L +    +
Sbjct: 192 IRQAITRTIANDARTIRLPIHVVEKLNKIKKAQRSLKQELKRNPNEGELAAALDITPAQL 251

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED+    P D   ++ LR     VLA  LT 
Sbjct: 252 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQQLQLPEDLMNESMLRREIVEVLAEVLTE 311

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  V+ +R+GI  +  +TLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 312 REMEVICLRYGIASHQSYTLEEVGNMFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 369


>gi|82545186|ref|YP_409133.1| RNA polymerase sigma factor RpoS [Shigella boydii Sb227]
 gi|81246597|gb|ABB67305.1| RNA polymerase sigma S factor [Shigella boydii Sb227]
 gi|332092174|gb|EGI97252.1| RNA polymerase sigma factor RpoS [Shigella boydii 3594-74]
          Length = 331

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 211 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 271 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 323


>gi|109900163|ref|YP_663418.1| RNA polymerase, sigma 28 subunit [Pseudoalteromonas atlantica T6c]
 gi|109702444|gb|ABG42364.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudoalteromonas atlantica
           T6c]
          Length = 327

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+ +NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  SRQRMIVSNLRLVVKIARRYNNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RT+R ++ K+  EPT EEIA+ +  PV  V
Sbjct: 145 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTSRELAQKLDHEPTAEEIAEAVQKPVADV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG E+ + L D I D N   P +     N++ +    L  L P+
Sbjct: 205 TKMLRLNERITSVDTPIGSENDNVLLDIIADDNGHDPEEDLQDKNVKLSIVGWLEDLNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+LK
Sbjct: 265 QREVLARRFGLLGYEPSTLEDVGVEIGLTRERVRQIQVEALRRLK 309


>gi|327405377|ref|YP_004346215.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320885|gb|AEA45377.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 288

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 104/253 (41%), Positives = 173/253 (68%), Gaps = 5/253 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + RK +     A +++  ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA+KFD 
Sbjct: 37  VELARKIKQGDQRALEKLTRANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQKFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+Q+  +R+P++    ++K+ +   R+  + +R P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQARIVRLPLNQVGSLNKINKAFSRLEQEFERPPSAE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSP-LDSAIQA- 607
           E+A+ L +P + +++ L ++   +S++ P+   ED   L D +   NA SP  D A+ A 
Sbjct: 157 ELAEALEVPEDKIKESLNVSGRHVSMDAPLSSSEDGGTLMDVM--ANADSPKADHALMAE 214

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L++   R L++LT +E  ++R+ FGIGMN   TLEE+G +F +TRER+RQI+ KAIR+L
Sbjct: 215 SLQKEIERSLSTLTDKEREIIRLFFGIGMNHGLTLEEIGAKFNLTRERVRQIKEKAIRRL 274

Query: 668 KHPSRSKKLRSFL 680
           +H SR+K L+++L
Sbjct: 275 RHTSRNKLLKAYL 287


>gi|329296050|ref|ZP_08253386.1| RNA polymerase sigma factor RpoS [Plautia stali symbiont]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 162/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|16761696|ref|NP_457313.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16766230|ref|NP_461845.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56414872|ref|YP_151947.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|62181426|ref|YP_217843.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157148284|ref|YP_001455603.1| RNA polymerase sigma factor RpoS [Citrobacter koseri ATCC BAA-895]
 gi|167550225|ref|ZP_02343982.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168230998|ref|ZP_02656056.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|168235962|ref|ZP_02661020.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|168242664|ref|ZP_02667596.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168261948|ref|ZP_02683921.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168463936|ref|ZP_02697853.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|168820376|ref|ZP_02832376.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|194442500|ref|YP_002042165.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451079|ref|YP_002046882.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194470798|ref|ZP_03076782.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194738113|ref|YP_002115873.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197263839|ref|ZP_03163913.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197363800|ref|YP_002143437.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198243199|ref|YP_002216890.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200388856|ref|ZP_03215468.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204928102|ref|ZP_03219302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|207858184|ref|YP_002244835.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213052392|ref|ZP_03345270.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213648321|ref|ZP_03378374.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|224584701|ref|YP_002638499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|237729723|ref|ZP_04560204.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|238909692|ref|ZP_04653529.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|283835495|ref|ZP_06355236.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|61236740|sp|P0A2E5|RPOS_SALTY RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236751|sp|P0A2E6|RPOS_SALTI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236761|sp|P0A2E7|RPOS_SALDU RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|1073666|pir||S49471 transcription initiation factor sigma kaltF - Salmonella
           choleraesuis
 gi|6010738|gb|AAF01235.1|AF184104_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|558645|emb|CAA57640.1| katF (rpoS) [Salmonella enterica]
 gi|602087|emb|CAA54798.1| KatF [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16421473|gb|AAL21804.1| sigma S (sigma 38) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503997|emb|CAD06030.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhi]
 gi|56129129|gb|AAV78635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|62129059|gb|AAX66762.1| sigma S (sigma 38) factor of RNA polymerase, major sigmafactor
           during stationary phase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157085489|gb|ABV15167.1| hypothetical protein CKO_04101 [Citrobacter koseri ATCC BAA-895]
 gi|194401163|gb|ACF61385.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194409383|gb|ACF69602.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194457162|gb|EDX46001.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194713615|gb|ACF92836.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195633598|gb|EDX52012.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197095277|emb|CAR60830.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|197242094|gb|EDY24714.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197290706|gb|EDY30060.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|197937715|gb|ACH75048.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|199605954|gb|EDZ04499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204322424|gb|EDZ07621.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205324779|gb|EDZ12618.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205334505|gb|EDZ21269.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205338030|gb|EDZ24794.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205342988|gb|EDZ29752.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|205349304|gb|EDZ35935.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|206709987|emb|CAR34342.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|224469228|gb|ACN47058.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|226908329|gb|EEH94247.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|261248060|emb|CBG25894.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. D23580]
 gi|267995054|gb|ACY89939.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|291068697|gb|EFE06806.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|301159483|emb|CBW19002.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. SL1344]
 gi|312913942|dbj|BAJ37916.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320087327|emb|CBY97092.1| RNA polymerase sigma factor rpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|321225598|gb|EFX50652.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614255|gb|EFY11186.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621681|gb|EFY18534.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624542|gb|EFY21375.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322628873|gb|EFY25656.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633400|gb|EFY30142.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636024|gb|EFY32732.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322639617|gb|EFY36303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646916|gb|EFY43419.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322652217|gb|EFY48576.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654704|gb|EFY51023.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322658925|gb|EFY55178.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322664508|gb|EFY60702.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668243|gb|EFY64400.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322673777|gb|EFY69878.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677838|gb|EFY73901.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681332|gb|EFY77364.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322683734|gb|EFY79744.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322715910|gb|EFZ07481.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323131276|gb|ADX18706.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323193878|gb|EFZ79081.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200347|gb|EFZ85429.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202369|gb|EFZ87413.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205603|gb|EFZ90568.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323210115|gb|EFZ95018.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323216417|gb|EGA01144.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323220766|gb|EGA05207.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323226390|gb|EGA10598.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230730|gb|EGA14848.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234919|gb|EGA19005.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238958|gb|EGA23008.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241658|gb|EGA25689.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248195|gb|EGA32131.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323251221|gb|EGA35094.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323257395|gb|EGA41091.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323263241|gb|EGA46779.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323264257|gb|EGA47763.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271083|gb|EGA54511.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624653|gb|EGE30998.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989795|gb|AEF08778.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|320662323|gb|EFX29720.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str. USDA
           5905]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|150005266|ref|YP_001300010.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212694793|ref|ZP_03302921.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|237710938|ref|ZP_04541419.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|237727237|ref|ZP_04557718.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D4]
 gi|254883735|ref|ZP_05256445.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|265750524|ref|ZP_06086587.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294777100|ref|ZP_06742557.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|319643459|ref|ZP_07998082.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
 gi|149933690|gb|ABR40388.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212662647|gb|EEB23221.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|229434093|gb|EEO44170.1| RNA polymerase sigma factor rpoD [Bacteroides dorei 5_1_36/D4]
 gi|229454782|gb|EEO60503.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|254836528|gb|EET16837.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|263237420|gb|EEZ22870.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294448969|gb|EFG17512.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|317384864|gb|EFV65820.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
          Length = 286

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 177/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   S +  +L     R L++LT RE+ +++M FGI    + TLEE+G +F
Sbjct: 199 VNDD---SPMADRSLVNESLAREIDRALSTLTEREKDIIQMFFGIN-TQEMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 255 GLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 285


>gi|307718699|ref|YP_003874231.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
 gi|306532424|gb|ADN01958.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
          Length = 338

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/224 (41%), Positives = 145/224 (64%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  M+ ANLRLV+S+AKKY +RGL  LDLI EGNIGL++A E+FD+  G +FSTY  WW+
Sbjct: 103 KNRMITANLRLVVSIAKKYQHRGLSLLDLIDEGNIGLIEAVERFDYTKGCRFSTYGTWWI 162

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAI +S+AD+S  IRIP+HM + I  V   ++ ++ ++ R+PT EE+++   +P   V 
Sbjct: 163 RQAIVKSLADKSRVIRIPIHMLNTIKNVFMLSKELAQELGRDPTEEELSRYTGLPDRRVA 222

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +++++++E  SL+  + +E+ + LGD + D     P +      L +     L  L+ RE
Sbjct: 223 EIMQVSQETASLDITVDEENMTTLGDLVSDDEDQGPFEKVFHRYLHDVLLEALGDLSERE 282

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             V+ +RFG+      TLEE GK   +TRER+RQI+ KA+ KL+
Sbjct: 283 RNVISLRFGLNGEGPLTLEETGKLLGITRERVRQIQEKALAKLR 326


>gi|253689710|ref|YP_003018900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251756288|gb|ACT14364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|317049278|ref|YP_004116926.1| RpoD subfamily RNA polymerase sigma-70 factor [Pantoea sp. At-9b]
 gi|316950895|gb|ADU70370.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pantoea sp.
           At-9b]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 162/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|16130648|ref|NP_417221.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|170082316|ref|YP_001731636.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238901878|ref|YP_002927674.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
 gi|1710676|sp|P13445|RPOS_ECOLI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|882634|gb|AAA69251.1| RNA polymerase sigma subunit RpoS (sigma-38) [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1789098|gb|AAC75783.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|23306700|gb|AAN15267.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|23306712|gb|AAN15273.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|169890151|gb|ACB03858.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238863502|gb|ACR65500.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|50122451|ref|YP_051618.1| RNA polymerase sigma factor RpoS [Pectobacterium atrosepticum
           SCRI1043]
 gi|227114060|ref|ZP_03827716.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
 gi|227327750|ref|ZP_03831774.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
 gi|49612977|emb|CAG76428.1| RNA polymerase sigma factor [Pectobacterium atrosepticum SCRI1043]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|73671310|gb|AAZ80066.1| RpoS variant [Escherichia coli LW1655F+]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|216659|dbj|BAA02747.1| RNA polymerase sigma subunit, sigma-38 [Escherichia coli]
 gi|23306698|gb|AAN15268.1| RNA polymerase sigma factor S variant [Escherichia coli]
 gi|260448208|gb|ACX38630.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           DH1]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|325287834|ref|YP_004263624.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324323288|gb|ADY30753.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 105/259 (40%), Positives = 172/259 (66%), Gaps = 3/259 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+ +E   +   +R G+ EA++ K  +  ANLR V+SVAK+Y N+GL+  DLI EGN+GL
Sbjct: 31  ITANEEVELAQKIRAGD-EAALEK--LTNANLRFVVSVAKQYQNQGLKLPDLINEGNVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKIKKAFSYLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
             +R P+ EEIAK+L + V  V++ +K +   +S++ P  + + S+L D I+   + +P 
Sbjct: 148 THERPPSAEEIAKELELSVSEVKQSMKNSGRHVSMDAPFKEGEDSNLYDVIKYGESPNPD 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  +  +L     R L +L+PRE  V+++ +GIG     TLEE+G+ F +TRER+RQI  
Sbjct: 208 EKLMHQSLNTEINRALETLSPREADVVKLYYGIGDKHSMTLEEIGQIFDLTRERVRQIRE 267

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KAIRKLKH SRSK L+++L
Sbjct: 268 KAIRKLKHNSRSKILKTYL 286


>gi|23306702|gb|AAN15269.1| RNA polymerase sigma factor S variant [Escherichia coli]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|89092114|ref|ZP_01165069.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
 gi|89083849|gb|EAR63066.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
          Length = 339

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 99/225 (44%), Positives = 151/225 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 99  ARKRMIESNLRLVVKIARRYINRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 158

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA+ +  PVE V
Sbjct: 159 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELAQKLDHEPSPEEIAELVDKPVENV 218

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L + +   S++TP+G +    L D I D  +  P      +N+     R L +L  +
Sbjct: 219 ERMLGLNERVSSVDTPMGKDSDKSLLDTIPDTVSSDPATLLQNSNISGNLDRWLDALPEK 278

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              VL  RFG+      TLEEVGK+  +TRER+RQI+ +A+RKL+
Sbjct: 279 HAEVLSRRFGLRGYEMSTLEEVGKEIGLTRERVRQIQVEALRKLR 323


>gi|15832849|ref|NP_311622.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           Sakai]
 gi|74313307|ref|YP_311726.1| RNA polymerase sigma factor RpoS [Shigella sonnei Ss046]
 gi|110642882|ref|YP_670612.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110806628|ref|YP_690148.1| RNA polymerase sigma factor RpoS [Shigella flexneri 5 str. 8401]
 gi|157157336|ref|YP_001464064.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|157162189|ref|YP_001459507.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|168749933|ref|ZP_02774955.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755487|ref|ZP_02780494.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|168778725|ref|ZP_02803732.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|168787997|ref|ZP_02813004.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|170019013|ref|YP_001723967.1| RNA polymerase sigma factor RpoS [Escherichia coli ATCC 8739]
 gi|170684160|ref|YP_001744890.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|191166775|ref|ZP_03028601.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|191171134|ref|ZP_03032684.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|193065048|ref|ZP_03046123.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|193069671|ref|ZP_03050623.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194431745|ref|ZP_03064036.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194438995|ref|ZP_03071079.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208812039|ref|ZP_03253368.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209395891|ref|YP_002272204.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920184|ref|YP_002294268.1| RNA polymerase sigma factor RpoS [Escherichia coli SE11]
 gi|217326648|ref|ZP_03442731.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218559734|ref|YP_002392647.1| RNA polymerase sigma factor RpoS [Escherichia coli S88]
 gi|218696339|ref|YP_002404006.1| RNA polymerase sigma factor RpoS [Escherichia coli 55989]
 gi|218706235|ref|YP_002413754.1| RNA polymerase sigma factor RpoS [Escherichia coli UMN026]
 gi|253772403|ref|YP_003035234.1| RNA polymerase sigma factor RpoS [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162672|ref|YP_003045780.1| RNA polymerase sigma factor RpoS [Escherichia coli B str. REL606]
 gi|256019474|ref|ZP_05433339.1| RNA polymerase sigma factor RpoS [Shigella sp. D9]
 gi|256024751|ref|ZP_05438616.1| RNA polymerase sigma factor RpoS [Escherichia sp. 4_1_40B]
 gi|260845388|ref|YP_003223166.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|260869420|ref|YP_003235822.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|261226035|ref|ZP_05940316.1| RNA polymerase sigma factor [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256708|ref|ZP_05949241.1| RNA polymerase, sigma S factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284068|ref|YP_003500886.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293406233|ref|ZP_06650159.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|293412096|ref|ZP_06654819.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|293415987|ref|ZP_06658627.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|293449062|ref|ZP_06663483.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|298381970|ref|ZP_06991567.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|300899982|ref|ZP_07118185.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|301027336|ref|ZP_07190677.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|306812377|ref|ZP_07446575.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|307139429|ref|ZP_07498785.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|307312831|ref|ZP_07592461.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|312973048|ref|ZP_07787221.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|331658855|ref|ZP_08359797.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331664297|ref|ZP_08365203.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331669480|ref|ZP_08370326.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331684360|ref|ZP_08384952.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|10197692|gb|AAG14975.1|AF242208_8 alternative sigma factor [Escherichia coli]
 gi|10197707|gb|AAG14988.1|AF242210_7 alternative sigma factor [Escherichia coli]
 gi|10197712|gb|AAG14992.1|AF242211_4 alternative sigma factor [Escherichia coli]
 gi|15529697|gb|AAL01412.1|AF410776_1 RpoS [Escherichia coli]
 gi|15529700|gb|AAL01414.1|AF410777_1 RpoS [Escherichia coli]
 gi|4887559|emb|CAB43502.1| alternative sigma factor, sigma 38 [Escherichia coli]
 gi|13363066|dbj|BAB37018.1| sigma factor RpoS [Escherichia coli O157:H7 str. Sakai]
 gi|37924617|gb|AAP59881.1| sigma S [Shigella boydii]
 gi|73856784|gb|AAZ89491.1| RNA polymerase, sigma S (sigma38) factor [Shigella sonnei Ss046]
 gi|83272618|gb|ABC00794.1| RpoS [Escherichia coli]
 gi|83272620|gb|ABC00795.1| RpoS [Escherichia coli]
 gi|83272622|gb|ABC00796.1| RpoS [Escherichia coli]
 gi|83272626|gb|ABC00798.1| RpoS [Escherichia coli]
 gi|110344474|gb|ABG70711.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110616176|gb|ABF04843.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|134036992|gb|ABO47833.1| sigma 38 factor [Escherichia coli]
 gi|134037004|gb|ABO47841.1| sigma 38 factor [Escherichia coli]
 gi|134037007|gb|ABO47843.1| sigma 38 factor [Escherichia coli]
 gi|134037010|gb|ABO47845.1| sigma 38 factor [Escherichia coli]
 gi|134037013|gb|ABO47847.1| sigma 38 factor [Escherichia coli]
 gi|157067869|gb|ABV07124.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|157079366|gb|ABV19074.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|169753941|gb|ACA76640.1| RNA polymerase, sigma 70 subunit, RpoD family [Escherichia coli
           ATCC 8739]
 gi|170521878|gb|ACB20056.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|188015788|gb|EDU53910.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003307|gb|EDU72293.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357252|gb|EDU75671.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|189372241|gb|EDU90657.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|190903146|gb|EDV62869.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|190908434|gb|EDV68023.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|192927345|gb|EDV81964.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|192957034|gb|EDV87485.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194420101|gb|EDX36179.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194422116|gb|EDX38119.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208733316|gb|EDZ82003.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209157291|gb|ACI34724.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209747660|gb|ACI72137.1| sigma factor RpoS [Escherichia coli]
 gi|209747662|gb|ACI72138.1| sigma factor RpoS [Escherichia coli]
 gi|209747664|gb|ACI72139.1| sigma factor RpoS [Escherichia coli]
 gi|209913443|dbj|BAG78517.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE11]
 gi|217319015|gb|EEC27440.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353071|emb|CAU98896.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli 55989]
 gi|218366503|emb|CAR04255.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli S88]
 gi|218433332|emb|CAR14232.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli UMN026]
 gi|222034438|emb|CAP77180.1| RNA polymerase sigma factor rpoS [Escherichia coli LF82]
 gi|242378296|emb|CAQ33073.1| RNA polymerase, sigma S (sigma 38) factor, subunit of RNA
           polymerase sigma 38 [Escherichia coli BL21(DE3)]
 gi|253323447|gb|ACT28049.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974573|gb|ACT40244.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253978740|gb|ACT44410.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|257760535|dbj|BAI32032.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|257765776|dbj|BAI37271.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|281179747|dbj|BAI56077.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE15]
 gi|290763941|gb|ADD57902.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291322152|gb|EFE61581.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|291426239|gb|EFE99271.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|291432176|gb|EFF05158.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|291468867|gb|EFF11358.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|298277110|gb|EFI18626.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|299879329|gb|EFI87540.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|300356491|gb|EFJ72361.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|305854415|gb|EFM54853.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|306907266|gb|EFN37772.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|307554720|gb|ADN47495.1| sigma factor RpoS [Escherichia coli ABU 83972]
 gi|307625683|gb|ADN69987.1| RNA polymerase sigma factor RpoS [Escherichia coli UM146]
 gi|309703100|emb|CBJ02432.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli ETEC
           H10407]
 gi|310332990|gb|EFQ00204.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|312947273|gb|ADR28100.1| RNA polymerase sigma factor RpoS [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062022|gb|ADT76349.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli W]
 gi|315615130|gb|EFU95767.1| RNA polymerase sigma factor RpoS [Escherichia coli 3431]
 gi|320186525|gb|EFW61253.1| RNA polymerase sigma factor RpoS [Shigella flexneri CDC 796-83]
 gi|320189070|gb|EFW63729.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194880|gb|EFW69509.1| RNA polymerase sigma factor RpoS [Escherichia coli WV_060327]
 gi|320202392|gb|EFW76962.1| RNA polymerase sigma factor RpoS [Escherichia coli EC4100B]
 gi|320651231|gb|EFX19666.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str. H
           2687]
 gi|320656781|gb|EFX24669.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320667375|gb|EFX34333.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323159951|gb|EFZ45921.1| RNA polymerase sigma factor RpoS [Escherichia coli E128010]
 gi|323167243|gb|EFZ52960.1| RNA polymerase sigma factor RpoS [Shigella sonnei 53G]
 gi|323172966|gb|EFZ58597.1| RNA polymerase sigma factor RpoS [Escherichia coli LT-68]
 gi|323180167|gb|EFZ65719.1| RNA polymerase sigma factor RpoS [Escherichia coli 1180]
 gi|323183273|gb|EFZ68670.1| RNA polymerase sigma factor RpoS [Escherichia coli 1357]
 gi|323188842|gb|EFZ74127.1| RNA polymerase sigma factor RpoS [Escherichia coli RN587/1]
 gi|323935702|gb|EGB32016.1| RNA polymerase sigma protein RpoS [Escherichia coli E1520]
 gi|323941428|gb|EGB37611.1| RNA polymerase sigma proteinRpoS [Escherichia coli E482]
 gi|323946373|gb|EGB42401.1| RNA polymerase sigma protein RpoS [Escherichia coli H120]
 gi|323951037|gb|EGB46913.1| RNA polymerase sigma proteinRpoS [Escherichia coli H252]
 gi|323957044|gb|EGB52769.1| RNA polymerase sigma proteinRpoS [Escherichia coli H263]
 gi|323960599|gb|EGB56225.1| RNA polymerase sigma proteinRpoS [Escherichia coli H489]
 gi|323966893|gb|EGB62322.1| RNA polymerase sigma proteinRpoS [Escherichia coli M863]
 gi|323971530|gb|EGB66763.1| RNA polymerase sigma proteinRpoS [Escherichia coli TA007]
 gi|323978651|gb|EGB73733.1| RNA polymerase sigma proteinRpoS [Escherichia coli TW10509]
 gi|324111374|gb|EGC05356.1| RNA polymerase sigma proteinRpoS [Escherichia fergusonii B253]
 gi|324119995|gb|EGC13873.1| RNA polymerase sigma proteinRpoS [Escherichia coli E1167]
 gi|325496210|gb|EGC94069.1| sigma factor RpoS [Escherichia fergusonii ECD227]
 gi|326339191|gb|EGD63006.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1044]
 gi|326342926|gb|EGD66694.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1125]
 gi|330908777|gb|EGH37291.1| RNA polymerase sigma factor RpoS [Escherichia coli AA86]
 gi|331053437|gb|EGI25466.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331058228|gb|EGI30209.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331063148|gb|EGI35061.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331077975|gb|EGI49181.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|332344623|gb|AEE57957.1| RNA polymerase sigma factor RpoS [Escherichia coli UMNK88]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|291618595|ref|YP_003521337.1| RpoS [Pantoea ananatis LMG 20103]
 gi|291153625|gb|ADD78209.1| RpoS [Pantoea ananatis LMG 20103]
 gi|327394975|dbj|BAK12397.1| RNA polymerase sigma factor RpoS [Pantoea ananatis AJ13355]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 322


>gi|260599105|ref|YP_003211676.1| RNA polymerase sigma factor RpoS [Cronobacter turicensis z3032]
 gi|260218282|emb|CBA33240.1| RNA polymerase sigma factor rpoS [Cronobacter turicensis z3032]
          Length = 351

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 111 SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 170

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 171 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 230

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 231 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 290

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 291 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 343


>gi|15803258|ref|NP_289290.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 EDL933]
 gi|12517195|gb|AAG57848.1|AE005502_2 RNA polymerase, sigma S (sigma38) factor; synthesis of many growth
           phase related proteins [Escherichia coli O157:H7 str.
           EDL933]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|319955596|ref|YP_004166863.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424256|gb|ADV51365.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 106/259 (40%), Positives = 170/259 (65%), Gaps = 3/259 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+ +E   +   +R+G+    +A +++  ANLR V+SVAK+Y N+GL   DLI EGN+GL
Sbjct: 31  ITANEEVDLAQRIREGD---QLALEKLTTANLRFVVSVAKQYQNQGLTLPDLINEGNVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++QAI +++A+QS  +R+P++    I+K+ +    +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLPLNKIGSINKIKKAFSYLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
             +R P+ EEIAK+L M V  V++ LK T   +S++ P+ + + S+L + I    + +P 
Sbjct: 148 AHERPPSAEEIAKELEMTVSEVQQSLKNTGRHVSMDAPLKEGEDSNLYNVIGSGESPNPD 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +Q +L     R L +L+ RE  V+++ +GIG     TLEE+G+ F +TRER+RQI  
Sbjct: 208 KQLLQQSLNIEINRALETLSQREADVVKLYYGIGDQHSMTLEEIGQTFDLTRERVRQIRE 267

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KAIRKLKH SRSK L+++L
Sbjct: 268 KAIRKLKHNSRSKILKTYL 286


>gi|91212108|ref|YP_542094.1| RNA polymerase sigma factor RpoS [Escherichia coli UTI89]
 gi|117624976|ref|YP_853964.1| RNA polymerase sigma factor RpoS [Escherichia coli APEC O1]
 gi|227888284|ref|ZP_04006089.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|237706630|ref|ZP_04537111.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|254037782|ref|ZP_04871840.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|300815849|ref|ZP_07096073.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300820522|ref|ZP_07100673.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300906754|ref|ZP_07124436.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300919222|ref|ZP_07135745.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300922264|ref|ZP_07138390.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300930600|ref|ZP_07145992.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300941124|ref|ZP_07155636.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300946980|ref|ZP_07161206.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300954984|ref|ZP_07167395.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300976231|ref|ZP_07173328.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300976795|ref|ZP_07173612.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|301027157|ref|ZP_07190526.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|301306156|ref|ZP_07212232.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|301326219|ref|ZP_07219602.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301645276|ref|ZP_07245227.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|309795208|ref|ZP_07689627.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|331643427|ref|ZP_08344558.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331648464|ref|ZP_08349552.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331654219|ref|ZP_08355219.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331674247|ref|ZP_08375007.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331678721|ref|ZP_08379395.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332280596|ref|ZP_08393009.1| sigma factor RpoS [Shigella sp. D9]
 gi|11036547|gb|AAG27177.1|AF270497_2 RpoS [Escherichia coli]
 gi|91073682|gb|ABE08563.1| sigma factor RpoS [Escherichia coli UTI89]
 gi|115514100|gb|ABJ02175.1| sigma factor RpoS [Escherichia coli APEC O1]
 gi|120538764|emb|CAM07120.1| sigma factor S [Escherichia coli]
 gi|226839406|gb|EEH71427.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|226899670|gb|EEH85929.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|227834553|gb|EEJ45019.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|300308576|gb|EFJ63096.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300318076|gb|EFJ67860.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300395189|gb|EFJ78727.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|300401448|gb|EFJ84986.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300409981|gb|EFJ93519.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|300413667|gb|EFJ96977.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300421394|gb|EFK04705.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300453367|gb|EFK16987.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300454167|gb|EFK17660.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300461542|gb|EFK25035.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300526786|gb|EFK47855.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300531778|gb|EFK52840.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300838588|gb|EFK66348.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|300847064|gb|EFK74824.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301076441|gb|EFK91247.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|308121179|gb|EFO58441.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|315254525|gb|EFU34493.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 85-1]
 gi|315289257|gb|EFU48652.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 110-3]
 gi|315293697|gb|EFU53049.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 153-1]
 gi|315298766|gb|EFU58020.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 16-3]
 gi|323377395|gb|ADX49663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           KO11]
 gi|324005707|gb|EGB74926.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 57-2]
 gi|324015519|gb|EGB84738.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 60-1]
 gi|324017012|gb|EGB86231.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 117-3]
 gi|331036898|gb|EGI09122.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331042211|gb|EGI14353.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331047601|gb|EGI19678.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331068341|gb|EGI39736.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331073551|gb|EGI44872.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332102948|gb|EGJ06294.1| sigma factor RpoS [Shigella sp. D9]
          Length = 342

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|320180825|gb|EFW55748.1| RNA polymerase sigma factor RpoS [Shigella boydii ATCC 9905]
          Length = 330

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|320173409|gb|EFW48608.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae CDC 74-1112]
          Length = 342

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|4100838|gb|AAD01001.1| RpoS [Escherichia coli]
 gi|4100840|gb|AAD01002.1| RpoS [Escherichia coli]
 gi|4100842|gb|AAD01003.1| RpoS [Escherichia coli]
          Length = 328

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|113475621|ref|YP_721682.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166669|gb|ABG51209.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 410

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 105/262 (40%), Positives = 165/262 (62%), Gaps = 8/262 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+++ E   I       + E   A+ +M+  NLRLV+S+AKKY NRG++ LDLIQEG +
Sbjct: 154 TGLNVKELEQI-------QTEGIEARHQMISTNLRLVVSIAKKYQNRGVELLDLIQEGTL 206

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL +A EKFD   GY+FSTYA WW++Q ITR+IA QS TIR+P+H+ +K++K+ +  +++
Sbjct: 207 GLERAVEKFDPQRGYRFSTYAYWWIRQGITRAIATQSRTIRLPIHVSEKLNKIKKVQQKI 266

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +       EEIA++L +    VR+VL      +SLET +G +  + LG+ +E K+A S
Sbjct: 267 FQEKGYTAKVEEIARELKITAAQVREVLVKIPHSVSLETKVGRDRDTELGELLETKDA-S 325

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +  I+ +L +    +L  LT RE  V+ MR+G+      +L E+     ++RER+RQI
Sbjct: 326 PEEMLIRESLVQALKELLLDLTQRERYVITMRYGLEDGRACSLSEIASALKLSRERVRQI 385

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E KA+ KL+ P    +++ +L+
Sbjct: 386 EVKALHKLRQPKFRNQIQDYLE 407


>gi|261822742|ref|YP_003260848.1| RNA polymerase sigma factor RpoS [Pectobacterium wasabiae WPP163]
 gi|5912456|emb|CAB56153.1| RpoS protein [Pectobacterium carotovorum]
 gi|261606755|gb|ACX89241.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           wasabiae WPP163]
          Length = 330

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 156/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|41861|emb|CAA78692.1| KatF [Escherichia coli]
          Length = 342

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|27735253|sp|P35540|RPOS_SHIFL RecName: Full=RNA polymerase sigma factor rpoS
 gi|332753598|gb|EGJ83977.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-671]
 gi|333000355|gb|EGK19938.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-218]
 gi|333015759|gb|EGK35097.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-304]
          Length = 330

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|269929031|ref|YP_003321352.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269788388|gb|ACZ40530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 359

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 151/229 (65%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A+++++  NLRLV+S+AKKY   GL  +DLIQEGNIGLM A E++D  LGY+FSTYA
Sbjct: 121 AKAAREKLIRHNLRLVVSIAKKYRTSGLPLIDLIQEGNIGLMTAVERYDPELGYRFSTYA 180

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            +W++QAI R++A+QS TIR+PVHM D I KV RT  ++     R  T +E+A+ L + V
Sbjct: 181 TFWIRQAIGRAVANQSRTIRVPVHMHDLISKVRRTEAQLEQLHGRPATDQELAQALDLDV 240

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E + +         SL+ PIG++  S +GD + D  +   +D A+ + +R+   R L SL
Sbjct: 241 ERIEQARSAIPRTSSLDKPIGEDGESTIGDLLPDPASDEVVDQAVTSAIRDQIRRSLESL 300

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + RE  VL +RFG+G     TL E+ + + ++RER+RQIE +A+ KL++
Sbjct: 301 SERERGVLTLRFGLGGQQPQTLAEIAEYYGISRERVRQIEKEALAKLRN 349


>gi|290511076|ref|ZP_06550445.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
 gi|289776069|gb|EFD84068.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
          Length = 347

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 107 SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 166

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 167 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 226

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 227 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 286

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 287 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 339


>gi|283786707|ref|YP_003366572.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
 gi|282950161|emb|CBG89797.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
          Length = 330

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|5804831|emb|CAB53534.1| RpoS protein [Escherichia coli O157:H7]
 gi|332087634|gb|EGI92761.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 155-74]
          Length = 298

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 58  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 118 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 177

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 178 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 237

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 238 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 290


>gi|1017750|gb|AAA79182.1| RpoS [Serratia entomophila]
          Length = 332

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV  V
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVHDV 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 212 SRMLRLNERMPSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 271

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 272 QREVLARRFGLLGYEAATLEDVGREIVLTRERVRQIQVEGLRRLR 316


>gi|301049496|ref|ZP_07196454.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
 gi|300298727|gb|EFJ55112.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
          Length = 342

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|289805538|ref|ZP_06536167.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 321

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|24114036|ref|NP_708546.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2a str. 301]
 gi|24053158|gb|AAN44253.1| similar to sigmaD(70) factor of RNA polymerase [Shigella flexneri
           2a str. 301]
 gi|281602111|gb|ADA75095.1| RNA polymerase sigma factor [Shigella flexneri 2002017]
          Length = 342

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|238896221|ref|YP_002920957.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae NTUH-K2044]
 gi|238548539|dbj|BAH64890.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 366

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 126 SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 185

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 186 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 245

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 246 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 305

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 306 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 350


>gi|120598086|ref|YP_962660.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146293843|ref|YP_001184267.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
           CN-32]
 gi|120558179|gb|ABM24106.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sp.
           W3-18-1]
 gi|145565533|gb|ABP76468.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           putrefaciens CN-32]
          Length = 326

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 98/231 (42%), Positives = 159/231 (68%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 83  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 140

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+KL +
Sbjct: 141 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQV 200

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           P   V ++LK+ ++  S++TP+G ++   L D + D ++V P D  +Q  ++  +  + L
Sbjct: 201 PSADVSRMLKLNEKITSVDTPLGGDNDKALIDILADDDSVGP-DYKVQDEDISNSVVKWL 259

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 260 NELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 310


>gi|126663248|ref|ZP_01734246.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
 gi|126624906|gb|EAZ95596.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
          Length = 287

 Score =  205 bits (521), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 162/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIAK+L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYALLEQSNERPPSAEEIAKELDMTVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    I  +L+    R L +LTPR
Sbjct: 170 KESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPNPDRELIHESLQTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|213859421|ref|ZP_03385125.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 319

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|57864855|gb|AAW57030.1| putative group 2 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 368

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 171/238 (71%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 130 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 189

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +
Sbjct: 190 IRQAITRTIANDARTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVSPSQL 249

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +  LR   + VL+  LT 
Sbjct: 250 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEELMNEGMLRYEVSAVLSDVLTQ 309

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 310 REKDVISLRYGLCTSQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 367


>gi|296104425|ref|YP_003614571.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058884|gb|ADF63622.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295097322|emb|CBK86412.1| RNA polymerase sigma factor RpoS [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 330

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 322


>gi|259909441|ref|YP_002649797.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224965063|emb|CAX56595.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
          Length = 277

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 158/225 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 37  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V
Sbjct: 97  IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAQKLDKPVDDV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 157 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 216

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 217 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 261


>gi|332297439|ref|YP_004439361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332180542|gb|AEE16230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 287

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 159/235 (67%), Gaps = 2/235 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ANLR V++VAKKY N GL  +DLI EGNIGLM A E+FD   GY F +YA+WW++Q+
Sbjct: 52  IVNANLRFVVNVAKKYQNHGLDLVDLISEGNIGLMTAIERFDVSKGYHFISYAVWWIRQS 111

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I ++I ++S  IR+P++  +++ ++    + ++     E    E+A  L M V  VR++L
Sbjct: 112 ILKAICEKSRMIRLPLNRANELVQIEHARKLVAQDKTEEEEITEVADMLNMDVSHVREML 171

Query: 568 KITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            I+++ ISL+  I   D+D++ +G+F+ED     P D+ + A++++    VL +LT +E 
Sbjct: 172 NISRDMISLDASIRSSDQDSASIGEFLEDSRYEDPADTVLNASMQDDIDGVLGTLTDKEA 231

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            VLR RFG+  N   +L+EVG +F +T+ERIRQIE KAI++L+HP+R+ +L +++
Sbjct: 232 DVLRYRFGLNGNKSMSLKEVGDKFNLTKERIRQIEKKAIKRLQHPARTVRLEAYV 286


>gi|82778108|ref|YP_404457.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae Sd197]
 gi|81242256|gb|ABB62966.1| RNA polymerase, sigma S factor [Shigella dysenteriae Sd197]
          Length = 330

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIDLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|67925121|ref|ZP_00518496.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853040|gb|EAM48424.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 374

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 106/239 (44%), Positives = 172/239 (71%), Gaps = 1/239 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IAK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA W
Sbjct: 135 IAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 194

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    
Sbjct: 195 WIRQAITRTIANDARTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVTPPQ 254

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LT 621
           +R++L++ ++ +SL   +G  + + L D +ED++   P +   +  L+   + VL+  LT
Sbjct: 255 LRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEELMNEGMLQYEVSAVLSDVLT 314

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 315 QREKDVISLRYGLCTSQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 373


>gi|161502017|ref|YP_001569129.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863364|gb|ABX19987.1| hypothetical protein SARI_00033 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 330

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFSFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|172035517|ref|YP_001802018.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
 gi|171696971|gb|ACB49952.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
          Length = 374

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 171/238 (71%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 136 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +
Sbjct: 196 IRQAITRTIANDARTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVSPSQL 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +  LR   + VL+  LT 
Sbjct: 256 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEELMNEGMLRYEVSAVLSDVLTQ 315

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 316 REKDVISLRYGLCTSQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 373


>gi|170727680|ref|YP_001761706.1| RpoD family RNA polymerase sigma factor [Shewanella woodyi ATCC
           51908]
 gi|169813027|gb|ACA87611.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella woodyi
           ATCC 51908]
          Length = 322

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 99/231 (42%), Positives = 159/231 (68%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C+ S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 79  CDKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA+KL +
Sbjct: 137 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEKLDL 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           P   V ++LK+ +   S++TP+G ++   L D + D + V P D  +Q  ++ ++  + L
Sbjct: 197 PSADVSRMLKLNERITSVDTPLGGDNDKALLDVLADDDNVGP-DYKVQDEDMSKSVVKWL 255

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 256 DELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 306


>gi|315224630|ref|ZP_07866455.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
 gi|314945415|gb|EFS97439.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
          Length = 287

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 161/237 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIA++L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAYLEQANERVPSAEEIARELDMSVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K     IS++ P+ + + S+L D I    + +P  + I  +LR    R L +LTPR
Sbjct: 170 KESMKNAGRHISMDAPLVEGEDSNLYDVIRSNESPNPDKALILDSLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLSDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|218701232|ref|YP_002408861.1| RNA polymerase sigma factor RpoS [Escherichia coli IAI39]
 gi|218371218|emb|CAR19049.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli IAI39]
 gi|327251469|gb|EGE63155.1| RNA polymerase sigma factor RpoS [Escherichia coli STEC_7v]
          Length = 330

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFSFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|88801442|ref|ZP_01116970.1| putative sigma factor A [Polaribacter irgensii 23-P]
 gi|88782100|gb|EAR13277.1| putative sigma factor A [Polaribacter irgensii 23-P]
          Length = 287

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+ EEIAKKL M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYAFLEQENERPPSAEEIAKKLDMTVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    +  +LR    R L +LTPR
Sbjct: 170 KESMKNSGRHVSMDAPLIEGEDSNLYDVLNSGESPNPDRKLLHESLRIEIDRALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+++ FG+G +   TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L ++L
Sbjct: 230 EADVVKLYFGLGEHQPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILMTYL 286


>gi|4929285|gb|AAD33933.1|AF144608_2 RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus]
          Length = 321

 Score =  204 bits (520), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 97/223 (43%), Positives = 152/223 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 146 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 206 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           ++ VL  RFG+      TLEEVG++  +TRER+R++    I++
Sbjct: 266 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRRLREILIKQ 308


>gi|300724640|ref|YP_003713965.1| sigma S (sigma 38) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|6643920|gb|AAF20816.1|AF198628_2 RpoS [Xenorhabdus nematophila]
 gi|297631182|emb|CBJ91877.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus nematophila ATCC
           19061]
          Length = 331

 Score =  204 bits (520), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARQRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA++L  PVE +
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPTVEEIAERLDKPVEDI 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++++ +   S++TPI  +    L D + D+N   P  +    +++++  + L  L  +
Sbjct: 211 SRMMRLNERITSVDTPISGDSDKALLDILSDENDSGPETTIQDDDMKQSIVKWLFELNAK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QREVLARRFGLLGYEAETLEDVGREIGLTRERVRQIQVEGLRRLR 315


>gi|91216377|ref|ZP_01253344.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
 gi|91185515|gb|EAS71891.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
          Length = 287

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 99/250 (39%), Positives = 169/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +K +    +A +++ +ANLR V+SV+K+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQKIKAGDDLALEKLTKANLRFVVSVSKQYQNQGLTLPDLINEGNLGLIKAAKRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I  ++A+QS  +R+P++    I+K+ +T   +  + +R P+P+
Sbjct: 97  TRGFKFISYAVWWIRQSILSALAEQSRVVRLPLNKIGSINKINKTFAILEQRHQRPPSPD 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK+L M V  V++ LK +   +S++ P+ + + S+L D ++   + +P +  +  +L+
Sbjct: 157 EIAKELEMTVNDVKESLKNSGRHLSMDAPLIEGEDSNLYDVLKFGESPNPENDLLHESLQ 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LT RE  V+R+ FG+G     TLEE+G+ F +TRER+RQI+ K +R+LKH 
Sbjct: 217 TEIERALETLTTREADVIRLYFGLGNQQPMTLEEIGETFGLTRERVRQIKEKGVRRLKHT 276

Query: 671 SRSKKLRSFL 680
           SRS  L+++L
Sbjct: 277 SRSTILKTYL 286


>gi|315137348|dbj|BAJ44507.1| RNA polymerase sigma factor RpoS [Escherichia coli DH1]
          Length = 330

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLTRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|223998999|ref|XP_002289172.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220974380|gb|EED92709.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 318

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 169/268 (63%), Gaps = 11/268 (4%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           ++E G+++++ +  +    +       AK  + E+NLRLVIS+AK+Y  RGL   DL QE
Sbjct: 57  AIEPGMTVTQIKKQIRRSLR-------AKAALTESNLRLVISIAKRYQGRGLNMQDLCQE 109

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL +A EKFD   G++FSTYA WW+KQ I R+IADQ+ TIR+PVH+ D++  V +  
Sbjct: 110 GTLGLTRACEKFDPERGFRFSTYATWWIKQGIMRAIADQARTIRLPVHIHDQLSIVRKAE 169

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIE 593
           R + N++ R+ T EE+A K+ M  + +  + + +   IS+E  +   G E +  + D + 
Sbjct: 170 RDLQNELGRDATKEEVAAKVGMKPDKIEFLKRASVGSISMEQELGTSGSERSFTIQDTLG 229

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +   P+D A    L++   R++ +L  RE+ V+RMRFG+      TLEE+GK+F VTR
Sbjct: 230 DPDQ-KPVDMAQYRMLQDDVGRLICTLNAREQAVIRMRFGLDDGKAKTLEEIGKKFSVTR 288

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEA+A+ KL+ P R+  ++ + +
Sbjct: 289 ERIRQIEARALHKLRQPYRNHTVKCYAN 316


>gi|260062909|ref|YP_003195989.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88784477|gb|EAR15647.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 102/259 (39%), Positives = 172/259 (66%), Gaps = 3/259 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+ +E   +   +++G+    +A +++ +ANLR V+SVAK+Y N+GL+  DLI EGN+GL
Sbjct: 31  ITANEEVELAQRIKQGD---QLALEKLTKANLRFVVSVAKQYQNQGLKLPDLINEGNVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNKIGSINKIKKTFSYLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
             +R P+ EEIAK+L M V  V++ +K +   +S++ P+ + + S+L D +    +  P 
Sbjct: 148 AHERPPSAEEIAKELDMTVSEVKQSIKNSGRHVSMDAPLREGEDSNLYDVLRSGESPKPD 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            S +  +L     R L +L+PRE  V+++ +GIG     TL E+G+ F +TRER+RQI  
Sbjct: 208 KSLMLQSLNTEINRALETLSPREADVVKLYYGIGDQQSMTLAEIGQTFDLTRERVRQIRE 267

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KAIRKL+H SRSK L+++L
Sbjct: 268 KAIRKLRHHSRSKLLKAYL 286


>gi|320640384|gb|EFX09923.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           G5101]
          Length = 330

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+++  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHQLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|167993163|ref|ZP_02574258.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205328726|gb|EDZ15490.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
          Length = 330

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRPLREILQTQGL 322


>gi|332308186|ref|YP_004436037.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332175515|gb|AEE24769.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 327

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 95/225 (42%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+ +NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 85  SRQRMIVSNLRLVVKIARRYNNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RT+R ++ K+  EPT EEIA+ +  PV  V
Sbjct: 145 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTSRELAQKLDHEPTAEEIAEAVQRPVADV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG ++ + L D I D N   P +     N++ +    L  L P+
Sbjct: 205 TKMLRLNERITSVDTPIGSDNDNVLLDIIADDNGHDPEEDLQDKNVKLSIVGWLEDLNPK 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+LK
Sbjct: 265 QREVLARRFGLLGYEPSTLEDVGVEIGLTRERVRQIQVEALRRLK 309


>gi|6010726|gb|AAF01229.1|AF184098_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A +KFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVQKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|1519382|gb|AAC46141.1| RNA polymerase subunit sigma 38 [Pectobacterium carotovorum]
          Length = 330

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 155/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L + +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLALNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|149911458|ref|ZP_01900075.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
 gi|149805489|gb|EDM65496.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
          Length = 319

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 79  SRKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++++  EPT E+IA KL  PV  V
Sbjct: 139 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELAHELDHEPTAEDIADKLDKPVADV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D+    P       +++ +  R L  L P+
Sbjct: 199 SKMLRLNERISSVDTPIGGDSEKALLDIISDEKGDGPESRTQNDDIKFSIIRWLEELNPK 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+R+L+
Sbjct: 259 QREVLARRFGLLGYDASTLEDVGREIGLTRERVRQIQVEALRRLR 303


>gi|12483895|gb|AAG53883.1|AF275947_2 sigma factor RpoS [Escherichia coli]
          Length = 366

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|19910024|dbj|BAB87263.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 431

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 118/259 (45%), Positives = 165/259 (63%), Gaps = 15/259 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRG-LQFLDLIQEGNIGLMK 483
           E RH   MVR G    ++A+  +V ANLR V++VAKKY   RG +   DLIQEGNIGL++
Sbjct: 176 ELRH---MVRVG----TLARDRLVRANLRWVVAVAKKYHKQRGTMSMQDLIQEGNIGLIR 228

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD  +GY+F+TYA WW++QAITRSI + S  IR+P H  +KI+++ R    +S  +
Sbjct: 229 AVEKFDPRMGYRFTTYATWWIRQAITRSIQNSSREIRLPAHRHEKINRIKRATVALSRSL 288

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED--TSHLGDFIEDKNAVS 599
            R+PT  EIA+ + +    +RK ++       +SL+ PI + D  ++ +GDFI  +N   
Sbjct: 289 GRQPTEAEIAEHVGLDPSRMRKFVESAAAVATVSLDVPINESDNQSATIGDFIRSENE-G 347

Query: 600 PLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           P D A +  +RE+  R LA +L+ RE  VLRMRFG+      TL +VG+   VTRER+RQ
Sbjct: 348 PADRAERELMRESVARTLAKALSEREYMVLRMRFGLDDGEPKTLNQVGETLGVTRERVRQ 407

Query: 659 IEAKAIRKLKHPSRSKKLR 677
           IE KA+RKL+ P  S  LR
Sbjct: 408 IEMKALRKLRRPGFSSALR 426


>gi|332999494|gb|EGK19079.1| RNA polymerase sigma factor RpoS [Shigella flexneri VA-6]
          Length = 359

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|254409611|ref|ZP_05023392.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196183608|gb|EDX78591.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 374

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 103/241 (42%), Positives = 169/241 (70%), Gaps = 1/241 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
             I+K++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +AAEKFD   GYKFSTYA
Sbjct: 133 GQISKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKFDPAKGYKFSTYA 192

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P   E+A+ L +  
Sbjct: 193 YWWIRQAITRTIANDARTIRLPIHIVEKLNKLKKVQRELKQKLQRTPDETELAEALDISR 252

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
             +R++L++ +  +SL   +G  + + L D +ED +   P     ++ +R+  + VL+  
Sbjct: 253 TNLRQLLQLRRRSLSLNHRVGKGEDTELVDLLEDNDLHLPEQQMSESMMRQEISDVLSDV 312

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE+ V+ +R+G+     +TLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +
Sbjct: 313 LTEREKDVISLRYGLATPESYTLEEVGSMFNLSRERVRQIQSKAMRKLRRPQVARRLQGW 372

Query: 680 L 680
           L
Sbjct: 373 L 373


>gi|41855|emb|CAA78689.1| KatF [Escherichia coli]
          Length = 377

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|6175918|gb|AAF05334.1|AF182102_2 RNA polymerase sigma subunit [Escherichia coli]
 gi|6175933|gb|AAF05344.1|AF182107_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 156/224 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRL 313


>gi|170765845|ref|ZP_02900656.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
 gi|170124991|gb|EDS93922.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
          Length = 434

 Score =  204 bits (519), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 194 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 253

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 254 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 313

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 314 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 373

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 374 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 426



 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 41/75 (54%), Positives = 61/75 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCT 518
           ++Q I R+I +Q+ T
Sbjct: 150 IRQTIERAIMNQTRT 164


>gi|2961260|emb|CAA73683.1| rpoS [Enterobacter cloacae]
          Length = 346

 Score =  204 bits (519), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 106 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 166 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 225

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 226 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 285

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 286 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 330


>gi|297184127|gb|ADI20246.1| hypothetical protein [uncultured Sphingobacterium sp. EB080_L08E11]
          Length = 287

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 99/250 (39%), Positives = 169/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + ++ +    IA +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD 
Sbjct: 37  VELAQRIKAGDQIALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+  
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAYLEQEHERPPSAA 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI+K L M    V++ ++ +   +S++ P+ + + S+L D +   ++  P +  +  +LR
Sbjct: 157 EISKHLEMSESDVKESMRNSGRHVSMDAPLVEGEDSNLYDVLNSSDSPHPDEDLMMDSLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R LA+LTPRE  V+R+ FG+G     TLEE+G++F +TRER+RQI+ KAIR++KH 
Sbjct: 217 TEIERSLATLTPREGDVIRLYFGLGGQHPMTLEEIGEKFDLTRERVRQIKEKAIRRMKHT 276

Query: 671 SRSKKLRSFL 680
           SRSK L+++L
Sbjct: 277 SRSKILKTYL 286



 Score = 39.3 bits (90), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL+E+G +EL++ E E+ +A+RI+AG  + +  L ++ L F  + + +   N G TL
Sbjct: 21  YLQEIGKVELITAEEEVELAQRIKAGDQIALEKLTKANLRF-VVSVAKQYQNQGLTL 76


>gi|10197699|gb|AAG14981.1|AF242209_6 alternative sigma factor [Escherichia coli]
          Length = 360

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|149370109|ref|ZP_01889960.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149356600|gb|EDM45156.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 287

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 98/237 (41%), Positives = 158/237 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++  ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA +FD   G+KF +YA+WW
Sbjct: 50  ALEKLTNANLRFVVSVAKQYQNQGLTLPDLINEGNVGLIKAASRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI +++A+QS  +R+P++    I+K+ +    +    +R P+PEEIAK+L M +  V
Sbjct: 110 IRQAILQALAEQSRIVRLPLNKIGSINKINKAFTHLEQAHQRPPSPEEIAKELDMTINDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   IS++ P+ + +  +L D +    + +P  + +  +LR    R L +LTPR
Sbjct: 170 KESIKNSGRSISMDAPLTEGEDYNLYDVLNTGESPNPDQALLLESLRTEIERALETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+++ FG+      TLEE+G  F +TRER+RQI+ KA+R+LKH SRS  L+++L
Sbjct: 230 ESDVIKLYFGLSDQRPMTLEEIGSTFDLTRERVRQIKEKAVRRLKHTSRSTILKTYL 286


>gi|332765694|gb|EGJ95907.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2930-71]
          Length = 330

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EG++GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGDLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLRETLQTQGL 322


>gi|322831414|ref|YP_004211441.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
 gi|321166615|gb|ADW72314.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
          Length = 328

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA++L  PV  V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAEEIAEQLDKPVHDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 208 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 268 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 312


>gi|309702135|emb|CBJ01450.1| putative RNA polymerase sigma factor [Escherichia coli ETEC H10407]
          Length = 697

 Score =  204 bits (518), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 113/255 (44%), Positives = 157/255 (61%), Gaps = 32/255 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K  + ANLRLV+++AKK+  RGL   DLIQEGN+GL+KA EKFD+  G+KFSTYA WW
Sbjct: 444 AWKGFIHANLRLVVAIAKKHCGRGLDIEDLIQEGNLGLIKAVEKFDFRRGFKFSTYASWW 503

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I+R+IADQ+  IR+PVH  +   +   +  ++ ++    PT   + +   +P    
Sbjct: 504 IRQKISRAIADQAQLIRLPVHFYEHFRRWRSSRDQLLHRQGITPTLRRLQEMTDLP---E 560

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-----------------AVSPLDSAIQ 606
           R++L++ K          +E T  +GDF ED                     +P+ S   
Sbjct: 561 RQLLQMAKY---------EEQTVLIGDFHEDAQDREAALSGDALLTRRDFTSAPVQS--- 608

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LRE  + VL +L PRE ++++MRFGIGM  D TLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 609 LELREHISSVLNTLLPRETQIIKMRFGIGMTQDFTLEEVGKQFDVTRERIRQIEAKALRK 668

Query: 667 LKHPSRSKKLRSFLD 681
           L+H SR+ KL  F++
Sbjct: 669 LRHHSRASKLGGFVE 683


>gi|332829288|gb|EGK01942.1| hypothetical protein HMPREF9455_00064 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 286

 Score =  204 bits (518), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 178/268 (66%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   ++KG+     A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQAIKKGD---RAALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R+P+ EE+A++L +PV+ +   LK++   IS++ P  + + + L D +
Sbjct: 139 SKAFSKFEQENERKPSAEELAEQLDIPVDKIADSLKVSGRHISMDAPFVEGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +A     + I  +L++   R L++LT RE  +++M FGIG   + TLEE+G +F +T
Sbjct: 199 VNDDAPIADRTLINESLQQEIERALSTLTERESEIIKMFFGIGYQ-EMTLEEIGDKFQLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAI++L+  SRSK L+S+L
Sbjct: 258 RERVRQIKEKAIKRLRQNSRSKLLKSYL 285


>gi|90407885|ref|ZP_01216060.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
 gi|90310976|gb|EAS39086.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
          Length = 313

 Score =  204 bits (518), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 96/226 (42%), Positives = 152/226 (67%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+K M+E+NLRLV+ ++++YTNRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 72  VARKRMIESNLRLVVKISRRYTNRGLSLLDLVEEGNLGLIRAVEKFDPEKGFRFSTYATW 131

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  K++  +RTAR +S+ +  EPT E+IA  L +P + 
Sbjct: 132 WIRQTIERAIMNQTRTIRLPIHIVKKLNVYLRTARELSHSLTHEPTAEDIALALDIPAKD 191

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V K+LK+ +   S++ PIG+     L D I D+  + P +     +++      L  L P
Sbjct: 192 VSKILKLNERISSVDIPIGNNSDKELLDIIPDRKEIIPENELENEDMKLRIVEWLEDLNP 251

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A++ L+
Sbjct: 252 KQREVLARRFGLLGYEAATLENVGKEIGLTRERVRQIQVEALKCLR 297


>gi|6175921|gb|AAF05336.1|AF182103_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  204 bits (518), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 156/224 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRL 313


>gi|224024118|ref|ZP_03642484.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
 gi|224017340|gb|EEF75352.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
          Length = 317

 Score =  204 bits (518), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 107/269 (39%), Positives = 177/269 (65%), Gaps = 6/269 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 53  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 109

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 110 LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 169

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 170 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 229

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D + ++   S +  +L     R L++LT RE+ +++M FGI    + TLEE+G +F +
Sbjct: 230 VNDDSPMAD-RSLVNESLSREIDRALSTLTEREKDIIQMFFGIN-TQEMTLEEIGDKFGL 287

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 288 TRERVRQIKEKAIRRLRQNSRSKLLKSYL 316


>gi|149378178|ref|ZP_01895895.1| nonessential primary sigma factor [Marinobacter algicola DG893]
 gi|149357540|gb|EDM46045.1| nonessential primary sigma factor [Marinobacter algicola DG893]
          Length = 333

 Score =  204 bits (518), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 98/240 (40%), Positives = 157/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +   + RKGE      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 82  YFARLARKGE---ESGRKRMIESNLRLVVKIARRYVNRGLTLLDLIEEGNLGLIRAVEKF 138

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 139 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNLYLRAARELTQKLDHEPS 198

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA+ +  PV  V+++L + +   S++TPIG      L D + D+ A  P D     N
Sbjct: 199 AEEIARMVDKPVADVKRMLGLNERVASMDTPIGTGGEKSLLDTVADEGASDPADLLQDNN 258

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     + +  L+ +++ VL  RFG+      TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 259 MCSCVEKWIDQLSDKQQEVLSRRFGLRGYPISTLEEVGQEIGLTRERVRQIQVEALRRLR 318


>gi|33867026|ref|NP_898585.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639627|emb|CAE09011.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 328

 Score =  204 bits (518), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 103/245 (42%), Positives = 159/245 (64%), Gaps = 8/245 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S  RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A
Sbjct: 82  SRHRHKIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERA 134

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  
Sbjct: 135 VDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFG 194

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS 603
           R+P   E+A  + +    +  ++  +    SL+    G+ED S LG+ I D N   P++ 
Sbjct: 195 RQPNRLELASAMGIEPRELEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEG 254

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             ++  +E     L+ L  RE+++LR+RFG+G     TL E+G+Q  V+RER+RQ+EAKA
Sbjct: 255 MDRSIQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKA 314

Query: 664 IRKLK 668
           I KL+
Sbjct: 315 ILKLR 319


>gi|326324968|dbj|BAJ84180.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Oranienburg]
          Length = 330

 Score =  203 bits (517), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  L+LI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|311694174|gb|ADP97047.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 331

 Score =  203 bits (517), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 98/241 (40%), Positives = 157/241 (65%), Gaps = 3/241 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +   + RKGE      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 80  YFARLARKGE---ESGRKRMIESNLRLVVKIARRYVNRGLTLLDLIEEGNLGLIRAVEKF 136

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 137 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNLYLRAARELTQKLDHEPS 196

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA+ +  PV  V+++L + +   S++TPIG      L D + D+ A  P D     N
Sbjct: 197 AEEIARMVDKPVADVKRMLGLNERVASMDTPIGAGGEKSLLDTVADEGASDPADLLQDNN 256

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     + +  L+ +++ VL  RFG+      TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 257 MCSCLEKWIDQLSDKQQEVLSRRFGLRGYPVSTLEEVGQEIGLTRERVRQIQVEALRRLR 316

Query: 669 H 669
            
Sbjct: 317 E 317


>gi|89109528|ref|AP_003308.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|218547743|ref|YP_002381534.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|85675562|dbj|BAE76818.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|218355284|emb|CAQ87891.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|320645931|gb|EFX14912.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str.
           493-89]
          Length = 291

 Score =  203 bits (517), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 51  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 111 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 170

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 171 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 230

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 231 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 283


>gi|254444043|ref|ZP_05057519.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198258351|gb|EDY82659.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 377

 Score =  203 bits (517), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 107/267 (40%), Positives = 170/267 (63%), Gaps = 2/267 (0%)

Query: 410 RNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN I++   E G I +      V++ R+ +     A+  M+++NLRLV+ +A  Y + GL
Sbjct: 78  RNSIRTYLQEIGRIDLLTPAQEVTLARRIQAGEKEARDLMIKSNLRLVVKIAHDYKDFGL 137

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI EGNIGL+KA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ DK
Sbjct: 138 PVLDLISEGNIGLVKAVERFDPDKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDK 197

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSH 587
           I ++ + A  ++ ++ REPT +E+A+ L MPV  V  +  ++  P SL  P+G D +++ 
Sbjct: 198 ISRMRKMALMLTEELGREPTDQELAEMLEMPVNKVSHLKSVSVRPTSLNAPVGEDGNSTE 257

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            G+ + D NA +P ++  + +LR     ++  L  RE  ++R+RFG+  ++  TLEEVG+
Sbjct: 258 FGEIVGDDNAPTPYENLHEKSLRGDLHEMIDGLEDREAEIIRLRFGLNGDSPLTLEEVGQ 317

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
            F +TRER+RQ++  A+ K++    SK
Sbjct: 318 VFDITRERVRQLQNIALSKMRKIMASK 344



 Score = 37.7 bits (86), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 30/42 (71%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++K+ A+    + +R YL+E+G I+LL+   E+ +A+RI+AG
Sbjct: 68  QKKEKAELPDRNSIRTYLQEIGRIDLLTPAQEVTLARRIQAG 109


>gi|170737511|ref|YP_001778771.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169819699|gb|ACA94281.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 627

 Score =  203 bits (517), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 95/237 (40%), Positives = 154/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW
Sbjct: 390 ARTKLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 449

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ V
Sbjct: 450 IRQAITHALADLGRTIRVPTHTVDTLNKLSRLARLHRQRTGDVADARALSTQMRLPVDKV 509

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  R
Sbjct: 510 RELMSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQLRAVVAELIDSLPVR 569

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 570 EAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 626



 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 76/154 (49%), Gaps = 17/154 (11%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I L   RGYVT+ E+   LP D      ++   +ML  +GI      D+ +  G+  + 
Sbjct: 33  LIALGIDRGYVTLGEIADALPDDATDGADVDAAASMLRELGI------DVREHAGAHTTW 86

Query: 94  DL----------ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L          AS   ++S  L      A R T+DP+R+YLREM +  LL R+ EIA+A
Sbjct: 87  TLDRHFAQVTEVASPLDDASTPLAADDLLAGR-TNDPIRLYLREMSATPLLERDEEIALA 145

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            R+E+GRA  + +L   P    A+    D++  G
Sbjct: 146 LRLESGRAACIDALSRDPAALAAVAAIADDIRAG 179


>gi|332298226|ref|YP_004440148.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181329|gb|AEE17017.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 332

 Score =  203 bits (517), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 152/226 (67%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + K +M++ANLRLV+S+AK+Y +RGL  LDLI EGNIGL++A ++F+     +FSTY +W
Sbjct: 95  VLKNKMIQANLRLVVSIAKRYQHRGLGLLDLIDEGNIGLIEAVDRFEPARNCRFSTYGIW 154

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAI +S+AD+   IR+PVHM + I+K    A+ ++ +  REPT  E+A+ L +  E 
Sbjct: 155 WIRQAIIKSLADKGRVIRVPVHMLNTINKCFFMAKLLTQEYGREPTTAELARFLCVTNEK 214

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V   +++++E  SLET + D++++ LGD + D+N  +P++    A L +T   VL  L+ 
Sbjct: 215 VEDYIRLSQEMSSLETNVDDDNSTRLGDLLTDENGEAPIERVFAAALTDTVNLVLNQLSE 274

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  ++R+R+G+      TL E G    +TRER+RQI+ K ++KL+
Sbjct: 275 REMSIIRLRYGLDGKAPRTLTETGNVLGITRERVRQIQEKTLKKLR 320


>gi|333001093|gb|EGK20663.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-272]
 gi|333015402|gb|EGK34741.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-227]
          Length = 330

 Score =  203 bits (517), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RT R +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTVRELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|330828425|ref|YP_004391377.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803561|gb|AEB48760.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 327

 Score =  203 bits (517), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 97/233 (41%), Positives = 157/233 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKIARRYNNRGLVLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+++  EPT E+IA  L   V+ V
Sbjct: 146 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELSHRLDHEPTAEDIAFALDRSVDDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+ ++  S++TPIG +    L D + D+  + P   + + ++R +    L  L P+
Sbjct: 206 NRMLKLNEKITSVDTPIGGDRDKALLDVLSDERGMGPELESQEDDMRSSIVHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+    S+ L
Sbjct: 266 QREVLARRFGLLGYEPATLEDVGAEIGLTRERVRQIQVEGLRRLREILLSQGL 318


>gi|23306706|gb|AAN15274.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306708|gb|AAN15270.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306710|gb|AAN15272.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 277

 Score =  203 bits (517), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 37  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 97  IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 157 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 216

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 217 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 269


>gi|108804071|ref|YP_644008.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765314|gb|ABG04196.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 294

 Score =  203 bits (516), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 110/240 (45%), Positives = 156/240 (65%), Gaps = 9/240 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++E NLRLV+SVAKKY   GL F DLIQEGNIGLMKA EKFD   G++FSTYA WW
Sbjct: 56  ARQKLIEKNLRLVVSVAKKYRGYGLPFEDLIQEGNIGLMKAVEKFDPERGFRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ R++AD+  TIR+PVHM +KI KV RT   +S +++REPT EEIA++L   VE V
Sbjct: 116 IRQAVQRAVADKGRTIRVPVHMTEKIRKVSRTFNELSLELEREPTDEEIARRLEWDVEDV 175

Query: 564 RKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQ----ANLRETTTRVLA 618
           R  +    +  SL+ P+  E++ S LGDFIED+      D+ ++    + L+E   R   
Sbjct: 176 RLTISAMPDATSLDQPVSSEESASELGDFIEDERTSDTPDTVLKELESSQLKEAIER--- 232

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  R   VL  R+G+      TL E+G +  ++RER+RQ++ +A R LK     + LR+
Sbjct: 233 -LPERARYVLVRRYGLDDREPATLAELGDELKISRERVRQLQREAERILKSGEHGRVLRN 291


>gi|212634213|ref|YP_002310738.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
 gi|212555697|gb|ACJ28151.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
          Length = 322

 Score =  203 bits (516), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 100/231 (43%), Positives = 157/231 (67%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 79  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA+KL +
Sbjct: 137 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEKLDL 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
               V ++LK+ +   S++TP+G E    L D + D + V P D  +Q  ++ ++  + L
Sbjct: 197 SSSDVSRMLKLNERITSVDTPLGGESDKALLDVLADDDNVGP-DYKVQDEDMSKSVVKWL 255

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 256 DELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 306


>gi|332885662|gb|EGK05908.1| hypothetical protein HMPREF9456_02172 [Dysgonomonas mossii DSM
           22836]
          Length = 286

 Score =  203 bits (516), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 177/268 (66%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   ++KG+     A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQAIKKGD---RAALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R+P+ EE+A++L +PV+ +   LK++   IS++ P  + + + L D +
Sbjct: 139 SKAFSKFEQENERKPSAEELAEQLDIPVDKIADSLKVSGRHISMDAPFVEGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +A       I  +L++   R L++LT RE  +++M FGIG   + TLEE+G +F +T
Sbjct: 199 VNDDAPIADRKLINESLQQEIERALSTLTERESEIIKMFFGIGYQ-EMTLEEIGDKFQLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAI++L+  SRSK L+S+L
Sbjct: 258 RERVRQIKEKAIKRLRQNSRSKLLKSYL 285


>gi|284929771|ref|YP_003422293.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
 gi|284810215|gb|ADB95912.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
          Length = 318

 Score =  203 bits (516), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 104/241 (43%), Positives = 162/241 (67%), Gaps = 5/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + S +  GE     AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EK
Sbjct: 71  RELHSAIASGEA----AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEK 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R +S    R+ 
Sbjct: 127 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRELSQARGRDA 186

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T  E+A++L +  + VR+ L+  ++P+SL+  +GD   + LGD +ED +  SP D A  +
Sbjct: 187 TIAELAEELDLTPKQVREYLERARQPLSLDLRVGDNQDTELGDLLED-DGPSPEDFATHS 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+     ++  LT +++ V+ +RFG+      TL ++G +  ++RER+RQIE +A+ KL
Sbjct: 246 SLQFDLEILMEDLTTQQKEVIALRFGLTDGQPLTLAKIGCRLNISRERVRQIEREALSKL 305

Query: 668 K 668
           +
Sbjct: 306 R 306



 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 24/33 (72%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +S  DPVR YLRE+G + LL+ E EI  AKR++
Sbjct: 5   KSNLDPVRSYLREIGRVPLLTHEEEILYAKRVQ 37


>gi|26665390|dbj|BAC44906.1| principal sigma factor [Scytonema sp. IAM M-262]
          Length = 188

 Score =  203 bits (516), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 101/188 (53%), Positives = 137/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  ++ +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIES-DSETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|195938492|ref|ZP_03083874.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 279

 Score =  203 bits (516), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 161/233 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 39  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 99  IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 158

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 159 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 218

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 219 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 271


>gi|126659670|ref|ZP_01730799.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126619015|gb|EAZ89755.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 369

 Score =  203 bits (516), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 169/238 (71%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 131 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 190

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +
Sbjct: 191 IRQAITRTIANDARTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVSPSQL 250

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED+    P +   +  LR   + VL+  LT 
Sbjct: 251 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQELQLPEELMNEGMLRYEVSAVLSDVLTQ 310

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+     HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 311 REKDVISLRYGLCTAQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 368


>gi|332711345|ref|ZP_08431277.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332349894|gb|EGJ29502.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 319

 Score =  203 bits (516), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 98/225 (43%), Positives = 154/225 (68%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++MVEANLRLV++VAKKY  R L+ LDLIQEG IGL +  EKFD   GY+FSTYA WW
Sbjct: 83  AKRKMVEANLRLVVAVAKKYIKRNLELLDLIQEGTIGLQRGVEKFDPTKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA++  TIR+P+H+ +K++K+ +  R++S K+ R  T  E+A +L +  + +
Sbjct: 143 IRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQKLGRTATISELAIELNLTPDQL 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+  +  ++P+SLE  +GD   + L + +ED     P D   Q+ ++    + +  LTP+
Sbjct: 203 REYFEQARQPLSLELRVGDNKDTELVELLED-TGPGPEDFVNQSLMQLDLEKFMDDLTPQ 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +VLR+R+G+      TL ++G+   ++RER+RQIE +AI KL+
Sbjct: 262 QRQVLRLRYGLAEVEPMTLAKIGQHLNISRERVRQIEREAIAKLR 306


>gi|206564209|ref|YP_002234972.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
 gi|198040249|emb|CAR56232.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
          Length = 628

 Score =  203 bits (516), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 95/237 (40%), Positives = 154/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW
Sbjct: 391 ARTKLFQSNLRLVVSVAKRYADRGLPFADLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 450

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ V
Sbjct: 451 IRQAITHALADLGRTIRVPAHTVDSLNKLSRLARIHRQRTGDVADARALSPQMRLPVDKV 510

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  R
Sbjct: 511 RELMSIVREPISADLPVSPDHDLTLCDVTIDADAPTPEEAASAGQLRAAVAELIDSLPVR 570

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 571 EAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 627



 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 47/138 (34%), Positives = 70/138 (50%), Gaps = 17/138 (12%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I L   RGYVT  E+   LP D      ++   +ML  +GI      D+ +  G+  + 
Sbjct: 34  LIALGIDRGYVTHGEIADALPDDAADGADVDAAASMLRELGI------DVREHAGAHTAW 87

Query: 94  DL----------ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L          AS  +++S  L      A R T+DP+R+YLREM +  LL R+ EIA+A
Sbjct: 88  TLDRHFAQVTEVASPLADASTPLAADDLLAGR-TNDPIRLYLREMSATPLLERDEEIALA 146

Query: 144 KRIEAGRAMMMASLCESP 161
            R+E+GRA  + +L   P
Sbjct: 147 LRLESGRAACIDALSRDP 164


>gi|254249954|ref|ZP_04943274.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
 gi|124876455|gb|EAY66445.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
          Length = 662

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 95/237 (40%), Positives = 154/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW
Sbjct: 425 ARTKLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 484

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ V
Sbjct: 485 IRQAITHALADLGRTIRVPAHTVDTLNKLSRLARLHRQRTGDVADARALSTQMRLPVDKV 544

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  R
Sbjct: 545 RELMSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQLRAAVAELIDSLPVR 604

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 605 EAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 661



 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 76/154 (49%), Gaps = 17/154 (11%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I L   RGYVT  E+   LP D      ++   +ML  +GI      D+ +  G+  + 
Sbjct: 68  LIALGIDRGYVTHGEIADALPDDATDGADVDTAASMLRELGI------DVREHTGAHTAW 121

Query: 94  DL----------ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L          AS  +++S  L      A R T+DP+R+YLREM +  LL R+ EIA+A
Sbjct: 122 TLDRHFAQVTEVASPLADASTPLAADDLLAGR-TNDPIRLYLREMSATPLLERDEEIALA 180

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            R+E+GRA  + +L   P    A+    D++  G
Sbjct: 181 LRLESGRAACIDALSRDPAALAAVAAIADDIRAG 214


>gi|296268951|ref|YP_003651583.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091738|gb|ADG87690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 311

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 149/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E ++ANLRLV++VA+KY  RG+  +DL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 80  AKDEFIKANLRLVVAVARKYAGRGMPLIDLVQEGNVGLVRAVEKFDYRRGYKFSTYATWW 139

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ RSI +Q   +R+P H  +++ +++R  R +  + + EP+ EE+A  L MP+E V
Sbjct: 140 IRQAVGRSIHEQGRPVRLPTHAGEQMTRLMRVRRDILAEQEMEPSDEELADVLDMPIERV 199

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ +   +P+SL+  +G+ED + LGD I D     P   AI    +E   R L  L  R
Sbjct: 200 RELRRWASDPVSLQLGVGEEDETELGDMIADDAWADPEQQAIDTLDKERLERWLTDLDGR 259

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +LR R+G+    +HTL EVG+++ + R+R R++E  A+R L+
Sbjct: 260 LSEMLRWRYGLVDGKEHTLTEVGERYGIGRDRARRMERDALRHLR 304


>gi|6175927|gb|AAF05340.1|AF182105_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 155/224 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRL 313


>gi|330836598|ref|YP_004411239.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
 gi|329748501|gb|AEC01857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
          Length = 293

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 158/237 (66%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE+NLR V+++AKKY N+GL   DLI EGNIGLM A EKFD   GY F +YA+WW
Sbjct: 56  ARNRLVESNLRFVVNIAKKYQNQGLPLGDLINEGNIGLMNAIEKFDVDKGYHFISYAVWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI ++I+++S T+R+P++  +++ ++ +  + + N+   EPT EEI +   +    V
Sbjct: 116 IRQAILKAISEKSRTVRLPLNRANELMQIQKAQKSLMNESGAEPTMEEIGRLTQLDPSHV 175

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++ I+KE +SL+ P+  D   S +GDFI+D  A SP D  I + L+E   +VLA+L+ 
Sbjct: 176 ADLIAISKEMVSLDAPVFTDSGNSSVGDFIQD-GADSPDDVIIDSALKEDINKVLATLSE 234

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +E  +L  RFG+      +L+E+G+ + +T+ERIRQIE KAI +L+ PSR K L  +
Sbjct: 235 KEMEILEFRFGLNGQHPMSLKEIGELYNLTKERIRQIEKKAIERLQQPSRIKMLVGY 291


>gi|23978298|dbj|BAC21128.1| principal sigma factor [Anabaena variabilis]
 gi|23978312|dbj|BAC21131.1| principal sigma factor [Nostoc linckia]
 gi|23978323|dbj|BAC21134.1| principal sigma factor [Anabaena variabilis]
 gi|23978327|dbj|BAC21135.1| principal sigma factor [Anabaenopsis circularis]
 gi|23978343|dbj|BAC21140.1| principal sigma factor [Chlorogloeopsis sp. PCC 6718]
 gi|23978354|dbj|BAC21143.1| principal sigma factor [Fischerella muscicola]
 gi|23978367|dbj|BAC21148.1| principal sigma factor [Chroococcidiopsis sp. PCC 7431]
 gi|26665388|dbj|BAC44905.1| principal sigma factor [Tolypothrix sp. IAM M-259]
 gi|26665392|dbj|BAC44907.1| principal sigma factor [Fischerella sp. IAM M-263]
 gi|26665394|dbj|BAC44908.1| principal sigma factor [Hapalosiphon sp. IAM M-264]
 gi|26665396|dbj|BAC44909.1| principal sigms factor [Hapalosiphon delicatulus IAM M-266]
 gi|26665398|dbj|BAC44910.1| principal sigma factor [Nostoc entophytum IAM M-267]
          Length = 188

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 101/188 (53%), Positives = 136/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIES-DGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|23978307|dbj|BAC21130.1| principal sigma factor [Calothrix brevissima]
          Length = 188

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 101/188 (53%), Positives = 136/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+ VH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLSVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+G     TLEE
Sbjct: 122 DSRLGDFIES-DGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLGDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|91792562|ref|YP_562213.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
 gi|91714564|gb|ABE54490.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
          Length = 327

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 102/239 (42%), Positives = 159/239 (66%), Gaps = 4/239 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 84  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 141

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR+++ K+  EPT EEIA KL +
Sbjct: 142 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARQLAQKLDHEPTAEEIAAKLDV 201

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
               V ++LK+ ++  S++TP+G ++   L D I D ++V P D  +Q  +L  +    L
Sbjct: 202 STSDVSRMLKLNEKITSVDTPLGGDNEKALLDVIADDDSVGP-DYQVQDEDLSNSIVGWL 260

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  ++  VL  RFG+      TLE VG +  +TRER+RQI+ +A+++LK    S+ L
Sbjct: 261 NELNTKQREVLARRFGLLGYEPSTLENVGAEIGLTRERVRQIQVEALKRLKDLLSSQGL 319


>gi|18073320|emb|CAC81021.1| mutant RpoS sigma factor [Escherichia coli]
          Length = 302

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN GL++A EKFD   G++FSTYA WW
Sbjct: 62  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNQGLIRAVEKFDPERGFRFSTYATWW 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 122 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 181

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 182 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 241

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 242 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 294


>gi|290476558|ref|YP_003469463.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
 gi|289175896|emb|CBJ82699.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
          Length = 331

 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 157/225 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 91  ARQRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA+KL  P++ V
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSVEEIAEKLDRPIDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +++++ +   S++TPI  +    L D + D+N   P  +    +++++  + L  L  +
Sbjct: 211 SRMMRLNERITSVDTPISGDSDKALLDILSDENDSGPETTIQDDDMKQSIVKWLFELNAK 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 271 QREVLARRFGLLGYEAETLEDVGREIGLTRERVRQIQVEGLRRLR 315


>gi|208821597|ref|ZP_03261917.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218690868|ref|YP_002399080.1| RNA polymerase sigma factor RpoS [Escherichia coli ED1a]
 gi|260856852|ref|YP_003230743.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|208741720|gb|EDZ89402.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218428432|emb|CAR09358.2| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli ED1a]
 gi|257755501|dbj|BAI27003.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|284922677|emb|CBG35765.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli 042]
          Length = 330

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|193222342|emb|CAL62001.1| Putative RNA polymerase sigma-70 factor [Herminiimonas
           arsenicoxydans]
          Length = 808

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 101/241 (41%), Positives = 161/241 (66%), Gaps = 5/241 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +M  ANL+LV S A KY+  G++FLDLIQEGNIGL++A EKFD+  G+KFSTYA+WW
Sbjct: 436 ARSQMAIANLKLVHSTATKYSWSGMEFLDLIQEGNIGLLRAIEKFDYRRGFKFSTYAIWW 495

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+  IR+PVH+ + I++V R   ++ + + +    +EI+  L+MP+  V
Sbjct: 496 IRQAITRAIADQTRLIRVPVHLVESINQVERHKNQVEHILGKSLKAQEISDALSMPLRKV 555

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS----AIQANLRETTTRVLAS 619
            + L      ++++  I  E  +     + ++N + P  +    AI+ +L +   R+L+ 
Sbjct: 556 EQCLAANVSILNIDDLIERETENQDEALVLEENLIDPSATPEQLAIKTSLSKVLNRILSD 615

Query: 620 LTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  +E  +LR+RFG+  N + HTLEEVG+   +TRER+RQIEAKA+ ++++P+R K +  
Sbjct: 616 LPEKEAHILRLRFGLYKNVEPHTLEEVGQLLGITRERVRQIEAKALTRIRYPNRRKDIAI 675

Query: 679 F 679
           F
Sbjct: 676 F 676


>gi|148909485|gb|ABR17840.1| unknown [Picea sitchensis]
          Length = 495

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 97/235 (41%), Positives = 157/235 (66%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++  NLRLVISVAK Y NRGL   DLIQ G++GLM++AEKFD+  G+KFSTYA WW++Q
Sbjct: 260 KIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGFKFSTYAYWWIRQ 319

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +IT+++ +QS TIR+PVH+ + + ++    R +  + KR+PT EE+A+   + +  +R V
Sbjct: 320 SITKALTEQSRTIRLPVHIVESMTRIRTAWRLLYQEHKRDPTKEEVAEVAGISMTRLRHV 379

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            + ++ P SL+  +G +      + + D N+ S      +   ++   RVL +LT RE++
Sbjct: 380 TRCSRVPTSLDRCVGKDMDEKFSEIVADTNSESTETIVSKELFKKDLDRVLDTLTAREKQ 439

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+R+R+G+      +L EVG+ F ++RER+RQIE KA+RKL+   R++ L+ +LD
Sbjct: 440 VVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAMRKLRQNHRTQHLKHYLD 494


>gi|114320976|ref|YP_742659.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227370|gb|ABI57169.1| RNA polymerase, sigma 38 subunit, RpoS [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 342

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 156/238 (65%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+ +   + A+  M+E+NLRLV+ +A++Y NRGL FLDLI+EGN+GL++A EKFD 
Sbjct: 90  VYFSRRAQRGDAAARARMIESNLRLVVKIARRYMNRGLAFLDLIEEGNLGLIRAVEKFDP 149

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +I++ +R AR+++ ++  EP+ E
Sbjct: 150 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVIKEINQYLRAARKLTQELDHEPSVE 209

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  +   VE VR++  + +   S++ PIG +    L D I D+N V P+ +    ++ 
Sbjct: 210 EIADHMGRDVEDVRRMRGLNEGTTSVDVPIGRDADRVLLDAIPDENNVDPVSALQDGDVF 269

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  LT ++  V+  RFG+  +   TLE+VG +  VTRER+RQI+  A+R+L+
Sbjct: 270 GNLEAWLGELTEKQRAVVERRFGLNGHDRATLEQVGNEIGVTRERVRQIQIDALRRLR 327


>gi|86143196|ref|ZP_01061598.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85830101|gb|EAQ48561.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 288

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 100/260 (38%), Positives = 171/260 (65%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+  E   +   +R+G+    +A + + +ANLR V+SVAK+Y N+GL+  DLI EGN+GL
Sbjct: 31  ITADEEVELAQRIREGD---QVALERLTKANLRFVVSVAKQYQNQGLKLPDLINEGNVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++Q+I ++I++ S T+R+P++    I K+ +    +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQSILQAISEHSRTVRLPLNKIGTISKINKAFSYLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSP 600
            ++R P+ EEIAK+L M V  V+  +K +   +S++ P  + E+ S+L D ++   + +P
Sbjct: 148 SLERPPSAEEIAKELDMTVAKVKLAMKNSGRNLSMDAPFKEGENDSNLYDVLKSGESPNP 207

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               +Q +L     R L +L+PRE  V+++ +G+G    HTL+E+G+ F ++RER+RQI 
Sbjct: 208 DADLMQESLGTEIERALETLSPRESDVIKLNYGLGGEQPHTLQEIGEMFDLSRERVRQIR 267

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            K IR+L+H SRSK L+++L
Sbjct: 268 EKGIRRLRHTSRSKVLKTYL 287


>gi|108804647|ref|YP_644584.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765890|gb|ABG04772.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 304

 Score =  202 bits (514), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 116/260 (44%), Positives = 161/260 (61%), Gaps = 17/260 (6%)

Query: 433 MVRKGECEAS--------IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           + R GE E S         A+++++E NLRLV+SVAKKY   GL F DLIQEGNIGLMKA
Sbjct: 48  LTRDGEIELSRRAKKGDRKARQKLIEKNLRLVVSVAKKYRGYGLPFEDLIQEGNIGLMKA 107

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD   G++FSTYA WW++QA+ R++AD+  TIR+PVHM +KI KV RT   +S +++
Sbjct: 108 VEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEKIRKVSRTFNELSLELE 167

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDS 603
           REPT EEIA++L   VE VR  +    +  SL+ P+  E++ S LGDFIED+      D+
Sbjct: 168 REPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPVSSEESASELGDFIEDERTSDTPDT 227

Query: 604 AIQ----ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            ++    + L+E   R    L  R   VL  R+G+      TL E+G +  ++RER+RQ+
Sbjct: 228 VLKELESSQLKEAIER----LPERARYVLVRRYGLDDREPATLAELGDELKISRERVRQL 283

Query: 660 EAKAIRKLKHPSRSKKLRSF 679
           + +A R LK   R    RS 
Sbjct: 284 QREAERLLKAGIRRTSPRSI 303


>gi|107025596|ref|YP_623107.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116693222|ref|YP_838755.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
 gi|105894970|gb|ABF78134.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116651222|gb|ABK11862.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
          Length = 628

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 95/237 (40%), Positives = 154/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW
Sbjct: 391 ARTKLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 450

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ V
Sbjct: 451 IRQAITHALADLGRTIRVPAHTVDTLNKLSRLARLHRQRTGDVADARALSTQMRLPVDKV 510

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  R
Sbjct: 511 RELMSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQLRAAVAELIDSLPVR 570

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 571 EAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 627



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/154 (31%), Positives = 74/154 (48%), Gaps = 17/154 (11%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I L   RGYVT  E+   LP D       +   +ML  +GI      D+ +  G+  + 
Sbjct: 34  LIALGIDRGYVTHGEIADALPDDATDGADADAAASMLRELGI------DVREHTGAHTAW 87

Query: 94  DL----------ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            L          AS  +++S  L    D     T+DP+R+YLREM +  LL R+ EIA+A
Sbjct: 88  TLDRHFAQVTEVASPLADASTPLPA-DDLLAGHTNDPIRLYLREMSATPLLERDEEIALA 146

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            R+E+GRA  + +L   P    A+    D++  G
Sbjct: 147 LRLESGRAACIDALSRDPAALAAVAALADDIRAG 180


>gi|23978319|dbj|BAC21133.1| principal sigma factor [Microcystis wesenbergii]
          Length = 188

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/188 (53%), Positives = 136/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S +++R+PT EEIA K+ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|150007022|ref|YP_001301765.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154495210|ref|ZP_02034215.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218256952|ref|ZP_03474423.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|255015941|ref|ZP_05288067.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_7]
 gi|256841904|ref|ZP_05547409.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262384222|ref|ZP_06077357.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298377447|ref|ZP_06987400.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|301308863|ref|ZP_07214815.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
 gi|149935446|gb|ABR42143.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154085357|gb|EDN84402.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218225859|gb|EEC98509.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|256736220|gb|EEU49549.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262293925|gb|EEY81858.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298265861|gb|EFI07521.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|300833387|gb|EFK64005.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
          Length = 286

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 176/268 (65%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +++G+  A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQAIKRGDRRAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L D +
Sbjct: 139 SKAFSKFEQENERRPSPEELADELDIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +A     S +  +L +   R LA+LT RE  +++M FGIG   + TLEE+G +F +T
Sbjct: 199 VNDDAPIADRSLMNESLAKEIDRALATLTERECEIIKMFFGIGCQ-EMTLEEIGDKFGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 258 RERVRQIKEKAIRRLRQGTRSKLLKSYL 285


>gi|50955189|ref|YP_062477.1| ECF subfamily RNA polymerase sigma-70 factor [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50951671|gb|AAT89372.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 308

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 104/235 (44%), Positives = 152/235 (64%), Gaps = 2/235 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +  +EANLRLV+S+AK+Y  RGL  +DLIQEGN+GL++A EKFD+  G KFSTYA WW
Sbjct: 75  AFERFIEANLRLVVSIAKRYAGRGLAVMDLIQEGNLGLVRAVEKFDYRTGNKFSTYATWW 134

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R IAD +  IRIPVH  +KI K+ R  R +  ++ R PT EEIA   ++    V
Sbjct: 135 IRQSILRGIADTARVIRIPVHTVEKIDKLDRIRRDLGGELGRTPTLEEIADAASLTPAEV 194

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA-IQANLRETTTRVLASLTP 622
            K+     E +SL  P+G+ + + LGD IED +A  P +   ++   R+   R L  L  
Sbjct: 195 HKLQMSDSETVSLAVPVGENEGAELGDLIEDGDAPGPSERVEVEFRHRDLEER-LRELPL 253

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           R+ +V+RMRFG+      TL+EVG  + +TRER+RQ+E +++++L+ P   + LR
Sbjct: 254 RDAKVVRMRFGLDGRKPMTLDEVGAVYGITRERVRQLETRSLKRLRSPELLEYLR 308



 Score = 38.5 bits (88), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 24/33 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T+DPVR YL  +G   LL+ E E+++AKRIE G
Sbjct: 12  TNDPVRDYLNSIGRTWLLTAEDEVSLAKRIEVG 44


>gi|124024683|ref|YP_001018990.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123964969|gb|ABM79725.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 344

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/242 (41%), Positives = 158/242 (65%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 101 RHKIRMGKR-------ARDRMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 153

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P
Sbjct: 154 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQP 213

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +  + +  ++  +    SL+    G+ED S LG+ I D N   P++   +
Sbjct: 214 NRLELAHAMGIQPQDLEDLIAQSAPCASLDAHARGEEDRSTLGELIPDPNGAEPMEGLDR 273

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 274 SIQKEHLGGWLSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRERVRQLEAKAILK 333

Query: 667 LK 668
           L+
Sbjct: 334 LR 335


>gi|83272624|gb|ABC00797.1| RpoS [Escherichia coli]
          Length = 330

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I + + TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNPTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|167623164|ref|YP_001673458.1| RpoD family RNA polymerase sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353186|gb|ABZ75799.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           halifaxensis HAW-EB4]
          Length = 321

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 99/231 (42%), Positives = 157/231 (67%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 78  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 135

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA++L +
Sbjct: 136 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEQLDL 195

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
               V ++LK+ +   S++TP+G E    L D + D + V P D  +Q  ++ ++  + L
Sbjct: 196 SSSDVSRMLKLNERITSVDTPLGGESDKALLDVLADDDNVGP-DYKVQDEDISKSVVKWL 254

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 255 DELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 305


>gi|291278687|ref|YP_003495522.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290753389|dbj|BAI79766.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 298

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 107/286 (37%), Positives = 178/286 (62%), Gaps = 10/286 (3%)

Query: 402 EVDSILKIRNEIKSISVET-GISISEFRHIVSMVRKGECEASI--------AKKEMVEAN 452
           E+++I +I N++ +  +E+  I ++E     ++ ++ E E S         AK  M+  N
Sbjct: 8   ELENIEEITNDVPTDDLESITIYLNEIIKYPTLSKEEEIELSKRIEQGDEEAKNLMINCN 67

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L+LV+S+AKKY NRGLQ +DLI EGNIGL+KA EKFD+  G+KFSTYA WW++QAI R++
Sbjct: 68  LKLVVSIAKKYNNRGLQLIDLINEGNIGLIKAVEKFDYRKGFKFSTYATWWIRQAIERAL 127

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+  +RIPVHM + I+KV +   ++  K+KREPT  E++ +  M +  ++K +   ++
Sbjct: 128 VNQTKMVRIPVHMNENINKVKKATEKLRRKLKREPTLFELSTECNMSLLTIQKTIDAMQQ 187

Query: 573 PISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            IS++  I ++D S L D + D ++   P    +Q   RE     +  L   E+ ++  R
Sbjct: 188 NISIDGTINEDDNSTLHDILPDPESKADPFKKIVQEKNRELIMNWIECLNENEKELIIKR 247

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           FG+      TL+++GK+  VTRER+RQIE + + KL++  ++K ++
Sbjct: 248 FGLDGKEPETLDKIGKRLGVTRERVRQIEKRILTKLRNHLKTKNIK 293


>gi|254794681|ref|YP_003079518.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14359]
 gi|254594081|gb|ACT73442.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O157:H7
           str. TW14359]
          Length = 330

 Score =  202 bits (514), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  +    L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWPFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|269101863|ref|ZP_06154560.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161761|gb|EEZ40257.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 333

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 95/227 (41%), Positives = 157/227 (69%), Gaps = 2/227 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA W
Sbjct: 89  VARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATW 148

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA +L  PV+ 
Sbjct: 149 WIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAIQLEKPVDD 208

Query: 563 VRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           V ++L++ +   S++ PI GD D + L D I D+   +P  S    +++ +    L  L 
Sbjct: 209 VNRMLRLNERVSSVDNPISGDADKALL-DIIPDEKGGTPEVSTQTDDIKSSIVDWLDELN 267

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 268 PKQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRRLR 314


>gi|255034849|ref|YP_003085470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947605|gb|ACT92305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 287

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 96/238 (40%), Positives = 159/238 (66%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A + + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+W
Sbjct: 49  LALERLTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVW 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I +++A+QS  +R+P++    ++K+ +T   +  + +REP+PEE+A+ L +    
Sbjct: 109 WIRQSILQALAEQSRIVRLPLNRVGSLNKISKTFSELEQRFEREPSPEELAEVLEISSSE 168

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V   +KI+   +S++ P    + + L D +E+     P    +  +LR+   R L +LT 
Sbjct: 169 VVDTMKISGRHVSMDAPFVQGEENSLLDVLENDLEDKPDSGLVNESLRKEVQRALCTLTQ 228

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  V+ + FG+      TLEE+G++F +TRER+RQI+ KAIR+L+H SRSK L+++L
Sbjct: 229 READVIALYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHVSRSKALKTYL 286


>gi|332087476|gb|EGI92604.1| RNA polymerase sigma factor RpoS [Shigella boydii 5216-82]
          Length = 330

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNSK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  V   RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVPARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 322


>gi|150026087|ref|YP_001296913.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772628|emb|CAL44111.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
          Length = 287

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 161/237 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLTLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +    +R P+ EEIAK+L M V  V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKMYALLEQSNERPPSAEEIAKELDMTVNDV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + +P    I  +LR    R L +LTPR
Sbjct: 170 KESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPNPDRELIIESLRTEIERSLETLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 230 EADVVRLYFGLADQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286


>gi|240047243|ref|YP_002960631.1| RNA polymerase sigma factor [Mycoplasma conjunctivae HRC/581]
 gi|239984815|emb|CAT04802.1| RNA polymerase sigma factor [Mycoplasma conjunctivae]
          Length = 533

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 109/256 (42%), Positives = 159/256 (62%), Gaps = 20/256 (7%)

Query: 433 MVRKGECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + RK E    + +K    +++ NLRLVI+ AK+Y NRGL F+DLI EGN+G+MKA  K+D
Sbjct: 274 LARKMEIPGRVGRKARDTLIKRNLRLVINNAKRYKNRGLNFIDLISEGNLGIMKAISKYD 333

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G+KFSTYA WW++Q+ITR++ADQ+  IRIPVHM + I+K+ +  R +  K    P+ 
Sbjct: 334 RTKGFKFSTYATWWIRQSITRAVADQARLIRIPVHMVETINKINKIERELQQKNGVTPSA 393

Query: 550 EEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEIA  +      E VR + KI  +PISL+  IG E+ S   DFI+D++ +SP D A Q 
Sbjct: 394 EEIADVMGADFTPEKVRYIRKINIDPISLDKAIGKEEDSSFSDFIKDESVISPSDYAEQ- 452

Query: 608 NLRETTTRVLA-----SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERI 656
              E  ++VL      +L   E+  +  R+GIG + +      H+ +E+     VT+ERI
Sbjct: 453 ---EEKSKVLIEMIKNNLEEEEQEFIMRRYGIGNDKNGRQYRAHSYDELAADRGVTKERI 509

Query: 657 RQIEAKAIRKLKHPSR 672
           RQIE+K ++KL+ P R
Sbjct: 510 RQIESKILKKLRAPQR 525


>gi|78214165|ref|YP_382944.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78198624|gb|ABB36389.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 328

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 102/245 (41%), Positives = 159/245 (64%), Gaps = 8/245 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S  RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A
Sbjct: 82  SRHRHKIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERA 134

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  
Sbjct: 135 VDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFG 194

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS 603
           R+P   E+A  + +    +  ++  +    SL+    G+ED S LG+ I D N   P++ 
Sbjct: 195 RQPNRLELASAMGIEPRELEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEG 254

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             ++  +E     L+ L  RE+++L++RFG+G     TL E+G+Q  V+RER+RQ+EAKA
Sbjct: 255 MDRSIQKEHLGGWLSQLNEREQKILKLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKA 314

Query: 664 IRKLK 668
           I KL+
Sbjct: 315 ILKLR 319


>gi|6010736|gb|AAF01234.1|AF184103_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +T ER+RQI+ + +R+L+   +++ L
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTCERVRQIQVEGLRRLREILQTQGL 322


>gi|213418760|ref|ZP_03351826.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 162

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 96/155 (61%), Positives = 125/155 (80%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 8   QKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 67

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 68  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 127

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 128 KLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 162


>gi|312129690|ref|YP_003997030.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Leadbetterella
           byssophila DSM 17132]
 gi|311906236|gb|ADQ16677.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leadbetterella
           byssophila DSM 17132]
          Length = 287

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 155/233 (66%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+
Sbjct: 54  LTKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQS 113

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +++A+QS  +R+P++    ++K+ +T   +  + +REP+PEE+A+ L +    V   +
Sbjct: 114 ILQALAEQSRIVRLPLNRVGSLNKISKTFSELEQRFEREPSPEELAEVLEISANEVVDTM 173

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI+   +S++ P    + + L D +E+   + P    +  +LR    R L++LT RE  V
Sbjct: 174 KISGRHVSVDAPFVQGEENSLLDVLENDTEIRPDQELMNDSLRREVLRALSTLTQREAEV 233

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   FG+      TLEE+G++F +TRER+RQI+ KAIR+L+  SRSK L+++L
Sbjct: 234 IMFYFGLNGEQAMTLEEIGEKFNLTRERVRQIKEKAIRRLRQTSRSKALKAYL 286


>gi|294141938|ref|YP_003557916.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
 gi|293328407|dbj|BAJ03138.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
          Length = 328

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 99/239 (41%), Positives = 159/239 (66%), Gaps = 2/239 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK       ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 75  VYFSRKSLKGCGKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDP 134

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT E
Sbjct: 135 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAE 194

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           EIA KL +P   V ++LK+ +   S++TP+G ++   L D +   ++V P D  +Q  ++
Sbjct: 195 EIAAKLDLPSSDVSRMLKLNERITSVDTPLGGDNDKALLDVLAADDSVGP-DYKVQDEDM 253

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  + L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 254 SKSVVKWLDELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 312


>gi|268315720|ref|YP_003289439.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
 gi|262333254|gb|ACY47051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
          Length = 279

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 98/244 (40%), Positives = 166/244 (68%), Gaps = 3/244 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA     ++  ANLR V+SVAKKY  +GL   DLI EGN GL+KAA++FD   G
Sbjct: 35  IKQGDEEAL---HKLTRANLRFVVSVAKKYQGQGLSLADLINEGNYGLIKAAQRFDETRG 91

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++QAI +++A+QS  +R+P++    I K+ + + R++ + +R P+ EE+A
Sbjct: 92  FKFISYAVWWIRQAILQALAEQSRVVRLPLNRIGTISKIRKVSARLAQEHERAPSAEELA 151

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L + VE +R+ L+ T   +S++ P  D+D + L D + ++   SP +  ++ +L+   
Sbjct: 152 EELNIDVEKIREALQHTGRALSMDAPFTDDDDNSLLDVLPNEEDTSPDEGLMEESLKIDI 211

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L++L PRE  ++R+ FGIG     TLEE+G++F +TRER+RQI+ KA+RKL+   R 
Sbjct: 212 ERALSTLHPREAEIIRLYFGIGREHPLTLEEIGQRFGLTRERVRQIKEKALRKLRQKHRR 271

Query: 674 KKLR 677
           ++L+
Sbjct: 272 EELQ 275


>gi|81299483|ref|YP_399691.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 7942]
 gi|123557285|sp|Q31QG5|RPOD3_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD3
 gi|81168364|gb|ABB56704.1| group2 RNA polymerase sigma factor SigD [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score =  201 bits (512), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/249 (40%), Positives = 161/249 (64%), Gaps = 8/249 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+SI E R    +   GE     AK++M+EANLRLV+SVAKKY  R +  LDLIQEG IG
Sbjct: 69  GLSIEELRQQQHL---GEQ----AKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIG 121

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           + +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S
Sbjct: 122 MQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLS 181

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ R  T  E+A  L +    VR  L+  + P+SL+  +GD   + LGD +E  +  +P
Sbjct: 182 QQLGRTATLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTELGDLLE-TDCTTP 240

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +  +QA++R    R+L  LT ++ +V+ +R+G+      TL  +G +  ++RER+RQ+E
Sbjct: 241 EEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLE 300

Query: 661 AKAIRKLKH 669
            +A+  L+ 
Sbjct: 301 REALHTLRQ 309


>gi|271963319|ref|YP_003337515.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270506494|gb|ACZ84772.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 312

 Score =  201 bits (512), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 151/225 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E ++ANLRLV++VA+KY+ RG+  +DL+QEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 82  AKDEFIQANLRLVVAVARKYSGRGMPLIDLVQEGNLGLVRAVEKFDYRRGYKFSTYATWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++ R+I +Q+  +R+P H  +++ +++R  R M  +  +EPT  ++A  L +P+E V
Sbjct: 142 IRQSVGRAIHEQARPVRLPTHAGEQMTRLMRVRRDMLAEFDQEPTDADLAAVLELPIERV 201

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++ +   +P+SL+  +GDED + LGD I D+    P   A+    RE   + L  L  +
Sbjct: 202 RELRRWASDPVSLQLGVGDEDETELGDMIADETWADPEQQAMDILERERLEQWLTGLEGQ 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +LR R+G+    +HTL EVG+++ + R+R R+IE  A+ +L+
Sbjct: 262 TREMLRWRYGLMDGREHTLTEVGERYGIGRDRARRIERDALARLR 306


>gi|23978331|dbj|BAC21136.1| principal sigma factor [Synechococcus leopoliensis]
          Length = 188

 Score =  201 bits (512), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 100/188 (53%), Positives = 136/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE    VL++L+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQLFNVT 188


>gi|23978358|dbj|BAC21144.1| principal sigma factor [Nodularia sp. PCC 73104]
          Length = 188

 Score =  201 bits (512), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 100/188 (53%), Positives = 136/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GY+FSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYRFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIES-DGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|312964996|ref|ZP_07779236.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
 gi|312290552|gb|EFR18432.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
          Length = 237

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 93/229 (40%), Positives = 158/229 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 181 LARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 229


>gi|312134852|ref|YP_004002190.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774903|gb|ADQ04390.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 273

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 95/226 (42%), Positives = 152/226 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++  AN RLV ++AK+Y   GL + DL+QEG IGLM A  K+D+  GY+F+TYA WW
Sbjct: 37  AKEKLFRANKRLVANIAKRYRGFGLDYEDLMQEGFIGLMNAVNKYDYRQGYRFATYATWW 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAIT++I +    IR+P+H+ +++ K+ +  R++  +  REPT  EIAK++    + V
Sbjct: 97  IRQAITKAIYNTGRNIRVPIHLHEQMFKIRKVYRKLLQENNREPTIREIAKEMNWSTKKV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K+L +  E +SL+TPIG++  + +GDF+ D  A S  ++  +  L E  T+    L+ +
Sbjct: 157 QKMLDLFNEIVSLDTPIGEDGLATIGDFMIDDKAFSYFENVEKQLLVEQLTKYFDKLSEK 216

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+RV+ +R+G+      TLEEVG    +TRERIRQIE KA+RK+++
Sbjct: 217 EKRVIVLRYGLADGKGRTLEEVGNALNLTRERIRQIEIKALRKIRY 262


>gi|260436326|ref|ZP_05790296.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260414200|gb|EEX07496.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 308

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 102/245 (41%), Positives = 159/245 (64%), Gaps = 8/245 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S  RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A
Sbjct: 62  SRHRHKIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERA 114

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  
Sbjct: 115 VDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFG 174

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS 603
           R+P   E+A  + +    +  ++  +    SL+    G+ED S LG+ I D N   P++ 
Sbjct: 175 RQPNRLELASAMGIEPRELEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEG 234

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             ++  +E     L+ L  RE+++L++RFG+G     TL E+G+Q  V+RER+RQ+EAKA
Sbjct: 235 MDRSIQKEHLGGWLSQLNEREQKILKLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKA 294

Query: 664 IRKLK 668
           I KL+
Sbjct: 295 ILKLR 299


>gi|78185860|ref|YP_378294.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78170154|gb|ABB27251.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 328

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 99/226 (43%), Positives = 152/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 94  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+A  + +    +
Sbjct: 154 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLELASAMGIEPREL 213

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N   P++   ++  +E     L+ L  
Sbjct: 214 EDLITQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEGMDRSIQKEHLGGWLSQLNE 273

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+++LR+RFG+G     TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 274 REQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|325857152|ref|ZP_08172442.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
 gi|325483215|gb|EGC86193.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
          Length = 327

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 171/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   +RKG+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 62  LQEIGHEEMISIEEEVELAQRIRKGDRKAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 118

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+
Sbjct: 119 LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKI 178

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+  EIA+   +P E +   +K++   +S++ P  D+D S L D I
Sbjct: 179 NKILNQFEQENERRPSIGEIAQSTDIPEEKIADAIKVSSRHVSVDAPFYDDDQSSLLDVI 238

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + N  S     ++ +LRE   RVL  L  RE++V+   FGI    + TLEE+G ++ +T
Sbjct: 239 PNDNVPSTDRGLVEESLREEIGRVLQVLEDREKKVVEAYFGINQR-EMTLEEIGSKYNLT 297

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  + SK L+++L
Sbjct: 298 RERVRQIKEKAIRRLRQQTNSKVLKAYL 325


>gi|87123382|ref|ZP_01079233.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86169102|gb|EAQ70358.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 293

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 102/242 (42%), Positives = 158/242 (65%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 50  RHQIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 102

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P
Sbjct: 103 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQP 162

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +  + +  ++  +    SL+    G+ED S LG+ I D N   P++   +
Sbjct: 163 NRLELAHAMGIEPKDLEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGAEPMEGMDR 222

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     LA L  RE+++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 223 SIQKEHLGGWLAQLNDREQKILRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILK 282

Query: 667 LK 668
           L+
Sbjct: 283 LR 284


>gi|327313374|ref|YP_004328811.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
 gi|326944913|gb|AEA20798.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
          Length = 327

 Score =  201 bits (512), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 171/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   +RKG+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 62  LQEIGHEEMISIEEEVELAQRIRKGDRKAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 118

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+
Sbjct: 119 LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKI 178

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+  EIA+   +P E +   +K++   +S++ P  D+D S L D I
Sbjct: 179 NKILNQFEQENERRPSIGEIAQSTDIPEEKIADAIKVSSRHVSVDAPFYDDDQSSLLDVI 238

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + N  S     ++ +LRE   RVL  L  RE++V+   FGI    + TLEE+G ++ +T
Sbjct: 239 PNDNVPSTDRGLVEESLREEIGRVLQVLEDREKKVVEAYFGINQR-EMTLEEIGSKYNLT 297

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  + SK L+++L
Sbjct: 298 RERVRQIKEKAIRRLRQQTNSKVLKAYL 325


>gi|332880149|ref|ZP_08447831.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332681908|gb|EGJ54823.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 286

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 105/271 (38%), Positives = 178/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   + +  +L     R L++L+ RE+ +++M FGI  + + TLEE+G +F
Sbjct: 199 VNDD---SPMADRTLVNESLSREIDRALSTLSEREKEIIQMFFGIN-HQEMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  ++SK L+S+L
Sbjct: 255 NLTRERVRQIKEKAIRRLRQNTKSKLLKSYL 285


>gi|119774181|ref|YP_926921.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
 gi|119766681|gb|ABL99251.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
          Length = 327

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 97/231 (41%), Positives = 157/231 (67%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 84  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 141

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA KL +
Sbjct: 142 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAAKLNL 201

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           P   V ++LK+ ++  S++ P+G ++   L D + D ++V P D  +Q  ++  +    L
Sbjct: 202 PSVEVSRMLKLNEKITSVDVPLGGDNDKALLDVLPDDDSVGP-DYKVQDEDISNSVVNWL 260

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 261 NELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 311


>gi|41853|emb|CAA34435.1| katF [Escherichia coli K-12]
          Length = 362

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+  EIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAVEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 334


>gi|148907004|gb|ABR16646.1| unknown [Picea sitchensis]
          Length = 592

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 97/235 (41%), Positives = 157/235 (66%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++  NLRLVISVAK Y NRGL   DLIQ G++GLM++AEKFD+  G+KFSTYA WW++Q
Sbjct: 357 KIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGFKFSTYAYWWIRQ 416

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +IT+++ +QS TIR+PVH+ + + ++    R +  + KR+PT EE+A+   + +  +R V
Sbjct: 417 SITKALTEQSRTIRLPVHIVESMTRIRTAWRLLYQEHKRDPTKEEVAEVAGISMTRLRHV 476

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            + ++ P SL+  +G +      + + D N+ S      +   ++   RVL +LT RE++
Sbjct: 477 TRCSRVPTSLDRCVGKDMDEKFSEIVADTNSESTETIVSKELFKKDLDRVLDTLTAREKQ 536

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+R+R+G+      +L EVG+ F ++RER+RQIE KA+RKL+   R++ L+ +LD
Sbjct: 537 VVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAMRKLRQNHRTQHLKHYLD 591


>gi|116071837|ref|ZP_01469105.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065460|gb|EAU71218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 284

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 99/226 (43%), Positives = 152/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 50  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+A  + +    +
Sbjct: 110 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLELASAMGIEPREL 169

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N   P++   ++  +E     L+ L  
Sbjct: 170 EDLITQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEGMDRSIQKEHLGGWLSQLNE 229

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+++LR+RFG+G     TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 230 REQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 275


>gi|56750866|ref|YP_171567.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 6301]
 gi|56685825|dbj|BAD79047.1| group2 RNA polymerase sigma factor RpoD3 [Synechococcus elongatus
           PCC 6301]
          Length = 326

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 101/249 (40%), Positives = 161/249 (64%), Gaps = 8/249 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+SI E R    +   GE     AK++M+EANLRLV+SVAKKY  R +  LDLIQEG IG
Sbjct: 75  GLSIEELRQQQHL---GEQ----AKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIG 127

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           + +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S
Sbjct: 128 MQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLS 187

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ R  T  E+A  L +    VR  L+  + P+SL+  +GD   + LGD +E  +  +P
Sbjct: 188 QQLGRTATLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTELGDLLE-TDCTTP 246

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +  +QA++R    R+L  LT ++ +V+ +R+G+      TL  +G +  ++RER+RQ+E
Sbjct: 247 EEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLE 306

Query: 661 AKAIRKLKH 669
            +A+  L+ 
Sbjct: 307 REALHTLRQ 315


>gi|256376033|ref|YP_003099693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255920336|gb|ACU35847.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 320

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 100/236 (42%), Positives = 160/236 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+ ANLRLV+SVAKK++ RGL  LD++QEGN+GL++A EKFD+  GYKFSTYA+WW
Sbjct: 83  AKDHMIRANLRLVVSVAKKHSFRGLPLLDVVQEGNLGLIRAVEKFDYSKGYKFSTYAIWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R +A+Q+ T+R+PVH+ +++ K+ +  R++  ++ REPT EE+A    +    V
Sbjct: 143 IRQAIERGLAEQTRTVRLPVHVVEELSKIKKAERKLRAELDREPTVEELAGATGLRAPRV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++    +  ISLETP+GDE ++ + D IED +A S  D+  QA        ++ +L  R
Sbjct: 203 AELRDAGRATISLETPVGDEGSASVADLIEDADAASAYDAVEQAAFSSELRALVETLPAR 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +  ++  R+G+     HTL+EV ++  +TRERIRQ+E +++R L+ P  ++ L ++
Sbjct: 263 QALIVSRRYGLTDGRVHTLQEVAEELGLTRERIRQLEKESLRFLRDPQHNRGLLAW 318


>gi|14970557|emb|CAC44359.1| RpoS protein [Erwinia chrysanthemi]
          Length = 332

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 92/227 (40%), Positives = 156/227 (68%), Gaps = 2/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    ++++   + L  L  +
Sbjct: 210 NRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK--AIRKLK 668
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ +   +R+L+
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVQVEGLRRLR 316


>gi|330995823|ref|ZP_08319720.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
 gi|329574553|gb|EGG56118.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
          Length = 286

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 105/271 (38%), Positives = 178/271 (65%), Gaps = 10/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +RKG+    +A +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRKGD---RVALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDF 591
            +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P +  ED S L   
Sbjct: 139 SKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 592 IEDKNAVSPLD--SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D    SP+   + +  +L     R L++L+ RE+ +++M FGI  + + TLEE+G +F
Sbjct: 199 VNDD---SPMADRTLVNESLAREIDRALSTLSEREKEIIQMFFGIN-HQEMTLEEIGDKF 254

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ KAIR+L+  ++SK L+S+L
Sbjct: 255 NLTRERVRQIKEKAIRRLRQNTKSKLLKSYL 285


>gi|325269188|ref|ZP_08135807.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|324988417|gb|EGC20381.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
          Length = 287

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 170/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   +RKG+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEEMISIEEEVELAQRIRKGDRKAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   R   + +R P+ +EIA+   +P + +   +K     +S++ P  D++ S L D I
Sbjct: 139 NKILNRFEQENERRPSIDEIAQSTDLPEDKIADAMKANSRHVSVDAPFYDDEQSSLLDVI 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + NA S     ++ +LRE   RVL  L  RE+ V+   FGI    + TLEE+G ++ +T
Sbjct: 199 PNDNAPSTDRGLVEESLREEIGRVLQILEDREKMVVEAYFGINQR-EMTLEEIGSKYNLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  + SK L+++L
Sbjct: 258 RERVRQIKEKAIRRLRQQTNSKVLKAYL 285


>gi|313206169|ref|YP_004045346.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|312445485|gb|ADQ81840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|315023147|gb|EFT36160.1| RNA polymerase sigma factor RpoD [Riemerella anatipestifer RA-YM]
 gi|325336386|gb|ADZ12660.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Riemerella anatipestifer RA-GD]
          Length = 288

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 98/250 (39%), Positives = 168/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +K      +A +++++ANLR V+SV+K+Y N+GL   DLI EGN+GLMKAA+++D 
Sbjct: 37  VELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+PE
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ L M  E +++ +K +   +S++ P+ + + S+L D +    + SP    +  +L+
Sbjct: 157 ELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQ 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  ++R+ FG+      TLEE+G+ F +TRER+RQI+ KAI++LKH 
Sbjct: 217 IEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHN 276

Query: 671 SRSKKLRSFL 680
           SRSK L+S+L
Sbjct: 277 SRSKILKSYL 286


>gi|254786794|ref|YP_003074223.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
 gi|237685659|gb|ACR12923.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
          Length = 337

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 152/225 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  ARKRMIESNLRLVVKISRRYVNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EP+ EEIA+ L  PVE V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPSAEEIAELLEKPVEDV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L + +   S++ PIG      + D + D+    P++    ++L  +    L  L+ +
Sbjct: 216 ERMLALNERVTSMDAPIGPASEKTVVDTVPDQQVSDPVELLEDSDLSTSLNSWLDELSEK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 276 QREVVARRFGLRGHETSTLEEVGREIGLTRERVRQIQVEALRRLR 320


>gi|75812337|ref|YP_319956.1| sigma-28 [Anabaena variabilis ATCC 29413]
 gi|75705093|gb|ABA24767.1| Sigma-28 [Anabaena variabilis ATCC 29413]
          Length = 316

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 100/237 (42%), Positives = 155/237 (65%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ ANLRLV+S+AKKY  R L+FLDL+QEG IGL +  EKFD   GYK STYA WW
Sbjct: 81  AKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPNRGYKLSTYAYWW 140

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V QAITR+IA++S T+R+P+H+ +K++++ +  R     + R P+  EIA+KL +    +
Sbjct: 141 VTQAITRAIAEKSRTVRLPIHVNEKLNQIKKVQREFFQTLGRRPSVAEIAQKLELEPSQI 200

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ LK+    ISL+  +GD   + L + +  +  VSP ++     LR+  + +LASL P 
Sbjct: 201 REYLKVASGTISLDLKVGDNQETELSELLASE-GVSPNENTTHEMLRQDLSDLLASLKPM 259

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK--HPSRSKKLRS 678
           +  VL +RFG+  N + +L ++ ++  ++RER+RQI+ KA+  L+   PS  + L S
Sbjct: 260 QREVLILRFGLLDNQEQSLAQISEKLNLSRERVRQIQQKAMTALRRQQPSIGQYLTS 316


>gi|23978363|dbj|BAC21146.1| principal sigma factor [Pleurocapsa sp. PCC 7327]
          Length = 188

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 100/188 (53%), Positives = 136/188 (72%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|163749990|ref|ZP_02157234.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
 gi|161330264|gb|EDQ01245.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
          Length = 323

 Score =  201 bits (511), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 94/225 (41%), Positives = 152/225 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  SRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA KL +P   V
Sbjct: 143 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAAKLDLPCSDV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+ +   S++TP+G ++   L D +   + V P       ++ ++  + L  L  +
Sbjct: 203 SRMLKLNERITSVDTPLGGDNDKALLDVLAADDNVGPDYKVQNEDMSKSVVKWLDELNTK 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK
Sbjct: 263 QREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLK 307


>gi|170077819|ref|YP_001734457.1| sigma-70 factor [Synechococcus sp. PCC 7002]
 gi|169885488|gb|ACA99201.1| sigma-70 factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score =  201 bits (511), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 99/237 (41%), Positives = 164/237 (69%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R L+FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNLEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q  TIR+P+H+ +K++K+ +T R+++  + R  T  EIA+ L +    +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKTQRQLAQDLGRAATIAEIAEALELEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+  ++++ PISL+  +GD   + L D +ED +  SP ++     L++    ++A LTP+
Sbjct: 212 REYFRVSRHPISLDVRVGDNQDTELMDLLED-SGESPDNNVTYELLKQDLRDLIADLTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++ V+ +RFG+    + +L ++GK+  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 271 QQEVIILRFGLNDGKELSLAKIGKRMNLSRERVRQLERQALNHLRR--RRSQIREYL 325


>gi|192358973|ref|YP_001982681.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
 gi|190685138|gb|ACE82816.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
          Length = 335

 Score =  201 bits (511), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 99/238 (41%), Positives = 149/238 (62%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK       A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 82  VFFARKALKGDEAARKRMIESNLRLVVKISRRYVNRGLALLDLIEEGNLGLIRAVEKFDP 141

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPE
Sbjct: 142 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPE 201

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V  +L + +   S++ PIG      + D I D +   P      ++L 
Sbjct: 202 EIANLLEKPVADVEHMLSLNERVTSIDAPIGASSDRTVADTIADTHVSDPAALLQDSDLT 261

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    L  LT ++  VL  RFG+      TLEEVG +  +TRER+RQI+ +A+++L+
Sbjct: 262 ASLDHWLEELTEKQREVLARRFGLRGYEVSTLEEVGHEIGLTRERVRQIQVEALKRLR 319


>gi|213029652|ref|ZP_03344099.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 322

 Score =  201 bits (511), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 91/224 (40%), Positives = 155/224 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R +
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRAV 313


>gi|117617733|ref|YP_855373.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559140|gb|ABK36088.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 327

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 95/225 (42%), Positives = 153/225 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKIARRYNNRGLVLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+++  EPT E+IA  L   V+ V
Sbjct: 146 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELSHRLDHEPTAEDIAFALDRSVDDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+ ++  S++TPIG +    L D + D+  + P   +   ++R +    L  L P+
Sbjct: 206 NRMLKLNEKITSVDTPIGGDRDKALLDVLSDERGMGPELESQDDDMRASIVHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+
Sbjct: 266 QREVLARRFGLLGYEPATLEDVGAEIGLTRERVRQIQVEGLRRLR 310


>gi|33241312|ref|NP_876254.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|33238842|gb|AAQ00907.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 339

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 102/242 (42%), Positives = 160/242 (66%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 96  RHQIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 148

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S+ + R+P
Sbjct: 149 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHNLGRQP 208

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A +L M  + +  ++  +    SL++   G+ED S LG+ I D N   P++   +
Sbjct: 209 NRVELANELGMEPKDLEDLMAQSAPCASLDSHARGEEDRSTLGELIPDPNYDEPMECMDR 268

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +E  +  L+ L  RE++++R+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 269 NMQKEHLSGWLSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILK 328

Query: 667 LK 668
           L+
Sbjct: 329 LR 330


>gi|304312494|ref|YP_003812092.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
 gi|301798227|emb|CBL46449.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
          Length = 342

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 94/225 (41%), Positives = 152/225 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 ARKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPTPEEI+  L  P+E V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPTPEEISALLDKPLEDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S+++P+G +    L D I D     P +    A+L+ +    L  L  +
Sbjct: 222 KRMLGLNERISSVDSPVGFDSDKSLLDTIADTKNTDPAELLQDADLKNSIDYWLDQLPGK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+      TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 282 QREVIARRFGLRGFEMSTLEEVGREIGLTRERVRQIQVEALKRLR 326



 Score = 37.7 bits (86), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 3/88 (3%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           D AS  S++  F  +R++     T D  ++YL E+G   LL+ E E+  A+R   G A  
Sbjct: 45  DFASDESDAETF--RRQEGGITKTLDATQIYLNEIGFSPLLTPEEEVYYARRALRGNADA 102

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLL 181
              + ES L    + I R  +N G +LL
Sbjct: 103 RKRMIESNLRL-VVKIARRYVNRGLSLL 129


>gi|309786170|ref|ZP_07680798.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
 gi|308925915|gb|EFP71394.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
          Length = 237

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/229 (40%), Positives = 158/229 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 181 LARRFGLLGYEAATLEDVGREIDLTRERVRQIQVEGLRRLREILQTQGL 229


>gi|281357254|ref|ZP_06243743.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281316285|gb|EFB00310.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 428

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 105/239 (43%), Positives = 155/239 (64%), Gaps = 5/239 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++M+EANLRLVIS+A+KY NRGL F DLIQEGN+GL++A EKFD+ LG KFSTYA WW+
Sbjct: 187 RQKMIEANLRLVISIAQKYRNRGLPFNDLIQEGNLGLLRALEKFDFRLGNKFSTYASWWI 246

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           K  I+RSIA+QS  IRIP HM   I+ +    +R      REP  +E+A  L MPV  + 
Sbjct: 247 KHNISRSIAEQSRVIRIPAHMVHAINSMTWAEQRFIQSHGREPEIDELAAVLEMPVARIS 306

Query: 565 KVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + K++ + ISL+ P+   ED + L D I D +  +P+    +  L +    +L +L  R
Sbjct: 307 AIRKMSCQTISLQAPVSSSEDGAMLEDLIADDSTANPVRDFARKILYDKLYEMLRTLPER 366

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +++++ +RFG+       L ++ ++F +TRERIRQ+EAK I  L+ P++ K    +LDG
Sbjct: 367 DQQIIILRFGLFGQPCLPLVDISRRFNLTRERIRQLEAKIIENLRSPAKLK----YLDG 421


>gi|17233195|ref|NP_490285.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17135717|dbj|BAB78263.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 316

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 155/237 (65%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ ANLRLV+S+AKKY  R L+FLDL+QEG IGL +  EKFD   GYK STYA WW
Sbjct: 81  AKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPNRGYKLSTYAYWW 140

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V QAITR+IA++S T+R+P+H+ +K++++ +  R     + R  T  EIA+KL +    +
Sbjct: 141 VTQAITRAIAEKSRTVRLPIHVNEKLNQIKKVQREFFQTLGRRATVAEIAQKLELEPSQI 200

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ LK+    ISL+  IGD   + L + +  +  VSP ++     LR+  + +LASL P 
Sbjct: 201 REYLKVASGTISLDLKIGDNKETELSELLASE-GVSPDENITHEMLRQDLSDLLASLKPM 259

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK--HPSRSKKLRS 678
           +  VL +RFG+  N + +L ++G++  ++RER+RQI+ KA+  L+   PS  + L S
Sbjct: 260 QREVLILRFGLLDNQEQSLAQIGEKLNLSRERVRQIQQKAMTALRRQQPSIGQYLTS 316


>gi|260591639|ref|ZP_05857097.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260536439|gb|EEX19056.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 287

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 108/268 (40%), Positives = 169/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   +RKG+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEEMISIEEEVELAQQIRKGDRKAL---ERLTKANLRFVVSVAKQYQNQGLSLSD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+
Sbjct: 79  LINEGNFGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+ +EIA+   +P E + +  KI    IS++ P  D+D S L D I
Sbjct: 139 NKVLNKFEQENERRPSIDEIAQDTDIPEEKIIEAFKINTHHISVDAPFHDDDESSLLDVI 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +    S   S ++ +LR    RVL  L  RE++V+   FGI    + TLEE+G ++ +T
Sbjct: 199 PNDAIPSTDKSLVEESLRAEIGRVLDILEDREKKVIEAYFGINQR-EMTLEEIGSKYGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  + SK L+++L
Sbjct: 258 RERVRQIKEKAIRRLRQQTNSKILKAYL 285


>gi|254255220|ref|ZP_04948536.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124900957|gb|EAY71707.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 241

 Score =  201 bits (510), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 96/237 (40%), Positives = 147/237 (62%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D+  G++FSTYA WW
Sbjct: 4   ARIALFDANLRLVVSIAKRYRDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 63

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++T ++AD   TIR+P H  D ++K+ R AR    +     TP ++A  +  PV+ V
Sbjct: 64  IRQSVTHALADLGRTIRVPTHTVDALNKLARLAREHRQRAGSAATPAQLAAHIGEPVDKV 123

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +L I KEP+S + P+  +      D   D    SP D+A    LR T    +  L  R
Sbjct: 124 RDLLAIVKEPVSADLPVSPDGDLTFIDVAPDTATPSPEDAADATQLRRTIAAAIERLPQR 183

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 184 EAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRASDALAVLRPFI 240


>gi|45128597|gb|AAS55059.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  201 bits (510), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 121/278 (43%), Positives = 165/278 (59%), Gaps = 13/278 (4%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    +  S K  V  E ++ +     L   ++  LV +L   
Sbjct: 218 EKFNQLRSTYQNLQLAINEYGYD--SPKATVANEMMLDVFKEFRLTPKQLXHLVXELRTA 275

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A   P  E       E
Sbjct: 276 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGXESSDAWLXEILASXXPYAEKIKRXEEE 335

Query: 403 VD-SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           +  SI K+      I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 336 IRRSIAKL----XMIEEETSLNVQNIKDISRRMSIGEAKAXRAKKEMVEANLRLVISIAK 391

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 392 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 451

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           PVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP
Sbjct: 452 PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMP 489



 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 2   KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 61

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 62  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 120

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 121 INQVQSSVAEYPGTIPYIL 139


>gi|298208827|ref|YP_003717006.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
 gi|83848754|gb|EAP86623.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
          Length = 288

 Score =  201 bits (510), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 103/273 (37%), Positives = 177/273 (64%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N ++ +S    I+  E   +   +R+G+    IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LNNYLQDVSKLDLITAEEEVELAQRIREGD---QIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+ S  +R+P++    
Sbjct: 75  RLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEHSRVVRLPLNKIGV 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSH 587
           I+K+ +T   +    +R P+  EIAK+L MPV  V+  +K +   +S++ P  + E+ S+
Sbjct: 135 INKINKTFSYLEQAYERPPSAAEIAKELDMPVSKVKTAMKNSGRSLSMDAPFQEGENDSN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++   + SP ++ +Q +L     R L +LT RE  V+R+ +G+G     TL+E+G+
Sbjct: 195 LYDVLKSGESPSPDNNLMQDSLSVEIERALDTLTEREADVIRLNYGLGGQQPLTLQEIGE 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  K IR+L+H S+SK L+ +L
Sbjct: 255 TFDLSRERVRQIREKGIRRLRHESKSKILKKYL 287


>gi|1396060|dbj|BAA13043.1| part of principal sigma factor homolog [Synechocystis sp.]
          Length = 186

 Score =  201 bits (510), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 100/187 (53%), Positives = 136/187 (72%), Gaps = 1/187 (0%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+
Sbjct: 1   RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHL 60

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I ++ +T + +S +++R+PT EEIA+K+ M +E +R + K  + PISLETPIG E+ 
Sbjct: 61  YETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEED 120

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+
Sbjct: 121 SRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEI 179

Query: 646 GKQFCVT 652
           G+ F VT
Sbjct: 180 GQIFNVT 186


>gi|152985831|ref|YP_001346901.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
 gi|150960989|gb|ABR83014.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
          Length = 344

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 93  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 149

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+
Sbjct: 150 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPS 209

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 210 PEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 269

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  + L+ LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 270 LSESIDQWLSELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 329


>gi|33864510|ref|NP_896070.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641290|emb|CAE22420.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 344

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 100/242 (41%), Positives = 158/242 (65%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 101 RHKIRMGKR-------ARDRMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 153

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P
Sbjct: 154 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQP 213

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +  + +  ++  +    SL+    G+ED S LG+ I D +   P++   +
Sbjct: 214 NRLELAHAMGIQPQDLEDLIAQSAPCASLDAHARGEEDRSTLGELIPDPDGAEPMEGLDR 273

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 274 SIQKEHLGGWLSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRERVRQLEAKAILK 333

Query: 667 LK 668
           L+
Sbjct: 334 LR 335


>gi|23978347|dbj|BAC21141.1| principal sigma factor [Oscillatoria sp. PCC 7112]
          Length = 188

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 100/188 (53%), Positives = 135/188 (71%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIES-DGETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|332666643|ref|YP_004449431.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332335457|gb|AEE52558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 289

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 96/241 (39%), Positives = 163/241 (67%), Gaps = 3/241 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALEKLTKANLRFVVSVAKQYQNQGLSLSDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    ++K+ +    +  + +REP+PEE+A+ L +P E V
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKVGSLNKINKAFSELEQEFEREPSPEELAEMLEIPTEEV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLT 621
              L +    +S++ P  + + + L D +E+ N     D+ +  N  LR    R L++LT
Sbjct: 170 ETTLGVAARHVSMDAPFVEGEDNSLLDVLEN-NTTPSTDAGLDYNESLRREIERSLSTLT 228

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            R+  V+++ FGIG+    +LE++G++F +TRER+RQI+ KAI KL+  +RSK L+++L 
Sbjct: 229 DRQCDVIKLYFGIGVEHPMSLEDIGEKFGLTRERVRQIKDKAINKLRSANRSKLLKNYLG 288

Query: 682 G 682
           G
Sbjct: 289 G 289


>gi|300871837|ref|YP_003786710.1| RNA polymerase sigma factor RpoD [Brachyspira pilosicoli 95/1000]
 gi|300689538|gb|ADK32209.1| RNA polymerase sigma factor, RpoD [Brachyspira pilosicoli 95/1000]
          Length = 314

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 95/234 (40%), Positives = 159/234 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V++NLRLVIS+AK+Y N G+ F+D+I EGNIGL++A ++F++  G+KFSTY +WW+KQ
Sbjct: 79  KLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYRKGFKFSTYGVWWIKQ 138

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I + I+ +   IR P+H+   I K ++ ++ ++ ++ REP+ +EIAK++ +  + +  +
Sbjct: 139 SIVKEISSKRHIIRFPMHIARLIKKSIQISKNLTQQLGREPSIDEIAKEMKIDRKTLSSI 198

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +  T+E  S+++   + D + +  FIEDKN  SP   A   +LR+T T  L +L  +E  
Sbjct: 199 IVFTQETASVDSFFKNSDNNDMTSFIEDKNFPSPHQDAFMESLRDTLTEALKALDEKERT 258

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+  RFG+      TLE+ GK+  +TRER+RQI+ KA++KL   + SK+L+SFL
Sbjct: 259 VIIERFGLYGKEPKTLEDTGKELNITRERVRQIQIKALKKLSGLNLSKELKSFL 312


>gi|323345452|ref|ZP_08085675.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093566|gb|EFZ36144.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 295

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 173/268 (64%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +RKG+ +A    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 31  LQEIGHEELISVEEEVELAQRIRKGDRKAL---EKLTKANLRFVVSVAKQYQNQGLSLPD 87

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 88  LINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 147

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R   +   + +R P+ EEIA ++ +P E +   +KI  + IS++ P  + + + L D +
Sbjct: 148 NRALNKFEQENERHPSIEEIADRIDLPEEKIIDAMKINGKHISVDAPFAEGEDNSLLDIM 207

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +  + +  +  +  +LR+  +RVL  L  RE  ++   FGI    D TLEE+G +F +T
Sbjct: 208 PNTESPTADERLVSESLRDEISRVLLLLNERERMIIEAFFGIN-QQDMTLEEIGDKFGLT 266

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L++ ++S  L+SFL
Sbjct: 267 RERVRQIKEKAIRRLRNNTKSSLLKSFL 294


>gi|262197687|ref|YP_003268896.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081034|gb|ACY17003.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 465

 Score =  200 bits (508), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 95/275 (34%), Positives = 179/275 (65%), Gaps = 5/275 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++ + +++++++S  T    ++FR+ V  VR  E  A  A+ E V+ANLRLV+S+A+++ 
Sbjct: 192 AMARRKSQVRNVSFST--RRADFRNYVDQVRAAEHAARNARNEFVKANLRLVVSIARRFN 249

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +  +   DLIQEGN+GL+KA E++D+  G++FSTYA WW++ AI R++AD+   +R+PVH
Sbjct: 250 HGRMSLADLIQEGNLGLIKAVERYDYRRGFRFSTYASWWIRHAIGRALADKGREVRLPVH 309

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE 583
           M D  H++++   +++N + R+PT EE+++   + VE + K+   +  + +SL+ P+ DE
Sbjct: 310 MLDAHHRLLKAQHQLTNTLGRQPTSEELSEAANLSVEKIEKMRTHLLDQALSLDRPMNDE 369

Query: 584 DTSHLGDFIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D   + + ++D +    S L+   Q  + +   + L +L P E  +LR RFG+  + + T
Sbjct: 370 DGRSVAEVLQDPHGEEHSALNVLAQRTMSDEVRKTLQTLRPIEADILRRRFGLDNDEELT 429

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+++G+Q+ ++RERIRQ++ +A+ K++   R K +
Sbjct: 430 LKQIGEQYNLSRERIRQLQEQALTKMRVALRRKAM 464


>gi|320538977|ref|ZP_08038652.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
 gi|320030910|gb|EFW12914.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
          Length = 332

 Score =  200 bits (508), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 91/234 (38%), Positives = 159/234 (67%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++++ M+E+NLRLV+ +A +Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA W
Sbjct: 91  LSRRRMIESNLRLVVKIALRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 150

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+++  EP+ EEIA++L  PV  
Sbjct: 151 WIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHRLDHEPSAEEIAEQLDKPVGD 210

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V  +L++ +   S++TP+G +    L D + D+    P  +    +++++  + L  L  
Sbjct: 211 VSHMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEGTTQDDDMKQSIVKWLFELNA 270

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 271 KQREVLARRFGLLGYESATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 324


>gi|23978316|dbj|BAC21132.1| principal sigma factor [Anabaena cylindrica]
          Length = 188

 Score =  200 bits (508), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 100/188 (53%), Positives = 135/188 (71%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEK D   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIES-DGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|299472559|emb|CBN79861.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 694

 Score =  200 bits (508), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 108/246 (43%), Positives = 157/246 (63%), Gaps = 7/246 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AS AK  M+ ANLRLV+SVAK+Y  + L F DLIQEG  GL+KAAEKFD   G+KFSTYA
Sbjct: 120 ASKAKMAMLAANLRLVVSVAKRYRFQKLSFQDLIQEGTFGLVKAAEKFDPERGFKFSTYA 179

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQ+I R IADQS  IR+PVH+ D +++V +    M++K  + PT +E+A+ L +  
Sbjct: 180 TWWIKQSIMRGIADQSRIIRLPVHVHDFLNRVRKATLEMTDKNGKLPTDDELAEHLEVSA 239

Query: 561 EGVRKVLKITKEPISLETP--IGDEDTSHLGDFIEDKNAVS-----PLDSAIQANLRETT 613
             ++      +  +S+E P  I  + ++  G  +E    VS     P   A    +++  
Sbjct: 240 VRIQYYRDAAQATLSMEAPRNIASKTSTSPGKKVEMGQGVSGPEKTPDKQAQSDVMKQKV 299

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           T +L +L+ RE+ V++ RFG+G     TLEEVG+ F +TRER+RQIEA+A+ KL+ P R+
Sbjct: 300 TELLMTLSIREQEVVKARFGLGGALPRTLEEVGRDFRLTRERVRQIEARALHKLRQPYRN 359

Query: 674 KKLRSF 679
            ++R F
Sbjct: 360 YRVRDF 365


>gi|296127362|ref|YP_003634614.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296019178|gb|ADG72415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 309

 Score =  200 bits (508), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 97/234 (41%), Positives = 158/234 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V++NLRLVIS+AK+Y N G+ F+D+I EGNIGL++A ++F++  G+KFSTY +WW+KQ
Sbjct: 74  KLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYKKGFKFSTYGVWWIKQ 133

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I + I+ +   IR P+H+   I K ++T++ ++ K+ REPT +EIAK++ +  + +  +
Sbjct: 134 SIVKEISSKRHIIRFPMHIARLIKKSIQTSKVLTQKLGREPTTDEIAKEMKIDRKTLSYI 193

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +  T++  S+++   + D + +   IEDKN  SP   A   +LR+T T  L  L  +E  
Sbjct: 194 MIFTQDTASVDSFFKNSDNNDMTSIIEDKNFPSPHQKAFMDSLRDTLTEALKCLDEKERT 253

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+  RFG+      TLE+ GK+  +TRER+RQI+ KAI+KL   + SK+L+SFL
Sbjct: 254 VIISRFGLYGKEAKTLEDTGKELNITRERVRQIQIKAIKKLAGLNLSKELKSFL 307


>gi|313109026|ref|ZP_07794999.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
 gi|310881501|gb|EFQ40095.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
          Length = 344

 Score =  200 bits (508), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 157/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 93  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 149

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+
Sbjct: 150 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPS 209

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 210 PEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 269

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  + L  LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 270 LSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 329


>gi|153001641|ref|YP_001367322.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS185]
 gi|160876377|ref|YP_001555693.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS195]
 gi|217972427|ref|YP_002357178.1| RNA polymerase sigma 70 subunit RpoD subfamily [Shewanella baltica
           OS223]
 gi|151366259|gb|ABS09259.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS185]
 gi|160861899|gb|ABX50433.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS195]
 gi|217497562|gb|ACK45755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS223]
 gi|315268567|gb|ADT95420.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS678]
          Length = 326

 Score =  199 bits (507), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 97/239 (40%), Positives = 159/239 (66%), Gaps = 2/239 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK     + ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 73  VYFSRKALKGCAKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDP 132

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E
Sbjct: 133 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAE 192

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           EIA+KL +    V ++LK+ ++  S++TP+G ++   L D + D + V P D  +Q  ++
Sbjct: 193 EIAEKLQVSSADVSRMLKLNEKITSVDTPLGGDNDKALLDILADDDNVGP-DYKVQDEDI 251

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  + L  L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 252 SNSVVKWLNELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 310


>gi|83644704|ref|YP_433139.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
 gi|83632747|gb|ABC28714.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
          Length = 332

 Score =  199 bits (507), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 160/240 (66%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   M R+G+ +    +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 81  HFARMARRGDEKG---RKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 137

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R +R ++ K+  EP+
Sbjct: 138 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRASRELTQKLDHEPS 197

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA  L  PV+ V+++L + +   S+++PIG      L D + D+ +  P +    ++
Sbjct: 198 AEEIADLLEKPVKDVKRMLGLNERITSVDSPIGGNAEKSLLDTVADEASNDPAELLQDSD 257

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+    R L  L+ +++ V+  RFG+      TLEEVG++  +TRER+RQI+ +A+++++
Sbjct: 258 LKGCLDRWLDQLSDKQQEVIARRFGLRGYPMSTLEEVGQEIGLTRERVRQIQVEALKRMR 317


>gi|29143180|ref|NP_806522.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|695759|emb|CAA57298.1| sigma S [Salmonella enterica subsp. enterica serovar Typhi]
 gi|3820469|emb|CAA76807.1| RNA polymerase sigma subunit [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|29138813|gb|AAO70382.1| RNA polymerase sigma subunit RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 384

 Score =  199 bits (507), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 91/222 (40%), Positives = 154/222 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLR 311


>gi|15598818|ref|NP_252312.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|116051619|ref|YP_789542.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218890153|ref|YP_002439017.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa LESB58]
 gi|254242320|ref|ZP_04935642.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|1173167|sp|P45684|RPOS_PSEAE RecName: Full=RNA polymerase sigma factor rpoS
 gi|9949780|gb|AAG07010.1|AE004782_8 sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|440378|dbj|BAA05131.1| RNA polymerase principal sigma factor [Pseudomonas aeruginosa]
 gi|52632371|gb|AAU85546.1| RNA polymerase sigma factor [Pseudomonas sp. M18]
 gi|115586840|gb|ABJ12855.1| sigma factor RpoS [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126195698|gb|EAZ59761.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|218770376|emb|CAW26141.1| sigma factor RpoS [Pseudomonas aeruginosa LESB58]
          Length = 334

 Score =  199 bits (507), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 157/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 83  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 139

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+
Sbjct: 140 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPS 199

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 200 PEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 259

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  + L  LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 260 LSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 319


>gi|237809473|ref|YP_002893913.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
 gi|237501734|gb|ACQ94327.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
          Length = 324

 Score =  199 bits (507), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 149/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+E+NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  ARNRMIESNLRLVVKIARRYNNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+I +Q+ TIR+P+H+  +++  +RTAR ++ ++  EPT E+IA  L  PVE V
Sbjct: 143 IRQTVERAIMNQTRTIRLPIHVVKELNVYLRTARELAQRLDHEPTAEDIASLLDKPVEEV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+ +   S++TPI  +    L D + D     P D     +++ +    L  L P+
Sbjct: 203 SRMLKLNERICSVDTPIAGDGDKSLIDILTDDRINCPEDQTQDDDMQHSIVIWLEQLNPK 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R++K
Sbjct: 263 QREVLARRFGLLGYEPATLEEVGEEIGLTRERVRQIQVEGLRRMK 307


>gi|296387874|ref|ZP_06877349.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAb1]
          Length = 334

 Score =  199 bits (507), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 157/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 83  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 139

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+
Sbjct: 140 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPS 199

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 200 PEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 259

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  + L  LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 260 LSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 319


>gi|193216316|ref|YP_001997515.1| RpoD family RNA polymerase, sigma 70 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193089793|gb|ACF15068.1| RNA polymerase, sigma 70 subunit, RpoD family [Chloroherpeton
           thalassium ATCC 35110]
          Length = 299

 Score =  199 bits (507), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/241 (40%), Positives = 161/241 (66%), Gaps = 1/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA  A +++++ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +Y
Sbjct: 58  EARRALEKLIKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAKRFDETRGFKFISY 117

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P+ EE+A  L M 
Sbjct: 118 AVWWIRQSILQALAEQSRIVRLPLNRVGTLNKIGKAFSQLEQEYERDPSTEELAHLLDMN 177

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              +   LKI    IS++ P    D + L D +++ ++  P    +Q +LR    R L++
Sbjct: 178 SSEITDTLKIAGRHISVDAPFAQGDDNRLLDVLQN-DSQRPDHGLLQESLRLEVERSLSA 236

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+PRE  V+R  FGIGM    TLEE+G++F +TRER+RQI+ KAIR+L+H   S  L+ +
Sbjct: 237 LSPREADVIRSYFGIGMENPLTLEEIGERFKLTRERVRQIKEKAIRRLRHSPYSNVLKEY 296

Query: 680 L 680
           +
Sbjct: 297 I 297


>gi|113954631|ref|YP_732094.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
 gi|113881982|gb|ABI46940.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
          Length = 340

 Score =  199 bits (507), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 100/242 (41%), Positives = 158/242 (65%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 97  RHRIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 149

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ +  R +S++  R+P
Sbjct: 150 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRKITRELSHRFGRQP 209

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +    + +++  +    SL+    G+ED S LG+ I D N   P++   +
Sbjct: 210 NRLELAHAMGIEPRDLEELIAQSAPCASLDAHARGEEDRSTLGELIPDPNGDEPMEGMDR 269

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     L+ L  RE+++LR+RFG+G     TL E+G+Q  V+RER+RQ+E+KAI K
Sbjct: 270 SIQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLESKAILK 329

Query: 667 LK 668
           L+
Sbjct: 330 LR 331


>gi|307155201|ref|YP_003890585.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306985429|gb|ADN17310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 295

 Score =  199 bits (507), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 101/229 (44%), Positives = 153/229 (66%), Gaps = 6/229 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ ANLRLV+S+AKKY  RGL FLDLIQEG+IGL++  EKFD   GYKFSTYA WW
Sbjct: 60  AKRKMINANLRLVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---V 560
           ++QA+TR+IADQS TIR+P H+ + ++K+ R  R+++ ++ R PT +E+A  L +    +
Sbjct: 120 IRQAMTRAIADQSRTIRLPSHLTESLNKLKRVTRQLTGELGRRPTEQELANALELSLHEL 179

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             +R+    T+   SL   + DE T  L + + D N+ +P D   Q  LR     +L SL
Sbjct: 180 HAIRQADHRTRS-YSLNMKMEDEQT-ELEELLAD-NSETPNDFVAQIELRSMVDELLESL 236

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PR++ ++ +R+G+      +LEEVG    ++RER+RQ++ +A+R LK+
Sbjct: 237 PPRQQEIIALRYGLKNGRQMSLEEVGNYCNLSRERVRQLQNRAMRTLKY 285


>gi|326794473|ref|YP_004312293.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
 gi|326545237|gb|ADZ90457.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
          Length = 329

 Score =  199 bits (507), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 95/226 (42%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKISRRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ ++  EP+PEEIA KL  PVE V
Sbjct: 146 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQQLDHEPSPEEIADKLDRPVEDV 205

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +K+L + +   S+++P+ G E    L + I D    +P D   + ++  +    L +L  
Sbjct: 206 QKMLSLNERISSIDSPLGGSEGDKSLVEVIPDTQHSNPEDERQEGDVLNSIDGWLDALNE 265

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  V+  RFG+      TLE+VG +  +TRER+RQI+ +A+RKL+
Sbjct: 266 KQREVIARRFGLRGYEPSTLEDVGAEIGLTRERVRQIQVEALRKLR 311


>gi|299140647|ref|ZP_07033785.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298577613|gb|EFI49481.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 287

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 101/268 (37%), Positives = 171/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +++G+  A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEDLISVEEEVELAQKIKRGDRRAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R   ++  + ++ PT EEIA K+ +P + V   +K     +S++ P+ + + + L D +
Sbjct: 139 KRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIKSNGRHVSVDAPLAEGEENSLLDIL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + NA       +Q +LR+     L SL  RE  ++   FGI   ++ TLEE+G +F +T
Sbjct: 199 PNNNAQMADSMLVQESLRDEVANALQSLNERERNIIEAFFGINQ-SEMTLEEIGDKFGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+H +++K L+++L
Sbjct: 258 RERVRQIKEKAIRRLRHNTKNKNLKAYL 285


>gi|253701007|ref|YP_003022196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775857|gb|ACT18438.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 325

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 150/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+ +NLRLV+ +AK+Y NRG+  LD+I+EGNIGL+KA E+F      +FSTYA WW
Sbjct: 83  ARKRMILSNLRLVVKIAKRYRNRGMPLLDIIEEGNIGLIKAVERFKLSKECRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +Q  TIR+PVH+ D+I+++ R  R +  K+ REPT +E+A  L + V+ +
Sbjct: 143 IRQSIERALINQVRTIRLPVHVSDEINRMFRENRVLELKLNREPTAKEVADNLGITVQRL 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+     L D I+D + V P +     N  E  + +L  L+  
Sbjct: 203 RELMVVLKKTFSIEQPMGERGDFCLTDTIQDTSTVLPTELLENQNRYELISNLLEFLSET 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E ++L +RFG+      TL+ +G+ F VTRERIRQIE KA+ KL+
Sbjct: 263 ERKILTLRFGLEDKAPQTLDTIGQGFGVTRERIRQIEVKALEKLR 307


>gi|257457314|ref|ZP_05622485.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257445236|gb|EEV20308.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 286

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 102/241 (42%), Positives = 159/241 (65%), Gaps = 5/241 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E+NLR V++VAKKY N+ +  +DLI EGNIGLM AA++FD   GYKF +YA+WW
Sbjct: 46  AKKILIESNLRFVVNVAKKYQNKNIPIMDLISEGNIGLMNAADRFDPDKGYKFISYAVWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV 560
           ++QAI ++I ++S  IR+P++  +++ ++ + AR+++ K   EP  +E   IA+ L +  
Sbjct: 106 IRQAILKAICEKSRMIRLPLNRANELVQIEK-ARKLTGKTGTEPEDKELTAIAQDLRIEP 164

Query: 561 EGVRKVLKITKEPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           E VR ++   ++P+SL+ P   D   +  GDFIED   + P   A+  +LRE    +LAS
Sbjct: 165 EMVRTIMNAARDPVSLDAPQFNDNSAASTGDFIEDTRYMQPESYALDIDLRENVDALLAS 224

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  +LR RFG+      +L+EVG +F +T+ERIRQIE KA+ +L+      +L SF
Sbjct: 225 LSEREAEILRYRFGLNGYEQLSLKEVGTRFNLTKERIRQIEKKALERLQSVGHQHELESF 284

Query: 680 L 680
           +
Sbjct: 285 V 285


>gi|325673633|ref|ZP_08153324.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|325555654|gb|EGD25325.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 448

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 110/238 (46%), Positives = 159/238 (66%), Gaps = 6/238 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+EANLRLV+S A+ Y  RGL  LDL+QEGN GL++A EKFD+ LG KFSTYA WW
Sbjct: 213 ARTRMIEANLRLVVSTAQNYEGRGLDMLDLVQEGNTGLIRAVEKFDYRLGNKFSTYATWW 272

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           ++QAITR IAD+S TIR+PVH+ + + ++  T  R+  +I+  R  T  E+A++  + +E
Sbjct: 273 IRQAITRGIADKSRTIRLPVHVVEDLSRM--TTVRVEGEIELGRALTDAEVAQRADLTLE 330

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR++    +  +S+E     +D + L   IED  A  P ++  +A++RE    VL +LT
Sbjct: 331 KVRELDDCDRTVLSIEALTDSDDGAGLD--IEDDCAHDPYEALHRADVRERIDIVLETLT 388

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            RE  V+++R G+      TLEE+GK + VTRERIRQIEAK ++ L+ PSR+ +LR F
Sbjct: 389 EREAGVMKLRHGLVDGVPRTLEEIGKVYKVTRERIRQIEAKTLQLLREPSRADELRPF 446


>gi|219883041|ref|YP_002478205.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
 gi|219862047|gb|ACL42388.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
          Length = 951

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 107/238 (44%), Positives = 146/238 (61%), Gaps = 2/238 (0%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V  NLRLV+S+AK++T RG+ FLDLIQEGN GL +A +KFD+  G+KFSTYA WW++Q
Sbjct: 531 KLVSCNLRLVVSIAKRHTGRGMDFLDLIQEGNAGLYRAVQKFDYTKGFKFSTYATWWIRQ 590

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR IADQS TIR+PVH  +++  V    R       R+ T EEIA+     V+ +  V
Sbjct: 591 AITRGIADQSRTIRLPVHFHEQVVSVFIAERNFLQSEGRDGTAEEIAEACGKTVDEINAV 650

Query: 567 LKITKEPISL--ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +    P SL  E P G      LG+ + D +  +  D+A+ A L+      L  L+ RE
Sbjct: 651 RRHRTPPASLDWEVPNGKGGVELLGETLYDPDEPTAYDAAVLAQLQSAVHGALDRLSERE 710

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             VL  RFG+      TL+++G  + VTRERIRQIEAKA   L+ P+ + +LR F DG
Sbjct: 711 AGVLAYRFGLATGEQLTLDQIGTIYGVTRERIRQIEAKAFAALREPAAAAQLRDFFDG 768


>gi|157414303|ref|YP_001485169.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388878|gb|ABV51583.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 339

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/226 (43%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 105 ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +
Sbjct: 165 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDL 224

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N   P++   +   +E     L+ L  
Sbjct: 225 EDLISQSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNE 284

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 285 REQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|226226576|ref|YP_002760682.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089767|dbj|BAH38212.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 286

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 163/268 (60%), Gaps = 3/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ IS    IS  E   +   +R+G+ EA     ++V +NLR V+SVAKKY N+G+   D
Sbjct: 21  LRDISAYPLISREEEAELARRIRQGDQEAL---DKLVRSNLRFVVSVAKKYQNQGVSLSD 77

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL++AA KFD   G KF +YA+WW++QAI +++A+QS  +R+P++    +H++
Sbjct: 78  LINEGNLGLIRAARKFDETKGIKFISYAVWWIRQAILQALAEQSRIVRVPLNRAGTLHRI 137

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            + A  +  ++ RE T  EIA  + +  E V K + I++  +SL+ P+   + + L D++
Sbjct: 138 GKRANALLQELGREATHAEIAHGMDITEEEVAKTMSISQVHLSLDAPLTPGEDNRLLDYL 197

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D    +P D      L E     L  L  RE ++LR+ FGI      TLEE+G Q  +T
Sbjct: 198 PDTVHPTPEDQTFDKALTEAIEESLGGLKEREAKILRLYFGIDGADPMTLEEIGSQLGIT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KA+ +L+H SRSK L SFL
Sbjct: 258 RERVRQIKEKALSRLRHVSRSKSLESFL 285


>gi|78780175|ref|YP_398287.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|123969439|ref|YP_001010297.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|126697226|ref|YP_001092112.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|78713674|gb|ABB50851.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
 gi|123199549|gb|ABM71190.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
 gi|126544269|gb|ABO18511.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 339

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/226 (43%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 105 ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +
Sbjct: 165 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDL 224

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N   P++   +   +E     L+ L  
Sbjct: 225 EDLISQSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNE 284

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 285 REQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|254526617|ref|ZP_05138669.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538041|gb|EEE40494.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 339

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/226 (43%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 105 ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +
Sbjct: 165 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDL 224

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N   P++   +   +E     L+ L  
Sbjct: 225 EDLISQSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNE 284

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 285 REQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|187764347|gb|ACD36026.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 322

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 157/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 77  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 133

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+
Sbjct: 134 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPS 193

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 194 PEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 253

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  + L  LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 254 LSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 313


>gi|168768834|ref|ZP_02793841.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
 gi|189362139|gb|EDU80558.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
          Length = 329

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 160/233 (68%), Gaps = 1/233 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L     +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFE-NAK 268

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 269 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 321


>gi|281425773|ref|ZP_06256686.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|281400034|gb|EFB30865.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
          Length = 287

 Score =  199 bits (506), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 101/268 (37%), Positives = 171/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +++G+  A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEDLISVEEEVELAQKIKRGDRRAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R   ++  + ++ PT EEIA K+ +P + V   +K     +S++ P+ + + + L D +
Sbjct: 139 KRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIKSNGRHVSVDAPLAEGEENSLLDIL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + NA       +Q +LR+     L SL  RE  ++   FGI   ++ TLEE+G +F +T
Sbjct: 199 PNNNAQMADSVLVQESLRDEVANALQSLNERERNIVEAFFGINQ-SEMTLEEIGDKFGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+H +++K L+++L
Sbjct: 258 RERVRQIKEKAIRRLRHNTKNKNLKAYL 285


>gi|148240837|ref|YP_001226224.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849376|emb|CAK24927.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 339

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 101/242 (41%), Positives = 157/242 (64%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 96  RHRIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 148

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P
Sbjct: 149 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRITRELSHRFGRQP 208

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +    + +++  +    SL+    G+ED S LG+ I D N   P++   +
Sbjct: 209 NRLELANAMGIEPRDLEELISQSAPCASLDAHARGEEDRSTLGELIPDPNGDEPMEGMDR 268

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 269 SIQKEHLGGWLSQLNDREQKILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILK 328

Query: 667 LK 668
           L+
Sbjct: 329 LR 330


>gi|145300341|ref|YP_001143182.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853113|gb|ABO91434.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 327

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 95/225 (42%), Positives = 152/225 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKIACRYNNRGLVLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+++  EPT E+IA  L   V+ V
Sbjct: 146 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELSHRLDHEPTAEDIAFALDRSVDDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+ ++  S++TPIG +    L D + D+  + P   +   ++R +    L  L P+
Sbjct: 206 NRMLKLNEKITSVDTPIGGDRDKALLDVLSDERGMGPELESQDDDMRASIVHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+
Sbjct: 266 QREVLARRFGLLGYEPATLEDVGSEIGLTRERVRQIQVEGLRRLR 310


>gi|318040855|ref|ZP_07972811.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 321

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 100/226 (44%), Positives = 149/226 (65%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 87  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P   E+A  + M  E +
Sbjct: 147 IRQGMTRAIDNSARTIRLPIHVSEKLSKMRRITRELSHRFGRQPNRLELAHAMGMQPEEL 206

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    GD+D S LG+ I D N+   +DS  +   +E     L+ L  
Sbjct: 207 EDLISQSAPCASLDAHARGDDDRSTLGELIADPNSNESMDSMDRNLQKEHLGTWLSQLNE 266

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE R++ +RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 267 RERRIIELRFGLEGQEPLTLAEIGRQINVSRERVRQLEAKAILKLR 312


>gi|115394497|gb|ABI97158.1| RNA polymerase sigma factor [Fusobacterium necrophorum]
          Length = 185

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 98/182 (53%), Positives = 133/182 (73%)

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + AR    +  ++ TPE +A++L 
Sbjct: 1   TYAPWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEILAERLG 60

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M VE V+ + ++ ++PISLETP+G E+ S LGDF+ED+  ++P +   ++ LRE    VL
Sbjct: 61  MEVEKVKSIQEMNQDPISLETPVGSEEDSELGDFVEDQKMLTPYELTNRSLLREQLDSVL 120

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SL+ REE+VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL 
Sbjct: 121 GSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLE 180

Query: 678 SF 679
            F
Sbjct: 181 DF 182


>gi|23978302|dbj|BAC21129.1| principal sigma factor [Oscillatoria agardhii]
          Length = 188

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 99/188 (52%), Positives = 135/188 (71%), Gaps = 1/188 (0%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL F DLIQEG++GL++AAEKF+   GYKFSTYA WW++QAITR+IADQS TIR+PVH
Sbjct: 2   NRGLSFQDLIQEGSLGLIRAAEKFEHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 61

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+
Sbjct: 62  LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEE 121

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE
Sbjct: 122 DSRLGDFIES-DGETPEDQVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEE 180

Query: 645 VGKQFCVT 652
           +G+ F VT
Sbjct: 181 IGQIFNVT 188


>gi|254430889|ref|ZP_05044592.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197625342|gb|EDY37901.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 327

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 166/271 (61%), Gaps = 8/271 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            E+ + +   G+  ++ R  +   R+       AK+ M++ANLRLV++VAKKY  RGL  
Sbjct: 60  GELTAWAGRCGVPPADLRQALHRGRR-------AKERMLQANLRLVVAVAKKYQRRGLDL 112

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEG +GL +A E++D   G++FSTYA WW++Q ITR++A QS TIR+PVH+ + ++
Sbjct: 113 LDLIQEGTLGLERAVERYDPRRGFRFSTYAYWWIRQGITRALASQSRTIRLPVHVTETLN 172

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++      ++ +  R+PT  E+A+ + +    +R  L     P+SLE  +G    + L D
Sbjct: 173 RIRTCQGELTREHGRQPTLAELARAVGLDEARLRSTLAHIPRPVSLEGRVGANADTPLVD 232

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +ED +A +P  +  +  L      +L  L+ RE  V+R RFG+  +T  TL E+G+Q  
Sbjct: 233 LLEDDHA-TPEQTLTRQQLHADLEALLDELSAREATVIRQRFGLDDDTPRTLAEIGEQLQ 291

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++RER+RQIE++A+ KL+ P    ++R +LD
Sbjct: 292 LSRERVRQIESRALLKLRQPQNRCRVRDYLD 322



 Score = 37.7 bits (86), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 26/32 (81%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           ++ DP+R+YLRE+G ++LL +E EI +A+ ++
Sbjct: 17  ASSDPIRLYLREIGRVDLLRQEEEILLARLVQ 48


>gi|221212018|ref|ZP_03584996.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
 gi|221168103|gb|EEE00572.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
          Length = 625

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 97/237 (40%), Positives = 151/237 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW
Sbjct: 388 AKMALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWW 447

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+IT ++AD   TIR+P H  D I+K+ R AR    +     TP+E+A ++  PV+ V
Sbjct: 448 IRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKV 507

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ I KEP+S++ PI  +      D + D +  SP D+A  A  R      +  L PR
Sbjct: 508 RELMAIVKEPVSVDLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPR 567

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++R+R+G+      +L ++G++  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 568 EALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDALAVLRPFV 624



 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/168 (33%), Positives = 82/168 (48%), Gaps = 18/168 (10%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           DD+L    +   +  +I L   RG+VT  ++   LP D+     ++   A+L+ +GI V 
Sbjct: 27  DDALAS--ASAPFAGLIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVS 84

Query: 79  DGDDLE-----DEEGSEDSLDLASSASNSSV----FLQKRKDSADRSTDDPVRMYLREMG 129
           D    E     D       L  A++  N +      L  R       T DPVR+YLREMG
Sbjct: 85  DAAHAETDWSLDRYFRPPPLSRAAAERNGAFAAFDLLAPR-------TTDPVRLYLREMG 137

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           ++ LL+ + EIA A+RIE GRA  +A LC  P    AL   R E+ +G
Sbjct: 138 TVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEG 185


>gi|72383143|ref|YP_292498.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002993|gb|AAZ58795.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 340

 Score =  199 bits (505), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 97/226 (42%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 106 ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+A  + +  + +
Sbjct: 166 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLELANAMGIEPQDL 225

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N+  P++   ++  +E     L+ L  
Sbjct: 226 EDLVSQSAPCASLDAHARGEEDRSTLGELIPDPNSDEPMEGMDRSIQKEHLGGWLSQLNE 285

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++R+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 286 REQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|255535549|ref|YP_003095920.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
 gi|255341745|gb|ACU07858.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
          Length = 294

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 96/250 (38%), Positives = 168/250 (67%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + +K      +A +++++ANLR V+SV+K+Y N+GL   DLI EGN+GLMKAA+++D 
Sbjct: 43  VDLAQKIRAGDRVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDE 102

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+PE
Sbjct: 103 TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPE 162

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ L M  + +++ +K +   +S++ P+ + + S+L D +    + SP    +  +L+
Sbjct: 163 ELAEVLDMSEDDIKESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQ 222

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R L +LTPRE  ++R+ FG+      TLEE+G+ F +TRER+RQI+ KAI++LKH 
Sbjct: 223 IEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHN 282

Query: 671 SRSKKLRSFL 680
           +RSK L+S+L
Sbjct: 283 TRSKILKSYL 292


>gi|124026883|ref|YP_001015998.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961951|gb|ABM76734.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 340

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 97/226 (42%), Positives = 153/226 (67%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 106 ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+A  + +  + +
Sbjct: 166 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLELANAMGIEPQDL 225

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N+  P++   ++  +E     L+ L  
Sbjct: 226 EDLVSQSAPCASLDAHARGEEDRSTLGELIPDPNSDEPMEGMDRSIQKEHLGGWLSQLNE 285

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++R+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 286 REQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|168000881|ref|XP_001753144.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162695843|gb|EDQ82185.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 581

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 108/268 (40%), Positives = 166/268 (61%), Gaps = 13/268 (4%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           S++V    ++ E R     +++G+C    AK ++V +NLRLV+S+ K Y  RG+   DLI
Sbjct: 321 SLAVGMNQTLFELR-----IKEGQC----AKDKLVNSNLRLVVSIVKNYQGRGMTLPDLI 371

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G++GL++ AEKFD  +G+KFSTYA WW++QA+TRSI DQS  IR+PVH+ + I ++ +
Sbjct: 372 QRGSLGLIRGAEKFDPEMGFKFSTYATWWIRQAVTRSITDQSRIIRLPVHIYEVISRINK 431

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           +   ++    R+   EE+A  + + VE +  +LK  + P S++  IG +    L + + D
Sbjct: 432 SRMMIAEDQGRQARDEEVATAVGISVEKLDFILKSARLPASMDQLIGRDKDLPLWEMVAD 491

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K   S  D      L++    VL +L+P E  VLR+RFG+      TL+++G  F VTRE
Sbjct: 492 KGFNSADDFLTNEVLKQDIDGVLQTLSPTEREVLRLRFGLDDAQSMTLKDIGIFFKVTRE 551

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIE +A+RKL+HP+R    R+ L G
Sbjct: 552 RIRQIEVRALRKLRHPTR----RNILQG 575


>gi|391964|gb|AAA03294.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 362

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 90/233 (38%), Positives = 159/233 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RT R +S+K+  EP+  EIA++L  PV+ V
Sbjct: 162 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTVRELSHKLDYEPSAVEIAEQLDKPVDDV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 222 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 281

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  V+  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 282 QREVIARRFGLLGYEAATLEDVGREIGLTRERVRQIQVQGLRRLREILQTQGL 334


>gi|33322905|gb|AAQ07189.1|AF496497_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 167

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 98/167 (58%), Positives = 127/167 (76%)

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ +PV+ VR+VLK+ +EP+
Sbjct: 1   QARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPV 60

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETPIG+ED SHLGDFIEDK+A SP   A    L++    VL +LT REE VLR+RFG+
Sbjct: 61  SLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGL 120

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                 TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR FL+
Sbjct: 121 DDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFLE 167


>gi|87300555|ref|ZP_01083397.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
 gi|87284426|gb|EAQ76378.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
          Length = 398

 Score =  198 bits (504), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 97/239 (40%), Positives = 154/239 (64%), Gaps = 1/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M++ANLRLV++VAKKY  RG++ LDL+QEG +GL +A EK+D   G++FSTYA WW
Sbjct: 158 ARDRMIQANLRLVVAVAKKYQKRGVELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAYWW 217

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+IA QS TIR+PVH+ +K++++ +  R+ ++   R  +  E+A+ L    E V
Sbjct: 218 IRQGVTRAIATQSRTIRLPVHVTEKLNRIKKAQRQFASDHGRTASLAELAEALQWSEEAV 277

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L      ISLE  +G +  + LGD +E   + +P  S  +  L      +L  L+ R
Sbjct: 278 RLTLLRVPRSISLEAKVGRDQDTPLGDLLE-ATSDTPEQSLTRQQLHSDLDALLDELSER 336

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  V+R+RFG+  +T  TL ++G+   ++RER+RQIE +A+ KL+ P+R  ++  +L G
Sbjct: 337 EAEVIRLRFGLADDTPRTLAQIGEGMQLSRERVRQIETRALHKLRQPARRCRVHDYLAG 395


>gi|91070519|gb|ABE11426.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-3E5]
          Length = 231

 Score =  198 bits (504), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 98/222 (44%), Positives = 151/222 (68%), Gaps = 1/222 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q 
Sbjct: 1   MMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQG 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++
Sbjct: 61  MTRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLI 120

Query: 568 KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
             +    SL+    G+ED S LG+ I D N   P++   +   +E     L+ L  RE++
Sbjct: 121 SQSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQK 180

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++R+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 181 IMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 222


>gi|209695924|ref|YP_002263854.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
 gi|208009877|emb|CAQ80190.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
          Length = 321

 Score =  198 bits (504), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 152/226 (67%), Gaps = 2/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+E+NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 78  ARSRMIESNLRLVVKIARRYNHRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPEEIA+KL  PV  V
Sbjct: 138 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPEEIAEKLDKPVSDV 197

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
            ++L++ +   S+++ +  +    L D I D     P +S  Q N + E+    L  L P
Sbjct: 198 SRMLRLNERVASVDSMVAGDSDKALLDIIPDTKHADP-ESETQTNDINESLVGWLGQLNP 256

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ V+  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 257 KQKEVVARRFGLLGYEASTLEQVGREIGLTRERVRQIQVEGLRRLR 302


>gi|297518365|ref|ZP_06936751.1| RNA polymerase sigma factor RpoS [Escherichia coli OP50]
          Length = 327

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 92/233 (39%), Positives = 159/233 (68%), Gaps = 3/233 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+    EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSDH---EPSAEEIAEQLDKPVDDV 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 207 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 266

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 267 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 319


>gi|218438398|ref|YP_002376727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171126|gb|ACK69859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 99/227 (43%), Positives = 152/227 (66%), Gaps = 4/227 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ ANLRLV+S+AKKY  RGL FLDLIQEG+IGL++  EKFD   GYKFSTYA WW
Sbjct: 60  AKRKMISANLRLVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IADQS TIR+P H+ + ++K+ R  R+++ ++ R PT EEIA +L + +  +
Sbjct: 120 IRQAMTRAIADQSRTIRLPSHLTESLNKLKRITRQLTGELGRRPTEEEIATELEISMNEL 179

Query: 564 RKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R + +        SL   + DE T  L + + D +A +P +   Q  L     ++L +L 
Sbjct: 180 RTIRQADHRTRSYSLNMKMDDEQT-ELAELLADDSA-NPNEFVAQIELSSMVEQLLETLP 237

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           PR++ ++ +R+G+      +LEEVG    ++RER+RQ++ +A+R LK
Sbjct: 238 PRQQEIIALRYGLKNGKQMSLEEVGHHCNLSRERVRQLQNRAMRTLK 284


>gi|195939453|ref|ZP_03084835.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 305

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 90/216 (41%), Positives = 150/216 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +  VL  RFG+      TLE+VG++  +TRER+RQI
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQI 305


>gi|24374942|ref|NP_718985.1| RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
 gi|24349657|gb|AAN56429.1|AE015779_6 RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
          Length = 326

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 96/231 (41%), Positives = 156/231 (67%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 83  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 140

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+KL +
Sbjct: 141 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQV 200

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
               V ++LK+ ++  S++ P+G ++   L D + D + V P D  +Q  ++  +  + L
Sbjct: 201 SSVDVSRMLKLNEKITSVDVPLGGDNDKALLDVLADDDNVGP-DYKVQDEDISNSVVKWL 259

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 260 NELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 310


>gi|159904372|ref|YP_001551716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889548|gb|ABX09762.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 338

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 100/242 (41%), Positives = 157/242 (64%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 95  RHQIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 147

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P
Sbjct: 148 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQP 207

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +  + +  ++  +    SL++   G+ED S LG+ I D N   P+    +
Sbjct: 208 NRVELANAMGIEPQDLEDLVAQSAPCASLDSHARGEEDRSTLGELIPDPNYDEPMAGMDR 267

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +E     L+ L  RE++++R+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 268 KMQKEHLGGWLSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILK 327

Query: 667 LK 668
           L+
Sbjct: 328 LR 329


>gi|219130701|ref|XP_002185497.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403028|gb|EEC42984.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 329

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 100/250 (40%), Positives = 160/250 (64%), Gaps = 14/250 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + E+N+RLV+S+AK+Y +RGL F DL QEG +GL +A EKFD   G++FSTYA WW
Sbjct: 77  AKAALTESNIRLVVSIAKRYQHRGLSFQDLAQEGILGLTRACEKFDPERGFRFSTYASWW 136

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I R+IADQ  TIR+PVH+ D+I+ + +  R +  ++ R+   EEI +K  +  E +
Sbjct: 137 IKQSIMRAIADQGRTIRLPVHIHDQINALRKVERELKAELGRDARLEEITEKSTLTAEKI 196

Query: 564 RKVLKITKEPISLETPI-------------GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
             + +++++ +S+E  +             G +    LGD + D  A  P + A    L+
Sbjct: 197 EFLNRVSQQDVSMEQELRTSKSKGSSAGLGGPDGGLTLGDVMGDPEA-QPAEEASYQMLK 255

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +  +R++ +L  RE+ V+RMRFG+      TLEE+G++F VTRERIRQIE++A+ KL+ P
Sbjct: 256 DDISRLICTLNSREQAVIRMRFGLDDGKAKTLEEIGRRFSVTRERIRQIESRALHKLRQP 315

Query: 671 SRSKKLRSFL 680
            R+  ++ ++
Sbjct: 316 YRNHAVKCYV 325


>gi|91070600|gb|ABE11500.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-8F9]
          Length = 340

 Score =  198 bits (503), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 97/222 (43%), Positives = 151/222 (68%), Gaps = 1/222 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q 
Sbjct: 110 MMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQG 169

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++
Sbjct: 170 MTRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLI 229

Query: 568 KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
             +    SL+    G+ED S LG+ I D N   P++   +   +E     L+ L  RE++
Sbjct: 230 SQSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQK 289

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 290 IMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|307546200|ref|YP_003898679.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
 gi|307218224|emb|CBV43494.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
          Length = 330

 Score =  197 bits (502), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + R+G+ +    +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 79  HYGRLARQGDPQG---RSRMIESNLRLVVKIARRYLNRGLTLLDLIEEGNLGLIRAVEKF 135

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +R AR ++ K+  E T
Sbjct: 136 DPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRAARELTQKLDHEAT 195

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA  L  PV  V++++ + +   S++ P+G E    L + + D N + P  + +  +
Sbjct: 196 AEEIADHLDKPVASVKRMMGLNERVSSVDYPVGSESDKPLIETLTDDNDLGPESTLVDGD 255

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++     LA LT ++  V+  RFG+  +   TLE+VG++  +TRER+RQI+ +A++KL+
Sbjct: 256 VKQHVDDWLAELTDKQREVVVRRFGLRGHEASTLEQVGEEIGLTRERVRQIQVEALKKLR 315


>gi|300777898|ref|ZP_07087756.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
 gi|57471279|gb|AAW50925.1| RpoD [Chryseobacterium indologenes]
 gi|300503408|gb|EFK34548.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
          Length = 288

 Score =  197 bits (502), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 95/237 (40%), Positives = 163/237 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++++ANLR V+SV+K+Y N+GL   DLI EGN+GLMKAA+++D   G+KF +YA+WW
Sbjct: 50  ALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+PEE+A+ L M  E +
Sbjct: 110 IRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDI 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++ +K +   +S++ P+ + + S+L D +    + SP    +  +L+    R L +LTPR
Sbjct: 170 KESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPSPDKDLMLESLQIEIERALNTLTPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++R+ FG+      TLEE+G+ F +TRER+RQI+ KAI++LKH +RSK L+S+L
Sbjct: 230 EADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNTRSKILKSYL 286


>gi|46201746|ref|ZP_00054445.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 756

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 115/268 (42%), Positives = 161/268 (60%), Gaps = 22/268 (8%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +VET  S  E R     +  G   A  A++    ANL+LV+  AKK+   GL + D IQE
Sbjct: 503 AVETDPSGGEARR---RMEAGLETARRARERFALANLKLVVWGAKKFG--GLTWPDRIQE 557

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GL+KA E+FD   G KFSTYA WW+KQA+TR++AD+  TIRIPVH ++ + K+ R  
Sbjct: 558 GNLGLLKAVERFDHRRGAKFSTYATWWIKQAVTRAVADKGRTIRIPVHAQEAMRKLRRAQ 617

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---- 592
             +     RE  PEE+ +   +P+  VR+ L + +EP SL+    +E   H  +      
Sbjct: 618 NEVFALTGREALPEEVGELTEIPLARVRRFLAVAEEPASLDV---EEVGLHAAEMASREP 674

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             E++ AV+ + + ++  L          L PRE  V+R+RFGIG   ++TLEE+G+QF 
Sbjct: 675 DPEERLAVAEIKAMVRGQLE--------LLPPREATVIRLRFGIGCEREYTLEEIGQQFG 726

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VTRERIRQIEAKA+RKL HP R K L+ 
Sbjct: 727 VTRERIRQIEAKALRKLSHPGRIKALQG 754


>gi|113969467|ref|YP_733260.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|114046700|ref|YP_737250.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117919573|ref|YP_868765.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
 gi|113884151|gb|ABI38203.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888142|gb|ABI42193.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117611905|gb|ABK47359.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
          Length = 326

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 96/231 (41%), Positives = 156/231 (67%), Gaps = 4/231 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 83  CEKS--RNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 140

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+KL +
Sbjct: 141 YATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQV 200

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
               V ++LK+ ++  S++ P+G ++   L D + D + V P D  +Q  ++  +  + L
Sbjct: 201 SSVDVSRMLKLNEKITSVDIPLGGDNDKALLDVLADDDNVGP-DYKVQDEDISNSVVKWL 259

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 260 NELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 310


>gi|330721381|gb|EGG99448.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC2047]
          Length = 321

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 150/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 81  GRKRMIESNLRLVVKISRRYVNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 140

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA+ L  PVE V
Sbjct: 141 IRQTIERALMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEEIAEMLDRPVENV 200

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++LK+ +   S++ P+G +    + + I  +N   P +     NL    T  L  L+ +
Sbjct: 201 KRMLKLNERVTSIDAPMGGDSERSMAENITGENVDDPSELLQNDNLHGNLTHWLGELSEK 260

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 261 QREVIARRFGLLGYEMSTLEQVGSEIGLTRERVRQIQVEALKRLR 305


>gi|319790059|ref|YP_004151692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114561|gb|ADU97051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 318

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 104/269 (38%), Positives = 171/269 (63%), Gaps = 3/269 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KSIS    +S  E   +    + G+ EA    K++VE+NLR V+SVAKKY   GL   D
Sbjct: 53  LKSISKIPLLSREEEIELAKRAKAGDKEAL---KKLVESNLRFVVSVAKKYLGCGLPLHD 109

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EG +GL++AA +FD   G KF +YA+WW++Q+I +++A Q+  ++IPV     ++K+
Sbjct: 110 LIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTGAVKIPVKQAVLVNKI 169

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R+   +  K+ REPT EE+A  + M  + V ++L I + P+SL+TPIGDE+ +   DF+
Sbjct: 170 TRSYGELLKKLGREPTIEELADYVGMEPKEVERLLSICQVPLSLDTPIGDEEDTTFKDFL 229

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           + +      +  +Q  L+++   +L  LTP+E++++ MRFG+  N   TL E+G++  ++
Sbjct: 230 KGEGTAEVEEKVVQEELKQSIQEMLEQLTPQEKKIIIMRFGLDGNEPKTLREIGEKLGIS 289

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQ+E +A +K+K  +  KKL  FL+
Sbjct: 290 RERVRQLETRAKKKMKEYALRKKLNVFLN 318


>gi|146281946|ref|YP_001172099.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri A1501]
 gi|145570151|gb|ABP79257.1| sigma factor RpoS [Pseudomonas stutzeri A1501]
          Length = 332

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 157/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKF
Sbjct: 81  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLVEEGNLGLIRAVEKF 137

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 138 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 197

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +  +  +
Sbjct: 198 PEEIANLLEKPVGEVKRMLGLNERVTSVDVSLGPDTDKTLLDTLTDDRPTDPCELLLDDD 257

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +  + L+ L+ ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 258 LSASIDQWLSDLSEKQREVVIRRFGLRGHEASTLEEVGQEIGLTRERVRQIQVEALRRLR 317


>gi|227536516|ref|ZP_03966565.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300773589|ref|ZP_07083458.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|227243593|gb|EEI93608.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300759760|gb|EFK56587.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 286

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 101/249 (40%), Positives = 168/249 (67%), Gaps = 8/249 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A +++ + NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G
Sbjct: 43  IREGD---QVALEKLTKTNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+ +   ++  + +REP+PEE+A
Sbjct: 100 FKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLSKISKAFSKLEQEYEREPSPEELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             L   V+ V   L  +   +S++ P   G+E+T  L D +E+ +  +   S I  +L E
Sbjct: 160 DILETTVDKVSDTLSNSGRHVSMDAPFVQGEENT--LLDVLENHDPDTD-SSLIDESLSE 216

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              R LA+LT RE  ++ + FG+G N   +LEE+G++F +TRER+RQI+ KA+++L+H S
Sbjct: 217 EIKRSLATLTEREREIIVLFFGLGSNHQLSLEEIGEKFNLTRERVRQIKDKALQRLRHTS 276

Query: 672 RSKKLRSFL 680
           RSK L+S+L
Sbjct: 277 RSKILKSYL 285


>gi|212550562|ref|YP_002308879.1| RNA polymerase primary sigma factor [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|212548800|dbj|BAG83468.1| putative RNA polymerase primary sigma factor [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 286

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 95/250 (38%), Positives = 160/250 (64%), Gaps = 1/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+       A  ++V ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAAEKFD 
Sbjct: 37  IELARRSRLGDRSALDKLVRANLRFVVSVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +   +   K +R+P+ E
Sbjct: 97  TRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGSLNKISKALSKFEQKHERKPSSE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A++L +P + V + L+I+   IS++ P  D + + L D + + +  +     I  +L 
Sbjct: 157 ELAQELELPEDKVSETLRISNRHISIDAPFADGEENSLLDVLTNDDTPAAYHGLIHESLS 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     L  L  RE+ +++M FGIG   +  LEE+G  F +TRER+RQI+ KAI+KLK  
Sbjct: 217 QEINNALLILNDREKEIIKMSFGIGQ-QEMNLEEIGDAFNLTRERVRQIKEKAIKKLKQN 275

Query: 671 SRSKKLRSFL 680
           +R+  L+++L
Sbjct: 276 NRNNGLKNYL 285


>gi|88809396|ref|ZP_01124904.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786615|gb|EAR17774.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 339

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 100/242 (41%), Positives = 157/242 (64%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 96  RHRIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 148

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P
Sbjct: 149 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRITRELSHRFGRQP 208

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E++  + +    + +++  +    SL+    G+ED S LG+ I D N   P++   +
Sbjct: 209 NRLELSNAMGIAPRDLEELIAQSAPCASLDAHARGEEDRSTLGELIPDPNGDEPMEGMDR 268

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 269 SIQKEHLGGWLSQLNEREQKILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILK 328

Query: 667 LK 668
           L+
Sbjct: 329 LR 330


>gi|158334481|ref|YP_001515653.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158304722|gb|ABW26339.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  197 bits (502), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 157/238 (65%), Gaps = 1/238 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS ++K       A ++MVE+NLRLV+S+AKKY    L+FLDLIQEG IGL +  EKFD 
Sbjct: 70  VSQLQKELKLGQTANRKMVESNLRLVVSIAKKYNKAKLEFLDLIQEGTIGLQRGVEKFDP 129

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++QA+TR+IA+Q  TIR+P+H+ +K++K+ +  R++S K+ R+PT  
Sbjct: 130 TKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEKLNKLRKVKRQLSLKLHRDPTVA 189

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A ++ +  + V   L   +  ISL+  +GD+  + L + +ED +A SP D A  + L+
Sbjct: 190 ELATEMELSPKKVEAFLSYARHSISLDVQVGDQQNTELWELLEDPHA-SPEDYATASYLQ 248

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               ++L  L P++  V+ +R+G+      TL +VG++  V+RE +R++E +A + L+
Sbjct: 249 SDLAKLLNVLNPQQREVITLRYGLIDQNPLTLAKVGERLNVSREWVRRVEREAFQLLR 306


>gi|123967121|ref|YP_001012202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201487|gb|ABM73095.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 339

 Score =  197 bits (501), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 101/245 (41%), Positives = 158/245 (64%), Gaps = 8/245 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S  RH++ + ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A
Sbjct: 93  SRNRHLIKVGKR-------ARDRMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERA 145

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S K  
Sbjct: 146 VDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRVSRELSQKSG 205

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS 603
           R+PT  E+A  + +  + +  ++  +    SL+    G+ED S LG+ I D N   P++ 
Sbjct: 206 RQPTRLEMATAMGIDQKDLEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEG 265

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   +E     L  L  RE++++++RFG+      TL E+G+Q  V+RER+RQ+EAKA
Sbjct: 266 MDRTIQKEHLGTWLTQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKA 325

Query: 664 IRKLK 668
           I KL+
Sbjct: 326 ILKLR 330


>gi|89890814|ref|ZP_01202323.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
 gi|89516959|gb|EAS19617.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
          Length = 287

 Score =  197 bits (501), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 100/259 (38%), Positives = 168/259 (64%), Gaps = 3/259 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+  E   +  +++KG+  A    +++  ANLR V+SVAK+Y N+GL+  DLI EGN GL
Sbjct: 31  ITAEEEVELAQLIKKGDQRAL---EKLTTANLRFVVSVAKQYQNQGLKLPDLINEGNAGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +    +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAFSHLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
             +R P+PEE+AK+L M V  V++ LK     +S++ P+ + +TS+L D +    + +P 
Sbjct: 148 LHERPPSPEELAKELDMTVSDVKQSLKNAGRHVSMDAPLKEGETSNLYDVVRSGESPNPD 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +  +L    TR L +L+ +E  V+ + FGIG     +LEE+G+ F +TRER+RQI+ 
Sbjct: 208 RELMHESLTLEITRALETLSQKEADVISLYFGIGNQQPMSLEEIGETFDLTRERVRQIKE 267

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           K I++L+  SRSK L+S+L
Sbjct: 268 KGIKRLRQNSRSKILKSYL 286


>gi|87301519|ref|ZP_01084359.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283736|gb|EAQ75690.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 322

 Score =  197 bits (501), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 97/226 (42%), Positives = 151/226 (66%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 88  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P   E++  + M ++ +
Sbjct: 148 IRQGMTRAIDNSARTIRLPIHVSEKLSKMRRITRELSHRFGRQPNRLELSHAMGMDIKDL 207

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D  +  P+D   ++  +E     L+ L  
Sbjct: 208 EDLISQSAPCASLDAHARGEEDRSTLGELIADPASTEPMDHMDRSIQKEHLGTWLSQLNE 267

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +LR+RFG+      TL E+G++  V+RER+RQ+EAKAI KL+
Sbjct: 268 REQEILRLRFGLEGKEPLTLAEIGRKINVSRERVRQLEAKAIMKLR 313


>gi|304410159|ref|ZP_07391778.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|307302130|ref|ZP_07581888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
 gi|304351568|gb|EFM15967.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|306914168|gb|EFN44589.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
          Length = 326

 Score =  197 bits (501), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 96/239 (40%), Positives = 158/239 (66%), Gaps = 2/239 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK     + ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 73  VYFSRKALKGCAKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDP 132

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E
Sbjct: 133 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAE 192

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           EIA+KL +    V ++LK+ ++  S++ P+G ++   L D + D + V P D  +Q  ++
Sbjct: 193 EIAEKLQVSSADVSRMLKLNEKITSVDMPLGGDNDKALLDILADDDNVGP-DYKVQDEDI 251

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  + L  L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 252 SNSVVKWLNELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 310


>gi|108803849|ref|YP_643786.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765092|gb|ABG03974.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 289

 Score =  197 bits (501), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 103/227 (45%), Positives = 150/227 (66%), Gaps = 3/227 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++E NLRLV+SVAKKY   GL F DLIQEGNIGLMKA EKFD   G++FSTYA WW
Sbjct: 51  ARQKLIEKNLRLVVSVAKKYRGYGLPFEDLIQEGNIGLMKAVEKFDPERGFRFSTYATWW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ R++AD+  TIR+PVHM +KI K+ RT   +S +++REPT EE+A+ L    E V
Sbjct: 111 IRQAVQRAVADKGRTIRVPVHMTEKIRKMARTYNELSAQLEREPTDEEVAEALGWTPEEV 170

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLT 621
           R+V     +  SL  P+  DED+S +G+F+ED+ A S    A+  ++     R  +  L 
Sbjct: 171 REVKGAMPDATSLNQPLSSDEDSSEIGEFVEDERA-SDTAGAVARDIENAALRKAIERLP 229

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R   VL  R+G+      TL E+ ++  V+RER+RQ++ +A R ++
Sbjct: 230 ERNRHVLVRRYGLDDREPATLAELSEELGVSRERVRQLQREAERMIQ 276


>gi|327404710|ref|YP_004345548.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320218|gb|AEA44710.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 289

 Score =  197 bits (501), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 100/239 (41%), Positives = 160/239 (66%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + +ANLR V+SV+K+Y N+GL   DLI EGN+GL+KAAE+FD   G+KF +YA+WW
Sbjct: 50  ALERLTKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLIKAAERFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+Q+  +R+P++    I+K+ R    +    +R P+ +E+A+ L   VE V
Sbjct: 110 IRQSILQALAEQARIVRLPLNKIGTINKINRAYSELEQVYERPPSADELAEFLECSVEDV 169

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R+ L  T   +S++ P+  GDE +S + D + +    SP +   + +LR+   R L+SL+
Sbjct: 170 RQSLANTARHLSMDAPLVDGDESSSSMYDVLPNDALPSPENELNKESLRKEIERSLSSLS 229

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE  V+R+ +G+      TLEE+G  F +TRER+RQI+ KAIR+LKH SRS+ L+S+L
Sbjct: 230 GREGDVVRLYYGLNGKHALTLEEIGDLFDLTRERVRQIKEKAIRRLKHTSRSRMLKSYL 288


>gi|325954752|ref|YP_004238412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
 gi|323437370|gb|ADX67834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
          Length = 288

 Score =  197 bits (501), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 163/238 (68%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+W
Sbjct: 49  VALEKLTKANLRFVVSVAKQYQNQGLSLPDLINEGNLGLIKAAQRFDETRGFKFISYAVW 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I +++A+QS  +R+P++    I+K+ +    +  + +R P+ EEI++ L M    
Sbjct: 109 WIRQSILQALAEQSRIVRLPLNKIGSINKINKAYALLEQEHERAPSAEEISEVLDMSEGD 168

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V++ LK +   +S++ P+ + + S+L D +    + SP ++ +  +LR    R L +LTP
Sbjct: 169 VKESLKNSGRHVSMDAPLVEGEDSNLYDVLNIGESPSPDNTLMIESLRVEIERALQTLTP 228

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  ++R+ FG+      TLEE+G+ F +TRER+RQI+ KAIR+LKH SRSK L++++
Sbjct: 229 READLIRLYFGLNGAHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILKTYI 286


>gi|189348175|ref|YP_001941371.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
 gi|189338313|dbj|BAG47381.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 612

 Score =  197 bits (500), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 97/237 (40%), Positives = 148/237 (62%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW
Sbjct: 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWW 434

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+IT ++AD   TIR+P H  D I+K+ R AR    +     TP E+A ++  PV+ V
Sbjct: 435 IRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGATATPAELAAQMGEPVDKV 494

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++ I KEP+S + PI  +      D + D +  SP D+A  A  R      +  L PR
Sbjct: 495 RDLMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPR 554

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++R+R+G+      +L ++G++  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 555 EALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASGTLAVLRPFV 611



 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 57/154 (37%), Positives = 81/154 (52%), Gaps = 12/154 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           +  +I L   RG+VT  +L   LP D+     ++   A+L+ +GI V   DD   E G  
Sbjct: 24  FAGLIALGLSRGFVTRGDLIDALPDDDAHDAGIDAATAVLAELGIAV--SDDAHAETGW- 80

Query: 91  DSLD-------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            SLD       L+ +A+  +           R+TD PVR+YLREMG++ LL+ + EIA A
Sbjct: 81  -SLDRYFRPAPLSRAAAERNGAFAAFDLLVPRTTD-PVRLYLREMGTVPLLTHDEEIAYA 138

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +RIE GRA  +A LC  P    AL   R E+ +G
Sbjct: 139 QRIERGRAASVAVLCGDPDALDALASIRREIAEG 172


>gi|317968319|ref|ZP_07969709.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 260

 Score =  197 bits (500), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 98/226 (43%), Positives = 150/226 (66%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 26  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P   E+A  + M  E +
Sbjct: 86  IRQGMTRAIDNSARTIRLPIHVSEKLSKMRRITRELSHRFGRQPNRLELAHAMGMQPEEL 145

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            +++  +    SL+    GD+D S LG+ I D N+   +DS  +   +E     L+ L  
Sbjct: 146 EELITQSAPCASLDAHARGDDDRSTLGELIADPNSNESMDSMDRNLQKEHLGTWLSQLNE 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +++ +RFG+      TL E+G+Q  V+RER+RQ+E+KAI KL+
Sbjct: 206 RERKIIELRFGLAGQEPLTLAEIGRQINVSRERVRQLESKAILKLR 251


>gi|161522996|ref|YP_001585925.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|160346549|gb|ABX19633.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
          Length = 625

 Score =  197 bits (500), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 97/237 (40%), Positives = 148/237 (62%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW
Sbjct: 388 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWW 447

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+IT ++AD   TIR+P H  D I+K+ R AR    +     TP E+A ++  PV+ V
Sbjct: 448 IRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGATATPAELAAQMGEPVDKV 507

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R ++ I KEP+S + PI  +      D + D +  SP D+A  A  R      +  L PR
Sbjct: 508 RDLMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPR 567

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++R+R+G+      +L ++G++  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 568 EALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASGTLAVLRPFV 624



 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/154 (37%), Positives = 81/154 (52%), Gaps = 12/154 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           +  +I L   RG+VT  +L   LP D+     ++   A+L+ +GI V   DD   E G  
Sbjct: 37  FAGLIALGLSRGFVTRGDLIDALPDDDAHDAGIDAATAVLAELGIAV--SDDAHAETGW- 93

Query: 91  DSLD-------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            SLD       L+ +A+  +           R+TD PVR+YLREMG++ LL+ + EIA A
Sbjct: 94  -SLDRYFRPAPLSRAAAERNGAFAAFDLLVPRTTD-PVRLYLREMGTVPLLTHDEEIAYA 151

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +RIE GRA  +A LC  P    AL   R E+ +G
Sbjct: 152 QRIERGRAASVAVLCGDPDALDALASIRREIAEG 185


>gi|1519640|gb|AAB07553.1| SigC [Chloroflexus aurantiacus J-10-fl]
          Length = 312

 Score =  197 bits (500), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 152/245 (62%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            +  A   + +++ +NLRLV+S+A++Y    L  LDLIQEG++GLM A +KFD   G KF
Sbjct: 66  AQVNAGTGRAQLINSNLRLVVSIARRYQGHALSLLDLIQEGSVGLMGAVDKFDASRGLKF 125

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA +W++Q+I R+IAD S T+R+PVH+ +++ ++ R  + +S ++ REPT EE+A   
Sbjct: 126 STYATYWIRQSIGRAIADHSRTVRLPVHLGERLSRLSRLRQELSQQLDREPTLEELAAGC 185

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                  R   +    P SL+ P  ++    L + + D    +P D   ++ L+      
Sbjct: 186 RPERRAGRTAEQAGLAPTSLDEPHTEDGGGALAEILTDPLQPTPFDEVSESMLQADVQHA 245

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L+PRE  +LR+R+G+     HTLE++G++  +TRER+RQ+E +A+RKL+ PS   +L
Sbjct: 246 LQQLSPRERSILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEHEALRKLRDPSLHPQL 305

Query: 677 RSFLD 681
           + +++
Sbjct: 306 QGYVN 310


>gi|209883307|ref|YP_002287164.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209871503|gb|ACI91299.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 387

 Score =  197 bits (500), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 113/246 (45%), Positives = 158/246 (64%), Gaps = 8/246 (3%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A  AK   VE+NL  V  +A +  N + L   DL QEG +GL+KA E FD  LG++F TY
Sbjct: 143 AEKAKARFVESNLLYVRKLANRKRNLKHLTADDLFQEGLMGLLKATELFDPELGFRFKTY 202

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q ++R++ D   TIR+PVH  +   K+ R   +++ ++ REPT  E+A +L + 
Sbjct: 203 ATWWIQQYMSRALDDGDRTIRLPVHRHEYFRKIKRKTAKLTFELGREPTLNELATELGLE 262

Query: 560 VEGVRKVL---KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            E + K+L    +T E +  + PIG EDT+ L  +  D++  S LD      LR    RV
Sbjct: 263 RERLAKLLWRLHVT-ECVEADAPIG-EDTTVLS-YKADESP-SILDLVALQQLRTMVARV 318

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA+L PREER++RMRFG+  + + TLE +G  F VTRERIRQIEAKA+RKLKHPSRS+ L
Sbjct: 319 LATLVPREERIIRMRFGLDGSGEQTLEAIGNVFGVTRERIRQIEAKALRKLKHPSRSRAL 378

Query: 677 RSFLDG 682
           R+FL+ 
Sbjct: 379 RTFLES 384


>gi|317502748|ref|ZP_07960858.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315666141|gb|EFV05698.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 287

 Score =  197 bits (500), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 102/268 (38%), Positives = 170/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +++G+  A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEDLISVEEEVELAQKIKRGDRRAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R   ++  + +  PT EEIA K+ +P E V   +K     +S++ P  + + + L D +
Sbjct: 139 KRVLNKLEQENEHFPTIEEIAAKVDIPEEKVADAIKSNGRHVSVDAPFAEGEENSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + NA    +  +Q +LR+  +  L SL  RE  ++   FGI    + TLEE+G +F +T
Sbjct: 199 PNSNAQMADNVLVQESLRDEISSALKSLNERERNIIEAFFGINQ-AEMTLEEIGDKFGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L++ S++K L+++L
Sbjct: 258 RERVRQIKEKAIRRLRNNSKNKSLKAYL 285


>gi|327480191|gb|AEA83501.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri DSM 4166]
          Length = 332

 Score =  197 bits (500), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 156/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKF
Sbjct: 81  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLVEEGNLGLIRAVEKF 137

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 138 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 197

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +  +  +
Sbjct: 198 PEEIANLLEKPVGEVKRMLGLNERVTSVDVSLGPDTDKTLLDTLTDDRPTDPCELLLDDD 257

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +    L+ L+ ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+R+L+
Sbjct: 258 LSNSIDLWLSDLSEKQREVVIRRFGLRGHEASTLEEVGQEIGLTRERVRQIQVEALRRLR 317


>gi|331006084|ref|ZP_08329420.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
 gi|330420121|gb|EGG94451.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
          Length = 342

 Score =  196 bits (499), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 98/238 (41%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK       A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 87  VFFARKSLKGEEAARKRMIESNLRLVVKISRRYVNRGLALLDLIEEGNLGLIRAVEKFDP 146

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EP+ E
Sbjct: 147 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPSAE 206

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V K+L + +   S++  IG +    L D I D++   P+     +++ 
Sbjct: 207 EIANLLDKPVADVEKMLGLNERVNSIDVNIGPQGDKTLSDTIPDQHVSDPVSLLQDSDMS 266

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    L  LT ++  VL  RFG+      TLEEVG++  +TRER+RQI+ +A+++LK
Sbjct: 267 ASIDGWLTELTEKQREVLCRRFGLRGYETSTLEEVGREIGLTRERVRQIQVEALKRLK 324


>gi|288926163|ref|ZP_06420090.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608876|ref|ZP_07883849.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337055|gb|EFC75414.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249403|gb|EFU29419.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 286

 Score =  196 bits (499), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 97/247 (39%), Positives = 163/247 (65%), Gaps = 4/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RKG+  A    +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAAEKFD   G
Sbjct: 43  IRKGDRHAL---EKLTKANLRFVVSVAKQYQNQGLSLPDLINEGNMGLIKAAEKFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+ R   +   + +R P+ +EIA
Sbjct: 100 FKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKINRMLNKFEQENERRPSIDEIA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +P + +   LK+    +S++ P  D D + L D + + +A     + +  +LRE  
Sbjct: 160 DSVDLPEDKIEDALKVNTRHVSVDAPFVDGDDNSLIDILPNSDAPMADKALVMESLREEI 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +R L +L  RE  ++   FGI  N + TLEE+G +F +TRER+RQI+ KAIR+L+H +++
Sbjct: 220 SRALRTLNERERNIIECFFGIN-NPEMTLEEIGDKFGLTRERVRQIKEKAIRRLRHNTKN 278

Query: 674 KKLRSFL 680
           + L+++L
Sbjct: 279 RVLKAYL 285


>gi|77919031|ref|YP_356846.1| DNA-directed RNA polymerase, sigma 70/sigma 32 subunit [Pelobacter
           carbinolicus DSM 2380]
 gi|77545114|gb|ABA88676.1| RNA polymerase, sigma 38 subunit, RpoS [Pelobacter carbinolicus DSM
           2380]
          Length = 347

 Score =  196 bits (499), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 95/226 (42%), Positives = 149/226 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW
Sbjct: 101 ARDRMIESNLRLVVKIAKRYMNRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWW 160

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R++ +QS TIR+PVH+ D I+K ++ +R + ++  REP  EEIA+ + +    +
Sbjct: 161 IRQSIERALVNQSRTIRLPVHVSDDINKFIKISRELVHQYNREPKVEEIAEYMGVEPAYI 220

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+++ + K+  S+E P+G+     L D IED  A +P       +          +L+  
Sbjct: 221 RRLMVLVKKTYSIEHPMGENRDYSLIDTIEDPKADNPSTFVDDIDKYAHVCNWFETLSEN 280

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E  +L +RFG+      TL+ +G++F VTRERIRQIEAK+++KL++
Sbjct: 281 EREILMLRFGLDDQEPQTLDTIGRRFGVTRERIRQIEAKSLQKLRN 326


>gi|325294741|ref|YP_004281255.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065189|gb|ADY73196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 322

 Score =  196 bits (499), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 94/238 (39%), Positives = 159/238 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++VE+NLR V+SVAKKY   GL   DLI EG +GL++AA +FD   G KF +YA+WW
Sbjct: 85  ALKKLVESNLRFVVSVAKKYLGCGLPLHDLIAEGILGLIEAARRFDPDKGVKFISYAVWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A Q+  ++IPV     ++K+ R+   +  K+ REPT EE+A+ + M  + +
Sbjct: 145 IRQSIMQALAQQTGAVKIPVKQAVLVNKITRSYGELLKKLGREPTTEELAEYVGMEPKEI 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L + + P+SL+TPIGDE+ +   DF++ +      +  +Q  L+++   +L  LTP+
Sbjct: 205 ERLLTVCQVPLSLDTPIGDEEDTTFKDFLKGEGTAEVEEKVVQEELKQSIQEMLEQLTPQ 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++++ MRFG+  N   TL E+G++  ++RER+RQ+E +A +K+K  +  KKL  FL+
Sbjct: 265 EKKIIIMRFGLDGNEPKTLREIGEKLGISRERVRQLETRAKKKMKEYALRKKLNVFLN 322


>gi|225621460|ref|YP_002722719.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225216281|gb|ACN85015.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 309

 Score =  196 bits (499), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 94/234 (40%), Positives = 158/234 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V++NLRLVIS+AK+Y N G+ F+D+I EGNIGL++A ++F++  G+KFSTY +WW+KQ
Sbjct: 74  KLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYKKGFKFSTYGVWWIKQ 133

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I + I+ +   IR P+H+   I K ++T++ ++ K+ R+PT +EI+K++ +  + +  +
Sbjct: 134 SIVKEISSKRHIIRFPMHIARLIKKSIQTSKTLTQKLGRDPTIDEISKEMKIDRKTLSYI 193

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +  T++  S+++   + D + +   IEDKN  SP   A   +LR+T T  L  L  +E  
Sbjct: 194 MIFTQDTASVDSFFRNSDNNDMTSIIEDKNFPSPHQKAFMDSLRDTLTEALKCLDEKERT 253

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+  R+G+      TLE+ GK+  +TRER+RQI+ KAI+KL   + SK+L+SFL
Sbjct: 254 VIISRYGLYGKEAKTLEDTGKELNITRERVRQIQIKAIKKLAGLNLSKELKSFL 307


>gi|42526449|ref|NP_971547.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|41816642|gb|AAS11428.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|325473389|gb|EGC76584.1| RNA polymerase sigma factor [Treponema denticola F0402]
          Length = 286

 Score =  196 bits (499), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 108/286 (37%), Positives = 171/286 (59%), Gaps = 7/286 (2%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           KN    E++S+     EI  I + T     E      +  KG+ +A   K  +V +NLR 
Sbjct: 6   KNNYDAEMNSLATYLKEINQIPLLTA---EEEIKYAKLAEKGDEDA---KNMLVNSNLRF 59

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V++VAKKY N+GL  +DLI EGNIGLM AAE+FD   GYKF +YA+WW+KQ+I ++I ++
Sbjct: 60  VVNVAKKYQNQGLPLMDLISEGNIGLMNAAERFDVSKGYKFISYAVWWIKQSILKAICEK 119

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S  IR+P++  +++ ++ +  + +           EIA  L M    V  ++   +EPIS
Sbjct: 120 SRMIRLPLNRANELVQIEKAKKEIDFSGNETKELNEIAGILNMDNSMVHTIMNAAREPIS 179

Query: 576 LETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           ++ P+ DE  +S + DF++D+    P D A+  +LR+    +L +L  RE  ++R RFG+
Sbjct: 180 IDAPVFDEPGSSSVNDFLQDETHQMPEDYAMDMSLRDEVNELLKNLDDREAEIIRYRFGL 239

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G     +L+EVG  F +T+ERIRQIE KA+++LK P+  +KL  ++
Sbjct: 240 GGYAPLSLKEVGLIFNLTKERIRQIEKKALQQLKKPAEKQKLAVYV 285


>gi|302345330|ref|YP_003813683.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302149662|gb|ADK95924.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 284

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 168/268 (62%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   +R G+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 19  LQEIGHEEMISIEEEVELAQKIRNGDRKAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 75

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+
Sbjct: 76  LINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKI 135

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+ +EIA+   +P + +   +K+    +S++ P  D++ S L D I
Sbjct: 136 NKILTQFEQENERRPSIDEIAQNTDIPEDKIVDAMKVNSRHVSVDAPFYDDEQSSLLDVI 195

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + N  S     ++ +LRE   R L  L  RE+ V+   FGI    + TLEE+G ++ +T
Sbjct: 196 PNDNTPSTDKELVEESLREEIGRALQILEDREKVVIEAYFGINQR-EMTLEEIGSKYNLT 254

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  S SK L+++L
Sbjct: 255 RERVRQIKEKAIRRLRQLSNSKVLKAYL 282


>gi|33862253|ref|NP_893814.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634471|emb|CAE20156.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 339

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/226 (43%), Positives = 149/226 (65%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL  LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 105 ARDRMMSANLRLVVSVAKKYQNQGLDLLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S K  R+PT  E+A  + +  + +
Sbjct: 165 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRVSRELSQKSGRQPTRLEMATAMGIEQKDL 224

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++  +    SL+    G+ED S LG+ I D N   P++   +   +E     L  L  
Sbjct: 225 EDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEGMDRTIQKEHLGTWLTQLNE 284

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 285 REQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|87118598|ref|ZP_01074497.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
 gi|86166232|gb|EAQ67498.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
          Length = 330

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 150/226 (66%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 87  SRKRMIESNLRLVVKISRRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ E+IA  L  PVE V
Sbjct: 147 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEDIADMLDRPVEDV 206

Query: 564 RKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +K+L + +   S+++P+G  DT   L + I D+    P D    +++       L  L  
Sbjct: 207 QKMLSLNERISSIDSPVGGMDTDKSLVEIIADEQHAGPEDERQFSDVVHNIDHWLNDLNE 266

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  V+  RFG+      TLE+VG +  +TRER+RQI+ +A+RKLK
Sbjct: 267 KQREVIARRFGLRGYEPSTLEDVGAEIGLTRERVRQIQVEALRKLK 312


>gi|126215762|gb|ABN81001.1| putative RNA polymerase sigma-B factor [Rhodococcus opacus]
          Length = 194

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 87/193 (45%), Positives = 138/193 (71%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ +
Sbjct: 1   MPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +++K+ R  R +  ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + 
Sbjct: 61  QVNKLARIKRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAP 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED  A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK
Sbjct: 121 LGDFIEDSEATSAENAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGK 180

Query: 648 QFCVTRERIRQIE 660
            F ++RER+RQIE
Sbjct: 181 LFGLSRERVRQIE 193


>gi|126175320|ref|YP_001051469.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125998525|gb|ABN62600.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS155]
          Length = 326

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/239 (40%), Positives = 158/239 (66%), Gaps = 2/239 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   RK     + ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 73  VYFSRKALKGCAKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDP 132

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E
Sbjct: 133 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAE 192

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           EIA+KL +    V ++LK+ ++  S++TP+  ++   L D + D + V P D  +Q  ++
Sbjct: 193 EIAEKLQVSSADVSRMLKLNEKITSVDTPLWGDNDKALLDILADDDNVGP-DYKVQDEDI 251

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  + L  L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+
Sbjct: 252 SNSVVKWLNELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLR 310


>gi|300727119|ref|ZP_07060538.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775663|gb|EFI72254.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 295

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 168/268 (62%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   ++KG+  A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 30  LQEIGHEDLISVDEEVELAQRIKKGDKRAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 86

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 87  LINEGNLGLIKAAKKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 146

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R       + +R P+ +EIA  + +P + +   L +    +S++ P  + + + L D +
Sbjct: 147 NRLVNSFEQENERRPSVDEIADNIDLPEDKIADALNVNTHHVSVDAPFQEGEDNSLLDVL 206

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +  S     +  +LRE   RVL +L  RE  V+   FGIG   + TLEE+G ++ +T
Sbjct: 207 PNTDIPSADSELVHESLREEIARVLETLNQRERNVVEAFFGIGQ-AEMTLEEIGDKYGLT 265

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+H +++K L+S+L
Sbjct: 266 RERVRQIKEKAIRRLRHNTKNKYLKSYL 293


>gi|326332710|ref|ZP_08198972.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
 gi|325949491|gb|EGD41569.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
          Length = 315

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 148/229 (64%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A +E + ANLRLV+S+A+KY    +  LDLIQEGN GL++A EKFD+  GYKFSTY
Sbjct: 78  EGHRATREFINANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYTKGYKFSTY 137

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+QAITR IA Q+  +R+PVH+ +++++V    R +  ++ R+P PEEIA +L M 
Sbjct: 138 ATWWVRQAITRGIAQQARVVRLPVHVVEELNQVGGARRTLERQLGRDPEPEEIAAELGMD 197

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ V  +L   ++ +SL+TPI ++  + LGD +  ++A SP    I    RE    ++  
Sbjct: 198 IDRVLDLLSWGRDHVSLDTPIDEDGDTSLGDLMAQESAPSPDMDVIDVESRERLNSLVGQ 257

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R   ++R R+G+     H L ++G +  ++ ER+RQ+E +A++KL+
Sbjct: 258 LDERSADIVRSRYGLTDGRQHKLADIGVKHGISAERVRQLEREALQKLR 306


>gi|94500747|ref|ZP_01307276.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
 gi|94427069|gb|EAT12050.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
          Length = 331

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 154/240 (64%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + RKG+ +    +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 75  HFARLARKGDEKG---RKRMIESNLRLVVKIARRYVNRGLTLLDLIEEGNLGLIRAVEKF 131

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPT
Sbjct: 132 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPT 191

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA  L  PV+ V+++L + +   S++TP+G      + D I D+    P       +
Sbjct: 192 AEEIADLLEKPVDDVKRMLGLNERVTSVDTPLGYNSDKAILDTIADEAVSDPCQVLQDDD 251

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +    L  LT ++  V+  RFG+      TLEEVG +  +TRER+RQI+ +A+++L+
Sbjct: 252 ISSSLDGWLDELTEKQREVIARRFGLRGYEISTLEEVGFEIGLTRERVRQIQVEALKRLR 311


>gi|220906009|ref|YP_002481320.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219862620|gb|ACL42959.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 372

 Score =  196 bits (498), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/241 (39%), Positives = 163/241 (67%), Gaps = 1/241 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
             +AK +M+ +NLRLV+S+AK+Y NRG+ FLDL+QEG +GL +A EKFD   G+KFSTYA
Sbjct: 131 GQVAKSKMIRSNLRLVVSIAKRYLNRGVPFLDLVQEGALGLNRATEKFDPEKGFKFSTYA 190

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q ITR+IA+ S TIR+P+H+ +K++K+ +  R +  +++R PT +E+A  L + +
Sbjct: 191 YWWIRQGITRAIANDSRTIRLPIHIVEKLNKLKKLQRHLKKELQRNPTEQELADALEITL 250

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E ++ + +  ++ +SL   +G E+ + L D +E  +  SP     +  +R+  +++L  +
Sbjct: 251 EQLQMLQRARQQALSLNRRVGREEDTELLDLLEADSTQSPEKQMGEVMMRQEISQLLDLV 310

Query: 621 TPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             ++ER V+ +R+G+     +TLEEV   F ++RER+RQI+ KAI KL+  + +  LR++
Sbjct: 311 LTKQERDVIILRYGLVSGEPNTLEEVSGLFNLSRERVRQIQNKAIGKLRRSAIAHHLRNW 370

Query: 680 L 680
           L
Sbjct: 371 L 371


>gi|198282770|ref|YP_002219091.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666687|ref|YP_002424966.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198247291|gb|ACH82884.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518900|gb|ACK79486.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 317

 Score =  196 bits (497), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/237 (41%), Positives = 148/237 (62%), Gaps = 3/237 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           MV+ G+     A+  M+E+NLRLV+ VA+ Y NRGL  LDLI+EGN+GL++A EKFD   
Sbjct: 70  MVQTGD---QAARCTMIESNLRLVVKVARHYLNRGLPLLDLIEEGNLGLIRAVEKFDPER 126

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  ++  V+R  R ++  ++R+PTPEE+
Sbjct: 127 GFRFSTYATWWIRQNIERALMNQTRTIRLPIHVMKELSAVLRATRCLAQTLQRDPTPEEV 186

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ L   V+ VR  L++     SL+ P G      L D + D NA          NL   
Sbjct: 187 AEALDRSVDAVRDCLEMDGRVTSLDMPYGKGSDRSLADLVADTNAPGVEQRLENQNLSRQ 246

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +A++T +   VL  RFG+      TLEEVG +  +TRER+RQI+ +A+  L+H
Sbjct: 247 VHQWIATMTEKHRLVLLWRFGLDGTDGATLEEVGSRLGITRERVRQIQVEALLVLRH 303


>gi|288803307|ref|ZP_06408740.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288334127|gb|EFC72569.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 287

 Score =  196 bits (497), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 168/268 (62%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   +R G+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEEMISIEEEVELAQKIRNGDRKAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+
Sbjct: 79  LINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+ +EIA+   +P + +   +K+    +S++ P  D++ S L D I
Sbjct: 139 NKILTQFEQENERRPSIDEIAQNTDIPEDKIVDAMKVNSRHVSVDAPFYDDEQSSLLDVI 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + N  S     ++ +LRE   R L  L  RE+ V+   FGI    + TLEE+G ++ +T
Sbjct: 199 PNDNTPSTDKELVEESLREEIGRALQILEDREKVVIEAYFGINQR-EMTLEEIGSKYNLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  S SK L+++L
Sbjct: 258 RERVRQIKEKAIRRLRQLSNSKVLKAYL 285


>gi|114562238|ref|YP_749751.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
 gi|114333531|gb|ABI70913.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 323

 Score =  196 bits (497), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 95/230 (41%), Positives = 152/230 (66%), Gaps = 2/230 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 80  CEKS--RNRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 137

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR+++ K+  EPT EEIA+KL +
Sbjct: 138 YATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARQLAQKLDHEPTAEEIAEKLDV 197

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               V ++LK+ +   S+++P+  ++   L D I D ++V P       +L  +    L 
Sbjct: 198 STGDVSRMLKLNERITSVDSPLSGDNEKALLDVIADDDSVGPDYRVQNEDLSNSIVGWLN 257

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  ++  VL  RFG+      TLE VG +  +TRER+RQI+ +A+++LK
Sbjct: 258 ELNTKQREVLARRFGLLGYEPSTLENVGAEIGLTRERVRQIQVEALKRLK 307


>gi|92114749|ref|YP_574677.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797839|gb|ABE59978.1| RNA polymerase, sigma 38 subunit, RpoS [Chromohalobacter salexigens
           DSM 3043]
          Length = 325

 Score =  196 bits (497), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 158/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      ++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 74  HYGRLAQKGD---PAGRQRMIESNLRLVVKIARRYLNRGLSLLDLIEEGNLGLIRAVEKF 130

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +R AR ++ ++  E T
Sbjct: 131 DPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRAARELTQRLDHEAT 190

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA+ L  PV  V+K+L + +   S++ P+G E    L D + D+N   P    +  +
Sbjct: 191 AEEIAEFLDKPVGTVKKMLGLNERVSSVDYPMGGESDKPLIDTLADENEAGPESLLVGND 250

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++     LA LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A++KL+
Sbjct: 251 VKQHVDDWLAELTDKQMEVVVRRFGLRGHEAATLEEVGEEIGLTRERVRQIQVEALKKLR 310


>gi|326319203|ref|YP_004236875.1| RpoD subfamily RNA polymerase sigma-70 subunit [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323376039|gb|ADX48308.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 878

 Score =  195 bits (496), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 106/247 (42%), Positives = 158/247 (63%), Gaps = 13/247 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IA+  M  ANL+L    A+KY   G    DL QEGN+GL+KA ++++W  G++FSTYA W
Sbjct: 520 IARDRMTAANLKLAFFHARKYLYSGETLDDLAQEGNVGLLKAVDRYNWRRGFRFSTYATW 579

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WV+Q I+R +AD++ TIR+PVH+ +K  +  R A+R      R P+ +E+A+++ MP   
Sbjct: 580 WVRQQISRYVADKARTIRMPVHIYEKAQRAERIAQRFEMLADRAPSLDELAERMEMPRHK 639

Query: 563 VRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLA 618
           +  +L+I  EP  + E+P+ DE  S     ++ ++A     P D+     +R    R ++
Sbjct: 640 LAALLRIAPEPSRIDESPV-DELIS-----LDARDAYWLPDPADAVETHQVRAALDRYIS 693

Query: 619 SLTPR---EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           SL+ R   EE VLR+R+GIG++   TL+EVG++F VTRERIRQIEAKAIRKLKH +RS+ 
Sbjct: 694 SLSTRDRKEEHVLRLRYGIGVHEALTLDEVGQRFGVTRERIRQIEAKAIRKLKHHARSEP 753

Query: 676 LRSFLDG 682
               + G
Sbjct: 754 FARLVLG 760


>gi|121998209|ref|YP_001002996.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
           SL1]
 gi|121589614|gb|ABM62194.1| RNA polymerase, sigma 38 subunit, RpoS [Halorhodospira halophila
           SL1]
          Length = 336

 Score =  195 bits (496), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 153/238 (64%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ R+ +   + A+  M+E+NLRLV+ +A++Y NRGL FLDLI+EGN+GL++A EKFD 
Sbjct: 84  VALARRVQQGDAAARARMIESNLRLVVKIARRYMNRGLAFLDLIEEGNLGLIRAVEKFDP 143

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R I +Q+ TIR+P+H+  +I++ +RT RR++  +  EPT +
Sbjct: 144 ERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHVIKEINQYLRTQRRLTQTLDHEPTVD 203

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  +    E VR++  + +   S++ PIG +    L D I D+    P +     ++ 
Sbjct: 204 EIADAMGRSPEDVRRMRGLNEGTTSVDVPIGKDSDRVLLDAIPDETQGMPENVLEDDDVV 263

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  LT ++  VL  RFG+  +  +TLE+VG Q  VTRER+RQI+  A+R+L+
Sbjct: 264 RHLQDWLGFLTDKQRAVLERRFGLNGHERYTLEQVGTQVGVTRERVRQIQIDALRRLR 321



 Score = 41.2 bits (95), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           R+  D  ++YL E+G   LL+ E E+A+A+R++ G A   A + ES L    + I R  +
Sbjct: 59  RTALDATQLYLNEIGHASLLTAEEEVALARRVQQGDAAARARMIESNLRL-VVKIARRYM 117

Query: 175 NDGTTLL 181
           N G   L
Sbjct: 118 NRGLAFL 124


>gi|238898782|ref|YP_002924464.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466542|gb|ACQ68316.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 335

 Score =  195 bits (496), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 162/246 (65%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 86  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 145

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 146 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 205

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 206 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 265

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           ++  + L  L+ ++  VL  RFG+      TLEEVG +  +TRER+RQI+ + + +LK  
Sbjct: 266 KSVVKWLFELSTKQREVLARRFGLLGYEPATLEEVGCEIGLTRERVRQIQVEGLLRLKEM 325

Query: 671 SRSKKL 676
            +++ L
Sbjct: 326 LQTQGL 331


>gi|261856530|ref|YP_003263813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
 gi|261836999|gb|ACX96766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
          Length = 343

 Score =  195 bits (495), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 103/272 (37%), Positives = 161/272 (59%), Gaps = 3/272 (1%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F A + +S+  +R  ++ +  E  ++  E    V   R+ +     A+++M+  NLRLV
Sbjct: 59  TFSASDSESVDPVRLYLRDVETERLLTAEEE---VIYSRRAQSGDESARQKMIVCNLRLV 115

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           I +A++Y NRGL  LDLI+EGNIGLM+A EKFD   G++FSTYA WW++Q I R + +QS
Sbjct: 116 IKIARRYMNRGLDLLDLIEEGNIGLMRAVEKFDPERGFRFSTYATWWIRQTIERGLMNQS 175

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            T+R+PVH+  ++H   R AR+++     E T E+IA  L  PV  V K++   +   S 
Sbjct: 176 RTVRLPVHVVKEVHTFNRAARKIAQNQNAEVTAEQIADHLDRPVNEVLKIMAFNERQSSF 235

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ++P+  +    L D I D+ +  P +    A +     +++A L  ++  VL  R+G+  
Sbjct: 236 DSPLKGDGEFSLLDLIPDQESNQPDELLQDAGVHGFLDQLIAQLESKQREVLVRRYGLRG 295

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              HTLEEVG    VTRER+RQI+ +A+R+LK
Sbjct: 296 YETHTLEEVGNHLGVTRERVRQIQLEAVRRLK 327


>gi|17158744|ref|NP_478255.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17134693|dbj|BAB77251.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 323

 Score =  195 bits (495), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 90/229 (39%), Positives = 153/229 (66%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + AK++M+ ANLRLV+++AKKY  R L+ +DLIQEG++GL +  EKFD   GYKFSTY
Sbjct: 83  QGTQAKQKMMVANLRLVVAIAKKYQRRNLELMDLIQEGSLGLERGVEKFDPTRGYKFSTY 142

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW+ QA+TR+I+ QS TIR+P+H+ +K++K  +  R +S K+KR P+ +EIA+K+ + 
Sbjct: 143 AYWWISQAMTRAISQQSRTIRLPIHITEKLNKFKKVQRELSQKLKRSPSADEIAEKMKLN 202

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              +R++L I+++P SL+  +GD + + L + + +    SP     Q  +R+     L  
Sbjct: 203 PAQIRELLMISRQPASLDKQVGDNEDTELQELLTEVPETSPEIQVTQNLMRQDIYLSLRE 262

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LTP++++VL + +G+  N + TL +V +   ++  R+R +E +A+  L+
Sbjct: 263 LTPQQQQVLILHYGLEDNYELTLTQVAQHLNISERRVRYLEKQALSYLR 311


>gi|254449272|ref|ZP_05062719.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
 gi|198261127|gb|EDY85425.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
          Length = 308

 Score =  194 bits (494), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 102/275 (37%), Positives = 167/275 (60%), Gaps = 5/275 (1%)

Query: 396 KNFVACEVDS--ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           ++F A E+ S  +   R  +K I     ++  +  H   +V++G+     A+++M+E+NL
Sbjct: 22  EHFTAAELSSSQLDATRLYLKEIEFSPLLTAEQEIHYGRLVQEGD---EAARRKMIESNL 78

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R + 
Sbjct: 79  RLVVKISRRYMNRGLPLLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERGLM 138

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +R AR M  +  REPTPEE+AK L  PV+ V ++  + +  
Sbjct: 139 NQTRTIRLPIHVIKELNVYLRAARAMQQEFAREPTPEEVAKHLDKPVDDVCRMYGLNERV 198

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++ PIG E  S L D I D +   P        +       L  L  +++ V+  RFG
Sbjct: 199 ASVDVPIGKEGDSLLLDLIADDSVPDPTALLQSEEVAAYVDHWLEELDAKQKAVVERRFG 258

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      TLE +G +  VTRER+RQI+ ++++KL+
Sbjct: 259 LHGQDYATLEVIGHELGVTRERVRQIQMESLKKLR 293


>gi|326800649|ref|YP_004318468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326551413|gb|ADZ79798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 286

 Score =  194 bits (494), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 102/241 (42%), Positives = 160/241 (66%), Gaps = 9/241 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + + NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALERLTKTNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I ++IA+QS  +R+P++    + K+ +   R+  + +REP+PEE+A  L   V+ +
Sbjct: 110 IRQSILQAIAEQSRIVRLPLNQVGSLSKISKAFSRLEQEYEREPSPEELADILETTVDKI 169

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLAS 619
              L  +   +S++ P   G+E+T  L D +E  D N  S L   I  +L E   R LA+
Sbjct: 170 SDTLSNSGRHVSMDAPFVQGEENT--LLDVLENHDPNTDSNL---IDESLSEEIKRSLAT 224

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE  ++ + FG+G N   +LEE+G+ F +TRER+RQI+ KA+++L+H SRSK L+S+
Sbjct: 225 LTEREREIIVLFFGLGSNHPLSLEEIGETFNLTRERVRQIKDKALQRLRHTSRSKILKSY 284

Query: 680 L 680
           L
Sbjct: 285 L 285


>gi|158336372|ref|YP_001517546.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158306613|gb|ABW28230.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  194 bits (494), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 152/225 (67%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MVE+NLRLV+S+AKKY    ++FLDLIQEG IGL +  EKFD   GY+FSTYA WW
Sbjct: 83  ANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGLQRGVEKFDPMKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IA+Q  TIR+P+H+ +K+ K+ +  R++S K+ R+PT +E+A ++ +  + +
Sbjct: 143 IRQAMTRAIAEQERTIRLPIHINEKLSKLRKVRRQLSQKLHRDPTVQELAVEMDLAPKKI 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L   +  ISL+  IGD+  + L + +ED N  SP   A  ++LR    ++L  L+P+
Sbjct: 203 EDYLNYARRSISLDIQIGDQQNTELWELLEDPNE-SPDTYATASSLRSDLAKLLQDLSPQ 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+ +R+G+      TL +VG++  V+RE +R++E +A + L+
Sbjct: 262 QREVITLRYGLIDQNPLTLAKVGERLNVSREWVRRVEREAFKILR 306


>gi|6463980|dbj|BAA86957.1| group 2 sigma factor RpoD3 [Synechococcus sp. PCC 7942]
          Length = 320

 Score =  194 bits (494), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 99/249 (39%), Positives = 157/249 (63%), Gaps = 8/249 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+SI E R    +   GE     AK++M+EANLRLV+SVAKKY  R +  LDLIQEG IG
Sbjct: 69  GLSIEELRQQQHL---GEQ----AKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIG 121

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           + +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S
Sbjct: 122 MQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLS 181

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++     P E+A  L +    VR  L+  + P+SL+  +GD   + LGD +E       
Sbjct: 182 QQLSTATLP-ELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTELGDLLETDMQRRR 240

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +  +QA++R    R+L  LT ++ +V+ +R+G+      TL  +G +  ++RER+RQ+E
Sbjct: 241 KEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLE 300

Query: 661 AKAIRKLKH 669
            +A+  L+ 
Sbjct: 301 REALHTLRQ 309


>gi|197335185|ref|YP_002156867.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
 gi|197316675|gb|ACH66122.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
          Length = 321

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 148/225 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+E+NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 78  ARARMIESNLRLVVKIARRYNHRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPEEIA+KL  PV  V
Sbjct: 138 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPEEIAEKLDKPVSDV 197

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S+++ +  E    L D + D     P     + ++  +    L  L P+
Sbjct: 198 SRMLRLNERVASVDSMVAGESDKALLDILPDTKNSDPESETQKDDINTSLVGWLGQLNPK 257

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ V+  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+
Sbjct: 258 QKEVVARRFGLLGYEAATLEQVGVEIGLTRERVRQIQVEGLRRLR 302


>gi|226945910|ref|YP_002800983.1| RNA polymerase sigma factor RpoS [Azotobacter vinelandii DJ]
 gi|16226165|gb|AAL16091.1|AF421351_3 stationary phase sigma factor [Azotobacter vinelandii]
 gi|226720837|gb|ACO80008.1| RNA polymerase sigma factor [Azotobacter vinelandii DJ]
          Length = 334

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 161/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     ++ +E  H   + ++G+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 67  LNEIGFSPLLTPAEEVHFARLAQRGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 123

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 124 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 183

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+ EEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 184 LRAARELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDVL 243

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P D     +L ++  + L  LT ++  V+  RFG+  +   TLEEVG++  +T
Sbjct: 244 TDDRPSDPCDLLQDDDLSQSIDQWLFDLTEKQREVVVRRFGLRGHESCTLEEVGQEIGLT 303

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ +A+++L+
Sbjct: 304 RERVRQIQVEALKRLR 319


>gi|320536473|ref|ZP_08036507.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320146682|gb|EFW38264.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 282

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 95/238 (39%), Positives = 159/238 (66%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK ++++ANLR V++VAKKY N+GL  +DLI EGNIGLM AA++FD   GYKF +YA+WW
Sbjct: 44  AKDKLIQANLRFVVNVAKKYQNQGLPLMDLISEGNIGLMNAADRFDVTKGYKFISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I ++I ++S  IR+P++   ++ ++ +T + + +    E   +E+A  LA+  + V
Sbjct: 104 IRQSILKAICEKSRMIRLPLNRVGELIQIEKTRKEIRSTASEEEELKEVADILALDHDTV 163

Query: 564 RKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + ++ I +EP+SL+ P+ D+  +  +GDFIED     P    +  +L+E+  +V+ +L  
Sbjct: 164 KMIVNIGREPVSLDAPLFDDAANGKMGDFIEDAQYEQPEAYMLDVSLKESIDKVINTLPK 223

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  +LR RFG+      +L++VGK F +T+ERIRQIE K++ +LK  S   KL +++
Sbjct: 224 REAEILRYRFGLNGYKQLSLKDVGKIFNLTKERIRQIEKKSLEQLKATSYKYKLDAYV 281


>gi|302876403|ref|YP_003845036.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307687066|ref|ZP_07629512.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579260|gb|ADL53272.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 427

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 114/238 (47%), Positives = 145/238 (60%), Gaps = 6/238 (2%)

Query: 448 MVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V AN +LV  +A   K+++       D+ Q G +GLMKAAEKFD   G +FSTYA WWV
Sbjct: 185 LVNANKKLVWEIALRYKQFSTVSFDNSDMYQAGVLGLMKAAEKFDISKGNQFSTYATWWV 244

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q+ITRSIAD S TIRIPVHMR+KI K V T  +  N+  R  + EE+A  L +  E V 
Sbjct: 245 RQSITRSIADYSTTIRIPVHMREKIIKYVSTENKFWNENGRVASKEELANLLGISSEEVN 304

Query: 565 --KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLT 621
             +V +      SL+ PIG ++ S LG+FI D    SP  SA +  L RE        LT
Sbjct: 305 YLQVYQDVANLTSLDIPIGADEGSFLGEFIPDDKHRSPEKSAEEGELKRELKEICEGRLT 364

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           P+E R+L  RFG      HTLEE+G    VTRERIRQIEAKAI KL++P   ++LR F
Sbjct: 365 PKETRILNFRFGFIDGRTHTLEEIGHVENVTRERIRQIEAKAISKLQNPKILERLRDF 422


>gi|313203522|ref|YP_004042179.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Paludibacter
           propionicigenes WB4]
 gi|312442838|gb|ADQ79194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paludibacter
           propionicigenes WB4]
          Length = 287

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 103/269 (38%), Positives = 176/269 (65%), Gaps = 5/269 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I++ E   +   +R G+    IA +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLITVEEEVELAQRIRAGD---RIALEKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R+P+PEE+A  L +PV+ +   +K++   IS++ P  + + + L D +
Sbjct: 139 NKAFSKFEQENERKPSPEELADVLDIPVDKIADTMKVSGRHISVDAPFVEGEDNSLLDVM 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            + ++ +     I  +L +   RVLA +L+ RE  +++  FGIG+  + TLEE+G +F +
Sbjct: 199 INDDSPNADRVLINESLSKEIERVLAFTLSDRERDIVKKFFGIGV-AEMTLEEIGDEFGL 257

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI+ KAIRKL+  ++SK L+ FL
Sbjct: 258 TRERVRQIKEKAIRKLRPNAKSKLLKGFL 286


>gi|302338230|ref|YP_003803436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635415|gb|ADK80842.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 291

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 98/238 (41%), Positives = 167/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++++NLR V++VAKKY N+GL   DLI EGNIGLM A E++D   GY F +YA+WW
Sbjct: 52  AKEMLIKSNLRFVVNVAKKYQNQGLPLADLINEGNIGLMNAIERYDVDKGYHFISYAVWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI ++I++++  IR+P++  +++ ++ +  + +  + K EP  EEIA+ + M  E V
Sbjct: 112 IRQAILKAISEKARMIRLPLNRANELVQIEKAKKGLQLEGKEEPEFEEIARVVGMDAEHV 171

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++ I+++ +SLE+PI  D   S LGDFIED +  SP ++ ++ +L+E   +VL +L+ 
Sbjct: 172 ASLVNISRDLVSLESPIYTDRSQSELGDFIEDVDYKSPDETLMEQSLKEDIAKVLDTLSE 231

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +E  ++R RFG+      +L+++G ++ +T+ERIRQIE KAI++L+HPSR + L S++
Sbjct: 232 KEADIIRHRFGLDGRAPLSLKDIGDRYNLTKERIRQIEKKAIKRLQHPSRRQYLESYI 289


>gi|59712674|ref|YP_205450.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
 gi|59480775|gb|AAW86562.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
          Length = 321

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 148/225 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+E+NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 78  ARARMIESNLRLVVKIARRYNHRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPEEIA+KL  PV  V
Sbjct: 138 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPEEIAEKLDKPVSDV 197

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S+++ +  E    L D + D     P     + ++  +    L  L P+
Sbjct: 198 SRMLRLNERVASVDSMVAGESDKALLDILPDTKNSDPESETQKDDINTSLVGWLGQLNPK 257

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ V+  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+
Sbjct: 258 QKEVVARRFGLLGYEAATLEQVGIEIGLTRERVRQIQVEGLRRLR 302


>gi|6175930|gb|AAF05342.1|AF182106_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 303

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 88/214 (41%), Positives = 148/214 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +  VL  RFG+      TLE+VG++  +TRER+R
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTRERVR 303


>gi|1769588|gb|AAB95226.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score =  194 bits (493), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 96/237 (40%), Positives = 162/237 (68%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++A+    R L+FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIARNIKKRNLEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA Q  TIR+P+H+ +K++K+ +T R+++  + R  T  EIA+ L +    +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKTQRQLAQDLGRAATIAEIAEALELEPAQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+  ++++ PISL+  +GD   + L D +ED +  SP ++     L++    ++A LTP+
Sbjct: 212 REYFRVSRHPISLDVRVGDNQDTELMDLLED-SGESPDNNVTYELLKQDLRDLIADLTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++ V+ +RFG+    + +L ++GK+  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 271 QQEVIILRFGLNDGKELSLAKIGKRMNLSRERVRQLERQALNHLRR--RRSQIREYL 325


>gi|45128577|gb|AAS55057.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  194 bits (492), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 118/278 (42%), Positives = 162/278 (58%), Gaps = 13/278 (4%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    +  S K  V  E ++ +     L   ++   V +    
Sbjct: 218 EKFNQLRSTYQNLQLAINEYGYD--SPKATVANEMMLDVFKEFRLTPKQLXHXVNEXRTA 275

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A   P  E       E
Sbjct: 276 MDRVXTQERLIMKSVVEYGKMPKKSFIALFTGXESSDAWLXEILASXXPYAEKIKRXEEE 335

Query: 403 VD-SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           +  SI K+      I  ET +++   + I   +  GE +A  AKKEMVEANLRLVIS+AK
Sbjct: 336 IRRSIAKL----XMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAK 391

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRG QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 392 KYTNRGXQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 451

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           PVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP
Sbjct: 452 PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMP 489



 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 2   KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 61

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 62  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 120

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 121 INQVQSSVAEYPGTIPYIL 139


>gi|146308041|ref|YP_001188506.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina ymp]
 gi|145576242|gb|ABP85774.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas mendocina ymp]
          Length = 335

 Score =  194 bits (492), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 156/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 84  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 140

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 141 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 200

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 201 AEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 260

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  + L+ LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 261 LSQSIDQWLSDLTDKQREVVVRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 320


>gi|325971114|ref|YP_004247305.1| RNA polymerase, sigma 70 family subunit [Spirochaeta sp. Buddy]
 gi|324026352|gb|ADY13111.1| putative RNA polymerase, sigma 70 family subunit [Spirochaeta sp.
           Buddy]
          Length = 293

 Score =  194 bits (492), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 95/250 (38%), Positives = 168/250 (67%), Gaps = 3/250 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + ++ +     A+K M+E+NLR V++VAKKY N+G+  +DLI EGNIGLM A EKFD   
Sbjct: 44  LAKRAQKGDEFARKRMIESNLRFVVNVAKKYQNQGMPLVDLINEGNIGLMTALEKFDPDK 103

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPEE 551
           GY F +YA+WW++Q+I ++I ++S  +R+P++  +++ ++ +  R +   +   +P+ EE
Sbjct: 104 GYHFISYAVWWIRQSIMKAINEKSRAVRLPLNRTNELLQMHKAQRSLMKDLSTDDPSMEE 163

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           I        + V  +L I+++ ISL+ P+  D   S++GDFIED++  +P  S + A+L+
Sbjct: 164 IGTLTGFDPKHVSNLLSISRDLISLDAPVFTDGSASNIGDFIEDESQ-NPEQSLLDASLK 222

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    +LA+L+ +E  ++ +RFG+   T  +L+E+G+ + +T+ERIRQIE KA+ +L++P
Sbjct: 223 EDVRSLLATLSDKERDIIELRFGLEGKTPMSLKEIGELYNLTKERIRQIEKKALERLRNP 282

Query: 671 SRSKKLRSFL 680
           S+SK + S++
Sbjct: 283 SKSKMVESYI 292


>gi|107103136|ref|ZP_01367054.1| hypothetical protein PaerPA_01004205 [Pseudomonas aeruginosa PACS2]
          Length = 236

 Score =  194 bits (492), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 91/221 (41%), Positives = 149/221 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L
Sbjct: 61  IERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L E+  + L  LT ++  V
Sbjct: 121 GLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 181 VIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLR 221


>gi|108805426|ref|YP_645363.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766669|gb|ABG05551.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 282

 Score =  194 bits (492), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 152/251 (60%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + R+       A++ ++E+NLRLV+++AK+Y  RG+ F DLIQEGN GL++A EKFD 
Sbjct: 28  VELSRRARAGDGAARRRLIESNLRLVVAIAKRYRGRGVPFEDLIQEGNAGLIRAVEKFDP 87

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            +G +FSTYA WW++QA+TR++ADQ   +R+P H+ D ++++ R    +S ++ REPT E
Sbjct: 88  EMGNRFSTYATWWIRQAVTRAVADQGRAVRLPAHVVDSVYRLRRAESALSVELGREPTDE 147

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E+A +L    E  R++ ++++   S+   +GD ED + LGD + D+ A            
Sbjct: 148 EVAGRLGTSPEEARRLREVSQPISSISARLGDEEDGAELGDLLPDEAASEEYARVEAGPW 207

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R      + SL  RE RVLR+R G+      TL EV +   +++ER RQ+E KA+R L+ 
Sbjct: 208 RGVLREAVGSLPEREARVLRLRHGLDGERARTLREVSEILGISQERARQVELKALRTLRS 267

Query: 670 PSRSKKLRSFL 680
              +  LR  L
Sbjct: 268 GRYAGSLRRGL 278


>gi|166368031|ref|YP_001660304.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166090404|dbj|BAG05112.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 377

 Score =  193 bits (491), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 168/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 139 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +   ++R P   E+A+ L M  E +
Sbjct: 199 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQDLQRNPNERELAEALEMTPEQL 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED +   P D   +  +R+    VL+  LT 
Sbjct: 259 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTE 318

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 319 REKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 376


>gi|1514627|emb|CAA62840.1| starvation sigma factor [Pseudomonas putida]
          Length = 335

 Score =  193 bits (491), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 160/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   +V+KG+      +K M+++NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFAPLVQKGD---PAGRKRMMQSNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|251771333|gb|EES51914.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           ferrodiazotrophum]
          Length = 307

 Score =  193 bits (491), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 97/247 (39%), Positives = 154/247 (62%), Gaps = 4/247 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE   +   +  G+ EA   ++ M+ +NLRLV+ +AK+Y  RGL F DLI+EGN+GL
Sbjct: 43  LSASEEVDLARRIATGDAEA---RERMILSNLRLVVMIAKRYAGRGLPFPDLIEEGNLGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +++D   G++FSTYA WW++Q+I R++ +    IR+PVHMR+K+++ +    +M +
Sbjct: 100 MKAVDRYDPEKGFRFSTYASWWIRQSIERAVINLGHMIRLPVHMREKVNRYLAAVEQMVS 159

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              REP P E A+K  + VE    +  +    ISL+ P+G++D + L D + D  A SPL
Sbjct: 160 T-GREPDPSEAARKAGLTVEEFESLYPLIAATISLDAPVGEQDENTLKDVLGDPEADSPL 218

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +   +          L+ L PRE  +L +RFG+      TL+E+G++  +TRER+RQIEA
Sbjct: 219 EVVSRREEGRELEAALSVLRPRERDILFLRFGLSGEDPKTLDEIGRRLGITRERVRQIEA 278

Query: 662 KAIRKLK 668
            A+ K++
Sbjct: 279 VALSKMR 285


>gi|37519772|ref|NP_923149.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35210763|dbj|BAC88144.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 356

 Score =  193 bits (491), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 101/232 (43%), Positives = 159/232 (68%), Gaps = 1/232 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  +   AK+++V+ANLRLV+S+AKKY NRG+ FLDLIQEG++GL++AAEKF+   G
Sbjct: 107 IAQGGPKGEWAKRKLVQANLRLVVSIAKKYLNRGVPFLDLIQEGSMGLIRAAEKFEHERG 166

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR++A Q+ T+R+PVH+ +KI++V +  R ++ ++ R P+  E+A
Sbjct: 167 YKFSTYAYWWIRQAITRAVASQARTVRLPVHLVEKINRVKKVRRTLAQELGRTPSQGELA 226

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L +  E +  +L+  +  +SL   +G E+ + L   IED     P     + ++R   
Sbjct: 227 EALELAEEDLEHILRAARRTVSLNITVGKEEDTELIHLIEDSQTDQPDVHIDRESMRVEV 286

Query: 614 TRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + +L   LTPRE  +L++RFG+      TL++VG+ F ++RERIRQI+AKA 
Sbjct: 287 SDLLDRHLTPRERDILQLRFGLRDGQQRTLDQVGRMFDLSRERIRQIQAKAF 338


>gi|158337702|ref|YP_001518878.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158307943|gb|ABW29560.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  193 bits (491), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 151/225 (67%), Gaps = 1/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MVE+NLRLV+S+AKKY    ++FLDLIQEG IGL +  EKFD   GY+FSTYA WW
Sbjct: 83  ANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGLQRGVEKFDPMKGYRFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+TR+IA+Q  TIR+P+H+ +K+ K+ +  R++S K+ R+PT +E+A ++ +  + +
Sbjct: 143 IRQAMTRAIAEQERTIRLPIHINEKLSKLRKVRRQLSQKLHRDPTVQELAVEMDLAPKKI 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L   +  ISL+  IGD+  + L + +ED N  SP      ++LR    ++L  L+P+
Sbjct: 203 EDYLNYARRSISLDIQIGDQQNTELWELLEDPNE-SPDTYVTASSLRSDLAKLLQDLSPQ 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+ +R+G+      TL +VG++  V+RE +R++E +A + L+
Sbjct: 262 QREVITLRYGLIDQNPLTLAKVGERLNVSREWVRRVEREAFKILR 306


>gi|116074244|ref|ZP_01471506.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069549|gb|EAU75301.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  193 bits (491), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 99/242 (40%), Positives = 156/242 (64%), Gaps = 8/242 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + M ++       A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +K
Sbjct: 98  RHKIRMGKR-------ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDK 150

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P
Sbjct: 151 FDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQP 210

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              E+A  + +    +  ++  +    SL+    G+ED S LG+ I D N    ++   +
Sbjct: 211 NRLELAHAMGIEPRDLEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEDSMEGMDR 270

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +  +E     L+ L  RE+++L++RFG+      TL E+G+Q  V+RER+RQ+EAKAI K
Sbjct: 271 SIQKEHLGGWLSQLNEREQKILKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILK 330

Query: 667 LK 668
           L+
Sbjct: 331 LR 332


>gi|325103187|ref|YP_004272841.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
 gi|324972035|gb|ADY51019.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
          Length = 286

 Score =  193 bits (491), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 162/240 (67%), Gaps = 7/240 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + + NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALERLTKTNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I ++IA+QS  +R+P++    + K+ +   ++  + +REP+PEE+A  L   V+ +
Sbjct: 110 IRQSILQAIAEQSRIVRLPLNQVGSLSKISKAFSKLEQEYEREPSPEELADILETTVDKI 169

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSA-IQANLRETTTRVLASL 620
              L  +   +S++ P   G+E+T  L D +E+ N  +  DS  I  +L E   R L++L
Sbjct: 170 SDTLSNSGRHVSMDAPFVQGEENT--LLDVLENDNPNT--DSMLIDESLSEEIKRSLSTL 225

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE  ++ + FG+G N   +LEE+G++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 226 TEREREIIVLFFGLGSNHPLSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285


>gi|88812406|ref|ZP_01127656.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88790413|gb|EAR21530.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 356

 Score =  193 bits (490), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+ +     A+K M+E+NLRLV+ +A++Y NRGL FLDLI+EGN+GL++A EKFD 
Sbjct: 104 VYYARRAQGGDESARKRMIESNLRLVVKIARRYMNRGLAFLDLIEEGNLGLIRAVEKFDP 163

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +I++ +R AR++  ++  EPT E
Sbjct: 164 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVIKEINQYLRVARQLVQRLDHEPTLE 223

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  +   +E VR ++ + +   S++ PIG +    L D I D+    P  +    ++ 
Sbjct: 224 EIAIAMDRSIEDVRHMMGLNEGVTSVDIPIGRDADRVLLDAIPDEVNPDPFAALQDEDVV 283

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  LT ++  V+  RFG+  +   TLEEVG +  VTRER+RQI+  A++KL+
Sbjct: 284 SHLDAWLNELTEKQRAVVERRFGLHGHEKATLEEVGDEIGVTRERVRQIQIDALKKLR 341


>gi|260911780|ref|ZP_05918352.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634106|gb|EEX52224.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 287

 Score =  193 bits (490), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 99/268 (36%), Positives = 170/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +RKG+ +A    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEELISVEEEVELAQRIRKGDRKAL---EKLTKANLRFVVSVAKQYQNQGLSLQD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+PV+    ++K+
Sbjct: 79  LINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPVNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+  EIA+K  +P + +   +K+T   IS++ P  D + + L D +
Sbjct: 139 NKILNKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGRHISVDAPFVDGEDNSLLDLL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +  +  +  ++ +LR      L  L  RE  V+   FGI    + TLEE+G ++ +T
Sbjct: 199 TNSDMPTVDNELVKESLRAEIAEALQFLNERERNVIEAFFGINQ-MEMTLEEIGDKYGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L++ +++K L+++L
Sbjct: 258 RERVRQIKEKAIRRLRNNTKNKMLKTYL 285


>gi|26988355|ref|NP_743780.1| RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148549360|ref|YP_001269462.1| RNA polymerase sigma factor RpoS [Pseudomonas putida F1]
 gi|167032190|ref|YP_001667421.1| RNA polymerase sigma factor RpoS [Pseudomonas putida GB-1]
 gi|24983106|gb|AAN67244.1|AE016351_6 RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148513418|gb|ABQ80278.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           F1]
 gi|166858678|gb|ABY97085.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           GB-1]
 gi|313500209|gb|ADR61575.1| RpoS [Pseudomonas putida BIRD-1]
          Length = 335

 Score =  193 bits (490), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 159/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|2289784|dbj|BAA21674.1| rpoS sigma factor [Pseudomonas tolaasii]
          Length = 336

 Score =  193 bits (490), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 155/240 (64%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 85  HFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 141

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 142 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 201

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 202 PEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 261

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 262 LSQSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 321


>gi|170723213|ref|YP_001750901.1| RNA polymerase sigma factor RpoS [Pseudomonas putida W619]
 gi|169761216|gb|ACA74532.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           W619]
          Length = 335

 Score =  193 bits (490), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 159/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|5305130|emb|CAB46191.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 335

 Score =  193 bits (490), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 159/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|325280730|ref|YP_004253272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312539|gb|ADY33092.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 289

 Score =  193 bits (490), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 112/288 (38%), Positives = 176/288 (61%), Gaps = 9/288 (3%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K     E  SI K   EI  I V   +S  E   +   +R G+     A++++V +NLR 
Sbjct: 8   KQITGRESYSIEKYLQEIGKIHV---LSPEEEADLAKKIRSGD---RAAREKLVLSNLRF 61

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+SVAK+Y N GL   DLI EGN+GL+KAAE FD   G+KF +YA+WW++Q+I ++IA+ 
Sbjct: 62  VVSVAKQYQNHGLTLGDLINEGNVGLIKAAECFDETKGFKFISYAVWWIRQSILQAIAEN 121

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +  IR+P++    I+KV R    +  + +REPT EEIA+K+ M  E V++ +KI  +P+S
Sbjct: 122 ARLIRLPLNKISTINKVNRCYTLLEQEFQREPTEEEIAEKMDMTPEEVKENMKIATKPVS 181

Query: 576 LETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           ++ P+  DE++  L D     D +  +P  S  Q +L+    R  A+L+ RE  +L M +
Sbjct: 182 MDAPLTTDEESISLYDVYIAPDPSIQAPESSLNQDSLKTDIERSFAALSVREATILSMYY 241

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+   +  +LEE+G +  +T ER+RQ++ KAIRKLK    +K+L+++L
Sbjct: 242 GLNGYSSMSLEEIGTKLGLTSERVRQVKTKAIRKLKEVKNNKRLKTYL 289


>gi|325277035|ref|ZP_08142696.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
 gi|324097832|gb|EGB96017.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
          Length = 335

 Score =  193 bits (490), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 159/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|104783164|ref|YP_609662.1| RNA polymerase sigma factor RpoS [Pseudomonas entomophila L48]
 gi|95112151|emb|CAK16878.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudomonas entomophila L48]
          Length = 335

 Score =  193 bits (490), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 159/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIASLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|87310114|ref|ZP_01092246.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87287104|gb|EAQ79006.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 516

 Score =  193 bits (490), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 106/247 (42%), Positives = 152/247 (61%), Gaps = 7/247 (2%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G C A   ++ +  ANLRLV+S+AK +  RGL +LDLIQEGN+GLM+A EKFD  LGYK
Sbjct: 266 EGLCRA---QRAITSANLRLVVSIAKSFRGRGLSYLDLIQEGNLGLMRAVEKFDPSLGYK 322

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+TYA WW++QA+ + +ADQ  TIR+P  M+D+I K+      +S + + EP  E  AK+
Sbjct: 323 FATYATWWIRQAVMKGLADQGRTIRLPARMQDRIQKINVAKAILSQEHRSEPPIELTAKQ 382

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             +    V    ++ +  +SL+    D+D+   GD +   +A     SA +  L     +
Sbjct: 383 AELTEREVVAADRLGRTIMSLDVSNNDDDS--FGDTLASGDAEQ--SSADEQRLPLAINQ 438

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  LT RE+ ++R RFG+      TLEEV + F VTRERIRQIE+ AIRKL+ P   +K
Sbjct: 439 LLQELTSREQEIVRRRFGMFDGRVQTLEEVSQAFSVTRERIRQIESAAIRKLRQPHLIRK 498

Query: 676 LRSFLDG 682
           L  FL+ 
Sbjct: 499 LDDFLEA 505


>gi|330504211|ref|YP_004381080.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
 gi|328918497|gb|AEB59328.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
          Length = 335

 Score =  193 bits (490), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 156/240 (65%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 84  HFARLAQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 140

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 141 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 200

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 201 AEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 260

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  + L+ LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 261 LSQSIDQWLSDLTDKQREVVVRRFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLR 320


>gi|312959424|ref|ZP_07773941.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
 gi|311286141|gb|EFQ64705.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
          Length = 335

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 155/240 (64%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 84  HFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 140

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 141 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 200

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 201 PEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 260

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 261 LSQSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|157688389|gb|ABV64841.1| RpoS [Pseudomonas sp. 122]
          Length = 334

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 155/240 (64%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 83  HFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 139

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 140 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 199

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 200 PEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 259

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 260 LSQSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 319


>gi|229588834|ref|YP_002870953.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens SBW25]
 gi|229360700|emb|CAY47558.1| RNA polymerase sigma factor [Pseudomonas fluorescens SBW25]
          Length = 334

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 155/240 (64%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 83  HFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKF 139

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+
Sbjct: 140 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPS 199

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +
Sbjct: 200 PEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDD 259

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 260 LSQSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 319


>gi|157169065|ref|YP_258338.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
 gi|1000294|gb|AAB02846.1| RpoS [Pseudomonas fluorescens Pf-5]
 gi|157061761|gb|AAY90494.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
          Length = 335

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera]
          Length = 575

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 99/237 (41%), Positives = 152/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA WW
Sbjct: 337 CKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 396

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  R P  EE+A+   + ++ +
Sbjct: 397 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 456

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   K P SL+  IG        + I D +A +  +  I+  +RE   +VL SL PR
Sbjct: 457 NAVLLTPKAPRSLDQKIGINQNLKPSEVIADPDAETAEELLIKQFMREDLEKVLNSLNPR 516

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++V+R R+G+      TL+E+G+   V+RERIRQIE+ A RKLK+  R+K L+ +L
Sbjct: 517 EKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQIESCAFRKLKNKRRTKHLQQYL 573


>gi|6010724|gb|AAF01228.1|AF184097_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 326

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 91/233 (39%), Positives = 157/233 (67%), Gaps = 4/233 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TI    H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTI----HIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 206 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 266 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 318


>gi|15419944|gb|AAK97216.1|AF300644_1 sigma factor RpoD [Lactobacillus acidophilus]
          Length = 162

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 96/162 (59%), Positives = 120/162 (74%)

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++R  R++   + REPTPEEI  ++ MP   VR +L+I +E +SLETP
Sbjct: 1   RIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDILRIAQERVSLETP 60

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+ED SHLGDFIEDK+A SP   A    L+E   +VL +LT REE VLR+RFG+     
Sbjct: 61  IGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLRLRFGLEYGRT 120

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+D
Sbjct: 121 RTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFMD 162


>gi|77457359|ref|YP_346864.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf0-1]
 gi|77381362|gb|ABA72875.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas fluorescens
           Pf0-1]
          Length = 335

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|186702713|gb|ACC91623.1| RNA polymerase sigma factor [Pseudomonas sp. CT07]
          Length = 336

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 84  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 143

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 144 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 203

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 204 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 263

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 264 QSIDQWLSELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 321


>gi|21219415|ref|NP_625194.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|256789543|ref|ZP_05527974.1| RNA polymerase principal sigma factor HrdC [Streptomyces lividans
           TK24]
 gi|289773432|ref|ZP_06532810.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
 gi|123520|sp|P18184|HRDC_STRCO RecName: Full=RNA polymerase principal sigma factor hrdC
 gi|48741|emb|CAA37173.1| unnamed protein product [Streptomyces coelicolor A3(2)]
 gi|6562877|emb|CAB62686.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|289703631|gb|EFD71060.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
          Length = 339

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 154/237 (64%), Gaps = 8/237 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  MV ANLRLV+S+AK++ +RGL  LD+IQEGN+GL++A EKFD   G+KFSTYA WW
Sbjct: 102 AKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYATWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R +A  + T+R+PVH+ +++ K+ +  R++   + REPT EE+A +  + V+ V
Sbjct: 162 IRQAIERGLATHARTVRLPVHVVEQLQKLAKVERKLRAGLDREPTTEEVAAESGIDVDKV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----SAIQANLRETTTRVLAS 619
             + ++ ++ +SL+TP+ +   + +GD I D   +   +     A+ A LRE     + +
Sbjct: 222 VWLRRVGRDAVSLDTPVDETGDTVVGDLIPDTEVLRAPEVAEFQALAAELRE----AVGT 277

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L PRE  +L +R+G+      TL++V +   +TRER+RQ+E +++  L+ P   ++L
Sbjct: 278 LAPRESLILSLRYGLHDGRPRTLQQVAQHVGLTRERVRQLEKESLAHLRAPENRERL 334


>gi|148243603|ref|YP_001228760.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851913|emb|CAK29407.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 323

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 96/226 (42%), Positives = 150/226 (66%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW
Sbjct: 89  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 148

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +TR+I + + TIR+P+H+ +K+ K+ R  R ++++  R+P   E+A  + M  + +
Sbjct: 149 IRQGMTRAIDNSARTIRLPIHISEKLSKMRRITRELTHRFGRQPNRLELAHAMGMEPDEL 208

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            ++L  +    SL+    G+ED S LG+ I D +    ++S  +   +E     +  L  
Sbjct: 209 EELLSQSAPCASLDAHARGEEDRSTLGELIPDPSCNDSMESMDRRIQKEHLGTWITQLNE 268

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+++L++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 269 REQKILKLRFGLEGAEPQTLAEIGRQINVSRERVRQLEAKAILKLR 314


>gi|237800176|ref|ZP_04588637.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331023033|gb|EGI03090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 335

 Score =  192 bits (488), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 149/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPTPEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPTPEEIANLLEKPVGEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 276 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|48727551|gb|AAT46075.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
          Length = 334

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 82  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 141

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 142 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 201

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 202 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 261

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 262 QSIDQWLSELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 319


>gi|225436223|ref|XP_002273602.1| PREDICTED: similar to SIGB (SIGMA FACTOR B); DNA binding /
           DNA-directed RNA polymerase/ transcription factor [Vitis
           vinifera]
          Length = 578

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 99/237 (41%), Positives = 152/237 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA WW
Sbjct: 340 CKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 399

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  R P  EE+A+   + ++ +
Sbjct: 400 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 459

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL   K P SL+  IG        + I D +A +  +  I+  +RE   +VL SL PR
Sbjct: 460 NAVLLTPKAPRSLDQKIGINQNLKPSEVIADPDAETAEELLIKQFMREDLEKVLNSLNPR 519

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++V+R R+G+      TL+E+G+   V+RERIRQIE+ A RKLK+  R+K L+ +L
Sbjct: 520 EKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQIESCAFRKLKNKRRTKHLQQYL 576


>gi|33150232|gb|AAP97086.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
 gi|103488976|gb|ABF71881.1| RpoS [Pseudomonas chlororaphis]
          Length = 334

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 82  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 141

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 142 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 201

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 202 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 261

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 262 QSIDQWLSELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 319


>gi|71278347|ref|YP_267823.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
 gi|71144087|gb|AAZ24560.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
          Length = 296

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 145/225 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 56  SRKRMIESNLRLVVKIARRYNNRGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R +R +  K+  EPT E+IA+ L  PV  V
Sbjct: 116 IRQTIERAIMNQTRTIRLPIHVVKELNIYLRASRELIQKLDHEPTAEDIAQHLDRPVADV 175

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TP   E    L D I D+ +  P       ++       L  L  +
Sbjct: 176 NKMLRLNERIASVDTPFAGESDKALLDVIADEKSTGPESDLQSEDMSNNIIHWLNELNTK 235

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  VL  RFG+      TLE VG++  +TRER+RQI+ +A+++L+
Sbjct: 236 QREVLARRFGLLGYEASTLENVGREIGLTRERVRQIQVEALKRLR 280


>gi|269126860|ref|YP_003300230.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311818|gb|ACY98192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 360

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/253 (37%), Positives = 156/253 (61%), Gaps = 9/253 (3%)

Query: 418 VETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           V  G++  E   +V+  VR        AK+  VEANLRLV+S+A+KY    L  +DLIQE
Sbjct: 59  VPPGVTRQELEELVAAGVR--------AKQRFVEANLRLVVSIARKYPTDALPLIDLIQE 110

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLM+A EKFD+  G+KFSTYA WW++Q+I R ++  + TIR+PVH+ +++ ++ R  
Sbjct: 111 GNLGLMRAVEKFDYRRGFKFSTYATWWIRQSIGRGLSHTARTIRLPVHVEEELSRLRRAE 170

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++  ++ REPT EE+A+ L   V+ V ++L+  ++P SL+  + D   + +GD +ED  
Sbjct: 171 RQLGRELGREPTREELAEALGAAVDHVDELLRWRRDPASLDAAVDDAGETPMGDLLEDPE 230

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            VSP    +  +      R+L  L  RE  +LR RFGI      +  ++G ++ ++  R+
Sbjct: 231 GVSPEAEVLALDDIAGLARLLDRLPERESAILRARFGIEDGQPLSYAQIGARYGLSHNRV 290

Query: 657 RQIEAKAIRKLKH 669
           RQI  +++R+L+ 
Sbjct: 291 RQITDRSLRRLRQ 303


>gi|239927194|ref|ZP_04684147.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291435537|ref|ZP_06574927.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291338432|gb|EFE65388.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
          Length = 339

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/256 (37%), Positives = 162/256 (63%), Gaps = 5/256 (1%)

Query: 429 HIVSMVRKGECEASI-----AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           H ++  R  E EA++     AK  M+ ANLRLV+S+AK++ +RGL  LD+IQEGN+GL++
Sbjct: 82  HHLTRERWRELEAAVHDGQAAKDRMIRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIR 141

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G+KFSTYA WW++QAI R +A  + T+R+PVH+ +++ K+ +  RR+   +
Sbjct: 142 AVEKFDHTKGFKFSTYATWWIRQAIERGVATHARTVRLPVHVVEQLQKLGKVERRLHLSL 201

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPT EE+A++  +  + V  + ++ ++ +SL+TP+ D   + +GD I D   +   + 
Sbjct: 202 DREPTVEEVARESGLAEKKVVWLRRVGRQVVSLDTPVDDTGDTVVGDLIPDTEVLQAPEV 261

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A    L E     + +L PRE  +L +R+G+      TL+EV     +TRER+RQ+E ++
Sbjct: 262 AEFQALAEELRGAVDTLAPREALILSLRYGLHDGQTRTLQEVADHVGLTRERVRQLEKQS 321

Query: 664 IRKLKHPSRSKKLRSF 679
           + +L+   + ++L ++
Sbjct: 322 LAQLREREQGERLLAW 337


>gi|163786482|ref|ZP_02180930.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159878342|gb|EDP72398.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 98/259 (37%), Positives = 164/259 (63%), Gaps = 3/259 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+  E   +  +++KG+    +A  ++  ANLR V+SVAK+Y N+GL+  DLI EGN GL
Sbjct: 31  ITAEEEVELAQLIKKGD---QVALDKLTTANLRFVVSVAKQYQNQGLKLPDLINEGNAGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++QAI +++A+QS  +R+P++    I+K+ +    +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLPLNKIGTINKINKAFSHLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
             +R P  EEIA++L +    V++ +K +   +S++ P+ D +T  L D +    +  P 
Sbjct: 148 LHQRPPNAEEIARELDISAREVKQSMKNSGRHLSMDAPLKDGETFSLYDVVSATESPRPD 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            + ++ +L     R L +LT +E  V+R+ FGIG     TLEE+G  + +TRER+RQI  
Sbjct: 208 KNLMKESLNLEVERALETLTQKESDVIRLNFGIGDQPPMTLEEIGGIYDLTRERVRQIRE 267

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           K IR+L+H S+SK L+++L
Sbjct: 268 KGIRRLRHASKSKILKTYL 286


>gi|254481825|ref|ZP_05095068.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
 gi|214037954|gb|EEB78618.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
          Length = 353

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 89/225 (39%), Positives = 149/225 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 114 GRKRMIESNLRLVVKISRRYINRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 173

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPT EEIA  L  P   V
Sbjct: 174 IRQTIERGIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPTAEEIADMLDRPAADV 233

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++TP+G +    + D I D +   P      ++++++    L  L+ +
Sbjct: 234 KRMLGLNERVTSMDTPVGPDSDKAVVDTIADTHESDPSQLLQDSDIKDSIGSWLDELSEK 293

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+      TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 294 QREVVARRFGLRGYESSTLEEVGREIGLTRERVRQIQVEALKRLR 338


>gi|26452898|dbj|BAC43527.1| putative plastid RNA polymerase sigma-subunit SIG1 [Arabidopsis
           thaliana]
          Length = 572

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 98/240 (40%), Positives = 152/240 (63%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA
Sbjct: 329 GTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYA 388

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA+   + +
Sbjct: 389 HWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSM 448

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +  VL   K P SL+  IG        + I D  AV+P D  I+  +R+   +VL SL
Sbjct: 449 KRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTPEDILIKEFMRQDLDKVLDSL 508

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  R+  L+ +L
Sbjct: 509 GTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYL 568


>gi|330807812|ref|YP_004352274.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327375920|gb|AEA67270.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 335

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|224824776|ref|ZP_03697883.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
 gi|224603269|gb|EEG09445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
          Length = 316

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 99/255 (38%), Positives = 159/255 (62%), Gaps = 3/255 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + +  +V +G+ EA   +++M+E NLRLV+++AK+Y NRGL  LDLI+EGNIGL
Sbjct: 59  LSPQEEQSLARLVVQGDFEA---RQKMIEHNLRLVVNIAKRYINRGLALLDLIEEGNIGL 115

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M A EKFD   G++FSTYA WW++Q+I R+I +QS TIR+PVH+  +++  +R +R + +
Sbjct: 116 MHALEKFDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHVIKELNVYLRASRHLES 175

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +I REP+ EEIA+ +  PVE VR+V+ + +   SL+ P+  +    +G+ I D     P 
Sbjct: 176 QIGREPSVEEIAQLVDKPVEDVRRVMNLNERMASLDAPLDIDPMLSIGESIPDDQHDEPE 235

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  L       +A L  ++  V+  R+G+  +   TLEE+     +TRER+RQI+ 
Sbjct: 236 IQLHNTQLENFVHEWMAQLNDKQRMVIERRYGLNGHEICTLEELASTLSLTRERVRQIQI 295

Query: 662 KAIRKLKHPSRSKKL 676
           + + +L+   R K +
Sbjct: 296 EGLEQLRRILRRKGI 310


>gi|148469868|gb|ABQ65863.1| stationary sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 EHGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|148241197|ref|YP_001226354.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849507|emb|CAK27001.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 324

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 157/247 (63%), Gaps = 1/247 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S F    +++R+       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++ 
Sbjct: 70  SSFGISPAVLRRRLINGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRG 129

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD   GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ 
Sbjct: 130 VEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITETLNKLKKGQRELSQELG 189

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R PT  E+A+ L +P   V+ +L   ++P+SLE  +GD D + L + +++ +A  P +  
Sbjct: 190 RTPTVGELAEFLELPEPEVKDLLSRARQPVSLEMKVGDSDDTELCELLQN-DAPMPHELV 248

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L+     +L  L P + RVL+MR+GI +    +L  +G++  ++R+R+R +E   +
Sbjct: 249 DGDCLKGDMRSLLEQLPPLQGRVLKMRYGIDVEEPMSLTGIGRELGMSRDRVRNLERDGL 308

Query: 665 RKLKHPS 671
             L+  S
Sbjct: 309 AGLRRLS 315


>gi|218440090|ref|YP_002378419.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172818|gb|ACK71551.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 94/257 (36%), Positives = 169/257 (65%), Gaps = 4/257 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +  V+  + + E  ++ +  +K   +  IAK++M++ANLRLV+S+AK+Y  RGL  LDLI
Sbjct: 31  ATKVQNMLPLLEKENLTAAEKKIVEQGQIAKRKMIQANLRLVVSIAKRYQRRGLSLLDLI 90

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG++GL++A EKFD   GYKFSTYA WWV+QAITR++A++S TIR+P+HM + ++++ +
Sbjct: 91  QEGSLGLIRAVEKFDPSKGYKFSTYAYWWVRQAITRALAEKSRTIRLPIHMTENLNQLKK 150

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFI 592
           + R ++ ++ R+P  +E+A+++ +PVE +R++       +  SL   + D++ + LG+ +
Sbjct: 151 SVRELTGELGRKPNEQEVAQRMEIPVEKLREIRHAVYRTDAKSLNITL-DDNQTELGEVL 209

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+ ++ P++   Q  L      +L  L PR+  ++ +RFG+      + +E+G+Q  ++
Sbjct: 210 PDETSL-PIEFVSQWELVTKINDLLEDLPPRQREIITLRFGLQTGKRMSYKEIGRQCGIS 268

Query: 653 RERIRQIEAKAIRKLKH 669
            ER RQ+  +A+R LK 
Sbjct: 269 HERARQLLNRAMRTLKQ 285


>gi|169883528|gb|ACA97859.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 377

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 105/238 (44%), Positives = 168/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 139 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +   ++R P   E+A+ L +  E +
Sbjct: 199 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQDLQRNPNERELAEALEITPEQL 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED +   P D   +  +R+    VL+  LT 
Sbjct: 259 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTE 318

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 319 REKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 376


>gi|28868771|ref|NP_791390.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|301383956|ref|ZP_07232374.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           Max13]
 gi|302064158|ref|ZP_07255699.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           K40]
 gi|302134085|ref|ZP_07260075.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|3132688|gb|AAC16326.1| sigma factor [Pseudomonas syringae pv. tomato]
 gi|28852010|gb|AAO55085.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|331016398|gb|EGH96454.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 335

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|159029420|emb|CAO90796.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 377

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 105/238 (44%), Positives = 168/238 (70%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 139 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +   ++R P   E+A+ L +  E +
Sbjct: 199 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQDLQRNPNERELAEALEITPEQL 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED +   P D   +  +R+    VL+  LT 
Sbjct: 259 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTE 318

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 319 REKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 376


>gi|213969149|ref|ZP_03397288.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
 gi|213926147|gb|EEB59703.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
          Length = 334

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 82  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 141

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 142 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 201

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 202 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 261

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 262 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 319


>gi|254430144|ref|ZP_05043847.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
 gi|197624597|gb|EDY37156.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
          Length = 318

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 98/229 (42%), Positives = 152/229 (66%), Gaps = 1/229 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA
Sbjct: 81  AQRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYA 140

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S+++ R+P   E++  + M  
Sbjct: 141 YWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRITRELSHRLGRQPNRLELSHAMDMRP 200

Query: 561 EGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           E + +++  +    SL+    GDED S LG+ I D  +    DS  +   +E     L+ 
Sbjct: 201 EELEELMAQSAPCASLDAHARGDEDRSTLGELIADPASNEHFDSMDRHIQKEHLGAWLSQ 260

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE++++++RFG+  +   TL E+G+   V+RER+RQ+EAKAI KL+
Sbjct: 261 LNEREQKIIKLRFGLEGSEPLTLAEIGRLINVSRERVRQLEAKAIMKLR 309


>gi|302187929|ref|ZP_07264602.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           642]
          Length = 335

 Score =  192 bits (487), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|289626003|ref|ZP_06458957.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289651481|ref|ZP_06482824.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330868573|gb|EGH03282.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 335

 Score =  191 bits (486), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|289208462|ref|YP_003460528.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
 gi|288944093|gb|ADC71792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
          Length = 359

 Score =  191 bits (486), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/256 (37%), Positives = 153/256 (59%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I     ++  E R    + R G+      ++ M+E NLRLV+ +A++Y NRGL  LD
Sbjct: 90  LRDIEYRPLLTPEEERKYARLARDGD---ESGRRRMIECNLRLVVKIARRYLNRGLPLLD 146

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GLM A EKFD   G++FSTYA WW++Q I R++ +Q  TIRIPVH+  ++   
Sbjct: 147 LIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERALMNQGRTIRIPVHVSKELRMH 206

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R AR ++ ++ R+PT EE+A++L  PV  ++K+  +++   S++ P G +    L D +
Sbjct: 207 ARIARNLTQELGRDPTEEELAQRLGKPVADIQKLRAMSEPSTSMDLPPGPDGERSLTDIL 266

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D NA  P       +++      L  L  ++  VL  RFG+      TLE+VG +  VT
Sbjct: 267 ADVNAQEPSSLLEDQDIQHLVDEWLGELDYKQREVLVRRFGLHGFERSTLEQVGAEIGVT 326

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+  A+++L+
Sbjct: 327 RERVRQIQMDALKRLR 342


>gi|330894625|gb|EGH27286.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. mori
           str. 301020]
          Length = 335

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|34540402|ref|NP_904881.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
 gi|34396715|gb|AAQ65780.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
          Length = 287

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 173/268 (64%), Gaps = 3/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +++G+ +A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLISVEEEVELAQAIKRGDRKAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGTLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           ++  ++   + +R P+  E+AK+L +  + +   +K++   IS++ P  + + + L D +
Sbjct: 139 IKAQQKFEQENERRPSSAELAKELDIAEDKIADTMKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +++  +   S I  +L     R L++LT RE  ++++ FGI    + TLEE+G +F +T
Sbjct: 199 VNEDTPNTDKSLINESLAVEIERALSTLTEREAEIVKLFFGIAGCQEMTLEEIGDKFGLT 258

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  ++ K L+ +L
Sbjct: 259 RERVRQIKEKAIRRLRQSNKCKNLKGYL 286


>gi|66044622|ref|YP_234463.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           B728a]
 gi|289675304|ref|ZP_06496194.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           FF5]
 gi|6644290|gb|AAF20993.1|AF208000_1 RpoS [Pseudomonas syringae pv. syringae]
 gi|24415296|gb|AAN59882.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|24415299|gb|AAN59884.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|63255329|gb|AAY36425.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Pseudomonas syringae pv. syringae B728a]
 gi|330896091|gb|EGH28312.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 335

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|294673737|ref|YP_003574353.1| RNA polymerase sigma factor RpoD [Prevotella ruminicola 23]
 gi|294473567|gb|ADE82956.1| putative RNA polymerase sigma factor RpoD [Prevotella ruminicola
           23]
          Length = 286

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 99/268 (36%), Positives = 170/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ IS ET IS  E   +   ++KG+ +A    + + +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEISKETMISAEEEVELAQRIKKGDTKAL---ERLTKANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAE+FD   G+KF +YA+WW++Q+I ++I++QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLLKAAERFDETRGFKFISYAVWWIRQSILQAISEQSRIVRLPLNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R   R     +R P+ +EIA+K+ +P E + + + I    IS++ P  + + + L D +
Sbjct: 139 NREINRFEQLNERRPSVDEIAEKVDLPQEKIDEAMAINGHQISVDAPFVEGEDNSLLDVM 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +A    +  ++ +L+      L++L  RE  V+   +GI    + TLEE+G +F +T
Sbjct: 199 ANSDAPLADNQLVEESLKSEIQNALSALNERERNVVEASYGINQ-PELTLEEIGTKFGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIRKL++   +K L+++L
Sbjct: 258 RERVRQIKEKAIRKLRNSKANKFLKTYL 285


>gi|167949417|ref|ZP_02536491.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 128

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 92/126 (73%), Positives = 106/126 (84%)

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED   VSP+DSA    LRE T  
Sbjct: 1   MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVVSPVDSATSEGLREATQN 60

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++
Sbjct: 61  MLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSER 120

Query: 676 LRSFLD 681
           +RSFLD
Sbjct: 121 MRSFLD 126


>gi|257487049|ref|ZP_05641090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|320323089|gb|EFW79178.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329639|gb|EFW85628.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330878042|gb|EGH12191.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330985141|gb|EGH83244.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331009312|gb|EGH89368.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 335

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|330968927|gb|EGH68993.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 335

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|330959229|gb|EGH59489.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 336

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 84  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 143

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 144 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 203

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 204 EIANLLERPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 263

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 264 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 321


>gi|330950646|gb|EGH50906.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae Cit 7]
          Length = 335

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLERPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|220934609|ref|YP_002513508.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219995919|gb|ACL72521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 344

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 102/285 (35%), Positives = 170/285 (59%), Gaps = 14/285 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  A D P+GE        +D+    R  +  I     ++  E  H   + +KG+     
Sbjct: 58  VYAAGDVPKGE--------LDAT---RLYLSEIEFSPLLTPEEEVHYARLAQKGD---EA 103

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +++M+E NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 104 GRRKMIECNLRLVVKIARRYMNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 163

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR+++ ++  EPT EE+A+ L  PV  V
Sbjct: 164 IRQTIERALMNQTRTIRLPIHVIKELNVYLRTARKLAQELDHEPTAEEVARHLDRPVGDV 223

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L +++   S++ PIG +    L D I D+    P       ++ +     L  L  +
Sbjct: 224 KRILALSERVTSVDLPIGKDGERALLDVIPDEQTPEPSILIQDEDVVQFVDEWLQELDEK 283

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+      TLE+VG +  VTRER+RQI+  A+++L+
Sbjct: 284 QREVIVRRFGLHGYERSTLEQVGAELGVTRERVRQIQMDALKRLR 328


>gi|116668483|gb|ABK15514.1| sigma factor [Pseudomonas alkylphenolia]
          Length = 335

 Score =  191 bits (486), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIASLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTDKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|312888769|ref|ZP_07748333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311298769|gb|EFQ75874.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 286

 Score =  191 bits (485), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 95/239 (39%), Positives = 160/239 (66%), Gaps = 5/239 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + + NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALERLTKTNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I ++IA+QS  +R+P++    + K+ +   ++  + +REP+PEE+A  L   V+ +
Sbjct: 110 IRQSILQAIAEQSRIVRLPLNQVGSLSKISKAFSKLEQEYEREPSPEELADILETTVDKI 169

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L  +   +S++ P   G+E+T  L D +++    +     I  +L E   R L++LT
Sbjct: 170 SDTLSNSGRHVSMDAPFVQGEENT--LLDVLDNHEPNTDFH-LINESLAEEIKRSLSTLT 226

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE  ++ + FG+G N+  +LEE+G++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 227 EREREIVVLFFGLGSNSPFSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285


>gi|238786819|ref|ZP_04630620.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
 gi|238725187|gb|EEQ16826.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
          Length = 306

 Score =  191 bits (485), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 87/220 (39%), Positives = 149/220 (67%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +  A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+
Sbjct: 79  VYFARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQT 138

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S+
Sbjct: 139 RTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSV 198

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +TP+G +    L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+  
Sbjct: 199 DTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG 258

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 259 YEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 298


>gi|304383342|ref|ZP_07365808.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335510|gb|EFM01774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 287

 Score =  191 bits (485), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 161/247 (65%), Gaps = 4/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+ +A    +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAAEKFD   G
Sbjct: 43  IRRGDRQAL---EKLTKANLRFVVSVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++IA+QS  +R+P++    ++++ +   R   + +R P+ EEIA
Sbjct: 100 FKFISYAVWWIRQSILQAIAEQSRIVRLPLNQIGSVNRINKMLNRFEQENERRPSMEEIA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            K+ +  E V  VLK+    +S++ P  + D + L D + + ++       ++ +LRE  
Sbjct: 160 DKVNLSQEKVADVLKVNSRQVSVDAPFTEGDETSLLDVLCNNDSPMADRELVRESLREEI 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L  RE  ++   FGI    + TLEE+G +F +TRER+RQI+ KAIR+L+  ++S
Sbjct: 220 NRTLQVLNERERNIVEAFFGINQG-EKTLEEIGNKFGLTRERVRQIKEKAIRRLRQNTKS 278

Query: 674 KKLRSFL 680
           + L+++L
Sbjct: 279 RLLKAYL 285


>gi|329848685|ref|ZP_08263713.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
 gi|328843748|gb|EGF93317.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
          Length = 699

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 98/177 (55%), Positives = 127/177 (71%), Gaps = 6/177 (3%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E E S D  + D +D + KK IK A+ RGYVT++ELN  LP +E +SEQ+EDT+AML+ M
Sbjct: 9   ESEASSDGPLLDLTDSAVKKFIKAAKARGYVTMDELNKVLPSEEFTSEQIEDTLAMLTEM 68

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           G+NV+     E EE + ++ ++A    + S+    +  + DR TDDPVRMYLREMGS+EL
Sbjct: 69  GVNVI-----ESEEEAGETTEVAVREESGSLVETAKTSAYDR-TDDPVRMYLREMGSVEL 122

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           LSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLREIIDLE  
Sbjct: 123 LSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGSGRILLREIIDLEGT 179


>gi|330872696|gb|EGH06845.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 335

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 90/238 (37%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q + R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTVERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|313672395|ref|YP_004050506.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939151|gb|ADR18343.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 337

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 85/233 (36%), Positives = 147/233 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+  NLRLV+S+AKKY N+G+   DLI EGNIGL++A EKFD+  G+KFSTYA WW
Sbjct: 99  AKETMINCNLRLVVSIAKKYANKGVPLEDLISEGNIGLIRAVEKFDYRKGFKFSTYATWW 158

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R+I   +  +R+PVH+ + I K+++    +   + R PT  E++    + +  +
Sbjct: 159 IRQAIERAIIANTKIVRVPVHVLEYIKKILKAKSELQETLGRNPTYTELSTYTGITLSNI 218

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K ++  +  +S++ PI +++  ++ + I D     P D A + N+++  ++ +  L   
Sbjct: 219 YKAVEAMRHDVSIDAPISEDEQENMHNLIPDNIHTDPFDHAFELNIQKLVSKWMGYLNET 278

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E+ ++ +R+G+      TL+EVGK+  +TRERIRQIE + + KL+    +K++
Sbjct: 279 EKLIITLRYGLDGKRSRTLDEVGKELNLTRERIRQIEKRVLNKLRSFFHNKRI 331


>gi|172037252|ref|YP_001803753.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
 gi|171698706|gb|ACB51687.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 297

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 96/230 (41%), Positives = 155/230 (67%), Gaps = 3/230 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +M++ANLRLV+S+AKKY N GL  LDLIQEG++GL++  EKFD   GYKFSTYA WW
Sbjct: 61  ARDKMIQANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA+QS TIR+P+H+ + ++K  ++ R ++ K+ R+PT +EIA+ + + V+ +
Sbjct: 121 IRQGITRAIAEQSRTIRLPIHINENLNKYRKSIRELTLKLGRKPTQQEIAENMDISVDKL 180

Query: 564 RKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R + +     +  SL   I DE+ + LG  + D+++VSP D   Q        R+L +L+
Sbjct: 181 RFLQQAAFKTKSRSLNIVI-DENHTELGQLLPDEDSVSPSDFVKQQEKISQINRMLENLS 239

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           PR++ V+ +RFG+      + + +G+Q  ++ ER RQI ++A+R L+  S
Sbjct: 240 PRQKEVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALRILRKQS 289


>gi|88802114|ref|ZP_01117642.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
 gi|88782772|gb|EAR13949.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
          Length = 287

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 91/233 (39%), Positives = 158/233 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ANLR V+SVAK+Y  +GL+  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+
Sbjct: 54  LVSANLRFVVSVAKQYQGQGLKLSDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQS 113

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +++A+QS  +R+P++    I+K+ +   R+    +R PT +EIAK+L M    V + L
Sbjct: 114 IMQALAEQSRIVRLPLNKIGSINKIKKIYARLEQNEQRMPTHKEIAKQLDMTEAEVEQSL 173

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           K +   +S++ P  + + S+L + ++  ++  P    +  +L+    R L +LT +E +V
Sbjct: 174 KNSGRHVSMDAPFKEGEDSNLYNVLQSGDSPRPDSQLMAQSLKIEIERALGTLTYKEAKV 233

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++M +GIG     +LEE+G++F +TRER+RQ++ KAIR+L+  S+++ LR++L
Sbjct: 234 IKMYYGIGNEAMASLEEIGEKFDLTRERVRQVKQKAIRRLQSGSKTQMLRTYL 286


>gi|298488362|ref|ZP_07006394.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298157184|gb|EFH98272.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 335

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 151/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 HSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|297580668|ref|ZP_06942594.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
 gi|297535084|gb|EFH73919.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
          Length = 236

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 90/209 (43%), Positives = 143/209 (68%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 8   SRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 67

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V K+L++ +   S++TP
Sbjct: 68  RLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISSVDTP 127

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D + D +   P  S    ++RE+    L  L P+++ VL  RFG+     
Sbjct: 128 IGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPKQKEVLARRFGLLGYEP 187

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 188 STLEEVGREINLTRERVRQIQVEGLRRLR 216


>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa]
 gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa]
          Length = 564

 Score =  191 bits (484), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 101/247 (40%), Positives = 155/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK    A + K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++  EKFD   G
Sbjct: 316 LRKRLNYAILCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGVEKFDASKG 375

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QA+ RS++DQS TIR+P HM D  ++V    ++  ++  R P  +E+A
Sbjct: 376 FKFSTYAHWWIRQAVRRSLSDQSRTIRLPFHMVDATYRVKEARKQFYSENGRHPDDKEVA 435

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  +G      L +   D  A +  D  ++  +++  
Sbjct: 436 EATGLSMKRLSAVLLTPKAPRSLDQKMGFNMDLKLSEVTADPEAETAEDLLMKEFMKKDL 495

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RVL SL+PRE +V+R RFG+      TL+E+G+   V+RERIRQIE  A RKLK+ +R+
Sbjct: 496 ERVLESLSPRENQVIRWRFGMEDGRMKTLQEIGELMGVSRERIRQIELSAFRKLKNKNRT 555

Query: 674 KKLRSFL 680
           K+LR +L
Sbjct: 556 KQLRQYL 562


>gi|254514875|ref|ZP_05126936.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
 gi|219677118|gb|EED33483.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
          Length = 367

 Score =  191 bits (484), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 92/258 (35%), Positives = 163/258 (63%), Gaps = 6/258 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           NEI  + +   +S  E +H   +V+KG+     A+K M+E+NLRLV+++A++Y +RG+  
Sbjct: 100 NEIGFVPL---LSADEEKHYARLVQKGD---EAARKRMIESNLRLVVNIARRYLHRGMSL 153

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLI+EGN+GLM+A EKFD   G++FSTYA WW++Q I R I +Q+ TIR+P+H+   ++
Sbjct: 154 LDLIEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIHVVKDLN 213

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
             +R AR ++ ++  +PT +EIA +       V +++ + +   S++ P+G    S + +
Sbjct: 214 GCLRAARELTQQLDHDPTTQEIASRTHKTATEVSRLMGLNERVSSMDAPLGPNSDSSVAE 273

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D++   P +     ++ ++    L  L+ ++  V+  RFG+      TLEEVG++  
Sbjct: 274 TIADEHGCDPSEQIQDDDVHDSVAHWLDELSEKQREVVVRRFGLLGYDSCTLEEVGQEIG 333

Query: 651 VTRERIRQIEAKAIRKLK 668
           +TRER+RQI+ +A+++L+
Sbjct: 334 LTRERVRQIQVEALKRLR 351


>gi|221134005|ref|ZP_03560310.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  191 bits (484), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 93/227 (40%), Positives = 152/227 (66%), Gaps = 3/227 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+ +NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 82  ARERMIVSNLRLVVKIARRYKDRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ T+R+P+H+  +++  +RTAR ++ ++  EPT EEIA KL +  E V
Sbjct: 142 IRQTIERAIMNQTRTVRLPIHVVKELNIYLRTARNLAQELDHEPTAEEIADKLDVSTEDV 201

Query: 564 RKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            K+L++ +   S+++ +  E D + L D + D N   P +   + +++      L  L P
Sbjct: 202 NKMLRLNERIKSVDSYLSHESDGNSLLDILPDSNHSGPEEKNQEDDIKNNIVMWLQELNP 261

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  VL  RFG+ G   D TLE VG +  +TRER+RQI+ +A+R+LK
Sbjct: 262 KQREVLSRRFGLMGFEPD-TLENVGAEIGLTRERVRQIQVEALRRLK 307


>gi|188994502|ref|YP_001928754.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
 gi|188594182|dbj|BAG33157.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
          Length = 287

 Score =  191 bits (484), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 172/268 (64%), Gaps = 3/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   +++G+ +A    +++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREDLISVEEEVELAQAIKRGDRKAL---EKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGTLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           ++  ++   + +R P+  E+AK+L +  + +   +K++   IS++ P  + + + L D +
Sbjct: 139 IKAQQKFEQENERRPSSAELAKELDIAEDKIADTMKVSGRHISVDAPFVEGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +++  +   S I  +L     R L++LT RE  ++++ FGI    + TLEE+G +F +T
Sbjct: 199 VNEDTPNTDKSLINESLAVEIERALSTLTEREAEIVKLFFGIAGCQEMTLEEIGDKFGLT 258

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L+  +  K L+ +L
Sbjct: 259 RERVRQIKEKAIRRLRQSNECKNLKGYL 286


>gi|149278388|ref|ZP_01884525.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255532892|ref|YP_003093264.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|149230758|gb|EDM36140.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255345876|gb|ACU05202.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  191 bits (484), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 96/239 (40%), Positives = 159/239 (66%), Gaps = 5/239 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + + NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALERLTKTNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I ++IA+QS  +R+P++    + K+ +   ++  + +REP+PEE+A  L   V+ +
Sbjct: 110 IRQSILQAIAEQSRIVRLPLNQVGSLSKISKAFSKLEQEYEREPSPEELADILETTVDKI 169

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L  +   +S++ P   G+E+T  L D +E+    +   S I  +L E   R L++LT
Sbjct: 170 SDTLSNSGRHVSMDAPFVQGEENT--LLDVLENHEPNTD-SSLINESLSEEIKRSLSTLT 226

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE  ++ + FG+  N   +LEE+G++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 227 EREREIIVLFFGLSTNHPLSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285


>gi|71736784|ref|YP_275947.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557337|gb|AAZ36548.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 335

 Score =  191 bits (484), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 151/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+      TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGYESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|149370424|ref|ZP_01890113.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149355975|gb|EDM44532.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 288

 Score =  190 bits (483), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 95/235 (40%), Positives = 154/235 (65%), Gaps = 1/235 (0%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++  ANLR VISVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q
Sbjct: 53  KLTRANLRFVISVAKQYQNQGLSLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQ 112

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I ++IA+QS  +R+P++    I+KV + +  +    +R PT +EIA +L + V  V+  
Sbjct: 113 SILQAIAEQSRIVRLPLNKIGDINKVKKASIHLQQVYERVPTAQEIANELDITVSSVKSS 172

Query: 567 LKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +K +   IS++ P  + E+ ++L D I    + +P +  +Q +L+    R L +L+ RE 
Sbjct: 173 MKNSNRSISMDAPFQEGENDNNLYDVISSGESPNPDNGLMQESLKTEIDRALDTLSQREA 232

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            V+++ FG+  N   TL+E+G  F ++RER+RQI  KAIR+L+H S+S  L  +L
Sbjct: 233 DVVKLNFGLSGNPVMTLQEIGDTFDLSRERVRQIREKAIRRLRHESKSHILMKYL 287


>gi|221636011|ref|YP_002523887.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
 gi|221157983|gb|ACM07101.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
          Length = 334

 Score =  190 bits (483), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 102/252 (40%), Positives = 155/252 (61%), Gaps = 7/252 (2%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           +E G    E R    +VRKG+     A+++++  NLRLV+S+AK+Y +  L  +DLIQEG
Sbjct: 80  IEAGEDTPELRE---LVRKGQE----AREKLIRHNLRLVVSIAKRYRSSELPLIDLIQEG 132

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLM A E++D  LGY+FSTYA +W++QAI R++A+ S TIR+PVHM D I K+ R   
Sbjct: 133 NIGLMTAVERYDPELGYRFSTYATFWIRQAIGRAVANLSRTIRVPVHMHDLIAKIRRAEA 192

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  R  T EE+A+ L + V  + +         SL+ PIG++  S +GD + D  +
Sbjct: 193 QIEQQKGRPATNEELAELLGIDVARIEQARTQIPRTSSLDKPIGEDGESSIGDLLPDPRS 252

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              ++ A+   +RE   R L  LT RE  VL MRFG+      TL E+     ++RER+R
Sbjct: 253 DDVVEEALTNAIREQIRRSLEQLTERERTVLVMRFGLDGEQPRTLAEIADALKISRERVR 312

Query: 658 QIEAKAIRKLKH 669
           Q+E +A++KL++
Sbjct: 313 QVEKEALQKLRN 324


>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 572

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 100/247 (40%), Positives = 154/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK     ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 322 LRKRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKG 381

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA
Sbjct: 382 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIA 441

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  AV+  D  I+  +R+  
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDL 501

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL  RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  RS
Sbjct: 502 DKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRS 561

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 562 NHLQQYL 568


>gi|330964173|gb|EGH64433.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 335

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 90/238 (37%), Positives = 152/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +IA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 DIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|288927719|ref|ZP_06421566.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330553|gb|EFC69137.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 287

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 97/268 (36%), Positives = 170/268 (63%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  IS+ E   +   ++KG+ +A    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGHEELISVEEEVELAQRIKKGDRKAL---EKLTKANLRFVVSVAKQYQNQGLSLQD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 79  LINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+  EIA+K  +P + +   +K+T   IS++ P  D + + L D +
Sbjct: 139 NKILSKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGRHISVDAPFVDGEDNSLLDLL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +  +  +  ++ +LR      L  L  RE  V+   FGI    + TLEE+G ++ +T
Sbjct: 199 ANTDTPTVDNELVKESLRAEIADALQYLNERERNVIEAFFGINQ-MEMTLEEIGDKYGLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIR+L++ +++K L+++L
Sbjct: 258 RERVRQIKEKAIRRLRNNTKNKMLKTYL 285


>gi|126660003|ref|ZP_01731125.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126618681|gb|EAZ89428.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 297

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 96/230 (41%), Positives = 153/230 (66%), Gaps = 3/230 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +M++ANLRLV+S+AKKY N GL  LDLIQEG++GL++  EKFD   GYKFSTYA WW
Sbjct: 61  ARDKMIQANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA+QS TIR+P+H+ + ++K  ++ R ++ K+ R+PT +EIA+ + + V+ +
Sbjct: 121 IRQGITRAIAEQSRTIRLPIHINENLNKYRKSIRELTLKLGRKPTQQEIAENMDITVDKL 180

Query: 564 RKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R + +     +  SL   I DE+ + LG  + D+  VSP D   Q        R+L +L+
Sbjct: 181 RFLQQAAFKTKSRSLNIVI-DENNTELGQLLPDEEGVSPSDFVKQQEKISQINRMLENLS 239

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           PR++ V+ +RFG+      + + +G+Q  ++ ER RQI ++A+R L+  S
Sbjct: 240 PRQKEVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALRILRKQS 289


>gi|25900789|emb|CAD57977.1| RNA polymerase sigma factor [Pseudomonas oleovorans]
          Length = 335

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 95/256 (37%), Positives = 156/256 (60%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I  Q+ TIR+P H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMSQTRTIRLPFHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 LRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + + +L+
Sbjct: 305 RERVRQIQVEGLERLR 320


>gi|327438872|dbj|BAK15237.1| DNA-directed RNA polymerase [Solibacillus silvestris StLB046]
          Length = 425

 Score =  190 bits (483), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 149/239 (62%), Gaps = 6/239 (2%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VEAN +LV  + K Y+     G    D+ Q G IGL+KAAEKFD  LGY+FSTYA WW+
Sbjct: 184 LVEANRKLVWKIVKHYSGLATVGFDENDMYQVGFIGLLKAAEKFDVSLGYQFSTYATWWI 243

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR IAD S  IRIPVH R+K++K ++    + N++ R  T  EI+K++  P   + 
Sbjct: 244 RQAITRGIADYSTLIRIPVHYREKMNKFIKIENELWNELARPATTFEISKEMEEPTNVIE 303

Query: 565 KV-LKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LT 621
           ++   I++  + SL+  +GD++ + LG+ + D N   P +   +  LR T   +  S LT
Sbjct: 304 ELRFYISQSNLDSLDRLVGDDENTSLGELVLDDNLKMPDEEYYKIELRNTIGEIFQSNLT 363

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE +VL  RFG   +   TLEEVG+ + +TRERIRQIEAKA+RKL+    +  L+ +L
Sbjct: 364 EREMQVLYYRFGFKNDETKTLEEVGQIYNLTRERIRQIEAKALRKLRKQKTTTVLKEYL 422


>gi|256420372|ref|YP_003121025.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256035280|gb|ACU58824.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 291

 Score =  190 bits (483), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 96/240 (40%), Positives = 160/240 (66%), Gaps = 5/240 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 52  ALEKLTKANLRFVVSVAKQYQNQGLSLSDLINEGNLGLIKAAQRFDETRGFKFISYAVWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS  +R+P++     +K+ +   ++  + +REP+P+E+A  L +  E V
Sbjct: 112 IRQSILQALAEQSRIVRLPLNKVGLSNKISKAYSQLEQEFEREPSPDELATILEINTEEV 171

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASL 620
              L +    +S++ P  D + + L D + + NAV+    LD     +LR    R L++L
Sbjct: 172 EATLGVAARHVSMDAPFIDGEDNSLLDVLANPNAVNADEELDH--HDSLRREIERSLSTL 229

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T R++ V+ + FGI +    +LE++G++F +TRER+RQI+ KAI KL+  SRSK LR++L
Sbjct: 230 TDRQKDVIILYFGIAVEHPMSLEDIGEKFGLTRERVRQIKDKAITKLRTTSRSKLLRNYL 289


>gi|28899327|ref|NP_798932.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
 gi|28807551|dbj|BAC60816.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
          Length = 319

 Score =  190 bits (482), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 93/213 (43%), Positives = 142/213 (66%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 146 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 206 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           ++ VL  RFG+      TLEEVG +     ER+
Sbjct: 266 QKEVLARRFGLLGYEPSTLEEVGLRLKKWDERL 298


>gi|186687052|ref|YP_001870195.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186469355|gb|ACC85154.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 316

 Score =  190 bits (482), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 106/250 (42%), Positives = 162/250 (64%), Gaps = 9/250 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S++++G+     AK++MV ANLRLV+SVAKKY N  L FLDL+QEG +GL +  EKFD  
Sbjct: 73  SVIQQGQK----AKQKMVTANLRLVVSVAKKYQNYSLDFLDLLQEGALGLQRGIEKFDPN 128

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYK STY  WW+ Q+ITR++AD+S TIR+P+H+ +K++K+ R  +++S  + R P   E
Sbjct: 129 KGYKLSTYVYWWITQSITRAVADKSRTIRLPIHINEKLNKIRRVQQQLSQSLGRPPVVAE 188

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           IA+ L +    +R+ L+I+K  +SLE  +GDE  S L D +   + +S LD  I   +L+
Sbjct: 189 IAESLNLSPNQIREYLQISKPLVSLEKRVGDEGESELADIL-PMDGIS-LDEQITLESLQ 246

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +   ++LA L PR+  VL +RFG+  N   TL +V K+  ++RE IR+ E  A+  L+  
Sbjct: 247 QDLAKLLALLKPRQREVLTLRFGLSDNQQLTLSQVAKRLNLSRETIRKTEHLALSILR-- 304

Query: 671 SRSKKLRSFL 680
           S   K++ +L
Sbjct: 305 SHQNKIKDYL 314


>gi|17545926|ref|NP_519328.1| RNA polymerase sigma factor RpoS [Ralstonia solanacearum GMI1000]
 gi|17428221|emb|CAD14909.1| rna polymerase sigma s (sigma-38) factor transcription regulator
           protein [Ralstonia solanacearum GMI1000]
          Length = 377

 Score =  189 bits (481), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 174/289 (60%), Gaps = 6/289 (2%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           PE +++  +  E+ +   +++ +  IS++  ++ +E  H  ++ + GE  A   ++ M+E
Sbjct: 88  PEEDFRTVLQAELAAD-TVQHYLNRISIKPLLTPAEELHFSTLAKAGEFAA---RQVMIE 143

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
            NLRLV+S+AK Y NRG+  LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R
Sbjct: 144 RNLRLVVSIAKGYLNRGVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIER 203

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +I +Q+ T+R+PVH+  ++++V+R  R +  S    R+ + E+IA  L    E V+ VL 
Sbjct: 204 AIMNQARTVRLPVHVIRELNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLS 263

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   SL+TP   +  + L DF+ D++  SP        L +     LA L+ +   V+
Sbjct: 264 LNEHTTSLDTPFDLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVV 323

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             RFG+      TLEE+  +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 324 ERRFGLNHIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQGVR 372


>gi|88705821|ref|ZP_01103530.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
 gi|88699892|gb|EAQ97002.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
          Length = 331

 Score =  189 bits (481), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 92/258 (35%), Positives = 163/258 (63%), Gaps = 6/258 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           NEI  + +   ++  E +H   + +KG+     A+K M+E+NLRLV+ +A++Y +RG+  
Sbjct: 64  NEIGFVPL---LTADEEKHYARLTQKGD---EAARKRMIESNLRLVVKIARRYLHRGMSL 117

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLI+EGN+GLM+A EKFD   G++FSTYA WW++Q I R I +Q+ TIR+P+H+   ++
Sbjct: 118 LDLIEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIHVVKDLN 177

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
             +R AR ++ ++  EPT +EIA +     + V +++ + +   S++ P+G +  S + +
Sbjct: 178 GCLRAARELTQQLDHEPTTQEIASRTHKSAKEVSRLMGLNERVSSVDAPLGPDSDSSVVE 237

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D +   P +     ++ ++    L  LT ++  V+  RFG+  +   TLEEVG++  
Sbjct: 238 TIADDHLCDPSEQLQNDDVHDSVADWLNELTDKQREVVMRRFGLLGHESSTLEEVGQEIG 297

Query: 651 VTRERIRQIEAKAIRKLK 668
           +TRER+RQI+ +A+++L+
Sbjct: 298 LTRERVRQIQVEALKRLR 315


>gi|117165089|emb|CAJ88642.1| putative RNA polymerase principal sigma factor HrdC [Streptomyces
           ambofaciens ATCC 23877]
          Length = 338

 Score =  189 bits (481), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 95/253 (37%), Positives = 156/253 (61%), Gaps = 12/253 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   VR G      AK  MV ANLRLV+S+AK++ +RGL  LD+IQEGN+GL++A EK
Sbjct: 89  RALEETVRDGRA----AKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEK 144

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G+KFSTYA WW++QAI R +A  + T+R+PVH+ +++ K+ +  R++  ++ REP
Sbjct: 145 FDHTKGFKFSTYATWWIRQAIERGLATHARTVRLPVHVVEQLQKLAKVERKLRGRLDREP 204

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----S 603
           T +E+A +  +  + V  + ++ ++ +SL+TP+ +   + +GD I D   +   +     
Sbjct: 205 TADEVAAESGIDGDKVVWLRRVGRDAVSLDTPVDEAGETVVGDLIPDTEVLQAPEVAEFQ 264

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+ A LRE     + +L PRE  +L +R+G+      TL +V +   +TRER+RQ+E  +
Sbjct: 265 ALAAELRE----AVGTLAPREAMILSLRYGLHDGRPRTLHQVAQHVGLTRERVRQLEKAS 320

Query: 664 IRKLKHPSRSKKL 676
           +  L+ P    +L
Sbjct: 321 LDHLRAPETRDRL 333


>gi|315499353|ref|YP_004088157.1| RNA polymerase, sigma 70 subunit, rpod [Asticcacaulis excentricus
           CB 48]
 gi|315417365|gb|ADU14006.1| RNA polymerase, sigma 70 subunit, RpoD [Asticcacaulis excentricus
           CB 48]
          Length = 696

 Score =  189 bits (481), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 100/177 (56%), Positives = 125/177 (70%), Gaps = 6/177 (3%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E +   D  + D +D   KK IK A+ RGYVT++ELN  LP +E +SEQ+EDT+AML+ M
Sbjct: 9   EADTPSDGPLLDLTDAGVKKFIKNAKARGYVTMDELNKVLPSEEFTSEQIEDTLAMLTEM 68

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           G+NVVD ++ E  EG E    +A       V + ++  + DR TDDPVRMYLREMGS+EL
Sbjct: 69  GVNVVDSEE-EATEGGE----IAVREETGGVVVAEKTSAYDR-TDDPVRMYLREMGSVEL 122

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           LSREGEIAIAKRIEAGR  M+  LCES LTF+A++IWR+EL  G  LLREIIDLE  
Sbjct: 123 LSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMIWREELESGRILLREIIDLEGT 179


>gi|257092978|ref|YP_003166619.1| RNA polymerase sigma factor RpoS [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257045502|gb|ACV34690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 319

 Score =  189 bits (481), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 99/249 (39%), Positives = 156/249 (62%), Gaps = 2/249 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V+  R+       A+++M+E NLRLV+++AK Y NRG+  LDLI+EGN+GL+ A EK+D 
Sbjct: 68  VNWARRARAGEFPARQKMIEHNLRLVVNIAKHYLNRGIPLLDLIEEGNLGLIHAIEKYDP 127

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q+I R+I +QS TIR+PVH+   I+ V+R  R + +   RE  P+
Sbjct: 128 ERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHVVKDINLVLRAIRHLESASGREICPD 187

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-L 609
            IA  +  PVE VR+V+ + +   SL+ P+  + +  +GD I D++ + P D  +Q+N L
Sbjct: 188 RIAHLIDRPVEDVRRVMALNERIASLDAPLQVDPSQTVGDLIADESLLDP-DELLQSNEL 246

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E     L  L  +  +VL  R+G+G +   TLEE+     +TRER+RQI+ +A+  L+ 
Sbjct: 247 GELLRNWLGQLAGKHRQVLERRYGLGGSEPSTLEEIAFDLNLTRERVRQIQIEALDHLRR 306

Query: 670 PSRSKKLRS 678
             R + + S
Sbjct: 307 IIRRRGVTS 315


>gi|91217671|ref|ZP_01254628.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
 gi|91184175|gb|EAS70561.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
          Length = 288

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 100/260 (38%), Positives = 167/260 (64%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I+  E   +   +R+G+ +A++ K  +  ANLR V+SVAK+Y N+GL+  DLI EGN+GL
Sbjct: 31  ITAEEEVELAQRIREGD-QAALEK--LTNANLRFVVSVAKQYQNQGLKLPDLINEGNVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    I+K+ +T   +  
Sbjct: 88  VKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNKIGVINKINKTFSHLEQ 147

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSP 600
             +R P+  EIAK+L M    V+  LK +   +S++ P  + E+ S+L D +    + +P
Sbjct: 148 VNERPPSAIEIAKELDMSEAQVKVALKNSGRHLSMDAPFKEGENDSNLYDVLSSAESPTP 207

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D  ++ +L     R L +L+ RE  V+R+ +GIG     TL+E+G  F ++RER+RQI 
Sbjct: 208 DDQLMRDSLSIEINRALETLSQREADVIRLNYGIGNQPAMTLQEIGDTFDLSRERVRQIR 267

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            K IR+LKH S++K L+ +L
Sbjct: 268 EKGIRRLKHQSKNKMLKKYL 287


>gi|34499137|ref|NP_903352.1| RNA polymerase sigma factor RpoS [Chromobacterium violaceum ATCC
           12472]
 gi|34104988|gb|AAQ61344.1| RNA sigma factor RpoS [Chromobacterium violaceum ATCC 12472]
          Length = 316

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 103/248 (41%), Positives = 154/248 (62%), Gaps = 4/248 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V  GE EA   +++M+E NLRLV+++AK Y NRGL  LDLI+EGNIGLM A EKFD   G
Sbjct: 71  VVAGEFEA---RQKMIEHNLRLVVNIAKHYINRGLALLDLIEEGNIGLMHALEKFDPERG 127

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q+I R+I +QS TIR+PVH+  +++  +R +R + ++I REP+ EEIA
Sbjct: 128 FRFSTYATWWIRQSIERAIMNQSRTIRLPVHVIKELNVYLRASRHLESQIGREPSVEEIA 187

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             +  PVE VRKVL + +   SL+ P+  +    +G+ I D+    P      + L    
Sbjct: 188 HLVGKPVEDVRKVLNLNERMASLDAPLDIDPMLSIGESIPDEQHEEPELQLHNSQLEMFV 247

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L+ L  ++  V+  R+G+      TLEE+     +TRER+RQI+ + + +L+   R 
Sbjct: 248 HDWLSQLNEKQRLVIERRYGLNGYEICTLEELAASLNLTRERVRQIQIEGLEQLRRILRR 307

Query: 674 KKL-RSFL 680
           K + R FL
Sbjct: 308 KGISRDFL 315


>gi|298500963|ref|ZP_07010764.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
 gi|297540211|gb|EFH76271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
          Length = 233

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 89/213 (41%), Positives = 145/213 (68%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           ++ ++++Y+NR L  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q
Sbjct: 1   MVKISRRYSNRRLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQ 60

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V K+L++ +   S
Sbjct: 61  TRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISS 120

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TPIG +    L D + D +   P  S    ++RE+    L  L P+++ VL  RFG+ 
Sbjct: 121 VDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPKQKEVLARRFGLL 180

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TLEEVG++  +TRER+RQI+ + +R+L+
Sbjct: 181 GYEPSTLEEVGREINLTRERVRQIQVEGLRRLR 213


>gi|6175878|gb|AAF05319.1|AF178851_2 sigma factor 38 [Pseudomonas putida]
          Length = 335

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 94/256 (36%), Positives = 157/256 (61%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  H   + +KG+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 68  LNEIGFSPLLSPEEEVHFARLSQKGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 124

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI +P+H+  +++  
Sbjct: 125 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIPLPIHVVKELNVY 184

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 185 SRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 244

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +T
Sbjct: 245 TDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLT 304

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + +++L+
Sbjct: 305 RERVRQIQVEGLKRLR 320


>gi|238926534|ref|ZP_04658294.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
 gi|238885480|gb|EEQ49118.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
          Length = 352

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 106/259 (40%), Positives = 161/259 (62%), Gaps = 12/259 (4%)

Query: 430 IVSMVRKGECEA----SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + +M+++G  +A     +  K++V+   +  +   K+Y +R L F D+ Q G IGL+ AA
Sbjct: 99  LCAMIQQGNLQAEQDLCVKNKKLVD---KYALGYEKRYRHR-LDFDDIEQAGFIGLITAA 154

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD  +GY FSTYA+WW+KQAITR I D    IRIPVHM ++I KV      M +++ R
Sbjct: 155 KKFDISMGYSFSTYAVWWIKQAITREIMDHGFVIRIPVHMMEQIIKVA-GVENMFSELNR 213

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           E    ++  +     E VR+ + + +  +   SL   +G+++T  LG+F+ D  A+S  +
Sbjct: 214 EERIVKVMDETGYKEERVRECMMLKEYVLTYSSLNVTVGEDETVELGEFLSDDGAISIEE 273

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                 LR     VL +LT +E++V+++RFG+  N   TLEEVGK F VTRERIRQIE+K
Sbjct: 274 MIENKELRRMLDDVLNTLTEKEKKVIKLRFGLEDNRQWTLEEVGKLFNVTRERIRQIESK 333

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKL+HPSR   ++SFL+
Sbjct: 334 ALRKLRHPSRLHNIKSFLE 352


>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
 gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
          Length = 569

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 99/247 (40%), Positives = 156/247 (63%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK     +I K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 321 LRKRINHGTICKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKG 380

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  R P  EE+A
Sbjct: 381 FKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPDDEEVA 440

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  A +  +  ++  +++  
Sbjct: 441 EAAGLSMKRLSAVLLTPKAPRSLDQKIGMNMDLKPSEVIADPEAETAEELLMKQFMKQDL 500

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL +L PRE +V+R RFG+      TL+E+G+   V+RERIRQIE+ A RKLK+  R+
Sbjct: 501 EKVLNTLNPRETQVVRWRFGLEDGRMKTLQEIGEIMGVSRERIRQIESSAFRKLKNKKRT 560

Query: 674 KKLRSFL 680
           K+L+ +L
Sbjct: 561 KQLKQYL 567


>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa]
 gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa]
          Length = 567

 Score =  189 bits (480), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 95/238 (39%), Positives = 153/238 (64%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA W
Sbjct: 328 LCKDKMIKSNVRLVISIAKNYQGTGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 387

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W+KQA+ +S++D+S TIR+P HM D  ++V    +++ ++  R P  +E+A+   + ++ 
Sbjct: 388 WIKQAVRKSLSDRSRTIRLPFHMVDATYRVKEARKQLYSENGRHPDDKEVAEAAGLSMKR 447

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  VL   K P SL+  +G      L +   D  A +  D  ++  +++   +VL SL+P
Sbjct: 448 LSAVLLTPKAPRSLDQKMGFNMDLKLSEVTADPEAETAEDLLMKEFMKKDLAKVLGSLSP 507

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +V+R RFG+      TL+E+G+   V+RER+RQIE  A RKLK+ +R+K+LR ++
Sbjct: 508 RENQVVRWRFGMEDGRMKTLQEIGELMGVSRERVRQIELSAFRKLKNKNRTKQLRQYM 565


>gi|1769413|dbj|BAA13122.1| RpoD2 sigma factor [Microcystis aeruginosa]
          Length = 376

 Score =  189 bits (479), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 105/238 (44%), Positives = 170/238 (71%), Gaps = 2/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 139 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 198

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K ++ A+ +   ++R P   E+A++L +  E +
Sbjct: 199 IRQAITRTIANDARTIRLPIHIVEKLNK-LKKAQILKQDLQRNPNERELAERLEITPEQL 257

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED +   P D   +  +R+    VL+  LT 
Sbjct: 258 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTE 317

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 318 REKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 375


>gi|309782329|ref|ZP_07677056.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
 gi|308918947|gb|EFP64617.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
          Length = 378

 Score =  189 bits (479), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 165/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 106 VQHYLNRISIKPLLTPAEELHFSTLAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 163 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 222

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 283 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNYIEPATLEELA 342

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 343 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 373


>gi|282877766|ref|ZP_06286579.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
 gi|281300082|gb|EFA92438.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
          Length = 298

 Score =  189 bits (479), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 101/270 (37%), Positives = 172/270 (63%), Gaps = 8/270 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  ISI E   +   ++KG+ +A    +++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 33  LQEIGHEDLISIEEEIELAQRIKKGDRKAL---EKLTKANLRFVVSVAKQYQNQGLSLPD 89

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 90  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 149

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R   +   + +R P  +EIA ++ +P + + + +K+  + IS++ PI +   S L D +
Sbjct: 150 NRILNKFEQEHERRPNVDEIADQIDLPEDKIVEAMKVNGKHISVDAPIMEGADSSLLDVL 209

Query: 593 EDKNAVSPL--DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
              N  SP+  +  +  +LRE     L  L  RE  ++   +GI    + TLEE+G +F 
Sbjct: 210 --PNTESPMADNELVMESLREEVASALNVLNERERNIIECFYGIN-QREMTLEEIGDKFG 266

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +TRER+RQI+ KA+R+L+  ++SK+L+++L
Sbjct: 267 LTRERVRQIKEKALRRLRQNTKSKQLKAYL 296


>gi|193089925|gb|ACF15191.1| RpoS [Pseudomonas sp. DF41]
          Length = 335

 Score =  189 bits (479), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 151/238 (63%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 143 ERGSRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 203 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QSIDQWLSELTDKQWEVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLR 320


>gi|241662747|ref|YP_002981107.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12D]
 gi|240864774|gb|ACS62435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ralstonia
           pickettii 12D]
          Length = 378

 Score =  189 bits (479), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 165/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 106 VQHYLNRISIKPLLTPAEELHFSTLAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 163 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 222

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 283 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNYIEPATLEELA 342

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 343 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 373


>gi|78188365|ref|YP_378703.1| RNA polymerase sigma factor rpoD (sigma-A) [Chlorobium
           chlorochromatii CaD3]
 gi|78170564|gb|ABB27660.1| RNA polymerase sigma factor rpoD (Sigma-A) [Chlorobium
           chlorochromatii CaD3]
          Length = 299

 Score =  189 bits (479), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/242 (38%), Positives = 155/242 (64%), Gaps = 1/242 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P   E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDPNTRELASLLEMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHM-PDYGLTRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIRSYFGIGMDNPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297

Query: 681 DG 682
            G
Sbjct: 298 GG 299


>gi|315185379|gb|EFU19152.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 292

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 99/259 (38%), Positives = 167/259 (64%), Gaps = 16/259 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   +  +G+ +A   K+++V ANLR V++VAKKY N+GL   DLI EGNIGL+ A E+F
Sbjct: 41  HYARLAAQGDQDA---KEKLVTANLRFVVNVAKKYQNQGLPLADLISEGNIGLLNAIERF 97

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD------KIHKVVRTARRMSNK 542
           D   GY F +YA+WW++QAI ++I+++S  IR+P++  +      K  K+V+T     N+
Sbjct: 98  DPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRANELVQIEKARKLVQTESGEHNE 157

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPL 601
           IK+      +A+ L    + V  +L ++KE +SL+TP+  D D++ LGD+++D+ +  P 
Sbjct: 158 IKK------VAETLDYDEDHVANLLNLSKEYVSLDTPVYEDRDSAMLGDYLKDEASRPPE 211

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D  ++  L+E    VLA+LT +E  +++ RFG+      +L+E+G  + +T+ERIRQIE 
Sbjct: 212 DVVLEKTLQEEIQEVLATLTEKEAEIIQYRFGLNGRHPMSLKEIGDMYNLTKERIRQIEK 271

Query: 662 KAIRKLKHPSRSKKLRSFL 680
           KA++K++   ++K L ++L
Sbjct: 272 KALKKIQQSEKAKVLETYL 290


>gi|46205316|ref|ZP_00048697.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 326

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 157/272 (57%), Gaps = 43/272 (15%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           AS +   +V     ++  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A
Sbjct: 45  ASGSRAVAVATPTTREPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIA 103

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDS 214
            LCESPLTFQA+IIWRDEL DG  LLR+IIDLEA   GP+++GG                
Sbjct: 104 GLCESPLTFQAIIIWRDELVDGKVLLRDIIDLEATYAGPDARGG---------------- 147

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
                            +      +D  +   PPE  +      DED+ ++  +L+AME 
Sbjct: 148 --------------PQVAEEGEESEDGEEGPVPPEGGD------DEDDMENNVSLAAMEA 187

Query: 275 QLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
           +++P+V+   D IA  YR+LR LQ+      A  G      + K   LK+ +V  V SLS
Sbjct: 188 EIKPRVLETFDNIASNYRKLRKLQNEEAEFKASGGTVTPAQTKKQAELKDIVVTDVKSLS 247

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
           LN  RI+  VEQ+YDI +R++ +EG L+  A+
Sbjct: 248 LNAKRIEAPVEQVYDIHERLISHEGRLICAAE 279


>gi|229496411|ref|ZP_04390127.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
 gi|229316639|gb|EEN82556.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
          Length = 287

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 102/268 (38%), Positives = 168/268 (62%), Gaps = 3/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I + E   +   +R+G   A   + ++  ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREELIDVDEEVRLAQEIRRGNRRA---QDKLTRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++      K+
Sbjct: 79  LIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGAQAKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P+  E+A  L    E V   LK   + +S++ P  D + + L D +
Sbjct: 139 KKAIEQFEQENERRPSIAELAIILDQSEEKVAVTLKSFSKHVSIDAPFVDGEDNSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +++A S   S ++ +L     RVL++L+ RE  ++++ FGIG N + TLEE+G +F +T
Sbjct: 199 VNEDAPSTDRSLMRDSLNTEIDRVLSTLSEREAEIIKLFFGIGPNPEMTLEEIGDKFGLT 258

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAIRKL+  ++  +L+SFL
Sbjct: 259 RERVRQIKEKAIRKLRAGNKCDQLKSFL 286


>gi|33241240|ref|NP_876182.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238770|gb|AAQ00835.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 328

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 103/257 (40%), Positives = 159/257 (61%), Gaps = 14/257 (5%)

Query: 416 ISVETGISISEF-RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++++ GIS+ E  + +   VR        AK+ MV ANLRLV+SVAKKYT R ++ LDLI
Sbjct: 72  LAIDAGISVRELSKRLKRGVR--------AKERMVSANLRLVVSVAKKYTKRNMELLDLI 123

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S  IR+P+H+ + ++K+ +
Sbjct: 124 QEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRIIRLPIHITELLNKLKK 183

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSHLGDFIE 593
             R +S  ++R PT +E++  + +PVE V+ ++    +P+SLE+ +GD EDTS L     
Sbjct: 184 GQRELSQHLERTPTMQELSAYVEIPVEEVKDLMFRASQPVSLESKVGDGEDTSLLDLLAI 243

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPR-EERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           D +     D  I+ +  +    VL    P  + RVLRMRFGI      TL  +G+   ++
Sbjct: 244 DTDLP---DQQIELDCMKGDLEVLLQKLPELQNRVLRMRFGINGEEPMTLTGIGRMLGIS 300

Query: 653 RERIRQIEAKAIRKLKH 669
           R+R+R +    ++ L+ 
Sbjct: 301 RDRVRNLLRDGLKGLRQ 317


>gi|262197834|ref|YP_003269043.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081181|gb|ACY17150.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 436

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 93/245 (37%), Positives = 148/245 (60%), Gaps = 3/245 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   +  V+      +  + E V ANLRLV+++A++Y   G+   DLIQEGN+GLM A  
Sbjct: 185 FGEYLRAVKSSFARGARLRNEFVHANLRLVVTMARRYDRGGMPLADLIQEGNLGLMHAVS 244

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD+  G +FSTYA WW++ AI R++AD+S  +RIPVHM +   ++ +   ++  ++ RE
Sbjct: 245 RFDYRRGLRFSTYACWWIRHAIGRALADKSRAVRIPVHMLEAQQQLAKVQAKLIGELGRE 304

Query: 547 PTPEEIAKKLAMPVEGVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDS 603
           PTP E+AK   +P+  + ++ + +  +P+SL+ P+ D+D    GD + D  +   SP+D 
Sbjct: 305 PTPSELAKAAQVPLAKLNQMHRYLMGQPMSLDRPLYDDDDRAFGDMLADPLSEDSSPVDD 364

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L      +L  LTP E  VLR RFG+  + + T  E+G Q+ ++RERIRQI+  A
Sbjct: 365 LTTQTLTSRVETLLDHLTPIEADVLRQRFGLMDDEERTFREIGDQYDLSRERIRQIQNAA 424

Query: 664 IRKLK 668
           + KL+
Sbjct: 425 LGKLR 429


>gi|187928144|ref|YP_001898631.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12J]
 gi|187725034|gb|ACD26199.1| RNA polymerase, sigma 70 subunit, RpoD family [Ralstonia pickettii
           12J]
          Length = 378

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 165/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 106 VQHYLNRISIKPLLTPAEELHFSTLAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 163 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 222

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 283 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNYIEPATLEELA 342

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 343 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 373


>gi|15223259|ref|NP_172330.1| SIG2 (RNA POLYMERASE SIGMA SUBUNIT 2); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana]
 gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana]
 gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana]
 gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana]
 gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
 gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana]
 gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana]
 gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana]
          Length = 572

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 97/240 (40%), Positives = 151/240 (62%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA
Sbjct: 329 GTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYA 388

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA+   + +
Sbjct: 389 HWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSM 448

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +  VL   K P SL+  IG        + I D  AV+  D  I+  +R+   +VL SL
Sbjct: 449 KRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSL 508

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  R+  L+ +L
Sbjct: 509 GTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYL 568


>gi|228471226|ref|ZP_04056039.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
 gi|228307041|gb|EEK16123.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
          Length = 286

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 160/240 (66%), Gaps = 7/240 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++VEANLR V+SVAK+Y N+GL   DLI EGNIG++KAAEKFD   G+KF +YA+WW
Sbjct: 50  ALNKLVEANLRFVVSVAKQYQNQGLSLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIP---VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++Q+I +++A+QS  +R+P   V ++ K++K +    +++    R P+P+EIA +L +P 
Sbjct: 110 IRQSILQALAEQSRIVRLPLNQVGLQQKMNKAIVKFEQLNG---RRPSPQEIADELELPE 166

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +R+ LK+  +  SL+ P  + + +++ D + +++  S   S I  +L     R+L  L
Sbjct: 167 DKIREALKVQGKHQSLDAPFVEGEDNNMLDVLVNEDTPSTDSSLINESLSAEIDRILEQL 226

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE  VLR  FGIG   + TLEE+G++  ++RER+RQI+ KAIR+LK   R + L+++L
Sbjct: 227 GDREAEVLRCFFGIGC-PEMTLEEIGERTKLSRERVRQIKEKAIRRLKQSDRCEYLKAYL 285


>gi|313886597|ref|ZP_07820310.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332300881|ref|YP_004442802.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
 gi|312923953|gb|EFR34749.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332177944|gb|AEE13634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 286

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 160/240 (66%), Gaps = 7/240 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++VEANLR V+SVAK+Y N+GL   DLI EGNIG++KAAEKFD   G+KF +YA+WW
Sbjct: 50  ALNKLVEANLRFVVSVAKQYQNQGLSLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIP---VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++Q+I +++A+QS  +R+P   V ++ K++K +    +++    R P+P+EIA +L +P 
Sbjct: 110 IRQSILQALAEQSRIVRLPLNQVGLQQKMNKAIVKFEQLNG---RRPSPQEIAAELELPE 166

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +R+ LK+  +  SL+ P  + + +++ D + +++  S   S I  +L     R+L  L
Sbjct: 167 DKIREALKVQGKHQSLDAPFVEGEDNNMLDVLVNEDTPSTDSSLINESLSAEIDRILDQL 226

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE  VLR  FGIG   + TLEE+G++  ++RER+RQI+ KAIR+LK   R + L+++L
Sbjct: 227 GDREAEVLRCFFGIGC-PEMTLEEIGERTKLSRERVRQIKEKAIRRLKQSDRCEYLKAYL 285


>gi|292491540|ref|YP_003526979.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580135|gb|ADE14592.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 311

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 99/248 (39%), Positives = 154/248 (62%), Gaps = 6/248 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +H   + ++G+ +A   +  M+E+NLR+VI +A ++ NRGL  +DLI+EGN+GL
Sbjct: 52  LSAEEEKHYARLAQQGDRKA---RDRMIESNLRMVIKMATRHVNRGLPLMDLIEEGNLGL 108

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A EKFD  LG++FSTYA WW++QAI R++ +Q  T+RIPVH+   I +  R A+R+  
Sbjct: 109 IHAVEKFDPELGFRFSTYASWWIEQAIERALMNQVRTVRIPVHVLKTIRRYQREAKRLGQ 168

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSP 600
               EP  EEIAK L  P+E +++ L       SL  P+ +++   L D + D +N  + 
Sbjct: 169 THNTEPRLEEIAKALNEPLEKIQRYLSFQIPETSLNDPLSEDNEDCLADLLPDERNNPAI 228

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           L      N+  T    L+ LT R++ VL+ R+G+      TLEEVG+   +TRER+RQI+
Sbjct: 229 LWEIFDKNI--TINHQLSQLTDRQQEVLKRRYGLDGYEATTLEEVGQTIGITRERVRQIQ 286

Query: 661 AKAIRKLK 668
             AI++L+
Sbjct: 287 QTAIKRLR 294


>gi|87301677|ref|ZP_01084517.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283894|gb|EAQ75848.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 349

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 96/228 (42%), Positives = 146/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 111 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 170

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V
Sbjct: 171 IRQGITRAIAEKSRTIRLPIHITETLNKLKKGQRELSQELGRTPTLSELAVCVELPEEEV 230

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L   ++P+SLET +GD + + L D ++    + P +S     LR     +L  L   
Sbjct: 231 KDLLCRARQPVSLETKVGDGEDTELLDLLQGDGTL-PAESVDSECLRGDMRALLEQLPEL 289

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +  VL MR+GI +    +L  +G+   ++R+RIR +E   +  L+  S
Sbjct: 290 QRSVLSMRYGIDVEEPMSLTGIGRILGMSRDRIRNLERDGLASLRRLS 337


>gi|119717204|ref|YP_924169.1| sigma-70 region 3 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119537865|gb|ABL82482.1| sigma-70 region 3 domain protein [Nocardioides sp. JS614]
          Length = 319

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 89/221 (40%), Positives = 143/221 (64%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            + ANLRLV+S+A+KY    +  LDLIQEGN GL++A EKFD+  GYKFSTYA WWV+QA
Sbjct: 90  FITANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYTKGYKFSTYATWWVRQA 149

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR IA Q+  +R+PVH+ +++++V    R +  K+ REP P EIA++L M V+ V  ++
Sbjct: 150 ITRGIAQQARVVRLPVHVVEELNQVGGARRTLERKLGREPEPREIAEELGMEVDRVLDLM 209

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
              +E +SL++P+ ++  + LGD +  + A  P  + I    R+    ++  L  R   +
Sbjct: 210 AWGREHVSLDSPVDEDGDTSLGDLMAQETAPGPDLNFIDVESRDRLNSLVGKLDDRAADI 269

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R R+G+     H L ++G +  ++ ER+RQ+E +A++KL+
Sbjct: 270 IRSRYGLVDGRQHKLADIGAKHGISAERVRQLEREALQKLR 310


>gi|78183723|ref|YP_376157.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78168017|gb|ABB25114.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 332

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 94/228 (41%), Positives = 148/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 97  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P + V
Sbjct: 157 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAQFVDLPEDEV 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +   N + P D   +  L+     +L  L   
Sbjct: 217 KDLMCRARQPVSLEMKVGDGDDTELLELLSGDNEL-PSDQVEEDCLKGDLRSLLGQLPHL 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +E+VLRMRFG+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 276 QEQVLRMRFGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRRVS 323


>gi|2353173|gb|AAB69385.1| sigma factor 2 [Arabidopsis thaliana]
          Length = 574

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 97/240 (40%), Positives = 151/240 (62%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA
Sbjct: 331 GTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYA 390

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA+   + +
Sbjct: 391 HWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSM 450

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +  VL   K P SL+  IG        + I D  AV+  D  I+  +R+   +VL SL
Sbjct: 451 KRLMAVLLSPKPPRSLDRKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSL 510

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  R+  L+ +L
Sbjct: 511 GTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYL 570


>gi|302555769|ref|ZP_07308111.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302473387|gb|EFL36480.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 339

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 155/247 (62%), Gaps = 5/247 (2%)

Query: 435 RKGECEASI-----AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           R+GE E +      AK  MV ANLRLV+S+A+++ +RGL  LD+IQEGN+GL++A EKFD
Sbjct: 88  RRGELEETARDGQRAKDHMVRANLRLVVSMARRHAHRGLPLLDVIQEGNLGLIRAVEKFD 147

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G+KFSTYA WW++Q+I R +A  + T+R+P+ + +++ K+ +  RR+   + REP+ 
Sbjct: 148 HTKGFKFSTYATWWIRQSIERGLAAHARTVRLPMQVVEQLQKIAKVERRLQLDLGREPSV 207

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            E+A++  +  + +  + ++ ++ +SL+TP+ D   + +GD I D   +   + A    L
Sbjct: 208 AEVARESGLAEDRIDWLRRVGRQAVSLDTPVDDTGETVVGDLIPDTEVLQAPEVAEYTAL 267

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E     + +L PRE  +L +R+G+      T +EV ++  +TRER+RQ+E  ++ +L+ 
Sbjct: 268 AEELREAVGTLGPREAMILSLRYGLHDGHTRTRDEVARRVGLTRERVRQLEKASLARLRE 327

Query: 670 PSRSKKL 676
           P   ++L
Sbjct: 328 PENRERL 334


>gi|206602787|gb|EDZ39268.1| RNA polymerase, RpoD-like sigma subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 499

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 108/274 (39%), Positives = 166/274 (60%), Gaps = 13/274 (4%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E D +  + + +K +     ++  E + +   VR G+  A   ++ M+++NLRLV+S+A
Sbjct: 41  LEDDHLSALGSYLKKLQKSHLLTFEEEQDLAKRVRAGDESA---RQAMIQSNLRLVVSIA 97

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K+Y  RGL   DLI+EGN+GLMKA  KFD   G++FSTYA WW++QAI R I +Q   IR
Sbjct: 98  KRYIGRGLLLEDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIR 157

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVHM +K++  +    R      ++P  E +A+K  + V  ++++  + K  +SL+TPI
Sbjct: 158 LPVHMMEKVNAYLNAIERQVAD-GQQPDIENLARKNGLKVRDLQEIQALLKNTVSLDTPI 216

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFGI--- 634
           GD + S L D + D  + SP+ S I++  RE   R+   LA L  +E RV+ +RFG+   
Sbjct: 217 GDREDSTLKDILVDPTSFSPI-STIES--REEGDRLRESLALLKDKERRVIHLRFGLPGE 273

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           G     TLE +G+   VTRER+RQIEA A+ KL+
Sbjct: 274 GPEEGMTLEAIGQMLGVTRERVRQIEASAMAKLR 307


>gi|307150096|ref|YP_003885480.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306980324|gb|ADN12205.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 298

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 89/228 (39%), Positives = 156/228 (68%), Gaps = 4/228 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M++ANLRLV+S+AK+Y  RGL  LDLIQEG++GL++A EKFD   GYKFSTYA WW
Sbjct: 62  AKQQMIQANLRLVVSIAKRYQRRGLSLLDLIQEGSLGLIRAVEKFDPSKGYKFSTYAYWW 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR++A++S TIR+P+HM + ++ + ++ R ++ ++ R+PT +E+A+++ +P+E +
Sbjct: 122 VRQAITRALAEKSRTIRLPIHMTENLNHLKKSVRELTGELGRKPTEQEVAQRMEIPLEKL 181

Query: 564 RKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +++       +  SL   + D++ + LG+ + D+ ++ P+D   +  L      +L  L 
Sbjct: 182 QEIRHAVYRTDAKSLNITL-DDNQTELGEVLPDETSL-PIDFVSERELMTKVDDLLEDLP 239

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           PR+  ++ +RFG+      + +E+G+Q  ++ ER RQ+  +A+R LK 
Sbjct: 240 PRQREIITLRFGLLTGKRMSYKEIGRQCGISHERARQLLNRAMRTLKQ 287


>gi|116071698|ref|ZP_01468966.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065321|gb|EAU71079.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 332

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 94/228 (41%), Positives = 148/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 97  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P + V
Sbjct: 157 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAQFVDLPEDEV 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +   N + P D   +  L+     +L  L   
Sbjct: 217 KDLMCRARQPVSLEMKVGDGDDTELLELLSGDNEL-PSDQVEEDCLKGDLRSLLGQLPHL 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +E+VLRMRFG+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 276 QEQVLRMRFGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRRVS 323


>gi|87303408|ref|ZP_01086196.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87282056|gb|EAQ74018.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 330

 Score =  188 bits (477), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 97/237 (40%), Positives = 152/237 (64%), Gaps = 3/237 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 95  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V
Sbjct: 155 IRQGITRAIAEKSRTIRLPIHITETLNKLKKGQRELSQELGRTPTLSELAVCVELPEEEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L   ++P+SLET +GD + + L D ++    + P +S     LR     +L  L   
Sbjct: 215 KDLLCRARQPVSLETKVGDGEDTELLDLLQGDGTL-PAESVDSECLRGDMRALLEQLPEL 273

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  VL MR+GI  +   +L  + +   ++R++ R +E +A+  ++  SRS +L  +L
Sbjct: 274 QRSVLSMRYGIDGDEPMSLTSIARTLGMSRDKTRNLERRALEGIR--SRSCRLEGYL 328


>gi|124514327|gb|EAY55841.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           rubarum]
          Length = 499

 Score =  187 bits (476), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 108/274 (39%), Positives = 166/274 (60%), Gaps = 13/274 (4%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E D +  + + +K +     ++  E + +   VR G+  A   ++ M+++NLRLV+S+A
Sbjct: 41  LEDDHLSALGSYLKKLQKSHLLTFEEEQDLAKRVRAGDESA---RQAMIQSNLRLVVSIA 97

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K+Y  RGL   DLI+EGN+GLMKA  KFD   G++FSTYA WW++QAI R I +Q   IR
Sbjct: 98  KRYIGRGLLLEDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIR 157

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVHM +K++  +    R      ++P  E +A+K  + V  ++++  + K  +SL+TPI
Sbjct: 158 LPVHMMEKVNAYLNAIERQVAD-GQQPDIETLARKNGLKVRDLQEIQALLKNTVSLDTPI 216

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFGI--- 634
           GD + S L D + D  + SP+ S I++  RE   R+   LA L  +E RV+ +RFG+   
Sbjct: 217 GDREDSTLKDILVDPTSFSPI-STIES--REEGDRLRESLALLKDKERRVIHLRFGLPGE 273

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           G     TLE +G+   VTRER+RQIEA A+ KL+
Sbjct: 274 GPEEGMTLEAIGQMLGVTRERVRQIEASAMAKLR 307


>gi|307718169|ref|YP_003873701.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
 gi|306531894|gb|ADN01428.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
          Length = 303

 Score =  187 bits (476), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 97/244 (39%), Positives = 161/244 (65%), Gaps = 13/244 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++V ANLR V++VAKKY N+GL   DLI EGNIGL+ A E+FD   GY F +YA+WW
Sbjct: 64  AKEKLVTANLRFVVNVAKKYQNQGLPLADLISEGNIGLLNAIERFDPDKGYHFISYAVWW 123

Query: 504 VKQAITRSIADQSCTIRIPVHMRD------KIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           ++QAI ++I+++S  IR+P++  +      K  K+V+T     N+IK+      +A+ L 
Sbjct: 124 IRQAILKAISEKSRMIRLPLNRANELVQIEKARKLVQTESGEHNEIKK------VAETLD 177

Query: 558 MPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              + V  +L ++KE +SL+TP+  D D++ LGD+++D+ +  P D  ++  L+E    V
Sbjct: 178 YDEDHVANLLNLSKEYVSLDTPVYEDRDSAMLGDYLKDEASRPPEDVVLEKTLQEEIQEV 237

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA+LT +E  +++ RFG+      +L+E+G  + +T+ERIRQIE KA++K++   ++K L
Sbjct: 238 LATLTEKEAEIIQYRFGLNGRHPMSLKEIGDLYNLTKERIRQIEKKALKKIQQSEKAKIL 297

Query: 677 RSFL 680
            ++L
Sbjct: 298 ETYL 301


>gi|189345950|ref|YP_001942479.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
 gi|189340097|gb|ACD89500.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
          Length = 299

 Score =  187 bits (476), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 154/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P   E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELANLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHL-PDHGLNKDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|54401868|gb|AAV34620.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401871|gb|AAV34621.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401874|gb|AAV34622.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 299

 Score =  187 bits (475), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 85/210 (40%), Positives = 144/210 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           +  VL  RFG+      TLE+VG++  +TR
Sbjct: 270 QREVLARRFGLLGYEAATLEDVGREIGLTR 299


>gi|254432638|ref|ZP_05046341.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627091|gb|EDY39650.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 335

 Score =  187 bits (475), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 97/242 (40%), Positives = 154/242 (63%), Gaps = 8/242 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 95  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V
Sbjct: 155 IRQGITRAIAEKSRTIRLPIHITETLNKLKKGQRELSQELGRTPTVTELAGYVELPEEEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L   ++P+SLET +GD + + L D +     + P +      L+     +L  L   
Sbjct: 215 KDLLCRARQPVSLETKVGDGEDTELLDLLAGDGEL-PEERVDGECLKGDLRALLEQLPEL 273

Query: 624 EERVLRMRFGI-----GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           + RVL+MR+G+     G+    +L  + K   ++R++ R +E KA+  ++  S+S++L  
Sbjct: 274 QGRVLKMRYGLDPEGQGLTEPMSLSSIAKNLGMSRDKTRNLERKALEGIR--SQSRRLEG 331

Query: 679 FL 680
           +L
Sbjct: 332 YL 333


>gi|119357820|ref|YP_912464.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
 gi|119355169|gb|ABL66040.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
          Length = 299

 Score =  187 bits (475), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 154/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P   E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELANLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHL-PDHGLNKDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKILKEYI 297


>gi|189500956|ref|YP_001960426.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
 gi|189496397|gb|ACE04945.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
          Length = 299

 Score =  187 bits (475), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 155/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELANLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++ +   P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQN-DGHKPDHGLTRDSLNLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAI++L+  + SK L+ ++
Sbjct: 238 APREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIKRLRQSAYSKVLKEYI 297


>gi|67920853|ref|ZP_00514372.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856970|gb|EAM52210.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 297

 Score =  187 bits (475), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 94/227 (41%), Positives = 151/227 (66%), Gaps = 3/227 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+EANLRLV+S+AKKY N GL  LDLIQEG++GL++  EKFD   GYKFSTYA WW
Sbjct: 61  ARERMIEANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPARGYKFSTYAYWW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA+QS TIR+P+H+ + ++K  ++ R ++ K+ R+PT  EIA+ + + V+ +
Sbjct: 121 IRQGITRAIAEQSRTIRLPIHINENLNKYRKSIRELTLKLGRKPTQREIAENMEISVDRL 180

Query: 564 RKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + + +     +  SL   I DE+ + LG  + D+ ++SP D   Q         +L SLT
Sbjct: 181 QFLQQAAFKTKSRSLNVVI-DENQTELGQLLPDEESISPSDFVKQEEKISQINNLLESLT 239

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           PR++ V+ +RFG+      + + +G++  V+ ER RQI ++A++ L+
Sbjct: 240 PRQKEVIILRFGLRDGKQMSYKAIGEKCGVSHERARQIYSRALKILR 286


>gi|311742672|ref|ZP_07716481.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
 gi|311314300|gb|EFQ84208.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
          Length = 320

 Score =  187 bits (475), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 89/230 (38%), Positives = 145/230 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   A +E ++ANLRLV+S+A+KY    +  LDL+QEGN GL++A EKFD+  G+KFST
Sbjct: 82  AEGERALQEFIQANLRLVVSIARKYGRSAMPMLDLVQEGNTGLIRAVEKFDYVKGFKFST 141

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WWV+QAITR IA Q+  +R+PVH+ +++++V    R +   +  +P P EI+ +L M
Sbjct: 142 YATWWVRQAITRGIAQQARVVRLPVHVVEELNQVTAARRNLERTLGYDPEPAEISAELGM 201

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V+ V  +L   ++ +SL+TP+ ++  + LGD I  + A  P  S +    R    +++ 
Sbjct: 202 DVDRVIDLLSWGRDHVSLDTPVDEDGDTSLGDLIARETAPGPDSSMMSDATRGMIAQLID 261

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE  ++R R+G+       L ++GK+  ++ ER+RQ+E +A+ KL+
Sbjct: 262 HLGEREADIVRARYGLLDGRQQKLADIGKRHGISAERVRQLEREALAKLR 311


>gi|237738339|ref|ZP_04568820.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
 gi|229420219|gb|EEO35266.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
          Length = 273

 Score =  187 bits (474), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 99/239 (41%), Positives = 151/239 (63%), Gaps = 8/239 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++  NLRLV+++AK Y NRGL  +DLI EGN GL+ A EKFD   G++FSTYA+WW
Sbjct: 40  AKNKLILCNLRLVVNIAKNYVNRGLSLIDLISEGNFGLIYAIEKFDMKKGFRFSTYAVWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPV 560
           +KQ+IT++I  +   IRIP +  D + KV    R + N+++ E   PT EEI++ L +  
Sbjct: 100 IKQSITKAIICKGRGIRIPSYKYDLLSKV---NRYVLNRVREEGIYPTVEEISEDLNVNK 156

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E + +++   ++P+SL   IGD+    L D I + +  S  D  I+   RE   +++  L
Sbjct: 157 EKIEEIMVAFQDPMSLSASIGDD--IQLEDIIANNSETSIEDDIIEEMGREQVRQIVKVL 214

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             RE+++L++RFG+     HTLEE+G+ F +TRER+RQIE K ++KLK      K + F
Sbjct: 215 DEREKQILKLRFGLDGEEIHTLEEIGQTFNITRERVRQIEKKTLKKLKMQCEKNKDKFF 273


>gi|82949200|dbj|BAE53364.1| sigma factor [Streptomyces sp. AJ9463]
          Length = 195

 Score =  187 bits (474), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 86/138 (62%), Positives = 111/138 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 58  AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 118 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 177

Query: 564 RKVLKITKEPISLETPIG 581
            +V K  +EPISL TP+G
Sbjct: 178 IEVQKYGREPISLHTPLG 195


>gi|153875311|ref|ZP_02003170.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
 gi|152068225|gb|EDN66830.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
          Length = 314

 Score =  187 bits (474), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 96/238 (40%), Positives = 147/238 (61%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+ +     A+  M+E NLRLV+ +A+ Y NRGL  LDLI+EGN+GLM+A  KFD 
Sbjct: 61  IKYARRAQQGNEAARNRMIEGNLRLVVKIARNYMNRGLALLDLIEEGNLGLMRAVNKFDP 120

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +I++ +RT   +S  +  EPT E
Sbjct: 121 EKGFRFSTYATWWIRQTIERAIMNQNRTIRLPIHVLKEINQCLRTNHVLSQTLDHEPTSE 180

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK L    + V K+L++ +  IS+++P  +     L D I D+    P      A++ 
Sbjct: 181 EIAKTLKKSKQEVEKLLEVNERAISMDSPWMNYSEKSLIDNIPDELNPDPRLILEDADII 240

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     L+ LT ++  V+  RFGIG   + TLEE+G +  +TRER+RQI+  A  +LK
Sbjct: 241 KCLHLWLSQLTDKQRLVVERRFGIGNGDEATLEEIGAELELTRERVRQIQITATERLK 298


>gi|254253609|ref|ZP_04946926.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898254|gb|EAY70097.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 773

 Score =  187 bits (474), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 97/222 (43%), Positives = 140/222 (63%), Gaps = 9/222 (4%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 467 VDEVRQVERQILHI------VVDKCGMPRSEFIARFPGNETDLDWAE--KIAAEGHPYSA 518

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 519 VLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 578

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 579 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 638

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 639 TIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 680



 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 85/158 (53%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 188 RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 247

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 248 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 307

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 308 GLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD 345


>gi|300691814|ref|YP_003752809.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
 gi|299078874|emb|CBJ51535.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
          Length = 377

 Score =  187 bits (474), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 101/271 (37%), Positives = 165/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 105 VQHYLNRISIKPLLTPAEELHFSTLAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 162 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 221

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    + V+ VL + +   SL+TP   +  +
Sbjct: 222 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPFDLDPGT 281

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 282 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 341

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 342 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 372


>gi|298373668|ref|ZP_06983657.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
 gi|298274720|gb|EFI16272.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
          Length = 287

 Score =  187 bits (474), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 104/269 (38%), Positives = 171/269 (63%), Gaps = 5/269 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  I+I +   +   +RKG+  A++ K  +V ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEIGREELITIEQEVELAQRIRKGD-HAALDK--LVRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGALNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSHLGDF 591
            +  +R   + +R P+ EEIA  L + ++ +   +K++   IS++ P  D ED + L   
Sbjct: 139 NKAFQRFEQEHERLPSVEEIATDLEISLDKITDTMKVSGRHISVDAPFVDGEDNTLLDVL 198

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D +  +      ++ L E    + A L  RE  +++M FGIG   + TLEE+G QF +
Sbjct: 199 MNDSSPATDQKLMSESLLTEIERALDALLQERERDIVKMFFGIGC-AEMTLEEIGDQFGL 257

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI+ KAIR+L+  S++K L+ +L
Sbjct: 258 TRERVRQIKEKAIRRLRGNSKNKLLKVYL 286


>gi|83747939|ref|ZP_00944970.1| RpoS [Ralstonia solanacearum UW551]
 gi|83725357|gb|EAP72504.1| RpoS [Ralstonia solanacearum UW551]
          Length = 381

 Score =  187 bits (474), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 109 VQHYLNRISIKPLLTPAEELHFSTRAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 165

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 166 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 225

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 226 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDSGT 285

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 286 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 345

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 346 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 376


>gi|302036606|ref|YP_003796928.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
 gi|300604670|emb|CBK41002.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
          Length = 332

 Score =  187 bits (474), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 88/225 (39%), Positives = 145/225 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++EM+EANLRLVIS+ K+Y NRG  F D+++EGN+GL+KA EKF++  G++FSTYA WW
Sbjct: 94  ARQEMIEANLRLVISIGKRYMNRGFPFADIVEEGNLGLIKAVEKFNYKRGFRFSTYASWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q   +R+PVH+ +++++ +    ++ +++ REP  +E+A KL   V  V
Sbjct: 154 IRQFIERAIINQGKLVRLPVHVVERLNRYLGKVEQLVHELGREPRADEVAAKLKTSVAEV 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             + ++ +   SL++PI D   + L D IED   ++P ++      R      +  L  +
Sbjct: 214 DDLKQLVRTTCSLDSPISDRQDTFLRDVIEDPLCLTPAETTEGVMRRAELMAWVKELPEK 273

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  V+  RFG+      TLEE+G++  +TRER+RQIE  A+ +L+
Sbjct: 274 ERTVILARFGLDGAESRTLEEIGQEMGLTRERVRQIETAALARLR 318


>gi|284104060|ref|ZP_06386126.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283830219|gb|EFC34468.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 271

 Score =  186 bits (473), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 95/257 (36%), Positives = 165/257 (64%), Gaps = 5/257 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E   +   +++G+ EA +   ++  ANLR V+SVAKK+  +GL   DLI EGN GL
Sbjct: 15  VTPAEEAELARRIKQGDEEALL---KLTRANLRFVVSVAKKFQGQGLHLTDLINEGNYGL 71

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA++FD   G+KF +YA+WW++Q+I +++A+Q   +R+P++    I K+ +++ R++ 
Sbjct: 72  IKAAKRFDETRGFKFISYAVWWIRQSILQALAEQGRVVRLPLNQIGTISKIRKSSARLAQ 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + +R+P  EE+A  L + +E VR  ++ T   +S++ P  +ED + L D +   N ++P 
Sbjct: 132 EHERDPNLEELATDLQIDIEKVRSAMQRTARHLSMDAPFNEEDENSLLDVLPS-NEIAPP 190

Query: 602 DSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  ++  +L+      L+SL PRE  + R+ FG+G     TLEE+G +F +TRER+RQI+
Sbjct: 191 DEPLRGESLKIDIEVALSSLCPREAEITRLYFGVGREHPLTLEEIGLRFDLTRERVRQIK 250

Query: 661 AKAIRKLKHPSRSKKLR 677
            KA+RKL+   R + L+
Sbjct: 251 EKALRKLRQKHRREDLK 267


>gi|158340842|ref|YP_001522010.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311083|gb|ABW32696.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 299

 Score =  186 bits (473), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 96/226 (42%), Positives = 141/226 (62%), Gaps = 2/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+  NLRLV+++AKKY  RG+  +DLIQEG++GL +A EKFD   GY+FSTYA WW
Sbjct: 62  AKHRMICGNLRLVVTIAKKYQKRGMDLIDLIQEGSLGLERAVEKFDPAKGYRFSTYAYWW 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+ITR+IA QS TIRIPVHM +K++++ R  R +S  + R PT +E+  +L + +E +
Sbjct: 122 IRQSITRAIAMQSHTIRIPVHMTEKLNRIKRVRRELSQTLGRTPTHQEMVAELGITLEQL 181

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +K L+  +   P SL   +G +    LGD +ED    SP +   Q  LR      LA L 
Sbjct: 182 QKTLQAAQISNPESLNIRVGKDQEMELGDLLEDLQMPSPNEVVEQDFLRNALWSALAQLN 241

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             E  VL +R+G+    + +L  V +Q  ++RE +R++E  A  KL
Sbjct: 242 DNERTVLILRYGLEDGRERSLYRVSQQMGISREWVRKLEQTAKSKL 287


>gi|299067258|emb|CBJ38455.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CMR15]
          Length = 376

 Score =  186 bits (473), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 101/271 (37%), Positives = 165/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTLAKAGEFPA---RQVMIERNLRLVVSIAKGYLNRGV 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 161 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 220

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    + V+ VL + +   SL+TP   +  +
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPFDLDPGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 281 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 340

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 341 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 371


>gi|146739110|gb|ABQ42602.1| chloroplast RNA-polymerase sigma factor precursor [Heterosigma
           akashiwo]
          Length = 404

 Score =  186 bits (473), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 100/256 (39%), Positives = 153/256 (59%), Gaps = 9/256 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK    AS +K  ++ ANLRLV+S AK Y  RG+ F DL+QEG  GL KA EKFD   G
Sbjct: 138 IRKNLKRASKSKSAIINANLRLVVSTAKAYQYRGVSFQDLVQEGTCGLHKATEKFDPRKG 197

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW+KQ I R++ DQS  +R+PVH+ D +  + R       +  REPT  E+A
Sbjct: 198 FRFSTYATWWIKQGIMRAVTDQSRVVRLPVHVHDALFHIRRAKANFWTEHLREPTLAELA 257

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG--------DEDTSHLGDFIEDKNAVSPLDSAI 605
           +   +  + +     +  +  S++  +G        ++    + D  +D     P ++A 
Sbjct: 258 EATGLTPQKIVFYDTVKDKVSSIDKTVGIGTKTNSMEKSQIAISDMCKDSRN-KPEETAQ 316

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             +LR+  +R++ +L+PRE+ V+RMR+G+      TLEE+G  F VTRER+RQIEA+A+ 
Sbjct: 317 VESLRQDISRLINTLSPREQDVVRMRYGLDDGEIRTLEEIGSIFSVTRERVRQIEARALH 376

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+ P R+ +L+  LD
Sbjct: 377 KLRQPYRNHRLKGQLD 392


>gi|110596913|ref|ZP_01385203.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
 gi|110341600|gb|EAT60060.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
          Length = 299

 Score =  186 bits (473), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 154/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P   E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELATLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHL-PDYGLNRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|78780107|ref|YP_398219.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713606|gb|ABB50783.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 344

 Score =  186 bits (473), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 95/229 (41%), Positives = 148/229 (64%), Gaps = 3/229 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 109 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 168

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P E V
Sbjct: 169 IRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSELAKYVELPEEDV 228

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
           + ++    +P+SLET +GD + + L D +     +   D  I+ + +R     +L  L  
Sbjct: 229 KDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMRGDLHSLLHQLPD 286

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 287 LQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLS 335


>gi|194334634|ref|YP_002016494.1| RNA polymerase sigma-32 subunit RpoH [Prosthecochloris aestuarii
           DSM 271]
 gi|194312452|gb|ACF46847.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris aestuarii
           DSM 271]
          Length = 299

 Score =  186 bits (473), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 153/240 (63%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEFERDPNTKELATVLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D ++  +   P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQ-HDGQKPDHGLTRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM    TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIRSYFGIGMENPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|283780188|ref|YP_003370943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438641|gb|ADB17083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 320

 Score =  186 bits (473), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 98/250 (39%), Positives = 158/250 (63%), Gaps = 11/250 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  + R + + +  G+  A   +  MV ANLRLV+++A+ YT +GL   DLI+EGN+GL
Sbjct: 56  LSARDERELAAAIADGDVRA---RDRMVRANLRLVVNIARGYTGKGLSLQDLIEEGNLGL 112

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E FD  +G +FSTYA +W+KQ+I R++ + + TIRIP +M + + K  R   R++ 
Sbjct: 113 LRAVEGFDPAVGTRFSTYASYWIKQSIKRALINSAKTIRIPAYMVELLSKWRRATARLTE 172

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL--ETPIGDEDTS--HLGDFIEDKNA 597
           ++ R PTPEE+A+ L +     +K L I K+ I +   TP  D+  +   LG+ + D+  
Sbjct: 173 ELGRGPTPEEVARVLGL----AKKKLPIIKKAIRIYNSTPQTDQSEAGWSLGEIVMDERL 228

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            +P D  ++ ++ +    +L ++  RE  VLRMRFG+G  T HTL+E+G+   +TRER+R
Sbjct: 229 KNPEDELVEQDVLKHVMEMLHTMDSREATVLRMRFGLGDTTPHTLKEIGESLGLTRERVR 288

Query: 658 QIEAKAIRKL 667
           QIE +A+ KL
Sbjct: 289 QIETEALGKL 298


>gi|86608620|ref|YP_477382.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557162|gb|ABD02119.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 319

 Score =  186 bits (473), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 102/248 (41%), Positives = 148/248 (59%), Gaps = 8/248 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S   GI ++E + I+   R+GE     AKK MVE NLRLV+S+AK+Y NRGL FLD
Sbjct: 52  VEGWSQRLGIPLAELQQIL---RQGEA----AKKRMVECNLRLVVSIAKRYRNRGLPFLD 104

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG IGL +A EKFD   GYKFSTYA WW++Q++ R I ++   IR+P HM +K+ +V
Sbjct: 105 LIQEGTIGLTRAVEKFDPTRGYKFSTYATWWIRQSVNRGIQNKGRMIRLPAHMYEKVSQV 164

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R  R +S +    P  EE+   L +       + +   E  SL   +GDED + L  FI
Sbjct: 165 KRRYRELSAERGSRPQAEEVFDSLDIGDNYRELITRHMAEMRSLNVGVGDEDGTELQHFI 224

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D++   P++   Q   RE    ++  L+ RE +V+  R+G+  +   TL E+G+   ++
Sbjct: 225 PDEDN-DPVEHLTQLARREEVRALVGQLSERERQVIVARYGLDGSRGLTLREIGEHIGLS 283

Query: 653 RERIRQIE 660
           RER+RQIE
Sbjct: 284 RERVRQIE 291


>gi|72383045|ref|YP_292400.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002895|gb|AAZ58697.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 335

 Score =  186 bits (472), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 100/269 (37%), Positives = 167/269 (62%), Gaps = 10/269 (3%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E++S L  + +I   + + GIS  + +  +   R+       AK+ MV ANLRLV+SVA
Sbjct: 64  TELESDLGEKPDINFFADKAGISPIQLKKKLKSGRR-------AKERMVAANLRLVVSVA 116

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S +IR
Sbjct: 117 KKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRSIR 176

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ + ++K+ +  R +S ++ R PT +E+++ + +P   V+ ++    +P+SLET I
Sbjct: 177 LPIHITEMLNKLKKGQRELSQELSRTPTLKELSEYVELPETDVKDLMSRAGQPVSLETKI 236

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           GD + + L D +   N +      I+++ ++     +L  L   + RVLRMR+GI  +  
Sbjct: 237 GDGEDTILLDLL--SNEIDMPSEQIESDCMKGDLETLLEQLPELQNRVLRMRYGIDGDDP 294

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  +G+   ++R+R+R +E   +R L+
Sbjct: 295 MSLTGIGRVLGISRDRVRNLERDGLRGLR 323


>gi|145219258|ref|YP_001129967.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris
           vibrioformis DSM 265]
 gi|145205422|gb|ABP36465.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeovibrioides
           DSM 265]
          Length = 299

 Score =  186 bits (472), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 155/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELANLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHL-PDHGLNRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V++  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIKSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|313810026|gb|EFS47747.1| sigma-70 region 2 [Propionibacterium acnes HL083PA1]
          Length = 464

 Score =  186 bits (472), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 85/137 (62%), Positives = 109/137 (79%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA W
Sbjct: 273 VAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 332

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E 
Sbjct: 333 WIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEK 392

Query: 563 VRKVLKITKEPISLETP 579
           V +V K  +EPISL TP
Sbjct: 393 VIEVQKYGREPISLHTP 409



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 209 ATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAG 242


>gi|2792523|gb|AAC38577.1| alternative RNA sigma factor RpoS [Ralstonia solanacearum]
          Length = 376

 Score =  186 bits (472), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTRAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 161 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 220

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 281 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 340

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 341 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 371


>gi|149188695|ref|ZP_01866986.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
 gi|148837356|gb|EDL54302.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
          Length = 296

 Score =  186 bits (472), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 100/258 (38%), Positives = 156/258 (60%), Gaps = 5/258 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            K ++    +S  + RHI    R G+   ++A++ ++ +NLRLVI  AK+Y+NRGL F D
Sbjct: 28  FKEVAGHDLLSAEDERHIARKARAGD---TLARQHLINSNLRLVIRTAKRYSNRGLDFYD 84

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIGL++A +KFD  LGY+FSTYA+WW++QAI R+I +Q  TIR+PVH+  +I + 
Sbjct: 85  LINEGNIGLIQAVDKFDPELGYRFSTYAVWWIQQAIDRAIMNQGRTIRVPVHVTKQIREC 144

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGD 590
            + A  +  +   EPT  EIA++     E V K+LK++++ +SL+    +E     HL  
Sbjct: 145 SKAAHELRKEGNHEPTSSEIAERTGRAPEEVSKLLKLSEQSLSLDNGWDEEGDKKDHLQT 204

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             +D     P    +  NL +    ++ SL  ++  +L  RFG+  +   TLE+VG+   
Sbjct: 205 IDDDDVFELPEQDIVTQNLNKALIDLVDSLPDKQRVILHHRFGLLDDDPKTLEQVGEIVG 264

Query: 651 VTRERIRQIEAKAIRKLK 668
           VTRER+RQI+  A+  L+
Sbjct: 265 VTRERVRQIQKSAMETLR 282


>gi|254526733|ref|ZP_05138785.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538157|gb|EEE40610.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 333

 Score =  186 bits (472), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 96/241 (39%), Positives = 153/241 (63%), Gaps = 3/241 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S+++K       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD  
Sbjct: 86  SIIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPA 145

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E
Sbjct: 146 RGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSE 205

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LR 610
           +AK + +P + V+ ++    +P+SLET +GD + + L D +     +   D  I+ + +R
Sbjct: 206 LAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMR 263

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +L  L   + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  
Sbjct: 264 GDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRL 323

Query: 671 S 671
           S
Sbjct: 324 S 324


>gi|33862185|ref|NP_893746.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634403|emb|CAE20088.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 333

 Score =  186 bits (471), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 95/231 (41%), Positives = 149/231 (64%), Gaps = 3/231 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 98  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V
Sbjct: 158 IRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTISELAKYVELPEDDV 217

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
           + ++    +P+SLET +GD + + L D +     +   D  I+ + +R     +L  L  
Sbjct: 218 KDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMRGDLHSLLHQLPD 275

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S S
Sbjct: 276 LQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSES 326


>gi|330946768|gb|EGH47674.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 184

 Score =  186 bits (471), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 96/179 (53%), Positives = 128/179 (71%), Gaps = 3/179 (1%)

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 8   FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 65

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 66  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 125

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 126 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 184


>gi|282880271|ref|ZP_06288987.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
 gi|281305866|gb|EFA97910.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
          Length = 292

 Score =  186 bits (471), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 96/268 (35%), Positives = 166/268 (61%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I  E  +S  E   +   ++KG+ +A     ++ +ANLR V+SVAK+Y N+GL   D
Sbjct: 27  LQEIGREDLLSTEEEIELAQRIKKGDRKAL---DKLTKANLRFVVSVAKQYQNQGLSLPD 83

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 84  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 143

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   + +R P   EIA+++ +P + V   +K   + +S++ P  D D + L D +
Sbjct: 144 NQLQNKFEQEFERRPNSSEIAERIDIPEDKVIDAMKANGKHVSVDAPFSDGDDNSLIDVL 203

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +     +  +  +LR+     L +L  RE  V+   +GI    + TLEE+G ++ +T
Sbjct: 204 PDSDIPMADNELVMESLRKEIADALHTLNERERNVIECFYGIN-QPEMTLEEIGDRYGLT 262

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI  KA+RKL+  +++K+L+S+L
Sbjct: 263 RERVRQIREKALRKLRKNTKNKQLKSYL 290


>gi|318066977|emb|CBY89103.1| RNA polymerase sigma70 factor [Halomonas ventosae]
          Length = 366

 Score =  186 bits (471), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 143/400 (35%), Positives = 202/400 (50%), Gaps = 61/400 (15%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                R + DL +        GF    EG       +  +E+ RD+ +      ++ AK 
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEAEVPEEEPRDEPRRMPTTEDAEAK- 130

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
                     PP++ E   R  ++  + +A   +A+ED  R           E   EL  
Sbjct: 131 ----EETTGGPPDSEEARAR-FEQIREQNAAAQAAIEDHGRGS--------KEAQEELAR 177

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           L      GQ      +  K++ +   +LVG + ++       VEQ+    K IMH     
Sbjct: 178 L------GQ----LFLPIKLVPKHFERLVGQVRIS-------VEQVRAQEKAIMH----- 215

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI--- 413
               +   + R  F++   G E +P W+    DF     K     E      +R +I   
Sbjct: 216 -LCVKKAKVSRKTFIKAFPGSESNPEWLD---DFSAANPKYAARLE-----PLRGDIQRA 266

Query: 414 -KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
            + I+ E     + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 267 QRKIAFEEEMIQLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 326

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 327 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 366


>gi|123967051|ref|YP_001012132.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201417|gb|ABM73025.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 333

 Score =  186 bits (471), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 148/229 (64%), Gaps = 3/229 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 98  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V
Sbjct: 158 IRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTISELAKYVELPEDDV 217

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
           + ++    +P+SLET +GD + + L D +     +   D  I+ + +R     +L  L  
Sbjct: 218 KDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMRGDLHSLLHQLPD 275

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 276 LQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLS 324


>gi|1519644|gb|AAB07555.1| SigA [Chlorobaculum tepidum]
          Length = 299

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 156/240 (65%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELADLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P  +  + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHM-PDYTLNRDSLSLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + +K L+ ++
Sbjct: 238 APREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYNKVLKEYI 297


>gi|973980|gb|AAB05357.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 609

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 107/278 (38%), Positives = 159/278 (57%), Gaps = 38/278 (13%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A++ +V ANLRLV+SVAK++TNRGL   DLIQEG+IGL+K AE+FD+  G++FSTYA
Sbjct: 330 AQRARESLVAANLRLVVSVAKQFTNRGLSMQDLIQEGSIGLIKGAERFDYRTGFRFSTYA 389

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           MWW++QA+ R+IAD S  IRIP  + D   ++ R    +S+ + R+PT  E+A  L + V
Sbjct: 390 MWWIRQAMQRAIADTSRPIRIPSTITDLSVQIYRARLELSSTLGRDPTDAELADFLDISV 449

Query: 561 EGVRKVLKITKE--PISLETPI--------------GDED----------------TSH- 587
           + ++ V   T +   +SL+ P+              GD D                + H 
Sbjct: 450 QRLQDVKLYTNQSATVSLDAPVSRQVTNTCIKSKGTGDTDVFSSKADGKLSKNGYGSRHK 509

Query: 588 -----LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                LGD ++   +VSP      + +R+     L+ L P E  V+RMRFG+      ++
Sbjct: 510 LGDFTLGDTVQTDESVSPEHMMADSLMRDDIECALSLLNPYEREVIRMRFGLDDGRMKSV 569

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +EV   +CV   RIR+IEA+A+RKL+HPS    LR ++
Sbjct: 570 DEVCAYYCVQTSRIRRIEARALRKLRHPSVWHMLRDYI 607


>gi|160872453|ref|ZP_02062585.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
 gi|159121252|gb|EDP46590.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
          Length = 330

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 98/256 (38%), Positives = 155/256 (60%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S  E  +   ++ KG+ +A   +K M+E+NLRLV+ +A+ Y NRGLQFLD
Sbjct: 63  LNEIGFSPLLSAEEEVYYARLIAKGDQDA---RKRMIESNLRLVVKIARHYNNRGLQFLD 119

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GLM A EKFD   G++FSTYA WWV+QAI R+I +Q+ T+R+P+H+  +++  
Sbjct: 120 LIEEGNLGLMHAVEKFDPERGFRFSTYATWWVRQAIERAIMNQARTVRLPIHVVKELNVY 179

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           ++ AR ++ K+  +PT +EIAK L  P E V ++L + +   S++ P   E    L + +
Sbjct: 180 LQAARELTQKLDHKPTSDEIAKWLDRPFEEVERMLGLNEHITSVDAPASSEADKPLLETL 239

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P       NLR+     L  L+  +  V+  R+G+      TLEEVG+   +T
Sbjct: 240 SDNRENDPEHILEGENLRKRLEGWLKQLSTNQREVIARRYGLLGCDRMTLEEVGEVIGLT 299

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQI+ + ++ L+
Sbjct: 300 RERVRQIQVEGLKTLR 315


>gi|301601105|dbj|BAJ13241.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 120/261 (45%), Positives = 151/261 (57%), Gaps = 42/261 (16%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DGD+  + EG E      + A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREG
Sbjct: 17  DGDEEAESEGGE-----LAPAGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREG 70

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKG 197
           EIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K 
Sbjct: 71  EIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKA 130

Query: 198 GF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              F   E     ++    +EK R      DD+    GD++   +  +D+          
Sbjct: 131 APQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEEDEDE-------- 182

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNG 304
                         S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G
Sbjct: 183 --------------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAG 228

Query: 305 QKDEKSSVKCKVLKEKLVKLV 325
                   + K LK++L+  V
Sbjct: 229 TLSSGQERRYKELKDQLITAV 249


>gi|226226116|ref|YP_002760222.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089307|dbj|BAH37752.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 295

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 152/237 (64%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V+ NLR VISVAKKY NRGL  +DLI EGN+GL+ AA KFD   G KF +YA+WW
Sbjct: 58  ALQELVKRNLRFVISVAKKYQNRGLPLIDLIGEGNVGLLTAARKFDPDQGVKFISYAVWW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI  S+A Q  T+R+P++    + ++++ +  +  K++REP+PEE+A+   + V+ V
Sbjct: 118 IRQAILSSLARQGRTVRVPLNRTADLSRIIKASEILRQKLRREPSPEELAQVTGLSVDVV 177

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + +  +    + L+ P+  D D S +  F+ D+   +  + A+   L +   + L++L P
Sbjct: 178 QSLAALNTGDVRLDAPMDPDGDRSLIERFVADEMPDTE-EEAMNRFLTDEIEQALSTLPP 236

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+ +VLR+ FG+    +HTLEE+G    VTRER+RQ+  +A+++L+     + L SF
Sbjct: 237 RDAKVLRLYFGLEGGREHTLEEIGSMLGVTRERVRQLRDRALKRLREGDVGRALSSF 293


>gi|54401876|gb|AAV34623.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401880|gb|AAV34625.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401882|gb|AAV34626.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401884|gb|AAV34627.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401886|gb|AAV34628.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401888|gb|AAV34629.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 85/210 (40%), Positives = 144/210 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 29  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 89  IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 149 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 208

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           +  VL  RFG+      TLE+VG++  +TR
Sbjct: 209 QREVLARRFGLLGYEAATLEDVGREIGLTR 238


>gi|260436019|ref|ZP_05789989.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260413893|gb|EEX07189.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 335

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/228 (40%), Positives = 147/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 100 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P + V
Sbjct: 160 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAEFVELPEDDV 219

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +     + P D   +  L+     +L  L   
Sbjct: 220 KDLMCRARQPVSLEMKVGDGDDTELLELLSGDGDL-PSDQVEEDCLKGDLRSLLGQLPHL 278

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +E+VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 279 QEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRRVS 326


>gi|54401878|gb|AAV34624.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 85/210 (40%), Positives = 144/210 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 29  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 89  IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 149 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 208

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           +  VL  RFG+      TLE+VG++  +TR
Sbjct: 209 QREVLARRFGLLGYEAATLEDVGREIGLTR 238


>gi|114155168|dbj|BAF31034.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|114155684|dbj|BAF31028.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|114155686|dbj|BAF31029.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|114155688|dbj|BAF31030.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|118562877|dbj|BAF37806.1| RNA polymerase major sigma factor [Agrobacterium vitis]
 gi|118562879|dbj|BAF37807.1| RNA polymerase major sigma factor [Agrobacterium vitis]
 gi|301601097|dbj|BAJ13237.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601101|dbj|BAJ13239.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601103|dbj|BAJ13240.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601112|dbj|BAJ13244.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601114|dbj|BAJ13245.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601116|dbj|BAJ13246.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601120|dbj|BAJ13248.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601126|dbj|BAJ13251.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601128|dbj|BAJ13252.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601130|dbj|BAJ13253.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601132|dbj|BAJ13254.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601138|dbj|BAJ13257.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 124/273 (45%), Positives = 156/273 (57%), Gaps = 47/273 (17%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+                        S  +L+AME +LRP+VM  LD IA+ Y++LR LQ
Sbjct: 179 DEDE----------------------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQ 216

Query: 299 DN------AVNGQKDEKSSVKCKVLKEKLVKLV 325
           D       A  G        + K LK++L+  V
Sbjct: 217 DQQVEARLACAGTLSSGQERRYKELKDQLITAV 249


>gi|301601142|dbj|BAJ13259.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 118/247 (47%), Positives = 147/247 (59%), Gaps = 41/247 (16%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+                        S  +L+AME +LRP+VM  LD IA+ Y++LR LQ
Sbjct: 179 DEDE----------------------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQ 216

Query: 299 DNAVNGQ 305
           D  V  +
Sbjct: 217 DQQVEAR 223


>gi|33864638|ref|NP_896197.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33632161|emb|CAE06617.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 332

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/228 (40%), Positives = 148/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 97  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P + V
Sbjct: 157 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTITELAQYVELPEDDV 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +   +A  P D   +  ++     +L  L   
Sbjct: 217 KDLMCRARQPVSLEMKVGDGDDTELLELLAG-DADLPSDQVEEDCMKGDLRSLLGQLPHL 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +E+VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 276 QEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRRIS 323


>gi|149916650|ref|ZP_01905152.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
 gi|149822367|gb|EDM81756.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
          Length = 398

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 98/283 (34%), Positives = 166/283 (58%), Gaps = 6/283 (2%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISE-FRHIVSMVRKGECEASIAKKEMVE 450
           +G++   V+ ++ +I   R ++  +S+      S  F   V   R        AK E V+
Sbjct: 107 DGKYGELVSVDLQAIEANRRDVVRLSITYPPRGSRPFARYVQRARSAHQALCWAKNEFVQ 166

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+++A++Y  R +   DLIQEGNIGLMKA ++FD   GY+FSTYA WW++ +I R
Sbjct: 167 ANLRLVVTIARRYDQRLMPLSDLIQEGNIGLMKAVDRFDGKRGYRFSTYATWWIRHSINR 226

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           ++A++  T+R+P H+   I ++ R  R +  +    P+ +E+AK+  +    VRK+ K++
Sbjct: 227 ALANKGRTVRLPAHVSADIQRIQRATRELETRTGESPSVDELAKETGLSKTRVRKLSKLS 286

Query: 571 -KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
              P+SL+ P  D+D+  L D +ED +A    D     ++ E     +++L P E  +LR
Sbjct: 287 LHNPVSLDAPSSDDDSRGLLDRLEDSSAPRLADMVELEDMSEHLREAMSALEPIEADILR 346

Query: 630 MRFGIGMNTDH----TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+G+G+  +     TL E+G+   ++RERIRQ++ +A+ KL+
Sbjct: 347 RRYGLGVAGEEFEAMTLRELGEMHQLSRERIRQLQQRALNKLR 389


>gi|126697159|ref|YP_001092045.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126544202|gb|ABO18444.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 344

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 96/243 (39%), Positives = 154/243 (63%), Gaps = 3/243 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S+++K       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD  
Sbjct: 97  SVIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPA 156

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E
Sbjct: 157 RGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSE 216

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LR 610
           +AK + +P + V+ ++    +P+SLET +GD + + L D +     +   D  I+ + +R
Sbjct: 217 LAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMR 274

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +L  L   + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  
Sbjct: 275 GDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRL 334

Query: 671 SRS 673
           S +
Sbjct: 335 SHN 337


>gi|157414236|ref|YP_001485102.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388811|gb|ABV51516.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 344

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 96/241 (39%), Positives = 153/241 (63%), Gaps = 3/241 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S+++K       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD  
Sbjct: 97  SIIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPA 156

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E
Sbjct: 157 RGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSE 216

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LR 610
           +AK + +P + V+ ++    +P+SLET +GD + + L D +     +   D  I+ + +R
Sbjct: 217 LAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMR 274

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +L  L   + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  
Sbjct: 275 GDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRL 334

Query: 671 S 671
           S
Sbjct: 335 S 335


>gi|114155164|dbj|BAF31032.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 118/247 (47%), Positives = 147/247 (59%), Gaps = 41/247 (16%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+                        S  +L+AME +LRP+VM  LD IA+ Y++LR LQ
Sbjct: 179 DEDE----------------------SNLSLAAMEAELRPQVMETLDLIADTYKKLRXLQ 216

Query: 299 DNAVNGQ 305
           D  V  +
Sbjct: 217 DQQVEAR 223


>gi|194476921|ref|YP_002049100.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
 gi|171191928|gb|ACB42890.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
          Length = 321

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 102/280 (36%), Positives = 171/280 (61%), Gaps = 6/280 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E +  L+++N IK    E   S+      ++ V++       AK++MV +NLRLV+S+AK
Sbjct: 48  ETEQKLELKNGIKPTQEELANSLDLS---INQVKRKIIHGKRAKEQMVSSNLRLVVSIAK 104

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYT R ++ LDL+QEG IGL++  EKFD   GYKFSTYA WW++Q ITR+I++QS TIR+
Sbjct: 105 KYTKRSMELLDLVQEGTIGLIRGVEKFDPTRGYKFSTYAYWWIRQGITRAISEQSRTIRL 164

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+ ++++K+ +  R +S  + R PT  E+AK + +  + V+++L   K+P+SLE  IG
Sbjct: 165 PIHITEELNKLKKAQRDLSQSLGRTPTVIELAKMIKLTEKEVKELLCHAKQPVSLEMKIG 224

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D D + L + +  +  + P +   +  LR     ++  L   + R+L+MR+G       T
Sbjct: 225 DGDDTVLLELLPSEIEL-PEEYVNRKCLRRDLLALVEQLPEIQVRILKMRYGFDSTEPLT 283

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           L  +G+   ++R+R+R +E   I +L+  S+S  +  +LD
Sbjct: 284 LTGIGRVLGMSRDRVRNLERDGINRLQKLSKS--IEGYLD 321


>gi|301601134|dbj|BAJ13255.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 118/247 (47%), Positives = 147/247 (59%), Gaps = 41/247 (16%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+                        S  +L+AME +LRP+VM  LD IA+ Y++LR LQ
Sbjct: 179 DEDE----------------------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQ 216

Query: 299 DNAVNGQ 305
           D  V  +
Sbjct: 217 DQQVEAR 223


>gi|261749591|ref|YP_003257277.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
 gi|261497684|gb|ACX84134.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
          Length = 287

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 96/250 (38%), Positives = 161/250 (64%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+     S A +++V ANLR V+SVAK+Y N+GL   DLI EGN+GL+K   +FD 
Sbjct: 37  VEYARRAREGDSSAIEKLVNANLRFVVSVAKQYQNQGLSLCDLINEGNLGLIKGILRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+K  +Y +WW++QAI ++IA+QS +IR P +    ++K+++T  ++  +++R P+  
Sbjct: 97  TRGFKCISYVVWWIRQAILQAIAEQSRSIRQPTNKLALLNKILKTLAQLEQELQRTPSAR 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+ L M  + V + +K +   +S++ P+ + + S+L D +    +  P +   + +LR
Sbjct: 157 EIAEHLDMNEKDVEESIKNSGRHVSMDAPLIEGEDSNLYDLVRSDESPRPDEHLERESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +   R+L +L+ RE RV+ + FG+  +   TLEEVG+   +TRER+RQIE+ A+++LKH 
Sbjct: 217 KDIKRILETLSERERRVIILHFGLNGSPPMTLEEVGQSCDLTRERVRQIESIALKRLKHS 276

Query: 671 SRSKKLRSFL 680
           SRSK L+ +L
Sbjct: 277 SRSKILKPYL 286


>gi|123969371|ref|YP_001010229.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199481|gb|ABM71122.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 344

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 148/229 (64%), Gaps = 3/229 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 109 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 168

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V
Sbjct: 169 IRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSELAKYVELPEDDV 228

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
           + ++    +P+SLET +GD + + L D +     +   D  I+ + +R     +L  L  
Sbjct: 229 KDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDLP--DEQIEMDCMRGDLHSLLHQLPD 286

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 287 LQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLS 335


>gi|78211648|ref|YP_380427.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196107|gb|ABB33872.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 335

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/228 (40%), Positives = 147/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 100 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P + V
Sbjct: 160 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAEFVELPEDDV 219

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +     + P D   +  L+     +L  L   
Sbjct: 220 KDLMCRARQPVSLEMKVGDGDDTELLELLSGDGDL-PSDQVEEDCLKGDLRSLLGQLPHL 278

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +E+VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 279 QEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRRVS 326


>gi|307824679|ref|ZP_07654903.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
 gi|307734333|gb|EFO05186.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
          Length = 342

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 86/225 (38%), Positives = 147/225 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GLM A EKFD   G++FSTYA WW
Sbjct: 103 ARKIMIESNLRLVVKISRRYLNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWW 162

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  ++  R +S  ++ EP  E+IA+ L +PV  V
Sbjct: 163 IRQTIERAIMNQTRTIRLPIHIVKEMNTYLKAQRHLSQLLEHEPNAEDIAEHLDIPVNKV 222

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+LK+ +   S++ P G +    L + I D  ++SP +   +  ++    + +  L+ +
Sbjct: 223 EKMLKLNERVTSIDMPGGKDFDKPLVESISDGESLSPAEKIQEDGIKHNIAKWVFQLSEK 282

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  R+G+      TLE+V ++  VTRER+RQI+   ++++K
Sbjct: 283 QREVICRRYGLCGYEGSTLEQVAQELGVTRERVRQIQMDGLKRMK 327


>gi|86134980|ref|ZP_01053562.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
 gi|85821843|gb|EAQ42990.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
          Length = 287

 Score =  185 bits (469), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 89/234 (38%), Positives = 159/234 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V+ANLR V+SVAK+Y N+GL+  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q
Sbjct: 53  KLVKANLRFVVSVAKQYQNQGLKLSDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQ 112

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I +S+A+QS  +R+P++    I K+ +   ++  + +R PT  EIA +L   V  V + 
Sbjct: 113 SIMQSLAEQSRIVRLPLNKIGSISKINKVYSKLEQRNERIPTYVEIANELDTTVRNVAQS 172

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K +   +S++ P  + + S+L + ++   +  P  + ++ +L     R L +L+ +E +
Sbjct: 173 MKNSGRHVSMDAPFREGEDSNLYNVLKSDESPRPDKNLMKQSLDIEIDRALETLSHKEAK 232

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V++M FG+G +T  +L E+G+ F +TRER+RQ++ +AIR+L++ SR++ LR +L
Sbjct: 233 VIKMFFGLGNHTASSLSEIGETFDLTRERVRQVKQRAIRRLQNKSRTEVLRYYL 286


>gi|194337394|ref|YP_002019188.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309871|gb|ACF44571.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 299

 Score =  184 bits (468), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 154/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P   E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELATLLEMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHL-PDYGLNRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V++  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 238 APREADVIKSYFGIGMDNPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKILKEYI 297


>gi|88809912|ref|ZP_01125417.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786102|gb|EAR17264.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 355

 Score =  184 bits (468), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/228 (40%), Positives = 146/228 (64%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 120 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P + V
Sbjct: 180 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEDEV 239

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++++   ++P+SLE  +GD D + L D +     + P +      L+     +L  L   
Sbjct: 240 KELMCRARQPVSLEMKVGDGDDTELLDLLAGDGEL-PSEQVEGECLKGDLRDLLGQLPEL 298

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +ERVLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 299 QERVLRMRYGMDGEEPMSLTGIGRVIGISRDRVRNLERDGLAGLRRLS 346


>gi|300704422|ref|YP_003746025.1| RNA polymerase sigma factor rpos [Ralstonia solanacearum CFBP2957]
 gi|299072086|emb|CBJ43418.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CFBP2957]
          Length = 376

 Score =  184 bits (468), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 101/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTRAKAGEFAA---RQVMIERNLRLVVSIAKGYLNRGV 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 161 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 220

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +  S    R+ + E+IA  L    + V+ VL + +   SL+TP   +  +
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPFDLDPGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 281 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 340

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 341 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 371


>gi|124026787|ref|YP_001015902.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961855|gb|ABM76638.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 335

 Score =  184 bits (468), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 91/226 (40%), Positives = 149/226 (65%), Gaps = 3/226 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 100 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S +IR+P+H+ + ++K+ +  R +S ++ R PT +E+++ + +P   V
Sbjct: 160 IRQGITRAIAEKSRSIRLPIHITEMLNKLKKGQRELSQELSRTPTLKELSEYVELPETDV 219

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
           + ++    +P+SLET IGD + + L D +   N +      I+++ ++     +L  L  
Sbjct: 220 KDLMSRAGQPVSLETKIGDGEDTILLDLL--SNEIDMPSEQIESDCMKGDLETLLEQLPE 277

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+
Sbjct: 278 LQNRVLRMRYGMDGDDPMSLTGIGRVLGISRDRVRNLERDGLRGLR 323


>gi|313673100|ref|YP_004051211.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939856|gb|ADR19048.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 327

 Score =  184 bits (468), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 87/248 (35%), Positives = 157/248 (63%), Gaps = 4/248 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA     +++ +N++ V+S+A +Y N G+   DLI +GN+GL++AA++FD   G
Sbjct: 84  IQQGDQEAL---NKLILSNIKFVVSMANRYKNTGVSLSDLINQGNLGLVEAAKRFDPDKG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF +YA+WW++QA+ + +A+QS T+++P+     ++K+      +S K  REPT EEI+
Sbjct: 141 VKFISYAVWWIRQAMIQLLAEQSGTVKLPIKQASLLYKINEAIETLSKKYHREPTSEEIS 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L +P E +  +L ++K  +S E+PI D +     D +E +  +   D  I   L++T 
Sbjct: 201 EYLNIPKENIENILMVSKNYLSFESPIKDGEDRTFLDLMESR-TIKVEDEVINHTLKDTL 259

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             ++  L  RE ++L+MR+G+      TLEEVG    ++RER+RQIE++A+ KL+  +  
Sbjct: 260 QSLIQELDEREAKILKMRYGLDGENPMTLEEVGNILNISRERVRQIESRALSKLRKKAVK 319

Query: 674 KKLRSFLD 681
           K+L+ +L+
Sbjct: 320 KRLQDYLN 327


>gi|301601136|dbj|BAJ13256.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  184 bits (468), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 119/247 (48%), Positives = 148/247 (59%), Gaps = 41/247 (16%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+                NL         +L+AME +LRP+VM  LD IA+ Y++LR LQ
Sbjct: 179 DEDES-------------NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQ 216

Query: 299 DNAVNGQ 305
           D  V  +
Sbjct: 217 DQQVEAR 223


>gi|160358239|dbj|BAF93440.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601099|dbj|BAJ13238.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  184 bits (468), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 119/255 (46%), Positives = 149/255 (58%), Gaps = 38/255 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEE   +  +LA  A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAK
Sbjct: 19  DEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAK 76

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHG 202
           RIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K    F  
Sbjct: 77  RIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQS 136

Query: 203 TEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            E     ++    +EK R      DD+    GD++   +  +D+                
Sbjct: 137 PEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEEDEDE-------------- 182

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKS 310
                   S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G      
Sbjct: 183 --------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQ 234

Query: 311 SVKCKVLKEKLVKLV 325
             + K LK++L+  V
Sbjct: 235 ERRYKELKDQLITAV 249


>gi|294507979|ref|YP_003572037.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
 gi|294344307|emb|CBH25085.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
          Length = 279

 Score =  184 bits (467), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 96/238 (40%), Positives = 155/238 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  ANLR V+SVAKKY  +GL   DLI EGN GL+KAA++FD   G+KF +YA+WW
Sbjct: 42  ALHKLCRANLRFVVSVAKKYQGQGLSLADLINEGNYGLIKAAKRFDETRGFKFISYAVWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI +++A+QS  +R+P++    I K+ + + R+   + R+P  EE+A++L + V+ V
Sbjct: 102 IRQAILQALAEQSRVVRLPLNRIGTISKIRKASARLQQDLDRKPNIEELAEELEIDVQKV 161

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ +K T   +S++ P  +ED + L D + D++  SP +  +  +++    R L++L  R
Sbjct: 162 REAMKHTSRHLSMDAPFNEEDDNSLLDVLPDEDNDSPDEEMLSESVKIDIERALSALHDR 221

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  + R+ FGIG     TLEE+GK+F +TRER+RQI+ KA+RKL+     + L+   D
Sbjct: 222 EAEITRLYFGIGREHPLTLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQDLQPHTD 279


>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]
          Length = 575

 Score =  184 bits (467), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 153/247 (61%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK     +  K  M+++N+RLVIS+AK Y   G+ F DL+QEG  GL++ AEKFD   G
Sbjct: 322 LRKRITHGTQCKDRMIKSNIRLVISIAKNYQGAGMDFQDLVQEGCRGLVRGAEKFDATKG 381

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  ++P  EE+A
Sbjct: 382 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKQPKNEEVA 441

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  A +  D  ++  +R+  
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIGINLNLKPSEVIADPEAETSEDILMKQFMRQDL 501

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL+ RE++V+R RFG+      TL+E+G+   V+RER+RQI+  A RKLK+  R+
Sbjct: 502 DKVLDSLSTREKQVIRWRFGMEDGRMKTLQEIGETMGVSRERVRQIDTSAFRKLKNKKRN 561

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 562 SHLQQYL 568


>gi|301601107|dbj|BAJ13242.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  184 bits (467), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 121/255 (47%), Positives = 152/255 (59%), Gaps = 30/255 (11%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DGD+  + EG E      + A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREG
Sbjct: 17  DGDEEAESEGGE-----LAPAGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREG 70

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKG 197
           EIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K 
Sbjct: 71  EIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKA 130

Query: 198 GF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
              F   E     ++    +EK R  V+ +E DI +          + +   E+      
Sbjct: 131 APQFQSPEKIEADRKAAEEKEKTR-RVRSSEDDITNVGGDMPMPEEEEEDEDES------ 183

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKS 310
           NL         +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G      
Sbjct: 184 NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQ 234

Query: 311 SVKCKVLKEKLVKLV 325
             + K LK++L+  V
Sbjct: 235 ERRYKELKDQLITAV 249


>gi|221198089|ref|ZP_03571135.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
 gi|221204352|ref|ZP_03577369.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221175209|gb|EEE07639.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221182021|gb|EEE14422.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
          Length = 338

 Score =  184 bits (467), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 103/278 (37%), Positives = 166/278 (59%), Gaps = 13/278 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 60  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 116

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 117 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 176

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 177 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 236

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 237 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 295

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 296 ATLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 333


>gi|301601095|dbj|BAJ13236.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  184 bits (466), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 119/255 (46%), Positives = 149/255 (58%), Gaps = 38/255 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEE   +  +LA  A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAK
Sbjct: 19  DEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAK 76

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHG 202
           RIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K    F  
Sbjct: 77  RIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQS 136

Query: 203 TEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            E     ++    +EK R      DD+    GD++   +  +D+                
Sbjct: 137 PEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEEDEDE-------------- 182

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKS 310
                   S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G      
Sbjct: 183 --------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQ 234

Query: 311 SVKCKVLKEKLVKLV 325
             + K LK++L+  V
Sbjct: 235 ERRYKELKDQLITAV 249


>gi|159897807|ref|YP_001544054.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159890846|gb|ABX03926.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
          Length = 303

 Score =  184 bits (466), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 98/225 (43%), Positives = 143/225 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ANLRLV+S+AK+Y   GL F DLIQEGNIGLM A E+FD   G +FSTYA WW
Sbjct: 74  AHEQLVRANLRLVVSIAKRYRGFGLPFQDLIQEGNIGLMNAIERFDATKGVRFSTYATWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRS+A+Q   IR+PVH  + + KV R   ++   + REP+  EI+  L +P E +
Sbjct: 134 IRQAITRSLANQGRLIRLPVHRWELLIKVRRIETKLLQALGREPSANEISTALGVPEEKI 193

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L I + PISL TP  +E    LGD + D++    L+  + +   + T  +L  L+ +
Sbjct: 194 CDLLSIAQVPISLATPKNEETDMLLGDSLPDEDWEDELECLLTSIDAQYTRAMLNQLSEQ 253

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ VL +R+G+      +L EVG     TR+RI+QIEA A++ L+
Sbjct: 254 EQEVLTLRYGLKDGKSRSLSEVGAVVGRTRQRIQQIEAGALQVLR 298


>gi|83721572|ref|YP_442747.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|167581696|ref|ZP_02374570.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis TXDOH]
 gi|167619812|ref|ZP_02388443.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis Bt4]
 gi|257138958|ref|ZP_05587220.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|83655397|gb|ABC39460.1| RpoS [Burkholderia thailandensis E264]
          Length = 363

 Score =  184 bits (466), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 102/269 (37%), Positives = 165/269 (61%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 85  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 141

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 142 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 201

Query: 529 IHKVVRTARRM-SNKI-------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +  N +       +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 202 LNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 261

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 262 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 320

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 321 ATLEELADEMGLTRERVRQIQQEALVRLK 349


>gi|269104472|ref|ZP_06157168.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161112|gb|EEZ39609.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 294

 Score =  184 bits (466), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 97/238 (40%), Positives = 149/238 (62%), Gaps = 4/238 (1%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK     + +KK M+E+NLRLV+S+AKKY   G+Q  D+I EGNIGL+ A EKFD   G+
Sbjct: 41  RKALVGDAKSKKVMIESNLRLVVSIAKKYRGSGMQLSDMIDEGNIGLITAVEKFDPERGF 100

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW+KQ I R+I +Q+ TIR+PVH+  +I+ ++RT +++      EPT EE+A 
Sbjct: 101 RFSTYATWWIKQTIERAIHNQARTIRLPVHVSKEINTILRTHKQLMKTNNSEPTHEEVAD 160

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN-LRE 611
           +L   VE +  +L      +S +  I  ED++   +  FI D +   P D+ I  N +++
Sbjct: 161 ELDKSVEDISALLSYDAPVMSFDQTISSEDSNSQTMASFISDDSDNGP-DAQIDKNDIQK 219

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  +L  L PR+  +L  RFG+      TL++V ++  +TRERIRQ++  ++ KLK+
Sbjct: 220 LTLTMLEGLNPRDREILCRRFGLMGYEAQTLQQVAEEVGLTRERIRQLQVSSLNKLKN 277


>gi|254252249|ref|ZP_04945567.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
 gi|124894858|gb|EAY68738.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
          Length = 361

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|152995337|ref|YP_001340172.1| RpoD family RNA polymerase sigma factor [Marinomonas sp. MWYL1]
 gi|150836261|gb|ABR70237.1| RNA polymerase, sigma 70 subunit, RpoD family [Marinomonas sp.
           MWYL1]
          Length = 338

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 147/226 (65%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 95  ARTRMIESNLRLVVKISRRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA+ L  PVE V
Sbjct: 155 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEEIAEMLDCPVEDV 214

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +K+L + ++  S++    GD +   L + + D     P       ++  +    L  L+ 
Sbjct: 215 QKMLGLNEKVSSIDATFGGDNNDKSLVEILADTLHQGPEADRQDGDVLNSIELWLDELSE 274

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  V+  RFG+  +   TLE VG +  +TRER+RQI+ +A+RKL+
Sbjct: 275 KQCEVITRRFGLRGHEASTLEHVGAEIGLTRERVRQIQVEALRKLR 320


>gi|325521809|gb|EGD00541.1| RNA polymerase sigma factor RpoS [Burkholderia sp. TJI49]
          Length = 339

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 103/278 (37%), Positives = 166/278 (59%), Gaps = 13/278 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 61  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 117

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 118 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 177

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 178 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 237

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 238 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 296

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 297 ATLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 334


>gi|262340892|ref|YP_003283747.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
 gi|262272229|gb|ACY40137.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
          Length = 287

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 160/246 (65%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E +AS   K +V ANLR V+SVAK+Y N+GL   DLI EGN+GL+K   +FD   G+
Sbjct: 42  RAREGDASAIDK-LVNANLRFVVSVAKQYQNQGLSLCDLINEGNLGLIKGILRFDETRGF 100

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K  +Y +WW++QAI ++IA+QS +IR P +    ++K+++T  ++  +++R P+  EIA+
Sbjct: 101 KCISYVVWWIRQAILQAIAEQSRSIRQPTNKLALLNKILKTLAQLEQELQRTPSAREIAE 160

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L M  + V + +K +   +S++ P+ + + S+L D +    +  P +   + +LR+   
Sbjct: 161 YLDMNEKDVEESIKNSGRHVSMDAPLIEGEDSNLYDLVRSDESPRPDEHLEKESLRKDIK 220

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           R+L +L+ RE RV+ + FG+  +   TLEEVG+   +TRER+RQIE+ A+++LKH SRSK
Sbjct: 221 RILETLSERERRVIILHFGLNGSPPMTLEEVGQSCDLTRERVRQIESIALKRLKHSSRSK 280

Query: 675 KLRSFL 680
            L+ +L
Sbjct: 281 ILKPYL 286


>gi|186682180|ref|YP_001865376.1| SigH/RpoD family RNA polymerase sigma factor [Nostoc punctiforme
           PCC 73102]
 gi|186464632|gb|ACC80433.1| RNA polymerase, sigma 70 subunit SigH, RpoD family [Nostoc
           punctiforme PCC 73102]
          Length = 321

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 142/218 (65%), Gaps = 3/218 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+S+AK+Y  R L+ +DLIQEG +GL +  EKF+  LGY+FSTYA WW
Sbjct: 94  AKHKMITANLRLVVSIAKQYQRRNLELMDLIQEGTLGLERGVEKFNPALGYRFSTYAYWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA Q   IR+P+H+ +K++K+ R  R +S  + R PT  EIA  L++    +
Sbjct: 154 IRQGITRAIAQQGRAIRLPIHINEKLNKIKRVQRELSQTLGRIPTSTEIANALSLKPSQI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTP 622
           R+ L +    ISL+  +  E    L D IED    S  +S I + +L +    +L++L+ 
Sbjct: 214 REFLLLATRTISLDIRVSSEKDLRLQDLIEDYKYSS--NSYITEESLNQEVNSLLSNLSR 271

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +++ +L + FG+    + +L+++G++  ++RER+RQIE
Sbjct: 272 QQQEILNLHFGLTDGEELSLQQIGQRLGISRERVRQIE 309



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
            F   +  + +++T D VR YL+E+G I LL++E EI  A+ ++     +M  L ES
Sbjct: 5   TFSDTKASNTNKATTDTVRAYLKEIGRIPLLTQEQEIIFAQEVQ----QLMTILAES 57


>gi|148238489|ref|YP_001223876.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847028|emb|CAK22579.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 355

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 92/228 (40%), Positives = 145/228 (63%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 120 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S  + R P+  E+A  + +P + V
Sbjct: 180 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQDLGRTPSVTELAAFVELPEDEV 239

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++++   ++P+SLE  +GD D + L D +     + P +      L+     +L  L   
Sbjct: 240 KELMCRARQPVSLEMKVGDGDDTELLDLLAGDGEL-PSEQVEGECLKGDLRDLLGQLPEL 298

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +ERVLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 299 QERVLRMRYGMDGEDPMSLTGIGRVIGISRDRVRNLERDGLAGLRRLS 346


>gi|167836384|ref|ZP_02463267.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis
           MSMB43]
          Length = 366

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 102/269 (37%), Positives = 165/269 (61%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRM-SNKI-------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +  N +       +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSLSTGAAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|161524626|ref|YP_001579638.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|189350618|ref|YP_001946246.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221212761|ref|ZP_03585737.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
 gi|160342055|gb|ABX15141.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia multivorans
           ATCC 17616]
 gi|189334640|dbj|BAG43710.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221166974|gb|EED99444.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
          Length = 361

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|114155170|dbj|BAF31035.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 119/255 (46%), Positives = 149/255 (58%), Gaps = 38/255 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEE   +  +LA  A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAK
Sbjct: 19  DEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAK 76

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHG 202
           RIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K    F  
Sbjct: 77  RIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQS 136

Query: 203 TEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            E     ++    +EK R      DD+    GD++   +  +D+                
Sbjct: 137 PEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEEDEDE-------------- 182

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKS 310
                   S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G      
Sbjct: 183 --------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQ 234

Query: 311 SVKCKVLKEKLVKLV 325
             + K LK++L+  V
Sbjct: 235 ERRYKELKDQLITAV 249


>gi|114155172|dbj|BAF31036.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|160358237|dbj|BAF93439.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601118|dbj|BAJ13247.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601144|dbj|BAJ13260.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  184 bits (466), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 125/267 (46%), Positives = 157/267 (58%), Gaps = 35/267 (13%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           LE    GPE+K    F   E     ++    +EK R  V+ +E DI +          + 
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR-RVRSSEDDITNVGGDMPMPEEEE 177

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---- 300
           +   E+      NL         +L+AME +LRP+VM  LD IA+ Y++LR LQD     
Sbjct: 178 EDEDES------NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEA 222

Query: 301 --AVNGQKDEKSSVKCKVLKEKLVKLV 325
             A  G        + K LK++L+  V
Sbjct: 223 RLACAGTLSSGQERRYKELKDQLITAV 249


>gi|53719139|ref|YP_108125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei K96243]
 gi|53723558|ref|YP_103014.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 23344]
 gi|67639892|ref|ZP_00438721.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|76810144|ref|YP_333760.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121600326|ref|YP_993163.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124385284|ref|YP_001026062.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126440772|ref|YP_001059233.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126450398|ref|YP_001080670.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|126452489|ref|YP_001066500.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|134277449|ref|ZP_01764164.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|167002252|ref|ZP_02268042.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|167719257|ref|ZP_02402493.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei DM98]
 gi|167738254|ref|ZP_02411028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 14]
 gi|167815444|ref|ZP_02447124.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 91]
 gi|167823855|ref|ZP_02455326.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 9]
 gi|167845396|ref|ZP_02470904.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei B7210]
 gi|167893937|ref|ZP_02481339.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 7894]
 gi|167902387|ref|ZP_02489592.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei NCTC
           13177]
 gi|167910629|ref|ZP_02497720.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 112]
 gi|167918658|ref|ZP_02505749.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei BCC215]
 gi|217421435|ref|ZP_03452939.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|226197238|ref|ZP_03792815.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237812557|ref|YP_002897008.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|242315690|ref|ZP_04814706.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|254178572|ref|ZP_04885227.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|254179542|ref|ZP_04886141.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|254189067|ref|ZP_04895578.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|254197294|ref|ZP_04903716.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|254199960|ref|ZP_04906326.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|254206293|ref|ZP_04912645.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|254261861|ref|ZP_04952915.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
 gi|254297419|ref|ZP_04964872.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|254358292|ref|ZP_04974565.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|28394113|gb|AAO34104.1| rpoS [Burkholderia pseudomallei]
 gi|52209553|emb|CAH35506.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52426981|gb|AAU47574.1| RNA polymerase sigma factor [Burkholderia mallei ATCC 23344]
 gi|76579597|gb|ABA49072.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121229136|gb|ABM51654.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124293304|gb|ABN02573.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126220265|gb|ABN83771.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126226131|gb|ABN89671.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|126243268|gb|ABO06361.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|134251099|gb|EBA51178.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|147749556|gb|EDK56630.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|147753736|gb|EDK60801.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|148027419|gb|EDK85440.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|157807858|gb|EDO85028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|157936746|gb|EDO92416.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|160699611|gb|EDP89581.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|169654035|gb|EDS86728.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|184210082|gb|EDU07125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|217395177|gb|EEC35195.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|225930617|gb|EEH26627.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237506433|gb|ACQ98751.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|238520504|gb|EEP83963.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|242138929|gb|EES25331.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|243062069|gb|EES44255.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|254220550|gb|EET09934.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
          Length = 359

 Score =  183 bits (465), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 81  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 137

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 138 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 197

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 198 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 257

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 258 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 316

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 317 ATLEELADEMGLTRERVRQIQQEALVRLK 345


>gi|194290015|ref|YP_002005922.1| RNA polymerase sigma factor rpos [Cupriavidus taiwanensis LMG
           19424]
 gi|193223850|emb|CAQ69859.1| RNA polymerase sigma factor rpoS [Cupriavidus taiwanensis LMG
           19424]
          Length = 395

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 100/271 (36%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ + G+     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 123 VQHYLNRISIKPLLSAPEELHFSTLAKDGDF---AARQVMIERNLRLVVSIAKGYLNRGV 179

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 180 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 239

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 240 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 299

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 300 SLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 359

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 360 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 390


>gi|114155166|dbj|BAF31033.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 119/241 (49%), Positives = 148/241 (61%), Gaps = 29/241 (12%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           LE    GPE+K    F   E     ++    +EK R  V+ +E DI +          + 
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR-RVRSSEDDITNVGGDMPMPEEEE 177

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           +                ED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD  V  
Sbjct: 178 ED---------------EDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEA 222

Query: 305 Q 305
           +
Sbjct: 223 R 223


>gi|167587040|ref|ZP_02379428.1| RNA polymerase sigma factor RpoS [Burkholderia ubonensis Bu]
          Length = 360

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 198

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 199 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 258

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 259 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 317

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 318 ATLEELADEMGLTRERVRQIQQEALVRLK 346


>gi|323453176|gb|EGB09048.1| hypothetical protein AURANDRAFT_53467 [Aureococcus anophagefferens]
          Length = 468

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 101/249 (40%), Positives = 154/249 (61%), Gaps = 14/249 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+ ANLRLV+S++K+Y +RGL F D+IQEG  GL +A EKFD   G+KFSTYA WW
Sbjct: 213 AKAAMINANLRLVVSISKRYQHRGLHFQDVIQEGTFGLTRAVEKFDPEKGFKFSTYATWW 272

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+ R+IADQS TIR+PVH+ D++  + +  R +  ++ RE T EE+A KL +    +
Sbjct: 273 IKQAVMRAIADQSRTIRLPVHVHDQLQSMKKVTRDLGAELGRECTDEELAGKLDLATTKM 332

Query: 564 RKVLKITKEPISLETPI------------GDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             +    ++ +S++  +            G  + + L D + D  A+ P + A   +L+ 
Sbjct: 333 DWLRSCERQTMSMDATVRVSGKGSSAGTGGAGNEAKLSDNLADAAAL-PDERAETKSLQS 391

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               +L  +L+ RE  V+R+RFG+      TLEE+G  F +TRER+RQIEA+A+ KL+ P
Sbjct: 392 DIHGLLRTALSDRECDVVRLRFGLDDGKARTLEEIGTVFSITRERVRQIEARALHKLRQP 451

Query: 671 SRSKKLRSF 679
            R+  L ++
Sbjct: 452 YRNHMLEAY 460


>gi|284031338|ref|YP_003381269.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810631|gb|ADB32470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 316

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 143/225 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  V ANLRLV+S+A++Y    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 83  AQQRFVTANLRLVVSIARRYGRSQMPLLDLVQEGNTGLIRAVEKFDYRKGFKFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR IA Q+  +R+PVH+ ++++++    R +  K+ REP  +EIA +L +  E V
Sbjct: 143 VRQAITRGIAQQARVVRLPVHVVEQLNQIGSARRTLERKLGREPEIDEIAAELDLDEERV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++I ++ ISL+ PI DE  + LGD I  + A  P      A+ R     ++  L PR
Sbjct: 203 TELIRIGRDHISLDNPIDDEGETSLGDLIAAETAPGPDQLVADASDRSGLFSLVDQLDPR 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              V+R R+G+       L ++G    ++ ER+RQIE +A+ +L+
Sbjct: 263 SADVIRRRYGLHDGRQAKLADIGAVHGISAERVRQIEREALGRLR 307


>gi|73541783|ref|YP_296303.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha JMP134]
 gi|72119196|gb|AAZ61459.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 391

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 100/271 (36%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ + G+  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 119 VQHYLNRISIKPLLSAPEELHFSTLAKDGDFSA---RQVMIERNLRLVVSIAKGYLNRGV 175

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 176 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 235

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 236 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 295

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 296 SLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 355

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 356 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 386


>gi|172060780|ref|YP_001808432.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria MC40-6]
 gi|171993297|gb|ACB64216.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MC40-6]
          Length = 361

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|107029001|ref|YP_626096.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia AU 1054]
 gi|105898165|gb|ABF81123.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
          Length = 362

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DPDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|301601109|dbj|BAJ13243.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 119/255 (46%), Positives = 149/255 (58%), Gaps = 38/255 (14%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DEE   +  +LA  A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAK
Sbjct: 19  DEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAK 76

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGF-FHG 202
           RIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K    F  
Sbjct: 77  RIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQS 136

Query: 203 TEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            E     ++    +EK R      DD+    GD++   +  +D+                
Sbjct: 137 PEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEEDEDE-------------- 182

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKS 310
                   S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G      
Sbjct: 183 --------SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQ 234

Query: 311 SVKCKVLKEKLVKLV 325
             + K LK++L+  V
Sbjct: 235 ERRYKELKDQLITAV 249


>gi|301601140|dbj|BAJ13258.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 119/241 (49%), Positives = 148/241 (61%), Gaps = 29/241 (12%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           LE    GPE+K    F   E     ++    +EK R  V+ +E DI +          + 
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR-RVRSSEDDITNVGGDMPMPEEEE 177

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           +   E+      NL         +L+AME +LRP+VM  LD IA+ Y++LR LQD  V  
Sbjct: 178 EDEDES------NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEA 222

Query: 305 Q 305
           +
Sbjct: 223 R 223


>gi|193212077|ref|YP_001998030.1| RNA polymerase sigma 32 subunit RpoH [Chlorobaculum parvum NCIB
           8327]
 gi|193085554|gb|ACF10830.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobaculum parvum NCIB
           8327]
          Length = 299

 Score =  183 bits (465), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 91/240 (37%), Positives = 154/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELANLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P  +  + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHM-PDHTLNRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V+R  FGIGM    TLEE+G++F +TRER+RQI+ KAIR+L+  +  + L+ ++
Sbjct: 238 APREADVIRSYFGIGMENPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYKEVLKEYI 297


>gi|88808921|ref|ZP_01124430.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786863|gb|EAR18021.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 322

 Score =  183 bits (465), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 91/226 (40%), Positives = 146/226 (64%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 86  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P + V
Sbjct: 146 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEDEV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++++   ++P+SLE  +GD D + L D +     + P +      L+     +L  L   
Sbjct: 206 KELMCRARQPVSLEMKVGDGDDTELLDLLAGDGEL-PSEQVEGECLKGDLRDLLGQLPEL 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +ERVLRMR+G+      +L  + K   ++R+R R++E + ++ L+ 
Sbjct: 265 QERVLRMRYGMDGEEPMSLTGIAKTLKMSRDRTRRLEREGLQSLRQ 310


>gi|270668763|ref|ZP_06222551.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
 gi|270316653|gb|EFA28454.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
          Length = 151

 Score =  183 bits (465), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 90/147 (61%), Positives = 113/147 (76%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D I +  N +      T ++I++ R I   V +GE +A  AKKEMVEANLRLVIS+AKKY
Sbjct: 5   DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKY 64

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 65  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 124

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPE 550
           HM + I+K+ R +R++  ++ RE TPE
Sbjct: 125 HMIETINKLNRISRQLLQEMGREATPE 151


>gi|78186275|ref|YP_374318.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
 gi|78166177|gb|ABB23275.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
          Length = 299

 Score =  183 bits (465), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 91/240 (37%), Positives = 154/240 (64%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA
Sbjct: 59  AKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYA 118

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  
Sbjct: 119 VWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEFERDPNTKELANLLDMDS 178

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V   LKI    +S++ P    D + L D +++   + P     + +L     R L+ L
Sbjct: 179 QDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHL-PDHGLNRDSLTLEVERSLSVL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            PRE  V++  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  +  K L+ ++
Sbjct: 238 APREADVIKSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRTSAYCKVLKEYI 297


>gi|78066590|ref|YP_369359.1| RNA polymerase sigma factor RpoS [Burkholderia sp. 383]
 gi|77967335|gb|ABB08715.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 362

 Score =  183 bits (465), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|288940519|ref|YP_003442759.1| RNA polymerase sigma-70 subunit RpoD subfamily [Allochromatium
           vinosum DSM 180]
 gi|288895891|gb|ADC61727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Allochromatium
           vinosum DSM 180]
          Length = 338

 Score =  183 bits (465), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 84/238 (35%), Positives = 149/238 (62%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R  +   + A++ M+  NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 86  IRFARLAQAGDNAARQRMIVCNLRLVVKIARRYLNRGLPLLDLIEEGNLGLIRAVEKFDP 145

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ T+R+P+H+  +I+  ++ +R+++  +  +PT E
Sbjct: 146 ERGFRFSTYATWWIRQTIERAIMNQTRTVRLPIHVVKEINIYLKASRQLAQSLDHDPTSE 205

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +IA+ L  P+  V+++L + +   S++TP   +    L D ++D  +  P +     ++ 
Sbjct: 206 DIAQLLDRPINEVKRMLGLNERITSVDTPYSKDADKPLVDMLQDDGSSDPTERIQDDDIH 265

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  L  ++  V+  RFG+  + + TLE V ++  VTRER+RQI+  A+R+L+
Sbjct: 266 VNIEHWLGLLNDKQREVVERRFGLHGHENSTLESVARELGVTRERVRQIQMDALRRLR 323


>gi|113868347|ref|YP_726836.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha H16]
 gi|113527123|emb|CAJ93468.1| DNA-directed RNA polymerase sigma subunit (sigma38) [Ralstonia
           eutropha H16]
          Length = 392

 Score =  183 bits (464), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 100/271 (36%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ + G+  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 120 VQHYLNRISIKPLLSAPEELHFSTLAKDGDFAA---RQVMIERNLRLVVSIAKGYLNRGV 176

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 177 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 236

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 237 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 296

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 297 SLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 356

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 357 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 387


>gi|115351809|ref|YP_773648.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria AMMD]
 gi|115281797|gb|ABI87314.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 361

 Score =  183 bits (464), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|206560255|ref|YP_002231019.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia J2315]
 gi|198036296|emb|CAR52192.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 362

 Score =  183 bits (464), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|171321354|ref|ZP_02910311.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
 gi|171093372|gb|EDT38562.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
          Length = 361

 Score =  183 bits (464), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|83815083|ref|YP_446059.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
 gi|83756477|gb|ABC44590.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
          Length = 313

 Score =  183 bits (464), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 96/238 (40%), Positives = 155/238 (65%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  ANLR V+SVAKKY  +GL   DLI EGN GL+KAA++FD   G+KF +YA+WW
Sbjct: 76  ALHKLCRANLRFVVSVAKKYQGQGLSLADLINEGNYGLIKAAKRFDETRGFKFISYAVWW 135

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI +++A+QS  +R+P++    I K+ + + R+   + R+P  EE+A++L + V+ V
Sbjct: 136 IRQAILQALAEQSRVVRLPLNRIGTISKIRKASARLQQDLDRKPNIEELAEELEIDVQKV 195

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ +K T   +S++ P  +ED + L D + D++  SP +  +  +++    R L++L  R
Sbjct: 196 REAMKHTSRHLSMDAPFNEEDDNSLLDVLPDEDNDSPDEEMLSESVKIDIERALSALHDR 255

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  + R+ FGIG     TLEE+GK+F +TRER+RQI+ KA+RKL+     + L+   D
Sbjct: 256 EAEITRLYFGIGREHPLTLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQDLQPHTD 313


>gi|170703618|ref|ZP_02894360.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
 gi|170131475|gb|EDT00061.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
          Length = 361

 Score =  183 bits (464), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|94311053|ref|YP_584263.1| RNA polymerase sigma factor RpoS [Cupriavidus metallidurans CH34]
 gi|93354905|gb|ABF08994.1| RNA polymerase sigma 38 (sigma S) factor [Cupriavidus metallidurans
           CH34]
          Length = 386

 Score =  183 bits (464), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 100/271 (36%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ + G+  A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 114 VQHYLNRISIKPLLSAPEELHFSTLAKGGDFSA---RQVMIERNLRLVVSIAKGYLNRGV 170

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 171 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 230

Query: 529 IHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 231 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 290

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 291 SLLDFLSDEHNAAPDQEVAHRELENLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 350

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 351 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 381


>gi|114155174|dbj|BAF31037.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 119/241 (49%), Positives = 148/241 (61%), Gaps = 29/241 (12%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           LE    GPE+K    F   E     ++    +EK R  V+ +E DI +          + 
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTR-RVRSSEDDITNVGGDMPMPEEEE 177

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           +   E+      NL         +L+AME +LRP+VM  LD IA+ Y++LR LQD  V  
Sbjct: 178 EDEDES------NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEA 222

Query: 305 Q 305
           +
Sbjct: 223 R 223


>gi|297626467|ref|YP_003688230.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922232|emb|CBL56802.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 309

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 90/229 (39%), Positives = 141/229 (61%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A +  V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTY
Sbjct: 75  EGERAMQHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTY 134

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+QAI+R IA Q   +R+PVH+ ++++++    R +  ++ REP   EIA +L + 
Sbjct: 135 ATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQISAVRRNLERQLGREPEVSEIANELGLE 194

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              V  +++ ++E +SL+ P+ D+  + LGD I  + A  P +  +    R     +LA+
Sbjct: 195 ENKVIDLIRYSREHVSLDAPVEDDGDTSLGDLIARETAPGPDELVLDLEDRSRLEALLAN 254

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R   V+R R+G+       L ++GK + +T ER+RQIE  A+ +L+
Sbjct: 255 LDDRSADVMRRRYGLLDGHQAKLSDIGKVWGITAERVRQIERAALNQLR 303


>gi|301601122|dbj|BAJ13249.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601124|dbj|BAJ13250.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 118/242 (48%), Positives = 146/242 (60%), Gaps = 41/242 (16%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+                NL         +L+AME +LRP+VM  LD IA+ Y++LR LQ
Sbjct: 179 DEDES-------------NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQ 216

Query: 299 DN 300
           D 
Sbjct: 217 DQ 218


>gi|281420881|ref|ZP_06251880.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405173|gb|EFB35853.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 287

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 172/271 (63%), Gaps = 9/271 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I+ E  +S  E   +   +RKG+  A    + + +ANLR V+SVAK+Y N+G+   D
Sbjct: 22  LQDIAHEELLSTDEEVELAQRIRKGDRRAL---ERLTKANLRFVVSVAKQYQNQGISLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+
Sbjct: 79  LINEGNVGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRLVRLPLNQVGSVNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGD 590
            R   +   + +R+P+ +EIA ++ +P + +   +K T     +S++ P  D++   + D
Sbjct: 139 NREMSKFEQEFERKPSVDEIADRIDLPEDKIEDAMKATSTSRHLSVDAPFSDDEDGSMLD 198

Query: 591 FIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            +   N+  P D  +Q  +LR    R+L +L  ++++++   +GIG   + TLEE+G ++
Sbjct: 199 LM--ANSDDPTDKELQTESLRAEIERLLKTLPDKDQKIIAAFYGIG-TPELTLEEIGTKY 255

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER+RQI+ K IR+L++ +  K L+S+L
Sbjct: 256 HLTRERVRQIKEKTIRRLRNKTTDKLLKSYL 286


>gi|169245684|gb|ACA50888.1| RpoD [Agrobacterium tumefaciens]
 gi|169245688|gb|ACA50890.1| RpoD [Agrobacterium tumefaciens str. C58]
 gi|169245694|gb|ACA50893.1| RpoD [Agrobacterium tumefaciens]
          Length = 174

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 96/174 (55%), Positives = 121/174 (69%), Gaps = 6/174 (3%)

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ
Sbjct: 1   QVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQ 60

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +   
Sbjct: 61  NRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAA 120

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             WK F   E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKK
Sbjct: 121 RGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKK 174


>gi|114155176|dbj|BAF31038.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 115/229 (50%), Positives = 143/229 (62%), Gaps = 24/229 (10%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DGD+  + EG E      + A N++V   K+K+  DR TDDPVRMYLREMGS+ELLSREG
Sbjct: 17  DGDEEAESEGGE-----LAPAGNTAVATAKKKEPTDR-TDDPVRMYLREMGSVELLSREG 70

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKG 197
           EIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE    GPE+K 
Sbjct: 71  EIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKA 130

Query: 198 GF-FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
              F   E     ++    +EK R  V+ +E DI +          + +   E+      
Sbjct: 131 APQFQSPEKIEADRKAAEEKEKTR-RVRSSEDDITNVGGDMPMPEEEEEDEDES------ 183

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
           NL         +L+AME +LRP+VM  LD IA+ Y++LR LQD  V  +
Sbjct: 184 NL---------SLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEAR 223


>gi|113954561|ref|YP_729335.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881912|gb|ABI46870.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 335

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 94/256 (36%), Positives = 156/256 (60%), Gaps = 8/256 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++   G+S ++ +  +   R+       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQ
Sbjct: 79  VAKAAGVSAAQLKRKLQAGRR-------AKERMVAANLRLVVSVAKKYTKRNMELLDLIQ 131

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ + 
Sbjct: 132 EGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKG 191

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +S ++ R P+  E+A  + +P E V+ ++   ++P+SLE  +GD D + L + +   
Sbjct: 192 QRELSQELGRTPSVTELASFVELPEEEVKDLMCRARQPVSLEMKVGDGDDTELLELLAGD 251

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
             + P D      L+     +L+ L   + +VLRMR+G+      +L  +G+   ++R+R
Sbjct: 252 GEL-PSDQVEGECLKGDLRDLLSQLPELQGKVLRMRYGMDGEEPMSLTGIGRIIGISRDR 310

Query: 656 IRQIEAKAIRKLKHPS 671
           +R +E   +  L+  S
Sbjct: 311 VRNLERDGLAGLRRLS 326


>gi|167562539|ref|ZP_02355455.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis EO147]
 gi|167569723|ref|ZP_02362597.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis C6786]
          Length = 362

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 165/269 (61%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE +A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFDA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRM-SNKI-------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +  N +       +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|169245678|gb|ACA50885.1| RpoD [Agrobacterium tumefaciens]
 gi|169245698|gb|ACA50895.1| RpoD [Agrobacterium tumefaciens]
 gi|169245702|gb|ACA50897.1| RpoD [Agrobacterium rhizogenes]
 gi|169245712|gb|ACA50902.1| RpoD [Agrobacterium tumefaciens]
          Length = 174

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 96/174 (55%), Positives = 121/174 (69%), Gaps = 6/174 (3%)

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ
Sbjct: 1   QVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQ 60

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +   
Sbjct: 61  NRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSIANLAA 120

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             WK F   E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKK
Sbjct: 121 RGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKK 174


>gi|20330084|emb|CAD30008.1| RNA polymerase sigma factor [Burkholderia cepacia]
          Length = 362

 Score =  182 bits (463), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|87123242|ref|ZP_01079093.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86168962|gb|EAQ70218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 309

 Score =  182 bits (462), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 95/235 (40%), Positives = 149/235 (63%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 74  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 133

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V
Sbjct: 134 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAGFVELPEEEV 193

Query: 564 RKVLKITKEPISLETPIGDEDTSHL-------GDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + ++   ++P+SLE  +GD D + L       G+  E++  V      ++ +LR+    +
Sbjct: 194 KDLMCRARQPVSLEMKVGDGDDTELLELLAGDGELPEEQVEV----ECLKGDLRD----L 245

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L  L   + RVLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 246 LEQLPDLQRRVLRMRYGMDGEEPMSLTGIGRVIGISRDRVRNLERDGLAGLRRLS 300


>gi|116689841|ref|YP_835464.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia HI2424]
 gi|170733180|ref|YP_001765127.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia MC0-3]
 gi|116647930|gb|ABK08571.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|169816422|gb|ACA91005.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           MC0-3]
          Length = 362

 Score =  182 bits (462), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 261 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|319955411|ref|YP_004166678.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424071|gb|ADV51180.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 286

 Score =  182 bits (462), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 90/247 (36%), Positives = 159/247 (64%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A   +V ANLR V+SVAK+Y   GL+  DLI EGN+GL+KAA++FD   G
Sbjct: 43  IREGD---QVALNTLVNANLRFVVSVAKQYQGSGLRLSDLINEGNVGLVKAAKRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++I++ S  +R+P++   +I K+ +    +   ++R P   EIA
Sbjct: 100 FKFISYAVWWIRQSILQAISELSRMVRLPLNKIGEIGKINKVFSYLEQSLQRPPNAIEIA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L M    V+  +K T + +S++ P  + ++S+L + ++ K A SP  + +Q +L    
Sbjct: 160 RELDMSTSQVKLAMKNTGKHLSMDAPFAEGESSNLYNVVQSKEANSPDTNLMQESLSSDI 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L++L  RE  ++R+ +GIG     +L E+G+ F ++RER+RQI  KAIR L+  S+ 
Sbjct: 220 GDLLSTLPSRESDIIRLYYGIGEKAPMSLTEIGEIFDISRERVRQIREKAIRVLRRKSQK 279

Query: 674 KKLRSFL 680
           + L+++L
Sbjct: 280 EVLKAYL 286


>gi|148239880|ref|YP_001225267.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 7803]
 gi|147848419|emb|CAK23970.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 322

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 91/226 (40%), Positives = 144/226 (63%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 86  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S  + R P+  E+A  + +P + V
Sbjct: 146 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQDLGRTPSVTELAAFVELPEDEV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++++   ++P+SLE  +GD D + L D +     + P +      L+     +L  L   
Sbjct: 206 KELMCRARQPVSLEMKVGDGDDTELLDLLAGDGEL-PSEQVEGECLKGDLRDLLGQLPEL 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +ERVLRMR+G+      +L  + K   ++R+R R++E + +  L+ 
Sbjct: 265 QERVLRMRYGMDGEDPMSLTGIAKTLKMSRDRTRRLEREGLESLRQ 310


>gi|86130344|ref|ZP_01048944.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332293359|ref|YP_004431968.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|85819019|gb|EAQ40178.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332171445|gb|AEE20700.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 288

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 101/273 (36%), Positives = 166/273 (60%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N ++ +S    I+  E   +   ++KG+  A  A   +  ANLR VISVAK+Y N+GL
Sbjct: 18  LNNYLQDVSKIDLITAEEEVELAQRIQKGDERALDA---LTRANLRFVISVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+ + T+R+P++   +
Sbjct: 75  SLSDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEHARTVRLPLNKIGE 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSH 587
           I K+ +    +    +R+PT  EIAK L +  E V+  LK     +S++ P  + E+ ++
Sbjct: 135 ISKINKAMVYLQQVHERKPTSGEIAKYLDISEEKVKISLKNVSRSLSMDAPFAEGENDNN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +    +  P    +Q +L     R L +LT +E  V+R+ +G+G     TL+E+G 
Sbjct: 195 LYDVLSSSESPRPDRELMQESLSIEINRALDTLTEKEAEVVRLNYGLGNQPAMTLQEIGD 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  KAI++L+H S+SK L  +L
Sbjct: 255 IFDLSRERVRQIREKAIKRLRHTSKSKILMKYL 287


>gi|238027063|ref|YP_002911294.1| RNA polymerase sigma factor RpoS [Burkholderia glumae BGR1]
 gi|76057940|emb|CAJ30487.1| stationary phase sigma factor [Burkholderia plantarii]
 gi|121663602|emb|CAM12359.1| stationary phase sigma factor [Burkholderia glumae]
 gi|237876257|gb|ACR28590.1| Stationary phase sigma factor [Burkholderia glumae BGR1]
          Length = 364

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 162/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 86  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 142

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 143 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 202

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE   ++IA       E V  +L + +   SL+ P+
Sbjct: 203 LNQVLRAKRHLEKNSMSTGEAAERREAGIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 262

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 263 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 321

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 322 ATLEELADEMGLTRERVRQIQQEALVRLK 350


>gi|239934542|emb|CAR94585.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 297

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 121/308 (39%), Positives = 183/308 (59%), Gaps = 26/308 (8%)

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+A LCESP+TFQA+I+WR+ELN+   LLR+IIDL+A +G   KG  
Sbjct: 6   IAIAKRIEAGRDTMIAGLCESPVTFQAIIVWREELNEERVLLRDIIDLDATLG---KG-- 60

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                    Q   +++      +    E  +++ A   +++ ++ D+P  +A   + + D
Sbjct: 61  -------PGQPGNEANNANAGGNAASNEA-VKAEAPAKQENAAEGDAPKTDASEADVSDD 112

Query: 260 EDEDDSAH--TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ--------KDEK 309
           +D+DD+    +L+AME  LRP+V+   D+IA  Y++L  L++  + G+        + EK
Sbjct: 113 DDDDDADSNMSLAAMEALLRPQVLEIFDKIAANYKKLHKLEEARIEGKVGNDPLSTQQEK 172

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
             VK   L+++ V LV SL LN +RI+ LV+ +Y I+KR++  EG LLRLA  +G+ R  
Sbjct: 173 RYVK---LRDETVTLVQSLHLNNNRIEALVDLMYSINKRLIGFEGRLLRLADYHGVDRAE 229

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL++++  ELD +W           W+ F   E   I +IR+EI  IS ETG+ I EFR 
Sbjct: 230 FLDQYRSHELDANWSRRVGRLKSKGWQEFTKKERVQIKEIRDEIAQISQETGLEIGEFRR 289

Query: 430 IVSMVRKG 437
           IV  V+KG
Sbjct: 290 IVHTVQKG 297


>gi|330817175|ref|YP_004360880.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
 gi|327369568|gb|AEA60924.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
          Length = 366

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 88  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 145 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 204

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 205 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 264

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 265 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNNIEP 323

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 324 ATLEELADEMGLTRERVRQIQQEALVRLK 352


>gi|254432550|ref|ZP_05046253.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627003|gb|EDY39562.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 319

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 95/233 (40%), Positives = 146/233 (62%), Gaps = 6/233 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 79  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V
Sbjct: 139 IRQGITRAIAEKSRTIRLPIHITETLNKLKKGQRELSQELGRTPTVTELAGYVELPEEEV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + +L   ++P+SLET +GD + + L D +     + P +      L+     +L  L   
Sbjct: 199 KDLLCRARQPVSLETKVGDGEDTELLDLLAGDGEL-PEERVDGECLKGDLRALLEQLPEL 257

Query: 624 EERVLRMRFGIG-----MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           + RVL+MR+GI      M    +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 258 QGRVLKMRYGIDPQSAEMAEPMSLTGIGRILGISRDRVRNLERDGLAGLRRLS 310


>gi|88854620|ref|ZP_01129287.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88816428|gb|EAR26283.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 1108

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 98/240 (40%), Positives = 144/240 (60%), Gaps = 3/240 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A      +N RLV S+A++Y N GL + DLIQEG +GL++A +KFD+  G+KFSTYA WW
Sbjct: 683 AFARFAASNYRLVFSIARRYVNNGLDYADLIQEGALGLLRAIQKFDYMKGFKFSTYATWW 742

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR++AD   TIRIPVHM ++ +K+ + AR    +  R+PT  E+A    +  +  
Sbjct: 743 VRQAITRALADLGSTIRIPVHMVEQQNKLRQAARSFELQNDRKPTISELAAGAEVTEQDA 802

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            + L      +S++  +   E    L + + D++ V+P+D  I A  R     VL++L  
Sbjct: 803 SRALGYEYSFLSIDKELDPGEGFGSLHNLLVDES-VAPVDLLIHAEFRGAMNNVLSALPK 861

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK-KLRSFLD 681
           RE   ++MRFGIG     TL+ +G  F VTRERIRQIE K +  L+  +  + +L  FLD
Sbjct: 862 RESTTIQMRFGIGGQDPATLDHIGDIFGVTRERIRQIEKKTMESLRSSAEVQGRLGDFLD 921


>gi|116074383|ref|ZP_01471645.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069688|gb|EAU75440.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 91/228 (39%), Positives = 145/228 (63%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 106 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V
Sbjct: 166 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAEFVELPEEEV 225

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +     + P +      L+     +L  L   
Sbjct: 226 KDLMCRARQPVSLEMKVGDGDDTELLELLAGDGEL-PSEQVEGECLKGDLRDLLEQLPEL 284

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           + +VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 285 QRKVLRMRYGMNGEDPMSLTGIGRIIGISRDRVRNLERDGLAGLRRLS 332


>gi|134295851|ref|YP_001119586.1| RNA polymerase sigma factor RpoS [Burkholderia vietnamiensis G4]
 gi|134139008|gb|ABO54751.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 361

 Score =  181 bits (460), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 100/269 (37%), Positives = 163/269 (60%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE +A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFDA---RQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
             +  S L D + D  + SP D+ +Q    ET TR  L+ L+ +   V+  RFG+     
Sbjct: 260 DLDPASSLLDLLPDDQSQSP-DAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEP 318

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 319 ATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|169245674|gb|ACA50883.1| RpoD [Agrobacterium tumefaciens]
 gi|169245676|gb|ACA50884.1| RpoD [Agrobacterium tumefaciens]
 gi|169245680|gb|ACA50886.1| RpoD [Agrobacterium tumefaciens]
 gi|169245682|gb|ACA50887.1| RpoD [Agrobacterium tumefaciens]
 gi|169245686|gb|ACA50889.1| RpoD [Agrobacterium tumefaciens]
 gi|169245690|gb|ACA50891.1| RpoD [Agrobacterium tumefaciens]
 gi|169245692|gb|ACA50892.1| RpoD [Agrobacterium tumefaciens]
 gi|169245696|gb|ACA50894.1| RpoD [Agrobacterium tumefaciens]
 gi|169245700|gb|ACA50896.1| RpoD [Agrobacterium tumefaciens]
 gi|169245704|gb|ACA50898.1| RpoD [Agrobacterium tumefaciens]
 gi|169245706|gb|ACA50899.1| RpoD [Agrobacterium tumefaciens]
 gi|169245708|gb|ACA50900.1| RpoD [Agrobacterium tumefaciens]
 gi|169245710|gb|ACA50901.1| RpoD [Agrobacterium tumefaciens]
          Length = 174

 Score =  181 bits (460), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 95/174 (54%), Positives = 121/174 (69%), Gaps = 6/174 (3%)

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ
Sbjct: 1   QVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKDLKDQLITAVKSLSLNQ 60

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +R+D LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +   
Sbjct: 61  NRVDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSIANLAA 120

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             WK F   E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKK
Sbjct: 121 RGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKK 174


>gi|159904297|ref|YP_001551641.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889473|gb|ABX09687.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 335

 Score =  181 bits (460), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 92/226 (40%), Positives = 145/226 (64%), Gaps = 3/226 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+S+AKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 100 AKERMVAANLRLVVSIAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 159

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R P+  E+A+ + +  E V
Sbjct: 160 IRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRDLSQQLSRTPSVAELAEYIDVSEEEV 219

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++    +P+SLE  +GD+D + L D +   N  SP    I+ +  +    +L    P 
Sbjct: 220 KDLMLKASQPVSLEMKVGDKDDTVLLDLLSTDND-SP-QQQIELDCMKGDLEILLEKLPE 277

Query: 624 -EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + RVLRMR+GI      +L  +G+   ++R+R+R +E   +R L+
Sbjct: 278 LQYRVLRMRYGIDGEEPMSLTGIGRVLGISRDRVRNLERSGLRGLR 323


>gi|86605925|ref|YP_474688.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
 gi|86554467|gb|ABC99425.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
          Length = 318

 Score =  181 bits (459), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 145/240 (60%), Gaps = 8/240 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GI + E + I+   R+GE     AKK MVE NLRLV+S+AK+Y NRGL FLDLIQEG IG
Sbjct: 60  GIPLEELQQIL---RQGEA----AKKRMVECNLRLVVSIAKRYRNRGLPFLDLIQEGTIG 112

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L +A EKFD   GYKFSTYA WW++Q++ R I ++   IR+P HM +K+ +V R  R +S
Sbjct: 113 LTRAVEKFDPTRGYKFSTYATWWIRQSVNRGIQNKGRLIRLPAHMYEKVSQVKRRYRELS 172

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +    P  EE+   L +       + +   E  SL   +GDED + L  FI D++   P
Sbjct: 173 AEKGSRPAAEEVFDSLDIGDNYRELITRHMAEIRSLNVGVGDEDGTELQHFIPDEDN-DP 231

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++   +    E    +++ L+ RE++V+  R+G+  +   TL E+G+   ++RER+RQIE
Sbjct: 232 IEHLNRVAHCEEVRALVSQLSEREQQVIVARYGLDGSKGLTLREIGEHIGLSRERVRQIE 291


>gi|54302639|ref|YP_132632.1| DNA-directed RNA polymerase sigma factor [Photobacterium profundum
           SS9]
 gi|90412658|ref|ZP_01220660.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
 gi|46916063|emb|CAG22832.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum SS9]
 gi|90326466|gb|EAS42878.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
          Length = 291

 Score =  181 bits (459), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 93/227 (40%), Positives = 144/227 (63%), Gaps = 1/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK M+E+NLRLV+S+AKKY   G+Q  DLI EGNIGL+ + EKFD   G++FSTYA WW
Sbjct: 48  AKKVMIESNLRLVVSIAKKYRGSGMQLSDLIDEGNIGLITSVEKFDPERGFRFSTYATWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I R I +Q+ TIR+PVH+  +I+ ++RT +++  K  +EPT EE+A+KL   V+ +
Sbjct: 108 IKQTIERCIHNQARTIRLPVHVSKEINTIIRTHKQLMKKNNQEPTREEVAEKLERSVDDI 167

Query: 564 RKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             VL      +S +  I D+  S  +  FI D ++  P     + +++     +L +L  
Sbjct: 168 SSVLAYDAPIVSFDQTINDDANSQSISVFIADDSSDKPESQVDKDDIKGLALAMLENLNQ 227

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+  +L  RFG+      TL++V  +  +TRERIRQ++  +++KLK+
Sbjct: 228 RDREILCRRFGLLGYEVQTLQQVANEVGLTRERIRQLQVSSLKKLKN 274


>gi|9621765|gb|AAF89531.1|AF160964_1 RNA polymerase sigma factor [Peanut witches'-broom phytoplasma]
          Length = 458

 Score =  181 bits (459), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 109/237 (45%), Positives = 144/237 (60%), Gaps = 10/237 (4%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLR+V+S+AKK + RG  FLDLI EGN+GLMK  +KFD+  G+KFSTYA WW++QAITR
Sbjct: 222 SNLRIVVSIAKKQSERGQYFLDLIHEGNMGLMKTVDKFDYTKGFKFSTYATWWIRQAITR 281

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGVR-KV 566
           ++ADQS TIR PVH+ D ++K      +++  + R+       EIAK  AM +E  +  +
Sbjct: 282 AVADQSRTIRCPVHVSDILNKNFAFKSKLTQDLARKARKAENHEIAK--AMNIETKKLMI 339

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREE 625
            K  K                   F +           +  N ++T    L  +LTPRE+
Sbjct: 340 YKWLKRNDFFRNIYSWWRWFFFRWFYKRSLRYFASWLYVTRNFKKTLEESLEEALTPREQ 399

Query: 626 RVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            VL+MR+GI  G N  HTLEEVG +  VTRERIRQIE KA+RKL+HPSRS  L SFL
Sbjct: 400 LVLKMRYGILEGDNRVHTLEEVGAKLGVTRERIRQIETKALRKLRHPSRSNPL-SFL 455


>gi|161899381|ref|XP_001712917.1| sigma 2 transcription factor [Bigelowiella natans]
 gi|75756411|gb|ABA27305.1| sigma 2 transcription factor [Bigelowiella natans]
          Length = 389

 Score =  181 bits (459), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 95/233 (40%), Positives = 156/233 (66%), Gaps = 2/233 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
             I+K+ +++ +L+L+IS+AK+Y   GL F DLI EG +GLMK   K+D+  G+KFSTYA
Sbjct: 147 GKISKEILIKRSLKLIISIAKRYNGCGLSFEDLIAEGILGLMKGIRKYDFSKGHKFSTYA 206

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q+I+RSI DQS  IR+PV++++ + K+ +   +     KR PT EEI+  + +P+
Sbjct: 207 HWWIRQSISRSIDDQSRIIRLPVYVKEILSKINKIKNKFYEDKKRYPTEEEISLLIGIPL 266

Query: 561 EGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           + +RK+L    + ISL++ I ++  D++ L D IED   ++    AI+ +L++   + L 
Sbjct: 267 KKLRKLLLSCNDLISLDSLIENDSNDSNMLNDSIEDSKVINSEVYAIEKSLKQDLNKALL 326

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +L+ RE  V+R+R+G+    + TLEE+G+   VTRER RQIE KA++KL+  +
Sbjct: 327 TLSDRESAVIRLRYGLDDGNERTLEEIGEYLNVTRERARQIEIKALKKLQFNT 379


>gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
 gi|300075048|gb|ADJ64447.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
          Length = 337

 Score =  181 bits (459), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 96/277 (34%), Positives = 169/277 (61%), Gaps = 6/277 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E K  +A E+ S    ++ +  I  +  ++ +E  H  +  + GE    +A+++M+E NL
Sbjct: 51  ELKKVLAAEL-STDTTQHYLNKIGAKPLLTAAEELHFATQAKAGEF---VARQKMIEHNL 106

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK Y NRG+  LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I 
Sbjct: 107 RLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIM 166

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKVLKITK 571
           +Q+ T+R+PVHM  ++++++R    +  + +  R+ + E+IA  +  PVE V+ VL +++
Sbjct: 167 NQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDVLALSE 226

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              SL+TP+ ++  + L D +       P   A    +       L SL+ ++  V+  R
Sbjct: 227 HAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEKQRVVVARR 286

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           FG+  +   TLE++  +  +TRER+RQ++ +A+ KLK
Sbjct: 287 FGLDNDDPSTLEQLASEMGITRERVRQVQQEALIKLK 323


>gi|58257340|gb|AAK30051.2| RpoS sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  181 bits (458), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 87/238 (36%), Positives = 149/238 (62%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +  AR ++ K+  EP+PE
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLGAARELTQKLDHEPSPE 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +  +    + D + D       +   + +L 
Sbjct: 203 EIANMLEKPVTEVKRMLGLNERVSSVDVSLDPDSDKTVLDTLTDDRPTDRCEVLQEDDLS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 263 QGIDQWLSELTEKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQIEGLKRLR 320


>gi|85813983|emb|CAD20831.2| sigma factor [Spinacia oleracea]
          Length = 575

 Score =  181 bits (458), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 92/240 (38%), Positives = 151/240 (62%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            +  K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G+KFSTYA
Sbjct: 334 GTFCKDKMIKSNVRLVISIAKNYQGSGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 393

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  ++P  EE+A+   + +
Sbjct: 394 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLLSENGKQPNNEEVAEATGLSM 453

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +  VL   K P SL+  IG        + I D  A +  D   +  +R+   +VL +L
Sbjct: 454 KRLTAVLMTPKAPRSLDQKIGFNMNLKPSEVIADPEAETAEDLLTKQFMRQDLEKVLDTL 513

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE++V+R RFG+      TL+E+G+   V+RERIRQIE+ A RKL++  ++  L+ ++
Sbjct: 514 SSREKQVIRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLQNKKKTINLQQYM 573


>gi|116073053|ref|ZP_01470315.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068358|gb|EAU74110.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 321

 Score =  181 bits (458), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 145/226 (64%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 86  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V
Sbjct: 146 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAEFVELPEEEV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +     + P +      L+     +L  L   
Sbjct: 206 KDLMCRARQPVSLEMKVGDGDDTELLELLSGDGEL-PSEQVESECLKGDLRDLLEQLPEL 264

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +VLRMR+G+      +L  + K   ++R+R R++E + +  L++
Sbjct: 265 QRKVLRMRYGMNGEDPMSLTGIAKTLKMSRDRTRRLEREGLEMLRN 310


>gi|158340427|ref|YP_001521783.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310668|gb|ABW32282.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 273

 Score =  180 bits (457), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 94/241 (39%), Positives = 155/241 (64%), Gaps = 2/241 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ +     AK+ M+E NLRLV+S+AKK+ NRGL F+DLIQEG+IGL +A EKF+ 
Sbjct: 26  IQLARQAKAGNLRAKQRMIECNLRLVVSIAKKHQNRGLPFMDLIQEGSIGLSRAVEKFEP 85

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++Q ITRSI + S  IR+PV      +++ +T R++S +  REPT  
Sbjct: 86  EQGYRFSTYAYWWIRQGITRSIQNNSRVIRLPVWHWQTGNQIKQTQRQLSQEFGREPTLA 145

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ + + ++ +++ +   ++ +SL+  +G E  + LG+ IE + + +P    +  N  
Sbjct: 146 ELAEAMEIDLDKLKQNMHHLQDVLSLDMQVGKEQDTTLGELIEAEQS-TPTHLEL-LNQS 203

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E  +  L+ L  R+  V+  R+G+      T++++G+Q  V+RERIRQI  KA++KL+  
Sbjct: 204 EEVSSYLSLLDERQRYVIVQRYGLEDGEAKTMQDIGQQLGVSRERIRQIINKAMKKLQKN 263

Query: 671 S 671
           S
Sbjct: 264 S 264


>gi|312796084|ref|YP_004029006.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
 gi|312167859|emb|CBW74862.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
          Length = 358

 Score =  180 bits (457), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 101/270 (37%), Positives = 163/270 (60%), Gaps = 14/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE +A   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 79  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFDA---RQMMIERNLRLVVSIAKGYLNRGV 135

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 136 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 195

Query: 529 IHKVVRTARRMSNKI---------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           +++V+R  R +              R+ + ++IA  +    E V  +L + +   SL+ P
Sbjct: 196 LNQVLRAKRHLERNASAPASGADEHRDASVDDIAYLIGKTPEEVADILALNEHTASLDAP 255

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER-VLRMRFGIGMNT 638
           +  +  S L D + D+ + SP D+  Q    ET TRV  S  P + R V+  RFG+    
Sbjct: 256 LELDPASSLLDLLSDEQSQSP-DAEAQHRELETLTRVWLSRLPDKHRHVIERRFGLNNIE 314

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 315 PATLEELADEMGLTRERVRQIQQEALARLK 344


>gi|23013686|ref|ZP_00053554.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 322

 Score =  180 bits (457), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 98/189 (51%), Positives = 127/189 (67%), Gaps = 3/189 (1%)

Query: 5   KKRNRDSDSEHED-SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           K  N    SE++D + D  + D    + KKM+   ++RGYVT +ELNA +PP+EVSSEQ+
Sbjct: 4   KSTNTAEVSENQDEAMDGPLLDTLGVAVKKMVAKGKERGYVTYDELNAAMPPEEVSSEQI 63

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           EDT+AMLS +GINVV+ ++ ED        +   +   S       +D     TDDPVRM
Sbjct: 64  EDTMAMLSELGINVVESEEGEDNAPEAAEEEATETEGYSGAGNVDEEDLG--RTDDPVRM 121

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +A++ W D L +G  LLR+
Sbjct: 122 YLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTLRAVVDWHDALVEGKMLLRD 181

Query: 184 IIDLEACIG 192
           IIDL+A  G
Sbjct: 182 IIDLDATYG 190


>gi|323388685|gb|ADX60147.1| SIGMA70-like transcription factor [Zea mays]
          Length = 428

 Score =  180 bits (456), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 92/237 (38%), Positives = 149/237 (62%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+AK++   G++F DLIQ+G  GL++ AEKFD   G++FSTY+ WW
Sbjct: 187 CKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEKFDASKGFRFSTYSHWW 246

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR P+ EEIA    M +  V
Sbjct: 247 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRLPSNEEIAVDTGMTIRRV 306

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +S  + +G  D ++  + + D +A +  ++  +  +++     L SL+PR
Sbjct: 307 EAAMSLPKYSVSFTSKVGCTDVTY-QEIMPDTSAETAEETLHRWLMKKDVNTALDSLSPR 365

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++V+R RFGI      TL ++G+   V+RERIRQIE  A RKL+  +R + L+ +L
Sbjct: 366 EKQVMRYRFGIEGGRARTLHDIGQLMGVSRERIRQIELGAFRKLRSKNRLQSLQHYL 422


>gi|207743818|ref|YP_002260210.1| rna polymerase sigma d (sigma-70) factor (partial sequence c
           terminus) protein [Ralstonia solanacearum IPO1609]
 gi|206595218|emb|CAQ62145.1| rna polymerase sigma d (sigma-70) factor (partial sequence c
           terminus) protein [Ralstonia solanacearum IPO1609]
          Length = 684

 Score =  180 bits (456), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 88/187 (47%), Positives = 127/187 (67%), Gaps = 3/187 (1%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGI 422
           G+ R  F+ R  G E +  W++      +G+ +   V   + ++ +++ ++  +     +
Sbjct: 498 GMSRGDFVSRFPGNETNLGWINTV--VADGKPYSAIVERNIPAVHELQQKLIDLQSRVVL 555

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 556 PLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 615

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +
Sbjct: 616 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQE 675

Query: 543 IKREPTP 549
              EP P
Sbjct: 676 TGNEPDP 682



 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V     D + L   +
Sbjct: 205 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLND 264

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 265 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 323

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 324 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 362


>gi|55274951|gb|AAV49275.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 205

 Score =  180 bits (456), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 83/204 (40%), Positives = 139/204 (68%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V +
Sbjct: 61  QTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSR 120

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 121 MLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 180

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQF 649
            VL  RFG+      TLE+VG++ 
Sbjct: 181 EVLARRFGLLGYEAATLEDVGREI 204


>gi|87124760|ref|ZP_01080608.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86167639|gb|EAQ68898.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 321

 Score =  180 bits (456), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 148/233 (63%), Gaps = 15/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 86  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V
Sbjct: 146 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAGFVELPEEEV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHL-------GDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + ++   ++P+SLE  +GD D + L       G+  E++  V      ++ +LR+    +
Sbjct: 206 KDLMCRARQPVSLEMKVGDGDDTELLELLAGDGELPEEQVEV----ECLKGDLRD----L 257

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L   + RVLRMR+G+      +L  + K   ++R+R R++E + +  L+ 
Sbjct: 258 LEQLPDLQRRVLRMRYGMDGEEPMSLTGIAKSLRMSRDRTRRLEREGLEMLRR 310


>gi|54401890|gb|AAV34630.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274947|gb|AAV49273.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 203

 Score =  180 bits (456), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 83/203 (40%), Positives = 139/203 (68%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V +
Sbjct: 61  QTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSR 120

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 121 MLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 180

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQ 648
            VL  RFG+      TLE+VG++
Sbjct: 181 EVLARRFGLLGYEAATLEDVGRE 203


>gi|55274937|gb|AAV49269.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score =  180 bits (456), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 83/202 (41%), Positives = 138/202 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDNDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 182 LARRFGLLGYEAATLEDVGREI 203


>gi|71894468|ref|YP_278576.1| RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 490

 Score =  180 bits (456), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 100/263 (38%), Positives = 154/263 (58%), Gaps = 18/263 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG      A+  +++ NLRLV++ AKKY NRGL F+DL+ EGN GL+KAA+KFD   G+K
Sbjct: 222 KGGSRGKRARDLIIKRNLRLVVNAAKKYKNRGLSFIDLVSEGNAGLLKAAQKFDIKKGFK 281

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q+I+R++ADQ+  IR+PVHM + I+K+ +  R +  +   E   EEIA +
Sbjct: 282 FSTYATWWIRQSISRAVADQARIIRVPVHMVETINKIYKIEREIQQENGGEIIDEEIAAR 341

Query: 556 LA-----MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           L           +R + KI   PISL+  +G E+ S  GDF++D++ +SP++ A +  L 
Sbjct: 342 LGGKSKKYDASYIRYIRKINTSPISLDKQVGKENDSFFGDFVKDESIISPVEFADKEELI 401

Query: 611 ETTTRVLASLTPREERVLRMRF-GIGMNT------DHTLEEVGKQF-----CVTRERIRQ 658
                 +  L    E  L  R+ GIG +         TL+E+ K F      +++ER+RQ
Sbjct: 402 TKINYYVEKLLSEAEADLIKRYHGIGYDAKGNPVRSATLDEISKDFRGEGKKISKERVRQ 461

Query: 659 IEAKAIRKLK-HPSRSKKLRSFL 680
           I  K  +KL+ +P   +   +F+
Sbjct: 462 IITKIYKKLRGYPEVVELFENFI 484


>gi|313837139|gb|EFS74853.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA2]
 gi|314927839|gb|EFS91670.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL044PA1]
 gi|314971910|gb|EFT16008.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA3]
 gi|328907302|gb|EGG27068.1| sigma-70 region 2 [Propionibacterium sp. P08]
          Length = 312

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 139/226 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 79  AMAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V
Sbjct: 139 VRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETSEIADELEITEERV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R     +L +L  R
Sbjct: 199 IELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRGRLEGLLDNLDER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 259 SADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALDSMRQ 304


>gi|55274976|gb|AAV49287.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/204 (40%), Positives = 139/204 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCV 651
           L  RFG+      TLE+VG++  +
Sbjct: 181 LARRFGLLGYEAATLEDVGREIGL 204


>gi|54401898|gb|AAV34634.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274877|gb|AAV49241.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
 gi|55274996|gb|AAV49295.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 201

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/201 (41%), Positives = 138/201 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQ 648
           L  RFG+      TLE+VG++
Sbjct: 181 LARRFGLLGYEAATLEDVGRE 201


>gi|44662845|gb|AAS47504.1| major sigma factor 70 [Meiothermus ruber DSM 1279]
          Length = 168

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 92/168 (54%), Positives = 117/168 (69%), Gaps = 2/168 (1%)

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTARRM  ++ REP+ EEIA  + 
Sbjct: 1   TYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARRMQQELGREPSYEEIADAMG 60

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E   +
Sbjct: 61  PGWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDSAAQSMLSEELEK 120

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            L  L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 121 ALGKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 168


>gi|54401894|gb|AAV34632.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401896|gb|AAV34633.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274921|gb|AAV49262.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274982|gb|AAV49290.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/202 (41%), Positives = 138/202 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 181 LARRFGLLGYEAATLEDVGREI 202


>gi|55274915|gb|AAV49259.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274917|gb|AAV49260.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274923|gb|AAV49263.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
 gi|55274925|gb|AAV49264.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274928|gb|AAV49265.1| RNA polymerase subunit sigma-38 [Shigella sonnei]
 gi|55274932|gb|AAV49267.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274939|gb|AAV49270.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274949|gb|AAV49274.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274955|gb|AAV49277.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274957|gb|AAV49278.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274959|gb|AAV49279.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274961|gb|AAV49280.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274974|gb|AAV49286.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274980|gb|AAV49289.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274991|gb|AAV49293.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274993|gb|AAV49294.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/202 (41%), Positives = 138/202 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 182 LARRFGLLGYEAATLEDVGREI 203


>gi|255020521|ref|ZP_05292585.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
 gi|254970041|gb|EET27539.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
          Length = 316

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 93/236 (39%), Positives = 145/236 (61%), Gaps = 3/236 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V++G+  A   +  M+E NLRLV+ VA++Y +RG+  LDLI+EGN+GL++A EKFD   
Sbjct: 69  LVQQGDVRA---RTRMIECNLRLVVRVARRYLHRGMPLLDLIEEGNLGLIRAVEKFDPER 125

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q I R++ +Q+ TIR+PVH+  ++  V+R AR +  +++REP+ +E+
Sbjct: 126 GFRFSTYATWWIRQNIERALMNQTRTIRLPVHVMKELAVVLRAARCLEQELRREPSVDEV 185

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  L  PV+ VR  L++     SL+     +    L + + D  A  P       NL   
Sbjct: 186 AAALDRPVDQVRGCLEMDGRVTSLDNSGQRDQGRDLNEVLSDAEAQGPEAMVAAQNLAVR 245

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               LA L+ +   VL  RFG+      TLEEVG +  +TRER+RQI+ +A+  L+
Sbjct: 246 LQSWLAGLSEKHRLVLSWRFGLDGGDGATLEEVGTRLGITRERVRQIQVEALLILR 301


>gi|119897381|ref|YP_932594.1| RNA polymerase sigma factor RpoS [Azoarcus sp. BH72]
 gi|119669794|emb|CAL93707.1| putative RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 311

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 92/235 (39%), Positives = 152/235 (64%), Gaps = 3/235 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR G+ +A   ++ M+E NLRLV+++AK Y NRG+  LDL++EGN+GLM A EKFD   G
Sbjct: 66  VRAGDFDA---RQTMIERNLRLVVNIAKHYLNRGIPLLDLVEEGNLGLMHALEKFDPERG 122

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R+I +QS TIR+PVH+  ++++V+R  R +      + + +EIA
Sbjct: 123 FRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKELNQVLRAQRVVEAASNGDFSLDEIA 182

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L  P+E VR +L +++   SL+ P+  + T  +G+ + D++A +P      A +    
Sbjct: 183 RRLDKPIEEVRAILALSEHTASLDAPLDIDPTLSIGESLADEHAETPESQIHNAEIEGLI 242

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  ++  V+R R+GIG     TLEE+  +  +TRER+RQI+ +A+ +L+
Sbjct: 243 RAWIDMLNDKQRLVIRHRYGIGECELMTLEELAARLELTRERVRQIQLEALGQLR 297


>gi|55274911|gb|AAV49257.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274963|gb|AAV49281.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 202

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/202 (41%), Positives = 138/202 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 181 LARRFGLLGYEAATLEDVGREI 202


>gi|15606622|ref|NP_214002.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
 gi|2983844|gb|AAC07398.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
          Length = 310

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 99/303 (32%), Positives = 172/303 (56%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K IS    ++  E + +    ++G+ EA    K++VE+NLR V+SVAK+Y   GL
Sbjct: 10  INQYLKKISKIPLLTPEEEKELARRAKQGDKEAL---KKLVESNLRFVVSVAKQYIGYGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F +LI  GN+GL++AA++FD   G KF +YA+WW++QAI ++++ Q+  +RIP+     
Sbjct: 67  PFSELIAAGNLGLLEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQSHI 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLA------------------------------- 557
           I+K+      +S K++REP+PEEIA++L+                               
Sbjct: 127 INKISHIYGELSKKLEREPSPEEIAEELSKQMIAKELEKELGREPTEEEIEERFKKEGYK 186

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E V K L++ + P+SL+ P+G+ + +   DF+         +  IQ  +++    +L
Sbjct: 187 ITPEEVEKYLQVCRVPLSLDAPVGENEDTFFIDFLSKHGTAEVEEKVIQEVIQKEIDDLL 246

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + LT +E +V+ +RFG+  N   TL E+G+   ++RER+RQ+E +A+RKL+  +  + L+
Sbjct: 247 SKLTDKERKVIELRFGLKGNEPKTLREIGEILGLSRERVRQLETRALRKLRSLAMKRHLK 306

Query: 678 SFL 680
            FL
Sbjct: 307 DFL 309


>gi|113954287|ref|YP_730230.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881638|gb|ABI46596.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 318

 Score =  179 bits (455), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 144/226 (63%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 83  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P E V
Sbjct: 143 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEEEV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L + +     + P D      L+     +L+ L   
Sbjct: 203 KDLMCRARQPVSLEMKVGDGDDTELLELLAGDGEL-PSDQVEGECLKGDLRDLLSQLPEL 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +VLRMR+G+      +L  + K   ++R+R R++E + +  L+ 
Sbjct: 262 QGKVLRMRYGMDGEEPMSLTGIAKSMKMSRDRTRRLEREGLEMLRR 307


>gi|302518878|ref|ZP_07271220.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302427773|gb|EFK99588.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 201

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 95/201 (47%), Positives = 139/201 (69%)

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++A EKFD+  G+KFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  R + 
Sbjct: 1   LIRAVEKFDYTRGFKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRGLL 60

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP+  E+A  L +  E V +VL++ +EP+SL TP+G ED   LGD IED +A SP
Sbjct: 61  QERGHEPSHAEVAALLGLTKERVGEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSP 120

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +SA    LR     VL++L  RE +V+++R+G+      TLEE+G  F VTRERIRQIE
Sbjct: 121 PESAALLLLRRHLEDVLSTLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIE 180

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AK + KL+  + + +LR +LD
Sbjct: 181 AKTLAKLRSHAFADQLRGYLD 201


>gi|55274913|gb|AAV49258.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274972|gb|AAV49285.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  179 bits (454), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 83/200 (41%), Positives = 137/200 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGK 647
           L  RFG+      TLE+VG+
Sbjct: 181 LARRFGLLGYEAATLEDVGR 200


>gi|323345487|ref|ZP_08085710.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093601|gb|EFZ36179.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  179 bits (454), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 94/263 (35%), Positives = 162/263 (61%), Gaps = 8/263 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +SI E   +  ++RKG  E   AK++++ ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  VSIDEETELAQLIRKGGKEGERAKEKLINANLRFVVSVAKQYQHQGLSLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+     +   
Sbjct: 91  VKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGALSKINSEVAKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R P+ +E+A    +    + + ++     +S++ P  D+D + + D +   +D  A 
Sbjct: 151 EHQRRPSTQELASLTNIDENKISQTMRADNHHMSIDAPFSDDDENSMADVLASGDDSRAD 210

Query: 599 SPLD-SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +D  ++ ++L +       +L PRE  +L+  FGIG  T+  LEE+G++F +TRER+R
Sbjct: 211 RIVDRESMNSDLDDAMAN---ALKPREVAILKESFGIGC-TEKGLEEIGEEFGLTRERVR 266

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QI  K+I+KL+    ++ L  +L
Sbjct: 267 QIREKSIQKLRESGYARILVKYL 289


>gi|25991939|gb|AAN76997.1|AF481773_1 putative sigma 70 transcription factor [Frankia sp. ACoN24d]
          Length = 185

 Score =  179 bits (453), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/168 (48%), Positives = 120/168 (71%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           + RG+  LDL+QEGN+GL++  +KFD+  GYKFSTYA WW++QAI R++ADQ  TIRIPV
Sbjct: 1   SGRGMTLLDLVQEGNLGLIRPVKKFDYAKGYKFSTYATWWIRQAIGRALADQGRTIRIPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            + ++I+K+ R  R++ + + REPT EE+A +L MP+E V ++ +  ++ +SLET +GD+
Sbjct: 61  XVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVVELRRYAQDTVSLETSVGDD 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             S LGDFIED +A SP D+A    +++    VL  L PRE  V+R+R
Sbjct: 121 GDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGGLNPREREVMRLR 168


>gi|42566466|gb|AAS21045.1| major sigma factor 70 [Meiothermus silvanus DSM 9946]
          Length = 168

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 91/168 (54%), Positives = 118/168 (70%), Gaps = 2/168 (1%)

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR+M  ++ REPT EEI++ + 
Sbjct: 1   TYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQMQQELGREPTYEEISEAMG 60

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E   +
Sbjct: 61  PGWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDSAAQSMLSEELEK 120

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            L  L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 121 ALGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 168


>gi|54401892|gb|AAV34631.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  178 bits (452), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 83/199 (41%), Positives = 136/199 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEVG 646
           L  RFG+      TLE+VG
Sbjct: 182 LARRFGLLGYEAATLEDVG 200


>gi|282854020|ref|ZP_06263357.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|282583473|gb|EFB88853.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|314922987|gb|EFS86818.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL001PA1]
 gi|314966764|gb|EFT10863.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA2]
 gi|314981098|gb|EFT25192.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA3]
 gi|315091924|gb|EFT63900.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA4]
 gi|315093320|gb|EFT65296.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL060PA1]
 gi|315103425|gb|EFT75401.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA2]
 gi|327327589|gb|EGE69365.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL103PA1]
          Length = 312

 Score =  178 bits (452), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 138/226 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 79  ALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V
Sbjct: 139 VRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFEIADELEITEERV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R     +L  L  R
Sbjct: 199 IELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRSRLEGLLDDLDER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 259 SADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|54401900|gb|AAV34635.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score =  178 bits (452), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 83/202 (41%), Positives = 137/202 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 181 LARRFGLLGYEAATLEDVGREI 202


>gi|55274945|gb|AAV49272.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 82/202 (40%), Positives = 138/202 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRL++ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLMVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 182 LARRFGLLGYEAATLEDVGREI 203


>gi|313812945|gb|EFS50659.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA1]
          Length = 312

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 138/226 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 79  ALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V
Sbjct: 139 VRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFEIADELEITEERV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R     +L  L  R
Sbjct: 199 IELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRSRLEGLLDDLDER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 259 SADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|258648419|ref|ZP_05735888.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851166|gb|EEX71035.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 286

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 97/265 (36%), Positives = 157/265 (59%), Gaps = 4/265 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  IS  E   +   + KG+ EA    +++ +ANLR V+SVAK+Y N+GL   DLI 
Sbjct: 25  IGREGLISTDEEVELAQRIHKGDAEAL---EKLTKANLRFVVSVAKQYQNQGLALNDLID 81

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++AA+KFD   G+KF +YA+WW++Q+I ++I++QS  +R+P++      K+ + 
Sbjct: 82  EGNLGLIRAAQKFDETRGFKFISYAVWWIRQSILQAISEQSRIVRMPLNQVGFQSKLTKA 141

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
                 + +R P+ +E+A  L   V  V++ +    + +S++ P  D+D++ L D + D+
Sbjct: 142 IVNFEQEFERRPSVQELADILDTDVAKVQEAMGTNGKKVSVDAPFQDDDSNSLIDIMTDE 201

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NA    D   + +L       L +LT RE  VL+M FGIG N + T EEV     +TRER
Sbjct: 202 NAPGTDDQMEKESLSSDLDAALGTLTERERLVLKMLFGIGRN-EMTAEEVANSLSLTRER 260

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           +RQI+ +A+R+L+       L  +L
Sbjct: 261 VRQIKERALRRLREADNIHILTKYL 285


>gi|50842514|ref|YP_055741.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289425060|ref|ZP_06426837.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289427240|ref|ZP_06428956.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|295130591|ref|YP_003581254.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|50840116|gb|AAT82783.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289154038|gb|EFD02726.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289159709|gb|EFD07897.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|291376720|gb|ADE00575.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|313764457|gb|EFS35821.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA1]
 gi|313772161|gb|EFS38127.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL074PA1]
 gi|313807516|gb|EFS46003.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA2]
 gi|313810025|gb|EFS47746.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA1]
 gi|313815996|gb|EFS53710.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA1]
 gi|313818558|gb|EFS56272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA2]
 gi|313820325|gb|EFS58039.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA1]
 gi|313822868|gb|EFS60582.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA2]
 gi|313825200|gb|EFS62914.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA1]
 gi|313827776|gb|EFS65490.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA2]
 gi|313830353|gb|EFS68067.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL007PA1]
 gi|313833726|gb|EFS71440.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL056PA1]
 gi|314915450|gb|EFS79281.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA4]
 gi|314918267|gb|EFS82098.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA1]
 gi|314920080|gb|EFS83911.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA3]
 gi|314925213|gb|EFS89044.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA3]
 gi|314931602|gb|EFS95433.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL067PA1]
 gi|314955755|gb|EFT00155.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA1]
 gi|314958169|gb|EFT02272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA1]
 gi|314960004|gb|EFT04106.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA2]
 gi|314967831|gb|EFT11930.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA1]
 gi|314973357|gb|EFT17453.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA1]
 gi|314976035|gb|EFT20130.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL045PA1]
 gi|314978426|gb|EFT22520.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA2]
 gi|314983943|gb|EFT28035.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA1]
 gi|314988127|gb|EFT32218.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA2]
 gi|314989932|gb|EFT34023.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA3]
 gi|315080642|gb|EFT52618.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL078PA1]
 gi|315084315|gb|EFT56291.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA2]
 gi|315085658|gb|EFT57634.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA3]
 gi|315088920|gb|EFT60896.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA1]
 gi|315095902|gb|EFT67878.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL038PA1]
 gi|315098533|gb|EFT70509.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA2]
 gi|315101109|gb|EFT73085.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA1]
 gi|315105655|gb|EFT77631.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA1]
 gi|315108329|gb|EFT80305.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA2]
 gi|327326184|gb|EGE67974.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA2]
 gi|327331941|gb|EGE73678.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA3]
 gi|327443142|gb|EGE89796.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA2]
 gi|327445926|gb|EGE92580.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA2]
 gi|327448094|gb|EGE94748.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA1]
 gi|327450785|gb|EGE97439.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA3]
 gi|327453871|gb|EGF00526.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA2]
 gi|328753473|gb|EGF67089.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL020PA1]
 gi|328754203|gb|EGF67819.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA1]
 gi|328754545|gb|EGF68161.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA2]
 gi|328760855|gb|EGF74421.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL099PA1]
 gi|332675431|gb|AEE72247.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           266]
          Length = 312

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 138/226 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 79  ALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V
Sbjct: 139 VRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFEIADELEITEERV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R     +L  L  R
Sbjct: 199 IELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRSRLEGLLDDLDER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 259 SADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|225440035|ref|XP_002276710.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/239 (37%), Positives = 149/239 (62%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLR+V+ +AK+Y  RGL   DL+QEG++GLM + EKF    G +F++YA WW
Sbjct: 321 SRQKLIYANLRMVVHIAKQYQGRGLNLQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWW 380

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ ++I   S TIR+P +M   + KV    R    +   +PT EEIA+++ + +E +
Sbjct: 381 IRQAVRKAIFQHSRTIRLPENMYSLLGKVKEAKRLFIQEGHHDPTKEEIAERVGITIEKL 440

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +++L  T+ P+S++ P+  D+DT+   +   D     P  S  +  +R+    +L  LTP
Sbjct: 441 QRLLLHTRMPLSMQQPVWADQDTT-FQEVTADTGIEIPDVSVAKQLMRQHVRNLLHVLTP 499

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +E R++R+RFGIG     TL E+G  F  ++ER+RQ+E +A+ KLK    S  L S+ D
Sbjct: 500 KERRIIRLRFGIGDGIPRTLSEIGLVFGFSKERVRQLEQRALHKLKQCLSSHGLESYTD 558


>gi|313792143|gb|EFS40244.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA1]
 gi|313801904|gb|EFS43138.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA2]
 gi|313838730|gb|EFS76444.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL086PA1]
 gi|314962802|gb|EFT06902.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA1]
 gi|315078018|gb|EFT50069.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA2]
 gi|327453138|gb|EGE99792.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL092PA1]
          Length = 312

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 138/226 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 79  ALARFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V
Sbjct: 139 VRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFEIADELEITEERV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R     +L  L  R
Sbjct: 199 IELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRSRLEGLLDDLDER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 259 SADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|327330254|gb|EGE72003.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL097PA1]
          Length = 312

 Score =  178 bits (451), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 138/226 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WW
Sbjct: 79  ALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V
Sbjct: 139 VRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRSLERQLGREPETFEIADELEITEERV 198

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R     +L  L  R
Sbjct: 199 IELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRSRLEGLLDDLDER 258

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 259 SADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|325109992|ref|YP_004271060.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
 gi|324970260|gb|ADY61038.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
          Length = 286

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 96/259 (37%), Positives = 159/259 (61%), Gaps = 11/259 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I+  + +S  E + + + +  G+ EA   +  MV ANLRLV+++A+ Y ++GL   D
Sbjct: 28  LREINETSLLSADEEKELANRIAMGDLEA---RDRMVRANLRLVVNIARGYASKGLPLQD 84

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A E FD  +  +FSTYA +W+KQ+I RS+ + + TIRIP +M + + K 
Sbjct: 85  LIEEGNLGLLRAVEGFDPNMNTRFSTYASYWIKQSIKRSLVNCAKTIRIPAYMVELLSKW 144

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL--ETPIGDEDTS--HL 588
            +   R+ +++ R PT EE+A +L +P    +K L I K+ I L   TP  D++ S   L
Sbjct: 145 RKATARLQDELNRTPTAEEVAAELGLP----KKKLNIVKKAIQLYNSTPQSDDEESGWSL 200

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ + D+ A+ P +  +  +      R+L  +  RE  +LRMRFG+      TL+E+G+ 
Sbjct: 201 GEMVADERAIGPEEELVNNDNLNHVYRMLDDMDDRESTILRMRFGLDHEEPKTLKEIGES 260

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE +A+ +L
Sbjct: 261 LGLTRERVRQIEQEALNRL 279


>gi|55274943|gb|AAV49271.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 204

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 82/202 (40%), Positives = 137/202 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+   ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDFSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 182 LARRFGLLGYEAATLEDVGREI 203


>gi|325264732|ref|ZP_08131461.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030024|gb|EGB91310.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 292

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 142/229 (62%), Gaps = 1/229 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK ++ E+ L LV+S+A +Y+ RGL F+DLIQEGNIGLM+AAEK+D+     FS YA  W
Sbjct: 61  AKLKLEESALCLVVSIAGQYSGRGLLFMDLIQEGNIGLMQAAEKYDYTKDGGFSGYARRW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEG 562
           ++ AI  ++ +QS  IR+P ++ + + KV + A  +  ++ RE T  EIA KL     E 
Sbjct: 121 IEDAIKHAVDEQSREIRVPAYVAENMKKVQKAAYELQQELGREATAGEIAGKLGDKSEEE 180

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  +L   K P+SL+ P+ D D  +L D I D+   +P D+      +E    +L SL+ 
Sbjct: 181 IESILTFLKNPVSLDAPVEDGDDENLEDTIADREEKTPEDAVNSLIQKEEVLHLLESLSE 240

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +E +V+  RFG+     HTLEEVG++  V+RERI QIE  A++KL+  +
Sbjct: 241 KERQVISKRFGLEDGRVHTLEEVGQELNVSRERISQIEEHAMKKLRQAA 289


>gi|300112902|ref|YP_003759477.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299538839|gb|ADJ27156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 310

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 86/240 (35%), Positives = 150/240 (62%), Gaps = 3/240 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +   + +KG    S  +K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL+ A EKF
Sbjct: 59  YYARLAKKGN---SAGRKRMIESNLRLVVKISRRYMNRGLALLDLIEEGNLGLIHAVEKF 115

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D  +G++FSTYA WW++Q I R++ +Q+ T+R+PVH+  +I    R A +++ +++ +P+
Sbjct: 116 DPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHVVKEIKSYQRVANKLAQELEHDPS 175

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A++L  PVE +++V  +     S++T   +     L D + D+ A  P       +
Sbjct: 176 FEELAQQLDKPVEEIKRVWSLKDNTASMDTGYRNNQEKTLLDALPDEGAPDPTVLLQNDD 235

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++      L+ L  ++  V+  RFG+      TLE+VG+   VTRER+RQI+ + +++L+
Sbjct: 236 MQARLELWLSQLNDKQREVVIRRFGLQGYEPQTLEQVGQAIGVTRERVRQIQLETLKRLR 295


>gi|7416823|dbj|BAA94072.1| rpoS [Rubrivivax gelatinosus]
          Length = 322

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 92/229 (40%), Positives = 144/229 (62%), Gaps = 4/229 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLV+S+AK Y  RG+  +DLI+EGN+GLM A  KF+   G++FSTYA WW
Sbjct: 80  ARQAMIERNLRLVVSIAKHYVGRGMPMIDLIEEGNLGLMHATGKFEPERGFRFSTYASWW 139

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN----KIKREPTPEEIAKKLAMP 559
           ++Q+I R+I  Q+  IR+PVH+  ++++V++  R + +    + +R  + +E+A  L  P
Sbjct: 140 IRQSIERAIMHQARLIRLPVHVVRELNQVLKARRALESARRGEAERPVSVDEVAAALQRP 199

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE V ++LK+ ++P SL+ P+  E    + D + D++A+ PL   +           LA 
Sbjct: 200 VEEVAELLKLAEQPTSLDMPLERESGESMLDTVADEDAIDPLGLTLSREAVHLLDNGLAE 259

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  VL  RFG+      TLEE+  +  +TRERIRQI+ +A+ KLK
Sbjct: 260 LNEREREVLAGRFGLRDREPETLEELAARLGLTRERIRQIQQEALLKLK 308


>gi|55274978|gb|AAV49288.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 82/200 (41%), Positives = 137/200 (68%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L+
Sbjct: 61  ERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 121 LNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 180

Query: 629 RMRFGIGMNTDHTLEEVGKQ 648
             RFG+      TLE+VG++
Sbjct: 181 ARRFGLLGYEAATLEDVGRE 200


>gi|284042443|ref|YP_003392783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283946664|gb|ADB49408.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 285

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 93/235 (39%), Positives = 141/235 (60%), Gaps = 3/235 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV +NLRLV+S+A+ Y  +GL   DL+QEG +GL++A EKFDW  G++FSTYA  W
Sbjct: 50  AKERMVNSNLRLVMSIARHYQGQGLGMGDLVQEGTLGLIRAVEKFDWRKGFRFSTYATLW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R + +   TIR+PVH+  +  KV R  R ++ K  R+ T EEIA+   +PVE V
Sbjct: 110 IRQSIQRGLENTGRTIRLPVHVGQRARKVARIRRELTAKHGRDATDEEIAEAARLPVEQV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASLTP 622
            +  +  +EP SL+ P+G++  + LG  I  K      D  +   LR ET  R +  L  
Sbjct: 170 IEAGRADREPTSLDAPVGEDGDTALGALI--KTDTPEPDEEVADTLRHETVQRAIDDLPD 227

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            E+ V+ +RFG       TL ++G++  V+  R R+IE +A+R+L   +    LR
Sbjct: 228 NEKTVIHLRFGTAGEPPQTLTQIGRRLGVSSSRAREIEEQALRRLSRETSLSALR 282


>gi|330982601|gb|EGH80704.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 459

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 141/225 (62%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 36  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 95

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE
Sbjct: 96  ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPE 155

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L  PV  V+++L + +   S++  +G +    L D + D     P +     +L 
Sbjct: 156 EIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS 215

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER
Sbjct: 216 QSIDQWLSELTEKQREVVIRRFGLRGHESSTLEDVGLEIGLTRER 260


>gi|299472557|emb|CBN79859.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 835

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 96/243 (39%), Positives = 151/243 (62%), Gaps = 13/243 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+ ANLRLV+S+A+ Y  RGL F DLIQEG +GL+KA EKF+  +G++F TYA WW
Sbjct: 300 AKEHMISANLRLVVSMARGYRGRGLAFPDLIQEGTMGLVKACEKFNPEMGFQFYTYARWW 359

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK---REPTPEEIAKKLAMPV 560
           +K++I   IA+QS  IR+P     ++H  + + R+ + ++    + PT EE+  KL   V
Sbjct: 360 IKKSILTGIANQSRVIRLPT----QVHAFLSSIRKYTYELTVDGKVPTDEELGDKLGATV 415

Query: 561 EGVR--KVLKITKEPISLE----TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           E ++  +   +  + ISL+      + D     LG  I +K+   P D+     ++   T
Sbjct: 416 EKIQHYRQAALRTDSISLDIRASNKVSDGAADDLGTQIGEKSTPDPEDATQAFYMKGKVT 475

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +LA+L  RE++V+R R+G+   T  TLEE+G+   +TRER+RQIE+KA+ KL+ P R+ 
Sbjct: 476 ALLATLKDREQKVVRARYGLDGATSKTLEEIGRDLGLTRERVRQIESKALSKLRQPYRNY 535

Query: 675 KLR 677
           ++R
Sbjct: 536 RVR 538


>gi|163783667|ref|ZP_02178655.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881072|gb|EDP74588.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 309

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 100/303 (33%), Positives = 168/303 (55%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K IS    +S  E + +    ++G+ E+    K++VE+NLR V+SVAK+Y   GL
Sbjct: 9   INQYLKRISKIPLLSPEEEKELARKAKEGDEESL---KKLVESNLRFVVSVAKQYIGYGL 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F +LI  GN+GL++AA++FD   G KF +YA+WW++QAI ++++ Q+  +RIP+     
Sbjct: 66  PFSELIAAGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQSHL 125

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLA------------------------------- 557
           I K+      ++ +++REPTPEE+A++L+                               
Sbjct: 126 ISKIGTIYAELAKELEREPTPEEVAEQLSKEMIAKELTKELGREPTDEEVQKKFKKEGYK 185

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E V K L++ + P+SL+ P+G+ + +   DF+         +S IQ  L +    +L
Sbjct: 186 ISPEEVEKYLQVCRIPLSLDAPVGENEDTFFVDFLSKHGTAEVEESVIQEVLEKEIYDLL 245

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L  +E RV+ +RFG+  N   TL E+G    V+RER+RQ+E +A+RKL+  +  + L+
Sbjct: 246 DKLPEKERRVVELRFGLKGNEPKTLREIGDILGVSRERVRQLETRALRKLRSLAMKRHLK 305

Query: 678 SFL 680
            FL
Sbjct: 306 DFL 308


>gi|56475838|ref|YP_157427.1| RNA polymerase sigma factor RpoS [Aromatoleum aromaticum EbN1]
 gi|56311881|emb|CAI06526.1| RNA sigma factor RpoS [Aromatoleum aromaticum EbN1]
          Length = 311

 Score =  177 bits (449), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 94/236 (39%), Positives = 151/236 (63%), Gaps = 5/236 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR G+  A   ++ M+E NLRLV+++AK Y NRG+  LDL++EGN+GLM A EKFD   G
Sbjct: 66  VRTGDFPA---RQIMIERNLRLVVNIAKHYLNRGIPLLDLVEEGNLGLMHALEKFDPERG 122

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R+I +QS TIR+PVH+  ++++V+R  R +      E T E++A
Sbjct: 123 FRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKELNQVLRAQRTLEASGNGEFTLEQVA 182

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRET 612
            +L   V+ VR +L +++   SL+ P+  + T  +G+ + D  A  P D+ IQ A + + 
Sbjct: 183 HRLDKSVDEVRAILALSEHTASLDAPLEIDPTLSIGESLADDQA-EPPDTHIQDAEVEKL 241

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  ++  V+R R+G+      TLEE+  + C+TRER+RQI+ +A+ +L+
Sbjct: 242 IQEWIGMLNEKQRLVIRHRYGLDECEVMTLEELASRLCLTRERVRQIQLEALGQLR 297


>gi|149177995|ref|ZP_01856592.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
 gi|148843188|gb|EDL57554.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
          Length = 279

 Score =  177 bits (449), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 98/259 (37%), Positives = 160/259 (61%), Gaps = 11/259 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K I+    +S  E R + + +  G+ EA   +  MV ANLRLV+++A+ Y+ +GL   D
Sbjct: 21  LKEINETALLSAEEERELSNRIEHGDKEA---RDRMVRANLRLVVNIARAYSGKGLPLQD 77

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A E FD  +G +FSTYA +W+KQ+I R++ + + TIRIP +M + + K 
Sbjct: 78  LIEEGNLGLLRAVEGFDPEMGTRFSTYASYWIKQSIKRALVNSAKTIRIPAYMVELLTKW 137

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL--ETPIGDEDTS--HL 588
            R   ++ + + R PT EE+A++L +P     K LKI K+ I L   +P  ++  +   L
Sbjct: 138 RRATAQLQDTLDRTPTTEEVARELDLPP----KKLKIVKKAIQLYNSSPQSEQHDAGWSL 193

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ I D     P D  ++ +  +   R+L  +  RE  +LRMRFG+  +   TL+E+G+ 
Sbjct: 194 GEMIPDDRLKGPDDELVENDNLKHVFRLLKEIPEREANILRMRFGLDGDEPKTLKEIGQA 253

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE++A++KL
Sbjct: 254 LGLTRERVRQIESEALKKL 272


>gi|282858973|ref|ZP_06268111.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588253|gb|EFB93420.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 286

 Score =  177 bits (448), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 155/247 (62%), Gaps = 4/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RKG+ +A    + +  ANLR V+SVAK+Y  +G+   DLI EGN+GL+KAA++FD   G
Sbjct: 43  IRKGDKKAL---ERLTRANLRFVVSVAKQYQTQGIDLPDLINEGNMGLIKAAKRFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++IA Q   IR+P +    ++K+ R   +   + +R P  +E+A
Sbjct: 100 FKFISYAVWWIRQSILQAIAAQGRLIRLPANQIGVVNKITRILNKFEQENERIPNIDELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ +  E +   L ++   +S+++P  D++   L D +   N  S   S +  +L+E  
Sbjct: 160 REVDLSEEHIEDALSLSFRQVSMDSPFKDDEGVSLLDVMPSTNVPSTDKSLVDESLKEEI 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +R L  L+ RE++VL   +GIG   + +LEE+G +F ++RER+RQI+ KAIR L+    +
Sbjct: 220 SRALKILSEREQKVLCAYYGIG-QLEMSLEEIGDKFGLSRERVRQIKEKAIRNLRKAGNN 278

Query: 674 KKLRSFL 680
           K LR +L
Sbjct: 279 KTLRVYL 285


>gi|289805026|ref|ZP_06535655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 196

 Score =  177 bits (448), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 97/178 (54%), Positives = 125/178 (70%), Gaps = 5/178 (2%)

Query: 370 FLERHQGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+    G E    W   + A + P  E  + VA EV   L+   +++ I  ETG++I + 
Sbjct: 22  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQV 78

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 79  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 138

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ R
Sbjct: 139 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 196


>gi|219111033|ref|XP_002177268.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411803|gb|EEC51731.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 324

 Score =  177 bits (448), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 150/251 (59%), Gaps = 12/251 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV++N+RLV+S+A+KY+N G+   DL+QEG++GL +AAEKF+   G+KFSTYA WW
Sbjct: 71  AKQRMVQSNMRLVVSIARKYSNVGVSLQDLVQEGSLGLSRAAEKFEPKKGFKFSTYASWW 130

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ RSIA  S TIR+PVH+ + +++V +    +  ++ R PT EE+A++L M ++  
Sbjct: 131 IQQAVFRSIAYHSRTIRLPVHVHNLLNRVRKVRNNLQRELSRTPTNEEMAEELGMTLQKY 190

Query: 564 RKVLKITKEPISLETP--------IGDEDTSHLGDFIEDKNAV----SPLDSAIQANLRE 611
            K+L++TK  ISLETP        +G E    LGD I   +A+    +P     +    E
Sbjct: 191 NKMLRLTKRSISLETPKYQSNPKDLGHESHDLLGDTISASSALFDESTPEKRVDRGIFHE 250

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L   E RV+  R+G+      T+  V  Q   ++  +R  E +A+RKL+ P 
Sbjct: 251 DLHEMLEILDEDERRVICSRYGLSDGLTRTVTAVASQMKQSKAWVRSQECRALRKLRRPW 310

Query: 672 RSKKLRSFLDG 682
             KKL+   D 
Sbjct: 311 YEKKLKEHQDA 321


>gi|162458864|ref|NP_001104924.1| sigma-like factor2B [Zea mays]
 gi|4336608|gb|AAD17855.1| sigma factor SIG2B [Zea mays]
          Length = 527

 Score =  177 bits (448), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 91/237 (38%), Positives = 149/237 (62%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+AK++   G++F DLIQ+G  GL++ AEKFD   G++FSTY+ WW
Sbjct: 286 CKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEKFDASKGFRFSTYSHWW 345

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR P+ EEIA    M +  V
Sbjct: 346 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRLPSNEEIAVDTGMTIRRV 405

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +S  + +G  D ++  + + D +A +  ++  +  +++     L SL+PR
Sbjct: 406 EAAMSLPKYSVSFTSKVGCTDVTY-QEIMPDTSAETAEETLHRWLMKKDVNTALDSLSPR 464

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +++V+R RFGI      TL ++G+   V+RERIRQIE  A RKL+  +R + L+ +L
Sbjct: 465 KKQVMRYRFGIEGGRARTLHDIGQLMGVSRERIRQIELGAFRKLRSKNRLQSLQHYL 521


>gi|55274919|gb|AAV49261.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 201

 Score =  177 bits (448), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 82/200 (41%), Positives = 137/200 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EG++GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGSLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEVGK 647
           L  RFG+      TLE+VG+
Sbjct: 182 LARRFGLLGYEAATLEDVGR 201


>gi|114776318|ref|ZP_01451363.1| RpoS [Mariprofundus ferrooxydans PV-1]
 gi|114553148|gb|EAU55546.1| RpoS [Mariprofundus ferrooxydans PV-1]
          Length = 282

 Score =  176 bits (447), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 91/227 (40%), Positives = 150/227 (66%), Gaps = 3/227 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV+ANLRLV+ ++++Y NRG+   DLI+EGN+GL++A EKFD   G +FSTYA WW
Sbjct: 43  AHHYMVQANLRLVVKISRRYMNRGVALADLIEEGNLGLIRAVEKFDVTHGCRFSTYATWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ R+I +QS TIR+PVH+  +++ + +   R+ ++++R+PT  EIA+ + + V+ +
Sbjct: 103 IRQAVERAIMNQSRTIRVPVHVGKELYALTKHTNRLRSELERDPTDVEIAEAMGVSVQRI 162

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTP 622
           ++++       S +  + D+    L D   D+ A SP D  +Q  LR    +V ++ L  
Sbjct: 163 QELMGAAVRTDSADDMLHDDSDFTLYDVTADEAAESPGDQ-MQTVLRNEILQVWMSKLEK 221

Query: 623 REERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E  V+R+R+G+    D  TLE +G+Q  VTRERIRQI+ +A++KL+
Sbjct: 222 KEREVVRLRYGLDDAGDPWTLEMIGEQLGVTRERIRQIQVQALQKLR 268


>gi|4100832|gb|AAD00998.1| RpoS [Escherichia coli]
          Length = 269

 Score =  176 bits (447), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 78/191 (40%), Positives = 133/191 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 77  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 136

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 137 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 196

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 197 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 256

Query: 624 EERVLRMRFGI 634
           +  VL  RFG+
Sbjct: 257 QREVLARRFGL 267


>gi|55275000|gb|AAV49297.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 203

 Score =  176 bits (447), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 82/202 (40%), Positives = 137/202 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  L LI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 181 LARRFGLLGYEAATLEDVGREI 202


>gi|77163721|ref|YP_342246.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254436220|ref|ZP_05049727.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
 gi|76882035|gb|ABA56716.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207089331|gb|EDZ66603.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
          Length = 321

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/225 (36%), Positives = 145/225 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL+ A EKFD  +G++FSTYA WW
Sbjct: 82  GRKRMIESNLRLVVKISRRYMNRGLALLDLIEEGNLGLIHAVEKFDPEMGFRFSTYATWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ T+R+PVH+  +I    R A +++ +++ +P+ EE+A++L  PVE +
Sbjct: 142 IRQTIERALMNQTRTVRLPVHVVKEIKSYQRVANKLAQELEHDPSFEELAQQLNKPVEEI 201

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++V  +     S++T   +     L D + D++A  P       +++      L+ L  +
Sbjct: 202 KRVWSLKDNTASMDTGYRNNQEKTLLDALPDEDAPDPTVLLQNDDMQSRLKLWLSQLNDK 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+      TLE+VG+   VTRER+RQI+ + +++L+
Sbjct: 262 QREVVIRRFGLQGYEPQTLEQVGQAIGVTRERVRQIQLETLKRLR 306


>gi|2564653|gb|AAC45358.1| group 2 alternative sigma factor [Nostoc punctiforme PCC 73102]
          Length = 321

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 85/218 (38%), Positives = 140/218 (64%), Gaps = 3/218 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+S+AK+Y  R L+ +DLIQEG +GL +  EKF+  LGY+ +TYA WW
Sbjct: 94  AKHKMITANLRLVVSIAKQYQRRNLELMDLIQEGTLGLERGVEKFNPALGYRKTTYAYWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA Q   IR+P+H+ +K++K+ R  R +S  + R PT  EIA  L++    +
Sbjct: 154 IRQGITRAIAQQGRAIRLPIHINEKLNKIKRVQRELSQTLGRIPTSTEIANALSLKPSQI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTP 622
           R+ L +    ISL+  +       L D IED    S  +S I + +L +    +L++L+ 
Sbjct: 214 REFLLLATRTISLDIRVSSAKDLRLQDLIEDYKYSS--NSYITEESLNQEVNSLLSNLSR 271

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +++ +L + FG+    + +L+++G++  ++RER+RQIE
Sbjct: 272 QQQEILNLHFGLTDGEELSLQQIGQRLGISRERVRQIE 309



 Score = 38.9 bits (89), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
            F   +  + +++T D VR YL+E+G I LL++E EI  A+ ++     +M  L ES
Sbjct: 5   TFSDTKASNTNKATTDTVRAYLKEIGRIPLLTQEQEIIFAQEVQ----QLMTILAES 57


>gi|14581457|gb|AAK29754.1| stationary phase sigma factor RpoS [Azotobacter vinelandii]
          Length = 238

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 147/241 (60%), Gaps = 3/241 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     ++ +E  H   + ++G+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 1   LNEIGFSPLLTPAEEVHFARLAQRGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 57

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 58  LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+ EEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 118 LRAARELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDVL 177

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P D     +L ++  + L  LT ++  V+  RFG+  +   TLEEVG++  +T
Sbjct: 178 TDDRPFDPCDLLQDDDLSQSIDQWLFDLTEKQREVVVRRFGLRGHESCTLEEVGQEIGLT 237

Query: 653 R 653
           R
Sbjct: 238 R 238


>gi|67925817|ref|ZP_00519113.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
 gi|67852341|gb|EAM47804.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
          Length = 386

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 100/255 (39%), Positives = 159/255 (62%), Gaps = 17/255 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E GIS+ E + I+   ++       AK++M++ANLRLV++V+KKY  +GL+F+DL+ EGN
Sbjct: 5   EIGISVRELQLILKRGKR-------AKEKMIQANLRLVVAVSKKYQGKGLEFMDLVSEGN 57

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A EKF++  GYKFSTYA  W++QA+ R+I D+  TIR+PVH+ ++I K+ +    
Sbjct: 58  LGLIRAVEKFEYDKGYKFSTYAYHWIRQALVRAICDKGRTIRVPVHINEEISKLKKVQLE 117

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNA 597
           +  K  R  T  E++++L +  E +R +  +    +SL+  + GDED S L  F+ D N 
Sbjct: 118 IRQKYGRSATVRELSERLEISPEKIRVLRSVNNPMLSLDQKVLGDEDNSTLLSFLADPNG 177

Query: 598 --VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRE 654
                LD+    N +E   + L  L P+E+RVLR  +   + T   TL E+GK+  ++RE
Sbjct: 178 DLQKFLDNL--GN-KELVEQCLCGLKPQEQRVLREYY---LETPSLTLNEIGKKMNLSRE 231

Query: 655 RIRQIEAKAIRKLKH 669
           R+R I+  A+ KLK 
Sbjct: 232 RVRHIKNNALDKLKQ 246


>gi|4100836|gb|AAD01000.1| RpoS [Escherichia coli]
          Length = 259

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 78/191 (40%), Positives = 133/191 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 67  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 126

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 127 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 186

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 187 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 246

Query: 624 EERVLRMRFGI 634
           +  VL  RFG+
Sbjct: 247 QREVLARRFGL 257


>gi|4100834|gb|AAD00999.1| RpoS [Escherichia coli]
          Length = 258

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 78/191 (40%), Positives = 133/191 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 66  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 126 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 185

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 186 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 245

Query: 624 EERVLRMRFGI 634
           +  VL  RFG+
Sbjct: 246 QREVLARRFGL 256


>gi|257452079|ref|ZP_05617378.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|257466122|ref|ZP_05630433.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917279|ref|ZP_07913519.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|317058628|ref|ZP_07923113.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313684304|gb|EFS21139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313691154|gb|EFS27989.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 272

 Score =  176 bits (445), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 99/242 (40%), Positives = 152/242 (62%), Gaps = 14/242 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++  NLRLV++VAK Y ++G+  +DLI EGN+GL++A EKFD   G++FSTYA+WW
Sbjct: 39  AKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVGKGFRFSTYAVWW 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I+++I  +   IRIP +  D ++K+ +            PT EE+A+ L MPV  V
Sbjct: 99  IKQSISKAIIFKGREIRIPSYRYDILNKINKYVTETVKLCGIYPTVEEVAEYLKMPVNKV 158

Query: 564 RKVLKITKEPISLETPIGD----EDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +V+   +EP+SL T IG+    EDT S   +  E+K         +Q  L++    +L+
Sbjct: 159 EEVMIEFQEPMSLSTEIGEDIYLEDTLSGAEEHFEEKVYY----KMMQQRLKD----ILS 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE+ +L++RFG+     HTLE++GK F +TRER+RQIE   ++KLK    +K+LR 
Sbjct: 211 RLESREQEILKLRFGLDGYEIHTLEDIGKNFNITRERVRQIEKNTLKKLKRKY-TKELRE 269

Query: 679 FL 680
            L
Sbjct: 270 TL 271


>gi|55274989|gb|AAV49292.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 199

 Score =  176 bits (445), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 82/198 (41%), Positives = 135/198 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGIGMNTDHTLEEV 645
           L  RFG+      TLE+V
Sbjct: 182 LARRFGLLGYEAATLEDV 199


>gi|55274998|gb|AAV49296.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 198

 Score =  176 bits (445), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 82/198 (41%), Positives = 135/198 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEV 645
           L  RFG+      TLE+V
Sbjct: 181 LARRFGLLGYEAATLEDV 198


>gi|310779070|ref|YP_003967403.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309748393|gb|ADO83055.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 275

 Score =  176 bits (445), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 98/245 (40%), Positives = 151/245 (61%), Gaps = 5/245 (2%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K  CE   AK +++ +NLRLV+++AK Y ++G+ F+DLI EGN GLM A EKFD   G++
Sbjct: 34  KSGCED--AKHKLILSNLRLVVNIAKSYVHKGMGFIDLISEGNFGLMHAIEKFDVEKGFR 91

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA+WW+KQ+I+++I  +   IRIP +  D ++KV +       K    P  E+IA  
Sbjct: 92  FSTYAVWWIKQSISKAIISKGREIRIPSYKHDLLNKVNKFIMEFVMKNSVYPNIEDIALG 151

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +  + V+KV+   ++ +SL   IGD+    L D I   +  S  D  +    R     
Sbjct: 152 LEITPKKVQKVMLEFQDLLSLNASIGDD--IFLEDTISQPDEESLEDEVLGEIGRNEIND 209

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  L PRE+ +L++R+G+     HTLEE+GK F +TRER+RQIE K ++KL++   S++
Sbjct: 210 ILEVLKPREKEILKLRYGLDGYEIHTLEEIGKSFSITRERVRQIEKKTLQKLRNKF-SEE 268

Query: 676 LRSFL 680
           L+ +L
Sbjct: 269 LKPYL 273


>gi|144575120|gb|AAZ43865.2| DNA-directed RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 798

 Score =  176 bits (445), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 99/253 (39%), Positives = 150/253 (59%), Gaps = 18/253 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG      A+  +++ NLRLV++ AKKY NRGL F+DL+ EGN GL+KAA+KFD   G+K
Sbjct: 530 KGGSRGKRARDLIIKRNLRLVVNAAKKYKNRGLSFIDLVSEGNAGLLKAAQKFDIKKGFK 589

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q+I+R++ADQ+  IR+PVHM + I+K+ +  R +  +   E   EEIA +
Sbjct: 590 FSTYATWWIRQSISRAVADQARIIRVPVHMVETINKIYKIEREIQQENGGEIIDEEIAAR 649

Query: 556 LA-----MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           L           +R + KI   PISL+  +G E+ S  GDF++D++ +SP++ A +  L 
Sbjct: 650 LGGKSKKYDASYIRYIRKINTSPISLDKQVGKENDSFFGDFVKDESIISPVEFADKEELI 709

Query: 611 ETTTRVLASLTPREERVLRMRF-GIGMNT------DHTLEEVGKQF-----CVTRERIRQ 658
                 +  L    E  L  R+ GIG +         TL+E+ K F      +++ER+RQ
Sbjct: 710 TKINYYVEKLLSEAEADLIKRYHGIGYDAKGNPVRSATLDEISKDFRGEGKKISKERVRQ 769

Query: 659 IEAKAIRKLK-HP 670
           I  K  +KL+ +P
Sbjct: 770 IITKIYKKLRGYP 782


>gi|90577776|ref|ZP_01233587.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440862|gb|EAS66042.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 291

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 143/236 (60%), Gaps = 1/236 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK  C  + +K  ++E+NLRLV+S+AKKY    +   DLI EGNIGLM A EKFD   G+
Sbjct: 40  RKSLCGDACSKNVLIESNLRLVVSIAKKYRGSSIHISDLIDEGNIGLMTAVEKFDPEKGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW+KQ I R+I +Q  TIR+PVH+  +I+ ++RT +++  K  +EP+ E +A+
Sbjct: 100 RFSTYATWWIKQTIERAIHNQGRTIRLPVHVSKEINTIIRTHKQLVKKNNQEPSTELVAE 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETT 613
            L   ++ V   L      +S +  I  E TS  +   I D+N+  P +      +++ T
Sbjct: 160 VLNKTLDDVSTTLSYDTPIVSYDQSITSEATSQSIAVLIADENSAKPDELVDDLAIQKIT 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             VL  L  R++ ++  RFG+      TL+EV ++  +TRERIRQ++  ++ KLK+
Sbjct: 220 ANVLKCLNNRDKEIICRRFGLLGYEAQTLQEVAEEVGLTRERIRQLQVTSLAKLKN 275


>gi|33862400|ref|NP_893960.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640513|emb|CAE20302.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 335

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 92/230 (40%), Positives = 143/230 (62%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 100 AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V
Sbjct: 160 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEV 219

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L   +       P +      ++     +L  L   
Sbjct: 220 KDLMCRARQPMSLEMKVGDGDETEL-LELLAGEEELPSEKVEVDCMKGDLRTLLEKLPEL 278

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           + RVLRMR+GI       L  +G+   ++R+R+R +E   +  L+  S +
Sbjct: 279 QGRVLRMRYGIDGGEPMNLTGIGRILDISRDRVRNLERHGLNGLRQLSET 328


>gi|327538655|gb|EGF25307.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica WH47]
          Length = 330

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 90/230 (39%), Positives = 147/230 (63%), Gaps = 10/230 (4%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+ +MV ANLRLV+++++ YT +GL   DLI+EGN+GL++A E FD   G +FSTYA +
Sbjct: 94  MARDQMVRANLRLVVNISRGYTGKGLGLQDLIEEGNLGLLRAVEGFDPIHGTRFSTYASY 153

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--- 559
           W+KQ+I R++ + + TIRIP +M + + K  R   R++ ++ R PT EE+A+ L +P   
Sbjct: 154 WIKQSIKRALINSAKTIRIPAYMVELLSKWRRATARLNEELGRTPTNEEVARVLGLPKKK 213

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  +RK +KI        TP  D+  +   LGD ++D+   +P +  +  ++ +    +L
Sbjct: 214 LPIIRKAIKINN-----STPQSDQTEAGWSLGDMVQDERLKAPDEEMLDHDILKHAMSLL 268

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L  RE  VL++RFG+G     TL+E+G +  +TRER+RQIE +A+R+L
Sbjct: 269 GDLEERESTVLKLRFGLGGVEPMTLKEIGAELGLTRERVRQIETEALRRL 318


>gi|149921691|ref|ZP_01910139.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149817429|gb|EDM76901.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 384

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 89/223 (39%), Positives = 140/223 (62%), Gaps = 1/223 (0%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +  +ANLRLV+S+A++ +N  L   DLIQEGNIGL+KA E+FD   G++FSTYA WW++ 
Sbjct: 153 DFAKANLRLVVSLARRLSNGRLPLQDLIQEGNIGLLKAIERFDHRKGFRFSTYASWWIRH 212

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +I+R+I ++   +R+PVH+ D   K+ R  RR   +I REPT EEIA ++ +P+  V K+
Sbjct: 213 SISRAIYNKGRQVRLPVHVYDVHQKITRVRRRYEAQIGREPTHEEIANEIGVPLAKVEKI 272

Query: 567 LKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             I   PI SL+ P+   D     D +ED+ +  P        L E     L++L P E 
Sbjct: 273 AAIELGPIVSLDAPLSRNDDRSGVDLLEDQVSPGPGFELELGELEEGLEDALSALRPMEA 332

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +LR R+G+      TL E+G+++ ++RERIRQ++ +A+ +++
Sbjct: 333 DILRRRYGLDGVEKETLREIGERYALSRERIRQLQERAVSRMR 375


>gi|124021877|ref|YP_001016184.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962163|gb|ABM76919.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 350

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 92/230 (40%), Positives = 143/230 (62%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 115 AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 174

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V
Sbjct: 175 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEV 234

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L   +       P +      ++     +L  L   
Sbjct: 235 KDLMCRARQPMSLEMKVGDGDETEL-LELLAGEEELPSEKVEVDCMKGDLRTLLEKLPEL 293

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           + RVLRMR+GI       L  +G+   ++R+R+R +E   +  L+  S +
Sbjct: 294 QGRVLRMRYGIDGGEPMNLTGIGRILDISRDRVRNLERHGLNGLRQLSET 343


>gi|158833999|gb|ABW81805.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 79/202 (39%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+  C    +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 67  VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDP 126

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +QS TIR+P+H+  +++  +RTAR +++K+  EP+ E
Sbjct: 127 ERGFRFSTYATWWIRQTIERAIMNQSRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAE 186

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S+++P+G +    L D + D +   P D+    +++
Sbjct: 187 EIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSEKALLDILSDDSENGPEDTTQNDDMK 246

Query: 611 ETTTRVLASLTPREERVLRMRF 632
            +  + L  L  ++  VL  RF
Sbjct: 247 HSIVKWLFELNAKQREVLARRF 268


>gi|312891071|ref|ZP_07750594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311296379|gb|EFQ73525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 89/239 (37%), Positives = 156/239 (65%), Gaps = 5/239 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + + NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALERLTKTNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I  ++A+QS  +R+P++    ++K+ +   ++  + +REP+  E+A  L    + +
Sbjct: 110 IRQSILSAVAEQSRIVRLPLNQIGSLNKIRQAFSKLEQQYEREPSQAELADILETTEDKI 169

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L  +   +S++ P   G+E+T  L D +++ N  +  D  ++ +L +   R L +L 
Sbjct: 170 CDSLSNSGRHVSMDAPFVQGEENT--LLDVLQN-NEPTTDDYLMEESLSQEIMRSLVTLA 226

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE  V+ + FG+G N   +LEE+G+++ +TRER+RQI+ KA+++L+H SRS  L+S+L
Sbjct: 227 EREREVIVLFFGLGNNYPLSLEEIGEKYNLTRERVRQIKDKALQRLRHTSRSNLLQSYL 285


>gi|114155162|dbj|BAF31031.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 250

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 114/236 (48%), Positives = 142/236 (60%), Gaps = 41/236 (17%)

Query: 76  NVVDGDDLED---------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           NVV+ +D ED         EE   +  +LA  A N++V   K+K+  DR TDDPVRMYLR
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAP-AGNTAVATAKKKEPTDR-TDDPVRMYLR 58

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIID
Sbjct: 59  EMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIID 118

Query: 187 LEACI-GPESKGGF-FHGTEGHSYQKREDSSQEKER------DDVQETEGDIESAAKVSK 238
           LE    GPE+K    F   E     ++    +EK R      DD+    GD++   +  +
Sbjct: 119 LETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRVRSSEDDITNVGGDMQMPEEEEE 178

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           D+                NL         +L+AME +LRP+VM  LD IA+ Y++L
Sbjct: 179 DEDES-------------NL---------SLAAMEAELRPQVMETLDLIADTYKKL 212


>gi|32472693|ref|NP_865687.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
 gi|32443930|emb|CAD73372.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
          Length = 355

 Score =  175 bits (443), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 90/230 (39%), Positives = 147/230 (63%), Gaps = 10/230 (4%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+ +MV ANLRLV+++++ YT +GL   DLI+EGN+GL++A E FD   G +FSTYA +
Sbjct: 119 MARDQMVRANLRLVVNISRGYTGKGLGLQDLIEEGNLGLLRAVEGFDPIHGTRFSTYASY 178

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--- 559
           W+KQ+I R++ + + TIRIP +M + + K  R   R++ ++ R PT EE+A+ L +P   
Sbjct: 179 WIKQSIKRALINSAKTIRIPAYMVELLSKWRRATARLNEELGRTPTNEEVARVLGLPKKK 238

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  +RK +KI        TP  D+  +   LGD ++D+   +P +  +  ++ +    +L
Sbjct: 239 LPIIRKAIKINN-----STPQSDQTEAGWSLGDMVQDERLKAPDEEMLDHDILKHAMSLL 293

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L  RE  VL++RFG+G     TL+E+G +  +TRER+RQIE +A+R+L
Sbjct: 294 GDLEERESTVLKLRFGLGGVEPMTLKEIGAELGLTRERVRQIETEALRRL 343


>gi|260773542|ref|ZP_05882458.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
 gi|260612681|gb|EEX37884.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
          Length = 297

 Score =  174 bits (442), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 82/189 (43%), Positives = 128/189 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 81  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 140

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPT EEIA +L  PVE V
Sbjct: 141 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTAEEIAAELDKPVEDV 200

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D + D N   P  S    ++R +    L  L P+
Sbjct: 201 NKMLRLNERISSVDTPIGGDGDKALLDILPDSNHSDPEVSTQDEDIRLSLLNWLDELNPK 260

Query: 624 EERVLRMRF 632
           ++ VL  R 
Sbjct: 261 QKEVLARRL 269


>gi|77165179|ref|YP_343704.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254434741|ref|ZP_05048249.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|76883493|gb|ABA58174.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207091074|gb|EDZ68345.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 303

 Score =  174 bits (442), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 155/250 (62%), Gaps = 10/250 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E RH   + ++G+ EA   +  ++E+NLR+VI +A ++ NRGL  +DLI+EGN+GL
Sbjct: 52  LSAEEERHYARLAQQGDREA---RNHIIESNLRIVIRMATRHINRGLPLMDLIEEGNLGL 108

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A EKF+  LG++FSTYA WW++QAI R++ +Q+ TIR+P+H+  KI    + AR    
Sbjct: 109 IDAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRVPIHVFKKIRCYQKEARYFRQ 168

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP   EIAK L  P+E +++ L +    ISL+ P+ ++    L D + D+      
Sbjct: 169 RYNIEPHLGEIAKLLHEPLERIQRYLSLQAPEISLDDPLSEDTDDCLVDLLPDERN---- 224

Query: 602 DSAIQANLRETTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           + AI   + +    +   L+ L  R++ +++ R+G+      TLEE+G++  +TRER+RQ
Sbjct: 225 NPAILWEIFDKKASIHNQLSQLPERQQEIIKCRYGLDGYEVTTLEEIGQKLGITRERVRQ 284

Query: 659 IEAKAIRKLK 668
           I+  AI++L+
Sbjct: 285 IQQTAIKRLR 294


>gi|158833997|gb|ABW81804.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  174 bits (441), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 78/202 (38%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+  C    +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 67  VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDP 126

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ E
Sbjct: 127 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAE 186

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S+++P+G +    L D + D +   P D+    +++
Sbjct: 187 EIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSEKALLDILSDDSENGPEDTTQNDDMK 246

Query: 611 ETTTRVLASLTPREERVLRMRF 632
            +  + L  L  ++  VL  RF
Sbjct: 247 HSIVKWLFELNAKQREVLARRF 268


>gi|317060654|ref|ZP_07925139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
 gi|313686330|gb|EFS23165.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 276

 Score =  174 bits (441), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 99/242 (40%), Positives = 151/242 (62%), Gaps = 14/242 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++  NLRLV++VAK Y ++G+  +DLI EGN+GL++A EKFD   G++FSTYA+WW
Sbjct: 43  AKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVEKGFRFSTYAVWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I+++I  +   IRIP +  D ++K+ R            P+ EE+A+ L MPV  V
Sbjct: 103 IKQSISKAIIFKGREIRIPSYRYDILNKINRYVTEEIKLYGVYPSVEEVAEYLNMPVNKV 162

Query: 564 RKVLKITKEPISLETPIGD----EDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +++   +EP+SL T IG+    EDT S   +  E+K         +Q  L++    +L 
Sbjct: 163 EEIMIEFQEPMSLSTEIGEDIYLEDTLSGTEEHFEEKVYY----KMMQQRLKD----ILN 214

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE+ +L++RFG+     HTLEE+GK F +TRER+RQIE   ++KLK    +K+LR 
Sbjct: 215 RLDTREQEILKLRFGLDGYEIHTLEEIGKNFNITRERVRQIEKNTLKKLKRKY-TKELRE 273

Query: 679 FL 680
            L
Sbjct: 274 TL 275


>gi|257463050|ref|ZP_05627452.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 272

 Score =  174 bits (441), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 99/242 (40%), Positives = 151/242 (62%), Gaps = 14/242 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++  NLRLV++VAK Y ++G+  +DLI EGN+GL++A EKFD   G++FSTYA+WW
Sbjct: 39  AKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVEKGFRFSTYAVWW 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I+++I  +   IRIP +  D ++K+ R            P+ EE+A+ L MPV  V
Sbjct: 99  IKQSISKAIIFKGREIRIPSYRYDILNKINRYVTEEIKLYGVYPSVEEVAEYLNMPVNKV 158

Query: 564 RKVLKITKEPISLETPIGD----EDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +++   +EP+SL T IG+    EDT S   +  E+K         +Q  L++    +L 
Sbjct: 159 EEIMIEFQEPMSLSTEIGEDIYLEDTLSGTEEHFEEKVYY----KMMQQRLKD----ILN 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE+ +L++RFG+     HTLEE+GK F +TRER+RQIE   ++KLK    +K+LR 
Sbjct: 211 RLDTREQEILKLRFGLDGYEIHTLEEIGKNFNITRERVRQIEKNTLKKLKRKY-TKELRE 269

Query: 679 FL 680
            L
Sbjct: 270 TL 271


>gi|149916815|ref|ZP_01905317.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149822532|gb|EDM81921.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 421

 Score =  174 bits (441), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 97/286 (33%), Positives = 163/286 (56%), Gaps = 9/286 (3%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISE-FRHIVSMVRKGECEASIAKKEMVE 450
           +G + + VA ++++I   R E  ++ V      S  F   V  VR        +K + V+
Sbjct: 127 DGNYSDCVAADLEAIDAHRREGVALEVSYPPKGSRPFARYVQKVRSSGHALRWSKNKFVK 186

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+++A+++ +  +   DL+QEGN+GLMKA ++FD   GY+FSTYA WW++ AI R
Sbjct: 187 ANLRLVVTIARRFDHGLMPLQDLVQEGNLGLMKAVDRFDPTRGYRFSTYATWWIRHAINR 246

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           ++A++  T+R+P H+   + ++ R  R +  K    PTPE++A+   +    VRK+ K+T
Sbjct: 247 ALANKGRTVRLPAHVSADLQRLRRVTRELEAKTGETPTPEQLAQAAGLSKTRVRKLSKLT 306

Query: 571 KEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +P +SL+ P  D+D   L D +ED +     D      L E     L +L P E  +L+
Sbjct: 307 LDPTVSLDAPSHDDDARGLLDRLEDASVPVAADILEHQALNEHLRDALYNLQPIELDILK 366

Query: 630 MRFGIGMNTDH-------TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+GI  +          TL ++G++  ++RERIRQ++ +A+ KL+
Sbjct: 367 RRYGIATSEAESVDFEPMTLRQLGERHSLSRERIRQLQERALTKLR 412


>gi|55274930|gb|AAV49266.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  174 bits (441), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 81/198 (40%), Positives = 134/198 (67%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V +
Sbjct: 61  QTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSR 120

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 121 MLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 180

Query: 626 RVLRMRFGIGMNTDHTLE 643
            VL  RFG+      TLE
Sbjct: 181 EVLARRFGLLGYEAATLE 198


>gi|42566462|gb|AAS21043.1| major sigma factor 70 [Deinococcus grandis]
 gi|42566464|gb|AAS21044.1| major sigma factor 70 [Deinococcus proteolyticus]
          Length = 168

 Score =  174 bits (440), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 89/168 (52%), Positives = 120/168 (71%), Gaps = 2/168 (1%)

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T EEIA+ + 
Sbjct: 1   TYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREATYEEIAEAMG 60

Query: 558 MPVEG--VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
              +   V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+++A +  L E   +
Sbjct: 61  PGWDAAKVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVENAAKTLLSEELEK 120

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            L+ LT RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA
Sbjct: 121 ALSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKA 168


>gi|158833995|gb|ABW81803.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  174 bits (440), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 78/202 (38%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R+  C    +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 67  VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDP 126

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ E
Sbjct: 127 ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAE 186

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S+++P+G +    L D + D +   P D+    +++
Sbjct: 187 EIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSEKALLDILSDDSENGPEDTTQNDDMK 246

Query: 611 ETTTRVLASLTPREERVLRMRF 632
            +  + L  L  ++  VL  RF
Sbjct: 247 HSIVKWLFELNAKQREVLARRF 268


>gi|326518320|dbj|BAJ88189.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326533296|dbj|BAJ93620.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 552

 Score =  173 bits (439), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 93/236 (39%), Positives = 152/236 (64%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  MV +N+RLVIS+A+++   GL+  DLIQEG  GL++ AEKFD   G++FSTY+ WW+
Sbjct: 312 KNRMVTSNVRLVISIAREFEGPGLELYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWI 371

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQA+ +S+++Q+   R+P HM +  ++V    +R+  K+KR P+ EEIA  + MPV+ V 
Sbjct: 372 KQAMRKSVSEQTQIFRLPAHMVEASYRVKECTKRLRRKLKRRPSNEEIAVDIGMPVKRVE 431

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             + + K  +SL++ IG  D ++  +   D +A +  +   + ++++   + L +L+PRE
Sbjct: 432 AAVSLPKYSVSLDSKIGSTDMTY-QEVTADPSAETAEEMLNRMSMKKDVHQALDTLSPRE 490

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +V+++RFGI      TL+E+G    V+RERIRQIE+ A RKL+   + K L  +L
Sbjct: 491 RQVVKLRFGINDGRIRTLQEIGNIMGVSRERIRQIESGAFRKLRGKKKVKCLMDYL 546


>gi|307822780|ref|ZP_07653011.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307736384|gb|EFO07230.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 448

 Score =  173 bits (439), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 89/237 (37%), Positives = 146/237 (61%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ + EAN  LV+ +A +Y    L F DL+QEG  GL++A +KFD+ LG++FSTYA +W
Sbjct: 213 SRQALAEANSGLVLFLANQYKCGFLDFDDLVQEGQTGLLRAIDKFDYHLGFQFSTYAAYW 272

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI+R+++     +R+P      IHKV+R    + +K  REP+ +E+ +   +P + +
Sbjct: 273 IKQAISRALSRNERVVRVPCEQVANIHKVLRAKNELLSKTGREPSIKELTEYSKIPDDQI 332

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L I++  +SLE    DED+    DF+E +   +P     Q++L+    + +  L PR
Sbjct: 333 NVILSISQTAVSLENLDDDEDSLAPIDFLEQQVFANPFKKIEQSDLKAWLGKAIKILDPR 392

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+   FGI    + TL+E+G +  +TRER+RQI+ KA+ K+K  S  K+L SFL
Sbjct: 393 ELKVICCHFGINTGNEMTLQEIGAELNLTRERVRQIQVKALNKMKL-SYGKQLMSFL 448


>gi|213621937|ref|ZP_03374720.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 197

 Score =  173 bits (439), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 78/190 (41%), Positives = 132/190 (69%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW+
Sbjct: 1   RRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V 
Sbjct: 61  RQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVS 120

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++
Sbjct: 121 RMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 180

Query: 625 ERVLRMRFGI 634
             VL  RFG+
Sbjct: 181 REVLARRFGL 190


>gi|89073765|ref|ZP_01160279.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89050540|gb|EAR56032.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 291

 Score =  173 bits (439), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 91/236 (38%), Positives = 142/236 (60%), Gaps = 1/236 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK     + +K  ++E+NLRLV+S+AKKY    +   DLI EGNIGLM A EKFD   G+
Sbjct: 40  RKSLSGDAYSKNVLIESNLRLVVSIAKKYRGSSIHISDLIDEGNIGLMTAVEKFDPEKGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW+KQ I R+I +Q  TIR+PVH+  +I+ ++RT +++  K  +EP+ E +A+
Sbjct: 100 RFSTYATWWIKQTIERAIHNQGRTIRLPVHVSKEINTIIRTHKQLVKKNNQEPSTELVAE 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETT 613
            L   ++ +   L      +S +  I  E +S  +   I D+N+  P D      +++ T
Sbjct: 160 VLNKTLDDISTTLSYDTPIVSYDQSITSEASSQSIAVLIADENSAKPDDLVDDLAIQKIT 219

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T VL  L  R++ ++  RFG+      TL+EV  +  +TRERIRQ++  ++ KLK+
Sbjct: 220 TNVLNCLNNRDKEIICRRFGLLGYEAQTLQEVADEVGLTRERIRQLQVTSLAKLKN 275


>gi|189501483|ref|YP_001957200.1| RNA polymerase sigma factor [Candidatus Amoebophilus asiaticus 5a2]
 gi|189496924|gb|ACE05471.1| RNA polymerase sigma factor, sigma-70 family [Candidatus
           Amoebophilus asiaticus 5a2]
          Length = 287

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 98/238 (41%), Positives = 159/238 (66%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IA +++ +ANLR V+SVAK+Y N+GL   DLI EGN+GL+K+A++FD   G+KF +YA+W
Sbjct: 49  IALEQLTKANLRFVVSVAKQYQNQGLSLSDLINEGNLGLIKSAQRFDETRGFKFISYAVW 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I +++A+QS  +R+P++    ++K+ RT  ++  K KREPT EE+A++L +    
Sbjct: 109 WIRQSILQALAEQSRIVRLPLNRVGTLNKLSRTFSQLEQKYKREPTAEELAEELEVTPGE 168

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +   +KI+   +S++ P    +   L D +ED +   P D+ I  +L +   R L+ LT 
Sbjct: 169 ISDTMKISGRHVSMDAPFVQGEEHSLLDVLEDDDEDKPDDTLIDESLCKDIERALSLLTE 228

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE  V+   FG+      TLEE+G +F +TRER+RQI+ KAI+KL+H + SK L+++L
Sbjct: 229 REAGVISYYFGLKGTNPMTLEEIGTRFNLTRERVRQIKEKAIKKLRHVASSKTLKNYL 286


>gi|55274875|gb|AAV49240.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 193

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 78/187 (41%), Positives = 130/187 (69%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGI 634
           L  RFG+
Sbjct: 181 LARRFGL 187


>gi|292492664|ref|YP_003528103.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
 gi|291581259|gb|ADE15716.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
          Length = 325

 Score =  173 bits (438), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 83/225 (36%), Positives = 143/225 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL+ A EKFD  +G++FSTYA WW
Sbjct: 86  GRKRMIESNLRLVVKIARRYMNRGLALLDLIEEGNLGLIHAVEKFDPEMGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ T+R+PVH+  +I    R A +++ +++ +PT EE+A++L   VE +
Sbjct: 146 IRQTIERALMNQTRTVRLPVHVVKEIKSYQRVASKLAQELEHDPTFEELAQQLDKSVEEI 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++  +     S++T    +    L D + D+    P       +++      L+ L  +
Sbjct: 206 KRMWSLKDNIASMDTGYRSDQEKTLLDTLPDEGTPDPTTLLQNDDMQSRLELWLSQLNNK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  V+  RFG+      TLE+VG+   VTRER+RQI+ +A+++L+
Sbjct: 266 QREVVIRRFGLQGYESQTLEQVGQAIGVTRERVRQIQLEALKRLR 310


>gi|302851352|ref|XP_002957200.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
 gi|300257450|gb|EFJ41698.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
          Length = 733

 Score =  173 bits (438), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 145/226 (64%), Gaps = 3/226 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++++N RLV++V K+Y  +G+   DL+ EG  GL++  E +D   G++F TYA WW
Sbjct: 474 AKELLLKSNYRLVMTVCKRYIGKGMHLQDLVSEGVKGLLRGVEMYDASRGFRFGTYAHWW 533

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++RS+A+    +R+PVHM +++ K+      ++ ++ REP+ EE+A+ + +P   V
Sbjct: 534 IRQAVSRSMAETGRAVRLPVHMIEQLTKLKNATAALAMELNREPSVEEMAEAVGLPPSRV 593

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTP 622
             +L   +   S+E+ IG +D   + D ++D+   +  D A  ++ +R     +L  L+ 
Sbjct: 594 ELLLDAARAASSMESAIGGDDGLTIKDAVQDERMAA--DEAFGSDSMRADVESMLEGLSD 651

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  VLR+RFG+    + TLE++G +  VTRERIRQ+EAKA+RKL+
Sbjct: 652 REACVLRLRFGLEDGVEWTLEDIGSRLGVTRERIRQLEAKALRKLQ 697


>gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor RpoS [Janthinobacterium sp. Marseille]
 gi|151280837|gb|ABR89247.1| RNA polymerase nonessential primary-like sigma factor
           [Janthinobacterium sp. Marseille]
          Length = 345

 Score =  173 bits (438), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 98/280 (35%), Positives = 168/280 (60%), Gaps = 12/280 (4%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E K  +A E+ S    ++ +  I     +++ E  H  ++ ++G   A   +++M+E NL
Sbjct: 59  ELKKVLATEL-STDATQHYLNQIGTRPLLTVPEEVHFATLAKQGNFAA---RQKMIEHNL 114

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK Y NRG+  LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I 
Sbjct: 115 RLVVSIAKHYINRGVILLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIM 174

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKVLKITK 571
           +Q+ T+R+PVH+  ++++ +R    +  +    ++ T E+IA  +   VE V+ +L +++
Sbjct: 175 NQARTVRLPVHVVRELNQTLRAKFHLEAQHHDGKDATAEDIAHLVDRSVEDVQDILALSE 234

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVL 628
              SL+ P+  +  S L D ++  +A  P D+  + N  E T  V   L  L  ++  V+
Sbjct: 235 HATSLDAPLDGDPQSSLMDLLQGDHANDP-DALAEHN--EMTVLVHDWLEKLPDKQRLVI 291

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RFG+  +   TLE +  +  VTRER+RQI+ +A+ KLK
Sbjct: 292 TRRFGLDNDDPATLEALAAEMHVTRERVRQIQQEALVKLK 331


>gi|332667453|ref|YP_004450241.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332336267|gb|AEE53368.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 288

 Score =  172 bits (437), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 94/248 (37%), Positives = 154/248 (62%), Gaps = 4/248 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+ +A +AK  +  ANLR V+SVAK+Y N+GL   DLI EGN+GLMKAA++FD   G
Sbjct: 43  IRQGDDDA-MAK--LTRANLRFVVSVAKQYQNQGLSLSDLINEGNVGLMKAAKRFDETKG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++I + S  +R+P++     +KV         + +REP+ EE+ 
Sbjct: 100 FKFISYAVWWIRQSILQAIVEYSRIVRLPLNKVGSYNKVNEAYLAFIQQFEREPSNEELG 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + L M    V  +LK     +S++ P+ G+E  S + D I D++ + P    ++ +L++ 
Sbjct: 160 ELLEMNPREVGNMLKGNGRHVSVDAPLSGEEGDSTMLDVITDEDDMGPDFRLMEQSLKDE 219

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + L+ L  RE  VL   +G+      TLEE+G+ + +TRER+RQI+ +AIR+L+    
Sbjct: 220 VKQGLSILNIREVEVLSAYYGLEGQKPLTLEEIGEMYGLTRERVRQIKERAIRRLRKSYN 279

Query: 673 SKKLRSFL 680
              LRS+L
Sbjct: 280 RNNLRSYL 287


>gi|55274970|gb|AAV49284.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 196

 Score =  172 bits (437), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 78/187 (41%), Positives = 130/187 (69%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 181

Query: 628 LRMRFGI 634
           L  RFG+
Sbjct: 182 LARRFGL 188


>gi|256425191|ref|YP_003125844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040099|gb|ACU63643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 285

 Score =  172 bits (437), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 147/237 (62%), Gaps = 2/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +   NLR V+SVAK+Y ++GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW
Sbjct: 50  ALERLTTGNLRFVVSVAKQYQHQGLSLSDLINEGNLGLIKAAQRFDETKGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+Q   +R+P +     +K  +       + +REP+ EE+A+ L M    +
Sbjct: 110 IRQSILQALAEQGRLVRLPQNKIGTYNKANKAYMAFEQENEREPSTEELAEILEMSESEI 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             + +     +SL+ P+ + +   +GD +E  +     D  ++ +LRE   RVL SL+PR
Sbjct: 170 NNIFQSNTRHMSLDAPVHEAEDVAMGDLLEGGDITD--DDVMRDSLREEIRRVLKSLSPR 227

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++   FG+      T+E++G+++ +T+ERIRQI+ +AI++L+    S  L+S+L
Sbjct: 228 EAEIVNAYFGLDGENGATIEQIGQKYDLTKERIRQIKERAIKRLQKARYSGALKSYL 284


>gi|33863339|ref|NP_894899.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640788|emb|CAE21243.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 320

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 91/228 (39%), Positives = 142/228 (62%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 85  AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V
Sbjct: 145 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L   +       P +      ++     +L  L   
Sbjct: 205 KDLMCRARQPMSLEMKVGDGDETEL-LELLAGEEELPSEKVEVDCMKGDLRTLLEKLPEL 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           + RVLRMR+GI       L  + K   ++R+R R++E + +  ++  S
Sbjct: 264 QGRVLRMRYGIDGGEPMNLTGIAKTLGMSRDRTRRLEREGLALMRTSS 311


>gi|303235908|ref|ZP_07322511.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
 gi|302483781|gb|EFL46773.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
          Length = 293

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 151/237 (63%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + +ANLR V+SVAK+Y N+GL   DLI EGN GL+KAA+K+D   G+KF +YA+WW
Sbjct: 56  ALERLTKANLRFVVSVAKQYQNQGLALPDLINEGNFGLIKAAQKYDETRGFKFISYAVWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I ++I++QS  +R+P++     +++ +   +   + +R P+  E+ + + +  E +
Sbjct: 116 IRQSIMQAISEQSRMVRVPINQMGSANRIRKFINQFEQEHERYPSLSELTEHIDLLEEKI 175

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + L +    +S++ P    +   L D + +KNA S  D  +  +L       LASL+ R
Sbjct: 176 VEALAMATTQVSMDAPFTSNEEGSLLDVLPNKNAPSADDLLVAESLSTEVANALASLSER 235

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ +++  FGI    + +LEE+G++  +TRER+RQI+ KAI +L+  S+S++L+SFL
Sbjct: 236 EQIIIKCFFGIN-QPEMSLEEIGERTGLTRERVRQIKEKAIIRLRKNSQSERLKSFL 291


>gi|213419842|ref|ZP_03352908.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 115

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 86/114 (75%), Positives = 94/114 (82%)

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +V
Sbjct: 1   KIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV 60

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 61  LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 114


>gi|159470255|ref|XP_001693275.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
 gi|42742499|gb|AAM88387.2|AF525691_1 RNA polymerase sigma factor [Chlamydomonas reinhardtii]
 gi|47076042|emb|CAF25319.1| sigma-like transcription factor [Chlamydomonas reinhardtii]
 gi|158277533|gb|EDP03301.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
          Length = 752

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 143/228 (62%), Gaps = 6/228 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++++N +LV++V K +  +G    DL+ EG  GL+K  EK+D   G++F TYA WW
Sbjct: 490 AKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGFRFGTYAHWW 549

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++RS+A+    +R+P+HM +++ ++   + ++  ++ REPT  E+AK   +PV  V
Sbjct: 550 IRQAVSRSLAETGRAVRLPMHMIEQLTRLKNLSAKLQTQLAREPTLPELAKAAGLPVTRV 609

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASL 620
           + +++  +   SL+TPIG  +   LG  ++D        +  +    +LR     +L  L
Sbjct: 610 QMLMETARSAASLDTPIGGNE---LGPTVKDSVEDEREAADEEFGSDSLRNDMEAMLLEL 666

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL+
Sbjct: 667 PEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKLR 714


>gi|330447824|ref|ZP_08311472.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492015|dbj|GAA05969.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 286

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 91/226 (40%), Positives = 137/226 (60%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK +VE+NLRLV+S+AKKY    L   DLI EGNIGLM A +KFD   G++FSTYA WW
Sbjct: 43  AKKILVESNLRLVVSIAKKYRASKLSLSDLIDEGNIGLMTAVDKFDPEKGFRFSTYASWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I R+I +Q+ TIR+PVH+  +I+ ++RT R +      EPT ++IA+ L   +  +
Sbjct: 103 IKQTIERAIHNQNRTIRLPVHVSKEINTLLRTHRELMKVNNNEPTQDDIARVLNRDINEI 162

Query: 564 RKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L      +SLE  +GD++ S+ +   + D+   SP       ++ + T  +L  L  
Sbjct: 163 SSLLASEVNVVSLEQTLGDDENSNTVAYLVADEQIASPSAEVDSDDIMKVTNMILHKLPS 222

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+  ++  R+G+     HTL+EV     +TRERIRQ++ K +  LK
Sbjct: 223 RDREIMCRRYGLMGYEPHTLQEVADSVGLTRERIRQLQIKTLNTLK 268


>gi|124022691|ref|YP_001016998.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962977|gb|ABM77733.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 320

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 91/228 (39%), Positives = 142/228 (62%), Gaps = 1/228 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW
Sbjct: 85  AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V
Sbjct: 145 IRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEV 204

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + ++   ++P+SLE  +GD D + L   +       P +      ++     +L  L   
Sbjct: 205 KDLMCRARQPMSLEMKVGDGDETEL-LELLAGEEELPSEKVEVDCMKGDLRTLLEKLPEL 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           + RVLRMR+GI       L  + K   ++R+R R++E + +  ++  S
Sbjct: 264 QGRVLRMRYGIDGGEPMNLTGIAKTLGMSRDRTRRLEREGLALMRTSS 311


>gi|299783172|gb|ADJ41170.1| RNA polymerase sigma factor [Lactobacillus fermentum CECT 5716]
          Length = 287

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 76/124 (61%), Positives = 100/124 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 143 AKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 202

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M  + V
Sbjct: 203 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDMDTQKV 262

Query: 564 RKVL 567
           R +L
Sbjct: 263 RDIL 266



 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 57/108 (52%), Gaps = 6/108 (5%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  ++++ M+  +  + + G++VVD      E G  D   L ++   SS  L+     + 
Sbjct: 51  PFGLNADGMDALLQNVEDAGVSVVD------ENGDPDLRALKATEKLSSKALKDTTAPSS 104

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              +DPVRMYL+E+G + LL+ + E+A+A RIE G       L E+ L
Sbjct: 105 IKINDPVRMYLKEIGRVNLLTADEEVALALRIEKGDETAKQELAEANL 152


>gi|318066935|emb|CBY89082.1| RNA polymerase sigma70 factor [Halomonas cupida]
          Length = 365

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 139/405 (34%), Positives = 201/405 (49%), Gaps = 72/405 (17%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                R + DL +        GF    EG       D  + +E    + T GD E     
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEADVPEIEE----EATAGDDEDDDAD 127

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA--LDEIAEVYREL 294
           +++D S     PE A       ++  + SA   +A+E   R        L  +AE++  +
Sbjct: 128 AEEDDSGGGPDPEEARA---RFEQIREQSALADAAIEAHGRQSAQAQEELARLAELFSPI 184

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                               K++ +   +LVG + ++       VEQ+    K +M    
Sbjct: 185 --------------------KLVPKHFERLVGQVRIS-------VEQVRAQEKSVMQ--- 214

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE---VDSILKIRN 411
               L +   + R  F++   G E    W+            +F+A      D + ++R 
Sbjct: 215 ---LLVKQAKVPRKSFIKAFPGNESRLDWLD-----------DFMAANARYADRLGELRA 260

Query: 412 EI----KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++    + I+ E     + +SE + +   +  GE +A  AKKEMVEANLRLVIS+AKKYT
Sbjct: 261 DVQRAQRKIAFEEEMVRLPVSEIKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYT 320

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 321 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 365


>gi|255312659|gb|ACU01739.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 132/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDLERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|6273430|emb|CAB60192.1| putative sigma-like transcription factor [Arabidopsis thaliana]
          Length = 487

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/238 (34%), Positives = 146/238 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+TYA WW
Sbjct: 247 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 306

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +SI   S TIR+P ++   + KV    +    +    P+ EE+A  + +  E +
Sbjct: 307 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKL 366

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L  T+ P+S++ PI  +  +   +   D    +P  S  +  +R     +L  L+P+
Sbjct: 367 DKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPK 426

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L ++ D
Sbjct: 427 ERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYAD 484


>gi|55274901|gb|AAV49252.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  171 bits (434), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 80/197 (40%), Positives = 133/197 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGKQF 649
           G+      TLE+VG++ 
Sbjct: 181 GLLGYEAATLEDVGREI 197


>gi|296535367|ref|ZP_06897567.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
 gi|296264309|gb|EFH10734.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
          Length = 1063

 Score =  171 bits (434), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 141/227 (62%), Gaps = 5/227 (2%)

Query: 444  AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            A++E+VE NL+ V+ +A++Y    + FLDL+QEG IGL++A ++FD   G++F TYA WW
Sbjct: 827  ARQEIVEGNLKRVVWLARRYARAAVPFLDLVQEGQIGLLRAIDRFDPDRGFRFGTYATWW 886

Query: 504  VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
            ++Q+++R + DQ  T+R+PVHM ++I K  R +  +  K    PTP+E+A  L   V  V
Sbjct: 887  IRQSMSRYVQDQGRTVRVPVHMLERIAKAKRASEALRAKTGVVPTPQELAAALEADVVSV 946

Query: 564  RKVLKITKEPISLE--TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             + L    E IS +    + DED + +   +++    +PL + +  +LR      L  L 
Sbjct: 947  ERALAADLEGISFDDMGSLPDEDAALVAPLVDE---ATPLTALLHHDLRRLLAASLRRLD 1003

Query: 622  PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R+ R++ +RFG+      TLEEVG+ + VTRERIRQIEAK++++L 
Sbjct: 1004 ARQARIIDLRFGLTDGNPLTLEEVGQFYGVTRERIRQIEAKSLKRLP 1050


>gi|255312689|gb|ACU01754.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  171 bits (434), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 132/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKSLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|257055481|ref|YP_003133313.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256585353|gb|ACU96486.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 315

 Score =  171 bits (434), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 85/233 (36%), Positives = 141/233 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+ ANLRLV++ A+K  +  L  LD IQEGN+GL++A EKFD+  G+KFSTYAMWW
Sbjct: 78  AKDHMIRANLRLVVTAARKNRHTNLPLLDAIQEGNLGLIRAVEKFDYAKGFKFSTYAMWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  A QS  IR+P+H+ +++ K+ R  R + ++   E T EE+A    MPVE V
Sbjct: 138 IRQAIQRGNAFQSNAIRLPMHVSEQVAKLDRLERTLQSRSNHELTVEELAAAAEMPVERV 197

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             + +  +  +SL+  + ++   +L D + D    +  +   +  + +     + SL P 
Sbjct: 198 EALRQAGRSTVSLDMSLDEDGELYLRDLVADGTVPAVGEGIERQAMVDQVRATIDSLPPM 257

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E  V+ +R+G+     HT+ E+ ++  ++R+R+R +E +A+  L+ P RS+ L
Sbjct: 258 EAAVVSLRYGLRDGHQHTIPEISQRLGLSRKRVRTLEQRAMAMLREPQRSEPL 310


>gi|182416213|ref|YP_001821279.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843427|gb|ACB77679.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 347

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 92/242 (38%), Positives = 142/242 (58%), Gaps = 14/242 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR+G+  A   +  M+ ANLRLV+ +AK Y   GL   DLI EGN+GL+ A ++FD  +G
Sbjct: 60  VRRGDAGA---RDHMIRANLRLVVRIAKDYAQYGLPLADLISEGNVGLIHAVDRFDPRIG 116

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K STYA WW++QAI R+ A  +  IR+PVHM D+I ++ R    +S +  RE T +E+A
Sbjct: 117 GKLSTYAAWWIRQAIRRAFAHHARAIRLPVHMLDRIARLRRAQASLSEQFGREATTDELA 176

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            +L  PVE +         P SL+  +G   ++  L + I D+ A +         LR+ 
Sbjct: 177 AELQAPVEKIALWKSAGDAPFSLDAAVGTGSESRRLSETIRDERAPTAF-----TQLRDA 231

Query: 613 TT-----RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           TT      ++A+L  RE  +LR+RFG+  +   TL  V  +F +TRER+RQ+E +A++ +
Sbjct: 232 TTARDLRAIIATLDVREATILRLRFGLDGDEPQTLHAVSLRFGITRERVRQLERRALQNV 291

Query: 668 KH 669
           ++
Sbjct: 292 RN 293


>gi|18404292|ref|NP_565856.1| SIGF (RNA POLYMERASE SIGMA-SUBUNIT F); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana]
 gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana]
 gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis
           thaliana]
 gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana]
          Length = 547

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 86/239 (35%), Positives = 149/239 (62%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+TYA WW
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 366

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +SI   S TIR+P ++   + KV    +    +    P+ EE+A  + +  E +
Sbjct: 367 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKL 426

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            K+L  T+ P+S++ PI  D+DT+   +   D    +P  S  +  +R     +L  L+P
Sbjct: 427 DKLLYNTRTPLSMQQPIWSDQDTT-FQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSP 485

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +E R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L ++ D
Sbjct: 486 KERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYAD 544


>gi|90577256|ref|ZP_01233067.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440342|gb|EAS65522.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 286

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 91/226 (40%), Positives = 136/226 (60%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +KK ++E+NLRLV+S+AKKY    L   DLI EGNIGLM A EKFD   G++FSTYA WW
Sbjct: 43  SKKILIESNLRLVVSIAKKYRASNLSLSDLIDEGNIGLMTAVEKFDPEKGFRFSTYASWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I R+I +Q+ TIR+PVH+  +I+ ++RT R +      EPT E+IA+ L    + +
Sbjct: 103 IKQTIERAIHNQNRTIRLPVHISKEINTLLRTHRELMKLNNNEPTHEDIAQALNKDSKEI 162

Query: 564 RKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +       ISL+  IGD + S  +   + D+   SP       ++ + T  +L  +  
Sbjct: 163 SALFSNEVNVISLDQTIGDTEKSQTIAYLVADEQITSPSAEVDNDDMVKITNLILNGINA 222

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R++ ++  RFG+     HTL+EV     +TRERIRQ++ K++  LK
Sbjct: 223 RDKEIICRRFGLMGYEPHTLQEVADAVGLTRERIRQLQIKSLSSLK 268


>gi|82701632|ref|YP_411198.1| RNA polymerase sigma factor RpoS [Nitrosospira multiformis ATCC
           25196]
 gi|82409697|gb|ABB73806.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosospira multiformis
           ATCC 25196]
          Length = 317

 Score =  171 bits (433), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 88/257 (34%), Positives = 150/257 (58%), Gaps = 8/257 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEAS--------IAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           T I  +E  H   +  K E E +         A+++M+E NLRLV+++AK YTN G+  L
Sbjct: 47  TQIYFNEIGHNALLTPKEEAELTRRVRQNDFAARQKMIECNLRLVVNIAKHYTNHGVALL 106

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+G+M A +KFD   G++FSTYA WW++Q I R I +QS TIR+PVH+   ++ 
Sbjct: 107 DLIEEGNMGMMHALDKFDPERGFRFSTYATWWIRQNIERCIMNQSRTIRLPVHVIKDLNI 166

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +++ AR +     ++P  E++A  L   V+ V+++L + +  +SL+ P+  +    +GD 
Sbjct: 167 ILQAARHLEAHTGKDPKAEDVAHLLGRTVKEVQRMLSLNQSMMSLDAPLDVDPLLSIGDA 226

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  +  P     Q+ ++      L  L  ++  ++  R+G+      TLE++     +
Sbjct: 227 IADDQSPGPDLMWEQSEIKGRVQDWLNRLNDKQRYIIEQRYGLNGYETQTLEQLAASLDL 286

Query: 652 TRERIRQIEAKAIRKLK 668
           TRER+RQI+ +A++ L+
Sbjct: 287 TRERVRQIQLEALQTLR 303


>gi|89072392|ref|ZP_01158971.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89051924|gb|EAR57376.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 286

 Score =  171 bits (433), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 93/235 (39%), Positives = 138/235 (58%), Gaps = 1/235 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK       +KK ++E+NLRLV+S+AKKY    L   DLI EGNIGLM A EKFD   G+
Sbjct: 34  RKSLTGDPASKKILIESNLRLVVSIAKKYRAANLSLSDLIDEGNIGLMTAVEKFDPEKGF 93

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW+KQ I R+I +Q+ TIR+PV++  +I+ ++RT R +      EPT E+IA+
Sbjct: 94  RFSTYASWWIKQTIERAIHNQNRTIRLPVNISKEINTLLRTHRELMKLNNNEPTHEDIAQ 153

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETT 613
            L    + +  +       +SL+  IGD + SH +   + D+   SP       ++ + T
Sbjct: 154 ALNKESKEISALFSNEVNVVSLDQTIGDNENSHTIAYLVADEQITSPSAEVDNDDMIKIT 213

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL  +  R+  ++  RFG+     HTL+EV     +TRERIRQ++ K++  LK
Sbjct: 214 NLVLNGINKRDREIICRRFGLMGYEPHTLQEVADAVGLTRERIRQLQIKSLNSLK 268


>gi|307107488|gb|EFN55731.1| hypothetical protein CHLNCDRAFT_35462 [Chlorella variabilis]
          Length = 267

 Score =  171 bits (433), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 93/242 (38%), Positives = 147/242 (60%), Gaps = 6/242 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS-TYAMW 502
           A++ MV  N+RLV+S+AKKY  RGL   DL+ EG +GL +A +KFD     + +  YA W
Sbjct: 26  AREHMVNCNMRLVVSIAKKYVGRGLALQDLVAEGMVGLQRAVDKFDASTRLQVTPAYAHW 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q++TR+I+DQ+  +R+PVH+ + + KV R  + + ++    P P+ +A +  +    
Sbjct: 86  WIRQSVTRAISDQARVVRLPVHLHEAMGKVRRAEQALWDETGLLPAPQAVADRCGLTHSK 145

Query: 563 VRKVLKITKEPISLE-TPI---GDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + K  + P S +  P    G  D    G+ ++E+     P + A    ++E    VL
Sbjct: 146 LMALYKSFRAPTSRDGVPTLGAGSVDAKAPGEQWVEEVGEEDPAELAHHRMMKEDLNHVL 205

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT RE  +++MR+G+    + TLEEVG+ F VTRERIRQIEAKAIRKL+ PSR  +L 
Sbjct: 206 LTLTERECGIIKMRYGLDDGEEKTLEEVGRAFNVTRERIRQIEAKAIRKLRSPSRVGQLV 265

Query: 678 SF 679
           ++
Sbjct: 266 TY 267


>gi|318066907|emb|CBY89068.1| RNA polymerase sigma70 factor [Chromohalobacter israelensis]
 gi|318066913|emb|CBY89071.1| RNA polymerase sigma70 factor [Chromohalobacter salexigens]
          Length = 367

 Score =  171 bits (433), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 138/411 (33%), Positives = 192/411 (46%), Gaps = 82/411 (19%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSILSAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                R        I P+       G  G +  +  +   E    D     GD+      
Sbjct: 81  EEAPGRLSDLFSGFIDPD------EGIPGVAEAEVPEPEPEPSAAD-----GDVSEDDDE 129

Query: 237 SKDDRSKVDSPPENA--------ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
           ++++ +     PE A        E +ER     E+    +  A  +Q R         +A
Sbjct: 130 AEEEETGGGPDPEEARARFEQIREQNERAKAAIEEHGLGSKEASAEQAR---------LA 180

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           E++  +                    K++ +   +LVG + ++       VEQ+    K 
Sbjct: 181 ELFSPI--------------------KLVPKHFERLVGQVRIS-------VEQIRGQEKA 213

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DS 405
           IM          +   + R  F+    G E D  W+             F+A      D 
Sbjct: 214 IMQI------FVKQAKVPRKTFIGSFPGAESDLEWLD-----------RFMAKHTKFADR 256

Query: 406 ILKIRNEI----KSISVETGISISEFRHIVSMVRK---GECEASIAKKEMVEANLRLVIS 458
           +   R +I    + I  E  + +    HI  + R+   GE +A  AKKEMVEANLRLVIS
Sbjct: 257 LEPFRADIQRAQRKIGFEEEMVLLPVSHIKEVNRRLSIGEAKARRAKKEMVEANLRLVIS 316

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 317 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|213417289|ref|ZP_03350433.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 277

 Score =  171 bits (432), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 76/188 (40%), Positives = 130/188 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269

Query: 624 EERVLRMR 631
           +  VL  R
Sbjct: 270 QREVLARR 277


>gi|281357500|ref|ZP_06243988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
 gi|281316103|gb|EFB00129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
          Length = 432

 Score =  171 bits (432), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 96/229 (41%), Positives = 138/229 (60%), Gaps = 6/229 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +++ANLRLV+ +A  +   GL  LDLI EGNIGLM+A EKFD   G KFS+YA WW
Sbjct: 196 ARSTLIKANLRLVVKIAHDFKGLGLPLLDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWW 255

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ++ R++A+QS TIRIPV    KI+K+     +++ ++ REP+  EIA+ L      V
Sbjct: 256 IKQSMRRALANQSRTIRIPVQSAGKINKIKSVRMKLAEELGREPSDAEIAEHLDFSERTV 315

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR---VLASL 620
             +        SL  PI   +     D I D++A++P    I  ++ E+  R   +L  L
Sbjct: 316 AGLRLADLRTFSLHDPIQQGEEGEFQDIIPDRHAMTP--DQILGDV-ESVFRLMDLLEKL 372

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRFG+  N   TLEEV ++   TRER+RQI+ +A+ KLK 
Sbjct: 373 EERERRILEMRFGLRGNRPLTLEEVSQEIGRTRERVRQIQNQALAKLKQ 421


>gi|55274885|gb|AAV49245.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|255312609|gb|ACU01714.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312611|gb|ACU01715.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312613|gb|ACU01716.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312615|gb|ACU01717.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312617|gb|ACU01718.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312619|gb|ACU01719.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312621|gb|ACU01720.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312623|gb|ACU01721.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312625|gb|ACU01722.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312627|gb|ACU01723.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312629|gb|ACU01724.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312631|gb|ACU01725.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312635|gb|ACU01727.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312637|gb|ACU01728.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312649|gb|ACU01734.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312651|gb|ACU01735.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312655|gb|ACU01737.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312657|gb|ACU01738.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312667|gb|ACU01743.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312673|gb|ACU01746.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312675|gb|ACU01747.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312677|gb|ACU01748.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312679|gb|ACU01749.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312681|gb|ACU01750.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312683|gb|ACU01751.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312685|gb|ACU01752.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312687|gb|ACU01753.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312691|gb|ACU01755.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312693|gb|ACU01756.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312695|gb|ACU01757.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312699|gb|ACU01759.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312701|gb|ACU01760.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312703|gb|ACU01761.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312705|gb|ACU01762.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  171 bits (432), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 132/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|55274967|gb|AAV49283.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score =  171 bits (432), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 77/186 (41%), Positives = 129/186 (69%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L+
Sbjct: 61  ERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 121 LNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 180

Query: 629 RMRFGI 634
             RFG+
Sbjct: 181 ARRFGL 186


>gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS [Herminiimonas arsenicoxydans]
 gi|133738387|emb|CAL61432.1| RNA polymerase sigma factor rpoS (Sigma-38) [Herminiimonas
           arsenicoxydans]
          Length = 344

 Score =  171 bits (432), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 96/280 (34%), Positives = 168/280 (60%), Gaps = 12/280 (4%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E K  ++ E+ S    ++ +  I     +++ E  H  ++ ++G   A   +++M+E NL
Sbjct: 58  ELKKVLSSEL-STDATQHYLNQIGARPLLTVPEEVHFATLAKQGNFAA---RQKMIEHNL 113

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK Y NRG+  LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I 
Sbjct: 114 RLVVSIAKHYINRGVVLLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIM 173

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKVLKITK 571
           +Q+ T+R+PVH+  ++++ +R    +  +    ++ T E+IA  +   VE V+ +L +++
Sbjct: 174 NQARTVRLPVHVVRELNQTLRAKFHLEAQHHDGKDATAEDIAHLVERSVEDVQDILALSE 233

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVL 628
              SL+ P+  +  S L D ++  +A  P    + A  +E    V   L  L+ ++  V+
Sbjct: 234 HASSLDAPLDGDPQSSLMDLLQGDHANDP---DVLAEHQEMIVLVRDWLDKLSDKQRLVI 290

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RFG+  +   TLEE+  +  VTRER+RQI+ +A+ KLK
Sbjct: 291 TRRFGLDNDDPATLEELATEMHVTRERVRQIQQEALVKLK 330


>gi|253582113|ref|ZP_04859337.1| RNA polymerase [Fusobacterium varium ATCC 27725]
 gi|251836462|gb|EES64999.1| RNA polymerase [Fusobacterium varium ATCC 27725]
          Length = 275

 Score =  171 bits (432), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 88/228 (38%), Positives = 147/228 (64%), Gaps = 8/228 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K +++ +NLRLV+++AK Y N+GL F+DLI EGN+GL+ A EKFD   G++FSTYA+WW
Sbjct: 41  SKNQLILSNLRLVVNIAKGYINKGLSFIDLISEGNLGLIYAIEKFDITKGFRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPV 560
           +KQ+I++++  +   IRIP +  D ++KV    R + +++K E   P  EEIA +L + V
Sbjct: 101 IKQSISKAVIVKGREIRIPSYKYDLLNKV---NRYVMSRLKDEGNYPPVEEIAAELNIDV 157

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + ++ ++   ++P+SL T IGD+   +L D +  +   S  +       R+    ++  L
Sbjct: 158 DKIQDIIMDFQDPMSLSTQIGDD--IYLEDTLAQQEDFSMEEEIFNEMGRKQVRDMVNQL 215

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L++R+G+     HTLEE+G    +TRER+RQIE K ++KL+
Sbjct: 216 EEREKEILKLRYGLDGYEIHTLEEIGNTLNITRERVRQIEKKTLQKLR 263


>gi|55274953|gb|AAV49276.1| RNA polymerase subunit sigma-38 [Shigella flexneri 2a]
          Length = 193

 Score =  171 bits (432), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 77/186 (41%), Positives = 129/186 (69%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L+
Sbjct: 61  ERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 121 LNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 180

Query: 629 RMRFGI 634
             RFG+
Sbjct: 181 ARRFGL 186


>gi|91202979|emb|CAJ72618.1| similar to DNA-directed RNA polymerase sigma subunit [Candidatus
           Kuenenia stuttgartiensis]
          Length = 256

 Score =  170 bits (431), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 91/250 (36%), Positives = 152/250 (60%), Gaps = 5/250 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I   V KG+ EA   ++++++ANLRLV+S+AK++ NRG  FLDLI+EGN+GL
Sbjct: 2   LTFEEELEIARKVAKGDAEA---REKLIKANLRLVVSIAKEFVNRGFSFLDLIEEGNLGL 58

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E FD   G +FSTYA WW+KQAI R+IA+++  IRIP +M  +I ++   +  +  
Sbjct: 59  IRAVEDFDITTGNRFSTYATWWIKQAIRRAIANKARIIRIPSYMLQRISQMKHASSGLLK 118

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
           K +R P+ +EIA ++ +  + V+ +    +   SL+ P+  G +    L D   +   + 
Sbjct: 119 KHERSPSEQEIAAEIDITAQNVKNIELSLQSMTSLDAPLVSGADIIWALSDITPNGKTLP 178

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +   +   +ET  ++L +L  R   V+ MR+G+      TLE++ K   ++RER+RQI
Sbjct: 179 PEEGLEETYEKETLKKLLDTLDKRAATVITMRYGLVDGESRTLEDISKILKISRERVRQI 238

Query: 660 EAKAIRKLKH 669
           E + I+KL +
Sbjct: 239 EKETIQKLHY 248


>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
 gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
          Length = 546

 Score =  170 bits (431), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 149/239 (62%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+TYA WW
Sbjct: 306 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 365

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +SI   S TIR+P ++   + KV    +    +    P+ E++A  + +  E +
Sbjct: 366 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEQLAGHVGVSTEKL 425

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            K+L  T+ P+S++ PI  D+DT+   +   D    +P  S  +  +R     +L  L+P
Sbjct: 426 DKLLYNTRTPLSMQQPIWSDQDTT-FQEITPDSGIETPTMSVGKQMMRNHVRNLLNVLSP 484

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +E R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L ++ D
Sbjct: 485 KERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQHMNSHGLHAYAD 543


>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa]
 gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa]
          Length = 535

 Score =  170 bits (431), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 83/238 (34%), Positives = 146/238 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLR+V+ +AK+Y NRGL   DL+QEG +GLMK+ EKF    G +F+TYA WW
Sbjct: 295 SREKLINANLRMVVHIAKRYQNRGLGLQDLLQEGTVGLMKSIEKFKPQAGCRFATYAYWW 354

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q IT++I   S TIR+P ++   + KV+   R    +   +PT EEIA+++ + ++ +
Sbjct: 355 IRQTITKAIFQHSRTIRLPENVYGLLGKVMEAKRSYIQEGNHQPTAEEIARRVGIAIDKL 414

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L  T+ P+S++  +  +  +   +   D     P  S  +  +R+    +L  L+ +
Sbjct: 415 EKLLCFTRTPLSMQQTVWSDQNTTFQEITADTEIEIPDMSVAKQLMRKHIRGLLNILSLK 474

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E R++R+RFGI      +L E+G  F +++ER+RQ+E++A+ KLK    S  L ++ D
Sbjct: 475 ERRIIRLRFGIEDGKQKSLSEIGNVFGLSKERVRQLESRALYKLKQCVGSHGLDAYAD 532


>gi|332753462|gb|EGJ83842.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 215

 Score =  170 bits (431), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 80/207 (38%), Positives = 139/207 (67%)

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  ++
Sbjct: 1   MLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKEL 60

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L 
Sbjct: 61  NVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALL 120

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++ 
Sbjct: 121 DILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREI 180

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +TRER+RQI+ + +R+L+   +++ L
Sbjct: 181 GLTRERVRQIQVEGLRRLREILQTQGL 207


>gi|302338308|ref|YP_003803514.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635493|gb|ADK80920.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 281

 Score =  170 bits (431), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 91/234 (38%), Positives = 143/234 (61%), Gaps = 2/234 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK +     A+  ++EANLRLV+ +AK Y   G   LDLIQEGN+GL++AAEK+D     
Sbjct: 37  RKIQSGDEAARHRLIEANLRLVVKIAKSYVTPGFGLLDLIQEGNMGLIRAAEKYDHRKQV 96

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q+I R+IA +   IR+P    + + K+ RT  ++S +++ EP+ EEIA 
Sbjct: 97  RFSTYAAWWIRQSIVRAIAKKQKAIRLPHRKNNLLKKIQRTYYQLSQELEHEPSAEEIAV 156

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ +    V ++L++    +SL+  IGD D S L D +ED +   P    I  +++E T 
Sbjct: 157 EIGIEPSIVDQMLQVGNPVVSLDCEIGD-DASTLLDMLED-STYEPERVCINKSMQEDTM 214

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  L  RE ++L  RF       +TL+++G +  ++ E +RQIE +AIRKL+
Sbjct: 215 HFLDHLKERERQILLYRFAFFGGKKYTLKKIGMEMGISPETVRQIEMRAIRKLR 268


>gi|87306425|ref|ZP_01088572.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
 gi|87290604|gb|EAQ82491.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
          Length = 296

 Score =  170 bits (430), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 94/226 (41%), Positives = 146/226 (64%), Gaps = 4/226 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  MV ANLRLV+++A+ YT +GL   DLI+EGN+GL++A E FD  +G +FSTYA +W
Sbjct: 50  ARDRMVRANLRLVVNIARGYTGKGLGLQDLIEEGNLGLLRAVEGFDPAMGTRFSTYASYW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I R++ + + TIRIP +M + + K  R   R++ ++ R PTPEEIA+ L +P + +
Sbjct: 110 IKQSIKRALINCAKTIRIPAYMVELLSKWRRATNRLTEELGRTPTPEEIARVLGLPKKKL 169

Query: 564 RKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             + K  K   S  TP  D+  S   LG+ + D    +P D  ++ +  +   ++L ++ 
Sbjct: 170 PIIKKAIKIYNS--TPQTDQADSGWSLGEMVMDDRLKNPEDEMVEHDDLKNVMQMLKTMD 227

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE  VLRMRFG+     HTL+E+G++  +TRER+RQIE +A+ KL
Sbjct: 228 GREATVLRMRFGLEGMDPHTLKEIGEKLGLTRERVRQIETEALGKL 273


>gi|318066957|emb|CBY89093.1| RNA polymerase sigma70 factor [Halomonas maura]
          Length = 365

 Score =  170 bits (430), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 131/396 (33%), Positives = 198/396 (50%), Gaps = 54/396 (13%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILDAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                R + DL +        GF    EG         ++ +  ++ + T GD + A + 
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIP-----GVAEAEVPEEPEATVGDADDADES 126

Query: 237 SKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           ++++      P PE A+     + E  + S   + A   +   +    L  +AE++  + 
Sbjct: 127 AEEEDDSGGGPDPEEAKARFEQIREQNEASRQAIDA-HGRGSAEAQAELARLAELFSPI- 184

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                              K++ +   +LVG + ++       VEQ+    K +M     
Sbjct: 185 -------------------KLVPKHFERLVGQVRIS-------VEQVRAQEKAVMQ---- 214

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF--PEGEWKNFVACEVDSILKIRNEI 413
                +   + R  F++   G E    W+    DF      + + +A     I + + +I
Sbjct: 215 --LCVKKAKVPRKTFIKAFPGNESRQDWLD---DFMGDNARYADRLAPLKADIQRAQRKI 269

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 270 AFEEEMVLLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 329

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 330 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 365


>gi|62734062|gb|AAX96171.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|125589330|gb|EAZ29680.1| hypothetical protein OsJ_13741 [Oryza sativa Japonica Group]
          Length = 563

 Score =  170 bits (430), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 147/236 (62%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD   G++FSTY+ WW+
Sbjct: 324 KNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWI 383

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EEIA    MP++ V 
Sbjct: 384 KQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEEIAADTGMPIKRVE 443

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             + + K  +SL++ IG  D ++  +   D  A +  +   + +++    + L +LT RE
Sbjct: 444 AAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRE 502

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   R   L+ +L
Sbjct: 503 RQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKKRVNALKDYL 558


>gi|297611772|ref|NP_001067832.2| Os11g0448400 [Oryza sativa Japonica Group]
 gi|62701714|gb|AAX92787.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|108864350|gb|ABA93405.2| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|255680064|dbj|BAF28195.2| Os11g0448400 [Oryza sativa Japonica Group]
          Length = 564

 Score =  170 bits (430), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 147/236 (62%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD   G++FSTY+ WW+
Sbjct: 324 KNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWI 383

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EEIA    MP++ V 
Sbjct: 384 KQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEEIAADTGMPIKRVE 443

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             + + K  +SL++ IG  D ++  +   D  A +  +   + +++    + L +LT RE
Sbjct: 444 AAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRE 502

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   R   L+ +L
Sbjct: 503 RQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKKRVNALKDYL 558


>gi|54401902|gb|AAV34636.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score =  170 bits (430), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 80/194 (41%), Positives = 131/194 (67%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+
Sbjct: 1   NLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 60

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +
Sbjct: 61  IMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNE 120

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  R
Sbjct: 121 RITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARR 180

Query: 632 FGIGMNTDHTLEEV 645
           FG+      TLE+V
Sbjct: 181 FGLLGYEAATLEDV 194


>gi|218442621|ref|YP_002380941.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
 gi|218174979|gb|ACK73711.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
          Length = 308

 Score =  170 bits (430), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 90/229 (39%), Positives = 143/229 (62%), Gaps = 6/229 (2%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   AK ++V+ NLRLVI++AKKY  RGL F DL+QEGNIGL++AAE F+   GYKFSTY
Sbjct: 79  EGQQAKNQLVQGNLRLVINLAKKYLGRGLSFEDLLQEGNIGLIRAAELFEPSKGYKFSTY 138

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q I R+I + + TIR+PVH+  +++++ +T  +++ ++ R PT +EIA  L M 
Sbjct: 139 AYWWIRQQIIRAINNSARTIRLPVHIIARLNRIKKTQHKLAAQLGRTPTVQEIATSLQMS 198

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + + K  ++ ++ ISL T + ++    L D I D N   P D   +    E     + +
Sbjct: 199 AQEIEKYREVAQKTISLSTIVDEQGRETLQDLIADPNP-QP-DFLERVFSYEQILEKMET 256

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PR + +L+ R    +  + TLE +G    +++ER+RQI  KA+ +L+
Sbjct: 257 LPPRYQDILKKR----IYEEQTLEAIGTSTKLSKERVRQIFQKALSRLR 301


>gi|318066933|emb|CBY89081.1| RNA polymerase sigma70 factor [Halomonas campisalis]
          Length = 367

 Score =  170 bits (430), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 137/404 (33%), Positives = 196/404 (48%), Gaps = 68/404 (16%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAWLPGAVDSILEAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                R + DL +        GF    EG       +  +E+ R    E+EGD +     
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEAEVPEEEPR---AESEGDGDEDDDE 128

Query: 237 SKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              +      P PE A      + E  ++ A    A   +  P+    L  +AE++  + 
Sbjct: 129 DAGEEETTGGPDPEEARARFEQIRE-LNERARAAIAAHGRGSPEARAELTRLAELFSPI- 186

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                              K++ +   +LVG + ++       VEQ+    K +M     
Sbjct: 187 -------------------KLVPKHFERLVGQVRIS-------VEQVRAQEKAVMQL--- 217

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE---VDSILKIRNE 412
                +   + R  F++   G E    W+             F+A      D +  +R +
Sbjct: 218 ---FVKKAKVPRKTFIKAFPGNESRQEWLD-----------EFIAAHGKYADRLSAMRGD 263

Query: 413 I----KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I    + I+ E     +++ E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 264 IQRAQRRIAFEEDMVQLAVPELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTN 323

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 324 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|253761922|ref|XP_002489335.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
 gi|241946983|gb|EES20128.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
          Length = 238

 Score =  170 bits (430), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 91/233 (39%), Positives = 150/233 (64%), Gaps = 1/233 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV +N+RLVIS+A+++   G+   DLIQEG  GL++ AEKFD   G++FSTY+ WW+KQA
Sbjct: 1   MVTSNVRLVISIAREFEGPGMDLYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWIKQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + +S+++QS   R+P HM +  ++V    +R+  K++R PT EEIA    MP++ V   +
Sbjct: 61  MRKSVSEQSQIFRLPAHMVEASYRVKECTKRLRRKLRRRPTNEEIALDTGMPIKRVEAAV 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + K  +SL++ IG  D ++  +   D +A +  +   + ++++   + L +LT RE++V
Sbjct: 121 NLPKYSVSLDSKIGSTDMTY-QEVTADPSAETAEEMLNRMSMKKDVHKALDTLTTREKQV 179

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +RFG+  +   TL+E+G    V+RERIRQIE+ A RKL+   R K L+ +L
Sbjct: 180 VVLRFGLEDDRIRTLQEIGNIMGVSRERIRQIESGAFRKLRSKKRVKALKDYL 232


>gi|46241495|gb|AAS82950.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 311

 Score =  170 bits (430), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 143/228 (62%), Gaps = 6/228 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++++N +LV++V K +  +G    DL+ EG  GL+K  EK+D   G++F TYA WW
Sbjct: 49  AKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGFRFGTYAHWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++RS+A+    +R+P+HM +++ ++   + ++  ++ REPT  E+AK   +PV  V
Sbjct: 109 IRQAVSRSLAETGRAVRLPMHMIEQLTRLKNLSAKLQTQLAREPTLPELAKAAGLPVTRV 168

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASL 620
           + +++  +   SL+TPIG  +   LG  ++D        +  +    +LR     +L  L
Sbjct: 169 QMLMETARSAASLDTPIGGNE---LGPTVKDSVEDEREAADEEFGSDSLRNDMEAMLLEL 225

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL+
Sbjct: 226 PEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKLR 273


>gi|224000633|ref|XP_002289989.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220975197|gb|EED93526.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 321

 Score =  170 bits (430), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 104/279 (37%), Positives = 161/279 (57%), Gaps = 18/279 (6%)

Query: 416 ISVETG--ISISEFRHIVS--MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +SVE G   SI+E+    S  + R+    A  AK+ MV+ N+RLV+S+A++Y   G+   
Sbjct: 30  LSVEMGRSPSIAEWAAACSPRLFREMMLTAKEAKQRMVQCNMRLVVSIARRYHGVGVNVQ 89

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+QEG++GL +AAEKFD   G+KFSTYA WW++QA+ RSIA  S TIR+PVH+ + ++K
Sbjct: 90  DLVQEGSLGLARAAEKFDPKKGFKFSTYASWWIQQAVFRSIAYHSRTIRLPVHVHNLLNK 149

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--------IGDE 583
           V R  + +  ++ R PT EE+A ++ M +E   K+++ T+  ISLE P        +G E
Sbjct: 150 VRRARQVLQQELGRTPTNEEMAVEMDMTIEKYNKMIRTTRNAISLERPKYKNNPKDLGHE 209

Query: 584 DTSHLGDFIEDKNAV-----SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
             + +GD + D +AV     +P  +     L      +L  L   E  VL +R+GI    
Sbjct: 210 SEALVGDMV-DSSAVIFDEKTPEQNVDHGLLHNDIEYMLGKLGEDERSVLCLRYGINDGI 268

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             T+  V  +   T+  +R  E +A+RKL+ P   K+L+
Sbjct: 269 TRTVTLVASEMRQTKSWVRSQECRALRKLRRPWYEKRLK 307


>gi|32351878|dbj|BAC78528.1| plastid sigma factor 2A [Oryza sativa Japonica Group]
          Length = 564

 Score =  170 bits (430), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 147/236 (62%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD   G++FSTY+ WW+
Sbjct: 324 KNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWI 383

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EEIA    MP++ V 
Sbjct: 384 KQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEEIAADTGMPIKRVE 443

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             + + K  +SL++ IG  D ++  +   D  A +  +   + +++    + L +LT RE
Sbjct: 444 AAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRE 502

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   R   L+ +L
Sbjct: 503 RQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKKRVNALKDYL 558


>gi|218194307|gb|EEC76734.1| hypothetical protein OsI_14770 [Oryza sativa Indica Group]
          Length = 563

 Score =  169 bits (429), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 147/236 (62%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD   G++FSTY+ WW+
Sbjct: 323 KNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWI 382

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EEIA    MP++ V 
Sbjct: 383 KQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEEIAADTGMPIKRVE 442

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             + + K  +SL++ IG  D ++  +   D  A +  +   + +++    + L +LT RE
Sbjct: 443 AAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRE 501

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   R   L+ +L
Sbjct: 502 RQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKKRVNALKDYL 557


>gi|149200267|ref|ZP_01877288.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
 gi|149136631|gb|EDM25063.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  169 bits (429), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 100/261 (38%), Positives = 154/261 (59%), Gaps = 5/261 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IRN + +IS  + ++  E   + + ++ G  +A   +++++ +NLRLV+ +A  +   GL
Sbjct: 8   IRNYMHNISDYSLVTKEEEVDLAADIKLGSDKA---REKLIVSNLRLVVKIAHDFKGLGL 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGLM+A EKFD   G KFS+YA WW+KQ++ R +A+QS TIRIPV    K
Sbjct: 65  PLSDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRGLANQSRTIRIPVQSAGK 124

Query: 529 IHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K +R AR  +  K+ REPT +EIA  L      V  +  +    ISL+  + D +   
Sbjct: 125 INK-IRNARIELKEKLMREPTDQEIATYLEFSKRTVSGLSTVGGSTISLQAKLQDGEDGE 183

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + DK + +  D   +A    +  + +  LT RE+ VL +RFG+      TLEEV +
Sbjct: 184 IQDIVADKASQTASDIIGEAESINSMMKFIVYLTDREKLVLELRFGLLSGRPKTLEEVSQ 243

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
               TRER+RQI+ +A++KL+
Sbjct: 244 AIGRTRERVRQIQNQALKKLR 264


>gi|158339245|ref|YP_001520422.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158309486|gb|ABW31103.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  169 bits (429), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 88/230 (38%), Positives = 139/230 (60%), Gaps = 2/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+E NLRLV+S+AKK+ + GL  +DLIQEG+IGL  A +KFD   G KFSTYA WW
Sbjct: 40  AKQRMIECNLRLVVSIAKKHQHLGLPLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + +AI R++  QS TI IP+H  ++ H++ +  R+++ +  R PT +E++    +    +
Sbjct: 100 ISEAIKRALKSQSRTIYIPIHQWERAHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLI 159

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L+  +   SL+ P+G E    L D I+ ++A  PL       + +  TR +A LT R
Sbjct: 160 RNTLQSFQAVSSLDQPVGPEQKDALIDLIQTEDA--PLSIMDGLEIEDALTRCMAYLTER 217

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E  ++  R+G+      ++  +GKQ  ++RER+RQI   A++K+    RS
Sbjct: 218 ERFIVDQRYGLTDGQPKSMGAIGKQIDISRERVRQILNIAMKKMTRQVRS 267


>gi|288800917|ref|ZP_06406374.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288332378|gb|EFC70859.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 287

 Score =  169 bits (428), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 155/250 (62%), Gaps = 1/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ RK +     A +++  ANLR V+SVAK+Y ++GL   DLI EGNIGL+KAAEKFD 
Sbjct: 37  ITLARKIKEGDKDALQKLTRANLRFVVSVAKQYQHQGLSLPDLINEGNIGLIKAAEKFDD 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++Q+I +++ADQS  +R+P++    ++K+ + + +   + +R+P+  
Sbjct: 97  TRGFKFISYAVWWIRQSIMQALADQSRLVRLPLNQVGSVNKINKISHKFEQEFERKPSIA 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ +P E V   +K     +S++ P+ D + + L D ++           +  +LR
Sbjct: 157 EIAEEINLPQERVSDAIKGNNRHVSMDAPLTDGNDNGLADLLQGNEGPDIDTHLLLESLR 216

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L  L  RE  V+   +GI    + TL+E+G +  +TRER RQI  KAIRKL+  
Sbjct: 217 EELKLALNILDERERFVIEAFYGINQ-PEMTLQEIGAKKGLTRERARQIREKAIRKLRKN 275

Query: 671 SRSKKLRSFL 680
           +++K L+S+L
Sbjct: 276 TQNKLLKSYL 285


>gi|186475727|ref|YP_001857197.1| RNA polymerase sigma factor RpoS [Burkholderia phymatum STM815]
 gi|184192186|gb|ACC70151.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phymatum
           STM815]
          Length = 364

 Score =  169 bits (428), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 86  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 142

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 143 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 202

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 203 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 262

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 263 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 321

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 322 ATLEELADEMGLTRERVRQIQQEALVRLK 350


>gi|2832900|emb|CAA04387.1| Sigma A [Lysinibacillus sphaericus]
          Length = 140

 Score =  169 bits (428), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/139 (61%), Positives = 106/139 (76%)

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED  A SP D
Sbjct: 2   LGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDSEAQSPSD 61

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAK
Sbjct: 62  HAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAK 121

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKL+HPSRSK+L+ FL+
Sbjct: 122 ALRKLRHPSRSKRLKDFLE 140


>gi|158340954|ref|YP_001522121.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311195|gb|ABW32807.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  169 bits (428), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 140/230 (60%), Gaps = 2/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+E NLRLV+S+AKK+ + GL  +DLIQEG+IGL  A +KFD   G KFSTYA WW
Sbjct: 40  AKQRMIECNLRLVVSIAKKHQHLGLPLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + +AI R++  QS TI IP+H  ++ H++ +  R+++ +  R PT +E++    +    +
Sbjct: 100 ISEAIKRALKSQSRTIYIPIHQWERAHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLI 159

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L+  +   SL+ P+G E    L D I+ ++A   +   ++  + +  TR +A LT R
Sbjct: 160 RNTLQSFQAVSSLDQPVGPEQKDALIDLIQTEDAALSIMDGLE--IEDALTRCMAYLTER 217

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E  ++  R+G+      ++  +GKQ  V+RER+RQI   A++K+    RS
Sbjct: 218 ERFIVDQRYGLTDGQPKSMGVIGKQIGVSRERVRQILNIAMKKMTRQVRS 267


>gi|288926192|ref|ZP_06420119.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608841|ref|ZP_07883815.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337084|gb|EFC75443.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249448|gb|EFU29463.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  169 bits (428), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 159/268 (59%), Gaps = 6/268 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS E  +SI E   +   +RKG  E   AK+++V ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  ISHEPMVSIDEETELAQAIRKGGREGERAKEKLVRANLRFVVSVAKQYQHQGLGLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQSRIVRLPLNQVGAVSKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--- 592
             +   +  R P+ +E+A+   +  + + + L      +S++ P  ++D + + D +   
Sbjct: 145 TSKFVQEHNRRPSIQELAQITGIDEQKIEQSLNADSHHMSIDAPFAEDDDNSMADVLASG 204

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           +D      +D    A+  E    +   L  RE R+++  FGIG + +  LEE+G++  +T
Sbjct: 205 DDSRTDKQVDFESMAS--ELNNVLKNVLKEREIRIVKECFGIGCH-EKGLEEIGEEMGLT 261

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI  K+I K++    ++ L  +L
Sbjct: 262 RERVRQIREKSILKIRESGNARILMKYL 289


>gi|255312697|gb|ACU01758.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 132/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  L+LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|197247378|ref|YP_002147821.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197211081|gb|ACH48478.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 269

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 73/172 (42%), Positives = 124/172 (72%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++T R
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSTER 261


>gi|209522220|ref|ZP_03270857.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
 gi|209497349|gb|EDZ97567.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
          Length = 363

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 85  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 141

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 142 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 201

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 202 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 261

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 262 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 320

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 321 ATLEELADEMGLTRERVRQIQQEALVRLK 349


>gi|148656381|ref|YP_001276586.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
 gi|148568491|gb|ABQ90636.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
          Length = 398

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 88/235 (37%), Positives = 138/235 (58%), Gaps = 2/235 (0%)

Query: 448 MVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++  NLRLV  +A +Y    R L F DL+QEG IGL+KA E+FD     + STYA++W++
Sbjct: 162 LMRCNLRLVAKIATRYMPYARHLTFDDLLQEGRIGLLKAIERFDQNCRGRLSTYAVYWIR 221

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q+I R++ADQ   +R+PVH+ +++H++ +T  +      REP   E+A  L + +  VR 
Sbjct: 222 QSIQRALADQDRMVRLPVHIVEQLHRLRKTCEQFRCIHGREPGDAELANALGVSLAKVRS 281

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + ++ +   S++ P+G +  + LG+ I D     P     Q  L      VL  L+ RE 
Sbjct: 282 LWRVAQHHTSIDRPVGADTNTFLGELIADDREEGPDFICEQQLLHAVLREVLGHLSSRER 341

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +L  R+G+     HTLEE+G+ F +TRERIRQIE KA+++L      + L+ FL
Sbjct: 342 DILERRYGLIDGQTHTLEEIGQIFGLTRERIRQIERKALKRLNRGEYRRILQPFL 396


>gi|74316856|ref|YP_314596.1| RNA polymerase sigma factor RpoS [Thiobacillus denitrificans ATCC
           25259]
 gi|74056351|gb|AAZ96791.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 316

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 143/236 (60%), Gaps = 6/236 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++ R+       A++ M+E NLRLV+++AK Y NRGL  LDL++EGN+GL+ A EKFD 
Sbjct: 65  VALARRTVLGDFEARQTMIERNLRLVVNIAKHYANRGLTLLDLVEEGNLGLIHALEKFDP 124

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +QS TIR+PVH+  +++  +R  R +      + T +
Sbjct: 125 ERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHIIKELNIYLRAQRHLETHGVTDATSD 184

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +IA     PV  VR+++++ +   SL+ P+  + T  LG+ I D NA  P D  +Q  L 
Sbjct: 185 DIAALTGHPVADVRRIMQLNERIASLDAPLDVDPTLSLGEAIADDNAHLP-DEMLQ--LE 241

Query: 611 ETTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           E    V   L  L  ++  V+  RFG+      TLE++  +  VTRER+RQI+ ++
Sbjct: 242 EIENHVQEWLTQLNDKQRWVIERRFGLNGCEACTLEDLALELEVTRERVRQIQMES 297


>gi|255312633|gb|ACU01726.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEI ++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEITEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTEDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|167932999|ref|ZP_02520086.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7b]
          Length = 211

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 76/129 (58%), Positives = 104/129 (80%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M EAN+RLV+S+AK+Y+ RGL FLDLIQEGN GL++A EKFD   G+KFSTYA WW
Sbjct: 83  AKDKMAEANMRLVVSIAKRYSGRGLDFLDLIQEGNTGLLRAVEKFDPDKGFKFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+  IRIPVHM + I+K++RT RRM+ ++ REPT EE++K+L M  + +
Sbjct: 143 IRQAITRAIADQARVIRIPVHMVETINKLLRTQRRMTQELNREPTIEELSKELDMEPDKI 202

Query: 564 RKVLKITKE 572
             V+KI ++
Sbjct: 203 EYVMKIKQD 211



 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D  +DD VR+YLRE+G I LLS E E+ +A R+  G
Sbjct: 44  DDVSDDSVRLYLREIGKIPLLSAEEEMELAHRVVQG 79


>gi|75812393|ref|YP_320012.1| sigma-70 [Anabaena variabilis ATCC 29413]
 gi|75705149|gb|ABA24823.1| Sigma-70 [Anabaena variabilis ATCC 29413]
          Length = 314

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 161/270 (59%), Gaps = 14/270 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+ ++ + G S +E   I+ + +K       AK++M+ ANLRLV+++AKKY    L+FLD
Sbjct: 56  IQQLAADMGKSETEVFQILRLGQK-------AKEKMIAANLRLVVAIAKKYRWSQLEFLD 108

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEG+IGL KA E+FD   GYKFST A WW++Q IT++IA++S TIR P HM D++ K+
Sbjct: 109 LVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRLIKL 168

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +  R +   + REP   EIA+   +    VR+ L   + P+SL+ P+G ED     DF+
Sbjct: 169 KKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEV---DFL 225

Query: 593 E--DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           E    +  SP +   +  LR+     L +L P +++VL +RFG+G     + +++ ++  
Sbjct: 226 EILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLN 285

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + + ++   + +AI+ L    +  ++R +L
Sbjct: 286 IKQAKVGTTQKQAIKVLHR--QQPQMREYL 313


>gi|295676469|ref|YP_003604993.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
 gi|295436312|gb|ADG15482.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
          Length = 362

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 261 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|91783466|ref|YP_558672.1| RNA polymerase sigma factor RpoS [Burkholderia xenovorans LB400]
 gi|296157776|ref|ZP_06840610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
 gi|91687420|gb|ABE30620.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia xenovorans
           LB400]
 gi|295892022|gb|EFG71806.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
          Length = 360

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 198

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 199 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 258

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 259 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 317

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 318 ATLEELADEMGLTRERVRQIQQEALVRLK 346


>gi|162458688|ref|NP_001104923.1| sigma factor SIG2A [Zea mays]
 gi|4336606|gb|AAD17854.1| sigma factor SIG2A [Zea mays]
          Length = 539

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 91/236 (38%), Positives = 150/236 (63%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  MV +N+RLVIS+A+++   G+ F DLIQEG  GL++ AEKFD   G++FSTY+ WW+
Sbjct: 299 KNRMVTSNVRLVISIAREFEGPGMDFYDLIQEGMQGLIRGAEKFDSSKGFRFSTYSHWWI 358

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQA+ +S+++QS   R+P HM +  ++V    +R+  K++R PT EEIA    +P++ V 
Sbjct: 359 KQAMRKSVSEQSQIFRLPAHMVEASYRVKECTKRLRRKLRRRPTNEEIAVDTGIPIKRVE 418

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             + + K  +SL++ IG  D ++  +   D +A +  +   + ++++     L +LT RE
Sbjct: 419 AAVNLPKYSVSLDSKIGSTDMTY-QEVTADPSAETAEEMLNRMSMKKDVHMALDTLTTRE 477

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   + K L+ +L
Sbjct: 478 KQVVVLRFGLEDGRIRTLQEIGNIMGVSRERIRQIESGAFRKLRSKKKVKALKDYL 533


>gi|124266448|ref|YP_001020452.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
 gi|124259223|gb|ABM94217.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
          Length = 343

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 142/245 (57%), Gaps = 8/245 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +M  +       A+++M+E NLRLV+S+AK Y +RGL   DLI+EGN+GLM A  KF+  
Sbjct: 85  AMATRARAGDFAARQQMIERNLRLVVSIAKSYLSRGLPMTDLIEEGNLGLMHAIGKFEPE 144

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-----RE 546
            G++FSTYA WW++Q+I R+I  Q+  +R+PVH+  ++++V++  R +  +       R 
Sbjct: 145 RGFRFSTYASWWIRQSIERAIMHQARLVRLPVHVVRELNQVLKARRALEGEAAASADGRT 204

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDS 603
              +EIA  L  PV  V ++L+  ++P SL+ P+          LGD + D+ A  PL  
Sbjct: 205 VRVDEIAAALGRPVTEVSELLRFAEQPTSLDAPLERQAGNGAETLGDMVADEQATDPLGH 264

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L       L  L+ RE  VL  R+G+      TLE + ++  +TRERIRQI+ +A
Sbjct: 265 TLNHELDVLLEHGLGELSEREREVLAGRYGLHDREPETLEVLAERLGLTRERIRQIQQEA 324

Query: 664 IRKLK 668
           + KLK
Sbjct: 325 LLKLK 329


>gi|300114080|ref|YP_003760655.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299540017|gb|ADJ28334.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 303

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 91/247 (36%), Positives = 148/247 (59%), Gaps = 4/247 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R+   +  +G+ EA   +  ++E+NLR+VI VA ++ NRGL  +DLI+EGN+GL
Sbjct: 52  LNAEEERYYARLALQGDREA---RNRIIESNLRIVIKVASRHVNRGLPLMDLIEEGNLGL 108

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A EKF+  LG++FSTYA WW++QAI R++ +Q+ TIR+PVH+  KI    +       
Sbjct: 109 INAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRLPVHVFKKIRSYQKEVILFRQ 168

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP   EIAK L  P+E V++ L +     SL+ P+ ++    L D + D+     L
Sbjct: 169 RYNIEPRSGEIAKLLHEPLERVQRYLSLQALETSLDDPLNEDTEDCLADLLPDERNNPAL 228

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              I  + + +    L+ L  R++ +L+ R+G+      TLEE+G    +TRER+RQI+ 
Sbjct: 229 LWEI-FDKKASIYNQLSQLPERQQEILKRRYGLDGYEVTTLEEIGHNLGITRERVRQIQQ 287

Query: 662 KAIRKLK 668
            AI++L+
Sbjct: 288 AAIKRLR 294


>gi|307729587|ref|YP_003906811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
 gi|307584122|gb|ADN57520.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
          Length = 362

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMNSGDAAERRDASIDDIAYLTGKTADEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 261 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 320 ATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|323526138|ref|YP_004228291.1| RNA polymerase sigma-70 subunit RpoD subfamily [Burkholderia sp.
           CCGE1001]
 gi|323383140|gb|ADX55231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1001]
          Length = 358

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 80  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 136

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 137 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 196

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 197 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 256

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 257 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 315

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 316 ATLEELADEMGLTRERVRQIQQEALVRLK 344


>gi|187923827|ref|YP_001895469.1| RNA polymerase sigma factor RpoS [Burkholderia phytofirmans PsJN]
 gi|187715021|gb|ACD16245.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phytofirmans
           PsJN]
          Length = 360

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 198

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 199 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 258

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 259 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 317

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 318 ATLEELADEMGLTRERVRQIQQEALVRLK 346


>gi|125585746|gb|EAZ26410.1| hypothetical protein OsJ_10293 [Oryza sativa Japonica Group]
          Length = 497

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 146/237 (61%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G++FSTY+ WW
Sbjct: 256 CKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGFRFSTYSHWW 315

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA    MP+  V
Sbjct: 316 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIASDTGMPLRRV 375

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +SL + +G  D ++  +   D +  +  +   +  ++E   R L  L+PR
Sbjct: 376 EAAMSLPKYTVSLTSKVGCTDMTY-QEITPDTSTETAEEMLHRWLMKEDVDRALDGLSPR 434

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + + L+ +L
Sbjct: 435 ERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKVQSLQHYL 491


>gi|320104603|ref|YP_004180194.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319751885|gb|ADV63645.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 277

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 102/276 (36%), Positives = 164/276 (59%), Gaps = 17/276 (6%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           ++ V   +++ L+  NE+  +S E      E + + + + KG+     A++ MV ANLRL
Sbjct: 9   RDTVQSPLETYLREINEMALLSAE------EEKELAARIAKGD---KTARERMVRANLRL 59

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+++A+ Y  +GL   DLI+EGN+GL++A E FD  +G +FSTYA +W+KQ+I R++ + 
Sbjct: 60  VVNIARGYVGKGLALQDLIEEGNLGLLRAVEGFDPKVGTRFSTYASYWIKQSIKRALVNT 119

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +  IRIP +M + + K  R A  + +++ R PT +EIA +L +P    +K L I K+ I 
Sbjct: 120 AKPIRIPAYMVELLCKWRRAAIELQDRLGRTPTTDEIAHELRIP----KKKLAIVKKAIK 175

Query: 576 LE--TPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           +    P  D+  S   LGD + D+    P    ++A+  +   R L  +  RE  VLRMR
Sbjct: 176 VYNLVPQSDQPESGWSLGDMLMDERTRPPDVEMVEADNLKLVMRRLEEMDKREATVLRMR 235

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           FG+      TL+E+G+Q  +TRER+RQIE +A+ KL
Sbjct: 236 FGLDDQPPCTLKEIGEQLGLTRERVRQIENEALNKL 271


>gi|71908137|ref|YP_285724.1| RNA polymerase sigma factor RpoS [Dechloromonas aromatica RCB]
 gi|71847758|gb|AAZ47254.1| RNA polymerase, sigma 38 subunit, RpoS [Dechloromonas aromatica
           RCB]
          Length = 309

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 93/239 (38%), Positives = 147/239 (61%), Gaps = 9/239 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR+G+  A   ++ M+E NLRLV+++AK Y NRG+  LDLI+EGN+GL+ A EKFD   
Sbjct: 63  LVREGDFSA---RQRMIEHNLRLVVNIAKHYLNRGIPLLDLIEEGNLGLIHALEKFDPER 119

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q I R I +QS TIR+PVH+  +I+ V+R  R + +  KR+ T E I
Sbjct: 120 GFRFSTYATWWIRQNIERGIMNQSRTIRLPVHIVKEINVVLRAMRHLESADKRDSTVERI 179

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  +  PV  VR++L + +   SL+ P+  +    + + I D     P +S +Q++  E 
Sbjct: 180 ALLIDRPVADVRRILSLNEHIASLDAPLEIDPNHTMAEVIADDGESDP-ESLLQSS--EV 236

Query: 613 TTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + V   L  LT R+  V+  R+G+      TL+ +     +TRER+RQI+ + + +L+
Sbjct: 237 GSLVDDWLEQLTERQRSVIERRYGLSGADLATLDVIACDLGLTRERVRQIQMEGLDRLR 295


>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila]
          Length = 547

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 149/239 (62%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+TYA WW
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 366

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +SI   S TIR+P ++   + KV    +         P+ E++A  + +  E +
Sbjct: 367 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCIQDGNYRPSKEQLASHVGVSTEKL 426

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            K+L  T+ P+S++ PI  D+DT+   +   D    +P  S  +  +R     +L  L+P
Sbjct: 427 DKLLYNTRTPLSMQQPIWSDQDTT-FQEVTPDSGIETPSMSVGKQLMRNHVRNLLNVLSP 485

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +E+R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L ++ D
Sbjct: 486 KEKRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMSSHGLNAYAD 544


>gi|15558898|dbj|BAB64922.1| chloroplast RNA polymerase sigma factor [Chlamydomonas reinhardtii]
          Length = 250

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 143/228 (62%), Gaps = 6/228 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++++N +LV++V K +  +G    DL+ EG  GL+K  EK+D   G++F TYA WW
Sbjct: 7   AKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGFRFGTYAHWW 66

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++RS+A+    +R+P+HM +++ ++   + ++  ++ REPT  E+AK   +PV  V
Sbjct: 67  IRQAVSRSLAETGRAVRLPMHMIEQLTRLKNLSAKLQTQLAREPTLPELAKAAGLPVTRV 126

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASL 620
           + +++  +   SL+TPIG  +   LG  ++D        +  +    +LR     +L  L
Sbjct: 127 QMLMETARSAASLDTPIGGNE---LGPTVKDSVEDEREAADEEFGSDSLRNDMEAMLLEL 183

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL+
Sbjct: 184 PEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKLR 231


>gi|261886011|ref|ZP_06010050.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 190

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 83/187 (44%), Positives = 126/187 (67%), Gaps = 1/187 (0%)

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           S       +QA+ R+IADQ+ TIRIP+HM + I+++ +       K  + P    I  ++
Sbjct: 3   SAACSLRARQAMCRAIADQALTIRIPIHMIETINRINKFIENFFQKKGKGPDVAFIPGEV 62

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + ++ V++V+KITKEPISLE PIG ED    GDF+EDK  +SP++  ++ +L+E    V
Sbjct: 63  GLSIDKVKQVIKITKEPISLEAPIGSEDDGKYGDFVEDKTNLSPMEQILKGDLKEQIDEV 122

Query: 617 LASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +K
Sbjct: 123 LDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRK 182

Query: 676 LRSFLDG 682
           L+++++G
Sbjct: 183 LKNYIEG 189


>gi|55274897|gb|AAV49250.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 79/197 (40%), Positives = 132/197 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  L LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGKQF 649
           G+      TLE+VG++ 
Sbjct: 181 GLLGYEAATLEDVGREI 197


>gi|318066905|emb|CBY89067.1| RNA polymerase sigma70 factor [Chromohalobacter canadensis]
          Length = 367

 Score =  168 bits (426), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 137/402 (34%), Positives = 198/402 (49%), Gaps = 64/402 (15%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLEAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ-EKERDDVQETEGDIESAAK 235
                R + DL +        GF    EG       D  + E ERD V   +GD      
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEADVPEPEPERDAV---DGDASEDDD 128

Query: 236 VSKDDRSKVDSPPENA--------ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
            ++++ +     PE A        E +ER     +     + +A ++Q R         +
Sbjct: 129 DAEEEETGGGPDPEEAKARFEQIREQNERAKAAIDKHGLGSSNADQEQAR---------L 179

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           AE++  +                    K++ +   +LVG + ++       +EQ+    K
Sbjct: 180 AELFSPI--------------------KLVPKHFERLVGQVRIS-------IEQIRGQEK 212

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
            IM      L + Q+  + R  F+    G E D  W+   K     ++   +      IL
Sbjct: 213 AIMQ-----LFVKQAK-VPRKTFIGSFPGAESDLEWLDRFKA-KHSKYAERIEPFRADIL 265

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + + +I        + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 266 RAQRKIGFEEEMVCLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 325

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 326 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|281420436|ref|ZP_06251435.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405493|gb|EFB36173.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 291

 Score =  168 bits (426), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 161/268 (60%), Gaps = 5/268 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  +SI E   +   +RKG  E   AK+++V+ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMVSIDEEIELAQKIRKGGREGERAKEKLVKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+   
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGALSKISAE 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIED 594
             +   + +R+P+  E+A+   M    + + +K     +S++ P G D+D + + D +  
Sbjct: 145 ISKFEQENQRKPSVAELAQITKMEESKIDQTIKADNHHMSIDAPFGSDDDDNAMVDVMAS 204

Query: 595 KNAVSPLDSAIQ-ANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +  S  D  +   ++     RVL S L  RE ++L   +GIG + +  LEE+G +F +T
Sbjct: 205 GDD-SRTDKGVDFESMASELDRVLNSVLKDRERKILCYCYGIGCH-EKGLEEIGSEFNLT 262

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI  K+I KL+   + K L  +L
Sbjct: 263 RERVRQIREKSIIKLRDSGKIKILMKYL 290


>gi|255312671|gb|ACU01745.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  168 bits (426), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|115452175|ref|NP_001049688.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|29893614|gb|AAP06868.1| unknown protein [Oryza sativa Japonica Group]
 gi|32351880|dbj|BAC78529.1| plastid sigma factor 2B [Oryza sativa Japonica Group]
 gi|108707414|gb|ABF95209.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|113548159|dbj|BAF11602.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|215704451|dbj|BAG93885.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|215765869|dbj|BAG87566.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 540

 Score =  168 bits (426), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 146/237 (61%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G++FSTY+ WW
Sbjct: 299 CKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGFRFSTYSHWW 358

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA    MP+  V
Sbjct: 359 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIASDTGMPLRRV 418

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +SL + +G  D ++  +   D +  +  +   +  ++E   R L  L+PR
Sbjct: 419 EAAMSLPKYTVSLTSKVGCTDMTYQ-EITPDTSTETAEEMLHRWLMKEDVDRALDGLSPR 477

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + + L+ +L
Sbjct: 478 ERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKVQSLQHYL 534


>gi|125543279|gb|EAY89418.1| hypothetical protein OsI_10924 [Oryza sativa Indica Group]
          Length = 540

 Score =  168 bits (425), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 146/237 (61%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G++FSTY+ WW
Sbjct: 299 CKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGFRFSTYSHWW 358

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA    MP+  V
Sbjct: 359 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIASDTGMPLRRV 418

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +SL + +G  D ++  +   D +  +  +   +  ++E   R L  L+PR
Sbjct: 419 EAAMSLPKYTVSLTSKVGCTDMTYQ-EITPDTSTETAEEMLHRWLMKEDVDRALDGLSPR 477

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + + L+ +L
Sbjct: 478 ERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKVQSLQHYL 534


>gi|255312665|gb|ACU01742.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312669|gb|ACU01744.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  168 bits (425), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ T R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTNRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|296121869|ref|YP_003629647.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296014209|gb|ADG67448.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 290

 Score =  168 bits (425), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 90/244 (36%), Positives = 152/244 (62%), Gaps = 11/244 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +  GE EA   +  MV ANLRLV+++A+ Y  +GL   DLI+EGN+GL++A E 
Sbjct: 47  RELANRIANGEKEA---RDRMVRANLRLVVNIARAYVGKGLPLQDLIEEGNLGLLRAVEG 103

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +  +FSTYA +W+KQ+I R++ +   TIRIP +M + + K  +   ++ ++ KR P
Sbjct: 104 FDPDMNTRFSTYASYWIKQSIKRALINCGKTIRIPAYMVELLSKWRKATAKLEDQFKRPP 163

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISL--ETPIGDEDTS--HLGDFIEDKNAVSPLDS 603
           T EE+A +L +P    +K L I K+ I L   TP  D++ S   + D + D+    P D 
Sbjct: 164 TQEEVAIELGLP----KKKLSIVKKAIHLYSSTPQTDDEESGWMMSDMVADERVKGPDDE 219

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  +  +    +L ++  RE ++LR+RFG+  +   TL+E+G++  +TRER+RQIE++A
Sbjct: 220 LLDVDNLKHVYAMLETMDEREAKILRLRFGLDDSEPKTLKEIGEEMGLTRERVRQIESEA 279

Query: 664 IRKL 667
           ++++
Sbjct: 280 LKRI 283


>gi|224007213|ref|XP_002292566.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971428|gb|EED89762.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 338

 Score =  168 bits (425), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 93/275 (33%), Positives = 161/275 (58%), Gaps = 23/275 (8%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-----------LQFLDLIQEG 477
           H V  +++    +  AK  ++EANLRLVI+VA++   +            +QF D  Q+G
Sbjct: 60  HTVPSLKQQIRRSQRAKAALIEANLRLVITVARQAVKKSPFRSSSHAASSVQFQDACQQG 119

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL +A EKFD  LG++FSTYA+WW+++ + +++ +QS T+R+P     KI+ +    R
Sbjct: 120 IIGLTRATEKFDPELGFRFSTYAIWWIQKEVAKNVNEQSRTVRVPGSAIKKINDIRIQER 179

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI------------GDEDT 585
            + N++ R P+ +E+A+K  + VE +    +  KE  SL+  I            GD+D 
Sbjct: 180 VLMNELGRRPSDDEVAEKCGLTVEKLNFYRQSAKEVKSLDKKIDSRTGKGSAASGGDDDG 239

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             +  F+ D    SP +   Q  +++   R++ +L+PRE+ V+R+RFG+      TL ++
Sbjct: 240 KTMEIFVRDTEHPSPSELIDQQMMQQDIRRLVKTLSPREQAVIRLRFGLDDGKPQTLGDI 299

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++F V +ERI++IEA+A+ KL+ PSRS  ++ ++
Sbjct: 300 GEKFGVEKERIKKIEARALLKLRQPSRSSVVKCYV 334


>gi|55274986|gb|AAV49291.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 196

 Score =  168 bits (425), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 78/195 (40%), Positives = 131/195 (67%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 60

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   
Sbjct: 61  QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERIT 120

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 121 SVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 180

Query: 635 GMNTDHTLEEVGKQF 649
                 TLE+VG++ 
Sbjct: 181 LGYEAATLEDVGREI 195


>gi|281420133|ref|ZP_06251132.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405933|gb|EFB36613.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 290

 Score =  168 bits (425), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 89/260 (34%), Positives = 154/260 (59%), Gaps = 2/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +SI E   +   +RKG      AK +++EANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  VSIDEEIELAQAIRKGGRAGERAKNKLIEANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAE+FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++KV +   +   
Sbjct: 91  IKAAERFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKVNQEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + +R P+ EE+A +  +  + + + +  +   +S++ P  D+D + + D +   +     
Sbjct: 151 ENQRRPSVEELAARTGVDEDKISQSMAASGHHVSIDAPFSDDDDNSMADVMASGDDARTD 210

Query: 602 DSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                 ++ +   +VL   L  RE +++   +GIG  T+  LEE+G +  +TRER+RQI 
Sbjct: 211 KQVDHESMAQDLRQVLKVCLKDRELKIICACYGIG-ETEKGLEEIGDKMGLTRERVRQIR 269

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            K+I KL+   +   L  +L
Sbjct: 270 EKSITKLRESGKIGILMKYL 289


>gi|170692344|ref|ZP_02883507.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
 gi|170142774|gb|EDT10939.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
          Length = 359

 Score =  168 bits (425), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 159/269 (59%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE EA   ++ M+E NLRLV+S+AK Y NRG+
Sbjct: 81  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFEA---RQVMIERNLRLVVSIAKGYLNRGV 137

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 138 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 197

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +R+ + ++IA       + V  +L + +   SL+ P+
Sbjct: 198 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 257

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTD 639
            D D +     +   +     D+ +Q    ET TR  LA L+ +   V+  RFG+     
Sbjct: 258 -DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEP 316

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLEE+  +  +TRER+RQI+ +A+ +LK
Sbjct: 317 ATLEELADEMGLTRERVRQIQQEALVRLK 345


>gi|255312647|gb|ACU01733.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312653|gb|ACU01736.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  167 bits (424), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L LV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LLLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|255312639|gb|ACU01729.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312641|gb|ACU01730.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312643|gb|ACU01731.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312645|gb|ACU01732.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  167 bits (424), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L LV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LGLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|55274894|gb|AAV49249.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 195

 Score =  167 bits (424), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  L LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|20151056|pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
 gi|20151057|pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
          Length = 241

 Score =  167 bits (424), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 81/153 (52%), Positives = 114/153 (74%), Gaps = 6/153 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 93  ELKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 148

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ R
Sbjct: 149 EKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGR 208

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISL 576
           EP+ EEIA+ +    +   V + LKI +EP+SL
Sbjct: 209 EPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241



 Score = 39.3 bits (90), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 24/33 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T DPVR YL E+G + LL+ E EI +A+++E G
Sbjct: 1   TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG 33


>gi|269123355|ref|YP_003305932.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
 gi|268314681|gb|ACZ01055.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
          Length = 280

 Score =  167 bits (423), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 132/229 (57%), Gaps = 11/229 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++ +NLRLV+S AKK    G+  +DLI EGN+GL+K+ +KFD+  G +FSTYA+WW
Sbjct: 49  AKHLLILSNLRLVVSEAKKLLGNGMPLIDLISEGNLGLIKSIDKFDYTKGLRFSTYAVWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I +SI +    IRIP +  +++ KV +      N+    PT E IA+ L M    V
Sbjct: 109 IKQTIKKSIVNLGRDIRIPSYKYEQLSKVNKVIESYQNEFGDIPTAEYIAEVLGMKPSKV 168

Query: 564 RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +    +E ISL   IGD    ED     D +ED       D      L E       +
Sbjct: 169 VLLQNEFQEIISLNDAIGDNIFLEDVIGQSDNVED-------DIIRNDQLSEMYNLFDKT 221

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PRE+ +L +R+G+  N  HTL+E+G++  +TRER+RQIE KAI KLK
Sbjct: 222 LNPREKEILELRYGLANNKIHTLKEIGEKLSITRERVRQIEKKAITKLK 270


>gi|318066911|emb|CBY89070.1| RNA polymerase sigma70 factor [Chromohalobacter nigrandesensis]
          Length = 367

 Score =  167 bits (423), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 130/396 (32%), Positives = 191/396 (48%), Gaps = 52/396 (13%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLDAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEG-HSYQKREDSSQEKERDDVQETEGDIESAAK 235
                R + DL +        GF    EG     + E    E E       +GD+     
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEAEVPGPEPE---PSAADGDVSEDDD 128

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
            ++++ +     PE A+     + E  +               +   A+D+         
Sbjct: 129 EAEEEETGGGPDPEEAKARFEQIREQNE---------------RAKAAIDK--------H 165

Query: 296 SLQDNAVNGQKDEKSSV--KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            L  +  N +++  + +    K++ +   +LVG + ++       +EQ+    K IM   
Sbjct: 166 GLGSSEANKEQERLAELFSPIKLVPKHFERLVGQVRIS-------IEQVRSQEKAIMQV- 217

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
                  +   + R  F+    G E D  W+   K       +       D IL+ + +I
Sbjct: 218 -----FVKQAKVPRKTFIGSFPGAESDLEWLDRFKAKHAKYAERLEPFRAD-ILRAQRKI 271

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 272 GFEEEMVRLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 331

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 332 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|148242708|ref|YP_001227865.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851018|emb|CAK28512.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 301

 Score =  167 bits (423), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 91/232 (39%), Positives = 147/232 (63%), Gaps = 7/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EKFD   G++FSTYA WW
Sbjct: 59  AKNQMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKFDPTRGHRFSTYAYWW 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+     R+     R+P  EE+A  L +P++ V
Sbjct: 119 IRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKARLFQSTGRQPIAEELADYLKLPLDEV 178

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +  + D S L D +  +  + P++ A      +T  ++L  A
Sbjct: 179 EDLLGCELRSVTVSLQGVVKSKSDPSELVDVLPSEE-MPPMERAELDERTQTVWKLLDQA 237

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +LTP+E  V+ +RFG+ G N   TL EV +Q   +RE  RQ+  +++RKL+ 
Sbjct: 238 NLTPKERTVVMLRFGLDGTNEWRTLAEVARQMSCSREYCRQVVQRSLRKLRR 289


>gi|55274883|gb|AAV49244.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274899|gb|AAV49251.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 193

 Score =  167 bits (423), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 79/193 (40%), Positives = 130/193 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEV 645
           G+      TLE+V
Sbjct: 181 GLLGYEAATLEDV 193


>gi|158338579|ref|YP_001519756.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158308820|gb|ABW30437.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  167 bits (423), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 89/237 (37%), Positives = 147/237 (62%), Gaps = 2/237 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ R+ +     AK++M+EANLRLV+S+AKK+ NRGL  LDLIQEGN+GL  A +KF+ 
Sbjct: 27  ITLARQVQAGNPRAKRKMIEANLRLVVSIAKKHQNRGLPLLDLIQEGNLGLSIAVDKFEP 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WW+ Q +TRS+ ++   +R+PV      +++ RT  ++S ++ REPT  
Sbjct: 87  EQGNRFSTYAYWWILQGVTRSLQNKGRVVRLPVKHWQVGNQIKRTRHQLSQELGREPTVV 146

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  + M +  ++K L   +E +SL+  +G E  + LGD IE  ++       +  +  
Sbjct: 147 EIADAMEMDLTRLKKYLHSLQETVSLDKFVGSEQDTTLGDLIEGNDSTQSYLDLLLQD-- 204

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  +  LA L  R+  V+  R+G+      ++E++G++  ++RER+RQI  KA++ L
Sbjct: 205 EELSGYLALLDDRQRFVISERYGLEDGKPKSMEKIGQKLGISRERVRQIIKKAMQTL 261


>gi|108707415|gb|ABF95210.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|215695353|dbj|BAG90544.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 343

 Score =  167 bits (423), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 146/237 (61%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G++FSTY+ WW
Sbjct: 102 CKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGFRFSTYSHWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA    MP+  V
Sbjct: 162 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIASDTGMPLRRV 221

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +SL + +G  D ++  +   D +  +  +   +  ++E   R L  L+PR
Sbjct: 222 EAAMSLPKYTVSLTSKVGCTDMTY-QEITPDTSTETAEEMLHRWLMKEDVDRALDGLSPR 280

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + + L+ +L
Sbjct: 281 ERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKVQSLQHYL 337


>gi|37362432|gb|AAO23112.1| sigma factor S [Vibrio vulnificus]
          Length = 167

 Score =  167 bits (422), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 74/153 (48%), Positives = 114/153 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 13  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV+ V
Sbjct: 73  IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVDDV 132

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            K+L++ +   S++TPIG +    L D I D N
Sbjct: 133 GKMLRLNERISSVDTPIGGDGEKALLDIIRDAN 165


>gi|261879347|ref|ZP_06005774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334050|gb|EFA44836.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  167 bits (422), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 93/262 (35%), Positives = 157/262 (59%), Gaps = 6/262 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I++ E   +   +RKG  E   AK+++V+ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ITVDEEIELAQAIRKGGKEGERAKEKLVKANLRFVVSVAKQYQHQGLGLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+     +   
Sbjct: 91  VKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGALSKINAEISKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           +  R P+ +E+A+   +    + + +K     +S++ P  ++D + + D +   +D  A 
Sbjct: 151 ENHRPPSVQELARLTNIEEAKIEQTMKADNHHMSIDAPFQEDDDNSMADVLSSGDDSRAD 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             +D   ++  +E  T +   L  RE  ++R  FGIG + +  LEE+G Q  +TRER+RQ
Sbjct: 211 RQVD--YESMSKELDTVLCNVLKERERTIVRECFGIGCH-EKGLEEIGDQLGLTRERVRQ 267

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           I  K+I KL+    ++ L  +L
Sbjct: 268 IREKSIVKLRESGHAQLLIKYL 289


>gi|255312663|gb|ACU01741.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  167 bits (422), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 131/195 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+ L++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|1526450|dbj|BAA13238.1| RNA polymerase sigma subunit, truncated form of sigma-38
           [Escherichia coli W3110]
 gi|23306704|gb|AAN15271.1| C-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 269

 Score =  167 bits (422), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 73/180 (40%), Positives = 126/180 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269


>gi|318066921|emb|CBY89075.1| RNA polymerase sigma70 factor [Halomonas almeriensis]
          Length = 366

 Score =  167 bits (422), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 132/403 (32%), Positives = 200/403 (49%), Gaps = 67/403 (16%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M +L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMFALAYLPGAVDSILEAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET-EGDIESAAK 235
                R        I P+       G  G +       ++  E   V +T EG+ +   +
Sbjct: 81  EEAPGRLSDLFSGFIDPD------EGIPGVA------EAEVPEPQPVHKTAEGEGDEDVE 128

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDD----SAHTLSAMEDQLRPKVMCALDEIAEVY 291
             +++      P E     E+  +++E       AH  +A E Q        L  +AE++
Sbjct: 129 AEEEETGGGPDPEEARARFEQIREQNEAARRAIEAHGRAAKEAQ------SELARLAELF 182

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
             +                    K++ +   +LVG + ++       VEQ+    K IM 
Sbjct: 183 SPI--------------------KLVPKHFERLVGQVRIS-------VEQVRAQEKAIMQ 215

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSIL-KI 409
                    +   + R  F++   G E +  W+ ++  D       +  A  ++ +  +I
Sbjct: 216 ------LCVKKAKLPRKTFIKSFPGNESNQEWLDAFMAD------NSRHAARLEPLKGEI 263

Query: 410 RNEIKSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +   + I+ E     +++++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 264 QRSQRKIAFEEEMVALAVTDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 323

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 324 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 366


>gi|242041441|ref|XP_002468115.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
 gi|241921969|gb|EER95113.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
          Length = 528

 Score =  166 bits (421), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 93/238 (39%), Positives = 146/238 (61%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  MV++N+RLVIS+AK++   G++F DLIQEG  GL++ AEKFD   G++FSTY+ WW
Sbjct: 287 CKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWW 346

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR P+ EEIA    M +  V
Sbjct: 347 IKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLRRELKRLPSNEEIAVDTGMTIRRV 406

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              + + K  +S  + +G  D ++  + + D +A +  +   +  +++     L SL+PR
Sbjct: 407 EAAMSLPKYSVSFTSKVGCTDVTYQ-EIMPDTSAETAEEVLHRWLMKKDVNTALESLSPR 465

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ V+R RFGI      TL ++G+   V+RERIRQIE  A RKL+   R + L+ +L 
Sbjct: 466 EKLVMRYRFGIEGGRPRTLHDIGQIMGVSRERIRQIELGAFRKLRSKKRVQSLQHYLQ 523


>gi|225848787|ref|YP_002728951.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643846|gb|ACN98896.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 282

 Score =  166 bits (421), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 97/261 (37%), Positives = 158/261 (60%), Gaps = 5/261 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R +    +KG+ EA    K++VE NLR V+++AK +   G+   DLI  GN+GL
Sbjct: 24  LTPEEERELAIRAKKGDKEAL---KKLVEGNLRFVVNIAKNFMGWGVPLTDLIAAGNLGL 80

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AA++FD     KF +YA+WW++QAI ++I  Q+  +RIP+     I KV     ++  
Sbjct: 81  IEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGAVRIPIKESLFISKVKNAYEKLKE 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVS 599
            + REPT EEIAK+L   V+ V+  L I ++PISL+ P+G+  E+   L D +  K    
Sbjct: 141 SLGREPTEEEIAKELKTSVKKVKNALAIVRQPISLDMPLGEGGEEDFTLLDILSKKGTED 200

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                +++ L+E   R+L  L  RE  ++++R+G+      TLEEVG+   ++RER+RQ+
Sbjct: 201 VEKDLVESTLKEEFERLLNVLDEREREIIKLRYGLEGLEPKTLEEVGEMLGISRERVRQL 260

Query: 660 EAKAIRKLKHPSRSKKLRSFL 680
           E +A++KLK  +  K L++FL
Sbjct: 261 EQRALKKLKAVALKKHLQNFL 281


>gi|15240693|ref|NP_196877.1| SIG4 (SIGMA FACTOR 4); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|3983260|gb|AAC97954.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972296|dbj|BAA78110.1| RNA polymerase sigma subunit SigD [Arabidopsis thaliana]
 gi|9758039|dbj|BAB08700.1| sigma-like factor [Arabidopsis thaliana]
 gi|332004550|gb|AED91933.1| sigma factor 4 [Arabidopsis thaliana]
          Length = 419

 Score =  166 bits (421), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 84/231 (36%), Positives = 138/231 (59%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    A++++     RLV+S+A  Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 174 CRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLST 233

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y  WW+KQAI R+IA +S  +++P  M +   KV   +  ++ K++R+P+ EEIA+ L +
Sbjct: 234 YVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNL 293

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V  VR  ++ ++ P+SL+          L + +   +   P +   + +++    ++L 
Sbjct: 294 NVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLG 353

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           SLT RE RVL + FG+   T  + EE+GK   ++RER+RQI   A++KL++
Sbjct: 354 SLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRN 404


>gi|255312661|gb|ACU01740.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/195 (40%), Positives = 130/195 (66%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L LV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LLLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S +TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSEDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEVGK 647
           G+      TLE+VG+
Sbjct: 181 GLLGYEAATLEDVGR 195


>gi|318066941|emb|CBY89085.1| RNA polymerase sigma70 factor [Halomonas eurihalina]
          Length = 367

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 132/395 (33%), Positives = 193/395 (48%), Gaps = 50/395 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILDAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ-EKERDDVQETEGDIESAAK 235
                R + DL +        GF    EG       D  + E ER      +G+      
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEADVPEPEPERS---AADGETSDEDD 128

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
            ++++ S     PE A                   A  +Q+R +   A   I E  R  +
Sbjct: 129 DAEEEESGGGPDPEEAR------------------ARFEQIRQQNEAARRAIEEHGRGAK 170

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
             Q+      +  +     K++ +   +LVG + ++       VEQ+    K IM     
Sbjct: 171 QAQNELA---RLAELFSPIKLVPKHFERLVGQVRIS-------VEQVRAQEKAIMQ---- 216

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
                +   + R  F++   G E    W+ ++  +     + + +A     I + + +I 
Sbjct: 217 --LCVKKAKVPRKTFIKSFPGNESRQDWLDTFMAE--HARYADRLAALKGDIQRAQRKIA 272

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
                  + + + + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 273 FEEEMVALVVPDLKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 332

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 333 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|158341079|ref|YP_001522246.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311320|gb|ABW32932.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 139/230 (60%), Gaps = 2/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M+E NLRLV+S+AKK+ + GL  +DLIQEG+IGL  A +KFD   G KFSTYA WW
Sbjct: 40  AKQRMIECNLRLVVSIAKKHQHLGLPLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + +AI R++  QS TI IP+H  ++ H++ +  R+++ +  R PT +E++    +    +
Sbjct: 100 ISEAIKRALKSQSRTIYIPIHQWERAHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLI 159

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R  L+  +   SL+ P+G E    L D I+ ++A   +   ++  + +  TR +A LT R
Sbjct: 160 RNTLQSFQAISSLDQPVGPEQKDALIDLIQTEDAALSIMDGLE--IEDALTRCMAYLTER 217

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E  ++  R+G+      ++  +GK   ++RER+RQI   A++K+    RS
Sbjct: 218 ERFIVDQRYGLTDGQPKSMGAIGKPIGISRERVRQILNIAMKKMTRQVRS 267


>gi|206901861|ref|YP_002251028.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
 gi|206740964|gb|ACI20022.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
          Length = 413

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 73/115 (63%), Positives = 95/115 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK+++EANLRLV+SVAK+Y  RGL FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW
Sbjct: 104 AKKKLIEANLRLVVSVAKRYIGRGLSFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWW 163

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           ++QAITR+IADQ+ TIRIPVHM + ++K+ +  R ++  + R+PT E+IAK L +
Sbjct: 164 IRQAITRAIADQARTIRIPVHMVETMNKIHKITRLLTQNLGRKPTEEDIAKFLVI 218



 Score =  128 bits (322), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 69/153 (45%), Positives = 104/153 (67%), Gaps = 15/153 (9%)

Query: 540 SNKIKREPTPEEIAKK-----------LAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           +NK+   PT EEI +K           +    E VR++  + +EP+SLE P+G+++ + L
Sbjct: 264 NNKV---PTKEEINEKAKELKHVLEEEIRQQTEKVREISMMGQEPLSLEMPVGEDEDNRL 320

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+E+K+ +SP D A+Q +L++    +L  L+ RE  +L++RFG+  N   TLEEVGK 
Sbjct: 321 ADFVENKD-LSPADIAVQKSLKKDIEELLNELSEREREILKLRFGLEDNQPRTLEEVGKL 379

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+R+L+HPSRSKK++ +L+
Sbjct: 380 FNVTRERIRQIEAKALRRLRHPSRSKKIKDYLE 412



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 31/49 (63%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           D   DDPV+MYL+E+G I LL+ E EI +AKR+E G       L E+ L
Sbjct: 65  DIELDDPVKMYLKEIGKIPLLTPEEEIELAKRVEQGDEEAKKKLIEANL 113


>gi|158833963|gb|ABW81787.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 75/202 (37%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDSDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L  L+ ++  VL  RF
Sbjct: 204 KSVVKWLFELSTKQREVLARRF 225


>gi|330448286|ref|ZP_08311934.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328492477|dbj|GAA06431.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 291

 Score =  166 bits (420), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 134/227 (59%), Gaps = 1/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +KK ++E+NLRLV+S+AKKY    +   DLI EGNIGL+ A EKFD   G++FSTYA WW
Sbjct: 49  SKKVLIESNLRLVVSIAKKYRGSPMHISDLIDEGNIGLITAVEKFDPEKGFRFSTYATWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I R+I +Q  TIR+PVH+  +I+ +VR  +++  K   EP+ E+IA  L   +  V
Sbjct: 109 IKQTIERAIHNQGRTIRLPVHVSKEINTIVRAHKQLVKKNNEEPSKEQIANILNKSLHDV 168

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              L      IS +  + G+ +   +   I D+    P        + + TT VL  L  
Sbjct: 169 STTLSYETPIISYDQSVNGEVNAQSMAVLIADETMAKPDQHVDDLAIEKITTNVLNCLNK 228

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R++ ++  RFG+      TL+EV ++  +TRERIRQ++  ++ KLK+
Sbjct: 229 RDKEIICRRFGLLGYEAQTLQEVAEEVGLTRERIRQLQVTSLSKLKN 275


>gi|55274909|gb|AAV49256.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 76/185 (41%), Positives = 127/185 (68%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E+NLRLV+ +A++Y NRGL  LDLI+EGN+ L++A EKFD   G++FSTYA WW++Q I 
Sbjct: 1   ESNLRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIE 60

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++
Sbjct: 61  RAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRL 120

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL 
Sbjct: 121 NERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLA 180

Query: 630 MRFGI 634
            RFG+
Sbjct: 181 RRFGL 185


>gi|313799121|gb|ADR82155.1| RNA polymerase sigma factor [Mycoplasma sp. 1220]
 gi|313799126|gb|ADR82156.1| RNA polymerase sigma factor [Mycoplasma anatis]
 gi|313799129|gb|ADR82157.1| RNA polymerase sigma factor [Mycoplasma anatis]
          Length = 183

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/159 (49%), Positives = 111/159 (69%), Gaps = 2/159 (1%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KAA+K++   G+KF
Sbjct: 25  GGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNAGILKAAQKYNVDKGFKF 84

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  ++ REP  EEIA K 
Sbjct: 85  STYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQELGREPLDEEIAAKF 144

Query: 557 --AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
             A   E VR + KI  +PISL+  IG E+ S   DF++
Sbjct: 145 GNAYTAEKVRYIRKINIDPISLDKQIGKENDSSFSDFVK 183


>gi|158833949|gb|ABW81780.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  166 bits (419), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 75/202 (37%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVNRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L  L+ ++  VL  RF
Sbjct: 204 KSVVKWLFELSTKQREVLARRF 225


>gi|89074640|ref|ZP_01161105.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89049578|gb|EAR55138.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 284

 Score =  166 bits (419), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 138/226 (61%), Gaps = 1/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++E+NLRLV+S+AKKY    L   D+I EGN+GL+ A EKFD   G++FSTYA WW
Sbjct: 41  AKEKLIESNLRLVVSIAKKYRAAHLLLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I R+I +Q+  IR+PVH+  +I+ ++RT R +  K   EPT E+IA +L    + +
Sbjct: 101 IKQNIERAIHNQNRAIRLPVHVSKEINALLRTHRDLMKKQNHEPTHEDIALQLNKETQDI 160

Query: 564 RKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L      +SL+  IGD+++   +   + D+   SP     + ++      +L  + P
Sbjct: 161 STLLSYELNIVSLDQTIGDDESKGTIASLVVDEQIPSPSHIVEENSMVNLAEGLLNKIKP 220

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  +L  RFG+      TL+EV     +TRER+RQ++ K++ +LK
Sbjct: 221 REREILCRRFGMMGYEPQTLQEVASALGLTRERVRQLQMKSLERLK 266


>gi|158833993|gb|ABW81802.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 75/202 (37%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L  L+ ++  VL  RF
Sbjct: 204 KSVVKWLFELSTKQREVLARRF 225


>gi|57996874|emb|CAI45885.1| negative response regulator [Escherichia coli]
 gi|57996882|emb|CAI45889.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 78/191 (40%), Positives = 128/191 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLE 643
           G+      TLE
Sbjct: 181 GLLGYEAATLE 191


>gi|226309754|ref|YP_002769648.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226092702|dbj|BAH41144.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 314

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 102/266 (38%), Positives = 151/266 (56%), Gaps = 17/266 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   ++   R G+ EA   ++ +V A LR V+S A ++  RG+ FLDLIQEG IGL  A 
Sbjct: 54  ELACLIRYQRDGDLEA---RETIVRAYLRYVVSTALRHLKRGMPFLDLIQEGTIGLFTAI 110

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD   G +   Y+ WW+ QAITR+I D++  IRIPVHM ++I +  +    + + + R
Sbjct: 111 DKFDVGRGVRLYHYSHWWISQAITRAINDKATLIRIPVHMHEQIRQYQKQVLHLVHALNR 170

Query: 546 EPTPEEIAKKLAMPVEGVRKV---LKITKEPISLE-------TPIGDEDTSHLGDFIEDK 595
            P  +EIA  L +P+E V  +   L +  E I  E       T   DE  S+  + ++D 
Sbjct: 171 TPDRQEIAVLLDIPLEKVEAIELALMMKMESIDAELDSEKWQTWHEDESLSY-AEIMDD- 228

Query: 596 NAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             +S LD  I+  +LR      L  L+PR + ++ MR+G+  +  +TLEEVGK F +TRE
Sbjct: 229 -GLSSLDDWIEKVDLRSQMRAALDRLSPRAQEIISMRYGLYDDQVYTLEEVGKMFGLTRE 287

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RIRQIEA  I +L+    S  L+ +L
Sbjct: 288 RIRQIEATTIDRLRTQKASHVLKDYL 313


>gi|158833991|gb|ABW81801.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 75/202 (37%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDGSSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L  L+ ++  VL  RF
Sbjct: 204 KSVVKWLFELSTKQREVLARRF 225


>gi|3249731|gb|AAC26668.1| RNA polymerase sigma-like factor [Streptomyces spectabilis]
          Length = 161

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 81/162 (50%), Positives = 116/162 (71%), Gaps = 1/162 (0%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EP+PEE+A  L +
Sbjct: 1   YATWWIRQAMSRAMADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPSPEEVAAHLDL 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR  L++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL+
Sbjct: 61  PHERVRG-LRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLS 119

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 120 TLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIE 161


>gi|291287615|ref|YP_003504431.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
 gi|290884775|gb|ADD68475.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
          Length = 301

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 80/238 (33%), Positives = 143/238 (60%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++  NL+ V+S+A +Y N GL   D+I +GN+GL++AA++FD     KF +YA+WW
Sbjct: 65  ALNTLILCNLKFVVSIANRYRNTGLPIADIINQGNLGLVEAAKRFDHTKDVKFISYAVWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +++A+QS T+++P+     ++K+     +++ K+ REPT  E+A++L M    +
Sbjct: 125 IRQSIIQALAEQSGTVKLPIKQAGILYKINGATEKLNKKLNREPTASELAEQLEMDEADI 184

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL++++  +SLE PI D +     D +E        D  I   L+     ++  L  R
Sbjct: 185 ENVLRVSRNYLSLEAPIKDGEDRSFIDLLESGTKDIEED-IISKTLKTALDDIVDELDER 243

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++  RFG+      TLEE+G+   ++RER+RQ+E +A+ KL+  +   KL+ FL+
Sbjct: 244 ESQIIEWRFGLNEEAPKTLEEIGELMDISRERVRQLETRALSKLRKKAMKNKLQDFLN 301


>gi|217967697|ref|YP_002353203.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
 gi|217336796|gb|ACK42589.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
          Length = 413

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 73/115 (63%), Positives = 94/115 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++EANLRLV+SVAK+Y  RGL FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW
Sbjct: 104 AKKRLIEANLRLVVSVAKRYIGRGLSFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWW 163

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           ++QAITR+IADQ+ TIRIPVHM + ++K+ +  R ++  + R+PT E+IAK L +
Sbjct: 164 IRQAITRAIADQARTIRIPVHMVETMNKIHKITRLLTQSLGRKPTEEDIAKFLVI 218



 Score =  127 bits (318), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 61/121 (50%), Positives = 92/121 (76%), Gaps = 1/121 (0%)

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VR++  + +EP+SLE P+G+++ + L DF+E+K+ +SP D A+Q +L++    +L  L
Sbjct: 293 EKVREISMMGQEPLSLEMPVGEDEDNRLADFVENKD-LSPADIAVQKSLKKDIEELLNEL 351

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  +L++RFG+  N   TLEEVGK F VTRERIRQIEAKA+R+L+HPSRSKK++ +L
Sbjct: 352 SEREREILKLRFGLEDNQPRTLEEVGKLFNVTRERIRQIEAKALRRLRHPSRSKKIKDYL 411

Query: 681 D 681
           +
Sbjct: 412 E 412



 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 30/45 (66%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           DDPV+MYL+E+G I LL+ E EI +AKR+E G       L E+ L
Sbjct: 69  DDPVKMYLKEIGKIPLLTPEEEIELAKRVEQGDEDAKKRLIEANL 113


>gi|158833951|gb|ABW81781.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833953|gb|ABW81782.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833955|gb|ABW81783.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833957|gb|ABW81784.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833961|gb|ABW81786.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833965|gb|ABW81788.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833981|gb|ABW81796.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833983|gb|ABW81797.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833985|gb|ABW81798.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833989|gb|ABW81800.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 75/202 (37%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L  L+ ++  VL  RF
Sbjct: 204 KSVVKWLFELSTKQREVLARRF 225


>gi|329902595|ref|ZP_08273157.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548742|gb|EGF33384.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 334

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 86/258 (33%), Positives = 152/258 (58%), Gaps = 5/258 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +++++  H  ++ + G+  A   ++ M+E NLRLV+S+AK Y NRG+  LD
Sbjct: 66  LNQIGARALLTVAQEVHYATLAKAGDFPA---RQVMIEHNLRLVVSIAKHYINRGVVLLD 122

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V
Sbjct: 123 LIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQV 182

Query: 533 VRTARRMS--NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           +R    +   +   ++ + ++IA       E V+ +L ++  P SL+ P+  +  S L D
Sbjct: 183 LRAKYHLEALHHDGKDASIDDIAHLTGRSAEDVQDILALSDHPASLDAPLDADPGSSLMD 242

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +       P   A Q          LA L+ ++  ++  RFG+  +   TLE +  +  
Sbjct: 243 LLPGDPGDGPEARAEQHETALLVRDWLARLSDKQRLIITRRFGLEDDDPATLEALAAEIG 302

Query: 651 VTRERIRQIEAKAIRKLK 668
           VTRER+RQ++ +A+ KLK
Sbjct: 303 VTRERVRQVQQEALIKLK 320


>gi|168036108|ref|XP_001770550.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
 gi|14669828|dbj|BAB62006.1| PpSIG1 [Physcomitrella patens]
 gi|14669830|dbj|BAB62007.1| PpSIG1 [Physcomitrella patens]
 gi|162678258|gb|EDQ64719.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
          Length = 677

 Score =  165 bits (418), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 96/257 (37%), Positives = 156/257 (60%), Gaps = 11/257 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VRK   EA  A+ +MV ANLRLV+SVAK+Y + GL+  DLIQEG+IGL++  EKFD   
Sbjct: 419 LVRK-LGEAEWARDKMVMANLRLVVSVAKQYHSFGLEMADLIQEGSIGLLRGVEKFDHTR 477

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYK STY  WW++Q +TR+IAD S T+R+PVH+ D + + +R A+          + +EI
Sbjct: 478 GYKLSTYVHWWIRQGVTRAIADHSRTVRLPVHVHDTLGR-IRKAKSTLLSEGCTASVQEI 536

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIG-----DEDTSHLGDFIEDKNAVS-PLDSAIQ 606
           ++   +    ++  L++TK+ +SL+  IG       D   L   + D++  + P     +
Sbjct: 537 SEATNLTGTKIKNTLQVTKKLVSLDKEIGRNTLQSGDGETLHSLVADRDIENQPWTIVER 596

Query: 607 ANLRETTTRVLAS-LTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +++   ++L S L PRE  ++R+ +G+G    +  +LE +  ++ V+RER+RQ+E  A
Sbjct: 597 MLMKDDVDKLLTSQLGPRERDIVRLHYGVGREDGSVMSLESISYRYGVSRERVRQLETAA 656

Query: 664 IRKLKHPSRSKKLRSFL 680
           +RKL+  SR + L  +L
Sbjct: 657 MRKLQIKSREQGLDRYL 673


>gi|291280296|ref|YP_003497131.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754998|dbj|BAI81375.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 313

 Score =  165 bits (417), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 137/219 (62%), Gaps = 1/219 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V +NL+ V+S+A +Y N GL   D+I +GN+GL++AA++FD   G KF +YA+WW
Sbjct: 77  ALEKLVLSNLKFVVSIANRYKNTGLPLADIINQGNLGLLEAAKRFDPERGVKFISYAVWW 136

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI +++A+QS T+++P+     ++K+      +S ++ REPTP+EIA  L M    +
Sbjct: 137 IRQAIIQALAEQSGTVKLPLKQASILYKINEAIEVLSKELGREPTPDEIAVYLDMDPADI 196

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             VL++++  +SLE PI D +     D +E     S  +      L+     ++  L  R
Sbjct: 197 ENVLRVSRNYLSLEAPIKDGEDRAFIDLLE-SGGKSVEEEIFLNTLKANIEEIVDELNER 255

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           E ++++ RFG+   T  TLEE+G+   ++RER+RQIEA+
Sbjct: 256 EAQIIKWRFGLEGETPKTLEEIGEILNISRERVRQIEAR 294


>gi|1621026|gb|AAB17121.1| RpoS [Yersinia enterocolitica]
          Length = 277

 Score =  165 bits (417), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 73/185 (39%), Positives = 128/185 (69%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+ L++A EKFD   G++FSTY+ WW
Sbjct: 91  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLCLIRAVEKFDPEPGFRFSTYSHWW 150

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++    TAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYFGTARELSHKLDHEPSAEEIAEQLNKPVDDV 210

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+N   P D+    +++++  + L  L  +
Sbjct: 211 SRMLRLNERITSVDTPLGGDSEKSLLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAK 270

Query: 624 EERVL 628
           +  VL
Sbjct: 271 QREVL 275


>gi|158340411|ref|YP_001521767.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310652|gb|ABW32266.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  165 bits (417), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 152/239 (63%), Gaps = 4/239 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ R+ +     AK+ M+E NLRLV+S+AKK+ NRGL  LDLIQEGNIGL +A EKFD 
Sbjct: 27  INLARQVKAGNLRAKQRMIECNLRLVVSIAKKHQNRGLPLLDLIQEGNIGLSRAVEKFDL 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WW+ Q ITR++ +++  IR+P+H+     K+ RT  +++ +  R+P+ +
Sbjct: 87  NQGCRFSTYAYWWIWQGITRALHNKTKMIRLPIHLNQLHSKIKRTYFQLNQEYGRQPSLD 146

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANL 609
           E+A  + +    +++ L++++E ISL+  + +     LG+ + +D ++    ++ +    
Sbjct: 147 EVAYAMDIDPTHIQEQLQLSQEVISLDKFVSENQGDTLGELVAKDHSSQKYFENLMN--- 203

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  ++++  L+ R++ ++  RFG+      TL E+ K   ++RE IR+IE KA ++LK
Sbjct: 204 KDELSKLMGHLSERQQFIIGQRFGLEDGQPKTLVEIAKLLDMSREGIRRIEKKAFQQLK 262


>gi|55274892|gb|AAV49248.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 190

 Score =  165 bits (417), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 75/182 (41%), Positives = 125/182 (68%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GI 634
           G+
Sbjct: 181 GL 182


>gi|55274903|gb|AAV49253.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 192

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 76/192 (39%), Positives = 129/192 (67%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+
Sbjct: 1   VKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQT 60

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S+
Sbjct: 61  RTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSV 120

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+  
Sbjct: 121 DTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG 180

Query: 637 NTDHTLEEVGKQ 648
               TLE+VG++
Sbjct: 181 YEAATLEDVGRE 192


>gi|55274965|gb|AAV49282.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 78/193 (40%), Positives = 129/193 (66%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLEEV 645
           G+      TLE+V
Sbjct: 181 GLLGYEAATLEDV 193


>gi|87303841|ref|ZP_01086550.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87281651|gb|EAQ73647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 215

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 85/185 (45%), Positives = 125/185 (67%), Gaps = 1/185 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW
Sbjct: 31  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P   EIA+ + +PVE +
Sbjct: 91  IRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPNRLEIAEAMDIPVEEL 150

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +L+      SL+ P+ G+E  S LGD I D +A  PLD   Q    E   R L+ L+ 
Sbjct: 151 DSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSADEPLDIVEQRIHHEQLGRWLSHLSE 210

Query: 623 REERV 627
           +E+ V
Sbjct: 211 QEQNV 215


>gi|169837518|ref|ZP_02870706.1| RNA polymerase sigma factor rpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 149

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 74/118 (62%), Positives = 100/118 (84%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW
Sbjct: 31  AKQKLIESNLRLVVSIAKKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++QAITR+IADQ  TIRIPVHM + I+K+ + +R +  +  +EPT EE+AKKL +PVE
Sbjct: 91  IRQAITRAIADQGRTIRIPVHMIETINKIKKESRIILQETGKEPTAEELAKKLELPVE 148


>gi|225849654|ref|YP_002729888.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
 gi|225646208|gb|ACO04394.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
          Length = 281

 Score =  164 bits (416), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 92/260 (35%), Positives = 153/260 (58%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + +    +KG+ EA    K++VE NLR V++VAK +   G+   DLI  GN+GL
Sbjct: 24  LTPEEEKELAKRAKKGDKEAL---KKLVEGNLRFVVNVAKNFMGWGVPLTDLIAAGNLGL 80

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AA++FD     KF +YA+WW++QAI ++I  Q+  +RIPV     I KV  T  ++  
Sbjct: 81  IEAAKRFDPERDVKFISYAVWWIRQAIMQTIFQQTGAVRIPVKESLFISKVKETYEKLKE 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSP 600
           ++KREPT EEIA+K+    + V+  L++ + P SL+ P+G+E +   L D +  K     
Sbjct: 141 ELKREPTIEEIAEKVGASPKKVKNALQVVRMPYSLDKPLGEEGEDLTLLDVLSKKGTEDV 200

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               ++ +L +    +L  L  RE  ++  RFG+      TL EVG+   ++RER+RQ+E
Sbjct: 201 EKEIVEESLHKELNTLLNVLDERERAIIEHRFGLNGEEPKTLTEVGEILGISRERVRQLE 260

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            +A++KL+  +  + L+ FL
Sbjct: 261 QRALKKLRALAMKRHLKDFL 280


>gi|237653675|ref|YP_002889989.1| RNA polymerase sigma factor RpoS [Thauera sp. MZ1T]
 gi|237624922|gb|ACR01612.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thauera sp. MZ1T]
          Length = 312

 Score =  164 bits (416), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 95/235 (40%), Positives = 149/235 (63%), Gaps = 5/235 (2%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   VR G+ +A   ++ M+E NLRLV+++AK Y NRG+  LDL++EGN+GLM A EKFD
Sbjct: 63  IARRVRMGDFDA---RQTMIERNLRLVVNIAKHYLNRGIPLLDLVEEGNLGLMHALEKFD 119

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WW++Q I R+I +QS TIR+PVH+  ++++V+R  R +      E + 
Sbjct: 120 PERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKELNQVLRAQRHIEADCNGESSL 179

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E+IA +L   +E VR +L + +   SL+ P+  + +  +G+ + D+  +S  D  IQ + 
Sbjct: 180 EQIANRLGKTIEEVRSILALGEHTASLDAPLDIDPSLSIGESLADEQHISA-DLRIQCSE 238

Query: 610 RETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            E   R  LA L  ++  V+R R+GI      TLEE+ ++  +TRER+RQI+ +A
Sbjct: 239 VEQLVREWLAILNDKQRMVIRHRYGIDECELLTLEELAERLELTRERVRQIQLEA 293


>gi|281423630|ref|ZP_06254543.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|299141293|ref|ZP_07034430.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|281402182|gb|EFB33013.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|298577253|gb|EFI49122.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 290

 Score =  164 bits (416), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 95/262 (36%), Positives = 155/262 (59%), Gaps = 6/262 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   ++KG  +   AK+++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSVAKQYQHQGLSLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+ R   +   
Sbjct: 91  VKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINREINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R+P+  E++    +  E + + L      +S++ P  + + + + D +   ED    
Sbjct: 151 EFQRKPSLAELSSATKIEEEKIDQSLMADSHHVSIDAPFQEGEDNSMVDVMAGGEDSRTD 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             +D    A   E+  R +  L  RE  ++R  FGIG + +  LEE+G Q  +TRER+RQ
Sbjct: 211 KQVDHESMALELESVLRKV--LKDREITIIRECFGIGCH-EKGLEEIGDQLGLTRERVRQ 267

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           I  K+I KL+    +K L  +L
Sbjct: 268 IREKSIAKLRDSGYAKILMKYL 289


>gi|332526107|ref|ZP_08402245.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
 gi|332109950|gb|EGJ10578.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
          Length = 320

 Score =  164 bits (416), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 92/229 (40%), Positives = 143/229 (62%), Gaps = 4/229 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLV+S+AK Y  RG+  +DLI+EGN+GLM A  KF+   G++FSTYA WW
Sbjct: 78  ARQTMIERNLRLVVSIAKHYVGRGMPMIDLIEEGNLGLMHATGKFEPERGFRFSTYASWW 137

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN----KIKREPTPEEIAKKLAMP 559
           ++Q+I R+I  Q+  IR+PVH+  ++++V++  R + +    + +R  + +E+A  L  P
Sbjct: 138 IRQSIERAIMHQARLIRLPVHVVRELNQVLKARRALESSRHGEAERPVSVDEVAAALGRP 197

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ V ++LK+ ++P SL+ P+  E    + D + D +AV PL   +           LA 
Sbjct: 198 VDEVAELLKLAEQPTSLDMPLEREGGESMLDTVADDDAVDPLGLTLSREAVHLLDHGLAE 257

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  VL  RFG+      TLEE+  +  +TRERIRQI+ +A+ KLK
Sbjct: 258 LNEREREVLAGRFGLHDREPETLEELAVRLGLTRERIRQIQQEALLKLK 306


>gi|188997117|ref|YP_001931368.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932184|gb|ACD66814.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 281

 Score =  164 bits (416), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 100/282 (35%), Positives = 165/282 (58%), Gaps = 5/282 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E D +  ++  ++ +     +S  E + +    ++G+ EA    K++VE NLR V+S+A
Sbjct: 2   AEQDELTTLQLYMQQMGKHPMLSPEEEKELAIRAKQGDKEAL---KKLVEGNLRFVVSIA 58

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K +   G+   DLI  GN+GL++AA++FD     KF +YA+WW++QAI ++I  Q+  +R
Sbjct: 59  KNFMGWGVPLTDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGAVR 118

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPV     I KV  T  ++  ++ REPT EEIAK+L   V+ V+  L I + PISL+ P+
Sbjct: 119 IPVKESLFIAKVKETYEKLKEELGREPTEEEIAKRLNTSVKKVKNALSIVRLPISLDMPL 178

Query: 581 GD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           G+  E+   L D +  K         I+  + +    +L  L  RE+ +++MR+G+    
Sbjct: 179 GEGGEEDFTLLDVLSKKGTEDIEKELIEETIHKELESMLDVLDEREKEIIKMRYGLDGEE 238

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             TLEEVG++  ++RER+RQ+E +A++KLK  +  K L+ FL
Sbjct: 239 PKTLEEVGEKLGISRERVRQLEQRALKKLKAVALKKHLKDFL 280


>gi|261879259|ref|ZP_06005686.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334090|gb|EFA44876.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 291

 Score =  164 bits (415), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 88/270 (32%), Positives = 157/270 (58%), Gaps = 3/270 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I+ E  +S  E   +   + KG  E   A+  +V  NLR V+SVAK+Y ++G+  +D
Sbjct: 22  LSEIAREPMLSPDEEAMLAQAIHKGGPEGDRARDRLVSGNLRFVVSVAKQYQHQGISLID 81

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I  ++A +S  +R+P++      KV
Sbjct: 82  LINEGNMGLVKAAEKFDETRGFKFISYAVWWIRQSIMEALAVKSRIVRMPLNQVGIYGKV 141

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +RT      +  R P+  E+A+ L +    +   +       S++ P+G+++   + D +
Sbjct: 142 IRTTESFLQEHGRVPSNHELAEILQVEEAQITAAMSAGARATSIDAPLGNDEDGSMADML 201

Query: 593 EDKNAVSPLDSAI-QANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
              ++    DS++ + ++ +    +L   L+ RE+R+++  FGIG+  + +LEE+     
Sbjct: 202 ASDDSGMKSDSSLDKESMNQFINDLLREVLSAREQRIIKESFGIGV-MEKSLEEIADSMG 260

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +TRERIRQ+  KA+RK++    +  LR +L
Sbjct: 261 MTRERIRQVREKALRKIRFSKYASTLRQYL 290


>gi|57996878|emb|CAI45887.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  164 bits (415), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 78/191 (40%), Positives = 127/191 (66%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLE 643
           G+      TLE
Sbjct: 181 GLLGYEAATLE 191


>gi|260911629|ref|ZP_05918210.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634235|gb|EEX52344.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 290

 Score =  164 bits (415), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 94/260 (36%), Positives = 150/260 (57%), Gaps = 2/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   +RKG  E   AK ++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+     +   
Sbjct: 91  IKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINHEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + +R P+  E++    +  E + + L      +S++ P  D + + + D +   +     
Sbjct: 151 ENQRHPSVSELSDATNLDEEKIGQSLMADGHHVSIDAPFQDGEDNCMLDVMASGDDSRTD 210

Query: 602 DSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             A   ++      VLA  L  RE  ++R  FGIG + +  LEE+G Q  +TRER+RQI 
Sbjct: 211 KQADHESMALELNSVLAKVLKDREITIIRECFGIGCH-EKGLEEIGDQLGLTRERVRQIR 269

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            K+I KL+    +K L  +L
Sbjct: 270 EKSIAKLRDSGNAKILMKYL 289


>gi|3249729|gb|AAC26667.1| RNA polymerase sigma-like factor [Streptomyces bluensis]
          Length = 161

 Score =  164 bits (415), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 83/161 (51%), Positives = 111/161 (68%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R +R+M   + REPTPEE+AK+L M
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVSRQMLQDLGREPTPEELAKELDM 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V +V K  +EPISL TP+G++  +  GD IED  AV P D+     L+E    VL 
Sbjct: 61  TPEKVIEVQKYGREPISLHTPLGEDGDTQFGDLIEDSEAVVPADAVSFTLLQEQLHSVLD 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQI
Sbjct: 121 TLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQI 161


>gi|55274934|gb|AAV49268.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 191

 Score =  164 bits (415), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 77/191 (40%), Positives = 128/191 (67%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 60

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   
Sbjct: 61  QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERIT 120

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 121 SVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 180

Query: 635 GMNTDHTLEEV 645
                 TLE+V
Sbjct: 181 LGYEAATLEDV 191


>gi|148242910|ref|YP_001228067.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851220|emb|CAK28714.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 293

 Score =  164 bits (414), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 90/232 (38%), Positives = 149/232 (64%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V+ANLRLV+ +AKK   RGL   DL+QEG+IGL +AAEK+D   GY+FSTYA WW
Sbjct: 58  ARGRLVQANLRLVVHLAKKQHLRGLAMEDLVQEGSIGLQRAAEKYDPSTGYRFSTYAYWW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+ R+I  Q+  +R+P  + +++ ++  T +R+S ++ R+P PEE+A+ +   ++ +
Sbjct: 118 IKQALHRAIQLQTPALRLPCRVSERLGRLRSTRQRLSQELGRQPRPEELAEAMGERIDQL 177

Query: 564 RKV--LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
           +++   ++     SL+TP+G D D   L D +ED +  SP+D   QA   E    +L+S 
Sbjct: 178 QELERAQVISRGCSLDTPMGSDPDHGSLVDLLED-DRTSPMDQLEQALRSEQLAELLSSA 236

Query: 620 -LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L+ RE  V++ R     + +H   +++  +F ++RER RQ+E  A+RKL+H
Sbjct: 237 GLSEREATVVQARH----SEEHIPYQQLADRFGISRERTRQLEHNALRKLRH 284


>gi|261880495|ref|ZP_06006922.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270332834|gb|EFA43620.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  164 bits (414), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 91/260 (35%), Positives = 152/260 (58%), Gaps = 2/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   +RKG  E   AK +++ +NLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELSQKIRKGGREGQRAKDKLITSNLRFVVSVAKQYQHQGLSLTDLINEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA EKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+ +       
Sbjct: 91  IKATEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGTLSKINKEINNFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + +R P+ +EIA+ + +    +R  +      +S++ P  +++++ + D +   +     
Sbjct: 151 RHERRPSTQEIAEAIDVEAGKIRMSMMADGHHVSIDAPFQEDESNSMADIMASGDDTRTD 210

Query: 602 DSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             A   ++ +    VL S L  RE  ++R  FGIG + +  LEE+G +  +TRER+RQI 
Sbjct: 211 KRADHESMAQELNTVLESVLKEREITIIRECFGIGCH-ELGLEEIGDRLGLTRERVRQIR 269

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            K+I KL+     K L  +L
Sbjct: 270 EKSIAKLRESGNIKILMKYL 289


>gi|158833975|gb|ABW81793.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833979|gb|ABW81795.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  164 bits (414), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 74/202 (36%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTY  WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L+ L+ ++  VL  RF
Sbjct: 204 KSVVKWLSELSTKQREVLARRF 225


>gi|57996876|emb|CAI45886.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  164 bits (414), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 77/191 (40%), Positives = 128/191 (67%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  L+LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLE 643
           G+      TLE
Sbjct: 181 GLLGYEAATLE 191


>gi|288927698|ref|ZP_06421545.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330532|gb|EFC69116.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 290

 Score =  164 bits (414), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 94/260 (36%), Positives = 150/260 (57%), Gaps = 2/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   +RKG  E   AK ++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+     +   
Sbjct: 91  IKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINHEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + +R P+  E++    +  E + + L      +S++ P  D + + + D +   +     
Sbjct: 151 ENQRHPSVSELSDATNIDEEKIGQSLMADGHHVSIDAPFQDGEDNCMLDVMASGDDSRTD 210

Query: 602 DSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             A   ++      VLA  L  RE  ++R  FGIG + +  LEE+G Q  +TRER+RQI 
Sbjct: 211 KQADHESMALELNSVLAKVLKDREITIIRECFGIGCH-EKGLEEIGDQLGLTRERVRQIR 269

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
            K+I KL+    +K L  +L
Sbjct: 270 EKSIAKLRDSGNAKILMKYL 289


>gi|294674467|ref|YP_003575083.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294473044|gb|ADE82433.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  164 bits (414), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 91/263 (34%), Positives = 154/263 (58%), Gaps = 8/263 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I E   +   +R+G  E   AK+ +V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  VTIDEEIELAQAIRRGGPEGEKAKERLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+ +   +   
Sbjct: 91  VKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQSGALSKINQEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R P+  E+A+   +    + +  K     +S++ P G++D + + D +   ED    
Sbjct: 151 QHQRRPSVTELAELTQIEESKIEQTAKADSHHMSIDAPFGEDDDNSMADMLSSGEDTRTD 210

Query: 599 SPLD-SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +D  ++ ++L      VL     RE ++++  FGIG   +  LEE+G +  +TRER+R
Sbjct: 211 KLVDYESLTSDLDNVLRNVLKD---RELKIVKECFGIGCQ-ERGLEEIGAEMGLTRERVR 266

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QI  K+I KL     ++ L  +L
Sbjct: 267 QIREKSITKLHDSGYARILMKYL 289


>gi|149200222|ref|ZP_01877244.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149136664|gb|EDM25095.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 279

 Score =  163 bits (413), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 95/261 (36%), Positives = 153/261 (58%), Gaps = 5/261 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ ++SI+    +S+ +   +  ++  G  +A   +++++ ANL+LV+ +A  Y + G+
Sbjct: 8   IKSYMQSIATLPLVSVEDEIELAKLIEAGSEDA---REKLIIANLKLVVKIAHDYKSLGV 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGLMKA EKF    G KFS+Y  WW+KQAI R++A+Q   IRIPV    K
Sbjct: 65  PLADLISEGNIGLMKAVEKFRPGHGAKFSSYGAWWIKQAIRRAVAEQGRVIRIPVQSAVK 124

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSH 587
           I K+   A  ++ K+ R P+ EE+A+     V  VR +   +  P +SL T +   +   
Sbjct: 125 IRKIHHEAMLLAEKLGRVPSMEEVAEATGFSVRSVRGMSVASTAPAVSLNTTLKTGEEGV 184

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVG 646
           L D I D     P D+  + ++++    V+ S LT RE+ +++MR+G+  +   TLEE+ 
Sbjct: 185 LEDVIPDTLLKLPGDNMNETDVKQVLLEVIDSKLTEREQMIIKMRYGLDGHQQKTLEELS 244

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
                TRER+RQI+ +A+RKL
Sbjct: 245 DMVGRTRERVRQIQYQALRKL 265


>gi|1542976|gb|AAB08043.1| sigma factor [Thermoanaerobacterium thermosulfurigenes]
          Length = 261

 Score =  163 bits (413), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 91/239 (38%), Positives = 143/239 (59%), Gaps = 4/239 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +VE N+RLV  VA  +   G++F DL+QEG IGL+ A +KFD   GYKFSTYA W+
Sbjct: 24  AKDVLVECNIRLVDKVAAGFLKSGVEFDDLVQEGLIGLLTAIDKFDHTKGYKFSTYATWY 83

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++ R I +    IR+P+H+ +KI+++++    +  K     T EEI++      E +
Sbjct: 84  IQQSMRRYIGNYGKIIRLPIHINEKINRILKARYLIEQKKGSLATTEEISRLTGYTEEEI 143

Query: 564 RKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              L    + ISL   + DE   + L +FI+D + +   + AI+  +++   ++L SL  
Sbjct: 144 EGYLSYATDVISLNQYVNDERVDAELINFIQD-DTIDVEEMAIEKEIKKEIRKILDSLPE 202

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK-KLRSFL 680
           RE  +L+MRFG G N   TL E+G  F +TRERIRQI+   I++L+H  + K +LR  +
Sbjct: 203 RERMILKMRFGFGCNL-KTLTEIGNIFGLTRERIRQIQNNTIKELRHNRKVKDRLREIM 260


>gi|317503800|ref|ZP_07961812.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315665097|gb|EFV04752.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 290

 Score =  163 bits (412), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 94/262 (35%), Positives = 155/262 (59%), Gaps = 6/262 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   ++KG  +   AK+++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSVAKQYQHQGLSLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+ R   +   
Sbjct: 91  VKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINREINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R+P+  E++    +  E + + L      +S++ P  + + + + D +   +D    
Sbjct: 151 EYQRKPSLSELSHATKIEEEKIDQSLMADSHHVSIDAPFQEGEDNSMVDVMAGGDDSRTD 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             +D    A   E+  R +  L  RE  ++R  FGIG + +  LEE+G Q  +TRER+RQ
Sbjct: 211 KQVDHESMALELESVLRKV--LKEREITIIRECFGIGCH-EKGLEEIGDQLGLTRERVRQ 267

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           I  K+I KL+    +K L  +L
Sbjct: 268 IREKSIAKLRDSGYAKILMKYL 289


>gi|167949416|ref|ZP_02536490.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 134

 Score =  163 bits (412), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 81/113 (71%), Positives = 96/113 (84%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 4   GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 63

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE  P
Sbjct: 64  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREGYP 116


>gi|55274907|gb|AAV49255.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 189

 Score =  163 bits (412), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 76/189 (40%), Positives = 127/189 (67%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 1   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 60

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 61  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 120

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+     
Sbjct: 121 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEA 180

Query: 640 HTLEEVGKQ 648
            TLE+VG++
Sbjct: 181 ATLEDVGRE 189


>gi|288919497|ref|ZP_06413828.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
 gi|288349100|gb|EFC83346.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
          Length = 936

 Score =  163 bits (412), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 95/238 (39%), Positives = 137/238 (57%), Gaps = 8/238 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E + A   +V  N RLV S+A KY  +GL+  DL Q G IGL++A +KFD   GYKFSTY
Sbjct: 470 ERARAHDALVLHNQRLVHSIALKYEGQGLELEDLSQHGMIGLLRAVQKFDATKGYKFSTY 529

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           + WW++QAITR++AD+   IR+P H  +K++KV R   ++   +         A      
Sbjct: 530 STWWIRQAITRALADEGRLIRLPAHFVEKVNKVRRVLGQLGMSVDGADVVTVAAAAGLSE 589

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-----EDKNAVSPLDSAIQANLRETTT 614
            E  R +L + +  + L+TP+GD   + LG+ +      D +  + LD   +  LR    
Sbjct: 590 QEVERCLLALHQRVVGLDTPVGDGGDTVLGELVGLPAPPDTDPDTVLD---RKWLRMAVA 646

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           R LA L+PR   V+R+RFG       TLE++G+ F VTRERIRQIE KA+ +L+ P R
Sbjct: 647 RSLAELSPRNAEVVRLRFGFDDGEPRTLEQIGQVFGVTRERIRQIEKKALEQLREPLR 704


>gi|325973333|ref|YP_004250397.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
 gi|325989768|ref|YP_004249467.1| RNA polymerase sigma factor [Mycoplasma suis KI3806]
 gi|323574853|emb|CBZ40513.1| RNA polymerase sigma factor [Mycoplasma suis]
 gi|323651935|gb|ADX98017.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
          Length = 530

 Score =  163 bits (412), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 142/240 (59%), Gaps = 12/240 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A+K+++ +NLRLVISVAKKY N G    DLIQEG  GL KA  KFD+  G KFSTYA 
Sbjct: 234 SFAEKQLMTSNLRLVISVAKKYLNCGFNLGDLIQEGVFGLRKAITKFDYKFGNKFSTYAT 293

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA---- 557
           WW++QAITRSIADQS  IRIPVHM + I+K+ +  + +  K    PT EE++ ++     
Sbjct: 294 WWIRQAITRSIADQSKIIRIPVHMMEVINKMTKAEKELVLKTGNPPTLEELSSEMQKYGT 353

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTT 614
              P++ + ++ KI  + +SL+ PI + ++S+  DF+ ED +  +P +     N+ E   
Sbjct: 354 QFTPIK-ISEIKKINVDLVSLDKPILNNESSNFADFVREDGDEANP-EWIASKNIYEEKL 411

Query: 615 RVLA--SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI-EAKAIRKLKHPS 671
           + L   +L   E  +L + FG+     HT+E++ + F    +    I   K I+KL  P+
Sbjct: 412 KSLLQETLKKDEYLILALHFGLNNQESHTVEQISQLFAKNSDYFSGILTNKKIKKLLTPT 471


>gi|187251192|ref|YP_001875674.1| DNA-directed RNA polymerase sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
 gi|186971352|gb|ACC98337.1| DNA-directed RNA polymerase, sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
          Length = 380

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 156/269 (57%), Gaps = 8/269 (2%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           VDSI +   +I  +S +  +S  E   +   ++KG+   + AK+ M+E NLRLVI  AK+
Sbjct: 5   VDSINQYFKKISEVSED--LSREEMEKLWKRIKKGD---TAAKQRMMELNLRLVIPAAKR 59

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +  + +  LDLI+EGN+GL++A EKFD   G++FSTYA++W+ QAI + I +QS  I+IP
Sbjct: 60  FMRKDIDLLDLIEEGNLGLLQAIEKFDPSKGFRFSTYAIYWIDQAIRKYIDEQSGAIKIP 119

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL---AMPVEGVRKVLKITKEPISLETP 579
            H    I K  RT   + + ++REP+  E++++L   A  ++ + + +   K   SL   
Sbjct: 120 SHAWGDIKKWTRTWNALKDSLEREPSLTEMSRELDWSARKIKSILETINAAKGIDSLALA 179

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+ED   L D + D    +P D   +++        L  L PR++ +L MR G+  N  
Sbjct: 180 IGEEDEVTLEDTLTDDGKGNPDDVFSRSSSNSALLAALEELNPRDKEILMMRNGLKTNEP 239

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL EV K   ++RER+RQIE +AI  ++
Sbjct: 240 MTLSEVSKIMGLSRERVRQIEERAISHIR 268


>gi|124025343|ref|YP_001014459.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123960411|gb|ABM75194.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 307

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 89/231 (38%), Positives = 147/231 (63%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+     R+  ++   P+  +IA ++ +P+E V
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSRLMQELGVHPSTNQIAIQMKIPLEEV 184

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
            ++L  ++    +SL+  +  + D S L D +  +  V P++ A  A    +   +L  +
Sbjct: 185 EELLACELRSITVSLQGAVKSKADPSELVDILPSEE-VPPMELAELAERSASAWSLLDKS 243

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  +L +RFG+ G N   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 244 NLTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLR 294


>gi|6010732|gb|AAF01232.1|AF184101_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 242

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 69/152 (45%), Positives = 114/152 (75%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            ++L++ +   S++TP+G +    L D + D+
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILADE 241


>gi|72381853|ref|YP_291208.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL2A]
 gi|72001703|gb|AAZ57505.1| possible type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
          Length = 307

 Score =  162 bits (411), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 89/231 (38%), Positives = 147/231 (63%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+     R+  ++   P+  +IA ++ +P+E V
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSRLMQELGVHPSTNQIAIQMKIPLEEV 184

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
            ++L  ++    +SL+  +  + D S L D +  +  V P++ A  A    +   +L  +
Sbjct: 185 EELLACELRSITVSLQGAVKSKADPSELVDILPSEE-VPPMELAELAERSASAWSLLDKS 243

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  +L +RFG+ G N   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 244 NLTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLR 294


>gi|57996884|emb|CAI45890.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 77/191 (40%), Positives = 127/191 (66%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  +    L  ++  VL  RF
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWRFELNAKQREVLARRF 180

Query: 633 GIGMNTDHTLE 643
           G+      TLE
Sbjct: 181 GLLGYEAATLE 191


>gi|262273681|ref|ZP_06051494.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
 gi|262222096|gb|EEY73408.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
          Length = 246

 Score =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 71/157 (45%), Positives = 113/157 (71%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 83  ARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWW 142

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT E+IA +L  PVE V
Sbjct: 143 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAFQLDKPVEDV 202

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++L++ +   S++ PIG +    L D I D+    P
Sbjct: 203 NRMLRLNERISSVDNPIGGDSEKALLDIIPDEKEGGP 239


>gi|134036998|gb|ABO47837.1| truncated sigma 38 factor [Escherichia coli]
 gi|134037001|gb|ABO47839.1| truncated sigma 38 factor [Escherichia coli]
          Length = 240

 Score =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 69/151 (45%), Positives = 113/151 (74%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED 594
            ++L++ +   S++TP+G +    L D + D
Sbjct: 210 SRMLRLNERITSVDTPLGGDSEKALLDILAD 240


>gi|158833959|gb|ABW81785.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/202 (36%), Positives = 133/202 (65%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRMIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q I R+I +Q+ TI +P+H+  +++  +R AR +++K+  +P+PE
Sbjct: 84  ERGFRFSTYATWWIRQTIERAIMNQTRTIHLPIHIVKELNVYLRAARELAHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L  L+ ++  VL  RF
Sbjct: 204 KSVVKWLFELSTKQREVLARRF 225


>gi|33240031|ref|NP_874973.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33237557|gb|AAP99625.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 310

 Score =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 92/231 (39%), Positives = 144/231 (62%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+ ANLRLV+++AKKY  +GL  LDLIQEG IGL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNHMITANLRLVVNLAKKYQGKGLDLLDLIQEGTIGLTRAVEKYDPKRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+      +  +    P+ E++AKKL++  + +
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSELMQEYGTPPSAEQLAKKLSVSKQII 184

Query: 564 RKVLKITKEPI--SLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L+     I  SL+  I  + D S LGD +   + + P++ A  A   ++   +L  A
Sbjct: 185 GDLLECEMRSITVSLQGVIQSKTDPSELGDVLPS-DEIPPMELAELAERNDSAWSLLNKA 243

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  ++ +RFG+ G N   TL EV K    +RE  RQ+  +A+RKL+
Sbjct: 244 NLTPKERTIVSLRFGLDGTNEWRTLAEVAKHMNCSREYCRQVVQRALRKLR 294


>gi|158833967|gb|ABW81789.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833969|gb|ABW81790.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833971|gb|ABW81791.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833973|gb|ABW81792.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833977|gb|ABW81794.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833987|gb|ABW81799.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  162 bits (409), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/202 (36%), Positives = 134/202 (66%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R+  C    +++ ++E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 24  IYFARRVLCGDESSRRRVIESNLRLVVKISRRYINRGLPLLDLIEEGNLGLIRAVEKFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTY  WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S+K+  +P+PE
Sbjct: 84  ERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSHKLDHDPSPE 143

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L  PV+ V ++L++ +   S++T  G+     L D + D+    P ++    +++
Sbjct: 144 EIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLLDVLSDETDNDPENTTQNDDMK 203

Query: 611 ETTTRVLASLTPREERVLRMRF 632
           ++  + L+ L+ ++  VL  RF
Sbjct: 204 KSVVKWLSELSTKQREVLARRF 225


>gi|257126034|ref|YP_003164148.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
 gi|257049973|gb|ACV39157.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
          Length = 273

 Score =  162 bits (409), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/229 (41%), Positives = 140/229 (61%), Gaps = 11/229 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ +NLRLVIS AKK    GL  +DLI EGNIGL+KA  KFD+  G++FSTYA+WW
Sbjct: 42  ARQLLILSNLRLVISTAKKSLGNGLPLIDLISEGNIGLIKAINKFDYEKGHRFSTYAVWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI ++I +    IRIP +  +++ KV +  +  +      P+ E IAKK+ +    +
Sbjct: 102 IKQAIKKAIINIGRDIRIPSYKYEQLSKVNKAIKDYTAIHGEAPSTEYIAKKVDLKESKI 161

Query: 564 RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +L   ++ +SL   IGD    ED     D +EDK  +   D  ++  +RE   R+   
Sbjct: 162 ILLLGEFQDIMSLNETIGDNIYLEDVIGKNDDVEDK--IIKEDQLLE--MRELLERI--- 214

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE ++L  R+G+  N  HTL+E+G+Q  +TRER+RQIE KAI KLK
Sbjct: 215 LNERERKILEYRYGLYDNKIHTLKEIGEQMGITRERVRQIEKKAITKLK 263


>gi|219124053|ref|XP_002182327.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406288|gb|EEC46228.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 317

 Score =  161 bits (408), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 103/282 (36%), Positives = 156/282 (55%), Gaps = 33/282 (11%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---------TNRG---- 467
           G+S  E R ++        E   A+  +V ANL LV ++AK+            RG    
Sbjct: 47  GVSAVELRRVLD-------EGQQARAALVAANLGLVTALAKRQLSTLQTATEAGRGVGTI 99

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG +GLMKAAE+F+   G++FSTYA WWV+Q I +S++D S TIR+P H+  
Sbjct: 100 LTLQDLIQEGTLGLMKAAERFEPERGWRFSTYATWWVRQRILKSVSDSSRTIRLPAHVHG 159

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI------G 581
            + ++ + A+        E T   +A+ L +PVE VR     ++  +SLETP+       
Sbjct: 160 TLQRIQK-AKAWFQAHGEEATLSSLAQYLELPVEKVRLYTDSSRNVMSLETPLKGRSAFK 218

Query: 582 DEDTSHLGDFIEDKNAVSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           DE+T  LGD +         D    A++ +L    T+V   LT  E+ VLR RFG+   T
Sbjct: 219 DENTRTLGDTLASDEKTPEEDVEAQALRLDLEHVMTQV---LTDVEQNVLRRRFGLEDGT 275

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++EE  +Q  V+R+RIR +E +A+ KL+HP ++ KL+S++
Sbjct: 276 CWSVEETARQLGVSRDRIRLVETRALNKLRHPQQNYKLQSYV 317


>gi|300726043|ref|ZP_07059501.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776650|gb|EFI73202.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  161 bits (408), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/263 (35%), Positives = 155/263 (58%), Gaps = 8/263 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   +++G  E   AK ++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIEEEIDLAQQIKRGGREGERAKSKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++QAI ++IA+QS  +R+P++    + KV +   +   
Sbjct: 91  IKAAEKFDETRGFKFISYAVWWIRQAILQAIAEQSRIVRLPLNQVGSLSKVNQEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           K +R PT +E++++  +  E + + +  + + +S++ P  + + + + D +   ED    
Sbjct: 151 KYQRVPTIQELSQRTDIDEEKIAQSMMASGKHVSIDAPFQEGEDNSMVDIMASGEDSRTD 210

Query: 599 SPLD-SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +D  ++  +L +    V   L  RE  ++R  FGIG   +  LEE+G    +TRER+R
Sbjct: 211 KEVDHESMSYDLNQVLETV---LNEREITIIRDCFGIGC-PEKGLEEIGDLLGLTRERVR 266

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QI  K+I KL+   +   L  +L
Sbjct: 267 QIREKSITKLRESGKIGVLMKYL 289


>gi|256372040|ref|YP_003109864.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008624|gb|ACU54191.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 294

 Score =  161 bits (407), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 139/239 (58%), Gaps = 2/239 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  VE N+ LV+S+A++Y   G+   DL+QEG IGL++A + +D   G++FSTYA WW
Sbjct: 56  ARERFVEGNMGLVVSIARRYVQPGISLDDLVQEGTIGLLRAIDLYDGRRGFRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI +++      + +P  +  ++ +V    R +   + R+P+  E+A    +    V
Sbjct: 116 IRQAIAQALTRTRRDVVLPRGIAAELARVEVQRRELEQALGRQPSMAELAAASGIDELRV 175

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTP 622
           R++    +  +SL+  +G+E    L D + D++A  P++  I+ A+LR      LA L P
Sbjct: 176 RELQGYARSVLSLDQAVGEERDVTLADIVPDRDA-EPIEETIEHADLRTVIAGALAHLEP 234

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE  VL  RFG+  N  H+LE+    F + RERIRQIEA+AI +L+    +  LR  L+
Sbjct: 235 REREVLAFRFGLEGNEPHSLEDAAAYFGIARERIRQIEARAIARLRRGDLAPVLRRVLE 293


>gi|300725901|ref|ZP_07059364.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776838|gb|EFI73385.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  161 bits (407), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 97/268 (36%), Positives = 156/268 (58%), Gaps = 6/268 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS E  I+I +   +   +RKG      AK ++V+ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  ISHEPMINIDQEIELAQAIRKGGRAGERAKDKLVKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+  T
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGALSKINAT 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--- 592
             +     +R P+ +EI++   +  E + + +K      S++ P  D + + + D +   
Sbjct: 145 ISKFEQDNQRRPSIQEISRLTGIEEEKIEQSIKADNHHTSIDAPFQDGEENSMVDIMASG 204

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED      +D    A  +E  + +   L  RE ++L   +GIG + +  LEE+G +  +T
Sbjct: 205 EDTRTDRQVDHDSMA--QELHSVLKNVLKDREIKILCECYGIGCH-EKGLEEIGDRMGLT 261

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI  K+I KL+    SK L  +L
Sbjct: 262 RERVRQIREKSILKLREAGCSKVLMKYL 289


>gi|307592489|ref|YP_003900080.1| RNA polymerase sigma-32 factor RpoH [Cyanothece sp. PCC 7822]
 gi|306986134|gb|ADN18014.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7822]
          Length = 307

 Score =  161 bits (407), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 143/226 (63%), Gaps = 8/226 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ANL+ VI +A +Y  RGL+  DLIQEG++GL++AAE+FD  LGY+FSTYA WW
Sbjct: 82  AADTLVRANLKFVIFIANRYVGRGLELSDLIQEGSLGLIRAAERFDPSLGYQFSTYANWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  +TR++A+QS TIR+P  + DK++K+ +T   ++  + R P+  E+A+ L + V  +
Sbjct: 142 VRAFMTRALANQSRTIRLPSQVNDKLNKIKKTRHNLAQLLGRSPSSSELAQALGISVLQL 201

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             + ++ K+ ISL   + ++    L D I   +  S LD  ++ +  E   ++L +L+PR
Sbjct: 202 HSLAQLDKKTISLSVWVDEQGRETLQDLIPSSDEPS-LDETLKPDEIE---QLLQTLSPR 257

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            + ++R+R   G     TL E+G+ F ++RER+R+I  +++  L+ 
Sbjct: 258 NQEIVRLRILEG----KTLSEIGQSFHLSRERVRKICLRSLTILRQ 299


>gi|288926119|ref|ZP_06420047.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608396|ref|ZP_07883384.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337159|gb|EFC75517.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249856|gb|EFU29857.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  161 bits (407), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 92/263 (34%), Positives = 155/263 (58%), Gaps = 8/263 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I E   +   +++G  +A  AK+++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  VTIEEEIELAQAIKRGGRDAERAKEKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++KV     R   
Sbjct: 91  IKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKVNHEINRFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           +  R P+ +E++ +  +  E +++ +      +S++ P  + + + + D +   +D    
Sbjct: 151 EHHRRPSVQELSDRTHIDEEKIQQSMMADGHHVSIDAPFQEGEDNSMVDVMAGSDDSRTD 210

Query: 599 SPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +D  ++   L     RV   L  RE+ ++R  FGIG   +  LEE+G Q  +TRER+R
Sbjct: 211 RQVDHDSMAMELNSVLDRV---LKEREQIIIRECFGIGCQ-EKGLEEIGDQLGLTRERVR 266

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QI  K+I KL+     K L  +L
Sbjct: 267 QIREKSITKLRESGNVKILMKYL 289


>gi|297736323|emb|CBI24961.3| unnamed protein product [Vitis vinifera]
          Length = 319

 Score =  161 bits (407), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 144/242 (59%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    +++ + ++  RLV+S+A +Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 77  CNGRESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYKLST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y  WW++QAI R+IA++S  IR+P  + + + K+      +S +++R PT +EIA+ + +
Sbjct: 137 YVYWWIRQAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIAEFIDV 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V  VR V + ++ PIS++  +  +    L + I   +  +P     +  +++   R L 
Sbjct: 197 NVSTVRLVSERSRTPISVDQAVTSQGCMTLQEIIPGPDETTPQKMVKRQLMKQEVERALN 256

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE  +LR+ FGI   T  + EE+G+   ++RER+RQI + A+ KL+  S    L+ 
Sbjct: 257 TLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQTSVVDYLKL 316

Query: 679 FL 680
           ++
Sbjct: 317 YM 318


>gi|289549268|ref|YP_003474256.1| RNA polymerase, sigma 70 family subunit [Thermocrinis albus DSM
           14484]
 gi|289182885|gb|ADC90129.1| putative RNA polymerase, sigma 70 family subunit [Thermocrinis
           albus DSM 14484]
          Length = 310

 Score =  160 bits (406), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 94/299 (31%), Positives = 164/299 (54%), Gaps = 34/299 (11%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K +S    ++  E + +    ++G+ EA    +++VE+NLR VIS+AK+Y   GL   +
Sbjct: 14  LKKVSKIPLLTPEEEKELARRAKEGDTEAL---RKLVESNLRFVISIAKQYQGYGLPLSE 70

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  GN GL++AA++FD   G KF +YA+WW++QAI ++++ QS  +RIP+     I+++
Sbjct: 71  LIAAGNYGLVEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQSGAVRIPLKQSHVINRI 130

Query: 533 VRTARRMSNKIKREPTPEEIA-------------KKLAMPV-----------EG------ 562
                ++  + ++EPT EE+A             ++L  P            EG      
Sbjct: 131 ASIYSKLYKEQEKEPTAEEVAYEYTKEILQKEMERELGRPPTEEEIERRIKKEGLKISPQ 190

Query: 563 -VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V K L+I K P+SL+ PIG+++ +   D +    +    +  +   L +    +L  L 
Sbjct: 191 EVEKCLQICKAPLSLDAPIGEDEDTFFVDLLSKHGSADVEEKVLTEFLEKEIEEMLDKLP 250

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +E RV+ +RFG+      TL E+G+   ++RER+RQ+E +A+RKL++ +  K L+ FL
Sbjct: 251 EKERRVIELRFGLRGEEPRTLREIGEILNISRERVRQLETRALRKLRNMAMKKHLKDFL 309


>gi|256370771|ref|YP_003108596.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
 gi|256009563|gb|ACU52923.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
          Length = 334

 Score =  160 bits (406), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 87/240 (36%), Positives = 145/240 (60%), Gaps = 1/240 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            S A ++++++NLR V+SVAK+Y N+GL   DLI EGN+GL+K   +FD   G+K  +Y 
Sbjct: 94  CSTALEQLIKSNLRFVVSVAKQYQNQGLSLSDLINEGNLGLIKGISRFDEKKGFKCISYC 153

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++QAI ++IADQ+  IR P +     +KVV+T  ++  K+K +PT  +I   L    
Sbjct: 154 VWWIRQAILQAIADQARCIRCPTNKLAFYNKVVKTYSKLEQKLKMQPTVNDIVVYLNSSE 213

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V + LK + +P SL+ PI + + ++L D ++ + +  P     + +  +   R+L +L
Sbjct: 214 KEVEEALKNSIQPTSLDAPILEGEDTNLYDVLKSETSPEPDFKLEKESFFKDIKRLLETL 273

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +E +V+ + +G G     TLE+V     +TRER RQIE   I++L+   R K LR +L
Sbjct: 274 SEKESQVISLHYGFGCK-PMTLEKVAFLLKLTRERCRQIEINGIKRLRISYRKKLLRPYL 332


>gi|149277811|ref|ZP_01883951.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149231499|gb|EDM36878.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 288

 Score =  160 bits (406), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 98/281 (34%), Positives = 167/281 (59%), Gaps = 11/281 (3%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           DS+ K  +EI  I +   +++ E   + S+VR+G+     A  ++V ANLR V+SVAK Y
Sbjct: 16  DSLEKYLSEISKIEL---LNVEEEVRLASIVREGD---RAALDKLVSANLRFVVSVAKNY 69

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            + GL+  DLI EGN+GL+KAA ++D   G+KF ++A+WW++Q+IT +IADQ   IR+P 
Sbjct: 70  QDMGLRLADLISEGNLGLIKAASRYDHTKGFKFISFAVWWIRQSITYAIADQHRMIRLPG 129

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--G 581
           +    I ++ RT+  +  K++R P+ EE+A+ L +P   V        +  SL+ PI  G
Sbjct: 130 NQIVGITRLNRTSDLLEQKLERRPSLEEVAEALDLPETKVVDYQMSALKTTSLDMPILLG 189

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +  T+  G  I + + V   D+ + + +L E   R+L+ L PRE+++L + +G+G     
Sbjct: 190 EPGTT-FGHMIRN-SEVEAADAVLDRQSLAENVRRLLSILPPREQKILSLYYGLGGMPQT 247

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            LE++   F +++ER+RQ++ KA++ LK       +  F +
Sbjct: 248 RLEDMVPVFHLSKERLRQLKDKAVKTLKACCSEVPMSGFFN 288


>gi|300727091|ref|ZP_07060510.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775635|gb|EFI72226.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  160 bits (406), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 158/268 (58%), Gaps = 6/268 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS E  +SI E   +   +RKG      AK+++V+ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  ISREPMVSIDEETELAQQIRKGGRAGDRAKEKLVKANLRFVVSVAKQYQHQGLTLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    + K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQSRIVRLPLNQVGAVSKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--- 592
             +   +  R P+ +E+A    +  + ++K L      +S++ P  D+D + + D +   
Sbjct: 145 TAKFVQEHNRRPSADELATLTGIDADKIQKSLNADSHQMSIDAPFSDDDDNSMSDMLSSG 204

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           +D      +D     N  E   +  + L  RE ++++  FGIG   +  LEE+G++  +T
Sbjct: 205 DDSRTDRQVDYESMQNDMEGVLK--SVLKDRELKIVKDCFGIG-GPEKGLEEIGEEMGLT 261

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI  K+I K++    +K L  +L
Sbjct: 262 RERVRQIREKSIMKIRQSGNAKLLMKYL 289


>gi|33862729|ref|NP_894289.1| RNA polymerase sigma-70 factor family protein [Prochlorococcus
           marinus str. MIT 9313]
 gi|33634645|emb|CAE20631.1| Sigma-70 factor family [Prochlorococcus marinus str. MIT 9313]
          Length = 308

 Score =  160 bits (406), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 92/244 (37%), Positives = 149/244 (61%), Gaps = 17/244 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+GE     AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G
Sbjct: 60  IRRGE----KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRG 115

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+       PT E++A
Sbjct: 116 HRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKSRLMQNNGLPPTAEQLA 175

Query: 554 KKLAMPVEGVRKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLR 610
           K + +P+  V  +L  ++    +SL+  +  + D S L D +  +  + P++   +A + 
Sbjct: 176 KTMRLPMAEVEDLLACELRSVTVSLQGVVKSKSDPSELADVLPSEE-IPPME---RAEMS 231

Query: 611 ETTTRVL-----ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           E T  V      A+LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+
Sbjct: 232 ERTASVWTLLNRANLTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVLQRAL 291

Query: 665 RKLK 668
           RKL+
Sbjct: 292 RKLR 295


>gi|289758832|ref|ZP_06518210.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714396|gb|EFD78408.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 170

 Score =  160 bits (405), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 83/170 (48%), Positives = 117/170 (68%)

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +
Sbjct: 1   MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAR 60

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+R
Sbjct: 61  EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLR 120

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 121 FGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 170


>gi|326523529|dbj|BAJ92935.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score =  160 bits (405), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 110/324 (33%), Positives = 172/324 (53%), Gaps = 25/324 (7%)

Query: 369 VFLERHQGRELDPH--WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           ++L     +EL  H   V  +K   +G W      ++  IL      K ++    IS  E
Sbjct: 193 IYLRGTVSKELLTHKQVVHLSKKIKDGIWLQQQRSKLTEILGNEPSYKQMAQSLRISTPE 252

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R   S +R    E+ +A++ +  +N+RLVIS+A+KY   G++  DLIQ G IGL++  E
Sbjct: 253 LR---SRMR----ESFLAREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIE 305

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G++ STY  WW++Q ++R++AD S T R+P +M +++   +R A+         
Sbjct: 306 KFDASRGFRISTYVYWWIRQGVSRALADNSKTFRLPTYMHERL-IAIRAAKYALEDQGVS 364

Query: 547 PTPEEIA-------KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAV 598
           PT + IA       KK+    E V K L + ++   SL    GD     L  +IED+N  
Sbjct: 365 PTTQNIAELLNISEKKVHNATEAVNKALSLDQQAFPSLNGLPGDT----LHSYIEDQNVA 420

Query: 599 S-PLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           + P     +  L+E    +L S LT RE  ++R+  GIG    HT E++ +QF ++RER+
Sbjct: 421 NDPWHGFEEWYLKEEVNNLLISNLTERERHIIRLYHGIGKQC-HTWEDISRQFGLSRERV 479

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQ+   A+ KLKH +R KKL + L
Sbjct: 480 RQVGLIAMEKLKHAARRKKLDALL 503


>gi|225450015|ref|XP_002272444.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 426

 Score =  160 bits (405), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 144/242 (59%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    +++ + ++  RLV+S+A +Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 184 CNGRESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYKLST 243

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y  WW++QAI R+IA++S  IR+P  + + + K+      +S +++R PT +EIA+ + +
Sbjct: 244 YVYWWIRQAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIAEFIDV 303

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V  VR V + ++ PIS++  +  +    L + I   +  +P     +  +++   R L 
Sbjct: 304 NVSTVRLVSERSRTPISVDQAVTSQGCMTLQEIIPGPDETTPQKMVKRQLMKQEVERALN 363

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE  +LR+ FGI   T  + EE+G+   ++RER+RQI + A+ KL+  S    L+ 
Sbjct: 364 TLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQTSVVDYLKL 423

Query: 679 FL 680
           ++
Sbjct: 424 YM 425


>gi|149197872|ref|ZP_01874921.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139093|gb|EDM27497.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  160 bits (404), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 137/229 (59%), Gaps = 8/229 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++  NLRLV+ +A  + + G+   DLI EGNIGLMKA EKF   +G KFS+Y  WW
Sbjct: 40  AREQLIVGNLRLVVKIAHDFKSLGVPLADLISEGNIGLMKAVEKFKPGMGAKFSSYGAWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI R +A+QS  IRIPV    K++K+ R A  ++ ++ R P+ +EIA+   M    V
Sbjct: 100 IKQAIRRCVAEQSRVIRIPVQSAVKMYKIQRVAMHLAEELGRVPSEKEIAEAADMSQRSV 159

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL----DSAIQANLRETTTRVLA 618
             + +  T   ISL T + D +   L D + D  A  P     D  +++ L++   +   
Sbjct: 160 HNLKVAATSPTISLSTSLKDGEDGVLEDMLPDLMAKMPGGEMDDRDVKSLLQDCVDQ--- 216

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LT RE+ ++ MR+G+     HTL+E+ +    TRER+RQI+ KA++KL
Sbjct: 217 HLTEREKLIINMRYGLNGGEQHTLDEISELIGRTRERVRQIQHKALKKL 265


>gi|326512474|dbj|BAJ99592.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score =  160 bits (404), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 110/324 (33%), Positives = 172/324 (53%), Gaps = 25/324 (7%)

Query: 369 VFLERHQGRELDPH--WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           ++L     +EL  H   V  +K   +G W      ++  IL      K ++    IS  E
Sbjct: 193 IYLRGTVSKELLTHKQVVHLSKKIKDGIWLQQQRSKLTEILGNEPSYKQMAQSLRISTPE 252

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R   S +R    E+ +A++ +  +N+RLVIS+A+KY   G++  DLIQ G IGL++  E
Sbjct: 253 LR---SRMR----ESFLAREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIE 305

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G++ STY  WW++Q ++R++AD S T R+P +M +++   +R A+         
Sbjct: 306 KFDASRGFRISTYVYWWIRQGVSRALADNSRTFRLPTYMHERL-IAIRAAKYALEDQGVS 364

Query: 547 PTPEEIA-------KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAV 598
           PT + IA       KK+    E V K L + ++   SL    GD     L  +IED+N  
Sbjct: 365 PTTQNIAELLNISEKKVHNATEAVNKALSLDQQAFPSLNGLPGDT----LHSYIEDQNVA 420

Query: 599 S-PLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           + P     +  L+E    +L S LT RE  ++R+  GIG    HT E++ +QF ++RER+
Sbjct: 421 NDPWHGFEEWYLKEEVNNLLISNLTERERHIIRLYHGIGKQC-HTWEDISRQFGLSRERV 479

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQ+   A+ KLKH +R KKL + L
Sbjct: 480 RQVGLIAMEKLKHAARRKKLDALL 503


>gi|149907981|ref|ZP_01896649.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
 gi|149808987|gb|EDM68918.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
          Length = 284

 Score =  160 bits (404), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 134/227 (59%), Gaps = 2/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+++NLRLVI++AK+Y +  L  +D+IQEGN GL+ A EKFD   G++FSTYA+WW
Sbjct: 43  ARQRMIQSNLRLVINIAKRYQHTSLSLVDIIQEGNTGLIHAVEKFDATKGFRFSTYAVWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I R I +QS TIR+P+H+     ++++ AR     +K     ++IA  L +  + V
Sbjct: 103 IKNNIERFIMNQSRTIRVPIHIGKTYKRILKNAREKVLDLKCNNDLKKIAINLELEFDDV 162

Query: 564 RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             VL       SL+  I  ++ S+  L D IED +   P D   + +       VL  L 
Sbjct: 163 VNVLSYYFTEASLDKTIATKNDSNTALVDLIEDSSICKPNDEIEKTDTSSYLITVLNHLC 222

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+  ++ +RFG+G     TL  +G++  ++RER+RQI   +++K+K
Sbjct: 223 DRDREIIELRFGLGREEPQTLNAIGERLFMSRERVRQIITASLQKIK 269


>gi|257886121|ref|ZP_05665774.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
 gi|257821977|gb|EEV49107.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
          Length = 383

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 98/229 (42%), Positives = 137/229 (59%), Gaps = 12/229 (5%)

Query: 448 MVEANLRLVISVAK---KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V+AN RLV+ +A+   KY    L   DL Q G IGL+KAA+KFD    Y FSTYA +W+
Sbjct: 133 LVKANRRLVLKIAQRYNKYLTSSLDIDDLEQFGMIGLLKAADKFDLSKEYAFSTYATYWI 192

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRT-ARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +Q+I+R I D S T+R+PVH+ +KI+K+ R  AR M+N    + +   I K++ +  E  
Sbjct: 193 RQSISRGIMDTSLTVRLPVHIFEKINKLNRLEARMMTNSSTTDISS--ILKEMDISEEQY 250

Query: 564 RKVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLAS 619
             +L I    +   SL+TPIG +  + +GD + D N    ++  I    LRE   + +  
Sbjct: 251 YDLLAIRSTYLSLPSLDTPIGIDGDATIGDMLPDNNY--DIEEVIDLGFLREDIKKSMTY 308

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E  VL +RFG       TLEE+G  F VTRERIRQIEAKAIRK+K
Sbjct: 309 LKEKEREVLYLRFGFDGEGRKTLEEIGNIFGVTRERIRQIEAKAIRKMK 357


>gi|255531277|ref|YP_003091649.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344261|gb|ACU03587.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 92/265 (34%), Positives = 155/265 (58%), Gaps = 6/265 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           DSI K   +I  I +   +S+ E   +   +RKG+  A      +V+ANLR V+SVAKKY
Sbjct: 16  DSIEKYLYDIARIDL---LSVEEEIVLAQKIRKGDQSAL---DRLVKANLRFVVSVAKKY 69

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N+G++  DLI EGN+GL+KAA++FD   G+KF ++A+WW++Q+I  +IA+Q   +R+P 
Sbjct: 70  QNQGIRLSDLIAEGNLGLIKAAQRFDETKGFKFISFAVWWIRQSIMIAIAEQKRIVRLPA 129

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           +    I K+ +    +  +++R P+ EE+ + + +P E V   L       SL+T I +E
Sbjct: 130 NQIGGIMKINKAMADLEQQLERVPSLEEVCEFIELPEEKVVDYLHHAPMTTSLDTVIAEE 189

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L + IED N      + +Q ++     R++  L  RE+ +L M +G+G      L+
Sbjct: 190 SGFTLAETIEDTNVEKTDTTVLQHSVTVDVKRLMRGLPEREKEILSMFYGLGGYPAIGLD 249

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G +  + +ER+RQI+ KA++ L+
Sbjct: 250 EIGGKMNLGKERVRQIKDKALKTLR 274


>gi|219123705|ref|XP_002182160.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406121|gb|EEC46061.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 319

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 101/279 (36%), Positives = 153/279 (54%), Gaps = 27/279 (9%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---------TNRG---- 467
           G+S+   R ++        E   A+  +V ANL LV ++AK+            RG    
Sbjct: 49  GVSVIVLRQVLD-------EGQQARAALVAANLGLVTALAKRQLSTLQTATEAGRGVGTI 101

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG +GLMKAAE+F+   G++FSTYA WWV+Q I +S++D S TIR+P H+  
Sbjct: 102 LTLQDLIQEGTLGLMKAAERFEPERGWRFSTYATWWVRQRILKSVSDSSRTIRLPAHVHG 161

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI------G 581
            + + ++ A+        E T   +A+ L +PVE VR     ++  +SLETP+       
Sbjct: 162 TLQR-IQKAKAWFRAHGEEATLSSLAQYLELPVEKVRLYTDSSRNVMSLETPLKGRSAFK 220

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+T  LGD +         +   QA   +    ++  LT  E+ VLR RFG+   T  +
Sbjct: 221 DENTRTLGDTLASDEKTPEENVEAQALRLDLEHVMIKVLTDVEQNVLRRRFGLEDGTSWS 280

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           LEE  KQ  ++R+RIR +EA+A+ KL+ P ++ KLRS++
Sbjct: 281 LEETAKQLGMSRDRIRLVEARALNKLRRPQQNYKLRSYM 319


>gi|321309570|ref|YP_004191899.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801414|emb|CBY92060.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 524

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 103/283 (36%), Positives = 155/283 (54%), Gaps = 45/283 (15%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A K+++ +NLRLVIS+AKKY NRG    DL+QEG  GLMK+ +KFD+  G KFSTYA W
Sbjct: 234 FAVKQLMTSNLRLVISIAKKYLNRGFSLGDLVQEGVFGLMKSIQKFDYKFGNKFSTYATW 293

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-----A 557
           W++Q+ITR+IADQ+  IRIPVHM + I+K V+  + +  K   EPT E++A+++      
Sbjct: 294 WIRQSITRAIADQARIIRIPVHMVEVINKFVKAEKDLILKNGEEPTIEQLAQEMQKYSPQ 353

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA--------IQANL 609
             V+ V  + K+  + +SL+ PI   +TS+  DF++D+ A S  + A        +Q  L
Sbjct: 354 YTVQKVSDIKKLNIDLVSLDKPIAHNETSNFSDFVQDEEAASSEEVAASTHKSMVLQEFL 413

Query: 610 RET----------------------TTRVLAS---LTPREERVLR---MRFGI-GMNTDH 640
             T                      T   + S   L P+ + +L+   + F I GM   H
Sbjct: 414 ESTLEDDELLMIHMHYGLMEYKSPHTIEQIVSERLLNPKYKGILKNKAINFVINGMLEKH 473

Query: 641 ---TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              T EE  K+       +R+  ++A+RKLK PS++ K R+  
Sbjct: 474 KVLTPEEWKKEKAKVENFVRKKISQALRKLKKPSKNGKYRTIF 516


>gi|156975281|ref|YP_001446188.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
 gi|156526875|gb|ABU71961.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
          Length = 287

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 139/230 (60%), Gaps = 1/230 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+ +NLRLV+++AK+Y  RGL FLDLI EGNIGLM+A EKFD   G++FSTYA  W
Sbjct: 50  ARTRMINSNLRLVVNIAKRYKGRGLTFLDLISEGNIGLMRAVEKFDPEKGFRFSTYATHW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I R + +Q+ T+R+PVH+  ++ + V+  + +S K +   TP +IA  L +PV  V
Sbjct: 110 IRQSIERELMNQARTVRLPVHINKELKRYVKATKELSQKTQ-TITPRDIADHLEIPVSSV 168

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K L+  K  ISL++    E+   L + +       P     + N      + +  L P 
Sbjct: 169 LKHLEFDKSTISLDSYQDKEEAKPLAETMACHRLRCPELELEEDNAFLMLLQWIEELEPD 228

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            + +L  R+G+  NT  +L+ VG +   +RERIR ++ + I+KL++ +++
Sbjct: 229 LKLILTRRYGLDGNTPTSLDTVGTELGYSRERIRHLQMQGIKKLQNLAKN 278


>gi|282881579|ref|ZP_06290248.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
 gi|281304565|gb|EFA96656.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
          Length = 290

 Score =  159 bits (402), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 93/262 (35%), Positives = 151/262 (57%), Gaps = 6/262 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+     R   
Sbjct: 91  IKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINHEINRFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           +  R P+  E++    +  E + + +      +S++ P  D + + + D +   +D    
Sbjct: 151 EHHRRPSITELSDATNIDEEKIGQSMMADGHHVSIDAPFQDGEDNTMLDVMPSGDDSRTD 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             +D    A  +E  T +   L  RE  +++  FGIG + +  LEE+G Q  +TRER+RQ
Sbjct: 211 RQVDHESMA--QELNTVLNKVLKDREITIIKECFGIGCH-EKGLEEIGDQLGLTRERVRQ 267

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           I  K+I KL+    +K L  +L
Sbjct: 268 IREKSIAKLRDSGNAKILMKYL 289


>gi|199601686|dbj|BAG70954.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens]
          Length = 153

 Score =  159 bits (402), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 96/188 (51%), Positives = 118/188 (62%), Gaps = 36/188 (19%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K+K+  DR TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQAL
Sbjct: 1   KKKEPTDR-TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAL 59

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           IIWRDELN+GTTLLREIIDLE           + G E  +  + + SS+    DD+    
Sbjct: 60  IIWRDELNEGTTLLREIIDLETT---------YSGPEAKAAPQFQSSSE----DDITNVG 106

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
           GD+    +  +D+                        S  +L+AME +LRP+VM  LD I
Sbjct: 107 GDMPMPEEEEEDEDE----------------------SNLSLAAMEAELRPQVMETLDLI 144

Query: 288 AEVYRELR 295
           A+ Y++LR
Sbjct: 145 ADTYKKLR 152


>gi|148239078|ref|YP_001224465.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847617|emb|CAK23168.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 308

 Score =  159 bits (402), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 88/231 (38%), Positives = 145/231 (62%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FS YA WW
Sbjct: 66  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSNYAYWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+  +  R+  +    P+ E++A  L +P+  V
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEKLTKLRASKARLMQRNGLSPSTEQLADDLNLPISEV 185

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +  + D S L D +  +  V P++ A  A    +  ++L  +
Sbjct: 186 EDLLGCELRSVTVSLQGVVKSKSDPSELVDVLPSEE-VPPMERAEIAERTASAWKLLDKS 244

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  V+ +RFG+ G N   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 245 NLTPKERTVVMLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLR 295


>gi|328947378|ref|YP_004364715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328447702|gb|AEB13418.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 283

 Score =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 87/228 (38%), Positives = 143/228 (62%), Gaps = 5/228 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++ +N+R VI +A +Y N+GL++ DLI EG +GLMKA + FD   GY F +YA+WW
Sbjct: 44  ARDKLLTSNMRFVIKIASQYLNKGLEYEDLISEGYLGLMKALDHFDVSKGYHFISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE--PTPEEIAKKLAMPVE 561
           ++Q+I ++I D    IR+PV+   ++ ++ R    ++   K+      EE+A KL M   
Sbjct: 104 IRQSIMKAIVDFGRPIRLPVNKDAELTEIKRACHSVNPHGKKSEEEELEEVALKLGMTKH 163

Query: 562 GVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            +R++L I++E ISL++PI GD DT+ L D +      +P D+AI A+L+    +    L
Sbjct: 164 HIREMLNISQEMISLDSPISGDSDTA-LVDTVS-AGTFTPEDAAIDASLKTEIDKAFVGL 221

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +   VL MR+G+    + TL+EVG++  ++RER+RQIE  AI K++
Sbjct: 222 DKKSVEVLNMRYGLNGQGERTLKEVGEKMNLSRERVRQIEKHAIAKIR 269


>gi|269102892|ref|ZP_06155589.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162790|gb|EEZ41286.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 282

 Score =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/265 (33%), Positives = 150/265 (56%), Gaps = 11/265 (4%)

Query: 420 TGISISEFRHIVSMVRKGECEASI--------AKKEMVEANLRLVISVAKKYTNRGLQFL 471
           TGI + + R    + ++ E E SI        A+ +++E+NLRLV+S+AKK  +RGL   
Sbjct: 7   TGIYLKQLRSRALLTKEEEIELSIKVQAGDQKARAKLIESNLRLVVSIAKKMQHRGLDLD 66

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+ A EKF+   GY+FSTYA WW+KQA+ R+I + S  +R+PVH+  ++  
Sbjct: 67  DLINEGNIGLITAVEKFNPDYGYRFSTYATWWIKQAMDRAIHNHSREVRLPVHISKELCT 126

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    + MS K   + T ++++     P E + K+LK  +   SL+     ++ +   + 
Sbjct: 127 IYSAFKEMSTK-SEQVTIDQVSALTGSPKEEIEKILKYERRYSSLDDQF--DEGAKFSEI 183

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D + +   +   + +  E    +LA L PR++ ++  RFG+     HTL+EV     +
Sbjct: 184 IPDHSKLDHTELLNEEDQTEVLAMLLAELKPRDQEIIARRFGLFGYEPHTLQEVATAVNL 243

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQ++  A ++L    R + +
Sbjct: 244 TRERVRQLQILAQQRLAAKMRDRNI 268


>gi|318041016|ref|ZP_07972972.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 323

 Score =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 138/230 (60%), Gaps = 4/230 (1%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  A ++MV ANLRLV+S+A++ ++R L   DLIQEG +GL++A ++FD   GYKFSTYA
Sbjct: 85  AERASEQMVTANLRLVVSLARRISHRRLDLDDLIQEGTLGLIRAVQRFDPSRGYKFSTYA 144

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW+++ + R++  QS TIR+P HM+D++ ++ R    +   + REP  EE+A+   +  
Sbjct: 145 TWWIREGMGRALQQQSRTIRLPAHMQDRLQRLRRCQMELRQMLGREPNLEELAEATELKP 204

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             +R+ L   +EP+SL++  G ED   L D +    A  P D    A+L+     +L  L
Sbjct: 205 LDIREALFRAQEPLSLDSGHGPEDDLRLLDTLR-CGAQLPSDQLTAAHLQTDLVALLDEL 263

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK---AIRKL 667
             +E  +LR+R+GI       L  V +Q  ++R++ R +E +   AIR+L
Sbjct: 264 PEKEAELLRLRYGIDQPAPMNLSAVARQMGLSRDQARGMERRANAAIRRL 313


>gi|158340730|ref|YP_001521898.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158310971|gb|ABW32584.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 269

 Score =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 83/237 (35%), Positives = 145/237 (61%), Gaps = 2/237 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ +  +  AK+ M+E NLRLV+S+AKK+ NRGL  LDLIQEG+IGL  A +KFD 
Sbjct: 28  IELARQAKAGSLRAKQRMIECNLRLVVSIAKKHQNRGLPLLDLIQEGSIGLSTAVDKFDL 87

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WW++Q IT ++ ++S  I +P +  DK +K+ +  R ++  + R+P+  
Sbjct: 88  AQGCRFSTYAYWWIRQGITAALREKSRPIYLPHNHWDKANKIKKHYRELNQTLGRKPSLS 147

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+++   +  + + + L++ ++  SL+ P+G E    L D +   +  +    ++Q  L 
Sbjct: 148 ELSEATDIKPKTINRTLQLFQKVSSLDQPVGPEQKDSLLDLLAGDDQPTQYMESLQ--LD 205

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  ++V+A+L  RE  VL  R+G+  N   +++ +G+Q  ++ E IR I  K ++KL
Sbjct: 206 EELSQVMANLDERERFVLSQRYGLEDNQPKSMKAIGQQIGLSHEAIRLILNKIMKKL 262


>gi|54401904|gb|AAV34637.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 183

 Score =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/180 (40%), Positives = 122/180 (67%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 60

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +   
Sbjct: 61  QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERIT 120

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 121 SVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 180


>gi|195953303|ref|YP_002121593.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
 gi|195932915|gb|ACG57615.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
          Length = 311

 Score =  158 bits (400), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 144/269 (53%), Gaps = 32/269 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +VEANLR V+SVAK+Y   G+   +LI  GN+GL++AA +FD     KF +YA+WW
Sbjct: 42  ALKALVEANLRFVVSVAKQYMGYGIPLSELIAAGNLGLLEAATRFDPDKNVKFISYAVWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA---------- 553
           V+QAI ++++ Q+  +RIPV     I  V      +  +++REPT +EIA          
Sbjct: 102 VRQAIMQALSQQTGAVRIPVKHSHLISAVGLAYNELLKELEREPTYKEIADYINKKNIIR 161

Query: 554 ----------------------KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                  K  +  E V+K L+I K P+SL+TP+GD   +   D 
Sbjct: 162 EFKKETGFAPTEEELEQSMTQEHKYTVTEEDVKKCLQICKTPLSLDTPVGDNPDTLFVDL 221

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +   +     +  I+  L +    +++ L  +E +VL +R+G+  N   TL E+G    +
Sbjct: 222 LSISDTDEIEEGVIKDVLEKELHDIISKLPEKERKVLELRYGLNGNEPLTLREIGDALGI 281

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +RER+RQ+E +AI+KL+  +  + L+ FL
Sbjct: 282 SRERVRQLETRAIKKLRSFALKRHLKDFL 310


>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 548

 Score =  158 bits (400), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 141/238 (59%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLR+V+ +AK+Y  RGL   DL+QEG++GLMK+ EKF   +G +F+TYA WW
Sbjct: 308 SREKLINANLRMVVHIAKQYQGRGLSLQDLLQEGSMGLMKSIEKFKPQVGCRFATYAYWW 367

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + ++I   S TIR+P ++   + KV    R    +    PT EE+AK++ +    +
Sbjct: 368 IRQTVRKAIFQHSRTIRLPENVYHTLGKVSEAKRSYIMEGNHNPTKEELAKRIGITTVRL 427

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L + + P+S++  +  +  +   +   D     P     +  +R+    +L  L PR
Sbjct: 428 ERLLYMARMPLSMQQTVWADQETTFQEITADIEVEIPELCVAKQLMRKHVLSLLNILNPR 487

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++R+R+GI      +L E+G  F +++ER+RQ+E++A+ KLK    S  L ++ D
Sbjct: 488 ERKIIRLRYGIEDGKKKSLSEIGSVFGLSKERVRQLESRALYKLKQCLASHGLEAYAD 545


>gi|33866043|ref|NP_897602.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639018|emb|CAE08024.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 308

 Score =  158 bits (400), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 91/243 (37%), Positives = 149/243 (61%), Gaps = 11/243 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +++R+GE     AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D  
Sbjct: 58  AVIRRGE----RAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPT 113

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +    PT E+
Sbjct: 114 RGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNGLTPTAEQ 173

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           +A  + +P+  V  +L  ++    +SL+  +    D S L D +   + + P++ A  A 
Sbjct: 174 LADFMEIPIAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPS-DELPPMERAEIAE 232

Query: 609 LRETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              +   +L  A+LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+R
Sbjct: 233 RSASVWTLLGKANLTPKERTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALR 292

Query: 666 KLK 668
           KL+
Sbjct: 293 KLR 295


>gi|288819153|ref|YP_003433501.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|288788553|dbj|BAI70300.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|308752737|gb|ADO46220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 310

 Score =  158 bits (400), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 92/303 (30%), Positives = 163/303 (53%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K ++    ++  E + +    ++G+ EA    +++VE+NLR VI++AK+Y   GL
Sbjct: 10  INQYLKKVAKIPLLTPEEEKEVARRAKEGDQEAF---RKLVESNLRFVINIAKQYLGYGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI  GN GL++AA++FD   G KF +YA+WW++QAI ++++ Q+  +RIP+     
Sbjct: 67  PLSELIAAGNHGLIEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQAHV 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIA-----------------------------KKLAMP 559
           I+++     R+  +++REPTPEE+A                             KK    
Sbjct: 127 INRIGSIYSRLFRELEREPTPEEVAIEYSKEILSRELERELGRKPTKDEVEQRFKKEGFK 186

Query: 560 V--EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E V K L++ + P+SL+ P+G+ + +   DF+         +  I   L +    +L
Sbjct: 187 ISPEEVEKCLQVCRIPLSLDAPVGENEDTFFVDFLSQHGTADVEERIINEVLEKEIGDML 246

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L  +E RV+ +RFG+      TL E+G    ++RER+RQ+E +A+RKL++ +  + L+
Sbjct: 247 DRLPEKERRVIELRFGLRGEEPRTLREIGDILNISRERVRQLETRALRKLRNMAMKRHLK 306

Query: 678 SFL 680
            FL
Sbjct: 307 DFL 309


>gi|213425678|ref|ZP_03358428.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 304

 Score =  158 bits (400), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 74/201 (36%), Positives = 132/201 (65%)

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           E N+ L++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RT
Sbjct: 96  ESNLRLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRT 155

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           AR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L D + D+
Sbjct: 156 ARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADE 215

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++  +TRER
Sbjct: 216 KENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRER 275

Query: 656 IRQIEAKAIRKLKHPSRSKKL 676
           +RQI+ + +R+L+   +++ L
Sbjct: 276 VRQIQVEGLRRLREILQTQGL 296


>gi|149908704|ref|ZP_01897365.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
 gi|149808246|gb|EDM68185.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
          Length = 284

 Score =  158 bits (399), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 85/227 (37%), Positives = 137/227 (60%), Gaps = 2/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+++NLRLVI++AK+Y +  L  +D+IQEGN GL+ A EKFD   G++FSTYA+WW
Sbjct: 43  ARQRMIQSNLRLVINIAKRYQHTSLPLVDIIQEGNTGLIHAVEKFDATKGFRFSTYAVWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I R I +QS TIR+P+H+     ++++TAR     ++       +A+ L M    V
Sbjct: 103 IKNNIERFIMNQSRTIRVPIHIGKVYKRILKTAREQELDLQCNHDVMTLAEFLEMQYAQV 162

Query: 564 RKVLKITKEPISLE-TPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +VL       SL+ T + D D+S  L D +ED +   P D    A+       VL  L+
Sbjct: 163 NEVLSYYFNEASLDKTIVTDRDSSTALVDMLEDYSICKPNDELEDADTLCYLNEVLGHLS 222

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+ +++ +RFG+G     TL  +G++  ++RERIRQI   +++K++
Sbjct: 223 ERDRKIIELRFGLGEEDPLTLHVIGERLSMSRERIRQIINLSLQKIQ 269


>gi|124023525|ref|YP_001017832.1| type II alternative sigma factor, sigma70 family [Prochlorococcus
           marinus str. MIT 9303]
 gi|123963811|gb|ABM78567.1| Putative type II alternative sigma factor, sigma70 family protein
           [Prochlorococcus marinus str. MIT 9303]
          Length = 308

 Score =  158 bits (399), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 90/241 (37%), Positives = 147/241 (60%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+GE     AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G
Sbjct: 60  IRRGE----KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRG 115

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+       PT E++ 
Sbjct: 116 HRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKSRLMQSNGLPPTAEQLV 175

Query: 554 KKLAMPVEGVRKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLR 610
           K + +P+  V  +L  ++    +SL+  +  + D S L D +  +  + P++ A  A   
Sbjct: 176 KTMRLPMAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPSEE-IPPMERAEMAERT 234

Query: 611 ETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +   +L  A+LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL
Sbjct: 235 ASVWTLLNRANLTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALRKL 294

Query: 668 K 668
           +
Sbjct: 295 R 295


>gi|55274872|gb|AAV49239.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 179

 Score =  158 bits (399), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 78/202 (38%), Positives = 128/202 (63%), Gaps = 25/202 (12%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 2   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 62  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 121

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP  D                         +++++  + L  L  ++  V
Sbjct: 122 RLNERITSVDTPQDD-------------------------DMKQSIVKWLFELNAKQREV 156

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 157 LARRFGLLGYEAATLEDVGREI 178


>gi|239934548|emb|CAR94588.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 231

 Score =  158 bits (399), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 107/246 (43%), Positives = 154/246 (62%), Gaps = 33/246 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI- 191
           LLSREGEIAIAKRIEAGR  M++ LCESPL+FQA+IIWRDELN+G  LLR+IIDLEA   
Sbjct: 1   LLSREGEIAIAKRIEAGREAMISGLCESPLSFQAIIIWRDELNEGKILLRDIIDLEATYA 60

Query: 192 GPESK----------GGFFHGTEGHSYQKREDSSQE-KERDDVQETEGDIESAAKVSKDD 240
           GP++K                       KRE +++E + +   +   GD      +S DD
Sbjct: 61  GPDAKKVEAPTPEERERKEKEARKAEADKREKAAEEMRAKSRSRRGGGD----DVLSADD 116

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                   E AE  + + D++++++  +L+AME +L+P V+   D IA+ Y+ LR LQD 
Sbjct: 117 F-------EPAEQPDDDDDDEDEEANVSLAAMEAELKPHVLETFDRIAKTYKSLRKLQDQ 169

Query: 301 AVNGQKDEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
            V+    EK+++      + + L+E++++ V SLSLN +RI+ LVEQLYDI++R++  EG
Sbjct: 170 EVS----EKTALSPSQGRRYRKLREEIIEDVKSLSLNAARIEALVEQLYDINRRLISLEG 225

Query: 355 ELLRLA 360
            LLRLA
Sbjct: 226 RLLRLA 231


>gi|288799880|ref|ZP_06405339.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288333128|gb|EFC71607.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 290

 Score =  158 bits (399), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 92/262 (35%), Positives = 150/262 (57%), Gaps = 6/262 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI +   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDDEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+     +   
Sbjct: 91  IKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINHEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R P+  E++    +  E + + L      +S++ P  D + + + D +   +D    
Sbjct: 151 ENQRHPSVSELSDATNIDEEKIGQSLMADGHHVSIDAPFQDGEDNCMLDVMPSSDDSRTD 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             +D    A   E     +  L  RE  ++R  FGIG + +  LEE+G Q  +TRER+RQ
Sbjct: 211 RQVDHESMAQELEAVLNKV--LKDREITIIRECFGIGCH-EKGLEEIGDQLGLTRERVRQ 267

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           I  K+I KL+    +K L  +L
Sbjct: 268 IREKSIAKLRDSGNAKILMKYL 289


>gi|6010722|gb|AAF01227.1|AF184096_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 228

 Score =  157 bits (398), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 66/138 (47%), Positives = 107/138 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETPIG 581
            ++L++ +   S++TP G
Sbjct: 210 SRMLRLNERITSVDTPAG 227


>gi|284030454|ref|YP_003380385.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
 gi|283809747|gb|ADB31586.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
          Length = 301

 Score =  157 bits (398), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 83/224 (37%), Positives = 134/224 (59%), Gaps = 13/224 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ M+E NLRLV+S+AK+YT +GL  LDLIQEGNIGLM+A E+FD+ LG++FSTYA+WW+
Sbjct: 80  RRRMIEGNLRLVVSLAKRYTGKGLSLLDLIQEGNIGLMRAVERFDYKLGHRFSTYAIWWI 139

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+ R+I+D+S  +R+P        +V    R +  +++REPT EE+A+  ++ V  V 
Sbjct: 140 RQALGRAISDRSRLVRMPAQAYVDAGRVAVVQRELIQRLEREPTIEELARATSLTVARVE 199

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L     P     P+   D+  +   I+D+  +       +A LR      L  L   +
Sbjct: 200 RALAWKLRP----EPLDGHDSDQV---IDDETLLQ------RAALRRDLHCQLEFLDDLK 246

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + VLR+R+G+      +LEE  +   +   R+R +E +A+R L+
Sbjct: 247 QDVLRLRYGLHNTPQSSLEETAEYLSLPPARVRSLELEALRHLR 290


>gi|197336747|ref|YP_002158681.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
 gi|197313999|gb|ACH63448.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
          Length = 294

 Score =  157 bits (398), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 147/247 (59%), Gaps = 6/247 (2%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFD 489
           + +KG+  A   +  ++E+NLRLV+ VA KY  R    L  LD+I+EGN+GL+KA +KF+
Sbjct: 44  LYKKGDLSA---RNTLIESNLRLVVKVANKYRKRNQTDLAILDIIEEGNLGLIKAIDKFN 100

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             LGY+FSTYA+WW++++I  ++ + S T+R+PVH+  +++  +R AR +S  +KREP+ 
Sbjct: 101 PELGYRFSTYAVWWIRESIESALFNHSRTVRLPVHITKELNTYLRAARELSKSLKREPSI 160

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +I+         V K++ +    ++  +   DE +    +   +  A+ P +S  Q NL
Sbjct: 161 RDISTYCEEEQIKVSKIISLIPNQLTCHSACSDELSPKFFELSSNNKALEPDNSLSQDNL 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +  + SL  RE+ ++  R+G+      TLE++GK   +++ER+RQI+++ + KL  
Sbjct: 221 EMNLSSWIDSLNYREKEIIINRYGLFGCKVKTLEDLGKDLDLSKERVRQIQSETLIKLNT 280

Query: 670 PSRSKKL 676
             +  KL
Sbjct: 281 IFKKNKL 287


>gi|323704529|ref|ZP_08116107.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535991|gb|EGB25764.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 339

 Score =  157 bits (398), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 143/250 (57%), Gaps = 19/250 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + +V+ N +LV+S A K   R    +   DL+Q G  GL+KAAE+FD     KF TYA
Sbjct: 94  ALEALVDRNKKLVMSRAYKCFKRYKLNIDEDDLVQYGYFGLIKAAERFDIKRETKFVTYA 153

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL---A 557
            WW+ QAI RSI D    IR+PVH  D+I+KV+         I  + + E I K L    
Sbjct: 154 TWWIDQAIKRSICDYGFIIRLPVHYFDEINKVLNIL-----SIHFDLSKEAIIKILEENG 208

Query: 558 MPVEGVRKVLKITKEPISLET-------PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +  +    ++ + +  +S+++         GD DT  L D I DK   +  +      L+
Sbjct: 209 ISKDKYDDIMFVIENVLSIDSLNKYVNPNSGDGDTELL-DLIVDKTNPTVEEEIDLKLLK 267

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           ET   +L +L  RE+ V+RMRFG+    + TLE +GK+F +TRERIRQIE KAI+KL+HP
Sbjct: 268 ETINNILDTLKSREKEVIRMRFGLDGGDEMTLERIGKEFNITRERIRQIEEKAIKKLRHP 327

Query: 671 SRSKKLRSFL 680
           SRSKKLR F+
Sbjct: 328 SRSKKLRDFI 337


>gi|260219679|emb|CBA26524.1| RNA polymerase sigma factor rpoS [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 340

 Score =  157 bits (398), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 147/247 (59%), Gaps = 12/247 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLVIS+AK Y  RG+   DLI+EGN+GLM A +KF+   G++FSTYA WW
Sbjct: 95  ARQSMIEHNLRLVISIAKGYAGRGVPMSDLIEEGNLGLMHAIDKFEPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK---IKREPTP---EEIAKKLA 557
           ++Q++ R++  Q   +R+PV++  ++ +V+R  R + N    + + P     E+IA  L 
Sbjct: 155 IRQSVDRALMYQGRAVRLPVNVVREVQQVLRARRLLENDAVLLAQRPEGIRVEDIAALLG 214

Query: 558 MPVEGVRKVLKITKEPISLET---PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
                V  +L + + P SL+      GDE +  LGD + D  A +P  +A+   +     
Sbjct: 215 RDAVDVTDLLAMAEAPRSLDARNDAGGDEHS--LGDSLADTLAAAPDSTALAHEVDALLE 272

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRS 673
           + +A+L PRE+ VL  RFG+      TLE + ++  +TRER+RQI+ +A+ KLK + +R 
Sbjct: 273 QWIATLNPREQEVLEARFGLHDRDPETLETLSERLGLTRERVRQIQNEALFKLKRYLARR 332

Query: 674 KKLRSFL 680
              R FL
Sbjct: 333 GIKREFL 339


>gi|209809124|ref|YP_002264662.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
 gi|208010686|emb|CAQ81073.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
          Length = 293

 Score =  157 bits (398), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 83/232 (35%), Positives = 141/232 (60%), Gaps = 3/232 (1%)

Query: 448 MVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+NLRLV+ +A KY +R    L  LD+I+EGN+GLMKA  KFD  LGY+FSTYA+WW+
Sbjct: 55  LIESNLRLVVKIANKYRHRNQRELAPLDIIEEGNLGLMKAVNKFDPELGYRFSTYAVWWI 114

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           K++I  ++ + S T+R+PVH+  +++  +R AR +S  +K+EP+  EI+       + V 
Sbjct: 115 KESIESALFNHSRTVRLPVHITKELNVYLRAARDLSRTLKKEPSISEISVHCNKDYKKVN 174

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+L +     +  +   D+ +S+L +   D +   P  S  ++NL    +  L  L  RE
Sbjct: 175 KILGLVPSSSTCHSASSDDMSSNLIELCADDHEQEPAQSLSKSNLESNLSSWLNLLQCRE 234

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++++  R+G+      TLEE+G+   +++ER+RQI+ + + KL    +  KL
Sbjct: 235 KQIIINRYGLFGTDVKTLEELGQDLQLSKERVRQIQTETLTKLNTIFKKNKL 286


>gi|269120610|ref|YP_003308787.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268614488|gb|ACZ08856.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 270

 Score =  157 bits (398), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 93/230 (40%), Positives = 138/230 (60%), Gaps = 13/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E++ +NLRLVIS+AKK    GL  +DLI EGNIGL+KA  KFD+  G++FSTYA+WW
Sbjct: 41  ARHELILSNLRLVISIAKKSLGNGLPLIDLISEGNIGLIKAINKFDYTKGHRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I ++I ++   IRIP +  +++ KV +      N     P+   IA++L +    V
Sbjct: 101 IKQSIKKAIINKGRDIRIPSYKYEQLAKVNKVMVNYINDHGETPSVAYIAEQLEIKEYKV 160

Query: 564 RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLA 618
             ++   ++ ISL   IGD    ED     D IE+K   +      Q N +RE    +  
Sbjct: 161 SLLINEFQDIISLNDVIGDNIFLEDVIGNEDNIEEKIIKND-----QINKMRELLDNI-- 213

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ RE  ++ +R+G+  N  HTL+E+G +  +TRER+RQIE KAI KLK
Sbjct: 214 -LSEREREIIELRYGLYNNKMHTLKEIGDELNITRERVRQIEKKAITKLK 262


>gi|55274905|gb|AAV49254.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 182

 Score =  157 bits (398), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 71/176 (40%), Positives = 120/176 (68%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ T
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++T
Sbjct: 61  IRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 120

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           P+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 121 PLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 176


>gi|59714198|ref|YP_206973.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
 gi|59482446|gb|AAW88085.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
          Length = 294

 Score =  157 bits (397), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 83/247 (33%), Positives = 146/247 (59%), Gaps = 6/247 (2%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFD 489
           + +KG+  A   +  ++E+NLRLV+ VA KY  R    L  LD+I+EGN+GL+KA +KF+
Sbjct: 44  LYKKGDVSA---RNTLIESNLRLVVKVANKYRKRNQTDLAILDIIEEGNLGLIKAIDKFN 100

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             LGY+FSTYA+WW++++I  ++ + S T+R+PVH+  +++  +R AR +S  +KREP+ 
Sbjct: 101 PELGYRFSTYAVWWIRESIESALFNHSRTVRLPVHITKELNTYLRAARELSKSLKREPSI 160

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +I+         V K++ +    ++  +   DE +    +   +  A+ P  S  Q NL
Sbjct: 161 RDISTYCEEEQIKVSKIISLIPNQLTCHSACSDELSPKFFELSSNNKALEPDSSLSQNNL 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +  + SL  RE+ ++  R+G+      TLE++GK   +++ER+RQI+++ + KL  
Sbjct: 221 EMNLSSWIDSLNYREKEIIINRYGLFGCKVKTLEDLGKDLDLSKERVRQIQSETLIKLNT 280

Query: 670 PSRSKKL 676
             +  KL
Sbjct: 281 IFKKNKL 287


>gi|323345236|ref|ZP_08085459.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093350|gb|EFZ35928.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  157 bits (397), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 91/263 (34%), Positives = 153/263 (58%), Gaps = 8/263 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI +   +   ++KG  E   AK+ +V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIEDEIELAQKIKKGGPEGERAKERLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+     +   
Sbjct: 91  IKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINHEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R P+  E++    +  E + + +      +S++ P  D + + + D +   +D    
Sbjct: 151 ENQRRPSISELSDATNIDEEKIGQSMMADGHHVSIDAPFQDGEDNTMLDVMPGGDDSRTD 210

Query: 599 SPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +D  ++   L    +RVL     RE  +++  FGIG + +  LEE+G Q  +TRER+R
Sbjct: 211 RNVDHESMAMELNSVLSRVLKD---REITIIKECFGIGCH-EKGLEEIGDQLGLTRERVR 266

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QI  K+I KL+    +K L  +L
Sbjct: 267 QIREKSIAKLRDSGNAKILMKYL 289


>gi|168986243|dbj|BAG11803.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986245|dbj|BAG11804.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986247|dbj|BAG11805.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986249|dbj|BAG11806.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986251|dbj|BAG11807.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986253|dbj|BAG11808.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986255|dbj|BAG11809.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986259|dbj|BAG11811.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|168986261|dbj|BAG11812.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|258642983|gb|ACV86055.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 177

 Score =  157 bits (397), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 71/176 (40%), Positives = 120/176 (68%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ T
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++T
Sbjct: 61  IRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 120

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           P+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 121 PLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 176


>gi|304383076|ref|ZP_07365551.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335762|gb|EFM02017.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 290

 Score =  157 bits (397), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 93/262 (35%), Positives = 151/262 (57%), Gaps = 6/262 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ISI E   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++GL   DLI EGNIGL
Sbjct: 31  ISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQGLTLTDLIDEGNIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+     +   
Sbjct: 91  IKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKINHEINKFEQ 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAV 598
           + +R P+  E++    +  E + + L      +S++ P  + + + + D +   ED    
Sbjct: 151 ENQRHPSVSELSDVTHIDEEKIGQSLMADGHHVSIDAPFQEGEENCMLDVMAGGEDSRTD 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             +D    A  +E  T +   L  RE  ++R  FGIG + +  LEE+G +  +TRER+RQ
Sbjct: 211 RLVDHESMA--QELNTVLCKVLKDREITIIRECFGIGCH-EKGLEEIGDRLGLTRERVRQ 267

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           I  K+I KL+     K L  +L
Sbjct: 268 IREKSIAKLRDSGNVKVLMKYL 289


>gi|3249719|gb|AAC26662.1| RNA polymerase sigma-like factor [Streptomyces lividans TK24]
          Length = 162

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 79/162 (48%), Positives = 116/162 (71%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +
Sbjct: 1   YATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDL 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL+
Sbjct: 61  APERVGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLS 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 121 TLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIE 162


>gi|260889708|ref|ZP_05900971.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260860314|gb|EEX74814.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 273

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 139/229 (60%), Gaps = 11/229 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ +NLRLVIS AKK    GL  +DLI EGNIGL+KA  KFD+  G++FSTYA+WW
Sbjct: 42  ARQLLILSNLRLVISTAKKSLGNGLPLIDLISEGNIGLIKAINKFDYEKGHRFSTYAVWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I ++I +    IRIP +  +++ KV +  +  +      P+ E IAK++ +    V
Sbjct: 102 IKQSIKKAIINIGRDIRIPSYKYEQLSKVNKVIKDYTAIHGEAPSTEYIAKEVDLKESKV 161

Query: 564 RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +L   ++ +SL   IGD    ED     D +EDK  +   D  I+  +++   RV   
Sbjct: 162 ILLLGEFQDIMSLNETIGDNIYLEDIIGKNDDVEDK--IIKEDQLIE--MKDLLERV--- 214

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  +L  R+G+  N  HTL+E+G+Q  +TRER+RQIE KAI KLK
Sbjct: 215 LNERERAILEYRYGLYDNKIHTLKEIGEQMGITRERVRQIEKKAITKLK 263


>gi|256371989|ref|YP_003109813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008573|gb|ACU54140.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 302

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 96/284 (33%), Positives = 151/284 (53%), Gaps = 16/284 (5%)

Query: 399 VACEVDSILK--------IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           V  EVDS L+        IR  +  ++     S +E   +   VR+G+ +A   K EMV 
Sbjct: 19  VQAEVDSALQAAGLGADSIRLFLDDLAKHPLPSAAEQVELAKRVREGDEDA---KAEMVA 75

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+  A++Y +RG++  DLIQEG  GL++A EKFDW  G+KFSTYA WWV+Q++ R
Sbjct: 76  ANLRLVVHWARRYQDRGVELADLIQEGTFGLIRAVEKFDWRRGFKFSTYATWWVRQSLQR 135

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           ++ +    IR+P+   ++  +V    R ++  + R PT EEIA    +    +  V    
Sbjct: 136 AVHNHGQAIRLPMEAAERSRRVDNVTRELAADLGRAPTEEEIAMAANLSASQLADVRHAA 195

Query: 571 KEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +   SL+  +G E  + LGD +  +D +    +D +I    RE   R +  L   E +V+
Sbjct: 196 RVVASLDQAVGPEGETSLGDLVVAQDTSFEEEVDESIS---REMLRRAVEELDELERQVV 252

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +RFG+  +   +LE   +   +   R R++EA A+ KL    R
Sbjct: 253 TLRFGLQGDRPASLEATARILGIGPRRARRLEASALAKLAENPR 296


>gi|290956130|ref|YP_003487312.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645656|emb|CBG68747.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 1033

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 87/221 (39%), Positives = 138/221 (62%), Gaps = 4/221 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V  N RLV S+ +   ++GL++ DL+Q G +GLM+AA KFD   GYKFSTYA WW
Sbjct: 250 ARDCLVLHNQRLVHSLIRSCLDQGLEYEDLVQHGVLGLMRAARKFDPAKGYKFSTYATWW 309

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+Q+++R+IAD+   IR+PVHM +++ KV    R ++ +  R     ++A +  M ++ V
Sbjct: 310 VRQSVSRAIADEGALIRVPVHMHEQMRKVAAAERALAAQ-GRPAGNVDVAVQCDMTLDRV 368

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASLTP 622
            ++ K+T+   SL+  IGD  T  LGDF+  + A+  +++  +   L E    V+ + + 
Sbjct: 369 EEIRKLTRRTDSLDRIIGDGAT--LGDFVGKRQALPSVENDVLHVLLMEDVMGVVGTFSE 426

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           R  R+L  R G+      TL+E+G++F VTRERIRQ+E KA
Sbjct: 427 RSARILVRRLGLDGEEPSTLDELGREFGVTRERIRQLEGKA 467


>gi|260435993|ref|ZP_05789963.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260413867|gb|EEX07163.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 309

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 158/271 (58%), Gaps = 25/271 (9%)

Query: 418 VETGISISEFRHIVS--------------MVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           V+  +SI+E  H+                ++R+GE     AK +M+ +NLRLV+++AK+Y
Sbjct: 31  VQAMVSITERCHLAGGTGPACEYSDEEKGVIRRGE----RAKNQMITSNLRLVVNLAKRY 86

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q + R+++ QS TIRIPV
Sbjct: 87  QGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPV 146

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPI- 580
           ++ +K+ K+     R+  +    P+ E++A+ + +P+  V  +L  ++    +SL+  + 
Sbjct: 147 NVNEKLTKLRAAKARLMQRNGLSPSGEQLAEFMEIPIAEVEDLLACELRSVTVSLQGVVK 206

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTPREERVLRMRFGI-GMN 637
              D S L D +  +  + PL+ A  A    +   +L  A+LTP+E  V+ +RFG+ G N
Sbjct: 207 SKSDPSELVDVLPSEE-LPPLERAEIAERTASAWSLLAKANLTPKEHTVVTLRFGLDGTN 265

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 266 EWRTLAEVARHMNCSREYCRQVVQRALRKLR 296


>gi|148645064|gb|ABR01057.1| RpoD [uncultured Geobacter sp.]
          Length = 102

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 73/102 (71%), Positives = 92/102 (90%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I
Sbjct: 1   LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           ADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+
Sbjct: 61  ADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAE 102


>gi|282877365|ref|ZP_06286188.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
 gi|281300417|gb|EFA92763.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
          Length = 290

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 153/270 (56%), Gaps = 10/270 (3%)

Query: 418 VETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           VE G    ISI E   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++GL   DL
Sbjct: 23  VEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQGLSLTDL 82

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           I EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    ++K+ 
Sbjct: 83  IDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLNKIN 142

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI- 592
               R   +  R P+  E++    +  + + + +      +S++ P  D + + + D + 
Sbjct: 143 HEINRFEQENHRRPSISELSDATNIDEDKISQSMMADGHHVSIDAPFQDGEDNTMLDVMP 202

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             ED      +D    A  +E    +   L  RE  +++  FGIG + +  LEE+G Q  
Sbjct: 203 SGEDSRTDRHVDHESMA--QELDAVLNKVLKEREIIIIKECFGIGRH-EKGLEEIGDQLG 259

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 260 LTRERVRQIREKSIAKLRDSGNAKILMKYL 289


>gi|254430393|ref|ZP_05044096.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197624846|gb|EDY37405.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 302

 Score =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 87/231 (37%), Positives = 145/231 (62%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y N+GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 62  AKNQMITANLRLVVNLAKRYQNKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ ++     R        P+P+ +A ++ +P+  V
Sbjct: 122 IRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARYLQSHGVSPSPKALAGEMQLPLAEV 181

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
            ++L  ++    +SL+  +  + D S L D +     ++P++ A  A    +  ++L S 
Sbjct: 182 EELLGCELRSITVSLQGVVKSKADPSELVDVLPSPE-LAPMERAELAERSASVWKLLESS 240

Query: 620 -LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+E  V+ +RFG+ G +   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 241 NLTPKERTVVMLRFGLDGSHEWRTLAEVARQLDCSREYCRQVVQRALRKLR 291


>gi|55274887|gb|AAV49246.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 199

 Score =  157 bits (396), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 80/199 (40%), Positives = 133/199 (66%), Gaps = 3/199 (1%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT---PEEIAKKLAMPVEGVRKVLKI 569
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+    EEIA++L  PV+ V ++L++
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEAEEIAEQLDKPVDDVSRMLRL 120

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL 
Sbjct: 121 NERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLA 180

Query: 630 MRFGIGMNTDHTLEEVGKQ 648
            RFG+      TLE+VG++
Sbjct: 181 RRFGLLGYEAATLEDVGRE 199


>gi|158341157|ref|YP_001522480.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158311398|gb|ABW33009.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 274

 Score =  157 bits (396), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 82/225 (36%), Positives = 139/225 (61%), Gaps = 2/225 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++E NLRLV+S+AKK+ NRGL   DLIQEG+IGL  A +KFD   G +FSTYA WW
Sbjct: 40  AKQRLIECNLRLVVSIAKKHQNRGLPLQDLIQEGSIGLSNAVDKFDLAQGCRFSTYAYWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q +T ++  +S  I +P +  + I K+ +  R ++ ++ REP+  E+AK   +  + +
Sbjct: 100 IRQGVTAALRAKSRPIYLPQYQWEMISKIKKHFRELNQQLGREPSLSELAKATNLKPKTI 159

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + L + ++  SL+ P+G +    L D +  ++  +    ++Q  L E  ++V+A L  R
Sbjct: 160 SRTLHLFQKVSSLDQPVGHQQKDTLLDLMAGEDQPTLYLESLQ--LDEQLSQVMAHLDKR 217

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ VL  RFG+  +   ++ E+G+Q  ++RE IR I  K ++KL+
Sbjct: 218 EQFVLSQRFGLEDDQPKSMREIGEQIGLSREGIRLILNKIMKKLQ 262


>gi|90580452|ref|ZP_01236258.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90438361|gb|EAS63546.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 231

 Score =  156 bits (395), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 83/213 (38%), Positives = 128/213 (60%), Gaps = 1/213 (0%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AKKY    L   D+I EGN+GL+ A EKFD   G++FSTYA WW+KQ I R+I +Q+
Sbjct: 1   MSIAKKYRAAHLLLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQN 60

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+PVH+  +I+ ++RT R +  K   EPT E+IA++L      +  +    ++ +SL
Sbjct: 61  RTIRLPVHVSKEINGLLRTHRDLMKKQNHEPTHEDIAQQLNKETHDISILFSYEQKIVSL 120

Query: 577 ETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +  IG DE+T  +   I D+   SP     + ++      +L  + PRE  +L  RFG+ 
Sbjct: 121 DQTIGDDENTGTIASLIVDEQIPSPSHIVEENSMVNLAEDILNKIKPREREILCRRFGVM 180

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL+EV     +TRER+RQ++AK++ +LK
Sbjct: 181 GYEPQTLQEVALALGITRERVRQLQAKSLERLK 213


>gi|310778262|ref|YP_003966595.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
 gi|309747585|gb|ADO82247.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
          Length = 263

 Score =  156 bits (395), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 93/234 (39%), Positives = 131/234 (55%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V +NLRLV+S+AKKY N G+  LDLIQEGNIGL+KA  KFD  +  +FSTYA +W
Sbjct: 35  AHEKLVTSNLRLVVSIAKKYINIGIPVLDLIQEGNIGLIKAVSKFDTTMDKRFSTYATFW 94

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I R I+     IR P ++ D I K+ +  R   NK    P+ E IA  L    + V
Sbjct: 95  IKQSILRYISSNKGVIRYPTYIYDNISKINKFIRDYKNKYGSVPSIEVIATGLEFKKKDV 154

Query: 564 RKVLKITKEPI-SLETPIGDEDTSH----LGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            K L I ++ + SLE   G+    H      D  E++     ++  + +NL+        
Sbjct: 155 EKYLNIFEQSLNSLEESYGENGDLHSIIPSDDLFEEQIITDSVNEELISNLK-------- 206

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  +E  V+  RFG+      TLEE+G    +TRERIRQI+ KAI KL+   R
Sbjct: 207 ILNSKERDVIIHRFGLFNKNVLTLEEIGNHLNLTRERIRQIQLKAIDKLRDKFR 260


>gi|3249725|gb|AAC26665.1| RNA polymerase sigma-like factor [Streptomyces glauceuces]
          Length = 162

 Score =  156 bits (395), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/162 (46%), Positives = 113/162 (69%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+I   L +
Sbjct: 1   YATWWIRQAMSRALADQADTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIGVDLDL 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  +L++ +EP+SL  P+G+ED    GD IED +A SP++SA+   LRE    VL+
Sbjct: 61  TPERVTDILRLGQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAVFLLLREHLEAVLS 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 121 TLGERERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIE 162


>gi|3769432|gb|AAC78468.1| RNA polymerase sigma factor 2 [Zea mays]
          Length = 349

 Score =  156 bits (395), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 145/252 (57%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +N+RLVIS+A KY N G+   DLIQ G IGL++  EKFD   G++ STY
Sbjct: 102 ESFLAREMLTMSNIRLVISIAHKYDNLGVDLADLIQGGLIGLLRGIEKFDASRGFRISTY 161

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
             WW++Q ++R++AD S T R+P ++ +++   +R A+         PT E IA+ L + 
Sbjct: 162 VYWWIRQGVSRALADNSKTFRLPTYLHERL-LAIRGAKYALEDQGIAPTIENIAESLNIS 220

Query: 560 V-------EGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
           V       E V KVL + ++   SL    GD     L  +IED+N  + P     +  L+
Sbjct: 221 VKKVHNATEAVHKVLSLDQQAFPSLNGLPGDT----LHSYIEDQNVANDPWHGFEEMYLK 276

Query: 611 ETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E    ++ S L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 277 EEVNNLINSNLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVRLVAMEKLKH 335

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 336 AARRKHLNALLE 347


>gi|37806470|dbj|BAC99905.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 388

 Score =  156 bits (394), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 148/252 (58%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 141 ESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 200

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++A+ S T R+P ++ +++   +R A+         PT E IA      
Sbjct: 201 VYWWIRQGVSRALAENSKTFRLPTYLHERL-IAIRGAKYELEDQGIAPTIENIAGSLNIS 259

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    G+     L  +IED+N  + P     +  L+
Sbjct: 260 EKKVLNATEAVNKVLSLDQQAFPSLNGLPGET----LHSYIEDQNVANDPWHGFEEWYLK 315

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 316 EEVNKLLNSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKH 374

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 375 AARRKNLEALLE 386


>gi|157833814|pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
           Escherichia Coli Rna Polymerase
          Length = 339

 Score =  156 bits (394), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 91/200 (45%), Positives = 125/200 (62%), Gaps = 6/200 (3%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 142 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 201

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + V+ EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 202 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ---KLQQIEEETGLTIEQVKDINRRMSI 258

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 259 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 318

Query: 497 STYAMWWVKQAITRSIADQS 516
           STYA WW++QAITRSIADQ+
Sbjct: 319 STYATWWIRQAITRSIADQA 338


>gi|167950928|ref|ZP_02538002.1| RNA polymerase sigma factor RpoS [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 216

 Score =  156 bits (394), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 78/201 (38%), Positives = 123/201 (61%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  
Sbjct: 1   MALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVK 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+  +R AR+++  +  EPT EEIA  L  P+  V+++L + +   S++TP G +    
Sbjct: 61  EINVYLRAARQLAQSLDHEPTSEEIADLLDKPISEVKRMLGLNERVTSVDTPFGKDADKP 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D I D+    P  +     L       L  L  ++  V+  RFG+    + TLE+V  
Sbjct: 121 LLDTIPDERVQDPTVNIQNDGLNTNLDTWLLKLNDKQREVVERRFGLHGYENSTLEQVAN 180

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  VTRER+RQI+  A+R+L+
Sbjct: 181 ELGVTRERVRQIQMDALRRLR 201


>gi|78212534|ref|YP_381313.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78196993|gb|ABB34758.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 309

 Score =  156 bits (394), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 89/243 (36%), Positives = 149/243 (61%), Gaps = 11/243 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R+GE     AK +M+ +NLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D  
Sbjct: 59  GVIRRGE----RAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPT 114

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +    P+ E+
Sbjct: 115 RGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNGLSPSGEQ 174

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           +A+ + +P+  V  +L  ++    +SL+  +    D S L D +   + + P++ A  A 
Sbjct: 175 LAEFMEIPIAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPS-DELPPMERAEIAE 233

Query: 609 LRETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              +   +L  A+LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+R
Sbjct: 234 RTASVWSLLAKANLTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALR 293

Query: 666 KLK 668
           KL+
Sbjct: 294 KLR 296


>gi|125560253|gb|EAZ05701.1| hypothetical protein OsI_27933 [Oryza sativa Indica Group]
          Length = 372

 Score =  155 bits (393), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 148/252 (58%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 125 ESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 184

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++A+ S T R+P ++ +++   +R A+         PT E IA      
Sbjct: 185 VYWWIRQGVSRALAENSKTFRLPTYLHERL-IAIRGAKYELEDQGIAPTIENIAGSLNIS 243

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    G+     L  +IED+N  + P     +  L+
Sbjct: 244 EKKVLNATEAVNKVLSLDQQAFPSLNGLPGET----LHSYIEDQNVANDPWHGFEEWYLK 299

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 300 EEVNKLLNSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKH 358

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 359 AARRKNLEALLE 370


>gi|33946401|gb|AAQ55816.1| truncated stationary phase specific sigma factor [Pseudomonas
           syringae]
          Length = 252

 Score =  155 bits (393), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 73/188 (38%), Positives = 118/188 (62%), Gaps = 3/188 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S +E  H   + + G+      +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 67  LNEIGFSPLLSPAEEVHFARLSQSGD---PAGRKRMIESNLRLVVKIARRYVNRGLSLLD 123

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 124 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 183

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 184 LRAARELTQKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTL 243

Query: 593 EDKNAVSP 600
            D     P
Sbjct: 244 TDDRPTDP 251


>gi|168986257|dbj|BAG11810.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
          Length = 177

 Score =  155 bits (393), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/176 (40%), Positives = 119/176 (67%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRGL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW++Q I R+I +Q+ T
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFLFSTYATWWIRQTIERAIMNQTRT 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++T
Sbjct: 61  IRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 120

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           P+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 121 PLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 176


>gi|158339615|ref|YP_001521004.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158309856|gb|ABW31472.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  155 bits (393), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 82/243 (33%), Positives = 148/243 (60%), Gaps = 2/243 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ +  +  AK+ M+E NLR V+S+AKKY NRGL  LDLIQEG+IGL  A +KFD 
Sbjct: 27  IQLARQAQAGSLRAKQRMIECNLRFVVSIAKKYQNRGLPLLDLIQEGSIGLSTAVDKFDL 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WW++Q IT ++  +S  I +P +  D + K+ +  R ++ ++ REP+  
Sbjct: 87  AQGCRFSTYAYWWIRQGITAAVRAKSRPIYLPHYHWDTVGKIKKHFRVLTQQLGREPSLS 146

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+++   +  + + + L++ ++  SL+  +G +    L D +  ++  +    ++Q  L 
Sbjct: 147 ELSEATNIKPKTISRTLQLFQQISSLDQLVGPQQKDTLLDMLAGEDQPTHYLESLQ--LD 204

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +  ++V+ASL  RE  VL  R+G+  +   +++E+G+Q  ++ E IR I  K ++KL+  
Sbjct: 205 DELSQVMASLDERERFVLSQRYGLEDDHPKSMKEIGQQIGLSHEGIRLILKKIMQKLERY 264

Query: 671 SRS 673
           ++S
Sbjct: 265 AQS 267


>gi|125602291|gb|EAZ41616.1| hypothetical protein OsJ_26150 [Oryza sativa Japonica Group]
          Length = 420

 Score =  155 bits (392), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 148/252 (58%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 173 ESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 232

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++A+ S T R+P ++ +++   +R A+         PT E IA      
Sbjct: 233 VYWWIRQGVSRALAENSKTFRLPTYLHERL-IAIRGAKYELEDQGIAPTIENIAGSLNIS 291

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    G+     L  +IED+N  + P     +  L+
Sbjct: 292 EKKVLNATEAVNKVLSLDQQAFPSLNGLPGET----LHSYIEDQNVANDPWHGFEEWYLK 347

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 348 EEVNKLLNSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKH 406

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 407 AARRKNLEALLE 418


>gi|158339957|ref|YP_001521127.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310198|gb|ABW31813.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  155 bits (392), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 84/243 (34%), Positives = 144/243 (59%), Gaps = 2/243 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + + R+ +  +  AK+ M+E NLRLV+S+AKK+ NRGL  LDLIQEG+IGL  A +KF+ 
Sbjct: 27  IELARQAKAGSLRAKQRMIECNLRLVVSIAKKHQNRGLPLLDLIQEGSIGLSTAVDKFEI 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WW++Q IT ++  +S  I +P +  + I+K+ +  R ++ K+ REP+  
Sbjct: 87  AQGCRFSTYAYWWIRQGITAALRAKSRPIYLPQYQWEMINKIKKHYRELNQKLGREPSLS 146

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+++   +  + +   L++ ++  SL+ P+G E    L D +   N  +    ++Q +  
Sbjct: 147 ELSESTEIKPKTINLTLQLFQKISSLDQPVGPEQKDSLLDLLPGDNQPTLYMESLQRD-- 204

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    V+A L  RE  VL  R+G+  +   ++ E+G+Q  ++ E IR I  K ++KL+  
Sbjct: 205 EQLFHVMAHLDERERLVLSQRYGLEDDQPKSMREIGEQIGLSHEGIRLILKKIMKKLERY 264

Query: 671 SRS 673
           + S
Sbjct: 265 AES 267


>gi|87302558|ref|ZP_01085375.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
 gi|87282902|gb|EAQ74859.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
          Length = 307

 Score =  155 bits (392), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 144/231 (62%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL++A EK+D   G++FSTYA WW
Sbjct: 66  AKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLVRAVEKYDPTRGHRFSTYAYWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+     R+        +P+E+A  + +P+  V
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLLQANGLTASPQELAATMHLPLAEV 185

Query: 564 RKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +    D + L D +   + + P++ A  +    +  R+L  +
Sbjct: 186 EDLLSCELRSITVSLQGVVKSKSDPTELVDVLAS-DEMPPMERAELSERSASVWRLLDVS 244

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTPRE  V+ +RFG+ G +   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 245 NLTPRERTVVMLRFGLDGGHEWRTLAEVARQLGCSREYCRQVVQRALRKLR 295


>gi|113953662|ref|YP_731106.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113881013|gb|ABI45971.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 307

 Score =  155 bits (392), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 146/234 (62%), Gaps = 7/234 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ ++     R+       P+ E++A+ + +P+  V
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARLMQSNGLAPSAEQLAECMKLPISEV 184

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +  + D S L D +   + + P++ A  A   ++   +L  +
Sbjct: 185 EDLLGCELRSVTVSLQGVVKSKSDPSELVDVLPS-DEIPPMERAEIAERTDSAWNLLDNS 243

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +LTP+E  ++ +RFG+ G +   TL EV +Q   +RE  RQ+  +A+RKL+  S
Sbjct: 244 NLTPKERTIVMLRFGLDGSHEWRTLAEVARQMNCSREYCRQVVQRALRKLRKTS 297


>gi|78184480|ref|YP_376915.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78168774|gb|ABB25871.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 309

 Score =  155 bits (391), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 90/242 (37%), Positives = 149/242 (61%), Gaps = 11/242 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R+GE     AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   
Sbjct: 60  VIRRGE----RAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTR 115

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +     T E++
Sbjct: 116 GHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARIMQRNGLTATGEQL 175

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A+ + +P+  V  +L  ++    +SL+  +    D S L D +   + + P++ A  A  
Sbjct: 176 AEFMNVPLTEVEDLLACELRSVTVSLQGIVKSKSDPSELVDILPS-DEIPPMERAEIAER 234

Query: 610 RETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +   +L  A+LTP+E +V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+RK
Sbjct: 235 SASVWALLSKANLTPKEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRK 294

Query: 667 LK 668
           L+
Sbjct: 295 LR 296


>gi|2780746|dbj|BAA24364.1| plastid RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 519

 Score =  155 bits (391), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 148/252 (58%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 272 ESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 331

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++A+ S T R+P ++ +++   +R A+         PT E IA      
Sbjct: 332 VYWWIRQGVSRALAENSKTFRLPTYLHERL-IAIRGAKYELEDQGIAPTIENIAGSLNIS 390

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    G+     L  +IED+N  + P     +  L+
Sbjct: 391 EKKVLNATEAVNKVLSLDQQAFPSLNGLPGET----LHSYIEDQNVANDPWHGFEEWYLK 446

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 447 EEVNKLLNSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKH 505

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 506 AARRKNLEALLE 517


>gi|317051905|ref|YP_004113021.1| sigma-70 family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946989|gb|ADU66465.1| RNA polymerase sigma factor, sigma-70 family [Desulfurispirillum
           indicum S5]
          Length = 305

 Score =  155 bits (391), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 92/274 (33%), Positives = 163/274 (59%), Gaps = 6/274 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+ ++ IS  T ++  E + +   +  G+ +A    + +VE+NLR V+ +A KY + G+
Sbjct: 35  LRDYLRRISRITLLTAEEEKELARRISAGDEQAF---RVLVESNLRFVVKIAMKYRDIGI 91

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI EGNIGL++AA +FD   G +F TYA+WW+KQ+I ++I   S T+R+P   + +
Sbjct: 92  NLLDLINEGNIGLLEAARRFDPERGNRFITYAVWWIKQSIIQAIISSSNTVRLP-GKQAR 150

Query: 529 IHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
               + +ARR    +   REPT +E+  +  + +  +  +L+ T+  ISL+TPIG++D  
Sbjct: 151 FASKLNSARREFARDHDGREPTEQELRDEYGLDISNIEDILRATRSYISLDTPIGEDDER 210

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E     S  +  ++  +      ++A L  R+  V+ +RFGI      TL+EVG
Sbjct: 211 TLKDVLESPEESSTEEQYVRQKISTEIRSIIAELESRDALVVDLRFGISEGIPQTLDEVG 270

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  +++ER+RQIE +A+++L+  + ++KL  +L
Sbjct: 271 TRLGLSKERVRQIEERALKRLQRKAMNRKLSEYL 304


>gi|299473209|emb|CBN78785.1| RNA polymerase [Ectocarpus siliculosus]
          Length = 627

 Score =  155 bits (391), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 92/251 (36%), Positives = 141/251 (56%), Gaps = 19/251 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRG------LQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A+  M+  NLRLV+ +A++   +G      +   D+IQ+G  GL+KA E+FD   G++FS
Sbjct: 235 ARDRMISCNLRLVVHIARRKFYKGASGTLKVSLEDMIQDGTAGLVKAVERFDPEKGFRFS 294

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WWV Q I    AD    +R+P+ +   + KV+R    M +++ R+PT +E++ +  
Sbjct: 295 TYATWWVHQGIHCGFADCGRVVRLPMSLHTMVCKVMRLQTAMVDQLGRQPTVQELSLESG 354

Query: 558 MPVEGVRKVLKITK-EPISLETPIGDEDTSHL-----------GDFIEDKNAVSPLDSAI 605
           +    V K L++ + EPISL+       + HL           GD ++      P+D A 
Sbjct: 355 LDERKVEKCLRVNQVEPISLDG-YRKSKSGHLNFENSFRRERVGDSVKSVQETEPVDGAD 413

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            + L+     +L  L+ RE  VLRMRFGIG ++  TLE VG++  VTRER+RQI+  AI+
Sbjct: 414 VSLLKTDVDTILGDLSEREAYVLRMRFGIGGSSPSTLETVGQELQVTRERVRQIQIAAIQ 473

Query: 666 KLKHPSRSKKL 676
           KL+  S S  L
Sbjct: 474 KLRGRSPSHDL 484


>gi|37806471|dbj|BAC99906.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 342

 Score =  155 bits (391), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 148/252 (58%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 95  ESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 154

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++A+ S T R+P ++ +++   +R A+         PT E IA      
Sbjct: 155 VYWWIRQGVSRALAENSKTFRLPTYLHERL-IAIRGAKYELEDQGIAPTIENIAGSLNIS 213

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    G+     L  +IED+N  + P     +  L+
Sbjct: 214 EKKVLNATEAVNKVLSLDQQAFPSLNGLPGET----LHSYIEDQNVANDPWHGFEEWYLK 269

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 270 EEVNKLLNSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKH 328

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 329 AARRKNLEALLE 340


>gi|297608012|ref|NP_001061065.2| Os08g0163400 [Oryza sativa Japonica Group]
 gi|255678168|dbj|BAF22979.2| Os08g0163400 [Oryza sativa Japonica Group]
          Length = 520

 Score =  155 bits (391), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 148/252 (58%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 273 ESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 332

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++A+ S T R+P ++ +++   +R A+         PT E IA      
Sbjct: 333 VYWWIRQGVSRALAENSKTFRLPTYLHERL-IAIRGAKYELEDQGIAPTIENIAGSLNIS 391

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    G+     L  +IED+N  + P     +  L+
Sbjct: 392 EKKVLNATEAVNKVLSLDQQAFPSLNGLPGET----LHSYIEDQNVANDPWHGFEEWYLK 447

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 448 EEVNKLLNSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKH 506

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 507 AARRKNLEALLE 518


>gi|297811483|ref|XP_002873625.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297319462|gb|EFH49884.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 273

 Score =  154 bits (390), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 77/207 (37%), Positives = 126/207 (60%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  +GL   DLIQEG+IGL++ AE+FD   GYK STY  WW+KQAI R+IA +S  +++P
Sbjct: 52  YQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLP 111

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             M +   KV   +  ++ K++R+P+ EEIA+ L + V  VR  ++ ++ P+SL+  +  
Sbjct: 112 GSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLHVSAVRLAVERSRSPVSLDRVVSQ 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                L + +   +   P +   + +++    ++L SLT RE RVL + FG+   T  + 
Sbjct: 172 NGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSF 231

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           EE+GK   ++RER+RQI   A++KL++
Sbjct: 232 EEIGKSLKLSRERVRQINGIALKKLRN 258


>gi|119503379|ref|ZP_01625463.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119461025|gb|EAW42116.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 430

 Score =  154 bits (390), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 82/225 (36%), Positives = 134/225 (59%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V  NLRLV S+A +Y  RG+ +LDL+QEG +GL++AAEKF++  G++FSTY   W
Sbjct: 188 ARDKLVMHNLRLVYSIAGRYKGRGVSYLDLVQEGTLGLIRAAEKFEFEKGFRFSTYCFNW 247

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + QA+ R + D    IR+P H+++++ ++ +       +   EP  E +A KL M +E  
Sbjct: 248 ITQAVRRYVGDVGTLIRLPTHVQEQMGRLYKEKAIEQLRTGVEPDEETLAAKLGMDIEKT 307

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++L++    +SL+ P  D+D   L D +  +      DSA QA+L +     + +L P 
Sbjct: 308 RQLLQMRNLGVSLDAPRFDDDEGTLLDTLSGEPYGGTEDSAEQASLHKFLGGAVDALEPS 367

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+RV+  R+G+      +  EV     V+RE +RQ+E  A+RKLK
Sbjct: 368 EQRVVVARWGLHDGPPLSRAEVADSLGVSREWVRQLERSALRKLK 412


>gi|87124019|ref|ZP_01079869.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168588|gb|EAQ69845.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 308

 Score =  154 bits (390), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 144/231 (62%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 66  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ K+     R+  +  +   PE++A+ + +P+  V
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQQHGQPANPEQLAEAMKIPLSEV 185

Query: 564 RKVL--KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +  + D S L D +   + + P++ A  A    +   +L  A
Sbjct: 186 EDLLACELRSVTVSLQGIVKSKADPSELVDVLPS-DELPPMERAEIAERTASAWTLLEKA 244

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 245 NLTPKERTVVMLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALRKLR 295


>gi|330862243|emb|CBX72404.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 113

 Score =  154 bits (390), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 77/103 (74%), Positives = 84/103 (81%)

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNT
Sbjct: 10  PIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNT 69

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 70  DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 112


>gi|281355585|ref|ZP_06242079.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281318465|gb|EFB02485.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 248

 Score =  154 bits (389), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/225 (37%), Positives = 132/225 (58%), Gaps = 3/225 (1%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           K ++E NLRLV  +A  +  RGL + DL+ EGN GLM AA ++D   G +FSTY+ WW+K
Sbjct: 16  KALIEENLRLVQKIANDFLGRGLPWEDLVSEGNRGLMTAARRYDPSRGARFSTYSAWWIK 75

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAI ++IA+Q+  +R+P+  +    K+ R    ++  +   P+ EE+A+   +P+  V +
Sbjct: 76  QAIRQAIAEQAQMVRVPIGTQTHWRKIRRIVNELTEALGHAPSDEEVAEAANLPLATVNR 135

Query: 566 VLKITKEPI-SLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +    +  + SL  PI  GD D     DF +D    +P    I+    E    +L +LT 
Sbjct: 136 LRGSRQIDVQSLNAPISDGDPDGGEFQDFFQDDTEPAPDQQLIKLEDVENLLSLLETLTE 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE++VLR+RFG+      TL+EVG +   T ER+RQI+ +A+RKL
Sbjct: 196 REQKVLRLRFGLDGEPIRTLDEVGTELNCTNERVRQIQNQALRKL 240


>gi|254526924|ref|ZP_05138976.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
 gi|221538348|gb|EEE40801.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
          Length = 307

 Score =  154 bits (388), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 89/232 (38%), Positives = 146/232 (62%), Gaps = 9/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPEEIAKKLAMPVEG 562
           ++Q + R+++ QS TIRIPV++ +K+ K +R+A+    ++K   PT +E+A+++ +  E 
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTK-LRSAKSKLMQLKGIPPTSDELAEEMKITKEE 183

Query: 563 VRKVLKITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-- 617
           + ++L      I++    T     D S L D +    A  P++ A  A    +  ++L  
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKSDPSELVDILPSDQA-PPMELAELAERTASAWKLLDK 242

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 243 ANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|302554830|ref|ZP_07307172.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472448|gb|EFL35541.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
          Length = 481

 Score =  154 bits (388), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 97/221 (43%), Positives = 129/221 (58%), Gaps = 12/221 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  N RLV  +A  Y  RGL   DL+Q G IGLM+A  KFD   G+KFSTYA WW+KQA
Sbjct: 250 LVLHNQRLVWKIALGYQGRGLDTEDLVQHGTIGLMRAVRKFDATKGFKFSTYATWWIKQA 309

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IAD+   IR+P H+ +K+ KV    R++ N+  R  T + +A    +    V KV 
Sbjct: 310 ITRAIADEGTLIRLPAHVHEKVSKVAVAERKLLNE-GRPRTVDNVAYVSGLTFAEVEKVR 368

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-----QANLRETTTRVLASLTP 622
           +I++   SL+  IGD DT+ LGD I   + +   D  +     QA LR     V+  L+ 
Sbjct: 369 RISRSTDSLDRIIGD-DTA-LGDLIIGPSRLPGPDVVLIRKEFQARLRH----VVEHLSE 422

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           RE  VL  R G+  +   TLE++G  F VTRERIRQIE KA
Sbjct: 423 RERHVLVRRTGLDGDEPDTLEDIGVVFGVTRERIRQIEPKA 463


>gi|123968168|ref|YP_001009026.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123198278|gb|ABM69919.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 307

 Score =  153 bits (387), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 89/232 (38%), Positives = 146/232 (62%), Gaps = 9/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPEEIAKKLAMPVEG 562
           ++Q + R+++ QS TIRIPV++ +K+ K +R+A+    ++K   PT +E+A+++ +  E 
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTK-LRSAKSKLMQLKGIPPTSDELAEEMKITKEE 183

Query: 563 VRKVLKITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-- 617
           V ++L      I++    T     D S L D +   +   P++ A  A    +  ++L  
Sbjct: 184 VDELLSCELRSITVSLQGTVKSKSDPSELVDILPS-DQTPPMELAELAERTASAWKLLDK 242

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 243 ANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|57996880|emb|CAI45888.1| negative response regulator [Escherichia coli]
          Length = 158

 Score =  153 bits (387), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 68/152 (44%), Positives = 109/152 (71%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 120

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
             S++TP+G +    L D + D+    P D+ 
Sbjct: 121 ITSVDTPLGGDSEKALLDILADEKENGPEDTT 152


>gi|15022434|dbj|BAB62255.1| RNA polymerase sigma 70 factor [Treponema medium]
          Length = 155

 Score =  153 bits (386), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 82/153 (53%), Positives = 107/153 (69%)

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV R +R++  K  REPT EEIA +L   VE V++V  + +EPISLETPIG+E+ S L
Sbjct: 2   INKVTRESRQLMQKFGREPTDEEIAAQLGWNVERVKQVKNVAREPISLETPIGEEEDSSL 61

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+  +P +      L+E    VL+ L  RE+ VL+MRFG+      TLEEVG  
Sbjct: 62  GDFIEDKDVENPSNLTEYILLQEQLRGVLSCLPLREQEVLKMRFGLDEGYALTLEEVGLY 121

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+R+L+HP +S KL+ +LD
Sbjct: 122 FNVTRERIRQIEAKALRRLRHPKQSCKLKDYLD 154


>gi|296125976|ref|YP_003633228.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
 gi|296017792|gb|ADG71029.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
          Length = 285

 Score =  152 bits (385), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/248 (36%), Positives = 146/248 (58%), Gaps = 6/248 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA   + +++ +NLR VI++AK+Y N GL   DLI EGN+GL+ AA++FD   G
Sbjct: 42  LKEGDAEA---RSKLIRSNLRFVITIAKQYKNSGLLLEDLISEGNMGLIIAADRFDPDKG 98

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y F +YA++W++Q+I R+I ++S  IR+P++    +  + RT  +   K    P   E+A
Sbjct: 99  YHFISYAVYWIRQSILRAINEKSRLIRLPLNKAMDLVDLERTVHQYYYKSGYTPDVNELA 158

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
             L      +  ++ ++ E ISLE     D     L D IEDK + +  ++AI   L E 
Sbjct: 159 AILNKDPNDILHIMSMSTEHISLEGEYNYDGMKDRLIDTIEDKTSKNVEETAINKELMEE 218

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               + SL+  E++++  R+GI      TL+EVG+ F  T+ERIRQIE KA+RK+ H  +
Sbjct: 219 LKTAIESLSDIEKQIINARYGIDQER-KTLKEVGEMFSFTKERIRQIEKKALRKM-HSQK 276

Query: 673 SKKLRSFL 680
              L+ FL
Sbjct: 277 YSSLKDFL 284


>gi|159903122|ref|YP_001550466.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159888298|gb|ABX08512.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 312

 Score =  152 bits (385), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 92/241 (38%), Positives = 148/241 (61%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+GE     AK +M+ +NLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G
Sbjct: 59  IRQGER----AKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRG 114

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     ++       P+ E +A
Sbjct: 115 HRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSQLMQANGLTPSSEMLA 174

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           KK+ +  E V ++L+     I  SL+  +    D S LGD +  +  + P++ A  A   
Sbjct: 175 KKMHLSKEEVEELLECELRSITVSLQGVVQSKSDPSELGDVLPSEE-IPPMEVAELAERN 233

Query: 611 ETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++   +L  A+LTP+E  ++ +RFG+ G N   TL EV K    +RE  RQ+  +A+RKL
Sbjct: 234 DSAWSLLNKANLTPKERTIVSLRFGLDGSNEWRTLAEVAKHMNCSREYCRQVVQRALRKL 293

Query: 668 K 668
           +
Sbjct: 294 R 294


>gi|293375845|ref|ZP_06622113.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325844994|ref|ZP_08168319.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
 gi|292645524|gb|EFF63566.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325488967|gb|EGC91357.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
          Length = 331

 Score =  152 bits (385), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 99/265 (37%), Positives = 150/265 (56%), Gaps = 25/265 (9%)

Query: 425 SEFRHIVSMVRKGECEA-SIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIG 480
           +E++H +  ++K   E    A + ++  N  LV  +  +YT   +  L + DL   G  G
Sbjct: 59  NEYQHNLEYLKKYRLENDETALEWLIFNNTNLVHKIIGRYTKFYHHKLDYDDLFSVGLEG 118

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA EKFD+     FSTYA +WVKQA+TR+IAD+  TIRIPVHM + I++V+R  +   
Sbjct: 119 LMKAIEKFDFTFDNNFSTYATYWVKQAVTRTIADEGFTIRIPVHMFESINQVMRYEQ--- 175

Query: 541 NKIKREPTP---EEIAKKLAMPV---EGVRKVLKITKEPISLETPIGDEDT-SHLGDFIE 593
            K  +E  P   + +  +L +P+   E V++V     +P SL   +  ED  + L D I 
Sbjct: 176 -KADQEDEPVDVDNLCGELKIPIEKYEAVKRVQTYMLKPTSLNGFVSKEDEDTELQDLIS 234

Query: 594 DKNAV----------SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           ++N +          +P   A+  +L+    +++ SL PRE+ V+  RFG+      TLE
Sbjct: 235 NENEMLVEGMSRIYDNPEKQAMDEDLKAYMDKMILSLNPREQFVIIHRFGLNGEEKKTLE 294

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G+   VTRERIRQIEAKA+RKL+
Sbjct: 295 EIGEIEGVTRERIRQIEAKAMRKLR 319


>gi|2624403|emb|CAA74653.1| plastid RNA polymerase sigma factor [Sorghum bicolor]
          Length = 500

 Score =  152 bits (385), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/252 (36%), Positives = 145/252 (57%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +N+RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 253 ESFLAREMLTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 312

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++AD S   R+P ++ +++   +R A+         PT E IA      
Sbjct: 313 VYWWIRQGVSRALADNSKAFRLPTYLHERL-IAIRGAKYALEDQGIAPTVENIAESLNIS 371

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    GD     L  +IED+N  + P     +  L+
Sbjct: 372 EKKVHNATEAVNKVLSLDQQAFPSLNGLPGDT----LHSYIEDQNVANDPWHGFEERYLK 427

Query: 611 ETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E    ++ S L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 428 EEVNNLINSNLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLVAMEKLKH 486

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 487 AARRKHLDALLE 498


>gi|168704138|ref|ZP_02736415.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 280

 Score =  152 bits (385), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/254 (36%), Positives = 142/254 (55%), Gaps = 23/254 (9%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E R +   +  G+     A+  MV ANLRLV+++A+ YT RGL   DL+ EGN+GL
Sbjct: 34  LSATEERELGGRILDGD---PAARDRMVRANLRLVVNLARGYTGRGLSLDDLVAEGNMGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E FD  +  +FSTYA +W+KQ+I R+I + + TIR+P +M   + +  R    + +
Sbjct: 91  LRAVEGFDPGMSTRFSTYASFWIKQSIQRAIVNTARTIRVPTYMAALVARWRRATAALGD 150

Query: 542 KIKREPTPEEIA-------KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           ++ R P PEE+A       +KLAM    V+  LK+            D+    L   I D
Sbjct: 151 ELGRAPAPEEVAGHLGLSRRKLAM----VQLALKVAGAGTQ-----ADDAEGGLEGLIPD 201

Query: 595 -KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +++ S  D+A Q  L       L  L PR+  VLR+RFG+      TL+EVG+   +T+
Sbjct: 202 TRDSGSDADAAEQLKL---VFEQLDRLNPRDADVLRLRFGLSGEEPKTLKEVGEALGLTK 258

Query: 654 ERIRQIEAKAIRKL 667
           ER+RQIE+ A+  L
Sbjct: 259 ERVRQIESAALSAL 272


>gi|242078297|ref|XP_002443917.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
 gi|241940267|gb|EES13412.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
          Length = 500

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 90/252 (35%), Positives = 146/252 (57%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +N+RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 253 ESFLAREMLTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTY 312

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++AD S   R+P ++ +++   +R A+         PT E IA      
Sbjct: 313 VYWWIRQGVSRALADNSKAFRLPTYLHERL-IAIRGAKYALEDQGIAPTVENIAESLNIS 371

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KVL + ++   SL    GD     L  +IED+N  + P     +  L+
Sbjct: 372 EKKVHNATEAVNKVLSLDQQAFPSLNGLPGDT----LHSYIEDQNVANDPWHGFEERYLK 427

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E    ++ ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 428 EEVNNLINSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLVAMEKLKH 486

Query: 670 PSRSKKLRSFLD 681
            +R K L + L+
Sbjct: 487 AARRKHLDALLE 498


>gi|327399101|ref|YP_004339970.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
 gi|327181730|gb|AEA33911.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
          Length = 289

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 92/256 (35%), Positives = 144/256 (56%), Gaps = 4/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K IS    +S  E + +   ++KG+ EA    K++V+ NLR V+SVAKKY N G+  LD
Sbjct: 30  LKEISKIPVLSAEEEKELGRRIKKGDKEAL---KKLVKHNLRFVVSVAKKYKNLGIPLLD 86

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAA+KFD     KF +YA WW+KQ+I + I +QS  IRIP+  + +I K+
Sbjct: 87  LINEGNLGLIKAAKKFDPDRNTKFISYAAWWIKQSIMKYITEQSTPIRIPLKAKSRISKI 146

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                    K   EP   EI++   +    ++          SL+  + D+     GD I
Sbjct: 147 DTIKEDYRQKFDEEPMNGEISEISDLSEREIKNAELARFYFDSLDDYVSDDKDILKGDLI 206

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
             K   S  D  IQ +L E   + L+ L  RE+ ++++R+G+      TL E+G+++ ++
Sbjct: 207 SLKEQ-SIEDEHIQKSLIEEVNKFLSELPEREQDIIKLRYGLYDGRPRTLREIGEKYGIS 265

Query: 653 RERIRQIEAKAIRKLK 668
           +ER+RQ+E   + KLK
Sbjct: 266 KERVRQLENNILNKLK 281


>gi|149278736|ref|ZP_01884871.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149230355|gb|EDM35739.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 286

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 94/279 (33%), Positives = 160/279 (57%), Gaps = 6/279 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E +SI K   +I  I +   +S+ E   +   ++KG+ EA++ K  +V+ NLR V+SVAK
Sbjct: 14  ETNSIDKYLTDIGRIGL---LSVEEELGLARRIKKGD-EAALDK--LVKTNLRFVVSVAK 67

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY N+GLQ  DLI EGN+GL+KAA++FD   G+KF ++A+WW++Q+I +++ADQ   IR+
Sbjct: 68  KYQNKGLQLADLISEGNLGLIKAAQRFDDTKGFKFISFAVWWIRQSIMQALADQKRMIRL 127

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P +    I K+ + A  +   ++R PT EE+A         V   L       SL+    
Sbjct: 128 PGNQVLGIIKINKAADELEQVLERAPTYEELAMATEFSEAKVADYLDSAPLSYSLDMTTH 187

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E    L D + ++N     +  ++ ++ E   R L+ L  RE+ ++   FG+  +T  T
Sbjct: 188 EESDFSLMDTLVNENTPDTDELMMKESMSEDVRRSLSILPEREKWIIIFFFGLDNHTALT 247

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L+++   F +++ERIRQ++ +A++ LK   R   L  ++
Sbjct: 248 LDDMTDVFQLSKERIRQLKDRALKTLKTSCRKSFLAEYI 286


>gi|2338708|gb|AAC46374.1| sigma factor RpoS [Vibrio cholerae]
          Length = 168

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 65/134 (48%), Positives = 104/134 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 35  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 94

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V
Sbjct: 95  IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDV 154

Query: 564 RKVLKITKEPISLE 577
            K+L++ +   S++
Sbjct: 155 TKMLRLNERITSVD 168


>gi|313647807|gb|EFS12253.1| RNA polymerase sigma factor rpoS [Shigella flexneri 2a str. 2457T]
          Length = 254

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 65/136 (47%), Positives = 106/136 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLETP 579
            ++L++ +   S++TP
Sbjct: 210 SRMLRLNERITSVDTP 225


>gi|302802267|ref|XP_002982889.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
 gi|302818650|ref|XP_002990998.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300141329|gb|EFJ08042.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300149479|gb|EFJ16134.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
          Length = 292

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 88/247 (35%), Positives = 137/247 (55%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+    A   +  MV +NL LVI VA+K+  +G    DLIQEG  GL+   EKFD   G
Sbjct: 37  LRRKLKHAKRCRTNMVSSNLGLVIKVARKFGLKGTTIEDLIQEGINGLLHGVEKFDTSRG 96

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++ STY +WW++ ++ R+   +S   ++P+H+ D   +V++T  R+  +    PT EE+A
Sbjct: 97  FRLSTYVLWWIELSVRRASVKRSIMCQVPMHLFDTHTRVLKTRARIFEERGTFPTNEEVA 156

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L    + V     + + P SL+  +   D   L + + D    S L  A +A L+E  
Sbjct: 157 TILGTTAQKVHLAANLMRHPKSLDDNVPGCDNVTLLEILPDPEVESSLLVAEKALLKEQL 216

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL  L PRE+ VL +R+GIG   D TLEE+   F ++RER+RQIE +A+ K+      
Sbjct: 217 DKVLNLLKPREKEVLTLRYGIGDGRDRTLEELSHHFNLSRERVRQIEKRALAKIHELGGK 276

Query: 674 KKLRSFL 680
           + L SF+
Sbjct: 277 ELLASFV 283


>gi|78778962|ref|YP_397074.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78712461|gb|ABB49638.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 307

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 88/232 (37%), Positives = 145/232 (62%), Gaps = 9/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPEEIAKKLAMPVEG 562
           ++Q + R+++ QS TIRIPV++ +K+ K +R+A+    ++K   P  +E+A++L +  E 
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTK-LRSAKSKLMQLKGITPNSDELAEELKITKEE 183

Query: 563 VRKVLKITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-- 617
           + ++L      I++    T     D S L D +   +   P++ A  A    +  ++L  
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKSDPSELVDILPS-DQTPPMELAELAERTASAWKLLDK 242

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 243 ANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|300689719|ref|YP_003750714.1| RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
 gi|299076779|emb|CBM09897.1| putative RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
          Length = 907

 Score =  151 bits (382), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 128/226 (56%), Gaps = 7/226 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  M++ANLRLV+ +A+   + GL+  DLIQEGN+GL+KA ++FDW  G++FST A+WW+
Sbjct: 550 RDHMMQANLRLVMDIARHRMHSGLRVEDLIQEGNLGLLKAVDRFDWRRGFRFSTMAIWWI 609

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQ I R I D +  IR+PVH+  KI +  R      +   +  +  E A    M ++   
Sbjct: 610 KQQIGRGIFDTALEIRLPVHIHQKISRGRRETESFEHVRGKPASLSERATICNMTLDKFE 669

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              +   EP+S+      E    +G + + + +  P     + +       VL  L  ++
Sbjct: 670 LAARALSEPLSI------EGAQQVG-YFKSEESDEPFARMSEDDDARLVEEVLTKLKTKD 722

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             VLR+RFGIG+    TLE++G+   VTRER+RQIEA A++KL  P
Sbjct: 723 AEVLRLRFGIGVLEALTLEQIGEILGVTRERVRQIEAAAMQKLSSP 768


>gi|296134902|ref|YP_003642144.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
 gi|295795024|gb|ADG29814.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
          Length = 351

 Score =  151 bits (382), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 135/230 (58%), Gaps = 8/230 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ MVE NLRLV+S+AK Y  RG    DLI+EGN+GL+ A EKF+   G++FSTYA WW
Sbjct: 111 ARQAMVEHNLRLVVSIAKAYVGRGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWW 170

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK--IKREPTPEEIAKKLAMPVE 561
           ++Q+I R++  Q  TIR+PVH+  ++++V+R  + +      + + + E++A  L    E
Sbjct: 171 IRQSIERALMQQVRTIRLPVHVIRELNQVLRARKHLEQAADYRGQTSDEDVAALLGRSTE 230

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LA 618
            V  +L + ++P SL+     +      D   D+NA+S  +   Q   RE    V   + 
Sbjct: 231 EVADLLALAEQPTSLDALRETQSGESYADQFADQNALSMEE---QTQTREVEALVDSWVG 287

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE  V+  RFG+      TLE + ++  +TRER+RQI+ +++ KLK
Sbjct: 288 ELAEREREVIEARFGLHGRELETLESLAQRLGLTRERVRQIQQESLLKLK 337


>gi|126695941|ref|YP_001090827.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126542984|gb|ABO17226.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 307

 Score =  151 bits (382), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 87/232 (37%), Positives = 146/232 (62%), Gaps = 9/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPEEIAKKLAMPVEG 562
           ++Q + R+++ QS TIRIPV++ +K+ K +R+A+    ++K   P+ +E+A+++ +  E 
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEKLTK-LRSAKSKLMQLKGIPPSTDELAEEMKITKEE 183

Query: 563 VRKVLKITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-- 617
           + ++L      I++    T     D S L D +   +   P++ A  A    +  ++L  
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKSDPSELVDILPS-DQTPPMELAELAERTASAWKLLDK 242

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 243 ANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|258648463|ref|ZP_05735932.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851219|gb|EEX71088.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 283

 Score =  151 bits (382), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 87/263 (33%), Positives = 148/263 (56%), Gaps = 4/263 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  IS E  I++ E    V + R+ +     A + +V ANLR V+SVAK+Y  +G+  +D
Sbjct: 23  LSEISREPRITVEEE---VELGRRAKNGDEAAVERLVRANLRFVVSVAKQYQGQGISLID 79

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL++AA +FD   G+KF +YA+WW++Q+I  +I ++S  IR+P +    I K+
Sbjct: 80  LINEGNLGLIQAAHRFDDTRGFKFISYAVWWIRQSILLAITEKSRLIRLPQNQMSSIQKI 139

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R   +     +R P+ EEI +++ +  E VR  L++  +P+S++ P+ +++   L + +
Sbjct: 140 LRFYNQYMQDYERPPSIEEICEQMQVTEERVRLALQLQNKPLSIDAPLTEDEARTLSERL 199

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S     ++   R    R+L  L P E  V+    G       +LEE+G +  ++
Sbjct: 200 RSDKGSSADGPLLKEAERWKVERMLNLLPPLERSVIEYYLGFK-GQGISLEEIGNRIGLS 258

Query: 653 RERIRQIEAKAIRKLKHPSRSKK 675
           RER+RQI+ KAI  L+    S K
Sbjct: 259 RERVRQIKVKAIMILRRHHESTK 281


>gi|318066969|emb|CBY89099.1| RNA polymerase sigma70 factor [Halomonas salina]
          Length = 366

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 123/397 (30%), Positives = 188/397 (47%), Gaps = 55/397 (13%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDATQD 80

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                R + DL +        GF    EG       D  +E         EG  +   + 
Sbjct: 81  EEAPGR-LSDLFS--------GFIDPDEGIPGVAEADVPEEP-----VVAEGASDEDDED 126

Query: 237 SKDDRSKVDSP-PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           ++D+      P PE A      + E  + +   + A   +   +    L  +AE++  + 
Sbjct: 127 AEDEDDSGGGPDPEEARARFEQIREQNESARQAIDA-NGRGSAQAQAELARLAELFSPI- 184

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                              K++ +   +LVG + ++       VEQ+    K +M     
Sbjct: 185 -------------------KLVPKHFERLVGQVRIS-------VEQIRAQEKAVMQ---- 214

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                +   + R  F++   G E    W+    DF                 +I+   + 
Sbjct: 215 --LCVKKAKVPRKTFIKAFPGNESRQDWLD---DFMAXXXXXXXXXXXXLKGEIQRSQRK 269

Query: 416 ISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I++E     +S+++ + +   +  G  +A  AKKEMVEA+LRLVIS+A+KY +RGL FLD
Sbjct: 270 IALEEEMVPLSVTDLKEVNRWLSIGRAKARRAKKEMVEAHLRLVISIAQKYPHRGLPFLD 329

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           L QEG+IGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 330 LFQEGHIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 366


>gi|303235620|ref|ZP_07322227.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
 gi|302484067|gb|EFL47055.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
          Length = 290

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 91/277 (32%), Positives = 151/277 (54%), Gaps = 24/277 (8%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    I K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGAISKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP------------IGDE 583
           +     K  R P+  E+A    +    +R+        +S++ P            +   
Sbjct: 145 SNEFIQKHNRRPSIHELADLTGIDEARIRQSQSADNHHMSIDAPFSDDDDNSMSDMLASG 204

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D S     ++ ++    L++ +Q  L++           RE R++   FGIG   +  LE
Sbjct: 205 DDSRTDKAVDFESMSDDLNAVLQNTLKD-----------RERRIVIECFGIGC-PEKGLE 252

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G +  +TRER+RQI  KAI K++    +K L  +L
Sbjct: 253 EIGTEMALTRERVRQIREKAIEKIRLSGNAKVLMKYL 289


>gi|213610106|ref|ZP_03369932.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 103

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 76/102 (74%), Positives = 83/102 (81%)

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTD
Sbjct: 1   IGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTD 60

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 61  HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 102


>gi|294338839|emb|CAZ87173.1| RNA polymerase sigma factor rpoS [Thiomonas sp. 3As]
          Length = 351

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 135/230 (58%), Gaps = 8/230 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ MVE NLRLV+S+AK Y  RG    DLI+EGN+GL+ A EKF+   G++FSTYA WW
Sbjct: 111 ARQAMVEHNLRLVVSIAKAYVGRGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWW 170

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK--IKREPTPEEIAKKLAMPVE 561
           ++Q+I R++  Q  TIR+PVH+  ++++V+R  + +      + + + E++A  L    E
Sbjct: 171 IRQSIERALMQQVRTIRLPVHVIRELNQVLRARKHLEQAADYRGQTSDEDVAALLGRSTE 230

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LA 618
            V  +L + ++P SL+     +      D   D+NA+S  +   Q   RE    V   + 
Sbjct: 231 EVTDLLALAEQPTSLDALRETQSGESYADQFADQNALSMEE---QTQTREVEALVDSWVG 287

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE  V+  RFG+      TLE + ++  +TRER+RQI+ +++ KLK
Sbjct: 288 ELAEREREVIEARFGLHGRELETLESLAQRLGLTRERVRQIQQESLLKLK 337


>gi|157412994|ref|YP_001483860.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157387569|gb|ABV50274.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 307

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 86/232 (37%), Positives = 146/232 (62%), Gaps = 9/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 65  AKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWW 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPEEIAKKLAMPVEG 562
           ++Q + ++++ QS TIRIPV++ +K+ K +R+A+    ++K   PT +E+++++ +  E 
Sbjct: 125 IRQGLNKALSTQSRTIRIPVNINEKLTK-LRSAKSKLMQLKGIPPTSDELSEEMKITKEE 183

Query: 563 VRKVLKITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-- 617
           + ++L      I++    T     D S L D +   +   P++ A  A    +  ++L  
Sbjct: 184 IEELLSCELRSITVSLQGTVKSKSDPSELVDILPS-DQTPPMELAELAERTASAWKLLDK 242

Query: 618 ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 243 ANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|3077740|dbj|BAA25788.1| SigC [Cyanidium caldarium]
          Length = 424

 Score =  151 bits (381), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 102/311 (32%), Positives = 167/311 (53%), Gaps = 57/311 (18%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--------- 467
           S   G+S  E R+ +   R+       A+  +V +NLRLV+++A +Y +R          
Sbjct: 123 STTVGVSEEEVRNEIERGRR-------ARARLVASNLRLVLAIANRYKSRAVVRSAWKSR 175

Query: 468 --------------LQ-----FL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
                         LQ     FL DLIQEG +GL++AAEKFD   G+KFSTYA WW++QA
Sbjct: 176 SKGGMDMPSHEKVRLQRQHNIFLGDLIQEGALGLIRAAEKFDPSKGFKFSTYATWWIRQA 235

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R +++ S TIR+P H+ + + ++ R   R+ + +KR PT EE+A+   M ++ ++K+ 
Sbjct: 236 IQRCVSEHSRTIRLPNHVTESLRQIYRMRARLQHVLKRPPTDEEVAEACNMTLKRLKKIT 295

Query: 568 KIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLD-------------SAIQAN-LRE 611
           +     + +SLE P  +E  S      + +   +PL               A++ N +RE
Sbjct: 296 QHAWKTQTLSLEGPPNNEAHS----LYKSQQGEAPLSIGSIIEATEETPEEALERNCMRE 351

Query: 612 TTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL +L  +E  +LR+R+GI  +   H+ EE+  +F +    IR IE++A+RKL+HP
Sbjct: 352 DVECVLRTLPFQEREILRLRYGISDDERPHSTEELSARFQLPVHTIRLIESRALRKLRHP 411

Query: 671 SRSKKLRSFLD 681
           S +  LR +++
Sbjct: 412 SLAAMLREYVN 422


>gi|318041996|ref|ZP_07973952.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 318

 Score =  150 bits (380), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 81/231 (35%), Positives = 145/231 (62%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 75  AKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 134

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ ++     R+  +   +P+ +++++ + +PV+ V
Sbjct: 135 IRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARLLQRHGSQPSAQQLSEAMDLPVQEV 194

Query: 564 RKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +    D + L D +  ++ + P++    A       ++L  +
Sbjct: 195 EDLLGCELRSVTVSLQGVVKSKSDPTELVDVLPSED-LPPMERCELAERNAAVWKLLDQS 253

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 254 NLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 304


>gi|116070855|ref|ZP_01468124.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116066260|gb|EAU72017.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 239

 Score =  150 bits (380), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 85/227 (37%), Positives = 141/227 (62%), Gaps = 7/227 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q 
Sbjct: 1   MITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQG 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R+++ QS TIRIPV++ +K+ K+     R+  +     T E++A+ + +P+  V  +L
Sbjct: 61  LNRALSTQSRTIRIPVNVNEKLTKLRAAKARVMQRNGLTATAEQLAEFMNLPLTEVEDLL 120

Query: 568 --KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTP 622
             ++    +SL+  +  + D S L D +  +  + P++ A  A    +   +L  A+LTP
Sbjct: 121 ACELRSVTVSLQGIVKSKSDPSELVDILPSEE-IPPMERAEIAERSASVWALLSKANLTP 179

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E +V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 180 KEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLR 226


>gi|225620189|ref|YP_002721446.1| DNA-directed RNA polymerase sigma-70/sigma-32 subunit RpoD
           [Brachyspira hyodysenteriae WA1]
 gi|225215008|gb|ACN83742.1| RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Brachyspira hyodysenteriae WA1]
          Length = 287

 Score =  150 bits (380), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 90/248 (36%), Positives = 145/248 (58%), Gaps = 6/248 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA   + +++ +NLR VI++AK+Y N GL   DLI EGN+GL+ AA++FD   G
Sbjct: 44  LKEGDAEA---RSKLIRSNLRFVITIAKQYKNSGLLLEDLISEGNLGLIIAADRFDPDKG 100

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y F +YA++W++Q+I R+I ++S  IR+P++    +  + R   +   K    P   E+A
Sbjct: 101 YHFISYAVYWIRQSILRAINEKSRLIRLPLNKAMDLVDLERAVHQYYYKSGYTPDVNELA 160

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
             L      +  ++ ++ E ISLE     D     L D IEDK + +  ++AI   L E 
Sbjct: 161 TILNKDPNDILHIMSMSTEHISLEGEYNYDGMKDRLIDTIEDKTSKNVEETAINKELMEE 220

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               + SL+  E++++  R+GI      TL+EVG+ F  T+ERIRQIE KA+RK+ H  +
Sbjct: 221 LKTAIESLSDIEKQIINARYGIDQER-KTLKEVGEMFSFTKERIRQIEKKALRKM-HSQK 278

Query: 673 SKKLRSFL 680
              L+ FL
Sbjct: 279 YSSLKDFL 286


>gi|194699556|gb|ACF83862.1| unknown [Zea mays]
 gi|223944677|gb|ACN26422.1| unknown [Zea mays]
          Length = 496

 Score =  150 bits (379), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 146/252 (57%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +N RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 249 ESFLAREMLAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDASRGFRISTY 308

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++AD S + R+P ++ +++   +R A+         PT E IA      
Sbjct: 309 VYWWIRQGVSRALADNSRSFRLPTYLHERL-VAIRGAKYALEDQGIAPTVENIAESLNIS 367

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KV+ + ++   SL    GD     L  +IED+N  + P     +  L+
Sbjct: 368 EKKVHNATEAVHKVISLDQQAFPSLNGLPGDT----LHSYIEDQNVANDPWHGFEERYLK 423

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E    ++ ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 424 EEVNSLINSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLVAMEKLKH 482

Query: 670 PSRSKKLRSFLD 681
            +R + L + L+
Sbjct: 483 AARREHLDALLE 494


>gi|307718430|ref|YP_003873962.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532155|gb|ADN01689.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 281

 Score =  150 bits (379), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 148/248 (59%), Gaps = 8/248 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +R+G+ EA   ++ ++ ANLRLV+ +A +++   +  LDLIQEGNIGL
Sbjct: 28  LSPEEERELGKRIRRGDPEA---RERLITANLRLVVKIALQFSVPDIPLLDLIQEGNIGL 84

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AAEKFD+    +FSTYA WW++QAI R++ ++   IR+P    D + K+ +  + +  
Sbjct: 85  IRAAEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRLPNRKEDVLRKIEKAKQLLEQ 144

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REP+ EEIA+ L M  E V +++ + +E +SLET I D  +  L D        SP 
Sbjct: 145 RLMREPSTEEIAELLGMETEEVEELINLGQEVVSLETQIND-GSMDLHDVC--PGGASPE 201

Query: 602 DSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +   +   RE T T +  +L  RE  V+  R+ +     +TL+ + +   ++ E +RQIE
Sbjct: 202 EEVCRKACREDTLTLIQRTLDSRESEVVLHRYAL-TGPRYTLKTLSEHLGISPETVRQIE 260

Query: 661 AKAIRKLK 668
            +A+RKL+
Sbjct: 261 IRALRKLR 268


>gi|94502401|ref|ZP_01308854.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
 gi|94451042|gb|EAT14014.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
          Length = 341

 Score =  150 bits (379), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 82/233 (35%), Positives = 142/233 (60%), Gaps = 1/233 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V+ANLR VIS+AK+Y N+GL   DLI EGN GL+K   +FD   G+K  +Y +WW++Q+
Sbjct: 108 LVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWWIRQS 167

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I ++I+D++  +R P +     +KV +T  ++  K+K  P+ + I+  L +  + V + L
Sbjct: 168 ILQAISDKARCVRYPTNKLAFYNKVNKTYSKLEQKLKMPPSIKYISDYLNVSEKDVEEAL 227

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             + +  SL+ P+G+ D S+L D I+   +     S  + +L++    +L +L+ RE ++
Sbjct: 228 INSIKHTSLDAPLGEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKILLETLSERESQI 287

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + + +G+G  +   LE++     +TRER RQIE  AI++LK  SR + L S+L
Sbjct: 288 ITLHYGLGCFS-MNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKEILLSYL 339


>gi|94499982|ref|ZP_01306517.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
 gi|94427840|gb|EAT12815.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
          Length = 368

 Score =  150 bits (379), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 74/224 (33%), Positives = 135/224 (60%), Gaps = 1/224 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V+ANLRL + VA++YT +G++  +LIQEG +GL+K AE+++   GY+F+TYA WW+
Sbjct: 139 RNQLVQANLRLAMHVARQYTGKGMELEELIQEGTLGLIKGAERYNINKGYRFTTYAYWWI 198

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAI  +++++   +RIP ++ D+I KV R          R P  +EI+  L M V+ +R
Sbjct: 199 QQAIKGALSEKRGIVRIPTNVTDRIVKVERCKYEFFKANGRYPNAKEISSILGMDVDHIR 258

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             L +T    S++ PI DE  + + + +  ++  +P     + +      +++  L  R+
Sbjct: 259 STLAVTNVGDSIDEPIYDEGLT-MQESMASESIATPSSQLDEEDGEAFLEKLIGELPKRQ 317

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R+  GIG+   +  +E+  Q  VT ER RQ+  ++IR+LK
Sbjct: 318 QFIVRLYHGIGIGQTYPFKEIAPQIGVTLERTRQLYHESIRQLK 361


>gi|161833810|ref|YP_001598006.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
 gi|152206300|gb|ABS30610.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
          Length = 351

 Score =  150 bits (379), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 82/233 (35%), Positives = 142/233 (60%), Gaps = 1/233 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V+ANLR VIS+AK+Y N+GL   DLI EGN GL+K   +FD   G+K  +Y +WW++Q+
Sbjct: 118 LVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWWIRQS 177

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I ++I+D++  +R P +     +KV +T  ++  K+K  P+ + I+  L +  + V + L
Sbjct: 178 ILQAISDKARCVRYPTNKLAFYNKVNKTYSKLEQKLKMPPSIKYISDYLNVSEKDVEEAL 237

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             + +  SL+ P+G+ D S+L D I+   +     S  + +L++    +L +L+ RE ++
Sbjct: 238 INSIKHTSLDAPLGEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKILLETLSERESQI 297

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + + +G+G  +   LE++     +TRER RQIE  AI++LK  SR + L S+L
Sbjct: 298 ITLHYGLGCFS-MNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKEILLSYL 349


>gi|317969234|ref|ZP_07970624.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 311

 Score =  150 bits (379), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 81/231 (35%), Positives = 142/231 (61%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW
Sbjct: 66  AKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q + R+++ QS TIRIPV++ +K+ ++     R+  +    P  +++A  L +P++ +
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARLMQRNGMAPNSQQLATALGLPLDEI 185

Query: 564 RKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--A 618
             +L  ++    +SL+  +    D + L D +  ++ + P++    A       ++L  +
Sbjct: 186 EDLLGCELRSVTVSLQGIVKSKSDPTELVDVLPSED-LPPMERCELAERNAAVWKLLDQS 244

Query: 619 SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 245 NLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 295


>gi|282859310|ref|ZP_06268422.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282587890|gb|EFB93083.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 290

 Score =  150 bits (379), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 93/280 (33%), Positives = 152/280 (54%), Gaps = 30/280 (10%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    I K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGAISKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--------------G 581
                 K  R P+  E+A+   +    +R+        +S++ P               G
Sbjct: 145 TNEFIQKHNRRPSIHELAEMTGIDEARIRQSQSADNHHMSIDAPFSDDDDNSMSDMLSSG 204

Query: 582 DEDTSHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D+  +  G DF   ++    L + +Q  L+E           RE +++   FGIG   + 
Sbjct: 205 DDSRTDKGVDF---ESMSDDLRAVLQNTLKE-----------REIKIVTECFGIGCQ-EK 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            LEE+G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 250 GLEEIGTEMALTRERVRQIREKAIEKIRESGNARVLMKYL 289


>gi|315185550|gb|EFU19319.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 281

 Score =  150 bits (379), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 89/248 (35%), Positives = 147/248 (59%), Gaps = 8/248 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +R+G+    +A++ ++ ANLRLV+ +A +++   +  LDLIQEGNIGL
Sbjct: 28  LSPEEERELGKRIRRGD---PVARERLITANLRLVVKIALQFSVPDIPLLDLIQEGNIGL 84

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+    +FSTYA WW++QAI R++ ++   IR+P    D + K+ +  R +  
Sbjct: 85  IRAVEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRLPNRKEDVLRKIEKARRLLEQ 144

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REP+ EEIA  L M  E V +++ + +E +SLET I D  +  L D        SP 
Sbjct: 145 RLMREPSTEEIADLLGMESEEVEELINLGQEVVSLETQIND-GSMDLHDVC--PGGASPE 201

Query: 602 DSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +   +   RE T T +  +L  RE  V+  R+ +     +TL+ + +Q  ++ E +RQIE
Sbjct: 202 EEVCRKACREDTLTLIQRTLDSRESEVVLHRYAL-TGPRYTLKTLSEQMGISPETVRQIE 260

Query: 661 AKAIRKLK 668
            +A+RKL+
Sbjct: 261 IRALRKLR 268


>gi|3893860|gb|AAC78467.1| RNA polymerase sigma factor 1 [Zea mays]
          Length = 398

 Score =  150 bits (379), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 88/252 (34%), Positives = 146/252 (57%), Gaps = 16/252 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +N RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 151 ESFLAREMLAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDASRGFRISTY 210

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++AD S + R+P ++ +++   +R A+         PT E IA      
Sbjct: 211 VYWWIRQGVSRALADNSRSFRLPTYLHERL-VAIRGAKYALEDQGIAPTVENIAESLNIS 269

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
            KK+    E V KV+ + ++   SL    GD     L  +IED+N  + P     +  L+
Sbjct: 270 EKKVHNATEAVHKVISLDQQAFPSLNGLPGDT----LHSYIEDQNVANDPWHGFEERYLK 325

Query: 611 ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E    ++ ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH
Sbjct: 326 EEVNSLINSTLNERERDIIRLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLVAMEKLKH 384

Query: 670 PSRSKKLRSFLD 681
            +R + L + L+
Sbjct: 385 AARREHLDALLE 396


>gi|3451022|gb|AAC32644.1| RNA polymerase sigma factor [Escherichia coli RS218]
          Length = 220

 Score =  150 bits (378), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 62/128 (48%), Positives = 101/128 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITK 571
            ++L++ +
Sbjct: 210 SRMLRLNE 217


>gi|320103352|ref|YP_004178943.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319750634|gb|ADV62394.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 287

 Score =  150 bits (378), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 92/262 (35%), Positives = 153/262 (58%), Gaps = 14/262 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K I+    +S +E R +   V +G+     A+  +V+ANLRLV+S+A+ Y  +GL   D
Sbjct: 20  LKQINETPLLSAAEERELGRRVSEGDY---FARDHLVKANLRLVVSIARGYNGKGLGLDD 76

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+E N+GL++A E FD+    +FSTYA +W+KQ+I R++ +    IR+P +M   + K 
Sbjct: 77  LIEERNLGLIRAVETFDYSQNIRFSTYASYWIKQSIRRAVMNNGKPIRLPAYMVTLLAKW 136

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMP---VEGVRKVLKITK-EPISLETPIGDEDTS-H 587
            +   +++ ++ R PTPEE+ K+L +    +  V K ++++K +P S     GDEDT   
Sbjct: 137 RQATTKLTARLGRPPTPEEVGKELRLSPRKIPIVSKAMEVSKLQPYS----EGDEDTGVP 192

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI--GMNTDHTLEEV 645
           L D + D N  SP +     + +     +L  L  RE  V+R+RFG+   +    TL ++
Sbjct: 193 LDDVLIDGNNRSPDELMAHDDDQARMKILLDELDERESAVIRLRFGLDESVPEAMTLRQI 252

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
           G++  +TRER+RQ+E  A+ KL
Sbjct: 253 GERLGLTRERVRQLEQAALTKL 274


>gi|294673146|ref|YP_003573762.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294474130|gb|ADE83519.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  150 bits (378), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 142/244 (58%), Gaps = 2/244 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RKG    + AK+++V ANLR V+SVAK+Y ++G+  +DLI EGN+GL+ AA+KFD   G
Sbjct: 43  IRKGGRTGAKAKEKLVNANLRFVVSVAKQYQHQGIPLIDLISEGNVGLITAADKFDETRG 102

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I ++IAD S  +R P       +K+         K +R P+ EE++
Sbjct: 103 FKFISYAIWWIRQSILQAIADYSGMVRRPQSQIAISNKIKNATNAFMLKNQRNPSAEELS 162

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + +++ +E + K ++      S++ PI D+DT+ + D I      +        ++    
Sbjct: 163 EIISLEIEKIEKAIQSEAHVASIDAPISDDDTTTMADSIASTAEYASDRKVDYESMCSDV 222

Query: 614 TRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             VL A L+ RE  ++   FGIG   +  L+++G    ++RER+RQI  + + K++  + 
Sbjct: 223 MLVLGAVLSERERAIVVQSFGIGC-PERGLDDIGSSMGLSRERVRQIRERGLDKIRKSNM 281

Query: 673 SKKL 676
           S  L
Sbjct: 282 SYIL 285


>gi|262038022|ref|ZP_06011434.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747975|gb|EEY35402.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 258

 Score =  150 bits (378), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 86/221 (38%), Positives = 130/221 (58%), Gaps = 7/221 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ +NLRLVIS AKK    GL  +DLI EGNIGL+KA  KFD+  G++FSTYA+WW
Sbjct: 42  ARQLLILSNLRLVISTAKKLLGNGLPLIDLISEGNIGLIKAINKFDYEKGHRFSTYAVWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I ++I +    IRIP +  +++ KV +       K    P  E IAK++ +    V
Sbjct: 102 IKQSIKKAIINTGRDIRIPSYKYEQLSKVNKVITDYVAKYGESPPTEYIAKEVDLKESKV 161

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLT 621
             +L   ++ ISL   IG  D  +L D + + + V    +     + +RE    +   LT
Sbjct: 162 ILLLNEFQDVISLNETIG--DNIYLEDIVGNTDDVEEKIIKEDQLSEMRELLENI---LT 216

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            RE  +L +R+G+  N  HTL+E+G +  +TRER+RQIE K
Sbjct: 217 DREREILELRYGLYNNKIHTLKEIGAKLNITRERVRQIEKK 257


>gi|307565781|ref|ZP_07628247.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
 gi|307345508|gb|EFN90879.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
          Length = 290

 Score =  150 bits (378), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 154/269 (57%), Gaps = 8/269 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMITVDEEIELAQEIHKGGLKGERAKEKLIKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    I K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGAISKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--- 592
                 K  R P+  E+A+   +    +R+        +S++ P  D+D + + D +   
Sbjct: 145 TNEFIQKHNRRPSIHELAEITGIDEARIRQSQSADNHHMSIDAPFSDDDDNSMSDMLSSG 204

Query: 593 EDKNAVSPLD-SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           ED      +D  ++  +LR        +L  RE +++   FGIG   +  LEE+G +  +
Sbjct: 205 EDSRTDKGVDFESMSDDLRAVLQN---TLKEREIKIVTECFGIGCQ-EKGLEEIGTEMAL 260

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQI  KAI K++    ++ L  +L
Sbjct: 261 TRERVRQIREKAIEKIRESGNARVLMKYL 289


>gi|4218586|emb|CAA10725.1| chloroplast sigma factor [Triticum aestivum]
          Length = 461

 Score =  149 bits (377), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 145/251 (57%), Gaps = 16/251 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E+ +A++ +  +N+RLVIS+A+KY   G++  DLIQ G IGL++  EKFD   G++ STY
Sbjct: 214 ESFLAREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTY 273

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++AD S T R+P ++ +++   +R A+         PT + IAK L + 
Sbjct: 274 VYWWIRQGVSRALADNSKTFRLPTYLHERL-IAIRGAKYALEDQGVSPTTQNIAKLLNIS 332

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLR 610
                   E V K L + ++   SL    GD     L  +IED+N  + P     +  L+
Sbjct: 333 EKKVHNATEAVNKALSLDQQAFPSLNGLPGDT----LHSYIEDQNVANDPWHGFEEWYLK 388

Query: 611 ETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   ++L S LT RE  ++++  GIG    HT E++ +QF ++RER+RQ+   A+ KLK 
Sbjct: 389 EEVNKLLNSNLTERERDIIQLYHGIGKQC-HTWEDISRQFGLSRERVRQVGLIAMEKLKQ 447

Query: 670 PSRSKKLRSFL 680
            +R KKL + L
Sbjct: 448 RARRKKLDALL 458


>gi|293977922|ref|YP_003543352.1| sigma-70 family RNA polymerase sigma factor [Candidatus Sulcia
           muelleri DMIN]
 gi|292667853|gb|ADE35488.1| RNA polymerase sigma factor, sigma-70 family [Candidatus Sulcia
           muelleri DMIN]
          Length = 342

 Score =  149 bits (377), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 82/233 (35%), Positives = 142/233 (60%), Gaps = 1/233 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V+ANLR VIS+AK+Y N+GL   DLI EGN GL+K   +FD   G+K  +Y +WW++Q+
Sbjct: 109 LVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWWIRQS 168

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I ++I+D++  +R P +     +KV +T  ++  K+K  P+ + I+  L +  + V + L
Sbjct: 169 ILQAISDKARCVRYPTNKLAFYNKVNKTYSKLEQKLKMPPSIKYISDYLNVSEKDVEEAL 228

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             + +  SL+ P+G+ D S+L D I+   +     S  + +L++    +L +L+ RE ++
Sbjct: 229 INSIKHTSLDAPLGEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKILLETLSERESQI 288

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + + +G+G  +   LE++     +TRER RQIE  AI++LK  SR + L S+L
Sbjct: 289 ITLHYGLGCFS-MNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKEILLSYL 340


>gi|3249723|gb|AAC26664.1| RNA polymerase sigma-like factor [Micromonospora olivasterospora]
          Length = 162

 Score =  149 bits (377), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 80/162 (49%), Positives = 113/162 (69%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R     + REPTPEE+AK++ +
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQREFFQDLGREPTPEELAKEMDI 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   + L++   +VL 
Sbjct: 61  TPEKVLEIQQYAREPISLDQTIGDEGDSSLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQ 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE
Sbjct: 121 TLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIE 162


>gi|6010720|gb|AAF01226.1|AF184095_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 254

 Score =  149 bits (377), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 64/135 (47%), Positives = 105/135 (77%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 149

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V
Sbjct: 150 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDV 209

Query: 564 RKVLKITKEPISLET 578
            ++L++ +   S++T
Sbjct: 210 SRMLRLNERITSVDT 224


>gi|116075407|ref|ZP_01472667.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116067604|gb|EAU73358.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 310

 Score =  149 bits (376), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 89/244 (36%), Positives = 146/244 (59%), Gaps = 17/244 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KGE     AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G
Sbjct: 60  IKKGE----KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRG 115

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +  +  TP ++A
Sbjct: 116 HRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNGQAATPAQLA 175

Query: 554 KKLAMPVEGVRKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           + + +    V  +L  ++    +SL+  +    D S L D +  +  + P++   QA + 
Sbjct: 176 EAMQISRAEVDDLLGCELRSVTVSLQGIVKSKSDPSELVDVLPSEE-LPPME---QAEID 231

Query: 611 ETTTRVL-----ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           E T         ++LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+
Sbjct: 232 ERTASAWTLLDRSNLTPKERTVVMLRFGLDGSNEWRTLAEVARHMGCSREYCRQVVQRAL 291

Query: 665 RKLK 668
           RKL+
Sbjct: 292 RKLR 295


>gi|325269444|ref|ZP_08136061.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325855020|ref|ZP_08171736.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|327313288|ref|YP_004328725.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
 gi|324988365|gb|EGC20331.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325483998|gb|EGC86938.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|326946004|gb|AEA21889.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
          Length = 290

 Score =  149 bits (376), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 93/280 (33%), Positives = 151/280 (53%), Gaps = 30/280 (10%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    I K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGAISKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--------------G 581
                 K  R P+  E+A+   +    +R+        +S++ P               G
Sbjct: 145 TNEFVQKHNRRPSIHELAELTGIDEARIRQSQSADNHHMSIDAPFSDDDDNSMSDMLSSG 204

Query: 582 DEDTSHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D+  +  G DF         +   ++A L+ T       L  RE +++   FGIG   + 
Sbjct: 205 DDSRTDRGVDF-------ESMSDDLRAVLQNT-------LKDREIKIVTECFGIGCQ-EK 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            LEE+G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 250 GLEEIGTEMGLTRERVRQIREKAIEKIRESGNARVLMKYL 289


>gi|89094249|ref|ZP_01167191.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081504|gb|EAR60734.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 411

 Score =  149 bits (376), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 135/228 (59%), Gaps = 6/228 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + +++E NLRLV  VA ++ + G+   DLIQEGNIGL+KAA++F++  GY+FSTYA W +
Sbjct: 176 RSKLIEKNLRLVYVVALRFKSSGVSLDDLIQEGNIGLLKAADRFNFVHGYRFSTYAFWCI 235

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  +  ++     TI  P ++++K+  + R + R  N+  R P   E+++  ++P   + 
Sbjct: 236 QNVLKTALQKNYHTISRPSYLQEKLSVIKRESVRFLNQYGRYPGTTELSELTSIPEAMLE 295

Query: 565 KVLKITKEPISLETPIG----DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           K+     EP+SL  P+      ED + +   +ED NA++       A  R    R+   L
Sbjct: 296 KIKSFPAEPLSLSQPVSRSQEGEDLT-VESTLED-NAMAAEKETDIALKRRMLERMSLRL 353

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE +VL+MRFGI  +T+HTLEE+  Q  V+ ER+RQ++  A+ KL+
Sbjct: 354 NEREYKVLKMRFGIDCHTEHTLEEISHQLNVSVERVRQLQKIALEKLQ 401


>gi|260590675|ref|ZP_05856133.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260537416|gb|EEX20033.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 290

 Score =  149 bits (376), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 93/280 (33%), Positives = 151/280 (53%), Gaps = 30/280 (10%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    I K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGAISKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--------------G 581
                 K  R P+  E+A+   +    +R+        +S++ P               G
Sbjct: 145 TNEFVQKHNRRPSIHELAELTGIEESRIRQSQSADNHHMSIDAPFSDDDDNSMSDMLSSG 204

Query: 582 DEDTSHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D+  +  G DF         +   ++A L+ T       L  RE +++   FGIG   + 
Sbjct: 205 DDSRTDKGVDF-------ESMSDDLRAVLQNT-------LKDREIKIVTECFGIGCQ-EK 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            LEE+G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 250 GLEEIGTEMGLTRERVRQIREKAIEKIRESGNARVLMKYL 289


>gi|198283622|ref|YP_002219943.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667581|ref|YP_002426250.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248143|gb|ACH83736.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519794|gb|ACK80380.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 316

 Score =  149 bits (375), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 131/227 (57%), Gaps = 1/227 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +VE NLRLV+ +A++Y  +  L  LDLI+EGN+GL++AAE FD   G++FSTYA W
Sbjct: 85  ARNRLVECNLRLVVRIARRYQRQHTLPLLDLIEEGNLGLIRAAELFDPTRGFRFSTYATW 144

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q I R I  QS  +R+P H+   +  V+R++R+++  ++ +P  E++A+ +   V  
Sbjct: 145 WIRQNIDRGIMQQSRVVRLPTHIIKNLSAVLRSSRQIAQTMQGDPRVEDVAQVMGKSVAY 204

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V   L+  +  +SL+ P   E +  L   + D +      S  + +L+    R L  L  
Sbjct: 205 VEDCLQQDRRVVSLDAPSRWEGSPSLAQTLVDADQADLGASLEEQDLQRQIHRALLGLDV 264

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R   +L  RFGI      +L  +GK+  V+ ER+RQ++ +A+  L+ 
Sbjct: 265 RHRTILIRRFGIDGQDGASLSAIGKELGVSHERVRQLQEEALDLLRQ 311


>gi|255532556|ref|YP_003092928.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255345540|gb|ACU04866.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 289

 Score =  149 bits (375), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 141/242 (58%), Gaps = 4/242 (1%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR +VS +R G+ EA      +++ NLR V+SVAKKY ++GL+  DLI EGNIGL+KAA
Sbjct: 36  EFR-LVSAIRNGDQEAL---HRLIKGNLRFVVSVAKKYQDKGLKLGDLINEGNIGLIKAA 91

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            +FD   G+KF T+A+WWV+QAI ++IA+Q   IR+P +    I ++ +   ++  +++R
Sbjct: 92  HRFDATRGFKFITFAVWWVRQAILQAIAEQRRLIRLPGNQLLGISRLNQAVLKLEQQLER 151

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            PT EE+A      V+ V           SL+  I +E  S L + I D+         +
Sbjct: 152 MPTVEELAVYTGFTVDKVMDYTANAAFTYSLDDVIKEESGSTLMEVIADEATHQTDHFTL 211

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A+L     R L  L+ RE++++ + +G+       +E++ K   +++ERIRQ++ KA +
Sbjct: 212 AASLSTDLNRALDILSKREQKIIILFYGLNGYPQTAIEDMQKILKLSKERIRQLKDKAHK 271

Query: 666 KL 667
            L
Sbjct: 272 TL 273


>gi|149908225|ref|ZP_01896889.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
 gi|149808767|gb|EDM68700.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
          Length = 284

 Score =  148 bits (374), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 87/228 (38%), Positives = 134/228 (58%), Gaps = 4/228 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  M+EANLRLVISVAK+Y    +  +D+IQEGN GL++A EKFD   G++FSTYA+WW
Sbjct: 43  AKNRMIEANLRLVISVAKRYQYSVIPLVDIIQEGNTGLIRAVEKFDPNKGFRFSTYAVWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHK-VVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I RSI +   TIRIP+H+  K+HK + + A+ +   +  +     IAK L   V+ 
Sbjct: 103 IKNNIERSIMNSDRTIRIPIHV-GKMHKSIAKVAKELGLDVGSDNDLVVIAKVLETDVDE 161

Query: 563 VRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           V  VL      +SL+  I   +E  + L D IED++  +P       + R+    +L +L
Sbjct: 162 VMDVLSYYFSELSLDKGIVTDNESVTTLVDIIEDQSIRTPSAEIEGGSTRDYLLALLENL 221

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              E +V+ +RFG+      +L  +G++  ++RE++R I    +R+LK
Sbjct: 222 PAYERQVVELRFGLTGEEPLSLSRIGERLSMSREKVRIIIRTTLRRLK 269


>gi|168704590|ref|ZP_02736867.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 278

 Score =  148 bits (374), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 87/257 (33%), Positives = 152/257 (59%), Gaps = 7/257 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I+    ++  + + +   + +G+ EA   + +MV ANLRLV+++A+ YT +GL   D
Sbjct: 20  LREINETALLTADQEKSLARAIAQGDTEA---RDQMVRANLRLVVNIARGYTGKGLALQD 76

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A E FD  +  +FSTYA +W+KQ+I R++ + + TIRIP +M + + K 
Sbjct: 77  LIEEGNLGLLRAVEGFDPTMNTRFSTYASYWIKQSIKRALVNTAKTIRIPAYMVELLAKW 136

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGD 590
            R   ++S+++ R PT EE+ K L +P + +  + K  +  +    P  D+      + +
Sbjct: 137 RRATNKLSDELGRPPTHEEVGKLLGLPKKKLAIIKKAIR--VYNAAPQADQGDQGWSIEE 194

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            + D  A +P    ++ +  +    +L  +  RE  VLRMRFG+      TL+E+G+   
Sbjct: 195 MLMDNRAKTPDTEMVETDDLKQVLILLEKMDQREATVLRMRFGLNDEEPKTLKEIGECLG 254

Query: 651 VTRERIRQIEAKAIRKL 667
           +TRER+RQIE +A+ KL
Sbjct: 255 LTRERVRQIEGEALAKL 271


>gi|254282580|ref|ZP_04957548.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
 gi|219678783|gb|EED35132.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
          Length = 429

 Score =  148 bits (373), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 136/244 (55%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  +  +R    + + A+  +V  NLRLV S+A +Y  RG+ +LDL+QEG +GL++AAEK
Sbjct: 172 RDSLKALRSALNDYTKARDALVMHNLRLVYSIAARYKGRGVNYLDLVQEGTLGLIRAAEK 231

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GY+FSTY   W+ Q++ R + D    IR P H+++++ ++ R     + +   EP
Sbjct: 232 FEFEKGYRFSTYCFNWITQSVRRYVGDVGSLIRFPTHVQEQMGRLYREKALETARTGIEP 291

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             E +AK L M ++  R++L++    +SL+ P  D+D   + D +         D+A Q 
Sbjct: 292 DEETLAKNLGMDLDKTRELLQLRNLGVSLDAPRFDDDEGTMVDSMTGDTFGDTEDTAEQD 351

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L    T  + +L P E  V+  R+G+      +  E+  +  V+RE +RQ+E   ++KL
Sbjct: 352 SLNRFLTNAIDTLEPAERDVVTARWGLHSGPPLSRAEIADKLGVSREWVRQLERSGLKKL 411

Query: 668 KHPS 671
           +  S
Sbjct: 412 RGQS 415


>gi|3249721|gb|AAC26663.1| RNA polymerase sigma-like factor [Micromonospora echinospora]
          Length = 161

 Score =  148 bits (373), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 78/162 (48%), Positives = 109/162 (67%), Gaps = 1/162 (0%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDI 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D A+  +L +   + + 
Sbjct: 61  TPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVD-AVSFSLLQDQLQQVL 119

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +P   RV  MRFG+      TL+E+G+ + VTRERIRQIE
Sbjct: 120 QGSPSVRRVWSMRFGLTDGQPRTLDEIGQVYGVTRERIRQIE 161


>gi|300870272|ref|YP_003785143.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
 gi|300687971|gb|ADK30642.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
          Length = 284

 Score =  148 bits (373), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 143/249 (57%), Gaps = 6/249 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG+ +A   + +++ +NLR VIS+AK+Y N GL   DLI EGN+GL+ A ++FD   G
Sbjct: 41  LKKGDSQA---RAKLIRSNLRFVISIAKQYKNSGLLLEDLIGEGNLGLIIATDRFDPDKG 97

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y F +YA++W++Q+I R+I ++S  IR+P++    +  + R   +   K    P  E++A
Sbjct: 98  YHFISYAVYWIRQSILRAINEKSRLIRLPLNKAMDLVDLERAVHQCYYKTGHMPDVEDLA 157

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
             L      +R ++ +  E +SLE     D     L D +EDKN+ +  D      L E 
Sbjct: 158 AILKKEPREIRNIMSMNNEYVSLEKDFNMDGVKDRLADVVEDKNSKTVEDILSDKELTEE 217

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               +  L+  E+ ++  R+G+      TL+EVG+++  T+ERIRQIE KA++K+ H  R
Sbjct: 218 LKIAMEELSDIEKEIINARYGLDQEK-KTLKEVGEKYSFTKERIRQIEKKALKKM-HSKR 275

Query: 673 SKKLRSFLD 681
              L+ FL+
Sbjct: 276 YSSLKDFLN 284


>gi|288801981|ref|ZP_06407422.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302347072|ref|YP_003815370.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|288335416|gb|EFC73850.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302150546|gb|ADK96807.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 290

 Score =  148 bits (373), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 92/280 (32%), Positives = 151/280 (53%), Gaps = 30/280 (10%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++GL   DLI 
Sbjct: 25  IGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQGLSLTDLID 84

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    I K+ + 
Sbjct: 85  EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGAISKINQV 144

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--------------G 581
                 +  R P+  E+A+   +    +R+        +S++ P               G
Sbjct: 145 TNEFVQQHNRRPSIHELAELTGIDEARIRQSQSADNHHMSIDAPFSDDDDNSMSDMLSSG 204

Query: 582 DEDTSHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D+  +  G DF         +   ++A L+ T       L  RE +++   FGIG   + 
Sbjct: 205 DDSRTDRGVDF-------ESMSDDLRAVLQNT-------LKDREIKIVTECFGIGCQ-EK 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            LEE+G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 250 GLEEIGTEMGLTRERVRQIREKAIEKIRESGNARVLMKYL 289


>gi|318066931|emb|CBY89080.1| RNA polymerase sigma70 factor [Halomonas campaniensis]
          Length = 368

 Score =  147 bits (372), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 84/199 (42%), Positives = 120/199 (60%), Gaps = 18/199 (9%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L +L   + L     + LV Q+    +++   E  +++L  +   I R  F++   G E
Sbjct: 179 RLAELFSPIKLVPKHFERLVNQVRISVEQVRAQEKAVMQLCVKKARIPRKTFIKAFPGSE 238

Query: 379 LDPHWVS-YAKDFPEGEWKNFVACEVDSILKIRNEI----KSISVE---TGISISEFRHI 430
            DP W++ +A D P+           D +  +R +I    + I+ E     + ++E + +
Sbjct: 239 SDPEWLTRFAADHPK---------YADRLEPLRADIARAQRKIAFEEEMVRLPVTEIKEV 289

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 290 NRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 349

Query: 491 CLGYKFSTYAMWWVKQAIT 509
             GYKFSTYA WW++QAIT
Sbjct: 350 RRGYKFSTYATWWIRQAIT 368


>gi|225849737|ref|YP_002729971.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
 gi|225645950|gb|ACO04136.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
          Length = 285

 Score =  147 bits (372), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 85/274 (31%), Positives = 155/274 (56%), Gaps = 9/274 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           + SIS    +S  E + I    ++G+ EA    ++++++NLR V++VAK YT  G+ F +
Sbjct: 14  LNSISKIPLLSPEEEKEIAKKAKEGDKEAL---EKLIKSNLRFVVNVAKNYTGYGIPFQE 70

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  GNIGL++AA++FD   G +F +YA+WW+KQ+I ++I  Q   I+IP   ++   K+
Sbjct: 71  LISAGNIGLIEAAKRFDPERGVRFISYAIWWIKQSILQTIQSQKDIIKIPQKTQNLSMKI 130

Query: 533 VRTARRMSNKIKREPTPEEIAKKLA------MPVEGVRKVLKITKEPISLETPIGDEDTS 586
                 +  ++ REP   EI + L       +  E +   L I +  +SL+TP+  ++ +
Sbjct: 131 DTAYLELKERLNREPKYSEIKEYLKEHENIDIDEETIENYLLIKRHSVSLDTPVDMDEGT 190

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              D I   +     ++ ++ ++ +    +L+ L+ RE  ++  RFG+      TL E+G
Sbjct: 191 FFIDLISKHSTKDIEENIVRESIEKEIEYILSHLSERERFIIVNRFGLNGEEPKTLREIG 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           K+  ++RER+RQIE +A++K++  +  K L+  L
Sbjct: 251 KELGISRERVRQIEIRALKKIRALATKKHLKDLL 284


>gi|115475493|ref|NP_001061343.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|30698490|dbj|BAC76602.1| Sig6 [Oryza sativa Japonica Group]
 gi|40253642|dbj|BAD05586.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|40253689|dbj|BAD05631.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|113623312|dbj|BAF23257.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|215712228|dbj|BAG94355.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 572

 Score =  147 bits (372), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 94/286 (32%), Positives = 157/286 (54%), Gaps = 14/286 (4%)

Query: 402 EVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASI-----AKKEMVEANLR 454
           ++  ++KI    + + V+ G   +++E+   V M  K E ++SI      +++M  +N R
Sbjct: 285 KIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSK-ELQSSIRTGRRCREKMARSNFR 343

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LVI VA+KY   GL   DL+Q+G  GLMK  EKF+   G +F TYA WW++Q+I +SI  
Sbjct: 344 LVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFK 403

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKITKEP 573
            S  IR+P  +   + KV +   RM   ++ E PT   +A++  + +E + K+   T++P
Sbjct: 404 NSRLIRLPESVYALLRKVGKA--RMECIMEGEQPTNANVARRAGITIEKLAKLRAKTRKP 461

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++  +  ++     +  ED N   P  S  +  +R+     L  L+PRE+ ++  RFG
Sbjct: 462 RSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFG 521

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           I      TL  +G  F +++ERIRQ++ +A+ KLK   RS  L+ F
Sbjct: 522 IHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK---RSASLQGF 564


>gi|3077738|dbj|BAA25787.1| SigB [Cyanidium caldarium]
          Length = 424

 Score =  147 bits (372), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 103/311 (33%), Positives = 165/311 (53%), Gaps = 57/311 (18%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--------- 467
           S   G+S  E R  +   R+       A++ +V +NLRLV+++A +Y  R          
Sbjct: 123 STTVGVSEEEVRKRIERGRR-------ARERLVASNLRLVLAIANRYKLRAVVCSAWKSR 175

Query: 468 --------------LQ-----FL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
                         LQ     FL DLIQEG +GL++AAEKFD   G+KFSTYA WW++QA
Sbjct: 176 SKGGMDMPSHEKVRLQRQHNIFLGDLIQEGALGLIRAAEKFDPSKGFKFSTYATWWIRQA 235

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R +++ S TIR+P H+ + + ++ R   R+ + +KR PT EE+A+   M ++ ++K+ 
Sbjct: 236 IQRCVSEHSRTIRLPNHVTESLRQIYRMRARLQHVLKRPPTDEEVAEACNMTLKRLKKIT 295

Query: 568 KITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLD-------------SAIQAN-LRE 611
           +   E   +SLE P   E  S      + +   +PL               A++ N +RE
Sbjct: 296 QHAWETQTLSLEGPPNSEAHS----LYKSQQGEAPLSIGSIIEATEETPEEALERNCMRE 351

Query: 612 TTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL +L  +E  +LR+R+GI  +   H+ EE+  +F +    IR IE++A+RKL+HP
Sbjct: 352 DVECVLRTLPFQEREILRLRYGISDDERPHSTEELSARFQLPVHTIRLIESRALRKLRHP 411

Query: 671 SRSKKLRSFLD 681
           S +  LR +++
Sbjct: 412 SLAAMLREYVN 422


>gi|218200736|gb|EEC83163.1| hypothetical protein OsI_28384 [Oryza sativa Indica Group]
          Length = 537

 Score =  147 bits (372), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 95/290 (32%), Positives = 157/290 (54%), Gaps = 14/290 (4%)

Query: 398 FVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASI-----AKKEMVE 450
           F+      ++KI    + + V+ G   +++E+   V M  K E ++SI      +++M  
Sbjct: 246 FIFRTAQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSK-ELQSSIRTGRRCREKMAR 304

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +N RLVI VA+KY   GL   DL+Q+G  GLMK  EKF+   G +F TYA WW++Q+I +
Sbjct: 305 SNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKK 364

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKI 569
           SI   S  IR+P  +   + KV +   RM   ++ E PT   +A++  + +E + K+   
Sbjct: 365 SIFKNSRLIRLPESVYALLRKVGKA--RMECIMEGEQPTNANVARRAGITIEKLAKLRAK 422

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T++P S++  +  ++     +  ED N   P  S  +  +R+     L  L+PRE+ ++ 
Sbjct: 423 TRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKEIIE 482

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            RFGI      TL  +G  F +++ERIRQ++ +A+ KLK   RS  L+ F
Sbjct: 483 HRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK---RSASLQGF 529


>gi|326801849|ref|YP_004319668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326552613|gb|ADZ80998.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 285

 Score =  147 bits (371), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 83/243 (34%), Positives = 141/243 (58%), Gaps = 4/243 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A + + +ANLR VISVAK+Y ++GL   DLI EGN GL+KAA +FD   G
Sbjct: 43  IREGD---QLALERLTKANLRFVISVAKQYQHQGLVLEDLINEGNAGLVKAARRFDETKG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KF +YA+WW++Q+I  +I+ QS  +R+P +    + K+ R+   M  +++REP+ EE+A
Sbjct: 100 FKFISYAVWWIRQSIMSAISIQSRAVRLPGNQISNLIKLRRSQAEMEQRLEREPSVEELA 159

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L    + +       +  +S++ P    +   L D +   +  +     IQ +L    
Sbjct: 160 VELGTTTDRIIASFTNAERQLSIDAPSVFSEEERLLDSLASSDPATD-QQLIQDSLFLRI 218

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL  L+ RE ++L M +G+  +   TL+E+  Q  +T ERIRQ++ KA+  +K+ S  
Sbjct: 219 DLVLKKLSSRERQILTMFYGLSNSEPQTLDEIAYQLKLTPERIRQLKTKALLHIKNSSSG 278

Query: 674 KKL 676
           + L
Sbjct: 279 RDL 281


>gi|168700059|ref|ZP_02732336.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 272

 Score =  147 bits (371), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 90/250 (36%), Positives = 145/250 (58%), Gaps = 11/250 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E R + + V  G+ +A   +  MV ANLRLV+++A+ YT +GL   DL+ EGN+GL
Sbjct: 24  LSAAEERDLGARVLTGDPQA---RDRMVRANLRLVVNIARGYTGKGLALDDLVSEGNMGL 80

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E F+  +  +FSTYA +W+KQ+I R+I + + TIRIP +M + + K  R   ++S+
Sbjct: 81  LRAVEGFEPSMNTRFSTYASYWIKQSIKRAIVNTAKTIRIPAYMAELLTKWRRATNQLSD 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE----DKNA 597
           ++ R PT +EIAK L +  + +  + K  +    +       D S  G  IE    D   
Sbjct: 141 ELGRPPTHDEIAKFLGLSKKKLAIIKKAIR----VANAGTQSDQSDAGWSIEETLMDSRG 196

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            +P     +++  +    +L  +  RE  VLRMRFG+      TL+E+G+   +TRER+R
Sbjct: 197 DAPDTELGKSDDLKQVLHLLDRMDQREATVLRMRFGLNDEEPRTLKEIGECLGLTRERVR 256

Query: 658 QIEAKAIRKL 667
           QIE +A+ KL
Sbjct: 257 QIENEALAKL 266


>gi|318066919|emb|CBY89074.1| RNA polymerase sigma70 factor [Halomonas alimentaria]
          Length = 362

 Score =  147 bits (370), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 81/192 (42%), Positives = 118/192 (61%), Gaps = 4/192 (2%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L +L   + L     + LV Q+    +++   E  +++L  +   I R  F++   G E
Sbjct: 173 RLAELFSPIKLVPKHFERLVNQVRISVEQVRAQEKAVMQLCVKKARIPRKTFIKAFPGSE 232

Query: 379 LDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            DP W+ ++A + P+  + + +A     I + + +I        + + E + +   +  G
Sbjct: 233 SDPEWLDAFAGEHPK--YADRLAPLRTDIQRAQRKIAFEEAMVRLPVQEIKEVNRRLSIG 290

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 291 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 350

Query: 498 TYAMWWVKQAIT 509
           TYA WW++QAIT
Sbjct: 351 TYATWWIRQAIT 362



 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILDAYDATQD 80


>gi|125602683|gb|EAZ42008.1| hypothetical protein OsJ_26557 [Oryza sativa Japonica Group]
          Length = 497

 Score =  146 bits (369), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 95/290 (32%), Positives = 157/290 (54%), Gaps = 14/290 (4%)

Query: 398 FVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASI-----AKKEMVE 450
           F+      ++KI    + + V+ G   +++E+   V M  K E ++SI      +++M  
Sbjct: 206 FIFRTAQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSK-ELQSSIRTGRRCREKMAR 264

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +N RLVI VA+KY   GL   DL+Q+G  GLMK  EKF+   G +F TYA WW++Q+I +
Sbjct: 265 SNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKK 324

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKI 569
           SI   S  IR+P  +   + KV +   RM   ++ E PT   +A++  + +E + K+   
Sbjct: 325 SIFKNSRLIRLPESVYALLRKVGKA--RMECIMEGEQPTNANVARRAGITIEKLAKLRAK 382

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T++P S++  +  ++     +  ED N   P  S  +  +R+     L  L+PRE+ ++ 
Sbjct: 383 TRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKEIIE 442

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            RFGI      TL  +G  F +++ERIRQ++ +A+ KLK   RS  L+ F
Sbjct: 443 HRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK---RSASLQGF 489


>gi|258592807|emb|CBE69116.1| RNA polymerase sigma factor RpoS [NC10 bacterium 'Dutch sediment']
          Length = 286

 Score =  146 bits (369), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 138/239 (57%), Gaps = 3/239 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++VEANLR V+ VA +Y   GL   DLI EGNIGL++AA ++      KF TYA+WW
Sbjct: 50  ALKQLVEANLRFVVKVALRYRGCGLSLPDLINEGNIGLLEAARRYSPDYNVKFITYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI +++A     +R+P+       ++      +S +++ EPT  E+ ++L +    +
Sbjct: 110 IRQAIMQALAISGGAVRLPLRKARLASQLDDVRADLSQQLQAEPTDSEVTEELDLSASDL 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD-SAIQANLRETTTRVLASLTP 622
              L    +   L   IG E    +G  + +   + P D   I+ +LRE   R+L SL  
Sbjct: 170 EGALHRAGQLAFLSDEIGLE--QRIGMELYESKQLPPADYELIRRSLREEVERMLRSLND 227

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE  ++ +RFG+G     TL+EVGK+  ++RER+RQIE +A +KL   ++S+ L+ +L+
Sbjct: 228 RERLIVELRFGLGKEEAMTLKEVGKRLKLSRERVRQIEERAKQKLCVWAKSRHLKDYLN 286


>gi|294856621|gb|ADF45248.1| RNA polymerase sigma S factor [Escherichia sp. B827]
 gi|294856623|gb|ADF45249.1| RNA polymerase sigma S factor [Escherichia sp. E1492]
 gi|294856625|gb|ADF45250.1| RNA polymerase sigma S factor [Escherichia sp. E807]
 gi|294856627|gb|ADF45251.1| RNA polymerase sigma S factor [Escherichia sp. H442]
 gi|294856629|gb|ADF45252.1| RNA polymerase sigma S factor [Escherichia sp. M863]
 gi|294856631|gb|ADF45253.1| RNA polymerase sigma S factor [Escherichia sp. TW10509]
 gi|294856633|gb|ADF45254.1| RNA polymerase sigma S factor [Escherichia sp. TW11930]
 gi|294856635|gb|ADF45255.1| RNA polymerase sigma S factor [Escherichia sp. TW11966]
 gi|294856639|gb|ADF45257.1| RNA polymerase sigma S factor [Escherichia sp. TW09231]
 gi|294856641|gb|ADF45258.1| RNA polymerase sigma S factor [Escherichia sp. TW09276]
 gi|294856643|gb|ADF45259.1| RNA polymerase sigma S factor [Escherichia sp. TW09254]
 gi|294856645|gb|ADF45260.1| RNA polymerase sigma S factor [Escherichia sp. TW09266]
 gi|294856647|gb|ADF45261.1| RNA polymerase sigma S factor [Escherichia sp. TA04]
 gi|294856649|gb|ADF45262.1| RNA polymerase sigma S factor [Escherichia sp. B685]
 gi|294856651|gb|ADF45263.1| RNA polymerase sigma S factor [Escherichia sp. TW14182]
 gi|294856653|gb|ADF45264.1| RNA polymerase sigma S factor [Escherichia albertii TW11588]
 gi|294856655|gb|ADF45265.1| RNA polymerase sigma S factor [Escherichia sp. H605]
 gi|294856657|gb|ADF45266.1| RNA polymerase sigma S factor [Escherichia sp. B49]
 gi|294856659|gb|ADF45267.1| RNA polymerase sigma S factor [Escherichia sp. TW09308]
 gi|294856661|gb|ADF45268.1| RNA polymerase sigma S factor [Escherichia sp. B1225]
 gi|294856663|gb|ADF45269.1| RNA polymerase sigma S factor [Escherichia sp. B646]
 gi|294856665|gb|ADF45270.1| RNA polymerase sigma S factor [Escherichia sp. E1118]
 gi|294856667|gb|ADF45271.1| RNA polymerase sigma S factor [Escherichia sp. E1195]
 gi|294856669|gb|ADF45272.1| RNA polymerase sigma S factor [Escherichia sp. E1196]
 gi|294856671|gb|ADF45273.1| RNA polymerase sigma S factor [Escherichia sp. E471]
 gi|294856673|gb|ADF45274.1| RNA polymerase sigma S factor [Escherichia sp. E472]
 gi|294856675|gb|ADF45275.1| RNA polymerase sigma S factor [Escherichia sp. E620]
 gi|294856677|gb|ADF45276.1| RNA polymerase sigma S factor [Escherichia sp. M1108]
 gi|294856679|gb|ADF45277.1| RNA polymerase sigma S factor [Escherichia sp. TA290]
 gi|294856681|gb|ADF45278.1| RNA polymerase sigma S factor [Escherichia sp. TW14263]
 gi|294856683|gb|ADF45279.1| RNA polymerase sigma S factor [Escherichia sp. TW14264]
 gi|294856685|gb|ADF45280.1| RNA polymerase sigma S factor [Escherichia sp. TW14265]
 gi|294856687|gb|ADF45281.1| RNA polymerase sigma S factor [Escherichia sp. TW14266]
 gi|294856689|gb|ADF45282.1| RNA polymerase sigma S factor [Escherichia sp. TW14267]
 gi|294856691|gb|ADF45283.1| RNA polymerase sigma S factor [Escherichia sp. RL325/96]
 gi|294856693|gb|ADF45284.1| RNA polymerase sigma S factor [Escherichia sp. Z205]
 gi|294856695|gb|ADF45285.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856697|gb|ADF45286.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856699|gb|ADF45287.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856701|gb|ADF45288.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856703|gb|ADF45289.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856705|gb|ADF45290.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856707|gb|ADF45291.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856709|gb|ADF45292.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856711|gb|ADF45293.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856713|gb|ADF45294.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856715|gb|ADF45295.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856717|gb|ADF45296.1| RNA polymerase sigma S factor [Escherichia fergusonii]
          Length = 157

 Score =  146 bits (368), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 64/157 (40%), Positives = 110/157 (70%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ T
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++T
Sbjct: 61  IRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 120

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           P+G +    L D + D+    P D+    +++++  +
Sbjct: 121 PLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVK 157


>gi|294856637|gb|ADF45256.1| RNA polymerase sigma S factor [Escherichia sp. B1147]
          Length = 157

 Score =  145 bits (367), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 64/157 (40%), Positives = 110/157 (70%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ T
Sbjct: 1   IARRYGNRGLALLDLIKEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++T
Sbjct: 61  IRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 120

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           P+G +    L D + D+    P D+    +++++  +
Sbjct: 121 PLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVK 157


>gi|260906263|ref|ZP_05914585.1| RNA polymerase, sigma 32 subunit, RpoH [Brevibacterium linens BL2]
          Length = 903

 Score =  145 bits (366), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 124/230 (53%), Gaps = 22/230 (9%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + + + A +EMV +NLRLV+S+AK++    L  LDLIQEGN+GL++A +KFD+  G KFS
Sbjct: 632 KADGAAAYEEMVTSNLRLVVSIAKRFNRSKLDLLDLIQEGNLGLVRAVQKFDYTKGNKFS 691

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R I D + TIR+P+H+ +K  +     R   ++   +    ++ + L 
Sbjct: 692 TYATWWIRQGIDRGIGDTAKTIRLPIHLFEKASEFWNCMRDDESRAACDHDHSKVEQALR 751

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLG-------DFIEDKNAVS--PLDSAIQAN 608
           M             +P+SLE  +  +   H         D I D +  +  P    +   
Sbjct: 752 M-------------QPVSLEGYLELQWDGHYAESLMSFDDRIADPDVFTDNPETKIVDGE 798

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           L ET   V+ SL  RE  ++R RFG       TL+ +G +F VTRERIRQ
Sbjct: 799 LLETVNSVVDSLPAREAEIIRRRFGWNGEPPQTLDAIGNRFAVTRERIRQ 848



 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 25/33 (75%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           TDD + +YL+++G   LLS   E+A+AKRIEAG
Sbjct: 575 TDDLLGVYLKQIGQYPLLSAAEEVAVAKRIEAG 607


>gi|33861134|ref|NP_892695.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33639866|emb|CAE19036.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 307

 Score =  145 bits (365), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 135/228 (59%), Gaps = 7/228 (3%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EM+ ANLRLV++++K+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q
Sbjct: 68  EMITANLRLVVNLSKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQ 127

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            + R+++ QS TIRIPV++ +K+ K+     ++       PT  E+A +L +  E + ++
Sbjct: 128 GLNRALSTQSRTIRIPVNINEKLTKLRAAKSKLMQLKGFPPTSIELANELKITKEEIDEL 187

Query: 567 LKITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLT 621
           L      I++    T     D S L D +   +   P++ A  A    +   +L  A+LT
Sbjct: 188 LSCELRSITVSLQGTVKSKSDPSELVDILPS-DQTPPMELAELAERTASAWTLLDKANLT 246

Query: 622 PREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 247 EKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|318066901|emb|CBY89065.1| RNA polymerase sigma70 factor [Carnimonas nigrificans]
          Length = 371

 Score =  145 bits (365), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 83/207 (40%), Positives = 121/207 (58%), Gaps = 6/207 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYG 364
           K+ + +    V +E+L +L   + L     + L+ Q+    +++  NE  ++++  +   
Sbjct: 168 KNGRDAPDVIVAQERLAELFSPIKLVPKHFERLILQVRITIEQVRANEKRIMQIFVKRAR 227

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV--DSILKIRNEIKSISVETGI 422
           + R  F+      E +  W+    +F     K     E+    IL+ +  I     E  +
Sbjct: 228 VPRKTFISSFPANESNQQWLD---EFIAKHPKYAEGLEIYRPDILRAQRRIAEEQEEVSL 284

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S++E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 285 SVAELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 344

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           KA +KF++  GYKFSTYA WW++QAIT
Sbjct: 345 KAVDKFEYRRGYKFSTYATWWIRQAIT 371



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 36/45 (80%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAFLP 65


>gi|323456432|gb|EGB12299.1| hypothetical protein AURANDRAFT_12561 [Aureococcus anophagefferens]
          Length = 233

 Score =  144 bits (364), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 130/228 (57%), Gaps = 13/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V  N+RLV+SVAK+YT  GL   DL+QEG++GLM+AA KFD   G KFSTYA WW
Sbjct: 7   ARQALVATNMRLVVSVAKRYTGLGLGLSDLVQEGSLGLMRAATKFDPARGCKFSTYACWW 66

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R++A QS  IR+P+H+   + K+ R  R  +    REP+  E+A+ L M    +
Sbjct: 67  IQQAILRAVAFQSRLIRLPMHVHQDLAKLKRGTRDFTAAHGREPSDGELAELLEMTPAKL 126

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTP 622
           RKV    ++           DT  L D +  K      ++A++ A L E     +  L  
Sbjct: 127 RKVRAAARQ----------GDTLKLEDTLASKEPTG--ETAVELALLHEDLHAAMDDLDA 174

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+RV+ +R+G+      T  +V      ++E +R+ E +AIRKL+ P
Sbjct: 175 DEKRVISLRYGLEDGVPCTPAQVAASCAESKEWVRRCEMRAIRKLRKP 222


>gi|196047982|ref|ZP_03115160.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
 gi|196021238|gb|EDX59967.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
          Length = 289

 Score =  144 bits (364), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 134/230 (58%), Gaps = 4/230 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ ++E NLRLV+SV   Y   G  + +D+IQ GN+GL++  E F+     K +TY  W
Sbjct: 43  ARRILIECNLRLVVSVVNSYPRVGNCEKMDMIQVGNVGLIRGIEAFEISKNCKLATYVTW 102

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++  I+R I      IR  V +++K+ K+ +     + K KR+   E+IA++L   VE 
Sbjct: 103 WIRHEISRFITFNKNDIRCSVTIQNKMDKLKKYFSNENGKAKRKLNIEQIAEELGYSVET 162

Query: 563 VRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLAS 619
           V +++   + KE +SL+ P  DED+  + + +++  A +P++    +  L +    +   
Sbjct: 163 VLQIMDTLMLKESVSLDAPSSDEDSRPVMNSVKNAKAPNPVELITSEEQLYQIEELLFTV 222

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  +EE V+R RFG     D TLEEV + F +TRERI+QIE KAI KLK+
Sbjct: 223 LNEKEESVIRYRFGFDTEKDLTLEEVARIFGITRERIQQIEKKAIGKLKN 272


>gi|226226008|ref|YP_002760114.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089199|dbj|BAH37644.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 302

 Score =  144 bits (364), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 96/259 (37%), Positives = 146/259 (56%), Gaps = 7/259 (2%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E R +  + +KG+  A+   + +V ANLR VIS  KKY   GL   +L+  GN GL+KA
Sbjct: 43  AEERRLARLAQKGDEAAA---ERLVTANLRFVISYVKKYQGHGLDLSELVAIGNEGLLKA 99

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             KFD   G KF +YA+WWV+QA+ +++A+Q+ ++RIP++   ++ ++ R    +S  + 
Sbjct: 100 VRKFDPDQGVKFISYAVWWVRQAVLKALAEQTRSVRIPLNQNSQLIRMARGEMILSQVLN 159

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLD 602
           REPT  E++K L  PVE VR   +I+   +SL+ PI   D + S LG+    +      D
Sbjct: 160 REPTDAELSKLLEEPVEQVRNARQISSTEVSLDAPIDRQDREASTLGERFAGETHADIED 219

Query: 603 SAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIE 660
                 +RE   RV    LTPRE ++L + +G+    +  TLE +G    VTRERIRQI 
Sbjct: 220 GTDFRLMREFIDRVFRKYLTPRERKILYLYYGLDEGAEAMTLERIGALMGVTRERIRQIR 279

Query: 661 AKAIRKLKHPSRSKKLRSF 679
            +A  KL+     + L  F
Sbjct: 280 ERAFEKLRESPDGRALSGF 298


>gi|123965877|ref|YP_001010958.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123200243|gb|ABM71851.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 307

 Score =  144 bits (364), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 136/227 (59%), Gaps = 7/227 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW++Q 
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R+++ QS TIRIPV++ +K+ K+     ++       PT  E+A+++ +  E + ++L
Sbjct: 129 LNRALSTQSRTIRIPVNINEKLTKLRAAKSKLMQLKGFPPTSFELAEEMKITKEEIDELL 188

Query: 568 KITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTP 622
                 I++    T     D S L D +   +   P++ A  A    +   +L  A+LT 
Sbjct: 189 SCELRSITVSLQGTVKSKSDPSELVDILPS-DQTPPMELAELAERTASAWTLLDKANLTE 247

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 248 KERKIVSLRFGLDGSNEWKTLAEVARHMSCSREYCRQVVQRALRKLR 294


>gi|311696748|gb|ADP99621.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 332

 Score =  144 bits (363), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 138/237 (58%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S  R+    A+  +++++++NLRL + +A++Y   G+   DLIQ+ N+GL+KA E+FD  
Sbjct: 84  SRCRRAFHLATACRRKLIQSNLRLAVHIARRYGQHGIPMSDLIQDANVGLIKAVERFDPT 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTYA WW+ + + R +   +  +  P ++ D+I ++ + + RM   + R P+  E
Sbjct: 144 KGFRFSTYAYWWISEEVKRCLQRGTRLVHTPENVVDEIRQLHKVSLRMHQSLGRTPSQSE 203

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+++      + ++  +    IS + P+ ++ +  LGD ++  + ++P       + + 
Sbjct: 204 LAREMEASPSRIGELRALATREISTDVPLVEDGSVTLGDSLDAGDQMAPDHPMSDRDRQR 263

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T   +L+ L  RE+ +L  R+G+G+    TL+ +     ++RER+RQIE  A++KL+
Sbjct: 264 TLKSMLSELNDREKDILSRRYGLGLPEPETLQVISDDLGISRERVRQIEKTALKKLQ 320


>gi|318066961|emb|CBY89095.1| RNA polymerase sigma70 factor [Halomonas muralis]
          Length = 367

 Score =  144 bits (362), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 86/211 (40%), Positives = 120/211 (56%), Gaps = 22/211 (10%)

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
           +SV+ K  K +L +L   + L     + LV Q+    ++I   E  +L++    G + R 
Sbjct: 168 ASVEAKTEKARLAELFSPIKLVPKHFERLVGQVRISVEQIRIQEKTILQVFVKKGKVPRK 227

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE---VDSILKIRNEI----KSISVETG 421
            F++     E +P W+             F+A      D +   R +I    + I+ E  
Sbjct: 228 TFIKAFPSNESNPQWLDV-----------FLANNAKYTDKLEPFRTDIARAQRKIAFEEA 276

Query: 422 I---SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +    + E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 277 LIQLPVGEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 336

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           IGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 337 IGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367



 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 43/60 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G   +M++L   P   ++++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGTREVMSALAYLPGAVESILDAYDATQD 80


>gi|312885799|ref|ZP_07745431.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311301606|gb|EFQ78643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 76/221 (34%), Positives = 129/221 (58%), Gaps = 1/221 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + + NLR V+SVAKKY ++GL   DLI EGN+GLMKAA+KFD   G+KF +YA+WW++Q 
Sbjct: 54  LTKTNLRFVVSVAKKYQHQGLPLSDLISEGNVGLMKAAKKFDETKGFKFISYAVWWIRQC 113

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I  +IA+ S  IR+P++    I K+ +    +  +++R+PT  E+A+ L    + V   L
Sbjct: 114 ILSAIAEHSRMIRLPMNQVGDITKMNKALALLEQQMERQPTTNELAEYLETSEDKVSDAL 173

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                  S + P   ED ++L D +      +  +  + +N +E   ++L++LT R++ V
Sbjct: 174 YFATRTASYDAPFRTEDENNLLDVLPGNEQATDHELMVLSNQQE-VRQLLSTLTSRDQEV 232

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R  FG+   T     ++     ++ ER+RQI  +A++ L+
Sbjct: 233 IRWTFGLDGKTALPPIDIAPLLGISAERVRQIRNQALQTLR 273


>gi|254384440|ref|ZP_04999781.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
 gi|194343326|gb|EDX24292.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
          Length = 1094

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 132/230 (57%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+   V  N  L   +A ++  +GL   DL+Q G +GL++AA KFD   GYKFSTYA WW
Sbjct: 261 ARNCFVVHNQGLAHGIALRHAGQGLDHEDLLQHGALGLIRAAVKFDPVKGYKFSTYATWW 320

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+++R++AD+   IRIPVH  ++I KV    RR+ ++  R  +   +A    + V+ V
Sbjct: 321 IRQSMSRAVADEGAVIRIPVHFHEQIRKVAAAERRLQSE-GRPWSAVHVAVACDLSVQRV 379

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLT- 621
            ++ ++++   SL+  IG  D  HLGD +  D+    PL SA    + E   + L SL  
Sbjct: 380 EEIRRVSRRTDSLDRVIG--DGVHLGDLVALDR----PLPSAEHLAMEEMGHKHLLSLLT 433

Query: 622 ---PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               R+ R+L  R G+      TL+++GK+F VTRERIRQ+E KA    +
Sbjct: 434 RFDARDARILLRRTGLDGGDRSTLDDLGKEFGVTRERIRQVEVKAFAAFR 483


>gi|307102796|gb|EFN51063.1| hypothetical protein CHLNCDRAFT_33233 [Chlorella variabilis]
          Length = 288

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 83/256 (32%), Positives = 144/256 (56%), Gaps = 31/256 (12%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ N+RLVI++AK+Y   G+  +DLI EG +GL K+ ++FD   G+KFSTYA WW++Q+I
Sbjct: 1   MQYNVRLVINIAKRYVGNGIDIVDLIPEGLVGLSKSLDRFDASKGFKFSTYAHWWIRQSI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +R++ DQ+  +R+P H+ + ++++ R    M+ +    P+ EEIA  + +PV  V   L+
Sbjct: 61  SRAVCDQARVVRLPSHVCETLYRINRAITSMTEQRDEMPSYEEIAAAVDLPVRRVIHYLR 120

Query: 569 ITKEPISLETPIGDEDTSHLG---------DFIED------KNAVSPLDSAIQANLRETT 613
           ++K P    +   D  T +L          + +ED             + A   ++R+ T
Sbjct: 121 LSKLPGGAASA-RDRPTQYLSGSSLKEVTYEALEDCAEDEDPGEEGEEEEAQHESIRQMT 179

Query: 614 TRVLASLTPREERVLRMRFGI--------GMNTD-------HTLEEVGKQFCVTRERIRQ 658
             +L++L  RE  +LR+R+G+        G++ D        +L EV   + +++ERIRQ
Sbjct: 180 DLLLSTLEKRERNILRLRYGLLGWGPAAGGLSWDDNVDGGSMSLGEVASAYGLSKERIRQ 239

Query: 659 IEAKAIRKLKHPSRSK 674
           IE KA+R L+ P R +
Sbjct: 240 IEDKAMRALRKPWRQQ 255


>gi|149377551|ref|ZP_01895291.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
 gi|149358164|gb|EDM46646.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
          Length = 332

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 136/234 (58%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+    A+ +++ ++ +NLRL + +A++Y NRG+   D+IQ+ N+GL+KA E+FD   G+
Sbjct: 87  RRAYHLATSSRQRLIRSNLRLAVHIARRYANRGIPMSDVIQDANVGLIKAVERFDPTKGF 146

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW+ + + R +   +  +  P ++ D+I  + RT+  +   + R P+  E+A+
Sbjct: 147 RFSTYAYWWISEEVKRCMKRGTRLVHTPENVVDEIRLLQRTSLALYQTLGRTPSQTELAR 206

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ +    + ++  +    +S++ P+  E    LG+ +   +  +P     Q + + T  
Sbjct: 207 EIEVSPSRIGELRALASMEVSVDLPVSTEGNITLGESLSADDQSAPDHDMAQRDRKRTLA 266

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +LA L+ RE+ VL  R+G+ +    TL+ +     ++RER+RQIE  A++KL+
Sbjct: 267 TLLAELSSREKDVLARRYGLDLPEPETLQVISDDLGISRERVRQIEKSALKKLQ 320


>gi|55274889|gb|AAV49247.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 180

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 69/182 (37%), Positives = 117/182 (64%), Gaps = 8/182 (4%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A++Y NRGL  L        GL++A EKFD   G++FSTYA WW++Q I R+I
Sbjct: 1   LRLVVKIARRYGNRGLALL--------GLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 52

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 53  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 112

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 113 ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 172

Query: 633 GI 634
           G+
Sbjct: 173 GL 174


>gi|323450165|gb|EGB06048.1| hypothetical protein AURANDRAFT_11909 [Aureococcus anophagefferens]
          Length = 325

 Score =  143 bits (361), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 96/301 (31%), Positives = 160/301 (53%), Gaps = 27/301 (8%)

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIA-----KKEMVEA 451
           +A EV +++ +R +   +    G   S  E+ +       G     +      ++E+++ 
Sbjct: 26  LATEVQALVALRAKRSELKAALGREPSGGEWANATGYANYGALRTRMGHMKACREELIQR 85

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+SVAK+Y + GL F DL QEGN GL KA ++FD   G++FSTYA+WW++QA+  +
Sbjct: 86  NLRLVLSVAKRYGDCGLAFTDLCQEGNFGLAKACDRFDPSKGFRFSTYAVWWIRQAVAHA 145

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +A QS TIR+P H+ +K+ ++ +    +  +  R+ T +EIA+++++  + +R++ +  +
Sbjct: 146 VAHQSRTIRLPTHVHEKLRRMKKHKVALEKQTGRDATDDEIAREMSLDADKLRRLRRAAR 205

Query: 572 EPISLETPI-------------GDEDTSH-----LGDFIEDKNAVSPLDSAIQANLRETT 613
             +S +                G    S+     L D + D     P   A ++ L++  
Sbjct: 206 GTVSTDVDAENLGSRRGAAPGNGRRGASYASGAQLADLLHDATQ-HPERDAAESLLKDEV 264

Query: 614 TRV-LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            R+    L  REE VL   FG+      TL E+  +F +TRERIRQIE  A  KL+ P R
Sbjct: 265 RRMLDDDLEDREEDVLNRHFGLDGRRPETLAEIAVRFDLTRERIRQIEKSAFAKLRQPHR 324

Query: 673 S 673
           S
Sbjct: 325 S 325


>gi|225848935|ref|YP_002729099.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225644026|gb|ACN99076.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 285

 Score =  143 bits (361), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 83/255 (32%), Positives = 144/255 (56%), Gaps = 9/255 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I+  ++ G+ EA    ++++ +NLR VI++AK+Y   G+   DLI  GNIGL++AA++
Sbjct: 29  KEILEKIKLGDKEAF---QKLILSNLRFVINIAKRYAGYGIPLQDLISAGNIGLIEAAKR 85

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G KF +YA+WW+KQ+I  +++ +   IR P  ++    K+      + + + REP
Sbjct: 86  FDPSKGVKFISYAIWWIKQSIINTLSQEGDIIRKPTKIQSLFQKISNAYFYLKDSLNREP 145

Query: 548 TPEEIAKKL---AMPVE--GVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPL 601
           + +EI   L    + VE   +   L   +  ISL+ PI  +D   HL D I +       
Sbjct: 146 SVDEIHSFLLREGLEVEKDTIENYLFFNQHFISLDEPILSQDEDIHLSDTISNSGTEDIE 205

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              I  ++ +    +L +L+PRE+++L  RFG+      TL+EVG    ++RER+RQIE 
Sbjct: 206 RKLIDEDILKFIDELLDTLSPREKQILIHRFGLYGEEPKTLKEVGNIVGISRERVRQIEI 265

Query: 662 KAIRKLKHPSRSKKL 676
           + ++KL+  +  +K+
Sbjct: 266 RLLKKLRKLATKRKI 280


>gi|188996015|ref|YP_001930266.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
 gi|188931082|gb|ACD65712.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
          Length = 285

 Score =  143 bits (361), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 90/274 (32%), Positives = 151/274 (55%), Gaps = 9/274 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KSI     +S  E   ++  V++G+ EA    ++++ +NLR VI++AK+Y   G+ F D
Sbjct: 14  LKSIYKIPLLSKEEEESLLKKVKEGDKEAL---QKLIISNLRFVINIAKRYAGYGIPFSD 70

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  GNIGL++AA+KFD   G +F +YA+WW++Q+I  +I  +S  I+ P  M     K+
Sbjct: 71  LISAGNIGLIEAAKKFDTSRGVRFISYAVWWIRQSIINTIQHESEIIKKPNRMYAYASKI 130

Query: 533 VRTARRMSNKIKREPTPEEI-----AKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTS 586
                 + + + REP+ +EI      + + +  E V          +SL+TPI G ++  
Sbjct: 131 NNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLDTPIEGTDNDL 190

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D I   N +       + +L+     +L +L+PRE  +L  RFG+      TL EVG
Sbjct: 191 VLEDTISVYNTLDIEKDINEEDLKRAIEALLDTLSPRERTILIHRFGLNGEEPKTLNEVG 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   ++RER+RQIE + ++KL+  ++ KKL   +
Sbjct: 251 EMVGLSRERVRQIENRILKKLRKIAKIKKLEDLI 284


>gi|119384818|ref|YP_915874.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
 gi|119374585|gb|ABL70178.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 728

 Score =  143 bits (360), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 85/237 (35%), Positives = 129/237 (54%), Gaps = 9/237 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++  +L  V   A +    G    D+ Q   +GL ++  +FD   GY+F  YA +W
Sbjct: 499 ATEHLIREHLPYVRRFASRNVEEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATYW 558

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR  +D+   IRIPVH  +KI K+ R   R+  ++    +  E+AK+L   ++ V
Sbjct: 559 MRQAITRWRSDEGAAIRIPVHRNEKITKLDRALERLDVRVGGAVSDLELAKELEWTIDEV 618

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +   I +E    E P   E      D + + + V   D   +A      T  LA L  R
Sbjct: 619 TQFRSIPREA---EYP---ESLDDWDDLLPEPSGVDVFD---EAETERIVTDALADLPER 669

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  V+RMRFGIG ++D TLEE+G+ + VTRERIRQIEAK + +L HP R ++L+  L
Sbjct: 670 QADVIRMRFGIGRDSDMTLEEIGQIYGVTRERIRQIEAKGLDRLSHPGRKRRLQELL 726


>gi|261416342|ref|YP_003250025.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261372798|gb|ACX75543.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326200|gb|ADL25401.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 282

 Score =  142 bits (359), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 90/262 (34%), Positives = 146/262 (55%), Gaps = 19/262 (7%)

Query: 430 IVSMVRKGECEA--SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           ++ +++ GE E     A + ++  NLR V+SVA+KY  RGL  LDLI EGN+GL KAA++
Sbjct: 27  LLKIIKNGETEEIRKSALQRLIRGNLRFVVSVARKYQGRGLSLLDLINEGNLGLFKAAKR 86

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF +YA+WW++Q+I +++ +Q   +RIP +    +++  R   +      +  
Sbjct: 87  FDMDKDVKFISYAVWWIRQSIQKALFEQVGAVRIPPNKLALVNRFKRALMQNGGDYDKTI 146

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-------EDTSHLGDFI-EDKNAVS 599
           + EE A      VE + K++      ISL+ PIGD       +  S L D +  D N   
Sbjct: 147 SMEEFAPYERDIVEVMEKIVD-----ISLDAPIGDDAGVSSADSVSTLMDVLGSDGNQDE 201

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            ++   +  L + T   L+SL  REE +LRM +G+    D TL+++G+   ++RER+RQI
Sbjct: 202 DMEREERKKLIQET---LSSLPQREEEILRMFYGLDTVEDTTLKDIGEDLKLSRERVRQI 258

Query: 660 EAKAIRKLKHPSRSK-KLRSFL 680
           + K +R+L+     K KL  +L
Sbjct: 259 KNKTLRRLQKSKEHKEKLADYL 280


>gi|306410397|gb|ADM85820.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410399|gb|ADM85821.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410401|gb|ADM85822.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410403|gb|ADM85823.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410405|gb|ADM85824.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|306410407|gb|ADM85825.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CpI1]
 gi|306410409|gb|ADM85826.1| RNA polymerase essential primary sigma 70 factor [Frankia sp.
           Cj1-82]
          Length = 106

 Score =  142 bits (358), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 61/106 (57%), Positives = 89/106 (83%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+
Sbjct: 1   LGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQ 60

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +   + REP+PEEIAK++ +  + VR++LK+++EP+SLETPIG+E+
Sbjct: 61  LLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVSLETPIGEEE 106


>gi|3249727|gb|AAC26666.1| RNA polymerase sigma-like factor [Pseudonocardia autotrophica]
          Length = 152

 Score =  142 bits (358), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 70/151 (46%), Positives = 100/151 (66%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDI 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V +  +  +EPISL+  IGDE  S LGDFIED  A SP D+     L++     L 
Sbjct: 61  TPEKVLETQQYAREPISLDQTIGDEGDSQLGDFIEDSEAASPSDAVSFTLLQDQLQSTLG 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           +L+ RE  V+R+RFG+      TL+E+G+ +
Sbjct: 121 TLSEREAGVVRLRFGLTDGRPRTLDEIGQVY 151


>gi|217968787|ref|YP_002354021.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
 gi|217506114|gb|ACK53125.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
          Length = 590

 Score =  142 bits (357), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 61/102 (59%), Positives = 79/102 (77%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  M+++NLRLVIS+AKKYT+ G  FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW+
Sbjct: 476 RNRMIKSNLRLVISIAKKYTHTGFPFLDLIQEGNLGLMKAVEKFDYRRGFKFSTYATWWI 535

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +QAITR IADQ   +R+PVHM + I+KV R  R +  +  R+
Sbjct: 536 RQAITRGIADQQRLVRVPVHMVESINKVSRVLRELEGRAPRK 577


>gi|330948232|gb|EGH48492.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 95

 Score =  141 bits (356), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 69/95 (72%), Positives = 78/95 (82%)

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRM
Sbjct: 1   KEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRM 60

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 61  RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 95


>gi|307128696|ref|YP_003880726.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
 gi|306483158|gb|ADM90028.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
          Length = 288

 Score =  141 bits (355), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 91/288 (31%), Positives = 159/288 (55%), Gaps = 12/288 (4%)

Query: 396 KNFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           K    CE +S+ K   EI  I +   E  I  ++F      ++        A   +++AN
Sbjct: 8   KQVTNCESESLDKYLYEIGKIPLLNNEEEIQFAKFARKTYNIK--------AINFLIKAN 59

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LR V+SVAK+Y N+GL   DLI EGN+GL+K   +FD   G+K  +Y++WW++Q+I ++I
Sbjct: 60  LRFVVSVAKQYQNQGLNLSDLINEGNLGLIKGIFRFDERKGFKCISYSVWWIRQSILQAI 119

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           AD+S  +R P +     +KV +    +    +  P+ ++I + L    + + + LK + +
Sbjct: 120 ADKSRCVRCPTNKLAFYNKVNKKYSELEQIYQIPPSIKQIGEYLNSNEKEIEEALKNSVK 179

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             SL+ PI + + S+L D I+   +  P     + +L++   R+L +L+ +E +++ + +
Sbjct: 180 HTSLDAPIIEGENSNLYDIIKYDESPHPDLDLEKESLKKDIKRLLDTLSEKEAQIITLHY 239

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+  +T + LEE+     +TRER RQIE   +R+LK  SR   LR +L
Sbjct: 240 GLESSTIN-LEEISFLLNLTRERCRQIEIYGLRRLKQSSRKNILRFYL 286


>gi|284053375|ref|ZP_06383585.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 183

 Score =  141 bits (355), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 69/180 (38%), Positives = 120/180 (66%), Gaps = 1/180 (0%)

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R  T ++IA +L M  +
Sbjct: 2   WWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKSRTATIDDIATELKMTPD 61

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R+VL      +SLET +G +  + LGD +E + + +P +  ++ +L      +LA L+
Sbjct: 62  QIREVLLRVPRSVSLETKVGTDKDTELGDLLETEES-TPEELLMRESLYRELQHILADLS 120

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  V++MR+G+G    ++L E+G+   ++RER+RQIEAKA++KL+ P R  ++R +LD
Sbjct: 121 GKERAVIQMRYGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRVRDYLD 180


>gi|310815187|ref|YP_003963151.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
 gi|308753922|gb|ADO41851.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
          Length = 809

 Score =  141 bits (355), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 87/237 (36%), Positives = 130/237 (54%), Gaps = 9/237 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++  +L  V   A +  + G    D+ Q   +GL ++  +FD   GY+F  YA +W
Sbjct: 580 ATEHLIREHLPYVRRFASRNVDEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATYW 639

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR  AD+   IRIPVH  +KI K+ R   R+  ++    +  E+A++L   ++ V
Sbjct: 640 MRQAITRWRADEGAAIRIPVHRNEKITKLDRALERLDVRVGGAVSDLELAEELEWTIDEV 699

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++   I +E    E P   +D  +L   + + +     D   Q          LA L  R
Sbjct: 700 KQFRGIPREA---EYPASLDDWDNL---LPEPSEADVFD---QTETERILADALAELPER 750

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  VLRMRFGIG  TD TLEEVG+ + VTRERIRQIEAKA+  L HP R ++L++ L
Sbjct: 751 QADVLRMRFGIGRETDMTLEEVGQIYGVTRERIRQIEAKALDHLSHPGRKRRLQALL 807


>gi|291060369|gb|ADD73104.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           str. Chicago]
          Length = 296

 Score =  140 bits (354), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 81/251 (32%), Positives = 136/251 (54%), Gaps = 14/251 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +V AN+R VISVA+ Y   GL   DLI EGNIGL+ AAE+F+   G +F +YA  W
Sbjct: 45  AKNALVRANVRFVISVARHYRTCGLPLADLISEGNIGLLTAAERFNPARGCRFISYAACW 104

Query: 504 VKQAITRSIADQSCTIRIPV---HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++Q+I +++ +++  IR+PV         ++ +     ++  I +        K+ A   
Sbjct: 105 IRQSILKALNEKARIIRLPVSRIRAAKSTYEYIPPVTSVNVGISKTQGGNRYGKRRATMC 164

Query: 561 EGVRKV--LKITKEPISLETPI---------GDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             V  V  + I   P+SL+ P+         GD D   +GD + D     P +  +   L
Sbjct: 165 RAVPTVEEVHIWHTPLSLDAPLGASGSRGESGDVDGLRIGDCVPDDLYAQPEEHMLACAL 224

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    ++L  L  R+ +V+R RFG+G     +L+E+G+ F +T+ER+RQIE KA+ +++ 
Sbjct: 225 QADIAKILRLLPARDAQVIRYRFGLGGYERRSLQEIGEIFQITKERVRQIEKKALLRIRS 284

Query: 670 PSRSKKLRSFL 680
            +R  +L S++
Sbjct: 285 CARQHRLDSYI 295


>gi|325002338|ref|ZP_08123450.1| RpoD family RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 425

 Score =  140 bits (354), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 124/226 (54%), Gaps = 24/226 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +  V ANLRLV+S+A  Y   GL  LDL+QEG +GL++A +KFD   G KFSTYA WW
Sbjct: 208 AYERFVTANLRLVLSIASGYGAPGLDALDLVQEGTLGLIRAVQKFDIAQGTKFSTYATWW 267

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK-KLAMPVEG 562
           ++QAITR+IADQS TIR PVH+ ++++   R A    +      T E +A     +P E 
Sbjct: 268 IRQAITRAIADQSRTIRYPVHLVERLNAFSRRALPDDDSA----TAELVATLPTTVPFES 323

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R VL             G+E    + D   D  A       ++    E     L+ L+ 
Sbjct: 324 ARDVL-------------GEEVLQDVADRYLDPPAPD-----LRGFTVEDVAAALSILSE 365

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  ++  RFG  +    TL+ +G +  VTRERIRQI++KA+ +L+
Sbjct: 366 RERTIVDRRFGF-VGDAATLDVIGGELGVTRERIRQIQSKALGRLE 410


>gi|297580650|ref|ZP_06942576.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
 gi|297535066|gb|EFH73901.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
          Length = 477

 Score =  140 bits (354), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 97/243 (39%), Positives = 131/243 (53%), Gaps = 29/243 (11%)

Query: 289 EVYRELRSLQDN---AVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           E + ELR    N   AVN       Q  E S +   + +E          L   + D LV
Sbjct: 248 EKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFRE--------FRLTPKQFDHLV 299

Query: 340 EQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS--YAKDFPEGEWK 396
           E L     R+   E  +++ + +   + +  F+    G E +  W+    A D      K
Sbjct: 300 ETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASD------K 353

Query: 397 NFVACEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +VA   +   +IR  I+ + +   ET +S+   + +   +  GE +A  A KEMVEANL
Sbjct: 354 TYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDLSRRMSIGEAKARRANKEMVEANL 413

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
            LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K ++  GY FSTYA WW++QAITRSIA
Sbjct: 414 PLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKSEYRRGYNFSTYATWWIRQAITRSIA 473

Query: 514 DQS 516
           DQS
Sbjct: 474 DQS 476



 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 27  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 86

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 87  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 145

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 146 INQVQSAIAEYPGTIPYIL 164


>gi|15639996|ref|NP_219449.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189026235|ref|YP_001934007.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
 gi|3323340|gb|AAC65963.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018810|gb|ACD71428.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 311

 Score =  140 bits (354), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 81/251 (32%), Positives = 136/251 (54%), Gaps = 14/251 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +V AN+R VISVA+ Y   GL   DLI EGNIGL+ AAE+F+   G +F +YA  W
Sbjct: 60  AKNALVRANVRFVISVARHYRTCGLPLADLISEGNIGLLTAAERFNPARGCRFISYAACW 119

Query: 504 VKQAITRSIADQSCTIRIPV---HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++Q+I +++ +++  IR+PV         ++ +     ++  I +        K+ A   
Sbjct: 120 IRQSILKALNEKARIIRLPVSRIRAAKSTYEYIPPVTSVNVGISKTQGGNRYGKRRATMC 179

Query: 561 EGVRKV--LKITKEPISLETPI---------GDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             V  V  + I   P+SL+ P+         GD D   +GD + D     P +  +   L
Sbjct: 180 RAVPTVEEVHIWHTPLSLDAPLGASGSRGESGDVDGLRIGDCVPDDLYAQPEEHMLACAL 239

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    ++L  L  R+ +V+R RFG+G     +L+E+G+ F +T+ER+RQIE KA+ +++ 
Sbjct: 240 QADIAKILRLLPARDAQVIRYRFGLGGYERRSLQEIGEIFQITKERVRQIEKKALLRIRS 299

Query: 670 PSRSKKLRSFL 680
            +R  +L S++
Sbjct: 300 CARQHRLDSYI 310


>gi|293392779|ref|ZP_06637097.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424638|gb|EFE97849.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 202

 Score =  140 bits (354), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 57/111 (51%), Positives = 90/111 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 92  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA+
Sbjct: 152 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAE 202


>gi|318066947|emb|CBY89088.1| RNA polymerase sigma70 factor [Halomonas halodenitrificans]
          Length = 360

 Score =  140 bits (353), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 80/199 (40%), Positives = 118/199 (59%), Gaps = 18/199 (9%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L +L   + L     + LV Q+    +++   E  +++L  +   I R  F++   G E
Sbjct: 171 RLAELFSPIKLVPKHFERLVNQVRISVEQVRAQEKAVMQLCVKKARIPRKTFIKAFPGSE 230

Query: 379 LDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEI----KSISVETG---ISISEFRHI 430
            +P W+  ++ + P+           + +  +R +I    + I+ E     + + E + +
Sbjct: 231 SNPEWLDGFSDEHPK---------YAERLRPLRTDIQRAQRKIAFEEAMVRLPVKEIKEV 281

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 282 NRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 341

Query: 491 CLGYKFSTYAMWWVKQAIT 509
             GYKFSTYA WW++QAIT
Sbjct: 342 RRGYKFSTYATWWIRQAIT 360



 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVGSILEAYDATQD 80


>gi|119476594|ref|ZP_01616904.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119449850|gb|EAW31086.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 194

 Score =  140 bits (353), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 65/176 (36%), Positives = 115/176 (65%)

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPTPEEI
Sbjct: 4   GFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPTPEEI 63

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ L  PV  V+++L++ +   S++TP+G +    L D I D +   P +     +++ +
Sbjct: 64  AELLDRPVADVKRMLRLNERVASVDTPLGADSDKSLLDTIPDTHVSDPAEMLQDDDMKAS 123

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  +  LT ++  V+  RFG+      TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 124 ISEWIGELTEKQREVVARRFGLRGYETSTLEEVGREIGLTRERVRQIQVEALKRLR 179


>gi|318066975|emb|CBY89102.1| RNA polymerase sigma70 factor [Halomonas variabilis]
          Length = 368

 Score =  140 bits (353), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 85/212 (40%), Positives = 122/212 (57%), Gaps = 16/212 (7%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYG 364
           K  + S + K  + +L  L   + L     + LV Q+    +++   E  +++L  +   
Sbjct: 165 KHGRGSAELKAEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAK 224

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI----KSISVE- 419
           + R  F++   G E    W+    DF   + K       D +  +R +I    + I+ E 
Sbjct: 225 VPRKTFIKSFPGNESRKTWLD---DFQAAQSKY-----ADRLEPLRADIARAQRKIAFEE 276

Query: 420 --TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +S+S+ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 277 DMVQLSVSDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 336

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           NIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 337 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 368



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILNAYDATQD 80


>gi|323144152|ref|ZP_08078788.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
 gi|322416060|gb|EFY06758.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
          Length = 311

 Score =  139 bits (351), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/241 (33%), Positives = 143/241 (59%), Gaps = 9/241 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V++G+ +A   +  M+ +NLRLVI VA+ Y  RG+  LDLI+EGN+GL+ A  KFD   
Sbjct: 67  LVQQGDVKA---RNSMITSNLRLVIKVARDYRTRGVPMLDLIEEGNLGLIHAVNKFDPER 123

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-EE 551
           G++FSTYA WW++Q I  ++ +QS  +R+P H+   +++V++  +++  K   +    ++
Sbjct: 124 GFRFSTYATWWIRQGIEHAVMNQSRLVRLPFHVIKDLNQVLKVKKKLQEKAHGQAVAVKD 183

Query: 552 IAKKLAMPVEGVRKVLKITKEPISL-ETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQA 607
           IAK+L +  + VR +L +  E IS+ +  + ++D+     L D + D+   +  +     
Sbjct: 184 IAKELDIDEDKVRSML-VVAEGISISDLNVKNKDSEKNVSLLDLLADEKTPTLEEQFGNT 242

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            + +     + SL  R++ ++  RFGI  N   TLEE+G+   +TRER+RQ++   +  L
Sbjct: 243 EIEKLLRSWIDSLNERQKIIVIHRFGINDNDIKTLEEIGEMLHLTRERVRQLQKTVLISL 302

Query: 668 K 668
           K
Sbjct: 303 K 303


>gi|307824191|ref|ZP_07654417.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734571|gb|EFO05422.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 391

 Score =  139 bits (351), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 132/228 (57%), Gaps = 4/228 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++M+  N+RL   VA K+    L F DL+QEG +GL+KA ++FD   GY+FSTYA+ W+
Sbjct: 149 RQQMIAGNVRLAAFVAHKHKTTVLSFDDLLQEGVVGLIKAVDRFDPYRGYQFSTYAIPWI 208

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           KQAI+R I  Q   +R+PV + ++   V    R    + +R P+ E++     +  + ++
Sbjct: 209 KQAISRLIVKQEKIVRLPVALAERACAVFEAMRNAYLQTERWPSIEQLKSLCDLSEDEIK 268

Query: 565 KVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +    +   SL+  +GD   ++   L   ++ +    PLD  I  NL     +V+A+L 
Sbjct: 269 TIRNYYQATHSLDA-VGDAEEDEGQALMARMKQRQFALPLDELIDRNLGRYLDQVVATLP 327

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +E  +L MRFG+  +T+ TL+ +  Q  V+RER+RQI+  A++KLK+
Sbjct: 328 DKEAAILNMRFGLKNHTEMTLQAIADQLQVSRERVRQIQNDALKKLKN 375


>gi|253583872|ref|ZP_04861070.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
 gi|251834444|gb|EES63007.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
          Length = 260

 Score =  139 bits (351), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 89/263 (33%), Positives = 143/263 (54%), Gaps = 6/263 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +L I   IK IS    ++  E R I    R G+ EA   ++++V +NLRLVIS+A+KYTN
Sbjct: 1   MLDISEYIKDISTYPLLTPKEEREIAVKARSGDREA---QEKLVTSNLRLVISIARKYTN 57

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G+  LDLIQEGN+GL++A EK++     +FSTY+ +W+KQ+I R I      IR P ++
Sbjct: 58  MGIPILDLIQEGNMGLIRAVEKYEPDKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSYV 117

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            D I ++ +  +   NK    P+ +EI + L M  +   + + + ++   +   +  E  
Sbjct: 118 YDGISRMKKYVQDYKNKNSHCPSIDEICRSLDMKKKEAERYIDVLEKGNGIGNEMYGEMV 177

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            +    I D       D  I  +      + +  L PRE  VL  R+G+      TL E+
Sbjct: 178 EYCSSIIYDDTFE---DEVIAKSSNIDLMKKVNKLPPREREVLIYRYGLLDEKVLTLGEI 234

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G++  +T+ERIRQI+ +AI +L+
Sbjct: 235 GQRMNLTKERIRQIQLEAIDRLR 257


>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 508

 Score =  139 bits (349), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 144/248 (58%), Gaps = 14/248 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY  
Sbjct: 263 SLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFRISTYVY 322

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA-------K 554
           WW++Q ++R++ + S T+R+P H+ +++  ++R A+    +    P+ + IA       K
Sbjct: 323 WWIRQGVSRALVENSRTLRLPNHLHERL-GLIRNAKIRLEEKGVTPSIDRIAESLNISQK 381

Query: 555 KLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+    E V KV  + +E   SL    G+   S++ D   + N   P        L++  
Sbjct: 382 KVRNATEAVSKVFSLDREAFPSLNGLPGETHHSYIADNCLENN---PWHGVDDWALKDEV 438

Query: 614 TRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +++  +L  RE+ ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KLKH +R
Sbjct: 439 NKLINLTLQEREQEIIRLYYGLD-NESLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497

Query: 673 SKKLRSFL 680
            KKL + L
Sbjct: 498 KKKLEAML 505


>gi|85706634|ref|ZP_01037726.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
 gi|85668692|gb|EAQ23561.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
          Length = 830

 Score =  139 bits (349), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 131/237 (55%), Gaps = 9/237 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++  +L  V   A +    G +  D+ Q   +GL ++  +FD   GY+F  YA +W
Sbjct: 499 ATEHLIREHLPYVRRFASRNVEEGEEPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATYW 558

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAI R  AD+   IRIPVH  +K+ K+ R   R+  ++    +  ++A++L   ++ V
Sbjct: 559 MRQAIMRWRADEGAAIRIPVHRNEKVTKLDRALDRLDVRVGGAVSDLDLAEELEWAIDEV 618

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+   I   P   E P   +D  +L   + + + V  LD   QA      T  LA L  R
Sbjct: 619 RQFRCI---PRKAEYPASLDDWDNL---LPEPSEVDVLD---QAETERIVTEALADLPER 669

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  V+RMRFGIG +++ TLEE+G+ + VTRERIRQIEAK +  L HP R ++L+  L
Sbjct: 670 QADVIRMRFGIGHDSEMTLEEIGQIYGVTRERIRQIEAKGLDLLSHPGRKRRLQELL 726


>gi|237757189|ref|ZP_04585608.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690651|gb|EEP59840.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 285

 Score =  139 bits (349), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 150/274 (54%), Gaps = 9/274 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KSI     +S  E   ++  V++G+ EA    ++++ +NLR VI++AK+Y   G+ F D
Sbjct: 14  LKSIYKIPLLSKEEEESLLKKVKEGDKEAL---QKLIISNLRFVINIAKRYAGYGIPFSD 70

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  GN+GL++AA+KFD   G +F +YA+WW++Q+I  +I  +S  I+ P  M     K+
Sbjct: 71  LISAGNVGLIEAAKKFDTSKGVRFISYAVWWIRQSIINTIQHESEIIKKPNRMYAYASKI 130

Query: 533 VRTARRMSNKIKREPTPEEI-----AKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTS 586
                 + + + REP+ +EI      + + +  E V          +SL+TPI G ++  
Sbjct: 131 NNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLDTPIEGTDNDL 190

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D I   N +       + +L+     +L +L+ RE  +L  RFG+      TL EVG
Sbjct: 191 VLEDTISVYNTLDIEKDINEEDLKRAIETLLDTLSQRERTILIHRFGLNGEEPKTLNEVG 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   ++RER+RQIE + ++KL+  ++ KKL   +
Sbjct: 251 EIVGLSRERVRQIENRVLKKLRKIAKIKKLEDLI 284


>gi|239814806|ref|YP_002943716.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus S110]
 gi|239801383|gb|ACS18450.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus S110]
          Length = 331

 Score =  139 bits (349), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 82/235 (34%), Positives = 136/235 (57%), Gaps = 12/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLV+++AK Y  RG+   DLI+EGN+GLM A  KF+   G++FSTYA WW
Sbjct: 85  ARQSMIEHNLRLVVNIAKAYLGRGVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWW 144

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK---IKREPTP---EEIAKKLA 557
           ++Q++ R++  Q+  IR+PVH+  ++ +V+R  R +      +   P     E++A  L 
Sbjct: 145 IRQSVERAVLTQARAIRLPVHVVRELQQVLRARRTLEGDAEFLAHRPDGVRVEDVAAFLG 204

Query: 558 MPVEGVRKVLKITKEPISLET--PIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETT 613
           + V+ V ++L + + P SL+     GDE  + L D +  ED+    P D      +    
Sbjct: 205 LEVQAVAELLALAEAPRSLDAGDAHGDEGFT-LADTVASEDEQG-DPTDVTHTHEVARLL 262

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + + +L  RE  VL  R+G+      TLE +  +  +TRER+RQI+ +A+ K++
Sbjct: 263 DQWVHALDAREREVLEGRYGLHDREPETLEVLSVRLGLTRERVRQIQNEALAKMR 317


>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [Arabidopsis thaliana]
          Length = 502

 Score =  138 bits (348), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 145/250 (58%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 255 ECHLAREKLAMSNVRLVMSIAQRYNNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 314

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 315 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 373

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V KV  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 374 QKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENN---PWHGYDDLALKE 430

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 431 EVSKLISATLGEREKEIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHA 489

Query: 671 SRSKKLRSFL 680
           +R +K+ + +
Sbjct: 490 ARKRKMEAMI 499


>gi|164690667|dbj|BAF98617.1| putative DNA helicase [Streptomyces argenteolus]
          Length = 1064

 Score =  138 bits (348), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 79/222 (35%), Positives = 129/222 (58%), Gaps = 4/222 (1%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  N+RLV +    Y  +G+   DL+Q G +G+M+AAEKFD   G +FSTYA WW++QA
Sbjct: 156 LVLHNIRLVHAAVAPYLGQGVDREDLVQHGVLGVMRAAEKFDPRAGTRFSTYATWWIRQA 215

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ++R++AD+  TIRIP H+RD + KV    RR   +  R P P+++A +L +P + V   L
Sbjct: 216 VSRAVADEGSTIRIPAHVRDVVLKVAVACRRSRERGLR-PRPQDLAAELDLPPDTVNLAL 274

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREER 626
           ++++   SL+        + L   I  ++A+   +  ++A   R+    +L  L  R   
Sbjct: 275 RVSRPADSLDRVADGVRPAELA--ISLRDAIPGPEETLRAAFGRQWVDWLLEPLPARNAD 332

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++R R G+      TL+++G  + VTRERIRQ E +A+  L+
Sbjct: 333 IVRRRNGVIKGEPQTLKDIGVLYGVTRERIRQNEKRALAVLR 374


>gi|318066929|emb|CBY89079.1| RNA polymerase sigma70 factor [Halomonas boliviensis]
          Length = 368

 Score =  138 bits (348), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 129/229 (56%), Gaps = 18/229 (7%)

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           E  RE  +L + A    K  + S + K  + +L  L   + L     + LV Q+    ++
Sbjct: 150 EQIREQNALVEAAFA--KHGRGSAELKSEQARLAVLFSPIKLVPKHFERLVGQVRISVEQ 207

Query: 349 IMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           +   E  +++L  +   + R  F++   G E    W+    DF   + K       D + 
Sbjct: 208 VRAQEKAVMQLCVKKAKVPRKTFIKSFPGNESRKTWLD---DFQAAQSKY-----ADRLE 259

Query: 408 KIRNEI----KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +R +I    + I+ E     +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+A
Sbjct: 260 PLRADIARAQRKIAFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIA 319

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 320 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 368



 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILDAYDATQD 80


>gi|325475291|gb|EGC78476.1| region 2 family RNA polymerase sigma-70 factor [Treponema denticola
           F0402]
          Length = 275

 Score =  138 bits (348), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 134/237 (56%), Gaps = 6/237 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V+KG  EA    + +V +NLRLVI +AKK+++   Q L+LIQEGN+GLMKAA KF     
Sbjct: 31  VKKGNTEAI---EVLVTSNLRLVIKMAKKFSSNENQILELIQEGNMGLMKAASKFSKSFK 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FS+YA WW+KQ+  R +      I++PV     I +V +       K    P+  ++A
Sbjct: 88  VRFSSYAAWWIKQSFIRYLNSADKVIKLPVRKEALIRQVNKEEENYKIKYGILPSYSQLA 147

Query: 554 KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + +   V+ + +V       I SL+ P+ +E +++L DFI   N  +P +  I    +E 
Sbjct: 148 EIMKEKVDIIAQVKSFNYTDICSLDDPVDNERSANLYDFIPC-NTYNPEEEFIDNEFKEK 206

Query: 613 TTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  L  RE+ VLR R+G+ G  T  T   +GK++ ++ E IRQ + +A++KL+
Sbjct: 207 LNKCLEILNDREKDVLRNRYGLDGTMTSTTFAVLGKKYSISAESIRQTQLRALKKLR 263


>gi|319792729|ref|YP_004154369.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus EPS]
 gi|315595192|gb|ADU36258.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus EPS]
          Length = 340

 Score =  138 bits (348), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 131/233 (56%), Gaps = 8/233 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLV+++AK Y  RG+   DLI+EGN+GLM A  KF+   G++FSTYA WW
Sbjct: 94  ARQSMIEHNLRLVVNIAKGYLGRGVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK---IKREPTP---EEIAKKLA 557
           ++Q++ R++  Q+  IR+PVH+  ++ +V+R  R +      + R P     E+IA  L 
Sbjct: 154 IRQSVERAVMTQARAIRLPVHVVRELQQVLRARRALEGDAEFVARRPDGVRVEDIAALLG 213

Query: 558 MPVEGVRKVLKITKEPISLET--PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             V+ V  +L +++ P SL+     GDE  +       D    +P        +     +
Sbjct: 214 RDVQEVADLLALSEAPRSLDAGDARGDEGFTLADTVASDDEQGNPSGVTQAHEVERLLDQ 273

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE  VL  R+G+      TLE +  +  +TRER+RQI+ +A+ K++
Sbjct: 274 WIHALDAREREVLEGRYGLHDREPETLEVLSVRLGLTRERVRQIQNEALAKMR 326


>gi|318066965|emb|CBY89097.1| RNA polymerase sigma70 factor [Halomonas pacifica]
          Length = 362

 Score =  138 bits (348), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 88/229 (38%), Positives = 126/229 (55%), Gaps = 18/229 (7%)

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           E  RE  +L   AV  +K    S + +  + +L +L   + L     + LV Q+    ++
Sbjct: 144 EQIREQNALVKAAV--EKHGYGSAEAQAEQARLAELFSPIKLVPKHFERLVGQVRISVEQ 201

Query: 349 IMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           +   E  ++++    G + R  F++   G E    W+         E+    A   D + 
Sbjct: 202 VRAQEKAIMQVFVKRGKVPRKAFIKSFPGNESRAEWMD--------EFLADNAKYADRLE 253

Query: 408 KIRNEI----KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
             R ++    + IS E     + + E + +   +  GE +A  AKKEMVEANLRLVIS+A
Sbjct: 254 PFRGDVQRAQRKISFEEDMVQLPVGELKEVNRRLSIGEAKARRAKKEMVEANLRLVISIA 313

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 314 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 362


>gi|239934550|emb|CAR94589.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 225

 Score =  138 bits (348), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 142/240 (59%), Gaps = 32/240 (13%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + L++R G IAIAKRIEAGR  M++ LCESPL+FQA+IIWRDELN+G  LLR+IIDLEA 
Sbjct: 1   LTLVAR-GRIAIAKRIEAGREAMISGLCESPLSFQAIIIWRDELNEGKILLRDIIDLEAT 59

Query: 191 I-GPESK----------GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
             GP++K                       KRE +++E          G   S   +S D
Sbjct: 60  YAGPDAKKVEAPTPEERERKEKEARKAEADKREKAAEEMRAKSGSRRGG---SDDVLSAD 116

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           D   V+ P ++ ++++   +        +L+AME +L+P V+   D IA+ Y+ LR LQD
Sbjct: 117 DFEPVEQPDDDDDDEDEEAN-------VSLAAMEAELKPHVLETFDRIAKTYKSLRKLQD 169

Query: 300 NAVNGQKDEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
             V+    EK+++      + + L+E++++ V SLSLN +RI+ LVEQLYDI++R++  E
Sbjct: 170 QEVS----EKTALSPSQGRRYRKLREEIIEDVKSLSLNAARIEALVEQLYDINRRLISLE 225


>gi|2385344|emb|CAA74896.1| sigma factorB [Arabidopsis thaliana]
          Length = 500

 Score =  138 bits (347), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 145/250 (58%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 253 ECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 312

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 313 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 371

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V KV  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 372 QKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENN---PWHGYDDLALKE 428

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 429 EVSKLISATLGEREKEIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHA 487

Query: 671 SRSKKLRSFL 680
           +R +K+ + +
Sbjct: 488 ARKRKMEAMI 497


>gi|295133351|ref|YP_003584027.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294981366|gb|ADF51831.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 284

 Score =  138 bits (347), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 143/252 (56%), Gaps = 8/252 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V + RK +     A   +V +NLR V+SVAK+Y  +GL   DLI EGN+GL+KAA +FD 
Sbjct: 37  VELTRKIKAGDKKALHTLVTSNLRFVVSVAKQYQFKGLSLSDLIAEGNLGLIKAANRFDE 96

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KF +YA+WW++QA+ +SI++ +  +R+P++    I+K+ +    +   ++RE + E
Sbjct: 97  TRGFKFISYAVWWIRQAMVQSISENARVVRLPLNKLTLINKIRKANSALQQLLQREASLE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++  L +P+  + +  K     +SL+ P+ +++     DF  ++   S ++   Q  L 
Sbjct: 157 EVSNFLNLPLTEIEEAGKSNATYLSLDKPLSNDN----DDFTLNQLITSKIEDPDQGLLN 212

Query: 611 ETTT----RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +T+    +++  L  RE+ V+ + FG+      +L ++     +T ER+RQI+   + K
Sbjct: 213 VSTSHEINQLMTILEKREKEVIILLFGLNGGEAKSLRDISTLLGLTSERVRQIKEMGLIK 272

Query: 667 LKHPSRSKKLRS 678
           L+   ++  L S
Sbjct: 273 LRRSPKAAILFS 284


>gi|15217767|ref|NP_176666.1| SIGA (SIGMA FACTOR A); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana]
 gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana]
 gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana]
 gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana]
 gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana]
 gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana]
          Length = 502

 Score =  138 bits (347), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 145/250 (58%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 255 ECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 314

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 315 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 373

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V KV  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 374 QKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENN---PWHGYDDLALKE 430

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 431 EVSKLISATLGEREKEIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHA 489

Query: 671 SRSKKLRSFL 680
           +R +K+ + +
Sbjct: 490 ARKRKMEAMI 499


>gi|2398851|dbj|BAA22214.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 502

 Score =  138 bits (347), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 145/250 (58%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 255 ECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 314

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 315 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 373

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V KV  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 374 QKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENN---PWHGYDDLALKE 430

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 431 EVSKLISATLGEREKEIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHA 489

Query: 671 SRSKKLRSFL 680
           +R +K+ + +
Sbjct: 490 ARKRKMEAMI 499


>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
          Length = 502

 Score =  137 bits (346), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 145/250 (58%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 255 ECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 314

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 315 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 373

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V KV  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 374 QKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENN---PWHGYDDLALKE 430

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 431 EVSKLISATLGEREKEIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHA 489

Query: 671 SRSKKLRSFL 680
           +R +K+ + +
Sbjct: 490 ARKRKMEAMI 499


>gi|42525589|ref|NP_970687.1| sigma-70 family RNA polymerase sigma factor [Treponema denticola
           ATCC 35405]
 gi|41815600|gb|AAS10568.1| RNA polymerase sigma-70 factor, region 2 family [Treponema
           denticola ATCC 35405]
          Length = 275

 Score =  137 bits (346), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 83/237 (35%), Positives = 134/237 (56%), Gaps = 6/237 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V+KG  EA    + +V +NLRLVI +AKK+++   Q L+LIQEGN+GLMKAA KF     
Sbjct: 31  VKKGNTEAI---EVLVTSNLRLVIKMAKKFSSNENQILELIQEGNMGLMKAASKFSKSFK 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FS+YA WW+KQ+  R +      I++PV     I +V +       K    P+  ++A
Sbjct: 88  VRFSSYAAWWIKQSFIRYLNSADKVIKLPVRKEALIRQVHKEEENYKIKYGILPSYSQLA 147

Query: 554 KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + +   V+ + ++       I SL+ P+ +E +++L DFI   N  +P +  I    +E 
Sbjct: 148 EIMKEKVDIIAQIKSFNYTDICSLDDPVDNERSANLYDFIPC-NTYNPEEEFIDNEFKEK 206

Query: 613 TTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  L  RE+ VLR R+G+ G  T  T   +GK++ ++ E IRQ + +A++KL+
Sbjct: 207 LNKCLEILNDREKDVLRNRYGLDGTMTSTTFAVLGKKYSISAESIRQTQLRALKKLR 263


>gi|218961053|ref|YP_001740828.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
 gi|167729710|emb|CAO80622.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
          Length = 292

 Score =  137 bits (346), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 143/264 (54%), Gaps = 10/264 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++N +  IS    +S  E   +    + G+ +A     ++++ANL+ V+ +A +Y NRGL
Sbjct: 13  LQNYLNEISKFKTLSREEEHDLAIKAKNGDMDAM---NKLIQANLKFVVKIASRYQNRGL 69

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGL+KA EKFD     K  +YA+WW+KQ I  +++++S  IR+P+     
Sbjct: 70  SLSELISEGNIGLIKAIEKFDPDKDIKLISYAIWWIKQRIMLAVSEKSSLIRVPMGKSSA 129

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            H+V  T  R   +  +  TP+E+++K+ +  + + ++     E  S +  I   D+   
Sbjct: 130 AHRVKLTQDRYFTETGKIATPDELSEKMNIAEKTIEQLQNKLPETSSFDDIITTSDSQDF 189

Query: 589 G--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH---TLE 643
              D +EDK+ + P     Q  ++E     ++ L  RE  ++R  F  G+N  H      
Sbjct: 190 TAKDLLEDKDTLDPQSLYYQERMQEKIQNAISKLDAREAEIIRNYF--GLNESHESRNFA 247

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           ++ ++  ++RER+RQI+ +A++K+
Sbjct: 248 QIAEKLGLSRERVRQIQKEALKKI 271


>gi|318066971|emb|CBY89100.1| RNA polymerase sigma70 factor [Halomonas sulfidaeris]
          Length = 368

 Score =  137 bits (346), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 87/229 (37%), Positives = 129/229 (56%), Gaps = 18/229 (7%)

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           E  RE  +L + A    K  + S + K  + +L  L   + L     + LV Q+    ++
Sbjct: 150 EQIREQNALVEAAFA--KHGRGSPELKAEQARLAVLFSPIKLVPKHFERLVGQVRISVEQ 207

Query: 349 IMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           +   E  +++L  +   + R  F++   G E    W+         E++   +   D + 
Sbjct: 208 VRAQEKAVMQLCVKKAKVPRKTFIKSFPGNESSKTWLD--------EFQAAQSKYADRLE 259

Query: 408 KIRNEI----KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +R +I    + I+ E     +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+A
Sbjct: 260 PLRADIARAQRKIAFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIA 319

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 320 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 368



 Score = 64.7 bits (156), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILDAYDATQD 80


>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa]
 gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa]
          Length = 559

 Score =  137 bits (346), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 133/234 (56%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+++    LV+ +A+ Y   G+   DLIQ GN+GL++ AE+FD   GY+FSTY  +W+++
Sbjct: 324 ELIKNTHSLVLYIARNYRGMGIAMEDLIQAGNLGLLQGAERFDPTRGYRFSTYVQYWIRK 383

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           ++ + +   +  I+IP  +   I+K+ +  + +SN   R P   E+AK   + +  +   
Sbjct: 384 SMLKIVERHARGIQIPYALSRSINKIQKARKALSNSHGRYPDDWEVAKFTGLSLAKIESA 443

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            K  +   SL+  IG+   +   +FI D +  +P ++ ++ ++RE    +L  L  RE++
Sbjct: 444 QKCLRVVASLDQKIGEGHYAKYSEFIPDMSIQNPEEAVMRQHMREEIYDLLRGLDSREKQ 503

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+ +R+G   N   +L E+G+ F V++ER+R+IE K + KL+     + L  ++
Sbjct: 504 VMVLRYGFKDNQPKSLAEIGRLFRVSKERVRKIEKKIMIKLRDEGIRRNLSRYM 557


>gi|318066963|emb|CBY89096.1| RNA polymerase sigma70 factor [Halomonas neptunia]
          Length = 368

 Score =  137 bits (346), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 87/229 (37%), Positives = 129/229 (56%), Gaps = 18/229 (7%)

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           E  RE  +L + A    K  + S + K  + +L  L   + L     + LV Q+    ++
Sbjct: 150 EQIREQNALVEAAFA--KHGRGSPELKAEQARLAVLFSPIKLVPKHFERLVGQVRISVEQ 207

Query: 349 IMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           +   E  +++L  +   + R  F++   G E    W+         E++   +   D + 
Sbjct: 208 VRAQEKAVMQLCVKKAKVPRKTFIKSFPGNESSKTWLD--------EFQAAQSKYADRLE 259

Query: 408 KIRNEI----KSISVE---TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +R +I    + I+ E     +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+A
Sbjct: 260 PLRADIARAQRKIAFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIA 319

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 320 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 368



 Score = 64.7 bits (156), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILDAYDATQD 80


>gi|326773499|ref|ZP_08232782.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636729|gb|EGE37632.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 147

 Score =  137 bits (345), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 73/145 (50%), Positives = 96/145 (66%)

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M   + REPTPEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  
Sbjct: 3   RQMLQDLGREPTPEELAVELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSE 62

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV P D+     L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERI
Sbjct: 63  AVVPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERI 122

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIE+K + KL+HPSRS+ LR +LD
Sbjct: 123 RQIESKTMSKLRHPSRSQVLRDYLD 147


>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa]
 gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa]
          Length = 509

 Score =  137 bits (345), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 143/250 (57%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + S+A++++  +N+RLV+S+A+KY N G +  DL+Q G IGL++  EKFD   G+K STY
Sbjct: 262 QCSLAREKLAMSNVRLVMSIAQKYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTY 321

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 322 VYWWIRQGVSRALVDNSRTLRLPNHLHERL-GLIRNAKIRLEEKGVTPSIDRIAESLNMS 380

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E + KV  + +E   SL    G+   S++ D   + N   P     +  L+E
Sbjct: 381 QRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRPENN---PWHGVDEWALKE 437

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +++ ++L  RE+ ++R+  G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 438 EVNKLIDSTLQEREKEIIRLYHGLDQEC-LTWEDISKRMGLSRERVRQVGLVALEKLKHA 496

Query: 671 SRSKKLRSFL 680
           +R +   + L
Sbjct: 497 ARKRNTEAML 506


>gi|120553093|ref|YP_957444.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
 gi|120322942|gb|ABM17257.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 330

 Score =  137 bits (345), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 136/235 (57%), Gaps = 2/235 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+    A   +  ++++NLRL + +A++Y + G+   DLIQ+ N+GL+KA E++D   G+
Sbjct: 87  RRAYHLALACRHRLIQSNLRLAVHIARRYGHHGIAMSDLIQDANVGLIKAVERYDPGKGF 146

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW+ + + R +      +  P ++ ++I ++ + + R+   + REPT  E+A+
Sbjct: 147 RFSTYAYWWISEEVRRCLQRGVRVVHTPENVVEEIRQLQKVSMRLHQSLGREPTQSELAR 206

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++      + ++  +    +S + P+ ++ +  L D + D  A +  D   +A  R    
Sbjct: 207 EMEATPSRIGELRALAAREVSTDVPLVEDGSVTLADSL-DAGADTRPDQPFRARDRMIRL 265

Query: 615 -RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R++ +L+ RE  +L  R+G+G+    TL+ + +Q  ++RER+RQIE  A+RKL+
Sbjct: 266 ERMMGALSDRERDILTRRYGLGLIEPETLQTISEQLGLSRERVRQIEKGALRKLQ 320


>gi|297837779|ref|XP_002886771.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
 gi|297332612|gb|EFH63030.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
          Length = 503

 Score =  137 bits (344), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 144/250 (57%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 256 ECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 315

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 316 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 374

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V K+  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 375 QKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRVENN---PWHGYDDLALKE 431

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++++ A+L  RE  ++R+ +G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 432 EVSKLISATLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHA 490

Query: 671 SRSKKLRSFL 680
           +R +K+ + +
Sbjct: 491 ARKRKMEAMI 500


>gi|194696078|gb|ACF82123.1| unknown [Zea mays]
 gi|323388703|gb|ADX60156.1| SIGMA70-like transcription factor [Zea mays]
          Length = 541

 Score =  137 bits (344), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 84/255 (32%), Positives = 137/255 (53%), Gaps = 6/255 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + S VR G       +++M  +N RLVI VA+KY   GL   DL+Q+G  GLMK  EK
Sbjct: 289 RELQSCVRTGR----RCREKMARSNFRLVIHVARKYEGCGLDIQDLVQDGCCGLMKTFEK 344

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV + AR        +P
Sbjct: 345 FNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGK-ARMECIMDGEQP 403

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E +A++  + +E + K+   T++  S++  +  +D     +  ED N   P  S  + 
Sbjct: 404 TNEVVARRAGITIEKLAKLRAKTRKVRSMQDRVWSDDGVTYQEITEDPNIEGPEVSVDRL 463

Query: 608 NLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +R+     L   L+PRE+ ++  RFGI      TL  +G  + +++ERIRQ++ KA+ K
Sbjct: 464 MMRQQVRSFLTGILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQVQNKALDK 523

Query: 667 LKHPSRSKKLRSFLD 681
           L++   ++    + D
Sbjct: 524 LRNSISAQGFHVYFD 538


>gi|291529642|emb|CBK95228.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 340

 Score =  137 bits (344), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 89/258 (34%), Positives = 140/258 (54%), Gaps = 23/258 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           K E+   N+RLV+ VAK+Y    + ++ +DLI E ++GL+KA +++D+  GYKFSTYA W
Sbjct: 82  KDEIFSRNIRLVVYVAKRYYKNLKHMEPIDLIDEASLGLLKAIDRYDYTTGYKFSTYAYW 141

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W+ QA TRSIA+ +  IR PVH+ + I KV +  R+           + IAK+L +  E 
Sbjct: 142 WINQACTRSIANDNDLIRQPVHIHEFIIKVKKAQRKWGQTHDNNAPVDYIAKELNVSEEK 201

Query: 563 VRKVLKIT---KEPISLETPI-------GDEDTSHL-----GDFIEDKNAVSPLDSAIQA 607
           VR +L I       ISL+  +       GD +   +     G+   +K  V+   + I  
Sbjct: 202 VRNILIIIDCQSNYISLDCTMSKGSEEPGDTEVGEIVLDPKGNVDFEKVEVNQFQNRIIE 261

Query: 608 NLRETTTRVLAS------LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            L +   +  A        T R   V++ RFG       TLEE+ + + V+RERIRQIEA
Sbjct: 262 ILSKANNKTSAKSNRSVEQTKRMIDVIKRRFGFDNCRIETLEEIAQSYGVSRERIRQIEA 321

Query: 662 KAIRKLKHPSRSKKLRSF 679
           +A++ L++P   ++L ++
Sbjct: 322 QALKILRNPKYKRELATW 339


>gi|291448259|ref|ZP_06587649.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
 gi|291351206|gb|EFE78110.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
          Length = 360

 Score =  137 bits (344), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 57/81 (70%), Positives = 72/81 (88%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 278 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 337

Query: 504 VKQAITRSIADQSCTIRIPVH 524
           ++QAITR++ADQ+ TIRIPVH
Sbjct: 338 IRQAITRAMADQARTIRIPVH 358



 Score = 42.4 bits (98), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 214 ATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAG 247


>gi|149190801|ref|ZP_01869066.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
 gi|148835363|gb|EDL52335.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
          Length = 289

 Score =  137 bits (344), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 145/263 (55%), Gaps = 44/263 (16%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAA 485
           H  ++ R+G+     A+  ++E+NLRLV+ +A+ YT RGL     LDLI+EGN+GL+KA 
Sbjct: 40  HYATLARRGD---KAARDVLIESNLRLVVKIARNYTKRGLSNHTILDLIEEGNLGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF+   G++FSTYA+WW++++I  S+ +   T+R+PVH+  +I+++ +    +   ++R
Sbjct: 97  DKFEPEKGFRFSTYAVWWIRESIESSLMNTGRTVRLPVHVIKEINRLSKQTNEIIADLQR 156

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            P+ +EIA+K A            ++  IS        D  H+  FIE  ++V  +D   
Sbjct: 157 PPSVKEIAEKTAK-----------SQAQIS--------DLIHMSGFIESSSSVDTIDKEF 197

Query: 606 QA-------------------NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           Q+                    L ++   V+ SL  +   ++  RFG+      TL+ +G
Sbjct: 198 QSLETCKSEAIPEPYDICHNEKLSQSLESVVLSLPEKYRDIVIHRFGLFGKEVLTLDNLG 257

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
           + F +++ER+RQ++ + I KL++
Sbjct: 258 EMFGLSKERVRQLQQEGISKLQN 280


>gi|162458769|ref|NP_001105507.1| sigma-like factor6 [Zea mays]
 gi|4336610|gb|AAD17856.1| sigma factor SIG6 [Zea mays]
          Length = 541

 Score =  136 bits (343), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 84/255 (32%), Positives = 137/255 (53%), Gaps = 6/255 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + S VR G       +++M  +N RLVI VA+KY   GL   DL+Q+G  GLMK  EK
Sbjct: 289 RELQSCVRTGR----RCREKMARSNFRLVIHVARKYEGCGLDIQDLVQDGCCGLMKTFEK 344

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV + AR        +P
Sbjct: 345 FNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGK-ARMECIMDGEQP 403

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E +A++  + +E + K+   T++  S++  +  +D     +  ED N   P  S  + 
Sbjct: 404 TNEVVARRAGITIEKLAKLRAKTRKVRSMQDRVWSDDGVTYQEITEDPNIEGPEVSVDRL 463

Query: 608 NLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +R+     L   L+PRE+ ++  RFGI      TL  +G  + +++ERIRQ++ KA+ K
Sbjct: 464 MMRQQVRSFLTGILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQVQNKALDK 523

Query: 667 LKHPSRSKKLRSFLD 681
           L++   ++    + D
Sbjct: 524 LRNSISAQGFHVYFD 538


>gi|20808499|ref|NP_623670.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
 gi|20517120|gb|AAM25274.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 265

 Score =  136 bits (343), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 142/239 (59%), Gaps = 7/239 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+ E+VE N+ LV+S+A  ++   G++  DLIQEG IGL+ A E FD   GY+FSTYA++
Sbjct: 26  ARDEIVEKNIGLVVSIAANFSKAYGVELDDLIQEGFIGLLAAIEGFDHTKGYRFSTYAVF 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++KQ I R I  +S TI +PV    K+++V+    ++  ++K E  PEEIA++  +  E 
Sbjct: 86  YIKQKIQRYIWGRSRTIHLPVKTYQKLNQVLSAQLKLE-QVKGEAFPEEIAEETGIKTEE 144

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLT 621
           V  +L +    +SL   + + D + L D I D+ + + +D       LR+     L  L 
Sbjct: 145 VVNLLSLKNPTVSLNQQLYENDNTELIDVILDEQSENEIDRNYSLEELRKILKECLEVLP 204

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +E  VL MR+G+   T  TL+++ +   ++++R  QIE +A+++L++   S+K+R+ L
Sbjct: 205 EKERSVLEMRYGLN-GTPMTLKQIAEILNISKQRAGQIEKRALQRLRN---SRKIRNAL 259


>gi|323454681|gb|EGB10551.1| hypothetical protein AURANDRAFT_23034 [Aureococcus anophagefferens]
          Length = 388

 Score =  136 bits (342), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 138/248 (55%), Gaps = 16/248 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +  ANLRLV+S+AK+Y   GL   DL+QEG  GL +A E+FD   G++FSTYA +W
Sbjct: 133 ARSTLTSANLRLVVSIAKRYRFCGLAQEDLLQEGAFGLSRAVERFDPERGFRFSTYATFW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA+ R+ A+QS  IR+P H+ D++  + + +  +S ++ R+ T +E+A  L +     
Sbjct: 193 IRQAVLRACAEQSRVIRLPAHVHDQLASMRKASAELSRRLGRDATDDELADHLELEKPEK 252

Query: 564 RKVLK--ITKEPISLE-------------TPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
              L+    ++P SL+                G    + + + + D   + P +   +A 
Sbjct: 253 LAFLRRCAAQDPSSLDEKHAIHAGRGSSVGGGGAAGATTIAESLSDDTILVPDEFVAEAA 312

Query: 609 LRETTTRVLASLTP-REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE    +LA++   RE  VL MRFG+  N   +  ++ ++  V+RER+RQIE +A+ KL
Sbjct: 313 SREYVGDLLATVCNDRERDVLGMRFGLYGNAPISKTKIAERLAVSRERVRQIEVRALTKL 372

Query: 668 KHPSRSKK 675
           +   R+ +
Sbjct: 373 RQTHRANR 380


>gi|318066995|emb|CBY89112.1| RNA polymerase sigma70 factor [Salinicola salarius]
          Length = 368

 Score =  135 bits (341), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 81/213 (38%), Positives = 118/213 (55%), Gaps = 16/213 (7%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           +K  + S +  + + +L +L   + L+    + LV Q+     ++   E  ++++    G
Sbjct: 164 EKHGRGSEEADIEQARLAELFSPIKLSPKHFERLVGQVRISVDQVRSQEKAIMQVFVKQG 223

Query: 365 -IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG-- 421
            + R  F+    G E    W      F E   KN      D +   R +++    + G  
Sbjct: 224 KVPRKTFISSFLGNETAEGW------FDEFIAKN--GKYADRLEPFRGDVQRAQRKIGFE 275

Query: 422 -----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                + + + + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 276 QEMVLLDVGQLKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 335

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           GNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 336 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 368



 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 42/60 (70%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D+  D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEILIAKRIEEGLREVMSSLAYLPGAVDSILDVYDQTQD 80


>gi|6682871|dbj|BAA88922.1| sigma factor [Nicotiana tabacum]
          Length = 502

 Score =  135 bits (341), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/256 (31%), Positives = 149/256 (58%), Gaps = 14/256 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R    E S+A++++  +N+RLV+S+A++Y   G +  DLIQ G IGL++  EKFD   G
Sbjct: 249 LRSTLIECSLAREKLAMSNVRLVMSIAQRYDTNGTEMADLIQGGLIGLLRGIEKFDHSRG 308

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +K STY  WW++Q ++R++ + S T+R+P+H+ +++  ++R A+    +    P+ E+IA
Sbjct: 309 FKISTYVYWWIRQGVSRALVENSRTLRLPIHLHERL-SLIRNAKIKLKENGITPSIEKIA 367

Query: 554 KKLAMPVEGVR-------KVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + L M  + VR       KV  + +E   SL    G+   S++ D   ++    P     
Sbjct: 368 ECLNMSQKKVRNATEASSKVFSLDREAFPSLNGLPGETLHSYIAD---NRLENIPWHGVD 424

Query: 606 QANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  L++    +++S L  RE  ++R+ +G+  N   T E++ ++  ++RER+RQ+   A+
Sbjct: 425 EWMLKDEVNNLISSTLREREREIVRLYYGLD-NECLTWEDISRRIGLSRERVRQVGLVAL 483

Query: 665 RKLKHPSRSKKLRSFL 680
            KLKH +R ++L + L
Sbjct: 484 EKLKHAARKRRLDAML 499


>gi|89901551|ref|YP_524022.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
 gi|89346288|gb|ABD70491.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
          Length = 350

 Score =  135 bits (340), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 132/232 (56%), Gaps = 7/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLV+S+AK Y  RG+  LDLI+EGN+GLM A +KF+   G++FSTYA WW
Sbjct: 105 ARQSMIEHNLRLVVSIAKAYMGRGVPLLDLIEEGNLGLMHAIDKFEPERGFRFSTYATWW 164

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK---IKREPTP---EEIAKKLA 557
           ++Q++ R++  Q   +R+PV++  ++ +V+R  R + +    +   P     E++A  L 
Sbjct: 165 IRQSVDRALMCQGRVVRLPVNVVRELQQVLRARRALESDAAFVVSRPDGIRVEDVAALLG 224

Query: 558 MPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                V  +L + + P SL+  +    +T   GD + D+    P        +       
Sbjct: 225 RDPVHVADLLGLAEAPRSLDAALDRSGETQTFGDSLVDEITADPSGVTQVHEVERLLEEW 284

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L+ RE+ VL  RFG+      TL+ +  +  +TRER+RQ++ +A+ KLK
Sbjct: 285 VGTLSEREKEVLEGRFGLHDREPETLDVLSARLDLTRERVRQVQNEALAKLK 336


>gi|330375231|gb|AEC12842.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens]
          Length = 200

 Score =  135 bits (340), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 66/185 (35%), Positives = 115/185 (62%)

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+
Sbjct: 1   AVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKL 60

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P + 
Sbjct: 61  DHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCEL 120

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +L ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + 
Sbjct: 121 LQDDDLSQSIDQWLSELTEKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEG 180

Query: 664 IRKLK 668
           +++L+
Sbjct: 181 LKRLR 185


>gi|6682869|dbj|BAA88921.1| sigma factor [Nicotiana tabacum]
          Length = 508

 Score =  135 bits (340), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 142/249 (57%), Gaps = 12/249 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E S+A++ +  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   GYK STY
Sbjct: 261 ECSLARERLAMSNVRLVMSIAQRYDNVGAEMADLVQGGLIGLLRGIEKFDPSKGYKISTY 320

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
             WW++Q ++R++ + S T+R+P ++ +++  ++R A+    +    P+   IA  L M 
Sbjct: 321 VYWWIRQGVSRALVENSRTLRLPTYLHERL-SLIRNAKARLEEKGITPSVNNIAASLNMS 379

Query: 560 VEGVR-------KVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + VR       K+  + +E   SL    G+   S++ D   + N    +D  + A   E
Sbjct: 380 QKKVRNATEASSKMYSLDREAFPSLNGLPGETLHSYIADNHLENNPWHGVD--VWALKDE 437

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               + ++L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KLKH +
Sbjct: 438 VNNLISSTLRDREREIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496

Query: 672 RSKKLRSFL 680
           R ++L + L
Sbjct: 497 RKRQLDAML 505


>gi|320537570|ref|ZP_08037508.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320145572|gb|EFW37250.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 274

 Score =  134 bits (338), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 131/226 (57%), Gaps = 2/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ +NLRLV+ +AK  T      +DLIQEGN+GLM AAEKF      +FS+YA WW
Sbjct: 38  ALQQLINSNLRLVVKMAKDRTPSENLLMDLIQEGNMGLMIAAEKFSSSFNARFSSYACWW 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q++ R +  +  TIR+P    D + K+ +T      K +R P+ EEIA+ + +P++ V
Sbjct: 98  IRQSLNRYLNGKHETIRLPFRKADLLRKIEKTIDLFKEKYRRTPSYEEIAEIIQVPLKSV 157

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTP 622
            ++   T++PIS ++P+    +++L D  E+ N  +P     +    E   + L  +L  
Sbjct: 158 IQICVFTEKPISFDSPLQIHFSANLYDLTEN-NDYNPEKEYFRKVQIEAFRKFLQNTLKS 216

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++  R  I      +L  +G ++ ++ E +RQ E +A++KL+
Sbjct: 217 REKDIIEERLPITDKNPKSLRSLGIKYGISAESVRQTEIRALKKLR 262


>gi|318066993|emb|CBY89111.1| RNA polymerase sigma70 factor [Salinicola halophilus]
          Length = 368

 Score =  134 bits (338), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 79/201 (39%), Positives = 113/201 (56%), Gaps = 22/201 (10%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRE 378
           +L  L   + L+    + LV Q+    +++   E  ++++    G + R  F+    G E
Sbjct: 179 RLAVLFSPIKLSPKHFERLVGQVRISVEQVREQEKSIMQVFVKQGKVPRKTFISEFLGSE 238

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEI----KSISVE---TGISISEFR 428
               W           + +FVA      D +   R ++    + I  E     +++ + +
Sbjct: 239 TTESW-----------FDDFVAKHTKYADRLAPFRGDVQRAQRKIDFEQEMVQLNVGQLK 287

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 288 EVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 347

Query: 489 DWCLGYKFSTYAMWWVKQAIT 509
           ++  GYKFSTYA WW++QAIT
Sbjct: 348 EYRRGYKFSTYATWWIRQAIT 368



 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 43/60 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++ + D+  D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGLREVMSSLAYLPGAVDSVLAFYDQTQD 80


>gi|300728464|ref|ZP_07061824.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
 gi|299774265|gb|EFI70897.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
          Length = 251

 Score =  134 bits (337), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 140/273 (51%), Gaps = 41/273 (15%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +  I  E  +S  E + + + ++ G+ E++I K  +  ANLR V+S+AK+Y +RGL
Sbjct: 18  LQTYLSEIGKENLLSEQEEQELSAKIQNGD-ESAIEK--LTTANLRFVVSIAKRYQDRGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN GL+KAA KFD   G +F  YA+ +++QAI  +I +QS    +P  M D 
Sbjct: 75  GINDLISEGNFGLIKAARKFDAAKGQRFVQYAVHFIRQAIENAIQEQSGIYTLPHSMDD- 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
                                         PVE     LK +K   S++ P+    T+ L
Sbjct: 134 ------------------------------PVE-----LKQSK-AFSVDAPLVQGKTASL 157

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG-MNTDHTLEEVGK 647
              + D NAV P    +   LR+   R L+ L  RE RV+ M +G+   N   T EE+G 
Sbjct: 158 LHVLSDPNAVIPDKPYLDDVLRQGLIRSLSVLNDRERRVVSMFYGLNDQNAGLTYEEIGT 217

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           Q  + RER+R I  KA RK+K  +++ +L+S+L
Sbjct: 218 QLGLKRERVRDIRKKAERKMKKYTKNDQLKSYL 250


>gi|302876248|ref|YP_003844881.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307686980|ref|ZP_07629426.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579105|gb|ADL53117.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 281

 Score =  134 bits (336), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 96/258 (37%), Positives = 140/258 (54%), Gaps = 29/258 (11%)

Query: 444 AKKEMVEANLRLVISVA--KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A+  ++  N RLV   A  KK T+  L + DL+QEG IGLM   EKF+     KFSTY  
Sbjct: 28  ARDYLIINNKRLVYKAASLKKDTSL-LAYDDLVQEGLIGLMIGIEKFNADYNSKFSTYIY 86

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-----RTARRMSNKIKREPTPEEIAKKL 556
           +W+KQ I R+I +   +IR+P+H+ +KI+KV+        + + N      T  +I  K 
Sbjct: 87  YWIKQRIDRAIYNTGTSIRLPIHLINKINKVMYVENKNNVKSLDNDSTDLCTDLDITDK- 145

Query: 557 AMPVEGVRKVLKITKEPISLETPI------GDEDTSHLGDFIEDK--NAVSP------LD 602
               +  + ++K  K  ISL + +      GDE+   L DFI++   N   P      +D
Sbjct: 146 --QYDYYKFLVKQFKNIISLNSALLSDNSEGDEE---LIDFIDENSSNFGDPGSKNYSID 200

Query: 603 S-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           S  I+  L      VL +L  RE+ VLRMRFG+      TLE++G  F VTRERIRQIE+
Sbjct: 201 SNIIKEELSHDLNEVLKTLNEREQHVLRMRFGLDDGEMKTLEQIGNHFNVTRERIRQIES 260

Query: 662 KAIRKLKHPSRSKKLRSF 679
           KA++KL++P    +L  +
Sbjct: 261 KALKKLRNPKILMRLEGY 278


>gi|320105081|ref|YP_004180672.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319752363|gb|ADV64123.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 322

 Score =  134 bits (336), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 71/225 (31%), Positives = 132/225 (58%), Gaps = 10/225 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++  AN+RLV  VAK++ +RG+ + DL+QEG  GL++A ++FD   G K +TYA WW+
Sbjct: 92  RSKLALANMRLVAHVAKRFRDRGVSYSDLLQEGFCGLLEAIDRFDLAHGTKLATYATWWI 151

Query: 505 KQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +QA+ R++A  +  +R+ P H+R          R    + +++ + EE     ++  E +
Sbjct: 152 RQAMQRAVAATAYPVRLSPRHLRQLARNQEEIERGGQPRTRKKASDEE-----SVSPEMI 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++   T+  +SL+  +  + +  L   + D       D   + ++ ET  +++ +L PR
Sbjct: 207 QRIHAATRPTVSLDATVDSDSSFSLLHTMSDPEG----DRTGEVDMDETIVKLMENLRPR 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E +VL +RFG+   T H+L +VGK   V++ER+RQI+ +A+ KL+
Sbjct: 263 EIQVLSLRFGLNGATRHSLSQVGKVLDVSKERVRQIQDRALEKLR 307


>gi|218848158|ref|YP_002454701.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
 gi|218546289|gb|ACK98682.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
          Length = 295

 Score =  134 bits (336), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 92/262 (35%), Positives = 140/262 (53%), Gaps = 16/262 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEK 487
           HI+    KG+ ++   ++ ++ +NLRLV+SVAK +   G    +++IQEG IGLMK  E 
Sbjct: 32  HIIKYKEKGDIDS---RELLICSNLRLVVSVAKSFPCYGNCDLMEMIQEGTIGLMKGLED 88

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D+  G K STY  WW++Q I++ ++     +R+   M+ KI +V         +     
Sbjct: 89  YDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKKITEVKNCYYENMGEKGTNL 148

Query: 548 TPEEIAKKLAMPVEGVRKVL---KITKEPISLETPIGDEDT------SHLGDFIEDKNAV 598
           T  E+A++L      V   L   +IT   IS+E  + +E T      S L   + +KNA 
Sbjct: 149 TTMEVAERLGYKESIVIDALVTDRITN-TISIEDDVQNEKTLLDRQQSTLA-ILANKNAP 206

Query: 599 SPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +P +  A +    E    +  +L PREE VLR RFG     + TLE+  +   VTRER++
Sbjct: 207 NPSEVMATEEEKFEFDELMFVTLNPREESVLRYRFGFDDGIELTLEDTARILGVTRERVQ 266

Query: 658 QIEAKAIRKLKHPSRSKKLRSF 679
           QIE KAI K+K    SKK+ SF
Sbjct: 267 QIEKKAIEKMKQRLSSKKINSF 288


>gi|318066903|emb|CBY89066.1| RNA polymerase sigma70 factor [Chromohalobacter beijerinckii]
          Length = 367

 Score =  133 bits (335), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 77/191 (40%), Positives = 110/191 (57%), Gaps = 2/191 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L +L   + L     + LV Q+    ++I   E  ++++  +   + R  F+    G E
Sbjct: 178 RLAELFSPIKLVPKHFERLVGQVRISIEQIRGQEKAIMQIFVKQAKVPRKTFIGSFPGAE 237

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            D  W+   +       +       D IL+ + +I        + ++  + +   +  GE
Sbjct: 238 SDLEWLDRFQTKHSKYAERLEPFRAD-ILRAQRKIGFEEEMVRLPVTNIKEVNRRLSIGE 296

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 297 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 356

Query: 499 YAMWWVKQAIT 509
           YA WW++QAIT
Sbjct: 357 YATWWIRQAIT 367



 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 35/45 (77%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P
Sbjct: 21  TTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLP 65


>gi|168029696|ref|XP_001767361.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
 gi|56603661|dbj|BAD80742.1| plastid sigma factor PpSIG5 [Physcomitrella patens]
 gi|162681425|gb|EDQ67852.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
          Length = 632

 Score =  133 bits (335), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 134/243 (55%), Gaps = 9/243 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A+ ++++ NLRLV+S A KY   +  L   DL QEG IGLM+A +KFD   GY+FSTY +
Sbjct: 394 ARTKLIQRNLRLVLSQAYKYHKDSMSLSIQDLCQEGVIGLMQAVDKFDPGKGYRFSTYGI 453

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +W++ +I R+       +R P ++      + R    + +++ R+PT +EI K L +  +
Sbjct: 454 YWIRNSILRAQTKSGHMLRSPHNVSTHRVNIQRAKVELFSELGRQPTNDEIRKHLGITAD 513

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL---DSAIQANLRETTTRVLA 618
             R +L+      SL           + + + +++A+  L    S +Q  L +    VL 
Sbjct: 514 RFRDILRTNMRTSSLHEHDRITGREKVENLVSEEDALDTLAGGTSMVQYGLDD----VLD 569

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SL P+E  VLR RFG+      +L EVG    ++RE +R+ E + I KL+HP+R + LR+
Sbjct: 570 SLRPKENLVLRQRFGLDGKGQRSLSEVGLILNLSREMVRRYELRGILKLQHPTRVEYLRN 629

Query: 679 FLD 681
           +L+
Sbjct: 630 YLN 632


>gi|2706544|emb|CAA75859.1| Sig1 [Sinapis alba]
          Length = 481

 Score =  133 bits (334), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 141/249 (56%), Gaps = 12/249 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 234 ECHLAREKLAMSNVRLVMSIAQRYDNMGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 293

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 294 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 352

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V K+  + ++   SL    G+   S++ D   + N     D+    +  E
Sbjct: 353 QKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRLENNPWHGYDALALKD--E 410

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +  +  +L  RE  ++R+ +G+      T E++ ++  ++RER+RQ+   A+ KLKH +
Sbjct: 411 VSKLISVTLGEREREIIRLYYGLDKEC-LTWEDISQRIGLSRERVRQVGLVALEKLKHAA 469

Query: 672 RSKKLRSFL 680
           R +K+ + +
Sbjct: 470 RKRKMEAMI 478


>gi|228949811|ref|ZP_04112021.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228809869|gb|EEM56280.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 295

 Score =  132 bits (333), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 92/261 (35%), Positives = 139/261 (53%), Gaps = 16/261 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEK 487
           HI+    KG+ ++   +  ++ +NLRLV+SVAK +   G    +++IQEG IGLMK  E 
Sbjct: 32  HIIKYKEKGDIDS---RDLLICSNLRLVVSVAKSFPCYGNCDLMEMIQEGTIGLMKGLED 88

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D+  G K STY  WW++Q I++ ++     +R+   M+ KI +V         +     
Sbjct: 89  YDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKKITEVKNCYYENMGEKGTNL 148

Query: 548 TPEEIAKKLAMPVEGVRKVL---KITKEPISLETPIGDEDT------SHLGDFIEDKNAV 598
           T +E+A+KL      V   L   +IT   IS+E  + +E T      S L   + +KNA 
Sbjct: 149 TTKEVAEKLGYKESIVIDALVTDRITN-TISIEDDVQNEKTLLDKQQSTLA-ILANKNAP 206

Query: 599 SPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +P +  A +    E    +  +L PREE VLR RFG     + TLE+  +   VTRER++
Sbjct: 207 NPSEVIATEEEKFEFDELMFVTLNPREESVLRYRFGFDDGIELTLEDTARILGVTRERVQ 266

Query: 658 QIEAKAIRKLKHPSRSKKLRS 678
           QIE KAI K+K    SKK+ S
Sbjct: 267 QIEKKAIEKMKQRLSSKKINS 287


>gi|218197356|gb|EEC79783.1| hypothetical protein OsI_21197 [Oryza sativa Indica Group]
          Length = 557

 Score =  132 bits (333), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 119/225 (52%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV  +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+
Sbjct: 330 LVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAE 389

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
            S  I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +
Sbjct: 390 NSGVIQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVV 449

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL T IG    +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+
Sbjct: 450 SLYTEIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGL 509

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
                 +LE++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 510 EDGKCRSLEQIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 554


>gi|168700394|ref|ZP_02732671.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gemmata obscuriglobus UQM 2246]
          Length = 335

 Score =  132 bits (332), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 128/226 (56%), Gaps = 7/226 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  +  AN+RL   VAK++ +  L + DL+QE   GLM+A ++FD   G + +TYA WW+
Sbjct: 100 KHRLASANIRLAAHVAKRFRHHSLAYSDLLQEAVCGLMQAIDRFDVSHGTRLATYATWWI 159

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q +  ++A QS  + +  H   ++  + + +  +++  K  P+P+E+A +    +E + 
Sbjct: 160 RQTLQIAVARQSHLVSLSPHHLQELGLLQQESEALAHGGKHLPSPQELASRTGSSLEHLT 219

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTP 622
            +   T+ P+SL   + D+    L + + D   +      +Q N   +E  + ++ +L P
Sbjct: 220 HLQTATRTPVSLNAVLDDDSDFKLTEAMPDTGTL-----VMQENNERQEALSFLMENLRP 274

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +VL +RFG+  N  H+L ++G    +++ER+RQI+ +A+ KLK
Sbjct: 275 RERKVLDLRFGLTGNGTHSLRQIGHLLRISKERVRQIQNRALEKLK 320


>gi|303282119|ref|XP_003060351.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226457822|gb|EEH55120.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 425

 Score =  132 bits (332), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 89/278 (32%), Positives = 141/278 (50%), Gaps = 33/278 (11%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAK------KYTNRGL-QFLDLIQEGNIGLM 482
           IV+ +  G+     A++++V  N+ L  S+A+       + +RGL    DL QEG  GL 
Sbjct: 55  IVTAIDAGQN----ARRQLVVKNVGLAYSIARDVFEKLNHADRGLLSVSDLAQEGCAGLA 110

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +AA+KFD   GYKFSTYA  W ++ +  +I +   TIR+P+HM + + +  +  R ++ K
Sbjct: 111 QAADKFDPSRGYKFSTYAYNWTRKYVVNAIQNNGRTIRLPIHMHEIMQRAKKATRELTQK 170

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET---------------PIGDEDTSH 587
             R PT EE+++ L +PV  V+++    +  +SL+                 + D     
Sbjct: 171 HGRAPTDEEMSRTLGVPVSRVQEINDWARSTLSLDVGGGGRSSDDGDGGAEGMMDGIVFA 230

Query: 588 LGDFIEDKNAVSPLDSA---IQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           LG        +SP ++A   ++A+ LR       A+L PRE  VLR RFG+       L 
Sbjct: 231 LGSKDGKDGMLSPHEAAEADMEADLLRRDLEEAFATLLPREAFVLRHRFGLAAAASTAL- 289

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             G    V+ E IR  E +A+ KLK PSR+ +   +LD
Sbjct: 290 --GTLLGVSHETIRTYERRALEKLKQPSRAARFVRYLD 325


>gi|49328110|gb|AAT58808.1| hypothetical protein [Oryza sativa Japonica Group]
          Length = 799

 Score =  132 bits (331), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 139/276 (50%), Gaps = 5/276 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           +++LK  +E+   S      I E     +++R    E    ++ ++     LV  +AK Y
Sbjct: 526 ENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKYIAKTY 580

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  I++P 
Sbjct: 581 AGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLPA 640

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T IG  
Sbjct: 641 RMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG 700

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+      +LE
Sbjct: 701 QNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLE 760

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 761 QIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 796


>gi|58698251|ref|ZP_00373170.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535223|gb|EAL59303.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 379

 Score =  132 bits (331), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 111/376 (29%), Positives = 197/376 (52%), Gaps = 45/376 (11%)

Query: 36  KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           K  ++ G++T +++N  L  +  SS+ ++D +++L + GINV+        E SED  D+
Sbjct: 21  KSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVL--------ESSEDEEDI 72

Query: 96  ASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            S++ +S +       +   +    DDPVR+YL++M S++LLSR  EI IAK+IE+ +  
Sbjct: 73  PSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEIAKKIESEKHN 132

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A           + ++ +   K E
Sbjct: 133 MLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAI----------YNSDFNVVPKEE 182

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA- 271
               E+  +DV+++E   E A   S D++   DS   + E D  N    ED S+  L+  
Sbjct: 183 SEESEESAEDVEDSEDVSEDAEYCSDDEK---DSKKSDDEKDGNN----EDISSVNLNVS 235

Query: 272 ---MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
              ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++  +   +
Sbjct: 236 ILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIWSIALQI 289

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQGRELDP 381
            L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+ +++  
Sbjct: 290 KLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHELKKISL 349

Query: 382 HWVSYAKDFPEGEWKN 397
             ++  +    GE KN
Sbjct: 350 LKINENQSSFTGELKN 365


>gi|228988887|ref|ZP_04148936.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228770801|gb|EEM19317.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 295

 Score =  131 bits (330), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 91/261 (34%), Positives = 139/261 (53%), Gaps = 16/261 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEK 487
           HI+    KG+ ++   +  ++ +NLRLV+SVAK +   G    +++IQEG IGLMK  E 
Sbjct: 32  HIIKYKEKGDIDS---RDLLICSNLRLVVSVAKSFPCYGNCDLMEMIQEGTIGLMKGLED 88

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D+  G K STY  WW++Q I++ ++     +R+   M+ KI +V         +     
Sbjct: 89  YDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKKITEVKNCYYENMGEKGTNL 148

Query: 548 TPEEIAKKLAMPVEGVRKVL---KITKEPISLETPIGDEDT------SHLGDFIEDKNAV 598
           T +E+A++L      V   L   +IT   IS+E  + +E T      S L   + +KNA 
Sbjct: 149 TTKEVAERLGYKESIVIDALVTDRITN-TISIEDDVQNEKTLLDKQQSTLA-ILANKNAP 206

Query: 599 SPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +P +  A +    E    +  +L PREE VLR RFG     + TLE+  +   VTRER++
Sbjct: 207 NPSEVIATEEEKFEFDELMFVTLNPREESVLRYRFGFDDGIELTLEDTARILGVTRERVQ 266

Query: 658 QIEAKAIRKLKHPSRSKKLRS 678
           QIE KAI K+K    SKK+ S
Sbjct: 267 QIEKKAIEKMKQRLSSKKINS 287


>gi|47777365|gb|AAT37999.1| putative RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 882

 Score =  131 bits (330), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 139/276 (50%), Gaps = 5/276 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           +++LK  +E+   S      I E     +++R    E    ++ ++     LV  +AK Y
Sbjct: 609 ENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKYIAKTY 663

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  I++P 
Sbjct: 664 AGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLPA 723

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T IG  
Sbjct: 724 RMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG 783

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+      +LE
Sbjct: 784 QNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLE 843

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 844 QIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 879


>gi|222632746|gb|EEE64878.1| hypothetical protein OsJ_19735 [Oryza sativa Japonica Group]
          Length = 1012

 Score =  131 bits (330), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 139/276 (50%), Gaps = 5/276 (1%)

Query: 404  DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +++LK  +E+   S      I E     +++R    E    ++ ++     LV  +AK Y
Sbjct: 739  ENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKYIAKTY 793

Query: 464  TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
               G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  I++P 
Sbjct: 794  AGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLPA 853

Query: 524  HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
             M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T IG  
Sbjct: 854  RMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG 913

Query: 584  DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+      +LE
Sbjct: 914  QNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLE 973

Query: 644  EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            ++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 974  QIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 1009


>gi|284044896|ref|YP_003395236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949117|gb|ADB51861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 300

 Score =  131 bits (330), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 80/228 (35%), Positives = 136/228 (59%), Gaps = 7/228 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           AK+ +V  NLRLV+S+A+++     L  LDL+QEG +GL++AAEKFDW  G++FSTYA  
Sbjct: 63  AKERLVNHNLRLVVSIARRFQGVSELTLLDLVQEGVVGLIRAAEKFDWRRGFRFSTYATL 122

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAI R IA    TIR+PV++  +  KV   ARR+  ++ R PT EEI+    +P + 
Sbjct: 123 WIRQAIQRGIATHGRTIRLPVNVAQRERKVAAAARRLEAELGRAPTVEEISSASDLPPDQ 182

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASL 620
           V  + ++++   SL+  +  +  + LG+ +  E       +D+ +QA   ET  R +  L
Sbjct: 183 VADLREVSRTLASLDQVVTADTDTTLGELLPSEAPEVEEQVDALLQA---ETVRRTVEHL 239

Query: 621 TPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              +  V+++RFG+  + T     ++G++  +   ++R IE +A+ +L
Sbjct: 240 PSPQRDVIKLRFGLEEDRTPLPHAQIGRRLALATAQVRAIEREALARL 287


>gi|257470234|ref|ZP_05634325.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064448|ref|ZP_07928933.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
 gi|313690124|gb|EFS26959.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
          Length = 260

 Score =  131 bits (329), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 78/225 (34%), Positives = 126/225 (56%), Gaps = 3/225 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V +NLRLVIS+A+KYTN G+  LDLIQEGN+GL++A EK++     +FSTY+ +W
Sbjct: 36  AQEKLVTSNLRLVISIARKYTNMGIPLLDLIQEGNMGLIRAVEKYEPEKNIRFSTYSTFW 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ+I R I      IR P ++ D I ++ +  +   NK    P+ EEI   L M  +  
Sbjct: 96  IKQSILRYITSSRGLIRFPSYVYDGISRMKKYVQDYKNKNSHLPSIEEICSSLDMRKKEA 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + +++ ++   +   +  E   +    I D       D  I  N      + +  L  +
Sbjct: 156 ERYIEVLEKGSCIGNEMYGEIAEYCSSIIFDDTFE---DKVIAKNSTIDLMKKVNKLPSK 212

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  VL  R+G+      TL E+G++  +T+ERIRQI+ +AI KL+
Sbjct: 213 EREVLIYRYGLLDEKVLTLGEIGERMNLTKERIRQIQLEAIDKLR 257


>gi|317505016|ref|ZP_07962964.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
 gi|315663898|gb|EFV03617.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
          Length = 260

 Score =  131 bits (329), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 125/247 (50%), Gaps = 38/247 (15%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G   +  A  ++  ANLR V+++AK+YT+RG+  LDLI EGNIGLMKAA  FD   G
Sbjct: 52  IQQGGASSERAINKLTSANLRFVVAIAKQYTDRGVAILDLISEGNIGLMKAAMSFDGSRG 111

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F  YA  +V++AI  ++ +QS   R+P H                     E +PEE A
Sbjct: 112 LRFVGYAEPFVRRAIEAAVNEQSGIFRLPKH---------------------ENSPEEKA 150

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              A                 S++ P+ +     L   + D NA  P    ++A+++E  
Sbjct: 151 NSRA----------------FSVDAPLENGKNMSLLSVLSDPNAARPDQEVLEASVKEEL 194

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            + +  L  RE+ V+   +GIG     T  E+ ++  + RER+RQI  KA+RKL   + S
Sbjct: 195 MQAMNILNQREKNVVEAFYGIG-QPHLTFAEIAEKMGLKRERVRQIRNKAVRKLNRNTTS 253

Query: 674 KKLRSFL 680
             L+++L
Sbjct: 254 DMLKAYL 260


>gi|225454599|ref|XP_002264964.1| PREDICTED: hypothetical protein isoform 2 [Vitis vinifera]
          Length = 496

 Score =  131 bits (329), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 144/250 (57%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G+K STY
Sbjct: 249 ECSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTY 308

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++ + S T+R+P H+ +++  ++R A+    +    P+ + IA      
Sbjct: 309 VYWWIRQGVSRALVENSRTLRLPSHLHERL-SLIRNAKIRLEEKGITPSIDRIAECLNMS 367

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            KK+    E + KV  + +E   SL    G+   S++ D   + N   P     +  L++
Sbjct: 368 QKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENN---PWHGVDEWALKD 424

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +++  +L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KLK+ 
Sbjct: 425 EVNKLINTTLGERERDIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVGLVALEKLKNA 483

Query: 671 SRSKKLRSFL 680
           +R  ++ + L
Sbjct: 484 ARKGRMEAML 493


>gi|255531368|ref|YP_003091740.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344352|gb|ACU03678.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  131 bits (329), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 132/237 (55%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V +NLR V++VAKKY +  L   DLI +GNIGL+KAAE+FD   G+KF +YA+WW
Sbjct: 50  ALQRLVSSNLRFVVTVAKKYESPDLSLADLISDGNIGLIKAAERFDEKRGFKFISYAVWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I + +      + +P+     I +V R+  ++  +++R P  EE+A  +    E V
Sbjct: 110 IRQSILQGMNTSKRMVHLPMSQISGIRQVKRSEIKLEQELQRIPCREELAGFMKTAEEVV 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L I+   +SL+ P   +D   +   ++     +P  S  + +L +   R++  L+PR
Sbjct: 170 YDYLYISGSQVSLDAPTEGQDGVLIPCIVQYDKGPAPDASLERESLEKDVQRMMDILSPR 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  +L + +G+G N     +++     ++ E IR+ + KA+ +L+     K +R +L
Sbjct: 230 ERSILFLAYGMGNNRPLQNDDISTLLGLSTETIRRSKNKALDRLRGLKEIKMMRRYL 286


>gi|284053747|ref|ZP_06383957.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 179

 Score =  130 bits (328), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 67/180 (37%), Positives = 113/180 (62%), Gaps = 5/180 (2%)

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IA  S TIR+P+H+ +K++K+ R  R +  +  R  TP EIAK L +   
Sbjct: 2   WWIRQAITRAIAQNSRTIRLPIHITEKLNKIKRVQRELFQQYGRNATPTEIAKALDLEPS 61

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASL 620
            +R  L  ++ P+SL+  +GD   + L D +ED++A +  DS + Q  LR+    ++A L
Sbjct: 62  QIRDYLLASRHPVSLDLRVGDNQDTELQDLLEDESASA--DSYVTQQLLRQDLKDMMADL 119

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TP++  VL +R+G+    + +L +VG Q  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 120 TPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRERVRQLENQALNHLRR--RKAQVREYL 177


>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera]
          Length = 611

 Score =  130 bits (328), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 129/238 (54%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E++ +   LV+ +A+ Y   G+ F D++Q GN+G+++ AE+FD   GY+FSTY  +W
Sbjct: 373 CRDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYW 432

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++++++  +A  +  ++IP  +   I ++ +  + +     R P   EIAK   + +  +
Sbjct: 433 IRKSMSTLVARHARGVKIPFTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGLSLAKI 492

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R      +   S +    D   + + +F  D +  SP +  +Q   R+    +L  L PR
Sbjct: 493 RSAGNCLRVVGSTDQSFQDCWGATILEFTPDTSIKSPEEGFMQQCKRKDIHNLLKGLDPR 552

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E ++L +R+G G     +LEE+G++F V++E IR++E  A+  L+     + LR ++D
Sbjct: 553 ERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRDEEICQNLRHYVD 610


>gi|225454597|ref|XP_002264928.1| PREDICTED: hypothetical protein isoform 1 [Vitis vinifera]
          Length = 507

 Score =  130 bits (328), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 144/250 (57%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G+K STY
Sbjct: 260 ECSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTY 319

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA------ 553
             WW++Q ++R++ + S T+R+P H+ +++  ++R A+    +    P+ + IA      
Sbjct: 320 VYWWIRQGVSRALVENSRTLRLPSHLHERL-SLIRNAKIRLEEKGITPSIDRIAECLNMS 378

Query: 554 -KKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            KK+    E + KV  + +E   SL    G+   S++ D   + N   P     +  L++
Sbjct: 379 QKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENN---PWHGVDEWALKD 435

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +++  +L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KLK+ 
Sbjct: 436 EVNKLINTTLGERERDIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVGLVALEKLKNA 494

Query: 671 SRSKKLRSFL 680
           +R  ++ + L
Sbjct: 495 ARKGRMEAML 504


>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa]
 gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa]
          Length = 499

 Score =  130 bits (328), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 141/250 (56%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + S+A++++  +N+RLV+S+A+K  N G +  DL+Q G IGL++  EKFD   G+K STY
Sbjct: 252 QCSLAREKLAMSNVRLVMSIAQKNDNMGAEMADLVQAGLIGLLRGIEKFDSSKGFKISTY 311

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ +   T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 312 VYWWIRQGVSRALVENPRTLRLPNHLHERL-GLIRNAKIRLEEKGVTPSIDRIAESLNMS 370

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E + KV  + +E   SL    G+   S++ D   + N   P     +  L+E
Sbjct: 371 QRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRLENN---PWHGVDEWALKE 427

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +++ ++L  RE  ++R+  G+      T E++ K+  ++RER+RQ+   A+ KLKH 
Sbjct: 428 EVNKLIDSALQEREREIIRLYHGLDKEC-LTWEDISKRMGLSRERVRQVGLVALEKLKHA 486

Query: 671 SRSKKLRSFL 680
           +R  KL + L
Sbjct: 487 ARKGKLEAML 496


>gi|329895346|ref|ZP_08270971.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
 gi|328922359|gb|EGG29703.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
          Length = 424

 Score =  130 bits (328), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 130/226 (57%), Gaps = 2/226 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V  N+RLV  +A++  NRG+   DL+QEG IGL++AAEKFD+ LG++FSTYA  W
Sbjct: 186 ARDKLVMHNVRLVYKLAREKQNRGIAVRDLVQEGIIGLVRAAEKFDYRLGFRFSTYAYNW 245

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
             Q I R        +  P H+  +++ + R      ++   EP+  E+A+     +E V
Sbjct: 246 TNQHIQRVCEGNGSLVTYPTHVTQEVNALYRVRNEWMDRRGEEPSLAELAEHSGFTLERV 305

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           R++ ++T   +S+++   DEDT+ L +  + D+ A   L+ A   +L+    + L  L  
Sbjct: 306 RELTQLTNLTVSIQSD-DDEDTNALPESALVDEAANPALEQAQSRSLKRLLEQQLKQLDR 364

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++  R+G+      TL ++  Q  V+RE +RQ+E  A+RKL+
Sbjct: 365 REQMIVTARWGLDGRPSRTLAQLADQLEVSRELVRQLEKSALRKLQ 410


>gi|32453269|gb|AAP82767.1| sigma 70 [Hydrogenothermus marinus]
          Length = 369

 Score =  130 bits (328), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 78/192 (40%), Positives = 109/192 (56%), Gaps = 8/192 (4%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISK----RIMHNEGELLRLAQSYG-IKRDVFLER 373
           +KL  L+    L+       +EQ+ DI +    ++  +E ++  L    G + RD FL+ 
Sbjct: 179 QKLRDLIAHELLHIRFTARYIEQVCDIVRGFIEQVRQHERQIQNLCTQIGTMPRDHFLKT 238

Query: 374 HQGRELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               E +  W+    +   G  W   +     S+L  +  I  I     + + E + I  
Sbjct: 239 FPPNETNLDWIK--NEIEAGHPWSESLVRVFPSVLDEQQRIIEIVERARVPLDELKDIFK 296

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE +   AK+EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 297 RMSQGEAKMRAAKREMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 356

Query: 493 GYKFSTYAMWWV 504
           GYKFSTYA WW+
Sbjct: 357 GYKFSTYATWWI 368


>gi|239934544|emb|CAR94586.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 241

 Score =  130 bits (327), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 93/258 (36%), Positives = 147/258 (56%), Gaps = 29/258 (11%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIAIAKRIEAGR +M+  +CESPL  +++I W   L DG  LLRE+IDL+A    E   
Sbjct: 6   GEIAIAKRIEAGRELMIGGICESPLAIESIIAWYKALQDGDILLREVIDLDATYSGE--- 62

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                        +ED +Q    D  +E E   ES  +  +D   K     E+ E+++ N
Sbjct: 63  -------------QEDFTQVSREDKEEEEEDSEESEDEEGEDGEEKGGESSEDDEDEDDN 109

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV----NGQK-DEKSSV 312
                   A +LSAME++L P+V     +I + Y++++ +Q+  +     G+K DEK+  
Sbjct: 110 --------AMSLSAMEEELAPQVFEIFGKIQKTYKKMQKVQNERLELLQKGRKADEKADK 161

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           K + LK  +V+L+  + LN SRI+ L+++LY +++ ++  EG++LR+A    +KR+ FLE
Sbjct: 162 KYEKLKHDMVELMNEVRLNNSRIEQLIDRLYTMNRELVSLEGKMLRMAVDCKVKREDFLE 221

Query: 373 RHQGRELDPHWVSYAKDF 390
            + G ELDP W++  K  
Sbjct: 222 HYYGAELDPRWLTKVKKL 239


>gi|148241530|ref|YP_001226687.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849840|emb|CAK27334.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 280

 Score =  130 bits (327), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 77/216 (35%), Positives = 125/216 (57%), Gaps = 11/216 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M++ANLRLV++VAK Y  RGL  +DL+QEG++GL++A EKFD  LGY+FSTYA  W++QA
Sbjct: 60  MIQANLRLVVTVAKTYQGRGLDLMDLVQEGSLGLIRAVEKFDPTLGYRFSTYAWNWIRQA 119

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR 564
           I+R +  +  T+R+P+H+  ++    R  RR   ++ ++    +   +A +  + ++   
Sbjct: 120 ISRGLETKGRTLRLPIHVTQQL----RALRRAHERLWQQGLSTDLVAVAAEAGVDLKAAS 175

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             L++    +SL+TP    ++  L      +   SPLD A + +  E   R L  L  R+
Sbjct: 176 LALRMAPGTLSLDTPAAGSESDLLQLLPSAEP--SPLDEAERHDGWERMGRQLRHLPERD 233

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++VL+ R+         L  VG+Q   +RER RQIE
Sbjct: 234 QQVLQWRYLT--PERQKLSVVGEQLGCSRERARQIE 267


>gi|255553456|ref|XP_002517769.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223543041|gb|EEF44576.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 389

 Score =  130 bits (327), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 119/217 (54%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C+   +++ +     RLV+S+A +Y  +GL   DLIQEG+IGL++ AE+FD   G K ST
Sbjct: 171 CKGRQSRERITGNYRRLVLSIANRYRGKGLSLQDLIQEGSIGLLRGAERFDPKRGNKLST 230

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y  WW+K+AI  SI+  S  +R P  + D+  K+      ++ ++ R P+  EIAK+L +
Sbjct: 231 YVYWWIKEAIITSISINSRIVRQPRSLWDRTTKIAEAKISLTERLGRLPSYREIAKELNV 290

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V  VR V   ++  +SL+  + D+    L + I     + P +   +  L++    ++ 
Sbjct: 291 HVSTVRLVFSRSRSTVSLDQAVSDQGGMTLQEIIPGPEEMMPENMVKKQLLKKELEELIQ 350

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +L  RE   LR+ FG+   T  + +E+G+   + RER
Sbjct: 351 TLGKREAHTLRLIFGLNGQTPQSCDEIGRSLKLCRER 387


>gi|302765387|ref|XP_002966114.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
 gi|300165534|gb|EFJ32141.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
          Length = 249

 Score =  130 bits (327), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 132/230 (57%), Gaps = 11/230 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ +NLRLV+++A++Y N G++  DLIQEG +GL+   EKFD   G+KFSTYA WW+ QA
Sbjct: 1   MILSNLRLVVAIARRYENMGVEIGDLIQEGTLGLIHGLEKFDVSRGFKFSTYAYWWIFQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + RS+  +   +R P H+ + I K+ +   R  +   R  + E + + L +P   +   L
Sbjct: 61  MIRSLDKRGKCVRYPFHLCEAIRKINQLRNRQVD--DRPVSVETMMQVLKLPRARIEIAL 118

Query: 568 KITKEPI-SLETPIGD----EDTSHLGDFIEDKNAVS-PLDSAIQANLRETTTRVLAS-L 620
           + +   + SL+  + +    E+   L DFI D+N  + P   A +  ++E   R+L S L
Sbjct: 119 QASNYRLTSLDRHVANKRCFEEGDPLEDFIVDQNVENQPWLMAERDAVKEELDRLLESKL 178

Query: 621 TPREERVLRMRFGIGMNTDHTL--EEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  V+R RFG+  N    L   E+G+   ++RER+RQ+E  A+ KL+
Sbjct: 179 DAREREVIRKRFGLHPNQTSPLSRHEIGRSCGISRERVRQLENDAMAKLR 228


>gi|225429414|ref|XP_002275831.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score =  130 bits (326), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 129/238 (54%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E++ +   LV+ +A+ Y   G+ F D++Q GN+G+++ AE+FD   GY+FSTY  +W
Sbjct: 323 CRDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYW 382

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++++++  +A  +  ++IP  +   I ++ +  + +     R P   EIAK   + +  +
Sbjct: 383 IRKSMSTLVARHARGVKIPFTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGLSLAKI 442

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R      +   S +    D   + + +F  D +  SP +  +Q   R+    +L  L PR
Sbjct: 443 RSAGNCLRVVGSTDQSFQDCWGATILEFTPDTSIKSPEEGFMQQCKRKDIHNLLKGLDPR 502

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E ++L +R+G G     +LEE+G++F V++E IR++E  A+  L+     + LR ++D
Sbjct: 503 ERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRDEEICQNLRHYVD 560


>gi|328948870|ref|YP_004366207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328449194|gb|AEB14910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 272

 Score =  130 bits (326), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 124/228 (54%), Gaps = 3/228 (1%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V +NLRLV+SVA ++       +DLIQEGN+GLM AA+KFD   G +FSTYA  W+ Q 
Sbjct: 42  LVNSNLRLVVSVAGRFNKGAFCIMDLIQEGNLGLMVAAKKFDPAFGTRFSTYAYRWIVQR 101

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + I+  S  I +PVH    + ++ +       +  RE   +E+A    +  E +  VL
Sbjct: 102 IMKFISANSSPILLPVHRETLLRRIQKFQNIFFQQNGREAAVKELALFAGISEERLNDVL 161

Query: 568 KITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           + +    SL+T + DE  T  LGD I D  A SP + AI+ + +      + SLT  E+ 
Sbjct: 162 ETSYTVASLDTEVADEGKTVSLGDIIPD-TAFSPEELAIREDSKSCVNFFMDSLTGIEKS 220

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           VLR R+    +    +L EVG+   +++E +RQ E +A + LK    S
Sbjct: 221 VLRHRYNFDYDLHSKSLREVGRIVGLSQEAVRQAELRAKKHLKSAMES 268


>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 560

 Score =  130 bits (326), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 137/238 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E++++   LV+  A+ Y   G+   DL+Q GN+G+++ AE+FD   GY+FSTY  +W
Sbjct: 322 CRDELIKSTRSLVLYFARNYRGTGIALEDLLQAGNLGVLEGAERFDHTRGYRFSTYVQYW 381

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++++++ ++  +  I+IP  +   I+++ +  + ++    + P  +EIAK   + +  +
Sbjct: 382 IRKSMSKIVSRLARGIQIPCTLSRAIYQIQKARKALTTSNGKYPDDDEIAKYTGLSLAKI 441

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
               +  +   S++  IG+   +   +F+ D +  SP +  ++ ++ +    +L SL  R
Sbjct: 442 ESASRCLRVVGSIDQKIGESLNAKYLEFLPDTSVQSPEEVVMRQHMIQDMHNLLRSLDSR 501

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VL +RFG+      +LEE+G+ F V++E +R++E + + +L++    + LR +++
Sbjct: 502 ERQVLILRFGLNDYQPKSLEEIGRHFHVSKEWVRRLEKRVMTRLRNEETCRNLRHYIN 559


>gi|318066939|emb|CBY89084.1| RNA polymerase sigma70 factor [Halomonas elongata]
          Length = 367

 Score =  129 bits (325), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 69/140 (49%), Positives = 92/140 (65%), Gaps = 15/140 (10%)

Query: 385 SYAKDFPEGE----WKNFVACE----VDSILKIRNEI----KSISVE---TGISISEFRH 429
           ++ K FP  E    W +    E     D +  ++ +I    + I+ E     + +++ + 
Sbjct: 228 TFIKSFPGNESRQTWLDKFMAENAKYADRLAPLKGDIQRAQRKIAFEEEMVALVVTDLKE 287

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 288 VNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 347

Query: 490 WCLGYKFSTYAMWWVKQAIT 509
           +  GYKFSTYA WW++QAIT
Sbjct: 348 YRRGYKFSTYATWWIRQAIT 367



 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 36/45 (80%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           T DPVRMY+REMG+++LL+REGEI IAKRIE G   +M+SL   P
Sbjct: 21  TTDPVRMYMREMGTVKLLTREGEIQIAKRIEEGTREVMSSLAYLP 65


>gi|223994539|ref|XP_002286953.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220978268|gb|EED96594.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 298

 Score =  129 bits (325), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 131/240 (54%), Gaps = 6/240 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++ +++  N+ LV  +AK+Y N      +LIQEG +G+M+AAE++D   G++FSTY   W
Sbjct: 62  SRTKLITGNVGLVTLIAKRYYN---MLRNLIQEGYMGIMEAAERYDPSKGFRFSTYGTHW 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+IA+ S  IR+PVH++  I  + +        I R P+  E+A ++ + ++ +
Sbjct: 119 IRQRIVRAIAESSRMIRLPVHVQATIRNINKKHEEFEATIGRSPSLPELAHEMGVSLDKL 178

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                +++  ISLE  +     ED   LGD I      +P + A+   LR     +L +L
Sbjct: 179 HLYQHLSRNVISLERAVDQHSPEDNRTLGDRIACTELPTPDEDAMSEALRGEVHSMLDAL 238

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              E  VL  RFG+      TL+E      ++ + +R +EAKA+ +L+ P  + +++ ++
Sbjct: 239 RDNERIVLTHRFGLDDGRPKTLKETAYGMGISIDSVRAVEAKALNRLRQPQLNYRVKDYV 298


>gi|297737220|emb|CBI26421.3| unnamed protein product [Vitis vinifera]
          Length = 555

 Score =  129 bits (325), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 144/250 (57%), Gaps = 14/250 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G+K STY
Sbjct: 308 ECSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTY 367

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ + S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 368 VYWWIRQGVSRALVENSRTLRLPSHLHERL-SLIRNAKIRLEEKGITPSIDRIAECLNMS 426

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E + KV  + +E   SL    G+   S++ D   + N   P     +  L++
Sbjct: 427 QKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENN---PWHGVDEWALKD 483

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +++  +L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KLK+ 
Sbjct: 484 EVNKLINTTLGERERDIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVGLVALEKLKNA 542

Query: 671 SRSKKLRSFL 680
           +R  ++ + L
Sbjct: 543 ARKGRMEAML 552


>gi|331028036|ref|YP_004421751.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
 gi|294805649|gb|ADF42487.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
          Length = 299

 Score =  129 bits (325), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 132/239 (55%), Gaps = 9/239 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++R+G+     AK+ M+  NLRLV+++AKKY  R   L+ LDL+Q+GN+GL +A E FD 
Sbjct: 52  IIRRGQR----AKERMIVRNLRLVVTIAKKYVKRCTSLEMLDLVQDGNMGLARATELFDP 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++Q+I+R + D+   IR+P+H  +K+ K             + PT  
Sbjct: 108 SRGYKFSTYAYWWIRQSISRGLQDRDRMIRLPIHRHEKVIKARAYMNHQLAMTGKMPTIA 167

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E A  +      ++  L + ++  SL+    G +D S + D I D  ++   D  +    
Sbjct: 168 ECAAAVDADPHELQASLVMAQDVCSLDAKASGRDDLSPILDLIPDPASLHKDDEYLIE-- 225

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE     +  L+  E+ ++R   G+G     TL ++G++  V+RE IRQ   KA+ K++
Sbjct: 226 REILHDAINMLSEDEQDIVRRHNGLGGAPKVTLGQLGQERGVSREAIRQKHTKAMNKVR 284


>gi|281425346|ref|ZP_06256259.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
 gi|281400509|gb|EFB31340.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
          Length = 252

 Score =  129 bits (323), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 83/269 (30%), Positives = 130/269 (48%), Gaps = 38/269 (14%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I  ET +S  E + +   +  G   A  A  ++  ANLR V+S+AK+Y +RG+  LD
Sbjct: 22  LNEIGKETILSDDEEKQLSQQIMAGGAAAEQAIGKLTSANLRFVVSIAKQYVDRGVAILD 81

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIGLMKAA  FD   G +F  YA  +V++A+  ++ +QS   R+P H        
Sbjct: 82  LISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNEQSGIFRLPKH-------- 133

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                        E + EE A   A                 S++ P+ +    +L   +
Sbjct: 134 -------------EHSAEEKANSRAF----------------SVDAPLQNGKNVNLLSIL 164

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D  A  P   A++ +++E     +  L  RE  V+   +GIG     T  E+G++  + 
Sbjct: 165 SDPTAARPDQEALETSVKEELLEAMNILDNRERNVVEAFYGIG-QPHLTFAEIGEKMGLK 223

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQI  KA+RKL   + S  L+++L+
Sbjct: 224 RERVRQIRNKAVRKLNRNTTSDMLKAYLE 252


>gi|321309572|ref|YP_004191901.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801416|emb|CBY92062.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 461

 Score =  129 bits (323), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 75/223 (33%), Positives = 130/223 (58%), Gaps = 13/223 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A K++  +NLRLV SVAKKY N G    DL+QEG  GLMKA +KF++ LG KFSTYA 
Sbjct: 173 SFAIKQLTISNLRLVQSVAKKYLNYGFPMEDLVQEGFFGLMKAVQKFNYNLGNKFSTYAT 232

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA---- 557
           WW++QAI RSIA++   IR+PVH+++ I +  + +  +  + K EP+ ++I  ++     
Sbjct: 233 WWIRQAIVRSIAEKYRVIRVPVHLQEIIKRFNKVSMTLMAE-KGEPSLQDILVEMQKYYP 291

Query: 558 -MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              +E +  + +++K+ +SL+  +  E+   L   I D++ +   + + +A   E    +
Sbjct: 292 NFDLEKITNIKQLSKDLLSLDGVLDSEEFFPLSGAIRDEDMMDAEELSFKAYRVEMLNDM 351

Query: 617 LAS-LTPREERVLRMRFGIGMNTDHTLEEVGK------QFCVT 652
           L + L P E  ++++R+G      H++ E+ +      +FC +
Sbjct: 352 LENELKPDEISLVKLRYGFLEYGKHSVREIVEEKLLDPEFCFS 394


>gi|299141532|ref|ZP_07034668.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298576868|gb|EFI48738.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 252

 Score =  129 bits (323), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 83/269 (30%), Positives = 130/269 (48%), Gaps = 38/269 (14%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I  ET +S  E + +   +  G   A  A  ++  ANLR V+S+AK+Y +RG+  LD
Sbjct: 22  LNEIGKETILSDDEEKQLSQQIMAGGAAAERAIGKLTSANLRFVVSIAKQYVDRGVAILD 81

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIGLMKAA  FD   G +F  YA  +V++A+  ++ +QS   R+P H        
Sbjct: 82  LISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNEQSGIFRLPKH-------- 133

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                        E + EE A   A                 S++ P+ +    +L   +
Sbjct: 134 -------------EHSAEEKANSRAF----------------SVDAPLQNGKNVNLLSIL 164

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D  A  P   A++ +++E     +  L  RE  V+   +GIG     T  E+G++  + 
Sbjct: 165 SDPTAARPDQEALETSVKEELLEAMNILDNRERNVVEAFYGIG-QPHLTFAEIGEKMGLK 223

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQI  KA+RKL   + S  L+++L+
Sbjct: 224 RERVRQIRNKAVRKLNRNTTSDMLKAYLE 252


>gi|207743452|ref|YP_002259844.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
 gi|206594849|emb|CAQ61776.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
          Length = 203

 Score =  129 bits (323), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 72/198 (36%), Positives = 115/198 (58%), Gaps = 2/198 (1%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM-- 539
           M A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +  
Sbjct: 1   MHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEK 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           S    R+ + E+IA  L    E V+ VL + +   SL+TP   +  + L DF+ D++  S
Sbjct: 61  SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDSGTSLLDFLSDEHGAS 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P        L +     LA L+ +   V+  RFG+      TLEE+  +  +TRER+RQI
Sbjct: 121 PDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELAAEMGLTRERVRQI 180

Query: 660 EAKAIRKLKHPSRSKKLR 677
           + +A+ KLK    S+ +R
Sbjct: 181 QQEALVKLKRHFASQGVR 198


>gi|317132579|ref|YP_004091893.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470558|gb|ADU27162.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 256

 Score =  128 bits (322), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 132/227 (58%), Gaps = 13/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++  NLRLV+SV +++TNRG    DL Q G IGLMK+ + FD     +FSTYA+  
Sbjct: 38  AREELISGNLRLVLSVIQRFTNRGENLDDLFQVGCIGLMKSIDNFDISQNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ N  +REPT EE+AK++ MP E +
Sbjct: 98  IIGEIRRYLRDNN-PIRVSRSLRDIAYKAMQCKERLMNANQREPTIEEMAKEMDMPKEEI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L+   EP+SL  P+  +  DT ++ D I DK   S  D   +  L+E     + +L+
Sbjct: 157 VMALESVVEPVSLYEPVYSDGGDTIYVMDQIGDKTVDS--DWLDEITLKEA----VGALS 210

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+R+L +RF  G    HT  EV  +  +++ ++ ++E  A+ K+K
Sbjct: 211 EREKRILYLRFFEG----HTQMEVASEIGISQAQVSRLEKGALSKIK 253


>gi|119474993|ref|ZP_01615346.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119451196|gb|EAW32429.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 491

 Score =  128 bits (322), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 78/223 (34%), Positives = 123/223 (55%), Gaps = 5/223 (2%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV  NLRLV  +AK+Y +  L  L+LIQEG  GL++A EKF    G +FSTYA  W++  
Sbjct: 253 MVNHNLRLVYHIAKRYNSGTLPMLELIQEGVFGLVRAVEKFQPASGNRFSTYAYLWIEAK 312

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +  +    +  +R+P      + K+ R+  +  +  +R  T   +A KL M    V  +L
Sbjct: 313 VRLTHEKLNSLVRLPSSNFQDVIKLRRSMEQSRSTGERFST-RNVAAKLDMTQAHVELLL 371

Query: 568 KITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   +P+SL+ P+G  D D S  G    ++  VS L   + ++++   T +L+ LT RE 
Sbjct: 372 RTKSQPLSLDQPVGGEDNDLSLSGTLQLEQPPVSSL--VLNSDMQRQVTELLSELTSREA 429

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L+ RFG+G     + E +GK   ++RER+RQIE  A+  LK
Sbjct: 430 YILQHRFGLGDMEPMSRESIGKNIGLSRERVRQIEKAALISLK 472


>gi|2398853|dbj|BAA22215.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 571

 Score =  128 bits (321), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 136/240 (56%), Gaps = 3/240 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E+V++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W
Sbjct: 332 CRDELVKSTRSLVLFLARNYRGMGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 391

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKV--VRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++++++  ++  +  + IP  +   I+ +   R   + S+ IK     EEIAK     V+
Sbjct: 392 IRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGIKYA-ADEEIAKLTGHSVK 450

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R   +  K   S++  +GD  T+   +F  D    SP ++ ++ + R     +L  L 
Sbjct: 451 KIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLE 510

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE++V+ +R+G+      +LEE+GK F V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 511 PREKQVMVLRYGLQDYRPKSLEEIGKLFKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570


>gi|218676616|ref|YP_002395435.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
 gi|218324884|emb|CAV26646.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
          Length = 298

 Score =  128 bits (321), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 131/230 (56%), Gaps = 6/230 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  M+E+NLRLV+ +AK Y  R       LDLI+EGNIGL+KA +K+D   GY+FSTYA
Sbjct: 61  ARDIMIESNLRLVVKIAKSYLKRKGNNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYA 120

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW+++ I  ++ ++  T+R+P H+  +I+ +      +S K+++E +  E++    +  
Sbjct: 121 VWWIRENIEAALMNKGRTVRLPAHVCKEINSLASKKLDVSKKMRKEISISELSNSSGVKA 180

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V +++ ++   I + T +G      + D  E +    P       +      +++ +L
Sbjct: 181 ERVDQLVALSGF-IDVTTTVGISHAPLVLDQCESEYIPDPQQDCEDQSFTHALEQIINTL 239

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQF--CVTRERIRQIEAKAIRKLK 668
            P+ ++VL  RFG   N   TL EVG+     V+ ER+RQ++ +A+ +++
Sbjct: 240 PPKLQKVLIHRFGFFDNKVKTLSEVGQMLDVNVSNERVRQMQKEAVERIQ 289


>gi|108762657|ref|YP_634340.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
 gi|585929|sp|Q07083|RPSC_MYXXA RecName: Full=RNA polymerase sigma-C factor
 gi|293866|gb|AAA25408.1| sigma factor [Myxococcus xanthus]
 gi|108466537|gb|ABF91722.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
          Length = 295

 Score =  128 bits (321), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 89/236 (37%), Positives = 130/236 (55%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ANLR V+ VA +Y + GL+  DLIQE NIGLMKA +KFD   G +  +YA+WW
Sbjct: 45  AGHQLVTANLRFVVKVAYEYRSYGLKMSDLIQEANIGLMKAVQKFDPDKGIRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTAR---RMSNKIKREPTPEEIAKKLAM 558
           ++  I   I      +++      R     + RT R   +M          EEIA+KL +
Sbjct: 105 IRAYIQNCILKNWSLVKLGTTQAQRRLFFSLARTRRELEKMGAGDANVVNAEEIARKLNV 164

Query: 559 PVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI---QANL-RET 612
               VR++  ++    +SL+ P+G D D +HL DF+E + +VS +D      QANL RE 
Sbjct: 165 KASEVREMEQRMGGRDLSLDAPMGEDGDATHL-DFVESE-SVSAVDEVADRQQANLTREL 222

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R L  L PRE  ++  R  +  + + TL E+G+ F  +RER RQ+E +A  KLK
Sbjct: 223 VQRALRRLDPRERFIIEQR--VMGDAEMTLSELGEHFGFSRERARQLEIRAKDKLK 276


>gi|213028661|ref|ZP_03343108.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 88

 Score =  127 bits (320), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 64/82 (78%), Positives = 69/82 (84%)

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 6   PLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 65

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HPSRS+ LRSFLD
Sbjct: 66  EAKALRKLRHPSRSEVLRSFLD 87


>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba]
          Length = 567

 Score =  127 bits (320), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 136/240 (56%), Gaps = 3/240 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E+V++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W
Sbjct: 328 CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVRYW 387

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKV--VRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++++++  ++  +  + IP  +   + ++   R   + S  IK  P  EEI+K     ++
Sbjct: 388 IRKSMSTMVSRHARGVHIPASIIRTMSQIQKARKTLKTSQGIK-YPADEEISKLTGYSLK 446

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R   +  K   S++  +GD  T+   +F  D    SP ++ ++ + R     +L  L 
Sbjct: 447 KIRAANQCLKVVGSIDKKVGDCFTTRFLEFTPDPTMESPEEAVMRQSARGEVHNLLEGLE 506

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE++V+ +R+G+   +  +LEE+GK   V++E IR+IE +A+ KL+   ++  LR +L+
Sbjct: 507 PREKQVMVLRYGLQDYSPKSLEEIGKILRVSKEGIRKIERRAMAKLRDQPKADNLRYYLN 566


>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
 gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
          Length = 568

 Score =  127 bits (319), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 139/240 (57%), Gaps = 3/240 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E++++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W
Sbjct: 329 CRDELLKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 388

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKV--VRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++++++  ++  +  + IP  +   I+++   R   + S+ IK  P  E+I+K  ++ V+
Sbjct: 389 IRKSMSMMVSRHARGVHIPSSIIRTINQIQKARKTLKTSHGIK-YPADEDISKLTSLSVK 447

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R   +  K   S+E  +GD  ++   +F  D    SP ++ ++ + R     +L  L 
Sbjct: 448 KIRAANQCLKVVGSIEKKVGDCFSTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLE 507

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE++V+ +R+G+      +LEE+GK   V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 508 PREKQVMVLRYGLQNYRPKSLEEIGKLLRVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 567


>gi|261415258|ref|YP_003248941.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371714|gb|ACX74459.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302327293|gb|ADL26494.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 283

 Score =  127 bits (318), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 131/227 (57%), Gaps = 10/227 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V +NLR V+++A  Y  RGL  ++LI EGN+GL++AA +FD  L  KF +YA+WW++Q 
Sbjct: 49  LVNSNLRFVVNIANLYKGRGLDIMELINEGNMGLIEAARRFDRSLKIKFISYAVWWIRQN 108

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-----EEIAKKLAMPVEG 562
           ITR+I+++   IRI       + +  R A+ +   I    T      E ++K  A  +E 
Sbjct: 109 ITRAISEKGRMIRISAEKELMLRRFNRHAKDVQQVIGGTFTINTQSLEGLSKYKASEIE- 167

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLT 621
             K+L +     SL+ P+ ++  + LGD I D  + +  + A   N  E   +VL  +L+
Sbjct: 168 --KILMMGNSTSSLDAPVNEDGDATLGDTISDSQSRTD-ELADNNNRAEVFDKVLDKNLS 224

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E+ ++++ +G  M++D  L+E+     +++ER+RQ++  A+ KL+
Sbjct: 225 NQEKEIIKLYYGFKMDSDLNLKEIAPMVGLSKERVRQLKENALNKLR 271


>gi|84385871|ref|ZP_00988901.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
 gi|84379187|gb|EAP96040.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
          Length = 262

 Score =  126 bits (317), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 132/230 (57%), Gaps = 6/230 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  M+E+NLRLV+ +AK Y  R       LDLI+EGNIGL+KA +K+D   GY+FSTYA
Sbjct: 25  ARDIMIESNLRLVVKIAKSYLKRKGNNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYA 84

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW+++ I  ++ ++  T+R+P H+  +I+ +      +S K+ +E +  E++    +  
Sbjct: 85  VWWIRENIEAALMNKGRTVRLPAHVCKEINSLASKKLDVSKKMSKEISISELSDSSGVKA 144

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V +++ ++   I + T +G      + D  E +    P       +  +   +++++L
Sbjct: 145 KRVDQLVALSGF-IDVTTTVGTNHAPMVLDQCESEYIPDPQRDCEDQSFTQALEQIISTL 203

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQF--CVTRERIRQIEAKAIRKLK 668
            P+ ++VL  RFG   N   TL EVG+     V+ ER+RQ++ +A+ +++
Sbjct: 204 PPKLQKVLIHRFGFFDNKVKTLSEVGQMLDVNVSSERVRQMQKEAVERIQ 253


>gi|22135904|gb|AAM91534.1| sigma factor SigC [Arabidopsis thaliana]
          Length = 291

 Score =  126 bits (316), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 134/237 (56%), Gaps = 3/237 (1%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W+++
Sbjct: 55  ELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRK 114

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKV--VRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +++  ++  +  + IP  +   I+ +   R   + S+ IK     EEIAK     V+ +R
Sbjct: 115 SMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGIK-YAADEEIAKLTGHSVKKIR 173

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              +  K   S++  +GD  T+   +F  D    SP ++ ++ + R     +L  L PRE
Sbjct: 174 AANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPRE 233

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++V+ +R+G+      +LEE+GK   V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 234 KQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 290


>gi|88799025|ref|ZP_01114606.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778252|gb|EAR09446.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 339

 Score =  126 bits (316), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 120/221 (54%), Gaps = 1/221 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ +N+RLV  VA ++T RGL  LDL QEG  GL++A E+F      +FSTYA  W+ Q 
Sbjct: 112 LIASNIRLVFKVAHRHTERGLSLLDLAQEGQFGLVRALERFRCDKELRFSTYATHWITQY 171

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I  +I  Q+ T+ IP +++D + +  R   R   +  R  +  E A+      +    ++
Sbjct: 172 IRLAIKKQTRTVPIPTNVQDDLARTNRALARAQQQQGRPVSVTEFARLSNQSTDAAEHLM 231

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +     SL+  + D+      D + D +   P     +++ +E    +LA LT RE+++
Sbjct: 232 SLNAPVQSLDERLSDDSEVSALDLL-DSDLARPESEHERSDNQERVQALLAHLTSREQQI 290

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L MR+GIGM  ++   E+  Q  ++RER+RQ+E +A+  L+
Sbjct: 291 LAMRYGIGMGAEYGYREIADQLNLSRERVRQLEKQALGFLR 331


>gi|207723156|ref|YP_002253555.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
 gi|206588350|emb|CAQ35313.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
          Length = 229

 Score =  125 bits (315), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 71/196 (36%), Positives = 114/196 (58%), Gaps = 2/196 (1%)

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM--SN 541
           A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +  S 
Sbjct: 29  AIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEKSG 88

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              R+ + E+IA  L    E V+ VL + +   SL+TP   +  + L DF+ D++  SP 
Sbjct: 89  IDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGTSLLDFLSDEHGASPD 148

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  L +     LA L+ +   V+  RFG+      TLEE+  +  +TRER+RQI+ 
Sbjct: 149 QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELAAEMGLTRERVRQIQQ 208

Query: 662 KAIRKLKHPSRSKKLR 677
           +A+ KLK    S+ +R
Sbjct: 209 EALVKLKRHFASQGVR 224


>gi|302810520|ref|XP_002986951.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
 gi|300145356|gb|EFJ12033.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
          Length = 326

 Score =  125 bits (315), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/255 (34%), Positives = 136/255 (53%), Gaps = 9/255 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKF 488
           V  +R+       A+ +M++ NLRLV   A+KY      L  LDL QEG  GLM A +KF
Sbjct: 75  VQTLRRLLQSGQAARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKF 134

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GY+FSTYA++WVK +I R+       +R+P ++  +   + R   ++S ++ REPT
Sbjct: 135 DPKKGYRFSTYAVYWVKNSILRAQTRLGHIVRVPYNVAAQKMTIQRKRAQLSLELDREPT 194

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLET---PIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            EE+  +L M      +VL+      SL       G+E    + D   D+N     ++  
Sbjct: 195 HEEVITELKMDSRRYFEVLRTGAPRRSLNARSKVTGEELIHSISD--PDENEAQYYNAG- 251

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A LR     VL SL P+E  ++R R+G+    + +  E+G+   ++RE +R+ E + + 
Sbjct: 252 -AQLRLGMDDVLDSLKPKESLIIRQRYGLDGKGERSFTEIGRNLNLSREMVRKYEIRGMM 310

Query: 666 KLKHPSRSKKLRSFL 680
           KLKHP+R K LR FL
Sbjct: 311 KLKHPTRVKYLREFL 325


>gi|302792318|ref|XP_002977925.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
 gi|300154628|gb|EFJ21263.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
          Length = 326

 Score =  125 bits (315), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/242 (35%), Positives = 132/242 (54%), Gaps = 9/242 (3%)

Query: 444 AKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A+ +M++ NLRLV   A+KY      L  LDL QEG  GLM A +KFD   GY+FSTYA+
Sbjct: 88  ARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPKKGYRFSTYAV 147

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +WVK +I R+       +R+P ++  +   + R   ++S ++ REPT EE+  +L M   
Sbjct: 148 YWVKNSILRAQTRLGHIVRVPYNVAAQKMTIQRKRAQLSLELDREPTHEEVITELKMDSR 207

Query: 562 GVRKVLKITKEPISLET---PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              +VL+      SL       G+E    + D   D+N     ++   A LR     VL 
Sbjct: 208 RYFEVLRTGAPRRSLNARSKVTGEELIHSISD--PDENEAQYFNAG--AQLRLGMDDVLD 263

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SL P+E  ++R R+G+    + +  E+G+   ++RE +R+ E + + KLKHP+R K LR 
Sbjct: 264 SLKPKESLIIRQRYGLDGKGERSFTEIGRNLNLSREMVRKYEIRGMMKLKHPTRVKYLRE 323

Query: 679 FL 680
           FL
Sbjct: 324 FL 325


>gi|326773494|ref|ZP_08232777.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636724|gb|EGE37627.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 164

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 56/81 (69%), Positives = 72/81 (88%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 84  AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 143

Query: 504 VKQAITRSIADQSCTIRIPVH 524
           ++QAITR++ADQ+ TIRIPVH
Sbjct: 144 IRQAITRAMADQARTIRIPVH 164



 Score = 42.0 bits (97), Expect = 0.39,   Method: Composition-based stats.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 19  ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 52


>gi|312281919|dbj|BAJ33825.1| unnamed protein product [Thellungiella halophila]
          Length = 562

 Score =  125 bits (314), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 138/238 (57%), Gaps = 5/238 (2%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++++   LV+ +++ Y   G+   DLIQ GN+G+++ AE+FD   GYKFSTY  +W+++
Sbjct: 326 ELLKSTRSLVLFLSRNYRGLGIAHEDLIQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRK 385

Query: 507 AITRSIADQSCTIRIP---VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++  ++  +  + IP   +    +I K  +T +  S+ IK  P  EEI+K+    ++ +
Sbjct: 386 SMSMMVSRHARGVYIPSSVIRTMSQIQKARKTLK-TSHGIK-YPADEEISKETGYSLKKI 443

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R   +  K   S++  +GD  T+   +F  D    SP ++ ++ +       +L  L PR
Sbjct: 444 RAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAWRDVHDLLQGLEPR 503

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++V+ +R+G+      +LEE+GK   V++E IR+IE +A+ KL+  + ++ LR +L+
Sbjct: 504 EKQVMVLRYGLQGFRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQANAENLRFYLN 561


>gi|149911320|ref|ZP_01899941.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
 gi|149805635|gb|EDM65637.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
          Length = 294

 Score =  125 bits (313), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 118/218 (54%), Gaps = 2/218 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  M+++NLRLV+ VAKKY N  L + ++IQEGN GLM A +KFD   G +FSTYA+WW
Sbjct: 42  ARDTMIQSNLRLVLMVAKKYQNYSLDWAEIIQEGNTGLMHAVDKFDPERGCRFSTYAVWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I + I + S TIRIP+H+     ++++ +  +   +       +IA++L +    V
Sbjct: 102 IRNNIEQYIMNHSRTIRIPIHVTRVYKQILKASSELGLDVDTNEGITKIAQELKISPRKV 161

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             +L       SL+  I  GD   + L D +  +    P     + +  E    +L  L 
Sbjct: 162 LNILGHYFNEGSLDKEIHSGDNLLATLKDLVAAEVDCQPDIRYEKCDYYEYMDALLEYLP 221

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            R + ++R+RFG       +L+ + +   ++RER+RQI
Sbjct: 222 VRSQNIIRLRFGFKGQDPMSLQAIAQLMDISRERVRQI 259


>gi|15232364|ref|NP_190960.1| SIGC (RNA POLYMERASE SIGMA-SUBUNIT C); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|2353175|gb|AAB69386.1| sigma factor 3 [Arabidopsis thaliana]
 gi|2463554|dbj|BAA22530.1| SigC [Arabidopsis thaliana]
 gi|5478585|dbj|BAA82450.1| sigma factor SigC [Arabidopsis thaliana]
 gi|7630012|emb|CAB88354.1| sigma factor SigC [Arabidopsis thaliana]
 gi|133778870|gb|ABO38775.1| At3g53920 [Arabidopsis thaliana]
 gi|332645638|gb|AEE79159.1| RNApolymerase sigma-subunit C [Arabidopsis thaliana]
          Length = 571

 Score =  125 bits (313), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 135/240 (56%), Gaps = 3/240 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E+V++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W
Sbjct: 332 CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 391

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKV--VRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++++++  ++  +  + IP  +   I+ +   R   + S+ IK     EEIAK     V+
Sbjct: 392 IRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGIKYA-ADEEIAKLTGHSVK 450

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R   +  K   S++  +GD  T+   +F  D    SP ++ ++ + R     +L  L 
Sbjct: 451 KIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLE 510

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE++V+ +R+G+      +LEE+GK   V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 511 PREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570


>gi|86145220|ref|ZP_01063551.1| RpoS-like sigma factor [Vibrio sp. MED222]
 gi|85836797|gb|EAQ54917.1| RpoS-like sigma factor [Vibrio sp. MED222]
          Length = 298

 Score =  125 bits (313), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 131/230 (56%), Gaps = 6/230 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  M+E+NLRLV+ +AK Y  R       LDLI+EGNIGL+KA +K+D   GY+FSTYA
Sbjct: 61  ARDIMIESNLRLVVKIAKSYLKRKGNNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYA 120

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW+++ I  ++ ++  T+R+P H+  +I+ +      +S K+++E +  E++    +  
Sbjct: 121 VWWIRENIEAALMNKGRTVRLPAHVCKEINSLASKKLDVSKKMRKEISISELSNISGVKA 180

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V +++ ++   I + T +G      + +  E +    P       +      +++ +L
Sbjct: 181 ERVDQLVALSGF-IDVTTTVGISHAPLVLEQCESEYIPDPQQDCEDQSFTHALEQIINTL 239

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQF--CVTRERIRQIEAKAIRKLK 668
            P+ ++VL  RFG   N   TL EVG+     V+ ER+RQ++ +A+ +++
Sbjct: 240 PPKLQKVLIHRFGFFDNKVKTLSEVGQMLDVNVSNERVRQMQKEAVERIQ 289


>gi|320103437|ref|YP_004179028.1| RpoD subfamily RNA polymerase sigma-70 factor [Isosphaera pallida
           ATCC 43644]
 gi|319750719|gb|ADV62479.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Isosphaera
           pallida ATCC 43644]
          Length = 286

 Score =  125 bits (313), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 87/259 (33%), Positives = 128/259 (49%), Gaps = 25/259 (9%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R +   V +G+  A   ++ M+EANLRLV  VA +Y   GL + DL+ EGN+GL
Sbjct: 33  LTAEEERELARRVLRGDASA---RRRMIEANLRLVAMVAARYRGLGLDWEDLVGEGNLGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A   +D   G +FSTYA  W++Q I  ++   + TIR+P HM  K+    R   R++ 
Sbjct: 90  IRAVSSYDPDRGVRFSTYAAHWIRQTIRVALTTTAATIRLPAHMVTKLALWRRAEARLTR 149

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVS 599
            + R PT EE+A +L       R  +K   E   +  E P   E     G   E +    
Sbjct: 150 NLGRSPTFEEVADELGWS-SSTRLSMKRAMESGRVHHEEPGATE-----GRGSESRR--- 200

Query: 600 PLDSAIQANLRET-----------TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           P+D A+                    R L  L  RE  VL +R+G+G      L EV   
Sbjct: 201 PIDQAVDPRPEPAWEIERRDELLELRRSLQRLGERERLVLALRYGLGDIAPKPLREVATT 260

Query: 649 FCVTRERIRQIEAKAIRKL 667
             VTRE +R+IEA+A+R+L
Sbjct: 261 LGVTREWVRRIEARALRQL 279


>gi|325520258|gb|EGC99421.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 167

 Score =  123 bits (309), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 66/165 (40%), Positives = 99/165 (60%), Gaps = 1/165 (0%)

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVH+ D+  +V R A R   +  R+PTP E+A +  +    +R VL +  EP+SL+
Sbjct: 4   TIRVPVHVGDQQQRVRRHALRFHQRTGRQPTPAELAAETGLDETRLRAVLALPAEPVSLD 63

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+ D DT  L D IED+++ SP +      +RE  T +L S+TP E  VLR RFG+G  
Sbjct: 64  TPLPDADTG-LVDLIEDQSSASPFERLADTRMRECVTSLLRSVTPAEADVLRRRFGLGGT 122

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              T + + K   ++RER+RQIE +A+  L+  + ++   SFLD 
Sbjct: 123 EPDTYDAIAKDAGMSRERVRQIEKRALAALRTIAEAEDAHSFLDA 167


>gi|88809561|ref|ZP_01125068.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786311|gb|EAR17471.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 211

 Score =  123 bits (309), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 55/135 (40%), Positives = 93/135 (68%), Gaps = 4/135 (2%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++++GE     AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   
Sbjct: 59  IIKRGE----KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTR 114

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+  +  R+  +    P+ E++
Sbjct: 115 GHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRASKARLMQRNGLSPSTEQL 174

Query: 553 AKKLAMPVEGVRKVL 567
           +  + +P+  V  +L
Sbjct: 175 SDDMNLPISEVEDLL 189


>gi|149198541|ref|ZP_01875585.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149138256|gb|EDM26665.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 282

 Score =  123 bits (309), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 125/228 (54%), Gaps = 3/228 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+  ANLRLV+++AK++ NRG+   +LI EGN GL+KAA++F    G KF++YA WW
Sbjct: 38  AIQELTLANLRLVVTIAKQFMNRGVALGELIAEGNHGLVKAAQRFRPGHGAKFASYAAWW 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ I R+I D    +R+PV    ++ K+     ++  +       + +AK++ +    V
Sbjct: 98  IKQNIRRAIRDDKRIVRVPVQSLLRMQKIKNARLKIQQETGDASNDKAVAKEVGISPRLV 157

Query: 564 RKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASL 620
           R   L +     S+   I  D   +  G+ I D  A +P +     +  +T   ++   L
Sbjct: 158 RTTSLHVDTSSFSINEQISQDGKATEKGELIPDSQAQTPGEVMEFHDGYKTLMEIVRQEL 217

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE ++L  RFG+      TL E  +   +T ER+RQ++ +A+R+L+
Sbjct: 218 TEREYKILSARFGLDDGEAKTLAETSELVGLTSERVRQLQQEALRRLR 265


>gi|222632729|gb|EEE64861.1| hypothetical protein OsJ_19718 [Oryza sativa Japonica Group]
          Length = 457

 Score =  123 bits (308), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 148/277 (53%), Gaps = 10/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TN 465
           + NE++S   +  ++ +    ++ M R  E     A+ ++++ NLRLV+    KY    +
Sbjct: 186 LENEVQSEPNDAQLAEAMNMSVLQMRRHLEV-GRAARNKLIKHNLRLVLYTINKYYPDMS 244

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              +F D+ Q G  GL+ A ++F+   G++ STYA++W++ +I R+I   + T R P  M
Sbjct: 245 NDERFDDICQAGANGLITAIDRFEPKRGFRISTYALFWIRHSIVRAITLSNFT-RFPFAM 303

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDE 583
             +  ++ R    ++ ++ R PT EE+ KK+ +     R V+++T+   SL     +  E
Sbjct: 304 ESERQEIHRAREELAFELGRAPTEEEVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQE 363

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L + + D +A+    S+    LR     +L SL P+E  V+R RFG+      TL 
Sbjct: 364 E---LINEVTDDDAIGVDTSSHNTLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLS 420

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+     ++RE +R+ E KA+ KLKHP+R + LR ++
Sbjct: 421 EIAGNLNISREMVRKYELKALMKLKHPTRVEYLRRYM 457


>gi|332703233|ref|ZP_08423321.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332553382|gb|EGJ50426.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 398

 Score =  122 bits (307), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 134/230 (58%), Gaps = 14/230 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +V ++LRLV+ +A  +  R +Q  LDL+QEGN+GLM+A +KFD   G KFS YA +W+K 
Sbjct: 155 LVTSHLRLVVKIAMDFQRRWMQNVLDLVQEGNVGLMRAVQKFDPEKGIKFSYYAAFWIKA 214

Query: 507 AITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            I + I D    ++I     + K+   +   R+       +PT   ++K L + VE + +
Sbjct: 215 YILKFIMDNWRMVKIGTTQTQRKLFYNLNKERQRLQSQGFDPTSSTLSKSLGVSVEDIEE 274

Query: 566 V-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP------LDSAIQANLRETTTRVLA 618
           +  ++++  +SL+  IGD+ T+   DF+    A+ P       +S I A LRE    ++ 
Sbjct: 275 MDQRLSRSDMSLDITIGDDTTATRMDFLP---ALGPGIEETLANSEISALLREHLASIVP 331

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ +E+ +L+ R  +  ++  TL E+G Q+ +TRER+RQIEA+ ++K++
Sbjct: 332 MLSDKEQDILQKR--LLSDSPVTLREIGDQYGITRERVRQIEARLLQKIR 379


>gi|310777993|ref|YP_003966326.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
 gi|309747316|gb|ADO81978.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
          Length = 329

 Score =  122 bits (307), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 145/256 (56%), Gaps = 15/256 (5%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS+ T I   + + IV   + G+ EA   ++ +V +NL+LV  +A KY+  G+ ++DLIQ
Sbjct: 78  ISLYTPIPKEKEKDIVKKAQDGDEEA---REMLVTSNLKLVAKIAMKYSKSGVNYIDLIQ 134

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           +G IGL+ A +K+D   G+ F++Y++WW+K+ I  SIA++   I+IP ++     K+   
Sbjct: 135 DGTIGLIAAIDKYDLSKGHSFTSYSVWWIKREIINSIANRINAIKIPSYVYLMNKKIRIF 194

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
                 +  ++P+ +EI++ L + +E V K+ + ++  +       D +   LGDF    
Sbjct: 195 EDDFMERNNKKPSYQEISEALNLSLEEVEKMKEASEIGVG---GFADGNEPDLGDF---- 247

Query: 596 NAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           N V  +D  +  NL E  +++   +  ++P E++V+ M +G+  N     +E+ K   V+
Sbjct: 248 NTVDQIDKEL--NLLEERSKISNLMRKISPEEQKVVEMYYGLDDNKRLGFKEISKIMGVS 305

Query: 653 RERIRQIEAKAIRKLK 668
            E+++ ++ +AI KLK
Sbjct: 306 VEKVKFLKERAILKLK 321


>gi|203288197|ref|YP_002223212.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
 gi|201085417|gb|ACH94991.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
          Length = 267

 Score =  122 bits (307), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 134/229 (58%), Gaps = 11/229 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+ + K+Y  +GL+  DLIQEGN+GL++AAEK+D     KFSTYA +W
Sbjct: 41  AKNQMINANLRLVLKIIKRYAGKGLKIEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ++ R++  ++  +++P    + I ++ +         ++ P  E+I ++  +     
Sbjct: 101 IKQSLQRALNTKTRLVKVPYRKENLILQINKYLMEE----EKSPKKEDIMERFNLTTAQY 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLT 621
            K++   ++  SL+  I   + S L +  ED N+++P +S ++ N  L+     +   L 
Sbjct: 157 VKIIPYLEKEYSLDKKIEGSENSTLLNLYED-NSLNP-ESTLEQNSTLKHLNYILETKLN 214

Query: 622 PREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E  +++ R+ +  N+D   TL+++  +  ++ E +RQIE + ++KL+
Sbjct: 215 EKERYIIKKRYNLD-NSDKKSTLKDISTELGISSETVRQIEKRVLKKLR 262


>gi|203284664|ref|YP_002222404.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
 gi|201084107|gb|ACH93698.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
          Length = 267

 Score =  122 bits (306), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 133/229 (58%), Gaps = 11/229 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+ + K+Y  +GL+  DLIQEGN+GL++AAEK+D     KFSTYA +W
Sbjct: 41  AKNQMINANLRLVLKIIKRYAGKGLKIEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ++ R++  ++  +++P    + I ++ +         ++ P  E+I ++  +     
Sbjct: 101 IKQSLQRALNTKTRLVKVPYRKENLILQINKYLMEE----EKSPKKEDIMERFNLTTAQY 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLT 621
            K++   ++  SL+  I   + S L +  ED N+ +P +S ++ N  L+     +   L 
Sbjct: 157 VKIIPYLEKEYSLDKKIEGSENSTLLNLYED-NSFNP-ESTLEQNSTLKHLNYILETKLN 214

Query: 622 PREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E  +++ R+ +  N+D   TL+++  +  ++ E +RQIE + ++KL+
Sbjct: 215 EKERYIIKKRYNLD-NSDKKSTLKDISTELGISSETVRQIEKRVLKKLR 262


>gi|269963639|ref|ZP_06177962.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269831652|gb|EEZ85788.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 279

 Score =  122 bits (305), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 132/243 (54%), Gaps = 7/243 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAA 485
           H   + R G+ EA   ++ M+E+NLRLV+ +AK Y   T      LDLI+EGNIGL+KA 
Sbjct: 32  HYAKLNRAGDKEA---REVMIESNLRLVVKIAKSYLKRTGNNFTLLDLIEEGNIGLIKAI 88

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +K+D   GY+FSTYA+WW+++ I  ++ +   T+R+P H+  +I+ +       S  + +
Sbjct: 89  DKYDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPAHVCKEINSLASKKHDASKTMSK 148

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + +  E++    + VE V +++ ++   I + T +       + +  E +    P     
Sbjct: 149 DISISELSHCSGVKVERVDELVALSG-FIDVSTTVDLNHAPFVLEQCESEYTTDPQQDCE 207

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                +    V+ +L  + ++VL  RFG+  +   TL EVG    V+ ER+RQ++ +A+ 
Sbjct: 208 DHCFTQALEHVVNTLPVKLQQVLIHRFGLFEHNVKTLAEVGDLLNVSNERVRQMQKEAVE 267

Query: 666 KLK 668
           +++
Sbjct: 268 RIQ 270


>gi|187918623|ref|YP_001884188.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
 gi|119861471|gb|AAX17266.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
          Length = 267

 Score =  122 bits (305), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 131/228 (57%), Gaps = 9/228 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+ + K+Y  +GL+  DLIQEGN+GL++AAEK+D     KFSTYA +W
Sbjct: 41  AKNKMINANLRLVLKIIKRYAGKGLKVEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ++ R++  ++  +++P    + I ++ +         ++ P  E+I ++  +     
Sbjct: 101 IKQSLQRALNTKTRLVKVPYRKENLILQINKYLMEE----EKSPKKEDIMERFNLTTAQY 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLT 621
            K++   ++  SL+  +   + S L +  ED N+ +P +S ++ N  L+     +   L 
Sbjct: 157 VKIIPYLEKEYSLDKKLEGSENSTLLNLYED-NSFNP-ESTLEQNSTLKHLNHILETKLN 214

Query: 622 PREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E  ++R R+ +  N    TL+++  +  ++ E +RQIE + ++KL+
Sbjct: 215 DKERYIIRKRYNLDNNDKKSTLKDISSELGISSETVRQIEKRVLKKLR 262


>gi|125553511|gb|EAY99220.1| hypothetical protein OsI_21178 [Oryza sativa Indica Group]
          Length = 500

 Score =  122 bits (305), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 148/277 (53%), Gaps = 10/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TN 465
           + NE++S   +  ++ +    ++ M R  E     A+ ++++ NLRLV+    KY    +
Sbjct: 229 LENEVQSEPNDAQLAEAMNMSVLQMRRHLEV-GRAARNKLIKHNLRLVLYTINKYYPDMS 287

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              +F D+ Q G  GL+ A ++F+   G++ STYA++W++ +I R+I   + T R P  M
Sbjct: 288 NDERFDDICQAGANGLITAIDRFEPKRGFRISTYALFWIRHSIVRAITLSNFT-RFPFAM 346

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDE 583
             +  ++ R    ++ ++ R PT EE+ KK+ +     R V+++T+   SL     +  E
Sbjct: 347 ESERQEIHRAREELAFELGRAPTEEEVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQE 406

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L + + D +A+    S+    LR     +L SL P+E  V+R RFG+      TL 
Sbjct: 407 E---LINEVTDDDAIGVDTSSHNTLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLS 463

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+     ++RE +R+ E KA+ KLKHP+R + LR ++
Sbjct: 464 EIAGNLNISREMVRKYELKALMKLKHPTRVEYLRRYM 500


>gi|115465727|ref|NP_001056463.1| Os05g0586600 [Oryza sativa Japonica Group]
 gi|30698488|dbj|BAC76601.1| Sig5 [Oryza sativa Japonica Group]
 gi|30698518|dbj|BAC76607.1| plastid sigma factor SIG5 [Oryza sativa Japonica Group]
 gi|113580014|dbj|BAF18377.1| Os05g0586600 [Oryza sativa Japonica Group]
          Length = 500

 Score =  122 bits (305), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 148/277 (53%), Gaps = 10/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TN 465
           + NE++S   +  ++ +    ++ M R  E     A+ ++++ NLRLV+    KY    +
Sbjct: 229 LENEVQSEPNDAQLAEAMNMSVLQMRRHLEV-GRAARNKLIKHNLRLVLYTINKYYPDMS 287

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              +F D+ Q G  GL+ A ++F+   G++ STYA++W++ +I R+I   + T R P  M
Sbjct: 288 NDERFDDICQAGANGLITAIDRFEPKRGFRISTYALFWIRHSIVRAITLSNFT-RFPFAM 346

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDE 583
             +  ++ R    ++ ++ R PT EE+ KK+ +     R V+++T+   SL     +  E
Sbjct: 347 ESERQEIHRAREELAFELGRAPTEEEVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQE 406

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L + + D +A+    S+    LR     +L SL P+E  V+R RFG+      TL 
Sbjct: 407 E---LINEVTDDDAIGVDTSSHNTLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLS 463

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+     ++RE +R+ E KA+ KLKHP+R + LR ++
Sbjct: 464 EIAGNLNISREMVRKYELKALMKLKHPTRVEYLRRYM 500


>gi|42524684|ref|NP_970064.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
 gi|39576894|emb|CAE78123.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
          Length = 373

 Score =  121 bits (304), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 134/233 (57%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V+ANLR V+ VA +Y+  G + +DLIQEGN+GLM A  +F+   G +  TYA+WW
Sbjct: 136 AAQALVKANLRFVVKVAAEYSKFGSKMIDLIQEGNVGLMHAVREFNPYKGARLITYAVWW 195

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   +  Q   +RI     + K+   ++  +   + +  EP    I+ +L +P + 
Sbjct: 196 IRGYIQEFLMRQYSMVRIGTTQNQRKLFYQLQKEKEALDAMGIEPNIGLISSRLGIPEDE 255

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-----LRETTTRV 616
           VR + ++++   +SL+ P+ DE  + LGD ++   +  PLD A+  N     L++    +
Sbjct: 256 VRDMTMRMSGRDVSLDRPVDDESGTTLGD-LQRGPSDQPLDEALAHNEQLEILKQKIEEI 314

Query: 617 LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L+ RE+ +L  R    +N D  TL+E+G++  +TRE +RQ+EA+ ++K+K
Sbjct: 315 RPELSEREKIILDERI---LNDDPLTLQEIGEKHGITREAVRQMEARLMKKIK 364


>gi|254454176|ref|ZP_05067613.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
 gi|198268582|gb|EDY92852.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
          Length = 715

 Score =  121 bits (303), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 109/223 (48%), Gaps = 12/223 (5%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A ++   GL+  DL QEG  GL ++ E F    G + +TY+ + ++Q I R++ D    
Sbjct: 504 LATRFPTEGLEEDDLFQEGYFGLTRSVEMFHAGRGNRLTTYSQYRIRQTIARAVDDHRSV 563

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL-E 577
           +RIPVH   K+  + R   R+S  I R      + K   + +  ++K+  I +  I   E
Sbjct: 564 VRIPVHFASKVRLIERFGERVSGNISRSDYHCALGKAFQIELAEIQKIENIPRLSIEFDE 623

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
               D D             + P    ++   +      L  L  R   ++  RFG+  N
Sbjct: 624 NLYSDADIE-----------LEPFQRVLEQQRQAIIKDFLEDLPERHADIIVRRFGLDGN 672

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            + TLE+ G+ + VTRERIRQ+EAKAI  L+HP R+K LR  L
Sbjct: 673 DEMTLEQCGQVYGVTRERIRQLEAKAIDWLRHPVRAKFLRELL 715


>gi|297812573|ref|XP_002874170.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297320007|gb|EFH50429.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 517

 Score =  121 bits (303), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 79/241 (32%), Positives = 131/241 (54%), Gaps = 7/241 (2%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A+ ++++ NLRLV+ V  KY    TN G +F DL Q G  GL+ A ++F+    ++ STY
Sbjct: 279 ARNKLIKHNLRLVLFVMNKYFHDFTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTY 337

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            ++W++ AI RS+   + T R+P  +     ++ +T   +  ++ R PT +E+ ++L + 
Sbjct: 338 GLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIFKTKTELLFELGRLPTEDEVVERLKIT 396

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E  R+VL+  K  +SL +         +   I D + V   +S   A LR     VL S
Sbjct: 397 PERYREVLRAAKPVLSLNSKHSVTQEEFING-ITDVDGVGANNSRQPALLRLALDDVLDS 455

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKH +R   LR +
Sbjct: 456 LKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQY 515

Query: 680 L 680
           +
Sbjct: 516 I 516


>gi|56606829|gb|AAW02799.1| sigma factor [Nonomuraea sp. ATCC 39727]
          Length = 92

 Score =  121 bits (303), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 56/91 (61%), Positives = 73/91 (80%)

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW+KQAITR++ADQ+ TIRIPVHM + I+KV R  RRM N++ REPTPEEI
Sbjct: 1   GYKFSTYATWWIKQAITRAMADQARTIRIPVHMVELINKVARVQRRMQNELGREPTPEEI 60

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           A++  + V+ V +V +  +EPISL TP+G+E
Sbjct: 61  AQESELEVDRVIEVQRYGREPISLHTPLGEE 91


>gi|85859725|ref|YP_461927.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
 gi|85722816|gb|ABC77759.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
          Length = 289

 Score =  121 bits (303), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 138/251 (54%), Gaps = 15/251 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR+ +   +    EA+   +++V +NLR V+ +A +Y N G++  DLIQEGNIGLM A 
Sbjct: 28  EFRYAIEWKKNQNMEAA---EKLVVSNLRFVVKIAHEYRNYGVKLADLIQEGNIGLMHAV 84

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKI 543
           +KFD   GY+  +YA+WW++  I   I      ++I      R    K+ +T + +    
Sbjct: 85  KKFDPYKGYRLISYAVWWIRAYIQNYIIKTWSLVKIGTTQAQRKLFFKLNKTKKDIQALS 144

Query: 544 KREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFI----EDKNAV 598
            + P   EIA+ L +    V ++ ++++   +SL+  IGD+  S   DF+    ED+   
Sbjct: 145 LKNPEFSEIAESLGVREGEVEEMDVRMSNRDLSLDMAIGDDGGSSHMDFLTYAGEDQE-- 202

Query: 599 SPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + L    +A L R+  T  LA L  +E  ++R R  +  +   TL+E+G  + +TRER R
Sbjct: 203 TALIRKEEAELVRKNITGALAVLNEKEMYIIRNR--VMADDPKTLQEIGDIYNITRERAR 260

Query: 658 QIEAKAIRKLK 668
           QIE +A++KL+
Sbjct: 261 QIEKQALKKLR 271


>gi|261415107|ref|YP_003248790.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371563|gb|ACX74308.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326239|gb|ADL25440.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 270

 Score =  121 bits (303), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 123/228 (53%), Gaps = 21/228 (9%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           IA+K+++ AN+R V+ VA +Y    +   DL+ EG +GL++A E F+   G KF +Y +W
Sbjct: 41  IARKKLISANMRFVLKVAIQYRGCPIPLPDLVSEGAMGLVRAIESFEHTRGLKFISYGVW 100

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W+K  ITR+I +Q   IR+P +   ++ K +    R           +EI        E 
Sbjct: 101 WIKAYITRAINEQGNLIRLPANQHLRVRKALHEQSR----------GKEIN-------EE 143

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-LDSAIQANLRETTTRVLASLT 621
           +R++++I +  +S ++P+  +  +   + + D  A +P  DS IQ+   E   R L    
Sbjct: 144 IRELIQIGQRGVSFDSPLKADSKATYAEVLPDSGASNPEADSEIQSV--EALARDLMEQL 201

Query: 622 P-REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P RE RV+   FGI      TL EVG+   ++ ER+RQ+  +A+R+++
Sbjct: 202 PEREARVITGIFGINQEAPQTLREVGESMNISHERVRQLRDQALRRIR 249


>gi|160933256|ref|ZP_02080645.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
 gi|156868330|gb|EDO61702.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
          Length = 260

 Score =  120 bits (302), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 143/248 (57%), Gaps = 16/248 (6%)

Query: 426 EFRHIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           E R +++ ++ G   E   A++E++  NLRLV+SV +++TNRG    DL Q G IGL+KA
Sbjct: 23  EKRALLTQMKNGTPQEQKKAREELINGNLRLVLSVIQRFTNRGENLDDLFQVGCIGLIKA 82

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     +FSTY +  +   I R + D + ++R+   +RD  +K ++   R++ +  
Sbjct: 83  IDNFDISQDVRFSTYGVPMIIGEIRRFLRDNN-SVRVSRSLRDTAYKAMQVKERLTTQNN 141

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSP-L 601
           +EP+ EEIAK+L +P E V   L+   EP+SL  P+  +  DT  + D + DKN  +  L
Sbjct: 142 KEPSIEEIAKELELPKEDVVLALEAIVEPVSLYEPVFSDGNDTIFVMDQVGDKNDDNNWL 201

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  L+E     + +L PRE+++L +RF  G     T  EV K+  +++ ++ ++E 
Sbjct: 202 D---EIALKEA----IRNLGPREKKILNLRFFQG----KTQMEVAKEIGISQAQVSRLEK 250

Query: 662 KAIRKLKH 669
            ++ ++K+
Sbjct: 251 GSLERIKN 258


>gi|56966075|pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
          Length = 81

 Score =  120 bits (302), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 61/80 (76%), Positives = 67/80 (83%)

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSA   +LR  T  VLA LT RE +VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEA
Sbjct: 1   DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 60

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS+ LRSFLD
Sbjct: 61  KALRKLRHPSRSEVLRSFLD 80


>gi|119953545|ref|YP_945755.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
 gi|119862316|gb|AAX18084.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
          Length = 267

 Score =  120 bits (301), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 132/229 (57%), Gaps = 11/229 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M+ ANLRLV+ + K+Y  +GL+  DLIQEGN+GL++AAEK+D     KFSTYA +W
Sbjct: 41  AKNKMINANLRLVLKIIKRYAGKGLKVEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQ++ R++  ++  +++P    + I ++ +         ++ P  E+I ++  +     
Sbjct: 101 IKQSLQRALNTKTRLVKVPYRKENLILQINKYLMEE----EKSPKKEDIMERFNLTTAQY 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLT 621
            K++   ++  SL+  I   + S L +  ED N+ +P +S ++ N  L+     +   L 
Sbjct: 157 IKIIPYLEKEYSLDKKIEGSENSTLLNLYED-NSFNP-ESTLEQNSTLKHLNHILETKLN 214

Query: 622 PREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E  ++  R+ +  N+D   TL+++  +  ++ E +RQIE + ++KLK
Sbjct: 215 EKERYIIIKRYNLD-NSDKKSTLKDISNELGISSETVRQIEKRVLKKLK 262


>gi|330938480|gb|EGH42083.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 82

 Score =  120 bits (301), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 59/81 (72%), Positives = 68/81 (83%)

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D A   +L+E T  VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 1   IDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 60

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HP+RS+ LRSFLD
Sbjct: 61  AKALRKLRHPTRSEHLRSFLD 81


>gi|212695902|ref|ZP_03304030.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212677025|gb|EEB36632.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 333

 Score =  120 bits (300), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 92/282 (32%), Positives = 151/282 (53%), Gaps = 26/282 (9%)

Query: 405 SILKIRNEIKSISVETGISISEF--RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +I KI+N + +      I +S+     IV   ++G   A  A   +V+ N  LV S A  
Sbjct: 60  NIHKIKNSLVAKKRSDIIRLSDLTNEQIVEQFQEGNQNALGA---LVDKNQGLVRSRASY 116

Query: 463 -YTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            Y + G  L+  DL+Q G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +  TI
Sbjct: 117 FYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTI 176

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-----VLKITKEPI 574
           RIP     K++K+ +       K   E + EE+ K L    EG+ K     +  I +  +
Sbjct: 177 RIPAGKYLKLNKLKQIL-----KANPEASEEELYKILKQ--EGIDKKQADDLFLINRNQV 229

Query: 575 ---SLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
              SL   +  ED++   L D + D +++   D  ++ ++ +   + L  L+ RE++++ 
Sbjct: 230 NSTSLNINLDSEDSTGDELMDMVGD-DSIPVDDQILKKDMEDFLMKALDQLSDREKQIII 288

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            R+G+      TLEE+G  + ++RERIRQIE +A+ KLK  S
Sbjct: 289 YRYGLDNEKPKTLEEIGTIYSLSRERIRQIENQALGKLKQYS 330


>gi|325845925|ref|ZP_08169123.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325481831|gb|EGC84863.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 333

 Score =  120 bits (300), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 92/282 (32%), Positives = 151/282 (53%), Gaps = 26/282 (9%)

Query: 405 SILKIRNEIKSISVETGISISEF--RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +I KI+N + +      I +S+     IV   ++G   A  A   +V+ N  LV S A  
Sbjct: 60  NIHKIKNSLVAKKRSDIIRLSDLTNEQIVEQFQEGNQNALGA---LVDKNQGLVRSRASY 116

Query: 463 -YTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            Y + G  L+  DL+Q G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +  TI
Sbjct: 117 FYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTI 176

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-----VLKITKEPI 574
           RIP     K++K+ +       K   E + EE+ K L    EG+ K     +  I +  +
Sbjct: 177 RIPAGKYLKLNKLKQIL-----KANPEASEEELYKILKQ--EGIDKKQADDLFLINRNQV 229

Query: 575 ---SLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
              SL   +  ED++   L D + D +++   D  ++ ++ +   + L  L+ RE++++ 
Sbjct: 230 NSTSLNINLDSEDSTGDELMDMVGD-DSIPVDDQILKKDMEDFLMKALDQLSDREKQIII 288

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            R+G+      TLEE+G  + ++RERIRQIE +A+ KLK  S
Sbjct: 289 YRYGLDNEKPKTLEEIGTIYSLSRERIRQIENQALGKLKQYS 330


>gi|315608976|ref|ZP_07883948.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|315249356|gb|EFU29373.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 287

 Score =  120 bits (300), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 127/237 (53%), Gaps = 38/237 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++  ANL+ V+++A+++  RGL   DLI EGNIGLM+AA KFD   G +F  YA  +
Sbjct: 87  ALEQLTRANLKFVVAMARRFRGRGLAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPY 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V++A+ R++  Q+   R+P   RD               I R+ +  E+           
Sbjct: 147 VRKAMERAVEQQAGLYRVP---RD---------------IMRQKSRHEV----------- 177

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   +P S++ P+ + +   L D +E+K+A+ P D      + E    ++A+L  R
Sbjct: 178 --------QPASVDAPLSEGNKFTLLDILENKDAIHPDDDYNVQAMIEALESLVATLDER 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+RV+R  +G+G     +L E+ +Q  + RER RQI  +A+RK+   ++++ L+ F+
Sbjct: 230 EQRVVRGFYGLGTGR-ISLAEIAEQMGIKRERARQIRDRALRKIARSTQNRALKIFI 285


>gi|242089037|ref|XP_002440351.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
 gi|241945636|gb|EES18781.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
          Length = 501

 Score =  119 bits (299), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 81/268 (30%), Positives = 148/268 (55%), Gaps = 19/268 (7%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV-ISVAKKYTNRGL--QFLDLIQE 476
           TG+++ + R  + + R        A+ ++++ NLRLV  ++ K Y + G   +F DL Q 
Sbjct: 246 TGMTVHQLRRRLDVGRA-------ARNKLIKHNLRLVPYAINKYYPDMGTDERFDDLCQA 298

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G  GL+ A ++F+   G++ STYA++W++ +I R++   S T R P  M  +  ++ +  
Sbjct: 299 GANGLITAIDRFEPKRGFRISTYALFWIRHSIVRAMTLSSFT-RFPFAMESERQEIGKAR 357

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDEDTSHLGDFIED 594
             ++ ++ R  T EE+ +K+ +  +  R VL++T+   SL     +  E+   L + + D
Sbjct: 358 EELAFELGRPATDEEVRRKVGISPQRYRDVLRMTRPTYSLHARNRVTQEE---LINEVTD 414

Query: 595 KNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +A+  +D+  + N  LR     +L SL P+E  V+R RFG+      TL E+     ++
Sbjct: 415 DDAIG-VDAGGRHNTLLRLAIDDLLDSLKPKESLVIRQRFGLDGRGKRTLSEIAGNLSIS 473

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +R+ E KA+ KLKHP+R + LR ++
Sbjct: 474 REMVRKYELKALMKLKHPTRVEYLRRYM 501


>gi|288927103|ref|ZP_06420991.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|288336130|gb|EFC74523.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
          Length = 287

 Score =  119 bits (299), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 127/237 (53%), Gaps = 38/237 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++  ANL+ V+++A+++  RGL   DLI EGNIGLM+AA KFD   G +F  YA  +
Sbjct: 87  ALEQLTRANLKFVVAMARRFRGRGLAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPY 146

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V++A+ R++  Q+   R+P   RD               I R+ +  E+           
Sbjct: 147 VRKAMERAVEQQAGLYRVP---RD---------------IMRQKSRHEV----------- 177

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   +P S++ P+ + +   L D +E+K+A+ P D      + E    ++A+L  R
Sbjct: 178 --------QPASVDAPLSEGNKFTLLDILENKDAIHPDDDYNVQAMIEALESLVATLDER 229

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+RV+R  +G+G     +L E+ +Q  + RER RQI  +A+RK+   ++++ L+ F+
Sbjct: 230 EQRVVRGFYGLGTGR-ISLAEIAEQMGIKRERARQIRDRALRKIARSTQNRALKIFI 285


>gi|121488749|emb|CAJ18259.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score =  119 bits (299), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/166 (35%), Positives = 102/166 (61%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  S  + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHSLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|15237896|ref|NP_197800.1| SIGE (SIGMA FACTOR E); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|4033838|emb|CAA77213.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972299|dbj|BAA78109.1| RNA polymerase sigma subunit SigE [Arabidopsis thaliana]
 gi|10178160|dbj|BAB11572.1| sigma-like factor [Arabidopsis thaliana]
 gi|222423237|dbj|BAH19595.1| AT5G24120 [Arabidopsis thaliana]
 gi|332005876|gb|AED93259.1| RNA polymerase sigma factor [Arabidopsis thaliana]
          Length = 517

 Score =  119 bits (298), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 78/241 (32%), Positives = 130/241 (53%), Gaps = 7/241 (2%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A+ ++++ NLRLV+ V  KY    TN G +F DL Q G  GL+ A ++F+    ++ STY
Sbjct: 279 ARNKLIKHNLRLVLFVMNKYFHEFTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTY 337

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            ++W++ AI RS+   + T R+P  +     ++ +    +  ++ R PT +E+ ++L + 
Sbjct: 338 GLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKIT 396

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E  R+VL+  K  +SL +         +   I D + V   +S   A LR     VL S
Sbjct: 397 PERYREVLRAAKPVLSLNSKHSVTQEEFING-ITDVDGVGANNSRQPALLRLALDDVLDS 455

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKH +R   LR +
Sbjct: 456 LKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQY 515

Query: 680 L 680
           +
Sbjct: 516 I 516


>gi|255017998|ref|ZP_05290124.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-515]
          Length = 209

 Score =  119 bits (298), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 63/73 (86%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW
Sbjct: 137 AKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWW 196

Query: 504 VKQAITRSIADQS 516
           ++QAITR+IADQ+
Sbjct: 197 IRQAITRAIADQA 209



 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 70/137 (51%), Gaps = 21/137 (15%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--------VDGDDLED 85
           +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V         D  +L  
Sbjct: 23  LIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEVSDDADDEDPDETELVK 82

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   +S DL   +    V             +DPVRMYL+E+G ++LL+ + EIA+AKR
Sbjct: 83  EE--TESFDLTDMSVPPGV-----------KINDPVRMYLKEIGRVDLLTADEEIALAKR 129

Query: 146 IEAGRAMMMASLCESPL 162
           IEAG       L E+ L
Sbjct: 130 IEAGDIEAKGRLAEANL 146


>gi|256546106|ref|ZP_05473459.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
 gi|256398223|gb|EEU11847.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
          Length = 333

 Score =  119 bits (297), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 92/279 (32%), Positives = 149/279 (53%), Gaps = 26/279 (9%)

Query: 408 KIRNEIKSISVETGISISEF--RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK-YT 464
           KI+N I +      I +S+     IV   ++G   A  A   +V+ N  LV S A   Y 
Sbjct: 63  KIKNSIVARQRSDIIRLSDLTNEQIVEQFQEGNQNALGA---LVDKNQGLVRSRASYFYR 119

Query: 465 NRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + G  L+  DL+Q G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP
Sbjct: 120 SHGNDLELEDLVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIP 179

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-----VLKITKEPI--- 574
                K++K+ +       K   E + EE+ K L    EG+ K     +  I +  +   
Sbjct: 180 AGKYLKLNKLKQIL-----KANPEASEEELYKILKQ--EGIDKKQADDLFLINRNQVNST 232

Query: 575 SLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           SL   +  ED++   L D + D +++   D  ++ ++ +   + L  L+ RE++++  R+
Sbjct: 233 SLNINLDSEDSTGDELMDMVGD-DSIPVDDQILKKDMEDFLMKALDQLSDREKQIIIYRY 291

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           G+      TLEE+G  + ++RERIRQIE +A+ KLK  S
Sbjct: 292 GLDNEKPKTLEEIGTIYNLSRERIRQIENQALGKLKQYS 330


>gi|224553536|gb|ACN55006.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553538|gb|ACN55007.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553540|gb|ACN55008.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553542|gb|ACN55009.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553546|gb|ACN55011.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553548|gb|ACN55012.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553550|gb|ACN55013.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553552|gb|ACN55014.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553554|gb|ACN55015.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553556|gb|ACN55016.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553558|gb|ACN55017.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553560|gb|ACN55018.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553562|gb|ACN55019.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553564|gb|ACN55020.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553566|gb|ACN55021.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553568|gb|ACN55022.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553570|gb|ACN55023.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553572|gb|ACN55024.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553574|gb|ACN55025.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553576|gb|ACN55026.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553578|gb|ACN55027.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553580|gb|ACN55028.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553582|gb|ACN55029.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553584|gb|ACN55030.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553586|gb|ACN55031.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553588|gb|ACN55032.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553594|gb|ACN55035.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553596|gb|ACN55036.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553598|gb|ACN55037.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553600|gb|ACN55038.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553602|gb|ACN55039.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553604|gb|ACN55040.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553608|gb|ACN55042.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553610|gb|ACN55043.1| RNA polymerase sigma factor [Escherichia coli ETEC H10407]
 gi|224553612|gb|ACN55044.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553614|gb|ACN55045.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553616|gb|ACN55046.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score =  119 bits (297), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 84/111 (75%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|254514436|ref|ZP_05126497.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
 gi|219676679|gb|EED33044.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
          Length = 432

 Score =  119 bits (297), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 120/224 (53%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +   NLRLV S+A +Y  +G+ +LDLIQEG +GL++AAEK+D   G++FSTY   W
Sbjct: 191 ARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHNKGFRFSTYCFNW 250

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + QAI R + D    IR P H++++++K+ R       +   EP    +A+   + +E  
Sbjct: 251 ITQAIRRHVGDTGGLIRYPTHVQEQVNKLYRLRITEKQRTGEEPGDAALAEAAGLSLEKT 310

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++L++    ISL+ P  D+D   L D +      +    A   +L +     +  L   
Sbjct: 311 RELLQLRNLGISLDAPQYDDDDGTLLDTMSGGPFEACEAEAETESLHDRLLVEMQGLDQA 370

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  V+  R+G+      +  E+  +  V+RE +RQ+E  A+ KL
Sbjct: 371 EREVVIARWGLHDGPPLSRAEIADRMSVSREWVRQLERAALTKL 414


>gi|224553534|gb|ACN55005.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score =  118 bits (296), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 84/111 (75%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIGRAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|312282679|dbj|BAJ34205.1| unnamed protein product [Thellungiella halophila]
          Length = 511

 Score =  118 bits (296), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/303 (28%), Positives = 154/303 (50%), Gaps = 24/303 (7%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKS----------ISVETGISISEFRHIVSMVRKGECEA 441
           E  W   +   + ++L++++E++           I+ E  +S +E +  + + R      
Sbjct: 218 EHAWLFKLMQPMKALLQVKDELQKSLGREPRETEIAGEINMSAAEVKRKIEIGRA----- 272

Query: 442 SIAKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             A+ ++++ NLRLV+ V  KY    TN G +F DL Q G  GL+ A ++F+    ++ S
Sbjct: 273 --ARNKLIKHNLRLVLFVMNKYFQDFTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLS 329

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TY ++W++ AI RS+   + T R+P  +     ++ +T   +  ++ R PT +E+ ++L 
Sbjct: 330 TYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKTKMELLFELGRLPTEDEVVERLK 388

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E  R+VL+  K   SL +         +   I D + V   +    A LR     VL
Sbjct: 389 ISPERYREVLRAAKPVFSLNSKHSVTQEEFING-ITDVDGVGADNRRQPAILRLALDDVL 447

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKH +R   LR
Sbjct: 448 DSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLR 507

Query: 678 SFL 680
            ++
Sbjct: 508 QYI 510


>gi|88705109|ref|ZP_01102821.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
 gi|88700804|gb|EAQ97911.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
          Length = 439

 Score =  118 bits (296), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 129/241 (53%), Gaps = 11/241 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A+  +   NLRLV S+A +Y  +G+ +LDLIQEG +GL++AAEK+D   G++FSTY  
Sbjct: 196 SDARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHSKGFRFSTYCF 255

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
            W+ QAI R + D    IR P H++++++K+ R       +   EP    +A+   + +E
Sbjct: 256 NWITQAIRRHVGDTGGLIRYPTHVQEQVNKLYRLRVTEKQRTGEEPGDAALAEAAGLTLE 315

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS----AIQANLRETTTRVL 617
             R +L++    +SL+ P  D+D   L D +       P D+    A   +L +     +
Sbjct: 316 KTRDLLQLRNLGVSLDAPQFDDDDGTLLDTMSG----GPFDASESEAETESLHDRLLLEM 371

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L   E  V+  R+G+      +  E+  +  V+RE +RQ+E  A+ KL   S ++++R
Sbjct: 372 EELDKAEREVVIARWGLHDGPPLSRAEIADRMSVSREWVRQLERAALTKL---SGNERIR 428

Query: 678 S 678
           S
Sbjct: 429 S 429


>gi|298250481|ref|ZP_06974285.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
 gi|297548485|gb|EFH82352.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
          Length = 313

 Score =  118 bits (296), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 121/247 (48%), Gaps = 42/247 (17%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +VEANLRLV SVA +Y   G+  +DLIQEGNIGL+ A EKFD   GY+FSTYA  W
Sbjct: 70  AKNRLVEANLRLVRSVAYQYRGFGVDIMDLIQEGNIGLIHAVEKFDPTKGYRFSTYATHW 129

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R +A Q   IRIP+++++++  +         +  ++    +   KL +  E  
Sbjct: 130 IRQYICRELARQIHKIRIPLYLQEQLRHLPEAPTTPDGQAMQD----QAHAKLMVAYERS 185

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASL 620
           +   +     P   E P                 A +P    +Q   R+   ++   A L
Sbjct: 186 KATHVSFDAVPFEFEDP-----------------APTPEQYCMQGAQRQLLHQLFLRAGL 228

Query: 621 TPREERVLRMRFGIGMNTDHTLE------------------EVGKQFCVTRERIRQIEAK 662
           T RE +VL +R+G+    +  LE                  ++G Q  ++ E +RQIE +
Sbjct: 229 TQRERQVLVLRYGLQQQREEGLEALLSGAISDQKQDESTYPQIGTQLGLSHEAVRQIEMR 288

Query: 663 AIRKLKH 669
           A+ KL++
Sbjct: 289 ALLKLRY 295


>gi|307776476|pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
 gi|307776477|pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
 gi|307776478|pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
          Length = 179

 Score =  118 bits (295), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/91 (57%), Positives = 71/91 (78%), Gaps = 4/91 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +  + + R+GE     A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A 
Sbjct: 92  ELKRYLHIAREGEA----ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 147

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           EKF++  G+ FSTYA WW++QAI R+IADQ+
Sbjct: 148 EKFEYKRGFAFSTYATWWIRQAINRAIADQA 178


>gi|326503440|dbj|BAJ86226.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326503904|dbj|BAK02738.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score =  118 bits (295), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 143/277 (51%), Gaps = 10/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TN 465
           +R+E++S   E  ++       V  +R+       A+ ++++ NLRLV+    KY     
Sbjct: 225 MRSELQSEPTEAEVA-EAMNMPVQRLRRLRDVGRAARNKLIKHNLRLVLYAINKYYPDMT 283

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              +F DL Q G  GL+ A ++F+   G++ STYA++W++ ++ R++   S T R P  M
Sbjct: 284 GDERFADLCQAGANGLITAIDRFEPKRGFRISTYALFWIRHSVVRAMTLSSFT-RFPFAM 342

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDE 583
             +  ++ R    +S ++ R PT EE  KK+ +     R V+++T+   SL +   +  E
Sbjct: 343 ESERQEINRAREELSFELGRTPTDEETMKKVGLSPARYRDVVRMTRPAYSLHSRNRVTQE 402

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L + + D +A+          LR     +L SL P+E  V+R RFG+      TL 
Sbjct: 403 E---LINEVTDVDAIGVDTHKHNRLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGRRTLS 459

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+     ++RE +R+ E KA+ KLKHP+R   LR ++
Sbjct: 460 EIAGNLRISREMVRKYELKALMKLKHPTRVDYLRRYM 496


>gi|121488745|emb|CAJ18257.1| sigma 70-type sigma factor [Chlorobaculum thiosulfatiphilum]
          Length = 165

 Score =  118 bits (295), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHGLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|225462725|ref|XP_002268709.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|302143685|emb|CBI22546.3| unnamed protein product [Vitis vinifera]
          Length = 518

 Score =  118 bits (295), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 126/240 (52%), Gaps = 5/240 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ ++++ NLRLV+ V  KY      G +F DL Q G  GL+ A ++F+    ++ STY 
Sbjct: 280 ARNKLIKHNLRLVLFVINKYFQEFANGPKFQDLCQAGVKGLITAIDRFEPKRSFRLSTYG 339

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++W++ AI RS+   S T R+   +     ++ R    +  K++R PT EEI +K+ +  
Sbjct: 340 LFWIRHAIMRSMTLSSFT-RVSFGLESVRVEIQRAKLELLFKLQRLPTEEEIIEKVGISP 398

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E   +V++ +K  +SL          ++   I D   V        A LR     VL SL
Sbjct: 399 ERYHEVMRASKSVLSLHARHATTQEEYING-ITDVEGVGGDRGRQLALLRLALDDVLDSL 457

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKHP+R   LR ++
Sbjct: 458 KPKESLVMRQRYGLDGKGDRTLGEIAGNLSISREMVRKHEVKALMKLKHPARVDYLRQYI 517


>gi|121488769|emb|CAJ18269.1| sigma 70-type sigma factor [Chlorobium limicola]
 gi|121488771|emb|CAJ18270.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score =  117 bits (294), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|121488773|emb|CAJ18271.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score =  117 bits (294), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLXPREADVIRSYFGIGMD 165


>gi|121488747|emb|CAJ18258.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score =  117 bits (294), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+K A++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKXAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  S  + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHSLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|242281118|ref|YP_002993247.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio salexigens
           DSM 2638]
 gi|242124012|gb|ACS81708.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           salexigens DSM 2638]
          Length = 322

 Score =  117 bits (294), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 84/253 (33%), Positives = 139/253 (54%), Gaps = 19/253 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKA 484
           EFR    +   G+ +A+     +V ++LRLV+ +A  +  R +Q  LDLIQEGN+GLMKA
Sbjct: 60  EFRLAKQVQENGDQQAAF---RLVSSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMKA 116

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKI 543
             KFD   G KFS YA +W+K  I + I D    ++I     + K+   +   R+    +
Sbjct: 117 VNKFDPDKGIKFSYYAAFWIKAYILKYIMDNWRMVKIGTTQTQRKLFYNLNKERQRLQAL 176

Query: 544 KREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             +PT  E++KKL +  E + ++  ++ K  +SL    G++  +   DF+ D   + P  
Sbjct: 177 GFDPTTSELSKKLNVSEEEITEMDQRLAKNDLSLNLKFGEDSEATRMDFLPD---LGPGV 233

Query: 603 SAIQANLRETTTRVL-------ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               AN +E +T +L        +L  +E+ +L  R  +  ++  TL E+G++F VTRER
Sbjct: 234 EETLAN-KEISTLLLDQLRAIVPNLNEKEQVILNDR--LLSDSPRTLREIGEEFGVTRER 290

Query: 656 IRQIEAKAIRKLK 668
           +RQIEA+ ++KL+
Sbjct: 291 VRQIEARLLKKLR 303


>gi|121488735|emb|CAJ18251.1| sigma 70-type sigma factor [Chlorobium chlorovibrioides]
          Length = 165

 Score =  117 bits (294), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 58/165 (35%), Positives = 101/165 (61%), Gaps = 1/165 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +++   + P  +  + +L     R L+ L PRE  V+R  FGIGM
Sbjct: 121 LQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFGIGM 164


>gi|108803518|ref|YP_643455.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764761|gb|ABG03643.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 274

 Score =  117 bits (293), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 110/209 (52%), Gaps = 1/209 (0%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + F DL+QEG + L+ A + +D   G +FSTYA WWVKQAI R+    +  +R+P     
Sbjct: 63  VPFEDLLQEGALALVHAVDHYDPSRGMRFSTYATWWVKQAIRRAAMAYARPMRVPERTWR 122

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              ++    R +  ++ RE    ++   L    E + +V +     +SLE+P+G+E+   
Sbjct: 123 LSERLAEAERELRAELGREIEDRDLRSGLGWSEEELSEVRRAMGPVVSLESPVGEEEEDV 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD + D+NA  P + A + + R      L++L  RE  VL  R+G+      T  ++G+
Sbjct: 183 LGDLVADENAEDPAELAARNDARRRLAHALSALPRRERAVLAGRYGL-TGEPRTFVDLGR 241

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  V+RER RQ+E  A  +L+   R   L
Sbjct: 242 ELGVSRERARQLERAAAERLREHGRRLGL 270


>gi|257067128|ref|YP_003153384.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
 gi|256799008|gb|ACV29663.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
          Length = 343

 Score =  117 bits (293), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 87/257 (33%), Positives = 137/257 (53%), Gaps = 26/257 (10%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
            IV   + G   A  A   +VE N  LV S A  +       L   DL+Q G +G+++AA
Sbjct: 95  QIVEQFQIGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAA 151

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ +       K   
Sbjct: 152 EKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQIL-----KANP 206

Query: 546 EPTPEEIAKKLAMPVEGVRK-----VLKITKEPI---SLETPIGDEDTS--HLGDFIEDK 595
           E + EE+ +   +  EG+ K     +  I +  +   SL   +  ED++   L D + D+
Sbjct: 207 EASDEELYR--ILEKEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDE 264

Query: 596 NAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +  +P+D  I + ++     + L  LT RE++++  R+G+      TLEE+GK + ++RE
Sbjct: 265 S--TPVDMLILEKDMENFLLKALDQLTDREKQIIIFRYGLDNEKPKTLEEIGKIYDLSRE 322

Query: 655 RIRQIEAKAIRKLKHPS 671
           RIRQIE +A+ KLK  S
Sbjct: 323 RIRQIENQALGKLKEFS 339


>gi|157826497|ref|YP_001495561.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801801|gb|ABV78524.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 81

 Score =  117 bits (293), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 56/67 (83%), Positives = 62/67 (92%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +LA+LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKK
Sbjct: 1   MLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKK 60

Query: 676 LRSFLDG 682
           L SF  G
Sbjct: 61  LNSFRRG 67


>gi|224553592|gb|ACN55034.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score =  117 bits (293), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 51/111 (45%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEI ++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEITEQLDKPVDDVSRMLRLNERITSVD 111


>gi|121488727|emb|CAJ18247.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score =  117 bits (293), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLXKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  +  + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|321309571|ref|YP_004191900.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801415|emb|CBY92061.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 424

 Score =  117 bits (292), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 99/326 (30%), Positives = 156/326 (47%), Gaps = 52/326 (15%)

Query: 404 DSILKIRNEIKSISVETGI----SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           D ILK R    SISV   +    +  E   +  ++   E   + A K +   NLRLV S 
Sbjct: 93  DLILKSRFSNTSISVALKLIGKLTFEEETALFKLLENPETR-NFAVKRLTIFNLRLVWSS 151

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+KY N G    DL+QEG  GL+KA  KFD   G +FSTYA WW++QA+ R++ D+S  I
Sbjct: 152 ARKYLNYGFPMEDLVQEGIFGLVKAIHKFDCAFGNRFSTYATWWIRQAMLRAVEDKSRII 211

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPI 574
           R+PVHM   I+ + R  + +  +   EPT E++ +++        V+ V  + K+  + +
Sbjct: 212 RVPVHMVPVINNLARIEKALILENGEEPTIEQLTQEMQKYDSQYTVQKVSDIKKLNIDWV 271

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFG 633
           SL+  I D D + L D + D+  +S  + AI  +        L ++L   E  VL M +G
Sbjct: 272 SLDKLI-DYDENFL-DSVPDEEVISSEEEAILTHKSMVLQEFLESTLEDDELLVLDMHYG 329

Query: 634 IG-MNTDHTLEEV---------------------------GKQFCVTRERIRQIEAK--- 662
           +    + +T+E++                           GKQ  +  E  ++ +AK   
Sbjct: 330 LMEFESPNTIEQIVSEILFNPEYRDVIKNKAINFVINEMLGKQDVLAPEEWKKEKAKVEN 389

Query: 663 --------AIRKLKHPSRSKKLRSFL 680
                   A+RKLK PS++ K R+  
Sbjct: 390 FVRKKISQALRKLKKPSKNGKYRTIF 415


>gi|196019865|ref|XP_002119058.1| hypothetical protein TRIADDRAFT_63024 [Trichoplax adhaerens]
 gi|190577137|gb|EDV18456.1| hypothetical protein TRIADDRAFT_63024 [Trichoplax adhaerens]
          Length = 349

 Score =  117 bits (292), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 98/338 (28%), Positives = 166/338 (49%), Gaps = 51/338 (15%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            DDPVRMYL+EMG   LL+R+GE+ +AKRIE  R   +  + ++P+  + +  W D++  
Sbjct: 54  NDDPVRMYLKEMGYRLLLTRDGEVEVAKRIEKSRINKLFYIIQTPMALKKMQDWYDDILT 113

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G  LLRE+ID++A    E    FF            D + EK                  
Sbjct: 114 GKKLLREVIDIDATASNEQ---FF------------DENSEKTD---------------- 142

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
                   D   +N E+   + D D+D  + ++SA+E+ L+PK++  L +I+E  + L  
Sbjct: 143 --------DFNTKNTESGNDDFDNDDDSDSTSISAIENDLKPKILDILLKISENCKSLLQ 194

Query: 297 LQD-------NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           L D       ++ N  K EK  +  K+    +  L+G L LN   I+ +  QL +I+K I
Sbjct: 195 LYDIKKDKKISSPNQSKTEKKLLDNKI--NDIANLLGELKLNDQFINEIFYQLKEINKDI 252

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG-EWKNFVACEVDSILK 408
           +  E EL +LA +  + R  F++ ++  +L+ +W+   K+   G ++   V        K
Sbjct: 253 IQIESELFKLASNSKLNRTKFIDVYRTIDLEKNWIDLLKN--RGVKYTKLVDENSSFFTK 310

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            + + + I V+ G+SI++F+ I   ++K E E    KK
Sbjct: 311 SQLKFEKIKVKAGLSITQFKKIFQDIQKWEREVQKLKK 348


>gi|227501074|ref|ZP_03931123.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227216847|gb|EEI82245.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 344

 Score =  116 bits (291), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/257 (33%), Positives = 137/257 (53%), Gaps = 26/257 (10%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
            IV   + G   A  A   +VE N  LV S A  +       L   DL+Q G +G+++AA
Sbjct: 96  QIVEQFQIGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAA 152

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ +       K   
Sbjct: 153 EKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQIL-----KANP 207

Query: 546 EPTPEEIAKKLAMPVEGVRK-----VLKITKEPI---SLETPIGDEDTS--HLGDFIEDK 595
           E + EE+ +   +  EG+ K     +  I +  +   SL   +  ED++   L D + D+
Sbjct: 208 EASDEELYR--ILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDE 265

Query: 596 NAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +  +P+D  I + ++     + L  LT RE++++  R+G+      TLEE+GK + ++RE
Sbjct: 266 S--TPVDMLILEKDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTLEEIGKIYDLSRE 323

Query: 655 RIRQIEAKAIRKLKHPS 671
           RIRQIE +A+ KLK  S
Sbjct: 324 RIRQIENQALGKLKEFS 340


>gi|262195735|ref|YP_003266944.1| RNA polymerase, sigma 70 family subunit [Haliangium ochraceum DSM
           14365]
 gi|262079082|gb|ACY15051.1| putative RNA polymerase, sigma 70 family subunit [Haliangium
           ochraceum DSM 14365]
          Length = 389

 Score =  116 bits (291), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 80/240 (33%), Positives = 129/240 (53%), Gaps = 11/240 (4%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E + A + ++EANLRLV+ ++ +Y       LDLIQEGNIGLM+A  K+D   G K S
Sbjct: 133 ENEDADAARRLIEANLRLVVKISYEYRRAYRNLLDLIQEGNIGLMQAVRKYDPYRGVKLS 192

Query: 498 TYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +YA WW++  I + I +    ++I     + K+   +R  R    ++   PTP  +A+ L
Sbjct: 193 SYAAWWIRAYILKFILNNWRLVKIGTTQAQRKLFFNLRKERERLEQLGFTPTPALLAENL 252

Query: 557 AMPVEGVRKVLKITKEP-ISLETPI-GDEDTSHLG--DFIEDKNAVSP----LDSAIQAN 608
            +  + V ++ K    P  SL+ P+ G+ED +     D++  +    P      S  Q  
Sbjct: 253 DVTEKEVVEMEKRLSAPDASLDAPMQGEEDGAPRTRMDYLPTEETDRPDRQVAQSQFQEL 312

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE   R   +L  REE + R R+    +T  TL+++G Q+ V+RER RQ+E + + +L+
Sbjct: 313 LREKLERFAETLEGREETIFRERWLT--DTPSTLQQIGDQYGVSRERARQLEKRLLGRLR 370


>gi|325479184|gb|EGC82281.1| sigma-70, region 4 [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 343

 Score =  116 bits (291), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/257 (33%), Positives = 137/257 (53%), Gaps = 26/257 (10%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
            IV   + G   A  A   +VE N  LV S A  +       L   DL+Q G +G+++AA
Sbjct: 95  QIVEQFQIGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAA 151

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ +       K   
Sbjct: 152 EKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQIL-----KANP 206

Query: 546 EPTPEEIAKKLAMPVEGVRK-----VLKITKEPI---SLETPIGDEDTS--HLGDFIEDK 595
           E + EE+ +   +  EG+ K     +  I +  +   SL   +  ED++   L D + D+
Sbjct: 207 EASDEELYR--ILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDE 264

Query: 596 NAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +  +P+D  I + ++     + L  LT RE++++  R+G+      TLEE+GK + ++RE
Sbjct: 265 S--TPVDMLILEKDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTLEEIGKIYDLSRE 322

Query: 655 RIRQIEAKAIRKLKHPS 671
           RIRQIE +A+ KLK  S
Sbjct: 323 RIRQIENQALGKLKEFS 339


>gi|229082715|ref|ZP_04215161.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
 gi|228700606|gb|EEL53146.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
          Length = 323

 Score =  116 bits (291), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 135/263 (51%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQ 469
           EIK I     +S  E   +    + GE +    +  +   N+ LV+S+A+KY N+   ++
Sbjct: 39  EIKEIGNYKVLSKQESLKLFQRYKHGEKDL---RDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA-DQSCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+K+++   I   +S   +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIKKSMLGIICRKKSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS 586
             + V    +      R P+ EE+AK+L +  E V K     K    ++L+    +ED  
Sbjct: 156 NLRYVELEDKYLQMYNRTPSVEEVAKELNVTSETVIKYNVYYKRATTMTLDVDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            L  F +D + +   +  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 ILNPFYDDSSTIPSTNEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
            K   +T ER+ QI+ +AI+KLK
Sbjct: 276 AKALMITTERVSQIKDEAIKKLK 298


>gi|224553590|gb|ACN55033.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score =  116 bits (291), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 52/111 (46%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFCFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|326490962|dbj|BAJ90342.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score =  116 bits (290), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 142/277 (51%), Gaps = 10/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TN 465
           +R+E++S   E  ++       V  +R+       A+ ++++ NLRLV+    KY     
Sbjct: 225 MRSELQSEPTEAEVA-EAMNMPVQRLRRLRDVGRAARNKLIKHNLRLVLYAINKYYPDMT 283

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              +F DL Q G  GL+ A ++F+   G++ STYA+ W++ ++ R++   S T R P  M
Sbjct: 284 GDERFADLCQAGANGLITAIDRFEPKRGFRISTYALSWIRHSVVRAMTLSSFT-RFPFAM 342

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDE 583
             +  ++ R    +S ++ R PT EE  KK+ +     R V+++T+   SL +   +  E
Sbjct: 343 ESERQEINRAREELSFELGRTPTDEETMKKVGLSPARYRDVVRMTRPAYSLHSRNRVTQE 402

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L + + D +A+          LR     +L SL P+E  V+R RFG+      TL 
Sbjct: 403 E---LINEVTDVDAIGVDTHKHNRLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGRRTLS 459

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+     ++RE +R+ E KA+ KLKHP+R   LR ++
Sbjct: 460 EIAGNLRISREMVRKYELKALMKLKHPTRVDYLRRYM 496


>gi|224553606|gb|ACN55041.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score =  116 bits (290), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 51/111 (45%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|302391629|ref|YP_003827449.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
 gi|302203706|gb|ADL12384.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
          Length = 260

 Score =  116 bits (290), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 130/248 (52%), Gaps = 13/248 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   ++ G+ EA   ++ +V  NL+LV+SV +++ NRG    DL Q G IGL
Sbjct: 18  LSNEEMRELFKKMQNGDREA---RQTIVGGNLKLVLSVLQRFNNRGEPIDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 75  MKAIDNFDLSRNVKFSTYAVPMIIGEIRRHLRDHN-PIRVSRSLRDTAYKALQMKESLEN 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K   EPT  EIA++L +P E + + L   ++PISL  PI  +     GD I   + VS  
Sbjct: 134 KTSEEPTLTEIAQELGIPREEIVQALDAIQDPISLFEPIYQDG----GDPIYVMDQVSDD 189

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           DS  ++ L     R  L  L  RE+ +L MRF  G     T  EV     +++ ++ ++E
Sbjct: 190 DSEDESWLEGIAVREALRQLEDREKLILSMRFYKG----KTQMEVADNIGISQAQVSRLE 245

Query: 661 AKAIRKLK 668
             A+  L+
Sbjct: 246 KAALENLE 253


>gi|325523156|gb|EGD01548.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 206

 Score =  115 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 53/94 (56%), Positives = 74/94 (78%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V++NLRLV+S+AK+Y +RGL   DLIQEGNIGL+KA E++D   G+KFSTYA WW
Sbjct: 104 ARTKLVKSNLRLVVSIAKRYPDRGLPLPDLIQEGNIGLLKAVERYDHRRGFKFSTYATWW 163

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           ++QAIT ++AD   TIR+P H  D ++K+ R AR
Sbjct: 164 IRQAITHALADLGRTIRVPAHTVDAVNKLARIAR 197


>gi|224116898|ref|XP_002331841.1| predicted protein [Populus trichocarpa]
 gi|222875079|gb|EEF12210.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score =  115 bits (289), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 129/245 (52%), Gaps = 7/245 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEK 487
           V  VRK       A+ ++++ NLRLV+ V  KY      G ++ DL Q G  GLM A ++
Sbjct: 263 VLQVRKQIEVGRAARNKLIKHNLRLVLFVINKYFQDYANGPRYQDLCQAGVKGLMTAIDR 322

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+    ++ STY ++W++ AI RS+   S T R+   +     ++ +    +  ++ R+P
Sbjct: 323 FEPKRRFRLSTYGLFWIRHAIIRSMTLSSFT-RVSFGLESIRSEIQKAKLELWFQLLRKP 381

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EEI +K+ + +E   +V++ +K  +SL +         L   + D N     D    A
Sbjct: 382 TGEEIIEKVGISIERYHEVMRASKPVLSLHSR-HKTTQEELISGVADVNGGD--DRRQSA 438

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR     VL SL P+E  V+R RFG+    D TL E+     ++RE +R+ EAKA+ KL
Sbjct: 439 LLRLALDDVLDSLKPKESLVVRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEAKALMKL 498

Query: 668 KHPSR 672
           KHP+R
Sbjct: 499 KHPTR 503


>gi|227485585|ref|ZP_03915901.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227236451|gb|EEI86466.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 340

 Score =  115 bits (289), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/258 (33%), Positives = 137/258 (53%), Gaps = 26/258 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAE 486
           IV   + G   A  A   +VE N  LV S A  +       L   DL+Q G +G+++AAE
Sbjct: 93  IVEQFQLGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAAE 149

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ +       K   E
Sbjct: 150 KFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQIL-----KANPE 204

Query: 547 PTPEEIAKKLAMPVEGVRK-----VLKITKEPI---SLETPIGDEDTS--HLGDFIEDKN 596
            + EEI +   +  EG+ K     +  I +  +   SL   +  ED++   L D + D++
Sbjct: 205 ASDEEIYR--ILENEGINKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDES 262

Query: 597 AVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
             +P+D  I + ++     + L  LT RE++++  R+G+      TLE++G  + ++RER
Sbjct: 263 --TPVDMLILEKDMENFLMQALDQLTDREKQIIIYRYGLDNEKPKTLEQIGAIYDLSRER 320

Query: 656 IRQIEAKAIRKLKHPSRS 673
           IRQIE +A+ KLK  S S
Sbjct: 321 IRQIENQALGKLKDYSDS 338


>gi|224110206|ref|XP_002333134.1| predicted protein [Populus trichocarpa]
 gi|222834948|gb|EEE73397.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 78/253 (30%), Positives = 130/253 (51%), Gaps = 7/253 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEK 487
           V  VRK       A+ ++++ NLRLV+ V KKY      G +F D  Q G  GL+ A ++
Sbjct: 263 VLQVRKQIAVGRAARNKLIKHNLRLVLFVIKKYFQDFANGTKFQDFCQAGVKGLITAIDR 322

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+    ++ STY ++W++ AI RS+   S T R+   +     ++ +    +  ++KR+P
Sbjct: 323 FEPKRRFRLSTYGLFWIRHAIIRSMTLSSFT-RVSFGLESIRSEIQKAKLELWFQLKRQP 381

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             +EI +K+ +  E   +V + +K  +SL +         +G   +         SA+  
Sbjct: 382 MEDEIIEKVRISPERYHEVTRASKPVLSLHSRHKTTQEEFIGGIADVDGGDDRRQSAL-- 439

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR     VL SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KL
Sbjct: 440 -LRLALDDVLDSLKPKESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKL 498

Query: 668 KHPSRSKKLRSFL 680
           KHP+R   LR ++
Sbjct: 499 KHPTRVDYLRRYV 511


>gi|258514354|ref|YP_003190576.1| sporulation sigma factor SigG [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778059|gb|ACV61953.1| RNA polymerase, sigma 28 subunit, SigG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 257

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 88/267 (32%), Positives = 142/267 (53%), Gaps = 25/267 (9%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     I  S+ R +   +++G+  A   + +++  NLRLV+SV +++TNR
Sbjct: 4   NKVEICGVNTAKLPVIPNSKMRELFEAIQQGDTSA---RPQLINGNLRLVLSVIQRFTNR 60

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +R
Sbjct: 61  GEYVDDLFQVGCIGLMKAIDNFDLAQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLR 119

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDE 583
           D  +K ++    + NK  REP+  EIAK+L MP E V   L   +EPISL  PI   G +
Sbjct: 120 DVAYKALQVRDTLVNKHSREPSVNEIAKELKMPREEVVFALDAIQEPISLFEPIYHDGGD 179

Query: 584 DTSHLGDFIEDKNA-VSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
               +    +DKN  ++ L+  AI+  LR+        L+ RE+ +L +RF  G     T
Sbjct: 180 PIFVMDQISDDKNQDLNWLEGIAIKDALRK--------LSDREKHILTLRFFDG----KT 227

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
             EV  +  +++ ++ ++E  A+  ++
Sbjct: 228 QMEVADEIGISQAQVSRLEKAALHHMR 254


>gi|121488785|emb|CAJ18277.1| sigma 70-type sigma factor [Pelodictyon clathratiforme]
          Length = 165

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELATLLEMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V++  FGIGM+
Sbjct: 121 LQNDGHL-PDYGLNRDSLTLEVERSLSVLAPREADVIKSYFGIGMD 165


>gi|91227014|ref|ZP_01261551.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|91188816|gb|EAS75102.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|210148643|gb|ACJ09227.1| RpoS-like sigma factor [Vibrio alginolyticus]
          Length = 279

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 74/257 (28%), Positives = 135/257 (52%), Gaps = 14/257 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
           H   + R G+ EA   ++ ++E+NLRLV+ +AK Y  R       LDLI+EGNIGL+KA 
Sbjct: 32  HYAKLNRAGDEEA---REMLIESNLRLVVKIAKGYLKRPGNNFTLLDLIEEGNIGLIKAV 88

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD   GY+FSTYA+WW+++ I  ++ +   T+R+P H+  +I+ +       S    +
Sbjct: 89  DKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPAHVCKEINSLALKKLDASKSESK 148

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           E +  E+++   +  E + +++ ++   I + T         + +  E +    P     
Sbjct: 149 ELSISELSRCSGVKAERIDELVALSGF-IDVSTTADLHRVPFVLELCESEYTPDPQQDCE 207

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                +    ++ +L  + ++VL  RFG+      TL E+G    V+ ER+RQ++ +A+ 
Sbjct: 208 NQCFTQAIENIIKTLPTKLQKVLIHRFGLFDQRVKTLSEIGLLLNVSNERVRQMQIEAVE 267

Query: 666 KLKHPSRSKKLRSFLDG 682
           +++     K+LR   DG
Sbjct: 268 RVQ-----KRLR--FDG 277


>gi|51599021|ref|YP_073209.1| RNA polymerase sigma factor [Borrelia garinii PBi]
 gi|51573592|gb|AAU07617.1| RNA polymerase sigma factor [Borrelia garinii PBi]
          Length = 266

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 77/258 (29%), Positives = 145/258 (56%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   + S +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIKLASQIQRGNAQA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q +  +    VL + L  +E  +++ R+ +  N    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTIKHLNYVLETKLNEKERYIIKKRYNLDNNPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|167770711|ref|ZP_02442764.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
 gi|167667306|gb|EDS11436.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
          Length = 263

 Score =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 132/233 (56%), Gaps = 16/233 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+ +A   ++EM+  NLRLV+SV +K+TNRG    DL Q G IGL+KA + FD    
Sbjct: 38  IRQGDQKA---RQEMINGNLRLVLSVVQKFTNRGENLDDLFQVGCIGLIKAIDNFDPNQN 94

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTY +  +   I R + D + ++R+   +RD  +K ++    + N+  +EPT EEIA
Sbjct: 95  VRFSTYGVPMIIGEIRRHLRDNN-SVRVSRSLRDLAYKAMQAKEALINRNSKEPTVEEIA 153

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K++    E V   L+   EP+SL  P+  +  DT ++ D I DKN+ S  D   +   RE
Sbjct: 154 KEMGAKKEDVVLALEAIVEPMSLYDPVYSDGGDTIYVMDQIGDKNSES--DWMDEIVFRE 211

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                + +L  RE+++L +RF  G     T  EV K+  +++ ++ ++E  A+
Sbjct: 212 A----MKNLGDREKQILSLRFFGG----KTQMEVAKEIGISQAQVSRLEKGAL 256


>gi|83589704|ref|YP_429713.1| sporulation sigma factor SigG [Moorella thermoacetica ATCC 39073]
 gi|83572618|gb|ABC19170.1| RNA polymerase, sigma subunit, RpsG/SigG [Moorella thermoacetica
           ATCC 39073]
          Length = 272

 Score =  115 bits (288), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 131/246 (53%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R +   ++ GE  A   +++++  NLRLV+SV +++TNRG    DL Q G IGLMKA 
Sbjct: 38  EIRQLFQQMQAGETGA---REKLITGNLRLVLSVIQRFTNRGEHVDDLFQVGCIGLMKAI 94

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + NK+ R
Sbjct: 95  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQIRDTLVNKLAR 153

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLD 602
           EP+  E+A++L +P E V   L   +EP+SL  PI   G +    +    ++KN     D
Sbjct: 154 EPSLAEVAQQLDLPQEEVIFALDAIQEPVSLFEPIYHDGGDPIFVMDQIGDEKNQ----D 209

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           S+   N+       +  L PRE  +L +RF  G       +E+G    +++ ++ ++E  
Sbjct: 210 SSWLENI--AIKEAMNKLNPRERLILSLRFFEGKTQMEVADEIG----ISQAQVSRLEKA 263

Query: 663 AIRKLK 668
           A++ ++
Sbjct: 264 ALQHMR 269


>gi|229113622|ref|ZP_04243069.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|228669818|gb|EEL25214.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|324323938|gb|ADY24981.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 323

 Score =  115 bits (288), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 79/262 (30%), Positives = 134/262 (51%), Gaps = 9/262 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQF 470
           I+ I     +S  E  H+    + GE +    +  +   N  LV+SVA+ Y N+   ++F
Sbjct: 40  IRGIGNYKVLSKEESLHLFKRYKHGEKDL---RDYLFHVNEGLVLSVARNYKNKHPDIEF 96

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-ADQSCTIRIPVHMRDKI 529
            DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I   +S   +IP H+    
Sbjct: 97  DDLVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFN 156

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSH 587
            K V    +   +  R P+ EE+ K+L +  E V   KV       ++L+    +ED   
Sbjct: 157 LKYVELEDKYLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGI 216

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              F +D++A+   +  I  +L      +    L P+++ VL + FG+     +  +E+ 
Sbjct: 217 SNPFFDDRSAIPSTNEMIIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEIA 276

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K   +T ER+ QI+ +AI+KLK
Sbjct: 277 KALMITTERVSQIKDEAIKKLK 298


>gi|224553544|gb|ACN55010.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score =  115 bits (288), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/111 (45%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FST A WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTSATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|302389526|ref|YP_003825347.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
 gi|302200154|gb|ADL07724.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
          Length = 257

 Score =  115 bits (287), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 137/248 (55%), Gaps = 13/248 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S+ + +   V++G+ EA   +++++  NLRLV+SV +++ NRG    DL Q G IGL
Sbjct: 19  LSNSKMKELFLRVKQGDKEA---REKLIHGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 76  MKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDSLVN 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K  REP+ EEIAK++ +P E +   L   +EPISL  PI  +     GD I   + +S  
Sbjct: 135 KNSREPSIEEIAKEMNIPSEEIVMALDAIQEPISLFEPIYHDG----GDPIFVMDQISDD 190

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +  +  LR  + +  +  L  RE+ +L +RF  G     T  EV ++  +++ ++ ++E
Sbjct: 191 KNNDENWLRSISIKEAMQKLNEREKLILTLRFFEG----KTQMEVAQEIGISQAQVSRLE 246

Query: 661 AKAIRKLK 668
             A++ LK
Sbjct: 247 KAALKHLK 254


>gi|295102494|emb|CBL00039.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii L2-6]
          Length = 255

 Score =  115 bits (287), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 143/265 (53%), Gaps = 20/265 (7%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     +S  E R +++  R G+ +A   ++ M+E NLRLV+SV ++++ R
Sbjct: 3   NKVELCGVNTAELPILSEQEKRDLLTRARAGDKKA---RQSMIEGNLRLVLSVVQRFSQR 59

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +R
Sbjct: 60  GENMDDLFQVGCIGLIKAIDNFDPAQQVRFSTYGVPMIIGEIRRFLRDNNA-LRVSRSLR 118

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--D 584
           D  ++ +++   +  ++ REPT +EIA+K  +    V   L+   EP+SLE P+  +  D
Sbjct: 119 DTAYRAMQSREELEKQLGREPTVDEIAQKTGLSRREVSAALESVVEPLSLEEPVYADGGD 178

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             ++ D + D +      S +Q   R+T    +A LTPRE+R++ +R+  G     T  E
Sbjct: 179 AVYVIDQVRDPDGEDSWISGLQ--FRQT----VAGLTPREKRIMELRYLKG----KTQME 228

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V ++  +++ ++ ++E  A+ +   
Sbjct: 229 VAREIGISQAQVSRLEKAALEQFHQ 253


>gi|146295967|ref|YP_001179738.1| sporulation sigma factor SigG [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409543|gb|ABP66547.1| RNA polymerase, sigma subunit, RpsG/SigG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 255

 Score =  115 bits (287), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 80/228 (35%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K+ +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARKQFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  +RI   ++D  +K ++   R  ++  REPT EEIA +L +  E +
Sbjct: 96  IIGEIRRYLRDNN-AMRISRSLKDTAYKALKIKERYISQNYREPTLEEIANELCISKEDL 154

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L   +EPISL  PI  +  DT ++ D + D+ +   L       L E + +  L+ L
Sbjct: 155 VFALDSIQEPISLYEPIFQDSTDTMYVVDQVSDQKSCENL------WLEEISLKDALSRL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE+ +L +R+  G     T  EV     +++ ++ +IE  AI  +K
Sbjct: 209 TKREKEILYLRYYKG----KTQMEVATIIGISQAQVSRIEKSAIGHIK 252


>gi|111115602|ref|YP_710220.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
 gi|110890876|gb|ABH02044.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
          Length = 266

 Score =  115 bits (287), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 146/258 (56%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +V  +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIQLVGQIQRGSAKA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q +  +    +L + LT +E  +++ R+ +  +    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTLQHLNYILETKLTEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea]
          Length = 548

 Score =  115 bits (287), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 129/238 (54%), Gaps = 1/238 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E++++   LV+ +++ Y   G+   DL+Q GNIG+++ AE+FD   GY+FSTY  +W
Sbjct: 311 CRDELLKSGRSLVLYLSRYYRGLGVAHEDLMQAGNIGILQGAERFDHTRGYQFSTYVQYW 370

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++A+++ ++     I++P  +   I++V +  + +     + P   E++K   + ++ +
Sbjct: 371 IRKAMSQLVSRHGRGIKVPTTLSTTINRVQKARKILKRSQGKHPDDVEVSKSTGLSLDKI 430

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +      +   SL+  +G        +   D     P  + ++ ++R    ++L  L P+
Sbjct: 431 KSADNCLRIVGSLDQKVGHFINMKYLECTPDTALEMPEKTVMKQHMRNDVHKLLQELDPK 490

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E RVL  R+G+  +   +L EVGK F V++E IR++E +A+ KL+       L+ +L+
Sbjct: 491 ERRVLIHRYGLEGHC-MSLHEVGKVFDVSKEWIRKMEKRALTKLRTEQNQTNLKHYLN 547


>gi|289751356|ref|ZP_06510734.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
 gi|289691943|gb|EFD59372.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
          Length = 470

 Score =  114 bits (286), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 46/66 (69%), Positives = 58/66 (87%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350

Query: 504 VKQAIT 509
           ++QAIT
Sbjct: 351 IRQAIT 356



 Score = 45.1 bits (105), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|121488765|emb|CAJ18267.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score =  114 bits (286), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 99/166 (59%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  F IGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFXIGMD 165


>gi|115372678|ref|ZP_01459985.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|310823838|ref|YP_003956196.1| RNA polymerase sigma-c factor [Stigmatella aurantiaca DW4/3-1]
 gi|115370399|gb|EAU69327.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|309396910|gb|ADO74369.1| RNA polymerase sigma-C factor [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  114 bits (286), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 132/245 (53%), Gaps = 18/245 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ +A      +V +NLR V+ VA +Y + GL+  DLIQE NIGLMKA +KFD   G 
Sbjct: 37  RQGDLQAG---HRLVTSNLRFVVKVAYEYRSYGLRMSDLIQEANIGLMKAVQKFDPDKGI 93

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRM---SNKIKREPTP 549
           +  +YA+WW++  I   +      +++      R     + RT R +    N        
Sbjct: 94  RLISYAVWWIRAYIQGYVLKNWSLVKLGTTQAQRRLFFALARTRRELEKQGNTDGNIVNA 153

Query: 550 EEIAKKLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI-- 605
           EEIA+KL +    VR++  ++    +SL+ P+G D D +H+ DF+   ++VS  D     
Sbjct: 154 EEIARKLNVKASEVREMEQRMGGRDLSLDAPMGEDGDATHM-DFVA-SDSVSQADEVADR 211

Query: 606 -QANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +A+L R    + L  L PRE  ++  R  +  +++ TL E+G+ F  +RER RQ+E +A
Sbjct: 212 QEADLARTRIQQALQRLDPRERFIIEKR--VMSDSEMTLSELGEHFGFSRERARQLEIRA 269

Query: 664 IRKLK 668
             KLK
Sbjct: 270 KDKLK 274


>gi|121488532|emb|CAJ18256.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score =  114 bits (286), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L P E  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHGLNRDSLTLEVERSLSVLAPGEADVIRSXFGIGMD 165


>gi|269968333|ref|ZP_06182353.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
 gi|269827051|gb|EEZ81365.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
          Length = 296

 Score =  114 bits (286), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 74/257 (28%), Positives = 135/257 (52%), Gaps = 14/257 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
           H   + R G+ EA   ++ ++E+NLRLV+ +AK Y  R       LDLI+EGNIGL+KA 
Sbjct: 49  HYAKLNRVGDEEA---REMLIESNLRLVVKIAKGYLKRPGNNFTLLDLIEEGNIGLIKAV 105

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD   GY+FSTYA+WW+++ I  ++ +   T+R+P H+  +I+ +       S    +
Sbjct: 106 DKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPAHVCKEINSLALKKLDASKSESK 165

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           E +  E+++   +  E + +++ ++   I + T         + +  E +    P     
Sbjct: 166 ELSISELSRCSGVKAERIDELVALSG-FIDVSTTADLHRVPFVLELCESEYTPDPQQDCE 224

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                +    ++ +L  + ++VL  RFG+      TL E+G    V+ ER+RQ++ +A+ 
Sbjct: 225 NQCFTQAIENIIKTLPIKLQKVLIHRFGLFDQRVKTLSEIGLLLNVSNERVRQMQIEAVE 284

Query: 666 KLKHPSRSKKLRSFLDG 682
           +++     K+LR   DG
Sbjct: 285 RVQ-----KRLR--FDG 294


>gi|67921068|ref|ZP_00514587.1| Sigma-70 region 3:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
 gi|67857185|gb|EAM52425.1| Sigma-70 region 3:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
          Length = 179

 Score =  114 bits (285), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 61/173 (35%), Positives = 106/173 (61%), Gaps = 1/173 (0%)

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IA QS  IR+PVH+ +K++K+ +  R++S    R  + EEI ++L M    VR+VL 
Sbjct: 5   TRAIATQSRIIRLPVHVTEKLNKIKQVQRKISQSKNRNASLEEIGQELGMTAAQVREVLM 64

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
                +SLE  +G E  + L D +E ++ +SP ++    +LR     +L  LT RE++V+
Sbjct: 65  KIPRSVSLEVKVGKEKDTELVDLLESED-ISPEENLAVESLRRDIGVLLKDLTEREQQVI 123

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++R+G      ++L  +G+   ++RER+RQIEAK ++KL+ P R  ++R + +
Sbjct: 124 KLRYGFEDGVAYSLAGIGRVLELSRERVRQIEAKTLQKLRQPRRRNQIRDYFE 176


>gi|229100411|ref|ZP_04231282.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
 gi|229107324|ref|ZP_04237193.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228676119|gb|EEL31095.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228683031|gb|EEL37038.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
          Length = 323

 Score =  114 bits (285), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 134/263 (50%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQ 469
           EIK I     +S  E   +    + GE +    +  +   N+ LV+S+A+KY N+   ++
Sbjct: 39  EIKEIGNYKVLSKQESLKLFQRYKHGEKDL---RDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA-DQSCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I   +S   +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTS 586
             K V    +      R PT EE+ K+L +  E V    V       ++L+    +ED  
Sbjct: 156 NLKYVELEDKYLQMYNRTPTVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
               F +D +A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 MSKPFYDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
            K   +T ER+ QI+ +AI+KLK
Sbjct: 276 AKALMITTERVSQIKEEAIKKLK 298


>gi|229051333|ref|ZP_04194847.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
 gi|229125362|ref|ZP_04254451.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228658091|gb|EEL13842.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228722026|gb|EEL73457.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
          Length = 325

 Score =  114 bits (285), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 77/253 (30%), Positives = 131/253 (51%), Gaps = 9/253 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQFLDLIQEGNI 479
           +S  E  H+    + GE +    +  +   N  LV+S+A+ Y N+   ++F DL+QEGN 
Sbjct: 51  LSKEESLHLFKRYKHGEKDL---RDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGNE 107

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-ADQSCTIRIPVHMRDKIHKVVRTARR 538
           G+++A E F+  LGY FSTYA WW+++++   I   +S   +IP H+     K V    +
Sbjct: 108 GMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLKYVELEDK 167

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
              +  R P+ EE+ K+L +  E V   KV       ++L+    +ED      F +DK+
Sbjct: 168 YLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTPFFDDKS 227

Query: 597 AVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           A+   +  I  +L      +    L P+++ VL + FG+     +  +E+ K   +T ER
Sbjct: 228 AIPSTNEMIIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTER 287

Query: 656 IRQIEAKAIRKLK 668
           + QI+ +AI+KLK
Sbjct: 288 VSQIKDEAIKKLK 300


>gi|330955106|gb|EGH55366.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae Cit 7]
          Length = 393

 Score =  114 bits (285), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 118/430 (27%), Positives = 205/430 (47%), Gaps = 50/430 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            +M ++   P T   ++     +      L +++            G+    +G +    
Sbjct: 131 EVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAE 179

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                + +    +  + D E +A  S D+  +V+S P+     +R              A
Sbjct: 180 VPPPVDPKAVKAEGADDDEEESADAS-DEEDEVESGPDPVIAQQR------------FGA 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           + DQ+            E+ R  ++L+       +D+K ++   V    L +L   + L 
Sbjct: 227 VSDQM------------EITR--KALKKFG----RDDKHAIAEMV---ALAELFMPIKLV 265

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWV-SYAKD 389
             + + LVE++    +R+   E  +++L  +   + R  FL +  G E+D  W  + AK 
Sbjct: 266 PKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKG 325

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  AKKEMV
Sbjct: 326 --KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRAKKEMV 383

Query: 450 EANLRLVISV 459
           EANLRLVIS+
Sbjct: 384 EANLRLVISI 393


>gi|255545052|ref|XP_002513587.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223547495|gb|EEF48990.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 501

 Score =  114 bits (284), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 79/257 (30%), Positives = 132/257 (51%), Gaps = 15/257 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEK 487
           V  VRK       A+ ++++ NLRLV+ V  KY      G +F DL Q G  GL+ A ++
Sbjct: 252 VEKVRKQLEVGRAARNKLIKHNLRLVMFVMNKYFQDFANGPRFQDLCQAGVKGLITAIDR 311

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+    ++ STY+++W++ AI RS+   S T ++   +     ++ +    +  +++R P
Sbjct: 312 FEPQRRFQLSTYSLFWIRHAIIRSMTLSSFT-KVSFGLESVRTEIQKAKLELLIELQRRP 370

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA--- 604
           T EEI +++ +  E   +V++  K  +SL          H     E  N ++ +D     
Sbjct: 371 TEEEIIERVGISAERYHEVIRAAKPALSLHA-------RHAVTQEEFINGITDIDGGDNR 423

Query: 605 -IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              A LR     VL SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA
Sbjct: 424 RQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKYEVKA 483

Query: 664 IRKLKHPSRSKKLRSFL 680
           + KLKHP+R   LR ++
Sbjct: 484 LMKLKHPARVDYLRRYV 500


>gi|296133647|ref|YP_003640894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032225|gb|ADG82993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 257

 Score =  114 bits (284), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 131/251 (52%), Gaps = 19/251 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE R I   ++ G+  A   + +++  NLRLV+SV +++TNRG    DL Q G IGL
Sbjct: 19  LSSSEMRKIFEQMQAGDKSA---RTKLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 76  MKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQVRDALVN 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K  REP+  EIA +L MP E V   L   +EPISL  PI  +  D  ++ D I D     
Sbjct: 135 KYSREPSINEIASELKMPREEVVFALDAIQEPISLFEPIYHDGGDPIYVMDQIGD----- 189

Query: 600 PLDSAIQANLRE--TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +  +  N  E  +    +  L  RE+ +L +RF  G       EE+G    +++ ++ 
Sbjct: 190 --EKNLDGNWLEGISVREAMRKLNEREKLILTLRFFEGKTQMEVAEEIG----ISQAQVS 243

Query: 658 QIEAKAIRKLK 668
           ++E  A++ ++
Sbjct: 244 RLEKAALKHMR 254


>gi|121488787|emb|CAJ18278.1| sigma 70-type sigma factor [Prosthecochloris aestuarii]
          Length = 165

 Score =  114 bits (284), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 57/165 (34%), Positives = 98/165 (59%), Gaps = 1/165 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL  EGN+GL+KAA++FD   G+KF +YA+WW++Q+  +++A+QS  +R+P++    ++K
Sbjct: 1   DLXXEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSXLQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANVLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ++  +   P  S  + +L     R L+ L PRE  V+R  FGIGM
Sbjct: 121 LQ-HDGQKPDYSLTKDSLTLEVERSLSVLAPREADVIRSYFGIGM 164


>gi|9368549|emb|CAB98133.1| unnamed protein product [Mycoplasma genitalium]
          Length = 100

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 52/78 (66%), Positives = 65/78 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V +NLRLV+S+AKK+  RGL F DLIQEGN+GL+KA  KF+W LG KFSTYA WW
Sbjct: 23  AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWW 82

Query: 504 VKQAITRSIADQSCTIRI 521
           +KQAITR+IADQ+ T+RI
Sbjct: 83  IKQAITRAIADQARTVRI 100


>gi|67078088|ref|YP_245708.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
 gi|66970394|gb|AAY60370.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
          Length = 323

 Score =  114 bits (284), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 135/263 (51%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQ 469
           EIK I     +S  E  ++    + GE +    +  +   N+ LV+S+A+KY N+   ++
Sbjct: 39  EIKEIGNYQVLSKQESLNLFQRYKHGEKDL---RDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ-SCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+K+ +   I  + S   +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIKKRMLGIICKKRSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTS 586
             K V    +      R P+ EE+ K+L +  E V    V       ++L+    +ED  
Sbjct: 156 NLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRVTTMTLDIDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
               F +DK+A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 ISNSFYDDKSAIPSINEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
            K   +T ER+ QI+ +AI+KLK
Sbjct: 276 AKALMITTERVSQIKEEAIKKLK 298


>gi|159137617|gb|ABW88899.1| HrdB [Streptomyces cacaoi subsp. asoensis]
          Length = 133

 Score =  114 bits (284), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 52/76 (68%), Positives = 67/76 (88%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 58  AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 117

Query: 504 VKQAITRSIADQSCTI 519
           ++QAITR++ADQ+ TI
Sbjct: 118 IRQAITRAMADQARTI 133


>gi|58699689|ref|ZP_00374359.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58533795|gb|EAL58124.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 256

 Score =  114 bits (284), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 71/182 (39%), Positives = 108/182 (59%), Gaps = 13/182 (7%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQGRELD 380
           + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+ +++ 
Sbjct: 12  IKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHELKKIS 71

Query: 381 PHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
              ++  +    GE KN    F+    + I    N IK    E   ++ EF+ ++  ++K
Sbjct: 72  LLKINENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQHIQED--NVQEFKELIKRIQK 129

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKF
Sbjct: 130 HEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKF 189

Query: 497 ST 498
           ST
Sbjct: 190 ST 191


>gi|326773500|ref|ZP_08232783.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636730|gb|EGE37633.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 311

 Score =  114 bits (284), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 47/70 (67%), Positives = 62/70 (88%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 224 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 283

Query: 504 VKQAITRSIA 513
           ++QAITR++A
Sbjct: 284 IRQAITRAMA 293



 Score = 41.6 bits (96), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +T DPV+ YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 159 ATADPVKDYLKQIGKVALLNAEQEVELAKRIEAG 192


>gi|113955141|ref|YP_730472.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882492|gb|ABI47450.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 282

 Score =  113 bits (283), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 80/237 (33%), Positives = 132/237 (55%), Gaps = 31/237 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK  M++ANLRLV++V++KY +R L   +F DL+QEG+IGL +A EKFD  LGYKFSTYA
Sbjct: 53  AKDRMIKANLRLVVTVSRKYLHRQLGQLEFGDLVQEGSIGLNRAVEKFDPELGYKFSTYA 112

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP- 559
            WW++Q+I+R+I   S TIR+P  M   + K+        N++ +    E+I + L +  
Sbjct: 113 YWWIRQSISRAIDQTSATIRVPTSMNLVLAKL--------NQLPQGLNDEQICELLEVSD 164

Query: 560 --VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDS----AIQANLRET 612
             ++ +R    + K   SL+  +G D D S L + + D+ +    D     A++ +L + 
Sbjct: 165 TQLKNLRHAF-VAKRIASLDMKLGADRDGSTLTELLCDEQSTLNYDEFQWEAVKRSLGDQ 223

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L +    ++ +LR      +  + +L+ +  +  ++RER+RQ   K  R  KH
Sbjct: 224 AKIALNN----DQELLRR----NVVDEQSLQSIANEIGISRERVRQ---KVDRAKKH 269


>gi|219684379|ref|ZP_03539323.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219685569|ref|ZP_03540385.1| RNA polymerase sigma factor [Borrelia garinii Far04]
 gi|219672368|gb|EED29421.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219672847|gb|EED29870.1| RNA polymerase sigma factor [Borrelia garinii Far04]
          Length = 266

 Score =  113 bits (283), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 144/258 (55%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +   +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIKLAGQIQRGNAQA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q +  +    VL + L  +E  +++ R+ +  N    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTIKHLNYVLETKLNEKERYIIKKRYNLDNNPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|229118995|ref|ZP_04248338.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
 gi|228664438|gb|EEL19936.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
          Length = 294

 Score =  113 bits (283), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 134/263 (50%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQ 469
           EIK I     +S  E   +    + GE +    +  +   N+ LV+S+A+KY N+   ++
Sbjct: 10  EIKEIGNYKVLSKQESLKLFQRYKHGEKDL---RDYLFHVNVGLVLSIARKYKNKHPDIE 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA-DQSCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I   +S   +IP ++   
Sbjct: 67  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQF 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTS 586
             K V    +      R PT EE+ K+L +  E V    V       ++L+    +ED  
Sbjct: 127 NLKYVELEDKYLQMYNRTPTVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINEDIG 186

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
               F +D +A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 187 MSKPFYDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 246

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
            K   +T ER+ QI+ +AI+KLK
Sbjct: 247 AKALMITTERVSQIKEEAIKKLK 269


>gi|134298555|ref|YP_001112051.1| sporulation sigma factor SigG [Desulfotomaculum reducens MI-1]
 gi|134051255|gb|ABO49226.1| RNA polymerase, sigma subunit, RpsG/SigG [Desulfotomaculum reducens
           MI-1]
          Length = 257

 Score =  113 bits (283), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 132/245 (53%), Gaps = 13/245 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ R +   +++G+ +A   + +++  NLRLV+SV +++TNRG    DL Q G IGLMKA
Sbjct: 22  TQMRTLFEAMQQGDKDA---RSQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGLMKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + NK  
Sbjct: 79  IDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQVRDTLVNKYS 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP+  EIA +L MP E +   L   +EPISL  PI  +     GD I   + +S   + 
Sbjct: 138 REPSINEIAGELKMPREDIVFALDAIQEPISLFEPIYHDG----GDPIFVLDQISDEKNL 193

Query: 605 IQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             + L E + R  L  L+ RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 194 DLSWLEEISIRDALRRLSDREKHILTLRFFEG----KTQMEVADEIGISQAQVSRLEKAA 249

Query: 664 IRKLK 668
           +  +K
Sbjct: 250 LNHMK 254


>gi|147678180|ref|YP_001212395.1| sporulation sigma factor SigG [Pelotomaculum thermopropionicum SI]
 gi|146274277|dbj|BAF60026.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 257

 Score =  113 bits (283), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 132/254 (51%), Gaps = 16/254 (6%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           + V TG   S+ + +   + KG+  A   + +++  NLRLV+SV +++TNRG    DL Q
Sbjct: 16  LPVLTG---SQMKALFEAMHKGDASA---RTKLINGNLRLVLSVIQRFTNRGEYVDDLFQ 69

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++ 
Sbjct: 70  VGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQV 128

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
              + NK  REP+  EIA +L MP E +   L   +EPISL  PI  +     GD I   
Sbjct: 129 RDALVNKYSREPSINEIACELKMPREEIVFALDAIQEPISLFEPIYHDG----GDPIFVM 184

Query: 596 NAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           + +S   +  Q  L     R  L  L+ RE+ +L +RF  G       EE+G    +++ 
Sbjct: 185 DQISDEKNQDQNWLEGIAIRDALRKLSDREKLILTLRFYEGKTQMEVAEEIG----ISQA 240

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E  A+  +K
Sbjct: 241 QVSRLEKAALNHMK 254


>gi|216263458|ref|ZP_03435453.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
 gi|215980302|gb|EEC21123.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
          Length = 266

 Score =  113 bits (283), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 145/258 (56%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +   +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIQLAGQIQRGSAKA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q +  +    +L + LT +E  +++ R+ +  +    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTLQHLNYILETKLTEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana]
          Length = 498

 Score =  113 bits (283), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 117/204 (57%), Gaps = 13/204 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G++ STY
Sbjct: 255 ECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTY 314

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
             WW++Q ++R++ D S T+R+P H+ +++  ++R A+    +    P+ + IA+ L M 
Sbjct: 315 VYWWIRQGVSRALVDNSRTLRLPTHLHERL-GLIRNAKLRLQEKGITPSIDRIAESLNMS 373

Query: 559 ------PVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   E V KV  + ++   SL    G+   S++ D   + N   P        L+E
Sbjct: 374 QKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENN---PWHGYDDLALKE 430

Query: 612 TTTRVL-ASLTPREERVLRMRFGI 634
             ++++ A+L  RE+ ++R+ +G+
Sbjct: 431 EVSKLISATLGEREKEIIRLYYGL 454


>gi|55274881|gb|AAV49243.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 184

 Score =  113 bits (283), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/142 (35%), Positives = 93/142 (65%)

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEI
Sbjct: 37  GFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEI 96

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A++L  PV+ V ++L++ +   S++TP+G +    L D + D+    P D+    +++++
Sbjct: 97  AEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 156

Query: 613 TTRVLASLTPREERVLRMRFGI 634
             + L  L  ++  VL  RFG+
Sbjct: 157 IVKWLFELNAKQREVLARRFGL 178


>gi|15894973|ref|NP_348322.1| sporulation sigma factor SigG [Clostridium acetobutylicum ATCC 824]
 gi|1350864|sp|P33658|RPSG_CLOAB RecName: Full=RNA polymerase sigma-G factor
 gi|15024660|gb|AAK79662.1|AE007679_8 Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|580960|emb|CAA80621.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|706854|gb|AAC43310.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|325509110|gb|ADZ20746.1| sporulation sigma factor SigG [Clostridium acetobutylicum EA 2018]
          Length = 257

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 134/245 (54%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R ++  +R G    + A+++ ++ NLRLV+SV +++ NRG    DL Q G IGL+K+ 
Sbjct: 23  EMRELLISMRNGN---TTAREKFIKGNLRLVLSVIQRFNNRGENADDLFQVGCIGLIKSI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  ++ ++   R+ +K  +
Sbjct: 80  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYRALQVRDRLISKNNK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
           EPT  +IAK+L +P E V   L   ++PISL  PI   D D  ++ D I D      LD 
Sbjct: 139 EPTVSQIAKELKIPREEVIFALDAIQDPISLFEPIYHDDGDAIYVMDQISDN---KNLDD 195

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +   N+  +    +  L+ RE+ +L MRF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 196 SWLQNI--SIKEAMKKLSDREKMILNMRFFDG----RTQMEVADEIGISQAQVSRLEKTA 249

Query: 664 IRKLK 668
           ++ +K
Sbjct: 250 LKHMK 254


>gi|51892360|ref|YP_075051.1| sporulation sigma factor SigG [Symbiobacterium thermophilum IAM
           14863]
 gi|51856049|dbj|BAD40207.1| RNA polymerase sigma factor similar to B. subtilis SigG
           [Symbiobacterium thermophilum IAM 14863]
          Length = 256

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 132/246 (53%), Gaps = 15/246 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ R +   +R GE     A+ E++  NLRLV+SV +++ NRG    DL Q G IGLMKA
Sbjct: 21  AQMRELFVRMRSGE---KAARDELITGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKA 77

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N++ 
Sbjct: 78  IDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDALVNRLS 136

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLD 602
           REPT +EIA +L +P+E +   L   +EP+SL  P+ ++  D  ++ D + D+   S  D
Sbjct: 137 REPTVQEIADELGLPLEEIVYALDSIQEPVSLFEPLYNDGGDPIYVMDQVSDE---SQQD 193

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           S     +  +  + L  L  RE  +L +RF  G       EE+G    +++ ++ ++E  
Sbjct: 194 SQWLEGI--SIRQALHRLNERERLILTLRFFEGKTQMEVAEEIG----ISQAQVSRLEKA 247

Query: 663 AIRKLK 668
           A+  ++
Sbjct: 248 ALSHMR 253


>gi|47565382|ref|ZP_00236424.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
 gi|208742286|ref|YP_002267738.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus]
 gi|47557736|gb|EAL16062.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
          Length = 325

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 134/263 (50%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQ 469
           EIK I     +S  E   +    + GE +    +  +   N+ LV+S+A+KY N+   ++
Sbjct: 41  EIKGIGNYKVLSKQESLKLFQRYKHGEKDL---RDYLFHVNVGLVLSIARKYKNKHPDIE 97

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA-DQSCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I   +S   +IP  +   
Sbjct: 98  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNSVNQF 157

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTS 586
             + V    +      R P+ EE+ K+L +  E V K  V       ++L+    +ED  
Sbjct: 158 NLRYVELEDKYLQMYNRPPSVEEVVKELNVTSETVIKHNVYYKRATTMTLDVDTINEDIG 217

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            L  F +D +A+   +  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 218 ILNPFYDDSSAIPSTNEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 277

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
            K   +T ER+ QI+ +AI+KLK
Sbjct: 278 AKALMITTERVSQIKDEAIKKLK 300


>gi|1143832|gb|AAA84899.1| RNA polymerase sigma C subunit [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 131/245 (53%), Gaps = 18/245 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ +A      +V +NLR V+ VA +Y + GL+  DLIQE NIGLMKA +KFD   G 
Sbjct: 37  RQGDLQAG---HRLVTSNLRFVVKVAYEYRSYGLRMSDLIQEANIGLMKAVQKFDPDKGI 93

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRM---SNKIKREPTP 549
           +  +YA+WW+   I   +      +++      R     + RT R +    N        
Sbjct: 94  RLISYAVWWILAYIQGYVLKNWSLVKLGTTQAQRRLFFALARTRRELEKQGNTDGNIVNA 153

Query: 550 EEIAKKLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI-- 605
           EEIA+KL +    VR++  ++    +SL+ P+G D D +H+ DF+   ++VS  D     
Sbjct: 154 EEIARKLNVKASEVREMEQRMGGRDLSLDAPMGEDGDATHM-DFVA-SDSVSQADEVADR 211

Query: 606 -QANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +A+L R    + L  L PRE  ++  R  +  +++ TL E+G+ F  +RER RQ+E +A
Sbjct: 212 QEADLARTRIQQALQRLDPRERFIIEKR--VMSDSEMTLSELGEHFGFSRERARQLEIRA 269

Query: 664 IRKLK 668
             KLK
Sbjct: 270 KDKLK 274


>gi|224534531|ref|ZP_03675107.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
 gi|224514208|gb|EEF84526.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
          Length = 266

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 145/258 (56%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +   +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIQLAGQIQRGNAQA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q +  +    +L + LT +E  +++ R+ +  +    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTIKHLNYILETKLTEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|319649652|ref|ZP_08003808.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
 gi|317398814|gb|EFV79496.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
          Length = 236

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 132/242 (54%), Gaps = 15/242 (6%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   + KG+     A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + 
Sbjct: 2   RELFKQMHKGDI---TAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMKSIDN 58

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++   R+ +K  REP
Sbjct: 59  FDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLMSKTSREP 117

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAI 605
           T EEIAK+L +P E +   L   ++P+SL  PI ++  D  ++ D + D+     +    
Sbjct: 118 TAEEIAKELDVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQLSDERN-KDIQWIE 176

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L+E   R    L  RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+
Sbjct: 177 EIALKEGMRR----LNEREKLILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIK 228

Query: 666 KL 667
           ++
Sbjct: 229 QM 230


>gi|296506459|ref|YP_003667693.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
 gi|296327046|gb|ADH09973.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
          Length = 323

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 131/253 (51%), Gaps = 9/253 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQFLDLIQEGNI 479
           +S  E  H+    + GE +    +  +   N  LV+S+A+ Y N+   ++F DL+QEGN 
Sbjct: 49  LSKEESLHLFKRYKHGEKDL---RDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGNE 105

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-ADQSCTIRIPVHMRDKIHKVVRTARR 538
           G+++A E F+  LGY FSTYA WW+++++   I   +S   +IP H+     K V    +
Sbjct: 106 GMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLKYVELEDK 165

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
              +  R P+ EE+ K+L +  E V   KV       ++L+    +ED      F +D++
Sbjct: 166 YLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTPFFDDRS 225

Query: 597 AVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           A+   +  I  +L      +    L P+++ VL + FG+     +  +E+ K   +T ER
Sbjct: 226 AIPSTNEMIIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTER 285

Query: 656 IRQIEAKAIRKLK 668
           + QI+ +AI+KLK
Sbjct: 286 VSQIKDEAIKKLK 298


>gi|121488781|emb|CAJ18275.1| sigma 70-type sigma factor [Chlorobium phaeovibrioides]
          Length = 165

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 99/163 (60%), Gaps = 1/163 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A +L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANQLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           +++   + P     + +L     R L+ L PRE  V++  FGI
Sbjct: 121 LQNDGHL-PDHGLNRDSLTLEVERSLSVLAPREADVIKSYFGI 162


>gi|294673921|ref|YP_003574537.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294472533|gb|ADE81922.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 250

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 134/262 (51%), Gaps = 47/262 (17%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I  E  ++  E R +   + KG+ E +++K  ++EANL+ V+SVA++Y  +G+   DL+ 
Sbjct: 29  IGREQLLTNEEERELAERIAKGD-ERALSK--LIEANLKFVVSVARQYKGKGVDMEDLVS 85

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GLMKAA KFD   G +F  +A  +++Q+I ++I  Q    ++P             
Sbjct: 86  EGNLGLMKAAAKFDASKGVRFVNFAFVYIRQSIEKAIDQQGGLYQVP------------- 132

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
                     +   +E+A++ A              + +S++ P+G      L   + +K
Sbjct: 133 ----------KDVKQEVARQQA--------------QAVSVDAPLGHRTNMSLLSVLVNK 168

Query: 596 NAVSPL-DSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVT 652
           +A  PL D  + +  + +     L +L  RE RV+   +GI  N +H T+ E+ +   V 
Sbjct: 169 DA--PLADERVHSEAIEDAIEFALGTLDARERRVINAFYGI--NQEHETMAEIAEDMDVK 224

Query: 653 RERIRQIEAKAIRKLKHPSRSK 674
           RER+RQI  KA+RKL+   R+K
Sbjct: 225 RERVRQIREKAVRKLRKAYRNK 246


>gi|323701302|ref|ZP_08112977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533904|gb|EGB23768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 257

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 130/245 (53%), Gaps = 13/245 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S+ R +   +++G  EA   + +++  NLRLV+SV +++TNRG    DL Q G IGLMKA
Sbjct: 22  SQMRTLFEAMQQGNKEA---RNQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGLMKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + NK  
Sbjct: 79  IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQVRDSLVNKFS 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP+  EIA +L MP E +   L   +EPISL  PI  +     GD I   + +S   + 
Sbjct: 138 REPSINEIAGELKMPREEIVFALDAIQEPISLFEPIYHDG----GDPIFVMDQISDEKNM 193

Query: 605 IQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             + L   + R  L  L+ RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 194 DLSWLEGISIRDALRRLSDREKHILTLRFFEG----KTQMEVADEIGISQAQVSRLEKAA 249

Query: 664 IRKLK 668
           +  ++
Sbjct: 250 LNHMR 254


>gi|312134672|ref|YP_004002010.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774723|gb|ADQ04210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 255

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 127/228 (55%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  NK +REPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYINKNQREPTLEEIAKELSITKEEL 154

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L   +EPISL  P+  +  DT ++ + + D+ +           L E + +  L+ L
Sbjct: 155 VFALDSIQEPISLYEPVFQDSSDTMYVVEKLCDQKSCE------NVWLEEISLKDALSKL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE+ +L +R+  G     T  EV +   +++ ++ +IE  AI  +K
Sbjct: 209 TKREKEILYLRYYKG----KTQMEVARIVGISQAQVSRIEKSAIGHIK 252


>gi|323699411|ref|ZP_08111323.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           ND132]
 gi|323459343|gb|EGB15208.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans ND132]
          Length = 375

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 133/236 (56%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A  ++V ++LRLV+ +A  +  R +Q  LDLIQEGN+GL+KA  KFD   G KFS YA +
Sbjct: 128 AAFKLVSSHLRLVVKIAMDFQRRWMQNGLDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAF 187

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I     + K+   +   R+    +  +P+ E ++++L +   
Sbjct: 188 WIKAYILKYIMDNWRMVKIGTTQTQRKLFYNLNKERQRLQTLGFDPSTEALSERLGVSEA 247

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDF-------IEDKNAVSPLDSAIQANLRETT 613
            + ++  +++K  +SL TP+GD+  +   DF       +E+  A   +   +  N+RE  
Sbjct: 248 EIDEMDQRLSKNDMSLNTPLGDDSDTTRMDFLPSLAPGVEESIANDQIVDLLLNNIRE-- 305

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + ASL  +E  +L  R    ++ D  TL E+G++F VTRER+RQIEA+ + K++
Sbjct: 306 --IRASLNDKEVAILDRRL---LSDDPVTLREIGEEFGVTRERVRQIEARLMAKIR 356


>gi|253576139|ref|ZP_04853471.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844482|gb|EES72498.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 260

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 22/272 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R +   +++    +  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFHSLQQDHVRS--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++    ++N+  REPT  EI++ L +P E V   L   ++P+SL  PI   G 
Sbjct: 120 RDIAYKALQMRDNLTNQNSREPTIFEISEALGLPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 583 EDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    +    +DKN  VS ++   +  LRE   R    L  RE+ +L MRF  G     T
Sbjct: 180 DPIYVMDQISDDKNKDVSWIE---EIALREAMQR----LGNREKMILSMRFFEG----KT 228

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             EV  +  +++ ++ ++E  AI +++   +S
Sbjct: 229 QMEVADEIGISQAQVSRLEKSAILQMQKHVKS 260


>gi|257438785|ref|ZP_05614540.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
 gi|257198753|gb|EEU97037.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
          Length = 254

 Score =  112 bits (281), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 124/224 (55%), Gaps = 13/224 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E NLRLV+SV +++  RG    DL Q G IGL+KA + FD     +FSTY +  +   
Sbjct: 41  MIEGNLRLVLSVVQRFAQRGENLDDLFQVGCIGLIKAIDNFDPAQPVRFSTYGVPMIIGE 100

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R + D +  +R+   +RD  +K ++    +  ++ REPT +E+A++  +    V   L
Sbjct: 101 IRRFLRDNNA-LRVSRSLRDAAYKAMQAREALEKQLGREPTVDEVARQAGLSRREVNAAL 159

Query: 568 KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   EPISLE P+  +  D  ++ D + D ++     S ++   R+T    +A LTPRE+
Sbjct: 160 ESVVEPISLEEPLYTDGGDAMYVIDQVRDPDSEDSWISGLE--FRQT----VAGLTPREK 213

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R++ +R+  G     T  EV ++  +++ ++ ++E  A+ + +H
Sbjct: 214 RIMELRYLKG----ETQMEVAREIGISQAQVSRLEKAALEQFRH 253


>gi|159795060|pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
           Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
          Length = 68

 Score =  112 bits (280), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 55/66 (83%), Positives = 60/66 (90%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLA LT RE +VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 62  LRSFLD 67


>gi|153811113|ref|ZP_01963781.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
 gi|149833001|gb|EDM88084.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
          Length = 259

 Score =  112 bits (280), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 133/243 (54%), Gaps = 17/243 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG+ EA   +++ ++ NLRLV+SV K++ N      DL Q G IGLMKA + FD  L 
Sbjct: 31  IKKGDSEA---REQYIKGNLRLVLSVIKRFQNSNENADDLFQIGCIGLMKAVDNFDDTLN 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   I R + D + +IR+   +RD  +K + T   M  K  +EPT +EIA
Sbjct: 88  VKFSTYAVPMIIGEIRRYLRDYN-SIRVSRSLRDIAYKAIYTKENMIKKNLKEPTIDEIA 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLR 610
            ++ +  E +   L   + P+SL  P+  E  DT ++ D I D+   +  D  ++  +LR
Sbjct: 147 DEIGIEKEMIVYALDAIQSPVSLFEPVYSEGGDTLYVMDQISDQK--NKEDHWLENLSLR 204

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   R    L  RE+ ++ MRF  G     T  EV  +  +++ ++ ++E  A++ +K+ 
Sbjct: 205 EAMNR----LNQREKHIIEMRFYEG----RTQMEVADEIGISQAQVSRLEKNALKTMKNY 256

Query: 671 SRS 673
            RS
Sbjct: 257 LRS 259


>gi|312622917|ref|YP_004024530.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203384|gb|ADQ46711.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 255

 Score =  112 bits (279), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 127/228 (55%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  NK ++EPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYINKNQKEPTLEEIAKELSITKEDL 154

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L   +EPISL  P+  +  DT ++ + + D  +   +       L E + +  L+ L
Sbjct: 155 VFALDSIQEPISLYEPVFQDSTDTMYVVERLCDHKSCESV------WLEEISLKDALSKL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE+ +L +R+  G     T  EV K   +++ ++ +IE  AI  +K
Sbjct: 209 TKREKEILYLRYYKG----KTQMEVAKIVGISQAQVSRIEKSAIGHIK 252


>gi|121488757|emb|CAJ18263.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 163

 Score =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 97/163 (59%), Gaps = 1/163 (0%)

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ + 
Sbjct: 1   EGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKA 60

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
             ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D +++ 
Sbjct: 61  YSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQND 120

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
             + P     + +L     R L+ L PRE  V+R  FGIGM+ 
Sbjct: 121 GHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFGIGMDN 162


>gi|223975681|gb|ACN32028.1| unknown [Zea mays]
          Length = 565

 Score =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 126/240 (52%), Gaps = 6/240 (2%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +VS ++ G C     +  ++     LV  +A+ YT  G    DL+Q G +G++  AEKFD
Sbjct: 318 LVSRLQAGYC----CRDRLLVTTEWLVRCIARTYTGMGTALDDLLQAGKMGVLDGAEKFD 373

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +FSTY  +W+++ +   +A+ S    +P  M   + KV    R +  +  R P+ 
Sbjct: 374 SRKGCRFSTYVKYWIRKGMLALLAENSGVTLLPARMESIMRKVKEARRGIRYRQGRNPSD 433

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QAN 608
            E+A  + + V  VR   K ++  +SL + +         + I D++A SP ++A+ +  
Sbjct: 434 SEVAAAVGVSVANVRLARKCSRRAVSLYSEVAIGQDVKFAEVIPDESA-SPDEAALFRGQ 492

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    VL  L  RE RVLR+R G+      +LEE+G  + V++E IR+IE  A+ +L+
Sbjct: 493 LRERLLLVLGRLPAREGRVLRLRHGLEDGRCRSLEEIGGIYGVSKEWIRKIEKSAMARLR 552


>gi|302871380|ref|YP_003840016.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574239|gb|ADL42030.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 255

 Score =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 126/228 (55%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  NK  REPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYINKNHREPTLEEIAKELSITKEEL 154

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L   +EPISL  P+  +  DT ++ + + D+ +           L E + +  L+ L
Sbjct: 155 VFALDSIQEPISLYEPVFQDSSDTMYVVEKLCDQKSCE------NVWLEEISLKDALSKL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE+ +L +R+  G     T  EV +   +++ ++ +IE  AI  +K
Sbjct: 209 TKREKEILYLRYYKG----KTQMEVARIVGISQAQVSRIEKSAIGHIK 252


>gi|325289982|ref|YP_004266163.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965383|gb|ADY56162.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 132/240 (55%), Gaps = 10/240 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +  ++ K +     A+++++  NL+L+ ++ +++T+RG +  DL Q G IGL+KA +KFD
Sbjct: 21  MTELLHKAQAGDHDAREQLINCNLKLIFNLIQRFTHRGYELEDLFQIGTIGLIKAIDKFD 80

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G KFSTYA+  +   I R + D    I++P   ++ ++K+ R+  ++S ++ REPT 
Sbjct: 81  FSYGVKFSTYAVPMIIGEIRRFLRDDH-PIKVPRSYKELVYKIHRSREKLSLELNREPTV 139

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA+ L +  E +   L   + P S+   +  +D+  +  +I D+  V      + A  
Sbjct: 140 NEIAQDLNVGSEEIVTALDAVQSPTSINDTLYQDDSDPI--YILDQIPVE--KDLVPAWF 195

Query: 610 RETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E   + VL  L  RE++VL MRF      D T  E+ K+  +++ +I +IE  A+  LK
Sbjct: 196 EEVALKDVLNKLPEREKQVLVMRF----YEDKTQSEIAKRLNLSQVQISRIERAALLHLK 251


>gi|312111757|ref|YP_003990073.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
 gi|311216858|gb|ADP75462.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
          Length = 271

 Score =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 141/265 (53%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+ EA   ++++V  NLRLV+SV +++ N
Sbjct: 15  RNKVEICGVDTSKLPVLKNEEMRELFKRMHEGDLEA---REKLVNGNLRLVLSVIQRFNN 71

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 72  RGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 130

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT EEIA  L +P E V   L   ++P+SL  PI ++  
Sbjct: 131 RDIAYKALQVREKLMGEAAKEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGG 190

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D +N  S     I   L+E   R    L  RE+ ++R RF  G       
Sbjct: 191 DPIYVMDQLSDERNGDSQWIEEIA--LKEGLCR----LNEREKMIIRKRFFQGKTQMEVA 244

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AIR++
Sbjct: 245 EEIG----ISQAQVSRLEKAAIRQM 265


>gi|295399724|ref|ZP_06809705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978127|gb|EFG53724.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 271

 Score =  111 bits (278), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 138/263 (52%), Gaps = 17/263 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+ EA   ++++V  NLRLV+SV +++ N
Sbjct: 15  RNKVEICGVDTSKLPVLKNEEMRELFKRMHEGDLEA---REKLVNGNLRLVLSVIQRFNN 71

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 72  RGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 130

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           RD  +K ++   ++  +  +EPT EEIA  L +P E V   L   ++P+SL  PI ++  
Sbjct: 131 RDIAYKALQVREKLMGEAAKEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDG- 189

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEE 644
              GD I   + +S   S     + E   +  L  L  RE+ ++R RF  G       EE
Sbjct: 190 ---GDPIYVMDQLSDERSGDNQWIEEIALKEGLCRLNEREKMIIRKRFFQGKTQMEVAEE 246

Query: 645 VGKQFCVTRERIRQIEAKAIRKL 667
           +G    +++ ++ ++E  AIR++
Sbjct: 247 IG----ISQAQVSRLEKAAIRQM 265


>gi|162463525|ref|NP_001105185.1| sigma factor protein [Zea mays]
 gi|20159761|gb|AAM12034.1| sigma factor protein [Zea mays]
          Length = 568

 Score =  111 bits (278), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 126/240 (52%), Gaps = 6/240 (2%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +VS ++ G C     +  ++     LV  +A+ YT  G    DL+Q G +G++  AEKFD
Sbjct: 321 LVSRLQAGYC----CRDRLLVTTEWLVRCIARTYTGMGTALDDLLQAGKMGVLDGAEKFD 376

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +FSTY  +W+++ +   +A+ S    +P  M   + KV    R +  +  R P+ 
Sbjct: 377 SRKGCRFSTYVKYWIRKGMLALLAENSGVTLLPARMESIMRKVKEARRGIRYRQGRNPSD 436

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QAN 608
            E+A  + + V  VR   K ++  +SL + +         + I D++A SP ++A+ +  
Sbjct: 437 SEVAAAVGVSVANVRLARKCSRRAVSLYSEVAIGQDVKFAEVIPDESA-SPDEAALFRGQ 495

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    VL  L  RE RVLR+R G+      +LEE+G  + V++E IR+IE  A+ +L+
Sbjct: 496 LRERLLLVLGRLPAREGRVLRLRHGLEDGRCRSLEEIGGIYGVSKEWIRKIEKSAMARLR 555


>gi|15615117|ref|NP_243420.1| sporulation sigma factor SigG [Bacillus halodurans C-125]
 gi|10175174|dbj|BAB06273.1| RNA polymerase sporulation forespore-specific (late) sigma-G factor
           [Bacillus halodurans C-125]
          Length = 261

 Score =  111 bits (278), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 149/274 (54%), Gaps = 25/274 (9%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R + + ++ G+  A   ++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNQEMRELFARLQSGDTSA---RETLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++   ++  + +R  EPT +EIAK+L +P E V   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDQLMGEKQREKEPTVQEIAKELGVPKEDVVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFI-EDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             D  ++ D I +D+N  V  +D   +  L+E   R    L  RE+ +L MRF  G    
Sbjct: 179 GGDPIYVMDQISDDRNKDVQWVD---EIALKEAMVR----LNDREKLILNMRFYQGKTQM 231

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              EE+G    +++ ++ ++E  AI+++   ++S
Sbjct: 232 EVAEEIG----ISQAQVSRLEKAAIQQMSKHAQS 261


>gi|153004710|ref|YP_001379035.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028283|gb|ABS26051.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
          Length = 307

 Score =  111 bits (278), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 80/238 (33%), Positives = 122/238 (51%), Gaps = 14/238 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ANLR V+ V+ +Y + G +  DLIQEGNIGLMKA +KFD   G +  +YA+WW
Sbjct: 46  AAHRLVTANLRFVVKVSYEYRSYGFKMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWW 105

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTAR---RMSNKIKREPTPEE---IAKK 555
           ++  I   I      +++      R     + RT R   +MS +  R+   ++   IAKK
Sbjct: 106 IRAYIQNYILKSWSLVKLGTTQAQRKLFFSLARTKRELDKMSVEHGRDSDAQDKGKIAKK 165

Query: 556 LAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRE 611
           L + P E      ++    +SL+ P+GD+      DF+  K+A       D+  Q  +  
Sbjct: 166 LRVKPAEVEEMEQRMDGRDLSLDAPMGDDGGYSHIDFVAAKSAAQDDELSDAEEQQIVSA 225

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             T  LA L  RE  ++  R  +  +   TL+E+G+ F  +RER RQ+E +A  KLK 
Sbjct: 226 KVTAALARLDQRERYIIEQR--VMSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKQ 281


>gi|312128104|ref|YP_003992978.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778123|gb|ADQ07609.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 255

 Score =  111 bits (278), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 125/226 (55%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  NK  REPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYINKNHREPTLEEIAKELSITKEEL 154

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EPISL  P+  + T  +  ++ +K  +    S     L E + +  L+ LT 
Sbjct: 155 VFALDSIQEPISLYEPVFQDSTDTM--YVVEK--LCDHKSCENVWLEEISLKDALSKLTK 210

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +R+  G     T  EV +   +++ ++ +IE  AI  +K
Sbjct: 211 REKEILYLRYYKG----KTQMEVARIVGISQAQVSRIEKSAIGHIK 252


>gi|331269711|ref|YP_004396203.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126261|gb|AEB76206.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 242

 Score =  111 bits (278), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 135/246 (54%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +R G+     ++++ +  NLRLV+SV +++ NRG    DL Q G IGL+KA 
Sbjct: 8   EMKELLIKMRDGDY---FSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKAI 64

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  +K ++   R+ NK  +
Sbjct: 65  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQVRDRLINKDNK 123

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           +P   +IAK+L +P E V   L   ++P+SL  PI  +  D  ++ D I D  +V   DS
Sbjct: 124 DPNVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDALYVMDQISDNKSVD--DS 181

Query: 604 AIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            I+  +++E   R    L  RE+ +L MRF  G     T  EV  +  +++ ++ ++E  
Sbjct: 182 WIENISIKEAMKR----LNEREKLILNMRFFQG----RTQMEVADEIGISQAQVSRLEKT 233

Query: 663 AIRKLK 668
           A++ ++
Sbjct: 234 ALKHMR 239


>gi|308173495|ref|YP_003920200.1| RNA polymerase sporulation-specific sigma factor sigma-G [Bacillus
           amyloliquefaciens DSM 7]
 gi|307606359|emb|CBI42730.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553575|gb|AEB24067.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens TA208]
 gi|328911632|gb|AEB63228.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens LL3]
          Length = 260

 Score =  111 bits (277), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 126/229 (55%), Gaps = 18/229 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  REPT EEIAK L +P E +
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSREPTAEEIAKVLEVPHEEI 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLA 618
              L   ++P+SL  PI ++  D  ++ D I D   K+     + A++  +R        
Sbjct: 158 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNKDTQWIEELALKEGMRR------- 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L  RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 211 -LNEREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 254


>gi|154685949|ref|YP_001421110.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens FZB42]
 gi|154351800|gb|ABS73879.1| SigG [Bacillus amyloliquefaciens FZB42]
          Length = 260

 Score =  111 bits (277), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 126/229 (55%), Gaps = 18/229 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  REPT EEIAK L +P E +
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSREPTAEEIAKVLEVPHEEI 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLA 618
              L   ++P+SL  PI ++  D  ++ D I D   K+     + A++  +R        
Sbjct: 158 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNKDTQWIEELALKEGMRR------- 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L  RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 211 -LNEREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 254


>gi|323452445|gb|EGB08319.1| hypothetical protein AURANDRAFT_5759 [Aureococcus anophagefferens]
          Length = 239

 Score =  111 bits (277), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 125/246 (50%), Gaps = 15/246 (6%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFST 498
           AK  +V AN  LV+S+A+ Y    T  G++ LD L+QEG +GL++A EK++   G +F T
Sbjct: 1   AKHALVRANGGLVVSIARGYQRLRTGAGVEALDDLVQEGTLGLIRAVEKYEPERGIRFGT 60

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA  W+K +I+  +      I++P  + D   +  R++  + N + R+ T EE+A+ L  
Sbjct: 61  YATAWIKASISAWLKRGDAMIKVPSRVADLGLRAARSSSALQNDLGRDATAEEVARDLGA 120

Query: 559 PVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               V            +S +   G +  S+    + D+      D A+  +L+   T  
Sbjct: 121 STAAVEAAASALHGSRVVSYDASAGGDSESNFVACLADE------DCAV-GDLKADLTNA 173

Query: 617 LAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           LA+ L  RE RV+R+R+G+   T  +  E      + +E +RQI  KA RKL+  ++   
Sbjct: 174 LAAVLDDRELRVVRLRYGLDDGTQRSTRECAAALGIGKESVRQICLKAFRKLRGTAQGSA 233

Query: 676 LRSFLD 681
           L S +D
Sbjct: 234 LLSHMD 239


>gi|150390630|ref|YP_001320679.1| sporulation sigma factor SigG [Alkaliphilus metalliredigens QYMF]
 gi|149950492|gb|ABR49020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 257

 Score =  111 bits (277), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 134/244 (54%), Gaps = 17/244 (6%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH+  ++++G+  A   ++E ++ NLRLV+SV +++ NRG    DL Q G IGL+KA + 
Sbjct: 25  RHLFGLIKQGDNSA---REEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGCIGLIKAIDN 81

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     +FSTYA+  +   I R + D + +IR+   +RD  +K ++   +++N+  +EP
Sbjct: 82  FDLRHNVRFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDTAYKALQVRDQLTNQKSKEP 140

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA  L +P E V   L   ++P+SL  PI  +  D   + D I D+   S  ++ I
Sbjct: 141 SVAEIAANLNIPREDVVFALDAIQDPVSLFEPIYHDSGDAIFVMDQIRDEK--SEDETWI 198

Query: 606 QA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               LRE   R    L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A+
Sbjct: 199 DGIALREAMRR----LNNREKHILNLRFFEG----RTQMEVADEIGISQAQVSRLEKTAL 250

Query: 665 RKLK 668
           + ++
Sbjct: 251 KHMR 254


>gi|224531828|ref|ZP_03672460.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
 gi|224511293|gb|EEF81699.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
          Length = 266

 Score =  111 bits (277), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 74/258 (28%), Positives = 143/258 (55%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +   +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIKLAGQIQRGSAQA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q + L+     +   L  +E  +++ R+ +  +    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTLKHLNYVLETKLNEKERYIIKKRYNLDNSPKKSTLKDISMELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|225175484|ref|ZP_03729478.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168813|gb|EEG77613.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
          Length = 277

 Score =  111 bits (277), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 129/246 (52%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R + + +R+G+     A++++V  NLRLV+SV +++ NRG    DL Q G IGL+KA 
Sbjct: 42  EMRRLFARLREGD---ESAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAI 98

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D +  IR+   +RD  +KV++    ++N+  R
Sbjct: 99  DNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKVLQVRDSLANRFAR 157

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLD 602
           EPT  EIAK+L +  E +   L   +EP+SL  PI   G +    +    +DKN  +   
Sbjct: 158 EPTISEIAKELNLKREDIVFALDAIQEPVSLFEPIYHDGGDPIFVMDQISDDKNHDNKWL 217

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  N        L  L  RE+ +L +RF  G       +E+G    +++ ++ ++E  
Sbjct: 218 EVLAIN------EALHKLNEREKLILTLRFYRGKTQMEVADEIG----ISQAQVSRLEKA 267

Query: 663 AIRKLK 668
           A+  L+
Sbjct: 268 ALSHLR 273


>gi|313115569|ref|ZP_07801028.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622084|gb|EFQ05580.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 255

 Score =  110 bits (276), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 125/226 (55%), Gaps = 13/226 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++MVE NLRLV+SV +++  RG    DL Q G IGL+KA + FD     +FSTY +  +
Sbjct: 38  REQMVEGNLRLVLSVVQRFAQRGENLDDLFQVGCIGLIKAIDHFDPAQPVRFSTYGVPMI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R + D +  +R+   +RD  ++ +++   +  ++ REPT +EIA+   +    V 
Sbjct: 98  IGEIRRFLRDNNA-LRVSRSLRDTAYRAMQSREALEKQLGREPTMDEIAQAAGLARREVT 156

Query: 565 KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L+   EPISLE P+  +  D  ++ D + D +      S +Q   R+T    +A LTP
Sbjct: 157 AALESVVEPISLEEPVYTDGGDAMYVIDQVRDPDGEDSWISGLQ--FRQT----VAGLTP 210

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+R++ +R+  G     T  EV ++  +++ ++ ++E  A+ + +
Sbjct: 211 REKRIMELRYLQG----KTQMEVAREIGISQAQVSRLEKGALSQFR 252


>gi|15595116|ref|NP_212905.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|195941591|ref|ZP_03086973.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 80a]
 gi|216264706|ref|ZP_03436698.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218249170|ref|YP_002375269.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221217974|ref|ZP_03589441.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223889406|ref|ZP_03623992.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224532620|ref|ZP_03673242.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225548870|ref|ZP_03769847.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225550031|ref|ZP_03770992.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225551867|ref|ZP_03772810.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226320640|ref|ZP_03796199.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|226321470|ref|ZP_03796997.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|2688700|gb|AAC67109.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|215981179|gb|EEC21986.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218164358|gb|ACK74419.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221192280|gb|EEE18500.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223885092|gb|EEF56196.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224512476|gb|EEF82855.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225369490|gb|EEG98942.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225370473|gb|EEG99909.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225371662|gb|EEH01089.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226233266|gb|EEH32018.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|226233963|gb|EEH32685.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|312148432|gb|ADQ31091.1| RNA polymerase sigma factor [Borrelia burgdorferi JD1]
 gi|312149704|gb|ADQ29775.1| RNA polymerase sigma factor [Borrelia burgdorferi N40]
          Length = 266

 Score =  110 bits (276), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 74/258 (28%), Positives = 143/258 (55%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +   +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIKLAGQIQRGNAKA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q + L+     +   L  +E  +++ R+ +  +    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTLKHLNYILETKLNEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|317129288|ref|YP_004095570.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474236|gb|ADU30839.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
          Length = 261

 Score =  110 bits (276), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 142/269 (52%), Gaps = 22/269 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ G+     A++E+V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNKEMRVLFEKMQNGD---EFAREELVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++    M N+ K  REPT +EIAK L +P E +   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDNMMNEKKREREPTVQEIAKVLDVPKEDIVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D  ++ D I D      +    +  L+E   R    L  RE+ +L MRF  G     T
Sbjct: 179 GGDPIYVMDQISDDKQ-KDIQWIEEIALKEAMIR----LNDREKMILDMRFFQG----KT 229

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
             EV  +  +++ ++ ++E  AI+++ KH
Sbjct: 230 QMEVADEIGISQAQVSRLEKAAIQQMNKH 258


>gi|295696452|ref|YP_003589690.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412054|gb|ADG06546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 261

 Score =  110 bits (276), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 141/265 (53%), Gaps = 19/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V T     ++ +E R + +  + G+  A   ++ ++  NLRLV+SV +++ N
Sbjct: 3   RNKVEISGVNTSQLPVLTNAEMRKLFAEFQAGDLSA---RERLIHGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGENVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   +++N+  REPT  EI+++L +P E V   L   ++P+SL  PI  +  
Sbjct: 119 RDIAYKALQVRDQLTNERLREPTITEISEQLNLPKEDVVFALDAIQDPVSLFEPIYHDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D      L    +  LRE   +    L  RE+++L MRF  G       E
Sbjct: 179 DPIYVMDQIRDDRNQDVL-WVEEIALREAMNK----LGQREQKILAMRFFEGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G    +++ ++ ++E  AI+ ++
Sbjct: 234 EIG----ISQAQVSRLEKSAIQHMQ 254


>gi|239826533|ref|YP_002949157.1| sporulation sigma factor SigG [Geobacillus sp. WCH70]
 gi|239806826|gb|ACS23891.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. WCH70]
          Length = 259

 Score =  110 bits (276), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 143/265 (53%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+ EA   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFKRMHEGDLEA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++ ++  +EP+ EEIAK L +P E V   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLMSETAKEPSAEEIAKVLGIPHEEVVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D +N  S     I   L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 DPIYVMDQLSDERNRDSQWIEEIA--LKEGMRR----LNEREKMIIRKRFFQGKTQMEVA 232

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AIR++
Sbjct: 233 EEIG----ISQAQVSRLEKAAIRQM 253


>gi|311029938|ref|ZP_07708028.1| sporulation sigma factor SigG [Bacillus sp. m3-13]
          Length = 259

 Score =  110 bits (276), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 84/264 (31%), Positives = 141/264 (53%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFREMQGGELSA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  REPT EEIAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVRERLMSETSREPTAEEIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+     +    +  L+E   R    L  RE+ +LR RF  G       +
Sbjct: 179 DPIYVLDQISDEKN-KDIQWIEEIALKEGMRR----LNDREKLILRKRFFQGKTQMEVAD 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 234 EIG----ISQAQVSRLEKAAIKQM 253


>gi|261880927|ref|ZP_06007354.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
 gi|270332314|gb|EFA43100.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
          Length = 243

 Score =  110 bits (276), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 138/279 (49%), Gaps = 43/279 (15%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E DSI +  N+I   ++   +S  E   +   ++ G+ +A    +E+  ANL  VI++A 
Sbjct: 6   EKDSINRYLNDIGHHNL---LSNEEELQLADRIQAGDSQAI---EELTSANLTYVITLAN 59

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y  RGL   DLI EGNIG+++AA KF    G +F  +A  +++ A+ ++I  Q+   R+
Sbjct: 60  QYVKRGLALEDLISEGNIGMLQAATKFSRDAGKRFVAFAAPYIRDAMEQAIEQQAGLYRV 119

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P           R A   +NK++++ +                       + +S++ P+ 
Sbjct: 120 P-----------RNAD--NNKLEKKRS-----------------------KALSIDEPLC 143

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 LG  I D+NA  P +   +  L    T ++A L  RE++V+R  +GIG     T
Sbjct: 144 GSHELSLGHVIPDRNATVPDEDLEKDMLLGELTELIADLDQREQQVIRALYGIGTEA-KT 202

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + E G    + RER+RQI  KAIRK+   ++S  L+ +L
Sbjct: 203 MLETGMAMGLKRERVRQIRNKAIRKICRLTKSSDLKDYL 241


>gi|160943880|ref|ZP_02091110.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444556|gb|EDP21560.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104729|emb|CBL02273.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii SL3/3]
          Length = 255

 Score =  110 bits (276), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 75/263 (28%), Positives = 142/263 (53%), Gaps = 20/263 (7%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V TG    ++ +E R ++++   G+     A+  MVE NLRLV+SV +++  R
Sbjct: 3   NKVELCGVNTGQLPVLTEAEKRQLLTLAHAGD---KAARARMVEGNLRLVLSVVQRFAQR 59

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +R
Sbjct: 60  GENLDDLFQVGCIGLIKAIDNFDPAQPVRFSTYGVPMIIGEIRRFLRDNNA-LRVSRTLR 118

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--D 584
           D  ++ ++    +  ++ REPT +EIA    +    V   L+   EP+SL+ P+  +  D
Sbjct: 119 DTAYRAMQARETLEKQLGREPTMDEIAAAAGLARREVTAALESVVEPLSLDEPVYTDGGD 178

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             ++ D + D ++     S +Q   R+T    +A+L+PRE+R++ +R+  G     T  E
Sbjct: 179 AMYVIDQVRDPDSEESWISGLQ--FRDT----VAALSPREKRIMELRYLRG----KTQME 228

Query: 645 VGKQFCVTRERIRQIEAKAIRKL 667
           V ++  +++ ++ ++E  A+++ 
Sbjct: 229 VAQEIGISQAQVSRLEKGALQQF 251


>gi|293376228|ref|ZP_06622471.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325845152|ref|ZP_08168461.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
 gi|292645120|gb|EFF63187.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325488817|gb|EGC91217.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
          Length = 259

 Score =  110 bits (275), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 79/271 (29%), Positives = 155/271 (57%), Gaps = 21/271 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           ++++  + V+T     +S +E   +    + G  EA   ++ +++ NLRLV+S+ KK+ +
Sbjct: 3   KHKVDIVGVDTAKLEVLSNAEMTELFKSFQNGNVEA---RESLIKGNLRLVLSIIKKFNH 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G +GLMKA + FD     KFSTYA+  +   I R + D + ++R+   +
Sbjct: 60  RGENLDDLFQVGCLGLMKAIDHFDLSHEVKFSTYAVPMIIGEIRRYLRDNN-SLRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDE- 583
           RD  +KV++   ++S +++R+PT EEIA  + + P++ V  V  I+ +P+S+ +PI ++ 
Sbjct: 119 RDTAYKVLQVKDQLSIELQRDPTNEEIAAAIGVEPIDVVLSVEAIS-DPVSIFSPIYNDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            DT HL D I+D ++++    +++  L E   R    L  RE+R++  R+ +G     T 
Sbjct: 178 GDTIHLIDQIKD-DSITDDKWSVKLMLEEGFKR----LGKREKRIIHDRYFMG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            E+  +  +++ ++ ++E  A++ ++   +S
Sbjct: 229 MEIAAEIGISQAQVSRLEKNALQVMEEMMKS 259


>gi|158522485|ref|YP_001530355.1| RNA polymerase sigma 70 family subunit [Desulfococcus oleovorans
           Hxd3]
 gi|158511311|gb|ABW68278.1| putative RNA polymerase, sigma 70 family subunit [Desulfococcus
           oleovorans Hxd3]
          Length = 321

 Score =  110 bits (275), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 127/238 (53%), Gaps = 29/238 (12%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +  +NLRLV+ +A ++    +Q  LDLIQEGNIGLM A +KFD     KFS YA +W+K 
Sbjct: 78  LATSNLRLVVKIALEFQRVWMQNLLDLIQEGNIGLMHAVQKFDPYKNVKFSYYASFWIKA 137

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----------EPTPEEIAKKL 556
            I + + D    ++I            +  R++  ++K+          EP P+ +A++L
Sbjct: 138 YILKFVMDNWRLVKI---------GTTQNQRKLFFRLKKEKQALIDQGFEPRPKLLAERL 188

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-----DSAIQANLR 610
            +P + V  +  ++    +SL+ P+  +  +  GD + D N   P+     D A++  + 
Sbjct: 189 GVPQKEVINMEQRLDMWDLSLDEPVSHDSDTQKGDLL-DINNTQPVDEQVGDKALRQLVG 247

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E       +LTPRE  + + R  I  +   TL+++G+++ ++RER+RQ+E   I+K++
Sbjct: 248 EHLVEFKKTLTPRERDIFKTR--IYTDQPMTLQDIGERYAISRERVRQLEVNIIKKMR 303


>gi|258404985|ref|YP_003197727.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
 gi|257797212|gb|ACV68149.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
          Length = 350

 Score =  110 bits (275), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 132/232 (56%), Gaps = 18/232 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ ++LRLV+ +A ++  R ++  LDL+QEGN+GLMKA +KFD   G KFS YA +W++ 
Sbjct: 108 LISSHLRLVVKIAMEFQRRWMKNVLDLVQEGNVGLMKAVQKFDPERGIKFSYYASFWIRA 167

Query: 507 AITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
            I + I D    +++      R   + + R  +R+  +   +P    +++ L +  E V 
Sbjct: 168 YILKFIMDNWRMVKLGTTQAQRKLFYNLSREKQRLQAQ-GFDPDASTLSENLDVSEESVV 226

Query: 565 KVL-KITKEPISLETPIGDEDTSHLGDF-------IEDKNAVSPLDSAIQANLRETTTRV 616
           ++  ++    +SL+ P+G++ +S   DF       IE+  A   + SA    LR+    +
Sbjct: 227 EMTQRLGGHDLSLDAPLGEDSSSSRMDFLPALGAGIEESLAQQEMGSA----LRQHLQTI 282

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  +E+ +L  R  +  ++  TL E+G+++ +TRER+RQIE++ ++KLK
Sbjct: 283 LPKLNDKEKEILEHR--LLTDSPVTLREIGEKYGITRERVRQIESRLLQKLK 332


>gi|294501013|ref|YP_003564713.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|295706362|ref|YP_003599437.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
 gi|294350950|gb|ADE71279.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|294804021|gb|ADF41087.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
          Length = 259

 Score =  110 bits (275), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 81/267 (30%), Positives = 143/267 (53%), Gaps = 25/267 (9%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ G+     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFKQMQAGD---GTAREKLVSGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EPT EEI+K L +P E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVRERLMSETSKEPTAEEISKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D  ++ D + D   +++    + A+Q  +R         L  RE+ +LR RF  G     
Sbjct: 179 DPIYVMDQLSDERNRDSTWIEEIALQEGMRR--------LNEREKLILRKRFFQGKTQME 230

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKL 667
             EE+G    +++ ++ ++E  AI+++
Sbjct: 231 VAEEIG----ISQAQVSRLEKAAIKQM 253


>gi|262277481|ref|ZP_06055274.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
 gi|262224584|gb|EEY75043.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
          Length = 300

 Score =  110 bits (275), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 134/250 (53%), Gaps = 29/250 (11%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ E++    ++V ++LRLV  +A  Y   GL   +L+ EGNIGLM A +KFD   G++
Sbjct: 47  KGDKESA---HKLVTSHLRLVAKIATGYRGYGLPMSELVSEGNIGLMTAVKKFDPERGFR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE- 550
            +TYAMWW+K ++   I      ++I      K  K+    R+M N+I R    +  PE 
Sbjct: 104 LATYAMWWIKASMQEYILRSWSLVKIGTTAAQK--KLFFNLRKMKNQIMRSDQTDLLPEQ 161

Query: 551 --EIAKKLAMPVEGVRKVLKITKEP-ISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             EIA +L +  + V  + +  K P  SL   I G+E  S   D++ D+NA    D  +Q
Sbjct: 162 VTEIANRLDVTEDEVNSMDQRMKGPEASLNATISGEEGESEWQDWVVDENA----DQELQ 217

Query: 607 ANLRETTT-------RVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQ 658
              R+ T        + ++ L  RE+ +L   F   +N +  TLEE+ +++ ++RERIRQ
Sbjct: 218 IAHRQETNKRKALLDKAMSILNEREKEIL---FDRRLNEEPKTLEELSQKYNISRERIRQ 274

Query: 659 IEAKAIRKLK 668
           IE +A  KL+
Sbjct: 275 IENRAFEKLQ 284


>gi|169831582|ref|YP_001717564.1| sporulation sigma factor SigG [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638426|gb|ACA59932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 255

 Score =  110 bits (275), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 132/248 (53%), Gaps = 14/248 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E R +   ++ G+  A   + +++  NLRLV+SV +++TNRG    DL Q G IGL
Sbjct: 18  LTAAEMRQLFQEMQAGDPSA---RSKLINGNLRLVLSVIQRFTNRGEFVDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    ++N
Sbjct: 75  IKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQIRDNLAN 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REP+  EIA++L +P E +   L   +EPISL  PI      H GD I   + VS  
Sbjct: 134 RFSREPSVSEIAQELNIPREEIVFALDSIQEPISLFEPI-----YHDGDPIFVMDQVSDE 188

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +A    L +   R  +  L  RE+ +L +RF  G       EE+G    +++ ++ ++E
Sbjct: 189 RNADANWLEDIAIRDAIRKLNEREKLILTLRFFEGKTQMEVAEEIG----ISQAQVSRLE 244

Query: 661 AKAIRKLK 668
             A+  ++
Sbjct: 245 KAALSHMR 252


>gi|115374575|ref|ZP_01461855.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823765|ref|YP_003956123.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|115368445|gb|EAU67400.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396837|gb|ADO74296.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 366

 Score =  110 bits (275), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 123/231 (53%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V +NLRLV+ +A +Y    L  LDL+QEGNIGLM+A +K+D   G K S+YA WW
Sbjct: 120 AAYRLVASNLRLVVKLAHEYHRNPLSLLDLVQEGNIGLMQAVKKYDPERGVKLSSYAAWW 179

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI---KREPTPEEIAKKLAMPV 560
           ++  I R I D    +++     +   K+    R+  +K+     EP P+ +A++L +  
Sbjct: 180 IRAYILRYIMDNWKMVKL--GTTEAQRKLFFKLRQEQDKLIAQGFEPNPKLLAERLNVTE 237

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           + V ++  ++  + +S++ P+GDE  +   D +   +AV   +      L+E     LA 
Sbjct: 238 QDVVEMDQRLGHDEVSIDAPVGDESRASRADRLLPSSAVGAEERLGNEELKELFREKLAE 297

Query: 620 LTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                E   R  F   +  D   TL+++G ++ V+RER RQIEA  I +++
Sbjct: 298 FAQTLEGKERFIFESRLTADEPLTLQDIGDKYGVSRERARQIEAALINRMR 348


>gi|222528794|ref|YP_002572676.1| sporulation sigma factor SigG [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455641|gb|ACM59903.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 255

 Score =  110 bits (274), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 77/228 (33%), Positives = 126/228 (55%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  N  ++EPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYINNNQKEPTLEEIAKELSITKEDL 154

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L   +EPISL  P+  +  DT ++ + + D  +   +       L E + +  L+ L
Sbjct: 155 VFALDSIQEPISLYEPVFQDSTDTMYVVERLCDHKSCESV------WLEEISLKDALSKL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE+ +L +R+  G     T  EV K   +++ ++ +IE  AI  +K
Sbjct: 209 TKREKEILYLRYYKG----KTQMEVAKIVGISQAQVSRIEKSAIGHIK 252


>gi|323449639|gb|EGB05525.1| hypothetical protein AURANDRAFT_60247 [Aureococcus anophagefferens]
          Length = 399

 Score =  110 bits (274), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 75/263 (28%), Positives = 132/263 (50%), Gaps = 27/263 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ--------------FLDLIQEGNIGLMKAAEKFD 489
           A++ M+ +N+RLV+++A++      Q                DL+ EG +GL KA ++F+
Sbjct: 137 AREVMMLSNMRLVVAMARRMQRSLPQASRLAVDRDGGSYALDDLVAEGTLGLAKAVDRFE 196

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WWV+QAI R+I  +   + +PVH++    K     + + ++  R PT 
Sbjct: 197 PDRGFRFSTYATWWVRQAIQRAI-RRRAVVAVPVHVQQLAKKCENATQELRDEYGRPPTS 255

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIE--------DKNAV 598
            E+A ++    + ++   +      SL+ P+        SH+ DF E        + +  
Sbjct: 256 AELAARVGASEKRLKLAGRAALATFSLDVPLSAARGGKGSHVADFAEAATLNEIVESDEP 315

Query: 599 SPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +P ++A    LR+     + A+L P E  VLR+R G+      T  +VG+    T ++IR
Sbjct: 316 APEEAATFHELRDAIDYAMHANLQPSERDVLRLRLGLDDGETRTRRQVGEICGQTEKKIR 375

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
            IE  A+ KL+H     +LR ++
Sbjct: 376 AIERAALTKLRHTRDCVQLREYV 398


>gi|315121811|ref|YP_004062300.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313495213|gb|ADR51812.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 300

 Score =  110 bits (274), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 126/238 (52%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV+ +A  Y   GL   ++I EGNIGLM+A +KFD   G++ +TY +WW
Sbjct: 49  AVHKLVTSHLRLVVKIAMGYRGYGLPISEVISEGNIGLMQAVKKFDPERGFRLATYGIWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPE---EIAKKL 556
           +K AI   I      ++I      K  ++    RR+  +++        PE   EIA KL
Sbjct: 109 IKAAIQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGRLQAVNDTNLKPEQVVEIATKL 166

Query: 557 AMP-VEGVRKVLKITK-EPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRE 611
            +   E +    +++  E +++     D+D+S   D +    D    + +D   + N R 
Sbjct: 167 NVSEAEVISMNCRLSGDESLNVLMNSSDKDSSQWQDLLVYNHDSQEQTLIDKEERKNRRN 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TR +++L PRE R+   R    +N +  TLE +  +F V+RERIRQIEA+A  K++
Sbjct: 227 MLTRSMSTLNPRERRIFEAR---RLNENPSTLENLSSEFAVSRERIRQIEARAFEKVQ 281


>gi|213018727|ref|ZP_03334535.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995678|gb|EEB56318.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 281

 Score =  110 bits (274), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 79/244 (32%), Positives = 134/244 (54%), Gaps = 18/244 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ ++L LV+ +A K+ N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ +
Sbjct: 37  LITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEAS 96

Query: 508 ITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVE 561
           +   I      ++I      R     + +  +R+     RE   +E    I+ +L++  E
Sbjct: 97  MKDFILKSWSLVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLSKEEIKAISNELSVSEE 156

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN----LRETT- 613
            V ++   L    + ++    IGD+    L D I   N VS  + A Q +    L+ET  
Sbjct: 157 DVVQMSYRLACKDQSLNNCIKIGDDSKKELQDMIPC-NLVSQ-EVAYQNHEEKALKETIL 214

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +  LASL  R   +   R+ +  NT  TL+E+ K++CV+RERIRQ+  +A+ K+K   +S
Sbjct: 215 SNALASLNERSRDIFISRY-LSENT-QTLDELSKKYCVSRERIRQLAEQAMSKVKQHIKS 272

Query: 674 KKLR 677
           + L+
Sbjct: 273 ESLK 276


>gi|224533396|ref|ZP_03673990.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
 gi|224513561|gb|EEF83918.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
          Length = 266

 Score =  110 bits (274), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 74/258 (28%), Positives = 145/258 (56%), Gaps = 10/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS+     I+  E   +   +++G  +A   K +M+ ANLRLV+ + K+Y  +GL+  D
Sbjct: 13  LKSVREHKLITHEEEIKLAGQIQRGNAKA---KNKMINANLRLVLKIIKRYAGKGLKIED 69

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I ++
Sbjct: 70  LIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQI 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +   + ++ P  EEI K+  +      K++   ++  SL+  I   + S L +  
Sbjct: 130 ----NKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNLY 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREER-VLRMRFGIGMNTDH-TLEEVGKQFC 650
           ED N+ +P  +  Q +  +    +L + +  +ER +++ R+ +  +    TL+++  +  
Sbjct: 186 ED-NSFNPEITLEQDSTLKHLNYILETKSNEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ E +RQIE + ++KLK
Sbjct: 245 ISSETVRQIEKRVLKKLK 262


>gi|121535758|ref|ZP_01667560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121305657|gb|EAX46597.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 243

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 127/236 (53%), Gaps = 10/236 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++ +     AK+ ++E N+ LV S+  ++ NRG ++ DL Q G IGLMKA E+FD    
Sbjct: 11  IKRAQAGDKQAKEYILEHNVNLVRSIVHRFLNRGYEWDDLFQIGCIGLMKAIERFDLNFN 70

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  V   I R I D + T ++   +++  ++V RT  R+ + + REPT  E+A
Sbjct: 71  VKFSTYAVPMVIGEIRRFIRDDNPT-KVSRPVKELAYRVYRTQERLQSLLGREPTIHEVA 129

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+LA+  + +   L+  + P SL      +D    GD I   + ++  D    A   +  
Sbjct: 130 KELALAPQEIVSALEAMQPPASLFEQAYHDD----GDPISRLDQIAQCDGQDNAYFEKLA 185

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R VL+ L P+E  V+ +RF      D T  E+     +++ ++ +IE +A+R ++
Sbjct: 186 LREVLSRLPPKERYVIHLRFF----EDKTQAEIANMIGLSQVQVSRIEKQALRLIR 237


>gi|219670064|ref|YP_002460499.1| sporulation sigma factor SigG [Desulfitobacterium hafniense DCB-2]
 gi|219540324|gb|ACL22063.1| RNA polymerase, sigma 28 subunit, SigG [Desulfitobacterium
           hafniense DCB-2]
          Length = 257

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 131/248 (52%), Gaps = 13/248 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S ++ + +    + GE EA   +++++  NLRLV+SV +++TNRG    DL Q G IGL
Sbjct: 19  LSSAKMKELFVAYQSGEKEA---REKLIYGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++   ++ N
Sbjct: 76  MKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDQLVN 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPT  EIA KL +P E V   L   +EPISL  PI  +     GD I   + +   
Sbjct: 135 ECSREPTVSEIADKLTLPREEVIFALDAIQEPISLFEPIYHDG----GDPIFVMDQIGDE 190

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +  + L     R  L  L+ RE+ +L +RF  G       +E+G    +++ ++ ++E
Sbjct: 191 KHSDNSWLEGIAVREALRRLSEREKLILSLRFFHGKTQMEVADEIG----ISQAQVSRLE 246

Query: 661 AKAIRKLK 668
             A+  ++
Sbjct: 247 KAALGHMR 254


>gi|291484084|dbj|BAI85159.1| sporulation sigma factor SigG [Bacillus subtilis subsp. natto
           BEST195]
          Length = 237

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 126/227 (55%), Gaps = 14/227 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 16  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPM 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  +EPT E+IAK L +P E +
Sbjct: 76  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEI 134

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI ++  D  ++ D I D +N  S     +   L+E   R    L
Sbjct: 135 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNTDSQWIEELA--LKEGMRR----L 188

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 189 NDREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 231


>gi|89895640|ref|YP_519127.1| sporulation sigma factor SigG [Desulfitobacterium hafniense Y51]
 gi|89335088|dbj|BAE84683.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 266

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 131/248 (52%), Gaps = 13/248 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S ++ + +    + GE EA   +++++  NLRLV+SV +++TNRG    DL Q G IGL
Sbjct: 28  LSSAKMKELFVAYQSGEKEA---REKLIYGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGL 84

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++   ++ N
Sbjct: 85  MKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDQLVN 143

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPT  EIA KL +P E V   L   +EPISL  PI  +     GD I   + +   
Sbjct: 144 ECSREPTVSEIADKLTLPREEVIFALDAIQEPISLFEPIYHDG----GDPIFVMDQIGDE 199

Query: 602 DSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +  + L     R  L  L+ RE+ +L +RF  G       +E+G    +++ ++ ++E
Sbjct: 200 KHSDNSWLEGIAVREALRRLSEREKLILSLRFFHGKTQMEVADEIG----ISQAQVSRLE 255

Query: 661 AKAIRKLK 668
             A+  ++
Sbjct: 256 KAALGHMR 263


>gi|190571331|ref|YP_001975689.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357603|emb|CAQ55044.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 297

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 79/244 (32%), Positives = 134/244 (54%), Gaps = 18/244 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ ++L LV+ +A K+ N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ +
Sbjct: 53  LITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEAS 112

Query: 508 ITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVE 561
           +   I      ++I      R     + +  +R+     RE   +E    I+ +L++  E
Sbjct: 113 MKDFILKSWSLVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLSKEEIKAISNELSVSEE 172

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN----LRETT- 613
            V ++   L    + ++    IGD+    L D I   N VS  + A Q +    L+ET  
Sbjct: 173 DVVQMSYRLACKDQSLNNCIKIGDDSKKELQDMIPC-NLVSQ-EVAYQNHEEKALKETIL 230

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +  LASL  R   +   R+ +  NT  TL+E+ K++CV+RERIRQ+  +A+ K+K   +S
Sbjct: 231 SNALASLNERSRDIFISRY-LSENT-QTLDELSKKYCVSRERIRQLAEQAMSKVKQHIKS 288

Query: 674 KKLR 677
           + L+
Sbjct: 289 ESLK 292


>gi|138894663|ref|YP_001125116.1| sporulation sigma factor SigG [Geobacillus thermodenitrificans
           NG80-2]
 gi|134266176|gb|ABO66371.1| Sporulation-specific sigma factor [Geobacillus thermodenitrificans
           NG80-2]
          Length = 264

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 142/265 (53%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+ EA   ++++V  NLRLV+SV +++ N
Sbjct: 8   RNKVEICGVDTSKLPVLKNEEMRELFQRMHEGDLEA---REKLVNGNLRLVLSVIQRFNN 64

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 65  RGEFVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 123

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+  +  +EP+ EEIAK+L +  E V   L   ++P+SL  PI ++  
Sbjct: 124 RDIAYKALQVRERLMGETAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGG 183

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D +N  S     I   L+E   R    L  RE+ ++R RF  G       
Sbjct: 184 DPIYVMDQLSDERNRDSQWIEEIA--LKEGLRR----LNEREKMIIRKRFFQGKTQMEVA 237

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AIR++
Sbjct: 238 EEIG----ISQAQVSRLEKAAIRQM 258


>gi|16078597|ref|NP_389416.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309407|ref|ZP_03591254.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313732|ref|ZP_03595537.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318656|ref|ZP_03599950.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322929|ref|ZP_03604223.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321315298|ref|YP_004207585.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
 gi|133475|sp|P19940|RPSG_BACSU RecName: Full=RNA polymerase sigma-G factor; AltName: Full=Stage
           III sporulation protein G
 gi|143430|gb|AAA22703.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|580764|emb|CAA40771.1| sigma-G factor [Bacillus subtilis subsp. subtilis str. 168]
 gi|2633906|emb|CAB13407.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|320021572|gb|ADV96558.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
          Length = 260

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 126/227 (55%), Gaps = 14/227 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  +EPT E+IAK L +P E +
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEI 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI ++  D  ++ D I D +N  S     +   L+E   R    L
Sbjct: 158 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNTDSQWIEELA--LKEGMRR----L 211

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 212 NDREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 254


>gi|196247722|ref|ZP_03146424.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196212506|gb|EDY07263.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 259

 Score =  109 bits (273), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 142/265 (53%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+ EA   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFQRMHEGDLEA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+  +  +EP+ EEIAK+L +  E V   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVRERLMGETAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D +N  S     I   L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 DPIYVMDQLSDERNRDSQWIEEIA--LKEGLRR----LNEREKMIIRKRFFQGKTQMEVA 232

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AIR++
Sbjct: 233 EEIG----ISQAQVSRLEKAAIRQM 253


>gi|34733392|gb|AAP82769.1| sigma 70 [Hydrogenobacter hydrogenophilus]
          Length = 310

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/98 (52%), Positives = 70/98 (71%), Gaps = 1/98 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L +  E+K +  E G    E   ++ ++++G  + + AK+ MV+ NLRLV+S+AK Y NR
Sbjct: 214 LSLEKEVKELRKEKGSFPEELDRVMHIIKEGRTKVTKAKQVMVKCNLRLVVSIAK-YVNR 272

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           GL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW+
Sbjct: 273 GLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWI 310



 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 29/44 (65%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           DPV++YLREMG I LL RE EI  AK+IE GR +M   L  +  
Sbjct: 1   DPVKLYLREMGRIPLLKREEEIMYAKQIEIGRKIMRRGLLRTSF 44


>gi|328948495|ref|YP_004365832.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
 gi|328448819|gb|AEB14535.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
          Length = 349

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 121/251 (48%), Gaps = 12/251 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDW 490
           +++ + +     A   M E  LR V+ ++  +       F +  Q G IGL++A + FD 
Sbjct: 109 NLIYEAQSGNVYAFNRMTEMYLRGVLRISYNFAKENYCDFEEAFQNGTIGLIRAIKNFDV 168

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F++Y    V   + R  + ++    +PVH   K  + +     +S  + +  TPE
Sbjct: 169 TSPNSFASYYSLSVLSEMQRKYSVKNSFFDLPVHFSQKTFEFLGI---ISKYLAKGKTPE 225

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E     ++ +      L+I  +      P  D D     +F  D   +   D  I  +L+
Sbjct: 226 E-----SIGIISDDFYLEINPKLKMYFLPYLDLDAISYENFAFD---IHIEDDIIYESLK 277

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L  RE +VL MRFG+      TLEEVGK + V+RERIRQIE KA+R+L+HP
Sbjct: 278 EQLNEVLHTLPERERKVLEMRFGLNNLKQMTLEEVGKYYNVSRERIRQIEKKALRRLRHP 337

Query: 671 SRSKKLRSFLD 681
            R+  LR ++D
Sbjct: 338 HRASGLRDYID 348


>gi|229541192|ref|ZP_04430252.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
 gi|229325612|gb|EEN91287.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
          Length = 258

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/267 (30%), Positives = 143/267 (53%), Gaps = 25/267 (9%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R ++  +  G+  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRDLLKKMHAGDASA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLNQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++ +   +EPT EEIA++L +P E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLMSATSKEPTTEEIARELDVPHEDIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIED-KNAVSPL--DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D  ++ D + D KN  S    + A+Q  +R         L  RE+ ++R RF  G     
Sbjct: 179 DPIYVMDQVSDEKNKDSQWIEEIALQEGMRR--------LNEREKMIIRKRFFQGKTQME 230

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKL 667
             EE+G    +++ ++ ++E  AI+++
Sbjct: 231 VAEEIG----ISQAQVSRLEKAAIKQM 253


>gi|56419663|ref|YP_146981.1| sporulation sigma factor SigG [Geobacillus kaustophilus HTA426]
 gi|261419325|ref|YP_003253007.1| sporulation sigma factor SigG [Geobacillus sp. Y412MC61]
 gi|297530705|ref|YP_003671980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766141|ref|YP_004131642.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
 gi|56379505|dbj|BAD75413.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-G) [Geobacillus kaustophilus HTA426]
 gi|261375782|gb|ACX78525.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC61]
 gi|297253957|gb|ADI27403.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111007|gb|ADU93499.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
          Length = 259

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 143/265 (53%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+ EA   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFRRMHEGDLEA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EP+ EEIAK+L +  E V   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVRERLMSETAKEPSTEEIAKELGVAHEEVVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D +N  S     I   L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 DPIYVMDQLSDERNRDSQWIEEIA--LKEGLRR----LNEREKMIIRKRFFQGKTQMEVA 232

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AIR++
Sbjct: 233 EEIG----ISQAQVSRLEKAAIRQM 253


>gi|330936784|gb|EGH40944.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 176

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/91 (50%), Positives = 66/91 (72%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   R  +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD 
Sbjct: 83  VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDP 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
             G++FSTYA WW++Q I R+I +Q+ TIR+
Sbjct: 143 ERGFRFSTYATWWIRQTIERAIMNQTRTIRL 173


>gi|160892497|ref|ZP_02073287.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
 gi|156865538|gb|EDO58969.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
          Length = 258

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 123/232 (53%), Gaps = 22/232 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV ++++N      DL Q G IGL+KA + FD  L  KFSTYA+  
Sbjct: 38  ARETFIKGNLRLVLSVIQRFSNSNENPDDLFQVGCIGLIKAIDNFDRSLNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +     R + D + +IR+   +RD  +K + T   +  K+ REPT +EIAK++ +  E +
Sbjct: 98  ILGECRRYLRDNN-SIRVSRSLRDIAYKAIYTKDALLKKLDREPTVDEIAKEIDVAPEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L     P+SL  P+  E  DT ++ D + DK     N V  +      +L+E     
Sbjct: 157 TTALDAISTPVSLYEPVYQEGGDTLYIVDQLSDKKNKEENWVENI------SLKEA---- 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  RE  +LR+RF  G     T  EV  +  +++ ++ +IE  AI+ LK
Sbjct: 207 MKKLNEREYNILRLRFFEG----KTQTEVASEIAISQAQVSRIEKSAIKSLK 254


>gi|121535240|ref|ZP_01667054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306125|gb|EAX47053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 257

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 83/269 (30%), Positives = 144/269 (53%), Gaps = 25/269 (9%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           I N+++   V T     +S ++ R +  ++++G  EA   +++++  NLRLV+SV +++ 
Sbjct: 2   IVNKVEICGVNTAKLPVLSANKMRELFEIMQQGNPEA---REQLIYGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---G 581
           MRD  +K ++    + +K  REP+  EIA +L +P E +   L   +EP+SL  PI   G
Sbjct: 118 MRDIAYKALQVRDALVSKFSREPSINEIADELKIPREEIIFALDAIQEPVSLFEPIYHDG 177

Query: 582 DEDTSHLGDFIEDKNA-VSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
            +    +    +DKN  ++ L+  AI+  LR+        L+ RE+ +L +RF  G    
Sbjct: 178 GDPIFVMDQISDDKNQDMNWLEGVAIKEALRK--------LSDREKHILTLRFFEGKTQM 229

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +E+G    +++ ++ ++E  A+  ++
Sbjct: 230 EVADEIG----ISQAQVSRLEKAALGHMR 254


>gi|253681759|ref|ZP_04862556.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
 gi|253561471|gb|EES90923.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
          Length = 257

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 136/247 (55%), Gaps = 19/247 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +R G+     ++++ +  NLRLV+SV +++ NRG    DL Q G IGL+KA 
Sbjct: 23  EMKELLIKMRDGDY---FSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  +K ++   R+ NK  +
Sbjct: 80  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQVRDRLINKDNK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLD 602
           +P   +IAK+L +P E V   L   ++P+SL  PI  +  D  ++ D I D KNA    D
Sbjct: 139 DPNVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDALYVMDQISDSKNAD---D 195

Query: 603 SAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           S I+  +++E   R    L  RE+ +L MRF  G     T  EV  +  +++ ++ ++E 
Sbjct: 196 SWIENISIKEAMKR----LNKREKLILNMRFFQG----RTQMEVADEIGISQAQVSRLEK 247

Query: 662 KAIRKLK 668
            A++ ++
Sbjct: 248 TALKHMR 254


>gi|296331109|ref|ZP_06873583.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674264|ref|YP_003865936.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151753|gb|EFG92628.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412508|gb|ADM37627.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 260

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 126/227 (55%), Gaps = 14/227 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  +EPT E+IAK L +P E +
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEI 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI ++  D  ++ D I D +N  S     +   L+E   R    L
Sbjct: 158 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNKDSQWIEELA--LKEGMRR----L 211

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 212 NDREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 254


>gi|304404022|ref|ZP_07385684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347000|gb|EFM12832.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 272

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 144/269 (53%), Gaps = 23/269 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + ++     A  A++++V  NLRLV+SV +++ N
Sbjct: 15  RNKVEICGVDTSKLPVLTNAEMRELFTALQTRNERA--AREKLVNGNLRLVLSVIQRFNN 72

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 73  RGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 131

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++    ++N   REPT  EI++ L +P E V   L   ++P+SL  PI   G 
Sbjct: 132 RDIAYKALQVRDSLTNANSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGG 191

Query: 583 EDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    +    +DKN  +S ++   +  LRE     +  L  RE+ +L MRF  G     T
Sbjct: 192 DPIYVMDQISDDKNKDISWIE---EIALREA----MHKLNDREKMILSMRFFEG----KT 240

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
             EV  +  +++ ++ ++E  AI+++ KH
Sbjct: 241 QMEVADEIGISQAQVSRLEKSAIQQMQKH 269


>gi|168180582|ref|ZP_02615246.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|168182609|ref|ZP_02617273.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|170757556|ref|YP_001782076.1| sporulation sigma factor SigG [Clostridium botulinum B1 str. Okra]
 gi|170761503|ref|YP_001787848.1| sporulation sigma factor SigG [Clostridium botulinum A3 str. Loch
           Maree]
 gi|187778872|ref|ZP_02995345.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226949887|ref|YP_002804978.1| sporulation sigma factor SigG [Clostridium botulinum A2 str. Kyoto]
 gi|237795971|ref|YP_002863523.1| sporulation sigma factor SigG [Clostridium botulinum Ba4 str. 657]
 gi|169122768|gb|ACA46604.1| RNA polymerase sigma-G factor [Clostridium botulinum B1 str. Okra]
 gi|169408492|gb|ACA56903.1| RNA polymerase sigma-G factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182668579|gb|EDT80558.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|182674221|gb|EDT86182.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|187772497|gb|EDU36299.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226842131|gb|ACO84797.1| RNA polymerase sigma-G factor [Clostridium botulinum A2 str. Kyoto]
 gi|229263792|gb|ACQ54825.1| RNA polymerase sigma-G factor [Clostridium botulinum Ba4 str. 657]
          Length = 257

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 129/245 (52%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +R GE E    ++E ++ NLRLV+SV K++ NRG    DL Q G IGL+KA 
Sbjct: 23  EMKKLLVRIRNGETEC---REEFIQGNLRLVLSVIKRFNNRGENVDDLFQVGCIGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  +K ++   ++     +
Sbjct: 80  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQARDKLIKNNNK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D   + D I D   V   D 
Sbjct: 139 EPTVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIFVMDQISDTKNV---DE 195

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               N+  +    +  L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 196 NWIENI--SIKEAMKKLNDREKLILNLRFFDG----RTQMEVADEIGISQAQVSRLEKTA 249

Query: 664 IRKLK 668
           ++ ++
Sbjct: 250 LKHMR 254


>gi|312794092|ref|YP_004027015.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181232|gb|ADQ41402.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 255

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 125/226 (55%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  N  ++EPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYINNNQKEPTLEEIAKELSVTKEEL 154

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EPISL  P+  + T  +  ++ +K  +    S     L E + +  L+ LT 
Sbjct: 155 VFALDSIQEPISLYEPVFQDSTDTM--YVVEK--LCDHKSCENVWLEEISLKDALSRLTK 210

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +R+  G     T  EV +   +++ ++ +IE  AI  +K
Sbjct: 211 REKEILYLRYYKG----KTQMEVARIVGISQAQVSRIEKSAIGHIK 252


>gi|251797866|ref|YP_003012597.1| sporulation sigma factor SigG [Paenibacillus sp. JDR-2]
 gi|247545492|gb|ACT02511.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. JDR-2]
          Length = 260

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 145/269 (53%), Gaps = 23/269 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + ++     A  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFTALQTQNEWA--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++    ++N+  REPT  EI++ L +P E V   L   ++P+SL  PI   G 
Sbjct: 120 RDIAYKALQVRDSLTNQNSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 583 EDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    +    +DKN  VS ++   +  LRE     +  L  RE+ +L MRF  G     T
Sbjct: 180 DPIYVMDQISDDKNKDVSWIE---EIALREA----MHKLNDREKMILSMRFFEG----KT 228

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
             EV  +  +++ ++ ++E  AI+++ KH
Sbjct: 229 QMEVADEIGISQAQVSRLEKSAIQQMQKH 257


>gi|220917834|ref|YP_002493138.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955688|gb|ACL66072.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 322

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 121/236 (51%), Gaps = 11/236 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G K S+YA WW
Sbjct: 69  AAYRLVASNLRLVVKIAHEYRRTAFQLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWW 128

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I R I +    +++     + K+   +   R        EPTP  +AK L +  + 
Sbjct: 129 IRAYIIRFIMENWRLVKLGTTQAQRKLFFNLSKEREKLLARGIEPTPRLLAKNLQVEEKD 188

Query: 563 VRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSP----LDSAIQANLRETTT 614
           V ++  ++  + +SL+ P+   GD+   +  D + D    SP     D  ++   RE   
Sbjct: 189 VEEMSARMAADDLSLDAPVGTEGDDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLD 248

Query: 615 RVLASLTPREER-VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +LT  +ER +   R      T   TL+EVG  F +TRER RQIEAK   +L+
Sbjct: 249 AFSGTLTDEKERYIFEHRLLPPDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLR 304


>gi|288958414|ref|YP_003448755.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288910722|dbj|BAI72211.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 323

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/241 (33%), Positives = 130/241 (53%), Gaps = 25/241 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLVI +A+ +   GL  +DL+ EGN+GLM+AA+KFD   G++F+TYA WW
Sbjct: 73  ALEQLVGSHLRLVIKIARGFGGYGLSLVDLVAEGNVGLMQAAQKFDPQRGFRFATYATWW 132

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE---EIAKKL 556
           ++ AI   I      +++      K  K+    RR+ +++    + + +PE    IA +L
Sbjct: 133 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKSQMAELEQGDLSPETVATIAAEL 190

Query: 557 AMP-VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +P  E V    ++     SL+  +  D +T+ L    +D+    P   A+ A+  E   
Sbjct: 191 DVPETEVVEMNRRLAANDSSLDATLSTDGETNWLELLADDR----PTQDAMLADADELAL 246

Query: 615 R------VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           R       L  L PRE R+L   F   +  D  TLE + +QF V+RER+RQIE +A  KL
Sbjct: 247 RRRLVGQALDRLDPRERRIL---FERRLKDDPSTLEALSQQFSVSRERVRQIEVRAFEKL 303

Query: 668 K 668
           +
Sbjct: 304 Q 304


>gi|197123044|ref|YP_002134995.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|196172893|gb|ACG73866.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
          Length = 322

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 121/236 (51%), Gaps = 11/236 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G K S+YA WW
Sbjct: 69  AAYRLVASNLRLVVKIAHEYRRTAFQLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWW 128

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I R I +    +++     + K+   +   R        EPTP  +AK L +  + 
Sbjct: 129 IRAYIIRFIMENWRLVKLGTTQAQRKLFFNLSKEREKLLARGIEPTPRLLAKNLQVEEKD 188

Query: 563 VRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSP----LDSAIQANLRETTT 614
           V ++  ++  + +SL+ P+   GD+   +  D + D    SP     D  ++   RE   
Sbjct: 189 VEEMSARMAADDLSLDAPVGTEGDDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLD 248

Query: 615 RVLASLTPREER-VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +LT  +ER +   R      T   TL+EVG  F +TRER RQIEAK   +L+
Sbjct: 249 AFSGTLTDEKERYIFEHRLLPPDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLR 304


>gi|332653369|ref|ZP_08419114.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
 gi|332518515|gb|EGJ48118.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
          Length = 256

 Score =  108 bits (271), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 123/227 (54%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++  NLRLV+SV  K+ NRG    DL Q G IGL+KA + FD  L  KFSTY +  
Sbjct: 37  AREELIAGNLRLVLSVIHKFANRGENVDDLFQVGCIGLIKAIDNFDTSLDVKFSTYGVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S  +R+   MRD  +KV++       + ++EP+ EEIA+ L +  E V
Sbjct: 97  IVGEIRRYLRDNS-AMRVSRAMRDTAYKVLQAKESYMAQHQKEPSVEEIAQMLGIKREEV 155

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L    +P+SL  PI  +  DT  + D ++D      +       L+E  +R    L+
Sbjct: 156 VFALDAILDPVSLYEPIYSDSGDTVCVMDQVKDSRNTDEMWLE-HIALKEAVSR----LS 210

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+++L MRF        T  EV ++  +++ ++ ++E  A+R+++
Sbjct: 211 EREQKILAMRF----YQSKTQVEVSREIGISQAQVSRLEKNALRQIR 253


>gi|308069872|ref|YP_003871477.1| RNA polymerase sigma-G factor (stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
 gi|305859151|gb|ADM70939.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
          Length = 260

 Score =  108 bits (271), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 146/272 (53%), Gaps = 22/272 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + +++    +  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFTSLQQNNERS--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++    ++N   REPT  EI++ L +P E V   L   ++P+SL  PI   G 
Sbjct: 120 RDIAYKALQVRDSLTNLNSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 583 EDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    +    +D+N  VS ++   +  LRE   R    L  RE+ +L MRF  G     T
Sbjct: 180 DPIYVMDQISDDRNKDVSWIE---EIALREAMHR----LGQREKMILSMRFYEG----KT 228

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             EV  +  +++ ++ ++E  AI++++   +S
Sbjct: 229 QMEVADEIGISQAQVSRLEKSAIQQMQKHVKS 260


>gi|95929333|ref|ZP_01312076.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134449|gb|EAT16105.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
          Length = 282

 Score =  108 bits (271), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 77/234 (32%), Positives = 129/234 (55%), Gaps = 15/234 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ANLR V+ +A +Y   GL+ +DL+QEGNIGLMKA +KFD     +  +YA+WW
Sbjct: 44  AAHKLVCANLRFVVKIAYEYQAYGLKMIDLVQEGNIGLMKAIKKFDPDRNIRLISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I +    ++I     R K+   ++  R    K+  +    EIA++L +  + 
Sbjct: 104 IRAYIHNYIINAWSLVKIGTTQARKKLFFKLKQTRDALQKMGNDADHAEIARQLNVSTDE 163

Query: 563 VRKV-LKITKEPISLE---TPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRV- 616
           V ++ +++     SL+   TP  D  TSHL   ++ DK+    L      +L  TT RV 
Sbjct: 164 VAEMSVRLGGRDSSLDGQLTP--DSTTSHLDTLVDHDKDQEQRLIELEHESL--TTHRVQ 219

Query: 617 --LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ L  RE+ ++  R  I  +   TL+++  Q+ +++ER+RQ+E +A+ KLK
Sbjct: 220 QALSHLNEREQHIVHSR--ILQDDKATLQDLADQYGISKERVRQLEKRALEKLK 271


>gi|126700256|ref|YP_001089153.1| sporulation sigma factor SigG [Clostridium difficile 630]
 gi|254976235|ref|ZP_05272707.1| sporulation sigma factor SigG [Clostridium difficile QCD-66c26]
 gi|255093622|ref|ZP_05323100.1| sporulation sigma factor SigG [Clostridium difficile CIP 107932]
 gi|255101810|ref|ZP_05330787.1| sporulation sigma factor SigG [Clostridium difficile QCD-63q42]
 gi|255307677|ref|ZP_05351848.1| sporulation sigma factor SigG [Clostridium difficile ATCC 43255]
 gi|255315370|ref|ZP_05356953.1| sporulation sigma factor SigG [Clostridium difficile QCD-76w55]
 gi|255518035|ref|ZP_05385711.1| sporulation sigma factor SigG [Clostridium difficile QCD-97b34]
 gi|255651151|ref|ZP_05398053.1| sporulation sigma factor SigG [Clostridium difficile QCD-37x79]
 gi|255656619|ref|ZP_05402028.1| sporulation sigma factor SigG [Clostridium difficile QCD-23m63]
 gi|260684217|ref|YP_003215502.1| sporulation sigma factor SigG [Clostridium difficile CD196]
 gi|260687876|ref|YP_003219010.1| sporulation sigma factor SigG [Clostridium difficile R20291]
 gi|296449925|ref|ZP_06891689.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296878307|ref|ZP_06902315.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
 gi|306521001|ref|ZP_07407348.1| sporulation sigma factor SigG [Clostridium difficile QCD-32g58]
 gi|115251693|emb|CAJ69528.1| RNA polymerase sigma-G factor [Clostridium difficile]
 gi|260210380|emb|CBA64761.1| RNA polymerase sigma-G factor [Clostridium difficile CD196]
 gi|260213893|emb|CBE05925.1| RNA polymerase sigma-G factor [Clostridium difficile R20291]
 gi|296261195|gb|EFH08026.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296430605|gb|EFH16444.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
          Length = 257

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 131/246 (53%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + ++  ++ G+ EA   +++ V  NLRLV+SV KK+ NRG    DL Q G IGL+KA 
Sbjct: 23  QMKELLLQIKNGDEEA---RQQFVRGNLRLVLSVIKKFNNRGENIDDLFQIGCIGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     +FSTYA+  +   I R + D +  IR+   ++D  +K ++   R+     +
Sbjct: 80  DNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLKDIAYKALQVRERLIRTNSK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  EIAK+L + VE V   L   ++PISL  P+  +  D   + D ++DK        
Sbjct: 139 EPTVSEIAKELELEVESVVMALDAIQDPISLFDPVYQDNGDAIFVMDQVQDKKDTD---- 194

Query: 604 AIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  L+E + +  +  L  RE+ VL +RF  G       +E+G    +++ ++ +IE  
Sbjct: 195 --ENWLQEISLKEAIKKLNSREKLVLDLRFYKGRTQIEVADEIG----ISQAQVSRIEKN 248

Query: 663 AIRKLK 668
           A++ ++
Sbjct: 249 ALKNMR 254


>gi|148380489|ref|YP_001255030.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933176|ref|YP_001384712.1| sporulation sigma factor SigG [Clostridium botulinum A str. ATCC
           19397]
 gi|153936833|ref|YP_001388233.1| sporulation sigma factor SigG [Clostridium botulinum A str. Hall]
 gi|153938804|ref|YP_001391829.1| sporulation sigma factor SigG [Clostridium botulinum F str.
           Langeland]
 gi|148289973|emb|CAL84086.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929220|gb|ABS34720.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152932747|gb|ABS38246.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. Hall]
 gi|152934700|gb|ABS40198.1| RNA polymerase sigma-G factor [Clostridium botulinum F str.
           Langeland]
 gi|295319855|gb|ADG00233.1| RNA polymerase sigma-G factor [Clostridium botulinum F str. 230613]
 gi|322806802|emb|CBZ04371.1| RNA polymerase sporulation specific sigma factor SigG [Clostridium
           botulinum H04402 065]
          Length = 257

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 76/245 (31%), Positives = 129/245 (52%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +R GE E    ++E ++ NLRLV+SV K++ NRG    DL Q G IGL+KA 
Sbjct: 23  EMKKLLVRIRNGETEC---REEFIQGNLRLVLSVIKRFNNRGENVDDLFQVGCIGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  +K ++   ++     +
Sbjct: 80  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQARDKLIKNNNK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D   + D I D      +D 
Sbjct: 139 EPTVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIFVMDQISD---TKNIDE 195

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               N+  +    +  L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 196 NWIENI--SIKEAMKKLNDREKLILNLRFFDG----RTQMEVADEIGISQAQVSRLEKTA 249

Query: 664 IRKLK 668
           ++ ++
Sbjct: 250 LKHMR 254


>gi|212639646|ref|YP_002316166.1| sporulation sigma factor SigG [Anoxybacillus flavithermus WK1]
 gi|212561126|gb|ACJ34181.1| DNA-directed RNA polymerase specialized sigma subunit sigG
           [Anoxybacillus flavithermus WK1]
          Length = 259

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 142/265 (53%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ G+  A   +++++  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFRQMQAGDISA---REKLITGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   +M ++  +EPT EEIAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKMMSETAKEPTAEEIAKILDVPHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D KN  +     I   L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 DPIYVMDQLSDEKNRDTNWIEEIA--LKEGLRR----LNEREKMIIRKRFFQGKTQMEVA 232

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AI+++
Sbjct: 233 EEIG----ISQAQVSRLEKAAIKQM 253


>gi|332982148|ref|YP_004463589.1| RNA polymerase sigma subunit RpsG/SigG [Mahella australiensis 50-1
           BON]
 gi|332699826|gb|AEE96767.1| RNA polymerase, sigma subunit, RpsG/SigG [Mahella australiensis
           50-1 BON]
          Length = 257

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 121/227 (53%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+S+ +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREEFIRGNLRLVLSIIQRFNNRGEHVDDLFQVGCIGLIKAIDNFDLGQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   ++  +  +EPT EEIAK + +P E V
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKALQVREQLVAQNGKEPTVEEIAKAMELPAEEV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RVLASLT 621
              +   ++PISL  P+  +     GD I   + VS  D     N  ET      +  L+
Sbjct: 157 VFAMDAIQDPISLFEPVYHDG----GDAIYVMDQVSD-DKNQDDNWLETIALKEAMQKLS 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L MRF  G       EE+G    +++ ++ ++E  A+  ++
Sbjct: 212 EREKTILAMRFFQGRTQMEVAEEIG----ISQAQVSRLEKSALSHMR 254


>gi|311068054|ref|YP_003972977.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
 gi|310868571|gb|ADP32046.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
          Length = 260

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 126/229 (55%), Gaps = 18/229 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  +EPT E+IAK L +P E +
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEI 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLA 618
              L   ++P+SL  PI ++  D  ++ D I D   K+     + A++  +R        
Sbjct: 158 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNKDTQWIEELALKEGMRR------- 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L  RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 211 -LNDREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 254


>gi|261405674|ref|YP_003241915.1| sporulation sigma factor SigG [Paenibacillus sp. Y412MC10]
 gi|315646040|ref|ZP_07899161.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|329922674|ref|ZP_08278226.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
 gi|261282137|gb|ACX64108.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. Y412MC10]
 gi|315278801|gb|EFU42115.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|328942016|gb|EGG38299.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
          Length = 260

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 127/231 (54%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMKA + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   +++N   REPT  EI++ L +P E V
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDQLTNANSREPTIFEISEALNVPKEDV 157

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLAS 619
              L   ++P+SL  PI   G +    +    +DKN  VS ++   +  LRE     +  
Sbjct: 158 VFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDDKNKDVSWIE---EIALREA----MHK 210

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
           L  RE+ +L MRF  G     T  EV  +  +++ ++ ++E  AI+++ KH
Sbjct: 211 LGQREKMILSMRFYEG----KTQMEVADEIGISQAQVSRLEKSAIKQMQKH 257


>gi|326791409|ref|YP_004309230.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
 gi|326542173|gb|ADZ84032.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
          Length = 257

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 127/230 (55%), Gaps = 18/230 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 38  AREEYIRGNLRLVLSVIQRFNNRGEHVDDLFQVGCIGLIKAIDNFDVTQNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++T  +++ K  +EPT +EIA +L +  E +
Sbjct: 98  IIGEIRRYLRDNNA-IRVSRSLRDTAYKALQTKEQLTRKNAKEPTVQEIADELGIKKEDI 156

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQAN--LRETTTRVLA 618
              L   ++PISL  P+   + DT ++ D + +DKN     D     N  L+E   R+  
Sbjct: 157 VFALDAIQDPISLFEPVYHDESDTLYIMDQVSDDKNQ----DDVWLENIALKEAMKRI-- 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               RE+++L +RF  G     T  EV  +  +++ ++ ++E  A++ +K
Sbjct: 211 --NDREKQILMLRFFAG----KTQMEVANEIGISQAQVSRLEKTALKHMK 254


>gi|325288838|ref|YP_004265019.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964239|gb|ADY55018.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 127/228 (55%), Gaps = 16/228 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++++++ NLRLV+SV ++++NRG    DL Q G IGLMKA + FD     KFSTYA+  +
Sbjct: 39  REQLIKGNLRLVLSVIQRFSNRGEHVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMI 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R + D + +IR+   +RD  +K ++   +++ +  REPT +EIA KL  P E V 
Sbjct: 99  IGEIRRYLRDNN-SIRVSRSLRDIAYKALQIRDKLATECSREPTIQEIAAKLETPQEEVI 157

Query: 565 KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSP--LDSAIQANLRETTTRVLASL 620
             L   +EP+SL  PI  +  D  ++ D I D        L+S    +++E   R    L
Sbjct: 158 LALDAIQEPVSLFEPIYHDGGDPIYVMDQIGDHKQSDRIWLES---LSIKEGIER----L 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+R++ +RF  G       EE+G    +++ ++ ++E  A++ ++
Sbjct: 211 GEREKRIISLRFFQGKTQMEVAEEIG----ISQAQVSRLEKAALKHMR 254


>gi|168335364|ref|ZP_02693458.1| sporulation sigma factor SigG [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 243

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 73/221 (33%), Positives = 115/221 (52%), Gaps = 13/221 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H+  ++  G+   ++A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + F
Sbjct: 26  HLFELIGAGD---NMAREEYIRGNLRLVLSVIQRFNNRGEHVDDLFQVGCIGLIKAIDNF 82

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G KFSTYA+  +   I R + D +  IR+   +RD  +K ++   ++  +  +EPT
Sbjct: 83  DTTQGVKFSTYAVPMIIGEIRRYLRDNNA-IRVSRSLRDTAYKALQVKEKLLRQNSKEPT 141

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI--- 605
            EEIA  L +  E +   L   ++PISL  P+  +D   L  FI D+ +       I   
Sbjct: 142 IEEIAAVLEIATENIVFALDAIQDPISLFEPVYHDDGDAL--FIMDQVSDEKSQDDIWLE 199

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              L+E   R    L  RE+ +L +RF  G       +E+G
Sbjct: 200 NIALKEAMKR----LNDREKHILTLRFFAGKTQMEVADEIG 236


>gi|158320421|ref|YP_001512928.1| sporulation sigma factor SigG [Alkaliphilus oremlandii OhILAs]
 gi|158140620|gb|ABW18932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 257

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 131/245 (53%), Gaps = 13/245 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S+ R +   + KG+   + A++E ++ NLRLV+SV +++ NRG    DL Q G IGL+KA
Sbjct: 22  SQMRVLFDRIHKGD---NSAREEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGCIGLIKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     +FSTYA+  +   I R + D + +IR+   +RD  +K ++   ++ NK  
Sbjct: 79  IDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDTAYKALQVREQLINKNS 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           +EPT  +IA++L +P E V   L   ++P+SL  PI  +     GD I   + V    S 
Sbjct: 138 KEPTIAQIAEELNLPREDVVFALDAIQDPVSLFEPIYQDS----GDAIFVMDQVCDEKSE 193

Query: 605 IQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  +     R  +  L  RE+ +L +RF  G       +E+G    +++ ++ ++E  A
Sbjct: 194 DECWIDGIALREAMRKLNSREKHILSLRFFEGRTQMEVADEIG----ISQAQVSRLEKTA 249

Query: 664 IRKLK 668
           ++ ++
Sbjct: 250 LKHMR 254


>gi|86157650|ref|YP_464435.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85774161|gb|ABC80998.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 322

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 122/236 (51%), Gaps = 11/236 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G K S+YA WW
Sbjct: 69  AAYKLVASNLRLVVKIAHEYRRTAFQLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWW 128

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I R I +    +++     + K+   +   R        EPTP  +AK L +  + 
Sbjct: 129 IRAYIIRFIMENWRLVKLGTTQAQRKLFFNLSKEREKLLARGIEPTPRLLAKNLQVEEKD 188

Query: 563 VRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSP----LDSAIQANLRETTT 614
           V ++  ++  + +SL+ P+   GD+   +  D + D    +P     D  ++   RE   
Sbjct: 189 VEEMSARMAADDLSLDAPVGTEGDDGRQNRLDRLADDGGQAPDAALGDEQLRRIFREKLD 248

Query: 615 RVLASLTPREER-VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +LT  +ER +   R      T   TL+EVG  F +TRER RQIEAK   +L+
Sbjct: 249 AFSGTLTDEKERYIFEHRLLPPDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLR 304


>gi|26249145|ref|NP_755185.1| hypothetical protein c3306 [Escherichia coli CFT073]
 gi|289829787|ref|ZP_06547302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|26109552|gb|AAN81755.1|AE016765_157 Hypothetical protein c3306 [Escherichia coli CFT073]
 gi|323154962|gb|EFZ41154.1| RNA polymerase sigma factor rpoS [Escherichia coli EPECa14]
          Length = 172

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 104/163 (63%)

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 2   NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 61

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 62  TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 121

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 122 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 164


>gi|167933077|ref|ZP_02520164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [candidate
           division TM7 single-cell isolate TM7b]
          Length = 103

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 52/101 (51%), Positives = 74/101 (73%)

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GDE+ S LGDFIED++  +P +SA    L+E    +L+SL+ RE+++++MRFG+     H
Sbjct: 3   GDEEDSVLGDFIEDEDTATPEESASSQLLKEQVQGILSSLSDREQKIIKMRFGLENGKSH 62

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVG++F VTRERIRQIEAKA+ KL+    +KKL  +L+
Sbjct: 63  TLEEVGQEFAVTRERIRQIEAKALAKLRKHKDAKKLHEYLN 103


>gi|34499661|ref|NP_903876.1| RNA polymerase factor sigma-32 [Chromobacterium violaceum ATCC
           12472]
 gi|34105511|gb|AAQ61866.1| RNA polymerase sigma-32 factor [Chromobacterium violaceum ATCC
           12472]
          Length = 287

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 127/232 (54%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV ++LR+V+SV++ Y   GLQ  DLIQEGNIGLMKA ++F+   G +  ++A+ W
Sbjct: 49  AARQMVLSHLRVVVSVSRGYAGYGLQQADLIQEGNIGLMKAVKRFEPGRGVRLFSFAIHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   I      +RI      +  K+    R M +      E   + IA+ L +  E
Sbjct: 109 IKAEIHEFILRNWRLVRIATTKPQR--KLFFNLRSMKSGFSALSEQEAKSIAEDLGVKPE 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS----AIQANLRETTTRV 616
            VR++ +++T + +SL     DED+    D++ D ++  P  +    A      E     
Sbjct: 167 EVREMEIRMTGQDVSLLADSDDEDSYAPIDWLADSHS-EPTRALERRAFDMLQSEGLEYA 225

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++L PR  R++  R+ +  ++  TL E+  +F V+ ERIRQIEAKA+ K+K
Sbjct: 226 LSTLDPRSRRIVEARW-LADDSGATLHELAAEFGVSAERIRQIEAKALSKMK 276


>gi|153005405|ref|YP_001379730.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152028978|gb|ABS26746.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 357

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 81/252 (32%), Positives = 127/252 (50%), Gaps = 13/252 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR  E     A   +V +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G
Sbjct: 94  VRYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAFQLLDLVQEGNMGLMQAVKKYDPWKG 153

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR--EPTPEE 551
            K S+YA WW++  I R I +    +++      +       A+     + R  EPTP  
Sbjct: 154 VKLSSYAAWWIRAYIIRFIMENWRMVKLGTTQAQR-KLFFNLAKEREKLLARGIEPTPRL 212

Query: 552 IAKKLAMPVEGVRKVL-KITKEPISLETPI-GDEDTSHLG--DFIEDKNAVSP----LDS 603
           +AK L +  + V ++  ++  E +SL+ P+ GDED S     D +    A +P     D 
Sbjct: 213 LAKNLDVEEKDVEEMTARMAGEDLSLDAPLRGDEDGSRQTRLDRVAGDGADAPDERLGDE 272

Query: 604 AIQANLRETTTRVLASLTPREERVL--RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            ++   RE       ++   +ER +  +     G     TL+E+G +F +TRER RQIEA
Sbjct: 273 QLRRLFREKLETFSKTIRDEKERYIFDKRLLPAGGEAPLTLQEIGDRFKLTRERARQIEA 332

Query: 662 KAIRKLKHPSRS 673
           K   +L+   R+
Sbjct: 333 KLTARLRDYLRA 344


>gi|197122293|ref|YP_002134244.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196172142|gb|ACG73115.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 307

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 76/242 (31%), Positives = 121/242 (50%), Gaps = 14/242 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ANLR V+ VA +Y + G +  DLIQEGNIGLMKA +KFD   G +  +YA+WW
Sbjct: 46  AAHRLVTANLRFVVKVAYEYRSYGFRMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWW 105

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPT------PEEIAKK 555
           ++  I   I      +++      R     + RT R +  + +            ++AKK
Sbjct: 106 IRAYIQNYILKSWSLVKLGTTQAQRKLFFSLARTKRELDKRSQEHGADSDGHDANKVAKK 165

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           L +    VR++  ++    +SL+ P+GD+      DF+    A    + +     +  + 
Sbjct: 166 LRVKPGEVREMEQRMEGRDLSLDAPMGDDGGYSHVDFLPSGTASQDDELSGVQEQKVVSG 225

Query: 615 RV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RV   L  L  RE  ++ MR  +  +   TL+E+G+ F  +RER RQ+E +A  KLK   
Sbjct: 226 RVGEALGRLDQRERYIIEMR--VMSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKEEL 283

Query: 672 RS 673
           R+
Sbjct: 284 RA 285


>gi|226313413|ref|YP_002773307.1| sporulation sigma factor SigG [Brevibacillus brevis NBRC 100599]
 gi|226096361|dbj|BAH44803.1| RNA polymerase sigma-G factor [Brevibacillus brevis NBRC 100599]
          Length = 259

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 141/270 (52%), Gaps = 19/270 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++  E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLTNKEMRDLFERLQSGELAA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    ++NK  REPT  EI+++L +  E V   L   ++P+SL  PI  +  
Sbjct: 119 RDIAYKALQVRDNLTNKHSREPTIIEISQELNVAKEDVVFALDAIQDPVSLFEPIYQDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+     +    +  LRE   R    L  RE+ +L MRF  G       E
Sbjct: 179 DPIYVMDQISDEKN-KDVTWVEEIALREGMQR----LGDREKMILSMRFYEGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G    +++ ++ ++E  AI  ++   +S
Sbjct: 234 EIG----ISQAQVSRLEKAAIAHMQKHVQS 259


>gi|310642978|ref|YP_003947736.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247928|gb|ADO57495.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 260

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 146/272 (53%), Gaps = 22/272 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + +++    +  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFTSLQQNNERS--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++    ++N   REPT  EI++ L +P E V   L   ++P+SL  PI   G 
Sbjct: 120 RDIAYKALQVRDSLTNLNSREPTIFEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 583 EDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    +    +D+N  VS ++   +  LRE   R    L  RE+ +L MRF  G     T
Sbjct: 180 DPIYVMDQISDDRNKDVSWIE---EIALREAMHR----LGQREKMILSMRFYEG----KT 228

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             EV  +  +++ ++ ++E  AI++++   +S
Sbjct: 229 QMEVADEIGISQAQVSRLEKSAIQQMQKHVKS 260


>gi|254478776|ref|ZP_05092144.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035288|gb|EEB75994.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 258

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 123/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E + +NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 39  AREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  EIAK+L +P E V
Sbjct: 99  IIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGEIAKELDLPSEEV 157

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI  +     GD I   + VS   +  +  L +   +  L  L  
Sbjct: 158 VMALDAIQEPVSLFEPIYHDG----GDAIYVMDQVSDDKNVDEVWLEKIALKEALEKLNE 213

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 214 REKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMR 255


>gi|20808063|ref|NP_623234.1| sporulation sigma factor SigG [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516644|gb|AAM24838.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 264

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 123/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E + +NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 45  AREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPM 104

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  EIAK+L +P E V
Sbjct: 105 IIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGEIAKELDLPSEEV 163

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI  +     GD I   + VS   +  +  L +   +  L  L  
Sbjct: 164 VMALDAIQEPVSLFEPIYHDG----GDAIYVMDQVSDDKNVDEVWLEKIALKEALEKLNE 219

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 220 REKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMR 261


>gi|304399205|ref|ZP_07381072.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
 gi|304353259|gb|EFM17639.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
          Length = 172

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 104/163 (63%)

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 2   NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 61

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 62  TSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 121

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 122 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 164


>gi|14346036|gb|AAK59987.1| RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 145

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 53/146 (36%), Positives = 98/146 (67%), Gaps = 2/146 (1%)

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  +    +  +L
Sbjct: 1   ITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELAEESGIEENKIEMLL 60

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREER 626
           + +++P+SL+ P+G ++ + LGDFIED  A    ++A+ A++R +  R V+ +L  RE+ 
Sbjct: 61  RQSRDPVSLDMPVGADEEAPLGDFIEDAEATDA-ETAVVASMRHSDIRDVIGTLEQREQD 119

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVT 652
           V+R+R+G+      TL+++G++F ++
Sbjct: 120 VIRLRYGLDDGVPRTLDQIGRKFGLS 145


>gi|288553150|ref|YP_003425085.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
 gi|288544310|gb|ADC48193.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
          Length = 261

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 145/272 (53%), Gaps = 21/272 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +  +E R + + ++ G+     A++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNTEMRELFTQLQSGD---DSAREVLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++   ++  + KR  EPT +EIAK L +P E V   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDQLMAEKKRENEPTVQEIAKVLDVPKEDVVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D   + D I D+     ++   +  L+E   R    L  RE+ +L MRF  G     T
Sbjct: 179 GGDPIFVMDQISDERN-KDVNWVEEIALKEAMIR----LNDREKMILNMRFFQG----KT 229

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             EV  +  +++ ++ ++E  AI+++   ++S
Sbjct: 230 QMEVADEIGISQAQVSRLEKAAIQQMNKHAQS 261


>gi|218132880|ref|ZP_03461684.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991753|gb|EEC57757.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
          Length = 259

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 130/240 (54%), Gaps = 14/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++RK     S A+++ ++ NLRLV+SV +++   G    DL Q G IGLMKA + FD   
Sbjct: 27  LLRKAIDGDSKAREKYIKGNLRLVLSVIQRFAGNGENADDLFQIGCIGLMKAIDNFDVTQ 86

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   + R + D + +IR+   +RD  +K +     ++ K + EPT  EI
Sbjct: 87  NVRFSTYAVPMIMGEVRRYMRDYN-SIRVSRSLRDTAYKAIHARDMLTKKNQHEPTVMEI 145

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           A ++ +P E +   L   + P+SL  P+  E  DT ++ D I DK   +  D+ ++   L
Sbjct: 146 AAEVGLPKEEIVMALDAMQTPLSLYEPVFSEGGDTLYVMDQISDKK--NREDNWVEDIAL 203

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE  +R    L  RE  ++R+RF  G     T  EV +   +++ ++ ++E  A+R +K+
Sbjct: 204 REAVSR----LPERERNIIRLRFFDG----RTQMEVARDVGISQAQVSRLEKNALRSMKN 255


>gi|323706111|ref|ZP_08117680.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534555|gb|EGB24337.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 256

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 76/227 (33%), Positives = 125/227 (55%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  AREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   ++ N+  +EPT  +IAK+L +P E V
Sbjct: 97  IIGEIRRYLRDNN-SIRVSRSLRDVAYKALQVRDKLVNENSKEPTVGDIAKELNIPREEV 155

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   ++P+SL  PI  +  D  ++ D I D+  V  +    Q  L+E   +    L 
Sbjct: 156 VFALDAIQDPVSLFEPIYHDGGDAIYVMDQIGDEKNVDEVWLE-QIALKEAIKK----LN 210

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 211 DREKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKSALSHMR 253


>gi|111035800|emb|CAL29427.1| RNA polymerase sigma-32 factor [Wolbachia endosymbiont of
           Onchocerca volvulus]
          Length = 297

 Score =  108 bits (269), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 133/245 (54%), Gaps = 18/245 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++ ++L LV+ +A K+ N GL  +DLI EGNIGLM A +KF+  LG++FSTYA+WW++ 
Sbjct: 52  KLITSHLNLVVKIAMKFKNYGLLLMDLIMEGNIGLMHAVKKFNPNLGFRFSTYAVWWIEA 111

Query: 507 AITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPV 560
           +I   I      I+I      R     + +  +R+     RE    E    I+ +LA+  
Sbjct: 112 SIKDFILKSWSFIKIGTTQAQRKLFFSLRKIKKRILQYTNRETLSNEEIKAISNELAVS- 170

Query: 561 EG--VRKVLKITKEPISLET--PIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETT 613
           EG  ++   ++  +  SL +   +GD     L D I   N+VS      +  +  L+ET 
Sbjct: 171 EGDVIQMSYRLAYKDQSLNSCLKVGDGSKKELQDMIPC-NSVSQEVTYQNHEEKELKETI 229

Query: 614 -TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               LA+L  R   +   R+ +  NT  TL+E+GK++ V+RERIRQ+  +A+ K+K   +
Sbjct: 230 LNNALANLNERSRDIFISRY-LSENT-QTLDELGKKYNVSRERIRQLAEQAMSKVKQYIQ 287

Query: 673 SKKLR 677
           S+ L+
Sbjct: 288 SESLK 292


>gi|220917075|ref|YP_002492379.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954929|gb|ACL65313.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 307

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 76/242 (31%), Positives = 121/242 (50%), Gaps = 14/242 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ANLR V+ VA +Y + G +  DLIQEGNIGLMKA +KFD   G +  +YA+WW
Sbjct: 46  AAHRLVTANLRFVVKVAYEYRSYGFRMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWW 105

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPT------PEEIAKK 555
           ++  I   I      +++      R     + RT R +  + +            ++AKK
Sbjct: 106 IRAYIQNYILKSWSLVKLGTTQAQRKLFFSLARTKRELDKRSQEHGADSDGHDANKVAKK 165

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           L +    VR++  ++    +SL+ P+GD+      DF+    A    + +     +  + 
Sbjct: 166 LRVKPGEVREMEQRMEGRDLSLDAPMGDDGGYSHVDFLPSGTASQDDELSGVQEQKVVSG 225

Query: 615 RV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RV   L  L  RE  ++ MR  +  +   TL+E+G+ F  +RER RQ+E +A  KLK   
Sbjct: 226 RVVEALGRLDQRERYIIEMR--VMSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKEEL 283

Query: 672 RS 673
           R+
Sbjct: 284 RA 285


>gi|114569135|ref|YP_755815.1| RNA polymerase factor sigma-32 [Maricaulis maris MCS10]
 gi|114339597|gb|ABI64877.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 295

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 143/279 (51%), Gaps = 30/279 (10%)

Query: 415 SISVETGIS--ISEFRHIVSM---------VRKGECEASIAKKEMVEANLRLVISVAKKY 463
           ++S E G+S  +SE R    +          R  E E   A +++V ++LRLV  +A  Y
Sbjct: 8   TLSPEQGLSSYLSEIRRFPMLEKDEEFMLGKRWREHEDGGAAEKLVTSHLRLVAKIAMGY 67

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++  
Sbjct: 68  RGYGLPIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 127

Query: 524 HMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPVEGVRKV-LKITKEPIS 575
               K  K+    RRM ++++       +    E IA KL +  + V  +  +++    S
Sbjct: 128 TAAQK--KLFFNLRRMKSQMQALDEGDLKPDQVEAIATKLGVTNDEVMSMNGRLSGPDAS 185

Query: 576 LETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS----LTPREERVLRM 630
           L  P+ G E      D++ D  A S  D   +++  +T  ++L S    L  RE+ +L+ 
Sbjct: 186 LNAPLRGTEGEGQWQDWLSDDTAESQEDELAESDEFDTRMQLLQSAMGELNEREQHILQE 245

Query: 631 RFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    ++ D  TLEE+ + + V+RERIRQIE +A  KL+
Sbjct: 246 RR---LSEDPKTLEELAEHYGVSRERIRQIEVRAFEKLQ 281


>gi|281421843|ref|ZP_06252842.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281404085|gb|EFB34765.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 136

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 50/96 (52%), Positives = 70/96 (72%), Gaps = 3/96 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RKG  E   AK++++ ANLR V+SVAK+Y +RGL   DLI EGNIGL+KA E+FD   G
Sbjct: 40  IRKGGSEGERAKEKLIRANLRFVVSVAKRYQHRGLALTDLIDEGNIGLIKAVERFDETRG 99

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           +KF  YA+WW++Q+I ++IA+Q+   RI +   DKI
Sbjct: 100 FKFIQYAIWWIRQSILQAIAEQNHITRISL---DKI 132


>gi|261342188|ref|ZP_05970046.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315521|gb|EFC54459.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 172

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 53/155 (34%), Positives = 100/155 (64%)

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 2   NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 61

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 62  TSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 121

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 122 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 156


>gi|167630136|ref|YP_001680635.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167592876|gb|ABZ84624.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 265

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 128/247 (51%), Gaps = 17/247 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E R +   ++ GE  A   +++++  NLRLV+SV +++TNRG    DL Q G IGLMKA
Sbjct: 30  AEMRTLFQAMQSGERSA---REKLISGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGLMKA 86

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N++ 
Sbjct: 87  IDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDHLVNELS 145

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPL 601
           REPT  EIA  L  P E V   L   +EPISL  PI   G +    +    ++KN  +  
Sbjct: 146 REPTVTEIADALGFPREEVVFALDAIQEPISLFEPIYHDGGDPIFVMDQIGDEKNQDAQW 205

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              I   +RE   R    L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E 
Sbjct: 206 LEGIA--VREALRR----LNDREKLILTLRFFEG----KTQMEVADEIGISQAQVSRLEK 255

Query: 662 KAIRKLK 668
            A+  ++
Sbjct: 256 AALTHMR 262


>gi|157692208|ref|YP_001486670.1| sporulation sigma factor SigG [Bacillus pumilus SAFR-032]
 gi|194014766|ref|ZP_03053383.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
 gi|157680966|gb|ABV62110.1| DNA-directed RNA polymerase sigma subunit SigG [Bacillus pumilus
           SAFR-032]
 gi|194013792|gb|EDW23357.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
          Length = 259

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 126/229 (55%), Gaps = 18/229 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     +FSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVRFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   R+ ++  +EPT E+IAK L +P E +
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEI 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLA 618
              L   ++P+SL  PI ++  D  ++ D I D   K+     + A++  +R        
Sbjct: 158 VFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNKDTQWVEELALKEGMRR------- 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L  RE+ +LR RF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 211 -LNDREKMILRKRFFQGKTQMEVAEEIG----ISQAQVSRLEKAAIKQM 254


>gi|167465669|ref|ZP_02330758.1| sporulation sigma factor SigG [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 260

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/267 (32%), Positives = 143/267 (53%), Gaps = 19/267 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + ++++     A  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNTEMRELFALLQTKNERA--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   +++N+  REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQVRDQLTNRNSREPTIYEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+     L       LRE     +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDERN-KDLFWIEGIALREA----MRKLGSREKMILSMRFFEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL-KH 669
           EV  +  +++ ++ ++E  AI ++ KH
Sbjct: 231 EVADEIGISQAQVSRLEKSAINQMQKH 257


>gi|308803162|ref|XP_003078894.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
 gi|116057347|emb|CAL51774.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
          Length = 485

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 82/262 (31%), Positives = 135/262 (51%), Gaps = 22/262 (8%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTN-------RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +  IA++++V AN+ L   VA    +       R +   D+I EG  GL++A+EKFD  L
Sbjct: 176 QGKIARQKLVSANIELAAKVATDVFHTFSPMERRSISRQDMIHEGVTGLVRASEKFDPAL 235

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP---VHMRDKIHKVVRTARRMSNKIKREPTP 549
           G  FSTYA  W KQA+TR + +   TIR+P   ++ R + H++   ++RM  ++ R PT 
Sbjct: 236 GCAFSTYAYNWTKQAVTRGVLNNGRTIRVPEQVLYERREAHEL---SKRMEIELGRRPTL 292

Query: 550 EEI-AKKLAMPVEGVRKVLKITKE-PISLET-PIGDE-----DTSHLGDFIEDKNAVSPL 601
            EI A+     V+ ++ ++ I K+ P+SL+   +GDE     +T   G +  +  +   +
Sbjct: 293 HEIAARSQKFSVDKLQLLVGIAKQHPLSLDILGVGDEERDGDETGLSGTWENEMGSTDEI 352

Query: 602 DSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
              I+   LR+   + L  L+  E  VL+ RFG+      T  E+G +   + E +R IE
Sbjct: 353 TRTIELEFLRDDIKKTLNELSSDEAYVLKHRFGLVGGEFMTNAEIGSRIGKSAEGVRYIE 412

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
            +A+ +LK       L   L G
Sbjct: 413 KRALERLKSTPDFSDLAQHLKG 434


>gi|301166786|emb|CBW26363.1| RNA polymerase sigma-32 factor [Bacteriovorax marinus SJ]
          Length = 350

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 140/275 (50%), Gaps = 33/275 (12%)

Query: 413 IKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           ++ IS    ++I E R +   +V  G+ E +   K++V ANLRLV+ +A +Y +     +
Sbjct: 82  LREISKYELLTIEEERELTQKLVETGDIEVA---KKLVAANLRLVVKIAMEYRSSFQNVM 138

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--I 529
           DLIQEGNIGLMKA  K+D   G K S YA WW+K  I + I D    ++I      K   
Sbjct: 139 DLIQEGNIGLMKAVSKYDPDKGAKLSYYASWWIKSYILKYILDNFRLVKIGTTNEQKKLF 198

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIG----- 581
           + +++   R++ K   EP  + +++ L +  + V  +   +  +   +SLETP+G     
Sbjct: 199 YNLMKEKDRLA-KQGIEPDHKLLSENLGVSEKAVALMDGRMSSSGGELSLETPLGHDSGS 257

Query: 582 --------DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
                   D+D S + + I D   +  L    Q NLR+     ++ L  R+  + + R  
Sbjct: 258 GVLSDILVDQDESDISEKIADAQGLEIL----QENLRD----FVSGLKERDRDIFKKR-- 307

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      +L+ +  ++ V+RERIRQIE + ++ LK
Sbjct: 308 LLSEVPPSLQNIADEYGVSRERIRQIEERLLKNLK 342


>gi|78043932|ref|YP_360874.1| sporulation sigma factor SigG [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996047|gb|ABB14946.1| RNA polymerase sigma-G factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score =  107 bits (268), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 131/246 (53%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +   V++G+ EA   +++++  NLRLV+S+ +++TNRG    DL Q G IGL+KA 
Sbjct: 23  EMKKLFLKVKEGDMEA---RQKLISGNLRLVLSIIQRFTNRGEYVDDLFQVGCIGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    +  +  R
Sbjct: 80  DNFDLEQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVAYKALQVRDNLVGRFSR 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLD 602
           EPT  EIA++L +P E V   L   ++P+SL  PI  +  D   + D I+D KN      
Sbjct: 139 EPTVSEIAQELKVPQEEVVFALDAIQDPVSLFEPIYQDGGDPIFVMDQIKDEKNTDHNWL 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             I   L+E   R    L  RE  +L++RF  G       EE+G    +++ ++ ++E  
Sbjct: 199 QGIA--LKEALER----LNERERLILKLRFYEGKTQMEVAEEIG----ISQAQVSRLEKA 248

Query: 663 AIRKLK 668
           A+  L+
Sbjct: 249 ALNHLR 254


>gi|332799104|ref|YP_004460603.1| RNA polymerase sigma-28 subunit SigG [Tepidanaerobacter sp. Re1]
 gi|332696839|gb|AEE91296.1| RNA polymerase, sigma 28 subunit, SigG [Tepidanaerobacter sp. Re1]
          Length = 257

 Score =  107 bits (268), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 81/267 (30%), Positives = 144/267 (53%), Gaps = 21/267 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           I N+++   V+T     +S ++ + +   ++KG+  A   +++++  NLRLV+SV +++ 
Sbjct: 2   IVNKVEICGVDTSKLPVLSNAKMKELFLQLQKGDKSA---REKLISGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-QIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    +  K  REP+  E+AK++ MP E V   L   +EP+SL  PI  + 
Sbjct: 118 LRDTAYKALQVRDSLVTKNSREPSINEVAKEMNMPSEEVVFALDAIQEPVSLFEPIYHDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            D   + D I D+      D  +Q  +++E   R    L  RE+++L +RF  G     T
Sbjct: 178 GDPIFVMDQISDEKNQD--DQWLQGISIKEAMQR----LGEREKKILNLRFFEG----KT 227

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
             EV ++  +++ ++ ++E  A++ ++
Sbjct: 228 QMEVAQEIGISQAQVSRLEKAALKHMR 254


>gi|144971|gb|AAA23295.1| ORF1 [Corynebacterium diphtheriae]
 gi|144975|gb|AAA23298.1| open reading frame [Corynebacterium diphtheriae PW8]
          Length = 143

 Score =  107 bits (267), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 54/142 (38%), Positives = 97/142 (68%), Gaps = 2/142 (1%)

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ RE T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A 
Sbjct: 1   MYQQLGREATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEAT 60

Query: 599 SPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              +SA+ A+LR +  R VL +L  RE+ V+R+R+G+      TL+++G+QF ++RER+R
Sbjct: 61  DA-ESAVVASLRHSDIRTVLDTLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVR 119

Query: 658 QIEAKAIRKLKHPSRSKKLRSF 679
           QIE + + KL+  +R++KLR++
Sbjct: 120 QIEREVMSKLRDGARAEKLRAY 141


>gi|89099621|ref|ZP_01172496.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
 gi|89085774|gb|EAR64900.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
          Length = 259

 Score =  107 bits (267), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 81/264 (30%), Positives = 140/264 (53%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   + +G+   + A++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFKQMHEGD---TYARECLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EPT EEIA+ L +P E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVRERLMSETSKEPTAEEIARVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+     +    +  L+E   R    L  RE+ +LR RF  G       E
Sbjct: 179 DPIFVMDQLSDERN-KDIQWIEEIALKEGMRR----LNEREKLILRKRFFQGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 234 EIG----ISQAQVSRLEKAAIKQM 253


>gi|229076790|ref|ZP_04209702.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
 gi|228706352|gb|EEL58613.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
          Length = 252

 Score =  107 bits (267), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 117/227 (51%), Gaps = 6/227 (2%)

Query: 448 MVEANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           M   N+ LV+S+A+KY  +   ++F DL+QEGN G+++A E FD  LGY FSTYA  W+K
Sbjct: 1   MFHVNIGLVLSIARKYKKKHPEIEFDDLVQEGNEGMLRAIEDFDPDLGYCFSTYAYCWIK 60

Query: 506 QAITRSIA-DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           +++   I   +S   +IP ++     K V    +      R PT EE+ K+L +  E V 
Sbjct: 61  KSMLGFICKKKSGPFKIPNYVNQFNVKYVEIEDKYLQMHNRIPTVEEVVKELDVTREKVV 120

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLT 621
              V       ++L+    +ED   L  F  D +A+   +  I  +L      +    L 
Sbjct: 121 RHNVYYNRVTTMTLDIDTINEDIGILNSFCNDNSAIPSTNEMIMEDLNYEIWIIFDEVLN 180

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P+++ VL + FG+     H  +E+ K   +T ER+ Q++ +AI +LK
Sbjct: 181 PKQKMVLNLCFGLLDGEIHLHKEIAKALMITTERVSQLKDEAINRLK 227


>gi|167751709|ref|ZP_02423836.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|167655517|gb|EDR99646.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|291558002|emb|CBL35119.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum
           V10Sc8a]
          Length = 261

 Score =  107 bits (267), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 136/247 (55%), Gaps = 18/247 (7%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SE   ++  +R G+     A+++++  NLRLV+SV ++++ RG    DL Q G IGLMKA
Sbjct: 27  SEKTELLRQMRSGD---PTAREKLINGNLRLVLSVIQRFSGRGENPDDLFQVGCIGLMKA 83

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + F      +FSTYA+  +   + R + D S +IR+   MRD  +K ++   +++N   
Sbjct: 84  IDNFSTDFNVRFSTYAVPMIMGELRRYLRD-SGSIRVSRSMRDLAYKAMQAREKLTNDNS 142

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKN-AVSPL 601
           +EPT E+IAK++    E V   L+   +PISL  P+  E  DT ++ D I D N   + L
Sbjct: 143 KEPTIEQIAKEIDAKREDVVIALEAVSDPISLYEPVFSESGDTIYMMDQIGDNNDDRNWL 202

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  L+E     +  L  RE+ +L++RF  G     T  EV ++  +++ ++ ++E 
Sbjct: 203 D---EIALKEA----IIGLDDREKNILKLRFFRG----KTQVEVAQEIGISQAQVSRLEK 251

Query: 662 KAIRKLK 668
            A+ K+K
Sbjct: 252 GALGKIK 258


>gi|317121713|ref|YP_004101716.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591693|gb|ADU50989.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score =  107 bits (267), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 142/263 (53%), Gaps = 17/263 (6%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     ++  + R +   +R+G+ EA   ++++V+ NLRLV+SV +++ +R
Sbjct: 8   NKVEICGVNTAELPVLTNEQMRVLFRRMRQGDEEA---RQQLVQGNLRLVLSVIQRFNHR 64

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +R
Sbjct: 65  GEPVDDLFQVGCIGLMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLR 123

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D  +K ++   +++++  REPT EEIA++L +P E V   L   ++P+SL  PI  +   
Sbjct: 124 DVAYKALQVRDQLTHRHGREPTLEEIARELGLPREEVVHALDAIQDPVSLFEPIYQDG-- 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             GD I   + VS      +  L     R  +A L  RE+ ++  RF  G     T  EV
Sbjct: 182 --GDPIYVVDQVSDDKQRDEQWLETIAVREAMARLDEREQLIITKRFYQG----KTQMEV 235

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
             +  +++ ++ ++E  A+++++
Sbjct: 236 ANEIGISQAQVSRLEKAALQRMR 258


>gi|164686360|ref|ZP_02210390.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
 gi|164601962|gb|EDQ95427.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
          Length = 257

 Score =  107 bits (267), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 132/246 (53%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + R ++  +++G+ +A   +++ V+ NLRLV+SV +K+ NRG    DL Q G +GL+KA 
Sbjct: 23  QMRELLVKIKQGDEDA---RQKFVKGNLRLVLSVIQKFNNRGENVDDLFQIGCVGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     +FSTYA+  +   I R + D +  IR+   ++D  +K ++   R+     +
Sbjct: 80  DNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLKDIAYKALQVRERLIRTNSK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  EIAK+L M VE V   L   ++PISL  P+  +  D   + D ++DK        
Sbjct: 139 EPTISEIAKELDMEVESVVMALDAIQDPISLFDPVYQDNGDAIFVMDQVQDKKDTD---- 194

Query: 604 AIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  L E   +  +  L+ RE+ VL +RF  G       +E+G    +++ ++ +IE  
Sbjct: 195 --ENWLEEIALKEAIKKLSSREKLVLDLRFYKGRTQIEVADEIG----ISQAQVSRIEKN 248

Query: 663 AIRKLK 668
           A++ ++
Sbjct: 249 ALKNMR 254


>gi|114570847|ref|YP_757527.1| RNA polymerase sigma 32 subunit RpoH [Maricaulis maris MCS10]
 gi|114341309|gb|ABI66589.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 305

 Score =  107 bits (267), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 79/237 (33%), Positives = 119/237 (50%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  E+ EA++RLVI+VA K+   GL F DLIQEGNIGLMKAA++FD     +FSTY  WW
Sbjct: 55  ALHELTEAHMRLVIAVAAKFKRYGLPFSDLIQEGNIGLMKAADRFDPERDVRFSTYVTWW 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTP---EEIAKKL 556
           ++  I   +      +R       K   +    RR+   I        TP   ++IAK L
Sbjct: 115 IRSCIQDYVLRNWSIVRTGTTSAQK--SLFFNLRRIRANIGDLDGSSITPDNRQKIAKDL 172

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +    V  + L+++    SL  P+GD + S   DF+ D  A    +   + +    +  
Sbjct: 173 RVRERDVENMALRLSASDRSLNAPVGDAEDSQWQDFLVDDTAAPETEVMNRTDSERRSAW 232

Query: 616 V---LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   L  L  RE+ ++R R    +  D  TL  +G    +++ER+RQIE  A+ KL+
Sbjct: 233 LGLALDGLNSREQFIIRER---RLREDGSTLASLGDSLGISKERVRQIENAALAKLR 286


>gi|52080136|ref|YP_078927.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|52785510|ref|YP_091339.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|319646086|ref|ZP_08000316.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
 gi|52003347|gb|AAU23289.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus licheniformis ATCC 14580]
 gi|52348012|gb|AAU40646.1| SigG [Bacillus licheniformis ATCC 14580]
 gi|317391836|gb|EFV72633.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
          Length = 259

 Score =  107 bits (266), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 128/231 (55%), Gaps = 18/231 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+
Sbjct: 37  TTAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAV 96

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R + D +  IR+   +RD  +K ++   R+ ++  REPT +EIAK+L +  E
Sbjct: 97  PMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSREPTAQEIAKELEVSHE 155

Query: 562 GVRKVLKITKEPISLETPIGDE--DTSHLGDFIED---KNAVSPLDSAIQANLRETTTRV 616
            +   L   ++P+SL  PI ++  D  ++ D I D   K++    + A++  +R      
Sbjct: 156 EIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNKDSQWIEELALKEGMRR----- 210

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              L  RE+ +LR RF  G     T  EV  +  +++ ++ ++E  AI+++
Sbjct: 211 ---LNEREKMILRKRFFQG----KTQMEVADEIGISQAQVSRLEKAAIKQM 254


>gi|317486415|ref|ZP_07945242.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
 gi|316922325|gb|EFV43584.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
          Length = 403

 Score =  107 bits (266), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 135/249 (54%), Gaps = 28/249 (11%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLG 493
           + G+ +A+     +V ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G
Sbjct: 151 KTGDSDAAF---RLVSSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPDKG 207

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPE 550
            KFS YA +W++  I + I D    ++I      +  K+     R   K+  E   P   
Sbjct: 208 IKFSYYAAFWIRAYILKFIMDNWRMVKIGTTQAQR--KLFYNLNRERQKLIAEGFDPDAA 265

Query: 551 EIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS--------HLGDFIEDKNAVSPL 601
            +A++L +  + + ++  ++    +SL+  +GDE  S         LG  IE+  A   +
Sbjct: 266 TLAERLGVGEDQIVEMQQRLDASDMSLDATVGDESGSATRMDFLPALGPGIEESLAGMEI 325

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQI 659
              +Q+ +R+    +L SL+ +E  +L  R    + TD   TL E+G+++ VTRER+RQ+
Sbjct: 326 AELLQSKIRD----ILPSLSEKEAYILEHR----LLTDDPVTLREIGERYNVTRERVRQL 377

Query: 660 EAKAIRKLK 668
           EA+ ++KLK
Sbjct: 378 EARLLQKLK 386


>gi|125972969|ref|YP_001036879.1| sporulation sigma factor SigG [Clostridium thermocellum ATCC 27405]
 gi|256004766|ref|ZP_05429741.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281417180|ref|ZP_06248200.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713194|gb|ABN51686.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium thermocellum
           ATCC 27405]
 gi|255991216|gb|EEU01323.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281408582|gb|EFB38840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940795|gb|ADU74829.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 1313]
          Length = 257

 Score =  107 bits (266), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 123/228 (53%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E ++ NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDVTQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   +++N+  +EPT EEIAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNNA-IRVSRSLRDIAYKALQAKEKLTNQNSKEPTIEEIAKELGLPKEEV 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++PISL   +  +  D  ++ D ++D KN        I        +  +  L
Sbjct: 157 VFALDAIQDPISLFESVYHDGGDAIYVMDQVKDEKNNDENWLEGI------ALSEAMRKL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G       EE+G    +++ ++ ++E  A+  ++
Sbjct: 211 NDREKLILNLRFFDGRTQMEVAEEIG----ISQAQVSRLEKTALMHMR 254


>gi|303238906|ref|ZP_07325437.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593539|gb|EFL63256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 257

 Score =  107 bits (266), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E ++ NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDVSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   R++NK  +EPT ++I+K+L +P E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALQAKERLTNKNSKEPTVDDISKELGIPKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++PISL   +  +  D  ++ D ++D KN        I  N        +  L
Sbjct: 157 VFALDAIQDPISLFESVYHDGGDAIYVMDQVKDEKNHDENWLEGIALN------EAMRKL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G       EE+G    +++ ++ ++E  A+  ++
Sbjct: 211 NDREKLILNLRFFDGRTQMEVAEEIG----ISQAQVSRLEKTALMHMR 254


>gi|302774234|ref|XP_002970534.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
 gi|300162050|gb|EFJ28664.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
          Length = 458

 Score =  107 bits (266), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 132/261 (50%), Gaps = 14/261 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL--DLIQEGNIGLM 482
           ++FR +   ++ GE     A+ +++E N RLV+ +A++Y      F   DL QEG  GL+
Sbjct: 204 TDFRTLRRRLQLGEA----AQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLI 259

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A + F+   G +FSTYA++W++ AI R+I      IR+P     K  ++ +  R +  +
Sbjct: 260 DAMDHFNPGKGTRFSTYAIFWIRTAIVRAITRTGQVIRLPFSFAAKKVEIRKARRELRVE 319

Query: 543 IKREPTPEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + R P+ EE+ ++  + PV+             SL   +   D   L    E  + VS  
Sbjct: 320 LGRNPSDEEVMERTGLDPVQFWNIYYYSNFRVRSLNETVRGTDEEFLEYLPETGDIVSE- 378

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQI 659
                + +RE     L  L  +E  VL+ R+G+  G     +L EVG++  +++E +R+ 
Sbjct: 379 ----SSEVREEIVTALQRLKDKERMVLQHRYGLEDGALAVKSLREVGRRLNMSQEMVRRY 434

Query: 660 EAKAIRKLKHPSRSKKLRSFL 680
           EA A+ +L+H   +K LRS L
Sbjct: 435 EASALERLRHQEEAKSLRSCL 455


>gi|322384112|ref|ZP_08057830.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151192|gb|EFX44501.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 272

 Score =  107 bits (266), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 86/267 (32%), Positives = 143/267 (53%), Gaps = 19/267 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + ++++     A  A++++V  NLRLV+SV +++ N
Sbjct: 15  RNKVEICGVDTAKLPVLTNTEMRELFALLQTKNERA--AREKLVNGNLRLVLSVIQRFNN 72

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 73  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 131

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   +++N+  REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 132 RDIAYKALQVRDQLTNRNSREPTIYEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGG 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+     L       LRE     +  L  RE+ +L MRF  G     T  
Sbjct: 192 DPIYVMDQISDERN-KDLFWIEGIALREA----MRKLGSREKMILSMRFFEG----KTQM 242

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL-KH 669
           EV  +  +++ ++ ++E  AI ++ KH
Sbjct: 243 EVADEIGISQAQVSRLEKSAINQMQKH 269


>gi|157803973|ref|YP_001492522.1| RNA polymerase factor sigma-32 [Rickettsia canadensis str. McKiel]
 gi|157785236|gb|ABV73737.1| hypothetical protein A1E_04050 [Rickettsia canadensis str. McKiel]
          Length = 296

 Score =  107 bits (266), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 125/237 (52%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I  +DT   G+ IE      P   A+  N +  TT+  
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINSDDTES-GELIELLPETRPTPEAMAINKQNYTTKKH 227

Query: 616 VLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LAS    L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLASAMKILNDRELRILTER--KLKDTPKTLDILSSEYNISKERIRQIENTAFEKIK 282


>gi|56964115|ref|YP_175846.1| sporulation sigma factor SigG [Bacillus clausii KSM-K16]
 gi|56910358|dbj|BAD64885.1| DNA-directed RNA polymerase sigma factor sigma-G [Bacillus clausii
           KSM-K16]
          Length = 261

 Score =  107 bits (266), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 142/269 (52%), Gaps = 22/269 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +  +E R + + ++ G      A++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSTLPVLKNAEMRELFTKLQAG---YEPARETLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++   +M  + KR  EPT +EIA  L +P E V   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDQMMAEKKREKEPTVQEIAAVLEVPKEDVVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D   + D I D+     ++   +  L+E   R    L  RE+ +L MRF  G      
Sbjct: 179 GGDPIFVMDQISDERN-KDINWVEEIALKEAMVR----LNDREKTILNMRFFQGKTQMEV 233

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
            EE+G    +++ ++ ++E  AI+++ KH
Sbjct: 234 AEEIG----ISQAQVSRLEKGAIQQMNKH 258


>gi|225175855|ref|ZP_03729848.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168779|gb|EEG77580.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 268

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 122/227 (53%), Gaps = 10/227 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++  NLRLV+SV +++ NRG    DL Q G IGLMKA + F       FSTYA+  
Sbjct: 38  ARQELINGNLRLVLSVLQRFKNRGENLDDLFQVGCIGLMKAVDNFSLDHNVHFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  +R+   ++   HK  ++   ++ K+ REPT +EIA  L +  E V
Sbjct: 98  IIGEIKRYLRDNNA-VRVSRSLKMLAHKAQQSREELTRKLLREPTLKEIAADLDITPEEV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
               +   +P+SL  P+  + T  +  F+ D   VS   S+ +  + + T R  +  L+ 
Sbjct: 157 VFAYQAINDPLSLHDPVFQDTTDPV--FVMD--LVSDQSSSAEIWVEDITLRQAMEILSE 212

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE R+L  RF  G     T  E+  +  +++ ++ +IE  A+R+++H
Sbjct: 213 RERRILESRFFEG----RTQTEIANEIGISQAQVSRIEKSALRQVRH 255


>gi|154500348|ref|ZP_02038386.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
 gi|150270853|gb|EDM98136.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
          Length = 256

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 131/239 (54%), Gaps = 10/239 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V+++++ +   + A++E++  NLRLV+SV +K++NRG    DL Q G IGL+KA + F+ 
Sbjct: 24  VALLKRTKEGDTAAREELIAGNLRLVLSVIQKFSNRGENVDDLFQVGCIGLIKAIDNFNT 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            L  +FSTY +  +   I R + D S ++R+   MRD  +KV++   +   + +REPT E
Sbjct: 84  DLDVRFSTYGVPMIVGEIRRYLRDNS-SMRVSRSMRDTAYKVLQAKEKFMAEHQREPTME 142

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK L +  E V   +    +P+SL  P+     S  GD I   + V    +  ++ L 
Sbjct: 143 EIAKMLDLKREDVVFAMDAIMDPVSLYEPV----YSDGGDAICVMDQVKDSKNTDESWLE 198

Query: 611 ETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  ++ L+ RE  +L +RF  G     T  EV  +  +++ ++ ++E  AI K++
Sbjct: 199 HIALKEAISHLSDRERHILSLRFFEG----RTQMEVSAEIGISQAQVSRLEKSAIWKIR 253


>gi|86158413|ref|YP_465198.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774924|gb|ABC81761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 307

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 125/244 (51%), Gaps = 18/244 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ANLR V+ VA +Y + G +  DLIQEGNIGLMKA +KFD   G +  +YA+WW
Sbjct: 46  AAHRLVTANLRFVVKVAYEYRSYGFRMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWW 105

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPT------PEEIAKK 555
           ++  I   I      +++      R     + RT R +  + + +          ++AKK
Sbjct: 106 IRAYIQNYILKSWSLVKLGTTQAQRKLFFSLARTKRELDKRSQEQGADSDGHDANKVAKK 165

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD--SAIQANLRET 612
           L +    VR++  ++    +SL+ P+GD+      DF+    + S  D  S +Q   +  
Sbjct: 166 LRVKPGEVREMEQRMEGRDLSLDAPMGDDGGYSHVDFLA-SGSTSQDDELSGVQEQ-KVV 223

Query: 613 TTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + R+   L  L  RE  ++ MR  +  +   TL+E+G+ F  +RER RQ+E +A  KLK 
Sbjct: 224 SGRIVEALGRLDQRERYIIEMR--VMSDRPLTLKELGEHFGFSRERARQLEIRAKDKLKE 281

Query: 670 PSRS 673
             R+
Sbjct: 282 ELRA 285


>gi|332976340|gb|EGK13196.1| DNA-directed RNA polymerase sigma subunit SigG [Desmospora sp.
           8437]
          Length = 259

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 122/227 (53%), Gaps = 14/227 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NLRLV+SV +++ NRG    DL Q G IGLMKA + FD     KFSTYA+  
Sbjct: 39  AREKLVNGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++    ++ +  REPT +EI+++L +  E V
Sbjct: 99  IIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDSLTYRHSREPTIQEISEELNVSKEEV 157

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI   G +    +    +D+N    L    +  LRE   R    L
Sbjct: 158 VFALDAIQDPVSLFEPIYQDGGDPIYVMDQLADDEN--KDLHWVEEIALREAMGR----L 211

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+ +L MRF  G       EE+G    +++ ++ ++E  AI+++
Sbjct: 212 NDREKMILSMRFFEGKTQMEVAEEIG----ISQAQVSRLEKAAIQQM 254


>gi|326392135|ref|ZP_08213612.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325991822|gb|EGD50337.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 256

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/226 (33%), Positives = 123/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  AREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  EIAK+L +P E V
Sbjct: 97  IIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGEIAKELDLPREEV 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI  +     GD I   + VS   +  +  L +   +  +  L+ 
Sbjct: 156 VMALDAIQEPVSLFEPIYHDG----GDAIYVMDQVSDDKNMDEVWLEKIALKEAIQKLSE 211

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 212 REKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMR 253


>gi|326204636|ref|ZP_08194492.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
 gi|325985203|gb|EGD46043.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
          Length = 257

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 121/227 (53%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  ARDEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDVSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   R++ +  +EPT  E+A++L +P E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALQAKERLTTQNSKEPTIAELAQELQLPKEDI 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RVLASLT 621
              L   ++PISL   +  +     GD I   + VS  D  I  N  ET +    +  L 
Sbjct: 157 VFALDAIQDPISLFESVYHDG----GDAIYVMDQVSD-DKNIDENWLETISLKEAMRKLN 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A+  +K
Sbjct: 212 DREKLILNLRFFEG----RTQMEVADEIGISQAQVSRLEKTALMHMK 254


>gi|268608170|ref|ZP_06141897.1| sporulation sigma factor SigG [Ruminococcus flavefaciens FD-1]
          Length = 259

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 124/228 (54%), Gaps = 15/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++++ NLRLV+SV +++T RG    DL Q G IGL+KA   FD     +FSTY +  
Sbjct: 39  ARDKLIKGNLRLVLSVIQRFTGRGEDIDDLFQIGVIGLIKAINNFDLTKEVRFSTYCVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D S  +++   +RD  +K +++  R++ +++REP+ +EIA+ +      +
Sbjct: 99  ISGELRRHLRDYS-HVKVSRSLRDLAYKAIQSKERLTVRLQREPSIDEIAEDIGEKRSEI 157

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L+   +P+SL  P+    +DT  + D I D+N        I++ L E T R  +  L
Sbjct: 158 VIALESISDPVSLYEPVYSDSDDTLFIMDQISDRN-------DIESRLNELTIRDAINQL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L +RF  G     T  EV  +  +++ ++ ++E  AIR +K
Sbjct: 211 GQRERNILYLRFFRG----KTQTEVAGEIGISQAQVSRLEKSAIRTVK 254


>gi|156636395|gb|ABU92468.1| RpoD [Vibrio vulnificus]
 gi|156636449|gb|ABU92495.1| RpoD [Vibrio vulnificus]
 gi|156636451|gb|ABU92496.1| RpoD [Vibrio vulnificus]
 gi|156636453|gb|ABU92497.1| RpoD [Vibrio vulnificus]
 gi|156636459|gb|ABU92500.1| RpoD [Vibrio vulnificus]
 gi|156636463|gb|ABU92502.1| RpoD [Vibrio vulnificus]
 gi|156636465|gb|ABU92503.1| RpoD [Vibrio vulnificus]
 gi|156636467|gb|ABU92504.1| RpoD [Vibrio vulnificus]
 gi|156636469|gb|ABU92505.1| RpoD [Vibrio vulnificus]
 gi|156636471|gb|ABU92506.1| RpoD [Vibrio vulnificus]
 gi|156636473|gb|ABU92507.1| RpoD [Vibrio vulnificus]
 gi|156636477|gb|ABU92509.1| RpoD [Vibrio vulnificus]
 gi|156636479|gb|ABU92510.1| RpoD [Vibrio vulnificus]
 gi|156636481|gb|ABU92511.1| RpoD [Vibrio vulnificus]
 gi|156636483|gb|ABU92512.1| RpoD [Vibrio vulnificus]
 gi|156636485|gb|ABU92513.1| RpoD [Vibrio vulnificus]
 gi|156636487|gb|ABU92514.1| RpoD [Vibrio vulnificus]
 gi|156636489|gb|ABU92515.1| RpoD [Vibrio vulnificus]
 gi|156636491|gb|ABU92516.1| RpoD [Vibrio vulnificus]
 gi|156636493|gb|ABU92517.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 68/175 (38%), Positives = 98/175 (56%), Gaps = 6/175 (3%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E ++ +     L   + D LV +L     R+   E  +++ A     + +  F+    G 
Sbjct: 29  ELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGN 88

Query: 378 ELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W+      D P  E    +    + I +  +++++I  ET +S+S  + I   + 
Sbjct: 89  ESSEEWLDKILVSDKPYAEK---IKLHEEDIRRSISKLRAIEEETSLSVSNIKDISRRMS 145

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|108760621|ref|YP_631554.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
 gi|108464501|gb|ABF89686.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
          Length = 246

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 122/232 (52%), Gaps = 16/232 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ANLR V+ VA +Y + G++  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 508 ITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPT--PEEIAKKLAMPVEGV 563
           I   I      +++      R     + RT R +      +     ++IA++L +    V
Sbjct: 61  IQNYILKSWSLVKLGTTQAQRKLFFSLARTRRELEKFGSGDAAVNVDDIARRLHVKPGEV 120

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----QANLRETTTR-VL 617
           R++  ++    +SL+ P+G++  +   DF+   +A +P D       +A L     R  L
Sbjct: 121 REMEQRMGGRDLSLDAPMGEDGGNSHVDFV--VSAAAPQDDEFADKEEAGLINARVRTAL 178

Query: 618 ASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L PRE  ++  R    MN    TL+E+G+ F  +RER RQ+E +A  KLK
Sbjct: 179 MRLDPRERFIIEQRV---MNERPMTLKELGEHFGFSRERARQLEIRAKDKLK 227


>gi|167037237|ref|YP_001664815.1| sporulation sigma factor SigG [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040623|ref|YP_001663608.1| sporulation sigma factor SigG [Thermoanaerobacter sp. X514]
 gi|300914664|ref|ZP_07131980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307267689|ref|ZP_07549143.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724102|ref|YP_003903853.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115656|ref|YP_004185815.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854863|gb|ABY93272.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856071|gb|ABY94479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|300889599|gb|EFK84745.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|306917291|gb|EFN47611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581163|gb|ADN54562.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928747|gb|ADV79432.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 256

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/226 (33%), Positives = 123/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  AREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  EIAK+L +P E V
Sbjct: 97  IIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGEIAKELDLPREEV 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI  +     GD I   + VS   +  +  L +   +  +  L+ 
Sbjct: 156 VMALDAIQEPVSLFEPIYHDG----GDAIYVMDQVSDDKNMDEVWLEKIALKEAIQKLSE 211

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 212 REKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMR 253


>gi|153003975|ref|YP_001378300.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152027548|gb|ABS25316.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 299

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 127/243 (52%), Gaps = 27/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++VEANLR V+ VA +Y + GL+  DLIQEGNIGLMKA +KFD     +  +YA+WW
Sbjct: 44  AAHKLVEANLRFVVKVAFEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-----------I 552
           ++  I   I      ++I      +  K+  +  R  ++I+R  TP             +
Sbjct: 104 IRAYIQNHILKSWSLVKIGTTQAQR--KLFFSLARTRHEIER-VTPGAGLDSEGIDVNLV 160

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL------GDFIEDKNAVSPLDSAI 605
           AKKL +    V ++  ++    +SL+ P+ D  ++HL       D  +D+ A +  D+ +
Sbjct: 161 AKKLRVRASDVVEMQQRMEGRDLSLDAPVADGTSTHLEFTPSDADPQDDELARAEEDAIV 220

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              + +  +R    L PRE  ++  R  I  +   TL ++G+ F  +RER RQ+E +A+ 
Sbjct: 221 NRRVNDAMSR----LDPRERHIVEAR--IMGDGKETLRDLGQHFGFSRERARQLEIRALE 274

Query: 666 KLK 668
           KL+
Sbjct: 275 KLR 277


>gi|288962535|ref|YP_003452830.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914801|dbj|BAI76286.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 296

 Score =  106 bits (264), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 131/256 (51%), Gaps = 21/256 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  + E S A  ++V ++LRLV  +A  Y   GL   +LI EGN+G+M+A ++FD   G+
Sbjct: 40  RWQQHEDSGAAHQLVTSHLRLVAKIAMGYRGYGLPLSELISEGNVGMMQAVKRFDPDRGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE 550
           + +TYAMWW++ AI   I      +++      K  K+    RR+  +++     + +PE
Sbjct: 100 RLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIEEGDLSPE 157

Query: 551 E---IAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           +   IA KL +P + V  + +    P  SL  P+  E      DF+ D++A   +  A +
Sbjct: 158 QVQAIATKLDVPEQDVVNMNRRLASPDHSLNAPLRAESEGEWQDFLVDESASQEIALADR 217

Query: 607 ANL---RETTTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             L   R+     +  L  RE  +L   R+R         TLE++ +++ ++RER+RQIE
Sbjct: 218 EELGKRRKLLVEAMTGLNERERDILTERRLR-----EAPTTLEDLSQKYGISRERVRQIE 272

Query: 661 AKAIRKLKHPSRSKKL 676
            +A  KL+   ++  L
Sbjct: 273 VRAFEKLQKAIKAAAL 288


>gi|110799379|ref|YP_696447.1| sporulation sigma factor SigG [Clostridium perfringens ATCC 13124]
 gi|168207288|ref|ZP_02633293.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210606|ref|ZP_02636231.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168214238|ref|ZP_02639863.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|168217048|ref|ZP_02642673.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
 gi|169342669|ref|ZP_02863710.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625828|ref|ZP_02953594.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|110674026|gb|ABG83013.1| RNA polymerase sigma-G factor [Clostridium perfringens ATCC 13124]
 gi|169299175|gb|EDS81245.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661342|gb|EDT14025.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711289|gb|EDT23471.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170714329|gb|EDT26511.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|177908862|gb|EDT71354.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380954|gb|EDT78433.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
          Length = 257

 Score =  106 bits (264), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 38  AREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + TIR+   +RD  +K +    ++ N+  +EPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-TIRVSRSLRDIAYKALLVRDKLVNENNKEPTVSQIAKELKIPREDV 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI  +  D  ++ D I D KN     D +   N+       +  L
Sbjct: 157 VFALDAIQDPVSLFEPIYHDGGDAIYVMDQISDSKNQ----DDSWLENI--AIKEAMKKL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 211 NDREKLILNLRFFNG----RTQMEVADEIGISQAQVSRLEKIALKHMR 254


>gi|148284686|ref|YP_001248776.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str.
           Boryong]
 gi|146740125|emb|CAM80313.1| RNA polymerase sigma-32 factor [Orientia tsutsugamushi str.
           Boryong]
          Length = 299

 Score =  106 bits (264), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 130/245 (53%), Gaps = 17/245 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V+++L+LV  +A  Y   GL  +DL+ EGNIGL++A +K++  LG++ STYA+WW
Sbjct: 52  AAHSLVKSHLKLVAKIALSYRGYGLPVVDLVSEGNIGLLQAVKKYNPELGFRLSTYAIWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-------EPTPEEIAKKL 556
           +K AI   I      +++      K  K+     ++ NKI +           ++IA + 
Sbjct: 112 IKAAIQDYILRSWSLVKLGTTAAQK--KLFFNLGKIKNKITKMHARAINSSDYKQIADES 169

Query: 557 AMPVEGVRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            + +  V +V  +++   +SL TPI   ++D + L + + +      +  A Q +L   +
Sbjct: 170 GVSIAEVSEVNQRLSNSDLSLNTPISYHEDDATELVELVPEHRPNQEIILANQQDLNLKK 229

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L +LT RE  ++R R     +   TLE++   F V++ERIRQIE+KA  KL+  
Sbjct: 230 EVLENALQTLTQRELYIIRAR--KLQDEPDTLEKLSLHFNVSKERIRQIESKAFEKLQQY 287

Query: 671 SRSKK 675
           + + K
Sbjct: 288 AMNTK 292


>gi|134298969|ref|YP_001112465.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134051669|gb|ABO49640.1| RNA polymerase, sigma subunit, RpoX/SigF [Desulfotomaculum reducens
           MI-1]
          Length = 260

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 131/237 (55%), Gaps = 10/237 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K +   S A++ +V  NL+LV ++ ++++NRG +  DL Q G IGLMKA +KFD   
Sbjct: 25  LLKKAQSGNSEARERLVNCNLKLVFNLVQRFSNRGYELEDLFQIGCIGLMKAIDKFDLSY 84

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R + D S  +++   +++  +K+ +T  R++ ++ REP+  EI
Sbjct: 85  DVKFSTYAVPMIVGEIRRFLRDDS-PVKVSRSLKETAYKIQQTRDRLTARLGREPSINEI 143

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A++L+   E V   L+  + P S+   +  +D    GD I   + +S  D      L + 
Sbjct: 144 AEELSYSREEVVNALEAAQMPTSIYETLHQDD----GDPIYILDQLSGEDEGDAPWLEKL 199

Query: 613 TTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +L  L  R+ ++L  RF      D T  EV  +  +++ ++ ++E +A+RKLK
Sbjct: 200 AVKQILIQLPERDRQILLWRF----FEDKTQSEVALRLGLSQVQVSRLERQALRKLK 252


>gi|189184203|ref|YP_001937988.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str. Ikeda]
 gi|189180974|dbj|BAG40754.1| heat shock sigma factor RpoH [Orientia tsutsugamushi str. Ikeda]
          Length = 299

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 130/245 (53%), Gaps = 17/245 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V+++L+LV  +A  Y   GL  +DL+ EGNIGL++A +K++  LG++ STYA+WW
Sbjct: 52  AAHSLVKSHLKLVAKIALSYRGYGLPVVDLVSEGNIGLLQAVKKYNPELGFRLSTYAIWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-------EPTPEEIAKKL 556
           +K AI   I      +++      K  K+     ++ NKI +           ++IA + 
Sbjct: 112 IKAAIQDYILRSWSLVKLGTTAAQK--KLFFNLGKIKNKITKLHARAINSSDYKQIADES 169

Query: 557 AMPVEGVRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            + +  V +V  +++   +SL TPI   ++D + L + + +      +  A Q +L   +
Sbjct: 170 GVSIAEVSEVNQRLSNSDLSLNTPISYHEDDATELVELVPEHRPNQEIILANQQDLNLKQ 229

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L +LT RE  ++R R     +   TLE++   F V++ERIRQIE+KA  KL+  
Sbjct: 230 EVLQNALQTLTQRELYIIRAR--KLQDEPDTLEKLSLHFNVSKERIRQIESKAFEKLQQY 287

Query: 671 SRSKK 675
           + + K
Sbjct: 288 AMNTK 292


>gi|256751992|ref|ZP_05492861.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749102|gb|EEU62137.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 256

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/226 (33%), Positives = 123/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  AREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  EIAK+L +P E V
Sbjct: 97  IIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGEIAKELDLPREEV 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI  +     GD I   + VS   +  +  L +   +  +  L+ 
Sbjct: 156 VMALDAIQEPVSLFEPIYHDG----GDAIYVMDQVSDDKNMDEVWLEKIALKEAIQKLSE 211

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 212 REKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMR 253


>gi|228931462|ref|ZP_04094387.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229188107|ref|ZP_04315191.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228595348|gb|EEK53084.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228828268|gb|EEM73978.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 323

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/268 (28%), Positives = 137/268 (51%), Gaps = 19/268 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG--LQ 469
           EIK I     +S  E  ++    + GE +    +  +   N+ LV+S+A+KY N+   ++
Sbjct: 39  EIKEIGNYQVLSKQESLNLFQRYKHGEKDL---RDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ-SCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA  W+++ +   I  + S   +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFCWIQKRMLGIICKKRSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-------RKVLKITKEPISLETPIG 581
             K V    +      R P+ EE+ K L +  E V       ++   +T +  ++   IG
Sbjct: 156 NLKYVELEDKYLQMYNRPPSVEEVVKDLDVTSEIVIRHNVYYKRATTMTLDIDTINEDIG 215

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDH 640
             ++SH     +DK+A+  ++  +  +L      +    L P+++ VL + FG+     +
Sbjct: 216 ISNSSH-----DDKSAIPSINEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVY 270

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E+ K   +T ER+ QI+ +AI+KLK
Sbjct: 271 LHKEIAKALMITTERVSQIKEEAIKKLK 298


>gi|197286218|ref|YP_002152090.1| RNA polymerase sigma factor RpoD [Proteus mirabilis HI4320]
 gi|227357334|ref|ZP_03841691.1| RNA polymerase sigma-70 factor [Proteus mirabilis ATCC 29906]
 gi|194683705|emb|CAR44685.1| RNA polymerase sigma-70 factor [Proteus mirabilis HI4320]
 gi|227162597|gb|EEI47586.1| RNA polymerase sigma-70 factor [Proteus mirabilis ATCC 29906]
          Length = 618

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 68/169 (40%), Positives = 99/169 (58%), Gaps = 9/169 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D+ D A  A+  +  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NSNDTDDDAVEAA--AQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            G   +  S+ E P     L+   D +  G   L ++I   A I P ++
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--AFIDPNAE 173


>gi|317154823|ref|YP_004122871.1| sigma-70 family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316945074|gb|ADU64125.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 397

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 79/246 (32%), Positives = 134/246 (54%), Gaps = 17/246 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A  ++V ++LRLV+ +A  +  R +Q  LDLIQEGN+GL+KA  KFD   G KFS YA +
Sbjct: 150 AAFKLVSSHLRLVVRIAMDFQRRWMQNALDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAF 209

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WVK  I + I D    +++     + K+   +   R+    +  +PT E ++K L +   
Sbjct: 210 WVKAYILKYIMDNWRMVKVGTTQTQRKLFYNLNKERQRLQAMGFDPTTEALSKSLGVSEA 269

Query: 562 GVRKV-LKITKEPISLETPIG-DEDTSH------LGDFIEDKNAVSPLDSAIQANLRETT 613
            + ++  ++++  +SL  P+G D D +       LG  IE+  A   +   +  NL+   
Sbjct: 270 EIDEMDQRLSRNDMSLNAPLGEDSDATRMDFLPSLGPGIEESLASDQIVELLLENLKA-- 327

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +  +L  +E  +L  R  +  +   TL E+G++F VTRER+RQIEA+ I K++    +
Sbjct: 328 --IRPTLNDKELAILDHR--LLSDDPMTLREIGERFEVTRERVRQIEARLIAKIRE-HMT 382

Query: 674 KKLRSF 679
           +K++ F
Sbjct: 383 EKIKGF 388


>gi|86157496|ref|YP_464281.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774007|gb|ABC80844.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 300

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 114/244 (46%), Gaps = 29/244 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +VEANLR V+ VA +Y + GL+  DLIQEGNIGLMKA +KFD     +  +YA+WW
Sbjct: 44  AGHRLVEANLRFVVKVAFEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE------IAKK 555
           ++  I   I      ++I      R     + RT   +          EE      +AKK
Sbjct: 104 IRAYIQNHILKSWSLVKIGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKK 163

Query: 556 LAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-------- 606
           L + P + V    ++    +SL+ P+ D  ++HL          +P D   Q        
Sbjct: 164 LRVRPSDVVEMTQRMEGRDLSLDAPVADGTSTHL--------EFTPADGEPQDEELARAE 215

Query: 607 --ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A L    +  +  L PRE  ++  R  I      TL ++G  F  +RER RQ+E +A+
Sbjct: 216 EDALLARRVSEAMGRLDPRERHIVEAR--IMGEGKETLRDLGHHFGFSRERARQLEIRAL 273

Query: 665 RKLK 668
            KL+
Sbjct: 274 EKLR 277


>gi|304317193|ref|YP_003852338.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778695|gb|ADL69254.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 256

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 124/227 (54%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  AREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   ++ N+  +EPT  +IAK+L +P E V
Sbjct: 97  IIGEIRRYLRDNN-SIRVSRSLRDVAYKALQIRDKLVNENSKEPTVGDIAKELNIPREEV 155

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   ++P+SL  PI  +  D  ++ D I D   V  +    Q  L+E   +    L 
Sbjct: 156 VFALDAIQDPVSLFEPIYHDGGDAIYVMDQIGDDKNVDEVWLE-QIALKEAIKK----LN 210

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L MRF  G     T  EV ++  +++ ++ ++E  A+  ++
Sbjct: 211 DREKMILTMRFFEG----KTQMEVAREIGISQAQVSRLEKSALTHMR 253


>gi|156636391|gb|ABU92466.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 68/175 (38%), Positives = 99/175 (56%), Gaps = 6/175 (3%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E ++ +     L   + D LV +L     R+   E  +++ A     + +  F+    G 
Sbjct: 29  ELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGN 88

Query: 378 ELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W+    A D P  E    +    + I +   ++++I  ET +S++  + I   + 
Sbjct: 89  ESNEEWLDQILASDKPYVEK---IKLHEEDIRRSIAKLRAIEEETSLSVNNIKDISRRMS 145

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|170744871|ref|YP_001773526.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168199145|gb|ACA21092.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 296

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 119/238 (50%), Gaps = 20/238 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 47  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  K+    R+   +I        R    ++IA +L
Sbjct: 107 IKAAIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKGRISALDEGDLRPEQVKQIATRL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P + V ++ +      SL  P+ +E      D++ D    SP   A+ A   E   R+
Sbjct: 165 GVPEQDVIEMNRRLSGDASLNAPLREEGEGEWQDWLVDD---SPSQEAVLAREEEGQNRL 221

Query: 617 ------LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L+ L PRE R+   R         TLE++  +F V+RER+RQIE +A  K++
Sbjct: 222 AALRDALSVLNPRERRIFEARR--LAEEPITLEDLSSEFGVSRERVRQIEVRAFEKVQ 277


>gi|332297914|ref|YP_004439836.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181017|gb|AEE16705.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 269

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 70/227 (30%), Positives = 115/227 (50%), Gaps = 4/227 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK ++V++NLRLV+S+A KY +  +  +DLIQEGN+GL+ AA KF +    +FSTYA  W
Sbjct: 38  AKLKLVQSNLRLVVSIANKYVSDRIGVMDLIQEGNLGLLTAASKFHYSFNTRFSTYAYSW 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + Q I R I ++   I +P    + + K+      +  +++ EPT  EIA  + +    +
Sbjct: 98  ITQYILRFIQNKIPYITLPHRKEEMLRKIHMAKIDLMQQLQSEPTLREIASYMDVSESDI 157

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP- 622
              L       S++  I         D I D +  SP    ++ NL     R L    P 
Sbjct: 158 SGALMHEYVYSSIDAEIDGTSNLTCADMIADPSP-SPEQLCLK-NLEAEDIRSLVETLPD 215

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +V+  RF         TL ++ +   ++ E +RQ+E +A++ L+
Sbjct: 216 RERQVIYYRFNFDNSRKPWTLRQISEMLGISAETVRQMELRALQFLR 262


>gi|18310743|ref|NP_562677.1| sporulation sigma factor SigG [Clostridium perfringens str. 13]
 gi|18145424|dbj|BAB81467.1| probable transcription initiation factor sigma G [Clostridium
           perfringens str. 13]
          Length = 270

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 51  AREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + TIR+   +RD  +K +    ++ N+  +EPT  +IAK+L +P E V
Sbjct: 111 IIGEIRRYLRDNN-TIRVSRSLRDIAYKALLVRDKLVNENNKEPTVSQIAKELKIPREDV 169

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI  +  D  ++ D I D KN     D +   N+       +  L
Sbjct: 170 VFALDAIQDPVSLFEPIYHDGGDAIYVMDQISDSKNQ----DDSWLENI--AIKEAMKKL 223

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 224 NDREKLILNLRFFNG----RTQMEVADEIGISQAQVSRLEKIALKHMR 267


>gi|260893400|ref|YP_003239497.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
 gi|260865541|gb|ACX52647.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
          Length = 256

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 129/229 (56%), Gaps = 16/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E+++ NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  ARSELIKGNLRLVLSVVQRFANRGEHLDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++    ++++  REP+  EIA+ L +P E V
Sbjct: 97  IIGEIRRYLRDNN-AIRVSRSLRDIAYKALQVRDVLASQYAREPSVAEIAEALKLPQEEV 155

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNA-VSPLDSAIQANLRETTTRVLAS 619
              L+  ++P+SL  P+  +  D  ++ D + D KN  V+ L++     ++E   R    
Sbjct: 156 VMALEAIQDPVSLFEPVYHDGGDPIYVMDQVGDEKNQDVNWLEN---IAIKEAMKR---- 208

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ RE ++++MRF  G       EE+G    +++ ++ ++E  A+  ++
Sbjct: 209 LSERERQIIKMRFFEGKTQMEVAEEIG----ISQAQVSRLEKAALNHMR 253


>gi|288287|emb|CAA39117.1| unnamed protein product [Myxococcus xanthus]
          Length = 246

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 121/232 (52%), Gaps = 16/232 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ANLR V+ VA +Y + G++  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGV 563
           I   I      +++       K+   +   RR   K          ++IA++L +    V
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKFGSGDAAVNVDDIARRLHVKPGEV 120

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----QANLRETTTR-VL 617
           R++  ++    +SL+ P+G++  +   DF+   +A +P D       +A L     R  L
Sbjct: 121 REMEQRMGGRDLSLDAPMGEDGGNSHVDFV--VSAAAPQDDEFADKEEAGLINARVRTAL 178

Query: 618 ASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L PRE  ++  R    MN    TL+E+G+ F  +RER RQ+E +A  KLK
Sbjct: 179 MRLDPRERFIIEQRV---MNERPMTLKELGEHFGFSRERARQLEIRAKDKLK 227


>gi|156636433|gb|ABU92487.1| RpoD [Vibrio vulnificus]
 gi|156636455|gb|ABU92498.1| RpoD [Vibrio vulnificus]
 gi|156636457|gb|ABU92499.1| RpoD [Vibrio vulnificus]
 gi|156636461|gb|ABU92501.1| RpoD [Vibrio vulnificus]
 gi|156636475|gb|ABU92508.1| RpoD [Vibrio vulnificus]
 gi|156636495|gb|ABU92518.1| RpoD [Vibrio vulnificus]
 gi|156636497|gb|ABU92519.1| RpoD [Vibrio vulnificus]
 gi|156636499|gb|ABU92520.1| RpoD [Vibrio vulnificus]
 gi|156636501|gb|ABU92521.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 68/175 (38%), Positives = 97/175 (55%), Gaps = 6/175 (3%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E ++ +     L   + D LV +L     R+   E  +++ A     + +  F+    G 
Sbjct: 29  ELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGN 88

Query: 378 ELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W+      D P  E    +    + I +   ++++I  ET +S+S  + I   + 
Sbjct: 89  ESSEEWLDKILVSDKPYAEK---IKLHEEDIRRSIAKLRAIEEETSLSVSNIKDISRRMS 145

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|205373280|ref|ZP_03226084.1| sporulation sigma factor SigG [Bacillus coahuilensis m4-4]
          Length = 258

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 140/261 (53%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + RK +   + +++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFRKMQAGDTYSREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT EEIAK L +P E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQAREKLMGETSKEPTAEEIAKVLDVPHEDIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+     ++   +  L+E   R    L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLSDERN-RDVNWIEEIALKEGLRR----LNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
            +  +++ ++ ++E  AI+ +
Sbjct: 233 DEIGISQAQVSRLEKAAIKHM 253


>gi|220931759|ref|YP_002508667.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
 gi|219993069|gb|ACL69672.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
          Length = 260

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 137/255 (53%), Gaps = 25/255 (9%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +++G+  A   +++++  NLRLV+SV +++ NRG    DL Q G IGL
Sbjct: 18  LSNEEMRKLFKKMQQGDWSA---RQKIINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     +FSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 75  IKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDTAYKALQMKESLKN 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFI-----ED 594
           K   EP+ +E++++L +P   +   L   ++PISL  PI  +  D   + D I     ED
Sbjct: 134 KKSEEPSLKEVSEELGIPRSEIIFALDAIQDPISLFEPIYHDGGDPIFVMDQISDEKTED 193

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +N +  +  A++  LR+        L+PRE+ +L  RF  G     T  EV  +  +++ 
Sbjct: 194 ENWLEGI--AVREGLRK--------LSPREKLILAYRFYEG----KTQMEVANEIGISQA 239

Query: 655 RIRQIEAKAIRKLKH 669
           ++ ++E  A+++LK 
Sbjct: 240 QVSRLEKAALKRLKR 254


>gi|110802253|ref|YP_699047.1| sporulation sigma factor SigG [Clostridium perfringens SM101]
 gi|110682754|gb|ABG86124.1| RNA polymerase sigma-G factor [Clostridium perfringens SM101]
          Length = 257

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 38  AREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + TIR+   +RD  +K +    ++ N+  +EPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-TIRVSRSLRDIAYKALLVRDKLVNENNKEPTVSQIAKELKIPREDV 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI  +  D  ++ D I D KN     D +   N+       +  L
Sbjct: 157 VFALDAIQDPVSLFEPIYYDGGDAIYVMDQISDSKNQ----DDSWLENI--AIKEAMKKL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 211 NDREKLILNLRFFNG----RTQMEVADEIGISQAQVSRLEKIALKHMR 254


>gi|197121539|ref|YP_002133490.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196171388|gb|ACG72361.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 300

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 114/244 (46%), Gaps = 29/244 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +VEANLR V+ VA +Y + GL+  DLIQEGNIGLMKA +KFD     +  +YA+WW
Sbjct: 44  AGHRLVEANLRFVVKVAFEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE------IAKK 555
           ++  I   I      ++I      R     + RT   +          EE      +AKK
Sbjct: 104 IRAYIQNHILKSWSLVKIGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKK 163

Query: 556 LAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-------- 606
           L + P + V    ++    +SL+ P+ D  ++HL          +P D   Q        
Sbjct: 164 LRVRPSDVVEMTQRMEGRDLSLDAPVADGTSTHL--------EFTPADGEPQDEELARAE 215

Query: 607 --ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A L    +  +  L PRE  ++  R  I      TL ++G  F  +RER RQ+E +A+
Sbjct: 216 EDALLARRVSEAMGRLDPRERHIVEAR--IMGEGKETLRDLGHHFGFSRERARQLEIRAL 273

Query: 665 RKLK 668
            KL+
Sbjct: 274 EKLR 277


>gi|144898533|emb|CAM75397.1| Sigma-70 region 2:Sigma-70 region 4 [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 290

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 127/245 (51%), Gaps = 22/245 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E + A  ++V ++LRLV  +A  Y + GL   DLI EGN+GLM+A +KF+   G++ S
Sbjct: 42  DYEDTAAAHQLVTSHLRLVAKIAMGYRHYGLPMADLISEGNLGLMRAVKKFEPERGFRLS 101

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPEE-- 551
           TYAMWW+K ++   + +    ++I      K  K+    R++  K++     E  P +  
Sbjct: 102 TYAMWWIKASLNEFVLNSWSLVKIGTLAAQK--KLFFNLRKVKTKLRLLDATELAPADVR 159

Query: 552 -IAKKLAMP-VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            IAK+L +   + V    ++     SL TP+G+  T  + + + D+        A    L
Sbjct: 160 AIAKELGVSETDVVNMNRRMGGRDSSLNTPVGESGTEII-ELLPDETDNQETGLAKHEEL 218

Query: 610 ---RETTTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              R+   + L SL  RE  +    R+R     +   TLEE+G +F V+RERIRQIE KA
Sbjct: 219 SKGRKLIAQALTSLNEREREIFVERRLR-----DEPLTLEELGARFGVSRERIRQIEVKA 273

Query: 664 IRKLK 668
             K++
Sbjct: 274 FEKVR 278


>gi|302793696|ref|XP_002978613.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
 gi|300153962|gb|EFJ20599.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
          Length = 458

 Score =  105 bits (262), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 132/261 (50%), Gaps = 14/261 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL--DLIQEGNIGLM 482
           ++FR +   ++ GE     A+ +++E N RLV+ +A++Y      F   DL QEG  GL+
Sbjct: 204 TDFRTLRRRLQLGEA----AQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLI 259

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A + F+   G +FSTYA++W++ A+ R+I      IR+P     K  ++ +  R +  +
Sbjct: 260 DAMDHFNPGKGTRFSTYAIFWIRTAMVRAITRTGQVIRLPFSFAAKKVEIRKARRELRVE 319

Query: 543 IKREPTPEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           + R P+ EE+ ++  + PV+             SL   +   D   L    E  + VS  
Sbjct: 320 LGRNPSDEEVMERTGLDPVQFWNIYYYSNFRVRSLNETVRGTDEEFLEYLPETGDIVSE- 378

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQI 659
                + +RE     L  L  +E  VL+ R+G+  G     +L EVG++  +++E +R+ 
Sbjct: 379 ----SSEVREEIVTALQRLKDKERMVLQHRYGLEDGAIAVKSLREVGRRLNMSQEMVRRY 434

Query: 660 EAKAIRKLKHPSRSKKLRSFL 680
           EA A+ +L+H   +K LRS L
Sbjct: 435 EASALERLRHQEEAKSLRSCL 455


>gi|156636373|gb|ABU92457.1| RpoD [Vibrio vulnificus]
 gi|156636375|gb|ABU92458.1| RpoD [Vibrio vulnificus]
 gi|156636377|gb|ABU92459.1| RpoD [Vibrio vulnificus]
 gi|156636379|gb|ABU92460.1| RpoD [Vibrio vulnificus]
 gi|156636381|gb|ABU92461.1| RpoD [Vibrio vulnificus]
 gi|156636383|gb|ABU92462.1| RpoD [Vibrio vulnificus]
 gi|156636385|gb|ABU92463.1| RpoD [Vibrio vulnificus]
 gi|156636387|gb|ABU92464.1| RpoD [Vibrio vulnificus]
 gi|156636389|gb|ABU92465.1| RpoD [Vibrio vulnificus]
 gi|156636393|gb|ABU92467.1| RpoD [Vibrio vulnificus]
 gi|156636397|gb|ABU92469.1| RpoD [Vibrio vulnificus]
 gi|156636399|gb|ABU92470.1| RpoD [Vibrio vulnificus]
 gi|156636401|gb|ABU92471.1| RpoD [Vibrio vulnificus]
 gi|156636403|gb|ABU92472.1| RpoD [Vibrio vulnificus]
 gi|156636405|gb|ABU92473.1| RpoD [Vibrio vulnificus]
 gi|156636407|gb|ABU92474.1| RpoD [Vibrio vulnificus]
 gi|156636409|gb|ABU92475.1| RpoD [Vibrio vulnificus]
 gi|156636411|gb|ABU92476.1| RpoD [Vibrio vulnificus]
 gi|156636413|gb|ABU92477.1| RpoD [Vibrio vulnificus]
 gi|156636415|gb|ABU92478.1| RpoD [Vibrio vulnificus]
 gi|156636417|gb|ABU92479.1| RpoD [Vibrio vulnificus MO6-24/O]
 gi|156636419|gb|ABU92480.1| RpoD [Vibrio vulnificus]
 gi|156636421|gb|ABU92481.1| RpoD [Vibrio vulnificus]
 gi|156636423|gb|ABU92482.1| RpoD [Vibrio vulnificus]
 gi|156636425|gb|ABU92483.1| RpoD [Vibrio vulnificus]
 gi|156636427|gb|ABU92484.1| RpoD [Vibrio vulnificus]
 gi|156636429|gb|ABU92485.1| RpoD [Vibrio vulnificus]
 gi|156636435|gb|ABU92488.1| RpoD [Vibrio vulnificus]
 gi|156636437|gb|ABU92489.1| RpoD [Vibrio vulnificus]
 gi|156636439|gb|ABU92490.1| RpoD [Vibrio vulnificus]
 gi|156636441|gb|ABU92491.1| RpoD [Vibrio vulnificus]
 gi|156636443|gb|ABU92492.1| RpoD [Vibrio vulnificus]
 gi|156636445|gb|ABU92493.1| RpoD [Vibrio vulnificus]
 gi|156636447|gb|ABU92494.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  105 bits (262), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 68/175 (38%), Positives = 99/175 (56%), Gaps = 6/175 (3%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E ++ +     L   + D LV +L     R+   E  +++ A     + +  F+    G 
Sbjct: 29  ELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGN 88

Query: 378 ELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E +  W+    A D P  E    +    + I +   ++++I  ET +S++  + I   + 
Sbjct: 89  ESNEEWLDQILASDKPYVEK---IKLHEEDIRRSIAKLRAIEEETSLSVNNIKDISRRMS 145

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|133470|sp|P19433|RPSB_MYXXA RecName: Full=RNA polymerase sigma-B factor
          Length = 246

 Score =  105 bits (262), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 121/232 (52%), Gaps = 16/232 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ANLR V+ VA +Y + G++  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGV 563
           I   I      +++       K+   +   RR   K          ++IA++L +    V
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKFGSGDAAVNVDDIARRLHVKPGEV 120

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----QANLRETTTR-VL 617
           R++  ++    +SL+ P+G++  +   DF+   +A +P D       +A L     R  L
Sbjct: 121 REMEQRMGGRDLSLDAPMGEDGGNSHVDFV--VSAAAPQDDEFADKEEAGLINARVRAAL 178

Query: 618 ASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L PRE  ++  R    MN    TL+E+G+ F  +RER RQ+E +A  KLK
Sbjct: 179 MRLDPREPFIIEQRV---MNERPMTLKELGEHFGFSRERARQLEIRAKDKLK 227


>gi|220916304|ref|YP_002491608.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954158|gb|ACL64542.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 300

 Score =  105 bits (262), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 119/240 (49%), Gaps = 21/240 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +VEANLR V+ VA +Y + GL+  DLIQEGNIGLMKA +KFD     +  +YA+WW
Sbjct: 44  AGHRLVEANLRFVVKVAFEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWW 103

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE------IAKK 555
           ++  I   I      ++I      R     + RT   +          EE      +AKK
Sbjct: 104 IRAYIQNHILKSWSLVKIGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKK 163

Query: 556 LAM-PVEGVRKVLKITKEPISLETPIGDEDTSHL------GDFIEDKNAVSPLDSAIQAN 608
           L + P + V    ++    +SL+ P+ D  ++HL      G+  +++ A +  D+ +   
Sbjct: 164 LRVRPSDVVEMTQRMEGRDLSLDAPVADGTSTHLEFTPADGEPQDEELARAEEDALLARR 223

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + E   R    L PRE  ++  R  I      TL ++G  F  +RER RQ+E +A+ KL+
Sbjct: 224 VSEAMGR----LDPRERHIVEAR--IMGEGKETLRDLGHHFGFSRERARQLEIRALEKLR 277


>gi|168186812|ref|ZP_02621447.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
 gi|169295146|gb|EDS77279.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
          Length = 256

 Score =  105 bits (262), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 126/230 (54%), Gaps = 14/230 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++++++ V  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+
Sbjct: 35  NLSREKFVRGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAV 94

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R + D + +IR+   +RD  +K ++   R+  K  ++P   +IAK+L +P E
Sbjct: 95  PMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQVRDRIIKKENKDPNVSQIAKELDLPRE 153

Query: 562 GVRKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLA 618
            V   L   ++P+SL  PI  +  D  ++ D I D KNA    D +   N+  +    + 
Sbjct: 154 EVVFALDAIQDPVSLFEPIYHDGGDALYVMDQISDNKNA----DESWIENI--SIKEAMK 207

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ +L MRF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 208 RLNEREKLILNMRFFQG----RTQMEVADEIGISQAQVSRLEKTALKHMR 253


>gi|160880600|ref|YP_001559568.1| sporulation sigma factor SigG [Clostridium phytofermentans ISDg]
 gi|160429266|gb|ABX42829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 260

 Score =  105 bits (262), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 128/238 (53%), Gaps = 15/238 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA   ++  ++ NLRLV+S+ ++++N      DL Q G IGLMKA + FD   G
Sbjct: 31  IKQGDKEA---RELYIKGNLRLVLSIIQRFSNSNENVDDLFQIGCIGLMKAIDNFDITQG 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   I R + D +  IR+   +RD  +K +     +  K  +EPT  EIA
Sbjct: 88  VKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSLRDTAYKAIYAKEMLLKKNDKEPTVCEIA 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            ++ +  E +   L   + P+SL  P+  E  DT ++ D + DK      +   + +L+E
Sbjct: 147 NEVGISQEDIVAALDAIQSPVSLYEPVYSEGGDTLYIMDQVSDKKNKEE-NWVEEISLKE 205

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              R    L+PRE  ++ +RF  G     T  EV ++  +++ ++ ++E  A++ +++
Sbjct: 206 AMAR----LSPRENNIINLRFFQG----KTQMEVAEEIQISQAQVSRLEKNALKNMRN 255


>gi|156636431|gb|ABU92486.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  105 bits (262), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 67/175 (38%), Positives = 98/175 (56%), Gaps = 6/175 (3%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           E ++ +     L   + D LV +L     R+   E  +++ A     + +  F+    G 
Sbjct: 29  ELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGN 88

Query: 378 ELDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E    W+      D P  E    +    + I +  +++++I  ET +S++  + I   + 
Sbjct: 89  ESSEEWLDKILVSDKPYAEK---IKLHEEDIRRSISKLRAIEEETSLSVNNIKDISRRMS 145

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 200


>gi|23014972|ref|ZP_00054764.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 292

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/239 (33%), Positives = 126/239 (52%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y + GL   DLI EGNIGLM+A +KF+   G++ +TYAMWW
Sbjct: 48  AAHKLVTSHLRLVAKIALGYRHYGLPVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE---IAKKL 556
           +K ++   + +    ++I      K  K+    RR+ ++++     +  PE    IA++L
Sbjct: 108 IKASLNEFVLNSWSMVKIGTLAAQK--KLFFNLRRIKSRLRLLESGDLAPEHVTTIAREL 165

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
            +    V  +  ++     SL TP+G E  + + D + D+        A +  L   R  
Sbjct: 166 DVDERDVVAMNRRMAGRDSSLNTPVG-EGGAEIQDLMADEADNQETSLAKREELSKGRTL 224

Query: 613 TTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R L SLT RE  V    R+R     +   TLEE+G ++ V+RERIRQIE KA  K++
Sbjct: 225 IARALDSLTEREREVFVERRLR-----DDPLTLEELGGRYGVSRERIRQIEVKAFEKVR 278


>gi|302382389|ref|YP_003818212.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302193017|gb|ADL00589.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 295

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 82/253 (32%), Positives = 132/253 (52%), Gaps = 21/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E + S +   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G+
Sbjct: 40  RWSEHQDSESAHRLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE 550
           + +TYAMWW++ +I   I      +++      K  K+    R+  ++I    + +  PE
Sbjct: 100 RLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQISAFEEGDLRPE 157

Query: 551 E---IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
               IA KL +  E V  + +      SL  P+  +  S   D++ D NAVS  ++A+ A
Sbjct: 158 HLAAIATKLGVSEEEVTNMNRRLGGDASLNAPLRVDGESEWQDWLSDDNAVSQ-ETAL-A 215

Query: 608 NLRETTTRV------LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIE 660
           +  E + R+      +  LT RE+ +L  R    +  D  TLEE+  Q+ V+RER+RQIE
Sbjct: 216 DSEEKSLRMGLLQEAMGELTEREKHILTER---RLKDDPVTLEELAGQYGVSRERVRQIE 272

Query: 661 AKAIRKLKHPSRS 673
            +A  KL+   R+
Sbjct: 273 VRAFEKLQKAMRA 285


>gi|220927320|ref|YP_002502622.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219951927|gb|ACL62319.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 296

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 118/238 (49%), Gaps = 20/238 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 47  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  K+    R+   +I        R    ++IA +L
Sbjct: 107 IKAAIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKGRISALDEGDLRPEQVKQIATRL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P + V  + +      SL  P+ +E      D++ D    SP   A+ A   E   R+
Sbjct: 165 GVPEQDVIDMNRRLSGDASLNAPLREEGEGEWQDWLVDD---SPSQEAVLAREEEGQNRL 221

Query: 617 ------LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L+ L PRE R+   R         TLE++  +F V+RER+RQIE +A  K++
Sbjct: 222 AALRDALSVLNPRERRIFEARR--LAEEPITLEDLSTEFGVSRERVRQIEVRAFEKVQ 277


>gi|283852956|ref|ZP_06370215.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
 gi|283571646|gb|EFC19647.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
          Length = 342

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 127/239 (53%), Gaps = 15/239 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   ++ ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G KFS YA +
Sbjct: 95  AAFRLISSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAY 154

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I     + K+   +   R     +  +P+  ++++ L +   
Sbjct: 155 WIKAYILKYIMDNWRMVKIGTTQAQRKLFYNLNKERHRLQTLGFDPSASQLSQALNVTES 214

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP------LDSAIQANLRETTT 614
            + ++  +++   +SL+  +GD+ TS   DF+    A++P          I   L +   
Sbjct: 215 DIVEMDQRLSGNDLSLDMTLGDDSTSTRLDFLP---ALTPGIEEILAGDEISHQLDKHIQ 271

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSR 672
            +   L  +E  +L  R  I  ++  TL E+G ++ +TRER+RQIEA+ + KLK H SR
Sbjct: 272 TIRPKLNEKELDLLDNR--ILSDSPATLREIGAKYGITRERVRQIEARLLEKLKEHLSR 328


>gi|188580210|ref|YP_001923655.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179343708|gb|ACB79120.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 297

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 116/239 (48%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 47  AAHRLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  K+    R+   +I        R    ++IA  L
Sbjct: 107 IKAAIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKGRISALDEGDLRPDQVQQIATSL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P + V  + +      SL  P+ +E      D++ D    SP    + A   E   R+
Sbjct: 165 GVPTQDVIDMNRRLSGDTSLNAPLREEGEGEWQDWLVDN---SPSQETVLAREEEGRNRL 221

Query: 617 ------LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  L PRE R+   R    +  D  TLE++  +F V+RER+RQIE +A  K++
Sbjct: 222 SALRDALGVLNPRERRIFEAR---RLADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQ 277


>gi|312876365|ref|ZP_07736350.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796859|gb|EFR13203.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 255

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 125/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +E NLRLV+SV +K+ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 36  ARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++RI   ++D  +K ++   +  +  ++EPT EEIAK+L++  E +
Sbjct: 96  IIGEIRRYLRDNN-SMRISRSLKDTAYKALKIKEKYISNNQKEPTLEEIAKELSITKEEL 154

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
              L   +EPISL  P+  +  DT ++ + + D        S+    L E + +  L+ L
Sbjct: 155 VFTLDSIQEPISLYEPVFQDSTDTMYVVEKLYDHK------SSENVWLEEISLKDALSRL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T RE+ +L + +  G     T  EV +   +++ ++ +IE  AI  +K
Sbjct: 209 TKREKEILYLHYYKG----KTQMEVARIVGISQAQVSRIEKSAIGHIK 252


>gi|153953967|ref|YP_001394732.1| sporulation sigma factor SigG [Clostridium kluyveri DSM 555]
 gi|219854581|ref|YP_002471703.1| hypothetical protein CKR_1238 [Clostridium kluyveri NBRC 12016]
 gi|146346848|gb|EDK33384.1| SigG [Clostridium kluyveri DSM 555]
 gi|219568305|dbj|BAH06289.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 257

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 123/227 (54%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   ++  +  +EPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALQVRDKLIRENNKEPTISQIAKELELPREEV 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   ++P+SL  PI  +  D  ++ D I D   V   D     N+  +    +  L 
Sbjct: 157 VFALDAIQDPVSLFEPIYHDGGDAIYVMDQISDTKNV---DENWLENI--SIKEAMKKLN 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A+R ++
Sbjct: 212 DREKLILNLRFFDG----RTQMEVAHEIGISQAQVSRLEKTALRHMR 254


>gi|89895050|ref|YP_518537.1| hypothetical protein DSY2304 [Desulfitobacterium hafniense Y51]
 gi|89334498|dbj|BAE84093.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 260

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 134/250 (53%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++   + G+ EA   ++ ++  NL+L+ ++ +++++RG +  DL Q G IGL
Sbjct: 16  LSDEEMMDLLHRAQNGDAEA---RERLINCNLKLIFNLVQRFSHRGYELEDLFQIGTIGL 72

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +KFD+  G KFSTYA+  +   I R + D    +++P   ++ ++KV +    +S 
Sbjct: 73  IKAIDKFDFTYGVKFSTYAVPMIIGEIRRFLRDDH-PVKVPRSYKELVYKVNKARESLSA 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + R+PT  EIA+ + +  E +   L+  + P S+   +  +D+  +  +I D+    P+
Sbjct: 132 TLGRDPTIGEIAESIGVDREDIVSALEAVQSPTSIHDTLYQDDSDPI--YILDQ---LPM 186

Query: 602 DSAIQANLRETTT--RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +  ++A   E      VL  L  RE+RVL MRF      D T  E+     +++ +I +I
Sbjct: 187 EKDLEAGWFEKIALKEVLDKLPEREKRVLMMRF----YEDKTQSEIAALLNLSQVQISRI 242

Query: 660 EAKAIRKLKH 669
           E  A+ +++ 
Sbjct: 243 ERAALHRIRQ 252


>gi|219669461|ref|YP_002459896.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
 gi|219539721|gb|ACL21460.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
          Length = 261

 Score =  105 bits (261), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 134/250 (53%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++   + G+ EA   ++ ++  NL+L+ ++ +++++RG +  DL Q G IGL
Sbjct: 17  LSDEEMMDLLHRAQNGDAEA---RERLINCNLKLIFNLVQRFSHRGYELEDLFQIGTIGL 73

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +KFD+  G KFSTYA+  +   I R + D    +++P   ++ ++KV +    +S 
Sbjct: 74  IKAIDKFDFTYGVKFSTYAVPMIIGEIRRFLRDDH-PVKVPRSYKELVYKVNKARESLSA 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + R+PT  EIA+ + +  E +   L+  + P S+   +  +D+  +  +I D+    P+
Sbjct: 133 TLGRDPTIGEIAESIGVDREDIVSALEAVQSPTSIHDTLYQDDSDPI--YILDQ---LPM 187

Query: 602 DSAIQANLRETTT--RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +  ++A   E      VL  L  RE+RVL MRF      D T  E+     +++ +I +I
Sbjct: 188 EKDLEAGWFEKIALKEVLDKLPEREKRVLMMRF----YEDKTQSEIAALLNLSQVQISRI 243

Query: 660 EAKAIRKLKH 669
           E  A+ +++ 
Sbjct: 244 ERAALHRIRQ 253


>gi|126650128|ref|ZP_01722361.1| sporulation sigma factor SigF [Bacillus sp. B14905]
 gi|126593300|gb|EAZ87262.1| sporulation sigma factor SigF [Bacillus sp. B14905]
          Length = 263

 Score =  105 bits (261), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 133/254 (52%), Gaps = 17/254 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  +S  E R +++  +KG+ EA   +K MVE N RLV S+ +++T RG++  DL Q 
Sbjct: 7   SSEKLLSQEEMRDLIARAQKGDHEA---RKRMVEGNTRLVWSIVQRFTTRGVELEDLFQI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGLMK+ +KFD     KFSTYA+  +   I R + D    +++   +R+   K+    
Sbjct: 64  GCIGLMKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGM-VKVSRSIRELNFKIRHAT 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIED 594
                K +  PT +E+A+ L +  E +       ++P SL   +   + D+  L D ++D
Sbjct: 123 DEFIKKNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKD 182

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           + +  P D      L+E  TR    L PRE+ ++ +R+     +D T  E+  +  +++ 
Sbjct: 183 EKSEQPFDY---IPLKEVLTR----LEPREQSIIYLRYF----SDCTQTEIANRLGISQV 231

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K + +LK
Sbjct: 232 QVSRLEKKILAQLK 245


>gi|220929478|ref|YP_002506387.1| sporulation sigma factor SigG [Clostridium cellulolyticum H10]
 gi|219999806|gb|ACL76407.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulolyticum
           H10]
          Length = 257

 Score =  104 bits (260), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 122/227 (53%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E ++ NLRLV+SV +++ NRG    DL Q G IGL+K+ + FD     KFSTYA+  
Sbjct: 38  ARDEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKSIDNFDVTQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K ++   R++ +  +EPT  E+A++L +P E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALQAKERLTTQNSKEPTIVELAQELQLPKEDI 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RVLASLT 621
              L   ++PISL   +  +     GD I   + VS  D  I  N  ET +    +  L 
Sbjct: 157 VFALDAIQDPISLFESVYHDG----GDAIYVMDQVSD-DKNIDENWLETISLKEAMRKLN 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A+  +K
Sbjct: 212 DREKLILNLRFFEG----RTQMEVADEIGISQAQVSRLEKTALMHMK 254


>gi|67458885|ref|YP_246509.1| RNA polymerase factor sigma-32 [Rickettsia felis URRWXCal2]
 gi|67004418|gb|AAY61344.1| RNA polymerase sigma-32 factor [Rickettsia felis URRWXCal2]
          Length = 293

 Score =  104 bits (260), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 82/276 (29%), Positives = 139/276 (50%), Gaps = 23/276 (8%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S L+  N+I S++ E      EF    S + + + +A+    ++V ++L+LV  +A  Y 
Sbjct: 18  SYLQKINKIPSLTQE-----EEFLLAKSYLEENDLQAA---HKLVTSHLKLVAKIASGYR 69

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++   
Sbjct: 70  TYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTT 129

Query: 525 MRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKV-LKITKEPISLET 578
              K     + +   +++N   R  T +   +IA +L + V  V ++  +I+   +SL  
Sbjct: 130 AAQKKLFFSLNKIKHKITNLYSRAITADDFIQIADELGVSVNEVSEMNTRISGPDLSLNN 189

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT------TRVLASLTPREERVLRMRF 632
           PI  +D    G+ IE      P    I  N +++T      +  +  L  RE R+   R 
Sbjct: 190 PINSDDAES-GELIELLPETRPTPETIAINKQDSTGKRKLLSNAMKILNDRELRIFTER- 247

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 248 -KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|33322911|gb|AAQ07192.1|AF496500_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 141

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 54/126 (42%), Positives = 84/126 (66%), Gaps = 3/126 (2%)

Query: 549 PEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PEE+A ++  P++  ++++ + K  E  SL+ P+G+E  S LGD +ED  A +P +    
Sbjct: 6   PEELAAEMNEPLQKXQEIITVAKNQETDSLDKPVGEEGDSQLGDLLEDNKATNPEEYTAF 65

Query: 607 ANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L++  + ++   LT RE +VL++RFG+  +  HTLEEVG+   VTRER+RQIEAKA++
Sbjct: 66  EMLKDQLSSMMGEFLTDREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQIEAKAVK 125

Query: 666 KLKHPS 671
           KLKH S
Sbjct: 126 KLKHHS 131


>gi|57239060|ref|YP_180196.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58579003|ref|YP_197215.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58617062|ref|YP_196261.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|57161139|emb|CAH58052.1| RNA polymerase sigma-70 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58416674|emb|CAI27787.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|58417629|emb|CAI26833.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 622

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 60/151 (39%), Positives = 95/151 (62%), Gaps = 2/151 (1%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-EDSLDLASS 98
           ++G+VT  ++N       +S++ +++T+++L + GINV++  D EDE  S  +S  L   
Sbjct: 20  KQGFVTFNDINDVFSDYVLSADNIDETISLLQDSGINVLEQSD-EDEASSIVESGRLKDG 78

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
             +  V     K      TDDP+RMYL EM S+ELLSREGEI IAK+I++ +  M+ SL 
Sbjct: 79  IDDDDVSDTSIKSWDFGQTDDPIRMYLCEMSSVELLSREGEIEIAKKIKSEKVNMLRSLV 138

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ESP+  +  + WRD+L +   +LR++IDL+A
Sbjct: 139 ESPMVLRTFMSWRDDLVNEQIMLRDLIDLDA 169


>gi|260425737|ref|ZP_05779717.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
 gi|260423677|gb|EEX16927.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
          Length = 292

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/259 (30%), Positives = 136/259 (52%), Gaps = 24/259 (9%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EAS+ +  ++ A +RL IS+A K+   G    DL+QE  +GLMKAA+KFD   G +FSTY
Sbjct: 39  EASLHR--LINAYMRLAISMASKFKRYGAPMGDLVQEAGLGLMKAADKFDPDRGVRFSTY 96

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--------- 550
           A+WW+K +I   +      +R       K   +    RR+  +++RE   E         
Sbjct: 97  AVWWIKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARLEREAAAEGKTLERHML 154

Query: 551 --EIAKKLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIED--KNAVSPLDSA 604
              IA+++ +P+  V  +  +++    SL  T   DED     D +ED  +   S ++  
Sbjct: 155 HAAIAQEIGVPLSDVEMMEGRLSGSDFSLNATQSSDEDGREWIDTLEDDGEQGSSVVEGR 214

Query: 605 I-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +  A LRE     +++L  RE  ++R R     +   TLE +G++  +++ER+RQ+EA A
Sbjct: 215 LDNAQLREWLVVAMSALNDRERFIVRER--KLRDETRTLESLGQELGLSKERVRQLEAAA 272

Query: 664 IRKLKHP--SRSKKLRSFL 680
             K++    ++S++++ FL
Sbjct: 273 FAKMRKSLEAQSREVQHFL 291


>gi|254519266|ref|ZP_05131322.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
 gi|226913015|gb|EEH98216.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
          Length = 259

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ NRG    DL Q G IGLMKA + FD     KFSTYA+  
Sbjct: 40  ARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPM 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +    R+  +  +EPT  +IAK+L +P E V
Sbjct: 100 IIGEIRRYLRDNN-SIRVSRSLRDIAYKALLVRDRLIKENNKEPTVSQIAKELNLPREEV 158

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   ++P+SL  PI  +  D  ++ D I D KN+    D +   N+  +    +  L
Sbjct: 159 VFALDAIQDPVSLFEPIYHDGGDAIYVMDQISDSKNS----DESWLENI--SIKEAMKKL 212

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 213 NDREKLILTLRFFNG----RTQMEVADEIGISQAQVSRLEKTALKHMR 256


>gi|255085668|ref|XP_002505265.1| predicted protein [Micromonas sp. RCC299]
 gi|226520534|gb|ACO66523.1| predicted protein [Micromonas sp. RCC299]
          Length = 477

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 85/289 (29%), Positives = 132/289 (45%), Gaps = 62/289 (21%)

Query: 444 AKKEMVEANLRLVISVAKKY------TNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           A++ +V  N+ L  +VA          +RGL    DL+QEG  GL  AA+KFD   GY+F
Sbjct: 85  ARRVLVTRNVGLARTVAADIHAKLNDADRGLLSVSDLMQEGCAGLATAADKFDPQRGYRF 144

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA +W+K+A+   + +   TIR+P+H+ + I K+ +  R +     R+PT +E+A +L
Sbjct: 145 STYAFFWIKKAVIDCVGNSGRTIRLPIHVNENIQKMKKATRELKEIKVRDPTEDELADRL 204

Query: 557 AMPVEGVRKV-LKITKEPISLETPI---GD---------------EDTSHLGDFIEDKNA 597
              V  +R++ +   + P+S++      GD                      DF    NA
Sbjct: 205 GWSVVKLRQMKVWAFRTPVSMDATTAKKGDPWEDADDAVAEAASLNAAMQSSDFGTGLNA 264

Query: 598 VSPLDSA---IQAN-LRETTTRVLASLTPREERVLRMRFGI------------------- 634
             P D+A   + A+ LR     V ++L PRE  +LR RFG+                   
Sbjct: 265 --PSDTAEADVDADLLRMALEEVFSTLLPREAFILRHRFGLAAASTAMEGGDWLKASRAE 322

Query: 635 ---------GMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
                    GM T      + +G    V+ E +R  E +A+ KLK P R
Sbjct: 323 VLSALRDDEGMGTRGGANFKTLGNLLGVSSESVRTYERRALAKLKQPDR 371


>gi|323702540|ref|ZP_08114203.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532514|gb|EGB22390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 260

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 129/237 (54%), Gaps = 10/237 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K +   + A++ +V  NL+LV ++ +++ NRG +  DL Q G IGLMKA +KFD   
Sbjct: 25  LIKKAQAGDADARERLVNCNLKLVFNLVQRFNNRGYELEDLFQIGCIGLMKAIDKFDLSY 84

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R + D S  +++   +++  +K+ +T  R++ ++ R+P+  EI
Sbjct: 85  DVKFSTYAVPMIVGEIRRFLRDDS-PVKVSRSLKETAYKIQQTRDRLTARLGRDPSINEI 143

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A++L    E V   L+  + P S+   +  +D    GD I   + +S  D      L + 
Sbjct: 144 AQELGCHREEVVSALEAAQTPTSIYETLHQDD----GDPIYILDQLSGADDGDSPWLEKL 199

Query: 613 TTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +L  L  R+ ++L  RF      D T  EV  +  +++ ++ ++E +A+RKLK
Sbjct: 200 AVKQLLIELPERDRQILLWRF----FEDKTQSEVALRLGLSQVQVSRLERQALRKLK 252


>gi|163850434|ref|YP_001638477.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|163662039|gb|ABY29406.1| RNA polymerase sigma factor RpoH [Methylobacterium extorquens PA1]
          Length = 297

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 115/239 (48%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 47  AAHRLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  K+    R+   +I        R    + IA  L
Sbjct: 107 IKAAIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKGRISALDEGDLRPDQVQHIATSL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P + V  + +      SL  P+ +E      D++ D    SP    + A   E   R+
Sbjct: 165 GVPAQDVIDMNRRLSGDTSLNAPLREEGEGEWQDWLVDN---SPSQETVLAREEEGRNRL 221

Query: 617 ------LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  L PRE R+   R    +  D  TLE++  +F V+RER+RQIE +A  K++
Sbjct: 222 SALRDALGVLNPRERRIFEAR---RLADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQ 277


>gi|114797392|ref|YP_759060.1| RNA polymerase factor sigma-32 [Hyphomonas neptunium ATCC 15444]
 gi|114737566|gb|ABI75691.1| alternative sigma factor RpoH [Hyphomonas neptunium ATCC 15444]
          Length = 298

 Score =  104 bits (260), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 129/248 (52%), Gaps = 21/248 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E + A ++MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G+
Sbjct: 42  RWHEHEDTEAAEKMVTSHLRLVAKIAMGYRGYGLPMAEVISEGNVGLMQAVKKFDPDKGF 101

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE 550
           + +TYAMWW++ AI   I      +++      K  K+    RR+  +++     +  PE
Sbjct: 102 RLATYAMWWIRAAIQEYILRSWSLVKLGTTAAQK--KLFFNLRRLKGEMQALEEGDLKPE 159

Query: 551 E---IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           +   IA+KL +    V  +  +++    SL  P+G +      D++ D     P  +   
Sbjct: 160 QARLIAEKLNVTETEVYSMNGRMSGSDASLNVPMGTDGDMEWQDWLADDE---PGTAETF 216

Query: 607 ANLRE------TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           AN +E        T+ +  L+ RE  +L  R  +  +   TLEE+ +Q+ V+RERIRQIE
Sbjct: 217 ANSQELDARMTLLTQAMEDLSERERHILTERRLV--DEPKTLEELSEQYNVSRERIRQIE 274

Query: 661 AKAIRKLK 668
            +A  KL+
Sbjct: 275 VRAFEKLQ 282


>gi|218528993|ref|YP_002419809.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|240137510|ref|YP_002961981.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254559688|ref|YP_003066783.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|218521296|gb|ACK81881.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|240007478|gb|ACS38704.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254266966|emb|CAX22766.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 297

 Score =  104 bits (259), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 115/239 (48%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 47  AAHRLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  K+    R+   +I        R    + IA  L
Sbjct: 107 IKAAIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKGRISALDEGDLRPDQVQHIATSL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P + V  + +      SL  P+ +E      D++ D    SP    + A   E   R+
Sbjct: 165 GVPAQDVIDMNRRLSGDTSLNAPLREEGEGEWQDWLVDN---SPSQETVLAREEEGRNRL 221

Query: 617 ------LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  L PRE R+   R    +  D  TLE++  +F V+RER+RQIE +A  K++
Sbjct: 222 SALRDALGVLNPRERRIFEAR---RLADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQ 277


>gi|313901760|ref|ZP_07835186.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467966|gb|EFR63454.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 261

 Score =  104 bits (259), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 141/263 (53%), Gaps = 17/263 (6%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     +S  + R +   +R+G+ EA   ++++V+ NLRLV+SV +++ +R
Sbjct: 8   NKVEICGVNTAELPVLSNEQMRVLFRRMREGDEEA---RQQLVQGNLRLVLSVIQRFNHR 64

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +R
Sbjct: 65  GEPVDDLFQVGCIGLMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLR 123

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D  +K ++   +++++  REPT EEIA++L  P E V   L   ++P+SL  PI  +   
Sbjct: 124 DVAYKALQVRDQLTHRHGREPTLEEIAQELGQPREEVVHALDAIQDPVSLFEPIYQDG-- 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             GD I   + VS      +  L     R  ++ L  RE+ ++  RF  G     T  EV
Sbjct: 182 --GDPIFVVDQVSDDKQRDERWLETIAVREAMSRLDEREQLIITKRFYQG----KTQMEV 235

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
             +  +++ ++ ++E  A+++++
Sbjct: 236 ANEIGISQAQVSRLEKAALQRMR 258


>gi|294676015|ref|YP_003576630.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294474835|gb|ADE84223.1| RNA polymerase sigma-32 factor-1 [Rhodobacter capsulatus SB 1003]
          Length = 292

 Score =  104 bits (259), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 132/253 (52%), Gaps = 26/253 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW+K +
Sbjct: 45  LVSAYMRLAISMASKFRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWWIKAS 104

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE-------EIAKKLAMPV 560
           I   +      +R       K   +    +R+  +I+RE   E       ++ +K+A+ +
Sbjct: 105 IQEFVMRNWSMVRTGSTSSQK--ALFFNLKRVQAQIQREAEAEGVVLDGAQLREKVAISI 162

Query: 561 EGVRKV------LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN----L 609
            GV          +++   +SL  P   DED     D +ED+   SP     +A+    +
Sbjct: 163 -GVSMADVEMMEGRLSGSDLSLNAPQSHDEDGREWVDTLEDEGG-SPETRVTEAHDGAKM 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + +  L+ RE  ++  R  I  +   TLE +G++  +++ERIRQ+EA+A  K++ 
Sbjct: 221 RDWLGQAMGQLSARERYIVAQRRLI--DEPRTLESLGEELGLSKERIRQLEAQAFSKMRK 278

Query: 670 P--SRSKKLRSFL 680
              SRS+++  F 
Sbjct: 279 SLESRSEEVIGFF 291


>gi|167628452|ref|YP_001678951.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591192|gb|ABZ82940.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 264

 Score =  104 bits (259), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 124/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ NLRLV ++ +++ +RG +  DL Q G IGL+KA +KFD     +FSTYA+  
Sbjct: 35  ARERLIQCNLRLVFNLVQRFQHRGYELEDLFQIGVIGLIKAIDKFDLSYNVRFSTYAVPM 94

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S  +++    ++   ++ R  + ++  + REPT +EIA  + MPVE V
Sbjct: 95  IVGEIRRFLRDDS-PVKVSRSYKEIAQRIHRVRQELNGSLGREPTVQEIAGAMNMPVEDV 153

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTP 622
            + L+  + P S+   +  +D   +  F+ D+ A V   +SA   +L      VL+ L  
Sbjct: 154 VEALEAVQLPTSIHETLYQDDGDPI--FLLDQLASVGTEESAWFDHL--ALKDVLSRLAA 209

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  +L MRF      D T  EV     +++ +I +IE  A++K++
Sbjct: 210 REREILEMRF----FQDKTQTEVATLVGLSQVQISRIERAALKKIR 251


>gi|303248805|ref|ZP_07335056.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
 gi|302489817|gb|EFL49747.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
          Length = 344

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 130/245 (53%), Gaps = 15/245 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   ++ ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G KFS YA +
Sbjct: 97  AAFRLISSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAY 156

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I     + K+   +   R     +  +P+  ++++ L +   
Sbjct: 157 WIKAYILKYIMDNWRMVKIGTTQAQRKLFYNLNKERNRLQTLGFDPSASQLSEALNVTES 216

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP------LDSAIQANLRETTT 614
            + ++  +++   +SL+  +G++ TS   DF+    A++P          I   L +   
Sbjct: 217 DIVEMDQRLSGNDLSLDVSLGEDSTSTRLDFLP---ALTPGIEEILAGDEISHQLEKHIQ 273

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +  SL  +E  +L  R  I  ++  TL E+G ++ +TRER+RQIEA+ + KLK    SK
Sbjct: 274 TIRPSLNEKELDLLDNR--ILSDSPVTLREIGAKYGITRERVRQIEARLLEKLKE-HLSK 330

Query: 675 KLRSF 679
           ++  F
Sbjct: 331 RIEDF 335


>gi|91205341|ref|YP_537696.1| RNA polymerase factor sigma-32 [Rickettsia bellii RML369-C]
 gi|91068885|gb|ABE04607.1| RNA polymerase sigma-32 factor [Rickettsia bellii RML369-C]
          Length = 294

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 141/276 (51%), Gaps = 23/276 (8%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S L+  N+I S++ E      EF    S + + + +A+    ++V ++L+LV  +A  Y 
Sbjct: 18  SYLQKINKIPSLTQE-----EEFLLAKSYLEQNDLQAA---HKLVTSHLKLVAKIATGYR 69

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++   
Sbjct: 70  TYGLPVTELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTT 129

Query: 525 MRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKV-LKITKEPISLET 578
              K     + +   +++N   R  T +   +IA +L + V  V  + ++++   +SL  
Sbjct: 130 AAQKKLFFSLSKIKNKITNLYSRAITSDDFVQIADELGVSVSEVSDMNIRLSGSDLSLNN 189

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-TRVLAS-----LTPREERVLRMRF 632
            I ++D S  G+ IE      P   AI  +  + T  R L S     L  RE R+L  R 
Sbjct: 190 TINNDDASS-GELIELLPETRPSPEAIAISKEDMTHKRALLSSAMKVLNARELRILTER- 247

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 248 -KLQDTPKTLDVLSSEYNISKERIRQIENTAFEKIK 282


>gi|23098931|ref|NP_692397.1| sporulation sigma factor SigG [Oceanobacillus iheyensis HTE831]
 gi|22777159|dbj|BAC13432.1| stage III sporulation protein G (RNA polymerase
           sporulation-specific sigma G factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 260

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 125/237 (52%), Gaps = 12/237 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            VR  E     A++E+V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD   
Sbjct: 28  FVRMQEDGDITAREELVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSH 87

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D +  IR+   +RD  +K ++   ++ +K  +EP+P EI
Sbjct: 88  NVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLISKTSKEPSPAEI 146

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK++ +P   V   L   ++P+SL  PI ++  D   + D I D+      DS+    L 
Sbjct: 147 AKEMDIPQTDVVFALDAIQDPVSLFEPIYNDGGDPIFVMDQISDE---KDKDSSWVDKL- 202

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +    +  L  RE+ +L  RF  G     T  EV  +  +++ ++ ++E  AI ++
Sbjct: 203 -SLKEGMHQLNEREKMILNKRFFQG----KTQMEVADEIGISQAQVSRLEKAAISQM 254


>gi|291544789|emb|CBL17898.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. 18P13]
          Length = 257

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 129/228 (56%), Gaps = 15/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++  NLRLV+SV +++  RG    DL Q G IGL+KA   FD     +FSTY +  
Sbjct: 39  ARDKLINGNLRLVLSVIQRFAGRGEDIDDLFQIGVIGLIKAINNFDLSKEVRFSTYCVPM 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D +  I++   +RD  +K ++   +++ + ++EPT +EIAK++      V
Sbjct: 99  ISGELRRFLRDYN-HIKVSRSLRDLAYKAMQAKEQLTAEQQKEPTMDEIAKRIDAKRSDV 157

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAV-SPLDSAIQANLRETTTRVLASL 620
              L+   +P+SL  P+  +  DT ++ D I D+N+V S LD   +  LR+     + +L
Sbjct: 158 VLALESVTDPVSLYEPVYSDAGDTLYVLDQISDQNSVDSWLD---EIALRDA----IKAL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PRE+R+L +RF  G     T  EV ++  +++ ++ ++E  A+ ++K
Sbjct: 211 QPREKRILYLRFFQG----KTQVEVAQEIGISQAQVSRLEKGALNQIK 254


>gi|302874724|ref|YP_003843357.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
 gi|302577581|gb|ADL51593.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
          Length = 256

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 131/245 (53%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R ++  ++ G+    I++++ +  NLRLV+SV +++ NRG    DL Q G IGL+KA 
Sbjct: 22  EMRELLDKMKAGDY---ISREKFIRGNLRLVLSVIQRFNNRGENADDLFQVGCIGLIKAL 78

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  ++ ++   ++  +  +
Sbjct: 79  DNFDLTQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYRALQVRDKLLTENNK 137

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  +IAK+L +  E V   L   +EP+SL  PI  +  D  ++ D I D      LD 
Sbjct: 138 EPTVYQIAKELDVAKEEVIFALDAIQEPVSLFEPIYHDGGDAIYVMDQISDS---KNLDE 194

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +   N+       +  L+ RE+ +L MRF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 195 SWLENI--AIKEAMKRLSDREKLILNMRFFDG----RTQMEVADEIGISQAQVSRLEKNA 248

Query: 664 IRKLK 668
           +R ++
Sbjct: 249 LRHMR 253


>gi|218289914|ref|ZP_03494104.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240054|gb|EED07240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 259

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 84/269 (31%), Positives = 143/269 (53%), Gaps = 24/269 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V T     ++ ++ R +   +R G+  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVNTSQLPVLTNAQMRELFEQLRAGDLSA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    +++K  REP+  EIA ++ +P E V   L   ++P+S+  PI  +  
Sbjct: 119 RDIAYKALQVRDMLASKNLREPSIVEIANEMNLPKEEVVFALDAIQDPVSMFEPIYHDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D  ++ D I D+      DSA      LRE   +    L+ RE+++L  RF  G     T
Sbjct: 179 DPIYVMDQIHDEREK---DSAWVEGIALREAMRK----LSDREKKILAKRFYEG----KT 227

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
             EV  +  +++ ++ ++E  AI ++ KH
Sbjct: 228 QMEVADEIGISQAQVSRLEKAAIHRMYKH 256


>gi|170752008|ref|YP_001758268.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170658530|gb|ACB27585.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 297

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 118/239 (49%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 47  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  K+    R+   KI        +    ++IA +L
Sbjct: 107 IKAAIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKGKISALDEGDLKPDQVKQIATRL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P + V  + +      SL  P+ +E      D++ D    SP    + A  +E   R+
Sbjct: 165 GVPEQDVIDMNRRLSGDTSLNAPLREEGEGEWQDWLVDN---SPSQETVLAREQEGQNRL 221

Query: 617 ------LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  L PRE R+   R    +  D  TLE++  +F V+RER+RQIE +A  K++
Sbjct: 222 SALKDALGVLNPRERRIFEARR---LAEDPITLEDLSGEFGVSRERVRQIEVRAFEKVQ 277


>gi|255525678|ref|ZP_05392611.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296185436|ref|ZP_06853846.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
 gi|255510664|gb|EET86971.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296050270|gb|EFG89694.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
          Length = 257

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 132/245 (53%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +R G+      +++ +++NLRLV+SV +++ NRG    DL Q G IGL+K+ 
Sbjct: 23  EMKELLLSMRNGDVSC---REKFIKSNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKSI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  ++ ++   R+ ++  +
Sbjct: 80  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYRALQVRDRLISENNK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D  ++ D I D      +D 
Sbjct: 139 EPTVSQIAKELKVPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQISDN---KNMDD 195

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +   N+       +  L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 196 SWLENI--AIKEAMKKLNDREKLILNLRFFDG----RTQMEVADEIGISQAQVSRLEKTA 249

Query: 664 IRKLK 668
           +R ++
Sbjct: 250 LRHMR 254


>gi|157828283|ref|YP_001494525.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165932987|ref|YP_001649776.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. Iowa]
 gi|157800764|gb|ABV76017.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165908074|gb|ABY72370.1| RNA polymerase sigma-32 factor [Rickettsia rickettsii str. Iowa]
          Length = 293

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 123/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTTAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I ++D    G+ IE      P   A+  N + +T++  
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINNDDAES-GELIELLPETRPTPEAMAINKQNSTSKRQ 227

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|254459542|ref|ZP_05072958.1| sigma 32 [Rhodobacterales bacterium HTCC2083]
 gi|206676131|gb|EDZ40618.1| sigma 32 [Rhodobacteraceae bacterium HTCC2083]
          Length = 292

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 77/258 (29%), Positives = 132/258 (51%), Gaps = 20/258 (7%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CEAS+ +  ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FST
Sbjct: 38  CEASLHR--LINAYMRLAISMASKFRRYGAPLNDLIQEAGLGLMKAADKFDPDRGVRFST 95

Query: 499 YAMWWVKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           YA+WW+K +I   +      +R         +  +MR    ++ R A++    + R    
Sbjct: 96  YAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQQRGEALDRHQLH 155

Query: 550 EEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSH-LGDFIEDKNAVSP---LDSA 604
           + I+ ++ +P+  V  +  +++    SL      ED      D +ED  A +     +  
Sbjct: 156 QMISTEIGVPLNDVEMMHGRLSGSDFSLNATQSVEDEGREWIDALEDDGAQAEEIVENEH 215

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A +RE     + +L  RE  ++R R    ++   TLE +G +  +++ERIRQ+EA A 
Sbjct: 216 DTAQMREWLLGAMNALNERERFIVRER--KLLDEPRTLESLGNELGLSKERIRQLEAAAF 273

Query: 665 RKLKHP--SRSKKLRSFL 680
           +K++    + S ++ +FL
Sbjct: 274 QKMRKTLEANSSEVHAFL 291


>gi|239906748|ref|YP_002953489.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
 gi|239796614|dbj|BAH75603.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
          Length = 348

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 133/243 (54%), Gaps = 11/243 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   ++ ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G KFS YA +
Sbjct: 101 AAFRLISSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAY 160

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I     + K+   +   R+    +  +P+  ++++ L +   
Sbjct: 161 WIKAYILKYIMDNWRMVKIGTTQAQRKLFYNLNKERQRLQSLGFDPSAAQLSQALNVTES 220

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLA 618
            + ++  +++   +SL+  +GD+ TS   DF+    A++P    I A   +     + + 
Sbjct: 221 DIVEMDQRLSGNDLSLDVSLGDDTTSTRLDFLP---ALTPGIEEILAGDEISHQLDKHIQ 277

Query: 619 SLTPR--EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           S+ P+  E+ +  +   I  ++  TL E+G ++ +TRER+RQIE++ + KLK    SK++
Sbjct: 278 SIRPKLNEKEIELLDNRILSDSPVTLREIGAKYGITRERVRQIESRLLEKLKD-HLSKRI 336

Query: 677 RSF 679
             F
Sbjct: 337 EDF 339


>gi|167835356|ref|ZP_02462239.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis MSMB43]
          Length = 311

 Score =  103 bits (258), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 128/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+SVA+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARQLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  I  G+E  + +    +  N  + + +A Q ++ +T    R
Sbjct: 189 EEVAEMETRLSGGDIALEGQIDDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAR 248

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 249 ALESLDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|222832319|gb|EEE70796.1| predicted protein [Populus trichocarpa]
          Length = 294

 Score =  103 bits (258), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 63/182 (34%), Positives = 95/182 (52%), Gaps = 16/182 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDE 86
            K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V     D + L   
Sbjct: 34  LKALIKLGKTRGYLTHSEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLN 93

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              + +     +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 94  NTGQSATTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRI 152

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  E  
Sbjct: 153 EGGLMDMMEAISASPATIAEILAMSEEIREGKVVISTIVD-----------GFVNANEDD 201

Query: 207 SY 208
            Y
Sbjct: 202 DY 203


>gi|115378280|ref|ZP_01465448.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|310821082|ref|YP_003953440.1| RNA polymerase sigma-b factor [Stigmatella aurantiaca DW4/3-1]
 gi|401024|sp|Q01624|RPSB_STIAD RecName: Full=RNA polymerase sigma-B factor
 gi|46680|emb|CAA78693.1| sigma factor (SigB) [Stigmatella aurantiaca DW4/3-1]
 gi|115364722|gb|EAU63789.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|309394154|gb|ADO71613.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
          Length = 296

 Score =  103 bits (258), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 78/254 (30%), Positives = 129/254 (50%), Gaps = 20/254 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E + +     KG+  A      +V +NLR V+ V+ +Y + G++  DLIQEGNIGL
Sbjct: 27  LSVEEEQALARKFVKGDLAAG---HRLVTSNLRFVVKVSYEYRSYGIKMSDLIQEGNIGL 83

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRM 539
           MKA +KFD   G +  +YA+WW++  I   I      +++      R     + RT R +
Sbjct: 84  MKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKLFFSLARTRREL 143

Query: 540 SNKIKREPT---PEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDK 595
                 +      +EIA KL +    VR++  ++    +SL+ P+G++  +   DF+   
Sbjct: 144 EKFGAGDGAVVNVDEIANKLNVKASEVREMEQRMGGRDLSLDAPMGEDGGNSHVDFV--A 201

Query: 596 NAVSPLDSAI----QANLRETTTRV-LASLTPREERVLRMRFGIGMN-TDHTLEEVGKQF 649
           +A +P D       +A L  +   + L  L PRE  ++  R    MN    TL+E+G+ F
Sbjct: 202 SAAAPQDDEFADKEEAGLINSRVHMALMRLDPRERFIIEQRV---MNERPMTLKELGEHF 258

Query: 650 CVTRERIRQIEAKA 663
             +RER RQ+E +A
Sbjct: 259 GFSRERARQLEIRA 272


>gi|188585937|ref|YP_001917482.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350624|gb|ACB84894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 269

 Score =  103 bits (258), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 130/245 (53%), Gaps = 11/245 (4%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SE + +   +R G+ E   A+++++  NLRLV+SV +++ NRG    DL Q G +GL+KA
Sbjct: 22  SEMKELFEKMRVGDDEDE-ARQKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCVGLIKA 80

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   I R + D + +IR+   +RD  +K ++    +  K  
Sbjct: 81  IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQIRDELVEKNS 139

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP   EIA+KL +  E V   L   ++P+SL  PI  +     GD I   + +S   + 
Sbjct: 140 REPAISEIAEKLDVSEEQVVFALDAIQDPVSLFEPIYHDG----GDPIFVMDQISDEKNQ 195

Query: 605 IQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  L E   +  L  L+ RE+ ++ +RF  G       EE+G    +++ ++ ++E  A
Sbjct: 196 DRTWLEEIAIKEGLHRLSSREKLIVNLRFFKGKTQMEVAEEIG----ISQAQVSRLEKAA 251

Query: 664 IRKLK 668
           + +LK
Sbjct: 252 LSQLK 256


>gi|328542558|ref|YP_004302667.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326412304|gb|ADZ69367.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 296

 Score =  103 bits (258), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 125/251 (49%), Gaps = 18/251 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E +   A + +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G+
Sbjct: 39  RYKEHDDPAAAERLVNSHLRLVAKIAMGYRGYGLPLGEVVSEGNVGLMQAVKRFEPDKGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K AI   I      +++      K  ++    RR+  +I+       +  
Sbjct: 99  RLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQALEEGDLKPE 156

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
             +EIA KL +P E V  + +      SL  PI   + D+    D++ D++       A 
Sbjct: 157 QVQEIATKLGVPEEDVVSMNRRLAGDASLNAPIRAAEADSGEWQDWLVDESESQETLLAN 216

Query: 606 QANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEA 661
           Q  L   R+     +  LT RE R+   R    +  D  TLEE+  +F V+RER+RQIE 
Sbjct: 217 QEELDIRRKLLGDAMDILTERERRIFEAR---RLAEDPITLEELSTEFGVSRERVRQIEV 273

Query: 662 KAIRKLKHPSR 672
           +A  K++   R
Sbjct: 274 RAFEKIQKAVR 284


>gi|209965510|ref|YP_002298425.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958976|gb|ACI99612.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 295

 Score =  103 bits (258), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 123/243 (50%), Gaps = 28/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  E+V +  RLV++ A ++ N GL   DL+QEGN+GLM+AA +F+     +FSTYA WW
Sbjct: 46  ALHELVRSYTRLVVATAARFRNYGLPMGDLVQEGNVGLMQAAARFEPDREVRFSTYAAWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP--------EEIAKK 555
           ++ A+   I      +R       K   +    RR+  KI+  P+           IA++
Sbjct: 106 IRSAMQDYILRNWSIVRTGTTAAQK--ALFFNLRRLRAKIEDSPSASALSPDGRRRIAEE 163

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           L +    V  + +++     SL +P+ +       DF+ D+   SP D  I   +R+   
Sbjct: 164 LNVDESDVESMEMRLAAADQSLNSPVAEGGDDEWQDFLSDQRP-SPEDVVI--GMRDGRM 220

Query: 615 R------VLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           R       L  L+PRE  ++   R+R     +   TLEE+G+   V++ER+RQ+E +A+ 
Sbjct: 221 RSRWLAEALGELSPRERTIIAQRRLR-----DDGATLEELGRVLGVSKERVRQLEHRALM 275

Query: 666 KLK 668
           KL+
Sbjct: 276 KLR 278


>gi|189424394|ref|YP_001951571.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
 gi|189420653|gb|ACD95051.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
          Length = 285

 Score =  103 bits (258), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 15/277 (5%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    DS  K  +EIKS  +       E R  V +  + +  A+   + ++ +NLR V+ 
Sbjct: 5   IPVTTDSFSKYLSEIKSFPLLD--EQEEHRLAVRLFEENDLSAA---QTLITSNLRFVVK 59

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A +Y N GL+ LDLIQEGNIGLM A  KF+   G++  TYA+WW++  I   I      
Sbjct: 60  IAAEYRNYGLKMLDLIQEGNIGLMLAVRKFNPYRGFRLITYAVWWIRAQIQSYIVSSWSL 119

Query: 519 IRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV---EGVRKVLKITKEPI 574
           ++I     + K+   ++ A+     +      +  A  L++ V   E     L++  E +
Sbjct: 120 LKIGTTQAQRKLFFKLKQAKNAILSMNGGDEGDLPATALSLDVREAEVEEMELRLMGE-V 178

Query: 575 SLET-PIGDEDTSHLGDFIEDK-NAVSPL-DSAIQANLRETTTRVLASLTPREERVLRMR 631
           SL+   +  E  S L   ++D+ N  S L D   Q  LR      ++ L  +E+ V++ R
Sbjct: 179 SLDAEQVAGEGGSLLETLVDDRPNQESQLADLQEQQALRVVVADAVSRLGEKEQFVVKQR 238

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             I  +   TL+E+   F ++RER+RQIE  A+RK+K
Sbjct: 239 --IVADDPMTLQEIADHFSISRERVRQIEENALRKIK 273


>gi|317403164|gb|EFV83689.1| RNA polymerase sigma factor [Achromobacter xylosoxidans C54]
          Length = 294

 Score =  103 bits (258), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 131/231 (56%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 61  AARELVLSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 120

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ R     +  E   + IA++L +  E 
Sbjct: 121 IKAEIHEYIIRNWRLVKVATTKAQRKLFFNLRSMRPDGQTLDPEQV-DHIARELNVRRED 179

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRET-TTRVL 617
           V ++ ++++   +SLE    D+D+     ++ D+    P   L+ A +  L+ +  +  L
Sbjct: 180 VSEMEVRLSGRDMSLENQDDDDDSYAPIAYLSDEGRQEPTRVLERAARDQLQSSGLSSAL 239

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L PR  R++  R+ +  +   TL E+ ++F V+ ERIRQIEA A++K++
Sbjct: 240 EALDPRSRRIVEARW-LQDDGGATLHELAQEFGVSAERIRQIEAAALKKMR 289


>gi|15892330|ref|NP_360044.1| RNA polymerase factor sigma-32 [Rickettsia conorii str. Malish 7]
 gi|15619475|gb|AAL02945.1| RNA polymerase sigma-32 factor [Rickettsia conorii str. Malish 7]
          Length = 293

 Score =  103 bits (258), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 122/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I  +D    G+ IE      P   A+  N + +T++  
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINSDDAES-GELIELLPETRPTPEAMAINKQNSTSKRQ 227

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|53724102|ref|YP_104622.1| RNA polymerase factor sigma-32 [Burkholderia mallei ATCC 23344]
 gi|121598782|ref|YP_991458.1| RNA polymerase factor sigma-32 [Burkholderia mallei SAVP1]
 gi|124383719|ref|YP_001027464.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10229]
 gi|126449925|ref|YP_001082430.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10247]
 gi|167001066|ref|ZP_02266867.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
 gi|238561338|ref|ZP_00442201.2| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|254175044|ref|ZP_04881705.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|254201710|ref|ZP_04908074.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|254207043|ref|ZP_04913394.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|254357524|ref|ZP_04973798.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|52427525|gb|AAU48118.1| RNA polymerase sigma-32 factor [Burkholderia mallei ATCC 23344]
 gi|121227592|gb|ABM50110.1| alternative sigma factor RpoH [Burkholderia mallei SAVP1]
 gi|124291739|gb|ABN01008.1| RNA polymerase sigma-32 factor [Burkholderia mallei NCTC 10229]
 gi|126242795|gb|ABO05888.1| alternative sigma factor RpoH [Burkholderia mallei NCTC 10247]
 gi|147747604|gb|EDK54680.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|147752585|gb|EDK59651.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|148026588|gb|EDK84673.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|160696089|gb|EDP86059.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|238524810|gb|EEP88241.1| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|243063136|gb|EES45322.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
          Length = 311

 Score =  103 bits (258), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 127/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+SVA+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  I  G+E  + +    +  N  + + +A Q ++ +T    R
Sbjct: 189 EEVAEMETRLSGGDIALEGQIDDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAR 248

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 249 ALESLDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|253997181|ref|YP_003049245.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera mobilis JLW8]
 gi|253983860|gb|ACT48718.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera mobilis JLW8]
          Length = 285

 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 121/233 (51%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LRLV S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++AM W
Sbjct: 49  AARQLIVSHLRLVASIARGYMGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAMHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAM-PV 560
           +K  I   I      ++I      +  K+    R M   I    T E   IA++L + P 
Sbjct: 109 IKAEIHEYIVRNWRLVKIATTKAQR--KLFFNLRSMKTGINTMQTSEIDHIARELNVKPE 166

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSP-LDSAIQANLRETT--TR 615
           E +    ++    ISLE+ I D+   H     +++D++   P    A Q  + ETT    
Sbjct: 167 EVLEMESRLNGHEISLESNIDDDSEEHYSPIAYLQDESLTPPEALEAKQFEMAETTGLAS 226

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R  RV+  R+ +  +   TL E+  +F V+ ERIRQIE KA+ K+K
Sbjct: 227 ALNHLDERSRRVVEARW-LQEDASKTLHELADEFGVSAERIRQIEQKAMLKMK 278


>gi|258511274|ref|YP_003184708.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478000|gb|ACV58319.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 259

 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 84/269 (31%), Positives = 143/269 (53%), Gaps = 24/269 (8%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V T     ++ ++ R +   +R G+  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVNTSQLPVLTNAQMRELFEQLRAGDPSA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    +++K  REP+  EIA ++ +P E V   L   ++P+S+  PI  +  
Sbjct: 119 RDIAYKALQVRDMLASKNLREPSIVEIANEMNLPKEEVVFALDAIQDPVSMFEPIYHDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D  ++ D I D+      DSA      LRE   +    L+ RE+++L  RF  G     T
Sbjct: 179 DPIYVMDQIHDEREK---DSAWVEGIALREAMRK----LSDREKKILAKRFYEG----KT 227

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
             EV  +  +++ ++ ++E  AI ++ KH
Sbjct: 228 QMEVADEIGISQAQVSRLEKAAIHRMYKH 256


>gi|289578664|ref|YP_003477291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544884|ref|YP_003677186.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528377|gb|ADD02729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842659|gb|ADH61175.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 256

 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 122/226 (53%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E +  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 37  AREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  EIAK+L +P E V
Sbjct: 97  IIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGEIAKELDLPREEV 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI  +     GD I   + VS   +  +  L +   +  +  L  
Sbjct: 156 VMALDAIQEPVSLFEPIYHDG----GDAIYVMDQVSDDKNIDEVWLEKIALKEAIQKLNE 211

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +RF  G     T  EV K+  +++ ++ ++E  A+  ++
Sbjct: 212 REKLILTLRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMR 253


>gi|261366888|ref|ZP_05979771.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
 gi|282571002|gb|EFB76537.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
          Length = 260

 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 129/249 (51%), Gaps = 16/249 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E   ++   R G+ EA   +++M++ NLRLV+SV +K+ NRG    DL Q G IGL
Sbjct: 19  LSETEKSALIRAARAGDAEA---RRKMIQGNLRLVLSVVQKFANRGENLDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD  L  +FSTY +  +   I R + D +  +R+   +RD  +  +R    +  
Sbjct: 76  IKAIDHFDPSLQVRFSTYGVPMIVGEIRRFLRDNN-AVRVSRSIRDLAYHSMRAREALQK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
           +  R+P   EIA ++    E V   L+   EP SL  P+    ED+  + D + D     
Sbjct: 135 ENGRDPKISEIAARVGASPENVAMALESVVEPASLYEPVYSDGEDSFAIVDQLHDATGEE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              S I    R+T    + SL+ RE R++ MR+  G     T  +V ++  +++ ++ ++
Sbjct: 195 SWISDIM--FRDT----VKSLSARERRIIAMRYLGG----KTQMQVAREIGISQAQVSRL 244

Query: 660 EAKAIRKLK 668
           E  A+ ++K
Sbjct: 245 EKGALNRIK 253


>gi|291531212|emb|CBK96797.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum 70/3]
          Length = 255

 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 133/244 (54%), Gaps = 18/244 (7%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SE   ++  +R G+     A+++++  NLRLV+SV ++++ RG    DL Q G IGLMKA
Sbjct: 27  SEKTELLRQMRSGD---PTAREKLINGNLRLVLSVIQRFSGRGENPDDLFQVGCIGLMKA 83

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + F      +FSTYA+  +   + R + D S +IR+   MRD  +K ++   +++N   
Sbjct: 84  IDNFSTDFNVRFSTYAVPMIMGELRRYLRD-SGSIRVSRSMRDLAYKAMQAREKLTNDNS 142

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKN-AVSPL 601
           +EPT E+IAK++    E V   L+   +PISL  P+  E  DT ++ D I D N   + L
Sbjct: 143 KEPTIEQIAKEIDAKREDVVIALEAVSDPISLYEPVFSESGDTIYMMDQIGDNNDDRNWL 202

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +  L+E     +  L  RE+ +L++RF  G     T  EV ++  +++ ++ ++E 
Sbjct: 203 D---EIALKEA----IIGLDDREKNILKLRFFRG----KTQVEVAQEIGISQAQVSRLEK 251

Query: 662 KAIR 665
           +  R
Sbjct: 252 RRSR 255


>gi|34580656|ref|ZP_00142136.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
 gi|28262041|gb|EAA25545.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
          Length = 293

 Score =  103 bits (257), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 121/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPMTELVSEGNIGLMQAVKKFNPALGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I  +D    G+ IE      P    +  N + +T++  
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINSDDAES-GELIELLPETRPTPETMAINKQNSTSKRQ 227

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|288961334|ref|YP_003451673.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288913642|dbj|BAI75129.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 287

 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 124/241 (51%), Gaps = 34/241 (14%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ +A+ Y   GL   DL+ EGN+GLM+AA+KFD   G++F+TYA WWV+ A
Sbjct: 38  LVGSHLRLVVKMARGYLGYGLPLADLVAEGNVGLMQAAQKFDPGKGFRFATYASWWVRAA 97

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAKKLAMPVEGV 563
           I   +      ++I      K  K+  + RR+  +++     + +PE         VE +
Sbjct: 98  IQEYVLHNWSLVKIGTTAGQK--KLFFSLRRLKARMQELDSGDLSPE--------AVESI 147

Query: 564 RKVLKITK-EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              L ++K E + +   +G++ + ++G   ED +A       + A+ R     VLA    
Sbjct: 148 ATELNVSKAEVVEMNRRLGNDRSLNVG-LSEDGDAEW---QDLLADDRPDQETVLADSEE 203

Query: 623 REERVLRMRFGIGMNTDH---------------TLEEVGKQFCVTRERIRQIEAKAIRKL 667
           R  R   ++ G+G+  D                TLEE+ + F V+RER+RQ+E +A  KL
Sbjct: 204 RRRRQQFLKLGLGVLDDRERRILVARRLRDEPLTLEELSQTFQVSRERVRQLEVRAFEKL 263

Query: 668 K 668
           +
Sbjct: 264 Q 264


>gi|121488737|emb|CAJ18252.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/164 (32%), Positives = 94/164 (57%), Gaps = 1/164 (0%)

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L  EGN+GL KA  +FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 2   LXNEGNLGLXKAXXRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKI 61

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D +
Sbjct: 62  SKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVL 121

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ++   + P  +  + +L     R L+ L PRE  V+R  F I M
Sbjct: 122 QNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFXIXM 164


>gi|53718144|ref|YP_107130.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei K96243]
 gi|76812253|ref|YP_332145.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1710b]
 gi|126441976|ref|YP_001057600.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 668]
 gi|126453430|ref|YP_001064846.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1106a]
 gi|134279764|ref|ZP_01766476.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|167717993|ref|ZP_02401229.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei DM98]
 gi|167737009|ref|ZP_02409783.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 14]
 gi|167814118|ref|ZP_02445798.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 91]
 gi|167822644|ref|ZP_02454115.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 9]
 gi|167844214|ref|ZP_02469722.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei B7210]
 gi|167892724|ref|ZP_02480126.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 7894]
 gi|167901220|ref|ZP_02488425.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei NCTC
           13177]
 gi|167909437|ref|ZP_02496528.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 112]
 gi|167917468|ref|ZP_02504559.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei BCC215]
 gi|217419877|ref|ZP_03451383.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|226199497|ref|ZP_03795054.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237810751|ref|YP_002895202.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242316271|ref|ZP_04815287.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254181885|ref|ZP_04888482.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|254187820|ref|ZP_04894332.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|254196825|ref|ZP_04903249.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|254260127|ref|ZP_04951181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
 gi|254296064|ref|ZP_04963521.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|52208558|emb|CAH34494.1| RNA polymerase sigma-32 factor [Burkholderia pseudomallei K96243]
 gi|76581706|gb|ABA51181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710b]
 gi|126221469|gb|ABN84975.1| alternative sigma factor RpoH [Burkholderia pseudomallei 668]
 gi|126227072|gb|ABN90612.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106a]
 gi|134248964|gb|EBA49046.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|157805888|gb|EDO83058.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|157935500|gb|EDO91170.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|169653568|gb|EDS86261.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|184212423|gb|EDU09466.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|217397181|gb|EEC37197.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|225928378|gb|EEH24408.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237503746|gb|ACQ96064.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242139510|gb|EES25912.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254218816|gb|EET08200.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
          Length = 311

 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 127/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+SVA+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  I  G+E  + +    +  N  + + +A Q ++ +T    R
Sbjct: 189 EEVAEMETRLSGGDIALEGQIDDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAR 248

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 249 ALESLDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|238650752|ref|YP_002916605.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
 gi|238624850|gb|ACR47556.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
          Length = 293

 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 122/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I  +D    G+ IE      P   A+  N + +T++  
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINSDDAES-GELIELLPETRPTPEAMAINKQNSTSKRQ 227

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|15604172|ref|NP_220687.1| RNA polymerase factor sigma-32 [Rickettsia prowazekii str. Madrid
           E]
 gi|3860864|emb|CAA14764.1| RNA POLYMERASE SIGMA-32 FACTOR (rpoH) [Rickettsia prowazekii]
 gi|292571903|gb|ADE29818.1| RNA polymerase sigma-32 factor [Rickettsia prowazekii Rp22]
          Length = 293

 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/276 (29%), Positives = 141/276 (51%), Gaps = 23/276 (8%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S L+  N+I S++ E      EF    S + + + +A+    ++V ++L+LV  +A  Y 
Sbjct: 18  SYLQKINKIPSLTQE-----EEFLLAKSYLEENDLQAA---HKLVTSHLKLVAKIASSYK 69

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K +I   I      +++   
Sbjct: 70  TYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKSWSLVKMGTT 129

Query: 525 MRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKV-LKITKEPISLET 578
              K     + +   +++N   R  T +   +IA +L + V  V ++  +I+   +SL  
Sbjct: 130 AAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRISGPDLSLNN 189

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR------VLASLTPREERVLRMRF 632
            I  +D    G+ IE    + P   A+  N +  T++       +  L  RE R+L+ R 
Sbjct: 190 SINSDDVES-GELIELLPELRPTPEAMAINKQNYTSKRKLLSNAMQILNDRELRILKDR- 247

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 248 -KLTDTPKTLDILSSEYNISKERIRQIENTAFEKIK 282


>gi|188588400|ref|YP_001920536.1| sporulation sigma factor SigG [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778549|ref|ZP_04821469.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498681|gb|ACD51817.1| RNA polymerase sigma-G factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082864|gb|EES48754.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 257

 Score =  103 bits (257), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 121/226 (53%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 38  ARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +    +      REPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALIVRDKFIKDNNREPTISQIAKELELPREEV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   ++P+SL  PI  +     GD I   + +S   +  ++ L   + +  +  LT 
Sbjct: 157 VFALDAIQDPVSLFEPIYHDG----GDAIFVMDQISDSKNTDESWLENISIKEAMKKLTD 212

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 213 REKLILNLRFFRG----RTQMEVADEIGISQAQVSRLEKTALKHMR 254


>gi|114798150|ref|YP_762122.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
 gi|114738324|gb|ABI76449.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
          Length = 295

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/254 (31%), Positives = 128/254 (50%), Gaps = 20/254 (7%)

Query: 429 HIVSMVRKG-ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           H  S+ R+  E E   A  E+  A +RLVIS+A K+ + GL   DL+ EGN+GLM+AA +
Sbjct: 29  HEASLARRWREAEDEAALHELTTAYMRLVISMAAKFRHYGLPMADLVSEGNVGLMQAAAR 88

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---- 541
           F+     +FSTYA WW++ +I   +      +R       K     + R   R+S+    
Sbjct: 89  FEPEREVRFSTYASWWIRSSIQDYVLRNWSIVRTGTTSAQKSLFFNLRRLRARISDLGDG 148

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            + RE   + ++  L +P+  V  +  +++    SL  P+  +  +   D I D+ A  P
Sbjct: 149 TMTRE-NKQWVSTHLGVPLRDVEIMSARLSGSDRSLNAPLTMDGDAEWQDMIADEGA--P 205

Query: 601 LDSAIQ-----ANLRETTTRVLASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCVTRE 654
            + A+      A   E  +  + +LTPRE  ++ R R         TLE +G +  V++E
Sbjct: 206 PEEAVMRSHDTARRHEWISEAMEALTPRETYIITRRRLS---EEPQTLEALGHELGVSKE 262

Query: 655 RIRQIEAKAIRKLK 668
           R+RQIE +A+ KLK
Sbjct: 263 RVRQIEHQALSKLK 276


>gi|300854419|ref|YP_003779403.1| putative RNA polymerase sigma-G factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434534|gb|ADK14301.1| predicted RNA polymerase sigma-G factor [Clostridium ljungdahlii
           DSM 13528]
          Length = 257

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 133/245 (54%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++  +++G+ E+   +++ ++ NLRLV+SV +++ NRG    DL Q G IGL+KA 
Sbjct: 23  EMKELLIKMQQGDNES---REKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     KFSTYA+  +   I R + D + +IR+   +RD  +K ++   ++  +  +
Sbjct: 80  DNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQVRDKLIRENNK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  +IA++L +P E V   L   ++P+SL  PI  +  D  ++ D I D      LD 
Sbjct: 139 EPTISQIAEELNIPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQISD---TKNLDE 195

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               N+  +    +  L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A
Sbjct: 196 NWLENI--SIKEAMKKLNDREKLILNLRFFDG----RTQMEVADEIGISQAQVSRLEKTA 249

Query: 664 IRKLK 668
           +R ++
Sbjct: 250 LRHMR 254


>gi|118443097|ref|YP_878334.1| sporulation sigma factor SigG [Clostridium novyi NT]
 gi|118133553|gb|ABK60597.1| Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           novyi NT]
          Length = 256

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 126/230 (54%), Gaps = 14/230 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++++++ V  NLRLV+SV +++ NRG    DL Q G IGL+KA + FD     KFSTYA+
Sbjct: 35  NLSREKFVRGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAV 94

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R + D + +IR+   +RD  +K ++   ++  K  ++P    IAK+L +P E
Sbjct: 95  PMIIGEIRRYLRDNN-SIRVSRSLRDIAYKALQVRDKIIKKENKDPNVSRIAKELDLPRE 153

Query: 562 GVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLA 618
            V   L   ++P+SL  PI  +  D  ++ D I D   V   +S I+  +++E   R   
Sbjct: 154 EVVFALDAIQDPVSLFEPIYHDGGDALYVMDQISDSKNVD--ESWIENISIKEAMKR--- 208

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ +L MRF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 209 -LNEREKMILNMRFFQG----RTQMEVADEIGISQAQVSRLEKTALKHMR 253


>gi|114764201|ref|ZP_01443439.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114543353|gb|EAU46369.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 292

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 129/249 (51%), Gaps = 18/249 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +
Sbjct: 45  LINAYMRLAISMAAKFKRYGAPMGDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKAS 104

Query: 508 ITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           I   +      +R         +  +MR    ++ R A      ++R      IAK++ +
Sbjct: 105 IQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAAAEGRALERHSLHAAIAKEVGV 164

Query: 559 PVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIED--KNAVSPLDSAIQAN-LRETT 613
           P+  V  +  +++    SL  T   DED     D +ED  + + S ++  +  + LRE  
Sbjct: 165 PLHDVEMMDGRLSGSDFSLNATQSTDEDGREWIDTLEDDGEQSASLVEGKLDNDQLREWL 224

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP--S 671
              L  L  RE  ++R R     +   TLE +G++  +++ER+RQ+EA A  K++    +
Sbjct: 225 VVALTGLNDRERFIVRER--KLRDETRTLESLGQELGLSKERVRQLEAAAFVKMRKSLEA 282

Query: 672 RSKKLRSFL 680
           +S+++  FL
Sbjct: 283 QSREVAQFL 291


>gi|78357159|ref|YP_388608.1| sigma 70 family protein [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78219564|gb|ABB38913.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 360

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 131/239 (54%), Gaps = 19/239 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           S A   +V ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G KFS YA
Sbjct: 112 SDAAFRLVSSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYA 171

Query: 501 MWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            +W+K  I + I D    ++I     + K+   +   R+       +P    ++++L + 
Sbjct: 172 AFWIKAYILKFIMDNWRLVKIGTTQAQRKLFYNLNKERQKLIAQGYDPDAAMLSERLDVT 231

Query: 560 VEGVRKV-LKITKEPISLETPIGDEDTS--------HLGDFIEDKNAVSPLDSAIQANLR 610
            E V ++  ++    +SL+  +GDE+ S         LG  IED  A + + + +Q  +R
Sbjct: 232 TEQVVEMEQRLDASDMSLDVQVGDENGSASRMDFLPALGPGIEDTLANNEIAAMVQERIR 291

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    ++  L  +E  +L  R    ++ D  TL E+G+++ +TRER+RQIEA+ ++K++
Sbjct: 292 D----IVPLLNDKELDILNSRL---LSEDPVTLREIGEKYDITRERVRQIEARLLQKIR 343


>gi|157825543|ref|YP_001493263.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
 gi|157799501|gb|ABV74755.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
          Length = 293

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 125/237 (52%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   G+   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGIPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEEIAK---KLAM 558
           +K AI   I      +++      K     + +   +++N   R  T ++ AK   +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAKIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--R 615
            V  V ++  +I+   +SL   I  +D +  G+ IE      P   A+  N +  T+  +
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINSDDAAS-GELIELLPETRPTPEAMAINKQNFTSKRK 227

Query: 616 VLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LA+    L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLANAMKILNDRELRILTER--KLTDTPTTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|46579995|ref|YP_010803.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120602593|ref|YP_966993.1| sigma-70 region 2 domain-containing protein [Desulfovibrio vulgaris
           DP4]
 gi|46449411|gb|AAS96062.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120562822|gb|ABM28566.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio vulgaris DP4]
 gi|311234006|gb|ADP86860.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           vulgaris RCH1]
          Length = 356

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 127/236 (53%), Gaps = 17/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   +V ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G KFS YA +
Sbjct: 110 AAFRLVSSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAF 169

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I     + K+   +   R+       +P    ++++L +  E
Sbjct: 170 WIKAYILKFIMDNWRMVKIGTTQAQRKLFYNLNKERQKLILQGYDPDAATLSERLNVTKE 229

Query: 562 GVRKV-LKITKEPISLETPIGDED--------TSHLGDFIEDKNAVSPLDSAIQANLRET 612
            V ++  ++    +SL+ P+GDE            LG  IED  +   + S +Q  L+  
Sbjct: 230 QVVEMEQRLDASDVSLDIPVGDEGGGASRMDFLPALGPGIEDALSNHEIASMVQNRLQS- 288

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++  L+ +E  +L+ R  +      TL E+G+++ +TRER+RQIEA+ ++K++
Sbjct: 289 ---IIPKLSDKEVDILQNR--LLSEEPVTLREIGEKYDITRERVRQIEARLLQKIR 339


>gi|157964378|ref|YP_001499202.1| RNA polymerase factor sigma-32 [Rickettsia massiliae MTU5]
 gi|157844154|gb|ABV84655.1| RNA polymerase sigma-32 factor [Rickettsia massiliae MTU5]
          Length = 310

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 122/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 66  AAHKLVTSHLKLVAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 126 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGV 185

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I  +D    G+ IE      P   A+  N + +T++  
Sbjct: 186 SVNEVSEMNTRISGPDLSLNNSINSDDAES-GELIELLPETRPTPEAMAINKQNSTSKRQ 244

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 245 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 299


>gi|56477835|ref|YP_159424.1| RNA polymerase factor sigma-32 [Aromatoleum aromaticum EbN1]
 gi|56313878|emb|CAI08523.1| Sigma-32 factor RpoH (RNA polymerase sigma factor) [Aromatoleum
           aromaticum EbN1]
          Length = 283

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 87/293 (29%), Positives = 151/293 (51%), Gaps = 24/293 (8%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +S A  FP      F    +D  ++  N I  ++ +  +S++       +  +G+ EA+ 
Sbjct: 1   MSQALSFP----VPFAVGSIDQYIQSVNRIPLLTEQEEVSLA-----TRLRNEGDLEAA- 50

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
             + +V ++LRLV+++++ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 51  --RGLVMSHLRLVVAISRGYLGYGLPHADLIQEGNIGLMKAVKRFDPDRGVRLVSFAIHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVE 561
           +K  I   I      ++I     + K+   +R+ ++ +  + R+     +AK+L + P E
Sbjct: 109 IKAEIHEYILKNWRLVKIATTKAQRKLFFNLRSLKQDTGTLNRDEV-VAVAKQLGVKPEE 167

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLR----ETTTR 615
            V    ++T   I LE    D+D  H     ++ D NA  P +   QA L     E  + 
Sbjct: 168 VVEMETRLTGRDIQLEGG-PDDDEHHFAPIAYLPDPNA-EPSEVLEQAQLARLQDEGLSD 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LASL  R   +++ R+ +      TL E+  ++ V+ ERIRQIEAKA++K++
Sbjct: 226 ALASLDDRSRTIVKRRW-LTEGDSATLHELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|284046869|ref|YP_003397209.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951090|gb|ADB53834.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 276

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 124/237 (52%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K MVE +L L   +A++Y++RG    DL+Q  ++GL+KA ++FD   G  F++YA+  
Sbjct: 50  ARKAMVEQHLGLAHHLARRYSDRGEPLDDLVQVASLGLLKAVDRFDPARGVSFASYAVPT 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R   D+   I +P   RD     +R    ++    R PTP ++ K+  + VE V
Sbjct: 110 ILGELRRHFRDRGWAIHVP---RDLKEAALRVESALAGHAGRSPTPSQLGKETGLDVEAV 166

Query: 564 RKVLKI--TKEPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + L++      +SL+ P G+E+   T+ L D +   +     D   +A  R T  R+ +
Sbjct: 167 LEALEVAGAHRALSLDAPAGNEEEGTTATLVDRLGRDD-----DELDRAGDRATIERLAS 221

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L PRE  +LR+RF      D T  E+G +  V++  + ++   A+ +++  S++ +
Sbjct: 222 VLEPREREILRLRF----VEDMTQSEIGARVGVSQMHVSRLIRTALTRMRLASQTSR 274


>gi|239947881|ref|ZP_04699634.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239922157|gb|EER22181.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 293

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 122/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            +  V ++  +I+   +SL   I  +D    G+ IE      P   A+  N + +T++  
Sbjct: 169 SINEVSEMNTRISGPDLSLNNSINSDDAES-GELIELLPETRPTPEAMAINKQNSTSKRK 227

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSSEYNISKERIRQIENTAFEKIK 282


>gi|296445492|ref|ZP_06887449.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296257058|gb|EFH04128.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 294

 Score =  102 bits (255), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 143/285 (50%), Gaps = 27/285 (9%)

Query: 411 NEIKSISVETGIS--ISEFRHIVSM---------VRKGECEASIAKKEMVEANLRLVISV 459
           N + ++S ++G+S  ++E R    +          R  E E   A +++V ++LRLV  +
Sbjct: 3   NALPTLSGDSGLSRYLAEIRRFPMLEPEQEYMLAKRWREHEDPNAAQKLVTSHLRLVAKI 62

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +
Sbjct: 63  AMGYRGYGLPIGEIVSEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWSLV 122

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKLAMPVEGVRKVLKITKE 572
           ++      K  K+    R+  +KI      + TPE   EIA++L +  + V ++ +    
Sbjct: 123 KMGTTASQK--KLFFNLRKAKSKISAFEDGDLTPEHVGEIARRLGVTNQDVIEMNRRMSG 180

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLR 629
             SL  P+ +E      D++ D ++      +D     N  +     L  L PRE R+  
Sbjct: 181 DASLNAPLREEGEGEWQDWLVDDSSDQERILVDQEEAGNRLDALRGALTVLNPRERRIFE 240

Query: 630 MRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R    ++ D  TLE++  +F V+RER+RQIE +A  K++   R+
Sbjct: 241 AR---RLSEDPVTLEDLSTEFGVSRERVRQIEVRAFEKVQSAVRA 282


>gi|256829638|ref|YP_003158366.1| RNA polymerase sigma-32 subunit RpoH [Desulfomicrobium baculatum
           DSM 4028]
 gi|256578814|gb|ACU89950.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfomicrobium baculatum
           DSM 4028]
          Length = 356

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 123/231 (53%), Gaps = 16/231 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ +NLRLV+ +A  +  R ++  LDLIQEGN+GLMKA +KFD   G KFS YA +W+K 
Sbjct: 113 LITSNLRLVVKIAMDFQRRWMKNVLDLIQEGNVGLMKAVQKFDPDKGIKFSYYASFWIKA 172

Query: 507 AITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-VEGVR 564
            I + I D    ++I     + K+   +   R+       +PT   ++K L +   + V 
Sbjct: 173 YILKFIMDNWRMVKIGTTQAQRKLFYNLGKERQRLQAQGFDPTTSTLSKNLQVSEADIVE 232

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDF-------IEDKNAVSPLDSAIQANLRETTTRVL 617
              ++ +  +SL+  IGD+ +    DF       IE++ A   +   I  N+      + 
Sbjct: 233 MGQRLGQHDVSLDMKIGDDSSFTPMDFIPALEAGIEEQMAADEISVLIHDNI----DAIR 288

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  +E  +L  R  +  ++  TL E+G ++ +TRER+RQIEA+ ++K+K
Sbjct: 289 DGLNEKELDILEQR--LLADSPITLREIGDKYGITRERVRQIEARLLQKIK 337


>gi|2529271|gb|AAB81191.1| sigma factor [Lysinibacillus sphaericus]
          Length = 263

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 79/265 (29%), Positives = 135/265 (50%), Gaps = 39/265 (14%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  +S  E R +++  ++G+ EA   +K MVE N RLV S+ +++T RG++  DL Q 
Sbjct: 7   SSEKLLSQEEMRDLIARAQQGDHEA---RKRMVEGNTRLVWSIVQRFTTRGVELEDLFQI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGLMK+ +KFD     KFSTYA+  +   I R + D            D + KV R+ 
Sbjct: 64  GCIGLMKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD------------DGMVKVSRSI 111

Query: 537 RRMSNKIK-----------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDE 583
           R ++ KI+             PT +E+A+ L +  E +       ++P SL   +   + 
Sbjct: 112 RELNFKIRHATDEFIKRNEHRPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEG 171

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D+  L D ++D+ +  P D      L+E  TR    L PRE+ ++ +R+     +D T  
Sbjct: 172 DSITLMDQMKDEKSEQPFDY---IPLKEVLTR----LEPREQSIIYLRYF----SDCTQT 220

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  +  +++ ++ ++E K + +LK
Sbjct: 221 EIANRLGISQVQVSRLEKKILAQLK 245


>gi|51473499|ref|YP_067256.1| RNA polymerase factor sigma-32 [Rickettsia typhi str. Wilmington]
 gi|51459811|gb|AAU03774.1| RNA polymerase sigma 32 subunit (heat shock sigma factor)
           [Rickettsia typhi str. Wilmington]
          Length = 293

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/276 (29%), Positives = 140/276 (50%), Gaps = 23/276 (8%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S L+  N+I S++ E      EF    S + + + +A+    ++V ++L+LV  +A  Y 
Sbjct: 18  SYLQKINKIPSLTQE-----EEFLLAKSYLEENDLQAA---HKLVTSHLKLVAKIASGYK 69

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K +I   I      +++   
Sbjct: 70  TYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKSWSLVKMGTT 129

Query: 525 MRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKV-LKITKEPISLET 578
              K     + +   +++N   R  T +   +IA +L + V  V ++  +I+   +SL  
Sbjct: 130 AAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVHEVSEMNTRISGPDLSLNN 189

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR------VLASLTPREERVLRMRF 632
            I  +D    G+ IE      P   A+  N +  T++       +  L  RE R+L+ R 
Sbjct: 190 SINSDDVES-GELIELLPETRPTPEAMAINKQNYTSKRKLLSNAMQILNDRELRILKDR- 247

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 248 -KLTDTPKTLDILSSEYNISKERIRQIENTAFEKIK 282


>gi|1552544|emb|CAA90874.1| sigma factor [Bacillus coagulans]
          Length = 252

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 126/242 (52%), Gaps = 16/242 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +++R+ E     A+  +VE N+RLV SV  ++ NRG +  DL Q G IGL+K+ +KFD
Sbjct: 19  VKNLIRRTEEGDQEARDLIVEKNIRLVWSVVHRFLNRGYEPDDLFQIGCIGLLKSVDKFD 78

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D   T+++   +++  +++ +    ++ K+ R PT 
Sbjct: 79  LSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETGNRIRKIRDELTKKLGRSPTV 137

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQ 606
            EIA +L MPVE V    +  K P S+   +   D D   L D I D+N     D  A+Q
Sbjct: 138 HEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDGDPITLLDQISDQNDQKWFDQIALQ 197

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +R         L  RE  ++ +R+      D T  E G++  +++ ++ ++E K +R 
Sbjct: 198 EAIR--------GLEERERLIVYLRY----YKDQTQSEAGERLGISQVQVSRLEKKILRV 245

Query: 667 LK 668
           +K
Sbjct: 246 MK 247


>gi|311103433|ref|YP_003976286.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
 gi|310758122|gb|ADP13571.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
          Length = 294

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 130/231 (56%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E++ ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 61  AARELILSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 120

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ R     +  +   + IA++L +  E 
Sbjct: 121 IKAEIHEYIIRNWRLVKVATTKAQRKLFFNLRSMRPDGQTLDPDQV-DHIARELNVRRED 179

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRET-TTRVL 617
           V ++ ++++   +SLE    D+D+     ++ D+    P   L+ A +  L+    T  L
Sbjct: 180 VSEMEVRLSGRDMSLENQDDDDDSYAPIAYLSDEGRQEPTRVLERAARDQLQSAGLTDAL 239

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L PR  R++  R+ +  +   TL E+ ++F V+ ERIRQIEA A++K++
Sbjct: 240 QALDPRSRRIVEARW-LQDDGGATLHELAQEFGVSAERIRQIEAAALKKMR 289


>gi|224369499|ref|YP_002603663.1| RpoH [Desulfobacterium autotrophicum HRM2]
 gi|223692216|gb|ACN15499.1| RpoH [Desulfobacterium autotrophicum HRM2]
          Length = 322

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 128/240 (53%), Gaps = 34/240 (14%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           MV +NLRLV+ +A  +    +Q  LDLIQEGNIGL+KA +KFD     KFS YA +W+K 
Sbjct: 80  MVTSNLRLVVKIALDFQRIWMQNLLDLIQEGNIGLVKAVKKFDPYKNVKFSYYASFWIKA 139

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE----------PTPEEIAKKL 556
            I + I D    ++I            +  R++  ++K+E          P P+ +++++
Sbjct: 140 YILKFIMDNWRLVKI---------GTTQGQRKLFFRLKKEKQKLIDEGFDPGPKLLSERM 190

Query: 557 AMPVEGVRKV-LKITKEPISLETPI-GDEDTSHL------GDFIEDKNAVSPLDSAIQAN 608
            +  + + ++  ++    +SL+ P+  D DT  +       D  ED+ A   ++  +   
Sbjct: 191 GVSEQEIIEMDQRLDGWDLSLDEPLRNDSDTERIEFINVESDSTEDRVARKEIEDILHVR 250

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ T    A+L PRE  +   R  I  +   TL+E+G+++ ++RER+RQIE   I+K+K
Sbjct: 251 VKKFT----ATLNPREMEIFSKR--IFSDEPRTLQEIGEEYNISRERVRQIENNIIKKMK 304


>gi|167949414|ref|ZP_02536488.1| RNA polymerase, sigma 70 subunit, RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 309

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/157 (37%), Positives = 95/157 (60%), Gaps = 1/157 (0%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
            K++I   +++G++T  E+N  LP   V  EQ+ED V M+++MGI V +   DLED+  S
Sbjct: 10  LKQLIAKGKEQGFLTYAEVNDHLPEGIVEPEQIEDIVRMINDMGITVHETAPDLEDKTLS 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++++     A+  +       DS    T DPVRMY+REMG++ELL+REGE+ IAKRIE G
Sbjct: 70  DEAVTSDDDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIAKRIEDG 129

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              + A+L   P+T + L     ++ +G   + ++I+
Sbjct: 130 LKQVSAALATFPVTIEMLHSMLTKVGEGEKRMADVIN 166


>gi|317470325|ref|ZP_07929717.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
 gi|316902189|gb|EFV24111.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
          Length = 258

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 121/228 (53%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++       DL Q G IGLMKA + FD  L  KFSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIQRFSGSNENADDLFQVGCIGLMKAIDNFDRSLNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + ++R+   +RD  +K +     ++ K  +EPT E IA+++ M  E V
Sbjct: 98  IIGEVRRYLRDNN-SMRVSRSLRDIAYKAITAKEALTKKFNKEPTIEAIAEEIEMKKEDV 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L     P+SL  P+  +  DT  L D ++DK     L     A L++     +  L 
Sbjct: 157 LFALDAIATPLSLYEPVYQDGGDTLFLMDQVKDKKNKEELWVESIA-LKDA----MEHLP 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++R+RF  G     T  EV  +  +++ ++ ++E  A++ +KH
Sbjct: 212 EREYNIIRLRFFDG----KTQTEVADEISISQAQVSRLEKNALKHMKH 255


>gi|225574955|ref|ZP_03783565.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037802|gb|EEG48048.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
          Length = 259

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 125/232 (53%), Gaps = 12/232 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E ++ NLRLV+SV K+++N      DL Q G IGL+KA + FD  L  KFSTYA+  
Sbjct: 38  AREEYIKGNLRLVLSVIKRFSNSNENADDLFQIGCIGLIKAIDNFDTTLDVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +    R+  +  +EPT EEI+K++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKAIYAKERIVKEELKEPTIEEISKEIGIEKEMI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   + P+SL  P+  E  D  ++ D I DK          + +LRE   R    L 
Sbjct: 157 VYALDAIQNPVSLFEPVYTEGGDALYVMDQISDKKNKEE-HWVEELSLREAMDR----LG 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RE+ ++ +RF  G     T  EV ++  +++ ++ ++E  A++ ++   RS
Sbjct: 212 EREKHIIDLRFYEG----KTQMEVAREIGISQAQVSRLEKNALKTMRTYLRS 259


>gi|167561467|ref|ZP_02354383.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis EO147]
 gi|167568698|ref|ZP_02361572.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis C6786]
          Length = 311

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 127/236 (53%), Gaps = 14/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARQLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  I  G+E  + +    +  N  + + +A Q ++ +T    R
Sbjct: 189 EEVAEMETRLSGGDIALEGQIDDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAR 248

Query: 616 VLASLTPREERVLRMRF---GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R  R++  R+   G   +   TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 249 ALESLDARSRRIIEARWLNVGDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|154485093|ref|ZP_02027541.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
 gi|149734046|gb|EDM50165.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
          Length = 258

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 126/246 (51%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +   ++KG     +A+++ +  NLRLV+S+ ++++N      DL Q G IGL+KA 
Sbjct: 23  EKKELFKEIKKGN---EVAREKYIRGNLRLVLSILQRFSNSNENVDDLFQIGCIGLIKAV 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD  L  KFSTYA+  +   + R + D +  IR+   ++D  +K +     +     R
Sbjct: 80  DNFDDTLNVKFSTYAVPMISGELKRYLRDNAA-IRVSRSIKDIAYKAIYCKENIIKTTHR 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLD 602
           EPT  EIAK++ +  E V   L   + P+SL  P+ D+  DT ++ D I D KN      
Sbjct: 139 EPTVVEIAKEIGVEPEDVVYALDAIQSPVSLYDPVYDQGGDTLYVMDQISDKKNKEEKWV 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             I  N        L  L+ RE +++ MRF  G       +E+G    +++ ++ ++E  
Sbjct: 199 ENIVLN------EALKGLSERERKIIDMRFFNGKTQMEIADEIG----ISQAQVSRLEKN 248

Query: 663 AIRKLK 668
           A++ +K
Sbjct: 249 ALKAMK 254


>gi|3219168|dbj|BAA28784.1| sigma-32 homolog [Achromobacter xylosoxidans]
          Length = 306

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 130/231 (56%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E++ ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 73  AARELILSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 132

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ R     +  E   E IA++L +  E 
Sbjct: 133 IKAEIHEYIIRNWRLVKVATTKAQRKLFFNLRSMRPDGQTLDPEQV-EHIARELNVRRED 191

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRET-TTRVL 617
           V ++ ++++   +SLE    D+D+     ++ D     P   L+ A +  L+ +  +  L
Sbjct: 192 VSEMEVRLSGRDMSLENQDDDDDSYAPIAYLSDDGRQEPTRVLERAARDQLQGSGLSDAL 251

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L PR  R++  R+ +  +   TL E+ ++F V+ ERIRQIEA A++K++
Sbjct: 252 EALDPRSRRIVEARW-LQDDGGATLHELAQEFGVSAERIRQIEAAALKKMR 301


>gi|83718896|ref|YP_441014.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|167579742|ref|ZP_02372616.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis TXDOH]
 gi|167617818|ref|ZP_02386449.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis Bt4]
 gi|257140333|ref|ZP_05588595.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|83652721|gb|ABC36784.1| RNA polymerase sigma-32 factor [Burkholderia thailandensis E264]
          Length = 311

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 127/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  I  G+E  + +    +  N  + + +A Q ++ +T    R
Sbjct: 189 EEVAEMETRLSGGDIALEGQIDDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAR 248

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDSLDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|118579103|ref|YP_900353.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501813|gb|ABK98295.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 282

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 123/233 (52%), Gaps = 13/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ +NLR V+ VA +Y + GL+ LDLIQEGNIGLM A +K++   G +  +YA+WW
Sbjct: 45  AAHTLITSNLRFVVRVAYEYRHYGLKMLDLIQEGNIGLMMAVKKYNPFKGVRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAKKLAM 558
           ++  I   +      ++I     + K+   +R AR   N I+     E   +  A+ L +
Sbjct: 105 IRAYIQNHVISAWSLLKIGTTQAQRKLFFKLREAR---NAIRHLNGGEDDLQSTARSLNV 161

Query: 559 PVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS--AIQANLRETTTR 615
               V ++ +  +   SL+  + G E  + L   ++D+     L S   +Q  LR     
Sbjct: 162 SDSEVVEMEQRLRGECSLDAELPGGEGVTGLDGLVDDRMNQEELLSECQLQRKLRTDVAT 221

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +++L  +E  V+  R  +  +T  TL+E+  +F ++RER+RQIE  A++KLK
Sbjct: 222 AVSALNEKERFVIEHR--VSADTPLTLQEIASRFSISRERVRQIEEAALKKLK 272


>gi|167748837|ref|ZP_02420964.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
 gi|167651807|gb|EDR95936.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
          Length = 275

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 121/228 (53%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++       DL Q G IGLMKA + FD  L  KFSTYA+  
Sbjct: 55  AREQYIKGNLRLVLSVIQRFSGSNENADDLFQVGCIGLMKAIDNFDRSLNVKFSTYAVPM 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + ++R+   +RD  +K +     ++ K  +EPT E IA+++ M  E V
Sbjct: 115 IIGEVRRYLRDNN-SMRVSRSLRDIAYKAITAKEALTKKFNKEPTIEAIAEEIEMKKEDV 173

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L     P+SL  P+  +  DT  L D ++DK     L     A L++     +  L 
Sbjct: 174 LFALDAIATPLSLYEPVYQDGGDTLFLMDQVKDKKNKEELWVESIA-LKDA----MEHLP 228

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++R+RF  G     T  EV  +  +++ ++ ++E  A++ +KH
Sbjct: 229 EREYNIIRLRFFDG----KTQTEVADEISISQAQVSRLEKNALKHMKH 272


>gi|237747428|ref|ZP_04577908.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
 gi|229378779|gb|EEO28870.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
          Length = 299

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/238 (32%), Positives = 128/238 (53%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  +YA+ W
Sbjct: 62  AAQELVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPGMGVRLVSYAIHW 121

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R+ +   + + R      +A+KL +  E 
Sbjct: 122 IKAEIHEYILRNWRMVKIATTKAQRKLFFNLRSHKNGLDSMTRAQI-RSLAEKLNVKDEE 180

Query: 563 VRKV-LKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAIQANLR-ETTTR 615
           V ++  ++    I+LET   D+D      ++L    E     S L++     ++ E    
Sbjct: 181 VAEMETRLNGHDIALETQHDDDDDNFAPIAYLSS--EQTEPASILEARQNDRMQSEGLAE 238

Query: 616 VLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            LA L PR  R++  R+   +N+D     TL  +  +F V+ ERIRQIEA A++K+K+
Sbjct: 239 ALAKLDPRSRRIVEARW---LNSDDGNSATLHALAAEFGVSAERIRQIEAAALKKMKN 293


>gi|242089059|ref|XP_002440362.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
 gi|241945647|gb|EES18792.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
          Length = 529

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 119/239 (49%), Gaps = 8/239 (3%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++S ++ G C     ++ ++     LV  +A+ YT  G    DL+Q G +G++  AEKFD
Sbjct: 277 LMSRLQTGYC----CRERLLVTTEWLVRCIARSYTGMGTALDDLLQAGKMGVLDGAEKFD 332

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +FSTY  +W+++ +   +A+ S    +P  M   + KV    R +     R P+ 
Sbjct: 333 TRKGCRFSTYVKYWIRKGMLALLAENSGVTLLPARMESIMRKVKEARRGIRYSEGRNPSD 392

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA----I 605
            E+A  + + V  VR   K ++ P+SL + IG    +   + I D+ A +          
Sbjct: 393 SEVAAAVGVSVANVRLARKCSRRPVSLYSEIGIGQHAKFAEVIPDEAAAAAEAPDEAALF 452

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  LRE    VL  L  RE  VLR+R G+      +LEE+G  + V++E IR+IE  A+
Sbjct: 453 RGQLRERLLLVLGRLPAREGHVLRLRHGLEDGRCRSLEEIGGMYRVSKEWIRKIEKSAM 511


>gi|302346408|ref|YP_003814706.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302150820|gb|ADK97081.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 228

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 127/255 (49%), Gaps = 39/255 (15%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+ I+ E  +S  E + +   ++ G+  A    +++ +ANL+ V+S+A +Y NRGL   D
Sbjct: 8   IEDIANEQLLSDKEEQELAEKIKVGDARAL---EKLTKANLKFVVSLAHQYRNRGLGEDD 64

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I +Q+   ++P          
Sbjct: 65  LISEGNIGMMYAAQKFDGSKGVRFVIFAAPYIRKAMEETIKEQATLYKLP---------- 114

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                      K E +  E  +  A+ ++          +P+    P+G  +   L   +
Sbjct: 115 -----------KNETSRFEQKRSHAISID----------QPV----PVGSNNNFTLQHIL 149

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E++NA    +   Q  L     + L  L  RE+RV+   +G+     +T+ E+ +   + 
Sbjct: 150 ENENAKHADEHLNQEILSNEIQKGLDVLDEREKRVITYIYGL-TGAHYTMAEIAEDMGLK 208

Query: 653 RERIRQIEAKAIRKL 667
           RER+RQI  KA+RKL
Sbjct: 209 RERVRQIRDKALRKL 223


>gi|86358940|ref|YP_470832.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283042|gb|ABC92105.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 302

 Score =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 127/247 (51%), Gaps = 20/247 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSAVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  ET  
Sbjct: 167 NVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHE-SQEDVLIEQDELETRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLE++  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMSVLNERERRIFEAR---RLAEDPVTLEDLSAEFDISRERVRQIEVRAFEKVQD 282

Query: 670 PSRSKKL 676
             R + L
Sbjct: 283 AVRKEAL 289


>gi|67921071|ref|ZP_00514590.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
 gi|67857188|gb|EAM52428.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
          Length = 250

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 45/68 (66%), Positives = 56/68 (82%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E+++ANLRLV+SVAKKY +RGL+ LDLIQEG +GL KA EKFD   GY+FSTYA WW
Sbjct: 179 AKDEIIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPVKGYRFSTYAYWW 238

Query: 504 VKQAITRS 511
           ++Q IT +
Sbjct: 239 IRQGITSA 246


>gi|42520871|ref|NP_966786.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|42410611|gb|AAS14720.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 297

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 129/244 (52%), Gaps = 16/244 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++ ++L LV+ +A K+ N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ 
Sbjct: 52  KLITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEA 111

Query: 507 AITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPV 560
           +I   I      ++I      R     + +  +R+     RE    E    I+ +L++  
Sbjct: 112 SIKDFILKSWSFVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSE 171

Query: 561 EGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETT- 613
             V ++   +    + ++    IGD+    L D I   N VS      +  +  L+ET  
Sbjct: 172 GDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIPC-NLVSQEVTYQNHEEKELKETIL 230

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              LASL  R   +   R+ +  N   TL+E+ K++CV+RERIRQ+  +A+ K+K   +S
Sbjct: 231 NNALASLNERARDIFISRY-LSENI-QTLDELSKKYCVSRERIRQLAEQAMAKVKQYIQS 288

Query: 674 KKLR 677
           + L+
Sbjct: 289 ESLK 292


>gi|114566373|ref|YP_753527.1| sporulation sigma factor SigG [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337308|gb|ABI68156.1| RNA polymerase sigma-G factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 234

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 124/226 (54%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++++ N+RLV+SV +++TNRG    DL Q G IGL+K+ + FD     +FSTYA+  
Sbjct: 15  AREKLIQGNIRLVLSVIQRFTNRGEYVDDLFQVGCIGLIKSIDNFDLSQNVRFSTYAVPM 74

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  +R+   +RD  +K ++   ++ N    EPT  +IA+ L +  E V
Sbjct: 75  IIGEIRRYLRDNNA-VRVSRSLRDIAYKALQVREKLINDNSAEPTVSQIAQHLDVSREEV 133

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI ++     GD I   + +S   S  +  L E + +  +  L  
Sbjct: 134 VFALDAIQEPVSLFEPIYNDG----GDPILVMDQLSDERSGDEQWLEEISIKEAMKKLND 189

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++ +RF  G       EE+G    +++ ++ ++E  A+++L+
Sbjct: 190 REKHIVSLRFFAGKTQMEVAEEIG----ISQAQVSRLEKAALKQLR 231


>gi|85373062|ref|YP_457124.1| RNA polymerase factor sigma-32 [Erythrobacter litoralis HTCC2594]
 gi|84786145|gb|ABC62327.1| RNA polymerase sigma-32 factor [Erythrobacter litoralis HTCC2594]
          Length = 301

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 79/254 (31%), Positives = 127/254 (50%), Gaps = 30/254 (11%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E   A  ++V ++LRLV  +A  Y   GL   DLI EGN+GLM+  +KF+   G+
Sbjct: 42  RYQEHEDPEAAAQLVSSHLRLVAKIAMGYRGYGLPVSDLISEGNVGLMQGVKKFEPDRGF 101

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPE 550
           + +TYAMWW+K ++   I      +++      K  K+    RRM  +++     + +PE
Sbjct: 102 RLATYAMWWIKASMQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKKQLEAYEDTDLSPE 159

Query: 551 E---IAKKLAMPVEGVRKVLKITKEPI-----SLETPI--GDEDTSHLGDFIEDKNAVSP 600
           +   IA  L +P +   +V+ + +  +     SL TP+  G++ +    D++ D     P
Sbjct: 160 DVTKIATDLGVPEQ---EVINMNRRMMMGGDGSLNTPMRNGEDGSGEWQDWLTDDR---P 213

Query: 601 LDSAIQANLRETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           L     AN  E   R       + +L  RE+ +L  R         TLEE+ + + V+RE
Sbjct: 214 LQDETVANAEEAQVRHEMLVEAMDALNEREQHILTERRLT--ENPQTLEELSQVYDVSRE 271

Query: 655 RIRQIEAKAIRKLK 668
           RIRQIE +A  KL+
Sbjct: 272 RIRQIEVRAFEKLQ 285


>gi|150016005|ref|YP_001308259.1| sporulation sigma factor SigG [Clostridium beijerinckii NCIMB 8052]
 gi|149902470|gb|ABR33303.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 257

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 120/226 (53%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 38  ARETFIKGNLRLVLSVIQRFNNRGENIDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +    +      +EPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALIMREKFIKDNNKEPTISQIAKELELPREEV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   ++P+SL  PI  +     GD I   + +S   +  +  L   + +  +  LT 
Sbjct: 157 VFALDAIQDPVSLFEPIYHDG----GDAIYVMDQISDAKNTDEHWLENISIKEAMKKLTD 212

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 213 REKLILNLRFFNG----RTQMEVADEIGISQAQVSRLEKTALKHMR 254


>gi|125972644|ref|YP_001036554.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125712869|gb|ABN51361.1| RNA polymerase, sigma subunit, RpoX/SigF [Clostridium thermocellum
           ATCC 27405]
          Length = 246

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 126/223 (56%), Gaps = 11/223 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE N+ LV S+ +++ NRG +  D+ Q G IGL+KA  KFD     KFSTYA+  +   
Sbjct: 27  LVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAINKFDCSYDVKFSTYAVPMIIGE 86

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R I D    I++   +++  +K   T   MS ++ REPT  EI+++L +PVE V   +
Sbjct: 87  IKRFIRDDG-MIKVSRSLKELANKARITKEIMSKELGREPTVGEISEQLGIPVEEVVMAM 145

Query: 568 KITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + +  P SL + +G+ D S   L D I +++    +D   + +LR    +VL +L PRE+
Sbjct: 146 EASCTPESLYSTLGEGDNSSTLLIDKIANESENQEVDIVDRIDLR----KVLDTLKPREK 201

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +R+      + T  ++ K   +++ ++ +IE K + +++
Sbjct: 202 QIIVLRYF----KEKTQVQIAKMLGISQVQVSRIEKKILEEIR 240


>gi|254363063|ref|ZP_04979122.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261492837|ref|ZP_05989384.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
 gi|261494798|ref|ZP_05991276.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|153094728|gb|EDN75518.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261309509|gb|EEY10734.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261311519|gb|EEY12675.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
          Length = 319

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 78/298 (26%), Positives = 153/298 (51%), Gaps = 28/298 (9%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           + P  VS +   P+G         +DS +++ N+   ++ E    ++E        R   
Sbjct: 35  MHPALVSGSMPVPQGN--------LDSYIRMANQYPILTAEQEKELAE--------RYYY 78

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   A K+++ +++R VI +A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  +
Sbjct: 79  DEDVEAAKQLILSHMRFVIHIARGYLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVS 138

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKL 556
           +A+ WVK  I   +      +++      +  K+    R+  N++    E   +++A  L
Sbjct: 139 FAVHWVKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKNKNRLAWFNEEEIKKVADDL 196

Query: 557 AMPVEGVRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + VE VR++  ++T + +  + P G  DED+     +IED ++    D   + +  + T
Sbjct: 197 GVSVEEVREMESRMTGQDLGFDLPAGDDDEDSYAPSMYIEDSSSNFADDLEDEQHNGQAT 256

Query: 614 TRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++   LA+L  R + +++ R+    +   TL+++  ++ ++ ER+RQ+E  A++K+K
Sbjct: 257 AQLAYALATLDERSQDIIKTRW--LDDNKATLQDLADKYNISAERVRQLENAALKKIK 312


>gi|256004731|ref|ZP_05429707.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281416836|ref|ZP_06247856.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|255991324|gb|EEU01430.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281408238|gb|EFB38496.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|316941118|gb|ADU75152.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 1313]
          Length = 248

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 126/223 (56%), Gaps = 11/223 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE N+ LV S+ +++ NRG +  D+ Q G IGL+KA  KFD     KFSTYA+  +   
Sbjct: 29  LVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAINKFDCSYDVKFSTYAVPMIIGE 88

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R I D    I++   +++  +K   T   MS ++ REPT  EI+++L +PVE V   +
Sbjct: 89  IKRFIRDDG-MIKVSRSLKELANKARITKEIMSKELGREPTVGEISEQLGIPVEEVVMAM 147

Query: 568 KITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + +  P SL + +G+ D S   L D I +++    +D   + +LR    +VL +L PRE+
Sbjct: 148 EASCTPESLYSTLGEGDNSSTLLIDKIANESENQEVDIVDRIDLR----KVLDTLKPREK 203

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +R+      + T  ++ K   +++ ++ +IE K + +++
Sbjct: 204 QIIVLRYF----KEKTQVQIAKMLGISQVQVSRIEKKILEEIR 242


>gi|58584688|ref|YP_198261.1| DNA-directed RNA polymerase sigma 32 subunit [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58419004|gb|AAW71019.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
           [Wolbachia endosymbiont strain TRS of Brugia malayi]
          Length = 297

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/260 (29%), Positives = 132/260 (50%), Gaps = 28/260 (10%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            +C+   +  +++ ++L LV+ +A K+ N GL  +DLI EGN+GL+ A +KF+  LG++F
Sbjct: 42  NQCKDISSAHKLITSHLNLVVKIAMKFKNYGLLLMDLIMEGNMGLIHAVKKFNPDLGFRF 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE--- 551
           STYA+WW++ +I   I      ++I      R     + +  +R+     RE    E   
Sbjct: 102 STYAVWWIEASIKDFILKSWSFVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIK 161

Query: 552 -IAKKLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ- 606
            I+ +L++    V ++   L    + ++    +G +    L D I       P +S  Q 
Sbjct: 162 AISNELSVSEGDVIQMNYRLACKDQSLNNCIKVGGDSKKELQDMI-------PCNSVNQE 214

Query: 607 --------ANLRETT-TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                     L+ET     LASL  R   +   R+ +  NT  TL+E+ K++CV+RERIR
Sbjct: 215 VTYQNREEKELKETILNNALASLNERSRDIFISRY-LSENT-QTLDELSKKYCVSRERIR 272

Query: 658 QIEAKAIRKLKHPSRSKKLR 677
           Q+  +A+ K+K   +S+ L+
Sbjct: 273 QLAEQAMSKVKQHIQSESLK 292


>gi|291559903|emb|CBL38703.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SSC/2]
          Length = 258

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 125/230 (54%), Gaps = 14/230 (6%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++  ++ NLRLV+S+ ++++       DL Q G IGLMKA + FD  L  KFSTYA+ 
Sbjct: 37  LAREHYIKGNLRLVLSIIQRFSGSNENADDLFQVGCIGLMKAIDNFDRNLNVKFSTYAVP 96

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   + R + D   ++R+   +RD  +K +     ++ K+  EPT + IAK++ M  E 
Sbjct: 97  MIIGEVKRYLRDNH-SMRVSRSLRDTAYKAINAREVLTKKLNHEPTIDVIAKEIDMKKED 155

Query: 563 VRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLAS 619
           V   L     P+SL  P+  +  DT +L D ++DK   +  DS +++  L+E     +  
Sbjct: 156 VLFALDAIATPLSLYEPVYQDGGDTLYLMDQVKDKK--NKEDSWVESIALKEA----MEH 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE  +++MRF  G     T  EV  +  +++ ++ ++E  A++ +K+
Sbjct: 210 LPDREYDIIKMRFFEG----KTQTEVADEIAISQAQVSRLEKNALKHMKN 255


>gi|187935615|ref|YP_001885389.1| sporulation sigma factor SigG [Clostridium botulinum B str. Eklund
           17B]
 gi|187723768|gb|ACD24989.1| RNA polymerase sigma-G factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 257

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 121/226 (53%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 38  ARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +    +      +EPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALIVRDKFIKDNNKEPTISQIAKELELPREEV 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   ++P+SL  PI  +     GD I   + +S   +  ++ L   + +  +  LT 
Sbjct: 157 VFALDAIQDPVSLFEPIYHDG----GDAIFVMDQISDSKNTDESWLENISIKEAMKKLTD 212

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 213 REKLILNLRFFRG----RTQMEVADEIGISQAQVSRLEKTALKHMR 254


>gi|229543947|ref|ZP_04433006.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
 gi|229325086|gb|EEN90762.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
          Length = 252

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 127/242 (52%), Gaps = 16/242 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +++R+ +     A+  +VE N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD
Sbjct: 19  VKNLIRRSQEGDQGARDLIVEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFD 78

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D   T+++   +++  +++ +T   ++ K+ R PT 
Sbjct: 79  LSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETGNRIRKTRDELTKKLGRSPTV 137

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQ 606
            EIA +L MPVE V    +  K P S+   +   D D   L D I D+N     D  A+Q
Sbjct: 138 HEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDGDPITLLDQISDQNDQKWFDQIALQ 197

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +R         L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K +  
Sbjct: 198 EAIR--------GLEERERLIVYLRY----YKDQTQSEVAERLGISQVQVSRLEKKILEV 245

Query: 667 LK 668
           +K
Sbjct: 246 MK 247


>gi|149924702|ref|ZP_01913051.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
 gi|149814429|gb|EDM74021.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
          Length = 371

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 82/251 (32%), Positives = 131/251 (52%), Gaps = 23/251 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFD 489
           V  V  G+ EA+   K +V +NLRLV+ +A +Y  RG Q  LDL+QEGN+GL+KA +KFD
Sbjct: 113 VRWVEHGDQEAA---KRLVTSNLRLVVKIANEY-RRGYQNLLDLVQEGNVGLLKAVQKFD 168

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPT 548
              G K STY+ WW++  + + I +    ++I     + K+   +R  R    +   +PT
Sbjct: 169 PYRGVKLSTYSGWWIRAYVLKHILNNWRLVKIGTTQNQRKLFFNLRKQREALIRAGIDPT 228

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLG---DFIEDKNA-----VS 599
            E IAK+L +  E V ++ K    P  SL  P+G  +        D +ED+       VS
Sbjct: 229 AENIAKELDVSTEEVVEMQKRMGAPDASLNAPLGSGEEPGARTRLDMLEDETTDPEGEVS 288

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIR 657
                 +  L +      A+L+ RE  +    FG  +  D   TL+ +G+++ V+RER R
Sbjct: 289 --GEEFKRLLHDKLRTFGATLSGREAEI----FGERLIADEPITLQALGERWGVSRERAR 342

Query: 658 QIEAKAIRKLK 668
           Q+E + + +L+
Sbjct: 343 QVEKRMVLRLR 353


>gi|94309217|ref|YP_582427.1| RNA polymerase factor sigma-32 [Cupriavidus metallidurans CH34]
 gi|93353069|gb|ABF07158.1| RNA polymerase sigma 32 (sigma H) factor [Cupriavidus metallidurans
           CH34]
          Length = 311

 Score =  102 bits (253), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 132/238 (55%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + MV ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 72  AARRMVMSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPEQGVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMP 559
           +K  I   +      +++     + K+   +R+ ++ S+      TPE+I   A++L + 
Sbjct: 132 IKAEIHEYVLKNWRMVKVATTKAQRKLFFNLRSHKQGSHTF----TPEQIEAVARELNVK 187

Query: 560 VEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKN-AVSPLDSAIQANLR-ETTT 614
            E V ++  +++   ++LE  I  G+E+ + +    ++ N     L++     L+ E   
Sbjct: 188 PEEVMEMETRMSGGDMALEGQIEDGEEEFAPIAYLADNHNEPTQVLEAKRHDRLQVEGLE 247

Query: 615 RVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  L PR  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 248 EALTKLDPRSRRIIEARW-LDVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMK 304


>gi|332799331|ref|YP_004460830.1| RNA polymerase sigma-28 subunit SigF [Tepidanaerobacter sp. Re1]
 gi|332697066|gb|AEE91523.1| RNA polymerase, sigma 28 subunit, SigF [Tepidanaerobacter sp. Re1]
          Length = 240

 Score =  101 bits (252), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 126/229 (55%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E+V  NL LV S+ K++ NRG +  DL Q G+IGL+KA EKFD+    KFSTYA+  
Sbjct: 20  ARDELVSLNLGLVWSIVKRFNNRGYEPEDLFQIGSIGLLKAIEKFDFSYDVKFSTYAVPM 79

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D    I++   +++  +K+ +T   ++N + REPT  EI+ ++ +PVE +
Sbjct: 80  IMGEIRRYIRDDK-PIKVSRSLKELGYKIQKTQEELTNTLDREPTINEISDEMEVPVEEI 138

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASL 620
              ++ ++  +SL   +  +D S +   I+  N     ++  Q NL   +      L+ L
Sbjct: 139 VMAMEASQSLVSLNDVVYQDDGSPIY-LIDQLN-----ENEYQENLLHDKIALKEALSKL 192

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              E +++ +R+      D T  +V K+  +T+ ++ ++E K + K+K+
Sbjct: 193 DRDERQIITLRYF----KDMTQIDVAKKLNMTQVQVSRLERKVLTKVKN 237


>gi|329890478|ref|ZP_08268821.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
 gi|328845779|gb|EGF95343.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
          Length = 294

 Score =  101 bits (252), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 87/288 (30%), Positives = 142/288 (49%), Gaps = 32/288 (11%)

Query: 411 NEIKSISVETGIS--ISEFRHIVSMV---------RKGECEASIAKKEMVEANLRLVISV 459
           N +  +S E G+S  ++E R    +          R  E +   A   +V ++LRLV  +
Sbjct: 4   NTLTVMSPEQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDPEAAHRLVTSHLRLVAKI 63

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +
Sbjct: 64  AMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLV 123

Query: 520 RIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKLAMPVEGVRKVLKITKE 572
           ++      K  K+    R+  ++I    + +  PE    IA KL +  E V  + +    
Sbjct: 124 KMGTTAAQK--KLFFNLRKAKSQISAFEEGDLHPEHLTAIATKLGVSEEEVTNMNRRLGG 181

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV------LASLTPREER 626
             SL  P+  +  S   D++ D +AVS  ++ +  N  E + R+      +  LT RE+ 
Sbjct: 182 DASLNAPLRADGESEWQDWLADDDAVSQ-ETQLAEN-EEKSIRMSLLQEAMEELTDREKH 239

Query: 627 VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L  R    +  D  TLEE+  Q+ V+RER+RQIE +A  KL+   R+
Sbjct: 240 ILTER---RLKDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRA 284


>gi|284050754|ref|ZP_06380964.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 159

 Score =  101 bits (252), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 48/90 (53%), Positives = 64/90 (71%), Gaps = 7/90 (7%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S + G+S SE   I++  R+       AK++M+EANLRLV+S+AKKY  R ++FLDLIQE
Sbjct: 77  SAKAGLSESEMTDIINRGRR-------AKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQE 129

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           G +GL +  EKFD   GYKFSTYA WW++Q
Sbjct: 130 GTLGLERGVEKFDPMRGYKFSTYAYWWIRQ 159


>gi|119632740|gb|ABL84377.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus suis]
          Length = 75

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 46/75 (61%), Positives = 62/75 (82%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 1   DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 60

Query: 532 VVRTARRMSNKIKRE 546
           +VR  R +  ++ ++
Sbjct: 61  LVREQRNLLQELGQD 75


>gi|167765669|ref|ZP_02437722.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
 gi|167712644|gb|EDS23223.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
          Length = 271

 Score =  101 bits (252), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 125/230 (54%), Gaps = 14/230 (6%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++  ++ NLRLV+S+ ++++       DL Q G IGLMKA + FD  L  KFSTYA+ 
Sbjct: 50  LAREHYIKGNLRLVLSIIQRFSGSNENADDLFQVGCIGLMKAIDNFDRNLNVKFSTYAVP 109

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   + R + D   ++R+   +RD  +K +     ++ K+  EPT + IAK++ M  E 
Sbjct: 110 MIIGEVKRYLRDNH-SMRVSRSLRDTAYKAINAREVLTKKLNHEPTIDVIAKEIDMKKED 168

Query: 563 VRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLAS 619
           V   L     P+SL  P+  +  DT +L D ++DK   +  DS +++  L+E     +  
Sbjct: 169 VLFALDAIATPLSLYEPVYQDGGDTLYLMDQVKDKK--NKEDSWVESIALKEA----MEH 222

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE  +++MRF  G     T  EV  +  +++ ++ ++E  A++ +K+
Sbjct: 223 LPDREYDIIKMRFFEG----KTQTEVADEIAISQAQVSRLEKNALKHMKN 268


>gi|307944600|ref|ZP_07659940.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
 gi|307772349|gb|EFO31570.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
          Length = 294

 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 128/249 (51%), Gaps = 21/249 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 48  AAERLVNSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   I      +++      K  ++    RR+  KI+       +    +EIA KL
Sbjct: 108 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGKIQALEEGDLKPHQVQEIATKL 165

Query: 557 AMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
            +  E V  + +      SL +P+  + D     D++ D+        A Q  L   RE 
Sbjct: 166 GVSEEEVISMNRRLGGDTSLNSPVRAEADAGEWQDWLVDEADSQETLLANQEELDQRREL 225

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRK----L 667
            ++ +  L  RE R+   R    ++ D  TLE++  +F V+RER+RQIE +A  K    +
Sbjct: 226 LSQAMDELNERERRIFTAR---RLSEDPITLEDLSTEFGVSRERVRQIEVRAFEKVQKAV 282

Query: 668 KHPSRSKKL 676
           K+ +R+K+L
Sbjct: 283 KNSARAKEL 291


>gi|255280674|ref|ZP_05345229.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
 gi|255268611|gb|EET61816.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
          Length = 258

 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 130/246 (52%), Gaps = 25/246 (10%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+ EA   ++  ++ NLRLV+SV K+++       DL Q G IGLMKA + F+  + 
Sbjct: 31  IRQGDMEA---RELYIKGNLRLVLSVIKRFSASNENADDLFQIGCIGLMKAIDNFNTEMD 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   I R + D + +IR+   +RD  +K + T      K  +EPT  E+A
Sbjct: 88  VKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDTAYKALYTREAYMKKHLKEPTINELA 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQ 606
           +++ +  E +   +   + P+SL  P+  E  DT ++ D I DK     N V  L     
Sbjct: 147 EEIGISREDIVFAMDAIQSPLSLYDPVYSEGGDTLYVMDQISDKKNKEENWVESLA---- 202

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E   R    L+ RE +++ MRF  G     T  EV  + C+++ ++ ++E  A++ 
Sbjct: 203 --LQEAMKR----LSDRERKIINMRFFEG----KTQMEVAAEICISQAQVSRLEKSALKS 252

Query: 667 LKHPSR 672
           +++  R
Sbjct: 253 MRNFLR 258


>gi|229586560|ref|YP_002845061.1| RNA polymerase factor sigma-32 [Rickettsia africae ESF-5]
 gi|228021610|gb|ACP53318.1| RNA polymerase sigma-32 factor [Rickettsia africae ESF-5]
          Length = 293

 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 121/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++L+LV  +A  Y   GL   +L+ EGNIGLM+A +KF+  LG++ STYAMWW
Sbjct: 49  AAHKLVTSHLKLVAKIASGYRTYGLPMTELVSEGNIGLMQAVKKFNPELGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K AI   I      +++      K     + +   +++N   R  T +   +IA +L +
Sbjct: 109 IKAAIQEYILKSWSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRTITTDDFVQIADELGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
            V  V ++  +I+   +SL   I  +D    G+ IE      P    +  N + +T++  
Sbjct: 169 SVNEVSEMNTRISGPDLSLNNSINSDDAES-GELIELLPETRPTPETMAINKQNSTSKRQ 227

Query: 616 ----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE R+L  R     +T  TL+ +  ++ +++ERIRQIE  A  K+K
Sbjct: 228 LLSNAMKILNDRELRILTER--KLTDTPKTLDILSNEYNISKERIRQIENTAFEKIK 282


>gi|108757418|ref|YP_634007.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
 gi|108461298|gb|ABF86483.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
          Length = 278

 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 126/234 (53%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V +NLRLV+ +A +Y    L  LDL+QEGNIGLM+A +K+D   G K S+YA WW
Sbjct: 30  AAYRLVASNLRLVVKLAHEYHRNPLSLLDLVQEGNIGLMQAVKKYDPERGVKLSSYAAWW 89

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I R I D    +++     + K+   +R  +        E +P+ +A++L +  + 
Sbjct: 90  IRAYILRYIMDNWKMVKLGTTEAQRKLFFKLRQEQEKLIAQGFEASPKLLAERLNVTEQD 149

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLD-----SAIQANLRETTT 614
           V ++  ++  + +S++ P+G++D S     D     N++ P D       ++A  RE  +
Sbjct: 150 VVEMDQRLGHDEMSIDAPLGNDDDSRTTRADRYLPSNSM-PADERLGAEQLKALFREKLS 208

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +L  +E  +   R  +  +   TL+++G ++ V+RER RQIEA  I +++
Sbjct: 209 EFARTLEGKERFIFESR--LVSDEPLTLQDIGDKYGVSRERARQIEAALINRMR 260


>gi|330814385|ref|YP_004358624.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327487480|gb|AEA81885.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 300

 Score =  101 bits (252), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 124/237 (52%), Gaps = 16/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +L+ EGNIGLM+A  KFD   G++ +TYAMWW
Sbjct: 52  AAHKLVTSHLRLVAKIAMGYRGYGLPVSELVSEGNIGLMQAVRKFDPEKGFRLATYAMWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE---EIAKKL 556
           +K +I   +      ++I      K  K+    +++ N+I    +    PE   EIA +L
Sbjct: 112 IKASIQEYVLRSWSLVKIGTTSAQK--KLFFNLKKIKNQIFAAEQGNMLPEHITEIATQL 169

Query: 557 AMPV-EGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +   E V    ++     SL  P+G ED+ +   D++ D+NA   L  + +  L +  +
Sbjct: 170 DVREDEVVSMNQRLAGHEHSLNAPVGGEDSDAEWQDWVVDENADQELQISQKQELNQRQS 229

Query: 615 ---RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  RE+ +L  R  I  +   TLEE+ ++  V+RERIRQIE +A  K++
Sbjct: 230 LLKNALHVLDEREKEILHNRRLI--DEPKTLEELSQKHKVSRERIRQIENRAFEKVQ 284


>gi|221195774|ref|ZP_03568827.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
 gi|221184248|gb|EEE16642.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
          Length = 276

 Score =  101 bits (251), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 119/225 (52%), Gaps = 17/225 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E   S  + +++ ++L LV  +A K+ NRG    DLIQ G IGL+KA ++FD   G +F+
Sbjct: 40  ETHDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGTIGLIKAIDRFDPSRGLEFT 99

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   +   I R   D+  ++R+P  +++   KV +    ++ +++R P+ EEIAKKL 
Sbjct: 100 TYATPTIMGEIKRHFRDKGWSVRVPRRLQELSAKVNQITDELTTELQRSPSIEEIAKKLG 159

Query: 558 MPVEGVRKVLKITKEPISLETPI--------GDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           + V+ V + ++ +    S+  P+        GDE  S +  +I +  A++  D  I    
Sbjct: 160 VSVDEVLEAMESSGAYSSV--PLEGGGSSVDGDEAPSIIDQYITEDEALAGSDDRI---- 213

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                  +A  +PRE+ ++RMRF  G+      E++G  Q  V+R
Sbjct: 214 --VLEDAIADFSPREQEIIRMRFVEGLTQVEIAEKLGISQVQVSR 256


>gi|88608622|ref|YP_506230.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600791|gb|ABD46259.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
          Length = 288

 Score =  101 bits (251), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 123/240 (51%), Gaps = 27/240 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +VEA LRLV+ V  ++ N G   +DL  EGNIGLMKA + F+  LG+  +TYA+WW
Sbjct: 46  AAQRLVEAYLRLVVKVTVRFRNYGFPLMDLASEGNIGLMKAIKNFNPTLGHGIATYAIWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-----IKREPTPEEIAKKLAM 558
           +K AI   +      ++I      +  ++    R++ N      +      + I++ LA+
Sbjct: 106 IKAAINEYVIRSWSMVKIGTTAAQR--RLFFNLRKLKNSGSVAGLDENQVVKRISEILAV 163

Query: 559 PVEGVRKVLKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRV 616
               V ++ +I     +SL   +G++D+S + D +       P   A Q A L ET  R 
Sbjct: 164 SKNDVEEMERILNARDVSLNMQLGEDDSSEVHDLV-------PFPEANQEAVLLETQERQ 216

Query: 617 LAS---------LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + S         L  R + +   R    +    TL+E+G++F +++ER+RQI A+A++K+
Sbjct: 217 MKSQLLYEAVEALEARHKEIFVARSLSAV--PRTLKELGEKFSISQERVRQIHARAMKKV 274


>gi|12744861|gb|AAK06822.1|AF326688_1 RNA polymerase sigma-32 factor [Burkholderia pseudomallei]
          Length = 281

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+SVA+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 42  AARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++     D+         R   K  +  TPEEI   A++L +  
Sbjct: 102 IKAEIHEYILRNWRMVKVG---DDEGAAQAFFNLRSHKKGTQAFTPEEIDGLAQELNVKR 158

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  I  G+E  + +    +  N  + + +A Q ++ +T    R
Sbjct: 159 EEVAEMETRLSGGDIALEGQIDDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAR 218

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 219 ALESLDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 274


>gi|296536196|ref|ZP_06898318.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
 gi|296263478|gb|EFH09981.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
          Length = 295

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 125/245 (51%), Gaps = 21/245 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +LI EGN+G+M+A  +FD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ AI   I      +++      K  K+    RR+  ++        +    E+IA+ L
Sbjct: 109 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMAALEEGDLQPEQVEKIARVL 166

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ---ANLRET 612
            +P + V  + +    P  SL  P+  +      D++ D++     + A +   +N RE 
Sbjct: 167 QVPEQDVVSMNRRLASPDNSLNAPVRADSEGEWQDWLVDESESQETEIAERQDMSNRREL 226

Query: 613 TTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L +L  RE  +L   R++     +   TLEE+ +Q+ ++RER+RQIE +A  KL+ 
Sbjct: 227 LGEALKTLNERERHILIERRLK-----DEPTTLEELSQQYNISRERVRQIEVRAFEKLQK 281

Query: 670 PSRSK 674
             +S+
Sbjct: 282 SMKSQ 286


>gi|212703179|ref|ZP_03311307.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
 gi|212673445|gb|EEB33928.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
          Length = 364

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   +V ++LRLV+ +A  +  R +Q  LDL+QEGN+GLM+A  KFD   G KFS YA +
Sbjct: 119 AAFRLVSSHLRLVVRIAMDFQRRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASF 178

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I    ++ K+   +   R+       +P    ++++L +  E
Sbjct: 179 WIKAYILKFIMDNWRMVKIGTTQVQRKLFYNLNRERQKLIAQGFDPDAAMLSERLGVSEE 238

Query: 562 GVRKV-LKITKEPISLETPIGDED--------TSHLGDFIEDKNAVSPLDSAIQANLRET 612
            + ++  ++    +SL   +G++            LG  IED       DS +   LRE 
Sbjct: 239 QITEMDQRLAANDLSLNAQVGEDAGGATRMDFLPALGPGIEDSLG----DSEVAELLREK 294

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +L  L  +E  +L+ R    + TD   TL E+G+++ VTRER+RQ+EA+ + K++ 
Sbjct: 295 LKTILPKLNEKELYILQNR----LLTDDPVTLREIGERYNVTRERVRQLEARLLEKIRQ 349


>gi|308233741|ref|ZP_07664478.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Atopobium vaginae DSM
           15829]
 gi|328943730|ref|ZP_08241195.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
 gi|327491699|gb|EGF23473.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
          Length = 286

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 129/228 (56%), Gaps = 9/228 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V A+L L   +A K+ NRG    DL+Q   IGL+KA ++FD   G +F+T+A   
Sbjct: 48  AREQLVLAHLNLARFLASKFKNRGESLDDLVQVATIGLIKAIDRFDISRGLEFTTFATPT 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+  ++R+P  +++   KV + + +++ K++R P+ +EIA+ L + V+ V
Sbjct: 108 IMGEIKRHFRDKGWSVRVPRRLQELSAKVTQVSDKLTEKLQRSPSVDEIAQALGVSVDEV 167

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
            + ++       +SL+ P GD+D       + DK A+  +D  ++ ++ R    + +   
Sbjct: 168 LEAMESAHAYSSVSLDVPQGDDDDGTQSSTVIDKYAL--VDEDLESSDDRIVLEQAIKDF 225

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + RE++++RMRF  G     T  E+ ++  +++ ++ ++  K ++K +
Sbjct: 226 SEREQQIIRMRFLEGF----TQVEIAQKLQISQVQVSRLLRKTLQKFQ 269


>gi|288802544|ref|ZP_06407983.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288335072|gb|EFC73508.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 257

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 127/255 (49%), Gaps = 39/255 (15%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+ I+ E  +S  E + +   ++ G+  A    +++ +ANL+ V+S+A +Y NRGL   D
Sbjct: 37  IEDIANEQLLSDKEEQDLAEKIKVGDARAL---EKLTKANLKFVVSLAHQYHNRGLGEDD 93

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I +Q+   ++P          
Sbjct: 94  LISEGNIGMMYAAQKFDGSKGVRFVVFAAPYIRKAMEEAIKEQATLYKLP---------- 143

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                      K E +  E  +  A+ ++          +P+    P+G  +   L   +
Sbjct: 144 -----------KNETSRFEQKRSHAISID----------QPV----PVGSNNNFTLQHIL 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E++NA    +   Q  L     + L  L  RE+RV+   +G+     +T+ E+ +   + 
Sbjct: 179 ENENAKHADEHLNQEILSNEIQKGLDVLDEREKRVITYIYGL-TGAHYTMAEIAEDMGLK 237

Query: 653 RERIRQIEAKAIRKL 667
           RER+RQI  KA+RKL
Sbjct: 238 RERVRQIRDKALRKL 252


>gi|32474462|ref|NP_867456.1| sigma-70 factor [Rhodopirellula baltica SH 1]
 gi|32445000|emb|CAD75002.1| sigma-70 factor [Rhodopirellula baltica SH 1]
          Length = 557

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 114/238 (47%), Gaps = 60/238 (25%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA   K ++V+ANLRLV+S+AK++      F  LI +GN+ L++A EKFD+  G KFSTY
Sbjct: 372 EAVKVKNKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAVEKFDYSRGNKFSTY 431

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A W + +   R+I ++          RD+                   TP+E+       
Sbjct: 432 ASWAIMKNFARTIPNE-------FKHRDRF----------------RATPDEMF------ 462

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                               +  +D   L  ++E+          +Q   +    R+L  
Sbjct: 463 --------------------VAHQD-ERLDPYLEE---------TVQLQRQRELARILDR 492

Query: 620 LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RE++++  RFG+    +  TL+EVG++  VT+ER+RQ+EA+A+ KL+  +R  K+
Sbjct: 493 LDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARALSKLRDAARDAKI 550


>gi|83311906|ref|YP_422170.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82946747|dbj|BAE51611.1| RNA polymerase sigma-32 factor [Magnetospirillum magneticum AMB-1]
          Length = 292

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 120/239 (50%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y + GL   DLI EGNIGLM+A +KF+   G++ +TYAMWW
Sbjct: 48  AAHRLVTSHLRLVAKIALGYRHYGLPVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAMP 559
           +K ++   + +    ++I      K  K+    RR+ ++++     +  PE +A      
Sbjct: 108 IKASLNEFVLNSWSMVKIGTLAAQK--KLFFNLRRIKSRLRLLEAGDLAPEHVATIAREL 165

Query: 560 VEGVRKVLKITKEPI----SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
               R V+ + +       SL  P+G E  + + D + D+          +  L   R  
Sbjct: 166 DVDERDVVAMNRRMAGRDSSLNAPVG-EGGTEIQDLMADEADNQETAYGKREELSKGRVL 224

Query: 613 TTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R L SLT RE  V    R+R     +   TLEE+G ++ V+RERIRQIE KA  K++
Sbjct: 225 IARALDSLTEREREVFVERRLR-----DDPVTLEELGGRYGVSRERIRQIEVKAFEKVR 278


>gi|198284078|ref|YP_002220399.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218665176|ref|YP_002426733.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248599|gb|ACH84192.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218517389|gb|ACK77975.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 285

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 133/251 (52%), Gaps = 29/251 (11%)

Query: 429 HIVSMVRKG-ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            ++  +R+G EC    A+  ++ A++ LV +VA+ Y N+GL   DL+QEG +GL++A ++
Sbjct: 45  QLIRRLRRGDEC----ARATLISAHMPLVRAVARGYRNKGLSQEDLLQEGYMGLLRAVDR 100

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN--KIKR 545
           F   LG +FS+YA WW+++A+ R++  +S  IR+P ++   +H  +++     +   ++R
Sbjct: 101 FQEGLGTRFSSYATWWIREAMQRALI-RSRFIRLPDYLAKSLHAYMQSGAEEDSDAGVRR 159

Query: 546 EPTPEEIAKK----LAMPVEGVRKVL---KITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           E   E +  +     A+    +R      +I+  P  +E   GD   S   D+  D    
Sbjct: 160 EQRREALGVRESTMRALDFADIRVFSLDEEISDGPGRIEQVTGDV-ASPDSDYDRD---- 214

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                AI   LRE  T     L  ++  V+  R+G+  +   TLE V ++  V+RE +RQ
Sbjct: 215 -----AICKALREHLT----ELNEKQREVMVFRYGMHGDAPMTLEAVAERMGVSREAVRQ 265

Query: 659 IEAKAIRKLKH 669
           ++ +A+ +L+ 
Sbjct: 266 LQVRALTRLRQ 276


>gi|327539462|gb|EGF26077.1| sigma-70 factor [Rhodopirellula baltica WH47]
          Length = 557

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 114/238 (47%), Gaps = 60/238 (25%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA   K ++V+ANLRLV+S+AK++      F  LI +GN+ L++A EKFD+  G KFSTY
Sbjct: 372 EAVKVKNKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAVEKFDYSRGNKFSTY 431

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A W + +   R+I ++          RD+                   TP+E+       
Sbjct: 432 ASWAIMKNFARTIPNE-------FKHRDRF----------------RATPDEMF------ 462

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                               +  +D   L  ++E+          +Q   +    R+L  
Sbjct: 463 --------------------VAHQD-ERLDPYLEE---------TVQLQRQRELARILDR 492

Query: 620 LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RE++++  RFG+    +  TL+EVG++  VT+ER+RQ+EA+A+ KL+  +R  K+
Sbjct: 493 LDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARALSKLRDAARDAKI 550


>gi|296284608|ref|ZP_06862606.1| RNA polymerase factor sigma-32 [Citromicrobium bathyomarinum JL354]
          Length = 280

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 82/252 (32%), Positives = 125/252 (49%), Gaps = 26/252 (10%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E   A  ++V ++LRLV  +A  Y   GL   DLI EGN+GLM+  +KF+   G+
Sbjct: 21  RYEEHEDPEAAAQLVSSHLRLVAKIAMGYRGYGLPVSDLISEGNVGLMQGVKKFEPDRGF 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPT---PE 550
           + +TYAMWW+K +I   I      +++      K  K+    RRM   +   E T   P+
Sbjct: 81  RLATYAMWWIKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRMKKNLDAYEDTDLHPD 138

Query: 551 E---IAKKLAMPVEGV----RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +   IA  L +P + V    R++L      +++     +E+ S   D++ D     PL  
Sbjct: 139 DVKKIATDLGVPEQEVINMNRRMLMGGDSSLNVSMRGDEENASQWQDWLTDDR---PLQD 195

Query: 604 AIQANLRETTTR------VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERI 656
              A+ +E   R       + SL  RE+ +L  R    +  D  TLEE+ K + V+RERI
Sbjct: 196 ETTADTQEAQVRHAMLLEAMDSLNDREKHILTER---RLTEDPQTLEELSKVYDVSRERI 252

Query: 657 RQIEAKAIRKLK 668
           RQIE +A  KL+
Sbjct: 253 RQIEVRAFEKLQ 264


>gi|288957081|ref|YP_003447422.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288909389|dbj|BAI70878.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 298

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 79/255 (30%), Positives = 121/255 (47%), Gaps = 47/255 (18%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V A  RLV++ A ++ N GL   DL+QEGN+GLM+AA +F+     +FSTYA WW
Sbjct: 46  ALHQLVRAYTRLVVATASRFRNYGLPMGDLVQEGNVGLMQAASRFEPDREVRFSTYAAWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-------EPTPEE----I 552
           ++ A+   I      +R       K   +    RR+  KI          P  +E    I
Sbjct: 106 IRSAMQDYILRNWSIVRTGTTAAQK--SLFFNLRRLRAKIDSATQNGSGAPLTKEGREWI 163

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A +L + V  V  + ++++    SL TP+ D       DF+ D+   SP D  I   +R+
Sbjct: 164 AGELRVEVAEVEAMEMRLSGADQSLNTPVADGSDDDWQDFLADQRP-SPEDVVI--GMRD 220

Query: 612 TTTR------VLASLTP-----------REERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             TR       L  L+P           REE               TLEE+G++  V++E
Sbjct: 221 ANTRSQWLAEALGELSPRERTIIRERRLREE-------------GATLEELGRELGVSKE 267

Query: 655 RIRQIEAKAIRKLKH 669
           R+RQ+E +A+ KL+ 
Sbjct: 268 RVRQLEHRALLKLRQ 282


>gi|225630797|ref|YP_002727588.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
 gi|225592778|gb|ACN95797.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
          Length = 270

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 129/249 (51%), Gaps = 16/249 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++ ++L LV+ +A K+ N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ 
Sbjct: 25  KLITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEA 84

Query: 507 AITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPV 560
           +I   I      ++I      R     + +  +R+     RE    E    I+ +L++  
Sbjct: 85  SIKDFILKSWSFVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSE 144

Query: 561 EGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETT- 613
             V ++   +    + ++    IGD+    L D I   N VS      +  +  L+E   
Sbjct: 145 GDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIPC-NLVSQEVTYQNHEEKELKEAIL 203

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              LASL  R   +   R+ +  N   TL+E+ K++CV+RERIRQ+  +A+ K+K   +S
Sbjct: 204 NNALASLNERARDIFISRY-LSENI-QTLDELSKKYCVSRERIRQLAEQAMAKVKQYIQS 261

Query: 674 KKLRSFLDG 682
           + L+  L  
Sbjct: 262 ESLKFCLHA 270


>gi|182418893|ref|ZP_02950150.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237667291|ref|ZP_04527275.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377176|gb|EDT74744.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237655639|gb|EEP53195.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 257

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 70/227 (30%), Positives = 119/227 (52%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     KFSTYA+  
Sbjct: 38  ARETFIKGNLRLVLSVIQRFNNRGENIDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +    +      +EPT  +IAK+L +P E V
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKALIVREKFIKDNNKEPTISQIAKELELPREEV 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   ++P+SL  PI  +  D  ++ D I D       D     N+  +    +  L+
Sbjct: 157 VFALDAIQDPVSLYEPIYHDGGDAIYVMDQISDSKDT---DENWLENI--SIKEAMKKLS 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 212 DREKLILNLRFFNG----RTQMEVADEIGISQAQVSRLEKTALKHMR 254


>gi|33594607|ref|NP_882251.1| RNA polymerase factor sigma-32 [Bordetella pertussis Tohama I]
 gi|33598734|ref|NP_886377.1| RNA polymerase factor sigma-32 [Bordetella parapertussis 12822]
 gi|33603808|ref|NP_891368.1| RNA polymerase factor sigma-32 [Bordetella bronchiseptica RB50]
 gi|33564683|emb|CAE44005.1| RNA polymerase sigma-32 factor [Bordetella pertussis Tohama I]
 gi|33574864|emb|CAE39527.1| RNA polymerase sigma-32 factor [Bordetella parapertussis]
 gi|33577933|emb|CAE35198.1| RNA polymerase sigma-32 factor [Bordetella bronchiseptica RB50]
 gi|332384018|gb|AEE68865.1| RNA polymerase factor sigma-32 [Bordetella pertussis CS]
          Length = 307

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 134/239 (56%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   +E+V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +
Sbjct: 68  EGDLEAA---RELVVSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVR 124

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +++     + K+   +R+ R     +  E   + IA+
Sbjct: 125 LVSFAVHWIKAEIHEFIIRNWRLVKVATTKAQRKLFFNLRSMRPDGQTLDPEQV-DHIAR 183

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLR 610
           +L +  E V ++ ++++   +SLE+   D+D+     ++ D+    P   LD     +L+
Sbjct: 184 ELNVRREDVSEMEVRLSGRDLSLESQDDDDDSFAPIAYLSDEGRQEPSRVLDRMAHDDLQ 243

Query: 611 ET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                R L +L  R  R++  R+ +  +   TL E+ ++F V+ ER+RQIEA A++K++
Sbjct: 244 GAGLGRALEALDARSRRIIEARW-LQDDGGLTLHELAQEFGVSAERVRQIEAAALKKMR 301


>gi|325270141|ref|ZP_08136748.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
 gi|324987442|gb|EGC19418.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
          Length = 228

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 122/246 (49%), Gaps = 39/246 (15%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   ++ G+ +A    +++ +ANL+ V+S+A +Y NRGL   DLI EGNIG+
Sbjct: 17  LSDREERTLAGRIKVGDAQAL---EKLTKANLKYVVSLAHQYRNRGLGEDDLISEGNIGM 73

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M AA++FD   G +F  +A  ++++A+  +I +Q+   R+P + ++      R+ ++ S+
Sbjct: 74  MHAAQRFDGSRGVRFVVFAAPYIRKAMEEAIKEQAALYRLPRNEKN------RSEQKRSH 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            I            +  PV                  P+G  +   L + +E+ NA    
Sbjct: 128 AI-----------SIDQPV------------------PVGSSNNFTLQNVLENDNAPHAD 158

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +   Q  L     + L  L  RE +V+   +G+     +T+ E  +   + RER+RQI  
Sbjct: 159 EQLNQEILSSEIQKGLGVLNERERQVIACLYGLS-GVHYTMAEAAEHMGLKRERVRQIRD 217

Query: 662 KAIRKL 667
           KA+RKL
Sbjct: 218 KALRKL 223


>gi|299134310|ref|ZP_07027503.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
 gi|298591057|gb|EFI51259.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
          Length = 299

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 120/248 (48%), Gaps = 21/248 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  K+    R+  +KI        RE   + IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALEEGDMREDQVKLIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +    V  + +      SL  PI D+ +     D++ D    SP   AI A      + 
Sbjct: 167 GVTERDVIDMNRRLGGDASLNAPIRDDGEPGEWQDWLVD---TSPNQEAIMAESEEYDHR 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R   T  +  L PRE R+   R         TLE++  +F V+RER+RQIE +A  K++ 
Sbjct: 224 RNALTGAMGVLNPRERRIFEARRLA--EEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQA 281

Query: 670 PSRSKKLR 677
             +S   R
Sbjct: 282 AVKSTVAR 289


>gi|92118359|ref|YP_578088.1| RNA polymerase factor sigma-32 [Nitrobacter hamburgensis X14]
 gi|91801253|gb|ABE63628.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter hamburgensis
           X14]
          Length = 299

 Score =  100 bits (250), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 122/239 (51%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P++   IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALEEGDMHPDQVKLIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +  + V  + +      SL  PI D+ +     D++ D    SP   AI A      + 
Sbjct: 167 GVTEQDVVDMNRRLGGDASLNAPIRDDGEAGEWQDWLVDH---SPTQEAIMAEHEELNHR 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+  T  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RQALTGAMGVLNPRERRIFEARR--LADEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQ 280


>gi|258515296|ref|YP_003191518.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779001|gb|ACV62895.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 259

 Score =  100 bits (249), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 138/247 (55%), Gaps = 19/247 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R +++  + G+   ++A++ +V  NL+LV ++ K++ NRG +  DL Q G+IGLMKA 
Sbjct: 20  EMRQLLAKAKLGD---AVARERLVNCNLKLVFNLVKRFNNRGYELEDLFQIGSIGLMKAI 76

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     KFSTYA+  +   I R + D +  +++   +++  +KV +T  R+  K+ R
Sbjct: 77  DKFDLNYDVKFSTYAVPMIVGEIRRFLRDDN-PVKVSRSVKEIAYKVQQTKERLIGKLGR 135

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDK--NAVSPL 601
           EP+  E+A+++ +  E V   L+  + P S+   +   D D  +L D +  K  N +  L
Sbjct: 136 EPSIGEVAEEIGLSKEEVVIALEAAQSPTSIYETLHQDDGDPIYLLDQLSSKEGNDLFWL 195

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   Q  ++E    +L +L  R+ ++L  RF      D T  ++ ++  +++ ++ ++E 
Sbjct: 196 D---QIEVKE----LLNNLHERDRQILIWRFF----EDKTQSDIARRLGLSQVQVSRLER 244

Query: 662 KAIRKLK 668
           +A+ KLK
Sbjct: 245 QALNKLK 251


>gi|74099847|gb|AAZ99132.1| RpoH [Rhizobium leguminosarum]
          Length = 302

 Score =  100 bits (249), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 127/247 (51%), Gaps = 20/247 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  +T  
Sbjct: 167 NVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDVLIEQDELDTRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLE++  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMSVLNERERRIFEAR---RLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQD 282

Query: 670 PSRSKKL 676
             R + L
Sbjct: 283 AVRKEAL 289


>gi|89053397|ref|YP_508848.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88862946|gb|ABD53823.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 292

 Score =  100 bits (249), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 133/265 (50%), Gaps = 26/265 (9%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R   CE S+ +  +V A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G 
Sbjct: 33  RDDRCEESLHR--LVTAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGV 90

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKR 545
           +FSTYA+WW+K +I   +      +R         +  +MR    ++ R A +  + + +
Sbjct: 91  RFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAMKSGDTLDK 150

Query: 546 EPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIED-----KNAV 598
               + IA ++ +P+  V  +  ++     SL      ED      D +ED     ++ V
Sbjct: 151 HQLRQMIATEVGVPLHDVEMMEGRLAGSDYSLNATQSAEDEGREWIDTLEDDGEQAEHIV 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIR 657
                  Q  LR+     + +L  RE  ++R R    +  D  TLE +G +  +++ER+R
Sbjct: 211 EHFHDTAQ--LRDWLIASMNALNDRERFIVRER---KLREDPRTLESLGTELGLSKERVR 265

Query: 658 QIEAKAIRKLKHP--SRSKKLRSFL 680
           Q+EA A  K++    ++SK++RSFL
Sbjct: 266 QLEAAAFGKMRKTLEAQSKEVRSFL 290


>gi|225019126|ref|ZP_03708318.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
 gi|224948099|gb|EEG29308.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
          Length = 288

 Score =  100 bits (249), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 131/231 (56%), Gaps = 21/231 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++  NL+LV+SV +++TNRG    DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 70  AREKLISGNLKLVLSVIQRFTNRGENLDDLFQVGCIGLIKAIDNFDISQNVRFSTYAVPM 129

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + ++R+   ++D  +K ++   +++    +EPT +EI++++ +  E V
Sbjct: 130 IIGEIRRYLRDNN-SVRVSRSLKDTAYKAMQAKEKLTTAHLKEPTIDEISQEMGVRREDV 188

Query: 564 RKVLKITKEPISLETPIGDE--DTSH----LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
              L+   +P+SL  P+  +  DT +    +GD  +DKN +  +  AI+  ++       
Sbjct: 189 VLALESIVDPVSLYEPVYSDGGDTIYVMDQIGDKSDDKNWLDEI--AIKEAIK------- 239

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  RE+++L +RF  G       E++G    +++ ++ ++E  A+ ++K
Sbjct: 240 -NLNEREKKILSLRFFNGKTQVEVAEDIG----ISQAQVSRLEKGALDRIK 285


>gi|75676615|ref|YP_319036.1| RNA polymerase factor sigma-32 [Nitrobacter winogradskyi Nb-255]
 gi|74421485|gb|ABA05684.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter winogradskyi
           Nb-255]
          Length = 299

 Score =  100 bits (249), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 119/239 (49%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  K+    R+  +KI        R    + IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDMRPDQVKLIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +  + V  + +      SL  PI D+ +     D++ D+   SP   AI A      + 
Sbjct: 167 GVTEQDVVDMNRRLGGDASLNAPIRDDGEAGEWQDWLVDQ---SPNQEAIMAEHEEFDHR 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R   T  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RRALTGAMGVLNPRERRIFEARRLA--DEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQ 280


>gi|291536437|emb|CBL09549.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           M50/1]
          Length = 259

 Score =  100 bits (249), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 120/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV K+++       DL Q G IGL+K+ + FD  +G KFSTYA+  
Sbjct: 38  ARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCIGLIKSIDNFDPTIGVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K + T   +S    +EPT +EIA +  +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIHTKEILSKTENKEPTLDEIAAESGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+  +  DT ++ D I DK     N V  L          +    
Sbjct: 157 VFALDAIQSPLSLYDPVYTDGGDTLYVMDQISDKKNREENWVEEL----------SLNDA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L  RE  +L++RF  G     T  EV  +  +++ ++ ++E  A++ ++H
Sbjct: 207 LDRLNERENYILKLRFFEG----KTQMEVADEIHISQAQVSRLEKSALKSIRH 255


>gi|94265020|ref|ZP_01288789.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|94270029|ref|ZP_01291635.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93450968|gb|EAT01953.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93454509|gb|EAT04794.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
          Length = 337

 Score =  100 bits (249), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 126/236 (53%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A  ++V ANLRLV+ VA  +    +Q FLDLIQEGNIGL++A +KFD     KFS YA +
Sbjct: 83  AAYQLVTANLRLVVKVAMDFQKYWMQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAY 142

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-V 560
           W++  I + I D    ++I     + K+   +   +++      EP P+ +A++L +   
Sbjct: 143 WIRAYILKFIMDNWRLVKIGTTQAQRKLFFNLNKEKKLLEAQGFEPEPKLLAQRLNVKES 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDF-------IEDKNAVSPLDSAIQANLRETT 613
           E +    ++    +SLE+P+ ++      DF       +E + A   +   + A L    
Sbjct: 203 EIIEMGQRLEHGDMSLESPLREDSDEQRKDFLPMLGPGVEQRVAEDEIRQWMAAML---- 258

Query: 614 TRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  +L  +E  +L  R    +N D  TL+E+  +F ++RER+RQIEA  ++K++
Sbjct: 259 DKLRLTLNEKELAILDQRL---LNDDPRTLQEIADRFTISRERVRQIEANLLKKMR 311


>gi|254796721|ref|YP_003081557.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
 gi|254589969|gb|ACT69331.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
          Length = 288

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 123/242 (50%), Gaps = 31/242 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +VEA LRLV+ V  ++ N G   +DL  EGNIGLMKA + F+  LG+  +TYA+WW
Sbjct: 46  AAQRLVEAYLRLVVKVTVRFRNYGFPLMDLASEGNIGLMKAIKNFNPTLGHGIATYAIWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-----IKREPTPEEIAKKLAM 558
           +K AI   +      ++I      +  K+    R++ N      +       +I++ L +
Sbjct: 106 IKAAINEYVIRSWSIVKIGTTAAQR--KLFFNLRKLKNSGSVAGLDEHQVVGKISEMLEV 163

Query: 559 P---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTT 614
               VE + ++L +    +SL   +G++ +S + D I       P   A Q A L ET  
Sbjct: 164 SKNDVEEMERILNV--RDVSLNMQLGEDGSSEVHDLI-------PFPEANQEAVLSETRE 214

Query: 615 R---------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           R          + SL  R + +   R    +    TL+E+G++F +++ER+RQI A+A++
Sbjct: 215 RQMKNRLLYEAVESLEARHKEIFVARSLSAV--PRTLKELGEKFSISQERVRQIHARAMK 272

Query: 666 KL 667
           K+
Sbjct: 273 KV 274


>gi|254456610|ref|ZP_05070039.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
 gi|207083612|gb|EDZ61038.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
          Length = 297

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 123/236 (52%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 51  AAEKLVTSHLRLVAKIAMGYKGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      ++I      K  K+    +++ N+I        R     EIA KL
Sbjct: 111 IKASIQEYILRSWSLVKIGTTTAQK--KLFFNLKKIKNQIAPQTEGDLRNEHVNEIANKL 168

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  E V  +  +++ +  SL   +G ED     D++ DK     L  A Q  + +    
Sbjct: 169 DVSKEEVVSMNRRLSGKEFSLNAQVG-EDGDEWQDWLVDKELDHDLKFAHQEEMEQRKDL 227

Query: 616 VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL-KH 669
           +  S+    +R   + +   +N D  TLE++ K++ ++RER+RQIE KA  KL KH
Sbjct: 228 LKNSIKVLNDREREILYSRRLNDDPTTLEDLSKKYKISRERVRQIENKAFEKLQKH 283


>gi|85707639|ref|ZP_01038705.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85689173|gb|EAQ29176.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 298

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 79/254 (31%), Positives = 126/254 (49%), Gaps = 30/254 (11%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E   A  ++V ++LRLV  +A  Y   GL   DLI EGN+GLM+  +KF+   G+
Sbjct: 39  RYAEHEDPEAASQLVSSHLRLVAKIAMGYRGYGLPVSDLISEGNVGLMQGVKKFEPDRGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPE 550
           + +TYAMWW+K +I   I      +++      K  K+    RRM  +++     +  P+
Sbjct: 99  RLATYAMWWIKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRMKKQLEAYEDSDLHPD 156

Query: 551 E---IAKKLAMPVEGVRKVLKITKEPI-----SLETPI--GDEDTSHLGDFIEDKNAVSP 600
           +   IA  L +P +   +V+ + +  +     SL TP+  G++ +    D++ D     P
Sbjct: 157 DVTKIATDLGVPEQ---EVVNMNRRMMMGGDGSLNTPMRNGEDGSGEWQDWLTDDR---P 210

Query: 601 LDSAIQANLRETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           L     A+  E   R       + SL  RE+ +L  R         TLEE+ + + V+RE
Sbjct: 211 LQDETVADAEEAEVRHEMLVEAMDSLNEREQHILTERRLT--EKPQTLEELSQVYDVSRE 268

Query: 655 RIRQIEAKAIRKLK 668
           RIRQIE +A  KL+
Sbjct: 269 RIRQIEVRAFEKLQ 282


>gi|83859721|ref|ZP_00953241.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852080|gb|EAP89934.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 301

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 129/244 (52%), Gaps = 18/244 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ EA  A   +  A +RLVIS+A K+ + GL F DL+ EGNIGLM+AA +F+     +
Sbjct: 46  KGDEEALHA---LTTAYMRLVISIAAKFRHYGLPFPDLVSEGNIGLMQAAARFEPEREVR 102

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPEE 551
           FSTYA WW++ +I   +      +R       K   +    RR+   IK     + TPE 
Sbjct: 103 FSTYATWWIRASIQDYVLRNWSIVRTGTTAAQK--SLFFNLRRLRALIKDTSSGQLTPEN 160

Query: 552 ---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDFIEDKNA---VSPLDSA 604
              +A+ L +  + V K+  ++     SL  P  ++      D + D+N       ++  
Sbjct: 161 RAYVAQALRVGEDDVEKMASRLAAVDRSLNAPFSEDGEGEWQDLLADENPDPETQVMEDR 220

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            QA   +     L+ L+ RE+ ++R R  +G ++  TLE++G++  +++ER+RQ+E +A+
Sbjct: 221 DQAQRAQWLGEALSRLSEREQLIIRER-RLGEDS-VTLEKLGERLGISKERVRQVEHQAL 278

Query: 665 RKLK 668
            KLK
Sbjct: 279 NKLK 282


>gi|325518946|gb|EGC98485.1| RNA polymerase factor sigma-32 [Burkholderia sp. TJI49]
          Length = 311

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 127/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I     T+++      K  + +    R   K  +  TPEEI   AK+L +  
Sbjct: 132 IKAEIHEYILRNWRTVKVAT---TKAQRKLFFNLRSHKKGVQAMTPEEIDGLAKELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|299538362|ref|ZP_07051645.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
 gi|298725949|gb|EFI66541.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
          Length = 247

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 128/244 (52%), Gaps = 17/244 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R +++  ++G+ EA   +K MVE N RLV S+ +++T RG++  DL Q G IGLMK+ +
Sbjct: 1   MRDLIARAQQGDHEA---RKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLMKSVD 57

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R + D    +++   +R+   K+         K +  
Sbjct: 58  KFDLTYDVKFSTYAVPMIIGEIQRFLRDDGM-VKVSRSIRELNFKIRHATDEFIKKNEHP 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSA 604
           PT +E+A+ L +  E +       ++P SL   +   + D+  L D ++D+ +  P D  
Sbjct: 117 PTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDEKSEQPFDY- 175

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L+E  TR    L PRE+ ++ +R+     +D T  E+  +  +++ ++ ++E K +
Sbjct: 176 --IPLKEVLTR----LEPREQSIIYLRYF----SDCTQTEIANRLGISQVQVSRLEKKIL 225

Query: 665 RKLK 668
            +LK
Sbjct: 226 AQLK 229


>gi|222087729|ref|YP_002546266.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221725177|gb|ACM28333.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 286

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 125/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 39  ARNKIATAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPEREVRFSTYASWW 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ R  T        EEIA  L
Sbjct: 99  IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLARGNTGVTVQSIHEEIAVAL 156

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDF-IEDKNAVSPLDSAIQANL--- 609
            + +  V+ +  +++    SL+ P   GD +++   DF I D+    PL     +N+   
Sbjct: 157 GVSLSDVQTMDARLSSNDASLQAPSISGDAESAERMDFLISDE----PLPDEQVSNMIDG 212

Query: 610 ---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R      L  L  RE +++R R  +      TLEE+G    +++ER+RQIE++A+ K
Sbjct: 213 ERRRVWLASALKHLNEREMKIIRARRLV--EDGATLEELGADLGISKERVRQIESRAMEK 270

Query: 667 LK 668
           L+
Sbjct: 271 LR 272


>gi|83592357|ref|YP_426109.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575271|gb|ABC21822.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 306

 Score =  100 bits (249), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 128/243 (52%), Gaps = 21/243 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y + GL   DL+ EGN+GLMKA +KF+   G++ +TYAMWW
Sbjct: 50  AAHRLVTSHLRLVAKIAMGYRHYGLPVSDLVAEGNMGLMKAVKKFEADRGFRLATYAMWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I +    +++      K  K+    RR+  K+    + + +PE+   IA +L
Sbjct: 110 IKASINEYILNSWSLVKVGTVAAQK--KLFFNLRRLKAKLGVYEEGDLSPEDVKTIATQL 167

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDK--NAVSPLDSAIQANLRETT 613
            +    V  + +    P  SL  P+G++ +    D + D+  N      +  + +L    
Sbjct: 168 KVTEADVVMMNRRLAGPDASLNVPVGEDQSMDRMDLLMDEGDNQEEVYAAHEEQSLGNRL 227

Query: 614 TR-VLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  L++LT RE  ++   R+R     +   TLEE+G ++ V+RER+RQIE +A  KL+ 
Sbjct: 228 LKDALSTLTERERHIITARRLR-----SEPVTLEELGGEYGVSRERVRQIENRAFEKLQT 282

Query: 670 PSR 672
             R
Sbjct: 283 AVR 285


>gi|322513377|ref|ZP_08066496.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
 gi|322120867|gb|EFX92727.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
          Length = 318

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/275 (26%), Positives = 147/275 (53%), Gaps = 22/275 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   +S E    ++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 51  LDSYIRMANQYPILSAEQEKELAE--------RYYYDEDLEAAKQLILSHMRFVIHIARG 102

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 103 YLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVA 162

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  N++    E   +++A+ L + VE VR++  ++T + +  + P
Sbjct: 163 TTKAQR--KLFFNLRKNKNRLAWFNEDEIKKVAEDLGVSVEEVREMESRMTGQDLGFDLP 220

Query: 580 IGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFGI 634
            G++D        +IED ++    +   + +  E T ++   LA+L  R + +++ R+  
Sbjct: 221 AGEDDDEAYAPSMYIEDNSSNFADELEDEEHTGEATAQLAYALATLDERSQDIIKTRW-- 278

Query: 635 GMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++ D  TL+++  ++ ++ ER+RQ+E  A++K+K
Sbjct: 279 -LDEDKATLQDLADKYGISAERVRQLENAALKKIK 312


>gi|297569322|ref|YP_003690666.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925237|gb|ADH86047.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 363

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 128/233 (54%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A  ++V ANLRLV+ VA  +    +Q FLDLIQEGNIGL++A +KFD     KFS YA +
Sbjct: 113 AAYKLVTANLRLVVKVAMDFQKYWMQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAY 172

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-V 560
           W++  I + I D    ++I     + K+   +   +++      +P P+ +A++L +   
Sbjct: 173 WIRAYILKFIMDNWRLVKIGTTQAQRKLFFSLNKEKKLLESQGFKPEPKLLAQRLNVKES 232

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVL-- 617
           E +    ++    +SLE+P+ ++      DF+    A   ++  + A+ +RE    +L  
Sbjct: 233 EVIEMSQRMDNWDMSLESPMREDSGDERKDFL--PVAGPSVEERVAADEVREWMAGILDK 290

Query: 618 --ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +L  +E  +LR R  +  +   TL+E+  +F ++RER+RQIEA  ++K++
Sbjct: 291 MRRTLNEKELAILRER--LLSDEPATLQEIADRFAISRERVRQIEANLLKKMR 341


>gi|284052567|ref|ZP_06382777.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 232

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 49/96 (51%), Positives = 67/96 (69%), Gaps = 1/96 (1%)

Query: 412 EIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           E+K I  E     +E  ++ V  +++ + E   AK  M++ANLRLV+SVAKKY NRGL+ 
Sbjct: 137 ELKQIMAEGKRCWAELANLSVEELKQVQREGIQAKDHMIKANLRLVVSVAKKYQNRGLEL 196

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q
Sbjct: 197 LDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQ 232


>gi|47028349|gb|AAT09107.1| RpoH-like sigma factor [Rhizobium sp. TAL11145]
          Length = 289

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 125/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 42  ARNKIATAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPEREVRFSTYASWW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ R  T        EEIA  L
Sbjct: 102 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLARGNTGVTVQSIHEEIAVAL 159

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDF-IEDKNAVSPLDSAIQANL--- 609
            + +  V+ +  +++    SL+ P   GD +++   DF I D+    PL     +N+   
Sbjct: 160 GVSLADVQTMDARLSSNDASLQAPSISGDAESAERMDFLISDE----PLPDEQVSNMIDG 215

Query: 610 ---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R      L  L  RE +++R R  +      TLEE+G    +++ER+RQIE++A+ K
Sbjct: 216 ERRRVWLASALKHLNEREMKIIRARRLV--EDGATLEELGADLGISKERVRQIESRAMEK 273

Query: 667 LK 668
           L+
Sbjct: 274 LR 275


>gi|85714568|ref|ZP_01045555.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85698453|gb|EAQ36323.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 272

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 119/239 (49%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 22  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 81

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  K+    R+  +KI        R    + IA++L
Sbjct: 82  IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDMRPDQVKLIARRL 139

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +  + V  + +      SL  PI D+ +     D++ D+   SP   A+ A      + 
Sbjct: 140 GVTEQDVVDMNRRLGGDASLNAPIRDDGEAGEWQDWLVDQ---SPTQEAVMAEHEEFDHR 196

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R   T  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 197 RRALTGAMGVLNPRERRIFEARRLA--DEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQ 253


>gi|117925612|ref|YP_866229.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117609368|gb|ABK44823.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 290

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 130/232 (56%), Gaps = 12/232 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A  ++V + LR V S+AK+Y    G++F+DL+QEG++GLM+A ++FD   G++ +TYAMW
Sbjct: 48  AAHKLVTSYLRYVASIAKEYQGYYGIKFMDLVQEGSVGLMQAVKRFDPHKGFRLATYAMW 107

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPV 560
           W+K +I   +      ++I      +  K+    R+  + ++R      EE+ ++  +  
Sbjct: 108 WIKASIQEFVLHHWSLVKIGTTAAQR--KLFFNLRKSKDTLERLDATQAEEMGQRFGVSG 165

Query: 561 EGVRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           E V ++  +++    SL   +   G+E  + L D   ++  +  L S  +   ++   + 
Sbjct: 166 EAVLEMDARLSGPDDSLNRCLVEGGEEIQNMLADSAPNQE-MRLLASESERLQQQMIKQA 224

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ L+ RE+ ++R R  I      TLE +G++  V+RERIRQ+E +A++KL+
Sbjct: 225 LSFLSEREQMIVRAR--IMCAEPVTLEVLGERLGVSRERIRQLETRALKKLR 274


>gi|240144182|ref|ZP_04742783.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
 gi|257203785|gb|EEV02070.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
          Length = 259

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 120/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV K+++       DL Q G IGL+K+ + FD  +G KFSTYA+  
Sbjct: 38  ARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCIGLIKSIDNFDPTIGVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K + T   +S    +EPT +EIA +  +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIHTKEILSKTENKEPTLDEIAAESGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+  +  DT ++ D I DK     N +  L          +    
Sbjct: 157 VFALDAIQSPLSLYDPVYTDGGDTLYVMDQISDKKNREENWIEEL----------SLNDA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L  RE  +L++RF  G     T  EV  +  +++ ++ ++E  A++ ++H
Sbjct: 207 LDRLNERENYILKLRFFEG----KTQMEVADEIHISQAQVSRLEKSALKSIRH 255


>gi|197103875|ref|YP_002129252.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
 gi|196477295|gb|ACG76823.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
          Length = 295

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/291 (28%), Positives = 141/291 (48%), Gaps = 37/291 (12%)

Query: 411 NEIKSISVETGIS--ISEFRHIVSMV---------RKGECEASIAKKEMVEANLRLVISV 459
           N +  +S E G+S  ++E R    +          R  E +   A   +V ++LRLV  +
Sbjct: 4   NALAVMSPEGGLSRYLTEIRKFPMLAKDEEFMLAKRWQEHQDPEAAHRLVTSHLRLVAKI 63

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +
Sbjct: 64  AMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLV 123

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPVEGVRKV-LKITK 571
           ++      K  K+    R+  ++I        R     +IA KL +  E V  +  ++  
Sbjct: 124 KMGTTAAQK--KLFFNLRKAKSEISALEEGDLRPEQVRQIATKLGVLDEEVISMNRRLAG 181

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV------LASLTPREE 625
              SL +P+  +  S   D++ D++  +P   ++ A   E   R+      +A LT RE 
Sbjct: 182 GDASLNSPLRADSESEWQDWLVDED--TPSQESVVAEAEERGIRMELLQEAMAELTDRER 239

Query: 626 RVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +L   R++     +   TLEE+  Q+ V+RER+RQIE +A  KL+   R+
Sbjct: 240 HILTERRLK-----DEPTTLEELASQYGVSRERVRQIEVRAFEKLQKSMRA 285


>gi|254419521|ref|ZP_05033245.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
 gi|196185698|gb|EDX80674.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
          Length = 286

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 123/242 (50%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 40  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I    + +  PE    IA KL
Sbjct: 100 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQISAFEEGDLHPEHLAAIATKL 157

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETT 613
            +  E V  + +      SL  P+  +  S   D++ D  AVS    L    +  +R + 
Sbjct: 158 GVSEEEVTNMNRRLGGDASLNAPLRADGESEWQDWLADDTAVSQETQLADDEEKGIRMSL 217

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +  +  LT RE+ +L  R    +  D  TLEE+  Q+ V+RER+RQIE +A  KL+   
Sbjct: 218 LQEAMEELTDREKHILTER---RLKDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAM 274

Query: 672 RS 673
           R+
Sbjct: 275 RA 276


>gi|78067614|ref|YP_370383.1| RNA polymerase factor sigma-32 [Burkholderia sp. 383]
 gi|77968359|gb|ABB09739.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. 383]
          Length = 311

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 85/280 (30%), Positives = 143/280 (51%), Gaps = 28/280 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +D+ ++  N I  ++VE      E R   +  R+G    S   + +V ++LRLV+S+++ 
Sbjct: 39  IDAYIQAVNRIPLLTVE------EERQYATEFREGNNLDS--ARRLVLSHLRLVVSISRN 90

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I     T+++ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTVKVA 150

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEGVRKV-LKITKEPISLET 578
                K  + +    R   K  +  TPEEI   AK+L +  E V ++  +++   I+LE 
Sbjct: 151 T---TKAQRKLFFNLRSHKKGLQAMTPEEIDGLAKELNVKREDVTEMETRLSGGDIALEG 207

Query: 579 PI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRF-- 632
            +  G+E  + +    +  N  + + +A Q +  +T    + L +L  R  R++  R+  
Sbjct: 208 QVEDGEESYAPIAYLADSHNEPTAVLAARQRDTLQTDGIAQALDALDARSRRIIEARWLH 267

Query: 633 ----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 268 VDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|39998179|ref|NP_954130.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|39985125|gb|AAR36480.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|298507117|gb|ADI85840.1| RNA polymerase sigma-70 factor RpoD [Geobacter sulfurreducens
           KN400]
          Length = 577

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/159 (37%), Positives = 92/159 (57%), Gaps = 4/159 (2%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T +E+N  LPPD +SSEQ++D ++M   M I++VD    +  
Sbjct: 5   STDEVKQLIDLGKEKGFLTYDEVNDLLPPD-ISSEQIDDVMSMFGEMDIDIVDSA--QKV 61

Query: 87  EGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +  +  LDL             + +  A   T DPVRMYLREMGS+ LL+REGE+ IAKR
Sbjct: 62  KIPKMKLDLEEEEEIEGEQEDFEYEPGALGRTSDPVRMYLREMGSVSLLTREGEVEIAKR 121

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           IE G   +   +  +P+T + +I   ++L  G     EI
Sbjct: 122 IEEGERDIAGVILNTPITVKEIIALGEKLLRGQVSAAEI 160


>gi|260592476|ref|ZP_05857934.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
 gi|260535522|gb|EEX18139.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
          Length = 228

 Score =  100 bits (248), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 129/255 (50%), Gaps = 39/255 (15%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+ I  E  +S  E + + + ++ G+ +A    +++ +ANL+ V+S+A  Y N+GL   D
Sbjct: 8   IEEIVQEQLLSSEEEQTLAAKIKLGDAKAL---EKLTKANLKFVVSLAHHYKNQGLGEDD 64

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+ EGNIG+M AA+KFD   G +F +YA  ++++A+  +I +Q+   ++P          
Sbjct: 65  LVSEGNIGMMHAAQKFDGTKGIRFVSYAAPYIRKAMEEAIKEQTALYKLP---------- 114

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                      K E +  E  +  A+ ++          +PI    P+G  +   L   +
Sbjct: 115 -----------KDEKSKFERKRTHAISID----------QPI----PVGSSNNFTLQHVL 149

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E+++A    +   +  L     + L  L  RE+R++   +G+   T +T+ E+ +   + 
Sbjct: 150 ENEDAPQADEHLNKELLNFEIQKGLNELNEREKRIIIAIYGLN-GTHYTMAEIAENMGLK 208

Query: 653 RERIRQIEAKAIRKL 667
           RER+RQI  KA+RKL
Sbjct: 209 RERVRQIRNKALRKL 223


>gi|312114652|ref|YP_004012248.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
 gi|311219781|gb|ADP71149.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
          Length = 308

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 126/256 (49%), Gaps = 17/256 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E + A +++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++FD   G+
Sbjct: 37  RWQEHEDAKAAQKLVTSHLRLVARIAMGYRGYGLPIGEVISEGNVGLMQAVKRFDPDKGF 96

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW++ AI   I      +++      K  K+    R+  ++++       R  
Sbjct: 97  RLATYAMWWIRAAIQEYILRSWSLVKMGTTASQK--KLFFNLRKAKSQLQALEEGDLRPD 154

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             + IA  L +P E V  + +      SL  P+  D ++    D++ D+        A  
Sbjct: 155 QVKTIATNLGVPEEDVVSMNRRLGGDASLNAPLRADSESGEWQDWLVDEGPNQETQLAES 214

Query: 607 ANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAK 662
             L   RE     + SL  RE R+   R    +  D  TLEE+  +F V+RERIRQIE +
Sbjct: 215 EELSRRREYLGAAMDSLNERERRIFTAR---RLADDPLTLEELSSEFNVSRERIRQIEVR 271

Query: 663 AIRKLKHPSRSKKLRS 678
           A  K++   +   L++
Sbjct: 272 AFEKVQKAVQKAALKA 287


>gi|325266382|ref|ZP_08133060.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
 gi|324982175|gb|EGC17809.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
          Length = 332

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 92/304 (30%), Positives = 142/304 (46%), Gaps = 49/304 (16%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           ++A   P G         ++  +   N I  +S E    ++E R I     KG+ EA+  
Sbjct: 45  AFALPVPSGH------GNLEQYIHTVNNIPMLSAEEETRLAE-RQI-----KGDLEAA-- 90

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ W+
Sbjct: 91  -KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRFEPHHGARLFSFAVHWI 149

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVE 561
           K  I   I      +R+      +  K+    R M N +K   +P+E   IA  L + V 
Sbjct: 150 KAEIHEFILRNWRLVRVATTKPQR--KLFFNLRSMRNSLK-ALSPKEAQDIADDLGVKV- 205

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLD---------------SA 604
                     E + +E  +   D   L D  +D   NA +P+D                A
Sbjct: 206 ---------SEVMEMEQRMTGHDIGLLADNQDDDENNAFAPIDWLSDSQHEPSHQLAQKA 256

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A   E     LA L  R  R++  R+ +      TL E+  +F V+ ERIRQIEAKAI
Sbjct: 257 HYALQTEGLQAALAQLDERSRRIVETRW-LHDGQAATLHELAAEFGVSAERIRQIEAKAI 315

Query: 665 RKLK 668
           +KL+
Sbjct: 316 QKLR 319


>gi|312797371|ref|YP_004030293.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
 gi|312169146|emb|CBW76149.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
          Length = 319

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 124/249 (49%), Gaps = 40/249 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 80  AARQLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPRQNVRLVSYAIHW 139

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   I      +++      K  + +    R   +  +  TP+EIA        G+
Sbjct: 140 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKQGMQAFTPDEIA--------GL 188

Query: 564 RKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA---- 618
            K L + +E ++ +ET +   D +  G F + + + +P+  A  A+ R   T VLA    
Sbjct: 189 AKELNVKREEVTEMETRLAGGDIALEGQFEDGEESFAPI--AYLADSRTEPTTVLASRQR 246

Query: 619 -------------SLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQI 659
                        SL  R  R++  R+      G G     TL E+  +F V+ ERIRQI
Sbjct: 247 DLLQTEGLAEALESLDARSRRIIEARWLQVQDDGSG---GATLHELADEFGVSAERIRQI 303

Query: 660 EAKAIRKLK 668
           EA A++K++
Sbjct: 304 EASAMKKMR 312


>gi|299535877|ref|ZP_07049197.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
 gi|298728629|gb|EFI69184.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
          Length = 257

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 127/245 (51%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +   ++ GE E    ++E+V  NLRLV+S+  ++  RG Q  DL Q G IGLMKA 
Sbjct: 22  EMKELFIRLQAGETEI---REELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIGLMKAI 78

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +      R
Sbjct: 79  DHFDLKHNVRFSTYAVPMIIGEIRRHLRDHHA-LRVSRSLRDIAYKAMQAKEQWITDNLR 137

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT EEIA+ + M  E V   L   ++P+SL+ PI  +  D  ++ D + D + VS    
Sbjct: 138 EPTIEEIAEMIDMKKEDVLFALDAIQDPVSLQEPIYSDGGDAVYMMDQLRDDD-VSEDQW 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +++E+    L  L  R++ ++  RF  G     T  E+ K+  +++ +I ++E  A
Sbjct: 197 VAYVSVKES----LQKLDERQQMIVAKRFYYG----ETQTEIAKELGISQAQISRLEKNA 248

Query: 664 IRKLK 668
           I  ++
Sbjct: 249 IETMQ 253


>gi|171320177|ref|ZP_02909239.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171094591|gb|EDT39643.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 311

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 126/237 (53%), Gaps = 20/237 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K
Sbjct: 74  RRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIK 133

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEG 562
             I   I      +++      K  + +    R   K  +  TPEEI   A++L +  E 
Sbjct: 134 AEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKRED 190

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVL 617
           V ++  +++   I+LE  +  G+E  + +    +  N  S + +A Q ++ +T    + L
Sbjct: 191 VTEMETRLSGGDIALEGQVDDGEESYAPIAYLADSHNEPSAVLAARQRDMLQTDGIAQAL 250

Query: 618 ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 251 EALDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|147677561|ref|YP_001211776.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273658|dbj|BAF59407.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 259

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 131/243 (53%), Gaps = 10/243 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +++K +   S A+ ++V  NL+LV ++ K++ NRG +  DL Q G IGLMKA +K
Sbjct: 19  REMRELLQKAKAGDSYARDKLVNCNLKLVFNLVKRFQNRGYELEDLFQIGCIGLMKAIDK 78

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D +  I++   +++K ++V +    ++ ++ REP
Sbjct: 79  FDVSYDVKFSTYAVPMIVGEIRRFLRDDN-PIKVSRSLKEKAYRVQQARDLLTARLGREP 137

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T  E++ +L +  E V   L+  + P S+   +  +D    GD I   + +   +     
Sbjct: 138 TVGEVSAELGLSREEVVNALEAAQVPASIYETLHQDD----GDPIYLLDQIKGSEEGDVP 193

Query: 608 NLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L + T + +L  L  R+ ++L  RF      D T  ++ K+  +++ ++ ++E +A++K
Sbjct: 194 WLEKITVKELLNKLPERDRQILAWRFF----EDRTQSDIAKRLGLSQVQVSRLERQALKK 249

Query: 667 LKH 669
           LK 
Sbjct: 250 LKE 252


>gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254040288|gb|ACT57084.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 302

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 85/289 (29%), Positives = 138/289 (47%), Gaps = 49/289 (16%)

Query: 415 SISVETGISISEFRH---IVSMVRKGECEASIAKK-----------EMVEANLRLVISVA 460
           SI V   I +S + H    + M+ K E E  +AK+            +V ++LRLV+ +A
Sbjct: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
             Y   GL   +++ EGNIGLM+A +KFD   G++ +TY+MWW+K A+   I      ++
Sbjct: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125

Query: 521 IPVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAMPVEGVRKVLKITK-EPIS 575
           I      K  ++    RR+   ++        PE++          + K L +++ E IS
Sbjct: 126 IGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVIS 175

Query: 576 LETPI-GDEDTSHLGDFIEDKNAVSPLDSAI---------------QANLRETTTRVLAS 619
           +   + GDE  + L +   DKN+    D  +               + N R   TR ++ 
Sbjct: 176 MNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 235 LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281


>gi|293602894|ref|ZP_06685333.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
 gi|292818688|gb|EFF77730.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
          Length = 294

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 129/231 (55%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E++ ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 61  AARELILSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 120

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ R     +  +   + IA++L +  E 
Sbjct: 121 IKAEIHEYIIRNWRLVKVATTKAQRKLFFNLRSMRPDGQTLDPDQV-DHIARELNVRRED 179

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRET-TTRVL 617
           V ++ ++++   +SLE    D+D+     ++ D     P   L+ A +  L+ T  T  L
Sbjct: 180 VSEMEVRLSGREMSLENQDDDDDSFAPIAYLSDDGRQEPTRVLERAARDELQSTGLTTAL 239

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R  R++  R+ +  +   TL E+ ++F V+ ERIRQIEA A++K++
Sbjct: 240 EALDARSRRIVEARW-LQDDGGATLHELAQEFGVSAERIRQIEAAALKKMR 289


>gi|241206034|ref|YP_002977130.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859924|gb|ACS57591.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 302

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 126/247 (51%), Gaps = 20/247 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D     D++ D +  S  D  I+ +  +T  
Sbjct: 167 KVSEEEVISMNRRLSGDASLNAPIKAAEGDGGQWQDWLVDDHD-SQEDVLIEQDELDTRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLE++  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMSVLNERERRIFEAR---RLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQD 282

Query: 670 PSRSKKL 676
             R + L
Sbjct: 283 AVRKEAL 289


>gi|254294740|ref|YP_003060763.1| RNA polymerase factor sigma-32 [Hirschia baltica ATCC 49814]
 gi|254043271|gb|ACT60066.1| RNA polymerase, sigma 32 subunit, RpoH [Hirschia baltica ATCC
           49814]
          Length = 295

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 123/243 (50%), Gaps = 27/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAEKMVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    RR+  +I+       R     EIA +L
Sbjct: 109 IRASIQEYILRSWSLVKLGTTAAQK--KLFFNLRRLKGEIQALEEGDLRPENVAEIATRL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +   E +    ++T    SL  PIG  D      D++ D N  +  +   Q +  E +T
Sbjct: 167 NVSETEVISMNRRMTGGDASLNAPIGGADGDGEWMDWLSDDNQQNQAEEYEQND--EFST 224

Query: 615 RV------LASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           R+      +  L  RE+ ++   R++     +   TLEE+   + V+RERIRQIE +A  
Sbjct: 225 RMSLLETAMEGLNEREKHIIAERRLK-----DEPSTLEELSAVYNVSRERIRQIEVRAFE 279

Query: 666 KLK 668
           KL+
Sbjct: 280 KLQ 282


>gi|116253507|ref|YP_769345.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258155|emb|CAK09256.1| putative RNA polymerase sigma-32 factor [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 302

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 126/247 (51%), Gaps = 20/247 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D     D++ D +  S  D  I+ +  +T  
Sbjct: 167 NVSEEEVISMNRRLSGDASLNAPIKAAEGDGGQWQDWLVDDHD-SQEDVLIEQDELDTRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLE++  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMSVLNERERRIFEAR---RLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQD 282

Query: 670 PSRSKKL 676
             R + L
Sbjct: 283 AVRKEAL 289


>gi|115352926|ref|YP_774765.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria AMMD]
 gi|170701101|ref|ZP_02892077.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|172061774|ref|YP_001809426.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria MC40-6]
 gi|115282914|gb|ABI88431.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           AMMD]
 gi|170134002|gb|EDT02354.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|171994291|gb|ACB65210.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MC40-6]
          Length = 311

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 126/237 (53%), Gaps = 20/237 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K
Sbjct: 74  RRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIK 133

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEG 562
             I   I      +++      K  + +    R   K  +  TPEEI   A++L +  E 
Sbjct: 134 AEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKRED 190

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVL 617
           V ++  +++   I+LE  +  G+E  + +    +  N  S + +A Q ++ +T    + L
Sbjct: 191 VTEMETRLSGGDIALEGQVDDGEESYAPIAYLADSHNEPSAVLAARQRDMLQTDGIAQAL 250

Query: 618 ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 251 EALDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|5911381|gb|AAD55771.1|AF177466_1 sigma-32 factor RpoH [Methylovorus sp. SS1]
          Length = 284

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/277 (32%), Positives = 148/277 (53%), Gaps = 22/277 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKG-ECEASIAKKEMVEANLRLVISVAK 461
           +DS+ +    IK+  V   +S+ E   + + +RKG + EA+   K ++ ++LRLV S+A+
Sbjct: 13  LDSLDQYLRTIKAFPV---LSVEEEYDLATRLRKGTDIEAA---KGLIVSHLRLVASIAR 66

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y+  GL   DLIQEGN+GLMKA  +FD   G +  ++AM W+K  I   I      +++
Sbjct: 67  GYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKV 126

Query: 522 P-VHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAM-PVEGVRKVLKITKEPISL 576
                + K+   +R+ ++ S+ +    +P E   IA++L + P E V    ++    ISL
Sbjct: 127 ATTKAQRKLFFNLRSMKKNSHTL----SPAEVADIARELRVKPEEVVEMESRMGGHEISL 182

Query: 577 ETPIGD--EDTSHLGDFIEDKNA-VSPLDSAIQANLRETT--TRVLASLTPREERVLRMR 631
           E    D  ED      ++ED+    S L +  +A   +T      L SL  R  R+++ R
Sbjct: 183 EGNSDDDTEDNFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDERSRRIVQAR 242

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +  N   TL ++  +F V+ ERIRQIE KA++K+K
Sbjct: 243 W-LQENNSATLHDLAAEFGVSAERIRQIEQKAMQKMK 278


>gi|218670385|ref|ZP_03520056.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 266

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 125/246 (50%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 13  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 73  IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 130

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  ET  
Sbjct: 131 NVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDVLIEQDELETRR 189

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R+L+     L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 190 RMLSKAMSVLNERERRIFEARR--LAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDA 247

Query: 671 SRSKKL 676
            R + L
Sbjct: 248 VRKEAL 253


>gi|298369543|ref|ZP_06980860.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282100|gb|EFI23588.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 287

 Score = 99.8 bits (247), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/267 (31%), Positives = 142/267 (53%), Gaps = 23/267 (8%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N I  +S E   S++E +      +KG+ EA+   K+++ ++LR+V+S+A+ Y   GL  
Sbjct: 25  NSIPMLSAEEESSLAERQ------QKGDLEAA---KQLILSHLRVVVSIARGYDGYGLNQ 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKI 529
            DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + K+
Sbjct: 76  ADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKL 135

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-----GDED 584
              +R+ R+  N +  +   +EIA  L + +    +VL++ +   S +  I      DED
Sbjct: 136 FFNLRSMRKSLNALSPKEA-QEIADDLGVKLS---EVLEMEQRMTSHDIGIMADNSDDED 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    D++ D +A      A QA+     E     LA L  R  R++  R+ +  +   T
Sbjct: 192 SFAPIDWLADHDAEPSRQLAKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLT 250

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 251 LHELADEYGVSAERIRQIEAKAMQKLR 277


>gi|209550663|ref|YP_002282580.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536419|gb|ACI56354.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 302

 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 125/243 (51%), Gaps = 20/243 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  +T  
Sbjct: 167 KVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDVLIEQDELDTRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLE++  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMSVLNERERRIFEAR---RLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQD 282

Query: 670 PSR 672
             R
Sbjct: 283 AVR 285


>gi|254453216|ref|ZP_05066653.1| sigma 32 [Octadecabacter antarcticus 238]
 gi|198267622|gb|EDY91892.1| sigma 32 [Octadecabacter antarcticus 238]
          Length = 292

 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 129/253 (50%), Gaps = 18/253 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMASKFRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  ++R    ++ R A +    + R    + IA 
Sbjct: 101 IKASIQDHVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAMKRGETLDRHDMRQMIAT 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIED---KNAVSPLDSAIQANL 609
           ++ +P+  V  +  +++    SL      ED      D +ED   + A +  +S     L
Sbjct: 161 EVGVPLRDVEMMEGRLSGSDFSLNATQSSEDEGREWIDALEDDGEQAADAVQNSHDTDTL 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     L +L+ RE+ ++R R     +   TLE +G +  +++ER+RQ+EA A  K++ 
Sbjct: 221 RQWLLTALTALSDREQFIVRER--KLRDAPRTLESLGTELSLSKERVRQLEAAAFGKMRK 278

Query: 670 P--SRSKKLRSFL 680
               +S+++ SFL
Sbjct: 279 SLEGQSQEVHSFL 291


>gi|329849869|ref|ZP_08264715.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
 gi|328841780|gb|EGF91350.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
          Length = 299

 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 125/250 (50%), Gaps = 27/250 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 57  AAHKLVTSHLRLVAKIAMGYRGYGLPVGEVISEGNVGLMQAVKKFDADRGFRLATYAMWW 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      +++      K  K+    R++ ++I        R    E+IA KL
Sbjct: 117 IKASIQEYVLRSWSLVKMGTTAAQK--KLFFNLRKVKSEISALEEGDLRHEQVEQIATKL 174

Query: 557 AMPVEGVRKVLKITKEP-ISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +    V  + +    P  SL  PI   E  S   D++ D   VS     + A+  E + 
Sbjct: 175 GVSETDVINMNRRMSSPDSSLNAPIRASEGESEWQDWLVDDKQVS--QETVLADSEEYSQ 232

Query: 615 RV------LASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           R+      +  L  RE  +L   R++     ++  TLE++ ++F V+RER+RQIE +A  
Sbjct: 233 RMGLLEAAMGELNAREREILTERRLK-----DSPTTLEDLAERFGVSRERVRQIEVRAFE 287

Query: 666 KLKHPSRSKK 675
           KL+    + K
Sbjct: 288 KLQKAMTASK 297


>gi|103487228|ref|YP_616789.1| RNA polymerase factor sigma-32 [Sphingopyxis alaskensis RB2256]
 gi|98977305|gb|ABF53456.1| RNA polymerase sigma factor RpoH [Sphingopyxis alaskensis RB2256]
          Length = 300

 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 120/250 (48%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KFD   G++ +TYAMWW
Sbjct: 53  AAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAMWW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAKKLAMP 559
           ++ +I   I      +++      K  K+    RRM N ++     + +PE +AK     
Sbjct: 113 IRASIQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKNNLEAFEDGDLSPEHVAK----- 165

Query: 560 VEGVRKVLKITKEPI-------------SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              +   L +T++ +             SL  P+G++  S   D + D     PL     
Sbjct: 166 ---IATDLGVTEDEVVSMNRRMAMGGDTSLNVPMGEDGDSQWQDLLGDD---GPLQDERV 219

Query: 607 ANLRETTTR------VLASLTPREERVLRMRFGIGMNTD--HTLEEVGKQFCVTRERIRQ 658
           A  +E   R       L +L  RE  +L  R      TD   TLE++ + + V+RER+RQ
Sbjct: 220 AEAQERDVRHDLLTEALETLNERERHILTER----RLTDDPKTLEDLSQLYDVSRERVRQ 275

Query: 659 IEAKAIRKLK 668
           IE +A  KL+
Sbjct: 276 IEVRAFEKLQ 285


>gi|126727088|ref|ZP_01742925.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126703516|gb|EBA02612.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 289

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 123/249 (49%), Gaps = 17/249 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + S A   +V ++LRL   +A  Y   GL   +++ E N+GLM+A +KFD   G++ S
Sbjct: 37  EHQDSGAAHRLVTSHLRLAAKIAMGYRGYGLPQAEVVSEANVGLMQAVKKFDPEKGFRLS 96

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIA 553
           TYAMWW++ +I   +      +++      K  K+    R+  N+I    + +  PE +A
Sbjct: 97  TYAMWWIRASIQEYVLRSWSLVKLGTTSAQK--KLFFNLRKAKNRIGALEEGDLRPENVA 154

Query: 554 KKLA----MPVEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQA 607
           K  +       E +    +++    SL   +G   E T+   D++ D +A    D   Q 
Sbjct: 155 KIASDLNVTETEVISMNRRMSGGDASLNVQVGGDGEGTAQWQDWLADDSADQAGDYEKQD 214

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            L   RE   + +A L  RE+ +L  R     +   TLEE+ + F V+RERIRQIE +A 
Sbjct: 215 ELDTRRELMAQAMAVLNDREKEILMERR--LQDKPKTLEELSEVFSVSRERIRQIEVRAF 272

Query: 665 RKLKHPSRS 673
            KL+   RS
Sbjct: 273 EKLQTEMRS 281


>gi|189423258|ref|YP_001950435.1| RNA polymerase, sigma 70 family subunit [Geobacter lovleyi SZ]
 gi|189419517|gb|ACD93915.1| putative RNA polymerase, sigma 70 family subunit [Geobacter lovleyi
           SZ]
          Length = 280

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 117/231 (50%), Gaps = 7/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ +NLR V+ VA +Y + GL+ LDLIQEGNIGLM A  KF+   G +  +YA+WW
Sbjct: 45  AAHTLITSNLRYVVKVASEYRHYGLKMLDLIQEGNIGLMMAVRKFNPYRGVRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  I   I      ++I      R   + + +T   +     R+    E++  L +P  
Sbjct: 105 IRAYIQNYIVSAWSLVKIGTTQAQRKLFYGLRKTKEALLKLTGRDSDAFEVSSMLHVPDH 164

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQAN-LRETTTRVLA 618
            V ++ +  K  +SL   I + D   + + I D   N    L    Q + L++     L 
Sbjct: 165 EVVEMEQRLKGEVSLNEEIIEGDGLTILETIADDRMNQEEMLGEYQQEHSLKKAIAHALQ 224

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  +E+ ++  R  I  +   TL+++   F ++RER+RQIE +A+ KLK+
Sbjct: 225 GLNEKEKYIVEHR--ITNDDPLTLQDIADHFSISRERVRQIEERALVKLKN 273


>gi|126649718|ref|ZP_01721954.1| sporulation sigma factor SigG [Bacillus sp. B14905]
 gi|126593437|gb|EAZ87382.1| sporulation sigma factor SigG [Bacillus sp. B14905]
          Length = 257

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 127/245 (51%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +   ++ GE E    ++E+V  NLRLV+S+  ++  RG Q  DL Q G IGLMKA 
Sbjct: 22  EMKELFIRLQAGEIEI---REELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIGLMKAI 78

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +   +  R
Sbjct: 79  DHFDLKHNVRFSTYAVPMIIGEIRRHLRDHH-ALRVSRSLRDIAYKAMQAKEQWITENLR 137

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT EEIA  + M  E V   L   ++P+SL+ PI  +  D  ++ D + D + VS    
Sbjct: 138 EPTIEEIADMIEMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLRDDD-VSEDQW 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +++E+    L  L  R++ ++  RF  G     T  E+ K+  +++ +I ++E  A
Sbjct: 197 VAYVSVKES----LQKLDERQQMIVAKRFYYG----ETQTEIAKELGISQAQISRLEKNA 248

Query: 664 IRKLK 668
           I  ++
Sbjct: 249 IETMQ 253


>gi|94987055|ref|YP_594988.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731304|emb|CAJ54667.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 385

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 136/255 (53%), Gaps = 28/255 (10%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCL 492
           V+K  C  S A   ++ ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   
Sbjct: 131 VQKKGC--SKAAFRLISSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPDK 188

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTP 549
           G KFS YA +W++  I + I D    ++I      +  K+     R   K+  E   P  
Sbjct: 189 GIKFSYYAAFWIRAYILKFIMDNWRMVKIGTTQAQR--KLFYNLNRERQKLLAEGFDPDT 246

Query: 550 EEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSP------ 600
             +A +L +  E + ++  ++    +SL+  +G+E  + S + DF+    A++P      
Sbjct: 247 SSLALRLGVGEEQIIEMQQRLDASDMSLDVTVGEETGNASRI-DFLP---AINPGIEESL 302

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQ 658
               I   L++    +L  L+ +E  +L  R    + TD   TL E+G+++ VTRER+RQ
Sbjct: 303 AGQEIAILLQDRIKDILPLLSEKEVYILHNR----LLTDDPVTLREIGEKYSVTRERVRQ 358

Query: 659 IEAKAIRKLK-HPSR 672
           +EA+ ++KL+ H SR
Sbjct: 359 LEARLLQKLRTHLSR 373


>gi|323137119|ref|ZP_08072198.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322397477|gb|EFX99999.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 127/249 (51%), Gaps = 20/249 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E   A +E+V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +
Sbjct: 39  EHEDPKAAQELVTSHLRLVAKIAMGYRGYGLPIGEIISEGNVGLMQAVKRFEPDRGFRLA 98

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPE 550
           TYAMWW++ +I   I      +++      K  K+    R+  ++I        R    E
Sbjct: 99  TYAMWWIRASIQEYILRSWSLVKMGTTASQK--KLFFNLRKAKSRISAFEEGDMRPENVE 156

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI----EDKNAVSPLDSAIQ 606
           +IA +L +  + V ++ +      SL  P+ +E      D++    ED+  +  L +  +
Sbjct: 157 KIATRLGVSQQDVIEMNRRMGGDASLNAPLREEGEGEWQDWLVDDSEDQERI--LVAQEE 214

Query: 607 ANLRETTTR-VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAI 664
            N R    R  L  L PRE R+   R    +  D  TLE++ ++F V+RER+RQIE +A 
Sbjct: 215 NNNRLKALRGALDVLNPRERRIFEAR---RLADDPVTLEQLSEEFGVSRERVRQIEVRAF 271

Query: 665 RKLKHPSRS 673
            K++   RS
Sbjct: 272 EKVQAAVRS 280


>gi|257469126|ref|ZP_05633220.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
          Length = 116

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 62/78 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++ +NLRLV+++AK Y N+GL F+DLI EGN+GL+ A EKFD   G++FSTYA+WW
Sbjct: 39  AKNQLILSNLRLVVNIAKGYINKGLSFIDLISEGNLGLIYAIEKFDITKGFRFSTYAVWW 98

Query: 504 VKQAITRSIADQSCTIRI 521
           +KQ+I++++  +   IRI
Sbjct: 99  IKQSISKAVIVKGREIRI 116


>gi|317063372|ref|ZP_07927857.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689048|gb|EFS25883.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 118

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 62/78 (79%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++ +NLRLV+++AK Y N+GL F+DLI EGN+GL+ A EKFD   G++FSTYA+WW
Sbjct: 41  AKNQLILSNLRLVVNIAKGYINKGLSFIDLISEGNLGLIYAIEKFDITKGFRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIRI 521
           +KQ+I++++  +   IRI
Sbjct: 101 IKQSISKAVIVKGREIRI 118


>gi|291538695|emb|CBL11806.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           XB6B4]
          Length = 259

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 119/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV K+++       DL Q G IGL+K+ + FD  +G KFSTYA+  
Sbjct: 38  ARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCIGLIKSIDNFDPTIGVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K + T   +S    +EPT +EIA +  +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIHTKEILSKTENKEPTLDEIAAESGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+  +  DT ++ D I DK     N +  L          +    
Sbjct: 157 VFALDAIQSPLSLYDPVYTDGGDTLYVMDQISDKKNREENWIEEL----------SLNDA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L  RE  +L++RF  G     T  EV  +  +++ ++ ++E  A+  ++H
Sbjct: 207 LDRLNERENYILKLRFFEG----KTQMEVADEIHISQAQVSRLEKSALNSIRH 255


>gi|307264154|ref|ZP_07545748.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|306870528|gb|EFN02278.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 619

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/156 (38%), Positives = 93/156 (59%), Gaps = 11/156 (7%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE      L 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDE------LM 68

Query: 95  LASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           LA + ++  V  +  K     +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  LAENIADEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              +  ++ E P     LI +  ++ +GT  L +++
Sbjct: 129 INEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLV 164


>gi|116749546|ref|YP_846233.1| sigma-70 region 2 domain-containing protein [Syntrophobacter
           fumaroxidans MPOB]
 gi|116698610|gb|ABK17798.1| sigma-70 region 2 domain protein [Syntrophobacter fumaroxidans
           MPOB]
          Length = 326

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 125/241 (51%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGY 494
           KG+ EA     +++ ANLRLV+ +A  +    +Q  +DLIQEGN+GLM+A +KFD   GY
Sbjct: 73  KGDIEAGY---KLITANLRLVVKIAMDFQRYWMQNLMDLIQEGNVGLMQAVKKFDPYRGY 129

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           KFS YA +W+K  I + I D    ++I     + K+   +R  +        E +P+ ++
Sbjct: 130 KFSYYASFWIKAYIIKFIMDNWKLVKIGTTQAQRKLFFNLRKEKERLEAQGIEASPKLLS 189

Query: 554 KKLAMP-VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-----QA 607
            +L +   E +    ++    ISL++P+ ++       F+   +   P+D  I     +A
Sbjct: 190 HRLDVKESEIIEMDQRLNSWEISLDSPLKEDSEDTHKSFLPSDDL--PVDDQIADREAKA 247

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L +        L  +E  +   R  +      TL+E+G +F ++RER+RQIE++  +KL
Sbjct: 248 ILHDKLLLFREQLKGKEAVIFDKR--LLTEEPMTLQEIGDRFGISRERVRQIESRLKKKL 305

Query: 668 K 668
           K
Sbjct: 306 K 306


>gi|190893168|ref|YP_001979710.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190698447|gb|ACE92532.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 302

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 125/246 (50%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  ET  
Sbjct: 167 NVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDVLIEQDELETRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R+L+     L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 226 RMLSKAMSVLNERERRIFEARR--LAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDA 283

Query: 671 SRSKKL 676
            R + L
Sbjct: 284 VRKEAL 289


>gi|260574108|ref|ZP_05842113.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259023574|gb|EEW26865.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 292

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/260 (31%), Positives = 127/260 (48%), Gaps = 32/260 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMAAKFRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-----------EEI 552
           +K +I   +      +R       K   +    +R+  K++RE              E +
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNLKRVQAKLEREAAQRGESLDGHQLREMV 158

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKN--AVSPLDSAI-QA 607
           A+++ +P+  V  +  ++     SL      ED      D +ED    A   ++ A   A
Sbjct: 159 AREVGVPLADVEMMEGRLAGSDFSLNATQSSEDEGREWIDALEDDGVQAAEAVEGAHDAA 218

Query: 608 NLRETTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            LR      +A+L PRE     ER LR   G G     TLE +G +  +++ER+RQ+EA 
Sbjct: 219 RLRGWLVVAMAALNPRERFIVTERKLR---GDG----RTLESLGAELGLSKERVRQLEAA 271

Query: 663 AIRKLKHP--SRSKKLRSFL 680
           A  KL+     ++++L  FL
Sbjct: 272 AFAKLRRSLEGQTRELHHFL 291


>gi|169827020|ref|YP_001697178.1| sporulation sigma factor SigG [Lysinibacillus sphaericus C3-41]
 gi|168991508|gb|ACA39048.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Lysinibacillus sphaericus C3-41]
          Length = 257

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 127/245 (51%), Gaps = 15/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +   ++ GE E    ++E+V  NLRLV+S+  ++  RG Q  DL Q G IGLMKA 
Sbjct: 22  EMKELFIRLQAGETEI---REELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIGLMKAI 78

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +   +  R
Sbjct: 79  DHFDLKHNVRFSTYAVPMIIGEIRRHLRDHHA-LRVSRSLRDIAYKAMQAKEQWITENLR 137

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT EEIA  + M  E V   L   ++P+SL+ PI  +  D  ++ D + D + VS    
Sbjct: 138 EPTIEEIADMIDMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLRDDD-VSEDQW 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +++E+    L  L  R++ ++  RF  G     T  E+ K+  +++ +I ++E  A
Sbjct: 197 VAYVSVKES----LQKLDERQQMIVAKRFYYG----ETQTEIAKELGISQAQISRLEKNA 248

Query: 664 IRKLK 668
           I  ++
Sbjct: 249 IETMQ 253


>gi|190150752|ref|YP_001969277.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|189915883|gb|ACE62135.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
          Length = 619

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/156 (38%), Positives = 93/156 (59%), Gaps = 11/156 (7%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE      L 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDE------LM 68

Query: 95  LASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           LA + ++  V  +  K     +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  LAENIADEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
              +  ++ E P     LI +  ++ +GT  L +++
Sbjct: 129 INEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLV 164


>gi|90422128|ref|YP_530498.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB18]
 gi|90104142|gb|ABD86179.1| sigma 32 (RpoH) [Rhodopseudomonas palustris BisB18]
          Length = 299

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 121/239 (50%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P++   IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDMHPDQVKLIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +  + V  + +      SL  PI D+ +     D++ D    SP   AI A      + 
Sbjct: 167 GVTEQDVVDMNRRLGGDASLNAPIRDDGEPGEWQDWLVDH---SPNQEAIMAEHEELDHR 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R   T  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RAALTGAIGVLNPRERRIFEARR--LADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQ 280


>gi|240142271|ref|YP_002966781.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
 gi|240012215|gb|ACS43440.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
          Length = 253

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/267 (29%), Positives = 124/267 (46%), Gaps = 39/267 (14%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ET +S  E   +V   R   C  S+ +  +V  + R+  SVA++++N      DL QEG 
Sbjct: 11  ETLLSPDEESGLVDAYRNDGCRKSLDR--LVRTHARMAFSVARRWSNNEAHMQDLAQEGM 68

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IG+M+AA+KF+   G +F+ Y  WW+  +I+   ++  C + +P    D++    R  R 
Sbjct: 69  IGIMRAADKFNPSFGKRFAQYCRWWILSSISSRASEVVCVVDMP----DRVFVAHRRKR- 123

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPI-GDEDTSHLGDFIEDKN 596
                                +EG    L       +S+  P+ GDE  + +GD +   +
Sbjct: 124 ---------------------LEGADAALVGAAVTAVSISEPLGGDEGGATVGDMLV-SD 161

Query: 597 AVSPLDSAIQANL----RETTTRVLASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCV 651
             SP  +A+Q+ +    R      +  LT RE  +L R R      T  TLE V   F +
Sbjct: 162 ETSPESAAVQSEMNWYYRTAVQTAMQGLTEREREILSRRRLA---ETPETLEVVADFFDL 218

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRS 678
           TRERIRQIE  A+ K++   R+   R+
Sbjct: 219 TRERIRQIENAAMAKVERNLRAAGFRA 245


>gi|291522675|emb|CBK80968.1| RNA polymerase, sigma subunit, RpsG/SigG [Coprococcus catus GD/7]
          Length = 259

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 14/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  +  NLRLV+SV ++++       DL Q G IGL+KA + FD   G +FSTYA+  
Sbjct: 38  ARERFINGNLRLVLSVIQRFSGTNENVNDLFQVGCIGLIKAIDNFDLTQGVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S  IR+   +RD  +K +     +  +  REPT  EIA++  +P E +
Sbjct: 98  IVGEIRRFLRDNSA-IRVSRSLRDTAYKAIYAREALITRNNREPTVMEIAEETGIPKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L   + P+SL  P+  +  D   + D + D KN  +     +  N        +  L
Sbjct: 157 VFALDAIQSPMSLYEPVYTDGGDALCIMDQVSDRKNGENSWVENLALN------DAMKRL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           + RE R+++MRF  G     T  EV  +  +++ +I +IE  A++ ++   R+
Sbjct: 211 SHRENRIIKMRFYEG----KTQMEVADELAISQAQISRIEKSALQNMRTYLRA 259


>gi|254503566|ref|ZP_05115717.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
 gi|222439637|gb|EEE46316.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
          Length = 287

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 144/277 (51%), Gaps = 39/277 (14%)

Query: 424 ISEFRHIVS-------MVRKGECEASI---------AKKEMVEANLRLVISVAKKYTNRG 467
           +SE RH+V        + R+ E E +I         A +++  +++RLVI+VA ++ N G
Sbjct: 1   MSERRHLVKTAMKAPYLTREEELELAIQWRDNKDEKALEKLSLSHMRLVIAVASRFKNFG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG++GL++AA +F+     +FSTYA WW++ +I   I      +R       
Sbjct: 61  LNIGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQ 120

Query: 528 KIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGVRKV------LKITKEPISLET 578
           K   +    RR+  K+    TP    E+ +K+A  + GV++        +++    SL  
Sbjct: 121 K--ALFFNLRRLRAKLSSNQTPLTDSELHQKIADAI-GVKQSDVAVMNARLSGPDTSLNA 177

Query: 579 PIGDEDTSHL--GDFIEDKNAVSP---LDSAIQANLRET-TTRVLASLTPREERVLRMRF 632
           P+ D + S     DF+   +A  P   +   I A  R T     L  L+ RE +++R R 
Sbjct: 178 PVTDTEGSSADRQDFLVS-DAPQPDEIVTENIDAERRNTWLASALDVLSERELKIVRER- 235

Query: 633 GIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++ D  TLE +GK+  +++ER+RQIE++A++KLK
Sbjct: 236 --RLSEDGATLESLGKKLGISKERVRQIESRALQKLK 270


>gi|307564926|ref|ZP_07627446.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
 gi|307346366|gb|EFN91683.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
          Length = 228

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 108/229 (47%), Gaps = 36/229 (15%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++ +ANL  V+S+A +Y  +GL   DLI EGNIG+M AA+KFD   G +F  +A  +
Sbjct: 36  ALEKLTKANLTFVVSIAHQYKEQGLDEDDLISEGNIGMMYAAQKFDGSKGIRFVKFAAPY 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++AI +SI +Q+   ++P               +  NK+          KK A PV   
Sbjct: 96  IRKAIEKSIKEQTTLYKVP---------------KKENKL--------FEKKRAKPVS-- 130

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   +PI    P+G  +   L + I + N     DS     L     + +  L  R
Sbjct: 131 ------LDQPI----PVGSNNKLTLQNLIPNNNNKDTDDSVNSNILNTILMQSINCLNER 180

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           E+ V+   +GI   T  T+ EV     + RER+RQI   A+RKL    R
Sbjct: 181 EKAVITQLYGIN-GTSLTMAEVATSLGLKRERVRQIRNTALRKLYRKMR 228


>gi|302392455|ref|YP_003828275.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
 gi|302204532|gb|ADL13210.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
          Length = 253

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 131/238 (55%), Gaps = 12/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K +     AK ++V  N++LV+ VA ++ N+   + +L Q G+IGL+KA E+FD   
Sbjct: 22  LLKKAQAGDQKAKDKLVNHNVKLVLKVAHRFANKNYDYEELFQIGSIGLLKAIERFDLER 81

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R + D    +++   ++ + H++      ++ ++ REPT +EI
Sbjct: 82  DVKFSTYAVPLIIGEIKRFLRDDDA-VKVSRSLKRRAHRINEVKESLTAELNREPTIQEI 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLR 610
           A+++ +  E +   L+  +EP S+ +P+ + +    G+ IE  D+ A S  +   + + R
Sbjct: 141 AEEMEVDKEEIVNALEAVREPTSIYSPVYENE----GNSIELVDQLAASSENQEQEID-R 195

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                V+  L  RE  +L++RF      + T +EV  +  V++ ++ ++E K I K++
Sbjct: 196 LALREVIDELKTRERLILKLRFF----DEKTQQEVADRIGVSQVQVSRLERKIIDKVR 249


>gi|295675387|ref|YP_003603911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
 gi|295435230|gb|ADG14400.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
          Length = 311

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 125/250 (50%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP+EI        EG
Sbjct: 132 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDEI--------EG 179

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + K L + +E ++ +ET +   D +  G   + + + +P+  A  A+     T VLAS  
Sbjct: 180 LAKELNVKREEVAEMETRLSGGDIALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQ 237

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L PR  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 238 RDRLQSDGIASALDALDPRSRRIIEARWLKVADDGSGGSTLH---ELADEFGVSAERIRQ 294

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 295 IEASAMKKMR 304


>gi|156972625|ref|YP_001443532.1| RNA polymerase factor sigma-32 [Vibrio harveyi ATCC BAA-1116]
 gi|156524219|gb|ABU69305.1| hypothetical protein VIBHAR_00277 [Vibrio harveyi ATCC BAA-1116]
          Length = 285

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 148/279 (53%), Gaps = 28/279 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E    ++E  H      KGE +A+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRSVNSYPMLTPEEERGLAERLHY-----KGEIDAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I 
Sbjct: 68  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++     + + P
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMP 185

Query: 580 IGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRM 630
           + D+D S+       ++EDK+  S +   I+A   ET T       LASL  R +R++R 
Sbjct: 186 MDDDDNSNSYTAPMFYLEDKS--SDVADNIEAANWETHTNNRLGHALASLDERSQRIVRS 243

Query: 631 RFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+   ++ D  TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 244 RW---LDDDKATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|134297011|ref|YP_001120746.1| RNA polymerase factor sigma-32 [Burkholderia vietnamiensis G4]
 gi|134140168|gb|ABO55911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia vietnamiensis
           G4]
          Length = 331

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 128/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 92  AARKLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 152 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKR 208

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 209 EEVTEMETRLSGGDIALEGQVEDGEEAYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 268

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 269 ALEALDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 324


>gi|326789987|ref|YP_004307808.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
 gi|326540751|gb|ADZ82610.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
          Length = 274

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 116/242 (47%), Gaps = 55/242 (22%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKK-YTNR--GLQFLDLIQEGNIGLMKAAEKFD 489
           +V+  +C  S A + ++EAN  L+  V+ K YT R   +   DL+QEG IGL+ AAEK+D
Sbjct: 6   LVKLYQCGDSKALERLLEANKGLIYKVSMKFYTERDNAIDQDDLVQEGRIGLIVAAEKYD 65

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                 F++YA +W+ Q                     K+H+ +   R M          
Sbjct: 66  INGDVPFASYAYYWIYQ---------------------KMHRFMYPKRNM---------- 94

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQA 607
                        ++  LK     +SL TPIG++    LGD +  E +   S  DS    
Sbjct: 95  -------------IKSSLKF----VSLNTPIGEDGEMELGDTLGEEQEEFCSVEDSIYHQ 137

Query: 608 NLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L E   + +  +LT ++ +VL  RFG   N  HTLEE GK+  VTRER+RQIE  ++RK
Sbjct: 138 ELAEELRQAMNDNLTLQQRQVLLFRFGFECNV-HTLEETGKEIGVTRERVRQIEVNSLRK 196

Query: 667 LK 668
           L+
Sbjct: 197 LR 198


>gi|218885581|ref|YP_002434902.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218756535|gb|ACL07434.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 474

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 132/244 (54%), Gaps = 20/244 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGY 494
           +G+ +A+     +V ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G 
Sbjct: 223 QGDSDAAF---RLVTSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPEKGI 279

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           KFS YA +W+K  I + I D    ++I     + K+   +   R+       +P    ++
Sbjct: 280 KFSYYAAFWIKAYILKFIMDNWRMVKIGTTQAQRKLFYNLNKERQRLIAQGYDPDATILS 339

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS--------HLGDFIEDKNAVSPLDSA 604
           +KL + VE V ++  ++    +SL+  +G++            LG  IE+  A    +S 
Sbjct: 340 EKLNVTVEQVIEMEQRLDSSDMSLDITVGEDSGGATRMDFLPALGPGIEETLA----NSE 395

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I   +++    +L  L+ +E  +L+ R  +      TL E+G+++ +TRER+RQIEA+ +
Sbjct: 396 IARMVQDRVQTILPKLSDKEAYILQHR--LLSEQPVTLREIGEKYDITRERVRQIEARLL 453

Query: 665 RKLK 668
           +KL+
Sbjct: 454 QKLR 457


>gi|257095687|ref|YP_003169328.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257048211|gb|ACV37399.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 286

 Score = 99.0 bits (245), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 125/236 (52%), Gaps = 19/236 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLVIS+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 49  AARQLVLSHLRLVISIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAHGVRLVSFAIHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM-SNKIKREPTP-EEIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R M +N     P    +IA +L++  E
Sbjct: 109 IKAEIHEYVLKNWRMVKLATTKAQR--KLFFNLRSMKANSEALSPGQVTDIAHRLSVKPE 166

Query: 562 GVRKV-LKITKEPISLETPIGDED-------TSHLGDFIEDKNAVSPLDSAIQANLR-ET 612
            V ++  ++T   ++L+   GD D        S+L D       V  L++  +  L  E 
Sbjct: 167 EVSEMEARLTGHDLALD---GDSDDDEVFAPISYLAD--HSSEPVHVLEARARERLHNEG 221

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               LASL PR  R++  R+ +   +  TL E+  +F V+ ERIRQ+E KA++K++
Sbjct: 222 LQGALASLDPRSRRIVEARW-LTDESPATLHELAAEFGVSAERIRQVEVKAMQKMR 276


>gi|331082586|ref|ZP_08331709.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
 gi|330400205|gb|EGG79847.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 259

 Score = 99.0 bits (245), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 130/243 (53%), Gaps = 17/243 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA   +++ ++ NLRLV+SV K++++      DL Q G +GL+KA + FD  L 
Sbjct: 31  IKEGDPEA---REQYIKGNLRLVLSVIKRFSSSNENADDLFQIGCVGLIKAIDNFDTTLN 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   I R + D +  IR+   +RD  +K +        +  +EPT  EIA
Sbjct: 88  VKFSTYAVPMIIGEIRRYLRDNNA-IRVSRSLRDVAYKAIYAKENYVKQNLKEPTINEIA 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLR 610
           +++ +  E +   L   + P+SL  P+  E  DT ++ D I DK   +  D+ I+   L+
Sbjct: 147 EEIGIDKEEIVYALDAIQSPVSLYEPVYTEGGDTLYVMDQISDKK--NKEDNWIENIALK 204

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L  L  RE+ ++ MRF  G       EE+G    +++ ++ ++E  A++ ++  
Sbjct: 205 EA----LKKLDDREQHIVTMRFYEGKTQMEVAEEIG----ISQAQVSRLEKHALKTMRTY 256

Query: 671 SRS 673
            RS
Sbjct: 257 LRS 259


>gi|254501465|ref|ZP_05113616.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
 gi|222437536|gb|EEE44215.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
          Length = 269

 Score = 99.0 bits (245), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 125/251 (49%), Gaps = 17/251 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E   A + +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G+
Sbjct: 13  RYKEHEDPEAAERLVNSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGF 72

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K AI   I      +++      K  ++    RR+  KI+       +  
Sbjct: 73  RLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGKIQALEEGDLKPH 130

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             +EIA +L +  E V  + +      SL  PI  + D     D++ D++       A Q
Sbjct: 131 QVQEIATRLGVSEEEVVSMNRRLGGDASLNAPIRAEADAGEWQDWLVDESDSQETLLANQ 190

Query: 607 ANL---RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAK 662
             L   R+  +  +  L  RE R+   R    ++ D  TLE++  +F V+RER+RQIE +
Sbjct: 191 EELDMRRKMLSDAMDVLNDRERRIFEAR---RLSEDPMTLEDLSGEFGVSRERVRQIEVR 247

Query: 663 AIRKLKHPSRS 673
           A  K++   R+
Sbjct: 248 AFEKVQKAVRN 258


>gi|91762259|ref|ZP_01264224.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718061|gb|EAS84711.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 293

 Score = 99.0 bits (245), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 130/247 (52%), Gaps = 13/247 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 47  AAEKLVTSHLRLVAKIAMGYRGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT----PE---EIAKKL 556
           ++ +I   I      ++I      K  K+    +++ N+I  +      PE   EIA KL
Sbjct: 107 IRASIQEYILRSWSLVKIGTTTAQK--KLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKL 164

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  +  +++ +  SL   +G ED     D++ DK     L  A Q  + +    
Sbjct: 165 DVNKDEVISMNRRLSGKEFSLNAQVG-EDGDEWQDWLVDKELDHDLKFAHQEEMGQRQNL 223

Query: 616 VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL-KHPSRS 673
           +  S+    ER   + +   +N +  TLE++ K++ ++RERIRQIE KA  KL KH   S
Sbjct: 224 LKDSIKILNEREKEILYSRRLNDEPTTLEDLSKKYKISRERIRQIENKAFEKLQKHMLLS 283

Query: 674 KKLRSFL 680
            K ++ L
Sbjct: 284 AKSKNLL 290


>gi|294085881|ref|YP_003552641.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
 gi|292665456|gb|ADE40557.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 312

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 125/255 (49%), Gaps = 26/255 (10%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ E++    ++V ++LRLV  +A  Y   GL   DLI EGN+G+M A +KF+   G++
Sbjct: 49  KGDVESA---HQLVTSHLRLVAKIAMGYRGYGLPVADLISEGNLGMMHAVKKFEPEKGFR 105

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE 551
            +TYAMWW+K AI   I      ++I      K  K+    RR+  +I+     +  PE+
Sbjct: 106 LATYAMWWIKAAIQEYILRSWSLVKIGTTAGQK--KLFFNLRRIKGQIQAIDEGDLKPEQ 163

Query: 552 ---IAKKLAMP-VEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSA- 604
              IA +L +   E +    ++     SL  P+    E T    D++ED         A 
Sbjct: 164 VTHIADELNVTEAEVMSMNQRMAGNDRSLNVPLSRDGEGTGEWQDWLEDDTVDQETSFAE 223

Query: 605 -----IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 +ANL       +  L  RE+R+L+ R         TLE++  +F V+RERIRQI
Sbjct: 224 HEEYSARANL---MMDAMKGLNEREQRILQARRLA--EPPLTLEDLAGEFNVSRERIRQI 278

Query: 660 EAKAIRKLKHPSRSK 674
           E +A  KL+   R K
Sbjct: 279 EVRAFEKLQKAVRDK 293


>gi|297616994|ref|YP_003702153.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144831|gb|ADI01588.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 256

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 122/226 (53%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++  NLRLV+SV +++ +RG    DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 37  AREELIRGNLRLVLSVIQRFNHRGEYVDDLFQVGCIGLIKAIDNFDLEQNVRFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  +R+   +RD  +K ++   ++  +  REPT  EIA +L +  E V
Sbjct: 97  IIGEIRRYLRDNN-PVRVSRSLRDVAYKALQVREQLLAEKSREPTIAEIADRLEVSQEEV 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTP 622
              L   +EP+SL  PI ++     GD I   + +S   +  +  L   + R  L  L+ 
Sbjct: 156 VFALDAIQEPVSLFEPIYNDG----GDPILVMDQISDDKTTDELWLEGISIREALKKLSE 211

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L +RF  G       EE+G    +++ ++ ++E  A++ +K
Sbjct: 212 REKLILTLRFFEGKTQMEVAEEIG----ISQAQVSRLEKAALKHMK 253


>gi|238924598|ref|YP_002938114.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
 gi|238876273|gb|ACR75980.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
          Length = 259

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 125/236 (52%), Gaps = 15/236 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG+     A+++ +  NLRLV+SV ++++N      DL Q G IGLMK+ + FD  +G
Sbjct: 31  IKKGD---KAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGCIGLMKSIDNFDPTIG 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   + R + D S   RIP  +RD  ++ +++  ++S K+  EP+  EI+
Sbjct: 88  VKFSTYAVPMIIGEVRRYLRDNSAY-RIPRSLRDTAYQAIKSKEKLSRKLVHEPSLAEIS 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K   +P   +   L   + P+SL  P+  +  DT ++ D I DK      + A   NL  
Sbjct: 147 KDCGIPENDILYALDAIQTPLSLFDPVYTDGGDTLYVMDQISDKKNK---EEAWVKNLVL 203

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                L     R+  ++++RF  G     T  EV ++  +++ ++ ++E  A++ +
Sbjct: 204 DDALKLLDDRARQ--IIKLRFFEG----KTQIEVAEEINISQAQVSRLEKNALKNM 253


>gi|213161043|ref|ZP_03346753.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 383

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/144 (40%), Positives = 88/144 (61%), Gaps = 13/144 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL---E 84
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +   +++  + A++   SSV      +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 70  NTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALI 168
           RIE G   +  S+ E P     L+
Sbjct: 124 RIEDGINQVQCSVAEYPEAITYLL 147



 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 37/134 (27%), Positives = 63/134 (47%), Gaps = 6/134 (4%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E
Sbjct: 253 KLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 312

Query: 379 LDPHW--VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W   + A + P  E  + VA EV   L+   +++ I  ETG++I + + I   +  
Sbjct: 313 TSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQ---KLRQIEEETGLTIEQVKDINRRMSI 369

Query: 437 GECEASIAKKEMVE 450
           GE +A  AKKEMVE
Sbjct: 370 GEAKARRAKKEMVE 383


>gi|222150148|ref|YP_002551105.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221737130|gb|ACM38093.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 285

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 128/253 (50%), Gaps = 27/253 (10%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR       +A+ ++  A++RLVI++A K+   GL   DLIQEG IGL++AA +F+    
Sbjct: 30  VRWKHGNDQVARNQIAHAHMRLVIAMASKFRGFGLPLGDLIQEGYIGLLEAAARFEPTRD 89

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-------E 546
            +FSTYA WW++ ++   I      +R       K   +    RR+  K+ +       +
Sbjct: 90  VRFSTYAGWWIRASMQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLAQGDQRLTDQ 147

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLD 602
              +EIA  L + +  V+ +  +++    SL+ PI   G+E    L     D+    P  
Sbjct: 148 AIHQEIATALGVSLADVQSMDARLSSNDTSLQAPISNNGEEGAERLDMLASDE----PTP 203

Query: 603 SAIQANLRETTTRV------LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRER 655
                ++ +T  R+      +A L  RE R++R R    ++ D  TLEE+G +  +++ER
Sbjct: 204 DEQVTDMIDTERRLDWLRGAMAHLNEREMRIIRARR---LSEDGATLEELGCELGISKER 260

Query: 656 IRQIEAKAIRKLK 668
           +RQIE +A+ KLK
Sbjct: 261 VRQIETRAMEKLK 273


>gi|226327186|ref|ZP_03802704.1| hypothetical protein PROPEN_01051 [Proteus penneri ATCC 35198]
 gi|225204404|gb|EEG86758.1| hypothetical protein PROPEN_01051 [Proteus penneri ATCC 35198]
          Length = 407

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 65/169 (38%), Positives = 97/169 (57%), Gaps = 9/169 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S  +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NS--NDTDDDAAEAAAQVLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            G   +  S+ E P     L+   D +  G   L ++I   A I P ++
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--AFIDPNAE 173


>gi|331090618|ref|ZP_08339469.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330401058|gb|EGG80653.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 259

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 120/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E ++ NLRLV+SV K+++N      DL Q G IGL+KA   F+  L  KFSTYA+  
Sbjct: 38  AKEEYIKGNLRLVLSVIKRFSNSNENPDDLFQIGCIGLIKAINNFNTELNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +           +EPT +EIA ++ +  E +
Sbjct: 98  IIGEIRRYMRDNN-SIRVSRSLRDTAYKAIYAKEGYMKTHLKEPTIQEIASEIGISKEEI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
            + L   + P+SL  PI ++  DT ++ D I DK     N V  L  A            
Sbjct: 157 VQALDAIQMPMSLHEPIYNDGGDTLYVMDQISDKKNKEENWVEELSLA----------EA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L  RE ++++MRF  G     T  E+ K+  +++ ++ ++E  A+  +K 
Sbjct: 207 MERLGERERKIIQMRFFEG----KTQMEIAKEIHISQAQVSRLEKNALEFMKQ 255


>gi|150389982|ref|YP_001320031.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949844|gb|ABR48372.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 258

 Score = 98.6 bits (244), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 126/241 (52%), Gaps = 14/241 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++ M +KG+ +A   ++++V  NL L+ SV K+++NRG    DL Q G+IGL+KA  KFD
Sbjct: 23  LIQMAQKGDLQA---QEKLVSHNLGLIRSVIKRFSNRGYDREDLFQLGSIGLIKAIRKFD 79

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +FSTYA+  +   I R + D    I++   ++    +V  T  ++  +  REPT 
Sbjct: 80  ISFNVRFSTYAVPMIIGEIKRFLRDDGI-IKVSRSLKQTASRVKVTKEKLFKEFGREPTL 138

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQA 607
            EIAK L +  E +   L     P  L   I  +D S  HL D I + +++   +   + 
Sbjct: 139 HEIAKVLEITKEEIVMALDSNMYPEYLYEVIHQDDGSPIHLIDKISETDSLDDSEVIDKI 198

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    V+  L PRE +++ +R+      D T  E+ K   +++ ++ +IE K ++ +
Sbjct: 199 MLKE----VIGRLEPRERQIIILRYF----KDKTQTEIAKVLGISQVQVSRIEKKVLQTM 250

Query: 668 K 668
           K
Sbjct: 251 K 251


>gi|225028119|ref|ZP_03717311.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
 gi|224954589|gb|EEG35798.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
          Length = 278

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 124/229 (54%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ V+ NLRLV+SV +++++      DL Q G IGLMKA + FD  L  KFSTYA+  
Sbjct: 57  AREQYVKGNLRLVLSVIQRFSSNHEHADDLFQVGCIGLMKAIDNFDRTLNVKFSTYAVPM 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +    +++  + R PT EE++KK  +P E +
Sbjct: 117 ILGEVRRYLRDNN-SIRVSRSLRDTAYKAIYAKEQLTKSMNRTPTIEEVSKKTEIPEEDI 175

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
              L     P+SL  P+  +  D   L D I DK   +  D+ I+  +L+E     +  L
Sbjct: 176 IYALDAIATPMSLFEPVYQDGNDPLFLMDQICDKK--NKEDTWIEHLSLQEA----MNQL 229

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + RE  ++  RF  G     T  EV  +  +++ ++ ++E  A++ +++
Sbjct: 230 SGREYHIIEKRFFEG----KTQTEVADEISISQAQVSRLEKNALKSIRN 274


>gi|327190963|gb|EGE58017.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 332

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 125/246 (50%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 79  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 139 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 196

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  ET  
Sbjct: 197 NVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDVLIEQDELETRR 255

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R+L+     L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 256 RMLSKAMSVLNERERRIFEARR--LAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDA 313

Query: 671 SRSKKL 676
            R + L
Sbjct: 314 VRKEAL 319


>gi|169351193|ref|ZP_02868131.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
 gi|169292255|gb|EDS74388.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
          Length = 258

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 121/225 (53%), Gaps = 12/225 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++V  N++LVIS+ K++ NR     DL Q G IGL+KA E F+     KFSTYA+  +
Sbjct: 39  KEKLVNDNIKLVISMTKRFYNRSDGCDDLFQVGMIGLIKAIENFNTSYDLKFSTYAVPLI 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R + D +  I+I   ++D  +K+++      NK +REPT +E+AKKL +    + 
Sbjct: 99  IGEMKRYLRD-NHQIKISRSLKDIAYKILKIKDEYLNKFQREPTIKELAKKLDIDQSVIV 157

Query: 565 KVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L  T    SL+  + + D + L   D + D+ A       ++ N R      L SL+ 
Sbjct: 158 EALLSTNSVASLQEEVKNSDGNSLKMIDSLSDEKA-----GVLKTNERIDLYDALKSLSQ 212

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +E  V++ R+  G++      E+ K+  +++ ++ +IE KA+  L
Sbjct: 213 KEHDVIKQRYFEGLSQ----SEIAKELFISQAQVSRIEKKALNTL 253


>gi|254251367|ref|ZP_04944685.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
 gi|124893976|gb|EAY67856.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
          Length = 311

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 127/239 (53%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   ++LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EEVAEMETRLSGGDVALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+   +N D       TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARW---LNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|261377878|ref|ZP_05982451.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
 gi|269145731|gb|EEZ72149.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
          Length = 290

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/272 (27%), Positives = 138/272 (50%), Gaps = 31/272 (11%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I +++    +++ E  H+    RKG+  A+   K+++ ++LR+V+S+A+ Y   GL   D
Sbjct: 24  IHTVNSIPMLTLDEETHLAERQRKGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQAD 80

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHK 531
           LIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + K+  
Sbjct: 81  LIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFF 140

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            +R+ R+  N +  +   +EIA  L + +           E + +E  +   D + + D 
Sbjct: 141 NLRSMRKNLNALSPKEA-QEIADDLGVKL----------SEVLEMEQRMTGHDIAIMADN 189

Query: 592 IEDKNAVSPLD---------------SAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
            +D+++ +P+D                A  A   E     LA L  R  R++  R+ +  
Sbjct: 190 SDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQD 248

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   TL ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 249 DGGLTLHQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|254973932|ref|ZP_05270404.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-66c26]
 gi|255091318|ref|ZP_05320796.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CIP 107932]
 gi|255312976|ref|ZP_05354559.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-76w55]
 gi|255515735|ref|ZP_05383411.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-97b34]
 gi|255648829|ref|ZP_05395731.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-37x79]
 gi|260682047|ref|YP_003213332.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260685645|ref|YP_003216778.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
 gi|306518943|ref|ZP_07405290.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-32g58]
 gi|260208210|emb|CBA60565.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260211661|emb|CBE01928.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
          Length = 233

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 124/233 (53%), Gaps = 19/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++E+++ N+ LV S+A+K+    +G ++ DL+  G IGL+ A  KFD   G KFS+Y+  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYI 62

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--- 559
            +K AI   I +QS    I  H   K++K  R   ++ +K+ REPT  EIAK+L +    
Sbjct: 63  KIKSAILDEIRNQSP---ISKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELNVSEKE 119

Query: 560 ---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              +E    +L I    +SL   I ++    + D I D+   +P +   +    E  ++ 
Sbjct: 120 LHDIESNIDMLNI----VSLNYVIFEDTNETVQDVISDREEEAPENIIEEEEKLEILSKA 175

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +++L  RE+ +L + +      D  L+E+GK   V+  R+ Q+  K+IR L++
Sbjct: 176 ISNLNEREKLILSLYYY----EDLNLKEIGKVLGVSESRVSQLHRKSIRNLRN 224


>gi|71083311|ref|YP_266030.1| RNA polymerase factor sigma-32 [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71062424|gb|AAZ21427.1| RNA polymerase sigma-32 factor (rpoH) RP303 [Candidatus
           Pelagibacter ubique HTCC1062]
          Length = 293

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 130/247 (52%), Gaps = 13/247 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 47  AAEKLVTSHLRLVAKIAMGYRGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT----PE---EIAKKL 556
           ++ +I   I      ++I      K  K+    +++ N+I  +      PE   EIA KL
Sbjct: 107 IRASIQEYILRSWSLVKIGTTTAQK--KLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKL 164

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  +  +++ +  SL   +G ED     D++ DK     L  A Q  + +    
Sbjct: 165 DVNKDEVISMNRRLSGKEFSLNAQVG-EDGDEWQDWLVDKELDHDLKFAHQEEMGQRQNL 223

Query: 616 VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL-KHPSRS 673
           +  S+    ER   + +   +N +  TLE++ K++ ++RER+RQIE KA  KL KH   S
Sbjct: 224 LKDSIKILNEREKEILYSRRLNDEPTTLEDLSKKYKISRERVRQIENKAFEKLQKHMLLS 283

Query: 674 KKLRSFL 680
            K ++ L
Sbjct: 284 AKSKNLL 290


>gi|239827600|ref|YP_002950224.1| sporulation sigma factor SigF [Geobacillus sp. WCH70]
 gi|239807893|gb|ACS24958.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. WCH70]
          Length = 250

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 127/253 (50%), Gaps = 17/253 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T I   E + ++   ++G+ EA   + E++E N+RLV SV +++ NRG +  DL Q G 
Sbjct: 9   QTPIKDQEMKELIRRSQEGDQEA---RDEIIEKNMRLVWSVVQRFLNRGYEPDDLFQIGC 65

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K+ +    
Sbjct: 66  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKEMGNKIRKAKDE 124

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S K  R PT  EIA  L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 125 LSKKQGRAPTVTEIADYLEISPEDVVLAQEAIRSPASIHETVYENDGDPITLLDQIADSD 184

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            VS  D            + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 185 EVSWFDKI-------ALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQV 233

Query: 657 RQIEAKAIRKLKH 669
            ++E K ++++K 
Sbjct: 234 SRLEKKILQQIKE 246


>gi|126697838|ref|YP_001086735.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile 630]
 gi|255099435|ref|ZP_05328412.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-63q42]
 gi|115249275|emb|CAJ67088.1| RNA polymerase sigma-28factor for flagellar operon [Clostridium
           difficile]
          Length = 233

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 124/233 (53%), Gaps = 19/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++E+++ N+ LV S+A+K+    +G ++ DL+  G IGL+ A  KFD   G KFS+Y+  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYI 62

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--- 559
            +K AI   I +QS    I  H   K++K  R   ++ +K+ REPT  EIAK+L +    
Sbjct: 63  KIKSAILDEIRNQSP---ISKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELKVSEKE 119

Query: 560 ---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              +E    +L I    +SL   I ++    + D I D+   +P +   +    E  ++ 
Sbjct: 120 LHDIESNIDMLNI----VSLNYVIFEDTNETVQDVISDREEEAPENIIEEEEKLEILSKA 175

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +++L  RE+ +L + +      D  L+E+GK   V+  R+ Q+  K+IR L++
Sbjct: 176 ISNLNEREKLILSLYYY----EDLNLKEIGKVLGVSESRVSQLHRKSIRNLRN 224


>gi|255305293|ref|ZP_05349465.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile ATCC 43255]
          Length = 233

 Score = 98.2 bits (243), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 124/233 (53%), Gaps = 19/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++E+++ N+ LV S+A+K+    +G ++ DL+  G IGL+ A  KFD   G KFS+Y+  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDTEKGAKFSSYSYI 62

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--- 559
            +K AI   I +QS    I  H   K++K  R   ++ +K+ REPT  EIAK+L +    
Sbjct: 63  KIKSAILDEIRNQSP---ISKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELKVSEKE 119

Query: 560 ---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              +E    +L I    +SL   I ++    + D I D+   +P +   +    E  ++ 
Sbjct: 120 LHDIESNIDMLNI----VSLNYVIFEDTNETVQDVISDREEEAPENIIEEEEKLEILSKA 175

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +++L  RE+ +L + +      D  L+E+GK   V+  R+ Q+  K+IR L++
Sbjct: 176 ISNLNEREKLILSLYYY----EDLNLKEIGKVLGVSESRVSQLHRKSIRNLRN 224


>gi|329910210|ref|ZP_08275256.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546240|gb|EGF31276.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 298

 Score = 98.2 bits (243), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 128/239 (53%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + MV ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 61  AAQGMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHW 120

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMP 559
           +K  +   I      +++     + K+   +R+ +   + +    TP   E +A+ L + 
Sbjct: 121 IKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDSM----TPAQVEALAQTLNVK 176

Query: 560 VEGVRKV-LKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRET--TT 614
            E V ++  +++   I+LE P  DED   + +     D+N  + +  A Q +  ++   +
Sbjct: 177 REEVIEMETRLSGRDIALEAPTDDEDDKFAPIAYLSSDRNEPTNVLEAQQYDRLQSDGLS 236

Query: 615 RVLASLTPREERVLRMRF-----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L  L  R  R++  R+     G G     TL E+ K+F V+ ERIRQIEA A++K+K
Sbjct: 237 QALNKLDERSRRIVEARWLANDDGSGA----TLHELAKEFGVSAERIRQIEAVALKKMK 291


>gi|326790567|ref|YP_004308388.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
 gi|326541331|gb|ADZ83190.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
          Length = 239

 Score = 98.2 bits (243), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 126/242 (52%), Gaps = 12/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H + ++++ +    IAK  +V+ NL LV S+ ++++NRG    DL Q G+IGL+K+ +KF
Sbjct: 3   HTLELIQRAQQGDEIAKNILVQENLGLVWSLVRRFSNRGYDMEDLFQIGSIGLLKSIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +KV      +  ++ REPT
Sbjct: 63  DLSFNVKFSTYAVPMIVGEIKRFLRDDGM-IKVSRSLKETAYKVRILKDELIRELNREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             EIA  L + VE V + L+   E  SL   I  GD     L D I++   V  L +++ 
Sbjct: 122 ISEIAAGLDLQVEEVVEALESNAEIESLNAVIYQGDGKPITLSDKIDE---VPTLQNSLV 178

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +    T ++  L P E  ++ MR+      D T  E+     +++ ++ +IE + ++K
Sbjct: 179 DKM--ILTELIERLLPIEREIIHMRYF----EDRTQTEIASALDISQVQVSRIEKRILKK 232

Query: 667 LK 668
           ++
Sbjct: 233 MR 234


>gi|206559184|ref|YP_002229944.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia J2315]
 gi|198035221|emb|CAR51095.1| RNA polymerase sigma-32 factor [Burkholderia cenocepacia J2315]
          Length = 311

 Score = 98.2 bits (243), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|158425877|ref|YP_001527169.1| RNA polymerase factor sigma-32 [Azorhizobium caulinodans ORS 571]
 gi|158332766|dbj|BAF90251.1| sigma-70 factor [Azorhizobium caulinodans ORS 571]
          Length = 300

 Score = 98.2 bits (243), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I        R    ++IA KL
Sbjct: 109 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQISALEEGDLRPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLG---DFIEDKNA---VSPLDSAIQANLR 610
            +  + V  + +      SL  P+  ED    G   D+++D +     + ++S    N R
Sbjct: 167 GVTEQDVVDMNRRLSGDASLNAPL-REDGDGGGEWQDWLQDDHQDQETNLVESEELDNRR 225

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  LA L PRE R+   R    ++ D  TLEE+  +F V+RER+RQIE +A  K++
Sbjct: 226 TALSSALAVLNPRERRIFEAR---RLSEDPVTLEELAAEFGVSRERVRQIEVRAFEKVQ 281


>gi|326794299|ref|YP_004312119.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas mediterranea
           MMB-1]
 gi|326545063|gb|ADZ90283.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas mediterranea
           MMB-1]
          Length = 610

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 63/148 (42%), Positives = 86/148 (58%), Gaps = 8/148 (5%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DG 80
           D      K++I   +++GY+T  E+N  LP D    EQ+E+ VAM+++MGI V     D 
Sbjct: 3   DTQQSRLKELIAKGKEQGYLTFTEVNDHLPDDLSDPEQVEEIVAMINDMGIVVSEYAPDK 62

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           + L  EEG  DS D  ++   ++       D A   T DPVRMY+REMG++ELL+R GEI
Sbjct: 63  ESLLMEEG--DSTDEEAAEEAAAALAAVEGDVA--RTTDPVRMYMREMGTVELLTRAGEI 118

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALI 168
           AIAKRIE G   +MASL   P     L+
Sbjct: 119 AIAKRIEEGTREVMASLSYFPGAVDVLL 146


>gi|260589168|ref|ZP_05855081.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
 gi|260540249|gb|EEX20818.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
          Length = 266

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 130/242 (53%), Gaps = 17/242 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+ EA   +++ ++ NLRLV+SV K++++      DL Q G +GL+KA + FD  L 
Sbjct: 38  IKEGDPEA---REQYIKGNLRLVLSVIKRFSSSNENADDLFQIGCVGLIKAIDNFDTTLN 94

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   I R + D +  IR+   +RD  +K +        +  +EPT  EIA
Sbjct: 95  VKFSTYAVPMIIGEIRRYLRDNNA-IRVSRSLRDVAYKAIYAKENYVKQNLKEPTINEIA 153

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLR 610
           +++ +  E +   L   + P+SL  P+  E  DT ++ D I DK   +  D+ I+   L+
Sbjct: 154 EEIGIDKEEIVYALDAIQSPVSLYEPVYTEGGDTLYVMDQISDKK--NKEDNWIENIALK 211

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L  L  RE+ ++ MRF  G       EE+G    +++ ++ ++E  A++ +++ 
Sbjct: 212 EA----LKKLDDREQHIVTMRFYEGKTQMEVAEEIG----ISQAQVSRLEKHALKTMRNY 263

Query: 671 SR 672
            R
Sbjct: 264 LR 265


>gi|294788977|ref|ZP_06754217.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
 gi|294483079|gb|EFG30766.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
          Length = 289

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 84/291 (28%), Positives = 152/291 (52%), Gaps = 24/291 (8%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           ++A   P G         ++  +   N I  +S+E    ++E R +     +G+ EA+  
Sbjct: 4   AFALPIPSGH------GSLEQYIHTVNAIPMLSLEEETKLAE-RQL-----RGDIEAA-- 49

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ W+
Sbjct: 50  -KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRFEPVHGARLFSFAVHWI 108

Query: 505 KQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           K  I   I      +RI     + K+   +R+ R+  N +  +   +EIA  L + +  V
Sbjct: 109 KAEIHEFILRNWRLVRIATTKPQRKLFFNLRSMRKSLNALSPKEA-QEIADDLGVKLTEV 167

Query: 564 RKV-LKITKEPISL--ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVL 617
            ++  ++T   ++L  E+   +ED+    D++ D ++      A QA+     E     L
Sbjct: 168 MEMEQRMTGNDVALLAESDDDNEDSFAPIDWLADNDSEPSQQIAKQAHYALQTEGLQNAL 227

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 228 AQLDERSRRIVETRW-LADDGGLTLHDLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|107023748|ref|YP_622075.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia AU 1054]
 gi|116690835|ref|YP_836458.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia HI2424]
 gi|170734160|ref|YP_001766107.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia MC0-3]
 gi|254247164|ref|ZP_04940485.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|105893937|gb|ABF77102.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia AU
           1054]
 gi|116648924|gb|ABK09565.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           HI2424]
 gi|124871940|gb|EAY63656.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|169817402|gb|ACA91985.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 311

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|86747581|ref|YP_484077.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris HaA2]
 gi|86570609|gb|ABD05166.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 299

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 121/239 (50%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P++   IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDMHPDQVKLIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  + +      SL  PI D+ +     D++ D+   SP   A+ A   E   R
Sbjct: 167 GVTEQDVIDMNRRLGGDASLNAPIRDDGEPGEWQDWLVDQ---SPNQEAVMAEHEELDHR 223

Query: 616 ------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RAALNGAIGVLNPRERRIFEARR--LADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQ 280


>gi|221211178|ref|ZP_03584157.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
 gi|221168539|gb|EEE01007.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
          Length = 281

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 42  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 102 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKR 158

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 159 EEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 218

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 219 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 274


>gi|118588309|ref|ZP_01545718.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118439015|gb|EAV45647.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 294

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 123/251 (49%), Gaps = 17/251 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E   A + +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G+
Sbjct: 39  RYKEHEDPEAAERLVNSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K AI   I      +++      K  ++    RR+  KI+       +  
Sbjct: 99  RLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGKIQALDEGDLKPH 156

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              EIA KL +  E V  + +      SL  P+  + D     D++ D++       A Q
Sbjct: 157 QVSEIATKLGVSEEEVVSMNRRLGGDASLNAPVRAEADAGEWQDWLVDESDSQETLLANQ 216

Query: 607 ANL---RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAK 662
             L   R+     +  L  RE R+   R    ++ D  TLE++  +F V+RER+RQIE +
Sbjct: 217 EELDMRRKMLNDAMDVLNERERRIFEAR---RLSEDPMTLEDLSGEFGVSRERVRQIEVR 273

Query: 663 AIRKLKHPSRS 673
           A  K++   R+
Sbjct: 274 AFEKVQKAVRN 284


>gi|27382448|ref|NP_773977.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1834373|emb|CAA70697.1| rpoH2 [Bradyrhizobium japonicum]
 gi|27355619|dbj|BAC52602.1| sigma32-like transcription factor [Bradyrhizobium japonicum USDA
           110]
          Length = 299

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 118/239 (49%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHQLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  K+    R+  +KI        R      IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKINALDEGDLRPDQVATIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +  + V  + +      SL  PI D+ +     D++ D    +P   A+ A      + 
Sbjct: 167 GVTDQDVIDMNRRLGGDASLNAPIRDDGEAGEWQDWLVDN---TPNQEAMMAEHEEYDHR 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+     +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RDALNGAMGVLNPRERRIFEARRLA--DEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQ 280


>gi|327314688|ref|YP_004330125.1| sigma-70, region 4 [Prevotella denticola F0289]
 gi|326944846|gb|AEA20731.1| sigma-70, region 4 [Prevotella denticola F0289]
          Length = 228

 Score = 97.8 bits (242), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/261 (27%), Positives = 127/261 (48%), Gaps = 41/261 (15%)

Query: 409 IRNE--IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           I NE  I+ I+    +S  E R +   ++ G+  A    +++ +ANL+ V+S+A +Y NR
Sbjct: 2   IANEKYIEEIAGGQPLSDVEERTLAERIKVGDAHAL---EKLTKANLKYVVSLAHQYRNR 58

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIG+M AA++FD   G +F  +A  ++++A+  +I +Q+   R+P + +
Sbjct: 59  GLGEDDLISEGNIGMMHAAQRFDGARGVRFVVFAAPYIRKAMEEAIKEQAALYRLPRNEK 118

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +      R+ ++ S+ I            +  PV                  P+G  +  
Sbjct: 119 N------RSEQKRSHAI-----------SIDQPV------------------PVGSSNNF 143

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L + +E+ NA    +   Q  L     + L  L  RE +V+   +G+     +T+ E  
Sbjct: 144 TLQNVLENDNAPHADEQLNQEILSAEIQKGLGVLNERERQVITCLYGLS-GIHYTMAEAA 202

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           +   + RER+RQI   A+RKL
Sbjct: 203 EHMGLKRERVRQIRDGALRKL 223


>gi|195970121|ref|NP_387362.2| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307302477|ref|ZP_07582234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307316193|ref|ZP_07595637.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|8131943|gb|AAF73147.1|AF149031_2 sigma factor RpoH2 [Sinorhizobium meliloti]
 gi|10129889|dbj|BAB13518.1| sigma factor [Sinorhizobium meliloti]
 gi|187904236|emb|CAC47835.2| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306898033|gb|EFN28775.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306903147|gb|EFN33737.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 288

 Score = 97.8 bits (242), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 126/240 (52%), Gaps = 21/240 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  +++RLVIS+A K+ + GL   DL+QEG+IGL++AA +F+     +FSTYA WW
Sbjct: 40  ARNKIAMSHMRLVISMAAKFRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAM 558
           ++ ++   +      +R       K     + R   R++    ++  +   EEIA  L +
Sbjct: 100 IRASMQDYVLRNWSIVRGGTSSAQKALFFNLRRLRARLAQGDRQLTSQAMHEEIAAALGV 159

Query: 559 PVEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL------ 609
            +  V+ +  +++    SL+ PI  GD D     DF+  +   +PL     ++L      
Sbjct: 160 SLADVQTMDARLSGNDASLQAPIGSGDPDAGARLDFLASE---APLPDEQVSDLIDGERA 216

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      L  L+ RE +++R R    +  D  TLEE+G    +++ER+RQIE +A+ KL+
Sbjct: 217 RRWLQVALGELSEREMKIIRARR---LTEDGATLEELGVALGISKERVRQIETRALEKLR 273


>gi|113866384|ref|YP_724873.1| RNA polymerase factor sigma-32 [Ralstonia eutropha H16]
 gi|113525160|emb|CAJ91505.1| DNA-directed RNA polymerase sigma subunit (RpoH) [Ralstonia
           eutropha H16]
          Length = 308

 Score = 97.8 bits (242), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 124/250 (49%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 69  AARQMVMSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHW 128

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R+ ++ ++      TPE+        VE 
Sbjct: 129 IKAEIHEYVLKNWRMVKVATTKAQRKLFFNLRSHKQGAHTF----TPEQ--------VEA 176

Query: 563 VRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV----- 616
           V + L +  E +  +ET +   D +  G   + +   +P+  A  A+     TRV     
Sbjct: 177 VARELNVKPEEVMEMETRLSGGDLALEGQIDDGEEEFAPI--AYLADNHNEPTRVLEAKR 234

Query: 617 ------------LASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                       L  L  R  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 235 HDRMQVEGLEEALGKLDERSRRIIEARWLHVEDDGSGGSTLH---ELADEFGVSAERIRQ 291

Query: 659 IEAKAIRKLK 668
           IEA A++K+K
Sbjct: 292 IEAAAMKKMK 301


>gi|153005080|ref|YP_001379405.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028653|gb|ABS26421.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 241

 Score = 97.8 bits (242), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 120/241 (49%), Gaps = 58/241 (24%)

Query: 429 HIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           H +++  RKG+  A   K+++V  NL  V+++A+K     ++  DLIQEGN+GLM+A EK
Sbjct: 35  HALALRARKGDVRA---KQKLVRHNLAFVVAIARKQRRGTVRLDDLIQEGNVGLMRAVEK 91

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G +FSTYA+WW++  I + + +   T+R                           
Sbjct: 92  FDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVR--------------------------- 124

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQ 606
                      P  G      + +  +SL++ I +E D +HL + IED +   P D+ +Q
Sbjct: 125 -----------PQSGT-----VAQPDLSLDSAIDEEGDATHL-ERIED-DGPGPEDTYLQ 166

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-----TDHTLEEVGKQFCVTRERIRQIEA 661
           A   E  + V  +L    +R+  + + I  N        TLEE+GK++ V+RER+RQ+E 
Sbjct: 167 A---EGDSDVRDALGKVRKRIGELGWDIVHNRLEQDQPRTLEEIGKRWGVSRERVRQVEL 223

Query: 662 K 662
           K
Sbjct: 224 K 224


>gi|47570318|ref|ZP_00240965.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
 gi|47553027|gb|EAL11431.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
          Length = 257

 Score = 97.8 bits (242), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 1   RNKVEICGVDTAKLPVLXNDEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 57

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 58  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 116

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 117 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 176

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 177 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 231

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 232 EIG----ISQAQVSRLEKSAIKQM 251


>gi|161523666|ref|YP_001578678.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|189351565|ref|YP_001947193.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|160341095|gb|ABX14181.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia multivorans
           ATCC 17616]
 gi|189335587|dbj|BAG44657.1| RNA polymerase sigma-32 factor [Burkholderia multivorans ATCC
           17616]
          Length = 311

 Score = 97.8 bits (242), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EDVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|167585406|ref|ZP_02377794.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ubonensis Bu]
          Length = 311

 Score = 97.4 bits (241), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|229013088|ref|ZP_04170253.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
 gi|229061509|ref|ZP_04198853.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|229168644|ref|ZP_04296366.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228614800|gb|EEK71903.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228717743|gb|EEL69393.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|228748342|gb|EEL98202.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
          Length = 259

 Score = 97.4 bits (241), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 137/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D ++D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 179 DPIFVMDQLKDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 234 EIG----ISQAQVSRLEKSAIKQM 253


>gi|163784595|ref|ZP_02179438.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880134|gb|EDP73795.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 154

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 55/144 (38%), Positives = 89/144 (61%), Gaps = 3/144 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K I+    IS  E +++   +++G+ +A     ++V+ANLR VI+VAK Y   G+ F +
Sbjct: 14  LKQIADIPLISPEEEKNLAKKIKEGDKQAL---DKLVKANLRFVINVAKNYIGYGVPFQE 70

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  GNIGL++AA++FD   G +F +YA+WW+KQ+I ++I  Q   IRIP    +   ++
Sbjct: 71  LISAGNIGLIEAAKRFDPDRGVRFISYAIWWIKQSIFQTIQQQKDLIRIPHRTSNMAVRI 130

Query: 533 VRTARRMSNKIKREPTPEEIAKKL 556
            +    +  K+ REPT +EI  KL
Sbjct: 131 DKVYLELKEKLGREPTYKEIKSKL 154


>gi|298715063|emb|CBJ27770.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Ectocarpus siliculosus]
          Length = 737

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 129/260 (49%), Gaps = 29/260 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++++V  NL LV+S+A KY            LIQEG IGL++AAE++D   G++F+TYA
Sbjct: 479 ARQKLVVCNLALVVSLANKYKRSHFDCGCLQTLIQEGTIGLIRAAERYDPSKGFRFTTYA 538

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++  +  S+  +   I +P+ ++++ + V R+  ++   + REPT EE+A ++   +
Sbjct: 539 IWWIEARLRVSVQTEERFIHVPMWVKNQYNTVHRSVPKLRKSLGREPTSEELAAQVE--I 596

Query: 561 EGVRKVLKITKE-------------------PISLETPIGDEDTSHLGDFIE--DKNAVS 599
           +   KV+   K                    P+ + TP+   D S + D ++  D +  S
Sbjct: 597 DTNSKVVVTPKRVEELETWVSFHRKHESLDVPLEVSTPV-PADCSTIEDGVKAPDPSTES 655

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +  IQ +  E+   +   L+  + ++LRM+ G+G       +E+ +   +    +   
Sbjct: 656 TSELEIQRDFLESC--LCQDLSKIQRKILRMKVGLGGEKGKNRQEISRALKMPFNNVISE 713

Query: 660 EAKAIRKLKHPSRSKKLRSF 679
           E KA  KL+   R     SF
Sbjct: 714 ERKAFYKLRGLQRGGGYPSF 733


>gi|330993273|ref|ZP_08317209.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
 gi|329759675|gb|EGG76183.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
          Length = 298

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 123/251 (49%), Gaps = 32/251 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ EA+    ++V ++LRLV  +A  Y   GL   +LI EGNIG+M+A  +FD   G++
Sbjct: 42  KGDTEAA---HKLVTSHLRLVAKIAMGYRGYGLPVGELISEGNIGMMQAVRRFDPDRGFR 98

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPT 548
            +TYAMWW++ AI   I      ++I      K  K+    RR+  +++       R   
Sbjct: 99  LATYAMWWIRAAIQEYILHSWSLVKIGTTAAQK--KLFFNLRRLKGQMQAIDDGDLRPEQ 156

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKN-------AVSP 600
             +IA+ L +P + V  + +    P  SL  P+  +      D++ D N       A S 
Sbjct: 157 VNKIAQSLGVPEQDVVNMNRRLAAPDHSLNAPLRMDGEGEWQDWLVDDNDNQEETLAQSE 216

Query: 601 LDSAIQANLRETTTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             S  QA L       L +L  RE  +L   R++     +   TLE++   + ++RER+R
Sbjct: 217 EYSGRQALL----ANALKTLNERERHILTERRLK-----DEPATLEDLSHVYNISRERVR 267

Query: 658 QIEAKAIRKLK 668
           QIE +A  KL+
Sbjct: 268 QIEVRAFEKLQ 278


>gi|209886261|ref|YP_002290118.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
 gi|209874457|gb|ACI94253.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
          Length = 299

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 119/248 (47%), Gaps = 21/248 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  K+    R+  +KI         E   + IAK+L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALEDGDMHEDQVKLIAKRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA------NL 609
            +    V  + +      SL  PI D+ +     D++ D    SP    I A      + 
Sbjct: 167 GVTERDVIDMNRRLGGDASLNAPIRDDGEPGEWQDWLVD---TSPNQETIMAESEEYDHR 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R   T  +  L PRE R+   R         TLE++  +F V+RER+RQIE +A  K++ 
Sbjct: 224 RNALTGAMGVLNPRERRIFEARRLA--EEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQA 281

Query: 670 PSRSKKLR 677
             +S   R
Sbjct: 282 AVKSTVAR 289


>gi|291525265|emb|CBK90852.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale DSM
           17629]
 gi|291529276|emb|CBK94862.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale
           M104/1]
          Length = 259

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 125/236 (52%), Gaps = 15/236 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG+     A+++ +  NLRLV+SV ++++N      DL Q G IGLMK+ + FD  +G
Sbjct: 31  IKKGD---KAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGCIGLMKSIDNFDPTIG 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   + R + D S   RIP  +RD  ++ +++  ++S K+  +P+  EI+
Sbjct: 88  VKFSTYAVPMIIGEVRRYLRDNSAY-RIPRSLRDTAYQAIKSKEKLSRKLVHDPSLAEIS 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K   +P   +   L   + P+SL  P+  +  DT ++ D I DK      + A   NL  
Sbjct: 147 KDCGIPENDILYALDAIQTPLSLFDPVYTDGGDTLYVMDQISDKKNK---EEAWVKNLVL 203

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                L     R+  ++++RF  G     T  EV ++  +++ ++ ++E  A++ +
Sbjct: 204 DDALKLLDDRARQ--IIKLRFFEG----KTQIEVAEEINISQAQVSRLEKNALKNM 253


>gi|149187051|ref|ZP_01865358.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
 gi|148829340|gb|EDL47784.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
          Length = 319

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 79/261 (30%), Positives = 125/261 (47%), Gaps = 30/261 (11%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A  ++V ++LRLV  +A  Y   GL   DLI EGN+GLM+  +KF+   G++ +TYAM
Sbjct: 67  SEAAAQLVTSHLRLVSKIAMGYRGYGLPVSDLISEGNVGLMQGVKKFEADRGFRLATYAM 126

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTP------EEIAK 554
           WW+K +I   I      +++      K  K+    RRM   +   E T       ++IA 
Sbjct: 127 WWIKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRMKKNLDAYEDTDLHPDDVQKIAT 184

Query: 555 KLAMPVEGVRKVLKITKEPI-----SLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            L +P +   +V+ + +  +     SL  P+  G+E +    D++ D     PL     A
Sbjct: 185 DLGVPEQ---EVVNMNRRMMMGGDGSLNVPMRNGEEGSGEWMDWLTDDR---PLQDETVA 238

Query: 608 NLRETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  E   R       + +L  RE+ +L  R         TLEE+ + + V+RERIRQIE 
Sbjct: 239 DAEEKEVRHEMLGEAMEALNEREQHILTERRLT--ENPQTLEELSQVYNVSRERIRQIEV 296

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           +A  KL+   ++      L G
Sbjct: 297 RAFEKLQKAMKAIAGERLLPG 317


>gi|260892756|ref|YP_003238853.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
 gi|260864897|gb|ACX52003.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
          Length = 245

 Score = 97.4 bits (241), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 121/228 (53%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V ANL LV  V +++  +G +  DL Q G IGL+KA ++FD   G  FSTYA+  
Sbjct: 26  ARELLVRANLGLVGKVVRRFAGQGREGEDLFQIGCIGLLKAIDRFDPQRGTCFSTYAVAT 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++   +V+RT   +   + REP+  EIA+ L + VE V
Sbjct: 86  ILGEIRRFLRDDG-MLKVSRSLKETSRRVIRTRASLKMALGREPSVAEIAESLGIAVEEV 144

Query: 564 RKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L+  K P  L+ P+  E    L   D +  +   S L++    +LRE+  R    L 
Sbjct: 145 VMALEAGKAPAFLQEPLAGEGEEALCWEDCLSSEKEESWLET---LSLRESLRR----LP 197

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++  RF  G    +T EEV KQ  +++ ++ ++E  A++KL+ 
Sbjct: 198 AREREIIWWRFFAG----YTQEEVAKQLGISQAQVSRLERNALQKLRE 241


>gi|149183910|ref|ZP_01862298.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
 gi|148848374|gb|EDL62636.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
          Length = 227

 Score = 97.4 bits (241), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 59/175 (33%), Positives = 98/175 (56%), Gaps = 8/175 (4%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ G+  A   ++++V  NLRLV+SV +++ N
Sbjct: 14  RNKVEICGVDTSKLPVLKNEEMRKLFREMQAGDISA---REKLVNGNLRLVLSVIQRFNN 70

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 71  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 129

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           RD  +K ++   ++  +  +EPT EEIAK L +P E +   +   ++P+SL  PI
Sbjct: 130 RDIAYKALQVREKLMGETSKEPTAEEIAKVLDVPHEDIVFAMDAIQDPVSLFEPI 184


>gi|259416055|ref|ZP_05739975.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
 gi|259347494|gb|EEW59271.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
          Length = 292

 Score = 97.4 bits (241), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 124/249 (49%), Gaps = 18/249 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL +S+A K+   G    DLIQE  +GLMKAAEKFD   G +FSTYA+WW+K +
Sbjct: 45  LITAYMRLAVSMASKFRRYGAPMNDLIQEAGLGLMKAAEKFDPDRGVRFSTYAVWWIKAS 104

Query: 508 ITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           I   +      +R         +  +MR    ++ R A     ++ R    + +A+++ +
Sbjct: 105 IQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLEREAESDGVELDRHKLHQMVAEEIGV 164

Query: 559 PVEGVRKV-LKITKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAI---QANLRETT 613
           P+  V  +  ++     SL      DED     D +ED +  +    A    +  LRE  
Sbjct: 165 PLRDVEMMDGRLAGADFSLNAVQSADEDGREWIDALEDDSEQAAERVAADHDRRQLREWL 224

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP--S 671
              L  L  RE  ++R R         TLE +G +  +++ER+RQ+EA A  K++     
Sbjct: 225 VTALNGLNERERFIVRER--KLREESRTLESLGNELGLSKERVRQLEAAAFLKMRKSLEG 282

Query: 672 RSKKLRSFL 680
           +S+++++FL
Sbjct: 283 QSREVQNFL 291


>gi|221199969|ref|ZP_03573012.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
 gi|221206876|ref|ZP_03579888.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221173531|gb|EEE05966.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221180208|gb|EEE12612.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
          Length = 311

 Score = 97.4 bits (241), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPV 560
           +K  I   I      +++      K  + +    R   K  +  TPEEI   A++L +  
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKR 188

Query: 561 EGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTR 615
           E V ++  +++   I+LE  +  G+E  + +    +  N  + + +A Q ++ +T    +
Sbjct: 189 EEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQ 248

Query: 616 VLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 249 ALDALDARSRRIIEARWLHVDDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|325860122|ref|ZP_08173248.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|325482407|gb|EGC85414.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
          Length = 228

 Score = 97.4 bits (241), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 73/261 (27%), Positives = 127/261 (48%), Gaps = 41/261 (15%)

Query: 409 IRNE--IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           I NE  I+ I+    +S  E R +   ++ G+  A    +++ +ANL+ V+S+A +Y NR
Sbjct: 2   IANEKYIEEIAGGQPLSDVEERTLAERIKVGDAHAL---EKLTKANLKYVVSLAHQYRNR 58

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIG+M AA++FD   G +F  +A  ++++A+  +I +Q+   R+P + +
Sbjct: 59  GLGEDDLISEGNIGMMHAAQRFDGTRGVRFVVFAAPYIRKAMEEAIKEQAVLYRLPRNEK 118

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +      R+ ++ S+ I            +  PV                  P+G  +  
Sbjct: 119 N------RSEQKRSHAI-----------SIDQPV------------------PVGSSNNF 143

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L + +E+ NA    +   Q  L     + L  L  RE +V+   +G+     +T+ E  
Sbjct: 144 TLQNVLENDNAPHADEQLNQEILSAEIQKGLGVLNERERQVITCLYGLS-GIHYTMAEAA 202

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           +   + RER+RQI   A+RKL
Sbjct: 203 EHMGLKRERVRQIRDGALRKL 223


>gi|308273291|emb|CBX29894.1| RNA polymerase sigma-32 factor [uncultured Desulfobacterium sp.]
          Length = 298

 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 128/236 (54%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A  E+V +NLRLV+ +A ++    +Q  LDLIQEGNIGLM+A  KFD     KFS YA +
Sbjct: 55  AAYEIVTSNLRLVVKIALEFQRIWMQNLLDLIQEGNIGLMQAVRKFDPYKNVKFSYYASF 114

Query: 503 WVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP- 559
           W+K  I + I D    ++I      R    K+ +  + + ++   +P P+ ++++L +  
Sbjct: 115 WIKAYILKFIMDNWRLVKIGTTQGQRKLFFKLKKEKQDLIDQ-GFDPKPKLLSERLGVTE 173

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-------EDKNAVSPLDSAIQANLRET 612
            E V    ++    +SL TP+ D+  S   +FI       E++ A   +D+ I + + E 
Sbjct: 174 KEIVDMDQRLDGWDVSLNTPLSDDSDSEKIEFISYDSDSAEEQVAKKQMDNLIYSKIDE- 232

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R L  +T RE  +  +R  I  +   TL+E+G ++ ++RER+RQ+E   I K++
Sbjct: 233 -FRKL--MTKRENEIFDLR--IFSDNPVTLQEIGDRYGISRERVRQLEKNIITKMR 283


>gi|222149598|ref|YP_002550555.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221736580|gb|ACM37543.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 300

 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 119/238 (50%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  ++    RR+  KI+       +     EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGKIQAIEEGDLKPDQVTEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-- 612
            +  E V  + +      SL  PI   + ++    D++ D +  S  D+ I+ +  ET  
Sbjct: 167 KVSEEEVISMNRRLSGDASLNAPIRASEGESGQWQDWLVDDHD-SQEDTLIEQDELETRR 225

Query: 613 --TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +R +  L  RE R+   R         TLEE+  +F ++RER+RQIE +A  K++
Sbjct: 226 NMLSRAMGVLNDRERRIFAARR--LAEEPVTLEELSSEFDISRERVRQIEVRAFEKVQ 281


>gi|30263905|ref|NP_846282.1| sporulation sigma factor SigG [Bacillus anthracis str. Ames]
 gi|47778237|ref|YP_020684.2| sporulation sigma factor SigG [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|165872304|ref|ZP_02216941.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167641114|ref|ZP_02399369.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170688856|ref|ZP_02880059.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|170708817|ref|ZP_02899253.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|177654919|ref|ZP_02936636.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190565736|ref|ZP_03018655.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035947|ref|ZP_03103349.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196045922|ref|ZP_03113151.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206976720|ref|ZP_03237624.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217961324|ref|YP_002339892.1| sporulation sigma factor SigG [Bacillus cereus AH187]
 gi|218233406|ref|YP_002368703.1| sporulation sigma factor SigG [Bacillus cereus B4264]
 gi|218905033|ref|YP_002452867.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225865885|ref|YP_002751263.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227813187|ref|YP_002813196.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228916541|ref|ZP_04080107.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229140552|ref|ZP_04269107.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|229152101|ref|ZP_04280296.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|229157482|ref|ZP_04285559.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|229174570|ref|ZP_04302100.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|229198015|ref|ZP_04324729.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|229602177|ref|YP_002868139.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
 gi|254721437|ref|ZP_05183226.1| sporulation sigma factor SigG [Bacillus anthracis str. A1055]
 gi|30258549|gb|AAP27768.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Ames]
 gi|47551942|gb|AAT33159.2| RNA polymerase sigma-G factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164711980|gb|EDR17520.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167510894|gb|EDR86285.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170126302|gb|EDS95193.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|170667211|gb|EDT17971.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|172080430|gb|EDT65517.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190562655|gb|EDV16621.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991596|gb|EDX55562.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196023362|gb|EDX62040.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206745030|gb|EDZ56433.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217067470|gb|ACJ81720.1| RNA polymerase sigma-G factor [Bacillus cereus AH187]
 gi|218161363|gb|ACK61355.1| RNA polymerase sigma-G factor [Bacillus cereus B4264]
 gi|218537241|gb|ACK89639.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225788717|gb|ACO28934.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227002358|gb|ACP12101.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228585494|gb|EEK43598.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|228608875|gb|EEK66167.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|228625932|gb|EEK82682.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|228631450|gb|EEK88084.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|228643113|gb|EEK99389.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|228843120|gb|EEM88202.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229266585|gb|ACQ48222.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
          Length = 259

 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 179 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 234 EIG----ISQAQVSRLEKSAIKQM 253


>gi|254439883|ref|ZP_05053377.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255329|gb|EDY79643.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 292

 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 128/253 (50%), Gaps = 18/253 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMASKFRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  ++R    ++ R A +    + R    + IA 
Sbjct: 101 IKASIQDHVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAMKRGETLDRHDMRQMIAT 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIED---KNAVSPLDSAIQANL 609
           ++ +P+  V  +  +++    SL      ED      D +ED   + A +  +S     L
Sbjct: 161 EVGVPLRDVEMMEGRLSGSDFSLNATQSSEDEGREWIDALEDDGEQAAETVQNSHDTDTL 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     L +L+ RE+ ++R R     +   TLE +G +  +++ER+RQ+EA A  K++ 
Sbjct: 221 RQWLLTALTALSDREQFIVRER--KLRDAPRTLESLGTELGLSKERVRQLEAAAFGKMRK 278

Query: 670 P--SRSKKLRSFL 680
               +S ++ +FL
Sbjct: 279 SLEGQSHEVHNFL 291


>gi|30021992|ref|NP_833623.1| sporulation sigma factor SigG [Bacillus cereus ATCC 14579]
 gi|206971353|ref|ZP_03232304.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218899057|ref|YP_002447468.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228902409|ref|ZP_04066563.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|228909729|ref|ZP_04073552.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228922656|ref|ZP_04085956.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228940992|ref|ZP_04103550.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954180|ref|ZP_04116208.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960121|ref|ZP_04121785.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966857|ref|ZP_04127901.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|229019106|ref|ZP_04175941.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|229025350|ref|ZP_04181768.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|229047588|ref|ZP_04193178.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|229071403|ref|ZP_04204625.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|229081156|ref|ZP_04213666.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|229104466|ref|ZP_04235133.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|229111373|ref|ZP_04240926.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|229129181|ref|ZP_04258154.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|229146475|ref|ZP_04274846.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|229162839|ref|ZP_04290796.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|229180179|ref|ZP_04307523.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|229192073|ref|ZP_04319042.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|296504397|ref|YP_003666097.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|29897548|gb|AAP10824.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 14579]
 gi|206734125|gb|EDZ51296.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218543268|gb|ACK95662.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228591399|gb|EEK49249.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|228603388|gb|EEK60865.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|228620721|gb|EEK77590.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|228637108|gb|EEK93567.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|228654418|gb|EEL10283.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|228672149|gb|EEL27440.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|228678908|gb|EEL33118.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|228702200|gb|EEL54676.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|228711694|gb|EEL63647.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|228723835|gb|EEL75190.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|228735935|gb|EEL86512.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|228742206|gb|EEL92371.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|228792956|gb|EEM40514.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799637|gb|EEM46590.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805500|gb|EEM52091.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818671|gb|EEM64738.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228837085|gb|EEM82426.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228850018|gb|EEM94849.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228857153|gb|EEN01659.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|296325449|gb|ADH08377.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|326941673|gb|AEA17569.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 259

 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 179 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 234 EIG----ISQAQVSRLEKSAIKQM 253


>gi|71909448|ref|YP_287035.1| RNA polymerase factor sigma-32 [Dechloromonas aromatica RCB]
 gi|71849069|gb|AAZ48565.1| RNA polymerase, sigma 32 subunit, RpoH [Dechloromonas aromatica
           RCB]
          Length = 286

 Score = 97.1 bits (240), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 78/254 (30%), Positives = 127/254 (50%), Gaps = 40/254 (15%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LRLVIS+A+ Y   GL   DLIQEGNIGLMKA ++FD   G + 
Sbjct: 45  GDVEAA---RQLVLSHLRLVISIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPSRGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT-----PEE 551
            ++AM W+K  I   I      +++      +  K+    R M +  +   T       E
Sbjct: 102 VSFAMHWIKAEIHEYILKNWRLVKVATTKAQR--KLFFNLRSMKSGYEGIDTLSGTQAAE 159

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L     GV++      E + +ET +   D +  G+  + + A +P+D    A+ R 
Sbjct: 160 VAARL-----GVKQ-----DEVVEMETRLSGRDIALDGNPDDGEEAFAPID--YLADSRY 207

Query: 612 TTTRV-----------------LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             TRV                 L +L PR  R++  R+ +      TL ++  +F V+ E
Sbjct: 208 EPTRVLENKAIARLQDEGLHEALEALDPRSRRIIEARW-LHDGETATLHDLADEFDVSAE 266

Query: 655 RIRQIEAKAIRKLK 668
           RIRQIE KA++K++
Sbjct: 267 RIRQIEVKALQKMR 280


>gi|77464172|ref|YP_353676.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126463015|ref|YP_001044129.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221640041|ref|YP_002526303.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332559048|ref|ZP_08413370.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|77388590|gb|ABA79775.1| sigma factor RpoH2 (Sigma-32 group [Rhodobacter sphaeroides 2.4.1]
 gi|126104679|gb|ABN77357.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221160822|gb|ACM01802.1| RNA polymerase, sigma 32 subunit, RpoH precursor [Rhodobacter
           sphaeroides KD131]
 gi|332276760|gb|EGJ22075.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 292

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 78/261 (29%), Positives = 128/261 (49%), Gaps = 34/261 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A KY   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMASKYRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A +    +      E +A 
Sbjct: 101 IKASIQDYVMRNWSLVRTGSTSSQKALFFNMRRVQARLEREASQRGEALDAHQLREMVAH 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSP------LDSAIQ 606
            + +P+  V  +  +++    SL  T   D++     D +ED +A +       LD+   
Sbjct: 161 DVGVPLSDVEMMEGRLSGSDFSLNATQSADDEGREWIDALEDDSAQAAEVVEGSLDA--- 217

Query: 607 ANLRETTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           A LR      +  L  RE     ER LR       +   TLE +G++  +++ER+RQ+EA
Sbjct: 218 ARLRGWLVSAMQQLNARERFIVTERKLR-------DVPRTLESLGEELKLSKERVRQLEA 270

Query: 662 KAIRKLKHP--SRSKKLRSFL 680
            A  K++    ++S+++  FL
Sbjct: 271 AAFAKMRRSLEAQSREVHHFL 291


>gi|298293645|ref|YP_003695584.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296930156|gb|ADH90965.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 293

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 126/241 (52%), Gaps = 28/241 (11%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A++RL I++A+++ N GL   DLIQEG+IGLM+AA +F+     +F+TYA WW++ A
Sbjct: 45  LIHAHMRLAIAIARRFRNYGLPMPDLIQEGHIGLMEAASRFETTHEVRFATYASWWIRAA 104

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR------EPTPEE----IAKKLA 557
           I   +      +R       K   +    RR+  +++R      E T EE    IA+KL 
Sbjct: 105 IQDYVLRNWSIVRGGTSSGQK--ALFFNLRRVRARLERANGGAGETTREEMHRSIAEKLG 162

Query: 558 MP-VEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPL-DSAIQANL---- 609
           +  +E  R   ++    +SL  P+  G+ED +   D +    A  PL D  +   +    
Sbjct: 163 VSEIEVARMDARLNVPDLSLNAPLSFGEEDGAERMDQL---VAADPLPDEQVSMEIDGER 219

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R      L  L  RE R++  R    +  D  TLE +G++  +++ER+RQIE++AI KL
Sbjct: 220 RRRWLQGALRGLNEREFRIIEARR---LTEDSETLEVLGERLGISKERVRQIESRAIEKL 276

Query: 668 K 668
           +
Sbjct: 277 R 277


>gi|318041080|ref|ZP_07973036.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 128/235 (54%), Gaps = 25/235 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQF----LDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A + +V ANLRLV++VA +Y  R        +DL+Q GN+GL++AAEK+D   GYKFSTY
Sbjct: 50  ALQRIVTANLRLVVTVALRYIRRLKHLAHDPMDLVQAGNLGLLRAAEKYDPTRGYKFSTY 109

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN--KIKREP-TPEEIAKKL 556
             WW++Q+I R + + S +IRIPV++       V  A R  +   ++  P + E++A+ L
Sbjct: 110 GYWWIRQSINRYLQEHSGSIRIPVNL-------VSLANRADSLQSLRSHPMSVEQLAEAL 162

Query: 557 AMPVEGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               + +   + I      +SL+  + G +    L D + D +   PL   I  + R   
Sbjct: 163 QESPQRLLYAMAIQHRSNTVSLDQQLSGSDGDMTLLDTVTDDH--QPL---ITDDYRWMH 217

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++    TP E  V+++R+  G +   +  EV +    ++++++++E  A+ KL+
Sbjct: 218 SQLQHLSTP-ELTVIQLRY--GEDKQRSFAEVARLIGRSKDQVQRLERHALTKLR 269


>gi|73540031|ref|YP_294551.1| RNA polymerase factor sigma-32 [Ralstonia eutropha JMP134]
 gi|72117444|gb|AAZ59707.1| Sigma-70 region 2 [Ralstonia eutropha JMP134]
          Length = 309

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 131/240 (54%), Gaps = 22/240 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 70  AARQLVMSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPNQGVRLVSYAMHW 129

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMP 559
           +K  I   +      +++     + K+   +R+ ++ S+      TPE+I   A+ L + 
Sbjct: 130 IKAEIHEYVLKNWRMVKVATTKAQRKLFFNLRSHKQGSHTF----TPEQIEAVARDLNVK 185

Query: 560 VEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKN-AVSPLDSAIQANLR-ETTT 614
            E V ++  +++   ++LE  +  G+E+ + +    ++ N     L++  Q  ++ E   
Sbjct: 186 PEEVMEMETRMSGGDLALEGQVDDGEEEFAPIAYLADNHNEPTRVLEAKRQDRMQVEGLE 245

Query: 615 RVLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LA L  R  R++  R+   +N +       TL E+  +F V+ ERIRQIE  A++K+K
Sbjct: 246 EALARLDERSRRIIEARW---LNVEDDGSGGATLHELADEFGVSAERIRQIEVAAMKKMK 302


>gi|15889716|ref|NP_355397.1| RNA polymerase factor sigma-32 [Agrobacterium tumefaciens str. C58]
 gi|15157628|gb|AAK88182.1| RNA polymerase sigma-32 factor [Agrobacterium tumefaciens str. C58]
          Length = 300

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 127/249 (51%), Gaps = 20/249 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + ++    D++ D +  S     I+ +  ET  
Sbjct: 167 QVSEEEVISMNRRLHGDASLNAPIKASEGESGQWQDWLVDDHE-SQEAVLIEQDELETRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLEE+  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMGVLNERERRIFEAR---RLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQE 282

Query: 670 PSRSKKLRS 678
             + + L +
Sbjct: 283 AVQKEALEA 291


>gi|84499725|ref|ZP_00998013.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84392869|gb|EAQ05080.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 292

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 122/246 (49%), Gaps = 30/246 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V A +RL IS+A KY   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLVTAYMRLAISMASKYRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    K+ R A      + +    + +A 
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAKLEREALGRGETLDKHQLHQLVAM 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---- 608
           ++ +P+  V+ +  +++    SL  T   DE+     D IED    +    A++A+    
Sbjct: 161 EVGVPLRDVQMMDGRLSGSDFSLNATQSVDEEGREWIDTIEDDGVQAA--EAVEADHDRE 218

Query: 609 -LRETTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            LR      ++ L  RE     ER LR       +   TLE +G++  +++ER+RQ+EA 
Sbjct: 219 TLRLWLAEAMSDLNDRETLIVTERKLR-------DAPRTLESLGQELGLSKERVRQLEAA 271

Query: 663 AIRKLK 668
           A +K++
Sbjct: 272 AFKKMR 277


>gi|260431476|ref|ZP_05785447.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260415304|gb|EEX08563.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 292

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 32/260 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A     ++ R    + IA 
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAASDGVELDRHQLHQMIAA 160

Query: 555 KLAMPVEGVRKVL-KITKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQA----- 607
           ++ +P+  V  +  ++     SL      DED     D +ED       DSA  A     
Sbjct: 161 EIGVPLRDVEMMHGRLAGSDFSLNAVQSADEDGREWIDALED-------DSAQAAELVEH 213

Query: 608 -----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                 LRE     + +L  RE  ++R R     +   TLE +G++  +++ER+RQ+EA 
Sbjct: 214 GHDTRQLREWLITAMQALNERERFIVRER--KLRDPARTLESLGQELGLSKERVRQLEAA 271

Query: 663 AIRKLKHP--SRSKKLRSFL 680
           A  K++     +S++++ FL
Sbjct: 272 AFAKMRKSLEGQSREVQHFL 291


>gi|83592446|ref|YP_426198.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575360|gb|ABC21911.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 299

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 121/239 (50%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPMGEVISEGNVGLMQAVKRFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPE---EIAKKL 556
           ++ AI   I      +++      K  K+    R+M  +++     +  P+   +IA KL
Sbjct: 109 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRKMKGQLQLMDEGDMHPDKVTQIATKL 166

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRET 612
            +P + V  + +    P  SL  P+  +      D++ D++     +  +S      R  
Sbjct: 167 GVPEQDVINMNRRLSSPDHSLNAPVRMDGDGEWQDWLVDESDDQETTLAESQEMGQRRAL 226

Query: 613 TTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L SL  RE  +L   R+R     +   TLE++ + + ++RER+RQIE +A  KL+
Sbjct: 227 LSGALKSLNERERHILTQRRLR-----DDPVTLEDLSQHYGISRERVRQIEVRAFEKLQ 280


>gi|167755749|ref|ZP_02427876.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
 gi|167704688|gb|EDS19267.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
          Length = 258

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 117/228 (51%), Gaps = 14/228 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  +V  N +LV+S+A+++  R     DL Q G IGL+KA E F+   G KFSTYA+  +
Sbjct: 39  KDRLVNDNTKLVLSMARRFYGREDSMDDLFQVGMIGLIKAIENFNTSFGLKFSTYAVPLI 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R + D +  I+I   +RD  +KV++       K+ REPT  E+A +L +    V 
Sbjct: 99  IGEMKRYLRD-NHQIKISRSIRDLAYKVLKVKDSYITKLNREPTINELANELEVEPSAVI 157

Query: 565 KVLKITKEPISLETPIGDEDTSHLG---DFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L  T    SL+  + ++D ++L       +DK  VS  +  I           L SL 
Sbjct: 158 EALLSTNSVSSLQEEVKNDDGNNLKMIDSITDDKTVVSRTNETIDL------YDALKSLN 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +E RV++ R+  G++      E+ K+  +++ ++ +IE KA+  L +
Sbjct: 212 QKEHRVIKQRYFEGLSQ----SEIAKELFISQAQVSRIERKALDNLHN 255


>gi|301155494|emb|CBW14960.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 280

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 78/276 (28%), Positives = 145/276 (52%), Gaps = 25/276 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++  ++  NE   ++ E   S++E      +   G+ EA+   K++V ++LR VI VA+ 
Sbjct: 15  IEGYIRAANEYPMLTAEEEKSLAE-----RLYYDGDIEAA---KKLVLSHLRFVIHVARG 66

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 67  YSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 126

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+      E   + +A +L +  E V ++  ++T   +  + P
Sbjct: 127 TTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMTGADVGFDLP 184

Query: 580 IGDEDTSHLGD-FIEDK--NAVSPLDSAIQANLRETTTR----VLASLTPREERVLRMRF 632
             D+D +++   ++EDK  N  + L+S    N  E  T      LA+L  R + +++ R+
Sbjct: 185 TDDDDEAYVPSLYLEDKSSNFAAELES---ENFEEQATEKLGTALANLDERSQEIIKARW 241

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +   TL ++  ++ V+ ERIRQ+EA A++KLK
Sbjct: 242 LD--DEKATLHDLAAKYNVSAERIRQLEANALKKLK 275


>gi|126739146|ref|ZP_01754840.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
 gi|126719763|gb|EBA16471.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
          Length = 292

 Score = 97.1 bits (240), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 123/243 (50%), Gaps = 24/243 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +  A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLTNAYMRLAISMAAKFNRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  ++R    ++ R A    +++ R    ++IA 
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQKTLFFNLRRVQAQLERRAYADGHRLDRHQLHQKIAS 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQA----- 607
           ++ +P+  V  +  +++    SL      D D     D +ED++A    + A Q      
Sbjct: 161 EIGVPLRDVEMMDGRLSGSDFSLNANQASDNDGREWIDALEDEHA----EGAEQVEGTHD 216

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LR+     + SLT RE  ++  R         TLE++G++  +++ER+RQ+EA A++
Sbjct: 217 RRQLRQWLVEAMQSLTERERFIIVAR--KLQEPFRTLEDLGQELNLSKERVRQLEAAALK 274

Query: 666 KLK 668
           K++
Sbjct: 275 KMR 277


>gi|307246764|ref|ZP_07528832.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307255748|ref|ZP_07537551.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307257933|ref|ZP_07539687.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307260200|ref|ZP_07541909.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306852339|gb|EFM84576.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306861308|gb|EFM93299.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306863580|gb|EFM95509.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865745|gb|EFM97624.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 316

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 148/285 (51%), Gaps = 42/285 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   ++ E    ++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--------RYYYDEDVEAAKQLILSHMRFVIHIARG 100

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 101 YLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVA 160

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  N++    E   +++A+ L + +E VR++  ++T + +  + P
Sbjct: 161 TTKAQR--KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSLEEVREMESRMTGQDLGFDLP 218

Query: 580 IGDED-------------TSHLGDFIEDKNAVSPLDSAIQANLRETT--TRVLASLTPRE 624
           +G++D             +S+  D +ED+          Q N + T      LA+L  R 
Sbjct: 219 VGEDDDEVYTPSMYLEDNSSNFADDLEDE----------QYNGQATAQLAYALATLDERS 268

Query: 625 ERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +++ R+   ++ +  TL+++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 269 QDIIKTRW---LDEEKATLQDLAEKYGISAERVRQLENAALKKIK 310


>gi|300690868|ref|YP_003751863.1| RNA polymerase sigma70 factor [Ralstonia solanacearum PSI07]
 gi|299077928|emb|CBJ50567.2| RNA polymerase sigma70 factor [Ralstonia solanacearum PSI07]
          Length = 876

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V     D + L   +
Sbjct: 262 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLND 321

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 322 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 380

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 381 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 419


>gi|150398305|ref|YP_001328772.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029820|gb|ABR61937.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 288

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 127/240 (52%), Gaps = 21/240 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  +++RLVIS+A K+ + GL   DL+QEG+IGL++AA +F+     +FSTYA WW
Sbjct: 40  ARNKIAMSHMRLVISMAAKFRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAM 558
           ++ ++   +      +R       K     + R   R++    ++  +   EEIA  + +
Sbjct: 100 IRASMQDYVLRNWSIVRGGTSSAQKALFFNLRRLRARLAQGDRQLTSQAVHEEIAAAIGV 159

Query: 559 PVEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL------ 609
            +  V+ +  +++    SL+ PI  GD D     DF+  +   +PL     ++L      
Sbjct: 160 SLADVQTMDARLSGNDASLQAPIGGGDPDAGARLDFLASE---APLPDEQVSDLIDGERA 216

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      L  L+ RE +++R R    ++ D  TLEE+G    +++ER+RQIE +A+ KL+
Sbjct: 217 RRWLHVALGELSEREMKIIRARR---LSEDGATLEELGVALGISKERVRQIETRALEKLR 273


>gi|220904711|ref|YP_002480023.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219869010|gb|ACL49345.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 433

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 124/231 (53%), Gaps = 17/231 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +V ++LRLV+ +A  +  R +Q  LDL+QEGN+GLM+A  KFD   G KFS YA +W+K 
Sbjct: 191 LVSSHLRLVVRIAMDFQRRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKA 250

Query: 507 AITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            I + I D    ++I    ++ K+   +   R+       +P    ++++L +  E + +
Sbjct: 251 YILKFIMDNWRMVKIGTTQVQRKLFYNLNRERQKLIMQGYDPDAAMLSERLGVTEEQINE 310

Query: 566 V-LKITKEPISLETPIGDEDTS--------HLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           +  ++    +SL   +G++            LG  IED  A + +   +++ L+     +
Sbjct: 311 MDQRLASTDMSLNAQVGEDSGGATRMDFLPALGPGIEDSLASTEIAGIVRSKLKT----I 366

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  L  +E+ +L  R  +  +   TL E+G+++ +TRER+RQ+EA+ + K+
Sbjct: 367 MPKLNEKEQYILHNR--LLSDEPITLREIGERYNITRERVRQLEARLVEKI 415


>gi|158312828|ref|YP_001505336.1| FliA/WhiG family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108233|gb|ABW10430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Frankia sp.
           EAN1pec]
          Length = 376

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 118/231 (51%), Gaps = 10/231 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +VS+  +G+ E +  + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 135 FVRLVSLP-EGDPERAALRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 193

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 194 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQSLGRS 253

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDS 603
           PT  EIA+ L M  E V + L+       +SL+ P  GD++   + D +  ++     +S
Sbjct: 254 PTVSEIARHLEMSEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD-----ES 308

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                 RE+   +L  L PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 309 LEGVEYRESLKPLLEKLPPREKRILLLRFFGNMTQSQIANELGISQMHVSR 359


>gi|56477911|ref|YP_159500.1| RNA polymerase sigma factor RpoD [Aromatoleum aromaticum EbN1]
 gi|56313954|emb|CAI08599.1| DNA-dependent RNA polymerase sigma subunits (Sigma70/32)
           [Aromatoleum aromaticum EbN1]
          Length = 663

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/158 (36%), Positives = 88/158 (55%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T  E++  LP D   +EQ+E  +A  +NMGI V D     ++    D
Sbjct: 47  KTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIRVFDEAPAAEDLLMSD 106

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++  +     +    ++   S D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 107 AVPSSVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 166

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   D++      + E+ID
Sbjct: 167 GLRHMVQAISACPTTIAEMLEITDKVARDEMRIDELID 204


>gi|325293796|ref|YP_004279660.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
 gi|1710644|sp|P50507|RP32_AGRTU RecName: Full=RNA polymerase sigma-32 factor
 gi|1143324|dbj|BAA09439.1| sigma-32 homolog [Agrobacterium tumefaciens]
 gi|325061649|gb|ADY65340.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
          Length = 300

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 127/249 (51%), Gaps = 20/249 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + ++    D++ D +  S     I+ +  ET  
Sbjct: 167 QVSEEEVISMNRRLHGDASLNAPIKASEGESGQWQDWLVDDHE-SQEAVLIEQDELETRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+LA     L  RE R+   R    +  D  TLEE+  +F ++RER+RQIE +A  K++ 
Sbjct: 226 RMLAKAMGVLNDRERRIFEAR---RLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQE 282

Query: 670 PSRSKKLRS 678
             + + L +
Sbjct: 283 AVQKEALEA 291


>gi|304320253|ref|YP_003853896.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303299155|gb|ADM08754.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 304

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 127/249 (51%), Gaps = 20/249 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E   A + ++ ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G+
Sbjct: 43  RFKEHEDPDAAQRLITSHLRLVAKIAMGYRGYGLPTGEVISEGNVGLMQAVKKFDPDKGF 102

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE 550
           + STYAMWW++ +I   I      ++I      K  K+    R++  +I    + +  PE
Sbjct: 103 RLSTYAMWWIRASIQEYILRSWSLVKIGTTAAQK--KLFFNLRKLKGQIDAVDEGDMRPE 160

Query: 551 E---IAKKLAMPVEGVRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDS 603
           E   IA +L +  + V  +  ++     SL +P+   GD   +   D++ D+NAV+    
Sbjct: 161 EVELIATRLGVTEDEVISMNRRMAGSDNSLNSPMRSDGD-GGAEWQDWLVDENAVNAESQ 219

Query: 604 AIQANLRETTTRVL----ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            ++ +  ET   +L      L  RE  +L  R         TLEE+  ++ V+RERIRQI
Sbjct: 220 LVKDDEFETRMELLQEAMVDLNDRERHILTERRLT--ENPKTLEELSGEYGVSRERIRQI 277

Query: 660 EAKAIRKLK 668
           E +A  KL+
Sbjct: 278 EVRAFEKLQ 286


>gi|84515923|ref|ZP_01003284.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510365|gb|EAQ06821.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 277

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 129/256 (50%), Gaps = 24/256 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLITAYMRLAISMASKFKRYGAPMNDLIQEASVGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-----------EEI 552
           +K +I   +      +R       K   +    RR+  +++RE              E+I
Sbjct: 86  IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARLEREAAAEGLHLETHELHEKI 143

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIED---KNAVSPLDSAIQA 607
           A ++ +P+  V+ +  +++    SL      ED      D +ED   + A    +S    
Sbjct: 144 AIEVGVPLHDVQMMDGRLSGSDFSLNATQSMEDEGREWIDALEDDAPQAAEKVENSHDTD 203

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            LR+     L +L  RE+ ++R R    +  D  TLE +G +  +++ER+RQ+EA A  K
Sbjct: 204 TLRQWLVTALTALNDREQFIVRER---KLRDDPRTLESLGSELGLSKERVRQLEAAAFGK 260

Query: 667 LKHP--SRSKKLRSFL 680
           ++    ++S +++SF 
Sbjct: 261 MRKSLEAQSTEVQSFF 276


>gi|148261701|ref|YP_001235828.1| RNA polymerase factor sigma-32 [Acidiphilium cryptum JF-5]
 gi|326405194|ref|YP_004285276.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
 gi|146403382|gb|ABQ31909.1| RNA polymerase, sigma 32 subunit, RpoH [Acidiphilium cryptum JF-5]
 gi|325052056|dbj|BAJ82394.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
          Length = 296

 Score = 97.1 bits (240), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 125/249 (50%), Gaps = 21/249 (8%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   A  ++V ++LRLV  +A  Y   GL   +LI EGN+G+M+A ++FD   G++ +TY
Sbjct: 37  EDQAAAHKLVTSHLRLVAKIAMGYRGYGLPLGELISEGNVGMMQAVKRFDPERGFRLATY 96

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR------EPTP-EEI 552
           AMWW++ AI   I      +++      K  K+    RR+  +++       +P   E+I
Sbjct: 97  AMWWIRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIEDGDMQPEQVEKI 154

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIED-----KNAVSPLDSAIQ 606
           A+ L +P + V  +  ++T    SL  PI  +      D++ D     + A+   D    
Sbjct: 155 ARVLGVPEQDVVSMNRRLTAPDHSLNAPIRMDGEGEWQDWLVDDADSQEEAIG--DHEEM 212

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIR 665
              R      L +L  RE  +L  R    +  D  TLE++ +Q+ ++RER+RQIE +A  
Sbjct: 213 TGRRALLATALKTLNDRERHILIQR---RLKDDPTTLEDLSQQYNISRERVRQIEVRAFE 269

Query: 666 KLKHPSRSK 674
           KL+   +++
Sbjct: 270 KLQKSMKAQ 278


>gi|163803403|ref|ZP_02197278.1| RNA polymerase sigma factor [Vibrio sp. AND4]
 gi|159172807|gb|EDP57652.1| RNA polymerase sigma factor [Vibrio sp. AND4]
          Length = 285

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 79/279 (28%), Positives = 147/279 (52%), Gaps = 28/279 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ +    ++E  H      KGE +A+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRSANSYPMLTADEERGLAERLHY-----KGEIDAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++     + + P
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMP 185

Query: 580 IGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRM 630
           + D+D S+       ++EDK+  S +   I+A   E  T       LASL  R +R++R 
Sbjct: 186 MDDDDNSNSYTAPMVYLEDKS--SDVADNIEAANWEAHTNNRLGHALASLDERSQRIVRS 243

Query: 631 RFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+   ++ D  TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 244 RW---LDDDKSTLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|222872026|gb|EEF09157.1| predicted protein [Populus trichocarpa]
          Length = 425

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 63/164 (38%), Positives = 93/164 (56%), Gaps = 13/164 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI V      E    +E
Sbjct: 38  LKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIAV-----YEQAPDAE 92

Query: 91  DSL--DLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             L  D A SA++     ++ +      DS    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 93  TLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 152

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIEAG   M+ ++   P+T   ++   + + +    + E +D
Sbjct: 153 AKRIEAGLKDMVMAISACPVTISEILASAERVANEEIKIDEFVD 196


>gi|121488755|emb|CAJ18262.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 51/166 (30%), Positives = 91/166 (54%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D   EG  G +KAA++ D   G+KF +YA+WW +Q+  +++A+QS  +R+P++    ++K
Sbjct: 1   DXXNEGXXGXIKAAKRXDETRGFKFISYAVWWXRQSXLQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYXQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  F IGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLXPREADVIRSYFXIGMD 165


>gi|325579283|ref|ZP_08149239.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159518|gb|EGC71652.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 293

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/276 (28%), Positives = 146/276 (52%), Gaps = 25/276 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  NE   ++ E   S++E      +   G+ EA+   K++V ++LR VI VA+ 
Sbjct: 28  IEAYIRAANEYPMLTAEEEKSLAE-----RLYYDGDIEAA---KKLVLSHLRFVIHVARG 79

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 80  YSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 139

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+      E   + +A +L +  E V ++  ++T   +  + P
Sbjct: 140 TTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMTGADVGFDLP 197

Query: 580 IGDEDTSHLGD-FIEDK--NAVSPLDSAIQANLRETTTR----VLASLTPREERVLRMRF 632
             D+D +++   ++EDK  N  + L+S    N  E  T      LA+L  R + +++ R+
Sbjct: 198 TDDDDEAYVPSLYLEDKSSNFAAELES---ENFEEQATEKLGTALANLDERSQDIIKARW 254

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +   TL ++  ++ V+ ERIRQ+EA A++KLK
Sbjct: 255 LD--DEKATLHDLAAKYNVSAERIRQLEANALKKLK 288


>gi|304311558|ref|YP_003811156.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
 gi|301797291|emb|CBL45511.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
          Length = 285

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 121/234 (51%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V A+LR V+ VA+ Y   GLQ  DL+QEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 50  AARQLVLAHLRFVVHVARGYNGYGLQLSDLVQEGNVGLMKAVKRFDPTMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R+ +R    +  +     IA +L +  E 
Sbjct: 110 IKAEIHEFILRNWRIVKIATTKSQRKLFFNLRSHKRRLGVLSGDEV-NMIATELNVSPED 168

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT----R 615
           VR++  ++     + + P+   DE  S    +  +  ++ P      A   + TT     
Sbjct: 169 VREMEGRLAAHDTAFDAPVDADDESASQAPVYYLEDASMDPAHQLEDAQWTDNTTDRLQL 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + SL  R   +L+ R+    N D  TL ++  Q+ V+ ERIRQ+EA A++K+K
Sbjct: 229 AMNSLDERSRDILQQRW---FNDDKATLHDLAAQYSVSAERIRQLEANAMKKIK 279


>gi|90407357|ref|ZP_01215542.1| RpoD protein [Psychromonas sp. CNPT3]
 gi|90311508|gb|EAS39608.1| RpoD protein [Psychromonas sp. CNPT3]
          Length = 282

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/269 (27%), Positives = 141/269 (52%), Gaps = 16/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I   I+S++    +S SE + +   +  +G+ +A+   K++V ++LR V  +AK Y   G
Sbjct: 16  IEAYIQSVNKFAMLSASEEKALAERLFYEGDLDAA---KKLVMSHLRFVAYIAKSYAGYG 72

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMR 526
           L   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     +
Sbjct: 73  LAIADLIQEGNVGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVIRNWRVVKIATTKAQ 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT 585
            K+   +R A++      ++   E +A  L +  + V ++  ++     S +    D+D 
Sbjct: 133 RKLFFNLRKAKKRLGWFSKDEV-ENVANNLNVSTKDVLEMESRLNGHDYSFDLTGDDDDE 191

Query: 586 SHLG--DFIEDKNAVSPLDSAI---QANLRETTTRVLASLTPREERVLRMRFGIGMN-TD 639
           +      ++EDKNA   L   +   Q+N++      L+SL  R + ++  R+   +N   
Sbjct: 192 NCFAPVQYLEDKNADVALLVEVENSQSNMKRQLHSALSSLDERSQDIISSRW---LNEPK 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  ++ ++ ER+RQ+EA AI+KL+
Sbjct: 249 ATLHDLAARYSISAERVRQLEANAIKKLQ 277


>gi|163747420|ref|ZP_02154772.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
 gi|161379273|gb|EDQ03690.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
          Length = 298

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/242 (32%), Positives = 118/242 (48%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  NKI        R     EIA +L
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSGQK--KLFFNLRKAKNKIGALEEGDLRPENVTEIATQL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +   E V    +++    SL   +G   E T    D++ED++A    D A +  L   R
Sbjct: 167 GVTEAEVVSMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYAERDELETRR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L  L  RE+ +L  R     +   TLE++  Q+ V+RERIRQIE +A  KL+  
Sbjct: 227 EMLADALDVLNDREKDILTQRR--LSDETVTLEDLSTQYDVSRERIRQIEVRAFEKLQKR 284

Query: 671 SR 672
            R
Sbjct: 285 MR 286


>gi|297539272|ref|YP_003675041.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera sp. 301]
 gi|297258619|gb|ADI30464.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera sp. 301]
          Length = 285

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/237 (33%), Positives = 128/237 (54%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LRLV S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++AM W
Sbjct: 49  AARQLIVSHLRLVASIARGYNGYGLPQSDLIQEGNIGLMKAVKRFDPERGVRLVSFAMHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAM- 558
           +K  +   I      ++I     + K+   +R+ +   N ++    P E   IAK+L + 
Sbjct: 109 IKAEMHEYIVRNWRMVKIATTKAQRKLFFNLRSMKTGLNSLQ----PAEVAHIAKELNVK 164

Query: 559 PVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDS--AIQANLRETT 613
           P E +    ++    ISLE  I    DE  S +  ++ D+  + PL++  + Q  + ETT
Sbjct: 165 PEEVLEMEARLNGHEISLEANIDDDSDEQYSPIA-YLPDE-GLEPLEALESKQIEIAETT 222

Query: 614 --TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L +L  R  RV+  R+ +      TL E+  +F V+ ERIRQIE KA++K+K
Sbjct: 223 GLANALQNLDDRSRRVVEARW-LQDQGGKTLHELADEFGVSAERIRQIEQKAMQKMK 278


>gi|219112653|ref|XP_002178078.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410963|gb|EEC50892.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 358

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 125/250 (50%), Gaps = 30/250 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL--QF--LDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           AK ++V +NLR+V SV   Y   GL  Q+   D++QEG I L++AAEKF+   G+KFSTY
Sbjct: 100 AKNQLVTSNLRMVQSVVNTYIRNGLTAQYNAGDMMQEGIIALIRAAEKFEPDRGWKFSTY 159

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM+WV+ ++ RS   QS  I +P  + +   ++++  R M   + R+P+  E+  ++ + 
Sbjct: 160 AMYWVRASVKRSQIYQSRVITVPQRLHENHKRLLKVEREMEADLGRKPSRIELGAEIGLS 219

Query: 560 --------------VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                          + + + L  +K P+S     GD     L + I  K   +  DS  
Sbjct: 220 KLQVDRCFAAMEQRCQSLDQKLSNSKRPMS-----GDTSKDTLMEIIGSKTEGNDFDSLN 274

Query: 606 QANLRETTTRVLA-SLTPREERVLRMRFGI------GMNTDHTLEEVGKQFCVTRERIRQ 658
           +  LRE     L   L P E  +L +R+G        +    T+ E+ +   +  +++R+
Sbjct: 275 RIFLREDLIETLHRHLDPAEVELLLLRYGFKEVASSKLGGQPTIAELSRTVGLKPDKVRR 334

Query: 659 IEAKAIRKLK 668
           +  ++++ LK
Sbjct: 335 MINRSLKHLK 344


>gi|163941643|ref|YP_001646527.1| sporulation sigma factor SigG [Bacillus weihenstephanensis KBAB4]
 gi|229134713|ref|ZP_04263522.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|163863840|gb|ABY44899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228648759|gb|EEL04785.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|322510150|gb|ADX05464.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 137/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 36  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 92

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 93  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 151

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 152 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 211

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D ++D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 212 DPIFVMDQLKDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 266

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 267 EIG----ISQAQVSRLEKSAIKQM 286


>gi|42782996|ref|NP_980243.1| sporulation sigma factor SigG [Bacillus cereus ATCC 10987]
 gi|49186753|ref|YP_030005.1| sporulation sigma factor SigG [Bacillus anthracis str. Sterne]
 gi|49478441|ref|YP_037965.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141585|ref|YP_085244.1| sporulation sigma factor SigG [Bacillus cereus E33L]
 gi|118479123|ref|YP_896274.1| sporulation sigma factor SigG [Bacillus thuringiensis str. Al
           Hakam]
 gi|196038711|ref|ZP_03106019.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|222097349|ref|YP_002531406.1| sporulation sigma factor sigg [Bacillus cereus Q1]
 gi|228928952|ref|ZP_04091984.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935219|ref|ZP_04098045.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228947623|ref|ZP_04109913.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987048|ref|ZP_04147173.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229092950|ref|ZP_04224083.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|229123417|ref|ZP_04252621.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|229186144|ref|ZP_04313313.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|254683387|ref|ZP_05147247.1| sporulation sigma factor SigG [Bacillus anthracis str. CNEVA-9066]
 gi|254739809|ref|ZP_05197502.1| sporulation sigma factor SigG [Bacillus anthracis str. Kruger B]
 gi|254750999|ref|ZP_05203038.1| sporulation sigma factor SigG [Bacillus anthracis str. Vollum]
 gi|254757943|ref|ZP_05209970.1| sporulation sigma factor SigG [Bacillus anthracis str. Australia
           94]
 gi|301055394|ref|YP_003793605.1| RNA polymerase sigma-G factor [Bacillus anthracis CI]
 gi|42738923|gb|AAS42851.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10987]
 gi|49180680|gb|AAT56056.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Sterne]
 gi|49329997|gb|AAT60643.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51975054|gb|AAU16604.1| RNA polymerase sigma-G factor [Bacillus cereus E33L]
 gi|118418348|gb|ABK86767.1| RNA polymerase, sigma subunit, RpsG/SigG [Bacillus thuringiensis
           str. Al Hakam]
 gi|196030434|gb|EDX69033.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|221241407|gb|ACM14117.1| RNA polymerase sigma-G factor [Bacillus cereus Q1]
 gi|228597320|gb|EEK54971.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|228660193|gb|EEL15829.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|228690454|gb|EEL44238.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|228772642|gb|EEM21083.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228812143|gb|EEM58474.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824384|gb|EEM70190.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830759|gb|EEM76364.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|300377563|gb|ADK06467.1| RNA polymerase sigma-G factor [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327802|gb|ADY23062.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 289

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 33  RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 89

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 90  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 149 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 208

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 209 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 263

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 264 EIG----ISQAQVSRLEKSAIKQM 283


>gi|293391709|ref|ZP_06636043.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952243|gb|EFE02362.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 616

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 92/158 (58%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D  D+   A+     L   +    R+TD PVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 70  NITDE-DVVEEATQ---VLSSVEAELGRTTD-PVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   + +++   P     LI   D + +G   L ++I
Sbjct: 125 EGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLI 162


>gi|86137868|ref|ZP_01056444.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85825460|gb|EAQ45659.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 298

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/254 (30%), Positives = 125/254 (49%), Gaps = 29/254 (11%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A   MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +
Sbjct: 43  EKEDSGAAHRMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKK 555
           TYAMWW++ +I   +      +++     + K+   +R A+ R+    + +  PE +AK 
Sbjct: 103 TYAMWWIRASIQEYVLRSWSMVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAK- 161

Query: 556 LAMPVEGVRKVLKITKEPI------------SLETPIGD--EDTSHLGDFIEDKNAVSPL 601
                  +   L +T++ +            SL   +G   E T    D++ED++A    
Sbjct: 162 -------IAHDLGVTEDEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAG 214

Query: 602 DSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           D   +  L   RE   + L  L  RE+ +L  R  +  N   TLEE+  Q+ V+RERIRQ
Sbjct: 215 DYEARDELEARRELLGQALEVLNDREKDILTKRR-LAENV-QTLEELSAQYSVSRERIRQ 272

Query: 659 IEAKAIRKLKHPSR 672
           IE +A  KL+   R
Sbjct: 273 IEVRAFEKLQKKMR 286


>gi|255505890|ref|ZP_05348671.3| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
 gi|255265373|gb|EET58578.1| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
          Length = 238

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 123/229 (53%), Gaps = 16/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++VE NL LV ++AK++T RG    DL Q G+IGL+KA + F+     KFSTYA+  
Sbjct: 18  AREQLVEENLGLVFTIAKRFTGRGTDVEDLFQIGSIGLLKAIDNFNLSYDVKFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++   +      ++  K+ REPT EE++ ++ +  E +
Sbjct: 78  IAGEIRRFLRDDGM-LKVSRSLKETAGRAAAAREQLEKKLGREPTMEELSGEVGITREEI 136

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP--LDSAIQANLRETTTRVLAS 619
              ++   E  SL  P+  GD    +L D IE+K +++   LD+ +        T V+  
Sbjct: 137 VLAMEAAAEVESLHRPVYQGDGTAIYLEDRIEEKESMNEKVLDNMV-------LTEVMEK 189

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L P E+ ++ MR+      D T  +V +    T+ ++ ++E K ++K++
Sbjct: 190 LEPEEQFLIIMRY----FKDKTQSQVAELLGRTQVQVSRMEKKILKKMR 234


>gi|323099956|gb|ADX23556.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 36  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 92

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 93  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 151

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 152 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 211

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 212 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 266

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 267 EIG----ISQAQVSRLEKSAIKQM 286


>gi|229075660|ref|ZP_04208642.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
 gi|229098374|ref|ZP_04229319.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|229117400|ref|ZP_04246776.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228666010|gb|EEL21476.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228684991|gb|EEL38924.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|228707436|gb|EEL59627.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
          Length = 289

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 33  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 89

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 90  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 149 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 208

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 209 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 263

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 264 EIG----ISQAQVSRLEKSAIKQM 283


>gi|317056324|ref|YP_004104791.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315448593|gb|ADU22157.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ruminococcus
           albus 7]
          Length = 256

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/225 (31%), Positives = 119/225 (52%), Gaps = 9/225 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++++ NLRLV+SV +KY+       DL Q G +GL+KA + FD  L  +FSTYA+  
Sbjct: 38  AREKLIKGNLRLVLSVLQKYSGGKENPDDLFQVGVVGLIKAIDNFDVGLNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    IR+   MRD  ++V++   R   + +REP+ +EIA+        +
Sbjct: 98  ILGEIKRYMRDFR-PIRVSRSMRDLAYRVMQAKERFIAEKQREPSIDEIAEITNEKRADI 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L+   +P+S+  P+  +    L   I D+   S  DS+    L  T    L  L PR
Sbjct: 157 VTALESVTDPVSIYEPVYTDGGDPL--CIADQICDSTDDSSWLEEL--TMKEALKELRPR 212

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ +L +RF  G    HT  EV  +  +++ ++ ++E  A+ K+K
Sbjct: 213 EKNILFLRFFKG----HTQVEVAHEIGISQAQVSRLEKNALNKIK 253


>gi|288917890|ref|ZP_06412250.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
 gi|288350679|gb|EFC84896.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 118/231 (51%), Gaps = 10/231 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +VS+  +G+ E +  + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 151 FARLVSLP-EGDPERAALRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 209

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 210 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQSLGRS 269

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDS 603
           PT  EIA+ L M  E V + L+       +SL+ P  GD++   + D +  ++     +S
Sbjct: 270 PTVSEIARHLEMTEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD-----ES 324

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                 RE+   +L  L PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 325 LEGVEYRESLKPLLEKLPPREKRILLLRFFGNMTQSQIANELGISQMHVSR 375


>gi|296114957|ref|ZP_06833602.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978475|gb|EFG85208.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
          Length = 299

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 125/250 (50%), Gaps = 20/250 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ EA+    ++V ++LRLV  +A  Y   GL   +LI EGNIG+M+A  +FD   G++
Sbjct: 43  KGDTEAA---HKLVTSHLRLVAKIAMGYRGYGLPVGELISEGNIGMMQAVRRFDPERGFR 99

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE 551
            +TYAMWW++ AI   I      ++I      K  K+    RR+  +++     +  PE+
Sbjct: 100 LATYAMWWIRAAIQEYILHSWSLVKIGTTAAQK--KLFFNLRRLKGQMQAIDDGDLQPEQ 157

Query: 552 ---IAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFI---EDKNAVSPLDSA 604
              IAK L +P + V  + +    P  SL  P+  +      D++    D    +  ++ 
Sbjct: 158 VDKIAKSLGVPEQDVVNMNRRLSAPDHSLNAPLRTDSEGEWQDWLVDDHDNQEQTLAENE 217

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKA 663
             +  +      + SL  RE  +L  R    +  D  TLE++   + ++RER+RQIE +A
Sbjct: 218 EYSGRKALLANAMQSLNERERHILTER---RLKDDPATLEDLSHVYNISRERVRQIEVRA 274

Query: 664 IRKLKHPSRS 673
             K+++  ++
Sbjct: 275 FEKVQNAMKA 284


>gi|86359605|ref|YP_471497.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283707|gb|ABC92770.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 287

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 124/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 40  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ R  T        +EIA  L
Sbjct: 100 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLARGDTQLTLQSIHQEIAAAL 157

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANL---- 609
            + +  V+ +  +++    SL+ P   GD +++   DF+   +   PL     +N+    
Sbjct: 158 GVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDD---PLPDEQVSNMIDGE 214

Query: 610 --RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             R      L  L  RE +++  R    +  D  TLEE+G    +++ER+RQIE++A+ K
Sbjct: 215 RRRVWLASALKHLNEREMKIISAR---RLAEDGATLEELGADLGISKERVRQIESRAMEK 271

Query: 667 LK 668
           L+
Sbjct: 272 LR 273


>gi|307546061|ref|YP_003898540.1| RNA polymerase sigma factor RpoD [Halomonas elongata DSM 2581]
 gi|307218085|emb|CBV43355.1| RNA polymerase sigma factor RpoD [Halomonas elongata DSM 2581]
          Length = 615

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/150 (38%), Positives = 89/150 (59%), Gaps = 11/150 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +++G++T  E+N  LP D    +Q+ED + M+++MGINVV+      E   ED
Sbjct: 12  KELIARGKEQGFLTYAEVNDHLPEDIADPDQVEDIIGMINDMGINVVE------EAPDED 65

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTD-----DPVRMYLREMGSIELLSREGEIAIAKRI 146
           +L +A  +++ S   +     A   +D     DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  TLMMADQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELND 176
           E G   +M++L   P    +++   D   D
Sbjct: 126 EEGTREVMSALAYLPGAVDSILEAYDATQD 155


>gi|154503257|ref|ZP_02040317.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
 gi|153796251|gb|EDN78671.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
          Length = 238

 Score = 96.7 bits (239), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 132/244 (54%), Gaps = 16/244 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++ K       A++++VE N+ L+  V K++  RG++  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIEKSHNGDKEAREQLVEENIGLIWCVVKRFYGRGIEAEDLFQIGSIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +++ +T  +M++ + REPT
Sbjct: 63  DLSYDVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKELSYRIFQTREKMTDGLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSP--LDSA 604
            EE+++++ +  E + + ++ + E  SL  PI  ++ S +   D +E+K       LD  
Sbjct: 122 LEELSQEMGVEKEELVQAMEASGEVESLYRPIHQKEGSEISLLDKLEEKEHREEKILDRM 181

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +   L       L  L  +E  ++ +R+      + T   VGK+  +++ ++ ++E K I
Sbjct: 182 LLGQL-------LEKLDGQERTLIYLRY----FAEKTQSAVGKEMGISQVQVSRMEKKII 230

Query: 665 RKLK 668
           + L+
Sbjct: 231 QNLR 234


>gi|228973923|ref|ZP_04134498.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980512|ref|ZP_04140822.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228779332|gb|EEM27589.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228785789|gb|EEM33793.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
          Length = 289

 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 33  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 89

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 90  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 149 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 208

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 209 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 263

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 264 EIG----ISQAQVSRLEKSAIKQM 283


>gi|209519627|ref|ZP_03268417.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
 gi|209499913|gb|EDZ99978.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
          Length = 311

 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 125/250 (50%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP+EI        +G
Sbjct: 132 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDEI--------DG 179

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + + L + +E ++ +ET +   D +  G   + + + +P+  A  A+     T VLAS  
Sbjct: 180 LARELNVKREEVAEMETRLSGGDIALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQ 237

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L PR  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 238 RDRLHSDGIASALDALDPRSRRIIEARWLKVADDGSGGSTLH---ELADEFGVSAERIRQ 294

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 295 IEASAMKKMR 304


>gi|228992638|ref|ZP_04152564.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
 gi|228998684|ref|ZP_04158271.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|229006186|ref|ZP_04163872.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228755027|gb|EEM04386.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228761152|gb|EEM10111.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|228766970|gb|EEM15607.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
          Length = 259

 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 134/265 (50%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI   G 
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +    +    +DK         +   L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 DPIFVMDQLSDDKQRDEQWVEELA--LKEGMKR----LNDREKMIIRKRFFQGKTQMEVA 232

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AI+++
Sbjct: 233 EEIG----ISQAQVSRLEKSAIKQM 253


>gi|170742915|ref|YP_001771570.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168197189|gb|ACA19136.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 293

 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 127/239 (53%), Gaps = 19/239 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 41  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPERDVRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E   +EI +++A  +
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTDERVGDEIHRRIATAI 158

Query: 561 EGVRKVL-----KITKEPISLETPIGDED--TSHLGDFIEDKNAVS--PLDSAIQANLRE 611
              R+ +     +++   +SL  PI DE   ++   DF+ D + +    +  A+    R 
Sbjct: 159 GVSREDVALMDARLSGPDMSLNAPITDEGDASAERVDFLVDTSPLPDEAVSDAVDGERRL 218

Query: 612 TTTR-VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T  R  L  L+ RE R+L  R    +  D  TLE +G +  +++ER+RQIE +A+ KL+
Sbjct: 219 TWLRQALTVLSERELRILHER---RLAEDQATLEALGHRLGISKERVRQIENRALEKLR 274


>gi|229031535|ref|ZP_04187535.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
 gi|228729824|gb|EEL80804.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
          Length = 289

 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 135/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 33  RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 89

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D    IR+   +
Sbjct: 90  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDND-PIRVSRSL 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 149 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 208

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 209 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 263

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 264 EIG----ISQAQVSRLEKSAIKQM 283


>gi|51246044|ref|YP_065928.1| RNA polymerase sigma-B factor [Desulfotalea psychrophila LSv54]
 gi|50877081|emb|CAG36921.1| probable RNA polymerase sigma-B factor [Desulfotalea psychrophila
           LSv54]
          Length = 332

 Score = 96.3 bits (238), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 123/237 (51%), Gaps = 20/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   +V +NLRLV+ VA  +    +Q F+DLIQEGN+GL++A +KFD   G KFS YA +
Sbjct: 80  AAYTLVSSNLRLVVKVAMDFQKYWMQNFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAY 139

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PV 560
           W++  + + I D    ++I     + K+   +   +++      +P P+ +A++L +   
Sbjct: 140 WIRAYVLKFIMDNWRLVKIGTTQAQRKLFFSLNKEKKLLESQGFDPKPKLLAERLNVREK 199

Query: 561 EGVRKVLKITKEPISLETPI----GDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETT 613
           E +    ++    +SLE+P+     DE  S L   G  IE   A       I+  L E  
Sbjct: 200 EVIEMGQRMDNWDVSLESPVRSDSDDEQKSFLPSNGPGIESVVA----GKEIKVKLTELI 255

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  +L  +E  +L  R    + TD   TL+ +  +F ++RER+RQIE   ++K+K
Sbjct: 256 DVLKVNLNDKERMILEKR----LLTDEPLTLQNIADKFGISRERVRQIEVNLLKKMK 308


>gi|315498780|ref|YP_004087584.1| RNA polymerase, sigma 32 subunit, rpoh [Asticcacaulis excentricus
           CB 48]
 gi|315416792|gb|ADU13433.1| RNA polymerase, sigma 32 subunit, RpoH [Asticcacaulis excentricus
           CB 48]
          Length = 344

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 118/240 (49%), Gaps = 21/240 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 102 AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWW 161

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K AI   +      +++      K  K+    R++ ++I        R     +IA KL
Sbjct: 162 IKAAIQEYVLRSWSLVKMGTTAAQK--KLFFNLRKVKSEISALEEGDMRHEQVAQIATKL 219

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V  + +    P  SL  P+   E  S   D++ D +  +P    + A+  E   
Sbjct: 220 GVSEDDVISMNRRMSSPDSSLNAPLRVSEGDSEWQDWLADDS--TPSQETVLADSEEYKL 277

Query: 615 RV------LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+      +  L  RE  +L  R         TLE++  +F V+RER+RQIE +A  KL+
Sbjct: 278 RMSLLEEAMGELNERERAILTARR--LQENPTTLEDLADRFGVSRERVRQIEVRAFEKLQ 335


>gi|162457339|ref|YP_001619706.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
 gi|161167921|emb|CAN99226.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
          Length = 443

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 124/229 (54%), Gaps = 11/229 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ANLRLV+ +A +Y       +DLIQEGNIGLM+A +++D   G K S+YA WW++  
Sbjct: 204 LVTANLRLVVKLAYEYRRAYKNIMDLIQEGNIGLMQAVKRYDPYRGVKLSSYAAWWIRAY 263

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           I R I +    +++     + K+   +   +   + +  EPT  EIAK+L++  + V  +
Sbjct: 264 ILRFILNNWRLVKLGTTQAQRKLFFNLNKEKAKLSAMGIEPTAAEIAKRLSVEEKEVVDM 323

Query: 567 -LKITKEPISLETPIGDEDTSHLGDF-IEDKNAVSPLDSAIQAN-----LRETTTRVLAS 619
             ++     SL+ P+GD +   +    +   +  SP D+A +A+     + +  ++   +
Sbjct: 324 DRRLASGEASLDAPVGDLEGRTIPRVELLVSSGASP-DTAFEASEMGMLVHDRLSKFRET 382

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  ++  +   R  +      TL+E+G +F ++RER+RQ+EA+   KL+
Sbjct: 383 LKGKDVIIFDKR--MAAEDPLTLQELGNEFGISRERVRQLEARLQSKLR 429


>gi|160871836|ref|ZP_02061968.1| alternative sigma factor RpoH [Rickettsiella grylli]
 gi|159120635|gb|EDP45973.1| alternative sigma factor RpoH [Rickettsiella grylli]
          Length = 290

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 18/239 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++  NLR V+ +A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 50  AAKKLIITNLRFVVHIAQTYMGYGLALADLIQEGNIGLMKAVKRFDPKVGVRLISFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   I      ++I      +  K+    R+M  ++    +   E +A  L +  E
Sbjct: 110 IKAEIQEFILRNWRIVKIATTKAQR--KLFFNLRKMKKRLGWFNQNEIEAVAHDLGVKPE 167

Query: 562 GVRKV-LKITKEPISLETPIGDEDTS----------HLGDFIEDKNAVSPLDSAIQANLR 610
            VR++  ++    +SL+    D + +          H  D   D   +    ++ ++N  
Sbjct: 168 TVREMEFRLASNDMSLDISHDDPNEAKSTRYPLLDIHFEDNRYDPARLLEASNSTESN-H 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +   + L  L  RE+ ++R R+   M    TL+E+ +++ V+ ERIRQ+E KA++ L+H
Sbjct: 227 DNLYKALTQLDEREQNIIRDRW--LMEPKMTLQELAQRYHVSAERIRQLEQKAMKALRH 283


>gi|254511947|ref|ZP_05124014.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
 gi|221535658|gb|EEE38646.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
          Length = 298

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 123/248 (49%), Gaps = 29/248 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVE 561
           ++ +I   +      +++     + K+   +R A+ R+    + +  PE +A+       
Sbjct: 109 IRASIQEYVLRSWSMVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAR------- 161

Query: 562 GVRKVLKITKEPI------------SLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
            + + L +T+E +            SL   +G   E T    D++ED++A    D   + 
Sbjct: 162 -IAEDLGVTEEEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARD 220

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            L   RE     L  L  RE+ +L  R    M+   TLEE+  Q+ V+RERIRQIE +A 
Sbjct: 221 ELEARRELLAAALDVLNDREKDILTQRR--LMDQVVTLEELSTQYNVSRERIRQIEVRAF 278

Query: 665 RKLKHPSR 672
            KL+   R
Sbjct: 279 EKLQKKMR 286


>gi|197116970|ref|YP_002137397.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
 gi|197086330|gb|ACH37601.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
          Length = 285

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 121/241 (50%), Gaps = 14/241 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ EA+     ++ ANLR V+ +A +Y + G++ LDLIQEGNIGLM A  KFD   G 
Sbjct: 39  REGDLEAA---HRLITANLRFVVKIAGEYRSYGMKMLDLIQEGNIGLMMAVRKFDPDKGV 95

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +  +YA+WW++  I   I      ++I     + K+   +  A++    +  E      A
Sbjct: 96  RLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQRKLFFKLNQAKQAIVNMTGEGDLHAAA 155

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L +     R++ +  +  +SL+  + + +    G F+E    +      + A  +ETT
Sbjct: 156 ISLDVKDNEAREMEQRLRGELSLDVEMFEGEGG--GTFLESLPDLRQNQEEMLAERQETT 213

Query: 614 ------TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                    L +L  +E+ V+  R  +      TL+E+   F ++RER+RQIE  A++K+
Sbjct: 214 ILERNVASALENLNEKEKFVIEQR--VAAEDPMTLQEIADHFSISRERVRQIEEGALKKM 271

Query: 668 K 668
           K
Sbjct: 272 K 272


>gi|303232785|ref|ZP_07319470.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
 gi|302481271|gb|EFL44346.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
          Length = 287

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 122/227 (53%), Gaps = 7/227 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V  +L L   +A K+ NRG    DLIQ   IGL+KA ++FD   G +F+T+A   
Sbjct: 59  ARNQLVLNHLNLARFLASKFKNRGESLDDLIQVATIGLIKAIDRFDIDRGLEFTTFATPT 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+S ++R+P  +++   KV +    ++ K++  P+ EEIA++L + V+ V
Sbjct: 119 ILGEIKRHFRDRSWSVRVPRRLQELSSKVSQATDMLTEKLQHSPSVEEIARELDVSVDEV 178

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + ++ ++    +SL+ P  D D       + D  A S  D     + +     ++ + T
Sbjct: 179 LEAMESSRAYSSVSLDVPTVDNDDGSAATSVLDTYA-SVDDDLESCDDKLVLQEIIKNCT 237

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++RMRF  GM    T  E+  +  V++ ++ ++    +RKL+
Sbjct: 238 EREQQIIRMRFLDGM----TQVEIADKLQVSQVQVSRLLRNTLRKLQ 280


>gi|111225338|ref|YP_716132.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
 gi|111152870|emb|CAJ64617.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
          Length = 299

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 113/222 (50%), Gaps = 9/222 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ E +  + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ ++FD   G +
Sbjct: 66  EGDAERAAIRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVE 125

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R PT  EIA+ 
Sbjct: 126 FSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQTLGRSPTVSEIARH 185

Query: 556 LAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           L M  E V + L+       +SL+ P  GD++   + D +  ++     +S      RE+
Sbjct: 186 LQMSEEDVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD-----ESLEGVEYRES 240

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 241 LKPLLEKLPPREKRILLLRFFGNMTQSQIATELGISQMHVSR 282


>gi|300023529|ref|YP_003756140.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525350|gb|ADJ23819.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 296

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 123/255 (48%), Gaps = 15/255 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  + E S A +++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++FD   G+
Sbjct: 41  RWQQHEDSDAAEKLVTSHLRLVARIAMGYRGYGLPIGEVISEGNVGLMQAVKRFDPEKGF 100

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW++ +I   I      +++      K  K+    RR  ++++       R  
Sbjct: 101 RLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRAKSQLQALDDGDLRPE 158

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             + IA KL +P E V  + +      SL  PI  + ++    D++ D            
Sbjct: 159 HVKAIATKLGVPEEDVVSMNRRLGGDASLNAPIRAESESGEWQDWLVDDTPTQEDRLVED 218

Query: 607 ANLRETTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             LR   + +   L+ L  RE RV   R         TLEE+  +F V+RERIRQIE +A
Sbjct: 219 EELRRRKSYLSSALSVLNDRERRVFEQRR--LAEEPATLEELSAEFGVSRERIRQIEVRA 276

Query: 664 IRKLKHPSRSKKLRS 678
             K++    S   R+
Sbjct: 277 FEKVQKAVTSTARRA 291


>gi|255019642|ref|ZP_05291721.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970865|gb|EET28348.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
          Length = 285

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 128/247 (51%), Gaps = 23/247 (9%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++ +R G+     A+  +V A++ LV ++A+ Y N+GL   DL+QEG +GLM+A ++F 
Sbjct: 46  VIAQIRSGD---EAARATLVSAHMPLVRAIARSYRNKGLSQEDLVQEGYMGLMRAMDRFQ 102

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             LG +FS+YA WW+++A+ R++  ++  IR+P ++   +H        +  K   E   
Sbjct: 103 EGLGTRFSSYATWWIREAMQRALI-RARFIRLPDYLAKSLHA-------LQQKSLDEVDG 154

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPL-----D 602
            +  +       GVR       +   +     DE+ +     IE    N  SP      D
Sbjct: 155 HDAQRAQRREALGVRDSTMRALDFADVRVCSLDEEMADGPSRIEQVVGNVASPAQDYDRD 214

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           ++++A LRE     L  L  ++  V+  RFG+  +   TLE + ++  V+RE +RQ++ +
Sbjct: 215 ASVRA-LREH----LKLLNEKQREVMIYRFGLHGDAPMTLEAIAERLGVSREAVRQLQVR 269

Query: 663 AIRKLKH 669
           A+ +L+ 
Sbjct: 270 ALLRLRQ 276


>gi|39933444|ref|NP_945720.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris CGA009]
 gi|192288802|ref|YP_001989407.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris TIE-1]
 gi|39647290|emb|CAE25811.1| RNA polymerase sigma 32 subunit, RpoH, stress response sigma factor
           [Rhodopseudomonas palustris CGA009]
 gi|192282551|gb|ACE98931.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 299

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 121/239 (50%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHQLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P++   IA +L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDLHPDQVKLIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  + +      SL  PI D+ +     D++ D+   SP   A+ A   E   R
Sbjct: 167 GVTEQDVVDMNRRLGGDASLNAPIRDDGEPGEWQDWLVDQ---SPSQEAVMAEHEELDQR 223

Query: 616 ------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RAALNGAIQVLNPRERRIFEARR--LADEPMTLEDLASEFGVSRERVRQIEVRAFEKVQ 280


>gi|83746507|ref|ZP_00943558.1| RNA polymerase sigma factor rpoD [Ralstonia solanacearum UW551]
 gi|83726838|gb|EAP73965.1| RNA polymerase sigma factor rpoD [Ralstonia solanacearum UW551]
          Length = 504

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 5/159 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +IKL + RGY+T  E+N  LP D V +E M+  VA L+++GI V     D + L   +
Sbjct: 262 KALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLND 321

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +   +   L        R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 322 NAPSVTTEEEAEEEAEAALSTVDSEFGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIE 380

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AG   M+ ++   P+T   ++   + + +    + E ID
Sbjct: 381 AGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID 419


>gi|255262130|ref|ZP_05341472.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
 gi|255104465|gb|EET47139.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
          Length = 292

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 131/262 (50%), Gaps = 20/262 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R   CE S+ +  ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G 
Sbjct: 34  RDERCEQSLHR--LITAYMRLAISMASKFKRYGAPMNDLIQEASLGLMKAADKFDPDRGV 91

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKR 545
           +FSTYA+WW+K +I   +      +R         +  ++R    ++ R A     ++ R
Sbjct: 92  RFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAATAGEELDR 151

Query: 546 EPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIE---DKNAVSP 600
               + IA ++ +P+  V  +  +++    SL      ED      D +E   D+ A + 
Sbjct: 152 HQMRQMIATEVGVPLHDVEMMEGRLSGSDYSLNATQSSEDEGREWIDALEDDSDQAAENV 211

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +      LR      L++L+ RE+ ++  R  I   T  TLE +G +  +++ERIRQ+E
Sbjct: 212 ENDHDTETLRSWLVTALSALSHREQYIVTER-KIKDQT-RTLESLGHELGLSKERIRQLE 269

Query: 661 AKAIRKLKHP--SRSKKLRSFL 680
           A A  K++     +S++L  F 
Sbjct: 270 AAAFIKMRKSLEGQSRELHHFF 291


>gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
 gi|151280836|gb|ABR89246.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
          Length = 298

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/241 (32%), Positives = 129/241 (53%), Gaps = 26/241 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  +Y+M W
Sbjct: 61  AAQKLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHW 120

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMP 559
           +K  +   I      +++     + K+   +R+ +   + +    TP   +E+AK L + 
Sbjct: 121 IKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDSM----TPDQVDELAKTLNVK 176

Query: 560 VEGVRKV-LKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAIQANLR-ET 612
            E V ++  +++   I+LE P  DED      ++L   +++   V  L+S     L+ E 
Sbjct: 177 REEVIEMETRLSGRDIALEAPTDDEDDKFAPIAYLSSDMQEPTKV--LESQQFDRLQTEG 234

Query: 613 TTRVLASLTPREERVLRMRF-----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +  L  L  R  R++  R+     G G     TL E+  +F V+ ERIRQIEA A++K+
Sbjct: 235 LSNALGKLDARSRRIVEARWLANDDGSGA----TLHELADEFGVSAERIRQIEAVALKKM 290

Query: 668 K 668
           K
Sbjct: 291 K 291


>gi|255263634|ref|ZP_05342976.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
 gi|255105969|gb|EET48643.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
          Length = 298

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 122/248 (49%), Gaps = 17/248 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S +  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A +KFD   G++ S
Sbjct: 43  ENEDSKSAHKLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKKFDPEKGFRLS 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPE 550
           TYAMWW++ AI   +      +++      K  K+    R+  ++I        R    E
Sbjct: 103 TYAMWWIRAAIQEYVLRSWSMVKLGTTSAQK--KLFFNLRKAKSRIGALEDGDLRPEHVE 160

Query: 551 EIAKKLAMPVEGVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
            IA  L +  + V  +  +++    SL   +G   E T    D++ED++A    D   + 
Sbjct: 161 RIANDLGVNEQEVINMNRRLSGGDASLNAQVGSEGEGTMQWQDWLEDEDADQAGDYEAKD 220

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            L   RE     ++ L  RE+ +L  R     +   TLEE+  Q+ V+RERIRQIE +A 
Sbjct: 221 ELDSRRELLADAMSVLNDREKDILMQRR--LQDKAITLEELSGQYDVSRERIRQIEVRAF 278

Query: 665 RKLKHPSR 672
            KL+   R
Sbjct: 279 EKLQKKMR 286


>gi|146338455|ref|YP_001203503.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. ORS278]
 gi|146191261|emb|CAL75266.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Bradyrhizobium sp. ORS278]
          Length = 299

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 121/245 (49%), Gaps = 21/245 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + S A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +
Sbjct: 43  EHDDSDAAHKLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPE 550
           TYAMWW+K +I   I      +++      K  K+    R+  +KI        R    +
Sbjct: 103 TYAMWWIKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDLRPDQVK 160

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA-- 607
            IAK+L +  + V  + +      SL  PI D+ +     D++ D    SP   AI A  
Sbjct: 161 LIAKRLGVTDQDVIDMNRRLGGDASLNAPIRDDGEAGEWQDWLVD---TSPNQEAIMAEH 217

Query: 608 ----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               + R+     +  L  RE R+   R     +   TLE++  +F V+RER+RQIE +A
Sbjct: 218 EEYDHRRQALNGAIGVLNARERRIFEARR--LADEPMTLEDLAAEFGVSRERVRQIEVRA 275

Query: 664 IRKLK 668
             K++
Sbjct: 276 FEKVQ 280


>gi|261868195|ref|YP_003256117.1| RNA polymerase sigma factor RpoD [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413527|gb|ACX82898.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 616

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 62/158 (39%), Positives = 92/158 (58%), Gaps = 9/158 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLIVQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDADDLMLNE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D  D+   A+     L   +    R+TD PVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 70  NITDE-DVVEEATQ---VLSSVEAELGRTTD-PVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   + +++   P     LI   D + +G   L ++I
Sbjct: 125 EGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLI 162


>gi|91974840|ref|YP_567499.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB5]
 gi|91681296|gb|ABE37598.1| RNA polymerase sigma factor RpoH [Rhodopseudomonas palustris BisB5]
          Length = 299

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 120/239 (50%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P++   IA +L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDMHPDQVKLIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  + +      SL  PI D+ +     D++ D+   SP   A+ A   E   R
Sbjct: 167 GVTEQDVIDMNRRLGGDASLNAPIRDDGEPGEWQDWLVDQ---SPSQEAVMAEHEELDHR 223

Query: 616 ------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RAALNGAIGVLNPRERRIFEARR--LADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQ 280


>gi|254510133|ref|ZP_05122200.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
 gi|221533844|gb|EEE36832.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
          Length = 292

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 22/255 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-----------I 552
           +K +I   +      +R       K   +    RR+  +++RE   E            I
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARLEREAATEGLDLDRHQLHQMI 158

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLET-PIGDEDTSHLGDFIED---KNAVSPLDSAIQA 607
           A ++ +P+  V  +  ++     SL      DED     D +ED   + A S   S    
Sbjct: 159 AAEIGVPLRDVEMMEGRLAGSDFSLNAVQSADEDGREWIDALEDDREQAAESVEHSHDTQ 218

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR+     + +L  RE  ++R R         TLE +G++  +++ER+RQ+EA A  K+
Sbjct: 219 QLRDWLVTAMQALNDRERFIVRER--KLREPARTLESLGQELGLSKERVRQLEAAAFTKM 276

Query: 668 KH--PSRSKKLRSFL 680
           +    ++S++++ F 
Sbjct: 277 RKNLEAQSREVQHFF 291


>gi|77919976|ref|YP_357791.1| RNA polymerase, sigma (32) factor [Pelobacter carbinolicus DSM
           2380]
 gi|77546059|gb|ABA89621.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter carbinolicus DSM
           2380]
          Length = 286

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 129/252 (51%), Gaps = 18/252 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR      R    EA+   ++++ ANLR V+ +A +Y   GL+ LD+IQEGNIGLMKA 
Sbjct: 31  EFRLTQDYHRNQNIEAA---QQLICANLRFVVKIAHEYRGYGLKLLDIIQEGNIGLMKAV 87

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD   G +F TYA+WW++  I   I      ++I      K  K+     ++ + I+R
Sbjct: 88  KKFDPDRGLRFITYAVWWIRAYIHNFIIRNWSLVKIGTTQAQK--KLFFKLNQVRSAIQR 145

Query: 546 EPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGD-EDTSHLGDFIEDKNAVSP 600
               E+   IA++L +  + V  +  ++     SL+  + + ED + L    +++ +   
Sbjct: 146 MTGSEDTKAIARELNVRDDEVEDMARRMAGRDTSLDMRLVEGEDFTLLDSLADERESQEE 205

Query: 601 LDSAIQANLRETTTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           L   I+   ++ TT      L  L  RE R++  R  I      TL+ +   F ++RER+
Sbjct: 206 L--LIKQQEKQITTSHIHGALQELNDRERRIVEER--ILQEEPRTLQALADDFGISRERV 261

Query: 657 RQIEAKAIRKLK 668
           RQ+E  A+ K++
Sbjct: 262 RQLEKNALEKIR 273


>gi|302389825|ref|YP_003825646.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
 gi|302200453|gb|ADL08023.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
          Length = 241

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 120/228 (52%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E+V  NL LV S+ K++TNRG +  DL Q G+IGL+KA EKFD+    KFSTYA+  
Sbjct: 20  AKSELVSLNLGLVWSIVKRFTNRGYEIEDLFQIGSIGLLKAIEKFDFSYNVKFSTYAVPM 79

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D    I++   +RD   K+     R++ ++ REPT  E+A++L    E +
Sbjct: 80  IIGEIRRYIRDDR-PIKMTRSLRDFSIKIQNAKERLAKELNREPTIAELAEELGATPEEL 138

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RVLASLT 621
              L+  +  ISL      ED S +  +++  N+    D   Q    +T      L+ L 
Sbjct: 139 VVGLEAAQPIISLNDVAFQEDGSPIY-YMDQLNS----DEHHQNQWLDTIALKEALSKLD 193

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E +++ +R+      D T  EV K   +T+ ++ ++E K + K+++
Sbjct: 194 KLERQIIILRYF----KDKTQTEVAKILGITQVQVSRLERKILAKIRN 237


>gi|220921709|ref|YP_002497010.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219946315|gb|ACL56707.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 293

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 126/239 (52%), Gaps = 19/239 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 41  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPERDVRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E   +EI  ++A  +
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTDERVGDEIHSRIATAI 158

Query: 561 EGVRKVL-----KITKEPISLETPIGDED--TSHLGDFIEDKNAVS--PLDSAIQANLRE 611
              R+ +     +++   +SL  PI DE   ++   DF+ D + +    +  A+    R 
Sbjct: 159 GVSREDVALMDARLSGPDMSLNAPITDEGDASAERVDFLVDTSPLPDEAVSDAVDGERRL 218

Query: 612 TTTR-VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T  R  L  L+ RE R+L  R    +  D  TLE +G +  +++ER+RQIE +A+ KL+
Sbjct: 219 TWLRQALTVLSERELRILHER---RLAEDQATLEALGHRLGISKERVRQIENRALEKLR 274


>gi|126728120|ref|ZP_01743936.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
 gi|126711085|gb|EBA10135.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
          Length = 277

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 127/253 (50%), Gaps = 18/253 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +++A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLIQAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A+ +  ++        IA 
Sbjct: 86  IKASIQDYVMRNWSMVRTGSTSSQKALFFNMRRVQARLEREAQAIGAQLDSHQLRHMIAS 145

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSP---LDSAIQANL 609
           ++ +P+  V  +  +++    SL      ED      D +ED +A       +S     L
Sbjct: 146 EIGVPLRDVEMMEGRLSGSDFSLNATQSVEDEGREWIDTLEDDSAHGAEIVENSHDTECL 205

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + + SL  RE  ++R R     +   TLE +G +  +++ER+RQ+EA A  K++ 
Sbjct: 206 RDWLVQAMGSLNERERFIVRER--KLRDEPRTLESLGNELGLSKERVRQLEAAAFGKMRK 263

Query: 670 P--SRSKKLRSFL 680
              ++S +++ FL
Sbjct: 264 ALEAQSGEVQHFL 276


>gi|46371303|gb|AAS90418.1| stationary phase sigma factor [Azotobacter chroococcum]
          Length = 172

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 94/157 (59%)

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA  L  PV  V+++L + +
Sbjct: 1   IMNQTGTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNE 60

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              S++  +G +    L D + +     P D     +L ++  + L  LT ++  V+  R
Sbjct: 61  RVTSVDVSLGPDSDRTLLDVLTEDRPSDPCDLLQDDDLSQSIDQWLFDLTDKQREVVVRR 120

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           FG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 121 FGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLR 157


>gi|326569916|gb|EGE19966.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC8]
          Length = 371

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 124/240 (51%), Gaps = 16/240 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 128 GDVEAT---RLLVMSHLRFVIHIARSYSGYGLSQADLIQEGNLGLMKAVKRFDPNKGVRL 184

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++       K+   +R+ ++ SN++  +     IA  
Sbjct: 185 VSFAVHWIKAEIHEFVIKNWRIVKVATTKAHRKLFFNLRSLKKSSNQLTLDEAT-AIAND 243

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET 612
           L + V+ V ++  ++T    S E    D+D        F+ED  AV+P D   +A+  E 
Sbjct: 244 LNVTVKQVLEMESRLTSYDASFEAQDSDDDEGRYAPQLFLED--AVNPADVVEEADWEEN 301

Query: 613 TTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TT  L     +L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+ K+K
Sbjct: 302 TTTALKDAMETLDERSRDIITQRWLADQKS--TLHELAATYNISAERVRQIEKNAMNKIK 359


>gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas arsenicoxydans]
 gi|133739970|emb|CAL63021.1| RNA polymerase sigma-32 factor [Herminiimonas arsenicoxydans]
          Length = 298

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 124/239 (51%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  +Y+M W
Sbjct: 61  AAQKLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHW 120

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMP 559
           +K  +   I      +++     + K+   +R+ +   + +    TP   E +AK L + 
Sbjct: 121 IKAEMHEYILKNWRLVKVATTKAQRKLFFNLRSHKTGLDAM----TPDQVEALAKTLNVK 176

Query: 560 VEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLR-ETTT 614
            E V ++  +++   I+LE P  DED           ++  P   L+S     L+ E  +
Sbjct: 177 REEVIEMETRLSGRDIALEAPTDDEDDKFAPIAYLSSDSQEPTRVLESQRYDRLQTEGLS 236

Query: 615 RVLASLTPREERVLRMRF-----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  L PR  R++  R+     G G     TL E+  +F V+ ERIRQIE  A++K+K
Sbjct: 237 SALGKLDPRSRRIVEARWLANDDGSGA----TLHELANEFGVSAERIRQIETVALKKMK 291


>gi|238917256|ref|YP_002930773.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872616|gb|ACR72326.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 258

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 124/229 (54%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+S+ ++++  G    DL Q G IG++KA + FD  L  +FSTYA+  
Sbjct: 38  ARETFIKGNLRLVLSIVQRFSQSGENLDDLFQIGCIGMIKAIDNFDISLNVQFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S TIR+   ++D  +K + T   +  K  +EP+  EIA+++ +    +
Sbjct: 98  IIGEIKRFLRDNS-TIRVSRSLKDTAYKAITTRETLMKKNLKEPSITEIAEEIGISKADI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
              L+     ISL  P+ ++  DT ++ D ++DK      D  ++   L+E   R    L
Sbjct: 157 VIALEAVTPSISLYEPVFNDGGDTLYVIDQVKDKKNTE--DRWVRNIALQEAINR----L 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +PRE +++ +RF   +    T  EV K   +++ ++ ++E  A+R +K 
Sbjct: 211 SPRERQIIILRFFDCL----TQTEVAKGLGISQAQVSRLEKCALRDMKR 255


>gi|303237309|ref|ZP_07323879.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
 gi|302482696|gb|EFL45721.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
          Length = 235

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 121/247 (48%), Gaps = 38/247 (15%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IK I+ E  +S  E + +   ++ G+ +A    +++ ++NL+ V+S+A +Y NRGL   D
Sbjct: 10  IKDIANEQLLSDKEEQELAKQIKIGDAKAL---EKLTKSNLKFVVSIAHQYKNRGLGEDD 66

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I +Q  T +  V  +D+    
Sbjct: 67  LISEGNIGMMYAAQKFDGTKGTRFVKFAAPYIRKAMEEAINEQLETFK--VQNKDEKKPR 124

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            RTA R+S                               +PI    P G   T  L   +
Sbjct: 125 KRTAHRVS-----------------------------IDQPI----PAGSNGTFTLQTIL 151

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E+ N+    ++  +  +RE   + ++ L  R+ +V+ + + I     +T++E      + 
Sbjct: 152 ENANSQHADENLTKQIVREEIKKAMSVLDARQRKVISLLYAIKDEEAYTMQETADIMDIK 211

Query: 653 RERIRQI 659
           RER+RQI
Sbjct: 212 RERVRQI 218


>gi|154503856|ref|ZP_02040916.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
 gi|153795455|gb|EDN77875.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
          Length = 259

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 120/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV K++++      DL Q G +GLMKA + FD     KFSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIKRFSSSSENADDLFQIGCVGLMKAVDHFDPSRLVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        K  +EPT +EIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIYAKEGFVKKYSKEPTVQEIAEEIGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+  +  DT ++ D + DK     N V  L          +    
Sbjct: 157 VFALDAIQMPVSLHEPVYSDGGDTLYIMDQVSDKKNREENWVEEL----------SLEAA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L  RE  ++++RF  G     T  EV +Q  +++ ++ ++E  A++ +K 
Sbjct: 207 MERLNERERFIIQLRFFEG----KTQMEVAEQIQISQAQVSRLEKNALKIMKQ 255


>gi|153873537|ref|ZP_02002087.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152069997|gb|EDN67913.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 288

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 126/235 (53%), Gaps = 14/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V+ +A  Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 51  AARTLVMSHLRFVMHIAHNYRGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R+A++    + ++   E +AK L +  + 
Sbjct: 111 IRAEIHEYILRNWRIVKVATTKSQRKLFFNLRSAKKRLGWLTQDEV-ETVAKDLGVSPKD 169

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD---FIEDKNAVSPLDSAIQANLRETTTR-- 615
           VR++ L++    +S + P+  D+D + +     ++ED N   P D   Q+  +    R  
Sbjct: 170 VREMELRLNSYDLSFDMPVDADDDNAEILSPVGYLED-NRYDPADLVEQSEWKTHGHRQL 228

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              LA L  R + +L+ R+     T  TL+E+   + V+ ERIRQIE  A++KLK
Sbjct: 229 HQALAKLDVRSQDILQKRWLSENKT--TLQELANHYKVSAERIRQIENNALKKLK 281


>gi|86139299|ref|ZP_01057869.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85824143|gb|EAQ44348.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 292

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/253 (28%), Positives = 127/253 (50%), Gaps = 18/253 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +  A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLTNAYMRLAISMAVKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAIWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K ++   +      +R         +  +MR    ++ R A     ++ +    ++IA 
Sbjct: 101 IKASVQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQTQLERQANAQGQRLDKHQLHQQIAS 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSP---LDSAIQANL 609
           ++ +P+  V  +  +++    SL      E +     + +ED +A +      S     L
Sbjct: 161 EIGVPIRDVEMMDGRLSGADFSLNAARSTEAEGQEWIEILEDDSAQAAELVERSHDHRKL 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     +  L+ RE+R++  R     N   TLE +G++  +++ER+RQ+EA A +K++ 
Sbjct: 221 RKWLVEAMQGLSGREQRIVVAR--KLSNPPRTLEALGRELSLSKERVRQLEAGAFQKMRK 278

Query: 670 P--SRSKKLRSFL 680
              +RS+++   L
Sbjct: 279 TLDTRSREVHKLL 291


>gi|99080297|ref|YP_612451.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036577|gb|ABF63189.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 292

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/251 (29%), Positives = 126/251 (50%), Gaps = 22/251 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL +S+A K+   G    DLIQE  +GLMKAAEKFD   G +FSTYA+WW+K +
Sbjct: 45  LITAYMRLAVSMASKFRRYGAPMNDLIQEAGLGLMKAAEKFDPDRGVRFSTYAVWWIKAS 104

Query: 508 ITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           I   +      +R         +  +MR    ++ R A     ++ R    + +A+++ +
Sbjct: 105 IQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLEREAAGEGVELDRHKLMQMVAEEIGV 164

Query: 559 PVEGVRKV-LKITKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-----LRE 611
           P+  V  +  ++     SL      DED     D +ED +  +     ++A+     LRE
Sbjct: 165 PLRDVEMMDGRLAGADFSLNAVQSADEDGREWIDALEDDSEQAA--DRVEADHDRRQLRE 222

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP- 670
                L  L  RE  ++R R         TLE +G +  +++ER+RQ+EA A  K++   
Sbjct: 223 WLLSALNGLNERERFIVRER--KLREEARTLESLGNELGLSKERVRQLEAAAFSKMRKSL 280

Query: 671 -SRSKKLRSFL 680
             +S+++++FL
Sbjct: 281 EGQSREVQNFL 291


>gi|229086468|ref|ZP_04218640.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
 gi|228696785|gb|EEL49598.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
          Length = 259

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 134/265 (50%), Gaps = 21/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GD 582
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI   G 
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +    +    +DK         +   L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 DPIFVMDQLSDDKQRDEQWVEELA--LKEGMKR----LNDREKMIIRKRFFQGKTQMEVA 232

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AI+++
Sbjct: 233 EEIG----ISQAQVSRLEKSAIKQM 253


>gi|303327038|ref|ZP_07357480.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
 gi|302863026|gb|EFL85958.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 126/239 (52%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A   +V ++LRLV+ +A  +  R +Q  LDL+QEGN+GLM+A  KFD   G KFS YA +
Sbjct: 106 AAFRLVSSHLRLVVRIAMDFQRRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASF 165

Query: 503 WVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           W+K  I + I D    ++I    ++ K+   +   R+       +P    ++++L +  +
Sbjct: 166 WIKAYILKFIMDNWRMVKIGTTQVQRKLFYNLNRERQKLIAQGYDPDAAMLSERLGVTED 225

Query: 562 GVRKV-LKITKEPISLETPIGDED--------TSHLGDFIEDKNAVSPLDSAIQANLRET 612
            + ++  ++    +SL   +G++            LG  IED  A   +   +++ L+  
Sbjct: 226 QINEMDQRLASTDLSLNVQVGEDSGGASRMDFLPALGPGIEDTLASDEIAGLVRSRLKT- 284

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              ++  L  +E  +L+ R    + TD   TL E+G+++ VTRER+RQ+EA+ + K++ 
Sbjct: 285 ---IMPKLNEKEVYILQNR----LLTDEPVTLREIGERYNVTRERVRQLEARLLEKIRQ 336


>gi|326564381|gb|EGE14609.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 12P80B1]
          Length = 371

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 124/240 (51%), Gaps = 16/240 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 128 GDVEAA---RLLVMSHLRFVIHIARSYSGYGLSQADLIQEGNLGLMKAVKRFDPNKGVRL 184

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++       K+   +R+ ++ SN++  +     IA  
Sbjct: 185 VSFAVHWIKAEIHEFVIKNWRIVKVATTKAHRKLFFNLRSLKKSSNQLTLDEAT-AIAND 243

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET 612
           L + V+ V ++  ++T    S E    D+D        F+ED  AV+P D   +A+  E 
Sbjct: 244 LNVTVKQVLEMESRLTSYDASFEAQDSDDDEGRYAPQLFLED--AVNPADVVEEADWEEN 301

Query: 613 TTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TT  L     +L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+ K+K
Sbjct: 302 TTTALKDAMETLDERSRDIITQRWLADQKS--TLHELAATYNISAERVRQIEKNAMNKIK 359


>gi|85704163|ref|ZP_01035266.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
 gi|85671483|gb|EAQ26341.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
          Length = 277

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 121/244 (49%), Gaps = 26/244 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-----------EEI 552
           +K +I   +      +R       K   +    RR+  +++RE              E I
Sbjct: 86  IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARLEREAMANGQQLDGYQLREMI 143

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQAN-- 608
           A ++ +P+  V  +  +++    SL      ED      D +ED+ A    D  ++ +  
Sbjct: 144 AHEVGVPLRDVEMMEGRLSGSDFSLNATQSAEDEGREWIDTLEDEGARG--DEIVERHHD 201

Query: 609 ---LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAI 664
              LR+     LA L  RE  ++R R    +  D  TLE +G++  +++ER+RQ+EA A 
Sbjct: 202 MHALRDWLADALARLNERERFIVRER---KLRDDPRTLESLGEELNLSKERVRQLEAAAF 258

Query: 665 RKLK 668
           +K++
Sbjct: 259 QKMR 262


>gi|148257972|ref|YP_001242557.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. BTAi1]
 gi|146410145|gb|ABQ38651.1| RNA polymerase, sigma 32 subunit, RpoH [Bradyrhizobium sp. BTAi1]
          Length = 299

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 123/243 (50%), Gaps = 17/243 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + S A +++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +
Sbjct: 43  EHDDSDAAQKLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEE---I 552
           TYAMWW+K +I   I      +++      K     + +   R+S   + +  P++   I
Sbjct: 103 TYAMWWIKASIQEYILRSWSLVKMGTTANQKKLFFNLRKAKSRISALDEGDLHPDQVKLI 162

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA---- 607
           AK+L +  + V  + +      SL  PI D+ +     D++ D    SP   AI A    
Sbjct: 163 AKRLGVTDQDVVDMNRRLGGDASLNAPIRDDGEAGEWQDWLVD---TSPNQEAIMAEHEE 219

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             + R+     +  L  RE R+   R     +   TLE++  +F V+RER+RQIE +A  
Sbjct: 220 YDHRRQALNGAIGVLNARERRIFEARR--LADEPMTLEDLAAEFGVSRERVRQIEVRAFE 277

Query: 666 KLK 668
           K++
Sbjct: 278 KVQ 280


>gi|167644630|ref|YP_001682293.1| RNA polymerase factor sigma-32 [Caulobacter sp. K31]
 gi|167347060|gb|ABZ69795.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter sp. K31]
          Length = 295

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/253 (30%), Positives = 127/253 (50%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E + S A  +MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G+
Sbjct: 39  RWKEHQDSEAAHKMVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDKGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE 550
           + +TYAMWW++ +I   I      +++      K  K+    R+  ++I      +  P+
Sbjct: 99  RLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQIAAFQDGDLHPD 156

Query: 551 E---IAKKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           +   IA KL  +  E +    ++     SL  P+  +  S   D++ D N VS     + 
Sbjct: 157 QVSYIATKLGVLDSEVISMNRRLGGPDASLNAPLRADGESEWQDWLADDNQVS--QETVV 214

Query: 607 ANLRETTTRV------LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQI 659
           A  +E + R+      +  LT RE  +L  R    +  D  TLE++  ++ V+RER+RQI
Sbjct: 215 AENQEKSMRMTLLEEAMVELTDRERHILTER---RLKDDPTTLEDLATEYGVSRERVRQI 271

Query: 660 EAKAIRKLKHPSR 672
           E +A  KL+   R
Sbjct: 272 EVRAFEKLQKSMR 284


>gi|226939164|ref|YP_002794235.1| RNA polymerase factor sigma-32 [Laribacter hongkongensis HLHK9]
 gi|226714088|gb|ACO73226.1| RpoH [Laribacter hongkongensis HLHK9]
          Length = 282

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 121/231 (52%), Gaps = 9/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ W
Sbjct: 49  AARQLVMSHLRVVVSIARGYAGYGLPQADLIQEGNIGLMKAVKRFEPERGVRLFSFAIHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   I      +R+      +  K+    R M          E  +IA  L +  E
Sbjct: 109 IKAEIHEFILRNWRLVRVATTKPQR--KLFFNLRSMKQGFSALSDTEARQIADDLGVKPE 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVL 617
            VR++  +++ + ISL     +E+     D++ D  +       +QA     RE   + L
Sbjct: 167 EVREMETRMSGQDISLLAEDNEEEGFAPIDWLADTRSEPTKQLEMQAYERLQREGIEQAL 226

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L PR  R++  R+ +  +   TL ++  +F V+ ERIRQIE KA++K+K
Sbjct: 227 QALDPRSRRIIEARW-LADDGGLTLHDLAAEFGVSAERIRQIEVKALKKMK 276


>gi|149202416|ref|ZP_01879389.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
 gi|149144514|gb|EDM32545.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
          Length = 277

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 119/243 (48%), Gaps = 24/243 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-----------EEI 552
           +K +I   +      +R       K   +    RR+  +++RE              E I
Sbjct: 86  IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARLEREALANGEQLDGYQLREMI 143

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS-HLGDFIEDKNA----VSPLDSAIQ 606
           A ++ +P+  V  +  +++    SL      ED      D +ED  A    +   D  + 
Sbjct: 144 AHEVGVPLRDVEMMEGRLSGSDFSLNATQSSEDEGRQWIDTLEDDGARGDEIVERDHDMH 203

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIR 665
           A LR      L+ L  RE  ++R R    +  D  TLE +G++  +++ER+RQ+EA A +
Sbjct: 204 A-LRTWLADALSRLNDRERFIVRER---KLRDDPRTLESLGEELNLSKERVRQLEAAAFQ 259

Query: 666 KLK 668
           K++
Sbjct: 260 KMR 262


>gi|307251409|ref|ZP_07533324.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306856577|gb|EFM88718.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 316

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 147/285 (51%), Gaps = 42/285 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   ++ E    ++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--------RYYYDEDVEAAKQLILSHMRFVIHIARG 100

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 101 YLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAIHWVKAEIHEYVLKNWRIVKVA 160

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  N++    E   +++A+ L +  E VR++  ++T + +  + P
Sbjct: 161 TTKAQR--KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLP 218

Query: 580 IGDED-------------TSHLGDFIEDKNAVSPLDSAIQANLRETT--TRVLASLTPRE 624
           +G++D             +S+  D +ED+          Q N + T      LA+L  R 
Sbjct: 219 VGEDDDEVYTPSMYLEDNSSNFADDLEDE----------QYNGQATAQLAYALATLDERS 268

Query: 625 ERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +++ R+   ++ +  TL+++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 269 QDIIKTRW---LDEEKATLQDLAEKYGISAERVRQLENAALKKIK 310


>gi|152976264|ref|YP_001375781.1| sporulation sigma factor SigG [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025016|gb|ABS22786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 259

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/264 (29%), Positives = 136/264 (51%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGETSA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IA+ L +  E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAQVLDVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       E
Sbjct: 179 DPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVAE 233

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+G    +++ ++ ++E  AI+++
Sbjct: 234 EIG----ISQAQVSRLEKSAIKQM 253


>gi|320353914|ref|YP_004195253.1| RNA polymerase sigma 32 subunit RpoH [Desulfobulbus propionicus DSM
           2032]
 gi|320122416|gb|ADW17962.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfobulbus propionicus
           DSM 2032]
          Length = 328

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 127/245 (51%), Gaps = 16/245 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCL 492
           VR  E     A   +V +NLRLV+ VA  +    +Q F+DLIQEGN+GL++A +KFD   
Sbjct: 60  VRFQETGDPDAAYRLVSSNLRLVVKVAMDFQKYWMQNFMDLIQEGNVGLVQATKKFDPYR 119

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           G KFS YA +W++  I + I D    ++I     + K+   +   +++      +P  + 
Sbjct: 120 GVKFSYYAAYWIRAYILKFIMDNWRLVKIGTTQAQRKLFFSLNKEKKLLESQGFKPEVKL 179

Query: 552 IAKKLAMP-VEGVRKVLKITKEPISLETPI----GDEDTS---HLGDFIEDKNAVSPLDS 603
           +A++L +   E +    ++    +SLE P+     DE  +   H G  IE+  A   +  
Sbjct: 180 LAERLNVKESEVIEMGQRMDNWDVSLEAPVRSDSEDEQKNFLPHEGPGIEEMVASQEMRE 239

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L + +TR    L  +E+ +L  R  +  +   TL+ +  +F ++RER+RQIE+  
Sbjct: 240 RLAGILADLSTR----LNEKEQVILTTR--LLSDEPKTLQTIADEFNISRERVRQIESNL 293

Query: 664 IRKLK 668
           ++KL+
Sbjct: 294 LKKLR 298


>gi|170691517|ref|ZP_02882682.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
 gi|170143722|gb|EDT11885.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
          Length = 311

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 124/250 (49%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP+EI        EG
Sbjct: 132 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGSF----TPDEI--------EG 179

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + K L + +E ++ +ET +   D +  G   + + + +P+  A  A+     T VLAS  
Sbjct: 180 LAKELNVKREEVAEMETRLSGGDIALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQ 237

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L  R  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 238 RDKLQSDGIATALEALDARSRRIIEARWLKVQDDGSGGSTLH---ELADEFGVSAERIRQ 294

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 295 IEASAMKKMR 304


>gi|229815207|ref|ZP_04445543.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
 gi|229809217|gb|EEP44983.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
          Length = 261

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/215 (33%), Positives = 115/215 (53%), Gaps = 10/215 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V ++L LV  +A K+ NRG    DLIQ G +GL+KA ++FD   G +F+T+A   
Sbjct: 31  AREKLVMSHLNLVRFIANKFKNRGEPIDDLIQVGYLGLLKAIDRFDPSRGLEFTTFATPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+  ++R+P  +++   KV +    ++++++R PT  EIA  L   V+ V
Sbjct: 91  IMGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDTLTSQLQRSPTIAEIADYLDATVDEV 150

Query: 564 RKVLK--ITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + ++       +SLE P G  D+DT      + D+ A    D A   + R      LAS
Sbjct: 151 LEAMESSSAYSSVSLEAPSGADDDDTPS----VIDRYATEDSDLAFTDD-RIIIEEALAS 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            +PRE  V+ MRF  GM      E++G  Q  V+R
Sbjct: 206 FSPRERDVIEMRFLKGMTQIEIAEKLGISQVQVSR 240


>gi|118578560|ref|YP_899810.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501270|gb|ABK97752.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 292

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 113/230 (49%), Gaps = 7/230 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V +NLR V+ +A +Y N G++ LDLIQEGNIGLM A  KF+     +  +YA+WW
Sbjct: 45  AAHTLVTSNLRYVVKIASEYRNYGMKMLDLIQEGNIGLMMAVRKFNPYRKIRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  I   I      I+I      R   + + +T   +      +    EIA  L +P  
Sbjct: 105 IRAYIQNYIVSAWSLIKIGTTQAQRKLFYGLRKTKEALLRMTGSDNDAAEIASMLQVPDH 164

Query: 562 GVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLA 618
            V  + +  K  +SL+  I + D  + L    +D+     L    Q  L  ++   + + 
Sbjct: 165 EVIDMEQRLKGEVSLDCQIVESDGLTFLETIADDRMNQEELLGENQQELQVKQRVIKAME 224

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  +E  ++  R  I  +   TL+++   F ++RER+RQ+E +A+ KLK
Sbjct: 225 GLNEKERYIVEHR--ITSDEPLTLQDIASHFSISRERVRQLEERALAKLK 272


>gi|253578148|ref|ZP_04855420.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850466|gb|EES78424.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39BFAA]
          Length = 259

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 124/232 (53%), Gaps = 14/232 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ N      DL Q G IGL+KA + FD  L  KFSTYA+  
Sbjct: 38  ARELYIKGNLRLVLSVIRRFQNSSENADDLFQIGCIGLIKAIDNFDTTLQVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K + T      +  +EPT  EIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKAIYTRENYMKQHLKEPTVTEIAQEIGIEKEMI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
              L   + P+SL  P+  E  DT ++ D I DK   +  +  I+   LRE   R    L
Sbjct: 157 VYALDAIQNPVSLFEPVYTEGGDTLYVMDQISDKK--NKEERWIENLALREAMQR----L 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RE+ ++ +RF  G     T  EV ++  +++ ++ ++E  A++ +++  R
Sbjct: 211 NSREKHIIELRFYEG----KTQMEVAQEIGISQAQVSRLEKNALKSMRNYLR 258


>gi|83859148|ref|ZP_00952669.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852595|gb|EAP90448.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 296

 Score = 95.9 bits (237), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 129/247 (52%), Gaps = 16/247 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E S A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G+
Sbjct: 40  RWQEHEDSDAAHQLVTSHLRLVAKIAMGYRGYGLPIAEVISEGNVGLMQAVKKFDPDKGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW++ +I   I      +++      K  K+    RRM ++++       R  
Sbjct: 100 RLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRMKSQMRALDEGDLRPD 157

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             EEIA KL +  + V  + +    P  SL  P+  +  +   D++ D +A    D   +
Sbjct: 158 QVEEIATKLGVTDDDVISMNRRLSGPDASLNAPMRADGEAEWQDWLADDDADDAEDELAE 217

Query: 607 AN---LRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           ++   +R T  +  + +L  RE+ +++ R         TLE++ + + V+RERIRQIE +
Sbjct: 218 SDEFSMRMTLLQEAMGALNEREQNIIQERRLT--EEPKTLEDLAQVYGVSRERIRQIEVR 275

Query: 663 AIRKLKH 669
           A  KL++
Sbjct: 276 AFEKLQN 282


>gi|209965454|ref|YP_002298369.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958920|gb|ACI99556.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 307

 Score = 95.5 bits (236), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V +++RL + +A KY   GL   DLI E NIGL+KA ++FD   G++ +TYA+WW++  
Sbjct: 51  LVRSHMRLAVKIASKYARSGLPMGDLISEANIGLVKAVQRFDPDRGFRLATYALWWIRAE 110

Query: 508 ITRSIADQSCTIR--IPVHMRDKIHKVVRTARRMS--NKIKREPTPEEIAKKLAMPVEGV 563
           +   +      ++      ++     + +T RR+   ++I  +   + +A +L   V+ V
Sbjct: 111 VQTYVLHNWSMLKGGNTAALKRLFFNLRQTQRRLGIQDRIMSDEEADRVADELGASVDEV 170

Query: 564 RKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLAS 619
           R++      P+ SL  P+G++      D + D+     +  A ++ L   +      L +
Sbjct: 171 REMEHRFATPVTSLNVPVGEDGDHEALDLLADETETVEVRLAEKSELAVRKALMVDALGA 230

Query: 620 LTPREERVLRMRFGIGMN-TDH--TLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE  +      +  N TD   TLE + +Q+ V++ERIRQIE+ A +K+
Sbjct: 231 LGDRERHIF-----VSRNLTDQPVTLETLAQQYGVSKERIRQIESGAYKKV 276


>gi|186475070|ref|YP_001856540.1| RNA polymerase factor sigma-32 [Burkholderia phymatum STM815]
 gi|184191529|gb|ACC69494.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phymatum
           STM815]
          Length = 311

 Score = 95.5 bits (236), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 123/249 (49%), Gaps = 40/249 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  SARKLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   I      +++      K  + +    R   +  +  TP+EI        +G+
Sbjct: 132 IKAEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKQGLQSFTPDEI--------DGL 180

Query: 564 RKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA---- 618
            K L + +E ++ +ET +   D +  G   + + A +P+  A  A+     T VLA    
Sbjct: 181 AKELNVKREEVAEMETRLSGGDVALEGQVEDGEEAFAPI--AYLADSHSEPTAVLAARQR 238

Query: 619 -------------SLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQI 659
                        SL  R  R++  R+      G G +T H   E+  +F V+ ERIRQI
Sbjct: 239 DRLHSDGIASALESLDSRSRRIIEARWLQVEDDGSGGSTLH---ELADEFGVSAERIRQI 295

Query: 660 EAKAIRKLK 668
           EA A++K++
Sbjct: 296 EASAMKKMR 304


>gi|165977273|ref|YP_001652866.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|190151190|ref|YP_001969715.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|303252711|ref|ZP_07338873.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307248906|ref|ZP_07530917.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307262328|ref|ZP_07543976.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307264539|ref|ZP_07546123.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|165877374|gb|ABY70422.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|189916321|gb|ACE62573.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|302648450|gb|EFL78644.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854601|gb|EFM86793.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306867991|gb|EFM99819.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306870138|gb|EFN01898.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 316

 Score = 95.5 bits (236), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 147/285 (51%), Gaps = 42/285 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   ++ E    ++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--------RYYYDEDVEAAKQLILSHMRFVIHIARG 100

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 101 YLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVA 160

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  N++    E   +++A+ L +  E VR++  ++T + +  + P
Sbjct: 161 TTKAQR--KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLP 218

Query: 580 IGDED-------------TSHLGDFIEDKNAVSPLDSAIQANLRETT--TRVLASLTPRE 624
           +G++D             +S+  D +ED+          Q N + T      LA+L  R 
Sbjct: 219 VGEDDDEVYTPSMYLEDNSSNFADDLEDE----------QYNGQATAQLAYALATLDERS 268

Query: 625 ERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +++ R+   ++ +  TL+++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 269 QDIIKTRW---LDEEKATLQDLAEKYGISAERVRQLENAALKKIK 310


>gi|312194695|ref|YP_004014756.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
 gi|311226031|gb|ADP78886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score = 95.5 bits (236), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 118/231 (51%), Gaps = 10/231 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +V +  +G+ E +  + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 152 FARLVELP-EGDAERAAIRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 210

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S K+ R 
Sbjct: 211 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQKLGRS 270

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDS 603
           PT  EIA  L M  E V + L+       +SL+ P  GD+++  + D +  ++     +S
Sbjct: 271 PTVAEIAAHLEMTEEEVLEGLESANAYSAVSLDAPDSGDDESPAVADTLGVQD-----ES 325

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                 RE+   +L  L PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 326 LEGVEYRESLKPLLEKLPPREKRILLLRFFGNMTQSQIAIELGISQMHVSR 376


>gi|146276534|ref|YP_001166693.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145554775|gb|ABP69388.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 292

 Score = 95.5 bits (236), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 130/258 (50%), Gaps = 28/258 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A KY   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMASKYRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A +   ++      E +A 
Sbjct: 101 IKASIQDYVMRNWSLVRTGSTSSQKALFFNMRRVQARLEREASQRGEQLDAHQLRELVAH 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSP--LDSAIQA-NL 609
            + +P+  V  +  +++    SL  T   D++     D +ED +A +   ++ ++ A  L
Sbjct: 161 DVGVPLSDVEMMEGRLSGSDFSLNATQSADDEGREWIDALEDDSAQASEVVEGSLDAERL 220

Query: 610 RETTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           R      +  L  RE     ER LR       +   TLE +G++  +++ER+RQ+EA A 
Sbjct: 221 RGWLVVAMQQLNARERFIVTERKLR-------DVPRTLESLGEELKLSKERVRQLEAAAF 273

Query: 665 RKLKHP--SRSKKLRSFL 680
            K++    ++S+++  FL
Sbjct: 274 AKMRRSLEAQSREVHHFL 291


>gi|91781700|ref|YP_556906.1| RNA polymerase factor sigma-32 [Burkholderia xenovorans LB400]
 gi|91685654|gb|ABE28854.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia xenovorans
           LB400]
          Length = 307

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 124/250 (49%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 68  SARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 127

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP+EI        EG
Sbjct: 128 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDEI--------EG 175

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + K L + +E +S +ET +   D +  G   + + + +P+  A  A+     T VLAS  
Sbjct: 176 LAKELNVKREEVSEMETRLSGGDIALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQ 233

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L  R  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 234 RDKLQSDGIASALDALDARSRRIIEARWLKVEDDGSGGSTLH---ELADEFGVSAERIRQ 290

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 291 IEASAMKKMR 300


>gi|187479755|ref|YP_787780.1| RNA polymerase factor sigma-32 [Bordetella avium 197N]
 gi|115424342|emb|CAJ50895.1| RNA polymerase sigma-32 factor [Bordetella avium 197N]
          Length = 307

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 129/231 (55%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +E+V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 73  SARELVLSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 132

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ R   + +  E   + IA++L +  E 
Sbjct: 133 IKAEIHEYIIRNWRLVKVATTKAQRKLFFNLRSMRPDGHTLDTEQV-DHIARELNVRRED 191

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLR-ETTTRVL 617
           V ++ ++++   +SLE    D+D      ++ D+    P   L+   + +L+ +  +  +
Sbjct: 192 VSEMEVRLSGRDLSLENQDDDDDGYAPIAYLSDECREEPTRVLERKARDDLQGKGLSDAI 251

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L PR  R++  R+ +      TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 252 TALDPRSRRIVEARW-LQDEGGATLHELAAEFGVSAERIRQIEAAALKKMR 301


>gi|218777994|ref|YP_002429312.1| RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
 gi|218759378|gb|ACL01844.1| putative RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
          Length = 328

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 130/246 (52%), Gaps = 18/246 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCL 492
           VR  E +   A   +V ANLRLV+ +A ++    +Q  LDLIQEGNIGLM+AA KFD   
Sbjct: 65  VRVQEFDDPDAAYRLVTANLRLVVKIALEFQRVWMQNLLDLIQEGNIGLMQAARKFDPYK 124

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
             KFS Y+ +W+K  I + I D    ++I     + K+   ++  ++   +   +P P+ 
Sbjct: 125 NVKFSYYSSFWIKAYILKFIMDNWRLVKIGTTQAQRKLFFKLKKEKQKLLEEGFDPKPKL 184

Query: 552 IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA------ 604
           +++KL +    +  +  ++    +SL+ P+ D+  S   +F+      +P +SA      
Sbjct: 185 LSEKLGVSERDIIDMDQRLNNWDLSLDAPVKDDSDSERIEFLS-----TPSESAEDQVAR 239

Query: 605 --IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++  LRE       +L  RE  +   R  +  ++  TL+++G +  ++RER+RQ+E+ 
Sbjct: 240 KEMETILREKIDIFRKTLKERELEIFDER--VFSDSPVTLQQIGDRHGISRERVRQVESG 297

Query: 663 AIRKLK 668
            ++KLK
Sbjct: 298 VVKKLK 303


>gi|254468686|ref|ZP_05082092.1| alternative sigma factor RpoH [beta proteobacterium KB13]
 gi|207087496|gb|EDZ64779.1| alternative sigma factor RpoH [beta proteobacterium KB13]
          Length = 281

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 125/235 (53%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LRLVI +A+ Y+  GL   DL+QEGNIGLMKA ++FD   G +  ++AM+W
Sbjct: 49  AARQLIMSHLRLVIKIARSYSGYGLNQADLVQEGNIGLMKAVKRFDPSRGVRLVSFAMYW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++      + K+   +R+ ++    +K+E   +EIAK+L +    
Sbjct: 109 IKAEIQEFVVRNWRLVKTATTKAQRKLFFNLRSMKKTLQPLKQEEI-KEIAKELNVKESD 167

Query: 563 VRKV-LKITKEPISLETPIGDEDTS----HLGDFIEDKNAVSPLDSAI----QANLRETT 613
           V+++  +     I+L+    DED          +++D+NA  P+   I    ++N     
Sbjct: 168 VKEMEYRFNGNEIALD--YQDEDNEDEVFRPISYLQDENA-DPVKQLISKESESNNLSAL 224

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  + S+  R   +L  R+ +      TL E+  +  V+ ERIRQIE  A++KLK
Sbjct: 225 SNAIKSIDERSRYILESRW-LNEEKSKTLHELADELGVSAERIRQIEQNALKKLK 278


>gi|295688294|ref|YP_003591987.1| RNA polymerase sigma 32 factor subunit RpoH [Caulobacter segnis
           ATCC 21756]
 gi|295430197|gb|ADG09369.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter segnis ATCC
           21756]
          Length = 295

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 125/245 (51%), Gaps = 24/245 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 48  AAHKMVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I    + +  PE+   IA KL
Sbjct: 108 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQIAAFQEGDLRPEQVSAIATKL 165

Query: 557 A-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-------LDSAIQAN 608
             +  E +    +++    SL  P+  +  S   D++ D+  VS         + +++ +
Sbjct: 166 GVLDSEVISMNRRLSGPDASLNAPLRSDSESEWQDWLADEEQVSQETRVAEDEEKSLRMS 225

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L E     +  LT RE  +L  R    +  D  TLEE+  Q+ V+RER+RQIE +A  KL
Sbjct: 226 LLE---EAMVELTDRERHILTER---RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKL 279

Query: 668 KHPSR 672
           +   R
Sbjct: 280 QKTMR 284


>gi|237749576|ref|ZP_04580056.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
 gi|229380938|gb|EEO31029.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
          Length = 299

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 124/236 (52%), Gaps = 16/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LRLV S+A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  +YA+ W
Sbjct: 62  AAQELVLSHLRLVASIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPKMGVRLVSYAIHW 121

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ +  +  + RE     +A+KL +  E 
Sbjct: 122 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKSGNEAMTREQI-RSLAEKLNVKDEE 180

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLR-ETTTRVL 617
           V ++  +++   I+LET   D+D +             P   L++     L+ E     L
Sbjct: 181 VSEMETRLSGHDIALETQHDDDDDNFAPIAYLSSEQTEPTRVLEAKQHDRLQSEGLAEAL 240

Query: 618 ASLTPREERVLRMRF-----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  R +R++  R+     G G     TL ++ ++F V+ ERIRQIEA A++K+K
Sbjct: 241 DKLDDRSKRIIEARWLKNDDGSGA----TLHDLAEEFGVSAERIRQIEAAALKKMK 292


>gi|323498063|ref|ZP_08103069.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
 gi|323316871|gb|EGA69876.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
          Length = 285

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 129/243 (53%), Gaps = 19/243 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE EA+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 45  GEIEAA---KGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAK 159

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDED--TSHLGD--FIEDKNAVSPLDSAIQANL 609
           +L +    VR++  ++  +  + E P  D+D  +S+     ++EDK A    D+   AN 
Sbjct: 160 ELGVEPAEVREMESRLAAQDSTFEMPTDDDDSVSSYTAPVLYLEDK-ASDVADNVEAANW 218

Query: 610 RETTTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              T       LASL  R + ++R R+    +   TL+E+ + + V+ ERIRQ+E  A++
Sbjct: 219 EAHTNNRLSLALASLDERSQHIVRSRWLD--DNKSTLQELAETYSVSAERIRQLEKNAMK 276

Query: 666 KLK 668
           KLK
Sbjct: 277 KLK 279


>gi|163815157|ref|ZP_02206538.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
 gi|158449566|gb|EDP26561.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
          Length = 260

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 121/228 (53%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E +E NLRLV+SV +++ +      DL Q G IGL+KA + FD  L  KFSTYA+  
Sbjct: 38  ARDEFIEGNLRLVLSVIQRFGSSNENPDDLFQVGCIGLIKALDNFDRSLNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +     R + D +  IR+   +RD  +K +     +     +EPT EEIA+++++P E +
Sbjct: 98  IIGECRRYLRDNN-AIRVSRSLRDIAYKAIYAKENLQKTRDKEPTIEEIAEEISIPKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L     P+SL  P+  E  DT ++ D I+D  +   L      +LRE   R    L 
Sbjct: 157 VMSLDAISAPLSLYEPVYQEGGDTLYIMDQIKDGKSREEL-WVENLDLREAMGR----LC 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++R+RF  G     T  EV ++  +++ ++ ++E  AI+ L+ 
Sbjct: 212 DREKNIVRLRFFEG----KTQTEVAEEISISQAQVSRLEKNAIKSLRR 255


>gi|329936108|ref|ZP_08285907.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329304426|gb|EGG48305.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 310

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 124/238 (52%), Gaps = 13/238 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  +  +V  +L LV  +A++Y NRG    DL Q   IGL+K+ ++FD   G
Sbjct: 76  LKDGSPEYAELRNRLVRMHLPLVEHLARRYRNRGEPLDDLTQVATIGLIKSVDRFDPDRG 135

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A
Sbjct: 136 VEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQQHGRSPTVHELA 195

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLR 610
           +KLA+  E V + L+       +SL+ P  D+D   + D +  D+ A+  ++   +A+LR
Sbjct: 196 EKLAISEEEVLEGLESANAYSTLSLDVPDTDDDAPAVADRLGADEAALESVE--YRASLR 253

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +L  L PRE+R+L +RF   M      +EVG    +++  + ++ A+ + KL+
Sbjct: 254 ----LLLEDLPPREKRILLLRFFGNMTQSQIAQEVG----ISQMHVSRLLARTLAKLR 303


>gi|296161515|ref|ZP_06844320.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
 gi|295888159|gb|EFG67972.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
          Length = 311

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 123/248 (49%), Gaps = 42/248 (16%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K
Sbjct: 74  RRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIK 133

Query: 506 QAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
             I   I      +++     + K+   +R+ ++         TP+EI        EG+ 
Sbjct: 134 AEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDEI--------EGLA 181

Query: 565 KVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS---- 619
           K L + +E +S +ET +   D +  G   + + + +P+  A  A+     T VLAS    
Sbjct: 182 KELNVKREEVSEMETRLSGGDIALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQRD 239

Query: 620 -------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                        L  R  R++  R+      G G +T H   E+  +F V+ ERIRQIE
Sbjct: 240 KLQSDGIASALDALDARSRRIIEARWLKVEDDGSGGSTLH---ELADEFGVSAERIRQIE 296

Query: 661 AKAIRKLK 668
           A A++K++
Sbjct: 297 ASAMKKMR 304


>gi|294011928|ref|YP_003545388.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
 gi|292675258|dbj|BAI96776.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
          Length = 304

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 127/251 (50%), Gaps = 26/251 (10%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E + S A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KF+   G+
Sbjct: 43  RYAEHQDSEAAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFEPDRGF 102

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE 550
           + +TYAMWW++ +I   I      +++      K  K+    RRM N I+     +  P+
Sbjct: 103 RLATYAMWWIRASIQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKNNIEAFEDGDLHPD 160

Query: 551 EIAKKLAMPVEGVRK--VLKITKE-----PISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           ++ KK+A  + GV +  V+ + +        SL  P+ ++      D++ D +   PL  
Sbjct: 161 DV-KKIATDL-GVTEEDVISMNRRMAMGGDTSLNVPMREDGEGQWQDWLADSD---PLQD 215

Query: 604 AIQANLRETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              A+ +E+  R       +  L  RE+ +L  R         TLEE+ + + V+RER+R
Sbjct: 216 ERVADRQESELRHDMLVEAMDDLNDREKHILAERRLA--EEPKTLEELSQVYGVSRERVR 273

Query: 658 QIEAKAIRKLK 668
           QIE +A  KL+
Sbjct: 274 QIEVRAFEKLQ 284


>gi|254000081|ref|YP_003052144.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. SIP3-4]
 gi|313202040|ref|YP_004040698.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. MP688]
 gi|253986760|gb|ACT51617.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. SIP3-4]
 gi|312441356|gb|ADQ85462.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. MP688]
          Length = 638

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/158 (37%), Positives = 88/158 (55%), Gaps = 21/158 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---------GDD 82
           K +I L ++RGY+T  E+N  LP D   SEQ++  + M+++MGI V +           D
Sbjct: 28  KSLIVLGKERGYLTYAEINDHLPDDVQDSEQIDGIIGMINDMGIQVYEETPDAEALLMSD 87

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                  ED+++ A  A ++        DS    T DPVRMY+REMG+++LL+REGEI I
Sbjct: 88  APPPVADEDAVEEAEQALSTV-------DSEFGRTTDPVRMYMREMGTVDLLTREGEIEI 140

Query: 143 AKRIEAGRAMMMASLCESPLTFQALI-----IWRDELN 175
           AKRIE G   M+ ++   P T   L+     + +DEL+
Sbjct: 141 AKRIEDGLKHMVQAIAACPTTIAELLAMVEKVEKDELS 178


>gi|256396809|ref|YP_003118373.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256363035|gb|ACU76532.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 353

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 115/230 (50%), Gaps = 11/230 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E    + E+V+ +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 120 EGSTERKQIRDELVQMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDTERGVE 179

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S + +R PT  E+A+ 
Sbjct: 180 FSTYATPTVIGEIKRHFRDKGWAVRVPRRLQELRLSLTSATSELSQRNRRSPTVAELAEY 239

Query: 556 LAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRE 611
           L +  E V + L+      +L   +   GDED+  + D +  +      D A++    RE
Sbjct: 240 LKISEEEVLEGLESANAYSTLSLDVSEGGDEDSPAVADSLGSE------DEALEGVEYRE 293

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIE 660
           +   +L  L PRE+++L +RF   M      EE+G  Q  V+R   R +E
Sbjct: 294 SLKPLLEQLPPREKKILLLRFFGNMTQSQIAEEIGISQMHVSRLLARTLE 343


>gi|188591091|ref|YP_001795691.1| RNA polymerase factor sigma-32 [Cupriavidus taiwanensis LMG 19424]
 gi|170937985|emb|CAP62969.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Cupriavidus taiwanensis LMG
           19424]
          Length = 309

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 129/237 (54%), Gaps = 16/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 70  AARRLVMSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHW 129

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R+ ++  +    E   E +A++L +  E 
Sbjct: 130 IKAEIHEYVLKNWRMVKVATTKAQRKLFFNLRSHKQGGHTFTPEQV-EAVARELNVKPEE 188

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKN-AVSPLDSAIQANLR-ETTTRVL 617
           V ++  +++   ++LE  +  G+E+ + +    ++ N     +++  Q  ++ E     L
Sbjct: 189 VMEMETRLSGGDLALEGQVDDGEEEFAPIAYLADNHNEPTRVMEAKRQDRMQVEGLEEAL 248

Query: 618 ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A L  R  R++  R+   +N +       TL E+  +F V+ ERIRQIEA A++K+K
Sbjct: 249 AKLDERSRRIIEARW---LNVEDDGSGGATLHELADEFGVSAERIRQIEAAAMKKMK 302


>gi|303251140|ref|ZP_07337324.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253519|ref|ZP_07535389.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649991|gb|EFL80163.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859020|gb|EFM91063.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 316

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 147/285 (51%), Gaps = 42/285 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   ++ E    ++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--------RYYYDEDVEAAKQLILSHMRFVIHIARG 100

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 101 YLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVA 160

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  N++    E   +++A+ L +  E VR++  ++T + +  + P
Sbjct: 161 TTKAQR--KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLP 218

Query: 580 IGDED-------------TSHLGDFIEDKNAVSPLDSAIQANLRETT--TRVLASLTPRE 624
           +G++D             +S+  D +ED+          Q N + T      LA+L  R 
Sbjct: 219 VGEDDDEVYTPSMYLEDNSSNFADDLEDE----------QYNGQATAQLAYALATLDKRS 268

Query: 625 ERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +++ R+   ++ +  TL+++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 269 QDIIKTRW---LDEEKATLQDLAEKYGISAERVRQLENAALKKIK 310


>gi|46143484|ref|ZP_00135165.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|126209296|ref|YP_001054521.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           L20]
 gi|126098088|gb|ABN74916.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 316

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 147/285 (51%), Gaps = 42/285 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   ++ E    ++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--------RYYYDEDVEAAKQLILSHMRFVIHIARG 100

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 101 YLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVA 160

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  N++    E   +++A+ L +  E VR++  ++T + +  + P
Sbjct: 161 TTKAQR--KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLP 218

Query: 580 IGDED-------------TSHLGDFIEDKNAVSPLDSAIQANLRETT--TRVLASLTPRE 624
           +G++D             +S+  D +ED+          Q N + T      LA+L  R 
Sbjct: 219 VGEDDDEVYTPSMYLEDNSSNFADDLEDE----------QYNGQATAQLAYALATLDERS 268

Query: 625 ERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +++ R+   ++ +  TL+++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 269 QDIIKTRW---LDEEKATLQDLAEKYGISAERVRQLENAALKKIK 310


>gi|241206826|ref|YP_002977922.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|86450985|gb|ABC96760.1| putative RNA polymerase sigma factor [Rhizobium leguminosarum bv.
           trifolii TA1]
 gi|240860716|gb|ACS58383.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 287

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 124/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 40  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ +  T        +EIA  L
Sbjct: 100 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAAL 157

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANL---- 609
            + +  V+ +  +++    SL+ P   GD +++   DF+   +   PL     +N+    
Sbjct: 158 GVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDD---PLPDEQVSNMIDGE 214

Query: 610 --RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             R      L  L  RE +++  R    +  D  TLEE+G    +++ER+RQIE++A+ K
Sbjct: 215 RRRVWLASALKHLNEREMKIISAR---RLAEDGATLEELGADLGISKERVRQIESRAMEK 271

Query: 667 LK 668
           L+
Sbjct: 272 LR 273


>gi|115522843|ref|YP_779754.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisA53]
 gi|115516790|gb|ABJ04774.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           BisA53]
          Length = 299

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 119/239 (49%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P++   IA +L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDMHPDQVKLIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  + +      SL  PI D+ +     D++ D    SP   A+ A   E   R
Sbjct: 167 GVTEQDVVDMNRRLGGDASLNAPIRDDGEPGEWQDWLVDH---SPSQEAVMAEHEELDHR 223

Query: 616 ------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RAALNGAIGVLNPRERRIFEARR--LADDPMTLEDLAAEFGVSRERVRQIEVRAFEKVQ 280


>gi|288962386|ref|YP_003452681.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914652|dbj|BAI76137.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 293

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 115/239 (48%), Gaps = 12/239 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+ +A  Y   GL   DLI EGN+GLM A +KF+   G++ STYAMWW
Sbjct: 49  AAHRLVTSHLRLVVKIAGGYRGYGLPLSDLIAEGNLGLMTAVKKFEPERGFRLSTYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           +K +I   I      ++I      K     + R  R++      +  P+    IA  LA+
Sbjct: 109 IKASIQDYILRSWSLVKIGTTAAQKKLFFSLGRLKRKLGEYGGGDLHPDSVTSIATDLAV 168

Query: 559 PVEGVRKVLKITKEPI-SLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTT-- 614
           P + V  + +    P+ SL  P+  E D+    D + D           +   R+ +   
Sbjct: 169 PEDDVVAMNRRLSAPVASLNAPMSAEGDSGEWQDLLADDRPSVEESLVERGEARQRSALL 228

Query: 615 -RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +  L  RE  +L  R     ++  TLE++  ++ V+RERIRQIE +A  K+   +R
Sbjct: 229 HEAMGVLNDRERDILTSRR--LSDSPLTLEDLSVRYGVSRERIRQIEERAFEKVARQTR 285


>gi|169831385|ref|YP_001717367.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638229|gb|ACA59735.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score = 95.5 bits (236), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 138/253 (54%), Gaps = 19/253 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R ++ + ++G+    +A++ ++ ANL+LV +V +++  RG    DL Q G IGL+KA 
Sbjct: 19  ETRRLLRLSQQGDV---LARETLINANLKLVCNVIRRFEGRGYDPDDLFQIGCIGLIKAI 75

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     KFSTYA+  +   I R + D +  +R+   +++   K   T  ++  ++ R
Sbjct: 76  DKFDLRFKVKFSTYAVPMIIGEIRRFLRDDT-PLRVSRSLKELAWKAQSTREQLQVRLDR 134

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISL-ETPIGDE-DTSHLGDFIEDK--NAVSPL 601
           +PT  E+A++L +P E +   L+  + P SL E    DE D  H+ D +++K  N  + +
Sbjct: 135 DPTIGELAEELGIPREELVGALEAAQSPTSLYEVLHQDEGDPIHVMDQVQNKEENEGAWV 194

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +       R     +L SL  R+ R++  RF      D T  EV +   +++ ++ ++E 
Sbjct: 195 E-------RIALQELLDSLPERDRRIVVWRFF----EDKTQAEVARNLGLSQVQVSRLER 243

Query: 662 KAIRKLKHPSRSK 674
           +A+RKLK  +R+K
Sbjct: 244 EALRKLKSMARAK 256


>gi|78224050|ref|YP_385797.1| sigma 32 (RpoH) [Geobacter metallireducens GS-15]
 gi|78195305|gb|ABB33072.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter metallireducens
           GS-15]
          Length = 279

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 14/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ ANLR V+ VA +Y + G++ LDLIQEGNIGLM A  KFD   G +  +YA+WW
Sbjct: 45  AAHRLITANLRFVVKVAAEYKSYGMKMLDLIQEGNIGLMMAVRKFDPHKGIRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRIPV-----HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           ++  I   I      ++I        +  K+++     RR++     E T   +  K + 
Sbjct: 105 IRAYIQNYIISAWSLLKIGTTQAQKKLFFKLNQAKNAIRRLTGGDDTEATALSLHVKESE 164

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQAN-LRETTTR 615
            +E  +++    +   SL+  + D +   + D + D  +N    L    +A+ L    T+
Sbjct: 165 VIEMDQRM----RGDYSLDAELVDGEGLTMLDTLVDERQNQEEALAEQQEASRLHGQVTQ 220

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  +E  V+  R  +  +   TL+E+   F ++RER+RQIE  A++K+K
Sbjct: 221 ALERLNEKERYVVENR--VTADEPLTLQEIADHFAISRERVRQIEEGALKKIK 271


>gi|29829555|ref|NP_824189.1| RNA polymerase sigma factor, sigH [Streptomyces avermitilis
           MA-4680]
 gi|29606663|dbj|BAC70724.1| putative RNA polymerase sigma factor, sigH [Streptomyces
           avermitilis MA-4680]
          Length = 391

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 114/225 (50%), Gaps = 10/225 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+  G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   
Sbjct: 156 MLPDGSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPER 215

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+
Sbjct: 216 GVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQQHGRSPTVHEL 275

Query: 553 AKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NL 609
           A+KLA+  E V + L+       +SL+ P  D+++  + D +  +      D A++    
Sbjct: 276 AEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEY 329

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           RE+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 330 RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 374


>gi|217969486|ref|YP_002354720.1| RNA polymerase factor sigma-32 [Thauera sp. MZ1T]
 gi|217506813|gb|ACK53824.1| RNA polymerase, sigma 32 subunit, RpoH [Thauera sp. MZ1T]
          Length = 283

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 128/234 (54%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR+V+++A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 48  AARQLVMSHLRVVVAIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHW 107

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAM- 558
           +K  I   I      ++I     + K+   +R  ++ S+ ++    P E   IA +L + 
Sbjct: 108 IKAEIHEYILKNWRLVKIATTKAQRKLFFNLRGMKQDSSTLQ----PAEVRSIAAQLGVK 163

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLG-DFIEDKNA--VSPLDSAIQANLRETTTR 615
           P E V    +++   I L+    DED       ++ D +A     ++ A  A L+++  R
Sbjct: 164 PEEVVEMETRLSGRDIPLDAGSDDEDERFAPIAYLPDPHAEPSEQVEQAQLARLQDSGLR 223

Query: 616 -VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LASL  R   +++ R+ +      TL E+  ++ V+ ERIRQIEAKA++K++
Sbjct: 224 DALASLDERSRAIVQRRW-LAEGDSATLHELAAEYGVSAERIRQIEAKAMQKMR 276


>gi|291545415|emb|CBL18523.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. SR1/5]
          Length = 259

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 121/232 (52%), Gaps = 12/232 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ N      DL Q G IGL+KA + FD  L  KFSTYA+  
Sbjct: 38  ARELYIKGNLRLVLSVIRRFQNSSENPDDLFQIGCIGLIKAIDNFDTTLQVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K + T      +  +EPT  EIA ++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDIAYKTIYTRENYMRQHLKEPTIAEIADEIGIDKEMI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              +   + P+SL  P+  E  DT ++ D I DK  +   +     +LR+   R    L 
Sbjct: 157 VYAMDAIQSPVSLFEPVYSEGGDTLYVMDQISDKKNLEE-NWVEDISLRDAMNR----LG 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RE  ++ +RF  G     T  EV  +  +++ ++ ++E  A+R +++  R+
Sbjct: 212 ERERHIIDLRFYEG----KTQMEVADEIGISQAQVSRLEKHALRSMRNYLRN 259


>gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
 gi|300076221|gb|ADJ65620.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
          Length = 299

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 125/239 (52%), Gaps = 22/239 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 62  AAQKMVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHW 121

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMP 559
           +K  I   I      +++     + K+   +R+ +   + +    TP   E +AK L + 
Sbjct: 122 IKAEIHEYILKNWRLVKVATTKAQRKLFFNLRSHKEGLDAM----TPAQVEALAKTLDVK 177

Query: 560 VEGVRKV-LKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQAN--LRETTT 614
            E V ++  +++   I+LE+P  DED   + +     D +  + +  A Q +    E   
Sbjct: 178 REEVIEMETRLSGRDIALESPTDDEDDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLE 237

Query: 615 RVLASLTPREERVLRMRF-----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ L  R  R++  R+     G G     TL E+  +F V+ ERIRQIEA A++K+K
Sbjct: 238 AALSKLDERSRRIVEARWLANDDGSGA----TLHELADEFGVSAERIRQIEAVALKKMK 292


>gi|316931591|ref|YP_004106573.1| RNA polymerase sigma 32 subunit RpoH [Rhodopseudomonas palustris
           DX-1]
 gi|315599305|gb|ADU41840.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           DX-1]
          Length = 299

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 120/239 (50%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHQLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    R+  +KI    + +  P+    IA +L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--KLFFNLRKAKSKISALDEGDLHPDHVKLIASRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  + V  + +      SL  PI D+ +     D++ D+   SP   A+ A   E   R
Sbjct: 167 GVTEQDVVDMNRRLGGDASLNAPIRDDGEPGEWQDWLVDQ---SPSQEAVLAEHEELDQR 223

Query: 616 ------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L PRE R+   R     +   TLE++  +F V+RER+RQIE +A  K++
Sbjct: 224 RAALNGAIQVLNPRERRIFEARR--LADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQ 280


>gi|315646368|ref|ZP_07899486.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
 gi|315278011|gb|EFU41331.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
          Length = 251

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/253 (26%), Positives = 132/253 (52%), Gaps = 17/253 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T +  +E + ++++ + G+   ++A+  +V  N+RLV SV +++ NRG +  DL Q G 
Sbjct: 10  QTYLDDAEVKRLIALSQSGD---NVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGC 66

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    
Sbjct: 67  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKEMANKVRKKRDE 125

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S ++ R PT +E+A++L +  E V    +  K P S+   +   D D   L D I D++
Sbjct: 126 LSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQIADES 185

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                D       +      +  LT RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 186 QERWFD-------KLALNEAIGGLTERERLIVYLRY----YRDQTQSEVASRLGISQVQV 234

Query: 657 RQIEAKAIRKLKH 669
            ++E K ++ +++
Sbjct: 235 SRLEKKILQSIRN 247


>gi|148645062|gb|ABR01056.1| RpoD [uncultured Geobacter sp.]
          Length = 72

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 42/71 (59%), Positives = 58/71 (81%)

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTY  WW++QAITR+J DQ+ TIRIPVHM + I+K++RT+R++  +
Sbjct: 1   KAVDKFEYQRGYKFSTYXTWWIRQAITRAJXDQARTIRIPVHMIETINKLIRTSRQLVQE 60

Query: 543 IKREPTPEEIA 553
           I REP PEEIA
Sbjct: 61  IGREPMPEEIA 71


>gi|116254340|ref|YP_770178.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258988|emb|CAK10097.1| putative rpoH sigma factor [Rhizobium leguminosarum bv. viciae
           3841]
          Length = 304

 Score = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 124/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 57  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ +  T        +EIA  L
Sbjct: 117 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAAL 174

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANL---- 609
            + +  V+ +  +++    SL+ P   GD +++   DF+   +   PL     +N+    
Sbjct: 175 GVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDD---PLPDEQVSNMIDGE 231

Query: 610 --RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             R      L  L  RE +++  R    +  D  TLEE+G    +++ER+RQIE++A+ K
Sbjct: 232 RRRVWLASALKHLNEREMKIISAR---RLAEDGATLEELGADLGISKERVRQIESRAMEK 288

Query: 667 LK 668
           L+
Sbjct: 289 LR 290


>gi|163794484|ref|ZP_02188455.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
 gi|159180208|gb|EDP64731.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
          Length = 298

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 82/286 (28%), Positives = 139/286 (48%), Gaps = 36/286 (12%)

Query: 410 RNEIKSISVETGIS--ISEFRHIVSMVRKGECEASIAK-----------KEMVEANLRLV 456
           R  + SISVE  +S  + E R    M+  GE E  +AK            ++V ++LRLV
Sbjct: 5   RANLPSISVEGNLSRYLQEIRKF-PMLEPGE-EYVLAKSWREHDDVESAHKLVTSHLRLV 62

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
             +A  Y   GL   +LI EGN+G+M+A ++FD   G++ +TYAMWW++ +I   I    
Sbjct: 63  AKIAMGYRGYGLPLAELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRASIQEYILHSW 122

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE---IAKKLAMPVEGVRKVLKI 569
             +++      K  K+    RR+  +++     + +PE    IA+KL +    V  + + 
Sbjct: 123 SLVKMGTTAAQK--KLFFNLRRLKGQMQAIEDGDLSPERVTAIAEKLDVSEADVVSMNRR 180

Query: 570 TKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREE 625
              P  SL  P+  +      D++ D+     +  A    L   R      + +L  RE 
Sbjct: 181 LASPDHSLNAPLRQDGEGEWQDWLVDEGQNQEVSFAEDEELSKRRRLLNVAMETLNDRER 240

Query: 626 RVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L   R+R     +   TLE++ +++ ++RER+RQIE +A  KL+
Sbjct: 241 HILTERRLR-----DNPTTLEDLSQEYDISRERVRQIEVRAFEKLQ 281


>gi|4103482|gb|AAD01786.1| sigma-E factor [Myxococcus xanthus]
          Length = 280

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 125/236 (52%), Gaps = 14/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLI--QEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A   +V  NLRLV+ +A +Y    L  LDL+  QEGNIGLM+A +K+D   G K S+YA 
Sbjct: 30  AAYRLVAWNLRLVVKLAHEYHRNPLSLLDLVLVQEGNIGLMQAVKKYDPERGVKLSSYAA 89

Query: 502 WWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           WW++  I R I D    +++     + K+   +R  +        E +P+ +A++L +  
Sbjct: 90  WWIRAYILRYIMDNWKMVKLGTTEAQRKLFFKLRQEQEKLIAQGFEASPKLLAERLNVTE 149

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLD-----SAIQANLRET 612
           + V ++  ++  + +S++ P+G++D S     D     N++ P D       ++A  RE 
Sbjct: 150 QDVVEMDQRLGHDEMSIDAPLGNDDDSRTTRADRYLPSNSM-PADERLGAEQLKALFREK 208

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    +L  +E  +   R  +  +   TL+++G ++ V+RER RQIEA  I +++
Sbjct: 209 LSEFARTLEGKERFIFESR--LVSDEPLTLQDIGDKYGVSRERARQIEAALINRMR 262


>gi|297562622|ref|YP_003681596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296847070|gb|ADH69090.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 267

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 116/229 (50%), Gaps = 16/229 (6%)

Query: 435 RKGECEASIAKK-----EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           R GE EA   ++     E+VE +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD
Sbjct: 28  RLGELEADSEERRRIRDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFD 87

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +FSTYA   +   I R   D+   +R+P  +++    + +    +S +  R PT 
Sbjct: 88  LERGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAVSDLSQREGRSPTV 147

Query: 550 EEIAKKLAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E+A  L M  E V + L+       +SL+ P  GDED   + D      ++  +D +++
Sbjct: 148 AELAAHLQMTEEEVLEGLESANAYSTVSLDAPDSGDEDAPAVAD------SLGIVDESLE 201

Query: 607 A-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
               RE+   +L  L PRE+R+L +RF   M      +E+G  Q  V+R
Sbjct: 202 GVEYRESLKPLLEQLPPREKRILLLRFFGNMTQSQIAQELGISQMHVSR 250


>gi|326571483|gb|EGE21498.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC7]
          Length = 371

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 124/240 (51%), Gaps = 16/240 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 128 GDVEAA---RLLVMSHLRFVIHIARSYSGYGLSQADLIQEGNLGLMKAVKRFDPNKGVRL 184

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++       K+   +R+ ++ SN++  +     IA  
Sbjct: 185 VSFAVHWIKAEIHEFVIKNWRIVKVATTKAHRKLFFNLRSLKKSSNQLTLDEAT-AIAND 243

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET 612
           L + V+ V ++  ++T    S E    D+D        F+ED  AV+P D   +A+  E 
Sbjct: 244 LNVTVKQVLEMESRLTSYDASFEAQDSDDDEGRYAPQLFLED--AVNPADVVEEADWEEN 301

Query: 613 TTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TT  L     +L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+ K+K
Sbjct: 302 TTTALKDAMETLDERSRDIITQRWLADQKS--TLHELAATYNISAERVRQIEKNAMNKIK 359


>gi|209551384|ref|YP_002283301.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209537140|gb|ACI57075.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 287

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 124/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 40  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ +  T        +EIA  L
Sbjct: 100 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAAL 157

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANL---- 609
            + +  V+ +  +++    SL+ P   GD +++   DF+   +   PL     +N+    
Sbjct: 158 GVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDD---PLPDEQVSNMIDGE 214

Query: 610 --RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             R      L  L  RE +++  R    +  D  TLEE+G    +++ER+RQIE++A+ K
Sbjct: 215 RRRVWLASALKHLNEREMKIISAR---RLAEDGATLEELGADLGISKERVRQIESRAMEK 271

Query: 667 LK 668
           L+
Sbjct: 272 LR 273


>gi|150397812|ref|YP_001328279.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029327|gb|ABR61444.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 301

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 121/251 (48%), Gaps = 28/251 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K AI   I      +++      K  ++    RR+  +I+     +  PE   EIA  L
Sbjct: 109 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQA------- 607
            +  + V  + +      SL  PI   + D+    D++ D+N     D+  Q        
Sbjct: 167 KVSEDEVISMNRRLSGDASLNAPIKASEGDSGQWQDWLVDEN-----DNQEQILIEQDEL 221

Query: 608 -NLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIR 665
            N R      L  L  RE R+   R    +  D  TLE++  +F ++RER+RQIE +A  
Sbjct: 222 DNRRALLANALKVLNDRERRIFEAR---RLTEDPITLEDLSTEFDISRERVRQIEVRAFE 278

Query: 666 KLKHPSRSKKL 676
           K++   R   L
Sbjct: 279 KVQEAVRKAAL 289


>gi|326386899|ref|ZP_08208513.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326208579|gb|EGD59382.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 300

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KFD   G++ +TYAMWW
Sbjct: 52  AAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPDRGFRLATYAMWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    RRM   ++     +  P++   IA  L
Sbjct: 112 IKASIQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKKNLEAFEDSDLHPDDVKKIATDL 169

Query: 557 AMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +P   V  + +  +     SL  P+ ++      D++ D+    PL     A+  E   
Sbjct: 170 GVPEADVVSMNRRMMMGGDASLNVPLREDGEGSWQDWLADER---PLQDEAVADAEEAQV 226

Query: 615 R------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R       +  L  RE  +L  R  +  +   TLEE+ + + V+RER+RQIE +A  KL+
Sbjct: 227 RHDLLVEAMQDLNDRERHILIDRRLV--DEPKTLEELSQVYHVSRERVRQIEVRAFEKLQ 284


>gi|302877701|ref|YP_003846265.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
 gi|302580490|gb|ADL54501.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
          Length = 284

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 127/232 (54%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR+V+SVA+ Y   GL   DLIQEGNIGLMKA + +D   G +  ++A+ W
Sbjct: 49  AARQLVLSHLRVVVSVARGYAGYGLPQADLIQEGNIGLMKAVKHYDPEFGVRLVSFALHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   +      ++I     + K+   +R+ ++    +K +    EIA++L +    
Sbjct: 109 IRAEINEFVVRNWRMVKIATTKAQRKLFFNLRSLKQGLESLKPKQI-SEIAEQLNVSEHD 167

Query: 563 VRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSP---LDSAIQANLR-ETTTR 615
           V ++  +     ++L+ P G  D+DT     ++ D     P   L+S+   +LR +   R
Sbjct: 168 VIEMEARFAGHEVALD-PAGSDDDDTYAPIQYLADSEEHEPSNILESSEGLSLRTQGLAR 226

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LASL  R  R++  R+ +  + + TL ++  +F V+ ERIRQIE KA+ K+
Sbjct: 227 ALASLDDRSRRIVEARW-LSEDQNATLHDLAAEFKVSAERIRQIEQKAMSKM 277


>gi|222086841|ref|YP_002545375.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221724289|gb|ACM27445.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 302

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 124/253 (49%), Gaps = 24/253 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDEGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  E V  + +      SL  PI   + ++    D++ D +         Q  L   R 
Sbjct: 167 KVSEEEVISMNRRLSGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELDTRRR 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              R ++ L  RE R+   R    ++ D  TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 227 MLARAMSVLNDRERRIFEAR---RLSEDPVTLEDLSSEFDISRERVRQIEVRAFEKVQEA 283

Query: 671 ------SRSKKLR 677
                  R+K LR
Sbjct: 284 VQKDALERAKALR 296


>gi|296112758|ref|YP_003626696.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|295920452|gb|ADG60803.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|326561004|gb|EGE11369.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 7169]
 gi|326566767|gb|EGE16906.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 103P14B1]
 gi|326567391|gb|EGE17506.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC1]
 gi|326575234|gb|EGE25162.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis CO72]
 gi|326576679|gb|EGE26586.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 101P30B1]
 gi|326577646|gb|EGE27523.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis O35E]
          Length = 371

 Score = 95.1 bits (235), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 124/240 (51%), Gaps = 16/240 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 128 GDVEAA---RLLVMSHLRFVIHIARSYSGYGLSQADLIQEGNLGLMKAVKRFDPNKGVRL 184

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++       K+   +R+ ++ SN++  +     IA  
Sbjct: 185 VSFAVHWIKAEIHEFVIKNWRIVKVATTKAHRKLFFNLRSLKKSSNQLTLDEAT-AIAND 243

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET 612
           L + V+ V ++  ++T    S E    D+D        F+ED  AV+P D   +A+  E 
Sbjct: 244 LNVTVKQVLEMESRLTSYDASFEAQDSDDDEGRYAPQLFLED--AVNPADVVEEADWEEN 301

Query: 613 TTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TT  L     +L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+ K+K
Sbjct: 302 TTTALKDAMETLDERSRDIITQRWLADQKS--TLHELAATYNISAERVRQIEKNAMNKIK 359


>gi|149915381|ref|ZP_01903908.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149810670|gb|EDM70511.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 292

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 123/248 (49%), Gaps = 25/248 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-----------EEI 552
           +K +I   +      +R       K   +    RR+  +I+RE              E I
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARIEREAMAKGEQLDGHQLREMI 158

Query: 553 AKKLAMP---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK----NAVSPLDSAI 605
           A ++ +P   VE +   L  T   ++    + DE    + D IED+    + +   D  +
Sbjct: 159 AHEVGVPLRDVEMMEGRLSGTDFSLNATQSVEDEGREWI-DTIEDEGPRGDQLVEQDHDL 217

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A LRE     ++ L  RE  ++R R     +   TLE +G++  +++ER+RQ+EA A +
Sbjct: 218 MA-LREWLGDAMSKLNDRERFIVRER--KLRDVPRTLESLGEELNLSKERVRQLEAAAFQ 274

Query: 666 KL-KHPSR 672
           K+ KH  R
Sbjct: 275 KMRKHLER 282


>gi|297202300|ref|ZP_06919697.1| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
 gi|297148082|gb|EDY54214.2| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
          Length = 381

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 115/224 (51%), Gaps = 10/224 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G
Sbjct: 147 MKDGSPEYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRG 206

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A
Sbjct: 207 VEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELA 266

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           +KLA+  E V + L+       +SL+ P  D+++  + D +  +      D A++    R
Sbjct: 267 EKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYR 320

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           E+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 321 ESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 364


>gi|33520062|ref|NP_878894.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia floridanus]
 gi|33504408|emb|CAD83301.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia floridanus]
          Length = 283

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 124/234 (52%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMK+  +F+  L  +  ++A+ W
Sbjct: 50  AAKKLIVSHLRFVIHVARNYSGYGLSQADLIQEGNIGLMKSIRRFNPELDVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      ++I      R     + +T +R+      E   E +AK L +  +
Sbjct: 110 IKSEIHEYVLKNWRIVKIATTKAQRKLFFNLRKTKQRLG--WFNEGEIEMVAKTLHVTCK 167

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTRV 616
            VR++  ++  + ++LE P  DED  ++      +++DK  +   +      +       
Sbjct: 168 DVREMESRMAAQDMTLEQPYLDEDDKNILSIPMLYLQDKITIIDDEEEWIDQVSNKLNIA 227

Query: 617 LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +L  R + ++R R+   +N D+  TL+E+  Q+ ++ ERIRQ+E  A++K+K
Sbjct: 228 LNTLDKRSQHIIRARW---LNADNKTTLQELANQYGISAERIRQLEKNAMKKMK 278


>gi|290957490|ref|YP_003488672.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260647016|emb|CBG70115.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 388

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 112/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 157 GSVEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 216

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A+KL
Sbjct: 217 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQQHGRSPTVHELAEKL 276

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
           A+  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 277 AISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 330

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 331 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 371


>gi|27884311|dbj|BAC55891.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus]
          Length = 318

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 112/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 87  GSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 146

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++L
Sbjct: 147 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAERL 206

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 207 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L +L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 261 KPLLEALPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 301


>gi|326201325|ref|ZP_08191197.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
 gi|325988893|gb|EGD49717.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
          Length = 248

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/241 (29%), Positives = 128/241 (53%), Gaps = 11/241 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++++ K +     A+  +VE N+ LV S+ K++ NRG +  DL Q G+IGL+KA  KFD
Sbjct: 9   VLTLIIKAKAGDKQAQSVLVERNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFD 68

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R I D    I++   +++   K   T   MS ++ REPT 
Sbjct: 69  TSYDVKFSTYAVPMIIGEIKRFIRDDGI-IKVSRSLKEISSKARITKEIMSKELGREPTI 127

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
            EIA+++ +  E +   ++    P SL + IGD D S   L D I+  +    +D   + 
Sbjct: 128 NEIAQRMNISPEELVMAIEAGCTPESLYSTIGDGDNSPILLIDRIDAADNNCEVDLIDKI 187

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +R+    +L +L  RE +++ +R+      + T  ++ K   +++ ++ +IE K +R +
Sbjct: 188 AIRQ----ILDTLDTRERQIIILRYF----KEKTQVQIAKLLGISQVQVSRIEKKILRDI 239

Query: 668 K 668
           K
Sbjct: 240 K 240


>gi|259417918|ref|ZP_05741837.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
 gi|259346824|gb|EEW58638.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
          Length = 298

 Score = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 122/250 (48%), Gaps = 18/250 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-- 560
           ++ +I   I      +++     + K+   +R A+     ++      E  KK+A  +  
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPEAVKKIATDLGV 168

Query: 561 ---EGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   +G   + T    D++ED+ A    D   Q  L   RE 
Sbjct: 169 TEDEVISMNRRMSGGDASLNAMVGGDGDSTMQWQDWLEDEGADQAGDYEAQDELQARREL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               ++ L  RE+ +L  R     +   TLEE+  Q+ V+RERIRQIE +A  KL+    
Sbjct: 229 LAEAMSVLNDREKDILTQRRLA--DQAKTLEELSVQYDVSRERIRQIEVRAFEKLQ---- 282

Query: 673 SKKLRSFLDG 682
            KK+R    G
Sbjct: 283 -KKMRELAAG 291


>gi|209542656|ref|YP_002274885.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209530333|gb|ACI50270.1| RNA polymerase, sigma 32 subunit, RpoH [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 295

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 20/245 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ EA+ A   +V ++LRLV  +A  Y   GL   +LI EGNIG+M+A  +FD   G++
Sbjct: 42  KGDTEAAHA---LVTSHLRLVAKIAMGYRGYGLPLGELISEGNIGMMQAVRRFDPDRGFR 98

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE 551
            +TYAMWW++ AI   I      +++      K  K+    RR+  +++     +  PE+
Sbjct: 99  LATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIDDGDLKPEQ 156

Query: 552 ---IAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDK--NAVSPLDSAI 605
              IA+ L +P + V  + +    P  SL  P+  +      D++ D+  N    L    
Sbjct: 157 VNKIAESLGVPEQDVINMNRRLSAPDHSLNAPLRADSEGEWQDWLVDEHDNQEQTLAENE 216

Query: 606 QANLRETTT-RVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKA 663
           + + R+      + +L  RE  +L  R    +  D  TLEE+   + ++RER+RQIE +A
Sbjct: 217 EFSGRKALLDNAMKTLNDRERHILTER---RLKDDPATLEELSHTYNISRERVRQIEVRA 273

Query: 664 IRKLK 668
             K++
Sbjct: 274 FEKVQ 278


>gi|56695321|ref|YP_165669.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56677058|gb|AAV93724.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 292

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 129/253 (50%), Gaps = 18/253 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A      + R    + IA 
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAATDGLALDRHQLHQMIAS 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---L 609
           ++ +P+  V  +  +++    SL  T   DE+     + +ED++  +    A + +   L
Sbjct: 161 EIGVPLRDVEMMEGRLSGSDFSLNATQASDEEGREWIEALEDESEQAAELVAHRHDTEQL 220

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     + +L  RE  ++R R     +   TLE +G +  +++ER+RQ+EA A  K++ 
Sbjct: 221 RDWLIEAMQALNERERFIVRER--KLRDEPRTLESLGDELGLSKERVRQLEAAAFAKMRK 278

Query: 670 P--SRSKKLRSFL 680
              +RS++++ FL
Sbjct: 279 SLEARSREVQHFL 291


>gi|298708236|emb|CBJ48299.1| rpoD [Ectocarpus siliculosus]
          Length = 381

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 130/265 (49%), Gaps = 44/265 (16%)

Query: 440 EASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E   A++ +   +  LV SVA +Y   +R L   DL QEGN+GL++A EKFD   G +FS
Sbjct: 109 EGRKAQRTLALCHQGLVRSVAYRYKQVSRNLSLDDLTQEGNVGLLEAVEKFDSTKGTRFS 168

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE-PTPEEIAKKL 556
           +YA++ +K ++ R+IAD+   +R+PVH +D   +++  +  +  +   + PT  ++A  L
Sbjct: 169 SYAVFRIKASVLRAIADKDRLVRVPVHAQDAAMRILAASHALQLESGGDVPTDAQLAVAL 228

Query: 557 AMPVEGV---RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS-------------- 599
            MP   V   RK L        L   I D D   L    + +                  
Sbjct: 229 GMPEASVALYRKSL--------LPQNIADLDNPALPSSPQGRGGSGAAGGGSLGGRVGGE 280

Query: 600 --PLDSA--IQANL--RETTTRVLASLTPREERVLRMRFGIGMNTDH----------TLE 643
             P +++   QA++  R+    + A L+P EER LR+RFG+G               T +
Sbjct: 281 QWPWEASQLAQAHVVRRDMMRAMQACLSPTEERALRLRFGLGGAEKEGAVADGGGALTFK 340

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G+   ++ E IR++  ++I KL+
Sbjct: 341 EIGRTMELSAEGIRKMVFRSIAKLQ 365


>gi|327441148|dbj|BAK17513.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 121/232 (52%), Gaps = 13/232 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           I ++++V  NLRLV+S+  +Y  RG Q  DL Q G IGL+KA + FD     +FSTYA+ 
Sbjct: 36  IVREQLVFCNLRLVLSIVGRYAYRGEQADDLFQVGCIGLLKAIDNFDLKHNVRFSTYAVP 95

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D    +R+   +RD  +K ++   +   +   EPT E++A+ + M  E 
Sbjct: 96  MIMGEIRRHLRDHH-ALRVSRSLRDIAYKAMKAKEQFIAEHLTEPTIEQLAQAIEMKKED 154

Query: 563 VRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           V   L   ++P+SL+ PI  +  D   + D I+DK        +I  +L+E+  +    L
Sbjct: 155 VLFALDAIQDPMSLQEPIYSDGGDAIFMIDQIKDKVTEEHWVGSI--SLQESMKK----L 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             R++ ++  RF +G     T  E+ +   +++ +I ++E  A+  +K   R
Sbjct: 209 NSRQKMIIEKRFFLG----ETQTEIAQSLGISQAQISRLEKSAVELMKRDFR 256


>gi|307728369|ref|YP_003905593.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
 gi|307582904|gb|ADN56302.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
          Length = 311

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 124/250 (49%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP+EI        +G
Sbjct: 132 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDEI--------DG 179

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + K L + +E ++ +ET +   D +  G   + + + +P+  A  A+     T VLAS  
Sbjct: 180 LAKELNVKREEVAEMETRLSGGDVALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQ 237

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L  R  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 238 RDKLQSDGIATALEALDARSRRIIEARWLKVQDDGSGGSTLH---ELADEFGVSAERIRQ 294

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 295 IEASAMKKMR 304


>gi|119715950|ref|YP_922915.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536611|gb|ABL81228.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 270

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 65/218 (29%), Positives = 113/218 (51%), Gaps = 11/218 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L LV   A+++ NRG    DL+Q G IGL+K+ ++FD   G +FSTYA   +   
Sbjct: 49  LVHLHLPLVEHCARRFRNRGEPLEDLVQVGTIGLIKSVDRFDADRGVEFSTYATPTIIGE 108

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R   D+   IR+P  +++   ++   +  ++  + R PTP E+A  +   VE + + +
Sbjct: 109 IKRYFRDKGWAIRVPRRLQELRMQISTASAELTQSLGRSPTPRELAGAIGCTVEEIVEGI 168

Query: 568 KITKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPR 623
           + +    +L    T  GD++T+ + D      A+   D  ++   +RE+   +L  L PR
Sbjct: 169 ESSNAYSTLSLDATDDGDDNTASMLD------AIGVDDEGLEHVEIRESLKPLLDRLEPR 222

Query: 624 EERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIE 660
           E+++L +RF   M      EE+G  Q  V+R   R +E
Sbjct: 223 EKKILLLRFFKNMTQSQIAEEIGVSQMHVSRLLNRTLE 260


>gi|253999699|ref|YP_003051762.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. SIP3-4]
 gi|253986378|gb|ACT51235.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. SIP3-4]
          Length = 284

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 128/243 (52%), Gaps = 31/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LRLV S+A+ Y+  GL   DLIQEGN+GLMKA  +FD   G +  ++AM W
Sbjct: 49  AAKGLIVSHLRLVASIARGYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++ S+ +    +P+E+A         
Sbjct: 109 IKAEIHEYIVRNWRLVKVATTKAQRKLFFNLRSMKKNSHTL----SPDEVAD-------- 156

Query: 563 VRKVLKI-TKEPISLETPIGDEDTSHLGD-------------FIEDKNA-VSPLDSAIQA 607
           + + LK+  +E + +E+ +G  + S  G+             ++ED+    S L +  +A
Sbjct: 157 IARELKVKPEEVVEMESRMGGHEISLEGNSDDDSEDSFSPIAYLEDQQPEPSELLAEREA 216

Query: 608 NLRETT--TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              +T      L SL  R  R+++ R+ +  N   TL ++  +F V+ ERIRQIE KA++
Sbjct: 217 EHNQTVGLAHALESLDDRSRRIVQARW-LQENNSATLHDLAAEFGVSAERIRQIEQKAMQ 275

Query: 666 KLK 668
           K+K
Sbjct: 276 KMK 278


>gi|239623454|ref|ZP_04666485.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521485|gb|EEQ61351.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 258

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 121/229 (52%), Gaps = 16/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++N      DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCIGLIKAIDNFDITQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +    +++    +EPT  EIA+++ +  E +
Sbjct: 98  ILGEVRRYLRDNN-SIRVSRSLRDTAYKALYAREQLTRVNSKEPTLVEIAQEIGVSKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV--LAS 619
              L   + P+SL  P+  +  D  ++ D I DK         ++ N  E  + V  +  
Sbjct: 157 TYALDAIQTPVSLYEPVYTDGGDPLYVMDQISDK-------KNLEENWVEDLSLVEAMKR 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K
Sbjct: 210 LPERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKSMK 254


>gi|160935677|ref|ZP_02083052.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441421|gb|EDP19131.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 120/229 (52%), Gaps = 16/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++N      DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCIGLIKAIDNFDITQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +    +++    +EPT  EIA+++ +  E +
Sbjct: 98  ILGEVRRYLRDNN-SIRVSRSLRDTAYKALYAREQLTRTNSKEPTLMEIAQEIGVSKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV--LAS 619
              L   + P+SL  P+  +  D   + D I DK         ++ N  E  + V  +  
Sbjct: 157 TYALDAIQTPVSLYEPVYTDGGDPLFVMDQISDK-------KNLEENWVEDLSLVEAMKR 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K
Sbjct: 210 LPERERHIIDMRFFEG----KTQTEVAQEIHISQAQVSRLEKNALKSMK 254


>gi|297158639|gb|ADI08351.1| RNA polymerase sigma factor, sigma L [Streptomyces bingchenggensis
           BCW-1]
          Length = 276

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 121/242 (50%), Gaps = 9/242 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++ R    E +  +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 30  LSRSLFLRLAALDRD-SVEHTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +T+  +S 
Sbjct: 89  IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELSQ 148

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVS 599
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D       + D+    
Sbjct: 149 KLDRSPTVTELATALGVSEEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE 206

Query: 600 PLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIR 657
             DSA++    RE+   +LA L PRE +++ +RF   M      EEVG  Q  V+R   R
Sbjct: 207 --DSALEGVEYRESLKPLLAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTR 264

Query: 658 QI 659
            +
Sbjct: 265 TL 266


>gi|269961508|ref|ZP_06175871.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
 gi|269833737|gb|EEZ87833.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
          Length = 285

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 146/278 (52%), Gaps = 26/278 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E    ++E  H       GE +A+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRSVNSYPMLTPEEERGLAERLHY-----NGEIDAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I 
Sbjct: 68  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++     + + P
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMP 185

Query: 580 IGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRM 630
           + D+D+++       ++EDK+  S +   I+A   ET T       LASL  R +R++R 
Sbjct: 186 MDDDDSANSYTAPMVYLEDKS--SDVADNIEAANWETHTNNRLGHALASLDERSQRIVRS 243

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+    +   TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 244 RWLD--DEKATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|190893879|ref|YP_001980421.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190699158|gb|ACE93243.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 287

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 125/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 40  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ +  T        +EIA  L
Sbjct: 100 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAAL 157

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + +  V+ +  +++    SL+ P   GD +++   DF+   +   PL     +N+ +  
Sbjct: 158 GVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDD---PLPDEQVSNMIDGE 214

Query: 614 TR------VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            R       L  L  RE +++  R    +  D  TLEE+G    +++ER+RQIE++A+ K
Sbjct: 215 RRRIWLASALKHLNEREMKIISAR---RLAEDGATLEELGADLGISKERVRQIESRAMEK 271

Query: 667 LK 668
           L+
Sbjct: 272 LR 273


>gi|282861039|ref|ZP_06270104.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563697|gb|EFB69234.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 323

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 92  GSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 151

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++L
Sbjct: 152 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQYGRSPTVHELAERL 211

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 212 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 265

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 266 KPLLEGLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 306


>gi|302343327|ref|YP_003807856.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301639940|gb|ADK85262.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 346

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 79/241 (32%), Positives = 127/241 (52%), Gaps = 30/241 (12%)

Query: 444 AKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A   +V +NLRLV+ +A   ++Y  R L  LDLIQEGN+GL++A +KFD   G KFS YA
Sbjct: 97  AAAMLVTSNLRLVVKIAMEHQRYWMRNL--LDLIQEGNMGLLQAVQKFDPFRGIKFSYYA 154

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLA 557
            +W+K  I + I D    +R+      +  K+    RR   K++ +   P P  + ++L 
Sbjct: 155 SFWIKAYILKFIMDNWRLVRVGTTQAQR--KLFYKLRREKEKLQAQGVTPGPRLLGQRLG 212

Query: 558 MPVEGVRKV-LKITKEPISLETPIGDE-DTSHLGDFIEDKNAV-SPLDSAIQ----ANLR 610
           +  + V  +  ++    +SL+ P+ D+ D +H       KN + SP  +A Q    + LR
Sbjct: 213 VSEKDVVDMEQRLDSWELSLDAPVRDDSDDTH-------KNLLPSPRPTAEQDLADSELR 265

Query: 611 ETTTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +   R L     +L  +E+ +L  R  +      TL EVG +  V+RERIRQ++ + + K
Sbjct: 266 QLFHRKLMEFRQTLDDKEQDILDNR--LLAENPQTLSEVGDRHGVSRERIRQLQVRLMEK 323

Query: 667 L 667
           L
Sbjct: 324 L 324


>gi|119899581|ref|YP_934794.1| RNA polymerase factor sigma-32 [Azoarcus sp. BH72]
 gi|119671994|emb|CAL95908.1| RNA polymerase sigma-32 factor [Azoarcus sp. BH72]
          Length = 284

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 125/231 (54%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR+V+++A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 49  AARQLVMSHLRVVVAIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVE 561
           +K  I   I      ++I     + K+   +R+ ++ +  + R+   E +A +L + P E
Sbjct: 109 IKAEIHEYILKNWRLVKIATTKAQRKLFFNLRSLKQDTGTLNRDEV-EAVATQLGVKPEE 167

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRETTTR-VL 617
            V    +++   I ++    DED            A  P   L+ A +A+L++T  +  L
Sbjct: 168 VVEMETRLSGRDIPIDGGNDDEDERFAPIAYLPAPAAEPSEVLERAERAHLQDTGLKQAL 227

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R   ++  R+ +      TL E+  ++ V+ ERIRQIEAKA++K++
Sbjct: 228 GALDERSRTIVERRW-LTDGDSATLHELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|222053896|ref|YP_002536258.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
 gi|221563185|gb|ACM19157.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
          Length = 283

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 114/247 (46%), Gaps = 39/247 (15%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +++ +NLR V+ +A +Y   G++ LDLIQEGN+GLM A  KF+   G++  +YA+WW
Sbjct: 45  AAHKLITSNLRFVVKIAGEYRAYGMKMLDLIQEGNVGLMMAVRKFNPHKGFRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   I      ++I            +  R++  K+ +       AK     + G 
Sbjct: 105 IRAYIQNHIISAWSLLKI---------GTTQAQRKLFFKLNQ-------AKSAIRNMTGG 148

Query: 564 RKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSP-------------------LDS 603
            +  + T E + + ET + + D    GDF  D   ++                    L  
Sbjct: 149 GEDFQATAEALDVKETEVAEMDQRMRGDFFLDAQVITGEGLTMLESLPDERRNQEELLAE 208

Query: 604 AIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           A ++ L E      L  L  +E  V+  R  +   +  TL+E+   F ++RER+RQIE  
Sbjct: 209 AQESALLEKQVASALTCLNEKERYVIEQR--VSAESPLTLQEIADHFSISRERVRQIEEG 266

Query: 663 AIRKLKH 669
           A++K+K 
Sbjct: 267 ALKKMKQ 273


>gi|225024603|ref|ZP_03713795.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
 gi|224942617|gb|EEG23826.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
          Length = 283

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 133/244 (54%), Gaps = 20/244 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 43  QGDLEAA---KKLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPNRGAR 99

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEE--- 551
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +    +PEE   
Sbjct: 100 LFSFAVHWIKAEIHEFILRNWRMVRVATTKPQRKLFFNLRSMRKSMNAL----SPEEAQT 155

Query: 552 IAKKLAMPVEGVRKV-LKITKEPISL--ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-- 606
           IA  L + ++ V ++  ++T + I+L  +    DED+    D++ D  +  P     Q  
Sbjct: 156 IADDLGVKMDEVLEMEQRMTGKDIALLPDNSDSDEDSYAPIDWLADTRS-EPTQQIAQKA 214

Query: 607 --ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A   E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQIEAKAI
Sbjct: 215 RYAMQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHELAAEYGVSAERIRQIEAKAI 273

Query: 665 RKLK 668
           +KL+
Sbjct: 274 QKLR 277


>gi|307328850|ref|ZP_07608020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885515|gb|EFN16531.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 276

 Score = 94.7 bits (234), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 113/228 (49%), Gaps = 8/228 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K   EA   +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +
Sbjct: 43  KDSAEAGYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVE 102

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D S ++R+P  +++    + + +  +S ++ R PT  E+A  
Sbjct: 103 FPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQRLDRSPTVPELATA 162

Query: 556 LAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L +  E V   L +       SL++P  ++D       + D+      DSA++    RE+
Sbjct: 163 LGVSEEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DSALEGVEYRES 218

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
              +LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 219 LKPLLAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 266


>gi|313201748|ref|YP_004040406.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. MP688]
 gi|312441064|gb|ADQ85170.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. MP688]
          Length = 290

 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 128/243 (52%), Gaps = 31/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LRLV S+A+ Y+  GL   DLIQEGN+GLMKA  +FD   G +  ++AM W
Sbjct: 55  AAKGLIVSHLRLVASIARGYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHW 114

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++ S+ +    +P+E+A         
Sbjct: 115 IKAEIHEYIVRNWRLVKVATTKAQRKLFFNLRSMKKNSHTL----SPDEVAD-------- 162

Query: 563 VRKVLKI-TKEPISLETPIGDEDTSHLGD-------------FIEDKNA-VSPLDSAIQA 607
           + + LK+  +E + +E+ +G  + S  G+             ++ED+    S L +  +A
Sbjct: 163 IARELKVKPEEVVEMESRMGGHEISLEGNSDDDSEDSFSPIAYLEDQQPEPSELLAEREA 222

Query: 608 NLRETT--TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              +T      L SL  R  R+++ R+ +  N   TL ++  +F V+ ERIRQIE KA++
Sbjct: 223 EHNQTVGLAHALESLDDRSRRIVQARW-LQENNSATLHDLAAEFGVSAERIRQIEQKAMQ 281

Query: 666 KLK 668
           K+K
Sbjct: 282 KMK 284


>gi|83950005|ref|ZP_00958738.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837904|gb|EAP77200.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 277

 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 119/240 (49%), Gaps = 18/240 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A KY   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLINAYMRLAISMASKYRRYGAPLNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K  I   +      +R         +  +MR    ++ R A     ++      E IA 
Sbjct: 86  IKAGIQDYVMRNWSMVRTGSTSSQKALFFNMRRVRAQIEREAEASGTRLDGHQLREMIAT 145

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSP---LDSAIQANL 609
           ++ +P+  V  +  +++   +SL      ED      D +ED    +     +   Q  L
Sbjct: 146 EVGVPLRDVEMMEGRLSGSDLSLNATQSTEDEGREWIDALEDDGPRAEEMVEEDHDQRVL 205

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      LA+L  RE  +LR R    ++ +  TLE +G++  +++ER+RQ+EA A+ K++
Sbjct: 206 RLWLRDALAALNDRERFILRHR---KLSEEVRTLESLGEELGLSKERVRQLEAAALVKMR 262


>gi|261405990|ref|YP_003242231.1| sporulation sigma factor SigF [Paenibacillus sp. Y412MC10]
 gi|329929773|ref|ZP_08283449.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
 gi|261282453|gb|ACX64424.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. Y412MC10]
 gi|328935751|gb|EGG32212.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
          Length = 251

 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 67/253 (26%), Positives = 131/253 (51%), Gaps = 17/253 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T +  +E + ++++ + G+   ++A+  +V  N+RLV SV +++ NRG +  DL Q G 
Sbjct: 10  QTYLDDAEVKRLIALSQSGD---NVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGC 66

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    
Sbjct: 67  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKEMANKVRKKRDE 125

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S ++ R PT +E+A++L +  E V    +  K P S+   +   D D   L D I D +
Sbjct: 126 LSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQIADDS 185

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                D       +      +  LT RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 186 QERWFD-------KLALNEAIGGLTERERLIVYLRY----YRDQTQSEVATRLGISQVQV 234

Query: 657 RQIEAKAIRKLKH 669
            ++E K ++ +++
Sbjct: 235 SRLEKKILQSIRN 247


>gi|86158019|ref|YP_464804.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|197122674|ref|YP_002134625.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|220917457|ref|YP_002492761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|85774530|gb|ABC81367.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|196172523|gb|ACG73496.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|219955311|gb|ACL65695.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 241

 Score = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 113/235 (48%), Gaps = 57/235 (24%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            RKGE  A   K+++V  NL  V+++A+K     ++  DLIQEGN+GLM+A EKFD   G
Sbjct: 41  ARKGEVSA---KQKLVRHNLAFVVAIARKQRRGTVRLDDLIQEGNVGLMRAVEKFDPHAG 97

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA+WW++  I + + +   T+R                                 
Sbjct: 98  TRFSTYAVWWIRAYIGKYLKEARSTVR--------------------------------- 124

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                P  G      + +  +SL++ I +E D +HL + IED +   P D+ +     E 
Sbjct: 125 -----PQSGT-----VAQPDLSLDSAIDEEGDATHL-ERIED-DGPGPEDTYLSG---EG 169

Query: 613 TTRVLASLTPREERVLRMRFGIGMN-----TDHTLEEVGKQFCVTRERIRQIEAK 662
              V  +L    +R+  + + I  N        TLEE+GK++ V+RER+RQ+E K
Sbjct: 170 DREVRDALGKVRKRIGELGWDIVHNRLEQDQPRTLEEIGKRWGVSRERVRQVELK 224


>gi|209965020|ref|YP_002297935.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958486|gb|ACI99122.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 294

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 120/244 (49%), Gaps = 21/244 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGN+G+M+A ++FD   G++ +TYAMWW
Sbjct: 50  AAHRLVTSHLRLVAKIAMGYRGYGLPLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ AI   I      +++      K  K+    R++  +++          T  +IA+ L
Sbjct: 110 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRKLKGQMQAIDEGDLHPETVRKIAETL 167

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
            +P   V  + +    P  SL  P+  +      D++ D++    +    +  L   +  
Sbjct: 168 DVPESDVVNMNRRLASPDHSLNAPLRVDGEGEWQDWLVDESESQEIRLGEREELGKRKAL 227

Query: 613 TTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + +L  RE  +L   R+R     +   TLE++ +Q+ ++RER+RQIE +A  KL+ 
Sbjct: 228 LAEAMKTLNDRERHILVERRLR-----DNPTTLEDLSQQYGISRERVRQIEVRAFEKLQK 282

Query: 670 PSRS 673
             RS
Sbjct: 283 AIRS 286


>gi|188587460|ref|YP_001919005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179352147|gb|ACB86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 273

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 119/225 (52%), Gaps = 8/225 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E++  NLRLV+SV  K+ NRG    DL Q G +GL+KA + FD   G KFSTYA+  
Sbjct: 38  AKQELINGNLRLVLSVINKFKNRGENLDDLFQVGCLGLVKAVDNFDPKQGVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S  +R+   ++    +  +   ++  +   EPT EE+A +L +  E +
Sbjct: 98  IMGEIKRYLRDDS-PMRVSRSLKLLGQEAAKAKEKLRKEKPYEPTIEELASELNISREEL 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + L  + EP+SL  P+  + T  +    + K+    L++ ++ N+  T    +A L  R
Sbjct: 157 VEALNSSSEPLSLYDPVYSDSTDPVLLVDQIKDEEERLENWVE-NM--TLKEAIAKLPER 213

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  ++  RF  G     T  EV  +  +++ ++ ++E  A+ +L+
Sbjct: 214 QRNIVNRRFFKG----QTQVEVSDELNISQAQVSRLEKSALLQLR 254


>gi|327191758|gb|EGE58760.1| RNA polymerase factor sigma-32 [Rhizobium etli CNPAF512]
          Length = 319

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 125/242 (51%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 72  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ +  T        +EIA  L
Sbjct: 132 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAAL 189

Query: 557 AMPVEGVRKV-LKITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + +  V+ +  +++    SL+ P   GD +++   DF+   +   PL     +N+ +  
Sbjct: 190 GVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDD---PLPDEQVSNMIDGE 246

Query: 614 TR------VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            R       L  L  RE +++  R    +  D  TLEE+G    +++ER+RQIE++A+ K
Sbjct: 247 RRRIWLASALKHLNEREMKIISAR---RLAEDGATLEELGADLGISKERVRQIESRAMEK 303

Query: 667 LK 668
           L+
Sbjct: 304 LR 305


>gi|254462386|ref|ZP_05075802.1| alternative sigma factor RpoH [Rhodobacterales bacterium HTCC2083]
 gi|206678975|gb|EDZ43462.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium HTCC2083]
          Length = 298

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 122/249 (48%), Gaps = 17/249 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + + A  +MV ++LRL   +A  Y   GL   +++ E N+GLM+A ++FD   G++ S
Sbjct: 43  EKQDTAAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVVSEANVGLMQAVKRFDPEKGFRLS 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIA 553
           TYAMWW++ AI   I      +++      K  K+    R+  N+I    + +  PE +A
Sbjct: 103 TYAMWWIRAAIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKNRIGALEEGDMRPENVA 160

Query: 554 KKL----AMPVEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
           +          E +    +++    SL   +G   E T    D++ED++A    D   + 
Sbjct: 161 RIAHDLGVTETEVISMNRRMSGGDASLNAQVGSEGEGTMQWQDWLEDEDADQAGDYEARD 220

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            L   RE     +  L  RE+ +L  R     +   TLE++  Q+ V+RERIRQIE +A 
Sbjct: 221 ELEARREMLADAMDVLNDREKDILVQRR--LSDKPVTLEDLSGQYDVSRERIRQIEVRAF 278

Query: 665 RKLKHPSRS 673
            KL+   RS
Sbjct: 279 EKLQERMRS 287


>gi|99080404|ref|YP_612558.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036684|gb|ABF63296.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 299

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 123/250 (49%), Gaps = 18/250 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-- 560
           ++ +I   I      +++     + K+   +R A+     ++      E+ KK+A  +  
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPEVVKKIATDLGV 168

Query: 561 ---EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   +G   + T    D++ED++A    D   +  L   RE 
Sbjct: 169 TEDEVISMNRRMSGGDASLNAMVGSDGDSTMQWQDWLEDEDADQAGDYEARDELQARREL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               ++ L  RE+ +L  R         TLEE+  Q+ V+RERIRQIE +A  KL+    
Sbjct: 229 LAEAMSVLNDREKDILTQRRLA--EQAKTLEELSVQYDVSRERIRQIEVRAFEKLQ---- 282

Query: 673 SKKLRSFLDG 682
            KK+R    G
Sbjct: 283 -KKMRELAAG 291


>gi|290769931|gb|ADD61700.1| putative protein [uncultured organism]
          Length = 259

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 122/237 (51%), Gaps = 22/237 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV +++ N      DL Q G IGL+KA + FD  L  KFSTYA+  
Sbjct: 38  ARELYIKGNLRLVLSVIRRFQNSSENPDDLFQIGCIGLIKAIDNFDTTLQVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K + T      +  +EPT  EIA ++ +  E +
Sbjct: 98  IVGEIRRYLRDNN-SIRVSRSLRDIAYKTIYTRENYMRQHLKEPTIAEIADEIGIDKEMI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              +   + P+SL  P+  E  DT ++ D I DK     N V  +      +LR+   R 
Sbjct: 157 VYAMDAIQSPVSLFEPVYSEGGDTLYVMDQISDKKNREENWVEDI------SLRDAMNR- 209

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  RE  ++ +RF  G     T  EV  +  +++ ++ ++E  A+R +++  R+
Sbjct: 210 ---LGERERHIIDLRFYEG----KTQMEVADEIGISQAQVSRLEKHALRSMRNYLRN 259


>gi|291613119|ref|YP_003523276.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
 gi|291583231|gb|ADE10889.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
          Length = 289

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 127/237 (53%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR+V+SVA+ Y   GL   DLIQEGNIGLMKA +++D   G +  ++A+ W
Sbjct: 49  AARQLVLSHLRVVVSVARGYAGYGLPQADLIQEGNIGLMKAVKRYDATRGVRLVSFALHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT-PE---EIAKKLAMP 559
           ++  I   +      ++I      +  K+    R M   +  EP  P+   EIA++L + 
Sbjct: 109 IRAEIHEYVVRNWRLVKIATTKSQR--KLFFNLRSMKQGL--EPLKPQQVREIAQQLNVS 164

Query: 560 VEGVRKV-LKITKEPISLETPIGDEDTSHLG-DFIEDKNAVSP---LDSAIQANLRET-T 613
              V ++  +     ++LE   G+ED S+    ++ D     P   L++A + +L     
Sbjct: 165 ERDVVEMEARFAGHEVALEPLSGEEDESYAPISYLADNAEHEPSYILEAAEREHLHTAGL 224

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + LASL  R  R++  R+ +    +H  TL E+  +F V+ ERIRQIE KA+ K++
Sbjct: 225 AQALASLDERSRRIVEARW-LRDEEEHAATLHELADEFKVSAERIRQIEQKALSKMQ 280


>gi|239930292|ref|ZP_04687245.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291438640|ref|ZP_06578030.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341535|gb|EFE68491.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
          Length = 300

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 110/216 (50%), Gaps = 8/216 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V   
Sbjct: 79  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 138

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R   D S ++R+P  +++    + +T+  +S K+ R PT  E+A  L +  E V   L
Sbjct: 139 IKRFFRDTSWSVRVPRRLQELRLALTKTSDELSQKLDRSPTVTELATALGVSEEDVVDGL 198

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPRE 624
            +       SL++P  ++D       + D+      D+A++    RE+   +LA L PRE
Sbjct: 199 AVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPLLAKLPPRE 254

Query: 625 ERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
            R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 255 RRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 290


>gi|296133159|ref|YP_003640406.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031737|gb|ADG82505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 260

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 125/227 (55%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NL+LV ++ +++ NRG +  DL Q G IGL+KA +KFD     KFSTYA+  
Sbjct: 35  AREKLVNCNLKLVFNLVQRFCNRGYEPEDLFQIGTIGLIKAIDKFDLSYDVKFSTYAVPL 94

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D +  +++   +++  +K+ R   ++S  + R+PT  EIAK++ M  E +
Sbjct: 95  IIGEIRRFLRDDN-PVKVSRSVKETANKINRAREKLSASLGRDPTISEIAKEVGMEREEI 153

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR--VLASLT 621
              ++ ++ P S+   +  +D    GD I   +A++   S  +    E      VL  L 
Sbjct: 154 VNAMEASQLPTSIYETLYQDD----GDPIYVMDAITG-SSGDEGQWFEHMALKDVLQKLP 208

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++VL +RF      D T  +V +   +++ ++ +IE +A++ ++
Sbjct: 209 EREKKVLLLRFF----EDKTQTQVAEILGISQVQVSRIERQALKTIR 251


>gi|210608669|ref|ZP_03287946.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
 gi|210152926|gb|EEA83932.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
          Length = 259

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 123/233 (52%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++ ++ NLRLV+SV K++TN      DL Q G IGL+KA   F+  L  KFSTYA+  
Sbjct: 38  AKEQYIKGNLRLVLSVIKRFTNSNENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        +  REPT +EI++++ +  E +
Sbjct: 98  IIGEIRRYMRDNN-SIRVSRSLRDTAYKAIYAKEGYMKRNLREPTLQEISEEIGIAKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              +   + P+SL  P+ ++  D  ++ D I DK     N +  L  A+QA         
Sbjct: 157 VFAMDAIQAPMSLNEPVYNDGGDALYVMDQISDKKNKEENWIEEL--ALQA--------A 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L  RE+ ++R+RF  G     T  EV +   +++ ++ ++E  A++ ++ 
Sbjct: 207 MEHLGEREKYIIRLRFFEG----RTQMEVAEDIDISQAQVSRLEKHALKVMRQ 255


>gi|254453399|ref|ZP_05066836.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
 gi|198267805|gb|EDY92075.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
          Length = 298

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 118/238 (49%), Gaps = 17/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   +      +++      K  K+    R+  N+I        R    + IA  L
Sbjct: 109 IRASIQEYVLRSWSMVKLGTTSAQK--KLFFNLRKAKNRIGALEEGDLRPENVQRIATDL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +   E V    +++    SL   +G   E T    D++ED++A    D   +  L   R
Sbjct: 167 GVTEAEVVSMNRRMSGGDASLNATVGSDGEGTMQWQDWLEDESADQAGDYEARDELTQRR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     +  L  RE+ +L M+  +   T  TLE++  Q+ V+RERIRQIE +A  KL+
Sbjct: 227 ELMAEAMEVLNDREKDIL-MQRRLAEKT-VTLEDLSGQYSVSRERIRQIEVRAFEKLQ 282


>gi|26249650|ref|NP_755690.1| hypothetical protein c3819 [Escherichia coli CFT073]
 gi|26110078|gb|AAN82264.1|AE016767_24 Putative conserved protein [Escherichia coli CFT073]
          Length = 368

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|110678526|ref|YP_681533.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109454642|gb|ABG30847.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 292

 Score = 94.4 bits (233), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/263 (28%), Positives = 130/263 (49%), Gaps = 20/263 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R   CE S+ +  ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G 
Sbjct: 34  RDERCEKSLHR--LITAYMRLAISMASKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGV 91

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKR 545
           +FSTYA+WW+K +I   +      +R         +  +MR    ++ R +      + R
Sbjct: 92  RFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLERESAASGEPLDR 151

Query: 546 EPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
               + I+ ++ +P+  V  +  +++    SL      ED      D +ED +A +    
Sbjct: 152 HQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNATQSTEDEGREWIDALEDDSAQAAETV 211

Query: 604 AIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               +   LR    + +  L  RE  ++R R     +   TLE +G++  +++ER+RQ+E
Sbjct: 212 EHHHDTEQLRAWLLQAMNDLNERERFIVRER--KLRDAPRTLESLGQELNLSKERVRQLE 269

Query: 661 AKAIRKLKHP--SRSKKLRSFLD 681
           A A  K++    ++S+++  FLD
Sbjct: 270 AAAFGKMRKSLENQSREVLYFLD 292


>gi|326563747|gb|EGE13998.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 46P47B1]
          Length = 371

 Score = 94.4 bits (233), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 123/240 (51%), Gaps = 16/240 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 128 GDVEAA---RLLVMSHLRFVIHIARSYSGYGLSQADLIQEGNLGLMKAVKRFDPNKGVRL 184

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++       K+   +R+ ++ SN++  +     IA  
Sbjct: 185 VSFAVHWIKAEIHEFVIKNWRIVKVATTKAHRKLFFNLRSLKKSSNQLTLDEAT-AIAND 243

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET 612
           L + V+ V ++  ++T    S E    D+D        F+ED  AV+P D   +A+  E 
Sbjct: 244 LNVTVKQVLEMESRLTSYDASFEAQDSDDDEGRYAPQLFLED--AVNPADVVEEADWEEN 301

Query: 613 TTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TT  L      L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+ K+K
Sbjct: 302 TTTALKDAMEILDERSRDIITQRWLADQKS--TLHELAATYNISAERVRQIEKNAMNKIK 359


>gi|323524659|ref|YP_004226812.1| RNA polymerase sigma-32 subunit RpoH [Burkholderia sp. CCGE1001]
 gi|323381661|gb|ADX53752.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1001]
          Length = 311

 Score = 94.4 bits (233), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 124/250 (49%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  AARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP+EI        +G
Sbjct: 132 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDEI--------DG 179

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + K L + +E ++ +ET +   D +  G   + + + +P+  A  A+     T VLAS  
Sbjct: 180 LAKELNVKREEVAEMETRLSGGDIALEGQVEDGEESYAPI--AYLADSHSEPTAVLASRQ 237

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L  R  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 238 RDKLQSDGIATALEALDARSRRIIEARWLKVQDDGSGGSTLH---ELADEFGVSAERIRQ 294

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 295 IEASAMKKMR 304


>gi|91227498|ref|ZP_01261835.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262392915|ref|YP_003284769.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269968648|ref|ZP_06182645.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
 gi|91188522|gb|EAS74814.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262336509|gb|ACY50304.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269826735|gb|EEZ81072.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
          Length = 285

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 78/269 (28%), Positives = 143/269 (53%), Gaps = 22/269 (8%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +  KGE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYKGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++     + + P  ++D+S+ 
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDEDDSSNA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRFGIGMNTD 639
                 ++EDK+  S +   I+A   E  T       LASL  R +R++R R+    +  
Sbjct: 195 YTAPMLYLEDKS--SDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLD--DEK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 251 ATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|254230128|ref|ZP_04923524.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
 gi|151937373|gb|EDN56235.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
          Length = 284

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 78/269 (28%), Positives = 143/269 (53%), Gaps = 22/269 (8%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +  KGE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYKGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++     + + P  ++D+S+ 
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDEDDSSNA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRFGIGMNTD 639
                 ++EDK+  S +   I+A   E  T       LASL  R +R++R R+    +  
Sbjct: 195 YTAPMLYLEDKS--SDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLD--DEK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 251 ATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|163735266|ref|ZP_02142701.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
 gi|161391480|gb|EDQ15814.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
          Length = 284

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 75/263 (28%), Positives = 130/263 (49%), Gaps = 20/263 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R   CE S+ +  ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G 
Sbjct: 26  RDERCEKSLHR--LITAYMRLAISMASKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGV 83

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKR 545
           +FSTYA+WW+K +I   +      +R         +  +MR    ++ R +      + R
Sbjct: 84  RFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLERESAASGEPLDR 143

Query: 546 EPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
               + I+ ++ +P+  V  +  +++    SL      ED      D +ED +A +    
Sbjct: 144 HQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNATQSTEDEGREWIDALEDDSAQAAETV 203

Query: 604 AIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               +   LR    + +  L  RE  ++R R     +   TLE +G++  +++ER+RQ+E
Sbjct: 204 EHHHDTEQLRAWLLQAMNDLNERERFIVRER--KLRDAPRTLESLGQELSLSKERVRQLE 261

Query: 661 AKAIRKLKH--PSRSKKLRSFLD 681
           A A  K++    ++S+++  FLD
Sbjct: 262 AAAFGKMRKNLENQSREVLYFLD 284


>gi|254384657|ref|ZP_04999996.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194343541|gb|EDX24507.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 334

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 112/222 (50%), Gaps = 10/222 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 102 EGSVERAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVE 161

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++
Sbjct: 162 FSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAER 221

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+
Sbjct: 222 LGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRES 275

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 276 LKPLLEGLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 317


>gi|182436064|ref|YP_001823783.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776688|ref|ZP_08235953.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178464580|dbj|BAG19100.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326657021|gb|EGE41867.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 318

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 87  GSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 146

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++L
Sbjct: 147 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAERL 206

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 207 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 261 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 301


>gi|162148038|ref|YP_001602499.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161786615|emb|CAP56197.1| putative RNA polymerase sigma-32 factor [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 325

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 20/245 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ EA+ A   +V ++LRLV  +A  Y   GL   +LI EGNIG+M+A  +FD   G++
Sbjct: 72  KGDTEAAHA---LVTSHLRLVAKIAMGYRGYGLPLGELISEGNIGMMQAVRRFDPDRGFR 128

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE 551
            +TYAMWW++ AI   I      +++      K  K+    RR+  +++     +  PE+
Sbjct: 129 LATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIDDGDLKPEQ 186

Query: 552 ---IAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDK--NAVSPLDSAI 605
              IA+ L +P + V  + +    P  SL  P+  +      D++ D+  N    L    
Sbjct: 187 VNKIAESLGVPEQDVINMNRRLSAPDHSLNAPLRADSEGEWQDWLVDEHDNQEQTLAENE 246

Query: 606 QANLRETTT-RVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKA 663
           + + R+      + +L  RE  +L  R    +  D  TLEE+   + ++RER+RQIE +A
Sbjct: 247 EFSGRKALLDNAMKTLNDRERHILTERR---LKDDPATLEELSHTYNISRERVRQIEVRA 303

Query: 664 IRKLK 668
             K++
Sbjct: 304 FEKVQ 308


>gi|294630218|ref|ZP_06708778.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833551|gb|EFF91900.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 302

 Score = 94.0 bits (232), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 113/226 (50%), Gaps = 12/226 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 73  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 132

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 133 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVAELAAVLGVS 192

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA-NLRETTT 614
            E V   L +       SL++P  ++D     L D +  +      DSA++    RE+  
Sbjct: 193 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYE------DSALEGVEYRESLK 246

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
            +LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 247 PLLAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 292


>gi|308205503|gb|ADO18993.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 158

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 48/148 (32%), Positives = 94/148 (63%), Gaps = 1/148 (0%)

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R +S  + R+PT  EIA++L +  E  R+ ++  ++ +SLE  +
Sbjct: 1   MPIHINEKLNKIKKIQRELSQSLGRKPTVVEIAEELKVKPEQAREYIQADRKLVSLEMRV 60

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+E  + L + + D+  +SPL+    + +R+    +LASL P +  VL +RFG+  +   
Sbjct: 61  GNEQETELSELLADEK-ISPLEELNSSLMRQNIKELLASLAPIQREVLTLRFGLENDHQL 119

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L ++G++  ++RERIRQ+E KA+  L+
Sbjct: 120 SLTQIGERLNLSRERIRQLEHKALSILR 147


>gi|219125233|ref|XP_002182890.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217405684|gb|EEC45626.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 312

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 81/277 (29%), Positives = 135/277 (48%), Gaps = 29/277 (10%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA-KKY----TNRGLQFLDLIQ 475
           G+S  E R +V+  R+       AK ++V ANL LV +V  ++Y    T+ G+   +LIQ
Sbjct: 44  GLSNKELRRVVNDYRR-------AKHDLVTANLGLVHAVVNQQYGSLKTHTGITKEELIQ 96

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG++GL++AAE FD   G +FSTYA+ W+K  ++ S   +   +R+P   + K +K+   
Sbjct: 97  EGSLGLLRAAELFDPERGLRFSTYAVVWIKGVLSNSHLPE--LVRLPAREKTKWNKIQTI 154

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGV----------RKVLKITKEPISLETPIGDEDT 585
            R +       PT EE+A    M V+ V          R +L +  E  S      D  T
Sbjct: 155 QREVETANGVVPTVEELATLTGMTVQEVVQTTRRMQQARSILSLDFEYSSHSRSGADTAT 214

Query: 586 SH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           S   L +    ++A     + +QA++     R   +L  RE R+LR+R+G+      +L 
Sbjct: 215 SSAALANQECPEDAKLAARTQLQADVIAAMAR---NLDAREARLLRLRYGLADGQTRSLA 271

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E      ++  R +QI    + KL+  + ++ L  +L
Sbjct: 272 ECADAMGLSPTRTQQIAQTCLSKLRQAAEAESLEEYL 308


>gi|303241077|ref|ZP_07327586.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302591337|gb|EFL61076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 246

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 129/250 (51%), Gaps = 33/250 (13%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K +     A+  +VE N+ LV S+ K++ NRG +  D+ Q G IGL+KA +KFD   
Sbjct: 12  LIKKAKSGDKQAQSILVERNVGLVWSIVKRFQNRGYETDDIYQIGCIGLIKAIKKFDDSF 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------- 544
             KFSTYA+  +   I R I D            D I KV R+ + +SNKI+        
Sbjct: 72  DVKFSTYAVPMIIGEIKRFIRD------------DGIIKVSRSLKELSNKIRVTKEIMMK 119

Query: 545 ---REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
              REP+  EI+ ++ +  E +   ++    P SL   +GD DTS   L D + +++   
Sbjct: 120 ELGREPSISEISLRMDVAAEELVMAMEANCSPESLYNTVGDSDTSTVLLIDKLNNESNDE 179

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D   + +LR     VL +L PRE++++ +R+      + T  ++ K   +++ ++ +I
Sbjct: 180 EVDLVDKIDLR----LVLNTLKPREKQIIILRYF----KEKTQVQIAKMLGISQVQVSRI 231

Query: 660 EAKAIRKLKH 669
           E K + ++K 
Sbjct: 232 EKKILDEIKK 241


>gi|254441831|ref|ZP_05055324.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
 gi|198251909|gb|EDY76224.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
          Length = 298

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 118/238 (49%), Gaps = 17/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   +      +++      K  K+    R+  N+I        R    + IA  L
Sbjct: 109 IRASIQEYVLRSWSMVKLGTTSAQK--KLFFNLRKAKNRIGALEEGDLRPENVQRIANDL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +   E V    +++    SL   +G   E T    D++ED++A    D   +  L   R
Sbjct: 167 GVTEAEVVSMNRRMSGGDASLNATVGSDGEGTMQWQDWLEDESADQAGDYEDRDELQQRR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     +  L  RE+ +L M+  +   T  TLE++  Q+ V+RERIRQIE +A  KL+
Sbjct: 227 ELMAEAMDVLNDREKDIL-MQRRLAEKT-VTLEDLSGQYSVSRERIRQIEVRAFEKLQ 282


>gi|319788352|ref|YP_004147827.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466864|gb|ADV28596.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 292

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 119/243 (48%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GLQ  DLIQEGNIGLMKA ++FD  LG +  ++A+ W
Sbjct: 57  AARELVHSHLRFVVHVARGYNGYGLQLGDLIQEGNIGLMKAVKRFDPDLGVRLVSFAVHW 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 117 IRAEIHEFILKNWRIVKV---------ATTKAQRKLFFNLRKAKT--RLGWMNAAEVSAV 165

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV------ 616
            K L ++ +E + +E+ +   D        ED+    P  +A   ++ E  ++       
Sbjct: 166 AKDLNVSEREVLEMESRLSGRDIGFDAPADEDEEHAPPSPAAYLVSMDEDPSQALEREDS 225

Query: 617 -----------LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                      LASL  R   ++  R+ +   +  TL+E+  ++ V+ ERIRQIEA A++
Sbjct: 226 EGHKLDLLRDGLASLDARSRDIIARRW-LDDESKVTLQELADEYGVSAERIRQIEANAMK 284

Query: 666 KLK 668
           K++
Sbjct: 285 KMR 287


>gi|188090484|gb|ACD49476.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
          Length = 284

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 57/142 (40%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            Q L+   ++  +G   L EI+
Sbjct: 123 VQTLLEDYEQHKEGKKRLAEIV 144


>gi|163758761|ref|ZP_02165848.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
 gi|162284051|gb|EDQ34335.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
          Length = 300

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 124/239 (51%), Gaps = 20/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  ++    R++ +KI+       R     EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKVKSKIQAVEDGDLRPDQVAEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + ++    D++ D++  S  D  ++ +  E+  
Sbjct: 167 NVSEEEVISMNRRLSGDASLNAPIKASEGESGQWQDWLVDESD-SQEDMLVEQDELESRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L S    L  RE+R+   R    +  D  TLE++  +F ++RER+RQIE +A  K++
Sbjct: 226 AMLKSALEVLNEREKRIFEAR---RLRDDPITLEDLSGEFDISRERVRQIEVRAFEKVQ 281


>gi|210633875|ref|ZP_03297890.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
 gi|210159044|gb|EEA90015.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
          Length = 261

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 117/220 (53%), Gaps = 20/220 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V ++L LV  +A K+ NRG    DL+Q G +GL+KA ++FD   G +F+T+A   
Sbjct: 31  AREKLVMSHLNLVRFIANKFKNRGEPIDDLVQVGYLGLLKAIDRFDPARGLEFTTFATPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+  ++R+P  +++   KV +    ++++++R PT  EIA+ L   V+ V
Sbjct: 91  IMGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDTLTSQLQRSPTIAEIAEYLDATVDEV 150

Query: 564 RKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRV--- 616
            + ++       +SLE P G          +ED +A S +D     +  L  T  R+   
Sbjct: 151 LEAMESSSAYSSVSLEAPSG----------MEDDDAPSVIDRYATEDEELAFTDDRIIIE 200

Query: 617 --LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             LAS +PRE  V+ MRF  GM      E++G  Q  V+R
Sbjct: 201 EALASFSPREREVIEMRFLQGMTQIEIAEKLGISQVQVSR 240


>gi|270487763|ref|ZP_06204837.1| putative RNA polymerase sigma factor RpoD [Yersinia pestis KIM D27]
 gi|270336267|gb|EFA47044.1| putative RNA polymerase sigma factor RpoD [Yersinia pestis KIM D27]
          Length = 402

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164



 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 69/143 (48%), Gaps = 2/143 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+      E
Sbjct: 250 KLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNE 309

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE
Sbjct: 310 TSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGE 368

Query: 439 CEASIAKKEMVEANLRLVISVAK 461
            +A  AKKEMVEANLRLVIS+AK
Sbjct: 369 AKARRAKKEMVEANLRLVISIAK 391


>gi|308069565|ref|YP_003871170.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           (sporulation sigma factor) [Paenibacillus polymyxa E681]
 gi|305858844|gb|ADM70632.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Paenibacillus polymyxa E681]
          Length = 251

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 128/246 (52%), Gaps = 17/246 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + ++++ + G+ EA   ++ +V +N+RLV SV +++ NRG +  DL Q G IGL+K+
Sbjct: 16  AEVKQLIALSQSGDNEA---RETLVNSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKS 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    +S ++ 
Sbjct: 73  VDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKETANKVRKMKDELSKRLN 131

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLD 602
           R PT +E+A +L +  E V    +  K P S+   +   D D   L D I D++     D
Sbjct: 132 RLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADESQERWFD 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++E K
Sbjct: 192 -------KLALNEAIGGLSERERLIVYLRY----YRDQTQSEVASRLGISQVQVSRLEKK 240

Query: 663 AIRKLK 668
            ++ ++
Sbjct: 241 ILQLIR 246


>gi|209696299|ref|YP_002264230.1| RNA polymerase factor sigma-32 [Aliivibrio salmonicida LFI1238]
 gi|208010253|emb|CAQ80584.1| RNA polymerase sigma-32 factor [Aliivibrio salmonicida LFI1238]
          Length = 286

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 78/278 (28%), Positives = 140/278 (50%), Gaps = 26/278 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS L+  N    ++VE    ++E  H      K E EA+   KE++ ++LR V+ VA+ 
Sbjct: 16  IDSYLRSVNRYPMLTVEKERDLAERLHY-----KEEIEAA---KELILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +  +R+      E   E +AK L +    VR++  ++  +  + E P
Sbjct: 128 TTKAQRKLFFNLRKNKKRLGWFNNGE--VEAVAKDLGVSPSEVREMESRLAAQDSTFEAP 185

Query: 580 IGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRM 630
             D+D          ++EDK   S +  +++ +  E  T       +A+L  R + +++ 
Sbjct: 186 TEDDDRDMAFTAPVYYLEDKQ--SDIAHSLEEDNWEDYTNNRLANAIATLDDRSQHIVQS 243

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+     T  TL+E+   + V+ ERIRQ+E  A++KLK
Sbjct: 244 RWLTDEKT--TLQELANTYSVSAERIRQLEKNAMKKLK 279


>gi|254464548|ref|ZP_05077959.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
 gi|206685456|gb|EDZ45938.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
          Length = 298

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 123/246 (50%), Gaps = 14/246 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A+ A K MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +
Sbjct: 44  EQDAASAHK-MVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           TYAMWW++ +I   I      +++     + K+   +R A+     ++      E  K++
Sbjct: 103 TYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPENVKRI 162

Query: 557 AMPV-----EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A  +     E +    +++    SL   +G   E T    D++ED++A    D   +  L
Sbjct: 163 ATDLGVTEDEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDEL 222

Query: 610 ---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              RE     L  L  RE+ +L  R    M+   TLE++  Q+ V+RERIRQIE +A  K
Sbjct: 223 EARRELLAEALDVLNDREKDILTQRR--LMDQAVTLEDLSAQYNVSRERIRQIEVRAFEK 280

Query: 667 LKHPSR 672
           L+   R
Sbjct: 281 LQKKMR 286


>gi|170765503|ref|ZP_02900314.1| RNA polymerase sigma factor RpoD [Escherichia albertii TW07627]
 gi|170124649|gb|EDS93580.1| RNA polymerase sigma factor RpoD [Escherichia albertii TW07627]
          Length = 613

 Score = 94.0 bits (232), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 88/138 (63%), Gaps = 3/138 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAE 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 70  NTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALI 168
             +  S+ E P     L+
Sbjct: 128 NQVQCSVAEYPEAITYLL 145


>gi|332977445|gb|EGK14221.1| DNA-directed RNA polymerase sigma subunit SigF [Desmospora sp.
           8437]
          Length = 254

 Score = 94.0 bits (232), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 127/249 (51%), Gaps = 17/249 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E + ++   +KG+ EA   +  +V+ N+RLV SV +++ NRG +  DL Q G IGL
Sbjct: 13  LSDTEVKELIQKSQKGDTEA---RDRLVQHNIRLVWSVVQRFLNRGYEAEDLFQIGCIGL 69

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +KFD     KFSTYA+  +   I R + D    +++   +++  +++ +    M+ 
Sbjct: 70  LKAVDKFDLAYDVKFSTYAVPMIIGEIQRFLRDDGM-VKVSRSLKELSNRIRKVKDEMTK 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
            + R PT +E+++++ +  E +    +  + P S+   +   D D   L D I D+    
Sbjct: 129 GLGRSPTIQELSEEMGVTPEEIVFAQEANRTPTSIHETVYENDGDPITLMDQIADEEEEG 188

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D       R      +  L  RE  ++ +RF      D T  EV ++  +++ ++ ++
Sbjct: 189 WFD-------RMALKEAIRQLEERERLIVYLRF----FKDQTQSEVAQRLGISQVQVSRL 237

Query: 660 EAKAIRKLK 668
           E K IR+++
Sbjct: 238 EKKIIRRMR 246


>gi|322421263|ref|YP_004200486.1| RNA polymerase sigma 32 subunit RpoH [Geobacter sp. M18]
 gi|320127650|gb|ADW15210.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M18]
          Length = 284

 Score = 94.0 bits (232), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 114/232 (49%), Gaps = 12/232 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +++ +NLR V+ +A +Y + G++ LDLIQEGNIGLM A  KFD   G +  +YA+WW
Sbjct: 45  AAHKLITSNLRFVVKIAGEYRSYGMKMLDLIQEGNIGLMMAVRKFDPAKGVRLISYAVWW 104

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      ++I     + K+   +  A++    +  E      A  L +    
Sbjct: 105 IRAYIQNHIISAWSLLKIGTTQAQRKLFFKLNQAKQAIINMTGEGDLHAAAISLDVKDTE 164

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT------TRV 616
            R++ +  +  +SL+  + D +    G F+E    +      + A  +ETT         
Sbjct: 165 AREMEQRLRGELSLDVEMFDGEG---GTFLETLPDLRQNQEEMLAERQETTILEQGVASA 221

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  +E  V+  R  +      TL+E+   F ++RER+RQIE  A++K+K
Sbjct: 222 LGHLNEKERFVIERR--VAAEEPLTLQEIADHFSISRERVRQIEEGALKKMK 271


>gi|188090488|gb|ACD49478.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
 gi|188090490|gb|ACD49479.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
          Length = 284

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 57/142 (40%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            Q L+   ++  +G   L EI+
Sbjct: 123 VQTLLEDYEQHKEGKKRLAEIV 144


>gi|241758558|ref|ZP_04756675.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
 gi|241321301|gb|EER57461.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
          Length = 287

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 129/240 (53%), Gaps = 11/240 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G 
Sbjct: 43  QKGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGA 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +  ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   +EIA
Sbjct: 100 RLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QEIA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL-- 609
             L + +  V ++  ++T   I +      DED     D++ D +A      + QA+   
Sbjct: 159 NDLGVKLSEVLEMEQRMTGHDIGIMAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYAL 218

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 219 QTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|239980906|ref|ZP_04703430.1| RNA polymerase sigma factor, sigma L [Streptomyces albus J1074]
 gi|291452768|ref|ZP_06592158.1| sigma L [Streptomyces albus J1074]
 gi|291355717|gb|EFE82619.1| sigma L [Streptomyces albus J1074]
          Length = 340

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 113/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 111 ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 170

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A  L + 
Sbjct: 171 AMPTVIGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELAHALGVS 230

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 231 EEDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 286

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 287 LAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 330


>gi|126666520|ref|ZP_01737498.1| RNA polymerase sigma factor RpoD [Marinobacter sp. ELB17]
 gi|126628908|gb|EAZ99527.1| RNA polymerase sigma factor RpoD [Marinobacter sp. ELB17]
          Length = 616

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 61/158 (38%), Positives = 93/158 (58%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V     D D L   +
Sbjct: 11  KDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDADTLIMTD 70

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  DS    ++ + ++  L   +  A R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 71  G--DSTADEAATAEAAAALAAVESDAGRTTD-PVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +MA++   P T   +I   D + +    L +I+
Sbjct: 128 EGIRDVMAAVAHFPGTTGTVIQGYDRIVENEGRLSDIV 165


>gi|121488741|emb|CAJ18254.1| sigma 70-type sigma factor [Chlorobaculum limnaeum]
          Length = 149

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 47/150 (31%), Positives = 86/150 (57%), Gaps = 1/150 (0%)

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P
Sbjct: 1   FDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDP 60

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             +E+A  L M  + V   LKI    +S++ P    D + L D +++   + P     + 
Sbjct: 61  NTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHM-PDHGLNRD 119

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 120 SLTLEVERSLSVLAPREADVIRSYFGIGMD 149


>gi|307293092|ref|ZP_07572938.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
 gi|306881158|gb|EFN12374.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
          Length = 304

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 126/251 (50%), Gaps = 26/251 (10%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E   S A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KF+   G+
Sbjct: 43  RYAEHADSEAAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFEPDRGF 102

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE 550
           + +TYAMWW++ +I   I      +++      K  K+    RRM N I+     +  P+
Sbjct: 103 RLATYAMWWIRASIQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKNNIEAFEDGDLHPD 160

Query: 551 EIAKKLAMPVEGVRK--VLKITKE-----PISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           ++ KK+A  + GV +  V+ + +        SL  P+ ++      D++ D +   PL  
Sbjct: 161 DV-KKIATDL-GVTEEDVISMNRRMAMGGDTSLNVPMREDGEGQWQDWLADTD---PLQD 215

Query: 604 AIQANLRETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              A+ +E+  R       +  L  RE+ +L  R         TLEE+ + + V+RER+R
Sbjct: 216 ERVADRQESELRHDMLVEAMDDLNDREKHILAERRLA--EEPKTLEELSQVYGVSRERVR 273

Query: 658 QIEAKAIRKLK 668
           QIE +A  KL+
Sbjct: 274 QIEVRAFEKLQ 284


>gi|325263641|ref|ZP_08130375.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
 gi|324031350|gb|EGB92631.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
          Length = 238

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 127/240 (52%), Gaps = 8/240 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A++++VE N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIKKSHDGDKKAREQLVEENVGLVWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K+ +T   ++  + REPT
Sbjct: 63  DLSYEVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKELSYKIFQTREALTGSLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A  + +  E + + ++   E  SL  PI  ++ + +   ++        +  I  +
Sbjct: 122 LEELANTMNVDKEEIVQAMEAGGEVESLYKPIHQKEGNEI-RLVDKLEEKERKEEKILDH 180

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     ++L SL   E +++ +R+      D T  +VGK+  +++ ++ ++E + I  L+
Sbjct: 181 M--LLAQLLESLDKEERQLIYLRY----FADETQSQVGKKLGISQVQVSRMEKRIIENLR 234


>gi|39995761|ref|NP_951712.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|39982525|gb|AAR33985.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|298504771|gb|ADI83494.1| RNA polymerase sigma-32 factor RpoH [Geobacter sulfurreducens
           KN400]
          Length = 284

 Score = 93.6 bits (231), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 77/271 (28%), Positives = 131/271 (48%), Gaps = 15/271 (5%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           DS+     EI+   V T     E+R  V      + EA+     ++ +NLR V+ +A +Y
Sbjct: 10  DSLTVYLREIRKFPVLT--PEEEYRFAVKFYEDKDLEAA---HSLITSNLRFVVKIAAEY 64

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            + GL+ LDLIQEGN+GLM A  KF+   G +  +YA+WW++  I   I      ++I  
Sbjct: 65  RSYGLKMLDLIQEGNVGLMMAVRKFNPYKGIRLISYAVWWIRAYIQNHIISAWSLLKIGT 124

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEGVRKVLKITKEPISLETPI 580
               K  K+     +  N IK     ++I   A  L +    V ++ +  +    L+  I
Sbjct: 125 TQAQK--KLFFKLNQAKNAIKGLTGTDDIEATATSLHVKESEVLEMDQRMRGDFYLDAEI 182

Query: 581 GDEDTSHLGDFIED--KNAVSPLDSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMN 637
            + D   + + + D  +N    L    ++  L++     L  L  +E  ++  R  +  +
Sbjct: 183 KNGDGLTILETLADERQNQEDTLAELQESELLKQHIAGALGKLNEKERFIVEQR--VTAD 240

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T  TL+E+  +F ++RER+RQIE  A+RK+K
Sbjct: 241 TPLTLQEIADRFSISRERVRQIEEAALRKIK 271


>gi|126734879|ref|ZP_01750625.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126715434|gb|EBA12299.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 277

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 127/256 (49%), Gaps = 24/256 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLITAYMRLAISMASKFKRYGAPMNDLIQEASVGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-----------I 552
           +K +I   +      +R       K   +    RR+  +++RE   E            I
Sbjct: 86  IKASIQDYVMRNWSMVRTGSTSSQK--SLFFNMRRVQARLEREAAAEGRVMDKQEMRELI 143

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIED---KNAVSPLDSAIQA 607
           A ++ +P+  V  +  +++    SL      ED      D +ED   + A +   +    
Sbjct: 144 AIEVGVPLHDVEMMEGRLSGSDFSLNATQSVEDEGREWIDALEDDGPQAAETVEHTHDND 203

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            LR+     L++L  RE+ ++R R    +  D  TLE +G +  +++ER+RQ+EA A  K
Sbjct: 204 TLRQWLLTALSNLNDREQFIVRER---KLREDPRTLESLGTELGLSKERVRQLEAAAFGK 260

Query: 667 LKHP--SRSKKLRSFL 680
           ++    S+S ++ +F 
Sbjct: 261 MRKSLESQSSEVHAFF 276


>gi|56696293|ref|YP_166650.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56678030|gb|AAV94696.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 298

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/238 (31%), Positives = 114/238 (47%), Gaps = 17/238 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW++ A
Sbjct: 53  MVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRAA 112

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPV 560
           I   I      +++      K  K+    R+   KI        R      IA  L +  
Sbjct: 113 IQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKAKIGALEEGDLRPENVARIAHDLGVSE 170

Query: 561 EGVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTT 614
           + V  +  +++    SL   +G   E T    D++ED++A    D   +  L   RE   
Sbjct: 171 DDVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAADYEARDELEARRELLA 230

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  L  RE+ VL  R  +      TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 231 SALDVLNEREKDVLTQRRLLDQTV--TLEDLSAQYNVSRERIRQIEVRAFEKLQKRMR 286


>gi|318060190|ref|ZP_07978913.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actG]
 gi|318078835|ref|ZP_07986167.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actF]
          Length = 356

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 425 SEFRHIVSMVRKGECEASIA---KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           SE R +   +R  E E++     +  +V  +L LV  +A+++ NRG    DL Q   IGL
Sbjct: 110 SEARALFVQLRTLEPESAAYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGL 169

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ ++FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S 
Sbjct: 170 IKSVDRFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQ 229

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVS 599
           +  R PT  E+A++L++  E V + L+       +SL+ P  D+++  + D +  +    
Sbjct: 230 QHGRSPTVHELAQRLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE---- 285

Query: 600 PLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             D A++    RE+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 286 --DEALEGVEYRESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 339


>gi|320008631|gb|ADW03481.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 320

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 112/222 (50%), Gaps = 10/222 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 88  EGSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVE 147

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++
Sbjct: 148 FSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAER 207

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+
Sbjct: 208 LGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRES 261

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 262 LKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 303


>gi|330818365|ref|YP_004362070.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
 gi|327370758|gb|AEA62114.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
          Length = 311

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 124/237 (52%), Gaps = 20/237 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K
Sbjct: 74  RRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPNQNVRLVSYAIHWIK 133

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEG 562
             I   I      +++      K  + +    R   K  +  TPEEI   A++L +  E 
Sbjct: 134 AEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKRED 190

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVL 617
           V ++  +++   I+LE  +  G+E  + +    +  N  + + ++ Q +  +T   +  L
Sbjct: 191 VAEMETRLSGGDIALEGQVDDGEESFAPIAYLADSHNEPTAVIASRQRDRLQTDGISEAL 250

Query: 618 ASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            SL  R  R++  R+      G G +T H L     +F V+ ERIRQIEA A++K++
Sbjct: 251 ESLDARSRRIIEARWLNVEDDGSGGSTLHDL---AAEFGVSAERIRQIEASAMKKMR 304


>gi|144897893|emb|CAM74757.1| RNA polymerase sigma-32 factor [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 288

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 121/245 (49%), Gaps = 23/245 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ ++LRLV  +A  Y   GL   +LI EGN+G+M+A ++FD   G++ +TYAMWW
Sbjct: 49  AADRLITSHLRLVAKIAMGYRGYGLPLGELISEGNVGMMQAVKRFDPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-------EPTPEEIAKKL 556
           ++ A+   I      +++      K  K+    R++  +++        + T   IA KL
Sbjct: 109 IRAAVQEYILHSWSLVKMGTTAAQK--KLFFNLRKLKGQMQAMDEGDLPQETVTSIATKL 166

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKN------AVSPLDSAIQANL 609
            +P   V  + +    P  SL  P+  +      D++ D++           +  I++ L
Sbjct: 167 NVPENDVINMNRRLASPDHSLNAPVRMDGEGEWQDWLVDESDDQETELADRQERGIRSKL 226

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             T    L +L  RE  +L  R    +  D  TLE++ +Q+ ++RER+RQIE +A  KL+
Sbjct: 227 LST---ALDTLNERERSILSQR---RLTEDPATLEDLSQQYGISRERVRQIEVRAFEKLQ 280

Query: 669 HPSRS 673
              R+
Sbjct: 281 KSIRA 285


>gi|239977584|sp|P0CAW9|RP32_CAUCR RecName: Full=RNA polymerase sigma-32 factor
 gi|239977655|sp|B8H3C3|RP32_CAUCN RecName: Full=RNA polymerase sigma-32 factor
 gi|1262200|gb|AAC43981.1| RpoH [Caulobacter vibrioides]
 gi|1588870|prf||2209377A heat shock sigma factor 32
          Length = 295

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 125/245 (51%), Gaps = 24/245 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 48  AAHKMVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE---EIAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I    + +  P+   +IA KL
Sbjct: 108 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKL 165

Query: 557 A-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-------LDSAIQAN 608
             +  E +    +++    SL  P+  +  S   D++ D+  VS         + +++ +
Sbjct: 166 GVLDSEVISMNRRLSGPDASLNAPLRADGESEWQDWLADEEQVSQETRVAEDEEKSLRMS 225

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L E     +  LT RE  +L  R    +  D  TLEE+  Q+ V+RER+RQIE +A  KL
Sbjct: 226 LLE---EAMVELTDRERHILTER---RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKL 279

Query: 668 KHPSR 672
           +   R
Sbjct: 280 QKTMR 284


>gi|282858710|ref|ZP_06267864.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588514|gb|EFB93665.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 228

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/255 (26%), Positives = 122/255 (47%), Gaps = 39/255 (15%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I++I  ET ++  E R +   ++ G+ +A    +++ +ANL  V+S+A +Y  +GL   D
Sbjct: 8   IENIIGETILTNEEERQLADRIKVGDAKAL---EKLTKANLTFVVSIAHQYKEQGLDEND 64

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I +Q+   ++P + +++  + 
Sbjct: 65  LISEGNIGMMYAAQKFDGTKGVRFVNFAASYIRKAMEDAIKEQTALYKVPKNEKNRFEQ- 123

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            + A+ +S               L  PV                  P+G  +   L + I
Sbjct: 124 -KRAKAIS---------------LDQPV------------------PVGSNNNFTLQNVI 149

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +  +  D      L     + +  L  RE  V+   +G+      T+ EV +   + 
Sbjct: 150 VNGDTANTDDDVTTNMLNTALKQSMKFLNERETAVITQLYGLD-GVHFTMAEVAETLGLK 208

Query: 653 RERIRQIEAKAIRKL 667
           RERIRQI   A+RKL
Sbjct: 209 RERIRQIRNTALRKL 223


>gi|162449128|ref|YP_001611495.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159710|emb|CAN91015.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 275

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 122/230 (53%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++EA L  V+++A +Y   GL   D++QEGNIGL+KAAE+FD   G + +TYA +W
Sbjct: 42  AGRRLIEACLPFVMTIALEYRRWGLPMEDIVQEGNIGLLKAAERFDPDRGCRLATYAAYW 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +A     +R+         K  R A R+  K   E  P  +A+   +  E  
Sbjct: 102 IRAEIREHVARGYRIVRL------GSSKSERRALRIYRKTH-EKDPAVLAELSGLSEERA 154

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR----VLA 618
            ++L  +    +SLE    ++  + +       +A +P D A  A+ R   +R    V+ 
Sbjct: 155 AELLPLLMARDVSLERSPTEDGIAPVERLA--SSAHTPEDEACDADERAQLSRALLQVVN 212

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+PRE  ++  R+    ++  TLE++G  F V++ER+RQIE +A ++++
Sbjct: 213 ELSPRERSIMNQRWLT--DSPVTLEQLGADFGVSKERVRQIEERAKKRMR 260


>gi|318060769|ref|ZP_07979492.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078700|ref|ZP_07986032.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025872|ref|ZP_08453936.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332745724|gb|EGJ76165.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 367

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 138 ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 197

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+AK L + 
Sbjct: 198 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELAKALGVS 257

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            + V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 258 EDDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 313

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 314 LAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 357


>gi|188090486|gb|ACD49477.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
          Length = 284

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 57/142 (40%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            Q L+   ++  +G   L EI+
Sbjct: 123 VQTLLEDYEQHKEGKKRLAEIV 144


>gi|239982221|ref|ZP_04704745.1| RNA polymerase sigma factor, sigH [Streptomyces albus J1074]
          Length = 287

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 56  GGPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEF 115

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A+KL
Sbjct: 116 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQRHGRSPTVHELAEKL 175

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 176 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 229

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 230 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 270


>gi|307943602|ref|ZP_07658946.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
 gi|307773232|gb|EFO32449.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
          Length = 291

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 122/232 (52%), Gaps = 19/232 (8%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ++ RLVISVA K+ N GL   DLIQEG++GL++AA +F+     +FSTYA WW++ +I  
Sbjct: 48  SHTRLVISVASKFRNFGLPLGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQD 107

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI---KREPTPEEIAKKLA-----MPVEG 562
            I      +R       K   +    RR+  K+   ++  T  E+ +K+A      P + 
Sbjct: 108 YILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLSGNQQNLTDSELHQKIADAIGVKPADV 165

Query: 563 VRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
                +++    SL  P+ D +  +S   DF+   +A  P D   ++   E   + LAS 
Sbjct: 166 ATMNARLSGPDTSLNAPVTDSEGSSSDRQDFLVS-DAPQPDDIVSESIDTERRRKWLASA 224

Query: 620 ---LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              LT RE +++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 225 MTVLTDRELKIVRERRLT--EEGATLESLGQKLGISKERVRQIESRAMEKLK 274


>gi|255068324|ref|ZP_05320179.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|261365915|ref|ZP_05978798.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
 gi|255047443|gb|EET42907.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|288565493|gb|EFC87053.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
          Length = 287

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 131/240 (54%), Gaps = 11/240 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G 
Sbjct: 43  QKGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGA 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +  ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA
Sbjct: 100 RLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QDIA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL-- 609
             L + +  V ++  ++T   I++      DED+    D++ D +A      + QA+   
Sbjct: 159 DDLGVKLSEVMEMEQRMTGHDIAIMADNNDDEDSFAPIDWLADHDAEPSRQLSKQAHYAL 218

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 219 QTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|1184690|gb|AAB01724.1| RNA polymerase sigma 32 subunit [Caulobacter crescentus CB15]
          Length = 295

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 125/245 (51%), Gaps = 24/245 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 48  AAHKMVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE---EIAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I    + +  P+   +IA KL
Sbjct: 108 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKL 165

Query: 557 A-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-------LDSAIQAN 608
             +  E +    +++    SL  P+  +  S   D++ D+  VS         + +++ +
Sbjct: 166 GVLDSEVISMNRRLSGPDASLNAPLRRDGESEWQDWLADEEQVSQETRVAEDEEKSLRMS 225

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L E     +  LT RE  +L  R    +  D  TLEE+  Q+ V+RER+RQIE +A  KL
Sbjct: 226 LLE---EAMVELTDRERHILTER---RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKL 279

Query: 668 KHPSR 672
           +   R
Sbjct: 280 QKTMR 284


>gi|295837881|ref|ZP_06824814.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826719|gb|EDY46528.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 57  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 116

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+AK L + 
Sbjct: 117 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELAKALGVS 176

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            + V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 177 EDDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 232

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 233 LAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 276


>gi|291447660|ref|ZP_06587050.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291350607|gb|EFE77511.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 318

 Score = 93.6 bits (231), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 86/298 (28%), Positives = 139/298 (46%), Gaps = 22/298 (7%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF-VACEVDSILKIRNEIKSISVETGI 422
           G+ R   +   Q R   PH V  A D PEG    F VA E  S  +   ++         
Sbjct: 18  GVVRPAGIPEQQAR---PHPVDGA-DGPEG----FDVAVEQQSQAERAGQMSEHGHHDPH 69

Query: 423 SISEFRHIVSMVRK---GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             S  R +   +R+   G  E +  +  +V  +L LV  +A+++ NRG    DL Q   I
Sbjct: 70  DRSGARALFFELRELPDGSPEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATI 129

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+K+ ++FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +
Sbjct: 130 GLIKSVDRFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAEL 189

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNA 597
           S +  R PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  +  
Sbjct: 190 SQQHGRSPTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE-- 247

Query: 598 VSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
               D A++    RE+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 248 ----DEALEGVEYRESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 301


>gi|229592968|ref|YP_002875087.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens SBW25]
 gi|229364834|emb|CAY52873.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas fluorescens
           SBW25]
          Length = 616

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 56/137 (40%), Positives = 85/137 (62%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D     D
Sbjct: 12  KELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|333024500|ref|ZP_08452564.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332744352|gb|EGJ74793.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 356

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 425 SEFRHIVSMVRKGECEASIA---KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           SE R +   +R  E E++     +  +V  +L LV  +A+++ NRG    DL Q   IGL
Sbjct: 110 SEARALFVQLRTLEPESAAYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGL 169

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ ++FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S 
Sbjct: 170 IKSVDRFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQ 229

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVS 599
           +  R PT  E+A++L++  E V + L+       +SL+ P  D+++  + D +  +    
Sbjct: 230 QHGRSPTVHELAQRLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE---- 285

Query: 600 PLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             D A++    RE+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 286 --DEALEGVEYRESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 339


>gi|261380105|ref|ZP_05984678.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
 gi|284797325|gb|EFC52672.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
          Length = 287

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 129/240 (53%), Gaps = 11/240 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G 
Sbjct: 43  QKGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGA 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +  ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   +EIA
Sbjct: 100 RLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QEIA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL-- 609
             L + +  V ++  ++T   I +      DED     D++ D +A      + QA+   
Sbjct: 159 DDLGVKLSEVLEMEQRMTGHDIGIMAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYAL 218

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 219 QTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|257453679|ref|ZP_05618966.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
 gi|257448913|gb|EEV23869.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
          Length = 393

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 78/267 (29%), Positives = 131/267 (49%), Gaps = 20/267 (7%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N +  I + T     E  H      +G+ EA+   + +V ++LR VI +A+ Y+  GL  
Sbjct: 126 NAVHQIPILTAEQEQELAH--RYTDEGDVEAA---RLLVMSHLRFVIHIARSYSGYGLPQ 180

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKI 529
            DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++       K+
Sbjct: 181 GDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHRKL 240

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
              +R+ ++ +N++  E   E IAK L + V+ V ++  ++T    S E    DED    
Sbjct: 241 FFNLRSLKKTNNQLTLEEA-EAIAKDLNVTVKQVLEMESRLTSYDASFEAQSDDEDEGRY 299

Query: 589 GD--FIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMNTDH-T 641
               F+ED  A  P D    A+  E     L      L  R   +++ R+   +N    T
Sbjct: 300 APQYFLED--AADPADMVEDADWEENNNSALMEAMEDLDDRSRDIVQQRW---LNEQKAT 354

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  ++ ++ ER+RQIE  A+ K+K
Sbjct: 355 LHELAAEYNISAERVRQIEKNAMDKIK 381


>gi|254465185|ref|ZP_05078596.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
 gi|206686093|gb|EDZ46575.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
          Length = 292

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 127/256 (49%), Gaps = 32/256 (12%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +
Sbjct: 45  LINAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKAS 104

Query: 508 ITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           I   +      +R         +  +MR    ++ R AR     + +    ++IA ++ +
Sbjct: 105 IQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLEREARSSGVPLDQHQLHQKIATEIGV 164

Query: 559 PVEGVRKV-LKITKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQA-----NLRE 611
           P+  V  +  +++    SL      DE+     D +ED    S  +  +Q       LR+
Sbjct: 165 PLRDVEMMEGRLSGADFSLNAVQSTDEEGREWIDALEDD--ASQAEDLVQERHDRRQLRK 222

Query: 612 TTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                L +L  RE     ER LR R         TLE +G +  +++ER+RQ+EA A +K
Sbjct: 223 WLVTALQALNDRERFIITERKLRDR-------PRTLESLGTELGLSKERVRQLEAGAFQK 275

Query: 667 LKHP--SRSKKLRSFL 680
           ++    S+S++++  L
Sbjct: 276 MRKSLESQSREVQKLL 291


>gi|16127328|ref|NP_421892.1| RNA polymerase factor sigma-32 [Caulobacter crescentus CB15]
 gi|221236131|ref|YP_002518568.1| RNA polymerase factor sigma-32 [Caulobacter crescentus NA1000]
 gi|13424754|gb|AAK25060.1| heat shock sigma factor RpoH [Caulobacter crescentus CB15]
 gi|220965304|gb|ACL96660.1| RNA polymerase sigma-32 factor [Caulobacter crescentus NA1000]
          Length = 298

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 125/245 (51%), Gaps = 24/245 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 51  AAHKMVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPE---EIAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I    + +  P+   +IA KL
Sbjct: 111 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKL 168

Query: 557 A-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-------LDSAIQAN 608
             +  E +    +++    SL  P+  +  S   D++ D+  VS         + +++ +
Sbjct: 169 GVLDSEVISMNRRLSGPDASLNAPLRADGESEWQDWLADEEQVSQETRVAEDEEKSLRMS 228

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L E     +  LT RE  +L  R    +  D  TLEE+  Q+ V+RER+RQIE +A  KL
Sbjct: 229 LLE---EAMVELTDRERHILTER---RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKL 282

Query: 668 KHPSR 672
           +   R
Sbjct: 283 QKTMR 287


>gi|254515828|ref|ZP_05127888.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
 gi|219675550|gb|EED31916.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
          Length = 303

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 123/234 (52%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V  +A+ Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 69  AARELVMSHLRFVAHIARSYRGYGLSEADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHW 128

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R+A++    +  +   + +A  L + V+ 
Sbjct: 129 IKAEIHEYILRNWRIVKIATTKAQRKLFFNLRSAKKSLAWLSADEA-QAVANDLGVDVQE 187

Query: 563 VRKV-LKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPL---DSAIQANLRETTTR 615
           V ++  +++   ++ + P G   DE       ++ED++A   +   DS  QA+ +     
Sbjct: 188 VHRMEGRLSSHDVAFDAPAGSDDDEGWQAPQYYLEDRSADPAIDVEDSEWQADSQAQLHA 247

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +A L  R   +L  R+   +  D  TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 248 AIADLDERSRNILAQRW---LTDDKATLHELAAEYGVSAERIRQLEQAAMKKIR 298


>gi|270158013|ref|ZP_06186670.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|289163720|ref|YP_003453858.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
 gi|269990038|gb|EEZ96292.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|288856893|emb|CBJ10704.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
          Length = 284

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 137/285 (48%), Gaps = 29/285 (10%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N     +D+ +   N+I  +S+E  I+ +E  H      +G+ EA+   + +V A+LR V
Sbjct: 11  NLPVGSIDAYIHRVNQIPMLSLEEEIACAERFH-----SEGDLEAA---RRLVLAHLRYV 62

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + VA+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +    
Sbjct: 63  VRVARGYLGYGLPLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNW 122

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKITKEPI 574
             ++I      +  K+    R+M N++      E   +A  L +  E    VL + +   
Sbjct: 123 RIVKIATTKAQR--KLFFNLRQMKNRLGWMSHEEVSAVANDLGVSRE---DVLVMEQRLN 177

Query: 575 SLETPIGDEDTSHLGDFI-----------EDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++TP    D     +F            +D + +   DSA     RE     L  L  R
Sbjct: 178 AMDTPYDAPDADDHDEFYTAPERYLFNTNDDPSVMLENDSASDQG-REKLMFALEQLDER 236

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L+ R+        TL ++ K++ V+ ER+RQ+E  A++KLK
Sbjct: 237 SQDILQQRW--LSEEKLTLHDLAKKYGVSAERVRQLEKNAMKKLK 279


>gi|160878636|ref|YP_001557604.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427302|gb|ABX40865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 238

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/241 (31%), Positives = 124/241 (51%), Gaps = 14/241 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++R  +    +A+  +V  N+ LV S+ +++  RG +  DL Q G+IGLMKA +KFD 
Sbjct: 4   LDLIRLSKQGDKVARDRVVTENVGLVWSIVRRFMGRGHEAEDLFQIGSIGLMKAIDKFDL 63

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++   K+      + +K  REPT E
Sbjct: 64  SYDVKFSTYAVPMITGEIKRFLRDDGM-IKVSRSLKETAGKIRLMRETLESKNGREPTIE 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI-QA 607
           EI + L +  E V   L+   E  SL   I  GD +   L D IE  +  S  D  I   
Sbjct: 123 EIGEALELAKEEVVMALESGAEVESLYKTIYQGDGNAIFLIDKIEQTDDAS--DEMIDHM 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE    V+ SL  +E+ ++R+R+      D T  E+ KQ  +++ ++ ++E K +R +
Sbjct: 181 ALRE----VMDSLDEKEKDIIRLRY----FKDKTQTEIAKQLGISQVQVSRLERKILRTM 232

Query: 668 K 668
           +
Sbjct: 233 R 233


>gi|319407753|emb|CBI81400.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 303

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 123/244 (50%), Gaps = 29/244 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD   G +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM-------SNKIKREPTPEEIAKKL 556
           ++ +I   I      +R       K   +    RR+        N + ++     I++KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLAQDDNTLTKQEIFRAISEKL 173

Query: 557 AMPVEGVRKV---LKITKEPISL------ETPIGDEDTSHLGDFIEDKNAV-SPLDSAIQ 606
            + V  V K+      T   +SL      ETPI   D+      I+D     S ++ AI 
Sbjct: 174 GVSVNDVEKMDFRFSGTDNSLSLSISENGETPIAKMDS-----LIDDHPLPDSVIEQAID 228

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAI 664
              R +     L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A+
Sbjct: 229 GQRRAQWLHEALQILNERELEIIRFR---RLNEEGTTLEVLGEKLGISKERVRQIEARAL 285

Query: 665 RKLK 668
           +KL+
Sbjct: 286 QKLR 289


>gi|297518949|ref|ZP_06937335.1| RNA polymerase sigma factor RpoD [Escherichia coli OP50]
          Length = 183

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 56/139 (40%), Positives = 88/139 (63%), Gaps = 3/139 (2%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
            K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D   +
Sbjct: 9   LKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLA 68

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E++ D  ++ + + V L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  ENTADEDAAEAAAQV-LSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 126

Query: 150 RAMMMASLCESPLTFQALI 168
              +  S+ E P     L+
Sbjct: 127 INQVQCSVAEYPEAITYLL 145


>gi|310815299|ref|YP_003963263.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
 gi|308754034|gb|ADO41963.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
          Length = 298

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAM 558
           ++ +I   I      +++     + K+   +R A+     ++    R    + IA  L +
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPEHVQRIAHDLGV 168

Query: 559 PVEGVRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
           P E V  +  +++    SL   +G  D+ ++   D++ED+++    D   +  L   R  
Sbjct: 169 PEEEVVNMNRRLSGGDASLNAMVGGDDDSSTQWQDWLEDEDSDQAADFEARDELDARRVL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE  VL MR     +   TLEE+ +++ V+RERIRQIE +A  KL+
Sbjct: 229 LEAAMEDLNDRERDVLMMRR--LQDPPVTLEELSEKYSVSRERIRQIEVRAFEKLQ 282


>gi|224002653|ref|XP_002290998.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220972774|gb|EED91105.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 345

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/250 (27%), Positives = 128/250 (51%), Gaps = 26/250 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           AK ++V +NLR+V  V   Y   GL       DL+Q+G + L++AAEK++   G++FSTY
Sbjct: 85  AKNQLVASNLRMVQRVVNLYIRNGLGSEYNAGDLMQDGTMALIRAAEKYEPERGFRFSTY 144

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM+W++ A+ RS   QS  + +P  + +   +V +T  R+  ++ R+PT  E++    + 
Sbjct: 145 AMYWIRSAVKRSQTMQSRIVNVPQRIHETYKRVTKTEARLRKELGRDPTKVELSAACDIT 204

Query: 560 VEGVRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQANLRETTTRVL 617
           V  + +  +  ++   SL+  +  ++T    +    K+ +  L  S +     E T R+L
Sbjct: 205 VVQLDRCRRAMQQAAFSLDAEV--QNTYKPNNSNSRKDTMYDLVASKVDETEYEKTQRLL 262

Query: 618 AS----------LTPREERVLRMRFGI--------GMNTDHTLEEVGKQFCVTRERIRQI 659
                       L+P E  +L +R+G+        GM+   T+ EV K   +  +++R+I
Sbjct: 263 MKEHLISTLRRYLSPHEVDLLLLRYGLMDERALPKGMSGPLTIAEVSKLVGLKPDKVRRI 322

Query: 660 EAKAIRKLKH 669
              + ++L+H
Sbjct: 323 IINSQKQLRH 332


>gi|126738732|ref|ZP_01754428.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
 gi|126719913|gb|EBA16620.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
          Length = 298

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 126/246 (51%), Gaps = 13/246 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E + A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +
Sbjct: 43  EKEDTGAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTAR-RMSNKIKREPTPE---EI 552
           TYAMWW++ +I   I      +++     + K+   +R A+ R+    + +  PE   +I
Sbjct: 103 TYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAQI 162

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A  L +  E V  +  +++    SL   +G   E T    D++ED++A    D   +  L
Sbjct: 163 AHDLGVTEEEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDEL 222

Query: 610 ---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              RE   + +  L  RE+ +L  R      T  TLE++  ++ V+RERIRQIE +A  K
Sbjct: 223 EARRELLVQAMEVLNDREKDILTQRRLSDQAT--TLEDLSGEYGVSRERIRQIEVRAFEK 280

Query: 667 LKHPSR 672
           L+   R
Sbjct: 281 LQKKMR 286


>gi|58038976|ref|YP_190940.1| RNA polymerase factor sigma-32 [Gluconobacter oxydans 621H]
 gi|58001390|gb|AAW60284.1| Heat shock sigma factor RpoH [Gluconobacter oxydans 621H]
          Length = 297

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 116/240 (48%), Gaps = 15/240 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E + A   +V ++LRLV  +A  Y   GL   +LI EGNIG+M+A  +FD   G++ +TY
Sbjct: 44  EDTSAAHRLVTSHLRLVAKIAMGYRGYGLPVNELISEGNIGMMQAVRRFDPERGFRLATY 103

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE---I 552
           AMWW++ A+   I      +++      K  K+    RR+  +++     +  PE+   I
Sbjct: 104 AMWWIRAAMQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIDDGDLKPEQVNSI 161

Query: 553 AKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-- 609
           A  L +P + V  + +    P  SL  P+  +      D++ D +       A       
Sbjct: 162 ATTLGVPEQDVVSMNQRLAAPDHSLNAPLRIDGEGEWQDWLVDDHENQEQTYAASEEFTG 221

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    + L +L  RE  +L  R         TLEE+   + V+RERIRQIEA+A+ KL+
Sbjct: 222 RKALLDQALMTLNERERHILSERR--LKEEPSTLEELSHHYNVSRERIRQIEARAMEKLQ 279


>gi|239929001|ref|ZP_04685954.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291437340|ref|ZP_06576730.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291340235|gb|EFE67191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 374

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 114/224 (50%), Gaps = 10/224 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G
Sbjct: 140 LQDGSPEYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRG 199

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A
Sbjct: 200 VEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELA 259

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           +KLA+  E V + L+       +SL+ P  D+++  + D +  +      D A++    R
Sbjct: 260 EKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYR 313

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           E+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 314 ESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 357


>gi|239944189|ref|ZP_04696126.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 284

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 53  GSPEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 112

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++L
Sbjct: 113 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAERL 172

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 173 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 227 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 267


>gi|159045518|ref|YP_001534312.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157913278|gb|ABV94711.1| RNA polymerase sigma 32 factor [Dinoroseobacter shibae DFL 12]
          Length = 293

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/254 (29%), Positives = 123/254 (48%), Gaps = 20/254 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 42  ALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 101

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A      + R    + IA 
Sbjct: 102 IKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAASAGEPLDRHQLRQMIAT 161

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSP----LDSAIQAN 608
           ++ +P+  V  +  ++     SL      ED      D +ED  A +      D  I+  
Sbjct: 162 EVGVPLHDVEMMEGRLAGSDYSLNATQSTEDEGREWIDTLEDTGAQAAELVEQDHDIE-T 220

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR      + +L  RE  ++R R     +   TLE +G++  +++ER+RQ+EA A  K++
Sbjct: 221 LRGWLITAMDALNERERFIVRER--KLRDQPRTLESLGQELGLSKERVRQLEAAAFGKMR 278

Query: 669 HP--SRSKKLRSFL 680
               ++S ++R F 
Sbjct: 279 KNLMNQSSEVRQFF 292


>gi|197103427|ref|YP_002128805.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480703|gb|ACG80230.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 316

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 116/235 (49%), Gaps = 12/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRL   +A  Y   GL   ++I EGN+GLM A +KFD   G++ +TYA+WW
Sbjct: 47  AAHRLVTSHLRLSAKIALSYRGYGLPLGEVISEGNLGLMHAVKKFDPDKGFRLATYAIWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAM 558
           ++ AI   I      +++      K     + R   R+S     +  P++   IA +L +
Sbjct: 107 IRAAIQEYILRSWSLVKLGTSAVQKKLFFNLRRAKARISALSDGDLKPDQVKAIASRLGV 166

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             E V  +  ++     SL +P+  +      D +ED+ AV P  +  +A  R     +L
Sbjct: 167 NEEEVVNMDRRLASRDASLNSPLAADAEQEWLDVLEDEAAVDPEAAVAEAEERALRMDLL 226

Query: 618 A----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A    +L  RE R+   R     +    LE++ K F V+RER+RQIE +A  K++
Sbjct: 227 AQAMQTLNARERRIFTARR--LQDPPALLEDLAKDFGVSRERVRQIEVRAFEKVQ 279


>gi|284033085|ref|YP_003383016.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283812378|gb|ADB34217.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 264

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 114/223 (51%), Gaps = 13/223 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ + S+A+  +V  ++ LV  +A+++ NRG  + DL+Q   IGL+KA ++FD   G +F
Sbjct: 33  GDPQHSLARDGLVSLHMPLVEHLARRFRNRGEPYDDLVQVATIGLIKAIDRFDSDRGVEF 92

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   +   I R   D+   IR+P  +++    +      ++ ++ R PT  E++ +L
Sbjct: 93  STYATPTILGEIKRYFRDKGWAIRVPRRLQELRLSLTAATAELTQELGRAPTVAELSTRL 152

Query: 557 AMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRE 611
            +     +EG+          +SL+ P  +E      D     + +   D A+++   RE
Sbjct: 153 GLSQDLVIEGLESANAYNT--LSLDAPDQNE-----ADATTVLDGLGGEDEALESVEFRE 205

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           +   +LA L  RE+R+L +RF  GM      EE+G  Q  V+R
Sbjct: 206 SLKPLLAQLETREKRILTLRFFRGMTQSQIAEEIGISQMHVSR 248


>gi|319403703|emb|CBI77288.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 305

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 128/247 (51%), Gaps = 20/247 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGNIGLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      ++I      K  ++    R++ NK++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKIGTTANQK--RLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V  + +      SL  P+     ++    D++ D ++ +   + I+ N  E   
Sbjct: 167 KVTEDEVVSMNRRLNGDASLNAPLLTNKGESYEWQDWLVD-DSNNQEQTLIEQNELENRY 225

Query: 615 RVLA----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +L     +L  RE+R+ + R    +  D  TLEE+  +F ++RER+RQIEA+A  K+++
Sbjct: 226 SILIHAMDNLNEREKRIFKAR---RLRDDPLTLEELSNEFNISRERVRQIEARAFEKIQN 282

Query: 670 PSRSKKL 676
             ++  L
Sbjct: 283 FIKTSAL 289


>gi|241661869|ref|YP_002980229.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12D]
 gi|240863896|gb|ACS61557.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12D]
          Length = 309

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 126/236 (53%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 69  AARRLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHW 128

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ +         + +A +L +    
Sbjct: 129 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQDAQATFTSDEIDAVAAELNVKGTE 188

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTTRV 616
           VR++  +++   I+LE  +  G+E  + +    +  N  + +  A ++N R   E     
Sbjct: 189 VREMETRLSGGDIALEGQMDDGEESYAPIAYLADTHNEPTRVIEA-RSNDRMQSEGIEAA 247

Query: 617 LASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 248 LAKLDDRSRRIIEARW-LNVNDDGSGGSTLHELADEFGVSAERIRQIESAAMKKMK 302


>gi|304393314|ref|ZP_07375242.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
 gi|303294321|gb|EFL88693.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
          Length = 300

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 122/247 (49%), Gaps = 18/247 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E + + A  +MV ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KFD   G+
Sbjct: 39  RYSEHDDTEAAHKMVTSHLRLVAKIAMGYRGYGLPVSEVISEGNVGLMQAVKKFDPEKGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K +I   +      +++      K  ++    R++  K+K       ++ 
Sbjct: 99  RLATYAMWWIKASIQEYVLRSWSLVKMGTTANQK--RLFFNLRKLKGKLKALEEGELKQE 156

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
             E+IA  L +  + VR + +      SL  PI   + ++    D++ D +         
Sbjct: 157 NVEKIASTLGVSHDEVRSMNQRLSGDASLNAPIKAAEGESGQWQDWLVDDSESQEQMLIK 216

Query: 606 QANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEA 661
           Q  L   R+     +  L  RE+R+   R    +  D  TLE +  +F ++RER+RQIE 
Sbjct: 217 QDELDVRRDMLAEAMDVLNDREKRIFMAR---RLEEDPLTLEVLSGEFDISRERVRQIEV 273

Query: 662 KAIRKLK 668
           +A  K++
Sbjct: 274 RAFEKVQ 280


>gi|28899727|ref|NP_799332.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260879104|ref|ZP_05891459.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|28807979|dbj|BAC61216.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|308089656|gb|EFO39351.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|328472446|gb|EGF43312.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus 10329]
          Length = 286

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 78/270 (28%), Positives = 142/270 (52%), Gaps = 23/270 (8%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +  KGE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYKGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++     + + P  D+D++  
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDDDDSATS 194

Query: 589 GD-----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRFGIGMNT 638
                  ++EDK+  S +   I+A   E  T       LASL  R +R++R R+    + 
Sbjct: 195 SYTAPMLYLEDKS--SDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLD--DE 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 251 KATLQDLADEFGVSAERIRQLEKNAMKKLK 280


>gi|224827256|ref|ZP_03700350.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
 gi|224600545|gb|EEG06734.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
          Length = 287

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 117/242 (48%), Gaps = 31/242 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++V ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ W
Sbjct: 49  AAKKLVLSHLRVVVSIARGYAGYGLPQADLIQEGNIGLMKAVKRFEPNRGVRLFSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE--IAKKLAMPVE 561
           +K  I   I      +R+      +  K+    R M          E   IA  L +  E
Sbjct: 109 IKAEIHEFILRNWRLVRVATTKPQR--KLFFNLRSMKKSFAALTDSEARVIADDLGVKPE 166

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT------- 614
            VR+          +ET +  +D + L D   D    +P+D    ++   T         
Sbjct: 167 EVRE----------METRMSGQDVALLAD-DNDDEGFAPIDWLADSDHEPTRQLEKKAFD 215

Query: 615 --------RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                   + L+SL  R  R++  R+ +  ++  TL E+  +F V+ ERIRQIEAKA+ K
Sbjct: 216 HLQTAGLEQALSSLDARSRRIIEARW-LADDSGATLHELAAEFGVSAERIRQIEAKALTK 274

Query: 667 LK 668
           +K
Sbjct: 275 MK 276


>gi|169351116|ref|ZP_02868054.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
 gi|169292178|gb|EDS74311.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
          Length = 239

 Score = 93.2 bits (230), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 16/241 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ K  C   IAK+ +V  NL LV S+  ++ N      DL Q G IGLMKA   FD 
Sbjct: 7   IELIEKARCGDEIAKELVVNQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAINNFDT 66

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA+  +   I R   D   TI++   +++   K+ +    + N+  ++PT E
Sbjct: 67  NYGVQFSTYAVPIIMGEIKRYFRDDG-TIKVSRSLKELNLKINKVKELLINQTGQDPTVE 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDK-NAVSPLDSAIQA 607
            IAK L + V+ V + +  +  P SL  PI ++D S +   + +EDK N +     A++ 
Sbjct: 126 AIAKYLNIDVQDVVEAIDSSYYPTSLSEPIYEKDGSSISMEERVEDKHNKMWFEKIALKM 185

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            + +        L  +E+ +L +R+ +  N     E+V K+  +++ ++ ++E K I KL
Sbjct: 186 EIDK--------LDEKEKLILYLRYQLDFNQ----EKVAKRLNISQVQVSRLEKKIIAKL 233

Query: 668 K 668
           +
Sbjct: 234 R 234


>gi|302520387|ref|ZP_07272729.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302429282|gb|EFL01098.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 338

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 115/226 (50%), Gaps = 12/226 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 109 ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 168

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+AK L + 
Sbjct: 169 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELAKALGVS 228

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA-NLRETTT 614
            + V   L +       SL++P  ++D     L D +  +      D+A++    RE+  
Sbjct: 229 EDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYE------DTALEGVEYRESLK 282

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
            +LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 283 PLLAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 328


>gi|145594674|ref|YP_001158971.1| sigma-70 region 2 domain-containing protein [Salinispora tropica
           CNB-440]
 gi|145304011|gb|ABP54593.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 284

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 115/229 (50%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 42  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E+A++L  P E +
Sbjct: 101 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATAALTSELSRAPTVAELARRLETPEEEI 160

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+      P SL  P+G E ++  GD + E  NA+  +D       R T + +L  L
Sbjct: 161 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESDNALESVDD------RVTVSGLLHRL 214

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF      + T  E+  +F +++  + ++ ++A+  L+ 
Sbjct: 215 PWRERRILAMRF----YGNQTQAEIAARFGISQMHVSRLLSRALTWLRQ 259


>gi|83944334|ref|ZP_00956789.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83844878|gb|EAP82760.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 295

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/253 (27%), Positives = 124/253 (49%), Gaps = 18/253 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 44  ALHRLITAYMRLAISMAGKFKRYGASMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 103

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A+     + +    + I+ 
Sbjct: 104 IKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMIST 163

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPL--DSAIQANL 609
           ++ +P+  V  +  +++    SL      ED     +   ++D    +    +S     L
Sbjct: 164 EIGVPMHDVEMMEGRLSGSDFSLNATQSAEDEGREWIDALVDDSAQAAERVEESHDTLTL 223

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R      + +L  RE+ ++R R     +   TLE +G +  +++ER+RQ+EA A  K++ 
Sbjct: 224 RSWLLSAMQALNEREQFIVRER--KLRDQPRTLESLGAELSLSKERVRQLEAAAFGKMRK 281

Query: 670 P--SRSKKLRSFL 680
              ++S ++R FL
Sbjct: 282 TLETQSSEVRHFL 294


>gi|72160963|ref|YP_288620.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71914695|gb|AAZ54597.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 267

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 110/214 (51%), Gaps = 11/214 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VE +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   +
Sbjct: 43  RDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLSRGVEFSTYATPTI 102

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    + +    +S +  R PT  E+A+ L M  E V 
Sbjct: 103 VGEIKRHFRDKGWAVRVPRRLQELKLSLTKAVSELSQRHGRAPTVAELAEYLKMSEEEVL 162

Query: 565 KVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASL 620
           + L+       +SL+ P  GDED   + D      ++  +D +++    RE+   +L  L
Sbjct: 163 EGLESANAYSTVSLDAPDNGDEDAPAVAD------SLGIMDESLEGVEYRESLKPLLERL 216

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            PRE+++L +RF   M       E+G  Q  V+R
Sbjct: 217 PPREKKILLLRFFGNMTQSQIAAELGISQMHVSR 250


>gi|312884403|ref|ZP_07744108.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367925|gb|EFP95472.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 285

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 129/242 (53%), Gaps = 17/242 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +A+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 45  GEIDAA---KGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNQGE--VETVAR 159

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +    VR++  ++  +  + E P  D+D  TS++   +  ++  S +   I+A   E
Sbjct: 160 ELGVEPSEVREMESRLAAQDATFEVPSDDDDAHTSYVAPMVYLEDKASDIADNIEAANWE 219

Query: 612 TTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             T       L SL  R + ++R R+    +   TL+E+ + + V+ ERIRQ+E  A++K
Sbjct: 220 AHTNNRLSLALKSLDERSQHIVRSRWLD--DNKSTLQELAETYQVSAERIRQLEKNAMKK 277

Query: 667 LK 668
           LK
Sbjct: 278 LK 279


>gi|239990645|ref|ZP_04711309.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 309

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 78  GSPEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 137

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++L
Sbjct: 138 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAERL 197

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 198 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 251

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 252 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 292


>gi|77462968|ref|YP_352472.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126461842|ref|YP_001042956.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221638824|ref|YP_002525086.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332557843|ref|ZP_08412165.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|1769585|gb|AAC46050.1| RpoH [Rhodobacter sphaeroides]
 gi|77387386|gb|ABA78571.1| sigma factor RpoH1 (Sigma-32 group, heat shock) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126103506|gb|ABN76184.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221159605|gb|ACM00585.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332275555|gb|EGJ20870.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 298

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 124/242 (51%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAM 558
           ++ +I   I      +++     + K+   +R A+     ++    R     +IAK L +
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLGV 168

Query: 559 P-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   IG   E ++   D++ED+++    D A +  L   RE 
Sbjct: 169 SETEVIDMNRRLSGSDASLNATIGSDGEGSTQWQDWLEDEDSDQAADYAERDELEIRREL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             + ++ L  RE+ +L  R      TD   TLEE+ + + V+RERIRQIE +A  KL+  
Sbjct: 229 LAQSMSVLNDREKDILVQR----RLTDDPVTLEELSEGYGVSRERIRQIEVRAFEKLQAK 284

Query: 671 SR 672
            R
Sbjct: 285 MR 286


>gi|296270865|ref|YP_003653497.1| Sig B/F/G subfamily RNA polymerase sigma-28 [Thermobispora bispora
           DSM 43833]
 gi|296093652|gb|ADG89604.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermobispora bispora DSM 43833]
          Length = 259

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 110/214 (51%), Gaps = 11/214 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VE ++ LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   +
Sbjct: 35  RDELVELHMPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLSRGVEFSTYATPTI 94

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    + +    +S +  R PT  E+A+ L M  E V 
Sbjct: 95  VGEIKRHFRDKGWAVRVPRRLQELKLSLTKAISELSQRESRAPTVAELAEHLQMSEEEVL 154

Query: 565 KVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASL 620
           + L+       +SL+ P  GDED   + D      ++  +D +++    RE+   +L  L
Sbjct: 155 EGLESANAYSTVSLDAPDSGDEDAPAVSD------SLGIVDESLEGVEYRESLKPLLERL 208

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 209 PPREKRILLLRFFGNMTQSQIANELGISQMHVSR 242


>gi|320009626|gb|ADW04476.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 288

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 59  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 118

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+AK L + 
Sbjct: 119 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELAKALGVS 178

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DAALEGVEYRESLKPL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 235 LAKLAPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 278


>gi|227823777|ref|YP_002827750.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342779|gb|ACP26997.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 288

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 127/242 (52%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  +++RLVI++A K+ + GL   DL+QEG+IGL++AA +F+     +FSTYA WW
Sbjct: 40  ARNKIAMSHMRLVIAMAAKFRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK---REPTP----EEIAKKL 556
           ++ ++   +      +R       K   +    RR+  ++    R+ T     +EIA  L
Sbjct: 100 IRASMQDFVLRNWSIVRGGTSSAQK--ALFFNLRRLRARLAQGDRQLTSLAMHQEIAAAL 157

Query: 557 AMPVEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---- 609
            + +  V+ +  +++    SL+ P+  GD D     DF+      +PL     +++    
Sbjct: 158 GVSLADVQTMDARLSGNDASLQAPVGHGDSDGGARLDFLPSD---APLPDEQVSDMIDGE 214

Query: 610 --RETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
             R      L  LT RE +++R R    ++ D  TLEE+G    +++ER+RQIE +A+ K
Sbjct: 215 RARRWLQVALTQLTEREMKIIRAR---RLSEDGATLEELGLALGISKERVRQIETRALEK 271

Query: 667 LK 668
           L+
Sbjct: 272 LR 273


>gi|161869654|ref|YP_001598821.1| RNA polymerase factor sigma-32 [Neisseria meningitidis 053442]
 gi|161595207|gb|ABX72867.1| RNA polymerase sigma-32 factor [Neisseria meningitidis 053442]
 gi|316983693|gb|EFV62674.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
 gi|325140133|gb|EGC62662.1| alternative sigma factor RpoH [Neisseria meningitidis CU385]
 gi|325200603|gb|ADY96058.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
          Length = 287

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/274 (27%), Positives = 137/274 (50%), Gaps = 37/274 (13%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N I  ++ E    ++E +H      KG+  A+   K+++ ++LR+V+S+A+ Y   GL  
Sbjct: 25  NRIPMLTQEEETRLAERQH------KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQ 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKI 529
            DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + K+
Sbjct: 76  ADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKL 135

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
              +R+ R+  N +  +   ++IA  L + +           E + +E  +   D + + 
Sbjct: 136 FFNLRSMRKNLNALSPKEA-QDIADDLGVKL----------SEVLEMEQRMTGHDIAIMA 184

Query: 590 DFIEDKNAVSPLD---------------SAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           D  +D+++ +P+D                A  A   E     LA L  R  R++  R+ +
Sbjct: 185 DNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-L 243

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +   TL ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 244 QDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|302536824|ref|ZP_07289166.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302445719|gb|EFL17535.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 332

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 112/222 (50%), Gaps = 10/222 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 100 EGSPERAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVE 159

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++
Sbjct: 160 FSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAER 219

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+
Sbjct: 220 LGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRES 273

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 274 LKPLLEGLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 315


>gi|56420843|ref|YP_148161.1| sporulation sigma factor SigF [Geobacillus kaustophilus HTA426]
 gi|56380685|dbj|BAD76593.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-F) (stage II sporulation protein AC) [Geobacillus
           kaustophilus HTA426]
          Length = 250

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 124/252 (49%), Gaps = 17/252 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ++ I   E + ++   ++G+ EA   + E++E N+RLV SV +++ NRG +  DL Q G 
Sbjct: 9   QSPIKDQEMKELIRRSQEGDQEA---RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGC 65

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    
Sbjct: 66  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE 124

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S    R PT  EIA  L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 125 LSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADAD 184

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D            + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 185 EASWFDKI-------ALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQV 233

Query: 657 RQIEAKAIRKLK 668
            ++E K ++ +K
Sbjct: 234 SRLEKKILQHIK 245


>gi|291446269|ref|ZP_06585659.1| sigma L [Streptomyces roseosporus NRRL 15998]
 gi|291349216|gb|EFE76120.1| sigma L [Streptomyces roseosporus NRRL 15998]
          Length = 307

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 78  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 137

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L + 
Sbjct: 138 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVS 197

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 198 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 253

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 254 LAKLAPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 297


>gi|261250002|ref|ZP_05942579.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
 gi|260939506|gb|EEX95491.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
          Length = 285

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 141/276 (51%), Gaps = 22/276 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E    ++E  H       GE EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRSANSYPMLTPEEERDLAERLHY-----DGEIEAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I 
Sbjct: 68  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++  +  + E P
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDATFEMP 185

Query: 580 IGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASLTPREERVLRMRF 632
             D++  TS+    +  ++  S +   ++A+  E  T       L SL  R + ++R R+
Sbjct: 186 TDDDETGTSYTAPMVYLEDKASDVADHVEASNWEAHTNNRLSLALKSLDDRSQHIVRSRW 245

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +   TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 246 LD--DNKSTLQELAETYSVSAERIRQLEKNAMKKLK 279


>gi|262364691|gb|ACY61248.1| RNA polymerase sigma factor RpoD [Yersinia pestis D182038]
          Length = 248

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 95/158 (60%), Gaps = 7/158 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V+    D DDL   E
Sbjct: 10  KLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDLMLAE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            + D+ D A+ A+     L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 70  NTTDTDDDAAEAAAQ--VLSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G   +  S+ E P     L+   D +  G + L ++I
Sbjct: 127 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI 164


>gi|83953376|ref|ZP_00962098.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83842344|gb|EAP81512.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 295

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/261 (28%), Positives = 125/261 (47%), Gaps = 34/261 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 44  ALHRLITAYMRLAISMAGKFKRYGASMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 103

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A+     + +    + I+ 
Sbjct: 104 IKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMIST 163

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL--DSAIQA---- 607
           ++ +P+  V  +  +++    SL      ED        E +  +  L  DSA  A    
Sbjct: 164 EIGVPMHDVEMMEGRLSGSDFSLNATQSAED--------EGREWIDALVDDSAQAAERIE 215

Query: 608 ------NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  LR      + +L  RE+ ++R R     +   TLE +G +  +++ER+RQ+EA
Sbjct: 216 ESHDTLTLRSWLLSAMQALNEREQFIVRER--KLRDQPRTLESLGAELSLSKERVRQLEA 273

Query: 662 KAIRKLKHP--SRSKKLRSFL 680
            A  K++    ++S ++R FL
Sbjct: 274 AAFGKMRKTLETQSSEVRHFL 294


>gi|328884955|emb|CCA58194.1| RNA polymerase sigma factor [Streptomyces venezuelae ATCC 10712]
          Length = 344

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 113/222 (50%), Gaps = 10/222 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 112 EGSPEKAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVE 171

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++
Sbjct: 172 FSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAER 231

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+
Sbjct: 232 LGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRES 285

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 286 LKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 327


>gi|325265256|ref|ZP_08131981.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
 gi|324029435|gb|EGB90725.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
          Length = 259

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E ++ NLRLV+SV K+++N      DL Q G +GLMKA + FD     KFSTYA+  
Sbjct: 38  AREEYIKGNLRLVLSVIKRFSNSNENADDLFQIGCVGLMKAVDHFDPNRLVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        K  +EPT +EIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIYAKEGYMKKHLKEPTVQEIAEEIGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+  +  DT ++ D + DK     N V  L          +    
Sbjct: 157 VFALDAIQMPMSLHEPVYSDGGDTLYVMDQVSDKKNKEENWVEEL----------SLEAA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L  RE  ++ +RF  G     T  EV ++  +++ ++ ++E  A++ +K 
Sbjct: 207 MERLNERERYIITLRFFEG----KTQMEVAEEIKISQAQVSRLEKNALKVMKQ 255


>gi|170731288|ref|YP_001776721.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M12]
 gi|167966081|gb|ACA13091.1| RNA polymerase sigma-32 factor [Xylella fastidiosa M12]
          Length = 288

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 126/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 56  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA +SP+   I           + N  
Sbjct: 165 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPLSPVGYLIANDGDPSQAYERGNSE 222

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 223 ETQLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 279

Query: 665 RKLK 668
           +K+K
Sbjct: 280 KKMK 283


>gi|163867808|ref|YP_001609012.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161017459|emb|CAK01017.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 294

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 124/246 (50%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  VA  Y   GL   ++I EGNIGLM+A ++F+   G++ +TYA+WW
Sbjct: 49  AAHRLVTSHLRLVAKVAMGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAIWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      +++      K  ++    R++ NK++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKMGTTANQK--RLFFNLRKLKNKLQALDSGDLNTEQVKEIATQL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP---LDSAIQANLRE 611
            +  + V  + +      SL  P+   + + S L D++ D++       ++ +   N R 
Sbjct: 167 NVTEDEVVSMNRRLGGDTSLNAPLRTKEGENSELQDWLVDESNNQEQILIEKSELENRRF 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                + +L  RE R+ + R    +N    TLEE+  +F ++RER+RQIE +A  K+++ 
Sbjct: 227 MLVNAMNNLNDRERRIFKAR---RLNDIPLTLEELSSEFNISRERVRQIEMRAFEKVQNS 283

Query: 671 SRSKKL 676
            R   L
Sbjct: 284 IRDSAL 289


>gi|83746847|ref|ZP_00943894.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|207727816|ref|YP_002256210.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|207742220|ref|YP_002258612.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
 gi|83726432|gb|EAP73563.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|206591057|emb|CAQ56669.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206593608|emb|CAQ60535.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
          Length = 306

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 128/237 (54%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W
Sbjct: 66  AARRLVLSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHW 125

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ ++        + +A++L +    
Sbjct: 126 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQDAHATFTSDEIDAVAQELNVKGAE 185

Query: 563 VRKV-LKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR-ETTTR 615
           VR++  +++   I+LE  I D + S     +L D   +   V  L++     L+ E    
Sbjct: 186 VREMETRLSGGDIALEGQIDDGEESFAPIAYLADTHNEPTRV--LETRGHDRLQSEGIET 243

Query: 616 VLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 244 ALAKLDDRSRRIIEARW-LNVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMK 299


>gi|302552550|ref|ZP_07304892.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470168|gb|EFL33261.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 301

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 72  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 131

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 132 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVTELASVLGVS 191

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 192 EEDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 247

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 248 LAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 291


>gi|163738663|ref|ZP_02146077.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|163742952|ref|ZP_02150335.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383635|gb|EDQ08021.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161387991|gb|EDQ12346.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 298

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 119/242 (49%), Gaps = 13/242 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S +  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAM
Sbjct: 47  SASAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAM 106

Query: 502 WWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           WW++ +I   I      +++     + K+   +R A+     ++      +  KK+A  +
Sbjct: 107 WWIRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLHPDSVKKIATDL 166

Query: 561 -----EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
                E +    +++    SL   +G   E T    D++ED++A    D   +  L   R
Sbjct: 167 GVTETEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     L  L  RE+ +L  R     +   TLE++  Q+ V+RERIRQIE +A  KL+  
Sbjct: 227 ELLASALEVLNDREKDILTQRRLA--DQAKTLEDLSTQYGVSRERIRQIEVRAFEKLQKK 284

Query: 671 SR 672
            R
Sbjct: 285 MR 286


>gi|15676610|ref|NP_273754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis MC58]
 gi|7225940|gb|AAF41127.1| RNA polymerase sigma-32 factor [Neisseria meningitidis MC58]
          Length = 290

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/274 (27%), Positives = 137/274 (50%), Gaps = 37/274 (13%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N I  ++ E    ++E +H      KG+  A+   K+++ ++LR+V+S+A+ Y   GL  
Sbjct: 28  NRIPMLTQEEETRLAERQH------KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQ 78

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKI 529
            DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + K+
Sbjct: 79  ADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKL 138

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
              +R+ R+  N +  +   ++IA  L + +           E + +E  +   D + + 
Sbjct: 139 FFNLRSMRKNLNALSPKEA-QDIADDLGVKL----------SEVLEMEQRMTGHDIAIMA 187

Query: 590 DFIEDKNAVSPLD---------------SAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           D  +D+++ +P+D                A  A   E     LA L  R  R++  R+ +
Sbjct: 188 DNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-L 246

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +   TL ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 247 QDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|110679109|ref|YP_682116.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109455225|gb|ABG31430.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 298

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           ++ +I   I      +++      K  K+    R+  NKI    + +  P+    IAK L
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSGQK--KLFFNLRKAKNKIGALEEGDLHPDNVARIAKDL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +   E +    +++    SL   +G   E T    D++ED++A    D   +  L   R
Sbjct: 167 GVTETEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     ++ L  RE  +L+ R         TLE++  ++ V+RERIRQIE +A  KL+  
Sbjct: 227 ELLADAMSVLNDRERDILQQRRLSEQTV--TLEDLSAEYNVSRERIRQIEVRAFEKLQKK 284

Query: 671 SR 672
            R
Sbjct: 285 MR 286


>gi|260438829|ref|ZP_05792645.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
 gi|292808819|gb|EFF68024.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
          Length = 260

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 128/253 (50%), Gaps = 15/253 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++  V+ G+     A++  ++ NLRLV+SV K+++  G    DL Q G IGL
Sbjct: 19  LSTKEKEELIIKVKNGD---KAARERYIKCNLRLVLSVVKRFSGNGENMDDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD  L  KFSTYA+  +   I R + D S  IR+   ++D   + +    R+  
Sbjct: 76  IKAIDNFDMSLNVKFSTYAVPMIIGEIRRFLRDNS-QIRVSRSLKDVAFRAIYAKERIMK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
             K EPT  E+A ++ +  E +   L   + P+SL  PI  +  D  ++ D I DK    
Sbjct: 135 TGKDEPTVNELATEIGVSKEELVMALDAIQTPVSLYEPIYTDGGDMLYVMDQIGDKKNTE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +   +  L++   R    L  RE+ ++++R+  G     T  EV K   +++ ++ ++
Sbjct: 195 E-NWVNEMALKDAIKR----LPDREKEIIKLRYFDG----KTQMEVSKMVRISQAQVSRL 245

Query: 660 EAKAIRKLKHPSR 672
           E  AI+ +++  R
Sbjct: 246 EKSAIKNMENYLR 258


>gi|253576354|ref|ZP_04853684.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844247|gb|EES72265.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 251

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/259 (28%), Positives = 134/259 (51%), Gaps = 18/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K IS E  +  +E + ++++ + G+   + A+  +V  N+RLV SV +++ NRG +  
Sbjct: 4   EVKQISREF-LDDTEVKRLIALSQSGD---NAARDRLVNCNIRLVWSVVQRFMNRGYEPE 59

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K
Sbjct: 60  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKEMANK 118

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           V +    +S ++ R PT +E+A +L +  E V    +  K P S+   +   D D   L 
Sbjct: 119 VRKKKDELSKQLGRLPTVKEVADELGVTPEDVVFAQEANKPPASIHETVFENDGDPITLM 178

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+      D   +  L E     +  LT RE  ++ +R+      D T  EV  + 
Sbjct: 179 DQIADETQERWFD---KLALHEA----IDGLTDRERLIVYLRY----YRDQTQSEVATRL 227

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++ ++
Sbjct: 228 GISQVQVSRLEKKILQSIR 246


>gi|187927337|ref|YP_001897824.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12J]
 gi|309779962|ref|ZP_07674716.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
 gi|187724227|gb|ACD25392.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12J]
 gi|308921321|gb|EFP66964.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
          Length = 309

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 126/236 (53%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 69  AARRLVLSHLRLVVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHW 128

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ +         + +A +L +    
Sbjct: 129 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQDAQATFTSDEIDAVAAELNVKGTE 188

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTTRV 616
           VR++  +++   I+LE  +  G+E  + +    +  N  + +  A ++N R   E     
Sbjct: 189 VREMETRLSGGDIALEGQMDDGEESFAPIAYLADTHNEPTRVIEA-RSNDRMQSEGIEAA 247

Query: 617 LASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 248 LAKLDDRSRRIIEARW-LNVNDDGSGGSTLHELADEFGVSAERIRQIESAAMKKMK 302


>gi|114327512|ref|YP_744669.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
 gi|114315686|gb|ABI61746.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
          Length = 375

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 118/239 (49%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGN+G+M+A  +FD   G++ +TYAMWW
Sbjct: 117 AAHRLVTSHLRLVAKIAMGYRGYGLPVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWW 176

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAK---KL 556
           ++ AI   I      +++      K  K+    RR+  +++     +  PE+++K    L
Sbjct: 177 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIDDGDLKPEQVSKIATSL 234

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +P + V ++ +    P  SL  P+  E      D++ D    +     + A+  E   R
Sbjct: 235 NVPEQDVVQMNRRMSAPDHSLNAPLRQEGEGEWQDWLVDD---AETQETVLADTEELGGR 291

Query: 616 ------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  L +L  RE  +L  R      T  TLE++ + + ++RER+RQIE +A  KL+
Sbjct: 292 KTLLANALKTLNDRERHILTERRLKDEPT--TLEDLSQHYNISRERVRQIEVRAFEKLQ 348


>gi|302544114|ref|ZP_07296456.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461732|gb|EFL24825.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 293

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 9/242 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++ R  E EA   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 47  LSRSLFLRLAALDRDSE-EAGYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 105

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  ++ 
Sbjct: 106 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQ 165

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVS 599
            + R PT  E+A  L +  E V   L +       SL++P   ED    G  + D+    
Sbjct: 166 TLDRSPTVTELATALGVSEEDVVDGLAVGNAYTASSLDSP-SPEDEGGEGS-LADRLGYE 223

Query: 600 PLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIR 657
             DSA++    RE+   +LA L PRE +++ +RF   M      EEVG  Q  V+R   R
Sbjct: 224 --DSALEGVEYRESLKPLLAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTR 281

Query: 658 QI 659
            +
Sbjct: 282 TL 283


>gi|290959142|ref|YP_003490324.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
 gi|260648668|emb|CBG71781.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
          Length = 306

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 113/226 (50%), Gaps = 12/226 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 77  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 136

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 137 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVTELAAVLGVS 196

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA-NLRETTT 614
            E V   L +       SL++P  ++D     L D +  +      D+A++    RE+  
Sbjct: 197 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYE------DTALEGVEYRESLK 250

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
            +LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 251 PLLAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 296


>gi|188090702|gb|ACD49585.1| RNA polymerase sigma factor [Stenotrophomonas maltophilia]
          Length = 284

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 55/142 (38%), Positives = 87/142 (61%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L + P++
Sbjct: 63  AAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGQFPVS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            ++L+   +   +G   L E+I
Sbjct: 123 VESLLNDYEAHKEGKKRLAEVI 144


>gi|253699229|ref|YP_003020418.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
 gi|251774079|gb|ACT16660.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
          Length = 285

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 119/241 (49%), Gaps = 14/241 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ EA+     ++ +NLR V+ +A +Y + G++ LDLIQEGNIGLM A  KFD   G 
Sbjct: 39  REGDLEAA---HRLITSNLRFVVKIAGEYRSYGMKMLDLIQEGNIGLMMAVRKFDPDKGV 95

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +  +YA+WW++  I   I      ++I     + K+   +  A++    +  E      A
Sbjct: 96  RLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQRKLFFKLNQAKQAIVNMTGEGDLHAAA 155

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L +     +++ +  +  +SL+  + + +    G F+E    +      + A  +ETT
Sbjct: 156 ISLDVKDHEAQEMEQRLRGELSLDVEMFEGEGG--GTFLESLPDLRQNQEEMLAERQETT 213

Query: 614 ------TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                    L  L  +E  V+  R  +      TL+E+   F ++RER+RQIE  A++K+
Sbjct: 214 ILERNVASALEDLNEKERFVIEQR--VAAENPMTLQEIADHFSISRERVRQIEEGALKKM 271

Query: 668 K 668
           K
Sbjct: 272 K 272


>gi|297250602|ref|ZP_06934149.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
 gi|296838520|gb|EFH22458.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
          Length = 290

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 127/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 47  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   +EIA 
Sbjct: 104 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QEIAD 162

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 163 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 212

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 213 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 271

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 272 EAKAMQKLR 280


>gi|21222437|ref|NP_628216.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256786489|ref|ZP_05524920.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289770380|ref|ZP_06529758.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|13122198|emb|CAC32374.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289700579|gb|EFD68008.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 318

 Score = 92.8 bits (229), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 89  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 148

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 149 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVGELAAVLGVS 208

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 209 EEDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 264

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 265 LAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 308


>gi|300692652|ref|YP_003753647.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
 gi|299079712|emb|CBJ52389.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
          Length = 306

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 128/237 (54%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W
Sbjct: 66  AARRLVLSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHW 125

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ ++        + +A++L +    
Sbjct: 126 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQDAHATFTSDEIDAVAQELNVKGTE 185

Query: 563 VRKV-LKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR-ETTTR 615
           VR++  +++   I+LE  I D + S     +L D   +   V  L++     L+ E    
Sbjct: 186 VREMETRLSGGDIALEGQIDDGEESFAPIAYLADAHNEPTRV--LEARGHDRLQSEGIET 243

Query: 616 VLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 244 ALAKLDDRSRRIIEARW-LNVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMK 299


>gi|300705271|ref|YP_003746874.1| RNA polymerase sigma h (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
 gi|299072935|emb|CBJ44291.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
          Length = 306

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 128/237 (54%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W
Sbjct: 66  AARRLVLSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHW 125

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ ++        + +A++L +    
Sbjct: 126 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQDAHATFTSDEIDAVAQELNVKGAE 185

Query: 563 VRKV-LKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR-ETTTR 615
           VR++  +++   I+LE  I D + S     +L D   +   V  L++     L+ E    
Sbjct: 186 VREMETRLSGGDIALEGHIDDGEESFAPIAYLADTHNEPTRV--LETRGHDRLQSEGIET 243

Query: 616 VLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 244 ALAKLDDRSRRIIEARW-LNVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMK 299


>gi|261417856|ref|YP_003251538.1| sporulation sigma factor SigF [Geobacillus sp. Y412MC61]
 gi|297529524|ref|YP_003670799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319767332|ref|YP_004132833.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
 gi|261374313|gb|ACX77056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC61]
 gi|297252776|gb|ADI26222.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317112198|gb|ADU94690.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
          Length = 252

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 124/252 (49%), Gaps = 17/252 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ++ I   E + ++   ++G+ EA   + E++E N+RLV SV +++ NRG +  DL Q G 
Sbjct: 11  QSPIKDQEMKELIRRSQEGDQEA---RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGC 67

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    
Sbjct: 68  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE 126

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S    R PT  EIA  L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 127 LSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADAD 186

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D            + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 187 EASWFDKI-------ALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQV 235

Query: 657 RQIEAKAIRKLK 668
            ++E K ++ +K
Sbjct: 236 SRLEKKILQHIK 247


>gi|163736875|ref|ZP_02144293.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|161389479|gb|EDQ13830.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 292

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/258 (28%), Positives = 129/258 (50%), Gaps = 28/258 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A+    ++ +    ++IA 
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLERQAQSDGARLDKHQLHQQIAT 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSP---LDSAIQANL 609
           ++ +P+  V+ +  ++     SL      ED      + +ED +A +     +S     L
Sbjct: 161 EIGVPLRDVQMMDGRLAGSDFSLNAVQSSEDEGREWIEALEDDSAQAAELVEESHDTRQL 220

Query: 610 RETTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           R+     + +L  RE     ER LR           TLE +G +  +++ER+RQ+EA A 
Sbjct: 221 RDWLVEAMQALNERERFIITERKLR-------EKPRTLESLGNELDLSKERVRQLEAGAF 273

Query: 665 RKLKHP--SRSKKLRSFL 680
           +K++    + S+++++FL
Sbjct: 274 QKMRKSLETCSREVQNFL 291


>gi|166031695|ref|ZP_02234524.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
 gi|166028672|gb|EDR47429.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
          Length = 244

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 125/244 (51%), Gaps = 12/244 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++++       A+  +VE N  LV  + K++ NRG++  DL Q GNIGL+KA +KF
Sbjct: 3   HTIALIQRSHEGDEEARARLVEENAGLVWCIVKRFHNRGVETEDLFQIGNIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K       + N+  REPT
Sbjct: 63  DLSYDVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKELAYKAYLLKEDLQNQWGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             E++++L +  E +   L    +  SL  PI  +D     L D +E+K+     +   Q
Sbjct: 122 VGELSERLGVEQEELVMALDAGGDVESLHKPIYQKDGQEIRLMDKLEEKS-----EEHEQ 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  T +L  L   E+R++ +R+      + T  +VG++  +++ ++ ++E K + +
Sbjct: 177 VLNHIVLTELLGVLNQDEKRLIYLRY----FAEQTQSQVGRELGISQVQVSRMEKKILGQ 232

Query: 667 LKHP 670
           LK+ 
Sbjct: 233 LKNA 236


>gi|94497521|ref|ZP_01304090.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
 gi|94422938|gb|EAT07970.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
          Length = 310

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 121/242 (50%), Gaps = 26/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KF+   G++ +TYAMWW
Sbjct: 58  AAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFEADRGFRLATYAMWW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAKKLAMP 559
           ++ +I   I      +++      K  K+    RRM N I+     +  PE++  K+A  
Sbjct: 118 IRASIQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKNNIEAFEDGDLRPEDVT-KIATD 174

Query: 560 VEGVRK--VLKITKE-----PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + GV +  V+ + +        SL  P+ ++      D++ D +   PL     A+ +E 
Sbjct: 175 L-GVSEDDVISMNRRMAMGGDTSLNVPMREDGEGQWQDWLADTD---PLQDERVADEQEK 230

Query: 613 TTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             R       +  L  RE+ +L  R         TLEE+ + + V+RER+RQIE +A  K
Sbjct: 231 VQRHDMLVEAMDDLNDREKHILAERRLA--EEPKTLEELSQVYGVSRERVRQIEVRAFEK 288

Query: 667 LK 668
           L+
Sbjct: 289 LQ 290


>gi|225375609|ref|ZP_03752830.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
 gi|225212588|gb|EEG94942.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
          Length = 259

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 128/248 (51%), Gaps = 27/248 (10%)

Query: 430 IVSMVRKGECEASIAKKEM-VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           + + +R+G+ EA    +EM ++ NLRLV+SV K+++       DL Q G IGL+K+ + F
Sbjct: 27  LFARIRQGDQEA----REMYIKGNLRLVLSVIKRFSGSHENLDDLFQIGCIGLIKSIDNF 82

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +  L  KFSTYA+  +   I R + D + +IR+   +RD  +K +     +S    +EPT
Sbjct: 83  NPDLQVKFSTYAVPMIIGEIRRYLRDNN-SIRVSRSLRDTAYKAIHAKEVLSKNSFKEPT 141

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPL 601
            +EIA++  +  E +   L   + P+SL  P+  +  DT ++ D I DK     N V  L
Sbjct: 142 LQEIAEESGVAAEDILYALDAIQSPVSLYDPVYTDGGDTLYVMDQISDKKNKEENWVEKL 201

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                     + +  +  L+ RE  ++ +RF  G     T  EV  +  +++ ++ ++E 
Sbjct: 202 ----------SLSDAMNHLSERENFIINLRFFEG----KTQMEVADEIHISQAQVSRLEK 247

Query: 662 KAIRKLKH 669
            A++ ++ 
Sbjct: 248 SALKTIRQ 255


>gi|319638161|ref|ZP_07992924.1| RNA polymerase sigma factor rpoD [Neisseria mucosa C102]
 gi|317400434|gb|EFV81092.1| RNA polymerase sigma factor rpoD [Neisseria mucosa C102]
          Length = 650

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/191 (32%), Positives = 108/191 (56%), Gaps = 20/191 (10%)

Query: 14  EHEDSDDS--LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           E++D DD+  L  +      +++I + ++RGY+T  E+N  LP D   +EQ+++ V+M+S
Sbjct: 9   EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMIS 68

Query: 72  NMGINVV----DGDD--LEDEEGS---EDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            +GI V     D +D  L D   +   +D+++ A +A +S+       DS    T DPVR
Sbjct: 69  GLGIQVTEQAPDAEDILLSDNAAALTDDDAVEEAEAALSSA-------DSEFGRTTDPVR 121

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    + 
Sbjct: 122 MYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVD 181

Query: 183 EIIDLEACIGP 193
           E++  EA I P
Sbjct: 182 EVV--EAIIDP 190


>gi|241760450|ref|ZP_04758543.1| RNA polymerase sigma factor RpoD [Neisseria flavescens SK114]
 gi|241318954|gb|EER55456.1| RNA polymerase sigma factor RpoD [Neisseria flavescens SK114]
          Length = 650

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/191 (32%), Positives = 108/191 (56%), Gaps = 20/191 (10%)

Query: 14  EHEDSDDS--LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           E++D DD+  L  +      +++I + ++RGY+T  E+N  LP D   +EQ+++ V+M+S
Sbjct: 9   EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMIS 68

Query: 72  NMGINVV----DGDD--LEDEEGS---EDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            +GI V     D +D  L D   +   +D+++ A +A +S+       DS    T DPVR
Sbjct: 69  GLGIQVTEQAPDAEDILLSDNAAAMTDDDAVEEAEAALSSA-------DSEFGRTTDPVR 121

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    + 
Sbjct: 122 MYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVD 181

Query: 183 EIIDLEACIGP 193
           E++  EA I P
Sbjct: 182 EVV--EAIIDP 190


>gi|295399044|ref|ZP_06809026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110351|ref|YP_003988667.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
 gi|294978510|gb|EFG54106.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215452|gb|ADP74056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
          Length = 250

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 119/238 (50%), Gaps = 14/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R+ +     A+ E+++ N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD   
Sbjct: 20  LIRRSQEGDQQARNEIIQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSY 79

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R I D   T+++   +++  +K+ +    +S K  R PT  EI
Sbjct: 80  DVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKETGNKIRKARDELSKKHGRAPTVTEI 138

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L +  E V    +  + P S+   +   D D   L D I D +  S  D        
Sbjct: 139 ADYLEISPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIADADEASWFDKI------ 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K ++++K
Sbjct: 193 -ALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQVSRLEKKILQQIK 245


>gi|291454068|ref|ZP_06593458.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291357017|gb|EFE83919.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 365

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 134 GGPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEF 193

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A+KL
Sbjct: 194 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQRHGRSPTVHELAEKL 253

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 254 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSE------DEALEGVEYRESL 307

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 308 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 348


>gi|291549326|emb|CBL25588.1| RNA polymerase sigma-F factor [Ruminococcus torques L2-14]
          Length = 239

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 134/242 (55%), Gaps = 16/242 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++RK       A++E+VE N+ L+  V K++  RG +  DL Q G+IGL+KA +KFD+
Sbjct: 5   IALIRKSHDGDKKAREELVEKNIGLIWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDF 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R + D    I++   +R+  +K ++   +M+  + REPT +
Sbjct: 65  SYEVQFSTYAVPMISGEIRRFLRDDG-MIKVSRSLRELSYKSLQAREKMTRILGREPTLK 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIE--DKNAVSPLDSAIQ 606
           E++++L +  E + + ++ + E  S+  PI  ++ S   L D +E  D+     LD  + 
Sbjct: 124 ELSEELQIDCEEIVQAMESSVEVESIYKPIHQKEGSEILLMDKLEEKDRQEEKVLDRIV- 182

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    VL +L  +E  ++ +R+  G     T  E+GK+  +++ ++ + E K + +
Sbjct: 183 --LKE----VLETLEAKERTIIYLRYFAG----KTQAEIGKKMGMSQVQVSRTEKKVLER 232

Query: 667 LK 668
           ++
Sbjct: 233 MR 234


>gi|163733965|ref|ZP_02141406.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
 gi|161392501|gb|EDQ16829.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
          Length = 298

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 122/242 (50%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEE---IAKKL 556
           ++ +I   I      +++      K  K+    R+  NKI    + +  P+    IAK L
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSGQK--KLFFNLRKAKNKIGALEEGDLHPDNVARIAKDL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +   E +    +++    SL   +G   E T    D++ED+ A    D   +  L   R
Sbjct: 167 GVTETEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEGADQAGDYEARDELEARR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     ++ L  RE+ +L+ R  +   T  TLE++  ++ V+RERIRQIE +A  KL+  
Sbjct: 227 ELLADAMSVLNDREKDILQQRR-LSEKT-VTLEDLSAEYNVSRERIRQIEVRAFEKLQKK 284

Query: 671 SR 672
            R
Sbjct: 285 MR 286


>gi|94499830|ref|ZP_01306366.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
 gi|94428031|gb|EAT13005.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
          Length = 288

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 129/233 (55%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V+ +AK Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 52  AARRLVLSHLRFVVHIAKSYNGYGLNQSDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+A++  N    E    +IA+ L +  + 
Sbjct: 112 IKAEIHEFILKNWRIVKVATTKAQRKLFFNLRSAKK-RNGWLNEAEAHKIAEDLGVSAKE 170

Query: 563 VRKV-LKITKEPISLETPIG-DEDTSHL--GDFIEDKNAVSPLDSAIQANLRETTTRV-- 616
           V ++  +++    + ++P+  DED+++    +++ED +    L    +   +++T R+  
Sbjct: 171 VYEMEGRLSSHDSTFDSPVADDEDSAYQAPANYLEDHSFDPALAVENENYEQDSTARLQD 230

Query: 617 -LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R + +L MR  +G +   TL E+  ++ V+ ERIRQ+E  A++K+K
Sbjct: 231 ALVQLDDRSKDIL-MRRWLGEHKA-TLHELADEYGVSAERIRQLEKNAMKKIK 281


>gi|82703854|ref|YP_413420.1| RNA polymerase factor sigma-32 [Nitrosospira multiformis ATCC
           25196]
 gi|82411919|gb|ABB76028.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosospira multiformis
           ATCC 25196]
          Length = 281

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 82/259 (31%), Positives = 140/259 (54%), Gaps = 16/259 (6%)

Query: 423 SISEFRHI-----VSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S+++FR +     + + R    E SI A +++V ++LRLV+++A+ Y   GL   DLIQE
Sbjct: 19  SVNQFRILTQEEELQLARSLRDEGSIDAARQLVLSHLRLVVAIARGYKGYGLPQADLIQE 78

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRT 535
           GNIGLMKA ++FD   G +  ++A+ W+K  I   I      ++I     + K+   +R+
Sbjct: 79  GNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFILRNWRLVKIATTKAQRKLFFNLRS 138

Query: 536 ARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLKITKEPISLETPIG---DEDTSHLGDF 591
            ++  + + ++    E+A++L + P E V    + +   ISLE P+    DE+T     +
Sbjct: 139 LKQALDTMSQKEVA-EVAEQLGVKPEEVVEMETRFSGRDISLE-PLSEDDDEETFSPIAY 196

Query: 592 IEDKNAVSP-LDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + D +  S  L+      LR E   + L SL  R   ++  R+    +T  TL E+  + 
Sbjct: 197 LTDGSEPSHVLEDEQTMRLRGEGLEQALESLDARSRHIIEARWLREKDTA-TLHELADEL 255

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+ ER+RQIEAKA++KL+
Sbjct: 256 GVSAERVRQIEAKAMQKLR 274


>gi|23099294|ref|NP_692760.1| sporulation sigma factor SigF [Oceanobacillus iheyensis HTE831]
 gi|22777523|dbj|BAC13795.1| stage II sporulation protein AC (RNA polymerase sigma-F factor)
           [Oceanobacillus iheyensis HTE831]
          Length = 250

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 122/240 (50%), Gaps = 11/240 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++R  +     A+  +VE N+RLV SV +++ NRG    DL Q G+IGL+K+ +KF
Sbjct: 16  QVKELIRLSQQGDQSARDRLVEKNIRLVWSVVQRFINRGYDPDDLFQIGSIGLIKSIDKF 75

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R I D   +I++   +++  +K+ R    M+ +  R PT
Sbjct: 76  DLSYDVKFSTYAVPMIIGEIQRFIRD-DGSIKVSRSLKEIGNKIRRKKDEMTKQYGRSPT 134

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A+ L +  E V    +  K P S+   + + D    GD I   + ++  DS     
Sbjct: 135 VNELAEALELQPEEVVHAQEAAKSPQSIYETVFEND----GDPITLLDQIADQDSKWFEK 190

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +    + SLT RE  ++ +R+      D T  EV ++  +++ ++ ++E K +  +K
Sbjct: 191 L--SLQEAIRSLTERERLIIYLRY----YKDKTQTEVAERLGISQVQVSRLEKKILEDMK 244


>gi|266624907|ref|ZP_06117842.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
 gi|288863210|gb|EFC95508.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
          Length = 258

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 116/229 (50%), Gaps = 16/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 38  AREEYIKGNLRLVLSVIQRFSGSNENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +     +  K  +EPT  EIA ++ +  E +
Sbjct: 98  ILGEVRRYLRDNN-SIRVSRSLRDTAYKAIYAKENLMKKNLKEPTIMEIADEIGVSKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE--TTTRVLAS 619
              L   + P+SL  P+  +  D   + D I DK         ++ N  E  +    +  
Sbjct: 157 TYALDAIQNPVSLYEPVYSDGGDPLFVMDQISDK-------KNLEENWVEDISLNEAMKR 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K
Sbjct: 210 LPERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKSMK 254


>gi|284043274|ref|YP_003393614.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947495|gb|ADB50239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 258

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 115/220 (52%), Gaps = 10/220 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++E  + LV S+A++Y NRG    DL Q G +GL+KA ++FD     +FST+A+  
Sbjct: 32  ARRALIERMMPLVRSLARRYANRGEPLDDLEQVGCVGLIKAVDRFDLSRELRFSTFAVPT 91

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++ ++R+   +++   +V R A R+S K+ R PT E++A+      E V
Sbjct: 92  ILGEIKRHFRDRAWSVRVSRGLQELSARVTREADRLSTKLGRSPTIEDLAEATNSTPEQV 151

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + L+  +    + LE P+GD+     G+ +    A  P      A  R   +R L  L+
Sbjct: 152 LEALQGAQAYSTVPLEEPLGDD-----GEPVARIGAEDP--EFELAEERIELSRGLHVLS 204

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIE 660
            RE R++ +RF  G+      E VG  Q  V+R   R +E
Sbjct: 205 ERERRIVLLRFFAGLTQREIAERVGISQMHVSRLLRRSLE 244


>gi|260434077|ref|ZP_05788048.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417905|gb|EEX11164.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 298

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 119/240 (49%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-- 560
           ++ +I   I      +++     + K+   +R A+     ++      +  K++A  +  
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLHPDNVKQIAHDLGV 168

Query: 561 ---EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   +G   E T    D++ED++A    D   +  L   RE 
Sbjct: 169 TEDEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDESADQAGDYETREELEVRREL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               L  L  RE+ +L  R    M+   TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 229 LAEALEVLNDREKDILTQRR--LMDQPVTLEELSSQYNVSRERIRQIEVRAFEKLQKKMR 286


>gi|238028681|ref|YP_002912912.1| RNA polymerase factor sigma-32 [Burkholderia glumae BGR1]
 gi|237877875|gb|ACR30208.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia glumae BGR1]
          Length = 311

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 124/234 (52%), Gaps = 14/234 (5%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K
Sbjct: 74  RRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAIHWIK 133

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEG 562
             I   I      +++      K  + +    R   K  +  TPEEI   A++L +  E 
Sbjct: 134 AEIHEYILRNWRMVKVAT---TKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKRED 190

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVL 617
           V ++  +++   I+LE  +  G+E  + +    +  N  + + ++ Q +  +T   +  L
Sbjct: 191 VAEMETRLSGGDIALEGQVEDGEESFAPIAYLADSHNEPTAVLASRQRDRLQTEGISEAL 250

Query: 618 ASLTPREERVLRMRF---GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            SL  R  R++  R+   G   +   TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 251 DSLDTRSRRIIEARWLNVGDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|118594538|ref|ZP_01551885.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440316|gb|EAV46943.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 286

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 123/236 (52%), Gaps = 17/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++L+LV+ +A+ Y+   L   DL+QEGNIGLMKA +KFD   G +  +YA++W
Sbjct: 48  AAKKLILSHLKLVMKIARSYSGYNLPHADLVQEGNIGLMKAVKKFDPDRGVRLVSYAIYW 107

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMP 559
           +K  I   +      ++      + K+   +R+ R+    +K    PEE   IA +L + 
Sbjct: 108 IKAEIQEYVVKNWRLVKTATTKAQRKLFFNLRSLRKTLQPLK----PEEIKSIANELNVK 163

Query: 560 VEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDS----AIQANLRET 612
              VR++  ++  +  +++    + +  H     ++ED+   SPL+       ++N+   
Sbjct: 164 ESEVREMEFRLNGKETTIDYSDDESEEDHFRPISYLEDETP-SPLEKIEMDQAESNVSAE 222

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L+ L  R   V+  R+ +  N   TL E+  +F V+ ERIRQIE  A +K++
Sbjct: 223 LQHALSELDSRSRSVVEARW-LNDNKSETLNELASKFKVSAERIRQIEKNAFKKIR 277


>gi|210617641|ref|ZP_03291672.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
 gi|210149188|gb|EEA80197.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
          Length = 237

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 127/245 (51%), Gaps = 16/245 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++R+       A++++VE N+ L+  + K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIRQSHDGDEKAREQLVEENIGLIWCIVKRFYGRGAEPEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      ++  K+ R+PT
Sbjct: 63  DMTYDVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKELSYKAYFAKEKLQEKLGRDPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSP--LDSA 604
            EE+A+ + +  E +   ++ + E  SL  PI  +D +   L D +E+  A     L+  
Sbjct: 122 LEELAETMEVEKEELVMAMESSGEVESLHKPIYQKDGNEIQLMDKLEETGAQEEKVLNQM 181

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           + A L       L  L   E +++ +R+      + T  +VGK   +++ ++ ++E K +
Sbjct: 182 LLAQL-------LEGLEKEERQLIYLRY----FANQTQSQVGKTLGISQVQVSRLEKKIL 230

Query: 665 RKLKH 669
           + L+ 
Sbjct: 231 KNLRQ 235


>gi|318041750|ref|ZP_07973706.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 45/91 (49%), Positives = 57/91 (62%), Gaps = 8/91 (8%)

Query: 448 MVEANLRLVISVAKKYTNR-----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           M++ NLRLV+ +AK Y  R      L+F DL+Q G IGL++A EKFD  LGY FSTYA W
Sbjct: 55  MIKENLRLVVCIAKPYHARIQRSSALEFSDLLQAGTIGLIRAVEKFDPALGYSFSTYASW 114

Query: 503 WVKQAITRSIADQSCTIRIPV---HMRDKIH 530
           W++QAI R I     +IR+      MR K H
Sbjct: 115 WIRQAIRREIEASESSIRLSARQQQMRLKAH 145


>gi|225076460|ref|ZP_03719659.1| hypothetical protein NEIFLAOT_01506 [Neisseria flavescens
           NRL30031/H210]
 gi|224952139|gb|EEG33348.1| hypothetical protein NEIFLAOT_01506 [Neisseria flavescens
           NRL30031/H210]
          Length = 650

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/191 (32%), Positives = 108/191 (56%), Gaps = 20/191 (10%)

Query: 14  EHEDSDDS--LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           E++D DD+  L  +      +++I + ++RGY+T  E+N  LP D   +EQ+++ V+M+S
Sbjct: 9   EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMIS 68

Query: 72  NMGINVV----DGDD--LEDEEGS---EDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            +GI V     D +D  L D   +   +D+++ A +A +S+       DS    T DPVR
Sbjct: 69  GLGIQVTEQAPDAEDILLSDNAAAMTDDDAVEEAEAALSSA-------DSEFGRTTDPVR 121

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    + 
Sbjct: 122 MYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVD 181

Query: 183 EIIDLEACIGP 193
           E++  EA I P
Sbjct: 182 EVV--EAIIDP 190


>gi|148552989|ref|YP_001260571.1| RNA polymerase factor sigma-32 [Sphingomonas wittichii RW1]
 gi|148498179|gb|ABQ66433.1| RNA polymerase sigma factor RpoH [Sphingomonas wittichii RW1]
          Length = 301

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 122/242 (50%), Gaps = 26/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KF+   G++ +TYAMWW
Sbjct: 53  AATRLVTSHLRLVAKIAMGYRGYGLPASELISEGNIGLMQGVKKFEPDRGFRLATYAMWW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAKKLAM- 558
           +K +I   I      +++      K  K+    RRM ++++     +  PE++ KK+A  
Sbjct: 113 IKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRMKSQLEAFEDGDLKPEDL-KKIATD 169

Query: 559 ------PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                  V  + + + +  +  SL   + ++      D + D+    PL     A + E 
Sbjct: 170 LGVSEEEVTSMNRRMSMGGDA-SLNVSMNEDGEGEWQDMLVDQG---PLQDERLAEVEEK 225

Query: 613 TTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + R       LA+L  RE+ +L  R  +  +   TLEE+ + + V+RER+RQIE +A  K
Sbjct: 226 SVRHNMLNEALAALNDREKHILVERRLV--DEPKTLEELSQVYGVSRERVRQIEVRAFDK 283

Query: 667 LK 668
           L+
Sbjct: 284 LQ 285


>gi|310822395|ref|YP_003954753.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309395467|gb|ADO72926.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 245

 Score = 92.4 bits (228), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/238 (29%), Positives = 107/238 (44%), Gaps = 54/238 (22%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +    RKG+     A++ +  +NL  V++VAKK+ NRG +  DLIQEGN+GLMKA E FD
Sbjct: 33  LARAARKGD---ESARQTLATSNLAFVVAVAKKFANRGARLDDLIQEGNVGLMKAIEHFD 89

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+TYA+WW++  ITR + D    +R     R  +                    
Sbjct: 90  PKKNVRFATYAVWWIRAYITRYLKDNRSQVRGGESERGSM-------------------- 129

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
                                    SL+  I +E  +   D +ED    SP D  +    
Sbjct: 130 ----------------------VDFSLDATIDEEGETTFMDRLED-GGPSPSDVYLS--- 163

Query: 610 RETTTRVLASLTPREERVLRMRFGI-----GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           RE    V  +L    +R+  + + I       +   TLEE+G+++ V+RER+RQ+E K
Sbjct: 164 REQDQEVHEALVKVRKRIGDLGWDILQERLTQDKPLTLEELGQRWGVSRERVRQVELK 221


>gi|301059188|ref|ZP_07200126.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
 gi|300446678|gb|EFK10505.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
          Length = 329

 Score = 92.4 bits (228), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 120/239 (50%), Gaps = 32/239 (13%)

Query: 448 MVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V +NLRLV+ +A    +Y  + L  LDLIQEGN+GL++A  KFD   G KFS YA +W+
Sbjct: 86  LVTSNLRLVVKIAMDFHRYWTKNL--LDLIQEGNLGLLQAVRKFDPYRGIKFSYYASFWI 143

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE----------PTPEEIAK 554
           K  I + I D    ++I            ++ R++   + +E          P P  +A+
Sbjct: 144 KAYILKFIMDNWKMVKI---------GTTQSQRKLFFNLAKERDKLIAQGFTPEPRLLAE 194

Query: 555 KLAMP-VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           KL +   E V    ++    ISL  P+G++     G F+ D  A++  D       +   
Sbjct: 195 KLDVKESEVVEMTQRLGGWEISLSAPVGEDSRESYGSFLPDP-AMAADDLLSNDESKNVL 253

Query: 614 TRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T+ L     +L+ +E  +   R  I      TL+++G ++ ++RERIRQI+ K I+ ++
Sbjct: 254 TKSLQEFRKTLSGKEADIFDNR--ILAEKPLTLQDLGDKYKISRERIRQIQEKIIKNIR 310


>gi|298529795|ref|ZP_07017198.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511231|gb|EFI35134.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 336

 Score = 92.4 bits (228), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 127/232 (54%), Gaps = 18/232 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ +NLRLV+ +A ++  + ++  LDLIQEGN+GLMKA +KFD   G KFS YA +W++ 
Sbjct: 94  LITSNLRLVVKIAMEFQRKWMKNVLDLIQEGNVGLMKALKKFDPDKGIKFSYYASFWIRA 153

Query: 507 AITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-VEGV 563
            I + I D    +++      R   + + +  +R+ + +      + I++ L +   + V
Sbjct: 154 YILKFIMDNWRMVKVGTTQAQRKLFYNLSKEKQRLES-MGITADADAISQSLDVSETDVV 212

Query: 564 RKVLKITKEPISLETPIG-DEDTS------HLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               ++ +  +SL+ P   D D +       LGD  E+          +Q N++E    +
Sbjct: 213 EMGQRLGQHDLSLDMPYNEDSDVTPMNVIPALGDGAEEILLQGETAQLLQQNIKE----L 268

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L+ +E+ ++ MR  +   +  TL E+G+++ +TRER+RQIE++ + K+K
Sbjct: 269 MPKLSDKEKDIIEMR--LLAESPVTLREIGEKYGITRERVRQIESRLLGKIK 318


>gi|251796351|ref|YP_003011082.1| sporulation sigma factor SigF [Paenibacillus sp. JDR-2]
 gi|247543977|gb|ACT00996.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. JDR-2]
          Length = 251

 Score = 92.4 bits (228), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/247 (26%), Positives = 125/247 (50%), Gaps = 17/247 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + ++++ + G+   +IA+  +V+ N+RLV SV +++ NRG +  DL Q G IGL+K+
Sbjct: 16  AEVKRLIALSQSGD---TIARDTLVQCNIRLVWSVVQRFINRGYEPEDLFQIGCIGLLKS 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    +S  + 
Sbjct: 73  VDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKETANKVRKMKDELSKTLG 131

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLD 602
           R PT  E+A +L +  E V    +  K P S+   +   D D   L D I D +     D
Sbjct: 132 RLPTVSEVADRLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADDSQERWFD 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++E K
Sbjct: 192 -------KLALIEAIEGLSERERLIVYLRY----YRDKTQSEVASRLGISQVQVSRLEKK 240

Query: 663 AIRKLKH 669
            ++ ++ 
Sbjct: 241 ILQSIRE 247


>gi|159037890|ref|YP_001537143.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
 gi|157916725|gb|ABV98152.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
          Length = 374

 Score = 92.4 bits (228), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 115/229 (50%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 42  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E+A++L  P E +
Sbjct: 101 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATAALTSELSRAPTVAELARRLETPEEEI 160

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+      P SL  P+G E ++  GD + E  NA+  +D       R T + +L  L
Sbjct: 161 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESDNALESVDD------RVTVSGLLHRL 214

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF      + T  E+  +F +++  + ++ ++A+  L+ 
Sbjct: 215 PWRERRILAMRF----YGNQTQAEIAARFGISQMHVSRLLSRALTWLRQ 259


>gi|188090472|gb|ACD49470.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. axonopodis]
 gi|188090630|gb|ACD49549.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. axonopodis]
          Length = 291

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 87/142 (61%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L++  +   +G   L EI+
Sbjct: 123 TEMLLVDYEAHKEGKKRLAEIV 144


>gi|154252145|ref|YP_001412969.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156095|gb|ABS63312.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 298

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 124/240 (51%), Gaps = 19/240 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  E+  A +RLVIS+A ++ N GL + DLIQEGN+GLM+AA +F+   G +FSTYA WW
Sbjct: 46  ALHELTCAYMRLVISLATRFRNYGLPYGDLIQEGNVGLMQAAARFEPERGVRFSTYASWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAM 558
           ++ AI   I      +R       K     + R    ++N  ++  T ++   IAK+L +
Sbjct: 106 IRAAIQDYILRNWSIVRTGTTAAHKSLFFNLRRLRALIANGTRQNLTEDDRIFIAKRLGV 165

Query: 559 PVEGVRKV-LKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               V  +  ++     SL   + D    E+ +   D +  +  + P +  ++ +  +  
Sbjct: 166 GASDVATIDARLMTGDRSLNATVSDSTSSENLTEWQDLLPCERPL-PEEEVMENHDSKQR 224

Query: 614 TR----VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     L SL  RE  ++R R    +  D  TLE +G +  +++ER+RQIE  A++KL+
Sbjct: 225 SRWIEGALESLNERELTIIRER---RLRDDVATLETLGVRLGISKERVRQIEHMALKKLR 281


>gi|261380693|ref|ZP_05985266.1| RNA polymerase sigma factor RpoD [Neisseria subflava NJ9703]
 gi|284796404|gb|EFC51751.1| RNA polymerase sigma factor RpoD [Neisseria subflava NJ9703]
          Length = 650

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 62/191 (32%), Positives = 108/191 (56%), Gaps = 20/191 (10%)

Query: 14  EHEDSDDS--LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           E++D DD+  L  +      +++I + ++RGY+T  E+N  LP D   +EQ+++ V+M+S
Sbjct: 9   EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMIS 68

Query: 72  NMGINVV----DGDD--LEDEEGS---EDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            +GI V     D +D  L D   +   +D+++ A +A +S+       DS    T DPVR
Sbjct: 69  GLGIQVTEQAPDAEDILLSDNAAAMTDDDAVEEAEAALSSA-------DSEFGRTTDPVR 121

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    + 
Sbjct: 122 MYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVD 181

Query: 183 EIIDLEACIGP 193
           E++  EA I P
Sbjct: 182 EVV--EAIIDP 190


>gi|188090584|gb|ACD49526.1| RNA polymerase sigma factor [Xanthomonas translucens pv. secalis]
 gi|188090586|gb|ACD49527.1| RNA polymerase sigma factor [Xanthomonas translucens]
 gi|188090588|gb|ACD49528.1| RNA polymerase sigma factor [Xanthomonas translucens pv. undulosa]
          Length = 285

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|149925644|ref|ZP_01913908.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
 gi|149825761|gb|EDM84969.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
          Length = 308

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 143/278 (51%), Gaps = 26/278 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +D+ +   ++I  +S E  + + E      + R  + EA+   + +V ++LRLV++VA++
Sbjct: 34  LDAYISATHQIPMLSPEEEVELGE-----RLQRDNDLEAA---RRLVLSHLRLVVAVARQ 85

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      +++ 
Sbjct: 86  YLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFALHWIKAEIHEYIIRNWRMVKM- 144

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKV-LKITKEPISLET 578
             +  K H+ +        K  +  +P+   E+A +L +  E V  +  ++     SL+ 
Sbjct: 145 --ITTKAHRKLFFNLNSFKKYGQTLSPDQINEVASELNVRPEDVYDMERRMAGHEFSLD- 201

Query: 579 PIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRM 630
           P+ D    E++ +   ++  + A  P +    AN+     E     LASL  R +R++  
Sbjct: 202 PVVDVDSEENSYNPVRYLAAEGA-EPTEVLEGANMERLHSEGLDMALASLDERSQRIISS 260

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+  G N   TL ++  +  V+ ER+RQIE +A++K+K
Sbjct: 261 RWLAGENAK-TLHDLAAELGVSAERVRQIETQAMKKMK 297


>gi|319406710|emb|CBI80343.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 305

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 74/257 (28%), Positives = 129/257 (50%), Gaps = 22/257 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E     A  ++V ++LRLV  +A  Y   GL   ++I EGNIGLM+A ++F+   G+
Sbjct: 40  RYHEYNDPKAAHKLVTSHLRLVAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K +I   +      ++I      K  ++    R++ NK++          
Sbjct: 100 RLATYAMWWIKASIQEYVLRSWSLVKIGTTANQK--RLFFNLRKLKNKLQMLDNGDLNAQ 157

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDF-IEDKNAVSPLDSA 604
             +EIA +L +  + V  + +      SL  P+     ++    D+ I+D N      + 
Sbjct: 158 QVKEIATRLKVTEDEVVSMNRRLNGDASLNAPLLTNKGESYEWQDWLIDDSNNQE--QTL 215

Query: 605 IQANLRETTTRVLA----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           I+ +  E    +L     +L  RE+R+ + R    +  D  TLEE+  +F ++RER+RQI
Sbjct: 216 IEQDELENRYSILIHAMDNLNEREKRIFKAR---RLRDDPLTLEELSNEFNISRERVRQI 272

Query: 660 EAKAIRKLKHPSRSKKL 676
           EA+A  K+K+  ++  L
Sbjct: 273 EARAFEKIKNFIKTSPL 289


>gi|182437345|ref|YP_001825064.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777955|ref|ZP_08237220.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465861|dbj|BAG20381.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658288|gb|EGE43134.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 288

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 59  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 118

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L + 
Sbjct: 119 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVS 178

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DAALEGVEYRESLKPL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 235 LAKLAPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 278


>gi|239942800|ref|ZP_04694737.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           15998]
          Length = 288

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 59  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 118

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L + 
Sbjct: 119 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVS 178

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 235 LAKLAPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 278


>gi|89092456|ref|ZP_01165410.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89083544|gb|EAR62762.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 284

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 143/275 (52%), Gaps = 21/275 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +D+ ++    I  +SVE   S++E  H       G+ EA+   +++V ++LR V+ VAK 
Sbjct: 17  LDAYVQNVTAIPVLSVEEERSLAERLHF-----DGDVEAA---RQLVMSHLRFVVHVAKT 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ WVK  +   I      +++ 
Sbjct: 69  YSGYGLPLGDLIQEGNVGLMKAVKRFDPTMGVRLVSFAVHWVKAEMHEFILRNWRIVKVA 128

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
               + K+   +R+ ++  + +  +     IA+ L +  + VR++  ++     + + P 
Sbjct: 129 TTKAQRKLFFNLRSKKKSLSWMTNDEV-NAIAEDLGVEAKVVRQMEGRMASVDTAFDAPE 187

Query: 581 GDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRVLAS----LTPREERVLRMRFG 633
           G +D         ++EDK+A  P     +AN  + + R L S    L  R + +L  R+ 
Sbjct: 188 GADDEQAAWAPAHYLEDKSA-DPSMQLEEANWEQDSQRRLMSAMSELDERSKDILARRWL 246

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +   TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 247 T--DDKATLHELAAEYGVSAERIRQLEKNAMKKIR 279


>gi|163854463|ref|YP_001628761.1| RNA polymerase factor sigma-32 [Bordetella petrii DSM 12804]
 gi|163258191|emb|CAP40490.1| RNA polymerase sigma-32 factor [Bordetella petrii]
          Length = 295

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 124/228 (54%), Gaps = 8/228 (3%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K 
Sbjct: 64  ELVLSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKA 123

Query: 507 AITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            I   I      +++     + K+   +R+ R     +  E   + IA++L +  E V +
Sbjct: 124 EIHEFIIRNWRMVKVATTKAQRKLFFNLRSMRPDGQTLDPEQV-DRIAQELNVRREDVSE 182

Query: 566 V-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRET-TTRVLASL 620
           + ++++   +SLE    DE+      ++ D+    P   LD      L+       L +L
Sbjct: 183 MEVRLSGRDLSLEKQDDDEEAFAPISYLSDEGRQEPTRVLDRRDHDELQGAGLAHALQAL 242

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R  R++  R+ +  +   TL+E+ ++F V+ ERIRQIE+ A++K++
Sbjct: 243 DARSRRIIEARW-LQDDGGVTLQELAQEFGVSAERIRQIESAALKKMR 289


>gi|188090534|gb|ACD49501.1| RNA polymerase sigma factor [Xanthomonas translucens pv. cerealis]
          Length = 285

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|289642895|ref|ZP_06475030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
 gi|289507278|gb|EFD28242.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
          Length = 332

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 114/231 (49%), Gaps = 10/231 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +V++    +  A I + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 91  FTQLVALPEGDQQRAEI-RDQLVRMHLPLVEYLARRFRNRGEPLDDLTQVATIGLIKSVD 149

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 150 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQTLGRS 209

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDS 603
           PT  EIA  L M  E V + L+       +SL+ P  GD++   + D +  ++     +S
Sbjct: 210 PTVSEIAAHLQMSEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD-----ES 264

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                 RE+   +L  L PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 265 LEGVEYRESLKPLLEKLPPREKRILLLRFFGNMTQSQIATELGISQMHVSR 315


>gi|188090700|gb|ACD49584.1| RNA polymerase sigma factor [Xanthomonas sacchari]
          Length = 286

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 84/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|298292657|ref|YP_003694596.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296929168|gb|ADH89977.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 303

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 117/238 (49%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 48  AAHKLVTSHLRLVAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPDKGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  K+    R+  ++I        R    ++IA KL
Sbjct: 108 IKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQISALEDGDLRPDQVQQIATKL 165

Query: 557 AMPVEGVRKVLKITKEPISLETPI-GD-EDTSHLGDFI---EDKNAVSPLDSAIQANLRE 611
            +  + V  + +      SL  P+ GD E      D++    D    +  D     N R 
Sbjct: 166 GVTEQEVVDMNRRLSGDASLNAPLRGDVEGGGEWQDWLADDRDDQETTLADLEETDNRRS 225

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L+ L  RE R+   R    ++ D  TLE++  +F V+RER+RQIE +A  K++
Sbjct: 226 ALAGALSVLNERERRIFEAR---RLSDDPMTLEDLASEFGVSRERVRQIEVRAFEKVQ 280


>gi|29830729|ref|NP_825363.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607842|dbj|BAC71898.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 307

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 113/226 (50%), Gaps = 12/226 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 78  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 137

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 138 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVAELAAVLGVS 197

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA-NLRETTT 614
            E V   L +       SL++P  ++D     L D +  +      D+A++    RE+  
Sbjct: 198 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYE------DTALEGVEYRESLK 251

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
            +LA L PRE R++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 252 PLLAKLPPRERRIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 297


>gi|293401521|ref|ZP_06645664.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305159|gb|EFE46405.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 259

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+++++ NL+LV+S+ ++++NR     DL Q G IGL+K+ + FD     +FSTYA+  
Sbjct: 38  AKEDLIQGNLKLVLSIVQRFSNRCENMDDLFQVGCIGLVKSIDNFDLKHEVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    IR+  H++D  +KV R      ++ ++EPT   +A++L +  + V
Sbjct: 98  IMGEIKRYLRDNQ-VIRVSRHLKDLAYKVFRLKEEYIHEHQKEPTIHWLAEQLQVKEKDV 156

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L  T+  +S+  P+   D D  +L D I +DK+ +  L + +      T  + + +L
Sbjct: 157 VDALDSTQSVVSIFEPVYNTDGDELYLLDQIKDDKDEIERLSNYM------TLKKSMRNL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E+ +++ R+      D T  E+  +  +++ ++ ++E  AI  LK
Sbjct: 211 KGKEKDIIQKRY----YQDKTQTEIANELGISQAQVSRLEKNAIALLK 254


>gi|169629597|ref|YP_001703246.1| RNA polymerase sigma factor SigF [Mycobacterium abscessus ATCC
           19977]
 gi|169241564|emb|CAM62592.1| Alternative sigma factor SigF [Mycobacterium abscessus]
          Length = 272

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 116/228 (50%), Gaps = 15/228 (6%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E+V   L L  +VA+ +  RG    DLIQ   +GL+ A  +FD   G  F  +A+  + 
Sbjct: 51  EEIVTRCLPLADNVARHFDRRGEDLEDLIQVARVGLLNAVNRFDPEKGASFLGFAVPTMM 110

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R   D   ++ +P  +RD+  ++ R    ++ +++R PT  E+A +L +  E V +
Sbjct: 111 GEVRRHFRDHGWSLHVPRAIRDRHAQISRATAELTQELQRAPTAGELAAELGIDREEVVE 170

Query: 566 VLKI--TKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
            L      +P S+E P+  GD+++ HL D + ++      D A++    RE    +LA+L
Sbjct: 171 SLIAADAYQPQSIEAPLSHGDQESKHLSDLLGNE------DPALEHVTNREAVRPLLANL 224

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  VL +RF  GM    T  ++  Q  V++  + +I +  +R L+
Sbjct: 225 PLRERTVLELRFFKGM----TQSQIAAQIGVSQMHVSRILSDTLRYLR 268


>gi|269127892|ref|YP_003301262.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312850|gb|ACY99224.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermomonospora curvata DSM 43183]
          Length = 276

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 114/223 (51%), Gaps = 11/223 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ E    + E+VE +L LV  +A+++ NRG    DLIQ   IGL+K+ ++FD   G +
Sbjct: 43  EGDPERQRVRDELVELHLPLVEYLARRFRNRGEWLDDLIQVATIGLIKSIDRFDLDRGVE 102

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   +   I R   D+   +R+P  +++    + +    ++ +  R PT  E+A+ 
Sbjct: 103 FSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAISDLAQREGRAPTVSELAEH 162

Query: 556 LAMPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRE 611
           L M  E V + L+       +SL+ P  GDED   + D      ++  +D +++    RE
Sbjct: 163 LQMSEEEVLEGLESANAYSTVSLDAPDSGDEDAPAVAD------SLGMVDDSLEGVEYRE 216

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           +   +L  L  RE+R+L +RF   M       E+G  Q  V+R
Sbjct: 217 SLKPLLEKLPAREKRILLLRFFGNMTQSQIANELGISQMHVSR 259


>gi|188090608|gb|ACD49538.1| RNA polymerase sigma factor [Xanthomonas theicola]
 gi|188090610|gb|ACD49539.1| RNA polymerase sigma factor [Xanthomonas theicola]
 gi|188090612|gb|ACD49540.1| RNA polymerase sigma factor [Xanthomonas theicola]
          Length = 286

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            ++L+   ++  +G   L EI+
Sbjct: 123 VESLLEDYEQHKEGKKRLAEIV 144


>gi|126733180|ref|ZP_01748927.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126716046|gb|EBA12910.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 298

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 118/238 (49%), Gaps = 17/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHQMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  N+I        R    E IA  L
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKNRIGALEDGDLRPENVERIANDL 166

Query: 557 AMPVEGVRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +  + V  +  +++    SL   +    E  +   D++ED++A +  D      L   R
Sbjct: 167 GVTEQEVISMNRRLSGGDASLNATVSADGEGAAQWQDWLEDESANTAADYEASDELTARR 226

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     +  L  RE+ +L M+  +   T  TLE++  Q+ V+RERIRQIE +A  KL+
Sbjct: 227 ELLAEAMEVLNDREKDIL-MQRRLSEET-VTLEDLSGQYDVSRERIRQIEVRAFEKLQ 282


>gi|188090576|gb|ACD49522.1| RNA polymerase sigma factor [Xanthomonas translucens pv. graminis]
          Length = 285

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|302558487|ref|ZP_07310829.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302476105|gb|EFL39198.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 281

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 113/224 (50%), Gaps = 10/224 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G
Sbjct: 47  LQDGTPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRG 106

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A
Sbjct: 107 VEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELA 166

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           +KLA+  E V + L+       +SL+ P  D+++  + D +  +      D A++    R
Sbjct: 167 EKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYR 220

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           E+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 221 ESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 264


>gi|188090696|gb|ACD49582.1| RNA polymerase sigma factor [Xanthomonas sacchari]
          Length = 286

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 84/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|162454145|ref|YP_001616512.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161164727|emb|CAN96032.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 283

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 118/224 (52%), Gaps = 7/224 (3%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLR V+S+A  Y   G+   DLI EGN G++ A  K+D   G +F TYA +W++  I   
Sbjct: 52  NLRHVVSIAISYRRYGIPLADLIAEGNFGIVHAIRKYDPDRGNRFVTYAAYWIRAYILNH 111

Query: 512 IADQSCTIRIPVH-MRDKIHKVVRTAR-RMSNKI-KREPTPEEIAKKLAMPVEGVRKVL- 567
           +      + +    +R K+   +R  R R++  + + E     +A+K   P E V ++  
Sbjct: 112 VIHSWSLVGVGSGPLRSKMFFRLRRERARIAGLVGEGEEGDRLLAEKFGAPAEKVLEMAH 171

Query: 568 KITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQ-ANLRETTTRVLASLTPRE 624
           ++    +SL+T + ++    L D +  +D++       A + A LRE  T+ + +L PRE
Sbjct: 172 RLEARDVSLDTKVFEDGARSLVDTLPADDQDQEERFSRAEEGALLRERLTQAVENLDPRE 231

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++  R       + +L E+G++  V+RER RQ+EA+A +KL+
Sbjct: 232 RYIVETRMMADPEEELSLAEIGRRLGVSRERARQLEARAKKKLR 275


>gi|238064463|ref|ZP_04609172.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237886274|gb|EEP75102.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 305

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 115/229 (50%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 65  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 123

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E+A++L  P E +
Sbjct: 124 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATATLTSELSRAPTVAELAERLETPQEEI 183

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+      P SL  P+G E ++  GD + E  NA+  +D       R T + +L  L
Sbjct: 184 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESDNALESVDD------RVTISGLLHRL 237

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF      + T  E+  +F +++  + ++ ++A+  L+ 
Sbjct: 238 PWRERRILAMRF----YGNQTQAEIAARFGISQMHVSRLLSRALTWLRQ 282


>gi|91775055|ref|YP_544811.1| sigma 32 (RpoH) [Methylobacillus flagellatus KT]
 gi|91709042|gb|ABE48970.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacillus flagellatus
           KT]
          Length = 285

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 122/232 (52%), Gaps = 8/232 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LRLV S+A+ Y   GL   DLIQEGNIGLMKA  +FD   G +  ++AM W
Sbjct: 49  AAKTLVVSHLRLVASIARNYAGYGLPQADLIQEGNIGLMKAVRRFDPDRGVRLVSFAMHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVE 561
           +K  I   I      +++     + K+   +R+ ++             IA++L + P E
Sbjct: 109 IKAEIHEYIVRNWRLVKVATTKAQRKLFFNLRSMKKGQTASLHSDEVAHIARELNVKPEE 168

Query: 562 GVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNA-VSPLDSAIQANLRETT--TRV 616
            +    +++   ISLE    D  ED      +++  +A  S +  A +A+   TT  +  
Sbjct: 169 VLEMEARMSGHEISLEGNADDDNEDMFSPISYLQASHAEPSEILEAQEADQLHTTGLSTA 228

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA L  R  R++  R+ +    + TL ++ ++F V+ ERIRQIE KA+++++
Sbjct: 229 LAKLDDRSRRIVEARW-LQEGHNATLHDLAEEFGVSAERIRQIEQKAMKQMR 279


>gi|239989259|ref|ZP_04709923.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           11379]
          Length = 288

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 59  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 118

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L + 
Sbjct: 119 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVS 178

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 179 EEDVIDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 235 LAKLAPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 278


>gi|330812146|ref|YP_004356608.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|327380254|gb|AEA71604.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 615

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/137 (40%), Positives = 85/137 (62%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D     D
Sbjct: 12  KELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|160915290|ref|ZP_02077503.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
 gi|158433089|gb|EDP11378.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
          Length = 240

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 126/241 (52%), Gaps = 17/241 (7%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++ +R G+ EA    ++ VEAN  LV ++ K++ NR +   DL Q G IGLMKA   FD
Sbjct: 9   LLAAIRYGDEEAL---EQFVEANQPLVYAIVKRFHNRRISQEDLFQIGCIGLMKAIHNFD 65

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R   D   +IRI   +++   ++++   +++  + +EPT 
Sbjct: 66  AAYEVKFSTYAVPIIMGEIKRFFRDDG-SIRISRSLKEGYLQMLKIKEQLTQTLGKEPTY 124

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
            +IA+ + + V  V    +  +   SL+ PI + D S   L D +ED       D  ++ 
Sbjct: 125 AQIAQAMNIEVGEVILAFEANQFMYSLDEPIYENDGSAIVLEDRVEDPKQT---DIVMKL 181

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR+   R    L  RE+ +L  R+ + M      E++ K+  +++ ++ ++E K + KL
Sbjct: 182 SLRKEFAR----LEQREQLILHYRYDLNMKQ----EDIAKRLHISQVQVSRLEKKILWKL 233

Query: 668 K 668
           K
Sbjct: 234 K 234


>gi|188090698|gb|ACD49583.1| RNA polymerase sigma factor [Xanthomonas sacchari]
          Length = 285

 Score = 91.7 bits (226), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 84/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 2   EVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 61

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   PL 
Sbjct: 62  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLA 121

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 122 VETLLEDYEQHKEGKKRLAEIV 143


>gi|294631337|ref|ZP_06709897.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292834670|gb|EFF93019.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 379

 Score = 91.7 bits (226), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 115/224 (51%), Gaps = 10/224 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G  + +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G
Sbjct: 145 LKEGSPQYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRG 204

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A
Sbjct: 205 VEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELA 264

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           +KLA+  E V + L+       +SL+ P  D+++  + D +  +      D A++    R
Sbjct: 265 EKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYR 318

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           E+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 319 ESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 362


>gi|188090494|gb|ACD49481.1| RNA polymerase sigma factor [Xanthomonas albilineans]
 gi|188090628|gb|ACD49548.1| RNA polymerase sigma factor [Xanthomonas albilineans]
          Length = 286

 Score = 91.7 bits (226), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|197302592|ref|ZP_03167647.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
 gi|197298490|gb|EDY33035.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
          Length = 259

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 119/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E ++ NLRLV+SV K++ +      DL Q G +GLMKA + FD     +FSTYA+  
Sbjct: 37  AREEYIKGNLRLVLSVIKRFDSSSESADDLFQIGCVGLMKAVDNFDPERLVRFSTYAVPM 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S +IR+   +RD  +K +        +  +EPT +EIA ++ +  E V
Sbjct: 97  IVGEIRRYLRDNS-SIRVSRSLRDTAYKAIYAKEGYVRRYMKEPTVQEIADEIGIAKEDV 155

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+ ++  D  ++ D + DK     N V  L  +++A         
Sbjct: 156 VFALDAVQTPMSLHEPVYNDGGDALYVMDQVSDKKNREENWVEEL--SLEA--------A 205

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L  RE  ++ +RF  G     T  EV  Q  +++ ++ ++E  A++ ++ 
Sbjct: 206 MERLNERERYIISLRFFEG----KTQTEVAGQIGISQAQVSRLEKNALKTMRQ 254


>gi|302542626|ref|ZP_07294968.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302460244|gb|EFL23337.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 351

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 120 GSAERAELRNNLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 179

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A+ L
Sbjct: 180 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQRHGRAPTVHELAEHL 239

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
           A+  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 240 AISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 293

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+++L +RF   M      +EVG  Q  V+R
Sbjct: 294 KPLLEDLPPREKKILLLRFFGNMTQSQIAQEVGISQMHVSR 334


>gi|297192165|ref|ZP_06909563.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197720190|gb|EDY64098.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 349

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 112/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  + +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 118 GSPQRAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEF 177

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++L
Sbjct: 178 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAERL 237

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 238 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 291

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 292 KPLLEGLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 332


>gi|307578942|gb|ADN62911.1| RNA polymerase factor sigma-32 [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 282

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 125/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 50  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 110 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 158

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA  SP+   I           + N  
Sbjct: 159 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPPSPVGYLIANDGDPSQAYERGNSE 216

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 217 ETQLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 273

Query: 665 RKLK 668
           +K+K
Sbjct: 274 KKMK 277


>gi|166031183|ref|ZP_02234012.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
 gi|166029030|gb|EDR47787.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
          Length = 278

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 120/233 (51%), Gaps = 22/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E ++ NLRLV+SV K++ +      DL Q G IGL+KA   F+  L  KFSTYA+  
Sbjct: 56  AKEEYIKGNLRLVLSVIKRFHSSNENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPM 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S +IR+   +RD  +K +        +  REPT +EIA+++ +  E +
Sbjct: 116 IIGEIRRYMRDNS-SIRVSRSLRDTAYKAIYAKENYVKQNMREPTVQEIAQEIGIAKEDI 174

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNA----VSPLDSAIQANLRETTTRV 616
              L   + P+SL+ P+  +  D  ++ D I D KN     V  L  ++QA         
Sbjct: 175 VYALDAIQAPMSLQEPVYSDGGDALYVMDQISDHKNKEEKWVESL--SLQA--------A 224

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L  RE  ++ +RF  G     T  EV +   +++ ++ ++E  A+R ++ 
Sbjct: 225 MEHLNERERYIISLRFFDG----RTQMEVARDVGISQAQVSRLEKNALRIMRQ 273


>gi|188090538|gb|ACD49503.1| RNA polymerase sigma factor [Xanthomonas albilineans]
          Length = 285

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL 
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFPLA 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   ++  +G   L EI+
Sbjct: 123 VETLLEDYEQHKEGKKRLAEIV 144


>gi|28199909|ref|NP_780223.1| RNA polymerase factor sigma-32 [Xylella fastidiosa Temecula1]
 gi|28058040|gb|AAO29872.1| RNA polymerase sigma-32 factor [Xylella fastidiosa Temecula1]
          Length = 293

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 125/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 61  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 121 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 169

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA  SP+   I           + N  
Sbjct: 170 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPPSPVGYLIANDGDPSQAYERGNSE 227

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 228 ETQLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 284

Query: 665 RKLK 668
           +K+K
Sbjct: 285 KKMK 288


>gi|188090526|gb|ACD49497.1| RNA polymerase sigma factor [Xanthomonas fragariae]
 gi|188090568|gb|ACD49518.1| RNA polymerase sigma factor [Xanthomonas fragariae]
          Length = 291

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L    G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNAGNSGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLAHYEAHKEGKKRLAEIV 144


>gi|299068068|emb|CBJ39282.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum CMR15]
          Length = 306

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 129/239 (53%), Gaps = 19/239 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W
Sbjct: 66  AARRLVLSHLRLVVSIARQYLGYGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHW 125

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ ++        + +A++L +    
Sbjct: 126 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQNAHATFTSDEIDAVAQELDVKGAE 185

Query: 563 VRKV-LKITKEPISLETPIGDEDTS-----HLGDFIEDKNAV---SPLDSAIQANLRETT 613
           VR++  +++   I+LE  I D + S     +L D   +   V     LD  +Q+   ET 
Sbjct: 186 VREMETRLSGGDIALEGQIDDGEESFAPIAYLADTHNEPTRVLEGRGLDR-LQSEGIETA 244

Query: 614 TRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 245 ---LAKLDDRSRRIIEARW-LHVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMK 299


>gi|159163074|pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
           Maritima
          Length = 87

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 46/78 (58%), Positives = 58/78 (74%)

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE KA
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSRSK L+S L 
Sbjct: 63  LRKLRHPSRSKYLKSLLS 80


>gi|329939708|ref|ZP_08289009.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329301278|gb|EGG45173.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 387

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 156 GSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 215

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A+KL
Sbjct: 216 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAEKL 275

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
           A+  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 276 AISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 329

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 330 KPLLEDLPPREKRILLLRFFANMTQSQIAQEVGISQMHVSR 370


>gi|254804595|ref|YP_003082816.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254668137|emb|CBA04749.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254669711|emb|CBA03845.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha153]
 gi|308388900|gb|ADO31220.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           alpha710]
 gi|319410084|emb|CBY90418.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           WUE 2594]
 gi|325127782|gb|EGC50690.1| alternative sigma factor RpoH [Neisseria meningitidis N1568]
 gi|325129864|gb|EGC52669.1| alternative sigma factor RpoH [Neisseria meningitidis OX99.30304]
 gi|325131835|gb|EGC54535.1| alternative sigma factor RpoH [Neisseria meningitidis M6190]
 gi|325133774|gb|EGC56430.1| alternative sigma factor RpoH [Neisseria meningitidis M13399]
 gi|325136066|gb|EGC58676.1| alternative sigma factor RpoH [Neisseria meningitidis M0579]
 gi|325137885|gb|EGC60460.1| alternative sigma factor RpoH [Neisseria meningitidis ES14902]
 gi|325141969|gb|EGC64407.1| alternative sigma factor RpoH [Neisseria meningitidis 961-5945]
 gi|325144085|gb|EGC66393.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240013]
 gi|325197931|gb|ADY93387.1| alternative sigma factor RpoH [Neisseria meningitidis G2136]
 gi|325203799|gb|ADY99252.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240355]
 gi|325206445|gb|ADZ01898.1| alternative sigma factor RpoH [Neisseria meningitidis M04-240196]
          Length = 287

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 127/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 44  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 101 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QDIAD 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 160 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 209

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 210 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 268

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 269 EAKAMQKLR 277


>gi|121602451|ref|YP_988610.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614628|gb|ABM45229.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 124/248 (50%), Gaps = 22/248 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGNIGLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAIGYRGYGLPMGEVISEGNIGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE-------EIAKKL 556
           +K +I   +      ++I      K  ++    R++ +K++     E       EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKIGTTTNQK--RLFFNLRKLKSKLQALDNGELNTEQVKEIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQA----NLR 610
            +  + V  +        SL  P+   +++ S   D + D+ A S     I+     N R
Sbjct: 167 NVTEDEVVSMNHRLSGDTSLNAPLRTNEDEHSEWQDCLVDE-ASSQEQVLIEKDELENRR 225

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A+L  RE+R+   R      +D   TLEE+  +F ++RER+RQIE +A  K++
Sbjct: 226 SLLIHAMANLNEREKRIFEAR----RLSDEVLTLEELSSEFNISRERVRQIEMRAFEKVQ 281

Query: 669 HPSRSKKL 676
              R+  L
Sbjct: 282 DFVRASAL 289


>gi|118591280|ref|ZP_01548678.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118435952|gb|EAV42595.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 287

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 127/236 (53%), Gaps = 27/236 (11%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +++RLVI+VA ++ N GL   DLIQEG++GL++AA +F+     +FSTYA WW++ +I  
Sbjct: 46  SHMRLVIAVASRFRNFGLSLGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQD 105

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGVRKV- 566
            I      +R       K   +    RR+  K+    TP    E+ +K+A  + GV++  
Sbjct: 106 YILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLSGNQTPLTDSELHQKIADAI-GVKQSD 162

Query: 567 -----LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPL-DSAIQANL-RETTTRVL 617
                 +++    SL  P+ D + S     DF+      +PL D  +  ++  E   R L
Sbjct: 163 VALMNARLSGPDTSLNAPVTDSEGSSADRQDFLVSD---APLPDEIVTVSIDTERRQRWL 219

Query: 618 AS----LTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +S    L+ RE +++R R    ++ D  TLE +G +  +++ER+RQIE++A+ KLK
Sbjct: 220 SSALEVLSERELKIVRER---RLSEDGATLESLGVKLGISKERVRQIESRAMEKLK 272


>gi|188090592|gb|ACD49530.1| RNA polymerase sigma factor [Xanthomonas fragariae]
 gi|188090606|gb|ACD49537.1| RNA polymerase sigma factor [Xanthomonas fragariae]
          Length = 291

 Score = 91.7 bits (226), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L    G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNAGNSGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLAHYEAHKEGKKRLAEIV 144


>gi|258622821|ref|ZP_05717838.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
 gi|258584882|gb|EEW09614.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
          Length = 286

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 143/269 (53%), Gaps = 21/269 (7%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    +S  E R +   +  KG+ +A+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNGYPMLSADEERELAERLHYKGDIDAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++  +  + E    D++    
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDAAFEMSAEDDENGMA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRE--TTTRV---LASLTPREERVLRMRFGIGMNTD 639
                 ++EDK+  S L   ++A   E  TT R+   LASL  R + ++R R+ +  +  
Sbjct: 195 YTAPVLYLEDKH--SDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNK 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++ + + V+ ERIRQ+E  A+RKLK
Sbjct: 252 TTLQDLAEMYGVSAERIRQLEKNAMRKLK 280


>gi|71901711|ref|ZP_00683785.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71728528|gb|EAO30685.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 125/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 56  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA  SP+   I           + N  
Sbjct: 165 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPPSPVGYLIANDGDPSQAYERGNSE 222

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 223 ETQLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 279

Query: 665 RKLK 668
           +K+K
Sbjct: 280 KKMK 283


>gi|15839280|ref|NP_299968.1| RNA polymerase factor sigma-32 [Xylella fastidiosa 9a5c]
 gi|9107932|gb|AAF85488.1|AE004075_3 RNA polymerase sigma-32 factor [Xylella fastidiosa 9a5c]
          Length = 293

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 125/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 61  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 121 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 169

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA  SP+   I           + N  
Sbjct: 170 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPPSPVGYLIANDGDPSQAYERGNSE 227

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 228 ETKLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 284

Query: 665 RKLK 668
           +K+K
Sbjct: 285 KKMK 288


>gi|291561536|emb|CBL40335.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SS3/4]
          Length = 258

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 117/232 (50%), Gaps = 22/232 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  ARETYIKGNLRLVLSVIQRFSGSSENLDDLFQIGCIGLIKAIDNFDLSQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +     ++ +  REPT  EIA ++ +  E +
Sbjct: 98  ILGEVRRYLRDNN-SIRVSRSLRDTAYKALSARELLTKRNLREPTIMEIADEVGISKEEI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              +   + P+SL  P+  +  D   + D I DK     N V       Q +L E   R 
Sbjct: 157 TYAMDAIQSPVSLYEPVYTDGGDPLCVMDQISDKKNREENWVE------QLSLSEAMKR- 209

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  RE R++ MRF  G     T  EV  +  +++ ++ ++E  A++ +K
Sbjct: 210 ---LPARERRIIDMRFFEG----KTQTEVAGEVGISQAQVSRLEKNALKAMK 254


>gi|226325489|ref|ZP_03801007.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
 gi|225206232|gb|EEG88586.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
          Length = 239

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 62/244 (25%), Positives = 126/244 (51%), Gaps = 8/244 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++R+       A+ ++VE N  L+  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIRRAHEGDENARAQLVEENTGLIWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++   +++  +K  +    ++ K+ REP 
Sbjct: 63  DLGYDVKFSTYAVPMITGEIKRFLRDDGM-LKVSRSLKEIAYKAYQAKEALTEKLGREPL 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA++  +  E +   ++   E  SL  P+G +D + +   +E        +  I  +
Sbjct: 122 LEEIAEETGVEKEELVMAMEAAGEVESLHRPVGMKDGNEVM-LLEKIADTGGAEEKILDH 180

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L    T ++  L   E ++L +R+      D T  E+G++  +++ ++ ++E K ++ ++
Sbjct: 181 L--LLTELIKELKKDERKLLYLRY----FADKTQTEIGEELGISQVQVSRMEKKILKTMR 234

Query: 669 HPSR 672
             ++
Sbjct: 235 EHAK 238


>gi|139436946|ref|ZP_01771106.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
 gi|133776593|gb|EBA40413.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
          Length = 263

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 124/230 (53%), Gaps = 15/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V +++ LV  +A K+ NRG    DL+Q G +GL+KA ++FD   G +F+T+A   
Sbjct: 32  AREQLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKAIDRFDPERGLEFTTFATPT 91

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+  ++R+P  +++   KV +   +++N+++R P  EEIA+ L + V+ V
Sbjct: 92  ILGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDKLTNELQRSPKVEEIAEYLDVTVDEV 151

Query: 564 RKVLKITK--EPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++ +     + +E P     D+  S L  + +D N +   D       R      + 
Sbjct: 152 LEAMESSSAYTSVPIEAPGASDSDDAPSILDRYADDDNELDFTDD------RLVIEEAIR 205

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +PRE  V+ +RF  GM    T  E+ K+  +++ ++ ++  + ++K++
Sbjct: 206 DFSPREREVIELRFVKGM----TQIEIAKKLGISQVQVSRLLRRTLKKIQ 251


>gi|229525043|ref|ZP_04414448.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
 gi|229338624|gb|EEO03641.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
          Length = 286

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 74/267 (27%), Positives = 141/267 (52%), Gaps = 17/267 (6%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    +S  E R +   +  KG+ +A+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNGYPMLSADEERELAERLHYKGDIDAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++  +  + E    D++    
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFGIGMNTDHT 641
                 ++EDK++    + A +     TT R+   LASL  R + ++R R+ +  +   T
Sbjct: 195 YTAPVLYLEDKHSDLADNLAAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNKTT 253

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++ + + V+ ERIRQ+E  A+RKLK
Sbjct: 254 LQDLAEMYGVSAERIRQLEKNAMRKLK 280


>gi|330447179|ref|ZP_08310829.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491370|dbj|GAA05326.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 286

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 126/235 (53%), Gaps = 14/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKALVMSHLRFVVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R +++       E     +A++L +  E 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKSKKRLGWFNNEEV-NMVAEQLGVEPEE 167

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTT 614
           VR++   L        ++    D D + +    F+EDK+   A++  ++  + +     +
Sbjct: 168 VREMESRLAAQDPTFEMQNDDDDRDAAPMAPAYFLEDKSSDVALTYEENNWENHANNRLS 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + LASL  R + ++R R+   ++ D  TL+++   + V+ ERIRQ+E  A++KLK
Sbjct: 228 QALASLDERSQHIVRSRW---LDDDKSTLQDLADSYGVSAERIRQLEKNAMKKLK 279


>gi|302386721|ref|YP_003822543.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197349|gb|ADL04920.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 118/228 (51%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 38  AREDYIKGNLRLVLSVIQRFSGSNENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +     +  K  +EPT  EIA+++ +  E +
Sbjct: 98  ILGEVRRYLRDNN-SIRVSRSLRDTAYKAIYAKENLMKKNLKEPTLMEIAEEIGVSKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   + P+SL  P+  +  D   + D I DK  +   +     +L E   R    L 
Sbjct: 157 TYALDAIQSPVSLYEPVYSDGGDPLFVMDQISDKKNLEE-NWVEDISLNEAMRR----LP 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K+
Sbjct: 212 ERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKTMKN 255


>gi|71275285|ref|ZP_00651572.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71902025|ref|ZP_00684069.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71164094|gb|EAO13809.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71728204|gb|EAO30391.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 125/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 56  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA  SP+   I           + N  
Sbjct: 165 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPPSPVGYLIANDGDPSQAYERGNSE 222

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 223 ETQLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 279

Query: 665 RKLK 668
           +K+K
Sbjct: 280 KKMK 283


>gi|163759996|ref|ZP_02167080.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
 gi|162282954|gb|EDQ33241.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
          Length = 278

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 121/239 (50%), Gaps = 18/239 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A K+ N GL   DL+QEG++GL++AA +FD     +FSTYA WW
Sbjct: 31  ALHKITMAHMRLVISMAAKFRNFGLPMGDLVQEGHVGLLEAAARFDPEREVRFSTYATWW 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EPTPE------EIAKKL 556
           ++ +I   I      +R       K   +    RR+  ++ + +PT        +IA  L
Sbjct: 91  IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLAQDDPTLTDSAIHIQIADSL 148

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-----DSAIQANLR 610
            + V+ V  +  +++    SL  P+ D ++    D ++   +  PL      + I    R
Sbjct: 149 GVHVKDVAVMDARLSGPDSSLNAPMSDGESGASSDRMDFLKSDEPLPDEQVSTIIDEERR 208

Query: 611 ET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            T     L +L PRE  ++R R         TLE +G    +++ER+RQIE +A+ KL+
Sbjct: 209 NTWLGDALNTLNPRELLIIRKRR--LAEEGATLEALGATLGISKERVRQIENRALEKLR 265


>gi|13377878|gb|AAK20883.1|AF334761_4 RNA polymerase sigma-32 [Aeromonas hydrophila]
          Length = 284

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 124/240 (51%), Gaps = 14/240 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G + 
Sbjct: 46  GDLEAA---RQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++     + K+   +R +++       +      A+ 
Sbjct: 103 VSFAVHWIKADIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWFSHDEVQAVAAEL 162

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA-NLRET 612
              P +      +++    + +    DED        ++EDK+  S L + I+  N  + 
Sbjct: 163 GVSPTDVTEMEARMSNYDQAFDLVGDDEDEGGFAPVHYLEDKS--SDLAATIENDNWDDH 220

Query: 613 TTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TR     LA+L  R + ++R R+ +  ++  TL+E+   + V+ ER+RQ+E  A++KLK
Sbjct: 221 ATRRLSSALATLDERSQHIIRARW-LDDDSKTTLQELADTYGVSAERVRQLEKNALKKLK 279


>gi|83312286|ref|YP_422550.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82947127|dbj|BAE51991.1| DNA-directed RNA polymerase, sigma subunit [Magnetospirillum
           magneticum AMB-1]
          Length = 296

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 121/242 (50%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGN+G+M+A  +FD   G++ +TYAMWW
Sbjct: 49  AANRLVTSHLRLVAKIAMGYRGYGLPLGELISEGNVGMMQAVRRFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAK---KL 556
           ++ AI   I      +++      K  K+    R++  +++     + + E +AK   KL
Sbjct: 109 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRKLKGQMQAIEEGDMSAENVAKIATKL 166

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
            +  + V  + +    P  SL  P+  E      D++ D +     +   +  L   R+ 
Sbjct: 167 EVTEDEVVTMNRRLSSPDHSLNAPVRAEGEGEWQDWLVDDHEDQETELGEREELGQRRQM 226

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            T  L +L  RE  +L  R    +  D  TLE++ +++ ++RER+RQIE +A  KL+   
Sbjct: 227 LTSALEALNDRERAILIQR---RLTEDPATLEDLSQRYGISRERVRQIEVRAFEKLQKSV 283

Query: 672 RS 673
           +S
Sbjct: 284 KS 285


>gi|17545093|ref|NP_518495.1| RNA polymerase factor sigma-32 [Ralstonia solanacearum GMI1000]
 gi|17427383|emb|CAD13902.1| probable rna polymerase sigma h (sigma-32) factor transcription
           regulator protein [Ralstonia solanacearum GMI1000]
          Length = 306

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 128/237 (54%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+S+A++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W
Sbjct: 66  AARRLVLSHLRLVVSIARQYLGYGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHW 125

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++ ++        + +A++L +    
Sbjct: 126 IKAEMHEYILKNWRMVKVATTKAQRKLFFNLRSHKQDAHATFTSDEVDAVAQELNVKGAE 185

Query: 563 VRKV-LKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR-ETTTR 615
           VR++  +++   I+LE  I D + S     +L D   +   V  L+   +  L+ E    
Sbjct: 186 VREMETRLSGGDIALEGQIDDGEESFAPIAYLADTHNEPTRV--LEGRGRDRLQSEGIET 243

Query: 616 VLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L  R  R++  R+ + +N D     TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 244 ALAKLDDRSRRIIEARW-LHVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMK 299


>gi|307330885|ref|ZP_07610018.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883426|gb|EFN14479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 263

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 113/222 (50%), Gaps = 10/222 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 31  EGSTERAEMRNHLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVE 90

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++
Sbjct: 91  FSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQRHGRAPTVHELAEQ 150

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L++  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+
Sbjct: 151 LSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRES 204

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+++L +RF   M      +EVG  Q  V+R
Sbjct: 205 LKPLLEDLPPREKKILLLRFFGNMTQSQIAQEVGISQMHVSR 246


>gi|317499023|ref|ZP_07957304.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|291560723|emb|CBL39523.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SSC/2]
 gi|316893673|gb|EFV15874.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 241

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 126/234 (53%), Gaps = 26/234 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++  N+ L+ SV +++TNRG +  DL Q G+IGLMKA +KFD     KFSTYA+  
Sbjct: 18  AREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLSYDVKFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++ ++K+++   +   + +RE T EEI+          
Sbjct: 78  ITGEIRRFLRDDGM-IKVSRSLKENVYKIMKAREKFCQQYQREATIEEIS---------- 126

Query: 564 RKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTT------ 614
            ++ KIT+E I  SLE    + ++ H   + +D + +S LD   +  N  E         
Sbjct: 127 -EITKITREEIVTSLEAS-NEVESIHQSAYQKDGSEISLLDKLSKGENESEKVVDHVLLK 184

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  +E++++  R+  G     T +E+ K F +++ ++ +IE + ++KL+
Sbjct: 185 EAMKHLEQKEQQMIYYRYFEG----KTQQEIAKIFHISQVQVSRIEKRILKKLR 234


>gi|320007063|gb|ADW01913.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 297

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 129/248 (52%), Gaps = 22/248 (8%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA ++FD
Sbjct: 55  LQVLEEGTHEYQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFD 114

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+T+A+ ++   I R   D + ++ +P  +++   ++ +   ++S K+ R+PT 
Sbjct: 115 LSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVELAKAKEQLSTKLDRDPTV 174

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSH----LGDFI-EDKNAVSP 600
            E+A  L +P    +EG+  V        SL+TP  D D+        D + ED   +  
Sbjct: 175 AELAAHLDLPEEEIIEGL--VAANGYSAGSLDTPNADSDSGSEQRAYADLLGEDDPGMES 232

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++     NL  T   +L  L  RE +++RMRFG  M    T  ++G +  V++  + ++ 
Sbjct: 233 VE-----NL-HTLAPLLRQLDDRERKIVRMRFGQEM----TQAQIGAELGVSQMHVSRLL 282

Query: 661 AKAIRKLK 668
           ++ +++L+
Sbjct: 283 SRIVQRLR 290


>gi|182682661|ref|YP_001830821.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M23]
 gi|182632771|gb|ACB93547.1| RNA polymerase, sigma 32 subunit, RpoH [Xylella fastidiosa M23]
          Length = 288

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 125/244 (51%), Gaps = 35/244 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++AM W
Sbjct: 56  AARELVHSHLRFVVRVARGYSGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSRT--RLGWMNAEEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-----------QANLR 610
            + L ++ +E + +E+ +   D     D  E+ NA  SP+   I           + N  
Sbjct: 165 ARDLNVSEREVLEMESRLSGRDIGF--DAPEEDNAPPSPVGYLIANDGDPSQAYERGNSE 222

Query: 611 ETTTRV----LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAI 664
           ET  R+    L+ L  R   +++ R+   + TD   TL+E+ +++ V+ ERIRQIEA A+
Sbjct: 223 ETQLRLLQEGLSVLDTRSRDIIQRRW---LETDKKITLQELAEEYGVSAERIRQIEANAL 279

Query: 665 RKLK 668
           +K+K
Sbjct: 280 KKMK 283


>gi|154245929|ref|YP_001416887.1| RNA polymerase factor sigma-32 [Xanthobacter autotrophicus Py2]
 gi|154160014|gb|ABS67230.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthobacter autotrophicus
           Py2]
          Length = 300

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/241 (29%), Positives = 120/241 (49%), Gaps = 25/241 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I      +  PE   +IA KL
Sbjct: 109 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKAKSQISALEDGDLKPEHVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQA-------N 608
            +  + V  + +      SL +PI  D +     D++ D+     LD   Q        N
Sbjct: 167 GVTEQDVVDMNRRLSGDASLNSPIREDSEGGEWQDWLVDER----LDQEEQLAESEELDN 222

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R   +  L+ L  RE R+   R    ++ D  TLE++  +F V+RER+RQIE +A  K+
Sbjct: 223 RRAALSGALSVLNDRERRIFEAR---RLSEDPMTLEDLASEFGVSRERVRQIEVRAFEKV 279

Query: 668 K 668
           +
Sbjct: 280 Q 280


>gi|302554065|ref|ZP_07306407.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302471683|gb|EFL34776.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 381

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 112/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 150 GSPEYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEF 209

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A+KL
Sbjct: 210 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAEKL 269

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
           ++  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 270 SISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 323

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 324 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 364


>gi|121634509|ref|YP_974754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis FAM18]
 gi|218767834|ref|YP_002342346.1| RNA polymerase factor sigma-32 [Neisseria meningitidis Z2491]
 gi|120866215|emb|CAM09955.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           FAM18]
 gi|121051842|emb|CAM08148.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           Z2491]
 gi|261392916|emb|CAX50501.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           8013]
          Length = 290

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 127/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 47  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 104 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QDIAD 162

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 163 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 212

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 213 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 271

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 272 EAKAMQKLR 280


>gi|167584375|ref|ZP_02376763.1| sigma 70 (RpoD) [Burkholderia ubonensis Bu]
          Length = 611

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 87/164 (53%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---------DD 82
           + +I L R+RGY+T  ++N  LP +   +  ME  V+  S+MG+ V +          +D
Sbjct: 2   RALIALGRERGYLTHADINDHLPDNFAQTAAMETIVSTFSDMGVAVYEQAPDAETLLLND 61

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  + A+ S+V      DS    T DPVRMY+REMG+ ELL+R GEI I
Sbjct: 62  ATAAVASDDQADEEAEAALSTV------DSEFGRTTDPVRMYMREMGASELLTRAGEIEI 115

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE+G   M+ ++   P     ++   D +  G   + E++D
Sbjct: 116 AKRIESGLQDMIQAIAACPTVVSTILADADRIAAGELRIDELVD 159


>gi|2529275|gb|AAB81194.1| sigma factor [Geobacillus stearothermophilus]
          Length = 250

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 125/255 (49%), Gaps = 14/255 (5%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           + V+ G S  + + +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q
Sbjct: 3   VDVKQGQSPIKDQEMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQ 62

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ + 
Sbjct: 63  IGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKA 121

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIE 593
              +S    R PT  EIA  L +  E V    +  + P S+   +   D D   L D I 
Sbjct: 122 KDELSKTRGRSPTITEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIA 181

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +  S  D            + +  L  RE  ++ +R+      D T  EV  +  +++
Sbjct: 182 DADEASWFDKI-------ALKKAIEELDERERLIVYLRY----YRDRTQSEVASRLGISQ 230

Query: 654 ERIRQIEAKAIRKLK 668
            ++ ++E K ++ +K
Sbjct: 231 VQVSRLEKKILQHIK 245


>gi|57239125|ref|YP_180261.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|57161204|emb|CAH58118.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 296

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 126/240 (52%), Gaps = 13/240 (5%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+ VA  + N GL  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K 
Sbjct: 50  KLVTSHLRLVVKVALSFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKA 109

Query: 507 AITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEG 562
           +I   I      I+I     + K+   +R  ++   K     T E+   IA + +   + 
Sbjct: 110 SIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLLKYHNNITKEDIKMIANECSTSEQE 169

Query: 563 VRKVLK-ITKEPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRET-TTR 615
           V ++ K  T    SL   +   G ++   L D I  ED N         + +++++  T+
Sbjct: 170 VEQMNKYFTYRDKSLNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQ 229

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            LA+L  R   +   R  I      TLE + K++ +++ERIRQIE  A  K+K+   SK+
Sbjct: 230 ALATLNERHRDIFIRRKLI--EEPDTLEILSKKYNISKERIRQIETHAFLKVKNFVISKR 287


>gi|312134334|ref|YP_004001672.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774385|gb|ADQ03872.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 256

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 99/190 (52%), Gaps = 7/190 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   +AKK+ NRG+ + DL Q   + L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNRHLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +     +S +Q    E   + +  L+P
Sbjct: 151 EVMEASNSYLPQSLDQTMYEDEEMTLGDVLGKSD-----ESILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRF 632
            E   L+ RF
Sbjct: 206 FEREFLQKRF 215


>gi|295836570|ref|ZP_06823503.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826098|gb|EDY44232.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 338

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 425 SEFRHIVSMVRKGECEASIA---KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           SE R +   +R  E E++     +  +V  +L LV  +A+++ NRG    DL Q   IGL
Sbjct: 92  SEARALFVRLRTLEPESAAYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGL 151

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ ++FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S 
Sbjct: 152 IKSVDRFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQ 211

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVS 599
              R PT  E+A++L++  E V + L+       +SL+ P  D+++  + D +  +    
Sbjct: 212 LHGRSPTVHELAQRLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE---- 267

Query: 600 PLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             D A++    RE+   +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 268 --DEALEGVEYRESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 321


>gi|15640181|ref|NP_229808.1| RNA polymerase factor sigma-32 [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121591866|ref|ZP_01679036.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|147674371|ref|YP_001218271.1| RNA polymerase factor sigma-32 [Vibrio cholerae O395]
 gi|153214854|ref|ZP_01949662.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|153803613|ref|ZP_01958199.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|153818953|ref|ZP_01971620.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|153824136|ref|ZP_01976803.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|153826296|ref|ZP_01978963.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|153830006|ref|ZP_01982673.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|227080385|ref|YP_002808936.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|229508425|ref|ZP_04397929.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229508894|ref|ZP_04398384.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229515820|ref|ZP_04405278.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229517008|ref|ZP_04406454.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229520061|ref|ZP_04409489.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229527110|ref|ZP_04416504.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229606698|ref|YP_002877346.1| RNA polymerase factor sigma-32 [Vibrio cholerae MJ-1236]
 gi|254291956|ref|ZP_04962737.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|254851536|ref|ZP_05240886.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255743901|ref|ZP_05417856.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|262163699|ref|ZP_06031440.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262172906|ref|ZP_06040584.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262190731|ref|ZP_06048960.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262404885|ref|ZP_06081439.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297581813|ref|ZP_06943734.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|298501088|ref|ZP_07010888.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|12644296|sp|P50511|RP32_VIBCH RecName: Full=RNA polymerase sigma-32 factor
 gi|9654552|gb|AAF93327.1| RNA polymerase sigma-32 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121546267|gb|EAX56564.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|124115097|gb|EAY33917.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|124120852|gb|EAY39595.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|126510515|gb|EAZ73109.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|126518343|gb|EAZ75566.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|146316254|gb|ABQ20793.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|148874491|gb|EDL72626.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|149739964|gb|EDM54143.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|150422166|gb|EDN14132.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|227008273|gb|ACP04485.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|227011849|gb|ACP08059.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|229335341|gb|EEO00824.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229342849|gb|EEO07839.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229346071|gb|EEO11043.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229347083|gb|EEO12044.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229354011|gb|EEO18944.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229354698|gb|EEO19620.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229369353|gb|ACQ59776.1| RNA polymerase sigma factor RpoH [Vibrio cholerae MJ-1236]
 gi|254847241|gb|EET25655.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255738384|gb|EET93774.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|261893982|gb|EEY39968.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262027915|gb|EEY46579.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262033375|gb|EEY51884.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262348969|gb|EEY98108.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297533907|gb|EFH72747.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|297540122|gb|EFH76183.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|327483048|gb|AEA77455.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 286

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 143/269 (53%), Gaps = 21/269 (7%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    +S  E R +   +  KG+ +A+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNGYPMLSADEERELAERLHYKGDIDAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++  +  + E    D++    
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRE--TTTRV---LASLTPREERVLRMRFGIGMNTD 639
                 ++EDK+  S L   ++A   E  TT R+   LASL  R + ++R R+ +  +  
Sbjct: 195 YTAPVLYLEDKH--SDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNK 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++ + + V+ ERIRQ+E  A+RKLK
Sbjct: 252 TTLQDLAEMYGVSAERIRQLEKNAMRKLK 280


>gi|182434526|ref|YP_001822245.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463042|dbj|BAG17562.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 300

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 127/245 (51%), Gaps = 16/245 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA ++FD
Sbjct: 58  LQLLEEGTHEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFD 117

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+T+A+ ++   I R   D + ++ +P  +++    + +   ++S ++ R+PT 
Sbjct: 118 LSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLAKAKEQLSGELDRDPTV 177

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +E+A  L +P    +EG+  V        SL+TP  D D+        D   +   D  +
Sbjct: 178 KELAAHLDLPEEEIIEGL--VAANGYSAGSLDTPSADSDSGQEQRAYAD--VLGEADPGM 233

Query: 606 QA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +   NL  T   +L  L  RE R+++MRFG  M    T  ++G +  V++  + ++ ++ 
Sbjct: 234 ETVENL-HTLAPLLDQLDERERRIVQMRFGAEM----TQSQIGAELGVSQMHVSRLLSRI 288

Query: 664 IRKLK 668
           +++L+
Sbjct: 289 VQQLR 293


>gi|227823295|ref|YP_002827267.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342296|gb|ACP26514.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 301

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 124/246 (50%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVMSEGNVGLMQAVKKFEPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K AI   I      +++      K  ++    RR+  +I+     +  PE   EIA  L
Sbjct: 109 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V  + +      SL  PI   + D+    D++ D++  +  +  I+ +  ++  
Sbjct: 167 KVSEDEVVSMNRRLSGDASLNAPIKASEGDSGQWQDWLVDEHD-NQEEILIEQDELDSRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +LAS    L  RE R+   R         TLEE+  +F ++RER+RQIE +A  K++  
Sbjct: 226 ALLASAMKVLNDRERRIFEARRLT--EEPVTLEELSTEFDISRERVRQIEVRAFEKVQEA 283

Query: 671 SRSKKL 676
            R   L
Sbjct: 284 VRKAAL 289


>gi|304387988|ref|ZP_07370160.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
 gi|304337987|gb|EFM04125.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
          Length = 290

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 127/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 47  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 104 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QDIAD 162

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 163 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 212

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 213 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 271

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 272 EAKAMQKLR 280


>gi|269958772|ref|YP_003328559.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
 gi|269848601|gb|ACZ49245.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
          Length = 307

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 126/236 (53%), Gaps = 22/236 (9%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+ VA  + N GL  ++LI EGNIGLM+A ++F+  LG + +TYA+WW+K 
Sbjct: 68  KLVTSHLRLVVKVAMGFKNYGLPLMELIMEGNIGLMQAVKRFNPDLGSRLATYAVWWIKA 127

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP------EEIAKKLAMPV 560
           +I   I      IR+      K  K+  + R++  ++    T       + IA++ A   
Sbjct: 128 SIKDYILRSWSCIRVGTTQAQK--KLFFSLRKIKKRLLGCGTSMTQKEVKTIAEECATSE 185

Query: 561 EGVRKVLK-ITKEPISLETPIGDEDTSHLGDFI------EDKNAVSPLDSAIQANLRETT 613
           E V ++ +      +SL  P+  E +  L D +      ++   ++  +SAI+ ++ +  
Sbjct: 186 EEVERMDRFFASRDVSLNEPVHGESSVELQDLVPSSLPSQEAMYLADEESAIKKSMFDAA 245

Query: 614 TRVLASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L++L  R   +  R R         TLE++ +++ V++ER+RQIE +A+ K+K
Sbjct: 246 ---LSTLDHRHRDIFTRRRL---QERPDTLEKLSEKYGVSKERVRQIELQALCKIK 295


>gi|167636574|ref|ZP_02394868.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
 gi|167527997|gb|EDR90803.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
          Length = 211

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 59/175 (33%), Positives = 96/175 (54%), Gaps = 8/175 (4%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPI 173


>gi|33151352|ref|NP_872705.1| RNA polymerase factor sigma-32 [Haemophilus ducreyi 35000HP]
 gi|33147572|gb|AAP95094.1| RNA polymerase sigma-32 factor [Haemophilus ducreyi 35000HP]
          Length = 319

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/275 (25%), Positives = 145/275 (52%), Gaps = 22/275 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +++ N+   ++ E   +++E        R    E   A K+++ +++R VI +A+ 
Sbjct: 51  LDSYIRMANQYPILTAEQEKTLAE--------RYYYDEDVDAAKQLILSHMRFVIHIARG 102

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++ 
Sbjct: 103 YMGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVA 162

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+  +++    E   +++A+ L +  E VR++  ++T + +  +  
Sbjct: 163 TTKAQR--KLFFNLRKNKHRLAWFNEDEIQQVAQDLGVSTEEVREMESRMTGQDVGFDIS 220

Query: 580 IGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFG 633
             +ED S +     ++ED ++    +   + +  E T ++   LA+L  R + +++ R+ 
Sbjct: 221 -ANEDESEVYVPSMYLEDNSSNFADELEEEQHTGEATAKLAYALATLDERSQDIIKTRW- 278

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  N   TL E+  ++ ++ ER+RQ+E  A++K+K
Sbjct: 279 LDENKA-TLHELAAKYSISAERVRQLENAALKKIK 312


>gi|54307376|ref|YP_128396.1| RNA polymerase factor sigma-32 [Photobacterium profundum SS9]
 gi|46911796|emb|CAG18594.1| putative RNA polymerase sigma-32 factor [Photobacterium profundum
           SS9]
          Length = 282

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 75/279 (26%), Positives = 142/279 (50%), Gaps = 22/279 (7%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A  +DS ++  N    +S E    ++E  H       G+ EA+   K +V +++R V+ V
Sbjct: 9   AGSLDSYIQTVNRHPMLSAEQEKELAERLHY-----DGDIEAA---KGLVMSHMRFVVHV 60

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +
Sbjct: 61  ARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIV 120

Query: 520 RIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISL 576
           ++      R     + ++ +R+      E   E +A++L +    VR++  ++  +  + 
Sbjct: 121 KVATTKAQRKLFFNLRKSKKRLGWFNNAE--VEMVAEQLGVNPSEVREMESRLAAQDPAF 178

Query: 577 ETPIGDED----TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           E P  D+D     +    F+EDK+   A+S  ++  + +     +  LA L  R + ++R
Sbjct: 179 ELPNEDDDRDAGYTAPVYFLEDKSSDVALSYEENNWENHTNNRLSNALAGLDERSQHIVR 238

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+     T  TL+++   + ++ ER+RQ+E  A++KLK
Sbjct: 239 SRWLDDEKT--TLQDLANHYGISAERVRQLEKNAMKKLK 275


>gi|319781136|ref|YP_004140612.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167024|gb|ADV10562.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 303

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 121/247 (48%), Gaps = 18/247 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E + A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G+
Sbjct: 39  RYAEHEDTSAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K +I   I      +++      K  ++    R++  KI+       +  
Sbjct: 99  RLATYAMWWIKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKVKGKIQALDDGDLKPD 156

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
              EIA +L +    V  + +      SL  PI   + ++    D++ D +  S  +  I
Sbjct: 157 QIAEIATRLNVSEAEVVSMNRRLSGDASLNAPIRASEGESGEWQDWLVDDHE-SQEEMLI 215

Query: 606 QA----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +     N R   +  LA L  RE R+   R         TLEE+  +F ++RER+RQIE 
Sbjct: 216 EQDELENRRGMLSGALAVLNERERRIFEARR--LAEEPLTLEELSSEFDISRERVRQIEV 273

Query: 662 KAIRKLK 668
           +A  K++
Sbjct: 274 RAFEKVQ 280


>gi|302036735|ref|YP_003797057.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
 gi|300604799|emb|CBK41131.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
          Length = 340

 Score = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 128/232 (55%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +++ ANLR+ +S+A +Y + G   +DLIQEGN+GL++A +KFD     +F  YA WW
Sbjct: 98  AAMKLILANLRVSVSIASEYLHTGADHMDLIQEGNVGLLQAIKKFDPTKNVRFYAYAAWW 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPV 560
            +  I R + +    I++      +  K+    ++   K++RE   P  + +A +L +  
Sbjct: 158 ARAYILRYLLNTYRLIKVGTTQDQR--KLFYNLKKEKAKLEREGFAPDSKLLADRLNVRE 215

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPL-DSAIQANLRETTTRV 616
             V ++  ++    +SL+ PIG E+   L D +   ++ A   L D+ ++A  R      
Sbjct: 216 RDVIEMDQRLGSWELSLDQPIGQENDGTLMDILPAHEQPADERLADTQLKALFRRKLAEF 275

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +L  REE +LR R  I   T  TLE++G ++ +T+ER RQ+EA+ I++L+
Sbjct: 276 TKTLDEREEDILRNR--ILSETPLTLEDMGAKYGITKERTRQLEARIIKRLR 325


>gi|89068061|ref|ZP_01155478.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046300|gb|EAR52357.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 281

 Score = 91.3 bits (225), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 117/244 (47%), Gaps = 34/244 (13%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +FSTYA+WW+K +
Sbjct: 35  LITAYMRLAISMAAKFRRYGAPMNDLIQEASLGLMKAADKFDPDRGVRFSTYAVWWIKAS 94

Query: 508 ITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           I   +      +R         +  ++R    ++ R A      I R+   E IA ++ +
Sbjct: 95  IQDYVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAAASGAPIDRQKMREMIAAEVGV 154

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQA--------- 607
           P+  V  +  +++    SL      ED        E +  +  L D  +QA         
Sbjct: 155 PLHDVEMMEGRLSGSDYSLNATQSAED--------EGREWIEALEDDGMQAAEKVENSHD 206

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAI 664
              LR      L+ L  RE  +++ R    +  D  TLE +G +  +++ER+RQ+EA A 
Sbjct: 207 IDTLRHWLLNALSQLNERERFIVKER---KLRDDPRTLESLGDELGLSKERVRQLEAAAF 263

Query: 665 RKLK 668
            K++
Sbjct: 264 GKMR 267


>gi|282863440|ref|ZP_06272499.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561775|gb|EFB67318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 288

 Score = 91.3 bits (225), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 113/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 59  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 118

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+AK L + 
Sbjct: 119 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVPELAKALGVS 178

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DAALEGVEYRESLKPL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 235 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 278


>gi|114707401|ref|ZP_01440298.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114537282|gb|EAU40409.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 304

 Score = 91.3 bits (225), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 125/247 (50%), Gaps = 18/247 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E +   A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G+
Sbjct: 40  RYAEHDDRNAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPERGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE 550
           + +TYAMWW+K +I   I      +++      K  ++    R+M ++I+     +  P+
Sbjct: 100 RLATYAMWWIKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSRIQALEDGDLNPD 157

Query: 551 ---EIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
              +IA +L +  + V  + +      SL +P+   + ++    D++ D+N       A 
Sbjct: 158 QVKQIATQLGVSDDEVISMNRRLSGDASLNSPLRATEGESGEWQDWLVDENESQEDVLAQ 217

Query: 606 QANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEA 661
           Q  L   R    R +  L  RE R+   R    ++ D  TLE +  +F ++RER+RQIE 
Sbjct: 218 QDELDQRRGMLKRAMGILNDRERRIFEAR---RLSEDPITLEALSGEFDISRERVRQIEV 274

Query: 662 KAIRKLK 668
           +A  K++
Sbjct: 275 RAFEKVQ 281


>gi|260774824|ref|ZP_05883726.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
 gi|260609249|gb|EEX35404.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
          Length = 285

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 141/277 (50%), Gaps = 24/277 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E    ++E  H       GE EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRTVNGYPMLTAEEERGLAERLHY-----NGEIEAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I 
Sbjct: 68  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++  +  + E  
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDAAFEMQ 185

Query: 580 IGDEDT--SHLGD--FIEDKNAVSPLDSAIQANLRETTTR----VLASLTPREERVLRMR 631
             D+D+  S+     ++EDK A    D+   AN    T       L+SL  R + ++R R
Sbjct: 186 NDDDDSGVSYTAPMLYLEDK-ASDVADNVEAANWEAHTNNRLSLALSSLDERSQHIVRSR 244

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    +   TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 245 W--LEDNKSTLQELAETYSVSAERIRQLEKNAMKKLK 279


>gi|310642622|ref|YP_003947380.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247572|gb|ADO57139.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 251

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 128/246 (52%), Gaps = 17/246 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + ++++ + G+ +A   ++ +V +N+RLV SV +++ NRG +  DL Q G IGL+K+
Sbjct: 16  TEVKRLIALSQSGDNDA---RETLVNSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKS 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    +S ++ 
Sbjct: 73  VDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKETANKVRKMKDELSKRLN 131

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLD 602
           R PT +E+A +L +  E V    +  K P S+   +   D D   L D I D++     D
Sbjct: 132 RLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADESQERWFD 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++E K
Sbjct: 192 -------KLALNEAIDGLSERERLIVYLRY----YRDQTQSEVASRLGISQVQVSRLEKK 240

Query: 663 AIRKLK 668
            ++ ++
Sbjct: 241 ILQLIR 246


>gi|239993653|ref|ZP_04714177.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 231

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE   ++
Sbjct: 10  KLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLMQE 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +     +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 70  ANADEDAAEAAAQALATVESEIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEDGIN 128

Query: 152 MMMASLCESPLTFQALI 168
            +  S+ E P     L+
Sbjct: 129 QVQCSVAEYPEAITYLL 145


>gi|163740703|ref|ZP_02148097.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161386561|gb|EDQ10936.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 292

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 73/258 (28%), Positives = 129/258 (50%), Gaps = 28/258 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A+    ++ +    ++IA 
Sbjct: 101 IKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLERQAQSEGTRLDQHQLHQQIAT 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANL 609
           ++ +P+  V+ +  ++     SL      +E+     + +ED +A +     +S     L
Sbjct: 161 EIGVPLRDVQMMDGRLAGADFSLNAVQSAEEEGREWIEALEDDSAQAAELVEESHDTRQL 220

Query: 610 RETTTRVLASLTPRE-----ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           R      + +L  RE     ER LR           TLE +G +  +++ER+RQ+EA A 
Sbjct: 221 RTWLVEAMQALNDRERFIITERKLR-------EKPRTLESLGTELGLSKERVRQLEAGAF 273

Query: 665 RKLKHP--SRSKKLRSFL 680
           +K++    + S+++++FL
Sbjct: 274 QKMRKSLETCSREVQNFL 291


>gi|319639187|ref|ZP_07993938.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
 gi|317399371|gb|EFV80041.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
          Length = 287

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 129/240 (53%), Gaps = 11/240 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G 
Sbjct: 43  QKGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGA 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +  ++A+ W+K  I   I      +R+     + K+   +R+ R+  + +  +   +EIA
Sbjct: 100 RLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLSALSPKEA-QEIA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL-- 609
             L + +  V ++  ++T   I +      DED     D++ D +A      + QA+   
Sbjct: 159 DDLGVKLSEVLEMEQRMTGHDIGIMAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYAL 218

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 219 QTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|145300817|ref|YP_001143658.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853589|gb|ABO91910.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 284

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 124/240 (51%), Gaps = 14/240 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G + 
Sbjct: 46  GDLEAA---RQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++     + K+   +R +++       +      A+ 
Sbjct: 103 VSFAVHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWFSHDEVQAVAAEL 162

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA-NLRET 612
              P +      +++    + +    DED        ++EDK+  S L + I+  N  + 
Sbjct: 163 GVSPTDVTEMEARMSNYDQAFDLVGDDEDEGGFAPVHYLEDKS--SDLAATIENDNWDDH 220

Query: 613 TTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TR     LA+L  R + ++R R+ +  ++  TL+E+   + V+ ER+RQ+E  A++KLK
Sbjct: 221 ATRRLSSALATLDERSQHIIRARW-LDDDSKTTLQELADTYGVSAERVRQLEKNALKKLK 279


>gi|302559791|ref|ZP_07312133.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477409|gb|EFL40502.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 301

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 71  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 130

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 131 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVPELAAVLGVS 190

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 191 EEDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 246

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 247 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 290


>gi|190576084|ref|YP_001973929.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia K279a]
 gi|190014006|emb|CAQ47646.1| putative RNA polymerase sigma-32 factor [Stenotrophomonas
           maltophilia K279a]
          Length = 291

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 116/243 (47%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLALGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWMNAAEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----------------- 605
            K L ++ +E + +E+ +   D        ED     P  +A                  
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDAPTDEDNEHAPPSPAAFLVADDEDPSMAYEREDS 224

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + N  +     LA L  R   ++R R+ +  ++  TL+E+  ++ V+ ERIRQ+EA A++
Sbjct: 225 EDNQMQLLREGLAELDARSRDIIRRRW-LDADSKVTLQELADEYGVSAERIRQVEANALK 283

Query: 666 KLK 668
           K+K
Sbjct: 284 KMK 286


>gi|209519886|ref|ZP_03268669.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
 gi|209499704|gb|EDZ99776.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
          Length = 665

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 56/164 (34%), Positives = 90/164 (54%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L +++GY+T  ++N  LP +   +  ++  V+  S+MG+ V     D + L    
Sbjct: 54  RALIQLGKEQGYLTHAQINDHLPDNFTQTAAIDSIVSAFSDMGVQVYEQAPDAETLLLNS 113

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEIAI
Sbjct: 114 NAPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEIAI 167

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE G   M+ ++   PL   A++    ++ DG   + E++D
Sbjct: 168 AKRIEDGLHEMVQAIAACPLAISAILASAQQIADGELRIDELVD 211


>gi|2529267|gb|AAB81186.1| sigma factor [Paenibacillus polymyxa]
          Length = 251

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 128/246 (52%), Gaps = 17/246 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + ++++ + G+ +A   ++ ++ +N+RLV SV +++ NRG +  DL Q G IGL+K+
Sbjct: 16  TEVKRLIALSQSGDNDA---RETLINSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKS 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    +S  + 
Sbjct: 73  VDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKETANKVRKMKDELSKPLN 131

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLD 602
           R PT +E+A +L +  E V    +  K P S+   +   D D   L D I D++     D
Sbjct: 132 RLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADESQERWFD 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++E K
Sbjct: 192 -------KLALNEAIDGLSERERLIVYLRY----YRDQTQSEVASRLGISQVQVSRLEKK 240

Query: 663 AIRKLK 668
            +++++
Sbjct: 241 ILQQIR 246


>gi|83955694|ref|ZP_00964274.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83839988|gb|EAP79164.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 279

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 19/243 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 30  AAHRMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIAKKLAMP 559
           ++ +I   I      +++      K  K+    R+  N+I    + +  P+ + K++A  
Sbjct: 90  IRASIQEYILRSWSLVKLGTTSGQK--KLFFNLRKAKNRIGALEEGDLHPDNV-KRIATD 146

Query: 560 V-----EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL--- 609
           +     E +    +++    SL   +G   E T    D++ED++A    D   +  L   
Sbjct: 147 LGVTETEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQATDYEERDELETR 206

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE     L  L  RE+ +L  R         TLE++  Q+ V+RERIRQIE +A  KL+ 
Sbjct: 207 REMLAEALDVLNDREKDILTQRRLSDQTV--TLEDLSSQYDVSRERIRQIEVRAFEKLQK 264

Query: 670 PSR 672
             R
Sbjct: 265 RMR 267


>gi|220929692|ref|YP_002506601.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
 gi|220000020|gb|ACL76621.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
          Length = 249

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 127/242 (52%), Gaps = 12/242 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +++ K +     A+  +VE N+ LV S+ K++ NRG +  DL Q G+IGL+KA  KFD
Sbjct: 9   VFTLIIKAKAGDKQAQSVLVEKNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFD 68

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R I D    I++   +++   K   T   MS ++ REPT 
Sbjct: 69  TSYDVKFSTYAVPMIIGEIKRFIRDDGI-IKVSRSLKEVSSKARITKEIMSKELGREPTI 127

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS-PLDSAIQ 606
            EIA+ + +  E +   ++    P SL + IGD + S   L D I+  N  S  +D   +
Sbjct: 128 NEIAQHMNISPEELVMAIEAGCTPESLYSTIGDGENSPILLIDRIDAANNNSCEVDLIDK 187

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +R+    +L +L  RE +++ +R+      + T  ++ K   +++ ++ +IE K +R 
Sbjct: 188 IAIRQ----ILDTLDTRERQIIILRYF----KEKTQVQIAKLLGISQVQVSRIEKKILRD 239

Query: 667 LK 668
           +K
Sbjct: 240 IK 241


>gi|32423705|gb|AAP81248.1| sigma-32 subunit of RNA polymerase [Candidatus Portiera
           aleyrodidarum]
          Length = 280

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 132/246 (53%), Gaps = 23/246 (9%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ +A+   + +V +NLR VI +A+ Y+  GLQ  D+IQEGN+GLMKA ++FD   G +
Sbjct: 38  KGDLDAA---RCLVISNLRFVIHIARSYSGYGLQNSDIIQEGNVGLMKAVKRFDPAHGVR 94

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   +      ++I     + K+   +R A+   N + RE   + IAK
Sbjct: 95  LVSFAIHWIKAEIHEYVLRNWRIVKIATTKSQRKLFFSLRCAKTSLNWLNREEI-KSIAK 153

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA-NL- 609
            L +    VR++  +++      +    +E  ++    +++ED    S  D A+Q  N  
Sbjct: 154 DLNVKPTVVREMECRLSSTDYGFDNKQKEEKNNYKNPSNYLED----SRFDPALQFENFD 209

Query: 610 --RETTTRVLASLTPREERV---LRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKA 663
             R +  R+  +L   +ERV   L+ R+   +N    TL E+   + V+ ERIRQ+E +A
Sbjct: 210 FERYSYRRLYVALNKLDERVRDILKQRW---LNEPKATLHELADIYGVSAERIRQLEQRA 266

Query: 664 IRKLKH 669
           I+K+K+
Sbjct: 267 IKKIKN 272


>gi|84515395|ref|ZP_01002757.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510678|gb|EAQ07133.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 303

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 118/238 (49%), Gaps = 17/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 54  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 113

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  N+I        R    ++IA  L
Sbjct: 114 IRASIQEYILRSWSLVKMGTTSAQK--KLFFNLRKAKNRIGALEEGDLRPENVKQIANDL 171

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---R 610
            +  + V  +  +++    SL   IG   E +    D++ED +A +  D      L   R
Sbjct: 172 GVTEDEVISMNRRLSGGDASLNAQIGSDGEGSMQWQDWLEDDSANTAADYEEHDELDARR 231

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +  L PRE+ +L  R  +   T  TLE++  ++ V+RERIRQIE +A  KL+
Sbjct: 232 ALLVEAMTLLNPREKDILVQR-RLAEET-VTLEDLSARYEVSRERIRQIEVRAFEKLQ 287


>gi|332286014|ref|YP_004417925.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
 gi|330429967|gb|AEC21301.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
          Length = 293

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 120/232 (51%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LRLV+S+A++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 61  AARQLITSHLRLVVSIARQYLGYGLAHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   I      +++      +  K+    RRM    +   T +  EIA++L +  E
Sbjct: 121 IKAEIHEYIVRNWRLVKVATTKAQR--KLFFNLRRMRPDGQTLDTEQVNEIARELNVRPE 178

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL----DSAIQANLRETTTRV 616
            V ++ ++++    +LE+   DED      ++ D+    P       A  A         
Sbjct: 179 DVSEMEVRMSGREFALESN-DDEDGYAPIAYLSDEGQQEPSRVLERRAYDALQGSGLADA 237

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  R  R+++ R+ +      TL E+  +F V+ ERIRQIEA A +KL+
Sbjct: 238 LDVLDERSRRIVQARW-LQDEGGATLHELAAEFGVSAERIRQIEAAAFKKLR 288


>gi|10952458|gb|AAG24943.1|AF128845_2 RpoH [Sinorhizobium meliloti]
          Length = 301

 Score = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 122/246 (49%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K AI   I      +++      K  ++    RR+  +I+     +  PE   EIA  L
Sbjct: 109 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  +     I+ +  E+  
Sbjct: 167 KVSEEEVVSMNRRLSGDASLNAPIKASEGDSGQWQDWLVDDHD-NQEQILIEQDELESRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +LA+    L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 226 ALLANAMKVLNDRERRIFEARRLT--EEPITLEDLSTEFDISRERVRQIEVRAFEKVQEA 283

Query: 671 SRSKKL 676
            R   L
Sbjct: 284 VRKAAL 289


>gi|311898315|dbj|BAJ30723.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 360

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 10/227 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S + +G  E    + ++V  ++ LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 123 LSELPEGSAERVEIRNQLVRMHIPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDH 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   +   I R   D+   +R+P  +++    +      +S +  R PT  
Sbjct: 183 ERGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATSELSQRHGRSPTVH 242

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA- 607
           E+A+ L +  E V + L+       +SL+ P  D+++  + D       +   D A++  
Sbjct: 243 ELAEHLGISEEDVLEGLESANAYSTLSLDVPDSDDESPAVAD------TLGATDEALEGV 296

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             RE+   +LA L PRE+++L +RF   M       EVG  Q  V+R
Sbjct: 297 EYRESLKPLLAQLPPREQKILVLRFFRNMTQSQIAAEVGISQMHVSR 343


>gi|284990614|ref|YP_003409168.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
 gi|284063859|gb|ADB74797.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
          Length = 360

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 111/211 (52%), Gaps = 11/211 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE +L LV   A++++NRG  F DL+Q G +GL+ A ++FD   G +F ++A+  +   
Sbjct: 140 LVEEHLPLVRHFARRFSNRGEPFDDLLQVGTLGLIAAIDRFDPTRGVEFLSFAVPTITGE 199

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R   DQ  ++R+P  +++    +      ++ K  R PTP E+A+ L +P   V + L
Sbjct: 200 IKRHFRDQGWSVRVPRRLQELHLSLNAAVGELAQKNGRAPTPSELAEHLGIPRAEVLEGL 259

Query: 568 KITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPR 623
            +       SL+  + G++D+  L   + ++      DSA++    RE+   +LA++  R
Sbjct: 260 AVANAYRSSSLDERLSGEDDSPTLAATLGEE------DSALEGVEYRESLQPLLATIPAR 313

Query: 624 EERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           E R+L +RF   M       ++G  Q  V+R
Sbjct: 314 ERRILILRFFGNMTQSQIAADIGISQMHVSR 344


>gi|88705470|ref|ZP_01103181.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
 gi|88700560|gb|EAQ97668.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
          Length = 338

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 122/234 (52%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V  +A+ Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 104 AARELVMSHLRFVAHIARSYRGYGLAEADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHW 163

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R+A++    +  +   + +A  L + V+ 
Sbjct: 164 IKAEIHEYILRNWRIVKIATTKAQRKLFFNLRSAKKSLAWLSADEA-KAVADDLGVDVQE 222

Query: 563 VRKV-LKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPL----DSAIQANLRETTTR 615
           V ++  +++   ++ + P+G  DE+      +  +  +V P     +S  QA+ +     
Sbjct: 223 VHRMEGRLSSHDVAFDAPVGADDEEGWQAPQYYLEDQSVDPATNVENSEWQADSQAQLHA 282

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +A L  R   +L  R+   +  D  TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 283 AIAELDERSRNILAQRW---LTDDKATLHELAAEYDVSAERIRQLEQAAMKKIR 333


>gi|10129883|dbj|BAB13517.1| sigma factor [Sinorhizobium meliloti]
          Length = 301

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 122/246 (49%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K AI   I      +++      K  ++    RR+  +I+     +  PE   EIA  L
Sbjct: 109 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  +     I+ +  E+  
Sbjct: 167 KVSEEKVVSMNRRLSGDASLNAPIKASEGDSGQWQDWLVDDHD-NQEQILIEQDELESRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +LA+    L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 226 GLLANAMKVLNDRERRIFEARRLT--EEPITLEDLSTEFDISRERVRQIEVRAFEKVQEA 283

Query: 671 SRSKKL 676
            R   L
Sbjct: 284 VRKAAL 289


>gi|298500980|ref|ZP_07010781.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MAK 757]
 gi|297540228|gb|EFH76288.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MAK 757]
          Length = 408

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 27  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 86

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 87  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 145

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 146 INQVQSAIAEYPGTIPYIL 164


>gi|187922577|ref|YP_001894219.1| RNA polymerase factor sigma-32 [Burkholderia phytofirmans PsJN]
 gi|187713771|gb|ACD14995.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phytofirmans
           PsJN]
          Length = 311

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 123/250 (49%), Gaps = 42/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W
Sbjct: 72  SARRLVLSHLRLVVSIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHW 131

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++         TP++I        + 
Sbjct: 132 IKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKQGLGAF----TPDQI--------DD 179

Query: 563 VRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
           + K L + +E +S +ET +   D +  G   + + A +P+  A  A+     T VLAS  
Sbjct: 180 LAKELNVKREEVSEMETRLSGGDIALEGQVEDGEEAYAPI--AYLADSHSEPTAVLASRQ 237

Query: 620 ---------------LTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERIRQ 658
                          L  R  R++  R+      G G +T H   E+  +F V+ ERIRQ
Sbjct: 238 RDKLHSDGIASALDALDARSRRIIEARWLKVEDDGSGGSTLH---ELADEFGVSAERIRQ 294

Query: 659 IEAKAIRKLK 668
           IEA A++K++
Sbjct: 295 IEASAMKKMR 304


>gi|317163755|gb|ADV07296.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 287

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 127/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 44  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 101 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNVLSPKEA-QDIAD 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 160 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 209

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 210 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 268

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 269 EAKAMQKLR 277


>gi|225389920|ref|ZP_03759644.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
 gi|225044021|gb|EEG54267.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
          Length = 258

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 120/232 (51%), Gaps = 22/232 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     KFSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIQRFSGNQENIDDLFQIGCIGLIKAIDNFDITQNVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +    +++    +EPT  EIA+++ +  E +
Sbjct: 98  ILGEVRRYLRDNN-SIRVSRSLRDTAYKAIYAREQLTRLNSKEPTLAEIAQEIGVSKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+  +  D  ++ D I DK     N V  L      +L E   R 
Sbjct: 157 TYALDAIQTPVSLYEPVYTDGGDPLYVMDQISDKKNLEENWVEDL------SLGEAMKR- 209

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  RE  ++ +RF  G     T  EV ++  +++ ++ ++E  A++ +K
Sbjct: 210 ---LPERERHIIDLRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKTMK 254


>gi|254473077|ref|ZP_05086475.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
 gi|211957798|gb|EEA93000.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
          Length = 297

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 119/240 (49%), Gaps = 22/240 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 48  AAEKLVNSHLRLVAKIAMGYRGYGLPLGEVISEGNVGLMQAVKRFEPDKGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  ++    RR+  KI+       R    ++IA  L
Sbjct: 108 IKASIQEYILRTWSLVKMGTTANQK--RLFFNLRRVKGKIQAFEDGDLRPEQVQQIATTL 165

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +    V  + +      SL  P+   + ++S   D++ D    S    A+ A   E   
Sbjct: 166 GVTENEVVSMNRRLGGDSSLNAPLRSSEGESSEWQDWLVDD---SESQEAVLAEQEEYDV 222

Query: 615 R------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R       ++ L  RE R+   R  +  N   TLEE+  +F V+RER+RQIE +A  K++
Sbjct: 223 RRDMLKNAMSVLNERETRIFEAR-RLSENPI-TLEELSTEFGVSRERVRQIEVRAFEKVQ 280


>gi|153827661|ref|ZP_01980328.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
 gi|149737861|gb|EDM52766.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
          Length = 305

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 53/140 (37%), Positives = 87/140 (62%), Gaps = 3/140 (2%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEG 88
            K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +    
Sbjct: 9   LKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALS 68

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 69  DDTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIED 127

Query: 149 GRAMMMASLCESPLTFQALI 168
           G   + +++ E P T   ++
Sbjct: 128 GINQVQSAIAEYPGTIPYIL 147


>gi|114763110|ref|ZP_01442536.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114544163|gb|EAU47172.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 298

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 116/234 (49%), Gaps = 17/234 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW++ +
Sbjct: 53  LVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRAS 112

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPV 560
           I   I      +++      K  K+    R+  ++I        R    E IA  L +  
Sbjct: 113 IQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKSRIGALEDGDLRPEHVERIATDLGVTH 170

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANL---RETTT 614
           + V  +  +++    SL   +G +D S +   D++ED++A    D A +  L   RE  T
Sbjct: 171 DEVISMNRRLSGGDASLNATVGSDDESSMQWQDWLEDESADQAGDYAERNELEARRELLT 230

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  RE  +L  R         TLEE+   + V+RERIRQIE +A  KL+
Sbjct: 231 EAMDVLNERERDILTQRRLAEQPV--TLEELSGVYDVSRERIRQIEVRAFEKLQ 282


>gi|163744692|ref|ZP_02152052.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
 gi|161381510|gb|EDQ05919.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
          Length = 292

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 128/255 (50%), Gaps = 22/255 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 41  ALHRLITAYMRLAISMAGKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 100

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A  +   + +    + I+ 
Sbjct: 101 IKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREASAVGETLDKHQLRQMIST 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSAIQ---A 607
           ++ +P+  V  +  +++    SL      ED     ++IE   D++A +      Q   A
Sbjct: 161 EIGVPLHDVEMMEGRLSGSDYSLNATQSAEDEGR--EWIEALADESAQAAERVEEQHDTA 218

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR      +  L+ RE+ ++R R     +   TLE +G +  +++ER+RQ+EA A  K+
Sbjct: 219 QLRNWLLTAMQGLSDREQFIVRER--KLRDPSRTLESLGDELSLSKERVRQLEAAAFGKM 276

Query: 668 KHP--SRSKKLRSFL 680
           +     +S+++ +FL
Sbjct: 277 RKSLEMQSREVFAFL 291


>gi|84393530|ref|ZP_00992284.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84375809|gb|EAP92702.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 291

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 74/278 (26%), Positives = 141/278 (50%), Gaps = 26/278 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E    ++E  H      KGE +A+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRSANSYPMLTPEEERGLAERLHY-----KGEIDAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I 
Sbjct: 68  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++  +  + E P
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDATFEAP 185

Query: 580 IGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTR-----VLASLTPREERVLRM 630
           + D+D          ++EDK   S +   ++A   E+ T       L SL  R + ++R 
Sbjct: 186 MDDDDGGSAYTAPVYYLEDK--ASDVAETVEAANWESHTNNRLGLALKSLDERSQHIVRS 243

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+    +   TL+++   + ++ ER+RQ+E  A++KLK
Sbjct: 244 RWLD--DNKSTLQDLADTYSISAERVRQLEKNAMKKLK 279


>gi|240013602|ref|ZP_04720515.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI18]
 gi|240112396|ref|ZP_04726886.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|240120672|ref|ZP_04733634.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID24-1]
 gi|268598456|ref|ZP_06132623.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|268582587|gb|EEZ47263.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
          Length = 290

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 131/239 (54%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 47  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 104 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNVLSPKEA-QDIAD 162

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL--- 609
            L + +  V ++  ++T   I++ T    DED+    D++ D ++      + QA+    
Sbjct: 163 DLGVKLSEVLEMEQRMTGHDIAIMTDNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQ 222

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 223 TEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|254476880|ref|ZP_05090266.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
 gi|214031123|gb|EEB71958.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
          Length = 292

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 129/255 (50%), Gaps = 30/255 (11%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +
Sbjct: 45  LINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKAS 104

Query: 508 ITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           I   +      +R         +  +MR    ++ R A     ++ +    ++IA ++ +
Sbjct: 105 IQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLEREAAASGEQLDQHQLHQKIATEIGV 164

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL--DSAIQANLRETT-- 613
           P+  V+ +  +++    SL      ED        E +  +  L  DSA  A L E +  
Sbjct: 165 PLRDVQMMDGRLSGADFSLNAVQSAED--------EGREWIEALEDDSAQAAELVEESHD 216

Query: 614 TRVLASLTPREERVL--RMRFGIG----MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           TR L +      + L  R RF I      +   TLE +G +  +++ER+RQ+EA A +K+
Sbjct: 217 TRQLRTWLVEAMQALNDRERFIITERKLRDKPRTLESLGDELGLSKERVRQLEAAAFQKM 276

Query: 668 KHP--SRSKKLRSFL 680
           +    + S+++++FL
Sbjct: 277 RKSLETCSREVQNFL 291


>gi|90415296|ref|ZP_01223230.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90332619|gb|EAS47789.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 278

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 129/236 (54%), Gaps = 16/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA  +F+   G +  ++A+ W
Sbjct: 43  AARRMVMAHLRFVVHIARSYNGYGLPLADLIQEGNVGLMKAVRRFNPEKGVRLVSFAVHW 102

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R+A++    +  +   + +A  L + V+ 
Sbjct: 103 IKAEIHEFILRNWRIVKIATTKAQRKLFFNLRSAKKQLQWLSADEA-KAVADDLGVQVKD 161

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLR-ETTTRV 616
           V ++ +++T    + + P G++D S        F+EDK ++ P   A   +   +  TR+
Sbjct: 162 VMEMEMRLTSRDPAFDAPAGEDDESSSFQAPVYFLEDK-SMDPAQLAENDDWEVDNNTRL 220

Query: 617 LASLTPREER---VLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A+++  ++R   +L+ R+   +N    TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 221 IAAVSDLDDRSRDILQRRW---LNDAKATLHELAAEYGVSAERIRQLEKNAMKKVR 273


>gi|15966479|ref|NP_386832.1| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307300484|ref|ZP_07580264.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307318349|ref|ZP_07597784.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|15075750|emb|CAC47305.1| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306896031|gb|EFN26782.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306904650|gb|EFN35234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 301

 Score = 90.9 bits (224), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 122/246 (49%), Gaps = 18/246 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K AI   I      +++      K  ++    RR+  +I+     +  PE   EIA  L
Sbjct: 109 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + D+    D++ D +  +     I+ +  E+  
Sbjct: 167 KVSEEEVVSMNRRLSGDASLNAPIKASEGDSGQWQDWLVDDHD-NQEQILIEQDELESRR 225

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +LA+    L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++  
Sbjct: 226 ALLANAMKVLNDRERRIFEARRLT--EEPITLEDLSTEFDISRERVRQIEVRAFEKVQEA 283

Query: 671 SRSKKL 676
            R   L
Sbjct: 284 VRKAAL 289


>gi|188090598|gb|ACD49533.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
 gi|188090644|gb|ACD49556.1| RNA polymerase sigma factor [Xanthomonas codiaei]
 gi|188090646|gb|ACD49557.1| RNA polymerase sigma factor [Xanthomonas codiaei]
          Length = 291

 Score = 90.5 bits (223), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090580|gb|ACD49524.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. manihotis]
 gi|188090650|gb|ACD49559.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 291

 Score = 90.5 bits (223), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090476|gb|ACD49472.1| RNA polymerase sigma factor [Xanthomonas vesicatoria ATCC 35937]
 gi|188090480|gb|ACD49474.1| RNA polymerase sigma factor [Xanthomonas vesicatoria]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|59800736|ref|YP_207448.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|194098013|ref|YP_002001061.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae NCCP11945]
 gi|239998477|ref|ZP_04718401.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|240016041|ref|ZP_04722581.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA6140]
 gi|240080183|ref|ZP_04724726.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|240115137|ref|ZP_04729199.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|240117420|ref|ZP_04731482.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|240122976|ref|ZP_04735932.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|240125228|ref|ZP_04738114.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|240127682|ref|ZP_04740343.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|254493195|ref|ZP_05106366.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|260441046|ref|ZP_05794862.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI2]
 gi|268594335|ref|ZP_06128502.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268596331|ref|ZP_06130498.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268600810|ref|ZP_06134977.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268603115|ref|ZP_06137282.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268681596|ref|ZP_06148458.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268683824|ref|ZP_06150686.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268686066|ref|ZP_06152928.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291044379|ref|ZP_06570088.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|293399564|ref|ZP_06643717.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
 gi|59717631|gb|AAW89036.1| putative RNA polymerase sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|193933303|gb|ACF29127.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512235|gb|EEH61580.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|268547724|gb|EEZ43142.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268550119|gb|EEZ45138.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268584941|gb|EEZ49617.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268587246|gb|EEZ51922.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268621880|gb|EEZ54280.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268624108|gb|EEZ56508.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268626350|gb|EEZ58750.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291011273|gb|EFE03269.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|291610133|gb|EFF39255.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 127/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 47  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 104 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNVLSPKEA-QDIAD 162

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 163 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 212

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 213 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 271

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 272 EAKAMQKLR 280


>gi|290796542|gb|ADD64841.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 289

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|258625092|ref|ZP_05720011.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
 gi|258582643|gb|EEW07473.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
          Length = 286

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 143/269 (53%), Gaps = 21/269 (7%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    +S  E R +   +  KG+ +A+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNGYPMLSADEERELAERLHYKGDIDAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++  +  + E    D++    
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRE--TTTRV---LASLTPREERVLRMRFGIGMNTD 639
                 ++EDK+  S L   ++A   E  TT R+   LASL  R + ++R R+ +  +  
Sbjct: 195 YTAPVLYLEDKH--SDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNK 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++ + + V+ ERIRQ+E  A+RKLK
Sbjct: 252 TTLQDLAEMYGVSAERIRQLEKNAMRKLK 280


>gi|254477747|ref|ZP_05091133.1| alternative sigma factor RpoH [Ruegeria sp. R11]
 gi|214031990|gb|EEB72825.1| alternative sigma factor RpoH [Ruegeria sp. R11]
          Length = 298

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 122/246 (49%), Gaps = 14/246 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A+ A K MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +
Sbjct: 44  EQDANSAHK-MVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           TYAMWW++ +I   I      +++     + K+   +R A+     ++      +  KK+
Sbjct: 103 TYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLHPDSVKKI 162

Query: 557 AMPV-----EGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANL 609
           A  +     E +    +++    SL   +G E    +   D++ED++A    D   +  L
Sbjct: 163 ATDLGVTEDEVISMNRRMSGGDASLNATVGTEGEGAMQWQDWLEDEDADQAGDYEARDEL 222

Query: 610 ---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              RE     L  L  RE+ +L  R     +   TLE++  Q+ V+RERIRQIE +A  K
Sbjct: 223 EARRELLASALEVLNDREKDILTQRRLA--DQAKTLEDLSTQYGVSRERIRQIEVRAFEK 280

Query: 667 LKHPSR 672
           L+   R
Sbjct: 281 LQKKMR 286


>gi|188090632|gb|ACD49550.1| RNA polymerase sigma factor [Xanthomonas melonis]
 gi|188090634|gb|ACD49551.1| RNA polymerase sigma factor [Xanthomonas melonis]
 gi|188090636|gb|ACD49552.1| RNA polymerase sigma factor [Xanthomonas melonis]
 gi|188090638|gb|ACD49553.1| RNA polymerase sigma factor [Xanthomonas melonis]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEIAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|323486723|ref|ZP_08092043.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692138|ref|ZP_08106382.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399942|gb|EGA92320.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503825|gb|EGB19643.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 258

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 118/228 (51%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++N      DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIQRFSNSSENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +     +  +  +EPT  EIA ++ +  E +
Sbjct: 98  ILGEVKRYLRDNN-SIRVSRSLRDTAYKAIYAREGLMKRNLKEPTICEIADEIGVSKESI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   + P+SL  P+  +  D  ++ D + DK   S        +L E   R    L 
Sbjct: 157 TYALDAIQSPVSLYEPVYTDGGDPLYVMDQLSDKKC-SEEHWIEDISLNEAMKR----LP 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +++
Sbjct: 212 ERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRLEKSALKNMRN 255


>gi|297200783|ref|ZP_06918180.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197712353|gb|EDY56387.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 297

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 68  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 127

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 128 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVAELASVLGVS 187

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 188 EEDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 243

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 244 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 287


>gi|188090528|gb|ACD49498.1| RNA polymerase sigma factor [Xanthomonas vesicatoria]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|212638845|ref|YP_002315365.1| sporulation sigma factor SigF [Anoxybacillus flavithermus WK1]
 gi|212560325|gb|ACJ33380.1| Stage II sporulation protein AC, DNA-directed RNA polymerase
           sporulation-specific sigma factor (sigma-F)
           [Anoxybacillus flavithermus WK1]
          Length = 247

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 123/241 (51%), Gaps = 15/241 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q G IGLMK+ +KFD
Sbjct: 15  IKELIRRSQQGDQQARDEIIEKNMRLVWSVVQRFLNRGYEPEDLFQIGCIGLMKSVDKFD 74

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R I D   ++++   +++  +K+ +    +S +  R PT 
Sbjct: 75  LSYDVKFSTYAVPMILGEIQRFIRDDG-SVKVSRSLKEIGNKIRKAKDELSKQNGRVPTV 133

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            EIA+ L +  E V    +  + P S+   +   D D   L D I D+  V     A++ 
Sbjct: 134 NEIAQFLQISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADEQDVWFDKIALKK 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            + E        L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K ++++
Sbjct: 194 AMEE--------LDERERLIVYLRY----YKDQTQSEVAARLGISQVQVSRLEKKILQQM 241

Query: 668 K 668
           K
Sbjct: 242 K 242


>gi|110635485|ref|YP_675693.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286469|gb|ABG64528.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 308

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 126/247 (51%), Gaps = 18/247 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G++ +TYAMWW
Sbjct: 48  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K AI   I      +++      K  ++    R++  KI+     +  PE   EIA +L
Sbjct: 108 IKAAIQEYILRSWSLVKMGTTANQK--RLFFNLRKVKGKIQALDEGDLNPEQVSEIATRL 165

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V  + +      SL  PI   + ++    D++ D++  +  +  ++ +  E+  
Sbjct: 166 NVSEEEVISMNRRLSGDASLNAPIRATEGESGEWQDWLVDEHE-NQEEMLVEQDELESRR 224

Query: 615 RVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R+L      L  RE R+   R     +   TLEE+  +F ++RER+RQIE +A  K++  
Sbjct: 225 RMLEDAMDVLNDRERRIFEARR--LSDEPMTLEELSGEFDISRERVRQIEVRAFEKVQEA 282

Query: 671 SRSKKLR 677
            ++   R
Sbjct: 283 VKASAKR 289


>gi|239945848|ref|ZP_04697785.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239992317|ref|ZP_04712981.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291449304|ref|ZP_06588694.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291352251|gb|EFE79155.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 298

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 128/245 (52%), Gaps = 16/245 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA ++FD
Sbjct: 56  LQVLEEGTHEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFD 115

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+T+A+ ++   I R   D + ++ +P  +++    + +   ++S ++ R+PT 
Sbjct: 116 LSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLAKAKEQLSAELDRDPTV 175

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +E+A  L +P    +EG+  V        SL+TP  D D+        D   +   D  +
Sbjct: 176 KELATHLDLPEEEIIEGL--VAANGYSAGSLDTPSADSDSGQEQRAYAD--VLGEADPGM 231

Query: 606 QA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +   NL  T   +L  L  RE R+++MRFG  M    T  ++G++  V++  + ++ ++ 
Sbjct: 232 ETVENL-HTLAPLLEQLDDRERRIVQMRFGAEM----TQSQIGEELGVSQMHVSRLLSRI 286

Query: 664 IRKLK 668
           +++L+
Sbjct: 287 VQQLR 291


>gi|188090582|gb|ACD49525.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola]
 gi|188090670|gb|ACD49569.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090516|gb|ACD49492.1| RNA polymerase sigma factor [Xanthomonas vasicola]
 gi|188090552|gb|ACD49510.1| RNA polymerase sigma factor [Xanthomonas vasicola]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090496|gb|ACD49482.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|223041647|ref|ZP_03611844.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
 gi|223017511|gb|EEF15925.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
          Length = 321

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 129/234 (55%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ +++R VI +A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 86  AAKQLILSHMRFVIHIARGYLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           VK  I   +      +++      +  K+    R+  N++    E   + +A  L +  E
Sbjct: 146 VKAEIHEYVLRNWRIVKVATTKAQR--KLFFNLRKNKNRLAWFNEEEIKRVAHDLGVSEE 203

Query: 562 GVRKV-LKITKEPISLETPIG-DEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VR++  ++T + +  + P G DED ++    ++ED ++    +   + +  E T ++  
Sbjct: 204 EVREMESRMTGQDLGFDLPSGDDEDEAYTPSMYLEDNSSNFADELEDEEHTGEATAQLAY 263

Query: 619 SLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +L+  +ER   +++ R+ +  N   TL ++  ++ ++ ER+RQ+E  A++K+K+
Sbjct: 264 ALSTLDERSQDIIKTRW-LDENK-LTLHDLAAKYQISAERVRQLENAALKKIKN 315


>gi|325202493|gb|ADY97947.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240149]
 gi|325207756|gb|ADZ03208.1| alternative sigma factor RpoH [Neisseria meningitidis NZ-05/33]
          Length = 287

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 126/249 (50%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA +++    G +
Sbjct: 44  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYKPGRGAR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 101 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QDIAD 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 160 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 209

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 210 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 268

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 269 EAKAMQKLR 277


>gi|254525091|ref|ZP_05137146.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
 gi|219722682|gb|EED41207.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 116/243 (47%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLALGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWMNAAEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----------------- 605
            K L ++ +E + +E+ +   D        ED     P  +A                  
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDAPTDEDNEHAPPSPAAFLVANDEDPSMAYERADS 224

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + N  +     LA L  R   ++R R+ +  ++  TL+E+  ++ V+ ERIRQ+EA A++
Sbjct: 225 EDNQMQLLREGLAELDARSRDIIRRRW-LDADSKVTLQELADEYGVSAERIRQVEANALK 283

Query: 666 KLK 668
           K+K
Sbjct: 284 KMK 286


>gi|188090520|gb|ACD49494.1| RNA polymerase sigma factor [Xanthomonas pisi]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090498|gb|ACD49483.1| RNA polymerase sigma factor [Xanthomonas cassavae]
 gi|188090624|gb|ACD49546.1| RNA polymerase sigma factor [Xanthomonas cassavae]
 gi|188090626|gb|ACD49547.1| RNA polymerase sigma factor [Xanthomonas cassavae]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090564|gb|ACD49516.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TELLLADYEAHKEGKKRLAEIV 144


>gi|188090518|gb|ACD49493.1| RNA polymerase sigma factor [Xanthomonas hortorum]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|297193425|ref|ZP_06910823.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
 gi|197723192|gb|EDY67100.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
          Length = 304

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 75  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 134

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+A  L + 
Sbjct: 135 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVPELAAVLGVS 194

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      DSA++    RE+   +
Sbjct: 195 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DSALEGVEYRESLKPL 250

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 251 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 294


>gi|23015588|ref|ZP_00055360.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 296

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 119/237 (50%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGN+G+M+A  +FD   G++ +TYAMWW
Sbjct: 49  AANRLVTSHLRLVAKIAMGYRGYGLPLGELISEGNVGMMQAVRRFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAK---KL 556
           ++ AI   I      +++      K  K+    R++  +++     + + E +AK   KL
Sbjct: 109 IRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRKLKGQMQAIEEGDMSAENVAKIATKL 166

Query: 557 AMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
            +  + V  + +    P  SL  P+  E      D++ D +     +   +  +   R  
Sbjct: 167 EVTEDEVITMNRRLSSPDHSLNAPVRTEGEGEWQDWLVDDHEDQETELGEREEMGQRRGM 226

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            T  LA+L  RE  +L  R    +  D  TLE++ +++ ++RER+RQIE +A  KL+
Sbjct: 227 LTSALAALNDRERAILIQR---RLTEDPATLEDLSQRYGISRERVRQIEVRAFEKLQ 280


>gi|188090562|gb|ACD49515.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. alfalfae]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090478|gb|ACD49473.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090482|gb|ACD49475.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090492|gb|ACD49480.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. begoniae]
 gi|188090506|gb|ACD49487.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vasculorum]
 gi|188090510|gb|ACD49489.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vasculorum]
 gi|188090530|gb|ACD49499.1| RNA polymerase sigma factor [Xanthomonas axonopodis]
 gi|188090540|gb|ACD49504.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090550|gb|ACD49509.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. ricini]
 gi|188090566|gb|ACD49517.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090570|gb|ACD49519.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. alfalfae]
 gi|188090590|gb|ACD49529.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vasculorum]
 gi|188090614|gb|ACD49541.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. ricini]
 gi|188090620|gb|ACD49544.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090654|gb|ACD49561.1| RNA polymerase sigma factor [Xanthomonas alfalfae subsp.
           citrumelonis]
 gi|188090656|gb|ACD49562.1| RNA polymerase sigma factor [Xanthomonas alfalfae subsp.
           citrumelonis]
 gi|188090658|gb|ACD49563.1| RNA polymerase sigma factor [Xanthomonas alfalfae subsp.
           citrumelonis]
 gi|188090666|gb|ACD49567.1| RNA polymerase sigma factor [Xanthomonas albilineans]
 gi|188090688|gb|ACD49578.1| RNA polymerase sigma factor [Xanthomonas perforans]
          Length = 291

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090464|gb|ACD49466.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris]
 gi|188090522|gb|ACD49495.1| RNA polymerase sigma factor [Xanthomonas campestris pv. incanae]
 gi|188090532|gb|ACD49500.1| RNA polymerase sigma factor [Xanthomonas campestris pv. raphani]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGTFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TELLLSDYEAHKEGKKRLAEIV 144


>gi|262167116|ref|ZP_06034830.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC27]
 gi|262024416|gb|EEY43103.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC27]
          Length = 621

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 129 INQVQSAIAEYPGTIPYIL 147


>gi|188090674|gb|ACD49571.1| RNA polymerase sigma factor [Xanthomonas bromi]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090470|gb|ACD49469.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. juglandis]
 gi|188090536|gb|ACD49502.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. celebensis]
 gi|188090548|gb|ACD49508.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090572|gb|ACD49520.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|188090602|gb|ACD49535.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090648|gb|ACD49558.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|188090652|gb|ACD49560.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|188090676|gb|ACD49572.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090678|gb|ACD49573.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090680|gb|ACD49574.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090682|gb|ACD49575.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090684|gb|ACD49576.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|290796520|gb|ADD64830.1| RNA polymerase sigma factor [Xanthomonas dyei pv. laureliae]
 gi|290796522|gb|ADD64831.1| RNA polymerase sigma factor [Xanthomonas dyei pv. laureliae]
 gi|290796524|gb|ADD64832.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796526|gb|ADD64833.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796528|gb|ADD64834.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796530|gb|ADD64835.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796532|gb|ADD64836.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796536|gb|ADD64838.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796540|gb|ADD64840.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090554|gb|ACD49511.1| RNA polymerase sigma factor [Xanthomonas oryzae]
          Length = 290

 Score = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090662|gb|ACD49565.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           aurantifolii]
 gi|188090664|gb|ACD49566.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           aurantifolii]
          Length = 287

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090512|gb|ACD49490.1| RNA polymerase sigma factor [Xanthomonas oryzae]
          Length = 289

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 2   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 61

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 62  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 121

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 122 TEMLLADYEAHKEGKKRLAEIV 143


>gi|188090502|gb|ACD49485.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
 gi|188090508|gb|ACD49488.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vignicola]
 gi|188090594|gb|ACD49531.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
 gi|188090622|gb|ACD49545.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           aurantifolii]
 gi|188090672|gb|ACD49570.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
          Length = 291

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090466|gb|ACD49467.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
 gi|188090468|gb|ACD49468.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
 gi|188090500|gb|ACD49484.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           malvacearum]
 gi|188090504|gb|ACD49486.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. glycines]
 gi|188090514|gb|ACD49491.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. cajani]
 gi|188090574|gb|ACD49521.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. glycines]
 gi|188090578|gb|ACD49523.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           malvacearum]
 gi|188090616|gb|ACD49542.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
 gi|188090660|gb|ACD49564.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
          Length = 291

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|27364575|ref|NP_760103.1| RNA polymerase factor sigma-32 [Vibrio vulnificus CMCP6]
 gi|37678299|ref|NP_932908.1| RNA polymerase factor sigma-32 [Vibrio vulnificus YJ016]
 gi|320154977|ref|YP_004187356.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
 gi|29611852|sp|Q8DD54|RP32_VIBVU RecName: Full=RNA polymerase sigma-32 factor
 gi|27360694|gb|AAO09630.1| alternative sigma factor RpoH [Vibrio vulnificus CMCP6]
 gi|37197038|dbj|BAC92879.1| RNA polymerase sigma-32 factor [Vibrio vulnificus YJ016]
 gi|319930289|gb|ADV85153.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
          Length = 285

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 133/246 (54%), Gaps = 23/246 (9%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KGE EA+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G +
Sbjct: 44  KGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQAN 608
           ++L +    VR++  ++     + + P  ++D+S +      ++EDK+  S +   ++A 
Sbjct: 159 RELGVEPAEVREMESRLAAVDSTFDLPNEEDDSSSVSTAPVLYLEDKS--SDVADNLEAQ 216

Query: 609 LRETTTR-----VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAK 662
             E  T       LASL  R + ++R R+   ++ D  TL+++ + + V+ ERIRQ+E  
Sbjct: 217 NWEAHTNNRLAMALASLDERSQHIVRSRW---LDDDKATLQDLAEMYGVSAERIRQLEKN 273

Query: 663 AIRKLK 668
           A++KLK
Sbjct: 274 AMKKLK 279


>gi|147674012|ref|YP_001216017.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|146315895|gb|ABQ20434.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|227012343|gb|ACP08553.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
          Length = 621

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSD 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + ++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTTITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +++ E P T   ++
Sbjct: 129 INQVQSAIAEYPGTIPYIL 147


>gi|188090694|gb|ACD49581.1| RNA polymerase sigma factor [Xanthomonas cynarae]
          Length = 291

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|302335912|ref|YP_003801119.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
 gi|301319752|gb|ADK68239.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
          Length = 276

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 124/232 (53%), Gaps = 19/232 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V ++L LV  +A K+ NRG    DL+Q G IGL+KA ++FD   G +F+T+A   
Sbjct: 47  AREQLVMSHLNLVRFLASKFKNRGEPLDDLVQVGTIGLIKAIDRFDPERGLEFTTFATPT 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+  ++R+P  +++   KV +    ++  ++R P+ EEIA  L   V+ V
Sbjct: 107 IMGEIKRHFRDKGWSVRVPRRLQELSAKVNQVTDELTKDLQRSPSVEEIAAALDTTVDEV 166

Query: 564 RKVLK----ITKEPISLETPIGDEDTSHLGDF---IEDKNAVSPLDSAIQANLRETTTRV 616
            + ++     +  P+    P  D+D   + D    +++  A S     I+  +R+     
Sbjct: 167 LEAMESSSAYSSVPLEGTGPGADDDAPSVIDHYATVDEDLAASDDRMVIEETVRD----- 221

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +PRE+ ++RMRF  G+    T  E+ ++  +++ ++ ++  + ++K++
Sbjct: 222 ---FSPREQEIIRMRFIEGL----TQVEIARRLGISQVQVSRLLRRTLQKVQ 266


>gi|188090556|gb|ACD49512.1| RNA polymerase sigma factor [Xanthomonas vasicola]
 gi|188090668|gb|ACD49568.1| RNA polymerase sigma factor [Xanthomonas vasicola]
          Length = 289

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 2   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 61

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 62  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 121

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 122 TEMLLADYEAHKEGKKRLAEIV 143


>gi|308273000|emb|CBX29604.1| hypothetical protein N47_J05850 [uncultured Desulfobacterium sp.]
          Length = 326

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 132/261 (50%), Gaps = 24/261 (9%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKE---------MVEANLRLVISVAKKYTNR-GLQFLDL 473
           IS++R    + R+ E E +I  K+         ++ +NLRLV+ +A  + +       DL
Sbjct: 53  ISQYRL---LSREEEIELAINVKDKDDKESASKLITSNLRLVVKIAFNFQHYLANNVPDL 109

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD-KIHKV 532
           IQEGNIGL+ A +K+D   G KFS YA +W++  I + I +    ++I    +  K+   
Sbjct: 110 IQEGNIGLIHAVKKYDPYKGVKFSYYAAFWIRAYIFKFIMNNWDMLKIGTTQKQRKLFFN 169

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDF 591
           +   RR        P P+ +A++L +    + +++ ++   P+SL  P+ ++    L + 
Sbjct: 170 LNKERRQITAEGLNPEPKLLAERLGVQENDIVQMIPRLDYSPLSLNQPLSEDSKECLEER 229

Query: 592 IEDKNA-----VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++DKNA     +S L+S  + NL     +    L   +  +  MR  I      +L+ +G
Sbjct: 230 VQDKNASTIDQLSVLES--KTNLERELKKFRKLLKGIKADIFDMR--IMAENPVSLQSIG 285

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
            ++ ++RER+RQI+   I K+
Sbjct: 286 DRYQISRERVRQIQEMIINKI 306


>gi|16079402|ref|NP_390226.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221310263|ref|ZP_03592110.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314586|ref|ZP_03596391.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319509|ref|ZP_03600803.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323785|ref|ZP_03605079.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321311821|ref|YP_004204108.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
 gi|133474|sp|P07860|RPSF_BACSU RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|143611|gb|AAA22788.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|1304000|dbj|BAA12655.1| SpoIIAC [Bacillus subtilis]
 gi|2634780|emb|CAB14277.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484775|dbj|BAI85850.1| sporulation sigma factor SigF [Bacillus subtilis subsp. natto
           BEST195]
 gi|320018095|gb|ADV93081.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
          Length = 255

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 127/245 (51%), Gaps = 17/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++   + G+ +A   +  ++E N+RLV SV +++ NRG +  DL Q G IGL+K+ 
Sbjct: 18  EVKELIKQSQNGDQQA---RDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSV 74

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     +FSTYA+  +   I R I D   T+++   +++  +K+ R    +S  + R
Sbjct: 75  DKFDLTYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGNKIRRAKDELSKTLGR 133

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
            PT +EIA  L +  E V    +  + P S+   +   D D   L D I D +     D 
Sbjct: 134 VPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQIADNSEEKWFD- 192

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  L+E     ++ L  RE+ ++ +R+      D T  EV ++  +++ ++ ++E K 
Sbjct: 193 --KIALKEA----ISDLEEREKLIVYLRY----YKDQTQSEVAERLGISQVQVSRLEKKI 242

Query: 664 IRKLK 668
           ++++K
Sbjct: 243 LKQIK 247


>gi|326775053|ref|ZP_08234318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655386|gb|EGE40232.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 300

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 127/245 (51%), Gaps = 16/245 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA ++FD
Sbjct: 58  LQVLEEGTHEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFD 117

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+T+A+ ++   I R   D + ++ +P  +++    + +   ++S ++ R+PT 
Sbjct: 118 LSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLAKAKEQLSGELDRDPTV 177

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +E+A  L +P    +EG+  V        SL+TP  D D+        D   +   D  +
Sbjct: 178 KELAAHLDLPEEEIIEGL--VAANGYSAGSLDTPSADSDSGQEQRAYAD--VLGEADPGM 233

Query: 606 QA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +   NL  T   +L  L  RE R+++MRFG  M    T  ++G +  V++  + ++ ++ 
Sbjct: 234 ETVENL-HTLAPLLDQLDERERRIVQMRFGAEM----TQSQIGAELGVSQMHVSRLLSRI 288

Query: 664 IRKLK 668
           +++L+
Sbjct: 289 VQQLR 293


>gi|240948113|ref|ZP_04752523.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
 gi|240297593|gb|EER48085.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
          Length = 321

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 129/234 (55%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ +++R VI +A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 86  AAKQLILSHMRFVIHIARGYLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           VK  I   +      +++      +  K+    R+  N++    E   + +A  L +  E
Sbjct: 146 VKAEIHEYVLRNWRIVKVATTKAQR--KLFFNLRKNKNRLAWFNEEEIKRVAHDLGVSEE 203

Query: 562 GVRKV-LKITKEPISLETPIG-DEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VR++  ++T + +  + P G DED ++    ++ED ++    +   + +  E T ++  
Sbjct: 204 EVREMESRMTGQDLGFDLPSGDDEDEAYTPSMYLEDNSSNFADELEDEEHTGEATAQLAY 263

Query: 619 SLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +L+  +ER   +++ R+ +  N   TL ++  ++ ++ ER+RQ+E  A++K+K+
Sbjct: 264 ALSTLDERSQDIIKTRW-LDENK-LTLHDLAAKYQISAERVRQLENAALKKIKN 315


>gi|188090474|gb|ACD49471.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. pruni]
          Length = 290

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|284431341|gb|ADB84485.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vitians]
          Length = 294

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|269960187|ref|ZP_06174562.1| RNA polymerase sigma factor [Vibrio harveyi 1DA3]
 gi|269834994|gb|EEZ89078.1| RNA polymerase sigma factor [Vibrio harveyi 1DA3]
          Length = 639

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 29  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 88

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 89  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 147

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 148 INQVQSSVAEYPGTIPYIL 166


>gi|329114085|ref|ZP_08242849.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
 gi|326696624|gb|EGE48301.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
          Length = 319

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 82/316 (25%), Positives = 157/316 (49%), Gaps = 37/316 (11%)

Query: 374 HQGRELDPHWVSYAKDFP-EGEWKNFVACEVD-----SILKIRNEIKS---ISVETGISI 424
           H GR  +P    ++++FP +G  ++ V+  ++     ++ +   EI+    ++ E  +S+
Sbjct: 2   HCGRYGNP---KHSREFPVQGSSQHMVSSVINVGPENNLSRYLQEIRKYPLLTPEEELSL 58

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           S          KG+ +A+    ++V ++LRLV  +A  Y   GL   +LI EGNIG+M+A
Sbjct: 59  SRL-----WRDKGDVKAA---HQLVTSHLRLVAKIAMGYRGYGLPINELISEGNIGMMQA 110

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++FD   G++ +TYAMWW++ AI   I      +++      K  K+    RR+  +++
Sbjct: 111 VKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQ 168

Query: 545 R----EPTPEE---IAKKLAMPVEGVRKVLKITKEP-ISLETPI-GDEDTSHLGDFIEDK 595
                +  PE+   IA  L +  + V  + +    P  SL  P+  D+D+      ++D 
Sbjct: 169 AIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSLNAPMRADQDSEWQDRLVDDH 228

Query: 596 NAVSPLDSAIQ--ANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVT 652
                + +  +  +  +   +  + +L  RE R+   R    +  D  TLEE+  ++ ++
Sbjct: 229 TNQEDVYAENEELSGRKALLSSAMENLNERERRIFTER---RLKDDPSTLEELAHEYGIS 285

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQIE +A  K++
Sbjct: 286 RERVRQIEVRAFEKVQ 301


>gi|188090604|gb|ACD49536.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris]
          Length = 290

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TELLLADYEAHKEGKKRLAEIV 144


>gi|188090542|gb|ACD49505.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. hederae]
 gi|188090558|gb|ACD49513.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. pelargonii]
 gi|188090560|gb|ACD49514.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. pelargonii]
 gi|290796546|gb|ADD64843.1| RNA polymerase sigma factor [Xanthomonas hortorum]
          Length = 291

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090642|gb|ACD49555.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           malvacearum]
          Length = 291

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|188090524|gb|ACD49496.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. taraxaci]
 gi|188090686|gb|ACD49577.1| RNA polymerase sigma factor [Xanthomonas gardneri ATCC 19865]
 gi|188090690|gb|ACD49579.1| RNA polymerase sigma factor [Xanthomonas cynarae]
 gi|188090692|gb|ACD49580.1| RNA polymerase sigma factor [Xanthomonas cynarae]
          Length = 291

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|156973168|ref|YP_001444075.1| RNA polymerase sigma factor RpoD [Vibrio harveyi ATCC BAA-1116]
 gi|156524762|gb|ABU69848.1| hypothetical protein VIBHAR_00848 [Vibrio harveyi ATCC BAA-1116]
          Length = 620

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 84/139 (60%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 92  SLDLASSASNSSVF--LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             ++    +  +    L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DTNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 129 INQVQSSVAEYPGTIPYIL 147


>gi|89055891|ref|YP_511342.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88865440|gb|ABD56317.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 298

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 121/248 (48%), Gaps = 15/248 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E E + A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A +KFD   G++ 
Sbjct: 42  AEKEDTEAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKKFDPEKGFRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIK----REPTPEE 551
           +TYAMWW++ AI   +      +++     + K+   +R A+     ++    R    E 
Sbjct: 102 ATYAMWWIRAAIQEYVLRSWSMVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVER 161

Query: 552 IAKKLAMP-VEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSA---- 604
           IA  L +   E V    +++    SL   +G ED  ++   D++ED++A    D A    
Sbjct: 162 IANDLGVTEAEVVSMNRRMSGGDASLNATVGSEDEGSAQWQDWLEDEDADQATDYAERDE 221

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            Q+ +       +  L  RE+ +L  R         TLE++   + V+RER+RQIE +A 
Sbjct: 222 FQSRM-ALMAEAMEVLNDREKDILTQRR--LQEKAVTLEDLSGVYNVSRERVRQIEVRAF 278

Query: 665 RKLKHPSR 672
            KL+   R
Sbjct: 279 EKLQKRMR 286


>gi|30024623|dbj|BAC75680.1| sigma L [Streptomyces griseus]
          Length = 288

 Score = 90.5 bits (223), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 113/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 59  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 118

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+ + L + 
Sbjct: 119 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELVRALGVS 178

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DAALEGVEYRESLKPL 234

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 235 LAKLAPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 278


>gi|332185869|ref|ZP_08387616.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
 gi|332014227|gb|EGI56285.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
          Length = 301

 Score = 90.5 bits (223), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 123/244 (50%), Gaps = 30/244 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KF+   G++ +TYAMWW
Sbjct: 53  AAAQLVTSHLRLVAKIAMGYRGYGLPTSELISEGNIGLMQGVKKFEPDRGFRLATYAMWW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEEIAKKLAMP 559
           ++ +I   I      +++      K  K+    RRM +K+      +  PE++  K+A  
Sbjct: 113 IRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRMKSKLDAFEDGDLRPEDVT-KIATD 169

Query: 560 VEGVR--KVLKITKE-----PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + GV   +V+ + +        SL   + ++      D++ D    +PL  ++ A  +E 
Sbjct: 170 L-GVNEDEVISMNRRMAMGGDTSLNVSMREDGEGQWQDWLADD---APLQDSVVAEQQEA 225

Query: 613 TTR------VLASLTPREERVLRMRFGIGMNTD--HTLEEVGKQFCVTRERIRQIEAKAI 664
             R       +  L  RE+ +L  R      TD   TLEE+ + + V+RER+RQIE +A 
Sbjct: 226 DVRHDMLVSAMDDLNDREKHILTER----RLTDDPKTLEELSQVYGVSRERVRQIEVRAF 281

Query: 665 RKLK 668
            KL+
Sbjct: 282 EKLQ 285


>gi|146277611|ref|YP_001167770.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145555852|gb|ABP70465.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 298

 Score = 90.5 bits (223), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 15/237 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAM 558
           ++ +I   I      +++     + K+   +R A+     ++    R     +IAK L++
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLSV 168

Query: 559 P-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   IG   +  +   D++ED+++    D A +  L   RE 
Sbjct: 169 TEAEVIDMNRRLSASDASLNATIGSDGDGATQWQDWLEDEDSDQASDYAERDELEIRREL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + ++ L  RE+ +L  R    +  D  TLEE+   + V+RERIRQIE +A  KL+
Sbjct: 229 LAQAMSVLNDREKDILVQR---RLTDDPVTLEELSDGYGVSRERIRQIEVRAFEKLQ 282


>gi|284431339|gb|ADB84484.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. vitians]
 gi|284431343|gb|ADB84486.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. vitians]
 gi|284431345|gb|ADB84487.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. vitians]
          Length = 294

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|261325797|ref|ZP_05964994.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261301777|gb|EEY05274.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 293

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 96  VRFSTYAFWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    +  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDIEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 214 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|223986354|ref|ZP_03636363.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
 gi|223961703|gb|EEF66206.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
          Length = 257

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 125/228 (54%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++  NL+LV+S+ +++ +R     DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 38  AKEKLINGNLKLVLSIVQRFAHRTENMDDLFQIGCIGLIKAIDNFDLSHEVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    IR+  H++D  +KV++      +  +REP+  E+A+ + +  + +
Sbjct: 98  IIGEIKRYLRDNQ-MIRVSRHLKDLAYKVLKEKEAFIHANQREPSLAELAEIMGVKEKDI 156

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
            + L+  +  +S+  PI   D DT +L D I +D + +  L S I   L+E+    +  L
Sbjct: 157 AESLESLQSVVSIFEPIYNDDGDTLYLLDQIKDDHDEIGKLSSLIA--LKES----MKHL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +E +++  R+  G     T  E+  +  +++ ++ ++E  A++ LK
Sbjct: 211 SDKEAQIINKRYYQG----QTQTEIASELGISQAQVSRLEKSALQCLK 254


>gi|51892950|ref|YP_075641.1| sporulation sigma factor SigF [Symbiobacterium thermophilum IAM
           14863]
 gi|51856639|dbj|BAD40797.1| RNA polymerase sigma factor similar to B. subtilis
           sporulation-specific sigma-F [Symbiobacterium
           thermophilum IAM 14863]
          Length = 255

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 124/253 (49%), Gaps = 14/253 (5%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E G    E R +V++ R G+ EA   +  +VE NLRLV S+  +++  G    DL Q G 
Sbjct: 9   ERGWPDEEVRRLVALARAGDKEA---RDRLVEGNLRLVRSLVSRFSASGADPEDLFQIGC 65

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA ++FD     +FSTYA+  +   I R + D    +R+   ++    +  R   R
Sbjct: 66  IGLLKAIDRFDLNYDVRFSTYAVPLIMGEIRRHLRDDG-PMRVSRSLKQLAQQARRVRER 124

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           ++ +++R+PT  E+A +L +  E V   L   + P S+   +  GD D  +L D +   +
Sbjct: 125 LAAQMERDPTVAEVAAELGVSPEEVVAALDGVRPPTSIHQTVHEGDGDPIYLLDQLAADD 184

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  LRE     L  L  RE  V+ +RF      D T  EV      ++ ++
Sbjct: 185 GQREGVWLDRVALREG----LNQLDERERTVILLRF----FRDKTQTEVASILGCSQVQV 236

Query: 657 RQIEAKAIRKLKH 669
            ++E +A+ ++++
Sbjct: 237 SRLERRALERIRN 249


>gi|13473215|ref|NP_104782.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14023963|dbj|BAB50568.1| sigma factor [Mesorhizobium loti MAFF303099]
          Length = 303

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 121/247 (48%), Gaps = 18/247 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E + A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G+
Sbjct: 39  RYAEHEDTSAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K +I   I      +++      K  ++    R++  KI+       +  
Sbjct: 99  RLATYAMWWIKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKVKGKIQALDDGDLKPD 156

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
              EIA +L +    V  + +      SL  PI   + ++    D++ D +  S  +  I
Sbjct: 157 QIAEIATRLNVTEAEVVSMNRRLSGDASLNAPIRATEGESGEWQDWLVDDHE-SQEEMLI 215

Query: 606 QA----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +     N R   +  LA L  RE R+   R         TLEE+  +F ++RER+RQIE 
Sbjct: 216 EQDELENRRGMLSGALAVLNERERRIFEARR--LAEEPLTLEELSAEFDISRERVRQIEV 273

Query: 662 KAIRKLK 668
           +A  K++
Sbjct: 274 RAFEKVQ 280


>gi|188090640|gb|ACD49554.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. populi]
          Length = 289

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TEMLLADYEAHKEGKKRLAEIV 144


>gi|260461535|ref|ZP_05809782.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032605|gb|EEW33869.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 303

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 121/247 (48%), Gaps = 18/247 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E E + A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A +KF+   G+
Sbjct: 39  RYAEHEDTSAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGF 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REP 547
           + +TYAMWW+K +I   I      +++      K  ++    R++  KI+       +  
Sbjct: 99  RLATYAMWWIKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKVKGKIQALDDGDLKPD 156

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
              EIA +L +    V  + +      SL  PI   + ++    D++ D +  S  +  I
Sbjct: 157 QIAEIATRLNVSEAEVVSMNRRLSGDASLNAPIRATEGESGEWQDWLVDDHE-SQEEMLI 215

Query: 606 QA----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +     N R   +  LA L  RE R+   R         TLEE+  +F ++RER+RQIE 
Sbjct: 216 EQDELENRRGMLSGALAVLNDRERRIFEARR--LAEEPLTLEELSAEFDISRERVRQIEV 273

Query: 662 KAIRKLK 668
           +A  K++
Sbjct: 274 RAFEKVQ 280


>gi|83941135|ref|ZP_00953597.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83846955|gb|EAP84830.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 298

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 19/243 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIAKKLAMP 559
           ++ +I   I      +++      K  K+    R+  N+I    + +  P+ + K++A  
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSGQK--KLFFNLRKAKNRIGALEEGDLHPDNV-KRIATD 165

Query: 560 V-----EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL--- 609
           +     E +    +++    SL   +G   E T    D++ED++A    D   +  L   
Sbjct: 166 LGVTETEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQATDYEERDELETR 225

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE     L  L  RE+ +L  R         TLE++  Q+ V+RERIRQIE +A  KL+ 
Sbjct: 226 REMLAEALDVLNDREKDILTQRRLSDQTV--TLEDLSSQYDVSRERIRQIEVRAFEKLQK 283

Query: 670 PSR 672
             R
Sbjct: 284 RMR 286


>gi|254389000|ref|ZP_05004231.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294814936|ref|ZP_06773579.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702718|gb|EDY48530.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294327535|gb|EFG09178.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 358

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 127 GSRERAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEF 186

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A++L
Sbjct: 187 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAERL 246

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 247 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 300

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 301 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 341


>gi|237746700|ref|ZP_04577180.1| RNA polymerase primary sigma factor [Oxalobacter formigenes HOxBLS]
 gi|229378051|gb|EEO28142.1| RNA polymerase primary sigma factor [Oxalobacter formigenes HOxBLS]
          Length = 827

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/158 (34%), Positives = 90/158 (56%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +IKL ++R ++T  E+N  LP + +  + +E  ++  ++MGI+V +   D ED   ++
Sbjct: 206 KMLIKLGKERSFLTYAEINDHLPDNVIDPDAIEGIISTFNDMGISVYEHAPDAEDLLLTD 265

Query: 91  DSLDLASSASNSSVFLQKRK--DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + + + S     +         DS    T DPVRMY+REMGS+ELL+REGEI IAKRIE 
Sbjct: 266 NVVTVTSDEEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEE 325

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   +I   +++ +    + E++D
Sbjct: 326 GLKDMIQAISSCPTTILEIIGQAEKIRNDEIRIDEVVD 363


>gi|188090544|gb|ACD49506.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
 gi|188090546|gb|ACD49507.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
          Length = 291

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 86/142 (60%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+   +   +G   L EI+
Sbjct: 123 TELLLADYEAHKEGKKRLAEIV 144


>gi|326443307|ref|ZP_08218041.1| sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 351

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +F
Sbjct: 120 GSRERAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEF 179

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   V   I R   D+   +R+P  +++    +      +S    R PT  E+A++L
Sbjct: 180 STYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAERL 239

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETT 613
            +  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+ 
Sbjct: 240 GISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESL 293

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 294 KPLLEDLPPREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 334


>gi|225568653|ref|ZP_03777678.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
 gi|225162581|gb|EEG75200.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
          Length = 259

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 121/231 (52%), Gaps = 18/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E ++ NLRLV+SV K++        DL Q G IGL+KA   F+  L  KFSTYA+  
Sbjct: 38  AKEEYIKGNLRLVLSVIKRFGGSNENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        +  +EPT +EIA+++ +  E +
Sbjct: 98  IIGEIRRYMRDNN-SIRVSRSLRDTAYKAIYAKENYVKRNLKEPTVQEIAEEIGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPL--DSAIQANLRETTTRVLA 618
              L   + P+SL+ P+ ++  D  ++ D I D KN       D +++A         + 
Sbjct: 157 VFALDAIQVPMSLQEPVYNDGGDALYVMDQISDTKNKEEKWVEDLSLEA--------AME 208

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  RE  ++++RF  G     T  EV ++  +++ ++ ++E  A+R +K 
Sbjct: 209 HLGERERYIIKLRFFEG----KTQMEVAEEINISQAQVSRLEKNALRVMKQ 255


>gi|330831381|ref|YP_004394333.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806517|gb|AEB51716.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 284

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 128/241 (53%), Gaps = 16/241 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G + 
Sbjct: 46  GDLEAA---RQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++     + K+   +R +++    +  E   + +A  
Sbjct: 103 VSFAVHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWLNHEEV-QAVAAD 161

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA-NLRE 611
           L +    V ++  ++     + +    DE+        ++EDK+  S L + I+  N  +
Sbjct: 162 LGVSAADVTEMEARMANYDQAFDLVGDDEEEGGFAPVHYLEDKS--SDLAATIENDNWDD 219

Query: 612 TTTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             TR     LA+L  R + ++R R+ +  ++  TL+E+   + V+ ER+RQ+E  A++KL
Sbjct: 220 HATRRLSSALATLDERSQHIIRARW-LDDDSKTTLQELADTYGVSAERVRQLEKNALKKL 278

Query: 668 K 668
           K
Sbjct: 279 K 279


>gi|296332278|ref|ZP_06874740.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674979|ref|YP_003866651.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150592|gb|EFG91479.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305413223|gb|ADM38342.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 255

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 127/245 (51%), Gaps = 17/245 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++   + G+ +A   +  ++E N+RLV SV +++ NRG +  DL Q G IGL+K+ 
Sbjct: 18  EVKELIKQSQNGDQQA---RDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSV 74

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     +FSTYA+  +   I R I D   T+++   +++  +K+ R    +S  + R
Sbjct: 75  DKFDLTYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGNKIRRAKDELSKTLGR 133

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
            PT +EIA  L +  E V    +  + P S+   +   D D   L D I D +     D 
Sbjct: 134 VPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQIADNSEEKWFD- 192

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  L+E     ++ L  RE+ ++ +R+      D T  EV ++  +++ ++ ++E K 
Sbjct: 193 --KIALKEA----ISDLEEREKLIVYLRY----YKDQTQSEVAERLGISQVQVSRLEKKI 242

Query: 664 IRKLK 668
           ++++K
Sbjct: 243 LKQIK 247


>gi|319778863|ref|YP_004129776.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
 gi|317108887|gb|ADU91633.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
          Length = 292

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 116/231 (50%), Gaps = 9/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++  +LRLV+SVA++Y   GL   DLIQEGNIGLMKA ++FD   G +  T+AM W
Sbjct: 58  AAQALILPHLRLVVSVARQYLGYGLPHADLIQEGNIGLMKAVKRFDVSRGVRLVTFAMHW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      ++I      +       + R   K         IAKKL +  E V
Sbjct: 118 IKAEIHEYVIRNWRLVKIATTKAQRKLFFNLNSLRPEGKSLDNDDIVGIAKKLNVRPEDV 177

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--- 619
            ++ K ++   I+L+T + ++D      ++ D  A  P +  +     +   + L S   
Sbjct: 178 VEMEKRMSGHDIALDTLMDEDDDYAPIQYLADDEAYEPENVMLAQEHDKLENQGLKSALD 237

Query: 620 -LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R   ++  R+   ++ D  TL ++  Q+ V+ ERIRQIE  AI+K++
Sbjct: 238 QLDDRSRHIIESRW---LSEDKPTLHDLAAQYNVSAERIRQIENAAIKKMR 285


>gi|225628325|ref|ZP_03786359.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
 gi|225616171|gb|EEH13219.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
          Length = 278

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 21  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 80

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 81  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 138

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 139 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGASRRMDFLVDDHPLQDEIA 198

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 199 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 255

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 256 ESRAMEKLK 264


>gi|312282731|dbj|BAJ34231.1| unnamed protein product [Thellungiella halophila]
          Length = 269

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/85 (47%), Positives = 58/85 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    A++++     RLV+S+A  Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 176 CRRREAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPERGYKLST 235

Query: 499 YAMWWVKQAITRSIADQSCTIRIPV 523
           Y  WW+KQAI R+IA +S  +++P+
Sbjct: 236 YVYWWIKQAILRAIAHKSRLVKLPL 260


>gi|89099055|ref|ZP_01171934.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
 gi|89086185|gb|EAR65307.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
          Length = 252

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 131/260 (50%), Gaps = 19/260 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +T +   E +    +++K +     A+  +V+ N+RLV SV +++ NRG +  
Sbjct: 4   EVKTDKTQTYLKDHEVKE---LIQKSQAGDQGARDTIVQKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKEMGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + +    ++    R PT  E++  L +P E +    +  + P S+   +   D D   L 
Sbjct: 120 IRKAKDELTKTFGRIPTVTELSAYLEIPPEDIILAQEAGRTPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I+D N     D  A++  +RE        L  RE  ++ +R+      D T  EV  +
Sbjct: 180 DQIDDGNDGKWFDQIALKEAIRE--------LDERERLIVYLRY----YKDQTQSEVAAR 227

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ ++ ++E K ++++K
Sbjct: 228 LGISQVQVSRLEKKILQQMK 247


>gi|299115565|emb|CBN75768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ectocarpus
           siliculosus]
          Length = 244

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/65 (60%), Positives = 53/65 (81%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK MVEAN+R+VIS+A+KY + G+   DLIQEG++GL++A EKFD   G+K STY+ WW
Sbjct: 82  AKKTMVEANMRMVISIARKYQHLGVPLTDLIQEGSLGLVRAVEKFDPERGFKLSTYSAWW 141

Query: 504 VKQAI 508
           ++QAI
Sbjct: 142 IQQAI 146


>gi|121730259|ref|ZP_01682638.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
 gi|121627991|gb|EAX60548.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
          Length = 259

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 132/245 (53%), Gaps = 20/245 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ +A+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G +
Sbjct: 17  KGDIDAA---KGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVR 73

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A
Sbjct: 74  LVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVA 131

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQAN 608
           ++L +    VR++  ++  +  + E    D++          ++EDK+  S L   ++A 
Sbjct: 132 RELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYLEDKH--SDLADNLEAE 189

Query: 609 LRE--TTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             E  TT R+   LASL  R + ++R R+ +  +   TL+++ + + V+ ERIRQ+E  A
Sbjct: 190 NWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNKTTLQDLAEMYGVSAERIRQLEKNA 248

Query: 664 IRKLK 668
           +RKLK
Sbjct: 249 MRKLK 253


>gi|20151162|pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
           Sigma Factor Spoiiab With The Sporulation Sigma Factor
           Sigmaf
          Length = 243

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 124/252 (49%), Gaps = 17/252 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ++ I   E + ++   ++G+ EA   + E++E N+RLV SV +++ NRG +  DL Q G 
Sbjct: 7   QSPIKDQEMKELIRRSQEGDQEA---RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGC 63

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    
Sbjct: 64  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE 122

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S    R PT  EIA  L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 123 LSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADAD 182

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D            + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 183 EASWFDKI-------ALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQM 231

Query: 657 RQIEAKAIRKLK 668
            ++E K ++ +K
Sbjct: 232 SRLEKKILQHIK 243


>gi|299472120|emb|CBN77105.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 555

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 45/128 (35%), Positives = 81/128 (63%), Gaps = 4/128 (3%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A++ +V AN+ L++ +A+++      RG    D+IQEG++ +++AAE FD  LGY+FSTY
Sbjct: 240 AQERIVGANVGLIVVMARRHHPATMARGTITSDVIQEGSLAVLRAAETFDPRLGYRFSTY 299

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+  +TR +  Q+  IR+P ++ +       T   +  ++ R PT +EIA+++ + 
Sbjct: 300 AGWWVRDRVTRCVTQQARIIRLPQYVHNFRRTASMTEAALLKELGRRPTYDEIAERMRVD 359

Query: 560 VEGVRKVL 567
           VE V +++
Sbjct: 360 VERVTRLM 367


>gi|317128506|ref|YP_004094788.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473454|gb|ADU30057.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
          Length = 252

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 127/244 (52%), Gaps = 14/244 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +  ++++ +  A  A+ ++V AN RLV SV +++ NRG +  DL Q G IGL+K+ +K
Sbjct: 18  KEVKRLIKEAQDGAQEARDQIVNANTRLVWSVVQRFLNRGYEADDLFQIGCIGLIKSVDK 77

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    +S  + R P
Sbjct: 78  FDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSIKESANKIRKMKEELSKTLGRTP 136

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAI 605
           T  EIA+KL +  E V    + +++  S+   +   D D   L D I D   +   D   
Sbjct: 137 TVNEIAEKLDLTPEEVVFAQEASRQLTSIHETVYENDGDPITLLDQISDDGDMKWFD--- 193

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  LR+   +    L  RE+ ++ +R+      D T  +V ++  +++ ++ ++E K ++
Sbjct: 194 KIALRDEIDK----LDEREKLIVYLRY----YKDQTQSQVAERLGISQVQVSRLEKKILK 245

Query: 666 KLKH 669
            LK 
Sbjct: 246 VLKE 249


>gi|90412724|ref|ZP_01220725.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90326299|gb|EAS42718.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 286

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/276 (26%), Positives = 141/276 (51%), Gaps = 22/276 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++VE    ++E  H       G+ EA+   K +V +++R V+ VA+ 
Sbjct: 16  LDSYIQTVNRHPMLTVEQEKELAERLHY-----DGDIEAA---KGLVMSHMRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++  +  + E P
Sbjct: 128 TTKAQRKLFFNLRKSKKRLGWFNNAE--VEMVAEQLGVNPSEVREMESRLAAQDPAFELP 185

Query: 580 IGDED----TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             D+D     +    F+EDK    A+S  ++  + +     +  LA L  R + ++R R+
Sbjct: 186 NEDDDRDAGYTAPVYFLEDKASDVALSYEENNWENHTNNRLSNALAGLDERSQHIVRSRW 245

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                T  TL+++   + ++ ER+RQ+E  A++KLK
Sbjct: 246 LDDEKT--TLQDLANHYGISAERVRQLEKNAMKKLK 279


>gi|261219345|ref|ZP_05933626.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222881|ref|ZP_05937162.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315875|ref|ZP_05955072.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316262|ref|ZP_05955459.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322406|ref|ZP_05961603.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|265987326|ref|ZP_06099883.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998840|ref|ZP_06111397.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|260921465|gb|EEX88118.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924434|gb|EEX91002.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261295096|gb|EEX98592.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295485|gb|EEX98981.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261304901|gb|EEY08398.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|262553529|gb|EEZ09298.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659523|gb|EEZ29784.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 293

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 96  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 214 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|254487022|ref|ZP_05100227.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
 gi|214043891|gb|EEB84529.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
          Length = 277

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 125/261 (47%), Gaps = 34/261 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KFD   G +FSTYA+WW
Sbjct: 26  ALHRLITAYMRLAISMAGKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWW 85

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +K +I   +      +R         +  +MR    ++ R A+     + +    + I+ 
Sbjct: 86  IKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMIST 145

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDE------------DTSHLGDFIEDKNAVSPL 601
           ++ +P+  V  +  +++    SL      E            DT+   + +E+ + +   
Sbjct: 146 EIGVPMHDVEMMEGRLSGSDYSLNATQSSEDEGREWIDALVDDTAQAAERVEESHDI--- 202

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  LR      + +L  RE+ ++R R     +   TLE +G++  +++ER+RQ+EA
Sbjct: 203 -----VTLRNWLLGAMQALNDREQFIVRER--KLRDQPRTLESLGQELNLSKERVRQLEA 255

Query: 662 KAIRKLKHP--SRSKKLRSFL 680
            A  K++    ++S ++  FL
Sbjct: 256 AAFAKMRKTLETQSAEVHHFL 276


>gi|85704966|ref|ZP_01036066.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670288|gb|EAQ25149.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 279

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 119/241 (49%), Gaps = 13/241 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 30  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWW 89

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-- 560
           ++ +I   I      +++     + K+   +R A+     ++      E+ KK+A  +  
Sbjct: 90  IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKAKIGALEDGDMRPEVVKKIATDLGV 149

Query: 561 ---EGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANL---RET 612
              E +    ++     SL   +G E    +   D++ED++A    D   +  +   RE 
Sbjct: 150 TEAEVISMNQRMAGADASLNATVGSEGEGSMQWQDWLEDEDADQAGDYERRDEMDARREL 209

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            T  +  L  RE  +L  R     +   TLE++  ++ V+RERIRQIE +A  KL+   R
Sbjct: 210 LTMAMDVLNERERDILTQRR--LSDETVTLEDLSAEYDVSRERIRQIEVRAFEKLQKRMR 267

Query: 673 S 673
           +
Sbjct: 268 A 268


>gi|261754167|ref|ZP_05997876.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743920|gb|EEY31846.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 293

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------RE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 96  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 214 ESSIDMERRNCWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|163941815|ref|YP_001646699.1| sporulation sigma factor SigF [Bacillus weihenstephanensis KBAB4]
 gi|229013283|ref|ZP_04170424.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
 gi|229061746|ref|ZP_04199079.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|229134882|ref|ZP_04263689.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|229168817|ref|ZP_04296536.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|163864012|gb|ABY45071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614665|gb|EEK71771.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|228648557|gb|EEL04585.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|228717492|gb|EEL69156.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|228748050|gb|EEL97914.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
          Length = 252

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 127/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +KV +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKVRKMRDELSKEFGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D++     D  A++  
Sbjct: 140 VAQALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQIADQSETKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|225574676|ref|ZP_03783286.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038103|gb|EEG48349.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
          Length = 239

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 127/242 (52%), Gaps = 12/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++ +       A+  + E N+ L+ S+ K++ NRG++  DL Q G+IGL+KA +KF
Sbjct: 5   HTLALIARAHQGDKEARDTIFEENIGLIWSIVKRFQNRGVELEDLFQIGSIGLLKAVDKF 64

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      ++  ++ R+P 
Sbjct: 65  DLSYDVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKEVCYKAYLAREKLEKELGRDPQ 123

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             E+A ++ +P E +   L    E  SL+  I  G+ +   L D +E+K   +  + ++ 
Sbjct: 124 IAEMAGEIGIPQEELMMALDSNVEIESLQKTIYQGEGNDIRLIDKLEEKK--NRQEESLN 181

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L E    +L  LT  E R++ MR+      + T  E+ ++  V++ ++ ++E K +++
Sbjct: 182 RILLEE---ILGQLTVSERRLIYMRY----FQERTQTEIARELGVSQVQVSRMEKKILKR 234

Query: 667 LK 668
           L+
Sbjct: 235 LR 236


>gi|290796538|gb|ADD64839.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 286

 Score = 90.1 bits (222), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/140 (40%), Positives = 84/140 (60%), Gaps = 4/140 (2%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSSVF 105
           N  LP D V  EQMED ++M++ MGI+V     D + L   +G+  + ++  +A+  +  
Sbjct: 1   NDHLPDDLVDPEQMEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAA 60

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
                D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ +
Sbjct: 61  ALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTE 120

Query: 166 ALIIWRDELNDGTTLLREII 185
            L+   +   +G   L EI+
Sbjct: 121 MLLADYEAHKEGKKRLAEIV 140


>gi|319404792|emb|CBI78393.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 247

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 121/241 (50%), Gaps = 29/241 (12%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD   G +FSTYA WW++ 
Sbjct: 3   QIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWWIRA 62

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRM-------SNKIKREPTPEEIAKKLAMP 559
           +I   I      +R       K   +    RR+        N + ++     I++KL + 
Sbjct: 63  SIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLAQDDNTLTKQEIFRAISEKLGVS 120

Query: 560 VEGVRKV---LKITKEPISL------ETPIGDEDTSHLGDFIEDKNAV-SPLDSAIQANL 609
           V  V K+      T   +SL      ETPI   D+      I+D     S ++ AI    
Sbjct: 121 VNDVEKMDFRFSGTDNSLSLSISENGETPIAKMDS-----LIDDHPLPDSVIEQAIDGQR 175

Query: 610 R-ETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           R +     L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIE +A++KL
Sbjct: 176 RAQWLHEALQILNERELEIIRFR---RLNEEGTTLEVLGEKLGISKERVRQIEVRALQKL 232

Query: 668 K 668
           +
Sbjct: 233 R 233


>gi|218710915|ref|YP_002418536.1| RNA polymerase factor sigma-32 [Vibrio splendidus LGP32]
 gi|218323934|emb|CAV20295.1| RNA polymerase sigma-32 factor [Vibrio splendidus LGP32]
          Length = 303

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 141/279 (50%), Gaps = 26/279 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ +    ++E  H      KGE +A+   K ++ ++LR V+ VA+ 
Sbjct: 34  LDSYIRSANSYPMLTPDEERGLAERLHY-----KGEIDAA---KGLILSHLRFVVHVARG 85

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I 
Sbjct: 86  YSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIA 145

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + ++ +R+      E   E +A++L +    VR++  ++  +  + E P
Sbjct: 146 TTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDATFEAP 203

Query: 580 IGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTR-----VLASLTPREERVLRM 630
           + D+D          ++EDK   S +   ++A   E+ T       L SL  R + ++R 
Sbjct: 204 MDDDDGGSAYTAPVYYLEDK--ASDVAETVEAANWESHTNNRLGLALKSLDERSQHIVRS 261

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    +   TL+++   + ++ ER+RQ+E  A++KLK 
Sbjct: 262 RWLD--DNKATLQDLADTYSISAERVRQLEKNAMKKLKQ 298


>gi|311068942|ref|YP_003973865.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
 gi|310869459|gb|ADP32934.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
          Length = 255

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 119/227 (52%), Gaps = 14/227 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD     +FSTYA+  
Sbjct: 33  ARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D   T+++   +++  +K+ R    +S    R PT +EIA+ L +  E V
Sbjct: 93  IIGEIQRFIRDDG-TVKVSRSLKELGNKIRRAKDELSKTYGRVPTVQEIAEHLEIDAEDV 151

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
               +  + P S+   +   D D   L D I D +     D   +  L+E     ++ L 
Sbjct: 152 VLAQEAVRAPSSIHETVYENDGDPITLLDQIADHSEEKWFD---KIALKEA----ISDLE 204

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 205 EREKLIVYLRY----YKDQTQSEVAERLGISQVQVSRLEKKILKQIK 247


>gi|260755457|ref|ZP_05867805.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758679|ref|ZP_05871027.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260884475|ref|ZP_05896089.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214728|ref|ZP_05929009.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261750913|ref|ZP_05994622.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|265984775|ref|ZP_06097510.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294851008|ref|ZP_06791684.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
 gi|260668997|gb|EEX55937.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260675565|gb|EEX62386.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260874003|gb|EEX81072.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916335|gb|EEX83196.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261740666|gb|EEY28592.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|264663367|gb|EEZ33628.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294821651|gb|EFG38647.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
          Length = 293

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------RE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 96  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 214 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|258543198|ref|YP_003188631.1| RNA polymerase factor sigma-32 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256634276|dbj|BAI00252.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637336|dbj|BAI03305.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640388|dbj|BAI06350.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643445|dbj|BAI09400.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646500|dbj|BAI12448.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649553|dbj|BAI15494.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652539|dbj|BAI18473.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655597|dbj|BAI21524.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 319

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 125/245 (51%), Gaps = 20/245 (8%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+ +A+    ++V ++LRLV  +A  Y   GL   +LI EGNIG+M+A ++FD   G++
Sbjct: 65  KGDVKAA---HQLVTSHLRLVAKIAMGYRGYGLPINELISEGNIGMMQAVKRFDPEKGFR 121

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE 551
            +TYAMWW++ AI   I      +++      K  K+    RR+  +++     +  PE+
Sbjct: 122 LATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK--KLFFNLRRLKGQMQAIDDGDLKPEQ 179

Query: 552 ---IAKKLAMPVEGVRKVLKITKEP-ISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              IA  L +  + V  + +    P  SL  P+  D+D+      ++D      + +  +
Sbjct: 180 VNKIATTLGVSEQDVVDMNRRMAAPDHSLNAPMRADQDSEWQDRLVDDHTNQEDVYAENE 239

Query: 607 --ANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKA 663
             +  +   +  + +L  RE R+   R    +  D  TLEE+  ++ ++RER+RQIE +A
Sbjct: 240 ELSGRKALLSSAMENLNERERRIFTER---RLKDDPSTLEELAHEYGISRERVRQIEVRA 296

Query: 664 IRKLK 668
             K++
Sbjct: 297 FEKVQ 301


>gi|126729201|ref|ZP_01745015.1| RNA polymerase sigma factor [Sagittula stellata E-37]
 gi|126710191|gb|EBA09243.1| RNA polymerase sigma factor [Sagittula stellata E-37]
          Length = 298

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 123/250 (49%), Gaps = 21/250 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E + A  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +
Sbjct: 43  EDEDTQAAHQLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLA 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPE 550
           TYAMWW++ +I   I      +++      K  K+    R+  ++I        R    E
Sbjct: 103 TYAMWWIRASIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKSRIGALEDGDLRPEHVE 160

Query: 551 EIAKKLAMPVEGVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
           +IA  L +  + V  +  +++    SL   +G   E T    D++ED++A    + A + 
Sbjct: 161 KIATDLGVTQDEVISMNRRLSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGEYAERN 220

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAK 662
            L   R    + +  L  RE  +L  R      +D   TLEE+  Q+ V+RERIRQIE +
Sbjct: 221 ELEARRALLEQAMDVLNDRERDILSQR----RLSDQAVTLEELSGQYDVSRERIRQIEVR 276

Query: 663 AIRKLKHPSR 672
           A  KL+   R
Sbjct: 277 AFEKLQKRMR 286


>gi|87201057|ref|YP_498314.1| RNA polymerase factor sigma-32 [Novosphingobium aromaticivorans DSM
           12444]
 gi|87136738|gb|ABD27480.1| RNA polymerase, sigma 32 subunit, RpoH [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 299

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KF+   G++ +TYAMWW
Sbjct: 52  AAAQLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----REPTPEE---IAKKL 556
           +K ++   I      +++      K  K+    RRM   ++     +  P++   IA  L
Sbjct: 112 IKASMQEFILRSWSLVKMGTTAAQK--KLFFNLRRMKKNLEAFEDSDLHPDDVRKIATDL 169

Query: 557 AMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +P + V  + +  +     SL   + ++      D++ D     PL     A+  E   
Sbjct: 170 GVPEQEVVNMNRRMMMGGDASLNVSMREDGEGSWQDWLTDDR---PLQDETVADAEEAQY 226

Query: 615 R------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R       + SL  RE  +L  R  I  +   TLEE+ + + V+RER+RQIE +A  KL+
Sbjct: 227 RHELLVEAMESLNERERHILTDRRLI--DDPKTLEELSQVYNVSRERVRQIEVRAFEKLQ 284


>gi|4972297|dbj|BAA78111.1| RNA polymerase sigma subunit SigD* [Arabidopsis thaliana]
 gi|16649075|gb|AAL24389.1| sigma-like factor [Arabidopsis thaliana]
 gi|21387209|gb|AAM48008.1| sigma-like factor [Arabidopsis thaliana]
          Length = 267

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/85 (47%), Positives = 58/85 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    A++++     RLV+S+A  Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 174 CRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLST 233

Query: 499 YAMWWVKQAITRSIADQSCTIRIPV 523
           Y  WW+KQAI R+IA +S  +++P+
Sbjct: 234 YVYWWIKQAILRAIAHKSRLVKLPL 258


>gi|271969498|ref|YP_003343694.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270512673|gb|ACZ90951.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 266

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 109/214 (50%), Gaps = 11/214 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VE +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   +
Sbjct: 42  RDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLGRGVEFSTYATPTI 101

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    + +    +S +  R PT  E+A  L M  E V 
Sbjct: 102 VGEIKRHFRDKGWAVRVPRRLQELKLSLTKAISELSQREGRAPTVGELAAFLKMSEEEVL 161

Query: 565 KVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASL 620
           + L+       +SL+ P  GD+D   + D      ++  +D +++    RE+   +L  L
Sbjct: 162 EGLESANAYSTVSLDAPDSGDDDAPAVAD------SLGIVDDSLEGVEYRESLKPLLERL 215

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 216 PPREKRILLLRFFGNMTQSQIATELGISQMHVSR 249


>gi|153854687|ref|ZP_01995937.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
 gi|149752791|gb|EDM62722.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
          Length = 258

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 24/234 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E ++ NLRLV+SV +++   G    DL Q G IGL+KA   F+  L  KFSTYA+  
Sbjct: 38  AKEEYIKGNLRLVLSVIRRFGASGENPDDLFQIGCIGLIKAINNFNTELEVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        K ++EPT +EIA+++ +  E +
Sbjct: 98  IIGEIRRYMRDNN-SIRVSRSLRDTAYKAIYAKENYMKKNQKEPTVQEIAEEIGISKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE------TTTR 615
              L   + P+SL+ P+ ++  D  ++ D + D           Q N  E      +   
Sbjct: 157 VFALDAIQVPMSLQEPVYNDGGDALYVMDQLSD-----------QTNKEEKWIEDLSLEE 205

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  L  RE  ++++RF  G     T  EV  +  +++ ++ ++E  A++ ++ 
Sbjct: 206 AMKHLGERERYIIKLRFFQG----KTQMEVADEIQISQAQVSRLEKNALKTMRQ 255


>gi|194367438|ref|YP_002030048.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia
           R551-3]
 gi|194350242|gb|ACF53365.1| RNA polymerase, sigma 32 subunit, RpoH [Stenotrophomonas
           maltophilia R551-3]
          Length = 291

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 116/243 (47%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLALGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWMNAAEVSAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----------------- 605
            K L ++ +E + +E+ +   D        ED     P  +A                  
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDAPTDEDNEHAPPSPAAYLVANDEDPSMAYERADS 224

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + N  +     LA L  R   ++R R+ +  ++  TL+E+  ++ V+ ERIRQ+EA A++
Sbjct: 225 EDNQMQLLREGLAELDARSRDIIRRRW-LDADSKVTLQELADEYGVSAERIRQVEANALK 283

Query: 666 KLK 668
           K+K
Sbjct: 284 KMK 286


>gi|117618742|ref|YP_854903.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560149|gb|ABK37097.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 284

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 128/241 (53%), Gaps = 16/241 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G + 
Sbjct: 46  GDLEAA---RQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPSVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   +      +++     + K+   +R +++    +  E   + +A  
Sbjct: 103 VSFAVHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWLNHEEV-QAVAAD 161

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA-NLRE 611
           L +    V ++  +++    + +    DE+        ++EDK+  S L + I+  N  +
Sbjct: 162 LGVSAADVTEMEARMSNYDQAFDLVGDDEEEGGFAPVHYLEDKS--SDLAATIENDNWDD 219

Query: 612 TTTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             TR     LA+L  R + ++R R+ +   +  TL+E+   + V+ ER+RQ+E  A++KL
Sbjct: 220 HATRRLSSALATLDERSQHIIRARW-LDDESKTTLQELADTYGVSAERVRQLEKNALKKL 278

Query: 668 K 668
           K
Sbjct: 279 K 279


>gi|261210147|ref|ZP_05924444.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
 gi|260840687|gb|EEX67236.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
          Length = 286

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 127/237 (53%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      ++I      R     + ++ +R+      E   E +A++L +   
Sbjct: 109 IKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVARELGVEPS 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRE--TTT 614
            VR++  ++  +  + E    D++          ++EDK+  S L   ++A   E  TT 
Sbjct: 167 EVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYLEDKH--SDLADNLEAENWEAHTTQ 224

Query: 615 RV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+   LASL  R + ++R R+ +  +   TL+++ + + V+ ERIRQ+E  A+RKLK
Sbjct: 225 RLSMALASLDERSQHIVRARW-LDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRKLK 280


>gi|182677344|ref|YP_001831490.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633227|gb|ACB94001.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 299

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 113/236 (47%), Gaps = 16/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 47  AAQRLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  ++I        R      IA +L
Sbjct: 107 IRASIQEYILRSWSLVKMGTTASQK--KLFFNLRKAKSQISALDEGDLRPDQVALIATRL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRETT 613
            +  + V  + +      SL  P+ +E      D++ D  A       D    AN     
Sbjct: 165 GVTGQEVIDMNRRMSGDASLNAPLREEGEGEWQDWLVDDQANQEHVLADQEESANRLGAL 224

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + L  L PRE R+   R    +  D  TLE +  +F ++RER+RQIE +A  K++
Sbjct: 225 RQALDVLNPRERRIFEAR---RLADDPVTLEALSDEFDISRERVRQIEVRAFEKVQ 277


>gi|86742435|ref|YP_482835.1| sigma 28 subunit [Frankia sp. CcI3]
 gi|86569297|gb|ABD13106.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Frankia sp. CcI3]
          Length = 338

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 110/220 (50%), Gaps = 9/220 (4%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E S  + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ ++FD   G +FS
Sbjct: 107 DPERSAVRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVEFS 166

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   +   I R   D+   IR+P  +++    + +    +S  + R PT  EIA+ L 
Sbjct: 167 TYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQTLGRSPTVSEIARHLQ 226

Query: 558 MPVEGVRKVLKITK--EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           M  + V + L+       +SL+ P  GD++   + D +  ++     +S      RE+  
Sbjct: 227 MSEDDVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD-----ESLEGVEYRESLK 281

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            +L  L  RE+R+L +RF   M       E+G  Q  V+R
Sbjct: 282 PLLEKLPAREKRILLLRFFGNMTQSQIATELGISQMHVSR 321


>gi|119715629|ref|YP_922594.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536290|gb|ABL80907.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 260

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 111/227 (48%), Gaps = 14/227 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  N+ +    A++Y  RG+   DL Q   +GL+KA   F+   G+ F ++A+  +
Sbjct: 27  RDEIVRLNMGVASDCARRYRQRGIATEDLDQVAYLGLVKAVRGFEPGRGHDFLSFAVPTI 86

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  + R   D    +R P  +++   ++      +S ++ R P P ++A+ L + +E V 
Sbjct: 87  RGEVRRHFRDLGWALRPPRSIQELQSRIHAAEGDLSQELGRSPRPSDLARHLGVDLEQVL 146

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLT 621
             L  T    P SL+    D D S LGD +         D A  QA  R T   VL  LT
Sbjct: 147 DALGATGCFAPASLDVVGADGDDS-LGDRL------GTADPAFDQAEARITLAAVLRGLT 199

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           PRE R+L +RF      +HT  E+G    VT+ ++ ++  + + +L+
Sbjct: 200 PRERRILELRF----FGNHTQAEIGADIGVTQMQVSRLLNRILARLR 242


>gi|26987129|ref|NP_742554.1| RNA polymerase sigma factor RpoD [Pseudomonas putida KT2440]
 gi|148545673|ref|YP_001265775.1| RNA polymerase sigma factor RpoD [Pseudomonas putida F1]
 gi|24981760|gb|AAN66018.1|AE016231_1 RNA polymerase sigma factor RpoD [Pseudomonas putida KT2440]
 gi|2654492|gb|AAB87749.1| DNA-directed RNA polymerase sigma subunit [Pseudomonas putida]
 gi|2731762|gb|AAC38073.1| sigma-70 [Pseudomonas putida]
 gi|148509731|gb|ABQ76591.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida F1]
 gi|313496752|gb|ADR58118.1| RpoD [Pseudomonas putida BIRD-1]
          Length = 616

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     +
Sbjct: 12  KELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAE 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDYIL 147


>gi|300788069|ref|YP_003768360.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299797583|gb|ADJ47958.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 273

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 57/228 (25%), Positives = 122/228 (53%), Gaps = 14/228 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++  +L L   +A++++ RG  F DL+Q    GL++A +++    G  F ++A+  +
Sbjct: 50  RERLITEHLPLAEHIARRFSGRGEPFEDLLQVARTGLIRAVDRYAADRGSDFVSFAVPTI 109

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D   ++R+P  ++D   K+ + +  +++++ R PTP E+A+ L + +E VR
Sbjct: 110 MGEVRRHFRDVGWSMRVPRALKDLKQKLAKASDVLAHELGRAPTPSELARHLDLDIETVR 169

Query: 565 KVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + L   +     SL+TP   G++D +  G   ED +     ++ I   LR      +A+L
Sbjct: 170 EGLLAAQAYRATSLDTPAREGEDDFAAAGRLAEDDSGFERFENHIA--LRA----AMATL 223

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PRE  +++MRF   +    T  ++ ++  V++  + ++ AK + +L+
Sbjct: 224 EPRERAIVKMRFADEL----TQSQIAQRIGVSQMHVSRLLAKTLEQLR 267


>gi|113461681|ref|YP_719750.1| RNA polymerase factor sigma-32 [Haemophilus somnus 129PT]
 gi|112823724|gb|ABI25813.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 129PT]
          Length = 280

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 123/231 (53%), Gaps = 10/231 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKTLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+     +E   + +A +L +  E
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFSDKE--VDMVANELGVSKE 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDK--NAVSPLDS-AIQANLRETTTRVL 617
            V ++  ++T   +  + P+ D+++     ++EDK  N  + L++   +    +     L
Sbjct: 167 DVLEMESRMTGSDVGFDLPVDDDESYAPALYLEDKSSNFAAELENENFETQAADQVANAL 226

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A L  R + +++ R+    +   TL ++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 227 AELDERSQDIIKSRWLD--DEKATLHDLAAKYNISAERVRQLETNALKKLK 275


>gi|289769170|ref|ZP_06528548.1| SigH protein [Streptomyces lividans TK24]
 gi|289699369|gb|EFD66798.1| SigH protein [Streptomyces lividans TK24]
          Length = 361

 Score = 89.7 bits (221), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 10/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 138 RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTV 197

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S    R PT  E+A+KL++  E V 
Sbjct: 198 VGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAEKLSISEEEVL 257

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLT 621
           + L+       +SL+ P  D+++  + D +  +      D A++    RE+   +L  L 
Sbjct: 258 EGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESLKPLLEDLP 311

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 312 PREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 344


>gi|189024846|ref|YP_001935614.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|189020418|gb|ACD73140.1| Sigma-70 factor family [Brucella abortus S19]
          Length = 306

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/252 (30%), Positives = 128/252 (50%), Gaps = 25/252 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 49  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 108

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 109 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 166

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPL-- 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D +   PL  
Sbjct: 167 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDH---PLQD 223

Query: 602 ---DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERI 656
              +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+
Sbjct: 224 EIAESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERV 280

Query: 657 RQIEAKAIRKLK 668
           RQIE++A+ KLK
Sbjct: 281 RQIESRAMEKLK 292


>gi|154686587|ref|YP_001421748.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens FZB42]
 gi|308174131|ref|YP_003920836.1| RNA polymerase sporulation-specific sigma factor sigma-F [Bacillus
           amyloliquefaciens DSM 7]
 gi|63146682|emb|CAG28933.1| Sigma F [Bacillus amyloliquefaciens FZB42]
 gi|154352438|gb|ABS74517.1| SigF [Bacillus amyloliquefaciens FZB42]
 gi|307606995|emb|CBI43366.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328552736|gb|AEB23228.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens TA208]
 gi|328912466|gb|AEB64062.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 255

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/259 (27%), Positives = 132/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  S    +   E + ++   ++G+ +A   +  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNSKNAQLKDHEVKELIKKSQEGDQQA---RDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + R    +S    R PT +EIA  L +  E V    +  + P S+   +   D D   L 
Sbjct: 120 IRRAKDELSKTYGRVPTVQEIADHLEIDAEDVVLAQEAVRAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D +     D   +  L+E     ++ L  RE+ ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADHSEEKWFD---KIALKEA----ISDLEEREKLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQIK 247


>gi|83590339|ref|YP_430348.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83573253|gb|ABC19805.1| RNA polymerase, sigma subunit, RpoX/SigF [Moorella thermoacetica
           ATCC 39073]
          Length = 270

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 125/241 (51%), Gaps = 16/241 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R+ +     A++ ++  NL+LV ++ +++  R  +  DL Q G IGL+KA +KFD   
Sbjct: 22  LLRRAKAGDKEARERLINCNLKLVFNLVQRFEKRNYELEDLFQIGTIGLIKAIDKFDLSY 81

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D S  +++   +++   KV RT   ++ K  REP   EI
Sbjct: 82  KVRFSTYAVPMILGEIRRFLRDDSA-VKVSRSLKETAFKVNRTREELAKKFGREPAIGEI 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP--LDSAIQAN 608
           A+ L +  E +   L+  + P S+   +   D D  ++ D +  ++   P  LD   +  
Sbjct: 141 AEALDLSREEIIAALEAVQMPSSIHDTVYQDDGDPIYVLDQLASEDGEEPEWLD---KIA 197

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL  L  +  RVL +RF      D T  EV  +  +++ +I +IE +A+++++
Sbjct: 198 LKE----VLRQLPEKHRRVLVLRF----FQDKTQAEVAARMGLSQVQISRIERQALQRIR 249

Query: 669 H 669
            
Sbjct: 250 E 250


>gi|70732951|ref|YP_262722.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
 gi|1710687|sp|P52326|RPOD_PSEFL RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|929808|emb|CAA59134.1| sigma 70 [Pseudomonas fluorescens]
 gi|68347250|gb|AAY94856.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
          Length = 615

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     +
Sbjct: 12  KELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAE 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|168187412|ref|ZP_02622047.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
 gi|169294714|gb|EDS76847.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
          Length = 251

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 124/241 (51%), Gaps = 14/241 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++K +     A  E+VE NL LV +++KK+ NRG ++ D+ Q G++GL+KA   FD 
Sbjct: 17  LELIKKAKLGDKKALDELVEKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R I D    I++   ++    K+     +++ K+ REPT E
Sbjct: 77  SYNVQFSTYAVPMIMGEIRRFIRDDGL-IKVSRSVKYTARKLHFDKEKLTKKLHREPTLE 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQA 607
           E++K   +  E +   ++   EP  L   I  +D S +  ++ DK  V   S +D   + 
Sbjct: 136 ELSKFSGIEKEQIIFAMEAINEPKYLYDTIHQDDGSPI--YLIDKVVVKDESEVDELDKI 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E     L  L  R  +++ +R+      D T  +V K   +++ ++ +IE K ++ +
Sbjct: 194 ALKEA----LNKLDQRSRQIIILRYF----KDITQVKVAKMLGISQVQVSRIEKKVLKTM 245

Query: 668 K 668
           K
Sbjct: 246 K 246


>gi|256785278|ref|ZP_05523709.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 354

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 10/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 131 RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTV 190

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S    R PT  E+A+KL++  E V 
Sbjct: 191 VGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAEKLSISEEEVL 250

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLT 621
           + L+       +SL+ P  D+++  + D +  +      D A++    RE+   +L  L 
Sbjct: 251 EGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESLKPLLEDLP 304

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 305 PREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 337


>gi|73667010|ref|YP_303026.1| sigma-70 region 2:sigma-70 region 4 [Ehrlichia canis str. Jake]
 gi|72394151|gb|AAZ68428.1| RNA polymerase, sigma 32 subunit, RpoH [Ehrlichia canis str. Jake]
          Length = 300

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/256 (28%), Positives = 125/256 (48%), Gaps = 48/256 (18%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ +A  + N GL  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K +
Sbjct: 57  LVTSHLRLVVKIALSFKNYGLPLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKAS 116

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLA-------MP 559
           I   I      I+I      +  K+  + R++  K+ K     ++  K +A         
Sbjct: 117 IKDYILKSWSCIKIGTTQAQR--KLFFSLRKIKQKLFKYNNITQDDIKLIANECSTSEQE 174

Query: 560 VEGVRKVLKI-------------------TKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           VE + +                        +E I  +TP   EDT  L +          
Sbjct: 175 VEQMNRYFTYRDRSLNEVVFSNDNQKGIELQEIIKCDTP-NQEDTYLLNE---------- 223

Query: 601 LDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                +A+L+ET  T+ L++L  R   +  +R  +  N D TL+ + +++ +++ER+RQI
Sbjct: 224 -----EASLKETLITQALSTLNERYRDIF-IRRRLIENPD-TLDTLSQEYKISKERVRQI 276

Query: 660 EAKAIRKLKHPSRSKK 675
           E  A  K+K+    KK
Sbjct: 277 EMHAFTKVKNFIMLKK 292


>gi|58617131|ref|YP_196330.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
 gi|58416743|emb|CAI27856.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
          Length = 319

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 126/240 (52%), Gaps = 13/240 (5%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+ VA  + N GL  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K 
Sbjct: 74  KLVTSHLRLVVKVALSFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKA 133

Query: 507 AITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEG 562
           +I   I      I+I     + K+   +R  ++   K     T E+   IA + +   + 
Sbjct: 134 SIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLLKYHNNITKEDIKMIANECSTSEQE 193

Query: 563 VRKVLK-ITKEPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRET-TTR 615
           V ++ K  T    SL   +   G ++   L D I  ED N         + +++++  T+
Sbjct: 194 VEQMNKYFTYRDKSLNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQ 253

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            LA+L  R   +   R  I      TLE + K++ +++ERIRQIE  A  K+K+   SK+
Sbjct: 254 ALATLNERHRDIFIRRKLI--EEPDTLEILSKKYNISKERIRQIETHAFLKVKNFVISKR 311


>gi|30248598|ref|NP_840668.1| RNA polymerase factor sigma-32 [Nitrosomonas europaea ATCC 19718]
 gi|30180193|emb|CAD84495.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 280

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/282 (28%), Positives = 135/282 (47%), Gaps = 32/282 (11%)

Query: 411 NEIKSISVETGISISEFRHIVSM--VRKGECEASIAKK-----------EMVEANLRLVI 457
           NEI ++ V  G  +  +    S   V   E EAS+AK+           ++V ++LR+V+
Sbjct: 2   NEIMALPVMAGGDLDSYIRATSSFPVLSREEEASLAKRMREEGDVNAAHQLVLSHLRVVV 61

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           ++A+ Y   GL   DLIQEGNIGLMKA  +FD   G +  ++A+ W++  I   I     
Sbjct: 62  TIARGYLGYGLPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIRAEIHEFIMRNWR 121

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKV-LKITKEPI 574
            ++I    + +  K+    R M   +      E   +A++L +  E V ++  + +   I
Sbjct: 122 LVKIATTKQQR--KLFFNLRSMKKGLDTMSQAEVASMAEQLGVKAEEVVEMETRFSGRDI 179

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSP--------LDSAIQANLRETTTRVLASLTPREER 626
           SLE P+ D D           +   P        L+    A L+ +    L SL  R  R
Sbjct: 180 SLE-PVTDSDEDDFSPIAWLTDGSDPSRELEKEQLERLTHARLKNS----LDSLDERSRR 234

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  R+ +  +   TL E+  +  V+ ER+RQIEAKA++K++
Sbjct: 235 IIEARW-LREDKAATLHELADELGVSAERVRQIEAKAMKKMR 275


>gi|21223610|ref|NP_629389.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|5912531|emb|CAB56114.2| SigH protein [Streptomyces coelicolor A3(2)]
 gi|9968693|emb|CAC05976.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 361

 Score = 89.7 bits (221), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 10/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 138 RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTV 197

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S    R PT  E+A+KL++  E V 
Sbjct: 198 VGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAEKLSISEEEVL 257

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLT 621
           + L+       +SL+ P  D+++  + D +  +      D A++    RE+   +L  L 
Sbjct: 258 EGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESLKPLLEDLP 311

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 312 PREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 344


>gi|219115846|ref|XP_002178718.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409485|gb|EEC49416.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 217

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 58/212 (27%), Positives = 109/212 (51%), Gaps = 17/212 (8%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           + ++A+  ++ +N+RLV+S+AKK+  N      + +QEG +GL KAA+++D   G +F+T
Sbjct: 6   DGALARDTLIASNVRLVVSIAKKWAKNAHKAARETVQEGILGLAKAADRYDPERGLRFAT 65

Query: 499 YAMWWVKQAITRSIADQSC-TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           YA +WV  ++       S   +R+PV   D   K  R  +   ++    P  +++A+++ 
Sbjct: 66  YATYWVTNSVRFCFQTASTGCLRVPVGFHDTKTKFKRLVKEYYDEFGDAPGIDDLAEQMG 125

Query: 558 MPVEGVRKVLKITKEPISLETPI----------GDEDTSH----LGDFIEDKNAVSPLDS 603
           +    +  +L+ T+  +S++ P+             D S     L D + D+ A+ P D 
Sbjct: 126 LTRPRLEVILRSTRPLVSIDAPLRTGAVTQAGKAGNDVSQTNLLLADLLTDEQALPPEDL 185

Query: 604 AIQANLRETTTRVLAS-LTPREERVLRMRFGI 634
              + LR+     +A+ L P E  VLR+R G+
Sbjct: 186 VELSFLRQNLENAMATELAPHERDVLRLRLGL 217


>gi|217978453|ref|YP_002362600.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
 gi|217503829|gb|ACK51238.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
          Length = 303

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 28/242 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 47  AAHKLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R++ ++I        R    ++IA +L
Sbjct: 107 IRASIQEYILRSWSLVKMGTTASQK--KLFFNLRKVKSQISALEEGDLRPEHVDKIAHRL 164

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETT 613
            +  + V  + +      SL  P+ +E      D++ D       DSA Q  L   RE T
Sbjct: 165 GVSKQDVIDMNRRMSGDASLNAPLREEGEGEWQDWLVD-------DSASQEKLLVDREET 217

Query: 614 TRVLAS-------LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              L +       L  RE R+   R     +   TLE +  +F ++RER+RQIE +A  K
Sbjct: 218 DNRLGALHTALNVLNDRERRIFEARR--LADDPMTLEALSDEFDISRERVRQIEVRAFEK 275

Query: 667 LK 668
           ++
Sbjct: 276 VQ 277


>gi|50123263|ref|YP_052430.1| RNA polymerase factor sigma-32 [Pectobacterium atrosepticum
           SCRI1043]
 gi|49613789|emb|CAG77240.1| RNA polymerase sigma-32 factor [Pectobacterium atrosepticum
           SCRI1043]
          Length = 285

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/279 (26%), Positives = 146/279 (52%), Gaps = 27/279 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++  ++  N    ++ E   +++E  H      +G+ EA+   K ++ ++LR VI VA+ 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHY-----QGDLEAA---KHLILSHLRFVIHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
               + K+   +R A+       ++   E +A++L +  + VR++  ++  + ++ + P 
Sbjct: 128 TTKAQRKLFFNLRKAKTRLGWFNQDEV-ELVARELGVTTKDVREMESRMAAQDMTFD-PT 185

Query: 581 GDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLR 629
            +ED SH G       +++DK+  S     I+ +  +T      T  L  L  R + ++R
Sbjct: 186 PEED-SHDGKAMSPMLYLQDKS--SDFADGIEEDNWDTHAADKLTYALEGLDERSQHIIR 242

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 243 ARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|304407011|ref|ZP_07388665.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343998|gb|EFM09838.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 251

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 123/246 (50%), Gaps = 17/246 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + ++++ + G+   ++++  +V  N+RLV SV +++ NRG +  DL Q G IGL+K+
Sbjct: 16  AEVKRLIALSQSGD---NVSRDTLVHCNIRLVWSVVQRFMNRGYEPEDLFQIGCIGLLKS 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    +S  + 
Sbjct: 73  VDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKETANKVRKMKDELSKTLG 131

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLD 602
           R PT  E+A+ L +  E V    +  K P S+   +   D D   L D I D +     D
Sbjct: 132 RLPTITEVAEGLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADDSQERWFD 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
               A         +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K
Sbjct: 192 KLALAE-------AIEGLAERERLIVYLRY----YRDQTQSEVASRLGISQVQVSRLEKK 240

Query: 663 AIRKLK 668
            ++ +K
Sbjct: 241 ILQLIK 246


>gi|329120658|ref|ZP_08249321.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327460882|gb|EGF07216.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 287

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 130/248 (52%), Gaps = 31/248 (12%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   K ++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G + 
Sbjct: 46  GDVEAA---KRLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPDRGARL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   I      +R+     + K+   +R+ R+  + +    +P+E A+ 
Sbjct: 103 FSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKSLSAL----SPKE-AQA 157

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------- 602
           +A  + GV+       E + +E  +   D + L D  +D+++ +P+D             
Sbjct: 158 IADDL-GVK-----LSEVMEMEQRMTGRDIALLADNSDDEDSFAPIDWLADHDNEPTRQI 211

Query: 603 --SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
              A  A   E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQIE
Sbjct: 212 ERKAHHALQTEGLQNALAKLDERSRRIVETRW-LQDDGGLTLHELAAEYGVSAERIRQIE 270

Query: 661 AKAIRKLK 668
           AKA++KL+
Sbjct: 271 AKAMQKLR 278


>gi|317497563|ref|ZP_07955881.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895122|gb|EFV17286.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 215

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 53/155 (34%), Positives = 87/155 (56%), Gaps = 3/155 (1%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A++  ++ NLRLV+S+ ++++       DL Q G IGLMKA + FD  L  KFSTYA+ 
Sbjct: 50  LAREHYIKGNLRLVLSIIQRFSGSSENADDLFQVGCIGLMKAIDNFDRNLNVKFSTYAVP 109

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   + R + D   ++R+   +RD  +K +     ++ K+  EPT + IAK++ M  E 
Sbjct: 110 MIIGEVKRYLRDNH-SMRVSRSLRDTAYKAINAREVLTKKLNHEPTIDVIAKEIDMKKED 168

Query: 563 VRKVLKITKEPISLETPIGDE--DTSHLGDFIEDK 595
           V   L     P+SL  P+  +  DT +L D ++DK
Sbjct: 169 VLFALDAIATPLSLYEPVYQDGGDTLYLMDQVKDK 203


>gi|296159716|ref|ZP_06842538.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295889930|gb|EFG69726.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 665

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 90/164 (54%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V     D + L    
Sbjct: 54  RALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQAPDAETLLLNS 113

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEIAI
Sbjct: 114 NAPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEIAI 167

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE G   M+ ++   PL   A++    ++ DG   + E++D
Sbjct: 168 AKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVD 211


>gi|144899360|emb|CAM76224.1| Sigma-70 region 2:Sigma-70 region 4:Sigma-70 region 1.2
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 291

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 121/239 (50%), Gaps = 12/239 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++ A+LRLV+  A ++   GL   DL+ EGN+GL++A E FD     +FSTYA WW
Sbjct: 44  ARTRLLSAHLRLVVKTAGQFKGYGLSGADLVAEGNLGLVRALESFDPGRNLRFSTYAQWW 103

Query: 504 VKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTAR-RMS----NKIKREPTPEEIAKKLA 557
           V+ A+   +   S  +   +   R K+   +R  + R++    N +    T  ++A +L 
Sbjct: 104 VRAAMFEYVLKFSTPVNFGLSAERKKLFFKLRGIKARLTGPSGNALSVAETA-QVADELG 162

Query: 558 MPVEGVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTT 614
           +  + V ++ + +T+ P SL+ P+G+          +D+ +V       Q  +  RE   
Sbjct: 163 VRDQRVAEMERLLTQSPRSLDAPVGESGIPFGELLADDRPSVEETLGERQELMYRRELLK 222

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                LT RE  ++  R          LE++ +++ ++RER+RQIE  A+ KLK   R+
Sbjct: 223 HAWEGLTERERDIVAQR--TLRENPLRLEDLAQRYSISRERVRQIEGSALTKLKALVRA 279


>gi|118443643|ref|YP_877879.1| sporulation sigma factor SigF [Clostridium novyi NT]
 gi|118134099|gb|ABK61143.1| RNA polymerase sigma-F factor [Clostridium novyi NT]
          Length = 251

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 124/241 (51%), Gaps = 14/241 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++K +     A  E+VE NL LV +++KK+ NRG ++ D+ Q G++GL+KA   FD 
Sbjct: 17  LELIKKAKLGDKKALDELVEKNLPLVTAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R I D    I++   ++    K+     +++ K+ REPT E
Sbjct: 77  SYNVQFSTYAVPMIMGEIRRFIRDDGL-IKVSRSVKYTARKLHFDKEKLTKKLNREPTVE 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQA 607
           E++K   +  E +    +   EP  L   I  +D S +  ++ DK  +   S +D   + 
Sbjct: 136 ELSKFSGIDKEQIIFATEAINEPKYLYDTIHQDDGSPI--YLIDKVVLKDESEIDELDKI 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E     L+ L  R  +++ +R+      D T  +V K   +++ ++ +IE K ++ +
Sbjct: 194 ALKEA----LSKLDQRSRQIIILRYF----KDITQVKVAKMLGISQVQVSRIEKKVLKTM 245

Query: 668 K 668
           K
Sbjct: 246 K 246


>gi|229075781|ref|ZP_04208758.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
 gi|229098543|ref|ZP_04229484.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|229104680|ref|ZP_04235342.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|229117569|ref|ZP_04246941.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228665889|gb|EEL21359.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228678744|gb|EEL32959.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|228684865|gb|EEL38802.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|228707333|gb|EEL59529.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
          Length = 252

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 127/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQGGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMRDELSKEFGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D++     D  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRPPSSIHETVYENDGDPITILDQIADQSETKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|58579073|ref|YP_197285.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417699|emb|CAI26903.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 320

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 126/240 (52%), Gaps = 13/240 (5%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+ VA  + N GL  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K 
Sbjct: 74  KLVTSHLRLVVKVALSFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKA 133

Query: 507 AITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEG 562
           +I   I      I+I     + K+   +R  ++   K     T E+   IA + +   + 
Sbjct: 134 SIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLLKYHNNITKEDIKMIANECSTSEQE 193

Query: 563 VRKVLK-ITKEPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRET-TTR 615
           V ++ K  T    SL   +   G ++   L D I  ED N         + +++++  T+
Sbjct: 194 VEQMNKYFTYRDKSLNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQ 253

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            LA+L  R   +   R  I      TLE + K++ +++ERIRQIE  A  K+K+   SK+
Sbjct: 254 ALATLNERHRDIFIRRKLI--EEPDTLEILSKKYNISKERIRQIETHAFLKVKNFVISKR 311


>gi|227113845|ref|ZP_03827501.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 285

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/280 (26%), Positives = 145/280 (51%), Gaps = 29/280 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++  ++  N    ++ E   +++E  H      +G+ EA+   K ++ ++LR VI VA+ 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHY-----QGDLEAA---KHLILSHLRFVIHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+   ++    +   E +A++L +  + VR++  ++  + ++ + P
Sbjct: 128 TTKAQR--KLFFNLRKSKTRLGWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFD-P 184

Query: 580 IGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVL 628
             +ED SH G       +++DK+  S     I+ +  ET      T  L  L  R + ++
Sbjct: 185 TPEED-SHDGKAMSPMLYLQDKS--SDFADGIEEDNWETHAADKLTYALEGLDERSQHII 241

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 242 RARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|292490206|ref|YP_003525645.1| RNA polymerase sigma factor RpoD [Nitrosococcus halophilus Nc4]
 gi|291578801|gb|ADE13258.1| RNA polymerase sigma factor RpoD [Nitrosococcus halophilus Nc4]
          Length = 602

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 56/154 (36%), Positives = 82/154 (53%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I   + RGY++  E+N  LP D +  EQ+ED + M ++MGI+V +     D     D
Sbjct: 10  KLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEADALAIMD 69

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +      A+  +       D     T DPVRMY+REMGS+ELL+REGEI IAKRIE G  
Sbjct: 70  TAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEIRIAKRIEEGMR 129

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            +  +L   P +   L+   + +  G   L ++I
Sbjct: 130 QVHTALSLFPGSVAELLRQYERVEAGDARLADMI 163


>gi|256061796|ref|ZP_05451931.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 311

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------RE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYAFWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    +  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDIEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|5732893|gb|AAD49326.1|AF162936_2 RNA polymerase alternative sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 354

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 10/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 131 RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTV 190

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S    R PT  E+A+KL++  E V 
Sbjct: 191 VGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHELAEKLSISEEEVL 250

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLT 621
           + L+       +SL+ P  D+++  + D +  +      D A++    RE+   +L  L 
Sbjct: 251 EGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRESLKPLLEDLP 304

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           PRE+R+L +RF   M      +EVG  Q  V+R
Sbjct: 305 PREKRILLLRFFGNMTQSQIAQEVGISQMHVSR 337


>gi|301644085|ref|ZP_07244098.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|301077566|gb|EFK92372.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
          Length = 283

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI +A++Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 47  AAKQLILSHLRFVIHIARQYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHW 106

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           VK  I   +      +++      R     + +T +R+    + E   + +A++L + V+
Sbjct: 107 VKSEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VDMVARELGVSVK 164

Query: 562 GVRKV-LKITKEPISLETPIGDE-DTSHLGD---FIEDKNAVSPLDSAIQ-----ANLRE 611
            VR++  +++ + ++ +    DE DT H      +++DK+  S     I+     A   +
Sbjct: 165 DVREMESRMSAQDMAYDIYPDDETDTHHPVSPSLYLQDKS--SDFAGMIEEDNWDAQATD 222

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + +L PR + ++R R+ +  +   TL E+ +++ ++ ER+RQ+E  A++KL+
Sbjct: 223 HLVAAMETLDPRSQDIIRARW-LDDDNKATLHELAERYGISAERVRQLENNAMKKLR 278


>gi|330468593|ref|YP_004406336.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
 gi|328811564|gb|AEB45736.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
          Length = 292

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 115/229 (50%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 42  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E++K+L  P E +
Sbjct: 101 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATAALTSELSRAPTVAELSKRLDTPEEEI 160

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
              L+      P SL  P+G E ++  GD + + + A+  +D       R T + +L  L
Sbjct: 161 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESDIALESVDD------RVTVSGLLHRL 214

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF      + T  E+  +F +++  + ++ ++A+  L+ 
Sbjct: 215 PWRERRILAMRF----YGNQTQAEIAARFGISQMHVSRLLSRALTWLRQ 259


>gi|265995632|ref|ZP_06108189.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|262766916|gb|EEZ12534.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 293

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------RE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 96  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 214 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|196248769|ref|ZP_03147469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196211645|gb|EDY06404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 250

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 124/252 (49%), Gaps = 17/252 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ++ I   E + ++   ++G+ EA   + E++E N+RLV SV +++ NRG +  DL Q G 
Sbjct: 9   QSPIKDQEMKELIRRSQEGDQEA---RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGC 65

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    
Sbjct: 66  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE 124

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S    R PT  EIA  L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 125 LSKTRGRAPTITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIADAD 184

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  +            + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 185 EASWFEKI-------ALKKAIEELDERERLIVYLRY----YKDQTQSEVAARLGISQVQV 233

Query: 657 RQIEAKAIRKLK 668
            ++E K ++ +K
Sbjct: 234 SRLEKKILQHIK 245


>gi|187921222|ref|YP_001890254.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
           PsJN]
 gi|187719660|gb|ACD20883.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
           PsJN]
          Length = 665

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 90/164 (54%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V     D + L    
Sbjct: 54  RALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQAPDAETLLLNS 113

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEIAI
Sbjct: 114 NAPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEIAI 167

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE G   M+ ++   PL   A++    ++ DG   + E++D
Sbjct: 168 AKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVD 211


>gi|295092809|emb|CBK78916.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium cf.
           saccharolyticum K10]
          Length = 258

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 119/228 (52%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +     +  K  +EPT  EIA+++ +  E +
Sbjct: 98  ILGEVKRYLRDNN-SIRVSRSLRDTAYKAIYARESLMKKNLKEPTLCEIAEEVGVSKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   + P+SL  P+  +  D  ++ D + DK   S  +     +L E   R    L 
Sbjct: 157 TYALDAIQSPVSLYEPVYTDGGDPLYVMDQLSDKKN-SEENWIEDISLSEAMRR----LP 211

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K+
Sbjct: 212 ERERHIIGMRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKAMKN 255


>gi|319898405|ref|YP_004158498.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319402369|emb|CBI75908.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 305

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 121/238 (50%), Gaps = 16/238 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGNIGLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      ++I      K  ++    R++ NK++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKIGTTANQK--RLFFNLRKLKNKLQMFDSGDLNAEQVKEIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDF-IEDKNAVSP--LDSAIQANLRE 611
            +  + V  + +      SL  P+     ++    D+ ++D N+     ++     N   
Sbjct: 167 KVTEDEVVSMNRRLSGDASLNAPLLTNKGESYEWQDWLVDDSNSQEQILIEQDELENRHS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              + + +L  RE+R+ + R     +   TLEE+  +F ++RER+RQIE +A  K+++
Sbjct: 227 MLIQAMDNLNEREKRIFKARR--LRDEPMTLEELSNEFNISRERVRQIEMRAFEKIQN 282


>gi|331086150|ref|ZP_08335232.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406309|gb|EGG85823.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 259

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 26/235 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV K++ +      DL Q G +GLMKA + F+  L  KFSTYA+  
Sbjct: 38  ARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCVGLMKAIDNFNTDLQVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        +  +EPT EEIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIYAKEGYMKRHLKEPTVEEIAEEIGIAKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS-------PLDSAIQANLRETTT 614
              L   + P+SL  P+ ++  D  ++ D I DK            L++A++        
Sbjct: 157 IFALDAIQAPMSLNEPVYNDSGDALYVMDQISDKKNREEYWVEGLSLEAAME-------- 208

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                L  RE  ++++RF  G     T  EV  Q  +++ ++ ++E  A++ ++ 
Sbjct: 209 ----RLNERERFIIQLRFFEG----KTQMEVASQVKISQAQVSRLEKNALKTMRQ 255


>gi|172087778|ref|YP_205833.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197336399|ref|YP_002157235.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
 gi|171902364|gb|AAW86945.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197317889|gb|ACH67336.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
          Length = 286

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 135/276 (48%), Gaps = 22/276 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS L+  N    ++V     ++E  H      K E EA+   KE++ ++LR V+ VA+ 
Sbjct: 16  IDSYLRSVNSYPMLTVAEERELAERLHY-----KEEIEAA---KELILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +  +R+      E   E +AK L +    VR++  ++  +  + E P
Sbjct: 128 TTKAQRKLFFNLRKNKKRLGWFNNGE--VEAVAKDLGVAPSEVREMEARLAAQDSTFEAP 185

Query: 580 IGDEDTSHLGD----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             D+D          ++EDK    A S  +   +          +A+L  R + +++ R+
Sbjct: 186 AEDDDRDMAFTAPVYYLEDKQSDVAYSLEEDNWEDYTNNRLANAIATLDERSQHIVQSRW 245

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +   TL+E+   + V+ ERIRQ+E  A++KLK
Sbjct: 246 --LADEKATLQELADTYQVSAERIRQLEKNAMKKLK 279


>gi|329938753|ref|ZP_08288149.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329302244|gb|EGG46136.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 291

 Score = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 62  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDPDRGVEFPTF 121

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  +S K+ R PT  E+A  L + 
Sbjct: 122 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQKLDRSPTVAELAVVLGVS 181

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 182 EEDVVDGLAVGNAYTASSLDSPAPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 237

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 238 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 281


>gi|307726409|ref|YP_003909622.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
 gi|307586934|gb|ADN60331.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
          Length = 664

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 90/164 (54%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V     D + L    
Sbjct: 53  RALIQLGKEQGYLTHAQINDHLPDNFTQTAAIDSIVSAFNDMGVQVYEQAPDAETLLLNS 112

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEIAI
Sbjct: 113 NTPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEIAI 166

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE G   M+ ++   PL   A++    ++ DG   + E++D
Sbjct: 167 AKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVD 210


>gi|240850016|ref|YP_002971409.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240267139|gb|ACS50727.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 294

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 124/247 (50%), Gaps = 20/247 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYA+WW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAIWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      +++      K  ++    R++ +K++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKMGTTANQK--RLFFNLRKLKSKLQALDNGDLNAEQVKEIATQL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFI----EDKNAVSPLDSAIQANLR 610
            +  + V  + +      SL  P+   + + S L D++     D+  V    S ++ N R
Sbjct: 167 NVSEDEVISMNRRLGGDTSLNAPLRTKEGENSELQDWLVDESNDQEQVLIEKSELE-NRR 225

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 + +L  RE+R+ + R    +N    TLEE+  +F ++RER+RQIE +A  K++ 
Sbjct: 226 SMLINAMDNLNEREKRIFKAR---RLNDIPLTLEELSGEFNISRERVRQIEMRAFEKVQD 282

Query: 670 PSRSKKL 676
             R   L
Sbjct: 283 SIRDSAL 289


>gi|169334044|ref|ZP_02861237.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258761|gb|EDS72727.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
          Length = 253

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 117/234 (50%), Gaps = 29/234 (12%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E +  NLRLV+SV ++++NR     DL Q G IGL+KA + FD   G KFSTYA+  +
Sbjct: 38  KNEFIRCNLRLVLSVVQRFSNRNENMDDLFQVGCIGLIKAIDNFDVKFGVKFSTYAVPMI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRT--ARRMSNKIKREPTPEEIAKKLAMPVEG 562
              + R + D   TIR+   ++D  +K ++   A + +N     PT  EIAKKL +  + 
Sbjct: 98  IGEVRRYLRDNG-TIRVSRSLKDMAYKALKYKEAHKDTN-----PTNREIAKKLGVKEKD 151

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-------TTTR 615
           +   L    EP SL   + +++    GD      ++S +D       RE       +   
Sbjct: 152 LNFALDSIVEPCSLYDQMYNDN----GD------SISLIDQVGDEKNREENWTEKLSLKE 201

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  L  RE+ ++  R+ +G     T  EV  +  +++ ++ ++E   +RK+K+
Sbjct: 202 AVEKLKGREKEIILKRYYLG----RTQIEVANEIGISQAQVSRLEKSGLRKIKN 251


>gi|226311983|ref|YP_002771877.1| sporulation sigma factor SigF [Brevibacillus brevis NBRC 100599]
 gi|226094931|dbj|BAH43373.1| RNA polymerase sigma-F factor [Brevibacillus brevis NBRC 100599]
          Length = 251

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 124/238 (52%), Gaps = 14/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +   + A++ +V +N+RLV SV +++ NRG +  DL Q G IGL+KA +KFD   
Sbjct: 21  LIAKSQAGDTEARELLVNSNIRLVWSVVQRFINRGYEADDLFQIGCIGLLKAVDKFDLSY 80

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D   T+++   +++  +KV RT   +  +  R PT  E+
Sbjct: 81  DVRFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKVRRTKDELYKQFGRAPTIAEV 139

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  + +  E V    +  + P S+   +   D D   L D I D+      +   +  L+
Sbjct: 140 ADAVGITPEEVVFAQEANRAPSSIHETVFENDGDPITLIDQIADEGVNKWFE---KIALK 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +R    L+ RE+ ++ +R+      D T  EV ++  +++ ++ ++E + ++ +K
Sbjct: 197 DAISR----LSEREQLIVYLRY----YKDQTQSEVAERLGISQVQVSRLEKRILQTIK 246


>gi|153006912|ref|YP_001381237.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152030485|gb|ABS28253.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 238

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 118/250 (47%), Gaps = 65/250 (26%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +    R+G+  A   K E+V  NL LV+ VA+K +   L+  +L+QEG +GL++A EK
Sbjct: 27  RALALRARRGDARA---KDELVRHNLALVVMVARKQSRGALRLEELVQEGMLGLLRAIEK 83

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G +FSTYA+WW++  + + +     ++R                           
Sbjct: 84  FDPNAGTRFSTYAVWWIRAYVWKYLKQARSSVR--------------------------- 116

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
                      P  G      +    +SL+T + +E      D +ED+ A SPL+   + 
Sbjct: 117 -----------PRSGA-----VAAADLSLDTAVDEEGDVSFLDRLEDEGA-SPLERYERV 159

Query: 608 NLRETTTRVLASLTPREERVLRMRFG-IGMNTDH---------TLEEVGKQFCVTRERIR 657
              E+  R+ ASL    E+V R R G +G +  H         TLE++G+++ V+RER+R
Sbjct: 160 ---ESGERLRASL----EKV-RKRIGDLGWDIVHTRLQQDPPDTLEQIGQRWGVSRERVR 211

Query: 658 QIEAKAIRKL 667
           Q+E +  R L
Sbjct: 212 QVELQTKRFL 221


>gi|145590108|ref|YP_001156705.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048514|gb|ABP35141.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 309

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/268 (27%), Positives = 128/268 (47%), Gaps = 36/268 (13%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E  H+    R+   E   A K +V ++LRLV+SVA++Y   G+   DLIQEGNIGL
Sbjct: 49  LSAAEELHLAQEFRR--TENVDAAKTLVLSHLRLVVSVARQYLGYGIPHADLIQEGNIGL 106

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +++D   G +  +YA+ W+K  I   I      ++       K  + +    R + 
Sbjct: 107 MKAVKRYDPNNGARLVSYAIHWIKAEIHEYILKNWRLVKTAT---TKAQRKLFFNLRSNK 163

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSP 600
                 TP E        V+ + K L +    +  +E  +   D +  GD  +D++A +P
Sbjct: 164 PTLSALTPSE--------VDALAKALDVKGSDVKEMEMRLAGGDIALEGDDSDDESAYAP 215

Query: 601 LDSAIQANLRETTTRV----------------LASLTPREERVLRMRFGIGM----NTDH 640
           +   +  N +E T R+                L SL  R   +++ R+ + M    N   
Sbjct: 216 IQW-LADNTQEPTARIASAEADALQGPRLDQALMSLDERSRNIVQSRW-LAMDAEGNGTK 273

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ ++ ER+RQIE  A++K++
Sbjct: 274 TLHDLAAEYGISAERVRQIETAALKKMR 301


>gi|23502620|ref|NP_698747.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619688|ref|YP_001593575.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|254703536|ref|ZP_05165364.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|260568841|ref|ZP_05839309.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|23348625|gb|AAN30662.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336499|gb|ABX62804.1| RNA polymerase sigma factor, sigma-70 family [Brucella canis ATCC
           23365]
 gi|260154225|gb|EEW89307.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
          Length = 311

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNCWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|167842198|ref|ZP_02468882.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 680

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +  + + E++D
Sbjct: 187 GLRHMVMAISACPTTIADILAMAERVANEESRVDELVD 224


>gi|138895880|ref|YP_001126333.1| sporulation sigma factor SigF [Geobacillus thermodenitrificans
           NG80-2]
 gi|134267393|gb|ABO67588.1| RNA polymerase sigma-F factorr [Geobacillus thermodenitrificans
           NG80-2]
          Length = 252

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 124/252 (49%), Gaps = 17/252 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ++ I   E + ++   ++G+ EA   + E++E N+RLV SV +++ NRG +  DL Q G 
Sbjct: 11  QSPIKDQEMKELIRRSQEGDQEA---RDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGC 67

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    
Sbjct: 68  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE 126

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S    R PT  EIA  L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 127 LSKTRGRAPTITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIADAD 186

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  +            + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 187 EASWFEKI-------ALKKAIEELDERERLIVYLRY----YKDQTQSEVAARLGISQVQV 235

Query: 657 RQIEAKAIRKLK 668
            ++E K ++ +K
Sbjct: 236 SRLEKKILQHIK 247


>gi|294501135|ref|YP_003564835.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|295706482|ref|YP_003599557.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|464690|sp|P35145|RPSF_BACME RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|39654|emb|CAA45288.1| spoIIAC [Bacillus megaterium]
 gi|294351072|gb|ADE71401.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|294804141|gb|ADF41207.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|383708|prf||1904152C spoIIAC gene
          Length = 253

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 122/238 (51%), Gaps = 14/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++++ +    IA+  +V+ N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD   
Sbjct: 22  LIKRSQQGDQIARDTIVQKNMRLVWSVVQRFINRGYEPDDLFQIGCIGLLKSVDKFDLSY 81

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R I D   T+++   +++  +K+ +    +S  + R PT  E+
Sbjct: 82  DVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKEMSNKIRKAKDELSKLLGRVPTVAEV 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ L +  E V    +  + P S+   +   D D   L D I D       D   +  L+
Sbjct: 141 AEHLDLTPEEVVLAQEANRAPSSIHETVYENDGDPITLLDQIADHTEAKWFD---KIALK 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     +  L  RE+ ++ +R+      D T  EV  +  +++ ++ ++E K ++++K
Sbjct: 198 EA----IEELDEREKLIVYLRY----YKDQTQSEVAARLGISQVQVSRLEKKILKQMK 247


>gi|302535694|ref|ZP_07288036.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444589|gb|EFL16405.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 300

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 71  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 130

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+A  L + 
Sbjct: 131 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVPELAAVLGVT 190

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P   ED    G  + D+      DSA++    RE+   +
Sbjct: 191 EEEVVDGLAVGNAYTASSLDSP-SPEDEGGEGS-LADRLGYE--DSALEGVEYRESLKPL 246

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 247 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 290


>gi|229180352|ref|ZP_04307695.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
 gi|228603099|gb|EEK60577.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
          Length = 252

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 127/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMRDELSKEFGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D++     D  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQIADQSEAKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|30022159|ref|NP_833790.1| sporulation sigma factor SigF [Bacillus cereus ATCC 14579]
 gi|30264150|ref|NP_846527.1| sporulation sigma factor SigF [Bacillus anthracis str. Ames]
 gi|42783188|ref|NP_980435.1| sporulation sigma factor SigF [Bacillus cereus ATCC 10987]
 gi|47529588|ref|YP_020937.1| sporulation sigma factor SigF [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47568126|ref|ZP_00238830.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49186981|ref|YP_030233.1| sporulation sigma factor SigF [Bacillus anthracis str. Sterne]
 gi|49478518|ref|YP_038132.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141420|ref|YP_085409.1| sporulation sigma factor SigF [Bacillus cereus E33L]
 gi|65321467|ref|ZP_00394426.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|75762406|ref|ZP_00742276.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118479276|ref|YP_896427.1| sporulation sigma factor SigF [Bacillus thuringiensis str. Al
           Hakam]
 gi|165871124|ref|ZP_02215774.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167633745|ref|ZP_02392069.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|167639441|ref|ZP_02397712.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|170687128|ref|ZP_02878346.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|170705887|ref|ZP_02896350.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|177652593|ref|ZP_02935009.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190565830|ref|ZP_03018749.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035002|ref|ZP_03102409.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196045861|ref|ZP_03113090.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206971277|ref|ZP_03232228.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206977400|ref|ZP_03238296.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217961566|ref|YP_002340136.1| sporulation sigma factor SigF [Bacillus cereus AH187]
 gi|218234550|ref|YP_002368877.1| sporulation sigma factor SigF [Bacillus cereus B4264]
 gi|218899234|ref|YP_002447645.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|218905210|ref|YP_002453044.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|222097523|ref|YP_002531580.1| sporulation sigma factor sigf [Bacillus cereus Q1]
 gi|225866059|ref|YP_002751437.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227816852|ref|YP_002816861.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228902583|ref|ZP_04066734.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|228909904|ref|ZP_04073725.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228916713|ref|ZP_04080278.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922825|ref|ZP_04086123.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228929122|ref|ZP_04092149.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935394|ref|ZP_04098212.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941224|ref|ZP_04103777.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947793|ref|ZP_04110080.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954358|ref|ZP_04116384.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960339|ref|ZP_04121992.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228967106|ref|ZP_04128142.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974156|ref|ZP_04134726.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980748|ref|ZP_04141053.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228987264|ref|ZP_04147385.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229019284|ref|ZP_04176110.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|229025528|ref|ZP_04181938.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|229047765|ref|ZP_04193345.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|229071577|ref|ZP_04204795.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|229081330|ref|ZP_04213833.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|229093131|ref|ZP_04224253.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|229111546|ref|ZP_04241097.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|229123596|ref|ZP_04252791.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|229129353|ref|ZP_04258324.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|229140809|ref|ZP_04269354.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|229146647|ref|ZP_04275014.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|229152275|ref|ZP_04280468.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|229157657|ref|ZP_04285732.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|229186319|ref|ZP_04313484.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|229192285|ref|ZP_04319250.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|229198196|ref|ZP_04324905.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|229603990|ref|YP_002868374.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|254683842|ref|ZP_05147702.1| sporulation sigma factor SigF [Bacillus anthracis str. CNEVA-9066]
 gi|254721677|ref|ZP_05183466.1| sporulation sigma factor SigF [Bacillus anthracis str. A1055]
 gi|254736189|ref|ZP_05193895.1| sporulation sigma factor SigF [Bacillus anthracis str. Western
           North America USA6153]
 gi|254744078|ref|ZP_05201761.1| sporulation sigma factor SigF [Bacillus anthracis str. Kruger B]
 gi|254754142|ref|ZP_05206177.1| sporulation sigma factor SigF [Bacillus anthracis str. Vollum]
 gi|254758168|ref|ZP_05210195.1| sporulation sigma factor SigF [Bacillus anthracis str. Australia
           94]
 gi|296504567|ref|YP_003666267.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|301055569|ref|YP_003793780.1| sporulation sigma factor SigF [Bacillus anthracis CI]
 gi|29897716|gb|AAP10991.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 14579]
 gi|30258795|gb|AAP28013.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Ames]
 gi|42739116|gb|AAS43043.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10987]
 gi|47504736|gb|AAT33412.1| RNA polymerase sigma-F factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47555116|gb|EAL13463.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49180908|gb|AAT56284.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Sterne]
 gi|49330074|gb|AAT60720.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974889|gb|AAU16439.1| RNA polymerase sigma-F factor [Bacillus cereus E33L]
 gi|74490099|gb|EAO53445.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118418501|gb|ABK86920.1| RNA polymerase, sigma subunit, RpoX/SigF [Bacillus thuringiensis
           str. Al Hakam]
 gi|164713043|gb|EDR18570.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167512500|gb|EDR87875.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|167531151|gb|EDR93838.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|170129427|gb|EDS98291.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|170668745|gb|EDT19490.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|172081928|gb|EDT66996.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190562749|gb|EDV16715.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992541|gb|EDX56502.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196023301|gb|EDX61979.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206734049|gb|EDZ51220.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206744391|gb|EDZ55802.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217063378|gb|ACJ77628.1| RNA polymerase sigma-F factor [Bacillus cereus AH187]
 gi|218162507|gb|ACK62499.1| RNA polymerase sigma-F factor [Bacillus cereus B4264]
 gi|218540139|gb|ACK92537.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|218540957|gb|ACK93351.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|221241581|gb|ACM14291.1| RNA polymerase sigma-F factor [Bacillus cereus Q1]
 gi|225790809|gb|ACO31026.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227007915|gb|ACP17658.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228585356|gb|EEK43465.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|228591235|gb|EEK49089.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|228597113|gb|EEK54768.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|228625614|gb|EEK82366.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|228631237|gb|EEK87873.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|228636817|gb|EEK93280.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|228642599|gb|EEK98885.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|228653958|gb|EEL09825.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|228659731|gb|EEL15376.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|228671928|gb|EEL27221.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|228690280|gb|EEL44073.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|228701952|gb|EEL54435.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|228711513|gb|EEL63470.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|228723557|gb|EEL74922.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|228735810|gb|EEL86395.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|228741969|gb|EEL92143.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|228772493|gb|EEM20938.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228778917|gb|EEM27179.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228785496|gb|EEM33505.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792475|gb|EEM40041.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799363|gb|EEM46327.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805290|gb|EEM51883.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228811780|gb|EEM58114.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818383|gb|EEM64455.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824146|gb|EEM69960.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830412|gb|EEM76022.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228836880|gb|EEM82223.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228842900|gb|EEM87983.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849739|gb|EEM94572.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228857024|gb|EEN01533.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|229268398|gb|ACQ50035.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|296325619|gb|ADH08547.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|300377738|gb|ADK06642.1| sporulation sigma factor SigF [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327980|gb|ADY23240.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941847|gb|AEA17743.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 252

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 127/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMRDELSKEFGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D++     D  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQIADQSETKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|237816135|ref|ZP_04595131.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
 gi|237788798|gb|EEP63010.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
          Length = 319

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 62  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 121

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 122 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 179

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 180 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 239

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 240 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 296

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 297 ESRAMEKLK 305


>gi|188090618|gb|ACD49543.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 290

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 2   EVNDHLPDDLVDLEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 61

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 62  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 121

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+       +G   L EI+
Sbjct: 122 TEMLLADYQAHKEGKKRLAEIV 143


>gi|149191850|ref|ZP_01870086.1| RNA polymerase sigma factor RpoD [Vibrio shilonii AK1]
 gi|148834326|gb|EDL51327.1| RNA polymerase sigma factor RpoD [Vibrio shilonii AK1]
          Length = 616

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS 89
           K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D  +     
Sbjct: 10  KLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALND 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++++    +A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 70  DNNITDEDAAEAAAAALSSVESEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALI 168
              + +S+ E P T   ++
Sbjct: 129 INQVQSSVAEYPGTIPYIL 147


>gi|257784260|ref|YP_003179477.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
 gi|257472767|gb|ACV50886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
          Length = 284

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 127/240 (52%), Gaps = 20/240 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + S  + +++ ++L LV  +A K+ NRG    DLIQ G IGL+KA ++F+   G +F+
Sbjct: 48  ETKDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGTIGLIKAIDRFEPDRGLEFT 107

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   +   I R   D+  ++R+P  +++   K+ +    ++ +++R P+ EEIA++L 
Sbjct: 108 TYATPTIMGEIKRHFRDKGWSVRVPRRLQELSSKINQVTDDLTKELQRSPSIEEIAQRLD 167

Query: 558 MPVEGVRKVLKITKEPISLETPI--------GDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             VE + + ++ +    S+  P+        GDE  S +  ++ +   ++  D  I    
Sbjct: 168 TNVEEILEAMESSSAYSSV--PLEGGGSGADGDETPSIIDQYVTEDEDLAGSDDRI---- 221

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  +   +PRE+ ++RMRF  G+    T  E+ ++  +++ ++ ++  + +++++ 
Sbjct: 222 --VLDEAIRDFSPREQEIIRMRFVEGL----TQVEIAEKLNISQVQVSRLLRRTLKRIQE 275


>gi|188090600|gb|ACD49534.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 291

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 56/142 (39%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHLPDDLVDLEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+       +G   L EI+
Sbjct: 123 TEMLLADYQAHKEGKKRLAEIV 144


>gi|196038743|ref|ZP_03106051.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
 gi|196030466|gb|EDX69065.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
          Length = 252

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 127/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMRDELSKEFGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D++     D  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQIADQSETKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|254473016|ref|ZP_05086414.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
 gi|211957737|gb|EEA92939.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
          Length = 289

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 120/229 (52%), Gaps = 20/229 (8%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVI+ A ++ + G+   DLIQEG+IGLM+AA +F      +FSTYA WW+K  I   + 
Sbjct: 53  RLVIAQALRFKSYGVPLSDLIQEGHIGLMEAANRFKLSKDVRFSTYASWWIKSFIQDYVL 112

Query: 514 DQSCTIRIPVHMRDKI--HKVVRTARRMSNK---IKREPTPEEIAKKLAMPVEGVRKV-L 567
                +R     R K+      R    +++K   +  +   ++I+ +    +  ++ +  
Sbjct: 113 RNQSIVRGGTSSRQKMLFFGFKRMRAELASKHPELSEDQLHQQISNQTGANMRDIKMMSS 172

Query: 568 KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPL-DSAIQANL-RETTTR----VLASL 620
           ++ +   SL   + G E    L D +    A  PL D  ++ +L  E   R     + +L
Sbjct: 173 RLGRSDTSLNATLKGSETNLQLQDTLA---ADEPLPDEIVEVHLDSERAERRLFDAIKTL 229

Query: 621 TPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PRE+RV+R R    +  D  TLE +GK+  V++ER+RQIE++A++KLK
Sbjct: 230 PPREQRVIRDR---KLREDGVTLEALGKKLGVSKERVRQIESRAMQKLK 275


>gi|171464209|ref|YP_001798322.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|171193747|gb|ACB44708.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 307

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 77/283 (27%), Positives = 141/283 (49%), Gaps = 34/283 (12%)

Query: 403 VDSILKIRNEIKSISVETGISIS-EFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVA 460
           +DS +   N +  +S    + ++ EFR          C  ++ A K +V ++LRLV+SVA
Sbjct: 36  LDSYIAYVNRVPMLSAAEELHLAQEFR----------CTENVDAAKTLVLSHLRLVVSVA 85

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           ++Y   G+   DLIQEGNIGLMKA +++D   G + ++YA+ W+K  I   I      ++
Sbjct: 86  RQYLGYGIPHADLIQEGNIGLMKAVKRYDPSNGARLASYAIHWIKAEIHEYILKNWRLVK 145

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEGVRKV-LKITKEPISL 576
                  K  + +    R +       TP E+   AK L +    V+++ +++    ++L
Sbjct: 146 TAT---TKAQRKLFFNLRSNKPTLSALTPNEVDALAKTLDVKGSDVKEMEMRLAGGDVAL 202

Query: 577 ETPIGDEDTSH-----LGDFIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           E    DED+++     L D  ++  A   S   +A+Q        + L +L  R   +++
Sbjct: 203 EGDDSDEDSAYAPIQWLADSSQEPTARIASAEANALQG---PKLDQALMALDERSRNIVQ 259

Query: 630 MRFGIGM----NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+ + M    N   TL ++  ++ ++ ER+RQIE  A++K++
Sbjct: 260 SRW-LAMDAEGNGTKTLHDLADEYGISAERVRQIETAALKKMR 301


>gi|323529380|ref|YP_004231532.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1001]
 gi|323386382|gb|ADX58472.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1001]
          Length = 664

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 90/164 (54%), Gaps = 15/164 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V     D + L    
Sbjct: 53  RALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQAPDAETLLLNS 112

Query: 88  G-----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                 S+D  D  +  + S+V      DS    T DPVRMY+REMG+ ELL+R GEIAI
Sbjct: 113 NAPAVVSDDQADEETEVALSTV------DSEFGRTTDPVRMYMREMGATELLTRAGEIAI 166

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           AKRIE G   M+ ++   PL   A++    ++ DG   + E++D
Sbjct: 167 AKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVD 210


>gi|326539488|gb|ADZ87703.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis M5-90]
          Length = 293

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 96  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 214 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|49475181|ref|YP_033222.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49237986|emb|CAF27191.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 294

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 124/245 (50%), Gaps = 16/245 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLMKA ++F+   G++ +TYA+WW
Sbjct: 49  AAHKLVTSHLRLVAKIAVGYRGYGLPIGEVISEGNVGLMKAVKRFEPERGFRLATYAIWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      +++      K  ++    R++ ++++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKMGTTANQK--RLFFNLRKLKSRLQALDNGDLNAEQVKEIAIQL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIED---KNAVSPLDSAIQANLRE 611
            +  + V  + +      SL  P+   + + S   D++ D       + ++     N R 
Sbjct: 167 NVTEDEVVSMNRRLGGDTSLNAPLRTKEGENSEWQDWLVDDSNNQEQTLIEQNELENRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             T  L +L  RE+R+ + R     +   TLEE+  +F ++RER+RQIE +A  K+++  
Sbjct: 227 MLTNALDNLNEREKRIFKARR--LSDIPLTLEELSSEFNISRERVRQIEMRAFEKIQNSI 284

Query: 672 RSKKL 676
           ++  L
Sbjct: 285 KASAL 289


>gi|254995008|ref|ZP_05277198.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Mississippi]
          Length = 296

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 126/235 (53%), Gaps = 22/235 (9%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ +A  + + GL  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +
Sbjct: 58  LVTSHLRLVVKIAMGFKSYGLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKAS 117

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV 563
           I   I      IR+     + K+   +R  ++         T +E   IA++ A   E V
Sbjct: 118 IKDYILRSWSCIRVGTTQAQKKLFFSLRKIKKRLLSCGSSMTKKEIKAIAEECATSEEEV 177

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHLGDFI------EDKNAVSPLDSAIQANLRETTTRV 616
            ++ +      +SL   +  E +  L D +      ++   ++  +SAI+ ++ ++    
Sbjct: 178 ERMDRFFANRDVSLNEQVHGESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSA--- 234

Query: 617 LASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA+L  R   +    R+R         TLE++ +++ V++ER+RQIE +A+ K+K
Sbjct: 235 LATLDDRHRDIFTRRRLR-----ERPDTLEKLSEEYGVSKERVRQIELQALCKIK 284


>gi|62290634|ref|YP_222427.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700548|ref|YP_415122.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|148559493|ref|YP_001259609.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|254689924|ref|ZP_05153178.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254700417|ref|ZP_05162245.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|254719758|ref|ZP_05181569.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|254730958|ref|ZP_05189536.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256258178|ref|ZP_05463714.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256370169|ref|YP_003107680.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260547128|ref|ZP_05822866.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297249027|ref|ZP_06932735.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306839453|ref|ZP_07472261.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
 gi|62196766|gb|AAX75066.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616649|emb|CAJ11731.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|148370750|gb|ABQ60729.1| RNA polymerase sigma-70 factor family protein [Brucella ovis ATCC
           25840]
 gi|256000332|gb|ACU48731.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260095493|gb|EEW79371.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297174160|gb|EFH33517.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306405398|gb|EFM61669.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
          Length = 311

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|254694416|ref|ZP_05156244.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
          Length = 311

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|297605001|ref|NP_001056480.2| Os05g0589200 [Oryza sativa Japonica Group]
 gi|255676623|dbj|BAF18394.2| Os05g0589200 [Oryza sativa Japonica Group]
          Length = 464

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 48/127 (37%), Positives = 68/127 (53%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV  +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+
Sbjct: 330 LVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAE 389

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
            S  I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +
Sbjct: 390 NSGVIQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVV 449

Query: 575 SLETPIG 581
           SL T IG
Sbjct: 450 SLYTEIG 456


>gi|254708375|ref|ZP_05170203.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708771|ref|ZP_05170582.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714614|ref|ZP_05176425.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717512|ref|ZP_05179323.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030297|ref|ZP_05443911.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256160470|ref|ZP_05458159.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255677|ref|ZP_05461213.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167971|ref|ZP_05754782.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|261757411|ref|ZP_06001120.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|261737395|gb|EEY25391.1| sigma-70 factor family [Brucella sp. F5/99]
          Length = 311

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|114770145|ref|ZP_01447683.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114548982|gb|EAU51865.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 294

 Score = 89.0 bits (219), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 120/237 (50%), Gaps = 20/237 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ A +RL IS+A K+   G+   DLIQE  +GLMKAA+KFD   G +FSTYA WWVK +
Sbjct: 45  LINAYMRLAISMASKFRRYGVSQQDLIQEAGMGLMKAADKFDPDKGVRFSTYAQWWVKAS 104

Query: 508 ITRSIADQSCTIRIPVHMRDK-----IHKVVRTARRMSNKIKREPTP----EEIAKKLAM 558
           I   +      +R       K     I +V     R + +  +  TP    E+++ +L +
Sbjct: 105 IQDFVMRNYSMVRTGSTTNQKSLFFNIKRVKAQLERDAVQNNQTVTPAQILEQVSTELGV 164

Query: 559 PVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI------QANLRE 611
           P+  V  +  +++   +SL     ++D     ++IE     +P  + I      +  L+ 
Sbjct: 165 PMRDVMMMNGRMSGGDMSLNAIQSNDDEGR--EWIETLADEAPGGAEIVEQSFDEEKLKI 222

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + +  L  RE+ ++  R  I  ++  TLE +G +  +++ERIRQIE  A+ KLK
Sbjct: 223 WIGQSMEVLNEREKYIVIQRKMI--DSPRTLESIGVELKLSKERIRQIENAALEKLK 277


>gi|149202313|ref|ZP_01879286.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
 gi|149144411|gb|EDM32442.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
          Length = 298

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 123/250 (49%), Gaps = 13/250 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E + + A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G+
Sbjct: 40  RWAEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGF 99

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           + +TYAMWW++ +I   I      +++     + K+   +R A+     ++      ++ 
Sbjct: 100 RLATYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKAKIGALEEGDMRPDVV 159

Query: 554 KKLAMPV-----EGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQ 606
           KK+A  +     E +    ++     SL   +G   E +    D++ED++A    D   +
Sbjct: 160 KKIATDLGVTEAEVISMNQRMAGADASLNATVGAEGEGSMQWQDWLEDEDADQAGDYERR 219

Query: 607 ANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             L   RE   + +  L  RE  +L  R     +   TLE++  ++ V+RERIRQIE +A
Sbjct: 220 DELDARRELLVQAMDVLNERERDILTQRR--LSDETVTLEDLSAEYDVSRERIRQIEVRA 277

Query: 664 IRKLKHPSRS 673
             KL+   R+
Sbjct: 278 FEKLQKRMRA 287


>gi|1163231|gb|AAC45341.1| DNA polymerase sigma 32 subunit [Vibrio cholerae]
          Length = 286

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    +S  E R +   +  KG+ +A+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNGYPMLSADEERELAERLHYKGDIDAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++  +  + E    D++    
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMA 194

Query: 589 GD----FIEDKNAVSPLDSAIQANLRE--TTTRV---LASLTPREERVLRMRFGIGMNTD 639
                 ++EDK+  S L   ++A   E  TT R+   LASL    + ++R R+ +  +  
Sbjct: 195 YTAPVLYLEDKH--SDLADNLEAENWEAHTTQRLSMALASLDDGSQHIVRARW-LDDDNK 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++  ++ V+ ERIRQ+E  A+RKLK
Sbjct: 252 TTLQDLAAKYGVSAERIRQLEKNAMRKLK 280


>gi|117927772|ref|YP_872323.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117648235|gb|ABK52337.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 287

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/215 (30%), Positives = 108/215 (50%), Gaps = 13/215 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V+ +L LV  +A+++ NRG    DL+Q   IGL+KA ++FD   G +FSTYA   +
Sbjct: 63  RSELVQTHLPLVEYLARRFRNRGEPHDDLVQVATIGLIKAIDRFDVERGVEFSTYATPTI 122

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----V 560
              I R   D+   IR+P  +++    + +    +S +  R PT  E+A  L M     +
Sbjct: 123 VGEIKRYFRDRGWAIRVPRRLQELKMSLAKATSELSQQYGRAPTVSELADHLGMSEDEIL 182

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLAS 619
           EG+      +   ISL+TP      +   D +   + +  +D A++    RE+   +L  
Sbjct: 183 EGLESANAYST--ISLDTP-----ETDDADALAVADTLGNIDEALEGVEYRESLKPLLEK 235

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L PRE+R+L +RF   M       E+G  Q  V+R
Sbjct: 236 LPPREKRILLLRFFRNMTQSQIAAELGISQMHVSR 270


>gi|315506253|ref|YP_004085140.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
 gi|315412872|gb|ADU10989.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
          Length = 377

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 114/229 (49%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 42  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E++ +L  P E +
Sbjct: 101 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATATLTSELSRAPTVAELSARLETPEEEI 160

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+      P SL  P+G E ++  GD + E  +A+  +D       R T + +L  L
Sbjct: 161 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESDHALESVDD------RVTVSGLLHRL 214

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF      + T  E+  +F +++  + ++ ++A+  L+ 
Sbjct: 215 PWRERRILAMRF----YGNQTQAEIAARFGISQMHVSRLLSRALTWLRQ 259


>gi|208779746|ref|ZP_03247090.1| alternative sigma factor RpoH [Francisella novicida FTG]
 gi|208744201|gb|EDZ90501.1| alternative sigma factor RpoH [Francisella novicida FTG]
          Length = 292

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 125/240 (52%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R + +KI    + +  E+A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSIKDKIGWLSSEDIKELAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+ P  D+D   TS    ++EDK++      +      N +    
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 233

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 234 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|307824539|ref|ZP_07654764.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734523|gb|EFO05375.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 285

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/288 (28%), Positives = 138/288 (47%), Gaps = 35/288 (12%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISIS-EFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           N      D+ L +  ++  ++VE    ++ +FR        G+ EA+   +E+V  NLR 
Sbjct: 10  NLSVGTFDAYLNVVRQMPKLTVEQERELALKFRD------DGDLEAA---RELVMTNLRF 60

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VI VA+ Y+  GL   D+IQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +   
Sbjct: 61  VIHVARGYSGYGLSMPDIIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVIKN 120

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLK-ITKE 572
              +++      +  K+    R+    +      E   IAK L + V  V ++ K +   
Sbjct: 121 WGIVKVATTKAQR--KLFFNLRKSKQDLGWLSNDEAVAIAKDLDVDVSTVYEMEKRLGSR 178

Query: 573 PISLETPIGDEDT------------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            +S + P+ DE T             H GD      AV   +S  + + ++     +A L
Sbjct: 179 DMSFDMPV-DESTEESYVAPASYLHQHGGD-----PAVLLENSDWEGHEQDLLADAMAEL 232

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R   +L  R+   M+   TL E+ +++ V+ ERIRQ+E  A++KL+
Sbjct: 233 DERSLDILSSRW--LMDKKATLHELAERYNVSAERIRQLEQNAMKKLR 278


>gi|239930843|ref|ZP_04687796.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 308

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 121/240 (50%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 73  LEEGTLEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEMSRG 132

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A
Sbjct: 133 VEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRAPTVAELA 192

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           ++L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 193 ERLGITNDEVVEGMAASNAYTASSLDAQ-PEEDDAEGALADRIGYE------DHGLEGIE 245

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L PR+ ++L +RF  GM    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 246 YIESLKPLIAELPPRDRKILSLRFVAGM----TQSEIGEELGISQMHVSRLLSRTLVKLR 301


>gi|84500884|ref|ZP_00999119.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84390951|gb|EAQ03369.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 298

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTAR-RMSNKIKREPTPE---EIAKKLAM 558
           ++ +I   I      +++     + K+   +R A+ R+    + +  P+   +IA  L +
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLHPDNVKQIANDLGV 168

Query: 559 P-VEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   +G   E      D++ED+ A    D A +  +   RE 
Sbjct: 169 TEAEVISMNRRMSGGDASLNATVGMDAESAMEWQDWLEDEEADQAGDYAERDEMDSRREL 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +A L  RE  +L  R  +   T  TLE++ +Q+ V+RERIRQIE +A  KL+
Sbjct: 229 LAEAMAVLNDRERDILTQR-RLSEET-ITLEDLSEQYGVSRERIRQIEVRAFEKLQ 282


>gi|330721841|gb|EGG99811.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC2047]
          Length = 614

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 54/134 (40%), Positives = 82/134 (61%), Gaps = 10/134 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V   D++  ++   D
Sbjct: 13  KELIARGKEQGYLTYAEVNDHLPQDISDPDQVEDIIRMINDMGITV---DEVAPDQ---D 66

Query: 92  SLDLASSASNSSVFLQKRKDSADRS----TDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           +L L  +  + +V       +A  +    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 67  TLQLNENTDDDAVEEAAAALAAVETEVGRTTDPVRMYMREMGSVELLTREGEIVIAKRIE 126

Query: 148 AGRAMMMASLCESP 161
            G   +M +L   P
Sbjct: 127 EGIREVMCALASFP 140


>gi|261819465|ref|YP_003257571.1| RNA polymerase factor sigma-32 [Pectobacterium wasabiae WPP163]
 gi|261603478|gb|ACX85964.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium wasabiae
           WPP163]
          Length = 285

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/280 (26%), Positives = 145/280 (51%), Gaps = 29/280 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++  ++  N    ++ E   +++E  H      +G+ EA+   K ++ ++LR VI VA+ 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHY-----QGDLEAA---KHLILSHLRFVIHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+   ++    +   E +A++L +  + VR++  ++  + ++ + P
Sbjct: 128 TTKAQR--KLFFNLRKTKTRLGWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFD-P 184

Query: 580 IGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVL 628
             +ED SH G       +++DK+  S     I+ +  +T      T  L  L  R + ++
Sbjct: 185 TPEED-SHDGKAMSPMLYLQDKS--SDFAGGIEEDNWDTHAADKLTYALEGLDERSQHII 241

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 242 RARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|170691126|ref|ZP_02882292.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia graminis
           C4D1M]
 gi|170144375|gb|EDT12537.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia graminis
           C4D1M]
          Length = 469

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 86/158 (54%), Gaps = 3/158 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +     +     D
Sbjct: 67  RALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLND 126

Query: 92  SLDLASSASNSSVFLQKRKDSADRS---TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +   ASS        +    + D     T DPVRMY+REMG++ELL+REGEI IAKRIE 
Sbjct: 127 NAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 187 GLKHMVMAISACPTTIADILAMAERVANEEIRIDELVD 224



 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 44/135 (32%), Positives = 70/135 (51%), Gaps = 9/135 (6%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE-WKN 397
           V+++  + ++I+H       +    G+ R  F+ R  G E D  W    K   EG  +  
Sbjct: 343 VDEVRQVERQILHT------VVDKCGMPRAEFIARFPGSETDLEWAD--KIVSEGHPYSA 394

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVI
Sbjct: 395 ILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVI 454

Query: 458 SVAKKYTNRGLQFLD 472
           S+AKKYTNRGLQFLD
Sbjct: 455 SIAKKYTNRGLQFLD 469


>gi|154816043|emb|CAO85715.1| putative RNA polymerase sigma factor rpoD [Clostridium sp.]
          Length = 75

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/74 (55%), Positives = 61/74 (82%), Gaps = 1/74 (1%)

Query: 609 LRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L +T + VL++L+PREER++R+R+G +G     TLEE+G++F +TRERIRQIEA+AIRKL
Sbjct: 2   LGDTLSNVLSTLSPREERIVRLRYGLVGDGESRTLEEIGREFNLTRERIRQIEARAIRKL 61

Query: 668 KHPSRSKKLRSFLD 681
           +HP+R KKL+ + +
Sbjct: 62  RHPTRIKKLQGYFE 75


>gi|302877609|ref|YP_003846173.1| RNA polymerase, sigma 70 subunit, RpoD [Gallionella
           capsiferriformans ES-2]
 gi|302580398|gb|ADL54409.1| RNA polymerase, sigma 70 subunit, RpoD [Gallionella
           capsiferriformans ES-2]
          Length = 655

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/179 (34%), Positives = 95/179 (53%), Gaps = 17/179 (9%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEG 88
           S K +I L ++RGY+T  E+N  LP D +  EQ+E   +M+++MGI V D   D E    
Sbjct: 35  SLKALIVLGKERGYLTYAEINDHLP-DMLEVEQIESVASMINDMGIRVCDVAPDAE---- 89

Query: 89  SEDSLDLASSASNSSVFLQKRK--------DSADRSTDDPVRMYLREMGSIELLSREGEI 140
              +L +  SA  ++      +        DS    T DPVRMY+REMG+++LL+RE EI
Sbjct: 90  ---ALIMTDSAPTAADEDAAEEAEAALSTVDSEFGRTTDPVRMYMREMGTVDLLTREKEI 146

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
            IAKRIE G+  M+ ++   P+T   ++    ++      + E+ID    I  E + G 
Sbjct: 147 EIAKRIEEGQRNMIQAISACPVTIAEILSLAAKIEIDEIRVNELIDGFVDIELEDESGL 205


>gi|83949442|ref|ZP_00958175.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837341|gb|EAP76637.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 298

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/260 (28%), Positives = 128/260 (49%), Gaps = 18/260 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E+    + V K + EA+     MV ++LRL   +A  Y   GL   ++I E N+GLM+A 
Sbjct: 34  EYMLAKAWVEKQDTEAA---HRMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAV 90

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIK 544
           ++FD   G++ +TYAMWW++ +I   I      +++     + K+   +R A+     ++
Sbjct: 91  KRFDPEKGFRLATYAMWWIRASIQEYILRSWSMVKLGTTSAQKKLFFNLRKAKARIGALE 150

Query: 545 REPTPEEIAKKLAMPV-----EGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNA 597
                 +  K++A  +     E +    +++    SL   +G   E T    D++ED++A
Sbjct: 151 EGDMHPDNVKRIATDLGVTEDEVISMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDA 210

Query: 598 VSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTR 653
               D   +  +    E  T  +  L  RE+ +L  R    +N +  TLE++  ++ V+R
Sbjct: 211 DQAGDYEKRNEMETRLELLTEAMDVLNDREKDILSQR---RLNDETVTLEDLSTEYGVSR 267

Query: 654 ERIRQIEAKAIRKLKHPSRS 673
           ERIRQIE +A  KL+   RS
Sbjct: 268 ERIRQIEVRAFEKLQKRMRS 287


>gi|228992811|ref|ZP_04152736.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
 gi|228998857|ref|ZP_04158442.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|229006374|ref|ZP_04164053.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228754873|gb|EEM04239.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228760873|gb|EEM09834.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|228766860|gb|EEM15498.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
          Length = 252

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 126/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMKDELSKEYGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D+      D  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITILDQIADQTETKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|170718627|ref|YP_001783826.1| RNA polymerase factor sigma-32 [Haemophilus somnus 2336]
 gi|168826756|gb|ACA32127.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 2336]
          Length = 280

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 122/231 (52%), Gaps = 10/231 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKTLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+     +E   + +A +L +  E
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFSDKE--VDMVANELGVSKE 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDK--NAVSPLDS-AIQANLRETTTRVL 617
            V ++  ++T   +  + P+ D+++     ++EDK  N  + L++   +    +     L
Sbjct: 167 DVLEMESRMTGSDVGFDLPVDDDESYAPALYLEDKSSNFAAELENENFETQAADQVANAL 226

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A L  R   +++ R+    +   TL ++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 227 AELDERSRDIIKSRWLD--DEKATLHDLAAKYNISAERVRQLETNALKKLK 275


>gi|291439213|ref|ZP_06578603.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342108|gb|EFE69064.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 304

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 121/240 (50%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 69  LEEGTLEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEMSRG 128

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A
Sbjct: 129 VEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRAPTVAELA 188

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           ++L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 189 ERLGITNDEVVEGMAASNAYTASSLDAQ-PEEDDAEGALADRIGYE------DHGLEGIE 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L PR+ ++L +RF  GM    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 242 YIESLKPLIAELPPRDRKILSLRFVAGM----TQSEIGEELGISQMHVSRLLSRTLVKLR 297


>gi|255003152|ref|ZP_05278116.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Puerto Rico]
 gi|255004281|ref|ZP_05279082.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Virginia]
          Length = 296

 Score = 88.6 bits (218), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 125/233 (53%), Gaps = 18/233 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ +A  + + GL  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +
Sbjct: 58  LVTSHLRLVVKIAMGFKSYGLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKAS 117

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV 563
           I   I      IR+     + K+   +R  ++         T +E   IA++ A   E V
Sbjct: 118 IKDYILRSWSCIRVGTTQAQKKLFFSLRKIKKRLLSCGSSMTKKEIKAIAEECATSEEEV 177

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHLGDFI------EDKNAVSPLDSAIQANLRETTTRV 616
            ++ +      +SL   +  E +  L D +      ++   ++  +SAI+ ++ ++    
Sbjct: 178 ERMDRFFANRDVSLNEQVHGESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSA--- 234

Query: 617 LASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA+L  R   +  R R         TLE++ +++ V++ER+RQIE +A+ K+K
Sbjct: 235 LATLDDRHRDIFTRRRL---QERPDTLEKLSEEYGVSKERVRQIELQALCKIK 284


>gi|239832766|ref|ZP_04681095.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
 gi|239825033|gb|EEQ96601.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
          Length = 303

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 18/234 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP---LDSAIQANLRE 611
            +  + V  + +      SL  P+   + ++    D++ D ++      ++     N R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSSSQEQILIEQDELDNRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R    ++ D  TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMDTLNDRERRIFEAR---RLSDDPMTLEDLSSEFSISRERVRQIEVRAF 277


>gi|319405171|emb|CBI78776.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 305

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 117/249 (46%), Gaps = 38/249 (15%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGNIGLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      ++I      K  ++    R++ NK++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKIGTTANQK--RLFFNLRKLKNKLQMLDSGDLNAQQVKEIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETP--------------IGDEDTSHLGDFIEDKNAVSPLD 602
            +  + V  + +      SL  P              + D+  +     IE     +   
Sbjct: 167 KVTEDEVVSMNRRLSGDASLNAPLLTNKGESYEWQDWLVDDSNNQEQILIEQDELENRYS 226

Query: 603 SAIQA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             IQA  NL E   R+  +   R+E +             TLEE+  +F ++RER+RQIE
Sbjct: 227 LLIQAMDNLNEREKRIFKARRLRDEPL-------------TLEELSNEFNISRERVRQIE 273

Query: 661 AKAIRKLKH 669
           A+A  K+++
Sbjct: 274 ARAFEKVQN 282


>gi|313901877|ref|ZP_07835297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
 gi|313467870|gb|EFR63364.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
          Length = 251

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 122/239 (51%), Gaps = 22/239 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+G+ EA   ++ +V  ++ LV  VA+++ + G    DLIQ G IGL++A + FD   G
Sbjct: 9   ARQGDGEA---RERLVALHMPLVRHVARRFASFGHDLDDLIQAGTIGLLQAIDGFDPSRG 65

Query: 494 YKFSTYAMWWVKQAITRSI--ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           Y+FSTYA+  +   I R +  +D +   R    MR ++ ++ R A  M  ++ R P    
Sbjct: 66  YQFSTYAVPVILGEIRRWLRASDPAGLSR---AMRARVAEIRRVADAMEQELGRRPPAAA 122

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDS-AIQANL 609
           +A++LA  V  V   L+  + P+SL+ P+  E D +  GD +         D+ A++A  
Sbjct: 123 VAQRLACDVADVTFALEAAQSPVSLDEPLSAEPDAACRGDRLPAPGDPDWSDTVAVRA-- 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  LA L PR   ++ +RF      D T  EV     +++ ++ ++E  A+ +L+
Sbjct: 181 ------ALAQLPPRLRTIIALRF----FRDLTQAEVAAAVGLSQPQVSRLEKMALARLR 229


>gi|285019635|ref|YP_003377346.1| RNA polymerase sigma-32 factor protein [Xanthomonas albilineans GPE
           PC73]
 gi|283474853|emb|CBA17352.1| probable rna polymerase sigma-32 factor protein [Xanthomonas
           albilineans]
          Length = 292

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 74/269 (27%), Positives = 129/269 (47%), Gaps = 39/269 (14%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  SE  H ++ VR  + E   A +E+V ++LR V+ VA+ Y   GL   DL+QEGNIGL
Sbjct: 36  VLTSEEEHALA-VRYRDQEDLDAARELVHSHLRFVVHVARGYNGYGLPLGDLVQEGNIGL 94

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA ++FD  +G +  ++A+ W++  +   I      +++            +  R++  
Sbjct: 95  MKAVKRFDPDMGVRLVSFAVHWIRAEMHEYILKNWRIVKV---------ATTKAQRKLFF 145

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +++  T   +    A  V  V K L ++ +E + +E+ +   D        ED +   P
Sbjct: 146 NLRKSKT--RLGWMNAAEVTAVAKDLNVSEREVLEMESRLSGRDIGFDAPSDEDDDHAPP 203

Query: 601 LDSA-IQAN--------------------LRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +A + AN                    LRE     LA L  R   ++  R+ +  ++ 
Sbjct: 204 SPAAYLMANEEDPSQAYERADSDDNQLQLLREG----LAELDARSRDIIERRW-LDADSK 258

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 259 ITLQELADEYGVSAERIRQIEANALKKMK 287


>gi|302867341|ref|YP_003835978.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302570200|gb|ADL46402.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 377

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 114/229 (49%), Gaps = 14/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 42  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E++ +L  P E +
Sbjct: 101 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATATLTSELSRAPTVAELSARLETPEEEI 160

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+      P SL  P+G E ++  GD + E  +A+  +D       R T + +L  L
Sbjct: 161 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESDHALESVDD------RVTVSGLLHRL 214

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF      + T  E+  +F +++  + ++ ++A+  L+ 
Sbjct: 215 PWRERRILAMRF----YGNQTQAEIAARFGISQMHVSRLLSRALTWLRQ 259


>gi|302871075|ref|YP_003839711.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302573934|gb|ADL41725.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 256

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 99/190 (52%), Gaps = 7/190 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L +   +AKK+ NRG+ + DL Q   + L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNKYLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S+K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRLYETSAKIKLVTEMLSSKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +     ++ +Q    E   + +  L+P
Sbjct: 151 EVMEASNSYLPQSLDQTMYEDEEMTLGDVLGKSD-----ENILQIENVEAVKKAIERLSP 205

Query: 623 REERVLRMRF 632
            E   ++ RF
Sbjct: 206 FEREFVQKRF 215


>gi|237809745|ref|YP_002894185.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
 gi|237502006|gb|ACQ94599.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
          Length = 284

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 129/242 (53%), Gaps = 18/242 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G + 
Sbjct: 46  GDLEAA---RQLVMSHLRFVVHIARTYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E     +A+
Sbjct: 103 VSFAVHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKTKKRLGWFNQDEVRA--VAE 160

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANLRE 611
           +L +  E V ++  +++    S +    D+  S+     ++EDK+  S L +  + N  +
Sbjct: 161 ELGVSPEDVTEMESRMSGLDHSFDGYDDDDSESNFAPAQYLEDKS--SDLATVYENNNWD 218

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           T         L  L  R ++++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 219 THAEHRLAYALQGLDERSQQIVRARW-LDEDNKQTLQELADRYGVSAERVRQLEKNALKK 277

Query: 667 LK 668
           LK
Sbjct: 278 LK 279


>gi|229031716|ref|ZP_04187709.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
 gi|228729600|gb|EEL80587.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
          Length = 252

 Score = 88.6 bits (218), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 121/228 (53%), Gaps = 16/228 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD     KFSTYA+  
Sbjct: 33  ARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D   ++++   +++  +K+ +    +S +  R PT  E+A+ L +  E V
Sbjct: 93  IIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMRDELSKEFGRAPTINEVAEALELTPEEV 151

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASL 620
               + ++ P S+   +   D D   + D I D++     D  A++  +RE        L
Sbjct: 152 VLAQEASRAPSSIHETVYENDGDPITILDQIADQSETKWFDKIALKEAIRE--------L 203

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 204 DERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|297157365|gb|ADI07077.1| putative sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 242

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 113/222 (50%), Gaps = 14/222 (6%)

Query: 440 EASIAKKEM----VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           E S A+ E+    V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +
Sbjct: 10  EGSTARAELRNTLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVE 69

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  E+A++
Sbjct: 70  FSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQRHGRAPTVHELAEQ 129

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRET 612
           L++  E V + L+       +SL+ P  D+++  + D +  +      D A++    RE+
Sbjct: 130 LSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAE------DEALEGVEYRES 183

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              +L  L PRE+++L +RF   M      +EVG  Q  V+R
Sbjct: 184 LKPLLEDLPPREKKILLLRFFGNMTQSQIAQEVGISQMHVSR 225


>gi|257063114|ref|YP_003142786.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256790767|gb|ACV21437.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 269

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 55/76 (72%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + +   AK+++V A+LRLV  +AK+Y  RG+ F+DL+ EGN+GL++AAE+FD   G  FS
Sbjct: 103 QSDGDAAKEQLVGASLRLVARIAKRYIFRGVSFMDLVHEGNMGLIRAAERFDPASGAAFS 162

Query: 498 TYAMWWVKQAITRSIA 513
            YA WW++ AI+R+  
Sbjct: 163 VYASWWIRAAISRATG 178



 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 9/78 (11%)

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ---FC-----V 651
           PLD +      E  T  L+S++ RE   +R RFG+   +  T  E   +    C     +
Sbjct: 186 PLDPSETFGEGEIET-ALSSMSERERDYIRFRFGLENGSSRTFGESAPEPGVVCTLPSGI 244

Query: 652 TRERIRQIEAKAIRKLKH 669
           TRER RQIEAK + KL++
Sbjct: 245 TRERARQIEAKFLAKLRN 262


>gi|229163011|ref|ZP_04290967.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
 gi|229174749|ref|ZP_04302273.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228608739|gb|EEK66037.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228620417|gb|EEK77287.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
          Length = 252

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 121/228 (53%), Gaps = 16/228 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD     KFSTYA+  
Sbjct: 33  ARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D   ++++   +++  +K+ +    +S +  R PT  E+A+ L +  E V
Sbjct: 93  IIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMRDELSKEFGRAPTINEVAEALELTPEEV 151

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASL 620
               + ++ P S+   +   D D   + D I D++     D  A++  +RE        L
Sbjct: 152 VLAQEASRAPSSIHETVYENDGDPITILDQIADQSETKWFDKIALKEAIRE--------L 203

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 204 DDRERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|291087795|ref|ZP_06347503.2| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
 gi|291073935|gb|EFE11299.1| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
          Length = 291

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 119/228 (52%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     +FSTYA+  
Sbjct: 71  AREQYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPM 130

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D + +IR+   +RD  +K +     +  K  +EPT  EIA+++ +  E +
Sbjct: 131 ILGEVKRYLRDNN-SIRVSRSLRDTAYKAIYARESLMKKNLKEPTLCEIAEEVGVSKEDI 189

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   + P+SL  P+  +  D  ++ D + DK   S  +     +L E   R    L 
Sbjct: 190 TYALDAIQSPVSLYEPVYTDGGDPLYVMDQLSDKKN-SEENWIEDISLSEAMRR----LP 244

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K+
Sbjct: 245 ERERHIIGMRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKAMKN 288


>gi|56416805|ref|YP_153879.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
 gi|56388037|gb|AAV86624.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
          Length = 290

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 125/233 (53%), Gaps = 18/233 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ +A  + + GL  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +
Sbjct: 52  LVTSHLRLVVKIAMGFKSYGLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKAS 111

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV 563
           I   I      IR+     + K+   +R  ++         T +E   IA++ A   E V
Sbjct: 112 IKDYILRSWSCIRVGTTQAQKKLFFSLRKIKKRLLSCGSSMTKKEIKAIAEECATSEEEV 171

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHLGDFI------EDKNAVSPLDSAIQANLRETTTRV 616
            ++ +      +SL   +  E +  L D +      ++   ++  +SAI+ ++ ++    
Sbjct: 172 ERMDRFFANRDVSLNEQVHGESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSA--- 228

Query: 617 LASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA+L  R   +  R R         TLE++ +++ V++ER+RQIE +A+ K+K
Sbjct: 229 LATLDDRHRDIFTRRRL---QERPDTLEKLSEEYGVSKERVRQIELQALCKIK 278


>gi|167758779|ref|ZP_02430906.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
 gi|167663519|gb|EDS07649.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
          Length = 258

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 128/245 (52%), Gaps = 21/245 (8%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + + ++ G+ EA   K+E ++ NLRLV+SV K++        DL Q G IGL+KA   F+
Sbjct: 27  LFARIKAGDAEA---KEEYIKGNLRLVLSVIKRFGGSNENPDDLFQIGCIGLIKAINNFN 83

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             L  KFSTYA+  +   I R + D + +IR+   +RD  +K +        +  +EPT 
Sbjct: 84  TELDVKFSTYAVPMIIGEIRRYMRDNN-SIRVSRSLRDTAYKAIYAKENYIKQNLKEPTV 142

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPL--DSA 604
           +EIA+++ +  E +   L   + P+SL+ P+ ++  D  ++ D I D KN       D +
Sbjct: 143 QEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYVMDQISDTKNKEEKWVEDLS 202

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++A ++         L  RE  ++++RF  G     T  EV  +  +++ ++ ++E  A+
Sbjct: 203 LEAAMQH--------LGERERYIIKLRFFEG----KTQMEVADEIKISQAQVSRLEKNAL 250

Query: 665 RKLKH 669
           R ++ 
Sbjct: 251 RLMRQ 255


>gi|294670676|ref|ZP_06735551.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307564|gb|EFE48807.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 287

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 130/249 (52%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 45  RGDVEAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPDRGAR 101

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  + +    +P+E A+
Sbjct: 102 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKSLSAL----SPKE-AQ 156

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            +A  + GV+       E + +E  +  +D + L D  +D +  +P+D            
Sbjct: 157 AIADDL-GVK-----LSEVLEMEQRMTGKDVALLADNSDDDDNFAPIDWLADHDNEPTRQ 210

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A      E     LA L  R  R++  R+ +  +   TL E+  ++ V+ ERIRQI
Sbjct: 211 IERKAHYTLQTEGLQNALAKLDDRSRRIVETRW-LQDDGGLTLHELAAEYGVSAERIRQI 269

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 270 EAKAMQKLR 278


>gi|256114330|ref|ZP_05455068.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 311

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|330946033|gb|EGH47317.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 166

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 46/149 (30%), Positives = 88/149 (59%)

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  
Sbjct: 3   RLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVS 62

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G +    L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +  
Sbjct: 63  LGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHES 122

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 123 STLEDVGLEIGLTRERVRQIQVEGLKRLR 151


>gi|222475169|ref|YP_002563585.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
 gi|222419306|gb|ACM49329.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
          Length = 307

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 125/233 (53%), Gaps = 18/233 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ +A  + + GL  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +
Sbjct: 69  LVTSHLRLVVKIAMGFKSYGLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKAS 128

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV 563
           I   I      IR+     + K+   +R  ++         T +E   IA++ A   E V
Sbjct: 129 IKDYILRSWSCIRVGTTQAQKKLFFSLRKIKKRLLSCGSSMTKKEIKAIAEECATSEEEV 188

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHLGDFI------EDKNAVSPLDSAIQANLRETTTRV 616
            ++ +      +SL   +  E +  L D +      ++   ++  +SAI+ ++ ++    
Sbjct: 189 ERMDRFFANRDVSLNEQVHGESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSA--- 245

Query: 617 LASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA+L  R   +  R R         TLE++ +++ V++ER+RQIE +A+ K+K
Sbjct: 246 LATLDDRHRDIFTRRRL---QERPDTLEKLSEEYGVSKERVRQIELQALCKIK 295


>gi|90418989|ref|ZP_01226900.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
 gi|90337069|gb|EAS50774.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
          Length = 303

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 117/249 (46%), Gaps = 32/249 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +++ EGN+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   I      +++      K  ++    R+M ++I+       R     +IA  L
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSRIQALDEGDLRPDQVSQIATNL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL----- 609
            +  E V  + +      SL  P+   + ++    D++ D       DS  Q +L     
Sbjct: 167 GVSDEEVVSMNRRLSGDASLNAPLRATEGESGEWQDWLVD-------DSETQEDLLARND 219

Query: 610 -----RETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKA 663
                R    + +  L  RE R+   R    +  D  TLE +  +F ++RER+RQIE +A
Sbjct: 220 ELDQRRGMLQQAMGVLNDRERRIFEAR---RLAEDPLTLETLSGEFEISRERVRQIEVRA 276

Query: 664 IRKLKHPSR 672
             K++   R
Sbjct: 277 FEKVQKAVR 285


>gi|50084493|ref|YP_046003.1| RNA polymerase factor sigma-32 [Acinetobacter sp. ADP1]
 gi|49530469|emb|CAG68181.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp.
           ADP1]
          Length = 289

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 124/236 (52%), Gaps = 16/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 171

Query: 563 VRKV-LKITKEPISLETPIGDED--TSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVL 617
           V ++  ++T    + ET   D+D  ++H+    ++ED N   P   A   +  E ++  L
Sbjct: 172 VLEMEGRLTAYDAAFETQGDDDDDSSTHVAPALYLED-NRYDPARLAENDDYEEQSSTAL 230

Query: 618 A----SLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 HEAMNQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|315635212|ref|ZP_07890490.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
 gi|315476174|gb|EFU66928.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
          Length = 283

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 124/233 (53%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++V ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AAKKLVLSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PV 560
           +K  I   +      +++      R     + +T +R+      E   + +A +L + P 
Sbjct: 110 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSPQ 167

Query: 561 EGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDK--NAVSPLDS-AIQANLRETTTR 615
           + V    ++T   ++ + P    DE+T     ++EDK  N  + L++   +A   +    
Sbjct: 168 DVVEMESRMTGADVAFDLPTDDHDEETYAPALYLEDKGSNFAAELENENYEAQATDQLVV 227

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R + +++ R+     T  TL+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 228 ALNNLDARSQDIIKARWLD--ETKATLQDLAAKYNISAERVRQLETNALKKLK 278


>gi|134102136|ref|YP_001107797.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291007613|ref|ZP_06565586.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133914759|emb|CAM04872.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 280

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 102/212 (48%), Gaps = 8/212 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L +   +A+++++RG    DL Q   +GL+ A ++FD   G  F +YA+  +
Sbjct: 41  RDRLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDPGRGVDFLSYAVPTI 100

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +R+P  +++    V     R+S +  R PTP EIA+ L +    V 
Sbjct: 101 MGEVRRHFRDTGWAVRMPRRLQELHLSVSAAIARLSQEFGRAPTPSEIAEHLGISTNDVY 160

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L+        SL+  + D D   LGD I   +A   LD   +   RET   +LA L  
Sbjct: 161 HGLEAGNAYRSASLDELLTDTDEIPLGDAIGSNDA--ELD---EVENRETIRPLLAELEE 215

Query: 623 REERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           RE R+L MRF  GM      E+VG  Q  V+R
Sbjct: 216 RERRILVMRFFRGMTQTQIAEQVGISQMHVSR 247


>gi|312794377|ref|YP_004027300.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312876651|ref|ZP_07736632.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796604|gb|EFR12952.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|312181517|gb|ADQ41687.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 256

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 99/190 (52%), Gaps = 7/190 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   +AKK+ NRG+ + DL Q   I L+ A E+F+   GY+F+++A   +
Sbjct: 31  RNELVNKHLYIAEIIAKKFVNRGIDYEDLYQVACIALINAVERFEPNKGYRFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEILSTKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +     ++ +Q    E   + +  L+P
Sbjct: 151 EVMEASSSYLPQSLDQTMYEDEEMTLGDVLGKSD-----ENILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRF 632
            E   ++ RF
Sbjct: 206 FEREFVQKRF 215


>gi|319651418|ref|ZP_08005547.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396949|gb|EFV77658.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 252

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 135/260 (51%), Gaps = 19/260 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +T +  +E + ++   + G+  A   + ++V+ N+RLV SV +++ NRG +  
Sbjct: 4   EVKAEKGQTYLKDNEVKELIKQSQSGDQGA---RDKIVQKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKEMGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + +    +S  + R PT  E+++ L +  E +    + ++ P S+   +   D D   L 
Sbjct: 120 IRKAKDELSKTLGRIPTVTELSEFLEISPEDIILAQEASRIPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I+D N     D  A++  +RE        L  RE  ++ +R+      D T  EV  +
Sbjct: 180 DQIDDGNEGKWFDKIALKEAIRE--------LDERERLIVYLRY----YKDQTQSEVAAR 227

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ ++ ++E K ++++K
Sbjct: 228 LGISQVQVSRLEKKILQQMK 247


>gi|262273588|ref|ZP_06051402.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
 gi|262222566|gb|EEY73877.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
          Length = 287

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR V+ +A+ Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKSLILSHLRFVVHIARGYSGYGLPISDLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R +++       E     +A++L +    
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKSKKRLGWFNAEEV-NMVAEQLGVDAAE 167

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLG----DFIEDKNA--VSPLDSAIQANLRETTTR 615
           VR++  ++  +    +  +GD++          ++EDK++   + L+S    N  + T R
Sbjct: 168 VREMESRLAAQDAGFDAGVGDDEREGGAVAPVFYLEDKSSDIATNLES---QNWEDHTNR 224

Query: 616 VLA----SLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA     L  R + ++R R+   ++ D+  TL+E+   + V+ ERIRQ+E  A+RKLK
Sbjct: 225 RLAQAMSGLDARSQHIIRSRW---LDDDNKVTLQELADHYQVSAERIRQLEKNAMRKLK 280


>gi|302560279|ref|ZP_07312621.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302477897|gb|EFL40990.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 304

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 121/240 (50%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 69  LEEGTPEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRG 128

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A
Sbjct: 129 VEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRSPTVAELA 188

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           ++L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 189 ERLGITNEEVVEGMAASNAYTASSLDAQ-PEEDDAEGALADRIGYE------DHGLEGIE 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L PR+ ++L +RF  GM    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 242 YVESLKPLIAELPPRDRKILSLRFVAGM----TQSEIGEELGISQMHVSRLLSRTLVKLR 297


>gi|197303315|ref|ZP_03168355.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
 gi|197297599|gb|EDY32159.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
          Length = 237

 Score = 88.2 bits (217), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 126/242 (52%), Gaps = 12/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +S++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTISLIRKSHHGDKEAREQLVKENVGLVWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   I R + D    I++   ++   +K  +    ++ ++ REPT
Sbjct: 63  DLSYDVQFSTYAVPMISGEIRRFLRDDG-MIKVSRSLKKLSYKCGKKKEELTERMGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQ 606
            EE+A  L    E + + ++   E  S+  PI  E  S L   D +E+K+   P +  + 
Sbjct: 122 MEELATSLGTEKEELVQAMEAATEVESIYRPIHQEGDSQLSILDRLEEKS--RPEEHLLN 179

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R   +++L  L   E +++ +R+      + T   VG+   +++ ++ ++E K + +
Sbjct: 180 ---RMMLSQILDGLDKEERQLIYLRY----FQEKTQAAVGEILGISQVQVSRMEKKILER 232

Query: 667 LK 668
           ++
Sbjct: 233 MR 234


>gi|269103879|ref|ZP_06156576.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163777|gb|EEZ42273.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 287

 Score = 88.2 bits (217), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 74/279 (26%), Positives = 143/279 (51%), Gaps = 22/279 (7%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A  +DS ++  N    ++ E    ++E  H       G+ +A+   K +V ++LR V+ +
Sbjct: 13  ADSLDSYIQAVNRYPMLTAEQEKELAERLHF-----DGDIDAA---KALVMSHLRFVVHI 64

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +
Sbjct: 65  ARGYSGYGLPMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLRNWRIV 124

Query: 520 RIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLE 577
           ++     + K+   +R +++       E     +A +L +    VR++  ++  +  + E
Sbjct: 125 KVATTKAQRKLFFNLRKSKKRLGWFNNEEI-NMVADQLGVEPSEVREMESRLAAQDATFE 183

Query: 578 TPIGDED----TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
               D+D     +    ++EDK+   A S  +S  + +     ++ LA L  R + ++R 
Sbjct: 184 MSNDDDDRDFTPTAPAYYLEDKSSDVARSYEESNWETHATNRLSQALAGLDERSQFIVRS 243

Query: 631 RFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+   ++ D  TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 244 RW---LDEDKSTLQDLADRFGVSAERIRQLEKNAMKKLK 279


>gi|89067929|ref|ZP_01155373.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046527|gb|EAR52583.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 297

 Score = 88.2 bits (217), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 48  AAHKLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWW 107

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTAR-RMSNKIKREPTPE---EIAKKLAM 558
           ++ +I   I      +++     + K+   +R A+ R+    + +  PE   +IA  L +
Sbjct: 108 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAQIANDLGV 167

Query: 559 P-VEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANL---RET 612
              E +    +++    SL   IG E  S     D++ED++A    D   +  L   RE 
Sbjct: 168 TETEVISMNRRLSGGDASLNAMIGTEGDSATQWQDWLEDESADQAGDYEERDELSTRREL 227

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE+ +L  R     +   TLEE+  Q+ V+RERIRQIE +A  KL+
Sbjct: 228 LGEAMDVLNDREKDILTQRR--LQDQAVTLEELSGQYGVSRERIRQIEVRAFDKLQ 281


>gi|240140689|ref|YP_002965169.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|240010666|gb|ACS41892.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
          Length = 262

 Score = 88.2 bits (217), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 125/250 (50%), Gaps = 41/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 13  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPEREVRFSTYATWW 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E    EI  ++A  +
Sbjct: 73  IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTEEQVGSEIHGRIATAI 130

Query: 561 EGVRKVL-----KITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              R+ +     +++   +SL  P+G+E   +S   DF+ D NA  P ++          
Sbjct: 131 GVSREDVALMDARLSGPDMSLNAPVGEESEASSERMDFLVD-NAALPDET---------- 179

Query: 614 TRVLASLTPREERVLRMRFGIGMNT---------------DHTLEEVGKQFCVTRERIRQ 658
              +++L   E R++ +R  + + +                 TLE +G +  +++ER+RQ
Sbjct: 180 ---VSALVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLEALGHRLGISKERVRQ 236

Query: 659 IEAKAIRKLK 668
           IE +A+ KL+
Sbjct: 237 IENRALEKLR 246


>gi|152976482|ref|YP_001375999.1| sporulation sigma factor SigF [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025234|gb|ABS23004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 252

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 126/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQGARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FDVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMKDELSKEYGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D+      D  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITILDQIADQAETKWFDKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|225853213|ref|YP_002733446.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|256263296|ref|ZP_05465828.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|225641578|gb|ACO01492.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis ATCC 23457]
 gi|263093265|gb|EEZ17362.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409772|gb|ADZ66837.1| RNA polymerase factor sigma-32 [Brucella melitensis M28]
          Length = 311

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|27380342|ref|NP_771871.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1613784|gb|AAC44755.1| sigma32-like factor RpoH1 [Bradyrhizobium japonicum]
 gi|27353506|dbj|BAC50496.1| sigma32-like factor [Bradyrhizobium japonicum USDA 110]
          Length = 308

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A +Y   GL   +++ EGNIGLM+A  +FD   G + +TYAMWW
Sbjct: 49  AAYHLVTSHLRLVAKIAMRYRGYGLPIAEIVSEGNIGLMQAVRRFDPDRGVRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAM 558
           ++ +I   I      ++I      K    K+ R    +S     +  PE+   IA++L +
Sbjct: 109 IRASIQEYILRSWSLVKIAASASQKKLFFKLRRAKSAISALQDGDLRPEQVRLIAERLKV 168

Query: 559 PVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRE---TTT 614
               V  + +  +   SL  PI DED      D++ D      +  A +   ++      
Sbjct: 169 AERDVVAMDRRLRGDASLNVPIHDEDEGGQTLDWLVDPAPTCEITLAEEQEAKQRRLALA 228

Query: 615 RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LA+L  RE  +   R+   +N +  TLEE+  ++ V+RER+RQIE +A +K+K
Sbjct: 229 NALANLNARERNIFTARW---LNEESTTLEELAAEYGVSRERVRQIEERAFQKVK 280


>gi|326442277|ref|ZP_08217011.1| RNA polymerase sigma factor, sigma L [Streptomyces clavuligerus
           ATCC 27064]
          Length = 292

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 63  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 122

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ ++ R PT  E+A  L + 
Sbjct: 123 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQRLDRSPTVPELAAVLGVS 182

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 183 EEEVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 238

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 239 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 282


>gi|254384107|ref|ZP_04999452.1| sigma factor [Streptomyces sp. Mg1]
 gi|194342997|gb|EDX23963.1| sigma factor [Streptomyces sp. Mg1]
          Length = 301

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 72  ERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 131

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+A  L + 
Sbjct: 132 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVPELAAVLGVS 191

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P   ED    G  + D+      D+A++    RE+   +
Sbjct: 192 EEEVVDGLAVGNAYTASSLDSP-SPEDEGGEGS-LADRLGYE--DTALEGVEYRESLKPL 247

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 248 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 291


>gi|167854819|ref|ZP_02477597.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219871694|ref|YP_002476069.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
 gi|167854117|gb|EDS25353.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219691898|gb|ACL33121.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
          Length = 315

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 129/234 (55%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA ++F+  +G + +++A+ W
Sbjct: 79  AAKQLIMSHLRFVVYIARGYLGYGLPLADLIQEGNIGLMKAVKRFNPEIGVRLASFAVHW 138

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           VK  I   +      +++      +  K+    R+   ++    E    ++A++L +  +
Sbjct: 139 VKAEIHEYVLKNWRIVKVATTKSQR--KLFFNLRKNKQRLAWFNEEEIRKVAEELGVSTD 196

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDK--NAVSPLDSAIQANLRETT--T 614
            V+++  ++  + I  +T +GD+D  +     ++ED+  N V  L+   + + R T    
Sbjct: 197 DVKEMESRMVGQDIGFDTSVGDDDDDNYVPSMYLEDESSNFVDELEYE-EYSGRATAQLA 255

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LA L  R + +++ R+ +  N   TL E+  Q+ ++ ER+RQ+E +A++K+K
Sbjct: 256 YALAQLDERSQNIIKTRW-LDENK-ATLHELAAQYNISAERVRQLENQALKKIK 307


>gi|167462564|ref|ZP_02327653.1| sporulation sigma factor SigF [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 251

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 125/246 (50%), Gaps = 17/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++++ + G+   +IA+  +V  N+RLV SV +++ NRG +  DL Q G IGL+K+ 
Sbjct: 17  EVKRLIALSQSGD---TIARDTLVNCNIRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSV 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF+     KFSTYA+  +   I R + D   T+++   +++  +KV +T   +S  ++R
Sbjct: 74  DKFNLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKELANKVRKTKDELSKNLER 132

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
            PT +E+A  L +  E V    +  K   S+   +   D D   L D I D +     D 
Sbjct: 133 LPTLKEVANALGITPEEVVFAQEANKPLSSIHETVFENDWDPITLMDQIADDSQEKWFD- 191

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++E K 
Sbjct: 192 ------KLALNEAIEGLSERERLIVYLRYF----KDQTQSEVANRLGISQVQVSRLEKKI 241

Query: 664 IRKLKH 669
           ++ +++
Sbjct: 242 LQSIRN 247


>gi|56459340|ref|YP_154621.1| RNA polymerase factor sigma-32 [Idiomarina loihiensis L2TR]
 gi|56178350|gb|AAV81072.1| DNA-directed RNA polymerase sigma 32 subunit [Idiomarina loihiensis
           L2TR]
          Length = 286

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 125/245 (51%), Gaps = 33/245 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A KE++ ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 51  AAKELIMSHLRFVVHVARSYSGYGLPQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      +++      +  K+    R+M  ++      E         VE V
Sbjct: 111 IKAEIHEYVLRNWRVVKVATTKAQR--KLFFNLRKMKKRLGWFSQKE---------VETV 159

Query: 564 RKVLKI-TKEPISLETPI----------GDEDTSHLGD------FIEDKNAVSPLDSAIQ 606
              L + TKE + +ET +           D+D S  G       ++EDK   S L + I+
Sbjct: 160 ANELGVSTKEVLEMETRMSAHDQAFELSSDDDDSKEGSAYSPAMYLEDKR--SDLAAEIE 217

Query: 607 ANLRETTT--RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKA 663
           A   E  T  ++L +++  +ER   +     ++ D  TL ++ +++ V+ ER+RQ+E  A
Sbjct: 218 AKDYENHTQQKLLGAMSHLDERSQDIVQSRWLSEDKTTLHDLAEKYEVSAERVRQLEQNA 277

Query: 664 IRKLK 668
           ++KL+
Sbjct: 278 MKKLR 282


>gi|62258694|gb|AAX77814.1| unknown protein [synthetic construct]
          Length = 327

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 123/240 (51%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 82  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI        +E+A++L +  E
Sbjct: 142 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSENIKELAEELGVKEE 199

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+ P  D+D   TS    ++EDK++      +      N +    
Sbjct: 200 TVIEMEKRMCQGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 259

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 260 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 317


>gi|46240842|dbj|BAD15074.1| RNA polymerase alternative sigma factor [Saccharopolyspora
           erythraea]
          Length = 280

 Score = 87.8 bits (216), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 102/212 (48%), Gaps = 8/212 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L +   +A+++++RG    DL Q   +GL+ A ++FD   G  F +YA+  +
Sbjct: 41  RDRLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDPGRGVDFLSYAVPTI 100

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +R+P  +++    V     R+S +  R PTP EIA+ L +    V 
Sbjct: 101 MGEVRRHFRDTGWAVRMPRRLQELHLSVSAAIARLSQEFGRAPTPSEIAEHLGISTNDVY 160

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L+        SL+  + D D   LGD I   +A   LD   +   RET   +LA L  
Sbjct: 161 HGLEAGNAYRSASLDELLTDTDEIPLGDAIGSNDA--ELD---EVENRETIRPLLAELEE 215

Query: 623 REERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           RE R+L MRF  GM      E+VG  Q  V+R
Sbjct: 216 RERRILVMRFFRGMTQTQIAEQVGISQMHVSR 247


>gi|302551910|ref|ZP_07304252.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302469528|gb|EFL32621.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 304

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 121/240 (50%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 69  LEEGTHEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRG 128

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A
Sbjct: 129 VEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVTELA 188

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           ++L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 189 ERLGISNDEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE------DHGLEGIE 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L PR+ ++L +RF  G+    T  E+G++  +++  + ++ ++ + +L+
Sbjct: 242 YVESLKPLIAELPPRDRKILSLRFVAGL----TQSEIGEELGISQMHVSRLLSRTLVRLR 297


>gi|224009562|ref|XP_002293739.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220970411|gb|EED88748.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 316

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 75/272 (27%), Positives = 140/272 (51%), Gaps = 24/272 (8%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN----RGLQFLDLIQEGN 478
           S +E R +VS  R        AK+E+V +N+ LV +V K Y+     RG+   +L+QEG+
Sbjct: 51  SPNELRKVVSEYRS-------AKQELVASNMGLVHAVVKNYSRKAYYRGITIDELVQEGS 103

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAE FD   G +FSTYA  W+K  ++ S  D+   + +P   R   +K+   ++ 
Sbjct: 104 LGLIRAAELFDPAKGLRFSTYATIWIKGVLSNSRVDE--MVLVPQRERQIWNKIREVSKD 161

Query: 539 MSNKIKREPTPEEIAKKLAM---PVEGVRKVLKITKEPISLE------TPIGDEDTSHLG 589
           + ++  R  T + IAKKL +    VE   + +      +SL+      T  G+ D S   
Sbjct: 162 VDDEDGRLST-DMIAKKLGLDKSSVEQNIQRMSSVNNMLSLDYQYASTTRSGETDGSKPF 220

Query: 590 DFIEDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           + +    + S  D A +A  + +    ++ +L  RE +++R+ +G+    ++++++  K 
Sbjct: 221 EALMADKSGSDADLAERAQFKADLVAGLVRNLNEREIQLIRLMYGMHDGHEYSVKDSAKI 280

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             + RE  R +    ++KL+  S  + L+ +L
Sbjct: 281 MGINRETARLLHHACLKKLREASNMESLQEYL 312


>gi|153008567|ref|YP_001369782.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560455|gb|ABS13953.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 303

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 18/234 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP---LDSAIQANLRE 611
            +  + V  + +      SL  P+   + ++    D++ D ++      ++     N R 
Sbjct: 167 KVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSSSQEQVLIEQDELENRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R    ++ D  TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMDTLNDRERRIFEAR---RLSDDPMTLEDLSSEFGISRERVRQIEVRAF 277


>gi|121602584|ref|YP_988464.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614761|gb|ABM45362.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 125/239 (52%), Gaps = 19/239 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  ++ +E +          IA+KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAQLVQEDSTLTKQDIFRSIAEKL 173

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSP--LDSAIQANLR- 610
           ++PV  V ++  + +    SL   I + + S +   D + D++ +    ++ AI    R 
Sbjct: 174 SVPVSDVERMDFRFSGADNSLSVSISENEESPVTKIDNLVDEHPLPDILIEKAIDGQRRT 233

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIE +A++KL+
Sbjct: 234 QWLYDALQILNEREMEIIRFR---RLNDESATLESLGERLGISKERVRQIEVRALQKLR 289


>gi|188090596|gb|ACD49532.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 291

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 55/142 (38%), Positives = 85/142 (59%), Gaps = 4/142 (2%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSS 103
           E+N  +P D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +
Sbjct: 3   EVNDHVPDDLVDLEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEA 62

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
                  D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+
Sbjct: 63  AAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLS 122

Query: 164 FQALIIWRDELNDGTTLLREII 185
            + L+       +G   L EI+
Sbjct: 123 TEMLLADYQAHKEGKKRLAEIV 144


>gi|167766746|ref|ZP_02438799.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
 gi|167711500|gb|EDS22079.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
          Length = 232

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 123/231 (53%), Gaps = 26/231 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++  N+ L+ SV +++TNRG +  DL Q G+IGLMKA +KFD     KFSTYA+  
Sbjct: 18  AREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLSYDVKFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++ ++K+++   +   + +RE T EEI+          
Sbjct: 78  ITGEIRRFLRDDGM-IKVSRSLKENVYKIMKAREKFCQQYQREATIEEIS---------- 126

Query: 564 RKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTT------ 614
            ++ KIT+E I  SLE    + ++ H   + +D + +S LD   +  N  E         
Sbjct: 127 -EITKITREEIVTSLEAS-NEVESIHQSAYQKDGSEISLLDKLSKGENESEKVVDHVLLK 184

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             +  L  +E++++  R+  G     T +E+ K F +++ ++ +I+ K ++
Sbjct: 185 EAMKHLEQKEQQMIYYRYFEG----KTQQEIAKIFHISQVQVSRIQKKILK 231


>gi|149181668|ref|ZP_01860161.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
 gi|148850646|gb|EDL64803.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
          Length = 253

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 114/228 (50%), Gaps = 16/228 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V+ N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD     KFSTYA+  
Sbjct: 33  ARDTIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D   T+++   +++  +++ R    +S    R PT  EIA  L +  E V
Sbjct: 93  IIGEIQRFIRDDG-TVKVSRSLKEMGNRIRRAKDELSKTFGRVPTVNEIAAHLELSPEEV 151

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASL 620
               + ++ P S+   +   D D   L D I D +     D  A++  +RE        L
Sbjct: 152 VMAQEASRSPSSIHETVYENDGDPITLLDQISDTSDQKWFDKIALKEAIRE--------L 203

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++ +R+      D T  EV  +  +++ ++ ++E K +  +K
Sbjct: 204 DERERLIVYLRY----YKDQTQSEVADRLGISQVQVSRLEKKILHNMK 247


>gi|158320823|ref|YP_001513330.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158141022|gb|ABW19334.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 256

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 124/249 (49%), Gaps = 11/249 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I E    + ++ + +     A++ +V  NL LV SV +++ NRG +  DL Q G IGL
Sbjct: 11  VEILEHDRTIELILQAQSGNMEAQEILVNHNLGLVRSVIRRFANRGYEREDLFQLGCIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +KFD     +FSTYA+  +   I R + D    I++   ++    +V  T  ++  
Sbjct: 71  IKAIKKFDTSFDVRFSTYAVPMIIGEIKRFLRDDGI-IKVSRSLKQTAARVKMTKEKLQK 129

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVS 599
           +  REPT +EIA  +    E +   L  +  P  L   I  +D S  HL D I + + + 
Sbjct: 130 ENGREPTLQEIADDMGATKEEIVMALDSSASPEYLYDVIHQDDGSPIHLIDKISENDTLE 189

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +   +  L+E  ++    L PRE +++ +R+      D T  ++ +   +++ ++ +I
Sbjct: 190 DSEVIDRIVLQEAISK----LEPRERQIIFLRYF----KDQTQTQIAQVLGISQVQVSRI 241

Query: 660 EAKAIRKLK 668
           E K ++ +K
Sbjct: 242 EKKVLQNMK 250


>gi|74316363|ref|YP_314103.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
 gi|74055858|gb|AAZ96298.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
          Length = 281

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 127/231 (54%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR+V+S+A+ Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 48  AARRLVLSHLRVVVSIARHYLGYGLPHADLIQEGNVGLMKAVKRFDPDRGVRLVSFALHW 107

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   +      +++     + K+   +R+ ++  N +  +   + +A++L +  + 
Sbjct: 108 IRAEIHEYVLKNYRMVKLATTKAQRKLFFNLRSLKQSLNALTVQQA-DAMAQELNVSRKD 166

Query: 563 VRKV-LKITKEPISLETPI--GDEDTSHLGDFIE-DKNAVSPLDSAIQANLRET-TTRVL 617
           V ++  +++   +S++  +  G++D S +      ++N    L+      LRE+  T  L
Sbjct: 167 VLEMETRLSGHDVSIDPMVDDGEDDYSPIAYLASAEENPAQRLEREQTERLRESGLTSAL 226

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  R   +++ R+ +      TL E+  Q+ V+ ERIRQIEA+A++K++
Sbjct: 227 EELDERSRHIIQARW-LSEGDVATLHELAAQYGVSAERIRQIEARALQKMR 276


>gi|254390381|ref|ZP_05005598.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294813859|ref|ZP_06772502.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197704085|gb|EDY49897.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294326458|gb|EFG08101.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 314

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 85  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 144

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ ++ R PT  E+A  L + 
Sbjct: 145 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQRLDRSPTVPELAAVLGVS 204

Query: 560 VEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 205 EEEVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 260

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 261 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 304


>gi|133473|sp|P26764|RPSF_BACLI RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|304173|gb|AAA22797.1| sporulation protein [Bacillus licheniformis]
          Length = 255

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 132/260 (50%), Gaps = 17/260 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  +  T +   E + ++   + G+ +A   +  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKENQNTQLKDHEVKELIKNSQNGDQKA---RDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + R    +S    R PT +EIA  L +  E V    +  + P S+   +   D D   L 
Sbjct: 120 IRRAKEELSKSNGRIPTVQEIADYLEISSEEVVMAQEAVRSPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D   +  L+E     +  L  RE+ ++ +R+      D T  EV  + 
Sbjct: 180 DQIADQSEEKWFD---KIALKEA----IKDLDEREKLIVYLRY----YKDKTQSEVADRL 228

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ ++E K ++++K+
Sbjct: 229 GISQVQVSRLEKKILKQIKN 248


>gi|329123705|ref|ZP_08252265.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
 gi|327469904|gb|EGF15369.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
          Length = 281

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 123/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G + +++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGA 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|311030733|ref|ZP_07708823.1| sporulation sigma factor SigF [Bacillus sp. m3-13]
          Length = 251

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 129/252 (51%), Gaps = 17/252 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T +   E + ++   + GE EA   +  +V+ N+RLV SV +++ NRG +  DL Q G 
Sbjct: 10  QTYLKDHEVKELIKRSQSGEQEA---RDTIVQKNMRLVWSVVQRFMNRGYEPDDLFQIGC 66

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R I D   ++++   +++  +K+ +    
Sbjct: 67  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-SVKVSRSLKEVANKIRKAKDE 125

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           +S +  R PT  EIA+ L +  E V    +  + P S+   +   D D   L D I D +
Sbjct: 126 LSKRYGRVPTINEIAEFLEITAEEVVLAQEAARAPSSIHETVYENDGDPITLLDQIADHS 185

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                D   +  L+E     +  L  RE+ ++ +R+      D T  EV ++  +++ ++
Sbjct: 186 EHRWFD---KIALKEA----IEELDEREKLIVYLRY----YKDQTQTEVAQRLGISQVQV 234

Query: 657 RQIEAKAIRKLK 668
            ++E K ++++K
Sbjct: 235 SRLEKKILQQMK 246


>gi|157692844|ref|YP_001487306.1| sporulation sigma factor SigF [Bacillus pumilus SAFR-032]
 gi|194016850|ref|ZP_03055463.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
 gi|157681602|gb|ABV62746.1| DNA-directed RNA polymerase sigma subunit SigF [Bacillus pumilus
           SAFR-032]
 gi|194011456|gb|EDW21025.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
          Length = 255

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/260 (27%), Positives = 134/260 (51%), Gaps = 19/260 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  + +  +S  E + ++   + G+ +A   +  +VE N+RLV SV +++ NRG +  
Sbjct: 4   EVKKQAKKAQLSNDEVKELIKKSQDGDQQA---RDLLVEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + R    +S    R PT +EIA+ L +  E V    +  + P S+   +   D D   L 
Sbjct: 120 IRRARDELSKSHGRMPTVQEIAEYLDITPEDVVLAQEAVRTPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I D +     D  A++  ++E        L  RE+ ++ +R+      D T  EV ++
Sbjct: 180 DQIADHSEERWFDKIALKEAIKE--------LEEREKLIVYLRY----YKDQTQSEVAER 227

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ ++ ++E K +++++
Sbjct: 228 LGISQVQVSRLEKKILKQIQ 247


>gi|145639818|ref|ZP_01795419.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|145271036|gb|EDK10952.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|309750314|gb|ADO80298.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2866]
          Length = 281

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 123/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDSA-IQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E  + 
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLSA 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|49473931|ref|YP_031973.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49239434|emb|CAF25783.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 294

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 124/245 (50%), Gaps = 16/245 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G + +TYA+WW
Sbjct: 49  AAHRLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGLRLATYAIWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      ++I      K  ++    R++ ++++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKIGTTANQK--RLFFNLRKLKSRLQVLDKGDLNAEQVKEIATQL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED---KNAVSPLDSAIQANLRE 611
            +  + V  + +      SL  P+  +  + S   D++ D       + ++ +   N R 
Sbjct: 167 NVTEDEVISMNRRLCGDTSLNAPLRTQEGENSEWQDWLVDDSNNQEQTLIEQSELENRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             T  +++L  RE+R+ + R     +   TLEE+  +F ++RER+RQIE +A  K+++  
Sbjct: 227 MLTYAMSNLNEREKRIFKARR--LSDKPLTLEELSSEFNISRERVRQIEMRAFEKVQNSI 284

Query: 672 RSKKL 676
           ++  L
Sbjct: 285 KASAL 289


>gi|290959865|ref|YP_003491047.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
 gi|260649391|emb|CBG72506.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
          Length = 304

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 119/240 (49%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 69  LEEGTYEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRG 128

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A
Sbjct: 129 VEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVGELA 188

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           ++L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 189 ERLGLTNDEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE------DHGLEGIE 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L PR+ ++L +RF   M    T  E+G +  +++  + ++ ++ + +L+
Sbjct: 242 YVESLKPLIAGLPPRDRQILSLRFVANM----TQSEIGDELGISQMHVSRLLSRTLVRLR 297


>gi|238899138|ref|YP_002924820.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466898|gb|ACQ68672.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 285

 Score = 87.8 bits (216), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 127/238 (53%), Gaps = 19/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AARQLILSHLRFVAHIARHYSGYGLPQADLIQEGNIGLMKAVRRFNPNMGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R A++      +    + +AK+L +  + 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFSQNEV-DMVAKELGVTSKD 167

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQAN-----LR 610
           VR++  +++ + ++ E P+  ED S  G       ++EDKN  S     I+ N       
Sbjct: 168 VREMESRMSAQDMAFELPL--EDESREGQSPAPVMYLEDKN--SDFADNIEKNNWGDHAA 223

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++    L  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 224 DSLWVALKGLDERSQDIIRARW-LDDDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 280


>gi|260913469|ref|ZP_05919947.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
 gi|260632409|gb|EEX50582.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
          Length = 281

 Score = 87.4 bits (215), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 122/232 (52%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   E +A +L +  E
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVEMVANELGVTPE 166

Query: 562 GVRKV-LKITKEPISLETPIGD-EDTSHLGDFIEDK--NAVSPL-DSAIQANLRETTTRV 616
            V ++  ++T   ++ + P  D E+T     ++EDK  N  + L D   +    E  +  
Sbjct: 167 DVMEMESRMTGSDVAFDLPTDDSEETYSPALYLEDKGSNFAAELEDENYETQATEQLSVA 226

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  R   +++ R+    +   TL+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 227 LEGLDERSLDIIKSRWLD--DNKATLQDLAAKYNISAERVRQLETNALKKLK 276


>gi|328883832|emb|CCA57071.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 303

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+
Sbjct: 74  ERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTF 133

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+A  L + 
Sbjct: 134 AMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVTELAAVLGVS 193

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
            E V   L +       SL++P  ++D       + D+      D+A++    RE+   +
Sbjct: 194 EEDVVDGLAVGNAYTASSLDSPSPEDDGGE--GSLADRLGYE--DTALEGVEYRESLKPL 249

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
           LA L PRE +++ +RF   M      EEVG  Q  V+R   R +
Sbjct: 250 LAKLPPRERQIIMLRFFANMTQSQIGEEVGISQMHVSRLLTRTL 293


>gi|306844750|ref|ZP_07477335.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
 gi|306274922|gb|EFM56692.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
          Length = 311

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 127/249 (51%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E++  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEESGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|115521899|gb|ABJ09417.1| RNA polymerase sigma factor [Brevundimonas diminuta]
          Length = 275

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 91/305 (29%), Positives = 149/305 (48%), Gaps = 34/305 (11%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           +GEIAIAKRIEAGR  M++ LCES LTF+A+++WR+EL +   LLRE+IDL+A  G  + 
Sbjct: 1   KGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWREELANNRILLREVIDLDATYGILNP 60

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
               H     +    E     +E DD    +G   S + +  + R  V    +    D  
Sbjct: 61  SSLPHNQPAPAQPTGEPDGDGEEDDDEDFDDGGAMSISALEAELRDGVMEVLDAIAVDFG 120

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
              + +D        +E +L+ +V+ A D+  + Y  L +   + +   K   ++ + + 
Sbjct: 121 EFRKLQD------KLVEARLKGEVLTAKDQ--KTYEALTASISDRLKTMK--LNNARIEA 170

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD-VFLERHQ 375
           L E+L  +   L   + R+  L +  Y IS+       E L+    +G + D  + ER  
Sbjct: 171 LVEQLYAINKRLIGQEGRLLRLADG-YGISR------PEFLK--AYFGSEMDPTWAERI- 220

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
            +E+   W      F E E     A ++D+   IR +I +++ E G+ I ++R IV MV+
Sbjct: 221 -KEMGVRWTK----FSENE-----AAQIDT---IRTQIAAVATEAGVPIDDYRRIVQMVQ 267

Query: 436 KGECE 440
           KGE E
Sbjct: 268 KGERE 272


>gi|163853281|ref|YP_001641324.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|218532097|ref|YP_002422913.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|254563204|ref|YP_003070299.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|163664886|gb|ABY32253.1| RNA polymerase sigma factor, sigma-70 family [Methylobacterium
           extorquens PA1]
 gi|218524400|gb|ACK84985.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|254270482|emb|CAX26482.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 290

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 125/250 (50%), Gaps = 41/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 41  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPEREVRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E    EI  ++A  +
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTEEQVGSEIHGRIATAI 158

Query: 561 EGVRKVL-----KITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              R+ +     +++   +SL  P+G+E   +S   DF+ D NA  P ++          
Sbjct: 159 GVSREDVALMDARLSGPDMSLNAPVGEESEASSERMDFLVD-NAALPDET---------- 207

Query: 614 TRVLASLTPREERVLRMRFGIGMNT---------------DHTLEEVGKQFCVTRERIRQ 658
              +++L   E R++ +R  + + +                 TLE +G +  +++ER+RQ
Sbjct: 208 ---VSALVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLEALGHRLGISKERVRQ 264

Query: 659 IEAKAIRKLK 668
           IE +A+ KL+
Sbjct: 265 IENRALEKLR 274


>gi|260575497|ref|ZP_05843496.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259022417|gb|EEW25714.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 298

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 120/244 (49%), Gaps = 17/244 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAM
Sbjct: 47  ATAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAM 106

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIAKKL- 556
           WW++ +I   I      +++      K  K+    R+   K+    + +  PE +A+   
Sbjct: 107 WWIRASIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKAKVGALEEGDLRPENVARIAH 164

Query: 557 ---AMPVEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL-- 609
                  E +    +++    SL   +G   E ++   D++ED+++    D A +  L  
Sbjct: 165 DLNVSETEVIDMNRRLSGGDASLNATVGSDGEGSTQWQDWLEDEDSDQANDYAERNELEM 224

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    + +A L  RE+ +L  R     +   TLE++   + V+RERIRQIE +A  KL+
Sbjct: 225 RRALLVQAMAVLNDREKDILMQRRLA--DEPVTLEDLSASYGVSRERIRQIEVRAFEKLQ 282

Query: 669 HPSR 672
              R
Sbjct: 283 ERMR 286


>gi|284028684|ref|YP_003378615.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283807977|gb|ADB29816.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 275

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 110/223 (49%), Gaps = 24/223 (10%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E +E NL +  S+A ++  RG++  DL Q   +GL+KAA  ++   G  F  YA+  ++
Sbjct: 47  NEAIELNLGIAHSIASRFRGRGVESDDLDQVAYLGLLKAARSYNPSTGTPFLAYAVPTIR 106

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM------- 558
             + R   D S T+RIP  +++    +     ++   ++R+PT EE+A +L         
Sbjct: 107 GEVKRYFRDCSWTVRIPRRLQELQGSIASVRPQLVQDLQRDPTLEELAAELGTDVAEVEA 166

Query: 559 --PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               +G   VL       SL+ P+  + T++L D I D+   S   +   A L      V
Sbjct: 167 AIAADGCFSVL-------SLDRPVDGDSTANLADTIADEEDTSFERTEAVAMLEP----V 215

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           L  LTPRE ++L +RF  G    HT  ++G +  V++ ++ ++
Sbjct: 216 LNDLTPRERKILELRFIEG----HTQADIGAEIGVSQMQVSRL 254


>gi|319406278|emb|CBI79915.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 303

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 119/247 (48%), Gaps = 35/247 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPEREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM-------SNKIKREPTPEEIAKKL 556
           ++ +I   I      +R       K   +    RR+        N + ++     I++KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLAQDDNTLTKQEIFSAISEKL 173

Query: 557 AMPVEGVRKV---LKITKEPISL------ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            + V  V K+      T   +SL      ETPI   D+      I+D     PL  A+  
Sbjct: 174 GVSVNDVEKMDFRFSGTDNSLSLSISESGETPIAKMDS-----LIDDH----PLPDAVIE 224

Query: 608 NLRETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            + +   R       L  L  RE  ++R R         TLE +G++  +++ER+RQIEA
Sbjct: 225 QVIDGQRRAQWLYEALQILNERELEIIRFRR--LKEEGATLEVLGEKLGISKERVRQIEA 282

Query: 662 KAIRKLK 668
           +A++KL+
Sbjct: 283 RALQKLR 289


>gi|238021049|ref|ZP_04601475.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
 gi|237868029|gb|EEP69035.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
          Length = 290

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 79/291 (27%), Positives = 152/291 (52%), Gaps = 24/291 (8%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           ++A   P G         ++  +   N I  +++E   S+++ R +     +G+ EA+  
Sbjct: 4   AFALSVPSGH------GSLEQYIHTVNSIPMLTLEEETSLAQ-RQL-----RGDLEAA-- 49

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            K+++ ++LR+V+S+A+ Y   GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+
Sbjct: 50  -KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNVGLMKAVKRFEPTHGARLFSFAVHWI 108

Query: 505 KQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           K  I   I      +RI     + K+   +R+ R+  + +  +   ++IA  L + +  V
Sbjct: 109 KAEIHEFILRNWRLVRIATTKPQRKLFFNLRSMRKSLSALSPKEA-QDIADDLGVKLSDV 167

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANL---RETTTRVL 617
            ++  ++T   ++L     D+D ++    D++ D ++      A +A+     E     L
Sbjct: 168 LEMEQRMTGNDVALLADNSDDDDNNFAPIDWLSDDSSEPSQQLAKKAHYALQTEGLRNAL 227

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L  R  R++  R+ +  +   TL E+  +F V+ ERIRQIEAKA++KL+
Sbjct: 228 SQLDERSRRIVETRW-LQDDGGLTLHELAAEFGVSAERIRQIEAKAMQKLR 277


>gi|332524130|ref|ZP_08400360.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
 gi|332107469|gb|EGJ08693.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
          Length = 306

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 128/254 (50%), Gaps = 28/254 (11%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+     +V ++LRLV+SV+++Y   GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 52  GDLEAA---GRLVLSHLRLVVSVSRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRL 108

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            +YA+ W+K  I   I      +++      +  K+    R M   +K E    ++ +  
Sbjct: 109 VSYALHWIKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGLKGEAAEADLHRST 166

Query: 557 AMP--VEGVRKVLKITK-EPISLETPIGDEDTSHLGDFIEDKNAVSPL----DSA----- 604
             P  VE V + L +   E + +ET +   D +      + + + +P+    D A     
Sbjct: 167 LTPAEVETVARELNVKPDEVVEMETRLAGGDVALEPQTDDSEESFAPIAYLADEASEPTR 226

Query: 605 -IQANLRETTT-----RVLASLTPREERVLRMRFGIGMNTDH----TLEEVGKQFCVTRE 654
            ++A  R+  +     + L+ L  R  R++  R+ + +N D     TL E+  ++ V+ E
Sbjct: 227 LLEARRRDWLSGDGIAQALSVLDARSRRIVEERW-LKVNDDSSGGMTLHELAAEYGVSAE 285

Query: 655 RIRQIEAKAIRKLK 668
           RIRQIE  A++K++
Sbjct: 286 RIRQIEVAAMKKMR 299


>gi|182418456|ref|ZP_02949750.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237666966|ref|ZP_04526951.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377838|gb|EDT75382.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237658165|gb|EEP55720.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 252

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 125/241 (51%), Gaps = 14/241 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++S+ +KG+ +A     +++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD
Sbjct: 19  LLSLAKKGDNDAM---NKLIEINLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++  +++    K+     +++NK+KR PT 
Sbjct: 76  LNYNVKFSTYAVPMIMGEIKRFLRDDGM-IKVSRNVKSLARKIHYYREQLTNKLKRSPTI 134

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQA 607
           EE+A+   +  E +   ++       L   I  +D +   L D + +K     ++   + 
Sbjct: 135 EELAEYAGVEKEEIVFAIESANSLQYLYDTIHQDDGAPVMLIDKLSEKKGEDDVNLIEKI 194

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E     L SL  +  +++ +R+      D T  +V K   +++ ++ +IE K + ++
Sbjct: 195 ALKEA----LRSLDEKARQIIMLRYF----KDKTQIQVAKMLGISQVQVSRIEKKVLLQM 246

Query: 668 K 668
           K
Sbjct: 247 K 247


>gi|145631055|ref|ZP_01786830.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148827424|ref|YP_001292177.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittGG]
 gi|144983340|gb|EDJ90822.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148718666|gb|ABQ99793.1| RNA polymerase sigma factor [Haemophilus influenzae PittGG]
 gi|301168923|emb|CBW28517.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus influenzae
           10810]
          Length = 281

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 123/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E  + 
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLSA 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|328542017|ref|YP_004302126.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326411767|gb|ADZ68830.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 289

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 79/236 (33%), Positives = 122/236 (51%), Gaps = 27/236 (11%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVI+VA ++ N GL   DLIQEG++GL++AA +F+     +FSTYA WW++ +I  
Sbjct: 48  AHMRLVIAVASRFRNFGLPMNDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQD 107

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI--KREPTPE-EIAKKLAMPVEGVRKV- 566
            I      +R       K   +    RR+  K+   R   PE E+ +++A  + GV+   
Sbjct: 108 YILRNWSIVRGGTSSTQK--ALFFNLRRLRAKLSSNRVDLPETELHRQIAEAI-GVKTAD 164

Query: 567 -----LKITKEPISLETPIGDEDTSHL--GDF-IEDKNAVSPL-DSAIQANL-RETTTRV 616
                 +++    SL  PI D D S     DF I D    +PL D  +  N+  E   R 
Sbjct: 165 VDLMNARLSGPDTSLNAPIIDSDGSSADRQDFLISD----APLPDETVSENIDSERQRRW 220

Query: 617 LAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L S    LT RE +++  R         TLE +G +  +++ER+RQIE +A+ KL+
Sbjct: 221 LRSAMNVLTERERKIVSERRLT--EEGATLEALGAKMGISKERVRQIENRALEKLR 274


>gi|253686510|ref|YP_003015700.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251753088|gb|ACT11164.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 285

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKHLILSHLRFVIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++    +   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQR--KLFFNLRKTKTRLGWFNQDEVELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-- 612
            VR++  ++  + ++ + P  +ED SH G       +++DK+  S     I+ +  +T  
Sbjct: 167 DVREMESRMAAQDMTFD-PTPEED-SHDGKAMSPMLYLQDKS--SDFADGIEEDNWDTHA 222

Query: 613 ---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 223 ADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|118497682|ref|YP_898732.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           novicida U112]
 gi|194323654|ref|ZP_03057430.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|254373048|ref|ZP_04988537.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|254374500|ref|ZP_04989981.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|118423588|gb|ABK89978.1| RNA polymerase sigma-32 factor [Francisella novicida U112]
 gi|151570775|gb|EDN36429.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3549]
 gi|151572219|gb|EDN37873.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|194322018|gb|EDX19500.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|332678395|gb|AEE87524.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida Fx1]
          Length = 292

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 124/240 (51%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI    + +  E+A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSEDIKELAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+ P  D+D   TS    ++EDK++      +      N +    
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 233

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 234 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|119776597|ref|YP_929337.1| RNA polymerase factor sigma-32 [Shewanella amazonensis SB2B]
 gi|119769097|gb|ABM01668.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella amazonensis
           SB2B]
          Length = 285

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 127/245 (51%), Gaps = 36/245 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      +++      +  K+    R+   ++      E     +AM  E  
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKAKQRLGWFSDDE-----VAMVAEN- 163

Query: 564 RKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKN---AVSPL------DSAIQANLR--- 610
              L ++K+ ++ +E+ +  +D +   D + D +     +P+       S + AN+    
Sbjct: 164 ---LGVSKDDVTEMESRMAAQDQAF--DLVNDHDDDEGFAPVHYLEDHSSDLAANIENDN 218

Query: 611 ---ETTTRVLASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKA 663
                  R++A++   +ER   +LR R+   ++ D  TL+E+ +Q+ V+ ERIRQ+E  A
Sbjct: 219 WESNAQNRLIAAIKTLDERSQHILRARW---LDDDKVTLQELAEQYQVSAERIRQLEKNA 275

Query: 664 IRKLK 668
           + KLK
Sbjct: 276 MNKLK 280


>gi|302867457|ref|YP_003836094.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|315506134|ref|YP_004085021.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|302570316|gb|ADL46518.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
 gi|315412753|gb|ADU10870.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 269

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 120/227 (52%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + +++EA L L   +A +Y+ RG    DL Q   +GL+KA ++FD   G  F+ +A+  +
Sbjct: 46  RNQVIEAWLPLANHLAARYSGRGEPAGDLAQTAALGLIKAVDRFDASRGVDFAGFAIPTI 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  +++   ++      ++  + R PT  +IA  L +  E V 
Sbjct: 106 LGEIKRHFRDRTWNIRVPRRLQELRLRISEANSTLTQTLNRAPTVADIAAHLDVTEEEVL 165

Query: 565 KVLKITK--EPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+  +    +SL TPIGD D+ + LGD +  ++    L     A+LR +    LA+L 
Sbjct: 166 EGLEGARAYNAVSLSTPIGDGDSATELGDTLGTEDNEYEL-----ADLRASLGPALATLD 220

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+++L +RF      + T  E+  +  V++  + ++ A+A+ KL+
Sbjct: 221 EREQKILTLRF----YGNLTQSEIAARVGVSQMHVSRLLARALTKLR 263


>gi|293391201|ref|ZP_06635535.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951735|gb|EFE01854.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 282

 Score = 87.4 bits (215), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 72/274 (26%), Positives = 144/274 (52%), Gaps = 20/274 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  NE   ++ E    ++E      +  K + EA+   K++V ++LR VI VA+ 
Sbjct: 16  IEAYIRAANEYPMLTAEEEKELAE-----RLYYKEDIEAA---KKLVLSHLRFVIHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+      E   + +A +L +  + V ++  ++T   ++ + P
Sbjct: 128 TTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSPQDVMEMESRMTGADVAFDLP 185

Query: 580 I--GDEDTSHLGDFIEDK--NAVSPLDSA-IQANLRETTTRVLASLTPREERVLRMRFGI 634
               DE+T     ++EDK  N  + L++   +A   +     L +L  R + +++ R+  
Sbjct: 186 GDEHDEETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDARSQDIIKARWLD 245

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              T  TL+++  ++ ++ ER+RQ+EA A++KLK
Sbjct: 246 --ETKATLQDLAAKYNISAERVRQLEANALKKLK 277


>gi|319945291|ref|ZP_08019553.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
 gi|319741861|gb|EFV94286.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
          Length = 298

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 121/236 (51%), Gaps = 14/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRLV+SVA++Y   GL   DLIQEGNIGLMKA ++FD     +  ++A+ W
Sbjct: 59  AARTLVTSHLRLVVSVARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDRSVRLVSFALHW 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPV 560
           +K  I   I      +++      +  K+    R M   +    TPE   +IA++L +  
Sbjct: 119 IKAEIHEYILKNWRLVKVATTKAQR--KLFFNLRSMKKDLD-TLTPEAVTDIAEQLNVRE 175

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR-----ETTT 614
           + V ++  ++T   I+LE    DE+ +  G         S     I+   R     E  +
Sbjct: 176 KDVTEMETRMTGHEIALEPQGDDEEGAGFGPAAYLAAPGSEPTEIIEDRQRDWLQTEGLS 235

Query: 615 RVLASLTPREERVLRMRF--GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LA+L  R   +++ R+          TL+++  ++ V+ ERIRQIEA+A++K+K
Sbjct: 236 NALATLDERSRNIVQSRWLRDEDEGGSRTLQDLANEYGVSAERIRQIEAQAMKKMK 291


>gi|20807766|ref|NP_622937.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|20516321|gb|AAM24541.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
          Length = 240

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 116/234 (49%), Gaps = 14/234 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K   +AS+ K  ++  N  L+ S+ KK+ NRG +  DL Q G IG +KA +KFD     K
Sbjct: 14  KNNDKASLEK--LILENSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAVQKFDESYNVK 71

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA+  +   I R + D    I++   +++   K       +SN++ REPT  EIA++
Sbjct: 72  FSTYAVPIIMGEIKRFLRDDGL-IKVSRSLKELSSKAFYMKEVLSNELNREPTINEIAER 130

Query: 556 LAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           L +  E +    +      SL   I  +E+   L + + DK     L+  +      T  
Sbjct: 131 LNVTPEEIAMAFESAATAESLYDSISHEEEDRQLIEMVGDKEDSVDLEEKL------TLH 184

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  L PRE++V+ +R+      D T  EV     +++ ++ +IE K + K++
Sbjct: 185 MIIDKLKPREKQVIFLRYF----KDMTQTEVANILGISQVQVSRIEKKVLEKIR 234


>gi|225569422|ref|ZP_03778447.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
 gi|225161630|gb|EEG74249.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
          Length = 237

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 122/241 (50%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A+ ++VE N  LV  + K++ NRG +  DL Q GNIGL+KA +KF
Sbjct: 3   HTIALIKKSHQGDEKARAQLVEENAGLVWCIVKRFYNRGAEAEDLFQVGNIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      ++   + REPT
Sbjct: 63  DMSYEVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELSYKAYLCQEKLQEALGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EIA+ L +  E +   L  + +  SL  PI  ++    G  I   + +   +   +  
Sbjct: 122 ITEIAEYLEVDREELTMALDASGDIESLHKPIYQKE----GQEIRLMDKLPEKEGGEEKI 177

Query: 609 LRETTTRVLASLTPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L     + L     ++ER ++ +R+      + T  +VG++  +++ ++ ++E K +++L
Sbjct: 178 LNHMLLQQLLEYLNKDERQLIYLRY----FANQTQSQVGQELGISQVQVSRLEKKILKRL 233

Query: 668 K 668
           +
Sbjct: 234 R 234


>gi|319760734|ref|YP_004124672.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318039448|gb|ADV33998.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 284

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 119/231 (51%), Gaps = 8/231 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ +A+ Y+  GL   DLIQEGNIGLMK+  +F+  L  +  ++A+ W
Sbjct: 51  AAKKLIVSHLRFVVHIARNYSGYGLAQADLIQEGNIGLMKSVRRFNPELDVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      ++I      R     + +T +R+      E   E +AK L +  +
Sbjct: 111 IKSEIHEYVLKNWRIVKIATTKAQRKLFFNLRKTKQRLG--WFNEEEIEMVAKTLHVTCK 168

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD---FIEDKNAVSPLDSAIQANLRETTTRVL 617
            VR++  ++  + ++ E    D++ + L     +++DK  +   +      +       L
Sbjct: 169 DVREMESRMAAQDMTFEQSSDDDEKNILSIPMLYLQDKVTMIDEEEEWINQVSNKLNIAL 228

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            SL  R + ++R R+    +   TL+E+  Q+ V+ ERIRQ+E  A++K+K
Sbjct: 229 NSLDKRSQHIIRARWLNTNDNKTTLQELANQYGVSAERIRQLEKNAMKKMK 279


>gi|299472548|emb|CBN77333.1| RNA polymerase sigma factor SigD [Ectocarpus siliculosus]
          Length = 825

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 81/279 (29%), Positives = 133/279 (47%), Gaps = 30/279 (10%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAE 486
           V  +R+   E   AK+E+V  NL LV  + K Y  T    +F   DL Q+  +GL++A E
Sbjct: 97  VESLRQALDEGEKAKQELVLDNLNLVDIIVKNYVGTFAYGRFTEKDLTQDATVGLIRAVE 156

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G+ F+TY  WWV++ +   + + +  +RIP     +I KV R    +  ++ R 
Sbjct: 157 KFDPEKGFFFATYGRWWVRKYLHEGVQNHNRMVRIPNSAAYRIAKVKRVRDELEGELGRA 216

Query: 547 PTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIGDEDT---SHLGD-FIEDKNA 597
           PT  EIA +  + V+ V   L     +I +    +    G  DT   SH G+ F+   + 
Sbjct: 217 PTKPEIALETDLTVQQVEACLEQDSFRIERLDGYMGHGFGMADTVFASHFGEGFLYGSDM 276

Query: 598 VS-PLDSA---------IQANLRETTTRVLASLTPREER-VLRMRFGIGMNTDHTLEEVG 646
           ++ P ++          IQ++LR   +     L    ER  L +R+G+     +++E+  
Sbjct: 277 LTHPGETPAPTVEGEKVIQSSLRGDLSSAFVRLLDATERECLVLRYGLHDGVTNSIEQTA 336

Query: 647 K--QFCVTRERIRQIEAKAIRKLKH---PSRSKKLRSFL 680
               FC   + +R I  +A+ KL+    P   KKL S+L
Sbjct: 337 AIMDFCDP-DDVRIITTQAMAKLRDGCLPEERKKLMSYL 374


>gi|114331030|ref|YP_747252.1| RNA polymerase factor sigma-32 [Nitrosomonas eutropha C91]
 gi|114308044|gb|ABI59287.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas eutropha C91]
          Length = 280

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 79/277 (28%), Positives = 134/277 (48%), Gaps = 27/277 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S E  IS+++      M   G+  A+    ++V ++LR V+ +A+ 
Sbjct: 15  LESYIRAANSFPVLSREEEISLAK-----KMQENGDINAA---HQLVLSHLRTVVMIARG 66

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +FD   G +  ++A+ W+K  I   I      ++I 
Sbjct: 67  YLGYGLPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIKAEIHEFIMRNWRLVKIA 126

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R M   +      E   +A++L +  E V ++  + +   ISLE P
Sbjct: 127 TTKPQR--KLFFNLRSMKEGLDTMNQAEVATMAEQLGVKAEEVVEMETRFSGRDISLE-P 183

Query: 580 IGDEDTSHLGDFIEDKNAVSP--------LDSAIQANLRETTTRVLASLTPREERVLRMR 631
           + D D           +   P        L+    A L+++    L SL  R  R++  R
Sbjct: 184 LTDSDEEDFSPIAYLTDGSDPSRELEKEQLERLTHAKLKDS----LDSLDERSRRIIEAR 239

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +  +   TL E+ K+  V+ ER+RQIEAKA++K++
Sbjct: 240 W-LREDKAATLHELAKELGVSAERVRQIEAKAMKKMR 275


>gi|52080862|ref|YP_079653.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|52786234|ref|YP_092063.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|319645181|ref|ZP_07999414.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
 gi|52004073|gb|AAU24015.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus licheniformis ATCC 14580]
 gi|52348736|gb|AAU41370.1| SigF [Bacillus licheniformis ATCC 14580]
 gi|317392990|gb|EFV73784.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
          Length = 255

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 132/260 (50%), Gaps = 17/260 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  +  T +   E + ++   + G+ +A   +  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKENQNTQLKDHEVKELIKNSQNGDQKA---RDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + R    +S    R PT +EIA  L +  E V    +  + P S+   +   D D   L 
Sbjct: 120 IRRAKDELSKSNGRIPTVQEIADYLEISSEEVVMAQEAVRSPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D   +  L+E     +  L  RE+ ++ +R+      D T  EV  + 
Sbjct: 180 DQIADQSEEKWFD---KIALKEA----IKDLDEREKLIVYLRY----YKDKTQSEVADRL 228

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ ++E K ++++K+
Sbjct: 229 GISQVQVSRLEKKILKQIKN 248


>gi|300782223|ref|YP_003762514.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299791737|gb|ADJ42112.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 259

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 110/223 (49%), Gaps = 15/223 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L L  ++A+K+ NR     DL+Q   +GL+ A ++FD   G  F  +A+  +   
Sbjct: 38  LVRTHLELARNLARKFRNRDEAMEDLVQIATVGLIHAVDRFDPAQGTDFLAFAVPTISGE 97

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +     D S ++R+P  +++    +      ++ ++ R P P EIA +L +P+E V + L
Sbjct: 98  LRHHFRDNSWSVRVPRRLKELNANISAAREELTVQLSRAPKPSEIAARLGVPIEDVYEGL 157

Query: 568 KITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  +         G    S  HL +        +P     QA LRE    +L SL  RE 
Sbjct: 158 RAGQ---------GRYGASLDHLLENAAHTRFGAPDAELGQAELREALRPMLESLPERER 208

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +RFG GM+      ++ ++  V++ ++ ++ A  ++KL+
Sbjct: 209 KIVALRFGSGMSQS----DIARRVGVSQMQVSRLLAATLKKLR 247


>gi|290796544|gb|ADD64842.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 284

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 4/137 (2%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +     
Sbjct: 3   LPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAAALT 62

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
             D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+
Sbjct: 63  ALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLL 122

Query: 169 IWRDELNDGTTLLREII 185
              +   +G   L EI+
Sbjct: 123 ADYEAHKEGKKRLAEIV 139


>gi|290796534|gb|ADD64837.1| RNA polymerase sigma factor [Xanthomonas dyei]
          Length = 283

 Score = 87.4 bits (215), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 83/137 (60%), Gaps = 4/137 (2%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +     
Sbjct: 1   LPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAAALT 60

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
             D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+
Sbjct: 61  ALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLL 120

Query: 169 IWRDELNDGTTLLREII 185
              +   +G   L EI+
Sbjct: 121 ADYEAHKEGKKRLAEIV 137


>gi|320539367|ref|ZP_08039036.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
 gi|320030492|gb|EFW12502.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
          Length = 285

 Score = 87.0 bits (214), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 124/235 (52%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ A+LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILAHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGD--FIEDKNAVSPLD---SAIQANLRETT 613
            VR++  ++  + ++ +    DE  D   L    +++DK++    D      ++N  +  
Sbjct: 167 DVREMESRMAAQDMTFDPAPDDETRDGQSLAPVLYLQDKSSDFAEDIEEDNWESNAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KLK
Sbjct: 227 AYALEGLDERSQHIIRARW-LDNDNKSTLQELADQYGVSAERVRQLEKNAMKKLK 280


>gi|319775860|ref|YP_004138348.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
 gi|317450451|emb|CBY86667.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
          Length = 281

 Score = 87.0 bits (214), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 123/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G + +++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGV 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|262278444|ref|ZP_06056229.1| EsvH [Acinetobacter calcoaceticus RUH2202]
 gi|262258795|gb|EEY77528.1| EsvH [Acinetobacter calcoaceticus RUH2202]
          Length = 288

 Score = 87.0 bits (214), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 121/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTAEQ 171

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 172 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLVENEDWEEQSTSALH 230

Query: 619 S----LTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 NAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|251793696|ref|YP_003008426.1| RNA polymerase factor sigma-32 [Aggregatibacter aphrophilus NJ8700]
 gi|247535093|gb|ACS98339.1| alternative sigma factor RpoH [Aggregatibacter aphrophilus NJ8700]
          Length = 282

 Score = 87.0 bits (214), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 125/233 (53%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++V ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKKLVLSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PV 560
           +K  I   +      +++      R     + +T +R     + E   + +A +L + P 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRFGWFSENE--VDMVANELGVSPQ 166

Query: 561 EGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDK--NAVSPLDSA-IQANLRETTTR 615
           + V    ++T   ++ + P    DE+T     ++EDK  N  + L++   +A   +    
Sbjct: 167 DVVEMESRMTGADVAFDLPTDDHDEETYAPALYLEDKGSNFAAELENENYEAQATDRLAV 226

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  R + +++ R+     T  TL+++ +++ ++ ER+RQ+E  A++KLK
Sbjct: 227 ALDNLDARSQDIIKARWLD--ETKATLQDLAEKYNISAERVRQLETNALKKLK 277


>gi|117926357|ref|YP_866974.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117610113|gb|ABK45568.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 297

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 121/230 (52%), Gaps = 9/230 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V A+LRLV+ +A++Y        DL+QEG+IGLM A +KFD   G + +TYA+WW
Sbjct: 56  AAHRLVHAHLRLVLKIAREYLYYRSSLPDLVQEGSIGLMHAVKKFDAQRGNRLATYAVWW 115

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++ AI   I + +  +++    ++  +   +R A+     + ++   EE+A K A   + 
Sbjct: 116 IRAAIHDFILNTAHMVKVATTKLKRHLFFKLRQAKSSLAPLNQQEA-EELAVKFATDAQT 174

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LA 618
           + ++  ++     SL  P+ DE    L + +ED+     L        +     V   L 
Sbjct: 175 ILEMDSRLAGADSSLNQPLFDEG-GELIELLEDERPNQELQLQSAQQQQRLGRLVKQGLK 233

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ ++  RF +G + +   E++ ++F ++ ER+RQIE +A+ KL+
Sbjct: 234 QLNEREQAIIISRF-MGEHAE-PREQLAQRFQISGERVRQIEQRAMAKLR 281


>gi|295698248|ref|YP_003602903.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|295698251|ref|YP_003602906.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157186|gb|ADD79631.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157289|gb|ADD79734.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
          Length = 286

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 126/240 (52%), Gaps = 22/240 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI ++K Y+  GL   DLIQEGN+GLMKA +KF+     +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHISKNYSGYGLLQADLIQEGNVGLMKAVQKFNPNASVRLVSFAIHW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   I      +++      +  K+    RR   KI      E   +AKKL +  +
Sbjct: 108 IKAEIHEYILRNWRIVKVATTKAQR--KLFFNLRRNKKKIGWFDQTEIDSVAKKLGVSKK 165

Query: 562 GVRKV--LKITKEPISLETPIGDEDTSHLGDF-------IEDKNAVSPLDSAIQANLRET 612
            VR++    + K+ +     I +E+     DF       +EDK++ +  +S  + N    
Sbjct: 166 DVREMESRMVAKDMV---FDINEEENRMKDDFFLIPALYLEDKSS-TFFESLEKDNWENH 221

Query: 613 T----TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T    T+ L+ L  R + +++ R+ +  +   TL+++ KQ+ V+ ERIRQ+E  A++K++
Sbjct: 222 TIKRLTQALSKLDKRSQEIIKKRW-LNQSGRETLQDLAKQYKVSAERIRQLEKNAMKKIR 280


>gi|188583534|ref|YP_001926979.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179347032|gb|ACB82444.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 290

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 125/250 (50%), Gaps = 41/250 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 41  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPERDVRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E    EI  ++A  +
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTEEQVGSEIHGRIASAI 158

Query: 561 EGVRKVL-----KITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              R+ +     +++   +SL  P+G+E   +S   DF+ D NA  P ++          
Sbjct: 159 GVSREDVALMDARLSGPDMSLNAPVGEESEASSERMDFLVD-NAALPDET---------- 207

Query: 614 TRVLASLTPREERVLRMRFGIGMNT---------------DHTLEEVGKQFCVTRERIRQ 658
              +++L   E R++ +R  + + +                 TLE +G +  +++ER+RQ
Sbjct: 208 ---VSALVDGERRLVWLRQALTVLSERELRILRERRLAEDQATLEALGHRLGISKERVRQ 264

Query: 659 IEAKAIRKLK 668
           IE +A+ KL+
Sbjct: 265 IENRALEKLR 274


>gi|291550016|emb|CBL26278.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus torques
           L2-14]
          Length = 260

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 95/164 (57%), Gaps = 6/164 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+G+    +A++E ++ NLRLV+SV K++ +      DL Q G +GL+KA + FD    
Sbjct: 31  IRQGD---KLAREEYIKGNLRLVLSVMKRFDSSNENADDLFQIGCVGLVKAVDNFDPDRQ 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +   I R + D S ++R+   +RD  +KV+ T      K  +EP+ +EIA
Sbjct: 88  VKFSTYAVPMIIGEIRRYLRDNS-SLRVSRSLRDIAYKVIYTREGYIRKNMKEPSIQEIA 146

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDK 595
           +++ +  E V   L   + P+SL+ P+ ++  D  ++ D + DK
Sbjct: 147 EEIGLSKEEVVYALDAVQTPMSLQEPVYNDGGDALYVMDQVSDK 190


>gi|115378523|ref|ZP_01465679.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
 gi|115364445|gb|EAU63524.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
          Length = 171

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 40/91 (43%), Positives = 58/91 (63%), Gaps = 3/91 (3%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +    RKG+     A++ +  +NL  V++VAKK+ NRG +  DLIQEGN+GLMKA E FD
Sbjct: 33  LARAARKGD---ESARQTLATSNLAFVVAVAKKFANRGARLDDLIQEGNVGLMKAIEHFD 89

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
                +F+TYA+WW++  ITR + D    +R
Sbjct: 90  PKKNVRFATYAVWWIRAYITRYLKDNRSQVR 120


>gi|328675965|gb|AEB28640.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida 3523]
          Length = 292

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 124/240 (51%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPEQGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI    + +  E+A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSEDIKELAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+ P  D+D   TS    ++EDK++      +      N +    
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 233

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 234 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|328955594|ref|YP_004372927.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
 gi|328455918|gb|AEB07112.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
          Length = 262

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 122/230 (53%), Gaps = 15/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V +++ LV  +A K+ NRG    DL+Q G +GL+KA ++F+   G +F+TYA   
Sbjct: 32  AREKLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKAIDRFEPARGLEFTTYATPT 91

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+  ++R+P  +++   KV +    ++ +++R P  EEIA+ L   V+ V
Sbjct: 92  ILGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDLLTTELQRSPKVEEIAEYLDATVDEV 151

Query: 564 RKVLKITK--EPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++ +     + LE   +   D+  S +  +  D N +S  D       R      L 
Sbjct: 152 LEAMESSSAYSSVPLEGTGSSENDDAPSIIDRYAIDDNVLSFTDD------RLIIEDALE 205

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           S +PRE  V+ +RF  GM    T  E+ +Q  +++ ++ ++  + ++K++
Sbjct: 206 SFSPREREVVNLRFLKGM----TQIEIAEQLGISQVQVSRLLRRTLKKIQ 251


>gi|256823783|ref|YP_003147746.1| RNA polymerase sigma-32 subunit RpoH [Kangiella koreensis DSM
           16069]
 gi|256797322|gb|ACV27978.1| RNA polymerase, sigma 32 subunit, RpoH [Kangiella koreensis DSM
           16069]
          Length = 283

 Score = 87.0 bits (214), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 126/235 (53%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V A+LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 50  AARQLVMAHLRFVVYIARSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++  N +  +     +A+ L +  E 
Sbjct: 110 IKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRSKKKTLNWLNNDEV-NAVAQDLGVSEEE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLG---DFIEDKNAVSPLDSAIQANLR-ETTTRVL 617
           VR++  ++     S + P   +D   +     ++E  N+  P  +  Q + + +   R++
Sbjct: 169 VRRMEGRLNAHDASFDAPNASDDDDAVYAPIHYLESPNS-DPAQAIEQEDWQDQREVRLM 227

Query: 618 ASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++L   +ER   +L+ R+    +   TL ++  ++ ++ ERIRQ+E  A+ K+K+
Sbjct: 228 SALKTLDERSQDILQQRW--LSDQKATLHDLADKYGISAERIRQLEKNAMNKIKN 280


>gi|311897125|dbj|BAJ29533.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 115/243 (47%), Gaps = 23/243 (9%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + FR +  +   G  E +  +  ++E NL LV   + ++ +R     D++Q G IGL
Sbjct: 50  LSRALFRRLAGL-ESGSAEHTYVRDTLIELNLPLVRYASARFRSRNEPMEDIVQVGTIGL 108

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +    +S 
Sbjct: 109 IKAIDRFDPDRGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKAGDELSQ 168

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVS 599
           ++ R PT  E+A  L            +T++ +     +G+  T+   D    ED     
Sbjct: 169 RLDRSPTVPELAAYLG-----------VTEDDVVEGLAVGNAYTASSLDSTPAEDDGGDG 217

Query: 600 PL-------DSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFC 650
           PL       D A++    RE+   +LA L PRE R++ +RF   +      EE+G  Q  
Sbjct: 218 PLADRLGYEDLALEGVEYRESLKPLLAKLPPRERRIIMLRFFGNLTQSQIGEEIGISQMH 277

Query: 651 VTR 653
           V+R
Sbjct: 278 VSR 280


>gi|42524687|ref|NP_970067.1| RNA polymerase sigma factor for flagellar operon [Bdellovibrio
           bacteriovorus HD100]
 gi|39576897|emb|CAE78126.1| RNA polymerase sigma factor for flagellar operon [Bdellovibrio
           bacteriovorus HD100]
          Length = 261

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 114/235 (48%), Gaps = 14/235 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A   K +++     L+  +A+K   R    ++  DLI  G IGLM A EK+D     KF 
Sbjct: 19  APTQKDDLIREYAPLIKFIAQKIAVRLPSNIELDDLISAGVIGLMDAIEKYDSTRDNKFK 78

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA + ++ AI   +  Q     +P  +RDK   + +T  ++   + R P+ EE+AK L 
Sbjct: 79  TYAEFRIRGAILDELRAQDW---VPRSIRDKAKLLDKTMVQLEADLGRTPSDEEVAKALN 135

Query: 558 MPVEG----VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + ++     V +V  ++  PI   T   + D   + D +E     SP +     N++E  
Sbjct: 136 VSIDEFHDLVNQVRPVSLLPIDQATSFSNTDKKSIMDILEGSRTNSPFNQLNVKNIKEVV 195

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +  L  R+  VL + +   +N    L+E+G+   VT  R+ Q+ A+A+ +L+
Sbjct: 196 AQAIEELPERQRLVLSLYYYEDLN----LKEIGQVLRVTESRVSQLHAQAVARLR 246


>gi|254369205|ref|ZP_04985217.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122155|gb|EDO66295.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 292

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 123/240 (51%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI        +E+A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSENIKELAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+ P  D+D   TS    ++EDK++      +      N +    
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 233

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 234 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|78043803|ref|YP_360778.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77995918|gb|ABB14817.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 124/245 (50%), Gaps = 13/245 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++   +KG+  A   +++++  NL+LV  V +++ +RG +  DL Q G IGL+KA 
Sbjct: 20  EIKELIEKAQKGDVAA---REKLINCNLKLVFKVVERFLHRGYEVEDLFQIGTIGLIKAI 76

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     KFSTYA+  +   I R + D    IRI    ++   K+++    ++ K+ R
Sbjct: 77  DKFDLKQQVKFSTYAVPMIVGEIRRFLRDDQA-IRISRSTKELGVKILKEKEALTVKLGR 135

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPT  E+ + L    E + + L+  +   SL   +  +D    GD I   + +       
Sbjct: 136 EPTIAELEETLGYSREAIVEALEAGQSLASLFETVHQDD----GDPIYLLDQIKQEGDEE 191

Query: 606 QANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           Q  L   + + VL+ L PRE  +L  RF      + T  E+ +   +++ ++ ++E +A+
Sbjct: 192 QTLLENISIKEVLSKLEPRERYILINRF----FKEKTQMEIARTLGISQVQVSRLERQAL 247

Query: 665 RKLKH 669
            KLK 
Sbjct: 248 LKLKR 252


>gi|75764482|ref|ZP_00743967.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488029|gb|EAO51760.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 260

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 76/265 (28%), Positives = 133/265 (50%), Gaps = 20/265 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR    +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRFCAFL 118

Query: 526 -RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
            R  +   ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++ 
Sbjct: 119 GRYALINXLQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDG 178

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D   + D + D+          +  L+E   R    L  RE+ ++R RF  G       
Sbjct: 179 GDPIFVMDQLSDEKQKDE-QWVEELALKEGMKR----LNDREKMIIRKRFFQGKTQMEVA 233

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           EE+G    +++ ++ ++E  AI+++
Sbjct: 234 EEIG----ISQAQVSRLEKSAIKQM 254


>gi|156936376|ref|YP_001440292.1| RNA polymerase factor sigma-32 [Cronobacter sakazakii ATCC BAA-894]
 gi|260599762|ref|YP_003212333.1| RNA polymerase factor sigma-32 [Cronobacter turicensis z3032]
 gi|156534630|gb|ABU79456.1| hypothetical protein ESA_04276 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218939|emb|CBA34294.1| RNA polymerase sigma-32 factor [Cronobacter turicensis z3032]
          Length = 285

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/276 (25%), Positives = 145/276 (52%), Gaps = 21/276 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    +S +   +++E  H      +G+ EA+   K+++ ++LR V+ +A+ 
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKLHY-----QGDLEAA---KKLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 580 IGDE--DTSHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             D+  D+  +    F++DK+   A    D   + +  +  T  +  L  R ++++R R+
Sbjct: 186 PDDDAGDSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARW 245

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 246 -LDEDNKSTLQELANRYGVSAERVRQLEKNAMKKLR 280


>gi|299769389|ref|YP_003731415.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
 gi|298699477|gb|ADI90042.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
          Length = 288

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTAEQ 171

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 172 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLVENEDWEEQSTSALH 230

Query: 619 ----SLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 DAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|56708190|ref|YP_170086.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670661|ref|YP_667218.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134302102|ref|YP_001122071.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|187931929|ref|YP_001891914.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|224457293|ref|ZP_03665766.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370677|ref|ZP_04986682.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254875002|ref|ZP_05247712.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604682|emb|CAG45745.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320994|emb|CAL09128.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134049879|gb|ABO46950.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151568920|gb|EDN34574.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|187712838|gb|ACD31135.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|254841001|gb|EET19437.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159406|gb|ADA78797.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 292

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 123/240 (51%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI        +E+A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSENIKELAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+ P  D+D   TS    ++EDK++      +      N +    
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 233

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 234 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|149917001|ref|ZP_01905502.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
 gi|149822279|gb|EDM81670.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
          Length = 411

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 112/234 (47%), Gaps = 22/234 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +   +LRLVIS+  +Y  + + F   +  G +GL KA ++F+   G++FSTYA WW+
Sbjct: 162 RRRLFADSLRLVISLVHRY-RKHMDFATGMLRGALGLDKAIDRFEPERGWQFSTYATWWI 220

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEG 562
           +Q ITRS  D +  +R+PVH  ++  +     + + ++    PT EE+  +      +E 
Sbjct: 221 RQNITRSSMDFATALRVPVHAAEQTTRFWMVQQELWSQTGVRPTDEEVLNQANFKFSIER 280

Query: 563 V-------RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +       R      ++ +     I D D   L +        +P    ++A +   T +
Sbjct: 281 LGDYRRHARTAHLTRRDQLGAAEAILDSDIPSLLE-------GNPASGWVRAAIDHATAQ 333

Query: 616 VLASLTPREER-----VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           V      R  R     +   R       ++TL E+G++F +TRERIRQ EAK I
Sbjct: 334 VDDKEHSRPSRGRWHAIFSRRILGDQIQNNTLRELGEEFDITRERIRQNEAKLI 387


>gi|294678332|ref|YP_003578947.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294477152|gb|ADE86540.1| RNA polymerase sigma-32 factor-2 [Rhodobacter capsulatus SB 1003]
          Length = 299

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 118/242 (48%), Gaps = 24/242 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ AI   I      +++      K  K+    R+  +KI        R     +IA  L
Sbjct: 109 IRAAIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKSKIGALDEGDLRPDAVAKIAHDL 166

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRET 612
            +  + V ++  ++     SL   +G  D    +   D++ED++A      A    L+  
Sbjct: 167 NVSEDDVIEMNRRLAGSDASLNAQVGASDGESATQWQDWLEDEDADQAEAYAEADELQAR 226

Query: 613 TTRVLAS---LTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              ++A+   L  RE  +L   R+R     +   TLEE+  Q+ V+RERIRQIE +A  K
Sbjct: 227 RAMLVAAMDVLNERERDILMARRLR-----DEPVTLEELSSQYDVSRERIRQIEVRAFEK 281

Query: 667 LK 668
           L+
Sbjct: 282 LQ 283


>gi|167507931|gb|ABZ81286.1| RpoD [Thalassospira sp. MCCC 1A01172]
          Length = 253

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 97  SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGETVPAATEKRYTKLKNEMV 156

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 157 ELMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPN 216

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK F+    + I K+R +I  +S E
Sbjct: 217 WMERVAGLPGKGWKTFIERYPEEIAKLREDIGGVSAE 253


>gi|167507901|gb|ABZ81271.1| RpoD [Thalassospira sp. MCCC 1A00370]
 gi|167507963|gb|ABZ81302.1| RpoD [Thalassospira sp. MCCC 1A02060]
          Length = 253

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 97  SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGETVPAATEKRYTKLKNEMV 156

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 157 ELMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPN 216

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK F+    + I K+R +I  +S E
Sbjct: 217 WMERVAGLPGKGWKTFIERYPEEIAKLREDIGGVSAE 253


>gi|319899398|ref|YP_004159495.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319403366|emb|CBI76925.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 303

 Score = 87.0 bits (214), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 126/243 (51%), Gaps = 27/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP---TPEE----IAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ ++    T +E    I++KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLAQDDSTLTKQEIFRTISEKL 173

Query: 557 AMPVEGVRKV-LKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAI--QANLR 610
            + V  V K+  + +    SL   +   G+   + +   ++D     PL  A+  QA   
Sbjct: 174 GVSVSDVEKMDFRFSAADNSLSLSVSENGENPIAKMDSLVDDH----PLPDAVIEQAIDG 229

Query: 611 ETTTR----VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  T+     L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A++
Sbjct: 230 QRRTKWLYEALKILNERELEIIRFR---RLNEEGATLEVLGQKLGISKERVRQIEARALQ 286

Query: 666 KLK 668
           KL+
Sbjct: 287 KLR 289


>gi|254490572|ref|ZP_05103758.1| alternative sigma factor RpoH [Methylophaga thiooxidans DMS010]
 gi|224464316|gb|EEF80579.1| alternative sigma factor RpoH [Methylophaga thiooxydans DMS010]
          Length = 287

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 123/244 (50%), Gaps = 19/244 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR V+ +AK Y+  GL   DLIQEGNIGLMKA ++F+   G + 
Sbjct: 47  GDLEAA---QRLVLSHLRFVVRIAKGYSGYGLPVADLIQEGNIGLMKAVKRFNPEKGVRL 103

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ WV+  I   +      ++I     + K+   +R+A++    + +E   E +A+ 
Sbjct: 104 VSFAVHWVRAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSAKQRLGWLNQEEV-EAVAED 162

Query: 556 LAMPVEGVRKVLKITKEP-ISLETPI--GDEDTSHLGD--FIEDKNAVSPLDSAIQANL- 609
           L +    V  + +   +P  S + P    D++ +H     ++       P     Q N  
Sbjct: 163 LGVTPANVMDMERRLAQPDASFDLPADSNDDEETHFSPVAYLAGPENSDPSQQLEQENYS 222

Query: 610 ---RETTTRVLASLTPREERVLRMRFGIGMNTD--HTLEEVGKQFCVTRERIRQIEAKAI 664
              ++  T  LA+L  R   ++  R+   +N D   TL  +  Q+ V+ ERIRQIE  A+
Sbjct: 223 DYQQQKLTNALATLDDRSRDIIMQRW---LNEDDKATLHTLADQYQVSAERIRQIENNAM 279

Query: 665 RKLK 668
           +KLK
Sbjct: 280 KKLK 283


>gi|260425792|ref|ZP_05779772.1| alternative sigma factor RpoH [Citreicella sp. SE45]
 gi|260423732|gb|EEX16982.1| alternative sigma factor RpoH [Citreicella sp. SE45]
          Length = 298

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW++ 
Sbjct: 52  KLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRA 111

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMP 559
           +I   I      +++      K  K+    R+  ++I        R    E+IA  L + 
Sbjct: 112 SIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKSRIGALEEGDLRPEHVEKIATDLGVS 169

Query: 560 VEGVRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANL---RETT 613
            + V  +  +++    SL   +G +D S +   D++ED+ A    D A +  L   R   
Sbjct: 170 KDEVISMNRRLSGGDASLNATVGSDDDSSMQWQDWLEDEGADQASDYAERNELEARRALL 229

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            + +  L  RE+ +L  R         TLE++   + V+RERIRQIE +A  KL+   R
Sbjct: 230 AQAMDVLNDREKDILTQRRLAEQPV--TLEDLSSVYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|330719751|gb|EGG98273.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC2047]
          Length = 283

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 122/234 (52%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 49  AARQLIMSHLRFVVHIAKSYSGYGLPQGDLIQEGNVGLMKAVKRFDPERGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R A++    +  +   + IA+ L +  + 
Sbjct: 109 IKAEIHEYILRNWRIVKVATTKAQRKLFFNLRGAKKSLAWLSNDEV-DAIAEDLGVDAKV 167

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHL-GDFIEDKNAVSPLDSAIQANLRETTTR--- 615
           VR++   L     P  +     D+       +++EDK    P+D   Q N +ET+ R   
Sbjct: 168 VRQMEGRLSAHDAPFDMGADDDDDSAYQAPANYLEDKRC-DPVDLLEQQNWQETSNRKLF 226

Query: 616 -VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +A L  R + +L  R+     +  TL ++  ++ V+ ERIRQ+E  A++K+K
Sbjct: 227 EAMADLDERSKDILNARWLSEQKS--TLHDLADKYGVSAERIRQLEKNAMKKIK 278


>gi|304397877|ref|ZP_07379753.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308188475|ref|YP_003932606.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
 gi|304354588|gb|EFM18959.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308058985|gb|ADO11157.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
          Length = 285

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/284 (24%), Positives = 140/284 (49%), Gaps = 37/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S E   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYVRAANTWPMLSAEEEKALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DL+QEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLVQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 580 IGDED---------------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             DE                TS   D IE+ N          A+  +  +  +  L  R 
Sbjct: 186 ADDESSEGRSMAPVLYLQDKTSDFADGIEEDN--------WDAHAADKLSYAMEGLDERS 237

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 238 QHIIRARW-LDEDNKTTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|312128428|ref|YP_003993302.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778447|gb|ADQ07933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 256

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 98/190 (51%), Gaps = 7/190 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   +AKK+  RG+ + DL Q   I L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNKHLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIARHLNMSTEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +     ++ +Q    E   + +  L+P
Sbjct: 151 EVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSD-----ENILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRF 632
            E   ++ RF
Sbjct: 206 FEREFVQKRF 215


>gi|303256291|ref|ZP_07342307.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|330998988|ref|ZP_08322713.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
 gi|302861020|gb|EFL84095.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|329575730|gb|EGG57256.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
          Length = 306

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 123/255 (48%), Gaps = 29/255 (11%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V +   G+ EA+    E+V ++LRLVIS+A++Y   GL F DLIQEGNIGLMKA ++F+ 
Sbjct: 55  VRLQEHGDMEAA---GELVMSHLRLVISIARQYQGYGLPFGDLIQEGNIGLMKAVKRFNP 111

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT-- 548
             G +  T+AM W+K  I   +      +++      +  K+    R++ +  K   T  
Sbjct: 112 NNGARLVTFAMTWIKSEIQEYVLRNWRLVKVATTKSQR--KLFFNLRKLKDDTKLLGTSE 169

Query: 549 PEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLG--------DFIEDKNAVS 599
            E+IA+ L + P E      ++    + ++ P G  D             D  E+  A  
Sbjct: 170 AEKIAETLDVKPSEVFEMEKRMLGSDVEIDEPSGGTDEGMAPSEWLTDERDTPENTIARG 229

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH------TLEEVGKQFCVTR 653
             ++ I+  L E   +    L  R  R++  R+   +  D       TL ++ K+  V++
Sbjct: 230 AYENTIENRLPEAVKK----LDDRSRRIIEARW---LYNDQDGSKGATLADLAKEMGVSQ 282

Query: 654 ERIRQIEAKAIRKLK 668
           ER+RQ+E KA   LK
Sbjct: 283 ERVRQLEKKAFATLK 297


>gi|145637130|ref|ZP_01792792.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145640200|ref|ZP_01795784.1| RNA polymerase sigma factor [Haemophilus influenzae R3021]
 gi|229846357|ref|ZP_04466465.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|145269575|gb|EDK09516.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145274786|gb|EDK14648.1| RNA polymerase sigma factor [Haemophilus influenzae 22.4-21]
 gi|229810450|gb|EEP46168.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|309972570|gb|ADO95771.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2846]
          Length = 281

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPALYLEDKSSNFAAALENENFESQATEQLGA 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|260767580|ref|ZP_05876516.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|260617480|gb|EEX42663.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|315178774|gb|ADT85688.1| RNA polymerase sigma-32 factor [Vibrio furnissii NCTC 11218]
          Length = 258

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 126/244 (51%), Gaps = 21/244 (8%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 18  GDIEAA---KGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRL 74

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A+
Sbjct: 75  VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAR 132

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANL 609
           +L +    VR++  ++  +  + E    D+D  +       ++EDK   S L   ++A  
Sbjct: 133 ELGVEPSEVREMESRLAAQDATFEMSNDDDDNPNAYTAPVLYLEDKQ--SDLAENVEAQN 190

Query: 610 RETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            E  T       L+SL  R + ++R R+        TL+E+ + + V+ ERIRQ+E  A+
Sbjct: 191 WEAHTNQRLALALSSLDERSQHIVRSRWLDDQKA--TLQELAEMYNVSAERIRQLEKNAM 248

Query: 665 RKLK 668
           +KLK
Sbjct: 249 KKLK 252


>gi|171060212|ref|YP_001792561.1| RNA polymerase sigma-32 subunit RpoH [Leptothrix cholodnii SP-6]
 gi|170777657|gb|ACB35796.1| RNA polymerase, sigma 32 subunit, RpoH [Leptothrix cholodnii SP-6]
          Length = 313

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 120/249 (48%), Gaps = 29/249 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 63  AAGRLVLSHLRLVVSVARQYLGYGLPHGDLIQEGNVGLMKAVKRFDPEQGVRLVSYAMHW 122

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVE 561
           +K  I   +      +++      +  K+    R M  ++K E    +  +       ++
Sbjct: 123 IKAEIHEYVLKNWRVVKLATTKAQR--KLFFNLRSMKRQLKGEAADGDTHRSSLTEAEID 180

Query: 562 GVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-- 618
            V + L + +E  I +E      D +      ED  + +P+  A  A+ R+  TR L   
Sbjct: 181 TVARELNVKREEVIEMEARFAGGDVALEPGSDEDDESYTPI--AYLADERQEPTRALEAA 238

Query: 619 ---------------SLTPREERVLRMRFGIGMNTDH----TLEEVGKQFCVTRERIRQI 659
                          +L  R  R++  R+ + +N D     TL ++  ++ V+ ERIRQI
Sbjct: 239 HRDELAGPGLLRALDALDARSRRIVEERW-LKVNDDGSGGLTLHDLAAEYGVSAERIRQI 297

Query: 660 EAKAIRKLK 668
           E  A++K++
Sbjct: 298 EVAAMKKMR 306


>gi|167507905|gb|ABZ81273.1| RpoD [Thalassospira sp. MCCC 1A00385]
 gi|167507921|gb|ABZ81281.1| RpoD [Thalassospira sp. MCCC 1A01109]
 gi|167507961|gb|ABZ81301.1| RpoD [Thalassospira sp. MCCC 1A02059]
          Length = 253

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 97  SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGETVPAATEKRYTKLKNEMV 156

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 157 ELMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPN 216

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK F+    + I K+R +I  +S E
Sbjct: 217 WMERVAGLPGKGWKTFIERYPEEIAKLREDIGGVSAE 253


>gi|319764144|ref|YP_004128081.1| RNA polymerase sigma factor rpoh [Alicycliphilus denitrificans BC]
 gi|330826499|ref|YP_004389802.1| RNA polymerase sigma-32 subunit RpoH [Alicycliphilus denitrificans
           K601]
 gi|317118705|gb|ADV01194.1| RNA polymerase sigma factor RpoH [Alicycliphilus denitrificans BC]
 gi|329311871|gb|AEB86286.1| RNA polymerase, sigma 32 subunit, RpoH [Alicycliphilus
           denitrificans K601]
          Length = 311

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/254 (28%), Positives = 121/254 (47%), Gaps = 38/254 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGRLVLSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVE 561
           +K  I   I      +++      +  K+    R M    K +    +  ++      ++
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADAIDADTHRETLSDHEID 177

Query: 562 GVRKVLKITKEP-ISLETPIGDEDT-----------------SHLGDFIEDKNAVSPLDS 603
            V + L + +E  I +ET +   D                  ++L D   +  A+     
Sbjct: 178 MVAEQLNVKREEVIEMETRLAGGDVLLDPAPSDDGEQAFGPIAYLADTAHEPTAM----- 232

Query: 604 AIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRE 654
            I++  R+       T  LASL  R  R++  R+ + +N D     TL E+  ++ V+ E
Sbjct: 233 -IESRQRDALATDGITSALASLDARSRRIVEQRW-LQVNDDGSGGMTLHELAAEYGVSAE 290

Query: 655 RIRQIEAKAIRKLK 668
           RIRQIE  A++K+K
Sbjct: 291 RIRQIEVAAMKKMK 304


>gi|296314331|ref|ZP_06864272.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
 gi|296838970|gb|EFH22908.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
          Length = 281

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 102/188 (54%), Gaps = 4/188 (2%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           RN++ + E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ 
Sbjct: 3   RNQNHE-EYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNI 61

Query: 67  VAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           V+M+S +GI V +   D ED   S+++      A   +       DS    T DPVRMY+
Sbjct: 62  VSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPVRMYM 121

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++
Sbjct: 122 REMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVV 181

Query: 186 DLEACIGP 193
             EA I P
Sbjct: 182 --EAIIDP 187


>gi|110835430|ref|YP_694289.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
 gi|110648541|emb|CAL18017.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
          Length = 289

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 121/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V  +A+ YT  GL   DL+QEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 55  AARSLVLSHLRFVAHIARSYTGYGLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHW 114

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R  ++   ++  E   + +A  L +    
Sbjct: 115 IKAEIHEYVIKNWRIVKVATTKAQRKLFFNLRGQKKRLGRLTLEEA-QRVADDLGVTAAQ 173

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V+++  ++     S + P  D+D S +     ++   N+  P D   + + ++  +R L+
Sbjct: 174 VKEMEGRLGAYDASFDGPTNDDDDSTVVSPAAYLHSDNS-DPADLLAEQDQQQRESRQLS 232

Query: 619 S----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           S    L  R   +L  R+     +  TL+E+  ++ V+ ERIRQ+E  AI+KL++
Sbjct: 233 SALMALDERSRDILERRWLADQKS--TLQELADEYSVSAERIRQLENNAIKKLRN 285


>gi|227329284|ref|ZP_03833308.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 285

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKHLILSHLRFVIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++    +   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQR--KLFFNLRKSKTRLGWFNQDEVELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-- 612
            VR++  ++  + ++ + P  +ED SH G       +++DK+  S     I+ +  ET  
Sbjct: 167 DVREMESRMAAQDMTFD-PTPEED-SHDGKAMSPMLYLQDKS--SDFADGIEEDNWETHA 222

Query: 613 ---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  L  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 223 ADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|281420137|ref|ZP_06251136.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
 gi|281405937|gb|EFB36617.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
          Length = 205

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 108/234 (46%), Gaps = 38/234 (16%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V  NL  V SVA +Y  +G++F DL+ EG + ++ AA KF    G  F  YA  +V +
Sbjct: 8   KIVSENLNYVKSVANQYKGKGVEFDDLVSEGTLAMLMAARKFQADRGTDFVAYAGPFVHK 67

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+++I  QS   R+P   +       + A R ++K                        
Sbjct: 68  AISQAIDKQSGLYRLPKDQK-------KFAPRNADK------------------------ 96

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                  +S++ P+   +   L D + D +     D+     +++     +A L PRE+ 
Sbjct: 97  ------AVSVDAPLSANNPYTLLDILNDPDVKIADDTLNIEMMKKKMAESIADLLPREKE 150

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++   +GIG+  + T+ E+ +   + RER+RQI    IR+L    R + LR++ 
Sbjct: 151 IITKFYGIGVPKE-TMAEIAEDMGLKRERVRQIRNLTIRRLNRSIRHQALRNYF 203


>gi|153814532|ref|ZP_01967200.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|317500575|ref|ZP_07958796.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089324|ref|ZP_08338225.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848026|gb|EDK24944.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|316898008|gb|EFV20058.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330405505|gb|EGG85037.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 260

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 115/232 (49%), Gaps = 22/232 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV K++ N      DL Q G +GLMKA + FD     KFSTYA+  
Sbjct: 38  AREKYIKGNLRLVLSVIKRFENSSENADDLFQIGCVGLMKAVDHFDPGRMVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D S  IR+   +RD  +K +        +  +EPT +EIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDNS-PIRVSRSLRDTAYKAIYAKEGYIKRHMKEPTVQEIAEEIGIAKEEI 156

Query: 564 RKVLKITKEPISLETPIGD--EDTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRV 616
              L   + P+SL  P+    +D   + D + DK     N +  L          +    
Sbjct: 157 VYALDAIQMPMSLHEPVYSDGQDALFVMDQVSDKKNKEENWIEEL----------SLEAA 206

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  RE  ++ +RF  G     T  EV +Q  +++ ++ ++E  A++ ++
Sbjct: 207 MERLNERERYIITLRFFEG----KTQMEVAEQINISQAQVSRLEKNALKIMR 254


>gi|167759902|ref|ZP_02432029.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
 gi|167662521|gb|EDS06651.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
          Length = 237

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 123/242 (50%), Gaps = 12/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A+  +VE N  LV  + K++ NRG++  DL Q GNIGL+KA +KF
Sbjct: 3   HTIALIQKSHDGDEEARARLVEENAGLVWCIVKRFYNRGVEAEDLFQVGNIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      R+  +  R+PT
Sbjct: 63  DMSYDVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELAYKAYLCQERLQEQWGRDPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA+ L +  E +   L  + +  SL  PI  ++     L D + +K      D  + 
Sbjct: 122 ITEIAESLNVEREELTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGE--DKILN 179

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L +   ++L  L   E +++ +R+      + T  +VG++  +++ ++ ++E K ++ 
Sbjct: 180 HMLLQ---QLLNYLDKDERQLIYLRY----FANQTQTQVGRELGISQVQVSRMEKKILKN 232

Query: 667 LK 668
           L+
Sbjct: 233 LR 234


>gi|212637488|ref|YP_002314013.1| RNA polymerase factor sigma-32 [Shewanella piezotolerans WP3]
 gi|212558972|gb|ACJ31426.1| RNA polymerase sigma-32 factor [Shewanella piezotolerans WP3]
          Length = 285

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 122/236 (51%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A KE++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKELIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E     +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNLRKTKKRLGWFSDNEVGM--VAESLGVSKA 169

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT--TRV 616
            V ++   +        L +   DE       ++ED +  S L S ++ +  E +  TR+
Sbjct: 170 DVTEMESRMAAQDPAFDLASDNDDEQDYAPMHYLEDHS--SDLASQVENDNWEQSNQTRL 227

Query: 617 LASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++   +ER   +L+ R+   +N D  TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 228 LSAIKTLDERSQHILQARW---LNEDKTTLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|254478671|ref|ZP_05092042.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035358|gb|EEB76061.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 215

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 108/218 (49%), Gaps = 12/218 (5%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           N  L+ S+ KK+ NRG +  DL Q G IG +KA +KFD     KFSTYA+  +   I R 
Sbjct: 3   NSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAVQKFDESYNVKFSTYAVPIIMGEIKRF 62

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           + D    I++   +++   K       +SN++ REPT  EIA++L +  E +    +   
Sbjct: 63  LRDDGL-IKVSRSLKELSSKAFYMKEVLSNELNREPTINEIAERLNVTPEEIAMAFESAA 121

Query: 572 EPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
              SL   I  +E+   L + + DK     L+  +      T   ++  L PRE++V+ +
Sbjct: 122 TAESLYDSISHEEEDRQLIEMVGDKEDSVDLEEKL------TLHMIIDKLKPREKQVIFL 175

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+      D T  EV     +++ ++ +IE K + K++
Sbjct: 176 RYF----KDMTQTEVANILGISQVQVSRIEKKVLEKIR 209


>gi|254428104|ref|ZP_05041811.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
 gi|196194273|gb|EDX89232.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
          Length = 287

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 121/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V  +A+ YT  GL   DL+QEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 53  AARSLVLSHLRFVAHIARSYTGYGLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R  ++   ++  E   + +A  L +    
Sbjct: 113 IKAEIHEYVIKNWRIVKVATTKAQRKLFFNLRGQKKRLGRLTMEEA-QRVADDLGVTATQ 171

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V+++  ++     S + P  D+D S +     ++   N+  P D   + + ++  +R L+
Sbjct: 172 VKEMEGRLGAYDASFDGPTNDDDDSTVVSPAAYLHSDNS-DPADLLAEQDKQQRESRQLS 230

Query: 619 S----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           S    L  R   +L  R+     +  TL+E+  ++ V+ ERIRQ+E  AI+KL++
Sbjct: 231 SALMALDERSRDILERRWLADQKS--TLQELADEYGVSAERIRQLENNAIKKLRN 283


>gi|15603449|ref|NP_246523.1| RNA polymerase factor sigma-32 [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|12721979|gb|AAK03668.1| RpoH [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 281

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 124/232 (53%), Gaps = 11/232 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PV 560
           +K  I   +      +++      R     + +T +R+      E   E +A +L + P 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVEMVANELGVSPA 166

Query: 561 EGVRKVLKITKEPISLETPIGD-EDTSHLGDFIEDK--NAVSPLDSA-IQANLRETTTRV 616
           + +    ++T   ++ + P  D E+T     ++EDK  N  + L++   +A   E  +  
Sbjct: 167 DVMEMESRMTGADVAFDLPTDDNEETYSPSLYLEDKGSNFAAELENENYEAQATEQLSVA 226

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  R   +++ R+ +  N   TL+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 227 LEGLDERSLDIIKARW-LDEN-KATLQDLAAKYNISAERVRQLETNALKKLK 276


>gi|192289929|ref|YP_001990534.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
 gi|192283678|gb|ACF00059.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 326

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 111/237 (46%), Gaps = 17/237 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ ++LRL   +A+ Y   G    DLI E N+GLM A +KFD   G +F+T A+WW++ A
Sbjct: 59  LITSHLRLAAKLARNYRRYGFPIGDLIAEANLGLMMALDKFDPTRGARFATCAVWWIRSA 118

Query: 508 ITRSIADQSCTIRI---PVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           I   I      +RI   P    +  ++   +R  R   +    +   E+I+  L +P+  
Sbjct: 119 IYDHIVRSWSLVRIGRTPAQKKLFFRLRGEIRRLRPDHHGALTKDLAEQISTSLDVPLRE 178

Query: 563 VRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQAN------LRETTTR 615
           V ++ +     +SL  P+ D D S    D I D    SP   AI A        R     
Sbjct: 179 VIEMEQRLSGDLSLNAPLSDLDESGEWQDLIADD---SPNAEAILAGHDELDRQRGALRD 235

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  L  RE  +   R  +G +   + E +G+   ++ ER+RQIEA+A  K+   +R
Sbjct: 236 ALVQLDARERYIFSARH-LG-DRPASFEAIGQSLSLSAERVRQIEARAFAKVATAAR 290


>gi|16272227|ref|NP_438438.1| RNA polymerase factor sigma-32 [Haemophilus influenzae Rd KW20]
 gi|68248876|ref|YP_247988.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 86-028NP]
 gi|260580848|ref|ZP_05848673.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|319896604|ref|YP_004134797.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
 gi|1173123|sp|P44404|RP32_HAEIN RecName: Full=RNA polymerase sigma-32 factor
 gi|1573235|gb|AAC21935.1| RNA polymerase sigma-32 factor (rpoH) [Haemophilus influenzae Rd
           KW20]
 gi|68057075|gb|AAX87328.1| RNA polymerase sigma-32 factor [Haemophilus influenzae 86-028NP]
 gi|260092471|gb|EEW76409.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|317432106|emb|CBY80457.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
          Length = 281

 Score = 86.7 bits (213), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGA 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|317046493|ref|YP_004114141.1| RNA polymerase,sigma 32 subunit,RpoH [Pantoea sp. At-9b]
 gi|316948110|gb|ADU67585.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. At-9b]
          Length = 285

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/284 (25%), Positives = 140/284 (49%), Gaps = 37/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S E   +++E  H      +G+ +A+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANVWPMLSAEEEKALAERLHY-----QGDLDAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 580 IGDED---------------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             DE+               TS   D IE+ N          A+  +  T  +  L  R 
Sbjct: 186 ADDENGESKTMAPVLYLQDKTSDFADGIEEDN--------WDAHAADKLTDAMQGLDERS 237

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +      TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 238 QHIIRARW-LDEENKTTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|325264312|ref|ZP_08131043.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030383|gb|EGB91667.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 288

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 113/246 (45%), Gaps = 20/246 (8%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++ + N   +  + +++  +G   LD L+QEG I L +A   FD      F  YA +W+K
Sbjct: 22  QLWQQNEPFIRMMGRRFAGQGKAELDDLMQEGYIALCEAVRHFDSEQAVPFINYAAFWIK 81

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---VEG 562
           Q + R I +   T+RIP H RD + +  +           +P  + +   L +    ++ 
Sbjct: 82  QGMKRYIENCCGTVRIPTHARDWVRRYGKIVAEYCKYYGSDPEDDVLCALLNISREKLQA 141

Query: 563 VRKVLKITKEPISLETPIGDEDTS-HLGDFIE-----DKNAVSPLDSAIQANLRETTTRV 616
           VRK   + K   SL  P+G ED   ++ +FI      +   V  LD     N++E     
Sbjct: 142 VRKSEHMGK-ICSLNEPLGQEDGDLNMEEFIASEEDLEGETVRRLDY---QNMKEMLWEA 197

Query: 617 LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +  L  ++  V+R RF      DH TL E G+   +T++ +   +  A+R L  P R +K
Sbjct: 198 VEGLEEKQAEVIRCRF-----LDHKTLRETGELIGITKDAVVHQQNNALRLLGQPGRCRK 252

Query: 676 LRSFLD 681
            R + +
Sbjct: 253 YRGYYE 258


>gi|145635177|ref|ZP_01790882.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
 gi|145267598|gb|EDK07597.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
          Length = 281

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETEIYSPSLYLEDKSSNFAAELENENFESQATEQLNT 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|282862754|ref|ZP_06271815.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282562440|gb|EFB67981.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 298

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/252 (26%), Positives = 126/252 (50%), Gaps = 40/252 (15%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA ++FD     
Sbjct: 61  EGTHEYQYARNTLIEMNLSLVRYAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREV 120

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+T+A+ ++   I R   D + ++ +P  +++   ++ +    +S ++ R+PT  E+A 
Sbjct: 121 EFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVELAKAKETLSAQLDRDPTVAELAT 180

Query: 555 KLAMP----VEGVRKVLKITKEPISLETPIGDEDTSH--------LG------DFIEDKN 596
            L +P    +EG+  V        SL+TP  D ++ +        LG      + +E+ +
Sbjct: 181 HLDLPEEEIIEGL--VAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGMESVENLH 238

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A++PL               L  L  RE  ++RMRFG  M    T  ++G +  V++  +
Sbjct: 239 ALAPL---------------LRQLDDRERTIVRMRFGQEM----TQAQIGAELGVSQMHV 279

Query: 657 RQIEAKAIRKLK 668
            ++ ++ +++L+
Sbjct: 280 SRLLSRIVQRLR 291


>gi|254432127|ref|ZP_05045830.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
 gi|197626580|gb|EDY39139.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
          Length = 335

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 116/229 (50%), Gaps = 21/229 (9%)

Query: 448 MVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           MV ANLRLV+ V ++Y  R     L+ LDL Q GNIGLM+A E FD   GY+ STYA  W
Sbjct: 108 MVTANLRLVVMVCRRYRGRIGNLQLEMLDLYQAGNIGLMRAVELFDPSRGYRLSTYAFSW 167

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + QA+ R +      IRIP  +R+  ++    A+ +    ++  +   IA  L    + +
Sbjct: 168 IHQAVQRCMTATGNGIRIPTALRNIAYR----AQLLEACAEQPLSIGAIAALLGEKEQRL 223

Query: 564 RKVLKITKE--PISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  L + ++    SL+ P     EDT+ L + I D+    P D      L E     L +
Sbjct: 224 QTALTVVRQCSTTSLDKPSASMGEDTT-LIEVIPDRRGNVPHDD--YRWLHEH----LDA 276

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+ +VL++R+G   +   +  +  +   V++  ++ +E + ++ L+
Sbjct: 277 LDLRDRQVLQLRYGD--DESRSCSKTARVLGVSKSCVQSVERRTLKNLR 323


>gi|300783890|ref|YP_003764181.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299793404|gb|ADJ43779.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 282

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 105/201 (52%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G  GL+ A EKFD   G +F TYAM  ++ AI   +  Q     +P  +R K  +
Sbjct: 81  DLVQSGIFGLVDAIEKFDPERGLRFETYAMQRIRGAILDDLRSQDW---VPRAVRSKAKE 137

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPI-GDEDTSH 587
             R   R+  ++ R PT  E+A +L + ++ +R     L++T   ++LE  +   +D+  
Sbjct: 138 AERAMERLGARLHRTPTDAELAAELGIGLDDLRDFYGQLQLTSV-VALEDLVAAGKDSGS 196

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D +AV P+   +  + R    + +A LT R++ V+ + +   +    TL E+GK
Sbjct: 197 LVDTLPDDDAVDPVAVLVDQDNRRQLAQAIAQLTERDKIVVSLYYFESL----TLAEIGK 252

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  R+ Q+  +A+ +L+
Sbjct: 253 VLGVTESRVSQLHTRAVMRLR 273


>gi|254486865|ref|ZP_05100070.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
 gi|214043734|gb|EEB84372.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
          Length = 298

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 113/240 (47%), Gaps = 21/240 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  N+I        R      IA  L
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSGQK--KLFFNLRKAKNRIGALEEGDMRPENVSRIATDL 166

Query: 557 AMP-VEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +   E V    +++    SL   +G   E T    D++ED++A    D   +  L    
Sbjct: 167 GVTEAEVVSMNRRMSGGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEEREELETRR 226

Query: 614 ---TRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  L  RE+ +L  R      +D   TLE++  Q+ V+RERIRQIE +A  KL+
Sbjct: 227 EMLAEALEVLNDREKDILTQR----RLSDETITLEDLSSQYDVSRERIRQIEVRAFEKLQ 282


>gi|319408110|emb|CBI81763.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 308

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 116/238 (48%), Gaps = 16/238 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGNIGLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           +K +I   +      +++      K  ++    R++ NK++            +EIA +L
Sbjct: 109 IKASIQEYVLRSWSLVKMGTTANQK--RLFFNLRKLKNKLQALDNGDLNAEQVKEIATRL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSP--LDSAIQANLRE 611
            +  + V  +        SL  P+     E T      ++D N+     ++     N R 
Sbjct: 167 NVTEDEVVSMNHRLSGDTSLNAPLRTKEGEKTEWQDWLVDDSNSQEQILIEQDELENRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                + +L  RE+ + + R     +   TLEE+   F ++RER+RQIE +A  K+++
Sbjct: 227 MLIHAIDNLNEREKHIFKARR--LSDESLTLEELSNTFNISRERVRQIEMRAFEKVRN 282


>gi|27375413|ref|NP_766942.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
 gi|1834377|emb|CAA70861.1| RNA polymerase subunit [Bradyrhizobium japonicum]
 gi|27348550|dbj|BAC45567.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
          Length = 307

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 112/234 (47%), Gaps = 11/234 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRL   +A+ Y   GL  +DLI E N+GL+ AA +F+   G +FSTYA+WW
Sbjct: 58  AADALVTSHLRLAAKLARGYKGYGLPMVDLIAEANLGLVIAASRFEPGRGARFSTYAIWW 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTP---EEIAKKLAM 558
           +K AI   I      ++I      K    K+    R+ +  +    TP   E IA KL +
Sbjct: 118 IKAAIHEYILRSWSLVKIGTTAAQKKLFFKLRSEIRKATGSVMSGLTPDVAELIAGKLDV 177

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDK--NAVSPLDSAIQANLRETTTR 615
               V ++       +SL   +G E++ + L   + D   +A + L    Q   R    R
Sbjct: 178 TAREVIEMDARLNGDMSLNARVGGEESGTELEALLVDGAVDAETMLADHEQTERRAKALR 237

Query: 616 V-LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V L  L  RE  V   R         TL+++ ++  ++ ER+RQIE +A  K+K
Sbjct: 238 VALGGLAARERHVFEARRLT--ECPVTLDQLARELSISSERVRQIEIRAFAKVK 289


>gi|160914281|ref|ZP_02076502.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
 gi|158433908|gb|EDP12197.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
          Length = 260

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 120/228 (52%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E++  NL+LV+S+ +++ NR     DL Q G IGL+K+ + FD     +FSTYA+  
Sbjct: 38  AKEELINGNLKLVLSIVQRFANRCENMDDLFQVGCIGLVKSIDHFDLKHEVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +R+  H++D  +K  R      ++ ++EP+   +A++L +  + +
Sbjct: 98  IMGEIKRYLRDNQ-VLRVSRHLKDLAYKCFRLKEEYVHQHQKEPSITWLAEQLEVREKDI 156

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASL 620
              L  T+  +S+  P+   D D  +L D I D K+ +  L++ +  +LR +    L  L
Sbjct: 157 VDALDSTQNVLSIFEPVYNSDGDELYLLDQIRDEKDEIDLLNNVL--SLRSS----LKQL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E  +L  R+      D T  E+  +  +++ ++ ++E  AI  L+
Sbjct: 211 KEKELEILDKRYY----QDMTQTEIANELGISQAQVSRLEKSAISTLR 254


>gi|222528460|ref|YP_002572342.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455307|gb|ACM59569.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 256

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 97/190 (51%), Gaps = 7/190 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L +   +AKK+  RG+ + DL Q   I L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNKYLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAQHLNMSAEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +     ++ +Q    E   + +  L+P
Sbjct: 151 EVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSD-----ENILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRF 632
            E   ++ RF
Sbjct: 206 FEREFVQKRF 215


>gi|2384764|gb|AAC97123.1| heat shock sigma factor [Rhodobacter capsulatus]
          Length = 299

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 123/243 (50%), Gaps = 26/243 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHRLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIAKKLAMP 559
           ++ AI   I      +++      K  K+    R+  +KI    + +  P+ +A K+A  
Sbjct: 109 IRAAIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKSKIGAFEEGDLRPDAVA-KIAHD 165

Query: 560 V---EG----VRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +   EG    + + L  +   ++ +   GD E  +   D++ED++A      A    L+ 
Sbjct: 166 LNVSEGDVIEMNRRLAGSDASLNAQVGAGDGESATQWQDWLEDEDADQAEAYAEADELQA 225

Query: 612 TTTRVLAS---LTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               ++A+   L  RE  +L   R+R     +   TLEE+  Q+ V+RERIRQIE +A  
Sbjct: 226 RRAMLVAAMDVLNERERDILMARRLR-----DEPVTLEELSSQYDVSRERIRQIEVRAFE 280

Query: 666 KLK 668
           KL+
Sbjct: 281 KLQ 283


>gi|167507971|gb|ABZ81306.1| RpoD [Thalassospira sp. MCCC 1A02411]
          Length = 258

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 89/157 (56%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   ++IA+ Y +L   Q+    A+N  +   ++ + +   LK+++V
Sbjct: 102 SLSKMEEELTEQVLEKFEKIAKTYEKLHKAQEQRLAALNKGESVPAATEKRYGKLKQEMV 161

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++ +QG ELDP+
Sbjct: 162 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRVKIKRPDFIKHYQGNELDPN 221

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK FV    + I  +R  +  +S E
Sbjct: 222 WMEKVGNLPGKGWKLFVERYPEEIANLREGVGGVSAE 258


>gi|163845340|ref|YP_001622995.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|163676063|gb|ABY40173.1| RNA polymerase sigma factor, sigma-70 family [Brucella suis ATCC
           23445]
          Length = 311

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 126/247 (51%), Gaps = 15/247 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLV S+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVTSMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMS---NKIKREPT 548
            +FSTYA WW++ ++   I      +R       K     + R   +++   + + +   
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLCRLRSKLAQTDDNMTKAEI 173

Query: 549 PEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--LDS 603
             EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     +S
Sbjct: 174 YREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAES 233

Query: 604 AIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEA 661
           +I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQIE+
Sbjct: 234 SIDMERRNCWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQIES 290

Query: 662 KAIRKLK 668
           +A+ KLK
Sbjct: 291 RAMEKLK 297


>gi|4103484|gb|AAD01787.1| sigma-D factor [Myxococcus xanthus]
          Length = 297

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 52/77 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++    +NL  V++VAKK+ NRG +  DLIQEGN+GLMKA E FD     +F+TYA+WW
Sbjct: 44  ARQTTASSNLAFVVAVAKKFANRGARLDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWW 103

Query: 504 VKQAITRSIADQSCTIR 520
           ++  ITR + D    +R
Sbjct: 104 IRAYITRYLKDNRSQVR 120


>gi|330945998|gb|EGH47306.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 163

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 45/148 (30%), Positives = 87/148 (58%)

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +
Sbjct: 1   MPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL 60

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +    L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   
Sbjct: 61  GPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHESS 120

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TLE+VG +  +TRER+RQI+ + +++L+
Sbjct: 121 TLEDVGLEIGLTRERVRQIQVEGLKRLR 148


>gi|119716157|ref|YP_923122.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536818|gb|ABL81435.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 282

 Score = 86.3 bits (212), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 114/234 (48%), Gaps = 13/234 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE E  + +  +V  N  +  +VA ++ NRG+   DL Q    GL KA  +FD  L    
Sbjct: 53  GEREEVLGR--VVVINRGVADAVAARFRNRGIPQEDLRQVAYEGLTKAVHRFDPELRNDL 110

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++  + R   DQ  T+R P  +++   +V +   R++ +  REP+ +EIA +L
Sbjct: 111 LTYAVPTIRGELQRYFRDQGWTVRPPRRIQELQWRVNQVIERLTQERGREPSEDEIAAEL 170

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
              VE  R         +P SL+ P+G E  + +G+ I   +A  P   A     R    
Sbjct: 171 DTTVEEYRDAASAFGCFQPTSLDQPVGHEGETPVGELIAGADADGPATEA-----RMLLA 225

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            V+  L  R  R+L +RF      D T EE+G+   VT+ ++ ++ ++ +  L+
Sbjct: 226 PVVRRLPERHRRILYLRF----FEDLTQEEIGRDLGVTQMQVSRLLSRILGDLR 275


>gi|221133912|ref|ZP_03560217.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola sp. HTCC2999]
          Length = 283

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 128/245 (52%), Gaps = 35/245 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ +AK Y+  GL   DL+QEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 50  AARELVMSHLRFVVHIAKSYSGYGLAQADLVQEGNIGLMKAVKRFDPNVGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + ++ +R+     +E   +++A++L     
Sbjct: 110 IKAEIHEFVLKNWRIVKVATTKAQRKLFFNLRKSKKRLGWFTHKE--VQKVAEEL----- 162

Query: 562 GVRKVLKITKEPISLETPIGDEDT-----SHLGD---------FIEDKN---AVSPLDSA 604
           GV +     KE + +E  +G +DT     S  GD         ++EDK+     + +++ 
Sbjct: 163 GVSE-----KEVLQMEARMGSQDTAFDLSSDDGDDNSNFSPAQYLEDKSENVEAAVINAD 217

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKA 663
             +N        + +L  R + ++  R+   +N +  TL+++  ++ V+ ER+RQIE  A
Sbjct: 218 YDSNASARLYSAIKTLDERSQYIIETRW---LNDNKMTLQDLAAKYEVSAERVRQIEKNA 274

Query: 664 IRKLK 668
           ++K++
Sbjct: 275 MKKIQ 279


>gi|167507973|gb|ABZ81307.1| RpoD [Thalassospira sp. MCCC 1A02450]
          Length = 258

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 89/157 (56%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   ++IA+ Y +L   Q+    A+N  +   ++ + +   LK+++V
Sbjct: 102 SLSKMEEELTEQVLEKFEKIAKTYEKLHKAQEQRLAALNKGESVPAATEKRYGKLKQEMV 161

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++ +QG ELDP+
Sbjct: 162 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRVKIKRPDFIKHYQGNELDPN 221

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK FV    + I  +R  +  +S E
Sbjct: 222 WMEKVGNLPGKGWKLFVERYPEEIANLREGVGGVSAE 258


>gi|88813090|ref|ZP_01128332.1| RpoH [Nitrococcus mobilis Nb-231]
 gi|88789723|gb|EAR20848.1| RpoH [Nitrococcus mobilis Nb-231]
          Length = 292

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 125/237 (52%), Gaps = 18/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 55  AARGLVLSHLRFVVHIARGYKGYGLPLTDLIQEGNIGLMKAVKRFDPAVGVRLVSFAVHW 114

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R A++    + R    + +A  L +  E 
Sbjct: 115 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRGAKKRLGWLNRAEV-DAVANDLGVKPET 173

Query: 563 VRKV-LKITKEPISLET-PIGDED-------TSHLGDFIEDKNAVSPLDSA-IQANLRET 612
           V+++ L+++ + +S +  P   ED        ++L D  +  N    ++S   Q +  E+
Sbjct: 174 VQEMELRLSGQEVSFDPGPDAAEDDDIVRAPAAYLRD--QRPNPAEEIESHDWQTHQSES 231

Query: 613 TTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               LA L  R   ++  R+   +N    TL+E+ +++ V+ ERIRQ+E  A++KL+
Sbjct: 232 LATALAHLDERSRAIVHERW---LNEPKATLQELAERYAVSAERIRQLEKNALKKLR 285


>gi|292489953|ref|YP_003532845.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|292900984|ref|YP_003540353.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291200832|emb|CBJ47966.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291555392|emb|CBA23800.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|312174141|emb|CBX82394.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC BAA-2158]
          Length = 284

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/274 (24%), Positives = 143/274 (52%), Gaps = 18/274 (6%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E   +++E  H      +G+ EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRAANAWPMLTAEEEKALAERLHY-----QGDLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLE-TP 579
               + K+   +R A++      ++   E +A++L +  + VR++  ++  + ++ + TP
Sbjct: 128 TTKAQRKLFFNLRKAKQRLGWFNQDEV-EMVARELGVSSKDVREMESRMAAQDMTFDPTP 186

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRFGI 634
             + +   +   +  ++  S   + I+ +  E       +  +  L  R + ++R R+ +
Sbjct: 187 DDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLSDAMQGLDERSQHIIRARW-L 245

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 246 DDDNKTTLQELADQYGVSAERVRQLEKNAMKKLR 279


>gi|153840380|ref|ZP_01993047.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
 gi|149745954|gb|EDM57084.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 136/262 (51%), Gaps = 23/262 (8%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +  KGE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYKGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
             + ++ +R+      E   E +A++L +    VR++  ++     + + P  D+D++  
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDDDDSATS 194

Query: 589 GD-----FIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRFGIGMNT 638
                  ++EDK+  S +   I+A   E  T       LASL  R +R++R R+    + 
Sbjct: 195 SYTAPMLYLEDKS--SDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLD--DE 250

Query: 639 DHTLEEVGKQFCVTRERIRQIE 660
             TL+++  +F V+ ERIRQ+E
Sbjct: 251 KATLQDLADEFGVSAERIRQLE 272


>gi|302525186|ref|ZP_07277528.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
 gi|302434081|gb|EFL05897.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
          Length = 282

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 102/201 (50%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G  GL+ A EKFD   G +F TYAM  ++ AI   +  Q     +P  +R K  +
Sbjct: 81  DLVQSGIFGLVDAIEKFDPERGLRFETYAMQRIRGAILDDLRSQDW---VPRAVRSKAKE 137

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPI-GDEDTSH 587
             R   R+  ++ R PT  E+A ++ + ++ +R     L++T   ++LE  +   +D   
Sbjct: 138 TARALERLGARLHRTPTDAELAGEMGISLDDLRDFYGQLRLTSV-VALEDLVAAGKDAGS 196

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D  AV P+   +  + R      +A LT R++ V+ + +   +    TL E+GK
Sbjct: 197 LVDTLPDDGAVDPVAVLVDQDNRRQLAEAIAQLTDRDKIVVSLYYFESL----TLAEIGK 252

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  R+ Q+  +A+ +L+
Sbjct: 253 VLGVTESRVSQLHTRAVMRLR 273


>gi|145628599|ref|ZP_01784399.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|145632513|ref|ZP_01788247.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148825451|ref|YP_001290204.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittEE]
 gi|144979069|gb|EDJ88755.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|144986708|gb|EDJ93260.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148715611|gb|ABQ97821.1| RNA polymerase sigma factor [Haemophilus influenzae PittEE]
          Length = 281

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDSA-IQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLGV 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|332977407|gb|EGK14184.1| DNA-directed RNA polymerase sigma subunit RpoH [Psychrobacter sp.
           1501(2011)]
          Length = 362

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 82/304 (26%), Positives = 140/304 (46%), Gaps = 34/304 (11%)

Query: 383 WVSYAKDFPEGEWKNFV-ACEVD------SILKIRNEIKSISVETGISISEFRHIVSMVR 435
           WVS+   +P+   ++ V A  V+      ++    N +  I + T     E  H      
Sbjct: 59  WVSH---YPDTSTRDLVPAMPVNLSAPGINLGAYMNSVHQIPILTTEQEQELAH--RYYD 113

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G +
Sbjct: 114 EGDVEAA---RILVMSHLRFVIHIARSYSGYGLPQADLIQEGNLGLMKAVKRFDPNKGVR 170

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
             ++A+ W+K  I   +      +++      K H+ +    R   K   + T EE A  
Sbjct: 171 LVSFAVHWIKAEIHEFVIRNWRIVKVAT---TKAHRKLFFNLRSLKKTNNQLTLEE-ADA 226

Query: 556 LAMPVEGVRKVL-----KITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQAN 608
           +A  +   RK +     ++T    S E    D++  H     F+ED   V P +    A+
Sbjct: 227 IAADLNVTRKQVLEMESRLTSYDASFEAQSSDDEDGHYAPQLFLED--GVDPAEMVEDAD 284

Query: 609 LRETTTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             E  T  L     +L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+
Sbjct: 285 WEENNTNALMDAMDTLDDRSRDIVEQRWLSEQKS--TLHELAAVYNISAERVRQIEKNAM 342

Query: 665 RKLK 668
            K++
Sbjct: 343 DKIR 346


>gi|166710450|ref|ZP_02241657.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 282

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 47  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 107 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 155

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAI-------QA------ 607
            K L ++ +E + +E+ +   D       D  +D    SP+   +       QA      
Sbjct: 156 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDS 215

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             N  +     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIEA A++
Sbjct: 216 EDNHLQLLREGMAGLDTRSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIEANALK 274

Query: 666 KLK 668
           K+K
Sbjct: 275 KMK 277


>gi|205373764|ref|ZP_03226566.1| sporulation sigma factor SigF [Bacillus coahuilensis m4-4]
          Length = 244

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 120/240 (50%), Gaps = 19/240 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + ++   + G+ +A   +  +V  N+RLV SV +++ NRG +  DL Q G+IGL+K+ 
Sbjct: 18  EIKQLIKRSQDGDVDA---RDMIVNRNMRLVWSVVQRFLNRGYEPDDLFQIGSIGLLKSV 74

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     KFSTYA+  +   I R I D   T+++   +++  +K+ R    +S  + R
Sbjct: 75  DKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKETGNKIRRAKEELSKTLNR 133

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
            PT  E+A  L +  E V    + ++ P S+   +   D D   L D I D+N     D 
Sbjct: 134 VPTISELADFLEITPEEVVLAQEASRTPSSIHETVYENDGDPITLLDQIADQNDQKWFDK 193

Query: 604 -AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A++  +RE        L  RE  ++ +R+      D T  EV  +  +++ ++ ++  K
Sbjct: 194 IALKEAIRE--------LDERERLIVFLRY----YKDQTQSEVADRLGISQVQVSRLRKK 241


>gi|260582846|ref|ZP_05850631.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
 gi|260094059|gb|EEW77962.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
          Length = 281

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLGV 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|283796413|ref|ZP_06345566.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|291075823|gb|EFE13187.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|295091441|emb|CBK77548.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Clostridium cf.
           saccharolyticum K10]
 gi|295114800|emb|CBL35647.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily
           [butyrate-producing bacterium SM4/1]
          Length = 245

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 115/233 (49%), Gaps = 23/233 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE N+ LV S+ +++  RG +  DL Q G+IGL+KA +KFD     +FSTYA+  
Sbjct: 24  ARDRLVEENMGLVWSIVRRFAGRGCETEDLFQIGSIGLIKAIDKFDTSYDVRFSTYAVPM 83

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++   KV     +++  + REPT EEIA  +    E V
Sbjct: 84  IAGEIRRFLRDDGM-IKVSRSVKEMGIKVSAAREKLAGTLGREPTLEEIAGSVGASREEV 142

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-------RETTTRV 616
              L+   +  SL  P G +DT+           +S LD   Q +        R    ++
Sbjct: 143 AASLEAGAQVESLYAPAGGDDTN-----------LSLLDRLSQESRENEEVLDRMVLKKL 191

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L SL  +E  ++  R+  G     T  ++  Q  +++ ++ ++E + ++K++ 
Sbjct: 192 LGSLGEKERELIVRRYFYG----QTQTKIAGQMGISQVQVSRMEKRILKKMRE 240


>gi|3219170|dbj|BAA28785.1| sigma-32 homolog [Hydrogenophilus thermoluteolus]
          Length = 309

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 116/234 (49%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ANLR V+ +A++Y   GL   DLIQEGN+GL+KA  +FD   G +F T+A +W
Sbjct: 70  AARKLVLANLRYVVMIARQYFGYGLPEADLIQEGNVGLLKAVRRFDPYKGVRFITFAAYW 129

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVE 561
           +K  I   I      ++I      K  K+    R++  S  + R    + IA+ LA+  E
Sbjct: 130 IKAEIHDYILRNWRLVKIATTKAQK--KLFFNLRKLLGSEPLTRAKA-DAIAETLAVKPE 186

Query: 562 GVRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLR---ETTT 614
            V ++  +     ++LE PI  DE+        ++ D +       A     R   E   
Sbjct: 187 EVAEMHARFAGGDVALEAPIDSDEEADWRAPLAYLPDPSGTPEEAVAEAEAERLSHEGLQ 246

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L  L  R   ++  R+        TL E+  ++ ++ ER+RQIEA A++KL+
Sbjct: 247 QALTQLDERSRAIVTRRW--LTEKPATLHELAAEYGISAERVRQIEAAALKKLR 298


>gi|238917528|ref|YP_002931045.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872888|gb|ACR72598.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 249

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 121/227 (53%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V  NL L+ ++ K++  RG +  DL Q G IGL+KA + F+  +   FSTYA+  
Sbjct: 28  AREKLVTDNLGLIWNIIKRFKGRGTEQEDLFQIGCIGLIKAIDNFNLDMDVAFSTYAVPM 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++   K ++ A ++ + +  EPT E+IA    + VE +
Sbjct: 88  ITGEIRRFLRDDG-MVKVSRSIKENAVKSMKAAGQLRDTLGCEPTVEQIAAACELSVEDI 146

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              +  + E  S+   I  GD     L D +EDK  +    S+     +    +++ +L+
Sbjct: 147 TLSMSASMEVESIYKTIYQGDGSEVMLMDKLEDKADIGETASS-----KVALVQLMETLS 201

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ ++RMR+      D+T  +V K+F +++ ++ ++E K +  ++
Sbjct: 202 QREKELIRMRY----YDDYTQMQVAKEFGISQVQVSRMEKKILSGMR 244


>gi|167507975|gb|ABZ81308.1| RpoD [Thalassospira sp. MCCC 1A02753]
 gi|167507991|gb|ABZ81316.1| RpoD [Thalassospira sp. MCCC 1A02878]
 gi|167507995|gb|ABZ81318.1| RpoD [Thalassospira sp. MCCC 1A02921]
          Length = 257

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 101 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMV 160

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 161 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 220

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK F+    D I ++R ++  +S E
Sbjct: 221 WMERVSELPGKGWKAFIERYPDEIAQLREQVGGVSAE 257


>gi|325928799|ref|ZP_08189966.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
 gi|325540772|gb|EGD12347.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
          Length = 282

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 47  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 107 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 155

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAI-------QA------ 607
            K L ++ +E + +E+ +   D       D  +D    SP+   +       QA      
Sbjct: 156 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDS 215

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             N  +     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIEA A++
Sbjct: 216 EDNQLQLLREGMAGLDARSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIEANALK 274

Query: 666 KLK 668
           K+K
Sbjct: 275 KMK 277


>gi|323138995|ref|ZP_08074055.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322395749|gb|EFX98290.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 131/245 (53%), Gaps = 30/245 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVI++A K+ + GL   DL+QEG++GL++AA +F      +FSTYA WW
Sbjct: 41  ALHKLTAAHMRLVIALAAKFRHYGLPIADLVQEGHVGLLEAAARFAPERDVRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP-------TPEEIAKKL 556
           ++ +I   +      +R       K   +    RR+  ++ R+P         + IAK L
Sbjct: 101 IRASIQDYVLRNWSIVRGGTSSSQK--ALFFNLRRLRARLARDPDAYGSGDAYQAIAKAL 158

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG---DFIEDKNAVSPL-DSAIQANLRE 611
            +    V  +  +++   +SL   + D+D+S      DF+ D +   PL D A+Q  + +
Sbjct: 159 GVSRADVEMMDSRLSGSDVSLNAQLVDDDSSGSAQRMDFLVDDH---PLPDEAVQETM-D 214

Query: 612 TTTR------VLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKA 663
           +  R       LA L+ RE R+++ R      TD+  TLE +G +  +++ER+RQIE++A
Sbjct: 215 SDRRARWLKDALAILSERELRIVQER----RLTDNLVTLETLGDKLGISKERVRQIESRA 270

Query: 664 IRKLK 668
           + KL+
Sbjct: 271 LIKLR 275


>gi|229086642|ref|ZP_04218811.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
 gi|228696724|gb|EEL49540.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
          Length = 252

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 126/240 (52%), Gaps = 16/240 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++K +     A+  +V++N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD  
Sbjct: 21  ALIQKSQDGDQGARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D   ++++   +++  +K+ +    +S +  R PT  E
Sbjct: 81  FEVKFSTYAVPMIIGEIQRFLRDDG-SVKVSRSLKETGNKIRKMKDELSKEYGRAPTINE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS-AIQAN 608
           +A+ L +  E V    + ++ P S+   +   D D   + D I D+      +  A++  
Sbjct: 140 VAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITILDQIADQTETKWFEKIALKEA 199

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +RE        L  RE  ++ +R+      D T  EV ++  +++ ++ ++E K ++++K
Sbjct: 200 IRE--------LDERERLIVYLRY----YKDQTQSEVAERIGISQVQVSRLEKKILKQMK 247


>gi|308051462|ref|YP_003915028.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
 gi|307633652|gb|ADN77954.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
          Length = 286

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/262 (27%), Positives = 133/262 (50%), Gaps = 10/262 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I++++    +S  E +++   V +G+ +A+   K ++ A+LR V+ VA+ Y   GL   D
Sbjct: 24  IQAVNAIPMLSAEEEQYLARQVEQGDLDAA---KHLIMAHLRFVVHVARSYAGYGLPQAD 80

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHK 531
           LIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++     + K+  
Sbjct: 81  LIQEGNIGLMKAVKRFDPNIGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQRKLFF 140

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHLG 589
            +R A++       E     +A +L +    V ++  ++     + +  P  D+D     
Sbjct: 141 NLRKAKKRLGWFSAEEV-STVADELGVSESEVMEMEARMAAVDAAFDIAPERDDDEGAFA 199

Query: 590 D--FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVG 646
              F+EDK +        +   R++  R+ A+L   +ER   +     ++    TL+E+ 
Sbjct: 200 PALFLEDKQSDHAEALEQEDWDRQSQQRLHAALNTLDERSRDILMARWLDEPKATLQELA 259

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
            ++ V+ ERIRQ+E  AI+KLK
Sbjct: 260 DRYQVSAERIRQLEKNAIKKLK 281


>gi|297200169|ref|ZP_06917566.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197713380|gb|EDY57414.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 304

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 119/240 (49%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 69  LEEGTYEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRG 128

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A
Sbjct: 129 VEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVAELA 188

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
            +L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 189 DRLGLSKEEVVEGMAASNAYTAASLDAQ-PEEDDSEGALADRIGYE------DHGLEGIE 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L  R+ ++L +RF  GM    T  E+G++  +++  + ++ ++ + +L+
Sbjct: 242 YVESLKPLIAELPSRDRQILSLRFVAGM----TQSEIGEELGISQMHVSRLLSRTLVRLR 297


>gi|260554461|ref|ZP_05826682.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
 gi|260411003|gb|EEX04300.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
          Length = 288

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 171

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 172 VMEMEGRLTAYDAAFEAQGDDDDDTPHTAPVLYLED-NRYDPARLVENEDWEEQSTSALH 230

Query: 619 ----SLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 DAMNQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|123440620|ref|YP_001004614.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332159850|ref|YP_004296427.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122087581|emb|CAL10362.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318607604|emb|CBY29102.1| RNA polymerase sigma factor RpoH [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664080|gb|ADZ40724.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330862604|emb|CBX72757.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica W22703]
          Length = 285

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 127/243 (52%), Gaps = 16/243 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ---- 606
           K+L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+    
Sbjct: 159 KELGVTSKDVREMESRMSAQDMTFDPTPDDEVRDGQSMAPVLYLQDKTSDFADGIEEDNW 218

Query: 607 -ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             +  +  T  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++
Sbjct: 219 DNHAADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMK 277

Query: 666 KLK 668
           KL+
Sbjct: 278 KLR 280


>gi|110635708|ref|YP_675916.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286692|gb|ABG64751.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 284

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 123/249 (49%), Gaps = 29/249 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   M+ A++RLVI++A K+ N GL   DLIQEG++GL++AA +FD     +FSTYA WW
Sbjct: 39  ALHRMIMAHMRLVIAMAGKFRNFGLSMSDLIQEGHVGLLEAAARFDPEREVRFSTYATWW 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE--PTP-----EEIAKKL 556
           ++ ++   I      +R       K   +    RR+  K+++    TP      E+A+ L
Sbjct: 99  IRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRMKLQKAGGTTPSEDVYREVAQAL 156

Query: 557 AMPVEGVRKV-LKITKEPISLETPI-GDED-TSHLGDFI------EDKNAVSPLDSAIQA 607
            +    V  +  ++     SL  P+  D D TS   DF+       D+     +D   +A
Sbjct: 157 RVSESDVAMMDSRLAAADASLNAPLRSDSDPTSERIDFLICDKPQPDELVREAIDGERKA 216

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              +   + L +L  RE  ++R R         TLE +G    +++ER+RQIE++A+ KL
Sbjct: 217 ---QWLHQALGTLNGRELTIVRERR--LSEEGATLEALGASLGISKERVRQIESRALEKL 271

Query: 668 K------HP 670
           +      HP
Sbjct: 272 RTALVKHHP 280


>gi|312623242|ref|YP_004024855.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203709|gb|ADQ47036.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 256

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 97/190 (51%), Gaps = 7/190 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L +   +AKK+  RG+ + DL Q   I L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNRYLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +     ++ +Q    E   + +  L+P
Sbjct: 151 EVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSD-----ENILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRF 632
            E   ++ RF
Sbjct: 206 FEREFVQKRF 215


>gi|260550924|ref|ZP_05825130.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
 gi|260406051|gb|EEW99537.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
          Length = 288

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 171

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 172 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLVENEDWEEQSTSALH 230

Query: 619 ----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 DAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|160939297|ref|ZP_02086648.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438260|gb|EDP16020.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
          Length = 240

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 57/176 (32%), Positives = 95/176 (53%), Gaps = 6/176 (3%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           ++ E   +++M  +G+     A+ ++V  N+ L+ S+ ++++ RG +  DL Q G+IGL+
Sbjct: 3   AMDETMKLINMAHEGD---KAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLI 59

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KFD     KFSTYA+  +   I R + D    I++   +++   KV      M+  
Sbjct: 60  KAIDKFDTGFDVKFSTYAVPMITGEIKRFLRDDGM-IKVSRSIKELGVKVRAAREEMTYA 118

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           + REPT EEIA +L    E V   L+   E  SL  P   GDE++++L D +   N
Sbjct: 119 LGREPTIEEIAGRLGTSREEVAASLEAAAEVESLYRPADSGDENSTYLMDRLAQDN 174


>gi|188574757|ref|YP_001911686.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188519209|gb|ACD57154.1| alternative sigma factor RpoH [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 282

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 47  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 107 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 155

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAI-------QA------ 607
            K L ++ +E + +E+ +   D       D  +D    SP+   +       QA      
Sbjct: 156 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDS 215

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             N  +     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIEA A++
Sbjct: 216 EDNQLQLLREGMAGLDTRSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIEANALK 274

Query: 666 KLK 668
           K+K
Sbjct: 275 KMK 277


>gi|32490821|ref|NP_871075.1| RNA polymerase factor sigma-32 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166027|dbj|BAC24218.1| rpoH [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 281

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 74/301 (24%), Positives = 148/301 (49%), Gaps = 48/301 (15%)

Query: 397 NFVAC----EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           N + C     ++S +K  N    +S+E    ++E  H       G+    +A K+++ ++
Sbjct: 5   NILTCVNQSSLESYIKKANSYSMLSIEEEKILTERLHY-----NGDL---LAAKKLILSH 56

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LR V+ +++ Y+  GLQ  DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   +
Sbjct: 57  LRFVVHISRNYSGYGLQRADLIQEGNVGLMKAVKRFNPAIGVRLVSFAVHWIKAEIHEYV 116

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKI 569
                 +++      +  K+    R+   K+    +   + +AK L +  + VR++  ++
Sbjct: 117 LRNWRIVKVATTKAQR--KLFFNLRKAKKKLGWFNQYEVDMLAKSLGVTSKDVREMESRM 174

Query: 570 TKEPISLETPIGDED-------------TSHLGDFIEDKN----AVSPLDSAIQANLRET 612
           + + ++ +    +ED             TS   D IE+ N    A   L +A        
Sbjct: 175 SAKDMAFDFN-SEEDKHKNNAILYLKDKTSDFADTIEEDNWDIHATDKLSAA-------- 225

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               L++L  R + ++R R+ +  +   TL+E+ K++ ++ ERIRQ+E  A++K++    
Sbjct: 226 ----LSNLDLRSQEIIRSRW-LRYDNKSTLKELAKKYGISAERIRQLEKNAMKKIRFAVE 280

Query: 673 S 673
           S
Sbjct: 281 S 281


>gi|297588048|ref|ZP_06946692.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
 gi|297574737|gb|EFH93457.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
          Length = 258

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 118/228 (51%), Gaps = 18/228 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE NL +   +AKKYT RG+++ DL Q   IGL+ A +++D   GY+FS+YA   +   
Sbjct: 33  LVEKNLYIAEILAKKYTGRGIEYDDLYQVACIGLIYAIDRYDPSKGYEFSSYATPTIVGE 92

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+   IR+P  +++   KV      ++  +++ PT E+IA  L++  E V +VL
Sbjct: 93  IKKYFRDKGWVIRVPRRIQELNKKVANAKIHLAQTMQKSPTVEDIADYLSISNEEVLEVL 152

Query: 568 KITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASL 620
           +  K   P SL+  I    D+  ++L D I  EDK+        ++   R+   R +  L
Sbjct: 153 EGAKVYAPQSLDQSIDQSSDDRDTNLSDLIGEEDKD-------MLKFENRDLINRCMEDL 205

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              E+++L  R+        T   + ++  +++  + ++E K ++K K
Sbjct: 206 NEVEKKILLGRYF----DKKTQIVIAEELDISQMTVSRMEKKILKKFK 249


>gi|167507913|gb|ABZ81277.1| RpoD [Thalassospira sp. MCCC 1A01051]
 gi|167507917|gb|ABZ81279.1| RpoD [Thalassospira sp. MCCC 1A01072]
 gi|167507945|gb|ABZ81293.1| RpoD [Thalassospira sp. MCCC 1A01448]
 gi|167507967|gb|ABZ81304.1| RpoD [Thalassospira sp. MCCC 1A02094]
          Length = 260

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 104 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGESVPAATEKRYAKLKGEMV 163

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 164 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 223

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK F+    D I ++R ++  +S E
Sbjct: 224 WMERVSELPGKGWKAFIERYPDEIAQLREQVGGVSAE 260


>gi|167507911|gb|ABZ81276.1| RpoD [Thalassospira sp. MCCC 1A01041]
 gi|167507923|gb|ABZ81282.1| RpoD [Thalassospira sp. MCCC 1A01140]
 gi|167507999|gb|ABZ81320.1| RpoD [Thalassospira sp. MCCC 1A03005]
 gi|167508001|gb|ABZ81321.1| RpoD [Thalassospira sp. MCCC 1A03052]
 gi|167508003|gb|ABZ81322.1| RpoD [Thalassospira sp. MCCC 1A03093]
          Length = 260

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 104 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGESVPAATEKRYAKLKGEMV 163

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 164 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 223

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK F+    D I ++R ++  +S E
Sbjct: 224 WMERVSELPGKGWKAFIERYPDEIAQLREQVGGVSAE 260


>gi|167507897|gb|ABZ81269.1| RpoD [Thalassospira xiamenensis]
          Length = 255

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 99  SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGESVPAATEKRYAKLKGEMV 158

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 159 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 218

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK F+    D I ++R ++  +S E
Sbjct: 219 WMERVSELPGKGWKAFIERYPDEIAQLREQVGGVSAE 255


>gi|134100730|ref|YP_001106391.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006467|ref|ZP_06564440.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133913353|emb|CAM03466.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 268

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 107/213 (50%), Gaps = 10/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L +   +A+++ +RG    DL+Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 36  RDRLVTEHLPVAEHIARRFRHRGETHDDLVQVATLGLIKAVDRFDPGRGVGFMSYAVPTI 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D   ++R+P  M++    V      +S ++ R PTP E+A  L + V+ V+
Sbjct: 96  MGEVRRHFRDAGWSVRMPRRMQELHLSVSAGISALSQELGRAPTPSELAAHLKLSVDDVQ 155

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+        SL+  +   D   LG+ I  D + ++ ++       RET   +LA L 
Sbjct: 156 QGLEAGNAYRSASLDDLLTGTDDVPLGEAIGFDDSELAEVED------RETIRPLLAELP 209

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            RE R+L MRF  GM      E+VG  Q  V+R
Sbjct: 210 ERERRILVMRFFRGMTQTEIAEQVGVSQMHVSR 242


>gi|293609550|ref|ZP_06691852.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828002|gb|EFF86365.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 288

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 171

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 172 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLVENEDWEEQSTSALH 230

Query: 619 ----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 DAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|21244548|ref|NP_644130.1| RNA polymerase factor sigma-32 [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|21110222|gb|AAM38666.1| RNA polymerase sigma-32 factor [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 291

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 121/248 (48%), Gaps = 40/248 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN------------ 608
            K L ++ +E + +E+ +   D       D  +D    SP+ S + AN            
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPV-SYLVANEEDPSQAYERHD 223

Query: 609 --------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                   LRE     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIE
Sbjct: 224 SEDNQLQLLREG----MAGLDARSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIE 278

Query: 661 AKAIRKLK 668
           A A++K+K
Sbjct: 279 ANALKKMK 286


>gi|121999080|ref|YP_001003867.1| RNA polymerase sigma-32 subunit RpoH [Halorhodospira halophila SL1]
 gi|121590485|gb|ABM63065.1| RNA polymerase, sigma 32 subunit, RpoH [Halorhodospira halophila
           SL1]
          Length = 287

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 127/247 (51%), Gaps = 16/247 (6%)

Query: 433 MVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + R+ + E  + A +++V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  
Sbjct: 41  LARRCQYEGDLDAARQLVLSHLRFVVHVARGYRGYGLALGDLIQEGNIGLMKAVKRFDPD 100

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPE 550
           +G +  ++A+ W++  I   I      +++     + K+   +R A++    + RE    
Sbjct: 101 VGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKLFFNLRGAKKRLGWMTREEV-N 159

Query: 551 EIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG---DFIEDKN-----AVSPL 601
            +A+ L +  E V ++  +++ + +  +  + +ED         ++ED+       V   
Sbjct: 160 AVAEDLGVQPETVLEMESRLSGQDLGFDPLVSEEDEEQARAPVAYLEDRRFDPAEVVESS 219

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D     +  ++  + L  L  R + +LR R+        TL+E+ +++ V+ ERIRQ+E 
Sbjct: 220 DWGTHQD--DSLHQALGQLDERSQNILRARW--LEEERQTLQELAERYGVSAERIRQLEK 275

Query: 662 KAIRKLK 668
            AI KL+
Sbjct: 276 NAISKLR 282


>gi|148265963|ref|YP_001232669.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
 gi|146399463|gb|ABQ28096.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
          Length = 280

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 110/246 (44%), Gaps = 39/246 (15%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ +NLR V+ +A +Y + G++ LDLIQEGNIGLM A  KF+   G++  +YA+WW
Sbjct: 41  AAHRLITSNLRFVVKIAGEYRSYGMKMLDLIQEGNIGLMMAVRKFNPYKGFRLISYAVWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   I      ++I            +  R++  K+ +       AK     + G 
Sbjct: 101 IRAYIQNHIVSTWSLLKI---------GTTQAQRKLFFKLNQ-------AKSAIRSMTGG 144

Query: 564 RKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSP-----LDSAI------------ 605
              L+     + + E+   + D    GD+  D   V+      L+S              
Sbjct: 145 GDDLQAAALSLDVKESEAQEMDQRMRGDYFLDAEVVTGEGLTMLESLPDERRNQEELLGE 204

Query: 606 ---QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
               A L       L  L  +E  V+  R  +  +   TL+E+   F ++RER+RQIE  
Sbjct: 205 AEESAILEREVAAALTCLNEKERYVIEQR--VSSDEPLTLQEIADHFSISRERVRQIEEG 262

Query: 663 AIRKLK 668
           A++K+K
Sbjct: 263 ALKKMK 268


>gi|238755238|ref|ZP_04616583.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
 gi|238706579|gb|EEP98951.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
          Length = 285

 Score = 85.5 bits (210), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 125/244 (51%), Gaps = 31/244 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQEE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDED----------------TSHLGDFIEDKNAVSPLDSA 604
            VR++  +++ + ++ + P  D+D                TS   D IE+ N        
Sbjct: 167 DVREMESRMSAQDMTFD-PTPDDDVRDGQSMAPVLYLQDKTSDFADGIEEDN-------- 217

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +++  +  +  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A+
Sbjct: 218 WESHAADKLSYALEGLDERSQHIIRARW-LDDDNKTTLQELADQYGVSAERVRQLEKNAM 276

Query: 665 RKLK 668
           +KL+
Sbjct: 277 KKLR 280


>gi|239832848|ref|ZP_04681177.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
 gi|239825115|gb|EEQ96683.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
          Length = 278

 Score = 85.5 bits (210), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 126/249 (50%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 21  IRWRELKDQEALHRITSAHMRLVISMAGRFRKFKLPMNDLIQEGYVGLLEAAARFDPERE 80

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 81  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQSDDTMSKA 138

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL  P+  E++  S   DF+ D + +     
Sbjct: 139 EIYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNSEESGASRRMDFLVDDHPLQDEIA 198

Query: 602 DSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R     V L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQI
Sbjct: 199 ESSIDMERRNQWLNVALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQI 255

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 256 ESRAMEKLK 264


>gi|325122820|gb|ADY82343.1| RNA polymerase factor sigma-32 [Acinetobacter calcoaceticus PHEA-2]
          Length = 276

 Score = 85.5 bits (210), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 41  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 100

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 101 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 159

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 160 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLVENEDWEEQSTSALH 218

Query: 619 ----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 219 DAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 270


>gi|255066480|ref|ZP_05318335.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
 gi|255049360|gb|EET44824.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
          Length = 649

 Score = 85.5 bits (210), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 55/184 (29%), Positives = 99/184 (53%), Gaps = 4/184 (2%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D + +D +  L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ V+M+S
Sbjct: 9   DYQEQDDNRPLTLEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMIS 68

Query: 72  NMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMG 129
            +GI V +   D ED   S+++  +    + +         DS    T DPVRMY+REMG
Sbjct: 69  GLGIQVTEQAPDAEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMG 128

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
            ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      + E++  EA
Sbjct: 129 QVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVV--EA 186

Query: 190 CIGP 193
            I P
Sbjct: 187 IIDP 190


>gi|312963434|ref|ZP_07777916.1| sigma-70 [Pseudomonas fluorescens WH6]
 gi|311282240|gb|EFQ60839.1| sigma-70 [Pseudomonas fluorescens WH6]
          Length = 616

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 82/137 (59%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|119384948|ref|YP_916004.1| RNA polymerase factor sigma-32 [Paracoccus denitrificans PD1222]
 gi|119374715|gb|ABL70308.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 301

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 120/243 (49%), Gaps = 24/243 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAQRLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKL 556
           ++ +I   I      +++      K  K+    R+  +K+        R     +IA  L
Sbjct: 109 IRASIQEYILRSWSLVKMGTTSAQK--KLFFNLRKAKSKLGALEEGDLRPENVTQIAHDL 166

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANL--- 609
            +  + V  +  +++    SL   +G    E T+   D++ED++A      A    L   
Sbjct: 167 NVTEQEVIDMNRRLSSGDASLNATVGSGDGESTAQWQDWLEDEDANQAEAFAEADELSAR 226

Query: 610 RETTTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           RE     +  L  RE+ +L   R+R     +   TLE++  ++ V+RERIRQIE +A  K
Sbjct: 227 REMLIAAMDVLNDREKDILMERRLR-----DDPMTLEDLSTRYGVSRERIRQIEVRAFEK 281

Query: 667 LKH 669
           L++
Sbjct: 282 LQN 284


>gi|261866928|ref|YP_003254850.1| RNA polymerase factor sigma-32 [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412260|gb|ACX81631.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 282

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/274 (25%), Positives = 143/274 (52%), Gaps = 20/274 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  NE   ++ E    ++E      +  K + EA+   K++V ++LR VI VA+ 
Sbjct: 16  IEAYIRAANEYPMLTAEEEKELAE-----RLYYKEDIEAA---KKLVLSHLRFVIHVARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+      E   + +A +L +  + V ++  ++T   ++ + P
Sbjct: 128 TTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSPQDVMEMESRMTGADVAFDLP 185

Query: 580 I--GDEDTSHLGDFIEDK--NAVSPLDSA-IQANLRETTTRVLASLTPREERVLRMRFGI 634
               DE+T     ++EDK  N  + L++   +A   +     L +L  R + +++ R+  
Sbjct: 186 GDEHDEETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDARSQDIIKARWLD 245

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              T  TL+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 246 --ETKATLQDLAAKYNISAERVRQLETNALKKLK 277


>gi|84688065|ref|ZP_01015924.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84663915|gb|EAQ10420.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 298

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 120/244 (49%), Gaps = 29/244 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHQLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVE 561
           ++ +I   I      +++     + K+   +R A+ R+      +  PE +A+       
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPENVAQ------- 161

Query: 562 GVRKVLKITKEPI------------SLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
            +   L +T+E +            SL   I +  + T    D++ED++A    D   + 
Sbjct: 162 -IAHDLNVTEEEVISMNRRMSGGDASLNATITNDGDSTMQWQDWLEDEDADQAGDYEQRD 220

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            L   RE   + +  L  RE+ +L  R     +   TLE++  Q+ V+RERIRQIE +A 
Sbjct: 221 ELTVRREMLAQAMDVLNDREKDILTQRR--LSDETVTLEDLSGQYDVSRERIRQIEVRAF 278

Query: 665 RKLK 668
            KL+
Sbjct: 279 EKLQ 282


>gi|324998294|ref|ZP_08119406.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 258

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 107/213 (50%), Gaps = 9/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V   L +   +A+++ +RG    DL+Q   +GL+ A ++FD   G +F ++A+  +
Sbjct: 31  RDRLVTGYLPVAQHIARRFNHRGEPLDDLVQVATVGLINAIDRFDPDKGGEFFSFAVPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   DQS ++R+P  ++D    +      +S  + R P P EIA+ L +PV  V 
Sbjct: 91  SGEVRRHFRDQSWSMRVPRRLKDMHVSINGAVSELSQTLGRSPRPSEIAEHLGLPVPEVL 150

Query: 565 KVLKITK--EPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+  +     SL+  +  ED  + +G+ + D +A   LD   + + RE+   +LA L 
Sbjct: 151 EGLEAAEAYRSSSLDEMLSSEDGGATVGELVGDADA--ELD---RVDYRESLRPLLAELA 205

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           PRE  ++ +RF           EVG  Q  V+R
Sbjct: 206 PRERTIVMLRFFGNRTQTQIANEVGISQMHVSR 238


>gi|167507977|gb|ABZ81309.1| RpoD [Thalassospira sp. MCCC 1A02758]
 gi|167507979|gb|ABZ81310.1| RpoD [Thalassospira sp. MCCC 1A02767]
 gi|167507981|gb|ABZ81311.1| RpoD [Thalassospira sp. MCCC 1A02785]
 gi|167507985|gb|ABZ81313.1| RpoD [Thalassospira sp. MCCC 1A02843]
 gi|167507987|gb|ABZ81314.1| RpoD [Thalassospira sp. MCCC 1A02866]
 gi|167507989|gb|ABZ81315.1| RpoD [Thalassospira sp. MCCC 1A02873]
 gi|167507997|gb|ABZ81319.1| RpoD [Thalassospira sp. MCCC 1A02935]
          Length = 257

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 101 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMV 160

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 161 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 220

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK FV    D I ++R ++  +S E
Sbjct: 221 WMERVGELPGKGWKAFVERYPDEIAQLREQVGGVSAE 257


>gi|114561466|ref|YP_748979.1| RNA polymerase factor sigma-32 [Shewanella frigidimarina NCIMB 400]
 gi|114332759|gb|ABI70141.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella frigidimarina
           NCIMB 400]
          Length = 285

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 122/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + ++ +R+      E T   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNIRKSKKRLGWFSDAEVTM--VAENLGVSKA 169

Query: 562 GVRKV--LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLR-ETTTRV 616
            V ++      ++P    T   D+D        ++ED ++    D    AN   ++ TR+
Sbjct: 170 DVTEMESRMAAQDPAFDLTNDSDDDHHDFAPALYLEDHSS-DVADQVEHANWEADSQTRL 228

Query: 617 LASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++   +ER   +LR R+    +T  TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 229 LSAIKTLDERSQHILRARWLD--DTKVTLQELASTYEVSAERIRQLEKNAMNKLK 281


>gi|167507937|gb|ABZ81289.1| RpoD [Thalassospira sp. MCCC 1A01300]
 gi|167507941|gb|ABZ81291.1| RpoD [Thalassospira sp. MCCC 1A01330]
          Length = 255

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 99  SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMV 158

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 159 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 218

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK F+    D I ++R ++  +S E
Sbjct: 219 WMERVGELPGKGWKAFIERYPDEIAQLREQVGGVSAE 255


>gi|255020686|ref|ZP_05292748.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
 gi|254969922|gb|EET27422.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
          Length = 285

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 128/236 (54%), Gaps = 20/236 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 50  AAKQLVLSHLRFVVRVARAYRGYGLPEADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+AR+ S  + +E +   IA+ L +  E 
Sbjct: 110 IKAEMHEFILRNWRIVKVATTKAQRKLFFNLRSARQSSGWLGQEESA-AIAEDLGVSQEA 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-------RETTT 614
           V ++  ++  +  SL+    DE+       +ED     P +S+++A +       R+   
Sbjct: 169 VLEMEGRMAGQDYSLQYESDDEEGHGRTLELED-----PGESSVEALIDRDWDQQRQRGL 223

Query: 615 R-VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R  L SL+ R+  +++ R+   ++ D  TL+ +G++  V+ ER+RQ+E   + KL+
Sbjct: 224 RAALQSLSERDRYIIQNRW---LSDDPKTLQALGEELGVSAERVRQLEKSGMEKLR 276


>gi|330938479|gb|EGH42082.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 183

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 82/137 (59%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|169632997|ref|YP_001706733.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii SDF]
 gi|169795347|ref|YP_001713140.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AYE]
 gi|184158784|ref|YP_001847123.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii ACICU]
 gi|213158666|ref|YP_002319964.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|215482881|ref|YP_002325084.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|239502880|ref|ZP_04662190.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB900]
 gi|301346949|ref|ZP_07227690.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB056]
 gi|301513493|ref|ZP_07238730.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB058]
 gi|301596794|ref|ZP_07241802.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB059]
 gi|332850459|ref|ZP_08432779.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332871911|ref|ZP_08440323.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
 gi|169148274|emb|CAM86139.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii AYE]
 gi|169151789|emb|CAP00610.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii]
 gi|183210378|gb|ACC57776.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii ACICU]
 gi|193077812|gb|ABO12685.2| EsvH [Acinetobacter baumannii ATCC 17978]
 gi|213057826|gb|ACJ42728.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|213986534|gb|ACJ56833.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|322507403|gb|ADX02857.1| rpoH [Acinetobacter baumannii 1656-2]
 gi|323518699|gb|ADX93080.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332730730|gb|EGJ62041.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332731125|gb|EGJ62426.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
          Length = 288

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 171

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 172 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPVLYLED-NRYDPARLVENEDWEEQSTSALH 230

Query: 619 ----SLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 DAMNQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|167040197|ref|YP_001663182.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           sp. X514]
 gi|300914281|ref|ZP_07131597.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|307265137|ref|ZP_07546696.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307724483|ref|YP_003904234.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|326391064|ref|ZP_08212611.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166854437|gb|ABY92846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889216|gb|EFK84362.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|306919759|gb|EFN49974.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307581544|gb|ADN54943.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|325992849|gb|EGD51294.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 111/222 (50%), Gaps = 12/222 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++  N  L+ S+ KK++NRG +  DL Q G IG +KA +KFD     K STYA+  +   
Sbjct: 30  LILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVKAIQKFDESYNVKLSTYAVPIIMGE 89

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R + D    I++   +++   K       +SN++ REPT  EIA++L +  E +    
Sbjct: 90  IKRFLRDDGL-IKVSRSLKELSTKAFYVKEILSNELNREPTINEIAERLNVSPEEIAMAF 148

Query: 568 KITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +      SL +    DED   L + + ++     +D  +   +      V+  L PRE++
Sbjct: 149 ESAATAESLYDNATHDEDDRLLIEMVSEEEKEVDIDDKLALQM------VINKLKPREKQ 202

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +R+      D T  EV     +++ ++ +IE K ++KL+
Sbjct: 203 IIFLRYF----KDMTQMEVASVLGISQVQVSRIEKKVLQKLR 240


>gi|88607306|ref|YP_505338.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
 gi|88598369|gb|ABD43839.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
          Length = 289

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 119/235 (50%), Gaps = 20/235 (8%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+ VA  + + GL  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K 
Sbjct: 50  KLVTSHLRLVVKVAMGFRSYGLPLMELIMEGNIGLMQAVKKFNPELGFRLSTYAIWWIKA 109

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI------KREPTPEEIAKKLAMPV 560
           +I   I      +RI      K  K+  + R++  +I        +     IA++     
Sbjct: 110 SIKDYILRSWSCMRIGTTQAQK--KLFFSLRKIKRRILGCSASASQSDIRAIAEECGTSE 167

Query: 561 EGVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR---- 615
           + V  + +  +   ISL   +  E  + L D I      SP    +  +  E+  +    
Sbjct: 168 KEVESMDRFFSNRDISLSDKVCCESGTELQDLIP---CSSPNQEVMYLSHEESVMKDQMV 224

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L++L  R   +   R  +  + D TLE + +++ V++ERIRQIE ++  K++
Sbjct: 225 KEALSTLDERHRDIFSRR-KLKEHPD-TLETLSEEYGVSKERIRQIELQSFSKVR 277


>gi|78049505|ref|YP_365680.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|294626531|ref|ZP_06705130.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|294665098|ref|ZP_06730402.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|78037935|emb|CAJ25680.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|292599221|gb|EFF43359.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292605140|gb|EFF48487.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 294

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 121/248 (48%), Gaps = 40/248 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 59  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 119 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 167

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN------------ 608
            K L ++ +E + +E+ +   D       D  +D    SP+ S + AN            
Sbjct: 168 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPV-SYLVANEEDPSQAYERHD 226

Query: 609 --------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                   LRE     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIE
Sbjct: 227 SEDNQLQLLREG----MAGLDARSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIE 281

Query: 661 AKAIRKLK 668
           A A++K+K
Sbjct: 282 ANALKKMK 289


>gi|297180174|gb|ADI16396.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured bacterium HF130_12L15]
          Length = 288

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 116/243 (47%), Gaps = 41/243 (16%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A K+   GL   DL+QEG++GL++AA +F+     +FSTYA WW++ ++  
Sbjct: 47  AHMRLVISMAGKFRYFGLPMSDLVQEGHVGLLEAAARFEPERDVRFSTYATWWIRASMQD 106

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKLAMPVEGV 563
            I      +R       K   +    RR+  ++ +   P       +EIA  + + V  V
Sbjct: 107 HILRNWSIVRGGTSSAQK--ALFFNLRRLRARLAQGTEPLKGAAVYQEIADAIGVSVADV 164

Query: 564 RKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             +  +++    SL  P+ D  E TS   DF+  ++     D  + A++ +         
Sbjct: 165 ALMDSRLSGPDSSLNAPVADGGESTSERMDFLVSEDPTP--DEVVSASIDD--------- 213

Query: 621 TPREERVLRMRFGIGMNTDH---------------TLEEVGKQFCVTRERIRQIEAKAIR 665
              E R + +   +G+  D                TLE +G +  +++ER+RQIE +A+ 
Sbjct: 214 ---ERRTMWLNRALGVLNDRELRIIRERRLRDEGATLESLGAKLGISKERVRQIENRALE 270

Query: 666 KLK 668
           KL+
Sbjct: 271 KLR 273


>gi|293393954|ref|ZP_06638260.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
 gi|291423514|gb|EFE96737.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
          Length = 285

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 126/243 (51%), Gaps = 16/243 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAI----- 605
           ++L +  + VR++  ++  + ++ +    DE  D   +   +  ++  S     I     
Sbjct: 159 RELGVTSKDVREMESRMAAQDMTFDPTPDDEARDGQSMAPVLYLQDKTSDFAEGIEEDNW 218

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           ++N  +     L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++
Sbjct: 219 ESNAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMK 277

Query: 666 KLK 668
           KLK
Sbjct: 278 KLK 280


>gi|296135250|ref|YP_003642492.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
 gi|294339349|emb|CAZ87705.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Thiomonas sp. 3As]
 gi|295795372|gb|ADG30162.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
          Length = 302

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 123/238 (51%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV+S A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W
Sbjct: 63  AAGKLVLSHLRLVVSTARQYLGYGLPHADLIQEGNIGLMKAVKRFDPAHGVRLVSYALHW 122

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVE 561
           +K  I   I      +++      +  K+    R M  +N    E   +++A+ L +  E
Sbjct: 123 IKAEIHEYILRNWRLVKVATTKSQR--KLFFNLRSMKTANAGMNEAQIDDMAQALNVKRE 180

Query: 562 GVRKV-LKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAIQANLR-ETTT 614
            V ++  ++    I+L+  + D +      S+L D  ++  AV  L++     L+ E   
Sbjct: 181 DVIEMESRMGGADIALDPTVEDGEESYAPISYLADNTQEPMAV--LEARSHDRLQVEGLE 238

Query: 615 RVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  L  R   ++  R+ + +N D     TL E+  ++ V+ ERIRQIE  A++K++
Sbjct: 239 NALELLDARSRAIVEQRW-LQVNDDGSGGKTLHELAAEYGVSAERIRQIEVAAMKKMR 295


>gi|154252606|ref|YP_001413430.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156556|gb|ABS63773.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 340

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 128/246 (52%), Gaps = 22/246 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E + A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +
Sbjct: 81  EHEDTEAAHQLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLA 140

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE-- 551
           TYAMWW++ +I   I      +++      K  K+    R++  +I+     +  PE+  
Sbjct: 141 TYAMWWIRASIQEYILRSWSLVKMGTTAAQK--KLFFNLRKVKGQIQAIEEGDLHPEQVK 198

Query: 552 -IAKKLAMPVEGVRKVLKITKEP-ISLETPI-GDEDTSHLGDFIEDKNA--VSPLDSAIQ 606
            I+ +L +  + V  + +    P  SL  P+  D +     D++ D  A   + L  A +
Sbjct: 199 VISDRLGVTEDEVISMNRRLSGPDNSLNAPLRQDSEGGEWQDWLVDDTADQEATLGEAEE 258

Query: 607 ANL-RETTTRVLASLTPREERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            +  RE     +A+L  RE  +L   R++     +   TLE++ +++ ++RER+RQIE +
Sbjct: 259 LDQRREMLAAAMATLNEREMHILTERRLK-----DEPATLEDLSQEYGISRERVRQIEVR 313

Query: 663 AIRKLK 668
           A  KL+
Sbjct: 314 AFEKLQ 319


>gi|239981813|ref|ZP_04704337.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 328

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 116/238 (48%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 95  EGTAEFAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 154

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A +
Sbjct: 155 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVRELADR 214

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     VEG+      T   +  + P  D+    L D I  +      D  I+     
Sbjct: 215 LGLSQEEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE------DHGIEGIEYV 267

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ R+L +RF   M    T  E+G++  +++  + ++  + + +L+
Sbjct: 268 ESLKPLIAELPARDRRILSLRFTANM----TQSEIGEELGISQMHVSRLLTRTLNRLR 321


>gi|297196439|ref|ZP_06913837.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197722266|gb|EDY66174.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 292

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 104/215 (48%), Gaps = 34/215 (15%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E   A+  ++E N+ LV  VA+++ NR     D++Q G IGL+KA ++FD     +
Sbjct: 59  EGTPEYQYARNTLIEMNISLVRYVARRFRNRAESDEDIVQVGTIGLIKAIDRFDLSREVE 118

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D S  + +P  +++   ++V+    +S K+ R PT  E+++ 
Sbjct: 119 FATFAVPYILGEIKRFFRDTSWAVHVPRRLQELRLELVQAVNELSGKLHRAPTAAELSEH 178

Query: 556 LAMPVEGVRKVLKITKEPI--SLETP---------------IGDEDTSHLGDFIEDKNAV 598
           L +PVE V + L      +  S + P                GD D + LG  +ED  A+
Sbjct: 179 LEIPVEEVTEGLVAMNGYVASSFDVPNTEGGPNAEAPFAERFGDLDPA-LG-LVEDLQAL 236

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            PL               +  L  R+  +LR+RFG
Sbjct: 237 KPL---------------IEELDDRDRLILRLRFG 256


>gi|284042121|ref|YP_003392461.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
 gi|283946342|gb|ADB49086.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
          Length = 300

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 127/252 (50%), Gaps = 21/252 (8%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKA 484
           R +V   + GE   + A+ E+V+  + L+ SVA+ Y  RG+  +   +L+Q G +GL+ A
Sbjct: 54  RALVLAAQGGE---TGARDELVDVFMPLIGSVARLY--RGVTSVHRAELMQAGVVGLLTA 108

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK---VVRTARRMSN 541
            E+FD      F TYA WWV+QA+ + +A+    +  PV M D+  +    +R ARR   
Sbjct: 109 LERFDPSRRAPFWTYASWWVRQAMQQVVAE----LARPVVMSDRGLRELARMRAARRDFT 164

Query: 542 KIK-REPTPEEIAKKLAMPVEGVRKVLKITKEPISLET--PIGDED--TSHLGDFIEDKN 596
           ++    P+   +A    +  E +  +L +   P +LE+     DED      G  +ED  
Sbjct: 165 RLHDAGPSSVRLAAATGLTRERIETLLALELVPETLESEPAWSDEDDLARRSGHPLEDPG 224

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A    D  +     +   R++  L  RE  +L  RFG+    + TL EV +   ++ ER+
Sbjct: 225 AEEAFDRVLDRVECDRLLRLIGDLRQRERVILHARFGLD-GQERTLREVARMVGLSAERV 283

Query: 657 RQIEAKAIRKLK 668
           RQ+E +A+ +L+
Sbjct: 284 RQLEHEALDELR 295


>gi|114705882|ref|ZP_01438785.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114538728|gb|EAU41849.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 300

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 126/251 (50%), Gaps = 23/251 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR  E     A  ++  A++RLVIS+A K+ + GL   DLIQEG++GL++AA +F+    
Sbjct: 43  VRWKENRDQEALHKITSAHMRLVISMASKFRHFGLAMNDLIQEGHVGLLEAAARFEPERE 102

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---- 549
            +FSTYA WW++ +I   I      +R       K   +    RR+  ++ +   P    
Sbjct: 103 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLSQGAEPISGN 160

Query: 550 ---EEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPL-D 602
               EIA  L +    V  +  +++    SL  P+ D+++      DF+    A  PL D
Sbjct: 161 AMYREIAGALKVSESDVALMDSRLSGPDSSLNAPLLDDESGSADRQDFL---VADDPLPD 217

Query: 603 SAIQANL---RETT--TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +  ++   R  T  T  L  L+ RE +++R R     +   TLE +G +  +++ER+R
Sbjct: 218 ETVSVSIDDERRVTWLTSALDVLSERELKIIRERR--LQDDGATLEALGTKLGISKERVR 275

Query: 658 QIEAKAIRKLK 668
           QIE +A+ KL+
Sbjct: 276 QIETRALEKLR 286


>gi|326775534|ref|ZP_08234799.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655867|gb|EGE40713.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 125/244 (51%), Gaps = 14/244 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFD 489
           + ++ +G      A+  ++E NL LV   AK++ NRG  +  D+IQ G IGL+KA ++F+
Sbjct: 50  LQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIIQVGTIGLIKAIDRFE 109

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+++A+ ++   I R   D +  + +P  +++    + +T   +S ++ REPT 
Sbjct: 110 LSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKTREALSTRLDREPTV 169

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSA 604
            E+A  L +     +EG+      T    SL+ PIG D++++    + + K  V P    
Sbjct: 170 AELAHHLELTEEEVIEGLIAANGYTAG--SLDLPIGADQNSAETVTYGDIKGDVDPAMEL 227

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++     T   +L  L  RE  ++ MRFG  M    T  ++G+   +++  + ++ ++ +
Sbjct: 228 VED--LHTLAPLLEQLDEREREIVAMRFGREM----TQAQIGEHLGISQMHVSRLLSRLL 281

Query: 665 RKLK 668
            KL+
Sbjct: 282 TKLR 285


>gi|260771645|ref|ZP_05880565.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
 gi|260613422|gb|EEX38621.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
          Length = 285

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 124/244 (50%), Gaps = 21/244 (8%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 45  GDIEAA---KTLILSHLRFVVHVARGYSGYGLPIADLVQEGNIGLMKAVKRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAR 159

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANL 609
           +L +    VR++  ++     + E    D+D  +       ++EDK   S L   I+A  
Sbjct: 160 ELGVEPAEVREMESRLAALDSTFEFSAEDDDNPNAYTAPVLYLEDKQ--SDLAENIEAQN 217

Query: 610 RETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            E  T       LASL  R + ++R R+        TL+E+   + V+ ERIRQ+E  A+
Sbjct: 218 WENHTNHRLSLALASLDERSQHIVRSRWLDDQKA--TLQELADLYQVSAERIRQLEKNAM 275

Query: 665 RKLK 668
           +KLK
Sbjct: 276 KKLK 279


>gi|1710646|sp|P50509|RP32_PROMI RecName: Full=RNA polymerase sigma-32 factor
 gi|1143374|dbj|BAA09441.1| sigma-32 homolog [Proteus mirabilis]
          Length = 284

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/277 (25%), Positives = 140/277 (50%), Gaps = 24/277 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E    ++E  H      +G+ EA+   K ++ ++LR VI VA+ 
Sbjct: 16  IEAYIRAANSYPMLTAEEEKELAERLHY-----EGDLEAA---KTLILSHLRFVIHVARS 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA   F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRHFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+   ++    +   E +AK+L +    VR++  +++ + ++ +  
Sbjct: 128 TTKSQR--KLFFNLRKNKKRLGWFNQDEVELVAKELGVSESDVREMESRMSAQDMAFDMS 185

Query: 580 IGDEDTSHLGD---FIEDKNAVSPLDSAIQA-----NLRETTTRVLASLTPREERVLRMR 631
             D D  H      F+EDK+  S     I+      +  +  T  + +L  R + ++R R
Sbjct: 186 ADDSDDPHPVAPVLFLEDKS--SDFADGIEEDNWDNHAADRLTLAIKTLDERSQDIIRAR 243

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 244 W-LEDDNKSTLQELADKYGVSAERVRQLEKNAMKKLR 279


>gi|168333394|ref|ZP_02691674.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family protein
           [Epulopiscium sp. 'N.t. morphotype B']
          Length = 249

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 114/228 (50%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +VE NL LV S+ K++TNRG    DL Q G+IGL+K+ EKFD      FSTYA+  
Sbjct: 27  AKELLVEQNLGLVWSLVKRFTNRGYDLDDLFQVGSIGLLKSIEKFDLKYPVAFSTYAVPM 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   ++D   K          +  REPT +EI+  L +P E +
Sbjct: 87  IVGEIKRFLRDDGL-IKVSRSLKDLASKARNVKEDFQRQENREPTLKEISDILNVPCEEI 145

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RVLASLT 621
              L+   E  SL   +    ++ +   + +K   SP +   Q N+ E      ++ +L+
Sbjct: 146 AVSLEANMEVESLNAVVNPNSSATIT--LAEKIDQSPDE---QKNIFENIYLKEIIKTLS 200

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E +++  R+      D T  E+  +  V++ +I +IE + + KL+ 
Sbjct: 201 SVERQIVNYRYF----EDLTQLEIANRLGVSQVQISRIEKRVLEKLRQ 244


>gi|291453672|ref|ZP_06593062.1| SigI protein [Streptomyces albus J1074]
 gi|291356621|gb|EFE83523.1| SigI protein [Streptomyces albus J1074]
          Length = 285

 Score = 85.5 bits (210), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 116/238 (48%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 52  EGTAEFAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 111

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A +
Sbjct: 112 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVRELADR 171

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     VEG+      T   +  + P  D+    L D I  +      D  I+     
Sbjct: 172 LGLSQEEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE------DHGIEGIEYV 224

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ R+L +RF   M    T  E+G++  +++  + ++  + + +L+
Sbjct: 225 ESLKPLIAELPARDRRILSLRFTANM----TQSEIGEELGISQMHVSRLLTRTLNRLR 278


>gi|84625707|ref|YP_453079.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|289664834|ref|ZP_06486415.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vasculorum NCPPB702]
 gi|289671390|ref|ZP_06492465.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           musacearum NCPPB4381]
 gi|84369647|dbj|BAE70805.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 291

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 121/248 (48%), Gaps = 40/248 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN------------ 608
            K L ++ +E + +E+ +   D       D  +D    SP+ S + AN            
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPV-SYLVANEEDPSQAYERHD 223

Query: 609 --------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                   LRE     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIE
Sbjct: 224 SEDNQLQLLREG----MAGLDTRSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIE 278

Query: 661 AKAIRKLK 668
           A A++K+K
Sbjct: 279 ANALKKMK 286


>gi|229844972|ref|ZP_04465109.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
 gi|229812106|gb|EEP47798.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
          Length = 281

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNENEVDMVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  +++   +  + P  D +T       ++EDK  N  + L++   ++   E    
Sbjct: 166 DVIEMESRMSGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLGV 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 226 ALQSLDVRSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|167507927|gb|ABZ81284.1| RpoD [Thalassospira sp. MCCC 1A01166]
 gi|167507929|gb|ABZ81285.1| RpoD [Thalassospira sp. MCCC 1A01167]
          Length = 255

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 99  SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGETVPAATEKRYAKLKNEMV 158

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 159 ELMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 218

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK F+    + I K+R ++  +S E
Sbjct: 219 WMERVAGLPGKGWKAFIERYPEEIAKLREDVGGVSAE 255


>gi|167507965|gb|ABZ81303.1| RpoD [Thalassospira sp. MCCC 1A02093]
          Length = 257

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 87/157 (55%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 101 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGEAVPAATEKRYNKLKNEMV 160

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ +  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 161 DLMEDVHLNNFRIEELLDHMTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 220

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    D I  +R  +  +S E
Sbjct: 221 WMERVGGLPGKGWKTFVERYADEIANLREGVGGVSAE 257


>gi|258511711|ref|YP_003185145.1| sporulation sigma factor SigF [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257478437|gb|ACV58756.1| RNA polymerase, sigma 28 subunit, SigF [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 256

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 124/249 (49%), Gaps = 17/249 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R ++     G+ EA   ++ ++  N RLV +V +++  RG +  DL Q G IGL
Sbjct: 19  LSDEEVRELLERSHNGDAEA---RERLIVHNQRLVWAVVQRFLGRGYEAEDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KFD     KFSTYA+  +   I R + D S T+++   +++   ++     R++ 
Sbjct: 76  MKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDS-TVKVSRSLKETAKQIRHVRDRLAK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
           ++ R+P   EIA+ + M    +    +  + P S+   +   D D  +L D I D+    
Sbjct: 135 ELGRQPHITEIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYLMDQIADEETEG 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D   +  L E    ++  L  RE  ++ MRF      D T  +V +   +++ ++ ++
Sbjct: 195 KFD---KVELHE----IIGRLPERERFIVYMRF----FRDKTQSDVARVLGISQVQVSRL 243

Query: 660 EAKAIRKLK 668
           E + +++++
Sbjct: 244 EKRILQQIR 252


>gi|148652168|ref|YP_001279261.1| RNA polymerase factor sigma-32 [Psychrobacter sp. PRwf-1]
 gi|148571252|gb|ABQ93311.1| RNA polymerase, sigma 32 subunit, RpoH [Psychrobacter sp. PRwf-1]
          Length = 372

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 83/304 (27%), Positives = 138/304 (45%), Gaps = 34/304 (11%)

Query: 383 WVSYAKDFPEGEWKNFV-ACEVD------SILKIRNEIKSISVETGISISEFRHIVSMVR 435
           WVS   D+P    ++ V A  V+      ++    N +  I + T     E  H      
Sbjct: 69  WVS---DYPNTSTRDLVPAMPVNLSAPGINLGAYMNSVHQIPILTTEQEQELAH--RYYD 123

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G+ EA+   + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G +
Sbjct: 124 DGDVEAA---RILVMSHLRFVIHIARSYSGYGLPQADLIQEGNLGLMKAVKRFDPNKGVR 180

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
             ++A+ W+K  I   +      +++      K H+ +    R   K   + T EE A  
Sbjct: 181 LVSFAVHWIKAEIHEFVIRNWRIVKVAT---TKAHRKLFFNLRSLKKTNNQLTLEE-ADA 236

Query: 556 LAMPVEGVRKVL-----KITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQAN 608
           +A  +   RK +     ++T    S E    D++  H     F+ED   V P +    A+
Sbjct: 237 IAADLNVTRKQVLEMESRLTSYDASFEAQSTDDEDGHYAPQLFLED--GVDPAEMVEDAD 294

Query: 609 LRETTTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             E  T  L     +L  R   ++  R+     +  TL E+   + ++ ER+RQIE  A+
Sbjct: 295 WEENNTNALMDAMDTLDERSRDIVEQRWLSEQKS--TLHELAAVYNISAERVRQIEKNAM 352

Query: 665 RKLK 668
            K++
Sbjct: 353 DKIR 356


>gi|330961076|gb|EGH61336.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 326

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 82/137 (59%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|289676146|ref|ZP_06497036.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 178

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/137 (39%), Positives = 82/137 (59%), Gaps = 1/137 (0%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D     D
Sbjct: 12  KELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLAD 71

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +    ++A  ++  L   +    R+TD PVRMY+REMG++ELL+REGEI IAKRIE G  
Sbjct: 72  ADTDEAAAEEAAAALAAVETDIGRTTD-PVRMYMREMGTVELLTREGEIEIAKRIEEGIR 130

Query: 152 MMMASLCESPLTFQALI 168
            +M ++   P T   ++
Sbjct: 131 EVMGAIAHFPGTVDHIL 147


>gi|148560551|ref|YP_001259508.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|294850906|ref|ZP_06791582.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
 gi|148371808|gb|ABQ61787.1| alternative sigma factor RpoH [Brucella ovis ATCC 25840]
 gi|294821549|gb|EFG38545.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
          Length = 303

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLSIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 277


>gi|124268355|ref|YP_001022359.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
 gi|124261130|gb|ABM96124.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
          Length = 319

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 120/249 (48%), Gaps = 29/249 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+SV+++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W
Sbjct: 69  AAGRLVLSHLRLVVSVSRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPSQGVRLVSYALHW 128

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE-- 561
           +K  I   +      +++      +  K+    R M    K + T  ++ +      E  
Sbjct: 129 IKAEIHEYVLRNWRMVKLATTKAQR--KLFFNLRSMKQGFKGDATDSDLHRSTLTDAEID 186

Query: 562 GVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
            V   LK+ +E  I +ET +   D +      +   + +P+  A  A+ R   TRVL + 
Sbjct: 187 IVASELKVKREEVIEMETRLSGGDVALDPQTDDGDESYAPI--AYLADDRHEPTRVLDAQ 244

Query: 620 ----------------LTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQI 659
                           L  R  R++  R+ + +N +     TL E+  ++ V+ ERIRQI
Sbjct: 245 RRDALAGDGIGEALDVLDARSRRIVEERW-LKVNDNGSGGMTLHELAAEYGVSAERIRQI 303

Query: 660 EAKAIRKLK 668
           E  A++K++
Sbjct: 304 EVAAMKKMR 312


>gi|319937136|ref|ZP_08011543.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807502|gb|EFW04095.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 259

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 116/227 (51%), Gaps = 14/227 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++V +NL+LV+S+ +KY  R     DL Q G IGL+KA + FD  L  +FSTYA+  +
Sbjct: 40  KEKLVLSNLKLVLSLVQKYHQRVSNLDDLFQVGVIGLIKAIDHFDTSLDVRFSTYAVPLI 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R I D S  +RIP  MRD  +K +        K  +E + +E++K L +    + 
Sbjct: 100 IGEIKRYIRDNS-PMRIPRSMRDLAYKALLANEEYMKKHHKEASTKELSKILDVDEFLLV 158

Query: 565 KVLKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L  T    SL   + ++    +       + KN +  + ++I  +L E     +  L 
Sbjct: 159 EALSSTNSVTSLSQEVQNDGNGQIDLESQIPDRKNQMEDMQNSI--DLYEA----MNHLD 212

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E +++  R+  G    HT  E+ K+  +++ ++ +IE +A+  LK
Sbjct: 213 EKELQIINERYFKG----HTQSEIAKELFISQAQVSRIEKQALSHLK 255


>gi|254392909|ref|ZP_05008077.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294811525|ref|ZP_06770168.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326440088|ref|ZP_08214822.1| putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|197706564|gb|EDY52376.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294324124|gb|EFG05767.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 289

 Score = 85.1 bits (209), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 117/240 (48%), Gaps = 18/240 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  +    +  ++E NL LV   A ++ NR  Q  D+IQ G IGL+KA ++F+     +
Sbjct: 54  EGTRDHQYVRNTLIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGLIKAIDRFELSREVE 113

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D S  + +P  +++    + +    +S ++ R PT  E+A+ 
Sbjct: 114 FATFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRIDLAKATDDLSQRLDRSPTTRELAEH 173

Query: 556 LAM----PVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           L +     +EGV      T    S++ P+    D  TS L D +   +A   +   +QA 
Sbjct: 174 LGIDEQEVIEGVVAANGYTAG--SIDMPLEDSSDHTTSSLSDRLGAPDAGLEIAENVQA- 230

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  ++  L  R+ R+LRMRFG     + T  E+G +  V++  + ++  +   +L+
Sbjct: 231 ----LKPLIEELGERDRRILRMRFG----EELTQSEIGAELGVSQMHVSRLLTRITTRLR 282


>gi|306844673|ref|ZP_07477258.1| alternative sigma factor RpoH [Brucella sp. BO1]
 gi|306274845|gb|EFM56615.1| alternative sigma factor RpoH [Brucella sp. BO1]
          Length = 303

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSSEFGISRERVRQIEVRAF 277


>gi|332875153|ref|ZP_08442986.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
 gi|332736597|gb|EGJ67591.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
          Length = 280

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 45  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 104

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E 
Sbjct: 105 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQ 163

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P       +  E +T  L 
Sbjct: 164 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPVLYLED-NRYDPARLVENEDWEEQSTSALH 222

Query: 619 ----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 223 DAMNQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 274


>gi|291547959|emb|CBL21067.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus sp.
           SR1/5]
          Length = 260

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 121/236 (51%), Gaps = 16/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E N  L+ SVAK++  RG++  DL Q G+IGL+KA +KFD     KFSTYA+  
Sbjct: 18  ARDLLFEENTGLIYSVAKRFLGRGVEMEDLFQIGSIGLLKAVDKFDMSYDVKFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++  +++ +    ++ +++REPT  E+A+++ + +E +
Sbjct: 78  IIGEIKRYLRDDG-ILKVSRSLKENHYRIYQVREALTRRLEREPTTGEMAEEMGISIEEL 136

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP--LDSAIQANLRETTTRVLAS 619
              ++   E  SL   I  G+     L D + +K       LD       R     +L +
Sbjct: 137 VMTMESGAEVESLHKTIYQGEGTEISLMDKLPEKENRQEKVLD-------RIFLEEILGT 189

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L  +E R++ MR+   M    T  E+  +  V++ ++ ++E + +R L+  +   K
Sbjct: 190 LEAKERRLIYMRYFQNM----TQMEIAHELGVSQVQVSRMEKRILRSLQESAEKNK 241


>gi|317494584|ref|ZP_07952997.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316917514|gb|EFV38860.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 283

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 124/233 (53%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVSEK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTTR 615
            V ++  ++  + ++ +    D+++S      F++DK+   A    D    ++  +  T 
Sbjct: 167 DVLEMESRMAAQDMAFDMSNDDDESSPAAPVLFLQDKSSDFANDIEDDNWDSHAADKLTL 226

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 AMEGLDERSQHIIRARW-LDDDNKATLQELADQYGVSAERVRQLEKNAMKKLR 278


>gi|251791618|ref|YP_003006339.1| RNA polymerase factor sigma-32 [Dickeya zeae Ech1591]
 gi|247540239|gb|ACT08860.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya zeae Ech1591]
          Length = 285

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-- 612
            VR++  ++  + ++ +     ED +  G       +++DK+  S     I+ +  ET  
Sbjct: 167 DVREMESRMAAQDMTFDP--SPEDDAQPGQPMAPMLYLQDKS--SDFADGIEEDNWETHA 222

Query: 613 ---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  L  L  R + ++R R+ +  +   TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 223 ADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADHYGVSAERVRQLEKNAMKKLR 280


>gi|21104386|dbj|BAB93463.1| putative rpoD gene [Variovorax sp. WFF52]
 gi|21104388|dbj|BAB93464.1| putative rpoD gene [Leptothrix discophora]
 gi|21104390|dbj|BAB93465.1| putative rpoD gene [Sphaerotilus natans]
          Length = 47

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 39/46 (84%), Positives = 43/46 (93%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 1   LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 46


>gi|226952985|ref|ZP_03823449.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|294650567|ref|ZP_06727924.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
 gi|226836306|gb|EEH68689.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|292823564|gb|EFF82410.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
          Length = 289

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 54  AAKLLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 113

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S ++  E   + IA  L +  E 
Sbjct: 114 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKRLTLEEA-QAIANDLNVTAEQ 172

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P   A + +    +T  L 
Sbjct: 173 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLAEEEDYEAQSTAALH 231

Query: 619 ----SLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 232 QAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|150019061|ref|YP_001311315.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
 gi|149905526|gb|ABR36359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
          Length = 242

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 122/237 (51%), Gaps = 17/237 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+++++  + LV  +A +     N+ +++ DL+  G +GLM A  KFD   G KFS+YA
Sbjct: 9   GKEQIIQEYIPLVKYIASRVMFGKNKYMEYEDLVSYGMVGLMDALNKFDDTKGMKFSSYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K A+   +        I     DK++K  +    +  ++ REPT +EIAK L + +
Sbjct: 69  SIRIKGAMIDELRRNR---PISKGAMDKLNKYNKAVDTLQLELLREPTNDEIAKYLGISM 125

Query: 561 EGVRKVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR-ETTTR 615
             V ++         +SLE  I   DED + +G  IEDKN+ SP D+ +Q   + E  T+
Sbjct: 126 SEVAEIENYINYISMVSLENVIFSDDEDVNLIG-IIEDKNSPSP-DAYLQDKEQLEILTK 183

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +  L  ++  VL + +  G+    TL+E+G    V+  R+ Q+ ++AI  L+   R
Sbjct: 184 AIDLLKEKDRIVLNLYYYEGL----TLKEIGTVLSVSESRVCQLHSRAISSLRECMR 236


>gi|291619275|ref|YP_003522017.1| RpoH [Pantoea ananatis LMG 20103]
 gi|291154305|gb|ADD78889.1| RpoH [Pantoea ananatis LMG 20103]
 gi|327395604|dbj|BAK13026.1| RNA polymerase sigma-32 factor RpoH [Pantoea ananatis AJ13355]
          Length = 285

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/284 (24%), Positives = 141/284 (49%), Gaps = 37/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S E   +++E  H      +G+ +A+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYVRAANTWPMLSAEEEKALAERLHY-----QGDLDAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 580 IGDED---------------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             DE                TS   D IE+ N         +++  +  T  +  L  R 
Sbjct: 186 ADDESGEGKSMAPVLYLQDKTSDFADGIEEDN--------WESHAADKLTYAMEGLDERS 237

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 238 QHIIRARW-LDEDNKTTLQELADRYGVSAERVRQLEKNAMKKLR 280


>gi|182435018|ref|YP_001822737.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463534|dbj|BAG18054.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 292

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 125/244 (51%), Gaps = 14/244 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFD 489
           + ++ +G      A+  ++E NL LV   AK++ NRG  +  D+IQ G IGL+KA ++F+
Sbjct: 50  LQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIIQVGTIGLIKAIDRFE 109

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+++A+ ++   I R   D +  + +P  +++    + +T   +S ++ REPT 
Sbjct: 110 LSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKTREALSTRLDREPTV 169

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSA 604
            E+A  L +     +EG+      T    SL+ PIG D++++    + + K  V P    
Sbjct: 170 AELAHHLELTEEEVIEGLIAANGYTAG--SLDLPIGADQNSAETVTYGDIKGDVDPAMEL 227

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++     T   +L  L  RE  ++ MRFG  M    T  ++G+   +++  + ++ ++ +
Sbjct: 228 VED--LHTLAPLLERLDEREREIVAMRFGREM----TQAQIGEHLGISQMHVSRLLSRLL 281

Query: 665 RKLK 668
            KL+
Sbjct: 282 TKLR 285


>gi|15614101|ref|NP_242404.1| sporulation sigma factor SigF [Bacillus halodurans C-125]
 gi|10174155|dbj|BAB05257.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           [Bacillus halodurans C-125]
          Length = 252

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/259 (27%), Positives = 131/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K    E   +  E + +++  + G+ EA   + ++V  N RLV SV +++ NRG +  
Sbjct: 4   EVKQNEKEQPFTDEEIKQLIAQSQAGDQEA---RDQIVSRNTRLVWSVVQRFLNRGYEAD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSIKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + +    M+  + R PT  EIA++L +  E V      ++   S+   +   D D   L 
Sbjct: 120 IRKLKDDMTKTLGRTPTVNEIAEQLEITPEEVVFAGDASRSLSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +ED++     D   +  L+E     + +L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQLEDQSETRWFD---KIALKEA----IHNLEERERLIVYLRY----YKDQTQSEVAQRL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K +  +K
Sbjct: 229 GISQVQVSRLEKKILETMK 247


>gi|271502546|ref|YP_003335572.1| RNA polymerase sigma-32 subunit RpoH [Dickeya dadantii Ech586]
 gi|270346101|gb|ACZ78866.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech586]
          Length = 285

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-- 612
            VR++  ++  + ++ +     ED +  G       +++DK+  S     I+ +  ET  
Sbjct: 167 DVREMESRMAAQDMTFDP--SPEDDAQPGQPMAPMLYLQDKS--SDFADGIEEDNWETHA 222

Query: 613 ---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  L  L  R + ++R R+ +  +   TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 223 ADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADHYGVSAERVRQLEKNAMKKLR 280


>gi|225025101|ref|ZP_03714293.1| hypothetical protein EIKCOROL_01993 [Eikenella corrodens ATCC
           23834]
 gi|224942062|gb|EEG23271.1| hypothetical protein EIKCOROL_01993 [Eikenella corrodens ATCC
           23834]
          Length = 648

 Score = 85.1 bits (209), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 88/164 (53%), Gaps = 14/164 (8%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           ++N  +  E ++S+  L  +      +++I   ++RGY+T  E+N  LP D   +EQ+++
Sbjct: 3   EQNNPATEEQDESNRPLTPEEQRARLRQLILQGKERGYITYAEINDALPDDMSDAEQIDN 62

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK--------DSADRST 117
            V M+S +GI V +      E    ++L +A + +N +      +        DS    T
Sbjct: 63  IVNMISGLGIQVTE------ETPDSETLLMADNTANMTDDDAVAEAEAALSSADSEFGRT 116

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            DPVRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P
Sbjct: 117 TDPVRMYMREMGQVDLLTREDEIVIAKKIETALRNMIQAISACP 160


>gi|253682486|ref|ZP_04863283.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
 gi|253562198|gb|EES91650.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
          Length = 252

 Score = 84.7 bits (208), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 118/226 (52%), Gaps = 16/226 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V+ NL LV S++KK+ NRG ++ D+ Q G++GL+KA   FD     +FSTYA+  +  
Sbjct: 34  ELVQKNLPLVSSISKKFLNRGYEYEDIFQIGSMGLIKAINNFDSSYDVQFSTYAVPMIMG 93

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R I D    I++   ++    K+     +++ ++ REP+ EE++K   +  E +   
Sbjct: 94  EIKRFIRDDGL-IKVSRSVKYTAKKLHYDKEKLTKELNREPSLEELSKFSGISKEDIIFS 152

Query: 567 LKITKEPISLETPIGDEDTS--HLGD--FIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            +   EP  L   I  +D S  +L D   ++DK  +  LD   +  L+E     L+ L  
Sbjct: 153 SEAINEPKYLYDTIHQDDGSPIYLIDKVVLDDKGEIDELD---KIALKEA----LSKLDQ 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R  +++ +R+      D T  +V K   +++ ++ +IE K ++ +K
Sbjct: 206 RSRQIIILRYF----KDITQVKVAKMLGISQVQVSRIEKKVLKSMK 247


>gi|71892394|ref|YP_278128.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|71796500|gb|AAZ41251.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 282

 Score = 84.7 bits (208), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 122/240 (50%), Gaps = 27/240 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ V++ Y+  GL   DLIQEGNIGLMKA  +F+  L  +  ++A+ W
Sbjct: 50  AAKKLIVSHLRFVVHVSRNYSGYGLPQADLIQEGNIGLMKAVRRFNPELDVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      ++I            +  R++   +++  T + +    A  +E V
Sbjct: 110 IKSEIHEYVLKNWRIVKIA---------TTKAQRKLFFNLRK--TKQRLGWFNAGEIEIV 158

Query: 564 RKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVS--PL----DSAIQAN-------- 608
            K L +T + +  +E+ +  +D +      ED   ++  P+    D  + +N        
Sbjct: 159 AKALNVTSKDVREMESRMSAQDMTFEQSSDEDNRGITIAPILYLQDKIVSSNEEEEWIDQ 218

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +     + +L  R + ++R R+ + ++   TL+E+  Q+ V+ ER+RQ+E  A++K+K
Sbjct: 219 VSDKLNAAIKTLDERSQHIIRARW-LNVDNKSTLQELANQYGVSAERVRQLEKNAMKKMK 277


>gi|329120411|ref|ZP_08249077.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327462095|gb|EGF08423.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 649

 Score = 84.7 bits (208), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 59/189 (31%), Positives = 102/189 (53%), Gaps = 18/189 (9%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E ED +  L  +      + +I   ++RGY+T  E+N  LP D   +EQ+++ V M+  +
Sbjct: 12  EQEDGNRPLTPEEQRQRLRLLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGL 71

Query: 74  GINVV----DGDDL-EDEEGS----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           GI V     D D L  ++ G+    +D+++ A +A +++       DS    T DPVRMY
Sbjct: 72  GIQVTEEAPDADTLLMNDTGTGMTDDDAVEEAEAALSNA-------DSEFGRTTDPVRMY 124

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++  G   + E+
Sbjct: 125 MREMGQVDLLTREDEIIIAKKIENALKNMIQAISACPGSIAEILGLIEQVRSGEIKVDEV 184

Query: 185 IDLEACIGP 193
           +  EA + P
Sbjct: 185 V--EAILDP 191


>gi|323154963|gb|EFZ41155.1| RNA polymerase sigma factor rpoS domain protein [Escherichia coli
           EPECa14]
          Length = 148

 Score = 84.7 bits (208), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 49/59 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA W
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 148


>gi|309778067|ref|ZP_07673006.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308914161|gb|EFP59962.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 259

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 128/247 (51%), Gaps = 17/247 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + +   +++G+ +A   K+ ++  NL+LV+S+ ++++NR     DL Q G IGL+K+
Sbjct: 22  AEMKELFVQLQQGDEQA---KETLINGNLKLVLSIVQRFSNRCENMDDLFQVGCIGLVKS 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     +FSTYA+  +   I R + D    IR+  H++D  ++  +      +K +
Sbjct: 79  IDNFDLKHEVRFSTYAVPMIMGEIKRYLRDNQ-VIRVSRHLKDLAYRAFKLKEEYVHKNQ 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFI-EDKNAVSPL 601
           +EPT   +A++L +  + +   L  T+  +S+  P+   D D   L D I +DK+ +  L
Sbjct: 138 KEPTIAWLAEQLEVKEKDIVDALDSTQSVLSIFEPVYNSDGDELFLLDQIKDDKDEIEHL 197

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ +         R L  L  +E  +++ R+      D T  E+  +  +++ ++ ++E 
Sbjct: 198 NNIM------ALKRSLKRLKGKELDIIQKRY----YQDMTQTEIAGELGISQAQVSRLEK 247

Query: 662 KAIRKLK 668
            AI  LK
Sbjct: 248 NAIAVLK 254


>gi|325924311|ref|ZP_08185855.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
 gi|325545176|gb|EGD16486.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
          Length = 291

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 121/248 (48%), Gaps = 40/248 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN------------ 608
            K L ++ +E + +E+ +   D       D  +D    SP+ S + AN            
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPV-SYLVANEEDPSQAYERHD 223

Query: 609 --------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                   LRE     L+ L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIE
Sbjct: 224 SEDNQLQLLREG----LSGLDTRSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIE 278

Query: 661 AKAIRKLK 668
           A A++K+K
Sbjct: 279 ANALKKMK 286


>gi|302871563|ref|YP_003840199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574422|gb|ADL42213.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 240

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 120/239 (50%), Gaps = 12/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD   
Sbjct: 9   LISKAKNGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSF 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 69  NVRFSTYAVPMIIGEIKRYLRDDG-RIKVSRKIKENQSKIKKLRNQFVSDNGREPTISEI 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  E +   +  + E  SL   I  E+     L D   D+   S     + A L+
Sbjct: 128 SQLTGLSSEEILLCMDASSEVASLSEVINQEEGKPITLMDLASDEEDYSTKLLDLMA-LK 186

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E     L  L  RE  ++ MR+      + T  E+ KQ  +++  + +IE +A+ ++K 
Sbjct: 187 EG----LKKLKGRERYIIFMRYF----KNKTQSEIAKQLNISQVHVSRIEKRALERIKR 237


>gi|291563747|emb|CBL42563.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SS3/4]
          Length = 239

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 117/229 (51%), Gaps = 16/229 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V  N  LV S+ +++  RG +  DL Q GNIGL+KA + FD  LG +FSTYA+  
Sbjct: 18  ARDRLVMENAGLVWSIVRRFIGRGPEPDDLFQIGNIGLIKAIDHFDTELGVRFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++   KV     ++   + REPT EE+A+ +    E V
Sbjct: 78  ITGEIRRFLRDDGM-IKVSRPLKELAGKVGAAREKLEADLGREPTVEELARSVGASREEV 136

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLAS 619
              ++      S+  P   GDE    L D I +K + +   LD  + A L       L+ 
Sbjct: 137 AASMEAGARVGSIYEPFDAGDESGGCLADKIAEKTSENDRVLDRIVLAEL-------LSG 189

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E+++++MR+      + T   +  +  +++ ++ ++E K +R+++
Sbjct: 190 LGEKEQQIIKMRY----FENMTQTVIAGRLGISQVQVSRMEKKILREMR 234


>gi|306841398|ref|ZP_07474101.1| alternative sigma factor RpoH [Brucella sp. BO2]
 gi|306288583|gb|EFM59932.1| alternative sigma factor RpoH [Brucella sp. BO2]
          Length = 303

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 277


>gi|283787904|ref|YP_003367769.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
 gi|282951358|emb|CBG91057.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
          Length = 284

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/283 (24%), Positives = 139/283 (49%), Gaps = 36/283 (12%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 580 IGDED--------------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             DE               TS+  D IE+ N      S +        T  +  L  R +
Sbjct: 186 PDDESDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAASKL--------THAMEGLDERSQ 237

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 238 AIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|167507919|gb|ABZ81280.1| RpoD [Thalassospira sp. MCCC 1A01103]
 gi|167507957|gb|ABZ81299.1| RpoD [Thalassospira sp. MCCC 1A02041]
 gi|167507959|gb|ABZ81300.1| RpoD [Thalassospira sp. MCCC 1A02042]
          Length = 261

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 87/157 (55%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 105 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMV 164

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 165 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 224

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    D I  +R  +  +S E
Sbjct: 225 WMERVGGLPGKGWKAFVERYPDEIANLREGVGGVSAE 261


>gi|292492240|ref|YP_003527679.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
 gi|291580835|gb|ADE15292.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
          Length = 287

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 120/236 (50%), Gaps = 17/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 53  AARQLVLSHLRFVVRIARGYSGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R+A++    + R+   +E+A+ L +    
Sbjct: 113 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKKRLGWLNRKEV-DEVARDLGV---S 168

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQA-------NLRET 612
            ++VL++     S +TP    +  +  D I    A       D A Q        +  + 
Sbjct: 169 PKQVLEMEARLSSQDTPFEGPNAENSEDDIPAPIAYLFDPTTDPARQMERLDQENHYGQR 228

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L +L PR   ++  R+     +  TL E+  ++ ++ ERIRQ+E  AI+KL+
Sbjct: 229 LQQALEALDPRSRAIIHRRW--LQESKSTLHELAAEYQISAERIRQLENNAIKKLR 282


>gi|153008471|ref|YP_001369686.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560359|gb|ABS13857.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 311

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/252 (29%), Positives = 128/252 (50%), Gaps = 25/252 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 54  IRWKELKDQDALHRITSAHMRLVISMAGRFRKFKLPMNDLIQEGYVGLLEAAARFDPERE 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------RE 546
            +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQSDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPL-- 601
               EI+ +L +    V  +  +++    SL  P+ +E++  +   DF+ D +   PL  
Sbjct: 172 EMYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNNEESGAVRRMDFLVDDH---PLQD 228

Query: 602 ---DSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERI 656
              +S+I    R     V L +L  RE  ++R R    ++ D  TLE +G++  +++ER+
Sbjct: 229 EIAESSIDMERRNQWLNVALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERV 285

Query: 657 RQIEAKAIRKLK 668
           RQIE++A+ KLK
Sbjct: 286 RQIESRAMEKLK 297


>gi|126664542|ref|ZP_01735526.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
 gi|126630868|gb|EBA01482.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
          Length = 286

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 69/279 (24%), Positives = 144/279 (51%), Gaps = 23/279 (8%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
              ++S ++  + I  ++V+   ++SE      +  +G+ +A+   ++++ ++LR VI +
Sbjct: 14  GANLESYIQAASRIPILTVDEERALSE-----RLYYEGDVDAA---RQLILSHLRFVIHI 65

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y+  GL   DL+QEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +
Sbjct: 66  ARSYSGYGLNQSDLVQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIV 125

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKV-LKITKEPISL 576
           ++      +  K+    R    K+      E   +A  L +    VR++  +++    + 
Sbjct: 126 KVATTKAQR--KLFFNLRGQKKKLAWLSHDELNAVAADLGVEARVVREMEGRLSSHDTAF 183

Query: 577 ETPIG-DEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTT----RVLASLTPREERVLR 629
           + P+  DED+++     ++ED  + +P     ++N  E +     + L+SL  R + +LR
Sbjct: 184 DGPMNDDEDSAYQAPAYYLEDHRS-NPATQLERSNWTEDSNGRLMQALSSLDDRSQDILR 242

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+     T  TL ++  ++ V+ ERIRQ+E  A++K++
Sbjct: 243 ERW--LSETKSTLHQLADRYGVSAERIRQLEKNAMKKIR 279


>gi|54298657|ref|YP_125026.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Paris]
 gi|296108313|ref|YP_003620014.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
 gi|53752442|emb|CAH13874.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Paris]
 gi|295650215|gb|ADG26062.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
          Length = 284

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/291 (25%), Positives = 136/291 (46%), Gaps = 39/291 (13%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N     +DS +   N+I  +++E  I+ +E  H      +G+ EA+   +++V A+LR V
Sbjct: 11  NLPVGSLDSYIHRVNQIPMLTLEEEIAYAERFH-----SEGDIEAA---RQLVLAHLRYV 62

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + VA+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +    
Sbjct: 63  VRVARGYLGYGLPLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNW 122

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +++      +  K+    R+M N++      E         V+ V K L +++E + L
Sbjct: 123 RIVKVATTKAQR--KLFFNLRQMKNRLGWFSNEE---------VDAVAKDLGVSREDVLL 171

Query: 577 -ETPIGDEDTSHLGDF-----------------IEDKNAVSPLDSAIQANLRETTTRVLA 618
            E  +   D+S+                     + D  AV   +       RE     + 
Sbjct: 172 MEQRLNVMDSSYDAPDVDDNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAME 231

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R + +L+ R+        TL ++ +++ V+ ER+RQ+E  A++K++ 
Sbjct: 232 QLDERSQDILQQRW--LAEEKLTLHDLAEKYGVSAERVRQLEKNAMKKIRQ 280


>gi|167037535|ref|YP_001665113.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256752057|ref|ZP_05492925.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|320115950|ref|YP_004186109.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166856369|gb|ABY94777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256749067|gb|EEU62103.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|319929041|gb|ADV79726.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 246

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 111/222 (50%), Gaps = 12/222 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++  N  L+ S+ KK++NRG +  DL Q G IG +KA +KFD     K STYA+  +   
Sbjct: 30  LILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVKAIQKFDESYNVKLSTYAVPIIMGE 89

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R + D    I++   +++   K       +SN++ REPT  EIA++L +  E +    
Sbjct: 90  IKRFLRDDGL-IKVSRSLKELSTKAFYVKEILSNELNREPTINEIAERLNVSPEEIAMAF 148

Query: 568 KITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +      SL +    DED   L + + ++     +D  +   +      V+  L PRE++
Sbjct: 149 ESAATAESLYDNATHDEDDKLLIEMVSEEEKEVDIDDKLALQM------VINKLKPREKQ 202

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +R+      D T  EV     +++ ++ ++E K ++KL+
Sbjct: 203 IIFLRYF----KDMTQMEVANILGISQVQVSRLEKKVLQKLR 240


>gi|254703436|ref|ZP_05165264.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261754065|ref|ZP_05997774.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743818|gb|EEY31744.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 300

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 46  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 106 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 163

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 164 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 223

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 224 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 274


>gi|307128894|ref|YP_003880910.1| RNA polymerase sigma-32 (sigma H) factor [Dickeya dadantii 3937]
 gi|306526423|gb|ADM96353.1| RNA polymerase, sigma 32 (sigma H) factor [Dickeya dadantii 3937]
          Length = 285

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-- 612
            VR++  ++  + ++ +     ED +  G       +++DK+  S     I+ +  ET  
Sbjct: 167 DVREMESRMAAQDMTFDP--SPEDDAQPGQPMAPMLYLQDKS--SDFADGIEEDNWETHA 222

Query: 613 ---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  L  L  R + ++R R+ +  +   TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 223 ADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADHYGVSAERVRQLEKNAMKKLR 280


>gi|167507953|gb|ABZ81297.1| RpoD [Thalassospira sp. MCCC 1A02039]
 gi|167507955|gb|ABZ81298.1| RpoD [Thalassospira sp. MCCC 1A02040]
          Length = 257

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 84/157 (53%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-AVNGQKDEKSSV----KCKVLKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+   V   K E   V    +   LK ++V
Sbjct: 101 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGEAVPVATEKRYNKLKNEMV 160

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ +  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 161 DLMEDVHLNNFRIEELLDHMTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 220

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    D I  +R  +  +S E
Sbjct: 221 WMERVGGLPGKGWKTFVERYSDEIANLREGVGGVSAE 257


>gi|163748787|ref|ZP_02156039.1| RNA polymerase sigma factor [Shewanella benthica KT99]
 gi|161331561|gb|EDQ02366.1| RNA polymerase sigma factor [Shewanella benthica KT99]
          Length = 286

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 120/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++      E   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKAKKRLGWFSDAEVGMVAENLGVSKA 169

Query: 562 GVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT--TRVL 617
            V ++      ++P        D+D       +  ++  S L S ++ +  E +  TR+L
Sbjct: 170 DVTEMESRMAAQDPAFDLVSDSDDDIQDYAPALYLEDHSSDLASQVETDNLEASNQTRLL 229

Query: 618 ASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A++   +ER   +L+ R+   +N D  TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 230 AAIKTLDERSQHILQARW---LNEDKTTLQELAATYQVSAERIRQLEKNAMNKLK 281


>gi|307611543|emb|CBX01223.1| RNA polymerase sigma-32 factor [Legionella pneumophila 130b]
          Length = 284

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/291 (25%), Positives = 136/291 (46%), Gaps = 39/291 (13%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N     +DS +   N+I  +++E  I+ +E  H      +G+ EA+   +++V A+LR V
Sbjct: 11  NLPVGSLDSYIHRVNQIPMLTLEEEIAYAERFH-----SEGDIEAA---RQLVLAHLRYV 62

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + VA+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +    
Sbjct: 63  VRVARGYLGYGLPLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNW 122

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +++      +  K+    R+M N++      E         V+ V K L +++E + L
Sbjct: 123 RIVKVATTKAQR--KLFFNLRQMKNRLGWFSNEE---------VDAVAKDLGVSREDVLL 171

Query: 577 -ETPIGDEDTSHLGDF-----------------IEDKNAVSPLDSAIQANLRETTTRVLA 618
            E  +   D+S+                     + D  AV   +       RE     + 
Sbjct: 172 MEQRLNVMDSSYDAPDVDDNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAME 231

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R + +L+ R+        TL ++ +++ V+ ER+RQ+E  A++K++ 
Sbjct: 232 QLDERSQDILQQRW--LAEEKLTLHDLAEKYGVSAERVRQLEKNAMKKIRQ 280


>gi|299534115|ref|ZP_07047467.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
 gi|298718024|gb|EFI59029.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
          Length = 314

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 124/253 (49%), Gaps = 33/253 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGRLVMSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP--TPEEIAKKLAMP-- 559
           +K  I   I      +++      +  K+    R M + +K +     EE+A +  +   
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKHDLKSDAAMADEELALRETLTSN 177

Query: 560 -VEGVRKVLKITKEP-ISLETPIGDEDT-----------------SHLGDFIEDKNAVSP 600
            ++ V   L + +E  I +ET +   D                  ++L D   +  A+  
Sbjct: 178 EIDAVAAKLNVKREEVIEMETRLAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAM-- 235

Query: 601 LDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRER 655
           L+S  + +L  +     L  L  R  R++  R+ + +N D     TL E+  ++ V+ ER
Sbjct: 236 LESRQRDHLATDGLVMALEGLDDRSRRIVEERW-LKVNDDGSGGMTLHELAAEYGVSAER 294

Query: 656 IRQIEAKAIRKLK 668
           IRQIE  A++K+K
Sbjct: 295 IRQIEVAAMKKMK 307


>gi|52842873|ref|YP_096672.1| RNA polymerase factor sigma-32 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52629984|gb|AAU28725.1| RNA polymerase sigma-32 factor RpoH [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 292

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/291 (25%), Positives = 136/291 (46%), Gaps = 39/291 (13%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N     +DS +   N+I  +++E  I+ +E  H      +G+ EA+   +++V A+LR V
Sbjct: 19  NLPVGSLDSYIHRVNQIPMLTLEEEIAYAERFH-----SEGDIEAA---RQLVLAHLRYV 70

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + VA+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +    
Sbjct: 71  VRVARGYLGYGLPLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNW 130

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +++      +  K+    R+M N++      E         V+ V K L +++E + L
Sbjct: 131 RIVKVATTKAQR--KLFFNLRQMKNRLGWFSNEE---------VDAVAKDLGVSREDVLL 179

Query: 577 -ETPIGDEDTSHLGDF-----------------IEDKNAVSPLDSAIQANLRETTTRVLA 618
            E  +   D+S+                     + D  AV   +       RE     + 
Sbjct: 180 MEQRLNVMDSSYDAPDVDDNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAME 239

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R + +L+ R+        TL ++ +++ V+ ER+RQ+E  A++K++ 
Sbjct: 240 QLDERSQDILQQRWLA--EEKLTLHDLAEKYGVSAERVRQLEKNAMKKIRQ 288


>gi|52424080|ref|YP_087217.1| RNA polymerase factor sigma-32 [Mannheimia succiniciproducens
           MBEL55E]
 gi|52306132|gb|AAU36632.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 282

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 124/233 (53%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFSDNE--LDLVANELGVTKE 166

Query: 562 GVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDK--NAVSPLDSA-IQANLRETTTR 615
            V ++  ++T   +  + P  D  E+T     ++EDK  N  + L+S   +    +  + 
Sbjct: 167 DVIEMESRMTGADVGFDLPTDDSEEETFAPSMYLEDKSSNFAAELESENFETQAIDQLSN 226

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  R + +++ R+    +T  TL E+  ++ ++ ER+RQ+E  A++KLK
Sbjct: 227 AMENLDERSKDIIQARWLD--DTKATLHELAAKYNISAERVRQLETNALKKLK 277


>gi|302531661|ref|ZP_07284003.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302440556|gb|EFL12372.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 258

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 59/224 (26%), Positives = 118/224 (52%), Gaps = 17/224 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L L  ++A+K+ NR     DL+Q   +GL+ A +++D   G  F  +A+  +   
Sbjct: 37  LVREHLELARNLARKFRNRDEAMDDLVQIATVGLIHAVDRYDPTQGTDFLAFAVPTISGE 96

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           +     D S ++R+P  +++ ++  +  AR  ++ ++ R P P EIA+ L +P+E V + 
Sbjct: 97  LRHHFRDNSWSVRVPRRLKE-LNATISAAREELTVRLSRAPKPSEIARHLDVPIEDVYEG 155

Query: 567 LKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           L+    +   SL+  +  E+++H      D N         QA LRE    +L SL  RE
Sbjct: 156 LRAGQGRYGASLDNLL--ENSAHTRFGAPDANLG-------QAELREALRPMLDSLPERE 206

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +++ +RFG GM+      ++ ++  V++ ++ ++ A  ++KL+
Sbjct: 207 RKIVALRFGSGMSQ----SDIARRVGVSQMQVSRLLAATLKKLR 246


>gi|254719685|ref|ZP_05181496.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|265984700|ref|ZP_06097435.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306840038|ref|ZP_07472825.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
 gi|264663292|gb|EEZ33553.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306404852|gb|EFM61144.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
          Length = 303

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 277


>gi|23502510|ref|NP_698637.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619585|ref|YP_001593472.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|163845234|ref|YP_001622889.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|225628222|ref|ZP_03786256.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|254708479|ref|ZP_05170307.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708670|ref|ZP_05170481.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714517|ref|ZP_05176328.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717415|ref|ZP_05179226.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030196|ref|ZP_05443810.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256061694|ref|ZP_05451831.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|256160370|ref|ZP_05458060.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255578|ref|ZP_05461114.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167873|ref|ZP_05754684.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|260568745|ref|ZP_05839213.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|261219245|ref|ZP_05933526.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222781|ref|ZP_05937062.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315977|ref|ZP_05955174.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316160|ref|ZP_05955357.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322306|ref|ZP_05961503.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261325699|ref|ZP_05964896.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261757310|ref|ZP_06001019.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|265987224|ref|ZP_06099781.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998739|ref|ZP_06111296.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|23348506|gb|AAN30552.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336396|gb|ABX62701.1| alternative sigma factor RpoH [Brucella canis ATCC 23365]
 gi|163675957|gb|ABY40067.1| alternative sigma factor RpoH [Brucella suis ATCC 23445]
 gi|225616068|gb|EEH13116.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|260154129|gb|EEW89211.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|260921365|gb|EEX88018.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924334|gb|EEX90902.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261294996|gb|EEX98492.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295383|gb|EEX98879.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261301679|gb|EEY05176.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261305003|gb|EEY08500.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261737294|gb|EEY25290.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|262553428|gb|EEZ09197.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659421|gb|EEZ29682.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 303

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 277


>gi|119503515|ref|ZP_01625598.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119460577|gb|EAW41669.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 282

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 125/237 (52%), Gaps = 21/237 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E+V A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K
Sbjct: 50  RELVLAHLRFVVHIARSYSGYGLAEGDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIK 109

Query: 506 QAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
             +   I      +++     + K+   +R+A++    +  E T + IA  L +    V+
Sbjct: 110 AEMHEFILRNWRIVKVATTKAQRKLFFNLRSAKKSLGWLNAEET-QAIAADLGVDEAEVQ 168

Query: 565 KV-LKITKEPISLETPI--GDEDT-----SHLGDFIED-KNAVSPLDSAIQANLRETTTR 615
           ++  +++   I+ + P    DED      ++L D   D    +   DSA     R+   R
Sbjct: 169 RMEGRLSSRDIAFDLPTDADDEDAWQSPQAYLDDISTDPARCIEAEDSA-----RDGENR 223

Query: 616 VLASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + A+L+  +ER   ++  R+        TL E+  ++ V+ ERIRQ+E  A++KLK+
Sbjct: 224 LRAALSDLDERSRNIVTQRWLAEQKA--TLHELAAEYGVSAERIRQLEVNAMKKLKN 278


>gi|265991792|ref|ZP_06104349.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263002748|gb|EEZ15151.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 293

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 126/249 (50%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 36  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 96  VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 153

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL   +  E+T  S   DF+ D + +     
Sbjct: 154 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIA 213

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  ++++R+RQI
Sbjct: 214 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKQRVRQI 270

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 271 ESRAMEKLK 279


>gi|262372449|ref|ZP_06065728.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
 gi|262312474|gb|EEY93559.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
          Length = 289

 Score = 84.7 bits (208), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 54  AAKLLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 113

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S ++  E   + IA  L +  E 
Sbjct: 114 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKRLTLEEA-QSIANDLNVTPEQ 172

Query: 563 VRKV-LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA 618
           V ++  ++T    + E     D+DT H     ++ED N   P     + +  E +T  L 
Sbjct: 173 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPALYLED-NRYDPARLIEEEDYEEQSTSALH 231

Query: 619 ----SLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 232 EAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|148358598|ref|YP_001249805.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
 gi|148280371|gb|ABQ54459.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
          Length = 284

 Score = 84.3 bits (207), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 75/295 (25%), Positives = 137/295 (46%), Gaps = 39/295 (13%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N     +DS +   N+I  +++E  I+ +E  H      +G+ EA+   +++V A+LR V
Sbjct: 11  NLPVGSLDSYIHRVNQIPMLTLEEEIAYAERFH-----SEGDIEAA---RQLVLAHLRYV 62

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + VA+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +    
Sbjct: 63  VRVARGYLGYGLPLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNW 122

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +++      +  K+    R+M N++      E         V+ V K L +++E + L
Sbjct: 123 RIVKVATTKAQR--KLFFNLRQMKNRLGWFSNEE---------VDAVAKDLGVSREDVLL 171

Query: 577 -ETPIGDEDTSHLGDF-----------------IEDKNAVSPLDSAIQANLRETTTRVLA 618
            E  +   D+S+                     + D  AV   +       RE     + 
Sbjct: 172 MEQRLNVMDSSYDAPDVDDNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAME 231

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  R + +L+ R+        TL ++ +++ V+ ER+RQ+E  A++K++    S
Sbjct: 232 QLDERSQDILQQRW--LAEEKLTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMES 284


>gi|167755690|ref|ZP_02427817.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|237734438|ref|ZP_04564919.1| sporulation sigma factor sigF [Mollicutes bacterium D7]
 gi|167704629|gb|EDS19208.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|229382668|gb|EEO32759.1| sporulation sigma factor sigF [Coprobacillus sp. D7]
          Length = 240

 Score = 84.3 bits (207), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 118/228 (51%), Gaps = 16/228 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V  NL LV S+  ++ N      DL Q G IGLMKA   FD   G +FSTYA+  
Sbjct: 20  AKELVVSQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAVNNFDTNYGVQFSTYAVPI 79

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D   TI++   +++   K+ +    ++N+  ++PT E+IA  L + V+ V
Sbjct: 80  IMGEIKRYFRDDG-TIKVSRSLKELNLKINKARELLTNQTGQDPTVEQIAAYLDVDVQDV 138

Query: 564 RKVLKITKEPISLETPIGDEDTSHLG--DFIEDK-NAVSPLDSAIQANLRETTTRVLASL 620
            + +  +  P SL  PI ++D S +   + IE+K N +     A++  + +        L
Sbjct: 139 VEAIDSSYYPTSLSEPIYEKDGSSISMEERIENKHNKMWFEKIALEMEIDK--------L 190

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E+ +L MR+ +  N     E V ++  +++ ++ ++E K I KL+
Sbjct: 191 DEKEKLILYMRYQLDFNQ----ERVAQRLNISQVQVSRLEKKIIAKLR 234


>gi|300718824|ref|YP_003743627.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
 gi|299064660|emb|CAX61780.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
          Length = 284

 Score = 84.3 bits (207), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 140/286 (48%), Gaps = 42/286 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E   +++E  H      +G+ EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRAANVWPMLTAEEEKALAERLHY-----QGDLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
               + K+   +R A++      +E   E +A++L +  + V ++  ++  + ++ +   
Sbjct: 128 TTKAQRKLFFNLRKAKQRLGWFNQEEV-EMVARELGVTSKDVLEMESRMAAQDMTFDPTP 186

Query: 581 GDED--------------TSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASLTP 622
            DE               +S   D IE+ N    A   L  A+Q             L  
Sbjct: 187 DDEGEGRSMAPMLYLQDKSSDFADGIEEDNWESHAADKLSDAMQG------------LDE 234

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 235 RSQNIIRARW-LDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLR 279


>gi|89076088|ref|ZP_01162448.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048240|gb|EAR53822.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 286

 Score = 84.3 bits (207), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 124/234 (52%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + K +V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  SAKALVMSHLRFVVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R +++       +     +A++L +    
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKSKKRLGWFNNDEV-NMVAEQLGVEPSD 167

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTT 614
           VR++   L        ++    + DT+ +    ++EDK+   A++  ++  + +     +
Sbjct: 168 VREMESRLAAQDPTFEMQNDDDERDTTPVAPAYYLEDKSSDVALTYEENNWENHANNRLS 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + LASL  R + ++R R+    +   TL+++   + V+ ERIRQ+E  A++KLK
Sbjct: 228 QALASLDERSQHIVRSRWLD--DEKSTLQDLANNYGVSAERIRQLEKNAMKKLK 279


>gi|333024988|ref|ZP_08453052.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332744840|gb|EGJ75281.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 316

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 120/238 (50%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 83  EGTHAHSYVRHTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 142

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PTP E+A+K
Sbjct: 143 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTPSELAEK 202

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     +EG+      T   +  + P  D+  S L D +  +      D +++     
Sbjct: 203 LGIEREEVIEGMAASNAYTASSLDAQ-PEEDDSESALADRLGYE------DHSLEGIEYI 255

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ ++L +RF   M    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 256 ESLKPMIARLPQRDRKILSLRFVANM----TQSEIGEELGISQMHVSRLLSRTLVKLR 309


>gi|319781051|ref|YP_004140527.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317166939|gb|ADV10477.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 287

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 117/235 (49%), Gaps = 26/235 (11%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A K+ + GL   DL+QEG++GL++AA +F+     +FSTYA WW++ ++  
Sbjct: 47  AHMRLVISMASKFRHYGLPLGDLVQEGHVGLLEAAARFEPEREVRFSTYATWWIRASMQD 106

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKLAMPVEGV 563
            I      +R       K   +    RR+  ++     P        E+++ L +    V
Sbjct: 107 YILRNWSIVRGGTSSAQK--ALFFNLRRLRARLANGAEPLSNATLYREVSEALGVSEADV 164

Query: 564 RKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR----- 615
             +  +++    SL  P+ D+   T  +   + D     PL   I  +  +   R     
Sbjct: 165 AMMDSRLSAPDSSLNMPVADDAGSTERMEFLVSD----DPLPDEIVGDKIDVARRSLWLR 220

Query: 616 -VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L +L  RE R++  R    +N +  TLE +G+   +++ER+RQIEA+A+ KLK
Sbjct: 221 EALRALNARELRIIEER---RLNDEGATLEALGETLGISKERVRQIEARAMEKLK 272


>gi|226323675|ref|ZP_03799193.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
 gi|225207859|gb|EEG90213.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
          Length = 205

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 60/191 (31%), Positives = 103/191 (53%), Gaps = 8/191 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++ ++ NLRLV+SV K+++       DL Q G IGL+KA   F+  L  KFSTYA+  
Sbjct: 13  AKEQYIKGNLRLVLSVIKRFSGSSENPDDLFQIGCIGLIKAINNFNPELEVKFSTYAVPM 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D + +IR+   +RD  +K +          ++EPT +EIA+++ +  E +
Sbjct: 73  IIGEIRRFIRDNN-SIRVSRSLRDTAYKAIYAKENYVKVNQKEPTVQEIAEEIGIAKEEI 131

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L   + P+SL  P+ ++  D  ++ D I DK   +  D  ++   + +    +  L 
Sbjct: 132 VYALDAIQMPVSLNEPVYNDNGDAMYVMDQISDKR--NKEDRWVE---KLSLQAAMDRLG 186

Query: 622 PREERVLRMRF 632
            RE+ ++R+RF
Sbjct: 187 KREKYIIRLRF 197


>gi|146295518|ref|YP_001179289.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409094|gb|ABP66098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 257

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 57/192 (29%), Positives = 101/192 (52%), Gaps = 11/192 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   VAKK+ NRG+++ DL Q   + L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNRHLYIAEIVAKKFINRGIEYDDLYQVACMALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+K+ P  EEIA+ + +  E V 
Sbjct: 91  MGEIKRYFRDRASLIRLPRRIYETSAKIKLATEILSAKLKQPPKIEEIAQYIGITPEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASL 620
           +V++ +    P SL+  + +++   LGD +   D+N V       Q    ET  + +  L
Sbjct: 151 EVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDENLV-------QIENTETVKKAIDKL 203

Query: 621 TPREERVLRMRF 632
           +P E   ++ RF
Sbjct: 204 SPLEREFVQKRF 215


>gi|239623681|ref|ZP_04666712.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521712|gb|EEQ61578.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 239

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 56/169 (33%), Positives = 93/169 (55%), Gaps = 6/169 (3%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++M  +G+     A+ ++V  N+ L+ S+ ++++ RG +  DL Q G+IGL+KA +KFD
Sbjct: 7   LINMAHEGD---KAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKAIDKFD 63

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++   +++   KV      M+  + REPT 
Sbjct: 64  TGFEVKFSTYAVPMITGEIKRFLRDDGM-IKVSRSIKELGFKVRAAREEMTYSLGREPTI 122

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKN 596
           EEIA +L    E V   ++   E  SL  P   GD++T  L D +E++N
Sbjct: 123 EEIAARLDTSREEVAASMEAGAEVESLYRPTGNGDDNTMFLMDRLEEEN 171


>gi|167507899|gb|ABZ81270.1| RpoD [Thalassospira sp. MCCC 1A00350]
 gi|167507915|gb|ABZ81278.1| RpoD [Thalassospira sp. MCCC 1A01057]
 gi|167507925|gb|ABZ81283.1| RpoD [Thalassospira sp. MCCC 1A01148]
 gi|167507933|gb|ABZ81287.1| RpoD [Thalassospira sp. MCCC 1A01275]
 gi|167507969|gb|ABZ81305.1| RpoD [Thalassospira sp. MCCC 1A02096]
          Length = 257

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 87/157 (55%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 101 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGEAVPAATEKRYNKLKNEMV 160

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ +  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 161 DLMEDVHLNNFRIEELLDHMTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 220

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    D I  +R  +  +S E
Sbjct: 221 WMERVGGLPGKGWKTFVERYSDEIANLREGVGGVSAE 257


>gi|90420276|ref|ZP_01228184.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90335610|gb|EAS49360.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 289

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 124/245 (50%), Gaps = 30/245 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A K+ + GL   DLIQEG++GL++AA +F+     +FSTYA WW
Sbjct: 40  ALHKITSAHMRLVISMAAKFRHFGLAMNDLIQEGHVGLLEAAARFEPEREVRFSTYATWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++ +I   I      +R       K     + R   R+S       T   + K++A    
Sbjct: 100 IRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLSQGADGGVTGSAMYKEIA---- 155

Query: 562 GVRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAV----------SPL-DSAIQANL 609
                LK+++  ++L ++ +   D+S     +ED++            SPL D  +  ++
Sbjct: 156 ---TALKVSEGDVALMDSRLSGPDSSLNAPLMEDESGSADRQDFLVSNSPLPDEMVSVSI 212

Query: 610 ---RETT--TRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKA 663
              R  T     L  L+ RE +++R R    +  D  TLE +G +  +++ER+RQIE +A
Sbjct: 213 DDERRVTWLHSALDVLSERELKIIRER---RLQDDGATLEALGTKLGISKERVRQIETRA 269

Query: 664 IRKLK 668
           + KL+
Sbjct: 270 LEKLR 274


>gi|332995320|gb|AEF05375.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 284

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 129/242 (53%), Gaps = 10/242 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR  E E   A +++V ++LR V+ +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G
Sbjct: 41  VRLREDEDLEAARKLVMSHLRFVVHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVG 100

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
            +  ++A+ W+K  I   +      +++     + K+   +R A++       E   + +
Sbjct: 101 VRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKLFFNLRKAKKRLGWFTHEEV-QTV 159

Query: 553 AKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNA---VSPLDSAIQ 606
           A +L +  + V ++  +++ +  + +    +++T +     F+EDK+    +  +++   
Sbjct: 160 ASELGVSTKEVLQMEARMSSQDQAFDLSADEDETGNFAPVQFLEDKSTDVEMDVINNDWD 219

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N  +     + +L  R + ++  R+    ++  TL+++  ++ V+ ER+RQIE  A++K
Sbjct: 220 TNASKRLYSAIKTLDDRSQDIIETRW--LADSKITLQDLADKYEVSAERVRQIEKNAMKK 277

Query: 667 LK 668
           L+
Sbjct: 278 LQ 279


>gi|318056726|ref|ZP_07975449.1| SigL-like sigma factor [Streptomyces sp. SA3_actG]
 gi|318075360|ref|ZP_07982692.1| SigL-like sigma factor [Streptomyces sp. SA3_actF]
          Length = 316

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 119/238 (50%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 83  EGTHAHSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 142

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PTP E+A+K
Sbjct: 143 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTPSELAEK 202

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     +EG+      T   +  + P  D+  S L D +  +      D  ++     
Sbjct: 203 LGIEREEVIEGMAASNAYTASSLDAQ-PEEDDSESALADRLGYE------DHGLEGIEYI 255

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ ++L +RF   M    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 256 ESLKPMIARLPQRDRKILSLRFVANM----TQSEIGEELGISQMHVSRLLSRTLVKLR 309


>gi|169823706|ref|YP_001691317.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302380124|ref|ZP_07268597.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|303234447|ref|ZP_07321085.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
 gi|167830511|dbj|BAG07427.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302312066|gb|EFK94074.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|302494402|gb|EFL54170.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
          Length = 258

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 118/228 (51%), Gaps = 18/228 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE NL +   +AKKYT RG+++ DL Q   IGL+ A +++D   GY+FS+YA   +   
Sbjct: 33  LVEKNLYIAEILAKKYTGRGIEYDDLYQVACIGLIYAIDRYDPSKGYEFSSYATPTIVGE 92

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+   IR+P  +++   KV      +S  +++ PT E+IA  L++  E V +VL
Sbjct: 93  IKKYFRDKGWVIRVPRRIQELNKKVATAKVHLSQTMQKSPTVEDIADYLSISNEEVLEVL 152

Query: 568 KITK--EPISLETPI--GDED-TSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASL 620
           +  K   P SL+  I   +ED  ++L D I  EDK+        ++   R+   R +  L
Sbjct: 153 EGAKVYAPQSLDQSIDQSNEDRETNLSDLIGEEDKD-------MLKFENRDLINRCMQDL 205

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              E ++L  R+        T   + ++  +++  + ++E K ++K K
Sbjct: 206 NKVERKILLGRYF----DKKTQIVIAEELDISQMTVSRMEKKILKKFK 249


>gi|298490935|ref|YP_003721112.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298232853|gb|ADI63989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 265

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 118/243 (48%), Gaps = 10/243 (4%)

Query: 423 SISEFRHIVSMVRK--GECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNI 479
           + +E +H +S + +   +C +   + ++V+ N  LV   A  + N+  + + DLIQ G +
Sbjct: 12  ATNELKHEISQLLREYQQCPSERLRNQLVKVNFGLVRKEAHYWINQCQESYDDLIQVGCL 71

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKF+   G  FS+YA+ +++  I   + D+  T+RIP        + +  +R +
Sbjct: 72  GLIRAIEKFELSKGNAFSSYAIPYIRGEIQHYLRDKGVTMRIPRRWLALQQQAIGLSRSL 131

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPI--GDEDTSHLGDFIEDK 595
             K  R+PT  E+A  LA+ +      K+  + + P+SL+ PI  G+E  S LG+ + D 
Sbjct: 132 REKYNRQPTDAELAAVLAISLSEWEEIKLAWMNRSPLSLDVPIKDGEEGASCLGELVPDP 191

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +  S    A +  +R    + L  L  R   VL   F   +      E +G        R
Sbjct: 192 HYRS-FQLAQEDQIR--LQQALVQLENRTREVLECVFLQDLTQKQVAEHLGISVVTVSRR 248

Query: 656 IRQ 658
           +++
Sbjct: 249 VKK 251


>gi|238921550|ref|YP_002935065.1| RNA polymerase factor sigma-32 [Edwardsiella ictaluri 93-146]
 gi|238871119|gb|ACR70830.1| alternative sigma factor RpoH, putative [Edwardsiella ictaluri
           93-146]
          Length = 284

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 68/275 (24%), Positives = 141/275 (51%), Gaps = 20/275 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E   ++ E  H      KG+ +A+   K+++ ++LR V+ VA+ 
Sbjct: 16  LEAYVRAANAYPMLTAEEERALGERLHY-----KGDLDAA---KQLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + V ++  ++  + ++ + P
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVSEKDVLEMESRMAAQDMAFDLP 185

Query: 580 IGDEDTSHLGD---FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
             DE          F++DK+   A    D   +++  +  +  L  L  R + ++R R+ 
Sbjct: 186 GDDEQEGAPAAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDERSQHIIRARW- 244

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 245 LDSDNKATLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|302521363|ref|ZP_07273705.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302430258|gb|EFL02074.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 312

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 119/238 (50%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 79  EGTHAHSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 138

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PTP E+A+K
Sbjct: 139 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTPSELAEK 198

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     +EG+      T   +  + P  D+  S L D +  +      D  ++     
Sbjct: 199 LGIEREEVIEGMAASNAYTASSLDAQ-PEEDDSESALADRLGYE------DHGLEGIEYI 251

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ ++L +RF   M    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 252 ESLKPMIARLPQRDRKILSLRFVANM----TQSEIGEELGISQMHVSRLLSRTLVKLR 305


>gi|167507949|gb|ABZ81295.1| RpoD [Thalassospira sp. MCCC 1A02030]
 gi|167507951|gb|ABZ81296.1| RpoD [Thalassospira sp. MCCC 1A02031]
          Length = 258

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 90/157 (57%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 102 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVALNKGEAVPAATEKRYAKLKNEMV 161

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 162 ELMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 221

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK F+    + I K+R ++  +S E
Sbjct: 222 WMERVAGLPGKGWKAFIERYPEEIAKLREDVGGVSAE 258


>gi|264680055|ref|YP_003279964.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
 gi|262210570|gb|ACY34668.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
          Length = 324

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 124/253 (49%), Gaps = 33/253 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 70  AAGRLVMSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 129

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP--TPEEIAKKLAMP-- 559
           +K  I   I      +++      +  K+    R M + +K +     EE+A +  +   
Sbjct: 130 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKHDLKSDAAMADEELALRETLTSN 187

Query: 560 -VEGVRKVLKITKEP-ISLETPIGDEDT-----------------SHLGDFIEDKNAVSP 600
            ++ V   L + +E  I +ET +   D                  ++L D   +  A+  
Sbjct: 188 EIDAVAAKLNVKREEVIEMETRLAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAM-- 245

Query: 601 LDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRER 655
           L+S  + +L  +     L  L  R  R++  R+ + +N D     TL E+  ++ V+ ER
Sbjct: 246 LESRQRDHLATDGLVMALEGLDDRSRRIVEERW-LKVNDDGSGGMTLHELAAEYGVSAER 304

Query: 656 IRQIEAKAIRKLK 668
           IRQIE  A++K+K
Sbjct: 305 IRQIEVAAMKKMK 317


>gi|312622111|ref|YP_004023724.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202578|gb|ADQ45905.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 117/228 (51%), Gaps = 12/228 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+++++E+NL LV SV KK+  +G++  DL Q G+IGL+KA ++FD     +FSTYA+ 
Sbjct: 19  LARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPSFNVRFSTYAVP 78

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D    I++   +++   K+ +   +  +   REPT  EI++   +  + 
Sbjct: 79  MIIGEIKRYLRDDG-KIKVSRKIKENQGKIKKLRNQFVSNHGREPTISEISQLTGLSNDE 137

Query: 563 VRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +   L  + E  SL   I  E+     L D   D+   S     + A L+E     L  L
Sbjct: 138 ILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA-LKEG----LKKL 192

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++ MR+      + T  E+ KQ  +++  + +IE +A+ ++K
Sbjct: 193 KGRERYIIFMRYF----KNKTQSEIAKQLNISQVHVSRIEKRALERIK 236


>gi|56963560|ref|YP_175291.1| sporulation sigma factor SigF [Bacillus clausii KSM-K16]
 gi|56909803|dbj|BAD64330.1| DNA-directed RNA polymerase sigma factor sigma-F [Bacillus clausii
           KSM-K16]
          Length = 254

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 131/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +S  + + +++  ++G+ EA   +  +V  N RLV SV +++ NRG +  
Sbjct: 4   EVKNGGKKKPLSDKQVKELIAKSQEGDTEA---RDSIVNHNTRLVWSVVQRFLNRGYEAD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSIKELSNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           + +    ++  ++R PT  EIA+ L +  E +       +   S+   +   D D   L 
Sbjct: 120 IRKAKDELTKTLRRAPTINEIAEHLGVTPEEIVFAGDANRSLSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D + V   D   +  L+E     +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADHSQVKWFD---KIALKEA----ICDLGERERLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K + ++K
Sbjct: 229 GISQVQVSRLEKKILEQMK 247


>gi|294138987|ref|YP_003554965.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
 gi|293325456|dbj|BAJ00187.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
          Length = 286

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 124/244 (50%), Gaps = 33/244 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      +++      +  K+    R+   ++      E         V  V
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKSKKRLGWFSDAE---------VGMV 160

Query: 564 RKVLKITKEPIS-LETPIGDED-----TSHLGDFIEDKNAVSPLD--SAIQANLRET--- 612
            + L ++K  ++ +E+ +  +D      S   D I+D      L+  S+  AN  ET   
Sbjct: 161 AENLGVSKADVTEMESRMAAQDPAFDLASDNDDDIQDYAPALYLEDHSSDLANQVETDNF 220

Query: 613 ----TTRVLASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAI 664
                TR+LA++   +ER   +L+ R+   +N D  TL+E+   + V+ ERIRQ+E  A+
Sbjct: 221 EADNQTRLLAAIKTLDERSQHILQARW---LNEDKTTLQELAATYQVSAERIRQLEKNAM 277

Query: 665 RKLK 668
            KLK
Sbjct: 278 NKLK 281


>gi|238750715|ref|ZP_04612214.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
 gi|238711105|gb|EEQ03324.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
          Length = 285

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 123/235 (52%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQA-----NLRETT 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S    +I+      +  +  
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWDDHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 SYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|254519401|ref|ZP_05131457.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
 gi|226913150|gb|EEH98351.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
          Length = 241

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 124/240 (51%), Gaps = 18/240 (7%)

Query: 438 ECEASIAKKE-MVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           EC++ I  KE +VE  + LV  +A +      + +++ DL+  G +GL+ A  ++D   G
Sbjct: 2   ECQSPIIHKEQIVEKYIPLVKYLASRVMLGKTKYIEYEDLVSYGIVGLLDAINRYDSTKG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEE 551
            KFS+YA   +K A+   I  + C    P+     DK+ K      ++ N+  REP+ +E
Sbjct: 62  MKFSSYATLRIKGAMIDEI--RKCR---PISKGAMDKLAKYNECVEKLQNRYMREPSLQE 116

Query: 552 IAKKLAMPVEGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           IA +L +  E V +V         ISLE+ I  D+D   + + +EDKN++SP +S     
Sbjct: 117 IALELNISEEEVSQVENYINYMSIISLESIIYSDDDDVTIMETLEDKNSISPEESLEDKE 176

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E     +  L  +++ +L + +   +    TL+E+G+   V+  R+ Q+ ++AIR L+
Sbjct: 177 KLEILAEAIEKLKDKDKLILNLYYYEKL----TLKEIGQILEVSESRVCQLHSRAIRNLR 232


>gi|1710647|sp|P50510|RP32_SERMA RecName: Full=RNA polymerase sigma-32 factor
 gi|1143376|dbj|BAA09442.1| sigma-32 homolog [Serratia marcescens]
          Length = 285

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 121/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAI-----QANLRETT 613
            VR++  ++  + ++ +    DE  D   +   +  ++  S     I     ++N  +  
Sbjct: 167 DVREMESRMAAQDMTFDPTPDDEARDGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KLK
Sbjct: 227 AYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLK 280


>gi|238798006|ref|ZP_04641495.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
 gi|238718109|gb|EEQ09936.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
          Length = 285

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 122/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETT 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S    +I+      +  +  
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWDGHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 AYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|302555286|ref|ZP_07307628.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472904|gb|EFL35997.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 264

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 116/234 (49%), Gaps = 16/234 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E +A   + E+VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 22  FRRLATLPAGPERDA--LRDEIVEAWLPMADRLAGRFRSRGESFEDLRQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-R 545
           ++D  LG  F +YA+  V   I R   D   T+ +P  ++D  ++V   ++ +S  I  R
Sbjct: 80  RYDPELGNAFESYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRVASQDLSQTISGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSP- 600
            PT  EIA+   M  + V+  L+     T   +  E P G ED   L D +    +V P 
Sbjct: 140 RPTIAEIAEHAKMSEDDVKAGLEALESFTALSLDAELP-GSEDGYSLSDAL---GSVDPA 195

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           LD+ +    RE+    LA+L  RE  +L MRF   M      EE+G  Q  V+R
Sbjct: 196 LDTVVD---RESVKARLAALPERERAILYMRFFGDMTQSRIAEELGISQMHVSR 246


>gi|153947554|ref|YP_001399239.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           31758]
 gi|152959049|gb|ABS46510.1| alternative sigma factor RpoH [Yersinia pseudotuberculosis IP
           31758]
          Length = 285

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 122/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRET-----T 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +  +T      
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWDTHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  L  R + ++R R+ +      TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 SYALEGLDERSQHIIRARW-LDDENKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|159901988|gb|ABX10718.1| RNA polymerase sigma factor [uncultured planctomycete 13FN]
          Length = 391

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 110/230 (47%), Gaps = 61/230 (26%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A   +  +++ANLRLV+S+A+++    +   +LI +GN+ LMKA ++F++ LG++FSTY
Sbjct: 205 DARQVRDHIIQANLRLVVSIARRFVTDFISLDELISDGNLILMKAVDRFNFSLGFRFSTY 264

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   V++   R+                      +  RR                     
Sbjct: 265 ATHAVQRDFYRN---------------------YKNGRR--------------------- 282

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
               R+V++I  +P  L   +   D       I D +AV+ L   +           + +
Sbjct: 283 ----RRVMEIATDPAVLFGSVVASDDEQQ---INDVHAVAYLKKLL-----------VDA 324

Query: 620 LTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+PRE+ +L MR G+   +   TL EVG++  +++ER+RQ++ +AI +++
Sbjct: 325 LSPREQTILDMRLGLKADDGGKTLREVGEKLSISKERVRQLQTRAIEQVR 374


>gi|270264290|ref|ZP_06192557.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
 gi|270041939|gb|EFA15036.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
          Length = 285

 Score = 84.3 bits (207), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 127/243 (52%), Gaps = 16/243 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLE-TPIGD-EDTSHLGDFIEDKNAVSPLDSAI----- 605
           ++L +  + VR++  ++  + ++ + TP  D  D   +   +  ++  S     I     
Sbjct: 159 RELGVTSKDVREMESRMAAQDMTFDPTPDDDARDGQSMAPVLYLQDKSSDFAEGIEEDNW 218

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           ++N  +     L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++
Sbjct: 219 ESNAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMK 277

Query: 666 KLK 668
           KLK
Sbjct: 278 KLK 280


>gi|325913818|ref|ZP_08176177.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325539893|gb|EGD11530.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 291

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 120/248 (48%), Gaps = 40/248 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN------------ 608
            K L ++ +E + +E+ +   D       D  +D    SP+ S + AN            
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPV-SYLVANEEDPSQAYERHD 223

Query: 609 --------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                   LRE     +A L  R   +++ R+ +   +  TL+E+  ++ V+ ERIRQIE
Sbjct: 224 SEDNQLQLLREG----MAGLDTRSRDIVKRRW-LDSESKVTLQELADEYGVSAERIRQIE 278

Query: 661 AKAIRKLK 668
           A A++K+K
Sbjct: 279 ANALKKMK 286


>gi|260589293|ref|ZP_05855206.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|331082700|ref|ZP_08331823.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540374|gb|EEX20943.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|330400319|gb|EGG79961.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 237

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 117/227 (51%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E N+ LV S+A+++ NRG +  DL+Q G IGL+KA +KFD     +FSTYA+  
Sbjct: 18  ARDILTEKNMGLVHSIARRFQNRGAELEDLVQIGCIGLLKAIDKFDLSYEVRFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++   K       +  K  +EP+ EEIAK+L++  E +
Sbjct: 78  ITGEIKRFLRDDGM-VKVSRSLKEAAGKAYAVREELLMKTGQEPSMEEIAKELSVSEEEL 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR--VLASLT 621
              ++ + +  SL+  I   D S +   +EDK    P +   Q  + +      +L SL 
Sbjct: 137 IMAMESSAQVESLQKTIYQSDGSDIA--LEDK---LPYEKDEQEEVLDKLLLEDILGSLN 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  ++ +RF      + T   + K   +++ ++ ++E K ++ L+
Sbjct: 192 ARERELIYLRF----FKEKTQTSIAKMMGMSQVQVSRLEKKILKALR 234


>gi|21233199|ref|NP_639116.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770141|ref|YP_244903.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|188993348|ref|YP_001905358.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. B100]
 gi|3046929|gb|AAC38329.1| heat shock sigma factor 32 [Xanthomonas campestris pv. campestris]
 gi|21115547|gb|AAM43471.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575473|gb|AAY50883.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|167735108|emb|CAP53320.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris]
          Length = 291

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 118/243 (48%), Gaps = 30/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 56  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 116 IRAEMHEFILKNWRIVKV---------ATTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 164

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAI-------QA------ 607
            K L ++ +E + +E+ +   D       D  +D    SP+   +       QA      
Sbjct: 165 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDS 224

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             N  +     +A L  R   +++ R+ +   +  TL+E+  ++ V+ ERIRQIEA A++
Sbjct: 225 EDNQLQLLREGMAGLDTRSRDIVKRRW-LDSESKVTLQELADEYGVSAERIRQIEANALK 283

Query: 666 KLK 668
           K+K
Sbjct: 284 KMK 286


>gi|259910110|ref|YP_002650466.1| RNA polymerase factor sigma-32 [Erwinia pyrifoliae Ep1/96]
 gi|224965732|emb|CAX57264.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae Ep1/96]
 gi|283480207|emb|CAY76123.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae DSM 12163]
 gi|310765698|gb|ADP10648.1| RNA polymerase factor sigma-32 [Erwinia sp. Ejp617]
          Length = 284

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 72/286 (25%), Positives = 141/286 (49%), Gaps = 42/286 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E   +++E  H      +G  EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRAANAWPMLTAEEEKALAERLHY-----QGCLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
               + K+   +R A++      ++   E +A++L +  + VR++  ++  + ++ +   
Sbjct: 128 TTKAQRKLFFNLRKAKQRLGWFNQDEV-EMVARELGVSSKDVREMESRMAAQDMTFDPTP 186

Query: 581 GDED--------------TSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASLTP 622
            DE               +S   + IE+ N    A   L+ A+Q             L  
Sbjct: 187 DDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQG------------LDE 234

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 235 RSQHIIRARW-LDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLR 279


>gi|90581423|ref|ZP_01237218.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90437400|gb|EAS62596.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 286

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 124/234 (52%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + K +V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  SAKALVMSHLRFVVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R +++       +     +A++L +    
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKSKKRLGWFNNDEV-NMVAEQLGVEPSD 167

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTT 614
           VR++   L        ++    + DT+ +    ++EDK+   A++  ++  + +     +
Sbjct: 168 VREMESRLAAQDPTFEMQNDDDERDTTPVAPAYYLEDKSSDLALTYEENNWENHANNRLS 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + LASL  R + ++R R+    +   TL+++   + V+ ERIRQ+E  A++KLK
Sbjct: 228 QALASLDERSQHIVRSRWLD--DEKSTLQDLADNYGVSAERIRQLEKNAMKKLK 279


>gi|22124334|ref|NP_667757.1| RNA polymerase factor sigma-32 [Yersinia pestis KIM 10]
 gi|45442990|ref|NP_994529.1| RNA polymerase factor sigma-32 [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51594579|ref|YP_068770.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           32953]
 gi|108806209|ref|YP_650125.1| RNA polymerase factor sigma-32 [Yersinia pestis Antiqua]
 gi|108810319|ref|YP_646086.1| RNA polymerase factor sigma-32 [Yersinia pestis Nepal516]
 gi|145600678|ref|YP_001164754.1| RNA polymerase factor sigma-32 [Yersinia pestis Pestoides F]
 gi|153997132|ref|ZP_02022265.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162418961|ref|YP_001605171.1| RNA polymerase factor sigma-32 [Yersinia pestis Angola]
 gi|165926363|ref|ZP_02222195.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165939186|ref|ZP_02227737.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166011667|ref|ZP_02232565.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166213537|ref|ZP_02239572.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167401873|ref|ZP_02307361.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167420986|ref|ZP_02312739.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167426241|ref|ZP_02317994.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|170026187|ref|YP_001722692.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis YPIII]
 gi|186893581|ref|YP_001870693.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis PB1/+]
 gi|218930813|ref|YP_002348688.1| RNA polymerase factor sigma-32 [Yersinia pestis CO92]
 gi|229837138|ref|ZP_04457303.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|229839498|ref|ZP_04459657.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229900061|ref|ZP_04515198.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229900493|ref|ZP_04515622.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|270488848|ref|ZP_06205922.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294505476|ref|YP_003569538.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957109|gb|AAM84008.1|AE013642_9 RNA polymerase, sigma(32) factor [Yersinia pestis KIM 10]
 gi|45437857|gb|AAS63406.1| RNA polymerase sigma-32 factor [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51587861|emb|CAH19464.1| RNA polymerase sigma-32 factor [Yersinia pseudotuberculosis IP
           32953]
 gi|108773967|gb|ABG16486.1| RNA polymerase sigma-32 factor [Yersinia pestis Nepal516]
 gi|108778122|gb|ABG12180.1| RNA polymerase sigma-32 factor [Yersinia pestis Antiqua]
 gi|115349424|emb|CAL22397.1| RNA polymerase sigma-32 factor [Yersinia pestis CO92]
 gi|145212374|gb|ABP41781.1| RNA polymerase sigma-32 factor [Yersinia pestis Pestoides F]
 gi|149289438|gb|EDM39516.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162351776|gb|ABX85724.1| alternative sigma factor RpoH [Yersinia pestis Angola]
 gi|165912959|gb|EDR31585.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165921887|gb|EDR39084.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165989436|gb|EDR41737.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166205210|gb|EDR49690.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166961115|gb|EDR57136.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167048766|gb|EDR60174.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167054760|gb|EDR64564.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169752721|gb|ACA70239.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           YPIII]
 gi|186696607|gb|ACC87236.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           PB1/+]
 gi|229682512|gb|EEO78599.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|229686841|gb|EEO78920.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695864|gb|EEO85911.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229706081|gb|EEO92090.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|262363541|gb|ACY60262.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367470|gb|ACY64027.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337352|gb|EFA48129.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294355935|gb|ADE66276.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320013591|gb|ADV97162.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 285

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 122/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETT 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S     I+     ++  +  
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWDSHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  L  R + ++R R+ +      TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 SYALEGLDERSQHIIRARW-LDDENKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|58583919|ref|YP_202935.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58428513|gb|AAW77550.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 329

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 121/248 (48%), Gaps = 40/248 (16%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 94  AARELVHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I      +++            +  R++   +++  T   +    A  V  V
Sbjct: 154 IRAEMHEFILKNWRIVKVA---------TTKAQRKLFFNLRKSKT--RLGWLNASEVTAV 202

Query: 564 RKVLKIT-KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN------------ 608
            K L ++ +E + +E+ +   D       D  +D    SP+ S + AN            
Sbjct: 203 AKDLNVSEREVMEMESRLSGRDIGFDASSDEDDDHGPPSPV-SYLVANEEDPSQAYERHD 261

Query: 609 --------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                   LRE     +A L  R   +++ R+ +  ++  TL+E+  ++ V+ ERIRQIE
Sbjct: 262 SEDNQLQLLREG----MAGLDTRSRDIVKRRW-LDSDSKVTLQELADEYGVSAERIRQIE 316

Query: 661 AKAIRKLK 668
           A A++K+K
Sbjct: 317 ANALKKMK 324


>gi|297157938|gb|ADI07650.1| SigL-like sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 322

 Score = 84.3 bits (207), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 121/241 (50%), Gaps = 16/241 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+   
Sbjct: 86  ILEEGTHEYAYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFELSR 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+
Sbjct: 146 GVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTAGEL 205

Query: 553 AKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA- 607
           A++L +     +EG+      T   +  + P  D+    L D I  +      D  ++  
Sbjct: 206 AERLGLTTAEVIEGMAASNAYTASSLDAQ-PEEDDTEGALADRIGYE------DHGLEGI 258

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E+   ++A L+PR+ ++L +RF   M    T  E+G +  +++  + ++ ++ + +L
Sbjct: 259 EYVESLKPLIADLSPRDRKILSLRFVANM----TQSEIGDELGISQMHVSRLLSRTLVRL 314

Query: 668 K 668
           +
Sbjct: 315 R 315


>gi|323345486|ref|ZP_08085709.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
 gi|323093600|gb|EFZ36178.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
          Length = 238

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 116/236 (49%), Gaps = 49/236 (20%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + + +ANL+ V+ +AK+Y ++G+   DL+ EGNIGL+ AA+K+      +F+ +A  +
Sbjct: 41  ALERLTKANLKFVVFIAKQYQHQGVDMEDLVSEGNIGLLYAAKKYTPSKEKRFAPFAAPF 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++ I + +  Q                   +  R+S  +  E                 
Sbjct: 101 IRKQIEQLLLRQGAD----------------SQSRLSASLTSE----------------- 127

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSP----LDSAIQANLRETTTRVL 617
                 +K+ +S+E PI  G  ++ +L   ++D NA+       D + +A L     RV 
Sbjct: 128 ------SKKVVSVEAPIPAGSRNSFNLLHVLKDTNALMADEHINDESFKAELERLMRRV- 180

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             L  R+++V+ + FGIG    HTL E+G    + RER+RQI  KA++K++  +++
Sbjct: 181 --LDQRQQQVISLFFGIGCE-KHTLMEIGDFMNLKRERVRQIRDKALQKIRKIAKT 233


>gi|164687591|ref|ZP_02211619.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
 gi|164603365|gb|EDQ96830.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
          Length = 255

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 120/241 (49%), Gaps = 14/241 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  V+ G+ EA   K  ++ +NL LV SV  K++N G +  DL Q G+IGL+KA  KFD
Sbjct: 22  LIQKVQNGDEEA---KALLISSNLGLVRSVIGKFSNIGYERDDLFQLGSIGLIKAIYKFD 78

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    +++   ++    KV      +S K+ R+PT 
Sbjct: 79  PSYNVKFSTYAVPMILGEIKRYLRDDGM-VKVSRSLKQLAIKVKMQGEMLSKKLGRDPTI 137

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
           EE+A+ + +  E V   ++       L+  I +E+ S   L D I  K            
Sbjct: 138 EELAEAIGVEKEDVVMAIESNFSVEYLQGVIHEEEGSPICLIDKISQKGEAEEDKVVDNI 197

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL  L  RE +++ +R+      D T  E+G+   +++ ++ +IE K + KL
Sbjct: 198 LLKE----VLGKLDKRERQIIMLRY----FEDKTQSEIGELLNISQVQVSRIEKKVLHKL 249

Query: 668 K 668
           K
Sbjct: 250 K 250


>gi|309378784|emb|CBX22610.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 287

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 129/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 44  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +    +P+E A+
Sbjct: 101 LFSFAVHWIKAEIHEFILKNWRLVRVATTKPQRKLFFNLRSMRKNLNAL----SPKE-AQ 155

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            +A  + GV+       E + +E  +   D + + D  +D +  +P+D            
Sbjct: 156 SIADDL-GVK-----LSEVLEMEQRMTGRDIAIMADNNDDDDNFAPIDWLADHDSEPSRQ 209

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 210 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 268

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 269 EAKAMQKLR 277


>gi|261400394|ref|ZP_05986519.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313668808|ref|YP_004049092.1| RNA polymerase sigma-32 factor [Neisseria lactamica ST-640]
 gi|269209833|gb|EEZ76288.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313006270|emb|CBN87733.1| putative RNA polymerase sigma-32 factor [Neisseria lactamica
           020-06]
          Length = 290

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 129/249 (51%), Gaps = 31/249 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 47  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 103

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +    +P+E A+
Sbjct: 104 LFSFAVHWIKAEIHEFILKNWRLVRVATTKPQRKLFFNLRSMRKNLNAL----SPKE-AQ 158

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            +A  + GV+       E + +E  +   D + + D  +D +  +P+D            
Sbjct: 159 SIADDL-GVK-----LSEVLEMEQRMTGRDIAIMADNNDDDDNFAPIDWLADHDSEPSRQ 212

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+ ERIRQI
Sbjct: 213 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVSAERIRQI 271

Query: 660 EAKAIRKLK 668
           EAKA++KL+
Sbjct: 272 EAKAMQKLR 280


>gi|146313497|ref|YP_001178571.1| RNA polymerase factor sigma-32 [Enterobacter sp. 638]
 gi|145320373|gb|ABP62520.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter sp. 638]
          Length = 285

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 128/242 (52%), Gaps = 14/242 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K ++ ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KTLILSHLRFVVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   +      +++     + K+   +R A++      +E   E +A+
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFNQEEV-EMVAR 159

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  ++  + ++ +    D  +D+  +   +  ++  S     I+ +  E
Sbjct: 160 ELGVSSKDVREMESRMAAQDMTFDMSSDDDAQDSQPMAPVLYLQDKTSNFADGIEEDNWE 219

Query: 612 -----TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  T  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 DQAANKLTHAMEGLDERSQAIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|291464148|gb|ADE05599.1| RNA polymerase sigma factor [Thalassospira tepidiphila]
          Length = 262

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 87/157 (55%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 106 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMV 165

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 166 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 225

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    + I  +R  I  +S E
Sbjct: 226 WMERVGGLPGKGWKTFVERYSEEIANLREGIGGVSAE 262


>gi|170750108|ref|YP_001756368.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170656630|gb|ACB25685.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 291

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 124/236 (52%), Gaps = 13/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 41  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPERDVRFSTYATWW 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E   +EI +++A  +
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTEEHVGDEIHRRIASAI 158

Query: 561 EGVRKVL-----KITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              R  +     +++   +SL  P+G++   +S   DF+ D   +     +   +     
Sbjct: 159 GVSRDDVALMDARLSGPDMSLNAPVGEDSDASSERMDFLVDGADLPDETVSATVDGERRL 218

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +  +LT   ER LR+     +  D  TLE +G++  +++ER+RQIE +A+ KL+
Sbjct: 219 SWLQQALTVLSERELRILRERRLAEDQATLEALGQRLGISKERVRQIENRALEKLR 274


>gi|188535384|ref|YP_001909181.1| RNA polymerase factor sigma-32 [Erwinia tasmaniensis Et1/99]
 gi|188030426|emb|CAO98320.1| RNA polymerase sigma-32 factor [Erwinia tasmaniensis Et1/99]
          Length = 284

 Score = 84.0 bits (206), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 71/286 (24%), Positives = 142/286 (49%), Gaps = 42/286 (14%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ E   +++E  H      +G+ EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRAANARPMLTAEEEKALAERLHY-----QGDLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
               + K+   +R A++      ++   E +A++L +  + VR++  ++  + ++ +   
Sbjct: 128 TTKAQRKLFFNLRKAKQRLGWFNQDEV-EMVARELGVSSKDVREMESRMAAQDMTFDPAP 186

Query: 581 GDED--------------TSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASLTP 622
            DE               +S   + IE+ N    A   L+ A+Q             L  
Sbjct: 187 DDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQG------------LDE 234

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 235 RSQHIIRARW-LDDDNKTTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|332289156|ref|YP_004420008.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
 gi|330432052|gb|AEC17111.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
          Length = 281

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 127/237 (53%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVIHIARGYSGYGLPQADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRM----SNKIKREPTPEEIAKKLA 557
           +K  I   +      +++      R     + +T +R+    +N++      + +A +L 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNANEV------DMVANELG 162

Query: 558 MPVEGVRKV-LKITKEPISLETPIGD-EDTSHLGDFIEDK--NAVSPLDSA-IQANLRET 612
           +  E V+++  +++   ++ + P  D E+T     ++EDK  N  + L+    +    + 
Sbjct: 163 VSAEDVQEMESRMSGIDMAFDLPTDDSEETYSPALYLEDKSSNFAAELEEENFENQATDQ 222

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  L  L  R   +++ R+    +   TL+E+   + V+ ERIRQ+E+ A++KL++
Sbjct: 223 LSEALEQLDERSRHIIQTRWLD--DNKATLQELADHYGVSAERIRQLESNALKKLRN 277


>gi|261407955|ref|YP_003244196.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|329929288|ref|ZP_08283041.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
 gi|261284418|gb|ACX66389.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|328936657|gb|EGG33100.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
          Length = 262

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 115/230 (50%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AKK+++E +L +V  V+ +      + +   DL   G +GL+ A EKFD+  G +F TYA
Sbjct: 26  AKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLASNGVMGLIDAIEKFDYKRGLQFETYA 85

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            W V+ AI  S+        +P  +R+K  K+    +++  K  R  +  E++  L +  
Sbjct: 86  SWRVRGAILDSLRQGDW---VPRSVREKAKKIETAYQQLEQKYLRSVSDSEMSDYLDVTE 142

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  R +L+        SLE PI +E++      + D+ A +P     +  LRE   + + 
Sbjct: 143 KEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNPDHKVHEFYLREALMKGIG 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 203 KLTPKERTVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|167507903|gb|ABZ81272.1| RpoD [Thalassospira lucentensis]
          Length = 267

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 84/157 (53%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-AVNGQKDEK----SSVKCKVLKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+   V   K E     +  +   LK ++V
Sbjct: 111 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAHNKGEAVPAATEKRYNKLKNEMV 170

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 171 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPN 230

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK F+    D I  +R  I  +S E
Sbjct: 231 WMERVSGLPGKGWKAFIERYPDEIANLREGIGGVSAE 267


>gi|313901043|ref|ZP_07834531.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
 gi|312954001|gb|EFR35681.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
          Length = 259

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 118/228 (51%), Gaps = 14/228 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++  NL+LV+S+ ++++NR     DL Q G IGL+K+ + FD     +FSTYA+  
Sbjct: 38  AKETLINGNLKLVLSIVQRFSNRCENMDDLFQVGCIGLVKSIDNFDLKHEVRFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    IR+  H++D  ++  +      +K ++EP+   +A++L +  + +
Sbjct: 98  IMGEIKRYLRDNQ-VIRVSRHLKDLAYRAFKLKEEYVHKHQKEPSVSWLAQQLEVKEKDI 156

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
              L  T+  +S+  P+   D D   L D I +DK+ +  L++ +         R L  L
Sbjct: 157 VDALDSTQSVLSIFEPVYNSDGDELFLLDQIKDDKDEIERLNNLM------ALKRSLTRL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E  +++ R+      D T  E+  +  +++ ++ ++E  AI  LK
Sbjct: 211 KGKELDIIQKRY----YQDMTQTEIAGELGISQAQVSRLEKNAIAVLK 254


>gi|152978131|ref|YP_001343760.1| RNA polymerase factor sigma-32 [Actinobacillus succinogenes 130Z]
 gi|150839854|gb|ABR73825.1| RNA polymerase, sigma 32 subunit, RpoH [Actinobacillus succinogenes
           130Z]
          Length = 281

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 122/233 (52%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 48  AAKALILSHLRFVIHVARGYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A +L +  E
Sbjct: 108 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFSENEVDLVANELGVSKE 165

Query: 562 GVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDK--NAVSPLDS-AIQANLRETTTR 615
            V ++  ++T   I  + P  D  E+T     ++EDK  N  + L++   +    +  T 
Sbjct: 166 DVIEMESRMTGADIGFDLPADDAEEETFAPSMYLEDKSSNFAAELENENFETQAVDQLTV 225

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  R + +++ R+ +  N   TL ++  ++ ++ ER+RQ+E+ A++KLK
Sbjct: 226 AMETLDARSQDIIKTRW-LDENK-ATLHDLAAKYNISAERVRQLESNALKKLK 276


>gi|331697274|ref|YP_004333513.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951963|gb|AEA25660.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 296

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 61/257 (23%), Positives = 130/257 (50%), Gaps = 21/257 (8%)

Query: 424 ISEFRHI------VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           ++E+ H+      ++ + KG    S  +  ++  +L L   +AK+++ RG    DL Q  
Sbjct: 1   MNEYSHLSPLFTELACLPKGHRRRSRLRDRLIIEHLPLARHIAKRFSQRGEPLQDLEQVA 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+ A ++FD   G +F  +A+  +   + R   D++ TIR+P  +++    +   A 
Sbjct: 61  VLGLINAVDRFDPARGPEFLAFAIPTITGEVLRWFRDRAWTIRVPRRLKELDMSISTAAD 120

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDE---DTSHLGDFI 592
           R++ ++ R PTP EIA +L + +  V + ++       +SL+ P+  E   ++ H G   
Sbjct: 121 RLTQELGRAPTPSEIAARLDVALSDVVESIQAREAYRCVSLDVPLSTESEDESVHNGILA 180

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                V+ ++       RE  + ++ +LT RE+R++ +RF      D T  E+G++  ++
Sbjct: 181 RTDPGVALVED------REVLSPLVDALTEREQRIVLLRF----FEDMTQNEIGQEIGIS 230

Query: 653 RERIRQIEAKAIRKLKH 669
           +  + ++   A+ +L+ 
Sbjct: 231 QMHVSRVLTAALERLRQ 247


>gi|13473307|ref|NP_104874.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14024055|dbj|BAB50660.1| RpoH-like sigma factor C [Mesorhizobium loti MAFF303099]
          Length = 287

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 117/234 (50%), Gaps = 24/234 (10%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A K+ + GL   DLIQEG++GL++AA +F+     +FSTYA WW++ ++  
Sbjct: 47  AHMRLVISMASKFRHYGLPLGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASMQD 106

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKLAMPVEGV 563
            I      +R       K   +    RR+  ++     P        E++  L +    V
Sbjct: 107 YILRNWSIVRGGTSSAQK--ALFFNLRRLRARLANGAEPLSNTTLYREVSVALGVSEADV 164

Query: 564 RKV-LKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR------ 615
             +  +++    SL  P+ D+   +   DF+   +   PL   I  +  +   R      
Sbjct: 165 AMMDSRLSAPDSSLNMPLADDAGATERMDFLVSDD---PLPDEIVGDKIDVARRSLWLKE 221

Query: 616 VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L  RE R++  R    +N +  TLE +G+   +++ER+RQIEA+A+ KLK
Sbjct: 222 ALHALNARELRIIEER---RLNDEGATLEALGETLGISKERVRQIEARAMEKLK 272


>gi|222529665|ref|YP_002573547.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456512|gb|ACM60774.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 232

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 120/238 (50%), Gaps = 12/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+ + +    +A+++++E NL LV SV KK+  +G++  DL Q G+IGL+KA ++FD   
Sbjct: 1   MISRAKNGDKLARQQLIENNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPSF 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 61  NVRFSTYAVPMIIGEIKRYLRDDG-KIKVSRKIKENQGKIKKLRNQFVSNHGREPTISEI 119

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   L  + E  SL   I  E+     L D   D+   S     + A L+
Sbjct: 120 SQLTGLSNDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA-LK 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     L  L  RE  ++ MR+      + T  E+ KQ  +++  + +IE +A+ ++K
Sbjct: 179 EG----LKKLKGRERYIIFMRYF----KNKTQSEIAKQLNISQVHVSRIEKRALERIK 228


>gi|238763647|ref|ZP_04624607.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238789414|ref|ZP_04633200.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238793542|ref|ZP_04637166.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
 gi|238698125|gb|EEP90882.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238722557|gb|EEQ14211.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238727132|gb|EEQ18662.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
          Length = 285

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 122/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETT 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S     I+      +  +  
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 SYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|88658518|ref|YP_507464.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
 gi|88599975|gb|ABD45444.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 297

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 119/249 (47%), Gaps = 45/249 (18%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LRLV+ VA  + N  L  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K  
Sbjct: 51  LVTSHLRLVVKVALSFKNYELPLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKAF 110

Query: 508 ITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEGV 563
           I   I      I+I     + K+   +R  ++   K     T E+I   A K +   + V
Sbjct: 111 IKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLFKYNHNITKEDIKLIANKCSTSEQEV 170

Query: 564 RKVLKI----------------------TKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            ++ +                        +E I  +TP   EDT  L + +  K A+   
Sbjct: 171 EQMNRYFLYRDRSLNELVFSNDNQNGVELQEIIKCDTP-NQEDTYLLNEELNIKKAL--- 226

Query: 602 DSAIQANLRETTTRVLASLTPREERV-LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                       ++ L++L  R   + +R R    +    TL+++ +++ +++ER+RQIE
Sbjct: 227 -----------ISQALSTLNERYRDIFIRRRL---IEEPDTLDKLSQEYNISKERVRQIE 272

Query: 661 AKAIRKLKH 669
             A  K+K+
Sbjct: 273 MHAFTKVKN 281


>gi|260439092|ref|ZP_05792908.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
 gi|292808404|gb|EFF67609.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
          Length = 241

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 126/245 (51%), Gaps = 17/245 (6%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + ++++  +G  EA   +  +V  N+ LV S+AK++ NRG +  D++  G IGL+KA +K
Sbjct: 5   KELIALAHEGNKEA---RDMLVMHNMGLVYSIAKRFANRGYEMDDIVSIGTIGLIKAIDK 61

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  +    STYA+  +   I R I D    I+I   +++   K+ +    +S K+KRE 
Sbjct: 62  FDLNMDVMLSTYAVPMISGEIKRFIRDDGI-IKISRSIKENGWKINQAKDYLSQKLKREV 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP----LDS 603
           T EEI+K+  +  E +   ++ +K+  S+   I   D + +  ++ DK A S      D 
Sbjct: 121 TIEEISKETGICTEDIVVAMEASKDVESIYQTIYQSDGNQI--YVVDKLAASAKESDHDK 178

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   + E T  +L      E+ ++ MR+      + T  EV K   +++ ++ ++E K 
Sbjct: 179 IMNHVMLEETMNILE---KDEKTIIEMRYF----QEKTQSEVAKILGISQVQVSRMEKKI 231

Query: 664 IRKLK 668
           + +++
Sbjct: 232 LLRMR 236


>gi|89256211|ref|YP_513573.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314678|ref|YP_763401.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502270|ref|YP_001428335.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167009752|ref|ZP_02274683.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367537|ref|ZP_04983563.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290952961|ref|ZP_06557582.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295313833|ref|ZP_06804405.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144042|emb|CAJ79290.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129577|gb|ABI82764.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253353|gb|EBA52447.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156252873|gb|ABU61379.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 292

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 122/240 (50%), Gaps = 13/240 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI        +E+A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSENIKELAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAV---SPLDSAIQANLRETTT 614
            V ++ K + +   SL+    D+D   TS    ++EDK++      +      N +    
Sbjct: 174 TVIEMEKRMCQGDASLDLSYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVK 233

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL+    R + ++  R+   ++   TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 234 DVLSGFDTRTKDIIMSRY--LLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|120556648|ref|YP_960999.1| RNA polymerase factor sigma-32 [Marinobacter aquaeolei VT8]
 gi|120326497|gb|ABM20812.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 286

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 147/281 (52%), Gaps = 27/281 (9%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
              ++S ++  + I  +SV+    ++E  H       G+ EA+   +++V ++LR VI +
Sbjct: 14  GANLESYIQAASRIPVLSVDEERELAERLHY-----HGDVEAA---RQLVLSHLRFVIHI 65

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y   GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +
Sbjct: 66  ARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIV 125

Query: 520 RIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLE 577
           ++     + K+   +R+ ++    +  +   + +A  L +    VR++  ++  +  + +
Sbjct: 126 KVATTKAQRKLFFNLRSQKKKLAWLNHDEL-KAVANDLGVEPHVVREMEGRLASQDTAFD 184

Query: 578 TPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQ---ANLRE-TTTRVLASLTPREER---V 627
            P+  DED ++     ++ED+ +    D A+Q   A+  E +  R++ +L   +ER   +
Sbjct: 185 GPMDDDEDNAYQAPAYYLEDRRS----DPAVQLENADWSEDSNGRLMQALEQLDERSQDI 240

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR R+     +  TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 241 LRERW--LSESKSTLHELADKYGVSAERIRQLEKNAMKKIR 279


>gi|311277614|ref|YP_003939845.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
 gi|308746809|gb|ADO46561.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
          Length = 285

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 72/290 (24%), Positives = 145/290 (50%), Gaps = 49/290 (16%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K+++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKLHY-----QGDLEAA---KKLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFD-- 183

Query: 580 IGDED-----------------TSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLA 618
           +G +D                 +S+  D IED N    A + L  A+Q            
Sbjct: 184 LGPDDDAQDGQPMAPVLYLQDKSSNFADGIEDDNWEEQAANKLTDAMQG----------- 232

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 -LDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 280


>gi|294813001|ref|ZP_06771644.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326441452|ref|ZP_08216186.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325600|gb|EFG07243.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 306

 Score = 84.0 bits (206), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 121/239 (50%), Gaps = 16/239 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+   G +
Sbjct: 73  EGTHEHAYVRNTLVELNLSLVRFAAARFRSRSEPMDDIVQVGTIGLIKAIDRFELSRGVE 132

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D S ++R+P  +++    + R    ++ ++ R PT  E+A+ 
Sbjct: 133 FPTFAMPTVIGEIKRFFRDTSWSVRVPRRLQELRLDLARAGDELTARLDRSPTVAELAEY 192

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     VEG+  V      P SL+    +E+  H G   E    +   D  ++     
Sbjct: 193 LGIGADEVVEGM--VASNAYTPSSLDARPQNEE--HDGTLAER---IGYEDGGLEGVEYI 245

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+   ++A L  R+ R+L +RFG     D T  ++G++  +++ ++ ++ ++ + +L+ 
Sbjct: 246 ESLKPLIAGLPDRDRRILSLRFG----ADMTQSDIGEELGISQMQVSRLLSRTLVRLRR 300


>gi|156933482|ref|YP_001437398.1| flagellar biosynthesis sigma factor [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531736|gb|ABU76562.1| hypothetical protein ESA_01300 [Cronobacter sakazakii ATCC BAA-894]
          Length = 229

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 103/201 (51%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L++P+E  R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATELEVAERLSIPLEEYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    ED    +PL   +++NLRE     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTEDNQNENPLHQLLESNLRERVMEAIESLPEREQMVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|167627742|ref|YP_001678242.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597743|gb|ABZ87741.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 292

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 128/242 (52%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI    + +  ++A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSEDIKQLAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQA-----NLRET 612
            V ++ K + +   SL+ P  D++   ++    ++EDK+  S ++  I       N +  
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDEGGQSNQQSFYLEDKS--SDIEHQIVQQDYYDNFKAI 231

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              V++    R + ++  R+   ++T  TL+++  ++ ++ ER+RQIE +A+ KL+   +
Sbjct: 232 VKDVISGFDTRTKDIIMSRY--LLDTKATLQDLAAKYNISAERVRQIEEEALVKLRKAIK 289

Query: 673 SK 674
           +K
Sbjct: 290 NK 291


>gi|152972335|ref|YP_001337481.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580698|ref|YP_002236168.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238896924|ref|YP_002921669.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae NTUH-K2044]
 gi|262040527|ref|ZP_06013768.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288933158|ref|YP_003437217.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|290511960|ref|ZP_06551328.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|329999131|ref|ZP_08303332.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
 gi|150957184|gb|ABR79214.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569756|gb|ACI11532.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238549251|dbj|BAH65602.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259042120|gb|EEW43150.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288887887|gb|ADC56205.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|289775750|gb|EFD83750.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|328538425|gb|EGF64546.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
          Length = 284

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 68/255 (26%), Positives = 129/255 (50%), Gaps = 41/255 (16%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KKLILSHLRFVVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVA 158

Query: 554 KKLAMPVEGVRKV----------------LKITKEPISLETPIGDEDTSHLGDFIEDKN- 596
           ++L +  + VR++                 +   +P++    + D+ TS+  D IED N 
Sbjct: 159 RELGVSSKDVREMESRMAAQDMTFDMSSDDESDSQPMAPVLYLQDK-TSNFADGIEDDNW 217

Query: 597 ---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
              A + L  A+Q             L  R + ++R R+ +  +   TL+E+  ++ V+ 
Sbjct: 218 EEQAANKLTDAMQG------------LDERSQDIIRARW-LDEDNKSTLQELADRYGVSA 264

Query: 654 ERIRQIEAKAIRKLK 668
           ER+RQ+E  A++KL+
Sbjct: 265 ERVRQLEKNAMKKLR 279


>gi|332142899|ref|YP_004428637.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|332143056|ref|YP_004428794.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552921|gb|AEA99639.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327553078|gb|AEA99796.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 284

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 141/269 (52%), Gaps = 16/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I+++S    +S  E R +   VR  E E   A +++V ++LR V+ +AK Y+  GL
Sbjct: 18  IEGYIQAVSSIDMLSAEEERELA--VRLREDEDLQAARKLVMSHLRFVVHIAKSYSGYGL 75

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRD 527
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++     + 
Sbjct: 76  PQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQR 135

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R A++       +   + +A +L +  + V ++  +++ +  + +    +++T 
Sbjct: 136 KLFFNLRKAKKRLGWFTHDEV-QTVANELGVSTKEVLQMEARMSSQDQAFDLSADEDETG 194

Query: 587 HLG--DFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRFGIGMNTD 639
           +     F+EDK+  S +++ +  N  +T         + +L  R + ++  R+    +  
Sbjct: 195 NFAPVQFLEDKS--SDVETDVINNDWDTAASKRLYSAIKTLDDRSQDIIETRW--LADNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++  ++ V+ ER+RQIE  A++KL+
Sbjct: 251 ITLQDLADKYQVSAERVRQIEKNAMKKLQ 279


>gi|256370062|ref|YP_003107573.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|256000225|gb|ACU48624.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
          Length = 303

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 117/233 (50%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGD-FIEDKNAVSP--LDSAIQANLRE 611
            +  + V  + +      SL  P+   + ++    D  ++D N+     ++     + R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDRLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERRIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 277


>gi|323492929|ref|ZP_08098069.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
 gi|323312822|gb|EGA65946.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
          Length = 285

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 127/243 (52%), Gaps = 19/243 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE EA+   K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 45  GEIEAA---KGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAR 159

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANL 609
           +L +    VR++  ++  +  + E P  D+D++        ++EDK A    D+   AN 
Sbjct: 160 ELGVEPAEVREMESRLAAQDATFEMPSDDDDSASSYTAPMVYLEDK-ASDVADNVEAANW 218

Query: 610 RETTTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              T       L +L  R + ++R R+    +   TL+E+ + + V+ ERIRQ+E  A++
Sbjct: 219 EAHTNNRLSLALKTLDDRSQHIVRSRWLD--DNKSTLQELAETYSVSAERIRQLEKNAMK 276

Query: 666 KLK 668
           KLK
Sbjct: 277 KLK 279


>gi|260598417|ref|YP_003210988.1| flagellar biosynthesis sigma factor [Cronobacter turicensis z3032]
 gi|260217594|emb|CBA31853.1| RNA polymerase sigma factor for flagellar operon [Cronobacter
           turicensis z3032]
          Length = 239

 Score = 84.0 bits (206), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 102/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L++P+E  R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATELEVAERLSIPLEEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    ED    +PL   ++ NLRE     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTEDNQNENPLHQLLEGNLRERVMEAIESLPEREQMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|239982297|ref|ZP_04704821.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291454142|ref|ZP_06593532.1| sigma factor [Streptomyces albus J1074]
 gi|291357091|gb|EFE83993.1| sigma factor [Streptomyces albus J1074]
          Length = 298

 Score = 83.6 bits (205), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/258 (24%), Positives = 126/258 (48%), Gaps = 39/258 (15%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFD 489
           +  + +G  E   A+  ++E NL LV   A ++ +RG  +  D++Q G IGL+KA ++FD
Sbjct: 53  LQTLEEGTPEHQYARNTLIEMNLSLVRYAAGRFRHRGPGEMEDIVQVGTIGLIKAIDRFD 112

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+T+A+ ++   I R   D S  + +P  +++    + +    ++ ++ REPT 
Sbjct: 113 LSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDMAKAKESLAAELDREPTV 172

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSH---------LG------D 590
           +E+A KL       VEG+      T   + + T  GD++ +          LG      +
Sbjct: 173 KELAAKLERTEEEVVEGLVAANGYTAGSLDVPTESGDDNRAGGSPRSLADTLGAPDPAQE 232

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +ED +A++PL               L +L  RE R++ MRFG     + T  ++G +  
Sbjct: 233 LVEDLHALAPL---------------LETLDERERRIVEMRFG----QELTQSQIGAELG 273

Query: 651 VTRERIRQIEAKAIRKLK 668
           +++  + ++ ++ + +L+
Sbjct: 274 ISQMHVSRLLSRILTRLR 291


>gi|121611388|ref|YP_999195.1| RNA polymerase sigma-32 subunit RpoH [Verminephrobacter eiseniae
           EF01-2]
 gi|121556028|gb|ABM60177.1| RNA polymerase, sigma 32 subunit, RpoH [Verminephrobacter eiseniae
           EF01-2]
          Length = 313

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 117/252 (46%), Gaps = 32/252 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGRLVLSHLRLVVSIARQYLGYGLPHGDLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---------------EPT 548
           +K  I   I      +++      +  K+    R M    K                E  
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADAGATDAATYRDTLSEHE 177

Query: 549 PEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            + +A +L +  E V ++  +++   + L+    D+     G      +A     + I++
Sbjct: 178 IDAVAAQLHVKREEVIEMETRMSGGDVLLDPAPSDDGEQAFGPIAYLADASHEPTALIES 237

Query: 608 NLRET-----TTRVLASLTPREERVLRMRF------GIGMNTDHTLEEVGKQFCVTRERI 656
             R+        + LASL  R  R+++ R+      G G  T H L  +   + V+ ERI
Sbjct: 238 RQRDALATDGIAKALASLDERSRRIVQERWLKVNDDGTGGMTLHDLAAI---YGVSAERI 294

Query: 657 RQIEAKAIRKLK 668
           RQIE  A++K+K
Sbjct: 295 RQIEVAAMKKMK 306


>gi|304406109|ref|ZP_07387766.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304344693|gb|EFM10530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 257

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 113/215 (52%), Gaps = 12/215 (5%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++  K   NR   F DL+Q G + L+K   ++D  +G +F  YAM  +   +   + D+S
Sbjct: 41  MAAGKIARNRPDLFEDLVQVGQMSLLKLFHQYDPSVGVQFEPYAMKSIIGHMKNYLRDKS 100

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPI 574
             I++P  +++K   V +    ++ K++R P  EEIA+++ + VE   ++L  +     +
Sbjct: 101 WYIQVPRRIKEKGIAVQQAIDELTVKLERSPRVEEIAERMELTVEETVEILGGRDLYHYV 160

Query: 575 SLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           SL+TPI +E+ T+ LG+ I      SPLD     + +      +A+L P E +VL++ F 
Sbjct: 161 SLDTPISEEESTTTLGELIG-----SPLDDFGLIDKKLDIEAAMAALKPEERQVLKLVFE 215

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            G         + +Q  V++  I +I+ +AI KLK
Sbjct: 216 DG----EPQRVIAEQLGVSQMSISRIQRRAIEKLK 246


>gi|17986563|ref|NP_539197.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|17982171|gb|AAL51461.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
          Length = 319

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 126/249 (50%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 62  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 121

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 122 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 179

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL   +  E+T  S   DF+ D + +     
Sbjct: 180 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIA 239

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  ++++R+RQI
Sbjct: 240 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKQRVRQI 296

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 297 ESRAMEKLK 305


>gi|312135430|ref|YP_004002768.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775481|gb|ADQ04968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 240

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 120/239 (50%), Gaps = 12/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD   
Sbjct: 9   LISKAKNGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSF 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 69  NVRFSTYAVPMIIGEIKRYLRDDG-RIKVSRKIKENQGKIKKLRNQFVSSNGREPTISEI 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   L  + E  SL   +  E+     L D   D+   S     + A L+
Sbjct: 128 SQLTGLSSDEILLCLDASSEVASLNEVVNQEEGKPITLMDIASDEEDYSTKLLDLMA-LK 186

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E     L  L  RE  ++ MR+      + T  E+ KQ  +++  + +IE +A+ ++K 
Sbjct: 187 EG----LKKLKGRERYIIFMRYF----KNKTQSEIAKQLNISQVHVSRIEKRALERIKR 237


>gi|256045366|ref|ZP_05448260.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260565741|ref|ZP_05836224.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260151114|gb|EEW86209.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
          Length = 311

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 126/249 (50%), Gaps = 19/249 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD    
Sbjct: 54  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRD 113

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KRE 546
            +FSTYA WW++ ++   I      +R       K+  +    RR+ +K+        + 
Sbjct: 114 VRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKV--LFFNLRRLRSKLAQTDDNMTKA 171

Query: 547 PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--L 601
               EI+ +L +    V  +  +++    SL   +  E+T  S   DF+ D + +     
Sbjct: 172 EIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIA 231

Query: 602 DSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQI 659
           +S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  ++++R+RQI
Sbjct: 232 ESSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKQRVRQI 288

Query: 660 EAKAIRKLK 668
           E++A+ KLK
Sbjct: 289 ESRAMEKLK 297


>gi|168235161|ref|ZP_02660219.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194737973|ref|YP_002116503.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194713475|gb|ACF92696.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197291332|gb|EDY30684.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 284

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 142/288 (49%), Gaps = 46/288 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASL 620
              +   +P++    + D+ +S+  D IED N    A + L  A+Q             L
Sbjct: 186 SDDESDSQPMAPVLYLQDK-SSNFADGIEDDNWEEQAANRLTDAMQ------------GL 232

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + ++R R+ +  +T  TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 DERSQDIIRARW-LDEDTKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|330466807|ref|YP_004404550.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328809778|gb|AEB43950.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 273

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 123/249 (49%), Gaps = 12/249 (4%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S ++  + ++ +  G    +  +   +EA L L   +A +Y+ RG    DL Q   +GL+
Sbjct: 27  SATDLLNAMAALPAGHPSRAALRDRAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLI 86

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KFD   G  F+ YA+  +   + R   D++  IR+P  +++    +      +   
Sbjct: 87  KAIDKFDPTRGVDFAGYAIPTIIGELKRHFRDRTWDIRVPRRLQELRLAISDANSSLLQT 146

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED-TSHLGDFIEDKNAVS 599
           + R PT  +IA  L +  E V + L+  +    +SL TP GD D  + LGD +  +++  
Sbjct: 147 LGRSPTVADIAAHLKLTEEEVLEGLEGARAYNAVSLSTPTGDGDRATELGDMLGGEDSEF 206

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L     A LR      LA+L  RE+++L +RF      + T  ++ +Q  V++  + ++
Sbjct: 207 EL-----AELRVALGPALATLDEREQKILTLRF----YGNLTQSQIAEQIGVSQMHVSRL 257

Query: 660 EAKAIRKLK 668
            A+A+ KL+
Sbjct: 258 LARALTKLR 266


>gi|304415276|ref|ZP_07395971.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304282866|gb|EFL91334.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 285

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 127/248 (51%), Gaps = 39/248 (15%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVTHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPAIGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R +++      ++   E +AK+L +  + 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKSKQRLGWFNQDEV-EMVAKELGVSKKD 167

Query: 563 VRKV-LKITKEPISLE-TP---------------IGDEDTSHLGDFIE---DKNAVSPLD 602
           V ++  +++ + ++ + +P               + D ++   GD  E   D +AV  L 
Sbjct: 168 VHEMESRMSAQDMTFDLSPDDDTRDGQLVAPVLYLQDRNSDFAGDVEEDNWDNHAVDKLS 227

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIE 660
            A++             L  R + ++R R+   +N D+  TL+E+  Q+ V+ ER+RQ+E
Sbjct: 228 FALE------------KLDERSQHIIRARW---LNDDNKATLQELANQYGVSAERVRQLE 272

Query: 661 AKAIRKLK 668
             A++KL+
Sbjct: 273 KNAMKKLR 280


>gi|269140667|ref|YP_003297368.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|267986328|gb|ACY86157.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|304560452|gb|ADM43116.1| RNA polymerase sigma factor RpoH [Edwardsiella tarda FL6-60]
          Length = 284

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/275 (24%), Positives = 141/275 (51%), Gaps = 20/275 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E   ++ E  H      KG+ +A+   K+++ ++LR V+ VA+ 
Sbjct: 16  LEAYVRAANAYPMLTAEEERALGERLHY-----KGDLDAA---KQLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + V ++  ++  + ++ + P
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVSEKDVLEMESRMAAQDMAFDLP 185

Query: 580 IGDEDTSHLGD---FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
             DE          F++DK+   A    D   +++  +  +  L  L  R + ++R R+ 
Sbjct: 186 GDDEQEGAPTAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDERSQHIIRARW- 244

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 245 LDSDNKATLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|167507983|gb|ABZ81312.1| RpoD [Thalassospira sp. MCCC 1A02803]
 gi|167507993|gb|ABZ81317.1| RpoD [Thalassospira sp. MCCC 1A02898]
          Length = 262

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 87/157 (55%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 106 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMV 165

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 166 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 225

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    + I  +R  I  +S E
Sbjct: 226 WMERVGGLPGKGWKTFVERYSEEIANLREGIGGVSAE 262


>gi|307328229|ref|ZP_07607407.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306886063|gb|EFN17071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 307

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 120/236 (50%), Gaps = 9/236 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E    +  ++E NL LV   A+++ NR ++  D++Q G IGL+KA ++FD     +
Sbjct: 71  EGTHEYQYVRNTLIELNLSLVRYAARRFHNRSVEMEDIVQVGTIGLIKAIDRFDLSREVE 130

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D S  + +P  +++    + +    +  ++ R PT  E+A+ 
Sbjct: 131 FTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRIDLAKANEELFQRLDRSPTTAELAEH 190

Query: 556 LAMPVEGVRKVLKITKEPI--SLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRET 612
           L +  + V   L  +   +  SL+ P   E   + +  + +    V P   A++ NL   
Sbjct: 191 LQLSEDEVVDGLVASNGYLTSSLDAPAEQESGATRVTTYADRFGDVDPAMEAVE-NLHAL 249

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++  L  R+ R+L++RFG  M    T  E+G +  V++  + ++ ++A+ +L+
Sbjct: 250 KP-LVEELGERDRRILQLRFGEEM----TQSEIGAELGVSQMHVSRLLSRALSRLR 300


>gi|221065333|ref|ZP_03541438.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
 gi|220710356|gb|EED65724.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
          Length = 324

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 125/253 (49%), Gaps = 33/253 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 70  AAGRLVMSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 129

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP--TPEEIAKKLAMP-- 559
           +K  I   I      +++      +  K+    R M +++K +     +E+A +  +   
Sbjct: 130 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKHELKSDAAMADDELALRETLTSN 187

Query: 560 -VEGVRKVLKITKEP-ISLETPIGDEDT-----------------SHLGDFIEDKNAVSP 600
            ++ V   L + +E  I +ET +   D                  ++L D   +  A+  
Sbjct: 188 EIDAVAAKLNVKREEVIEMETRLAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAM-- 245

Query: 601 LDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRER 655
           L+S  + +L  +     L  L  R  R++  R+ + +N D     TL E+  ++ V+ ER
Sbjct: 246 LESRQRDHLATDGLVMALEGLDDRSRRIVEERW-LKVNDDGSGGMTLHELAAEYGVSAER 304

Query: 656 IRQIEAKAIRKLK 668
           IRQIE  A++K+K
Sbjct: 305 IRQIEVAAMKKMK 317


>gi|167507907|gb|ABZ81274.1| RpoD [Thalassospira sp. MCCC 1A01013]
 gi|167507909|gb|ABZ81275.1| RpoD [Thalassospira sp. MCCC 1A01017]
          Length = 258

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 49/157 (31%), Positives = 89/157 (56%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 102 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMV 161

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 162 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPN 221

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+    + P   WK F+    D I ++R ++  +  E
Sbjct: 222 WMERVGELPGKGWKAFIERYPDEIAQLREQVGGVPAE 258


>gi|242241268|ref|YP_002989449.1| RNA polymerase factor sigma-32 [Dickeya dadantii Ech703]
 gi|242133325|gb|ACS87627.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech703]
          Length = 285

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVIHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T RR+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKRRLGWFNQDE--VELVARELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET-- 612
            VR++  ++  + ++ + P  D+D +  G       +++DK+  S     I+ +  ET  
Sbjct: 167 DVREMESRMAAQDMTYD-PTPDDD-AQPGQPMAPMLYLQDKS--SDFADGIEEDNWETHA 222

Query: 613 ---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  L  L  R + ++R R+ +  +   TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 223 ADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADYYGVSAERVRQLEKNAMKKLR 280


>gi|182418318|ref|ZP_02949613.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237666658|ref|ZP_04526643.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|182377700|gb|EDT75244.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237657857|gb|EEP55412.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 243

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 117/232 (50%), Gaps = 15/232 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K++++E  + LV  +A +     N+ +++ DL+  G IGL+ A  KFD   G KFS+YA
Sbjct: 10  GKEQIIEEYIPLVKYIASRVMFAKNKYMEYEDLVSYGMIGLIDAINKFDNSKGMKFSSYA 69

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K A+   +        I     DK+++  +    +  ++ REPT +EI+  L +  
Sbjct: 70  SIRIKGAMIDELRKNRP---ISKGAMDKLNRYNKAIEELQGRLLREPTTQEISNYLGISS 126

Query: 561 EGVRKVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             V ++         +SLE+ I   DED + +G  IEDKN+ SP          E  T+ 
Sbjct: 127 SEVAEIENYINYISMVSLESVIFSDDEDVNLMG-VIEDKNSPSPHSYLEDKEKLEILTQA 185

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  ++  +L + +  G+    TL+E+GK   V+  R+ Q+ +++IR L+
Sbjct: 186 IELLKEKDRMILNLYYYEGL----TLKEIGKILEVSESRVCQLHSRSIRNLR 233


>gi|317121977|ref|YP_004101980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
 gi|315591957|gb|ADU51253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
          Length = 250

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 119/239 (49%), Gaps = 22/239 (9%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ EA   ++ +V  ++ LV  VA+++   G +  DL+Q G IGL++A + FD   GY
Sbjct: 10  RRGDAEA---RERLVALHMPLVRHVARRFAGFGHEMDDLVQAGTIGLLQAIDGFDPARGY 66

Query: 495 KFSTYAMWWVKQAITRSI--ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           +FSTYA+  +   I R +  +D +   R    MR ++  + R A  M  ++   P    +
Sbjct: 67  QFSTYAVPAILGEIRRWLRASDPAGLTRA---MRARVAAIRRVAEAMEQELGHRPPAAAV 123

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS-AIQANLR 610
           A++L   V  V   L+ ++ P+SL+ P+  D D S  G  +         D+ A++A L 
Sbjct: 124 AERLGCDVADVTFALEASQVPVSLDEPLSSDPDASARGQRLAAPAEPDWSDAVAVRAALT 183

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +        L PR   ++ +RF      D T  EV     +++ ++ ++E  A+ +L+ 
Sbjct: 184 Q--------LPPRLRTIVTLRF----FRDMTQAEVAAAVGLSQPQVSRLEKLALGQLRQ 230


>gi|241668310|ref|ZP_04755888.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254876843|ref|ZP_05249553.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254842864|gb|EET21278.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 292

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 128/242 (52%), Gaps = 17/242 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V  +A+ ++  GL   DLIQEGNIGLMKA  KFD   G +  ++A+ W
Sbjct: 56  AAQQLVLSHLRFVTKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  +   +      +++      +  K+    R   +KI    + +  ++A++L +  E
Sbjct: 116 IKAEMHDYVLKNWKIVKVATTKAQR--KLFFNLRSSKDKIGWLSSEDIKQLAEELGVKEE 173

Query: 562 GVRKVLK-ITKEPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQA-----NLRET 612
            V ++ K + +   SL+ P  D++   ++    ++EDK+  S ++  I       N +  
Sbjct: 174 TVIEMEKRMCQGDASLDLPYTDDEGGQSNQQSLYLEDKS--SDIEHQIVQQDYYDNFKAI 231

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              V++    R + ++  R+   ++T  TL+++  ++ ++ ER+RQIE +A+ KL+   +
Sbjct: 232 VKDVISGFDTRTKDIIMSRY--LLDTKATLQDLATKYNISAERVRQIEEEALVKLRKAIK 289

Query: 673 SK 674
           +K
Sbjct: 290 NK 291


>gi|15803973|ref|NP_290009.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 EDL933]
 gi|15833564|ref|NP_312337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           Sakai]
 gi|16131333|ref|NP_417918.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|26250076|ref|NP_756116.1| RNA polymerase factor sigma-32 [Escherichia coli CFT073]
 gi|74314061|ref|YP_312480.1| RNA polymerase factor sigma-32 [Shigella sonnei Ss046]
 gi|82545824|ref|YP_409771.1| RNA polymerase factor sigma-32 [Shigella boydii Sb227]
 gi|82778725|ref|YP_405074.1| RNA polymerase factor sigma-32 [Shigella dysenteriae Sd197]
 gi|89110551|ref|AP_004331.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|91212950|ref|YP_542936.1| RNA polymerase factor sigma-32 [Escherichia coli UTI89]
 gi|110643701|ref|YP_671431.1| RNA polymerase factor sigma-32 [Escherichia coli 536]
 gi|117625739|ref|YP_859062.1| RNA polymerase factor sigma-32 [Escherichia coli APEC O1]
 gi|157158396|ref|YP_001464926.1| RNA polymerase factor sigma-32 [Escherichia coli E24377A]
 gi|157162938|ref|YP_001460256.1| RNA polymerase factor sigma-32 [Escherichia coli HS]
 gi|168747045|ref|ZP_02772067.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|168753229|ref|ZP_02778236.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|168759499|ref|ZP_02784506.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|168765824|ref|ZP_02790831.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|168772630|ref|ZP_02797637.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|168779560|ref|ZP_02804567.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|168785282|ref|ZP_02810289.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|168797247|ref|ZP_02822254.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|170018307|ref|YP_001723261.1| RNA polymerase factor sigma-32 [Escherichia coli ATCC 8739]
 gi|170082975|ref|YP_001732295.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170683649|ref|YP_001745710.1| RNA polymerase factor sigma-32 [Escherichia coli SMS-3-5]
 gi|170766775|ref|ZP_02901228.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|187730400|ref|YP_001882152.1| RNA polymerase factor sigma-32 [Shigella boydii CDC 3083-94]
 gi|188495507|ref|ZP_03002777.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|191169502|ref|ZP_03031234.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|191170346|ref|ZP_03031899.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|193061907|ref|ZP_03043004.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|193068783|ref|ZP_03049743.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194427076|ref|ZP_03059628.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194431093|ref|ZP_03063386.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194435828|ref|ZP_03067931.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|195934955|ref|ZP_03080337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|208806017|ref|ZP_03248354.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814463|ref|ZP_03255792.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821158|ref|ZP_03261478.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209398124|ref|YP_002272905.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920920|ref|YP_002295004.1| RNA polymerase factor sigma-32 [Escherichia coli SE11]
 gi|215488736|ref|YP_002331167.1| RNA polymerase factor sigma-32 [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217325718|ref|ZP_03441802.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218550723|ref|YP_002384514.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ATCC 35469]
 gi|218556012|ref|YP_002388925.1| RNA polymerase factor sigma-32 [Escherichia coli IAI1]
 gi|218560529|ref|YP_002393442.1| RNA polymerase factor sigma-32 [Escherichia coli S88]
 gi|218691746|ref|YP_002399958.1| RNA polymerase factor sigma-32 [Escherichia coli ED1a]
 gi|218697144|ref|YP_002404811.1| RNA polymerase factor sigma-32 [Escherichia coli 55989]
 gi|218702206|ref|YP_002409835.1| RNA polymerase factor sigma-32 [Escherichia coli IAI39]
 gi|218707055|ref|YP_002414574.1| RNA polymerase factor sigma-32 [Escherichia coli UMN026]
 gi|227883607|ref|ZP_04001412.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|237703208|ref|ZP_04533689.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|238902552|ref|YP_002928348.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|253771710|ref|YP_003034541.1| RNA polymerase factor sigma-32 [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038629|ref|ZP_04872685.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|254163385|ref|YP_003046493.1| RNA polymerase factor sigma-32 [Escherichia coli B str. REL606]
 gi|254795381|ref|YP_003080218.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           TW14359]
 gi|256020809|ref|ZP_05434674.1| RNA polymerase factor sigma-32 [Shigella sp. D9]
 gi|256025815|ref|ZP_05439680.1| RNA polymerase factor sigma-32 [Escherichia sp. 4_1_40B]
 gi|260846245|ref|YP_003224023.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260857567|ref|YP_003231458.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260870186|ref|YP_003236588.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|261224744|ref|ZP_05939025.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261254361|ref|ZP_05946894.1| RNA polymerase, sigma 32 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284801|ref|YP_003501619.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293407042|ref|ZP_06650966.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|293412884|ref|ZP_06655552.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|293416865|ref|ZP_06659502.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|293453766|ref|ZP_06664185.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|297517521|ref|ZP_06935907.1| RNA polymerase factor sigma-32 [Escherichia coli OP50]
 gi|298382788|ref|ZP_06992383.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|300815334|ref|ZP_07095559.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300822733|ref|ZP_07102870.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300898837|ref|ZP_07117141.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300907388|ref|ZP_07125036.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300917205|ref|ZP_07133887.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300930998|ref|ZP_07146356.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300936478|ref|ZP_07151398.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300946790|ref|ZP_07161034.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300956796|ref|ZP_07169063.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300985247|ref|ZP_07177344.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300987360|ref|ZP_07178168.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|301018548|ref|ZP_07182926.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|301021811|ref|ZP_07185775.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|301050314|ref|ZP_07197203.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|301302348|ref|ZP_07208480.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301645904|ref|ZP_07245818.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|306816195|ref|ZP_07450333.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|307140144|ref|ZP_07499500.1| RNA polymerase factor sigma-32 [Escherichia coli H736]
 gi|307311872|ref|ZP_07591510.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|309794740|ref|ZP_07689162.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|312968227|ref|ZP_07782437.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|331644161|ref|ZP_08345290.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331649268|ref|ZP_08350354.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331655044|ref|ZP_08356043.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331659757|ref|ZP_08360695.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331665070|ref|ZP_08365971.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331670287|ref|ZP_08371126.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331674946|ref|ZP_08375703.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331679529|ref|ZP_08380199.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331685107|ref|ZP_08385693.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332282016|ref|ZP_08394429.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|84028120|sp|P0AGB5|RP32_ECO57 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028121|sp|P0AGB4|RP32_ECOL6 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028122|sp|P0AGB3|RP32_ECOLI RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|12518117|gb|AAG58570.1|AE005569_10 RNA polymerase, sigma(32) factor; regulation of proteins induced at
           high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|26110505|gb|AAN82690.1|AE016768_108 RNA polymerase sigma-32 factor [Escherichia coli CFT073]
 gi|147732|gb|AAA24587.1| RNA polymerase sigma-32 subunit [Escherichia coli]
 gi|466597|gb|AAB18436.1| RNA polymerase sigma-32 subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|1789871|gb|AAC76486.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13363784|dbj|BAB37733.1| RNA polymerase sigma32 factor [Escherichia coli O157:H7 str. Sakai]
 gi|73671328|gb|AAZ80075.1| RpoH [Escherichia coli LW1655F+]
 gi|73857538|gb|AAZ90245.1| RNA polymerase, sigma(32) factor [Shigella sonnei Ss046]
 gi|81242873|gb|ABB63583.1| RNA polymerase, sigma(32) factor [Shigella dysenteriae Sd197]
 gi|81247235|gb|ABB67943.1| RNA polymerase sigma(32) factor [Shigella boydii Sb227]
 gi|85676582|dbj|BAE77832.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|91074524|gb|ABE09405.1| component of RNA polymerase, sigma 32 factor [Escherichia coli
           UTI89]
 gi|110345293|gb|ABG71530.1| RNA polymerase sigma-32 factor [Escherichia coli 536]
 gi|115514863|gb|ABJ02938.1| RNA polymerase sigma factor [Escherichia coli APEC O1]
 gi|157068618|gb|ABV07873.1| alternative sigma factor RpoH [Escherichia coli HS]
 gi|157080426|gb|ABV20134.1| alternative sigma factor RpoH [Escherichia coli E24377A]
 gi|169753235|gb|ACA75934.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli ATCC 8739]
 gi|169890810|gb|ACB04517.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170124213|gb|EDS93144.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|170521367|gb|ACB19545.1| alternative sigma factor RpoH [Escherichia coli SMS-3-5]
 gi|187427392|gb|ACD06666.1| alternative sigma factor RpoH [Shigella boydii CDC 3083-94]
 gi|187771635|gb|EDU35479.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|188018405|gb|EDU56527.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|188490706|gb|EDU65809.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|189002511|gb|EDU71497.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|189359084|gb|EDU77503.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|189364663|gb|EDU83082.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|189369524|gb|EDU87940.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|189374649|gb|EDU93065.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|189380077|gb|EDU98493.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|190900463|gb|EDV60280.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|190909154|gb|EDV68740.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|192932697|gb|EDV85294.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|192957859|gb|EDV88302.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194415037|gb|EDX31307.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194420548|gb|EDX36624.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194425371|gb|EDX41355.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|208725818|gb|EDZ75419.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735740|gb|EDZ84427.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741281|gb|EDZ88963.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209159524|gb|ACI36957.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209756038|gb|ACI76331.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756040|gb|ACI76332.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756042|gb|ACI76333.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756044|gb|ACI76334.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756046|gb|ACI76335.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209914179|dbj|BAG79253.1| RNA polymerase sigma-32 factor [Escherichia coli SE11]
 gi|215266808|emb|CAS11249.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|217321939|gb|EEC30363.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353876|emb|CAV00268.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli 55989]
 gi|218358264|emb|CAQ90911.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia fergusonii
           ATCC 35469]
 gi|218362780|emb|CAR00406.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI1]
 gi|218367298|emb|CAR05076.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli S88]
 gi|218372192|emb|CAR20054.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI39]
 gi|218429310|emb|CAR10124.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli ED1a]
 gi|218434152|emb|CAR15069.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli UMN026]
 gi|222035167|emb|CAP77912.1| RNA polymerase sigma-32 factor [Escherichia coli LF82]
 gi|226839135|gb|EEH71158.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|226902472|gb|EEH88731.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|227839486|gb|EEJ49952.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|238863499|gb|ACR65497.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|242378982|emb|CAQ33780.1| RNA polymerase, sigma 32 (sigma H) factor, subunit of RNA
           polymerase sigma 32 [Escherichia coli BL21(DE3)]
 gi|253322754|gb|ACT27356.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975286|gb|ACT40957.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979442|gb|ACT45112.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|254594781|gb|ACT74142.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257756216|dbj|BAI27718.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257761392|dbj|BAI32889.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257766542|dbj|BAI38037.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|260447523|gb|ACX37945.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli DH1]
 gi|281180490|dbj|BAI56820.1| RNA polymerase sigma-32 factor [Escherichia coli SE15]
 gi|284923451|emb|CBG36546.1| RNA polymerase sigma-32 factor [Escherichia coli 042]
 gi|290764674|gb|ADD58635.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291321892|gb|EFE61323.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|291425853|gb|EFE98887.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|291431441|gb|EFF04426.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|291468531|gb|EFF11024.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|294492777|gb|ADE91533.1| alternative sigma factor RpoH [Escherichia coli IHE3034]
 gi|298276624|gb|EFI18142.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|299881444|gb|EFI89655.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|300297943|gb|EFJ54328.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|300306228|gb|EFJ60748.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|300316435|gb|EFJ66219.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300357522|gb|EFJ73392.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300399667|gb|EFJ83205.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|300400897|gb|EFJ84435.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300408118|gb|EFJ91656.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300415544|gb|EFJ98854.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300453547|gb|EFK17167.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300458400|gb|EFK21893.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300461176|gb|EFK24669.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300524733|gb|EFK45802.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300532226|gb|EFK53288.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300842511|gb|EFK70271.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301075893|gb|EFK90699.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|305850591|gb|EFM51048.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|306908016|gb|EFN38516.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|307555555|gb|ADN48330.1| component of RNA polymerase [Escherichia coli ABU 83972]
 gi|307628534|gb|ADN72838.1| RNA polymerase factor sigma-32 [Escherichia coli UM146]
 gi|308121790|gb|EFO59052.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|309703867|emb|CBJ03208.1| RNA polymerase sigma-32 factor [Escherichia coli ETEC H10407]
 gi|312287052|gb|EFR14962.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|312948014|gb|ADR28841.1| RNA polymerase factor sigma-32 [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062740|gb|ADT77067.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli W]
 gi|315138035|dbj|BAJ45194.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315256058|gb|EFU36026.1| alternative sigma factor RpoH [Escherichia coli MS 85-1]
 gi|315286128|gb|EFU45566.1| alternative sigma factor RpoH [Escherichia coli MS 110-3]
 gi|315291684|gb|EFU51040.1| alternative sigma factor RpoH [Escherichia coli MS 153-1]
 gi|315295969|gb|EFU55278.1| alternative sigma factor RpoH [Escherichia coli MS 16-3]
 gi|320175708|gb|EFW50796.1| RNA polymerase sigma factor RpoH [Shigella dysenteriae CDC 74-1112]
 gi|320187771|gb|EFW62446.1| RNA polymerase sigma factor RpoH [Shigella flexneri CDC 796-83]
 gi|320191521|gb|EFW66171.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194037|gb|EFW68670.1| RNA polymerase sigma factor RpoH [Escherichia coli WV_060327]
 gi|320199638|gb|EFW74228.1| RNA polymerase sigma factor RpoH [Escherichia coli EC4100B]
 gi|320639745|gb|EFX09339.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           G5101]
 gi|320645244|gb|EFX14260.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str.
           493-89]
 gi|320650555|gb|EFX19021.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str. H
           2687]
 gi|320655748|gb|EFX23671.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320661531|gb|EFX28946.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320666554|gb|EFX33537.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154300|gb|EFZ40503.1| alternative sigma factor RpoH [Escherichia coli EPECa14]
 gi|323174100|gb|EFZ59728.1| alternative sigma factor RpoH [Escherichia coli LT-68]
 gi|323376672|gb|ADX48940.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli KO11]
 gi|323934553|gb|EGB30953.1| sigma protein RpoH [Escherichia coli E1520]
 gi|323939321|gb|EGB35532.1| sigma proteinRpoH [Escherichia coli E482]
 gi|323944315|gb|EGB40390.1| sigma protein RpoH [Escherichia coli H120]
 gi|323950129|gb|EGB46012.1| sigma proteinRpoH [Escherichia coli H252]
 gi|323954785|gb|EGB50566.1| sigma proteinRpoH [Escherichia coli H263]
 gi|323959687|gb|EGB55338.1| sigma proteinRpoH [Escherichia coli H489]
 gi|323966125|gb|EGB61562.1| sigma proteinRpoH [Escherichia coli M863]
 gi|323970059|gb|EGB65334.1| sigma proteinRpoH [Escherichia coli TA007]
 gi|323974898|gb|EGB70009.1| sigma proteinRpoH [Escherichia coli TW10509]
 gi|324009349|gb|EGB78568.1| alternative sigma factor RpoH [Escherichia coli MS 57-2]
 gi|324014559|gb|EGB83778.1| alternative sigma factor RpoH [Escherichia coli MS 60-1]
 gi|324018638|gb|EGB87857.1| alternative sigma factor RpoH [Escherichia coli MS 117-3]
 gi|324111782|gb|EGC05762.1| sigma proteinRpoH [Escherichia fergusonii B253]
 gi|324116341|gb|EGC10260.1| sigma proteinRpoH [Escherichia coli E1167]
 gi|325499010|gb|EGC96869.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ECD227]
 gi|326337569|gb|EGD61404.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1044]
 gi|326344680|gb|EGD68429.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1125]
 gi|330909502|gb|EGH38016.1| RNA polymerase sigma factor RpoH [Escherichia coli AA86]
 gi|331036455|gb|EGI08681.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331041766|gb|EGI13910.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331047059|gb|EGI19137.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331052972|gb|EGI25005.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331057580|gb|EGI29566.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331062349|gb|EGI34269.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331067855|gb|EGI39253.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331072701|gb|EGI44026.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331077478|gb|EGI48690.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332085344|gb|EGI90516.1| alternative sigma factor RpoH [Shigella boydii 5216-82]
 gi|332085690|gb|EGI90854.1| alternative sigma factor RpoH [Shigella dysenteriae 155-74]
 gi|332090225|gb|EGI95323.1| alternative sigma factor RpoH [Shigella boydii 3594-74]
 gi|332104368|gb|EGJ07714.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|332345416|gb|AEE58750.1| alternative sigma factor RpoH [Escherichia coli UMNK88]
          Length = 284

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 139/288 (48%), Gaps = 46/288 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    +S +   +++E  H       G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKLHY-----HGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASL 620
                  +P++    + D+ +S+  D IED N    A + L  A+Q             L
Sbjct: 186 SDDDSDSQPMAPVLYLQDK-SSNFADGIEDDNWEEQAANRLTDAMQG------------L 232

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 DERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|294638156|ref|ZP_06716412.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
 gi|291088723|gb|EFE21284.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
          Length = 284

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 122/234 (52%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVARELGVSEK 166

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD---FIEDKN---AVSPLDSAIQANLRETTT 614
            V ++  ++  + ++ + P  DE          F++DK+   A    D   +++  +  +
Sbjct: 167 DVLEMESRMAAQDMAFDLPNDDEQEGAPAAPVLFLQDKSSDFANEIEDDNWESHAADKLS 226

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  L  R + ++R R+ +      TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 227 VALEGLDERSQHIIRARW-LDSENKATLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|332981002|ref|YP_004462443.1| RNA polymerase sigma-28 subunit SigF [Mahella australiensis 50-1
           BON]
 gi|332698680|gb|AEE95621.1| RNA polymerase, sigma 28 subunit, SigF [Mahella australiensis 50-1
           BON]
          Length = 256

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 126/246 (51%), Gaps = 15/246 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   ++  VR+G  +A+   + + E NL LV +V +K+ NRG ++ DL Q G++GL+KA 
Sbjct: 21  EIEDLIVKVRQGNKQAA---EILAERNLGLVHNVVRKFMNRGYEYDDLFQVGSMGLVKAI 77

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
             +D     KFSTYA+  +   I R + D   +I++   ++   +K+     R+  ++ R
Sbjct: 78  NNYDLSYNVKFSTYAVPMIMGEIKRFLRDDG-SIKVSRSVKIAAYKIHNAQDRIKKELGR 136

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISL-ETPIGDEDTS-HLGDFIEDKNAVSPLDS 603
           EP+ +E+A  L M    V   ++    P+SL ++   D ++S  L D I D + +   D 
Sbjct: 137 EPSVQELATALDMEPADVVYAMEADTVPVSLYDSAYEDGESSISLIDRISDGDELDT-DV 195

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  L+E     +A L  +  +V+ +R+      D T  EV +   +T+ ++ +IE K 
Sbjct: 196 IDRVALKEC----IAQLDAKGRQVILLRYF----KDKTQSEVAQMLGITQVQVCRIEKKV 247

Query: 664 IRKLKH 669
           +  ++ 
Sbjct: 248 LEFMRQ 253


>gi|157368473|ref|YP_001476462.1| RNA polymerase factor sigma-32 [Serratia proteamaculans 568]
 gi|157320237|gb|ABV39334.1| RNA polymerase, sigma 32 subunit, RpoH [Serratia proteamaculans
           568]
          Length = 285

 Score = 83.6 bits (205), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 129/244 (52%), Gaps = 18/244 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVA 158

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD-----FIEDKN---AVSPLDSA 604
           ++L +  + VR++  ++  + ++ + P  D+D           +++DK+   A    +  
Sbjct: 159 RELGVTSKDVREMESRMAAQDMTFD-PTPDDDAREGQSMAPVLYLQDKSSDFAEGIEEDN 217

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            ++N  +     +  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A+
Sbjct: 218 WESNAADKLAYAMEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAM 276

Query: 665 RKLK 668
           +KLK
Sbjct: 277 KKLK 280


>gi|54295507|ref|YP_127922.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Lens]
 gi|53755339|emb|CAH16835.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Lens]
          Length = 284

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/285 (25%), Positives = 135/285 (47%), Gaps = 39/285 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS +   N+I  +++E  I+ +E  H      +G+ EA+   +++V A+LR V+ VA+ 
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAERFH-----SEGDIEAA---RQLVLAHLRYVVRVARG 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 69  YLGYGLPLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVA 128

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL-ETPIG 581
                +  K+    R+M N++      E         V+ V K L +++E + L E  + 
Sbjct: 129 TTKAQR--KLFFNLRQMKNRLGWFSNEE---------VDAVAKDLGVSREDVLLMEQRLN 177

Query: 582 DEDTSHLGDF-----------------IEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             D+S+                     + D  AV   +       RE     +  L  R 
Sbjct: 178 VMDSSYDAPDVDDNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERS 237

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +L+ R+        TL ++ +++ V+ ER+RQ+E  A++K++ 
Sbjct: 238 QDILQQRW--LAEEKLTLHDLAEKYGVSAERVRQLEKNAMKKIRQ 280


>gi|238784413|ref|ZP_04628423.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
 gi|238714705|gb|EEQ06707.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
          Length = 285

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 121/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETT 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S     I+      +  +  
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 AYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|295109704|emb|CBL23657.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus obeum
           A2-162]
          Length = 259

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 123/233 (52%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++ ++ NLRLV+SV +++ N      DL Q G IGLMKA + FD  L  KFSTYA+  
Sbjct: 38  AREQYIKGNLRLVLSVIRRFQNSNENPDDLFQIGCIGLMKAVDNFDDTLMVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        +  +EPT EEIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDYN-SIRVSRSLRDIAYKAIYAKENYIRQNLKEPTMEEIAEEIGIEKEMI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSP--LDSAIQANLRETTTRVLAS 619
              L   + P+SL  P+  E  DT ++ D I D+       L++    +L+E   R    
Sbjct: 157 VYALDAIQSPVSLYEPVYSEGGDTLYVMDQISDRKNKEEHWLEN---LSLKEAMNR---- 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  RE  ++ MRF  G     T  EV  +  +++ ++ ++E  A++ +++  R
Sbjct: 210 LGSRERHIIEMRFYEG----KTQMEVADEIGISQAQVSRLEKNALKTMRNYLR 258


>gi|297195554|ref|ZP_06912952.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197721376|gb|EDY65284.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 291

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 124/251 (49%), Gaps = 13/251 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           IS S F  + S+  +G  E    +  ++E NL LV   A ++ NR  Q  D+IQ G IGL
Sbjct: 43  ISKSFFVRLASL-EEGTHEYQYVRNTLIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGL 101

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++F+     +F+T+A+ ++   I R   D S  + +P  +++    + +    +S 
Sbjct: 102 IKAIDRFELSREVEFATFAVPYIIGEIKRFFRDTSWAVHVPRRLQELRIDLAKAVDELSQ 161

Query: 542 KIKREPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           K+   PT  E+A+ L M     +EGV      T    S++ P+ D+ + H    + D+  
Sbjct: 162 KLDHTPTTAELAEHLGMDEEEIIEGVVASNGYTAG--SIDMPM-DDASDHGAVPLSDRLG 218

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
               +  I  N+ +    ++  L  R+ ++L+MRFG  M    T  E+G +  V++  + 
Sbjct: 219 APDAELEIAENV-QALKPLIEELDERDRQILQMRFGEEM----TQSEIGAELGVSQMHVS 273

Query: 658 QIEAKAIRKLK 668
           ++ ++   +L+
Sbjct: 274 RLLSRITARLR 284


>gi|256787303|ref|ZP_05525734.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 308

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 119/240 (49%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 73  LEEGTHEHAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRG 132

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A
Sbjct: 133 VEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTVSELA 192

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           + L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 193 EHLGLSKDEVVEGMAASNAYTASSLDAQ-PEEDDAEGALADRIGYE------DHGLEGIE 245

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L  R+ ++L +RF  GM    T  E+G++  +++  + ++ ++ + +L+
Sbjct: 246 YVESLKPLIAELPSRDRKILSLRFVAGM----TQSEIGEELGISQMHVSRLLSRTLVRLR 301


>gi|21221509|ref|NP_627288.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289771198|ref|ZP_06530576.1| SigI protein [Streptomyces lividans TK24]
 gi|5911753|emb|CAB55836.1| SigI protein [Streptomyces coelicolor A3(2)]
 gi|7672251|emb|CAB89440.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701397|gb|EFD68826.1| SigI protein [Streptomyces lividans TK24]
          Length = 304

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 119/240 (49%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G
Sbjct: 69  LEEGTHEHAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRG 128

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A
Sbjct: 129 VEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTVSELA 188

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           + L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 189 EHLGLSKDEVVEGMAASNAYTASSLDAQ-PEEDDAEGALADRIGYE------DHGLEGIE 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A L  R+ ++L +RF  GM    T  E+G++  +++  + ++ ++ + +L+
Sbjct: 242 YVESLKPLIAELPSRDRKILSLRFVAGM----TQSEIGEELGISQMHVSRLLSRTLVRLR 297


>gi|238759635|ref|ZP_04620796.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
 gi|238702178|gb|EEP94734.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
          Length = 285

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 123/235 (52%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETT 613
            VR++  +++ + ++ +    DE  D   +   +  ++  S     I+     ++  +  
Sbjct: 167 DVREMESRMSAQDMTFDPSPDDEARDGHSMAPVLYLQDKSSDFADGIEEDNWDSHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 227 SYAMEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|27904539|ref|NP_777665.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340406|sp|Q89B27|RP32_BUCBP RecName: Full=RNA polymerase sigma-32 factor
 gi|27903936|gb|AAO26770.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
          Length = 287

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI V++ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 50  AAKTLILSHLRFVIHVSRNYSGYGLLQADLIQEGNIGLMKAVRRFNPKIGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   E +A++L +  E
Sbjct: 110 IKSEIHEYVLRNWRIVKVATTKSQRKLFFNLRKTKQRLGWFNDHE--LELVAQELGVKRE 167

Query: 562 GVRKV-LKITKEPISLE---------------TPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            VR++  +++ + I+L                 P   +  S   + +E+ N         
Sbjct: 168 DVREMESRMSAQDIALHHVPDNFREEQNFSYTIPYLKDSLSDFANHVEEDNW-------- 219

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +A+     +  L+SL  R   ++  R+    +   TL E+   + ++ ER+RQ+E  A++
Sbjct: 220 EAHKTNKLSNALSSLDERSRNIIHARWLDDSDHKMTLREIAHNYGISAERVRQLEKNAMK 279

Query: 666 KLK 668
           KLK
Sbjct: 280 KLK 282


>gi|225026956|ref|ZP_03716148.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
 gi|224955721|gb|EEG36930.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
          Length = 275

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 81/133 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++EANL   + +AK+Y  RGL   DLIQEGNIGLM A  +F+  +   F  ++   
Sbjct: 138 ARNLLIEANLSRAVEIAKEYEGRGLLLSDLIQEGNIGLMVAVNEFEPDIDKDFHAFSEKM 197

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++ +  ++ + + + R  V M ++++++   A   + + +RE  P EIA+++ +  E V
Sbjct: 198 IRKHLEETLEEYNSSTRSAVKMANRVNEMNDIATAFAKEYEREAKPSEIAERMGITEEEV 257

Query: 564 RKVLKITKEPISL 576
           R+++K++ + I++
Sbjct: 258 RELMKVSLDAIAV 270


>gi|325662347|ref|ZP_08150956.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471349|gb|EGC74572.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 234

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/154 (33%), Positives = 86/154 (55%), Gaps = 3/154 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++  ++ NLRLV+SV K++ +      DL Q G +GLMKA + F+  L  KFSTYA+  
Sbjct: 38  ARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCVGLMKAIDNFNTDLQVKFSTYAVPM 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D + +IR+   +RD  +K +        +  +EPT EEIA+++ +  E +
Sbjct: 98  IIGEIRRYLRDNN-SIRVSRSLRDTAYKAIYAKEGYMKRHLKEPTVEEIAEEIGIAKEDI 156

Query: 564 RKVLKITKEPISLETPIGDE--DTSHLGDFIEDK 595
              L   + P+SL  P+ ++  D  ++ D I DK
Sbjct: 157 IFALDAIQAPMSLNEPVYNDSGDALYVMDQISDK 190


>gi|331269204|ref|YP_004395696.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329125754|gb|AEB75699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 252

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 118/226 (52%), Gaps = 16/226 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V+ NL LV +++KK+ NRG ++ D+ Q G++GL+KA   FD     +FSTYA+  +  
Sbjct: 34  QLVQKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDSSYNVQFSTYAVPMIMG 93

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R I D    I++   ++    K+     +++ ++ REP+ EE++K   +  E +   
Sbjct: 94  EIKRFIRDDGL-IKVSRSVKYTAKKLHYDKEKLTKQLNREPSIEELSKFSGISKEEIIFS 152

Query: 567 LKITKEPISLETPIGDEDTS--HLGD--FIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            +   EP  L   I  +D S  +L D   ++DK  +  LD   +  L+E     L+ L  
Sbjct: 153 SEAINEPKYLYDTIHQDDGSPIYLIDKVVVDDKGEIDELD---KIALKEA----LSKLDQ 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R  +++ +R+      D T  +V K   +++ ++ +IE K ++ +K
Sbjct: 206 RSRQIIILRYF----KDITQVKVAKMLGISQVQVSRIEKKVLKSMK 247


>gi|253580606|ref|ZP_04857870.1| RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847977|gb|EES75943.1| RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 237

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 126/242 (52%), Gaps = 12/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++ K +     A+  + + N  LV S+AK++  R ++  D++Q G+IGL+KA ++F
Sbjct: 3   HTLALIMKSQQGDKEARDTVFKENAGLVYSMAKRFAGRSVEMEDIVQIGSIGLLKAIDRF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++  ++++   ++      +  ++ REP 
Sbjct: 63  DISYDVKFSTYAVPMIIGEIRRYLRDDGM-LKVSRNLKENCARIYSAREALEKELGREPI 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            EE+AK   + V+ V   ++   E  SL   I  GD +   L D +++K   +  D+A+ 
Sbjct: 122 LEEVAKATELSVDEVVMSMESGAEVESLHKIIYQGDGNDISLMDRLQEKE--NGQDAALN 179

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     +L  L  RE +++ MR+      D T  E+  +  +++ ++ ++E + +++
Sbjct: 180 ---RIFLDEILKKLDARERQLIGMRY----FKDMTQTEIAAEMGISQVQVSRMEKRILKE 232

Query: 667 LK 668
           LK
Sbjct: 233 LK 234


>gi|326318574|ref|YP_004236246.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375410|gb|ADX47679.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 313

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 118/250 (47%), Gaps = 28/250 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV ++LRLV+S+A++Y   GL   DLIQEGN+GLMKA ++FD     +  +YAM W
Sbjct: 60  AAGRMVMSHLRLVVSIARQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-----------REPTPEE- 551
           +K  I   I      +++      +  K+    R M    K           RE   E+ 
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKSQR--KLFFNLRSMKQGFKADSAAGNTGTHRETLSEQE 177

Query: 552 ---IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +A++L +  E V ++  +++   + L+    D+     G      +      + I++
Sbjct: 178 IDVVAQQLNVKREEVIEMETRLSGGDVMLDPAPSDDGEQAYGPIAYLADGTHEPTAMIES 237

Query: 608 NLRET-----TTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQ 658
             R+          LA+L  R  R++  R+ + +N D     TL E+   + V+ ERIRQ
Sbjct: 238 RQRDVLATDGIANALATLDDRSRRIVEERW-LKVNDDGSGGMTLHELAAVYGVSAERIRQ 296

Query: 659 IEAKAIRKLK 668
           IE  A++K+K
Sbjct: 297 IEVAAMKKMK 306


>gi|90023234|ref|YP_529061.1| RNA polymerase factor sigma-32 [Saccharophagus degradans 2-40]
 gi|89952834|gb|ABD82849.1| CheW protein [Saccharophagus degradans 2-40]
          Length = 284

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 122/235 (51%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W
Sbjct: 50  AARKMVMAHLRFVVHIAKSYSGYGLSQSDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   I      ++I      R     +    +R++     E   E +A+ L + V+
Sbjct: 110 IKAEIHEFILRNWRIVKIATTKAQRKLFFNLRGQKKRLAWLTNSE--AEAVAQDLNVDVK 167

Query: 562 GVRKV-LKITKEPISLETPIG-DEDTSHL--GDFIEDKNA-VSPL--DSAIQANLRETTT 614
            VR++  ++     + +     D+DT++    +++ED+    S L  D     N     T
Sbjct: 168 HVREMEGRLASFDATFDAGADEDDDTAYQAPANYLEDRRYDPSTLLEDEDWTENSVSGLT 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L SL  R   +L+ R+   ++ D  TL ++  Q+ V+ ERIRQ+E  A++K+K
Sbjct: 228 TALESLDDRSRDILQQRW---LSDDKSTLHDLAAQYGVSAERIRQLEKNAMKKVK 279


>gi|126642303|ref|YP_001085287.1| EsvH [Acinetobacter baumannii ATCC 17978]
          Length = 233

 Score = 83.2 bits (204), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 118/231 (51%), Gaps = 15/231 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  
Sbjct: 2   LVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAE 61

Query: 508 ITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           I   +      ++I     + K+   +R+ ++ S K+  E   + IA  L +  E V ++
Sbjct: 62  IHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEA-QSIANDLNVTPEQVLEM 120

Query: 567 -LKITKEPISLETPI-GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA---- 618
             ++T    + E     D+DT H     ++ED N   P       +  E +T  L     
Sbjct: 121 EGRLTAYDAAFEAQGDDDDDTPHTAPVLYLED-NRYDPARLVENEDWEEQSTSALHDAMN 179

Query: 619 SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 180 QLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 227


>gi|167507895|gb|ABZ81268.1| RpoD [Thalassospira profundimaris]
          Length = 262

 Score = 83.2 bits (204), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 87/157 (55%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   + IA+ Y +L   Q+    A+N  +   ++ + +   LK ++V
Sbjct: 106 SLSKMEEELTEQVLEKFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMV 165

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 166 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPN 225

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+      P   WK FV    + I  +R  I  +S E
Sbjct: 226 WMERVGGLPGKGWKTFVERYSEEIASLREGIGGVSAE 262


>gi|120600694|ref|YP_965268.1| RNA polymerase factor sigma-32 [Shewanella sp. W3-18-1]
 gi|146291400|ref|YP_001181824.1| RNA polymerase factor sigma-32 [Shewanella putrefaciens CN-32]
 gi|120560787|gb|ABM26714.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. W3-18-1]
 gi|145563090|gb|ABP74025.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           CN-32]
 gi|319428373|gb|ADV56447.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           200]
          Length = 285

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 122/235 (51%), Gaps = 16/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R A++       E     +A+ L +    
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNIRKAKKRLGWFSDEEVT-MVAENLGVSKAD 170

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RVL 617
           V ++   +        L +   DE       ++ED +  S L   I+ +  E+    R+L
Sbjct: 171 VTEMESRMAAQDPAFDLTSDNDDEQDFAPVHYLEDHS--SDLAENIENDNWESNAQGRLL 228

Query: 618 ASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++   +ER   +LR R+   ++ D  TL+E+ + + V+ ERIRQ+E  A+ KLK
Sbjct: 229 SAIKTLDERSQHILRARW---LDDDKTTLQELAETYQVSAERIRQLEKNAMNKLK 280


>gi|109900247|ref|YP_663502.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
 gi|109702528|gb|ABG42448.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
          Length = 289

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 123/235 (52%), Gaps = 14/235 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A ++++ ++LR V+ +AK Y+  GL   DLIQEGNIGLMKA  +FD  +G +  ++A+ 
Sbjct: 56  LAARKLIMSHLRFVVHIAKSYSGYGLPQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVH 115

Query: 503 WVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           W+K  I   +      +++      R     + +  +R+      E   +++A  L +  
Sbjct: 116 WIKAEIHEFVLRNWRIVKVATTKAQRKLFFNLRKNKKRLGWFTHAE--VQKVASDLGVSE 173

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V ++  +++    + +    D+++       F+EDK+A    D  + A+   T ++ L
Sbjct: 174 KEVLQMEARMSSHDQAFDLSADDDESGSFAPVQFLEDKSADVETD-VVNADWDATASQKL 232

Query: 618 AS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            S    L  R + +++ R+     T  TL+++  ++ V+ ER+RQIE  A++KL+
Sbjct: 233 YSAIKTLDERSQHIIQTRWLSDDKT--TLQDLADKYQVSAERVRQIEKNAMKKLQ 285


>gi|149923127|ref|ZP_01911542.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
 gi|149816035|gb|EDM75549.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
          Length = 304

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 110/234 (47%), Gaps = 16/234 (6%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A + ++EA+LR V+++A+ Y N G    +L+ EGN+GL++A E FD   G +F TY  +
Sbjct: 52  LAGQRLIEAHLRDVVAIARGYRNYGHPMAELVAEGNVGLVRALESFDPERGLRFMTYGRY 111

Query: 503 WVKQAITRSIADQSCTIRI---PVHMR--DKIHKVVRTARRMSNKIKREPTPEE--IAKK 555
           WV+  I   +      +R+     H R    +H+     R  +   +R+   E   +A+ 
Sbjct: 112 WVRARILAHVQRSWSLVRVGSSSAHTRLFYGLHRA--RGRFQATAGERDGAAERAALAEY 169

Query: 556 LAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
                  V  +  +I    +SL+ P      S      E     +  +  +   +RE   
Sbjct: 170 FGCSEAHVEAMAARIDGRDLSLDHPSSAALVS------ESTVEATIFEREVGELVRERIA 223

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            V+  L PRE  +LR R      +  +L EVG++  ++RER RQ+E +   KL+
Sbjct: 224 AVIRELDPRERVILRRRLLDESGSPPSLVEVGRELGLSRERTRQLEQRVKTKLR 277


>gi|315648111|ref|ZP_07901212.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
 gi|315276757|gb|EFU40100.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
          Length = 262

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 115/230 (50%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AKK+++E +L +V  V+ +      + +   DL   G +GL+ A EKFD+  G +F TYA
Sbjct: 26  AKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLASNGVMGLIDAIEKFDYKRGLQFETYA 85

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            W V+ AI  S+        +P  +R+K  ++    +++  K  R  +  E++  L +  
Sbjct: 86  SWRVRGAILDSLRQGDW---VPRSVREKAKRIETAYQQLEQKYLRSVSDSEMSDYLDVTE 142

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  R +L+        SLE PI +E++      + D+ A +P     +  LRE   + + 
Sbjct: 143 KEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNPDHKVHEFYLREALMKGIG 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTP+E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 203 KLTPKERTVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|49474699|ref|YP_032741.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49240203|emb|CAF26671.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 303

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 121/245 (49%), Gaps = 31/245 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           ++ +I   I      +R         +  ++R    K+V+      N + ++     IA+
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLVQD----DNALTKQDIFRTIAE 171

Query: 555 KLAMPVEGVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +L + V  V     +            +   D   + +   ++D    SPL  A+   + 
Sbjct: 172 RLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPIAKMDALVDD----SPLPDALIEQVI 227

Query: 611 ETTTRV------LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKA 663
           ++  R       L SL  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A
Sbjct: 228 DSQRRTQWLHDALQSLNERELEIIRFR---RLNEEGATLEVLGEKLGISKERVRQIEARA 284

Query: 664 IRKLK 668
           ++KL+
Sbjct: 285 LQKLR 289


>gi|325660705|ref|ZP_08149334.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331085570|ref|ZP_08334654.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325473012|gb|EGC76221.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330407457|gb|EGG86959.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 240

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++++       A++++VE N  LV  + K++  RG    DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIQRSHDGDEKAREQLVEENTGLVWCIVKRFFGRGTDSEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      R+  K  REPT
Sbjct: 63  DLNYDVKFSTYAVPMISGEIRRFLRDDGM-IKVSRSLKETAYKAFLARERLQKKYNREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A +L +  E +   L  + E  SL  PI  +D    G+ I+  + +   +   +  
Sbjct: 122 MEELAAELEVEKEELAMALDASGEVESLHKPIYQKD----GNEIQLLDKLEEEEGQEETI 177

Query: 609 LRETTTRVLASLTPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L     R L     REER ++ +R+      + T  E+GK+  +++ ++ ++E K ++ +
Sbjct: 178 LNHMLIRQLLEELDREERQLIYLRY----FANQTQSEIGKKLGISQVQVSRLEKKILKNM 233

Query: 668 K 668
           +
Sbjct: 234 R 234


>gi|222112015|ref|YP_002554279.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax ebreus TPSY]
 gi|221731459|gb|ACM34279.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax ebreus TPSY]
          Length = 311

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 119/248 (47%), Gaps = 26/248 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGRLVLSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK---------REPTPEE--- 551
           +K  I   I      +++      +  K+    R M    K         RE   +    
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADALDADTHRETLSDHEID 177

Query: 552 -IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +A++L +  E V ++  +++   + L+    D+     G      +A     + I++  
Sbjct: 178 LVAEQLNVKREEVIEMETRLSGGDVLLDPAPSDDGEQAFGPIAYLADAGHEPTAMIESRQ 237

Query: 610 RET-----TTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIE 660
           R+          L SL  R  R++  R+ + +N D     TL E+  ++ V+ ERIRQIE
Sbjct: 238 RDALATDGIATALDSLDARSRRIVEQRW-LQVNDDGSGGMTLHELAAEYGVSAERIRQIE 296

Query: 661 AKAIRKLK 668
             A++K+K
Sbjct: 297 VAAMKKMK 304


>gi|332969043|gb|EGK08083.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Kingella kingae
           ATCC 23330]
          Length = 287

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 86/302 (28%), Positives = 144/302 (47%), Gaps = 44/302 (14%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +++A   P G         ++  +   N I  +S+E  + ++E R I     KG+ EA+ 
Sbjct: 1   MNFALPIPSGH------GSLEQYIHTVNNIPMLSLEEEVGLAE-RQI-----KGDLEAA- 47

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
             K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +  ++A+ W
Sbjct: 48  --KKLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPNHGARLFSFAVHW 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV 560
           +K  I   I      +R+      +  K+    R M + +    +P+E   IA  L + +
Sbjct: 106 IKAEIHEFILRNWRLVRVATTKPQR--KLFFNLRSMRSSLS-ALSPKEAQSIADDLGVKL 162

Query: 561 EGVRKV-LKITKEPISL-----------ETPI-GDEDTSH-LGDFIEDKNAVSPLDSAIQ 606
             V ++  ++T   I L             PI    D SH     +E K   +     +Q
Sbjct: 163 SEVMEMEQRMTGRDIGLLADNNDDDDAAFAPIEWLSDASHEPSQQLERKAHYALQTDGLQ 222

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A         LA L  R  R++  R+ +      TL E+  ++ V+ ERIRQIE KA++K
Sbjct: 223 A--------ALAQLDERSRRIVETRW-LQDEGALTLHELAAEYGVSAERIRQIEVKAMQK 273

Query: 667 LK 668
           LK
Sbjct: 274 LK 275


>gi|289578314|ref|YP_003476941.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544594|ref|YP_003676896.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528027|gb|ADD02379.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842369|gb|ADH60885.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 120/239 (50%), Gaps = 12/239 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++R  +     + ++++  N  L+ S+ KK++NRG +  DL Q G +G +KA +KFD 
Sbjct: 13  LTLIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCMGFVKAVQKFDE 72

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               K STYA+  +   I R + D    I++   +++   K       +S+++ REPT  
Sbjct: 73  SYNVKLSTYAVPIIMGEIKRFLRDDGL-IKVSRSLKELSTKAFYLKEVLSSELNREPTIN 131

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA++L +  E V    +      SL +    DED   L + + ++     +D  +   +
Sbjct: 132 EIAERLKVSPEEVAMAFESAATAESLYDNATHDEDDRLLIEMVSEEEKEVDIDDKLALQM 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 V+  L PRE++++ +R+      D T  E+     +++ ++ +IE K ++KL+
Sbjct: 192 ------VINKLKPREKQIIFLRYF----KDMTQMEIASILGISQVQVSRIEKKVLQKLR 240


>gi|332529979|ref|ZP_08405929.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
 gi|332040452|gb|EGI76828.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
          Length = 326

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 126/255 (49%), Gaps = 31/255 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV++ A++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W
Sbjct: 66  AAGKLVLSHLRLVVATARQYMGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHW 125

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARR---------------MSNKIKREP 547
           +K  I   I      +++     + K+   +R+ ++               +     RE 
Sbjct: 126 IKAEIHEYILKNWRMVKVATTKAQRKLFFNLRSKKQGYKAASAADSSLHDGLDAATHRET 185

Query: 548 TPE----EIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             E    ++A++L +  E V ++  +++   + L+   G++     G      +A     
Sbjct: 186 LSEHEIDQMARELNVKREEVIEMETRLSGGDVMLDPGPGEDGEDSFGPIAYLTDAGHEPT 245

Query: 603 SAIQANLR-----ETTTRVLASLTPREERVLRMRFGIGMNTDH----TLEEVGKQFCVTR 653
           + I+A  R     +   + L +L PR  R++  R+ + +N D     TL E+  ++ V+ 
Sbjct: 246 AMIEARQRDRLATDGIAKALDALDPRSRRIVEERW-LKVNDDASGGMTLHELAAEYGVSA 304

Query: 654 ERIRQIEAKAIRKLK 668
           ERIRQIE  A++K+K
Sbjct: 305 ERIRQIEVAAMKKMK 319


>gi|254412979|ref|ZP_05026751.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196180143|gb|EDX75135.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/156 (30%), Positives = 89/156 (57%), Gaps = 5/156 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            + ++V  N+ LV   A  + N+  + + DL+Q G +GL++A E+F    G  FS++A+ 
Sbjct: 30  TRNQLVYLNIGLVRREAHYWVNQCTESYEDLLQVGCLGLIRAIERFAPSKGNAFSSFAIP 89

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +++  I   + D+   IRIP        + +   R++  ++ R+PT  E+A+ L +P+  
Sbjct: 90  YIRGEIQHYLRDRGGCIRIPRRWLALQQQSIAIIRQLRAQLNRQPTDAEVAEALEIPLAE 149

Query: 563 VR--KVLKITKEPISLETPIGDED--TSHLGDFIED 594
            +  K+    +EP+SL+TP+GDE+  T+ LGD + D
Sbjct: 150 WQEIKLAHQNREPLSLDTPVGDEEDGTTSLGDIVPD 185


>gi|114776576|ref|ZP_01451621.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114553406|gb|EAU55804.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 281

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 128/249 (51%), Gaps = 26/249 (10%)

Query: 432 SMVRKGECEASIAK-KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ RK + +  +A  ++++ ANL +V ++A++Y + GL   DLIQEG +GLM+A ++FD 
Sbjct: 33  ALARKWQRDHDLASVQQLINANLHVVAAIAREYRHFGLPEEDLIQEGTLGLMQAVKRFDP 92

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++  TYA +W++ +I   I      +++  +         +  RR+   +++     
Sbjct: 93  DRGFRLKTYAAYWIRASIHDFILRSWSIVKMGTN---------KLQRRIFAGLQKAECA- 142

Query: 551 EIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQ 606
            IA      +EGV     ++ E    +       D S   D  ED N +   +P D+  Q
Sbjct: 143 -IAALEGRGLEGVASQYGVSGESYQQIAASFLRRDYSIDSDATEDGNIIELPAPGDTPEQ 201

Query: 607 A----NLRETTT----RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           A    + +  TT    + + +L+ R+  ++R R+ +      TL+E+ +   ++ ER+RQ
Sbjct: 202 ALVAKDWQSFTTMQLKQAMEALSERDRNIIRQRYLV--EPPSTLKELSEDLGISIERVRQ 259

Query: 659 IEAKAIRKL 667
           +EA+A++K+
Sbjct: 260 LEARAMKKI 268


>gi|325983562|ref|YP_004295964.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
 gi|325533081|gb|ADZ27802.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
          Length = 281

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 125/240 (52%), Gaps = 14/240 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   ++++ ++LR V+++A+ Y   GL   DLIQEGNIGLMKA ++FD   G +
Sbjct: 42  RGDIEAA---QQLIMSHLRFVVAIARGYKGYGLPQADLIQEGNIGLMKAVKRFDPERGVR 98

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI--- 552
             ++A+ W+K  I   I      ++I    + +  K+    R M + +     P+E+   
Sbjct: 99  LVSFAVHWIKAEIHEFIMRNWRLVKIATTKQQR--KLFFNLRSMKHGLD-TMNPQEVDAM 155

Query: 553 AKKLAMPVEGVRKVLK-ITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQ-ANL 609
           A +L +  E V ++ K      ISLE    DE DT    +++ D    S L    Q  +L
Sbjct: 156 AAQLGVKAEEVIEMEKRFNGSDISLEPVSEDEDDTFSPINYLTDGTEPSQLLEKEQITHL 215

Query: 610 RET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE    + L  L  R   ++  R+    +T  TL ++  +  V+ ER+RQIE KA++K++
Sbjct: 216 REKGLQKSLDCLDKRSRHIIEARWLREKDTA-TLHDLADELGVSAERVRQIEVKALQKMR 274


>gi|302556259|ref|ZP_07308601.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302473877|gb|EFL36970.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 281

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/258 (23%), Positives = 134/258 (51%), Gaps = 34/258 (13%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKA 484
           +F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA
Sbjct: 36  QFFDRLAVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKA 95

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++FD     +F+++A+ ++   I R   D +  + +P  +++   ++ R    + +++ 
Sbjct: 96  IDRFDLSREAEFTSFAVPYIVGEIKRFFRDTTWAVHVPRRLQEARVQLARATEELRSRLG 155

Query: 545 REPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPI--GDEDTSHLGDFI-------- 592
           R PT +E+++ +++P + VR  ++        SL+  I   D+  + L DFI        
Sbjct: 156 RTPTVKELSELMSLPEQEVREARIAANGYNSSSLDATISGSDDGEAALQDFIGAEDQAME 215

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             ED +A++PL               LA L  R+  ++RMRF      + T  ++G++  
Sbjct: 216 LVEDFHALAPL---------------LAELDERDRHIIRMRF----VEELTQAQIGERLG 256

Query: 651 VTRERIRQIEAKAIRKLK 668
           V++ ++ ++ ++ + +L+
Sbjct: 257 VSQMQVSRLLSRTLARLR 274


>gi|297194001|ref|ZP_06911399.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152057|gb|EFH31507.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 305

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 113/240 (47%), Gaps = 33/240 (13%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + F  + S+  +G  E +  +  +VE NL LV   A ++  R     D+IQ G IGL
Sbjct: 59  LSKTLFARLASL-EEGTHEYAYVRNTLVELNLALVKFAASRFRTRSEPMEDIIQVGTIGL 117

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    +S 
Sbjct: 118 IKAIDRFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQ 177

Query: 542 KIKREPTPEEIAKKLAMP----VEGVRKVLKITKEPI-----------SLETPIGDEDTS 586
           ++ R PT +E+A++L +     VEG+      T   +           +L   IG ED  
Sbjct: 178 QLDRAPTVDELAQRLDIGRDEVVEGMAASNAYTASSLDAQPEEDDSEGALANRIGYED-- 235

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           H  + IE   ++ P+               +ASL PR+ ++L +RF   M      EE+G
Sbjct: 236 HGLEGIEYIESLRPM---------------IASLPPRDRKILSLRFVANMTQSEIGEELG 280


>gi|303304828|emb|CBL59288.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304830|emb|CBL59289.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304832|emb|CBL59290.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304834|emb|CBL59291.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304836|emb|CBL59292.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304838|emb|CBL59293.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304840|emb|CBL59294.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304842|emb|CBL59295.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304844|emb|CBL59296.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304846|emb|CBL59297.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304848|emb|CBL59298.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304850|emb|CBL59299.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
          Length = 246

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 51/132 (38%), Positives = 80/132 (60%), Gaps = 4/132 (3%)

Query: 58  VSSEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +       D+ 
Sbjct: 1   VDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAAALTALDTE 60

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 61  GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 120

Query: 174 LNDGTTLLREII 185
             +G   L EI+
Sbjct: 121 HKEGKKRLAEIV 132


>gi|120612533|ref|YP_972211.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax citrulli AAC00-1]
 gi|120590997|gb|ABM34437.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax citrulli
           AAC00-1]
          Length = 313

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 119/250 (47%), Gaps = 28/250 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   MV ++LRLV+S+A++Y   GL   DLIQEGN+GLMKA ++FD     +  +YAM W
Sbjct: 60  AAGRMVMSHLRLVVSIARQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-----------REPTPEE- 551
           +K  I   I      +++      +  K+    R M    K           RE   E+ 
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKSQR--KLFFNLRSMKQGFKADAAAGDAGTHRETLSEQE 177

Query: 552 ---IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +A++L +  E V ++  +++   + L+    D+     G      + +    + I++
Sbjct: 178 IDVVAQQLNVKREEVIEMETRLSGGDVMLDPAPSDDGEQAYGPIAYLADGMHEPTAMIES 237

Query: 608 NLRET-----TTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQ 658
             R+          LA+L  R  R++  R+ + +N D     TL E+   + V+ ERIRQ
Sbjct: 238 RQRDVLATDGIANALATLDDRSRRIVEERW-LKVNDDGSGGMTLHELAAVYGVSAERIRQ 296

Query: 659 IEAKAIRKLK 668
           IE  A++K+K
Sbjct: 297 IEVAAMKKMK 306


>gi|71280363|ref|YP_266929.1| RNA polymerase factor sigma-32 [Colwellia psychrerythraea 34H]
 gi|71146103|gb|AAZ26576.1| RNA polymerase sigma-32 factor [Colwellia psychrerythraea 34H]
          Length = 285

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 127/245 (51%), Gaps = 31/245 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E++ ++LR VI VAK Y+  GL   DL+QEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAQELIMSHLRFVIHVAKGYSGYGLPHADLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++    T E   +A+ L +  +
Sbjct: 108 IKAEIHEFVLKNWRIVKVATTKAQR--KLFFNLRKNKKRLGWFSTEEVNTVAENLGVTTK 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLG-------DFIEDKNAVSPLDSAIQ------- 606
            V ++  +++    + E    D+D  +LG        +++DK +    D A++       
Sbjct: 166 DVMEMESRMSSHDQAFELSKDDDD--NLGSSSFSPAQYLQDKQS----DLAVEVENDNWD 219

Query: 607 --ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             AN R +T   L +L  R + +++ R+     T  TL+E+  ++ ++ ER+RQ+E  A+
Sbjct: 220 NHANKRLST--ALVTLDERSQDIIKTRWLTEDKT--TLQELANKYQISAERVRQLEKNAL 275

Query: 665 RKLKH 669
            KLK+
Sbjct: 276 SKLKN 280


>gi|157373363|ref|YP_001471963.1| RNA polymerase factor sigma-32 [Shewanella sediminis HAW-EB3]
 gi|157315737|gb|ABV34835.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sediminis
           HAW-EB3]
          Length = 285

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 124/243 (51%), Gaps = 32/243 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      +++      K  + +    R S K     + EE+          V
Sbjct: 112 IKAEIHEYVLKNWRIVKVAT---TKAQRKLFFNLRKSKKRLGWFSDEEVGM--------V 160

Query: 564 RKVLKITKEPIS-LETPIGDEDTSH-LGDFIEDKNAVSPL--------DSAIQA---NLR 610
              L ++K  ++ +E+ +  +D +  L    +D +  +P+        D A Q    NL 
Sbjct: 161 ADNLGVSKADVTEMESRMAAQDPAFDLASDNDDDHDFAPMHYLEDHSSDLASQVENDNLE 220

Query: 611 ETT-TRVLASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIR 665
            +   R+L+++   +ER   +L+ R+   +N D  TL+E+   + V+ ERIRQ+E  A+ 
Sbjct: 221 ASNQARLLSAIKTLDERSQHILQARW---LNEDKTTLQELAATYQVSAERIRQLEKNAMN 277

Query: 666 KLK 668
           KLK
Sbjct: 278 KLK 280


>gi|315127793|ref|YP_004069796.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
 gi|315016307|gb|ADT69645.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
          Length = 287

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 122/234 (52%), Gaps = 11/234 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVAHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +  +R+    + E +   +A +L +  +
Sbjct: 112 IKAEIHEFVLKNWRIVKVATTKAQRKLFFNLRKNKKRLGWFNQAEVST--VASELGVSEK 169

Query: 562 GVRKV-LKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            VR++  +++ + +  +    D D     T     ++ D +A    D   Q    ++ TR
Sbjct: 170 EVREMESRMSGQDMGFDLTGDDNDDAPTSTYSPVQYLTDGSADLADDIEQQQWQEQSHTR 229

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++L   +ER   +     ++ D  TL+E+ +++ V+ ER+RQ+E  A++KL+
Sbjct: 230 LFSALKTLDERSQDIVSARWLSDDKATLQELAEKYSVSAERVRQLEKTAMKKLQ 283


>gi|312793875|ref|YP_004026798.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181015|gb|ADQ41185.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 120/239 (50%), Gaps = 12/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD   
Sbjct: 9   LISKAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSF 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 69  NVRFSTYAVPMIIGEIKRYLRDDG-KIKVSRKIKENQSKIKKLRNQFVSSNGREPTISEI 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   +  T E  SL   +  E+     L D   D+   S     + A L+
Sbjct: 128 SQLTGLSSDEILLCMDATSEVASLNDVVNQEEGKPITLMDIASDEEDYSTKLLDLMA-LK 186

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E     L  L  RE  ++ MR+      + T  E+ K+  +++  + +IE +A+ ++K 
Sbjct: 187 EG----LKKLKGRERYIIFMRYF----KNKTQSEIAKELNISQVHVSRIEKRALERIKR 237


>gi|328952031|ref|YP_004369365.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452355|gb|AEB08184.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
          Length = 328

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 120/238 (50%), Gaps = 20/238 (8%)

Query: 444 AKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A   ++ +NLRLV+ +A   +K+  R L  LDLIQEGNIGLM+A +KFD   G K S YA
Sbjct: 79  AAYTLITSNLRLVVKIALDFQKFWMRNL--LDLIQEGNIGLMQAIKKFDPYRGIKLSYYA 136

Query: 501 MWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            +W+K  I + I D    ++I     + K+   ++  +        E  P+ I+ +L + 
Sbjct: 137 SFWIKAYILKFIMDNWKLVKIGTTQAQRKLFFSLKKEKERLRAQGYEADPKLISTRLNVK 196

Query: 560 -VEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             E +    ++     SL+ P+  D +  H+      + A    +   +  +++     L
Sbjct: 197 EAEVIEMDQRLGSWEFSLDAPLKSDSEELHINFLTSGETAAD--EHLAREEMKDIFLMRL 254

Query: 618 A----SLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           A    +L   E  +L +R    +  +H  TL+E+G +  ++RER+RQIE + ++KL+ 
Sbjct: 255 AEFRNTLKDNERDILDLR----LLAEHPLTLQEIGARHNISRERVRQIEERLLKKLRQ 308


>gi|225389231|ref|ZP_03758955.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
 gi|225044710|gb|EEG54956.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
          Length = 239

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 53/155 (34%), Positives = 85/155 (54%), Gaps = 3/155 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V  N+ L+ S+ +++  RG +  DL Q G+IGLMKA +KFD     KFSTYA+  
Sbjct: 18  ARDQLVMDNVGLIWSIVRRFAGRGYEMEDLFQIGSIGLMKAIDKFDTTFEVKFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++   KV      M+ ++ REPT EEIA  + +  E V
Sbjct: 78  ITGEIKRFLRDDG-MIKVSRSIKELGLKVKCAREEMTYELGREPTIEEIAGSVGVSREEV 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLG--DFIEDKN 596
              ++   E  SL  P+G  D + L   D +E++N
Sbjct: 137 AASMEAGAEVESLYRPVGGSDDNQLCLMDRLEEEN 171


>gi|30424475|dbj|BAC76410.1| heat shock sigma-32 factor [Colwellia maris]
          Length = 285

 Score = 82.8 bits (203), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 125/243 (51%), Gaps = 27/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E++ ++LR VI VAK Y+  GL   DL+QEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 48  AAQELIMSHLRFVIHVAKGYSGYGLPHADLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHW 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++    T E   +A+ L +  +
Sbjct: 108 IKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKNKKRLGWFSTEEVNTVAENLGVTTK 165

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGDF-----IEDKNAVSPLDSAIQ--------- 606
            V ++  +++    + E    D+D     +F     ++DK +    D A++         
Sbjct: 166 DVMEMESRMSSYDQAFELSKDDDDNLGASNFSPAQYLQDKQS----DLAVEVENDNWDNH 221

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           AN R +T   L +L  R + +++ R+     T  TL+E+  ++ ++ ER+RQ+E  A+ K
Sbjct: 222 ANKRLST--ALVTLDERSQDIIKTRWLTEDKT--TLQELANKYQISAERVRQLEKNALSK 277

Query: 667 LKH 669
           LK+
Sbjct: 278 LKN 280


>gi|332975259|gb|EGK12159.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella kingae
           ATCC 23330]
          Length = 654

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 57/166 (34%), Positives = 88/166 (53%), Gaps = 8/166 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           +++I L ++RGY+T  E+N  LP D   +EQ++  V M+ ++GI V     D D L   +
Sbjct: 32  RRLIMLGKERGYITYAEINDSLPDDMSDAEQIDGIVNMIQSLGIQVTEEAPDADALLMND 91

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S    D  + A   +   Q   DS    T DPVRMY+REMG +ELL+RE EI IAK IE
Sbjct: 92  NSTGITDDDAVAEAEAALSQ--ADSEFGRTTDPVRMYMREMGQVELLTREDEIKIAKEIE 149

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
                M+ ++   P +   ++   +++      + E++  EA I P
Sbjct: 150 NALKNMIQAISACPGSVGEILELIEQIKKDEIRVDEVV--EAIIDP 193


>gi|295836990|ref|ZP_06823923.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
 gi|197697450|gb|EDY44383.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
          Length = 312

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 118/238 (49%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 79  EGTHAHSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 138

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PTP E+A +
Sbjct: 139 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTPSELADR 198

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     +EG+      T   +  + P  D+  S L D +  +      D  ++     
Sbjct: 199 LGIEREEVIEGMAASNAYTASSLDAQ-PEEDDSESALADRLGYE------DHGLEGIEYI 251

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ ++L +RF   M    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 252 ESLKPMIARLPQRDRKILSLRFVANM----TQSEIGEELGISQMHVSRLLSRTLVKLR 305


>gi|121595815|ref|YP_987711.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax sp. JS42]
 gi|120607895|gb|ABM43635.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax sp. JS42]
          Length = 321

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 119/248 (47%), Gaps = 26/248 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 70  AAGRLVLSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 129

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK---------REPTPEE--- 551
           +K  I   I      +++      +  K+    R M    K         RE   +    
Sbjct: 130 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADALDADTHRETLSDHEID 187

Query: 552 -IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +A++L +  E V ++  +++   + L+    D+     G      +A     + I++  
Sbjct: 188 LVAEQLNVKREEVIEMETRLSGGDVLLDPAPSDDGEQAFGPIAYLADAGHEPTALIESRQ 247

Query: 610 RET-----TTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIE 660
           R+          L SL  R  R++  R+ + +N D     TL E+  ++ V+ ERIRQIE
Sbjct: 248 RDALATDGIATALDSLDARSRRIVEQRW-LQVNDDGSGGMTLHELATEYGVSAERIRQIE 306

Query: 661 AKAIRKLK 668
             A++K+K
Sbjct: 307 VAAMKKMK 314


>gi|239934552|emb|CAR94590.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 237

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 44/54 (81%), Gaps = 1/54 (1%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESK 196
           KRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLR+IIDLEA   GP+ K
Sbjct: 8   KRIEAGREAMIAGLCESPLTFQAIIIWRDELNETKILLRDIIDLEATYDGPDKK 61


>gi|312127292|ref|YP_003992166.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311777311|gb|ADQ06797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 120/238 (50%), Gaps = 12/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD   
Sbjct: 9   LISKAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSF 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 69  NVRFSTYAVPMIIGEIKRYLRDDG-KIKVSRKIKENQGKIKKLRNQFVSNHGREPTISEI 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   L  + E  SL   I  E+     L D   D+   S     + A L+
Sbjct: 128 SQLTGLSSDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA-LK 186

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     L  L  RE  ++ MR+      + T  E+ K+  +++  + +IE +A+ ++K
Sbjct: 187 EG----LKKLKGRERYIIFMRYF----KNKTQSEIAKELNISQVHVSRIEKRALERIK 236


>gi|17986661|ref|NP_539295.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|62290526|ref|YP_222319.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700442|ref|YP_415016.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|189024748|ref|YP_001935516.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|225853116|ref|YP_002733349.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|237816032|ref|ZP_04595028.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|254689824|ref|ZP_05153078.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254694316|ref|ZP_05156144.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|254697972|ref|ZP_05159800.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254730858|ref|ZP_05189436.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256045266|ref|ZP_05448160.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114225|ref|ZP_05454970.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|256258077|ref|ZP_05463613.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256263396|ref|ZP_05465928.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|260547226|ref|ZP_05822964.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260565841|ref|ZP_05836324.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260755355|ref|ZP_05867703.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758577|ref|ZP_05870925.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260762409|ref|ZP_05874746.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884371|ref|ZP_05895985.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214622|ref|ZP_05928903.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|265991691|ref|ZP_06104248.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995528|ref|ZP_06108085.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|297248928|ref|ZP_06932636.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|17982279|gb|AAL51559.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
 gi|62196658|gb|AAX74958.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616543|emb|CAJ11621.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|189020320|gb|ACD73042.1| Sigma-70 factor family [Brucella abortus S19]
 gi|225641481|gb|ACO01395.1| alternative sigma factor RpoH [Brucella melitensis ATCC 23457]
 gi|237788695|gb|EEP62907.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|260095591|gb|EEW79469.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260151214|gb|EEW86309.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260668895|gb|EEX55835.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260672835|gb|EEX59656.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675463|gb|EEX62284.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260873899|gb|EEX80968.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916229|gb|EEX83090.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|262766812|gb|EEZ12430.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|263002647|gb|EEZ15050.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263093393|gb|EEZ17462.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|297174061|gb|EFH33418.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|326409662|gb|ADZ66727.1| Sigma-70 factor family [Brucella melitensis M28]
 gi|326539369|gb|ADZ87584.1| alternative sigma factor RpoH [Brucella melitensis M5-90]
          Length = 303

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 114/233 (48%), Gaps = 16/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    R+M +KI+     +  P+   +IA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RE 611
            +  + V  + +      SL  P+   + ++    D++ D +         Q  L   R 
Sbjct: 167 NVSEDEVVSMNRRLSGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRS 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + + +L  RE  +   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 227 MLEQAMETLNDRERHIFEARRLA--EEPMTLEDLSGEFGISRERVRQIEVRAF 277


>gi|239994826|ref|ZP_04715350.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 284

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 144/269 (53%), Gaps = 16/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I+++S    +S  E R +   VR  E E   A +++V ++LR V+ +AK Y+  GL
Sbjct: 18  IEGYIQAVSSIDMLSAEEERELA--VRLREDEDLQAARKLVMSHLRFVVHIAKSYSGYGL 75

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRD 527
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++     + 
Sbjct: 76  PQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQR 135

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R A++       +   + +A +L +  + V ++  +++ +  + +    +++T 
Sbjct: 136 KLFFNLRKAKKRLGWFTHDEV-QTVANELGVSTKEVLQMEARMSSQDQAFDLTADEDETG 194

Query: 587 HLG--DFIEDKNAVSPLDSAIQANLRETTT--RVLASLTPREER---VLRMRFGIGMNTD 639
           +     ++EDK+  S +++ +  N  +T    R+ +++   +ER   ++  R+    +  
Sbjct: 195 NFAPVQYLEDKS--SDVETDVINNDWDTAASKRLYSAIKTLDERSQDIIETRW--LADNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+++  ++ V+ ER+RQIE  A++KL+
Sbjct: 251 ITLQDLADKYQVSAERVRQIEKNAMKKLQ 279


>gi|161505889|ref|YP_001573001.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867236|gb|ABX23859.1| hypothetical protein SARI_04068 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 284

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 142/287 (49%), Gaps = 44/287 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--------------- 566
               + K+   +R A++      ++   E +A++L +  + VR++               
Sbjct: 128 TTKAQRKLFFNLRKAKQRLGWFNQDEV-EMVARELGVSSKDVREMESRMAAQDMTFDMSS 186

Query: 567 -LKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASLT 621
             +   +P++    + D+ +S+  D IED N    A + L  A+Q             L 
Sbjct: 187 DDESDSQPMAPVLYLQDK-SSNFADGIEDDNWEEQAANRLTDAMQ------------GLD 233

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 234 ERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|319409355|emb|CBI82999.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 303

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 121/241 (50%), Gaps = 23/241 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVISIASRFKRFKMPLSDLVQEGYVGLLEAAARFEPDRDVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIR---------IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           ++ +I   I      +R         +  ++R    ++V+    MS    ++     I++
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAQLVQDDSTMS----KQDIFRVISE 171

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLR 610
           KL + V  V  +  + +    SL   + + D    + L   +++K     L   +    R
Sbjct: 172 KLGVSVSDVETMDFRFSGTDNSLSMSVSENDDNSVTKLDTLVDEKPLPDSLIEKVIDGQR 231

Query: 611 ETT--TRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKL 667
            T      L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A++KL
Sbjct: 232 RTQWLYDALQILNERELEIIRFR---RLNEESATLEFLGEKLGISKERVRQIEARALQKL 288

Query: 668 K 668
           +
Sbjct: 289 R 289


>gi|158341591|ref|YP_001522756.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311832|gb|ABW33441.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/263 (28%), Positives = 126/263 (47%), Gaps = 21/263 (7%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-Q 469
           N   S S+ETG    + ++    + + +     A+   +  N RLV + AK+Y  RGL  
Sbjct: 5   NVFNSQSLETGPFSRKVQY--PQIERAQAGDRRAEDRFIRKNQRLVFNEAKRY--RGLVD 60

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMRDK 528
           + DL+  G +GL  A +KFD   G++FSTYA+  ++  I + I +Q    R I  H++  
Sbjct: 61  WDDLVNAGTLGLSIAIQKFDLSRGFQFSTYAVKPIRTEIRQLICEQRGLSREITKHLK-- 118

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTS 586
             K+    + +  +++R+PT +E+A++       +       +  +  SL    G E   
Sbjct: 119 --KIDEAEQDLKLELERKPTLDELAERTGYSHRVITNAWSKARVVDTSSLNVLTGTEQGI 176

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              DF+ED   +   D A   N+++     +A L  RE  ++R R        H+  E+G
Sbjct: 177 ECLDFVEDLEQLDSWDFAESINMKD----YIAQLPDRESFIVRAR-----RDGHSYREIG 227

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               ++ ERIRQ+  KA+  LKH
Sbjct: 228 TMLKLSGERIRQLYQKALEYLKH 250


>gi|29830033|ref|NP_824667.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607143|dbj|BAC71202.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 306

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 117/238 (49%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +
Sbjct: 73  EGTHEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVE 132

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A++
Sbjct: 133 FPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTVSELAER 192

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLR 610
           L +     VEG+      T   +  + P  D+    L D I  +      D  ++     
Sbjct: 193 LGISNGEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE------DHGLEGIEFV 245

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++A L  R+ ++L +RF   M    T  E+G +  +++  + ++ ++ + +L+
Sbjct: 246 ESLKPLIAQLPSRDRKILSLRFVANM----TQSEIGDELGISQMHVSRLLSRTLVRLR 299


>gi|170724574|ref|YP_001758600.1| RNA polymerase factor sigma-32 [Shewanella woodyi ATCC 51908]
 gi|169809921|gb|ACA84505.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella woodyi ATCC
           51908]
          Length = 283

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 119/243 (48%), Gaps = 32/243 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 50  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      +++      K  + +    R S K     + EE+          V
Sbjct: 110 IKAEIHEYVLKNWRIVKVAT---TKAQRKLFFNLRKSKKRLGWFSDEEVGM--------V 158

Query: 564 RKVLKITKEPIS-LETPIGDEDTSH-LGDFIEDKNAVSPL---------------DSAIQ 606
              L ++K  ++ +E+ +  +D +  L    +D    SP+               +  ++
Sbjct: 159 ADNLGVSKADVTEMESRMAAQDPAFDLASDNDDDQDFSPVHYLEDHSSDLASQVENDNLE 218

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIR 665
           +N +      + +L  R + +L+ R+   +N D  TL+E+   + V+ ERIRQ+E  A+ 
Sbjct: 219 SNNQARLLSAIKTLDERSQHILQARW---LNEDKTTLQELAATYQVSAERIRQLEKNAMN 275

Query: 666 KLK 668
           KLK
Sbjct: 276 KLK 278


>gi|21672319|ref|NP_660386.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|25091196|sp|Q8KA76|RP32_BUCAP RecName: Full=RNA polymerase sigma-32 factor
 gi|21622919|gb|AAM67597.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 285

 Score = 82.4 bits (202), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 124/235 (52%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI +++ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKTLILSHLRFVIHISRNYSGYGLLQADLIQEGNIGLMKAVRRFNPDIGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R  ++      +E   E +A++L +  E 
Sbjct: 109 IKSEIHEYVLRNWRIVKVATTKSQRKLFFNLRKNKKRLGWFNQEEI-EIVARELGVSSED 167

Query: 563 VRKV-LKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI-QANLRETTTRVL 617
           VR++  +++ + I+   P  +ED       G+    ++  S   + + Q N  + TT  L
Sbjct: 168 VREMESRMSAQDITF-NPFPEEDLKDGKINGNMFYLQDKTSNFANGLEQDNWNKHTTSKL 226

Query: 618 AS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++    L  R   ++R R+ +     +TL+++   + ++ ER+RQ+E  A++KLK
Sbjct: 227 SNALLRLDERSRNIIRARW-LDKKEKNTLQKIANNYGISAERVRQLEKNAMKKLK 280


>gi|158341383|ref|YP_001522549.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311624|gb|ABW33234.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score = 82.4 bits (202), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 74/263 (28%), Positives = 125/263 (47%), Gaps = 21/263 (7%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-Q 469
           N   S S+ETG    + ++    + + +     A+   +  N RLV   AK+Y  RGL  
Sbjct: 5   NVFNSQSLETGPFSRKVQY--PQIERAQAGDRRAEDRFIRKNQRLVFKEAKRY--RGLVD 60

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMRDK 528
           + DL+  G +GL  A +KFD   G++FSTYA+  ++  I + I +Q    R I  H++  
Sbjct: 61  WDDLVNAGTLGLSIAIQKFDLSRGFQFSTYAVKPIRTEIRQLICEQRGLSREITKHLK-- 118

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTS 586
             K+    + +  +++R+PT +E+A++       +       +  +  SL    G E   
Sbjct: 119 --KIDEAEQDLELELERKPTLDELAERTGYSHRVITNAWNKARVVDTSSLNVLTGTEQGI 176

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              DF+ED   +   D A   N+++     +A L  RE  ++R R        H+  E+G
Sbjct: 177 ECLDFVEDFEQLDSWDFAESINMKD----YIAQLPDRESFIVRAR-----RDGHSYREIG 227

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               ++ ERIRQ+  KA+  LKH
Sbjct: 228 TMLKLSGERIRQLYQKALEYLKH 250


>gi|4102217|gb|AAD11814.1| sigma-like factor [Streptomyces sp. A21]
          Length = 343

 Score = 82.4 bits (202), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/252 (25%), Positives = 125/252 (49%), Gaps = 40/252 (15%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           +G  +   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA ++FD     
Sbjct: 106 EGTHDYQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREV 165

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+T+A+ ++   I R   D + ++ +P  +++   ++ +    +S  + R+PT  E+A 
Sbjct: 166 EFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVELAKAKEALSADLDRDPTVAELAA 225

Query: 555 KLAMP----VEGVRKVLKITKEPISLETPIGDEDTSH--------LG------DFIEDKN 596
           +L +     +EG+  V        SL+TP  D ++ +        LG      + +E+ +
Sbjct: 226 RLDLSEEEIIEGL--VAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGMESVENLH 283

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A++PL               L  L  RE  ++RMRFG  M    T  ++G +  V++  +
Sbjct: 284 ALAPL---------------LRQLDDRERAIVRMRFGQEM----TQAQIGAELGVSQMHV 324

Query: 657 RQIEAKAIRKLK 668
            ++ ++ +R+L+
Sbjct: 325 SRLLSRIVRRLR 336


>gi|254283645|ref|ZP_04958613.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
 gi|219679848|gb|EED36197.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
          Length = 291

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 119/242 (49%), Gaps = 17/242 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GEC AS   +E+V A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G + 
Sbjct: 52  GECVAS--ARELVLAHLRFVVHIARSYSGYGLAEADLIQEGNVGLMKAVKRFDPNKGVRL 109

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  +   I      +++     + K+   +R+A++  + +    T + IA+ 
Sbjct: 110 VSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKLFFNLRSAKKNLSWLTHSET-QAIAED 168

Query: 556 LAMPVEGVRKV--------LKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQ 606
           L +P   V+++        +       + +         +L D   D   AV   +S+  
Sbjct: 169 LGVPEAEVQRMEGRLSCRDMAFDAPSDADDDDAWQAPQHYLQDLSSDPAVAVEAANSSAD 228

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R      LA L  R + +L  R+        TL E+  +  V+ ERIRQ+EA A++K
Sbjct: 229 DETRLHAA--LAQLDARSQDILARRW--LAEKKATLHELAAEHGVSAERIRQLEANAMKK 284

Query: 667 LK 668
           L+
Sbjct: 285 LR 286


>gi|241764416|ref|ZP_04762441.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
 gi|241366206|gb|EER60777.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
          Length = 312

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 115/255 (45%), Gaps = 39/255 (15%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S+A++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGRLVMSHLRLVVSIARQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---V 560
           +K  I   I      +++      +  K+    R M    K +   +    +  +    +
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADAAVDAATHRDTLSEQEI 177

Query: 561 EGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIED-------KNAVSPLDSAIQANLRET 612
           + V   L + +E  I +ET +        GD + D       + A  P+     A+   T
Sbjct: 178 DAVATQLNVKREEVIEMETRMAG------GDVLLDPAPSDDGEQAFGPIGYLADASHEPT 231

Query: 613 T---------------TRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTR 653
                              LA L  R  R++  R+ + +N D     TL E+   + V+ 
Sbjct: 232 AMIESRQRDALATDGIAMALARLDDRSRRIVEERW-LKVNDDGTGGMTLHELAAVYGVSA 290

Query: 654 ERIRQIEAKAIRKLK 668
           ERIRQIE  A++K+K
Sbjct: 291 ERIRQIEVAAMKKMK 305


>gi|83643468|ref|YP_431903.1| RNA polymerase factor sigma-32 [Hahella chejuensis KCTC 2396]
 gi|83631511|gb|ABC27478.1| RNA polymerase sigma-32 factor RpoH [Hahella chejuensis KCTC 2396]
          Length = 284

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 126/234 (53%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V A+LR V+ +AK Y+  GL   DL+QEGNIGLMKA ++F+   G +  ++A+ W
Sbjct: 50  AARQLVMAHLRFVVHIAKSYSGYGLSQADLVQEGNIGLMKAVKRFNPEFGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+A++    +  +   + +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKKRLAWLTNDEA-KAVAEDLGVDTHV 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRE-TTTRVL 617
           VR++  ++  +  S +    ++D +      +++ED+    P       N  E + +R+ 
Sbjct: 169 VREMESRLAGQDTSFDAGADEDDETAFKAPANYLEDRR-YDPAMMLENENWEEDSNSRLH 227

Query: 618 ASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +LT  +ER   +++ R+ +  N   TL E+  ++ V+ ERIRQ+E  A++K+K
Sbjct: 228 DALTQLDERSKDIIQKRW-LAENKA-TLHELADEYGVSAERIRQLEKNAMKKVK 279


>gi|146410|gb|AAA23991.1| heat shock regulatory protein [Escherichia coli]
          Length = 284

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/287 (25%), Positives = 141/287 (49%), Gaps = 44/287 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    +S +   +++E  H       G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKLHY-----HGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLE-- 577
                R     + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLA 185

Query: 578 ----------TPI--GDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASLT 621
                      P+    + +S+  D IED N    A + L  A+Q             L 
Sbjct: 186 SDDDSDSHAMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQ------------GLD 233

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 234 ERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|300926841|ref|ZP_07142609.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|301329786|ref|ZP_07222521.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
 gi|300417191|gb|EFK00502.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|300844135|gb|EFK71895.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
          Length = 284

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 139/288 (48%), Gaps = 46/288 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    +S +   +++E  H       G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKLHY-----HGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDQS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASL 620
                  +P++    + D+ +S+  D IED N    A + L  A+Q             L
Sbjct: 186 SDDDSDSQPMAPVLYLQDK-SSNFADGIEDDNWEEQAANRLTDAMQG------------L 232

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 DERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|159045149|ref|YP_001533943.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157912909|gb|ABV94342.1| RNA polymerase [Dinoroseobacter shibae DFL 12]
          Length = 298

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 121/250 (48%), Gaps = 33/250 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +MV ++LRL   +A  Y   GL   ++I E N+GLM+A ++FD   G++ +TYAMWW
Sbjct: 49  AAHKMVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI----KREPTPEEIAKKLAMP 559
           ++ +I   I      +++      K  K+    R+  N+I    + +  PE +A+     
Sbjct: 109 IRASIQEYILRSWSLVKLGTTSAQK--KLFFNLRKAKNRIGALEEGDLRPENVAR----- 161

Query: 560 VEGVRKVLKITKEPI------------SLETPIGD--EDTSHLGDFIEDKNAVSPLDSAI 605
              +   L +T++ +            SL   IG   E  +   D++ED++A    D A 
Sbjct: 162 ---IANDLNVTEDEVISMNRRMSGGDASLNAMIGSDGEGATEWQDWLEDEDADQADDFAE 218

Query: 606 QANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  L   RE     +  L  RE+ +L  R     +   TLEE+ + + V+RERIRQIE +
Sbjct: 219 KDELMVRRELLAEAMGVLNDREKDILMKRR--LEDKPATLEELSEVYGVSRERIRQIEVR 276

Query: 663 AIRKLKHPSR 672
           A  KL+   R
Sbjct: 277 AFEKLQKAMR 286


>gi|332763556|gb|EGJ93795.1| alternative sigma factor RpoH [Shigella flexneri 2930-71]
          Length = 280

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/284 (25%), Positives = 138/284 (48%), Gaps = 38/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    +S +   +++E  H       G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 12  LDSYIRAANAWPMLSADEERALAEKLHY-----HGDLEAA---KTLILSHLRFVVHIARN 63

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 64  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 123

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 124 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLS 181

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
                  +P++    + D+ +S+  D IED N         QA  R   T  +  L  R 
Sbjct: 182 SDDDSDSQPMAPVLYLQDK-SSNFADGIEDDNWEE------QAANR--LTDAMHGLDERS 232

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 QDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 275


>gi|24114721|ref|NP_709231.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 301]
 gi|30065262|ref|NP_839433.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 2457T]
 gi|110807289|ref|YP_690809.1| RNA polymerase factor sigma-32 [Shigella flexneri 5 str. 8401]
 gi|24053937|gb|AAN44938.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|30043524|gb|AAP19244.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str.
           2457T]
 gi|110616837|gb|ABF05504.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|281602809|gb|ADA75793.1| Sigma(32) factor of RNA polymerase [Shigella flexneri 2002017]
 gi|313647240|gb|EFS11692.1| alternative sigma factor RpoH [Shigella flexneri 2a str. 2457T]
 gi|332749439|gb|EGJ79856.1| alternative sigma factor RpoH [Shigella flexneri K-671]
 gi|332750286|gb|EGJ80697.1| alternative sigma factor RpoH [Shigella flexneri 4343-70]
 gi|332751371|gb|EGJ81774.1| alternative sigma factor RpoH [Shigella flexneri 2747-71]
 gi|332996248|gb|EGK15875.1| alternative sigma factor RpoH [Shigella flexneri VA-6]
 gi|332996590|gb|EGK16215.1| alternative sigma factor RpoH [Shigella flexneri K-272]
 gi|332997356|gb|EGK16972.1| alternative sigma factor RpoH [Shigella flexneri K-218]
 gi|333012512|gb|EGK31893.1| alternative sigma factor RpoH [Shigella flexneri K-304]
 gi|333012998|gb|EGK32374.1| alternative sigma factor RpoH [Shigella flexneri K-227]
          Length = 284

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/284 (25%), Positives = 138/284 (48%), Gaps = 38/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    +S +   +++E  H       G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKLHY-----HGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
                  +P++    + D+ +S+  D IED N         QA  R   T  +  L  R 
Sbjct: 186 SDDDSDSQPMAPVLYLQDK-SSNFADGIEDDNWEE------QAANR--LTDAMHGLDERS 236

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 237 QDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|29828415|ref|NP_823049.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29605518|dbj|BAC69584.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/215 (32%), Positives = 106/215 (49%), Gaps = 12/215 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+VEA L +   +A ++ NRG  + DL Q  ++GL+KA +++D  LG  F +YA+  +
Sbjct: 38  REEIVEAWLPMAERLAGRFRNRGENYEDLRQVASLGLVKAVDRYDPELGNAFESYAVPTI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V   ++ +S  I  R PT  EIA+   M  E V
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRFASQDLSQTISGRRPTVAEIAEHANMSEEDV 157

Query: 564 RKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R  L+     T   +  E P G ED   L D +   +A   LD  +    RE     L +
Sbjct: 158 RAGLEALESFTALSLDAELP-GSEDGYSLSDAL--GSADPALDIVVD---REAVKPRLQA 211

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  RE  +L MRF   M      E++G  Q  V+R
Sbjct: 212 LPERERDILYMRFFGDMTQSRIAEQLGISQMHVSR 246


>gi|317501595|ref|ZP_07959789.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897012|gb|EFV19089.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 239

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/158 (29%), Positives = 91/158 (57%), Gaps = 1/158 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KFD 
Sbjct: 5   IALIRKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDL 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++  +K V+   R+ + + REPT E
Sbjct: 65  TYNVKFSTYAVPLISGEIKRFLRDDG-MIKVSRSLKEIAYKSVQARERLISSLGREPTIE 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           E+++++ +  E + + ++   E  S+  P+  ++ S +
Sbjct: 124 ELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEI 161


>gi|284008659|emb|CBA75293.1| RNA polymerase sigma-32 factor [Arsenophonus nasoniae]
          Length = 292

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 130/239 (54%), Gaps = 21/239 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 56  AAKQLILSHLRFVIHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   +I    +   + +AK+L +  +
Sbjct: 116 IKAEIHEYVLRNWRIVKVATTKAQR--KLFFNLRKNKKRIGWFNQNEVDMVAKELGVTSK 173

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLGD--------FIEDKN---AVSPLDSAIQANL 609
            VR++  ++  + ++ +  + D+D S  G+        +++DK+   A S  +   + + 
Sbjct: 174 DVREMESRMAAQDMAFD--MNDDDDS--GENTTIAPVLYLQDKSSDFADSIEEDNWENHA 229

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  T+ L++L  R + ++R R+    N   TL+++  ++ V+ ER+RQ+E  A++KL+
Sbjct: 230 TDKLTQALSTLDERSQDIIRARWLDDENKT-TLQDLADKYSVSAERVRQLEKNAMKKLR 287


>gi|157145286|ref|YP_001452605.1| flagellar biosynthesis sigma factor [Citrobacter koseri ATCC
           BAA-895]
 gi|157082491|gb|ABV12169.1| hypothetical protein CKO_01023 [Citrobacter koseri ATCC BAA-895]
          Length = 229

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 103/201 (51%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++LA+PVE  R++L  T           DE     GD 
Sbjct: 90  VAQAMGQLEQELGRNATETEVAERLAIPVEEYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   +++NLR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTEEHQQENPLQQLLESNLRQRVMDAIESLPEREQLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|296164736|ref|ZP_06847300.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295899907|gb|EFG79349.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 288

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 111/228 (48%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +V   L L   VA  +  RG    DL+Q   +GLM A  +FD   G  F  +A+  +
Sbjct: 65  RERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPDKGPSFIGFAVPTM 124

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +R+   ++ RT   ++ K+ R PT  E+++ L +P E + 
Sbjct: 125 MGEVRRYFRDYSWGMRVPRRLRELHVQISRTTGDLAQKLGRAPTAGELSRALEVPHEEIV 184

Query: 565 KVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASL 620
           + L +  +     SL+ P+G  D+S     + D  AV  +D  I+        RVL A+L
Sbjct: 185 ECL-VAGDAYRLDSLDAPMG-TDSSGTPRLVAD--AVGGIDPQIEHITNREALRVLVAAL 240

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  VLRMRF   M      E +G    V++ ++ +I A  +R L+
Sbjct: 241 PEREREVLRMRFFESMTQSQIAERIG----VSQMQVSRILAGTLRCLR 284


>gi|306021726|gb|ADM80299.1| RNA-polymerase sigma subunit [Geobacillus pallidus]
          Length = 256

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 100/200 (50%), Gaps = 10/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 56  DLISFGLMGLYDALEKFDPTRDLKFDTYASFRIRGAILDGLRKEDW---LPRSFREKAKK 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD-EDTSHL 588
           V     R+  K  R  TP E+A++L M  E V  V+        +S++  + D E+   +
Sbjct: 113 VEAAIERLEQKYHRNVTPNEVAEELGMTPEEVVHVVNENFFANVLSIDEQLHDQEEGEQM 172

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              ++D   ++P +  ++  L E  T++++ L  +E+ VL + +      + TL E+G  
Sbjct: 173 NIVLKDDKTLTPEEHLLKEELFEHLTKLISQLNDKEQLVLSLFY----KEELTLTEIGNV 228

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             ++  RI QI +KA+ KLK
Sbjct: 229 LNLSTSRISQIHSKALYKLK 248


>gi|293400808|ref|ZP_06644953.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305834|gb|EFE47078.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 241

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 106/213 (49%), Gaps = 10/213 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK   VE N  LV S+ ++++ + +   DL Q G +GLMKA   FD     KFSTYA+  
Sbjct: 21  AKSIFVEKNSPLVYSIVRRFSRQRIAMDDLFQIGCVGLMKALNNFDTSYQVKFSTYAVPI 80

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D    +RI   +++   ++ +    +  K+ REPT +EIA  L+M V  V
Sbjct: 81  IMGEIKRFFRDDG-NMRISRSLKEGYLQMSKKKEELLQKLNREPTYQEIADALSMDVADV 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
               +  +   SL+  I + D S +   +EDK +    +  +   ++ +    +A L  R
Sbjct: 140 ILAFEANQFVYSLDETIYENDGSPI--LLEDKVSNRKEEDVV---MKVSLQNEIAHLEQR 194

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           E+ +L  R+ +GM      EE+ K+  +++ ++
Sbjct: 195 EQLLLHYRYDLGMKQ----EEIAKKLQISQVQV 223


>gi|114321809|ref|YP_743492.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
 gi|114228203|gb|ABI58002.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 285

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 121/233 (51%), Gaps = 12/233 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V+ +A+ Y   GL   D+IQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 53  AARALVLSHLRFVVHIARSYRGYGLPLGDIIQEGNVGLMKAVKRFDPAQGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   +      +++     + K+   +R+ R+    +  E   + +A+ L +  E 
Sbjct: 113 IRAEIHEYVLRNWRIVKVATTKAQRKLFFNLRSGRKHLGWLTSEEV-DAMARDLGVKPET 171

Query: 563 VRKV-LKITKEPISLE-TPIGDEDTSHLG-DFIEDKNAVSPLDSAIQANLR----ETTTR 615
           VR++  ++T    + + TP  D++  H    ++EDK    P  +  +A+      +   +
Sbjct: 172 VREMEARMTGNDTTFDPTPGQDDEGIHAPVAYLEDKR-YDPATAVEEADWEQHRDQNLHQ 230

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L  R + +L  R+        TL+E+ + + V+ ERIRQ+E  A+ +LK
Sbjct: 231 ALAGLDERSQDILARRWLSERKA--TLKELAEHYQVSAERIRQLEKNAMGRLK 281


>gi|86747323|ref|YP_483819.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
 gi|86570351|gb|ABD04908.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 329

 Score = 82.0 bits (201), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 115/246 (46%), Gaps = 27/246 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ ++LRL   +A+ +   G    DLI E N+GLM A ++FD   G +FST A+WW
Sbjct: 55  AADALITSHLRLAAKLARDFRRYGFPLGDLIAEANLGLMMALDRFDPERGARFSTCAVWW 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR-EP---------TPEEIA 553
           ++ AI   I      +RI    R    K  +   R+  +I+R +P           E+I+
Sbjct: 115 IRSAIYDHIIRSWSLVRI---GRTPAQK--KLFFRLRGEIRRLQPDHHGTLTKELAEQIS 169

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQA----- 607
             L +P+  V ++ +      SL TP+ D D S    D I D    +P   A+ A     
Sbjct: 170 ATLDVPLREVIEMEQRLSGDRSLNTPLSDLDESGEWQDLIADD---APNAEAVLAGHDEL 226

Query: 608 -NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            + R      L  L  RE  +   R  +G     + E +G+   ++ ER+RQIEA+A  K
Sbjct: 227 DHQRRALQDALVQLDARERYIFSARH-LG-ERPASFETIGQSLSISAERVRQIEARAFAK 284

Query: 667 LKHPSR 672
           + + +R
Sbjct: 285 VANSAR 290


>gi|108804196|ref|YP_644133.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765439|gb|ABG04321.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 258

 Score = 81.6 bits (200), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 105/215 (48%), Gaps = 10/215 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++++  L L   +A+K+  RG    DL+Q  ++GL+KA ++FD     +FSTYA   
Sbjct: 28  AREQVIQEQLPLAEFLARKFAGRGEPLEDLVQVASVGLIKAVDRFDVDRNIEFSTYATPN 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D+   +R+P  +++    V    R  + +  R PT +E+A++L   VE V
Sbjct: 88  ILGEIKRHFRDKGWAMRVPRGLQELRQAVKEAIREETVRTGRSPTMDELAERLDTDVESV 147

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQANLRETTTRVLAS 619
            + L + +     SL+ PI  +D    GD I D  A    P++      L +   R    
Sbjct: 148 AEALTLGRAYNTTSLDAPISQDDAE--GDTIMDLQADENQPIEGIEDKLLLQEAMR---G 202

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  ++  +LR+RF  G       E +G  Q  V+R
Sbjct: 203 LREQQREILRLRFNEGKTQTEIAERIGVSQMHVSR 237


>gi|16762736|ref|NP_458353.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|16766854|ref|NP_462469.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|29144223|ref|NP_807565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62182067|ref|YP_218484.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161616616|ref|YP_001590580.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167549215|ref|ZP_02342974.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167990783|ref|ZP_02571882.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168232714|ref|ZP_02657772.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168241719|ref|ZP_02666651.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168260704|ref|ZP_02682677.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|168465152|ref|ZP_02699044.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168818616|ref|ZP_02830616.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443524|ref|YP_002042813.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194449082|ref|YP_002047593.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194469731|ref|ZP_03075715.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|197250526|ref|YP_002148491.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197265856|ref|ZP_03165930.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198244039|ref|YP_002217526.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387614|ref|ZP_03214226.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204928638|ref|ZP_03219837.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205354814|ref|YP_002228615.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858806|ref|YP_002245457.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213426834|ref|ZP_03359584.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213619347|ref|ZP_03373173.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213649997|ref|ZP_03380050.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|213857359|ref|ZP_03384330.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|224585360|ref|YP_002639159.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238910431|ref|ZP_04654268.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|289829445|ref|ZP_06547057.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|25288476|pir||AB0992 RNA polymerase sigma-32 factor [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16422128|gb|AAL22428.1| sigma H factor of RNA polymerase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|16505042|emb|CAD08062.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139860|gb|AAO71425.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62129700|gb|AAX67403.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock proteins induced by cytoplasmic stress [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|161365980|gb|ABX69748.1| hypothetical protein SPAB_04433 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194402187|gb|ACF62409.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194407386|gb|ACF67605.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194456095|gb|EDX44934.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195632472|gb|EDX50956.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197214229|gb|ACH51626.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197244111|gb|EDY26731.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197938555|gb|ACH75888.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199604712|gb|EDZ03257.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204322071|gb|EDZ07269.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205274595|emb|CAR39645.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205325609|gb|EDZ13448.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205330694|gb|EDZ17458.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205333102|gb|EDZ19866.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205338892|gb|EDZ25656.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205344405|gb|EDZ31169.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205350317|gb|EDZ36948.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710609|emb|CAR34967.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224469888|gb|ACN47718.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|261248721|emb|CBG26559.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995798|gb|ACY90683.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301160107|emb|CBW19627.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312914591|dbj|BAJ38565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|320087978|emb|CBY97740.1| RNA polymerase sigma-32 factor Heat shock regulatory protein F33.4
           [Salmonella enterica subsp. enterica serovar Weltevreden
           str. 2007-60-3289-1]
 gi|321226618|gb|EFX51668.1| RNA polymerase sigma factor RpoH [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614066|gb|EFY11002.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617958|gb|EFY14851.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625428|gb|EFY22254.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322629893|gb|EFY26666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322632218|gb|EFY28969.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636431|gb|EFY33138.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643092|gb|EFY39666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322644713|gb|EFY41249.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322651265|gb|EFY47649.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322652822|gb|EFY49161.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659124|gb|EFY55376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322663174|gb|EFY59378.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322668661|gb|EFY64814.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322674536|gb|EFY70629.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322678259|gb|EFY74320.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322682485|gb|EFY78506.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322684198|gb|EFY80204.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716555|gb|EFZ08126.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131927|gb|ADX19357.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323192247|gb|EFZ77479.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196326|gb|EFZ81478.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323201872|gb|EFZ86935.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323206415|gb|EFZ91376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212008|gb|EFZ96835.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323216913|gb|EGA01636.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222313|gb|EGA06696.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323224327|gb|EGA08616.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323228255|gb|EGA12386.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233477|gb|EGA17570.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237061|gb|EGA21128.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323243724|gb|EGA27740.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323246034|gb|EGA30021.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323250810|gb|EGA34688.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323255821|gb|EGA39571.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323261903|gb|EGA45470.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267705|gb|EGA51187.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323268585|gb|EGA52052.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326625307|gb|EGE31652.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629958|gb|EGE36301.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990419|gb|AEF09402.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 284

 Score = 81.6 bits (200), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 141/288 (48%), Gaps = 46/288 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASL 620
              +   +P++    + D+ +S+  D IED N    A + L  A+Q             L
Sbjct: 186 SDDESDSQPMAPVLYLQDK-SSNFADGIEDDNWEEQAANRLTDAMQG------------L 232

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 DERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|301155442|emb|CBW14908.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 629

 Score = 81.6 bits (200), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 85/155 (54%), Gaps = 2/155 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS-NMGINVVDGDDLEDEEGSE 90
           +++++L R +GY+T  E+N  LP D +  E  +  +  L  + GI V+D     DE    
Sbjct: 17  EQLMELGRTQGYLTYAEINDLLPEDLIDPEYYDKLLQTLQHDAGIPVLDEAPESDEMMLN 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++    +   ++  L   +    R+TD PVRMY+REMG+++LL+RE EI+IAKRIE G 
Sbjct: 77  DTIPDEDAVEEATQILSNVESEIGRTTD-PVRMYMREMGTVDLLTREDEISIAKRIEEGI 135

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             +  ++   P     L+   D++  G   L ++I
Sbjct: 136 DEVQTAIAAYPEALTELLDNYDQVEAGNYRLADLI 170


>gi|296448000|ref|ZP_06889906.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296254510|gb|EFH01631.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 289

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 119/244 (48%), Gaps = 25/244 (10%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A  ++  A++RLVI++A ++ + GL   DL+QEG++GL++AA +F      +FSTYA W
Sbjct: 40  VALHKLASAHMRLVIALAVRFRHYGLPVADLVQEGHVGLLEAAARFAPERDVRFSTYATW 99

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++ +I   +      +R       K   +    RR+  K+   P   + A +     + 
Sbjct: 100 WIRASIQDYVLRNWSIVRGGTSSSQK--ALFFNLRRLRAKLAHAP---QTAAESGDAFDA 154

Query: 563 VRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVS-----------PLDSAIQANLR 610
           +   + +++  + L  + +   D S     IED +A S           PL   I  +  
Sbjct: 155 IAGAIGVSRADVELMNSRLAGSDVSLNSQLIEDDSASSAERMDFLVDDRPLPDEIVEDRL 214

Query: 611 ETTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++  R       L  L+ RE R+++ R      +  TLE +G +  +++ER+RQIE +A+
Sbjct: 215 DSDRRARWLADALKLLSERELRIVQERR--LSESLVTLESLGDRLGISKERVRQIENRAL 272

Query: 665 RKLK 668
            KL+
Sbjct: 273 CKLR 276


>gi|89900482|ref|YP_522953.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
 gi|89345219|gb|ABD69422.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
          Length = 313

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 38/255 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV+SV+++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W
Sbjct: 60  AAGKLVLSHLRLVVSVSRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDHGVRLVSYALHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL------- 556
           +K  I   I      +++      +  K+    R M  + K +    ++           
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQRYKSDDAAADLGTHRDTLNEDQ 177

Query: 557 --AMPVEGVRKVLKITKEPI-SLETPI--------------GDEDTSHLGDFIEDKNAVS 599
             AM +E     L++ +E +  +ET +              GD+    +    + ++  +
Sbjct: 178 IDAMALE-----LRVKREEVMEMETRLSGGDVLLDPSPTDDGDDAFGPIAYLTDTRHEPT 232

Query: 600 PLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMNTDH----TLEEVGKQFCVTR 653
            +  A Q +L   +     L +L  R  R++  R+ + +N D+    TL E+   + V+ 
Sbjct: 233 EMIEAHQRDLLASDGIATALEALDERSRRIVEERW-LKVNDDNSGGMTLHELAAVYGVSA 291

Query: 654 ERIRQIEAKAIRKLK 668
           ERIRQIE  A++K+K
Sbjct: 292 ERIRQIEVAAMKKMK 306


>gi|54023854|ref|YP_118096.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54015362|dbj|BAD56732.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 273

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 121/244 (49%), Gaps = 38/244 (15%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ ++E++   L L  ++A+++TNRG++F DL+Q   +GL+ A ++FD   G  F  +A+
Sbjct: 40  AVVREEILHRCLPLAHNIARRFTNRGVEFEDLLQIARLGLVHAVDRFDLEHGDSFLGFAV 99

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPV 560
             +   + R   D    +R+P  M++ +H+++  A  R+++++ R+PT  E+A +L + +
Sbjct: 100 PTIMGEVRRYFRDHGWAVRVPRRMKE-LHQLLGPATDRLTHQLGRQPTARELASELGVEL 158

Query: 561 EGVRKVLKITKEPISLET--------------PIGDE--DTSHLGDFIEDKNAVSPLDSA 604
             V + L + +   + E+              PI D           +ED  AV PL   
Sbjct: 159 TEVTQAL-VARNAFTTESLDGGERTGEEGGALPIADRLGAVEPCYGLLEDAMAVRPL--- 214

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                       +A+L  RE +VL +RF      + T  E+G+    ++ ++ +I AK +
Sbjct: 215 ------------IAALPERERQVLILRF----YDNKTQAEIGRLLGCSQMQVSRILAKTL 258

Query: 665 RKLK 668
             L+
Sbjct: 259 TMLR 262


>gi|126172428|ref|YP_001048577.1| RNA polymerase factor sigma-32 [Shewanella baltica OS155]
 gi|153002659|ref|YP_001368340.1| RNA polymerase factor sigma-32 [Shewanella baltica OS185]
 gi|217975235|ref|YP_002359986.1| RNA polymerase factor sigma-32 [Shewanella baltica OS223]
 gi|304412289|ref|ZP_07393897.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|307306073|ref|ZP_07585818.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
 gi|125995633|gb|ABN59708.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS155]
 gi|151367277|gb|ABS10277.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS185]
 gi|217500370|gb|ACK48563.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS223]
 gi|304349324|gb|EFM13734.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|306910946|gb|EFN41373.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
          Length = 285

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 126/242 (52%), Gaps = 30/242 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +  +R+      E T   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNIRKAKKRLGWFSDAEVTM--VAENLGVSKA 169

Query: 562 GVRKVLKITKEPISLETP----IGDEDTSHLGDF-----IEDKNAVSPLDSAIQANLRET 612
            V ++    +  ++ + P      D+D  H  DF     +ED +  S L   I+ +  E+
Sbjct: 170 DVTEM----ESRMAAQDPAFDLTNDQDEEH--DFAPVHYLEDHS--SDLAENIENDNWES 221

Query: 613 TT--RVLASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRK 666
               R+L+++   +ER   +LR R+   ++ D  TL+E+ + + V+ ERIRQ+E  A+ K
Sbjct: 222 NAQGRLLSAIKTLDERSQHILRARW---LDDDKTTLQELAETYQVSAERIRQLEKNAMNK 278

Query: 667 LK 668
           LK
Sbjct: 279 LK 280


>gi|325674621|ref|ZP_08154308.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
 gi|325554207|gb|EGD23882.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
          Length = 262

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+   +  +  +V  +L L  ++A+++++RG +  DL Q   +GL+ A ++FD   G  F
Sbjct: 32  GDERGTALRDRIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLINAVDRFDPAQGSSF 91

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           + YA+  +   + R   D +   R+P  ++D    V +    +S ++ R PT  E+A +L
Sbjct: 92  AAYAVPTIMGEVRRYFRDHAWAARVPRRLKDLTLDVGKATEALSQRLGRSPTAHELATEL 151

Query: 557 AMPVEGVRKVLKITK--EPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               + V + +      +  SL++P+G D +++ L D +    A   +D   Q  L    
Sbjct: 152 GTDPDSVMEAIAAAGAYQTHSLDSPVGRDGESATLADTL----ATDDVDLE-QTELHLAL 206

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++  L PRE+R++ MRF      + T  E+ ++  V++ +I ++ +K + +++
Sbjct: 207 QPLIDQLEPREKRIVVMRF----FEERTQTEIAREIGVSQVQISRLLSKILARIR 257


>gi|127514531|ref|YP_001095728.1| RNA polymerase factor sigma-32 [Shewanella loihica PV-4]
 gi|126639826|gb|ABO25469.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella loihica PV-4]
          Length = 285

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 119/234 (50%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VAK Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVIHVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R A++       E     +A+ L +    
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNLRKAKKRLGWFSDEEVT-MVAENLGVSKSD 170

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVL 617
           V ++   +        L +   D+       ++ED +  S + S ++ +  E    TR+L
Sbjct: 171 VTEMESRMAAQDPAFDLASDNDDDQDYAPVHYLEDHS--SDIASQVENDNFEADNQTRLL 228

Query: 618 ASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A++   +ER   +L+ R+     T  TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 229 AAIKTLDERSQHILQARWLDEEKT--TLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|183598031|ref|ZP_02959524.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
 gi|188022810|gb|EDU60850.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
          Length = 292

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 124/238 (52%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVIHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   +      ++I      +  K+    R+   ++    +   + +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKIATTKSQR--KLFFNLRKNKKRLGWFNQDEVDMVAKELGVSTK 166

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRET--T 613
            VR++               D+D+  LG       F++DK+  S    +I+ +  E+  T
Sbjct: 167 DVREMESRMAAQDMAFDMSDDDDSGDLGQPIAPVLFLQDKS--SDFAGSIEEDNWESHAT 224

Query: 614 TRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+   L SL  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 225 DRLADALDSLDERSQDIIRARW-LDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|290473624|ref|YP_003466496.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
 gi|289172929|emb|CBJ79700.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
          Length = 285

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 125/234 (53%), Gaps = 11/234 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVVHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R A++      ++   + +AK+L +  + 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFNQDEV-DLVAKELGVTSKD 167

Query: 563 VRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TT 614
           VR++  +++ + ++ +    D+  D+  +   +  ++  S     I+ +  E       +
Sbjct: 168 VREMESRMSAQDMAFDMSSNDDSHDSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLS 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 228 MAIEGLDERSQDIIRARW-LDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|257056691|ref|YP_003134523.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256586563|gb|ACU97696.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 266

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 104/219 (47%), Gaps = 8/219 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E++   L L   +A+++  RG    DL+Q   +GL+ A ++FD   G +F  +A+  +
Sbjct: 45  REEIITRCLPLAEHIARRFVGRGEPRDDLVQVARLGLLNAIDRFDASRGTEFVAFAVPTI 104

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +++    + + + +++ ++ R PTP E+A +L +  E V 
Sbjct: 105 MGEVRRHFRDSSWAVRVPRRLKELHLSLSQASSKLAQRLGRAPTPSELAAELGLSPEDVW 164

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L      + +S++    DE T  L + +   +              E+   +LASL  
Sbjct: 165 DGLLAGNAYQSVSMDAAYDDEGTLPLAETVGHDDV-----ELEHVEYHESLQPLLASLPE 219

Query: 623 REERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIE 660
           RE RVL +RF   M      E VG  Q  V+R   R +E
Sbjct: 220 RERRVLILRFFGNMTQTQIAERVGISQMHVSRLLARTLE 258


>gi|91787153|ref|YP_548105.1| sigma 32 (RpoH) [Polaromonas sp. JS666]
 gi|91696378|gb|ABE43207.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas sp. JS666]
          Length = 322

 Score = 81.6 bits (200), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 118/244 (48%), Gaps = 25/244 (10%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+S+++KY   GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K 
Sbjct: 75  KLVLSHLRLVVSISRKYLGYGLPHGDLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKA 134

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK------------REPTPEEIAK 554
            I   I      +++      +  K+    R M    K             E   + +AK
Sbjct: 135 EIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKDDADVATHRDTLTEGQIDSMAK 192

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET- 612
            L +  E V ++  +++   + L+    D+     G      +A     + +++  R++ 
Sbjct: 193 TLNVKREEVIEMEQRMSGGDVLLDPSPSDDGEDAFGPIAYLADATQEPTALMESRQRDSL 252

Query: 613 ----TTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAI 664
                +  L  L PR  R++  R+ + +N D     TL ++  ++ V+ ERIRQIE  A+
Sbjct: 253 ASDGISAALQELDPRSRRIVEERW-LKVNDDGSGGMTLHDLADEYQVSAERIRQIEVSAM 311

Query: 665 RKLK 668
           +K+K
Sbjct: 312 KKMK 315


>gi|329937605|ref|ZP_08287124.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329303004|gb|EGG46892.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 292

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/258 (23%), Positives = 126/258 (48%), Gaps = 34/258 (13%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   +S++ +G  E   A+  ++E N+ LV   A ++ NRG    D++Q G IGL+KA 
Sbjct: 40  QFFQRLSVLEEGTHEYQYARNTLIEMNMSLVRFAAGRFRNRGDDMEDIVQVGMIGLIKAI 99

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +S+++ R
Sbjct: 100 DRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELSSRLDR 159

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDT---SHLGDFI-------- 592
           +PT  E+A  + +P + V   ++        SL+  +  ED    + L DFI        
Sbjct: 160 DPTVAELATLMNLPEKDVVEAQIAANGYNSSSLDAALSGEDQDGEAVLSDFIGAEDEAMG 219

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             ED + ++PL               +A L+ R+ R++ MRF      + T  ++G Q  
Sbjct: 220 LVEDFHTLAPL---------------VAELSERDRRIIHMRF----VEEATQADIGAQLG 260

Query: 651 VTRERIRQIEAKAIRKLK 668
            ++  + ++  + I +L+
Sbjct: 261 CSQMHVSRLIKRIIEQLR 278


>gi|325678908|ref|ZP_08158506.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
 gi|324109412|gb|EGC03630.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
          Length = 217

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 108/212 (50%), Gaps = 11/212 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E NL LV   A ++  RG+++ DL   G IGL+KA++ FD   G KFSTYA+  
Sbjct: 3   AESHLPEDNLGLVHLCANRFRGRGIEYDDLYGAGCIGLLKASKAFDSGRGVKFSTYAVPV 62

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D   T+++   +++   ++   A+  ++K  REPT EE+AK +  PVE V
Sbjct: 63  ILGEIKRLFRDGG-TVKVSRSLKELSLRLTGEAQVFAHKNGREPTVEELAKIVGTPVEDV 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + L   +  ISL   +GD++     D      A +P D  I   L     +VL  L  +
Sbjct: 122 IEALNAAQPVISLT--VGDDENETQADL----PAPAP-DEDITDRL--ALRQVLTELDDK 172

Query: 624 EERVLRMRFGIGMNTDHTLEEVG-KQFCVTRE 654
           + +++ +R+  GM        +G  Q  V+R+
Sbjct: 173 DRQLIELRYFQGMTQSAAAAVLGMTQVQVSRK 204


>gi|37527948|ref|NP_931293.1| RNA polymerase factor sigma-32 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787384|emb|CAE16473.1| RNA polymerase sigma-32 factor [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 285

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/247 (26%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGDED---------------TSHLGDFIEDKN----AVSPL 601
            VR++  +++ + ++ +    D+                 S   D IE+ N    A   L
Sbjct: 167 DVREMESRMSAQDMAFDMSADDDSQEGQPVAPVLYLQDKASDFADGIEEDNWENHAADKL 226

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             AI+            SL  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E 
Sbjct: 227 SVAIE------------SLDERSQDIIRCRW-LDDDNKSTLQELADKYGVSAERVRQLEK 273

Query: 662 KAIRKLK 668
            A++KL+
Sbjct: 274 NAMKKLR 280


>gi|225026792|ref|ZP_03715984.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
 gi|224955911|gb|EEG37120.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
          Length = 245

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 113/239 (47%), Gaps = 24/239 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE N  L+ SV K++  RG    DL Q G+IGL+K  E FD     KFSTYA+  
Sbjct: 18  AQSILVEENSGLIWSVVKRFQGRGYDKEDLFQIGSIGLLKCIENFDLERNVKFSTYAVPL 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++  +K+ R          REPT +EIA  L M    +
Sbjct: 78  IMGEIKRFLRDDG-IVKVSRSLKEASYKIKREKEHYQKLYNREPTLKEIAVTLDMDESDI 136

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT------R 615
              ++  +E  SL   I   + D  HL D +E            QA+L E T        
Sbjct: 137 LMAMESGQEVCSLHQVIYQSEGDEIHLEDKLEQ-----------QADLIEQTVDNIYVQE 185

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +L  L  +E +++ MR+      + T   + K+  +++ ++ ++E K + KL+  + +K
Sbjct: 186 LLKKLNEQERQIIHMRYF----QNQTQAAIAKKIGISQVQVSRMEKKILNKLRKNANTK 240


>gi|93005058|ref|YP_579495.1| RNA polymerase factor sigma-32 [Psychrobacter cryohalolentis K5]
 gi|92392736|gb|ABE74011.1| sigma 32 (RpoH) [Psychrobacter cryohalolentis K5]
          Length = 287

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 125/269 (46%), Gaps = 24/269 (8%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N +  I + T     E  H      +G+ EA+   + +V ++LR VI +A+ Y+  GL  
Sbjct: 17  NTVHQIPILTPTQEQELAH--RYYDEGDVEAA---RLLVMSHLRFVIHIARSYSGYGLPQ 71

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++      K H
Sbjct: 72  ADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVAT---TKAH 128

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIGDEDT 585
           + +    R   K   + T EE A  +A  +   RK +     ++T    S E    D+D 
Sbjct: 129 RKLFFNLRSLKKTNNQLTLEE-ADAIANDLNVTRKQVLEMESRLTSYDASFEAQSSDDDD 187

Query: 586 SHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMNTD 639
                  F+ED   + P +   +++  E  +  L     +L  R   ++  R+     + 
Sbjct: 188 GRYAPQLFLED--GIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWLSEQKS- 244

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+   + ++ ER+RQIE  A+ K++
Sbjct: 245 -TLHELAAVYSISAERVRQIEKNAMDKIR 272


>gi|256784015|ref|ZP_05522446.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 266

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VEA L +   +A ++ +RG  F DL Q   +GL+KA +++D   G  F +YA+  +
Sbjct: 37  RDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFESYAVPTI 96

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  +++  ++V    + +S  I  R PT  EIA++  +  E V
Sbjct: 97  TGEIKRHFRDHMWTLHVPRRVQELRNRVRFAGQDLSQTIPGRRPTVAEIAERAELSEEDV 156

Query: 564 RKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R  L+     T   +  E P G ED   LGD +   +    LD+ +    RE     LA+
Sbjct: 157 RVGLEALESFTALSLDAELP-GSEDGYSLGDALGAPDPA--LDTVVD---REAVKDRLAA 210

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L PRE  +L MRF   M      E++G  Q  V+R
Sbjct: 211 LPPRERAILYMRFFDDMTQSRIAEQLGISQMHVSR 245


>gi|257054261|ref|YP_003132093.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256584133|gb|ACU95266.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 267

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 110/239 (46%), Gaps = 36/239 (15%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L L   +A++++ RG+   DL+Q   +GL+ A ++FD   G  F ++A+  V
Sbjct: 40  RDRLVTGHLPLAEHIAQRFSGRGVAKEDLVQVARVGLINAVDRFDPSRGSDFLSFAVPTV 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    IR+P  +++    +   + ++S ++ R PTP EIA  L + +E V 
Sbjct: 100 MGEVRRHFRDTGWVIRVPRRLKELHLSINNASTQLSQRLGRAPTPSEIADHLGLTLEEVF 159

Query: 565 ---------------KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
                          +VL    E ++L   +G+ED +  G  +E+   + PL        
Sbjct: 160 EGLEAGNAYHSMSLDEVLSADTENLALGDTLGEEDAALAG--VENHETLQPL-------- 209

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L  RE  +L +RF   M      E +G    +++  + ++ A+ ++KL+
Sbjct: 210 -------VKQLPERERTILALRFVHNMTQTQIAERIG----ISQMHVSRLLARTLKKLR 257


>gi|319935952|ref|ZP_08010376.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809066|gb|EFW05562.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 241

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 120/236 (50%), Gaps = 15/236 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR G+ +A   K+++V+ NL LV S+  ++ N      DL Q G IGLMKA   FD    
Sbjct: 13  VRSGDEQA---KEQVVKDNLGLVWSIVHRFKNSYYDKEDLFQIGCIGLMKAINHFDPSYN 69

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA+  +   I R   D   TI++   +++   KV +    +  +   EPT EE+A
Sbjct: 70  VQFSTYAVPIIMGEIKRYFRDDG-TIKVSRSLKELNIKVTKAKEILQAENNEEPTVEEVA 128

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L + V  V + +  +  P SL  PI ++D S +   +ED+     +D +      +  
Sbjct: 129 RYLEVDVHDVVEAIDSSYYPTSLSEPIYEKDGSTIS--MEDR----LIDKSDHMWFEKIA 182

Query: 614 TRV-LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  +E+ ++ MR+ +    D+  E + ++  +++ ++ ++E K + KL+
Sbjct: 183 LEMEMEKLDEKEKMIIYMRYQL----DYNQEAIAQRLGISQVQVSRLEKKIVTKLR 234


>gi|56415467|ref|YP_152542.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364396|ref|YP_002144033.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129724|gb|AAV79230.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095873|emb|CAR61447.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 284

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 141/288 (48%), Gaps = 46/288 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASL 620
              +   +P++    + D+ +S+  D IED N    A + L  A+Q             L
Sbjct: 186 SDDESDSQPMAPVLYLQDK-SSNFADGIEDDNWEEQAANRLTDAMQG------------L 232

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 233 DERSQDIIRARW-LDEDNKSTLQELADRYGVSVERVRQLEKNAMKKLR 279


>gi|71064787|ref|YP_263514.1| RNA polymerase factor sigma-32 [Psychrobacter arcticus 273-4]
 gi|71037772|gb|AAZ18080.1| putative Sigma 32 (RpoH) [Psychrobacter arcticus 273-4]
          Length = 341

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 125/269 (46%), Gaps = 24/269 (8%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N +  I + T     E  H      +G+ EA+   + +V ++LR VI +A+ Y+  GL  
Sbjct: 71  NTVHQIPILTPTQEQELAH--RYYDEGDVEAA---RLLVMSHLRFVIHIARSYSGYGLPQ 125

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++      K H
Sbjct: 126 ADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVAT---TKAH 182

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIGDEDT 585
           + +    R   K   + T EE A  +A  +   RK +     ++T    S E    D+D 
Sbjct: 183 RKLFFNLRSLKKTNNQLTIEE-ADAIANDLNVTRKQVLEMESRLTSYDASFEAQSSDDDD 241

Query: 586 SHLGD--FIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMNTD 639
                  F+ED   + P +   +++  E  +  L     +L  R   ++  R+     + 
Sbjct: 242 GRYAPQLFLED--GIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWLSEQKS- 298

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+   + ++ ER+RQIE  A+ K++
Sbjct: 299 -TLHELAAVYSISAERVRQIEKNAMDKIR 326


>gi|167507935|gb|ABZ81288.1| RpoD [Thalassospira sp. MCCC 1A01288]
 gi|167507939|gb|ABZ81290.1| RpoD [Thalassospira sp. MCCC 1A01318]
 gi|167507943|gb|ABZ81292.1| RpoD [Thalassospira sp. MCCC 1A01423]
 gi|167507947|gb|ABZ81294.1| RpoD [Thalassospira sp. MCCC 1A01449]
          Length = 266

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 89/157 (56%), Gaps = 5/157 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN---AVNGQKDEKSSVKCKV--LKEKLV 322
           +LS ME++L  +V+   ++IA+ Y +L   Q+    A+N  +   ++ + +   LK+++V
Sbjct: 110 SLSKMEEELTEQVLEKFEKIAKTYEKLHKAQEQRLAAMNKGETVPAATEKRYGKLKQEMV 169

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+  + LN  RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+
Sbjct: 170 DLMEDVHLNNFRIEELLDHLTGLNNRLLGLEGKLLRYADRCKIKRPDFVKQYQGNELDPN 229

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           W+          WK FV    D I ++R  I  +S E
Sbjct: 230 WMERVGALSGKGWKLFVERYPDEIAQLREGIGGVSAE 266


>gi|187935068|ref|YP_001885063.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723221|gb|ACD24442.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 242

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 115/232 (49%), Gaps = 15/232 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+++V+  + LV  +A +     N+ +++ DL+  G IGLM A  KF+   G KFS+YA
Sbjct: 9   VKEQIVKEYIPLVKYIASRIMIGKNKYMEYEDLVSYGIIGLMDAISKFNPEKGMKFSSYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K AI   I       +      DK+++       + NK+ REP   EIAK L + +
Sbjct: 69  SIRIKGAIIDQIRKNRPITK---GAMDKLNRYNGAIEALQNKLLREPNILEIAKYLELSL 125

Query: 561 EGVRKVLKITKE--PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           E V ++         +SLE  I   DE+ + LG  IEDKN+ SP     +    E  +  
Sbjct: 126 EEVSQIENYINHISMVSLENIIFSDDEEVNLLG-IIEDKNSPSPEGELEEKEKLEVLSDA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  +E+ +L + +   +    TL+E+G    V+  R+ Q+ A++I  L+
Sbjct: 185 IKLLKEKEQLILNLYYYEKL----TLKEIGAILSVSESRVCQLHARSISNLR 232


>gi|154707560|ref|YP_001423635.1| RNA polymerase factor sigma-32 [Coxiella burnetii Dugway 5J108-111]
 gi|154356846|gb|ABS78308.1| RNA polymerase sigma-32 factor [Coxiella burnetii Dugway 5J108-111]
          Length = 288

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 118/236 (50%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G + +++A+ W
Sbjct: 51  AARKLVLSHLRFVVRIARGYSGYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLASFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           ++  I   I      ++I      +  K+    R+ + K       E   +A++L +  +
Sbjct: 111 IRAEIHEFILKNWRIVKIATTKAQR--KLFFNLRKHAKKRGWFSDHEAFALAEELNVSTK 168

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLG---DFIEDK--NAVSPLDSAIQANLRETT 613
            VR++   L    E         D  T   G    ++EDK  N    L+ +  A+ +E  
Sbjct: 169 DVRQMEERLNSYDEAFDGADEESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHR 228

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  R   +L  R+     +  TL E+  Q+ V+ ERIRQ+E  A++K++
Sbjct: 229 LHNAMQSLDDRSRDILYQRWLSEKKS--TLHELAAQYAVSAERIRQLEKNAMQKIR 282


>gi|312138386|ref|YP_004005722.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311887725|emb|CBH47037.1| putative sigma-70 factor [Rhodococcus equi 103S]
          Length = 262

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+   +  +  +V  +L L  ++A+++++RG +  DL Q   +GL+ A ++FD   G  F
Sbjct: 32  GDERGTALRDRIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLINAVDRFDPAQGSSF 91

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           + YA+  +   + R   D +   R+P  ++D    V +    +S ++ R PT  E+A +L
Sbjct: 92  AAYAVPTIMGEVRRYFRDHAWAARVPRRLKDLTLDVGKATEALSQRLGRSPTAHELATEL 151

Query: 557 AMPVEGVRKVLKITK--EPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               + V + +      +  SL++P+G D +++ L D +    A   +D   Q  L    
Sbjct: 152 GTDPDSVMEAIAAAGAYQTHSLDSPVGRDGESATLADTL----ATDDVDLE-QTELHLAL 206

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++  L PRE+R++ MRF      + T  E+ ++  V++ +I ++ +K + +++
Sbjct: 207 RPLIDQLEPREKRIVVMRF----FEERTQTEIAREIGVSQVQISRLLSKILARIR 257


>gi|21224822|ref|NP_630601.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|3559995|emb|CAA20617.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 266

 Score = 81.3 bits (199), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VEA L +   +A ++ +RG  F DL Q   +GL+KA +++D   G  F +YA+  +
Sbjct: 37  RDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFESYAVPTI 96

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  +++  ++V    + +S  I  R PT  EIA++  +  E V
Sbjct: 97  TGEIKRHFRDHMWTLHVPRRVQELRNRVRFAGQDLSQTIPGRRPTVAEIAERAELSEEDV 156

Query: 564 RKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R  L+     T   +  E P G ED   LGD +   +    LD+ +    RE     LA+
Sbjct: 157 RVGLEALESFTALSLDAELP-GSEDGYSLGDALGAPDPA--LDTVVD---REAVKDRLAA 210

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L PRE  +L MRF   M      E++G  Q  V+R
Sbjct: 211 LPPRERAILYMRFFNDMTQSRIAEQLGISQMHVSR 245


>gi|322833177|ref|YP_004213204.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
 gi|321168378|gb|ADW74077.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
          Length = 240

 Score = 81.3 bits (199), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERFDAMQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +       K+ R P+  E+A+ L +P+E  R++L  T    S +    DE     GD 
Sbjct: 100 VSQAMHSAEQKLGRPPSEGEVAQVLDIPIEEYRQILMDTN---SSQLFSYDEWREEHGDT 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL   ++ NLR      + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALMEGHEEANPLHHLLEGNLRHRVMEAIDALPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLDVGESRVSQLHSQAIKRLR 233


>gi|309785782|ref|ZP_07680413.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|308926902|gb|EFP72378.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|315614730|gb|EFU95370.1| alternative sigma factor RpoH [Escherichia coli 3431]
 gi|323162701|gb|EFZ48540.1| alternative sigma factor RpoH [Escherichia coli E128010]
 gi|323164790|gb|EFZ50582.1| alternative sigma factor RpoH [Shigella sonnei 53G]
 gi|323179012|gb|EFZ64586.1| alternative sigma factor RpoH [Escherichia coli 1180]
 gi|323182926|gb|EFZ68327.1| alternative sigma factor RpoH [Escherichia coli 1357]
 gi|323188948|gb|EFZ74232.1| alternative sigma factor RpoH [Escherichia coli RN587/1]
 gi|327251097|gb|EGE62790.1| alternative sigma factor RpoH [Escherichia coli STEC_7v]
          Length = 257

 Score = 81.3 bits (199), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 66/254 (25%), Positives = 124/254 (48%), Gaps = 41/254 (16%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   K ++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 18  GDLEAA---KTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 74

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+      +   E +A+
Sbjct: 75  VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNQDEVEMVAR 132

Query: 555 KLAMPVEGVRKV----------------LKITKEPISLETPIGDEDTSHLGDFIEDKN-- 596
           +L +  + VR++                     +P++    + D+ +S+  D IED N  
Sbjct: 133 ELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQDK-SSNFADGIEDDNWE 191

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A + L  A+Q             L  R + ++R R+ +  +   TL+E+  ++ V+ E
Sbjct: 192 EQAANRLTDAMQG------------LDERSQDIIRARW-LDEDNKSTLQELADRYGVSAE 238

Query: 655 RIRQIEAKAIRKLK 668
           R+RQ+E  A++KL+
Sbjct: 239 RVRQLEKNAMKKLR 252


>gi|6175924|gb|AAF05338.1|AF182104_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 147

 Score = 81.3 bits (199), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 48/57 (84%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 146


>gi|113972098|ref|YP_735891.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-4]
 gi|114049328|ref|YP_739878.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-7]
 gi|117922401|ref|YP_871593.1| RNA polymerase factor sigma-32 [Shewanella sp. ANA-3]
 gi|113886782|gb|ABI40834.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-4]
 gi|113890770|gb|ABI44821.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-7]
 gi|117614733|gb|ABK50187.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. ANA-3]
          Length = 285

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 121/243 (49%), Gaps = 32/243 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK--KLAMPVE 561
           +K  I   +      +++            +  R++   I++  T        ++AM  E
Sbjct: 112 IKAEIHEYVLKNWRIVKVA---------TTKAQRKLFFNIRKAKTRLGWFSDDEVAMVAE 162

Query: 562 --GVRKV--------LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             GV K         +        L +   DE       ++ED +  S L   I+ +  E
Sbjct: 163 NLGVSKADVTEMESRMAAQDPAFDLSSDNDDEQDFAPVHYLEDHS--SDLAENIENDNWE 220

Query: 612 TTT--RVLASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIR 665
           +    R+L+++   +ER   +LR R+   ++ D  TL+E+ + + V+ ERIRQ+E  A+ 
Sbjct: 221 SNAQGRLLSAIKTLDERSQHILRARW---LDDDKTTLQELAETYQVSAERIRQLEKNAMN 277

Query: 666 KLK 668
           KLK
Sbjct: 278 KLK 280


>gi|319940794|ref|ZP_08015133.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319805676|gb|EFW02457.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 281

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 123/244 (50%), Gaps = 29/244 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLVIS+A+ +   GL + DLIQEGNIGLMKA  ++D   G +  T+A+ W
Sbjct: 37  AAQKLVLSHLRLVISIARGFLGYGLPYADLIQEGNIGLMKAIRRYDPDRGARLMTFAVHW 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   I      +++      +  K+    R++    +   T +E A+++A+ ++ V
Sbjct: 97  IRSEIQEYIIRNWRIVKLATTKNQR--KLFFNLRQLKEDSQAALTNQE-AQRIALTLD-V 152

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLD----------SAIQANLR-- 610
           +      KE + +E  +  ++TS  G    D +   SP D          + ++A  R  
Sbjct: 153 K-----PKEVLDMEERMYGQETSIDGPADSDDDDRFSPSDWLTRTSDQPEAILEAEDRQH 207

Query: 611 ---ETTTRVLASLTPREERVLRMRF----GIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              E     LA+L PR  RV+  R+      G     TL+ +  +  V+ ER+RQIE  A
Sbjct: 208 LEGEGLQTALAALDPRSRRVIEARYLTVDADGTAKPVTLQALAHELGVSAERVRQIEKLA 267

Query: 664 IRKL 667
           I+K+
Sbjct: 268 IKKM 271


>gi|238063793|ref|ZP_04608502.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
 gi|237885604|gb|EEP74432.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
          Length = 294

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 111/223 (49%), Gaps = 12/223 (5%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EA L L   +A +Y+ RG    DL Q   +GL+KA +KFD   G  F+ YA+  +   +
Sbjct: 74  IEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDKFDPSRGVDFAGYAIPTIIGEL 133

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R   D++  IR+P  +++    +      +   + R PT  +IA  L +  E V + L+
Sbjct: 134 KRHFRDRTWDIRVPRRLQELRLAISDANSTLLQTLGRSPTVADIAAHLKLTEEEVLEGLE 193

Query: 569 ITK--EPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +    +SL TP GD D  + LGD +  ++    L     A LR      LA+L  RE+
Sbjct: 194 GARAYNAVSLSTPTGDGDRATELGDMLGGEDTEFEL-----AELRVALGPALATLDEREQ 248

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L +RF      + T  ++  Q  V++  + ++ A+A+ KL+
Sbjct: 249 KILTLRF----YGNLTQSQIADQIGVSQMHVSRLLARALTKLR 287


>gi|146296669|ref|YP_001180440.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410245|gb|ABP67249.1| RNA polymerase, sigma subunit, RpoX/SigF [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 231

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 120/241 (49%), Gaps = 17/241 (7%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+ K +     A++E++E NL LV S+ KK+  +G++  DL Q G IGL+KA ++FD   
Sbjct: 1   MISKAKNGDKKARQELIENNLALVWSIVKKFVVKGIEADDLFQIGCIGLIKAVDRFDLSF 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I+I   +++  +K+ R       +  REPT  EI
Sbjct: 61  NVRFSTYAVPMIIGEIKRYLRDDG-KIKISRKIKENQNKLKRFRDEFLFQNGREPTISEI 119

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPL--DSAIQAN 608
           ++   +  + +   +  + +  SL   I  E+     L D   D++  S L    A++  
Sbjct: 120 SEATGLSQDDILLCIDASLDVTSLNEVINQEEGKPITLMDIAADEDYSSRLLDIMALKEG 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+        L  RE  ++ MR+      + T  E+ K+  +++  + +IE KA+ ++K
Sbjct: 180 LRK--------LKGRERYIIFMRYF----KNKTQSEIAKELNISQVHVSRIEKKALERIK 227

Query: 669 H 669
            
Sbjct: 228 R 228


>gi|54025575|ref|YP_119817.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017083|dbj|BAD58453.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 315

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 118/251 (47%), Gaps = 32/251 (12%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ V  G  E +  + E++   + L   +A+K++ RG  F DL Q   +GL+ A ++FD 
Sbjct: 78  LAAVEPGTAEHAALRDELISRCVPLADHIARKFSGRGEPFDDLTQVARVGLVHAVDRFDP 137

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F ++A+  +   + R   D +  +R+P  +++   ++      +S  + R PT +
Sbjct: 138 ARGSNFLSFAVPTIMGEVRRYFRDHTWAMRVPRRVKETHLRIGAAIDTLSQSLGRSPTAK 197

Query: 551 EIAKKLAM-PVEGVRKVLKITK-EPISLE-TPIGDEDTSHLGDF----------IEDKNA 597
           EIA +L + P E  + V+     +P S++   +G E  + L D           +E+  A
Sbjct: 198 EIAAELRVDPDEVTQAVIAGNAYQPSSIDAAALGRESDASLLDTLGEEEAQFERVEEYVA 257

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + PL               LA L  RE R+L MRF   M    T  ++ KQ  +++  + 
Sbjct: 258 IRPL---------------LAGLPERERRILTMRFFESM----TQTQIAKQMGISQMHVS 298

Query: 658 QIEAKAIRKLK 668
           +I AK + +L+
Sbjct: 299 RILAKTLARLR 309


>gi|312972274|ref|ZP_07786448.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
 gi|310334651|gb|EFQ00856.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
          Length = 257

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 66/254 (25%), Positives = 124/254 (48%), Gaps = 41/254 (16%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   K ++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 18  GDLEAA---KTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 74

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+      +   E +A+
Sbjct: 75  VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG--WFNQDEVEMVAR 132

Query: 555 KLAMPVEGVRKV----------------LKITKEPISLETPIGDEDTSHLGDFIEDKN-- 596
           +L +  + VR++                     +P++    + D+ +S+  D IED N  
Sbjct: 133 ELGVTSKDVREMESRMAAQDMTFDLSSNDDSDSQPMAPVLYLQDK-SSNFADGIEDDNWE 191

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A + L  A+Q             L  R + ++R R+ +  +   TL+E+  ++ V+ E
Sbjct: 192 EQAANRLTDAMQG------------LDERSQDIIRARW-LDEDNKSTLQELADRYGVSAE 238

Query: 655 RIRQIEAKAIRKLK 668
           R+RQ+E  A++KL+
Sbjct: 239 RVRQLEKNAMKKLR 252


>gi|302866675|ref|YP_003835312.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302569534|gb|ADL45736.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 273

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 112/223 (50%), Gaps = 12/223 (5%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EA L L   +A +Y+ RG    DL Q   IGL+KA +KFD   G  F+ YA+  +   +
Sbjct: 53  IEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAIPTIIGEL 112

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R   D++  IR+P  +++    +      +   + R PT  +IA  L +  E V + L+
Sbjct: 113 KRHFRDRTWDIRVPRRLQELRLAISDANSTLLQTLGRSPTVADIAAHLKLTEEEVLEGLE 172

Query: 569 ITK--EPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +    +SL TP GD E  + LGD +  ++    L     A +R      LA+L  RE+
Sbjct: 173 GARAYNAVSLSTPTGDGERATELGDLLGGEDGEFEL-----AEMRVALGPALATLDQREQ 227

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L +RF      + T  ++ +Q  V++  + ++ A+A+ KL+
Sbjct: 228 KILTLRF----YGNLTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|261342189|ref|ZP_05970047.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315522|gb|EFC54460.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 147

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 48/57 (84%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 146


>gi|24376056|ref|NP_720099.1| RNA polymerase factor sigma-32 [Shewanella oneidensis MR-1]
 gi|24351072|gb|AAN57543.1|AE015890_4 RNA polymerase sigma-32 factor [Shewanella oneidensis MR-1]
          Length = 285

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 123/236 (52%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++     + K+   +R A+ R+      E T   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNIRKAKTRLGWFSDDEVTM--VAENLGVSKA 169

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--RV 616
            V ++   +        L +   DE       ++ED +  S L   I+ +  E+    R+
Sbjct: 170 DVTEMESRMAAQDPAFDLSSDNDDEHDFAPVHYLEDHS--SDLAENIENDNWESNAQGRL 227

Query: 617 LASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++   +ER   +LR R+   ++ D  TL+E+ + + V+ ERIRQ+E  A+ KLK
Sbjct: 228 LSAIKTLDERSQHILRARW---LDDDKTTLQELAETYQVSAERIRQLEKNAMNKLK 280


>gi|332531759|ref|ZP_08407644.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038735|gb|EGI75177.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 287

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 121/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVAHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +  +R+    + E +   +A +L +  +
Sbjct: 112 IKAEIHEFVLKNWRIVKVATTKAQRKLFFNLRKNKKRLGWFNQAEVST--VASELGVSEK 169

Query: 562 GVRKV-LKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAIQANLRETT-T 614
            VR++  +++ + +  +    D D     T     ++ D  A    D   Q   +E   T
Sbjct: 170 EVREMESRMSGQDMGFDLTGDDNDDAPTSTYSPVQYLTD-GAADLADDVEQEQWKEQAHT 228

Query: 615 RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+ ++L   +ER   +     ++ D  TL+E+ +++ V+ ER+RQ+E  A++KL+
Sbjct: 229 RLFSALKTLDERSQDIVSARWLSDDKATLQELAQKYSVSAERVRQLEKTAMKKLQ 283


>gi|294629742|ref|ZP_06708302.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292833075|gb|EFF91424.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 305

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/253 (25%), Positives = 124/253 (49%), Gaps = 17/253 (6%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S S F  + S+  +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IG
Sbjct: 58  ALSKSLFERLESL-EEGTHEHAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIG 116

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++
Sbjct: 117 LIKAIDRFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELA 176

Query: 541 NKIKREPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            ++ R PT  E+A+ L +     VEG+      T   +  + P  +E    L D I  + 
Sbjct: 177 QRLDRAPTVSELAEHLGLSAEEVVEGMAASNAYTASSLDAQ-PEENESEGALADRIGYE- 234

Query: 597 AVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                D  I+     E+   ++A L  R+ ++L +RF   M    T  E+G++  +++  
Sbjct: 235 -----DHGIEGIEYVESLKPLIAELPSRDRKILSLRFVANM----TQSEIGEELGISQMH 285

Query: 656 IRQIEAKAIRKLK 668
           + ++ ++ + +L+
Sbjct: 286 VSRLLSRTLVRLR 298


>gi|157149048|ref|YP_001456366.1| RNA polymerase factor sigma-32 [Citrobacter koseri ATCC BAA-895]
 gi|157086253|gb|ABV15931.1| hypothetical protein CKO_04887 [Citrobacter koseri ATCC BAA-895]
          Length = 284

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 74/284 (26%), Positives = 141/284 (49%), Gaps = 38/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKLHY-----QGDLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDMS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              +   +P++    + D+ TS+  D IE+ N     D A  AN     T  +  L  R 
Sbjct: 186 SDDESDSQPMAPVLYLQDK-TSNFADGIEEDNWE---DQA--AN---KLTHAMEGLDERS 236

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 237 QDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|56551645|ref|YP_162484.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241761228|ref|ZP_04759316.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752767|ref|YP_003225660.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|59803027|sp|P50512|RP32_ZYMMO RecName: Full=RNA polymerase sigma-32 factor
 gi|56543219|gb|AAV89373.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374135|gb|EER63632.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552130|gb|ACV75076.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 302

 Score = 80.9 bits (198), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KFD   G++ +TYA+WW
Sbjct: 53  AASRLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    RR+ + +      +  P+E   IA  L
Sbjct: 113 IKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNL 170

Query: 557 AMPVEGVRKVLKITKEPI-----SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            +  E   +V+ + +        SL   + ++    + D++ D+    PL         E
Sbjct: 171 GVSNE---EVVNMNRRMAMGGDSSLNITMREDGEGQMQDWLVDQ---EPLQDQQIEEEEE 224

Query: 612 TTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  R       +  L  RE+ +L  R     +   TLEE+ + + V+RER+RQIE +A  
Sbjct: 225 SLVRHKLLIEAMDKLNDREKHILTERR--LSDNPKTLEELSQVYGVSRERVRQIEVRAFD 282

Query: 666 KLK 668
           KL+
Sbjct: 283 KLQ 285


>gi|315503089|ref|YP_004081976.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|315409708|gb|ADU07825.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 273

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 112/223 (50%), Gaps = 12/223 (5%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EA L L   +A +Y+ RG    DL Q   IGL+KA +KFD   G  F+ YA+  +   +
Sbjct: 53  IEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAIPTIIGEL 112

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R   D++  IR+P  +++    +      +   + R PT  +IA  L +  E V + L+
Sbjct: 113 KRHFRDRTWDIRVPRRLQELRLAISDANSTLLQTLGRSPTVADIAAHLKLTEEEVLEGLE 172

Query: 569 ITK--EPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +    +SL TP GD E  + LGD +  ++    L     A +R      LA+L  RE+
Sbjct: 173 GARAYNAVSLSTPTGDGERATELGDLLGGEDGEFEL-----AEMRVALGPALATLDQREQ 227

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L +RF      + T  ++ +Q  V++  + ++ A+A+ KL+
Sbjct: 228 KILTLRF----YGNLTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|160877394|ref|YP_001556710.1| RNA polymerase factor sigma-32 [Shewanella baltica OS195]
 gi|160862916|gb|ABX51450.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS195]
 gi|315269598|gb|ADT96451.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS678]
          Length = 285

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 24/239 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +  +R+      E T   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNIRKAKKRLGWFSDAEVTM--VAENLGVSKA 169

Query: 562 GVRKVLKITKEPISLETP----IGDEDTSHLGDF-----IEDKNAVSPLDSAIQANLRET 612
            V ++    +  ++ + P      D+D  H  DF     +ED +  S L   I+ +  E+
Sbjct: 170 DVTEM----ESRMAAQDPAFDLTNDQDEEH--DFAPVHYLEDHS--SDLAENIENDNWES 221

Query: 613 TT--RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               R+L+++   +ER   +     ++ D  TL+E+ + + V+ ERIRQ+E  A+ KLK
Sbjct: 222 NAQGRLLSAIKTLDERSQHILHARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLK 280


>gi|47122|emb|CAA48660.1| whiG-Stv [Streptomyces griseocarneus]
          Length = 278

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGIFGLIDAIEKFDPARAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + +E +  V       +SL   +  ED  H G  
Sbjct: 132 VERAYATLEAELRRTPTEAEVAAEMGIALEELHSVFS----QLSLANVVALEDLLHAGDE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGERLSLMDTLEDTAADDPVEVAEDHELRRLLARAINTLPEREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G+   VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGQVLGVTESRVSQIHTKSVLQLR 270


>gi|302385959|ref|YP_003821781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302196587|gb|ADL04158.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 240

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 118/230 (51%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V  N  LV S+ +++T RG +  DL Q G+IGLMKA +KFD     KFSTYA+  
Sbjct: 21  ARDQLVTDNFGLVWSIVRRFTGRGYEAEDLFQIGSIGLMKAIDKFDLSYEVKFSTYAVPM 80

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++   KV      +  ++ REPT EEIA ++    E V
Sbjct: 81  ITGEIKRFLRDDGM-IKVSRSIKEMGLKVKNVREELIYRLGREPTVEEIAGEIGASKEEV 139

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLAS 619
              ++   E  SL   +   DE++  L D IE+       +S+ Q  L  R     +L +
Sbjct: 140 AASIEAGAEVESLYRSVNKNDENSILLIDKIEE-------ESSAQEELLNRMVLRELLTA 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L+ ++  ++  R+      + T  ++  +  +++ ++ ++E K +++++ 
Sbjct: 193 LSDKDREIIIRRY----YYNETQSQIAAKLGISQVQVSRLEKKILKQMRE 238


>gi|167464139|ref|ZP_02329228.1| DNA-directed RNA polymerase sigma subunit D [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322382365|ref|ZP_08056272.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321153718|gb|EFX46093.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 262

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 121/244 (49%), Gaps = 12/244 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ ++E  L LV  V+ + +N   R +   DL   G +GLM A EKFD   G +F TYA
Sbjct: 26  AKQSLLEQYLPLVDYVSSRMSNGLPRNVAKEDLASFGVLGLMDAVEKFDHTRGLQFETYA 85

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            W +  A+   +        +P  +R+K  K+    +++     R  T  EI++ L +  
Sbjct: 86  SWRILGAVIDGLRQGDW---VPRSLREKAKKIEDAYQKLEQHYLRTVTDAEISEYLGVEE 142

Query: 561 EGVRKVLK-ITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           E  R++L+ I    I S++ PI +E++      + D+ A +P     +  L+ET  R + 
Sbjct: 143 EEFRQMLQEINVTSICSVDDPIKEEESETRLSLLIDEKAKNPEYKVNEFYLKETLARAIE 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT +E+ V+ + +      + +L E+ +   ++  RI Q+ +KAI +L+      K++ 
Sbjct: 203 KLTEKEKIVVSLFYF----EELSLSEIAEVMSLSPSRISQLHSKAILRLRGTLNKYKIQL 258

Query: 679 FLDG 682
           F D 
Sbjct: 259 FQDS 262


>gi|315444787|ref|YP_004077666.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263090|gb|ADT99831.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 270

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 105/223 (47%), Gaps = 10/223 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++   L L    A+++  RG    DL Q  ++GL+ A ++FD   G  F  YA+  +   
Sbjct: 35  IIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLVNAVKRFDPDSGSDFLAYAVPTIMGE 94

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R   D S  +++P  ++D   ++ +    ++ ++ R PTP E+A  L +  E V +  
Sbjct: 95  VRRYFRDCSWAVKVPRRLKDLNSQLAKARAELTQQLGRAPTPSEVAAHLGIDREEVVQAT 154

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREER 626
             +    +L T   D  +   GDF+  +  +   D+ + A +   T R L   L PRE+ 
Sbjct: 155 IASSNYATLST---DSTSGPDGDFVALRETLGEPDARLDAVVDNETIRPLIEKLPPREQA 211

Query: 627 VLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLK 668
           VL++RF   M      E +G  Q  V+R     + AKA+  L+
Sbjct: 212 VLKLRFFDEMTQTQIAERMGYSQMHVSR-----LLAKALATLR 249


>gi|262195942|ref|YP_003267151.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262079289|gb|ACY15258.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 298

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 116/242 (47%), Gaps = 27/242 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V + LR V+ +A+KY   G+   DL+ EGN+GL++A  +F+   G +F TYA  W
Sbjct: 44  AADALVSSQLRSVLKIARKYRGYGIYLSDLVAEGNLGLLEAVNRFEPERGLRFFTYARHW 103

Query: 504 VKQAITR------SIADQSCTI---RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           V+  I        SI D   T    ++   ++ +  +++ T    S++++R     ++A 
Sbjct: 104 VRAFILAHVLKHWSIVDLGTTAQQSKMFFRLQSEHARLLTTLGDQSDQVER-----QLAD 158

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDFI-------EDKNAVSPLDSAIQ 606
                 E VR  L ++ +   SL+ P+ D   + L D +       E + A + L S + 
Sbjct: 159 TFKTSPEQVRANLQRLARRDASLDVPVVDGGITFL-DMLQADTTDQETQTAAAELSSVV- 216

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R   + +  +L  RE  ++  R         TL  +G+Q  +TRER+RQ+EA    +
Sbjct: 217 ---RNAVSELWPTLDCRERLIVDERLLPADGDPRTLAALGRQLGLTRERVRQLEAGVKDR 273

Query: 667 LK 668
           L+
Sbjct: 274 LR 275


>gi|289767896|ref|ZP_06527274.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289698095|gb|EFD65524.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 270

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VEA L +   +A ++ +RG  F DL Q   +GL+KA +++D   G  F +YA+  +
Sbjct: 41  RDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFESYAVPTI 100

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  +++  ++V    + +S  I  R PT  EIA++  +  E V
Sbjct: 101 TGEIKRHFRDHMWTLHVPRRVQELRNRVRFAGQDLSQTIPGRRPTVAEIAERAELSEEDV 160

Query: 564 RKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R  L+     T   +  E P G ED   LGD +   +    LD+ +    RE     LA+
Sbjct: 161 RVGLEALESFTALSLDAELP-GSEDGYSLGDALGAPDPA--LDTVVD---REAVKDRLAA 214

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L PRE  +L MRF   M      E++G  Q  V+R
Sbjct: 215 LPPRERAILYMRFFDDMTQSRIAEQLGISQMHVSR 249


>gi|145224454|ref|YP_001135132.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216940|gb|ABP46344.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium gilvum
           PYR-GCK]
          Length = 270

 Score = 80.9 bits (198), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 105/223 (47%), Gaps = 10/223 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++   L L    A+++  RG    DL Q  ++GL+ A ++FD   G  F  YA+  +   
Sbjct: 35  IIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLVNAVKRFDPDSGSDFLAYAVPTIMGE 94

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R   D S  +++P  ++D   ++ +    ++ ++ R PTP E+A  L +  E V +  
Sbjct: 95  VRRYFRDCSWAVKVPRRLKDLNSQLAKARAELTQQLGRAPTPSEVAAHLGIDREEVVQAT 154

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREER 626
             +    +L T   D  +   GDF+  +  +   D+ + A +   T R L   L PRE+ 
Sbjct: 155 IASSNYATLST---DSTSGPDGDFVALRETLGEPDARLDAVVDNETIRPLIEKLPPREQA 211

Query: 627 VLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLK 668
           VL++RF   M      E +G  Q  V+R     + AKA+  L+
Sbjct: 212 VLKLRFFDEMTQTQIAERMGYSQMHVSR-----LLAKALATLR 249


>gi|295696440|ref|YP_003589678.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412042|gb|ADG06534.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 256

 Score = 80.9 bits (198), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 121/254 (47%), Gaps = 17/254 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S +  ++  + R +++  + G+  A   ++ +V  N RLV SV +++  RG +  DL Q 
Sbjct: 9   STKAKLTDQQVRELIAQSQSGDAGA---RETLVLFNQRLVWSVVQRFLGRGYEPEDLFQI 65

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGLMKA +KFD     KFSTYA+  +   I R + D   T+++   +++    + R  
Sbjct: 66  GCIGLMKAIDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSVKETARHIRRAR 124

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIED 594
             ++ ++ R+P   E+A++L M    V       + P S+   +   D D   L D I D
Sbjct: 125 DELAKRLGRQPHINELAEELGMDPAEVVFTQDAMRAPASIHETVFENDGDPILLMDQIAD 184

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +      D       R   T  L  L  RE  ++ +RF      D T  EV +   +++ 
Sbjct: 185 EEQEKWFD-------RLALTDALNRLPERERLIVFLRF----FRDKTQSEVAEVLGISQV 233

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K + +++
Sbjct: 234 QVSRLEKKILNRIR 247


>gi|297203565|ref|ZP_06920962.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|297148443|gb|EFH28990.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 265

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 107/216 (49%), Gaps = 14/216 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++VEA L +   +A ++ +RG  F DL Q   +GL+KA +++D  LG+ F +YA+  +
Sbjct: 38  RGQVVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPALGHAFESYAVPTI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVE-- 561
              I R   D   T+ +P  ++D  ++V   ++ ++  I  R PT  EIA+  +M  E  
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRIASQDLAQTIPGRRPTVAEIAEHASMSEEDV 157

Query: 562 --GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLA 618
             G+  +   +   +  E P G ED   L D      A+   D A+   + RE+    LA
Sbjct: 158 LVGLEALESFSALSLDAELP-GSEDGYSLAD------ALGSFDPALDTVVDRESVKPRLA 210

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           +L  RE  +L MRF   M      E++G  Q  V+R
Sbjct: 211 ALPERERAILYMRFFGDMTQSRIAEQLGISQMHVSR 246


>gi|192362020|ref|YP_001983950.1| RNA polymerase factor sigma-32 [Cellvibrio japonicus Ueda107]
 gi|190688185|gb|ACE85863.1| alternative sigma factor RpoH [Cellvibrio japonicus Ueda107]
          Length = 286

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 116/234 (49%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 52  AARKLVMAHLRFVVHIARSYNGYGLPLGDLIQEGNVGLMKAVKRFDPDKGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R A++    +  +   E +A  L + V+ 
Sbjct: 112 IKAEIHEFILRNWRIVKIATTKAQRKLFFNLRGAKKRLAWLSNDEA-EAVALDLGVDVKQ 170

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR---- 615
           VR++   L              D++     +++ED N   P     +AN  E +      
Sbjct: 171 VREMEGRLASYDAGFDASDDDEDDNYVAPANYLED-NRYDPAARLEEANWEEASVNGLEM 229

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L  R   +L+ R+   +N D  TL ++  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 230 AMEKLDDRSRVILQRRW---LNDDKATLHDLAAEYGVSAERIRQLEKNAMNKVK 280


>gi|188586278|ref|YP_001917823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350965|gb|ACB85235.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 253

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 124/234 (52%), Gaps = 10/234 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +KG+ EA   +K ++E N+ LV SV K++   G++  DL Q G +GL+KA +KFD+    
Sbjct: 24  QKGDREA---RKIIIEENINLVKSVVKRFVGSGIEEEDLTQLGLMGLIKAIDKFDYRKEV 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA+  +   I   + D    I++  ++++  ++     R ++ K++REPT  E+A 
Sbjct: 81  RFSTYAVPLIIGEIKTFLRD-DHPIKVSRNLKELFNRSKEVKRWLTLKLRREPTISEVAD 139

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L +  E +    +  +E ISL+ P+ DE        + D    +  D+ I   L  T  
Sbjct: 140 ELEVSKEELATAEEANQELISLDKPVSDEHNHESEKALIDTIPDNSFDAKIHNEL--TIQ 197

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  L  ++ R++ +R+ +    + + +E G    +++ ++ ++E + +  L+
Sbjct: 198 ELLKKLDQKKRRLIVLRYFL----EKSQQETGVILGMSQVQVSRMERRILNNLQ 247


>gi|331088539|ref|ZP_08337452.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330407801|gb|EGG87295.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 239

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 46/158 (29%), Positives = 91/158 (57%), Gaps = 1/158 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KFD 
Sbjct: 5   IALIRKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDL 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++  +K V+   R+ + + R+PT E
Sbjct: 65  TYNVKFSTYAVPLISGEIKRFLRDDG-MIKVSRSLKEIAYKSVQARERLISSLGRDPTIE 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           E+++++ +  E + + ++   E  S+  P+  ++ S +
Sbjct: 124 ELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEI 161


>gi|1143379|dbj|BAA09444.1| sigma-32 homolog [Zymomonas mobilis]
          Length = 302

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV  +A  Y   GL   +LI EGNIGLM+  +KFD   G++ +TYA+WW
Sbjct: 53  AASRLVTSHLRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPEE---IAKKL 556
           +K +I   I      +++      K  K+    RR+ + +      +  P+E   IA  L
Sbjct: 113 IKASIQEYILRSWSLVKMGTTAAQK--KLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNL 170

Query: 557 AMPVEGVRKVLKITKEPI-----SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            +  E   +V+ + +        SL   + ++    + D++ D+    PL         E
Sbjct: 171 GVSNE---EVVNMNRRMAMGGDSSLNITMREDGEGQMQDWLVDQ---EPLQDQQIEEEEE 224

Query: 612 TTTR------VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  R       +  L  RE+ +L  R     +   TLEE+ + + V+RER+RQIE +A  
Sbjct: 225 SLVRHKLLIEAMDRLNDREKHILTERR--LSDNPKTLEELSQVYGVSRERVRQIEVRAFD 282

Query: 666 KLK 668
           KL+
Sbjct: 283 KLQ 285


>gi|92115102|ref|YP_575030.1| RNA polymerase factor sigma-32 [Chromohalobacter salexigens DSM
           3043]
 gi|91798192|gb|ABE60331.1| RNA polymerase, sigma 32 subunit, RpoH [Chromohalobacter salexigens
           DSM 3043]
          Length = 288

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 132/248 (53%), Gaps = 22/248 (8%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +  +G+ EA+   + +V ++LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++FD   
Sbjct: 42  LYEQGDLEAA---RRLVMSHLRFVVHIARSYSGYGLPQADLIQEGNVGLMKAVKRFDPTQ 98

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           G +  ++A+ W+K  I   +      ++I     + K+   +R A++    +  +   + 
Sbjct: 99  GVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRGAKKRLAWLNNDEV-DA 157

Query: 552 IAKKLAMPVEGVRKV-LKITKEPISLE-TPIGDEDTSHL--GDFIEDKNAVSPLDSAIQ- 606
           IAK L +  + VR++  +++      + TP  +ED  +     +++D+      D A Q 
Sbjct: 158 IAKDLDVKPQVVREMEGRLSAFDAGYDATPSEEEDQGYQAPAHYLDDER----FDPAAQL 213

Query: 607 --ANLRE-TTTRVLASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             A+  E +T R+ A+L   +ER   +L+ R+     +  TL E+   + V+ ERIRQ+E
Sbjct: 214 EAADWEEDSTHRLQAALGELDERSRDILQRRW--LAESKATLHELADVYGVSAERIRQLE 271

Query: 661 AKAIRKLK 668
             A++K+K
Sbjct: 272 KNAMKKIK 279


>gi|219856135|ref|YP_002473257.1| hypothetical protein CKR_2792 [Clostridium kluyveri NBRC 12016]
 gi|219569859|dbj|BAH07843.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 254

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 120/239 (50%), Gaps = 11/239 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++   R+G+ EA     ++VE NL LV +++KK+ NRG ++ D+ Q G +GLMKA   FD
Sbjct: 22  LIKCAREGDKEAL---NKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVNNFD 78

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++   +++   K+      ++ K+ REPT 
Sbjct: 79  ETYNVKFSTYAVPMILGEIKRFLRDDGM-IKVSRSIKNTAKKLHYDREALTKKLNREPTI 137

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+   +  E +    + T     L   I  +D S +   + DK + +P +  ++   
Sbjct: 138 EELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPV--LLIDKISENPKED-VEVID 194

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      L +L  +  +++ +R+      D T  +V K   + + ++ +IE K ++ ++
Sbjct: 195 RIALKEALRNLDVKSRQIIMLRYF----KDKTQVQVAKMLGINQVQVSRIEKKVLKTMR 249


>gi|153814969|ref|ZP_01967637.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
 gi|145847537|gb|EDK24455.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
          Length = 243

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 46/158 (29%), Positives = 91/158 (57%), Gaps = 1/158 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KFD 
Sbjct: 5   IALIRKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDL 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++  +K V+   R+ + + R+PT E
Sbjct: 65  TYNVKFSTYAVPLISGEIKRFLRDDG-MIKVSRSLKEIAYKSVQARERLISSLGRDPTIE 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           E+++++ +  E + + ++   E  S+  P+  ++ S +
Sbjct: 124 ELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEI 161


>gi|186684907|ref|YP_001868103.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186467359|gb|ACC83160.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 269

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 108/220 (49%), Gaps = 8/220 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            + ++V+ N  LV   A  +TN+  + + DL+Q G +GL++A EKF+   G+ FS+YA+ 
Sbjct: 39  VRNKLVKLNFGLVRKEAHYWTNQCHETYDDLLQVGCLGLIRAIEKFELSKGHAFSSYALP 98

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVE 561
           +++  I   + D+  T+RIP        + +  +R    K  R+PT  E+A  L + P E
Sbjct: 99  YIRGEIQHYLRDKGVTVRIPRKWLALQQQAIGVSRSWREKHNRQPTDTELAAALEISPNE 158

Query: 562 GVR-KVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               K+  I + P+SL+ PI  G+E ++ LG+ + D +  S    A +  LR    + L 
Sbjct: 159 WQEIKLAWINRAPLSLDVPIQDGEEGSTCLGELVPDPHYRS-FQLAQEDQLR--LQQALV 215

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            L  R   VL   F   +      E +G        R+++
Sbjct: 216 QLEQRTRDVLECVFLQDLTQKQVAEHLGISVVTVSRRVKK 255


>gi|148244663|ref|YP_001219357.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326490|dbj|BAF61633.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 277

 Score = 80.5 bits (197), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 125/238 (52%), Gaps = 23/238 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V +++R V  +A  Y   GL+  DL+QEG IGLMKA ++F+     + +++A++W
Sbjct: 45  AARKLVLSHMRFVAFIAHSYKGYGLEQADLVQEGTIGLMKAVKRFNPHRNVRLASFAVYW 104

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  I   I      +++      R    K+ +    + N +  E   ++IAK L     
Sbjct: 105 IRAEIHEFIFKNWKIVKVATTKAQRKLFFKLKQAKAHIYNSLNEEQA-DKIAKDL----- 158

Query: 562 GVRK--VL----KITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETT- 613
           GVR+  VL    ++    ++ E  + DE+ SH  + ++ ++N  +P    +  + ++T  
Sbjct: 159 GVRRKDVLEMESRLQFSDVTFE--VFDEEDSHAPEQYLTNENIQTPEQLLLTDDSKKTQQ 216

Query: 614 ---TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + L+SL  R   +L+ R+     T  TL  +  ++ +++ER+RQ+E KA++KLK
Sbjct: 217 QRLYKALSSLDERSLDILQSRYLKEEKT--TLYTLADKYSISKERVRQLETKAMQKLK 272


>gi|239941779|ref|ZP_04693716.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239988239|ref|ZP_04708903.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291445225|ref|ZP_06584615.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348172|gb|EFE75076.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 329

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 119/240 (49%), Gaps = 16/240 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+   G
Sbjct: 94  LEEGTHEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFELSRG 153

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    +S ++ R PT  E++
Sbjct: 154 VEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQQLDRAPTVAELS 213

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-N 608
           ++L +     VEG+      T   +  + P  D+    L D I  +      D  ++   
Sbjct: 214 ERLGITPDEVVEGMSASNAYTASSLDAK-PEEDDSEGALADRIGYE------DHGLEGIE 266

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++A+L  R+  +L +RF   M    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 267 YVESLKPLIAALPARDRMILSLRFVSNM----TQSEIGEELNISQMHVSRLLSRTLTKLR 322


>gi|297196939|ref|ZP_06914336.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197715922|gb|EDY59956.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 281

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 60/253 (23%), Positives = 134/253 (52%), Gaps = 34/253 (13%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           ++++ +G  E S A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA ++F+
Sbjct: 41  LAVLEEGTPEYSYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFE 100

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+++A+ ++   I R   D +  + +P  +++   ++ R    + +++ R PT 
Sbjct: 101 LTREVEFTSFAIPYIVGEIKRFFRDTTWAVHVPRRLQEARVQLARATEELRSRLGRTPTV 160

Query: 550 EEIAKKLAMPVEGVR--KVLKITKEPISLETPI-GDEDT-SHLGDFI----------EDK 595
           +E+++ +++  E VR  ++   +    SL+  I G ED  S L DFI          ED 
Sbjct: 161 KELSELMSLSEEEVREARLASNSYNSSSLDAAISGSEDGESALADFIGAEDRALELVEDF 220

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +A++PL               +A+L  R+ +++ MRF      + T  ++G++  V++  
Sbjct: 221 HALAPL---------------IAALDDRDRQIIHMRF----VEELTQAQIGERLGVSQMH 261

Query: 656 IRQIEAKAIRKLK 668
           + ++ ++ + +L+
Sbjct: 262 VSRLLSRTLARLR 274


>gi|326203397|ref|ZP_08193262.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325986655|gb|EGD47486.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 249

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 111/227 (48%), Gaps = 13/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L L   ++KK+ NRG+ F D+ Q   + L+KA E+F    G KF ++A   +
Sbjct: 29  RNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALIKAVERFSPEKGVKFISFATPTI 88

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+S TI+IP  + +    V +    ++ K+ R P  +EIA+ + + V+ V 
Sbjct: 89  LGEIKRFFRDKSTTIKIPRRIYESRQGVNKARDELTQKLSRVPRADEIAEYMGISVDTVL 148

Query: 565 KVLKITKEPI--SLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLT 621
           ++L+     I  SL+  I  E+ S LGD +  D+     +D+      ++   + L S  
Sbjct: 149 EILEAGSSSIVKSLDQSINQENDSELGDTLGYDEKTYEMIDN------KDFLEKALTSFN 202

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+  ++ R+   M      E +G    V++  I ++E K + K +
Sbjct: 203 DIEKEFIKYRYIQNMTQKQIAEILG----VSQMYISRMEKKILDKFR 245


>gi|326566649|gb|EGE16790.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 48

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 38/47 (80%), Positives = 43/47 (91%)

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           M +DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 1   MPSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 47


>gi|85710830|ref|ZP_01041891.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
 gi|85695234|gb|EAQ33171.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
          Length = 286

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 123/238 (51%), Gaps = 19/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A KE++ ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 51  AAKELIMSHLRFVVHIARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+M  ++    +   E +AK+L +  +
Sbjct: 111 IKAEIHEYVLRNWRVVKVATTKAQR--KLFFNLRKMKKRLGWFNQDEVETVAKELGVSSK 168

Query: 562 GVRKV-LKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            V ++  +++    + E    D+D     T     ++EDK   S L   I+    E  T+
Sbjct: 169 EVMEMEARMSAHDQAFELSSDDDDSKEGSTYSPAMYLEDKR--SDLAEEIETEDYEAHTQ 226

Query: 616 -----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 ++ L  R + +++ R+     +  TL ++  ++ V+ ER+RQ+E  A++KL+
Sbjct: 227 KKLFSAMSELDERSQDIVQSRW--LSESKVTLHDLAAKYEVSAERVRQLEQNAMKKLR 282


>gi|133286|sp|P11539|RP32_CITFR RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein
 gi|40469|emb|CAA33083.1| unnamed protein product [Citrobacter freundii]
          Length = 284

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 141/284 (49%), Gaps = 38/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKLHY-----QGDLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL+  DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLRQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+      +   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLG--WFNQDEVEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              +   +P++    + D+ +S+  D IE+ N     D A  AN     T  +  L  R 
Sbjct: 186 SDDESDSQPMAPVLYLQDK-SSNFADGIEEDNWE---DQA--AN---KLTHAMEGLDERS 236

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 237 QDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|70733139|ref|YP_262912.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf-5]
 gi|68347438|gb|AAY95044.1| transcription initiation factor sigma 32 [Pseudomonas fluorescens
           Pf-5]
          Length = 284

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 121/237 (51%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQ---ANLRETTT- 614
           VR++  ++T + ++ +     +D S      +++ED       D A+Q   A+  + +T 
Sbjct: 169 VREMESRLTGQDMAFDPAAEADDDSAFQSPANYLEDHR----YDPALQLEDADWSDNSTS 224

Query: 615 ---RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 225 NLHEALEVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|283780334|ref|YP_003371089.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283438787|gb|ADB17229.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 556

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 40/107 (37%), Positives = 64/107 (59%), Gaps = 8/107 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+++   S  T + + E  H+         EA   K  +V+ANLRLV+S+AK++ N   
Sbjct: 350 LRDKLDPASARTSV-MDEIEHLYE-------EAVAVKNSIVQANLRLVVSIAKRHVNGSE 401

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
            F  L+ +GN+ L++AAEKFD+  G KFSTYA W + +   R+I ++
Sbjct: 402 DFFGLVSDGNMSLIRAAEKFDFSRGNKFSTYASWAIMKNFARTIPEE 448



 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 40/55 (72%), Gaps = 1/55 (1%)

Query: 615 RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L  L  RE++++  RFG+  + +  TL+EVG +  VT+ER+RQIEA+A+ KL+
Sbjct: 489 KILEKLDEREQKIIISRFGLDHSHEPLTLKEVGHELGVTKERVRQIEARALNKLR 543


>gi|320010407|gb|ADW05257.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 326

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 118/241 (48%), Gaps = 16/241 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E +  +  +VE NL LV   A ++  R     D++Q G IGL+KA ++F+   G
Sbjct: 89  LEEGTHEYAYVRNTLVELNLALVKFAASRFRTRSEPMEDIVQVGTIGLIKAIDRFELSRG 148

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    +S ++ R PT  E+A
Sbjct: 149 VEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQQLDRAPTVAELA 208

Query: 554 KKLAMP----VEGVRKVLKITKEPISLET-PIGDEDTSHLGDFI-EDKNAVSPLDSAIQA 607
            +L +     VEG+      T   +  +    GD +   L D +  + N +  ++     
Sbjct: 209 DRLGLSRDEVVEGMAASNAYTASSLDAKPDDHGDGNEGALADRLGYEDNGLEGIEYI--- 265

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E+   ++ASL  R+  +L MRF   M    T  E+G++  +++  + ++ ++ + KL
Sbjct: 266 ---ESLKPLIASLPLRDRTILSMRFVSNM----TQSEIGEELGISQMHVSRLLSRTLVKL 318

Query: 668 K 668
           +
Sbjct: 319 R 319


>gi|91794849|ref|YP_564500.1| RNA polymerase factor sigma-32 [Shewanella denitrificans OS217]
 gi|91716851|gb|ABE56777.1| RNA polymerase sigma factor RpoH [Shewanella denitrificans OS217]
          Length = 284

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 121/234 (51%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + ++ +R+      E T   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQRKLFFNIRKSKKRLGWFSDAEVTM--VAENLGVSKA 169

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKN---AVSPLDSAIQANLRETTTR 615
            V ++  ++  +  + +    ++D +      ++ED +   A    ++  ++N +     
Sbjct: 170 DVTEMESRMAAQDPAFDIASDNDDETDFSPVHYLEDHSSDVAQQVENANWESNSQSRLFS 229

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  R + +L+ R+   ++ D  TL+E+ + + V+ ERIRQ+E  A+ KLK
Sbjct: 230 AIKTLDERSQHILQARW---LDDDKTTLQELAETYQVSAERIRQLEKNAMNKLK 280


>gi|290475011|ref|YP_003467895.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
 gi|289174328|emb|CBJ81122.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
          Length = 240

 Score = 80.5 bits (197), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 104/203 (51%), Gaps = 18/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERFDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
           V +T R++  ++ R  + +E+AK+L + +   R++L  T       + +   D  H    
Sbjct: 100 VTQTIRKLEQELGRPASEQEVAKELKINLIEYRQILLDTN-----NSQLFSYDEWHEIHG 154

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                 IED++  +PL   ++ +LR+    V+ SL  RE+ VL + +   +N    L+E+
Sbjct: 155 ESCEPVIEDEHETNPLQQLLEGDLRQRVIDVIESLPEREKMVLTLYYQEELN----LKEI 210

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ Q+ ++AI++L+
Sbjct: 211 GAVLNVGESRVSQLHSQAIKRLR 233


>gi|260461453|ref|ZP_05809700.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032523|gb|EEW33787.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 287

 Score = 80.5 bits (197), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 118/231 (51%), Gaps = 18/231 (7%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A K+ + GL   DLIQEG++GL++AA +F+     +FSTYA WW++ ++  
Sbjct: 47  AHMRLVISMASKFRHYGLPLGDLIQEGHVGLLEAAARFEPERDVRFSTYATWWIRASMQD 106

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVRK 565
            I      +R       K     + R   R++N    +  E    E++  L +    V  
Sbjct: 107 YILRNWSIVRGGTSSAQKALFFNLRRLRARLANGAEPLSNETLYREVSVALGVSEADVAM 166

Query: 566 V-LKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL------ 617
           +  +++    SL  P+ D+   +   DF+   +   PL   + ++  +   R +      
Sbjct: 167 MDSRLSAPDSSLNVPLADDAGATERMDFLVSDD---PLPDEVVSDRIDVARRSVWLKAAL 223

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+L  RE R++  R     +   TLE +G+   +++ER+RQIEA+A+ KLK
Sbjct: 224 AALNARELRIIEERR--LSDEGATLEALGETLGISKERVRQIEARAMEKLK 272


>gi|118602568|ref|YP_903783.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
 gi|118567507|gb|ABL02312.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 280

 Score = 80.5 bits (197), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 124/241 (51%), Gaps = 29/241 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V +++R V  +A  Y   GL+  DL+QEG IGLMKA ++F+     + +++A++W
Sbjct: 45  AARKLVLSHMRFVAFIAHGYKGYGLEQADLVQEGTIGLMKAVKRFNPNRNVRLASFAVYW 104

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP------EEIAKKLA 557
           ++  I   I      +++            +  R++  K+K+          EE A K+A
Sbjct: 105 IRAEIHEFIFKNWKIVKVA---------TTKAQRKLFFKLKQAKAHIYSSLNEEQADKIA 155

Query: 558 MPVEGVRK--VL----KITKEPISLETPIGDEDTSHLGDFIEDKNAVSP----LDSAIQA 607
             + GVR+  VL    ++    ++ E    DED+     ++ ++N  +P    L +  + 
Sbjct: 156 NDL-GVRRKDVLEMESRLQFNDVTFEVS-DDEDSLAPEQYLTNENVQTPEQLLLINDSKQ 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N ++   + L+SL  R   +L+ R+     T  TL  +  ++ +++ER+RQ+E KA++KL
Sbjct: 214 NQQQQLYKALSSLDERSLDILQSRYLKEEKT--TLHTLADKYGISKERVRQLETKAMQKL 271

Query: 668 K 668
           K
Sbjct: 272 K 272


>gi|319795672|ref|YP_004157312.1| RNA polymerase, sigma 32 subunit, rpoh [Variovorax paradoxus EPS]
 gi|315598135|gb|ADU39201.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus EPS]
          Length = 313

 Score = 80.5 bits (197), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 28/250 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGALILSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP------------TPEE 551
           +K  I   I      +++      +  K+    R M    K +             +P+E
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADSAASDNGTHRETLSPDE 177

Query: 552 I---AKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +   A +L + P E +    +++   + L+    D+     G      +A     + +++
Sbjct: 178 VSQMATRLNVKPEEVLEMETRLSGGDVLLDPGPSDDGDEAFGPIAYLADATQEPTALLES 237

Query: 608 NLRETTTR-----VLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQ 658
             R+  +       L +L  R  R++  R+ + +N D     TL ++   + V+ ERIRQ
Sbjct: 238 QQRDRLSSDGIATALEALDARSRRIVEERW-LKVNDDGSGGMTLHDLAAVYGVSAERIRQ 296

Query: 659 IEAKAIRKLK 668
           IE  A++K+K
Sbjct: 297 IEVAAMKKMK 306


>gi|302385749|ref|YP_003821571.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
 gi|302196377|gb|ADL03948.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
          Length = 203

 Score = 80.5 bits (197), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 39/141 (27%), Positives = 80/141 (56%), Gaps = 2/141 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK--FSTYAM 501
           AKK +VE NLR  +  A++Y  RG+   DL+QE N+ LM A E+F      +  F ++  
Sbjct: 38  AKKRLVEGNLRTALEYAREYDGRGVLITDLVQEANMALMMAVEEFSAMENGRLAFDSFTG 97

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +++A+T ++ +Q    +    +  +++ + + ++ ++ ++ RE T EE+A K+ M VE
Sbjct: 98  RKIREALTAAVEEQQSACQTGEELAARVNVLQKVSQALAGELGREATVEELADKMKMSVE 157

Query: 562 GVRKVLKITKEPISLETPIGD 582
            ++ ++K+  + +S+     D
Sbjct: 158 EIKGIMKMAMDAMSMNAETMD 178


>gi|332308280|ref|YP_004436131.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175609|gb|AEE24863.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 283

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A ++++ ++LR V+ +AK Y+  GL   DLIQEGNIGLMKA  +FD  +G +  ++A+ 
Sbjct: 50  LAARKLIMSHLRFVVHIAKSYSGYGLPQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVH 109

Query: 503 WVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           W+K  I   +      +++      R     + +  +R+      E   +++A  L +  
Sbjct: 110 WIKAEIHEFVLRNWRIVKVATTKAQRKLFFNLRKNKKRLGWFTHAE--VQKVASDLGVSE 167

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNA---VSPLDSAIQANLRETTT 614
           + V ++  +++    + +    D+++       F+EDK+       +++   A   +   
Sbjct: 168 KEVLQMEARMSSHDQAFDLSADDDESGSFAPVQFLEDKSPDVETEVVNADWDATASQKLY 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +L  R + +++ R+     T  TL+++  ++ V+ ER+RQIE  A++KL+
Sbjct: 228 SAIKTLDERSQHIIQTRWLSDDKT--TLQDLADKYQVSAERVRQIEKNAMKKLQ 279


>gi|182438259|ref|YP_001825978.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326778910|ref|ZP_08238175.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178466775|dbj|BAG21295.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326659243|gb|EGE44089.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 323

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/250 (25%), Positives = 119/250 (47%), Gaps = 36/250 (14%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +G  E S  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+   G
Sbjct: 88  LEEGTHEYSYVRNTLVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFELSRG 147

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  +   I R   D S ++R+P  +++    + +    +S ++ R PT  E++
Sbjct: 148 VEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQQLDRAPTVAELS 207

Query: 554 KKLAMP----VEGVRKVLKITKEPI-----------SLETPIGDEDTSHLGDFIEDKNAV 598
           ++L +     VEG+      T   +           +L   IG ED S  G  IE   ++
Sbjct: 208 ERLGISPEEVVEGMSASNAYTASSLDAKPEEDDGEGALADRIGYEDHSLEG--IEYVESL 265

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PL               +A+L  R+  +L +RF   M    T  E+G++  +++  + +
Sbjct: 266 KPL---------------IAALPARDRMILSLRFVSNM----TQSEIGEELNISQMHVSR 306

Query: 659 IEAKAIRKLK 668
           + ++ + KL+
Sbjct: 307 LLSRTLTKLR 316


>gi|53802588|ref|YP_112675.1| RNA polymerase factor sigma-32 [Methylococcus capsulatus str. Bath]
 gi|53756349|gb|AAU90640.1| RNA polymerase sigma-32 factor [Methylococcus capsulatus str. Bath]
          Length = 286

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 117/238 (49%), Gaps = 18/238 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ANLR V  +A+ Y   GL   DLIQEGNIGLMKA +++D  +G +  ++A+ W
Sbjct: 49  AARRLVLANLRFVAYIARGYLGYGLPLADLIQEGNIGLMKAVKRYDPDVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPV 560
           ++  I   I      ++I      +  K+    R+M N++    TP     +A +L + V
Sbjct: 109 IRAEIHEFIIQNWRIVKIATTKAQR--KLFFNLRKMKNRLG-WLTPEEAAAVAAELGVDV 165

Query: 561 EGVRKVLKITKEP-ISLETPI---GDEDTSHLGDFIEDKNAVSPL----DSAIQANLRET 612
           E V K+      P ++LE      GD+  SH       +    P      S  +   +E 
Sbjct: 166 EDVYKMENRLNNPDMALEAHGEDDGDDRESHAPIHYLQQEGGDPALLIEHSEWENRQQEK 225

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +  L  R   ++  R+   ++ D  TL ++  ++ V+ ERIRQ+E+ A++KL++
Sbjct: 226 LQEAIGQLDERSRDIVASRW---LSEDKLTLHDLAARYNVSAERIRQLESSAMKKLRN 280


>gi|239817346|ref|YP_002946256.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
 gi|239803923|gb|ACS20990.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
          Length = 313

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 28/250 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W
Sbjct: 60  AAGALILSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP------------TPEE 551
           +K  I   I      +++      +  K+    R M    K +             +P+E
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGFKADSAAADNGTHRDTLSPDE 177

Query: 552 I---AKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +   A +L + P E +    +++   + L+    D+     G      +A     + +++
Sbjct: 178 VSQMATRLNVKPEEVLEMETRLSGGDVLLDPGPSDDGDEAFGPIAYLADATQEPTALLES 237

Query: 608 NLRETTTR-----VLASLTPREERVLRMRFGIGMNTDH----TLEEVGKQFCVTRERIRQ 658
             R+  +       L +L  R  R++  R+ + +N D     TL ++   + V+ ERIRQ
Sbjct: 238 QQRDRLSSDGIATALEALDDRSRRIVEERW-LKVNDDGSGGMTLHDLAAVYGVSAERIRQ 296

Query: 659 IEAKAIRKLK 668
           IE  A++K+K
Sbjct: 297 IEVAAMKKMK 306


>gi|153955768|ref|YP_001396533.1| sporulation sigma factor SigF [Clostridium kluyveri DSM 555]
 gi|146348626|gb|EDK35162.1| RNA polymerase sigma-F factor [Clostridium kluyveri DSM 555]
          Length = 251

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 120/239 (50%), Gaps = 11/239 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++   R+G+ EA     ++VE NL LV +++KK+ NRG ++ D+ Q G +GLMKA   FD
Sbjct: 19  LIKCAREGDKEAL---NKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVNNFD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++   +++   K+      ++ K+ REPT 
Sbjct: 76  ETYNVKFSTYAVPMILGEIKRFLRDDGM-IKVSRSIKNTAKKLHYDREALTKKLNREPTI 134

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A+   +  E +    + T     L   I  +D S +   + DK + +P +  ++   
Sbjct: 135 EELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPV--LLIDKISENPKED-VEVID 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      L +L  +  +++ +R+      D T  +V K   + + ++ +IE K ++ ++
Sbjct: 192 RIALKEALRNLDVKSRQIIMLRYF----KDKTQVQVAKMLGINQVQVSRIEKKVLKTMR 246


>gi|284050443|ref|ZP_06380653.1| RNA polymerase sigma factor SigF [Arthrospira platensis str.
           Paraca]
 gi|291567732|dbj|BAI90004.1| group 3 RNA polymerase sigma factor SigF [Arthrospira platensis
           NIES-39]
          Length = 261

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 124/255 (48%), Gaps = 20/255 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N++KS S+E    + E++H           ++  + ++V+ N+ LV      + N+  
Sbjct: 5   VSNQLKSESLEL---LREYQH---------SPSNSIRNQLVQINIGLVRKEVHHWLNQCT 52

Query: 469 Q-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + + DL+Q G IGL++A E+FD   G+ FS++A+ +++  I   + D+S ++R+P     
Sbjct: 53  ESYDDLLQVGCIGLIRAIERFDMSKGHAFSSFAIPYIRGEIQHYLRDKSPSVRVPRQWLT 112

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE--GVRKVLKITKEPISLETPIGDED- 584
            + K     + +  K+ R+PT  EIA  L + VE     K+    +  +SL+ PI DE+ 
Sbjct: 113 LLRKATPCIQELQVKLGRKPTDVEIASALEISVEEWNQVKLASQNRSLLSLDAPIQDEEE 172

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            ++ LGD + D    S    A +  +R    + L  L     +VL   F   +    T E
Sbjct: 173 GSTSLGDLVPDTRYRS-FQLAQEDQIR--LQQALGHLEDGTRKVLEFVFLYDLTQKETAE 229

Query: 644 EVGKQFCVTRERIRQ 658
           ++G        R+++
Sbjct: 230 KLGISAVTVSRRVKR 244


>gi|197103189|ref|YP_002128567.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480465|gb|ACG79992.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 310

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 116/240 (48%), Gaps = 22/240 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ ++LRL   +A  Y   GL   D+I E N+GL+ A  KFD     + STYA WW
Sbjct: 52  AAHRLMTSHLRLAAKIACGYRGYGLPLEDMISEANVGLLHAIYKFDLERDCRLSTYAAWW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ A+   I      +++      K  ++    RR   +++  P+         ++A+  
Sbjct: 112 IRAALQDYILRHWSIVKLGTSATQK--RLFFGFRRARARVEACPSELLAGDSIAKMAELF 169

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +P   +  +  ++    +SL    GDE      + + D+NA  P  +  +A+ R+  TR
Sbjct: 170 HVPPGDITGMEARLGWRDLSLSALHGDEGEPDRLERLADENAQDPETALSEADERDYRTR 229

Query: 616 VLA-SLTP---REERVL---RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L  +L+P   RE R+    R+R     +    L E+ +++ V+ ERIRQIE +A  K++
Sbjct: 230 LLTQALSPLGSREHRIFVARRLR-----DPPAPLAELAQEYGVSCERIRQIEMRAFEKVQ 284


>gi|300721688|ref|YP_003710964.1| sigma H (sigma 32) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297628181|emb|CBJ88736.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus nematophila ATCC
           19061]
          Length = 285

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/234 (25%), Positives = 123/234 (52%), Gaps = 11/234 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      +++     + K+   +R A++      ++   E +AK+L +  + 
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFNQDEI-ELVAKELGVTSKD 167

Query: 563 VRKV-LKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TT 614
           VR++  +++ + ++ +    D+  D+  +   +  ++  S     I+ +  E       +
Sbjct: 168 VREMESRMSAQDMAFDMSADDDNHDSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLS 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  R + ++R R+ +      TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 228 VAMEGLDERSQDIIRARW-LDDENKTTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|226359630|ref|YP_002777408.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226238115|dbj|BAH48463.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 265

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 121/233 (51%), Gaps = 14/233 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EAS  + E++   L L   +A+++  RG    DL+Q   +GL+KA ++FD   G+ F +Y
Sbjct: 37  EASALRDEIITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSY 96

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  +   + R   D   ++R+P  M++    + +    +S ++ R P+  EIA +L + 
Sbjct: 97  AVPTIMGEVRRYFRDTGWSMRVPRRMQELHALIAKAVDELSQELGRSPSASEIAAELELD 156

Query: 560 VEGVRKVL--KITKEPISLETPIGDE-DTSHLGDFI-EDKNAVSPLDSAIQANLRETTTR 615
           V  V + L  K   + +S++  +GD+ D   L + + E+   ++ ++S   A++R     
Sbjct: 157 VREVSEGLLAKNAYQTLSMDAAMGDDPDDLPLAETLGEEDPELANVES--HASVRPA--- 211

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L P E RVL +RF   M    T  E+ ++  V++ ++ +I A+ +  L+
Sbjct: 212 -LEKLPPLERRVLMLRFFGSM----TQTEIAQRVGVSQMQVSRILARTLSGLR 259


>gi|209524790|ref|ZP_03273336.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Arthrospira
           maxima CS-328]
 gi|209494669|gb|EDZ94978.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Arthrospira
           maxima CS-328]
          Length = 255

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 124/255 (48%), Gaps = 20/255 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N++KS S+E    + E++H           ++  + ++V+ N+ LV      + N+  
Sbjct: 5   VSNQLKSESLEL---LREYQH---------SPSNSVRNQLVQINIGLVRKEVHHWLNQCT 52

Query: 469 Q-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + + DL+Q G IGL++A E+FD   G+ FS++A+ +++  I   + D+S ++R+P     
Sbjct: 53  ESYDDLLQVGCIGLIRAIERFDMSKGHAFSSFAIPYIRGEIQHYLRDKSPSVRVPRQWLT 112

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE--GVRKVLKITKEPISLETPIGDED- 584
            + K     + +  K+ R+PT  EIA  L + VE     K+    +  +SL+ PI DE+ 
Sbjct: 113 LLRKATPCIQDLQVKLGRKPTDAEIASALEISVEEWNQVKLASQNRSLLSLDAPIQDEEE 172

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            ++ LGD + D    S    A +  +R    + L  L     +VL   F   +    T E
Sbjct: 173 GSTSLGDLVPDTRYRS-FQLAQEDQIR--LQQALGHLEDGTRKVLEFVFLYDLTQKETAE 229

Query: 644 EVGKQFCVTRERIRQ 658
           ++G        R+++
Sbjct: 230 KLGISAVTVSRRVKR 244


>gi|84872788|gb|ABC67485.1| RpoH2 [Sinorhizobium sp. BL3]
          Length = 286

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 126/246 (51%), Gaps = 17/246 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  +++RLV+++A K+ + GL   DL+QEG+IGL++AA +F+     +FSTYA WW
Sbjct: 40  ARNKIAMSHMRLVVAMAAKFRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWW 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAM 558
           ++ ++   +      +R       K     + R   R++    ++  +   EEIA  L +
Sbjct: 100 IRASMQDYVLRNWSIVRGGTSSAQKALFFNLRRLRARLAQGDRQLTSQAMHEEIAAALGV 159

Query: 559 PVEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +  V+ +  +++    SL+ P+  GD ++    DF+   +A  P +   +    E   R
Sbjct: 160 SLADVQTMDARLSGNDASLQAPVGHGDAESGARLDFLPS-DAPLPDEQVSEMIDGERARR 218

Query: 616 VLAS----LTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            L S    L+ RE +++R R    ++ D  TLEE+G    +++ER+R    ++   ++  
Sbjct: 219 WLHSALRELSEREMKIIRARR---LSEDGATLEELGVALGISKERVRSKRGRSKSCVRRS 275

Query: 671 SRSKKL 676
            R+  L
Sbjct: 276 PRAPAL 281


>gi|262369666|ref|ZP_06062994.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
 gi|262315734|gb|EEY96773.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
          Length = 289

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 122/246 (49%), Gaps = 36/246 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKLLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRT------------ARRMSNKIKREPTPE 550
           +K  I   +      ++I     + K+   +R+            A+ ++N +    TPE
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLKEAQSIANDLN--VTPE 170

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGD--FIEDKNAVSPLDSAIQ 606
           ++     + +EG     ++T    + E    D+D  ++H+    ++ED N   P   A +
Sbjct: 171 QV-----LEMEG-----RLTAYDAAFEAQGDDDDEGSTHVAPALYLED-NRYDPARLAEE 219

Query: 607 ANLRETTTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            +  E +T  L      L  R   +L+ R+    +   TL E+  ++ V+ ERIRQ+E  
Sbjct: 220 EDYEEQSTNALHDAMEQLDDRSRNILQRRWLD--DEKSTLHELAAEYNVSAERIRQLEKN 277

Query: 663 AIRKLK 668
           A+ K+K
Sbjct: 278 AMEKIK 283


>gi|113867637|ref|YP_726126.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia
           eutropha H16]
 gi|113526413|emb|CAJ92758.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia
           eutropha H16]
          Length = 656

 Score = 80.1 bits (196), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 79/145 (54%), Gaps = 14/145 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L RQRGY+T  +++  LP +   +  ME  V+  + MG+ +     D + L   +
Sbjct: 46  RALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVSTFAEMGVKIYEQTPDAETLLLSD 105

Query: 88  G----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           G    S+D  D  +  + ++V      DS    T DPVRMY+REM S  LL+R+ E+ IA
Sbjct: 106 GPVVASDDQADEEAEVALATV------DSEFGRTTDPVRMYMREMSSATLLTRKQEVEIA 159

Query: 144 KRIEAGRAMMMASLCESPLTFQALI 168
           KRIE G   M+ ++   P T  A++
Sbjct: 160 KRIEEGLNNMVHAISACPFTIAAIL 184


>gi|329295846|ref|ZP_08253182.1| RNA polymerase factor sigma-32 [Plautia stali symbiont]
          Length = 285

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/284 (23%), Positives = 139/284 (48%), Gaps = 37/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    ++ E   +++E  H      +G+ +A+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYVRAANNWPVLTAEEEKALAERLHY-----QGDLDAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++  
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKAA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +A++L +  + V ++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVLEMESRMAAQDMTFDMS 185

Query: 580 IGD---------------EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             D               + TS   D IE+ N          A+  +  +  + SL  R 
Sbjct: 186 SDDDAGEGKPMAPVLYLQDKTSDFADGIEEDN--------WDAHAADKLSDAMLSLDERS 237

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 238 QHIIRARW-LDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|295836278|ref|ZP_06823211.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
 gi|197697357|gb|EDY44290.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
          Length = 279

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 104/214 (48%), Gaps = 18/214 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 76  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 132

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE--TPIGDEDTSH 587
           V R    +  K++R P+  E+A+++ + VE +  V         ++LE    +G E    
Sbjct: 133 VERAYATLEAKLRRTPSEAEVAREMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGR 192

Query: 588 LG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L   D +ED +A +P++ A    LR   +R + SL  RE+ V+ + +  G+    TL E+
Sbjct: 193 LSIMDTLEDTDADNPVEVAEGRELRRLLSRAINSLPEREKTVVMLYYYEGL----TLAEI 248

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 249 GHVLGVTESRVSQIHTKSVLQLR-----AKLSSF 277


>gi|165922507|ref|ZP_02219678.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212211687|ref|YP_002302623.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuG_Q212]
 gi|165916712|gb|EDR35316.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212010097|gb|ACJ17478.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuG_Q212]
          Length = 288

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 117/236 (49%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 51  AARKLVLSHLRFVVRIARGYSGYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           ++  I   I      ++I      +  K+    R+ + K       E   +A++L +  +
Sbjct: 111 IRAEIHEFILKNWRIVKIATTKAQR--KLFFNLRKHAKKRGWFSDHEAFALAEELNVSTK 168

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLG---DFIEDK--NAVSPLDSAIQANLRETT 613
            VR++   L    E         D  T   G    ++EDK  N    L+ +  A+ +E  
Sbjct: 169 DVRQMEERLNSYDEAFDGADEESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHR 228

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  R   +L  R+     +  TL E+  Q+ V+ ERIRQ+E  A++K++
Sbjct: 229 LHNAMQSLDDRSRDILYQRWLSEKKS--TLHELAAQYAVSAERIRQLEKNAMQKIR 282


>gi|160933635|ref|ZP_02081023.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
 gi|156867512|gb|EDO60884.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
          Length = 217

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 115/229 (50%), Gaps = 24/229 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +E+N+ LV + AK++  RG+++ DL+Q G +GL+KA + FD   G +FSTYA+  +
Sbjct: 4   REQAIESNMGLVHACAKRFRGRGIEYDDLVQAGCLGLVKAVDHFDEGRGLQFSTYAVPVI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    I++   +++   K  R     S +  R+PT  E+A++L +      
Sbjct: 64  LGEMRRLFRD-GGAIKVGRALKELSLKAARACNEFSLREGRQPTISELAEQLGVEPAEAS 122

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLAS 619
           + L  +++P+SL                +++N    +D   +A   + +      +V+  
Sbjct: 123 QALGASQQPLSLSA--------------DEENGGGQIDVPTEAPEEKISELIALKQVVGE 168

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PR+  ++ MRF        T E +G    +T+ ++ + E K +++LK
Sbjct: 169 LDPRDRSLIVMRFFKSRTQTQTAEVLG----MTQVQVSRREKKILQELK 213


>gi|85058065|ref|YP_453767.1| RNA polymerase factor sigma-32 [Sodalis glossinidius str.
           'morsitans']
 gi|84778585|dbj|BAE73362.1| RNA polymerase sigma-32 factor RpoH [Sodalis glossinidius str.
           'morsitans']
          Length = 285

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/288 (23%), Positives = 142/288 (49%), Gaps = 45/288 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E   +++E  H      +G+ EA+   K+++ ++LR V+ +A+ 
Sbjct: 16  LEAYVRAANAYPMLTAEEERALAERLHY-----QGDLEAA---KKLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                R     + +T +R+    + E   E +AK+L +  + VR++  ++  + ++ +  
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVAKELGVTSKDVREMESRMAAQDMTFDPT 185

Query: 580 IGDE---------------DTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASL 620
             DE                +S   D IE+ N    A   L +A++             L
Sbjct: 186 PEDEAREGQPMAPMLYLQDKSSDFADGIEEDNWDDHAADKLSAALEG------------L 233

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K++
Sbjct: 234 DERSQDIIRARW-LDDDNKSTLQELADRYGVSAERVRQLEKNAMKKMR 280


>gi|266620503|ref|ZP_06113438.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
 gi|288867868|gb|EFD00167.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
          Length = 237

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 123/258 (47%), Gaps = 41/258 (15%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   ++ M  +G+ EA   +  +V  N+ L+ S+ +++T RG    DL Q G+IGLMKA 
Sbjct: 3   ETMRLIEMAHEGDKEA---RDRLVTENMGLIWSIVRRFTGRGYDPEDLFQIGSIGLMKAI 59

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK- 544
           +KFD     KFSTYA+  +   I R + D            D + KV R+ + M  ++K 
Sbjct: 60  DKFDMSFDVKFSTYAVPMITGEIKRFLRD------------DGMIKVSRSIKEMGTRVKC 107

Query: 545 ----------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFI 592
                     REPT EEIA +L    E V   ++   E  SL   +   DE++  L D I
Sbjct: 108 VREALGFTLGREPTIEEIAGELGASKEEVAASIEAGAEVESLYRTVNKNDENSILLIDKI 167

Query: 593 EDKNAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           E+       +S+ Q  L  R     +L  L+ ++  ++  R+      + T  ++     
Sbjct: 168 EE-------ESSAQEELLNRMVLRELLTGLSDKDREIIIRRY----YYNETQSQIASHLG 216

Query: 651 VTRERIRQIEAKAIRKLK 668
           +++ ++ ++E K +++++
Sbjct: 217 ISQVQVSRLEKKILKQMR 234


>gi|78221650|ref|YP_383397.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78192905|gb|ABB30672.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           metallireducens GS-15]
          Length = 250

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 99/201 (49%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+    IGL+ AAE+FD   G +F T+A   ++  I   +  Q    R    +RDK  K
Sbjct: 50  DLMSAAVIGLITAAERFDPSRGVQFKTFAEQRIRGTIIDELRSQDWLTR---SLRDKFKK 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + R    + +++ R PT EE+AK L + V+    +L+       +SL+    DED S  G
Sbjct: 107 LEREFVMLEHRLGRNPTSEEVAKSLEISVDDYHHMLEEIHLLSFVSLDESWEDEDGSPFG 166

Query: 590 --DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D +EDK   +P    +   + +T T  +  L  +E  V+   +   +N    L+E+G 
Sbjct: 167 LLDILEDKGVENPQSQLMARQMLDTLTEAIEGLPEKERLVITFYYYEELN----LKEIGA 222

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+ ++AI +L+
Sbjct: 223 VLDLSESRISQLHSQAIVRLR 243


>gi|153209360|ref|ZP_01947367.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212217703|ref|YP_002304490.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuK_Q154]
 gi|120575393|gb|EAX32017.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212011965|gb|ACJ19345.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuK_Q154]
          Length = 288

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 117/236 (49%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 51  AARKLVLSHLRFVVRIARGYSGYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           ++  I   I      ++I      +  K+    R+ + K       E   +A++L +  +
Sbjct: 111 IRAEIHEFILKNWRIVKIATTKAQR--KLFFNLRKHAKKRGWFSDHEAFALAEELNVSTK 168

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLG---DFIEDK--NAVSPLDSAIQANLRETT 613
            VR++   L    E         D  T   G    ++EDK  N    L+ +  A+ +E  
Sbjct: 169 DVRQMEERLNSYDEAFDGADEESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHR 228

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  R   +L  R+     +  TL E+  Q+ V+ ERIRQ+E  A++K++
Sbjct: 229 LHNAMQSLDDRSRDILYQRWLSEKKS--TLHELAAQYAVSAERIRQLEKNAMQKIR 282


>gi|251795840|ref|YP_003010571.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
 gi|247543466|gb|ACT00485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
          Length = 258

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 125/239 (52%), Gaps = 15/239 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A+ A  +  E+ +R+ +S  K   NR   + DL Q G + +++  +++D   G  F  Y
Sbjct: 27  DAATALLQHFESLVRMAVS--KISRNRPDLYEDLYQVGQMSMLRLFKQYDSDKGVPFEGY 84

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   +   + D+S  I++P +M++K   + +    ++ K++R P  +EIA  L + 
Sbjct: 85  AMKSVIGQLKNYLRDKSWYIQVPRNMKEKGLLIQKAIDELTTKLERSPKMDEIAAYLGLS 144

Query: 560 VEGVRKVL--KITKEPISLETPIGDE-DTSHLGDFIED-KNAVSPLDSAIQANLRETTTR 615
           VE   +VL  + + + +SL+TP+  E D++ +GD I D  +  S +D+ I        + 
Sbjct: 145 VEETIEVLSSRESYQYVSLDTPLSSEGDSATIGDVISDHSDKYSHVDNQI------ALSD 198

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +A L   E +VL + +  G +     +++G  Q  V+R + R ++   +R+L HP +S
Sbjct: 199 AMAQLKEEERKVLVLVYQHGQSQREIADQLGVSQMSVSRFQKRALD--KLRQLLHPPQS 255


>gi|238022360|ref|ZP_04602786.1| hypothetical protein GCWU000324_02267 [Kingella oralis ATCC 51147]
 gi|237866974|gb|EEP68016.1| hypothetical protein GCWU000324_02267 [Kingella oralis ATCC 51147]
          Length = 654

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 87/166 (52%), Gaps = 8/166 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           +++I   ++RGY+T  E+N  LP D   +EQ+++ V M+  +GI V     D D L   +
Sbjct: 32  RRLIIQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDADSLLMND 91

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S    D  + A   +   Q   DS    T DPVRMY+REMG ++LL+RE EI IAK IE
Sbjct: 92  NSTAITDEDAVAEAEAALSQA--DSEFGRTTDPVRMYMREMGQVDLLTREDEIKIAKEIE 149

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
                M+ ++   P +   ++   +++      + E++  EA I P
Sbjct: 150 NALKNMIQAISACPGSIGEILDLINQIKKDEIKVDEVV--EAIIDP 193


>gi|237728776|ref|ZP_04559257.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|283835854|ref|ZP_06355595.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
 gi|226909398|gb|EEH95316.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|291068027|gb|EFE06136.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
          Length = 284

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 73/284 (25%), Positives = 141/284 (49%), Gaps = 38/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ VA+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKLHY-----QGDLEAA---KTLILSHLRFVVHVARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-------------- 566
                R     + +T +R+    + E   E +A++L +  + VR++              
Sbjct: 128 TTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMS 185

Query: 567 --LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              +   +P++    + D+ +S+  D IE+ N     D A  AN     T  +  L  R 
Sbjct: 186 SDDESDSQPMAPVLYLQDK-SSNFADGIEEDNWE---DQA--AN---KLTHAMEGLDERS 236

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 237 QDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|119485331|ref|ZP_01619659.1| sigma factor SigF [Lyngbya sp. PCC 8106]
 gi|119457087|gb|EAW38213.1| sigma factor SigF [Lyngbya sp. PCC 8106]
          Length = 259

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 119/234 (50%), Gaps = 9/234 (3%)

Query: 431 VSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKF 488
           + ++R  +C  S   + ++V+ N+ LV      + N+  + + DL+Q G IGL++A E+F
Sbjct: 14  LELLRDYQCSNSKELRNQLVQLNIGLVRKEVHHWVNQCTENYDDLLQVGCIGLIRAIERF 73

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G+ FS++A+ +++  I   + D+S  +R+P H      + ++ A+ +  K+KR+PT
Sbjct: 74  DLSKGHAFSSFAIPYIRGEIQHYLRDKSLPLRVPRHWLTLQRQGMKLAQELQVKLKRQPT 133

Query: 549 PEEIAKKLAMP-VEGVR-KVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSA 604
             EIA+ L +   E  + K+    +  +SL+ P+ DE+  T+ LG+ + D N       A
Sbjct: 134 DTEIARGLNISETEWSQVKLAGYNRSLLSLDAPVQDENEGTTCLGELVPD-NRYRSFQLA 192

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            +  +R    + L+ L     +VL   F   +    T E +G        R+++
Sbjct: 193 QEDQIR--LQQGLSKLEEGTRKVLEFVFLYDLTQKETAERLGISAVTVSRRVKK 244


>gi|261344963|ref|ZP_05972607.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
 gi|282567106|gb|EFB72641.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
          Length = 291

 Score = 79.7 bits (195), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/286 (23%), Positives = 137/286 (47%), Gaps = 40/286 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    +S E    ++E  H       G+ EA+   K+++ ++LR VI +A+ 
Sbjct: 16  IEAYIRAANTYPMLSAEEEKELAERLHY-----DGDLEAA---KQLILSHLRFVIHIARS 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-------------- 566
                +  K+    R+   ++    +   + +A++L +  + V ++              
Sbjct: 128 TTKSQR--KLFFNLRKNKKRLGWFNQDEVDMVAQELGVSTKDVLEMESRMAAQDMAFDMS 185

Query: 567 ----LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     PI+    + D+ +   G  IED N         +++  +  +  LASL  
Sbjct: 186 DDDDSGDFGGPIAPVLYLQDKSSDFAGS-IEDDN--------WESHATDRLSDALASLDE 236

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R + ++R R+ +  ++  TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 237 RSQDIIRARW-LDDDSKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|318075685|ref|ZP_07983017.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actF]
          Length = 259

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 18/214 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 56  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE--TPIGDEDTSH 587
           V R    +  K+ R PT  E+A ++ + VE +  V         ++LE    +G E    
Sbjct: 113 VERAYATLEAKLHRTPTEVEVASEMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGR 172

Query: 588 LG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L   D +ED  A +P++ A    LR+  +R + SL  RE+ V+ + +  G+    TL E+
Sbjct: 173 LSIMDTLEDTGADNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYYEGL----TLAEI 228

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 229 GHVLGVTESRVSQIHTKSVLQLR-----AKLSSF 257


>gi|111017120|ref|YP_700092.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110816650|gb|ABG91934.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 120/233 (51%), Gaps = 14/233 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EAS  + E++   L L   +A+++  RG    DL+Q   +GL+KA ++FD   G+ F +Y
Sbjct: 37  EASALRDEVITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSY 96

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  +   + R   D   ++R+P  M++    + +    +S ++ R P+  EIA +L + 
Sbjct: 97  AVPTIMGEVRRYFRDTGWSMRVPRRMQELHALITKAVDELSQELGRSPSASEIAAQLELD 156

Query: 560 VEGVRKVL--KITKEPISLETPIGDE-DTSHLGDFI-EDKNAVSPLDSAIQANLRETTTR 615
           V  V + L  K   + +S++  +GD+ D   L + + E+   ++ ++S   A +R     
Sbjct: 157 VREVSEGLLAKNAYQTLSMDAAMGDDPDDLPLAETLGEEDPELANVES--HAAVRPA--- 211

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L P E RVL +RF   M    T  E+ ++  V++ ++ +I A+ +  L+
Sbjct: 212 -LQKLPPLERRVLMLRFFGSM----TQTEIAQRVGVSQMQVSRILARTLSGLR 259


>gi|226939286|ref|YP_002794357.1| RpoS [Laribacter hongkongensis HLHK9]
 gi|226714210|gb|ACO73348.1| RpoS [Laribacter hongkongensis HLHK9]
          Length = 170

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/161 (30%), Positives = 86/161 (53%)

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +QS TIR+PVH+  +++  +R +R + ++I R+PT +EIA  +  P E VR+V+ + +  
Sbjct: 2   NQSRTIRLPVHVIKELNVYLRASRHLESQIGRDPTIDEIAHLVGKPPEEVRRVMSLNERM 61

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            SL+ P+  +    +G+ I D+    P        +       L  LT ++  V+  R+G
Sbjct: 62  ASLDAPLDIDPMLTIGESIPDEQQEEPDIKLHGMQVNRYVQTWLKQLTDKQRLVIERRYG 121

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +      TLEE+     +TRER+RQI+ + +  L+   R K
Sbjct: 122 LNGYEICTLEELADSLSLTRERVRQIQIEGLESLRRILRRK 162


>gi|307546422|ref|YP_003898901.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
 gi|307218446|emb|CBV43716.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
          Length = 288

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 131/250 (52%), Gaps = 32/250 (12%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   + +V ++LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G +
Sbjct: 45  EGDLEAA---RRLVMSHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFDPNQGVR 101

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRM-----SNKIKREPTP 549
             ++A+ W+K  I   +      +++     + K+   +R A++      SN++      
Sbjct: 102 LVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKLFFNLRGAKKRLAWLNSNEV------ 155

Query: 550 EEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS------HLGDFIEDKNAVSPLD 602
           E IAK L +  E VR++  +++      +   G+++ S      H  D      A    D
Sbjct: 156 EAIAKDLDVKPEVVREMEGRLSAHDAGFDAAPGEDEESAYQAPVHYLDDASQDPATQLED 215

Query: 603 SAIQANLRETTTRVLASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQ 658
           S  +    ++T R+ A+L+  +ER   +L+ R+   ++ D  TL ++   + V+ ERIRQ
Sbjct: 216 SDWE---EDSTQRLQAALSELDERSRDILQRRW---LSDDKSTLHDLADVYGVSAERIRQ 269

Query: 659 IEAKAIRKLK 668
           +E  A++K++
Sbjct: 270 LEKNAMKKIR 279


>gi|254729575|ref|YP_003084257.1| RNAP sigma factor [Cyanophage PSS2]
 gi|254211727|gb|ACT65675.1| RNAP sigma factor [Cyanophage PSS2]
 gi|265524923|gb|ACY75815.1| predicted protein [Cyanophage PSS2]
          Length = 284

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/173 (34%), Positives = 90/173 (52%), Gaps = 16/173 (9%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK-YTNRGL---QFLDLIQEGNIGLMKAAEKFDW 490
           RKG+     A + +V+ NLRLV ++ KK Y  R +     L+++QEG IGL  AA +FD 
Sbjct: 39  RKGQA----ALQRIVKGNLRLVAAIWKKRYLKRNIAPAHSLEILQEGAIGLNDAAMRFDP 94

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FST+A WW+ +++     D    +R    M  K  K V    +M +  K + + E
Sbjct: 95  SSGYRFSTFASWWIIKSMKEYQRDSERLVRFKGDMHWKALKAV----KMLHTEKGQHSTE 150

Query: 551 EIAKKLAMPVE-GVRKVLKITK-EPISLETP--IGDEDTSHLGDFIEDKNAVS 599
           EI K L MP +  +   +  T+  P SL+ P  +   D S L +FI D +  +
Sbjct: 151 EIEKALKMPAKRAINLAMTFTQLHPKSLDVPNQLSGNDASPLHEFIADPSTTT 203


>gi|302544308|ref|ZP_07296650.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461926|gb|EFL25019.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 288

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 116/235 (49%), Gaps = 9/235 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  +    +  ++E NL LV   A+++ NR ++  D++Q G IGL+KA ++FD     +
Sbjct: 35  EGTHDYQYVRNTLIELNLSLVRYAARRFRNRSVEMEDVVQVGTIGLIKAIDRFDLSREVE 94

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D S  + +P  +++    + +    +  +  R PT  E+A+ 
Sbjct: 95  FTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRIDLAKANEELFQRFDRSPTTTELAEH 154

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRET 612
           L +  + V   L  +      SL+ P   E  T+ +  + +    V P    ++ NL   
Sbjct: 155 LNLSEDEVLDGLVASNGYSTSSLDAPADPETGTTRVTTYADRIGEVDPAMEVVE-NLHAL 213

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              ++  L  R+ R+L+MRFG  M    T  E+G +  V++  + ++  K++ +L
Sbjct: 214 KP-LVEQLGERDRRILQMRFGEEM----TQSEIGAELGVSQMHVSRLLTKSLTRL 263


>gi|256393983|ref|YP_003115547.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256360209|gb|ACU73706.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 265

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 56/214 (26%), Positives = 106/214 (49%), Gaps = 13/214 (6%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VA ++  RG    DL Q   +GL+KA + FD   G  F TYA   +   + R   D +  
Sbjct: 53  VAARFRLRGETQADLEQVAYLGLVKAVDNFDPDYGATFLTYATPMIAGEVRRHFRDTTWH 112

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISL 576
           + +P   ++    V    R ++ ++ R P+  EI ++L +  + V +  + +      SL
Sbjct: 113 VHVPRRAQENALAVRAVERELTQQLGRAPSAAEIGRRLDLSADEVAEAYEASAAHHTASL 172

Query: 577 ETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           + P+   D D + LGD + D++     DS +    RE    +LA L+PR++R+L M+F  
Sbjct: 173 DVPVAMADGDGASLGDLLGDED--PGFDSVVD---REALKPLLAELSPRDKRILLMKFFR 227

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            M+      ++G +  V++ ++ ++ ++ I  L+
Sbjct: 228 NMSQ----AQIGAEIGVSQMQVSRLLSQIIGSLR 257


>gi|289422547|ref|ZP_06424390.1| RNA polymerase sigma-B factor [Peptostreptococcus anaerobius 653-L]
 gi|289157119|gb|EFD05741.1| RNA polymerase sigma-B factor [Peptostreptococcus anaerobius 653-L]
          Length = 257

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 117/228 (51%), Gaps = 18/228 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L L   +++KY N+G+ + D+ Q  ++ L+ A +++D   G++FS++A   +   
Sbjct: 34  LIEKHLYLAKILSRKYMNKGVDYEDIFQVASLALIFAIDRYDVSKGFEFSSFATPTIVGE 93

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  T+R+P  +++   K+  T   +  ++KR P P EIA+ L + +E V + +
Sbjct: 94  IKKYFRDKVWTLRVPRRIQELSKKISNTKTLLEQELKRSPKPIEIAEYLEVDLEDVLEAM 153

Query: 568 KIT--KEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +   +P+SL+TP  +++      LGD I  E+KN     D        ET       L
Sbjct: 154 EASYGYQPMSLDTPSNEDNEDKDITLGDKIGFEEKNFSQIEDMDFLDKFMET-------L 206

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              E  +++ RF      + T   +  +  +++  + ++E K + KLK
Sbjct: 207 NELEVSIVKGRFF----ENKTQSVIAGELGISQMTVSRLEKKIVEKLK 250


>gi|326332872|ref|ZP_08199129.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
 gi|325949230|gb|EGD41313.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
          Length = 265

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 117/231 (50%), Gaps = 9/231 (3%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E + A++E+V  N+ LV   A ++  RG    DL+Q G +GL+ A +++D     +FS
Sbjct: 38  DAERTAAREELVHLNMALVEYCASQFYGRGEPHEDLVQVGVVGLLNAVDRYDLARDVEFS 97

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  +   I R   D    + +P  +RD    +      +S ++ R PT  ++A +L 
Sbjct: 98  TYAVPTILGEIKRYFRDSRWAVSVPRRLRDLQQNLRDATAELSQELGRSPTARDLATRLG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + +E V + L+ +    +L      ++T+ + D +   +    LD      +RE+   VL
Sbjct: 158 VSLETVVEGLESSNAYAALSLDSESDETAPMLDSLTAHDL--RLDD---VEVRESIKPVL 212

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            SL+  E++VL ++F      + T  E+  +  V++ ++ ++  +++ +L+
Sbjct: 213 DSLSAHEKQVLMLKF----FRNKTQTEIAGELGVSQMQVSRLLNRSLAQLR 259


>gi|257055039|ref|YP_003132871.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
 gi|256584911|gb|ACU96044.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
          Length = 295

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 100/205 (48%), Gaps = 16/205 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G  GL+ A EKFD   G +F TYAM  ++ AI   +  Q     +P  +R +  +
Sbjct: 90  DLIQSGIFGLVDAIEKFDPERGLRFETYAMQRIRGAILDDLRSQDW---VPRAVRSRARE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIG-----DE 583
           + R   R+  +++R PT  E+A +L + +  +R +   L++T   ++L+  +G       
Sbjct: 147 IERAHERLGARLRRTPTDAEVAAELGITLRELRDLYGQLRLTSV-LALDDLMGASKDNGN 205

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            T    D + D  AV P    +  + R      +A L  R+  V+ + +   +    TL 
Sbjct: 206 GTGSPADTLPDDGAVDPAAVLVDQDNRRQLAEAIAQLNERDRIVVSLYYFENL----TLA 261

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+GK   VT  R+ Q+  +A+ +L+
Sbjct: 262 EIGKVLGVTESRVSQLHTRAVLRLR 286


>gi|160895319|ref|ZP_02076090.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
 gi|156863012|gb|EDO56443.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
          Length = 225

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 104/213 (48%), Gaps = 20/213 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++++E NL LV SVA+++T RG    DL Q G IGL+K  +KF +    KFSTYA+  
Sbjct: 18  AKEKLIEQNLGLVWSVARRFTGRGYDIEDLFQIGCIGLIKCIDKFSFEYDVKFSTYAVPL 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I R + D S  I++   +++   KV +  +++  +   EP   EIA  L+     +
Sbjct: 78  IQGEIRRFLRD-SGAIKVSRSLKEMNMKVEQYRQKIKKEKGYEPEITEIAAALSFDAGDI 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              ++ + E  SL+TP     T      I D   +S L               L  L P 
Sbjct: 137 VMAMEASMEIESLDTPGVLSKTEEYSQDIVDHITLSQL---------------LDRLDPD 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           E+ ++R+R+      D T  E GK   +++ ++
Sbjct: 182 EQMLIRLRY----FEDRTQTETGKALGLSQVQV 210


>gi|150015700|ref|YP_001307954.1| sporulation sigma factor SigF [Clostridium beijerinckii NCIMB 8052]
 gi|149902165|gb|ABR32998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 251

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 121/243 (49%), Gaps = 19/243 (7%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++++ R G+ +A      ++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD
Sbjct: 19  LLALARSGDTDAM---NTLIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++  +++    K+      ++ K+KR PT 
Sbjct: 76  LNYNVKFSTYAVPMIIGEIKRFLRDDGM-IKVSRNVKSLARKIHFQKEILTKKLKRSPTI 134

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
           EE+A    +  E +   ++ +     L   I  +D +   L D + +K       SA   
Sbjct: 135 EELADYANVDKEEILFAIESSNSLQYLYDTIHQDDGAPVLLIDKLSEK-------SADDE 187

Query: 608 NLRETTT--RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           NL E       L SL  + ++++ +R+      D T  +V K   +++ ++ +IE K + 
Sbjct: 188 NLIEKIALKEALNSLDNKAKQIIMLRYF----KDKTQVQVAKMLGISQVQVSRIEKKVLA 243

Query: 666 KLK 668
           +++
Sbjct: 244 EMR 246


>gi|15616654|ref|NP_239866.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681412|ref|YP_002467797.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219681968|ref|YP_002468352.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|257471086|ref|ZP_05635085.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|7994684|sp|O05385|RP32_BUCAI RecName: Full=RNA polymerase sigma-32 factor
 gi|25288470|pir||H84932 DNA-directed RNA polymerase (EC 2.7.7.6) sigma-32 factor [imported]
           - Buchnera sp. (strain APS)
 gi|1929472|gb|AAB51433.1| heat shock sigma factor 32 [Buchnera aphidicola]
 gi|10038717|dbj|BAB12752.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219621701|gb|ACL29857.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219624255|gb|ACL30410.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311085774|gb|ADP65856.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086927|gb|ADP67007.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 284

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 121/235 (51%), Gaps = 14/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K ++ ++LR VI +++ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKTLILSHLRFVIHISRNYSGYGLLQSDLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+      E   + +A++L +   
Sbjct: 109 IKSEIHEYVLRNWRIVKVATTKSQRKLFFNLRKTKKRLG--WFNEEEIQIVARELGVSSR 166

Query: 562 GVRKV-LKITKEPISLE-TP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            VR++  +++ + ++   +P    D  T+    +++DK + +  +   Q N  E     L
Sbjct: 167 DVREMESRMSAQDVAFNPSPEEHCDSKTNSSIQYLQDKTS-NFANGVEQDNWEEHAANKL 225

Query: 618 AS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +S    L  R   ++  R+ +  N  +TL+ +   + ++ ER+RQ+E  A++KLK
Sbjct: 226 SSALLRLDERSRHIIHARW-LDKNKKNTLQNIANNYGISAERVRQLEKNAMKKLK 279


>gi|254818833|ref|ZP_05223834.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 242

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 111/228 (48%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +V   L L   VA  +  RG    DLIQ   +GLM A  +FD   G  F  +A+  +
Sbjct: 19  REYIVARCLPLADHVASHFARRGEGLEDLIQVARLGLMNAVNRFDPAKGPSFIGFAVPTM 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +R+   ++ R    ++ ++ R P   E+++ L +P E + 
Sbjct: 79  MGEVRRYFRDYSWGMRVPRRLRELHVQISRATADLAQQLGRAPNAGELSQMLEVPREEIV 138

Query: 565 KVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
           + L +  +     SL+ P+G  D+S     + D  +V  +D  I+    RE    ++A+L
Sbjct: 139 ECL-VAGDAYRLDSLDAPLG-ADSSGTPRSVAD--SVGDIDPQIEHITNREALRALVATL 194

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PRE  VLRMRF   M      E +G    V++ ++ +I A  +R L+
Sbjct: 195 PPRERDVLRMRFFESMTQSQIAERIG----VSQMQVSRILANTLRCLR 238


>gi|295095481|emb|CBK84571.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 229

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     ++  ++ R  T  E+A++L +PVE  R++L  T           DE     GD 
Sbjct: 90  VAHAMGQLEQELGRNATETEVAERLGIPVEEYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    +    +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDEHQQENPLHHLLEGNLRQRVMEAIEALPEREQLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|254455073|ref|ZP_05068509.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
 gi|198263775|gb|EDY88046.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
          Length = 249

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 105/206 (50%), Gaps = 15/206 (7%)

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP--VHMRDKIHK 531
           +Q  NIGL+KAA++FD   G++FSTYA WW++  I          +++P     R   + 
Sbjct: 1   MQHANIGLLKAADRFDPDKGFRFSTYAAWWIRAEIQDYKLQGWSLVKLPNSAFGRKLFYN 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLA-----MPVEGVRKVLKITKEPISLETPIGDE-DT 585
           + R   R+    + E  PE +  ++A      P + V    ++     SL  P+ D+  T
Sbjct: 61  LKRVETRLV--AEGEVPPEHLVDRIATDLGVTPEQVVLMQQRLAAPDGSLNRPVSDDGGT 118

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LASLTPREERVLRMRFGIGMNTDHTL 642
           + L D +ED +A    + + + + R   T +   L  L+ RE+ ++ +   +  +T  TL
Sbjct: 119 AQLQDLLEDPDADVEKEVSARLDSRAFWTTLSFHLNRLSKREQEII-IEIYVS-DTPKTL 176

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+G+QF V+ ERIRQI   A+ +L+
Sbjct: 177 YELGEQFSVSHERIRQIREAALTRLR 202


>gi|254439671|ref|ZP_05053165.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255117|gb|EDY79431.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 235

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 111/224 (49%), Gaps = 19/224 (8%)

Query: 458 SVAKKYTNRGLQFL--DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           ++AK+++  GLQ    DL+Q+ NIGLMKAA++FD   GY+FSTY++WW++  I       
Sbjct: 4   TMAKRFSA-GLQAAEPDLVQQANIGLMKAADRFDPERGYRFSTYSVWWIRAEIQSYKLAS 62

Query: 516 SCTIRIP--VHMRDKIHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKV-LKIT 570
              +R P     R+ + K+ R    +SN   I R      +AK L + ++ +  +  +++
Sbjct: 63  MSIVRRPNSADFRNAVGKLGRLDEAVSNDPTINRTDADALVAKALGVNLQRLNDLRQQVS 122

Query: 571 KEPISLETP-IGDEDTSHLGDFI-----EDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
               SL  P  GD+    +   +     ED + +  LD      LR     ++ SL  RE
Sbjct: 123 GTDYSLNLPSFGDDGEERMARLVDPASTEDADTMHRLDI---KKLRGLLVEIIGSLPDRE 179

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +++ M   +  +   TL  +G  F ++ ER+RQ+      +L+
Sbjct: 180 RKII-MATQL-QDPPATLTALGIHFGISTERVRQLREMGFERLR 221


>gi|143615|gb|AAA22791.1| sporulation protein [Bacillus subtilis]
          Length = 195

 Score = 79.7 bits (195), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/141 (33%), Positives = 78/141 (55%), Gaps = 1/141 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E N+RLV SV +++ NRG +  DL Q G IGL+K+ +KFD     +FSTYA+  
Sbjct: 33  ARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLTYDVRFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D   T+++   +++  +K+ R    +S  + R PT +EIA  L +  E V
Sbjct: 93  IIGEIQRFIRDDG-TVKVSRSLKELGNKIRRAKDELSKTLGRVPTVQEIADHLEIEAEDV 151

Query: 564 RKVLKITKEPISLETPIGDED 584
               +  + P S+   + + D
Sbjct: 152 VLAQEAVRAPSSIHETVYEND 172


>gi|282866278|ref|ZP_06275324.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282558864|gb|EFB64420.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 318

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 120/238 (50%), Gaps = 16/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+   G +
Sbjct: 85  EGTHEYAYVRNTLVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVE 144

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  E+A++
Sbjct: 145 FPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRAPTVVELAER 204

Query: 556 LAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLR 610
           L +     VEG+      T   +  + P  D++   L D +  + N +  ++        
Sbjct: 205 LGITHEEVVEGMTASNAYTASSLDAK-PEDDDNEGALADRLGYEDNGLEGIEYI------ 257

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+   ++ASL  R+  +L +RF   M    T  E+G++  +++  + ++ ++ + KL+
Sbjct: 258 ESLKPLIASLPLRDRTILSLRFVANM----TQSEIGEELGISQMHVSRLLSRTLVKLR 311


>gi|167745425|ref|ZP_02417552.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|317473026|ref|ZP_07932327.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655146|gb|EDR99275.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|316899509|gb|EFV21522.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
          Length = 241

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 131/247 (53%), Gaps = 15/247 (6%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + E R ++ + ++G+ +A   ++++V  N+ L+ SV K++T RG +  DL Q G+IGL+K
Sbjct: 1   MDETRELLKLTKEGDQDA---REKIVLDNMGLIWSVVKRFTGRGHEPEDLFQIGSIGLLK 57

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KFD     KFSTYA+  +   I R + D    I++   +++  ++V +     + K 
Sbjct: 58  AVDKFDLSYDVKFSTYAVPMITGEIKRFLRDDGM-IKVSRSLKEIAYQVRQAGEAFAMKY 116

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK--NAVSPL 601
            RE T +E++++  +  + +   L+  K+  S+  P    D S +   + DK     +  
Sbjct: 117 NREATIDELSRETKIARDEIVVALEANKDVESIYQPSYQSDDSQV--LLVDKLPGEENES 174

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+ I   + E    ++ +L+  E  ++ MR+  G     T +E+ K+  +++ ++ ++E 
Sbjct: 175 DTVINHVMLE---ELMDTLSGDERELITMRYFHG----KTQQEIAKKLSISQVQVSRMEK 227

Query: 662 KAIRKLK 668
           K + +++
Sbjct: 228 KILLRMR 234


>gi|167622231|ref|YP_001672525.1| RNA polymerase factor sigma-32 [Shewanella halifaxensis HAW-EB4]
 gi|167352253|gb|ABZ74866.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella halifaxensis
           HAW-EB4]
          Length = 285

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 120/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++      E   +A  L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKAKKRLGWFSDSEVGMVADSLGVSKA 169

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE--TTTRV 616
            V ++   +        L +   DE       ++ED +  S L S ++++  E     R+
Sbjct: 170 DVTEMESRMAAQDPAFDLASDNDDEHDYAPMHYLEDHS--SDLASQVESDNWEQNNQARL 227

Query: 617 LASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++   +ER   +L+ R+   ++ D  TL+++   + V+ ERIRQ+E  A+ KLK
Sbjct: 228 LSAIKTLDERSQHILKARW---LDEDKTTLQDLASTYQVSAERIRQLEKNAMSKLK 280


>gi|49476176|ref|YP_034217.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49238984|emb|CAF28284.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 303

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 117/243 (48%), Gaps = 27/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ ++ +          IA+KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLVQDDSALSKQDIFRSIAEKL 173

Query: 557 AMPVEGVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            + V  V     +            +   D   + +   ++D    SPL  A+   + + 
Sbjct: 174 GVSVRDVETMDFRFSSSDNSLSVSVSENSDNPVAKMDALVDD----SPLPDALIEQVIDG 229

Query: 613 TTRV------LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIR 665
             R       L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A++
Sbjct: 230 QRRTQWLYDALQILNERELEIIRFR---RLNEEGATLEVLGEKLGISKERVRQIEARALQ 286

Query: 666 KLK 668
           KL+
Sbjct: 287 KLR 289


>gi|160897140|ref|YP_001562722.1| RNA polymerase sigma 32 subunit RpoH [Delftia acidovorans SPH-1]
 gi|160362724|gb|ABX34337.1| RNA polymerase, sigma 32 subunit, RpoH [Delftia acidovorans SPH-1]
          Length = 314

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/253 (27%), Positives = 120/253 (47%), Gaps = 33/253 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +V ++LRLV+S++++Y   GL   DLIQEGN+GLMKA ++FD     +  +YAM W
Sbjct: 60  AAGRLVMSHLRLVVSISRQYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHW 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-----AM 558
           +K  I   I      +++      +  K+    R M   +K +    E    L     + 
Sbjct: 120 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGLKSDAAMAEDGAMLRDTLTSG 177

Query: 559 PVEGVRKVLKITKEPI-SLETPIGDEDT-----------------SHLGDFIEDKNAVSP 600
            ++ V + L + +E +  +ET +   D                  ++L D   +  A+  
Sbjct: 178 EIDAVAEKLNVKREEVMEMETRLAGGDVLLDPSPSDDGEQAFGPIAYLADGAHEPTAM-- 235

Query: 601 LDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRER 655
           ++S  + +L  +     L SL  R  R++  R+ + +N D     TL E+   + V+ ER
Sbjct: 236 IESRQRDHLATDGIAMALDSLDDRSRRIVEERW-LKVNDDGSGGMTLHELAAVYGVSAER 294

Query: 656 IRQIEAKAIRKLK 668
           IRQIE  A++K+K
Sbjct: 295 IRQIEVAAMKKMK 307


>gi|296101730|ref|YP_003611876.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295056189|gb|ADF60927.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 239

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     ++  ++ R  T  E+A++L +PVE  R++L  T           DE     GD 
Sbjct: 100 VAHAMGQLEQELGRNATETEVAERLGIPVEEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    +    +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDEHQQENPLHHLMEGNLRQRVMEAIEALPEREQLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|283785667|ref|YP_003365532.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
 gi|282949121|emb|CBG88728.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
          Length = 239

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 102/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L +PVE  R++L  T           DE     GD 
Sbjct: 100 VAQAMGQLEQELGRNATETEVAERLGIPVEEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   +++NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTEEHQQENPLQQLLESNLRQRVMDAIEALPEREQLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|149378434|ref|ZP_01896128.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
 gi|149357284|gb|EDM45812.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
          Length = 289

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 141/288 (48%), Gaps = 41/288 (14%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
              ++S ++  + I  +SVE    ++E  H       G+ +A+   +E+V ++LR VI +
Sbjct: 14  GANLESYIQAASRIPVLSVEEERKLAERLHY-----DGDVDAA---RELVLSHLRFVIHI 65

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y   GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +
Sbjct: 66  ARSYAGYGLSQADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIV 125

Query: 520 RIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           ++     + K+   +R+ ++    +  +     +A  L +    VR+          +E 
Sbjct: 126 KVATTKAQRKLFFNLRSQKKRLAWLSHDEV-NAVASDLGVEPRVVRE----------MEG 174

Query: 579 PIGDEDTSHLGD--------------FIEDKNAVSPLDSAIQANLR-ETTTRVLASLTPR 623
            +   DT+  G               ++EDK + +P     Q++   ++  R++A+L   
Sbjct: 175 RLASHDTAFDGPQDDDDDNAYQAPAYYLEDKRS-NPATQLEQSDWTDDSNGRLMAALEQL 233

Query: 624 EER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +ER   +LR R+    ++  TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 234 DERSQDILRERW--LSDSKSTLHELADRYGVSAERIRQLEKNAMKKIR 279


>gi|302522171|ref|ZP_07274513.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318056578|ref|ZP_07975301.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actG]
 gi|302431066|gb|EFL02882.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
          Length = 279

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 18/214 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 76  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 132

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE--TPIGDEDTSH 587
           V R    +  K+ R PT  E+A ++ + VE +  V         ++LE    +G E    
Sbjct: 133 VERAYATLEAKLHRTPTEVEVASEMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGR 192

Query: 588 LG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L   D +ED  A +P++ A    LR+  +R + SL  RE+ V+ + +  G+    TL E+
Sbjct: 193 LSIMDTLEDTGADNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYYEGL----TLAEI 248

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 249 GHVLGVTESRVSQIHTKSVLQLR-----AKLSSF 277


>gi|257062124|ref|YP_003140012.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|256592290|gb|ACV03177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 258

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/250 (24%), Positives = 121/250 (48%), Gaps = 13/250 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDL 473
           S  ++  + +   R  +   + G  +    + +++E N  LV   A  + N   + + DL
Sbjct: 2   STPIKENLKLDTLRLFLDYQKTGSIQL---RNQILELNFGLVRKEAYHWVNHCSESYEDL 58

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +Q G++GL++A E+F+   G+ FS++A+ +++  I   + D+  T+RIP    +   +V 
Sbjct: 59  LQVGSLGLIRAIERFNSEKGHAFSSFALPYIRGEIQHYLRDKGYTVRIPRRWLEIGQQVK 118

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLG 589
              +    +  R+PT  EIA+ L +P++  +++      +EP+SL+  +G++    + L 
Sbjct: 119 SIKQDFRERFNRQPTDSEIAQILEIPLKEWQEIQLAFQNREPLSLDLKVGNDSDGQTSLA 178

Query: 590 DFIEDKNAVS-PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D + D N  S  L    Q  L++     LA L  R  R+L   F   +    T E++G  
Sbjct: 179 DLVPDPNYRSFQLSQEDQIRLQQG----LAQLEERTRRILEFVFLQDLTQRETAEQLGIS 234

Query: 649 FCVTRERIRQ 658
                 R+++
Sbjct: 235 VVTVSRRVKK 244


>gi|121603798|ref|YP_981127.1| RNA polymerase sigma-32 subunit RpoH [Polaromonas naphthalenivorans
           CJ2]
 gi|120592767|gb|ABM36206.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas
           naphthalenivorans CJ2]
          Length = 322

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 117/244 (47%), Gaps = 25/244 (10%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LRLV+S+++KY   GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K 
Sbjct: 75  KLVLSHLRLVVSISRKYLGYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAMHWIKA 134

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK------------REPTPEEIAK 554
            I   I      +++      +  K+    R M    K             E   + +A+
Sbjct: 135 EIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQGYKDDADVATHRDTLTESQIDSMAR 192

Query: 555 KLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR--- 610
            L +  E V ++  +++   + L+    D+     G      +A     + +++  R   
Sbjct: 193 TLNVKREEVIEMEQRMSGGDVLLDPSPNDDGDDAFGPIAYLADAAQEPTALMESRERDDL 252

Query: 611 --ETTTRVLASLTPREERVLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAI 664
             +  +  L  L PR  R++  R+ + +N D     TL ++  ++ V+ ERIRQIE  A+
Sbjct: 253 MTDGLSTALQELDPRARRIVEERW-LNVNDDGSGGMTLHDLAAEYKVSAERIRQIEVAAM 311

Query: 665 RKLK 668
           +K+K
Sbjct: 312 KKMK 315


>gi|304320154|ref|YP_003853797.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
 gi|303299057|gb|ADM08656.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
          Length = 283

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/260 (27%), Positives = 120/260 (46%), Gaps = 23/260 (8%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +SI E R ++      + E ++ K  +  A++R+ +S A K+   GL   DLIQEG IGL
Sbjct: 22  LSIEEERSLMRRWVDDQDERALGK--LTRAHMRMAVSTAIKFRGYGLPLADLIQEGAIGL 79

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-RTARRMS 540
           ++AA++FD     +F TYA WW++ ++   I      +R+        HK +     R+ 
Sbjct: 80  LEAAKRFDPDREVRFCTYAGWWIRASMQDYILRNWSIVRVGSK---SAHKTIFFNLSRIR 136

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRK------VLKITKEPISLETPIGDEDTSHLGDFIED 594
           + I+   T    A+  A     V +        ++ +   SL   + D+      D I D
Sbjct: 137 SMIEDADTAPRTARIKAAERFNVSESDIEFMTSRLGRRDQSLNAMLTDDGDIERQDLIPD 196

Query: 595 KN------AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           +       A   LD   QA  +    + L +L+ RE  ++  RF        TL  +G  
Sbjct: 197 EREGPDSLAEGTLD---QARRKSWIGKALKTLSNRERMIIEHRFFT--EEKMTLSRLGDD 251

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ER+RQIE +A+ KLK
Sbjct: 252 LSLSKERVRQIEKQAMGKLK 271


>gi|188589224|ref|YP_001920224.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778902|ref|ZP_04821822.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499505|gb|ACD52641.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083217|gb|EES49107.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 242

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 115/232 (49%), Gaps = 15/232 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+++V+  + LV  +A +     N+ +++ DL+  G IGLM A  KF+   G KFS+YA
Sbjct: 9   VKEQIVKEYIPLVKYIASRIMIGKNKYMEYEDLVSYGIIGLMDAISKFNPDKGMKFSSYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K AI   I       +      DK+++       + NK+ REP   EIA+ L + +
Sbjct: 69  SIRIKGAIIDQIRKNRPITK---GAMDKLNRYNSAIESLQNKLLREPNILEIAQYLELSL 125

Query: 561 EGVRKVLKITKE--PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + V ++         +SLE  I   DE+ + LG  IEDKN+ SP     +    E  +  
Sbjct: 126 QEVSQIENYINHISMVSLENIIFSDDEEVNLLG-IIEDKNSPSPEGELEEKEQLEVLSDA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  +E+ +L + +   +    TL+E+G    V+  R+ Q+ A++I  L+
Sbjct: 185 IKLLKEKEQLILNLYYYEKL----TLKEIGSILSVSESRVCQLHARSISNLR 232


>gi|114776846|ref|ZP_01451889.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114552932|gb|EAU55363.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 274

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 116/232 (50%), Gaps = 13/232 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ANL  V ++A++Y + GL  +DLIQEG +GLM A ++FD   G++  TYA WW
Sbjct: 43  AARQLVVANLGGVAAIAREYRHFGLPEMDLIQEGTLGLMHAVKRFDPERGFRLMTYASWW 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPV- 560
           V+ AI   I      +++  +   +  +V    ++  N I        +++A    +   
Sbjct: 103 VRAAIHDFILHSWSIVKLGTNKLQR--RVFAGLQKAKNAIAAFDGSRADDVAADFGITAG 160

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRV 616
           E         +  +SL+    DE    +   +E  +A SP       N  E         
Sbjct: 161 EYQEAAGAFLQRDLSLDCAC-DEGGDAMVHNLESMDA-SPEQIVTDNNWSEHRQAGLYHA 218

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++L  R+  +L+ R     +   TL+++ ++F V+ ERIRQ+EA+A+++L+
Sbjct: 219 LSTLPERDRLILQRRH--LSDEPATLKDLSEEFGVSMERIRQLEARAMKQLR 268


>gi|323702739|ref|ZP_08114399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532256|gb|EGB22135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 232

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 111/247 (44%), Gaps = 55/247 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + ++S +++G+    +A+  +VE NLRLV ++A K+ +RG+   DL Q G IGL
Sbjct: 33  LSAEEEQELLSRLQQGD---QLARSVLVERNLRLVATIANKHKDRGIDKQDLFQVGVIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     KF+TYA   ++  +                            R M  
Sbjct: 90  IKAVNTFNPARTNKFATYAGVCIENEM----------------------------RMMLR 121

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E     +++ L    EG          P+ L+  +  +D               P+
Sbjct: 122 KNKDEYRCLSLSEPLDYDKEG---------NPLELQDTLMADDV--------------PV 158

Query: 602 DSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  +  NL  E     +  LTPRE  V+ +RFG+    + T  EVGKQ  ++R  I +IE
Sbjct: 159 DEQVVHNLETERLGAAMQKLTPRERVVINLRFGLNGGRELTQREVGKQLNISRSFISRIE 218

Query: 661 AKAIRKL 667
           +K+I KL
Sbjct: 219 SKSISKL 225


>gi|77461555|ref|YP_351062.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf0-1]
 gi|77385558|gb|ABA77071.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas fluorescens
           Pf0-1]
          Length = 284

 Score = 79.3 bits (194), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 115/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  ++T   ++ +     +D S      +++ED     A    D+    N       
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHRYDPARQLEDADWSDNSNHNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 ALEVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|290956233|ref|YP_003487415.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645759|emb|CBG68850.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 262

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EA L +   +A ++ +RG  + DL Q  ++GL+KA +++D  LG  F +YA+  +
Sbjct: 36  RDRIIEAWLPMAERLAGRFRSRGESYEDLRQVASLGLVKAVDRYDPELGNAFESYAVPTI 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V    + +S  I  R PT  EIA+   M  E V
Sbjct: 96  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRFATQDLSQTISGRRPTVAEIAEHANMSEEDV 155

Query: 564 RKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R  L+     T   +  E P G ED   L D +   +A   LD+ +    RE     LA+
Sbjct: 156 RVGLEALESFTALSLDAELP-GSEDGYSLSDAL--GSADPALDTVVD---REAVKPRLAA 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  RE  +L MRF   M      +E+G  Q  V+R
Sbjct: 210 LPERERAILYMRFFGDMTQSRIADELGISQMHVSR 244


>gi|218249036|ref|YP_002374407.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|218169514|gb|ACK68251.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
          Length = 258

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/220 (26%), Positives = 111/220 (50%), Gaps = 10/220 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + N   + + DL+Q G++GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRKEAYHWVNHCSESYEDLLQVGSLGLIRAIERFNSEKGHAFSSFALPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   +V    +    +  R+PT  EIA+ L +P++  
Sbjct: 89  IRGEIQHYLRDKGYTVRIPRRWLEIGQQVKSIKQDFRERFNRQPTDSEIAQILEIPLKEW 148

Query: 564 RKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVS-PLDSAIQANLRETTTRVLA 618
           +++      +EP+SL+  +G++    + L D + D N  S  L    Q  L++     LA
Sbjct: 149 QEIQLAFQNREPLSLDLKVGNDSDGQTSLADLVPDPNYRSFQLSQEDQIRLQQG----LA 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            L  R  R+L   F   +    T E++G        R+++
Sbjct: 205 QLEERTRRILEFVFLQDLTQRETAEQLGISVVTVSRRVKK 244


>gi|119511848|ref|ZP_01630948.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119463490|gb|EAW44427.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 258

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 87/155 (56%), Gaps = 5/155 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ N  LV   A  + N+  + + DL+Q G +GL++A EKF+   G+ FS++A+ +
Sbjct: 29  RNKLVKLNFGLVRKEAHYWMNQCRENYDDLVQVGYLGLIRAIEKFEISKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP        + +  +R +  K  R+PT  E+A  LA+ +   
Sbjct: 89  IRGEIQHYLRDKGVTVRIPRRYLALQQQAIGVSRDLCEKYNRQPTDSELAAALAISLNEW 148

Query: 564 R--KVLKITKEPISLETPIGD--EDTSHLGDFIED 594
           +  K+  + + P+SL+ P+ D  E T+ LG+ + D
Sbjct: 149 QEIKLAWVNRSPLSLDVPVLDSEEGTTSLGELVPD 183


>gi|157963788|ref|YP_001503822.1| RNA polymerase factor sigma-32 [Shewanella pealeana ATCC 700345]
 gi|157848788|gb|ABV89287.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella pealeana ATCC
           700345]
          Length = 285

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 120/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++      E   +A+ L +   
Sbjct: 112 IKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKAKKRLGWFSDSEVGMVAESLGVSKA 169

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE--TTTRV 616
            V ++   +        L +   DE       ++ED +  S L S ++ +  E     R+
Sbjct: 170 DVTEMESRMAAQDPAFDLASDNDDEQDYAPMHYLEDHS--SDLASQVENDNWEQNNQARL 227

Query: 617 LASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++   +ER   +L+ R+   ++ D  TL+++   + V+ ERIRQ+E  A+ KLK
Sbjct: 228 LSAIKTLDERSQHILKARW---LDEDKTTLQDLAATYQVSAERIRQLEKNAMNKLK 280


>gi|212711019|ref|ZP_03319147.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
 gi|212686187|gb|EEB45715.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
          Length = 291

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/283 (23%), Positives = 132/283 (46%), Gaps = 34/283 (12%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E    ++E  H       G+ EA+   K+++ ++LR VI +A+ 
Sbjct: 16  IEAYMRAANAYPMLTAEEEKELAERLHY-----DGDLEAA---KQLILSHLRFVIHIARS 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 V--HMRDKIHKVVRTARRMS-------NKIKRE---PTPEEIAKKLAMPVEGVRKVLKIT 570
                R     + +  +R+        N + +E    T + +  +  M  + +   +   
Sbjct: 128 TTKSQRKLFFNLRKNKKRLGWFNQDEVNMVAQELGVSTKDVLEMESRMAAQDMAFDMSDD 187

Query: 571 KEPISLETPIG-----DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            +      P+       +  S   + IED N         +++  +     LASL  R +
Sbjct: 188 DDSGDFGGPVAPVLYLQDKASDFANTIEDDN--------WESHATDRLADALASLDERSQ 239

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 240 DIIRARW-LDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|685227|dbj|BAA04283.1| sigma factor [Streptomyces setonii]
          Length = 259

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/247 (24%), Positives = 120/247 (48%), Gaps = 15/247 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           + ++ +G  E   A+  ++E NL LV   A ++ NRG   + D++Q G IGL+KA ++FD
Sbjct: 14  LQVLEEGTHEYQYARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAIDRFD 73

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+++A+ ++   I R   D S  + +P  +++    + +    ++  + R+PT 
Sbjct: 74  LSREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDLAKAKESLAGDLDRDPTV 133

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSA 604
            E+A+ L +      EG+      T   + + T   +     H G    D   +   D A
Sbjct: 134 RELAQDLGIEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQHSGRTFAD--VLGEPDPA 191

Query: 605 IQA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           ++   NL      +L  L  RE R++ MRFG  M    T  ++G +  +++  + ++ ++
Sbjct: 192 METVENLHALAP-LLGELDERERRIIDMRFGQEM----TQAQIGAELGISQMHVSRLLSR 246

Query: 663 AIRKLKH 669
            + KL++
Sbjct: 247 MLGKLRN 253


>gi|296105152|ref|YP_003615298.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059611|gb|ADF64349.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 285

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/256 (25%), Positives = 127/256 (49%), Gaps = 42/256 (16%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K+++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVA 158

Query: 554 KKLAMPVEGVRKV-----------------LKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           ++L +  + VR++                      +P++    + D+ TS+  D IE+ N
Sbjct: 159 RELGVSSKDVREMESRMAAQDMTFDMSSDDDASDSQPMAPVLYLQDK-TSNFADGIEEDN 217

Query: 597 ----AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
               A + L  A++             L  R + ++R R+ +  +   TL+E+  ++ V+
Sbjct: 218 WEDQAANKLSYAMEG------------LDERSQDIIRARW-LDEDNKSTLQELADRYGVS 264

Query: 653 RERIRQIEAKAIRKLK 668
            ER+RQ+E  A++KL+
Sbjct: 265 AERVRQLEKNAMKKLR 280


>gi|153852719|ref|ZP_01994156.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
 gi|149754361|gb|EDM64292.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
          Length = 237

 Score = 79.0 bits (193), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 121/241 (50%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A+ ++VE N  LV  + +++T RG +  DL Q G IGL+KA +KF
Sbjct: 3   HTIALIQKSHEGDEEARAQIVEENTGLVWCIVRRFTGRGTELEDLFQIGTIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K  +    +  K+ REP+
Sbjct: 63  DLSYEVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKELSYKGYQAQEVLGRKLGREPS 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A+ L +  E +   +    +  SL  P+  ++    G  I     V   D A +  
Sbjct: 122 VTELAEYLDVSPEELTMAMDACTDVESLHRPVYKKE----GQEISLMEKVGKEDGAEERV 177

Query: 609 LRETTTRVLASLTPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L     + L +   +EER ++ +R+      + T  ++GK+  +++ ++ ++E K ++ L
Sbjct: 178 LDHLLLKELLTSLDKEERKLIYLRY----FAEKTQTQIGKEMGISQVQVSRMEKKILKNL 233

Query: 668 K 668
           +
Sbjct: 234 R 234


>gi|320101986|ref|YP_004177577.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319749268|gb|ADV61028.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 565

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/77 (42%), Positives = 52/77 (67%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA   K +++ ANLRLV+S+AK++      F DL+ +GN+ L++A EKFD+  G KFSTY
Sbjct: 384 EALAVKNQIISANLRLVVSIAKRHVGPSNNFFDLVSDGNMSLIRAVEKFDFARGNKFSTY 443

Query: 500 AMWWVKQAITRSIADQS 516
           A W + +   R+I +++
Sbjct: 444 ASWAIMKNFARTIPEEN 460



 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 50/71 (70%)

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q  +RE    +L+ L PRE++++  RFGI    + TLE++GK+  +T+ER+RQIEA+A +
Sbjct: 491 QRRMREGVNGMLSKLEPREQKIIVSRFGINGAKEMTLEQLGKELGITKERVRQIEARAQQ 550

Query: 666 KLKHPSRSKKL 676
           KL+  ++ +K+
Sbjct: 551 KLRKIAQEEKI 561


>gi|182440616|ref|YP_001828335.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178469132|dbj|BAG23652.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 290

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/249 (24%), Positives = 124/249 (49%), Gaps = 16/249 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G      A+  ++E NL LV   AK++ NRG  +  D++Q G IGL+KA 
Sbjct: 44  FFERLQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIVQVGTIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +    ++ ++ R
Sbjct: 104 DRFELSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKAKEELAGRLDR 163

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +PT  E+A  L +     VEG+      T    SL+ PIG E  S   + I   +    L
Sbjct: 164 DPTVGELAAHLGLTDEEVVEGLIASNGYTAG--SLDLPIGTEQNS--AETITYGDIKGDL 219

Query: 602 DSAIQA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           D AI+   NL      +L  L  R+  ++ MRFG     + T  ++G++  +++  + ++
Sbjct: 220 DPAIELVENLHALAP-LLEGLGDRDREIVAMRFG----QELTQAQIGERLGISQMHVSRL 274

Query: 660 EAKAIRKLK 668
             + + +L+
Sbjct: 275 LNRLLTQLR 283


>gi|283832678|ref|ZP_06352419.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
 gi|291072353|gb|EFE10462.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
          Length = 229

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 102/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++LA+PV+  R++L  T           DE     GD 
Sbjct: 90  VAQAMGQLEQELGRNATETEVAERLAIPVQEYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTEEHQQENPLQQLLEGNLRQRVMDAIEALPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|254498663|ref|ZP_05111381.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
 gi|254352111|gb|EET10928.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
          Length = 280

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 74/284 (26%), Positives = 137/284 (48%), Gaps = 27/284 (9%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N     +D+ +   N+I  +++E  I+ +E  H      +G+ EA+   + +V A+LR V
Sbjct: 7   NLPVGSLDAYIHRVNQIPMLTMEEEIACAERFH-----SEGDIEAA---RRLVLAHLRYV 58

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + VA+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +    
Sbjct: 59  VRVARGYLGYGLPLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNW 118

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKITKEPI 574
             ++I      +  K+    R+M N++      E   +AK L +  +   +VL + +   
Sbjct: 119 RIVKIATTKAQR--KLFFNLRQMKNRLGWFSNEEVAAVAKDLGVSTD---EVLVMEQRLN 173

Query: 575 SLETPIGDEDTSHLGDF----------IEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +++ P    D     DF          + D  A+     +     RE     L  L  R 
Sbjct: 174 AMDAPYDAPDADDNDDFHMAPERYLFNVNDDPALVLEKESTGDRGREQLLLALEQLDERS 233

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L+ R+    +   TL ++ +++ ++ ER+RQ+E  A++KL+
Sbjct: 234 QDILQQRW--LADDKLTLHDLAEKYAISAERVRQLEKNAMKKLR 275


>gi|256379368|ref|YP_003103028.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923671|gb|ACU39182.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 268

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 116/227 (51%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   +A+++ +RG    DL+Q   +GL+ A ++FD   G  F ++A+  +
Sbjct: 46  RDELVTEHLPVARHIARRFGHRGEPHDDLVQVATVGLINAVDRFDPERGSDFLSFAVPTI 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + +   D S ++R+P  +++    +   + R+S ++ R PTP E+A+ L +  E V 
Sbjct: 106 MGEVRKYFRDSSWSVRMPRRLKELHLAINAGSARLSQELGRAPTPSELAQHLGLSREEVH 165

Query: 565 KVLKITKEPISL---ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L       S    +  + D+ +  LG  + +++   P   AI+   RE+   +L  L 
Sbjct: 166 EGLAAGNAYHSASLDDLLVADDSSISLGSTLGEED---PELEAIEQ--RESLHPLLEKLP 220

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE R++ MRF   M      ++VG    +++  + ++ AK +R+L+
Sbjct: 221 ERERRIVVMRFFGNMTQTQIAQKVG----ISQMHVSRLLAKTLRQLR 263


>gi|29655194|ref|NP_820886.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 493]
 gi|6716381|gb|AAF26609.1|AF120928_1 heat-shock sigma factor [Coxiella burnetii]
 gi|29542466|gb|AAO91400.1| RNA polymerase sigma-32 factor [Coxiella burnetii RSA 493]
          Length = 288

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 117/236 (49%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 51  AARKLVLSHLRFVVRIARGYSGYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           ++  I   I      ++I      +  K+    R+ + K       E   +A++L +  +
Sbjct: 111 IRAEIHEFILKNWRIVKIATTKAQR--KLFFNLRKHAKKRGWFSDHEAFALAEELNVSTK 168

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLG---DFIEDK--NAVSPLDSAIQANLRETT 613
            VR++   L    E         D  T   G    ++EDK  N    L+ +  A+ +E  
Sbjct: 169 DVRQMEERLNSYDEAFDGADEESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHR 228

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + S+  R   +L  R+     +  TL E+  Q+ V+ ERIRQ+E  A++K++
Sbjct: 229 LHNAMQSMDDRSRDILYQRWLSEKKS--TLHELAAQYAVSAERIRQLEKNAMQKIR 282


>gi|332708995|ref|ZP_08428965.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
 gi|332352184|gb|EGJ31754.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
          Length = 258

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 118/236 (50%), Gaps = 15/236 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V  NL LV   A  +  +  + + DL+Q G IGL+ A E+FD   G  FS++A+ +
Sbjct: 29  RNQLVALNLGLVRREAHHWVKQCNESYEDLLQVGCIGLIVAIERFDSTKGIAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  +IRIP        K V   + +   + R+PT EEIA  L + +E  
Sbjct: 89  IRGEIQHYLRDRGYSIRIPRRWLALRQKSVEITQNLRATLNRQPTEEEIAAALNISLEEW 148

Query: 564 RKVL--KITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+TP+GD +   + LG+ + D    S    A +  +R    + LA 
Sbjct: 149 QEITLAHQNREPLSLDTPVGDSEDRNTSLGELVPDPRYRS-FQLAQEDQIR--IQQALAH 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQF---CVTRERIRQIEAKAIRKLKHPSR 672
           L  R   VL   F      D T +EV ++     VT  R  +   +A++KL  P++
Sbjct: 206 LEKRTREVLEFVFL----HDLTQKEVAQRLDISVVTVSRRVKKGLEALQKLMTPTQ 257


>gi|302558953|ref|ZP_07311295.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302476571|gb|EFL39664.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 282

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 128/247 (51%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           FR + +++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 39  FRRL-TVLEEGTHEYQYARNTLIEMNMSLVRYAAGRFRSRGPEEMEDIVQVGMIGLIKAI 97

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S ++ +P  +++   ++ R    + +++ R
Sbjct: 98  DRFELSREVEFTSFAIPYIVGEIKRFFRDTSWSVHVPRRLQEARVQLARATEELRSRLGR 157

Query: 546 EPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPL 601
            PT  E+A+ +++  E V   ++        SL+  IG E    S L DFI  ++A   L
Sbjct: 158 TPTVGELAQLMSLTEEEVNEARIASNGYNSASLDAAIGSEPDGESVLADFIGSEDAALEL 217

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  RE +++  RF      + T  E+G++   ++  + ++ +
Sbjct: 218 VEDFHA-----LAPMIADLDERERKIVHWRF----VEELTQAEIGQRLGCSQMHVSRLLS 268

Query: 662 KAIRKLK 668
           + +++L+
Sbjct: 269 RTLKRLR 275


>gi|253991200|ref|YP_003042556.1| RNA polymerase factor sigma-32 [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782650|emb|CAQ85814.1| component of rna polymerase, sigma 32 factor [Photorhabdus
           asymbiotica]
          Length = 285

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 122/235 (51%), Gaps = 13/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKKLILSHLRFVVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +T +R+    + E   E +AK+L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVAKELGVTSK 166

Query: 562 GVRKV-LKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRET-----T 613
            VR++  +++ + ++ +    D  ++   +   +  ++  S     I+ +  E       
Sbjct: 167 DVREMESRMSAQDMAFDMSADDDNQEGQSVAPVLYLQDKASDFAGGIEEDNWENHAADKL 226

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 227 SVAIEGLDERSQDIIRCRW-LDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|84502385|ref|ZP_01000521.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
 gi|84389197|gb|EAQ01994.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
          Length = 249

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 109/225 (48%), Gaps = 32/225 (14%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ ++ R   S+A ++T+  +   DL  EG IGL++AA+ FD     +FSTYA WWV   
Sbjct: 39  LLRSHARQAWSMAARWTDNPVHLEDLAAEGVIGLIRAADNFDLGQDVRFSTYAAWWVMNG 98

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ++ + A              +I  V+    R   +++     +E    + M ++G+    
Sbjct: 99  VSAAAA--------------RIRSVIDVPPRAVTEMRSGRLADEDNTVITMAMQGI---- 140

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPR 623
                 ++L+ P+GD   S L   +     ++P ++A   +L +   R++A     L  +
Sbjct: 141 ------VALDAPVGDGTHSLLDALVSSD--LTPEETAAAESLHDVQRRLIAKAMSGLNAQ 192

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  ++R R    +    TLE++     +TR+R+RQ+E +A+ +L+
Sbjct: 193 EAEIIRRRRLQAV--PETLEDLADAMNMTRDRLRQVERRAMTRLR 235


>gi|118470482|ref|YP_886176.1| RNA polymerase sigma factor SigF [Mycobacterium smegmatis str. MC2
           155]
 gi|25396413|dbj|BAC24795.1| alternative sigma factor SigF [Mycobacterium smegmatis]
 gi|118171769|gb|ABK72665.1| RNA polymerase sigma-F factor [Mycobacterium smegmatis str. MC2
           155]
          Length = 250

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 68/256 (26%), Positives = 129/256 (50%), Gaps = 24/256 (9%)

Query: 425 SEFRHIVSMVRK--GECEASIA----KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           SE+  ++ M R+  G  E S +    ++++VE  L L   +A+++  RG    DL+Q   
Sbjct: 3   SEYADVLDMFRELAGTTEGSPSYVRQREKIVERCLPLADHIARRFDGRGEPREDLVQVAR 62

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL+ A  +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      
Sbjct: 63  VGLVNAVNRFDVEAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAE 122

Query: 539 MSNKIKREPTPEEIAKKLAMP----VEGVRKVLKITKEPISLET-PIGDEDTSHLGDFIE 593
           +S ++ R PT  E+A +L M     VEG+  +   +   +S+++   GDE+   + D + 
Sbjct: 123 LSQRLGRAPTASELAHELDMDREEVVEGL--IAGSSYNTLSIDSGGGGDEEAPAIVDTLG 180

Query: 594 DKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           D      LD  + Q + RE+   +LASL  RE  VL +RF   M      E VG    ++
Sbjct: 181 D------LDMGLDQIDNRESLRPLLASLPERERTVLVLRFFESMTQTQIAERVG----IS 230

Query: 653 RERIRQIEAKAIRKLK 668
           +  + ++ AK++ +L+
Sbjct: 231 QMHVSRLLAKSLARLR 246


>gi|197287411|ref|YP_002153283.1| RNA polymerase factor sigma-32 [Proteus mirabilis HI4320]
 gi|227358346|ref|ZP_03842687.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
 gi|194684898|emb|CAR47059.1| RNA polymerase sigma-32 factor [Proteus mirabilis HI4320]
 gi|227161682|gb|EEI46719.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
          Length = 284

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 71/277 (25%), Positives = 142/277 (51%), Gaps = 24/277 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E    ++E  H      +G+ EA+   K ++ ++LR VI VA+ 
Sbjct: 16  IEAYIRAANSYPMLTAEEEKELAERLHY-----EGDLEAA---KTLILSHLRFVIHVARS 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETP 579
                +  K+    R+   ++    +   E +AK+L +    VR++  +++ + ++ +  
Sbjct: 128 TTKSQR--KLFFNLRKNKKRLGWFNQDEVELVAKELGVSESDVREMESRMSAQDMAFDMS 185

Query: 580 IGDEDTSHLGD---FIEDKNAVSPLDSAIQA-----NLRETTTRVLASLTPREERVLRMR 631
             D D SH      F+EDK+  S     I+      +  +  T  + +L  R + ++R R
Sbjct: 186 ADDSDDSHPVAPVLFLEDKS--SDFADGIEEDNWDNHAADRLTLAIKTLDERSQDIIRAR 243

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 244 W-LEDDNKSTLQELADKYGVSAERVRQLEKNAMKKLR 279


>gi|154484272|ref|ZP_02026720.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
 gi|149734749|gb|EDM50666.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
          Length = 304

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 84/145 (57%), Gaps = 4/145 (2%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + S++ K +VEANL LV  +A+ +  +G+ F DLIQEGN+GLM A   +   +G  F ++
Sbjct: 130 DTSVSSK-IVEANLSLVAKIAESHRGKGVNFGDLIQEGNVGLMLAVSDYTESVG-DFHSF 187

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
               ++ AI  ++  Q  + RI  H+ DK++++    + +S K+ R P  +E+AK + + 
Sbjct: 188 ISGRIEDAINNTVNVQINSDRIGQHLADKLNRLDEVTKNLSEKLGRVPELDELAKAMNIS 247

Query: 560 VEGVRKVLKITKEPISL--ETPIGD 582
            +    +LK + + +S+  +T I D
Sbjct: 248 KDEASILLKTSLDTLSVNEDTQITD 272


>gi|288555973|ref|YP_003427908.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
 gi|288547133|gb|ADC51016.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
          Length = 256

 Score = 79.0 bits (193), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 125/246 (50%), Gaps = 19/246 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + +++  ++G+ +A   +  +V  N RLV SV +++ NRG +  DL Q G IGL+K+ 
Sbjct: 20  EVKELIARSQEGDQQA---RDLIVNRNTRLVWSVVQRFMNRGYEADDLFQIGCIGLIKSV 76

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    ++  + R
Sbjct: 77  DKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSIKELGNKIRKMKDELTKSLGR 135

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EIA++L +  E V    + ++   S+   +   D D   L D I D+      D 
Sbjct: 136 VPTVNEIAEQLEITPEEVVFAGEASRSLTSIHETVYENDGDPITLLDQIADQTETKWFDK 195

Query: 604 -AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A++  +R+        L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K
Sbjct: 196 IALKEAIRD--------LDERERLIVFLRY----YKDQTQSEVATRLGISQVQVSRLEKK 243

Query: 663 AIRKLK 668
            + ++K
Sbjct: 244 ILEQMK 249


>gi|302392368|ref|YP_003828188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
 gi|302204445|gb|ADL13123.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
          Length = 260

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 118/240 (49%), Gaps = 17/240 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+E++   + LV  VA +         +F DL   G IGL+ A E+FD   G KFSTYA
Sbjct: 24  AKEELMLRFMPLVKYVANRVAINLPDKFEFEDLQNYGIIGLIDAIERFDHRRGMKFSTYA 83

Query: 501 MWWVKQAITRSIADQSCTIR-IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           +      I  SI DQ   +  +P  +R K  +V      ++NK+ R PT EEI ++L + 
Sbjct: 84  I----SRIRGSIIDQLRRLDWVPTTIRRKAKQVAEINSELANKLGRLPTDEEIRQELDLD 139

Query: 560 VEGVRKVLKITKEP--ISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +   +++     P   SL++ I     D   L + I D++A  P  +     ++     
Sbjct: 140 SDEYSQLMSEINIPQETSLDSFINSRQADGVTLIEVIADEDAARPEQTFRYEEIKRILGE 199

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSK 674
            +  L P+E +V+ + +  G+N    L E+G+   VT  RI Q+  KAI +L+ + SR K
Sbjct: 200 AIEKLKPQERKVVTLYYYEGLN----LTEIGEVLEVTTARISQLHTKAIYRLRGYLSRKK 255


>gi|331092383|ref|ZP_08341209.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401407|gb|EGG80993.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 237

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 118/240 (49%), Gaps = 8/240 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++++       A+ ++VE N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIKRSHKGDEKARTQLVEENVGLVWCVVKRFYGRGTEPEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K       M  ++ REPT
Sbjct: 63  DLSYDVKFSTYAVPMISGEIKRFLRDDGM-IKVSRSLKELAYKAYLAKEEMKERLNREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A+KL +  E +   L+   E  SL  PI  +D + +   ++        +  I  +
Sbjct: 122 VEELAEKLEVEKEELALALESGGEVESLHKPIYQKDGNEI-QLMDKLEEKEEQEEKILNH 180

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +             R+  ++ MR+      + T  E+GK   +++ ++ ++E K +  L+
Sbjct: 181 MLLQQLLEQLKKEERQ--LIYMRY----FANKTQSEIGKTMGISQVQVSRLEKKILGYLR 234


>gi|302544852|ref|ZP_07297194.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302462470|gb|EFL25563.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 315

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/288 (24%), Positives = 131/288 (45%), Gaps = 29/288 (10%)

Query: 380 DPHWVSYA---------KDFPEGEWKNFVACEVDSILKIRNEIKSISVET-------GIS 423
           DP W + A         +  P+ + +       D + ++ +  +  S ET        +S
Sbjct: 11  DPSWSTRATVSSAHVPEQFVPDADAQALAGYSFDELTELSDLPEIPSFETVSPVDARALS 70

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
            + F  I  ++ +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+K
Sbjct: 71  KTLFERI-EVLEEGTHEYAYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIK 129

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++
Sbjct: 130 AIDRFEPGRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRL 189

Query: 544 KREPTPEEIAKKL----AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            R PT  E+A++L    A  VEG+      T   +  + P  D+    L D I  +    
Sbjct: 190 DRAPTVHELAQRLDITTAEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE---- 244

Query: 600 PLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             D  ++     E+   ++A L  R++++L +RF   M      EE+G
Sbjct: 245 --DHGLEGIEYVESLKPLIADLPARDKQILSLRFVANMTQSEIGEELG 290


>gi|261341953|ref|ZP_05969811.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
 gi|288315861|gb|EFC54799.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
          Length = 285

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/256 (26%), Positives = 126/256 (49%), Gaps = 42/256 (16%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K ++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVA 158

Query: 554 KKLAMPVEGVRKV-----------------LKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           ++L +  + VR++                      +P++    + D+ TS+  D IE+ N
Sbjct: 159 RELGVSSKDVREMESRMAAQDMTFDMSSDDDASDSQPMAPVLYLQDK-TSNFADGIEEDN 217

Query: 597 ----AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
               A + L  A++             L  R + ++R R+ +  +   TL+E+  ++ V+
Sbjct: 218 WEDQAANKLSFAMEG------------LDERSQDIIRARW-LDEDNKSTLQELADRYGVS 264

Query: 653 RERIRQIEAKAIRKLK 668
            ER+RQ+E  A++KL+
Sbjct: 265 AERVRQLEKNAMKKLR 280


>gi|161829709|ref|YP_001597727.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 331]
 gi|161761576|gb|ABX77218.1| alternative sigma factor RpoH [Coxiella burnetii RSA 331]
          Length = 288

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 117/236 (49%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 51  AARKLVLSHLRFVVRIARGYSGYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVE 561
           ++  I   I      ++I      +  K+    R+ + K       E   +A++L +  +
Sbjct: 111 IRAEIHEFILKNWRIVKIATTKAQR--KLFFNLRKHAKKRGWFSDHEAFALAEELNVSTK 168

Query: 562 GVRKV---LKITKEPISLETPIGDEDTSHLG---DFIEDK--NAVSPLDSAIQANLRETT 613
            VR++   L    E         D  T   G    ++EDK  N    L+ +  A+ +E  
Sbjct: 169 DVRQMEERLNSYDEAFDGADEESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHR 228

Query: 614 TR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + S+  R   +L  R+     +  TL E+  Q+ V+ ERIRQ+E  A++K++
Sbjct: 229 LHNAMQSMDDRSRDILYQRWLSEKKS--TLHELAAQYSVSAERIRQLEKNAMQKIR 282


>gi|329941096|ref|ZP_08290375.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329299627|gb|EGG43526.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 319

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 122/254 (48%), Gaps = 19/254 (7%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S + F+ + S+  +G  E +  +  +VE NL LV   A ++  R     D+IQ G IG
Sbjct: 72  ALSKTLFQRLESL-EEGTYEHAYVRHTLVELNLALVKFAAARFRTRSEPMEDIIQVGTIG 130

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++
Sbjct: 131 LIKAIDRFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELA 190

Query: 541 NKIKREPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--ED 594
            ++ R PT  E+A +L +     VEG+      T   +  + P  D+    L D I  ED
Sbjct: 191 QQLDRAPTVTELADRLGLSNEEVVEGMVASNAYTASSLDAQ-PEEDDSEGALADRIGYED 249

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                           E+   ++A L  R+ ++L +RF   M    T  E+G++  +++ 
Sbjct: 250 HELEG-------VEYVESLKPLIAGLPQRDRKILSLRFVANM----TQSEIGEELGISQM 298

Query: 655 RIRQIEAKAIRKLK 668
            + ++ ++ + +L+
Sbjct: 299 HVSRLLSRTLVRLR 312


>gi|77359323|ref|YP_338898.1| RNA polymerase factor sigma-32 [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874234|emb|CAI85455.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Pseudoalteromonas haloplanktis TAC125]
          Length = 287

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 122/234 (52%), Gaps = 11/234 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR V  +AK Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 52  AAKQLIMSHLRFVAHIAKGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   +      +++      R     + +  +R+    + E +   +A +L +  +
Sbjct: 112 IKAEIHEFVLKNWRIVKVATTKAQRKLFFNLRKNKKRLGWFNQAEVST--VASELGVSEK 169

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHLG-----DFIEDKNAVSPLDSAIQANLRETTTR 615
            VR++  +++ + +  +    D+D++         ++ D  A    D   Q    ++ TR
Sbjct: 170 EVREMESRMSGQDMGFDLTGDDDDSAPSSTYSPVQYLTDGTADLADDIEQQQWQEQSHTR 229

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++L   +ER   +     +  D  TL+E+ +++ V+ ER+RQ+E  A++KL+
Sbjct: 230 LFSALKTLDERSQDIVSARWLTDDKATLQELAEKYSVSAERVRQLEKTAMKKLQ 283


>gi|289207353|ref|YP_003459419.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
 gi|288942984|gb|ADC70683.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
          Length = 289

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 115/236 (48%), Gaps = 15/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++  NLR V+ VA+ Y   GL   DLIQEGN+GLMKA  +FD   G +  ++A+ W
Sbjct: 53  AARQLILHNLRFVVHVARGYQGYGLPLGDLIQEGNVGLMKAVRRFDPNQGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R+A++    +  +     +A+ L +    
Sbjct: 113 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKQRLGWMSNDEV-SAVARDLGVSEND 171

Query: 563 VRKV-LKITKEPISLE-TPIGDEDTSHLG--------DFIEDKNAVSPLDSAIQANLRET 612
           V ++  +++ +  S +  P  D++ ++L         D  +D   V+  D     + +E 
Sbjct: 172 VWEMERRLSSQDASFDPAPDSDDEHTYLAPAQRLSIEDMSDDPAQVAE-DEDWDRHYQER 230

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  L  R   +L  R+        TL E+  ++ V+ ERIRQIE  AI++++
Sbjct: 231 LASTLGELDERSRDILARRY--MSEPKATLHELAAEYGVSAERIRQIENNAIKRIR 284


>gi|229593148|ref|YP_002875267.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens SBW25]
 gi|312963636|ref|ZP_07778117.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
 gi|229365014|emb|CAY53168.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens SBW25]
 gi|311282145|gb|EFQ60745.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
          Length = 284

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 115/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  ++T   ++ +     +D S      +++ED     A    D+    N       
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHRYDPARQLEDADWSDNSNHNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 ALEVLDDRSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|133478|sp|P12254|RPSK_BACSU RecName: Full=RNA polymerase sigma-K factor; AltName:
           Full=Sigma-27; AltName: Full=Stage IV sporulation
           protein CB; Flags: Precursor
          Length = 294

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/237 (27%), Positives = 112/237 (47%), Gaps = 20/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+K  E +    G K +TYA   
Sbjct: 51  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARC 110

Query: 504 VKQ--AITRSIADQSCTIR-----IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           ++    IT+        IR     + +H  +  H  V     +    K  P    +  ++
Sbjct: 111 IENEIVITKGGCIHPSLIRFNIYGVRIHNGNFFHDKVNNCFFI---FKSMPPLFVMNNEI 167

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ET 612
            M +  ++K    TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E 
Sbjct: 168 LMHLRALKK----TKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEK 221

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +  L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 222 VKQYIDILDDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 278


>gi|307131576|ref|YP_003883592.1| RNA polymerase sigma-28 (sigma F) factor [Dickeya dadantii 3937]
 gi|306529105|gb|ADM99035.1| RNA polymerase, sigma 28 (sigma F) factor [Dickeya dadantii 3937]
          Length = 240

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++    + R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAQAMQQAEQSLGRAPTEQEVAQTLNISLEEYRQILLDTNNSQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL+  +  NLR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEEANPLNQLMDVNLRQRVMDAIESLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|297202660|ref|ZP_06920057.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197713235|gb|EDY57269.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 280

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 102/218 (46%), Gaps = 26/218 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDLDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A +L + V+ +  V       +SL   +  E+  H+G  
Sbjct: 134 VERAYATLEARLRRTPTEGEVAGELGIAVDDLHAVFS----QLSLANVVALEELLHVGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 GGDGLSFMDTLEDPAADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR-----AKLASF 278


>gi|312139980|ref|YP_004007316.1| sigma-70 factor sigf [Rhodococcus equi 103S]
 gi|311889319|emb|CBH48635.1| sigma-70 factor SigF [Rhodococcus equi 103S]
          Length = 259

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 114/229 (49%), Gaps = 15/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++   L L   +A+++  RG  F DL+Q  +IGL+ A +++D   G  F  +A+  +
Sbjct: 36  RESIITRCLPLAQHIARRFDRRGEPFEDLVQVASIGLVNAVDRYDVERGSDFLAFAVPTI 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +R+P  +++    +V+T+ ++S ++ R PT  E+A++L + VE V 
Sbjct: 96  MGEVRRHFRDTGWAVRVPRRLKELHLDLVKTSAQLSQRLGRSPTTREMAEELGIEVEEVA 155

Query: 565 KVLKITK--EPISLETPIGD-EDT-SHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLAS 619
           + L+     + +S++   G   DT S LGD + D       DS I      ET   VL  
Sbjct: 156 QGLQAANGYQALSVDAAAGSGPDTGSTLGDLLGDN------DSDIAGVEDHETLRVVLEG 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  VL +RF      + T  ++     V++  + +I +  + +L+
Sbjct: 210 LPERERTVLLLRF----FGNQTQSQIAAHVGVSQMHVSRILSDTLARLR 254


>gi|311279128|ref|YP_003941359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
 gi|308748323|gb|ADO48075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
          Length = 243

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 101/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + VE  R++L  T           DE     GD 
Sbjct: 100 VAQAMGQLEQELGRNATETEVAQRLGIAVEEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   +++NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTEENQQENPLHQLMESNLRQRVIEAIEALPEREQLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLDVGESRVSQLHSQAIKRLR 233


>gi|320012478|gb|ADW07328.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 290

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 117/242 (48%), Gaps = 19/242 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           +G  E   A+  ++E NL LV   A ++ NRG   + D++Q G IGL+KA ++FD     
Sbjct: 50  EGTPEHQYARNTLIEMNLSLVRFAAGRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLAREV 109

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+++A+ ++   I R   D +  + +P  +++    + +    ++ ++ R+PT +E+A 
Sbjct: 110 EFTSFAVPYIVGEIKRFFRDTTWAVHVPRRLQELRVDLAKAKEALAVELDRDPTVQELAG 169

Query: 555 KLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL---DSAIQA 607
            L +      EG+      T   + +    GD    H G     +     L   D A++ 
Sbjct: 170 YLDLEEEEITEGLVAANGYTAGSLEMPADAGD----HAGRTTAGRTYADVLGEPDPAMET 225

Query: 608 --NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             NL      +L  L  RE R++ MRFG  M    T  ++G +  +++  + ++ ++ +R
Sbjct: 226 VENLHALAP-LLGELDARERRIIDMRFGQEM----TQAQIGDELGISQMHVSRLLSRILR 280

Query: 666 KL 667
           KL
Sbjct: 281 KL 282


>gi|239928675|ref|ZP_04685628.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291436999|ref|ZP_06576389.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291339894|gb|EFE66850.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
          Length = 280

 Score = 78.6 bits (192), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 102/218 (46%), Gaps = 26/218 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGIFGLIDAIEKFDVDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A +L + VE +  V       +SL   +  E+  H+G  
Sbjct: 134 VERAYATLEARLRRTPSESEVAGELGIAVEELHAVFS----QLSLANVVALEELLHVGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 GGDRLSLMDTLEDTAADNPVEVAEDRELRRFLVRAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR-----AKLASF 278


>gi|307243397|ref|ZP_07525554.1| putative RNA polymerase sigma-B factor [Peptostreptococcus stomatis
           DSM 17678]
 gi|306493207|gb|EFM65203.1| putative RNA polymerase sigma-B factor [Peptostreptococcus stomatis
           DSM 17678]
          Length = 257

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 109/216 (50%), Gaps = 19/216 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L L   +++KY N+G+ + DL Q  ++ L+ A +++D   G++FS++A   +   
Sbjct: 34  LIEKHLYLAKILSRKYMNKGVDYEDLYQVASLALIYAIDRYDISKGFEFSSFATPTIVGE 93

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  T+R+P  +++   K+      +  +++R PTP EIA  L +  E V + +
Sbjct: 94  IKKYFRDKVWTLRVPRRIQELSKKISNAKVYLEQELRRSPTPSEIAGYLDITEEEVLEAM 153

Query: 568 KIT--KEPISLETPIGDEDTSH---LGDFI--EDKNA--VSPLDSAIQANLRETTTRVLA 618
           + +   +P+SL+TP  D+       LGD +  E+KN   +  +D              + 
Sbjct: 154 EASYGYQPVSLDTPSNDDSEDKDMTLGDRVGTEEKNFRHIEEMD---------FINHFMK 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           +L   E +++R RF          EE+G  Q  V+R
Sbjct: 205 TLNELEVQIIRGRFFDNKTQSVIAEELGISQMTVSR 240


>gi|240851254|ref|YP_002972657.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240268377|gb|ACS51965.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 303

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 117/243 (48%), Gaps = 27/243 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ ++ +          IA+KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLIQDDSALSKQDIFRTIAEKL 173

Query: 557 AMPVEGVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            + V  V     +            +   D   + +   ++D    SPL  A+   + + 
Sbjct: 174 GVSVRDVETMDFRFSSSDNSLSVSVSENSDNPIAKMDVLVDD----SPLPDALIEQVIDG 229

Query: 613 TTRV------LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIR 665
             R       L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A++
Sbjct: 230 QRRTQWLYDALQILNERELEIIRFR---RLNEEGATLEVLGEKLGISKERVRQIEARALQ 286

Query: 666 KLK 668
           KL+
Sbjct: 287 KLR 289


>gi|145225367|ref|YP_001136045.1| RNA polymerase sigma factor SigF [Mycobacterium gilvum PYR-GCK]
 gi|145217853|gb|ABP47257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 262

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 114/246 (46%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G       +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELAEL-EEGSAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVI 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVTAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRA 141

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           PTP E+A +L M     VEG+          I      G+ED   + D + D +    LD
Sbjct: 142 PTPSELAAELEMDRDEVVEGLVAGSSYNTLSIDSGGGSGNEDAPAIADTLGDVDLT--LD 199

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              Q   RE    +LA+L  RE  VL +RF   M      E VG    +++  + ++ AK
Sbjct: 200 ---QIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRLLAK 252

Query: 663 AIRKLK 668
           ++ +L+
Sbjct: 253 SLTRLR 258


>gi|188589198|ref|YP_001920238.1| sporulation sigma factor SigF [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778416|ref|ZP_04821336.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499479|gb|ACD52615.1| RNA polymerase sigma-F factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082731|gb|EES48621.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 251

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 119/246 (48%), Gaps = 23/246 (9%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            ++ + + G+ EA      ++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   F
Sbjct: 18  QLLPLAKDGDTEAM---NRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNF 74

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++  +++    ++  T   ++ K+ R PT
Sbjct: 75  DLSYNVKFSTYAVPMIIGEIKRFLRDDGM-IKVSRNVKSLAKRIHFTKEELTKKLNRSPT 133

Query: 549 PEEIAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLD 602
            EE+A+       GV K  ++   +   SL+      DT H  D     + DK +    D
Sbjct: 134 IEELAE-----YSGVDKEEIIFAIESATSLQYLY---DTIHQDDGAPVLLIDKLSEKGED 185

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                N +      L SL  +  +++ +R+      D T  +V K   +++ ++ +IE K
Sbjct: 186 DIGMIN-KIALKEALRSLDEKARQIIVLRYF----KDKTQVQVAKLLGISQVQVSRIEKK 240

Query: 663 AIRKLK 668
            + K++
Sbjct: 241 VLLKMR 246


>gi|313637835|gb|EFS03172.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL S4-171]
          Length = 56

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 38/55 (69%), Positives = 46/55 (83%)

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 2   VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 56


>gi|282864142|ref|ZP_06273199.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561220|gb|EFB66765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 290

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 56/245 (22%), Positives = 118/245 (48%), Gaps = 13/245 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFD 489
           + ++ +G  E   A+  ++E NL LV   A ++ +RG   + D++Q G +GL+KA ++FD
Sbjct: 45  LQLLDEGTPEHQYARNTLIEMNLSLVRFAAGRFRSRGSGDMEDIVQVGTVGLIKAIDRFD 104

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+++A+ ++   I R   D + ++ +P  +++    + R    ++  + R+PT 
Sbjct: 105 LAREVEFTSFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLARAKETLAVGLDRDPTV 164

Query: 550 EEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDS 603
           +E+A  L +      +G+      T   + +    GD      G   F +      P   
Sbjct: 165 QELAAHLGLDEQEVTDGIVAANGYTAGSLDMPAEAGDPAGRATGGRTFADVLGEPDPAME 224

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            ++ NL      +L  L  RE R++ MRFG     + T  ++G +  +++  + ++  + 
Sbjct: 225 TVE-NLHALAP-LLEDLDARERRIIEMRFG----QELTQAQIGDELGISQMHVSRLLGRT 278

Query: 664 IRKLK 668
           +RKL+
Sbjct: 279 LRKLR 283


>gi|296120653|ref|YP_003628431.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296012993|gb|ADG66232.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 558

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 52/75 (69%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++ +NLRLV+S+AKK+++    F ++I +GN+ L+KA EKFD+  G+KFSTYA W +
Sbjct: 380 KNFLIRSNLRLVVSIAKKHSHPTANFFEMISDGNMSLIKAIEKFDYTRGFKFSTYASWAI 439

Query: 505 KQAITRSIADQSCTI 519
            +   RSI  ++  +
Sbjct: 440 MKNFARSIPAENTRL 454



 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIE 660
           D  +    RE    +L  L  RE  ++  R+G+       TLE+VG +  VT+ERIRQIE
Sbjct: 478 DEIVNYRQREALMGILGQLELRERDIIMHRYGLETGQQPQTLEQVGHRLGVTKERIRQIE 537

Query: 661 AKAIRKLKHPSRSKKL 676
           A+A++KLK  +  ++L
Sbjct: 538 ARALKKLKRIATDERL 553


>gi|291300290|ref|YP_003511568.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290569510|gb|ADD42475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Stackebrandtia nassauensis DSM 44728]
          Length = 267

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 8/212 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V+  L L   +A+++ +RG    DL Q   +GL+ A + F    G  F+ +A+  +
Sbjct: 46  RNTVVQRALPLADRLARRFEHRGQPLEDLTQVARLGLINAVDNFKCGRGGGFTHFAVPSI 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D+   +R+P  +++        ++ +S ++ R PT E+ A+ L+MPVE VR
Sbjct: 106 LGELKRHFRDKGWLVRVPRRLQETRLAFNEASKDLSQRLGRSPTLEDYAEYLSMPVEQVR 165

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +      E +SL TP   E +  L D +   +      +   A  R      +  LTP
Sbjct: 166 AGINCVGAYEGVSLHTPAHRESSEELIDSLGGSDP-----AMASAEARMLLRPAIKELTP 220

Query: 623 REERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           RE R+L +RF   ++      EVG  Q  V+R
Sbjct: 221 RECRILSLRFVDDLHQSEIAREVGLSQMHVSR 252


>gi|328880412|emb|CCA53651.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 283

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/258 (22%), Positives = 128/258 (49%), Gaps = 34/258 (13%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG +  D++Q G IGL+KA +
Sbjct: 39  FFQELTVLEEGTHEYQYARNTLIEMNMSLVRYAAGRFRHRGDEMEDIVQVGMIGLIKAID 98

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+T+A+ ++   I R   D S  + +P  +++   ++ +    +S ++ R 
Sbjct: 99  RFELSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELAKATEELSTRLGRT 158

Query: 547 PTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDED---TSHLGDFI--------- 592
           PT +E+A+ +++  E V   ++        SL+  +  E+    + L DFI         
Sbjct: 159 PTSKELAELMSLTEEEVNEARLASNGYHSSSLDAALSGENEDSEASLADFIGSEDPAMEL 218

Query: 593 -EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            ED +A++PL               +A L  R+ +++ +RF      + T  ++G++   
Sbjct: 219 VEDFHALAPL---------------IAELDERDRQIIHLRF----VEELTQAQIGERLGC 259

Query: 652 TRERIRQIEAKAIRKLKH 669
           ++  + ++ ++ I+ L+ 
Sbjct: 260 SQMHVSRLLSRTIKSLRQ 277


>gi|300722632|ref|YP_003711922.1| sigma F (sigma 28) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297629139|emb|CBJ89735.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           nematophila ATCC 19061]
          Length = 240

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 104/203 (51%), Gaps = 18/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERFDSMQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
           V +T R++  ++ R  + +E+AK+L + +   R++L  T       + +   D  H    
Sbjct: 100 VTQTIRKLEQELGRPASEQEVAKELKINLIEYRQILLDTN-----NSQLFSYDEWHEIHG 154

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                 IE+++  +PL   ++ +LR+    ++ SL  RE+ VL + +   +N    L+E+
Sbjct: 155 ESCEPVIEEEHETNPLQQLLEGDLRQRVINIIESLPEREKMVLTLYYQEELN----LKEI 210

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ Q+ ++AI++L+
Sbjct: 211 GAVLNVGESRVSQLHSQAIKRLR 233


>gi|326781290|ref|ZP_08240555.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326661623|gb|EGE46469.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 290

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 124/249 (49%), Gaps = 16/249 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G      A+  ++E NL LV   AK++ NRG  +  D++Q G IGL+KA 
Sbjct: 44  FFERLQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIVQVGTIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +    ++ ++ R
Sbjct: 104 DRFELSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKAKEELAGRLDR 163

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +PT  E+A  L +     +EG+      T    SL+ PIG E  S   + I   +    L
Sbjct: 164 DPTVGELAAHLGLTDEEVIEGLIASNGYTAG--SLDLPIGTEQNS--AETITYGDIKGDL 219

Query: 602 DSAIQA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           D AI+   NL      +L  L  R+  ++ MRFG     + T  ++G++  +++  + ++
Sbjct: 220 DPAIELVENLHALAP-LLEGLGDRDREIVAMRFG----QELTQAQIGERLGISQMHVSRL 274

Query: 660 EAKAIRKLK 668
             + + +L+
Sbjct: 275 LNRLLTQLR 283


>gi|325674546|ref|ZP_08154234.1| RNA polymerase sigma-F factor [Rhodococcus equi ATCC 33707]
 gi|325554806|gb|EGD24480.1| RNA polymerase sigma-F factor [Rhodococcus equi ATCC 33707]
          Length = 259

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 114/229 (49%), Gaps = 15/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++   L L   +A+++  RG  F DL+Q  +IGL+ A +++D   G  F  +A+  +
Sbjct: 36  RESIITRCLPLAEHIARRFDRRGEPFEDLVQVASIGLVNAVDRYDVERGSDFLAFAVPTI 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +R+P  +++    +V+T+ ++S ++ R PT  E+A++L + VE V 
Sbjct: 96  MGEVRRHFRDTGWAVRVPRRLKELHLDLVKTSAQLSQRLGRSPTTREMAEELGIEVEEVA 155

Query: 565 KVLKITK--EPISLETPIGD-EDT-SHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLAS 619
           + L+     + +S++   G   DT S LGD + D       DS I      ET   VL  
Sbjct: 156 QGLQAANGYQALSVDAAAGSGPDTGSTLGDLLGDN------DSDIAGVEDHETLRVVLEG 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  VL +RF      + T  ++     V++  + +I +  + +L+
Sbjct: 210 LPERERTVLLLRF----FGNQTQSQIAAHVGVSQMHVSRILSDTLARLR 254


>gi|282861385|ref|ZP_06270450.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
 gi|282564043|gb|EFB69580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
          Length = 278

 Score = 78.6 bits (192), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDLERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQLRRTPTEAEVAAEMGIALEELHSVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADNPVEIAEDRELRRMLARAINTLPEREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|331091330|ref|ZP_08340170.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404491|gb|EGG84035.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 206

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 68/250 (27%), Positives = 112/250 (44%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ SE R+ +    +G+ EA   K  ++E NLRLV  + KKY +      DL+  G IGL
Sbjct: 8   LTASEERYYLQKYTEGDLEA---KHILIERNLRLVAHIVKKYQHLDEDPEDLLSIGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+   G + +TYA                                   AR + N
Sbjct: 65  IKAVSTFNLEKGNRLATYA-----------------------------------ARCIEN 89

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAV 598
           +I              M + G +K    T + +SL  PIG +   +   L D IE     
Sbjct: 90  EI-------------LMMLRGKKK----TSKEVSLYEPIGTDREGNEIQLFDVIESDEED 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P   A++ +++    +V + L+PRE  VL+MR+G+    ++T  E+ +Q  ++R  + +
Sbjct: 133 APSKVALKDDIKMLYEKVSSELSPRERLVLKMRYGLYEGEEYTQREIARQLGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE  AI KL+
Sbjct: 193 IEKSAIEKLR 202


>gi|5327289|emb|CAB46360.1| FliA, sigma 28 [Xenorhabdus nematophila]
 gi|139522465|gb|ABO77651.1| FliA [Xenorhabdus nematophila]
          Length = 230

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 104/203 (51%), Gaps = 18/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERFDSMQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
           V +T R++  ++ R  + +E+AK+L + +   R++L  T       + +   D  H    
Sbjct: 90  VTQTIRKLEQELGRPASEQEVAKELKINLIEYRQILLDTN-----NSQLFSYDEWHEIHG 144

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                 IE+++  +PL   ++ +LR+    ++ SL  RE+ VL + +   +N    L+E+
Sbjct: 145 ESCEPVIEEEHETNPLQQLLEGDLRQRVINIIESLPEREKMVLTLYYQEELN----LKEI 200

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ Q+ ++AI++L+
Sbjct: 201 GAVLNVGESRVSQLHSQAIKRLR 223


>gi|302537203|ref|ZP_07289545.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
 gi|302446098|gb|EFL17914.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
          Length = 278

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + VE +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQLRRTPTEGEVAGEMGIAVEELHTVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|284992377|ref|YP_003410931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
 gi|284065622|gb|ADB76560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
          Length = 266

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 102/201 (50%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A  ++      KF +YAM  ++ AI   I +   T  IP  +R K  +
Sbjct: 66  DLVSYGTFGLIDAITRYQPSREVKFESYAMARIRGAI---IDELRSTDWIPRSVRMKARQ 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED--TSH 587
             RT   + ++++R P+ EE+A ++ M VE VRK L        ++L+  + D++     
Sbjct: 123 FERTVALLESRLQRSPSEEEVAAEMDMDVEDVRKFLGQLSLVNVVALDELLSDDEGGAPR 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++D +A+ P   A  +  R+   R +  L  RE+ V+ + +  G+    TL ++G+
Sbjct: 183 LVDTLQDTSALDPQAMAEHSEARQLLARAVEQLPEREKVVVSLYYFEGL----TLADIGR 238

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  RI Q+  KA+  L+
Sbjct: 239 VLGVTESRICQLHTKAVLHLR 259


>gi|167036147|ref|YP_001671378.1| RNA polymerase factor sigma-32 [Pseudomonas putida GB-1]
 gi|166862635|gb|ABZ01043.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida GB-1]
          Length = 284

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     AV   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPAAEADDDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSASNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGLDERSRDILYQRW--LAEEKATLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|17231345|ref|NP_487893.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17132987|dbj|BAB75552.1| group 3 sigma 37-type sigma factor [Nostoc sp. PCC 7120]
          Length = 258

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 112/231 (48%), Gaps = 12/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            + ++V+ NL LV   A  + N+  + + DL+Q G +GL++A E+F+   G+ FS++A+ 
Sbjct: 28  VRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQVGCLGLIRAIERFEIAKGHAFSSFAIP 87

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +++  I   + D+  T+RIP        + +  +R +  +  R+PT  E+A  L +  + 
Sbjct: 88  YIRGEIQHYLRDKGVTVRIPRRYLAIQQRAIGVSRSLREQYNRQPTDSELATALEISPDE 147

Query: 563 VR--KVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +  K+  + + P+SL+ P+  G+E  + LG+ + D +  S    A +  +R    + L 
Sbjct: 148 WQEIKLAWVNRAPLSLDVPVQDGEEGATSLGELVPDHHYRS-FQLAQEDQIR--LQQALF 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R   VL   F   +      E +G        R++    K +  LKH
Sbjct: 205 QLEQRTREVLECVFLQDLTQKQVAEHLGISVVTVSRRVK----KGLDLLKH 251


>gi|237731968|ref|ZP_04562449.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
 gi|226907507|gb|EEH93425.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
          Length = 239

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 101/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A +LA+PV+  R++L  T           DE     GD 
Sbjct: 100 VAQAMGQLEQELGRNATETEVAARLAIPVQEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTEEHQQENPLQQLLEGNLRQRVMDAIEALPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|195940831|ref|ZP_03086213.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|1710645|sp|P50508|RP32_ENTCL RecName: Full=RNA polymerase sigma-32 factor
 gi|1143326|dbj|BAA09440.1| sigma-32 homolog [Enterobacter cloacae]
 gi|295097059|emb|CBK86149.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 285

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/256 (26%), Positives = 126/256 (49%), Gaps = 42/256 (16%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ EA+   K ++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +
Sbjct: 44  QGDLEAA---KTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A
Sbjct: 101 LVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVA 158

Query: 554 KKLAMPVEGVRKV-----------------LKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           ++L +  + VR++                      +P++    + D+ TS+  D IE+ N
Sbjct: 159 RELGVSSKDVREMESRMAAQDMTFDMSADDDASDSQPMAPVLYLQDK-TSNFADGIEEDN 217

Query: 597 ----AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
               A + L  A++             L  R + ++R R+ +  +   TL+E+  ++ V+
Sbjct: 218 WEDQAANKLTFAMEG------------LDERSQDIIRARW-LDEDNKSTLQELADRYGVS 264

Query: 653 RERIRQIEAKAIRKLK 668
            ER+RQ+E  A++KL+
Sbjct: 265 AERVRQLEKNAMKKLR 280


>gi|148550183|ref|YP_001270285.1| RNA polymerase factor sigma-32 [Pseudomonas putida F1]
 gi|148514241|gb|ABQ81101.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida F1]
          Length = 284

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     AV   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPAAEADDDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGLDERSRDILYQRWLAEEKA--TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|26991784|ref|NP_747209.1| RNA polymerase factor sigma-32 [Pseudomonas putida KT2440]
 gi|8885996|gb|AAF80334.1|AF157048_1 heat shock sigma factor RpoH [Pseudomonas putida]
 gi|24986895|gb|AAN70673.1|AE016711_1 RNA polymerase sigma-32 factor [Pseudomonas putida KT2440]
          Length = 284

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     AV   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPAAEADDDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGLDERSRDILYQRWLAEEKA--TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|302532223|ref|ZP_07284565.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302441118|gb|EFL12934.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 307

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 121/258 (46%), Gaps = 46/258 (17%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +G  E   A+  ++E NL LV   A+++  R    GL   D+IQ G IGL+KA ++FD  
Sbjct: 65  EGTREYQYARNTLIEMNLSLVHYAARRFRARVSGGGLDMDDVIQVGTIGLIKAIDRFDLD 124

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FST A+ ++   I R   D +  + +P  +++   ++ +    ++  + R PT +E
Sbjct: 125 REVEFSTLALPYITGEIKRHFRDTTWAVHVPRRLQELRSELAKAQESLTEALHRAPTVKE 184

Query: 552 IAKKLAMPVEGVRKVL--------------------KITKEPI-SLETPIGDEDTSHLGD 590
           +A+ L +  E V   L                    + T  P  +L   +G+ D +   +
Sbjct: 185 VAQHLGLSEEEVIDGLVAANGYTSGSLDTADEAEEARGTGRPARALAEKLGESDPAM--E 242

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             ED + ++PL       LRE        L PRE  +L MRFG     + T  E+G +  
Sbjct: 243 LFEDFHTLAPL-------LRE--------LQPRERLILSMRFG----QEKTQAEIGAELH 283

Query: 651 VTRERIRQIEAKAIRKLK 668
           +++ ++ ++ ++ + +L+
Sbjct: 284 ISQMQVSRLLSRTLARLR 301


>gi|317492397|ref|ZP_07950826.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
 gi|316919736|gb|EFV41066.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
          Length = 240

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 116/243 (47%), Gaps = 45/243 (18%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + + E +   +RL  SV         +  DL+Q G IGL+ A E++D   G  F+TYA
Sbjct: 21  APLVRHEALRLQVRLPASV---------ELDDLLQAGGIGLLHAVERYDAMQGTAFTTYA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  ++ A+   +  +     +P  +R    +V    +R   ++ R PT  EIA++L MP+
Sbjct: 72  VQRIRGAMLDELRSRDW---VPRSVRRNAREVSAAMQRAEQRLHRAPTETEIAQELDMPL 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHL----------GD-----FIEDKNAVSPLDSAI 605
              +++L              D +TSHL          GD     F + ++A +PL   +
Sbjct: 129 VEYQQILL-------------DTNTSHLFSYDEWREEHGDSAEPVFQQHEDA-NPLKQLL 174

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + +LR+     + +L  RE+ VL + +   +N    L+E+G    V   R+ Q+ ++AI+
Sbjct: 175 EGDLRQRVIAAIEALPEREKLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIK 230

Query: 666 KLK 668
           +L+
Sbjct: 231 RLR 233


>gi|325275633|ref|ZP_08141532.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
 gi|313501084|gb|ADR62450.1| RpoH [Pseudomonas putida BIRD-1]
 gi|324099220|gb|EGB97167.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
          Length = 284

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     AV   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPAAEADDDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGLDERSRDILYQRWLAEEKA--TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|161502922|ref|YP_001570034.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160864269|gb|ABX20892.1| hypothetical protein SARI_00981 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 229

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 102/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L +PVE  R++L  T           DE     GD 
Sbjct: 90  VAQAMGQLEQELGRNATETEVAERLGIPVEEYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++++LR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTEEHQKENPLHQLLESDLRQRVMGAIESLPEREQLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|218289600|ref|ZP_03493820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240250|gb|EED07433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 222

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 92/183 (50%), Gaps = 6/183 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R ++     G+ EA   ++ ++  N RLV +V +++  RG +  DL Q G IGL
Sbjct: 19  LSDEEVRELLERSHNGDAEA---RERLIVHNQRLVWAVVQRFLGRGYEAEDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KFD     KFSTYA+  +   I R + D S T+++   +++   ++     R++ 
Sbjct: 76  MKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDS-TVKVSRSLKETAKQIRHVRDRLAK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
           ++ R+P   EIA+ + M    +    +  + P S+   +   D D  +L D I D+    
Sbjct: 135 ELGRQPHITEIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYLMDQIADEETEG 194

Query: 600 PLD 602
             D
Sbjct: 195 KFD 197


>gi|22298280|ref|NP_681527.1| RNA polymerase sigma factor SigF [Thermosynechococcus elongatus
           BP-1]
 gi|22294459|dbj|BAC08289.1| group 3 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 261

 Score = 78.2 bits (191), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 88/164 (53%), Gaps = 13/164 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-----FLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +VE N+ LV    +K  +R +Q     F DL+Q G +GL++A E+FD   G  FS++
Sbjct: 30  RNRLVELNIGLV----RKEAHRWVQCTQESFDDLMQVGTLGLIRAIERFDPTKGVAFSSF 85

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+ +++  I   + D+S  IR+P   +    +  R  + +  +++R PT  EIA+ L +P
Sbjct: 86  AIPYIRGEIQHYLRDKSPQIRLPRRWQTLQSQGKRVIQELRQQLERPPTDSEIAQALDVP 145

Query: 560 VE--GVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
           +E     K       P+SL+ P   G+E++  LGD + D+   S
Sbjct: 146 LEEWQAAKFASYHTTPVSLDAPTFEGEEESVALGDILPDQRYQS 189


>gi|329940311|ref|ZP_08289592.1| putative RNA polymerase sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329300372|gb|EGG44269.1| putative RNA polymerase sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 270

 Score = 78.2 bits (191), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 114/237 (48%), Gaps = 14/237 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + ++FR + ++    E +A   +  +VEA L +   +A ++ NRG  + DL Q   +GL+
Sbjct: 18  TAADFRRLAALPDGPERDA--LRSRVVEAWLPMAERLAGRFRNRGESYEDLRQVAALGLV 75

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++++  LG  F +YA+  V   I R   D   T+ +P  ++D  ++V    + +S  
Sbjct: 76  KAVDRYEPDLGNAFESYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRFATQDLSQT 135

Query: 543 IK-REPTPEEIAKKLAMPVEGVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           I  R PT  EIA    +  E V+     +   T   +  E P G ED   L D +   +A
Sbjct: 136 ISGRRPTVAEIAAHAHLSEEDVKAGQEALESFTALSLDAELP-GSEDGYSLSDAL--GSA 192

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              LD+ +    RE+    LA+L  RE  +L MRF   M      E++G  Q  V+R
Sbjct: 193 DPALDTVVD---RESVKPRLAALPERERAILYMRFFGDMTQSRIAEQLGISQMHVSR 246


>gi|290962991|ref|YP_003494173.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652517|emb|CBG75650.1| sigma factor [Streptomyces scabiei 87.22]
          Length = 283

 Score = 78.2 bits (191), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 120/243 (49%), Gaps = 31/243 (12%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 39  FFEQLTVLEEGTREYQYARNTLIEMNISLVRYAAGRFRSRGADEMEDIVQVGMIGLIKAI 98

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+T+A+ ++   I R   D S  + +P  +++   ++ R    +S+++ R
Sbjct: 99  DRFELSREVEFTTFAVPYIVGEIRRFFRDTSWAVHVPRRLKEARVELARATDELSSRLGR 158

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDT--SHLGDFI--------- 592
            PT +E+A+ + +  + V   ++        SL+  IG ++T  + L DFI         
Sbjct: 159 SPTVKELAELMNLSEDEVIEARLAANGYNSSSLDAAIGGDETGEAALADFIGSEDAGMEL 218

Query: 593 -EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFC 650
            ED +A++PL               L+ L  R+ R++ MRF   +      E +G  Q  
Sbjct: 219 VEDFHALAPL---------------LSELGDRDRRIIHMRFVEELTQAQIAEHLGCSQMH 263

Query: 651 VTR 653
           V+R
Sbjct: 264 VSR 266


>gi|170719544|ref|YP_001747232.1| RNA polymerase factor sigma-32 [Pseudomonas putida W619]
 gi|169757547|gb|ACA70863.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida W619]
          Length = 284

 Score = 78.2 bits (191), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     AV   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPAAEADDDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGLDERSRDILYQRWLAEEKA--TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|312877562|ref|ZP_07737521.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795637|gb|EFR12007.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 240

 Score = 78.2 bits (191), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 119/239 (49%), Gaps = 12/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++F    
Sbjct: 9   LISKAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELDDLFQIGCIGLIKAVDRFAPSF 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 69  NLRFSTYAVPMIIGEIKRYLRDDG-KIKVSRKIKENQSKIKKLRNQFVSSNGREPTISEI 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   +  + E  SL   +  E+     L D   D+   S     + A L+
Sbjct: 128 SQLTGLSSDEILLCMDASSEVASLNEVVNQEEGKPITLMDIASDEEDYSTKLLDLMA-LK 186

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E     L  L  RE  ++ MR+      + T  E+ K+  +++  + +IE +A+ ++K 
Sbjct: 187 EG----LKKLKGRERYIIFMRYF----KNKTQSEIAKELNISQVHVSRIEKRALERIKR 237


>gi|75908065|ref|YP_322361.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75701790|gb|ABA21466.1| Sigma 32 (RpoH) [Anabaena variabilis ATCC 29413]
          Length = 258

 Score = 78.2 bits (191), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 112/231 (48%), Gaps = 12/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            + ++V+ NL LV   A  + N+  + + DL+Q G +GL++A E+F+   G+ FS++A+ 
Sbjct: 28  VRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQVGCLGLIRAIERFEIAKGHAFSSFAIP 87

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +++  I   + D+  T+RIP        + +  +R +  +  R+PT  E+A  L +  + 
Sbjct: 88  YIRGEIQHYLRDKGVTVRIPRRYLAIQQRAIGVSRSLREQYNRQPTDSELATALDISPDE 147

Query: 563 VR--KVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +  K+  + + P+SL+ P+  G+E  + LG+ + D +  S    A +  +R    + L 
Sbjct: 148 WQEIKLAWVNRAPLSLDVPVQDGEEGATSLGELVPDHHYRS-FQLAQEDQIR--LQQALF 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R   VL   F   +      E +G        R++    K +  LKH
Sbjct: 205 QLEQRTREVLECVFLQDLTQKQVAEHLGISVVTVSRRVK----KGLDLLKH 251


>gi|307330561|ref|ZP_07609702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883810|gb|EFN14855.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 315

 Score = 77.8 bits (190), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 108/221 (48%), Gaps = 12/221 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+ 
Sbjct: 77  LEVLEEGTHEYAYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFET 136

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  
Sbjct: 137 GRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTVS 196

Query: 551 EIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           E+A++L +     VEG+      T   +  + P  D+    L D I  +      D  ++
Sbjct: 197 ELAQRLDISQSEVVEGMAASNAYTASSLDAQ-PEEDDSEGALADRIGYE------DHGLE 249

Query: 607 A-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                E+   ++A L+ R+ ++L +RF   M      EE+G
Sbjct: 250 GIEYVESLKPLIADLSARDRKILSLRFVANMTQSEIGEELG 290


>gi|163869170|ref|YP_001610422.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161018869|emb|CAK02427.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 303

 Score = 77.8 bits (190), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 122/242 (50%), Gaps = 25/242 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 56  AMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWW 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ ++ +          IA+KL
Sbjct: 116 IRASIQDYILRNWSIVRGGTSSSQK--ALFFNLRRLRAKLVQDDSALSKQDIFRTIAEKL 173

Query: 557 AMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETT 613
            + V  V  +  + +    SL   + +   S +   D + D+   SPL  A+   + +  
Sbjct: 174 GVSVRDVETMDFRFSSSDNSLSVSVSENSDSPVAKMDVLVDE---SPLPDALIEQVIDGQ 230

Query: 614 TRV------LASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            R       L  L  RE  ++R R    +N +  TLE +G++  +++ER+RQIEA+A++K
Sbjct: 231 RRTQWLYDALQILNERELEIIRFR---RLNEEGATLEVLGEKLGISKERVRQIEARALQK 287

Query: 667 LK 668
           L+
Sbjct: 288 LR 289


>gi|54024680|ref|YP_118922.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54016188|dbj|BAD57558.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 261

 Score = 77.8 bits (190), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 61/255 (23%), Positives = 113/255 (44%), Gaps = 38/255 (14%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ +  G+   +  + E+++  L L   +A+++  RG  F DL+Q   +GL++AA++FD 
Sbjct: 22  IAALDPGDPRRTALRAEVIDRALPLAEHIARRFAGRGESFDDLLQVARLGLVQAADRFDV 81

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   + R   D +  +R+P   ++    +  T   +S ++ R P   
Sbjct: 82  GRGSSFLAFAVPTIMGEVRRHFRDNTWAVRVPRRTKEIQGSIGATVEELSQRLGRMPRAR 141

Query: 551 EIAKKLAMPVEGVRKVLKITKE-----------------PISLETPIGDEDTSHLGDFIE 593
           EIA +L + V  V + L                      P+ L   +G E+ S   +F++
Sbjct: 142 EIAAELGIDVVEVTQALIAGNAYQSSSLDSTAGDDGENTPLPLSESLGAEEPSF--EFVD 199

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  AV PL               +A L  RE +VL MRF  G     T  ++     V++
Sbjct: 200 DYLAVRPL---------------IAELPERERQVLVMRFFEG----KTQTQIADVLGVSQ 240

Query: 654 ERIRQIEAKAIRKLK 668
             + +I +K +  L+
Sbjct: 241 MHVSRILSKTLHALR 255


>gi|330812379|ref|YP_004356841.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327380487|gb|AEA71837.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 284

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 115/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  ++T   ++ +     +D S      +++ED     A    D+    N       
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHRYDPARQLEDADWSDNSNTNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 ALEVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|297559507|ref|YP_003678481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296843955|gb|ADH65975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 58/247 (23%), Positives = 114/247 (46%), Gaps = 11/247 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   ++  + +G+ +A+  ++ ++     L+  +A++Y  RG    DL Q   +GL KA 
Sbjct: 35  ELLSVLVRLGEGDPQANGLRERVMVLYQPLINKIARRYGGRGEPLEDLKQTAMVGLAKAV 94

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
             +D   G  F +Y +  V   I R   D +  +R+P   ++   K+ R       +  R
Sbjct: 95  RGYDPARGKPFISYLLPTVTGEIKRHFRDHTWAVRVPRRHQENRVKLRRVTSEFQQRHAR 154

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAV--SPL 601
            PT  E+A  + +P   V ++ ++++    +SL+ P   +     G  +ED      + L
Sbjct: 155 TPTIAELAHDMGLPEAEVSELTQVSESYRSLSLDAPDSSDSEGQEGTRLEDHLGCEDAAL 214

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D  ++   RE+    LA L  RE  +LR+RF      DHT  E+  +   ++  + ++ +
Sbjct: 215 DRVVE---RESLKPALARLPAREREILRLRF----FGDHTQSEIADRLGYSQMHVSRLLS 267

Query: 662 KAIRKLK 668
             + +L+
Sbjct: 268 GVLEQLR 274


>gi|29829172|ref|NP_823806.1| RNA polymerase sigma factor WhiG [Streptomyces avermitilis MA-4680]
 gi|29606278|dbj|BAC70341.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 280

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 102/218 (46%), Gaps = 26/218 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDIGREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + V+ +  V       +SL   +  E+  H+G  
Sbjct: 134 VERAYATLEARLRRTPTEGEVATEMGIAVDELHSVFS----QLSLANVVALEELLHVGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 GGDRLSLMDTLEDTAADNPVEVAEDRELRRFLARAINTLPDREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR-----AKLASF 278


>gi|311900244|dbj|BAJ32652.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 310

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 57/246 (23%), Positives = 120/246 (48%), Gaps = 32/246 (13%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E S  +  ++E NL LV    +++ +    + DL+Q G++GL+KA ++FD  LG +
Sbjct: 77  EGTREFSYVRTTLIELNLTLVRFAIRRFGHSKEPYEDLLQVGSVGLIKAIDRFDPSLGVE 136

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+TYA+  +   I R   D + ++ +P  +++    + +    ++  + REPT  ++A+ 
Sbjct: 137 FTTYAVPTIIGEIRRHFRDTTWSVHVPRRLQELRLDLAKAQDALAQTLDREPTVADLAEY 196

Query: 556 LAMP----VEGVRKVLKITKEPISLETPI---GDEDTSHLG------DFIEDKNAVSPLD 602
           L++     +EG+      T   + L +P    G +    LG        +E+  A+ PL 
Sbjct: 197 LSISEEEVIEGLAAANAHTAGSLDLTSPGEGDGQQPAERLGRVDGRFALVENLVALKPL- 255

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                         +A L  R+ ++L MRF    + D T  ++G +  +++  + ++ ++
Sbjct: 256 --------------IAQLPERDRQILAMRF----SEDLTQSQIGARLGLSQMHVSRLLSR 297

Query: 663 AIRKLK 668
            + +L+
Sbjct: 298 TLARLR 303


>gi|297560171|ref|YP_003679145.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844619|gb|ADH66639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 313

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 103/218 (47%), Gaps = 11/218 (5%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           L+  +A++Y  RG    DL Q   +GL+KA   +D   G  F +Y +  V   I R   D
Sbjct: 92  LINKIARRYGGRGEPLEDLKQTAMVGLVKAVRGYDPARGKPFISYLLPTVTGEIKRHFRD 151

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
            +  +R+P   ++   K+ R          R PT  E+++++ +P   V +++++++   
Sbjct: 152 HTWAVRVPRRHQENRVKLRRVTGEFQQAHARTPTVHELSEEMGLPEAEVGELIQVSESYR 211

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +SL+ P   +     G  +ED      + LD  ++   RE+    LA L  RE  +LR+
Sbjct: 212 SLSLDAPDSSDSEGQEGTRLEDHLGCEDAALDRVVE---RESLKPALARLPAREREILRL 268

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RF      DHT  E+  +   ++  + ++ +  + +L+
Sbjct: 269 RF----FGDHTQSEIADRLGYSQMHVSRLLSGVLEQLR 302


>gi|152967736|ref|YP_001363520.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151362253|gb|ABS05256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 326

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 101/220 (45%), Gaps = 28/220 (12%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+   +L L   +A ++  RG    DL+Q   IGL+KA ++FD   G  F  YA+  +
Sbjct: 106 REELTRRHLPLADHLAARFLGRGEPQDDLVQVATIGLLKALDRFDPSRGVPFGAYAVPTM 165

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +++++ R PT  E+A++     E V 
Sbjct: 166 LGEIKRHFRDRGWAMRVPRRIQEAGRALGDAREALTHELGRAPTVAELAERTGYDPEDVV 225

Query: 565 KVLKI----------TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            VL+           T  P SL   +G +D +     +E++ A+ PL             
Sbjct: 226 DVLESANAYSTLPLDTGSPTSLVASLGADDDAL--QNVENREALRPL------------- 270

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             LA L  RE R+L +RF  GM+      EVG  Q  V+R
Sbjct: 271 --LAGLPARERRILALRFVRGMSQSQIAAEVGISQMHVSR 308


>gi|297196321|ref|ZP_06913719.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722899|gb|EDY66807.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 307

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 121/251 (48%), Gaps = 32/251 (12%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++ +G  E S  +  +VE NL LV   A ++ NR     D+IQ G IGL+KA  +FD 
Sbjct: 62  LAVLEEGTPEYSYVRNTLVELNLSLVKFAALRFANRAEPMEDIIQVGTIGLIKAINRFDL 121

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +F+++A+  V   I R   D S ++R+P  +++    + +    +  ++ R PT  
Sbjct: 122 EREVEFASFALPTVIGEIKRFFRDSSWSVRVPRRLQELRIDLAKALDVLEQRLGRRPTTA 181

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSH-----LG------DFIEDKNA 597
           E+A  L +  E V +  + +      SL+  + DED S+     LG      D I+   A
Sbjct: 182 ELAAYLGVSEEEVVEGERASNGYTAQSLDATVNDEDASNAVNRRLGIDDPAFDIIDSLEA 241

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + PL               +A+L  R+  +L +RF      + T  E+G++  +++  + 
Sbjct: 242 LKPL---------------IATLDERDRLILSLRF----REELTQSEIGERLGISQMHVS 282

Query: 658 QIEAKAIRKLK 668
           ++ A+ + KL+
Sbjct: 283 RLLARILEKLR 293


>gi|315445714|ref|YP_004078593.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315264017|gb|ADU00759.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 262

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 114/246 (46%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G       +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELAEL-EEGSAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVI 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVNAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRA 141

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           PTP E+A +L M     VEG+          I      G+ED   + D + D +    LD
Sbjct: 142 PTPSELAAELEMDRDEVVEGLVAGSSYNTLSIDSGGGSGNEDAPAIADTLGDVDLT--LD 199

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              Q   RE    +LA+L  RE  VL +RF   M      E VG    +++  + ++ AK
Sbjct: 200 ---QIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRLLAK 252

Query: 663 AIRKLK 668
           ++ +L+
Sbjct: 253 SLTRLR 258


>gi|300856558|ref|YP_003781542.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
 gi|300436673|gb|ADK16440.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
          Length = 251

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 126/246 (51%), Gaps = 25/246 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++   +KG+ +A     ++VE NL LV S++KK+ NRG ++ D+ Q G +GLMKA   F+
Sbjct: 19  LIKYAKKGDKDAL---NKLVELNLPLVASISKKFLNRGYEYEDIFQIGCMGLMKAVNNFN 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++   +++   K+      ++ K+ REPT 
Sbjct: 76  EEYNVKFSTYAVPMILGEIKRFLRDDGM-IKVSRSVKNTAKKIHYDREALTKKLNREPTI 134

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSP---LD 602
           +E+A+   + VE   +++  T+   SL+      DT H  D     + DK + +P   ++
Sbjct: 135 QELAEYSGVEVE---ELIFATESASSLQYLY---DTIHQDDGSPVLLIDKISENPKEDVE 188

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              +  L+E     L +L  +  +++ +R+      D T  +V K   + + ++ +IE K
Sbjct: 189 MVDKIALKEA----LNNLDVKSRQIIMLRYF----KDKTQVQVAKMLGINQVQVSRIEKK 240

Query: 663 AIRKLK 668
            ++ ++
Sbjct: 241 VLKTMR 246


>gi|154499842|ref|ZP_02037880.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
 gi|150271440|gb|EDM98697.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
          Length = 235

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 118/241 (48%), Gaps = 18/241 (7%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++   R+G+ +A      M+E N  L+ S+ ++Y  RG+   DL Q G +G +KA   FD
Sbjct: 8   LLEAARQGDNDAC---ARMMEENSGLIWSIVRRYYGRGVDPEDLYQLGCMGFLKAVRGFD 64

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPT 548
              G +FSTYA+  +   I R + D    +++   ++++    +RTAR R+   + REPT
Sbjct: 65  PAFGCQFSTYAVPKIAGEIRRFLRDDG-AVKVSRGLKERAGS-IRTARDRLQADLGREPT 122

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A++  +  E +    +      SL+   GD      G  +E       ++  I   
Sbjct: 123 LSELAEETGLEPEEIAAAEEANAPVASLQMETGD------GFTLESVLGTEGMEEGIVE- 175

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE     ++SL  RE +V+ +R+  G+  D T   +G    V++ +I ++E KA+  L+
Sbjct: 176 -REALRSAVSSLPDRERQVIVLRYFRGLTQDRTARIMG----VSQVQISRVEKKAMEYLR 230

Query: 669 H 669
            
Sbjct: 231 R 231


>gi|71737989|ref|YP_276878.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|257482996|ref|ZP_05637037.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289624653|ref|ZP_06457607.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289648492|ref|ZP_06479835.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|289672442|ref|ZP_06493332.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           FF5]
 gi|298485264|ref|ZP_07003357.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|302187226|ref|ZP_07263899.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           642]
 gi|71558542|gb|AAZ37753.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|298160252|gb|EFI01280.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320326376|gb|EFW82429.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320331634|gb|EFW87572.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330871135|gb|EGH05844.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330872356|gb|EGH06505.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891333|gb|EGH23994.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. mori str.
           301020]
 gi|330898959|gb|EGH30378.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330954977|gb|EGH55237.1| RNA polymerase factor sigma-32 [Pseudomonas syringae Cit 7]
 gi|330982560|gb|EGH80663.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
 gi|330985905|gb|EGH84008.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
 gi|331011765|gb|EGH91821.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 284

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 116/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  ++T   ++ +     +D S      +++ED     A    DS    N      +
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHRYDPARQLEDSDWTDNSTANLHQ 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 ALDVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|148266118|ref|YP_001232824.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter
           uraniireducens Rf4]
 gi|146399618|gb|ABQ28251.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           uraniireducens Rf4]
          Length = 251

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 96/201 (47%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL     IGL+ AAE+FD   G  F T+A   ++  I   +  Q    R    +RDK  +
Sbjct: 50  DLRSAAVIGLISAAERFDPSRGVMFKTFAEQRIRGTIMDELRSQDWLTR---SLRDKFKR 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + R    +  ++ R PT EE+A  + + +EG   +L+       +SL+    DED S LG
Sbjct: 107 LEREFSCLEQRLGRNPTSEEVAAAMGLELEGYFHLLEEIHFLSFVSLDDAWMDEDGSPLG 166

Query: 590 --DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D +EDK   SP +  I     E     +  L  +E  V+ + +   +N    L+E+G 
Sbjct: 167 LLDVLEDKGVESPQNQLIARQTVENLAEAIDGLPEKERIVITLYYYEELN----LKEIGS 222

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  RI Q+ ++A+ +L+
Sbjct: 223 VLSLTESRISQLHSQALLRLR 243


>gi|242238998|ref|YP_002987179.1| flagellar biosynthesis sigma factor [Dickeya dadantii Ech703]
 gi|242131055|gb|ACS85357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya dadantii
           Ech703]
          Length = 240

 Score = 77.8 bits (190), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 96/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V    R+    + R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAHAMRQAEQLLGRAPTEQEVAQSLNISLEEYRQILLDTNNSQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL   +  NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEEANPLHQLMDVNLRQRVMEAIENLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|134102478|ref|YP_001108139.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
 gi|133915101|emb|CAM05214.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 311

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 105/201 (52%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G  GL+ A EKF+   G KF TYAM  ++ AI   +  Q     +P  +R +   
Sbjct: 112 DLIQSGIFGLVDAIEKFEPERGLKFETYAMQRIRGAILDDLRAQDW---VPRSVRSRARD 168

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIG-DEDTSH 587
           V R   R+  K++R  +  E+A++L + V+ +R++   L++T   ++L+  IG  + TS 
Sbjct: 169 VERALERLEAKLQRTASDAELAEELELSVDELRELFAQLQMTS-VVALDDLIGAGQTTSS 227

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L + + D  A  P+ + +  + R      +  L+ R+  V+ + +   +    TL E+GK
Sbjct: 228 LAETLPDDRAEDPVATLVDRDSRRQLAEAVERLSDRDRIVVTLYYFENL----TLAEIGK 283

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  R+ Q+  +A+ +L+
Sbjct: 284 VLGVTESRVCQLHTRAVLRLR 304


>gi|153440|gb|AAC36891.1| minor sigma-like factor [Streptomyces aureofaciens]
 gi|743686|prf||2013252A RNA polymerase:SUBUNIT=sigma factor
          Length = 278

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + VE +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQLRRTPTEGEVAGEMGIGVEELHTVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDHAADDPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|329936708|ref|ZP_08286415.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
 gi|329303938|gb|EGG47821.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
          Length = 279

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 99/206 (48%), Gaps = 20/206 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EK+D     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKYDIGREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A +L + V+ +  V       +SL   +  E+  H+G  
Sbjct: 134 VERAYTTLEARLRRTPTESEVAAELGIRVDDLHAVFS----QLSLANVVALEEILHIGGE 189

Query: 590 -------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                  D +ED +A +P++ A    LR    R + +L  RE+ V+ + +  G+    TL
Sbjct: 190 GGGLSLMDTLEDTSADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYFEGL----TL 245

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+G    VT  R+ QI  K++ +L+
Sbjct: 246 AEIGNVLGVTESRVSQIHTKSVLQLR 271


>gi|294815383|ref|ZP_06774026.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
 gi|294327982|gb|EFG09625.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 278

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A+++ + VE +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQLRRTPSEGEVAEEMGIAVEELHAVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADDPVEVAEGRELRRLLARAINTLPDREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|268590799|ref|ZP_06125020.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
 gi|291313578|gb|EFE54031.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
          Length = 292

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 120/236 (50%), Gaps = 14/236 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K+++ ++LR VI VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AAKQLILSHLRFVIHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVE 561
           +K  I   +      +++      +  K+    R+   ++    +   + +A++L +  +
Sbjct: 109 IKAEIHEYVLRNWRIVKVATTKSQR--KLFFNLRKNKKRLGWFNQDEVDMVAQELGVSTK 166

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGD------FIEDKN---AVSPLDSAIQANLRET 612
            VR++               D+D+S  G       +++DK    A S  D   +++  + 
Sbjct: 167 DVREMESRMAAQDMAFDMSDDDDSSDFGGPVAPVLYLQDKASDFAGSIEDDNWESHATDR 226

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L SL  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 227 LADALDSLDERSQDIIRARW-LDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|54022121|ref|YP_116363.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54013629|dbj|BAD54999.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 266

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 52/212 (24%), Positives = 106/212 (50%), Gaps = 5/212 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E++E  L L   +A+K++ RG  F DL+Q   +G++ A ++FD   G  F  +A+  +
Sbjct: 41  REELIERCLPLAEHIARKFSGRGENFEDLLQIARVGMVAAVDRFDPTQGAPFLGFAVPTI 100

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D + ++R+P  +++    +      ++ ++ R P   E+A++L + +  V 
Sbjct: 101 MGEVRRHFRDHTWSVRVPRRLKELQATLNPAIETLTQRLGRMPKARELAEELGVDIAEVT 160

Query: 565 KVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L  +   +  S++   GD+  S      +   A  P    ++  L      ++A+L  
Sbjct: 161 QALVARNAYQTSSIDGSSGDDGESSAPALADTLGAEDPEFGTVENYL--AVKPLIAALPE 218

Query: 623 REERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           RE+RVL MRF   M+ +   +++G  Q  V+R
Sbjct: 219 REQRVLVMRFFHSMSQEQIAQQIGCSQMQVSR 250


>gi|294631664|ref|ZP_06710224.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
 gi|292834997|gb|EFF93346.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
          Length = 280

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 102/218 (46%), Gaps = 26/218 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDIDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + V+ +  V       +SL   +  E+  H+G  
Sbjct: 134 VERAYATLEARLRRTPTETEVAGEMGIAVDELHAVFS----QLSLANVVALEELLHVGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 DGDGLSFMDTLEDTAADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR-----AKLASF 278


>gi|239926901|ref|ZP_04683854.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
 gi|291435248|ref|ZP_06574638.1| HasL [Streptomyces ghanaensis ATCC 14672]
 gi|291338143|gb|EFE65099.1| HasL [Streptomyces ghanaensis ATCC 14672]
          Length = 281

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 58/247 (23%), Positives = 127/247 (51%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           FR + +++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 38  FRQL-AVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   + R   D S ++ +P  +++   ++ R    +  ++ R
Sbjct: 97  DRFELSREVEFTSFAIPYIVGEMKRFFRDTSWSVHVPRRLQEARVQLARATEELRTRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPL 601
            PT  E+A+ +++  E V   ++        SL+  IG E    S L DFI  ++A   L
Sbjct: 157 TPTTRELAQLMSLTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFIGSEDAALEL 216

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  RE +++  RF      + T  E+G++   ++  + ++ +
Sbjct: 217 VEDFHA-----LAPMIAELDERERKIIHWRF----VEELTQAEIGERLGCSQMHVSRLIS 267

Query: 662 KAIRKLK 668
           + +++L+
Sbjct: 268 RILKRLR 274


>gi|66047972|ref|YP_237813.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           B728a]
 gi|237802354|ref|ZP_04590815.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|63258679|gb|AAY39775.1| Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas syringae pv.
           syringae B728a]
 gi|330957082|gb|EGH57342.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. maculicola
           str. ES4326]
 gi|330970950|gb|EGH71016.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aceris
           str. M302273PT]
 gi|331025211|gb|EGI05267.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 284

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 116/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  ++T   ++ +     +D S      +++ED     A    DS    N      +
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHRYDPARQLEDSDWTDNSTANLHQ 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 ALDVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|302554440|ref|ZP_07306782.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472058|gb|EFL35151.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 280

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 101/218 (46%), Gaps = 26/218 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDIDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + VE +  V       +SL   +  E+  H G  
Sbjct: 134 VERAYATLEARLRRTPTEGEVAAEMGIGVEELHAVFS----QLSLANVVALEELLHAGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 GGDGLSVMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR-----AKLASF 278


>gi|255526140|ref|ZP_05393061.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296187150|ref|ZP_06855547.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
 gi|255510189|gb|EET86508.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296048185|gb|EFG87622.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
          Length = 251

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 114/225 (50%), Gaps = 8/225 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +++E NL LV +++KK+ NRG ++ D+ Q G +GL+KA   FD     KFSTYA+  
Sbjct: 30  ALNKLIEVNLPLVSAISKKFLNRGYEYEDIFQIGCMGLVKAVNNFDEKYNVKFSTYAVPM 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D    I++   +++   K+      ++ +I REPT EE+++   + VE +
Sbjct: 90  ILGEIKRFIRDDGM-IKVSRSVKNTAKKLHYAKEALTKQISREPTIEELSEYSGIGVEDI 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              ++ +     L   I  +D + +   I+  +  S  DS I    R      L +L  +
Sbjct: 149 IFAMESSNSLQYLYDTIHQDDGAPVL-LIDKLSESSDRDSEIVD--RIALKEALKNLDVK 205

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +++ +R+      D T  +V K   +++ ++ +IE K ++ ++
Sbjct: 206 SRQIIMLRYF----KDKTQIQVAKMLGISQVQVSRIEKKVLKVMR 246


>gi|205352349|ref|YP_002226150.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205272130|emb|CAR36983.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|326627399|gb|EGE33742.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 239

 Score = 77.4 bits (189), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  K+ R  T  E+A++L +PV   R++L  T           DE     GD 
Sbjct: 100 VAQAMGQLEQKLGRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++ +LR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|87121174|ref|ZP_01077065.1| sigma factor RpoH [Marinomonas sp. MED121]
 gi|86163666|gb|EAQ64940.1| sigma factor RpoH [Marinomonas sp. MED121]
          Length = 291

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 121/251 (48%), Gaps = 36/251 (14%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   +++V ++LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++F+  +G + 
Sbjct: 46  GDLEAA---RQLVMSHLRFVVHIAKSYSGYGLNQGDLIQEGNVGLMKAVKRFNPEVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   I      +++     + K+   +R+A++  +    +   E +A  
Sbjct: 103 VSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKMFFNLRSAKKTLSWFSNDEV-ESVAGD 161

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--------------GDFIEDKNAVSPL 601
           L +  E VR+          +E  +   DT+                 +++ED +   P 
Sbjct: 162 LGVSPEVVRQ----------MEGRMSSSDTTFDASSDDDDDSAYQAPANYLED-HRYDPA 210

Query: 602 DSAIQANLRETTTR----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                 N  E + R     ++ L  R   +L  R+    ++  TL ++  ++ V+ ERIR
Sbjct: 211 SLTENGNWEEDSNRRLQEAMSELDERSRNILVQRW--LSDSKSTLHDLADEYGVSAERIR 268

Query: 658 QIEAKAIRKLK 668
           Q+E  A+ K++
Sbjct: 269 QLEKNAMAKIR 279


>gi|330944706|gb|EGH46637.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 284

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 116/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  ++T   ++ +     +D S      +++ED     A    DS    N      +
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHRYDPARQLEDSDWTDNSPANLHQ 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 ALDVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|206208346|gb|ACI06117.1| RNA polymerase sigma subunit [Parvibaculum sp. P31]
          Length = 269

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/50 (70%), Positives = 42/50 (84%), Gaps = 1/50 (2%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESK 196
           AGR  M+A LCESPLTFQA+IIWRDELN+G  LLR+IIDL+A   GP++K
Sbjct: 1   AGRETMIAGLCESPLTFQAIIIWRDELNEGKILLRDIIDLDATYAGPDAK 50


>gi|116514965|ref|YP_802594.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256819|gb|ABJ90501.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 291

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 120/239 (50%), Gaps = 22/239 (9%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           K ++ +NLR VI VAK Y+  GL   DLIQEGNIGLMKA  +F+  +  +  ++A+ W+K
Sbjct: 54  KLLILSNLRFVIHVAKNYSGYGLPQADLIQEGNIGLMKAIRRFNPNINVRLVSFAVHWIK 113

Query: 506 QAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
             I   +      ++I     + K+   +R +++      R    + ++++L +  + V+
Sbjct: 114 SEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNRHEI-DTVSQELGVSTQEVK 172

Query: 565 KV-LKITKEPISLETPIGDEDTSHLGDF---------IEDKNAVSPL-----DSAIQANL 609
           ++  +++ + I+ +    D   SHL            +EDK +   +     + A+ A  
Sbjct: 173 EMEARMSAQDITFDLSAKD---SHLDSITNNLRTSFHLEDKKSNFSIKIEKDNWALHAT- 228

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  L  L  R +++++ R+        TL+ + + + ++ ER+RQ+E  A++KLK
Sbjct: 229 -NKLTNALLILDKRSQQIIKRRWLDDDKPKITLQAIARDYGISAERVRQLEKNAMKKLK 286


>gi|317055657|ref|YP_004104124.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447926|gb|ADU21490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 218

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 101/205 (49%), Gaps = 11/205 (5%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E NL LV   A ++  RG+++ DL   G +GL+KA+  FD   G KFSTYA+  +   I 
Sbjct: 10  EDNLGLVHLCANRFRGRGIEYDDLYGAGCMGLVKASRAFDASRGVKFSTYAVPVILGEIK 69

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R   D   T+++   +++   K+ R ++  ++K  REPT  E++       + V + L  
Sbjct: 70  RLFRD-GGTVKVSRSLKELSLKITRASQTFAHKNGREPTVSELSDITGADPDDVIEALNA 128

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           ++  +SL   IGDED     D         P D  I   L     +VL+ L+  + +++ 
Sbjct: 129 SQPTVSLT--IGDEDGESQTDL-----PTEPPDEDITDRL--ALRQVLSELSADDRKLID 179

Query: 630 MRFGIGMNTDHTLEEVG-KQFCVTR 653
           +R+  GM      E++G  Q  V+R
Sbjct: 180 LRYFKGMTQTAAAEKLGMTQVQVSR 204


>gi|307153354|ref|YP_003888738.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306983582|gb|ADN15463.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 258

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 108/219 (49%), Gaps = 8/219 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++    + DL+Q G +GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRREAYHWVSQCNENYEDLLQVGCLGLIRAIERFETGKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  ++RIP    D   + +   R    ++ R+P+ EEIA+ L +  +  
Sbjct: 89  IRGEIQHYLRDKGYSVRIPRRWLDLGRQAMTIRRDFQTRLNRQPSDEEIAEILEISAKEW 148

Query: 564 R--KVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  K+    +EP+SL+  I  +D   + LGD + D    S     +  + R    + LA 
Sbjct: 149 QEIKLAFQNREPLSLDVSINHDDDGQTSLGDLVPDPKYRS---FQLSEDDRIRLQQALAQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           L  R  RVL   F   +    T E++G        R+++
Sbjct: 206 LEERTRRVLEFVFLYDLTQRETAEQLGISVVTVSRRVKK 244


>gi|258546170|ref|ZP_05706404.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
 gi|258518595|gb|EEV87454.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
          Length = 287

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 123/233 (52%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++  +L+ V+ +A+ +T  GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W
Sbjct: 53  AAQTLIVHHLKFVVHIARGFTGYGLPLGDLIQEGNVGLMKAVKRFEPQRGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      ++I     + K+   +R+ ++  N +  E   + IA +L +  + 
Sbjct: 113 IKSEIHEYIIRNWRMVKIATTKAQRKLFFNLRSMKKSLNWLN-EAEAKAIADELNVSTKD 171

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANLRETTTRVLA- 618
           V ++  +I  + I+ E    DED  H     ++ D +++ P +    A       R LA 
Sbjct: 172 VFEMESRIHGQDIAFELNDDDEDNDHFSPSQWLAD-DSIDPAEHTEHAEHENLMQRKLAK 230

Query: 619 ---SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +L PR   +++ R+ +  ++  TL+ +  ++ V+ ERIRQIE +A+ +L+
Sbjct: 231 GLQALDPRSRAIVQARW-LNEDSKATLQTLASEYNVSAERIRQIEQQAMHQLR 282


>gi|187934214|ref|YP_001885077.1| sporulation sigma factor SigF [Clostridium botulinum B str. Eklund
           17B]
 gi|187722367|gb|ACD23588.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 251

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 42/125 (33%), Positives = 70/125 (56%), Gaps = 4/125 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            ++ + + G+ EA      ++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   F
Sbjct: 18  QLLPLAKDGDNEAM---NRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNF 74

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++  +++    ++  T   ++ K+ R PT
Sbjct: 75  DLSYNVKFSTYAVPMIIGEIKRFLRDDGM-IKVSRNVKSLAKRIHFTKEELTKKLNRSPT 133

Query: 549 PEEIA 553
            EE+A
Sbjct: 134 IEELA 138


>gi|291004131|ref|ZP_06562104.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 328

 Score = 77.4 bits (189), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 105/201 (52%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G  GL+ A EKF+   G KF TYAM  ++ AI   +  Q     +P  +R +   
Sbjct: 129 DLIQSGIFGLVDAIEKFEPERGLKFETYAMQRIRGAILDDLRAQDW---VPRSVRSRARD 185

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIG-DEDTSH 587
           V R   R+  K++R  +  E+A++L + V+ +R++   L++T   ++L+  IG  + TS 
Sbjct: 186 VERALERLEAKLQRTASDAELAEELELSVDELRELFAQLQMTS-VVALDDLIGAGQTTSS 244

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L + + D  A  P+ + +  + R      +  L+ R+  V+ + +   +    TL E+GK
Sbjct: 245 LAETLPDDRAEDPVATLVDRDSRRQLAEAVERLSDRDRIVVTLYYFENL----TLAEIGK 300

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  R+ Q+  +A+ +L+
Sbjct: 301 VLGVTESRVCQLHTRAVLRLR 321


>gi|300787087|ref|YP_003767378.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299796601|gb|ADJ46976.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 263

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 105/225 (46%), Gaps = 29/225 (12%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + + ++V   L L   +A +++ RG    DL+Q   IGL+ A ++FD   G+ F ++A+ 
Sbjct: 37  VVRSKLVTELLPLAEHIATRFSGRGEPREDLVQVARIGLINAVDRFDPARGHDFLSFAVP 96

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   + R   D   ++R+P  +++    + + +  +S ++ R PTP E+A+ L + V+ 
Sbjct: 97  TIMGEVRRHFRDTGWSVRVPRRLKELHLSLSQGSAVLSQRLGRAPTPTELAEHLNLDVDE 156

Query: 563 VRKVLKI--TKEPISLETPIGDE-----------DTSHLGDFIEDKNAVSPLDSAIQANL 609
           VR+ L      + +S++ P+ D+           +  H    +E+  A+ PL        
Sbjct: 157 VREGLLAGNAYQALSVDKPVHDDAEALSLADTMGEPDHEMAMVENHEALQPL-------- 208

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                  L  L  RE  +L MRF  G+      + VG  Q  V+R
Sbjct: 209 -------LQELPKRERAILVMRFFGGLTQTQIADRVGISQMHVSR 246


>gi|328882855|emb|CCA56094.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 296

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 116/251 (46%), Gaps = 39/251 (15%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  + +  +  +VE NL LV   A ++  R     D++Q G IGL+KA ++F+   G +
Sbjct: 60  EGTHDHAYVRNTLVELNLALVRFAAARFGTRSEPMEDIVQVGTIGLIKAIDRFELTRGVE 119

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  +   I R   D S ++ +P  +++    + R    ++ ++ R PT  E+A++
Sbjct: 120 FPTFAMPTIIGEIKRFFRDTSWSVHVPRRLQELRLDLARAGDTLAQRLDRAPTVAELAEE 179

Query: 556 LAMP----VEGVRKVLKITKEPI--------------SLETPIGDEDTSHLGDFIEDKNA 597
           L +     VEG+      T   +              +L   +G ED    G  IE   +
Sbjct: 180 LGIAPEEVVEGMAASNAYTASSLDAQPDEEEGGGGEATLADRLGYEDHGLTG--IEYIAS 237

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + P+               +ASL  RE ++L +RF  G+    T  E+G +  +++  + 
Sbjct: 238 LKPM---------------IASLPARERQILSLRFVSGL----TQSEIGTELGISQMHVS 278

Query: 658 QIEAKAIRKLK 668
           ++ A+ + +L+
Sbjct: 279 RLLARTLARLR 289


>gi|28211847|ref|NP_782791.1| sporulation sigma factor SigF [Clostridium tetani E88]
 gi|28204289|gb|AAO36728.1| RNA polymerase sigma-F factor [Clostridium tetani E88]
          Length = 255

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 113/232 (48%), Gaps = 22/232 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++VE NL LV +++KK+ NRG  + D+ Q G +GL+KA   FD     KFSTYA+  
Sbjct: 33  ATDKLVELNLPLVSAISKKFLNRGYDYEDIYQIGCMGLVKAINNFDSSYNVKFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D    I++   ++    K+      +  K+ REP+ EE+++   + +E +
Sbjct: 93  IMGEIKRFIRDDGI-IKVSRSLKIMARKLYYHRETLCKKLGREPSIEELSEYTGLEIEEI 151

Query: 564 RKVLKITKEPISLETPIGDEDTSHLG-------DFIEDKNAVSPLDSAIQANLRETTTRV 616
              ++ +     L   I  +D + +        ++ ED + ++ L       L+E     
Sbjct: 152 VYAMESSSNLQYLHDVIHQDDGAPIMLIDKISENYSEDSDIINKL------ALKEA---- 201

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  +  +++ +R+      D T  EV K   +++ ++ +IE + ++ +K
Sbjct: 202 LGKLDAKSRQIIMLRYF----KDKTQIEVAKMLGISQVQVSRIEKRVLKTMK 249


>gi|311030102|ref|ZP_07708192.1| RNA polymerase sigma factor SigD [Bacillus sp. m3-13]
          Length = 254

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 98/193 (50%), Gaps = 10/193 (5%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL  A EKFD     KF TYA + ++ +I   +  +     +P  +R+K  ++  T   
Sbjct: 62  VGLFDAIEKFDPSRDLKFDTYASFRIRGSIIDGLRKEDW---LPRSVREKAKRIESTLEN 118

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISL-ETPIGDEDTSHLGDFIEDK 595
           +  K+ R  T EE+A  L MP E V  V+        +S+ E P  +++ SH    ++D+
Sbjct: 119 LEQKLMRNATLEEVAAHLDMPEEEVSTVMHEVFYSNILSMDEMPKENDEQSHGAYVLKDE 178

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
             +SP +  I++ L +     + +LT  E+ V+ + +      + TL E+G+   +T  R
Sbjct: 179 KVISPEEELIKSELIQLLGEQIENLTENEQIVISLFY----KEELTLTEIGQVLGLTTSR 234

Query: 656 IRQIEAKAIRKLK 668
           I QI +KAI KL+
Sbjct: 235 ISQIHSKAIFKLR 247


>gi|262376306|ref|ZP_06069536.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
 gi|262308907|gb|EEY90040.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
          Length = 289

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 115/235 (48%), Gaps = 14/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   +      ++I     + K+   +R+ ++ S K+      + IA  L +  E 
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLAEA-QSIANDLNVTPEQ 171

Query: 563 VRKV---LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRETTTRVL 617
           V ++   L          +   DE ++H+    ++ED N   P       +  E +T  L
Sbjct: 172 VLEMEGRLTAYDAAFDASSDDDDEGSTHVAPALYLED-NRYDPARLIENEDYEEQSTSAL 230

Query: 618 A----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L  R   +L+ R+    +   TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 231 HEAMDQLDDRSRNILQRRWLD--DEKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|104779584|ref|YP_606082.1| RNA polymerase factor sigma-32 [Pseudomonas entomophila L48]
 gi|95108571|emb|CAK13265.1| sigma H (sigma 32) factor of RNA polymerase RpoH [Pseudomonas
           entomophila L48]
          Length = 284

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 115/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     A+   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPASEADDDSAFQSPAHYLEDHRYDPALQLEDADWSDNSSSNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  R   +L  R+        TL E+ +++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGLDDRSRDILYQRWLAEEKA--TLHELAEKYSVSAERIRQLEKNAMNKVK 279


>gi|239944630|ref|ZP_04696567.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           15998]
 gi|239991094|ref|ZP_04711758.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           11379]
          Length = 247

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 44  DFVSSGVFGLIDAIEKFDIERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  + +R P+  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 101 VERAYATLEAQFRRTPSEAEVASEMGIALEELHAVFS----QLSLANVVALEELLHVGGE 156

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 157 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEGL----T 212

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 213 LAEIGNVLGVTESRVSQIHTKSVLQLR 239


>gi|28867660|ref|NP_790279.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213967796|ref|ZP_03395943.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382433|ref|ZP_07230851.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           Max13]
 gi|302061175|ref|ZP_07252716.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           K40]
 gi|302132032|ref|ZP_07258022.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|28850895|gb|AAO53974.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213927572|gb|EEB61120.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|330965442|gb|EGH65702.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. actinidiae
           str. M302091]
 gi|331014973|gb|EGH95029.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 284

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 118/234 (50%), Gaps = 13/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTT---- 614
           VR++  ++T   ++ +     +D S      +++ED     P      A+  + +T    
Sbjct: 169 VREMESRLTGHDMAFDPAAEADDDSAFQSPANYLEDHR-YDPARQLEDADWTDNSTANLH 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 228 QALDVLDERSRDILYQRWLAEEKA--TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|297616717|ref|YP_003701876.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144554|gb|ADI01311.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 248

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 111/226 (49%), Gaps = 10/226 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ + ++NL LV    +++ N    F DL Q G IGL+KA  +FD+  G KFSTYA+  
Sbjct: 26  AEEAVFQSNLGLVYMALERFKNTPYDFEDLFQIGAIGLLKAIARFDFGYGVKFSTYAVPM 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R + D    +++   +++  ++V      +  +  +EPT  EIA++L + +  V
Sbjct: 86  IIGELKRYLRDDGI-LKVQRSIKEIYYRVKSAQDDLRREFGKEPTIGEIAERLGLELNDV 144

Query: 564 RKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              ++  + P  +   + GDE    L    +  +     D   +  L+E   R    L P
Sbjct: 145 VMAVEACQPPTYIYNLLPGDEKEQPLPLISKVSDREGTEDLLEKVALKEAVMR----LDP 200

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  V+  RF      D T   + +   +++ ++ ++E +A++KL+
Sbjct: 201 REREVIVRRF----FKDETQSAIAEDLGISQVQVSRLEKRALKKLR 242


>gi|254519896|ref|ZP_05131952.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
 gi|226913645|gb|EEH98846.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
          Length = 251

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 114/232 (49%), Gaps = 20/232 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  +++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD     KFSTYA+  
Sbjct: 30  AMNKVIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFDDKFNVKFSTYAVPM 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R I D    I++  +++    K+     +++ K+ REPT EE+++       GV
Sbjct: 90  IIGEIKRFIRDDGI-IKVSRNVKSLARKLHFDKEQLTKKLDREPTIEELSQ-----FSGV 143

Query: 564 RK--VLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTRVL 617
            K  +L   +   S++      DT H  D     + DK +    D +   N R      L
Sbjct: 144 DKEEILFAIESSASMQYLY---DTIHQDDGAPVLLIDKLSEKGEDDSDMIN-RIALKEAL 199

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            SL  +  +++ +R+      D T  +V K   +++ ++ +IE K +  +K 
Sbjct: 200 RSLDSKARQIIMLRYF----KDKTQVQVAKMLGISQVQVSRIEKKVLVLMKQ 247


>gi|153876074|ref|ZP_02003579.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152067462|gb|EDN66421.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 242

 Score = 77.0 bits (188), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 120/234 (51%), Gaps = 17/234 (7%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           K++V ++LR V+ +A  Y   GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W++
Sbjct: 8   KKLVISHLRFVLYIAHGYRGYGLPLADLIQEGNIGLMKAVKRFNPNVGVRLVSFAVHWIR 67

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV 563
             I   I      +++      +  K+    R M  ++      E  ++A+ L +  + V
Sbjct: 68  AEIHEFILRNWRIVKVVTTKAQR--KLFFNLRSMKKRLGWLSQAEVDKVAQDLGVSSKDV 125

Query: 564 RKVLK-ITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQ----ANLRETTTR 615
            ++ K ++ + ++ + P+  +D   +     ++ED N   P     Q    A+  +    
Sbjct: 126 LEMEKRLSMQDVAFDAPVDSDDDDEVFAPAAYLED-NRYDPAALVEQDEWEAHGHKQLLH 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  R + +L+ R+   ++ D  TL+E+   + V+ ERIRQIE+ A++KLK
Sbjct: 185 AFKKLDVRSQDILQQRW---LSEDKATLQELANHYKVSAERIRQIESNALKKLK 235


>gi|148381038|ref|YP_001255579.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933259|ref|YP_001385409.1| sporulation sigma factor SigF [Clostridium botulinum A str. ATCC
           19397]
 gi|153935896|ref|YP_001388816.1| sporulation sigma factor SigF [Clostridium botulinum A str. Hall]
 gi|153939970|ref|YP_001392365.1| sporulation sigma factor SigF [Clostridium botulinum F str.
           Langeland]
 gi|170754271|ref|YP_001782722.1| sporulation sigma factor SigF [Clostridium botulinum B1 str. Okra]
 gi|226950516|ref|YP_002805607.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|148290522|emb|CAL84650.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929303|gb|ABS34803.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152931810|gb|ABS37309.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. Hall]
 gi|152935866|gb|ABS41364.1| RNA polymerase sigma-F factor [Clostridium botulinum F str.
           Langeland]
 gi|169119483|gb|ACA43319.1| RNA polymerase sigma-F factor [Clostridium botulinum B1 str. Okra]
 gi|226844449|gb|ACO87115.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|295320356|gb|ADG00734.1| RNA polymerase sigma-F factor [Clostridium botulinum F str. 230613]
 gi|322807388|emb|CBZ04962.1| RNA polymerase sporulation specific sigma factor SigF [Clostridium
           botulinum H04402 065]
          Length = 251

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 113/222 (50%), Gaps = 8/222 (3%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++VE NL LV +++KK+ NRG ++ D+ Q G IGL+KA   F+     KFSTYA+  +  
Sbjct: 33  KLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAINNFETKYNVKFSTYAVPMIMG 92

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    I++   ++    K+     ++  ++ REPT EE+++     V+ +   
Sbjct: 93  EIKRFLRDDGI-IKVSRSIKTAAKKLHYDKEKLCKELNREPTIEELSQFSGYTVDEILMA 151

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            + +  P  L   I  +D + +   I+  +  +  D+ I  N+       L +L  +  +
Sbjct: 152 TESSSSPQYLYDVIHQDDGAPVL-LIDKISENTEEDNKIVDNI--ALKEALKNLDIKSRQ 208

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +R+      D T  EV KQ  +++ ++ +IE K ++ +K
Sbjct: 209 IIILRYF----KDKTQIEVAKQLGISQVQVSRIEKKVLKLMK 246


>gi|302535451|ref|ZP_07287793.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444346|gb|EFL16162.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 288

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 118/257 (45%), Gaps = 38/257 (14%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++ + +G  + S  +  +VE NL LV   A+++  R     D++Q G IGL+KA  +F
Sbjct: 46  HRLAELDEGTADYSYVRNTLVELNLSLVKYAARRFRGRSEPMEDIVQVGTIGLIKAINRF 105

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G +F+T+AM  +   I R   D S  +++P  +++      +    +   + REPT
Sbjct: 106 DPERGVEFTTFAMPTISGEIKRFFRDTSWAVKVPRRLQELRIDSAKAHDALEQDLGREPT 165

Query: 549 PEEIAKKLAMPVEGVRKVLKIT-----------------KEPISLETPIGDEDTSHLGDF 591
             E+A++L +  E   +  K                   ++P +    +G+E+ ++  D 
Sbjct: 166 DTEMARELDVTPEEFSEGRKAASAYSARSLDAPVQEDSERDPAAERASLGEEEPAY--DR 223

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE   ++ P+               LA L  RE  +L +RFG     + T  E+G +  +
Sbjct: 224 IECLESLKPM---------------LAVLPERERELLSLRFG----QELTQSEIGARLGL 264

Query: 652 TRERIRQIEAKAIRKLK 668
           ++  + ++  + + +L+
Sbjct: 265 SQMHVSRLLNRTLTRLR 281


>gi|254482649|ref|ZP_05095887.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
 gi|214037008|gb|EEB77677.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
          Length = 284

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 124/235 (52%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +E+V ++LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W
Sbjct: 50  AARELVMSHLRFVVHIARSYSGYGLAEADLIQEGNVGLMKAIKRFDPEKGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R+ ++  + +  +   + +A+ L + V+ 
Sbjct: 110 IKAEMHEYILRNWRIVKVATTKAQRKLFFNLRSKKKSLSWLSADEA-KAVAEDLGVDVKE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGD---FIEDKNAVSPLDSAIQANLRETTT---- 614
           V ++  ++T   ++ +     +D         ++ED ++  P  +  + + ++ +     
Sbjct: 169 VHRMEGRLTSRDLAYDMSTDSDDDDAWQAPQYYLEDHSS-DPAQTVEEGDWKQNSQAQLH 227

Query: 615 RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LA L  R   +L  R+   +  D  TL E+  Q+ V+ ERIRQ+EA A++KLK
Sbjct: 228 SALADLDERSRNILAQRW---LAEDKSTLHELADQYGVSAERIRQLEANAMKKLK 279


>gi|187778269|ref|ZP_02994742.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
 gi|187771894|gb|EDU35696.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
          Length = 251

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 113/222 (50%), Gaps = 8/222 (3%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++VE NL LV +++KK+ NRG ++ D+ Q G IGL+KA   F+     KFSTYA+  +  
Sbjct: 33  KLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAINNFETKYNVKFSTYAVPMIMG 92

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    I++   ++    K+     ++  ++ REPT EE+++     V+ +   
Sbjct: 93  EIKRFLRDDGI-IKVSRSIKTAAKKLHYDKEKLCKELNREPTIEELSQFSGYTVDEILMA 151

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            + +  P  L   I  +D + +   I+  +  +  D+ I  N+       L +L  +  +
Sbjct: 152 TESSSSPQYLYDVIHQDDGAPVL-LIDKISENTEEDNKIIDNI--ALKEALKNLDIKSRQ 208

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +R+      D T  EV KQ  +++ ++ +IE K ++ +K
Sbjct: 209 IIILRYF----KDKTQIEVAKQLGISQVQVSRIEKKVLKLMK 246


>gi|157161393|ref|YP_001458711.1| flagellar biosynthesis sigma factor [Escherichia coli HS]
 gi|157067073|gb|ABV06328.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           HS]
          Length = 239

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           VV+   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VVQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|220927856|ref|YP_002504765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
 gi|219998184|gb|ACL74785.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
          Length = 249

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L L   ++KK+ NRG+ F D+ Q   + L+ A E+F    G KF ++A   +
Sbjct: 29  RNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALINAVERFSPDKGVKFISFATPTI 88

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+S TI+IP  + +    V +    ++ K+ R P  +EIA+ + +PVE V 
Sbjct: 89  LGEIKRFFRDKSTTIKIPRRIYESRQGVNKARDELTQKLSRVPRADEIAEYMGIPVETVL 148

Query: 565 KVLKITKEPI--SLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLT 621
           ++++     I  SL+  I  ++ + LGD +  D+     +D+      ++   +VL S  
Sbjct: 149 EIIEAGSSTIVKSLDQTINQDNDAELGDTLGYDEKTYEMIDN------KDFLEKVLISFN 202

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E + +  R+      + T +++ +   V++  + ++E K + K +
Sbjct: 203 DVERQFVTYRYI----QNKTQKQIAEILGVSQMYVSRMERKILDKFR 245


>gi|168179581|ref|ZP_02614245.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|168181777|ref|ZP_02616441.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|170761116|ref|YP_001788407.1| sporulation sigma factor SigF [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237796543|ref|YP_002864095.1| sporulation sigma factor SigF [Clostridium botulinum Ba4 str. 657]
 gi|169408105|gb|ACA56516.1| RNA polymerase sigma-F factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182669805|gb|EDT81781.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|182675139|gb|EDT87100.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|229260985|gb|ACQ52018.1| RNA polymerase sigma-F factor [Clostridium botulinum Ba4 str. 657]
          Length = 251

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 113/222 (50%), Gaps = 8/222 (3%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++VE NL LV +++KK+ NRG ++ D+ Q G IGL+KA   F+     KFSTYA+  +  
Sbjct: 33  KLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAINNFETKYNVKFSTYAVPMIMG 92

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    I++   ++    K+     ++  ++ REPT EE+++     V+ +   
Sbjct: 93  EIKRFLRDDGI-IKVSRSIKTAAKKLHYDKEKLCKELNREPTIEELSQFSGYTVDEILMA 151

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            + +  P  L   I  +D + +   I+  +  +  D+ I  N+       L +L  +  +
Sbjct: 152 TESSSSPQYLYDVIHQDDGAPVL-LIDKISENTEEDNKIIDNI--ALKEALKNLDIKSRQ 208

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +R+      D T  EV KQ  +++ ++ +IE K ++ +K
Sbjct: 209 IIILRYF----KDKTQIEVAKQLGISQVQVSRIEKKVLKLMK 246


>gi|309775720|ref|ZP_07670717.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916525|gb|EFP62268.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 241

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 114/228 (50%), Gaps = 15/228 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  +R G+ EA   K   V+ N  LV S+ ++++ + +   DL Q G +GLMKA   FD
Sbjct: 10  LIERIRLGDEEA---KSCFVQQNSALVYSIIRRFSRQRISNEDLFQIGCVGLMKALNNFD 66

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R   D   +IRI   +++   ++V+T   +  K+  EPT 
Sbjct: 67  TSYEVKFSTYAVPIIMGEIKRFFRDDG-SIRISRSLKEGYLQMVKTKEMLLQKLNHEPTY 125

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQAN 608
           +EIA  + + V  V    +  +   SL+  I + D S +   +EDK +     D  ++ +
Sbjct: 126 QEIADAMELDVADVILAFEANQFIYSLDETIYENDGSPI--LLEDKVSNKKEEDVVMKVS 183

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           LR+   +    L  RE+ +L  R+ + M      E++ K+  +++ ++
Sbjct: 184 LRDEIQK----LDQREQLLLHYRYDLSMKQ----EDIAKKLNISQVQV 223


>gi|213583576|ref|ZP_03365402.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
          Length = 201

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 5   DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 61

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L +PV   R++L  T           DE     GD 
Sbjct: 62  VAQAMGQLEQELGRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSY---DEWREEHGDS 118

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++ +LR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 119 IELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYYQEELN----LKEIGA 174

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 175 VLEVGESRVSQLHSQAIKRLR 195


>gi|82776398|ref|YP_402747.1| flagellar biosynthesis sigma factor [Shigella dysenteriae Sd197]
 gi|81240546|gb|ABB61256.1| alternative sigma factor 28 [Shigella dysenteriae Sd197]
          Length = 239

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQCIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDYQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  V   R+ Q+ ++AI++L+
Sbjct: 213 ELEVGESRVSQLHSQAIKRLR 233


>gi|300114350|ref|YP_003760925.1| RNA polymerase sigma 32 subunit RpoH [Nitrosococcus watsonii C-113]
 gi|299540287|gb|ADJ28604.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus watsonii
           C-113]
          Length = 287

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 116/238 (48%), Gaps = 21/238 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR VI +A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 53  AARQLVLSHLRFVIRIARGYNGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R+A++    + R+    E+A+ L +    
Sbjct: 113 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKKRLGWLNRKEV-NEVAQDLGI---S 168

Query: 563 VRKVLKITKEPISLETPIGDEDT-----------SHLGDFIEDKNAVSPLDSAIQANLRE 611
            ++V+++     S +TP    +T           ++L D   D      ++   Q N   
Sbjct: 169 PKQVMEMEARLSSQDTPFDGTNTEESENSLPAPMAYLADPSAD--PAQKMELLDQENYYG 226

Query: 612 TTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R  L  L  R   ++  R+        TL E+  ++ ++ ERIRQ+E  AI+K++
Sbjct: 227 QRLRQALEVLDLRSRTIINRRW--LQENKSTLHELAAEYQISAERIRQLENNAIKKMR 282


>gi|119475401|ref|ZP_01615754.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451604|gb|EAW32837.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 282

 Score = 77.0 bits (188), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 120/230 (52%), Gaps = 10/230 (4%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E+V A+LR V+ +A+ Y   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ WVK
Sbjct: 51  RELVMAHLRFVVHIARSYNGYGLPLADLIQEGNIGLMKAVKRFNPEKGVRLVSFAVHWVK 110

Query: 506 QAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
             +   I      +++     + K+   +R A++    +  E     IA+ L + V+ VR
Sbjct: 111 AEMHEYILRNWRIVKVATTKAQRKLFFNLRGAKKKLAWLN-EKEAHAIAEDLNVDVKEVR 169

Query: 565 KV-LKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPL---DSAIQANLRETTTRVLA 618
           ++  ++T   +  +    DED   +    ++ED +A   +   D+  + N  +     L 
Sbjct: 170 RMESRLTASDLGFDAGADDEDDGFVAPAHYLEDHSANPAMLLEDADWEQNSNQHLQLALE 229

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R   +++ R+    ++  TL ++  ++ V+ ER+RQ+E  A++K++
Sbjct: 230 QLDERSRDIIQARW--LSDSKSTLHDLAGKYGVSAERVRQLEKNAMKKVR 277


>gi|322834883|ref|YP_004214910.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
 gi|321170084|gb|ADW75783.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
          Length = 285

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/275 (24%), Positives = 139/275 (50%), Gaps = 19/275 (6%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++ ++  N    ++ E   +++E  H       G+ EA+   KE++ ++LR V  +A+ 
Sbjct: 16  LEAYVRAANAYPMLTAEEERALAERLHY-----NGDLEAA---KELILSHLRFVAHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 127

Query: 523 -VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
               + K+   +R  ++       +   E +A++L +  + V ++  ++  + ++ +   
Sbjct: 128 TTKAQRKLFFNLRKNKQRLGWFSHDEV-EHVARELGVTSKDVLEMESRMAAQDMTFDPTP 186

Query: 581 GDE--DTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLAS----LTPREERVLRMRFG 633
            DE  D + +   +  ++  S     I+  N  +  T  L+S    L  R + ++R R+ 
Sbjct: 187 DDEPRDGAAMAPMLYLQDKSSDFAETIEEDNWDQDATDKLSSAMEGLDERSQDIIRARW- 245

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 246 LDDENKSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|323487067|ref|ZP_08092375.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694575|ref|ZP_08108741.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399568|gb|EGA91958.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501343|gb|EGB17239.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 237

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 117/226 (51%), Gaps = 8/226 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V  N+ LV S+ +++T RG +  DL Q G+IGL+KA +KFD     +FSTYA+  
Sbjct: 18  ARERLVMDNVGLVWSIVRRFTGRGCETEDLFQIGSIGLIKAIDKFDTSYDVRFSTYAVPM 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   +++   KV      +S  + REPT EEI++ L +  E V
Sbjct: 78  ITGEIKRFLRDDG-MIKVSRSIKELGFKVSAVRESLSGSLGREPTLEEISEALEVSKEEV 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L+   +  SL  P G  + + L   + DK A    ++ +  + R     +L SL  +
Sbjct: 137 AASLEAGCQVESLYAPSGSGEDNTLS--LIDKVAEEKEENEMLLD-RMVLGELLKSLEKK 193

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  ++  R+      + T  ++ +   +++ ++ ++E K +R+++ 
Sbjct: 194 QREIIVRRY----FYNQTQTQIAEILGISQVQVSRMERKILREMRE 235


>gi|164686436|ref|ZP_02210464.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
 gi|164604447|gb|EDQ97912.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
          Length = 256

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 116/227 (51%), Gaps = 16/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NL LV  +AKKY N+G++F DL Q G++ L+ A E++D   GY+FS++A   +   
Sbjct: 35  LIERNLYLVSILAKKYINKGVEFEDLYQVGSLALIYAIERYDISKGYEFSSFATPTIIGE 94

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  T+R+P  +++   KV      +  + K++P   EIA+ +    E V + L
Sbjct: 95  IKKYFRDKVWTMRVPRRVQELNKKVNEAKLLLEQQNKKKPKVNEIAEYIGCREEEVLEAL 154

Query: 568 KIT--KEPISLETPIGDE----DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + +   +P+SL++P+  +    + S +      +N  S ++       ++   +  + L 
Sbjct: 155 EASYGYQPVSLDSPVNSDSEEAEISLIDKIGSQENNFSDIE------YKDFIEKFTSKLN 208

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E  +   RF      + T   + K+  +++  I +IE K ++KL+
Sbjct: 209 ELERNIFEGRFF----KEKTQSALAKELDISQMTISRIERKVVQKLR 251


>gi|5821404|dbj|BAA83808.1| sigma factor 32 [Pseudomonas putida]
          Length = 284

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 113/233 (48%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVMAHLRFVVHIARSYAGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  +     +A+ L +    
Sbjct: 110 IKAEIPEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKN---AVSPLDSAIQANLRETTTR 615
           VR++  +++ + ++ +     +D S       ++ED     AV   D+    N       
Sbjct: 169 VREMESRLSGQDMAFDPAAEADDDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHE 228

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L     R   +L  R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 229 ALQGWNERSRDILYQRW--LAEEKATLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|309789348|ref|ZP_07683938.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
 gi|308922742|gb|EFP68259.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
          Length = 229

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQCIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDDYQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  V   R+ Q+ ++AI++L+
Sbjct: 203 ELEVGESRVSQLHSQAIKRLR 223


>gi|297154338|gb|ADI04050.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 268

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 111/234 (47%), Gaps = 12/234 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +EF  I  +    + EA   ++++VEA + +   +A +Y NRG    DL Q   +GL+KA
Sbjct: 24  AEFERIAELPDGPQKEA--LRQQVVEAWIPMADRLAGQYRNRGESLEDLRQVAALGLVKA 81

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI- 543
             ++D   G  F ++A+  V   I R   D    + +P  +++  ++V    R +S+ + 
Sbjct: 82  VNRYDPGRGSAFESFAVPTVVGEIKRHFRDHLWALHVPRRVQELRNRVRTAHRELSHSLD 141

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKNAVSP 600
            R P  EEIA +  +  E VR  +    +  P+SL+ P+ G +D   L D + ++     
Sbjct: 142 DRAPDVEEIADRTGLSEEDVRTGVAALDSFAPLSLDAPLTGTDDGYALRDTLGEQEPA-- 199

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            D  +    RE     L  L  RE R+L MRF   M      E++G  Q  V+R
Sbjct: 200 YDRVVD---REAVRSGLCRLPERERRILYMRFFCDMTQSRIAEQLGISQMHVSR 250


>gi|218133795|ref|ZP_03462599.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991170|gb|EEC57176.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
          Length = 256

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 128/257 (49%), Gaps = 19/257 (7%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S +  + ++    +G+ EA   +  +V  N+ L+ S+ K++T RG +  DL Q G+IGL+
Sbjct: 4   SYNHTKELIEQAHRGDKEA---RNRLVTENMGLIWSIVKRFTGRGHELEDLFQIGSIGLI 60

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KFD     +FSTYA+  +   + R + D    I++   +++ + KV R   ++  +
Sbjct: 61  KAIDKFDTSYDVRFSTYAVPMITGEVKRFLRDDGM-IKVSRSLKEIVVKVQRAREQLQKE 119

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNA--- 597
           +  EP+ E IA+ + +P E +   L+   E  S+   I   D +   L D + D+ +   
Sbjct: 120 MGEEPSMEMIARAIDVPEEDIVMALEAGSEIESIYKTIYQSDGNEITLIDRVADRGSSGA 179

Query: 598 -VSP----LDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            + P     D   +  +     + +L  L   E+ ++ +R+      D T  +V K+  +
Sbjct: 180 GIVPECEWTDYEKEQLINHMVLKQILDELPENEKNLILLRY----FRDQTQTQVAKEMGI 235

Query: 652 TRERIRQIEAKAIRKLK 668
           ++ ++ +IE + + +L+
Sbjct: 236 SQVQVSRIEKRILLRLR 252


>gi|220909315|ref|YP_002484626.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219865926|gb|ACL46265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 262

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/156 (28%), Positives = 91/156 (58%), Gaps = 5/156 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V+ NL LV   A ++ +   + + DL+Q G++GL++A E+FD   G+ FS++AM +
Sbjct: 33  RNRLVQMNLGLVRKEAHRWLSYSTETYEDLVQVGSLGLIRAIERFDITKGHAFSSFAMPY 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S  +RIP   +    +    A+ +  ++ R PT +E+A  L + ++  
Sbjct: 93  IRGEIQHYLRDKSPQVRIPRRWQVLQKQASLVAQELREQLHRVPTDDEMALALGIGLQEW 152

Query: 564 R--KVLKITKEPISLETPIGDED--TSHLGDFIEDK 595
           +  K+    + P+SL+ P+G++D  ++ LG+ + D+
Sbjct: 153 QQVKLSSYNRSPLSLDAPVGEDDFGSTCLGEMVPDQ 188


>gi|160946612|ref|ZP_02093815.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
 gi|158446996|gb|EDP23991.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
          Length = 254

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 122/229 (53%), Gaps = 17/229 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++E NL +   +AKKY NRG+ + DL Q  ++GL+ A +++D   G++FS++AM  +  
Sbjct: 31  KLIEKNLYMAEILAKKYVNRGIDYDDLFQVASLGLIYAIDRYDISKGFEFSSFAMPTIVG 90

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R   D+   IR+P  +++   KV      ++ ++ R PT ++IA  + +  E V ++
Sbjct: 91  EIKRYFRDKGWVIRVPRRIQENSKKVNNAKYHLTQELGRTPTIKDIADYVELSEEEVLEI 150

Query: 567 LKITK--EPISLETPIGDEDT----SHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ +K   P SL+    + D+    ++L D + E+      +D+  Q  +R+T    L  
Sbjct: 151 MEASKVYTPQSLDQSFENSDSEDKDTNLIDIVGEEDKEFDFIDN--QDFIRKT----LDK 204

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LT  E++++  R+        T   + K+  +++  + ++E KA+ K +
Sbjct: 205 LTEVEKQIILGRYF----EQKTQVALAKELNISQMTVSRLEKKALAKFR 249


>gi|220931546|ref|YP_002508454.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
 gi|219992856|gb|ACL69459.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
          Length = 257

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 73/260 (28%), Positives = 127/260 (48%), Gaps = 35/260 (13%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E RH    ++K +     A  ++VE NLRLV+ V  ++ + G    DL Q G IGL
Sbjct: 14  LSEEETRH---YIKKAQNNDQKALDKLVEHNLRLVLKVINRFKSSGYDPQDLFQIGVIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-IHKVVRTARRMS 540
           +KA + FD   G KFSTY       A++R I +      I +H+RD  I KV R+ ++++
Sbjct: 71  IKAIKNFDLDRGVKFSTY-------AVSRIIGE------IRLHIRDDGIIKVSRSLKKIA 117

Query: 541 NKIKR-----------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           N +++            P+  E++KK     E + + L+  K P S+   + ++D S L 
Sbjct: 118 NDVRKKEEELKKKNNCSPSILELSKKTGYSKEEIVQALEANKAPTSIYETVYEDDGSEL- 176

Query: 590 DFIEDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            ++ D  A    D     +  +     +L  L  R  +++ +R+      D T +EV  +
Sbjct: 177 -YVVDNLANESKDEEKIPDFNKILLVDLLKKLDERSRKIIYLRYF----EDKTQQEVADE 231

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V++ +I ++E K + KL+
Sbjct: 232 IGVSQVQISRLEKKILHKLR 251


>gi|326443735|ref|ZP_08218469.1| RNA polymerase sigma factor WhiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 258

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 55  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A+++ + VE +  V       +SL   +  E+  H+G  
Sbjct: 112 VERAYATLEAQLRRTPSEGEVAEEMGIAVEELHAVFS----QLSLANVVALEELLHVGGE 167

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 168 GGDRLSLMDTLEDTAADDPVEVAEGRELRRLLARAINTLPDREKTVVTLYYYEGL----T 223

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 224 LAEIGNVLGVTESRVSQIHTKSVLQLR 250


>gi|146344240|ref|YP_001202096.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
 gi|146188052|emb|CAM96382.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
          Length = 291

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 130/278 (46%), Gaps = 39/278 (14%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
             +D+ L + + I ++S E    +SE      +V   + +A+   +E+V + LR V+ +A
Sbjct: 20  SNLDAYLTVIHSIPNMSAEEERRLSE-----RLVEHNDMDAA---RELVTSQLRFVVHIA 71

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           + Y+  GL   DLIQEGNIGL+KA ++F+     +  T+ + W++  I   I      +R
Sbjct: 72  RSYSGYGLPLSDLIQEGNIGLIKAVKRFNPAAQVRLITFGVHWIRAEINEFIIRNGRMVR 131

Query: 521 IP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           +     + K+   +R   R  N +  + T   IA  L + V  V++          +ET 
Sbjct: 132 LATTKAQRKLFFNLRKQPRSRNWLTADET-RHIADTLNVSVLDVKE----------METR 180

Query: 580 IGDEDTSH--LGDFIEDKNAVSP--------LDSAIQ----ANLRETTTRVLASLTPREE 625
           +   DTS     D  ++   ++P         D A Q    A+   +T  + A+L   +E
Sbjct: 181 MAGNDTSFDPAADADDESAYITPSHQIGDHRYDPAYQYETEADAGTSTDDLHAALNNLDE 240

Query: 626 R---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           R   +L  RF     +  TL ++  ++ V+ ERIRQIE
Sbjct: 241 RSRDILAQRF--LSESKATLNDLASKYNVSAERIRQIE 276


>gi|30250410|ref|NP_842480.1| RNA polymerase sigma-70 factor family protein [Nitrosomonas
           europaea ATCC 19718]
 gi|30181205|emb|CAD86403.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 236

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 104/209 (49%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL+ A  +++   G +F +YA   ++ +I   + +      +P  +R 
Sbjct: 36  VQVDDLIQAGMIGLLDAINRYEGSYGRQFESYAAQRIRGSILDELREADW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDT 585
           K+ ++    R +  ++   P+ +EIA ++ +P+   +++L+     + I  E    DE+ 
Sbjct: 93  KMRQIETAMRALEQRLGYPPSEQEIANEMNLPLVEYQEMLQEAGGGQLIYYEDFQEDEE- 151

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            H  D +    +  PLD  ++ NLRE     +  L  +E+ V+ M +   MN    L E+
Sbjct: 152 DHFLDRLRGDQSNEPLDRLLEKNLRELLVAAIEKLPAKEKLVMGMYYEQEMN----LREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           GK   V+  R+ Q+  +AI +L+   R K
Sbjct: 208 GKVLGVSESRVCQLHTQAISRLRTHLRDK 236


>gi|320008281|gb|ADW03131.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces
           flavogriseus ATCC 33331]
          Length = 278

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQLRRTPSEAEVASEMGVALEELHAVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADDPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|149188340|ref|ZP_01866634.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837929|gb|EDL54872.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 285

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 115/239 (48%), Gaps = 30/239 (12%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V  +LR V+ +AK +   GL  +D+IQ GNIGL+KA +KF+  LG++  ++A+ W+K 
Sbjct: 52  KLVLPHLRYVVYIAKGFAGYGLPLVDMIQSGNIGLLKAVKKFNPELGFRLVSFAVHWIKS 111

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            IT  I      ++I            ++ R++   +K+    +E   +     E +   
Sbjct: 112 EITDFIIKNWSIVKIA---------TTKSQRKLFFNLKKYKQSQEWMSE--SEAENLASK 160

Query: 567 LKITKEPI-SLETPIGDEDTSHLGDFIEDKNAV---------SPLDSAIQANLRETTTRV 616
           LK++K+ + S++  +   D+       ED++ V           LD AI+   ++    +
Sbjct: 161 LKVSKKDVLSMDGRLSARDSYIDPKIGEDEDQVISTGEVFAEPQLDVAIEYETQDWDRHI 220

Query: 617 -------LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  LA L  R   ++  R+ +      TL E+ ++  V+ ER+RQIE   + KLK
Sbjct: 221 NDELNAGLAKLDARSRDIIVSRWLLSEKV--TLNELAERHRVSAERVRQIELMTLEKLK 277


>gi|94312634|ref|YP_585843.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
 gi|93356486|gb|ABF10574.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
          Length = 238

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 110/224 (49%), Gaps = 14/224 (6%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           R+ + +A K     +Q  DLIQ G IGL+ AA++++   G +F TYA   ++ A+   + 
Sbjct: 23  RIALQLAAKLPA-SVQIDDLIQAGMIGLLDAAKRYEDNHGARFETYASQRIRGAMLDEVR 81

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
                 R    +R    K+ RT R++  K+ R P   E+AK+L M +E  +++L      
Sbjct: 82  ANDWQSR---SLRQFTRKIERTQRQLEQKLGRSPIDSEVAKELEMGLEEYQELLNEVHGC 138

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVS----PLDSAIQANLRETTTRVLASLTPREERVLR 629
             L     D + S   DF++    V+    PL   +++ +R+   R +  L  RE+ VL 
Sbjct: 139 QLLHYE--DFERSGEEDFLDRHLGVTDEANPLTVLMESGMRDALIRAIEKLPEREKLVLS 196

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           + +   +N    L E+G    VT  R+ QI ++AI +L++  R 
Sbjct: 197 LCYDQELN----LREIGAVLEVTESRVCQIRSQAITRLRNQLRG 236


>gi|226313041|ref|YP_002772935.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
 gi|226095989|dbj|BAH44431.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score = 76.6 bits (187), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 100/201 (49%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GL+ A  KFD   G +F TYAMW ++ A+   + +      IP  +RDK  K
Sbjct: 58  DLISYGRFGLLDALAKFDHTRGLQFETYAMWRIRGAMIDGLRENDW---IPRTVRDKAKK 114

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           +      +  ++ R PT +E++  L +  + +++V   T     +S++  +GDED     
Sbjct: 115 IEEAYTTLEQQMLRMPTDQEVSDYLGISKKELQQVFLETSLASMVSIDEAVGDEDEQKTA 174

Query: 590 --DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
              +I D+    P + A  ++L+E    V+  L  +E  V+ + +   M    TL E+ +
Sbjct: 175 RHSYIIDELTPRPDNVAEVSSLKEVLVTVIDKLPEKERLVISLFYFEEM----TLSEIAE 230

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+ +KA+ +L+
Sbjct: 231 IMSLSPSRISQLHSKALFRLR 251


>gi|188592109|ref|YP_001796707.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; sigma-f factor; sigma-27; sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
 gi|170938483|emb|CAP63470.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; Sigma-F factor; Sigma-27; Sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
          Length = 238

 Score = 76.3 bits (186), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 116/243 (47%), Gaps = 20/243 (8%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +  + + ++V+A+  LV  +A +   R    +Q  DLIQ G IGL+ AA++++   G +F
Sbjct: 5   QGKLEQADVVKAHAPLVRRIALQLAARLPASVQIDDLIQAGMIGLLDAAKRYEDTHGARF 64

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA   ++ A+   +       R    +R    ++ RT R +  K+ R P   E+A+ +
Sbjct: 65  ETYASQRIRGAMLDEVRANDWQSR---SLRQFTRRIERTQRNLEQKLGRTPIDSEVAEAM 121

Query: 557 AMPVEGVRKVLKITKEPISLETP----IGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR 610
            MP++  + +L        L        G+ED    HLG   +D N   PL   +++ +R
Sbjct: 122 EMPLDEYQLLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGS-DDGN---PLTVLMESGMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   R +  L  RE+ VL + +   +N    L E+G    VT  R+ QI  +AI +L+  
Sbjct: 178 EALVRAIERLPEREKLVLSLCYDQELN----LREIGAVLDVTESRVCQIRGQAINRLRTQ 233

Query: 671 SRS 673
            R 
Sbjct: 234 LRG 236


>gi|261855188|ref|YP_003262471.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
 gi|261835657|gb|ACX95424.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
          Length = 291

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 14/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA ++F+     +  T+A+ W
Sbjct: 53  AAQKLIMSHLRFVVHIARGYRGYGLPLADLIQEGNIGLMKAVKRFEPEQKVRLVTFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMP-V 560
           ++  I   I      ++I      +  K+    R+M + +      E   IA +L +P  
Sbjct: 113 IRAEIHEYILKNWRIVKIATTKAQR--KLFFKMRQMKSGLGWLTADETRAIAAELNVPER 170

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRE---TT 613
           E V    ++    I+++ P+ D +    G   E    D++ VS  D   Q +  +     
Sbjct: 171 EVVTMESRLYSHDIAIDAPVYDSEQEGSGPSYEQILVDQHQVSVEDMTAQRDEDDRVTAM 230

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T  L  L  R   +L  R+        TL+ +  ++ V+ ER+RQIE  A++KL+
Sbjct: 231 THALHDLDARSRDILERRW--LQEPKATLQTLADEYQVSAERVRQIENAALKKLR 283


>gi|328885347|emb|CCA58586.1| RNA polymerase sigma factor for flagellar operon [Streptomyces
           venezuelae ATCC 10712]
          Length = 258

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 55  DFVSSGVFGLIDAIEKFDVERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 112 VERAYATLEAQLRRTPSETEVAAEMDISLEDLHAVFS----QLSLANVVALEELLHVGGE 167

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 168 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 223

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 224 LAEIGHVLGVTESRVSQIHTKSVLQLR 250


>gi|297191780|ref|ZP_06909178.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197721703|gb|EDY65611.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 278

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + V+ +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQLRRTPSESEVAAEMGITVDELHSVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGERLSLMDTLEDTAADNPVEVAEGRELRRLLARAINTLPDREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|270262372|ref|ZP_06190644.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
 gi|270044248|gb|EFA17340.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
          Length = 240

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 99/198 (50%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRHARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  R++  ++ R  +  E+A+ L +P++  R++L  T            E+     + 
Sbjct: 100 VAQVMRQLEQRLGRPASEVEVAQTLNIPLDEYRQILLDTNNSQLFSYDEWREEHGESAEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEEANPLHHLLEGNLRQRVIDAIDALPEREKMVLTLYYQEELN----LKEIGAVLD 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|197303735|ref|ZP_03168772.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
 gi|197297255|gb|EDY31818.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
          Length = 265

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 70/266 (26%), Positives = 119/266 (44%), Gaps = 61/266 (22%)

Query: 409 IRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I N ++ +S++T    ++  E ++      +G+ EA   K  ++E NLRLV  + +KY N
Sbjct: 51  ISNVLRGVSLKTFPNPLTPDEEKYYFQKYTEGDLEA---KHILIERNLRLVAHIVRKYQN 107

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G +  DLI  G IGL+KA   FD   G + + YA        +R + ++     I +++
Sbjct: 108 LGEEMEDLISIGTIGLIKAVISFDPEKGNRLAAYA--------SRCVENE-----ILMYL 154

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---D 582
           R         AR+   K                               ISL  PIG   D
Sbjct: 155 R---------ARKKGGK------------------------------EISLYEPIGTDRD 175

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            +   L D IE  +   P    ++ N+++   +V + L+PRE  VL+MR+G+    ++T 
Sbjct: 176 GNEIRLYDIIETTDTDVPEKLYLKENIQKLYEKVESELSPRERLVLKMRYGLYNGEEYTQ 235

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+     ++R  + +IE  A+ KL+
Sbjct: 236 REIASLLGISRSYVSRIEKSAVEKLR 261


>gi|20151058|pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment, Region 4
 gi|20151059|pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
 gi|20151062|pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
          Length = 73

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 42/72 (58%), Positives = 52/72 (72%), Gaps = 1/72 (1%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-H 669
           E   + L+ L+ RE  VL+MR G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61

Query: 670 PSRSKKLRSFLD 681
            SR++KLR FL+
Sbjct: 62  ESRTRKLRDFLE 73


>gi|261340320|ref|ZP_05968178.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
 gi|288317411|gb|EFC56349.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
          Length = 229

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     ++  ++ R  T  E+A++L + VE  R++L  T           DE     GD 
Sbjct: 90  VAHAMGQLEQELGRNATETEVAERLGIAVEDYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    +    +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDEHQQENPLHHLMEGNLRQRVMEAIEALPEREQLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|311696378|gb|ADP99251.1| RNA polymerase, sigma 32 subunit, RpoH [marine bacterium HP15]
          Length = 286

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/287 (25%), Positives = 141/287 (49%), Gaps = 45/287 (15%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  + I  ++V+    ++E  H      +G+ EA+   +++V ++LR VI +A+ 
Sbjct: 17  LESYIQAASRIPVLTVDEERELAERLHY-----EGDVEAA---RQLVMSHLRFVIHIARS 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+  GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +++ 
Sbjct: 69  YSGYGLAQADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVA 128

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKITKEPISLETPI 580
                +  K+    R    K+      E   +A+ L +    VR+          +E  +
Sbjct: 129 TTKAQR--KLFFNLRSQKKKLAWLSHDELNAVAEDLGVEPRVVRE----------MEGRL 176

Query: 581 GDEDTSHLGD--------------FIED--KNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             +DT+  G               ++ED   N  + L++A  ++  ++  R++ +L   +
Sbjct: 177 ASQDTAFDGPQDDDDDNAYQAPAYYLEDARSNPATQLENADWSD--DSNGRLMQALGQLD 234

Query: 625 ER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ER   +LR R+     +  TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 235 ERSQDILRERW--LSESKSTLHELADRYGVSAERIRQLEKNAMKKIR 279


>gi|3929539|gb|AAC79983.1| HasR [Streptomyces ambofaciens]
 gi|117164812|emb|CAJ88361.1| putative sigma factor [Streptomyces ambofaciens ATCC 23877]
          Length = 281

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/247 (23%), Positives = 129/247 (52%), Gaps = 14/247 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   +S++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 37  FFQQLSVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 97  DRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVQLARATEELRSRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPI-GDEDT-SHLGDFIEDKNAVSPL 601
            PT +E+++ +++P + V   ++        SL+  I G ED  S L DFI   +A   L
Sbjct: 157 NPTTKELSELMSLPEDEVVEARLAANGYNSASLDAAISGSEDGESALADFIGADDATLAL 216

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  R+ +++  RF      + T +++G++  V++  + ++ +
Sbjct: 217 VDDFHA-----LAPMIAELDERDRQIIHWRF----VEELTQKDIGERLGVSQMHVSRLIS 267

Query: 662 KAIRKLK 668
           + + +L+
Sbjct: 268 RLLARLR 274


>gi|331696957|ref|YP_004333196.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951646|gb|AEA25343.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 288

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/209 (25%), Positives = 103/209 (49%), Gaps = 18/209 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +V  +L +V  +A+++  RG    DL Q G +GL+ A ++FD   G  F +YA+  +
Sbjct: 67  RERLVTGHLPVVRHIARRFAGRGEPVDDLEQAGTVGLINAVDRFDPARGVDFLSYAVPTI 126

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
              + R   D++ ++R+P  +++    +      ++ ++ R P P EIA ++   V+ V 
Sbjct: 127 TGEVRRHFRDRTWSMRVPRRLKELQSSINSAVGGLAQELGRAPRPSEIADRIGRDVDEVI 186

Query: 564 -----RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
                R+V + T    SL+  + D D       + +   ++  D+ ++  + R+T   +L
Sbjct: 187 EGLEARQVYRST----SLDELVADSDA-----MLSETLGIA--DAELEKVDYRQTLAPLL 235

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             L  RE  +L +RF  GM      +EVG
Sbjct: 236 DELPTRERTILVLRFFAGMTQTQIADEVG 264


>gi|323144379|ref|ZP_08078987.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
 gi|322415832|gb|EFY06558.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
          Length = 295

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 124/240 (51%), Gaps = 24/240 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA + FD  +G + + +A+ W
Sbjct: 53  AARKLVLSHLRLVVSIARGYLGYGLPISDLIQEGNIGLMKAVKHFDPDVGGRLAAFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMS-------NKIKRE--PTPEEI 552
           +K  I   +      +++      R    K+ +  +R+        NK+  +   + +++
Sbjct: 113 IKAEIHDYVIKNWRVVKVATTKAQRKLFFKLRQNKQRLGWFSDSERNKVADDLGVSADDV 172

Query: 553 AK---KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A+   +LA    G         +  S  +P     +++L D  E+ N  +  ++    N 
Sbjct: 173 AEMETRLAGQDIGFDADSDDDSDKGSSFSP-----SAYLED--ENSNFANTFENIDYENY 225

Query: 610 RETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ R  L SL  R   +++ R+ +  N   TL+E+ ++  V+ ER+RQIE +A++K+K
Sbjct: 226 ELSSLRKALDSLDERSRYIVQRRW-LDENK-ATLQELSEKLNVSIERVRQIENQALKKIK 283


>gi|50120672|ref|YP_049839.1| flagellar biosynthesis sigma factor [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611198|emb|CAG74644.1| RNA polymerase sigma factor for flagellar operon [Pectobacterium
           atrosepticum SCRI1043]
          Length = 240

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++   ++ R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAQAMQQTEQQLGRTPTEQEVAQTLNITLEDYRQILLDTNNSQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL   ++ NLR      + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEDANPLHQLMEGNLRHRVMDAIENLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|46241492|gb|AAS82949.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 182

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 47/120 (39%), Positives = 70/120 (58%), Gaps = 6/120 (5%)

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA---N 608
           +AK   +PV  V+ +++  +   SL+TPIG    + LG  ++D        +  +    +
Sbjct: 28  LAKAAGLPVTRVQMLMETARSAASLDTPIGG---NELGPTVKDSVEDEREAADEEFGSDS 84

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR     +L  L  RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL+
Sbjct: 85  LRNDMEAMLLELPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKLR 144


>gi|217958581|ref|YP_002337129.1| RNA polymerase sigma factor SigB [Bacillus cereus AH187]
 gi|217065197|gb|ACJ79447.1| RNA polymerase sigma-B factor [Bacillus cereus AH187]
          Length = 257

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 123/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      ++++++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|41407572|ref|NP_960408.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395925|gb|AAS03791.1| SigF_1 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 269

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 108/228 (47%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +V   L L   VA  +  RG    DL+Q   +GLM A  +FD   G  F  +A+  +
Sbjct: 46  RERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPAKGPSFIGFAVPTM 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +R+   ++ RT   ++ ++ R P   E+++ L +P E + 
Sbjct: 106 MGEVRRYFRDYSWGMRVPRRLRELHVQISRTTADLAQQLGRAPNAGELSQVLEVPREEIV 165

Query: 565 KVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L +  +     SL+ P G  D+S     + D  +V  +D  I+        RVL +  
Sbjct: 166 ECL-VAGDAYRLDSLDAPQG-ADSSGTPRSVAD--SVGDIDPQIEHITNREALRVLVATL 221

Query: 622 PREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P  ER VLRMRF   M      E +G    V++ ++ +I A  +R L+
Sbjct: 222 PHREREVLRMRFFESMTQSQIAERIG----VSQMQVSRILANTLRCLR 265


>gi|271500098|ref|YP_003333123.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Dickeya
           dadantii Ech586]
 gi|270343653|gb|ACZ76418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dickeya
           dadantii Ech586]
          Length = 240

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++    + R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAQAMQQAEQSLGRAPTEQEVAQTLNISLEEYRQILLDTNNSQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL+  +  NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEDANPLNLLMDVNLRQRVMDAIENLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|158340157|ref|YP_001521327.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
 gi|158310398|gb|ABW32013.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
          Length = 421

 Score = 76.3 bits (186), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 114/226 (50%), Gaps = 21/226 (9%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +  N RLV   A +Y  RGL  + DL+  GN GL +A EKFD   G KFS+YA+  ++ 
Sbjct: 40  FIRKNQRLVFKEANRY--RGLDDWNDLVTAGNWGLARAIEKFDVSKGCKFSSYAVKVIRT 97

Query: 507 AITRSIADQ-SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            I + + DQ   +  I  H++D    + + ++++  +++R+PT EE++++       +  
Sbjct: 98  EIQQFLNDQRGLSKEIAKHLKD----IKQASQKLEWELERQPTLEELSERTGYSQRIITS 153

Query: 566 VLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            L   +  E  SL  P+G+   +   D +E  + +   D A   + +E     +A L  R
Sbjct: 154 TLDRARVVETSSLNIPVGENLKAEQIDLVEGDDDL--WDYAENIDEKE----YIAQLPER 207

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              ++R R        H+   +G+ F ++ ERIRQ+  +A+  LKH
Sbjct: 208 YNVIVRAR-----RDGHSYRAIGRMFGLSGERIRQLFKEALAYLKH 248


>gi|295109465|emb|CBL23418.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus
           obeum A2-162]
          Length = 238

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 112/227 (49%), Gaps = 12/227 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +   N  L+   AK++  RG+   DL Q G+IGL+KA +KFD     KFSTYA+  
Sbjct: 19  ARERLFHENTGLIYCAAKRFLGRGVDMEDLFQIGSIGLLKAVDKFDTSYDVKFSTYAVPM 78

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++  +++ R    +   + REPT  E+A+ + M  E +
Sbjct: 79  IIGEIKRFLRDDGI-LKVSRSVKENQYRIGRKREELEKTLGREPTLGELAESVQMLPEEL 137

Query: 564 RKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              +    +  S+   I  G+ +   L D I +K  +   D  +     E    +L SL 
Sbjct: 138 AMTMDAANDVESIYQIIYQGEGNELRLLDKIPEKENLH--DRLLNKIFLE---ELLRSLN 192

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E ++L MR+      + T  EV  +F V++ +I ++E K + +L+
Sbjct: 193 AEERKLLYMRY----FREMTQTEVADEFGVSQVQISRMEKKILNRLR 235


>gi|222094730|ref|YP_002528790.1| RNA polymerase sigma factor sigb [Bacillus cereus Q1]
 gi|221238788|gb|ACM11498.1| RNA polymerase sigma-B factor [Bacillus cereus Q1]
          Length = 257

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 123/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      ++++++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|161613481|ref|YP_001587446.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167993526|ref|ZP_02574620.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168234127|ref|ZP_02659185.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168244804|ref|ZP_02669736.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168259759|ref|ZP_02681732.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168822997|ref|ZP_02834997.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194445382|ref|YP_002041220.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194450090|ref|YP_002046006.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471287|ref|ZP_03077271.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197251137|ref|YP_002146068.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197362055|ref|YP_002141692.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242943|ref|YP_002215131.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200390898|ref|ZP_03217509.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|213053507|ref|ZP_03346385.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213650343|ref|ZP_03380396.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855803|ref|ZP_03384043.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|238912471|ref|ZP_04656308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289824078|ref|ZP_06543676.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|56127386|gb|AAV76892.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. ATCC 9150]
 gi|161362845|gb|ABX66613.1| hypothetical protein SPAB_01198 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194404045|gb|ACF64267.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194408394|gb|ACF68613.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194457651|gb|EDX46490.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197093532|emb|CAR58994.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. AKU_12601]
 gi|197214840|gb|ACH52237.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197937459|gb|ACH74792.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199603343|gb|EDZ01889.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205328422|gb|EDZ15186.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205331884|gb|EDZ18648.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205336383|gb|EDZ23147.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205340661|gb|EDZ27425.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350810|gb|EDZ37441.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|312912946|dbj|BAJ36920.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321224599|gb|EFX49662.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322616949|gb|EFY13857.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322618189|gb|EFY15081.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322625859|gb|EFY22678.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626311|gb|EFY23121.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322632726|gb|EFY29471.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322639068|gb|EFY35761.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640509|gb|EFY37162.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647255|gb|EFY43754.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649897|gb|EFY46318.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322655505|gb|EFY51813.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322660283|gb|EFY56521.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662964|gb|EFY59171.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668149|gb|EFY64308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322674091|gb|EFY70185.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675556|gb|EFY71630.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322683032|gb|EFY79048.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686726|gb|EFY82704.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195385|gb|EFZ80565.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199276|gb|EFZ84371.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204441|gb|EFZ89447.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323207531|gb|EFZ92479.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323211856|gb|EFZ96687.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323217516|gb|EGA02235.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323219591|gb|EGA04075.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223594|gb|EGA07909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231538|gb|EGA15651.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235981|gb|EGA20060.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240551|gb|EGA24594.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245443|gb|EGA29443.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323253976|gb|EGA37800.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323255497|gb|EGA39258.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262094|gb|EGA45657.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323266217|gb|EGA49707.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270674|gb|EGA54115.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326622879|gb|EGE29224.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
          Length = 229

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L +PV   R++L  T           DE     GD 
Sbjct: 90  VAQAMGQLEQELGRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++ +LR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|319399556|gb|EFV87811.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis FRI909]
          Length = 256

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 124/243 (51%), Gaps = 20/243 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S+A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKH 669
               R+L  L+ RE ++++  F  G++   T E +G  Q  V+R     ++  AI+KL+ 
Sbjct: 198 MILERILPILSERERQIIQCTFIEGLSQKETGERIGLSQMHVSR-----LQRTAIKKLQE 252

Query: 670 PSR 672
            +R
Sbjct: 253 AAR 255


>gi|299143454|ref|ZP_07036534.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298517939|gb|EFI41678.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 260

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 119/227 (52%), Gaps = 16/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L +   ++KKY+ RG+ + D+ Q  +IGL+ A +++D+  GY+FS++A   +   
Sbjct: 37  LIEEHLYIAEILSKKYSGRGIDYDDIFQVASIGLIYAIDRYDFEKGYEFSSFATPTIIGE 96

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  TIR+P  +++   K+     +++ +++R PT E+IA  L    E V + +
Sbjct: 97  IKKYFRDKGWTIRVPRRIQELSKKINNAKTQLTQELQRIPTVEDIADYLETTPEEVIEAM 156

Query: 568 KITK--EPISLETPI---GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + +K   P SL+      GD+   +L D + E++     ++      +++   R ++ L 
Sbjct: 157 EASKVYTPQSLDVTYDTNGDDKELNLADLVGENEKYFEKIE------MKDFLERAMSELN 210

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E  +L  R+        T   + ++  +++  I +IE K ++K++
Sbjct: 211 DMERTILIERYF----EKKTQVAIAEKLDISQMTISRIEKKVLKKMR 253


>gi|289754806|ref|ZP_06514184.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695393|gb|EFD62822.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 84

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/66 (54%), Positives = 50/66 (75%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ 
Sbjct: 19  VLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQV 78

Query: 676 LRSFLD 681
           LR +LD
Sbjct: 79  LRDYLD 84


>gi|291448094|ref|ZP_06587484.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|1655819|gb|AAB41960.1| sporulation sigma factor [Streptomyces filamentosus]
 gi|291351041|gb|EFE77945.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 278

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  + +R P+  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQFRRTPSEAEVASEMGIALEELHAVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|16760902|ref|NP_456519.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765294|ref|NP_460909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29141406|ref|NP_804748.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|62180530|ref|YP_216947.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|161936245|ref|YP_150204.2| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|194736051|ref|YP_002114988.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195873263|ref|ZP_02696436.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197263158|ref|ZP_03163232.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197301170|ref|ZP_02664251.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204931059|ref|ZP_03221885.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205357293|ref|ZP_02346566.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|207856530|ref|YP_002243181.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|224583543|ref|YP_002637341.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|289810757|ref|ZP_06541386.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
 gi|61224055|sp|P0A2E8|FLIA_SALTY RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|61224057|sp|P0A2E9|FLIA_SALTI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|25331353|pir||AF0750 RNA polymerase sigma transcription factor for flagellar operon fliA
           [imported] - Salmonella enterica subsp. enterica serovar
           Typhi (strain CT18)
 gi|556579|dbj|BAA00389.1| sigma factor [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|4115509|dbj|BAA36397.1| FliA [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16420491|gb|AAL20868.1| sigma F (sigma 28) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503199|emb|CAD05705.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137033|gb|AAO68597.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi str.
           Ty2]
 gi|62128163|gb|AAX65866.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|194711553|gb|ACF90774.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195634506|gb|EDX52858.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197241413|gb|EDY24033.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197288040|gb|EDY27427.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204320103|gb|EDZ05308.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205322652|gb|EDZ10491.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|206708333|emb|CAR32636.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|224468070|gb|ACN45900.1| flagellar biosynthesis sigma factor FliA [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|261247122|emb|CBG24945.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|267993942|gb|ACY88827.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158470|emb|CBW17980.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|320085426|emb|CBY95207.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|322715006|gb|EFZ06577.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130234|gb|ADX17664.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323250213|gb|EGA34105.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|332988845|gb|AEF07828.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 239

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L +PV   R++L  T           DE     GD 
Sbjct: 100 VAQAMGQLEQELGRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           I    E+    +PL   ++ +LR+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|313887713|ref|ZP_07821395.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312846322|gb|EFR33701.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 261

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 47/149 (31%), Positives = 82/149 (55%), Gaps = 4/149 (2%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L +   ++KKYT RG+ + D+ Q  +IGL+ A E++D   G++FS++A   +   
Sbjct: 37  LIEEHLYIAEILSKKYTGRGIDYDDIYQVASIGLIYAIERYDPEKGFEFSSFATPTIIGE 96

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D   TIR+P  +++   K+      +S K ++ PT +EIA+ L    E V + +
Sbjct: 97  IKKYFRDNGWTIRVPRRIQELSKKISNATVSLSQKYQKTPTIDEIAEYLDSTPEEVMEAM 156

Query: 568 KITK--EPISLETPI--GDEDTSHLGDFI 592
           + +K   P SL+     GDE   +L D I
Sbjct: 157 EASKVYTPQSLDVTYESGDESEVNLSDLI 185


>gi|77165402|ref|YP_343927.1| RpoH [Nitrosococcus oceani ATCC 19707]
 gi|254433859|ref|ZP_05047367.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
 gi|76883716|gb|ABA58397.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus oceani ATCC
           19707]
 gi|207090192|gb|EDZ67463.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
          Length = 287

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 112/243 (46%), Gaps = 31/243 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR VI +A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W
Sbjct: 53  AARQLVLSHLRFVIRIARGYNGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R+A++    + R+   +E+A+ L +    
Sbjct: 113 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKKRLGWLNRKEV-DEVAQDLGVS--- 168

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------------- 608
                   K+ + +E  +  +D    G   E+     P   A  A+              
Sbjct: 169 -------PKQVMEMEARLSSQDAPFDGSNAEESENGIPAPMAYLADPSADPAQKMELLDQ 221

Query: 609 ---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                +   + L  L  R   ++  R+        TL E+  ++ ++ ERIRQ+E  AI+
Sbjct: 222 ENYYGQRLQQALEVLDLRSRTIINRRW--LQENKSTLHELAAEYQISAERIRQLENNAIK 279

Query: 666 KLK 668
           K++
Sbjct: 280 KMR 282


>gi|182435659|ref|YP_001823378.1| RNA polymerase sigma factor WhiG [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326776293|ref|ZP_08235558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
 gi|178464175|dbj|BAG18695.1| putative RNA polymerase sigma factor WhiG [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656626|gb|EGE41472.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
          Length = 278

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  + +R P+  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 132 VERAYATLEAQFRRTPSEAEVASEMGIALEELHAVFS----QLSLANVVALEELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|254775435|ref|ZP_05216951.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
          Length = 242

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 108/228 (47%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +V   L L   VA  +  RG    DL+Q   +GLM A  +FD   G  F  +A+  +
Sbjct: 19  RERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPAKGPSFIGFAVPTM 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +R+   ++ RT   ++ ++ R P   E+++ L +P E + 
Sbjct: 79  MGEVRRYFRDYSWGMRVPRRLRELHVQISRTTADLAQQLGRAPNAGELSQVLEVPREEIV 138

Query: 565 KVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L +  +     SL+ P G  D+S     + D  +V  +D  I+        RVL +  
Sbjct: 139 ECL-VAGDAYRLDSLDAPQG-ADSSGTPRSVAD--SVGDIDPQIEHITNREALRVLVATL 194

Query: 622 PREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P  ER VLRMRF   M      E +G    V++ ++ +I A  +R L+
Sbjct: 195 PHREREVLRMRFFESMTQSQIAERIG----VSQMQVSRILANTLRCLR 238


>gi|118465934|ref|YP_882149.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118167221|gb|ABK68118.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 269

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 108/228 (47%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +V   L L   VA  +  RG    DL+Q   +GLM A  +FD   G  F  +A+  +
Sbjct: 46  RERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPAKGPSFIGFAVPTM 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +R+   ++ RT   ++ ++ R P   E+++ L +P E + 
Sbjct: 106 MGEVRRYFRDYSWGMRVPRRLRELHVQISRTTADLAQQLGRAPNAGELSQVLEVPREEIV 165

Query: 565 KVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L +  +     SL+ P G  D+S     + D  +V  +D  I+        RVL +  
Sbjct: 166 ECL-VAGDAYRLDSLDAPQG-ADSSGTPRSVAD--SVGDIDPQIEHITNREALRVLVATL 221

Query: 622 PREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P  ER VLRMRF   M      E +G    V++ ++ +I A  +R L+
Sbjct: 222 PHREREVLRMRFFESMTQSQIAERIG----VSQMQVSRILANTLRCLR 265


>gi|308205773|gb|ADO19206.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 124

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +  +AK  M+ ANLRLV++VAKKY    L+FLDLIQEG IGL KA EKF+   GYKFSTY
Sbjct: 41  QGQLAKHLMITANLRLVVAVAKKYRWSNLEFLDLIQEGAIGLQKAVEKFEPNRGYKFSTY 100

Query: 500 A 500
           A
Sbjct: 101 A 101


>gi|73539441|ref|YP_299808.1| sigma-70 region 4 [Ralstonia eutropha JMP134]
 gi|72122778|gb|AAZ64964.1| Sigma-70 region 4 [Ralstonia eutropha JMP134]
          Length = 238

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 114/244 (46%), Gaps = 18/244 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G+ E +   K   +   R+ + +A K     +Q  DLIQ G IGL+ AA++++   G +
Sbjct: 5   QGKLEQADVVKTHAQLVRRIALQLAAKLPA-SVQIDDLIQAGMIGLLDAAKRYEDTHGAR 63

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F TYA   ++ A+   +       R    +R    ++ RT R +  K+ R P   E+A++
Sbjct: 64  FETYASQRIRGAMLDEVRANDWQSR---SLRQFTRRIERTQRGLEQKLGRAPLDSEVAQE 120

Query: 556 LAMPVEGVRKVLKITKEPISLETP----IGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           L MP++  + +L        L        G+ED    HLG   ED N   PL   ++  +
Sbjct: 121 LEMPLDEYQTLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGS-EDGN---PLTQLMENGM 176

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    R +  L  RE+ VL + +   +N    L E+G    VT  R+ QI  +AI +L++
Sbjct: 177 RAALIRAIERLPEREKLVLSLCYDQELN----LREIGAVLDVTESRVCQIRGQAITRLRN 232

Query: 670 PSRS 673
             R 
Sbjct: 233 QLRG 236


>gi|255319457|ref|ZP_05360671.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262378519|ref|ZP_06071676.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
 gi|255303397|gb|EET82600.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262299804|gb|EEY87716.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
          Length = 289

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 114/245 (46%), Gaps = 34/245 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W
Sbjct: 53  AAKMLVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPSMGVRLVSFAVHW 112

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREP----------TPEEI 552
           +K  I   +      ++I     + K+   +R+ ++ S K+  E           TPE++
Sbjct: 113 IKAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEARSIANDLNVTPEQV 172

Query: 553 --------AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
                   A   A   +G       +     L       D + L   +ED++     +SA
Sbjct: 173 LEMEGRLTAYDAAFEAQGDDDDDSSSHVAPVLYLEDSRYDPARL---VEDEDWEEQSNSA 229

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKA 663
           +           +  L  R   +L+ R+   ++ D  TL E+  ++ V+ ERIRQ+E  A
Sbjct: 230 LH--------NAMDQLDDRSRNILQRRW---LDDDKSTLHELAAEYNVSAERIRQLEKNA 278

Query: 664 IRKLK 668
           + K+K
Sbjct: 279 MEKIK 283


>gi|307330048|ref|ZP_07609199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306884309|gb|EFN15344.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 99/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 74  DFVSSGVFGLIDAIEKFDPERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + +E +  V       +SL   +  E+  H+G  
Sbjct: 131 VERAYATLEAQLRRTPSEAEVAAEMDISIEELHGVFS----QLSLANVVALEELLHVGGE 186

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 187 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 242

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G+   VT  R+ QI  K++ +L+
Sbjct: 243 LAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|254382042|ref|ZP_04997404.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194340949|gb|EDX21915.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 278

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGVFGLIDAIEKFDIDRSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R PT  E+A ++ + VE +  V       +SL   +  ++  H+G  
Sbjct: 132 VERAYATLEAQLRRTPTECEVADEMGIAVEELHTVFS----QLSLANVVALDELLHVGGE 187

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 188 GGDRLSLMDTLEDTAADNPVEVAEGRELRRLLARAINTLPEREKTVVTLYYYEGL----T 243

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 244 LAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|88858433|ref|ZP_01133075.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
 gi|88820050|gb|EAR29863.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
          Length = 288

 Score = 75.9 bits (185), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 118/244 (48%), Gaps = 29/244 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LR V  +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 52  AARQLIMSHLRFVAHIAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHW 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV 560
           +K  I   +      +++      K  + +    R + K      PEE   +A +L +  
Sbjct: 112 IKAEIHEYVLKNWRIVKVAT---TKAQRKLFFNLRKNKKRLGWFNPEEVSTVANELGVTE 168

Query: 561 EGVRK----------VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           + VR+          V  +T +     +        +L D     N+V   D   +    
Sbjct: 169 KDVREMEARMSSQDMVFDLTTDDDDSTSATQYSPVQYLTD-----NSVDLADKIEEEQWE 223

Query: 611 ETT----TRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIR 665
           E T       L SL  R + +++ R+   ++ D  TL+++  ++ V+ ER+RQ+E  A++
Sbjct: 224 EQTHNRLFHALKSLDERSQDIVQTRW---LSDDKATLQDLAVKYDVSAERVRQLEKTAMK 280

Query: 666 KLKH 669
           KL+H
Sbjct: 281 KLQH 284


>gi|328880278|emb|CCA53517.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 290

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 115/230 (50%), Gaps = 15/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E N+ LV+  A ++  RG +  D++Q G IGL+KA ++FD     +F+T+A+ ++
Sbjct: 60  RNTLIEMNMSLVVYAAGRFRARGDEMEDIVQVGMIGLIKAIDRFDLSREVEFATFAVPYI 119

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
              I R   D +  + +P  +++   ++ +    +S+++ R P   E+A  + +  E V 
Sbjct: 120 VGEIKRFFRDSTWAVHVPRRLQEARVELAKATDELSSRLGRAPRVAELAPAMDLSEEQVV 179

Query: 564 -RKVLKITKEPISLETPI--GD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             +V        SL+  +  GD  +D + L D I  ++    L          T   ++ 
Sbjct: 180 EAQVAANGYHSTSLDAAVAGGDSEDDDAALADLIGQEDPAIELFEDFH-----TLAPLVE 234

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L PR+  +L +RF      + T  E+G++  V++  + ++ A+ I +L+
Sbjct: 235 ALGPRDRLLLHLRF----VEELTQSEIGERLGVSQMHVSRLLARNIERLR 280


>gi|239929464|ref|ZP_04686417.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
          Length = 245

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 108/211 (51%), Gaps = 11/211 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           FR + +++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 35  FRQL-AVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 93

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   + R   D S ++ +P  +++   ++ R    +  ++ R
Sbjct: 94  DRFELSREVEFTSFAIPYIVGEMKRFFRDTSWSVHVPRRLQEARVQLARATEELRTRLGR 153

Query: 546 EPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPL 601
            PT  E+A+ +++  E V   ++        SL+  IG E    S L DFI  ++A   L
Sbjct: 154 TPTTRELAQLMSLTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFIGSEDAALEL 213

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRF 632
                A        ++A L  RE +++  RF
Sbjct: 214 VEDFHA-----LAPMIAELDERERKIIHWRF 239


>gi|318060086|ref|ZP_07978809.1| sigma factor [Streptomyces sp. SA3_actG]
 gi|318076269|ref|ZP_07983601.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 286

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 123/249 (49%), Gaps = 35/249 (14%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E   A+  ++E N+ LV   A+++ +RG    D++Q G IGL+KA ++F+     +
Sbjct: 50  EGTREFQDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVE 109

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D +  + +P  +++   ++ +    +S ++ R P   E+A  
Sbjct: 110 FTTFAVPYIVGEIKRFFRDTTWAVHVPRRLQEARVELAKANEELSTRLGRAPKVSELAAL 169

Query: 556 LAMPVEGV--RKVLKITKEPISLETPIGDEDT----SHLGDFI----------EDKNAVS 599
           +++  + V   ++        SL+  IG ED+    + L DFI          ED +A++
Sbjct: 170 MSLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAALSDFIGAEDPGMELVEDLHALA 229

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PL               LA L PR+ ++L +RFG     + T  ++G++  V++  + ++
Sbjct: 230 PL---------------LAGLEPRDRQILELRFG----QELTQAQIGERLGVSQMHVSRL 270

Query: 660 EAKAIRKLK 668
             + +  L+
Sbjct: 271 LNRTLGTLR 279


>gi|45643442|gb|AAC79984.2| HasL [Streptomyces ambofaciens]
 gi|126347729|emb|CAJ89446.1| putative sigma factor [Streptomyces ambofaciens ATCC 23877]
          Length = 281

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/257 (22%), Positives = 132/257 (51%), Gaps = 34/257 (13%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   +S++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 37  FFQQLSVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 97  DRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVQLARATEELRSRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPI-GDEDT-SHLGDFI--------- 592
            PT +E+++ +++P + V   ++        SL+  I G ED  S L DFI         
Sbjct: 157 NPTTKELSELMSLPEDEVVEARLAANGYNSASLDAAISGSEDGESALADFIGAEDTALAL 216

Query: 593 -EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            ED +A++P+               +A L  R+ +++  RF      + T +++G++  V
Sbjct: 217 VEDFHALAPM---------------IAELDERDRQIIHWRF----VEELTQKDIGERLGV 257

Query: 652 TRERIRQIEAKAIRKLK 668
           ++  + ++ ++ + +L+
Sbjct: 258 SQMHVSRLISRLLARLR 274


>gi|303242484|ref|ZP_07328964.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302589952|gb|EFL59720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 252

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 14/157 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E+V   L L   ++KK+ NRG+ + D+ Q  +I L+KA E+FD   G KF+++A   
Sbjct: 30  VRNEIVSKYLYLAEIISKKFVNRGIDYEDIYQVASIALIKAVERFDPDKGVKFASFATPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  IRIP  + +   KV      ++ ++ R P  +EIAK L +  E V
Sbjct: 90  LIGEIKRFFRDKASVIRIPRRIYEVYQKVSHARESLTQELSRPPRIDEIAKYLNISEETV 149

Query: 564 RKVLK--------------ITKEPISLETPIGDEDTS 586
            ++++               T + + L   IG+ED +
Sbjct: 150 MEIIESNNAHNLQSFDQNVYTDDDLELHETIGEEDAT 186


>gi|296501716|ref|YP_003663416.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
 gi|296322768|gb|ADH05696.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
          Length = 257

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 122/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIADFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|257469127|ref|ZP_05633221.1| RNA polymerase sigma factor RpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 157

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 48/150 (32%), Positives = 85/150 (56%), Gaps = 8/150 (5%)

Query: 522 PVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           P +  D ++KV    R + +++K E   P+ EEIA +L +  + V+ ++   ++P+SL T
Sbjct: 1   PSYKYDLLNKV---NRYVMSRLKDEGNYPSVEEIAAELNIEADKVQDIIMDFQDPMSLST 57

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            IGD+   +L D +  +   S  +       R+    ++  L  RE+ +L++R+G+    
Sbjct: 58  QIGDD--IYLEDTLAQQEDFSMEEEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYE 115

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            HTLEE+G    +TRER+RQIE K ++KL+
Sbjct: 116 IHTLEEIGNTLNITRERVRQIEKKTLQKLR 145


>gi|153487|gb|AAA26829.1| sigma factor (whiG) (put. alt.) (gtg start codon); putative
           [Streptomyces coelicolor]
          Length = 258

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 55  DFVSSGVFGLIDAIEKFDVDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + VE +  V       +SL   +  E+  H G  
Sbjct: 112 VERAYATLEARLRRTPSESEVAVEMGIAVEDLHAVFS----QLSLANVVALEELLHAGGE 167

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 168 GGGRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 223

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 224 LAEIGNVLGVTESRVSQIHTKSVLQLR 250


>gi|256267|gb|AAC60414.1| RpoD1 [Synechococcus]
          Length = 48

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/47 (74%), Positives = 42/47 (89%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS T
Sbjct: 2   DLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRT 48


>gi|47564960|ref|ZP_00236004.1| sigma-B [Bacillus cereus G9241]
 gi|47558333|gb|EAL16657.1| sigma-B [Bacillus cereus G9241]
          Length = 257

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 122/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|331663420|ref|ZP_08364330.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
 gi|331059219|gb|EGI31196.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
          Length = 239

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGS 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|298243403|ref|ZP_06967210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
 gi|297556457|gb|EFH90321.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
          Length = 294

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 107/202 (52%), Gaps = 12/202 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+ A +++D   G +F  +A   ++ A+   I   +   R  V    +I +
Sbjct: 53  DLIGYGMIGLINAIDRYDLSRGVRFEAFATPRIRGAVIDQIRQLNWLPRSSV---SRIRQ 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG----DEDTS 586
           + RT   +  ++ R  T  E AK L + VE  R++L +++   +SL+ P+G    +++++
Sbjct: 110 IERTHAELEQQLGRPATEAEAAKALDVSVERYRQMLTEMSVSVLSLDAPMGSSIQEDESA 169

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LGD +ED++   P ++     L ++ +  L  L PRE+ +L + +      + T++E+ 
Sbjct: 170 SLGDMLEDESQQDPGEAVEHEELIQSLSAALQHLPPREQLLLSLYY----KEELTMKEIS 225

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   V+  R+ Q+  +A+ +L+
Sbjct: 226 RIMNVSESRVCQLRMQALVRLR 247


>gi|302558130|ref|ZP_07310472.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
 gi|302475748|gb|EFL38841.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
          Length = 280

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDVDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A +L + V+ +  V       +SL   +  E+  H+G  
Sbjct: 134 VERAYATLEARLRRTPSESEVAGELGIAVDELHAVFS----QLSLANVVALEELLHVGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 SGDRLSLMDTLEDTAADDPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR 272


>gi|218513990|ref|ZP_03510830.1| RNA polymerase factor sigma-32 [Rhizobium etli 8C-3]
          Length = 217

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 82/160 (51%), Gaps = 11/160 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EIAKKL 556
           +K +I   I      +++      K  ++    RR+  +I+     +  PE   EIA KL
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKL 166

Query: 557 AMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIED 594
            +  E V  + +      SL  PI   + D+    D++ D
Sbjct: 167 NVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVD 206


>gi|333028638|ref|ZP_08456702.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332748490|gb|EGJ78931.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 310

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 123/249 (49%), Gaps = 35/249 (14%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E   A+  ++E N+ LV   A+++ +RG    D++Q G IGL+KA ++F+     +
Sbjct: 74  EGTREFQDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVE 133

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D +  + +P  +++   ++ +    +S ++ R P   E+A  
Sbjct: 134 FTTFAVPYIVGEIKRFFRDTTWAVHVPRRLQEARVELAKANEELSTRLGRAPKVSELAAL 193

Query: 556 LAMPVEGV--RKVLKITKEPISLETPIGDEDT----SHLGDFI----------EDKNAVS 599
           +++  + V   ++        SL+  IG ED+    + L DFI          ED +A++
Sbjct: 194 MSLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAALSDFIGAEDPGMELVEDLHALA 253

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PL               LA L PR+ ++L +RFG     + T  ++G++  V++  + ++
Sbjct: 254 PL---------------LAGLEPRDRQILELRFG----QELTQAQIGERLGVSQMHVSRL 294

Query: 660 EAKAIRKLK 668
             + +  L+
Sbjct: 295 LNRTLGTLR 303


>gi|262164053|ref|ZP_06031792.1| RNA polymerase sigma factor RpoD [Vibrio mimicus VM223]
 gi|262027581|gb|EEY46247.1| RNA polymerase sigma factor RpoD [Vibrio mimicus VM223]
          Length = 595

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/118 (38%), Positives = 73/118 (61%), Gaps = 3/118 (2%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
           +P + V SEQ+ED + M+++MGI VV+   D  +     + ++    +A  ++  L   +
Sbjct: 1   MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
               R+TD PVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++
Sbjct: 61  SEIGRTTD-PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAVAEYPGTIPYIL 117


>gi|290957086|ref|YP_003488268.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
 gi|260646612|emb|CBG69709.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
          Length = 258

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/218 (28%), Positives = 101/218 (46%), Gaps = 26/218 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 55  DFVSSGVFGLIDAIEKFDIDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    + ++++R P+  E+A ++ + V+ +  V       +SL   +  E+  H G  
Sbjct: 112 VERAYATLESRLRRTPSEGEVAAEMGIAVDELHAVFS----QLSLANVVALEELLHAGGE 167

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A  P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 168 GGDRLSLMDTLEDTAADDPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEGL----T 223

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 224 LAEIGNVLGVTESRVSQIHTKSVLQLR-----AKLASF 256


>gi|158333719|ref|YP_001514891.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158303960|gb|ABW25577.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 264

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 56/208 (26%), Positives = 107/208 (51%), Gaps = 10/208 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V+ NL LV   A ++     + F DL+Q G++GL++A E+FD   G+ FS++A+ +
Sbjct: 29  RNRLVQMNLGLVRREAHRWVGHSTESFDDLMQVGSLGLIRAIERFDPFKGHAFSSFAVPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S  +RIP    +   + +   R M ++++R+PT  E+A  L +  +  
Sbjct: 89  IRGEIQHYLRDKSPQVRIPRKWHELQRQAINVTREMRDELQRQPTDVEVAAALDICQKEW 148

Query: 564 R--KVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS-PLDSAIQANLRETTTRVLA 618
           +  K+    +  +SL+ P+   ++++  LG+ + D++  S  L    Q  LR+     L+
Sbjct: 149 QEVKLASCNRSVLSLDAPVHNSEQESMSLGELLPDRHYHSFQLAQEDQIRLRQA----LS 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L  R   VL   F   +    T E +G
Sbjct: 205 KLEKRTSDVLEFVFFHDLTQKETAEVLG 232


>gi|302542195|ref|ZP_07294537.1| RNA polymerase sigma factor WhiG [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459813|gb|EFL22906.1| RNA polymerase sigma factor WhiG [Streptomyces himastatinicus ATCC
           53653]
          Length = 277

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 98/207 (47%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 74  DFVSSGVFGLIDAIEKFDPERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +   ++R PT  E+A ++ + V+ +  V       +SL   +  E+  H+G  
Sbjct: 131 VERAYATLEAALRRTPTEVEVAAEMDISVDELHGVFS----QLSLANVVALEELLHVGGE 186

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 187 GGDRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 242

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G+   VT  R+ QI  K++ +L+
Sbjct: 243 LAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|242241477|ref|ZP_04795922.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
 gi|242235020|gb|EES37331.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
          Length = 256

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 124/243 (51%), Gaps = 20/243 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S+A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKH 669
               R+L  L+ RE ++++  F  G++   T E +G  Q  V+R     ++  A++KL+ 
Sbjct: 198 MILERILPILSERERQIIQCTFIEGLSQKETGERIGLSQMHVSR-----LQRTAVKKLQE 252

Query: 670 PSR 672
            +R
Sbjct: 253 AAR 255


>gi|294673112|ref|YP_003573728.1| sigma factor [Prevotella ruminicola 23]
 gi|294471705|gb|ADE81094.1| putative sigma factor [Prevotella ruminicola 23]
          Length = 238

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 109/235 (46%), Gaps = 46/235 (19%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++M+++NL+LV+S+A  Y    +   DLIQ GNIGL+KA  +F+  LGY+F  YA   
Sbjct: 46  AEEQMIKSNLKLVVSIANSYRPM-MSMEDLIQNGNIGLIKAVREFNPELGYRFVFYASMM 104

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++ I   I + S      VH  D     + +                  + L +P  G 
Sbjct: 105 IRKYIIMGIRNDSGI----VHSSDYEQAFISS------------------ESLDVPGSG- 141

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                            G +DTS     + D +  S LDS + A+L+     V   L+P 
Sbjct: 142 -----------------GYKDTSKADMLVGDMDVESDLDS-LSADLKRAMCSV---LSPC 180

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
              ++    G+G    +T E +GK+  + + R+R+I  ++I  L++  R KKL S
Sbjct: 181 AVDIVCKVMGLGCTPMYT-ESIGKELNMPKSRVRKIYQESIGILQNNERVKKLLS 234


>gi|331653330|ref|ZP_08354335.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
 gi|323174562|gb|EFZ60183.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LT-68]
 gi|331049428|gb|EGI21500.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
          Length = 239

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|91211141|ref|YP_541127.1| flagellar biosynthesis sigma factor [Escherichia coli UTI89]
 gi|117624064|ref|YP_852977.1| flagellar biosynthesis sigma factor [Escherichia coli APEC O1]
 gi|218558780|ref|YP_002391693.1| flagellar biosynthesis sigma factor [Escherichia coli S88]
 gi|237705878|ref|ZP_04536359.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|91072715|gb|ABE07596.1| flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli UTI89]
 gi|115513188|gb|ABJ01263.1| flagellar biosynthesis sigma factor FliA [Escherichia coli APEC O1]
 gi|218365549|emb|CAR03276.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli S88]
 gi|226900635|gb|EEH86894.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|294492788|gb|ADE91544.1| flagellar operon sigma factor FliA [Escherichia coli IHE3034]
 gi|323952417|gb|EGB48290.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H252]
 gi|323956319|gb|EGB52062.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H263]
          Length = 239

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMETIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|294811026|ref|ZP_06769669.1| Putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|326439632|ref|ZP_08214366.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294323625|gb|EFG05268.1| Putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
          Length = 277

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 109/226 (48%), Gaps = 18/226 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+V A L +   +A+++ +RG    DL Q   +GL+KA +++D   G  F+++A+  +
Sbjct: 51  RQELVNAWLPMSERLARRFRDRGESLEDLRQVAALGLVKAVDRYDPARGCAFASFAVPTI 110

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAM-PV-- 560
              + R   D   T+ +P  ++D+ ++V    + ++  +  R PT  EIA++  + P   
Sbjct: 111 TGEVKRHFRDHMWTLHVPRRVQDQRNRVRAAQQELAQTVTGRAPTEAEIAERAGLTPAQT 170

Query: 561 -EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            EG+  +       +  E P GD D   + D +   +    LD  I    RE     L  
Sbjct: 171 REGLAAIGSYRTLSLDAEAP-GDGDGCTMADALGGPDPA--LDVVID---REAVRPRLRE 224

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR------ERIRQ 658
           L  RE R+L MRF  GM      E++G  Q  V+R      +R+RQ
Sbjct: 225 LPERERRILYMRFFRGMTQSRIAEDLGISQMHVSRLISHSCDRLRQ 270


>gi|167768028|ref|ZP_02440081.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|317498378|ref|ZP_07956673.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710357|gb|EDS20936.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|291561028|emb|CBL39828.1| Sigma-70 region 3./Sigma-70 region 2 [butyrate-producing bacterium
           SSC/2]
 gi|316894272|gb|EFV16459.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 256

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/144 (31%), Positives = 84/144 (58%), Gaps = 6/144 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V KG+ EA      ++E+ L  ++ +A+ +T +G+ F DL+QEGNIGL++A   +    
Sbjct: 111 LVEKGDGEA------VIESFLPQILEIARTHTGKGVLFGDLVQEGNIGLLEAMAIYQGKD 164

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
              F  +A   V+ +I  +IA Q  +  +   M  K +++   +  +S ++ REP  EE+
Sbjct: 165 AEGFLAHAKSAVEDSILDAIAIQRGSDSVGEAMAIKANRLDDASTFLSKELGREPKIEEL 224

Query: 553 AKKLAMPVEGVRKVLKITKEPISL 576
           AK L+M  E V++V+KI+ + +S+
Sbjct: 225 AKYLSMTEEEVKEVMKISLDALSV 248


>gi|15802357|ref|NP_288383.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7
           EDL933]
 gi|15831915|ref|NP_310688.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           Sakai]
 gi|26248189|ref|NP_754229.1| flagellar biosynthesis sigma factor [Escherichia coli CFT073]
 gi|49176170|ref|NP_416432.3| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|74311731|ref|YP_310150.1| flagellar biosynthesis sigma factor [Shigella sonnei Ss046]
 gi|89108757|ref|AP_002537.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|110642027|ref|YP_669757.1| flagellar biosynthesis sigma factor [Escherichia coli 536]
 gi|157158016|ref|YP_001463226.1| flagellar biosynthesis sigma factor [Escherichia coli E24377A]
 gi|170019740|ref|YP_001724694.1| flagellar biosynthesis sigma factor [Escherichia coli ATCC 8739]
 gi|170081570|ref|YP_001730890.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170684004|ref|YP_001743321.1| flagellar biosynthesis sigma factor [Escherichia coli SMS-3-5]
 gi|187776391|ref|ZP_02802353.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188025223|ref|ZP_02776870.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|189010650|ref|ZP_02808323.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189402557|ref|ZP_02783240.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189403603|ref|ZP_02796533.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189404441|ref|ZP_02789463.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189405427|ref|ZP_02815329.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189406256|ref|ZP_02827273.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|191168296|ref|ZP_03030089.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|191173335|ref|ZP_03034865.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|193066383|ref|ZP_03047431.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|193071158|ref|ZP_03052082.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194429934|ref|ZP_03062444.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194439580|ref|ZP_03071653.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208810387|ref|ZP_03252263.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209399914|ref|YP_002271036.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209919344|ref|YP_002293428.1| flagellar biosynthesis sigma factor [Escherichia coli SE11]
 gi|215487127|ref|YP_002329558.1| flagellar biosynthesis sigma factor [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218554506|ref|YP_002387419.1| flagellar biosynthesis sigma factor [Escherichia coli IAI1]
 gi|218689915|ref|YP_002398127.1| flagellar biosynthesis sigma factor [Escherichia coli ED1a]
 gi|218695529|ref|YP_002403196.1| flagellar biosynthesis sigma factor [Escherichia coli 55989]
 gi|218699514|ref|YP_002407143.1| flagellar biosynthesis sigma factor [Escherichia coli IAI39]
 gi|218705417|ref|YP_002412936.1| flagellar biosynthesis sigma factor [Escherichia coli UMN026]
 gi|238901131|ref|YP_002926927.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253773125|ref|YP_003035956.1| flagellar biosynthesis sigma factor [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254793572|ref|YP_003078409.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           TW14359]
 gi|260844326|ref|YP_003222104.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260855902|ref|YP_003229793.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260868514|ref|YP_003234916.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|291283099|ref|YP_003499917.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|293405408|ref|ZP_06649400.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|293410281|ref|ZP_06653857.1| conserved hypothetical protein [Escherichia coli B354]
 gi|293446304|ref|ZP_06662726.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|298381052|ref|ZP_06990651.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|307314171|ref|ZP_07593781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|312967123|ref|ZP_07781341.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|312973866|ref|ZP_07788038.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|331642544|ref|ZP_08343679.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331668616|ref|ZP_08369464.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331673440|ref|ZP_08374208.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331677807|ref|ZP_08378482.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331683474|ref|ZP_08384075.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332278907|ref|ZP_08391320.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|84028136|sp|P0AEM8|FLIA_ECO57 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028137|sp|P0AEM7|FLIA_ECOL6 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028138|sp|P0AEM6|FLIA_ECOLI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|12516023|gb|AAG56937.1|AE005415_2 flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli O157:H7 str. EDL933]
 gi|26108593|gb|AAN80796.1|AE016762_49 RNA polymerase sigma factor for flagellar operon [Escherichia coli
           CFT073]
 gi|556180|gb|AAC37011.1| sigma factor 28 [Escherichia coli]
 gi|687650|gb|AAC43543.1| sigma F [Escherichia coli]
 gi|1736581|dbj|BAA15742.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|1788231|gb|AAC74989.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13362129|dbj|BAB36084.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli O157:H7 str. Sakai]
 gi|73855208|gb|AAZ87915.1| alternative sigma factor 28 [Shigella sonnei Ss046]
 gi|110343619|gb|ABG69856.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           536]
 gi|157080046|gb|ABV19754.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E24377A]
 gi|169754668|gb|ACA77367.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli ATCC
           8739]
 gi|169889405|gb|ACB03112.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170521722|gb|ACB19900.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SMS-3-5]
 gi|187767374|gb|EDU31218.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014157|gb|EDU52279.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|188999325|gb|EDU68311.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354876|gb|EDU73295.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359713|gb|EDU78132.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189365564|gb|EDU83980.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370194|gb|EDU88610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189375693|gb|EDU94109.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|190901668|gb|EDV61424.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|190906452|gb|EDV66061.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|192925968|gb|EDV80614.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|192955553|gb|EDV86032.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194412023|gb|EDX28335.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194421489|gb|EDX37503.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208724903|gb|EDZ74610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209161314|gb|ACI38747.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209748392|gb|ACI72503.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748394|gb|ACI72504.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748396|gb|ACI72505.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209912603|dbj|BAG77677.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE11]
 gi|215265199|emb|CAS09588.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|218352261|emb|CAU98017.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli 55989]
 gi|218361274|emb|CAQ98858.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI1]
 gi|218369500|emb|CAR17267.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI39]
 gi|218427479|emb|CAR08375.2| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli ED1a]
 gi|218432514|emb|CAR13407.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli UMN026]
 gi|222033663|emb|CAP76404.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LF82]
 gi|238863498|gb|ACR65496.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253324169|gb|ACT28771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254592972|gb|ACT72333.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257754551|dbj|BAI26053.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257759473|dbj|BAI30970.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257764870|dbj|BAI36365.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|260448961|gb|ACX39383.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli DH1]
 gi|284921835|emb|CBG34908.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           042]
 gi|290762972|gb|ADD56933.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|291323134|gb|EFE62562.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|291427616|gb|EFF00643.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|291470749|gb|EFF13233.1| conserved hypothetical protein [Escherichia coli B354]
 gi|298278494|gb|EFI20008.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|306906140|gb|EFN36658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|307553936|gb|ADN46711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ABU 83972]
 gi|309702217|emb|CBJ01534.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ETEC H10407]
 gi|310332461|gb|EFP99696.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|312288587|gb|EFR16489.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|315061222|gb|ADT75549.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli W]
 gi|315617855|gb|EFU98453.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           3431]
 gi|320191897|gb|EFW66544.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC1212]
 gi|320194366|gb|EFW68997.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           WV_060327]
 gi|320198616|gb|EFW73216.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EC4100B]
 gi|323158594|gb|EFZ44608.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E128010]
 gi|323165278|gb|EFZ51066.1| RNA polymerase sigma factor for flagellar operon [Shigella sonnei
           53G]
 gi|323180827|gb|EFZ66367.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1180]
 gi|323186802|gb|EFZ72122.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           RN587/1]
 gi|323378201|gb|ADX50469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli KO11]
 gi|323937197|gb|EGB33477.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1520]
 gi|323940415|gb|EGB36606.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E482]
 gi|323948197|gb|EGB44185.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H120]
 gi|323961971|gb|EGB57570.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H489]
 gi|323968339|gb|EGB63746.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli M863]
 gi|323972715|gb|EGB67916.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TA007]
 gi|323977897|gb|EGB72983.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TW10509]
 gi|324118976|gb|EGC12865.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1167]
 gi|326342331|gb|EGD66112.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1044]
 gi|326344837|gb|EGD68584.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1125]
 gi|327253053|gb|EGE64707.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           STEC_7v]
 gi|331039342|gb|EGI11562.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331063810|gb|EGI35721.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331069638|gb|EGI41025.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331074267|gb|EGI45587.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331079689|gb|EGI50886.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332089656|gb|EGI94758.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           5216-82]
 gi|332101259|gb|EGJ04605.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|332343648|gb|AEE56982.1| RNA polymerase sigma factor for flagellar operon protein
           [Escherichia coli UMNK88]
 gi|332756073|gb|EGJ86426.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           4343-70]
 gi|333003239|gb|EGK22785.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-218]
 gi|333004180|gb|EGK23712.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-272]
 gi|333017792|gb|EGK37099.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-227]
          Length = 239

 Score = 75.5 bits (184), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|21223976|ref|NP_629755.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|256784937|ref|ZP_05523368.1| RNA polymerase sigma factor WhiG [Streptomyces lividans TK24]
 gi|289768830|ref|ZP_06528208.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
 gi|133480|sp|P17211|RPSW_STRCO RecName: Full=RNA polymerase sigma factor whiG
 gi|153486|gb|AAA26828.1| sigma factor (whiG) (put. alt.); putative [Streptomyces coelicolor]
 gi|3192014|emb|CAA19413.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|289699029|gb|EFD66458.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
          Length = 280

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDVDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + VE +  V       +SL   +  E+  H G  
Sbjct: 134 VERAYATLEARLRRTPSESEVAVEMGIAVEDLHAVFS----QLSLANVVALEELLHAGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 GGGRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR 272


>gi|302517710|ref|ZP_07270052.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302426605|gb|EFK98420.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 286

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 123/249 (49%), Gaps = 35/249 (14%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E   A+  ++E N+ LV   A+++ +RG    D++Q G IGL+KA ++F+     +
Sbjct: 50  EGTREFQDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVE 109

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D +  + +P  +++   ++ +    +S ++ R P   E+A  
Sbjct: 110 FTTFAVPYIVGEIKRFFRDTTWAVHVPRRLQEARVELAKANEELSTRLGRAPKVSELAAL 169

Query: 556 LAMPVEGV--RKVLKITKEPISLETPIGDEDT----SHLGDFI----------EDKNAVS 599
           +++  + V   ++        SL+  IG ED+    + L DFI          ED +A++
Sbjct: 170 MSLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAALSDFIGAEDPGMELVEDLHALA 229

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PL               LA L PR+ ++L +RFG     + T  ++G++  V++  + ++
Sbjct: 230 PL---------------LADLEPRDRQILELRFG----QELTQAQIGERLGVSQMHVSRL 270

Query: 660 EAKAIRKLK 668
             + +  L+
Sbjct: 271 LNRTLGTLR 279


>gi|254380542|ref|ZP_04995908.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339453|gb|EDX20419.1| sigma factor [Streptomyces sp. Mg1]
          Length = 304

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/256 (24%), Positives = 124/256 (48%), Gaps = 24/256 (9%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLM 482
           FR + ++  +G  E    +  ++E +L LV   A+++  R    GL   D+IQ G IGL+
Sbjct: 53  FRRLRTL-EEGTREYQYTRNTLIEMSLSLVQFAARRFRARVLGGGLDMDDIIQVGTIGLI 111

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++FD     +FST A+ ++   I R   D + ++ +P  +++   ++ +    +++ 
Sbjct: 112 KAIDRFDPEREVEFSTLALPYIVGEIKRHFRDTTWSVHVPRRLQELRSELAKAQEALTDV 171

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS--------HLGDFI 592
           + R PT +E+A+ L +  E V   L         SL+   G+ +TS         L D +
Sbjct: 172 LGRAPTVKEVAEHLELTEEQVIDGLVAANGYTSGSLDAAAGESETSPSTGRSTRPLADLV 231

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +    L   +      T   +L  L  R+  +L+MRFG     D T  E+G +  ++
Sbjct: 232 GDVDPAMELFEDLH-----TLAPLLRQLDERDRLILQMRFG----QDRTQAEIGSELGIS 282

Query: 653 RERIRQIEAKAIRKLK 668
           + ++ ++ ++ + +L+
Sbjct: 283 QMQVSRLLSRTLARLR 298


>gi|333003010|gb|EGK22564.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           VA-6]
          Length = 239

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|114332399|ref|YP_748621.1| RNA polymerase, sigma 28 subunit [Nitrosomonas eutropha C91]
 gi|114309413|gb|ABI60656.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosomonas
           eutropha C91]
          Length = 236

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 113/239 (47%), Gaps = 13/239 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
            +I K + V     LV  +A     R    +Q  DLIQ G IGL+ A  +++   G +F 
Sbjct: 6   GTIDKDQFVIEFTPLVKRIAYHMMARLPASVQVDDLIQAGMIGLLDAINRYEGSYGRQFE 65

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           +YA   ++ ++   + +      +P  +R K+ ++    R +  ++   P+ +EIA +L 
Sbjct: 66  SYAAQRIRGSMLDELREADW---LPRSLRRKMRQIETAMRTLEQRLGCPPSEQEIADELN 122

Query: 558 MPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +P+   +++L+     + I  E    DE+  H  D + +     PLD  ++ NLRE    
Sbjct: 123 LPLAEYQEMLQEAGGGQLIYYEDFQVDEE-DHFLDHLCNDQGNEPLDQLLEKNLRELLVA 181

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +  L  +E+ V+ M +   MN    L E+G    V+  RI Q+  +AI +L+   R K
Sbjct: 182 AIEKLPAKEKLVMGMYYEQEMN----LREIGDVLGVSESRICQLHTQAISRLRTRLRDK 236


>gi|301029374|ref|ZP_07192470.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
 gi|299877729|gb|EFI85940.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
          Length = 239

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNSTETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|30019159|ref|NP_830790.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 14579]
 gi|29894702|gb|AAP07991.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 14579]
          Length = 258

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 122/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 19  LIADFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 76

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 77  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPRI 136

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 137 IEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 186

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 187 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 242

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 243 KRQAISKLKQAA 254


>gi|320647130|gb|EFX15963.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           493-89]
 gi|320652413|gb|EFX20711.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           H 2687]
          Length = 228

 Score = 75.1 bits (183), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|110805895|ref|YP_689415.1| flagellar biosynthesis sigma factor [Shigella flexneri 5 str. 8401]
 gi|195939226|ref|ZP_03084608.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           EC4024]
 gi|208816591|ref|ZP_03257711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208820391|ref|ZP_03260711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217328583|ref|ZP_03444664.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227885651|ref|ZP_04003456.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|256017880|ref|ZP_05431745.1| flagellar biosynthesis sigma factor [Shigella sp. D9]
 gi|256022420|ref|ZP_05436285.1| flagellar biosynthesis sigma factor [Escherichia sp. 4_1_40B]
 gi|261227583|ref|ZP_05941864.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261255813|ref|ZP_05948346.1| RNA polymerase, sigma 28 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|300818654|ref|ZP_07098862.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300822306|ref|ZP_07102447.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300899176|ref|ZP_07117454.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300904809|ref|ZP_07122636.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300917364|ref|ZP_07134033.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300925015|ref|ZP_07140938.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300951546|ref|ZP_07165380.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300956562|ref|ZP_07168843.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300982291|ref|ZP_07176001.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300993927|ref|ZP_07180602.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|301018228|ref|ZP_07182743.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|301050723|ref|ZP_07197582.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|301305263|ref|ZP_07211360.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|301327712|ref|ZP_07220918.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301645559|ref|ZP_07245489.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|306814254|ref|ZP_07448420.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|307138589|ref|ZP_07497945.1| flagellar biosynthesis sigma factor [Escherichia coli H736]
 gi|309795968|ref|ZP_07690381.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|110615443|gb|ABF04110.1| flagellar biosynthesis sigma factor FliA [Shigella flexneri 5 str.
           8401]
 gi|208730934|gb|EDZ79623.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208740514|gb|EDZ88196.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217317930|gb|EEC26357.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227837224|gb|EEJ47690.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|300297591|gb|EFJ53976.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|300307268|gb|EFJ61788.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300316625|gb|EFJ66409.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300357213|gb|EFJ73083.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300399815|gb|EFJ83353.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|300403277|gb|EFJ86815.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300406428|gb|EFJ89966.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|300415410|gb|EFJ98720.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300418834|gb|EFK02145.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300449221|gb|EFK12841.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300525189|gb|EFK46258.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300528826|gb|EFK49888.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300839469|gb|EFK67229.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|300845756|gb|EFK73516.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301076168|gb|EFK90974.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|305852413|gb|EFM52864.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|308120418|gb|EFO57680.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|312946514|gb|ADR27341.1| flagellar biosynthesis sigma factor [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|315136559|dbj|BAJ43718.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315257247|gb|EFU37215.1| flagellar biosynthesis sigma factor [Escherichia coli MS 85-1]
 gi|315290288|gb|EFU49666.1| flagellar biosynthesis sigma factor [Escherichia coli MS 153-1]
 gi|315296505|gb|EFU55802.1| flagellar biosynthesis sigma factor [Escherichia coli MS 16-3]
 gi|320641770|gb|EFX11158.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           G5101]
 gi|320658015|gb|EFX25777.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320658587|gb|EFX26281.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320668485|gb|EFX35312.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323152745|gb|EFZ39017.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EPECa14]
 gi|323186302|gb|EFZ71652.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1357]
 gi|324007273|gb|EGB76492.1| flagellar biosynthesis sigma factor [Escherichia coli MS 57-2]
 gi|324013514|gb|EGB82733.1| flagellar biosynthesis sigma factor [Escherichia coli MS 60-1]
 gi|324017957|gb|EGB87176.1| flagellar biosynthesis sigma factor [Escherichia coli MS 117-3]
          Length = 229

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|300854227|ref|YP_003779211.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
 gi|300434342|gb|ADK14109.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
          Length = 241

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 115/231 (49%), Gaps = 15/231 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  L LV  +A +      + +++ DL+  G +GL+ A  KFD   G KFSTYA 
Sbjct: 10  KEELVKKYLPLVKYIASRVIIGKTKYIEYEDLVSYGMLGLIDAINKFDKDRGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +   S    I     DK++K       +  K+ REP+ EEIA +L MP++
Sbjct: 70  IRIKGSMIDELRRNSP---ISKGAMDKLNKYNAAMDSLRTKLGREPSSEEIANELGMPLK 126

Query: 562 GVRKVLKITK--EPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + ++         +SLE  I   D+D   +G  +ED  + SP  S  +  + E   + L
Sbjct: 127 KMMEIENYINYISIVSLEDLIFSEDDDIPLMGT-VEDTKSPSPEKSLEKKEMLEYLAKAL 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  V+ + +   +    TL+E+G    V+  R+ Q+ ++AI  L+
Sbjct: 186 DLLNEKDNLVITLYYYEKL----TLKEIGHILNVSESRVCQLHSRAILHLR 232


>gi|302557289|ref|ZP_07309631.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302474907|gb|EFL38000.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 269

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 113/238 (47%), Gaps = 16/238 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + + FR + ++    E EA   + E+VEA L +   +A ++ +RG  F DL Q   +GL+
Sbjct: 22  TAAAFRRLTALPACPEREA--LRDEIVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLV 79

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +++D  LG  F +YA+  +   I R   D   T+ +P  +++  ++V   ++ +S  
Sbjct: 80  KAVDRYDSELGNAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQELRNRVRYASQDLSGT 139

Query: 543 IK-REPTPEEIAKKLAMPVEGVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
              R PT  EIA+   +  E VR     +   +   +  E P G +D   LGD +    A
Sbjct: 140 TPGRRPTVTEIAEHAHLSEEDVRTGQEALESFSALSLDAELP-GSDDGYSLGDAL---GA 195

Query: 598 VSP-LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             P LD+ +    RE     LA L  RE  +L MRF          EE+G  Q  V+R
Sbjct: 196 PDPALDTVVD---REAVKERLAELPERERAILYMRFFDDRTQSSIAEELGISQMHVSR 250


>gi|58699726|ref|ZP_00374383.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533758|gb|EAL58100.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 216

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 52/75 (69%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++ ++L LV+ +A K+ N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ 
Sbjct: 48  KLITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEA 107

Query: 507 AITRSIADQSCTIRI 521
           +I   I      ++I
Sbjct: 108 SIKDFILKSWSFVKI 122


>gi|300935898|ref|ZP_07150854.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|300458917|gb|EFK22410.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|307626601|gb|ADN70905.1| flagellar biosynthesis sigma factor [Escherichia coli UM146]
 gi|315286624|gb|EFU46057.1| flagellar biosynthesis sigma factor [Escherichia coli MS 110-3]
          Length = 229

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDDHQRENPLQQLLDSNLRQRVMETIETLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|119944398|ref|YP_942078.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
 gi|119863002|gb|ABM02479.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
          Length = 283

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 117/242 (48%), Gaps = 30/242 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++V ++LR V+ +AK Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 49  AAKKLVMSHLRFVVYIAKSYAGYGLAQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K  I   +      ++I      +  K+    RR   ++      E         V  V
Sbjct: 109 IKAEIHEYVIRNWRMVKIATTKAQR--KLFFNLRRAKKRLGWFSHDE---------VATV 157

Query: 564 RKVLKI-TKEPISLETPIGDEDTSHLG-------------DFIEDKNAVSPLDSAIQANL 609
            + L + TK+ + +E+ +  +D S                 ++EDK+A      A +   
Sbjct: 158 AENLNVSTKDVLEMESRLNAQDQSFDLSDSDDDESGFAPVQYLEDKSADVFQVVATENTQ 217

Query: 610 RETTTRVLASLTPREER---VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             T  ++ ++L+  +ER   ++  R+        TL ++  ++ ++ ERIRQ+E  A++K
Sbjct: 218 LHTKNKLYSALSTLDERSQDIVSSRW--LSEPKATLHDLAARYGISAERIRQLEENAMKK 275

Query: 667 LK 668
           L+
Sbjct: 276 LQ 277


>gi|218778853|ref|YP_002430171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760237|gb|ACL02703.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
          Length = 252

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/213 (27%), Positives = 111/213 (52%), Gaps = 16/213 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A +K+D   G KF TYA + ++ A+   +        +P  +R K+ +
Sbjct: 48  DLISAGIMGLLDALDKYDEGRGVKFRTYAEFRIRGAMLDELRAMDW---VPRSVRKKVQE 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + +   R+  +  R    EEIA +L + ++  + +L      E +SL+ P+   D +  G
Sbjct: 105 IEQAVNRVEKRESRPADAEEIANELGVDMDTYQNMLSKAGGIELVSLDEPLWSNDNTKDG 164

Query: 590 -----DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
                D +ED NA +P    + +  ++   + ++SLTP+E+++L + +      + TL+E
Sbjct: 165 RRTHVDLLED-NA-NPDRDLMDSEFKKILAQSISSLTPKEQQILSLYY----QDELTLKE 218

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           VG+   +T  RI QI  + + KL+   ++++ R
Sbjct: 219 VGEVMGLTESRICQIHTQCMIKLRSKLKTQEAR 251


>gi|297582861|ref|YP_003698641.1| LuxR family transcriptional regulator [Bacillus selenitireducens
           MLS10]
 gi|297141318|gb|ADH98075.1| transcriptional regulator, LuxR family [Bacillus selenitireducens
           MLS10]
          Length = 268

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 124/234 (52%), Gaps = 22/234 (9%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV ++A+K++       DL+Q G IGL+ A  +FD   G  F ++A+  +   I R I D
Sbjct: 48  LVHALARKFSRGQRHDEDLVQVGMIGLLAALRRFDPSFGRSFESFAVPTIVGEIKRFIRD 107

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   K+      ++ +++R P  EEIA  L +  E + + +++ K  +
Sbjct: 108 KTWSVHVPRRIKELGPKIKSAVENLTTELQRSPQVEEIADYLEVSEEEILETMEMGKSYQ 167

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLD--SAIQANLRETTTRVLAS-----LTPREE 625
            +S++  I  +D         + +AV+ LD   ++++   +T  ++L       LT RE+
Sbjct: 168 ALSVDRSIEADD---------EGSAVTLLDLVGSVESGYEQTDQQLLLEKAFQVLTDREK 218

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ++L++ +   M+     +E G+Q  +++  + +++ +A++KLK   R +   +F
Sbjct: 219 QILQLTYFENMSQ----KETGEQLGISQMHVSRLQRRALQKLKDSIRIEATEAF 268


>gi|86605313|ref|YP_474076.1| RNA polymerase sigma factor SigF [Synechococcus sp. JA-3-3Ab]
 gi|86553855|gb|ABC98813.1| RNA polymerase sigma factor, group 3 [Synechococcus sp. JA-3-3Ab]
          Length = 299

 Score = 75.1 bits (183), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 105/207 (50%), Gaps = 9/207 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +VE NL LV   A  + N+  + + DL+Q G IGL++A E+FD   G  FS++AM +
Sbjct: 71  RNRLVEINLGLVRKEAHHWRNQCDEGYDDLVQVGCIGLIQAIERFDISRGLAFSSFAMPY 130

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S TIRIP        +  +   R+  ++ R P+  E+ + L +  +  
Sbjct: 131 IRGEIQHYLRDKSPTIRIPRRWATLQRQAKKVIARLRQELGRSPSEAEVREALQLTEQEW 190

Query: 564 RKVLKITKEP---ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R+ L++ ++    +SL+ P+  +ED+  LGD I D+   S    A +  +R      LA 
Sbjct: 191 RE-LELAQQNSLLLSLDAPVQVEEDSVALGDTIPDQRYRS-FQLAEEDRIR--LQNALAK 246

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG 646
           L  R  ++L   F   +    T E +G
Sbjct: 247 LEERTRQILEFVFFYDLTQKETAERLG 273


>gi|290962881|ref|YP_003494063.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652407|emb|CBG75540.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 275

 Score = 74.7 bits (182), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 57/259 (22%), Positives = 126/259 (48%), Gaps = 35/259 (13%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   ++++ +G       +  ++E NL LV   A ++  R     D++Q G IGL+KA 
Sbjct: 27  QFFDRLAVLDEGTHTYQYVRNTLIEMNLSLVRYAASRFRGREDSLEDIVQVGTIGLIKAI 86

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+T+A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 87  DRFELSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELARATDELQSRLGR 146

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI----GDEDTSHLGDFI------- 592
            PT  E+++ +++  E V +  K +      SL+  +    GD+  + LGD I       
Sbjct: 147 MPTTRELSELMSLSEEEVIEARKASNGYNTSSLDAALTSDGGDDGDAVLGDLIGEEDHAL 206

Query: 593 ---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              ED ++++PL               +A L  RE R++ +RF      + T  ++ ++ 
Sbjct: 207 QLVEDFHSLAPL---------------IAQLDDRERRIIHLRF----VEEWTQSQIAEEL 247

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V++  + ++ ++ I++L+
Sbjct: 248 GVSQMHVSRLISRIIKRLR 266


>gi|40787125|gb|AAR90090.1| WhiG-like protein [Streptomyces ambofaciens]
          Length = 280

 Score = 74.7 bits (182), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 77  DFVSSGVFGLIDAIEKFDVDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 133

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  +++R P+  E+A ++ + VE +  V       +SL   +  E+  H G  
Sbjct: 134 VERAYTTLEARLRRTPSESEVAVEMGIAVEDLHAVFS----QLSLANVVALEELLHAGGE 189

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 190 GGGRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G    VT  R+ QI  K++ +L+
Sbjct: 246 LAEIGNVLGVTESRVSQIHTKSVLQLR 272


>gi|76664996|emb|CAJ17940.1| DNA-directed RNA polymerase sigma subunit [Candidatus Phytoplasma
           solani]
          Length = 110

 Score = 74.7 bits (182), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 31/51 (60%), Positives = 43/51 (84%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +A +AK  +VE+N RLV+S+AK+Y  RG+ FLDLIQEGN+GLM+A +KFD+
Sbjct: 58  QAQLAKDSLVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDY 108


>gi|146312155|ref|YP_001177229.1| flagellar biosynthesis sigma factor [Enterobacter sp. 638]
 gi|145319031|gb|ABP61178.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter sp.
           638]
          Length = 239

 Score = 74.7 bits (182), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 99/198 (50%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     ++  ++ R  T  E+A++L + V+  R++L  T            E+     + 
Sbjct: 100 VAHAIGQLEQELGRNATETEVAERLGIAVQDYRQMLLDTNNSQLFSYDEWREEHGDSVEL 159

Query: 592 IEDKNAV-SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           + D+N   +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 VTDENQHENPLHQLLEGNLRQRVMDAIEALPEREQLVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|163816725|ref|ZP_02208088.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
 gi|158447982|gb|EDP24977.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
          Length = 224

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 117/232 (50%), Gaps = 32/232 (13%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  N+ LV+SVAK+Y  RG +  DLIQ G IGL+KA ++FD      FSTY++  
Sbjct: 18  ARDRLITENMGLVVSVAKRYIGRGQELEDLIQIGLIGLIKAVDRFDLEYDVMFSTYSVPL 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEG 562
           ++  I R + D    +R+  +++   ++  +  +       REPT +EI  K+   P E 
Sbjct: 78  IQGEIRRFLRDDGL-VRVSRNLKTIHYRAEKYRQEYQRTNGREPTVDEICAKIGSDPEEL 136

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFI----EDKNAVSPLDSAIQANLRETTTRVLA 618
           V          +++E+ +   +   +G+      E++  V  L             ++L 
Sbjct: 137 V----------MAMESAVDISNIEEMGELQTSRREEERVVEKL----------YVKQLLD 176

Query: 619 SLTPREERVLRMR-FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +L  RE++++ +R FG     + T  E+G+   +++ ++ ++E K +R+LK 
Sbjct: 177 TLPEREKKLITLRYFG-----EKTQGEIGRILGMSQVQVSRLEKKILRELKR 223


>gi|300864899|ref|ZP_07109744.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
 gi|300337103|emb|CBN54894.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
          Length = 292

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 109/221 (49%), Gaps = 10/221 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            + E+V+ N+ LV      + ++  + + DL+Q G+IGL++A E+FD   G  FS++A+ 
Sbjct: 65  VRNELVKLNIGLVRKEVHHWLHQCTESYDDLLQVGSIGLIRAIERFDMSKGNAFSSFAIP 124

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +++  I   + D+S ++R+P H      +     + +  ++ R PT  E+A  L + V G
Sbjct: 125 YIRGEIQHYLRDKSPSVRVPRHWLTLERQSSSIVKDLQVRLNRHPTDIEVATALNISV-G 183

Query: 563 VRKVLKIT---KEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             + +K+    + P+SL+ P+ DE+   + LG+ + D N       A +  +R    + L
Sbjct: 184 EWQEIKLACRNRSPLSLDAPLQDEEEGATCLGELVPD-NRYRSFQLAQEDRIR--LQQAL 240

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           A L  R   +L   F   +    T E +G        R+++
Sbjct: 241 AKLEERTREILEFVFLYDLTQKETAERLGISAVTVSRRVKK 281


>gi|29830728|ref|NP_825362.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607841|dbj|BAC71897.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 309

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 114/241 (47%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R G  E S  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 75  LRPGSPEHSRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 134

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 135 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIA 194

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  E V   ++  +     SLE     ++   L   ++      P    ++   R+
Sbjct: 195 ERLRITEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RD 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++  +L+  +
Sbjct: 250 LVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFARLRSAN 305

Query: 672 R 672
           R
Sbjct: 306 R 306


>gi|42543555|pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
           Sigma-Region4 Of Thermus Aquaticus Bound To Dna
          Length = 73

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 41/72 (56%), Positives = 52/72 (72%), Gaps = 1/72 (1%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-H 669
           E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H
Sbjct: 2   EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61

Query: 670 PSRSKKLRSFLD 681
            SR++KLR FL+
Sbjct: 62  ESRTRKLRDFLE 73


>gi|119718035|ref|YP_925000.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119538696|gb|ABL83313.1| sigma-70 region 2 domain protein [Nocardioides sp. JS614]
          Length = 257

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 109/227 (48%), Gaps = 17/227 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++  N+ + +   +++  RG+   DL Q   +GL+KA + FD   G+ F ++A+  ++ 
Sbjct: 34  QLIRLNMAVAVDATRRFRGRGIATDDLEQVAYVGLVKAVKGFDPDRGHDFLSFAIPTIRG 93

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            + R   D   T+R P  +++   K++     +  ++ R P P EIA+ L +  + V + 
Sbjct: 94  EVRRHFRDLGWTVRPPRSIQEAQTKIIACEGELYQQLGRAPRPSEIAEHLGLDRDLVVEA 153

Query: 567 LKITK--EPISLETPIGDEDTSHLG---DFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           L  +    P SL+ P  + D   +G    F ++   V        A  R     VLA L+
Sbjct: 154 LGASGCFAPASLDAPAHEGDDDPIGRRLGFTDEGFDV--------AEARAVLAPVLAKLS 205

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  ++ MRF  G     T  ++G+   VT+ ++ ++  + + +L+
Sbjct: 206 KRERIIVEMRFFRGC----TQAQIGEAIGVTQMQVSRLLTRLMARLR 248


>gi|220936149|ref|YP_002515048.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997459|gb|ACL74061.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 281

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 116/233 (49%), Gaps = 11/233 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V  NLR V+ +A+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W
Sbjct: 47  AARKLVMHNLRFVVHIARGYSGYGLGLGDLIQEGNIGLMKAVKRFDPEMGVRLISFAVHW 106

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVE 561
           ++  I   I      +++     + K+   +R+A++       E     +A  L + P +
Sbjct: 107 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKQRLGWFNSEEV-NAVADDLGVTPAQ 165

Query: 562 GVRKVLKITKEPISLE-TPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTRV 616
            +    ++  + +S +  P  DED   L        E  +    L++   A   ET    
Sbjct: 166 VLEMESRLAGQDVSFDPAPASDEDGPSLSPAETLIDESGDPAERLEADDWAAHHETRLHS 225

Query: 617 -LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L +L PR   ++  R+        TL E+  ++ ++ ER+RQ+E+ A+RKL+
Sbjct: 226 GLEALDPRSRDIVARRWLTEQKA--TLHELAAEYGISAERVRQLESNAMRKLR 276


>gi|313901053|ref|ZP_07834541.1| RNA polymerase sigma-F factor [Clostridium sp. HGF2]
 gi|312954011|gb|EFR35691.1| RNA polymerase sigma-F factor [Clostridium sp. HGF2]
          Length = 241

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 113/228 (49%), Gaps = 15/228 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  +R G+ EA   K   V+ N  LV S+ ++++ + +   DL Q G +GLMKA   FD
Sbjct: 10  LIERIRLGDEEA---KSCFVQQNSALVYSIIRRFSRQRISNEDLFQIGCVGLMKALNNFD 66

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R   D   +IRI   +++   ++V+    +  K+  EPT 
Sbjct: 67  TSYEVKFSTYAVPIIMGEIKRFFRDDG-SIRISRSLKEGYLQMVKAKEVLLQKLNHEPTY 125

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQAN 608
           +EIA  + + V  V    +  +   SL+  I + D S +   +EDK +     D  ++ +
Sbjct: 126 QEIADAMELDVADVILAFEANQFIYSLDETIYENDGSPI--LLEDKVSNKKEEDVVMKVS 183

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           LR+   +    L  RE+ +L  R+ + M      EE+ ++  +++ ++
Sbjct: 184 LRDEIQK----LDQREQLLLHYRYDLSMKQ----EEIARKLNISQVQV 223


>gi|291537993|emb|CBL11104.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis XB6B4]
          Length = 248

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 115/228 (50%), Gaps = 8/228 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  NL LV ++A ++ +RG +  +L Q G IGLMKA +KFD  L   FSTYA+  
Sbjct: 18  ARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLSLNLAFSTYAVPV 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++  +K  R    +  ++ REP   EIA++  +    +
Sbjct: 78  IMGEIRRFLRDDG-MVKVSRTLKENAYKAGRAKEELWGELGREPGLLEIAERTGLSSGEI 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANL-RETTTRVLASL 620
              ++  ++  S+  P+ ++D   L   D + +K      +   +A L R    +++  L
Sbjct: 137 IMAMESARDVESIYQPVYEKDGDELLMVDQLCEKEENGKDEPEKEAVLNRMVIEQLMELL 196

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ ++R R+      + T  E  K+  +T+ ++ ++E K +  L+
Sbjct: 197 DEREQNLIRCRY----FENRTQSETAKELGMTQVQVSRLEKKILLCLR 240


>gi|325846834|ref|ZP_08169712.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481206|gb|EGC84249.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 256

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 120/230 (52%), Gaps = 18/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY+FS++A   +
Sbjct: 30  RNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGYEFSSFATPTI 89

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D+   IR+P  +++   K+    + +  +++R PT ++IA  L    E + 
Sbjct: 90  MGELKRYFRDKGWVIRVPRRIQNLYKKINVAKKILPQELQRTPTIKDIAAYLGEDEETIL 149

Query: 565 KVLKITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVL 617
           + ++ +K   P SL+        E++  L D I  +DKN     DS    +L E +T  L
Sbjct: 150 ETMEASKVYTPQSLDMKYQVQKGENSVDLSDMIGEDDKN----FDSIELKDLIEKSTERL 205

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L   E+++L +R+  G     T  ++ K+  +++  + +IE K ++K 
Sbjct: 206 NDL---EKQILELRYYEG----RTQVDIAKKLSISQMTVSRIEKKILQKF 248


>gi|291437789|ref|ZP_06577179.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
 gi|291340684|gb|EFE67640.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
          Length = 285

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 108/211 (51%), Gaps = 11/211 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           FR + +++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 75  FRQL-AVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 133

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   + R   D S ++ +P  +++   ++ R    +  ++ R
Sbjct: 134 DRFELSREVEFTSFAIPYIVGEMKRFFRDTSWSVHVPRRLQEARVQLARATEELRTRLGR 193

Query: 546 EPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPL 601
            PT  E+A+ +++  E V   ++        SL+  IG E    S L DFI  ++A   L
Sbjct: 194 TPTTRELAQLMSLTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFIGSEDAALEL 253

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRF 632
                A        ++A L  RE +++  RF
Sbjct: 254 VEDFHA-----LAPMIAELDERERKIIHWRF 279


>gi|1276889|gb|AAC44103.1| stress response/stationary phase sigma factor [Mycobacterium
           tuberculosis H37Rv]
 gi|1589717|prf||2211432A RNA polymerase sigma factor
          Length = 261

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 125/248 (50%), Gaps = 19/248 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +V +   G  E    + ++V+  L L   +A+++  RG    DLIQ   +GL+ AA 
Sbjct: 23  FRELVGLP-AGSPEFQRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKR 545
           +FD   G  F ++A+  +   + R   D S ++++P  +++ +H  + TA   +S ++ R
Sbjct: 82  RFDVKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKE-LHLRLGTATADLSQRLGR 140

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSP 600
            P+  E+A +L M     +EG+  +   +   +S+++  G D+D   + D + D +A   
Sbjct: 141 APSASELAAELGMDRAEVIEGL--LAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA--G 196

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LD   Q   RE    +L +L  RE  VL +RF   M      E VG    +++  + ++ 
Sbjct: 197 LD---QIENREVLRPLLEALPERERTVLVLRFFDSMTQTQIAERVG----ISQMHVSRVL 249

Query: 661 AKAIRKLK 668
           AK++ +L+
Sbjct: 250 AKSLARLR 257


>gi|215432251|ref|ZP_03430170.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           EAS054]
 gi|289755409|ref|ZP_06514787.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis EAS054]
 gi|289695996|gb|EFD63425.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis EAS054]
          Length = 261

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 125/248 (50%), Gaps = 19/248 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +V +   G  E    + ++V+  L L   +A+++  RG    DLIQ   +GL+ AA 
Sbjct: 23  FRELVGLP-AGSPEFQRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKR 545
           +FD   G  F ++A+  +   + R   D S ++++P  +++ +H  + TA   +S ++ R
Sbjct: 82  RFDMKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKE-LHLRLGTATADLSQRLGR 140

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSP 600
            P+  E+A +L M     +EG+  +   +   +S+++  G D+D   + D + D +A   
Sbjct: 141 APSASELAAELGMDRAEVIEGL--LAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA--G 196

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LD   Q   RE    +L +L  RE  VL +RF   M      E VG    +++  + ++ 
Sbjct: 197 LD---QIENREVLRPLLEALPERERTVLVLRFFDSMTQTQIAERVG----ISQMHVSRLL 249

Query: 661 AKAIRKLK 668
           AK++ +L+
Sbjct: 250 AKSLARLR 257


>gi|332096706|gb|EGJ01697.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           3594-74]
          Length = 229

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 98/200 (49%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKL 667
              V   R+ Q+ ++AI++L
Sbjct: 203 VLEVGESRVSQLHSQAIKRL 222


>gi|295840299|ref|ZP_06827232.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295827905|gb|EDY46913.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 121/249 (48%), Gaps = 35/249 (14%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E   A+  ++E N+ LV   A+++ +RG    D++Q G IGL+KA ++F+     +
Sbjct: 50  EGTREFQDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVE 109

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+ ++   I R   D +  + +P  +++   ++ +    +S ++ R P   E+A  
Sbjct: 110 FTTFAVPYIVGEIKRFFRDTTWAVHVPRRLQEARVELAKANEELSTRLGRAPRVSELAAL 169

Query: 556 LAMPVEGV--RKVLKITKEPISLETPIGDEDTSH----LGDFI----------EDKNAVS 599
           + +  + V   ++        SL+  IG ED+      L DFI          ED +A++
Sbjct: 170 MNLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAVLSDFIGADDPGMELVEDLHALA 229

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PL               LA L PR+ ++L +RFG     + T  ++G++  V++  + ++
Sbjct: 230 PL---------------LAGLEPRDRQILELRFG----QELTQAQIGERLGVSQMHVSRL 270

Query: 660 EAKAIRKLK 668
             + +  L+
Sbjct: 271 LNRTLGTLR 279


>gi|94676476|ref|YP_588537.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94219626|gb|ABF13785.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 286

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 138/284 (48%), Gaps = 38/284 (13%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++  +K  N    ++ E  + ++E  H      +G+ EA+   K ++ ++LR VI++A+ 
Sbjct: 17  LEDYVKAANAYPMLTAEEELKLAEKLHY-----QGDIEAA---KLLILSHLRFVINIART 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+   L   DLIQEGNIGLMKA  KF+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 69  YSGYNLPQADLIQEGNIGLMKAVRKFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 128

Query: 523 VHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV------LKITKEPI 574
                +  ++    R++  ++    +   E +AK+L +  + VR++        I  +PI
Sbjct: 129 TTKAQR--RLFFNLRKIKQRLGWFNQEEVEMVAKELGVTSKDVREMESRMAAQDIAFDPI 186

Query: 575 S--------LETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
                    L  PI    +  S   D IE++N      +A + N+       L  L  R 
Sbjct: 187 PNDEVPDKLLMAPILYLQDKGSDFADRIEEQN--WEYHAADKLNI------ALDKLDERS 238

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++  R+    N   TL+++  ++ V+ ERIRQ+E  A++K++
Sbjct: 239 KNIIAARW--LDNKKSTLQDLANKYGVSAERIRQLEKNAMKKIR 280


>gi|72161738|ref|YP_289395.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915470|gb|AAZ55372.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 308

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 115/235 (48%), Gaps = 15/235 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A I + E+V   + LV   A++Y NRG    DL Q G +GLMKA + FD   G  F 
Sbjct: 80  ETSARI-RDELVRLYMPLVRREARRYRNRGEPMDDLYQVGMLGLMKAIKGFDPSYGKPFV 138

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            Y +  V   + R   D +  +R+P   +++  ++ R     + K  R PT  EIA  L 
Sbjct: 139 AYLLPMVTGELKRHFRDTTWAVRVPRVHQERRSELNRVIAEFTQKHGRTPTTREIADALE 198

Query: 558 MPVEGVRKVLKITK--EPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           M +E   +++  +     +SL+TP GD ED S LGD       +   D  ++  + +T+ 
Sbjct: 199 MDLESAIELIDASSAYSALSLDTPFGDTEDESALGD------TLGVADGDLETVVDKTSL 252

Query: 615 R-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  L  RE RV+ +RF      + T  E+     +++  + ++ ++ +R+L+
Sbjct: 253 KDALDRLPERERRVILLRF----FGNKTQSEIAADVGLSQMHVSRLLSQTLRQLR 303


>gi|82543610|ref|YP_407557.1| flagellar biosynthesis sigma factor [Shigella boydii Sb227]
 gi|81245021|gb|ABB65729.1| alternative sigma factor 28 [Shigella boydii Sb227]
 gi|320176074|gb|EFW51142.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae CDC 74-1112]
 gi|320184751|gb|EFW59543.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           CDC 796-83]
          Length = 239

 Score = 74.7 bits (182), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 98/200 (49%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKL 667
              V   R+ Q+ ++AI++L
Sbjct: 213 VLEVGESRVSQLHSQAIKRL 232


>gi|198284457|ref|YP_002220778.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667652|ref|YP_002427124.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198248978|gb|ACH84571.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519865|gb|ACK80451.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 286

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 118/237 (49%), Gaps = 20/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K++V ++LR V+ VA+ Y   GLQ  DLIQEGNIGLMKA +++D   G +  ++A+ W
Sbjct: 50  AAKDLVLSHLRFVVRVARGYRGYGLQEADLIQEGNIGLMKAVKRYDPDHGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPE-----EIAKKLA 557
           VK  I   I      +++     + K+   +R++R  +  +  E +        + +   
Sbjct: 110 VKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSSRSHTGWMSGEESAAMADDLGVTQAQV 169

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-- 615
           + +EG     +++    SL     +E        + D    SP++  ++ +  +   R  
Sbjct: 170 LEMEG-----RMSGYDYSLNLEPDEEREGGRAPDLADPTG-SPIEQLVERDWDQQQHRAL 223

Query: 616 --VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              L++L  R+  ++  R+   ++ D  TL+ +G +  V+ ER+RQ+E  ++ KL+ 
Sbjct: 224 HTALSALPQRDRYIIENRW---LSDDPKTLQVLGDELGVSAERVRQLEKSSMGKLRQ 277


>gi|138894766|ref|YP_001125219.1| RNA polymerase sigma factor SigD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247611|ref|ZP_03146313.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
 gi|134266279|gb|ABO66474.1| RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           thermodenitrificans NG80-2]
 gi|196212395|gb|EDY07152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
          Length = 253

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 96/199 (48%), Gaps = 11/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  +RDK+ K
Sbjct: 57  ELVSLGLVGLYDALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSVRDKVKK 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLG 589
           +  TA R+  +  R  T +E+A +L M  E V+  +  T     +SL     +ED   L 
Sbjct: 114 IEETAERLEQRYMRSVTAKEVAAELGMTEEEVQAAVNETFFSNWLSLGQTACEEDDEPLA 173

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D  AV P +  ++  + E     +  L  +E+ V+ + +      + T  E+G   
Sbjct: 174 --IRDDRAVLPEEQVVKQEMIEKLAVGIGQLNEKEQLVISLFY----KEELTFTEIGSIL 227

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++  RI QI AKA+ KL+
Sbjct: 228 QLSTSRISQIHAKALWKLR 246


>gi|114566161|ref|YP_753315.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114337096|gb|ABI67944.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 243

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 120/249 (48%), Gaps = 15/249 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S S +++  +++R  +     AK ++ EAN+ L+  V +++ N      DL Q G +GL+
Sbjct: 3   SSSSYQNNEALLRLAQGGDQEAKAQLYEANVGLIYLVLERFKNTSYDQEDLFQVGAMGLL 62

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA E+FD+    +FSTYA+  +   I + + D    +++   +++   +V     ++   
Sbjct: 63  KAIERFDFSFDVRFSTYAVPMIIGEIKKFLRDDGM-VKVQRGIKELYARVRWAQDKLRGD 121

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED---TSHLGDFIEDKNAVS 599
           + REP   EIA  L M  E +   ++  + P  +   +  E+    S L   + ++  V+
Sbjct: 122 LGREPGVNEIASLLEMEKEDIVVAMEACQAPAYIHDVVPSEEKEQLSLLDKLVHEEGNVA 181

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L+   +  LRE     LA L  RE  V+  RF      D T   + +   V++ +I +I
Sbjct: 182 ILE---KLALREA----LAKLDERERVVIIRRF----FQDETQTVIAEDLGVSQVQISRI 230

Query: 660 EAKAIRKLK 668
           E  AI KL+
Sbjct: 231 EKSAILKLR 239


>gi|325523159|gb|EGD01550.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 126

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/125 (32%), Positives = 68/125 (54%)

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P+  V  ++ I +EP+S + P+  +     G+ + D+    P D+A    LR     
Sbjct: 1   MDLPLAKVLDLMAIVREPVSTDVPVSPDGDMTFGEVVPDQATPLPEDAAAATQLRAAMAA 60

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L  RE  VLR+R+GIG     +L ++G+Q  ++ ER+RQIEA A+ +++       
Sbjct: 61  TLGGLPAREATVLRLRYGIGTADGVSLRDIGRQLNLSAERVRQIEASALERIRASGALHG 120

Query: 676 LRSFL 680
           LRSF+
Sbjct: 121 LRSFM 125


>gi|291545019|emb|CBL18128.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 220

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/197 (28%), Positives = 98/197 (49%), Gaps = 10/197 (5%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E NL LV   A ++  RG+++ DL   G IGLMKA   FD   G +FSTYA+  +   I 
Sbjct: 11  EENLGLVHLCANRFRGRGVEYDDLYSAGCIGLMKAVNAFDTERGVRFSTYAVPVILGEIK 70

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R   D   T+++   M++   +VVR    +  +  +EPT +++A+++ +    + + L +
Sbjct: 71  RLFRDGG-TVKVSRSMKELSMRVVRLRDELRMQSGKEPTVQQLAREMGVEEAEIVQALCV 129

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +  P+SL  P G+     L D       V P D+ I   L     +++ +L+ R+  +L 
Sbjct: 130 SVPPVSLTDP-GESGEGQL-DI-----PVPPPDTEIGDVL--ALRQIMQTLSERDRMLLT 180

Query: 630 MRFGIGMNTDHTLEEVG 646
           MR+        T + +G
Sbjct: 181 MRYYQNKTQSQTAQALG 197


>gi|229542547|ref|ZP_04431607.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
 gi|229326967|gb|EEN92642.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
          Length = 259

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 122/230 (53%), Gaps = 14/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V    +LV S+A+KY+       D+ Q G IGL+ A ++FD  +G  F ++A+  
Sbjct: 27  AQEILVAHYQKLVESLARKYSKGRAYQEDIFQVGIIGLLGAIQRFDPNIGKSFESFAIPT 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   ++  T  +++N+++R P   EIA  L +  E V
Sbjct: 87  IIGEIKRFLRDKTWSVHVPRRIKELGPRIKSTVEKLTNELQRSPKIAEIAAHLEISEEEV 146

Query: 564 RKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++++K    +S++  I    D  T  L D +  ++     D   + N R    +VL 
Sbjct: 147 LEAMEMSKSYHALSVDHSIESDSDGSTVTLLDMVGSED-----DGYEKVNQRLVLEKVLH 201

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ RE +V+   +   ++   T E++G    +++  + +++ +AI+KL+
Sbjct: 202 VLSERERQVIHYTYIENLSQKDTGEKLG----ISQMHVSRLQRRAIKKLR 247


>gi|5911749|emb|CAB55833.1| SigJ protein [Streptomyces coelicolor A3(2)]
          Length = 266

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/247 (23%), Positives = 128/247 (51%), Gaps = 14/247 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 22  FFEQLTVLEEGTPEHQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 81

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 82  DRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVQLARATEELRSRLGR 141

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPI-GDEDT-SHLGDFIEDKNAVSPL 601
            PT  E+++ +++P + V   ++        SL+  I G ED  S L DFI   +A   L
Sbjct: 142 TPTTAELSELMSLPEDEVVEARLAANGYNSASLDAAINGSEDGESALADFIGADDAALAL 201

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  R+ +++  RF      + T +++G++  V++  + ++ +
Sbjct: 202 VDDFHA-----LAPMIAELDERDRQIIHWRF----VEELTQKDIGERLGVSQMHVSRLIS 252

Query: 662 KAIRKLK 668
           + + +L+
Sbjct: 253 RLLARLR 259


>gi|253990087|ref|YP_003041443.1| flagellar biosynthesis sigma factor [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253781537|emb|CAQ84700.1| rna polymerase sigma factor for flagellar operon (sigma-f factor
           (sigma-27) (sigma-28) [Photorhabdus asymbiotica]
          Length = 244

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 102/201 (50%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 47  DLLQAGGIGLLNAVERFDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +T R++   + R  + +E+AK+L + +   R++L  T           DE     G+ 
Sbjct: 104 VTQTIRKLEQDLGRPASEQEVAKELKIDLVEYRQILLDTNNSQLFSY---DEWHEMHGES 160

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               IE+ +  +PL   +++++R+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 161 CEPVIEEGHETNPLQQLLESDVRQRVIDAIDSLPEREKMVLTLYYQEELN----LKEIGA 216

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   RI Q+ ++AI++L+
Sbjct: 217 VLEVGESRISQLHSQAIKRLR 237


>gi|294669660|ref|ZP_06734727.1| hypothetical protein NEIELOOT_01561 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308573|gb|EFE49816.1| hypothetical protein NEIELOOT_01561 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 146

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 51/141 (36%), Positives = 80/141 (56%), Gaps = 16/141 (11%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           E ED +  L  +      +++I   + RGY+T  E+N  LP D   +EQ+++ V M+  +
Sbjct: 9   EQEDDNRPLTAEEQRARLRQLILQGKDRGYITYAEINDALPDDMSDAEQIDNIVNMIQGL 68

Query: 74  GINVV----DGDDL-EDEEGS----EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           GI V     D D L  ++ G+    +D+++ A +A +++       DS    T DPVRMY
Sbjct: 69  GIQVTEEAPDADSLLMNDSGTGMTDDDAVEEAEAALSNA-------DSEFGRTTDPVRMY 121

Query: 125 LREMGSIELLSREGEIAIAKR 145
           +REMG +ELL+RE EI IAK+
Sbjct: 122 MREMGQVELLTREDEIIIAKK 142


>gi|116694211|ref|YP_728422.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
 gi|113528710|emb|CAJ95057.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
          Length = 238

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 117/243 (48%), Gaps = 20/243 (8%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +  + + ++V+A+ +LV  +A +   R    +Q  DLIQ G IGL+ AA++++   G +F
Sbjct: 5   QGKLEQADVVKAHAQLVRRIALQLAARLPASVQIDDLIQAGMIGLLDAAKRYEDTHGARF 64

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA   ++ A+   +       R    +R    ++ RT R +  K+ R P   E+A+ +
Sbjct: 65  ETYASQRIRGAMLDEVRANDWQSR---SLRQFTRRIERTQRGLEQKLGRAPLDSEVAEAM 121

Query: 557 AMPVEGVRKVLKITKEPISLETP----IGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR 610
            M ++  + +L        L        G+ED    HLG   +D N   PL   +++ +R
Sbjct: 122 EMALDEYQLLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGS-DDGN---PLTVLMESGMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   R +  L  RE+ VL + +   +N    L E+G    VT  R+ QI  +AI +L++ 
Sbjct: 178 EALIRAIDRLPEREKLVLSLCYDQELN----LREIGAVLDVTESRVCQIRGQAITRLRNQ 233

Query: 671 SRS 673
            R 
Sbjct: 234 LRG 236


>gi|157692327|ref|YP_001486789.1| RNA polymerase sigma factor SigD [Bacillus pumilus SAFR-032]
 gi|157681085|gb|ABV62229.1| DNA-directed RNA polymerase sigma subunit D [Bacillus pumilus
           SAFR-032]
          Length = 255

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 98/201 (48%), Gaps = 10/201 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 54  DLISLGMLGLYDALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGD-EDTSHL 588
           V     ++  +  R  TP E+A++L M  + V   +        +S++  + D ED  ++
Sbjct: 111 VEAAIEKLEQRYLRNVTPTEVAEELGMSEQDVVTTMNEGFFANLLSIDEKLHDQEDGENV 170

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D+  V+P +  ++  L E     +  L+ +E+ V+ + +      + TL E+G  
Sbjct: 171 QVMIRDEKTVTPEEKMLKDELIEQLAEKMTELSEKEKLVISLFY----KEELTLTEIGHV 226

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  RI QI +KA+ KLKH
Sbjct: 227 LNLSTSRISQIHSKALFKLKH 247


>gi|188495466|ref|ZP_03002736.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|293415233|ref|ZP_06657876.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|331647515|ref|ZP_08348607.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
 gi|188490665|gb|EDU65768.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|281178984|dbj|BAI55314.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE15]
 gi|291432881|gb|EFF05860.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|330911730|gb|EGH40240.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           AA86]
 gi|331043239|gb|EGI15377.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
          Length = 239

 Score = 74.3 bits (181), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   +  NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDNNLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|15610422|ref|NP_217803.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Rv]
 gi|15842877|ref|NP_337914.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           CDC1551]
 gi|31794466|ref|NP_856959.1| RNA polymerase sigma factor SigF [Mycobacterium bovis AF2122/97]
 gi|121639175|ref|YP_979399.1| RNA polymerase sigma factor SigF [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148663149|ref|YP_001284672.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|148824488|ref|YP_001289242.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis F11]
 gi|167968918|ref|ZP_02551195.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|215405299|ref|ZP_03417480.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           02_1987]
 gi|215413164|ref|ZP_03421865.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           94_M4241A]
 gi|215428770|ref|ZP_03426689.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T92]
 gi|215447591|ref|ZP_03434343.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|218755069|ref|ZP_03533865.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis GM
           1503]
 gi|219559346|ref|ZP_03538422.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T17]
 gi|224991668|ref|YP_002646357.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253800329|ref|YP_003033330.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           1435]
 gi|254233896|ref|ZP_04927221.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis C]
 gi|254365909|ref|ZP_04981954.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis str. Haarlem]
 gi|254552388|ref|ZP_05142835.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260188335|ref|ZP_05765809.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|260202448|ref|ZP_05769939.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T46]
 gi|260206638|ref|ZP_05774129.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis K85]
 gi|289444868|ref|ZP_06434612.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T46]
 gi|289448975|ref|ZP_06438719.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|289555564|ref|ZP_06444774.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           605]
 gi|289571513|ref|ZP_06451740.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T17]
 gi|289576006|ref|ZP_06456233.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis K85]
 gi|289747104|ref|ZP_06506482.1| sigma factor SigF [Mycobacterium tuberculosis 02_1987]
 gi|289751981|ref|ZP_06511359.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T92]
 gi|289759427|ref|ZP_06518805.1| sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|289763474|ref|ZP_06522852.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis GM 1503]
 gi|294993773|ref|ZP_06799464.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis 210]
 gi|297635940|ref|ZP_06953720.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           4207]
 gi|297732937|ref|ZP_06962055.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           R506]
 gi|298526762|ref|ZP_07014171.1| sigma factor SigF [Mycobacterium tuberculosis 94_M4241A]
 gi|306777615|ref|ZP_07415952.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu001]
 gi|306782337|ref|ZP_07420674.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu002]
 gi|306786159|ref|ZP_07424481.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu003]
 gi|306790527|ref|ZP_07428849.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu004]
 gi|306795048|ref|ZP_07433350.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu005]
 gi|306799245|ref|ZP_07437547.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu006]
 gi|306805094|ref|ZP_07441762.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu008]
 gi|306809281|ref|ZP_07445949.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu007]
 gi|306969383|ref|ZP_07482044.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu009]
 gi|306973735|ref|ZP_07486396.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu010]
 gi|307081445|ref|ZP_07490615.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu011]
 gi|307086048|ref|ZP_07495161.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu012]
 gi|313660269|ref|ZP_07817149.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           V2475]
 gi|5917771|gb|AAD56032.1|AF181975_3 sigma factor SigF [Mycobacterium bovis]
 gi|1877341|emb|CAB07069.1| ALTERNATE RNA POLYMERASE SIGMA FACTOR SIGF [Mycobacterium
           tuberculosis H37Rv]
 gi|13883208|gb|AAK47728.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis CDC1551]
 gi|31620062|emb|CAD95406.1| PROBABLE RNA POLYMERASE SIGMA FACTOR SIGF [Mycobacterium bovis
           AF2122/97]
 gi|121494823|emb|CAL73304.1| Probable rna polymerase sigma factor sigF [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|124599425|gb|EAY58529.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis C]
 gi|134151422|gb|EBA43467.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis str. Haarlem]
 gi|148507301|gb|ABQ75110.1| sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|148723015|gb|ABR07640.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis F11]
 gi|224774783|dbj|BAH27589.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253321832|gb|ACT26435.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           1435]
 gi|289417787|gb|EFD15027.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T46]
 gi|289421933|gb|EFD19134.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|289440196|gb|EFD22689.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           605]
 gi|289540437|gb|EFD45015.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis K85]
 gi|289545267|gb|EFD48915.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T17]
 gi|289687632|gb|EFD55120.1| sigma factor SigF [Mycobacterium tuberculosis 02_1987]
 gi|289692568|gb|EFD59997.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T92]
 gi|289710980|gb|EFD74996.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis GM 1503]
 gi|289714991|gb|EFD79003.1| sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|298496556|gb|EFI31850.1| sigma factor SigF [Mycobacterium tuberculosis 94_M4241A]
 gi|308214036|gb|EFO73435.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu001]
 gi|308325087|gb|EFP13938.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu002]
 gi|308329308|gb|EFP18159.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu003]
 gi|308333139|gb|EFP21990.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu004]
 gi|308336826|gb|EFP25677.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu005]
 gi|308340659|gb|EFP29510.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu006]
 gi|308344393|gb|EFP33244.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu007]
 gi|308348397|gb|EFP37248.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu008]
 gi|308353234|gb|EFP42085.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu009]
 gi|308356974|gb|EFP45825.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu010]
 gi|308360831|gb|EFP49682.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu011]
 gi|308364515|gb|EFP53366.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu012]
 gi|323718155|gb|EGB27337.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CDC1551A]
 gi|326902486|gb|EGE49419.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis W-148]
 gi|328460063|gb|AEB05486.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           4207]
          Length = 261

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 125/248 (50%), Gaps = 19/248 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +V +   G  E    + ++V+  L L   +A+++  RG    DLIQ   +GL+ AA 
Sbjct: 23  FRELVGLP-AGSPEFQRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKR 545
           +FD   G  F ++A+  +   + R   D S ++++P  +++ +H  + TA   +S ++ R
Sbjct: 82  RFDVKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKE-LHLRLGTATADLSQRLGR 140

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSP 600
            P+  E+A +L M     +EG+  +   +   +S+++  G D+D   + D + D +A   
Sbjct: 141 APSASELAAELGMDRAEVIEGL--LAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA--G 196

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LD   Q   RE    +L +L  RE  VL +RF   M      E VG    +++  + ++ 
Sbjct: 197 LD---QIENREVLRPLLEALPERERTVLVLRFFDSMTQTQIAERVG----ISQMHVSRLL 249

Query: 661 AKAIRKLK 668
           AK++ +L+
Sbjct: 250 AKSLARLR 257


>gi|317121837|ref|YP_004101840.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591817|gb|ADU51113.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 97/201 (48%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GLM+A  ++D   G KF TYA   ++ A+   +        +P  +R +   
Sbjct: 57  DLISYGIFGLMEAIRRYDPARGVKFETYAYTRIRGAMLDGLRAMDW---VPQTLRRRARD 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE--TPIGDEDTSH 587
           V    RR+ N++ R    +E+A +L +  E    +L+       +SL+   P   +D + 
Sbjct: 114 VEACYRRLENRLGRPANDDEVAAELGLKPEEFAGLLQELARTTVVSLDDVLPSDSDDPAA 173

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D  A  PL +A  A+LR      LA L  RE  V+ + +  G+    T++E+ +
Sbjct: 174 VLDRLADPGATDPLQAATLADLRRRLADALAGLPERERLVVSLYYYEGL----TVKEIAE 229

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ Q+  +AI +L+
Sbjct: 230 VMGVSPSRVSQLHTRAILRLR 250


>gi|224477054|ref|YP_002634660.1| RNA polymerase sigma factor SigB [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421661|emb|CAL28475.1| sigma factor B [Staphylococcus carnosus subsp. carnosus TM300]
          Length = 256

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 123/238 (51%), Gaps = 14/238 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD   G KF  +
Sbjct: 27  ENTDAQDKLVKHYQKLIESLAFKYSKGQSHHEDLVQVGMVGLIGAINRFDINFGRKFEAF 86

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            +  V   I R + D++ ++ +P  +++   ++ +T   ++N+++R P+  EIA++L + 
Sbjct: 87  LVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKTTDELTNELERSPSISEIAERLEVT 146

Query: 560 VEGVRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            E V + +++ +    +S++  I    D  T  L D + ++     L        R    
Sbjct: 147 DEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGEQEGGYDLTEK-----RMILE 201

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           R+L  LT RE  +++  F  G++   T E +G    +++  + +++  AI+KL+  ++
Sbjct: 202 RILPILTDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRNAIKKLQQAAK 255


>gi|329735692|gb|EGG71975.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU028]
          Length = 256

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 123/243 (50%), Gaps = 20/243 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKH 669
               R+L  L+ RE ++++  F  G++   T E +G  Q  V+R     ++  AI+KL+ 
Sbjct: 198 MILERILPILSERERQIIQCTFIEGLSQKETGERIGLSQMHVSR-----LQRTAIKKLQE 252

Query: 670 PSR 672
            +R
Sbjct: 253 AAR 255


>gi|149177082|ref|ZP_01855690.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148844147|gb|EDL58502.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 556

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 50/73 (68%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E++  K  ++ +NLRLV+S+AK++   G  F +++ +GN+ L++A EKFD+  G KFSTY
Sbjct: 373 ESTDVKNFLIRSNLRLVVSIAKRHIRPGGNFFEMVSDGNMSLIRAIEKFDYTKGNKFSTY 432

Query: 500 AMWWVKQAITRSI 512
           A W + +   RSI
Sbjct: 433 ASWAIMKNYARSI 445



 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 39/54 (72%), Gaps = 1/54 (1%)

Query: 616 VLASLTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L  L  RE+ +L  R+G+   N   TLE+VG +F VT+ERIRQ+E++A++KL+
Sbjct: 490 ILDQLDGREKDILIYRYGLNARNEPQTLEQVGDRFGVTKERIRQLESRALKKLR 543


>gi|146344354|ref|YP_001202210.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
 gi|146188166|emb|CAM96497.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
          Length = 533

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/200 (30%), Positives = 108/200 (54%), Gaps = 19/200 (9%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
            N+GL +A  +F   +G++FST A+ W+  +I+R +ADQ  +IR+P  M    HK     
Sbjct: 330 ANMGLTRAVYRFAPEMGFRFSTIALTWINVSISRDLADQE-SIRLPEGM----HK----H 380

Query: 537 RRM-SNKIKREP--TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGD 590
           RRM SN ++ +P  +   +A+   +  + VR ++       S++T     D+S    L +
Sbjct: 381 RRMISNMLRDQPNVSINSLAEATKLEQDVVRDLVHFAGGQRSIDTAFQGTDSSDADGLHE 440

Query: 591 FIEDKNAVSPLDSAIQAN-LRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + D N  +   S I+ + +R+     L   LT RE  V+  RFG+G   + TL E+  +
Sbjct: 441 LLADTN--NDFMSEIEDDSMRQFVESALGDVLTQREIFVIVNRFGMGDAREKTLAELSVE 498

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ER+RQ+E +A+ K++
Sbjct: 499 MNLSKERVRQLEIQALSKIR 518


>gi|17226799|gb|AAL37943.1|AF359562_4 SigB [Staphylococcus epidermidis]
          Length = 256

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 123/243 (50%), Gaps = 20/243 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKH 669
               R+L  L+ RE ++++  F  G++   T E +G  Q  V+R     ++  AI+KL+ 
Sbjct: 198 MILERILPILSERERQIIQCTFIEGLSQKETGERIGLSQMHVSR-----LQRTAIKKLQE 252

Query: 670 PSR 672
            +R
Sbjct: 253 AAR 255


>gi|253688938|ref|YP_003018128.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251755516|gb|ACT13592.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 240

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++   ++ R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAQAMQQAEQQLGRTPTEQEVAQALNITLEDYRQILLDTNNSQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL   ++ NLR      + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEDANPLHQLMEGNLRHRVMDAIESLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|120402666|ref|YP_952495.1| RNA polymerase sigma factor SigF [Mycobacterium vanbaalenii PYR-1]
 gi|119955484|gb|ABM12489.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 262

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 66/254 (25%), Positives = 121/254 (47%), Gaps = 22/254 (8%)

Query: 426 EFRHIVSMVRK-GECEASIA-----KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           E+  +  M R+  E E   A     +  +VE  L L   +A+++  RG    DL+Q   +
Sbjct: 16  EYADVAPMFRELAELEEGTAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARV 75

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A  +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +
Sbjct: 76  GLVNAVIRFDVNAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAEL 135

Query: 540 SNKIKREPTPEEIAKKLAM----PVEGVRKVLKITKEPISLET-PIGDEDTSHLGDFIED 594
           S ++ R PT  E+A +L M     VEG+  V   +   +S+++   G+ED   + D + D
Sbjct: 136 SQRLGRAPTATELAAELEMDRDEVVEGL--VAGSSYNTLSIDSGGSGNEDAPAIADTLGD 193

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +      S  Q   RE    +LA+L  RE  VL +RF   M      E VG    +++ 
Sbjct: 194 VDL-----SLDQIENREALRPLLAALPERERTVLALRFFESMTQTQIAERVG----ISQM 244

Query: 655 RIRQIEAKAIRKLK 668
            + ++ AK++ +L+
Sbjct: 245 HVSRLLAKSLARLR 258


>gi|331657967|ref|ZP_08358929.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
 gi|331056215|gb|EGI28224.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
          Length = 239

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     +  L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIEMLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|329896515|ref|ZP_08271573.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
 gi|328921732|gb|EGG29105.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
          Length = 286

 Score = 74.3 bits (181), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 123/234 (52%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V ++LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W
Sbjct: 50  AARQLVMSHLRFVVHIARSYSGYGLAEADLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  +   I      +++     + K+   +R++++    +  E   + +A  L + V  
Sbjct: 110 IKAEMHEFILRNWRIVKVATTKAQRKLFFNLRSSKKALAWLSAEEA-QAVADDLGVDVRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLRE-TTTRVLA 618
           V  +  +++   ++ + P   +D        ++ED  A  P       N +E + +R+  
Sbjct: 169 VATMEARMSSRDVAFDAPSDSDDDDVYAPQYYLEDHRA-DPAQQVESTNWQEDSESRLHY 227

Query: 619 SLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   +ER   +L  R+   +N +  TL ++  Q+ V+ ERIRQ+E  A++K++
Sbjct: 228 ALEQLDERSRDILAQRW---LNDEKATLHDLAAQYGVSAERIRQLEQNAMQKVR 278


>gi|240171602|ref|ZP_04750261.1| RNA polymerase sigma factor SigF [Mycobacterium kansasii ATCC
           12478]
          Length = 262

 Score = 73.9 bits (180), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 114/233 (48%), Gaps = 23/233 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++VE  L L   +A+++  RG    DLIQ   +GL+ A  +FD   G  F ++A+  +
Sbjct: 40  RDKIVERCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAVVRFDVETGSDFVSFAVPTI 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----V 560
              + R   D S ++++P  +++   ++      +S ++ R PT  E+A +L M     V
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHLRLGTATAELSQRLGRAPTATELAAELGMDRGEVV 159

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-----RETTTR 615
           EG+  V   +   +S+++  G+ED        +D  A++     + A L     RE+   
Sbjct: 160 EGL--VAGSSYNTLSIDSGGGNED--------DDARAIADTLGDMDAGLDRIEDRESLRP 209

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L +L  RE  VL +RF   M      E VG    +++  + ++ AK++ +L+
Sbjct: 210 LLEALPERERTVLILRFFESMTQTQIAERVG----ISQMHVSRLLAKSLARLR 258


>gi|21219133|ref|NP_624912.1| RNA polymerase sigma factor sig8 [Streptomyces coelicolor A3(2)]
 gi|256789847|ref|ZP_05528278.1| RNA polymerase sigma factor sig8 [Streptomyces lividans TK24]
 gi|289773730|ref|ZP_06533108.1| SigB [Streptomyces lividans TK24]
 gi|6670923|gb|AAF23070.1|AF068267_4 SigB [Streptomyces coelicolor A3(2)]
 gi|6448735|emb|CAB61294.1| RNA polymerase sigma factor sig8 [Streptomyces coelicolor A3(2)]
 gi|289703929|gb|EFD71358.1| SigB [Streptomyces lividans TK24]
          Length = 281

 Score = 73.9 bits (180), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 57/247 (23%), Positives = 128/247 (51%), Gaps = 14/247 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG + + D++Q G IGL+KA 
Sbjct: 37  FFEQLTVLEEGTPEHQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 97  DRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVQLARATEELRSRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPI-GDEDT-SHLGDFIEDKNAVSPL 601
            PT  E+++ +++P + V   ++        SL+  I G ED  S L DFI   +A   L
Sbjct: 157 TPTTAELSELMSLPEDEVVEARLAANGYNSASLDAAINGSEDGESALADFIGADDAALAL 216

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  R+ +++  RF      + T +++G++  V++  + ++ +
Sbjct: 217 VDDFHA-----LAPMIAELDERDRQIIHWRF----VEELTQKDIGERLGVSQMHVSRLIS 267

Query: 662 KAIRKLK 668
           + + +L+
Sbjct: 268 RLLARLR 274


>gi|304398826|ref|ZP_07380696.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308187260|ref|YP_003931391.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
 gi|304353530|gb|EFM17907.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308057770|gb|ADO09942.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
          Length = 240

 Score = 73.9 bits (180), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 96/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     R+   + R  + +E+A++L + +E  R++L  T           DE     GD 
Sbjct: 100 VAGAMHRVEQSLGRSASEQEVAQQLNVSMEEYRQILLDTNNSQLFSY---DEYREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ +LRE     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AELVTEGHEEANPLHQLLEGSLRERVIEAIEALPDREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLDVGESRVSQLHSQAIKRLR 233


>gi|262204122|ref|YP_003275330.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily [Gordonia
           bronchialis DSM 43247]
 gi|262087469|gb|ACY23437.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily [Gordonia
           bronchialis DSM 43247]
          Length = 276

 Score = 73.9 bits (180), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 116/244 (47%), Gaps = 15/244 (6%)

Query: 426 EFRHIVSMVRKGECE---ASIAKK--EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           ++  +V+ +R+   E   A+ AKK   ++E  L L   VA ++++RG  F DL+Q   IG
Sbjct: 24  DYADVVAALRELSAETDAAAHAKKRDNIIERCLPLAEHVAWRFSDRGEPFDDLLQVARIG 83

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           ++ A ++FD   G  F ++A+  V   + R   D    IR+P   ++    + +    + 
Sbjct: 84  VVNAVDRFDGERGDSFLSFAVPTVMGEVRRHFRDSMWAIRVPRRAKETSLSIGKATDELV 143

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNA- 597
            ++ R P P E+A  L +PV+ V   L  +   +  S++    D+D   + D + D +A 
Sbjct: 144 QRLGRSPRPSELAAHLGLPVDEVIDGLLARSAYQARSIDATPEDDDGRSIRDTLGDDDAR 203

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERI 656
           ++ +D  +      T   VL  L  RE  ++ +RF   M+       VG  Q  V+R   
Sbjct: 204 LAQIDEFV------TLRPVLDQLPDREREIVTLRFFHAMSQSEIAARVGISQMHVSRLLS 257

Query: 657 RQIE 660
           R +E
Sbjct: 258 RTLE 261


>gi|332970514|gb|EGK09503.1| RNA polymerase sigma factor SigB [Desmospora sp. 8437]
          Length = 261

 Score = 73.9 bits (180), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 122/225 (54%), Gaps = 18/225 (8%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV ++A K+T     F DL+Q G IGL+ A +++D   G  F ++A+  +   I R I D
Sbjct: 41  LVETLASKFTKGSEPFEDLVQVGMIGLLAALKRYDPDFGKSFESFAVPTIVGEIKRHIRD 100

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   ++ + A  ++ + +R P+ +EIA+ L +  E V + +++ +   
Sbjct: 101 KTWSVHVPRRIKELGPRIKKAAEELTIRYQRSPSVDEIAQYLDVTPEEVLETMEMGRSYN 160

Query: 573 PISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +S+++PI     G + T  L D + +++A    +   Q  L +   +V   LT RE+ +
Sbjct: 161 AVSVDSPIEANNEGSQVT--LLDLVGNRDA--GFEKVDQQLLLQKAFQV---LTDREQAI 213

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +RM F   ++     ++VG +  +++  + +++ +A+ KL+   R
Sbjct: 214 IRMTFFDNLSQ----KQVGDELGISQMHVSRLQRRALGKLREAIR 254


>gi|223986127|ref|ZP_03636150.1| hypothetical protein HOLDEFILI_03458 [Holdemania filiformis DSM
           12042]
 gi|223961932|gb|EEF66421.1| hypothetical protein HOLDEFILI_03458 [Holdemania filiformis DSM
           12042]
          Length = 241

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 126/247 (51%), Gaps = 22/247 (8%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKA 484
           EF  ++   ++G+ +A   +++ V  N+ LV S+  ++ T+   Q  DL Q G +GLMKA
Sbjct: 6   EFFDLLHQAQQGDEQA---REQCVLRNVGLVWSIVNRFKTHSSAQ--DLFQIGCLGLMKA 60

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              FD      FSTYA+  +   I R   D+   ++I   ++++  +V ++  R++ K++
Sbjct: 61  INNFDTSYNVMFSTYAVPIILGEIKRYFRDEG-QMKISRSLKERYLQVQKSRERLAQKLQ 119

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVS-PL 601
           REPT  EI + L +    V   ++  +   S++     +D  T  L D +ED++    P+
Sbjct: 120 REPTYREIGEDLGVEENDVMLAMEANQFLASMDEAFYQKDGSTIKLEDKVEDRHGEDVPM 179

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             A++        + +  L  RE+ ++ +R+ +  N     E + K+  +++ ++ ++E 
Sbjct: 180 KLALK--------KEIGHLEQREQYLIYLRYELEYNQ----EAIAKKMGISQVQVSRLEK 227

Query: 662 KAIRKLK 668
           K + KLK
Sbjct: 228 KILNKLK 234


>gi|304316787|ref|YP_003851932.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778289|gb|ADL68848.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 247

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 111/241 (46%), Gaps = 37/241 (15%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++RK +    ++ +++++ N  L+ S+ KK++NRG +  DL Q G IG +KA  KFD   
Sbjct: 15  LIRKSKNNDKLSLEKLLKENSGLIWSIVKKFSNRGYEAEDLYQIGCIGFVKAINKFDESY 74

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K STYA+  +   I R + D    I++   +++  +K       +  ++ REPT +EI
Sbjct: 75  NVKLSTYAVPIILGEIKRFLRDDGL-IKVSRSLKELSNKAYYIKDELEKELNREPTIQEI 133

Query: 553 AKKLAMPVEGVRKVLKITK--------------EPISLETPIGDEDTSHLGDFIEDKNAV 598
           A KL +  E +    + T               + + L   IG ED  +    IEDK A+
Sbjct: 134 ASKLNVSAEEIAMAFESTATAEYLYDNSQHSEDDNMLLIEKIGSEDNEY---DIEDKLAL 190

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                            VL  L  RE +++ +R+      D T  EV K   +++ ++ +
Sbjct: 191 RM---------------VLKKLDSRERQIIVLRYF----KDMTQTEVSKILGISQVQVSR 231

Query: 659 I 659
           I
Sbjct: 232 I 232


>gi|317048579|ref|YP_004116227.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Pantoea sp.
           At-9b]
 gi|316950196|gb|ADU69671.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           At-9b]
          Length = 240

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 95/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  T +E+A +L + +E  R++L  T           DE     GD 
Sbjct: 100 VAGAMHQVEQAMGRAATEQEVADQLNVSLEEYRQILLDTNNSQLFSY---DEYREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ NLRE     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AELVTEGHEEANPLHQLMEGNLRERVIEAIEALPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|256392583|ref|YP_003114147.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256358809|gb|ACU72306.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 262

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 51/214 (23%), Positives = 106/214 (49%), Gaps = 13/214 (6%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VA ++  RG    DL Q   +GL+KA + FD   G  F TYA   +   + R   D +  
Sbjct: 52  VAGRFRQRGESQADLEQVAYLGLVKAVDNFDPDYGAAFLTYATPMIAGEVRRHFRDTTWD 111

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISL 576
           + +P  +++    V    R ++ ++   P+  +IA++L +  + V +  + +      SL
Sbjct: 112 VHVPRRVQENALAVRAAERELTQQLGHAPSAAQIAERLDLSADEVAEAYEASAAHHTASL 171

Query: 577 ETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           + P+   D D + +G+ + D +     D  +    RE    +LA L+PR++R+L M+F  
Sbjct: 172 DVPVAMADGDGASMGELMGDDD--PGYDLVVD---REALKPLLAELSPRDKRILLMKFFR 226

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            M+      ++G +  V++ ++ ++ ++ + +L+
Sbjct: 227 NMSQ----AQIGAELGVSQMQVSRLLSQILGRLR 256


>gi|5360738|dbj|BAA82139.1| sigma factor of sigB family [Streptomyces griseus]
          Length = 259

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 59/255 (23%), Positives = 119/255 (46%), Gaps = 43/255 (16%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           +G      A+  ++E NL LV   A ++ NRG   + D++Q G IGL+KA ++FD     
Sbjct: 19  EGTHAYQYARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLSREV 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+++A+ ++   I R   D S  + +P  +++    + +    ++  + R+PT +E+A+
Sbjct: 79  EFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDLAKAKEALAGVLDRDPTAKELAE 138

Query: 555 KLAMP----VEGVRKVLKITKEPISLET-----------------PIGDEDTSHLGDFIE 593
            L +      EG+      T   + + T                  +GD D +   + +E
Sbjct: 139 YLGIEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQTAGRTFADVLGDPDPAM--EAVE 196

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           + +A++PL               L  L  RE R++ MRFG  M    T  ++G +  +++
Sbjct: 197 NLHALAPL---------------LDELDERERRIIDMRFGQEM----TQAQIGAELGISQ 237

Query: 654 ERIRQIEAKAIRKLK 668
             + ++ ++ + KL+
Sbjct: 238 MHVSRLLSRMLGKLR 252


>gi|331695379|ref|YP_004331618.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950068|gb|AEA23765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 259

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 113/241 (46%), Gaps = 21/241 (8%)

Query: 426 EFRHIVSMVRKGECEASIA---------KKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           E+ H+V ++   E  A +A         + E+V   L +   +A+++ +RG    DL Q 
Sbjct: 7   EYGHLVPLL---EEYAGLAPDDPRREALRDELVRGYLPVAQHIARRFAHRGEPLDDLTQV 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
             +GL+ A ++F    G  F ++A+  +   + R   D   ++R+P  ++D    +    
Sbjct: 64  ATVGLINAIDRFAPDKGSDFFSFAVPTISGEVRRHFRDLGWSMRVPRRLKDLHVSLNGAV 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIE 593
             +S ++ R P P EIA+ L MPV  V + L+        SL+  +  E  S  +G+ + 
Sbjct: 124 SDLSQRLGRAPKPTEIAEYLGMPVADVLEGLEAADAYRSSSLDEMLSSEQGSATVGELVG 183

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVT 652
           + +A   LD   + + R+    VLA L  RE  ++ +RF   M      E+VG  Q  V+
Sbjct: 184 EADA--ELD---RVDTRQALRPVLAELGERERTIVMLRFFGNMTQTQIAEKVGISQMHVS 238

Query: 653 R 653
           R
Sbjct: 239 R 239


>gi|255523683|ref|ZP_05390649.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296186687|ref|ZP_06855089.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
 gi|255512552|gb|EET88826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296048724|gb|EFG88156.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
          Length = 241

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 119/239 (49%), Gaps = 15/239 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+V+  + LV  +A +      + +++ DL+  G +GLM A  KFD   G KFSTY+
Sbjct: 9   VKEELVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMLGLMDAIGKFDNTRGMKFSTYS 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K A+   I   S    I     DK+++      R+   + REP+ +EIA +L + +
Sbjct: 69  SIRIKGAMIDEIRKNSP---ISKGAMDKLNRYNAAVERLQKTLGREPSDKEIANELNITL 125

Query: 561 EGVRKVLKITK--EPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + + ++         +SLE  I   D+D   +G  I+D  + SP  S  +    E   + 
Sbjct: 126 KEMIEIENYINYISIVSLEDLIFSEDDDIPLIGT-IQDNKSPSPEKSLEEKEELEYLAKA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L  L  +++ VL + +  G+    TL+E+GK   V+  R+ Q+ ++AI  L++  +  K
Sbjct: 185 LDLLNEKDKTVLSLYYYEGL----TLKEIGKVLSVSESRVCQLHSRAIVHLRNAMQKLK 239


>gi|240146182|ref|ZP_04744783.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|257201716|gb|EEV00001.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|291536709|emb|CBL09821.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis M50/1]
          Length = 248

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 115/228 (50%), Gaps = 8/228 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  NL LV ++A ++ +RG +  +L Q G IGLMKA +KFD  L   FSTYA+  
Sbjct: 18  ARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLSLNLAFSTYAVPV 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    +++   +++  +K  R    +  ++ REP   EIA++  +    +
Sbjct: 78  IMGEIRRFLRDDG-MVKVSRTLKENAYKAGRAKEELWGELGREPGLLEIAERTGLSSGEI 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANL-RETTTRVLASL 620
              ++  ++  S+  P+ ++D   L   D + +K      +   +A L R    +++  L
Sbjct: 137 IMAMESARDVESIYQPVYEKDGDELLMVDQLCEKEENGRDEPEKEAVLNRMVIEQLMELL 196

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ ++R R+      + T  E  K+  +T+ ++ ++E K +  L+
Sbjct: 197 DEREQNLIRCRY----FENRTQSETAKELGMTQVQVSRLEKKILLCLR 240


>gi|149174362|ref|ZP_01852989.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
 gi|148846907|gb|EDL61243.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
          Length = 309

 Score = 73.9 bits (180), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 104/237 (43%), Gaps = 60/237 (25%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + + E++  N+RLV S+ KK T  G+ F +L  +G + ++KA +KFD+  G++FSTYA
Sbjct: 123 AQLVRDEILRRNMRLVASIVKKCTTTGVSFDELFSDGCLTMLKAIDKFDYSRGFRFSTYA 182

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +     R IA++                                  +E AK   +P 
Sbjct: 183 YHAISNFAYRKIANRK---------------------------------KERAKYKQLPP 209

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E   +     K P+ + T   DE                         L E   + + +L
Sbjct: 210 EQSMEETGAVKNPL-MGTDTWDE-------------------------LSELLNQSIDTL 243

Query: 621 TPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             RE+ +++ RF +G +    T +++  Q  +++ER+RQ+E +A+ KLK  ++  +L
Sbjct: 244 DEREQLIVKSRFALGKHRKTLTFQKLADQLGISKERVRQLEQRAVAKLKAVTQGTRL 300


>gi|311894139|dbj|BAJ26547.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 281

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 114/230 (49%), Gaps = 10/230 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S  +  ++E N+ LV  VA ++ +R  +  D++Q G +GL+KA + FD   G +F TYA+
Sbjct: 28  SYVRGTVIELNMPLVRFVASRFRHRPEELDDIVQVGTVGLIKAVDGFDPDRGVEFVTYAI 87

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D S  +R+P  ++++    VR + R+   + R P   E+A +L +  +
Sbjct: 88  PTISGEIKRFFRDTSWPLRVPRSVQERYLAAVRASDRLEQALGRLPDTAELAAELHVTED 147

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLA 618
              + L+  +     SL++ + D+ +   G  +   N +   D  ++ A LR   T  L+
Sbjct: 148 EAAEGLEAGRLCRCDSLDS-LRDDGSDDAGSAL--INRLGGCDPELEVAELRVMATPFLS 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE  VL +RF  G+    T  E+  +  V++  + +I A  +  L+
Sbjct: 205 RLPERERTVLLLRFWGGL----TQSEIAARIGVSQMHVSRILAATLAGLR 250


>gi|254974392|ref|ZP_05270864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-66c26]
 gi|255091783|ref|ZP_05321261.1| RNA polymerase sigma-F factor [Clostridium difficile CIP 107932]
 gi|255099887|ref|ZP_05328864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-63q42]
 gi|255305776|ref|ZP_05349948.1| RNA polymerase sigma-F factor [Clostridium difficile ATCC 43255]
 gi|255313518|ref|ZP_05355101.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-76w55]
 gi|255516203|ref|ZP_05383879.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-97b34]
 gi|255649300|ref|ZP_05396202.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-37x79]
 gi|255654820|ref|ZP_05400229.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-23m63]
 gi|260682470|ref|YP_003213755.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260686069|ref|YP_003217202.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296449564|ref|ZP_06891341.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296878113|ref|ZP_06902128.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
 gi|306519396|ref|ZP_07405743.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-32g58]
 gi|260208633|emb|CBA61376.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260212085|emb|CBE02685.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296261628|gb|EFH08446.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296430866|gb|EFH16698.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
          Length = 254

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 11/227 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ +NL LV SV  ++ N G    DL Q G+IGL+K+  KFD     KFSTYA+  
Sbjct: 33  AKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSIGLIKSIYKFDPKFNVKFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   ++    K    +  ++ K+ REP+ EE+AK + +  E +
Sbjct: 93  ILGEIKRYLRDDGM-IKVSRSLKQIAVKAKMESEALTKKLGREPSIEELAKAIDVEKEDL 151

Query: 564 RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              ++       L+  I +E+ S   L D I  K      +  +  N+      +L  L 
Sbjct: 152 VMAMEANFNVEYLQGVIHEEEGSPICLIDKISMKGESE--EEKVVDNI--LLKDILGRLD 207

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE +++ +R+      D T  E+G+   +++ ++ +IE K + KLK
Sbjct: 208 KRERQIIVLRY----FEDMTQSEIGEMLNISQVQVSRIEKKVLSKLK 250


>gi|300928953|ref|ZP_07144457.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
 gi|300463107|gb|EFK26600.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
          Length = 229

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 146

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE    D    +PL   + +NLR+     +  L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 IELVTDDHQRENPLQQLLDSNLRQRVMEAIEMLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|227112555|ref|ZP_03826211.1| flagellar biosynthesis sigma factor [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
 gi|227329198|ref|ZP_03833222.1| flagellar biosynthesis sigma factor [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 230

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 33  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++   ++ R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 90  VAQAMQQAEQQLGRTPTEQEVAQTLNITLEDYRQILLDTNNSQLFSY---DEWREEHGDS 146

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL   ++ NLR      + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 147 AEALLEGNEDANPLHQLMEGNLRHRVMDAIESLPEREKLVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLEVGESRVSQLHSQAIKRLR 223


>gi|126698352|ref|YP_001087249.1| RNA polymerase sigma-F factor [Clostridium difficile 630]
 gi|115249789|emb|CAJ67606.1| RNA polymerase sigma-F factor [Clostridium difficile]
          Length = 254

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 11/227 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++ +NL LV SV  ++ N G    DL Q G+IGL+K+  KFD     KFSTYA+  
Sbjct: 33  AKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSIGLIKSIYKFDPKFNVKFSTYAVPM 92

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D    I++   ++    K    +  ++ K+ REP+ EE+AK + +  E +
Sbjct: 93  ILGEIKRYLRDDGM-IKVSRSLKQIAIKAKMESEALTKKLGREPSIEELAKAIDVEKEDL 151

Query: 564 RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              ++       L+  I +E+ S   L D I  K      +  +  N+      +L  L 
Sbjct: 152 VMAMEANFNVEYLQGVIHEEEGSPICLIDKISMKGESE--EEKVVDNI--LLKDILGRLD 207

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE +++ +R+      D T  E+G+   +++ ++ +IE K + KLK
Sbjct: 208 KRERQIIVLRY----FEDMTQSEIGEMLNISQVQVSRIEKKVLSKLK 250


>gi|269139471|ref|YP_003296172.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
 gi|267985132|gb|ACY84961.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
          Length = 240

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 109/232 (46%), Gaps = 23/232 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + + E +   +RL  SV         +  DL+Q G IGL+ A E++D   G  F+TYA
Sbjct: 21  APLVRHEALRLQVRLPASV---------ELDDLLQAGGIGLLHAVERYDAMQGTAFTTYA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  ++ A+   +  +     +P  +R     V    +R   ++ R P   EIA+++ +P+
Sbjct: 72  IQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRTPGDSEIAQEMGIPL 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTRV 616
           E  +++L  T           DE     GD     +E     +PL   ++++LR      
Sbjct: 129 EEYQQILLDTNTSQLFSY---DEWREDHGDSAEPVLEQSEEANPLRQLLESDLRGRVIAA 185

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L  RE+ VL + +   +N    L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 186 IEALPEREKLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|182440445|ref|YP_001828164.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326781114|ref|ZP_08240379.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178468961|dbj|BAG23481.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326661447|gb|EGE46293.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 293

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 59/255 (23%), Positives = 119/255 (46%), Gaps = 43/255 (16%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           +G      A+  ++E NL LV   A ++ NRG   + D++Q G IGL+KA ++FD     
Sbjct: 53  EGTHAYQYARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLSREV 112

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+++A+ ++   I R   D S  + +P  +++    + +    ++  + R+PT +E+A+
Sbjct: 113 EFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDLAKAKEALAGVLDRDPTAKELAE 172

Query: 555 KLAMP----VEGVRKVLKITKEPISLET-----------------PIGDEDTSHLGDFIE 593
            L +      EG+      T   + + T                  +GD D +   + +E
Sbjct: 173 YLGIEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQTAGRTFADVLGDPDPAM--EAVE 230

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           + +A++PL               L  L  RE R++ MRFG  M    T  ++G +  +++
Sbjct: 231 NLHALAPL---------------LDELDERERRIIDMRFGQEM----TQAQIGAELGISQ 271

Query: 654 ERIRQIEAKAIRKLK 668
             + ++ ++ + KL+
Sbjct: 272 MHVSRLLSRMLGKLR 286


>gi|313901496|ref|ZP_07834946.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313468234|gb|EFR63698.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 258

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 101/201 (50%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GLM+A +++D   G KF TYA   ++ A+   +        +P  +R +  +
Sbjct: 57  DLISYGIFGLMEAIKRYDPSRGVKFETYAYTRIRGAMLDGLRAMDW---VPQGLRRRARE 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDE--DTSH 587
           V    RR+ N++ R     E+A +L +  +   ++LK       ISL+  +  E  D + 
Sbjct: 114 VEACYRRLENRLGRPAEDAEVAAELGLTPDEFGELLKDLARTTVISLDDVLRSESDDPAA 173

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D  A  PL +A  A+LR+   + LA L  RE  V+ + +  G+    T++E+ +
Sbjct: 174 VLDRLADPGAADPLAAATLADLRQRLAQALAVLPERERLVITLYYYEGL----TVKEIAE 229

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ Q+  +AI +L+
Sbjct: 230 VMGVSPSRVSQLHTRAILRLR 250


>gi|326938732|gb|AEA14628.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 257

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 59/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C    A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCNE--AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|261821180|ref|YP_003259286.1| flagellar biosynthesis sigma factor [Pectobacterium wasabiae
           WPP163]
 gi|261605193|gb|ACX87679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           wasabiae WPP163]
          Length = 240

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++   ++ R PT +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAQAMQQAEQQLGRTPTEQEVAQTLNITLEDYRQILLDTNNTQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL   ++ NLR      + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEDANPLHQLMEGNLRHRVMDAIESLPEREKLVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|302874980|ref|YP_003843613.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
 gi|307690403|ref|ZP_07632849.1| sporulation sigma factor SigF [Clostridium cellulovorans 743B]
 gi|302577837|gb|ADL51849.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
          Length = 265

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 40/132 (30%), Positives = 75/132 (56%), Gaps = 1/132 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           SI+++   V +++  +   + A  ++++ N+ LV +++KK+ NRG ++ D+ Q G +GL+
Sbjct: 23  SINDYTDNVELIKLAQGGDNEALNDLIKKNMPLVAAISKKFLNRGYEYDDIFQIGCMGLI 82

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA   F+     KFSTYA+  +   I R + D    I+I   ++    K+      ++N 
Sbjct: 83  KAVNNFNTDFNVKFSTYAVPMIMGEIKRFLRDDGI-IKISRSIKATAKKLHYDRENLTNI 141

Query: 543 IKREPTPEEIAK 554
           + REPT EE++K
Sbjct: 142 LNREPTIEELSK 153


>gi|87306557|ref|ZP_01088704.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87290736|gb|EAQ82623.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 556

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 52/74 (70%), Gaps = 1/74 (1%)

Query: 440 EASI-AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           EA++  K ++V++NLRLV+S+AK++     +F +L+ +GN+ L++A EKFD+  G KFST
Sbjct: 371 EAAVEVKNQIVQSNLRLVVSIAKRHLGAADEFFELVSDGNMSLIRAVEKFDYSRGNKFST 430

Query: 499 YAMWWVKQAITRSI 512
           Y  W + +   R+I
Sbjct: 431 YCSWAIMKNFARTI 444



 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 43/63 (68%), Gaps = 5/63 (7%)

Query: 617 LASLTPREERVLRMRFGIGMNTDH---TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           L  L  RE++++  R+G  ++ DH   TL+EVG +  VT+ERIRQIEA+A+ KL+  ++ 
Sbjct: 490 LNRLDEREQKIIIRRYG--LDHDHEPQTLKEVGAELGVTKERIRQIEARALNKLRVAAQE 547

Query: 674 KKL 676
            KL
Sbjct: 548 AKL 550


>gi|317132447|ref|YP_004091761.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470426|gb|ADU27030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 237

 Score = 73.9 bits (180), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 40/124 (32%), Positives = 73/124 (58%), Gaps = 2/124 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +R G+ +A+ A+ ++VE NL LV + A+ +  +G+++ DL Q G +GL+KA   FD   
Sbjct: 11  FIRAGKGDAA-AQTQLVEENLGLVHAAARHFNGKGIEYDDLYQAGCMGLVKAVTGFDITR 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +FSTYA+  +   + R   D    +++   +++   K +R   ++S ++ REPT  E+
Sbjct: 70  GVQFSTYAVPVIMGEMRRLFRDDG-PVKVSRSLKELSLKAMRAREKLSARLCREPTLSEL 128

Query: 553 AKKL 556
           A +L
Sbjct: 129 AAEL 132


>gi|21225555|ref|NP_631334.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256783425|ref|ZP_05521856.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767301|ref|ZP_06526679.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|4835317|emb|CAB42939.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289697500|gb|EFD64929.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 295

 Score = 73.6 bits (179), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 60/260 (23%), Positives = 125/260 (48%), Gaps = 40/260 (15%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA +
Sbjct: 48  FRRLTEL-EEGTAEYQFARNTLIEMNMSLVRFAAGRFRGRGNDMEDIVQTGMIGLIKAID 106

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+++A+ ++   I R   D +  + +P  +++   ++ R    +S ++ RE
Sbjct: 107 RFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELARAREELSTRLDRE 166

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPI---GDEDT-SHLGDFI------ 592
           PT  E+A  + +     +EG  ++        SL+  +   G E+  S L DFI      
Sbjct: 167 PTVAELATLMNIGEDQVIEG--QIASNGYNSSSLDAALTGDGPENGESVLADFIGVEEDG 224

Query: 593 ----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
               ED ++++PL               +A L+ R+ +++ +RF      + T  E+G++
Sbjct: 225 LRLVEDFHSLAPL---------------MAELSERDRQIIHLRF----VEEATQAEIGER 265

Query: 649 FCVTRERIRQIEAKAIRKLK 668
              ++  + ++  + I +L+
Sbjct: 266 LGCSQMHVSRLIKRIITRLR 285


>gi|224370767|ref|YP_002604931.1| FliA [Desulfobacterium autotrophicum HRM2]
 gi|223693484|gb|ACN16767.1| FliA [Desulfobacterium autotrophicum HRM2]
          Length = 238

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 106/222 (47%), Gaps = 15/222 (6%)

Query: 455 LVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  +A ++  R    + F +L+  G++GL+ A +KFD        TYA + +K AI   
Sbjct: 8   LVRQIASRFARRLPSSVLFDELVSAGSLGLIDAVDKFDSGKHVSLKTYAQYRIKGAILDE 67

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-IT 570
           +       R    MR KI  + R  + + +K K   +  E+AK L +P+E    +L  I 
Sbjct: 68  LRSMDTYSR---SMRKKIQDISRAVKAIEDKKKGPASDNEVAKLLEVPLESYYDMLTDIH 124

Query: 571 KEPI-SLETPI--GDEDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREER 626
              I SL+  I  GD DTS +  F    K   +P D   +  L+    R + +LT +E+ 
Sbjct: 125 GAAILSLDAFIRTGDNDTSSMTRFQAGIKGEHTPADLLDREELKGVLARAVTTLTEKEQL 184

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+ + +      + TL+E+G+   +T  RI QI    + KLK
Sbjct: 185 VVSLYY----YEELTLKEIGEVLTLTESRICQIHTAILIKLK 222


>gi|304559365|gb|ADM42029.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda FL6-60]
          Length = 237

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 108/229 (47%), Gaps = 17/229 (7%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + + E +   +RL  SV         +  DL+Q G IGL+ A E++D   G  F+TYA
Sbjct: 18  APLVRHEALRLQVRLPASV---------ELDDLLQAGGIGLLHAVERYDAMQGTAFTTYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  ++ A+   +  +     +P  +R     V    +R   ++ R P   EIA+++ +P+
Sbjct: 69  IQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRTPGDSEIAQEMGIPL 125

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           E  +++L  T            ED     +  +E     +PL   ++++LR      + +
Sbjct: 126 EEYQQILLDTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRGRVIAAIEA 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+ VL + +   +N    L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 186 LPEREKLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIKRLR 230


>gi|218232670|ref|YP_002365766.1| RNA polymerase sigma factor SigB [Bacillus cereus B4264]
 gi|218160627|gb|ACK60619.1| RNA polymerase sigma-B factor [Bacillus cereus B4264]
          Length = 257

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +V     LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIADFQQNQCDE--AQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      ++++ +R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRFQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|108743436|dbj|BAE95539.1| putative RNA polymerase sigma factor [Streptomyces kanamyceticus]
          Length = 278

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 103/216 (47%), Gaps = 14/216 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+VE  L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F +YA+  V
Sbjct: 52  RQEVVEVWLPMSERLAGRFRNRGESLDDLRQVAALGLVKAVDRYDPRRGTAFESYAVPTV 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIK-REPTPEEIAKKLAMPVE- 561
              I R   D   T+ +P  ++D +   VR AR+ ++  +  R PT  EIA++  M  E 
Sbjct: 112 TGEIKRHFRDHMWTLHVPRRVQD-LRNRVRFARQDLAQTVSGRAPTTAEIAERAQMSEED 170

Query: 562 ---GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              G+  +   T   +  E P G ED   L D +   +    LD  I    RE+    +A
Sbjct: 171 AKAGLEALDSFTALSLDAELP-GSEDGYSLSDALGGPDPA--LDVVID---RESVKPRIA 224

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            L  RE  +L MRF   M      +E+G  Q  V+R
Sbjct: 225 QLPERERTILYMRFFGDMTQSRIADEMGISQMHVSR 260


>gi|206968111|ref|ZP_03229067.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
 gi|206737031|gb|EDZ54178.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
          Length = 257

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +V     LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIADFQQNQCDE--AQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      ++++ +R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRFQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|325111003|ref|YP_004272071.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324971271|gb|ADY62049.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 555

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 48/73 (65%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA   K  ++ +NLRLV+S+AK++      F +++ +GN+ L++A EKFD+  G KFSTY
Sbjct: 372 EAVAVKNFLIRSNLRLVVSIAKRHFKPQANFFEMVSDGNMSLIRAIEKFDYSQGNKFSTY 431

Query: 500 AMWWVKQAITRSI 512
           A W + +   RSI
Sbjct: 432 ATWAIMKNYARSI 444



 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 616 VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +L  L PRE  ++  RFG+   T+  TLE+VG +F VT+ERIRQIE++A+ KLK  +  +
Sbjct: 489 ILGQLDPRERDIILHRFGLNKGTEPETLEQVGHRFGVTKERIRQIESRALSKLKKIAVEE 548

Query: 675 KL 676
           KL
Sbjct: 549 KL 550


>gi|188996275|ref|YP_001930526.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188931342|gb|ACD65972.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 590

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/171 (32%), Positives = 89/171 (52%), Gaps = 18/171 (10%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDDL--ED 85
           D  + +I LAR++GYVT  E++ ++  +  SS E +E  +  L+ + I+V D + +  ED
Sbjct: 8   DDVRTLINLAREKGYVTYAEISTYVEEEFFSSDENIESLIEYLNELNIDVRDDEKIKSED 67

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E+ SE    L    S+  V+            DDPV++YLREMG I LL R+ EI  +  
Sbjct: 68  EDISEH---LGIDLSDDDVW---------NKADDPVKLYLREMGKIPLLKRDEEIKYSME 115

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           IE GR  +   L  +    + L+    ++ DG   + +I++L+    PE K
Sbjct: 116 IERGRKKVFRGLLRTSFLTERLLDEWAKVIDGKARVHDILNLDE---PEVK 163


>gi|300814743|ref|ZP_07094991.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|300511130|gb|EFK38382.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 258

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 116/226 (51%), Gaps = 15/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L +   ++KKY  +G+ + D+ Q  +IGL+ + ++FD   GY+FS++A   +   
Sbjct: 34  LIEEYLYIAEILSKKYIGKGIDYDDIYQVASIGLIYSVDRFDPTKGYEFSSFATPTIIGE 93

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  TIR+P  +++   K++    ++S + +R PT E+IA+ L    E + + +
Sbjct: 94  IKKYFRDKGWTIRVPRRIQELSKKIMIAKNKLSQEYQRTPTVEDIAEFLNASPEEIIESM 153

Query: 568 KITK--EPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + +K   P SL+     GD+    L D I ED+     +D      L++   + + +L  
Sbjct: 154 EASKVYTPQSLDIVYDSGDDKKMSLQDLIGEDEKYFDKID------LKDFLLKSMKNLNE 207

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+ +L  R+        T   + K+  +++  + +IE K + K++
Sbjct: 208 VEKTILIDRYF----NKKTQIVIAKKLNISQMTVSRIEKKVLEKMR 249


>gi|222053730|ref|YP_002536092.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. FRC-32]
 gi|221563019|gb|ACM18991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. FRC-32]
          Length = 251

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 96/201 (47%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL     IGL+ AAE+FD   G  F T+A   ++  I   +  Q    R    +RDK  +
Sbjct: 50  DLRSAAVIGLISAAERFDPTRGVMFKTFAEQRIRGTIMDELRSQDWLTR---SLRDKFKR 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + R    +  ++ R P+ +E+A  + + +E    +L+       +SL+    DED S LG
Sbjct: 107 LEREFSALEQRLGRNPSSDEVAAAMGLDLEAYFHLLEEIHFLSFVSLDDAWMDEDGSPLG 166

Query: 590 --DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D +EDK   SP +  I     E     + +L  +E  V+ + +   MN    L+E+G 
Sbjct: 167 LLDVLEDKGIESPQNQLIARQTVENLAEAIDNLPEKERIVITLYYYEEMN----LKEIGA 222

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  RI Q+ ++A+ +L+
Sbjct: 223 VLHLTESRISQLHSQALLRLR 243


>gi|317063374|ref|ZP_07927859.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689050|gb|EFS25885.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 151

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 41/122 (33%), Positives = 71/122 (58%), Gaps = 2/122 (1%)

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+ EEIA +L +  + V+ ++   ++P+SL T IGD+   +L D +  +   S  +    
Sbjct: 20  PSVEEIAAELNIEADKVQDIIMDFQDPMSLSTQIGDD--IYLEDTLAQQEDFSMEEEIFN 77

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R+    ++  L  RE+ +L++R+G+     HTLEE+G    +TRER+RQIE K ++K
Sbjct: 78  EMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIHTLEEIGNTLNITRERVRQIEKKTLQK 137

Query: 667 LK 668
           L+
Sbjct: 138 LR 139


>gi|20808064|ref|NP_623235.1| sporulation sigma factor SigE [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516645|gb|AAM24839.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 241

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 53/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEESYLISKMEKGDNEA---KSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++     I +++R             +N
Sbjct: 98  IKAINTFNPRKKIKLATYA--------SRCIENE-----ILMYLRR------------NN 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K + E + +E    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 133 KTRLEVSFDE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   RE  T  L  L  RE++++R+RFG+   T+ T +EV     +++  I ++E 
Sbjct: 176 --------RELLTSALKKLPDREKKIIRLRFGLEGGTEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLK 668
           K +++LK
Sbjct: 228 KILKRLK 234


>gi|163938900|ref|YP_001643784.1| RNA polymerase sigma factor SigB [Bacillus weihenstephanensis
           KBAB4]
 gi|163861097|gb|ABY42156.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
          Length = 257

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/252 (22%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +V     LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCDE--AQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  + +P  ++D   K+      +++ ++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGVHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIANHLGLSEEEVLEIMDAKN----------NYQVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    +T  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEQTERRLVLDDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|288942274|ref|YP_003444514.1| RNA polymerase sigma-32 subunit RpoH [Allochromatium vinosum DSM
           180]
 gi|288897646|gb|ADC63482.1| RNA polymerase, sigma 32 subunit, RpoH [Allochromatium vinosum DSM
           180]
          Length = 279

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 116/240 (48%), Gaps = 26/240 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +V ++LR VI +A+ Y   GL   DLIQEG +GLMKA  +F+  +G +  ++A+ W
Sbjct: 46  AAKRLVTSHLRFVIRIARGYLGYGLPLPDLIQEGTVGLMKAVRRFEPDMGVRLVSFAVHW 105

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      +++     + K+   +R++++    + ++   +E+A  L +  E 
Sbjct: 106 IRAEIHEYILRNWRIVKVATTKAQRKLFFNLRSSKKRLGWLTKQEV-DEVAADLGVKPEV 164

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLG-------------DFIEDKNAVSPLDSAIQANL 609
           V          + +E+ + ++D S  G              ++ D           +   
Sbjct: 165 V----------LQMESRLSNQDLSFDGLEDDDDDSPAAPSTYLPDVRMEPSRLLEHEDTD 214

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+   R+ A+L   +ER   + F   ++    TL E+ ++F V+ ERIRQIE  A++K++
Sbjct: 215 RDQRERLYAALADLDERSKTILFERWLSEKKQTLHELAEKFGVSAERIRQIEKNAMKKVR 274


>gi|329937639|ref|ZP_08287158.1| RNA polymerase sigma factor sig8 [Streptomyces griseoaurantiacus
           M045]
 gi|329303038|gb|EGG46926.1| RNA polymerase sigma factor sig8 [Streptomyces griseoaurantiacus
           M045]
          Length = 287

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 106/225 (47%), Gaps = 35/225 (15%)

Query: 428 RHI---VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMK 483
           RH    ++ + +G  E    +  ++E NL LV   A ++ +RG  +  D++Q G IGL+K
Sbjct: 39  RHFFARLATLEEGTPEYQYVRNTLIEMNLSLVRYAASRFRSRGADEMEDIVQVGTIGLIK 98

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    +S + 
Sbjct: 99  AIDRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELARATEELSRRT 158

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEP------ISLETPIGDEDTSHLGDF------ 591
            R+PT  E++  +++P E V +  K +          SL    G +  S L DF      
Sbjct: 159 GRQPTVRELSALMSLPEEEVIEARKASNAYRSSSLDASLSGDGGLDGESALADFIGVEER 218

Query: 592 ----IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
               IED ++++PL               +A L  R+  +L +RF
Sbjct: 219 GLELIEDLHSLAPL---------------VAGLPERDRTILHLRF 248


>gi|300717210|ref|YP_003742013.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
 gi|299063046|emb|CAX60166.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
          Length = 240

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 95/198 (47%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     ++   + R  T +E+A  L + ++  R++L  T            E+     + 
Sbjct: 100 VAGAMHKVEQSLGRTATEQEVAASLDVSLQEYRQILLDTNNSQLFSYDEFREEHGDTAEL 159

Query: 592 IEDKN-AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           + D +   +PL   ++ NLRE     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 VTDGHEEANPLHQLMEGNLRERVIEAIEALPDREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|251789202|ref|YP_003003923.1| flagellar biosynthesis sigma factor [Dickeya zeae Ech1591]
 gi|247537823|gb|ACT06444.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya zeae Ech1591]
          Length = 240

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 98/201 (48%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  ++    + R P+ +E+A+ L + +E  R++L  T           DE     GD 
Sbjct: 100 VAQAMQQAEQSLGRAPSEQEVAQTLNISLEEYRQILLDTNNSQLFSY---DEWREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               +E     +PL+  +  +LR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AEALLEGNEDANPLNQLMDVSLRQRVMDAIENLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|212697380|ref|ZP_03305508.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675572|gb|EEB35179.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 256

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 120/230 (52%), Gaps = 18/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY+FS++A   +
Sbjct: 30  RNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGYEFSSFATPTI 89

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D+   IR+P  +++   K+    + +  +++R PT ++IA  L    E + 
Sbjct: 90  MGELKRYFRDKGWVIRVPRRIQNLYKKINVAKKILPQELQRTPTIKDIAAYLGEDEETIL 149

Query: 565 KVLKITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVL 617
           + ++ +K   P SL+        E++  L D I  +DKN     DS    +L E +T  L
Sbjct: 150 ETMEASKVYTPQSLDMKYQVQKGENSVDLSDMIGEDDKN----FDSIELKDLIEKSTERL 205

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L   E+++L +R+  G     T  ++ ++  +++  + +IE K ++K 
Sbjct: 206 NDL---EKQILELRYYEG----RTQVDIAQKLSISQMTVSRIEKKILQKF 248


>gi|219129831|ref|XP_002185083.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403578|gb|EEC43530.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 435

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 110/246 (44%), Gaps = 57/246 (23%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG IGL +A ++++  +G KFSTYA++WV+ AI R IA++   +R+P H+   + K
Sbjct: 184 DLIQEGAIGLARAVDRWNPEIGGKFSTYAVYWVRAAILRCIAERDDLVRVPEHVSAAVRK 243

Query: 532 VVRTARRMSNKI----------------KREPTPEEIAKKLAMPVEGVRKVLKITKE--- 572
           + R AR++   I                K     + +A++  +    V + +K+      
Sbjct: 244 ISRAARQLGIDIDGNDLISSVYSKDASWKEAQAAKALAEEAGLTPRQVSEAIKVKARRRG 303

Query: 573 -PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
             +S E  +  G +  + L   + D N   PL S     L+ T ++    L P+E   L 
Sbjct: 304 GMLSFEAWMQQGQDFATDLTPVVADDN---PLASLETEQLKSTLSKF---LRPKEMEALS 357

Query: 630 MRFGIGMNTDHTLE---------------------------EVGKQFCVTRERIRQIEAK 662
            R+  G+  D+  E                           EVGK+  V+ E  R++  K
Sbjct: 358 WRY--GLQRDYVAEAEEELFGRSPRAPITVKGRWGEAMSFTEVGKKMKVSAEYGRRLCHK 415

Query: 663 AIRKLK 668
           A+ KL+
Sbjct: 416 ALNKLR 421


>gi|138896107|ref|YP_001126560.1| sporulation sigma factor SigK [Geobacillus thermodenitrificans
           NG80-2]
 gi|196249000|ref|ZP_03147700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134267620|gb|ABO67815.1| RNA polymerase sigma-K factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211876|gb|EDY06635.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 237

 Score = 73.6 bits (179), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 101/237 (42%), Gaps = 72/237 (30%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G +  DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNRLIEHNLRLVAHIVKKFENTGEEVEDLISIGTIGLIKAIESYSPNKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLRS------------------------------------ 120

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----------SAIQANLR-ET 612
              LK T++ +SL  PIG +         ++ N +S LD            IQ N+  E 
Sbjct: 121 ---LKKTRKDVSLHEPIGQD---------KEGNEISLLDILKSEGQDIVDEIQLNMELEQ 168

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + ++ L  RE+ V+  RFG+G   + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 169 VKKYISVLDEREKEVIVNRFGLGRQREKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|282881777|ref|ZP_06290435.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
 gi|281298387|gb|EFA90825.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
          Length = 261

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 116/226 (51%), Gaps = 15/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L +   ++KKY  +G+ + D+ Q  +IGL+ + ++FD   GY+FS++A   +   
Sbjct: 37  LIEEYLYIAEILSKKYIGKGIDYDDIYQVASIGLIYSVDRFDPTKGYEFSSFATPTIIGE 96

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  TIR+P  +++   K++    ++S + +R PT E+IA+ L    E + + +
Sbjct: 97  IKKYFRDKGWTIRVPRRIQELSKKIMIAKNKLSQEYQRTPTVEDIAEFLNASPEEIIESM 156

Query: 568 KITK--EPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + +K   P SL+     GD+    L D I ED+     +D      L++   + + +L  
Sbjct: 157 EASKVYTPQSLDIVYDSGDDKKMSLQDLIGEDEKYFDKID------LKDFLLKSMKNLNE 210

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+ +L  R+        T   + K+  +++  + +IE K + K++
Sbjct: 211 IEKTILIDRYF----NKKTQIVIAKKLNISQMTVSRIEKKVLEKMR 252


>gi|256832234|ref|YP_003160961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
 gi|256685765|gb|ACV08658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
          Length = 283

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 113/235 (48%), Gaps = 15/235 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           ++ ++E++     LV  +A +   +    ++  DL+  G  GL+ A +KFD     KF T
Sbjct: 46  ALGREELILHYAPLVTMIAGRVGMKLPNTVEAADLVSYGMFGLIDAIDKFDPSRDIKFET 105

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   V+ AI   I +      IP  +R +  +  R    + N + REPT  EIA+ L +
Sbjct: 106 YASTRVRGAI---IDELRALDWIPRSVRSRAREYDRACEHLENTLHREPTSGEIAQHLGV 162

Query: 559 PVEGVRKV-LKITK-EPISLETPI--GDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           P + V ++  +++    I+L+  +  GD  D     D +++  AV P  S  Q  +RE  
Sbjct: 163 PEKDVWQLQWQVSSGHVIALDEVVSTGDRVDQISAMDSVQETLAVDPAQSFAQGEMREIL 222

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +  L  RE  V+ + +   M    TL E+GK   VT  R+ Q+ +  I KL+
Sbjct: 223 AQAVDHLNERERAVVTLYYFRSM----TLSEIGKLLGVTESRVSQMHSAIIVKLR 273


>gi|157371179|ref|YP_001479168.1| flagellar biosynthesis sigma factor [Serratia proteamaculans 568]
 gi|157322943|gb|ABV42040.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Serratia
           proteamaculans 568]
          Length = 240

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 98/198 (49%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRHARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  R++  ++ R  +  E+A+ L + ++  R++L  T            E+     + 
Sbjct: 100 VAQVMRQLEQQLGRPASEVEVAQTLNLSLDEYRQILLDTNNSQLFSYDEWREEHGESAEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEEANPLHHLLEGNLRQRVIDAIEALPEREKMVLTLYYQEELN----LKEIGAVLD 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|284045116|ref|YP_003395456.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283949337|gb|ADB52081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 116/235 (49%), Gaps = 18/235 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A++ +V A   LV  VA +  + GL    +  DLI  G IGL+ A E+FD     KF TY
Sbjct: 25  ARERLVVAYSPLVKYVAGRMAS-GLPAHVEEADLISYGLIGLISAIERFDLGREIKFETY 83

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  ++ AI   I +      +P  +R K  ++ R   ++ +K++R PT EE+A +L M 
Sbjct: 84  AIPRIRGAI---IDELRSLDWVPRSVRAKAREIERANAKLEHKLQRAPTDEEMAHELDMS 140

Query: 560 VEGVRKVL-KITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++  +  L +I+   I+    +        D   L D ++D +A  P      + L++  
Sbjct: 141 MDEFQDALIQISNSTIAALDELWTVSDASGDQISLLDTLQDPDAPDPEKIVDASELKDRV 200

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +A L  RE+ V+ + +      + TL E+G+   VT  RI Q+  KA+ +L+
Sbjct: 201 ADAIARLPEREKLVIALYY----YENLTLREIGEVLGVTESRISQLHTKAVLRLR 251


>gi|296168913|ref|ZP_06850582.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896382|gb|EFG76035.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 262

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 121/258 (46%), Gaps = 38/258 (14%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + + V  G  E    + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELAT-VGAGSMEFQRQRDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVDAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATAELSQRLGRA 141

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIG-DEDTSH-----LGDF----- 591
           PT  E+A +L M     VEG+  V   +   +S+++  G DED +      LGD      
Sbjct: 142 PTATELAAELGMDREEVVEGL--VAGSSYNTLSIDSGGGSDEDEARAIADTLGDVDTGLD 199

Query: 592 -IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IED+ ++ PL               L +L  RE  VL +RF   M      E VG    
Sbjct: 200 RIEDQESLRPL---------------LEALPERERTVLVLRFFESMTQTQIAERVG---- 240

Query: 651 VTRERIRQIEAKAIRKLK 668
           +++  + ++ AK++ +L+
Sbjct: 241 ISQMHVSRLLAKSLTRLR 258


>gi|258488938|gb|ACV72475.1| RpoD [Xanthomonas axonopodis pv. axonopodis]
 gi|258488940|gb|ACV72476.1| RpoD [Xanthomonas axonopodis pv. axonopodis]
          Length = 261

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L++  +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLVDYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|254387389|ref|ZP_05002636.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346181|gb|EDX27147.1| sigma factor [Streptomyces sp. Mg1]
          Length = 266

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/244 (25%), Positives = 114/244 (46%), Gaps = 22/244 (9%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +G  E    +  ++E N  LV    +++ +R  G    D++Q G IGL+KA ++FD    
Sbjct: 22  EGTPEHQYVRNTLIEMNASLVQYAVRRFRSRCDGGDIEDVVQVGTIGLIKAIDRFDPARE 81

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FST AM ++   I R   D S  +R+P  +++    + +    ++ ++ R PT  ++A
Sbjct: 82  NEFSTLAMPYITGEIKRHFRDTSWAVRVPRRLQELRIDIAKAKEELTVRLDRSPTVTDLA 141

Query: 554 KKLAMP----VEGVRKVLKITKEPISLETPIGDED----TSH-LGDFIEDKNAVSPLDSA 604
             L +     VEG+      T    SL+ P  D      T H L D + ++     L   
Sbjct: 142 GHLGLTDEEVVEGLVAANGHTSG--SLDAPHSDHGDGPTTGHTLADVMGEEEPALALVED 199

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +QA        +L  L+ RE  +LRMRFG     + T  ++G    +++ ++ ++  + +
Sbjct: 200 VQA-----LAPLLQRLSERERSMLRMRFG----EELTQAQIGTALGISQMQVSRLLNRIL 250

Query: 665 RKLK 668
             L+
Sbjct: 251 AHLR 254


>gi|293366035|ref|ZP_06612723.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|291319758|gb|EFE60116.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
          Length = 256

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 123/243 (50%), Gaps = 20/243 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V+   +L+ S+A +Y+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  VFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKH 669
               R+L  L+ RE ++++  F  G++   T E +G  Q  V+R     ++  AI+KL+ 
Sbjct: 198 MILERILPILSERERQIIQCTFIEGLSQKETGERIGLSQMHVSR-----LQRTAIKKLQE 252

Query: 670 PSR 672
            +R
Sbjct: 253 AAR 255


>gi|229827370|ref|ZP_04453439.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
 gi|229788308|gb|EEP24422.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
          Length = 268

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 451 ANL-RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           ANL +++      Y    +++ DL+  G  GL+ A +KFD   G KF TYA   +K AI 
Sbjct: 38  ANLVKIIAGRMSIYLGYNVEYDDLVGYGIFGLIDAIDKFDHVKGVKFETYASLRIKGAIL 97

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
             I        IP  MR +  K+    R +  K  R  T EEIA +L + V+        
Sbjct: 98  DQIRKMDW---IPRTMRQRQKKLEAAERAIEEKYGRMATDEEIAAELGISVDEYGS---- 150

Query: 570 TKEPISLETPIGDEDTSHLG-DFIEDKNAV--------SPLDSAIQANLRETTTRVLASL 620
            +  +S+   I  +D    G D + DK+           P ++  +  L+E+    +  L
Sbjct: 151 WQSQVSMSGIISLDDYLEQGSDLVADKSGSKLGISGFEQPEEAVEKEELKESLAVAIEGL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T +E++V+ + +      + TL+E+ +   V+  R+ Q+  KA+ KLK     +KL  ++
Sbjct: 211 TEKEQKVIALYY----YEELTLKEISRVLSVSESRVSQLHTKALTKLK-----EKLGDYI 261

Query: 681 D 681
           D
Sbjct: 262 D 262


>gi|237755496|ref|ZP_04584118.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237692360|gb|EEP61346.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 570

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/171 (32%), Positives = 89/171 (52%), Gaps = 18/171 (10%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDDL--ED 85
           D  + +I LAR++GYVT  E++ ++  +  SS E +E  +  L+ + I+V D + +  ED
Sbjct: 8   DDVRTLINLAREKGYVTYAEISTYVDEEFFSSDENIESLIEYLNELNIDVRDDEKIKSED 67

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E+ SE    L    S+  V+            DDPV++YLREMG I LL R+ EI  +  
Sbjct: 68  EDISEH---LGIDLSDDDVW---------NKADDPVKLYLREMGKIPLLKRDEEIKYSME 115

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           IE GR  +   L  +    + L+    ++ DG   + +I++L+    PE K
Sbjct: 116 IERGRKKVFRGLLRTSFLTERLLDEWAKVIDGKARVHDILNLDE---PEVK 163


>gi|226310092|ref|YP_002769986.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
 gi|226093040|dbj|BAH41482.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 123/251 (49%), Gaps = 22/251 (8%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE +    ++++V A   LV S+AKK+    + + DL+Q G IGL+ +  +FD      F
Sbjct: 23  GETKDPTIQEQLVRAYTPLVESLAKKFVRGQVMYEDLVQVGLIGLLASFRRFDPSFERTF 82

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            ++A+  +   I R I D++ ++ +P  +++   K+ R    ++ K++R P   +IA  L
Sbjct: 83  ESFAIPTIVGEIKRYIRDKTWSVYVPRRVKELSPKIKRVVDELTIKLQRSPQIADIANSL 142

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD---------SAIQA 607
            +  E + + L++ +   SL       D+    D   D N +S LD          A++ 
Sbjct: 143 GVSEEAILETLEMGRSYHSLSM-----DSELEADL--DGNTISLLDLVGTMEEGYGAVEQ 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           NL     R L  L  RE+ ++++ F   ++     ++ G    +++  I +++ +A+ KL
Sbjct: 196 NL--MLERALQILDHREKEIIQLTFYQNLSQ----KQAGDIMGMSQMHISRLQRRALGKL 249

Query: 668 KHPSRSKKLRS 678
           +   R ++L +
Sbjct: 250 REALRVEQLET 260


>gi|27468586|ref|NP_765223.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis ATCC
           12228]
 gi|57867587|ref|YP_189242.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis RP62A]
 gi|251812213|ref|ZP_04826686.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876523|ref|ZP_06285389.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|27316133|gb|AAO05267.1|AE016749_213 sigma factor B [Staphylococcus epidermidis ATCC 12228]
 gi|57638245|gb|AAW55033.1| RNA polymerase sigma-37 factor [Staphylococcus epidermidis RP62A]
 gi|251804310|gb|EES56967.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281294775|gb|EFA87303.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|329726159|gb|EGG62631.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU144]
 gi|329734176|gb|EGG70494.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU045]
          Length = 256

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 123/243 (50%), Gaps = 20/243 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V+   +L+ S+A +Y+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLKH 669
               R+L  L+ RE ++++  F  G++   T E +G  Q  V+R     ++  AI+KL+ 
Sbjct: 198 MILERILPILSERERQIIQCTFIEGLSQKETGERIGLSQMHVSR-----LQRTAIKKLQE 252

Query: 670 PSR 672
            +R
Sbjct: 253 AAR 255


>gi|253573548|ref|ZP_04850891.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251847076|gb|EES75081.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 262

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 112/230 (48%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AKK+++E  L +V  V+ +      + +   DL   G +GL+ A EKFD+  G +F TYA
Sbjct: 26  AKKQLIEKYLPIVDYVSGRLAVGLPKNVSKDDLASNGVMGLIDAVEKFDYKRGLQFETYA 85

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            W V+ AI   +        +P  +R+K  K+    + +  +  R  T  E++  L +  
Sbjct: 86  SWRVRGAILDGLRQGDW---VPRSVREKAKKIEEGYQHLEQQYLRSVTDAEMSSYLNVSE 142

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  + +L+        SLE PI +E++      + D+ A +P     +  LRE+  + + 
Sbjct: 143 KEFQSMLQEVAVMTLCSLEDPIREEESETRLTLLVDEKAKNPDYKVREFYLRESLAKGIE 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LT +E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 203 KLTEKERTVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|254478789|ref|ZP_05092157.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035301|gb|EEB76007.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 244

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 53/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 44  LSVEEESYLISKMEKGDNEA---KSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++     I +++R             +N
Sbjct: 101 IKAINTFNPRKKIKLATYA--------SRCIENE-----ILMYLRR------------NN 135

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K + E + +E    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 136 KTRLEVSFDE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 178

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   RE  T  L  L  RE++++R+RFG+   T+ T +EV     +++  I ++E 
Sbjct: 179 --------RELLTSALKKLPDREKKIIRLRFGLEGGTEKTQKEVADMLGISQSYISRLEK 230

Query: 662 KAIRKLK 668
           K +++LK
Sbjct: 231 KILKRLK 237


>gi|160944585|ref|ZP_02091813.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444367|gb|EDP21371.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|295103334|emb|CBL00878.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 224

 Score = 73.2 bits (178), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 116/225 (51%), Gaps = 15/225 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++  +  NL LV + A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA+  +
Sbjct: 8   REAFITQNLGLVHACAGRFRGRGMEYDDLYSAGCVGLIKAYDNFDESRGVCFSTYAVPVI 67

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              I +   D   T+++   +++ +   V+ AR  + K+   EPT +++A++L  P+E V
Sbjct: 68  LGEIKKLFRDGG-TVKVSRSLKE-LGMRVQAAREHTMKLCGAEPTLQQLAEQLDEPIENV 125

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              ++  +  +SL TP G ED    GD   D    SP +       R +   V+ +L  +
Sbjct: 126 ALAIQAAQPAMSL-TPEGGED----GDRQLDIPVESPEEELAD---RISLAEVIEALPEQ 177

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++++R+RF      + T  E  K    T+ +I + E K + +L+
Sbjct: 178 DKQLIRLRF----YGNRTQSETAKALHTTQVQISRRERKILIRLR 218


>gi|46204236|ref|ZP_00050286.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 182

 Score = 73.2 bits (178), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/153 (29%), Positives = 81/153 (52%), Gaps = 10/153 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+     +FSTYA WW
Sbjct: 26  ALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPEREVRFSTYATWW 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPV 560
           ++ +I   I      +R       K   +    RR+  ++ +   E    EI  ++A  +
Sbjct: 86  IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRARLMQSTEEQVGSEIHGRIATAI 143

Query: 561 EGVRKVL-----KITKEPISLETPIGDEDTSHL 588
              R+ +     +++   +SL  P+G+E  S L
Sbjct: 144 GVSREDVALMDARLSGPDMSLNAPVGEERRSFL 176


>gi|320537994|ref|ZP_08037899.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
 gi|320145151|gb|EFW36862.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
          Length = 262

 Score = 73.2 bits (178), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 108/207 (52%), Gaps = 14/207 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMR 526
           ++F DL+  G  GL  A +K+D     +F+TYA+  ++ AI     D+  +I  +P  +R
Sbjct: 53  IEFDDLVSYGIFGLFDAIDKYDPEKNIRFNTYAVTRIRGAIY----DELRSIDWVPRSVR 108

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKIT-KEPISL-ETPIGDE 583
            +I ++  T   +  K+ R  T EEIA +L + +E   + +LKI+    ISL +T  G E
Sbjct: 109 QQIKQIEDTIAAIEAKLGRSATDEEIAFELNISLEEYHQLLLKISGTSVISLADTKFGGE 168

Query: 584 DTSHL--GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D+  +  GD IE   +++P     +  ++      +  L+ RE++VL + +      D T
Sbjct: 169 DSGQIAVGDSIEAPASLNPDVIVEREEIKRVIVEAIKELSEREQQVLILYY----YEDMT 224

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+GK   VT  R+ QI   A  KLK
Sbjct: 225 LKEIGKVLKVTESRVSQIHTSANLKLK 251


>gi|15614994|ref|NP_243297.1| RNA polymerase sigma factor SigD [Bacillus halodurans C-125]
 gi|10175051|dbj|BAB06150.1| RNA polymerase sigma-D factor [Bacillus halodurans C-125]
          Length = 256

 Score = 73.2 bits (178), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 106/202 (52%), Gaps = 11/202 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A EKF+     KF TYA + V+ AI   +  +     +P  MR+KI K
Sbjct: 55  DLISHGMLGLLDALEKFNPDRDLKFDTYASFRVRGAILDGLRKEDW---LPRSMREKIKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDED--TSH 587
           +     ++  K+ R  + EE+AK++ +    V + +   +    +S++    D D   ++
Sbjct: 112 IEAATEKLEQKLGRNVSVEEVAKEVGISENEVSQTMTESLVANLLSMDEKTNDSDREETY 171

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               I DK ++SP +  ++   +E  ++++A++   +E+++    G+    + TL E+G+
Sbjct: 172 TATII-DKQSLSPEEKLLEEAQKEELSQLIANILNEKEQLV---IGLFYFEELTLTEIGQ 227

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++  RI QI +KA+ +L+ 
Sbjct: 228 ILKLSTSRISQIHSKALFRLQQ 249


>gi|294634103|ref|ZP_06712658.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829917|gb|EFF88271.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 294

 Score = 73.2 bits (178), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/261 (22%), Positives = 122/261 (46%), Gaps = 40/261 (15%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G  E   A+  ++E N+ LV   A ++ NR     D++Q G IGL+KA +
Sbjct: 47  FRRLTEL-EEGTHEYQYARNTLIEMNMSLVRFAAGRFRNRSDDMEDIVQTGMIGLIKAID 105

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+++A+ ++   I R   D +  + +P  +++   ++ R    +S+++ R+
Sbjct: 106 RFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELARAREELSSRLDRD 165

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--------EPISLETPIGDEDTSHLGDFI------ 592
           PT  E+A  + +    V +    +           ++ + P G E    L DFI      
Sbjct: 166 PTVAELATLMNLSESEVVEAQIASNGYNSSSLDAALTGDGPEGGEAV--LADFIGVEEHG 223

Query: 593 ----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
               ED +A++PL               +A L+ R+ R++ +RF      + T  E+G+Q
Sbjct: 224 IRLVEDFHALAPL---------------VADLSERDRRIIHLRF----VEEATQAEIGEQ 264

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
              ++  + ++  + I +L+ 
Sbjct: 265 LGCSQMHVSRLIKRIITQLRQ 285


>gi|310641572|ref|YP_003946330.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309246522|gb|ADO56089.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 262

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AKK+++E  L +V  V+ +      + +   DL   G +GL+ A EKFD+  G +F TYA
Sbjct: 26  AKKQLIEKYLHIVEYVSGRLAVGLPKNVSKDDLASNGVMGLIDALEKFDYERGLQFETYA 85

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            W V+ AI   +        +P  +R+K  K+    + +  +  R  + EE++  L +  
Sbjct: 86  SWRVRGAILDGLRQGDW---VPRSVREKAKKIEDAYQHLEQRYLRTVSDEEMSHYLDVSE 142

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  + +++       +SLE PI +E++      + D+ A +P     +  LR+   + + 
Sbjct: 143 KEFQSMIQEVAVMSIVSLEDPIREEESETRLSLLVDEKAKNPDHKVNEFTLRDALAQGID 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LT +E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 203 KLTEKERIVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|308068681|ref|YP_003870286.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
 gi|305857960|gb|ADM69748.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
          Length = 262

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AKK+++E  L +V  V+ +      + +   DL   G +GL+ A EKFD+  G +F TYA
Sbjct: 26  AKKQLIEKYLHIVEYVSGRLAVGLPKNVSKDDLASNGVMGLIDALEKFDYERGLQFETYA 85

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            W V+ AI   +        +P  +R+K  K+    + +  +  R  + EE++  L +  
Sbjct: 86  SWRVRGAILDGLRQGDW---VPRSVREKAKKIEDAYQHLEQRYLRTVSDEEMSHYLDVSE 142

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  + +++       +SLE PI +E++      + D+ A +P     +  LR+   + + 
Sbjct: 143 KEFQNMIQEVAVMSIVSLEDPIREEESETRLSLLVDEKAKNPDHKVNEFTLRDALAQGID 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LT +E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 203 KLTEKERIVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|88797598|ref|ZP_01113187.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88779770|gb|EAR10956.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 290

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 111/234 (47%), Gaps = 17/234 (7%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V ++LR V+ +AK Y+  GL   DLIQEGN+GLMKA  +F+  +G +  ++A+ W+K
Sbjct: 56  RRLVMSHLRFVVHIAKSYSGYGLNQGDLIQEGNVGLMKAIRRFNPEVGVRLVSFAVHWIK 115

Query: 506 QAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMP 559
             I   I      ++I      R     +  + +R+    +RE         + KK+   
Sbjct: 116 AEIHEYILKNWRIVKIATTKAQRKLFFNLRSSKKRLGWLNEREAQAIADDLGVEKKIVYD 175

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +EG  ++               D    H  D++ ++ A  P  +  QAN  +     L S
Sbjct: 176 MEG--RLTASDAAFDGFNDDDDDGAAFHPSDYLMNE-ADDPAAAVEQANYTDDAHGQLFS 232

Query: 620 ----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  R   +++ R+   +N +  TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 233 ALEDLDDRSRDIIQQRW---LNEEKATLHELADKYGVSAERIRQLEKNAMNKVK 283


>gi|239934572|emb|CAR94600.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 219

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 47/69 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLTFQ ++   + +  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTFQHILNSYESVKQ 60

Query: 177 GTTLLREII 185
           G   L +II
Sbjct: 61  GQGRLVDII 69


>gi|152998320|ref|YP_001343155.1| RNA polymerase factor sigma-32 [Marinomonas sp. MWYL1]
 gi|150839244|gb|ABR73220.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas sp. MWYL1]
          Length = 288

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 111/238 (46%), Gaps = 21/238 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V ++LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARTLVMSHLRFVVHIAKSYSGYGLAQGDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+A++  +        E +A  L +  E 
Sbjct: 110 IKAEIHEFILKNWRIVKVATTKAQRKMFFNLRSAKKSLSWFSNSEV-ESVASDLGVTPEV 168

Query: 563 VRKV--------LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           VR++        +         +       + +L D   D     P       N  E + 
Sbjct: 169 VRQMEGRLSSSDMAFDASADDDDDSAFQAPSQYLEDHRSD-----PATLLENGNWEEDSN 223

Query: 615 R----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     +A L  R   +L  R+    +   TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 224 QRLEVAMADLDERSRNILVQRW--LSDAKSTLHELADEYGVSAERIRQLEKNAMKKIR 279


>gi|297197353|ref|ZP_06914750.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197714848|gb|EDY58882.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 263

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 98/222 (44%), Gaps = 28/222 (12%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VE  L +   +A ++  RG    DL Q   +GL+KA + +D   G  F  YA+  V
Sbjct: 38  RDELVELWLPMAERIAVRFRGRGESLEDLYQVAALGLVKAVDHYDPARGSAFEAYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D   T+ +P  ++D  ++V + ++ +S    R PT  EIA++  +  + VR
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRQASKELSQTPGRAPTVAEIAERAHLTEDEVR 157

Query: 565 KVLKITK--EPISLETPIGDEDTSHLG----------DFIEDKNAVSPLDSAIQANLRET 612
              +  +    +SLE  +   D   LG          D + D+ AV P            
Sbjct: 158 AGAEALECFSALSLEAEMPGTDGYALGDALGVPDPGYDVVVDRVAVGP------------ 205

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
               L +L  RE  +L +RF  GM      EE+G  Q  V+R
Sbjct: 206 ---CLKALPERERTILYLRFFRGMTQSCIAEELGISQMHVSR 244


>gi|134300227|ref|YP_001113723.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134052927|gb|ABO50898.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfotomaculum
           reducens MI-1]
          Length = 251

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 123/245 (50%), Gaps = 19/245 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+++++  +L LV  +A +   +   F+   DL   G IGLM+A +K+D  +G+ F +YA
Sbjct: 18  ARQKIILLHLPLVKHLAGRVAVKLPSFILREDLESYGVIGLMEALDKYDPAMGHSFDSYA 77

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +  Q+    +P     K   +  T  R+  +     T E +AK++ +PV
Sbjct: 78  YHRIRGAMLDEVRRQNW---LPRTAWQKNQLLKNTRERLEREQGEVITNEVLAKEMGIPV 134

Query: 561 EGVRK-VLKITKEPI-SLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRV 616
           E VR+ +    K  I SL+  +   D S +   + +ED N+  PL    +   +      
Sbjct: 135 EEVRQLIFNANKMYIQSLDEEVAGHDGSQMSKLELLEDTNSPDPLSIVEEKESKRLLAEA 194

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + +L+ RE+ +L + +  G+    TL+E+G+   V+  R+ Q+ ++ +++LK     K L
Sbjct: 195 IETLSEREKLILALYYSEGL----TLKEIGQVLEVSESRVCQLHSQVMKRLK-----KTL 245

Query: 677 RSFLD 681
            S L+
Sbjct: 246 ESMLN 250


>gi|256545958|ref|ZP_05473313.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
 gi|256398380|gb|EEU12002.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
          Length = 256

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 119/230 (51%), Gaps = 18/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY+FS++A   +
Sbjct: 30  RNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGYEFSSFATPTI 89

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D+   IR+P  +++   K+    + +  +++R PT ++IA  L    E + 
Sbjct: 90  MGELKRYFRDKGWVIRVPRRIQNLYKKINVAKKILPQELQRTPTIKDIAAYLGEDEETIL 149

Query: 565 KVLKITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVL 617
           + ++ +K   P SL+        E++  L D I  +DKN     DS    +L + +T  L
Sbjct: 150 ETIEASKVYSPQSLDMKYQVQKGENSVDLSDMIGEDDKN----FDSVELKDLIDKSTERL 205

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L   E+++L +R+  G     T  ++  +  +++  + +IE K ++K 
Sbjct: 206 NDL---EKQILELRYYEG----RTQVDIANKLSISQMTVSRIEKKILQKF 248


>gi|221133291|ref|ZP_03559596.1| flagellar biosynthesis sigma factor [Glaciecola sp. HTCC2999]
          Length = 243

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 112/237 (47%), Gaps = 17/237 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +C  S++ +E+VE +  LV  +A     R    +   DLIQ G +GL++AA+ F+   G 
Sbjct: 7   DCNQSLSSEELVEKHTILVKRIAHHLLARLPPNILVDDLIQAGMLGLLEAAKNFNSTKGA 66

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F T+A   ++ ++   I     T R  VH   +   + +    + N++  +    +IAK
Sbjct: 67  SFETFAGIRIRGSMLDDIRKGDWTPR-SVHKNSR--AITQAISSVENEMNSDAKDSDIAK 123

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED---KNAVSPLDSAIQANLRE 611
           +L + +    K+L      +++   +G ED     D I     K+  +P D  +    ++
Sbjct: 124 RLGIELPQYHKMLN----EVNIGKLVGIEDLGISEDVIATPDFKSTNTPYDELVHGCFQK 179

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + + SL  RE  VL + +    + D +L E+G+   V+  R+ QI ++A  KLK
Sbjct: 180 ALAKAIVSLPEREAIVLSLYY----DEDLSLREIGQALNVSESRVSQIHSQAKSKLK 232


>gi|108798252|ref|YP_638449.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119867348|ref|YP_937300.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126433912|ref|YP_001069603.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108768671|gb|ABG07393.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119693437|gb|ABL90510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126233712|gb|ABN97112.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 263

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 108/228 (47%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+  +
Sbjct: 41  RDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVDAGSDFVSFAVPTI 100

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----V 560
              + R   D S ++++P  +++   ++      +S ++ R PT  E+A++L M     V
Sbjct: 101 MGEVRRHFRDNSWSVKVPRRLKELHLRLGSATAELSQRLGRAPTASELAEELGMDRDEVV 160

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           EG+          I      G+ED   + D + D +    LD   Q   RE    +LA+L
Sbjct: 161 EGLVAGSSYNTLSIDSGGNSGNEDAPAIADTLGDVDL--GLD---QIENREALRPLLAAL 215

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  VL +RF   +      E VG    +++  + ++ AK++ +L+
Sbjct: 216 PERERMVLLLRFFENLTQTQIAERVG----ISQMHVSRLLAKSLTRLR 259


>gi|218896055|ref|YP_002444466.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
 gi|218544560|gb|ACK96954.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
          Length = 257

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C    A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCNE--AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    +T  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEQTERRLVLEDIFNVLNDTEKSVIHYIFGENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|29827282|ref|NP_821916.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604380|dbj|BAC68451.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 279

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/253 (22%), Positives = 125/253 (49%), Gaps = 34/253 (13%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFD 489
           ++++ +G  E   A+  ++E N+ LV   A ++ +R   +  D++Q G IGL+KA ++F+
Sbjct: 39  LAVLEEGTPEYQYARNTLIEMNVTLVRFAAARFRSRSQDEMEDIVQVGTIGLIKAIDRFE 98

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+++A+ ++   I R   D S  + +P  +++   ++ +    + +++ R PT 
Sbjct: 99  LTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARIQLAKATEELQSRLDRMPTV 158

Query: 550 EEIAKKLAMPVEGVR--KVLKITKEPISLETPI--GDEDTSHLGDFI----------EDK 595
           +E+++ + +  E V   ++        SL+  I   ++  + L DFI          ED 
Sbjct: 159 KELSELMCLSEEEVNEARLASNGYTSSSLDATISSSNDGEAALADFIGTDDNALELVEDF 218

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NA++P+               +A L  RE R++ MRF      + T  ++G+   V++  
Sbjct: 219 NALAPM---------------IAELDDRERRIIHMRF----VDELTQAQIGEHLGVSQMH 259

Query: 656 IRQIEAKAIRKLK 668
           + ++ ++ + KL+
Sbjct: 260 VSRLLSRTLAKLR 272


>gi|154499126|ref|ZP_02037504.1| hypothetical protein BACCAP_03120 [Bacteroides capillosus ATCC
           29799]
 gi|150271966|gb|EDM99192.1| hypothetical protein BACCAP_03120 [Bacteroides capillosus ATCC
           29799]
          Length = 340

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 46/64 (71%), Gaps = 4/64 (6%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ LT REE VLR+RF  G+    T  E GK+F VTRERI QIE  A+RKL+HPSRSK L
Sbjct: 111 LSQLTTREEEVLRLRFFEGL----TGAECGKKFGVTRERIHQIEVTALRKLRHPSRSKFL 166

Query: 677 RSFL 680
           + F+
Sbjct: 167 KPFV 170


>gi|256269|gb|AAC60415.1| RpoD2 [Synechococcus]
          Length = 48

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/48 (68%), Positives = 38/48 (79%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           LDLIQEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA QS T
Sbjct: 1   LDLIQEGTLGLERGVEKFDPSKGYKFSTYAYWWIRQAITRAIAQQSRT 48


>gi|51894120|ref|YP_076811.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
 gi|51857809|dbj|BAD41967.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
          Length = 253

 Score = 72.8 bits (177), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 122/238 (51%), Gaps = 23/238 (9%)

Query: 442 SIAKKEMVEANLRLVISVAKK-------YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + A+  +V+  L LV  VA +       + ++G    D+   G  GL++A  ++D   G 
Sbjct: 16  TAARDALVQHYLWLVRYVAGRLMVGMPDHVDQG----DVEGHGCFGLLEAIARYDPDRGV 71

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F T+A+ W++ A    +      ++    +R ++ ++ R    +   + REP+  E+A+
Sbjct: 72  RFETFAIPWIRGACLEGLR----AMQWAPALRRRVRQLERVRDELMAVLGREPSAAELAE 127

Query: 555 KLAMPVEGVRKVLK--ITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++ + VE   + L+   T   +SL+  +   D +T+ L D + D+ AV P   + +A  R
Sbjct: 128 QMGISVEEAERRLQEAGTLAVLSLDEALAFDDGETTALADRVADEEAVDPELESQRAERR 187

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   R +ASLT +E+ V+ + +  G+      +EV +   +++ RI Q+ +KAI +L+
Sbjct: 188 EVLARAIASLTEQEQLVIALIYQEGLIA----KEVSEILGLSQARISQVHSKAILRLR 241


>gi|302552488|ref|ZP_07304830.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470106|gb|EFL33199.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 285

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/260 (21%), Positives = 123/260 (47%), Gaps = 38/260 (14%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   ++++ +G  E   A+  ++E N+ LV   A+++ + G    D++Q G IGL+KA 
Sbjct: 40  QFLDRLAVLEEGTPEHQYARNTLIEMNMSLVRFAARRFRSSGQAMEDVVQVGVIGLIKAI 99

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ +    +++++ R
Sbjct: 100 DRFEVSREVQFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARTELAKATEELASRLGR 159

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPIS-----------------LETPIGDEDTSHL 588
            P   E+A  + +  E V +        +S                 L   IG+ED    
Sbjct: 160 APRVAELAALMNLSEEEVVEAQVAANGYLSSSLDATISGDSEDSDSTLSEFIGEEDPGL- 218

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + +ED +A++PL               +A L  R+  +L +RF      + T  E+GK+
Sbjct: 219 -ELVEDFHALAPL---------------IAELDERQRLILHLRF----VEELTQAEIGKR 258

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++  + ++ A+ + +L+
Sbjct: 259 LGISQMHVSRLIARTVARLR 278


>gi|194289649|ref|YP_002005556.1| RNA polymerase sigma 70 (sigma d) factor [Cupriavidus taiwanensis
           LMG 19424]
 gi|193223484|emb|CAQ69489.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus taiwanensis
           LMG 19424]
          Length = 655

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 71/141 (50%), Gaps = 6/141 (4%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEE 87
           + +I+L RQRGY+T  +++  LP +   +  ME  V   + MG+ +     D + L   +
Sbjct: 44  RALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVGTFAEMGVKIYEQTPDAETLLLSD 103

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G    +     A   +       DS    T DPVRMY+REM S  LL+R+ E+ IAKRIE
Sbjct: 104 GP--VVASDEQAEEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRIE 161

Query: 148 AGRAMMMASLCESPLTFQALI 168
            G   M+ ++   P T   ++
Sbjct: 162 DGLNNMVHAISACPFTIATIL 182


>gi|302338101|ref|YP_003803307.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635286|gb|ADK80713.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 262

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 107/209 (51%), Gaps = 14/209 (6%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVH 524
           + ++F DL+  G  GL  A EKFD     KF TYA+  ++ AI     D+  +I  +P  
Sbjct: 51  QNVEFDDLVGFGVFGLFDAIEKFDPEKHVKFKTYAVTRIRGAIY----DELRSIDWVPRS 106

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI--- 580
           +R K  ++  T  R+   + R  + +EIA +L + V   +K+ LKI+   +     +   
Sbjct: 107 VRQKAREIEETIHRLEASLGRAASDKEIADELGISVADFQKLMLKISGTSVLSLNDVWYT 166

Query: 581 GDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           GDE DT  + D IE   +++P     +  +R    + ++ L  +E++VL + +      D
Sbjct: 167 GDENDTVAIVDGIESPQSLNPDIIIEKEEIRRVIVQAISELPEKEKKVLVLYY----YED 222

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+GK   VT  R+ Q+  KAI +L+
Sbjct: 223 LTLKEIGKVLDVTESRVSQLHTKAIMRLR 251


>gi|37525878|ref|NP_929222.1| flagellar biosynthesis sigma factor [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36785307|emb|CAE14248.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 240

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERFDSLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V    R++   + R  + +E+AK+L + +   R++L  T           DE     G+ 
Sbjct: 100 VTHIIRKLEQDLGRPASEQEVAKELKIDLVEYRQILLDTNNSQLFSY---DEWHEMHGES 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               IE+ +  +PL   +++++R+     + SL  RE+ VL + +   +N    L+E+G 
Sbjct: 157 CEPVIEEGHETNPLQQLLESDVRQRVIEAIDSLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   RI Q+ ++AI++L+
Sbjct: 213 VLEVGESRISQLHSQAIKRLR 233


>gi|254422308|ref|ZP_05036026.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196189797|gb|EDX84761.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 259

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 107/219 (48%), Gaps = 8/219 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V+ N+ LV   A ++    G  F DL+Q G++GL+ A E+FD   GY FS++A+ +
Sbjct: 29  RNRLVQLNIGLVRQEAYRWLGYSGETFDDLMQIGSLGLINAIERFDLEKGYAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+   +RIP   +   ++  +  R + N++ R+P   E+A +L + VE  
Sbjct: 89  IRGEIQHYLRDKGTVVRIPRKWQALQNQAAQAIRHLQNELNRKPNDYEVAARLNVTVEEW 148

Query: 564 R--KVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  K+    +  +SL+ PI ++    S LG+ + D    S    A +  +R    + L  
Sbjct: 149 QQVKLASSNRHLLSLDAPIREDRNGASSLGELLPDARYRS-FQLAQEDRIR--LQQALEQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           L  R   VL   F   +    T +++G        R+R+
Sbjct: 206 LEKRTREVLEFVFLQDLTQKETAKKLGISSVTVSRRVRK 244


>gi|271964601|ref|YP_003338797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270507776|gb|ACZ86054.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 258

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 111/246 (45%), Gaps = 36/246 (14%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E  A   ++ +VE +  L + +A++Y  RG    DL+Q   +GLMKA   FD  LG+ F 
Sbjct: 27  EYRAERLRERIVEMHRPLAMEIARRYRYRGEPLEDLLQAAYVGLMKAINGFDPTLGHAFR 86

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA+  +   + R   D++  IR+P   +++  ++ R    +S  + R PT  E+A K+ 
Sbjct: 87  GYAVVTMTGEVKRHFRDRTWAIRVPRVYQERRAELNRLVADLSQDLGRAPTVAELAVKMR 146

Query: 558 MPVEGVRKVLKITKEPISLETP---------------IGDEDTSHLGDFIEDKNAVSPLD 602
           +  E V   L  +    +L                  I DED + LG  + D+ AV PL 
Sbjct: 147 ISEEDVLLTLDASAAYSALSLDAPLGADDDAAALGDIIPDEDDA-LGVLV-DREAVKPL- 203

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                         +  L  RE+ +L +RF   M    T  E+  +F +++  + +I  K
Sbjct: 204 --------------IDKLPTREKNILLLRFFGNM----TQAEIAAEFGISQMHVSRILRK 245

Query: 663 AIRKLK 668
            + +L+
Sbjct: 246 VLDQLR 251


>gi|118443948|ref|YP_877996.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
 gi|118134404|gb|ABK61448.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
          Length = 242

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 114/231 (49%), Gaps = 15/231 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + ++F DL+  G +GLM A  KFD   G KFSTYA 
Sbjct: 10  KEEIVKKYIPLVKYIASRVIIGKTKYIEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I   S    I     DK++K       +  +   EP  ++IAK+L M V+
Sbjct: 70  IRIRGSMIDEIRKNSP---ISKGAMDKLNKYNSAIESLQKRNLAEPNIKDIAKELDMTVK 126

Query: 562 GVRKVLKITK--EPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V ++         +SLE  I   D+D S +G  IED N+ +P +        E  ++ L
Sbjct: 127 QVGEIENFINYISIVSLEDLIFSEDDDISLMGT-IEDINSPNPEEEYENDEKLEYLSKGL 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL + +      + TL+E+GK   V+  R+ Q+ ++AI  L+
Sbjct: 186 DMLNEKDRTVLSLYY----YEEMTLKEIGKILGVSESRVCQLHSRAIVHLR 232


>gi|302556969|ref|ZP_07309311.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474587|gb|EFL37680.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 295

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/260 (22%), Positives = 124/260 (47%), Gaps = 40/260 (15%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA +
Sbjct: 48  FRRLAEL-EEGTREYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIGLIKAID 106

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +++++ RE
Sbjct: 107 RFELAREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELASRLDRE 166

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSH----LGDFI------ 592
           PT  E+A  + +     VEG  ++        SL+  +  +   +    L DFI      
Sbjct: 167 PTVAELATLMNITEQQVVEG--QIAANGYNSSSLDAALTGDGPEYGEAVLADFIGVEEEG 224

Query: 593 ----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
               ED ++++PL               +A L+PR+  +L +RF      + T  E+G++
Sbjct: 225 LRLVEDFHSLAPL---------------MAELSPRDREILHLRF----VEEATQAEIGER 265

Query: 649 FCVTRERIRQIEAKAIRKLK 668
              ++  + ++  + I +L+
Sbjct: 266 LGCSQMHVSRLIKRIIARLR 285


>gi|302874610|ref|YP_003843243.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|307690779|ref|ZP_07633225.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|302577467|gb|ADL51479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
          Length = 241

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 110/228 (48%), Gaps = 13/228 (5%)

Query: 447 EMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E++   + LV  +A +     ++ ++F DL+  G +GLM A  KFD   G KFS+YA   
Sbjct: 12  EIITKYIPLVKYIASRVIIGKSKHIEFDDLVSNGILGLMDALNKFDESKGMKFSSYASIR 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K A+   +   S    IP    DK+++       + N + REPT +EIA ++A+ +  V
Sbjct: 72  IKGAMIDELRRNS---PIPKGAMDKLNRYNSAIDSLRNTLLREPTVDEIACEMAIDIADV 128

Query: 564 RKVLKITK--EPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            ++         +SLE  I  ED    L   I+D  + SP          E   + +  L
Sbjct: 129 IEIENHINYLSVVSLEELIYSEDDDMPLIGTIKDNKSPSPEKDLEDKEKMEYLAKAIELL 188

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +++ VL + +  G+    TL+E+GK   V+  R+ Q+  +AI  L+
Sbjct: 189 NEKDKLVLNLYYYEGL----TLKEIGKILEVSESRVCQLHTRAIAHLR 232


>gi|256379908|ref|YP_003103568.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
 gi|255924211|gb|ACU39722.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
          Length = 272

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 101/205 (49%), Gaps = 16/205 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G  GL+ A EKF+   G KF TYAM  ++ AI   +  Q     +P  +R +   
Sbjct: 67  DLIQSGIFGLVDAIEKFEPERGLKFETYAMQRIRGAILDDLRSQDW---VPRSVRSRARD 123

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPI-----GDE 583
           V R   R+  +++R PT  E+A +L + +  +R++    ++T   ++L+  I        
Sbjct: 124 VERALERLGGRLQRTPTDRELAAELKIGLGELRELYAQFQLTS-VVALDELIAAGRAAGS 182

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S L + + D+ A  P+ S +  + R      +A L  R+  V+ + +      + TL 
Sbjct: 183 AGSSLAESLPDEGAEDPVASLVDQDSRRQLADAIAQLAERDRVVVTLYY----FENLTLA 238

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+GK   VT  R+ Q+  +A+ +L+
Sbjct: 239 EIGKVLGVTESRVCQLHTRAVLRLR 263


>gi|297200782|ref|ZP_06918179.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197712352|gb|EDY56386.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 285

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 115/241 (47%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  +  ++EANL LV   A ++ +R     D+IQ G IGL+ A ++FD   G
Sbjct: 51  LQPGTPEHNRVRTALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPDRG 110

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 111 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAFGRTPTTAEIA 170

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++  +     SLE     ++   L   ++      P    ++   R+
Sbjct: 171 QRLRITEDEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RD 225

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +
Sbjct: 226 LVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSAN 281

Query: 672 R 672
           R
Sbjct: 282 R 282


>gi|328880523|emb|CCA53762.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 325

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/249 (23%), Positives = 124/249 (49%), Gaps = 10/249 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + F  + S+  +G    S  +  +VE NL LV   A ++ +    + DL+Q G +GL
Sbjct: 49  LSTALFERLRSL-EEGTASYSYVRNTLVELNLSLVKYAATRFRHSSENWEDLVQVGTVGL 107

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA  +FD   G +F ++A+  V   I R + D S ++ +P  +++    V +    +  
Sbjct: 108 IKAINRFDPARGNEFMSFALPTVLGEIRRHLRDTSWSVHVPRRLQELRLDVAKANDALEQ 167

Query: 542 KIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++ R PT  E++ +L +  + +R  ++        SL+ P+ DED    G  +  +   S
Sbjct: 168 ELGRPPTAAELSDRLHITEDELREGRIAANGFASRSLDVPVDDEDA---GPGMLARCLGS 224

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D+  +    E    ++A+L+ R+  +L +RFG     + T  E+G++  +++  + ++
Sbjct: 225 DDDAFEKVLNLEALKPLVAALSERDRTILALRFG----GELTQAEIGERLGLSQMHVSRL 280

Query: 660 EAKAIRKLK 668
            ++ +  L+
Sbjct: 281 LSRILGGLR 289


>gi|228919826|ref|ZP_04083184.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839842|gb|EEM85125.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 224

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 111/234 (47%), Gaps = 24/234 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  I +P  ++D   K+      ++++++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR-----VL 617
                         +   S L D +E   D ++V+ ++S   ++    ET  R     + 
Sbjct: 121 DAKN----------NYRVSSLDDVVENSSDGSSVARIESVGEVEQGYEETERRLVLKDIF 170

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             L   E+ V+   FG  +N   T    G++  +++  + +I+ +AI KLK  +
Sbjct: 171 NVLNETEKSVIHYIFGENLNQKDT----GERLGISQMHVSRIKRQAISKLKQAA 220


>gi|21222438|ref|NP_628217.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|585925|sp|P37971|RPOF_STRCO RecName: Full=RNA polymerase sigma-F factor
 gi|153455|gb|AAA93052.1| sigma factor [Streptomyces coelicolor A3(2)]
 gi|13122128|emb|CAC32306.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 287

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 112/238 (47%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 56  GTPEHDRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 115

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 116 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERL 175

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 176 RITEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 230

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 231 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 284


>gi|168186139|ref|ZP_02620774.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
 gi|169295860|gb|EDS77993.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
          Length = 242

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 113/231 (48%), Gaps = 15/231 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + ++F DL+  G +GLM A  KFD   G KFSTYA 
Sbjct: 10  KEEIVKKYIPLVKYIASRVIIGKTKYIEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I   S    I     DK++K       +  K   EP  ++IA++L M V 
Sbjct: 70  IRIRGSMIDEIRKNSP---ISKGAMDKLNKYNAAIENLQRKNLSEPNIKDIAQELDMTVS 126

Query: 562 GVRKVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V ++         +SLE  I   D+D S +G  IED N+  P +   +    E  ++ L
Sbjct: 127 QVGEIENFINYISIVSLEDLIFSDDDDISLIGT-IEDINSPDPEEEFERDEKLEYLSKGL 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL + +      + TL+E+GK   V+  R+ Q+ ++AI  L+
Sbjct: 186 DMLNDKDRTVLSLYY----YEEMTLKEIGKVLGVSESRVCQLHSRAIVHLR 232


>gi|294630217|ref|ZP_06708777.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833550|gb|EFF91899.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 314

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 113/238 (47%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 83  GTSEHARVRGALIEANLPLVRYAAGRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQF 142

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 143 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERL 202

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 203 RITEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 257

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 258 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 311


>gi|291278833|ref|YP_003495668.1| RNA polymerase sigma factor for flagellar operon FliA
           [Deferribacter desulfuricans SSM1]
 gi|290753535|dbj|BAI79912.1| RNA polymerase sigma factor for flagellar operon FliA
           [Deferribacter desulfuricans SSM1]
          Length = 243

 Score = 72.4 bits (176), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/192 (27%), Positives = 100/192 (52%), Gaps = 10/192 (5%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            G ++A +++D      F  YA   VK AI   +       R   ++R KI  +     R
Sbjct: 53  FGFVEALKRYDKSRNIDFKYYAEKRVKGAILDVLRKMDILSR---NVRTKIKDLEDKIAR 109

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKN 596
           +S+K+ R+P P EIAK+  + ++ V K+L++    + +SL+   G++D+S L +FI+  +
Sbjct: 110 LSSKLGRKPHPSEIAKEYNLDIDEVNKLLELLENSDQVSLDITFGEDDSSSLINFIKS-D 168

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            ++P +S  +  L E   + +  L  +E  V+ + +      D T++E+G    ++  R+
Sbjct: 169 ILTPEESIEKKELIEVLGKEIEKLNEKERLVITLYYY----EDLTMKEIGSVLGISESRV 224

Query: 657 RQIEAKAIRKLK 668
            Q+   A++KLK
Sbjct: 225 SQLHNSAVKKLK 236


>gi|210624023|ref|ZP_03294140.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
 gi|210153230|gb|EEA84236.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
          Length = 255

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/223 (22%), Positives = 112/223 (50%), Gaps = 9/223 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L L   +AKKY N+G+ + D+ Q  ++ L+ A +++D   G++FS++A   +   
Sbjct: 34  LIERHLYLARILAKKYINKGVDYEDIYQVASLALIYAIDRYDISKGFEFSSFATPTIIGE 93

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+  T+R+P  +++   K+      +  + KR P+ ++IA+ +    E V + +
Sbjct: 94  IKKYFRDKVWTMRVPRRIQELSKKISNAKIAIEQEKKRHPSVKDIAEYIGCREEDVLEAM 153

Query: 568 K--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   + +P+SL+   GD+    L   + D+  V   D       ++   R + +L   E 
Sbjct: 154 EASYSYQPVSLDASSGDDSEDDLT--LSDRVGVEEKDFG-NIEQKDFLNRFMQTLNELEV 210

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L  RF      + T   +  +  +++  + ++E K + KL+
Sbjct: 211 KILEDRFF----HNKTQSVIATELNISQMTVSRLEKKVVEKLR 249


>gi|291436144|ref|ZP_06575534.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291339039|gb|EFE65995.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 282

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VEA L +   +A ++ +RG  F DL Q   +GL+KA +++D  LG  F +YA+  +
Sbjct: 53  RGEIVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTI 112

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS-NKIKREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  +++  ++V   ++ +S +   R PT  EIA+   +  E V
Sbjct: 113 TGEIKRHFRDHMWTLHVPRRVQELRNRVRSASQDLSLSGSGRPPTVAEIAEHADLSEEDV 172

Query: 564 R----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R     +   T   +  E   GD+  S LGD +   +    LD+ +    RE     LA+
Sbjct: 173 RTGQGALDSFTALSLDAELTSGDDGYS-LGDTLGAPDPA--LDTVVD---REAVRERLAA 226

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  RE+ +L MRF   M       E+G  Q  V+R
Sbjct: 227 LPEREQAILYMRFFGDMTQSSIAAELGISQMHVSR 261


>gi|75761672|ref|ZP_00741618.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490828|gb|EAO54098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 258

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C    A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 19  LIAEFQQNQCNE--AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 76

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 77  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 136

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 137 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENSSDGSSVARIESVGE 186

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    +T  R     +   L   E+ V+   FG  +N   T E +G    +++  + +I
Sbjct: 187 VEQGYEQTERRLVLEDIFNVLNDMEKSVIHYIFGENLNQKDTRERLG----ISQMHVSRI 242

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 243 KRQAISKLKQAA 254


>gi|256786488|ref|ZP_05524919.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 291

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 112/238 (47%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 60  GTPEHDRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 119

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 120 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERL 179

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 180 RITEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 234

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 235 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 288


>gi|223043961|ref|ZP_03614002.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|314934140|ref|ZP_07841501.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
 gi|222442676|gb|EEE48780.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|313653045|gb|EFS16806.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
          Length = 256

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 123/242 (50%), Gaps = 18/242 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKISDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VSDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R+L  L+ RE ++++  F  G++   T E +G    +++  + +++  AI+KL+  
Sbjct: 198 MILERILPILSDRERQIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQEA 253

Query: 671 SR 672
           ++
Sbjct: 254 AK 255


>gi|47569335|ref|ZP_00240019.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228967406|ref|ZP_04128439.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|47554006|gb|EAL12373.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228792294|gb|EEM39863.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 228

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 27  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 83

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 84  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 109

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 110 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 151

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 152 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 211

Query: 666 KLKH 669
           K+ H
Sbjct: 212 KMFH 215


>gi|206975995|ref|ZP_03236905.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
 gi|206745747|gb|EDZ57144.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
          Length = 237

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 36  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 92

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 93  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 118

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 119 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 160

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 161 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEETQREIAKALGISRSYVSRIEKRALM 220

Query: 666 KLKH 669
           K+ H
Sbjct: 221 KMFH 224


>gi|149183717|ref|ZP_01862127.1| sigma factor B [Bacillus sp. SG-1]
 gi|148848576|gb|EDL62816.1| sigma factor B [Bacillus sp. SG-1]
          Length = 265

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 54/216 (25%), Positives = 113/216 (52%), Gaps = 8/216 (3%)

Query: 455 LVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           LVIS+A+KY+ +G  F  D++Q G IGL+ A  ++D   G  F  +A+  +   I R + 
Sbjct: 41  LVISIARKYS-KGKSFHEDIVQVGMIGLLGAIRRYDDSFGKTFEAFAIPTIVGEIKRFLR 99

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           D++ ++ +P  +++   K+  T   ++N ++R P  EEIA  + +  E V + +++ K  
Sbjct: 100 DKTWSVHVPRRIKELGPKIKSTVEELTNTLERSPKVEEIADYIGVTEEEVLEAMEMGKSY 159

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRF 632
            +L      E  S  G  +   + V  +D   +  N +    +VL  L+ RE  +++  +
Sbjct: 160 QALSVDHSIEADSE-GSTVTLLDIVGNVDEGYERINQKLVLEKVLHVLSERERLIIQYTY 218

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++     ++ G++  +++  + +++ +AI+KLK
Sbjct: 219 LDNLSQ----KDAGEKLGISQMHVSRLQRRAIKKLK 250


>gi|259908158|ref|YP_002648514.1| flagellar biosynthesis sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963780|emb|CAX55281.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           pyrifoliae Ep1/96]
 gi|283478078|emb|CAY73994.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
 gi|310767931|gb|ADP12881.1| flagellar biosynthesis sigma factor [Erwinia sp. Ejp617]
          Length = 240

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 95/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  T +E+A +L +P+E  R++L  T           DE     GD 
Sbjct: 100 VAGAMHQVEQALGRTATEQEVAAQLDVPLEEYRQILLDTNNSQLFSF---DEYREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ +LR+     +  L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AELVTEGHEQENPLHQLLEGDLRDRVIEAIDGLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|225181587|ref|ZP_03735028.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
 gi|225167695|gb|EEG76505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
          Length = 239

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 102/197 (51%), Gaps = 12/197 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G +GL++A ++FD   G KF ++A   ++ A+   +  + C   +P  +  ++ +
Sbjct: 49  DLLQAGMLGLLEALQRFDPTRGVKFESFAALRIRGAMLDEL-RRLCW--VPRSVVREMRE 105

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + R  + ++ ++ REP  EEIA+K+ + +  +RK+  +    I+  + +  EDT  L   
Sbjct: 106 MDRAVQELATQLGREPAEEEIAEKMGITIPQLRKITGM----INSSSLLSLEDTL-LAVP 160

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             D   V  LD  I A  R+     +  L  R +++L + +      D TL+EVG    V
Sbjct: 161 AVDGPEVEALDRLIAAEDRQRLAEAIGQLPERHQQLLALYY----QEDLTLKEVGLVLGV 216

Query: 652 TRERIRQIEAKAIRKLK 668
           T  R+ Q+ A+ I +L+
Sbjct: 217 TESRVCQLHARIIARLR 233


>gi|331007677|ref|ZP_08330813.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
 gi|330418520|gb|EGG93050.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
          Length = 288

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 115/236 (48%), Gaps = 16/236 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V A+LR V+ +AK Y   GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W
Sbjct: 50  AARGLVMAHLRFVVHIAKSYAGYGLSQSDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  +   I      +++      R     +    +R+      E T   +A  L + V+
Sbjct: 110 IKAEMHEFILRNWRIVKVATTKAQRKLFFNLRGQKKRLGWLSYDEATA--VAADLNVEVK 167

Query: 562 GVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDK--NAVSPLDSAIQANLRETTTR 615
            V     ++        +      +       +++ED   N    L+++  ++   +  R
Sbjct: 168 HVHEMESRLSAYDASFDADNDDDDESAYKAPANYLEDHRYNPAQELEASDWSDDNASRLR 227

Query: 616 V-LASLTPREERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LA+L  R + +++ R+   +N D+  TL E+  +F V+ ERIRQ+E  A++K+K
Sbjct: 228 TALATLDERSQVIIQRRW---LNDDNKSTLHELAAEFGVSAERIRQLEKNAMKKVK 280


>gi|319893019|ref|YP_004149894.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162715|gb|ADV06258.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 256

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 120/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++N++ R P+  EIA++L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELGRSPSISEIAERLEVSDEDV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    R+
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQHDDNYELTEKRMILERI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  LT RE  +++  F  G++   T E +G    +++  + +++  AI+KL+  +R
Sbjct: 204 LPILTDREREIIQCTFIDGLSQKETGERIG----LSQMHVSRLQRTAIKKLQEAAR 255


>gi|302552549|ref|ZP_07304891.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470167|gb|EFL33260.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 289

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/241 (23%), Positives = 114/241 (47%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 55  LQPGTSEHDRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 114

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 115 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTSFGRTPTTAEIA 174

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++  +     SLE     ++   L   ++      P    ++   R+
Sbjct: 175 ERLRITEDEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RD 229

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +
Sbjct: 230 LVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSAN 285

Query: 672 R 672
           R
Sbjct: 286 R 286


>gi|297156863|gb|ADI06575.1| RNA polymerase sigma factor WhiG [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 97/207 (46%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 74  DFVSSGVFGLIDAIEKFDPERAIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARA 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
           V R    +   ++R P+  E+A ++ + ++ +  V       +SL   +  ED  H    
Sbjct: 131 VERAYATLEAALRRTPSEAEVAAEMDIGLDELHGVFS----QLSLANVVALEDLLHASGE 186

Query: 588 ------LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 187 GGERLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEGL----T 242

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G+   VT  R+ QI  K++ +L+
Sbjct: 243 LAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|292488613|ref|YP_003531497.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292899773|ref|YP_003539142.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291199621|emb|CBJ46740.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291554044|emb|CBA21132.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|312172755|emb|CBX81011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 240

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 95/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  T +E+A +L +P+E  R++L  T           DE     GD 
Sbjct: 100 VAGAMHQVEQALGRTATEQEVAAQLDVPLEEYRQILLDTNNSQLFSF---DEYREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ +LR+     +  L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AELVTEGHEQENPLHQLLEGDLRDRVIEAIDGLPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|289770379|ref|ZP_06529757.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
 gi|289700578|gb|EFD68007.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
          Length = 287

 Score = 72.4 bits (176), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 112/238 (47%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 56  GTPEHDRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 115

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 116 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERL 175

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 176 RITEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 230

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 231 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 284


>gi|294636855|ref|ZP_06715188.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
 gi|291089930|gb|EFE22491.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
          Length = 240

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 113/232 (48%), Gaps = 23/232 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + + E +   +RL  SV         +  DL+Q G IGL+ A E++D   G  F+TYA
Sbjct: 21  APLVRHEALRLQVRLPASV---------ELDDLLQAGGIGLLHAVERYDAMQGTAFTTYA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  ++ A+   +  +     +P  +R     V    +R   ++ R P+  EIA+++ +P+
Sbjct: 72  IQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRVPSDGEIAQEMGIPL 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRV 616
              +++L  T    S +    DE     GD  E    ++ + +PL   ++++LR      
Sbjct: 129 AEYQQILLDTN---SSQLFSYDEWREEHGDNAEPVWGEEESANPLRQLLESDLRGRVIAA 185

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L  RE+ VL + +   +N    L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 186 IEALPEREKLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|291617817|ref|YP_003520559.1| FliA [Pantoea ananatis LMG 20103]
 gi|291152847|gb|ADD77431.1| FliA [Pantoea ananatis LMG 20103]
          Length = 240

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 96/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  + +E+A++L + +E  R++L  T           DE     GD 
Sbjct: 100 VAGAMHQVEQMLGRAASEQEVAQQLNVSIEEYRQILLDTNNSQLFSY---DEYREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ +LRE     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AELVTEGHEEANPLHQLMEGSLRERVIEAIEALPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLDVGESRVSQLHSQAIKRLR 233


>gi|238784716|ref|ZP_04628720.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238714395|gb|EEQ06403.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 240

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+AK L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQQVEQRVGRPATEQEVAKILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|242371561|ref|ZP_04817135.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
 gi|242350713|gb|EES42314.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
          Length = 256

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 123/242 (50%), Gaps = 18/242 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSINEIAERLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VTDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R+L  L+ RE ++++  F  G++   T E +G    +++  + +++  AI+KL+  
Sbjct: 198 MILERILPILSDRERQIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQEA 253

Query: 671 SR 672
           ++
Sbjct: 254 AK 255


>gi|225019367|ref|ZP_03708559.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
 gi|224947998|gb|EEG29207.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
          Length = 221

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 71/131 (54%), Gaps = 1/131 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            V+ NL LV S A ++T +G+++ DL   G +GL+KA + FD   G KFSTYA+  +   
Sbjct: 11  FVKQNLGLVHSCAHRFTGKGIEYDDLFSAGCMGLVKATDAFDEDRGVKFSTYAVPVILGE 70

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R   D   ++++   +++   +  +   R   K  REPT  E+A  L +  E   + L
Sbjct: 71  IRRLFRD-GGSVKVSRSLKELSMRATKERERFMLKTGREPTVSELADLLEVTPEQAIEAL 129

Query: 568 KITKEPISLET 578
           +++  P+SL T
Sbjct: 130 EVSVPPMSLTT 140


>gi|194014777|ref|ZP_03053394.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
 gi|194013803|gb|EDW23368.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
          Length = 255

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 98/201 (48%), Gaps = 10/201 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 54  DLISLGMLGLYDALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGD-EDTSHL 588
           V     ++  +  R  TP E+A++L M  + V   +        +S++  + D ED  ++
Sbjct: 111 VEAAIEKLEQRYLRNVTPTEVAEELGMSEQDVVTTMNEGFFANLLSIDEKLHDQEDGENV 170

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D+  V+P +  ++  L E     +  L+ +E+ V+ + +      + TL E+G  
Sbjct: 171 QVMIRDEKTVTPEEKMLKDELIEQLAEKMTELSEKEKLVISLFY----KEELTLTEIGHV 226

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  RI QI +KA+ KLK+
Sbjct: 227 LNLSTSRISQIHSKALFKLKY 247


>gi|107099361|ref|ZP_01363279.1| hypothetical protein PaerPA_01000373 [Pseudomonas aeruginosa PACS2]
          Length = 274

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 120/237 (50%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 40  AARQMVLAHLRFVVHIAKSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 99

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 100 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 158

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDK--NAVSPLDSA-----IQANLRE 611
           VR++  ++T + ++ +     +D S       ++ED   +    L+ A       ANL E
Sbjct: 159 VREMESRLTGQDMAFDPAADADDESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHE 218

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  R   +L+ R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 219 A----LEGLDERSRDILQQRW--LSEEKATLHDLAEKYNVSAERIRQLEKNAMSKLK 269


>gi|330959578|gb|EGH59838.1| putative RNA polymerase sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 532

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/200 (30%), Positives = 108/200 (54%), Gaps = 19/200 (9%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
            N+GL +A  +F   +G++FST A+ W+  +I+R +ADQ  +IR+P  M    HK     
Sbjct: 329 ANMGLTRAVYRFAPEMGFRFSTIALTWINVSISRDLADQE-SIRLPEGM----HK----H 379

Query: 537 RRM-SNKIKREP--TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGD 590
           RRM +N ++  P  + + +A+   +  + VR ++       S++T     D+S    L +
Sbjct: 380 RRMIANMLRDHPNVSIKTLAEATKLEQDVVRDLVHFAGGQRSIDTAFQGTDSSEADGLHE 439

Query: 591 FIEDKNAVSPLDSAIQAN-LRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + D N  +   S I+ + +R+     L   LT RE  VL  RFG+G   + TL E+  +
Sbjct: 440 LLADTN--NDFISEIEDDSMRQFVESALGDVLTQREIFVLVNRFGMGDAREKTLAELSIE 497

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ER+RQ+E +A+ K++
Sbjct: 498 MKLSKERVRQLEIQALGKIR 517


>gi|30264411|ref|NP_846788.1| sporulation sigma factor SigK [Bacillus anthracis str. Ames]
 gi|47529862|ref|YP_021211.1| sporulation sigma factor SigK [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187232|ref|YP_030484.1| sporulation sigma factor SigK [Bacillus anthracis str. Sterne]
 gi|49481469|ref|YP_038392.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141167|ref|YP_085663.1| sporulation sigma factor SigK [Bacillus cereus E33L]
 gi|163942095|ref|YP_001646979.1| sporulation sigma factor SigK [Bacillus weihenstephanensis KBAB4]
 gi|165873242|ref|ZP_02217852.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167634588|ref|ZP_02392908.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|167638535|ref|ZP_02396811.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|170687349|ref|ZP_02878566.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|170707389|ref|ZP_02897843.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|177653302|ref|ZP_02935554.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190566875|ref|ZP_03019791.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196034403|ref|ZP_03101812.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196039171|ref|ZP_03106477.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|196044956|ref|ZP_03112190.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|206969450|ref|ZP_03230404.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217961829|ref|YP_002340399.1| sporulation sigma factor SigK [Bacillus cereus AH187]
 gi|218231149|ref|YP_002369149.1| sporulation sigma factor SigK [Bacillus cereus B4264]
 gi|218899507|ref|YP_002447918.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225866320|ref|YP_002751698.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227817116|ref|YP_002817125.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229603939|ref|YP_002868629.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|254684096|ref|ZP_05147956.1| sporulation sigma factor SigK [Bacillus anthracis str. CNEVA-9066]
 gi|254721930|ref|ZP_05183719.1| sporulation sigma factor SigK [Bacillus anthracis str. A1055]
 gi|254736444|ref|ZP_05194150.1| sporulation sigma factor SigK [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741481|ref|ZP_05199168.1| sporulation sigma factor SigK [Bacillus anthracis str. Kruger B]
 gi|254750920|ref|ZP_05202959.1| sporulation sigma factor SigK [Bacillus anthracis str. Vollum]
 gi|254757752|ref|ZP_05209779.1| sporulation sigma factor SigK [Bacillus anthracis str. Australia
           94]
 gi|300118668|ref|ZP_07056396.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|49065844|sp|P62180|RP28_BACCR RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065845|sp|P62181|RP28_BACTK RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065846|sp|P62182|RP28_BACAN RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|580953|emb|CAA40024.1| sigma factor 28 [Bacillus thuringiensis serovar kurstaki]
 gi|19918928|gb|AAL99379.1| sigma factor 28 [Bacillus thuringiensis serovar israelensis]
 gi|30259069|gb|AAP28274.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Ames]
 gi|47505010|gb|AAT33686.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181159|gb|AAT56535.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Sterne]
 gi|49333025|gb|AAT63671.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974636|gb|AAU16186.1| RNA polymerase sigma-28 factor [Bacillus cereus E33L]
 gi|163864292|gb|ABY45351.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|164711001|gb|EDR16568.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167513383|gb|EDR88753.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|167530040|gb|EDR92775.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|170127633|gb|EDS96506.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|170668544|gb|EDT19290.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|172081584|gb|EDT66656.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190561866|gb|EDV15835.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992945|gb|EDX56904.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196024444|gb|EDX63117.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|196029798|gb|EDX68399.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|206735138|gb|EDZ52306.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217066768|gb|ACJ81018.1| RNA polymerase sigma-27 factor [Bacillus cereus AH187]
 gi|218159106|gb|ACK59098.1| RNA polymerase sigma-27 factor [Bacillus cereus B4264]
 gi|218543613|gb|ACK96007.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225788740|gb|ACO28957.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227007199|gb|ACP16942.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229268347|gb|ACQ49984.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|298723917|gb|EFI64631.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|324328243|gb|ADY23503.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326942122|gb|AEA18018.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 237

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 36  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 92

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 93  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 118

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 119 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 160

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 161 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 220

Query: 666 KLKH 669
           K+ H
Sbjct: 221 KMFH 224


>gi|118618107|ref|YP_906439.1| RNA polymerase sigma factor SigF [Mycobacterium ulcerans Agy99]
 gi|183981270|ref|YP_001849561.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
 gi|118570217|gb|ABL04968.1| alternate RNA polymerase sigma factor SigF [Mycobacterium ulcerans
           Agy99]
 gi|183174596|gb|ACC39706.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
          Length = 262

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 112/233 (48%), Gaps = 23/233 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+  +
Sbjct: 40  RDTIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVETGSDFVSFAVPTI 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----V 560
              + R   D S ++++P  +++   ++      +S ++ R PT  E+A +L M     V
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRAPTATELAAELEMDRAEVV 159

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-----RETTTR 615
           EG+  V   +   +S+++  G ED        +D  A++     + A L     RE+   
Sbjct: 160 EGL--VAGSSYNTLSIDSGSGSED--------DDARAIADTLGDMDAGLDRIEDRESLRP 209

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L +L  RE  VL +RF   M      E VG    +++  + ++ AK++ +L+
Sbjct: 210 LLEALPERERTVLVLRFFDSMTQTQIAERVG----ISQMHVSRLLAKSLARLR 258


>gi|324325029|gb|ADY20289.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 257

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/262 (22%), Positives = 125/262 (47%), Gaps = 26/262 (9%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +
Sbjct: 8   TNLTKEDVMKLIAEFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGML 65

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+      +
Sbjct: 66  GLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEEL 125

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKN 596
           ++ ++R P   EIA  L +  E V +++              +   S L D +E   D +
Sbjct: 126 TDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDGS 175

Query: 597 AVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           +V+ ++S   ++    ET  R     +   L   E+ V+   F   +N   T E +G   
Sbjct: 176 SVARIESVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDTGERLG--- 232

Query: 650 CVTRERIRQIEAKAIRKLKHPS 671
            +++  + +I+ +AI KLK  +
Sbjct: 233 -ISQMHVSRIKRQAISKLKQAA 253


>gi|30022417|ref|NP_834048.1| sporulation sigma factor SigK [Bacillus cereus ATCC 14579]
 gi|228902866|ref|ZP_04067008.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
 gi|228910177|ref|ZP_04073996.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228916971|ref|ZP_04080532.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228929384|ref|ZP_04092407.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935660|ref|ZP_04098474.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941506|ref|ZP_04104056.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954625|ref|ZP_04116649.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960610|ref|ZP_04122256.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228974436|ref|ZP_04135004.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981030|ref|ZP_04141332.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|229025805|ref|ZP_04182204.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|229031990|ref|ZP_04187975.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|229048046|ref|ZP_04193621.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|229062038|ref|ZP_04199363.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|229071846|ref|ZP_04205059.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|229076014|ref|ZP_04208987.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|229098811|ref|ZP_04229749.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|229104971|ref|ZP_04235627.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|229111812|ref|ZP_04241358.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|229117837|ref|ZP_04247201.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|229123878|ref|ZP_04253071.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|229129620|ref|ZP_04258588.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|229141077|ref|ZP_04269619.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|229157954|ref|ZP_04286026.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|229163288|ref|ZP_04291242.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|229169087|ref|ZP_04296802.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|229175013|ref|ZP_04302532.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|229180616|ref|ZP_04307957.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|229192552|ref|ZP_04319513.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|229198467|ref|ZP_04325171.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|29897975|gb|AAP11249.1| RNA polymerase sigma-K factor [Bacillus cereus ATCC 14579]
 gi|228584970|gb|EEK43084.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|228590859|gb|EEK48717.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|228602859|gb|EEK60339.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|228608474|gb|EEK65777.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|228614315|gb|EEK71425.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|228620195|gb|EEK77067.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|228625514|gb|EEK82269.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|228642355|gb|EEK98644.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|228653737|gb|EEL09607.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|228659592|gb|EEL15239.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|228665634|gb|EEL21112.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|228671568|gb|EEL26866.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|228678465|gb|EEL32686.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|228684655|gb|EEL38595.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|228707126|gb|EEL59326.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|228711276|gb|EEL63238.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|228717190|gb|EEL68865.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|228723290|gb|EEL74660.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|228729345|gb|EEL80337.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|228735513|gb|EEL86109.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|228778690|gb|EEM26955.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|228785272|gb|EEM33283.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228799038|gb|EEM46009.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805071|gb|EEM51666.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818156|gb|EEM64231.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824020|gb|EEM69838.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830290|gb|EEM75904.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842692|gb|EEM87779.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849460|gb|EEM94295.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228856740|gb|EEN01258.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
          Length = 240

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 39  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 95

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 96  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 122 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 163

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 164 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 223

Query: 666 KLKH 669
           K+ H
Sbjct: 224 KMFH 227


>gi|254381060|ref|ZP_04996425.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339970|gb|EDX20936.1| sigma factor [Streptomyces sp. Mg1]
          Length = 302

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 118/257 (45%), Gaps = 45/257 (17%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E    +  ++E N+ LV   A+++ +R   G+   D++Q G IGL+KA ++FD   
Sbjct: 61  EGTREYQYTRNTLIEMNISLVNFAARRFRSRAGGGVDIEDIVQVGTIGLIKAIDRFDPDR 120

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FST A+ ++   I R   D +  + +P  +++   ++ ++   ++    R PT +EI
Sbjct: 121 EVEFSTLALPYISGEIKRFFRDTTWAVHVPRRLQELRSELAKSQDALTEVFGRAPTVKEI 180

Query: 553 AKKLAMP----VEGVRKVLKITKEPI-----------------SLETPIGDEDTSHLGDF 591
           A+ L +     +EG+      T   I                 SL   +G+ D     + 
Sbjct: 181 AEHLELSEDDVIEGLVAANGYTSGSIDAATSSRQRTSGETEGRSLAETVGEVDPDM--EL 238

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            E+ + ++PL               L SL  R+ R+L MRFG  M    T  E+G +  +
Sbjct: 239 FEEFHTLAPL---------------LQSLKERDRRILAMRFGEEM----TQAEIGTELGI 279

Query: 652 TRERIRQIEAKAIRKLK 668
           ++ ++ ++  + + +L+
Sbjct: 280 SQMQVSRLLTRVLTRLR 296


>gi|165973130|gb|ABY76244.1| sigma-K factor [Bacillus thuringiensis]
          Length = 237

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 36  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 92

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 93  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 118

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 119 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 160

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 161 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 220

Query: 666 KLKH 669
           K+ H
Sbjct: 221 KMFH 224


>gi|126659553|ref|ZP_01730685.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619192|gb|EAZ89929.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 258

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/219 (25%), Positives = 107/219 (48%), Gaps = 8/219 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++  + + DL+Q G++GL++A E+F    G+ FS++A+ +
Sbjct: 29  RNKILELNFGLVRKEAHHWVHQCPESYEDLVQVGSLGLIRAIERFSIEKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   + +   R    K  R+PT  EIA+ L + ++  
Sbjct: 89  IRGEIQHYLRDKKYTVRIPRRWLELGRQSMNVRREFREKFNRQPTDSEIAQVLEISLKEW 148

Query: 564 R--KVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  K+    +EP+SL+  +    E  + LGD + D N  S    A +  +R    + L  
Sbjct: 149 QEIKLAFQNREPVSLDVKVSSEGEGQTSLGDLVPDANYRS-FQLAQEDQIR--LQQALEQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           L  R   +L   F   +    T E++G        R+++
Sbjct: 206 LEERTRNILEFVFLKDLTQRETAEQLGISVVTVSRRVKK 244


>gi|493078|gb|AAA92723.1| RpoH (sigma 32) [Pseudomonas aeruginosa]
          Length = 284

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 120/237 (50%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIAKSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDK--NAVSPLDSA-----IQANLRE 611
           VR++  ++T + ++ +     +D S       ++ED   +    L+ A       ANL E
Sbjct: 169 VREMESRLTGQDMAFDPAADADDESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHE 228

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  R   +L+ R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 A----LEGLDERSRDILQQRW--LSEEKATLHDLAEKYNVSAERIRQLEKNAMSKLK 279


>gi|65321710|ref|ZP_00394669.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|228923092|ref|ZP_04086384.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228948053|ref|ZP_04110338.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987592|ref|ZP_04147708.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229013560|ref|ZP_04170693.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|229019564|ref|ZP_04176380.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|229081603|ref|ZP_04214099.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|229135165|ref|ZP_04263965.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|229146910|ref|ZP_04275274.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|229152543|ref|ZP_04280733.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|229186579|ref|ZP_04313740.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228596838|gb|EEK54497.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228630909|gb|EEK87548.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|228636509|gb|EEK92975.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|228648293|gb|EEL04328.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|228701709|gb|EEL54199.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|228741730|gb|EEL91914.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|228747720|gb|EEL97590.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|228772133|gb|EEM20583.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228811639|gb|EEM57975.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228836590|gb|EEM81939.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 243

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 42  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 98

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 99  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 124

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 125 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 166

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 167 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 226

Query: 666 KLKH 669
           K+ H
Sbjct: 227 KMFH 230


>gi|16332163|ref|NP_442891.1| RNA polymerase sigma factor SigF [Synechocystis sp. PCC 6803]
 gi|1653792|dbj|BAA18703.1| RNA polymerase sigma-37 [Synechocystis sp. PCC 6803]
          Length = 258

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 103/220 (46%), Gaps = 10/220 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  ++E NL LV   A  +T +  + F DL Q G +GL++A E+FD   G  FS++A+ +
Sbjct: 29  RNRIMEVNLGLVRKEAHHWTAQCNESFEDLSQVGCLGLIRAIERFDVSKGNAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  I   + D+S  +RIP    D   + +   +    K  R  T EEIA+ LA+P+   
Sbjct: 89  VRGEIQHFLRDKSNCVRIPRRWLDLGRQAIAVQQEFRLKYDRAATDEEIAQILAVPLADW 148

Query: 564 R--KVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVS-PLDSAIQANLRETTTRVLA 618
           +  K+    +E +SL+T +   DE   +LGD +      S  L    Q  L++     LA
Sbjct: 149 QETKLALQNRELVSLDTKVNGDDEGQVNLGDCLAHHEFRSFQLSQEDQIRLQQA----LA 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            L  R  R++   F          E +G        RI+Q
Sbjct: 205 GLEERTRRIVEFVFLHDFTHKEAAEMMGVSVITVSRRIKQ 244


>gi|18311030|ref|NP_562964.1| sporulation sigma factor SigF [Clostridium perfringens str. 13]
 gi|110799417|ref|YP_696728.1| sporulation sigma factor SigF [Clostridium perfringens ATCC 13124]
 gi|110803821|ref|YP_699329.1| sporulation sigma factor SigF [Clostridium perfringens SM101]
 gi|168205856|ref|ZP_02631861.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|168208750|ref|ZP_02634375.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168212915|ref|ZP_02638540.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|168215675|ref|ZP_02641300.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
 gi|182623955|ref|ZP_02951743.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145712|dbj|BAB81754.1| RNA polymerase sigma-F factor [Clostridium perfringens str. 13]
 gi|110674064|gb|ABG83051.1| RNA polymerase sigma-F factor [Clostridium perfringens ATCC 13124]
 gi|110684322|gb|ABG87692.1| RNA polymerase sigma-F factor [Clostridium perfringens SM101]
 gi|170662589|gb|EDT15272.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|170712973|gb|EDT25155.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170715517|gb|EDT27699.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|177910848|gb|EDT73202.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|182382022|gb|EDT79501.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
          Length = 251

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 119/245 (48%), Gaps = 24/245 (9%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++ M ++G  EA     +++E N  LV S+ K++TNRG  + D+ Q G++GL+KA   F+
Sbjct: 19  LIVMAKEGNKEAM---NKLIEVNTPLVSSICKRFTNRGYDYEDIFQIGSMGLVKAINNFN 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++    +    K+      +  K+ R+PT 
Sbjct: 76  DSFNVKFSTYAVPMIIGEIKRFLRDDGI-IKVSRSTKTLAKKLHYNKEELIKKLNRDPTV 134

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDT-----SHLGDFIEDKNAVSPLDS 603
           +E+A+   +  E V   L+       L   I  DE T       L +  ED + V+ +  
Sbjct: 135 DELAEYSGVDKEEVIVALESASSMQYLYDTIHHDEGTPVLLIDKLSEKGEDDDMVNKI-- 192

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                LRE     ++SL  + ++++ +R+      D T  +V K   +++ ++ +IE K 
Sbjct: 193 ----ALREA----ISSLDSKGKQIIMLRYF----KDKTQIQVAKMLGISQVQVSRIEKKV 240

Query: 664 IRKLK 668
           ++ +K
Sbjct: 241 LKIMK 245


>gi|323705419|ref|ZP_08116994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535321|gb|EGB25097.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 246

 Score = 72.0 bits (175), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/199 (28%), Positives = 96/199 (48%), Gaps = 12/199 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI +G IGL+ A  K+D   G KF TYA   +K  I   +  +     IP  ++ +   
Sbjct: 51  DLISQGMIGLIDAVNKYDVSKGVKFETYASIRIKGEIIDYLRKKDW---IPRSLKKRYKS 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLG 589
           + +T  ++  + KREPT EEI +   +    V K L         SL+  I  E+   + 
Sbjct: 108 IEKTIEQLEQEYKREPTIEEIMEATKLSKNDVLKTLSYMNAGYISSLDEVI--ENNLKIT 165

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D    +P +  +  +L++  ++ + +L  +E  ++ + +   +N     +E+ K  
Sbjct: 166 S-ITDNEVTNPENEVMMFDLKQNISKAIDTLQEKERLIISLYYYEDLN----YKEISKIM 220

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +T  RI QI +KAI+KLK
Sbjct: 221 GLTESRISQIHSKAIKKLK 239


>gi|258488878|gb|ACV72445.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488934|gb|ACV72473.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488986|gb|ACV72499.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489036|gb|ACV72524.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489040|gb|ACV72526.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489042|gb|ACV72527.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
          Length = 261

 Score = 72.0 bits (175), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488860|gb|ACV72436.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258488862|gb|ACV72437.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258488880|gb|ACV72446.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258488882|gb|ACV72447.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258489014|gb|ACV72513.1| RpoD [Xanthomonas axonopodis pv. manihotis]
          Length = 261

 Score = 72.0 bits (175), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258489044|gb|ACV72528.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
          Length = 260

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGTFPLSTELLLSDYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|323463926|gb|ADX76079.1| RNA polymerase sigma-B factor [Staphylococcus pseudintermedius
           ED99]
          Length = 256

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 119/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++N++ R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELGRSPSISEIADRLEVSDEDV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    R+
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQHDDNYELTEKRMILERI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  LT RE  +++  F  G++   T E +G    +++  + +++  AI+KL+  +R
Sbjct: 204 LPILTDREREIIQCTFIDGLSQKETGERIG----LSQMHVSRLQRTAIKKLQEAAR 255


>gi|296504831|ref|YP_003666531.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
 gi|296325883|gb|ADH08811.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
          Length = 196

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 8   ARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYA--- 64

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 65  -----ARCIENE-----ILMHLR------------------------------------- 77

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ ++  E     +  L 
Sbjct: 78  --VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILD 135

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 136 EREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 183


>gi|164688589|ref|ZP_02212617.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
 gi|164603002|gb|EDQ96467.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
          Length = 234

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 105/226 (46%), Gaps = 51/226 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V+ N+RLV  ++KKY N G +  DLI  G IGL+KA + F+   G + +TYA   
Sbjct: 31  AKEVLVQRNMRLVAHISKKYNNSGEELDDLISIGTIGLIKAIDTFNVDKGIRLATYASKC 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  +I       ++ V ++D I                                GV
Sbjct: 91  IENEILMNIRSNKKN-KMQVSLQDPI--------------------------------GV 117

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            K        ISL   +G DED  ++ D +E K  +S L   I+             LT 
Sbjct: 118 DK----EGNAISLIDILGTDED--YIVDKVELKMKISKLYEKIE-----------KVLTE 160

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++++R+G+  +   T  E+ +Q  ++R  + +IE KA++KLK
Sbjct: 161 REKEIIKLRYGLTPSGYKTQREIAQQLDISRSYVSRIEKKALKKLK 206


>gi|90579944|ref|ZP_01235752.1| flagellar biosynthesis sigma factor FliA [Vibrio angustum S14]
 gi|90438829|gb|EAS64012.1| flagellar biosynthesis sigma factor FliA [Vibrio angustum S14]
          Length = 240

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 96/200 (48%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F T+A   ++ A+   I        +P  +     K
Sbjct: 44  DLIQAGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRK 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      + N++ R+P  +EIA+ L MP+E   + L      ++    +G  D     D 
Sbjct: 101 ISEAISHLENELGRDPNDQEIAQYLDMPLEQYHQALN----DVNCGRLVGISDLGVAEDT 156

Query: 592 IEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           + ++ ++   +PL   +  N R +    + +L  RE  VL + +   +N    L+E+G  
Sbjct: 157 VANEESIGENTPLQGVVDDNFRASLAEAIETLPEREALVLSLYYDEELN----LKEIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  RI QI ++A+++L+
Sbjct: 213 IGVSESRICQIHSQAMQRLR 232


>gi|304404273|ref|ZP_07385935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347251|gb|EFM13083.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 262

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 116/241 (48%), Gaps = 15/241 (6%)

Query: 435 RKGECEASI-AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDW 490
           RK + E  I AKK+++E  L LV  V  +      + +   DL   G +GL+ A EKFD+
Sbjct: 16  RKWKTEKDIEAKKQLIEQYLPLVDYVTSRMAIGLPKTVSKDDLYSNGVMGLIDAIEKFDY 75

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F TYA W ++  I   +        +P  +RDK  ++    + +  K  R  T  
Sbjct: 76  ERGLQFETYASWRIRGGIIDGLRQGDW---VPRSVRDKAKRIEEAYQLLEQKYLRSVTDA 132

Query: 551 EIAKKLAMP---VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EI+  L +      G+ + + +T    SLE PI +E++      + D+ A +P     + 
Sbjct: 133 EISDYLNVSEKEFTGILQEIAVTT-ICSLEDPIREEESETRLSLLVDEKAKNPDYKVHEF 191

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E+  + +  LT +E  V+ + +      + +L E+ +   ++  RI Q+ +KAI +L
Sbjct: 192 YLKESLVKGIERLTEKERTVVSLFY----YEELSLSEIAEVMSLSPSRISQLHSKAILRL 247

Query: 668 K 668
           +
Sbjct: 248 R 248


>gi|15595573|ref|NP_249067.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAO1]
 gi|116054106|ref|YP_788549.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|152989115|ref|YP_001345866.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PA7]
 gi|218889117|ref|YP_002437981.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa LESB58]
 gi|254243475|ref|ZP_04936797.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|296386874|ref|ZP_06876373.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAb1]
 gi|313112005|ref|ZP_07797792.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
 gi|2507390|sp|P42378|RP32_PSEAE RecName: Full=RNA polymerase sigma-32 factor
 gi|9946228|gb|AAG03765.1|AE004475_7 sigma factor RpoH [Pseudomonas aeruginosa PAO1]
 gi|765096|dbj|BAA08769.1| heat-shock sigma factor [Pseudomonas aeruginosa]
 gi|998760|gb|AAB33935.1| heat-shock sigma factor sigma 32 [Pseudomonas aeruginosa]
 gi|115589327|gb|ABJ15342.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126196853|gb|EAZ60916.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|150964273|gb|ABR86298.1| alternative sigma factor RpoH [Pseudomonas aeruginosa PA7]
 gi|218769340|emb|CAW25100.1| sigma factor RpoH [Pseudomonas aeruginosa LESB58]
 gi|310884294|gb|EFQ42888.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
          Length = 284

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 120/237 (50%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +AK Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIAKSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +K  I   I      +++     + K+   +R+ ++    +  E     +A+ L +    
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNEEV-HRVAESLGVEPRE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDK--NAVSPLDSA-----IQANLRE 611
           VR++  ++T + ++ +     +D S       ++ED   +    L+ A       ANL E
Sbjct: 169 VREMESRLTGQDMAFDPAADADDESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHE 228

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  R   +L+ R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 A----LEGLDERSRDILQQRW--LSEEKATLHDLAEKYNVSAERIRQLEKNAMSKLK 279


>gi|327394234|dbj|BAK11656.1| RNA polymerase sigma factor for flagellar operon FliA [Pantoea
           ananatis AJ13355]
          Length = 230

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 96/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  + +E+A++L + +E  R++L  T           DE     GD 
Sbjct: 90  VAGAMHQVEQMLGRAASEQEVAQQLNVSIEEYRQILLDTNNSQLFSY---DEYREEHGDS 146

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ +LRE     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 147 AELVTEGHEEANPLHQLMEGSLRERVIEAIEALPEREKMVLTLYYQEELN----LKEIGA 202

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 203 VLDVGESRVSQLHSQAIKRLR 223


>gi|308273536|emb|CBX30138.1| RNA polymerase sigma factor whiG [uncultured Desulfobacterium sp.]
          Length = 255

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 103/214 (48%), Gaps = 18/214 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGL  A E FD   G KF TYA + ++ AI   +        IP  +R  I K
Sbjct: 57  DLNSAGIIGLFDAIENFDSSRGIKFETYASYRIRGAILDEMRKLDW---IPRSVRKDIQK 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETP-IGDEDTSHL 588
           V         K+ R P   EIA++L + +E   K++  T     +SL+ P +G   T+  
Sbjct: 114 VETAVTAAQTKLGRTPEDHEIAEELGVNLEDFYKIIDRTHNVNLLSLDEPALGTSVTT-- 171

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + +E  N  SPLD   ++ + +     LA+L  + + V+ + +   M    TL+E+ + 
Sbjct: 172 VNRLESDNP-SPLDKVKKSEIEKVIASALANLPEKVQMVISLYYYDEM----TLKEIAEI 226

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             +T  RI QI +KAI  L+      KL+++ +G
Sbjct: 227 MGLTESRISQIHSKAIIILR-----SKLKAYFEG 255


>gi|239980907|ref|ZP_04703431.1| RNA polymerase sigma factor, sigma F [Streptomyces albus J1074]
 gi|291452769|ref|ZP_06592159.1| transcription initiation factor sigma F [Streptomyces albus J1074]
 gi|291355718|gb|EFE82620.1| transcription initiation factor sigma F [Streptomyces albus J1074]
          Length = 294

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 113/241 (46%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V  G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 60  VEPGTAEHARVRSALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 119

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 120 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTSATEDLTTAHGRSPTTAEIA 179

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++  +     SLE     ++   L   ++      P    ++   R+
Sbjct: 180 ERLRISEDEVLACIEAGRSYHATSLEA---AQEGDGLPGLLDRLGYEDPALDGVEH--RD 234

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++  +L+  +
Sbjct: 235 LVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFARLRSAN 290

Query: 672 R 672
           R
Sbjct: 291 R 291


>gi|258488942|gb|ACV72477.1| RpoD [Xanthomonas campestris pv. campestris]
          Length = 260

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGTFPLSTELLLSDYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488864|gb|ACV72438.1| RpoD [Xanthomonas axonopodis pv. manihotis]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488994|gb|ACV72503.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489002|gb|ACV72507.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489004|gb|ACV72508.1| RpoD [Xanthomonas axonopodis pv. allii]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488970|gb|ACV72491.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488870|gb|ACV72441.1| RpoD [Xanthomonas axonopodis pv. begoniae]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|238752744|ref|ZP_04614214.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
 gi|238709075|gb|EEQ01323.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
          Length = 240

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQKVEQRLGRPATEQEVAQNLEIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLQHLLEGNLRQRVIDAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|258488962|gb|ACV72487.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488964|gb|ACV72488.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
          Length = 260

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488840|gb|ACV72426.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
          Length = 260

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|89073430|ref|ZP_01159953.1| flagellar biosynthesis sigma factor FliA [Photobacterium sp. SKA34]
 gi|89050694|gb|EAR56175.1| flagellar biosynthesis sigma factor FliA [Photobacterium sp. SKA34]
          Length = 240

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 95/200 (47%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F T+A   ++ A+   I        +P  +     K
Sbjct: 44  DLIQSGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRK 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      + N++ R+P  +EIA+ L MP+E   + L      ++    +G  D     D 
Sbjct: 101 ISEAISHLENELGRDPNDQEIAQYLDMPLEQYHQALN----DVNCGRLVGISDLGVAEDT 156

Query: 592 IEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           + ++ ++   SP    +  N R +    + +L  RE  VL + +   +N    L+E+G  
Sbjct: 157 VANEESIGENSPFQGVVDDNFRASLAEAIKTLPEREALVLSLYYDEELN----LKEIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  RI QI ++A+++L+
Sbjct: 213 IGVSESRICQIHSQAMQRLR 232


>gi|315127302|ref|YP_004069305.1| flagellar biosynthesis sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315015816|gb|ADT69154.1| flagellar biosynthesis sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 236

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 105/232 (45%), Gaps = 26/232 (11%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 12  IVEKHASLVKKVACHLIARLPASVQLDDLIQSGMIGLIEASKNFDASKGASFETFAGIRI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +       R  VH + ++  V  T   + N + REP   E+A+KL + +    
Sbjct: 72  RGAMIDEMRRGDWVPR-SVHRKSRL--VAETIVALENSLNREPKDSEVAEKLEISLNEYH 128

Query: 565 KVLKITKEPISLETPIGDED--------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +L      +++   +G ED        T H  D   DK    P ++       E+    
Sbjct: 129 HILN----DVNVSKVLGIEDLGIDDDVITPHGQDLALDK----PFNNVKNERFNESLLSA 180

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + SL  ++  VL + +   MN    L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 181 IKSLPEKDAMVLSLYYNDEMN----LKEIGHILDVSESRVSQIHGQAMIKLK 228


>gi|258489074|gb|ACV72543.1| RpoD [Xanthomonas axonopodis pv. glycines]
          Length = 259

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 2   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 61

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 62  GKKRLAEIV 70


>gi|258488848|gb|ACV72430.1| RpoD [Xanthomonas axonopodis pv. glycines]
 gi|258489072|gb|ACV72542.1| RpoD [Xanthomonas axonopodis pv. glycines]
          Length = 260

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|329938754|ref|ZP_08288150.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329302245|gb|EGG46137.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 305

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 74  GSPEHDRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 133

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 134 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERL 193

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  E V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 194 RIGEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 248

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 249 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 302


>gi|258488908|gb|ACV72460.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
          Length = 259

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488842|gb|ACV72427.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488844|gb|ACV72428.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488850|gb|ACV72431.1| RpoD [Xanthomonas perforans]
 gi|258488868|gb|ACV72440.1| RpoD [Xanthomonas perforans]
 gi|258488904|gb|ACV72458.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488912|gb|ACV72462.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488924|gb|ACV72468.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
 gi|258488926|gb|ACV72469.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
 gi|258488928|gb|ACV72470.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488930|gb|ACV72471.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488932|gb|ACV72472.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488948|gb|ACV72480.1| RpoD [Xanthomonas perforans]
 gi|258488950|gb|ACV72481.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488952|gb|ACV72482.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488954|gb|ACV72483.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488956|gb|ACV72484.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488958|gb|ACV72485.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488960|gb|ACV72486.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488966|gb|ACV72489.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488968|gb|ACV72490.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488976|gb|ACV72494.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488978|gb|ACV72495.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258488980|gb|ACV72496.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258488982|gb|ACV72497.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258488984|gb|ACV72498.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258488996|gb|ACV72504.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258488998|gb|ACV72505.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489000|gb|ACV72506.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489006|gb|ACV72509.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489008|gb|ACV72510.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489010|gb|ACV72511.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258489012|gb|ACV72512.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258489016|gb|ACV72514.1| RpoD [Xanthomonas perforans]
 gi|258489018|gb|ACV72515.1| RpoD [Xanthomonas perforans]
 gi|258489076|gb|ACV72544.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
 gi|258489078|gb|ACV72545.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|126348048|emb|CAJ89768.1| putative RNA polymerase secondary sigma factor [Streptomyces
           ambofaciens ATCC 23877]
          Length = 264

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 60/214 (28%), Positives = 100/214 (46%), Gaps = 11/214 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+++  L +   +A ++  RG    DL Q   +GL+KA + +D   G+ F  YA+  V
Sbjct: 39  RDELIQVWLPMSERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPRRGHAFEAYAVPTV 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V ++A+ ++     R PT EEIA    +    V
Sbjct: 99  TGEIKRHFRDHMWTLHVPRRIQDLRNRVRKSAKELAQVTPGRAPTVEEIADHAHLTTVEV 158

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
           R  ++  +    +SLE  +   D   LGD      A+   D A  A +     R  L +L
Sbjct: 159 RTGMEALECFSALSLEAEMPGTDGYALGD------ALGGPDPAFDAVVDRVAVRPCLEAL 212

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             RE  +L +RF  GM      +++G  Q  V+R
Sbjct: 213 PERERTILYLRFFGGMTQSRIAQQLGISQMHVSR 246


>gi|238758082|ref|ZP_04619262.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
 gi|238703620|gb|EEP96157.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
          Length = 240

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VATAMQKVEQRVGRPATEQEVAQTLDIELSEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLQHLLEGNLRQRVIDAIEALPDREKMVLTLYYQEELN----LKEIGAVLD 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|293374267|ref|ZP_06620595.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
 gi|292647100|gb|EFF65082.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
          Length = 229

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/273 (24%), Positives = 118/273 (43%), Gaps = 59/273 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F+     +++ +   I + +    +S  E  H ++++  G+  A   +++++E NLRLV 
Sbjct: 6   FIVSLFSNLIPLMGSISNQAFPNPLSAEEEEHYLTLMANGDKNA---REKLIEHNLRLVA 62

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KKY N+     DLI  G IGL+KA + F    G K +TYA   +             
Sbjct: 63  HIVKKYQNQTDDKEDLISIGTIGLIKAIDSFSPDKGTKLATYAARCID------------ 110

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                    ++I  + R+ ++M N                                +SL 
Sbjct: 111 ---------NEILMLFRSTKKMRN-------------------------------DVSLY 130

Query: 578 TPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++D+N     D  IQ    E   + L SLT RE  ++  RFG+
Sbjct: 131 DPIGYDKEGNEICLIDVVKDENK-DLNDIIIQQLAFEKIEKNLKSLTQRERDIIVRRFGL 189

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             + + T +E+ K + ++R  + +IE +A+ KL
Sbjct: 190 ENHEEETQQEIAKSYGISRSYVSRIEKRALMKL 222


>gi|167770367|ref|ZP_02442420.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
 gi|167667689|gb|EDS11819.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
          Length = 225

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 97/202 (48%), Gaps = 10/202 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  N+ LV S A ++  RG+++ DL Q G +GL KA + FD   G K STYA+  +
Sbjct: 12  REQTISENIGLVHSCAHRFKGRGIEYDDLFQAGCMGLCKAVDAFDPQRGVKLSTYAVPVI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +++   +++   ++ R   +++  + REP+  E+A+ + +P E V 
Sbjct: 72  LGEMRRLFRDGG-AVKVSRTLKELSLRIGRAREQLALALGREPSVSELAQAMELPEEQVV 130

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L     P+SL     DED     D   D    SP D         +  +V+  L  ++
Sbjct: 131 EALCAAAPPLSLTE--SDEDGGGQIDLPAD----SPEDQLADVI---SLNQVVEKLEDKD 181

Query: 625 ERVLRMRFGIGMNTDHTLEEVG 646
             ++ +R+  GM    T   +G
Sbjct: 182 RALIELRYYSGMTQVQTAARLG 203


>gi|258488888|gb|ACV72450.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488914|gb|ACV72463.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488916|gb|ACV72464.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488920|gb|ACV72466.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
          Length = 257

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488856|gb|ACV72434.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488858|gb|ACV72435.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488884|gb|ACV72448.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488890|gb|ACV72451.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258488892|gb|ACV72452.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258488906|gb|ACV72459.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488936|gb|ACV72474.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488988|gb|ACV72500.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488990|gb|ACV72501.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488992|gb|ACV72502.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489020|gb|ACV72516.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489022|gb|ACV72517.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489024|gb|ACV72518.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489026|gb|ACV72519.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489030|gb|ACV72521.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489032|gb|ACV72522.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489034|gb|ACV72523.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489046|gb|ACV72529.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489048|gb|ACV72530.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489050|gb|ACV72531.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489052|gb|ACV72532.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489054|gb|ACV72533.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489056|gb|ACV72534.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489058|gb|ACV72535.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489060|gb|ACV72536.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489062|gb|ACV72537.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489064|gb|ACV72538.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489066|gb|ACV72539.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489068|gb|ACV72540.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489070|gb|ACV72541.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489090|gb|ACV72551.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258489092|gb|ACV72552.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258489094|gb|ACV72553.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258489096|gb|ACV72554.1| RpoD [Xanthomonas citri pv. anacardii]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258488838|gb|ACV72425.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488846|gb|ACV72429.1| RpoD [Xanthomonas axonopodis pv. glycines]
 gi|258488854|gb|ACV72433.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488866|gb|ACV72439.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
 gi|258488872|gb|ACV72442.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488876|gb|ACV72444.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
 gi|258488886|gb|ACV72449.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488910|gb|ACV72461.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488918|gb|ACV72465.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488944|gb|ACV72478.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488946|gb|ACV72479.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488972|gb|ACV72492.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
 gi|258488974|gb|ACV72493.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|296125231|ref|YP_003632483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
 gi|296017047|gb|ADG70284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
          Length = 272

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 107/211 (50%), Gaps = 12/211 (5%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +++ ++F DL+  G+ GLM A +K++     KF TYA+  ++ AI   +        +P 
Sbjct: 59  SHKHIEFQDLVGFGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDELRKLDY---LPR 115

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLET--P 579
            +R  + ++ +    +  ++ R   P+EIA  L +P+    + +K  I   P SL     
Sbjct: 116 SIRKDVKEIEKAREILEARLSRNIKPQEIADMLGIPISKYNETMKRYIEASPTSLSDVWY 175

Query: 580 IGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +GD+ D   + D ++  +  +P   A + +++      L  L  +E++VL + +      
Sbjct: 176 VGDDSDEISVIDTLKSNDKTNPEYLAEREDVKNKIVAALKKLPEKEKQVLILYY----YD 231

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           D TL+E+GK   V+  RI Q+  KAI++L++
Sbjct: 232 DLTLKEIGKVLEVSESRISQLHTKAIQQLRY 262


>gi|258488922|gb|ACV72467.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|258489038|gb|ACV72525.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489080|gb|ACV72546.1| RpoD [Xanthomonas perforans]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|21225616|ref|NP_631395.1| RNA polymerase secondary sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|2687404|gb|AAC01582.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
 gi|8246836|emb|CAB92887.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
          Length = 263

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 100/214 (46%), Gaps = 11/214 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + +++   L +   +A ++  RG    DL Q   +GL+KA + +D   G+ F  YA+  V
Sbjct: 38  RDDLIRVWLPMAERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPERGHAFEAYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V ++A+ ++     R PT EEIA+   +    V
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRIQDLRNRVRKSAKELAQTTPGRAPTVEEIAEHAQLTTAEV 157

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
           R  ++  +    +SLE  +   D   LGD      A+   D A  A +     R  L +L
Sbjct: 158 RTGMEALECFSALSLEAEMPGTDGYALGD------ALGGPDPAFDAVVDRVAVRPCLEAL 211

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             RE  +L +RF  GM      +++G  Q  V+R
Sbjct: 212 PERERTILYLRFFGGMTQSRIAQQLGISQMHVSR 245


>gi|258488874|gb|ACV72443.1| RpoD [Xanthomonas axonopodis pv. glycines]
          Length = 261

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|123442749|ref|YP_001006726.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332161358|ref|YP_004297935.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122089710|emb|CAL12562.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318605283|emb|CBY26781.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665588|gb|ADZ42232.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859514|emb|CBX69857.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 240

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQKVEQRLGRPATEQEVAQNLDIDLTEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 MLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|229010401|ref|ZP_04167605.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
 gi|228750821|gb|EEM00643.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
          Length = 224

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 110/234 (47%), Gaps = 24/234 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR-----VL 617
                         +   S L D +E   D ++V+ ++S   ++    +T  R     + 
Sbjct: 121 DAKN----------NYQVSSLDDVVENSSDGSSVARIESVGEVEQGYEQTERRLVLDDIF 170

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             L   E+ V+   FG  +N   T    G++  +++  + +I+ +AI KLK  +
Sbjct: 171 NVLNDTEKSVIHYIFGENLNQKDT----GERLGISQMHVSRIKRQAISKLKQAA 220


>gi|330959691|gb|EGH59951.1| putative RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 291

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 112/252 (44%), Gaps = 49/252 (19%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++V + LR V+ +A++Y+  GL   DLIQEGNIGL+KA ++F+     +  T+A+  
Sbjct: 55  AARQLVTSQLRFVVHIARRYSGYGLPLSDLIQEGNIGLIKAVKRFNPAAQVRLITFAVHG 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP------TPEE---IAK 554
           +K  I   I      +R+            +  R++   ++++P      T +E   IA 
Sbjct: 115 IKAEINEYILRNCRMVRM---------ATTKAQRKLLFNLRKQPRSRTWLTADETKHIAD 165

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTS------------------HLGDFIEDKN 596
            L + V  V++          +ET +   DTS                   LGD   D  
Sbjct: 166 ILNVSVRDVKE----------METRMAGNDTSFDPAADADDDSALLTPAHQLGDHRYDPA 215

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            +   ++    +  +  T  L SL  R   +L  RF        TL ++  ++ V+ ERI
Sbjct: 216 HLYETENDADTSSYDLHT-ALNSLDERSRDILAQRFLSERKA--TLHDLATKYKVSAERI 272

Query: 657 RQIEAKAIRKLK 668
           RQIE  A+ KLK
Sbjct: 273 RQIEKLALAKLK 284


>gi|225619299|ref|YP_002720525.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
 gi|225214118|gb|ACN82852.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
          Length = 275

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 107/211 (50%), Gaps = 12/211 (5%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +++ ++F DL+  G+ GLM A +K++     KF TYA+  ++ AI   +        +P 
Sbjct: 62  SHKHIEFQDLVGFGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDELRKLDY---LPR 118

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLET--P 579
            +R  + ++ +    +  ++ R   P+EIA  L +P+    + +K  I   P SL     
Sbjct: 119 SIRKDVKEIEKAREILEARLSRNIKPQEIADMLGIPISKYNETMKRYIEASPTSLSDVWY 178

Query: 580 IGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +GD+ D   + D ++  +  +P   A + +++      L  L  +E++VL + +      
Sbjct: 179 VGDDSDEISVIDTLKSNDKTNPEYLAEREDVKNKIIAALKKLPEKEQQVLILYY----YD 234

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           D TL+E+GK   V+  RI Q+  KAI++L++
Sbjct: 235 DLTLKEIGKVLEVSESRISQLHTKAIQQLRY 265


>gi|238756654|ref|ZP_04617944.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
 gi|238705123|gb|EEP97550.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
          Length = 240

 Score = 71.6 bits (174), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 99/201 (49%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +  R++  K+ R  + +E+A+ L + +   R++L  T           DE     G+ 
Sbjct: 100 VAQAMRQVEQKVGRPASEQEVAQILDISLVEYRQILLDTNNSQLFSY---DEWREEHGES 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +E      +  +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 VEPVLDGLDDANPLQQLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 213 VLEVGESRVSQLHSQAIKRLR 233


>gi|227500978|ref|ZP_03931027.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
 gi|227216751|gb|EEI82149.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
          Length = 256

 Score = 71.6 bits (174), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 117/229 (51%), Gaps = 20/229 (8%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A E++D   G+ FS++A   +  
Sbjct: 31  ELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIERYDPSKGFAFSSFATPTIMG 90

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVEGVRK 565
            + R   D+   IR+P  +++ ++K + TA++ +  +++R PT  +IA  L    E + +
Sbjct: 91  ELKRYFRDKGWVIRVPRRIQN-LYKKINTAKKILPQELQRTPTVADIADYLGEDEETILE 149

Query: 566 VLKITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
            ++ +K   P SL+        E+   L D I  EDKN     DS     L++   + + 
Sbjct: 150 TMEASKVYTPQSLDMKYQVQKGENAVDLSDMIGEEDKN----FDS---IELKDLIDKSME 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L   E+ +L +R+  G     T  ++     +++  + +IE K ++K 
Sbjct: 203 RLNDLEKEILELRYYEG----RTQVDIANSLDISQMTVSRIEKKILQKF 247


>gi|126348115|emb|CAJ89836.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 295

 Score = 71.6 bits (174), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 61/263 (23%), Positives = 126/263 (47%), Gaps = 43/263 (16%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA 
Sbjct: 46  QFFQRLTELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIGLIKAI 105

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +S+++ R
Sbjct: 106 DRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELSSRLDR 165

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLET------PIGDEDTSHLGDFI--- 592
           EPT  E+A  + +     VEG  ++        SL+       P G E  S L DFI   
Sbjct: 166 EPTVAELATLMNISENEVVEG--QIASNGYNSSSLDAALTGDGPEGGE--SVLADFIGVE 221

Query: 593 -------EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                  ED ++++PL               +A L+ R+ +++ MRF      + T  E+
Sbjct: 222 EDGLRLVEDFHSLAPL---------------MAELSERDRQIIHMRF----VEEATQAEI 262

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G++   ++  + ++  + I +L+
Sbjct: 263 GERLGCSQMHVSRLIKRIITRLR 285


>gi|283779412|ref|YP_003370167.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283437865|gb|ADB16307.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 374

 Score = 71.6 bits (174), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 55/85 (64%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R ++  + +   +A   +  +V ANLRLV+S+AKK+++    F DL+ EG   L++A EK
Sbjct: 178 RELIVSIERLIAQALADRNRIVRANLRLVVSIAKKFSDARNSFDDLLSEGITSLLRAVEK 237

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSI 512
           FD+  G++FSTYA   V++ + RS+
Sbjct: 238 FDYDRGFRFSTYATQAVRRTLCRSL 262



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           LR    ++L+ L PRE  ++R RFG+       TL+ +  +F V +ER+RQ+E +AI KL
Sbjct: 300 LRRALAKMLSKLDPRERSIIRCRFGLDRKEQVQTLQSLAGEFGVCKERVRQLEMRAISKL 359

Query: 668 K 668
           +
Sbjct: 360 R 360


>gi|258488852|gb|ACV72432.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488894|gb|ACV72453.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488896|gb|ACV72454.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488898|gb|ACV72455.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488900|gb|ACV72456.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488902|gb|ACV72457.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489082|gb|ACV72547.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489084|gb|ACV72548.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489086|gb|ACV72549.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489088|gb|ACV72550.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
          Length = 261

 Score = 71.6 bits (174), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|255994576|ref|ZP_05427711.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
 gi|255993289|gb|EEU03378.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
          Length = 249

 Score = 71.6 bits (174), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 108/211 (51%), Gaps = 8/211 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VE  L +V  + +KY N+G+++ DL Q G + L+ A E+FD   G++FS++A   +   
Sbjct: 22  IVEDYLYIVDILVRKYLNKGVEYDDLYQVGAMALIMAVERFDASRGFEFSSFATPTILGE 81

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           I +   D+   +++P  +++  +  +++AR  +  K++R+PT +EIA++  M  E V K+
Sbjct: 82  IKKYFRDKEWKLKVPRSVKEA-NAAIQSARESLFAKLQRDPTVKEIAEEKNMKEEEVAKL 140

Query: 567 L--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPR 623
           +   +    +SL+    D  +       E   AV    S I++    E    +L+ L+ +
Sbjct: 141 IDSSMAYNTLSLDVTFDDSGSDSGVSRYEKYMAVEG--SGIESLEYEEMIESILSVLSEK 198

Query: 624 EERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
              + + RF  G       E++G  Q  ++R
Sbjct: 199 NRYIFKKRFLEGKTQSEIAEKLGVSQMTISR 229


>gi|238798562|ref|ZP_04642039.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238717582|gb|EEQ09421.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 240

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+AK L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQQVEQRVGRPATEQEVAKILDIDLVEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|56421070|ref|YP_148388.1| sporulation sigma factor SigK [Geobacillus kaustophilus HTA426]
 gi|56380912|dbj|BAD76820.1| sporulation mother cell-specific RNA polymerase sigma-27 factor
           precursor (sigma K) (stage IV sporulation protein CB)
           [Geobacillus kaustophilus HTA426]
          Length = 237

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 115/268 (42%), Gaps = 75/268 (27%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IK+ +    +S  E    ++++ KG+ +A   +  ++E NLRLV  + KK+ N G +  D
Sbjct: 22  IKNNAFPQPLSAQEEEKYLALMAKGDEQA---RNRLIEHNLRLVAHIVKKFENTGEEVED 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA E +    G K +TYA         R I ++     I +H+R      
Sbjct: 79  LISIGTIGLIKAIESYSPGKGTKLATYA--------ARCIENE-----ILMHLRS----- 120

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                                             LK T++ +SL  PIG +         
Sbjct: 121 ----------------------------------LKKTRKDVSLHEPIGQD--------- 137

Query: 593 EDKNAVSPLD----------SAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++ N +S LD            I  N+  E   + ++ L  RE+ V+  RFG+G   + T
Sbjct: 138 KEGNEISLLDILKAEGEDIADEIHLNMELEQVKQYISVLDEREKEVIINRFGLGRQREKT 197

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 198 QREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|210621718|ref|ZP_03292767.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
 gi|210154600|gb|EEA85606.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
          Length = 252

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 125/247 (50%), Gaps = 13/247 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++S+ +KG+ ++   K ++++ N+ LV     K++   L   DL Q G IGL
Sbjct: 14  VSYDEILSLISLAQKGDLKS---KNKLIKLNIGLVKKAVSKFSFSSLDNDDLYQLGCIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA E+FD  LG  FS+YA+  ++  I R + D    I+I   ++    K  +   +   
Sbjct: 71  VKAIERFDPNLGNMFSSYAVPLIEGEIKRFLRDDGI-IKISRELKTIGWKAKKYKTQYFK 129

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K  +E + + ++K+L +P+E ++  L I   P+     I + D+ +    ++  N +   
Sbjct: 130 KTGKEASLQALSKELNIPIEKIQSAL-IALSPVEYFN-IYESDSEYTQ--LDLSNNIIME 185

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DS     L E    ++  L   E++V+++R+      D T  + G+   +++ ++ +IE 
Sbjct: 186 DSIPYTELIE-LNEIIDELPDLEKKVMKLRYF----EDFTQAKTGEILGISQVQVSRIER 240

Query: 662 KAIRKLK 668
           KA+  LK
Sbjct: 241 KALMLLK 247


>gi|154249080|ref|YP_001409905.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
 gi|154153016|gb|ABS60248.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
          Length = 233

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 103/203 (50%), Gaps = 10/203 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG I L++AAEK+D   G  F T+A   VK A+   +        +P ++R  I K
Sbjct: 34  DLIQEGVIALLQAAEKYDPRYGATFKTFAYTRVKGAMIDYLRKLDY---LPKNVRQDIKK 90

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
             R       + KR PT +E+++ L + VE V ++ +    K+ ++L+  + + D +  G
Sbjct: 91  FDRELLNFYEQNKRLPTYDEMSEILGIDVEEVEEIYRELALKQSLNLDQYLFESDENSYG 150

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I+ K+  +  ++A ++ L E     +  L  +E+ +L MRF      + +L+E+ +  
Sbjct: 151 S-IDIKSEENVKENAWKSILHEQLVEAINKLDEKEKIILSMRF----EHELSLKEIAEVL 205

Query: 650 CVTRERIRQIEAKAIRKLKHPSR 672
            VT  R+ QI    + KL+   R
Sbjct: 206 GVTESRVSQILGVILSKLRKMLR 228


>gi|297193426|ref|ZP_06910824.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197723191|gb|EDY67099.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 282

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 57/241 (23%), Positives = 116/241 (48%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E S  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 48  LQAGTAEHSRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 107

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 108 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRSPTTAEIA 167

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++  +     SLE     ++   +   ++      P  + ++   R+
Sbjct: 168 ERLKIGEDEVLACIEAGRSYHATSLE---AAQEGDGMPGLLDRLGYEDPALAGVEH--RD 222

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+     ++ T  ++ ++  V++  + ++ A++  +L+  +
Sbjct: 223 LVRHLLVQLPEREQRILMLRY----YSNLTQSQISQELGVSQMHVSRLLARSFARLRSAN 278

Query: 672 R 672
           R
Sbjct: 279 R 279


>gi|258489028|gb|ACV72520.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
          Length = 246

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 49/69 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   +
Sbjct: 4   TTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE 63

Query: 177 GTTLLREII 185
           G   L EI+
Sbjct: 64  GKKRLAEIV 72


>gi|261418447|ref|YP_003252129.1| sporulation sigma factor SigK [Geobacillus sp. Y412MC61]
 gi|319767593|ref|YP_004133094.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
 gi|261374904|gb|ACX77647.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC61]
 gi|317112459|gb|ADU94951.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
          Length = 245

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 115/268 (42%), Gaps = 75/268 (27%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IK+ +    +S  E    ++++ KG+ +A   +  ++E NLRLV  + KK+ N G +  D
Sbjct: 30  IKNNAFPQPLSAQEEEKYLALMAKGDEQA---RNRLIEHNLRLVAHIVKKFENTGEEVED 86

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA E +    G K +TYA         R I ++     I +H+R      
Sbjct: 87  LISIGTIGLIKAIESYSPGKGTKLATYA--------ARCIENE-----ILMHLRS----- 128

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                                             LK T++ +SL  PIG +         
Sbjct: 129 ----------------------------------LKKTRKDVSLHEPIGQD--------- 145

Query: 593 EDKNAVSPLD----------SAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++ N +S LD            I  N+  E   + ++ L  RE+ V+  RFG+G   + T
Sbjct: 146 KEGNEISLLDILKAEGEDIVDEIHLNMELEQVKQYISVLDEREKEVIINRFGLGRQREKT 205

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 206 QREIAKELGISRSYVSRIEKRALMKMFH 233


>gi|149175161|ref|ZP_01853784.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148846139|gb|EDL60479.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 349

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 56/230 (24%), Positives = 103/230 (44%), Gaps = 60/230 (26%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +++ANLRLV+S+AK  T+R   F D++ +G++ L++A E FD   G +FSTY  W V   
Sbjct: 170 IIQANLRLVVSIAKNLTDRANLFEDIVSDGHLPLIRAVEIFDVDRGNRFSTYGTWAV--- 226

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
                             R+ + +  +  R      K   T    A+ LA+ +  +R  +
Sbjct: 227 ------------------RNFLFRTTKKGR------KYRKTFLNGAETLALGLSDIRSTM 262

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           +               +T H             +D  +Q        +VL +L  RE+ +
Sbjct: 263 R-------------SHETYH-----------QNIDDVLQ--------KVLHTLDEREQVI 290

Query: 628 LRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L+ RFG+   +T     E+ +   V+ ER+RQ+  +++++++     +KL
Sbjct: 291 LKRRFGLAQSDTPEKFREIAEDLGVSTERVRQLTIRSLQRMREAIEEQKL 340


>gi|39998144|ref|NP_954095.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
 gi|39985090|gb|AAR36445.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
          Length = 250

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 105/210 (50%), Gaps = 13/210 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+    IGL+ AAE+FD   G +F T+A   ++  I   +  Q    R    +RDK  K
Sbjct: 50  DLMSAAIIGLITAAERFDPTRGVQFKTFAEQRIRGTIIDELRSQDWLTR---SLRDKFKK 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + +    + +++ R PT EE+A  L M V+   ++L+       +SL+    D+D S  G
Sbjct: 107 LEKEFVLLEHQLGRNPTSEEVATALKMSVDEYYQMLEEIHLLSFVSLDESWEDDDGSPFG 166

Query: 590 --DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D + D +  +P    +   + ++ T  + SL  +E  V+ + +   +N    L+E+G 
Sbjct: 167 LLDILADTSIENPQSQLMARQMLDSLTESIESLPEKERLVITLYYYEELN----LKEIGA 222

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
              ++  RI Q+ ++AI +L+  ++ K +R
Sbjct: 223 VLELSESRISQLHSQAIVRLR--AKMKNMR 250


>gi|325844829|ref|ZP_08168281.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
 gi|325489016|gb|EGC91404.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
          Length = 229

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 67/273 (24%), Positives = 118/273 (43%), Gaps = 59/273 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F+     +++ +   I + +    +S  E  H ++++  G+  A   +++++E NLRLV 
Sbjct: 6   FIVSLFSNLIPLMGSISNQAFPNPLSPEEEEHYLTLMANGDKNA---REKLIEHNLRLVA 62

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KKY N+     DLI  G IGL+KA + F    G K +TYA   +             
Sbjct: 63  HIVKKYQNQTDDKEDLISIGTIGLIKAIDSFSPDKGTKLATYAARCID------------ 110

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                    ++I  + R+ ++M N                                +SL 
Sbjct: 111 ---------NEILMLFRSTKKMRND-------------------------------VSLY 130

Query: 578 TPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++D+N     D  IQ    E   + L SLT RE  ++  RFG+
Sbjct: 131 DPIGYDKEGNEICLIDVVKDENK-DLNDIIIQQLAFEKIEKNLKSLTQRERDIIVRRFGL 189

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             + + T +E+ K + ++R  + +IE +A+ KL
Sbjct: 190 ENHEEETQQEIAKSYGISRSYVSRIEKRALMKL 222


>gi|228993082|ref|ZP_04153005.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
 gi|228999132|ref|ZP_04158714.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|229006680|ref|ZP_04164314.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228754541|gb|EEM03952.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228760749|gb|EEM09713.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|228766730|gb|EEM15370.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
          Length = 228

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 40  ARNLLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSAGKGTKLATYA--- 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 97  -----ARCIENE-----ILMHLR------------------------------------- 109

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ ++  E     +  L 
Sbjct: 110 --VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILD 167

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 168 EREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 215


>gi|238794024|ref|ZP_04637642.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
 gi|238726656|gb|EEQ18192.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
          Length = 240

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQKVEQRVGRPATEQEVAQILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|310657328|ref|YP_003935049.1| RNA polymerase sigma-37 factor (sigma-b) [Clostridium sticklandii
           DSM 519]
 gi|308824106|emb|CBH20144.1| RNA polymerase sigma-37 factor (sigma-B) [Clostridium sticklandii]
          Length = 273

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 59/241 (24%), Positives = 116/241 (48%), Gaps = 38/241 (15%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V+ +L +   ++KK+ N+G+++ D+ Q  ++GL+ A E+FD   G++FS++A   +
Sbjct: 46  RNELVKRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIFAIERFDVSKGFEFSSFATPTI 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  +IR+P  +++   KV      +  ++ R P  E+IAK L    E V 
Sbjct: 106 IGEIKKYFRDKGWSIRVPRRIQELSKKVNTAKSYLQQELHRVPKIEDIAKYLDCTEEEVL 165

Query: 565 KVLKITK--EPISLETP---------------IGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           + ++ +   +P SL+                 +GDED S   + IE+K+ +         
Sbjct: 166 EAIEASHVYKPKSLDLSYDNEGDDKDILLLDLVGDEDKSF--NMIENKDFIE-------- 215

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                    L+ L   E ++++ RF       H   ++G    V++  + ++E K + KL
Sbjct: 216 -------NALSKLNEIETKIIKDRFFKNKTQMHVANDLG----VSQMTVSRMEKKILAKL 264

Query: 668 K 668
           K
Sbjct: 265 K 265


>gi|254700317|ref|ZP_05162145.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261750811|ref|ZP_05994520.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261740564|gb|EEY28490.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
          Length = 262

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 59/101 (58%), Gaps = 2/101 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV  +A  Y   GL   ++I EGN+GLM+A ++F+   G++ +TYAMWW
Sbjct: 49  AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           +K +I   I      +++      K  ++    R+M +KI+
Sbjct: 109 IKASIQEYILRSWSLVKMGTTANQK--RLFFNLRKMKSKIQ 147


>gi|229086911|ref|ZP_04219070.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
 gi|228696421|gb|EEL49247.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
          Length = 228

 Score = 71.2 bits (173), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 40  ARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYA--- 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 97  -----ARCIENE-----ILMHLR------------------------------------- 109

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ ++  E     +  L 
Sbjct: 110 --VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILD 167

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 168 EREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 215


>gi|297529299|ref|YP_003670574.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297252551|gb|ADI25997.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 245

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 115/268 (42%), Gaps = 75/268 (27%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IK+ +    +S  E    ++++ KG+ +A   +  ++E NLRLV  + KK+ N G +  D
Sbjct: 30  IKNNAFPQPLSAQEEEKYLALMAKGDEQA---RNRLIEHNLRLVAHIVKKFENTGEEVED 86

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA E +    G K +TYA         R I ++     I +H+R      
Sbjct: 87  LISIGTIGLIKAIESYSPGKGTKLATYA--------ARCIENE-----ILMHLRS----- 128

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                                             LK T++ +SL  PIG +         
Sbjct: 129 ----------------------------------LKKTRKDVSLHEPIGQD--------- 145

Query: 593 EDKNAVSPLD----------SAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++ N +S LD            I  N+  E   + ++ L  RE+ V+  RFG+G   + T
Sbjct: 146 KEGNEISLLDILKAEGQDIVDEIHLNMELEQVKQYISVLDEREKEVIINRFGLGRQREKT 205

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 206 QREIAKELGISRSYVSRIEKRALMKMFH 233


>gi|91200244|emb|CAJ73289.1| strongly similar to RNA polymerase sigma factor for flagellar
           operon [Candidatus Kuenenia stuttgartiensis]
          Length = 259

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 112/240 (46%), Gaps = 19/240 (7%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           I ++++V  NL LV  V  K+      F+D   LI+ G IGL++A+E+FD C+  KF T+
Sbjct: 24  IDREKLVTENLSLVKYVVNKFIIYLPSFVDKEDLIEYGVIGLLEASERFDPCMDTKFGTF 83

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  ++ AI   +  Q     +P  +R+K+         +  K+ R P PEEIA +L + 
Sbjct: 84  AVSRIRGAILDHLRAQDW---LPRSVREKVSLAREAYATLEQKLNRHPLPEEIAAELKID 140

Query: 560 VEGVRKVLK-------ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                K+L        ++ E ++ ++  G+++   +G    D     PL +      +E 
Sbjct: 141 TAEWEKLLVEINFGMFLSLEEMNAKSEDGNKEA--VGMLFADSKIGDPLSNIETEEEKEL 198

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               +  L  RE+ V+ + +      D  L E+ +   ++  R+ QI  + +  L+   R
Sbjct: 199 LVAAIKELPAREKLVITLYY----YEDLMLREISQMLDISESRVSQIHHQGLFMLRSKVR 254


>gi|306821834|ref|ZP_07455426.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550141|gb|EFM38140.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 268

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 56/231 (24%), Positives = 116/231 (50%), Gaps = 18/231 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+++ NL +   ++KKY N+G+++ D+ Q  ++GL+ A E++D   G++FS++A   +
Sbjct: 42  RNELIQRNLYIAEILSKKYINKGIEYEDIYQVASLGLIYAIERYDITKGFEFSSFATPTI 101

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  +IR+P  +++   +V      +  +  + P   +IA+KL +  E V 
Sbjct: 102 IGEIKKYFRDKGWSIRVPRRIQELSKRVNTVKNELQQETHKTPRISDIAEKLGITQEEVL 161

Query: 565 KVLKI--TKEPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVL 617
           + +       PISL+      G++    L + I  +DK+     D     N       V+
Sbjct: 162 ETMDAAGAYAPISLDVKYDNEGEDKDVALHELIGKDDKSFAEIEDGDFLRN-------VM 214

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            SL+  E++++  R+      + T   V K+  +++  + ++E K + KLK
Sbjct: 215 ESLSEVEKKIIMDRYF----DNKTQMTVAKELDISQMTVSRMEKKILTKLK 261


>gi|1706832|sp|P52621|FLIA_YEREN RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|790557|gb|AAC43394.1| FliA [Yersinia enterocolitica (type O:9)]
          Length = 230

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDRLQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 90  VASAMQKVEQRLGRPATEQEVAQNLDIDLTEYRQILLDTNNSQLFSYDEWREEHGESVEP 149

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 150 MLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 205

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 206 VGESRVSQLHSQAIKRLR 223


>gi|116334961|ref|YP_802456.1| putative RNA polymerase sigma factor rpoD [Candidatus Carsonella
           ruddii PV]
 gi|116235242|dbj|BAF35090.1| putative RNA polymerase sigma factor rpoD [Candidatus Carsonella
           ruddii PV]
          Length = 320

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 49/73 (67%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           NL      ++  L  +E+ ++R+RFGIG    +TLEE+G  + +T+ERIRQIE   + KL
Sbjct: 241 NLNNLIRLIILELPKKEQIIIRLRFGIGFPKSYTLEEIGLMYYLTKERIRQIELNVLFKL 300

Query: 668 KHPSRSKKLRSFL 680
           +HP+RS+ L+ ++
Sbjct: 301 RHPTRSEVLKPYI 313


>gi|229016304|ref|ZP_04173251.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
 gi|229022543|ref|ZP_04179074.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228738763|gb|EEL89228.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228744996|gb|EEL95051.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
          Length = 224

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 112/234 (47%), Gaps = 24/234 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVDHYKNLVHSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  I +P  ++D   K+      ++++++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR-----VL 617
                         +   S L D +E   D ++V+ ++S   ++    +T  R     + 
Sbjct: 121 DAKN----------NYRVSSLDDVVENSSDGSSVARIESVGEVEQGYEQTERRLILDDIF 170

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             L   E+ V+   FG  +N   T    G++  +++  + +I+ +AI KLK  +
Sbjct: 171 NVLNDTEKSVIHYIFGENLNQKDT----GERLGISQMHVSRIKRQAISKLKQAA 220


>gi|325106726|ref|YP_004267794.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324966994|gb|ADY57772.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 332

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 104/250 (41%), Gaps = 75/250 (30%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A+  +  ++ ANLRLV+SVA+K+    L F +L  +G I LM A EKFD+  GY+FSTY
Sbjct: 148 QANSVRDLLIRANLRLVVSVARKFVTPQLTFDELFSDGVIALMNAVEKFDYDRGYRFSTY 207

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A + + +++ R          I V  +++IH  V                          
Sbjct: 208 AYYSISRSLYRF---------IKVQRKNRIHSDV-------------------------- 232

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLG------DFIEDKNAVSPLDSAIQANLRETT 613
                           LE  +  +D    G      DF+ ++     LDS +        
Sbjct: 233 ----------------LEQVVEADDDGQSGWNQESWDFVNEE-----LDSML-------- 263

Query: 614 TRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               A L  RE  ++R R+         T + + ++  V  ER+RQ+E +A+ KL++ S 
Sbjct: 264 ----AQLDQRERWIIRQRYTFDSEGKAPTYKVLAEKLGVCNERVRQLEKRALSKLRNLSD 319

Query: 673 SKKLRSFLDG 682
             +    L+ 
Sbjct: 320 DGRFSDILEA 329


>gi|146284301|ref|YP_001174454.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri A1501]
 gi|145572506|gb|ABP81612.1| sigma factor RpoH [Pseudomonas stutzeri A1501]
 gi|327482685|gb|AEA85995.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri DSM 4166]
          Length = 284

 Score = 71.2 bits (173), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 122/236 (51%), Gaps = 17/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  I   I      +++      R     +    +R++     E T   +A  L +   
Sbjct: 110 IRAEIHEFILRNWRIVKVATTKAQRKLFFNLRSQKKRLAWLNNDEVTA--VADSLGVEPH 167

Query: 562 GVRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            VR++  ++T   ++ +     +D S       ++ED +   P      A+  +++T  L
Sbjct: 168 EVREMESRLTGHDMAFDPAADADDDSAYQSPAHYLED-HRYDPARQLEDADWSDSSTSSL 226

Query: 618 -ASLTPREER---VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            A+L   +ER   +L+ R+   +N D  TL ++  ++ V+ ERIRQ+E  A+ KLK
Sbjct: 227 HAALEGLDERSRDILQQRW---LNEDKATLHDLAAKYNVSAERIRQLEKNAMNKLK 279


>gi|254381148|ref|ZP_04996513.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194340058|gb|EDX21024.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 306

 Score = 70.9 bits (172), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 61/257 (23%), Positives = 121/257 (47%), Gaps = 45/257 (17%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  +   A+  ++E N+ LV   A+++T   N G++  D+IQ G IGL+KA ++FD   
Sbjct: 65  EGTRDYQYARNTLIEMNISLVRFAARRFTARINAGIELDDVIQVGTIGLIKAIDRFDPDR 124

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FST A+ ++   I R   D +  + +P  +++   ++ +    ++  + R P+ +EI
Sbjct: 125 EVEFSTLALPYITGEIKRYFRDTTWAVHVPRRLQELRVELAKCQETLTEVLGRAPSVKEI 184

Query: 553 AKKLAMPVEGVRKVL---------------KITKEPISLET------PIGDEDTSHLGDF 591
           A+ L +  E V + L                 T  P +L         +GD D + +   
Sbjct: 185 AEHLELSEEEVIEGLVAANGYSSASLDSTAGTTDRPAALSEGRPLADTVGDIDPAMV--L 242

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            ED + ++PL               L+ L  R+ ++LRMRF   M    T  E+G +  +
Sbjct: 243 FEDVHTLAPL---------------LSELDERDLQILRMRFAREM----TQAEIGTELGI 283

Query: 652 TRERIRQIEAKAIRKLK 668
           ++ ++ ++  + + +L+
Sbjct: 284 SQMQVSRLLTRILTRLR 300


>gi|319644916|ref|ZP_07999149.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392725|gb|EFV73519.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 241

 Score = 70.9 bits (172), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 100/230 (43%), Gaps = 58/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLAS 619
              LK TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E   + +  
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEKVKKYIDI 175

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 176 LDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|326797246|ref|YP_004315066.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
 gi|326548010|gb|ADZ93230.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
          Length = 288

 Score = 70.9 bits (172), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 119/241 (49%), Gaps = 16/241 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+ EA+   + +V ++LR V+ +AK Y+  GL   DL+QEGN+GLMKA ++F+  +G + 
Sbjct: 46  GDLEAA---RALVMSHLRFVVHIAKSYSGYGLSQGDLVQEGNVGLMKAVKRFNPEVGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            ++A+ W+K  I   I      +++     + K+   +R+A++  + +      + +A  
Sbjct: 103 VSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKMFFNLRSAKKTLSWLNNSEV-DAVAND 161

Query: 556 LAMPVEGVRKV--------LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           L +  + VR++        +         +        S+L D   D  A+   D   +A
Sbjct: 162 LGVSPDVVRQMEGRMSSTDMAFDATTDDDDDSAFQAPASYLEDGRYDP-AMLLEDGNWEA 220

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +      + ++ L  R   +L  R+ +  N   TL ++  ++ V+ ERIRQ+E  A++K+
Sbjct: 221 DSNRRLQQAMSDLDERSRNILVQRW-LSENKS-TLHDLADEYGVSAERIRQLEKNAMKKI 278

Query: 668 K 668
           +
Sbjct: 279 R 279


>gi|294501329|ref|YP_003565029.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|295706676|ref|YP_003599751.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
 gi|294351266|gb|ADE71595.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|294804335|gb|ADF41401.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
          Length = 242

 Score = 70.9 bits (172), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 115/259 (44%), Gaps = 57/259 (22%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+ +    +S +E +  +S++ +G+ EA   +  ++E NLRLV  + KK+ N G    D
Sbjct: 22  VKNNAFPQPLSAAEEKRYLSLMEQGDQEA---RNLLIEHNLRLVAHIVKKFENTGEDAED 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA E +    G K +TYA         R I ++     I +H+R      
Sbjct: 79  LISIGTIGLIKAIESYSQGKGTKLATYA--------ARCIENE-----ILMHLR------ 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDF 591
                                             LK TK+ +SL  PIG D++ + +   
Sbjct: 120 ---------------------------------ALKKTKKDVSLHDPIGQDKEGNEISLI 146

Query: 592 IEDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
              K+    +   IQ N+  E     +  L  RE+ V+  RFG+ +  + T  E+ K+  
Sbjct: 147 DVLKSESDDVIDMIQLNMELEKIKEYIDILDDREKEVIVGRFGLDLQDEKTQREIAKELN 206

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++R  + +IE +A+ K+ H
Sbjct: 207 ISRSYVSRIEKRALMKMFH 225


>gi|256271|gb|AAC60416.1| RpoD3 [Synechococcus]
          Length = 48

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+++ T
Sbjct: 1   LDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKART 48


>gi|256783362|ref|ZP_05521793.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289767236|ref|ZP_06526614.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289697435|gb|EFD64864.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
          Length = 263

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 99/214 (46%), Gaps = 11/214 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++   L +   +A ++  RG    DL Q   +GL+KA + +D   G+ F  YA+  V
Sbjct: 38  RDNLIRVWLPMAERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPERGHAFEAYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V ++A+ ++     R PT EEIA+   +    V
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRIQDLRNRVRKSAKELAQTTPGRAPTVEEIAEHAQLTTAEV 157

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASL 620
           R  ++  +    +SLE  +   D   LGD      A+   D A  A +     R  L +L
Sbjct: 158 RTGMEALECFSALSLEAEMPGTDGYALGD------ALGGPDPAFDAVVDRVAVRPCLEAL 211

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             RE  +L +RF  GM      +++G  Q  V+R
Sbjct: 212 PERERTILYLRFFGGMTQSRIAQQLGISQMHVSR 245


>gi|152976769|ref|YP_001376286.1| sporulation sigma factor SigK [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025521|gb|ABS23291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 237

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 49  ARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYA--- 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 106 -----ARCIENE-----ILMHLR------------------------------------- 118

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ ++  E     +  L 
Sbjct: 119 --VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILD 176

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 177 EREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 224


>gi|282863441|ref|ZP_06272500.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561776|gb|EFB67319.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 285

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 111/239 (46%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 53  PGTPEHDRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQ 112

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 113 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTAEIAQR 172

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  E V   ++  +     SLE     ++   L   ++      P  + ++   R+  
Sbjct: 173 LKISEEEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLV 227

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+      + T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 228 RHLLVQLPEREQRILLLRY----YNNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 282


>gi|218548541|ref|YP_002382332.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ATCC
           35469]
 gi|218356082|emb|CAQ88699.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia fergusonii
           ATCC 35469]
 gi|324113640|gb|EGC07615.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           fergusonii B253]
 gi|325496958|gb|EGC94817.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ECD227]
          Length = 238

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 97/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  +  E+AK+L +  E  R++L  T            E+     + 
Sbjct: 100 VAQAIGQLEQELGRNASETEVAKRLGISTEEYRQMLLDTNNSQLFSYDEWREEHGDSAEL 159

Query: 592 I-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           I E+    +PL   ++++LR+     +  L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 ITEEHQQANPLHQLLESDLRQQVMDAIERLPEREKLVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|167630319|ref|YP_001680818.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
 gi|167593059|gb|ABZ84807.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
          Length = 266

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 67/218 (30%), Positives = 105/218 (48%), Gaps = 28/218 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GLM A EKFD   G KF TYA+  ++ ++   +        +PV +R K  +
Sbjct: 60  DLISYGVFGLMDAIEKFDLARGLKFETYAIARIRGSMLDGLRAMDW---VPVSVRQKTRE 116

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +T   +S ++ RE T EE+A+ L + +    K+L+  +      T I   D   L D 
Sbjct: 117 LEKTYATLSQRLGREATDEEVAQALGLTLNEFAKLLQDVQ-----ATTIMSLDEYWLTD- 170

Query: 592 IEDK-NAVSPLDSAIQANLRETT-------TRVLAS-----LTPREERVLRMRFGIGMNT 638
             DK + V  +DS     + E T       TR+L +     L  +E  V+ + +  G+  
Sbjct: 171 -SDKGDPVRLIDSLADEQVEEPTAALEFEETRLLLAQAIDKLPEKERTVIALYYYEGL-- 227

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
             TL+E+G    V+  RI Q+  KAI +L+   +R KK
Sbjct: 228 --TLKEIGAVIGVSESRISQLHTKAILRLRGQLARQKK 263


>gi|238788344|ref|ZP_04632138.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
 gi|238723590|gb|EEQ15236.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
          Length = 240

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQKVEQRLGRPATEQEVAQILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|304439070|ref|ZP_07398989.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372429|gb|EFM26016.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 260

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 57/247 (23%), Positives = 118/247 (47%), Gaps = 26/247 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++++E NL +   +AKKY  RG+ + D+ Q  +IGL+ A +++D   G++FS++A   +
Sbjct: 29  REKLIEDNLYIAEILAKKYYGRGIDYDDIYQVASIGLIYAVDRYDPSKGFEFSSFATPTI 88

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  TIR+P  +++   K+      ++  +++ PT  +IA+ L    E V 
Sbjct: 89  IGEIKKYFRDKGWTIRVPRRIQELSKKINNARVYLAQNLQKAPTVSDIAEYLNTTEEEVL 148

Query: 565 KVLKITK--EPISLETPI---GDEDTSHLGDFIE------DKNAVSPLDSAIQANLRETT 613
           + ++ ++  +P SL+       D+   +L D I       +K  ++ L  ++  NL E  
Sbjct: 149 EAIEASRVYQPQSLDISYESQSDDKEVNLADIIGQDEEYFEKIEMNDLMESLFKNLNEVE 208

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L       ER    +  +          + +Q  +++  + +IE K + +LK     
Sbjct: 209 KTILV------ERYFNRKTQVA---------IAEQLNISQMTVSRIEKKVLERLKKDVEG 253

Query: 674 KKLRSFL 680
           K +   L
Sbjct: 254 KTMGEVL 260


>gi|322421664|ref|YP_004200887.1| RNA polymerase sigma 28 subunit FliA/WhiG [Geobacter sp. M18]
 gi|320128051|gb|ADW15611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M18]
          Length = 250

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 113/233 (48%), Gaps = 14/233 (6%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +++ E+V ++L LV  +  +  +     LD   L     IGL+ AAE+FD   G +F T+
Sbjct: 18  MSRDELVVSHLPLVKFIVDRIASSLPPHLDRDDLRSAAVIGLISAAERFDPSRGVQFKTF 77

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++  I   +  Q    R    +RDK  K+ +   ++  ++ R P+ +E+A  + + 
Sbjct: 78  AEQRIRGTIMDELRAQDWLTR---SLRDKFKKLEKEFSQLEQRLGRNPSSDEVATAMGLE 134

Query: 560 VEGVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTR 615
           ++   ++L+       +SL+    DED +  G  D +EDK   SP +  I     E    
Sbjct: 135 LKDYFRLLEEIHLLSFVSLDDAWHDEDGAPFGLLDVLEDKGTESPQNQLIARQTVERLAE 194

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  +E  V+ + +   +N    L+E+G    +T  RI Q+ ++AI +L+
Sbjct: 195 AIDTLPEKERIVITLYYYEELN----LKEIGAVLDLTESRISQLHSQAIIRLR 243


>gi|197120125|ref|YP_002140552.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           bemidjiensis Bem]
 gi|253702434|ref|YP_003023623.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M21]
 gi|197089485|gb|ACH40756.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           bemidjiensis Bem]
 gi|251777284|gb|ACT19865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M21]
          Length = 250

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 114/236 (48%), Gaps = 20/236 (8%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +++ E+V  +L LV  +  +  +     LD   L     IGL+ AAE+FD   G +F T+
Sbjct: 18  MSRDELVVTHLPLVKFIVDRIASSLPPHLDRDDLRSAAVIGLISAAERFDPARGVQFKTF 77

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++  I   +  Q    R    +RDK  K+ R   ++  ++ R P+ +E+A  LAM 
Sbjct: 78  AEQRIRGTIMDELRAQDWLTR---SLRDKFKKLEREFSQLEQRLGRNPSSDEVA--LAMG 132

Query: 560 VEGVRKVLKITKEP-----ISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRET 612
           +E ++   ++ +E      +SL+    DED +  G  D +EDK   SP    I     E 
Sbjct: 133 LE-LKDYFRLLEEIHLLSFVSLDDAWHDEDGAPFGLLDVLEDKGTESPQSQLIARQTVER 191

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  +E  V+ + +   +N    L+E+G    +T  RI Q+ ++AI +L+
Sbjct: 192 LAEAIDALPEKERIVVTLYYYEELN----LKEIGAVLDLTESRISQLHSQAIIRLR 243


>gi|229543758|ref|ZP_04432818.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
 gi|229328178|gb|EEN93853.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
          Length = 241

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 112/252 (44%), Gaps = 61/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE R  +  + +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL
Sbjct: 31  LSASEERKYLKRMAEGDADA---RNILIEHNLRLVAHIVKKFENTGEDTEDLISIGTIGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA E +    G K +TYA         R I ++     I +H+R               
Sbjct: 88  IKAIESYSEGKGTKLATYA--------ARCIENE-----ILMHLR--------------- 119

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                    LK TK+ +SL  PIG +   +   L D ++ + A 
Sbjct: 120 ------------------------ALKKTKKDVSLHDPIGQDKEGNEISLIDVLQSE-AE 154

Query: 599 SPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              D+ IQ N+  E   +    L  RE++V+  RFG+ +  + T  E+ K+  ++R  + 
Sbjct: 155 DVFDT-IQLNMELEKVKQFFDILDEREKQVIIGRFGLNLKKEKTQREIAKELGISRSYVS 213

Query: 658 QIEAKAIRKLKH 669
           +IE +A+ K+ H
Sbjct: 214 RIEKRALMKMFH 225


>gi|229093408|ref|ZP_04224513.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
 gi|228690002|gb|EEL43805.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
          Length = 258

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 39  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 95

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 96  YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 122 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 163

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 164 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 223

Query: 666 KLKH 669
           K+ H
Sbjct: 224 KMFH 227


>gi|229165937|ref|ZP_04293702.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
 gi|228617490|gb|EEK74550.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
          Length = 224

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 55/234 (23%), Positives = 110/234 (47%), Gaps = 24/234 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  + +P  ++D   K+      +++ ++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGVHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR-----VL 617
                         +   S L D +E   D ++V+ ++S   ++    +T  R     + 
Sbjct: 121 DAKN----------NYQVSSLDDVVENSSDGSSVARIESVGEVEQGYEQTERRLVLDDIF 170

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             L   E+ V+   FG  +N   T    G++  +++  + +I+ +AI KLK  +
Sbjct: 171 NVLNDTEKSVIHYIFGENLNQKDT----GERLGISQMHVSRIKRQAISKLKQAA 220


>gi|77359758|ref|YP_339333.1| flagellar biosynthesis sigma factor [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874669|emb|CAI85890.1| Polar Flagellar-specific RNA polymerase sigma factor FliA (sigma F)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 236

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 110/228 (48%), Gaps = 18/228 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 12  IVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAGIRI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +       R  VH + +  +V+     + + + REPT  E+A+KL + +E   
Sbjct: 72  RGAMLDEMRRGDWAPR-SVHRKSR--QVIEAISALESSLNREPTDSEVAQKLEITLEQYH 128

Query: 565 KVLK--ITKEPISLETPIGDEDT-SHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            +L    + + + +E    DED  + +G D   DK    P ++       E+    + SL
Sbjct: 129 HILTDVNSSKILGIEDLGIDEDVITPVGHDLALDK----PFNNVKNERFNESLLSAIKSL 184

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R+  VL + +   MN    L+E+G+   V+  R+ QI  +A+ KLK
Sbjct: 185 PERDAMVLSLYYNDEMN----LKEIGQILDVSESRVSQIHGQAMIKLK 228


>gi|117928753|ref|YP_873304.1| RNA polymerase sigma factor WhiG [Acidothermus cellulolyticus 11B]
 gi|117649216|gb|ABK53318.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 289

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 100/203 (49%), Gaps = 13/203 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A EKFD     KF TYA+  +K AI   I +      IP  +R K  +
Sbjct: 85  DLVSYGIFGLIDAIEKFDLDRAIKFETYAINRIKGAI---IDELRAIDWIPRSVRYKARE 141

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI---GDE-DT 585
           V +    + +K+ R PT  E+A +L + ++ +  +         I+L+  +   GD  D 
Sbjct: 142 VEKAYAALEHKLHRTPTEAEVAAELGISLDELHAIFSQVSFVNVIALDELLNVGGDRGDR 201

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D +ED  A  P+++      +   +R + +L  RE+ V+ + +  G+    TL E+
Sbjct: 202 LSLVDTLEDTKAEDPVEAFETEETKYLLSRAINALPEREKIVITLYYYEGL----TLAEI 257

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+   VT  RI Q+  KA+ +L+
Sbjct: 258 GQVLGVTESRICQMHTKAVLQLR 280


>gi|42783467|ref|NP_980714.1| sporulation sigma factor SigK [Bacillus cereus ATCC 10987]
 gi|42739396|gb|AAS43322.1| RNA polymerase sigma-27 factor [Bacillus cereus ATCC 10987]
          Length = 265

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 64  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 120

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 121 YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 146

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 147 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 188

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 189 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 248

Query: 666 KLKH 669
           K+ H
Sbjct: 249 KMFH 252


>gi|222097784|ref|YP_002531841.1| sporulation sigma factor sigk [Bacillus cereus Q1]
 gi|221241842|gb|ACM14552.1| RNA polymerase sigma-27 factor [Bacillus cereus Q1]
          Length = 263

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 62  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 118

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 119 YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 144

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 145 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 186

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 187 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 246

Query: 666 KLKH 669
           K+ H
Sbjct: 247 KMFH 250


>gi|207109684|ref|ZP_03243846.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 84

 Score = 70.9 bits (172), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 37/81 (45%), Positives = 56/81 (69%), Gaps = 1/81 (1%)

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQI 659
           +D  ++ +L+     VL  L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQI
Sbjct: 2   IDHIMREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQI 61

Query: 660 EAKAIRKLKHPSRSKKLRSFL 680
           E+ AI+KL+ P   + LR++L
Sbjct: 62  ESSAIKKLRSPQYGRILRNYL 82


>gi|52081127|ref|YP_079918.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52786504|ref|YP_092333.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52004338|gb|AAU24280.1| RNA polymerase sporulation-specific sigma factor [Bacillus
           licheniformis ATCC 14580]
 gi|52349006|gb|AAU41640.1| SpoIIIC [Bacillus licheniformis ATCC 14580]
          Length = 241

 Score = 70.9 bits (172), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 100/230 (43%), Gaps = 58/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLAS 619
              LK TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E   + +  
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEKVKKYIDI 175

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 176 LDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|291438641|ref|ZP_06578031.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
 gi|291341536|gb|EFE68492.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
          Length = 303

 Score = 70.9 bits (172), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 71  PGTPEHTRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 130

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R P+  EIA++
Sbjct: 131 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAFGRSPSTAEIAER 190

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  E V   ++  +     SLE     +    L D +  ++    LD       R+  
Sbjct: 191 LRITEEDVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPA--LDG---VEHRDLV 245

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 246 RHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 300


>gi|238764885|ref|ZP_04625825.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
 gi|238696904|gb|EEP89681.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
          Length = 240

 Score = 70.9 bits (172), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQKVEQRLGRPATEQEVAQILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 MLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|226946813|ref|YP_002801886.1| RNA polymerase factor sigma-32 [Azotobacter vinelandii DJ]
 gi|226721740|gb|ACO80911.1| RNA polymerase sigma-32 factor [Azotobacter vinelandii DJ]
          Length = 284

 Score = 70.9 bits (172), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 120/237 (50%), Gaps = 19/237 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQSDLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           ++  I   I      ++I     + K+   +R+ ++    +  E   + +A+ L +    
Sbjct: 110 IRAEIHEFILRNWRIVKIATTKAQRKLFFNLRSQKKRLAWLNNEEV-DAVAESLGVEPHE 168

Query: 563 VRKV-LKITKEPISLETPIGDEDTSHL---GDFIEDK--NAVSPLDSA-----IQANLRE 611
           VR++  +++ + ++ +     +D S       ++ED+  +    L+ A       ANL E
Sbjct: 169 VREMESRLSGQDMAFDPAADADDDSVFQAPAHYLEDQRYDPARQLEEADWSDSAAANLHE 228

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  R   +L  R+        TL ++  ++ V+ ERIRQ+E  A+ KLK
Sbjct: 229 A----LEGLDERSRDILYQRW--LAEEKATLHDLAAKYKVSAERIRQLEKSALNKLK 279


>gi|307718622|ref|YP_003874154.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
 gi|306532347|gb|ADN01881.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
          Length = 262

 Score = 70.9 bits (172), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 100/207 (48%), Gaps = 12/207 (5%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++F DLI  G  GL+ A EKFD     KF TYA+  ++ AI   +        +P  +R
Sbjct: 52  SVEFDDLIGFGTFGLLDAIEKFDPEKHVKFKTYAVTRIRGAIYDELRAMDW---VPRSVR 108

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPI-SLET--PIGD 582
            K  ++     R+ + + R  T EE+A+++ M    ++K L KI+   I SL+     GD
Sbjct: 109 QKSREIEDALHRLESSLGRAATDEELAREMNMSSRELQKTLQKISSTSILSLQELWYTGD 168

Query: 583 E-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           E D   + D +E   A  P     +  ++      +  L  +E++VL + +      D T
Sbjct: 169 ENDRVAIADMLEAPQAYDPAARVEREEIKRVVAEAIKELPEKEKKVLVLYY----YEDLT 224

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+G    VT  R+ Q+  KAI +L+
Sbjct: 225 LKEIGAILNVTESRVSQLHTKAISRLR 251


>gi|118479504|ref|YP_896655.1| sporulation sigma factor SigK [Bacillus thuringiensis str. Al
           Hakam]
 gi|118418729|gb|ABK87148.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Bacillus
           thuringiensis str. Al Hakam]
          Length = 271

 Score = 70.9 bits (172), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 70  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 127 YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 152

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 153 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 194

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 195 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 254

Query: 666 KLKH 669
           K+ H
Sbjct: 255 KMFH 258


>gi|311031146|ref|ZP_07709236.1| RNA polymerase sigma factor SigB [Bacillus sp. m3-13]
          Length = 261

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 125/237 (52%), Gaps = 18/237 (7%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFS 497
           CE S  + ++VE    LV S+A+KY+ RG  F  DL Q G IGL+ A ++FD   G  F 
Sbjct: 24  CEVS--QLQLVEHYTALVESIARKYS-RGKAFHEDLSQVGMIGLLGAMKRFDASFGRSFE 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            +A+  +   I R + D++ ++ +P  +++   K+      ++N+++R P   EIA  L 
Sbjct: 81  AFAVPTIIGEIKRFLRDKTWSVHVPRRIKEIGPKIKSAVEELTNELQRSPKVFEIADYLE 140

Query: 558 MPVEGVRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +  E V + +++++  + +S++  I    D  T  + D + +++A    D   Q  L + 
Sbjct: 141 VTEEEVLEAMEMSQNYQALSVDNAIEADSDGSTVTILDIVGNQDA--GFDQVDQQLLLQ- 197

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++   L+ RE++++   F   M+   T E++G    +++  + +++ KA+ KLK 
Sbjct: 198 --KIFHVLSEREKQIIECTFFKNMSQKETGEKLG----ISQMHVSRLQRKALTKLKQ 248


>gi|294998208|gb|ADF57908.1| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
 gi|308154182|gb|ADF57907.2| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
          Length = 271

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 70  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 127 YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 152

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 153 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 194

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 195 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 254

Query: 666 KLKH 669
           K+ H
Sbjct: 255 KMFH 258


>gi|239932973|ref|ZP_04689926.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441326|ref|ZP_06580716.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291344221|gb|EFE71177.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 295

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 59/260 (22%), Positives = 126/260 (48%), Gaps = 40/260 (15%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA +
Sbjct: 48  FRRLAEL-EEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDIVQTGMIGLIKAID 106

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +++++ RE
Sbjct: 107 RFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELASRLDRE 166

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPI---GDEDT-SHLGDFI------ 592
           PT  E+A  + +     +EG  ++        SL+  +   G E+  + L DFI      
Sbjct: 167 PTVAELATLMNITEDQVIEG--QIAANGYNSSSLDAALTGDGPENGEAVLADFIGVEEEG 224

Query: 593 ----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
               ED +A++PL               +A L+ R+ +++ MRF      + T  E+G++
Sbjct: 225 LRLVEDFHALAPL---------------MAELSERDRQIIHMRF----VEEATQAEIGER 265

Query: 649 FCVTRERIRQIEAKAIRKLK 668
              ++  + ++  + I +L+
Sbjct: 266 LGCSQMHVSRLIKRIIARLR 285


>gi|304316881|ref|YP_003852026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778383|gb|ADL68942.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 246

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 56/206 (27%), Positives = 93/206 (45%), Gaps = 26/206 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI +G IGL+ A  K+D   G KF TYA   +K  I   +  +     IP  ++ +   
Sbjct: 51  DLISQGMIGLIDAVNKYDISKGVKFETYASIRIKGEIIDYLRKKDW---IPRSLKKRYKS 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +T  R+  + KREPT EEI     +    V K L          + +     S L + 
Sbjct: 108 IEKTIERLEQEYKREPTIEEIMDATKLSKNDVLKTL----------SYMNAGYISSLDEV 157

Query: 592 IEDKNAVS---------PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           IE+   +S         P +  +  +L++   + +  L  +E  ++ + +   +N     
Sbjct: 158 IENNLKISSITESEITNPENEVLMYDLKQNIAKAIDMLQEKERLIISLYYYEDLN----Y 213

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+ K   +T  RI QI +KAI+KLK
Sbjct: 214 KEISKIMGLTESRISQIHSKAIKKLK 239


>gi|307328849|ref|ZP_07608019.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885514|gb|EFN16530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 59/244 (24%), Positives = 116/244 (47%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S +  G  E +  +  ++EANL LV   A ++ +R     D+IQ G IGL+ A ++FD 
Sbjct: 40  LSGLTPGTPEHTRVRAALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDP 99

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  
Sbjct: 100 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTVLHGRSPTTA 159

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  E V   ++  +     SLE     ++   L   ++      P  + ++  
Sbjct: 160 EIAERLKLSEEEVLACIEAGRSYHATSLE---AAQEGDGLPGLVDRLGYEDPALAGVEH- 215

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ +++  +L+
Sbjct: 216 -RDLVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLSRSFARLR 270

Query: 669 HPSR 672
             +R
Sbjct: 271 SANR 274


>gi|225850934|ref|YP_002731168.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
 gi|225645790|gb|ACO03976.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
          Length = 241

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 61/200 (30%), Positives = 99/200 (49%), Gaps = 10/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A  K+D   G K STYA   ++  I  S+        +P ++R K   
Sbjct: 39  DLINTGVLGLIDAINKYDPSKGVKLSTYAEIRIRGQIIDSLRKLDW---VPRNVRQKARH 95

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEP-ISLETPIG-DEDTSHL 588
           +      +  K+ RE TPEEIA+ L M VE   K   KI+    IS++T +G DED +  
Sbjct: 96  IEAAILEVEQKLGREATPEEIAEYLGMDVEEYMKYAEKISNSGLISIDTTVGSDEDANTK 155

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I   N  +P     +  L++  + +++ L  RE  V+ + +      + +++E+G+ 
Sbjct: 156 LWQIISINDDTPDKYVEEEELKKIISDIISKLNERERLVITLYY----YEELSMKEIGEV 211

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +T  RI QI  K + K+K
Sbjct: 212 LGLTESRISQIHTKTMMKIK 231


>gi|254517024|ref|ZP_05129082.1| flagellar biosynthesis sigma factor FliA [gamma proteobacterium
           NOR5-3]
 gi|219674529|gb|EED30897.1| flagellar biosynthesis sigma factor FliA [gamma proteobacterium
           NOR5-3]
          Length = 243

 Score = 70.5 bits (171), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 94/201 (46%), Gaps = 21/201 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL++A E +D   G  FSTYA   +K A+   I        +P  ++ ++ +
Sbjct: 52  DLMQVGLIGLLRARESYDAAQGASFSTYAGIRIKGAMLDEIRSHDW---LPRSVQSQLRQ 108

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     R   ++ R     EIA +L MP++  ++          L   +     +H+ D 
Sbjct: 109 VSEAIDRADARLGRPANDAEIAGELDMPLDEYQQ----------LSGQLACARMTHIEDS 158

Query: 592 IEDKNAV----SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +E + AV    +PLD   +   RE     +  L  +E  ++ + +  G+N    L+E+G 
Sbjct: 159 VEAETAVLNTHTPLDEVGEEGFREALAESVTQLPEKERLMMSLYYSEGLN----LKEIGA 214

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ Q+  +A+ +L+
Sbjct: 215 VLGVSESRVSQLHGQALARLR 235


>gi|50262051|gb|AAT72766.1| putative sigma factor 32 [Dichelobacter nodosus]
          Length = 283

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 69/288 (23%), Positives = 140/288 (48%), Gaps = 22/288 (7%)

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            P G+W    + ++D  +    +I  +  +      EFR + + +++    A  A + ++
Sbjct: 1   MPHGQWLT-PSSDIDQYIAKVRQIPILDAD-----EEFR-LATELQQNHSLA--AAQTLI 51

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
             +L+ V+ +A+ +   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I 
Sbjct: 52  VHHLKFVVHIARGFLGYGLPLGDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIH 111

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV- 566
             +      ++I      +  K+    R M   +    +   + IA+ L + V+ V ++ 
Sbjct: 112 EYVIRNWRLVKIATTKAQR--KLFFNLRSMKKNMHWLSDAEAQTIAEDLNVSVKDVLEME 169

Query: 567 LKITKEPISLETPI---GDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASL 620
            +I  + I+ + P+    DE+      ++ D++   A+S      +  L+   T+ L  L
Sbjct: 170 SRIHGQDIAFD-PLDENDDEENVAPAAWLTDESVDPALSTEHHEQKHLLQHQLTQGLNQL 228

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R   ++  R+ +  +   TL+ +  ++ ++ ERIRQIE +A+ +LK
Sbjct: 229 DARSREIIESRW-LNEHEKVTLQTLASKYHISAERIRQIEQQALLQLK 275


>gi|75761264|ref|ZP_00741246.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74491246|gb|EAO54480.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 271

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 57/244 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 70  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 127 YSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 152

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQ 606
                             VLK TK+ +SL  PIG +   +    I+  K+    +   IQ
Sbjct: 153 ------------------VLKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQ 194

Query: 607 ANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++  E     +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ 
Sbjct: 195 LSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALM 254

Query: 666 KLKH 669
           K+ H
Sbjct: 255 KMFH 258


>gi|161898871|gb|ABX80425.1| SigB [Listeria monocytogenes]
          Length = 229

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 9   AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 68

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 69  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 128

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 129 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 184

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 185 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 229


>gi|229195303|ref|ZP_04322075.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
 gi|228588158|gb|EEK46204.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
          Length = 242

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 3   LIAEFQQNQCDE--AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 61  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 120

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 121 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGE 170

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   F   +N   T E +G    +++  + +I
Sbjct: 171 VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRI 226

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 227 KRQAISKLKQAA 238


>gi|218441823|ref|YP_002380152.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218174551|gb|ACK73284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 258

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 105/220 (47%), Gaps = 10/220 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  +T +    + DL+Q G +GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRREAHHWTTQCNENYEDLLQVGCLGLIRAIERFELGKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  ++RIP    D   + +   R    +  R+PT  EIA  L + ++  
Sbjct: 89  IRGEIQHYLRDKGYSVRIPRRWLDLGRQAMIIRREFQTQFNRQPTDTEIAYGLEVSLKEW 148

Query: 564 R--KVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVS-PLDSAIQANLRETTTRVLA 618
           +  K+    +EP+SL+  I   +E  + L D + D    S  L    Q  L++     L+
Sbjct: 149 QEIKLAFQNREPLSLDVSINHDEEGQTSLADLVPDPKYRSFQLSQDDQIRLQQA----LS 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            L  R  RVL   F   +      E++G        R+++
Sbjct: 205 QLEERTRRVLEFVFLQDLTQREAAEQLGISVVTVSRRVKK 244


>gi|206901181|ref|YP_002249992.1| SigD [Dictyoglomus thermophilum H-6-12]
 gi|206740284|gb|ACI19342.1| SigD [Dictyoglomus thermophilum H-6-12]
          Length = 171

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 36/88 (40%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E+   + D IED  ++   ++  Q ++R    R L +L+ RE  +L+ R+G       T
Sbjct: 78  EENIYAIQDLIEDPRSIE--ETIEQIDIRREIERALDALSEREREILKWRYGFKDGKPRT 135

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LEEVGK F +TRER+RQIE +A+RKL+H
Sbjct: 136 LEEVGKLFNITRERVRQIEERALRKLRH 163


>gi|315186365|gb|EFU20125.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Spirochaeta
           thermophila DSM 6578]
          Length = 262

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 100/207 (48%), Gaps = 12/207 (5%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++F DLI  G  GL+ A EKFD     KF TYA+  ++ AI   +        +P  +R
Sbjct: 52  SVEFDDLIGFGTFGLLDAIEKFDPEKHVKFKTYAVTRIRGAIYDELRAMDW---VPRSVR 108

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPI-SLET--PIGD 582
            K  ++     R+ + + R  T EE+A+++ M    ++K L KI+   I SL+     GD
Sbjct: 109 QKSKEIEDALHRLESSLGRAATDEELAREMNMSSRELQKTLQKISSTSILSLQELWYTGD 168

Query: 583 E-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           E D   + D +E   A  P     +  ++      +  L  +E++VL + +      D T
Sbjct: 169 ENDRVAIADMLEAPQAYDPAARVEREEIKRVVAEAIKELPEKEKKVLVLYY----YEDLT 224

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+G    VT  R+ Q+  KAI +L+
Sbjct: 225 LKEIGAILNVTESRVSQLHTKAISRLR 251


>gi|256273|gb|AAC60417.1| RpoD4 [Synechococcus]
          Length = 48

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 40/48 (83%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           LDLIQEG++GL +A EKFD  LGYKFSTYA WW++Q++TR+I + + T
Sbjct: 1   LDLIQEGSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAIDNHART 48


>gi|312110136|ref|YP_003988452.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
 gi|311215237|gb|ADP73841.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
          Length = 236

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNILIEHNLRLVAHIVKKFENTGEDVEDLISIGTIGLIKAIESYSSNKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLRS------------------------------------ 120

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK T++ +SL  PIG +   +    I+  K+  + +   IQ N+  E   + +  L 
Sbjct: 121 ---LKKTRKDVSLHEPIGQDKEGNEISLIDVLKSEGNDIIDEIQLNMELEQVKKYIDVLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ M  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 EREKEVIINRFGLDMQQEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|313115504|ref|ZP_07800969.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310622214|gb|EFQ05704.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 223

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 114/223 (51%), Gaps = 18/223 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            +E NL LV + A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA+  +   
Sbjct: 11  FIEQNLGLVHACAGRFRGRGIEYDDLYSAGCMGLVKACDNFDESRGVCFSTYAVPVILGE 70

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGVRKV 566
           I +   D S T+++   +++ +   V+ AR    K+   EPT  ++A++L  P E +   
Sbjct: 71  IKKLFRD-SGTVKVSRSLKE-LGMRVQAAREHHMKVCGTEPTLSQLAEELNEPAENITLA 128

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREE 625
           ++  +  +SL TP  +E         ED+    P++S  +A   R +   VL +L  ++ 
Sbjct: 129 IQAAQPAMSL-TPENEE---------EDRQMDIPVESPEEALAERISLEEVLHALPEQDR 178

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++R+RF      + T  E  K    T+ +I + E K + +L+
Sbjct: 179 QLIRLRF----YGNKTQSETAKVLHTTQVQISRRERKILVQLR 217


>gi|157693076|ref|YP_001487538.1| sporulation sigma factor SigK [Bacillus pumilus SAFR-032]
 gi|157681834|gb|ABV62978.1| DNA-directed RNA polymerase sigma subunit SigK carboxy-terminus
           [Bacillus pumilus SAFR-032]
          Length = 289

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 66/237 (27%), Positives = 104/237 (43%), Gaps = 59/237 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 98  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATYA--- 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 155 -----ARCIENE-----ILMHLR------------------------------------- 167

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLAS 619
              LK TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E     +  
Sbjct: 168 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEKVKEYIDI 223

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP-SRSKK 675
           L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H  SR++K
Sbjct: 224 LDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFHEFSRAEK 280


>gi|86609923|ref|YP_478685.1| RNA polymerase sigma factor SigF [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558465|gb|ABD03422.1| RNA polymerase sigma factor, group 3 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 293

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 105/207 (50%), Gaps = 9/207 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +VE NL LV   A  + N+  + + DL+Q G +GL++A E+FD   G  FS++A+ +
Sbjct: 65  RNRLVEMNLGLVRKEAHHWRNQCNEGYDDLVQVGCLGLIQAIERFDISRGLAFSSFALPY 124

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S T+RIP        +  +   R+  ++ R P+  E+ + L +  +  
Sbjct: 125 IRGEIQHYLRDKSPTMRIPRRWTTLQRQAKKVIARLRQELGRSPSEAEVREALQLTEQEW 184

Query: 564 RKVLKITKEP---ISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R+ L++ ++    +SL+ PI  +ED+  LG+ + D+   S    A +  +R      LA 
Sbjct: 185 RE-LELAQQNSLLLSLDAPIQTEEDSVALGEVVPDQRYRS-FQLAEEDRIR--LQHALAQ 240

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG 646
           L  R  ++L   F   +    T E +G
Sbjct: 241 LEERTRKILEFVFFYDLTQKETAERLG 267


>gi|239930293|ref|ZP_04687246.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 305

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 73  PGTPEHTRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 132

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R P+  EIA++
Sbjct: 133 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAFGRSPSTAEIAER 192

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  E V   ++  +     SLE     +    L D +  ++    LD       R+  
Sbjct: 193 LRITEEDVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPA--LDG---VEHRDLV 247

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 248 RHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 302


>gi|251797416|ref|YP_003012147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
 gi|247545042|gb|ACT02061.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
          Length = 256

 Score = 70.5 bits (171), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 111/234 (47%), Gaps = 20/234 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-------DLIQEGNIGLMKAAEKFDWCLGYKF 496
           AKK ++E  L LV  V    TNR    L       DL   G +GL+ A EKFD+C G +F
Sbjct: 21  AKKRLIEQFLPLVDYV----TNRMAIGLPKNVLKDDLASNGVMGLIDAIEKFDYCRGLQF 76

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA W ++ +I   +        +P  +R+K  ++    + +  K  R  +  EI++ L
Sbjct: 77  ETYASWRIRGSIIDGLRQGDW---VPRSVREKAKRIEEAYQSLEQKYLRSVSDAEISQYL 133

Query: 557 AMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  +    +L         SLE PI +E++      + D+ A +P   A +  L+++  
Sbjct: 134 NVSEKEFTTMLHEIAITTVCSLEDPIREEESETRLSLLIDERAKNPDHKAHEFFLKDSLI 193

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  LT +E  V+ + +      + +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 194 SGIEKLTEKERTVISLFY----YEELSLSEIAEVMSLSPSRISQLHSKAILRLR 243


>gi|302037625|ref|YP_003797947.1| flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
 gi|300605689|emb|CBK42022.1| Flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
          Length = 247

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 95/200 (47%), Gaps = 10/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GLM A +K+D     KF TYA + ++ A+   I        IP  + ++I  
Sbjct: 47  DLISVGIMGLMDAMDKYDPTREAKFKTYAEFRIRGAMLDEIRSMDW---IPRSVHERITL 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL---ETPIGDEDTSHL 588
           + +T   + +++ R PT +E+ K+L M  E + + L  ++  + +   +  + D D   +
Sbjct: 104 LQKTYSELLHRLGRPPTDQEVGKELKMSAEELDEFLTRSRGAVVISLDDLGVQDADGHKI 163

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              + D N   PL   +    R      +  L  +E  VL + +      + T++E+G+ 
Sbjct: 164 ISVLTDSNQPDPLSVLVNERARHVLEAAIHDLPEKERLVLSLYY----FEELTMKEIGQA 219

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             VT  R+ QI +KAI  LK
Sbjct: 220 LKVTESRVCQIHSKAILHLK 239


>gi|239933042|ref|ZP_04689995.1| RNA polymerase secondary sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291441393|ref|ZP_06580783.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344288|gb|EFE71244.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 263

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 97/213 (45%), Gaps = 9/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V+A L +   +A ++  RG    DL Q   +GL+KA + +D   G  F  YA+  +
Sbjct: 38  RDDLVQAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPVRGNAFEAYAVPTI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS-NKIKREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V   AR ++   + R PT  EIA    +    V
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRHAARELAQTTVGRAPTVPEIAAYARLTESEV 157

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R  ++  +    +SLE  +   D   LGD +   +     D+ +    R T    L +L 
Sbjct: 158 RTGMEALECFSALSLEAEMPGTDGYALGDSVGGPDPA--FDTVVD---RVTVRPFLEALP 212

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            RE  +L +RF  GM      E +G  Q  V+R
Sbjct: 213 ERERLILYLRFFRGMTQSTIAEHLGISQMHVSR 245


>gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Herminiimonas
           arsenicoxydans]
          Length = 216

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/205 (24%), Positives = 93/205 (45%), Gaps = 9/205 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A  +++   G +F TYA+  ++ A+   +        +P  MR  + K
Sbjct: 13  DLIQAGMIGLLDAVGRYEETHGAQFETYAVQRIRGAMLDELRSSDW---MPRSMRQNMRK 69

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +      +  K+ R P   E+AK+L + +   + +L      + +  E     ED  H  
Sbjct: 70  IEVAMNSLQQKLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFL 129

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D      +  PL + +    R      + +L  RE+ ++ + +   MN    L+E+G   
Sbjct: 130 DRYCTDESPDPLQNLMNTGFRSAVIAAIEALPEREKILMSLYYEQEMN----LKEIGAVM 185

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSK 674
            VT  R+ Q+ ++AI +++   R K
Sbjct: 186 GVTESRVSQLHSQAIARMRANLREK 210


>gi|146329254|ref|YP_001209773.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
 gi|146232724|gb|ABQ13702.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
          Length = 297

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 69/287 (24%), Positives = 140/287 (48%), Gaps = 22/287 (7%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P G+W    + ++D  +    +I  +  +      EFR + + +++    A  A + ++ 
Sbjct: 16  PHGQWLT-PSSDIDQYIAKVRQIPILDAD-----EEFR-LATELQQNHSLA--AAQTLIV 66

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
            +L+ V+ +A+ +   GL   DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I  
Sbjct: 67  HHLKFVVHIARGFLGYGLPLGDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHE 126

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKV-L 567
            +      ++I      +  K+    R M   +    +   + IA+ L + V+ V ++  
Sbjct: 127 YVIRNWRLVKIATTKAQR--KLFFNLRSMKKNMHWLSDAEAQTIAEDLNVSVKDVLEMES 184

Query: 568 KITKEPISLETPI---GDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLT 621
           +I  + I+ + P+    DE+      ++ D++   A+S      +  L+   T+ L  L 
Sbjct: 185 RIHGQDIAFD-PLDENDDEENVAPAAWLTDESVDPALSTEHHEQKHLLQHQLTQGLNQLD 243

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R   ++  R+ +  +   TL+ +  ++ ++ ERIRQIE +A+ +LK
Sbjct: 244 ARSREIIESRW-LNEHEKVTLQTLASKYHISAERIRQIEQQALLQLK 289


>gi|260220134|emb|CBA27368.1| RNA polymerase sigma-32 factor [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 354

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/103 (36%), Positives = 58/103 (56%), Gaps = 2/103 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W
Sbjct: 69  AAGKLVLSHLRLVVSVARQYLGYGLPHGDLIQEGNVGLMKAVKRFDPEQGVRLVSYALHW 128

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +K  I   I      +++      +  K+    R M  + K E
Sbjct: 129 IKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQRFKGE 169


>gi|29827628|ref|NP_822262.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604728|dbj|BAC68797.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 295

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/262 (24%), Positives = 128/262 (48%), Gaps = 41/262 (15%)

Query: 428 RHI---VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMK 483
           RH    +S++ +G  +    +  ++E NL LV   A ++ +RG  +  D++Q G IGL+K
Sbjct: 45  RHFFARLSVLEEGTQDYQYVRNTLIEMNLTLVRYAASRFRSRGSGEMEDIVQVGTIGLIK 104

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ +    +S + 
Sbjct: 105 AIDRFELSREVEFASFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELAQATDELSRRT 164

Query: 544 KREPTPEEIAKKLAMPVEGV---RKVLKITKEPISLETPI-GD---EDTSHLGDF----- 591
            R PT  E+A+ +++  E V   RK     +   SL+  + GD   ++ S L DF     
Sbjct: 165 GRTPTVRELAELMSLTEEEVIEARKAANAYRSS-SLDASLSGDGSADNESVLADFIGREE 223

Query: 592 -----IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IED ++++PL               +A L  R+ R+L +RF      + T  ++G
Sbjct: 224 TALELIEDMHSLAPL---------------VAQLDERDRRILHLRF----VDELTQAQIG 264

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           ++  +++  + ++  K I  L+
Sbjct: 265 ERLGISQMHVSRLINKIITTLR 286


>gi|256396292|ref|YP_003117856.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256362518|gb|ACU76015.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 263

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/215 (23%), Positives = 106/215 (49%), Gaps = 15/215 (6%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VA K+  RG    DL Q   +GL+KA + FD   G  F TYA   +   + R   D +  
Sbjct: 52  VAGKFRQRGESQADLEQVAYLGLVKAVDNFDPDYGAAFLTYATPMIAGEVRRHFRDTTWD 111

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISL 576
           + +P  +++    V    R ++ ++   P+  +IA++L +  + V +  + +      SL
Sbjct: 112 VHVPRRVQENALAVRAAERELTQQLGHAPSAAQIAERLDLSADEVAEAYEASAAHHTASL 171

Query: 577 ETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFG 633
           + P+   D D + +G+ + D+      D   +  + RE    +LA L+ R++R+L M+F 
Sbjct: 172 DVPVAMADGDGASMGELMGDE------DPGFELVVDREALKPLLAELSTRDKRILLMKFF 225

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             M+      ++G +  V++ ++ ++ ++ + +L+
Sbjct: 226 RNMSQ----AQIGAELGVSQMQVSRLLSQILGRLR 256


>gi|149909450|ref|ZP_01898105.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149807560|gb|EDM67509.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 287

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/267 (23%), Positives = 125/267 (46%), Gaps = 56/267 (20%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W
Sbjct: 49  AARQLIMSHLRFVVHVARGYAGYGLAQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           VK  I   +      +++            +  R++   +++  + + +    +  V+ V
Sbjct: 109 VKAEIHEFVLRNWRVVKVA---------TTKAQRKLFFNLRK--SKKRLGWFTSAEVKTV 157

Query: 564 RKVLKI-TKEPISLETPIGDEDTSH------------------LGDFIEDKNAVSPLDSA 604
            + L + TK+ + +E+ +   D +                      ++ED  +    D A
Sbjct: 158 AETLGVSTKDVVEMESRMSYSDQAFDLYADDDSDKDSGSTSFSPAQYLEDNAS----DVA 213

Query: 605 IQANLRE--------TTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRER 655
           +Q   RE        + T  ++ L  R + +++ R+   +  D  TL+ +  ++ V+ ER
Sbjct: 214 LQVE-RENWDKSASLSLTNAISELDERSQDIVKSRW---LAEDKATLQYLADRYGVSAER 269

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +RQ+E  A+         KKLR F+ G
Sbjct: 270 VRQLEKNAM---------KKLREFISG 287


>gi|125975381|ref|YP_001039291.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|281419342|ref|ZP_06250357.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|125715606|gb|ABN54098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Clostridium
           thermocellum ATCC 27405]
 gi|281406962|gb|EFB37225.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|316939496|gb|ADU73530.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 252

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 81/163 (49%), Gaps = 14/163 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++   + ++V   L L   +AKK+ NRG+ + D+ Q  +I L+KA E+FD   G KF 
Sbjct: 24  ETKSVEVRNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVASIALIKAVERFDPDKGVKFI 83

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           ++A   +   I R   D+   IRIP  + +   K+      ++ ++KR P  +E+A+ L 
Sbjct: 84  SFATPTIIGEIKRYFRDKGSVIRIPRRIYEVYQKINHARESLTQELKRPPRIDELARHLN 143

Query: 558 MPVEGVRKVLK--------------ITKEPISLETPIGDEDTS 586
           +  E V ++++                 + + L   IGD+D++
Sbjct: 144 ISEESVVEIIESYNAYNIQSFSQNVYANDELELHEVIGDQDST 186


>gi|153953960|ref|YP_001394725.1| sporulation sigma factor SigK [Clostridium kluyveri DSM 555]
 gi|219854574|ref|YP_002471696.1| hypothetical protein CKR_1231 [Clostridium kluyveri NBRC 12016]
 gi|146346841|gb|EDK33377.1| SigE1 [Clostridium kluyveri DSM 555]
 gi|219568298|dbj|BAH06282.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 233

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 108/243 (44%), Gaps = 54/243 (22%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R+ +  +++G+    +AK  +VE NLRLV  + KKY+  G    DLI  G +GL+KA 
Sbjct: 35  EERYYLRKLKEGDL---LAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGLIKAI 91

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD C G + +TYA   ++  I   I +    I+  V+++D I                
Sbjct: 92  DSFDSCKGTRLATYAAKCIENEILMLIRNNK-KIKNEVYLQDPI---------------- 134

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSA 604
                           GV K        ISL   +  DED+  + + +E K  V  L S 
Sbjct: 135 ----------------GVDK----EGNEISLMDVLSSDEDS--IIEIVEQKIQVKKLYSK 172

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I              L+ RE+ V+ MR+G+      T  E+ K   ++R  + +IE KA+
Sbjct: 173 IN-----------TCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKKAL 221

Query: 665 RKL 667
           +KL
Sbjct: 222 KKL 224


>gi|49480184|ref|YP_035252.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49331740|gb|AAT62386.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 258

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 19  LIAEFQQNQCDE--AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 76

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 77  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKI 136

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 137 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGE 186

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   F   +N   T E +G    +++  + +I
Sbjct: 187 VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRI 242

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 243 KRQAISKLKQAA 254


>gi|254384106|ref|ZP_04999451.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
 gi|194342996|gb|EDX23962.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
          Length = 302

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 114/241 (47%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 68  LQPGTSEHTRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 127

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 128 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNAATEDLTTLHGRTPTTPEIA 187

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  E V   ++  +     SLE     ++   L   ++      P  + ++   R+
Sbjct: 188 ERLRITEEEVLSCIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPELAGVEH--RD 242

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+      + T  ++  +  V++  + ++ A++  +L+  +
Sbjct: 243 LVRHLLVQLPEREQRILLLRY----YNNLTQSQISAELGVSQMHVSRLLARSFARLRSAN 298

Query: 672 R 672
           R
Sbjct: 299 R 299


>gi|332533108|ref|ZP_08408977.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332037390|gb|EGI73844.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 236

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 109/228 (47%), Gaps = 18/228 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 12  IVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAGIRI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +       R  VH +++  +V      + + + REPT  E+A+KL + +    
Sbjct: 72  RGAMLDEMRRGDWAPR-SVHRKNR--QVAEAITELESSLNREPTDIEVAEKLEISLNEYH 128

Query: 565 KVLK--ITKEPISLETPIGDEDT-SHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            +L    T + + +E    DED  + +G D  +DK    P ++       E+    + SL
Sbjct: 129 HILNDANTSKILGIEDLGVDEDVITPVGQDLAQDK----PFNNVKNDRFNESLLSAIKSL 184

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R+  VL + +   MN    L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 185 PERDAMVLSLYYNDEMN----LKEIGHILDVSESRVSQIHGQAMIKLK 228


>gi|229131899|ref|ZP_04260765.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
 gi|228651574|gb|EEL07543.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
          Length = 224

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 110/234 (47%), Gaps = 24/234 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D++Q G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  + +P  ++D   K+      +++ ++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGVHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIM 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR-----VL 617
                         +   S L D +E   D ++V+ ++S   ++    +T  R     + 
Sbjct: 121 DAKN----------NYQVSSLDDVVENSSDGSSVARIESVGEVEQGYEQTERRLVLKDIF 170

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             L   E+ V+   FG  +N   T    G++  +++  + +I+ +AI KLK  +
Sbjct: 171 NVLNDTEKSVIHYIFGENLNQKDT----GERLGISQMHVSRIKRQAISKLKQAA 220


>gi|254784503|ref|YP_003071931.1| RNA polymerase factor sigma-32 [Teredinibacter turnerae T7901]
 gi|237687248|gb|ACR14512.1| alternative sigma factor RpoH [Teredinibacter turnerae T7901]
          Length = 284

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 110/235 (46%), Gaps = 15/235 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +V A+LR V+ +AK Y   GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W
Sbjct: 50  AARRLVMAHLRFVVHIAKSYAGYGLAQGDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +K  I   I      +++      R     +    +R++     E     +A+ L + V+
Sbjct: 110 IKAEIHEFILRNWRIVKVATTKAQRKLFFNLRGQKKRLAWLTNDEANA--VAQDLNVDVK 167

Query: 562 GVR----KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT--- 614
            VR    ++        +      +       +++ED+    P      A+  E +    
Sbjct: 168 NVREMESRLSAYDAAFDAGADDDDETAYQAPANYLEDRR-YDPSTMLENADWTENSVAGL 226

Query: 615 -RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R +  L  R   +L+ R+    ++  TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 227 ERAMDQLDDRSRDILQQRW--LSDSKATLHELADKYGVSAERIRQLEKNAMKKMR 279


>gi|302527791|ref|ZP_07280133.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
 gi|302436686|gb|EFL08502.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
          Length = 243

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 96/211 (45%), Gaps = 33/211 (15%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A ++T RG    DL+Q   IGL+ A ++F    G  F ++A+  +   I R   D   +
Sbjct: 33  IATRFTGRGEPREDLVQVARIGLINAIDRFTPDRGPDFLSFAVPTIMGEIRRYFRDTGWS 92

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR---------KVLKI 569
           +R+P  +++    + R +  +S  + R PTP E+A+ L + +  V          + L +
Sbjct: 93  VRVPRRLKELHLSLSRGSATLSQTLGRAPTPTELAEHLGLELSEVHEGLVAGHAYQTLSV 152

Query: 570 TK------EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K      EP+ L   +G +D     + IE+  A+ PL       LRE        L  R
Sbjct: 153 DKPVHDDAEPLLLADTLGSDDPEI--EHIENHEALQPL-------LRE--------LPKR 195

Query: 624 EERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           E  +L MRF  G+      E+VG  Q  V+R
Sbjct: 196 ERAILVMRFFGGLTQTQIAEQVGISQMHVSR 226


>gi|298507081|gb|ADI85804.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           sulfurreducens KN400]
          Length = 250

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 100/201 (49%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+    IGL+ AAE+FD   G +F T+A   ++  I   +  Q    R    +RDK  K
Sbjct: 50  DLMSAAIIGLITAAERFDPTRGVQFKTFAEQRIRGTIIDELRSQDWLTR---SLRDKFKK 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + +    + +++ R PT +E+A  L M V+   ++L+       +SL+    D+D S  G
Sbjct: 107 LEKEFVLLEHQLGRNPTSDEVATALKMSVDEYYRMLEEIHLLSFVSLDESWEDDDGSPFG 166

Query: 590 --DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D + D +  +P    +   + ++ T  + SL  +E  V+ + +   +N    L+E+G 
Sbjct: 167 LLDILADTSIENPQSQLMARQMLDSLTESIESLPEKERLVITLYYYEELN----LKEIGA 222

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+ ++AI +L+
Sbjct: 223 VLELSESRISQLHSQAIVRLR 243


>gi|163856407|ref|YP_001630705.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii
           DSM 12804]
 gi|163260135|emb|CAP42436.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii]
          Length = 246

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/204 (27%), Positives = 99/204 (48%), Gaps = 11/204 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL+ AA ++      +F TYA   ++ A+   +  Q     +P  +R 
Sbjct: 30  VQLDDLIQAGMIGLLDAARRYQETPDAQFETYATARIRGAMLDELRSQDW---LPRSVRS 86

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTS 586
           K  ++    +R  +++ R P+  EIA +L +P++  + +L   +    L    IG  D  
Sbjct: 87  KGKRIEAAIQRKEHELMRPPSESEIADELELPLDEYQAMLNDARGIQILHYDDIGSNDPD 146

Query: 587 HLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             G  D   D     PLD+ +  +LR      + +L  RE+ VL + +  G+N    L+E
Sbjct: 147 ERGWRDVPADSGG-DPLDALLTGDLRRALVNAIETLPEREKLVLSLCYEQGLN----LKE 201

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    VT  R+ Q+ ++A  +++
Sbjct: 202 IGAVLEVTEARVCQLRSQATARIR 225


>gi|29827692|ref|NP_822326.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604792|dbj|BAC68861.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 295

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/222 (22%), Positives = 107/222 (48%), Gaps = 30/222 (13%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   +S + +G  +   A+  ++E N+ LV   A ++ NRG    D++Q G IGL+KA 
Sbjct: 44  QFFRRLSELEEGTHDYQYARNTLIEMNMSLVRFAAGRFRNRGDDMEDIVQVGMIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +S+++ R
Sbjct: 104 DRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELSSRLDR 163

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDT---SHLGDFI-------- 592
           EP+  E+A  + +    V   ++        SL+  +  +D    + L DFI        
Sbjct: 164 EPSVAELATLMNLSENEVVEAQIASNGYNSSSLDAALSGDDQEGEAVLADFIGEEDDGMQ 223

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             ED + ++PL               +A L+ R+ +++ MRF
Sbjct: 224 LVEDFHTLAPL---------------VAELSDRDRQIIHMRF 250


>gi|297531625|ref|YP_003672900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297254877|gb|ADI28323.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 256

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/219 (26%), Positives = 113/219 (51%), Gaps = 14/219 (6%)

Query: 455 LVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           L+ + AKK       F  DL Q G +  ++  + +D   G  F +YAM  +   +   + 
Sbjct: 39  LIAAAAKKMARSRPDFYEDLFQIGRLSFLRLLDHYDPKQGTSFESYAMKSLIGYMKNYLR 98

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITK 571
           D++  I++P  +++K  KV +    ++ K++R PT +EIA  L + VE   ++L  +   
Sbjct: 99  DKAWYIQVPRKVKEKGSKVQQAIDELTVKLERSPTLDEIAGHLGLSVEETIEILAGRDHY 158

Query: 572 EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           + +SL+ P+  G++D + +GDF+ D+   + ++S I+   R    + +  L+ +E+ V+ 
Sbjct: 159 QAVSLDAPVQDGEKDATTIGDFVADE--ANEIESLIE---RMDLEQAIGKLSEQEQIVID 213

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             F  G       E +G    V++  I +I+ +AI KLK
Sbjct: 214 AIFRRGETQRALAERLG----VSQMTISRIQKRAIAKLK 248


>gi|254383401|ref|ZP_04998753.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194342298|gb|EDX23264.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 311

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 67/269 (24%), Positives = 126/269 (46%), Gaps = 23/269 (8%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N     +V+TG    +S + FR +  +  +G  E S  +  +VE NL LV   A+++  R
Sbjct: 21  NRTDLTAVDTGEARALSATLFRRLAEL-HEGSPEYSYVRNTLVELNLSLVRYAARRFRAR 79

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
                D++Q G IGL+KA  +FD   G +F+++AM  +   I R   D S  +++P  ++
Sbjct: 80  SEPMEDIVQVGTIGLIKAINRFDPGRGVEFTSFAMPTITGEIKRFFRDTSWAVKVPRRLQ 139

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED 584
           +      +    +   + R P+  E+A +L +  E + +  K        SL+ P  +E 
Sbjct: 140 ELRIDAAKAHDALEQDLGRPPSDVELAGRLHVSPEELAEGQKAAHGYSARSLDAPSQEE- 198

Query: 585 TSHLGDFIEDKNAVS-----PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               GD      A +     P    I+    E+   +LA+L  RE  +L +RFG     +
Sbjct: 199 ----GDLASYSGAPAIGEEEPAYDRIEC--LESLKPILAALPDRERTLLSLRFG----QE 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            T  E+G +  +++  + ++ ++ + +L+
Sbjct: 249 LTQAEIGDRLGLSQMHVSRLLSRTLARLR 277


>gi|193222293|emb|CAL61487.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Herminiimonas arsenicoxydans]
          Length = 243

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/205 (24%), Positives = 93/205 (45%), Gaps = 9/205 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A  +++   G +F TYA+  ++ A+   +        +P  MR  + K
Sbjct: 40  DLIQAGMIGLLDAVGRYEETHGAQFETYAVQRIRGAMLDELRSSDW---MPRSMRQNMRK 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +      +  K+ R P   E+AK+L + +   + +L      + +  E     ED  H  
Sbjct: 97  IEVAMNSLQQKLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFL 156

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D      +  PL + +    R      + +L  RE+ ++ + +   MN    L+E+G   
Sbjct: 157 DRYCTDESPDPLQNLMNTGFRSAVIAAIEALPEREKILMSLYYEQEMN----LKEIGAVM 212

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSK 674
            VT  R+ Q+ ++AI +++   R K
Sbjct: 213 GVTESRVSQLHSQAIARMRANLREK 237


>gi|295837882|ref|ZP_06824815.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|197699594|gb|EDY46527.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 274

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 43  GSPEHGRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V   A  ++    R PT  EIA++L
Sbjct: 103 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSAAEDLTTAHGRSPTTAEIAERL 162

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 163 RIAEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 217

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+      + T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 218 HLLVQLPEREQRILLLRY----YNNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 271


>gi|133481|sp|P26768|RPSX_BACTK RecName: Full=Putative RNA polymerase sigma-G factor; AltName:
           Full=ORF3
 gi|580955|emb|CAA40027.1| unnamed protein product [Bacillus thuringiensis serovar kurstaki]
          Length = 125

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/126 (35%), Positives = 70/126 (55%), Gaps = 8/126 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE  A   ++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISA---REKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHK 531
           RD  +K
Sbjct: 119 RDIAYK 124


>gi|291454422|ref|ZP_06593812.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
 gi|291357371|gb|EFE84273.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 279

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 98/215 (45%), Gaps = 19/215 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 75  DFVSSGIFGLIDAIEKFDPERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 131

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-------ITKEPISLETPIGDED 584
           V R    +  ++ R PT  E+A ++ + VE +  V         +  E +      G  D
Sbjct: 132 VERAYASLEAELHRTPTEAEVAAEMGIAVEDLHAVFSQLSLANVVALEELLHGGGEGGGD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              + D +ED +A +P++ A    LR    R +  L  RE+ V+ + +  G+    TL E
Sbjct: 192 RLSIMDTLEDTSADNPVELAEDRELRRLLARAINLLPEREKTVVTLYYYEGL----TLAE 247

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 248 IGHVLGVTESRVSQIHTKSVLQLR-----AKLSSF 277


>gi|30266005|gb|AAN16080.1| SigB [Listeria seeligeri]
 gi|30266007|gb|AAN16081.1| SigB [Listeria seeligeri]
 gi|66968476|gb|AAY59617.1| SigB [Listeria seeligeri]
 gi|66968478|gb|AAY59618.1| SigB [Listeria seeligeri]
 gi|66968480|gb|AAY59619.1| SigB [Listeria seeligeri]
 gi|66968482|gb|AAY59620.1| SigB [Listeria seeligeri]
 gi|66968484|gb|AAY59621.1| SigB [Listeria seeligeri]
 gi|66968486|gb|AAY59622.1| SigB [Listeria seeligeri]
 gi|313634111|gb|EFS00776.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL N1-067]
 gi|313638716|gb|EFS03817.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL S4-171]
          Length = 259

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 115/229 (50%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V    +LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|323705323|ref|ZP_08116898.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535225|gb|EGB25001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 247

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 112/228 (49%), Gaps = 11/228 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++RK +     + +++++ N  L+ S+ KK++ RG +  DL Q G IG +KA  KFD   
Sbjct: 15  LIRKSKNNDKSSMEKLLKENSGLIWSIVKKFSYRGYEAEDLYQIGCIGFVKAINKFDESY 74

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K STYA+  +   I R + D    I++   +++  +K      ++  ++ REPT +EI
Sbjct: 75  NVKLSTYAVPIIIGEIKRFLRDDGL-IKVSRSLKELSNKAYFMKDKLEKELNREPTIQEI 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A KL +  E V    + T     L +    +ED + L   + +K  +   +  I+  L  
Sbjct: 134 ASKLDVSAEEVAMAFESTATAEYLYDNSQHNEDDNLL---LIEKIGIDEQEYEIEDKL-- 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               VL +L  RE +++ +R+      D T  EV K   +++ ++ +I
Sbjct: 189 ALRMVLKNLNSRERQIIVLRYF----KDMTQTEVSKILGISQVQVSRI 232


>gi|239934554|emb|CAR94591.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 210

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 46/69 (66%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLTFQ ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTFQHILNSYESVKQ 60

Query: 177 GTTLLREII 185
           G   L +II
Sbjct: 61  GQGRLVDII 69


>gi|239982580|ref|ZP_04705104.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 259

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 98/215 (45%), Gaps = 19/215 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 55  DFVSSGIFGLIDAIEKFDPERSIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-------ITKEPISLETPIGDED 584
           V R    +  ++ R PT  E+A ++ + VE +  V         +  E +      G  D
Sbjct: 112 VERAYASLEAELHRTPTEAEVAAEMGIAVEDLHAVFSQLSLANVVALEELLHGGGEGGGD 171

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              + D +ED +A +P++ A    LR    R +  L  RE+ V+ + +  G+    TL E
Sbjct: 172 RLSIMDTLEDTSADNPVELAEDRELRRLLARAINLLPEREKTVVTLYYYEGL----TLAE 227

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 228 IGHVLGVTESRVSQIHTKSVLQLR-----AKLSSF 257


>gi|51596050|ref|YP_070241.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|153949581|ref|YP_001401249.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|170024605|ref|YP_001721110.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           YPIII]
 gi|186895155|ref|YP_001872267.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|51589332|emb|CAH20954.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
 gi|152961076|gb|ABS48537.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 31758]
 gi|169751139|gb|ACA68657.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis YPIII]
 gi|186698181|gb|ACC88810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 240

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 96/198 (48%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQQVEQRVGRPATEQEVAQVLDIGLVEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLKHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|302520386|ref|ZP_07272728.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318060770|ref|ZP_07979493.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078699|ref|ZP_07986031.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025873|ref|ZP_08453937.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|302429281|gb|EFL01097.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|332745725|gb|EGJ76166.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 274

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 43  GSPEHGRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQF 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V   A  ++    R PT  EIA++L
Sbjct: 103 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSAAEDLTTAHGRSPTTAEIAERL 162

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V   ++  +     SLE     ++   L   ++      P    ++   R+   
Sbjct: 163 RIGEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALDGVEH--RDLVR 217

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+      + T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 218 HLLVQLPEREQRILLLRY----YNNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 271


>gi|225055401|gb|ACN80687.1| Tsr7 [Streptomyces laurentii]
          Length = 336

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 104 PGTPEHQHVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 163

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 164 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRSPTTAEIAER 223

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+  
Sbjct: 224 LKIGEDEVLACIEAGRSYHATSLEA---AQEGDGLPGLLDRLGYEDPALAGVEH--RDLV 278

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 279 RHLLVQLPEREQRILMLRY----YSNLTQSQISQELGVSQMHVSRLLARSFARLRSANR 333


>gi|37522237|ref|NP_925614.1| RNA polymerase sigma factor SigF [Gloeobacter violaceus PCC 7421]
 gi|35213237|dbj|BAC90609.1| glr2668 [Gloeobacter violaceus PCC 7421]
          Length = 254

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/202 (27%), Positives = 97/202 (48%), Gaps = 11/202 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYK 495
           GE  ++  + E+V  NL LV  +A +      + L DL+Q G IGLM+A E+FD  LG+ 
Sbjct: 19  GESPSTALRNELVCRNLGLVRKIAHQLARGSSEPLEDLVQVGAIGLMRAVERFDPSLGHA 78

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FS++A   ++ A+   + D   ++R+P  + +   +  R A  +S +    P+  ++A  
Sbjct: 79  FSSFATPCIRGAMQHYLRDHGHSVRLPRRLLELDSRARRAAHALSQRHGCTPSERQVASA 138

Query: 556 LAMPVEG--VRKVLKITKEPISLETPIGDE-DTSHLGDFI--EDKNAVSPLDSAIQANLR 610
           L +  E     ++ +  +  +SL+ P G   DT  L + +   D   VSP     +   R
Sbjct: 139 LDISAEEWLQMRLARANRTLVSLDAPAGPHPDTPPLVELLPGPDTPEVSP-----EGQER 193

Query: 611 ETTTRVLASLTPREERVLRMRF 632
               R LA L    + V+R  +
Sbjct: 194 AHLARALAQLEAATQVVVRQVY 215


>gi|302544115|ref|ZP_07296457.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461733|gb|EFL24826.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 284

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/244 (23%), Positives = 116/244 (47%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +S +  G  E +  +  ++EANL LV   A ++ +R     D+IQ G IGL+ A ++FD 
Sbjct: 45  LSGLTAGTPEHNRVRDALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDP 104

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  
Sbjct: 105 GRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTVLHGRSPTTA 164

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  + V   ++  +     SLE     ++   L   ++      P  + ++  
Sbjct: 165 EIAERLGLGEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLVDRLGYEDPALAGVEH- 220

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ +++  +L+
Sbjct: 221 -RDLVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLSRSFARLR 275

Query: 669 HPSR 672
             +R
Sbjct: 276 SANR 279


>gi|302549049|ref|ZP_07301391.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466667|gb|EFL29760.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 263

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 96/213 (45%), Gaps = 9/213 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VEA L +   +A ++  RG    DL Q   +GL+KA + +D   G  F  YA+  V
Sbjct: 38  RDELVEAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPARGNAFEAYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS-NKIKREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V    + +S   + R PT  EIA+   +    V
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRHAVKELSQTTLGRAPTVAEIAEYAHLTEGEV 157

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R   +  +    +SLE  +   D   LGD I   +     D+ +    R      L +L 
Sbjct: 158 RTGTEALECFSALSLEAEMPGTDGYALGDAIGGPDPA--FDTVVN---RVAVKPCLEALP 212

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            RE  +L +RF  GM      E++G  Q  V+R
Sbjct: 213 ERERIILYLRFFKGMTQSRIAEQLGISQMHVSR 245


>gi|108799863|ref|YP_640060.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119868973|ref|YP_938925.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126435506|ref|YP_001071197.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108770282|gb|ABG09004.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119695062|gb|ABL92135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126235306|gb|ABN98706.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 269

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/258 (24%), Positives = 113/258 (43%), Gaps = 38/258 (14%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR ++S++  G  +    ++ +V   L L   +A +Y  +G    DL+Q   +GLM A  
Sbjct: 30  FR-LLSVLSPGTPDHDRQRERIVTRCLPLADHIAFRYHRKGENLDDLVQIARVGLMHAVN 88

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   I R   D    + +P  ++D   ++ R   R++  + R 
Sbjct: 89  RFDPENGANFLSFAVPTMLGEIRRHFRDNGWAMHVPRRLKDLHVQITRATPRLTQSLGRP 148

Query: 547 PTPEEIAKKLAMPVEGVRKVL----------------KITKEPISLETPIGDEDTSHLGD 590
           PTP ++A +L    + V + L                       SL   +G+ D     +
Sbjct: 149 PTPTDLAAELGADRQEVVECLVAGDAYSLRSIDSPISSSDDTTRSLADTLGEVDGEM--E 206

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D+ ++ PL               LA+LT RE  V+ +RF   M      E +G    
Sbjct: 207 HITDRESLRPL---------------LAALTERERTVISLRFFASMTQTQIAERIG---- 247

Query: 651 VTRERIRQIEAKAIRKLK 668
           V++ ++ +I AK +++L+
Sbjct: 248 VSQMQVSRILAKTLQQLR 265


>gi|254390382|ref|ZP_05005599.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
 gi|197704086|gb|EDY49898.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
          Length = 326

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 114/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 94  PGSPEHTRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 153

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 154 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRIPTTAEIAER 213

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+  
Sbjct: 214 LRIGEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLV 268

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 269 RHLLVQLPEREQRILMLRY----YSNLTQSQISQELGVSQMHVSRLLARSFARLRSANR 323


>gi|290959143|ref|YP_003490325.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
 gi|260648669|emb|CBG71782.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
          Length = 287

 Score = 70.1 bits (170), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/257 (24%), Positives = 118/257 (45%), Gaps = 19/257 (7%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T +   E +H+      G  E +  +  ++EANL LV   A ++ +R     D++Q G I
Sbjct: 43  TQVLFGELKHLA----PGTPEHNRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTI 98

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A ++FD   G +F T+AM  V   I R   D   T+ +P  + +   +V      +
Sbjct: 99  GLINAIDRFDPDRGVQFPTFAMPTVIGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDL 158

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFI--EDK 595
           +    R P+  EIA++L +  E V   ++  +     SLE     +    L D +  ED 
Sbjct: 159 TTAFGRTPSTAEIAERLRITEEEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDP 218

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                LD       R+    +L  L  RE+R+L +R+     ++ T  ++  +  V++  
Sbjct: 219 E----LDG---VEHRDLVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMH 267

Query: 656 IRQIEAKAIRKLKHPSR 672
           + ++ A++  +L+  +R
Sbjct: 268 VSRLLARSFARLRSANR 284


>gi|239934568|emb|CAR94598.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 224

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 47/69 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLTF  ++   +++  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRHALSNYPLTFAFMLNQYEQVKA 60

Query: 177 GTTLLREII 185
           G   L +II
Sbjct: 61  GQGRLVDII 69


>gi|149188355|ref|ZP_01866649.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837944|gb|EDL54887.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 290

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 119/258 (46%), Gaps = 31/258 (12%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + V    C  S+   E++  +LR V  +AK +   G+  LD+IQ GN+GL+KA +K
Sbjct: 35  RTLANKVVTENCSQSL--NELILPHLRYVAYIAKNFVGYGMSTLDIIQAGNVGLIKAIKK 92

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK--IKR 545
           F+   G +  ++A+ W+K  I   I      +++      +  K+    R+  N      
Sbjct: 93  FNPARGIRLVSFAIHWIKSEINEYIIKNWSMVKVATTKEQR--KLFFNLRKHKNDSGWVS 150

Query: 546 EPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS-----------HLGDFI- 592
           E   ++IAK L + V  V  +  +++ +   LE+   DE+             H  DF  
Sbjct: 151 EEQAKDIAKNLKVRVRDVFVMDGRLSNKDKQLESHNYDEEFHCPYTEDNYFREHRDDFAD 210

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             E++N  + L S ++  +++        L  R + ++  R+    N   TL E+  +  
Sbjct: 211 NHEEENWSNHLSSELKIAIQK--------LDERSKDIIFHRW--LTNEKATLSELADKHQ 260

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++ ERIRQIE   + KLK
Sbjct: 261 LSAERIRQIEVATLAKLK 278


>gi|331269335|ref|YP_004395827.1| RNA polymerase sigma 28 subunit FliA/WhiG [Clostridium botulinum
           BKT015925]
 gi|329125885|gb|AEB75830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium botulinum
           BKT015925]
          Length = 242

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 101/208 (48%), Gaps = 12/208 (5%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           ++ ++F DL+  G IGLM A  KFD   G KFSTYA   ++ ++   I   S    I   
Sbjct: 33  SKYIEFEDLLGYGMIGLMDALNKFDESKGMKFSTYASIRIRGSMIDEIRKNSP---ISKG 89

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIG- 581
             DK+++       +  K   EP  ++IA++L M V  V ++         +SLE  I  
Sbjct: 90  AMDKLNRYNNAIETLQKKNLTEPNIKDIAQELQMTVNEVGEIENFINYISIVSLEDLIFS 149

Query: 582 -DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            D+D S +G  IED+ + +P          E   + L  L  +++ VL + +  GM    
Sbjct: 150 EDDDISLMGT-IEDEKSPNPEKDFEDQERLEYLAKALDMLNDKDKTVLSLYYYEGM---- 204

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+G    V+  R+ Q+ ++AI  L+
Sbjct: 205 TLKEIGSVLGVSESRVCQLHSRAIVHLR 232


>gi|227485765|ref|ZP_03916081.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
 gi|227236320|gb|EEI86335.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
          Length = 258

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 112/228 (49%), Gaps = 18/228 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++E +L +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY FS++A   +  
Sbjct: 32  ELIEEHLYIVDILSNKYVGKGIEKDDLYQVASLGLINAVDRYDPSKGYAFSSFATPTIMG 91

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R   D+   I++P  +++   K+    + +  +++R PT  +IA  L    E + + 
Sbjct: 92  EIKRYFRDKGWVIKVPRRIQNLYKKINVAKKVLPQELQRVPTIADIADYLGEDEETILET 151

Query: 567 LKITK--EPISLETPIG---DEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ +K   P SL+        E+   L + I  EDKN     DS    +L E +   L  
Sbjct: 152 MEASKVYTPQSLDMKYSVQKGENAIDLAEIIGEEDKN----FDSVELKDLIEKSKERLTD 207

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L   E+ +L +R+  G     T  ++ +   +++  + +IE K + K 
Sbjct: 208 L---EKEILELRYYEG----RTQVDIAESLDISQMTVSRIEKKILNKF 248


>gi|161898883|gb|ABX80431.1| SigB [Listeria monocytogenes]
          Length = 235

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 15  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 74

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 75  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 134

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 135 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 190

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 191 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 235


>gi|225376836|ref|ZP_03754057.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
 gi|225211332|gb|EEG93686.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 119/239 (49%), Gaps = 9/239 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R+ +     A+ ++V  NL LV ++ +++  RG    +L Q G IGL+KA + FD  L
Sbjct: 7   LIRQAQDGDKKARDKVVSDNLGLVHAIVRRFEKRGHDREELFQIGCIGLIKAIDHFDLSL 66

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
              FSTYA+  +   I R + D    +++   +++  +K+ R    ++ ++ R+P+  E+
Sbjct: 67  NLAFSTYAVPMITGEIRRFLRDDG-MVKVSRSLKENGYKISRAKEVLTTELGRDPSLLEL 125

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +    +  E +   L   +   S+  P+   D D   L D I D++ V   +   +A L 
Sbjct: 126 SAMTELGTEEIVMALDANRGVESIYQPVCGSDGDELLLIDQIGDQSDVYE-EPEKEAVLN 184

Query: 611 ETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   R L  +L   E++++R+R+      + T  EV     VT+ +I + E K + KL+
Sbjct: 185 KMVIRQLMDTLDETEQQIIRLRY----FENKTQCEVAGILAVTQVQISRNERKILAKLR 239


>gi|161898857|gb|ABX80418.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|89100825|ref|ZP_01173677.1| SpoIIIC [Bacillus sp. NRRL B-14911]
 gi|89084471|gb|EAR63620.1| SpoIIIC [Bacillus sp. NRRL B-14911]
          Length = 240

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/269 (25%), Positives = 118/269 (43%), Gaps = 57/269 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  I+ + + +K+ +    +S ++ R  + ++ +G+  A   +  ++E NLRLV  + KK
Sbjct: 12  VKEIVFLVSYVKNNAFPQPLSAADERKYLRLMAEGDAHA---RNMLIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G    DLI  G IGL+KA E +    G K +TYA         R I ++     I 
Sbjct: 69  FENTGEDSEDLISIGTIGLIKAIESYSEGKGTKLATYA--------ARCIENE-----IL 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+R                                        LK TK+ +SL  PIG 
Sbjct: 116 MHLR---------------------------------------ALKKTKKDVSLHDPIGQ 136

Query: 583 EDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +   +    I+  K+    + + IQ N+  E     +  L  RE+ V+  RFG+ +  + 
Sbjct: 137 DKEGNEISLIDVLKSESEDVINTIQLNMELEKVKEYIDVLDDREKEVIIGRFGLDLKKEK 196

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|169834796|ref|YP_001715634.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169408903|gb|ACA57313.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 296

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 106/224 (47%), Gaps = 29/224 (12%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E N  L+  VA KY N+ ++  DL Q+G +G +KA +KFD     KFSTYA +W++  
Sbjct: 90  LIEKNQNLIFKVANKYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIEAE 149

Query: 508 ITRSI---ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           I+       D S +I      R                 K +     I  +  +P E V+
Sbjct: 150 ISSFFNFNVDGSLSISSSYQHR-----------------KLKGYENGILSEDELP-ELVK 191

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             +++    IS+++ +  ++  +  D++  K  ++   + I++ +       L+ L+ +E
Sbjct: 192 NHIQLKNNSISVDSIVHGKENENSADYLLGKTDINY--NNIESKI--VMKNALSGLSEKE 247

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++  R    +  +   +++ K+F V+ + I+ +   AI KLK
Sbjct: 248 KSIIISR----IIYEKKYKDIAKEFKVSYQYIQYLYKNAIGKLK 287


>gi|166368033|ref|YP_001660306.1| RNA polymerase sigma factor SigF [Microcystis aeruginosa NIES-843]
 gi|166090406|dbj|BAG05114.1| group 3 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 258

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 108/222 (48%), Gaps = 14/222 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E NL LV   A  + N+  + + DL+Q G++GL++A E+FD   G+ FS++A+ +
Sbjct: 29  RDQIMELNLGLVRREAHHWVNQCHENYEDLVQVGSMGLIRAIERFDSSKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S T+RIP    D   +     R       R+P   EI++ L +  E  
Sbjct: 89  IRGEIQHHLRDKSYTVRIPRRWLDLGRQATNVRRDFQTIHNRQPNDTEISRALNISSEEW 148

Query: 564 R--KVLKITKEPISLETPI-GDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRV--- 616
           +  K+    +EP+SL+  +  DED +  L D + D     P   + Q   +E   R+   
Sbjct: 149 QEVKLAFQNREPLSLDVTVNNDEDNNTCLKDLVPD-----PRYRSFQL-CQEDRIRLQQA 202

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           LA L  +   ++   F   +    T E++G        R+++
Sbjct: 203 LAQLEEKTRHIIEFVFLKDLTQRETAEQLGISVVTVSRRVKK 244


>gi|255022641|ref|ZP_05294627.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-208]
 gi|22770504|gb|AAN06627.1|AF497199_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|307327205|ref|ZP_07606393.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306887096|gb|EFN18094.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 272

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 112/234 (47%), Gaps = 12/234 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +EF  +  +    E EA   ++ +VEA + +   +A++Y NRG    DL Q   +GL+KA
Sbjct: 28  AEFAEMARLPDGPEKEA--LRRRVVEAWMPMAERLARQYRNRGESLEDLEQVAALGLVKA 85

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI- 543
            +++D   G  F+ +A+  +   I R   D    + +P  ++D  ++V    R +S+   
Sbjct: 86  VKRYDPEHGTAFAGFAVPTIVGEIKRHFRDHLWVLHVPRRVQDLRNRVRAAHRELSHSAD 145

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPI-GDEDTSHLGDFIEDKNAVSP 600
            R P  ++IA++  +  + VR  ++      P+SL+  + G +D   L D +  + A   
Sbjct: 146 DRPPRTQDIAERTGLTEKEVRAGMEAMGSFTPLSLDAQLTGSDDGYSLADTLGAQEAA-- 203

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            D  +    RE     L+ L  RE ++L MRF   M      E++G  Q  V+R
Sbjct: 204 YDRVVD---REAVRPGLSRLPERERQILYMRFFCDMTQSRIAEQLGISQMHVSR 254


>gi|161898889|gb|ABX80434.1| SigB [Listeria monocytogenes]
 gi|161898893|gb|ABX80436.1| SigB [Listeria monocytogenes]
 gi|161898909|gb|ABX80444.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 69.7 bits (169), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|188533568|ref|YP_001907365.1| flagellar biosynthesis sigma factor [Erwinia tasmaniensis Et1/99]
 gi|188028610|emb|CAO96472.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           tasmaniensis Et1/99]
          Length = 240

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 95/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     R+   + R  + +E+A +L + +E  R++L  T           DE     GD 
Sbjct: 100 VAGAMHRVEQALGRSASEQEVAAQLDVSLEEYRQILLDTNNSQLFSF---DEYREEHGDS 156

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E     +PL   ++ +LR+     + +L  RE+ VL + +   +N    L+E+G 
Sbjct: 157 AELVTEGHEQENPLHQLLEGDLRDRVIEAIEALPDREKMVLTLYYQEELN----LKEIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++A+++L+
Sbjct: 213 VLEVGESRVSQLHSQAVKRLR 233


>gi|161898895|gb|ABX80437.1| SigB [Listeria monocytogenes]
 gi|161898903|gb|ABX80441.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKINNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 237


>gi|239827809|ref|YP_002950433.1| sporulation sigma factor SigK [Geobacillus sp. WCH70]
 gi|239808102|gb|ACS25167.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. WCH70]
          Length = 236

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNILIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSPGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLRS------------------------------------ 120

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK T++ +SL  PIG +   +    I+  K+  + +   IQ N+  E   + +  L 
Sbjct: 121 ---LKKTRKDVSLHEPIGQDKEGNEISLIDVLKSEGNDIIDEIQLNMELEQVKKYIDVLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ M  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 EREKEVIISRFGLDMQQEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|302559792|ref|ZP_07312134.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477410|gb|EFL40503.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 298

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 66  PGTPEHARVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQ 125

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R P+  EIA++
Sbjct: 126 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPSTAEIAER 185

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  + V   ++  +     SLE     +    L D +  ++    LD       R+  
Sbjct: 186 LRISEDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPA--LDG---VEHRDLV 240

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 241 RHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFQRLRSANR 295


>gi|161898847|gb|ABX80413.1| SigB [Listeria monocytogenes]
          Length = 233

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 13  AQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 73  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 132

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 133 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 188

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 189 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 233


>gi|46907127|ref|YP_013516.1| RNA polymerase sigma factor SigB [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092103|ref|ZP_00229896.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|217965008|ref|YP_002350686.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|226223514|ref|YP_002757621.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           Clip81459]
 gi|254823836|ref|ZP_05228837.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|254852389|ref|ZP_05241737.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|254931278|ref|ZP_05264637.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|254994246|ref|ZP_05276436.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-064]
 gi|255521165|ref|ZP_05388402.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-175]
 gi|290892914|ref|ZP_06555904.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|300764104|ref|ZP_07074099.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|22770514|gb|AAN06632.1|AF497204_1 sigma factor B [Listeria monocytogenes]
 gi|22770518|gb|AAN06634.1|AF497206_1 sigma factor B [Listeria monocytogenes]
 gi|22770520|gb|AAN06635.1|AF497207_1 sigma factor B [Listeria monocytogenes]
 gi|22770522|gb|AAN06636.1|AF497208_1 sigma factor B [Listeria monocytogenes]
 gi|22770524|gb|AAN06637.1|AF497209_1 sigma factor B [Listeria monocytogenes]
 gi|22770526|gb|AAN06638.1|AF497210_1 sigma factor B [Listeria monocytogenes]
 gi|22770528|gb|AAN06639.1|AF497211_1 sigma factor B [Listeria monocytogenes]
 gi|22770530|gb|AAN06640.1|AF497212_1 sigma factor B [Listeria monocytogenes]
 gi|3298584|gb|AAC38789.1| sigma B [Listeria monocytogenes]
 gi|3298589|gb|AAC38792.1| Sigma B [Listeria monocytogenes]
 gi|26000673|gb|AAN75465.1| SigB [Listeria monocytogenes]
 gi|46880394|gb|AAT03693.1| RNA polymerase sigma-B factor [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47019543|gb|EAL10283.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|112960117|gb|ABI27557.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960121|gb|ABI27560.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960125|gb|ABI27563.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960129|gb|ABI27566.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960133|gb|ABI27569.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960137|gb|ABI27572.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960141|gb|ABI27575.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960145|gb|ABI27578.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960149|gb|ABI27581.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960153|gb|ABI27584.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960157|gb|ABI27587.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960161|gb|ABI27590.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960165|gb|ABI27593.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960169|gb|ABI27596.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960173|gb|ABI27599.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960177|gb|ABI27602.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960181|gb|ABI27605.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960185|gb|ABI27608.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960189|gb|ABI27611.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960193|gb|ABI27614.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960197|gb|ABI27617.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960201|gb|ABI27620.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960205|gb|ABI27623.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960209|gb|ABI27626.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960213|gb|ABI27629.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960217|gb|ABI27632.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960221|gb|ABI27635.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960225|gb|ABI27638.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960229|gb|ABI27641.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960233|gb|ABI27644.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960237|gb|ABI27647.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960241|gb|ABI27650.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960245|gb|ABI27653.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960249|gb|ABI27656.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960253|gb|ABI27659.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960257|gb|ABI27662.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960261|gb|ABI27665.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960265|gb|ABI27668.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960269|gb|ABI27671.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960273|gb|ABI27674.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960277|gb|ABI27677.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960281|gb|ABI27680.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960285|gb|ABI27683.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960289|gb|ABI27686.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960293|gb|ABI27689.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960297|gb|ABI27692.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960301|gb|ABI27695.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960305|gb|ABI27698.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960309|gb|ABI27701.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960313|gb|ABI27704.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960317|gb|ABI27707.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960321|gb|ABI27710.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960325|gb|ABI27713.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960329|gb|ABI27716.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960333|gb|ABI27719.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960337|gb|ABI27722.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960341|gb|ABI27725.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960345|gb|ABI27728.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960349|gb|ABI27731.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960353|gb|ABI27734.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960357|gb|ABI27737.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960361|gb|ABI27740.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962434|gb|ABI28932.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962439|gb|ABI28936.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962444|gb|ABI28940.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962449|gb|ABI28944.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962454|gb|ABI28948.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962459|gb|ABI28952.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962464|gb|ABI28956.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962469|gb|ABI28960.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962474|gb|ABI28964.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962479|gb|ABI28968.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962484|gb|ABI28972.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962489|gb|ABI28976.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962494|gb|ABI28980.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962499|gb|ABI28984.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962504|gb|ABI28988.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962509|gb|ABI28992.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962514|gb|ABI28996.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962519|gb|ABI29000.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962524|gb|ABI29004.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962529|gb|ABI29008.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962534|gb|ABI29012.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962539|gb|ABI29016.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962544|gb|ABI29020.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962549|gb|ABI29024.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962554|gb|ABI29028.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962559|gb|ABI29032.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962564|gb|ABI29036.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962569|gb|ABI29040.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962574|gb|ABI29044.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962579|gb|ABI29048.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962584|gb|ABI29052.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962589|gb|ABI29056.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962594|gb|ABI29060.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962599|gb|ABI29064.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962604|gb|ABI29068.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962609|gb|ABI29072.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962614|gb|ABI29076.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962619|gb|ABI29080.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962624|gb|ABI29084.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962629|gb|ABI29088.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962634|gb|ABI29092.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962644|gb|ABI29100.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962649|gb|ABI29104.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962654|gb|ABI29108.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962659|gb|ABI29112.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962664|gb|ABI29116.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962669|gb|ABI29120.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962674|gb|ABI29124.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962679|gb|ABI29128.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962684|gb|ABI29132.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962689|gb|ABI29136.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962694|gb|ABI29140.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962699|gb|ABI29144.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962704|gb|ABI29148.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962709|gb|ABI29152.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962714|gb|ABI29156.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962719|gb|ABI29160.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962724|gb|ABI29164.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962729|gb|ABI29168.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962734|gb|ABI29172.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962739|gb|ABI29176.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962744|gb|ABI29180.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|118084623|gb|ABI16055.2| sigma B [Listeria monocytogenes]
 gi|118084625|gb|ABI16057.2| sigma B [Listeria monocytogenes]
 gi|153582301|emb|CAO79792.1| sigma factor B [Listeria monocytogenes]
 gi|153582307|emb|CAO79795.1| sigma factor B [Listeria monocytogenes]
 gi|217334278|gb|ACK40072.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|225875976|emb|CAS04680.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258605695|gb|EEW18303.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|290557490|gb|EFD91014.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|293582827|gb|EFF94859.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|293593059|gb|EFG00820.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|300515094|gb|EFK42146.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|302034435|gb|ADK92371.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034437|gb|ADK92372.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|307570432|emb|CAR83611.1| RNA polymerase sigma-B factor [Listeria monocytogenes L99]
 gi|313609777|gb|EFR85233.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL F2-208]
 gi|328467051|gb|EGF38146.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 1816]
 gi|328475458|gb|EGF46224.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 220]
 gi|332311302|gb|EGJ24397.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. Scott A]
          Length = 259

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|239637364|ref|ZP_04678346.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
 gi|239596964|gb|EEQ79479.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
          Length = 256

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/242 (23%), Positives = 122/242 (50%), Gaps = 18/242 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  EDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA +L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAARLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VTDEEVLEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R+L  L+ RE+ +++  F  G++   T E +G    +++  + +++  AI+KL+  
Sbjct: 198 MILERILPILSDREKEIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQEA 253

Query: 671 SR 672
           ++
Sbjct: 254 AK 255


>gi|311105912|ref|YP_003978765.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans A8]
 gi|310760601|gb|ADP16050.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans A8]
          Length = 259

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 95/204 (46%), Gaps = 14/204 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A  ++      +F TYA   ++ A+   +  Q     +P  +R K  K
Sbjct: 42  DLIQAGMIGLLDAVRRYQETADAQFETYATTRIRGAMLDELRGQDW---LPRSVRAKARK 98

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-------ITKEPISLETPIGDED 584
           + +  +++  ++ R P+  EIA++L MP+   + +L        +  E  + E       
Sbjct: 99  IEQAIQQLEQRLMRAPSEAEIAQQLDMPLGDYQSLLHDAQGVQIVHYEDFATEPDSASGQ 158

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           +             +PLDS +  + R+     + SL  RE+ +L + +  G+N    L+E
Sbjct: 159 SDWAATLNHGAAGGNPLDSLLAGDFRQALVHAIDSLPEREKLLLSLCYEQGLN----LKE 214

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    VT  R+ Q+ ++A  +++
Sbjct: 215 IGAILNVTEARVCQLRSQATARIR 238


>gi|289578665|ref|YP_003477292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528378|gb|ADD02730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 241

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 116/247 (46%), Gaps = 53/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  ++VS + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEETYLVSKMEKGDNEA---KTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++     I +++R             ++
Sbjct: 98  IKAINTFNPKKKIKLATYA--------SRCIENE-----ILMYLRR------------NS 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + EE    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 133 KTKLEVSFEE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   RE  T  L  L  RE++++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 176 --------RELLTSALKKLPDREKKIIGLRFGLDGGVEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLK 668
           K +++LK
Sbjct: 228 KILKRLK 234


>gi|161898845|gb|ABX80412.1| SigB [Listeria monocytogenes]
 gi|161898851|gb|ABX80415.1| SigB [Listeria monocytogenes]
 gi|161898853|gb|ABX80416.1| SigB [Listeria monocytogenes]
 gi|161898861|gb|ABX80420.1| SigB [Listeria monocytogenes]
 gi|161898863|gb|ABX80421.1| SigB [Listeria monocytogenes]
 gi|161898867|gb|ABX80423.1| SigB [Listeria monocytogenes]
 gi|161898869|gb|ABX80424.1| SigB [Listeria monocytogenes]
 gi|161898873|gb|ABX80426.1| SigB [Listeria monocytogenes]
 gi|161898875|gb|ABX80427.1| SigB [Listeria monocytogenes]
 gi|161898877|gb|ABX80428.1| SigB [Listeria monocytogenes]
 gi|161898879|gb|ABX80429.1| SigB [Listeria monocytogenes]
 gi|161898887|gb|ABX80433.1| SigB [Listeria monocytogenes]
 gi|161898891|gb|ABX80435.1| SigB [Listeria monocytogenes]
 gi|161898901|gb|ABX80440.1| SigB [Listeria monocytogenes]
 gi|161898911|gb|ABX80445.1| SigB [Listeria monocytogenes]
 gi|161898919|gb|ABX80449.1| SigB [Listeria monocytogenes]
 gi|161898925|gb|ABX80452.1| SigB [Listeria monocytogenes]
 gi|161898927|gb|ABX80453.1| SigB [Listeria monocytogenes]
 gi|161898929|gb|ABX80454.1| SigB [Listeria monocytogenes]
 gi|161898935|gb|ABX80457.1| SigB [Listeria monocytogenes]
 gi|161898941|gb|ABX80460.1| SigB [Listeria monocytogenes]
 gi|161898943|gb|ABX80461.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 237


>gi|119491111|ref|ZP_01623269.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
 gi|119453656|gb|EAW34816.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
          Length = 304

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 108/229 (47%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ N+ LV      +  +  + + DL Q G IGL++A E+FD   G  FS++A+ +
Sbjct: 72  RNQIVQLNMGLVRQEVHHWVKKCPESYDDLFQIGCIGLIQAIERFDLTKGCAFSSFAVPY 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S  IR+P        +  +    +  K+ R+PT  EIA  L + +E  
Sbjct: 132 IRGEILHYLRDKSLLIRVPRRCSQLKQEAAKLVILLQEKLHRKPTDLEIANSLGISIEKW 191

Query: 564 RKVLKITKEP--ISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +V    K    +SL+ P+ DE  +   LG+ I D N  + +    + +L       L  
Sbjct: 192 NQVKLTVKNSSVLSLDIPLNDEFNEKHCLGELIVDSNPNASMSQEEKIDLE----MALLK 247

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L      +L + F   +    T +EV KQ  ++   + +   +++R LK
Sbjct: 248 LKAENRDILELVFFKNL----TYKEVAKQMNISVMTVSRRLKQSLRDLK 292


>gi|71906382|ref|YP_283969.1| sigma-70 region 4 [Dechloromonas aromatica RCB]
 gi|71846003|gb|AAZ45499.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Dechloromonas
           aromatica RCB]
          Length = 248

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 109/229 (47%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++++V+  + LV  +A     R    +QF DL+Q G IGL+ A ++F    G +F TYA 
Sbjct: 10  REQLVQRFVPLVKRIAYHLMARLPPSVQFDDLVQNGMIGLLDAIDRFQEGFGAQFETYAT 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + +      +P ++R ++ ++     ++ ++  R P+ +E+A+ L M + 
Sbjct: 70  QRIRGAMLDGLRENDW---LPRNLRRELRRIETAINQLEHEHGRVPSEKELAEALGMSLA 126

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +K L+  +  + +  +   G+ D   L     D NA  P       +++ T    +  
Sbjct: 127 DYQKTLQDARGHQLVYFDDLAGEGDEGFLERHFTD-NAADPAAILEDKSVKATLITAIGE 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE    +M   +    D  L E+G+   VT  R+ Q+  +AI +L+
Sbjct: 186 LPERE----KMMMALYYEQDLNLREIGEVMGVTESRVCQLHTQAIARLR 230


>gi|330684827|gb|EGG96520.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU121]
          Length = 256

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/242 (23%), Positives = 122/242 (50%), Gaps = 18/242 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E + S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  EDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA +L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAARLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LR 610
           +  E V + +++ +   +L          H  +  +D + V+ LD   Q +        R
Sbjct: 145 VTDEEVLEAIEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               R+L  L+ RE+ +++  F  G++   T E +G    +++  + +++  AI+KL+  
Sbjct: 198 MILERILPILSDREKEIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQEA 253

Query: 671 SR 672
           ++
Sbjct: 254 AK 255


>gi|255030138|ref|ZP_05302089.1| RNA polymerase sigma factor SigB [Listeria monocytogenes LO28]
          Length = 245

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|161898931|gb|ABX80455.1| SigB [Listeria monocytogenes]
 gi|161898937|gb|ABX80458.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 237


>gi|28211312|ref|NP_782256.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
 gi|28203752|gb|AAO36193.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
          Length = 242

 Score = 69.7 bits (169), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 121/246 (49%), Gaps = 18/246 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           EC+    K+ +V+  + LV  +A +      + + + DL+  G +GLM A +KFD   G 
Sbjct: 6   ECDV---KEGLVKKYIPLVKYIASRVIIGKTKYIDYDDLVGYGMLGLMDAMQKFDPSKGM 62

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA   ++ ++   +   S    I     DK+++      ++  K  +EP  EE+AK
Sbjct: 63  KFSTYASIRIRGSMIDELRRISP---ISKSAMDKLNRYNEAVEKLQMKNFKEPKLEEVAK 119

Query: 555 KLAMPVEGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L M ++ V ++         +SLE  I  DE+   L   + DKN+ SP     +  L E
Sbjct: 120 ELDMSLKEVAQIENYINYISIVSLEDFIFSDEEDMSLMATVVDKNSPSPEKILEEKELIE 179

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + +  L  R+  VL + +   +    TL+E+GK   V+  R+ Q+ ++AI  L+  S
Sbjct: 180 YLEKAINKLKERDRIVLSLYYYERL----TLKEIGKVLDVSESRVCQLHSRAIVHLR--S 233

Query: 672 RSKKLR 677
             KKL+
Sbjct: 234 ELKKLK 239


>gi|167757711|ref|ZP_02429838.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
 gi|167664593|gb|EDS08723.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
          Length = 208

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 110/252 (43%), Gaps = 62/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E R+ +    +G+ EA   K  ++E NLRLV  + KKY +      DL+  G IGL
Sbjct: 11  LTAAEERYYMQKYTEGDLEA---KHILIERNLRLVAHIVKKYQSFEEDTEDLLSIGTIGL 67

Query: 482 MKAAEKF--DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           +KA   F  D C+  +  TYA         R I ++     I +H+R K           
Sbjct: 68  IKAVVTFNPDKCV--RLGTYA--------ARCIENE-----ILMHLRAK----------- 101

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKN 596
                                       K +   ISL  PIG +   +   L D IE + 
Sbjct: 102 ----------------------------KKSSREISLYEPIGTDREGNEIQLFDIIETEE 133

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             +     ++ ++R    RV + L+PRE  VL+MR+G+    ++T  E+ KQ  ++R  +
Sbjct: 134 DDAHKKVELRDDIRMLYYRVESELSPRERLVLKMRYGLYNEEEYTQREIAKQLGISRSYV 193

Query: 657 RQIEAKAIRKLK 668
            +IE  AI KL+
Sbjct: 194 SRIEKSAIEKLR 205


>gi|257438786|ref|ZP_05614541.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
 gi|257198754|gb|EEU97038.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
          Length = 188

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 103/226 (45%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++  NLRLV+ +AKKY N G+   D+I  G IGL+KA   F      K +TYA   
Sbjct: 8   ARDDLITHNLRLVVYLAKKYENSGVPQEDMISIGTIGLIKAVNTFTPARNIKLATYA--- 64

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   R+ SN+ ++E + +             
Sbjct: 65  -----SRCIGNE----------------ILMYLRKSSNR-RQEASID------------- 89

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                   EP++ +   GD +   L D +  D+N V       QA  R T  R +  L P
Sbjct: 90  --------EPLNTD---GDGNELLLSDVLGSDENLVGL--QLEQAAERATLRRSVEQLAP 136

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +++ +RFG+    +HT +E      +++  I ++E + IR+LK
Sbjct: 137 RERQIMELRFGLVDGVEHTQKEAADALGISQSYISRLEKRIIRQLK 182


>gi|302549129|ref|ZP_07301471.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466747|gb|EFL29840.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 295

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/264 (22%), Positives = 124/264 (46%), Gaps = 43/264 (16%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA 
Sbjct: 46  QFFQRLTELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMEDIVQTGMIGLIKAI 105

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +    +++++ R
Sbjct: 106 DRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVDLAKAREELASRLDR 165

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLET------PIGDEDTSHLGDFI--- 592
           EPT  E+A  + +     VEG  ++        SL+       P G E    L DFI   
Sbjct: 166 EPTVAELATLMNISENQVVEG--QIAANGYNSSSLDAALTGDGPEGGEAV--LADFIGVE 221

Query: 593 -------EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                  ED ++++PL               +A L+ R+ +++ MRF      + T  E+
Sbjct: 222 EDGLRLVEDFHSLAPL---------------MAELSERDRQIIHMRF----VEEATQAEI 262

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
           G++   ++  + ++  + I +L+ 
Sbjct: 263 GERLGCSQMHVSRLIKRIITRLRQ 286


>gi|161898881|gb|ABX80430.1| SigB [Listeria monocytogenes]
 gi|161898907|gb|ABX80443.1| SigB [Listeria monocytogenes]
          Length = 233

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 13  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 73  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 132

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 133 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 188

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 189 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 233


>gi|238800552|gb|ACR56097.1| RNA polymerase sigma factor SigB [Listeria innocua]
          Length = 248

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 19  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 78

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 79  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 138

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 139 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 194

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 195 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 239


>gi|293604981|ref|ZP_06687378.1| DNA-directed RNA polymerase sigma subunit FliA [Achromobacter
           piechaudii ATCC 43553]
 gi|292816809|gb|EFF75893.1| DNA-directed RNA polymerase sigma subunit FliA [Achromobacter
           piechaudii ATCC 43553]
          Length = 251

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 101/210 (48%), Gaps = 26/210 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A  ++      +F TYA   ++ A+   +  Q     +P  +R K  K
Sbjct: 34  DLIQAGMIGLLDAVRRYQETADAQFETYATTRIRGAMLDELRGQDW---LPRSVRTKARK 90

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPV----------EGVRKVLK--ITKEPISLETP 579
           + +  +++  ++ R PT  EIA +L MP+          +GV+ V     T EP   ++ 
Sbjct: 91  IEQAIQQLEQRLMRAPTEAEIAAQLEMPIGEYQSLLHDAQGVQIVHYEDFTTEP---DSA 147

Query: 580 IGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            G  D T+ L       N   PLD+ +  + R+     + +L  RE+ +L + +  G+N 
Sbjct: 148 SGQSDWTATLNHGSAGGN---PLDALLAGDFRQALVHAIDALPDREKLLLSLCYEQGLN- 203

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L+E+G    VT  R+ Q+ ++A  +++
Sbjct: 204 ---LKEIGAIMNVTEARVCQLRSQATARIR 230


>gi|293395614|ref|ZP_06639897.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
 gi|291421933|gb|EFE95179.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
          Length = 240

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 95/198 (47%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R     
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRHARD 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V +  +R+  ++ R     E+A+ + M +   R++L  T            E+     + 
Sbjct: 100 VAQAMQRLEQQLGRPAGELEVAQAMNMSLADYRQILMDTNNSQLFSYDEWREEQGESAEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ +LR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHAEANPLHQLLEGSLRQRVIDAIEALPEREKLVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|225418674|ref|ZP_03761863.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
 gi|225041795|gb|EEG52041.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
          Length = 216

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 99/229 (43%), Gaps = 55/229 (24%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+  ++E N+RLV  V KKY +      DL+  G IGL+KA   F    G + +TYA  
Sbjct: 32  LARDVLIERNMRLVAHVVKKYQSPDYDIEDLLSVGTIGLIKAVNTFKVDKGSRLATYAAK 91

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+                     ++I  + R ++++S ++                   
Sbjct: 92  CVE---------------------NEILMLFRASKKLSKEV------------------- 111

Query: 563 VRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                       SL  PIG   D +   L D IE +N  +     ++ +++E      + 
Sbjct: 112 ------------SLFEPIGVDKDGEAVSLVDIIEMENKETIDTMILKQDVKELYEAFDSC 159

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+  E+ V+RMR+G+    +HT  E+  Q  ++R  + +IE KA+ KLK
Sbjct: 160 LSDTEKTVIRMRYGLFRGKEHTQREIAAQLGISRSYVSRIEKKALEKLK 208


>gi|315302306|ref|ZP_07873197.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
 gi|313629329|gb|EFR97571.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|294813860|ref|ZP_06772503.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326442278|ref|ZP_08217012.1| RNA polymerase sigma factor, sigma F [Streptomyces clavuligerus
           ATCC 27064]
 gi|294326459|gb|EFG08102.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 335

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 114/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 103 PGSPEHTRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 162

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 163 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRIPTTAEIAER 222

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+  
Sbjct: 223 LRIGEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLV 277

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 278 RHLLVQLPEREQRILMLRY----YSNLTQSQISQELGVSQMHVSRLLARSFARLRSANR 332


>gi|313619763|gb|EFR91370.1| RNA polymerase sigma-B factor [Listeria innocua FSL S4-378]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|296333262|ref|ZP_06875715.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|296149460|gb|EFG90356.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
          Length = 241

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/252 (26%), Positives = 110/252 (43%), Gaps = 61/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE +  + ++ KG+  A   +  ++E NLRLV  + KK+ N G    DLI  G IGL
Sbjct: 31  LSSSEEKKYLELMAKGDEHA---RNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K  E +    G K +TYA         R I ++     I +H+R               
Sbjct: 88  IKGIESYSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------- 119

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                    LK TK+ +SL  PIG +   +   L D ++ +N  
Sbjct: 120 ------------------------ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN-- 153

Query: 599 SPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +   IQ N+  E   + +  L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + 
Sbjct: 154 EDVIDTIQLNMELEKVKQYIDILDDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVS 213

Query: 658 QIEAKAIRKLKH 669
           +IE +A+ K+ H
Sbjct: 214 RIEKRALMKMFH 225


>gi|327441027|dbj|BAK17392.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/199 (26%), Positives = 92/199 (46%), Gaps = 9/199 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL  A  KFD     KF TYA + V+ AI   +  +     +P   R+K  K
Sbjct: 55  DLMSLGMMGLFDALNKFDINRDLKFDTYASFRVRGAILDGLRKEDW---LPRSAREKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +      +  K+ R  T EE+A  + +PVE V +  +       +S+   +  E++    
Sbjct: 112 LESQIESLEQKLMRHATAEEVAAHMNLPVEEVYQTFQEHFFSNVLSINEQLDQEESEGKS 171

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D N  +P   ++   L       +  L  +E+ V+ + +    + + TL E+G+  
Sbjct: 172 FVIRDDNTKTPEQHSVHVELLGDLAENIKKLNEKEQLVISLFY----SEELTLTEIGEIL 227

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++  RI QI +KA+ KL+
Sbjct: 228 DLSTSRISQIHSKALFKLR 246


>gi|16802936|ref|NP_464421.1| RNA polymerase sigma factor SigB [Listeria monocytogenes EGD-e]
 gi|47094902|ref|ZP_00232516.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499433|ref|ZP_03667782.1| RNA polymerase sigma factor SigB [Listeria monocytogenes Finland
           1988]
 gi|224503136|ref|ZP_03671443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           R2-561]
 gi|254827839|ref|ZP_05232526.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|254832139|ref|ZP_05236794.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 10403S]
 gi|254898932|ref|ZP_05258856.1| RNA polymerase sigma factor SigB [Listeria monocytogenes J0161]
 gi|254911580|ref|ZP_05261592.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|254935906|ref|ZP_05267603.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284801225|ref|YP_003413090.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284994367|ref|YP_003416135.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289434163|ref|YP_003464035.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|315281577|ref|ZP_07870178.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
 gi|22770508|gb|AAN06629.1|AF497201_1 sigma factor B [Listeria monocytogenes]
 gi|22770512|gb|AAN06631.1|AF497203_1 sigma factor B [Listeria monocytogenes]
 gi|22770532|gb|AAN06641.1|AF497213_1 sigma factor B [Listeria monocytogenes]
 gi|3298587|gb|AAC38791.1| Sigma B [Listeria monocytogenes]
 gi|16410298|emb|CAC98973.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           EGD-e]
 gi|47016784|gb|EAL07703.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|66968488|gb|AAY59623.1| SigB [Listeria seeligeri]
 gi|112363462|gb|ABI16056.1| sigma B [Listeria monocytogenes]
 gi|153582303|emb|CAO79793.1| sigma factor B [Listeria monocytogenes]
 gi|153582305|emb|CAO79794.1| sigma factor B [Listeria monocytogenes]
 gi|223700498|gb|ACN20365.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700502|gb|ACN20368.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700506|gb|ACN20371.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700514|gb|ACN20377.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700518|gb|ACN20380.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700522|gb|ACN20383.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700526|gb|ACN20386.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700530|gb|ACN20389.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700534|gb|ACN20392.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700538|gb|ACN20395.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700542|gb|ACN20398.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700546|gb|ACN20401.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700550|gb|ACN20404.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700554|gb|ACN20407.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700558|gb|ACN20410.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700562|gb|ACN20413.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700566|gb|ACN20416.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700570|gb|ACN20419.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700574|gb|ACN20422.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700578|gb|ACN20425.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700582|gb|ACN20428.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700586|gb|ACN20431.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700590|gb|ACN20434.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700594|gb|ACN20437.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700598|gb|ACN20440.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700602|gb|ACN20443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700606|gb|ACN20446.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700610|gb|ACN20449.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700614|gb|ACN20452.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700618|gb|ACN20455.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700622|gb|ACN20458.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700626|gb|ACN20461.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700630|gb|ACN20464.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700634|gb|ACN20467.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700638|gb|ACN20470.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700642|gb|ACN20473.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700646|gb|ACN20476.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700650|gb|ACN20479.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700654|gb|ACN20482.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700658|gb|ACN20485.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700662|gb|ACN20488.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700666|gb|ACN20491.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700670|gb|ACN20494.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700674|gb|ACN20497.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700678|gb|ACN20500.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700682|gb|ACN20503.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700686|gb|ACN20506.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700690|gb|ACN20509.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700694|gb|ACN20512.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700698|gb|ACN20515.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700702|gb|ACN20518.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700706|gb|ACN20521.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700710|gb|ACN20524.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700714|gb|ACN20527.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700718|gb|ACN20530.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700722|gb|ACN20533.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700726|gb|ACN20536.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700730|gb|ACN20539.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700734|gb|ACN20542.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700738|gb|ACN20545.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700742|gb|ACN20548.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700746|gb|ACN20551.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700750|gb|ACN20554.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700754|gb|ACN20557.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700758|gb|ACN20560.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700762|gb|ACN20563.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700766|gb|ACN20566.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700770|gb|ACN20569.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700774|gb|ACN20572.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700778|gb|ACN20575.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700782|gb|ACN20578.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700786|gb|ACN20581.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700790|gb|ACN20584.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700794|gb|ACN20587.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700798|gb|ACN20590.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700802|gb|ACN20593.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700806|gb|ACN20596.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700810|gb|ACN20599.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700814|gb|ACN20602.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700818|gb|ACN20605.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700822|gb|ACN20608.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700826|gb|ACN20611.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700830|gb|ACN20614.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700834|gb|ACN20617.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700838|gb|ACN20620.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700842|gb|ACN20623.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700846|gb|ACN20626.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700850|gb|ACN20629.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700854|gb|ACN20632.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700858|gb|ACN20635.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700862|gb|ACN20638.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700866|gb|ACN20641.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700870|gb|ACN20644.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700874|gb|ACN20647.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700878|gb|ACN20650.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700882|gb|ACN20653.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700886|gb|ACN20656.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700890|gb|ACN20659.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700894|gb|ACN20662.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700898|gb|ACN20665.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700902|gb|ACN20668.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700906|gb|ACN20671.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700910|gb|ACN20674.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700914|gb|ACN20677.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700918|gb|ACN20680.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700922|gb|ACN20683.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700926|gb|ACN20686.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700930|gb|ACN20689.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700934|gb|ACN20692.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700938|gb|ACN20695.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700942|gb|ACN20698.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700946|gb|ACN20701.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700950|gb|ACN20704.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700954|gb|ACN20707.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700958|gb|ACN20710.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700962|gb|ACN20713.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700966|gb|ACN20716.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700970|gb|ACN20719.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700974|gb|ACN20722.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700978|gb|ACN20725.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700982|gb|ACN20728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700986|gb|ACN20731.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700990|gb|ACN20734.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700994|gb|ACN20737.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700998|gb|ACN20740.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|258600220|gb|EEW13545.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|258608494|gb|EEW21102.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284056787|gb|ADB67728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284059834|gb|ADB70773.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289170407|emb|CBH26947.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|293589526|gb|EFF97860.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|302034427|gb|ADK92367.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034429|gb|ADK92368.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034431|gb|ADK92369.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034433|gb|ADK92370.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034439|gb|ADK92373.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034441|gb|ADK92374.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034443|gb|ADK92375.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034445|gb|ADK92376.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|313614786|gb|EFR88329.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|325478815|gb|EGC81925.1| putative RNA polymerase sigma-F factor [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 255

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 116/229 (50%), Gaps = 20/229 (8%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A ++FD   GY FS++A   +  
Sbjct: 31  ELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRFDPTKGYAFSSFATPTIMG 90

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVEGVRK 565
            + R   D+   IR+P  +++ ++K + TA++ +  +++R PT  +IA  L    E + +
Sbjct: 91  ELKRYFRDKGWVIRVPRRIQN-LYKKINTAKKILPQELQRTPTVADIADYLGEDEETILE 149

Query: 566 VLKITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
            ++ +K   P SL+        E+   L + I  EDKN     DS     L++   +   
Sbjct: 150 TMEASKVYAPQSLDMKYQVQKGENAIDLSEMIGEEDKN----FDS---IELKDLIDKSKE 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L   E+ +L +R+  G     T  ++     +++  + +IE K I+K 
Sbjct: 203 RLNDLEKEILELRYYEG----RTQVDIANTLDISQMTVSRIEKKIIQKF 247


>gi|16799967|ref|NP_470235.1| RNA polymerase sigma factor SigB [Listeria innocua Clip11262]
 gi|16413344|emb|CAC96126.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria innocua
           Clip11262]
 gi|30266013|gb|AAN16084.1| SigB [Listeria monocytogenes]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 110/218 (50%), Gaps = 12/218 (5%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  +   I R + D
Sbjct: 41  LVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPTIVGEIKRFLRD 100

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V + +++ K  +
Sbjct: 101 KTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQ 160

Query: 573 PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRM 630
            +S++  I  D D    G  I   + V   D   +  N R    +VL  L  RE+++L+ 
Sbjct: 161 ALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPVLDEREQKILQY 216

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 217 TF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|196044126|ref|ZP_03111362.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218902186|ref|YP_002450020.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
 gi|196024765|gb|EDX63436.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218534787|gb|ACK87185.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
          Length = 257

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 113/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 30  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 90  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 149

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    ET  R   
Sbjct: 150 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEETERRLVL 199

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 200 KDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 253


>gi|197723817|gb|ACH72688.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 256

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 29  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 89  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 148

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 149 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 204

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 205 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 249


>gi|305675234|ref|YP_003866906.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|161168469|dbj|BAF93933.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto]
 gi|291485028|dbj|BAI86103.1| hypothetical protein BSNT_03833 [Bacillus subtilis subsp. natto
           BEST195]
 gi|305413478|gb|ADM38597.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 242

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/252 (26%), Positives = 110/252 (43%), Gaps = 61/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE +  + ++ KG+  A   +  ++E NLRLV  + KK+ N G    DLI  G IGL
Sbjct: 32  LSSSEEKKYLELMAKGDEHA---RNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K  E +    G K +TYA         R I ++     I +H+R               
Sbjct: 89  IKGIESYSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------- 120

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                    LK TK+ +SL  PIG +   +   L D ++ +N  
Sbjct: 121 ------------------------ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN-- 154

Query: 599 SPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +   IQ N+  E   + +  L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + 
Sbjct: 155 EDVIDTIQLNMELEKVKQYIDILDDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVS 214

Query: 658 QIEAKAIRKLKH 669
           +IE +A+ K+ H
Sbjct: 215 RIEKRALMKMFH 226


>gi|319651643|ref|ZP_08005770.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396710|gb|EFV77421.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 98/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNMLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSEGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK TK+ +SL  PIG +   +    I+  K+    + + IQ N+  E     +  L 
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVINTIQLNMELEKVKEYIDVLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 DREKEVIVGRFGLDLQKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|317063373|ref|ZP_07927858.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689049|gb|EFS25884.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 54

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/54 (51%), Positives = 42/54 (77%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           + F+DLI EGN+GL+ A EKFD   G++FSTYA+WW+KQ+I++++  +   IRI
Sbjct: 1   MSFIDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRI 54


>gi|254673642|emb|CBA09200.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha275]
          Length = 268

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 112/233 (48%), Gaps = 31/233 (13%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KG+  A+   K+++ ++LR+V+S+A+ Y   GL   DLIQEGNIGLMKA ++++   G +
Sbjct: 44  KGDLNAA---KQLILSHLRVVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGAR 100

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             ++A+ W+K  I   I      +R+     + K+   +R+ R+  N +  +   ++IA 
Sbjct: 101 LFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKLFFNLRSMRKNLNALSPKEA-QDIAD 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD------------ 602
            L + +           E + +E  +   D + + D  +D+++ +P+D            
Sbjct: 160 DLGVKL----------SEVLEMEQRMTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQ 209

Query: 603 ---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
               A  A   E     LA L  R  R++  R+ +  +   TL ++  ++ V+
Sbjct: 210 LSKQAHYALQTEGLQNALAQLDDRSRRIVESRW-LQDDGGLTLHQLAAEYGVS 261


>gi|239934586|emb|CAR94607.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/69 (49%), Positives = 47/69 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSNYPLTYTFMLNQYEQVKA 60

Query: 177 GTTLLREII 185
           G   L +II
Sbjct: 61  GQGRLVDII 69


>gi|172037479|ref|YP_001803980.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171698933|gb|ACB51914.1| group 3 sigma-70 RNA polymerase sigma factor F [Cyanothece sp. ATCC
           51142]
          Length = 269

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 107/219 (48%), Gaps = 8/219 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++  + + DL+Q G++GL++A E+F    G  FS++A+ +
Sbjct: 40  RNQILELNFGLVRKEAHHWVHQCPESYEDLVQVGSLGLIRAIERFSIDKGNAFSSFAIPY 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   + +   +    K  R+PT  EIA+ L + ++  
Sbjct: 100 IRGEIQHYLRDKKYTVRIPRRWLELGRQSMNVRQEFREKFNRQPTDSEIAQVLEISLKEW 159

Query: 564 R--KVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  K+    +EP+SL+  + +  E  + LGD + D N  S    A +  +R    + L  
Sbjct: 160 QEIKLAFQNREPVSLDVKVSNDGEGQTSLGDLVPDANYRS-FQLAQEDQIR--LQQALEQ 216

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           L  R   +L   F   +    T E++G        R+++
Sbjct: 217 LEERTRHILEFVFLKDLTQRETAEQLGISVVTVSRRVKK 255


>gi|197723819|gb|ACH72689.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 257

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|320009625|gb|ADW04475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 285

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 111/238 (46%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 54  GTTEHHRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 113

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 114 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTGEIAERL 173

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+   
Sbjct: 174 KISEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLVR 228

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+      + T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 229 HLLVQLPEREQRILLLRY----YNNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 282


>gi|22770506|gb|AAN06628.1|AF497200_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 206 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 249


>gi|197723821|gb|ACH72690.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 238

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|154484618|ref|ZP_02027066.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
 gi|149734466|gb|EDM50383.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
          Length = 237

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/242 (22%), Positives = 124/242 (51%), Gaps = 15/242 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++ +      +A+ +++  N  L+ S+ +++ NRG +  DL Q G IG++KA ++FD 
Sbjct: 4   LTLINRAHQGDKLARDKILIENTGLIWSIVRRFLNRGHEGEDLFQIGCIGMLKAIDRFDT 63

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                FSTYA+  +   I R I D    ++I   +++   K++       N+ K+EPT E
Sbjct: 64  EFDVAFSTYAVPMIAGEIRRFIRDDGI-VKISRKIKENQMKIMHQREIYINEKKQEPTIE 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANL 609
           E+ K   +  E +   +  ++   S++  +  +D+++ L D  ED       D+ I+  +
Sbjct: 123 ELEKVCDLTKEEIVMAMDASRNVESIDKEMYSKDSAYTLMDLAED-------DTNIEETV 175

Query: 610 --RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +    +++  L  +E +++ +R+      + T  +V K+  +T+ ++ ++E K +  +
Sbjct: 176 LNKIMVQQLMDMLESKERKIINLRYF----KNKTQSQVAKEMGMTQVQVSRLEKKILNSM 231

Query: 668 KH 669
           ++
Sbjct: 232 RN 233


>gi|160939772|ref|ZP_02087119.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437206|gb|EDP14971.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
          Length = 209

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 99/229 (43%), Gaps = 57/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E N+RLV  V KKY        DL+  G IGL+KA   F+   G + +TYA   
Sbjct: 27  ARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGLIKAVNTFNVDKGSRLATYAARC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+                     ++I  ++R +R+ S ++                    
Sbjct: 87  VE---------------------NEILMLLRASRKYSKEV-------------------- 105

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLAS 619
                      SL  PIG   D +T  L D IE  N    LD+ I + +++E      + 
Sbjct: 106 -----------SLFEPIGVDKDGETVSLVDVIEMDNK-ETLDTMILKQDVKELYEAFESC 153

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LT  E+ VL MR+G+    +HT  E+  +  ++R  + +IE KAI K++
Sbjct: 154 LTETEKTVLGMRYGLYRGKEHTQREIAGKLGISRSYVSRIEKKAIEKIR 202


>gi|161898897|gb|ABX80438.1| SigB [Listeria monocytogenes]
          Length = 235

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 15  AQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 74

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 75  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 134

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 135 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 190

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 191 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 235


>gi|89099505|ref|ZP_01172381.1| sigma factor B [Bacillus sp. NRRL B-14911]
 gi|89085891|gb|EAR65016.1| sigma factor B [Bacillus sp. NRRL B-14911]
          Length = 264

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 52/218 (23%), Positives = 113/218 (51%), Gaps = 12/218 (5%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV ++A+KY+       D+ Q G IGL+ A  ++D   G  F  +A+  +   I R + D
Sbjct: 41  LVETIARKYSKGRSYHEDIAQVGIIGLLGAIRRYDETFGKSFEAFAVPTIIGEIKRFLRD 100

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   K+  T   ++ ++ R P  +EIA ++ +  E V + +++ K  +
Sbjct: 101 KTWSVHVPRRIKELGPKIKTTVEELTTQLHRSPRVDEIADEIGVSEEEVLEAMEMGKSYQ 160

Query: 573 PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRM 630
            +S++  I  D D    G  +   + V  +D   +  N R    RVL  LT RE+++++ 
Sbjct: 161 ALSVDHSIEADSD----GGTVTLLDIVGNVDEGFEKVNQRMVLERVLHVLTDREKQIIQY 216

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +   M+     ++ G +  +++  + +++ +AI+KL+
Sbjct: 217 TYLENMSQ----KDAGDKLGISQMHVSRLQRRAIKKLQ 250


>gi|161898923|gb|ABX80451.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|315179524|gb|ADT86438.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           NCTC 11218]
          Length = 244

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 95/200 (47%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +  ++ R+PT  E+AK L M ++    VL      I+    +G ED     D 
Sbjct: 103 IGQAIAVLEGELNRDPTDSEVAKHLGMSLDQYHSVLT----DINCSRIVGIEDLGVTDDA 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   +D    SP       + R+     + SL  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPVDDDEDNSPFKGVADESFRKALVESIKSLPEREALVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++A+++L+
Sbjct: 215 LGVSESRVSQILSQAMQRLR 234


>gi|30266009|gb|AAN16082.1| SigB [Listeria ivanovii]
 gi|30266011|gb|AAN16083.1| SigB [Listeria ivanovii]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|3298591|gb|AAC38793.1| Sigma B [Listeria innocua]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 110/218 (50%), Gaps = 12/218 (5%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  +   I R + D
Sbjct: 41  LVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPTIVGEIKRFLRD 100

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V + +++ K  +
Sbjct: 101 KTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQ 160

Query: 573 PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRM 630
            +S++  I  D D    G  I   + V   D   +  N R    +VL  L  RE+++L+ 
Sbjct: 161 ALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPVLDEREQKILQY 216

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 217 TF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|73541439|ref|YP_295959.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72118852|gb|AAZ61115.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 653

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 47/145 (32%), Positives = 74/145 (51%), Gaps = 14/145 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD------LED 85
           + +I+L RQRGY+T  +++  L  +   +  ME  V   + MG+ + +         L D
Sbjct: 41  RALIQLGRQRGYLTHADISDHLQENFTDTAAMESIVTTFAEMGVKIFEQTPDAETLLLSD 100

Query: 86  EE--GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                S+D  D  +  + S+V      DS    T DPVRMY+REM S  LL+R+ E+ +A
Sbjct: 101 NAVVASDDQADEEAEVALSTV------DSEFGRTTDPVRMYMREMSSATLLTRKEEVELA 154

Query: 144 KRIEAGRAMMMASLCESPLTFQALI 168
           KRIE G   M+ ++   P T   ++
Sbjct: 155 KRIEDGLNNMVHAISACPSTIATIL 179


>gi|22770516|gb|AAN06633.1|AF497205_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 206 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 249


>gi|325288837|ref|YP_004265018.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964238|gb|ADY55017.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 250

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 109/227 (48%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +++K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 69  VKGTLIERNLRLVVYISRKFENTGISIEDLVSIGTIGLIKAVNTFDPTKKIKLATYA--- 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NKI+ E + +             
Sbjct: 126 -----SRCIENE-----ILMYLRR------------NNKIRSEVSFD------------- 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +N +   P++  +    R+   + ++SL+
Sbjct: 151 --------EPLNIDW---DGNELLLSDVLGTENDIISKPIEEEVD---RQLLAQAMSSLS 196

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ ++ +RFG+G   + T +EV  +  +++  I ++E K I++L+
Sbjct: 197 EREQLIMELRFGMGGKEEKTQKEVADKLGISQSYISRLEKKIIKRLR 243


>gi|319944142|ref|ZP_08018420.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
 gi|319742636|gb|EFV95045.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
          Length = 241

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 108/218 (49%), Gaps = 12/218 (5%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           R+ + +A +  +  ++  DLIQ G IGL+ A  +FD  +G +F T+AM  V+ A+   + 
Sbjct: 26  RVAVQMAARLPS-SIELDDLIQAGLIGLVDAVSRFDAAMGVQFDTFAMQRVRGAMLDELR 84

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +      +P  +R     + +    +  ++ R     EIA +L +P+E  +++L   K  
Sbjct: 85  NADW---MPRSVRKSQRSIEQAIHAVEQRLGRPAQEREIADELQVPLEEYQRLLSSAKGS 141

Query: 574 ISL---ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             L   ++   D+D S +   + D +A +P      A  RE+    +  L  RE+ ++ +
Sbjct: 142 QLLYFEDSASEDDDESRIEQMLPD-DAPTPDRRLEDARFRESLVAAIDGLPEREKLLMNL 200

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      + TL+E+G+   VT  R+ Q+ ++A+ +L+
Sbjct: 201 YY----VEELTLKEIGEVLGVTESRVSQLHSQAVARLR 234


>gi|269836601|ref|YP_003318829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
 gi|269785864|gb|ACZ38007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
          Length = 264

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 95/204 (46%), Gaps = 16/204 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G IGL++A ++FD   G KF T+A+  ++ AI  ++        +P   R +   
Sbjct: 60  DLLGYGTIGLIEAIDRFDPERGVKFETFAIQRIRGAIIDAVRTLDL---VPRTARQRARA 116

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT---SHL 588
           + +  R +     R P  EE+A  L M ++  R+ L+     I    P+   D      L
Sbjct: 117 IEQAYREIFAATGRMPPEEEVAAHLGMTIDAFRQALQDAACAI---LPLQQSDRDGEGTL 173

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + D  A  PLD+A++++L       L  L  R+  ++ + +      + TL E+ + 
Sbjct: 174 EDTLPDAQATEPLDAAVRSDLVHRLAAALERLPERDRLIVTLYY----YEELTLREISEV 229

Query: 649 FCVTRERIRQIEAKA---IRKLKH 669
             +T  R+ Q+ ++A   +R L H
Sbjct: 230 LGITESRVSQLLSRARLQLRALLH 253


>gi|206975667|ref|ZP_03236579.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
 gi|206746129|gb|EDZ57524.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
          Length = 257

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 121/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCDE--AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDCLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   F   +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
 gi|151280463|gb|ABR88873.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
          Length = 243

 Score = 69.3 bits (168), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/205 (24%), Positives = 93/205 (45%), Gaps = 9/205 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A  +++   G +F TYA+  ++ A+   +        +P  MR  + K
Sbjct: 40  DLIQAGMIGLLDAVSRYEETHGAQFETYAVQRIRGAMLDELRSSDW---MPRSMRQNMRK 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +      +  ++ R P   E+AK+L + +   + +L      + +  E     ED  H  
Sbjct: 97  IEVAMNTLQQRLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFL 156

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D      +  PL + +    R      + +L  RE+ ++ + +   MN    L+E+G   
Sbjct: 157 DRYCTDESPDPLQNLMNTGFRAAVIEAIQALPEREKILMGLYYEQEMN----LKEIGAVM 212

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSK 674
            VT  R+ Q+ ++AI +++   R K
Sbjct: 213 GVTESRVSQLHSQAIARMRANLREK 237


>gi|284007149|emb|CBA72430.1| flagellar biosynthesis sigma factor [Arsenophonus nasoniae]
          Length = 243

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 99/203 (48%), Gaps = 18/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E+FD   G  F+TYA+  V+ A+   +  +     +P  +R +  +
Sbjct: 46  DLVQAGGIGLLDALERFDASQGTAFTTYAVQRVRGAMLDELRARDW---VPRSVRRQARE 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
             +  +++   + R  T +EIA KL + +   +++L+ T       + +   D  H    
Sbjct: 103 ATKVMQQLEQALGRPATEQEIADKLHIGLLEYQQLLQDTN-----NSQLCSYDEWHEVHG 157

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                 IE  +  +PL + I  ++R+   + +  L  RE+ VL + +      D  L+E+
Sbjct: 158 ESCEPIIEVDDERNPLQTLIATDIRKNIIKAIECLPEREKMVLTLYY----QEDLNLKEI 213

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ Q+ ++AI++L+
Sbjct: 214 GAVLNVGESRVSQLHSQAIKRLR 236


>gi|161898917|gb|ABX80448.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKINNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 236


>gi|161898913|gb|ABX80446.1| SigB [Listeria monocytogenes]
 gi|161898915|gb|ABX80447.1| SigB [Listeria monocytogenes]
 gi|161898939|gb|ABX80459.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 193 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 237


>gi|118476614|ref|YP_893765.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis str. Al
           Hakam]
 gi|301052635|ref|YP_003790846.1| sigma factor B [Bacillus anthracis CI]
 gi|118415839|gb|ABK84258.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Bacillus thuringiensis
           str. Al Hakam]
 gi|300374804|gb|ADK03708.1| sigma factor B [Bacillus cereus biovar anthracis str. CI]
          Length = 258

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 113/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 31  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 91  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    ET  R   
Sbjct: 151 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEETERRLVL 200

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 201 KDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 254


>gi|3386359|gb|AAC34827.1| RNA polymerase sigma B [Listeria monocytogenes]
          Length = 266

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 37  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 97  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 156

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 157 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 212

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 213 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 257


>gi|183220350|ref|YP_001838346.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910466|ref|YP_001962021.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167775142|gb|ABZ93443.1| RNA polymerase sigma subunit [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167778772|gb|ABZ97070.1| RNA polymerase sigma factor for flagellar operon [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 266

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 109/223 (48%), Gaps = 24/223 (10%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVH 524
           + ++F DL+  G  GL+ A EKFD     KF TYAM      I  SI D+  ++  IP  
Sbjct: 53  QNVEFEDLVSYGVFGLLDAIEKFDPSREIKFKTYAM----TRIRGSIFDELRSVDWIPRS 108

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +R K  ++      + NK  ++   EEIAK+L + +E    +L      +S  + +   D
Sbjct: 109 IRQKAKQLENIIAMLENKEGKKVDDEEIAKELGVSMEEYNSLLA----KLSGTSLVSLND 164

Query: 585 TSHLGDFIEDKNAVSPLDSAIQAN---------LRETTTRVLASLTPREERVLRMRFGIG 635
              LGD  ++ + +  L+S +  N         ++      + SL  +E++V+ + +   
Sbjct: 165 IWFLGDENDEVSFMETLESPMNMNPDNIIEKEEIKNVIVEAIQSLPEKEKKVIVLYY--- 221

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
              D TL+E+G+   VT  RI Q+  KA+ +L+  S+  K++S
Sbjct: 222 -YEDLTLKEIGEVLEVTESRISQLHTKAVARLR--SKLSKVKS 261


>gi|312879616|ref|ZP_07739416.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
 gi|310782907|gb|EFQ23305.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
          Length = 247

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 105/224 (46%), Gaps = 17/224 (7%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+ +V   L LV  VA +       GL F DL+  G +GL+ A E+FD   G+ F T+A+
Sbjct: 21  KERLVRRYLPLVRYVAGRMAVSPPPGLDFEDLLSFGAMGLLDAIERFDLDRGFCFQTFAV 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +       R     R+K+ K+ RT  R + + +  P  E +   L M  +
Sbjct: 81  PRIRGAILDELRRYDWISRTG---REKLQKLERTVERFA-RTQGNPDDETLMDALGMNEK 136

Query: 562 GVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +++L+I      +SL+  +  ED     + I + +A SPLD   Q   +E   RVLA 
Sbjct: 137 AYKELLEIASRSYVVSLDEVLALEDGDVQREGILEDDAPSPLDRMEQ---KEEVDRVLAG 193

Query: 620 LT--PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           L+  P  ER+L     +      TL+E+G    VT  R  Q+  
Sbjct: 194 LSELPERERLL---ISLYYYEGLTLKEIGGVLGVTESRASQLHG 234


>gi|256005472|ref|ZP_05430434.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255990527|gb|EEU00647.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
          Length = 252

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 81/163 (49%), Gaps = 14/163 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++   + ++V   L L   +AKK+ NRG+ + D+ Q  +I L+KA E+FD   G KF 
Sbjct: 24  ETKSVEVRNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVVSIALIKAVERFDPDKGVKFI 83

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           ++A   +   I R   D+   IRIP  + +   K+      ++ ++KR P  +E+A+ L 
Sbjct: 84  SFATPTIIGEIKRYFRDKGSVIRIPRRIYEVYQKINHARESLTQELKRPPRIDELARHLN 143

Query: 558 MPVEGVRKVLK--------------ITKEPISLETPIGDEDTS 586
           +  E V ++++                 + + L   IGD+D++
Sbjct: 144 ISEESVVEIIESYNAYNIQSFSQNVYANDELELHEVIGDQDST 186


>gi|119514598|gb|ABL76111.1| SigB [Listeria monocytogenes]
 gi|119514600|gb|ABL76112.1| SigB [Listeria monocytogenes]
 gi|119514604|gb|ABL76114.1| SigB [Listeria monocytogenes]
 gi|119514612|gb|ABL76118.1| SigB [Listeria monocytogenes]
 gi|119514616|gb|ABL76120.1| SigB [Listeria monocytogenes]
 gi|119514620|gb|ABL76122.1| SigB [Listeria monocytogenes]
 gi|119514622|gb|ABL76123.1| SigB [Listeria monocytogenes]
 gi|119514624|gb|ABL76124.1| SigB [Listeria monocytogenes]
 gi|119514628|gb|ABL76126.1| SigB [Listeria monocytogenes]
 gi|119514634|gb|ABL76129.1| SigB [Listeria monocytogenes]
 gi|119514636|gb|ABL76130.1| SigB [Listeria monocytogenes]
 gi|119514638|gb|ABL76131.1| SigB [Listeria monocytogenes]
          Length = 249

 Score = 68.9 bits (167), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 206 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 249


>gi|302528260|ref|ZP_07280602.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302437155|gb|EFL08971.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 261

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/219 (27%), Positives = 105/219 (47%), Gaps = 11/219 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E S  ++ ++E +L L   +A+++  RG    DL+Q   IGL+ A +++D      F  +
Sbjct: 28  EHSRLRRRLIEEHLPLAEHIARRFARRGQPTEDLLQVARIGLINAVDRYDPARQTDFVAF 87

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  V   + R   D + ++R+P  +++    V + A  +  ++ R PT  E+A  L + 
Sbjct: 88  AVPTVMGEVRRYFRDHTWSVRVPRRLKELHLTVGQAATELGQRLGRAPTARELADHLDLD 147

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIEDKNA-VSPLDSAIQANLRETTTR 615
           ++ V + L      +  S++ P  D+  S  L D + D++  +  L+       RET   
Sbjct: 148 LDEVAEALHAGNAYQASSIDYPAHDDSGSVALADTLGDEDPEIEKLED------RETLKP 201

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           +L SL  RE  +L MRF   M      E VG  Q  V+R
Sbjct: 202 LLRSLPERERAILVMRFFSNMTQSQIAERVGLSQMQVSR 240


>gi|113477360|ref|YP_723421.1| RNA polymerase sigma factor SigF [Trichodesmium erythraeum IMS101]
 gi|110168408|gb|ABG52948.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 254

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 106/218 (48%), Gaps = 8/218 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ N+ LV   A  + N+  + + DL+Q G IGL+ A E+FD      FS++A  +
Sbjct: 29  RNKLVQLNVGLVRKEAYHWLNKCSETYDDLLQVGYIGLILAIERFDVSKARAFSSFATPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S ++RIP +      +  +  + +  K +R+PT +E+A  L + ++  
Sbjct: 89  IRGEIKHYLRDKSPSVRIPRNWLAIDRQATKVIQDLRMKFQRKPTDQEVASALGISLDQW 148

Query: 564 RKVLKITKE--PISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            K+    +   P+SL+ P+ D+   ++ LG+ + D    S    A +  +R    + L+ 
Sbjct: 149 HKIQMACRNLAPLSLDAPVQDQAYGSTSLGELVPDSQYRS-FQLAQEDQIR--LQQALSK 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           L     +VL   F   +    T E +G        R++
Sbjct: 206 LEESTRKVLEFVFLCDLTQKETAERMGISAVTVSRRVK 243


>gi|297544885|ref|YP_003677187.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842660|gb|ADH61176.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 241

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 116/247 (46%), Gaps = 53/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  ++VS + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSMEEETYLVSKMEKGDNEA---KTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++     I +++R             ++
Sbjct: 98  IKAINTFNPKKKIKLATYA--------SRCIENE-----ILMYLRR------------NS 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + EE    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 133 KTKLEVSFEE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   RE  T  L  L  RE++++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 176 --------RELLTSALKKLPDREKKIIGLRFGLDGGVEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLK 668
           K +++LK
Sbjct: 228 KILKRLK 234


>gi|212709528|ref|ZP_03317656.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
 gi|212687866|gb|EEB47394.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
          Length = 242

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 100/206 (48%), Gaps = 14/206 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A E+FD  LG  F+TYA+  ++ ++   +  +     +P  +R +  +
Sbjct: 47  DLIQAGGIGLLHALERFDASLGASFATYAVQRIRGSMLDELRSRDW---VPRSVRRQARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +   + R  T  EIAK L + +   R+VL  T           DE     G+ 
Sbjct: 104 MTKAIGELEQSLGRSATEPEIAKALDIDLAEYRQVLLDTNNSQLFSY---DEWHEVHGES 160

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E    + +  +PL   ++++L++     +  L  RE+ VL + +   +N    L+E+G 
Sbjct: 161 CEPSMDEDDGGNPLSLLMESSLKDQIVAAIEQLPEREKMVLTLYYQEELN----LKEIGA 216

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              V   R+ Q+ ++AI++L+   RS
Sbjct: 217 VLEVGESRVSQLHSQAIKRLRSKLRS 242


>gi|72161291|ref|YP_288948.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
 gi|71915023|gb|AAZ54925.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
          Length = 307

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/200 (29%), Positives = 97/200 (48%), Gaps = 11/200 (5%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRG    DL Q   +GL  A   FD   G +F +YA+  +   + R   D++  
Sbjct: 97  IARQYRNRGEPEEDLRQVAMVGLYNAIRNFDPAYGKEFISYALPMMTGEVKRHFRDRTWA 156

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISL 576
           IR+P   ++K  ++ R     + +  R PT  E+A+ L M  E   +++   +    +SL
Sbjct: 157 IRVPRKYQEKRAELNRVTAEFTQRHGRSPTVRELAELLEMDEEQTLELIDAARAYSTLSL 216

Query: 577 ETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGI 634
           + P G D+D + LGD       +  LD A++  +        LA+L+PR+ R+L +RF  
Sbjct: 217 DVPFGPDDDGATLGD------TLGGLDDALERVVDHAALRPALAALSPRDRRILLLRFAG 270

Query: 635 GMNTDHTLEEVG-KQFCVTR 653
                   E VG  Q  V+R
Sbjct: 271 DKTQAQIAEIVGLSQMHVSR 290


>gi|297616583|ref|YP_003701742.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144420|gb|ADI01177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 235

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 97/225 (43%), Gaps = 53/225 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  V KK+   G    DLI  G IGL+KA   FD+  G + +TYA   
Sbjct: 52  AKHILIEHNLRLVAHVIKKFEGTGEDTEDLISIGTIGLIKAINTFDYARGTRLATYA--- 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                                           AR + N++              M     
Sbjct: 109 --------------------------------ARCIENEV-------------LMWFRNS 123

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTP 622
           RKV    K+ +S+  PIG +   +   F++     + +   ++  L+E   R  L +L+ 
Sbjct: 124 RKV----KQEVSIYEPIGYDKEGNEITFLDILTTDNEIVDVVETRLQEEKIRQKLGALSK 179

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE +V+ MR+G+      T  E+ ++  ++R  + +IE +A++KL
Sbjct: 180 RERQVIEMRYGLFSGLKATQREIARKLGISRSYVSRIEKRALKKL 224


>gi|220934511|ref|YP_002513410.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219995821|gb|ACL72423.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 241

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 113/229 (49%), Gaps = 15/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +V+A++ LV  +A     R    +Q  DLIQ G +GL++AA+++D   G  F TYA 
Sbjct: 9   RNRLVDAHVPLVKRIAYHLLGRLPSSVQVDDLIQAGVVGLLEAAQQYDATQGASFETYAG 68

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +     T R  VH   +  +V    R + N++ RE  P E+A +L + ++
Sbjct: 69  IRIRGAMLDEVRRSDWTPR-SVHRNAR--RVSEAMRLVENRLGREAQPAEVAAELGVSLD 125

Query: 562 GVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             + ++    + + +S E  I + D+   G+ +   +  SP ++      R    R + +
Sbjct: 126 EYQHMVSDAASCKVLSFED-IFEPDSE--GEDLLPGDEPSPFEALQSDGFRAALAREVGA 182

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  V+ + +   +N    L E+G+   V+  R+ Q+  +A+ +L+
Sbjct: 183 LPERERLVMSLYYDDELN----LREIGEVLGVSESRVCQLHGQALVRLR 227


>gi|149183156|ref|ZP_01861605.1| SpoIIIC [Bacillus sp. SG-1]
 gi|148849139|gb|EDL63340.1| SpoIIIC [Bacillus sp. SG-1]
          Length = 238

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 98/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNILIEHNLRLVAHIVKKFENTGEDPEDLISIGTIGLIKAIESYSEGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK TK+ +SL  PIG +   +    I+  K+    +   IQ ++  E   + +  L 
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDILKSDADDVIETIQLSMELEKVRKYICVLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ M  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 DREKEVIIGRFGLDMKEEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|311031586|ref|ZP_07709676.1| sporulation sigma factor SigK [Bacillus sp. m3-13]
          Length = 237

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 97/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +TYA   
Sbjct: 50  ARNLLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESFHSGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRV-LASLT 621
              LK TK+ +SL  PIG +   +    I+  K+    +   IQ N+     +V +  L 
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMELEKIKVYIDVLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 EREREVIVGRFGLDLKDEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|197723815|gb|ACH72687.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 242

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 23  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 82

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 83  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 142

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 143 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 198

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 199 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 242


>gi|257065529|ref|YP_003151785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256797409|gb|ACV28064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 255

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 116/229 (50%), Gaps = 20/229 (8%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+++ ++ +V  ++ KY  +G++  DL Q  ++GL+ A E++D   GY FS++A   +  
Sbjct: 31  ELIKEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAVERYDPTKGYAFSSFATPTIMG 90

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVEGVRK 565
            + R   D+   IR+P  +++ ++K + TA++ +  +++R PT  +IA  L    E + +
Sbjct: 91  ELKRYFRDKGWVIRVPRRIQN-LYKKINTAKKILPQELQRTPTIADIADYLGEDEETILE 149

Query: 566 VLKITK--EPISLETPI---GDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
            ++ +K   P SL+        E+   L D I  EDKN     DS     L++   +   
Sbjct: 150 TMEASKVYTPQSLDMKYQVQKGENAIDLSDMIGEEDKN----FDS---IELKDLIDKSKE 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L   E+ +L +R+  G     T  ++     +++  + +IE K ++K 
Sbjct: 203 RLNDLEKEILELRYYEG----RTQVDIANTLDISQMTVSRIEKKILQKF 247


>gi|56419781|ref|YP_147099.1| RNA polymerase sigma factor SigD [Geobacillus kaustophilus HTA426]
 gi|56379623|dbj|BAD75531.1| DNA-directed RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           kaustophilus HTA426]
          Length = 251

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 15/201 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  MRDK  K
Sbjct: 55  ELVSLGLVGLYDALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSMRDKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG----DEDTSH 587
           +     R+  +  R  T +EIA +L M  E V+     T    S   P+G    DED   
Sbjct: 112 IEEAIERLEQRHMRSVTAKEIAAELGMTEEEVQAAASETF--FSHWLPLGQTTVDEDEGL 169

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D  A  P +  ++  + E     +  L  +E+ V+ + +      + T  E+G 
Sbjct: 170 LA--VRDDRAPLPEEQIVKQEMIEKLAEAIGQLNEKEQLVISLFY----KEELTFTEIGS 223

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI QI AKA+ KL+
Sbjct: 224 LLHLSTSRISQIHAKALWKLR 244


>gi|328883833|emb|CCA57072.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 281

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 49  PGTPEHHRVRGALIEANLPLVRYAADRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 108

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 109 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRSPTTAEIAER 168

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+  
Sbjct: 169 LRIGEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLV 223

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 224 RHLLVQLPEREQRILMLRY----YSNLTQSQISQELGVSQMHVSRLLARSFARLRSANR 278


>gi|158320542|ref|YP_001513049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
 gi|158140741|gb|ABW19053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
          Length = 245

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 115/231 (49%), Gaps = 19/231 (8%)

Query: 444 AKKEMVEANLRLVISVAKK-YTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK  ++E  +RLV  +A + Y + G  +++ DL+  G  GL+ A EKFD     KF TYA
Sbjct: 19  AKALLIEEYIRLVKFIAGRLYISYGSNIEYDDLVSYGIFGLIDAIEKFDLNKQVKFETYA 78

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ AI  S+        +P  +R K  K+      + NK+ R  T  E+++ L + V
Sbjct: 79  QIRIRGAIIDSLRSLDW---VPRSIRQKSKKIEEAYSSLENKLGRSATDVEVSEALDISV 135

Query: 561 EGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQANLRETTTRVL 617
           + ++++L  T     ISLE  I   +   +G+  E++     +       NL++T    +
Sbjct: 136 KELQEILLNTASFNVISLEEVIF--EVGLIGNTAEEQLTEDLICRRETYNNLKDT----I 189

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE +V+ + +      + T +E+GK   ++  R+ Q+ +KAI +LK
Sbjct: 190 VQLPERERQVISLYYY----NNLTYKEIGKVLDISESRVSQLHSKAISRLK 236


>gi|239942801|ref|ZP_04694738.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           15998]
 gi|239989260|ref|ZP_04709924.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           11379]
 gi|291446270|ref|ZP_06585660.1| sigma F [Streptomyces roseosporus NRRL 15998]
 gi|291349217|gb|EFE76121.1| sigma F [Streptomyces roseosporus NRRL 15998]
          Length = 285

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 112/239 (46%), Gaps = 11/239 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 53  PGTPEHRRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQ 112

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 113 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTAEIAER 172

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+  
Sbjct: 173 LKISEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLV 227

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 228 RHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 282


>gi|311068169|ref|YP_003973092.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
 gi|310868686|gb|ADP32161.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
          Length = 254

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 96/201 (47%), Gaps = 10/201 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 54  DLMSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS-HL 588
           V     ++  +  R  +P EIA++L M  + V   +        +S++  + D+D   ++
Sbjct: 111 VEAAIEKLEQRYLRNVSPAEIAEELGMTEQDVVSTMNEGFFANLLSIDEKLHDQDDGENI 170

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D   V P +  ++  L       +  L+ +E+ V+ + +      + TL E+G+ 
Sbjct: 171 QVMIRDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFY----KEELTLTEIGQV 226

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  RI QI +KA+ KLKH
Sbjct: 227 LSLSTSRISQIHSKALFKLKH 247


>gi|124516296|gb|EAY57804.1| putative RNA polymerase sigma 28 subunit, FliA/WhiG [Leptospirillum
           rubarum]
          Length = 251

 Score = 68.9 bits (167), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 104/218 (47%), Gaps = 16/218 (7%)

Query: 460 AKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           A +Y++R    L   DLI  G  GL+ AA +FD   G KF T A   ++ A+   I    
Sbjct: 21  ALRYSHRLPPELDVDDLISAGMGGLLDAARRFDPSRGIKFKTLAEHRIRGAMLDEIRAAD 80

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--- 573
               +P  +R+K+  V +    +  + KREPT +EIA ++ M  E   + L +  EP   
Sbjct: 81  W---MPRSVREKLTHVQQVKTELIARYKREPTRQEIAARMDMTEEEFDR-LSVDIEPHHL 136

Query: 574 ISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           +SLE  +  E  D+  L D +       PL S +Q+ + E   + L  L  ++  VL + 
Sbjct: 137 VSLEDLMDPEDGDSPSLLDRLSAPQEGDPLASLLQSEVSEKLCQALDRLPEKQRLVLSLY 196

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      + T++EV +   V+  R+ QI  +A+  LK 
Sbjct: 197 Y----YEELTMKEVARVVGVSESRVSQIHGQALAALKQ 230


>gi|154504525|ref|ZP_02041263.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
 gi|153795007|gb|EDN77427.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
          Length = 208

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 97/228 (42%), Gaps = 55/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  V KKY        DLI  G IGL+KA   F+   G + + YA   
Sbjct: 27  AKHILIERNLRLVAHVIKKYQYVDEDPEDLISIGTIGLIKAIVTFNPSKGNRLAAYASKC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  I              +H+R         AR+ ++K                     
Sbjct: 87  VENEIL-------------MHLR---------ARKKTSK--------------------- 103

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                     ISL  PIG +   +   L D IE      P    ++ N+++   +V   L
Sbjct: 104 ---------EISLYEPIGTDREGNEIKLYDIIETDEDDIPERVCLKENIQKLYEKVENEL 154

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + RE+ VL+MR+G+    ++T  EV KQ  ++R  + +IE  A+ KL+
Sbjct: 155 SQREKLVLKMRYGLYGGEEYTQREVAKQLGISRSYVSRIEKSAVEKLR 202


>gi|56421959|ref|YP_149277.1| DNA-directed RNA polymerase sigma-37 factor [Geobacillus
           kaustophilus HTA426]
 gi|56381801|dbj|BAD77709.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B) [Geobacillus
           kaustophilus HTA426]
          Length = 256

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 112/219 (51%), Gaps = 14/219 (6%)

Query: 455 LVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           L+ + AKK       F  DL Q G +  ++  + +D   G  F +YAM  +   +   + 
Sbjct: 39  LIAAAAKKMARSRPDFYEDLFQIGRLSFLRLLDHYDPSQGASFESYAMKSLIGYMKNYLR 98

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITK 571
           D++  I++P  +++K  KV +    ++ K++R P  +EIA  L + VE   ++L  +   
Sbjct: 99  DKAWYIQVPRKVKEKGSKVQQAIDELTVKLERSPNIDEIAAHLGLSVEETIEILAGRDHY 158

Query: 572 EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           + ISL+ P+  G++D + +G+F+ D+   + ++S I+   R    + +  L+ +E+ V+ 
Sbjct: 159 QAISLDAPVQDGEKDATTIGEFVADE--ANEIESLIE---RMDLEQAIGKLSEQEQIVID 213

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             F  G       E +G    V++  I +I+ +AI KLK
Sbjct: 214 AVFRRGETQRSLAERLG----VSQMTISRIQKRAIAKLK 248


>gi|125973527|ref|YP_001037437.1| sporulation sigma factor SigK [Clostridium thermocellum ATCC 27405]
 gi|256003345|ref|ZP_05428336.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281417730|ref|ZP_06248750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713752|gb|ABN52244.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Clostridium
           thermocellum ATCC 27405]
 gi|255992635|gb|EEU02726.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281409132|gb|EFB39390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940233|gb|ADU74267.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 1313]
          Length = 236

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 66/259 (25%), Positives = 114/259 (44%), Gaps = 58/259 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +H + +++KG+ EA   +  ++E NLRLV  + KKY++      DLI  G IGL
Sbjct: 33  LSPEEEQHYLDLLKKGDEEA---RNILIERNLRLVAHIVKKYSSTINDSDDLISIGTIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+   G + +TYA         R I ++     I +H+R               
Sbjct: 90  IKAISTFNHEKGTRLATYA--------ARCIENE-----ILMHIRSN------------- 123

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAV 598
                                     K T+  +SL+ PIG   D +   L D I +++  
Sbjct: 124 --------------------------KKTQSEVSLQDPIGVDRDGNEIALIDVIGNESES 157

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +  ++  ++    ++   L  RE+ VL +R+G+   T  T  E+ K   ++R  + +
Sbjct: 158 VVEEVELKMQVKRLYNKMKDVLKAREKMVLELRYGLLNGTGKTQREIAKMLGISRSYVSR 217

Query: 659 IEAKAIRKLKHPSRSKKLR 677
           IE KAI+KL    +S+  +
Sbjct: 218 IEKKAIKKLGKELKSESFK 236


>gi|154686064|ref|YP_001421225.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens FZB42]
 gi|308173610|ref|YP_003920315.1| RNA polymerase sigma-28 factor sigma-D [Bacillus amyloliquefaciens
           DSM 7]
 gi|154351915|gb|ABS73994.1| SigD [Bacillus amyloliquefaciens FZB42]
 gi|307606474|emb|CBI42845.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328553458|gb|AEB23950.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens TA208]
 gi|328911751|gb|AEB63347.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 254

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 96/201 (47%), Gaps = 10/201 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 54  DLMSLGMLGLYDALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS-HL 588
           V     ++  +  R  TP EIA++L M  + V   +        +S++  + D+D   ++
Sbjct: 111 VEAAIEKLEQRYLRNVTPSEIAEELGMTEQDVVSTMNEGFFANLLSIDEKLHDQDDGENI 170

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D   V P +  ++  L       +  L+ +E+ V+ + +      + TL E+G+ 
Sbjct: 171 QVMIRDDKNVPPEEKIMKDELIAQLAGKIHELSEKEQLVVSLFY----KEELTLTEIGQV 226

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  RI QI +KA+ KLKH
Sbjct: 227 LNLSTSRISQIHSKALFKLKH 247


>gi|328912710|gb|AEB64306.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 242

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 98/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+K  E +    G K +TYA   
Sbjct: 51  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYA--- 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 108 -----ARCIENE-----ILMHLR------------------------------------- 120

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK TK+ +SL  PIG D++ + +      K+    +   IQ N+  E   + +  L 
Sbjct: 121 --ALKKTKKDVSLHDPIGQDKEGNEISRIDVLKSESEDVIDTIQLNMELEKVKKYIDILD 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 179 DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 226


>gi|297560730|ref|YP_003679704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845178|gb|ADH67198.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 287

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 110/231 (47%), Gaps = 17/231 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+V     LV  +A++Y  RG    DL Q   +GL+KA   +    G  F +Y M  V
Sbjct: 56  REEVVVRYQPLVNKLARRYNGRGEPLEDLKQTAMVGLVKAIRGYRPDRGKPFISYLMPTV 115

Query: 505 KQAITRSIADQSCTIRIPVHM---RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
              I R   D +  IR+P      R K+ +V+ T ++   ++   PT  EIAK++ +  E
Sbjct: 116 TGEIKRHFRDHTWAIRVPRRHQENRIKLRQVLNTFQQTHARV---PTNAEIAKEMGLDEE 172

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVL 617
            V ++++ ++    +SL+ P   +     G  +ED        L+  +Q   RE+    L
Sbjct: 173 EVVELVQASESYRSLSLDAPDSSDSDGQEGSRLEDHLGSEDEGLERVVQ---RESLKPAL 229

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A L  RE  +L++RF  G   DHT  E+  +   ++  + ++    + +L+
Sbjct: 230 ARLPEREREILKLRF-FG---DHTQTEIADRMGYSQMHVSRLLKNTLEQLR 276


>gi|297158638|gb|ADI08350.1| RNA polymerase sigma factor, sigma F [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 112/238 (47%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 46  GTPEHGRVRDALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 105

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 106 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTVLHGRSPTTAEIAERL 165

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+   
Sbjct: 166 GLGEDEVLACIEAGRSYHATSLEA---AQEGDGLPGLVDRLGYEDPALAGVEH--RDLVR 220

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ +++  +L+  +R
Sbjct: 221 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLSRSFARLRSANR 274


>gi|225862940|ref|YP_002748318.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
 gi|225786058|gb|ACO26275.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
          Length = 257

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 112/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 30  AQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 90  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 149

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    ET  R   
Sbjct: 150 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEETERRLVL 199

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 200 KDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 253


>gi|22770510|gb|AAN06630.1|AF497202_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 113/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      +  +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELXRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|297530579|ref|YP_003671854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297253831|gb|ADI27277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 251

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 15/201 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  MRDK  K
Sbjct: 55  ELVSLGLVGLYDALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSMRDKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG----DEDTSH 587
           +     R+  +  R  T +EIA +L M  E V+     T    S   P+G    DED   
Sbjct: 112 IEEAIERLEQRHMRSVTAKEIAAELGMTEEEVQAAASETF--FSHWLPLGQTTVDEDEGL 169

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D  A  P +  ++  + E     +  L  +E+ V+ + +      + T  E+G 
Sbjct: 170 LS--VRDDRAPLPEEQIVKQEMIEKLAEAIGQLNEKEQLVISLFY----KEELTFTEIGS 223

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI QI AKA+ KL+
Sbjct: 224 LLHLSTSRISQIHAKALWKLR 244


>gi|170078529|ref|YP_001735167.1| RNA polymerase sigma factor SigF [Synechococcus sp. PCC 7002]
 gi|5359699|gb|AAD42767.1|AF121848_2 SigF [Synechococcus sp. PCC 7002]
 gi|169886198|gb|ACA99911.1| SigF [Synechococcus sp. PCC 7002]
          Length = 259

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 114/233 (48%), Gaps = 20/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V  N+ LV   A  ++ +  + F DL+Q G++GL++A E+F    G  FS++A  +
Sbjct: 32  RNQIVSLNIGLVRKEAHHWSRQCSENFDDLMQVGSLGLLRAIERFTLERGNAFSSFANPY 91

Query: 504 VKQAITRSIADQSCTIRIP---VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++  I   + D+S T+RIP   + +R + ++ + T R+  N   R+P+  EIA+ L + V
Sbjct: 92  IRGEIQHYLRDKSSTVRIPRRMLQLRQQSNRFIHTFRQEHN---RQPSAIEIAEHLNISV 148

Query: 561 EGVRKV--LKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
              + +      ++P+SL+  +     E+TS LGD + D    S    AI+  +R    +
Sbjct: 149 TEWQSINLAYQNRDPVSLDVSVKADQGENTS-LGDLVPDPGYKS-FQLAIEDQIR--IQQ 204

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L     +VL   F   +      + +G        RI+    K I  LK
Sbjct: 205 GLAQLEEHTRKVLEFVFLHDLTQKEAADLLGVSVITVSRRIK----KGINSLK 253


>gi|220911344|ref|YP_002486653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219858222|gb|ACL38564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 310

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/277 (23%), Positives = 132/277 (47%), Gaps = 21/277 (7%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           ++F    VDS     +E++S  ++   S  +     S  R G+   +  + ++V   L L
Sbjct: 3   ESFSPAAVDS--PYIHEVQSTPIQKTASPHD-----SQARSGQLRETF-ENDLVLGYLDL 54

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
             ++A ++  RG +  DL Q   +GL+KAA  FD   G  F  YA   +   + R + D+
Sbjct: 55  AEALAARFEARGRERADLNQVAYLGLVKAARGFDRSKGESFPAYAAPTITGELKRYLRDR 114

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EP 573
           +  +R P +++D   ++ R    ++  + R P+ EE+A +L      V++ +  +    P
Sbjct: 115 TWVVRPPRNIQDLRTRLFRAEPELTQALGRSPSVEELAGELETDPAAVQEAMSASSSMHP 174

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRF 632
            SL+    + D   +GD +   +  +PL+   + A LR+     +  L P +  +L  R+
Sbjct: 175 DSLDAVNPNSDAPSIGDMLACPD--TPLERLEELACLRD----AMHDLAPADRELLYRRY 228

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 + T  ++GK+  +++ ++ +  A+ + +L+H
Sbjct: 229 ----FCEETQVQLGKRLGMSQMQVSRRLARVLVELQH 261


>gi|229492301|ref|ZP_04386108.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229320710|gb|EEN86524.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 260

 Score = 68.6 bits (166), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/224 (25%), Positives = 111/224 (49%), Gaps = 12/224 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L L   VA++Y  RG  F DL Q   +GL++A ++FD   G  F ++A+  V   
Sbjct: 39  IIELCLPLATHVARRYQGRGQPFEDLEQVARVGLIQAVQRFDVDKGSDFLSFAVPTVMGE 98

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + +   D   ++R+P  ++++   + R    +S  + R PT  E+AK+L +  + V + L
Sbjct: 99  VRKHFRDHGWSVRVPRSLQERHLALNRALTTLSQTLGRAPTVAELAKELDIEPDEVEQGL 158

Query: 568 KITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAI-QANLRETTTRVLASLTPRE 624
             T       TP+   DT+  GD   +   + +   D AI + +  ET    L +L  RE
Sbjct: 159 --TAGNSYRTTPL---DTASAGDGSGLTLIDTLGQYDEAISRIDNHETLRPALLALPERE 213

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +RF   +      E+VG    +++  + +I  +++++L+
Sbjct: 214 RTIVVLRFFGHLTQSQIAEKVG----ISQMHVSRILTQSLKQLR 253


>gi|119514602|gb|ABL76113.1| SigB [Listeria monocytogenes]
 gi|119514606|gb|ABL76115.1| SigB [Listeria monocytogenes]
 gi|119514608|gb|ABL76116.1| SigB [Listeria monocytogenes]
 gi|119514610|gb|ABL76117.1| SigB [Listeria monocytogenes]
 gi|119514614|gb|ABL76119.1| SigB [Listeria monocytogenes]
 gi|119514618|gb|ABL76121.1| SigB [Listeria monocytogenes 690]
 gi|119514626|gb|ABL76125.1| SigB [Listeria monocytogenes]
 gi|119514630|gb|ABL76127.1| SigB [Listeria monocytogenes]
 gi|119514632|gb|ABL76128.1| SigB [Listeria monocytogenes]
          Length = 249

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 249


>gi|206603135|gb|EDZ39615.1| Putative RNA polymerase sigma 28 subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 251

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 103/218 (47%), Gaps = 16/218 (7%)

Query: 460 AKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           A +Y++R    L   DLI  G  GL+ AA +FD   G KF T A   ++ A+   I    
Sbjct: 21  ALRYSHRLPPELDIDDLISAGMGGLLDAARRFDPARGIKFKTLAEHRIRGAMLDEIRAAD 80

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--- 573
               +P  +R+K+  V +    +  + KREPT +EIA ++ M  E   + L +  EP   
Sbjct: 81  W---MPRSVREKLTHVQQVKTELIARYKREPTRQEIAARMEMTEEEFDR-LSVDIEPHHL 136

Query: 574 ISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           +SLE  +  E  D+  L D +       PL S +Q  + E   + L  L  ++  VL + 
Sbjct: 137 VSLEDLMDPEDGDSPSLLDRLSAPQEGDPLASLLQNEVSEKLCQALDRLPEKQRLVLSLY 196

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      + T++EV +   V+  R+ QI  +A+  LK 
Sbjct: 197 Y----YEELTMKEVARVVGVSESRVSQIHGQALAALKQ 230


>gi|41409504|ref|NP_962340.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|254776692|ref|ZP_05218208.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|41398335|gb|AAS05956.1| SigF_2 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 262

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 115/241 (47%), Gaps = 39/241 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+  +
Sbjct: 40  RDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTI 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMP---- 559
              + R   D S ++++P  +++ +H  + TA   +S ++ R PT  E+A +L M     
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKE-LHLRLGTATADLSQRLGRAPTATELAAELEMDREEV 158

Query: 560 VEGVRKVLKITKEPISLETPIGDED------TSHLGDF------IEDKNAVSPLDSAIQA 607
           VEG+  V   +   +S+++  G E+         LGD       IED+ ++ PL      
Sbjct: 159 VEGL--VAGSSYNTLSIDSGGGSEEEEVRAIADTLGDVDTGLDRIEDQESLRPL------ 210

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                    L +L  RE  VL +RF   M      E VG    +++  + ++ AK++ +L
Sbjct: 211 ---------LEALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRLLAKSLTRL 257

Query: 668 K 668
           +
Sbjct: 258 R 258


>gi|239927803|ref|ZP_04684756.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 220

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 98/202 (48%), Gaps = 14/202 (6%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A ++ +RG  F DL Q   +GL+KA +++D  LG  F +YA+  +   I R   D   T
Sbjct: 5   LAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTITGEIKRHFRDHMWT 64

Query: 519 IRIPVHMRDKIHKVVRTARRMS-NKIKREPTPEEIAKKLAMPVEGVR----KVLKITKEP 573
           + +P  +++  ++V   ++ +S +   R PT  EIA+   +  E VR     +   T   
Sbjct: 65  LHVPRRVQELRNRVRSASQDLSLSGSGRPPTVAEIAEHADLSEEDVRTGQGALDSFTALS 124

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSP-LDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           +  E   GD+  S LGD +    A  P LD+ +    RE     LA+L  RE+ +L MRF
Sbjct: 125 LDAELTSGDDGYS-LGDTL---GAPDPALDTVVD---REAVRERLAALPEREQAILYMRF 177

Query: 633 GIGMNTDHTLEEVG-KQFCVTR 653
              M       E+G  Q  V+R
Sbjct: 178 FGDMTQSSIAAELGISQMHVSR 199


>gi|229492054|ref|ZP_04385868.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229321078|gb|EEN86885.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 259

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 110/229 (48%), Gaps = 12/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + +++E  L L   +A +Y  RG    DL+Q  ++GL+ A  +FD   G  F  +A+  +
Sbjct: 30  RTQIIELCLPLTRHIALRYRGRGQALDDLVQAASVGLVSAVNRFDLAKGKDFLAFAIPTM 89

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGV 563
              + +   D+   +R+P  +++    + +    ++  + REPT  E+AK+L + P E  
Sbjct: 90  MGEVRKHFRDRGWDVRVPRSLQENCLALNKARTALTQDLGREPTVPELAKELGVEPAE-- 147

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTP 622
             V +I     S        D + +GD     +A+   D+A+   + +ET    L +L  
Sbjct: 148 --VAEIVAAGDSYHA--ASLDAAAVGDGRSIADALGEFDAALDGIDNQETLRPALLALPE 203

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RE  ++  RF      + T  E+ ++  V++  + ++ A+++ KL+  S
Sbjct: 204 RERIIVIYRF----FGELTQAEIAEKIGVSQMHVSRLLAQSLAKLRASS 248


>gi|297199468|ref|ZP_06916865.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197712989|gb|EDY57023.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 282

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 54/257 (21%), Positives = 127/257 (49%), Gaps = 34/257 (13%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +R  + + D++Q G IGL+KA 
Sbjct: 38  FFQQLTVLDEGTPEYQYARNTLIEMNISLVRYAASRFRSRDPEEMEDIVQVGVIGLIKAI 97

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++++ ++   I R   D +  + +P  +++   ++ R    +S ++ R
Sbjct: 98  DRFELSREVEFTSFSIPYIVGEIKRFFRDTTWAVHVPRRLQEARVQLARATEELSTRLGR 157

Query: 546 EPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPI--GDEDTSHLGDFI--------- 592
            PT  E+A+ + +  + V   ++        SL+  I  GD+  + L DFI         
Sbjct: 158 TPTVAELAQLMNLEEKEVIEARLASNGYRSSSLDAAIGNGDDGETALADFIGTDDGALEL 217

Query: 593 -EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            ED +A++P+               +A+L  R  ++L  RF      + T  ++G++  +
Sbjct: 218 VEDFHALAPM---------------IAALDERSRKILHWRF----VEEATQAQIGERLGI 258

Query: 652 TRERIRQIEAKAIRKLK 668
           ++  + ++ ++ + +L+
Sbjct: 259 SQMHVSRLLSRTLAQLR 275


>gi|93007309|gb|ABE97157.1| SigF [Pasteuria ramosa]
          Length = 131

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 45/132 (34%), Positives = 76/132 (57%), Gaps = 17/132 (12%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E R ++   +KG+ +A   +  +V  N+RLV SV +++ NRG +  D+ Q G IGL+KA
Sbjct: 17  TEVRELIISSQKGDTKA---RDRLVSHNIRLVWSVVQRFLNRGYESDDIFQIGCIGLLKA 73

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF+     KFSTYA+  +   I R + D            D I KV R+ + M+++++
Sbjct: 74  VDKFNLEYEVKFSTYAVPMILGEIQRFLRD------------DGIVKVSRSLKEMAHRVR 121

Query: 545 REPTPEEIAKKL 556
           +  T +E++KKL
Sbjct: 122 K--TRDELSKKL 131


>gi|261366790|ref|ZP_05979673.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
 gi|282571621|gb|EFB77156.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
          Length = 232

 Score = 68.6 bits (166), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 99/205 (48%), Gaps = 11/205 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + + E +E NL LV + A ++  RG+++ +L   G +GL+KA + FD   G  FSTYA+ 
Sbjct: 9   LPRAEFIEKNLGLVHACAGRFKGRGIEYEELYAAGCLGLVKACDGFDTSRGVCFSTYAVP 68

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I +   D   T+++   +++   K+     R   K  +EP   ++A+ L    E 
Sbjct: 69  VILGEIKKLFRDGG-TVKVSRSLKELSLKINAERERCLKKTGQEPGVTQLAEILQTTPEQ 127

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLT 621
           +   ++ +   ISL TP  +ED     D         P+DS  ++ + R     V+  L+
Sbjct: 128 IALAIRASLPAISL-TPTDEEDGQREWDV--------PVDSPEESLSDRIGLAEVMEKLS 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG 646
           P + +++R+RF  G     T   +G
Sbjct: 179 PTDRQMIRLRFFGGRTQSETARVLG 203


>gi|182437344|ref|YP_001825063.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777954|ref|ZP_08237219.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465860|dbj|BAG20380.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658287|gb|EGE43133.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 112/238 (47%), Gaps = 11/238 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 61  GTPEHRRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQF 120

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L
Sbjct: 121 PTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTAEIAERL 180

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +  + V   ++  +     SLE     ++   L   ++      P  + ++   R+   
Sbjct: 181 KISEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH--RDLVR 235

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 236 HLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFARLRSANR 289


>gi|257440909|ref|ZP_05616664.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
 gi|257196689|gb|EEU94973.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
          Length = 222

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 117/233 (50%), Gaps = 28/233 (12%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           I +   +E NL LV + A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA+ 
Sbjct: 6   IRRSAFIEQNLGLVHACAGRFRGRGIEYDDLYGAGCMGLVKATDGFDEGRGVCFSTYAVP 65

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVE 561
            +   I + +  +  T+++   +++ +   V  AR    K+   EPT  ++A++L   VE
Sbjct: 66  VILGEI-KKLFREGGTVKVSRSLKE-LGLRVNAAREHHRKLCGTEPTLSQLAEELGESVE 123

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS-----AIQANLRETTTRV 616
            +   ++  +  +SL TP G+ +         D+    P++S     A +  L E    V
Sbjct: 124 NITLAIQAAQPALSL-TPEGENN---------DRQIDIPVESPEEELADKIGLAE----V 169

Query: 617 LASLTPREERVL-RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L SL P E+R+L R+RF      + T  E  K    T+ +I + E K +RK++
Sbjct: 170 LESL-PEEDRLLIRLRF----YANRTQSETAKVLHTTQVQISRRERKILRKMR 217


>gi|253682632|ref|ZP_04863429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
 gi|253562344|gb|EES91796.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
          Length = 242

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 101/208 (48%), Gaps = 12/208 (5%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           ++ ++F DL+  G IGLM A  KFD   G KFSTYA   ++ ++   I   S    I   
Sbjct: 33  SKYIEFEDLLGYGMIGLMDALNKFDESKGMKFSTYASIRIRGSMIDEIRKNSP---ISKG 89

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIG- 581
             DK++K       +  +   EP  ++IA++L M V  V ++         +SLE  I  
Sbjct: 90  AMDKLNKYNSAIETLQKRNLTEPNIKDIAEELEMTVNEVGEIENFINYISVVSLEDLIFS 149

Query: 582 -DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            D+D S +G  IED+ + +P          E   + L  L  +++ VL + +  GM    
Sbjct: 150 EDDDISLMGT-IEDEKSPNPEKDFEDQERLEYLAKALDMLNDKDKTVLSLYYYEGM---- 204

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+G    V+  R+ Q+ ++AI  L+
Sbjct: 205 TLKEIGIVLGVSESRVCQLHSRAIVHLR 232


>gi|332305676|ref|YP_004433527.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173005|gb|AEE22259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 242

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 97/204 (47%), Gaps = 22/204 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  FD   G  F T+A   ++ ++   I     T R        +HK
Sbjct: 44  DLIQAGMIGLLEASRNFDGSKGASFETFAGIRIRGSMLDEIRKGDWTPR-------SVHK 96

Query: 532 VVRTARRMSNKIKREPTPE----EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             R      NK++RE   +    +IAKKL + +E   ++L      ++    IG ED   
Sbjct: 97  NGRAITDAINKVERETGRDARDVDIAKKLEVSIEQYHQMLS----EVNAGKIIGMEDLGV 152

Query: 588 LGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D +   + K + +P +  +Q + ++     + +L  RE  VL + +   +N    L E
Sbjct: 153 TEDVVTTEQTKGSDTPFEDLLQGSFQKALAHAITTLPEREAIVLSLYYDEELN----LRE 208

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+   V+  R+ QI ++A+ KLK
Sbjct: 209 IGEVLDVSESRVSQIHSQAMLKLK 232


>gi|196035080|ref|ZP_03102486.1| RNA polymerase sigma-B factor [Bacillus cereus W]
 gi|195992144|gb|EDX56106.1| RNA polymerase sigma-B factor [Bacillus cereus W]
          Length = 257

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 113/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 30  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 90  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 149

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    +T  R   
Sbjct: 150 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEQTERRLVL 199

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 200 EDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 253


>gi|30266015|gb|AAN16085.1| SigB [Listeria welshimeri]
          Length = 259

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 113/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+ +L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQMILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|152965379|ref|YP_001361163.1| RNA polymerase sigma factor WhiG [Kineococcus radiotolerans
           SRS30216]
 gi|151359896|gb|ABS02899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 312

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 59/205 (28%), Positives = 98/205 (47%), Gaps = 17/205 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A EKFD     KF TYA+  ++ AI   I +      IP  +R K  +
Sbjct: 110 DLVSYGIFGLIDAIEKFDIERAIKFETYAISRIRGAI---IDELRSIDWIPRSVRSKARE 166

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--------EPISLETPIGDE 583
           V RT   +  ++ R PT  E+A ++ + +  +  +             E +S+    GD+
Sbjct: 167 VERTYAALEAELHRTPTEVEVAARMEIKLSELHHIFSQVSYVNVVALDELLSVSGEKGDK 226

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +  L D +ED  A  P+ S  +   +   +R +  L  RE+ V+ + +  G+    TL 
Sbjct: 227 LS--LVDTLEDTKAEDPVQSFEKEETKFLLSRAINQLPEREKIVVTLYYYEGL----TLA 280

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G+   VT  RI Q+  KA+ +L+
Sbjct: 281 EIGRVLGVTESRICQMHTKAVLQLR 305


>gi|308174363|ref|YP_003921068.1| RNA polymerase sporulation-specific sigma-K factor [Bacillus
           amyloliquefaciens DSM 7]
 gi|307607227|emb|CBI43598.1| RNA polymerase sporulation-specific sigma-K factor precursor
           (Sigma-27) (C-terminal fragment) [Bacillus
           amyloliquefaciens DSM 7]
          Length = 240

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 97/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+K  E +    G K +TYA   
Sbjct: 50  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK TK+ +SL  PIG +   +    I+  K+    +   IQ N+  E   + +  L 
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|221635447|ref|YP_002523323.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
 gi|221157679|gb|ACM06797.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
          Length = 262

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 95/191 (49%), Gaps = 13/191 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL++A ++FD   G KF TYA   ++ AI  ++  ++  I +P   R +  +
Sbjct: 55  DLIGYGTIGLLEALDRFDDTRGVKFETYAAMRIRGAILDAL--RTLDI-VPRSARSRARQ 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHL 588
           + +  R    +  R P+  E+A  L M    +++ +    +   L  P+    D DT  L
Sbjct: 112 IEQATREFFAEYGRMPSENELADHLGMTTTELQQAI---SDAACLFLPLQASEDPDTLTL 168

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + + D NA+ P + A + +L++     LA+L+ R+  ++ + +      D T+ E+ + 
Sbjct: 169 EEQLADPNALEPGEVAAEEDLKQRIAAALATLSERDRLIVSLYY----YEDLTMREISQL 224

Query: 649 FCVTRERIRQI 659
             ++  R+ QI
Sbjct: 225 LGISESRVSQI 235


>gi|284044899|ref|YP_003395239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949120|gb|ADB51864.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 273

 Score = 68.2 bits (165), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 104/216 (48%), Gaps = 11/216 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++   L L   +A +Y +      DL+Q  ++GL+KA ++F+      F++YA+  
Sbjct: 47  AREELITRFLPLARQLALRYYHGREPLDDLVQVASVGLVKAVDRFEVRRTTAFASYAVPV 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   + R   D    + +P  ++++   V RTA R+       PTP +IA++L + VE V
Sbjct: 107 MLGELRRYFRDNGWALHVPRGLQERALAVDRTADRLQVAQGAAPTPAQIAEQLKLTVEEV 166

Query: 564 RKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASL 620
            + +   +  + +SL+ P    D     D + D       DS ++    RE     L +L
Sbjct: 167 VEAMAAARATDTVSLDAPRPSADGER--DALVDSLGAD--DSRLELVEYREAIAGALDAL 222

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             RE  +LR+RF      D T  E+  +  V++ +I
Sbjct: 223 PVREREILRLRF----EEDRTQSEIAARLGVSQMQI 254


>gi|239626528|ref|ZP_04669559.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516674|gb|EEQ56540.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 209

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 94/229 (41%), Gaps = 57/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E N+RLV  V KKY        DL+  G IGL+KA   F+   G + +TYA   
Sbjct: 27  ARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGLIKAVNTFNADKGSRLATYAARC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  I   +                         R S K  +E                 
Sbjct: 87  VENEILMLL-------------------------RASKKFSKE----------------- 104

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLAS 619
                     +SL  PIG   D +T  L D IE  N    LD+ I + +++E      + 
Sbjct: 105 ----------VSLFEPIGVDKDGETVSLVDVIEMDNK-ETLDTMILKQDVKELYEAFESC 153

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LT  E+ VL MR+G+    +HT  E+     ++R  + +IE KAI K++
Sbjct: 154 LTETEKTVLGMRYGLYRGKEHTQREIAGNLGISRSYVSRIEKKAIEKIR 202


>gi|315444719|ref|YP_004077598.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263022|gb|ADT99763.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 275

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 55/208 (26%), Positives = 102/208 (49%), Gaps = 7/208 (3%)

Query: 428 RHIVSMVRKGE-CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           + + SM   G+  E    ++ ++   L L   +A ++  RG    DLIQ   IGL+K+ +
Sbjct: 30  KQLSSMAACGDRAERRRRRQHIITECLPLADHIACRFAGRGEPSDDLIQVARIGLVKSVD 89

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G +F  +A+  ++  + R   D + ++R+P  ++D   ++   A  +S ++KR 
Sbjct: 90  RYVPDKG-RFMAFAVPTIRGEVRRHFRDSTWSMRVPRKIQDTQLRMRHAAEELSQRLKRA 148

Query: 547 PTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  EIA++L +    V +         P+SL+ P GD +    G   E + A  P   +
Sbjct: 149 PTDREIARELGVDDGEVSRCHSAHWAYRPVSLDAPRGDAEQECAG-IGELRGADDPGFDS 207

Query: 605 IQANLRETTTRVLASLTPREERVLRMRF 632
           ++  +    + V+A L PR   +L MRF
Sbjct: 208 VEDLI--VLSGVIAELDPRRRAILGMRF 233


>gi|154686834|ref|YP_001421995.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens FZB42]
 gi|154352685|gb|ABS74764.1| SpoIIIC [Bacillus amyloliquefaciens FZB42]
          Length = 240

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 97/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+K  E +    G K +TYA   
Sbjct: 50  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK TK+ +SL  PIG +   +    I+  K+    +   IQ N+  E   + +  L 
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|317403792|gb|EFV84272.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans C54]
          Length = 253

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 52/215 (24%), Positives = 98/215 (45%), Gaps = 22/215 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A  ++      +F TYA   ++ A+   +  Q     +P  +R K  K
Sbjct: 34  DLIQAGMIGLLDAVRRYQETADAQFETYATTRIRGAMLDELRGQDW---LPRSVRAKARK 90

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK------------ITKEPISLETP 579
           + +  + +  ++ R PT  EIA+++ +P+   + +L                EP   +T 
Sbjct: 91  IEQAIQSLEQRLMRAPTEAEIAQQMEIPLNEYQTLLHDAQGVQIVHYEDFATEP---DTG 147

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
            G   +           + +PLDS +  + R+     + SL  RE+ +L + +  G+N  
Sbjct: 148 SGSGQSDWTATLNHGAASGNPLDSLLAGDFRQALIHAIDSLPDREKLLLSLCYEQGLN-- 205

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L+E+G    VT  R+ Q+ ++A  +++   R +
Sbjct: 206 --LKEIGAIMNVTEARVCQLRSQATARIRAKLREQ 238


>gi|311897124|dbj|BAJ29532.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 301

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 98/221 (44%), Gaps = 10/221 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E +  +  ++E N+ LV   A ++ +R     D++Q G IGL+ A ++FD   G +F
Sbjct: 70  GTPERARVRSALIEINIPLVRYAAIRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQF 129

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  +   I R   D   T+ +P  +++   +V      ++    R P   EIA  L
Sbjct: 130 PTYALPTILGEIKRYFRDNVRTMHVPRRLQELWVQVSGAMEELTVAHGRAPKVPEIAANL 189

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETT 613
            +P E VR  L   +     SLE     E    L D +  +      DSA+     R+  
Sbjct: 190 RIPEEDVRACLDAGRAYNAASLEAAQEHEGGLALLDRLGYE------DSALTDVEHRDMV 243

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L  L  RE R++ +RF   +       E+G  Q  V+R
Sbjct: 244 RHLLVQLPERERRIIMLRFFANLTQSQISTELGMSQMHVSR 284


>gi|238920292|ref|YP_002933807.1| flagellar biosynthesis sigma factor [Edwardsiella ictaluri 93-146]
 gi|238869861|gb|ACR69572.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           ictaluri 93-146]
          Length = 240

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 107/232 (46%), Gaps = 23/232 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A + + E +   +RL  SV         +  DL+Q G IGL+ A E++D   G  F+TYA
Sbjct: 21  APLVRHEALRLQVRLPASV---------ELDDLLQAGGIGLLHAVERYDAMQGTAFTTYA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  ++ A+   +  +     +P  +R     V    +R   ++ R P   EIA+++ + +
Sbjct: 72  IQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRVPGDSEIAQEMGISL 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLRETTTRV 616
              +++L  T           DE     GD     +E     +PL   ++++LR      
Sbjct: 129 AEYQQILLDTNTSQLFSY---DEWREEHGDSAEPVVEQSEESNPLHQLLESDLRGRVIAA 185

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L  RE+ VL + +   +N    L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 186 IEALPEREKLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|261420836|ref|YP_003254518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC61]
 gi|319768505|ref|YP_004134006.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC52]
 gi|261377293|gb|ACX80036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC61]
 gi|317113371|gb|ADU95863.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC52]
          Length = 256

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 113/219 (51%), Gaps = 14/219 (6%)

Query: 455 LVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           L+ + AKK       F  DL Q G +  ++  + +D   G  F +YAM  +   +   + 
Sbjct: 39  LIAAAAKKMARSRPDFYEDLFQIGRLSFLRLLDHYDPKQGTSFESYAMKSLIGYMKNYLR 98

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITK 571
           D++  I++P  +++K  KV +    ++ K++R PT +EIA  L + VE   ++L  +   
Sbjct: 99  DKAWYIQVPRKVKEKGSKVQQAIDELTVKLERSPTIDEIAGHLGLSVEETIEILAGRDHY 158

Query: 572 EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           + +SL+ P+  G++D + +G+F+ D+   + ++S I+   R    + +  L+ +E+ V+ 
Sbjct: 159 QAVSLDAPVQDGEKDATTIGEFVADE--ANEIESLIE---RMDLEQAIGKLSEQEQIVID 213

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             F  G       E +G    V++  I +I+ +AI KLK
Sbjct: 214 AIFRRGETQRSLAERLG----VSQMTISRIQKRAIAKLK 248


>gi|328554314|gb|AEB24806.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens TA208]
          Length = 241

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 97/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+K  E +    G K +TYA   
Sbjct: 50  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLT 621
              LK TK+ +SL  PIG +   +    I+  K+    +   IQ N+  E   + +  L 
Sbjct: 120 --ALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 178 DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|23099454|ref|NP_692920.1| sporulation sigma factor SigK [Oceanobacillus iheyensis HTE831]
 gi|22777683|dbj|BAC13955.1| RNA polymerase sigma 28 (sigam K) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 234

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 97/231 (41%), Gaps = 58/231 (25%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +A+ +++E NLRLV  + KK+ N G    DLI  G IGL+K  E F    G K +TYA  
Sbjct: 49  VARNKLIEHNLRLVAHIVKKFENTGEDMEDLISIGTIGLIKGVESFSTDKGTKLATYA-- 106

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                  R I ++     I +H+R                                    
Sbjct: 107 ------ARCIENE-----ILMHLR------------------------------------ 119

Query: 563 VRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLA 618
               LK  K+ +SL  PIG +   +   L D +E +N    +   IQ N+      +  +
Sbjct: 120 ---ALKKVKKDVSLHDPIGQDKEGNEISLIDILEAEN--ENVIEYIQLNMEISKMQKYFS 174

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  RE  V+  R+G+    + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 175 VLDKREREVIVYRYGLNDREEMTQREIAKKLNISRSYVSRIEKRALMKVFH 225


>gi|302878264|ref|YP_003846828.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
 gi|302581053|gb|ADL55064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
          Length = 236

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 53/203 (26%), Positives = 96/203 (47%), Gaps = 10/203 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  D+IQ G +GL+ AA ++D   G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VQIDDIIQAGMMGLLDAATRYDEIHGAQFETYATQRIRGAMLDELRSADW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDT 585
            + ++ +   R+  K+ R P   EIAK+L + +   +++L+ ++  + I  E    DED 
Sbjct: 93  DMRRIEQGVSRLQQKLGRAPNETEIAKELEVSLVEYQQMLQESRGAQLIYYED-FQDEDH 151

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               +  E  N   PL        +    R +  L  RE    R+   +    +  L EV
Sbjct: 152 EDFFERFEFANDTDPLALLQDDRFKSELARAIDVLPERE----RLLMALIYEQELNLREV 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+ F V+  RI Q+ ++A+ +L+
Sbjct: 208 GEVFGVSESRISQLHSQAVLRLR 230


>gi|52144331|ref|YP_082499.1| RNA polymerase sigma factor SigB [Bacillus cereus E33L]
 gi|51977800|gb|AAU19350.1| RNA polymerase sigma-B factor [Bacillus cereus E33L]
          Length = 258

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 113/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 31  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 91  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    +T  R   
Sbjct: 151 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEQTERRLVL 200

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 201 EDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 254


>gi|30261116|ref|NP_843493.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Ames]
 gi|47526271|ref|YP_017620.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|65318395|ref|ZP_00391354.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165871654|ref|ZP_02216299.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167635453|ref|ZP_02393766.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|167638886|ref|ZP_02397160.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|170687593|ref|ZP_02878809.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|170707965|ref|ZP_02898414.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|177653505|ref|ZP_02935679.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190566700|ref|ZP_03019617.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196037492|ref|ZP_03104803.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227816152|ref|YP_002816161.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229604478|ref|YP_002865547.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
 gi|254682827|ref|ZP_05146688.1| RNA polymerase sigma factor SigB [Bacillus anthracis str.
           CNEVA-9066]
 gi|254725613|ref|ZP_05187395.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. A1055]
 gi|254734239|ref|ZP_05191952.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Western
           North America USA6153]
 gi|254740112|ref|ZP_05197804.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Kruger B]
 gi|254753453|ref|ZP_05205489.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Vollum]
 gi|254758550|ref|ZP_05210577.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Australia
           94]
 gi|17369088|sp|Q9K5J6|RPSB_BACAN RecName: Full=RNA polymerase sigma-B factor
 gi|8670945|emb|CAB95034.1| sigB [Bacillus anthracis]
 gi|30254730|gb|AAP24979.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Ames]
 gi|47501419|gb|AAT30095.1| RNA polymerase sigma-B factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164712555|gb|EDR18087.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167513016|gb|EDR88388.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|167529071|gb|EDR91825.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|170127125|gb|EDS96003.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|170668406|gb|EDT19153.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|172081309|gb|EDT66383.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190562252|gb|EDV16220.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196031734|gb|EDX70330.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227003869|gb|ACP13612.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229268886|gb|ACQ50523.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
          Length = 257

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 113/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 30  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 90  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 149

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    +T  R   
Sbjct: 150 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEQTERRLVL 199

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 200 KDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 253


>gi|116872297|ref|YP_849078.1| RNA polymerase sigma factor SigB [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|55535652|gb|AAV52891.1| SigB [Listeria welshimeri]
 gi|116741175|emb|CAK20295.1| RNA polymerase sigma-37 (sigma-B) [Listeria welshimeri serovar 6b
           str. SLCC5334]
          Length = 259

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 113/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+ +L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQMILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|23098085|ref|NP_691551.1| RNA polymerase sigma factor SigB [Oceanobacillus iheyensis HTE831]
 gi|22776310|dbj|BAC12586.1| RNA polymerase general stress sigma factor (sigma B)
           [Oceanobacillus iheyensis HTE831]
          Length = 263

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 114/222 (51%), Gaps = 10/222 (4%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV S+A+KY+       DL+Q G IGL+ A  ++D   G  F ++A+  +   I R I D
Sbjct: 42  LVGSIARKYSKNSAIHEDLVQVGMIGLLAAVRRYDPTYGKSFESFAIPTIIGEIKRFIRD 101

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKE 572
           ++ ++ +P  +++   K+ +    ++   ++ PT  EIAK +    E V + +++  + +
Sbjct: 102 KTWSVHVPRRIKELGPKIRKGVDELTTDNQKSPTVAEIAKYIGTSEEEVLETMEMGQSYK 161

Query: 573 PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            +S++  I  D D S +       N+    D+  Q  + E   ++L  L+ RE+++L   
Sbjct: 162 ALSVDRKIEADSDGSTVAILDLVGNSEDGYDNVEQRMMLE---KILPILSEREQQILECT 218

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +   M+     +E G+   +++  + +++ +++RKL+   +S
Sbjct: 219 YFKNMSQ----KETGELLGISQMHVSRLQRRSLRKLREAIQS 256


>gi|328958265|ref|YP_004375651.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
 gi|328674589|gb|AEB30635.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
          Length = 238

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/205 (27%), Positives = 98/205 (47%), Gaps = 11/205 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGLM A EKFD      F  YA   +K +I   I   +   R  +    K+++
Sbjct: 36  DLYNIGVIGLMDALEKFDKSKKVPFEGYAYIRIKGSIIDEIRKTAPVSRTRM---GKLNE 92

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS--H 587
             R   ++   + R PT +EI ++L +  + + K+ +       ISLE  +  +D +   
Sbjct: 93  YYRAKEKLEATLMRTPTEKEICEELKIDEKALTKIHETVHNLASISLEKVMFSDDGNSIE 152

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L DF+EDK+     D+ +    ++  T+ ++ L  RE+ +L + +      + +L+E+  
Sbjct: 153 LIDFLEDKHETGSEDTLLDKERQQLLTKNVSKLDKREQTILNLYYV----EELSLKEIAY 208

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSR 672
            F ++  R+ QI  K I KLK   R
Sbjct: 209 IFDISVPRVSQIHGKMILKLKELMR 233


>gi|150390456|ref|YP_001320505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
 gi|149950318|gb|ABR48846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
          Length = 243

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 109/230 (47%), Gaps = 15/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKK-YTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K E++E  + LV  +A + YT+ G  + + DL+  G  GL+ A EKFD     KF TYA
Sbjct: 18  TKNELIEKYIALVKIIAGRLYTSYGSNVDYDDLVSYGIFGLIDAIEKFDINKNVKFETYA 77

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ AI   + +      +P  +R K  K+     +  N++ R     E+A++L M +
Sbjct: 78  QIRIRGAIIDQLRNLDW---VPRSIRQKSKKIEDAYAKAENRLGRSVLDFEVAQELEMSI 134

Query: 561 EGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               + L+       +SLE  +   DT H    I D+N + P         R      + 
Sbjct: 135 GDFHRTLQQINSFNIVSLEERLS--DTHHNQIPIGDENDL-PEQIICNKEERLLLRSSIE 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SL+ RE+ V+ + +  G     T +E+G+   V+  R+ Q+ +KAI +LK
Sbjct: 192 SLSEREKTVVTLYYYEGF----TYKEIGQVLDVSESRVSQLHSKAIVRLK 237


>gi|312621597|ref|YP_004023210.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202064|gb|ADQ45391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 246

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 119/230 (51%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 19  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K AI   + +Q     +P  +R K  ++ R    +  K  + PT +E+AK++ + VE
Sbjct: 79  TRIKGAIIDCVRNQDF---LPRSIRQKAKEIERAYIEI-EKEGKTPTNQEVAKRIGISVE 134

Query: 562 GVRKVL-KITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLA 618
            ++K+  +I+    ISLE+ +     S +G     ++ VS  +  I+   LR+   + + 
Sbjct: 135 ELQKLQDRISSGMIISLESFLEQNYESKIGGL---EDFVSQPEHFIENEELRKVLRQQID 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   E  V+ + +      D +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 192 NLMENERMVIVLYY----YEDLSIKEIAKVLGVSESRVSQLHTRALLKLR 237


>gi|261419446|ref|YP_003253128.1| RNA polymerase sigma factor SigD [Geobacillus sp. Y412MC61]
 gi|319766261|ref|YP_004131762.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
 gi|261375903|gb|ACX78646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC61]
 gi|317111127|gb|ADU93619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
          Length = 251

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 15/201 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  MRDK  K
Sbjct: 55  ELVSLGLVGLYDALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSMRDKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG----DEDTSH 587
           +     R+  +  R  T +EIA +L M  E V+     T    S   P+G    DED   
Sbjct: 112 IEGAIERLEQRHMRSVTAKEIAAELGMTEEEVQAAASETF--FSHWLPLGQTTVDEDEGL 169

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D  A  P +  ++  + E     +  L  +E+ V+ + +      + T  E+G 
Sbjct: 170 LS--VRDDRAPLPEEQIVKQEMIEKLAEAIGQLNEKEQLVISLFY----KEELTFTEIGS 223

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI QI AKA+ KL+
Sbjct: 224 LLHLSTSRISQIHAKALWKLR 244


>gi|194017684|ref|ZP_03056294.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
 gi|194010584|gb|EDW20156.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
          Length = 289

 Score = 68.2 bits (165), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 98/237 (41%), Gaps = 72/237 (30%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 98  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATYA--- 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 155 -----ARCIENE-----ILMHLR------------------------------------- 167

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----------SAIQANLR-ET 612
              LK TK+ +SL  PIG +         ++ N +S +D            IQ N+  E 
Sbjct: 168 --ALKKTKKDVSLHDPIGQD---------KEGNEISLIDVLKSESEDVIDTIQLNMELEK 216

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +  L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 217 VKEYIDILDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 273


>gi|294638491|ref|ZP_06716692.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|291088426|gb|EFE20987.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
          Length = 205

 Score = 67.8 bits (164), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 49/80 (61%), Gaps = 2/80 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  
Sbjct: 10  TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEA 69

Query: 177 GTTLLREIIDLEACIGPESK 196
           G   L ++I   A I P ++
Sbjct: 70  GEARLSDLIT--AFIDPNAE 87


>gi|112981046|gb|ABI29247.1| DNA-dependent RNA polymerase sigma factor D subunit [Comamonas
           denitrificans]
          Length = 268

 Score = 67.8 bits (164), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 50/88 (56%), Gaps = 11/88 (12%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   MM ++  SP T   ++    ++ +G  +
Sbjct: 1   VRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISTSPATIAEVLKMAADIREGKVI 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSY 208
           +  ++D           GF +  E   Y
Sbjct: 61  ISTVVD-----------GFVNANENDDY 77


>gi|258404724|ref|YP_003197466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfohalobium
           retbaense DSM 5692]
 gi|257796951|gb|ACV67888.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfohalobium
           retbaense DSM 5692]
          Length = 241

 Score = 67.8 bits (164), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 93/192 (48%), Gaps = 10/192 (5%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ AA +FD   G  F T+A   ++ AI   +       R    MRDK  ++  T R +
Sbjct: 51  GLINAANRFDPNQGVLFKTFAEHRIRGAIFDEVRRLDWFSR---SMRDKHQRLAETIREL 107

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSH-LGDFIEDKN 596
              ++R P   E+A  + M + G  ++L        +SL+  + D DT     D +ED +
Sbjct: 108 EISLERAPNENEVAAAMDMDLTGYHRMLGEVSHLGCMSLQEVLSDSDTGQSFLDVLEDTD 167

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            + P ++  QA L      +L  L+ +E++V+ + +  G++     +E+     +T  RI
Sbjct: 168 GMPPEEAVEQAELTREVAGMLHELSEKEQQVIALLYHEGLSQ----KEIADVLSLTEGRI 223

Query: 657 RQIEAKAIRKLK 668
            Q+ ++A+ KL+
Sbjct: 224 SQLHSQALAKLR 235


>gi|161898855|gb|ABX80417.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 67.8 bits (164), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 55/232 (23%), Positives = 112/232 (48%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-------QANLRETTTRV 616
            + +++ K   +L      E  S       D + ++ LD A        + N R    +V
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADS-------DGSTITLLDVAGGTDDGFERVNQRMLLEKV 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 190 LPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 237


>gi|158319069|ref|YP_001511576.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158139268|gb|ABW17580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 270

 Score = 67.8 bits (164), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 116/230 (50%), Gaps = 16/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++  +L +   ++KK+ N+G+++ D+ Q  ++GL+ A E++D   G++FS++A   +
Sbjct: 43  RNELINRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIYAIERYDVTKGFEFSSFATPTI 102

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  +IR+P  +++   KV  +   +   ++R PT ++IA+ L    E V 
Sbjct: 103 IGEIKKYFRDKGWSIRVPRRIQELSKKVNVSKNTLQQTLQRTPTVKDIAEYLNCTEEEVI 162

Query: 565 KVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLA 618
           + ++ ++   P SL+      GD+    L D I        LD        ++   + + 
Sbjct: 163 EAMEASQVYTPKSLDLIYDNDGDDKDIQLLDLI------GELDKRFDDIENKDFFQKAID 216

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L   E++VL+ RF      + T  +V ++  V++  + ++E + I K K
Sbjct: 217 KLNEVEKKVLKDRFF----NNKTQMKVSEELNVSQMTVSRMEKRIIEKFK 262


>gi|295695806|ref|YP_003589044.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411408|gb|ADG05900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 238

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 98/243 (40%), Gaps = 72/243 (29%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +TYA   
Sbjct: 50  ARNLLIEHNLRLVAHIVKKFENTGEDTEDLISIGTIGLIKAIESFQPHKGTKLATYAARC 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +H+R                                     
Sbjct: 110 IENEIL-------------MHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----------SAIQANL-RET 612
              LK T++ +SL  PIG +         ++ N V+ LD            ++  L +  
Sbjct: 120 --ALKKTRKDVSLHDPIGTD---------KEGNEVTLLDILSSDADDVVDIVEMKLEKHQ 168

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               L  L  RE+ V+R RFG+    + T  E+ ++  ++R  + +IE +A+ KL H  R
Sbjct: 169 IYEKLQELDEREQEVIRGRFGLQNGEEKTQREIAEELGISRSYVSRIEKRALMKLLHDLR 228

Query: 673 SKK 675
            ++
Sbjct: 229 PRR 231


>gi|23099037|ref|NP_692503.1| RNA polymerase sigma factor SigD [Oceanobacillus iheyensis HTE831]
 gi|22777265|dbj|BAC13538.1| RNA polymerase sigma-D factor [Oceanobacillus iheyensis HTE831]
          Length = 258

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 56/197 (28%), Positives = 92/197 (46%), Gaps = 12/197 (6%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL  A +KFD     KF TYA + +K +I   +  +     +P  +R+K  KV +  
Sbjct: 60  GILGLYDALKKFDPSRDLKFDTYASFRIKGSIMDGLRKEDW---LPRSIREKTKKVEQAM 116

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISL-ETPIGDEDT--SHLGDF 591
                  +RE    EIA    M  E V   +K  +    +S+ E P G+ D     +G  
Sbjct: 117 EEYEQSYQREANSSEIANLTGMTTEEVETTMKDALFSNILSIEEKPKGNSDQLKEGIGYS 176

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D+ A+ P +  +   L+E   + +  L  +E+ V+ + +    N + T  E+G+   +
Sbjct: 177 ISDERAILPENHIVNEELKEELIQGIKLLNEKEQLVVSLFY----NEELTFTEIGQVVGL 232

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI QI  ++I KLK
Sbjct: 233 TTSRISQIHKRSIFKLK 249


>gi|56964009|ref|YP_175740.1| RNA polymerase sigma factor SigD [Bacillus clausii KSM-K16]
 gi|56910252|dbj|BAD64779.1| DNA-directed RNA polymerase sigma-28 factor sigma-D [Bacillus
           clausii KSM-K16]
          Length = 254

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 98/198 (49%), Gaps = 20/198 (10%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A  KFD     KF TYA + ++ AI   +  +    R+P  +RDK+ K+ +   ++
Sbjct: 58  GLLDAIAKFDSKRALKFDTYASFRIRGAIIDGLRKED---RLPRTIRDKVKKLEQITEQL 114

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI------- 592
             +  R   P E+A  + +P    +++  + +E  +  T +  +D  H+ D +       
Sbjct: 115 EQEKGRSVLPGEVAAAMGLPE---KEIEALKREQFASHT-LSLDDVMHMNDHLDPSAVAY 170

Query: 593 --EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             ED+ A+ P D  ++ + R+    ++  L   E+ V+++ +      + +L E+G+   
Sbjct: 171 QFEDEQAIMPDDKLVEEDTRKELAEMIKELGRNEQLVIQLSY----YEELSLTEIGRILN 226

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++  RI QI A+AI KL+
Sbjct: 227 LSTSRISQIHARAIAKLR 244


>gi|15895412|ref|NP_348761.1| sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|15025135|gb|AAK80101.1|AE007715_6 Sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|325509558|gb|ADZ21194.1| Sigma factor of SigD/WhiG family [Clostridium acetobutylicum EA
           2018]
          Length = 241

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 60/211 (28%), Positives = 101/211 (47%), Gaps = 18/211 (8%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           ++ +++ DL+  G IGLM A +KFD   G KFSTY+   +K A+   +   S    I   
Sbjct: 33  SKYIEYEDLVGYGMIGLMDALKKFDQSKGMKFSTYSSIRIKGAMIDELRKNSP---ISKG 89

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP------VEGVRKVLKITKEPISLET 578
             DK+++      R+  ++ REPT  EIA  L +       +EG    + +    +SLE 
Sbjct: 90  AMDKLNRYNLVVERLEKELSREPTELEIASGLGVGRKEVGEIEGYINYISV----VSLED 145

Query: 579 PIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            I  ED    L   IED+ + SP  +  +    E   + +  L  ++  VL + +  G+ 
Sbjct: 146 LIFSEDDDMPLIGTIEDEKSPSPEKALEEKEEIEYLAKGIELLNEKDRMVLSLYYYEGL- 204

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL+++G    V+  R+ Q+  +AI  L+
Sbjct: 205 ---TLKKIGNILNVSESRVCQLHTRAIMHLR 232


>gi|108804234|ref|YP_644171.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765477|gb|ABG04359.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 264

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 65/219 (29%), Positives = 110/219 (50%), Gaps = 19/219 (8%)

Query: 455 LVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  VA +   R   G++  DL+  G +GL+KA E FD   G KF TYA+  ++ AI   
Sbjct: 54  LVKYVAGRMAARIPGGVEQEDLVSWGVVGLLKAVETFDPARGAKFETYAISKIRWAILDE 113

Query: 512 I--ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           +  AD      +P  +R ++ +  R A  ++  ++R PT  EIA+++ + +   R+ L+ 
Sbjct: 114 LRKADP-----LPRRVRRRVRETQRAASALTQTLRRAPTEAEIAREVGVGLAEHRETLER 168

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
                +      +E  S +G+   + +   P  +A  A LRE     L SL+ RE  V+ 
Sbjct: 169 YHRARTWSL---EELLSGMGEGGRELSVSDP--TAETAELRERLAEALESLSERERVVIT 223

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  G+    TL E+G+   +T  RI QI  +A+++L+
Sbjct: 224 FYYYQGL----TLREIGRALNLTEGRISQILRRALQRLR 258


>gi|49183950|ref|YP_027202.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Sterne]
 gi|49177877|gb|AAT53253.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Sterne]
          Length = 258

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 113/238 (47%), Gaps = 24/238 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  
Sbjct: 31  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V
Sbjct: 91  IVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA--IQANLRETTTR--- 615
            +++              +   S L D +E   D ++V+ ++S   ++    +T  R   
Sbjct: 151 LEIMDAKN----------NYRVSSLDDVVENASDGSSVARIESVGEVEQGYEQTERRLVL 200

Query: 616 --VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +   L   E+ V+   F   +N   T E +G    +++  + +I+ +AI KLK  +
Sbjct: 201 KDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRIKRQAISKLKQAA 254


>gi|42528183|ref|NP_973281.1| RNA polymerase sigma factor WhiG [Treponema denticola ATCC 35405]
 gi|41819453|gb|AAS13200.1| RNA polymerase sigma-27 factor [Treponema denticola ATCC 35405]
 gi|325474612|gb|EGC77798.1| RNA polymerase sigma-27 factor [Treponema denticola F0402]
          Length = 262

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 101/208 (48%), Gaps = 14/208 (6%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHM 525
            ++F DL+  G  GL+ A EK+D     KF+TYA+  ++ AI     D+  +I  +P  +
Sbjct: 52  NVEFDDLVGYGVFGLLDAIEKYDLDKNVKFNTYAVNRIRGAIF----DELRSIDWVPRSV 107

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKITKEPI----SLETPI 580
           R K  ++  T   +  ++ R  + EEIA  + + +E     +LKI+   +     L    
Sbjct: 108 RQKSREIEETIADLEARLGRSASNEEIAYAMGLDIEEYNSLLLKISATSVISLTDLRFSN 167

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            D +   +GD IE  ++++P     + +++      +  L  RE++VL M +      D 
Sbjct: 168 DDSEEFSVGDIIEAPSSLNPDVIVEREDIKRVIVEAIKELPDREKKVLIMYY----YEDM 223

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+G+   VT  R+ QI   A  KL+
Sbjct: 224 TLREIGEVLHVTESRVSQIHTSANIKLR 251


>gi|311069177|ref|YP_003974100.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
 gi|310869694|gb|ADP33169.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
          Length = 242

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 67/259 (25%), Positives = 109/259 (42%), Gaps = 75/259 (28%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE +  + ++ KG+  A   +  ++E NLRLV  + KK+ N G    DLI  G IGL
Sbjct: 32  LSGSEEKKYLELMAKGDEHA---RNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K  E +    G K +TYA         R I ++     I +H+R               
Sbjct: 89  IKGIESYSAGKGTKLATYA--------ARCIENE-----ILMHLR--------------- 120

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                                    LK TK+ +SL  PIG +         ++ N +S +
Sbjct: 121 ------------------------ALKKTKKDVSLHDPIGQD---------KEGNEISLI 147

Query: 602 D----------SAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           D            IQ N+  E   + +  L  RE+ V+  RFG+ +  + T  E+ K+  
Sbjct: 148 DVLKSESEDVIDTIQLNMELEKVKKYIDILDDREKEVIVGRFGLDLKKEKTQREIAKELG 207

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++R  + +IE +A+ K+ H
Sbjct: 208 ISRSYVSRIEKRALMKMFH 226


>gi|56752504|ref|YP_173205.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|81300319|ref|YP_400527.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|56687463|dbj|BAD80685.1| group3 RNA polymerase sigma factor SigF1 [Synechococcus elongatus
           PCC 6301]
 gi|81169200|gb|ABB57540.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 259

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 44/155 (28%), Positives = 85/155 (54%), Gaps = 5/155 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +VE NL LV   A ++  R  + F +L+Q G++GL+ A ++F+   G  FS++A+ +
Sbjct: 29  RNRLVELNLGLVRQEAYRWVQRCPESFEELVQIGSLGLIAAIDRFELERGKAFSSFAVPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+S T+R+P    +   ++     ++  ++ R PT EE+ + L +  E  
Sbjct: 89  IRGEIQHYLRDRSGTVRVPRRWAELHQQIDPLRHKLQRELGRSPTEEELRQGLGLDAEEW 148

Query: 564 RKVLKI--TKEPISLETPI--GDEDTSHLGDFIED 594
           ++V  I   +  +SL+ P+   +E  + LGD I D
Sbjct: 149 QEVRLIGRNRTTLSLDQPLYADEEQVTSLGDSIAD 183


>gi|268610009|ref|ZP_06143736.1| sporulation sigma factor SigK [Ruminococcus flavefaciens FD-1]
          Length = 227

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 106/237 (44%), Gaps = 52/237 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +  +  C    A+K+++E NLRLV  + KKYT+   +  +LI  G IGL+KA   FD   
Sbjct: 34  LFERSSCGDEYARKKLIEHNLRLVAHIVKKYTSSFDEQDELISIGTIGLIKAVSSFDHTK 93

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G KF+TYA        +R I ++     I +H R                     + ++ 
Sbjct: 94  GSKFATYA--------SRCIENE-----ILMHFR---------------------SAKKS 119

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQANLRE 611
           A  L M             EP+  +    D +   + D ++D + ++  +D  I++ +  
Sbjct: 120 ASDLYM------------NEPVETDK---DGNALTIMDLLDDGSDINEQVDLLIRSKM-- 162

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +   L PRE  ++  R+G+   + HT  E  ++  ++R  + +IE KA+ KLK
Sbjct: 163 LYRFIEQCLDPRETDIMIYRYGLYGTSPHTQSETAEKLGISRSYVSRIEKKAVGKLK 219


>gi|254819525|ref|ZP_05224526.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 262

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 68/261 (26%), Positives = 121/261 (46%), Gaps = 44/261 (16%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + S V     E    + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELAS-VAADSMELQRQRDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKR 545
           +FD   G  F ++A+  +   + R   D S ++++P  +++ +H  + TA   +S ++ R
Sbjct: 82  RFDVDAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKE-LHLRLGTATADLSQRLGR 140

Query: 546 EPTPEEIAKKLAM----PVEGVRKVLKITKEPISLET--------------PIGDEDTSH 587
            PT  E+A +L M     VEG+  V   +   +S+++               +GD DT  
Sbjct: 141 APTATELAAELEMDREEVVEGL--VAGSSYNTLSIDSGGGGEEEEARAIADTLGDVDTGL 198

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D IED+ ++ PL               L +L  RE  VL +RF   M      E VG 
Sbjct: 199 --DRIEDQESLRPL---------------LEALPERERTVLVLRFFESMTQTQIAERVG- 240

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +++  + ++ AK++ +L+
Sbjct: 241 ---ISQMHVSRLLAKSLTRLR 258


>gi|30266017|gb|AAN16086.1| SigB [Listeria welshimeri]
          Length = 259

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 113/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+ +L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 206 LDEREQMILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 250


>gi|78486471|ref|YP_392396.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
 gi|78364757|gb|ABB42722.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
          Length = 283

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 125/247 (50%), Gaps = 43/247 (17%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA ++F+     +  T+A+ W
Sbjct: 51  AARQLILSSLRYVVPIARSYNGYGLPLNDLIQEGNIGLMKAVKRFNPAEKVRLMTFAVHW 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA-----RRMSNKIKR-EPTPEEIAKKLA 557
           V+  I   +               K  ++V+TA     R++  K++  + + E +  K A
Sbjct: 111 VRAEINEYVI--------------KNWRIVKTATTKAQRKLFFKLRSTKKSLEWLGDKDA 156

Query: 558 MPVEGVRKVLKIT-KEPISLETPIGDEDTS-HLGDFIEDKNAVS-------PLDSAIQ-A 607
              + + K L +T K+ + +ET +  +D S  L    E+ N+ +        LD   Q A
Sbjct: 157 ---DTIAKELGVTRKDVLEMETRLYGQDMSVDLSPDEEEANSKTYPVLVSQELDPETQLA 213

Query: 608 NLRET------TTRVLASLTPREERVLRMRFGIGMNTDHT-LEEVGKQFCVTRERIRQIE 660
           N  ++        + L  L  R   +L+ R+   ++ D T L+ + +++ V+ ERIRQIE
Sbjct: 214 NDSQSDHELGKMHQALKQLDQRSRDILQQRW---LSEDKTGLKALSEKYGVSMERIRQIE 270

Query: 661 AKAIRKL 667
            +AI+ L
Sbjct: 271 QQAIKTL 277


>gi|16078710|ref|NP_389529.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309525|ref|ZP_03591372.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313849|ref|ZP_03595654.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318772|ref|ZP_03600066.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323044|ref|ZP_03604338.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|296330862|ref|ZP_06873337.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674380|ref|YP_003866052.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315414|ref|YP_004207701.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
 gi|1350863|sp|P10726|RPSD_BACSU RecName: Full=RNA polymerase sigma-D factor; AltName: Full=Sigma-28
 gi|289304|gb|AAA61470.1| sigma factor 28 [Bacillus subtilis]
 gi|2634019|emb|CAB13520.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291484202|dbj|BAI85277.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151867|gb|EFG92741.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412624|gb|ADM37743.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021688|gb|ADV96674.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
          Length = 254

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 97/201 (48%), Gaps = 10/201 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 54  DLMSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS-HL 588
           V     ++  +  R  +P EIA++L M V+ V   +        +S++  + D+D   ++
Sbjct: 111 VEAAIEKLEQRYLRNVSPAEIAEELGMTVQDVVSTMNEGFFANLLSIDEKLHDQDDGENI 170

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D   V P +  ++  L       +  L+ +E+ V+ + +      + TL E+G+ 
Sbjct: 171 QVMIRDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFY----KEELTLTEIGQV 226

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  RI QI +KA+ KLK+
Sbjct: 227 LNLSTSRISQIHSKALFKLKN 247


>gi|317129180|ref|YP_004095462.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
 gi|315474128|gb|ADU30731.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
          Length = 254

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 109/246 (44%), Gaps = 13/246 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLV-ISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E    +A   +V+A L LV   V +   N  R +Q  DL   G +GL  A EKFD  
Sbjct: 16  RWSEDRDEVACDRLVQAYLPLVDYHVQRIGANLPRNVQLDDLRSNGMLGLYDALEKFDEK 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +        +P  +R+K  K+ +   ++  +  R   P+E
Sbjct: 76  RELKFDTYASFRIRGAIIDGLRQMDW---LPRSVREKTKKIDQATEKLEQQYGRYVNPKE 132

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQAN 608
           +A  L M  E V K +        +S++ P  D E        I D+  ++P     +  
Sbjct: 133 VADYLGMNEEDVYKTINESYLAHQLSIDEPAQDSEKEDSFTATIMDEKTLTPEQHIDKKG 192

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E    ++ +   +E+ ++ + +      + TL E+G+   V+  R+ QI +K I KL+
Sbjct: 193 QMEELAEIIKTFNEKEQLIISLFYF----EELTLTEIGEILNVSTSRVSQIHSKTIFKLQ 248

Query: 669 HPSRSK 674
               SK
Sbjct: 249 QKLLSK 254


>gi|134300490|ref|YP_001113986.1| sporulation sigma factor SigK [Desulfotomaculum reducens MI-1]
 gi|134053190|gb|ABO51161.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Desulfotomaculum reducens MI-1]
          Length = 232

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 102/226 (45%), Gaps = 52/226 (23%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  ++E NLRLV  +A K  + G+   DL Q G IGL+K  + FD     KFSTYA  
Sbjct: 51  LAKTILIERNLRLVAKIANKLKDSGVDKQDLFQVGVIGLIKGVDTFDIKKARKFSTYA-- 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                               V +++++  ++R  +   N I        I++ L    +G
Sbjct: 109 -------------------GVCIQNEMLMMLRKQKSERNTI-------SISEPLDFDKDG 142

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLT 621
                     P+ L+  + + +               P+D  ++ +L  E   + L +L 
Sbjct: 143 ---------SPLELQDTLANNEI--------------PVDELVEKSLDVERLEKALQTLN 179

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           PRE+ V+++R+G+    + T  EVGK+  ++R  I +IE+  I KL
Sbjct: 180 PREKIVIKLRYGLEGERELTQREVGKRLDISRSFISRIESSTINKL 225


>gi|218458675|ref|ZP_03498766.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 138

 Score = 67.8 bits (164), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 50/77 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 61  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWW 120

Query: 504 VKQAITRSIADQSCTIR 520
           ++ +I   I      +R
Sbjct: 121 IRASIQDYILRNWSIVR 137


>gi|222151972|ref|YP_002561132.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
 gi|222121101|dbj|BAH18436.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
          Length = 255

 Score = 67.8 bits (164), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 116/235 (49%), Gaps = 22/235 (9%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A+KE+V    +LV S+A +Y+       DL+Q G +GL+ A  +FD     KF  + + 
Sbjct: 28  FAQKELVLHYQKLVESLAYRYSKGQSHHEDLVQVGMVGLLGAINRFDVTFERKFEAFLVP 87

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V   I R + D++ ++ +P  +++   K+ R    ++N++ R P   EIA+++    E 
Sbjct: 88  TVIGEIKRYLRDKTWSVHVPRRIKEIGPKIKRATDELTNELGRSPKIIEIAQRIEATEEE 147

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE---------TT 613
           V + +++ +   +L       D S   D  +D + V+ LD  +  N  E           
Sbjct: 148 VLEAMEMGQSYNALSV-----DHSIEAD--KDGSTVTLLD--VMGNTEEGYDLTEKRMIL 198

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +VL  L+ RE  +++  F  G++   T E++G    +++  + +++  AI+KL+
Sbjct: 199 EKVLPILSDREREIIQCTFLDGLSQKETGEKIG----LSQMHVSRLQRTAIKKLR 249


>gi|326791514|ref|YP_004309335.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
 gi|326542278|gb|ADZ84137.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
          Length = 249

 Score = 67.8 bits (164), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 111/227 (48%), Gaps = 14/227 (6%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  ++E  + LV  VA +   Y N+ +   DL+  G +GL+ A +KFD     KF TYA 
Sbjct: 22  KSSLIEHYVYLVKLVAGRLGIYLNQYVDSDDLVGYGVLGLIDAVDKFDPGKNVKFETYAS 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI  +I        +P  +R K   + +    +  ++ R+P  EE+A  L + +E
Sbjct: 82  LRIRGAILDAIRKLDW---VPRTLRKKQKDIDKAYIELEGRLGRQPLDEEVADFLEISIE 138

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              ++LK     +++ + I  ++  +  + ++D +A  P +      ++E     + SL 
Sbjct: 139 EYNELLK----EVNISSLISIDEYMYQFESVKDPSAPIPENYIEDTEVKEMLAEFIDSLP 194

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++V+ + +      + TL+E+     V+  R+ Q+  KA+ +L+
Sbjct: 195 EREKKVIFLYY----YEELTLKEISHVLEVSESRVSQLHTKAVSRLR 237


>gi|145224387|ref|YP_001135065.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216873|gb|ABP46277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 301

 Score = 67.8 bits (164), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 55/208 (26%), Positives = 102/208 (49%), Gaps = 7/208 (3%)

Query: 428 RHIVSMVRKGE-CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           + + SM   G+  E    ++ ++   L L   +A ++  RG    DLIQ   IGL+K+ +
Sbjct: 56  KQLSSMAACGDRAERRRRRQHIITECLPLADHIACRFAGRGEPSDDLIQVARIGLVKSVD 115

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G +F  +A+  ++  + R   D + ++R+P  ++D   ++   A  +S ++KR 
Sbjct: 116 RYVPDKG-RFMAFAVPTIRGEVRRHFRDSTWSMRVPRKIQDTQLRMRHAAEELSQRLKRA 174

Query: 547 PTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  EIA++L +    V +         P+SL+ P GD +    G   E + A  P   +
Sbjct: 175 PTDREIARELGVDDGEVSRCHSAHWAYRPVSLDAPRGDAEQECAG-IGELRGADDPGFDS 233

Query: 605 IQANLRETTTRVLASLTPREERVLRMRF 632
           ++  +    + V+A L PR   +L MRF
Sbjct: 234 VEDLI--VLSGVIAELDPRRRAILGMRF 259


>gi|327537603|gb|EGF24315.1| RNA polymerase ECF-type sigma factor [Rhodopirellula baltica WH47]
          Length = 340

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 52/86 (60%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + ++      A   +  +VEANLRLV S+ KK+ N    F DL+ +G + L++A EK
Sbjct: 145 RHRLELIELFVALADWHRDRIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEK 204

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIA 513
           FD+  G++FSTYA   V++   R++ 
Sbjct: 205 FDFDRGFRFSTYATQVVRRNSYRTVV 230



 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           LR   + +L  L  RE+ ++R RF +G +   HTL+ +  +  V++ER+RQ+E +A+ KL
Sbjct: 267 LRSRLSVMLGDLDRREKFIIRARFSLGPHRKVHTLQSLADRLGVSKERVRQLERRAMDKL 326

Query: 668 K 668
           +
Sbjct: 327 R 327


>gi|289444245|ref|ZP_06433989.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
 gi|289417164|gb|EFD14404.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
          Length = 375

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 46/62 (74%), Gaps = 4/62 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  ++ R ++ + R G+     AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL
Sbjct: 273 LPAAQRRDMMWICRDGD----RAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 328

Query: 482 MK 483
           ++
Sbjct: 329 IR 330



 Score = 44.7 bits (104), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|32471396|ref|NP_864389.1| RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
 gi|32443237|emb|CAD72068.1| probable RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
          Length = 340

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 52/86 (60%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + ++      A   +  +VEANLRLV S+ KK+ N    F DL+ +G + L++A EK
Sbjct: 145 RHRLELIELFVALADWHRDRIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEK 204

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIA 513
           FD+  G++FSTYA   V++   R++ 
Sbjct: 205 FDFDRGFRFSTYATQVVRRNSYRTVV 230



 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           LR   + +L  L  RE+ ++R RF +G +   HTL+ +  +  V++ER+RQ+E +A+ KL
Sbjct: 267 LRSRLSVMLGDLDRREKFIIRARFSLGPHRKVHTLQSLADRLGVSKERVRQLERRAMDKL 326

Query: 668 K 668
           +
Sbjct: 327 R 327


>gi|109899335|ref|YP_662590.1| flagellar biosynthesis sigma factor [Pseudoalteromonas atlantica
           T6c]
 gi|109701616|gb|ABG41536.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudoalteromonas
           atlantica T6c]
          Length = 242

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 97/204 (47%), Gaps = 22/204 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  FD   G  F T+A   ++ ++   I     T R        +HK
Sbjct: 44  DLIQAGMIGLLEASRNFDGTKGASFETFAGIRIRGSMLDEIRKGDWTPR-------SVHK 96

Query: 532 VVRTARRMSNKIKREPTPE----EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             R      NK++RE   +    +IAKKL + +E   ++L      ++    IG ED   
Sbjct: 97  NGRAITDAINKVERETGRDARDVDIAKKLEVSIEQYHQMLG----EVNAGKIIGMEDLGV 152

Query: 588 LGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D +   + K + +P +  +Q + ++     + +L  RE  VL + +   +N    L E
Sbjct: 153 SEDVVTTEQTKGSDTPFEDLLQGSFQKALAHAITTLPEREAIVLSLYYDEELN----LRE 208

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+   V+  R+ QI ++A+ KLK
Sbjct: 209 IGEVLDVSESRVSQIHSQAMLKLK 232


>gi|302539934|ref|ZP_07292276.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302457552|gb|EFL20645.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 274

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 110/234 (47%), Gaps = 12/234 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +EFR +  +    E EA   ++ +VEA + +   +A++Y NRG    DL Q   +GL+KA
Sbjct: 28  AEFREMARLPEGPEKEA--LRQRVVEAWMPMAQRLARQYRNRGESLEDLEQVAALGLVKA 85

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +++D   G  F+ +A+  V   I R   D    + +P  +++  ++V    R +S+ + 
Sbjct: 86  VKRYDPEHGTAFAGFAVPTVVGEIKRHFRDHLWVLHVPRRVQELRNRVRAAHRELSHSLD 145

Query: 545 REPTP-EEIAKKLAMPVEGVRKVLKITKE--PISLETPI-GDEDTSHLGDFIEDKNAVSP 600
               P E IA++  +  + VR  ++      P+SL+  + G +D   L D +  +     
Sbjct: 146 DATVPTEAIAERTGLSEKEVRIGMEAMGSFTPLSLDAQLTGADDGYSLADTLGGQEPA-- 203

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            D  +    RE     L  L  RE ++L MRF   M      E++G  Q  V+R
Sbjct: 204 YDRVVD---REAVRPGLGRLPARERQILYMRFFCDMTQSRIAEQLGISQMHVSR 254


>gi|196249822|ref|ZP_03148518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196210698|gb|EDY05461.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 256

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 59/220 (26%), Positives = 110/220 (50%), Gaps = 16/220 (7%)

Query: 455 LVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           L+ + AKK       F  DL Q G +  ++  E +D   G  F +YAM  +   +   + 
Sbjct: 39  LIAAAAKKMARSRPDFYEDLFQVGRLSFLRLLEHYDPNQGTSFESYAMKSLIGYMKNYLR 98

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITK 571
           D++  I++P  +++   KV +    ++  ++R P  EEIA  L + VE   ++L  +   
Sbjct: 99  DKAWYIQVPRRVKENGSKVQKAIDELTVTLERSPNIEEIANHLGLSVEETIEILAGRDHY 158

Query: 572 EPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + IS++ P+  G++D + +G+F+ +D N V  L   +  +L+E     +  L+ +E  V+
Sbjct: 159 QAISIDAPVQDGEKDATTIGEFLADDTNEVEALIERL--DLQEA----IGKLSEQERIVI 212

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              F  G     T   + K+  V++  I +I+ +AI KLK
Sbjct: 213 EAVFRRG----ETQRSLAKRLGVSQMTISRIQKRAIEKLK 248


>gi|296133019|ref|YP_003640266.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031597|gb|ADG82365.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 262

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 64/211 (30%), Positives = 102/211 (48%), Gaps = 14/211 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GL+ A EKF+     KF TYA+  +K AI   +        IP  +R K  +
Sbjct: 56  DLISYGIFGLIDAIEKFEPERNIKFETYAISRIKGAIWDGLRSMDW---IPYSIRQKAKE 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE-TPIGDEDTSH- 587
           +  T  R+ N++ R  T EE+ + L +  +    +L+ T     +SLE   + D D ++ 
Sbjct: 113 LEETYARLENELGRPATDEEMCETLGITKQQFYSLLQETSCTSLLSLEDLFVFDRDGTNG 172

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D I D     P+ + +    ++     +  L  RE+ V+ + +  G+    TL+E+
Sbjct: 173 VKMIDTIADSRVPDPVAAVMFEEQKKILGEAINKLPEREKMVIALYYYEGL----TLKEI 228

Query: 646 GKQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
           GK   VT  RI Q+  KAI +L+   SR KK
Sbjct: 229 GKVLGVTESRISQLHTKAILRLRGRLSRVKK 259


>gi|255026033|ref|ZP_05298019.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-003]
          Length = 259

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 113/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +A +KL+
Sbjct: 206 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAXKKLR 250


>gi|161898865|gb|ABX80422.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 55/232 (23%), Positives = 112/232 (48%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-------QANLRETTTRV 616
            + +++ K   +L      E  S       D + ++ LD A        + N R    +V
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADS-------DGSTITLLDVAGGTDDGFERVNQRMLLEKV 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 190 LPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 237


>gi|209695722|ref|YP_002263652.1| flagellar biosynthesis sigma factor [Aliivibrio salmonicida
           LFI1238]
 gi|208009675|emb|CAQ79974.1| RNA polymerase sigma factor for flagellar regulon FliA [Aliivibrio
           salmonicida LFI1238]
          Length = 243

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 95/200 (47%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F TYA   ++ ++   I       R  VH   ++  
Sbjct: 46  DLIQSGMIGLLEAQQNYDGSKGASFETYAGIRIRGSMLDEIRRGDWVPR-SVHKNSRM-- 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V    + +  K+ REPT +EIA+ L +P++   ++L      ++    +G ED     D 
Sbjct: 103 VNAAIKALEAKLSREPTDKEIAEHLELPLDQYYQILN----DVNCGKLVGMEDLGVSEDV 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   E  +   P    +  + R      + +L  RE  VL + +   +N    L+E+G  
Sbjct: 159 ITTEEHADDNIPFQGVVDEHFRVALVEAIKTLPEREALVLSLYYDEELN----LKEIGAV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 IGVSESRVSQIHSQSMQRLR 234


>gi|153953795|ref|YP_001394560.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219854411|ref|YP_002471533.1| hypothetical protein CKR_1068 [Clostridium kluyveri NBRC 12016]
 gi|146346676|gb|EDK33212.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219568135|dbj|BAH06119.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 241

 Score = 67.4 bits (163), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 111/235 (47%), Gaps = 23/235 (9%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  L LV  +A +      + +++ DL+  G +GLM A  KFD   G KFSTYA 
Sbjct: 10  KEELVKKYLPLVKYIASRVIIGKTKYIEYEDLVSYGTLGLMDAINKFDKDRGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +   S    I     DK+++       +  ++ REP   EIA KL + ++
Sbjct: 70  IRIKGSMIDELRRNSP---ISKGAMDKLNRYNAAVEYLQGELGREPNSVEIASKLGISLK 126

Query: 562 GVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-----TT 613
            + ++         +SLE  +  DED   +   IED  + SP     + NL E       
Sbjct: 127 EMMEIENYINYISMVSLEDLVFSDEDNIPIMGTIEDTKSPSP-----ERNLEEKEKLKYL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + L  L  ++  VL + +      + TL+E+G    V+  R+ Q+ ++AI  L+
Sbjct: 182 AKALELLNEKDNLVLTLYY----YEELTLKEIGHILNVSESRVCQLHSRAIVHLR 232


>gi|325262838|ref|ZP_08129574.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
 gi|324031932|gb|EGB93211.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
          Length = 212

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 110/260 (42%), Gaps = 68/260 (26%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD---- 472
           S    ++ SE ++ +    +G+ +A   K  ++E NLRLV  V KKY     Q+LD    
Sbjct: 10  SFPNPLTPSEEKYYMQKYTEGDLQA---KHVLIERNLRLVAHVIKKY-----QYLDEDPE 61

Query: 473 -LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
            LI  G IGL+KA   F+   G + + YA   V+  I              +++R K   
Sbjct: 62  DLISIGTIGLIKAVVTFNPDKGNRLAAYASKCVENEIL-------------MYLRAK--- 105

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---L 588
                                               K T + ISL  PIG +   +   L
Sbjct: 106 ------------------------------------KKTSKEISLYEPIGTDREGNEIKL 129

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D IE   A  P    ++ N+++   +V   L+ RE  VL+MR+G+    ++T  E+ +Q
Sbjct: 130 YDIIETDEADVPEKIHLKENIQKLYDKVENELSQRERLVLKMRYGLYNGEEYTQREIARQ 189

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             ++R  + +IE  A+ KL+
Sbjct: 190 LGISRSYVSRIEKSAVEKLR 209


>gi|326332680|ref|ZP_08198943.1| hypothetical protein NBCG_04120 [Nocardioidaceae bacterium Broad-1]
 gi|325949508|gb|EGD41585.1| hypothetical protein NBCG_04120 [Nocardioidaceae bacterium Broad-1]
          Length = 264

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 111/230 (48%), Gaps = 21/230 (9%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E++  N  +  S+A +YT RG+   DL Q   I L++AA+ F       F TYA+  ++
Sbjct: 39  EEVILLNAAVARSIAHRYTGRGIPRADLEQVAYIALVRAAKSFHPDRADDFLTYAVPTIR 98

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R   D   T+R P      I ++  T  R+ ++    PT  E+A+   +P + VR+
Sbjct: 99  GEVKRWFRDHGWTVRPP----RPIQELQSTLLRIGSERGNLPT-SELAEIAEVPEQKVRE 153

Query: 566 VL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-----LA 618
            L  +    P SL+ P+   D+   G+       +  +   +   L +  TR+     + 
Sbjct: 154 ALDARGCFTPSSLDAPLRSGDSQSSGE-----ATIGDMLPGVDGGLSDCETRLALEQAIH 208

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L PR++ V+R+RF      D +  E+G+   VT+ ++ +I  + I +L+
Sbjct: 209 ALCPRDQLVVRLRF----LEDRSQAEIGEAIGVTQTQVSRILTRIIDELR 254


>gi|218669755|gb|ACL00354.1| Bcp26 [Bacillus phage Bcp1]
          Length = 256

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 116/239 (48%), Gaps = 31/239 (12%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE EA+   + +VE N RLV  V ++  N   ++ DL Q G IGL+ A  KFD   G +F
Sbjct: 32  GEEEAT---ESLVEHNARLVTYVVRRKNNPYHEYDDLFQLGMIGLITAIAKFDTSKGLQF 88

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA+ W+   I   + +++  +++P  +   ++K+      ++ K+K E  P  I +KL
Sbjct: 89  STYAVRWIDAEIGNYLKNRTSILKVPREIGAIVNKI------LAVKLKNEE-PAIIMEKL 141

Query: 557 ---AMPVEGVRKVLKIT-KEPISLETPIGDEDTSHLGDFI-EDKNA--VSPLDSAIQANL 609
              A  ++ V   L+I   E ISL+   G+E    L   + +D N    S L        
Sbjct: 142 KLDASQLDNVTIALEIIHNEVISLDKQTGEEKDDSLSSIVGQDVNQDWFSGL-------- 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 ++  L  +E+ VL +++   M+++    ++   F     +I ++E  A+ KL+
Sbjct: 194 --AFYDIIRFLDDKEQSVLTLKYVHDMSSN----KIATLFGTYANKISRLEKVALDKLR 246


>gi|317123623|ref|YP_004097735.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Intrasporangium calvum DSM 43043]
 gi|315587711|gb|ADU47008.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Intrasporangium calvum DSM 43043]
          Length = 282

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 110/225 (48%), Gaps = 13/225 (5%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V  +L L   VA +Y  R +   DL+Q   + L+ A +++    G  F  YA+  +  
Sbjct: 52  EIVRLHLDLCDGVAARYAGRSIPTEDLVQVARLALLVAIKRYQPGPGSSFIGYALPTISG 111

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            + R   D    +R P  +++ +  V+R AR     +    PT +++A+++ +  E V +
Sbjct: 112 ELKRHFRDHGWMVRPPRRLQE-LGPVLRLAREHWEQEHGTSPTTQDLAEEVGVDPEQVSE 170

Query: 566 VLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            L    +  P+SL+   GD+++  L + + +     P D    A  R +    L+SL+ +
Sbjct: 171 CLSAEHSYHPLSLDLTFGDDESRSLAESLAE-----PQDELESAADRVSLGTALSSLSQK 225

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  +L+MRF  GM    T +E+G    V++ ++ ++    + +L+
Sbjct: 226 DRELLQMRFVDGM----TQKEIGLALGVSQMQVSRLVRAVLDRLR 266


>gi|318066967|emb|CBY89098.1| RNA polymerase sigma70 factor [Halomonas pantelleriensis]
          Length = 363

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 45/62 (72%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P   ++++    E+ D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVESIL----EIYD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|146309186|ref|YP_001189651.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina ymp]
 gi|145577387|gb|ABP86919.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas mendocina ymp]
          Length = 284

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 50/78 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSIADQSCTIRI 521
           ++  I   I      +++
Sbjct: 110 IRAEIHEFILKNWRIVKV 127


>gi|318066973|emb|CBY89101.1| RNA polymerase sigma70 factor [Halomonas taeanensis]
          Length = 366

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 45/62 (72%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P   ++++    E+ D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIKIAKRIEEGTREVMSALAYLPGAVESVL----EVYD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|114566068|ref|YP_753222.1| sporulation sigma factor SigK [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337003|gb|ABI67851.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 244

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 99/228 (43%), Gaps = 59/228 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY + G    DLI  G IGL+KA   +++  G + +TYA   
Sbjct: 52  ARNILIEHNLRLVAHVVKKYESSGEDLEDLISIGTIGLIKAIRTYNFERGVRLATYA--- 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     + +H+R                                     
Sbjct: 109 -----ARCIDNE-----VLMHLRSS----------------------------------- 123

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
               K  K+ +SL  PIG +   +   L D + + N +  L   ++A ++E   +   +L
Sbjct: 124 ----KKQKQEVSLYDPIGHDKEGNEISLIDILTNDNEIVDL---VEAKMQEEKIKEKINL 176

Query: 621 TPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R ER V+ MR+G+      T  ++ K+  ++R  + +IE KAI+KL
Sbjct: 177 LSRRERQVIEMRYGLFNGLKETQRDIAKKLGISRSYVSRIEKKAIKKL 224


>gi|138897001|ref|YP_001127454.1| sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
 gi|134268514|gb|ABO68709.1| Sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
          Length = 258

 Score = 67.4 bits (163), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 59/220 (26%), Positives = 110/220 (50%), Gaps = 16/220 (7%)

Query: 455 LVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           L+ + AKK       F  DL Q G +  ++  E +D   G  F +YAM  +   +   + 
Sbjct: 41  LIAAAAKKMARSRPDFYEDLFQVGRLSFLRLLEHYDPNQGTSFESYAMKSLIGYMKNYLR 100

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITK 571
           D++  I++P  +++   KV +    ++  ++R P  EEIA  L + VE   ++L  +   
Sbjct: 101 DKAWYIQVPRRVKENGSKVQKAIDELTVTLERSPNIEEIANHLGLSVEETIEILAGRDHY 160

Query: 572 EPISLETPI--GDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + IS++ P+  G++D + +G+F+ +D N V  L   +  +L+E     +  L+ +E  V+
Sbjct: 161 QAISIDAPVQDGEKDATTIGEFLADDTNEVEALIERL--DLQEA----IGKLSEQERIVI 214

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              F  G     T   + K+  V++  I +I+ +AI KLK
Sbjct: 215 EAVFRRG----ETQRSLAKRLGVSQMTISRIQKRAIEKLK 250


>gi|126651479|ref|ZP_01723683.1| sigma factor B [Bacillus sp. B14905]
 gi|126591732|gb|EAZ85828.1| sigma factor B [Bacillus sp. B14905]
          Length = 261

 Score = 67.4 bits (163), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 123/230 (53%), Gaps = 14/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+N    + D++Q G +GL+ A  +FD  +G  F  +A+  
Sbjct: 30  AQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++  + +P  +++   ++  T   ++ +++R P+ +EIA++L +  E V
Sbjct: 90  IVGEIKRFLRDKTWDVHVPRRIKEIGPRIKSTVEALTIELQRSPSIQEIAERLEVAEEEV 149

Query: 564 RKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + +++++  + +S++  I    D  T  L D +  ++     D     + R   +  + 
Sbjct: 150 LEAMEMSRSYQALSMDHSIESDSDGSTVTLFDILGRED-----DGYEMTDKRMIVSEAMV 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE++++++ +   ++     +E G+Q  +++  + +I+ KAI+KL+
Sbjct: 205 VLNEREKQIIQLTYLEQLSQ----KEAGEQLGISQMHVSRIQRKAIKKLQ 250


>gi|28203259|gb|AAO35702.1| RNA polymerase sigma-E factor [Clostridium tetani E88]
          Length = 261

 Score = 67.4 bits (163), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 106/221 (47%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 84  LIERNLRLVVYIARKFENTGIGIEDLVSVGTIGLIKAVNTFDPSKKIKLATYA------- 136

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NKIK E +  E    L +  +G   +L
Sbjct: 137 -SRCIENE-----ILMYLRR------------NNKIKSEISFYE---PLNVDWDGNELLL 175

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   DT  + D+IE++     +D       +E     +  L  RE+++
Sbjct: 176 ----------SDILGTDTDIVYDYIEEE-----VD-------KELLLIAMDKLNNREKQI 213

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+G  T+ T +EV     +++  I ++E + I++LK
Sbjct: 214 VNLRFGLGGKTEKTQKEVADMLGISQSYISRLEKRIIKRLK 254


>gi|74317198|ref|YP_314938.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056693|gb|AAZ97133.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 236

 Score = 67.0 bits (162), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 95/199 (47%), Gaps = 10/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM A  +FD   G +F +YA   ++ A+   + +      +P H+R K  +
Sbjct: 38  DLIQVGLIGLMDAVSRFDGTQGAQFESYATQRIRGAMLDELREADW---LPRHVRQKSRQ 94

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDEDT-SHLG 589
           +     ++  +  + P+  EI+ +L +P++  + +L   K   +       DED+ S L 
Sbjct: 95  IEAAIHKLEQRHGKAPSESEISAELGIPIDQYQSMLGDVKCSQLLYYEDFSDEDSASFLE 154

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            ++ D  +  PL        R +    +  L  RE  ++ M +   MN    L+E+G   
Sbjct: 155 RYLVD-GSNDPLAVLEDEGFRASLIAAIHHLPERERSMMGMYYEQDMN----LKEIGAVL 209

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ Q+ ++A+ +L+
Sbjct: 210 GVSESRVCQLHSQAVARLR 228


>gi|187478163|ref|YP_786187.1| RNA polymerase sigma factor for flagellar operon [Bordetella avium
           197N]
 gi|115422749|emb|CAJ49277.1| RNA polymerase sigma factor for flagellar operon [Bordetella avium
           197N]
          Length = 244

 Score = 67.0 bits (162), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 101/210 (48%), Gaps = 25/210 (11%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL+ A  ++      +F TYA   ++ A+   +  Q     +P  +R 
Sbjct: 30  VQLDDLIQAGMIGLLDAVRRYQKNPDAQFETYATARIRGAMLDELRSQDW---LPRSVRS 86

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-------ITKEPISLETPI 580
           K  ++    +R    + R PT  EIA++L +P++  + +L        +  E I  E   
Sbjct: 87  KSRRIETAIQRQEQVLMRPPTEIEIAQELGLPLDEYQAMLSDAQGIQILHYENIDAE--- 143

Query: 581 GDEDTSHLGDFIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           GD      GD+ E       +PL++ + A+LR +  + +  L  RE+ +L + +  G+N 
Sbjct: 144 GD------GDWHEGAGDGGGNPLNALLAADLRASLIQAIERLPEREQLLLSLYYEQGLN- 196

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L+E+G    VT  R+ Q+  +A  +L+
Sbjct: 197 ---LKEIGAVLNVTEARVCQLRTQATARLR 223


>gi|119470003|ref|ZP_01612808.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
 gi|119446713|gb|EAW27986.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
          Length = 240

 Score = 67.0 bits (162), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 106/228 (46%), Gaps = 18/228 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 16  IVEKHASLVKKVACHLIARLPASVQLDDLIQSGMIGLIEASKSFDATKGASFETFAGIRI 75

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +       R  VH + ++  V  T   +   + REPT  E+A+KL + +    
Sbjct: 76  RGAMLDEMRRGDWAPR-SVHRKSRL--VAETIAFLEKSLNREPTDIEVAEKLEISLNEYH 132

Query: 565 KVLK--ITKEPISLETPIGDEDT-SHLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            +L      + + +E    DED  S +G D   DK    P ++       E+    + SL
Sbjct: 133 HILNDVNASKVLGIEDLGVDEDAISPVGQDLALDK----PFNNVKNERFNESLLGAIKSL 188

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R+  VL + +   MN    L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 189 PERDAMVLSLYYNDEMN----LKEIGHILDVSESRVSQIHGQAMIKLK 232


>gi|168700558|ref|ZP_02732835.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 260

 Score = 67.0 bits (162), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 63/252 (25%), Positives = 113/252 (44%), Gaps = 45/252 (17%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE  L LV   A++  +R   G++  DLI  G  GL+ A + FD   G KF TY +
Sbjct: 26  RNRLVERYLSLVKYNAERIWSRLPDGVELDDLISAGVFGLLDAIDAFDLTRGVKFETYCV 85

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  K+    +++   + R P PEE+++KL +P+E
Sbjct: 86  PRIRGAMLDELRTMDW---VPRLVRSKASKMEAARKQLEAALGRPPKPEELSEKLGIPLE 142

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLG------------------DFIEDKNAVSPLDS 603
                         LE+ +GD    +L                   D +EDK A SP   
Sbjct: 143 -------------QLESYVGDATAVNLVSLNKKWYETDSYKDVREIDILEDKKAESPTGR 189

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +L +  TR L     R ER++ + +      + T++E+G    ++  R+ Q+ +  
Sbjct: 190 LQNRDLMKLVTRGLN----RNERLIVILY---YYEEMTMKEIGATLNLSESRVSQMHSSI 242

Query: 664 IRKLK-HPSRSK 674
           + +L+ H ++ K
Sbjct: 243 VARLQSHLAKRK 254


>gi|94500298|ref|ZP_01306831.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
 gi|94427597|gb|EAT12574.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
          Length = 245

 Score = 67.0 bits (162), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 109/243 (44%), Gaps = 48/243 (19%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE    LV  +A     R    +Q  DLIQ G IGL++AA+K++   G  F TYA    
Sbjct: 19  LVEEYASLVKRIAHHLKGRLPDSVQVDDLIQSGMIGLIEAAQKYEPSKGASFETYA---- 74

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------REPTPE 550
                         IRI   M D+I K       V R +RR+S  I+       R+   +
Sbjct: 75  -------------GIRIRGSMLDEIRKGDWAPRSVHRNSRRISEAIRYVESQTGRDAQDQ 121

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAI 605
           E+AK L M +E   + L+        S E  +   G++++  +G   E     SPL    
Sbjct: 122 EVAKALGMELEEYHQHLQDGAGSRLFSFEDLLEQRGEQESDFMGHDDE-----SPLQDLQ 176

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             + ++   + ++ L  RE+ VL + +   +N    L+E+G    V+  R+ QI ++A  
Sbjct: 177 SEHFQQQLAKAISQLPEREQLVLALYYDEELN----LKEIGAVLEVSESRVSQIHSQAAH 232

Query: 666 KLK 668
           +L+
Sbjct: 233 RLR 235


>gi|317128262|ref|YP_004094544.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473210|gb|ADU29813.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 98/228 (42%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N   +  DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNLLIEHNLRLVAHIVKKFENTREENEDLISIGTIGLIKAIESYSPGKGTKLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANL-RETTTRVLASLT 621
              LK  ++ +SL  PIG +   +    I+   A    +   IQ N+ ++   + +  L 
Sbjct: 120 --ALKKVRKDVSLHDPIGQDKEGNEISLIDVLQAETEDVVETIQLNMEKKQIYQYIHVLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ MN + T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 178 EREKEVVVGRFGLDMNKERTQREIAKELGISRSYVSRIEKRALMKLFH 225


>gi|222530110|ref|YP_002573992.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456957|gb|ACM61219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 246

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 118/230 (51%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 19  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K AI   +  Q     +P  +R K  ++ R    +  +  + PT +E+AK++ + VE
Sbjct: 79  TRIKGAIIDCVRSQDF---LPRSIRQKAKEIERVYIEIEKE-GKTPTNQEVAKRIGISVE 134

Query: 562 GVRKVL-KITK-EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLA 618
            ++K+  +I+    ISLE+ +     S +G     ++ VS  +  I+   LRE   + + 
Sbjct: 135 ELQKLQDRISSGMIISLESFLEQNYESKIGGL---EDFVSQPEHFIENEELREVLRQQID 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 192 NLLENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLR 237


>gi|229587526|ref|YP_002860564.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
 gi|229260255|gb|ACQ51292.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
          Length = 296

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/228 (22%), Positives = 107/228 (46%), Gaps = 29/228 (12%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E N  L+  VA KY N+ ++  DL Q+G +G +KA +KFD     KFSTYA +W++  
Sbjct: 90  LIEKNENLIFKVANKYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIEAE 149

Query: 508 ITRSI---ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           I+       D S +I      R                 K +     I  +  +P + V+
Sbjct: 150 ISSFFNFNVDGSLSISSSYQHR-----------------KLKGYENGILSEDELP-KLVK 191

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             +++    IS+++ +  ++  +  D++  K  ++   + I++ +       L+ L+ +E
Sbjct: 192 NHIQLKNNSISVDSIVHGKENENSADYLLGKTDINY--NNIESKI--VMENALSGLSDKE 247

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           + ++  R    +  +   +++ K+F V+ + I+ +   AI KL+   +
Sbjct: 248 KNIIISR----IIYEKKYKDIAKEFKVSYQYIQYLYNNAIEKLRQTVK 291


>gi|169829726|ref|YP_001699884.1| RNA polymerase sigma-B factor [Lysinibacillus sphaericus C3-41]
 gi|168994214|gb|ACA41754.1| RNA polymerase sigma-B factor (Sigma-37) (General stress protein
           84) (GSP84) [Lysinibacillus sphaericus C3-41]
          Length = 261

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 123/230 (53%), Gaps = 14/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+N    + D++Q G +GL+ A  +FD  +G  F  +A+  
Sbjct: 30  AQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++  + +P  +++   ++  T   ++ +++R P+ +EIA++L +  E V
Sbjct: 90  IVGEIKRFLRDKTWDVHVPRRIKEIGPRIKTTVEALTIELQRSPSIQEIAERLEVAEEEV 149

Query: 564 RKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + +++++  + +S++  I    D  T  L D +  ++     D     + R   +  + 
Sbjct: 150 LEAMEMSRSYQALSMDHSIESDSDGSTVTLFDILGRED-----DGYEMTDKRMIVSEAMV 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE++++++ +   ++     +E G+Q  +++  + +I+ KAI+KL+
Sbjct: 205 VLNEREKQIIQLTYLEQLSQ----KEAGEQLGISQMHVSRIQRKAIKKLQ 250


>gi|161486847|ref|NP_781765.2| sporulation sigma factor SigE [Clostridium tetani E88]
          Length = 235

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 106/221 (47%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGIGIEDLVSVGTIGLIKAVNTFDPSKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NKIK E +  E    L +  +G   +L
Sbjct: 111 -SRCIENE-----ILMYLRR------------NNKIKSEISFYE---PLNVDWDGNELLL 149

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   DT  + D+IE++     +D       +E     +  L  RE+++
Sbjct: 150 ----------SDILGTDTDIVYDYIEEE-----VD-------KELLLIAMDKLNNREKQI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+G  T+ T +EV     +++  I ++E + I++LK
Sbjct: 188 VNLRFGLGGKTEKTQKEVADMLGISQSYISRLEKRIIKRLK 228


>gi|56963382|ref|YP_175113.1| sporulation sigma factor SigK [Bacillus clausii KSM-K16]
 gi|56909625|dbj|BAD64152.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus
           clausii KSM-K16]
          Length = 235

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 105/242 (43%), Gaps = 61/242 (25%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R  E +AS A+  ++E NLRLV  + KK+ N      DLI  G IGL+KA E +    
Sbjct: 40  LARMAEGDAS-ARNMLIEHNLRLVAHIVKKFENTREDVEDLISIGTIGLIKAIESYSEGK 98

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G K +TYA         R I ++     I +H+R                          
Sbjct: 99  GTKLATYA--------ARCIENE-----ILMHLR-------------------------- 119

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIED--KNAVSPLDSAIQA 607
                         LK  K+ +SL  PIG +   +   L D ++D  ++ V  L + ++ 
Sbjct: 120 -------------ALKKVKKDVSLHDPIGTDKEGNEITLIDILKDDGEDIVDVLQTEME- 165

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             ++     +  L  RE+ V+  RFG+ M  + T  E+ K+  ++R  + +IE +A+ KL
Sbjct: 166 --KKQIYEYIHVLDEREKEVIIGRFGLNMEEERTQREIAKELNISRSYVSRIEKRALMKL 223

Query: 668 KH 669
            H
Sbjct: 224 FH 225


>gi|311900799|dbj|BAJ33207.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/248 (22%), Positives = 117/248 (47%), Gaps = 33/248 (13%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G  E S  +  +VE NL LV    +++ +      DL+Q G +GL+KA ++F+   G +
Sbjct: 63  EGTREYSYVRASLVELNLSLVRFALRRFGSHRESTEDLMQVGAVGLIKAIDRFETERGLE 122

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A+  +   + R   D +  + +P  +++    +V+    +S  + R PT  E+++ 
Sbjct: 123 FTTFAIPTILGELRRHFRDTTWAVHVPRRLQELRLALVKAQDALSQALDRAPTVAELSEH 182

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDED------TSHLG------DFIEDKNAVSPL 601
           L +  E V + L+        SL+ P G +D       + +G        +ED  ++ PL
Sbjct: 183 LGITQEEVIEGLQAANAHSTDSLDLPAGPDDDGPGALAAKIGGTDERLGMVEDLVSLQPL 242

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                          +A+L  R+  +L MRF      + T  ++G++  +++  + ++ +
Sbjct: 243 ---------------IAALPERDRLILSMRF----TEELTQSQIGERLGLSQMHVSRLLS 283

Query: 662 KAIRKLKH 669
           + + KL+ 
Sbjct: 284 RTLAKLRQ 291


>gi|113473821|ref|YP_718084.1| RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
 gi|112821501|dbj|BAF03372.1| Probable RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
          Length = 328

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 46/61 (75%)

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           T  L+ L+ REERV+R+RFG+G + + TL+++G +F V  +RIRQIE KA+R+L+H  R 
Sbjct: 55  TAALSCLSAREERVIRLRFGLGGHGEWTLQQIGDEFGVNPQRIRQIEMKALRRLRHQFRK 114

Query: 674 K 674
           +
Sbjct: 115 R 115


>gi|256004813|ref|ZP_05429788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 2360]
 gi|281417227|ref|ZP_06248247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|255991263|gb|EEU01370.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 2360]
 gi|281408629|gb|EFB38887.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940748|gb|ADU74782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 1313]
          Length = 256

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 100/217 (46%), Gaps = 28/217 (12%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y    +++ DLI  G  GL+ A EKFD   G KF TYA   ++ +I  SI +      +P
Sbjct: 45  YFGSNVEYDDLIGYGIFGLIDAIEKFDINKGVKFETYASLRIRGSIIDSIRELDW---VP 101

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +R K  ++ +    + N++ R  + +E+A KL + V+ + K+L      ++L + I  
Sbjct: 102 RSLRQKNKELEKVYAEIENELGRSASDKEVADKLGITVDELNKLLN----EVNLSSMIS- 156

Query: 583 EDTSHLGDFIEDKNAVS-----------PLDSAIQANLRETTTRVLASLTPREERVLRMR 631
                L +F+E    +            P      A LRE     ++ L  +E+ V+ + 
Sbjct: 157 -----LEEFLEQNYEIGVTTAPESRDEKPEGYIEMAELREILADAISKLPEKEKMVITLY 211

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      D TL+E+     V+  RI Q+  KAI +L+
Sbjct: 212 YF----EDLTLKEISAIMKVSESRISQLHTKAILRLR 244


>gi|330505413|ref|YP_004382282.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
 gi|328919699|gb|AEB60530.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
          Length = 284

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 47/69 (68%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAITRSI 512
           ++  I   I
Sbjct: 110 IRAEIHEFI 118


>gi|299472406|emb|CBN77594.1| RpoD family RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 242

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/208 (26%), Positives = 98/208 (47%), Gaps = 13/208 (6%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T   L  +DLIQEG I L  AAE++D   G +F TYA W ++ A  R+ A Q+ TI IP 
Sbjct: 7   TVTALSSMDLIQEGAIALHLAAERYDPQRGVRFFTYADWSLRAAFERAEASQATTIAIPR 66

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +       V    RR+   + +   P   +++A  L +    + K+L+  K+  S+   +
Sbjct: 67  Y-------VYVQKRRLKAILGQHCGPQTSQDLATSLGISERQLAKLLRRAKDCQSMNRVL 119

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                + LG+ I    +   +   + A    +   +L +L P+EE V+  R+G+      
Sbjct: 120 VSSGVA-LGEMIPGAQSCEDILRRLDAE--ASLVGLLGTLKPQEEEVIVHRYGLFGRRRK 176

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   V     V+R+ + ++   A+ K++
Sbjct: 177 STPAVAAVMGVSRQYVGRVHRSALEKMR 204


>gi|153803716|ref|ZP_01958302.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
 gi|124120749|gb|EAY39492.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
          Length = 242

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 96/200 (48%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +  ++ R+PT  E+AK L M +E    VL      I+    +G ED     D 
Sbjct: 103 ISQAIAVLEGELNRDPTDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVSDDA 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   E+    SP     + + R+     + SL  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPFEEGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 LGVSESRVSQILSQSMQRLR 234


>gi|29833942|ref|NP_828576.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29611067|dbj|BAC75111.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/214 (28%), Positives = 101/214 (47%), Gaps = 10/214 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A +Y  RG    DL Q   +GL+KA +++D   G  F +YA+  +
Sbjct: 38  RDEIVRAWLPMAERIAWRYRGRGESTEDLCQVAAVGLVKAVDRYDPARGNAFESYAVPTI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              I R   D    + +P  ++D  ++V   A+ +S  +   EPT  EIA+   +  + V
Sbjct: 98  TGEIKRHFRDHMWVLHVPRRVQDLRNRVRVAAKELSQTVPGHEPTVTEIAEHAQLSEDDV 157

Query: 564 RKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +  L+   T   +SL+  + G +D   L D +   +  S  D  +    RE     L +L
Sbjct: 158 QIGLEAMDTFTALSLDAELPGSDDGYALSDALGGPD--SGYDLVVD---REAVKPSLRAL 212

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             RE  +L +R+  GM      E++G  Q  V+R
Sbjct: 213 PERERTILYLRYFRGMTQSSIAEQLGISQMHVSR 246


>gi|323703189|ref|ZP_08114842.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531848|gb|EGB21734.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 251

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 109/232 (46%), Gaps = 14/232 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+++++   L LV  +A +   +   F+   DL   G IGLM+A +KFD  +G  F  YA
Sbjct: 18  ARQQLILHYLPLVKHLAGRLAVKLPSFIQREDLEGYGVIGLMEALDKFDHTMGNSFDAYA 77

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ AI   +  Q+    +P     K+  + +T  R+  ++      E +A+++ + V
Sbjct: 78  YHRIRGAILDQVRRQNW---LPRTAWQKLQHLKQTRERLERELGGAVPDEILAREMGISV 134

Query: 561 EGVRKVL----KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + +  +     K+    +  E P  D       D +ED  +  PL    +   R+   R 
Sbjct: 135 DELNHLASSAGKMYLMSLDEEVPGSDGSVVRKLDLVEDTGSPDPLSIVEEKENRKLLARA 194

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  R++ +L + +  G+    TL+E+G+   V+  R+ Q+  + +RKL+
Sbjct: 195 IEKLGQRDQLILSLYYTEGL----TLKEIGQVLEVSESRVCQLHGQVMRKLR 242


>gi|218677311|ref|ZP_03525208.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 171

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/144 (31%), Positives = 76/144 (52%), Gaps = 10/144 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW
Sbjct: 25  ARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPDRDVRFSTYASWW 84

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP-------EEIAKKL 556
           ++ +I   I      +R       K   +    RR+  K+ +  T        +EIA  L
Sbjct: 85  IRASIQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAAL 142

Query: 557 AMPVEGVRKV-LKITKEPISLETP 579
            + +  V+ +  +++    SL+ P
Sbjct: 143 GVSLADVQTMDARLSGNDASLQAP 166


>gi|317122054|ref|YP_004102057.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
 gi|315592034|gb|ADU51330.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
          Length = 251

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 99/242 (40%), Gaps = 59/242 (24%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +  +R G+     A+  ++E NLRLV  +AKK+   G    DLI  G +GL+K  + +
Sbjct: 41  HYLERMRHGD---ERARDVLIERNLRLVAHIAKKFDETGEDPEDLISIGTVGLIKGVDTY 97

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR---MSNKIKR 545
           D   G + +TYA   ++  I              +H+R       R  RR   + N I  
Sbjct: 98  DPSKGTRLATYAARCIENEIL-------------MHLR-----ATRRNRREVFLQNPIGV 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +    E+     +P +                            D +ED      L   I
Sbjct: 140 DREGNEVTLMDMLPAD---------------------------DDAVEDTVGRRLLARRI 172

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  +RE        L PRE RVL +RFG+     +T  EV +   ++R  + +IE +A+R
Sbjct: 173 REAVRE--------LGPRERRVLELRFGLDGQRRYTQREVARVLGISRSYVSRIEKRAVR 224

Query: 666 KL 667
           KL
Sbjct: 225 KL 226


>gi|313810027|gb|EFS47748.1| conserved domain protein [Propionibacterium acnes HL083PA1]
          Length = 52

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/52 (59%), Positives = 40/52 (76%)

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 1   MRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 52


>gi|258621167|ref|ZP_05716201.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
 gi|258626709|ref|ZP_05721533.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258581005|gb|EEW05930.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258586555|gb|EEW11270.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
          Length = 244

 Score = 67.0 bits (162), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 96/200 (48%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +  ++ R+PT  E+AK L M +E    VL      I+    +G ED     D 
Sbjct: 103 ISQAIAVLEGELNRDPTDAEVAKFLEMSLEQYHSVLM----DINCSRIVGIEDLGVSDDA 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   E+    SP     + + R+     + SL  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPFEEGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 LGVSESRVSQILSQSMQRLR 234


>gi|282599758|ref|ZP_05971750.2| motility sigma factor FliA [Providencia rustigianii DSM 4541]
 gi|282567697|gb|EFB73232.1| motility sigma factor FliA [Providencia rustigianii DSM 4541]
          Length = 242

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 100/206 (48%), Gaps = 14/206 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A E+FD  LG  F+TYA+  ++ ++   +  +     +P  +R +  +
Sbjct: 47  DLIQAGGIGLLHALERFDASLGASFATYAVQRIRGSMLDELRSRDW---VPRSVRRQARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +  K+ R  +  EIA+ L + +   R+VL  T           DE     G+ 
Sbjct: 104 MTKAIGELEQKLGRSASEPEIAQSLDIELSEYRQVLLDTNNSQLFSY---DEWHEIHGES 160

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E    + +  +PL   ++++LR+     +  L  RE  VL + +   +N    L+E+G 
Sbjct: 161 CEPSMDEDDGGNPLSLLMESSLRDQIMGAIEQLPEREMLVLTLYYQEELN----LKEIGA 216

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              V   R+ Q+ ++AI++L+   +S
Sbjct: 217 VLEVGESRVSQLHSQAIKRLRSKLKS 242


>gi|213423374|ref|ZP_03356362.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 271

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/104 (42%), Positives = 61/104 (58%), Gaps = 13/104 (12%)

Query: 72  NMGINVV----DGDDL---EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           +MGI V+    D DDL   E+   +++  + A++   SSV      +S    T DPVRMY
Sbjct: 1   DMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQVLSSV------ESEIGRTTDPVRMY 54

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+
Sbjct: 55  MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLL 98


>gi|239934562|emb|CAR94595.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 217

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 46/69 (66%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSNYPLTYTFMLNQYEQVKA 60

Query: 177 GTTLLREII 185
           G   L +II
Sbjct: 61  GQGRLVDII 69


>gi|119963836|ref|YP_945938.1| RNA polymerase sigma (70) factor [Arthrobacter aurescens TC1]
 gi|119950695|gb|ABM09606.1| putative RNA polymerase sigma (70) factor [Arthrobacter aurescens
           TC1]
          Length = 258

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 73/151 (48%), Gaps = 5/151 (3%)

Query: 437 GECEASIAKK---EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           G  E SI +     +V  +L L  S+A +Y+       D+ Q   +GL+KA+  +D   G
Sbjct: 16  GAPEGSIRQSFQDSLVLDHLNLAKSIAARYSAHTHDLDDVRQVAYMGLIKASRGYDEAKG 75

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  YA   +   + R + D    +R P  ++D   +V+     M+  ++R P+PEE+A
Sbjct: 76  VSFPAYAAPTIAGEVKRYLRDHCWVVRPPRTIQDVRRQVLARTEEMTQTLQRTPSPEEVA 135

Query: 554 KKLAMPVEGVRKVL--KITKEPISLETPIGD 582
           + L +    VR+ L    +K P SL+ P  D
Sbjct: 136 EDLNLEPCQVREALMAGTSKRPDSLDAPASD 166


>gi|188997568|ref|YP_001931819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932635|gb|ACD67265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 242

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/208 (28%), Positives = 101/208 (48%), Gaps = 25/208 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G +GL  A EKFD   G KFSTYA   V+  I   +        IP ++R+K+  
Sbjct: 39  DLFQVGVLGLYDALEKFDPAKGVKFSTYAEIRVRGYILDHLRQLDW---IPRNIRNKVKN 95

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVE--------GVRKVLKITKEPISLETPIG-- 581
           +      +  K+ RE  PEEIA+ L M +E         V K+L      ISL++ +   
Sbjct: 96  LENKIVELETKLGREAKPEEIAEYLGMSLEEYMIYAEKAVNKIL------ISLDSDVSKD 149

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH 640
           D+++ HL + I   N  +P     +  L+E  + ++ + L  RE+ ++ + +   +N   
Sbjct: 150 DDESLHLWEVI-STNDDTPEKYVEEKQLKEILSDIIMNKLDEREKLIVTLYYYEDLN--- 205

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++E+ +    T  R+ Q+  K + K++
Sbjct: 206 -MKEIAEILGCTESRVSQLHTKIMLKIR 232


>gi|15642066|ref|NP_231698.1| flagellar biosynthesis sigma factor [Vibrio cholerae O1 biovar El
           Tor str. N16961]
 gi|121586929|ref|ZP_01676709.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121727398|ref|ZP_01680537.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|147674794|ref|YP_001217593.1| flagellar biosynthesis sigma factor [Vibrio cholerae O395]
 gi|153213706|ref|ZP_01948958.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|153821715|ref|ZP_01974382.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|153826072|ref|ZP_01978739.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|153828895|ref|ZP_01981562.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|227082193|ref|YP_002810744.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|229507844|ref|ZP_04397349.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229511920|ref|ZP_04401399.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229513722|ref|ZP_04403184.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229519056|ref|ZP_04408499.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229522025|ref|ZP_04411442.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229524074|ref|ZP_04413479.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229528916|ref|ZP_04418306.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229607389|ref|YP_002878037.1| flagellar biosynthesis sigma factor [Vibrio cholerae MJ-1236]
 gi|254226075|ref|ZP_04919673.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|254286814|ref|ZP_04961767.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|254849153|ref|ZP_05238503.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297579572|ref|ZP_06941500.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|298497906|ref|ZP_07007713.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|9656612|gb|AAF95212.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O1 biovar El Tor str. N16961]
 gi|121548865|gb|EAX58908.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121630290|gb|EAX62688.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|124115767|gb|EAY34587.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|125621387|gb|EAZ49723.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|126520813|gb|EAZ78036.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|146316677|gb|ABQ21216.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|148875601|gb|EDL73736.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|149740189|gb|EDM54342.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|150423105|gb|EDN15053.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|227010081|gb|ACP06293.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|227013963|gb|ACP10173.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|229332690|gb|EEN98176.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229337655|gb|EEO02672.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229340950|gb|EEO05955.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229343745|gb|EEO08720.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229348903|gb|EEO13860.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229351885|gb|EEO16826.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229355349|gb|EEO20270.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229370044|gb|ACQ60467.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MJ-1236]
 gi|254844858|gb|EET23272.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297537166|gb|EFH75999.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|297542239|gb|EFH78289.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|327484600|gb|AEA79007.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 96/200 (48%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +  ++ R+PT  E+AK L M +E    VL      I+    +G ED     D 
Sbjct: 103 ISQAIAVLEGELNRDPTDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVSDDA 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   E+    SP     + + R+     + SL  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPFEEGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 LGVSESRVSQILSQSMQRLR 234


>gi|302556917|ref|ZP_07309259.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
 gi|302474535|gb|EFL37628.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
          Length = 263

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/218 (27%), Positives = 100/218 (45%), Gaps = 9/218 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E  + + E+V A L +   +A ++  RG    DL Q   +GL+KA + +D   G  F  Y
Sbjct: 33  ERRMLRDELVTAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPARGNAFEAY 92

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAM 558
           A+  V   I R   D   T+ +P  ++D  ++V ++A+ ++     R PT  EIA    +
Sbjct: 93  AVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRQSAKELAQTTPGRAPTVAEIAAHARL 152

Query: 559 PVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             + VR  ++  +    +SL+  +   D   LGD +   +     D+ +    R      
Sbjct: 153 TEDEVRTGMEALECFTALSLDAEMPGTDGYALGDALGGPD--PGYDTVVD---RVAVRPC 207

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L +L  RE  +L +RF  GM      E++G  Q  V+R
Sbjct: 208 LEALPERERLILYLRFFRGMTQSGIAEQLGISQMHVSR 245


>gi|266624394|ref|ZP_06117329.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288863758|gb|EFC96056.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 216

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 95/228 (41%), Gaps = 55/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E N+RLV  VAKKY N      DL+  G IGL+KA   F    G + +TYA   
Sbjct: 27  ARATLIERNMRLVAHVAKKYQNTDYDMEDLLSVGTIGLIKAVNTFHTDRGSRLATYAAKC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+                     ++I  ++R  ++ S +                     
Sbjct: 87  VE---------------------NEILMLLRANKKYSKE--------------------- 104

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                     +SL  PIG   D +T  L D IE +N  +     +  ++RE        L
Sbjct: 105 ----------VSLFEPIGVDKDGETVSLVDVIEMENKEALETIILSQDIRELYDAFDHCL 154

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              E++V+ MR+G+    +HT  E+     ++R  + +IE K+I KL+
Sbjct: 155 RDTEKKVIGMRYGLYGGKEHTQREIADMLGISRSYVSRIEKKSIEKLR 202


>gi|160943881|ref|ZP_02091111.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444557|gb|EDP21561.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104730|emb|CBL02274.1| RNA polymerase, sigma 29 subunit, SigE [Faecalibacterium
           prausnitzii SL3/3]
          Length = 234

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 102/226 (45%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++  NLRLV+ +AKKY N G+   DL+  G IGL+KA   F      K +TYA   
Sbjct: 54  AREELITHNLRLVVYLAKKYENSGVPAEDLVSIGTIGLIKAVNTFTPARSIKLATYA--- 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   R+ SN+ ++E +               
Sbjct: 111 -----SRCIGNE----------------ILMYLRKSSNR-RQEAS--------------- 133

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                   EP++++   GD +   L D +  D NAVS      Q   R      +A+L+ 
Sbjct: 134 ------IDEPLNVD---GDGNELLLSDILGSDANAVS--QQLEQDAERAVLRSAVAALSA 182

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +++ +RFG+    + T +E      +++  I ++E + IR LK
Sbjct: 183 RERQIMELRFGLTDGVERTQKEAADALGISQSYISRLEKRIIRTLK 228


>gi|112962639|gb|ABI29096.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
          Length = 258

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 114/229 (49%), Gaps = 13/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGV-TEEV 148

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 149 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 204

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 205 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 249


>gi|328474969|gb|EGF45763.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 47

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 38/46 (82%)

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           M     LEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 2   MVVRALLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 47


>gi|307109682|gb|EFN57919.1| hypothetical protein CHLNCDRAFT_141989 [Chlorella variabilis]
          Length = 509

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 101/212 (47%), Gaps = 6/212 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +  AN  LV  +A K+  RGL   DL+ EG + L +AA  F      +F T+A   
Sbjct: 69  AAAMLAHANRPLVTWLAAKFAGRGLAKEDLVAEGMLALERAAGSFHPDREARFGTFAAAA 128

Query: 504 VKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTA-RRMSNKIKREPTPEEIAKKLAMPVE 561
           +  A++R+I  QS  IRIP  H RD    VVR A   +S ++ R P  EEIA+   + V+
Sbjct: 129 ISNALSRAIRRQSRVIRIPETHYRDM--AVVRQAMAELSAELGRPPRCEEIAQSCVLTVK 186

Query: 562 GVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
               +L+ +  +          E+   + D +E++   S      Q  LR+  +  LA L
Sbjct: 187 HTLHLLRAMGTQQQQGGGSEAAEEYDVVDDSLEEEE-CSFAQEERQGMLRQELSSRLAQL 245

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
             ++  ++ +R G+      + +E+G++   T
Sbjct: 246 DSKQALIVSLRHGLHDGRAWSCKEIGERLDCT 277


>gi|260899647|ref|ZP_05908042.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
 gi|308106738|gb|EFO44278.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
          Length = 120

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 4/97 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +  KGE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYKGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEI 113


>gi|188025882|ref|ZP_02960155.2| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
 gi|188020848|gb|EDU58888.1| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
          Length = 246

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 95/203 (46%), Gaps = 18/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A E+FD   G  F+TYA+  ++ ++   +  +      P  +R +  +
Sbjct: 47  DLIQAGGIGLLHALERFDASQGASFATYAVQRIRGSMLDELRSRDWA---PRSVRRQARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
           + +    +   + R  T  EIA+ L + V   R+ L  T       + +   D  H    
Sbjct: 104 MAKVIGELEQSLSRSATESEIAQALNIDVTEYRQALLDTN-----NSQLYSYDEWHEIHG 158

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
                 I++ +  +PL   +++NLR      +  L  RE+ VL + +   +N    L+E+
Sbjct: 159 ESCEPAIDESDGGNPLSLLMESNLRAQIIEAIEQLPEREKLVLTLYYQEELN----LKEI 214

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ Q+ ++AI++L+
Sbjct: 215 GAVLEVGESRVSQLHSQAIKRLR 237


>gi|161898841|gb|ABX80410.1| SigB [Listeria monocytogenes]
          Length = 234

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 112/226 (49%), Gaps = 12/226 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+    + ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVKELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|161898859|gb|ABX80419.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+ +G  F +  Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVIHYKNLVESIARKYS-QGKSFHEDSQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|329904712|ref|ZP_08273913.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327547856|gb|EGF32614.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 244

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 97/207 (46%), Gaps = 12/207 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ-SCTIRIPVHMRDKIH 530
           DLIQ G IGL  A  +++   G +F TYA+    Q I  S+ D+   +  +P  MR  + 
Sbjct: 40  DLIQAGMIGLFDAINRYEDTHGAQFETYAV----QRIRGSMLDELRSSDWLPRSMRQNMR 95

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGD--EDTSH 587
           K+    + +  K+ R P   E+AK + + +   + +L +     +       D  E   H
Sbjct: 96  KIEVAMQALQQKLGRAPLEAEVAKHMKLSLAEYQNLLGEGGGHQLVYYEDFHDSSEGNEH 155

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D      + +PL S + A  R+   R + +L  RE+ ++ + +   MN    L+E+G 
Sbjct: 156 FLDRYCTDLSDNPLQSLLNAGFRDAVIRAIEALPEREKILMGLYYEQEMN----LKEIGA 211

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
              VT  RI Q+ ++AI +++   R K
Sbjct: 212 VLGVTESRISQLHSQAIARMRAFLREK 238


>gi|161898837|gb|ABX80408.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 112/226 (49%), Gaps = 12/226 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+    + ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVKELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|161898933|gb|ABX80456.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+ +G  F +  Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYS-QGKSFHEDSQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 192 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|167040624|ref|YP_001663609.1| sporulation sigma factor SigE [Thermoanaerobacter sp. X514]
 gi|300914665|ref|ZP_07131981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724101|ref|YP_003903852.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|166854864|gb|ABY93273.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889600|gb|EFK84746.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581162|gb|ADN54561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
          Length = 241

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 66/247 (26%), Positives = 115/247 (46%), Gaps = 53/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEEMYLISKMEKGDNEA---KTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++                ++   RR ++
Sbjct: 98  IKAINTFNPKKKIKLATYA--------SRCIENE----------------ILMYLRR-NS 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + +E    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 133 KTKLEVSFDE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   +E  T  L  L  RE++++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 176 --------KELLTSALKKLPDREKKIIGLRFGLEGGVEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLK 668
           K +++LK
Sbjct: 228 KILKRLK 234


>gi|327438482|dbj|BAK14847.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 261

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 119/234 (50%), Gaps = 14/234 (5%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           CE S  +  +V    +LV S+A+KY++    + D++Q G +GL+ A  +FD   G  F  
Sbjct: 27  CEES--QTNLVLHYQQLVESIARKYSHGKSYYDDIVQVGMLGLLGAIRRFDPSFGRSFEA 84

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A+  +   I R + D++  + +P  +++   ++      ++  ++R P+  EIA  L +
Sbjct: 85  FAVPTIVGEIKRFLRDKTWDVHVPRRIKELGPRIKAAVEALTTSLQRSPSITEIATYLEV 144

Query: 559 PVEGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTT 614
             E V + +++ +  + +S++  I  D D S +  F    + V   D+  +  N R    
Sbjct: 145 QDEDVLEAMEMGRSYQALSMDHSIESDSDGSTVTLF----DVVGREDTGYEVTNRRMIVA 200

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  RE +++++ +   ++     +E G++  +++  + +I+ KAI+KL+
Sbjct: 201 DAMNVLNERERQIIQLTYLEQLSQ----KEAGERLGISQMHVSRIQRKAIKKLQ 250


>gi|260361298|ref|ZP_05774403.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
 gi|308111826|gb|EFO49366.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
          Length = 158

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 4/97 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +  KGE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYKGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEI 113


>gi|237653596|ref|YP_002889910.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
 gi|237624843|gb|ACR01533.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
          Length = 257

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/236 (23%), Positives = 112/236 (47%), Gaps = 13/236 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +    + K  +VE    LV  +A +  +R    +   DLIQ G +GL+ A  +++  LG 
Sbjct: 3   DAHGKLDKGGLVENYAPLVKRIAYQLMSRLPASVDVDDLIQNGMMGLLDALGRYEQGLGA 62

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F TYA+  ++ A+   + +      +P  +R  + ++      +  +  R P+  E+A 
Sbjct: 63  QFETYAVQRIRGAMLDGLRENDW---LPRSLRRDMRRIEAAIHSLEQQNGRPPSESELAA 119

Query: 555 KLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L +P+E  +++L+  +  + + LE    +ED  +L   +  +    PL      +LR  
Sbjct: 120 ALDLPLEDYQRMLQDARGHQLVYLEDFNREEDDDYLDRHLA-QEGNDPLTLLEDTDLRRR 178

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE+ V+ + +   +N    L E+G+   VT  R+ Q+ ++A+ +L+
Sbjct: 179 LVGAIEHLPEREQLVMALYYDEELN----LREIGEVLGVTESRVCQLHSQAVARLR 230


>gi|92114133|ref|YP_574061.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797223|gb|ABE59362.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Chromohalobacter
           salexigens DSM 3043]
          Length = 232

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/198 (26%), Positives = 92/198 (46%), Gaps = 11/198 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A E+FD   G  FST+A   V+ A+   +  +     +P  +R     
Sbjct: 40  DLIQAGMVGLLDALERFDATQGASFSTFANQRVRGAMIDELRSRDW---MPRSVRRSARA 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++   + R P   EIA  L M VE   ++L        L     D+  S LG+ 
Sbjct: 97  LDQAVHKLEQTLGRAPDEREIANALGMSVEEYHQLLLDANNGYLLGF---DDVVSELGEP 153

Query: 592 I-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
              D    +P D+ +Q + R      +  L  RE+ +L + +   +N    L+E+G    
Sbjct: 154 PGGDTAPATPHDALLQGDARTHLVAAIEHLPEREKLLLGLYYQEELN----LKEIGAVLG 209

Query: 651 VTRERIRQIEAKAIRKLK 668
           V+  R+ Q+ ++A+ +L+
Sbjct: 210 VSESRVCQLHSQAVARLR 227


>gi|330445383|ref|ZP_08309035.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328489574|dbj|GAA03532.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 240

 Score = 66.6 bits (161), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 94/200 (47%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F T+A   ++ A+   I        +P  +     K
Sbjct: 44  DLIQSGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRK 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      + N++ R+P  +EIA+ L MP+E   + L      ++    +G  D     D 
Sbjct: 101 ISEAISHLENELGRDPNDQEIAQYLDMPLEQYHQALN----DVNCGRLVGISDLGVAEDS 156

Query: 592 IEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           + ++ ++   +P       + R +    + +L  RE  VL + +   +N    L+E+G  
Sbjct: 157 VANEESIEENAPFQDVADDSFRASLAEAIKTLPEREALVLSLYYDEELN----LKEIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  RI QI ++A+++L+
Sbjct: 213 IGVSESRICQIHSQAMQRLR 232


>gi|311898622|dbj|BAJ31030.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 276

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 95/207 (45%), Gaps = 21/207 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ AI   I +      IP  +R K   
Sbjct: 74  DFVSSGVFGLIDAIEKFDIDRAIKFETYAISRIRGAI---IDELRALDWIPRSVRQKAKA 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---- 587
           V R    +  +++R P   E+A ++ + ++ +  +       +SL   +  ++  H    
Sbjct: 131 VERAYATLEARLRRTPYDPEVAAEMGISLDDLHTIFS----QLSLANVVALDELLHSAGE 186

Query: 588 ------LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L + + D  A +P++ A    LR      + +L  RE+ V+ + +  G+    T
Sbjct: 187 GGDRLTLMETLPDSGADNPVEIAEDRELRRLLASAVNTLPEREKTVVTLYYYEGL----T 242

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+G+   VT  R+ QI  K++ +L+
Sbjct: 243 LAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|225018077|ref|ZP_03707269.1| hypothetical protein CLOSTMETH_02014 [Clostridium methylpentosum
           DSM 5476]
 gi|224949074|gb|EEG30283.1| hypothetical protein CLOSTMETH_02014 [Clostridium methylpentosum
           DSM 5476]
          Length = 267

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 99/224 (44%), Gaps = 54/224 (24%)

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           ++T  G+ + DL+QE    +++A E FD     KF++Y                   +  
Sbjct: 47  RFTRLGVDYDDLVQECYFAMVEAVEAFDPESELKFTSY-------------------LNF 87

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+  R       RT+R+     K +PT                  L  T    SL+  +G
Sbjct: 88  PIKKRLNAISNNRTSRQ-----KNDPT------------------LSCT----SLDIEVG 120

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMN 637
            E    LG+ I DK A  P +   Q +    L+E    VL +LT  ++ V+R+RF     
Sbjct: 121 AEGDCPLGELIPDKTAGIPFEVIEQQDWNRALQEAIETVLDTLTENQQEVIRLRF----Y 176

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            D +L E+ ++   +RERIRQI+ ++++ +K P   K L+ F D
Sbjct: 177 EDKSLIEISEETGRSRERIRQIQGQSLKAMKKPLPRKILKPFYD 220


>gi|56460225|ref|YP_155506.1| flagellar biosynthesis sigma factor [Idiomarina loihiensis L2TR]
 gi|56179235|gb|AAV81957.1| DNA-directed RNA polymerase specialized sigma 28 subunit
           [Idiomarina loihiensis L2TR]
          Length = 241

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 106/231 (45%), Gaps = 18/231 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  ++E +  LV  +A     R    +Q  DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  RNAIIEQHTGLVKRIAHHMMARLPASVQVDDLIQAGMIGLLEAARNFDNSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH   +  +V+   R++ N+  R+    E+A KL M ++
Sbjct: 74  IRIRGAMLDEIRRGDWAPR-SVHRNHR--RVLEAIRQVENETGRDAKDTEVAAKLNMGMD 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK----NAVSPLDSAIQANLRETTTRVL 617
               +L+     +S    +G ED     D I  +    +A  P      A   +     +
Sbjct: 131 EYHHILR----DVSTGRIVGIEDLGVSEDAIMPEQVTGSAYEPQKDVENAAFHKALVSTI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +SL  RE  VL + +   +N    L+E+G+   V+  R+ QI ++A+ +LK
Sbjct: 187 SSLPEREALVLSLYYDEELN----LKEIGEVLSVSESRVSQIHSQAMLRLK 233


>gi|310643955|ref|YP_003948713.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248905|gb|ADO58472.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 257

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/209 (26%), Positives = 104/209 (49%), Gaps = 14/209 (6%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NR   + DL Q G + L++  +++D  LG  F  YAM  +   +   + D+S  I++P  
Sbjct: 51  NRPDLYEDLYQTGQMALIRLLQQYDISLGIPFEPYAMKSMLGHMKNYLRDKSWYIQVPRR 110

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD 582
           +++K   V      ++ K++R P   EIA+ L + VE   +VL  +     +SL++P+  
Sbjct: 111 IKEKGALVQHAIDELTVKLERSPNVNEIAEYLDLTVEETIEVLAGRECYHYVSLDSPLSQ 170

Query: 583 EDTSH-LGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           E+++  LG+ I  D N    ++       R    + L+ L  +E++VL + F  G +   
Sbjct: 171 EESAATLGELISSDANDFDTVEK------RMDLQQALSQLKEQEQKVLLLAFQDGQSQRA 224

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +G    V++  + +I+ +A  KLK 
Sbjct: 225 IAQTLG----VSQMSVSRIQKRATEKLKQ 249


>gi|308070731|ref|YP_003872336.1| DNA-directed RNA polymerase specialized sigma subunit
           [Paenibacillus polymyxa E681]
 gi|305860010|gb|ADM71798.1| DNA-directed RNA polymerase specialized sigma subunit
           [Paenibacillus polymyxa E681]
          Length = 257

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/209 (26%), Positives = 104/209 (49%), Gaps = 14/209 (6%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NR   + DL Q G + L++  +++D  LG  F  YAM  +   +   + D+S  I++P  
Sbjct: 51  NRPDLYEDLYQTGQMALIRLLQQYDISLGIPFEPYAMKSMLGHMKNYLRDKSWYIQVPRR 110

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD 582
           +++K   V      ++ K++R P  +EIA  L + VE   +VL  +     +SL++P+  
Sbjct: 111 IKEKGALVQHAIDELTVKLERSPNVDEIATYLDLTVEETIEVLAGRECYHYVSLDSPLSQ 170

Query: 583 EDTSH-LGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           E+++  LG+ I  D N    ++       R    + L+ L  +E++VL + F  G +   
Sbjct: 171 EESAATLGELISSDANDYDTVEK------RMDLQQALSQLKEQEQKVLLLAFQDGQSQRA 224

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +G    V++  + +I+ +A  KLK 
Sbjct: 225 IAQTLG----VSQMSVSRIQKRATEKLKQ 249


>gi|205373400|ref|ZP_03226204.1| RNA polymerase sigma factor SigD [Bacillus coahuilensis m4-4]
          Length = 257

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 101/199 (50%), Gaps = 9/199 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G +GL+ A +KFD     KF TYA + ++ +I   +  +     +P + RDK  K
Sbjct: 55  DLKSLGMMGLLDALQKFDIERDLKFDTYASFRIRGSIIDGLRKEDW---LPRNTRDKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           + +T  R+   + R+  PE++AK+L M  + V +++        +S++    +E+     
Sbjct: 112 IEKTISRLEQTLMRKIVPEDVAKELDMSADEVIQIMNEHFFANVLSMDEMTREEEKDSPK 171

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             ++D+ + SP +  +++       + +  L  +E+ VL + +      + TL E+G+  
Sbjct: 172 FQMQDEKSRSPEEELVKSEQIRDLEQHIRGLNEKEQLVLSLFY----QEELTLTEIGEVL 227

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++  RI QI +KA+ KL+
Sbjct: 228 QLSTSRISQIHSKALFKLR 246


>gi|297197437|ref|ZP_06914834.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197716285|gb|EDY60319.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 298

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/261 (20%), Positives = 124/261 (47%), Gaps = 39/261 (14%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA 
Sbjct: 49  QFFQRLTELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMEDIVQTGMIGLIKAI 108

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +++++ R
Sbjct: 109 DRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELASRLDR 168

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITK--------EPISLETPIGDEDTSHLGDFI----- 592
           +PT  E+A  + +  + V +    +           ++ + P G E    L DFI     
Sbjct: 169 DPTVAELATLMNISEKEVIEAQIASNGYNSSSLDAALTGDGPEGGEAV--LADFIGVEED 226

Query: 593 -----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                ED ++++PL               +A L+ R+ +++ MRF      + T  E+G+
Sbjct: 227 GLRLVEDFHSLAPL---------------MAELSERDRQIIHMRF----VEEATQSEIGE 267

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +   ++  + ++  + I +L+
Sbjct: 268 RLGCSQMHVSRLIKRIITRLR 288


>gi|167770197|ref|ZP_02442250.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
 gi|167667519|gb|EDS11649.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
          Length = 257

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 102/213 (47%), Gaps = 14/213 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +++ +G I L+ + ++FD   G KFSTYA   VK AI   +  Q     +P  +R    +
Sbjct: 57  EMVNQGVIALIDSVDRFDPDHGVKFSTYAFTKVKGAIIDYVRKQDW---LPRRVRHNAIR 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMP-VEGVRKVLKITKEPI-SLETPIGDEDTSHLG 589
           V      +  K+ R PT  E+AK+L M   E  + + +++ E I S E+ + D   +   
Sbjct: 114 VNNAYNDLPMKLGRNPTRSEMAKQLDMSEREFDQCIYEMSGESIFSYESLLADGPQNQNM 173

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            +  +   V+P        LRE     + SL  +E  VL + +      + T++E+G   
Sbjct: 174 LWPMEGEIVNPEGCVDAKELREQLGMAIDSLNEQERHVLSLYY----YENLTMKEIGGVL 229

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            V+ +RI QI  K I+KL++     KL  ++ G
Sbjct: 230 GVSEQRIGQINRKLIQKLRN-----KLEQYMKG 257


>gi|217077805|ref|YP_002335523.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
 gi|217037660|gb|ACJ76182.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
          Length = 226

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 97/199 (48%), Gaps = 14/199 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG +  ++A EKFD   G K  +Y +  VK A+   +        +P ++R  I K
Sbjct: 34  DLIQEGLVAFIQAIEKFDPKKGAKLRSYLLTRVKGAMYDYLRKIDW---MPKNLRHDI-K 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +V  A         +   E+IAK   +P+E V++       K+ + L++ I D D+  + 
Sbjct: 90  LVEDAIVNMESDTNDIDFEKIAKITNLPIENVKRAYNELTRKQLLMLDSYISD-DSELID 148

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
               D+N   P   AI   L+E     +  L  +E+ +L +RF      + +L+E+GK  
Sbjct: 149 KIASDEN---PYSYAINELLKEQLIEAIKKLDDKEQLLLSLRF----EHELSLKEIGKVL 201

Query: 650 CVTRERIRQIEAKAIRKLK 668
            VT  R+ Q+ AK + KLK
Sbjct: 202 NVTESRVSQLLAKTLAKLK 220


>gi|150387863|ref|YP_001317912.1| RinA family phage transcriptional regulator [Alkaliphilus
           metalliredigens QYMF]
 gi|149947725|gb|ABR46253.1| phage transcriptional regulator, RinA family [Alkaliphilus
           metalliredigens QYMF]
          Length = 266

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 113/230 (49%), Gaps = 14/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + E+V   L +   ++KK+ N+G+ + D+ Q  ++GL+ A E+FD   G++FS++A   
Sbjct: 38  VRNELVNRYLYIAEILSKKFLNKGIDYEDIYQVASLGLIYAIERFDLSRGFEFSSFATPT 97

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I +   D+  +IR+P  +++   KV      +   ++R P  ++IA+ L    E V
Sbjct: 98  IIGEIKKHFRDKGWSIRVPRRIQELSKKVNTAKMTLHQNLQRTPMIKDIAEYLNCTQEEV 157

Query: 564 RKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++ ++   P SL+      G++    L D I +K+      +  +   R+   + + 
Sbjct: 158 MEAMEASQVYTPKSLDLTYDNDGEDKDIQLIDLIGEKDK-----NFDEIENRDFLKKAMR 212

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   E++VL  RF        T   V ++  V++  + ++E + I K +
Sbjct: 213 NLNEVEKKVLEDRFF----NSKTQMNVAEELNVSQMTVSRMEKRIIEKFR 258


>gi|284029882|ref|YP_003379813.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Kribbella
           flavida DSM 17836]
 gi|283809175|gb|ADB31014.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Kribbella
           flavida DSM 17836]
          Length = 272

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 102/217 (47%), Gaps = 12/217 (5%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E+VE N+ +   +A+++  RG +  DL Q   +GL+KAA  +       F  +A+  ++
Sbjct: 46  EEVVELNIEMARGIARRFRGRGAEADDLEQVAYLGLVKAAHHYRLDADTPFIGFAIPTIR 105

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R   D + T+RIP  +++    +      +   + REPTP EIA  L + +  V +
Sbjct: 106 GEVKRYFRDCAWTVRIPRRLQEMQGTIAAKLPYLEQLLNREPTPAEIADHLGVELSEVEQ 165

Query: 566 VL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            L  K     +SL+ P   D D +     + D  A     +  Q    +    VLA L  
Sbjct: 166 ALAAKGCFNVLSLDRPAEADADLT-----LADVVADDDDATIDQLEAVDMLQPVLADLGE 220

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           RE R+L++RF  G     T  E+G    V++ ++ ++
Sbjct: 221 RERRILQLRFVEGW----TQSEIGADIGVSQMQVSRV 253


>gi|197335206|ref|YP_002156660.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio fischeri MJ11]
 gi|197316696|gb|ACH66143.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio fischeri MJ11]
          Length = 243

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 96/201 (47%), Gaps = 16/201 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F TYA   ++ ++   I       R  VH   K  +
Sbjct: 46  DLIQAGMIGLLEAQQNYDGSKGASFETYAGIRIRGSMLDEIRRGDWVPR-SVH---KNSR 101

Query: 532 VVRTA-RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++ +A R +  K+ R+PT +EIA  L +P++   ++L      ++    +G ED     D
Sbjct: 102 MINSAIRELEAKLSRDPTDKEIADYLELPLDQYYQILN----DVNCGKLVGMEDLGVSDD 157

Query: 591 FI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            I   E  +   P       + R      + +L  RE  VL + +   +N    L+E+G 
Sbjct: 158 VIATEEQADDNIPFQGVADEHFRVALVEAIKTLPEREALVLSLYYDEELN----LKEIGA 213

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI ++++++L+
Sbjct: 214 VIGVSESRVSQIHSQSMQRLR 234


>gi|322381761|ref|ZP_08055715.1| sporulation sigma factor SigF-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154149|gb|EFX46471.1| sporulation sigma factor SigF-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 200

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/207 (26%), Positives = 100/207 (48%), Gaps = 14/207 (6%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG +  DL Q G IGL+K+ +KF+     KFSTYA+  +   I R + D   T+++   
Sbjct: 2   NRGYEADDLFQIGCIGLLKSVDKFNLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRS 60

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GD 582
           +++  +KV +T   +S  ++R PT +E+A  L +  E V    +  K   S+   +   D
Sbjct: 61  LKELANKVRKTKDELSKNLERLPTLKEVANALGITPEEVVFAQEANKPLSSIHETVFEND 120

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D   L D I D +     D       +      +  L+ RE  ++ +R+      D T 
Sbjct: 121 WDPITLMDQIADDSQEKWFD-------KLALNEAIEGLSERERLIVYLRYF----KDQTQ 169

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV  +  +++ ++ ++E K ++ +++
Sbjct: 170 SEVANRLGISQVQVSRLEKKILQSIRN 196


>gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase sigma factor [Herbaspirillum
           seropedicae SmR1]
 gi|300074130|gb|ADJ63529.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           protein [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/233 (22%), Positives = 110/233 (47%), Gaps = 17/233 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K +++E +  LV  +A +   +    ++  DLIQ G +GL+ A  +++   G +F TYA
Sbjct: 9   GKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQFETYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  ++ A+   +        +P  +R    KV    + +  ++ R+P   E+A+ + + +
Sbjct: 69  VQRIRGAMLDELRSSDW---LPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQHMQISL 125

Query: 561 EGVRKVL-KITKEPISLETPIGDEDTSHLGDFIEDKNAVS----PLDSAIQANLRETTTR 615
           E  + +L +     +       D+D  H  +   D++  S    PL + I    RE    
Sbjct: 126 EDYQSLLSECGGHQLIYYEDFHDDDGGH--EHFLDRHQTSDSDDPLQNLINGGFREAVVD 183

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE+ ++ + +   MN    L+E+G    V+  R+ Q+ ++AI +++
Sbjct: 184 SIKALPEREQILMALYYEQEMN----LKEIGAVMGVSESRVCQLHSQAISRMR 232


>gi|313895821|ref|ZP_07829375.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320529404|ref|ZP_08030492.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
 gi|312975246|gb|EFR40707.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320138370|gb|EFW30264.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
          Length = 246

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 94/201 (46%), Gaps = 21/201 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A E+++   G KF TYA   V+ A+   +  +     IPV +R  I K
Sbjct: 53  DLLSSGFFGLLDAIERYELTRGNKFETYAGVRVRGAMLDHLRSKDW---IPVSVRQNIKK 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             +    +  K+ R  T EE+A +L +  EG+R           LE+ +       L ++
Sbjct: 110 YEKAVASLEGKLGRTATDEELAAELGLTREGLRH----------LESQVSAATVIPLEEY 159

Query: 592 IEDKNAVS----PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +   + VS    P++ A    ++ET    + +L  +E  V+ + +      + TL+E+  
Sbjct: 160 LRTDSPVSLEDGPVEHAEWTEVKETLAAAIENLPEKERTVVALYY----YDEMTLKEIAA 215

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+  KAI +++
Sbjct: 216 ILHLSEARISQLHTKAIFRMR 236


>gi|304316726|ref|YP_003851871.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778228|gb|ADL68787.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 231

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 96/224 (42%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY+N G    DLI  G IGL+KA   +D   G   +TYA   
Sbjct: 51  AKNILIERNLRLVAHIVKKYSNTGKDVDDLISIGTIGLIKAISTYDASKGTHLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  S+                         R   KIK E + ++       P+ G+
Sbjct: 111 IENEILMSL-------------------------RSEKKIKSEISLQD-------PI-GI 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E T  + D +E +  +  L S I + L+            R
Sbjct: 138 DK----EGNAISLIDILGTE-TDEVSDQVELEMQIKKLYSKINSVLKN-----------R 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  ++ +R+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 182 ERLIIELRYGLVNGGAKTQREIAKMLGISRSYVSRIEKKALSKL 225


>gi|261409324|ref|YP_003245565.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Paenibacillus
           sp. Y412MC10]
 gi|329928598|ref|ZP_08282465.1| putative RNA polymerase sigma factor SigB [Paenibacillus sp. HGF5]
 gi|261285787|gb|ACX67758.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. Y412MC10]
 gi|328937714|gb|EGG34123.1| putative RNA polymerase sigma factor SigB [Paenibacillus sp. HGF5]
          Length = 256

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 107/216 (49%), Gaps = 12/216 (5%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++  K   NR   + DL Q G + L++  +++D  LG  F  YAM  +   +   + D+S
Sbjct: 43  MAAGKIARNRPDLYEDLYQVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKS 102

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPI 574
             I++P  +++K   V +    +  K++R P   EIA  L + VE   +VL  +     +
Sbjct: 103 WYIQVPRRIKEKGALVQQAIDELMVKLERSPDVNEIASYLDLSVEETVEVLAGRECYHYV 162

Query: 575 SLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           SL++P+  E+T + LG+ I   + V+  DS      R    + ++ L  +E++VL + F 
Sbjct: 163 SLDSPLSQEETGATLGELI--SSDVNDFDS---VEKRMDLQQAMSQLKEQEQKVLLLAFQ 217

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            G +     + +G    V++  + +I+ +A  KLK 
Sbjct: 218 EGQSQRAIAQRLG----VSQMSVSRIQKRATEKLKQ 249


>gi|59712441|ref|YP_205217.1| flagellar biosynthesis sigma factor [Vibrio fischeri ES114]
 gi|59480542|gb|AAW86329.1| RNA polymerase, sigma-28 (sigma-F, FliA) factor [Vibrio fischeri
           ES114]
          Length = 243

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 96/201 (47%), Gaps = 16/201 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F TYA   ++ ++   I       R  VH   K  +
Sbjct: 46  DLIQAGMIGLLEAQQNYDGSKGASFETYAGIRIRGSMLDEIRRGDWVPR-SVH---KNSR 101

Query: 532 VVRTA-RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++ +A R +  K+ R+PT +EIA  L +P++   ++L      ++    +G ED     D
Sbjct: 102 MINSAIRELEAKLSRDPTDKEIADYLELPLDQYYQILN----DVNCGKLVGMEDLGVSDD 157

Query: 591 FI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            I   E  +   P       + R      + +L  RE  VL + +   +N    L+E+G 
Sbjct: 158 VIATEEQADDNLPFQGVADEHFRVALVEAIKTLPEREALVLSLYYDEELN----LKEIGA 213

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI ++++++L+
Sbjct: 214 VIGVSESRVSQIHSQSMQRLR 234


>gi|83749399|ref|ZP_00946393.1| RNA polymerase sigma-f factor for flagellar operon (fliA)
           [Ralstonia solanacearum UW551]
 gi|83723926|gb|EAP71110.1| RNA polymerase sigma-f factor for flagellar operon (fliA)
           [Ralstonia solanacearum UW551]
          Length = 253

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 96/206 (46%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 50  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  +++  +  R PT  EIA  L M +   +K+L   +    L     D D      F
Sbjct: 107 IEQAIQKLQQQKGRAPTETEIAAALEMSLADYQKLLVELQGSQLLYYE--DFDREDADAF 164

Query: 592 IEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           IE++   N  +PLD  +  +LRE+    + +L  RE+ ++ + +      D  L E+G  
Sbjct: 165 IENRAAENDATPLDQLLDHDLRESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAV 220

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             V+  R+ QI ++AI +++   R +
Sbjct: 221 MGVSESRVCQIHSQAIARIRARLRER 246


>gi|313624456|gb|EFR94462.1| RNA polymerase sigma-B factor [Listeria innocua FSL J1-023]
          Length = 215

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/214 (23%), Positives = 107/214 (50%), Gaps = 12/214 (5%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  +   I R + D++ +
Sbjct: 1   IARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWS 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISL 576
           + +P  +++   K+      ++ +++  P   +IA  + +  E V + +++ K  + +S+
Sbjct: 61  VHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSV 120

Query: 577 ETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGI 634
           +  I  D D    G  I   + V   D   +  N R    +VL  L  RE+++L+  F  
Sbjct: 121 DHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPVLDEREQKILQYTF-- 174

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 175 --IENRSQKETGELLDISQMHVSRIQRQAIKKLR 206


>gi|254479124|ref|ZP_05092475.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214034938|gb|EEB75661.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 234

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 75/271 (27%), Positives = 115/271 (42%), Gaps = 54/271 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            V   V  IL +     + S  + +S  E R  +   R+G+ EA   +  ++E NLRLV 
Sbjct: 11  LVGTIVKEILNLGYLTNTNSFPSPLSPEEERKYLEAYRRGDEEA---RNILIERNLRLVA 67

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA + +D+  G   +TYA   ++  I  SI     
Sbjct: 68  HVVKKYSGTGRDLDDLISIGTIGLIKAIDTYDFEKGTHLATYAAKCIENEILMSI----- 122

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                               R   K+K E   ++       P+ GV K        ISL 
Sbjct: 123 --------------------RAEKKMKGEVFLQD-------PI-GVDK----EGNEISLM 150

Query: 578 TPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
             +G DED   + + +E K  +  L S + + L+            RE  ++ MR+G+  
Sbjct: 151 DVLGTDED--EVSEQVEKKIQIKKLYSKLNSVLKN-----------RERMIIEMRYGLYN 197

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               T  E+ K   ++R  + +IE KA+ KL
Sbjct: 198 GRVRTQREIAKMLGISRSYVSRIEKKALNKL 228


>gi|169827149|ref|YP_001697307.1| RNA polymerase sigma factor SigD [Lysinibacillus sphaericus C3-41]
 gi|168991637|gb|ACA39177.1| RNA polymerase sigma-D factor (Sigma-28) [Lysinibacillus sphaericus
           C3-41]
          Length = 271

 Score = 66.2 bits (160), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/190 (27%), Positives = 86/190 (45%), Gaps = 9/190 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGL  A  KFD     KF TYA + V+ AI   +  +     +P   R+K  K
Sbjct: 70  DLTSLGMIGLFDALNKFDINRDLKFDTYASFRVRGAIIDGLRKEDW---LPRSAREKAKK 126

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +     ++  K  R  TPEE+AK + +PVE V + ++       +S+      E+     
Sbjct: 127 LDAQIEQLEQKYMRHVTPEELAKHMEVPVEDVYQTVQEHFFSNVLSINEQQDQEEVDGKS 186

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D    +P  S +++ L +     +  L  +E+ VL + +      + TL E+G+  
Sbjct: 187 FVIRDDTTKTPEQSVVKSELLDDLAENIQKLNEKEQLVLSLFY----TEELTLTEIGEML 242

Query: 650 CVTRERIRQI 659
            ++  RI QI
Sbjct: 243 ELSTSRISQI 252


>gi|20807708|ref|NP_622879.1| sporulation sigma factor SigK [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516259|gb|AAM24483.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 231

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 75/271 (27%), Positives = 115/271 (42%), Gaps = 54/271 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            V   V  IL +     + S  + +S  E R  +   R+G+ EA   +  ++E NLRLV 
Sbjct: 8   LVGTIVKEILNLGYLTNTNSFPSPLSPEEERKYLEAYRRGDEEA---RNILIERNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA + +D+  G   +TYA   ++  I  SI     
Sbjct: 65  HVVKKYSGTGRDLDDLISIGTIGLIKAIDTYDFEKGTHLATYAAKCIENEILMSI----- 119

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                               R   K+K E   ++       P+ GV K        ISL 
Sbjct: 120 --------------------RAEKKMKGEVFLQD-------PI-GVDK----EGNEISLM 147

Query: 578 TPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
             +G DED   + + +E K  +  L S + + L+            RE  ++ MR+G+  
Sbjct: 148 DVLGTDED--EVSEQVEKKIQIKKLYSKLNSVLKN-----------RERMIIEMRYGLYN 194

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               T  E+ K   ++R  + +IE KA+ KL
Sbjct: 195 GRVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|22126347|ref|NP_669770.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM 10]
 gi|45441369|ref|NP_992908.1| flagellar biosynthesis sigma factor [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807215|ref|YP_651131.1| flagellar biosynthesis sigma factor [Yersinia pestis Antiqua]
 gi|108812441|ref|YP_648208.1| flagellar biosynthesis sigma factor [Yersinia pestis Nepal516]
 gi|145598571|ref|YP_001162647.1| flagellar biosynthesis sigma factor [Yersinia pestis Pestoides F]
 gi|149366211|ref|ZP_01888246.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CA88-4125]
 gi|165925981|ref|ZP_02221813.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165938720|ref|ZP_02227275.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010831|ref|ZP_02231729.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166210907|ref|ZP_02236942.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167401029|ref|ZP_02306532.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167420291|ref|ZP_02312044.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167425870|ref|ZP_02317623.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470709|ref|ZP_02335413.1| flagellar biosynthesis sigma factor [Yersinia pestis FV-1]
 gi|218928962|ref|YP_002346837.1| flagellar biosynthesis sigma factor [Yersinia pestis CO92]
 gi|229896290|ref|ZP_04511460.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Pestoides A]
 gi|229897227|ref|ZP_04512383.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229897954|ref|ZP_04513105.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229902815|ref|ZP_04517932.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Nepal516]
 gi|270486604|ref|ZP_06203678.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM D27]
 gi|294503994|ref|YP_003568056.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|21959330|gb|AAM86021.1|AE013850_3 alternative sigma factor 28 [Yersinia pestis KIM 10]
 gi|45436229|gb|AAS61785.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108776089|gb|ABG18608.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Nepal516]
 gi|108779128|gb|ABG13186.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Antiqua]
 gi|115347573|emb|CAL20483.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CO92]
 gi|145210267|gb|ABP39674.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides F]
 gi|149292624|gb|EDM42698.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CA88-4125]
 gi|165913334|gb|EDR31956.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165922185|gb|EDR39362.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165990175|gb|EDR42476.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166208087|gb|EDR52567.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166961986|gb|EDR58007.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167049418|gb|EDR60826.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167055269|gb|EDR65066.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229680262|gb|EEO76361.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Nepal516]
 gi|229688995|gb|EEO81060.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229693564|gb|EEO83613.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229701213|gb|EEO89242.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Pestoides A]
 gi|262361821|gb|ACY58542.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D106004]
 gi|262366043|gb|ACY62600.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D182038]
 gi|270335108|gb|EFA45885.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM D27]
 gi|294354453|gb|ADE64794.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|320015417|gb|ADV98988.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 240

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 95/198 (47%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G I L+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIDLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++ R  T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQQVEQRVGRPATEQEVAQVLDIGLVEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLKHLLEGNLRQRVIDAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|239995147|ref|ZP_04715671.1| flagellar biosynthesis sigma factor [Alteromonas macleodii ATCC
           27126]
          Length = 243

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 108/230 (46%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K ++VE +  LV  +A     R    +   DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  KAQLVERHAPLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I     T R  VH   +   +     ++ ++  R+    +IA KL + ++
Sbjct: 74  IRIRGAMLDEIRKGDWTPR-SVHRNGR--AITEAISQVESETGRDARDSDIADKLNVSLQ 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLA 618
              ++L      ++    +G ED     D I   +++ + +PL+  +Q   ++     + 
Sbjct: 131 DYHQMLN----EVNAGKLVGIEDLGVSEDVISTEQNRGSDAPLEDLMQGAFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ KLK
Sbjct: 187 TLPEREAIVLSLYYDEELN----LREIGEVLDVSESRVSQIHSQAMLKLK 232


>gi|116668918|ref|YP_829851.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116609027|gb|ABK01751.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
          Length = 275

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/219 (23%), Positives = 108/219 (49%), Gaps = 13/219 (5%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L L  ++A ++  RG    DL Q   +GL+KAA  FD   G  F  YA   +   + R +
Sbjct: 36  LDLAEALAARFQARGRDRADLNQVAYLGLVKAARGFDEARGASFPAYAAPTITGELKRYL 95

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK- 571
            D+   +R P H++D   +++R    ++  + R P+  E+A++LA+  E V +       
Sbjct: 96  RDRCWMVRPPRHVQDLRSELLRAEPALAQSLGRPPSAAELARELAVSPEAVNEATAAAAS 155

Query: 572 -EPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
             P SL+    + DT+ L + +   ++ ++ L+  I  N      + +  LT  ++ +L 
Sbjct: 156 LHPDSLDAVDANTDTAPLAETLSSGEDPLARLEELICLN------QAIHELTAEDQELLY 209

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+      + +  E+G++F V++ ++ +  ++ + +L+
Sbjct: 210 RRY----FCEESQAELGRRFGVSQMQVSRRLSRVLVQLQ 244


>gi|210610056|ref|ZP_03288235.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
 gi|210152667|gb|EEA83673.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
          Length = 208

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 114/260 (43%), Gaps = 68/260 (26%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD---- 472
           S    ++ +E ++ +    +G+ EA   K  ++E NLRLV  V KKY     Q+LD    
Sbjct: 6   SFPIPLTAAEEQYYIQKYIEGDLEA---KHILIERNLRLVAHVIKKY-----QYLDDDPE 57

Query: 473 -LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
            LI  G IGL+KA   F+     +  TYA                               
Sbjct: 58  DLISIGTIGLIKAVATFNPSKNNRLGTYA------------------------------- 86

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGD 590
               AR + N+I            L M    +R   K++KE ISL  PIG D + + +  
Sbjct: 87  ----ARCIENEI------------LMM----LRSKKKVSKE-ISLYEPIGTDREGNEIQL 125

Query: 591 FIEDKNAVSPLDS--AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           F   +       +  A++ +++   T+V + L+PRE  VL+MR+G+    ++T  E+  Q
Sbjct: 126 FDIIEADDDDAQTKVALKEDIKMLYTKVESELSPRERLVLKMRYGLYDEEEYTQREIAAQ 185

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             ++R  + +IE  AI KL+
Sbjct: 186 LGISRSYVSRIEKSAIEKLR 205


>gi|126653717|ref|ZP_01725635.1| sigma factor SigD [Bacillus sp. B14905]
 gi|126589681|gb|EAZ83817.1| sigma factor SigD [Bacillus sp. B14905]
          Length = 256

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/190 (27%), Positives = 86/190 (45%), Gaps = 9/190 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGL  A  KFD     KF TYA + V+ AI   +  +     +P   R+K  K
Sbjct: 55  DLTSLGMIGLFDALNKFDINRDLKFDTYASFRVRGAIIDGLRKEDW---LPRSAREKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +     ++  K  R  TPEE+AK + +PVE V + ++       +S+      E+     
Sbjct: 112 LDAQIEQLEQKYMRHVTPEELAKHMEVPVEDVYQTVQEHFFSNVLSINEQQDQEEVDGKS 171

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D    +P  S +++ L +     +  L  +E+ VL + +      + TL E+G+  
Sbjct: 172 FVIRDDTTKTPEQSVVKSELLDDLAENIQKLNEKEQLVLSLFY----TEELTLTEIGEML 227

Query: 650 CVTRERIRQI 659
            ++  RI QI
Sbjct: 228 ELSTSRISQI 237


>gi|10834759|gb|AAG23813.1|AF274004_5 SigB [Staphylococcus epidermidis]
          Length = 246

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/216 (25%), Positives = 110/216 (50%), Gaps = 14/216 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E S A+ ++V+   +L+ S+A +Y+       DL+Q G +GL+ A  +FD     KF 
Sbjct: 25  ENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFE 84

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA++L 
Sbjct: 85  AFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSISEIAQRLE 144

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA--NLRETTTR 615
           +  E V + +++ +   +L       D S   D  +D + V+ LD   Q   N   T  R
Sbjct: 145 VSDEEVLEAMEMGQSYNALSV-----DHSIEAD--KDGSTVTLLDIMGQQDDNYDLTEKR 197

Query: 616 -----VLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                +L  L+ RE ++++  F  G++   T E +G
Sbjct: 198 MILECILPILSERERQIIQCTFIEGLSQKETGERIG 233


>gi|307546921|ref|YP_003899400.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
 gi|307218945|emb|CBV44215.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
          Length = 235

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 109/235 (46%), Gaps = 15/235 (6%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            +  I + +++E  L LV   A     R    ++  DLIQ G +GL++A  +FD   G  
Sbjct: 4   AQGKIEQGDLLEEYLPLVRRQALALQVRLPASIELDDLIQAGTVGLLEALGRFDAAQGAS 63

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FST+A   ++ A+   +  +     +P  +R          RR+   + R P   EIA+ 
Sbjct: 64  FSTFASQRIRGAMLDELRSRDW---LPRSVRRGARAADEAVRRLEQSLGRPPEEAEIAEA 120

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L M ++  R++L  T   + +  E  + +     L D   ++ A +P+   +    R   
Sbjct: 121 LDMDIDAYRRLLSDTNSGQLLPFEDLMSEGGEGRLRD---NETAETPVSLLVDDERRRQL 177

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T  + +L  RE+ ++ + +   +N    L+E+G    VT  R+ Q+ ++A+ +L+
Sbjct: 178 TAGIEALPEREKLLMALYYQEELN----LKEIGAVLGVTESRVCQLHSQAVSRLR 228


>gi|253580726|ref|ZP_04857990.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848097|gb|EES76063.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 209

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 115/254 (45%), Gaps = 66/254 (25%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +SIS+ ++ +   ++G+   S AK  ++E NLRLV  V KKY   G    DLI  G IGL
Sbjct: 8   LSISQEKYYLQKYQEGD---SQAKNILIEHNLRLVAHVVKKYQGTGEDTDDLISIGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     + STYA         R I ++     + ++ R               
Sbjct: 65  IKAVTTFNPQKASRLSTYA--------ARCIENE-----LLMYFR--------------- 96

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAV 598
                      AKK            K +KE +SL  PIG +   +  +L D IE     
Sbjct: 97  -----------AKK------------KHSKE-VSLYEPIGTDKEGNEINLLDVIES---- 128

Query: 599 SPLDSAIQANLRETTTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +P+D      +RE T  +L S    L+ +E +V+  R+G+    + T  E+ ++ C++R 
Sbjct: 129 APVDIVEDCYIRENTDYLLRSLKKVLSDKEYQVICCRYGLFGMEEETQREIARKLCISRS 188

Query: 655 RIRQIEAKAIRKLK 668
            + +IE  A++KL+
Sbjct: 189 YVSRIEKTALQKLR 202


>gi|307264896|ref|ZP_07546458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306920154|gb|EFN50366.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 246

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/202 (28%), Positives = 93/202 (46%), Gaps = 12/202 (5%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           ++ DLI +G IGL+ A EK+    G KF TYA   ++  I   +  +     +P  ++ K
Sbjct: 48  EYEDLINQGVIGLIDAIEKYQPSKGVKFETYATLRIRGEIIDYLRRKDW---MPRSLKKK 104

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITKEPI-SLETPIGDEDTS 586
             K+  T   +  K  REPT EEI +   +    V K L  I    I SLE  I +    
Sbjct: 105 YKKIEETVETLQQKYNREPTVEEITEACGLNETDVLKTLSYINVSNINSLEEAIENNLKL 164

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           H    +E KN   P +  +   L+      + SL  +E  V+ + +   +N     +++ 
Sbjct: 165 HAISNVELKN---PEEEVLYKELKRKLASAIESLPDKERLVITLYYYEDLN----YKDIS 217

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K   +T  RI QI  KAI++++
Sbjct: 218 KILNLTESRISQIHTKAIKRIR 239


>gi|254449115|ref|ZP_05062567.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
 gi|198261307|gb|EDY85600.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
          Length = 227

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 51/78 (65%), Gaps = 3/78 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ +A+   +++V ++LR V  +A+ Y   GL   D+IQEGNIGLMKA ++FD  +G 
Sbjct: 72  REGDLDAA---RQLVFSHLRFVTHIARGYKGYGLPLADVIQEGNIGLMKAVKRFDPNVGV 128

Query: 495 KFSTYAMWWVKQAITRSI 512
           +  ++A+ W++  I   I
Sbjct: 129 RLVSFAVHWIRAEIHEYI 146


>gi|158338094|ref|YP_001519270.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308335|gb|ABW29952.1| RNA polymerase sigma factor, group3 [Acaryochloris marina
           MBIC11017]
          Length = 266

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/158 (27%), Positives = 83/158 (52%), Gaps = 8/158 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V  N+ LV  VA + T++  + + DL Q G +GL+ A E+FD   GY FS++A+ +
Sbjct: 27  RNRLVRLNMGLVRKVAHRLTHQCAEPYEDLEQCGFLGLITAIERFDPSQGYAFSSFAVPY 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D++ T+RIP   +       +  + ++ ++ R+P  +EIA  L++ ++  
Sbjct: 87  IRGEILHFLRDRANTVRIPRRWQQLSRDAAKARQALTMELGRQPNDQEIADALSLSMQEW 146

Query: 564 R--KVLKITKEPISLETPIG-----DEDTSHLGDFIED 594
           R  K+    + P+SL   +       +    LGD + D
Sbjct: 147 RSVKLATTNRVPLSLNARVSSGHSQSDSAMTLGDTLMD 184


>gi|291165879|gb|EFE27926.1| RNA polymerase sigma-B factor [Filifactor alocis ATCC 35896]
          Length = 273

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/160 (28%), Positives = 83/160 (51%), Gaps = 17/160 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+++ NL +   ++KKY N+G+++ D+ Q  ++GL+ A E++D   G+KFS++A   +
Sbjct: 44  RNELIQKNLYIAEILSKKYLNKGIEYDDIFQVASLGLILAIERYDVTKGFKFSSFATPTI 103

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  +IR+P  +++   KV +    + N+    P  ++IA+ L +  E V 
Sbjct: 104 IGEIKKYFRDKGWSIRVPRKIQELSKKVTQAREYLQNEKGAIPEVKDIAEYLEISEEEVM 163

Query: 565 -----------KVLKITKE------PISLETPIGDEDTSH 587
                      K L +T E       +SL   +GDED S 
Sbjct: 164 EVMEASQVYHLKSLDVTYENGGEDKEVSLIDVLGDEDKSF 203


>gi|313902394|ref|ZP_07835797.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467325|gb|EFR62836.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
          Length = 247

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 103/249 (41%), Gaps = 59/249 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  H +  +R   C    A++ ++E NLRLV  +AKK+   G    DLI  G +GL
Sbjct: 34  LSPEEEAHYLERMR---CGDERAREVLIERNLRLVAHIAKKFDETGEDPEDLISIGTVGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--- 538
           +K  + +D   G + +TYA   ++  I              +H+R       R  RR   
Sbjct: 91  IKGVDTYDPSKGTRLATYAARCIENEIL-------------MHLR-----ATRRNRREVF 132

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + N I  +    E+     +P                      DED       +E+    
Sbjct: 133 LQNPIGVDREGNEVTLMDMLPA---------------------DEDA------VEETVGR 165

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             L   I+  +RE        L PRE RVL +RFG+     +T  EV +   ++R  + +
Sbjct: 166 RLLARRIREAVRE--------LGPRERRVLELRFGLDGRRRYTQREVARVLGISRSYVSR 217

Query: 659 IEAKAIRKL 667
           IE +A+RKL
Sbjct: 218 IEKRAVRKL 226


>gi|332140599|ref|YP_004426337.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550621|gb|AEA97339.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 243

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 109/235 (46%), Gaps = 17/235 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K ++VE +  LV  +A     R    +   DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  KSQLVERHASLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I     T R  VH   +   +     ++ ++  R+    +IA KL + ++
Sbjct: 74  IRIRGAMLDEIRKGDWTPR-SVHRNGR--AITEAISQVESETGRDARDSDIADKLNVSLQ 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLA 618
              ++L      ++    +G ED     D I   + + + +PL+  +Q   ++     + 
Sbjct: 131 DYHQMLN----EVNAGKLVGIEDLGVSEDVITTEQSRGSDAPLEDLMQGAFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ KLK   +S
Sbjct: 187 TLPEREAIVLSLYYDEELN----LREIGEVLDVSESRVSQIHSQAMLKLKSRMKS 237


>gi|323701301|ref|ZP_08112976.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533903|gb|EGB23767.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 243

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 112/244 (45%), Gaps = 61/244 (25%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  + +G+ + SI K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD
Sbjct: 49  LIGRLGEGDIDGSI-KSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFD 107

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                K +TYA        +R I ++     I +++R             +NK + E + 
Sbjct: 108 PNKKIKLATYA--------SRCIENE-----ILMYLRR------------NNKTRSEVSF 142

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +                     EP++++    D +   L D +  +N +      I  N+
Sbjct: 143 D---------------------EPLNIDW---DGNELLLSDVLGTENDI------IYKNI 172

Query: 610 RETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            E   +      L  L+ RE R++ +RFG+   T+ T +EV     +++  I ++E + I
Sbjct: 173 EEEVDKKLLHQALLKLSGRERRIMELRFGLNNGTEKTQKEVADMLGISQSYISRLEKRII 232

Query: 665 RKLK 668
           ++LK
Sbjct: 233 KRLK 236


>gi|187778769|ref|ZP_02995242.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
 gi|187772394|gb|EDU36196.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
          Length = 242

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 13/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA
Sbjct: 10  VKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYA 69

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K ++   +   S    I     DK+++      R+  K+ +EP   +IA +L + +
Sbjct: 70  SIRIKGSMIDELRRNSP---ISKGAMDKLNRYNEAIERLQKKLNKEPNLIQIADELNISL 126

Query: 561 EGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V ++         ISLE  I   ED   L   I+D  + SP     +    +   + +
Sbjct: 127 KEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDDKSPSPEKHVEENEQLDYLAKAI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK
Sbjct: 187 ELLNEKDRLVVTLYYY----EELTLKEIGKILSVSESRVCQLHSRAIIHLK 233


>gi|161898921|gb|ABX80450.1| SigB [Listeria monocytogenes]
          Length = 231

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 111/226 (49%), Gaps = 12/226 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 14  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 73

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 74  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 133

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 134 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 189

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 190 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 231


>gi|167037236|ref|YP_001664814.1| sporulation sigma factor SigE [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|307266545|ref|ZP_07548078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307267688|ref|ZP_07549142.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|320115655|ref|YP_004185814.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326392136|ref|ZP_08213613.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166856070|gb|ABY94478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|306917290|gb|EFN47610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306918464|gb|EFN48705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|319928746|gb|ADV79431.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325991823|gb|EGD50338.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 241

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 114/247 (46%), Gaps = 53/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEEIYLISKMEKGDNEA---KTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++                ++   RR S 
Sbjct: 98  IKAINTFNPKKKIKLATYA--------SRCIENE----------------ILMYLRRNS- 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + +E    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 133 KTKLEVSFDE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   +E  T  L  L  RE++++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 176 --------KELLTSALKKLPDREKKIIGLRFGLEGGVEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLK 668
           K +++LK
Sbjct: 228 KILKRLK 234


>gi|297584063|ref|YP_003699843.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
 gi|297142520|gb|ADH99277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
          Length = 253

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 94/201 (46%), Gaps = 10/201 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  +RDK  K
Sbjct: 56  DLRSHGLMGLFDALEKFDRKRELKFDTYASFRIRGAIIDGLRQEDW---LPRTLRDKAKK 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDED-TSHL 588
           + +    +  ++ R  +P+EIA +  +    V K          +S++ P  + D T   
Sbjct: 113 IEQVTESLEQQLGRNVSPKEIADEAGLTEADVIKTSNENFFSHLLSIDEPTQEGDQTETY 172

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D+  ++P +S  +    +     + +L  +E+ V+ + +   +    TL E+G+ 
Sbjct: 173 ASSIADQQTLTPAESLSKQADYDELADAIQNLNEKEQLVISLFYYEEL----TLTEIGEA 228

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  RI QI +KA+ KL+ 
Sbjct: 229 LSLSTSRISQIHSKAVYKLQQ 249


>gi|15613092|ref|NP_241395.1| RNA polymerase sigma factor SigB [Bacillus halodurans C-125]
 gi|10173142|dbj|BAB04248.1| RNA polymerase general stress sigma factor(sigma B) [Bacillus
           halodurans C-125]
          Length = 261

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 114/221 (51%), Gaps = 18/221 (8%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV S+A+K++       DLIQ G +GL+ A E++D   G  F ++A+  +   I R I D
Sbjct: 41  LVHSLARKFSRSRAHDDDLIQVGMVGLLAAFERYDPKYGRSFESFAVPTIIGEIKRFIRD 100

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           ++ ++ +P  +++   K+ + A  ++++++R P  EEIA  L +  E V + +++ K   
Sbjct: 101 KTWSVHVPRRIKELGPKIKKAADELASELQRSPRVEEIADFLGVSEEEVLETMEMGKSYQ 160

Query: 575 SLET-------PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           +L         P G E T  L D +  ++     + A Q  L E   +V   L  RE+++
Sbjct: 161 ALSVDRSLEADPEGGEVT--LLDLVGQEDG--GYEKADQQMLLEKAFQV---LDEREKQI 213

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L   +   ++     +E G +  +++  + +++ +A++KL+
Sbjct: 214 LLCTYFEHLSQ----KETGHRLGISQMHVSRLQRRALKKLR 250


>gi|320012666|gb|ADW07516.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 294

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 123/249 (49%), Gaps = 15/249 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  +VE N+ LV   A+++ NRG   + D+ Q G IGL+KA 
Sbjct: 49  FFERLQVLEEGTHEYQYARNTLVEMNISLVRFAARRFRNRGSGDMEDITQVGTIGLIKAI 108

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+T+A+ ++   I R   D +  + +P  +++   ++ +    ++ ++ R
Sbjct: 109 DRFELSREVEFATFAVPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAKDELAVRLDR 168

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +PT +E+A  L       +EG+      T   + + T  G+   +    F    + +   
Sbjct: 169 DPTVKELAAHLDRTEDEVIEGIIASNGYTAGSLDMPTDTGETTGTASRTF---ADILGEP 225

Query: 602 DSAIQA--NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           DSA++   NL      +L  L  RE R++ MRFG  M    T  ++G +  V++  + ++
Sbjct: 226 DSAMETVENLHALAP-LLEQLDDRERRLIEMRFGQEM----TQSQIGAELDVSQMHVSRL 280

Query: 660 EAKAIRKLK 668
             + + KL+
Sbjct: 281 LTRTLGKLR 289


>gi|161898905|gb|ABX80442.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 111/226 (49%), Gaps = 12/226 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|15613848|ref|NP_242151.1| sporulation sigma factor SigK [Bacillus halodurans C-125]
 gi|10173901|dbj|BAB05004.1| RNA polymerase sigma factor (sigma K) precursor [Bacillus
           halodurans C-125]
          Length = 235

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 116/268 (43%), Gaps = 61/268 (22%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +L   + +K+ +    +S  E RH +  + +G+ EA   +  ++E NLRLV  + KK+ N
Sbjct: 15  VLVFVSYVKNNAFPQPLSKEEERHYLKRMAEGDEEA---RNRLIEHNLRLVAHIVKKFEN 71

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                 DLI  G IGL+KA E F    G K +TYA         R I ++     I +H+
Sbjct: 72  TREHTEDLISIGTIGLIKAIESFSEGKGTKLATYA--------ARCIENE-----ILMHL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           R                                        LK  K+ +SL  PIG +  
Sbjct: 119 R---------------------------------------ALKKVKKDVSLHDPIGTDKE 139

Query: 586 SH---LGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            +   L D +++ +    +  +IQ  + ++     +  L  RE+ V+  RFG+ +  + T
Sbjct: 140 GNEITLIDVLQEDS--EDIADSIQLKMEKKQIYEYIHVLDDREKEVIVGRFGLDLEEERT 197

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E+ K+  ++R  + +IE +A+ KL H
Sbjct: 198 QREIAKELGISRSYVSRIEKRALMKLFH 225


>gi|332527910|ref|ZP_08403946.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
 gi|332112486|gb|EGJ12279.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
          Length = 237

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 96/202 (47%), Gaps = 15/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL  A  +FD   G +F T+A   ++ A+   +       R      D+ H+
Sbjct: 40  DLIQVGMIGLSDALSRFDAAQGVQFETFATQRIRGAMLDELRGNDWMSR-----GDRRHQ 94

Query: 532 --VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDE-DTS 586
             +     ++  K+ R P   EIAK++ + +   +++L   +  + I LE   GD+ D  
Sbjct: 95  RSIEAAVHKLEQKLHRAPNESEIAKEMGLSLAEYQELLTKVRGTQLIYLEDMSGDDGDED 154

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +L   + D  A +PL       +R+     + +L  RE+ V+ M +   MN    L+E+ 
Sbjct: 155 YLDRHVHDDEA-NPLGRLQDQRMRQALVDAIKNLPEREQYVMSMYYEHDMN----LKEIA 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               VT  R+ Q+ +++I +L+
Sbjct: 210 AVLKVTESRVCQLHSQSIARLR 231


>gi|17549609|ref|NP_522949.1| flagellar biosynthesis sigma factor [Ralstonia solanacearum
           GMI1000]
 gi|17431863|emb|CAD18541.1| probable rna polymerase sigma factor for flagellar operon (sigma-f
           factor) transcription regulator protein [Ralstonia
           solanacearum GMI1000]
          Length = 253

 Score = 65.9 bits (159), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 96/206 (46%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 50  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  +++  +  R PT  EIA  L M +   +K+L   +    L     D D      F
Sbjct: 107 IEQAIQKLQQQKGRAPTETEIAAALNMSLADYQKLLVELQGSQLLYYE--DFDREDADAF 164

Query: 592 IEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           IE++   N  +PLD  +  +LRE+    + +L  RE+ ++ + +      D  L E+G  
Sbjct: 165 IENRAPENDATPLDQLLDHDLRESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAV 220

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             V+  R+ QI ++AI +++   R +
Sbjct: 221 MGVSESRVCQIHSQAIARIRSRLRER 246


>gi|332981685|ref|YP_004463126.1| RNA polymerase sigma-27/28 subunit,RpsK/SigK [Mahella australiensis
           50-1 BON]
 gi|332699363|gb|AEE96304.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Mahella
           australiensis 50-1 BON]
          Length = 236

 Score = 65.9 bits (159), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/247 (26%), Positives = 106/247 (42%), Gaps = 54/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E RH + +  +G+ +A   K  ++E NLRLV  + KKY N      DLI  G IGL
Sbjct: 33  LSYEEERHYLELYEQGDQQA---KNILIEHNLRLVAHIVKKYNNAVKDPEDLISIGTIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K    FD   G + +TYA   ++  I   +                         R S 
Sbjct: 90  IKGITTFDSNKGTRLATYAARCIENEILMYV-------------------------RASK 124

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSP 600
           K K+E   +E    +    EG           ++L   +G DEDT  + D + DK  ++ 
Sbjct: 125 KEKKEVFLQE---PIGTDKEG---------NEVTLIDILGTDEDT--ITDQVSDKMQIAK 170

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           L   + + L++           RE  +L +R+G+    D T  E+ +   ++R  + +IE
Sbjct: 171 LYKKMGSVLKD-----------RERLILELRYGLINGNDKTQREIAQMLGISRSYVSRIE 219

Query: 661 AKAIRKL 667
            KA+ KL
Sbjct: 220 KKALNKL 226


>gi|94968665|ref|YP_590713.1| sigma 28 [Candidatus Koribacter versatilis Ellin345]
 gi|94550715|gb|ABF40639.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Candidatus
           Koribacter versatilis Ellin345]
          Length = 262

 Score = 65.9 bits (159), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 101/203 (49%), Gaps = 17/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ AA K+D     +F +YA + ++ AI  S+ D   +   P  +R K   
Sbjct: 48  DLINAGILGLIDAAGKYDSEKNVQFQSYAKFRIRGAILDSLRDLDWS---PRDLRRKARA 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV------LKITKEPISLETPIGDEDT 585
           +     R++++    P  +E+A++L M ++G R++      L I+    SL+  +  E  
Sbjct: 105 LEAAELRLTSETGHPPLEDELARELGMDLDGFRELTRELEGLGIS----SLQEGLPAEGF 160

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               + + + +  SPLD+ +++   E     +  L  RE +VL + +      + T++EV
Sbjct: 161 GEEREVVVESHEESPLDAFLRSENHELLVEAIEQLPARERQVLALYY----FEELTMKEV 216

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ QI ++A+ +++
Sbjct: 217 GDVLGVGESRVSQIHSQALTRVR 239


>gi|218288661|ref|ZP_03492938.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218241318|gb|EED08493.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 239

 Score = 65.9 bits (159), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 96/236 (40%), Gaps = 58/236 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  +AKKY + G +  DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNRLIEHNLRLVAHLAKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATYAARC 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                         R S K +R+                 
Sbjct: 110 IENEILMYL-------------------------RSSKKHRRDAF--------------- 129

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLAS 619
                       L  P+G   D +   L D +  D + V  +D+   +  ++     L  
Sbjct: 130 ------------LSDPVGTDKDGNEMTLADLLGSDPDDV--IDAVDMSWEKQKMFECLPL 175

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L PRE  VL  RFG+    + T  E+ K+  ++R  + +IE KAI KL    R +K
Sbjct: 176 LAPREREVLCKRFGLPDGEERTQREIAKELGISRSYVSRIEQKAIVKLYENMRQRK 231


>gi|318066917|emb|CBY89073.1| RNA polymerase sigma70 factor [Cobetia marina]
 gi|318066949|emb|CBY89089.1| RNA polymerase sigma70 factor [Halomonas halodurans]
          Length = 364

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 34/62 (54%), Positives = 43/62 (69%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++    E  D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIKIAKRIEEGTREVMSSLAFLPGAVDSIL----EAYD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|258511987|ref|YP_003185421.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478713|gb|ACV59032.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 239

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 96/236 (40%), Gaps = 58/236 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  +AKKY + G +  DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNRLIEHNLRLVAHLAKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATYAARC 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                         R S K +R+                 
Sbjct: 110 IENEILMYL-------------------------RSSKKHRRDAF--------------- 129

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLAS 619
                       L  P+G   D +   L D +  D + V  +D+   +  ++     L  
Sbjct: 130 ------------LSDPVGTDKDGNEMTLADLLGSDPDDV--IDAVDMSWEKQKMFECLPL 175

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L PRE  VL  RFG+    + T  E+ K+  ++R  + +IE KAI KL    R +K
Sbjct: 176 LAPREREVLCKRFGLPDGEERTQREIAKELGISRSYVSRIEQKAIVKLYENMRQRK 231


>gi|161898849|gb|ABX80414.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 111/226 (49%), Gaps = 12/226 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 193 LDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|312794234|ref|YP_004027157.1| RNA polymerase, sigma 70 family subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181374|gb|ADQ41544.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 206

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 39/108 (36%), Positives = 68/108 (62%), Gaps = 5/108 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E + +V  +++G+ +A+   +E++ A   L+IS+A KY N+   F DL QEG + +
Sbjct: 4   LSLDEQKELVCRIKQGDKKAA---EELIRAYEPLIISIASKY-NKPDIFEDLKQEGAVAI 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           ++AA+KFD  LG  F T A++++K+   R +  +S TIR P +  D I
Sbjct: 60  LQAAQKFDESLGVSFITLAVYYIKRNTDRCV-KRSQTIRPPFNKFDAI 106


>gi|153938360|ref|YP_001391942.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|152934256|gb|ABS39754.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|295319962|gb|ADG00340.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. 230613]
          Length = 242

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 112/233 (48%), Gaps = 13/233 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           S  K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFST
Sbjct: 8   SYVKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFST 67

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   +K ++   +   S    I     DK+++      ++  K+ +EP   +IA +L +
Sbjct: 68  YASIRIKGSMIDELRRNSP---ISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIAGELNI 124

Query: 559 PVEGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            ++ V ++         ISLE  I   ED   L   I+D+ + SP     +    +   +
Sbjct: 125 SLKEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAK 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK
Sbjct: 185 AIELLNEKDRLVVTLYY----YEELTLKEIGKILNVSESRVCQLHSRAIIHLK 233


>gi|301165903|emb|CBW25476.1| RNA polymerase sigma factor WhiG [Bacteriovorax marinus SJ]
          Length = 260

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 105/232 (45%), Gaps = 17/232 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E++     L+  +A++  +R    ++  DLI  G IGLM A EKFD     KF TYA 
Sbjct: 23  KDEIIIEYAPLIKYIAQRIASRLPSNVELDDLISCGVIGLMDAIEKFDPSRDNKFKTYAE 82

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + ++ +I   +  Q     +P  +R+K   V R   ++     R  T EE+  +L +  E
Sbjct: 83  FRIRGSILDELRAQDW---VPRSVREKAKLVERAYAKIEAAEGRPATDEEMCAELGVNQE 139

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGD-----FIEDKNAVSPLDSAIQANLRETTTRV 616
               +L   K    L   I D  + + GD      +ED    +P  +      R+     
Sbjct: 140 EFYDLLNKAKSVSVLN--IDDSASFNKGDKKLIAGLEDNRNSNPFHAVANKGSRDKIKEG 197

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A L  ++  VL + +   +N    L+E+G+   VT  R+ Q+  +AI KLK
Sbjct: 198 IAQLPEKQRLVLSLYYYEDLN----LKEIGQVLNVTESRVSQLHTQAIMKLK 245


>gi|207724998|ref|YP_002255395.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum MolK2]
 gi|207738855|ref|YP_002257248.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum IPO1609]
 gi|206590225|emb|CAQ37186.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum MolK2]
 gi|206592225|emb|CAQ59131.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum IPO1609]
          Length = 243

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 96/206 (46%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 40  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  +++  +  R PT  EIA  L M +   +K+L   +    L     D D      F
Sbjct: 97  IEQAIQKLQQQKGRAPTETEIAAALEMSLADYQKLLVELQGSQLLYYE--DFDREDADAF 154

Query: 592 IEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           IE++   N  +PLD  +  +LRE+    + +L  RE+ ++ + +      D  L E+G  
Sbjct: 155 IENRAAENDATPLDQLLDHDLRESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAV 210

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             V+  R+ QI ++AI +++   R +
Sbjct: 211 MGVSESRVCQIHSQAIARIRARLRER 236


>gi|315649479|ref|ZP_07902564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily protein
           [Paenibacillus vortex V453]
 gi|315274952|gb|EFU38327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily protein
           [Paenibacillus vortex V453]
          Length = 256

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 107/216 (49%), Gaps = 12/216 (5%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++  K   NR   + DL Q G + L++  +++D  LG  F  YAM  +   +   + D+S
Sbjct: 43  MAAGKIARNRPDLYEDLYQVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKS 102

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPI 574
             I++P  +++K   V +    +  K++R P   EIA  L + VE   +VL  +     +
Sbjct: 103 WYIQVPRRIKEKGALVQQAIDELMVKLERSPDVNEIAAYLDLSVEETVEVLAGRECYHYV 162

Query: 575 SLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           SL++P+  E+T + LG+ I   + V+  DS      R    + ++ L  +E++VL + F 
Sbjct: 163 SLDSPLSQEETGATLGELI--SSDVNDFDS---VEKRMDLQQAMSQLKEQEQKVLLLAFQ 217

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            G     +   + ++  V++  + +I+ +A  KLK 
Sbjct: 218 EG----QSQRAIAQRLGVSQMSVSRIQKRATEKLKQ 249


>gi|300697965|ref|YP_003748626.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CFBP2957]
 gi|299074689|emb|CBJ54246.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CFBP2957]
          Length = 245

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 96/206 (46%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 42  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 98

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  +++  +  R PT  EIA  L M +   +K+L   +    L     D D      F
Sbjct: 99  IEQAIQKLQQQKGRAPTETEIAASLEMSLAEYQKLLVELQGSQLLYYE--DFDREDADAF 156

Query: 592 IEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           IE++   N  +PLD  +  +LRE+    + +L  RE+ ++ + +      D  L E+G  
Sbjct: 157 IENRAAENDATPLDQLLDHDLRESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             V+  R+ QI ++AI +++   R +
Sbjct: 213 MGVSESRVCQIHSQAIARIRARLRER 238


>gi|284045933|ref|YP_003396273.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950154|gb|ADB52898.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 263

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 94/209 (44%), Gaps = 21/209 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q  ++GL+KA ++FD   G+ FST+A   +   + R   D    + +    ++   K
Sbjct: 68  DLVQVASVGLIKAVDRFDPDRGHSFSTFAQPTIVGELLRHFRDTGWGVHVARGTQELALK 127

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDED----- 584
           V   A  +  +     TP +IA++    +E V + L     +  +SL TP G +D     
Sbjct: 128 VRSAAEAIETETGAVATPRQIAERTGAELEAVVEALGALANRTALSLATPAGHDDEGDAT 187

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               LGD  E   A         A  R      L  L  RE+R++RMRF      D T  
Sbjct: 188 IADTLGDVEEGYRA---------AEARALLGPALRHLPEREQRIIRMRF----VDDLTQS 234

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           E+  +  V++ +I ++  +++ KL   +R
Sbjct: 235 EIATEIGVSQMQISRLLRQSLDKLHELTR 263


>gi|253998499|ref|YP_003050562.1| flagellar biosynthesis sigma factor [Methylovorus sp. SIP3-4]
 gi|313200585|ref|YP_004039243.1| RNA polymerase sigma-28 subunit FliA/WhiG [Methylovorus sp. MP688]
 gi|253985178|gb|ACT50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           SIP3-4]
 gi|312439901|gb|ADQ84007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           MP688]
          Length = 244

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/200 (24%), Positives = 98/200 (49%), Gaps = 11/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G +GL+ A  +++   G +F TYA   ++ A+   + +      +P  +R  +  
Sbjct: 41  DLVQAGMMGLLDAINRYEDTHGAQFETYAAQRIRGAMIDELRNADW---LPRSIRKNMRD 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R PT  E+AK+L M ++    +L      + +  E     E   H  
Sbjct: 98  VEGAINQLEQVLGRPPTEGEVAKQLKMSLDDYYDMLGECSGHQLLYYEDFHESEGGDHFL 157

Query: 590 D-FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D F++D +  +P+   + +N RET    + +L  RE+ ++ + +   +N    L+E+G  
Sbjct: 158 DRFLQDDSG-NPIKGLLDSNFRETLIEAIENLPEREQILMGLYYEQELN----LKEIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ Q+ ++AI +L+
Sbjct: 213 MNVSESRVCQLHSQAIARLR 232


>gi|226304764|ref|YP_002764722.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
 gi|226183879|dbj|BAH31983.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
          Length = 272

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 55/224 (24%), Positives = 108/224 (48%), Gaps = 12/224 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L L   VA++Y  RG  F DL Q   +GL++A ++FD   G  F ++A+  V   
Sbjct: 51  IIELCLPLATHVARRYQGRGQPFEDLEQVARVGLVQAVQRFDVDKGSDFLSFAVPTVMGE 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + +   D   ++R+P  ++++   + R    +S  + R PT  E+A +L +  + V + L
Sbjct: 111 VRKHFRDHGWSVRVPRSLQERHLALNRALTSLSQTLGRAPTVAELATELDIEPDEVEQGL 170

Query: 568 KITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAI-QANLRETTTRVLASLTPRE 624
                     TP+   DT+  GD   +   + +   D AI + +  ET    L +L  RE
Sbjct: 171 TAGNS--YRTTPL---DTASAGDGSGLTLIDTLGQYDEAISRIDNHETLRPALLALPERE 225

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +RF   +      E++G    +++  + +I  + +++L+
Sbjct: 226 RTIVVLRFFGHLTQSQIAEKIG----ISQMHVSRILTQTLKQLR 265


>gi|168703207|ref|ZP_02735484.1| sigma-70 factor [Gemmata obscuriglobus UQM 2246]
          Length = 566

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 41/67 (61%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++  N RLV + AK+    G    DL+ +GN+ LM+A EKFD+  G KFSTYA W + + 
Sbjct: 394 LINCNQRLVYAQAKQKLALGENIDDLVSDGNLSLMRAVEKFDYARGNKFSTYATWAIMKN 453

Query: 508 ITRSIAD 514
             RSI D
Sbjct: 454 FARSIPD 460



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 39/65 (60%)

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+    R    R+L  L  R   V+RMR G+  + + TLE++G+ F +T+ER+RQI  + 
Sbjct: 491 ALADQARARVNRLLDHLDARTREVIRMRTGLDGSEEMTLEQIGQHFGITKERVRQINVRG 550

Query: 664 IRKLK 668
           ++ L+
Sbjct: 551 MKMLR 555


>gi|261886056|ref|ZP_06010095.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 262

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/141 (29%), Positives = 72/141 (51%), Gaps = 7/141 (4%)

Query: 41  RGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDGDDL----EDEEGSEDSLD 94
           +GYVT E+L       P   + +++E    +     I+ V+   +    E ++  ED L 
Sbjct: 20  KGYVTFEKLVRLFDKAPTVATIKKVETLAELYKIQLISAVEAAKIKNIQEAKKSEEDKLK 79

Query: 95  LASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           +  +A      L    D  + S +D PVRMYLREMG I LL++E E+ I+K+IE G  ++
Sbjct: 80  IIDTALEEEFDLTSENDLLEWSRSDSPVRMYLREMGQISLLTKEEEVEISKKIELGEDII 139

Query: 154 MASLCESPLTFQALIIWRDEL 174
           + + C  P     ++ +++ L
Sbjct: 140 IDAFCSVPYLIDFILDYKEPL 160


>gi|299822364|ref|ZP_07054250.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
 gi|299815893|gb|EFI83131.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
          Length = 259

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 114/229 (49%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q G IGL+ A +++D   G  F  +A+  
Sbjct: 30  AQTNLVLHYHNLVESIARKYSQGKSFHEDLVQVGVIGLLGAIKRYDPDFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  +    E +
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIANFIGATEEEI 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V  +D    Q N R    ++L  
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGVDEGFEQVNQRMILEKILPV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+++L+  F      + + +E G+   +++  + +++ +AI+KL+
Sbjct: 206 LDEREQKILQYTF----IENRSQKETGELLDISQMHVSRVQRQAIKKLR 250


>gi|239934564|emb|CAR94596.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/67 (47%), Positives = 45/67 (67%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  G 
Sbjct: 2   DPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTYNFMLNQYEQVKAGQ 61

Query: 179 TLLREII 185
             L +II
Sbjct: 62  GRLVDII 68


>gi|225028516|ref|ZP_03717708.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
 gi|224954159|gb|EEG35368.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
          Length = 209

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/255 (26%), Positives = 105/255 (41%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S +  +   E R+ + M R G+ +A   K++++E NLRLV  + KKY +      DLI  
Sbjct: 3   SFKKPLKAEEERYYLKMYRDGDEKA---KEKLIEHNLRLVAHIVKKYNSPDRDLDDLISI 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   FD   G +  TYA                                   A
Sbjct: 60  GTIGLIKAVNTFDLNKGGRLVTYA-----------------------------------A 84

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLG--DFIE 593
           R + N             +L M +   +K+L+     +SL  PIG D++ +H+   D I 
Sbjct: 85  RCIEN-------------ELLMMIRQEKKILR----EVSLYEPIGTDQEGNHISLLDIIS 127

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            + A        +  L      V      RE  ++  R+G+  N  HT +EV     ++R
Sbjct: 128 TEEAELIEQYLHKYYLSRLEQEVFLLTDDREREIILKRYGLCGNEPHTQKEVAAMMGISR 187

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE KA+ KL+
Sbjct: 188 SYVSRIEKKALEKLR 202


>gi|152964789|ref|YP_001360573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151359306|gb|ABS02309.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 267

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/190 (29%), Positives = 90/190 (47%), Gaps = 18/190 (9%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +++V  +L L  SVA  Y NRG  + DL+Q   +GL+KAA++FD   G++F+ YA   + 
Sbjct: 16  EDLVLEHLPLARSVAAHYRNRGEPYDDLVQVAYLGLVKAAQRFDPDTGHRFAAYAAPTIT 75

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI-AKKLAMPVEGVR 564
             + R   D    +R P  +++        AR ++       TPEE+ A++L   V  VR
Sbjct: 76  GEVRRHFRDHGWNVRPPRRLQEL------RARLLAEDAD---TPEEVLAQRLDATVAEVR 126

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              + +     +SL+   G ED   L + + D             +   T  R+ A L  
Sbjct: 127 AARQASNAYSAVSLDAAHGPEDVP-LCELLADDAD-----DTAAVDDALTLRRITAGLDE 180

Query: 623 REERVLRMRF 632
           RE R+L +RF
Sbjct: 181 RERRILHLRF 190


>gi|85712287|ref|ZP_01043338.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
 gi|85693914|gb|EAQ31861.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
          Length = 241

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 104/231 (45%), Gaps = 18/231 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ ++E +  LV  +A     R    +Q  DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  RQAIIEQHTGLVKRIAHHMMARLPASVQVDDLIQSGMIGLLEAARNFDNSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH   +  +V+   R++ N+  R+    E+A+KL MP+E
Sbjct: 74  IRIRGAMLDEIRRGDWAPR-SVHRNHR--RVLEAIRQVENETGRDAKDVEVAEKLEMPLE 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS----PLDSAIQANLRETTTRVL 617
               +L+     ++    IG ED     D I  +        P                +
Sbjct: 131 EYHAILR----DVNSGRIIGIEDLGVSEDAIMPEQVTGANYEPQKDVENDAFHRALVETI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L  RE  VL + +   +N    L+E+G+   V+  R+ QI ++A+ +LK
Sbjct: 187 SGLPEREALVLSLYYDEELN----LKEIGEVLSVSESRVSQIHSQAMMRLK 233


>gi|20807860|ref|NP_623031.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478885|ref|ZP_05092249.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
 gi|20516424|gb|AAM24635.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|214035198|gb|EEB75908.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
          Length = 246

 Score = 65.5 bits (158), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 109/230 (47%), Gaps = 15/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++   L LV  + KK     +   ++ DLI +G +GL+ A EK+    G KF TYA
Sbjct: 20  ARNEIIVKYLPLVKHIVKKLVISDIAQSEYEDLIHQGILGLIDAIEKYQPDKGVKFETYA 79

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +  +     +P  ++ K  K+  T  ++  +  REPT EEI +   +  
Sbjct: 80  TLRIRGEIIDYLRKRDW---MPRSLKKKYKKIEETVEKLQQRYNREPTVEEITEACGLEE 136

Query: 561 EGVRKVLK-ITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           E V K L  I    I SLE  I +    H    I+ KN   P +  +   L++     + 
Sbjct: 137 EDVLKTLSYINVSNINSLEEAIENNLKIHSISEIDLKN---PEEELLYKELKKKLAHAIE 193

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ +E  V+ + +   +N     +++ K   +T  RI QI +KAI+K++
Sbjct: 194 KLSEKERLVITLYYYEDLN----YKDISKILNLTESRISQIHSKAIKKIR 239


>gi|904172|gb|AAB38522.1| flagellin sigma factor [Yersinia enterocolitica (type O:8)]
          Length = 229

 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 93/198 (46%), Gaps = 9/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+    Q I   + +       P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAV----QRIAPMLDELRQRDWAPRRLRRNARE 88

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++    T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 89  VASAMQKVEQRLGAPATEQEVAQNLDIDLTEYRQILLDTNNSQLFSYDEWREEHGRTVEP 148

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 149 MLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 204

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 205 VGESRVSQLHSQAIKRLR 222


>gi|226364233|ref|YP_002782015.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226242722|dbj|BAH53070.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 285

 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 55/223 (24%), Positives = 101/223 (45%), Gaps = 27/223 (12%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++ ++E  L L   +A+++  RG    DLIQ   +GL+KA ++FD   G  F +YA+ 
Sbjct: 57  LLRQRLIERCLPLAEHIARRFLGRGEPLDDLIQVARLGLVKAVDRFDARCGASFVSYAVP 116

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   + R   D    + +P  M++    +      ++  + R PT  E+A+ L +  + 
Sbjct: 117 TITGEVRRHFRDTGWAMHVPRSMQELHLSLTNATTELTTTLGRAPTASELAEALGIDKDE 176

Query: 563 VRKVLKIT--KEPISLETPIGDED---TSHLGDF------IEDKNAVSPLDSAIQANLRE 611
           V + L+++     +S++ P+G+++   +  +GD       +ED   + PL          
Sbjct: 177 VARGLRVSDAYSTLSVDFPLGEDERPLSETIGDVDPSLAHVEDHVVLEPL---------- 226

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                L SL   E  VL +RF   M        VG  Q  V+R
Sbjct: 227 -----LGSLPDLERTVLVLRFFGNMTQSQIAARVGVSQMQVSR 264


>gi|585927|sp|P37970|RPOF_STRAU RecName: Full=RNA polymerase sigma-F factor
 gi|153450|gb|AAA93050.1| minor sigma-like factor [Streptomyces aureofaciens]
          Length = 297

 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/241 (23%), Positives = 113/241 (46%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 63  LQPGTREHERVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERG 122

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 123 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNAATEDLTTLHGRTPTTPEIA 182

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++  +     SLE     ++   +   ++      P  + ++   R+
Sbjct: 183 ERLRISEDEVLSCIEAGRSYHATSLE---AAQEGDGMPGLLDRLGYEDPELAGVEH--RD 237

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+      + T  ++  +  V++  + ++ A++  +L+  +
Sbjct: 238 LVRHLLVQLPEREQRILLLRY----YNNLTQSQISAELGVSQMHVSRLLARSFARLRSAN 293

Query: 672 R 672
           R
Sbjct: 294 R 294


>gi|119476300|ref|ZP_01616651.1| RNA polymerase sigma factor for flagellar operon [marine gamma
           proteobacterium HTCC2143]
 gi|119450164|gb|EAW31399.1| RNA polymerase sigma factor for flagellar operon [marine gamma
           proteobacterium HTCC2143]
          Length = 240

 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 112/247 (45%), Gaps = 55/247 (22%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           EMVE    LV  +A     R    +Q  DL+Q G IGL++AA  +D   G  F TYA   
Sbjct: 12  EMVERYAPLVKRIAHHLMARMPSSVQVEDLVQAGLIGLLEAARNYDASKGASFETYA--- 68

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------REPTP 549
                          IRI   M D + +       + R +RR+S  +K       R+ T 
Sbjct: 69  --------------GIRIRGSMIDDVRRGDWAPRSIHRNSRRVSEALKIVESRLGRDATD 114

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-------NAVSPLD 602
           +E+A +L++ ++   ++L   ++  S +    DE TS      EDK       +  SP D
Sbjct: 115 QEVAAELSVSLDDYYRML---QDSASSKLFSFDEITSG-----EDKPEEQLPSSTASPFD 166

Query: 603 SAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             IQAN LR+     + +L  RE  VL + +   +N    L+E+G    V+  R+ QI +
Sbjct: 167 -GIQANALRQGLADAIGTLPERERLVLALYYDEELN----LKEIGLILGVSESRVSQIHS 221

Query: 662 KAIRKLK 668
           +A  +L+
Sbjct: 222 QAATRLR 228


>gi|325001881|ref|ZP_08122993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia sp. P1]
          Length = 258

 Score = 65.1 bits (157), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 52/227 (22%), Positives = 104/227 (45%), Gaps = 13/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +VE +  LV  +  K   R    ++  DL+Q G  GL+ A ++FD   G +F  YA 
Sbjct: 33  RRLLVEHHAPLVRGIGAKLATRLPSSIELADLLQSGTFGLIDAVDRFDPARGVRFEGYAA 92

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+ A+   +  Q     +P  +R +  ++ R    + +K+ R  +  E+A +L +   
Sbjct: 93  QRVRGAMLDELRAQDW---VPRTVRSRSREIERAREAVQSKVGRPASDRELAAELGI--- 146

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           G+R + +  +  + +     D + +     +   +   P+ +A++          +A L 
Sbjct: 147 GLRDLRQAVRPALLVSADDLDGNAAPGPAALAAADTADPVATAVRRETGAELRAAIAQLG 206

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+  VLR+ +      DHTL E+G    VT  R+ Q+  + + +L+
Sbjct: 207 ERDRTVLRLYY----VEDHTLAEIGALLGVTESRVCQLHTRMLTRLR 249


>gi|149191506|ref|ZP_01869755.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148834694|gb|EDL51682.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 125

 Score = 65.1 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/97 (36%), Positives = 60/97 (61%), Gaps = 4/97 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           I+S++    ++  E R +   +   GE EA+   K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 20  IRSVNSYPMLTADEERELAERLHYDGEIEAA---KGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEI 113


>gi|118475308|ref|YP_891711.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp. fetus
           82-40]
 gi|118414534|gb|ABK82954.1| RNA polymerase sigma factor [Campylobacter fetus subsp. fetus
           82-40]
          Length = 623

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 42/141 (29%), Positives = 72/141 (51%), Gaps = 7/141 (4%)

Query: 41  RGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDGDDL----EDEEGSEDSLD 94
           +GYVT E+L       P   + +++E    +     I+ V+   +    E ++  ED L 
Sbjct: 20  KGYVTFEKLVRLFDKAPTVATIKKVETLAELYKIQLISAVEAAKIKNIQEAKKSEEDKLK 79

Query: 95  LASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           +  +A      L    D  + S +D PVRMYLREMG I LL++E E+ I+K+IE G  ++
Sbjct: 80  IIDTALEEEFDLTSENDLLEWSRSDSPVRMYLREMGQISLLTKEEEVEISKKIELGEDII 139

Query: 154 MASLCESPLTFQALIIWRDEL 174
           + + C  P     ++ +++ L
Sbjct: 140 IDAFCSVPYLIDFILDYKEPL 160


>gi|91792701|ref|YP_562352.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91714703|gb|ABE54629.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 239

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 103/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  ++E    LV  +A     R    +Q  DL+Q G +GL++AA KFD   G KF T+A 
Sbjct: 13  KSSVIEQYAPLVKKIAHHMLARLPASVQLDDLLQAGMMGLLEAASKFDGTKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH   +  +V +    +     R+    EIA+KL M ++
Sbjct: 73  IRIRGAMIDEIRRGDWVPR-SVHRNQR--RVAQVIDELEQHFGRDARDTEIAEKLDMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D I  E+ +     D  ++   +      + +
Sbjct: 130 EYHHILN----DVSVGKIIGIEDLGVSQDVIITEETSMDESFDELVETQFQSALVEAIKT 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|167037640|ref|YP_001665218.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167040301|ref|YP_001663286.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|256750769|ref|ZP_05491654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914385|ref|ZP_07131701.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724379|ref|YP_003904130.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320116055|ref|YP_004186214.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|166854541|gb|ABY92950.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|166856474|gb|ABY94882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256750352|gb|EEU63371.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889320|gb|EFK84466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581440|gb|ADN54839.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319929146|gb|ADV79831.1| RNA polymerase sigma factor, FliA/WhiG family [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 246

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/202 (28%), Positives = 93/202 (46%), Gaps = 12/202 (5%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           ++ DLI +G IGL+ A EK+    G KF TYA   ++  I   +  +     +P  ++ K
Sbjct: 48  EYEDLINQGVIGLIDAIEKYQPSKGVKFETYATLRIRGEIIDYLRKKDW---MPRSLKKK 104

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITKEPI-SLETPIGDEDTS 586
             K+  T   +  K  REPT EEI +   +    V K L  I    I SLE  I +    
Sbjct: 105 YRKIEETVETLQQKYNREPTVEEITEACGLNETDVLKTLSYINVSNINSLEEAIENNFKL 164

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           H    +E KN   P +  +   L+      + +L  +E  V+ + +   +N     +++ 
Sbjct: 165 HAISDVELKN---PEEEVLYKELKRKLANAIENLPDKERLVITLYYYEDLN----YKDIS 217

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K   +T  RI QI  KAI++++
Sbjct: 218 KILNLTESRISQIHTKAIKRIR 239


>gi|299538306|ref|ZP_07051591.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
 gi|298726508|gb|EFI67098.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
          Length = 261

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 122/230 (53%), Gaps = 14/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+N    + D++Q G +GL+ A  +FD  +G  F  +A+  
Sbjct: 30  AQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++  + +P  +++   ++  T   ++ +++R P+ ++IA++L +  E V
Sbjct: 90  IVGEIKRFLRDKTWDVHVPRRIKELGPRIKSTVEALTIELQRSPSIKDIAERLEVAEEEV 149

Query: 564 RKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + +++++  + +S++  I    D  T  L D +  ++     D     N R      L 
Sbjct: 150 LEAMEMSRSYQALSMDHSIESDSDGSTVTLFDILGRED-----DGYEMTNQRMIVQDALV 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE++++++ +   ++     +E G++  +++  + +I+ KAI+KL+
Sbjct: 205 VLNEREKQIIQLTYLEQLSQ----KEAGERLGISQMHVSRIQRKAIKKLQ 250


>gi|318066983|emb|CBY89106.1| RNA polymerase sigma70 factor [Kushneria aurantia]
          Length = 370

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 43/62 (69%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++    E  D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAHLPGAVDSIL----EAYD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|77463598|ref|YP_353102.1| sigma factor FliA (sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126462430|ref|YP_001043544.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332558454|ref|ZP_08412776.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
 gi|77388016|gb|ABA79201.1| sigma factor FliA (Sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126104094|gb|ABN76772.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332276166|gb|EGJ21481.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
          Length = 239

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 436 KGECEASIAKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E +   + +V A++ LV  +A        R ++  DLIQ G +GL+ A+ +++   
Sbjct: 5   RGYAEQTQTPERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPRE 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+ YA   ++ +I   +   S   R  + M+ K+   V   +R+  ++ R P   E+
Sbjct: 65  GVSFAAYAAIRIRGSIMDFLRSNSALCRTTILMQQKVKAAV---QRLEGRLMRAPETPEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV------SPLDSAIQ 606
           A +L+MPV   +  L                 T+ L +  +D++A+      S  D    
Sbjct: 122 AAELSMPVGEYQDWL----------AQFAGSQTASLDEVYDDQSALFEGHDPSAEDRLQA 171

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + +R    + L  +  RE  +L++ F   +N    + EVG+   VT  R+ QI+  AI +
Sbjct: 172 SQMRGLLRQALGRMPEREALLLQLIFVEELN----VYEVGEILGVTTGRVSQIKKAAIER 227

Query: 667 LK 668
           L+
Sbjct: 228 LR 229


>gi|318066943|emb|CBY89086.1| RNA polymerase sigma70 factor [Halomonas halmophila]
          Length = 367

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 43/62 (69%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M +L   P    +++    E+ D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMMALAYLPGAVDSIL----EVYD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|299069774|emb|CBJ41053.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CMR15]
          Length = 253

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 96/206 (46%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 50  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  +++  +  R PT  EIA  L M +   +K+L   +    L     D D      F
Sbjct: 107 IEQAIQKLQQQKGRAPTETEIAAFLNMSLADYQKLLVELQGSQLLYYE--DFDREDADAF 164

Query: 592 IEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           IE++   N  +PLD  +  +LRE+    + +L  RE+ ++ + +      D  L E+G  
Sbjct: 165 IENRAPENDATPLDQLLDHDLRESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAV 220

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             V+  R+ QI ++AI +++   R +
Sbjct: 221 MGVSESRVCQIHSQAIARIRSRLRER 246


>gi|239934560|emb|CAR94594.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/67 (47%), Positives = 45/67 (67%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  G 
Sbjct: 1   DPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALANYPLTYTFMLNQYEQVKMGQ 60

Query: 179 TLLREII 185
             L +II
Sbjct: 61  GRLVDII 67


>gi|169334413|ref|ZP_02861606.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259130|gb|EDS73096.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
          Length = 250

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 118/232 (50%), Gaps = 18/232 (7%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+   N  L+ S+ K+Y +  + + DL Q G IGL+KA ++F +    KFSTYA++ +  
Sbjct: 32  ELTVINTPLINSILKRYLSYSISYDDLFQIGAIGLIKAIKRFSFEFNTKFSTYAVYVING 91

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPVEGV 563
              R   D+   I++  +++  I+   +T R   + +K+   EP+ + +++K+ +  E V
Sbjct: 92  EYKRYFRDEGI-IKVGRNLKT-IYLKTKTIRE--DYVKKNGVEPSIDYLSEKIGVSSEDV 147

Query: 564 RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L+  ++P SL   + + + +   L D I+D+N     DS  +   +      + +L 
Sbjct: 148 LMALEACRQPESLSKELNNNENTPILLMDKIKDEN-----DSNEKIVEKLDLKNAIMNLE 202

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R+ +++ +R+      + T +EV +   +++ ++ ++E K I  +K    S
Sbjct: 203 KRDRQIIVLRYF----KNKTQKEVAEVLGLSQVQVSRLEKKIIENMKKTFES 250


>gi|331696243|ref|YP_004332482.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950932|gb|AEA24629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 273

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 122/247 (49%), Gaps = 24/247 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +S + + + E    + E++ A L +   +  +Y T+R     D+ Q  +  +++A + +D
Sbjct: 34  LSTLPRDDPEHDALRTELILAFLPVAERLVGRYATSRPWSRDDIAQAASEAVVRAVDHWD 93

Query: 490 W------CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
                   LGY         V+ AI R   DQS ++R+P  ++D    + +    +S ++
Sbjct: 94  PDRARGDVLGYLVPC-----VRGAILRWFRDQSWSLRVPRRVKDLSVAIRQAVGPLSQEL 148

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            R P P E+A++L + V+ + + L      +  +L+ P GD+D+S  G+ I D   V P 
Sbjct: 149 GRAPRPSELARRLDVDVDEIVEALYAEDNHQAATLDAPAGDDDSSP-GERIGD---VDPR 204

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              ++    ET   +LA L+ RE R++ +RF  G     T  ++G++  V++  + ++ A
Sbjct: 205 LGRVEDV--ETLRPLLAGLSERERRIVVLRFFCG----RTQSQIGEEIGVSQMHVSRLLA 258

Query: 662 KAIRKLK 668
             + KL+
Sbjct: 259 GTLAKLR 265


>gi|326389454|ref|ZP_08211021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325994459|gb|EGD52884.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 56/202 (27%), Positives = 91/202 (45%), Gaps = 12/202 (5%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           ++ DLI +G IGL+ A EK+    G KF TYA   ++  I   +  +     +P  ++ K
Sbjct: 48  EYEDLINQGVIGLIDAIEKYQPSKGVKFETYATLRIRGEIIDYLRRKDW---MPRSLKKK 104

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+  T   +  K  REPT EEI +   +    V K L         SLE  I +    
Sbjct: 105 YKKIEETVETLQQKYNREPTVEEITEACGLNEIDVLKTLSYINVSNVNSLEEAIENNFKL 164

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           H    +E KN   P +  +   L+      + SL  +E  V+ + +   +N     +++ 
Sbjct: 165 HAISNVELKN---PEEEVLYKELKRKLASAIESLPDKERLVITLYYYEDLN----YKDIS 217

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K   +T  RI QI  KAI++++
Sbjct: 218 KILNLTESRISQIHTKAIKRIR 239


>gi|325981885|ref|YP_004294287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Nitrosomonas sp.
           AL212]
 gi|325531404|gb|ADZ26125.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Nitrosomonas sp.
           AL212]
          Length = 238

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/240 (23%), Positives = 111/240 (46%), Gaps = 15/240 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           +I K + +     LV  +A     R    +Q  DLIQ G IGL+ A  +++   G +F +
Sbjct: 9   AIDKDQFIAEFTPLVKRIAYHMMTRLPASVQVDDLIQAGMIGLLDAINRYEGSYGRQFES 68

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++ +I   + +      +P  +R K+ ++      +  +    P   ++AK+L M
Sbjct: 69  YAAQRIRGSILDELREADW---LPRSIRKKMRRIEAAVNLLEQRNGCAPNELDLAKELDM 125

Query: 559 PVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            ++   + L+  +  + I  E    D++   L     D     PL++ +  N R      
Sbjct: 126 SLDEYHETLQSARGAQLIYYEDFQQDDEEPFLDRLFIDSEG-DPLNALLDENFRNQLIAA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + +L PRE++++ M +   MN    L E+G+   V+  R+ Q+  +A+ +L+  SR + L
Sbjct: 185 IDNLPPREKQMMGMHYEQEMN----LREIGEVLGVSESRVCQLHTQAVARLR--SRLRNL 238


>gi|42780162|ref|NP_977409.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 10987]
 gi|42736080|gb|AAS40017.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10987]
          Length = 257

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 59/252 (23%), Positives = 122/252 (48%), Gaps = 26/252 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D+IQ G +GL+ A  ++D
Sbjct: 18  LIAEFQQNQCDE--AQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + +G  F  +A+  +   I + + D++  I +P  ++D   K+      ++++++R P  
Sbjct: 76  YSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDQLQRSPKI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSA-- 604
            EIA  L +  E V +++              +   S L D +E   D ++V+ ++S   
Sbjct: 136 IEIADHLELSEEEVLEIMDAK----------NNYRVSSLDDVVENASDGSSVARIESVGE 185

Query: 605 IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++    ET  R     +   L   E+ V+   F   +N   T E +G    +++  + +I
Sbjct: 186 VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDTGERLG----ISQMHVSRI 241

Query: 660 EAKAIRKLKHPS 671
           + +AI KLK  +
Sbjct: 242 KRQAISKLKQAA 253


>gi|161898839|gb|ABX80409.1| SigB [Listeria monocytogenes]
          Length = 222

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 95/193 (49%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 15  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 74

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+    + ++ +++  P   +IA  + +  E V
Sbjct: 75  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVKELTRELQSSPQISDIADFIGVTEEEV 134

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 135 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 190

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 191 LDEREQKILQFTF 203


>gi|221639440|ref|YP_002525702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
 gi|221160221|gb|ACM01201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
          Length = 239

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 436 KGECEASIAKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E +   + +V A++ LV  +A        R ++  DLIQ G +GL+ A+ +++   
Sbjct: 5   RGYAEQTQTPERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPRE 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+ YA   ++ +I   +   S   R  + M+ K+   V   +R+  ++ R P   E+
Sbjct: 65  GVTFAAYAAIRIRGSIMDFLRSNSALCRTTILMQQKVKAAV---QRLEGRLMRAPETPEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV------SPLDSAIQ 606
           A +L+MPV   +  L                 T+ L +  +D++A+      S  D    
Sbjct: 122 AAELSMPVGEYQDWL----------AQFAGSQTASLDEVYDDQSALFEGHDPSAEDRLQA 171

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + +R    + L  +  RE  +L++ F   +N    + EVG+   VT  R+ QI+  AI +
Sbjct: 172 SQMRGLLRQALGRMPEREALLLQLIFVEELN----VYEVGEILGVTTGRVSQIKKAAIER 227

Query: 667 LK 668
           L+
Sbjct: 228 LR 229


>gi|120403519|ref|YP_953348.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium
           vanbaalenii PYR-1]
 gi|119956337|gb|ABM13342.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium
           vanbaalenii PYR-1]
          Length = 242

 Score = 65.1 bits (157), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 59/248 (23%), Positives = 113/248 (45%), Gaps = 17/248 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + +++ +G       +  ++E  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 2   FREL-ALLDEGSAPYRRQRDAIIERCLPLADHIARRFRGRGEAHEDLVQVARVGLLNAVN 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD      F  +A+  +   + R   D   ++++P  +++   ++      +++++ R 
Sbjct: 61  RFDVDSANDFLAFAVPTMMGEVRRYFRDHGWSLKVPRRLKELNVRLNSARSELTHQLNRA 120

Query: 547 PTPEEIAKKLAMP----VEGVRKVLKITKEPISLET-PIGDEDTSHLGDFIEDKNAVSPL 601
           PTP E+A+ L M     VEG+      +      ET   GD D   L D I         
Sbjct: 121 PTPSELAEFLGMERDEIVEGLVAANAYSTRSTEQETMRTGDGDGLTLLDTIGGP------ 174

Query: 602 DSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           D  IQ  +  +T   +LA L  R+  VL++RF   +      E +G    V++  + ++ 
Sbjct: 175 DEGIQRVIDIQTVQPLLAKLPARDRLVLQLRFFDNLTQSQIAERIG----VSQMHVSRLL 230

Query: 661 AKAIRKLK 668
           A+A+  L+
Sbjct: 231 ARALATLR 238


>gi|319649539|ref|ZP_08003695.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398701|gb|EFV79383.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 251

 Score = 64.7 bits (156), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 92/196 (46%), Gaps = 12/196 (6%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   RDK  K+    
Sbjct: 59  GLMGLYDALEKFDPARDLKFDTYASFRIRGAILDGLRKEDW---LPRSTRDKAKKIDAAI 115

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISL-ETPIGDEDTSHLGDFIE 593
            ++  ++ R  T  EIA++  M  + V  V+        +S+ E P  DE        I+
Sbjct: 116 EKLEQRLMRNATVHEIAEEAEMQEDEVYSVMNEHFYANILSIDEQPDADEKDGSYS--IK 173

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D+ A+ P +  ++  L E     +  L  +E+ VL + +      + TL E+G+   ++ 
Sbjct: 174 DEKAIIPEEKVLKNELLEEMAEKILQLNEKEQMVLSLFY----KEELTLTEIGEVMGLST 229

Query: 654 ERIRQIEAKAIRKLKH 669
            RI QI +K+I KL+ 
Sbjct: 230 SRISQIHSKSIFKLRQ 245


>gi|89099620|ref|ZP_01172495.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
 gi|89085773|gb|EAR64899.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
          Length = 239

 Score = 64.7 bits (156), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 108/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +  +   D  ++AN+ ++   + L  LT 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTEEDIITKD--LEANVDKKLLLKALHQLTD 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+G   + T ++V     +++  I ++E + I++LK
Sbjct: 187 REKQIMELRFGLGSGEEKTQKDVADMLGISQSYISRLEKRIIKRLK 232


>gi|302535695|ref|ZP_07288037.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
 gi|302444590|gb|EFL16406.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
          Length = 355

 Score = 64.7 bits (156), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 60/121 (49%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 123 PGTSEHHRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQ 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++
Sbjct: 183 FPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNAATEDLTTLHGRTPTTPEIAER 242

Query: 556 L 556
           L
Sbjct: 243 L 243


>gi|89335089|dbj|BAE84684.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 238

 Score = 64.7 bits (156), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 104/223 (46%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 61  LIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYA------- 113

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +H+            R +NK + E + +                 
Sbjct: 114 -SRCIENE-----ILMHL------------RRNNKTRTEVSFD----------------- 138

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLTPREE 625
               EP++++    D +   L D +  +N +   PL+  +    R+     +A LT RE+
Sbjct: 139 ----EPLNID---WDGNELLLSDVLGTENDIISRPLEEKVD---RQLLHLAMARLTDREK 188

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++ +RFG+    + T +EV  +  +++  I ++E + IR+L+
Sbjct: 189 LIMELRFGLDNGEEKTQKEVADRLGISQSYISRLEKRIIRRLR 231


>gi|251798285|ref|YP_003013016.1| sporulation sigma factor SigK [Paenibacillus sp. JDR-2]
 gi|247545911|gb|ACT02930.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. JDR-2]
          Length = 232

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 96/228 (42%), Gaps = 61/228 (26%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +T+A       
Sbjct: 53  LIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFA------- 105

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
             R I ++     I +H+R                                        L
Sbjct: 106 -ARCIENE-----ILMHLRS---------------------------------------L 120

Query: 568 KITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           K T++ +SL  PIG +   +   L D +  E  + V  +   I+   +    R L  L  
Sbjct: 121 KKTRKDVSLHDPIGTDKEGNEITLIDILGTEADDVVDRVQLKIE---KSKIYRNLDILDE 177

Query: 623 REERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+ V+R RFG+    D  T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 178 REQEVIRGRFGLDHGGDERTQREIAKELGISRSYVSRIEKRALMKLYH 225


>gi|308205502|gb|ADO18992.1| RNA polymerase sigma 70 subunit [Nostoc flagelliforme str.
           Sunitezuoqi]
          Length = 165

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 37/82 (45%), Positives = 54/82 (65%), Gaps = 5/82 (6%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L++  E  +  + T +  SE   + S++ +GE     AK++MV ANLRLV+++AKKY NR
Sbjct: 49  LQLNREPTTRELATSLGQSE-AEVESILHQGE----RAKQKMVTANLRLVVAIAKKYQNR 103

Query: 467 GLQFLDLIQEGNIGLMKAAEKF 488
            L+FLDLIQEG +GL +  EK 
Sbjct: 104 NLEFLDLIQEGTLGLYRGVEKL 125


>gi|296129329|ref|YP_003636579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Cellulomonas flavigena
           DSM 20109]
 gi|296021144|gb|ADG74380.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Cellulomonas flavigena
           DSM 20109]
          Length = 328

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 107/234 (45%), Gaps = 16/234 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++ ++   + LV +VA +   R    ++  DL+  G  GL+ A EK+      KF +YA
Sbjct: 93  AREVLILHYVPLVTAVAGRIGMRLPSTVEHADLVSYGMFGLIDAIEKYCTDRAVKFESYA 152

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ AI   I +      +P  +R K   V R    +   + R PT  E+A++L +PV
Sbjct: 153 SSRIRGAI---IDELRAMDWVPRSVRTKARAVDRAYGELEATLHRAPTEAEVAQRLELPV 209

Query: 561 EGVRKVL-KITKEPISL--ETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             +R V  ++    I+   E   G +D    + L D + D+ A  P  S      +   +
Sbjct: 210 SELRAVYSQLASVNIAALDEMLAGSDDRPGAATLADTLGDRRADDPAGSVEAQETKYLLS 269

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R +  L  RE  V+ + +   M    TL E+G+   VT  RI QI   A+ +L+
Sbjct: 270 RAIECLGERERLVVVLYYYESM----TLAEIGRVLGVTESRISQIHTAAMGRLR 319


>gi|167037477|ref|YP_001665055.1| sporulation sigma factor SigK [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040139|ref|YP_001663124.1| sporulation sigma factor SigK [Thermoanaerobacter sp. X514]
 gi|256752531|ref|ZP_05493387.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914223|ref|ZP_07131539.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724542|ref|YP_003904293.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115891|ref|YP_004186050.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854379|gb|ABY92788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856311|gb|ABY94719.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256748597|gb|EEU61645.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889158|gb|EFK84304.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581603|gb|ADN55002.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928982|gb|ADV79667.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 231

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 96/224 (42%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   
Sbjct: 51  ARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  SI                     RT ++M  ++            L  P+ GV
Sbjct: 111 IENEILMSI---------------------RTEKKMKGEV-----------FLQDPI-GV 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E+   + + +E K  +  L S + + L+            R
Sbjct: 138 DK----EGNEISLMDVLGTEE-DEISEQVEKKLQIKKLYSKMNSVLKN-----------R 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E+ ++ MR+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 182 EKLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|331006368|ref|ZP_08329678.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330419828|gb|EGG94184.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 251

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 95/210 (45%), Gaps = 25/210 (11%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++AA+K+D   G  F TYA   ++ AI   I       R  VH   
Sbjct: 49  VQVDDLIQSGMIGLLEAAKKYDGSRGASFETYAGIRIRGAIVDEIRKGDWVPR-SVHRNS 107

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE---------GVRKVLKITKEPISLET 578
           ++  +  T  ++   + R+    EIA+ + + ++            ++  I +   S E+
Sbjct: 108 RL--ISNTIHQLEASLGRDAKDSEIAEAMGVDIDEYYAMSRDASSSRLFSIDESFESDES 165

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            I +E  S           V P D A    L+ +    +  L  RE+ VL + +   +N 
Sbjct: 166 VISNEKNSPF---------VDPHDGAQHQALKSSLVTAIDKLPEREKLVLSLYYDEELN- 215

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L+E+G+   VT  R+ QI ++A  +LK
Sbjct: 216 ---LKEIGQILGVTESRVSQIHSQAALRLK 242


>gi|319654668|ref|ZP_08008747.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
 gi|317393584|gb|EFV74343.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
          Length = 264

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 117/235 (49%), Gaps = 14/235 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV ++A+KY+       D++Q G IGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQNTLVLQYQNLVEAIARKYSKGRSYHEDIVQVGIIGLLGAIRRYDESFGKTFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+  T   ++ ++ R P  +EIA  L +  E V
Sbjct: 90  IIGEIKRFLRDKTWSVHVPRRIKELGPKIKATVEELTTELHRSPRVDEIADVLGVSEEEV 149

Query: 564 RKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + +++ K  + +S++  I    D  T  L D + +++     +   + N      +VL 
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSDGGTVTLLDIVGNED-----EGYEKVNQMLVLDKVLH 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L+ RE+ +++  +   M+     +E G +  +++  + +++ +AI+KL+    S
Sbjct: 205 VLSEREKLIIQYTYLENMSQ----KEAGDKLGISQMHVSRLQRRAIKKLQEAIHS 255


>gi|318066989|emb|CBY89109.1| RNA polymerase sigma70 factor [Kushneria marisflavi]
          Length = 373

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 42/60 (70%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P +  +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALASLPGSVDSILQAYDATQD 80


>gi|37680648|ref|NP_935257.1| flagellar biosynthesis sigma factor [Vibrio vulnificus YJ016]
 gi|37199396|dbj|BAC95228.1| polar Flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           vulnificus YJ016]
          Length = 245

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++K  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 16  SQKLFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  ++ +    +   + R+PT  E+AK + + +
Sbjct: 76  GIRIRGAMLDDIRRGDWVPR-SVHKSNR--EISQAIAELEGLLNRDPTDAEVAKHMGLSL 132

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           E     L      I+    IG ED     D I   ED    +P         R+     +
Sbjct: 133 EQYHGALT----DINCSRLIGIEDLGVSDDVITSVEDSENNTPFKGVADEYFRKALVESI 188

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G+   V+  R+ QI ++++++L+
Sbjct: 189 KQLPEREALVLSLYYDEELN----LKEIGEILSVSESRVSQILSQSMQRLR 235


>gi|71281710|ref|YP_268261.1| flagellar biosynthesis sigma factor [Colwellia psychrerythraea 34H]
 gi|71147450|gb|AAZ27923.1| motility sigma factor FliA [Colwellia psychrerythraea 34H]
          Length = 239

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 17/242 (7%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
           MV+       I K  ++E    LV  +A     R    +Q  DLIQ G IGL +AA  FD
Sbjct: 1   MVKVNSYNNQIDKAALLEQQTVLVKRIAYHLLARLPASVQVDDLIQSGMIGLFEAANNFD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F T+A   ++ A+   I     T R  VH   ++  +    +++  ++ R+ + 
Sbjct: 61  NTKGASFETFAGIRIRGAMLDEIRRGDWTPR-SVHKNSRM--ISEAIKQLEAQLGRDVSD 117

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQ 606
            E+A+KL + ++   ++L      +S    +G +D     D I   +D     P  S  +
Sbjct: 118 VEVAEKLDISLKDYHQILS----EVSTGKILGIDDLGVNEDAIKPSDDYIGDDPYQSIER 173

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              ++  T+ + SL  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ +
Sbjct: 174 IAFKKGLTQCIKSLPEREALVLSLYYDEELN----LREIGQVLDVSESRVSQIHSQAMHR 229

Query: 667 LK 668
           LK
Sbjct: 230 LK 231


>gi|170760209|ref|YP_001787962.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
 gi|169407198|gb|ACA55609.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
          Length = 242

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA
Sbjct: 10  VKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYA 69

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K ++   +   S    I     DK+++      ++  K+ +EP   +IA +L + +
Sbjct: 70  SIRIKGSMIDELRRNSP---ISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNISL 126

Query: 561 EGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + +
Sbjct: 127 KEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK
Sbjct: 187 ELLNEKDRLVVTLYYY----EELTLKEIGKILNVSESRVCQLHSRAIVHLK 233


>gi|27365297|ref|NP_760825.1| flagellar biosynthesis sigma factor [Vibrio vulnificus CMCP6]
 gi|320155681|ref|YP_004188060.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
 gi|27361444|gb|AAO10352.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           CMCP6]
 gi|319930993|gb|ADV85857.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
          Length = 244

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++K  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQKLFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDASKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  ++ +    +   + R+PT  E+AK + + +
Sbjct: 75  GIRIRGAMLDDIRRGDWVPR-SVHKSNR--EISQAIAELEGLLNRDPTDAEVAKHMGLSL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           E     L      I+    IG ED     D I   ED    +P         R+     +
Sbjct: 132 EQYHGALT----DINCSRLIGIEDLGVSDDVITSVEDSENNTPFKGVADEYFRKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G+   V+  R+ QI ++++++L+
Sbjct: 188 KQLPEREALVLSLYYDEELN----LKEIGEILSVSESRVSQILSQSMQRLR 234


>gi|238916719|ref|YP_002930236.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872079|gb|ACR71789.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 223

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 109/255 (42%), Gaps = 50/255 (19%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL--DLI 474
           + E  +S  E + ++  +R+G+   S A+  ++E N+RLV  + KKYT+    ++  DLI
Sbjct: 9   TFEKPLSAQEEKELLIKLREGD---SAARNALIEKNMRLVAHIVKKYTSTERDYINEDLI 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+KA + FD     +FSTYA   +   I                          
Sbjct: 66  SVGTIGLIKAVDSFDIERNVRFSTYAAKCIDNEILMLF---------------------- 103

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              R   K +RE +  E    +    EG           ISL+  IG++      D +ED
Sbjct: 104 ---RQDKKKEREVSLNE---PIGKDKEG---------NEISLKDIIGEDSEKKQPDAVED 148

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                 +   I  N+ +        L PRE  +L+ R+G+    + T  E+  +  ++R 
Sbjct: 149 YMFYEQI-KCIYGNIEKV-------LAPREIEILKYRYGLFGAKECTQNELADRLGISRS 200

Query: 655 RIRQIEAKAIRKLKH 669
            + +IE KA+ KL+ 
Sbjct: 201 YVSRIEKKALGKLRE 215


>gi|148380599|ref|YP_001255140.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 3502]
 gi|153931945|ref|YP_001384886.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|153937160|ref|YP_001388355.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|168182725|ref|ZP_02617389.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|170754752|ref|YP_001782258.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|226950054|ref|YP_002805145.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|237796081|ref|YP_002863633.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
 gi|148290083|emb|CAL84202.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152927989|gb|ABS33489.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|152933074|gb|ABS38573.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|169119964|gb|ACA43800.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|182674219|gb|EDT86180.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|226840945|gb|ACO83611.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|229261699|gb|ACQ52732.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
          Length = 242

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA
Sbjct: 10  VKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYA 69

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K ++   +   S    I     DK+++      ++  K+ +EP   +IA +L + +
Sbjct: 70  SIRIKGSMIDELRRNSP---ISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNISL 126

Query: 561 EGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + +
Sbjct: 127 KEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK
Sbjct: 187 ELLNEKDRLVVTLYYY----EELTLKEIGKILNVSESRVCQLHSRAIIHLK 233


>gi|108804004|ref|YP_643941.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765247|gb|ABG04129.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 257

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 36/116 (31%), Positives = 64/116 (55%), Gaps = 2/116 (1%)

Query: 455 LVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           L+ S+A++Y  + G  + DL+Q G +GLMKA   +D   G  FS+YA   ++  I   + 
Sbjct: 41  LLKSIARRYAGSSGEPYEDLLQAGYVGLMKAVNGYDPSSGAAFSSYAYSMMEGEIRHHLR 100

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           D S  +R P        +V      ++ ++ R P PEE+A++  +  EG+R+++K+
Sbjct: 101 D-SGLVRRPRWASGLYARVSEATAHLTRELGRPPLPEEVAREANITPEGIRELMKV 155


>gi|298708238|emb|CBJ48301.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 516

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 67/122 (54%), Gaps = 8/122 (6%)

Query: 444 AKKEMVEANLRLVISVAK---KYTNRGLQ--FLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           AK+ +VE N+ +VI + +   ++  RG Q  F DL+QEG   L  AAE+FD  +  +F T
Sbjct: 214 AKQTLVERNMPMVIRMVEGQYRWRLRGGQVSFADLLQEGAYALGVAAERFDPTMPNRFLT 273

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA++ V+  +  ++A  +  I +P     ++H   R  R ++ ++ R P+  E+A   A 
Sbjct: 274 YALYTVRDKLDVALARGNSAISVPATALKEVH---RARRELTGRLGRTPSEAELANFFAN 330

Query: 559 PV 560
            V
Sbjct: 331 GV 332


>gi|302540326|ref|ZP_07292668.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302457944|gb|EFL21037.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 263

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 103/201 (51%), Gaps = 13/201 (6%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A ++ N+G    DL Q  ++ L+KA ++++  LG+ F +YA+  +   + R   D   T
Sbjct: 53  LALRFRNKGENMEDLTQVASLALVKAVDRYNPDLGHAFPSYAIPVITGELKRHFRDYLWT 112

Query: 519 IRIPVHMRDKIHKVVRTAR-RMSNKI-KREPTPEEIAKKLAMPVEGVRKVLKITKE--PI 574
           + IP ++++ +    R+AR  +  ++  R PT  EI+ +  MP E VR  L+ +    P+
Sbjct: 113 LHIPRNIQE-VRSRTRSARDALEQELGGRTPTVGEISTRTGMPQEDVRAGLEASASCTPL 171

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFG 633
           SL   +   +   L +       V   D+AI+  +   + RVL A+L+ ++  VL +RF 
Sbjct: 172 SLNAAVQGAEERLLAE------TVGADDAAIERVVNRESLRVLIANLSEQDRYVLYLRFF 225

Query: 634 IGMNTDHTLEEVG-KQFCVTR 653
            G++     E +G  Q  ++R
Sbjct: 226 AGLSQSQIGEILGFSQMHISR 246


>gi|161353798|ref|YP_519128.2| sporulation sigma factor SigE [Desulfitobacterium hafniense Y51]
 gi|219670065|ref|YP_002460500.1| sporulation sigma factor SigE [Desulfitobacterium hafniense DCB-2]
 gi|219540325|gb|ACL22064.1| RNA polymerase, sigma 28 subunit, SigE [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 104/223 (46%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 72  LIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYA------- 124

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +H+R             +NK + E + +                 
Sbjct: 125 -SRCIENE-----ILMHLRR------------NNKTRTEVSFD----------------- 149

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLTPREE 625
               EP++++    D +   L D +  +N +   PL+  +    R+     +A LT RE+
Sbjct: 150 ----EPLNID---WDGNELLLSDVLGTENDIISRPLEEKVD---RQLLHLAMARLTDREK 199

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++ +RFG+    + T +EV  +  +++  I ++E + IR+L+
Sbjct: 200 LIMELRFGLDNGEEKTQKEVADRLGISQSYISRLEKRIIRRLR 242


>gi|291613029|ref|YP_003523186.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
 gi|291583141|gb|ADE10799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
          Length = 247

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 48/199 (24%), Positives = 95/199 (47%), Gaps = 10/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ AA ++D   G +F TYA   ++ A+   +        +P  +R  + +
Sbjct: 51  DLIQAGMMGLLDAASRYDELRGAQFETYAAQRIRGAMLDELRGADW---LPRSLRRDMRR 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           +     R+  ++ + P   EIA++L + +   +++L+  +  + +  E   G+E      
Sbjct: 108 IETAVSRLQQQMGKTPNETEIARELGVSLHEYQQMLQEGRGAQLLYYEDFHGEEGEDFFE 167

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E     +PL+       RE     +  L  RE +++ M +   MN    L E+G+  
Sbjct: 168 RF-EFSGDSNPLELLQDERFREALIHAIERLPERERQMMGMHYEQDMN----LREIGEVM 222

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ Q+ ++A+ +L+
Sbjct: 223 GVSESRVCQLHSQAVARLR 241


>gi|91223562|ref|ZP_01258827.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269965686|ref|ZP_06179799.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
 gi|91191648|gb|EAS77912.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269829754|gb|EEZ83990.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
          Length = 244

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 104/231 (45%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   + D      +P  +     ++ +    +  ++ R+PT  E+A  L M +
Sbjct: 75  GIRIRGAM---LDDMRKGDWVPRSVHKNNREINQAIAELEGELNRDPTDSEVATHLGMTL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P    +  + R+     +
Sbjct: 132 DQYHSALT----DINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVVDESFRKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G    V+  R+ QI ++A+++L+
Sbjct: 188 KQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQAMQRLR 234


>gi|74317267|ref|YP_315007.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056762|gb|AAZ97202.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 246

 Score = 64.7 bits (156), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 109/230 (47%), Gaps = 14/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K +++E  + +V  +A     R    ++  DL+Q G IGL+ A  ++D     +F  YA+
Sbjct: 13  KNDLLEQYMPMVKRLAHHMMGRLPPSVEEDDLVQAGMIGLLDAVSRYDEAQSAQFEAYAI 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +        +P   R  + K+ +    + +++ R+P+  EIA+ + +P+ 
Sbjct: 73  QRIRGSMIDELRQSDW---MPRSARQSMRKIEQAIAALQHQLGRQPSEGEIAEAMKIPLA 129

Query: 562 GVRKVLKITKEPISL---ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + +L   +    L   +    DED S L     D+ A  PL   + ANLR      + 
Sbjct: 130 DYQSMLGDARGHQLLYFEDFGESDEDDSFLDKQSADE-ATMPLPQLLDANLRACIIAGIE 188

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L  RE+ ++ + +   +N    L E+ + F V+  RI Q+  +AI +L+
Sbjct: 189 NLPEREQLLMSLYYEQELN----LREIAEVFGVSESRICQLHGQAIARLR 234


>gi|300854412|ref|YP_003779396.1| putative RNA polymerase sigma-K factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434527|gb|ADK14294.1| predicted RNA polymerase sigma-K factor precursor [Clostridium
           ljungdahlii DSM 13528]
          Length = 233

 Score = 64.7 bits (156), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 96/225 (42%), Gaps = 49/225 (21%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  +VE NLRLV  + KKY+    +  +LI  G +GL+KA + FD   G + +TYA  
Sbjct: 49  LAKSILVERNLRLVAHIVKKYSYPSKEVDELISIGTVGLIKAIDSFDMSKGTRLATYAAK 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++  I   I +    IR  V++ D I                                G
Sbjct: 109 CIENEILMLIRNNK-KIRNEVYLEDPI--------------------------------G 135

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V K        ISL   +  ++ S + + +E K  V  L S I   L E           
Sbjct: 136 VDK----EGNEISLMDVLSSDEGSII-EIVEQKLQVKKLYSKINTCLSE----------- 179

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE+ V+ MR+G+      T  E+ K   ++R  + +IE KA++KL
Sbjct: 180 REKSVVEMRYGLLEGKPRTQREIAKLLGISRSYVSRIEKKALKKL 224


>gi|322806971|emb|CBZ04541.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           botulinum H04402 065]
          Length = 242

 Score = 64.7 bits (156), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA
Sbjct: 10  VKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYA 69

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K ++   +   S    I     DK+++      ++  K+ +EP   +IA +L + +
Sbjct: 70  SIRIKGSMIDELRRNSP---ISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNISL 126

Query: 561 EGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + +
Sbjct: 127 KEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK
Sbjct: 187 ELLNEKDRLVVTLYYY----EELTLKEIGKILNVSESRVCQLHSRAIIHLK 233


>gi|239934556|emb|CAR94592.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 207

 Score = 64.7 bits (156), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 33/65 (50%), Positives = 44/65 (67%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLTFQ ++   + +  G   
Sbjct: 1   VRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTFQHILNSYELVKQGQGR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LVDII 65


>gi|239934580|emb|CAR94604.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 223

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 45/69 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREII 185
            T  L +II
Sbjct: 61  QTVRLADII 69


>gi|197285477|ref|YP_002151349.1| flagellar biosynthesis sigma factor [Proteus mirabilis HI4320]
 gi|6959882|gb|AAF33246.1|AF221596_2 FliA [Proteus mirabilis]
 gi|194682964|emb|CAR43378.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           HI4320]
          Length = 240

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 99/209 (47%), Gaps = 30/209 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDSMQGAAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP----------ISLET--P 579
           V ++  ++   + R P+ +E+A  L + +   R++L  T             I  E+  P
Sbjct: 100 VTQSIHQLEQDLGRPPSEQEVADHLQIELAEYRQILLDTNNSQLFSYDEWHEIYGESCEP 159

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             DED         D N   PL   +++++R+     +  L  RE+ VL + +   +N  
Sbjct: 160 SQDED--------HDDN---PLQMLLESDIRQRVIDAIELLPEREKMVLTLYYQEELN-- 206

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 207 --LKEIGAVLNVGESRVSQLHSQAIKRLR 233


>gi|303239292|ref|ZP_07325820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593078|gb|EFL62798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 236

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 105/249 (42%), Gaps = 58/249 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +H + ++++G+ EA   +  ++E NLRLV  + KKY        DLI  G IGL
Sbjct: 33  LSPDEEQHYIKLLKEGDEEA---RNILIERNLRLVAHIVKKYNATIGDCDDLISIGTIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+   G + +TYA   ++  I   I                         R S 
Sbjct: 90  IKAIATFNHEKGTRLATYAARCIENEILMQI-------------------------RSSK 124

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAV 598
           KI+ E                           +SL+ PIG   + +   L D I ++   
Sbjct: 125 KIQSE---------------------------VSLQDPIGVDREGNEIALIDVIGNEAES 157

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +  ++  ++    ++   L  RE+ VL +R+G+   T  T  E+ K   ++R  + +
Sbjct: 158 VVEEVELKMQVKRLYNKMKVVLKSREKVVLELRYGLLNGTSKTQREIAKMLGISRSYVSR 217

Query: 659 IEAKAIRKL 667
           IE KAI+KL
Sbjct: 218 IEKKAIKKL 226


>gi|282861223|ref|ZP_06270288.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563881|gb|EFB69418.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 296

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 60/264 (22%), Positives = 128/264 (48%), Gaps = 45/264 (17%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E N+ LV   A+++ NRG   + D+ Q G +GL+KA 
Sbjct: 51  FFAQLQVLEEGTHEYQYARNTLIEMNISLVRFAARRFRNRGSGDMEDITQVGIVGLIKAI 110

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+T+A+ ++   I R   D +  + +P  +++   ++ +    ++ ++ R
Sbjct: 111 DRFELSREVEFATFAVPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAKEELAVRLDR 170

Query: 546 EPTPEEIAKKLAMP----VEGVRKVLKITKEPISLETP-----------------IGDED 584
           +PT +E+A+ L +     VEG+      T    SL+ P                 +G+ D
Sbjct: 171 DPTVKELAEYLGLTEDEVVEGIVASNGYTAG--SLDLPTDANEATATATRTFADILGEPD 228

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            +   + +E+ +A++PL               L  L  RE R++ MRFG  M    T  +
Sbjct: 229 AAM--ETVENLHALAPL---------------LEELDDRERRIIEMRFGQEM----TQAQ 267

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G +  +++  + ++ ++ + KL+
Sbjct: 268 IGAELGISQMHVSRLLSRTLGKLR 291


>gi|283796304|ref|ZP_06345457.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291075701|gb|EFE13065.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|295091614|emb|CBK77721.1| Sigma-70 region 3. [Clostridium cf. saccharolyticum K10]
          Length = 177

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 76/133 (57%), Gaps = 3/133 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E  L +   ++++Y +RGL   DL+QE N+ L+    +++   G  F   A   
Sbjct: 45  AKKRLIEGCLAMAAELSEEYRDRGLPAGDLVQEANMALLLLVSEYE---GGNFRAQAEER 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++A+  ++  Q    +I   M  +++ +   + +M+ ++ RE T EE+A ++ M VE +
Sbjct: 102 IREALETALDIQDTEQKIEEEMLARVNVLKDISAQMAEELGREATVEELAARMKMTVEEI 161

Query: 564 RKVLKITKEPISL 576
           + ++K+T + +S+
Sbjct: 162 KDIMKLTLDAMSV 174


>gi|302343749|ref|YP_003808278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
 gi|301640362|gb|ADK85684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
          Length = 260

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 56/213 (26%), Positives = 100/213 (46%), Gaps = 17/213 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A +KFD     KF TYA + V+ AI   +        +P  +R K   
Sbjct: 56  DLIGAGVLGLIDAVDKFDPEKNVKFKTYAEFRVRGAILDELRAMDW---VPRSVRKKSSD 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISL---ETPIGDEDTS 586
           +     R+ N++ R    EEIA++L + ++ + ++L        +SL   ++P+G+ D+ 
Sbjct: 113 LEDAIGRLQNRLGRPAEDEEIAQELGIGLDDLHRLLDEVSGVNLLSLDDADSPLGNLDSE 172

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + + +  +    PL       LR      +  L  +E+ V+ + +      + T+ E+G
Sbjct: 173 QVMEAMGREGLEDPLVMLGLVELRRVIASAIEGLPEKEKLVVSLYY----YDELTMREIG 228

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +    T  RI Q+  KAI +L+      +LR F
Sbjct: 229 EVLGYTESRISQMHTKAILRLR-----ARLRDF 256


>gi|118464372|ref|YP_883398.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118165659|gb|ABK66556.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 241

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 114/241 (47%), Gaps = 39/241 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+  +
Sbjct: 19  RDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMP---- 559
              + R   D S ++++P  +++ +H  + TA   +S ++ R  T  E+A +L M     
Sbjct: 79  MGEVRRHFRDNSWSVKVPRRLKE-LHLRLGTATADLSQRLGRAHTATELAAELEMDREEV 137

Query: 560 VEGVRKVLKITKEPISLETPIGDED------TSHLGDF------IEDKNAVSPLDSAIQA 607
           VEG+  V   +   +S+++  G E+         LGD       IED+ ++ PL      
Sbjct: 138 VEGL--VAGSSYNTLSIDSGGGSEEEEVRAIADTLGDVDTGLDRIEDQESLRPL------ 189

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                    L +L  RE  VL +RF   M      E VG    +++  + ++ AK++ +L
Sbjct: 190 ---------LEALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRLLAKSLTRL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|295399836|ref|ZP_06809817.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111652|ref|YP_003989968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
 gi|294978239|gb|EFG53836.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216753|gb|ADP75357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
          Length = 254

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 98/202 (48%), Gaps = 14/202 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  +R+K  K
Sbjct: 55  ELISLGLVGLYDALEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDW---LPRSIREKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE---TPIGDEDTS 586
           +  T  ++  +  R  T +E+A +L +    V  V+        +S +   T   +E+ +
Sbjct: 112 IEETIEKLEQRYMRSVTAKEVADELGITEAEVYTVVNEHFFANVLSFQHVATENDEEENA 171

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L   I D+  +SP +  ++  L E    V+  L+ +E+ V+ + +      + T  E+G
Sbjct: 172 LLA--IRDEKTLSPEEEVLKQELYEKLAEVIQQLSEKEQLVISLFY----KEELTFTEIG 225

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   ++  RI Q+ +KAI KL+
Sbjct: 226 EILGLSTSRISQLHSKAIFKLR 247


>gi|227355968|ref|ZP_03840360.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
 gi|227163956|gb|EEI48858.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
          Length = 244

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 99/209 (47%), Gaps = 30/209 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 47  DLLQAGGIGLLNAVERYDSMQGAAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP----------ISLET--P 579
           V ++  ++   + R P+ +E+A  L + +   R++L  T             I  E+  P
Sbjct: 104 VTQSIHQLEQDLGRPPSEQEVADHLQIELAEYRQILLDTNNSQLFSYDEWHEIYGESCEP 163

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             DED         D N   PL   +++++R+     +  L  RE+ VL + +   +N  
Sbjct: 164 SQDED--------HDDN---PLQMLLESDIRQRVIDAIELLPEREKMVLTLYYQEELN-- 210

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 211 --LKEIGAVLNVGESRVSQLHSQAIKRLR 237


>gi|224992858|gb|ACN76144.1| SigB [Listeria monocytogenes]
 gi|224992860|gb|ACN76145.1| SigB [Listeria monocytogenes]
 gi|224992862|gb|ACN76146.1| SigB [Listeria monocytogenes]
 gi|224992864|gb|ACN76147.1| SigB [Listeria monocytogenes]
 gi|224992866|gb|ACN76148.1| SigB [Listeria monocytogenes]
 gi|224992868|gb|ACN76149.1| SigB [Listeria monocytogenes]
 gi|224992870|gb|ACN76150.1| SigB [Listeria monocytogenes]
 gi|224992872|gb|ACN76151.1| SigB [Listeria monocytogenes]
 gi|224992876|gb|ACN76153.1| SigB [Listeria monocytogenes]
 gi|224992878|gb|ACN76154.1| SigB [Listeria monocytogenes]
 gi|224992880|gb|ACN76155.1| SigB [Listeria monocytogenes]
 gi|224992882|gb|ACN76156.1| SigB [Listeria monocytogenes]
 gi|224992884|gb|ACN76157.1| SigB [Listeria monocytogenes]
 gi|224992888|gb|ACN76159.1| SigB [Listeria monocytogenes]
 gi|224992890|gb|ACN76160.1| SigB [Listeria monocytogenes]
 gi|224992892|gb|ACN76161.1| SigB [Listeria monocytogenes]
 gi|224992894|gb|ACN76162.1| SigB [Listeria monocytogenes]
 gi|224992896|gb|ACN76163.1| SigB [Listeria monocytogenes]
 gi|224992900|gb|ACN76165.1| SigB [Listeria monocytogenes]
          Length = 214

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 12  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 72  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 131

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 132 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 187

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 188 LDEREQKILQFTF 200


>gi|134298554|ref|YP_001112050.1| sporulation sigma factor SigE [Desulfotomaculum reducens MI-1]
 gi|134051254|gb|ABO49225.1| RNA polymerase, sigma 29 subunit, SigE [Desulfotomaculum reducens
           MI-1]
          Length = 241

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 103/230 (44%), Gaps = 60/230 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 60  VKNVLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFDPHKKIKLATYA--- 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 117 -----SRCIENE-----ILMHLRR------------NNKTRSEVSFD------------- 141

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLA 618
                   EP++++    D +   L D +  +N +      I  N+ E   +      L 
Sbjct: 142 --------EPLNIDW---DGNELLLSDVLGTENDI------IYKNIEEEVDKKLLHQALL 184

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ RE R++ +RFG+   ++ T +EV     +++  I ++E + I++LK
Sbjct: 185 KLSGRERRIMELRFGLNNGSEKTQKEVADMLGISQSYISRLEKRIIKRLK 234


>gi|168180934|ref|ZP_02615598.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
 gi|182668292|gb|EDT80271.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
          Length = 242

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA
Sbjct: 10  VKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYA 69

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              +K ++   +   S    I     DK+++      ++  K+ +EP   +IA +L + +
Sbjct: 70  SIRIKGSMIDELRRNSP---ISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNVSL 126

Query: 561 EGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + +
Sbjct: 127 KEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK
Sbjct: 187 ELLNEKDRLVVTLYYY----EELTLKEIGKILNVSESRVCQLHSRAIIHLK 233


>gi|323705266|ref|ZP_08116841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535168|gb|EGB24944.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 231

 Score = 64.3 bits (155), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 95/224 (42%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  V KKY+N G    DLI  G IGL+KA   +D   G   +TYA   
Sbjct: 51  AKNILIERNLRLVAHVVKKYSNAGKDVDDLISIGTIGLIKAILTYDSSKGTHLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  S+                         R   KIK E +  +       P+ GV
Sbjct: 111 IENEILMSL-------------------------RAEKKIKSEISLHD-------PI-GV 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E T  + D +E +  V  L   + + L+            R
Sbjct: 138 DK----EGNEISLIDILGTE-TDEVSDQVELRMQVKKLYHKLNSVLKN-----------R 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E+ ++ +R+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 182 EKLIIELRYGLINGGAKTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|260776433|ref|ZP_05885328.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607656|gb|EEX33921.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 244

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 94/204 (46%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I        +P  +  
Sbjct: 42  VQVEDLIQAGMIGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHK 98

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              ++ +   ++  ++ R+PT  E+AK+L M +E     L      I+    IG +D   
Sbjct: 99  NSREISQAIAQLEGELNRDPTDAEVAKRLEMSLEQYHSALT----DINSSRLIGIDDLGV 154

Query: 588 LGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D I  ++A     P         R      + SL  RE  VL + +   +N    L+E
Sbjct: 155 SEDAISHEDADEENIPFQGVADEYFRTALVESIKSLPEREALVLSLYYDEELN----LKE 210

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+   V+  R+ QI ++++++L+
Sbjct: 211 IGEVIGVSESRVSQILSQSMQRLR 234


>gi|225174854|ref|ZP_03728851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169494|gb|EEG78291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 219

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 101/231 (43%), Gaps = 25/231 (10%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           I   E  E +L LV S+ K+Y     +  DL Q G IGL+KA +KFD   G  F+TYA+ 
Sbjct: 2   IVMAETFEKHLPLVHSLVKRYQGEYAESDDLFQVGCIGLLKALKKFDPARGNAFATYAVP 61

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I   +  Q   ++    +  +  ++ R    +   + R+PT  E+A    +  E 
Sbjct: 62  VIAGEIKMYLRGQGA-MKFSRSLVTQAGRIKRVQNELEQALGRQPTLGELAAASGLGREE 120

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-----L 617
           +   L   + P+SL+  +  E T+ L              +  QA   E   RV     L
Sbjct: 121 LLMALDAVRSPVSLDAAVPGE-TAEL--------------AVTQAETDEVVDRVALREAL 165

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE R++  RF        + +EV +   +++  + ++E K + +LK
Sbjct: 166 TDLPERERRIVLYRF----FRHKSQQEVAEILGISQMHVSRLEKKVLARLK 212


>gi|257457436|ref|ZP_05622606.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
 gi|257445165|gb|EEV20238.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
          Length = 262

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 98/207 (47%), Gaps = 14/207 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMR 526
           ++F DL+  G  GL+ A +K+D     KF+TYA+  ++ AI     D+  +I  +P  +R
Sbjct: 53  VEFDDLVGYGVFGLLDAIDKYDPEKNVKFNTYAVTRIRGAIF----DELRSIDWVPRSVR 108

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPI----SLETPIG 581
            +  ++      +  ++    T  EIA+ L M VE   +V LKI+   I     L     
Sbjct: 109 QQSREIEEVIADLEARLGHAATDSEIAEALGMSVEEFHQVLLKISGTSIISLTDLRFGAD 168

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D + + + D IE   +++P     +  ++      +  L  RE++VL M +      D T
Sbjct: 169 DSEQTPVADSIEAPTSLNPDVIVEREEMKRIIVDAINELPDREKKVLIMYY----YEDMT 224

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+GK   VT  R+ QI   A  KLK
Sbjct: 225 LREIGKVLEVTESRVSQIHTSANLKLK 251


>gi|295835999|ref|ZP_06822932.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295825822|gb|EFG64505.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 297

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 64/271 (23%), Positives = 127/271 (46%), Gaps = 42/271 (15%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F   ++++ +G      A+  ++E N  LV   A+++ NRG   + D++Q G +GL+KA 
Sbjct: 47  FFDQLTVLEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTVGLIKAI 106

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D +  + +P  +++    + R   R++  + R
Sbjct: 107 DRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELRVDLARAKERLAVDLDR 166

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS-------------HLGD 590
           +P  +E+A +L +  + V   L      +  SL+ P  D  TS              LGD
Sbjct: 167 DPGVKELAAELGISEDEVIDGLIAANGYMSDSLDLP-ADSTTSGKPDQKTATTYADFLGD 225

Query: 591 F------IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           +      +ED  A+ PL               L +L  RE  +L +RFG     + T  +
Sbjct: 226 WDPAMELVEDFTALRPL---------------LGTLDDRERYLLELRFG----QELTQAQ 266

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +G +  V++  + ++ ++ + KL+    S+K
Sbjct: 267 IGAELGVSQMHVSRLLSRTLGKLREGLLSEK 297


>gi|307717588|gb|ADN88847.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717632|gb|ADN88869.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 95/193 (49%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V    +LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|317133468|ref|YP_004092782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
 gi|315471447|gb|ADU28051.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
          Length = 248

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 106/227 (46%), Gaps = 28/227 (12%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V A +  V+SV+  Y        DL   G IGL+KA EKFD   G +FST+A + ++  
Sbjct: 35  LVRAIVHRVMSVSGSYAESD----DLTSCGTIGLIKAIEKFDSDKGVQFSTFATYRIRGE 90

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I   +        +P  +R ++ ++      +++ + R P+  E+ ++L +P     +VL
Sbjct: 91  ILDFVRRSDW---VPRGVRKRVLEMESAESELASSLGRRPSDSELCERLGVP----DRVL 143

Query: 568 KITKEP------ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             T+        IS E  + D      GD        SP ++  ++ L E  T+ +  L 
Sbjct: 144 AKTRASMERFNVISFEEMLRDAARDMAGDD-------SPENALQESELLEVLTKAVEDLP 196

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+  V+ + +      D TL E+ +   VT  R+ QI ++A+ ++K
Sbjct: 197 ERDRLVITLYY----YEDLTLREISEVIGVTESRVSQIHSRAVGRMK 239


>gi|300694351|ref|YP_003750324.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum PSI07]
 gi|299076388|emb|CBJ35704.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum PSI07]
          Length = 245

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 51/207 (24%), Positives = 96/207 (46%), Gaps = 14/207 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 42  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 98

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHLGD 590
           + +  +++  +  R PT  EIA  L M +    R+++++    +        ED      
Sbjct: 99  IEQAIQKLQQQKGRAPTETEIAAALDMSLADYQRQLVELQGSQLLYYEDFDREDADA--- 155

Query: 591 FIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           FIE++   N  +PLD  +  +LRE+    +  L  RE+ ++ + +      D  L E+G 
Sbjct: 156 FIENRAAENDATPLDQLLDHDLRESVVAAIEGLPEREKLMMSLYY----EQDLNLREIGA 211

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
              V+  R+ QI ++AI +++   R +
Sbjct: 212 VMGVSESRVCQIHSQAIARIRARLRER 238


>gi|289578405|ref|YP_003477032.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544681|ref|YP_003676983.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528118|gb|ADD02470.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842456|gb|ADH60972.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 56/202 (27%), Positives = 93/202 (46%), Gaps = 12/202 (5%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           ++ DLI +G +GL+ A EK+    G KF TYA   ++  I   +  +     +P  ++ K
Sbjct: 48  EYEDLINQGVLGLIDAIEKYQPSKGVKFETYATLRIRGEIIDYLRKKDW---MPRSLKKK 104

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITKEPI-SLETPIGDEDTS 586
             K+  T   +  K  REPT EEI +   +    V K L  I    I SLE  I +    
Sbjct: 105 YKKIEETVETLQQKYNREPTVEEITEACGLNETDVLKTLSYINVSNINSLEEAIENNFKL 164

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           H    +E KN   P +  +   L+      + +L  +E  V+ + +   +N     +++ 
Sbjct: 165 HAISDVELKN---PEEEVLYKELKRKLANAIKNLPDKERLVITLYYYEDLN----YKDIS 217

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K   +T  RI QI  KAI++++
Sbjct: 218 KILNLTESRISQIHTKAIKRIR 239


>gi|332994104|gb|AEF04159.1| flagellar biosynthesis sigma factor [Alteromonas sp. SN2]
          Length = 243

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 109/235 (46%), Gaps = 17/235 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K ++VE +  LV  +A     R    +   DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  KSQLVERHASLVKRIAHHLMARLPASVLVDDLIQSGMIGLLEAARNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I     T R  VH   +   +     ++  +  R+    +IA K+ + ++
Sbjct: 74  IRIRGAMLDEIRKGDWTPR-SVHKNGR--AITEAISQVEGETGRDARDVDIAAKMNVSMQ 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLA 618
              ++L      ++    +G ED     D I   +++ + +PL+  +Q   ++     + 
Sbjct: 131 DYHQMLN----EVNAGKLVGIEDLGVSEDVISTEKNRGSDAPLEDLMQGAFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ KLK   +S
Sbjct: 187 TLPEREAIVLSLYYDEELN----LREIGEVLDVSESRVSQIHSQAMLKLKSRMKS 237


>gi|330874700|gb|EGH08849.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 202

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 29/65 (44%), Positives = 46/65 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAI 508
           +K  I
Sbjct: 110 IKAEI 114


>gi|224992874|gb|ACN76152.1| SigB [Listeria monocytogenes]
 gi|224992886|gb|ACN76158.1| SigB [Listeria monocytogenes]
 gi|224992898|gb|ACN76164.1| SigB [Listeria monocytogenes]
 gi|224992902|gb|ACN76166.1| SigB [Listeria monocytogenes]
          Length = 214

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 12  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 72  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 131

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 132 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 187

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 188 LDEREQKILQYTF 200


>gi|319649653|ref|ZP_08003809.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398815|gb|EFV79497.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 109/226 (48%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  ++ +   D  ++AN+ ++   + L  L+ 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTEDDIITKD--LEANVDKKLLLKALHQLSD 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+G   + T ++V     +++  I ++E + I++LK
Sbjct: 187 REKQIMELRFGLGSGEEKTQKDVADMLGISQSYISRLEKRIIKRLK 232


>gi|294497070|ref|YP_003560770.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|295702435|ref|YP_003595510.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
 gi|294347007|gb|ADE67336.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|294800094|gb|ADF37160.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
          Length = 264

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/234 (20%), Positives = 121/234 (51%), Gaps = 12/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V     LV S+A++Y+       D++Q G +GL+ A  ++D   G  F ++A+  
Sbjct: 30  AQSDLVVHYKNLVESIARRYSKGRSLHEDIVQVGMLGLLGAIRRYDASFGRSFESFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++R P  +EIA  + +  E +
Sbjct: 90  IIGEIKRFLRDKTWSVHVPRRIKELGPKIKAAVEELTTRLQRSPQVKEIADHIGVTEEEI 149

Query: 564 RKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++  + + +S++  I  D D    G  +   + V   +S  +  + R    ++L  
Sbjct: 150 LETMEMGQSYQALSVDHSIEADSD----GSTVTILDLVGEQESGYEKTDQRLVLEKILHV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           L+ RE+ V+R  F   ++     ++ G++  +++  + +++ +A+ KL+  +RS
Sbjct: 206 LSDREKEVIRYTFIENLSQ----KDAGEKLGISQMHVSRLQRRALDKLRTAARS 255


>gi|284032127|ref|YP_003382058.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Kribbella
           flavida DSM 17836]
 gi|283811420|gb|ADB33259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Kribbella
           flavida DSM 17836]
          Length = 269

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 58/254 (22%), Positives = 115/254 (45%), Gaps = 24/254 (9%)

Query: 420 TGISISEFRH-------IVSMVRKGECEASIAKKEMVEA----NLRLVISVAKKYTNRGL 468
           +G ++++  H       +  ++R    E    + E++E      + +  ++A +Y  RG+
Sbjct: 12  SGPAVTQVEHRNQQAAQVERLLRLAAEETGARRTELIEQAVVEGVPMARTLAARYHRRGV 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+Q  ++GL+KAA  +       F +YA+  ++  + R   DQ+  +R P  ++D 
Sbjct: 72  DSDDLLQVASVGLVKAAHGYRPGPDTDFRSYAIPTIRGELRRHFRDQAWMVRPPRRIQDL 131

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTS 586
              +      +++ ++  PT E++A  + +PVE +    +      P SL+  +      
Sbjct: 132 QTAINAAEADLASTLQHWPTTEDLAAAIGVPVEDIVDAQRAQGCFRPASLDAKLTGAPAL 191

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEV 645
            LG  I DK     L   I     ET   V+  L  R+  +L  RF      DH T  E+
Sbjct: 192 SLGTVIADKTNTYELVDHI-----ETLRPVVEDLPARDRLILHRRF-----VDHRTQAEI 241

Query: 646 GKQFCVTRERIRQI 659
           G++  V++ ++ ++
Sbjct: 242 GEEIGVSQMQVSRL 255


>gi|222530382|ref|YP_002574264.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457229|gb|ACM61491.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 210

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 113/240 (47%), Gaps = 60/240 (25%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + ++  ++KG+ EA+   + ++ A   L+IS+A KY N+   F DL QEG + +
Sbjct: 8   LSFDEQKELIGRIKKGDKEAA---ETLIMAYEPLIISLAAKY-NKPDIFEDLKQEGAVAI 63

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++AA+KFD  LG  F T A++++K+ + R   ++S TIR P +                 
Sbjct: 64  LQAAQKFDESLGVSFVTLAIYYIKRNMDRC-TNKSRTIRPPFN----------------- 105

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-----GDEDTSHLGDFIEDKN 596
               +P  E       +P            + IS+E+ I      D++   + D ++D  
Sbjct: 106 ----KPNTE-------IP------------QVISMESVINTNSHADDEELKVKDTVQDTA 142

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            V       QA   ET  R++  L+  E ++L +R        ++ +E+ K+  +T +++
Sbjct: 143 NVEE-----QAMYNETLQRLIKMLSDEERKILLLRLK-----QYSFKEIAKELGLTEKQV 192


>gi|318066987|emb|CBY89108.1| RNA polymerase sigma70 factor [Kushneria indalinina]
          Length = 372

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 42/60 (70%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P +  +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALSSLPGSVDSILEAYDATQD 80


>gi|224992794|gb|ACN76112.1| SigB [Listeria innocua]
 gi|224992800|gb|ACN76115.1| SigB [Listeria innocua]
 gi|224992802|gb|ACN76116.1| SigB [Listeria innocua]
 gi|224992804|gb|ACN76117.1| SigB [Listeria innocua]
 gi|224992806|gb|ACN76118.1| SigB [Listeria innocua]
 gi|224992808|gb|ACN76119.1| SigB [Listeria innocua]
 gi|224992812|gb|ACN76121.1| SigB [Listeria innocua]
 gi|224992816|gb|ACN76123.1| SigB [Listeria innocua]
 gi|224992818|gb|ACN76124.1| SigB [Listeria innocua]
 gi|224992820|gb|ACN76125.1| SigB [Listeria innocua]
 gi|224992822|gb|ACN76126.1| SigB [Listeria innocua]
 gi|224992824|gb|ACN76127.1| SigB [Listeria innocua]
 gi|224992826|gb|ACN76128.1| SigB [Listeria innocua]
 gi|224992828|gb|ACN76129.1| SigB [Listeria innocua]
 gi|224992830|gb|ACN76130.1| SigB [Listeria innocua]
 gi|224992836|gb|ACN76133.1| SigB [Listeria innocua]
 gi|224992838|gb|ACN76134.1| SigB [Listeria innocua]
 gi|224992840|gb|ACN76135.1| SigB [Listeria innocua]
 gi|224992842|gb|ACN76136.1| SigB [Listeria innocua]
 gi|224992844|gb|ACN76137.1| SigB [Listeria innocua]
 gi|224992846|gb|ACN76138.1| SigB [Listeria innocua]
 gi|224992852|gb|ACN76141.1| SigB [Listeria innocua]
 gi|224992854|gb|ACN76142.1| SigB [Listeria innocua]
          Length = 214

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 12  AQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 72  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 131

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 132 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 187

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 188 LDEREQKILQYTF 200


>gi|116328490|ref|YP_798210.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116331220|ref|YP_800938.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116121234|gb|ABJ79277.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124909|gb|ABJ76180.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 266

 Score = 64.3 bits (155), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 112/225 (49%), Gaps = 24/225 (10%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVH 524
           + ++F DL+  G  GL+ A EKFD     KF TYAM      I  SI D+  +I  IP  
Sbjct: 53  QNVEFDDLVSYGVFGLLDAIEKFDPDRLIKFKTYAM----TRIRGSIFDELRSIDWIPRS 108

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +R K  ++ +    + NK  ++   + IAK+L + +E    +L  TK  IS  + +   D
Sbjct: 109 IRQKAKQLEQIIGMLENKEGQQVDDDAIAKELGISMEEYNSLL--TK--ISGTSLVSLND 164

Query: 585 TSHLGDFIEDKNAVSPLDSAIQAN---------LRETTTRVLASLTPREERVLRMRFGIG 635
              LGD  ++ + +  L+S +  N         ++      + +L  +E++V+ + +   
Sbjct: 165 IWFLGDENDEVSFMETLESPMNMNPDTIIEKEEIKNVIVEAIKTLPEKEKKVIVLYY--- 221

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              D TL+E+G+   VT  RI Q+  +A+ +L+  S+  K++S +
Sbjct: 222 -YEDLTLKEIGEVLEVTESRISQLHTRAVSRLR--SKLGKVKSVI 263


>gi|318066955|emb|CBY89092.1| RNA polymerase sigma70 factor [Halomonas magadiensis]
          Length = 370

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILEAYDATQD 80


>gi|225017509|ref|ZP_03706701.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
 gi|224949748|gb|EEG30957.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
          Length = 231

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 101/227 (44%), Gaps = 50/227 (22%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A+  ++E NLRLV  +AKKY +   +  DLI  G IGL+KA   FD+  G +F+TYA 
Sbjct: 47  SAARDRLIEHNLRLVAHIAKKYYSVTNEQDDLISIGTIGLIKAVGTFDYTKGTRFATYA- 105

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
                  +R I ++     I +H R+               +K+      I   +    +
Sbjct: 106 -------SRCIENE-----ILMHFRN---------------VKKTAGDVYINDTIDTDKD 138

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           G           ISL   I DE            N V  +D  +++     + + L  LT
Sbjct: 139 G---------NSISLIDVIADE-----------TNIVDTIDLKLKSEQLHKSIKNL--LT 176

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ ++ +R+G+  +   T  EV  +  ++R  + +IE K++ +LK
Sbjct: 177 EREQMIVILRYGLNGHRPMTQREVADRLKISRSYVSRIEKKSLEQLK 223


>gi|315444786|ref|YP_004077665.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263089|gb|ADT99830.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 284

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 111/233 (47%), Gaps = 22/233 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++   L L   +A+++  RG    DL+Q   +GL+ A  +FD      F  +A+  +
Sbjct: 54  REAIIARCLPLADHIARRFRGRGEGHEDLVQVARVGLLNAVNRFDVDSANDFLAFAVPTM 113

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D   ++++P  +++   ++      ++ ++ R PTP E+AK L +  E V 
Sbjct: 114 MGEVRRYFRDHGWSLKVPRRLKELNVRLNAARADLTQELNRAPTPSELAKYLGIDREEVV 173

Query: 565 KVL--------KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR- 615
           + L        + T++P +     GD      G+ +  ++     D  IQ  +   T + 
Sbjct: 174 EGLVAANAYSTRSTEQPTTFS---GD------GEGLSLQDTFGAPDDNIQKVIDVNTVQP 224

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LA+L  R+  VL++RF      D T  ++ +Q  V++  + ++ A+A+  L+
Sbjct: 225 LLAALPERDRLVLKLRF----FEDRTQSQIAEQIGVSQMHVSRLLARALATLR 273


>gi|228474927|ref|ZP_04059656.1| RNA polymerase sigma-B factor [Staphylococcus hominis SK119]
 gi|228271159|gb|EEK12539.1| RNA polymerase sigma-B factor [Staphylococcus hominis SK119]
          Length = 256

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 118/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDISFDRKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ +    ++N++ R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVGDELTNELGRSPSILEIANRLEVNEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L       D S   D  +D + V+ LD   Q +        R    R+
Sbjct: 151 LEAMEMGQSYNALSV-----DHSIEAD--KDGSTVTLLDIMGQQDDNYDLTEKRMILERI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AIRKL+  +R
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIRKLQQAAR 255


>gi|211906943|gb|ACJ11990.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906945|gb|ACJ11991.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906947|gb|ACJ11992.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906949|gb|ACJ11993.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
          Length = 222

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 18  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 78  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 137

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 138 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 193

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 194 LDEREQKILQFTF 206


>gi|85679195|gb|ABC72014.1| SigB [Listeria monocytogenes]
 gi|85679205|gb|ABC72019.1| SigB [Listeria monocytogenes]
 gi|85679211|gb|ABC72022.1| SigB [Listeria monocytogenes]
 gi|85679213|gb|ABC72023.1| SigB [Listeria monocytogenes]
 gi|307717608|gb|ADN88857.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717616|gb|ADN88861.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQFTF 204


>gi|224992792|gb|ACN76111.1| SigB [Listeria innocua]
 gi|224992796|gb|ACN76113.1| SigB [Listeria innocua]
 gi|224992810|gb|ACN76120.1| SigB [Listeria innocua]
 gi|224992814|gb|ACN76122.1| SigB [Listeria innocua]
 gi|224992832|gb|ACN76131.1| SigB [Listeria innocua]
 gi|224992834|gb|ACN76132.1| SigB [Listeria innocua]
 gi|224992848|gb|ACN76139.1| SigB [Listeria innocua]
 gi|224992850|gb|ACN76140.1| SigB [Listeria innocua]
 gi|224992856|gb|ACN76143.1| SigB [Listeria innocua]
          Length = 214

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 12  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 72  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 131

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 132 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 187

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 188 LDEREQKILQYTF 200


>gi|54308132|ref|YP_129152.1| flagellar biosynthesis sigma factor [Photobacterium profundum SS9]
 gi|46912558|emb|CAG19350.1| Putative flagellar-specific RNA polymerase sigma factor, FliA
           [Photobacterium profundum SS9]
          Length = 240

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 96/204 (47%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F T+A   ++ A+   I        +P  +  
Sbjct: 40  VQVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDDIRRGDW---VPRSVYK 96

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              ++     ++ NK+ R+PT  EIA+ L M ++   + L      ++    +G +D   
Sbjct: 97  NNRRITEAMAQLENKLGRDPTDTEIAEHLEMTLDQYHQALN----DVNCGRLVGMDDLGV 152

Query: 588 LGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D +  + +     P    +  N R++    + +L  RE  VL + +   +N    L+E
Sbjct: 153 SEDAVTTEASREENLPFQGVVDDNFRQSLADAIKTLPEREALVLSLYYDEELN----LKE 208

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    V+  RI QI ++A+++L+
Sbjct: 209 IGVVVGVSESRICQIHSQAMQRLR 232


>gi|188011585|gb|ACD45089.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011587|gb|ACD45090.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011589|gb|ACD45091.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011591|gb|ACD45092.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011593|gb|ACD45093.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011595|gb|ACD45094.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011597|gb|ACD45095.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011599|gb|ACD45096.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011601|gb|ACD45097.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011603|gb|ACD45098.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011605|gb|ACD45099.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011607|gb|ACD45100.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011609|gb|ACD45101.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011611|gb|ACD45102.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011613|gb|ACD45103.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011615|gb|ACD45104.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011617|gb|ACD45105.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011619|gb|ACD45106.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011621|gb|ACD45107.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011623|gb|ACD45108.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011625|gb|ACD45109.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011627|gb|ACD45110.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011629|gb|ACD45111.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011631|gb|ACD45112.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011633|gb|ACD45113.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011635|gb|ACD45114.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011637|gb|ACD45115.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011639|gb|ACD45116.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011641|gb|ACD45117.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011643|gb|ACD45118.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011645|gb|ACD45119.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011647|gb|ACD45120.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011649|gb|ACD45121.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011651|gb|ACD45122.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011653|gb|ACD45123.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011655|gb|ACD45124.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011657|gb|ACD45125.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011659|gb|ACD45126.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011661|gb|ACD45127.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011663|gb|ACD45128.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011665|gb|ACD45129.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011667|gb|ACD45130.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011669|gb|ACD45131.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011671|gb|ACD45132.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011673|gb|ACD45133.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011675|gb|ACD45134.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011677|gb|ACD45135.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011679|gb|ACD45136.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011681|gb|ACD45137.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011683|gb|ACD45138.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011685|gb|ACD45139.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011687|gb|ACD45140.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011689|gb|ACD45141.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011691|gb|ACD45142.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011693|gb|ACD45143.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011695|gb|ACD45144.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011697|gb|ACD45145.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011699|gb|ACD45146.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011701|gb|ACD45147.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011703|gb|ACD45148.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011705|gb|ACD45149.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011707|gb|ACD45150.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011709|gb|ACD45151.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011711|gb|ACD45152.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011713|gb|ACD45153.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011715|gb|ACD45154.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011717|gb|ACD45155.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011719|gb|ACD45156.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011721|gb|ACD45157.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011723|gb|ACD45158.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011725|gb|ACD45159.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011727|gb|ACD45160.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011729|gb|ACD45161.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011731|gb|ACD45162.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011733|gb|ACD45163.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011735|gb|ACD45164.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011737|gb|ACD45165.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011739|gb|ACD45166.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011741|gb|ACD45167.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011743|gb|ACD45168.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011745|gb|ACD45169.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011747|gb|ACD45170.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011749|gb|ACD45171.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011751|gb|ACD45172.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011753|gb|ACD45173.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011755|gb|ACD45174.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011757|gb|ACD45175.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011763|gb|ACD45178.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011865|gb|ACD45229.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011871|gb|ACD45232.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011873|gb|ACD45233.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011945|gb|ACD45269.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011947|gb|ACD45270.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011949|gb|ACD45271.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|211906951|gb|ACJ11994.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906953|gb|ACJ11995.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906955|gb|ACJ11996.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906957|gb|ACJ11997.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906959|gb|ACJ11998.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906961|gb|ACJ11999.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906963|gb|ACJ12000.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|281324219|gb|ADA60651.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324223|gb|ADA60653.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324225|gb|ADA60654.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324227|gb|ADA60655.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324229|gb|ADA60656.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324231|gb|ADA60657.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324233|gb|ADA60658.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324235|gb|ADA60659.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324237|gb|ADA60660.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324241|gb|ADA60662.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324243|gb|ADA60663.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324245|gb|ADA60664.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324247|gb|ADA60665.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324249|gb|ADA60666.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324251|gb|ADA60667.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324253|gb|ADA60668.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324255|gb|ADA60669.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324257|gb|ADA60670.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324259|gb|ADA60671.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324261|gb|ADA60672.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324263|gb|ADA60673.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324265|gb|ADA60674.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324267|gb|ADA60675.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324269|gb|ADA60676.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324271|gb|ADA60677.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324275|gb|ADA60679.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324277|gb|ADA60680.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324279|gb|ADA60681.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324281|gb|ADA60682.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324283|gb|ADA60683.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 18  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 78  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 137

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 138 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 193

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 194 LDEREQKILQFTF 206


>gi|161898843|gb|ABX80411.1| SigB [Listeria monocytogenes]
          Length = 228

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 14  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 73

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 74  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 133

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 134 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 189

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 190 LDEREQKILQFTF 202


>gi|317502438|ref|ZP_07960602.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331090300|ref|ZP_08339184.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316896176|gb|EFV18283.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330401435|gb|EGG81020.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 206

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 67/255 (26%), Positives = 109/255 (42%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ SE ++ +    +G+ EA   K  ++E NLRLV  V KKY N      DLI  
Sbjct: 3   SFPNPLTPSEEKYYIRKYTEGDLEA---KHILIERNLRLVAHVIKKYQNSEEDPEDLISI 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+   G + + YA        +R I ++     I +++R K        
Sbjct: 60  GTIGLIKAVVTFNPDKGNRLAAYA--------SRCIENE-----ILMYLRSK-------- 98

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
                            KK A              + ISL  PIG +   +   L D IE
Sbjct: 99  -----------------KKAA--------------KEISLYEPIGTDREGNEIKLYDIIE 127

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                      ++ N++    +V   L+ RE  +L+MR+G+    ++T  E+ +Q  ++R
Sbjct: 128 TDEEEVAEKIHLKENIQTLYEKVEKELSQRERIILKMRYGLYNGEEYTQREIARQLGISR 187

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE  A+ KL+
Sbjct: 188 SYVSRIEKGAVEKLR 202


>gi|253577386|ref|ZP_04854702.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251843186|gb|EES71218.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 257

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 54/217 (24%), Positives = 107/217 (49%), Gaps = 14/217 (6%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++  K   NR   + DL Q G + L++  +++D  LG  F  YAM  +   +   + D+S
Sbjct: 43  MAAGKIARNRPDLYEDLYQVGEMALVRLLQQYDSDLGIPFEPYAMKSMIGHMKNYLRDKS 102

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPI 574
             I++P  +++K   V +    ++ K++R P  +EIA+ L + VE   +VL  +     +
Sbjct: 103 WYIQVPRRIKEKGALVQQAIDELTLKLERSPNVQEIAEYLELSVEETVEVLAGRDCYHYV 162

Query: 575 SLETPIG-DEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           SL++P+  DE    LG+ I  D +    L++      R    + L  L  +E++VL M +
Sbjct: 163 SLDSPLSPDESAVTLGEVISADADDYDALEN------RMDLQQALGQLKAQEQQVLLMAY 216

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             G     +   + ++  +++  + +I+ +A  +LK 
Sbjct: 217 QEG----QSQRAIARKLGISQMSVSRIQKRATERLKQ 249


>gi|307717606|gb|ADN88856.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 95/193 (49%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA+ + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIAEFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|187926255|ref|YP_001892600.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12J]
 gi|241665743|ref|YP_002984102.1| flagellar biosynthesis sigma factor [Ralstonia pickettii 12D]
 gi|309778948|ref|ZP_07673718.1| RNA polymerase sigma factor for flagellar operon [Ralstonia sp.
           5_7_47FAA]
 gi|187728009|gb|ACD29173.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12J]
 gi|240867770|gb|ACS65430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12D]
 gi|308922295|gb|EFP67922.1| RNA polymerase sigma factor for flagellar operon [Ralstonia sp.
           5_7_47FAA]
          Length = 253

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 94/206 (45%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F  YA   ++ AI   +        +P  +R     
Sbjct: 50  DLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNART 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  +++  +  R PT  EIA  L M +   +K L   +    L     D D      F
Sbjct: 107 IEQAIQKLQQQKGRAPTETEIAVALGMSLAEYQKQLVDLQGSQLLYYE--DFDREDADAF 164

Query: 592 IEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           IE++   N  +PLD  +  +LRE+    +  L  RE+ ++ + +      D  L E+G  
Sbjct: 165 IENRAPENDATPLDQLLDHDLRESVVAAIEGLPEREKLMMSLYY----EQDLNLREIGAV 220

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             V+  R+ QI ++AI +++   R +
Sbjct: 221 MGVSESRVCQIHSQAIARIRSRLRDR 246


>gi|323490578|ref|ZP_08095784.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
 gi|323395844|gb|EGA88684.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
          Length = 260

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 52/229 (22%), Positives = 117/229 (51%), Gaps = 12/229 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V    RLV S+A+KY+N      D+ Q G +GL+ A  ++D   G  F  +A+  
Sbjct: 30  AQTNLVLNYKRLVESIARKYSNGKSYHEDIAQVGMLGLLGAIRRYDPSYGRSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++  I +P  +++   ++  T   ++ +++R P   EIA+ L +  + +
Sbjct: 90  IIGEIKRFLRDKTWAIHVPRRIKELGPRIKATVEVLTTELQRSPQVWEIAEYLDVEEDDI 149

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  +  D D S +  F    + V   D   + A+ R      +  
Sbjct: 150 LEAMEMGKSYQALSMDHSLEADSDGSTITLF----DVVGQEDDGYEKADQRMLVAEAMNV 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ RE+++++  +   ++     +E G +  +++  + +++ KAI+KL+
Sbjct: 206 LSEREKQIIQFTYIEQLSQ----KEAGDKLGISQMHVSRLQRKAIKKLQ 250


>gi|318066981|emb|CBY89105.1| RNA polymerase sigma70 factor [Halotalea alkalilenta]
          Length = 370

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 43/62 (69%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++    E  D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAFLPGAVDSIL----EAFD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|253578603|ref|ZP_04855875.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850921|gb|EES78879.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39BFAA]
          Length = 238

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 106/232 (45%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 55  AKSVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNIKLATYA--- 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR S                       
Sbjct: 112 -----SRCIENE----------------ILMYLRRNSK---------------------- 128

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVS-PLDSAIQANLRETTTRVLA 618
                 TK  +S++ P+    D +   L D +  D++ +S  L+  ++ +L    ++ + 
Sbjct: 129 ------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDVISRRLEDEVEISL---LSKAIR 179

Query: 619 SLTPREERVLRMRFGIGMN--TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+PRE+ ++R+RFG+G     + T +EV     +++  I ++E + +++LK
Sbjct: 180 KLSPREQTIIRLRFGLGKENAAEKTQKEVADLLGISQSYISRLEKRIMKRLK 231


>gi|314935979|ref|ZP_07843329.1| RNA polymerase sigma-B factor [Staphylococcus hominis subsp.
           hominis C80]
 gi|313655985|gb|EFS19727.1| RNA polymerase sigma-B factor [Staphylococcus hominis subsp.
           hominis C80]
          Length = 256

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 118/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDISFDRKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ +    ++N++ R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVGDELTNELGRSPSILEIANRLEVNEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L       D S   D  +D + V+ LD   Q +        R    R+
Sbjct: 151 LEAMEMGQSYNALSV-----DHSIEAD--KDGSTVTLLDIMGQQDDNYDLTEKRMILERI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AIRKL+  +R
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIRKLQQAAR 255


>gi|317127083|ref|YP_004093365.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315472031|gb|ADU28634.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 262

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 117/223 (52%), Gaps = 22/223 (9%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV ++A+K++       DLIQ G IGL+ A  +FD  +G  F ++A+  +   I R I D
Sbjct: 42  LVHALARKFSRGQRHDEDLIQVGMIGLLAAIRRFDPTIGKSFESFAVPTIIGEIKRFIRD 101

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   KV      ++ +++R P  EEIA  +    E V + +++ K  +
Sbjct: 102 KTWSVHVPRRIKEMGPKVKNAVDTLTTQLQRSPKVEEIAAHIDASEEEVLETMEMGKSYQ 161

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLD--SAIQANLRETTTRVL-----ASLTPREE 625
            +S++  I  +D         + +AV+ LD   + +    +T  ++L       L+ RE+
Sbjct: 162 ALSVDRSIEADD---------EGSAVTLLDLVGSTEGGYEKTDQQMLLEKAFTVLSDREK 212

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L + +   ++   T E++G    +++  + +++ +A++KL+
Sbjct: 213 QILHLTYFENLSQKDTGEKLG----ISQMHVSRLQRRALQKLR 251


>gi|161898885|gb|ABX80432.1| SigB [Listeria monocytogenes]
          Length = 217

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 13  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 73  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 132

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 133 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 188

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 189 LDEREQKILQFTF 201


>gi|289607021|emb|CBI60914.1| unnamed protein product [Sordaria macrospora]
          Length = 72

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 47/60 (78%)

Query: 17 DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
          D+ D+ + D ++ S KK++  A++RGY+T+++LN  LP D+++SEQ+ED ++ L++MG+N
Sbjct: 13 DTGDAPLIDLNEGSIKKLVARAKKRGYITVDQLNEMLPQDQMTSEQIEDIMSALNDMGVN 72


>gi|318066923|emb|CBY89076.1| RNA polymerase sigma70 factor [Halomonas anticariensis]
          Length = 371

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDATQD 80


>gi|85679193|gb|ABC72013.1| SigB [Listeria monocytogenes]
 gi|85679197|gb|ABC72015.1| SigB [Listeria monocytogenes]
 gi|85679199|gb|ABC72016.1| SigB [Listeria monocytogenes]
 gi|85679201|gb|ABC72017.1| SigB [Listeria monocytogenes]
 gi|85679203|gb|ABC72018.1| SigB [Listeria monocytogenes]
 gi|85679207|gb|ABC72020.1| SigB [Listeria monocytogenes]
 gi|85679209|gb|ABC72021.1| SigB [Listeria monocytogenes]
 gi|85679215|gb|ABC72024.1| SigB [Listeria monocytogenes]
 gi|307717584|gb|ADN88845.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717618|gb|ADN88862.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717628|gb|ADN88867.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQFTF 204


>gi|111021699|ref|YP_704671.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110821229|gb|ABG96513.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 249

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 100/223 (44%), Gaps = 27/223 (12%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++ ++E  L L   +A+++  RG    DLIQ   +GL+KA ++FD   G  F +YA+ 
Sbjct: 20  VLRQRLIERCLPLAEHIARRFHGRGEPLDDLIQVARLGLVKAVDRFDARCGANFVSYAVP 79

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   + R   D    +R+P  M++    +      ++  + R PT  E+A+ + +  + 
Sbjct: 80  TITGEVRRHFRDTGWAMRVPRSMQELHLSLTNATTELTTTLGRAPTASELAEAVGIDKDE 139

Query: 563 VRKVLKITKEPISLET--PIGDED---TSHLGDF------IEDKNAVSPLDSAIQANLRE 611
           V + L++     +L T  P+G+ +   +  +GD       +ED   ++PL          
Sbjct: 140 VVQGLRVADAYSTLSTDFPLGENERPLSETIGDVDPALAHVEDHVVLAPL---------- 189

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                L SL   E  VL +RF   M        VG  Q  V+R
Sbjct: 190 -----LESLPDLERTVLVLRFFGNMTQSQIAARVGVSQMQVSR 227


>gi|318066925|emb|CBY89077.1| RNA polymerase sigma70 factor [Halomonas aquamarina]
 gi|318066927|emb|CBY89078.1| RNA polymerase sigma70 factor [Halomonas axialensis]
 gi|318066959|emb|CBY89094.1| RNA polymerase sigma70 factor [Halomonas meridiana]
          Length = 370

 Score = 63.9 bits (154), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILEAYDATQD 80


>gi|318066945|emb|CBY89087.1| RNA polymerase sigma70 factor [Halomonas halocynthiae]
          Length = 368

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 42/60 (70%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG+++LL+REGEI IAKRIE G   +MA+L   P   ++++   D   D
Sbjct: 21  TTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGIREVMAALAYVPGAVESILEAYDATQD 80


>gi|318066951|emb|CBY89090.1| RNA polymerase sigma70 factor [Halomonas hydrothermalis]
          Length = 370

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILDAYDATQD 80


>gi|14530750|emb|CAC42416.1| RpoH protein [Ralstonia metallidurans CH34]
          Length = 317

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 38/54 (70%), Gaps = 6/54 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD------WC 491
           A + MV ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD      WC
Sbjct: 91  AARRMVMSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPEQACAWC 144


>gi|15895573|ref|NP_348922.1| sporulation sigma factor SigF [Clostridium acetobutylicum ATCC 824]
 gi|15025312|gb|AAK80262.1|AE007731_7 Sporulation-specific sigma factor F [Clostridium acetobutylicum
           ATCC 824]
 gi|325509722|gb|ADZ21358.1| sporulation sigma factor SigF [Clostridium acetobutylicum EA 2018]
          Length = 252

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 54/246 (21%), Positives = 118/246 (47%), Gaps = 25/246 (10%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  V +G  EA     +++E NL LV ++++K+ NRG ++ D+ Q G +GL+KA   F+
Sbjct: 20  LIKSVHEGNKEAL---NKIIENNLPLVSAISRKFLNRGYEYDDIFQIGCMGLVKAVNNFN 76

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R + D    I++   ++    ++     ++  ++ REPT 
Sbjct: 77  SDYKVKFSTYAVPMIMGEIKRFLRDDGI-IKVSRSVKSTARQLHYDREKLVKELNREPTI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS------HLGD-FIEDKNAVSPLD 602
           +E++K   +  E +    + T     L   +  +D S       L D + ED + +  + 
Sbjct: 136 DELSKFSGIDKEEIIMATESTTSMQYLYDVVHQDDGSPVLLIDKLSDPYSEDSDVIDKI- 194

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                       +++ SL  + ++++ +R+      D T  +V     +++ ++ +IE +
Sbjct: 195 ---------VLKQIIKSLDNKSKQIIMLRYF----KDKTQTQVANMLGISQVQVSRIEKR 241

Query: 663 AIRKLK 668
            ++ ++
Sbjct: 242 ILKAIR 247


>gi|167758775|ref|ZP_02430902.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
 gi|167663515|gb|EDS07645.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
          Length = 247

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 108/228 (47%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 64  AKKTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPEKNIKLATYA--- 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NK K E + +E    L +  +G 
Sbjct: 121 -----SRCIENE----------------ILMYLRR-NNKTKMEVSIDE---PLNVDWDG- 154

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DEDT +             L++ ++   R+   + ++ L+ 
Sbjct: 155 --------NELLLSDILGTDEDTIY-----------KDLENEVE---RKLLVKAISRLSG 192

Query: 623 REERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  +++MRFG+G     + T +EV     +++  I ++E K +++LK
Sbjct: 193 RERTIIKMRFGLGTPDGEEKTQKEVADMLGISQSYISRLEKKIMQRLK 240


>gi|83647839|ref|YP_436274.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
 gi|83635882|gb|ABC31849.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
          Length = 275

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 92/208 (44%), Gaps = 22/208 (10%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++AA+K+D   G KF TYA   ++ A+   I        +P  +  
Sbjct: 74  VQVEDLIQAGMIGLLEAAQKYDAGKGAKFETYAGIRIRGAMVDEIRKGDW---VPRSVHR 130

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-------ITKEPISLETPI 580
               +      +  +  R+ +  E+A +L +P+E     L+        + E +      
Sbjct: 131 NARNIAEAIHTIEARTGRDASDAEVAAELGVPLEQYHASLRDASSGKLFSLEELGFHGEG 190

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +D        E   A +PL    Q    E  +  +  L  RE+ VL + +   +N   
Sbjct: 191 GSDD--------ETLTADNPLSDIEQNAFLEKLSAAIDGLPEREKLVLSLYYDEELN--- 239

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+E+G+   V+  R+ QI ++A  +L+
Sbjct: 240 -LKEIGQVLSVSESRVSQIHSQATLRLR 266


>gi|161898899|gb|ABX80439.1| SigB [Listeria monocytogenes]
          Length = 229

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQFTF 204


>gi|114562377|ref|YP_749890.1| flagellar biosynthesis sigma factor [Shewanella frigidimarina NCIMB
           400]
 gi|114333670|gb|ABI71052.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 239

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 104/230 (45%), Gaps = 18/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHMLARLPASVQLDDLLQAGMMGLLEASSKFDNSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH  +++  V      +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMIDEIRRGDWVPR-SVHRNNRL--VAHAIDELGQLLGRDANDTEIAEKLDMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLA 618
               +L      +S+   IG ED     D +   N  SP    DS  +   +      + 
Sbjct: 130 EYHHILN----DVSVGKIIGIEDLGVSQDVLITDNE-SPDETFDSLAEIQFQSALVEAIK 184

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 185 TLPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|323499559|ref|ZP_08104529.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
 gi|323315432|gb|EGA68473.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
          Length = 244

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 94/204 (46%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH  +
Sbjct: 42  VQVEDLIQAGMIGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHN 100

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +  ++ +    +  ++ R+PT  E+A+ L M +      L      I+    +G ED   
Sbjct: 101 R--EISQAISVLEGELNRDPTDAEVAQHLGMSLAQYHSALA----DINCSRLVGIEDLGV 154

Query: 588 LGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D I   +D  A +P         R+     + +L  RE  VL + +   +N    L+E
Sbjct: 155 SEDVISPEDDDEANTPFQGVADEYFRKALVDSIKALPEREALVLSLYYDEELN----LKE 210

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    V+  R+ QI ++++++L+
Sbjct: 211 IGDVIGVSESRVSQILSQSMQRLR 234


>gi|161723249|ref|YP_095808.2| flagellar biosynthesis sigma factor [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|307610482|emb|CBX00054.1| sigma factor 28 [Legionella pneumophila 130b]
          Length = 238

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 112/254 (44%), Gaps = 63/254 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F TYA
Sbjct: 14  TQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYA 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMS-------NKIKRE 546
                             IRI  HM D++ +       V R +R +S       +K+ RE
Sbjct: 74  -----------------GIRIRGHMLDEVRRNDWVPRSVYRNSRMISDAVRILEHKLGRE 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF------------IED 594
               EIA++L + ++    +L+             D  +SHL  F             E 
Sbjct: 117 AKDNEIAEELGVSLDDYHDMLQ-------------DSISSHLYGFDDLGVTDDVLFDHEG 163

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             +  P  + +++++    T+V+ SL PR+ER++     +    D  L+E+G+   V+  
Sbjct: 164 NGSTEPHRNVMRSDMMNRLTQVIDSL-PRKERLV---LSLYYEQDLNLKEIGEILEVSES 219

Query: 655 RIRQIEAKAIRKLK 668
           RI QI ++A  +++
Sbjct: 220 RISQILSQATHRIR 233


>gi|331027965|ref|YP_004421515.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
 gi|294805578|gb|ADF42417.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
          Length = 261

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 47/84 (55%), Gaps = 8/84 (9%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFL--------DLIQEGNIGLMKAAEKFDWCLGYKFST 498
           ++ + NLRLV    + Y   G + L        DL+QEG  GL +AA KFD   GY F+T
Sbjct: 46  KLCQHNLRLVAKFTRAYMKGGTRKLTWGGDETMDLLQEGYFGLRRAANKFDPERGYTFAT 105

Query: 499 YAMWWVKQAITRSIADQSCTIRIP 522
           YA  WV+QA+ +   D+   IR+P
Sbjct: 106 YANAWVRQALGKYHVDKLSLIRVP 129


>gi|318066979|emb|CBY89104.1| RNA polymerase sigma70 factor [Halomonas venusta]
          Length = 370

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILDAYDATQD 80


>gi|192362157|ref|YP_001982606.1| FliA [Cellvibrio japonicus Ueda107]
 gi|190688322|gb|ACE86000.1| FliA [Cellvibrio japonicus Ueda107]
          Length = 247

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 62/213 (29%), Positives = 102/213 (47%), Gaps = 28/213 (13%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A++K+D   G  F TYA   ++ AI   +       R  VH   
Sbjct: 44  VQVEDLIQAGMIGLIEASQKYDASRGASFETYAGIRIRGAIVDEMRRGDWAPR-SVH--- 99

Query: 528 KIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLET 578
                 R  RR+S  +        R+ +  EIA +L + ++   ++L+ +      S E 
Sbjct: 100 ------RNGRRISQAMAAVEARTGRDASDTEIAAELDVGLDEYYQMLQDSSGSRLFSYEE 153

Query: 579 PIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
             G+ED++  G    D ++V  SPL+S  +  L+      +A L  RE  VL + +   +
Sbjct: 154 TFGEEDSNIDG---SDHSSVFASPLESIQRDGLKRALADAIALLPERERLVLALYYDEEL 210

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           N    L+E+G    V+  RI QI ++A  +L+ 
Sbjct: 211 N----LKEIGLVLGVSESRISQIHSQAAARLRQ 239


>gi|24215303|ref|NP_712784.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45657258|ref|YP_001344.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24196402|gb|AAN49802.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45600496|gb|AAS69981.1| RNA polymerase sigma-28 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 266

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 112/225 (49%), Gaps = 24/225 (10%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVH 524
           + ++F DL+  G  GL+ A EKFD     KF TYAM      I  SI D+  +I  IP  
Sbjct: 53  QNVEFDDLVSYGVFGLLDAIEKFDPERLIKFKTYAM----TRIRGSIFDELRSIDWIPRS 108

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +R K  ++ +    + NK  ++   + IAK+L + +E    +L  TK  IS  + +   D
Sbjct: 109 IRQKAKQLEQIIGMLENKEGQQVDDDAIAKELGISMEEYNSLL--TK--ISGTSLVSLND 164

Query: 585 TSHLGDFIEDKNAVSPLDSAIQAN---------LRETTTRVLASLTPREERVLRMRFGIG 635
              LGD  ++ + +  L+S +  N         ++      + +L  +E++V+ + +   
Sbjct: 165 IWFLGDENDEVSFMETLESPMNMNPDTIIEKEEIKNVIVEAIKTLPEKEKKVIVLYY--- 221

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              D TL+E+G+   VT  RI Q+  +A+ +L+  S+  K++S +
Sbjct: 222 -YEDLTLKEIGEVLEVTESRISQLHTRAVSRLR--SKLGKVKSVI 263


>gi|213027483|ref|ZP_03341930.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 253

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 35/106 (33%), Positives = 62/106 (58%), Gaps = 8/106 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI 113


>gi|168334573|ref|ZP_02692729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 247

 Score = 63.9 bits (154), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 108/229 (47%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++E    LV  VA +   Y N  L+  DL+  G IGL+ A +K+D+    KF TYA 
Sbjct: 20  KEQLIEHYAPLVKIVAGRLGIYLNSYLELDDLLGFGVIGLIDAIDKYDYDKKIKFETYAS 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I        +P  +R K  + +R   R+  KI   PT  ++ K+L +   
Sbjct: 80  LRIRGAIIDEIRKLDW---VPRSIRQKQKEYIRAYERVEAKIGHSPTDTDVRKELNINES 136

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDF-IEDKNAVSPLDSAIQANLRETTTRVLASL 620
              K++  T   IS    I   D S L +F IED    +P          E     + +L
Sbjct: 137 EYNKLVHDTN--ISTLVSI---DESELYEFNIEDITTKNPYQELENKEALEILEHEILAL 191

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T RE+ ++++ +      + TL+E+     ++  R+ QI +K + KL++
Sbjct: 192 TEREQLLIKLYYY----EELTLKEISLILEISESRVSQIHSKLMVKLRN 236


>gi|330980004|gb|EGH78270.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 214

 Score = 63.9 bits (154), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/65 (44%), Positives = 46/65 (70%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++MV A+LR V+ +A+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W
Sbjct: 50  AARQMVLAHLRFVVHIARSYSGYGLAQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHW 109

Query: 504 VKQAI 508
           +K  I
Sbjct: 110 IKAEI 114


>gi|328951994|ref|YP_004369328.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452318|gb|AEB08147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
          Length = 258

 Score = 63.9 bits (154), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 96/201 (47%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+ A +KFD      F TYA + +K AI   + +      IP  +R K  +
Sbjct: 57  DLISSGMIGLLDAIKKFDPQKNISFKTYAEFRIKGAI---LDELRALDWIPRSIRKKTSQ 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-----PIGDEDTS 586
           + +   ++  ++ R    EE+A  + + +E    ++  TK    L+       + +   +
Sbjct: 114 LEKAYTKLEKELGRPAEAEEVAHSMGLSMEEFYHLIDETKGVSLLDIDAVRRNLNEFSEA 173

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L + ++D+++ SP  S   A LR+   R L  L  +E+ ++ + +      + T++E+G
Sbjct: 174 ELYEILQDESSRSPFISVHFAELRDLLMRALEDLPDKEKLLISLYY----YEELTMKEIG 229

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           +    T  RI QI  +AI  L
Sbjct: 230 EIMGYTESRISQIHTQAIFHL 250


>gi|318059283|ref|ZP_07978006.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075250|ref|ZP_07982582.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 294

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/255 (25%), Positives = 125/255 (49%), Gaps = 25/255 (9%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F  +V ++ +G      A+  ++E N  LV   A+++ NRG   + D++Q G IGL+KA 
Sbjct: 45  FDQLV-VLEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D +  + +P  +++    + R   R++ ++ R
Sbjct: 104 DRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELRVDLARAKERLAVELDR 163

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSH---------LGDFIED 594
           +P  +E+A +L +  E V   L      +  SL+ P  D  TS            DF+ D
Sbjct: 164 DPGVKELAAELGISEEEVIDGLIAANGYMSDSLDLP-ADSSTSGKPDQKTATTYADFLGD 222

Query: 595 KNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                  D A++     T  R +L +L  RE  +L +RFG     + T  ++G +  V++
Sbjct: 223 ------WDPAMELVENFTALRPLLGTLDDRERYLLELRFG----QELTQAQIGAELGVSQ 272

Query: 654 ERIRQIEAKAIRKLK 668
             + ++ ++ + KL+
Sbjct: 273 MHVSRLLSRTLGKLR 287


>gi|291464752|gb|ADE05834.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 300

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/69 (49%), Positives = 44/69 (63%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+   
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEA 60

Query: 177 GTTLLREII 185
               L +II
Sbjct: 61  EQLRLSDII 69


>gi|126659593|ref|ZP_01730724.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619136|gb|EAZ89874.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 245

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 70/118 (59%), Gaps = 1/118 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +VE NL LV  VA + + +  + + DL Q G +GL++A E+FD   G  FS++A+ +
Sbjct: 16  RNRLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFDPQQGCAFSSFAIPY 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  +   + D+   +RIP   ++  +K  +  ++++  +KR PT +EIA  L +P++
Sbjct: 76  IRGEMLHYLRDKGSVMRIPRRWQELHNKAKKIRKQLTVSLKRPPTDQEIANALEVPLK 133


>gi|308048769|ref|YP_003912335.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
 gi|307630959|gb|ADN75261.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
          Length = 237

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 108/245 (44%), Gaps = 32/245 (13%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE +  LV  +A     R    +Q  DL+Q G +GL++AA  FD   G  F T+A 
Sbjct: 13  RAALVERHTPLVKRIAHHLLARLPASVQLDDLLQSGMVGLLEAARNFDGSKGASFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I     T R  VH   +  +V     ++  ++ R+PT  E+A  L + V+
Sbjct: 73  IRIRGAMLDEIRRGDWTPR-SVHRNSR--RVTDAMEQLERQLGRDPTGTEVADYLELSVD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-------LDSAIQANLRETTT 614
               +L      +S    +G      L D    ++A+ P        D       +    
Sbjct: 130 EYHHIL----HDVSAGKLVG------LDDLGVSEDAIGPGEESSEHFDHLADGRFQSALV 179

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             + +L  RE  VL + +   +N    L+E+G+   V+  R+ QI ++++ +LK      
Sbjct: 180 EAIKTLPEREALVLSLYYDEELN----LKEIGQVLGVSESRVSQIHSQSMVRLK-----T 230

Query: 675 KLRSF 679
           KLR++
Sbjct: 231 KLRAW 235


>gi|188011951|gb|ACD45272.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 222

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 18  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 78  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 137

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 138 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDYGFERVNQRMLLEKVLPV 193

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 194 LDEREQKILQFTF 206


>gi|90411040|ref|ZP_01219054.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
 gi|90328253|gb|EAS44564.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
          Length = 240

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 95/204 (46%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F T+A   ++ A+   I        +P  +  
Sbjct: 40  VQVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDDIRRGDW---VPRSVYK 96

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              ++      + NK+ R+PT  EIA+ L M ++   + L      ++    +G +D   
Sbjct: 97  NNRRITEAMALLENKLGRDPTDTEIAEHLEMTLDQYHQALN----DVNCGRLVGMDDLGV 152

Query: 588 LGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D +  + +     P    +  N R++    + +L  RE  VL + +   +N    L+E
Sbjct: 153 SEDAVTTEASREENLPFQGVVDDNFRQSLADAIKTLPEREALVLSLYYDEELN----LKE 208

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    V+  RI QI ++A+++L+
Sbjct: 209 IGAVVGVSESRICQIHSQAMQRLR 232


>gi|331698492|ref|YP_004334731.1| RNA polymerase sigma 28 subunit FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953181|gb|AEA26878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
          Length = 429

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 100/203 (49%), Gaps = 22/203 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G  GL+ A  +FD   G +F TYA   ++ A+   +  Q     +P  +R +I +
Sbjct: 234 DLVQAGVFGLLDAIARFDPTRGIRFETYAAQRIRGAMLDELRAQDW---VPRTVRSRIRE 290

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVE-----GVRKVLKITKEPISLETPIGDEDTS 586
           + RT  ++  ++ R P   EIA +L +P+      G R+ L      +S+E     E  S
Sbjct: 291 IERTREQLERRLGRAPDRREIAAELGLPLRELVRAGQRRRL------VSVEA--LAESAS 342

Query: 587 HLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + + + D++A  P +  A+Q   RE    V   L  R+  V+++ +      + TL E+
Sbjct: 343 SVAESVVDESAPDPAEVFALQETHRELAAAVRL-LDERDRLVVQLYY----VENRTLAEI 397

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+   VT  R+ Q+ A+ + +L+
Sbjct: 398 GRLLGVTESRVCQLHARMVVRLR 420


>gi|159029418|emb|CAO90794.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 258

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 102/219 (46%), Gaps = 8/219 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++  NL LV   A  + N+  + + DL+Q G +GL++A ++FD   G+ FS++A+ +
Sbjct: 29  RDQIIRLNLGLVRREAHHWVNQCHENYEDLVQVGCMGLIRAIKRFDSSKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    D   +     R       R+P   EI+  L + +E  
Sbjct: 89  IRGEIQHYLRDKGYTVRIPRRWLDLGRQAANMRRDFQTIHNRQPNDTEISLALNISLEEW 148

Query: 564 R--KVLKITKEPISLETPI-GDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  K+    +EP+SL+  +  DED  + L D + D    S     +    R    + LA 
Sbjct: 149 QEVKLAFQNREPLSLDATVNNDEDNNTCLKDIVPDPGYRS---FQLCQEDRIRLQQALAQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           L  +   +L   F   +    T E++G        R+++
Sbjct: 206 LEEKTRYILEFVFLKDLTQRETAEQLGISIVTVSRRVKK 244


>gi|148273835|ref|YP_001223396.1| putative RNA polymerase sigma factor SigF [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
 gi|147831765|emb|CAN02734.1| putative RNA polymerase sigma factor, SigF-homolog (stress
           response/stationary phase sigma factor) [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
          Length = 335

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 108/224 (48%), Gaps = 11/224 (4%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V  +L L   +A++++ R   + DL Q G +GL+KAA ++D   G  F ++A+  +  
Sbjct: 88  QIVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAIPTISG 147

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    +R P H+++  H ++     ++ ++ R PT  E+A       E V + 
Sbjct: 148 EIKRHLRDNGWVVRPPRHVQELRHALLAVVPALTQRLGRTPTDAELAAHTGHAREEVVEA 207

Query: 567 LKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           L    +  P SL+  + +++   L D I    A  P  +  +  +     R    L+ R+
Sbjct: 208 LAAHSSLRPASLDFTVHEDEGISLADTI---GADDPGYARAERTVLLDAAR--GVLSDRD 262

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+L +RF      + +  E+  +  VT+ ++ ++ A+ +  L+
Sbjct: 263 RRILHLRF----VDECSQSEIAAELGVTQMQVSRLLARILGALR 302


>gi|172038499|ref|YP_001805000.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171699953|gb|ACB52934.1| group 3 sigma-70 RNA polymerase sigma factor J [Cyanothece sp. ATCC
           51142]
          Length = 282

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 70/118 (59%), Gaps = 1/118 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE NL LV  VA + + +  + + DL Q G +GL++A E+FD   G  FS++A+ +
Sbjct: 53  RNQLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFDPQQGCAFSSFAIPY 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  +   + D+   +RIP   ++  +K  +  ++++  +KR P+  EIA  L +P+E
Sbjct: 113 IRGEMLHYLRDKGSVMRIPRRWQELYNKAKKIRKQLTVSLKRPPSDWEIADALGVPLE 170


>gi|307717642|gb|ADN88874.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|213421295|ref|ZP_03354361.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 191

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/106 (33%), Positives = 62/106 (58%), Gaps = 8/106 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI 113


>gi|89895149|ref|YP_518636.1| sporulation sigma factor SigK [Desulfitobacterium hafniense Y51]
 gi|89334597|dbj|BAE84192.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 98/234 (41%), Gaps = 60/234 (25%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  A+ ++VE NLRLV  + KK+   G    DLI  G IGL+K  + FD   G K +T
Sbjct: 59  TKAEYARNKLVEHNLRLVAHLVKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLAT 118

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I              +H+R                                
Sbjct: 119 YAARCIENEIL-------------MHLRS------------------------------- 134

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVL 617
                   LK ++  +S+  PIG +     G+ I   + ++    AI   +  E   RVL
Sbjct: 135 --------LKKSRGEVSIYDPIGVDKE---GNEISLMDVLASEGEAISDRIENEFEQRVL 183

Query: 618 ----ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                +LT RE  VL++R+G+  +   T  E+ K   ++R  + +IE KAI+KL
Sbjct: 184 LDKVKNLTRRERLVLQLRYGLMNSPRRTQREIAKALGISRSYVSRIEKKAIQKL 237


>gi|224826337|ref|ZP_03699439.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601438|gb|EEG07619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 248

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 109/249 (43%), Gaps = 39/249 (15%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           VE +  LV  +AK    +    ++  DL Q G IGL++AA +FD   G +F T+A   ++
Sbjct: 22  VELHAPLVKKIAKLLIAKLPASVELDDLAQVGIIGLIEAARQFDPTQGVQFETFASQRIR 81

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   +  +     +P   R    ++     ++  +  R P   EIA  L +P+   + 
Sbjct: 82  GAMLDELRREDW---LPRQARRHSKQIEDAIHQLEQREGRPPQESEIADFLGLPLAEYQT 138

Query: 566 VLKITKEPISLETPIGDEDTSHLGDF--------------IEDKNAVSPLDSAIQANLRE 611
           +L   K  +SL+         H  DF              + D NAV P  S    + R 
Sbjct: 139 MLGECKG-VSLQ---------HFSDFDDEDGVGAEAAVANVADDNAVDPFASLADGDFRG 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                + +L  R++ V+ + +   +N    L+E+G    V+  R+ Q+ ++AI +++   
Sbjct: 189 ALVDAIKALPERDQLVMALYYEQELN----LKEIGAVLGVSESRVSQLHSQAIARVR--- 241

Query: 672 RSKKLRSFL 680
              KLR +L
Sbjct: 242 --SKLREWL 248


>gi|188011759|gb|ACD45176.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011761|gb|ACD45177.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011765|gb|ACD45179.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011767|gb|ACD45180.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011769|gb|ACD45181.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011771|gb|ACD45182.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011773|gb|ACD45183.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011775|gb|ACD45184.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011777|gb|ACD45185.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011779|gb|ACD45186.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011781|gb|ACD45187.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011783|gb|ACD45188.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011785|gb|ACD45189.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011787|gb|ACD45190.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011789|gb|ACD45191.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011791|gb|ACD45192.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011793|gb|ACD45193.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011795|gb|ACD45194.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011797|gb|ACD45195.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011799|gb|ACD45196.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011801|gb|ACD45197.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011803|gb|ACD45198.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011805|gb|ACD45199.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011807|gb|ACD45200.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011809|gb|ACD45201.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011811|gb|ACD45202.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011813|gb|ACD45203.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011815|gb|ACD45204.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011817|gb|ACD45205.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011819|gb|ACD45206.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011821|gb|ACD45207.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011823|gb|ACD45208.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011825|gb|ACD45209.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011827|gb|ACD45210.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011829|gb|ACD45211.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011831|gb|ACD45212.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011833|gb|ACD45213.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011835|gb|ACD45214.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011837|gb|ACD45215.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011839|gb|ACD45216.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011841|gb|ACD45217.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011843|gb|ACD45218.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011845|gb|ACD45219.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011847|gb|ACD45220.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011849|gb|ACD45221.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011851|gb|ACD45222.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011853|gb|ACD45223.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011855|gb|ACD45224.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011857|gb|ACD45225.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011859|gb|ACD45226.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011861|gb|ACD45227.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011863|gb|ACD45228.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011867|gb|ACD45230.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011869|gb|ACD45231.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011875|gb|ACD45234.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011877|gb|ACD45235.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011879|gb|ACD45236.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011881|gb|ACD45237.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011883|gb|ACD45238.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011885|gb|ACD45239.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011887|gb|ACD45240.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011889|gb|ACD45241.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011891|gb|ACD45242.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011893|gb|ACD45243.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011895|gb|ACD45244.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011899|gb|ACD45246.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011903|gb|ACD45248.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011905|gb|ACD45249.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011907|gb|ACD45250.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011909|gb|ACD45251.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011911|gb|ACD45252.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011913|gb|ACD45253.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011917|gb|ACD45255.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011919|gb|ACD45256.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011921|gb|ACD45257.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011923|gb|ACD45258.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011925|gb|ACD45259.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011927|gb|ACD45260.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011929|gb|ACD45261.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011931|gb|ACD45262.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011933|gb|ACD45263.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011935|gb|ACD45264.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011937|gb|ACD45265.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011939|gb|ACD45266.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011941|gb|ACD45267.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011943|gb|ACD45268.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|281324217|gb|ADA60650.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324221|gb|ADA60652.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324239|gb|ADA60661.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324273|gb|ADA60678.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 18  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 77

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 78  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 137

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 138 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 193

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 194 LDEREQKILQYTF 206


>gi|162418642|ref|YP_001606497.1| flagellar biosynthesis sigma factor [Yersinia pestis Angola]
 gi|162351457|gb|ABX85405.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Angola]
          Length = 240

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/198 (23%), Positives = 94/198 (47%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G I L+ A E++D   G  F+TYA+  ++ A+   +  +      P  +R    +
Sbjct: 43  DLLQAGGIDLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---PRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++    T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 100 VASAMQQVEQRVGSPATEQEVAQVLDIGLVEYRQILLDTNNSQLFSYDEWREEHGESVEP 159

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+     + +L  RE+ VL + +   +N    L+E+G    
Sbjct: 160 LLEGHEDANPLKHLLEGNLRQRVIDAIEALPEREKMVLTLYYQEELN----LKEIGAVLE 215

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 216 VGESRVSQLHSQAIKRLR 233


>gi|229189193|ref|ZP_04316217.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
 gi|228594237|gb|EEK52032.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
          Length = 203

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/210 (23%), Positives = 100/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G IGL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMIGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      ++++++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IRLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|307717596|gb|ADN88851.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717598|gb|ADN88852.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717600|gb|ADN88853.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717602|gb|ADN88854.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|89098615|ref|ZP_01171497.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
 gi|89086577|gb|EAR65696.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
          Length = 253

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/196 (26%), Positives = 92/196 (46%), Gaps = 10/196 (5%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL  A EKFD     KF TYA + ++ +I   +  +     +P   R+K  K+   A
Sbjct: 59  GLMGLYDALEKFDPTRDLKFDTYASFRIRGSIIDGLRKEDW---LPRSTREKAKKIEAAA 115

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFI-E 593
            R+   + R+ T  EI K++ +  + V+ V+        +S++    D+D      +I +
Sbjct: 116 ERLEQHLMRKATAAEIGKEVDLHEDEVQTVMSEHFFANVLSMDEQPQDQDEKDGATYILK 175

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  AV P +   +  L       ++ L  +E+ V+ + +      + TL E+G+   ++ 
Sbjct: 176 DHRAVVPEEKVAKDELLSEMADAVSCLNEKEQLVISLFY----KEELTLTEIGQVMGLST 231

Query: 654 ERIRQIEAKAIRKLKH 669
            RI QI  KAI  L+H
Sbjct: 232 SRISQIHTKAIFSLRH 247


>gi|255280061|ref|ZP_05344616.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255269152|gb|EET62357.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 243

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 96/230 (41%), Gaps = 57/230 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV  VAKKY  +G    +LI  G IGL+KA   F+     K +TYA   
Sbjct: 62  AKKILIERNLRLVAHVAKKYQKQGEDGEELIAVGTIGLIKAVSTFNHARTNKLATYAARC 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  +                             R   KI RE                 
Sbjct: 122 VENELLMLF-------------------------RSRKKISRE----------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
                     +SL  PIG +   +   L D IE +N        +  N R T  R+L + 
Sbjct: 140 ----------VSLNEPIGTDKEGNEISLIDVIEGENIDVIERMELDRNTR-TLYRLLENV 188

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LT RE+ +L++R+G+   ++ T  E+  +  ++R  + +IE  A+ KL+ 
Sbjct: 189 LTEREKEILKLRYGLYGKSEMTQREIADKMGISRSYVSRIEKSAVAKLRQ 238


>gi|148976430|ref|ZP_01813136.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
 gi|145964253|gb|EDK29509.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
          Length = 244

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 92/200 (46%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMIGLIEAQQNYDGTKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKNNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      + + + R+P+  E+AK + + +E     L      I+    +G ED     D 
Sbjct: 103 ISSAIAELESTLNRDPSDAEVAKHMGLSLEQYHSALT----DINCSRLVGIEDLGVSDDV 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   ED    +P       + R+     +  L  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPNEDSQDNAPFQGVADESFRQALIDSIKQLPEREGLVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 LGVSESRVSQILSQSMQRLR 234


>gi|119775415|ref|YP_928155.1| flagellar biosynthesis sigma factor [Shewanella amazonensis SB2B]
 gi|119767915|gb|ABM00486.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella amazonensis
           SB2B]
          Length = 239

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 106/232 (45%), Gaps = 20/232 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +K  +VE    LV  +A     R    +Q  DL+Q G IGL++A+ KFD   G KF T+A
Sbjct: 12  SKTSIVEQYAPLVKRIAHHMLARLPASVQLDDLLQAGMIGLLEASAKFDGGKGAKFETFA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH   +  +V +    +  ++ R+    EIA++L M +
Sbjct: 72  GIRIRGAMLDEIRKGDWVPR-SVHRNQR--RVAQVIDELEQELGRDARDTEIAERLDMSM 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI----EDKNAVSPLDSAIQANLRETTTRV 616
           E    +L      +S+   IG ED     D +    E  N +   D   Q+  ++     
Sbjct: 129 EEYHHILN----DVSVGKIIGIEDLGVSHDVLVPDGEQTNDI--YDDLAQSQFQQALADA 182

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 183 IRQLPERDALVLSLYYDEALN----LKEIGAILDVSESRVCQIHSQAMLRLK 230


>gi|330721193|gb|EGG99303.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC2047]
          Length = 246

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 107/233 (45%), Gaps = 29/233 (12%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A     R    +Q  DL+Q G +GL++AA+KFD   G  F T+A   V
Sbjct: 22  LVEQHAPLVKRIAHHLMARLPSTVQLNDLVQSGMVGLLEAAQKFDASKGASFETFAGIRV 81

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-------REPTPEEIAKKLA 557
           + A+   +       R           V R ARR+S  IK       R+ + +E+A ++ 
Sbjct: 82  RGAMLDDVRKDDWAPR----------SVHRNARRVSEAIKAVEGRTGRDASDQEVAAEMG 131

Query: 558 MPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +P+E     L+ +      S +     +D+S L   +      +P ++  +   ++   +
Sbjct: 132 IPLEDYYAYLQDSAGTRLFSYDEVTEQDDSSIL---LAASATPTPHENVQRQAFKDNLAQ 188

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE  VL + +   +N    L+E+G    V+  R+ QI ++A  +L+
Sbjct: 189 AIEALPERERMVLALYYQEELN----LKEIGSVLGVSESRVSQIHSQAALRLR 237


>gi|188011897|gb|ACD45245.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011901|gb|ACD45247.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717586|gb|ADN88846.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717610|gb|ADN88858.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717630|gb|ADN88868.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717636|gb|ADN88871.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
 gi|307717638|gb|ADN88872.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
 gi|307717646|gb|ADN88876.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|256751991|ref|ZP_05492860.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749101|gb|EEU62136.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 236

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 106/235 (45%), Gaps = 53/235 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + KG+ EA   K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEEMYLISKMEKGDNEA---KTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA        +R I ++                ++   RR S 
Sbjct: 98  IKAINTFNPKKKIKLATYA--------SRCIENE----------------ILMYLRRNS- 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + EE    L +  +G   +L          + I   D   +  +IED+      
Sbjct: 133 KTKLEVSFEE---PLNVDWDGNELLL----------SDILGTDNETVYKYIEDEVE---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                   +E  T  L  L  RE++++ +RFG+G   + T +EV     +++  I
Sbjct: 176 --------KELLTSALKKLPDREKKIIGLRFGLGGGVEKTQKEVADMLGISQSYI 222


>gi|219669565|ref|YP_002460000.1| sporulation sigma factor SigK [Desulfitobacterium hafniense DCB-2]
 gi|219539825|gb|ACL21564.1| RNA polymerase, sigma 28 subunit, SigK [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 98/234 (41%), Gaps = 60/234 (25%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  A+ ++VE NLRLV  + KK+   G    DLI  G IGL+K  + FD   G K +T
Sbjct: 60  TKAEYARNKLVEHNLRLVAHLVKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLAT 119

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I              +H+R                                
Sbjct: 120 YAARCIENEIL-------------MHLRS------------------------------- 135

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVL 617
                   LK ++  +S+  PIG +     G+ I   + ++    AI   +  E   RVL
Sbjct: 136 --------LKKSRGEVSIYDPIGVDKE---GNEISLMDVLASEGEAISDRIENEFEQRVL 184

Query: 618 ----ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                +LT RE  VL++R+G+  +   T  E+ K   ++R  + +IE KAI+KL
Sbjct: 185 LDKVKNLTRRERLVLQLRYGLMNSPRRTQREIAKALGISRSYVSRIEKKAIQKL 238


>gi|307717634|gb|ADN88870.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVNYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|238924178|ref|YP_002937694.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|238875853|gb|ACR75560.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|291529048|emb|CBK94634.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           M104/1]
          Length = 230

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/267 (22%), Positives = 109/267 (40%), Gaps = 61/267 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIA------KKEMVEANLRLVISVAKKYT 464
           N I    + TG  ++ F   +S+ R+ EC   +A      K E++  N+RLV  V KKY 
Sbjct: 12  NIIYYKQIMTGCYVNTFLSPLSLERETECLKKVAQNDKEAKDELILHNMRLVAHVTKKYA 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
               +  +LI  G IGL+KA   F    G +F+T+A+  ++  I              +H
Sbjct: 72  VSEDEMEELISIGTIGLIKAVSSFKADYGNRFATFAIRCIENEIL-------------MH 118

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
            R +                                       K ++  +S+  PIG + 
Sbjct: 119 FRSR---------------------------------------KKSRGDVSIFEPIGTDK 139

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +  HL D IE+  +    D  +  +L+     + + L+ RE  ++  RFG+    + T
Sbjct: 140 EGNQIHLVDVIENGQSDVVSDIEVSESLKILRQNMRSVLSDREYYIITKRFGLDGEKELT 199

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ K   ++R  + +IE   ++KL+
Sbjct: 200 QRQIAKTLSISRSYVSRIEKAGLKKLR 226


>gi|145224453|ref|YP_001135131.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216939|gb|ABP46343.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 342

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 111/233 (47%), Gaps = 22/233 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++   L L   +A+++  RG    DL+Q   +GL+ A  +FD      F  +A+  +
Sbjct: 112 REAIIARCLPLADHIARRFRGRGEGHEDLVQVARVGLLNAVNRFDVDSANDFLAFAVPTM 171

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D   ++++P  +++   ++      ++ ++ R PTP E+AK L +  E V 
Sbjct: 172 MGEVRRYFRDHGWSLKVPRRLKELNVRLNAARADLTQELNRAPTPSELAKYLGIDREEVV 231

Query: 565 KVL--------KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR- 615
           + L        + T++P +     GD      G+ +  ++     D  IQ  +   T + 
Sbjct: 232 EGLVAANAYSTRSTEQPTTFS---GD------GEGLSLQDTFGAPDDNIQKVIDVNTVQP 282

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +LA+L  R+  VL++RF      D T  ++ +Q  V++  + ++ A+A+  L+
Sbjct: 283 LLAALPERDRLVLKLRF----FEDRTQSQIAEQIGVSQMHVSRLLARALATLR 331


>gi|326791235|ref|YP_004309056.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
 gi|326541999|gb|ADZ83858.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
          Length = 220

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/251 (26%), Positives = 105/251 (41%), Gaps = 62/251 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +H +   + G+ EA  AK  ++E NLRLV  + KKY N      DLI  G IGL
Sbjct: 20  LSAEEEKHYLECYQDGD-EA--AKNILIERNLRLVAHIVKKYNNINNDVDDLISIGTIGL 76

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K    FD     + +TYA   ++  I  SI                     R  R+   
Sbjct: 77  IKGISSFDPNKCTRLATYAARCIENEILMSI---------------------RAGRK--- 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLG--DFI--EDKN 596
             +R  T                          SL  PIG D++ + +   D +  E+  
Sbjct: 113 --QRYET--------------------------SLHAPIGMDQEGNEISLLDILCTENDT 144

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
               +D  I+        R+L  L PRE+ +L +R+G+    + T  E+ +Q  ++R  +
Sbjct: 145 IFDQVDLDIEVRKLYQHIRIL--LKPREKEILLLRYGLNNQEEKTQREIAEQMGISRSYV 202

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 203 SRIEKKALKKL 213


>gi|291524907|emb|CBK90494.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           DSM 17629]
          Length = 230

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/267 (22%), Positives = 109/267 (40%), Gaps = 61/267 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIA------KKEMVEANLRLVISVAKKYT 464
           N I    + TG  ++ F   +S+ R+ EC   +A      K E++  N+RLV  V KKY 
Sbjct: 12  NIIYYKQIMTGCYVNTFLSPLSLERETECLKKVAQNDKEAKDELILHNMRLVAHVTKKYA 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
               +  +LI  G IGL+KA   F    G +F+T+A+  ++               I +H
Sbjct: 72  VSEDEMEELISIGTIGLIKAVSSFKADYGNRFATFAIRCIEN-------------EILMH 118

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
            R +                                       K ++  +S+  PIG + 
Sbjct: 119 FRSR---------------------------------------KKSRGDVSIFDPIGTDK 139

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +  HL D IE+  +    D  +  +L+     + + L+ RE  ++  RFG+    + T
Sbjct: 140 EGNQIHLVDVIENGQSDVVSDIEVSESLKILRQNMRSVLSDREYYIITKRFGLDGEKELT 199

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ K   ++R  + +IE   ++KL+
Sbjct: 200 QRQIAKTLSISRSYVSRIEKAGLKKLR 226


>gi|302522454|ref|ZP_07274796.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
 gi|302431349|gb|EFL03165.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
          Length = 297

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/255 (25%), Positives = 125/255 (49%), Gaps = 25/255 (9%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F  +V ++ +G      A+  ++E N  LV   A+++ NRG   + D++Q G IGL+KA 
Sbjct: 48  FDQLV-VLEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAI 106

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D +  + +P  +++    + R   R++ ++ R
Sbjct: 107 DRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELRVDLARAKERLAVELDR 166

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSH---------LGDFIED 594
           +P  +E+A +L +  E V   L      +  SL+ P  D  TS            DF+ D
Sbjct: 167 DPGVKELAAELGISEEEVIDGLIAANGYMSDSLDLP-ADSSTSGKPDQKTATTYADFLGD 225

Query: 595 KNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                  D A++     T  R +L +L  RE  +L +RFG     + T  ++G +  V++
Sbjct: 226 ------WDPAMELVENFTALRPLLGTLDDRERYLLELRFG----QELTQAQIGAELGVSQ 275

Query: 654 ERIRQIEAKAIRKLK 668
             + ++ ++ + KL+
Sbjct: 276 MHVSRLLSRTLGKLR 290


>gi|34496477|ref|NP_900692.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
 gi|34102331|gb|AAQ58697.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
          Length = 248

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 113/244 (46%), Gaps = 14/244 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
           S  R G   A+ + +  VEA   LV  +A     R    ++  DL+Q G IGL++AA +F
Sbjct: 5   SFRRSGYAAAAPSVEIDVEAYAPLVRKLASIMIARLPASVELGDLVQVGMIGLIEAARQF 64

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G +F T+A   ++ A+   +  +     +P   R    ++     ++  ++ R P 
Sbjct: 65  DPAQGVQFETFASQRIRGAMLDELRREDW---LPRQARRNSRQIEEAISKLEQRLGRAPL 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISL---ETPIGDEDTSHLG-DFIEDKNAVSPLDSA 604
             EIA ++ + +E  + +L   K    L   +   GD++ SH     I D ++  PL + 
Sbjct: 122 ESEIAAEMGVELEQYQDMLGDCKGTTLLHFEDFGGGDDEGSHNPVTNIADDDSPDPLAAL 181

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + R      +  L  R++ V+ + +   +N    L+E+G    VT  R+ Q+ ++AI
Sbjct: 182 SDDSFRRQLVSAIKFLPERDQLVMALYYEQELN----LKEIGAVLGVTESRVCQLHSQAI 237

Query: 665 RKLK 668
            +L+
Sbjct: 238 ARLR 241


>gi|318066953|emb|CBY89091.1| RNA polymerase sigma70 factor [Halomonas koreensis]
          Length = 365

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 41/60 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDATQD 80


>gi|114566413|ref|YP_753567.1| RNA polymerase sigma factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337348|gb|ABI68196.1| putative RNA polymerase sigma factor [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 260

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 102/209 (48%), Gaps = 12/209 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G  GL+ A EKFD     KF TYA+  ++ ++   +        IPV +R K  +
Sbjct: 55  ELISYGIEGLIDAIEKFDHKRNIKFETYAITRIRGSMIDGLRSMDW---IPVSLRQKSKE 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-- 587
           + +    +  ++ R  +  E+A++L + ++    +L+       ISL+  +  ED     
Sbjct: 112 LEKAYMNVEARLGRSASDAEVAEELGLNLDEFAVLLRDVAATTIISLDDFLPGEDGEQKK 171

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D +ED N++S  +      +++   + ++ L  +E+ V+ + +  G+    TL+E+G
Sbjct: 172 RMLDLLEDHNSISASEIVEFNEVKDLLAKAISRLPDKEKLVVYLYYYEGL----TLKEIG 227

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
               ++  RI Q+  KAI +L+     KK
Sbjct: 228 ATISLSESRISQLHTKAILRLRGSLSKKK 256


>gi|188011915|gb|ACD45254.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 221

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 17  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 77  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 136

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 137 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 192

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 193 LDEREQKILQYTF 205


>gi|86157781|ref|YP_464566.1| sigma 28 (flagella/sporulation) [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774292|gb|ABC81129.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 232

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/206 (25%), Positives = 95/206 (46%), Gaps = 21/206 (10%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T   ++  DL   G +GL++AA ++D     +F T+A   V+ A+   +        +P 
Sbjct: 41  TGHAVEPGDLWSAGAMGLLEAARRYDASQDVRFETFAEHRVRGAMLDELRRMD---HLPR 97

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            +R    +V+    R+   + REP P EIA+   +P E V ++L +   P+ +E      
Sbjct: 98  RLRADADRVLAARARLEQALGREPDPVEIAEAAGLPAEQVGELLLLASPPVPVE------ 151

Query: 584 DTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                 D +    AV P D A+  A  R    R +A+L  R + +L + +   +    T 
Sbjct: 152 ------DDVAPAPAV-PADEALGAAERRGALARAVAALPERLQVLLALYYDEAL----TY 200

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+ K   V+  R+ Q+ ++A ++L+
Sbjct: 201 REIAKVLGVSEPRVCQLHSEAAKRLR 226


>gi|78485092|ref|YP_391017.1| sigma 28 (flagella/sporulation) [Thiomicrospira crunogena XCL-2]
 gi|78363378|gb|ABB41343.1| sigma 28 (Flagella/Sporulation) [Thiomicrospira crunogena XCL-2]
          Length = 241

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 111/228 (48%), Gaps = 22/228 (9%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EA L LV  +A     R    +   DLIQ G IGL+++++KFD   G  F TYA   ++
Sbjct: 21  IEAFLPLVKRIAYHLKGRLPDSVMVDDLIQSGIIGLIESSQKFDATQGASFETYAGIRIR 80

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   I     T   P  +  K  +V     ++ ++  RE   EEIA+ + + ++    
Sbjct: 81  GAMLDEIRKGDWT---PRSVYRKSREVSEAILKVESEKGREARDEEIAEVMGVSLDEYYH 137

Query: 566 VLKITK--EPISLETPIGDEDTSHLGDFIEDK---NAVSPLDSAIQANLRETTTRVLASL 620
           +L+ T   + +S++ P  DE         ED+      +P+   ++++ +      +  L
Sbjct: 138 ILQDTNSAQLLSIDEPDHDE-------LAEDRMVGTIKTPITELVESDFQGALAEQINEL 190

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E+ V+ + +   +N    L+E+G+   V+  R+ QI ++AI++LK
Sbjct: 191 PEKEKLVMALYYDEELN----LKEIGEVLEVSESRVSQIHSQAIKRLK 234


>gi|304317194|ref|YP_003852339.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778696|gb|ADL69255.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 241

 Score = 63.5 bits (153), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 105/243 (43%), Gaps = 60/243 (24%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ K E   + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+ 
Sbjct: 47  IFLIAKMESGDNAAKSMLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGLIKAINTFNP 106

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               K +TYA        +R I ++                ++   RR S          
Sbjct: 107 HKKIKLATYA--------SRCIENE----------------ILMYLRRNSK--------- 133

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAV--SPLDSAI 605
                              T+  +S + P+    D +   L D +   N +    ++  +
Sbjct: 134 -------------------TRMEVSFDEPLNIDWDGNELLLSDILGTDNEIVYKMIEDEV 174

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L +T    L  L+ RE+R++ +RFG+G   + T +EV     +++  I ++E + ++
Sbjct: 175 DKQLLKTA---LKKLSEREKRIIGLRFGLGGGAEMTQKEVADMLGISQSYISRLEKRILK 231

Query: 666 KLK 668
           +LK
Sbjct: 232 RLK 234


>gi|148359326|ref|YP_001250533.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|296107373|ref|YP_003619073.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148281099|gb|ABQ55187.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|295649274|gb|ADG25121.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 238

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 113/245 (46%), Gaps = 45/245 (18%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F TYA
Sbjct: 14  TQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYA 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMS-------NKIKRE 546
                             IRI  HM D++ +       V R +R +S       +K+ RE
Sbjct: 74  -----------------GIRIRGHMLDEVRRNDWVPRSVYRNSRMISDAVRILEHKLGRE 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDS 603
               EIA++L + +     +L   ++ IS     G +D     D +   E   +  P  +
Sbjct: 117 AKDNEIAEELGVSLNDYHDML---QDSISSHL-YGFDDLGVTDDILFDDEGNGSTEPHRN 172

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +++++    T+V+ SL PR+ER++     +    D  L+E+G+   V+  RI QI ++A
Sbjct: 173 VMRSDMMNRLTQVIDSL-PRKERLV---LSLYYEQDLNLKEIGEILEVSESRISQILSQA 228

Query: 664 IRKLK 668
             +++
Sbjct: 229 THRIR 233


>gi|307717594|gb|ADN88850.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717604|gb|ADN88855.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717614|gb|ADN88860.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717620|gb|ADN88863.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717622|gb|ADN88864.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|170780849|ref|YP_001709181.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155417|emb|CAQ00524.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 337

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 108/224 (48%), Gaps = 11/224 (4%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V  +L L   +A++++ R   + DL Q G +GL+KAA ++D   G  F ++A+  +  
Sbjct: 90  QIVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAIPTISG 149

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    +R P  +++  H ++     ++ ++ R PT  E+A     P E V + 
Sbjct: 150 EIKRHLRDNGWMVRPPRQIQELRHALLAVVPALTQRLGRTPTDAELAAHTGHPREEVMEA 209

Query: 567 LKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           L    +  P SL+  + + +   L D +    A  P  +  +  +     R +  L+ R+
Sbjct: 210 LAAHSSLRPASLDHTVHEHEGISLADTL---GADDPGYARAERTVLLDAARGV--LSERD 264

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+L +RF      + +  E+  +  VT+ ++ ++ A+ +  L+
Sbjct: 265 RRILHLRF----VDECSQSEIAAELGVTQMQVSRLLARILGALR 304


>gi|307717644|gb|ADN88875.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 90/190 (47%), Gaps = 2/190 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTP 622
            + +++ K   +L      E  S  G  I   + V   D   +  N R    +VL  L  
Sbjct: 136 LEAMEMGKSYQALSVDHSMEADSD-GSTITLLDVVGGTDDGFERVNQRMLLEKVLPVLDE 194

Query: 623 REERVLRMRF 632
           RE+++L+  F
Sbjct: 195 REQKILQYTF 204


>gi|332755592|gb|EGJ85955.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2747-71]
          Length = 133

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/44 (56%), Positives = 38/44 (86%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EK
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEK 133


>gi|323486720|ref|ZP_08092041.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692141|ref|ZP_08106384.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323400101|gb|EGA92478.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503715|gb|EGB19534.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 246

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 110/228 (48%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +++E NLRLV+ +AKK+ N  +   DLI  G+IGL+KA   F+     K +TYA   
Sbjct: 63  AKSKLIEHNLRLVVYIAKKFDNTSVGVEDLISIGSIGLIKAINTFNIDKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NK K E + +E    L +  +G 
Sbjct: 120 -----SRCIENE----------------ILMYLRR-NNKTKMEVSIDE---PLNVDWDG- 153

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DED  +    +ED+   S L++AI            + L P
Sbjct: 154 --------NELLLSDILGTDEDVIYRD--LEDEIEKSLLNTAI------------SRLNP 191

Query: 623 REERVLRMRFGIGM-NTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+G  N D  T +EV     +++  I ++E K +++LK
Sbjct: 192 REQKIVELRFGLGTENEDEMTQKEVADLLGISQSYISRLEKKIMKRLK 239


>gi|324997618|ref|ZP_08118730.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 277

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/217 (27%), Positives = 98/217 (45%), Gaps = 9/217 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  ++++      +V  +A +Y +RG    DL Q G IGL+ A ++FD   G  F  Y
Sbjct: 38  ERAALREQLARGFHPVVRHIAGRYRHRGEPADDLEQVGAIGLLNALDRFDPEQGTPFLAY 97

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  +   I R   D++ ++R+P  ++D   ++ R    ++ +  R P   E+A+ L   
Sbjct: 98  AVPTITGEIRRHFRDRTWSMRVPRRLKDFQTRMTRAQEELAVRHGRAPKVSELAEHLGTS 157

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            E V + L+   +    SL+   GD + S LG+ +   +A            RE     L
Sbjct: 158 REEVIEGLQAQDSYRSDSLDRLAGDTE-SPLGEIVGGADA-----GIGTVEDREALRPAL 211

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             L  RE  +L +RF          EEVG  Q  V+R
Sbjct: 212 RRLPERERTILLLRFFGNRTQTQIAEEVGLSQMHVSR 248


>gi|288555607|ref|YP_003427542.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
 gi|288546767|gb|ADC50650.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
          Length = 235

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/253 (25%), Positives = 105/253 (41%), Gaps = 75/253 (29%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++++G+ EA   +  ++E NLRLV  + KK+ N      DLI  G IGL+KA E 
Sbjct: 37  RKYLKLMQEGDAEA---RNLLIEHNLRLVAHIVKKFENTREDTEDLISIGTIGLIKAIES 93

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +    G K +TYA         R I ++     I +H+R                     
Sbjct: 94  YSDGKGTKLATYA--------ARCIENE-----ILMHLR--------------------- 119

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----- 602
                              LK  K+ +SL  PIG +         ++ N +S +D     
Sbjct: 120 ------------------ALKKVKKDVSLHDPIGTD---------KEGNEISLIDVLQED 152

Query: 603 -----SAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  IQ  + ++     +  L  RE+ V+  RFG+ M  + T  E+ K+  ++R  +
Sbjct: 153 ADDIVDVIQTKMEKKQIYEYIHVLDEREKEVIVGRFGLDMEDELTQREIAKKLGISRSYV 212

Query: 657 RQIEAKAIRKLKH 669
            +IE +A+ KL H
Sbjct: 213 SRIEKRALMKLFH 225


>gi|328948392|ref|YP_004365729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
 gi|328448716|gb|AEB14432.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
          Length = 262

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 100/206 (48%), Gaps = 12/206 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++F DL+  G  GL+ A  KFD   G KF TYA   ++ AI   + +      +P  +R 
Sbjct: 53  VEFDDLVGFGQFGLLDAINKFDIDKGVKFKTYATTRIRGAIFDELRELDW---VPRSVRQ 109

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-VEGVRKVLKITKEPISLETPI---GDE 583
           K  ++  T   + +K+ R  +  EIAK + M   E    V+K++   +     +   GDE
Sbjct: 110 KSREIEDTIVELESKLGRTASDAEIAKAMNMTEAEYQSAVMKVSGTSVLSLNDVWYSGDE 169

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            +   +GD IE  N+++P     +  +R    + +  L   E+ V+ + +    + D + 
Sbjct: 170 SEHVSIGDSIEAPNSLNPDVIVEREEIRRVIIQAINELPKNEKMVIVLYY----HEDLSF 225

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+G+   V+  RI Q+ +KA  +L+
Sbjct: 226 KEIGQVLNVSESRISQLHSKANLRLR 251


>gi|70725968|ref|YP_252882.1| RNA polymerase sigma factor SigB [Staphylococcus haemolyticus
           JCSC1435]
 gi|68446692|dbj|BAE04276.1| sigma factor B [Staphylococcus haemolyticus JCSC1435]
          Length = 256

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 120/234 (51%), Gaps = 14/234 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V    +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDRLVNHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSIAEIADRLEVSEEEV 150

Query: 564 RKVLKI--TKEPISLETPI-GDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + +++  +   +S++  I  D+D  T  L D +  K+     D+      R    R+L 
Sbjct: 151 LEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQKD-----DNYDLTEKRMILERILP 205

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+  ++
Sbjct: 206 ILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQQAAK 255


>gi|226326542|ref|ZP_03802060.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
 gi|225205141|gb|EEG87495.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
          Length = 244

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 97/209 (46%), Gaps = 30/209 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ ++   +  +      P  +R    +
Sbjct: 47  DLLQAGGIGLLNAVERYDSMQGAAFTTYAVQRIRGSMLDELRSRDWA---PRSVRRNARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP----------ISLET--P 579
           V  +  ++   + R P  +E+A  L + +   R++L  T             I  E+  P
Sbjct: 104 VTHSIHQLEQDLGRPPLEQEVADHLQIELAEYRQILLDTNNSQLFSYDEWHEIYGESCEP 163

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             DED         D N   PL   +++++R+     +  L  RE+ VL + +   +N  
Sbjct: 164 SQDED--------HDDN---PLQMLLESDIRQRVIDAIELLPEREKMVLTLYYQEELN-- 210

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 211 --LKEIGAVLNVGESRVSQLHSQAIKRLR 237


>gi|149201624|ref|ZP_01878598.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
 gi|149144672|gb|EDM32701.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
          Length = 242

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 102/226 (45%), Gaps = 18/226 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE ++ LV  +A  +  R  +F+   DL+Q G +GL+ A++++  C G  F+ YA   +
Sbjct: 17  LVEQHMPLVQRLAWHFHGRVGRFIEIDDLLQAGYLGLIDASQRYSVCDGVSFAAYATIRI 76

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + +I   +   S   R  + MR KI     T R++S K+ REP   E+A+ L +  E  +
Sbjct: 77  RGSIIDHLRRNSNLCRNSITMRQKIEA---TRRKLSQKLGREPEVPELAQSLELSTEEFQ 133

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                  T +  SL+    D         +   +  +P D      L+      L  L  
Sbjct: 134 DWENRFQTNQLQSLDEVYTDH------SLLFSDHGSTPEDEVEHIQLKALLQSALQDLPE 187

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R   VL++ +   +N    + E+     VT  R+ QI+  AI +L+
Sbjct: 188 RSALVLQLYYVEELN----VYEIAAILDVTTGRVSQIKKAAIGQLR 229


>gi|167756988|ref|ZP_02429115.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
 gi|167703163|gb|EDS17742.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
          Length = 228

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 108/258 (41%), Gaps = 59/258 (22%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IKS S E  ++  E    +     G+ EA   +  ++E NLRLV  +AKKY N      D
Sbjct: 18  IKSKSFELPLTAKEEERYLEQFFNGDKEA---RNVLIERNLRLVAHIAKKYENNKDMQED 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA + +      K +TYA        +R I ++     I +H+R      
Sbjct: 75  LISIGTIGLIKAVDSYKQNHKTKLATYA--------SRCIENE-----ILMHLRTN---- 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSH--LG 589
                                              K T   ISL   IG D+D S   LG
Sbjct: 118 -----------------------------------KKTNLDISLNETIGIDKDGSEIVLG 142

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I  K     +D   + +  +  T   + L PRE+  L MR+G+     +T +++ K+ 
Sbjct: 143 DIIAAKQE-EFIDIVDKKDTLDKFTTYFSVLEPREKDTLIMRYGLNNTKKYTQKDIAKKL 201

Query: 650 CVTRERIRQIEAKAIRKL 667
            ++R  + ++E +A+ KL
Sbjct: 202 NISRSYVSRLEKRALIKL 219


>gi|331090616|ref|ZP_08339467.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401056|gb|EGG80651.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 246

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 109/230 (47%), Gaps = 56/230 (24%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA  
Sbjct: 62  VAKKTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPMKNIKLATYA-- 119

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                 +R I ++     I +++R             +NK + E + +            
Sbjct: 120 ------SRCIENE-----ILMYLRR------------NNKTRLEVSID------------ 144

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASL 620
                    EP++++    D +   L D +  E+      L++ ++   R+   + +  L
Sbjct: 145 ---------EPLNVD---WDGNELLLSDILGTEEDTIYRDLETEVE---RKLLMKAINRL 189

Query: 621 TPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + RE+ +++MRFGIG     + T +EV     +++  I ++E K +++LK
Sbjct: 190 SSREKTIVQMRFGIGTKDGEEKTQKEVADILGISQSYISRLEKKIMQRLK 239


>gi|310659013|ref|YP_003936734.1| RNA polymerase sigma-28 factor (sigma-d) [Clostridium sticklandii
           DSM 519]
 gi|308825791|emb|CBH21829.1| RNA polymerase sigma-28 factor (sigma-D) [Clostridium sticklandii]
          Length = 247

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 108/222 (48%), Gaps = 17/222 (7%)

Query: 453 LRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           + LV  +A K   Y    +++ DL+  G IGL+ A +K+D     KF TYA   ++ +I 
Sbjct: 32  INLVKIIAGKLYNYYASNIEYDDLMSYGVIGLIDAIDKYDPTKNIKFETYASIRIRGSII 91

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
             I +      IP  +R K  K+++ A   + +K  RE + +EIAK L    + V  +++
Sbjct: 92  DQIRNLDW---IPRSIRQK-SKILKDANEALESKYGREASYQEIAKYLGKSEQEVLTLIE 147

Query: 569 ITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            T     +S+E    +     L D   +    SP D  +  +  +   R ++ L  RE+ 
Sbjct: 148 ETSVYNVLSIEDDFNESFKIQLKD---ESLESSPEDLTVYNDTVKELERTISELNEREQL 204

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ + +  G+    T +E+G+   ++  R+ QI +KAI K++
Sbjct: 205 IINLYYYEGL----TYKEIGEILNISESRVSQIHSKAISKMR 242


>gi|295102468|emb|CBL00013.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 224

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 97/199 (48%), Gaps = 13/199 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +   +E NL LV S A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA+  +
Sbjct: 8   RSAFIEQNLGLVHSCAGRFRGRGIEYDDLYSAGCMGLVKAYDGFDESRGVCFSTYAVPVI 67

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D   T+++   +++   ++       S     EPT  ++A++L   VE + 
Sbjct: 68  LGEIKKLFRDGG-TVKVSRSLKELSLRINAAREHHSKLCGAEPTLSQLAEELGESVENIT 126

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASLTPR 623
             ++  +  +SL TP   E+    GD   D    SP +  A +  L E    VL SL P 
Sbjct: 127 LAIQAAQPAVSL-TPENREE----GDRQMDIPVESPEEELADKIGLAE----VLKSL-PE 176

Query: 624 EER-VLRMRFGIGMNTDHT 641
           E+R ++++RF  G     T
Sbjct: 177 EDRLIIQLRFYGGKTQSDT 195


>gi|224992798|gb|ACN76114.1| SigB [Listeria innocua]
          Length = 214

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 93/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 12  AQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D+  ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 72  IVGEIKRFLRDKKWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 131

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 132 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 187

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 188 LDEREQKILQYTF 200


>gi|54297695|ref|YP_124064.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Paris]
 gi|53751480|emb|CAH12898.1| sigma factor 28 [Legionella pneumophila str. Paris]
          Length = 238

 Score = 63.2 bits (152), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 112/254 (44%), Gaps = 63/254 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F TYA
Sbjct: 14  TQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYA 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------RE 546
                             IRI  HM D++ +       V R +R +S+ ++       RE
Sbjct: 74  -----------------GIRIRGHMLDEVRRNDWVPRSVYRNSRMISDAVRILEHKFGRE 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF------------IED 594
               EIA++L + ++    +L+             D  +SHL  F             E 
Sbjct: 117 AKDNEIAEELGVSLDDYHDMLQ-------------DSISSHLYGFDDLGVTDDVLFDHEG 163

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             +  P  + +++++    T+V+ SL PR+ER++     +    D  L+E+G+   V+  
Sbjct: 164 NGSTEPHRNVMRSDMMNRLTQVIDSL-PRKERLV---LSLYYEQDLNLKEIGEILEVSES 219

Query: 655 RIRQIEAKAIRKLK 668
           RI QI ++A  +++
Sbjct: 220 RISQILSQATHRIR 233


>gi|307265198|ref|ZP_07546757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306919820|gb|EFN50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 230

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 94/224 (41%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   
Sbjct: 50  ARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARC 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  SI                         R   K+K E   ++       P+ GV
Sbjct: 110 IENEILMSI-------------------------RAEKKMKGEVFLQD-------PI-GV 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E+   + + +E K  +  L S + + L+            R
Sbjct: 137 DK----EGNEISLMDVLGTEE-DEISEQVEKKLQIKKLYSKMNSVLKN-----------R 180

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  ++ MR+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 181 ERLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRIEKKALNKL 224


>gi|159469913|ref|XP_001693104.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158277362|gb|EDP03130.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 525

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/136 (25%), Positives = 64/136 (47%), Gaps = 15/136 (11%)

Query: 444 AKKEMVEANLRLVISVAK---------------KYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           A+  + + N RLV++ AK                  +  L F D +  G  GLM+   KF
Sbjct: 116 ARAILAQKNYRLVVACAKWACKNGVGGGGAGSGHDGSYELAFEDALTAGMEGLMRGIHKF 175

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
               GY+ STY  WW++ +I ++++ QS  +++P+ +   +  +V    R++      PT
Sbjct: 176 RPDSGYRLSTYCTWWIRMSIRKTLSRQSTALQLPLSVLQSVEALVSARLRLTKPGASPPT 235

Query: 549 PEEIAKKLAMPVEGVR 564
            E +A +L   +  +R
Sbjct: 236 DEAVAAELGWSMTRIR 251


>gi|326390169|ref|ZP_08211730.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993817|gb|EGD52248.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 231

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 94/224 (41%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   
Sbjct: 51  ARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  SI                     R  ++M  +I            L  P+ GV
Sbjct: 111 IENEILMSI---------------------RAEKKMKGEI-----------FLQDPI-GV 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E+   + + +E K  +  L S + + L+            R
Sbjct: 138 DK----EGNEISLMDVLGTEE-DEISEQVEKKLQIKKLYSKMNSVLKN-----------R 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  ++ MR+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 182 ERLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|307717640|gb|ADN88873.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+++L+  F
Sbjct: 192 LDEREQKILQYTF 204


>gi|194016072|ref|ZP_03054687.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
 gi|194012427|gb|EDW21994.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
          Length = 262

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 114/227 (50%), Gaps = 8/227 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +VE    LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQLTLVECYTNLVDMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPLVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++      ++ + ++ P  +EIA+ L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDHLTTETQKSPQVQEIAEYLDVTEEE 148

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLT 621
           V + +++ K   +L    G E  S  G  +   + V   +   +  N +     VL  LT
Sbjct: 149 VLETMEMGKSYQALSVDQGVEADSE-GSTVTILDVVGSQEEGYERVNQKMMLESVLHVLT 207

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ ++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 208 DREKEIINLTY----LQNKSQKETGDLLGISQMHVSRLQRKAVKKLR 250


>gi|126215794|gb|ABN81017.1| putative sigma factor sigma 70 type group 3 [Rhodococcus opacus]
          Length = 139

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/114 (28%), Positives = 61/114 (53%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EAS+ + E++   L L   +A+++  RG    DL Q   +GL+KA ++FD   G+ F +Y
Sbjct: 25  EASVLRDEVITRCLPLADHIARRFGGRGEAHEDLRQVARLGLVKAVDRFDPDRGFDFVSY 84

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           A+  +   + R   D   ++R+P  M++    + +    +S ++ R P+  EIA
Sbjct: 85  AVPTIMGEVRRYFRDTGWSMRVPRRMQELHALITKAVDDLSQELGRSPSASEIA 138


>gi|303240258|ref|ZP_07326777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302592168|gb|EFL61897.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/211 (28%), Positives = 96/211 (45%), Gaps = 16/211 (7%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y    +++ DLI  G  GL+ A  KFD   G KF TYA   ++ AI  SI +      +P
Sbjct: 45  YFGSNVEYDDLIGYGVFGLIDAINKFDINKGVKFETYASLRIRGAIIDSIRELDW---VP 101

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI 580
             +R K  ++ R    + N++    T +E+A+KL + V+   K+L        ISLE  +
Sbjct: 102 RSLRQKNKELERVYTEVENELGHSATDQEVAQKLGVSVDEFYKLLNEVNLSSLISLEEFL 161

Query: 581 ---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
               +   +  G   ED+    P        LRE     +  L  +E+ V+   +     
Sbjct: 162 EQNYEAGVNIAGGCKEDR----PEGYMEITELREILVDAIGKLPEKEKTVVSFYY----F 213

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            D TL+E+ +   V+  RI Q+  KAI +L+
Sbjct: 214 EDLTLKEISEIMKVSESRISQLHTKAILRLR 244


>gi|260222460|emb|CBA32046.1| RNA polymerase sigma factor for flagellar operon [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 273

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 101/207 (48%), Gaps = 14/207 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL  A  +++   G +F T+A   ++ A+   + +     R       K  K
Sbjct: 75  DLIQVGLIGLSDALSRYEASQGVQFETFATQRIRGAMLDELRENDWMSRGS----RKSQK 130

Query: 532 VVRTA-RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTS 586
            + TA R++ +K+ R P   EIA +L M +   + +L   +  + + LE      ++D +
Sbjct: 131 EIETALRKLEHKLGRSPAESEIATELGMSLSDYQSLLGKVRGTQLVYLEDMARRNEDDDT 190

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +L   + D++A  PL+      LR++    +  L  RE+ ++ M +   MN    L+E+ 
Sbjct: 191 YLDRHVADQDA-DPLNMLRDQRLRQSLVDAIKCLPEREQYIMSMYYEQDMN----LKEIA 245

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRS 673
               VT  R+ Q+ +++I +L+   RS
Sbjct: 246 AVLDVTESRVCQLHSQSIARLRAKMRS 272


>gi|256390724|ref|YP_003112288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
 gi|256356950|gb|ACU70447.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
          Length = 411

 Score = 63.2 bits (152), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 99/207 (47%), Gaps = 13/207 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   D +  G  GL+ A E+F+     KF TYA+  ++ AI   I +      IP  +R 
Sbjct: 205 LDSADFVSSGIFGLIDAIERFEPHRHVKFETYAIARIRGAI---IDELRALDWIPRSLRQ 261

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPIS-----LETPIG 581
           K  ++ + + R+  +  R P+  EIA++L + +  +R++  K++   ++     L  P  
Sbjct: 262 KAREIEQASVRLEQEFGRTPSESEIARELGIGLGELRQIFSKLSLVNVAALDELLALPTQ 321

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D   L + +ED +A  P+        R    R + SL  R++ V+ + +  GM    T
Sbjct: 322 SGDRIPLMETLEDGDAPDPVALFEVQETRALLARAVNSLPERDKTVVTLYYFEGM----T 377

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++G+   V+  R+ QI  KA+  L+
Sbjct: 378 LAQIGEVLGVSESRVCQIHTKAVLTLR 404


>gi|318066937|emb|CBY89083.1| RNA polymerase sigma70 factor [Halomonas desiderata]
          Length = 375

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 36/45 (80%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P
Sbjct: 21  TTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAWLP 65


>gi|289550312|ref|YP_003471216.1| RNA polymerase sigma factor SigB [Staphylococcus lugdunensis
           HKU09-01]
 gi|315660227|ref|ZP_07913082.1| RNA polymerase sigma-B factor [Staphylococcus lugdunensis M23590]
 gi|289179844|gb|ADC87089.1| RNA polymerase sigma factor SigB [Staphylococcus lugdunensis
           HKU09-01]
 gi|315494654|gb|EFU82994.1| RNA polymerase sigma-B factor [Staphylococcus lugdunensis M23590]
          Length = 256

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 119/236 (50%), Gaps = 18/236 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDISFDRKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSPSITEIANRLEVTEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    R+
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDNYDLTEKRMILERI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+  ++
Sbjct: 204 LPILSEREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQQAAK 255


>gi|83590422|ref|YP_430431.1| sporulation sigma factor SigK [Moorella thermoacetica ATCC 39073]
 gi|83573336|gb|ABC19888.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Moorella
           thermoacetica ATCC 39073]
          Length = 226

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 94/221 (42%), Gaps = 53/221 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G +GL+KA   ++   G K +TYA   
Sbjct: 52  ARNILIEHNLRLVAHITKKFENTGEDTEDLISIGTVGLIKAINTYNKAKGTKLATYA--- 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 109 -----ARCIENE-----ILMHLR------------------------------------- 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTP 622
              LK T+  ISL  PIG +   +    I+   +   +   ++++  +   R  +++LTP
Sbjct: 122 --TLKKTRGEISLYDPIGVDREGNEIALIDILGSEQDVAEMVESSYEQQRVRQKISTLTP 179

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           RE +VL MR+G+      T  ++ ++  ++R  + +IE  A
Sbjct: 180 RERKVLEMRYGLWHGLRRTQRDIARKMGISRSYVSRIEKPA 220


>gi|88858091|ref|ZP_01132733.1| flagellar biosynthesis sigma factor FliA [Pseudoalteromonas
           tunicata D2]
 gi|88819708|gb|EAR29521.1| flagellar biosynthesis sigma factor FliA [Pseudoalteromonas
           tunicata D2]
          Length = 227

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 100/226 (44%), Gaps = 14/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E ++ LV  +A     R    +Q  DL Q G IGL++AA+ FD   G  F TYA   +
Sbjct: 4   LIERHVSLVKRIAYHLLARLPASVQLDDLTQSGMIGLIEAAKNFDGTKGASFETYAGIRI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I       R  VH   ++  V +    +  ++ RE    E+A+KL + +    
Sbjct: 64  RGAMLDEIRKGDWVPR-SVHKNARM--VAQATAELEAELGREVKDVEVAEKLDITLNEYH 120

Query: 565 KVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            +L        I +E    DED  H  D +   +  SP +         +    + SL  
Sbjct: 121 DILNDVNSGRIIGIEDLGVDEDVLHSDDQVHAFD--SPFNHTQTEKFNLSLVEAIKSLPE 178

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+  VL + +   MN    L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 179 RDALVLSLYYNDEMN----LKEIGLILEVSESRVSQIHGQAMVKLK 220


>gi|116748823|ref|YP_845510.1| FliA/WhiG family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697887|gb|ABK17075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 279

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 93/201 (46%), Gaps = 15/201 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+ A +K+D   G  F  YA   ++ A+   I        +P  +R K + 
Sbjct: 62  DLISAGVIGLIDAVDKYDSGQGIPFKFYAKIRIRGAMLDEIRAMDW---VPRSLRQKGNV 118

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + RT   +  K+ R P+ E++A +L + +E   ++L   K    L   I +     L + 
Sbjct: 119 LERTFSALEQKLGRCPSDEQVAGELNIGIEDYHRLLDEIKGISFLPENINEA----LLEN 174

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E  +  S  +   Q   R+   R LA    +LT +E+ VL + +      + T++EVG 
Sbjct: 175 GESGSLASDSEELFQHAYRQEIQRHLADAIRTLTEKEQLVLSLYY----YDELTMKEVGT 230

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
               T  RI QI  KAI KL+
Sbjct: 231 ALGYTESRISQIHTKAIIKLR 251


>gi|312622918|ref|YP_004024531.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203385|gb|ADQ46712.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 244

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 104/226 (46%), Gaps = 54/226 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK +VE NLRLV+ +A+++ N  +   DL+  G IGL+KA   ++     K +TYA   +
Sbjct: 64  KKILVERNLRLVVYIARRFENTKINLEDLVSIGTIGLIKAINTYNPNKNIKLATYASKCI 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +                        ++++   RR SN            KKL + ++   
Sbjct: 124 E------------------------NEILMFLRRNSN------------KKLELSID--- 144

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                  EP++++    D +   L D +  + +   + ++S+++   RE   R +  L  
Sbjct: 145 -------EPLNVD---WDGNELLLSDVLGTDTEEIYNRIESSVE---REALLRAIQKLPS 191

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+R++ +RFG G   + T +EV     +++  I ++E K I +LK
Sbjct: 192 REKRIVELRFGFGDGGEKTQKEVADMLGISQSYISRLEKKIITRLK 237


>gi|288553039|ref|YP_003424974.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
 gi|288544199|gb|ADC48082.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 257

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/207 (26%), Positives = 97/207 (46%), Gaps = 17/207 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G +GL  A EKF+     KF TYA + V+ AI   +  +     +P  MR+KI +
Sbjct: 55  DLTSHGMLGLYDALEKFNPNRDLKFDTYASFRVRGAIIDGLRKEDW---LPRSMREKIKR 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDED----- 584
           V    +++  +  R  + +E+  KL MP E V +++        +S++    D D     
Sbjct: 112 VEACIQQLEQEFGRNVSAKEVGVKLDMPEEEVYQIMNEHYLSNLLSIDERTNDSDRSDSN 171

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              S+    I DK   +P +S +   ++E   + +  L+  E+ V+ + +      + TL
Sbjct: 172 NSASYSATLI-DKQTKTPEESLMFEAVKEELIKGINRLSENEKLVISLFYF----DELTL 226

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E+G    ++  RI QI +KA+ ++  
Sbjct: 227 TEIGHILNLSTSRISQIHSKALFRMNQ 253


>gi|218680389|ref|ZP_03528286.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 209

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/194 (29%), Positives = 94/194 (48%), Gaps = 20/194 (10%)

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPT 548
           G++ +TYAMWW+K +I   I      +++      K  ++    RR+  +I+     +  
Sbjct: 5   GFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLK 62

Query: 549 PE---EIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDS 603
           PE   EIA KL +  E V  + +      SL  PI   + D+    D++ D +  S  D 
Sbjct: 63  PEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDV 121

Query: 604 AIQANLRETTTRVLAS----LTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQ 658
            I+ +  +T  R+LA     L  RE R+   R    +  D  TLE++  +F ++RER+RQ
Sbjct: 122 LIEQDELDTRRRMLAKAMSVLNERERRIFEAR---RLAEDPVTLEDLSTEFDISRERVRQ 178

Query: 659 IEAKAIRKLKHPSR 672
           IE +A  K++   R
Sbjct: 179 IEVRAFEKVQDAVR 192


>gi|118581847|ref|YP_903097.1| FliA/WhiG family RNA polymerase sigma factor [Pelobacter
           propionicus DSM 2379]
 gi|118504557|gb|ABL01040.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pelobacter
           propionicus DSM 2379]
          Length = 250

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 95/201 (47%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+    IGL+ AA++FD   G  F T+A   ++  I   +       R    MRDK  +
Sbjct: 49  DLMSAAMIGLIHAADRFDPNRGVLFKTFAEQHIRGTIIDELRSYDVLSRT---MRDKYKR 105

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL----KITKEPISLETPIGDEDTSH 587
           + R    + +++ R PT EE+A+ L + +E   ++L      +   I       + ++  
Sbjct: 106 LSRQLVSLEHQLGRNPTSEEVAESLGIGLEEYYELLDDVHAYSFISIDDSWDDDEGNSLC 165

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD + +  A SP    +   L E   + + +L  ++  V+ + +      D  L+E+G+
Sbjct: 166 LGDVLCESEAKSPQQQVMTMQLAEELGKAIDALPEKDRLVVTLYY----KEDLRLKEIGE 221

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  RI QI ++A+ +L+
Sbjct: 222 AMGLTESRISQILSQAMVRLR 242


>gi|127512314|ref|YP_001093511.1| flagellar biosynthesis sigma factor [Shewanella loihica PV-4]
 gi|126637609|gb|ABO23252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           loihica PV-4]
          Length = 239

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 103/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KASIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASAKFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  ++ +    +  ++ R+    EIA +L M ++
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RIAQVIDELEQELGRDAKDNEIADRLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +  ED +     +S  +    E     +  
Sbjct: 130 EYHHILN----DVSVGKVVGIEDLGVSVDVVRQEDDHQDDAFESLAETQFHEALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYYDEALN----LKEIGAVLDVSESRVSQIHSQAMLRLK 230


>gi|291522735|emb|CBK81028.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus catus
           GD/7]
          Length = 206

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 102/230 (44%), Gaps = 59/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KKY N G +  ++I  G +GL+KA   +++  G + +TYA   
Sbjct: 27  ARDILIERNLRLVAHIVKKYMNSGKETDEMISVGIVGLVKAVNTYNFEKGSRLATYA--- 83

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                                           AR + N             +L M + G 
Sbjct: 84  --------------------------------ARCIDN-------------ELLMLMRGD 98

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI-----EDKNAVSPLDSAIQANLRETTTRVLA 618
           RK+       +SL  PIG +   +    +     ED++ +  LD   + +LR+ +  +  
Sbjct: 99  RKL----SREVSLYDPIGTDKEGNEITLLSILEHEDEDIIDQLDK--KQSLRKLSKILSK 152

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LTPRE  V+  R+G+  + + T  E+ +Q  ++R  + +IE KA+ KL+
Sbjct: 153 VLTPREYFVVIRRYGLYGHHETTQRELAEQLNISRSYVSRIEKKALEKLR 202


>gi|312882106|ref|ZP_07741856.1| flagellar biosynthesis sigma factor [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309370242|gb|EFP97744.1| flagellar biosynthesis sigma factor [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 244

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 106/230 (46%), Gaps = 15/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++++ +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQRDFLEKYSVLVRRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGNKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  +V +    +   + R+PT  E+AKKL + +
Sbjct: 75  GIRIRGAMLDDIRRGDWVPR-SVHKHNR--EVSQAIATLEGILNRDPTDAEVAKKLGLEL 131

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +    +L        I +E     EDT  +G   E+     P         R+     + 
Sbjct: 132 DQYHNILTDINCSRLIGIEDLGVSEDTITMGGCDEEN---LPFQGVSDEFFRKALVDSIK 188

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SL  RE  VL + +   +N    L+E+G+   V+  R+ QI ++++++L+
Sbjct: 189 SLPERESLVLSLYYDEELN----LKEIGEVIGVSESRVSQILSQSMQRLR 234


>gi|333023850|ref|ZP_08451914.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332743702|gb|EGJ74143.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 294

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/255 (25%), Positives = 125/255 (49%), Gaps = 25/255 (9%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAA 485
           F  +V ++ +G      A+  ++E N  LV   A+++ NRG   + D++Q G IGL+KA 
Sbjct: 45  FDQLV-VLEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D +  + +P  +++    + R   R++ ++ R
Sbjct: 104 DRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELRVDLARAKERLAVELDR 163

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSH---------LGDFIED 594
           +P  +E+A +L +  E V   L      +  SL+ P  D  TS            DF+ D
Sbjct: 164 DPGVKELAAELNISEEEVIDGLIAANGYMSDSLDLP-ADSSTSGKPDQKTATTYADFLGD 222

Query: 595 KNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                  D A++     T  R +L +L  RE  +L +RFG     + T  ++G +  V++
Sbjct: 223 ------WDPAMELVENFTALRPLLGTLDDRERYLLELRFG----QELTQAQIGAELGVSQ 272

Query: 654 ERIRQIEAKAIRKLK 668
             + ++ ++ + KL+
Sbjct: 273 MHVSRLLSRTLGKLR 287


>gi|323484667|ref|ZP_08090029.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323694798|ref|ZP_08108953.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
 gi|323402050|gb|EGA94386.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323501114|gb|EGB17021.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
          Length = 192

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/133 (25%), Positives = 76/133 (57%), Gaps = 3/133 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A K +VE  L   + +A++Y +RGL   DL+QE NI L+  A+++    G  F + +   
Sbjct: 60  AVKRLVEGKLGRAVRMAEEYRDRGLSMNDLVQEANIALLLTAQEYK---GGDFDSQSEER 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +++ I  ++  Q+   ++   M  +++ +   +  M+ ++ RE T EE+A+++ M  + +
Sbjct: 117 IRRMIEDALELQNTEYKVEEEMLARVNVLKDISAGMAEELGREATVEELAERMKMTEQEI 176

Query: 564 RKVLKITKEPISL 576
           + ++K+T + +S+
Sbjct: 177 KDIMKLTLDAMSV 189


>gi|297626395|ref|YP_003688158.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922160|emb|CBL56728.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 272

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 112/258 (43%), Gaps = 49/258 (18%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQE 476
            G S  E R +V+    GE    +A ++  E N+ LV  V  ++   T+   +  DL+ E
Sbjct: 42  CGASAEELRQVVA---HGE----LAWQKFFEGNISLVRCVVARWVPVTHPDSE--DLVHE 92

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT-RSIADQSCTIRIPVHMRDKIHKVVRT 535
           G +GL++A  +FD  LG++FST A + V Q +   ++ ++SC      H R    +V R 
Sbjct: 93  GCMGLVEAIMRFDHALGWRFSTLAWYLVSQQVAIAAVGNRSCGSGTVAHAR----RVARI 148

Query: 536 ARRMSNKIKREPTP---EEIAKKLAMPVEGVRKVL----KITKEPISLETPIGDEDTSHL 588
            R  S        P    E+A  +   VE VR+ L    ++  +   LE  I DE   H 
Sbjct: 149 ERARSRASASRGAPVSDREVADLVGRSVEAVRRDLGQARRVEADQDILEQTIPDERPVHD 208

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
             F                         L+ L  +E RVL + FGI      TL ++ + 
Sbjct: 209 VSF-------------------------LSELADQERRVLELNFGIRNGRAQTLVQIAEH 243

Query: 649 FCVTRERIRQIEAKAIRK 666
             ++   + +++ +A+R+
Sbjct: 244 MGMSVSAVSRLKQRALRR 261


>gi|223984205|ref|ZP_03634353.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
 gi|223963820|gb|EEF68184.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
          Length = 234

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/286 (23%), Positives = 120/286 (41%), Gaps = 73/286 (25%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F +C + SI       ++ S    ++  E +  +  + KG+ EA   + +++E NLRLV 
Sbjct: 12  FFSCFIGSI-------RTTSFPQPLTAEEEQDALQRMAKGDVEA---RADLIEHNLRLVA 61

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+  R  Q  DLI  G IGL+K  + F    G+K +TY        ++R I ++  
Sbjct: 62  HIVKKFDIRREQTEDLISIGTIGLIKGIDTFKVDKGHKLATY--------VSRCIENE-- 111

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
              I +H+R+  H                                         +  SL+
Sbjct: 112 ---ILMHLRNNKHAF---------------------------------------QTRSLD 129

Query: 578 TPIG-DEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
             IG D+D S L   D I   +   P+D  +    +   T+ +  L  RE  ++  R+G+
Sbjct: 130 DAIGQDKDGSELTLIDVIPAPDQPDPIDKLMLEENKRKLTQFMGLLDEREHSIIVRRYGL 189

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             + + T  ++ +Q  ++R  + +IE +A  KL        LR+F+
Sbjct: 190 EGHQEMTQRDIARQEHISRSYVSRIEKRAFMKL--------LRAFM 227


>gi|206900763|ref|YP_002250593.1| SigF [Dictyoglomus thermophilum H-6-12]
 gi|206739866|gb|ACI18924.1| SigF [Dictyoglomus thermophilum H-6-12]
          Length = 235

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 105/230 (45%), Gaps = 28/230 (12%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++E    L+   A K+T+ G    DL+Q G +G +KA E +D   G   STY   +V  
Sbjct: 23  ELLEVFDDLIYYWASKFTSYGEPLEDLVQIGYLGFLKAVENYDPEKG-DLSTYISHYVLG 81

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I   + D+   I+IP  ++  I+K+    + +  K  R P+ EEIAK L + VE V ++
Sbjct: 82  EIRHHLRDKIDKIKIPRSVKGLINKMDNFIKEVWEKENRSPSCEEIAKHLNITVESVEEL 141

Query: 567 LKITKEPIS-----LETPIGDEDTSHLGDF---IEDKNAVSPLDSAIQANLRETTTRVLA 618
            KI +  ++     LE  +       L  F   IEDK A+                + LA
Sbjct: 142 FKIKEAMMTVSLEDLEIEMDRIRAEKLESFKLPIEDKIALE---------------QALA 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L   + +V+   F      D T  EV K   +++ ++ +I   A+ KLK
Sbjct: 187 KLPDIQRKVIEYIF----YQDLTQTEVAKILKISQSQVSRILRSALEKLK 232


>gi|167587836|ref|ZP_02380224.1| flagellar biosynthesis sigma factor [Burkholderia ubonensis Bu]
          Length = 244

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 98  VEHAVHQVEQHLGRAASEAEIAQHLNMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 153

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL S +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRVDHADPLSSLLDEHLREALIEAIERLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|158341138|ref|YP_001522305.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
 gi|158311379|gb|ABW32991.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
          Length = 427

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 23/231 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+   +  N  LV   A K+  RGL  + DL+  GN+GL  A +KFD   GYKFS+YA+ 
Sbjct: 36  ARDRFIRQNEGLVFQQAHKF--RGLADWDDLVNAGNLGLAIAIQKFDVAKGYKFSSYAVK 93

Query: 503 WVKQAITRSIAD-QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
            ++  I R I + +  +I I +H+++    + + ++ +   + REPT  E++ +     +
Sbjct: 94  VIRTEIRRLIHEFKGISIEISLHLKE----IEQASQAIRMDLDREPTITELSDETGYSQQ 149

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLA 618
            +          E  SL  P+ D+      D I  D       ++  Q N        +A
Sbjct: 150 VIFNAWNKANVVETASLNIPLNDDQGCEQLDVIGVDDRTWEFTETLDQKNY-------IA 202

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  RE  ++R +         + +E+G    ++ ER+RQ+  +A   LKH
Sbjct: 203 QLPDREAFIVRAK-----RDGFSNKEIGTMLSLSGERVRQLLKQARAFLKH 248


>gi|33592168|ref|NP_879812.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis Tohama I]
 gi|33601519|ref|NP_889079.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           bronchiseptica RB50]
 gi|33571813|emb|CAE41322.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis Tohama I]
 gi|33575955|emb|CAE33034.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           bronchiseptica RB50]
 gi|332381584|gb|AEE66431.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis CS]
          Length = 245

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/205 (25%), Positives = 96/205 (46%), Gaps = 14/205 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DL+Q G IGL+ A  ++      +F TYA   ++ A+   +  Q     +P  +R 
Sbjct: 30  VQLDDLVQAGMIGLLDAVRRYQESPDAQFETYATARIRGAMLDELRSQDW---LPRSVRS 86

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE----TPIGDE 583
           K  ++    +R   ++ R P+  EIA++L +P+   + +L   +    L        GD 
Sbjct: 87  KSRRIETAIQRKEQELMRAPSEGEIAEELGVPLAEYQGMLADAQGVQILHYEDFNTDGDS 146

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D+       E  +   PLD+ +  +LR      +  L  RE+ +L + +  G+N    L+
Sbjct: 147 DSPWAESSAEHAD---PLDALLAGDLRRALIDAIDGLPEREKLLLSLCYEQGLN----LK 199

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G    VT  R+ Q+ A+A  +++
Sbjct: 200 EIGAVLNVTEARVCQLRAQATARIR 224


>gi|157691239|ref|YP_001485701.1| RNA polymerase sigma factor SigB [Bacillus pumilus SAFR-032]
 gi|157679997|gb|ABV61141.1| DNA-directed RNA polymerase sigma subunit SigB [Bacillus pumilus
           SAFR-032]
          Length = 262

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 114/227 (50%), Gaps = 8/227 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +VE    LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQLTLVECYTNLVDMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPLVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++      ++ + ++ P  +EIA+ L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDHLTTETQKSPKVQEIAEYLDVTEEE 148

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLT 621
           V + +++ K   +L    G E  S  G  +   + V   +   +  N +     VL  LT
Sbjct: 149 VLETMEMGKSYQALSVDQGVEADSE-GSTVTILDVVGSQEEGYERVNQKMMLESVLHVLT 207

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ ++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 208 DREKEIINLTY----LQNKSQKETGDLLGISQMHVSRLQRKAVKKLR 250


>gi|333022810|ref|ZP_08450874.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332742662|gb|EGJ73103.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 275

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 113/245 (46%), Gaps = 20/245 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VE  L +   +A +Y  RG    DL Q   +GL+KA ++FD  +   F +YA+  +
Sbjct: 40  RSRLVETWLPMAHRIAGRYRERGENLEDLCQVAALGLVKAVDRFDPEVSDAFESYAVPTI 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
           +  + R   D +  + +P  +++ +   VRTA +        R P+  E+A+   +  E 
Sbjct: 100 RGELKRHFRDNTWGVHVPRRVQE-LRNAVRTALQELAPRTAPRTPSVAELAESAKLGEEE 158

Query: 563 VRKVLKI--TKEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           VR+ L+   +  P+SL+   TP G+         + D+        AI  + RE+    L
Sbjct: 159 VRRGLEALDSYRPVSLDGTPTPEGEHP-------LRDRLGADDPAYAIVVD-RESVRPAL 210

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A L  RE  +L +RF        T   +  +  +++  + ++  +A  ++KH   ++  R
Sbjct: 211 AELPERERYILYLRF----FHARTQRAIAAELGLSQMHVSRLITQACAQVKHRVEARPPR 266

Query: 678 SFLDG 682
           + L G
Sbjct: 267 AVLTG 271


>gi|297617167|ref|YP_003702326.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297145004|gb|ADI01761.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 258

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 103/206 (50%), Gaps = 20/206 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G  GL+ A  +FD     KF TYA+  +K AI   +        IPV +R K  +
Sbjct: 53  ELISYGIEGLIDAVHRFDPKRKVKFETYALARIKGAIIDGLRAMDW---IPVSLRHKAKE 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPI-GDED--TS 586
           + +    + +++ R  T EE+A +L M +   + +LK       I LE  I GDE     
Sbjct: 110 LEKAYCLLEHRLGRAATDEEMACELGMSIPEFQNLLKEVNLATIIYLEDLIPGDEGDKNK 169

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLA---SLTPREER-VLRMRFGIGMNTDHTL 642
            + D I+D+ A    +  ++    E + R+LA   +L P +ER V+ + +  G+    TL
Sbjct: 170 RIADVIKDERA----EDGLELIEFEESKRLLAEAIALLPEKERTVVTLYYYEGL----TL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+G+   ++  RI Q+  KAI +L+
Sbjct: 222 KEIGEVLGLSESRISQLHTKAILRLR 247


>gi|300871802|ref|YP_003786675.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
 gi|300689503|gb|ADK32174.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
          Length = 270

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/212 (25%), Positives = 104/212 (49%), Gaps = 18/212 (8%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVH 524
           R ++F DL+  G +GL+ A EK+D     KF TYA   +K     SI D+   I ++P  
Sbjct: 59  RDIEFDDLVGYGALGLIDAIEKYDPNKEVKFKTYATTRIKG----SIYDELRKIDKLPRS 114

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG--- 581
           +R +I  +      + +K+ R    +EIA  + +P+  + + ++ + E  +  T +    
Sbjct: 115 IRREIKDIEIAREFLESKLGRNVNSQEIADTMGIPLSKINETMRYSIEAST--TSLSEVW 172

Query: 582 ----DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
               D D   + D ++  +  +P   A + ++++     L  L  +E  VL + +     
Sbjct: 173 YHGDDSDEISIMDTLKASDKNNPEYLAERKDVQKKIVEALDKLPEKERSVLILYY----Y 228

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            D TL+E+GK   V+  R+ Q+  KA+++L++
Sbjct: 229 EDLTLKEIGKVLDVSESRVSQLHTKAVQQLRY 260


>gi|229490177|ref|ZP_04384024.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229322925|gb|EEN88699.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 264

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 103/225 (45%), Gaps = 8/225 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++   L L   +A+++  RG    DL+Q   +GL+ A ++FD   G  F ++A+  V
Sbjct: 43  RTALITRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNAVDRFDSTRGSDFVSFAVPTV 102

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +R+P  M++   ++ +    +S ++   PT +E+A+ L +  E V 
Sbjct: 103 MGEVRRHFRDTGWALRVPRRMKELHFQLGQAISELSQQLGHAPTVDELAETLGIEREEVA 162

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPR 623
           + L       + +T   D   S+  D +     +   D+A++     E    +L  L  R
Sbjct: 163 QALIAGN---AYQTVSVDGAASNHTDDLPLVETLGDYDAALENVENHEALRPLLDKLPER 219

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  VL +RF   +      E+VG    V++  + ++ AK +  L+
Sbjct: 220 ERTVLMLRFFGNLTQTQIAEKVG----VSQMHVSRLLAKTLSNLR 260


>gi|30024622|dbj|BAC75679.1| sigma F [Streptomyces griseus]
          Length = 293

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/243 (23%), Positives = 111/243 (45%), Gaps = 18/243 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +
Sbjct: 60  PGTPEHRRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQ 119

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH----KVVRTARRMSNKIKREPTPEE 551
           F T+AM  V   I R   D       P    D++H    +V      ++    R PT  E
Sbjct: 120 FPTFAMPTVVGEIKRYFRDNCAH---PSTSPDRLHELWVQVTGATEDLTTAHGRSPTTAE 176

Query: 552 IAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           IA++L +  + V   ++  +     SLE     ++   L   ++      P  + ++   
Sbjct: 177 IAERLKISEDEVLACIEAGRSYHATSLE---AAQEGDGLPGLLDRLGYEDPALAGVEH-- 231

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    +L  L  RE+R+L +R+     ++ T  ++  +  V++  + ++ A++  +L+ 
Sbjct: 232 RDLVRHLLVQLPEREQRILLLRY----YSNLTQSQISAELGVSQMHVSRLLARSFARLRS 287

Query: 670 PSR 672
            +R
Sbjct: 288 ANR 290


>gi|163789630|ref|ZP_02184068.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
 gi|159875162|gb|EDP69228.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
          Length = 238

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/201 (26%), Positives = 93/201 (46%), Gaps = 11/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGLM A EKFD      F  YA   +K  I   I   +   R  +    K+++
Sbjct: 36  DLYNIGVIGLMDALEKFDKSKKVPFEGYAYIRIKGTIIDEIRKTAPVSRTRM---GKLNE 92

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS--H 587
             R   ++  ++ R PT +EI  +L +  + + K+ +       +SLE  +  +D +   
Sbjct: 93  YYRGKEKLEAELMRTPTEKEICAELKIDEKSLAKIHETVHNLASVSLEKVMFSDDGNSIE 152

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L DF+ED +     D+ +    +   T+ +  L  RE+ +L + +      + +L+E+  
Sbjct: 153 LLDFLEDTHETGSEDTLLDKERQHLLTKHVGQLDKREQTILNLIY----VEELSLKEIAY 208

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
            F ++  R+ QI  K I KLK
Sbjct: 209 IFDISVPRVSQIHGKMILKLK 229


>gi|289810010|ref|ZP_06540639.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 227

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 37/52 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+
Sbjct: 41  TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLL 92


>gi|332187909|ref|ZP_08389642.1| RNA polymerase sigma factor, FliA/WhiG family protein [Sphingomonas
           sp. S17]
 gi|332012070|gb|EGI54142.1| RNA polymerase sigma factor, FliA/WhiG family protein [Sphingomonas
           sp. S17]
          Length = 265

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 56/197 (28%), Positives = 99/197 (50%), Gaps = 12/197 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G + L++AA  F+   G +F  Y    ++ A+   +  Q+ T R  +  R + H+
Sbjct: 74  DLVQVGLVALVEAAASFEE-RGVEFGHYLKARLRGAMIDELRRQATTTRGAMRRRRQYHE 132

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            V    +++ ++   PT E +A+KL +  E +R   K T E + +E PI D     L  F
Sbjct: 133 AVTALSQVAGQV---PTDEAVAEKLGVTTEKLRTDYK-TAEAVRME-PIDDVYADDLPWF 187

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            +D       +   +++LR+     +ASL  RE  V+++ +   +N    LEE+G+   V
Sbjct: 188 ADDTP--DAFEQLAESDLRDALIAAIASLPEREAMVIQLYYVEELN----LEEIGQVLGV 241

Query: 652 TRERIRQIEAKAIRKLK 668
              R+ QI++ A  +LK
Sbjct: 242 GAARVCQIKSAAHARLK 258


>gi|295849257|gb|ADG45292.1| sigma 70 factor-like protein [uncultured bacterium]
          Length = 173

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 46/72 (63%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  K +++ ANLRLV+S+A+++    +  ++L+ EG + LM+A + FD   G+KFSTYA
Sbjct: 18  ATDTKNQIIRANLRLVVSIARRHLRGSVSLMELVSEGTMTLMRAVDSFDAHRGHKFSTYA 77

Query: 501 MWWVKQAITRSI 512
              + +   R +
Sbjct: 78  TLALMKGFARCV 89


>gi|292669753|ref|ZP_06603179.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
 gi|292648550|gb|EFF66522.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
          Length = 251

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 25/242 (10%)

Query: 435 RKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDW 490
           R  E E ++A +  + E  L LV  VA +      Q +D   L+  G  GL+ A E+++ 
Sbjct: 17  RAYETEKTVAVRNRIAEHYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLLDAIERYEL 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G KF TYA   V+ A+   +  +     IPV +R  I K  +    +  ++ R  T E
Sbjct: 77  ARGNKFETYAGVRVRGAMLDHLRAKDW---IPVSVRQNIKKYEKAVAHLEGELGRTATDE 133

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS----PLDSAIQ 606
           E+A++L + +EG+            LE  +       L +++   +  S    P++ A  
Sbjct: 134 ELAEELDLTIEGLHH----------LEGQVSAATVIPLEEYLRTDSPTSLEDGPVEHAEW 183

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             ++ET    +  L  +E  V+ + +   M    TL+E+     ++  RI Q+  KAI +
Sbjct: 184 TEVKETLAAAIEKLPEKERTVITLYYYDEM----TLKEIAAILHLSEARISQLHTKAIFR 239

Query: 667 LK 668
           ++
Sbjct: 240 MR 241


>gi|226305067|ref|YP_002765025.1| RNA polymerase sigma factor SigF [Rhodococcus erythropolis PR4]
 gi|226184182|dbj|BAH32286.1| RNA polymerase sigma factor SigF [Rhodococcus erythropolis PR4]
          Length = 264

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 103/225 (45%), Gaps = 8/225 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++   L L   +A+++  RG    DL+Q   +GL+ A ++FD   G  F ++A+  V
Sbjct: 43  RTALITRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNAVDRFDSTRGSDFVSFAVPTV 102

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +R+P  M++   ++ +    +S ++   PT +E+A+ L +  E V 
Sbjct: 103 MGEVRRHFRDTGWALRVPRRMKELHFQLGQAISELSQQLGHAPTVDELAETLGIEREEVA 162

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLASLTPR 623
           + L       + +T   D   S+  D +     +   D+A++     E    +L  L  R
Sbjct: 163 QALIAGN---AYQTVSVDGAASNHTDDLPLVETLGDYDAALENVENHEALRPLLDKLPER 219

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  VL +RF   +      E+VG    V++  + ++ AK +  L+
Sbjct: 220 ERTVLMLRFFGNLTQTQIAEKVG----VSQMHVSRLLAKTLSNLR 260


>gi|225028118|ref|ZP_03717310.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
 gi|224954588|gb|EEG35797.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
          Length = 247

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 109/227 (48%), Gaps = 52/227 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA + F      K +TYA   
Sbjct: 64  AKALLIERNLRLVVYIAKKFENTGIGVEDLISIGTIGLIKAIQTFKLDKKIKLATYA--- 120

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R       RT     NK K E + +E    L +  +G 
Sbjct: 121 -----SRCIENE-----ILMYLR-------RT-----NKTKMEVSIDE---PLNVDWDGN 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L          + I   D+  +   IED+     +D       R+   + + +L+ R
Sbjct: 156 ELLL----------SDILGTDSDVISKDIEDE-----ID-------RKMLNKAMETLSDR 193

Query: 624 EERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++R+RFGIG   + + T +EV     +++  I ++E K I +LK
Sbjct: 194 EKLIIRLRFGIGGEESEEKTQKEVADLLGISQSYISRLEKKIIHRLK 240


>gi|293392778|ref|ZP_06637096.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424637|gb|EFE97848.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 119

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 61/104 (58%)

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 1   MLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQR 60

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+ 
Sbjct: 61  EVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLRE 104


>gi|91776300|ref|YP_546056.1| flagellar biosynthesis sigma factor [Methylobacillus flagellatus
           KT]
 gi|91710287|gb|ABE50215.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Methylobacillus
           flagellatus KT]
          Length = 244

 Score = 62.8 bits (151), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 114/233 (48%), Gaps = 20/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+++ +  LV  +A +   +    +   DLIQ G +GL+ A+ +++   G +F TYA 
Sbjct: 11  KEELLKQHASLVKKIAYQLKAKLPASVDIDDLIQAGMMGLLDASNRYEDNHGAQFETYA- 69

Query: 502 WWVKQAITRSIADQSCTIR----IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
               Q I  S+ D+   +R    +P  +R  +  V      +  K+ R PT  E+A++L 
Sbjct: 70  ---AQRIRGSMIDE---LRRADWLPRSVRKNMRDVESAVHLLEQKLGRPPTEGELARELN 123

Query: 558 MPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + ++  + +L   +   +       ++D+  H  D  +  ++  PL + + ++ RE    
Sbjct: 124 LSMDDFQGMLDDCSGHQLIYYEDFSEQDSGDHFLDRYQSDDSGDPLKALLSSDFREALIE 183

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE+ ++ + +   MN    L+++G    V+  R+ Q+  +A+ +L+
Sbjct: 184 AIEALPEREKILMGLYYEQEMN----LKDIGAIMSVSESRVCQLHTQAVARLR 232


>gi|332654157|ref|ZP_08419901.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
 gi|332517243|gb|EGJ46848.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 110/227 (48%), Gaps = 14/227 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A ++++E N  L+ SV ++Y  RG++  DL Q G +G +KA   FD   G +FSTYA+  
Sbjct: 21  ACEQVLEENNGLIWSVVRRYYGRGVEPDDLYQLGCLGFLKAVRGFDPAFGTQFSTYAVPK 80

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVEG 562
           +   I R + D    +++   ++++   ++R  R ++ + + REP   E+A+   +  E 
Sbjct: 81  IAGEIRRFLRDDGA-VKVSRGLKEQ-GALIRGVRSQLWSTLGREPALSELAQATGLTPEE 138

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +          +SL+      +T   G  +E   +   ++  +    R      L  L  
Sbjct: 139 IAAAETAADPVVSLQA-----ETGEGGLTLEGVLSAGGMEEGLVE--RIALRGALEQLPE 191

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE  VL +R+  G+   +T   +G    V++ +I ++E +A+ +L+ 
Sbjct: 192 REREVLLLRYYKGLTQTNTARVLG----VSQVQISRLERRAVDRLRQ 234


>gi|187778862|ref|ZP_02995335.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
 gi|187772487|gb|EDU36289.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
          Length = 234

 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 107/242 (44%), Gaps = 52/242 (21%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E ++ +  ++KG+   ++AK  +VE NLRLV  + KKY+  G    DLI  G +GL+KA 
Sbjct: 35  EEKYYLDRLKKGD---ALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGLIKAI 91

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD   G + +TYA   ++  I   I +   T +  V+++D I                
Sbjct: 92  DSFDNSKGTRLATYAARCIENEILMLIRNNKKT-KGEVYLQDPI---------------- 134

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                           GV K        ISL   +  ++ S + + +  K  V  L   I
Sbjct: 135 ----------------GVDK----EGNEISLMDILSSDEDSII-EIVSTKIEVKKLYGKI 173

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  LR            RE++V++MR+G+      T  E+     ++R  + +IE KA++
Sbjct: 174 ETCLR-----------GREKKVIQMRYGLKDGRPRTQREIAGILNISRSYVSRIEKKALK 222

Query: 666 KL 667
           KL
Sbjct: 223 KL 224


>gi|54294669|ref|YP_127084.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Lens]
 gi|53754501|emb|CAH15985.1| sigma factor 28 [Legionella pneumophila str. Lens]
          Length = 238

 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 113/245 (46%), Gaps = 45/245 (18%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F TYA
Sbjct: 14  TQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYA 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------RE 546
                             IRI  HM D++ +       V R +R +S+ ++       RE
Sbjct: 74  -----------------GIRIRGHMLDEVRRNDWVPRSVYRNSRMISDAVRILEHKFGRE 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDS 603
               EIA++L + +     +L   ++ IS     G +D     D +   E   +  P  +
Sbjct: 117 AKDNEIAEELGVSLNDYHDML---QDSISSHL-YGFDDLGVTDDVLFDDEGNGSTEPHRN 172

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +++++    T+V+ SL PR+ER++     +    D  L+E+G+   V+  RI QI ++A
Sbjct: 173 VMRSDMMNRLTQVIDSL-PRKERLV---LSLYYEQDLNLKEIGEILEVSESRISQILSQA 228

Query: 664 IRKLK 668
             +++
Sbjct: 229 THRIR 233


>gi|86146119|ref|ZP_01064445.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218708840|ref|YP_002416461.1| flagellar biosynthesis sigma factor [Vibrio splendidus LGP32]
 gi|85836066|gb|EAQ54198.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218321859|emb|CAV17839.1| RNA polymerase sigma factor for flagellar operon [Vibrio splendidus
           LGP32]
          Length = 244

 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMIGLIEAQQNYDGTKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKNNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +   + R+P+  E+AK + + ++     L      I+    +G ED     D 
Sbjct: 103 ISSAIAELEGTLNRDPSDAEVAKHMGLSLDQYHSALT----DINCSKLVGIEDLGVSDDV 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   ED    +P       + R+     +  L  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPNEDSQDNTPFQGVADESFRQALIDSIKQLPEREGLVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 LGVSESRVSQILSQSMQRLR 234


>gi|332701290|ref|ZP_08421378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332551439|gb|EGJ48483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 264

 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/197 (26%), Positives = 95/197 (48%), Gaps = 10/197 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+  G++GLM+A +KF+  L  KF TYA   +K A+   +       R    +R ++  
Sbjct: 66  ELMSAGSLGLMEALQKFNPELRIKFETYAESRIKGAMLDELRRMDWYSR---GLRQRLRL 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +  T R +  +  R  T +EIAK+  +  + V   L++ +  + L      E  + + D 
Sbjct: 123 MEHTVREIEQETGRPATVQEIAKRTGLSEKDVDMGLEMLQNQLCLSLDAISECVASVSDA 182

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             D +   P  SA    L +  T ++  LTPRE+ VL + +G  +N    + E      +
Sbjct: 183 GVDGD---PYQSAAFQELIDKITLLIDELTPREKLVLSLYYGEELN----MRETANVMEI 235

Query: 652 TRERIRQIEAKAIRKLK 668
           T  R+ Q+ ++A+ KL+
Sbjct: 236 TEGRVSQLHSQALGKLR 252


>gi|84388128|ref|ZP_00991024.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
 gi|84377195|gb|EAP94065.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
          Length = 244

 Score = 62.4 bits (150), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMIGLIEAQQNYDGTKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKNNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +   + R+P+  E+AK + + ++     L      I+    +G ED     D 
Sbjct: 103 ISSAIAELEGALNRDPSDAEVAKHMGLSLDQYHNALT----DINCSRLVGIEDLGVSDDV 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           I   ED    +P       + R+     +  L  RE  VL + +   +N    L+E+G+ 
Sbjct: 159 ISPNEDSQDNTPFQGVADESFRQALIDSIKQLPEREGLVLSLYYDEELN----LKEIGEV 214

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 215 LGVSESRVSQILSQSMQRLR 234


>gi|313901762|ref|ZP_07835188.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467968|gb|EFR63456.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
          Length = 244

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 102/231 (44%), Gaps = 61/231 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 62  VRHTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYA--- 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                ++ I ++     I +H+R       RT+R                          
Sbjct: 119 -----SKCIENE-----ILMHLR-------RTSR-------------------------- 135

Query: 564 RKVLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVL 617
                 T+  +SL+ P+     G+E    L D I   +    +   ++A + R    R L
Sbjct: 136 ------TRYEVSLDEPLNVDWEGNELL--LSDVIPATDG-DVIYRDLEAKVDRHLLHRAL 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A LTPRE  ++ +RFG+    + T ++V     +++  I ++E + I +L+
Sbjct: 187 ARLTPRERLIMELRFGLVDGIERTQKQVADHLGISQSYISRLEKRIINRLR 237


>gi|297538886|ref|YP_003674655.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Methylotenera
           sp. 301]
 gi|297258233|gb|ADI30078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylotenera sp. 301]
          Length = 244

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 92/200 (46%), Gaps = 11/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ-SCTIRIPVHMRDKIH 530
           DLIQ G +GL+ A  +++   G +F TYA     Q I  S+ D+      +P  +R  + 
Sbjct: 41  DLIQAGMMGLLDAINRYEDTHGAQFETYA----AQRIRGSMLDELRSADWLPRSVRKSMR 96

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHL 588
            V     ++  ++ + PT  E+AKKL + +     +L      + I  E     E+  H 
Sbjct: 97  DVEIAISQLEQQLGKPPTENEVAKKLQLSLSDYYDMLGDCSGHQLIYYEDFHESENGEHF 156

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D         P+ S ++ + RE     + +L P  E++L    G+    +  L+E+G  
Sbjct: 157 LDRFNADTTGDPIKSLLEGDFREALVGAITAL-PEREKIL---MGLYYEQELNLKEIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ Q+ ++A+ +L+
Sbjct: 213 MNVSESRVCQLHSQAVARLR 232


>gi|52629120|gb|AAU27861.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 262

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 112/254 (44%), Gaps = 63/254 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F TYA
Sbjct: 38  TQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYA 97

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMS-------NKIKRE 546
                             IRI  HM D++ +       V R +R +S       +K+ RE
Sbjct: 98  -----------------GIRIRGHMLDEVRRNDWVPRSVYRNSRMISDAVRILEHKLGRE 140

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF------------IED 594
               EIA++L + ++    +L+             D  +SHL  F             E 
Sbjct: 141 AKDNEIAEELGVSLDDYHDMLQ-------------DSISSHLYGFDDLGVTDDVLFDHEG 187

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             +  P  + +++++    T+V+ SL PR+ER++     +    D  L+E+G+   V+  
Sbjct: 188 NGSTEPHRNVMRSDMMNRLTQVIDSL-PRKERLV---LSLYYEQDLNLKEIGEILEVSES 243

Query: 655 RIRQIEAKAIRKLK 668
           RI QI ++A  +++
Sbjct: 244 RISQILSQATHRIR 257


>gi|254491912|ref|ZP_05105091.1| RNA polymerase sigma factor, FliA/WhiG family [Methylophaga
           thiooxidans DMS010]
 gi|224463390|gb|EEF79660.1| RNA polymerase sigma factor, FliA/WhiG family [Methylophaga
           thiooxydans DMS010]
          Length = 234

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 56/230 (24%), Positives = 101/230 (43%), Gaps = 15/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +K E+VE N  LV  +A     R    +   DLIQ G IGL+ A+ +FD   G  F TYA
Sbjct: 7   SKSELVEQNAALVKRIAYHLIARLPASVDVEDLIQAGMIGLLDASHQFDSSQGASFETYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I         P  +  K  ++  T + +  +  R  +  E+A+ + + +
Sbjct: 67  GIRIRGAMLDEIRRNDWA---PRSVHRKAREISSTMQVIEQQKGRNASDAEVAQAMGLDI 123

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               + L+     +  SL+    D D  H           +P +   Q + ++   R + 
Sbjct: 124 SEYHQQLQDSTGHQLFSLDE-FSDNDEVHARPI--SSGPAAPEEEVQQDDFQQAMVRAID 180

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SL  RE    R+   +  N +  L+E+G+   V+  R+ QI ++ + +L+
Sbjct: 181 SLPERE----RLLMSLYYNDELNLKEIGEVLGVSESRVSQIHSQTVIRLR 226


>gi|213580121|ref|ZP_03361947.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 143

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/106 (33%), Positives = 62/106 (58%), Gaps = 8/106 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S ++  N    +S +   +++E  H      +G+ EA+   K ++ ++LR V+ +A+ 
Sbjct: 16  LESYIRAANAWPMLSADEERALAERLHY-----QGDLEAA---KTLILSHLRFVVHIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI 113


>gi|289575401|ref|ZP_06455628.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis K85]
 gi|289539832|gb|EFD44410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis K85]
          Length = 470

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 32/37 (86%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN G
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNRG 327



 Score = 44.7 bits (104), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 209 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 268


>gi|288942618|ref|YP_003444858.1| RNA polymerase sigma-28 subunit FliA/WhiG [Allochromatium vinosum
           DSM 180]
 gi|288897990|gb|ADC63826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Allochromatium vinosum
           DSM 180]
          Length = 248

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 106/239 (44%), Gaps = 15/239 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           R G   A      +V  ++ LV  +A     R    +Q  DLIQ G +GL++AA +F   
Sbjct: 7   RMGYASAGDEAARLVSEHVDLVRRIAHHLVARLPASVQVEDLIQSGMVGLIEAARQFQTG 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F+TYA   V+ A+   +     T R  VH   +  ++     ++ ++  R  +  E
Sbjct: 67  QGATFATYAGIRVRGAMIDELRRADWTPR-SVHRNSR--RIAEAIHQVESREGRAASDRE 123

Query: 552 IAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           IA+ L + ++    +L+ T   + + LE   G++  S   D        +P +   +   
Sbjct: 124 IAETLGVTLDDYHGMLQDTASCQILGLEDLFGEDADS---DRFLPGAGTAPTEQLEREQF 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     LA L  RE  VL + +   +N    L E+G    VT  R+ QI ++A+ +L+
Sbjct: 181 AQALAEALADLPERERLVLALYYDEELN----LREIGAVLDVTESRVSQIRSQALHRLR 235


>gi|312792676|ref|YP_004025599.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179816|gb|ADQ39986.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 246

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 117/233 (50%), Gaps = 23/233 (9%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 19  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLAM 558
             +K AI   +  Q     +P  +R K  ++     +   +I+RE   PT +E+AK++ +
Sbjct: 79  TRIKGAIIDCVRSQDF---LPRSIRQKAKEI----EKAYVEIEREGKTPTDQEVAKRVGI 131

Query: 559 PVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTR 615
            V  ++K+ +       ISL++ +     S +G     ++ VS  +  I+   L+E   +
Sbjct: 132 SVNELQKLQERISSGMIISLDSFLEQNYESKIGGL---EDFVSQPEHFIENEELKEVLRQ 188

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KLK
Sbjct: 189 QIENLMENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLK 237


>gi|323484320|ref|ZP_08089687.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694680|ref|ZP_08108842.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402314|gb|EGA94645.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501272|gb|EGB17172.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 209

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 65/252 (25%), Positives = 106/252 (42%), Gaps = 62/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ SE R  +   ++G+ EA   K  ++E NLRLV  V KKY     +  DL+  G IGL
Sbjct: 8   LTASEEREYLKRCKEGDEEA---KAVLIERNLRLVAHVIKKYQYTDYEMEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F    G + +TYA   V+                     ++I  + R  ++ S 
Sbjct: 65  IKAVNTFKMDRGSRLATYAAKCVE---------------------NEILMLFRAGKKHS- 102

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIE--DKN 596
                                         + +SL  PIG   D +T +L D IE  DK 
Sbjct: 103 ------------------------------KDVSLYDPIGVDKDGETVNLIDVIEADDKA 132

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+  +   ++ ++ E        L   E+ VL MR+G+    + T  E+  +  ++R  +
Sbjct: 133 ALETI--ILEQDVSELYDAYRKCLKNTEQEVLSMRYGLFGEQERTQREIAGKMGISRSYV 190

Query: 657 RQIEAKAIRKLK 668
            +IE KA+ KL+
Sbjct: 191 SRIEKKALEKLR 202


>gi|307717590|gb|ADN88848.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717592|gb|ADN88849.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717624|gb|ADN88865.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717626|gb|ADN88866.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 93/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+ +L+  F
Sbjct: 192 LDEREQMILQYTF 204


>gi|297162318|gb|ADI12030.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 261

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 108/215 (50%), Gaps = 13/215 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++ A L +   +A ++ N+G    DL Q  ++ L+KA +++D  LG+ F +YA+  +
Sbjct: 37  REAIICAWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVDRYDPDLGHAFPSYAIPVI 96

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKI-KREPTPEEIAKKLAMPVEG 562
              + R   D   T+ +P ++++ +    R+AR  +  ++  R PT  EI+ +  MP E 
Sbjct: 97  TGELKRHFRDYLWTLHVPRNIQE-VRSRTRSARDALEQELGGRTPTITEISTRTGMPKED 155

Query: 563 VRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLAS 619
           V   L+ +    P+SL   +   +   L +       V   D+AI+  + RE    ++  
Sbjct: 156 VMAGLEASASCTPLSLNAAVQGAEERLLAE------TVGADDAAIERVVNREALRALITH 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L+ ++  VL +RF +G++     E +G  Q  ++R
Sbjct: 210 LSEQDRYVLYLRFFVGLSQSQIGEILGFSQMHISR 244


>gi|318066991|emb|CBY89110.1| RNA polymerase sigma70 factor [Modicisalibacter tunisiensis]
          Length = 373

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 40/60 (66%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+RE EI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVELLTREAEIEIAKRIEEGTREVMSSLAYLPGAVDSILEAYDATQD 80


>gi|28899006|ref|NP_798611.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153836996|ref|ZP_01989663.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|260365248|ref|ZP_05777805.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|260878798|ref|ZP_05891153.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|260899951|ref|ZP_05908346.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|28807225|dbj|BAC60495.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149749769|gb|EDM60514.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|308094185|gb|EFO43880.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|308107226|gb|EFO44766.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|308115412|gb|EFO52952.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|328474457|gb|EGF45262.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus 10329]
          Length = 244

 Score = 62.4 bits (150), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   + D      +P  +     ++ +    +   + R+PT  E+A  L M +
Sbjct: 75  GIRIRGAM---LDDMRKGDWVPRSVHKNNREINQAVAELEGVLNRDPTDSEVAAHLGMSL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P       + R+     +
Sbjct: 132 DQYHSALT----DINCSRLVGIEDLGVSDDVISPADETDDSNPFKGVADESFRKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G    V+  R+ QI ++A+++L+
Sbjct: 188 KQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQAMQRLR 234


>gi|228943728|ref|ZP_04106130.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976238|ref|ZP_04136717.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977712|ref|ZP_04138098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|229042834|ref|ZP_04190570.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|229143711|ref|ZP_04272133.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228639767|gb|EEK96175.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228726494|gb|EEL77715.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|228782010|gb|EEM30202.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|228783483|gb|EEM31583.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228815947|gb|EEM62170.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 203

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|210608671|ref|ZP_03287948.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
 gi|210152928|gb|EEA83934.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
          Length = 247

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 103/227 (45%), Gaps = 52/227 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NK K E + +             
Sbjct: 120 -----SRCIENE----------------ILMYLRR-NNKTKLEVSID------------- 144

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   EP++++    D +   L D +  +      D   +A  R+   + +  L+ R
Sbjct: 145 --------EPLNVD---WDGNELLLSDILGTEEDTIYRDLENEAE-RKLLVKAIGRLSNR 192

Query: 624 EERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  ++RMRFG+G     + T +EV     +++  I ++E K +++LK
Sbjct: 193 ERMIVRMRFGLGTLDGEEKTQKEVADLLGISQSYISRLEKKIMQRLK 239


>gi|206558549|ref|YP_002229309.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           J2315]
 gi|198034586|emb|CAR50452.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia cenocepacia J2315]
          Length = 243

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 97  VEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 152

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYRVDHADPLSALLDEHLREALVEAIERLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVLEVSESRVCQLHSQAVARLR 230


>gi|239826640|ref|YP_002949264.1| RNA polymerase sigma factor SigD [Geobacillus sp. WCH70]
 gi|239806933|gb|ACS23998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp. WCH70]
          Length = 254

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 97/202 (48%), Gaps = 14/202 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P  +R+K  K
Sbjct: 55  ELISLGLMGLYDALEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDW---LPRSVREKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIG---DEDTS 586
           +  T  ++  +  R  T +E+A +L +  E V   +        +S +  I    +E+ +
Sbjct: 112 IEETIEKLEQRYMRSVTAKEVADELGITEEEVYMAVNENFFANVLSFQHVITENKEEENA 171

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L   I D+   SP +  ++  L E    V+  L+ +E+ V+ + +      + T  E+G
Sbjct: 172 LLA--IRDEKTPSPEEEVLKQELYEKLAEVIQQLSEKEQLVISLFY----KEELTFTEIG 225

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   ++  RI Q+ +KAI KL+
Sbjct: 226 EILGLSTSRISQLHSKAIFKLR 247


>gi|284041831|ref|YP_003392171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283946052|gb|ADB48796.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 112/242 (46%), Gaps = 17/242 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           KG  E + A+ ++V A   +V  VA +   R    +   DLI +G  GL+ A E+F+   
Sbjct: 18  KGTGERA-ARDDLVLAYSPIVKYVAGRVAARMPAHVDVADLISDGFKGLLDAVERFEPVR 76

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F  YA   ++ AI   +        +P  +R +  ++ R    ++ +++R PT  E+
Sbjct: 77  GVRFEAYADTRIRGAIFDGLRSLDW---VPRAVRAEAREIERATAELAMRLQRMPTDPEL 133

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIG----DEDTSHLGDFIEDKNAVSPLDSAIQ 606
           A  L+M    +   L+   +   ++L+ P G    D     L D + D +AV P   + +
Sbjct: 134 AGALSMSRRQLAASLQRVSDSRIVALDEPWGPVLADGRPVALLDTLPDLDAVDPAADSDE 193

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               E     +  L  RE+ VL +R+    + D TL ++G+   ++  R  Q+  KA  +
Sbjct: 194 TERSERIGAAVRQLPAREQVVLGLRY----HHDLTLLQIGEVLGISESRTSQLHTKAALQ 249

Query: 667 LK 668
           LK
Sbjct: 250 LK 251


>gi|332284050|ref|YP_004415961.1| RNA polymerase sigma factor for flagellar operon [Pusillimonas sp.
           T7-7]
 gi|330428003|gb|AEC19337.1| RNA polymerase sigma factor for flagellar operon [Pusillimonas sp.
           T7-7]
          Length = 255

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 102/210 (48%), Gaps = 23/210 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G +GL+ A  ++      +F TYA+  ++ A+   +  Q     +P  +R K   
Sbjct: 35  DLMQAGMMGLLDAIRRYQQTADAQFETYAVTRIRGAMLDELRSQDW---LPRSVRSKTRN 91

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMP-------VEGVRKVLKITKEPISLETPIGDED 584
           + +    +++++ R P   EIA+++ +P       +E  R V  +  E ++ +   G++ 
Sbjct: 92  IEQAIHTLTHRLLRAPAESEIAEEMGVPLPEYQQLLEEARGVQILHYEDLAGQ---GEDA 148

Query: 585 TSHLGDFIEDKNAV------SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            S L    ED++A       +PL+  +   LR      + +L  RE+ +L ++F   +N 
Sbjct: 149 GSSLDRSSEDESATQAAHWSNPLNQLVSKGLRRALVEAIKALPEREQLLLSLQFEQDLNQ 208

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +E+G    +T  R+ Q+ ++A+ +++
Sbjct: 209 ----KEIGLVMGITEGRVSQLRSQAVARIR 234


>gi|78064851|ref|YP_367620.1| flagellar biosynthesis sigma factor [Burkholderia sp. 383]
 gi|77965596|gb|ABB06976.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia sp.
           383]
          Length = 244

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 98  VEHAVHQVEQNLGRSASETEIAQHLNMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 153

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRVDHADPLSALLDEHLREALVEAIERLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|54025772|ref|YP_120014.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017280|dbj|BAD58650.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 281

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/225 (24%), Positives = 97/225 (43%), Gaps = 31/225 (13%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++   L L   +A++++ RG  F DL Q   +GL++A ++FD   G  F  +A+  +
Sbjct: 50  REHIIGLCLPLADHIARRFSGRGEAFDDLHQTARLGLVQAVDRFDVRRGSSFLAFAVPTI 109

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-VEGV 563
              + R   D +  +R+P   ++    +     ++S +  R PT  EIA +L +  VE  
Sbjct: 110 MGEVRRHFRDHTWALRVPRRAKELQAMIGPATEKLSQRHGRMPTAREIAAELDVELVEVT 169

Query: 564 RKVLKITKEPISLETPIGDEDTSHLG--------------DFIEDKNAVSPLDSAIQANL 609
           R ++       +    +G +D  ++G                +ED  AV PL        
Sbjct: 170 RALVAANAYSTNTLHAVGRDDDGNVGLSIGDSLGTEEPCYRLMEDAMAVRPL-------- 221

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
                  +A+L  RE +VL  RF   +      E +G  Q  V+R
Sbjct: 222 -------IAALPERERQVLIWRFYDSLTQSQIAERLGVSQMQVSR 259


>gi|78217835|gb|ABB37184.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 227

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 53/198 (26%), Positives = 93/198 (46%), Gaps = 12/198 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G +GLM+A  KF   LG KF TYA   ++ A+   +         P  +R ++  
Sbjct: 28  ELISAGTLGLMEAFGKFQPKLGIKFDTYAENRIRGAMLDELRRLDW---FPRSLRQRVRL 84

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-D 590
           +  T  R+ ++  R P+ EE+ K   +  + +R  L+  +  + +      E  +  G D
Sbjct: 85  LEDTINRLEHEKGRRPSEEELQKATGLEEKDLRSGLEALQNHLCISLDAIQETFAADGRD 144

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E +    P  S     L E    ++  LTPRE+ VL + +   +N   T E +G    
Sbjct: 145 HLEGE----PFHSTATQELIERIASLIDQLTPREKLVLSLYYSDELNMRETAEVMG---- 196

Query: 651 VTRERIRQIEAKAIRKLK 668
           VT  R+ Q+ ++A+ +L+
Sbjct: 197 VTEGRVSQLHSQALNRLR 214


>gi|195953358|ref|YP_002121648.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195932970|gb|ACG57670.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 245

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 114/238 (47%), Gaps = 22/238 (9%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNR-------GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           I KKE  E  +   I + KK   +        + + DL+  G IGL+ A +  D     +
Sbjct: 11  IEKKEQREKKILEYIPLVKKICGKMSRNLPPSVDYNDLVSNGIIGLINAIDHLDELKNPE 70

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
             +Y    VK AI   +       R   ++RDK HK+    R   N+ +REPT EEI+  
Sbjct: 71  --SYIKIRVKGAIYDYLRSLDFGSR---NIRDKEHKIKEIIRTFQNEYQREPTDEEISSI 125

Query: 556 LAMPVEGVRKVL-KITKEPI-SLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           L   +E  +  L KI+   + SLE     I +E+ S   +F+   +  +P + A++++L 
Sbjct: 126 LGESLEEYQNSLYKISFSYLQSLEDMVYKITEENESSYDNFV-ISSIETPEEYAVKSDLA 184

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     +  L  RE+ VL++ F      +  ++EV +   V+  R+ QI+++A+ KL+
Sbjct: 185 EKLKEAIDKLEEREKLVLQLLFY----EEFGIKEVAEILNVSLSRVSQIKSQALEKLR 238


>gi|229149313|ref|ZP_04277550.1| RNA polymerase sigma-B factor [Bacillus cereus m1550]
 gi|229154668|ref|ZP_04282783.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 4342]
 gi|228628616|gb|EEK85328.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 4342]
 gi|228634127|gb|EEK90719.1| RNA polymerase sigma-B factor [Bacillus cereus m1550]
          Length = 203

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENASDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|119897398|ref|YP_932611.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
 gi|119669811|emb|CAL93724.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 256

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/240 (22%), Positives = 114/240 (47%), Gaps = 21/240 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + E ++ K  +V A   LV  +A +   +    ++  DLIQ G +GL+ A  +++  LG 
Sbjct: 3   DAEGNLDKDHLVVAYAPLVKRIAFQLMAKLPASVEVEDLIQNGMMGLLDAIGRYEEGLGA 62

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F TYA+  V+ A+   + +      +P  +R  + ++      +  +  R P+  E+A+
Sbjct: 63  QFETYAVQRVRGAMLDGLRENDW---LPRSLRRDMRRIESAIHVLEQQHGRPPSETELAE 119

Query: 555 KLAMPVEGVRKVLKITK--EPISLETPIGDEDTS----HLGDFIEDKNAVSPLDSAIQAN 608
            L +P+   +++L+  +  + +  E     E       HLG      +  +P +    A+
Sbjct: 120 SLGVPLPEYQRMLQDARGHQLVYFEDFTDGEGEDFLDRHLG-----AHESNPAELLEDAD 174

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R    R +  L  RE+ V+ + +   +N    L E+G+   VT  R+ Q+ ++A+ +L+
Sbjct: 175 MRANLIRAIDDLPEREKLVMALYYEEELN----LREIGEVLGVTESRVCQLHSQAVARLR 230


>gi|307717612|gb|ADN88859.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 93/193 (48%), Gaps = 8/193 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 16  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 76  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIAYFIGVTEEEV 135

Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLAS 619
            + +++ K  + +S++  I  D D    G  I   + V   D   +  N R    +VL  
Sbjct: 136 LEAMEMGKSYQALSVDHSIEADSD----GSTITLLDVVGGTDDGFERVNQRMLLEKVLPV 191

Query: 620 LTPREERVLRMRF 632
           L  RE+ +L+  F
Sbjct: 192 LDEREQMILQYTF 204


>gi|241763670|ref|ZP_04761720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax delafieldii
           2AN]
 gi|241367145|gb|EER61511.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax delafieldii
           2AN]
          Length = 246

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 96/206 (46%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL  A  +++   G +F T+A   ++ A+   + +     R     R     
Sbjct: 48  DLIQVGMMGLADALSRYEATQGVQFETFATQRIRGAMLDELREGDWMSRSS---RKSQKD 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE-TPIGDE-DTSH 587
           +  + RR+  K+ R P   EIA  + M +   + +L   +  + + LE    GDE D   
Sbjct: 105 IEHSLRRLEQKLGRPPLESEIAADMGMSLAEYQSLLGKVRGTQLVYLEDMTHGDEGDEGF 164

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D +A  PL+      LR +  + + SL  RE+ ++ M +   MN    L+E+  
Sbjct: 165 LDRHVADSSA-DPLELLRDHRLRASLVQAIQSLPEREQHIMGMYYEHDMN----LKEIAA 219

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  R+ Q+ +++I +L+   RS
Sbjct: 220 VLGVTESRVCQLHSQSIARLRAKMRS 245


>gi|318066915|emb|CBY89072.1| RNA polymerase sigma70 factor [Chromohalobacter sarecensis]
          Length = 369

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 35/45 (77%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P
Sbjct: 21  TTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLP 65


>gi|325290052|ref|YP_004266233.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965453|gb|ADY56232.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 248

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 98/243 (40%), Gaps = 58/243 (23%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E   A+ +++E NLRLV  + KKY   G    DLI  G IGL+K    F+   G + +
Sbjct: 59  EIEVENARNKLIEHNLRLVAHLVKKYDGTGEDSDDLISIGTIGLIKGINTFNTDKGTRLA 118

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   ++  I              +++R                               
Sbjct: 119 TYAARCIENEIL-------------MYLR------------------------------- 134

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETT 613
                    LK T+  +S+  PIG +   +  + I+    D +A+S  D       +   
Sbjct: 135 --------TLKKTRGEVSMYDPIGTDKEGNSINLIDILGTDPDAIS--DQVESEFEQRIV 184

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  LT RE  VL++RFG+  +   T  E+ +   ++R  + +IE KA++KL    + 
Sbjct: 185 LEKLKCLTKRERMVLQLRFGLLNSPKKTQREIARMLGISRSYVSRIEKKAVQKLTEEMKE 244

Query: 674 KKL 676
            +L
Sbjct: 245 HRL 247


>gi|302872543|ref|YP_003841179.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302575402|gb|ADL43193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 246

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 117/230 (50%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 19  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K AI   +  Q     +P  +R K  ++ +    +  +  R PT +E+AK++ + + 
Sbjct: 79  TRIKGAIIDCVRSQDF---LPRSIRQKAKEIEKAYIEIERE-GRTPTDDEVAKRVGLSIS 134

Query: 562 GVRKVL-KITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLA 618
            ++K+  KI+   I SL++ +     S +G     ++ VS  +  I+   L+E   + + 
Sbjct: 135 ELQKLQEKISSGMIVSLDSFLEQNYESKIGGL---EDFVSQPEHFIENEELKEVLRQQID 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 192 NLLENERMVIVLYY----YEELSIKEIAKILGVSESRVSQLHTRALLKLR 237


>gi|229068653|ref|ZP_04201951.1| RNA polymerase sigma-B factor [Bacillus cereus F65185]
 gi|229078304|ref|ZP_04210868.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-2]
 gi|229177534|ref|ZP_04304912.1| RNA polymerase sigma-B factor [Bacillus cereus 172560W]
 gi|228605896|gb|EEK63339.1| RNA polymerase sigma-B factor [Bacillus cereus 172560W]
 gi|228704979|gb|EEL57401.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-2]
 gi|228714400|gb|EEL66277.1| RNA polymerase sigma-B factor [Bacillus cereus F65185]
          Length = 203

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      ++++ +R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|15834951|ref|NP_296710.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270285123|ref|ZP_06194517.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270289144|ref|ZP_06195446.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Weiss]
 gi|301336518|ref|ZP_07224720.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum
           MopnTet14]
 gi|7190373|gb|AAF39194.1| RNA polymerase sigma factor, sigma-70 family [Chlamydia muridarum
           Nigg]
          Length = 253

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 110/241 (45%), Gaps = 39/241 (16%)

Query: 448 MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++EA L LV +VA +  +     ++  DL   G  GL++A E+FD     +F +YA++ +
Sbjct: 25  LIEAYLPLVKNVAHRLASGMPSHVKIEDLYASGVEGLVRAVERFDPEKSKRFESYALFII 84

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           K AI   +  Q     +P  +  + +++      +   + +EPT  ++ + L +  + + 
Sbjct: 85  KAAIIDDLRKQDW---VPRSVYQRANRLADAMDALRQTLGKEPTDGDLCEYLNISQQELS 141

Query: 564 ------RKVLKIT----------KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
                 R  L ++           E ++LE  I DE   +  D I  K A+S L      
Sbjct: 142 HWFSSSRPALVLSLNDDFSCQDEDEGLALEERIADERAENGYDVIRKKEAISIL------ 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 T  L SL  +E +V+ + +      D  L+E+GK   V+  R+ QI +KA+ KL
Sbjct: 196 ------TEALLSLDEKERQVMALYY----YDDLVLKEIGKILGVSESRVSQIHSKALLKL 245

Query: 668 K 668
           +
Sbjct: 246 R 246


>gi|255527843|ref|ZP_05394691.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296185444|ref|ZP_06853854.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
 gi|255508454|gb|EET84846.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296050278|gb|EFG89702.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
          Length = 233

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 99/225 (44%), Gaps = 49/225 (21%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +AK  +VE NLRLV  + KKY+  G +  DLI  G +GL+KA + FD   G + +TYA  
Sbjct: 49  LAKNILVERNLRLVAHIVKKYSYPGKEVDDLISIGTVGLIKAIDSFDASKGTRLATYAAK 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++  I   I +   T +  ++++D I                            +  EG
Sbjct: 109 CIENEILMLIRNNKKT-KGEIYLQDPI---------------------------GIDKEG 140

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                    E   L+    DED+            +  ++S IQ  +++   ++   L  
Sbjct: 141 --------NEISLLDVLSSDEDS-----------IIEIVESKIQ--VKKLYDKMNTCLAE 179

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE+ V+ MR+G+      T  E+ K   ++R  + +IE +A++KL
Sbjct: 180 REKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKRALKKL 224


>gi|318041689|ref|ZP_07973645.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0101]
          Length = 263

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 51/89 (57%), Gaps = 1/89 (1%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +C  +  +  ++ ANL LV  VA++ + R G  F DL QEG  GL+KA E+FD   G+  
Sbjct: 23  QCRTTANRNAVIHANLPLVWRVARQESQRSGHSFDDLTQEGCFGLIKAVERFDPGRGHSL 82

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHM 525
           ST A+ W++ AI   + D+S  I    H+
Sbjct: 83  STAAVPWIRGAIRHYLRDRSHPISGSHHL 111


>gi|6952813|gb|AAF32414.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus]
          Length = 245

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 16  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   + D      +P  +     ++ +    +   + R+PT  E+A  L M +
Sbjct: 76  GIRIRGAM---LDDMRKGDWVPRSVHKNNREINQAVAELEGVLNRDPTDSEVAAHLGMSL 132

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P       + R+     +
Sbjct: 133 DQYHSALT----DINCSRLVGIEDLGVSDDVISPADETDDSNPFKGVADESFRKALVESI 188

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G    V+  R+ QI ++A+++L+
Sbjct: 189 KQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQAMQRLR 235


>gi|318066909|emb|CBY89069.1| RNA polymerase sigma70 factor [Chromohalobacter marismortui]
          Length = 367

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 40/60 (66%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D   D
Sbjct: 21  TTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLEAYDATQD 80


>gi|168182618|ref|ZP_02617282.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
 gi|182674200|gb|EDT86161.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
          Length = 234

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 106/242 (43%), Gaps = 52/242 (21%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E ++ +  ++KG+   ++AK  +VE NLRLV  + KKY+  G    DLI  G +GL+KA 
Sbjct: 35  EEKYYLDRLKKGD---ALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGLIKAI 91

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD   G + +TYA   ++  I   I +   T +  V+++D I                
Sbjct: 92  DSFDNSKGTRLATYAARCIENEILMLIRNNKKT-KGEVYLQDPI---------------- 134

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                           GV K        ISL   +  ++ S + + +  K  V  L   I
Sbjct: 135 ----------------GVDK----EGNEISLMDILSSDEDSII-EIVSTKIEVKKLYGKI 173

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LR            RE++V++MR+G+      T  E+     ++R  + +IE KA++
Sbjct: 174 DTCLR-----------GREKKVIQMRYGLKDGRHRTQREIAGILNISRSYVSRIEKKALK 222

Query: 666 KL 667
           KL
Sbjct: 223 KL 224


>gi|239934574|emb|CAR94601.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 223

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 44/69 (63%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREII 185
            T  L +II
Sbjct: 61  QTVRLADII 69


>gi|297561355|ref|YP_003680329.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845803|gb|ADH67823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/218 (23%), Positives = 98/218 (44%), Gaps = 11/218 (5%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV  +A++Y  RG    DL Q   +GL+KA   F+   G  F +Y +  V   I R   D
Sbjct: 64  LVNKLARRYNGRGEPLDDLQQTAMLGLVKAIHGFNPDRGKPFISYLLPTVTGEIKRHFRD 123

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-- 572
            +  +R+    ++   K+ +          R PT  E+++++ +P   V +++++++   
Sbjct: 124 HTWAVRVSRRHQENRIKLRQALNDFQQAHARTPTVHELSEEMGLPEAEVGELIQVSESYR 183

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +SL+ P   +     G  +ED        L+  +Q   RE+    LA L  RE  +L +
Sbjct: 184 SLSLDAPDTSDSDGQEGTRLEDHLGSEDEGLELVVQ---RESLKPALARLPEREREILML 240

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RF      DHT  E+      ++  + ++    + +L+
Sbjct: 241 RF----FGDHTQSEIADCLGYSQMHVSRLLNGVLGQLR 274


>gi|229126412|ref|ZP_04255427.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-Cer4]
 gi|228656992|gb|EEL12815.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-Cer4]
          Length = 203

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPRIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|107024379|ref|YP_622706.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia AU
           1054]
 gi|116688295|ref|YP_833918.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           HI2424]
 gi|170731608|ref|YP_001763555.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|105894568|gb|ABF77733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia AU 1054]
 gi|116646384|gb|ABK07025.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia HI2424]
 gi|169814850|gb|ACA89433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 243

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 97  VEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 152

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYRVDHADPLSALLDDHLREALVEAIERLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVLEVSESRVCQLHSQAVARLR 230


>gi|311071144|ref|YP_003976067.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
 gi|310871661|gb|ADP35136.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
          Length = 262

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ +V+    LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQETLVQVYTNLVEVLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPVVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++      ++ + +R P  EEIA+ L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDTLTTETQRSPKVEEIAEYLDVSEEE 148

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      D   + N +     VL
Sbjct: 149 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----DGYERVNQQMMLKSVL 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 204 HVLSEREKQIIDLTY----IQNKSQKETGDILGISQMHVSRLQRKAVKKLR 250


>gi|312876527|ref|ZP_07736510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796738|gb|EFR13084.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 246

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 117/233 (50%), Gaps = 23/233 (9%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 19  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE---PTPEEIAKKLAM 558
             +K AI   +  Q     +P  +R K  ++     +   +I+RE   PT +E+AK++ +
Sbjct: 79  TRIKGAIIDCVRSQDF---LPRSIRQKAKEI----EKAYVEIEREGKTPTDQEVAKRVGI 131

Query: 559 PVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTR 615
            V  ++K+ +       ISL++ +     S +G     ++ VS  +  I+   L+E   +
Sbjct: 132 SVNELQKLKERISSGMIISLDSFLEQNYESKIGGL---EDFVSQPEHFIENEELKEVLRQ 188

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KLK
Sbjct: 189 QIENLMENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLK 237


>gi|239934584|emb|CAR94606.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 230

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 37/52 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +M +L   P   Q ++
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIVIAKRIEEGVRELMHALAYWPGAVQQIL 52


>gi|261252375|ref|ZP_05944948.1| RNA polymerase sigma factor for flagellar operon [Vibrio orientalis
           CIP 102891]
 gi|260935766|gb|EEX91755.1| RNA polymerase sigma factor for flagellar operon [Vibrio orientalis
           CIP 102891]
          Length = 203

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 97/206 (47%), Gaps = 18/206 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH  +
Sbjct: 1   MQVEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHN 59

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +  +V +    +  ++ R+PT  E+A+++ + +E    +L      I+    +G ED   
Sbjct: 60  R--EVSQVIAILEGELNRDPTDAEVAQRMGISLEQYHVILT----DINCSRLVGIEDLGI 113

Query: 588 LGDFI-----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
             D I     ED N   P         R+     + +L  RE  VL + +   +N    L
Sbjct: 114 SEDSISPGDSEDDNL--PFKGVADEYFRKALVDSIKTLPEREALVLSLYYDEELN----L 167

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+G+   V+  R+ QI ++++++L+
Sbjct: 168 KEIGEVIGVSESRVSQILSQSMQRLR 193


>gi|239934576|emb|CAR94602.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 37/52 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   ++  L   P T Q ++
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGIYQVLKPLAHYPETTQLVL 52


>gi|114320145|ref|YP_741828.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226539|gb|ABI56338.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 242

 Score = 62.0 bits (149), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 60/221 (27%), Positives = 98/221 (44%), Gaps = 20/221 (9%)

Query: 455 LVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  +A     R    +Q  DLIQ G +GL++AA +FD   G  F TYA   ++ A+   
Sbjct: 25  LVKRIAHHLAGRLPPSVQLDDLIQAGMVGLLEAARQFDPGQGASFQTYAGIRIRGAMLDE 84

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           I     T R  VH + +   V    R + ++  R+    E+A++L + ++   ++L+   
Sbjct: 85  IRRLDWTPR-SVHRKGR--SVAEAIRAVEHRTGRDARDHEVAQELGITLDEYHQILQDVS 141

Query: 572 E----PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                 I  E P   E     GD  E    ++  D   Q  L E   R    L  RE+ +
Sbjct: 142 TSRIFSIDQEDPATGEPHQLPGDHPEPFAEIT--DEGFQRALAEAIRR----LPEREQLI 195

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + + +   +N    L E+G+   VT  R+ QI  + + KL+
Sbjct: 196 MALYYDEELN----LREIGEVLNVTESRVSQIHGRIVVKLR 232


>gi|188586048|ref|YP_001917593.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350735|gb|ACB85005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 250

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 103/218 (47%), Gaps = 20/218 (9%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI  G IGL+ A +KFD      F  YA   ++ AI   +        +P ++R
Sbjct: 43  GLNRDDLISFGVIGLIDAIKKFDINRNVPFEAYANIRIRGAILDGLRKFDF---VPRNLR 99

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI-GDE 583
           +++  +    R++  K+ R PT  E+A ++++    + K+ + T    P  L   I  +E
Sbjct: 100 EEMKTLHSEYRKLEQKLGRTPTNNELAYQMSISEAELDKLWQATNCVIPSYLSDYITAEE 159

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASLTPREERVLRMRFGIGMNT 638
               L D   D N+  P     Q+ + E TT+      + +L  +E+ VL + +      
Sbjct: 160 GELTLEDIYPDSNSPDP-----QSRIDEKTTKQELGQAIDTLPQKEKLVLSLYY----YE 210

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + TL+E+ K   +T  RI Q+ +KA+ +L+     KKL
Sbjct: 211 ELTLKEIAKILELTESRISQLHSKAVLRLRGKLAKKKL 248


>gi|167769451|ref|ZP_02441504.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
 gi|167668419|gb|EDS12549.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
          Length = 234

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 110/249 (44%), Gaps = 57/249 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R  +  + +G+ EA   K  ++E NLRLV  + KKY +      DLI  G IGL
Sbjct: 28  LSAKEERECLEGIARGDEEA---KTRLIEHNLRLVAHIIKKYYSAFKDQDDLISIGTIGL 84

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F    G +F+TYA        +R I ++     + +H R+K             
Sbjct: 85  IKAVSTFKPEKGTRFATYA--------SRCIENE-----VLMHFRNK------------- 118

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSP 600
                       KK A  V           +PI  +    D ++  L D + ED N V  
Sbjct: 119 ------------KKSAQDV--------YISDPIDTDK---DGNSLTLQDIMAEDDNIVDC 155

Query: 601 LDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +D  I++   E   R +  +L  RE +++ MR+G+G     T  EV K+  ++R  + +I
Sbjct: 156 IDLRIKS---EQLYRFIEGALDERERQIIIMRYGLGGTRSLTQREVAKKLDISRSYVSRI 212

Query: 660 EAKAIRKLK 668
           E KAI  L+
Sbjct: 213 EKKAISILR 221


>gi|268612026|ref|ZP_06145753.1| anti-sigma F factor [Ruminococcus flavefaciens FD-1]
          Length = 219

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 95/202 (47%), Gaps = 11/202 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+   E NL LV   A ++ NRG+++ +L   G +GL+KA + FD   G +FSTYA+  +
Sbjct: 6   KRPAAEENLGLVHLCANRFRNRGIEYEELYSAGCVGLLKAVKAFDPDRGAQFSTYAVPVI 65

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D    IR+   +++   ++ +       +  REPT  E+A         V 
Sbjct: 66  LGEIRRLFRDGG-AIRVSRSLKELSMRIQKMCTDFRQREMREPTISELAVISGESEADVS 124

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L +++  +SL    GD+D   +     D    +P D AI   L     ++++ L  R+
Sbjct: 125 EALCVSQPMLSLTA--GDDDEGQI-----DIPTDAP-DEAIVDVL--ALRQIMSGLDSRD 174

Query: 625 ERVLRMRFGIGMNTDHTLEEVG 646
             +L +R+   +    T + +G
Sbjct: 175 RALLELRYFRCLTQTKTAQALG 196


>gi|228957370|ref|ZP_04119129.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229028783|ref|ZP_04184888.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228732530|gb|EEL83407.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228802319|gb|EEM49177.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 203

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|93007303|gb|ABE97152.1| Sigma-70 [Pasteuria ramosa]
          Length = 241

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 101/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 64  LIERNLRLVVYIARKFENTGIHIEDLVSTGTIGLIKAVNTFDPEKKIKLATYA------- 116

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                 +    R +NKI+ E + +E    L +  +G     
Sbjct: 117 -SRCIENE-----------------ILMFLRRNNKIRSEISFDE---PLNIDWDG----- 150

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                 + L   +G E+ +   D IED+     L +A            L+ L+ RE R+
Sbjct: 151 ----NELLLSDVLGTENDTIYRD-IEDEVDKEILRTA------------LSMLSDRERRI 193

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+G   + T ++V     +++  I ++E K I +L+
Sbjct: 194 VILRFGLGGGEEKTQKDVADLLGISQSYISRLEKKVIGRLR 234


>gi|172058807|ref|YP_001815267.1| RNA polymerase sigma factor SigB [Exiguobacterium sibiricum 255-15]
 gi|171991328|gb|ACB62250.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Exiguobacterium
           sibiricum 255-15]
          Length = 265

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/217 (24%), Positives = 114/217 (52%), Gaps = 10/217 (4%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV ++A+K++       DL+Q G IGL+ A  +FD   G  F ++A+  +   I R I D
Sbjct: 42  LVEALARKFSRGRPIHDDLVQVGMIGLLAALRRFDKEFGRSFESFAVPTIIGEIKRFIRD 101

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   K+ +    ++ +++R P  +EIA +L +  E V + L++ K  +
Sbjct: 102 KTWSVHVPRRIKELGPKIKKAVEELTTELQRSPRIDEIAARLEVSEEEVLETLEMGKSYQ 161

Query: 573 PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            +S+++ I  D++ S +       N  +  DS  Q  + E   +  A LT RE  +L   
Sbjct: 162 ALSVDSSIEADQEGSTVTLLDLVGNQENGYDSVDQKLILE---KAFAVLTDRERSILECA 218

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   M+     +E G+   +++  + +++ +A++KL+
Sbjct: 219 YYRNMSQ----KETGELLGISQMHVSRLQRRALQKLR 251


>gi|46581631|ref|YP_012439.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120601210|ref|YP_965610.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           vulgaris DP4]
 gi|46451054|gb|AAS97699.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120561439|gb|ABM27183.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           vulgaris DP4]
 gi|311235273|gb|ADP88127.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio vulgaris RCH1]
          Length = 265

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 102/222 (45%), Gaps = 10/222 (4%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
            +R +    K    R ++  +LI  G +GLM+A  KF   LG +F TYA   ++ A+   
Sbjct: 46  KIRFLALRLKAKLPRNVELGELISAGTLGLMEALGKFKPQLGIRFETYAESRIRGAMLDE 105

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +         P  +R ++ ++    +R+ ++  R  T E++ K   +  + VR  L+  +
Sbjct: 106 LRRLDW---FPRSLRQRVRQLDEAMQRIEHETGRRATEEDLQKATGLDEKDVRLGLEALQ 162

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             + L      +  +  G    D +   P+ +A    L E    ++  LTPRE+ VL + 
Sbjct: 163 NQLCLSLEAMQDSLAGEGGPQSDAD---PMQTAATQELIERVASLIDELTPREKLVLSLY 219

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +   +N   T E +G    +T  R+ Q+ ++A+ +L+   R+
Sbjct: 220 YSDELNMRETAEVMG----ITEGRVSQLHSQALGRLRREFRN 257


>gi|254228448|ref|ZP_04921874.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262393605|ref|YP_003285459.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
 gi|151939036|gb|EDN57868.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262337199|gb|ACY50994.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
          Length = 244

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   + D      +P  +     ++ +    +  ++ R+PT  E+A  L M +
Sbjct: 75  GIRIRGAM---LDDMRKGDWVPRSVHKNNREINQAIAELEGELNRDPTDSEVATHLGMTL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P       + R+     +
Sbjct: 132 DQYHSALT----DINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVADESFRKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  RE  VL + +   +N    L+E+G    V+  R+ QI ++A+++L+
Sbjct: 188 KQIPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQAMQRLR 234


>gi|239934578|emb|CAR94603.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 233

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 44/69 (63%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREII 185
            T  L +II
Sbjct: 61  QTVRLADII 69


>gi|167462462|ref|ZP_02327551.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B)
           [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322381881|ref|ZP_08055835.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154269|gb|EFX46591.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 260

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/215 (21%), Positives = 106/215 (49%), Gaps = 12/215 (5%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++  K   NR   + DL Q G + L+K  ++FD   G +F  Y M  +   +   + D+S
Sbjct: 42  MAAGKMSRNRPDLYEDLYQVGQMSLLKLFKQFDPSHGVQFEAYMMKSIIGHMKNYLRDKS 101

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPI 574
             I++P  +++K  ++ +    ++ K++R P  +EIA +L +  E   ++L  +     +
Sbjct: 102 WYIQVPRRIKEKGFQIQQAIDSLTMKLERSPNVDEIANELGLSTEETIEILAGRECYHYV 161

Query: 575 SLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           SL+ P+  +E+ S +GD +  +      D  +  + R      +  L P E++ L + + 
Sbjct: 162 SLDMPLSTEENGSTIGDVLGIQE-----DEYLHVDNRLDLQEAMEHLKPEEKKALILAYI 216

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            G    ++   + ++  +++  + +++ +A+ KL+
Sbjct: 217 DG----YSQRTIAQELDISQMSVSRMQRRALSKLR 247


>gi|146277655|ref|YP_001167814.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
 gi|145555896|gb|ABP70509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 239

 Score = 62.0 bits (149), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 62/255 (24%), Positives = 113/255 (44%), Gaps = 35/255 (13%)

Query: 436 KGECEASIAKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E +   + +V A++ LV  +A        R ++  DLIQ G +GL+ A+ +++   
Sbjct: 5   RGYAEQAQTPERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQIGYMGLVDASRRYEPRD 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+ YA   ++ +I   +   S   R  + M+ K+   V   +R+ +++ R P   E+
Sbjct: 65  GVTFAAYAAIRIRGSIMDFLRSNSALCRTTILMQQKVKAAV---QRLESRLMRAPETPEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV------SPLDSAIQ 606
           A +L MPV   +  L                 T+ L +  +D++++      S  D    
Sbjct: 122 AAELGMPVGEYQDWL----------AQFAGSQTASLDEVYDDQSSLFQGSEPSAEDRLQA 171

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +R    + L  +  RE  +L++ F   MN    + EV +   VT  R+ QI+  AI  
Sbjct: 172 TQMRGLLRQALGKMPEREALLLQLIFVEEMN----VYEVAEILGVTTGRVSQIKKAAI-- 225

Query: 667 LKHPSRSKKLRSFLD 681
                  ++LR F+D
Sbjct: 226 -------ERLRGFID 233


>gi|258514353|ref|YP_003190575.1| sporulation sigma factor SigE [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778058|gb|ACV61952.1| RNA polymerase, sigma 28 subunit, SigE [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 241

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 103/222 (46%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 64  LIERNLRLVVYIARKFENTGISIEDLVSIGTIGLIKAVNTFDPAKKIKLATYA------- 116

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NK + E + +                 
Sbjct: 117 -SRCIENE-----ILMYLRR------------NNKTRSEVSFD----------------- 141

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREER 626
               EP++++    D +   L D +  +N V  +   I+  + R+     L  L+ RE R
Sbjct: 142 ----EPLNID---WDGNELLLSDVLGTENDV--IYKYIEEEVDRKLLHLALQKLSGRERR 192

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +RFG+   ++ T +EV     +++  I ++E + I++LK
Sbjct: 193 IMELRFGLNNGSEKTQKEVADMLGISQSYISRLEKRIIKRLK 234


>gi|318066985|emb|CBY89107.1| RNA polymerase sigma70 factor [Kushneria avicenniae]
          Length = 373

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 32/62 (51%), Positives = 42/62 (67%), Gaps = 4/62 (6%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+ EGEI IAKRIE G   +M++L   P    +++    E  D
Sbjct: 21  TTDPVRMYMREMGTVELLTLEGEIEIAKRIEEGTREVMSALASLPGAVDSIL----EAYD 76

Query: 177 GT 178
           GT
Sbjct: 77  GT 78


>gi|291538524|emb|CBL11635.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis XB6B4]
          Length = 254

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 101/227 (44%), Gaps = 28/227 (12%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +R+V      Y    +++ DL+  G  GL+ A +KFD     KF TYA   ++ +I   I
Sbjct: 33  VRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDRGKDVKFETYASLRIRGSILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                   IP  +R K  K+    +++  K  R  + EEIA++L +  E          E
Sbjct: 93  RKMDW---IPRTVRQKRKKIEEAIKQIETKTGRNASDEEIAQELGIGEE----------E 139

Query: 573 PISLETPIGDEDTSHLGDFIE-----------DKNAVSPLDSAIQANLRETTTRVLASLT 621
               +T +   +   L +F+E           + + + P +S  +  L++     L  LT
Sbjct: 140 LNDWQTQLNVTNVISLNEFVEQGGEPVMDAKNNSHFIQPEESVQEEELKKVLMESLELLT 199

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E++V+ + +      D TL+E+     V+  R+ Q+  KA+ K++
Sbjct: 200 EKEKKVILLYY----YEDMTLKEISSILEVSESRVSQLHTKALLKMR 242


>gi|167750689|ref|ZP_02422816.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|167656368|gb|EDS00498.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|291558233|emb|CBL35350.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 221

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 99/215 (46%), Gaps = 10/215 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            +  +  LV S+A ++ NRG+++ +L   G +GL+KA   FD   G KFSTYA+  +   
Sbjct: 9   FITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D   T+++   +++   K+ R  R    K   EP    +A+KL +  E     L
Sbjct: 69  IKQLFRDGG-TVKVSRSLKELSLKICRL-RDELIKNGEEPHISVLAEKLGITPEEASLAL 126

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             +  P+SL +   +E+     D   +      LD   +  LR+  +R    L P + R+
Sbjct: 127 GASLPPVSLSSYDDEENDEGSFDLPVEPEQPKALD---RMALRQLVSR----LEPLDRRL 179

Query: 628 LRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEA 661
           + +R+        T E +G  Q  V+R   + +E 
Sbjct: 180 IILRYSEECTQSRTAEILGMTQVQVSRREKKILEG 214


>gi|116625262|ref|YP_827418.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116228424|gb|ABJ87133.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 255

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 95/209 (45%), Gaps = 11/209 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL  A  K+D      F +YA   +K AI  S+       R    +R +  +
Sbjct: 49  DLIHAGVMGLFDAVTKYDGDKNVAFHSYAKHRIKGAILDSLRQLDWASR---DLRRRQKQ 105

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL--ETPIGDEDTSHLG 589
           V    R +  K+ R P   EIA+++ + +   R+ ++I    + L   TP  D+D     
Sbjct: 106 VESVTRDLGVKLGRSPHDSEIAEQMGVGLARWRQ-MQIEMRTVGLVSATPNPDQDRERAQ 164

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           +F    N + P     Q  L  T  R + +L  R ++V+ + +      D T++E+G+  
Sbjct: 165 EFPAKPN-LQPDRMCEQRQLESTLARAIGTLPLRYQKVVFLYY----TNDLTMKEIGEVL 219

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            V   R+ QI   A++K+     S+ +RS
Sbjct: 220 GVNESRVSQIHKIALKKMAGVLESEGIRS 248


>gi|222528793|ref|YP_002572675.1| sporulation sigma factor SigE [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455640|gb|ACM59902.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 244

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 105/226 (46%), Gaps = 54/226 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK +VE NLRLV+ +A+++ N  +   DL+  G IGL+KA   ++     K +TYA    
Sbjct: 64  KKLLVERNLRLVVYIARRFENTKINLEDLVSIGTIGLIKAINTYNPNKNIKLATYA---- 119

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
               ++ I ++                ++   RR SN            KKL + ++   
Sbjct: 120 ----SKCIENE----------------ILMFLRRNSN------------KKLELSID--- 144

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                  EP++++    D +   L D +  + +   + ++S+++   RE   R +  L  
Sbjct: 145 -------EPLNVD---WDGNELLLSDVLGTDTEEIYNRIESSVE---REALLRAIQKLPS 191

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG G   + T +EV     +++  I ++E K I +LK
Sbjct: 192 REKKIVELRFGFGDGGEKTQKEVADMLGISQSYISRLEKKIITRLK 237


>gi|148380498|ref|YP_001255039.1| sporulation sigma factor SigK [Clostridium botulinum A str. ATCC
           3502]
 gi|170759231|ref|YP_001787857.1| sporulation sigma factor SigK [Clostridium botulinum A3 str. Loch
           Maree]
 gi|226949896|ref|YP_002804987.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|237795980|ref|YP_002863532.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
 gi|148289982|emb|CAL84095.1| RNA polymerase sigma-28 factor [Clostridium botulinum A str. ATCC
           3502]
 gi|169406220|gb|ACA54631.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A3
           str. Loch Maree]
 gi|226844119|gb|ACO86785.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|229261319|gb|ACQ52352.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
          Length = 234

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 106/242 (43%), Gaps = 52/242 (21%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E ++ +  ++KG+   ++AK  +VE NLRLV  + KKY+  G    DLI  G +GL+KA 
Sbjct: 35  EEKYYLDRLKKGD---ALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGLIKAI 91

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD   G + +TYA   ++  I   I +   T +  V+++D I                
Sbjct: 92  DSFDNSKGTRLATYAARCIENEILMLIRNNKKT-KGEVYLQDPI---------------- 134

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                           GV K        ISL   +  ++ S + + +  K  V  L   I
Sbjct: 135 ----------------GVDK----EGNEISLMDILSSDEDSII-EIVSTKIEVKKLYGKI 173

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LR            RE++V++MR+G+      T  E+     ++R  + +IE KA++
Sbjct: 174 DTCLR-----------GREKKVIQMRYGLKDGRPRTQREIAGILNISRSYVSRIEKKALK 222

Query: 666 KL 667
           KL
Sbjct: 223 KL 224


>gi|212639647|ref|YP_002316167.1| sporulation sigma factor SigE [Anoxybacillus flavithermus WK1]
 gi|212561127|gb|ACJ34182.1| DNA-directed RNA polymerase specialized sigma subunit sigE
           [Anoxybacillus flavithermus WK1]
          Length = 239

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 108/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK++ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKVRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  ++ V   D  ++AN+ R    R L  L+ 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTEDDVITKD--LEANIDRNLLFRALDQLSD 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232


>gi|228951468|ref|ZP_04113574.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228808175|gb|EEM54688.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 203

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      ++++ +R P  +EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDRFQRSPKIKEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    E   R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEEAERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|302386724|ref|YP_003822546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197352|gb|ADL04923.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 246

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 105/235 (44%), Gaps = 68/235 (28%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKSELIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPNKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NK K E                 
Sbjct: 120 -----SRCIENE----------------ILMYLRR-NNKTKME----------------- 140

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                     +S++ P+    D +   L D +  E+      L++ ++ NL  T    ++
Sbjct: 141 ----------VSIDEPLNVDWDGNELLLSDILGTEEDVIYKDLETEVERNLLNTA---IS 187

Query: 619 SLTPREERVLRMRFGIGMNTDH-----TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+PRE +++ +RFG+   TD      T +EV     +++  I ++E K +++LK
Sbjct: 188 RLSPRERKIVELRFGL---TDEEGEEMTQKEVADLLGISQSYISRLEKKIMKRLK 239


>gi|302391216|ref|YP_003827036.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
 gi|302203293|gb|ADL11971.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
          Length = 235

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 103/225 (45%), Gaps = 52/225 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++E N+RLV  + KKY N  +   DLI  G+IGL+KA E +D     K +TYA   
Sbjct: 53  AKEVLIEHNMRLVAHIVKKYNNSNVDKEDLISIGSIGLIKAIETYDPSKKVKLATYA--- 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H R             + K  RE        KL  P+   
Sbjct: 110 -----SRCIENE-----ILMHFRQ------------NKKTNREV-------KLHDPLSSD 140

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTP 622
           ++               G+E T  L D  E D+ AV  L+    A   E     +  L+ 
Sbjct: 141 KE---------------GNEMT--LMDVYETDEEAV--LEKVEMALAEERLYDKIEGLSE 181

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE++V++MR+G+    + T  E+  +  ++R  + +IE +A++KL
Sbjct: 182 REQKVVKMRYGLNNVEELTQREIANKLGISRSYVSRIEKRALQKL 226


>gi|290962882|ref|YP_003494064.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652408|emb|CBG75541.1| probable sigma factor [Streptomyces scabiei 87.22]
          Length = 280

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 103/217 (47%), Gaps = 16/217 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ NRG    DL Q   +GL+KA ++F+   G  F +YA+  +
Sbjct: 51  RDELVRAWLPMAHRIASRFRNRGESLEDLRQVAAMGLVKAVDRFEPERG-AFESYAVPTI 109

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVE 561
              I R   D+  T+R+P  ++D  +K VR ARR    ++    EP+  +IA    +  E
Sbjct: 110 TGEIKRHFRDRMWTLRVPRRVQDLRNK-VRVARRELSQTSGGSAEPSVADIAALAGLTEE 168

Query: 562 ----GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
               G+  +   +   +  E   GD D  +L D +   +A    D  +    RE+  + L
Sbjct: 169 EVHAGMEALDSFSALSLDAEMASGD-DGYNLADTLGAPDAA--YDVVVD---RESVKQGL 222

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           + L  RE  +L MRF   M  +   + +G  Q  V+R
Sbjct: 223 SRLPERERAILYMRFFEDMTQNRIADRLGISQMHVSR 259


>gi|326319090|ref|YP_004236762.1| RNA polymerase sigma-28 subunit FliA/WhiG [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375926|gb|ADX48195.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 237

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 97/205 (47%), Gaps = 11/205 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +++   G +F T+A   ++ A+   + +     R     + +I  
Sbjct: 40  DLIQVGMIGLSEALSRYEVTQGVQFETFASQRIRGAMLDELREGDWMSRSSRKSQKEIEH 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE-TPIGDEDTSHL 588
            V    R+  K+ R P   EIA +L + +   + +L   +  + + LE    GD+D   L
Sbjct: 100 AV---TRLEQKLGRSPLESEIATELELSLAEYQSLLSKVRGTQLVYLEDMTHGDDDDGFL 156

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              + D +A  P+       LR +    + +L  RE++++ M +   MN    L+E+   
Sbjct: 157 DRHVAD-SAADPMAMLRDQRLRASLVAAIKALPEREQQIMGMYYEHDMN----LKEIAAV 211

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             VT  RI Q+ +++I +L+   RS
Sbjct: 212 LGVTESRICQLHSQSIARLRAKMRS 236


>gi|226329393|ref|ZP_03804911.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
 gi|225202579|gb|EEG84933.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
          Length = 137

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/65 (44%), Positives = 44/65 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++ ++LR VI VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W
Sbjct: 49  AARTLILSHLRFVIHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108

Query: 504 VKQAI 508
           +K  I
Sbjct: 109 IKAEI 113


>gi|289805024|ref|ZP_06535653.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 145

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 27/63 (42%), Positives = 42/63 (66%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           K ++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K
Sbjct: 39  KRLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIK 98

Query: 506 QAI 508
             I
Sbjct: 99  AEI 101


>gi|296332841|ref|ZP_06875301.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673187|ref|YP_003864859.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150121|gb|EFG91010.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411431|gb|ADM36550.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 262

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ +V     LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQETLVRVYTNLVDMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPVVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++     +++ + +R P  EEIA+ L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAEFLDVSEEE 148

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      D   + N +     VL
Sbjct: 149 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----DGYERVNQQMMLQSVL 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 204 HVLSDREKQIIDLTY----IQNKSQKETGDILGISQMHVSRLQRKAVKKLR 250


>gi|302387774|ref|YP_003823596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302198402|gb|ADL05973.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score = 61.6 bits (148), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 111/247 (44%), Gaps = 24/247 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E+V   + +V S++ +  +  L F    D++ EG + +M   EKFD  +  KF TY  
Sbjct: 26  KHELVMRYMYMVRSISIQMRDVYLSFAQVEDIVNEGVLTIMSGIEKFDPEMNVKFETYIS 85

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I      Q     IP  +R    ++      + N++ R P+P E A+ + + +E
Sbjct: 86  KRIRGMIIDMARKQDW---IPRSVRKNAKELDNAVMELCNRLGRFPSPRETAEYMNISLE 142

Query: 562 ------GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                 G   V  +    + LE    ++ T  L    E++    P D  +Q   ++   +
Sbjct: 143 KYQEALGKTNVYSVLSLDMVLEAGNDNKKTVQLPAVNENE---QPEDHYLQEEFKQILVQ 199

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            + +L   E++V+ + +   +N    ++E+ +   V+  RI QI + AI+KLK       
Sbjct: 200 AINNLKENEQKVISLYYMDELN----MKEIAQVMNVSEPRISQIHSNAIQKLK-----LY 250

Query: 676 LRSFLDG 682
           L  F++G
Sbjct: 251 LTGFING 257


>gi|229101713|ref|ZP_04232430.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
 gi|228681661|gb|EEL35821.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
          Length = 203

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 101/210 (48%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTRVLAS-----LTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    +T  R++ +     L   E+ V+   FG  +N   T
Sbjct: 114 VENASDGSSVARIESVGEVEQGYEQTERRLVLNDIFNVLNETEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAINKLKQAA 199


>gi|52080135|ref|YP_078926.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|52785509|ref|YP_091338.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|319646087|ref|ZP_08000317.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
 gi|52003346|gb|AAU23288.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus licheniformis ATCC 14580]
 gi|52348011|gb|AAU40645.1| SigE [Bacillus licheniformis ATCC 14580]
 gi|317391837|gb|EFV72634.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
          Length = 239

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 107/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +N +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTENDIITKD--IEANVDKKLLKKALEQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLVGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|331696322|ref|YP_004332561.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951011|gb|AEA24708.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 283

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 102/231 (44%), Gaps = 33/231 (14%)

Query: 445 KKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDW-CLGYKFSTYAMW 502
           + E++ A L +V  +A +++      + DL+Q G +GL+ A +++D    G     Y + 
Sbjct: 59  RSELILAFLPIVRHLALRHSAGYPGGYDDLVQVGTVGLISAIDRWDPDRAGADLLGYLVP 118

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+  + R   D++  +R+P  ++D    + +    +S ++ R P P E+A  L + V  
Sbjct: 119 CVRGEMLRYFRDRTWAVRVPRRLKDLAVAINKATGPLSQQLGRAPRPSELAAHLGVDVSE 178

Query: 563 VRKVLKITK-------EPISLETPIGDEDTSHLG------DFIEDKNAVSPLDSAIQANL 609
           V + L           EP+  ET  G+     LG      D +E ++A+ PL        
Sbjct: 179 VVEALTAKAGHHSDPLEPVDPET--GESSHERLGELDGELDHVEYRHALRPL-------- 228

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQI 659
                  L SL  RE  +L +RF   M      EE+G  Q  V+R   R +
Sbjct: 229 -------LESLPERERTILMLRFFRDMTQTQIAEEIGISQMHVSRLLARSL 272


>gi|26249146|ref|NP_755186.1| hypothetical protein c3307 [Escherichia coli CFT073]
 gi|26109553|gb|AAN81756.1|AE016765_158 Putative conserved protein [Escherichia coli CFT073]
          Length = 144

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 37/43 (86%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A E
Sbjct: 102 SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVE 144


>gi|1419613|emb|CAA67397.1| signma factor 28 [Legionella pneumophila str. Corby]
          Length = 238

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 59/220 (26%), Positives = 103/220 (46%), Gaps = 42/220 (19%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           + +Q  DLIQ G +GL++AA  +D   G  F TYA                  IRI  HM
Sbjct: 39  QSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYA-----------------GIRIRGHM 81

Query: 526 RDKIHK-------VVRTARRMS-------NKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
            D++ +       V R +R +S       +K+ RE    EIA++L + +     +L   +
Sbjct: 82  LDEVRRNDWVPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGVSLNDYHSML---Q 138

Query: 572 EPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + IS     G +D     D +   E   +  P  + +++++    T+V+ SL PR+ER++
Sbjct: 139 DSISSHL-YGFDDLGVTDDILFDDEGNGSTEPHRNVMRSDMMNRLTQVIDSL-PRKERLV 196

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +    D  L+E+G+   V+  RI QI ++A  +++
Sbjct: 197 ---LSLYYEQDLNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|88704270|ref|ZP_01101984.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
 gi|88701321|gb|EAQ98426.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
          Length = 236

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 50/201 (24%), Positives = 90/201 (44%), Gaps = 21/201 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL++A E +D   G  F+TYA   +K A+   I        +P  ++ ++ +
Sbjct: 45  DLMQVGLIGLLRARESYDASQGASFATYAGIRIKGAMLDEIRAHDW---LPRSVQTQLRQ 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     R   ++       +IA +L MP+           E   L   +     +H+ D 
Sbjct: 102 VSVAIERADARLGHPAQDADIAAELDMPL----------AEYQQLSGQLACARMTHIEDS 151

Query: 592 IEDKNA----VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E +NA    V+P D   +   RE     +A L  +E  ++ + +   +N    L+E+G 
Sbjct: 152 AEAENAVLNTVNPFDEVGEEGFREALAESVAQLPEKERLMMSLYYAEDLN----LKEIGA 207

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ Q+  +A+ +L+
Sbjct: 208 VLGVSESRVSQLHGQALARLR 228


>gi|291525957|emb|CBK91544.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           DSM 17629]
          Length = 224

 Score = 61.6 bits (148), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 35/95 (36%), Positives = 53/95 (55%), Gaps = 3/95 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  N+ L+  V K++ NRG+   DL Q G +GL KAA++FD   G+ FSTYA+  +   
Sbjct: 9   LVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKIHK--VVRTARRMS 540
           I R + D    + I   +RD   K  ++R   RM+
Sbjct: 69  IQRFLRDDGM-VHISRKIRDDARKIAIIREKYRMN 102


>gi|256379404|ref|YP_003103064.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923707|gb|ACU39218.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 243

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 97/219 (44%), Gaps = 29/219 (13%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V   L +   +A ++  RG    DL Q   +GL+ A ++FD   G  F  +A+  +
Sbjct: 28  RDQLVTEYLPVAWHIADRFAERGESVEDLRQVAAVGLIHAVDRFDVQRGIDFLAFAVPTI 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R + DQ   +R+P  +++    +      ++    R PTP E+A+ L + +  V 
Sbjct: 88  TGEVRRHLRDQGWAVRVPRRLKELCLAIDAARVELARASGRTPTPSEVARHLNLSLAEVY 147

Query: 565 KVLKIT--KEPISLETPIGDEDTSH-LG------DFIEDKNAVSPLDSAIQANLRETTTR 615
           + L  T     +SL+    + D+ H LG      + +E ++A+ P+              
Sbjct: 148 EGLHATSANHMVSLD----EVDSDHRLGVDDPALEVVELQHALDPM-------------- 189

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            L  L  RE R++ +RF   M      + VG  Q  V+R
Sbjct: 190 -LRGLPKRERRIVLLRFFRNMTQSQIADSVGVSQMHVSR 227


>gi|254506869|ref|ZP_05119008.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
 gi|219550154|gb|EED27140.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
          Length = 220

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 93/204 (45%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH   
Sbjct: 18  VQVEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHS 76

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +  ++ +    +  ++ R+PT  E+A+ L + +      L      I+    +G ED   
Sbjct: 77  R--EISQAISVLEGELNRDPTDAEVAQHLGLSLTQYHTALT----DINCSRLVGIEDLGV 130

Query: 588 LGDFIE---DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D I    D+ A +P         R+     + SL  RE  VL + +   +N    L+E
Sbjct: 131 SEDVITPDGDEEANTPFQGVADEYFRKALIDSIKSLPEREALVLSLYYDEELN----LKE 186

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    V+  R+ QI ++++++L+
Sbjct: 187 IGDVIGVSESRVSQILSQSMQRLR 210


>gi|320354339|ref|YP_004195678.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
 gi|320122841|gb|ADW18387.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
          Length = 244

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 113/230 (49%), Gaps = 13/230 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + +++  N+ LV  V ++ T +   F+   D+I    +GL+ AA KFD   G KF T+A 
Sbjct: 11  RSQLIRENMPLVELVVQRMTPQVPSFMTKEDMISAAMVGLVDAANKFDPTKGVKFKTFAE 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + V+ AI   +       R    MRDK + + +T  R+  ++ R P  EE+A+++A+ ++
Sbjct: 71  YRVRGAIFDEMRKLDWFSR---SMRDKQNTLTQTMLRLERQLGRSPEEEEMAREMALSID 127

Query: 562 GVRKVLKITKEP--ISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             R +L        +SL ET    ED     D +ED     P D  ++   +E  TRV+A
Sbjct: 128 EYRDLLAEVSHLGCVSLHETLDHTEDGRSFLDSLEDIGGPVP-DDLLE---KEEMTRVMA 183

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +        R+   +    + T +E+ +   V+  R+ Q+ ++A+ KL+
Sbjct: 184 EILEELSEKERLVIALYYYEELTQKEIAEVLSVSEGRVSQLHSQALLKLR 233


>gi|119715356|ref|YP_922321.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119536017|gb|ABL80634.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 244

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 94/200 (47%), Gaps = 21/200 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+ +G IGL+ A +KFD   G +F TYA+  ++ A+   +        +P  +R+KI  
Sbjct: 55  DLVSDGVIGLLDALDKFDPERGLQFQTYAVSRIRGAMVDGLRAADW---VPRSVREKIRD 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSH-L 588
           +      +  ++ R P   E+A +L + V  +RK+   T     +S ET + +EDT    
Sbjct: 112 INTAQTELERRLGRAPKDAEVADRLGISVGDLRKIYSQTAHTSVVSFETVLDEEDTPRAT 171

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D     + + P      A +RE        L  R++ V+ + +   +    TL E+G+ 
Sbjct: 172 TDLPGADDDIPP---GFLAAVRE--------LPERDQVVVALYYWERL----TLAEIGQV 216

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ Q+ ++A   L+
Sbjct: 217 LGVSESRVSQLHSRATLALR 236


>gi|240145473|ref|ZP_04744074.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|257202447|gb|EEV00732.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|291536032|emb|CBL09144.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis M50/1]
          Length = 254

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 101/227 (44%), Gaps = 28/227 (12%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +R+V      Y    +++ DL+  G  GL+ A +KFD     KF TYA   ++ +I   I
Sbjct: 33  VRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDRGKDVKFETYASLRIRGSILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                   IP  +R K  K+    +++  K  R  + EEIA++L +  E          E
Sbjct: 93  RKMDW---IPRTVRQKRKKIEEAIKQIETKTGRNASDEEIAQELGIGEE----------E 139

Query: 573 PISLETPIGDEDTSHLGDFIE-----------DKNAVSPLDSAIQANLRETTTRVLASLT 621
               +T +   +   L +F+E           + + + P +S  +  L++     L  LT
Sbjct: 140 LNDWQTQLNVTNVISLNEFVEQGGEPVMDAKNNSHFIQPEESVQEEELKKVLMESLELLT 199

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E++V+ + +      D TL+E+     V+  R+ Q+  KA+ K++
Sbjct: 200 EKEKKVILLYY----YEDLTLKEISSILEVSESRVSQLHTKALLKMR 242


>gi|291532029|emb|CBK97614.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           70/3]
          Length = 221

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 99/215 (46%), Gaps = 10/215 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            +  +  LV S+A ++ NRG+++ +L   G +GL+KA   FD   G KFSTYA+  +   
Sbjct: 9   FITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D   T+++   +++   K+ R    +  K   EP    +A+KL +  E     L
Sbjct: 69  IKQLFRDGG-TVKVSRSLKELSLKICRLRDELI-KNGEEPHISVLAEKLGITPEEASLAL 126

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             +  P+SL +   +E+     D   +      LD   +  LR+  +R    L P + R+
Sbjct: 127 GASLPPVSLSSYDDEENDEGSFDLPVEPEQPKALD---RMALRQLVSR----LEPIDRRL 179

Query: 628 LRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEA 661
           + +R+        T E +G  Q  V+R   + +E 
Sbjct: 180 IILRYSEECTQSRTAEILGMTQVQVSRREKKILEG 214


>gi|147678181|ref|YP_001212396.1| sporulation sigma factor SigE [Pelotomaculum thermopropionicum SI]
 gi|146274278|dbj|BAF60027.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 101/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 66  LIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPAKKIKLATYA------- 118

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R       R+ +  +     EP        L +  +G     
Sbjct: 119 -SRCIENE-----ILMYLR-------RSVKNRAEVSFDEP--------LNIDWDG----- 152

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                 + L   +G E+   +  FIED+     L  A+Q             L+ RE R+
Sbjct: 153 ----NELLLSDVLGTEN-DIIYKFIEDEIEKKLLHLALQ------------KLSGRERRI 195

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+   T+ T +EV     +++  I ++E + I++LK
Sbjct: 196 MELRFGLNNGTEKTQKEVADLLGISQSYISRLEKRIIKRLK 236


>gi|332981462|ref|YP_004462903.1| RNA polymerase sigma-28 subunit FliA/WhiG [Mahella australiensis
           50-1 BON]
 gi|332699140|gb|AEE96081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Mahella australiensis
           50-1 BON]
          Length = 247

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 112/220 (50%), Gaps = 20/220 (9%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N G    DLI  G  GL+ A E++D     KF TYA   ++ AI  ++  +     IP  
Sbjct: 46  NTGDDLDDLIGYGVFGLLDAIERYDPSRDVKFETYASHRIRGAIIDNLRKKDV---IPRS 102

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITK-EPISLETPIGD 582
           +RDK+  +    +++     +  + E++ + L + +E +  +   I +   ISL+    D
Sbjct: 103 VRDKVKHLDAVYKQLEATSDKPVSDEDVCRYLGISIEQLDALYADINRFNCISLDEIFVD 162

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E   ++GD  E   +V       +  L++  +  ++ L+ RE+++L++ +  G+    TL
Sbjct: 163 E--WNIGD-TESSESVYD-----RIELKQVLSEAVSKLSDREKQLLQLYYYDGL----TL 210

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +E+GK   ++  R+ Q+  KA+ +L+  SR +K++ F+ G
Sbjct: 211 KEIGKVLGISESRVSQLHTKALLQLR--SRLRKMQ-FIAG 247


>gi|257095368|ref|YP_003169009.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
 gi|257047892|gb|ACV37080.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 248

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/233 (22%), Positives = 104/233 (44%), Gaps = 13/233 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             + + ++V+  + LV  +A     R    +Q  DLIQ G +GL+ A  +F+  +G +F 
Sbjct: 6   GQLNRDQLVQHFVPLVKRIACHLMARLPASVQVDDLIQNGMLGLLDAISRFEATMGAQFE 65

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA   V+ A+   + +      +P  +R    ++     R+  +  R PT +E+A  L 
Sbjct: 66  AYAAQRVRGAMLDGLRENDW---LPRSLRSDCRRIEVAIARLEQEHGRAPTEKELADSLG 122

Query: 558 MPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           M +   +K+L+  +  + + LE  + +     L   + D +A  P     +   R    +
Sbjct: 123 MALADYQKMLQDARGHQLVYLEDMVAERGEDFLERHLVDADA-DPSKLLEEETFRRLLVQ 181

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L  RE    R+   +    D  + E+G+   VT  R+ Q+ ++ + +L+
Sbjct: 182 AIDGLPERE----RLLMALYYEQDLNMREIGEVMGVTESRVCQLHSQVVLRLR 230


>gi|182420443|ref|ZP_02641505.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182382221|gb|EDT79700.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 237

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 62/249 (24%), Positives = 110/249 (44%), Gaps = 65/249 (26%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +V + ++GE +A     E++E N +L+  VA K+ +     ++F DL+QEG IG + A  
Sbjct: 16  LVVLYQQGEKKAL---DELLENNDKLIYKVASKFYSEKTSSIEFDDLLQEGRIGFILACS 72

Query: 487 KFD--WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           K+D  +    KF TYA +W+ Q                     KIH+           I 
Sbjct: 73  KYDIEYIKSTKFITYAFYWIYQ---------------------KIHRF----------IT 101

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDS 603
           R  T EE                      ISL TP+ +E+   L + IE + N ++  + 
Sbjct: 102 RYNTNEE----------------------ISLNTPVSEENKDELINSIESNSNEINDREE 139

Query: 604 AIQ-ANLRETTTRVLASLTPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +  ++LR     ++       ER +L++ +G     + ++E++   F  +   ++ I+ 
Sbjct: 140 ELYLSDLRIELESIMDRYNTLNEREILKLYYGWD-TEELSIEQIADIFETSSNEVKSIKG 198

Query: 662 KAIRKLKHP 670
           KAIRKL++ 
Sbjct: 199 KAIRKLRNS 207


>gi|296121384|ref|YP_003629162.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013724|gb|ADG66963.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 376

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 45/67 (67%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+ANLRLV+++A+K      Q  +L+ EG + L+++ E FD  LG +FSTYA W 
Sbjct: 194 ARNQIVQANLRLVVALARKCCGSIEQLAELVSEGVMPLIRSVELFDISLGNRFSTYATWA 253

Query: 504 VKQAITR 510
           V+  + R
Sbjct: 254 VRNQMHR 260



 Score = 39.7 bits (91), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 614 TRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T +L +L+ RE  V+  RFG+ G     +L E+  +  +++ER+RQI  KA+ KLK
Sbjct: 306 TSLLETLSDRERAVIAARFGLDGQPRGQSLSEISGRIGLSKERVRQIVLKALDKLK 361


>gi|284028883|ref|YP_003378814.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283808176|gb|ADB30015.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 287

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/215 (24%), Positives = 100/215 (46%), Gaps = 11/215 (5%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +++  N  +  S+A +Y ++G+   DL Q   +GL+KAA  +       F  YA+  ++ 
Sbjct: 63  QVILLNSPIARSIASRYRSKGVDSDDLEQVAYLGLVKAANGYRPSESTAFLAYAVPTIRG 122

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVE-GVR 564
            + R   D + T+R P  +++    +      ++ K+   PT  E A+ L   P E    
Sbjct: 123 ELKRYFRDCAWTVRPPRRVQEMQGSIAAAEPELTQKLGHLPTDRETAEALGTEPGEIAEA 182

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             ++     +SL+ P   E  + L D + D      L   +      T T  +A L  R+
Sbjct: 183 TAVRACFSTLSLDAPGSGEGGASLMDTVADAEDGYDLVENVH-----TLTPAVADLDDRD 237

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            R+L++RF  G    +T EE+G++  V++ ++ ++
Sbjct: 238 RRILQLRFCHG----YTQEEIGQELGVSQMQVSRL 268


>gi|167747162|ref|ZP_02419289.1| hypothetical protein ANACAC_01876 [Anaerostipes caccae DSM 14662]
 gi|317473634|ref|ZP_07932923.1| hypothetical protein HMPREF1011_03274 [Anaerostipes sp. 3_2_56FAA]
 gi|167654122|gb|EDR98251.1| hypothetical protein ANACAC_01876 [Anaerostipes caccae DSM 14662]
 gi|316898924|gb|EFV20949.1| hypothetical protein HMPREF1011_03274 [Anaerostipes sp. 3_2_56FAA]
          Length = 249

 Score = 61.2 bits (147), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 43/141 (30%), Positives = 80/141 (56%), Gaps = 9/141 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++E+ L  V   A+ YT  G+   DLIQEGN+GL++A     + LG +    A  ++
Sbjct: 110 QNELIESMLADVALDARNYTGHGVLLGDLIQEGNMGLIEAV----FELGDREPKEAEKFL 165

Query: 505 KQ----AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++    A+ +++++Q  T  +   M  K +++   AR ++  + RE T  E+A  L M  
Sbjct: 166 REAAESAMKKAVSEQMNTDSVGEQMARKANRLDEAARFLAEDLGREATAGELADHLKMTE 225

Query: 561 EGVRKVLKITKEPIS-LETPI 580
           E V++++K++ + IS +ET I
Sbjct: 226 EEVKEIMKMSLDAISVVETDI 246


>gi|78044674|ref|YP_359860.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996789|gb|ABB15688.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 254

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 53/194 (27%), Positives = 94/194 (48%), Gaps = 9/194 (4%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL++A E +D   G KF +YA   ++ AI   +  Q+    +P  + DKI KV  + 
Sbjct: 59  GIIGLIEAVETYDQNRGVKFESYASLKIRAAIIDELRKQNF---LPRSVWDKIKKVTTSE 115

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIED 594
             + N +  E   E++A++L + V  V K+  L   K  +SL+  I  E +      + D
Sbjct: 116 EMLLNALGEEVPVEKVAEQLGVSVSDVLKIKTLIALKNHLSLDEIIDPEGSVDRFAGLAD 175

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
               SP +  ++    E     L  L+ RE  +L++ +      + +L+E+     ++  
Sbjct: 176 DEKYSPENKFLKRVEIEELREALKRLSDRERLILQLFY----VEELSLKEIAAVLDISTS 231

Query: 655 RIRQIEAKAIRKLK 668
           R+ QI +KA+ KL+
Sbjct: 232 RVSQIASKALGKLR 245


>gi|304570578|ref|YP_386879.2| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
          Length = 265

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 53/198 (26%), Positives = 93/198 (46%), Gaps = 12/198 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G +GLM+A  KF   LG KF TYA   ++ A+   +         P  +R ++  
Sbjct: 66  ELISAGTLGLMEAFGKFQPKLGIKFDTYAENRIRGAMLDELRRLDW---FPRSLRQRVRL 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-D 590
           +  T  R+ ++  R P+ EE+ K   +  + +R  L+  +  + +      E  +  G D
Sbjct: 123 LEDTINRLEHEKGRRPSEEELQKATGLEEKDLRSGLEALQNHLCISLDAIQETFAADGRD 182

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E +    P  S     L E    ++  LTPRE+ VL + +   +N   T E +G    
Sbjct: 183 HLEGE----PFHSTATQELIERIASLIDQLTPREKLVLSLYYSDELNMRETAEVMG---- 234

Query: 651 VTRERIRQIEAKAIRKLK 668
           VT  R+ Q+ ++A+ +L+
Sbjct: 235 VTEGRVSQLHSQALNRLR 252


>gi|313672893|ref|YP_004051004.1| RNA polymerase, sigma 28 subunit, sigd/flia/whig [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939649|gb|ADR18841.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 242

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 102/201 (50%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L     +GL+++ +KFD      F +YA   +K AI  ++        +P ++R K+ +
Sbjct: 45  ELYSAACMGLVESLQKFDKGRSVDFYSYAERRIKGAILDALRQMDF---LPRNVRTKLKQ 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLG 589
                + ++ K+ R+P  +EI +   +  E V   L +  T +  SL+T + ++    L 
Sbjct: 102 FEEKLQELTVKLGRKPNTDEIVEYTNLSQEDVFNFLNLIETGQLTSLDTSLDEDGDISLL 161

Query: 590 DFIEDKNAV-SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I  K+ V  P DSAI+  L      ++ SL  +E+ V+ + +      + T++E+G+ 
Sbjct: 162 DTI--KSFVEGPEDSAIKEQLISKLGEIIDSLPDKEKLVITLYY----YEELTMKEIGEV 215

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             ++  R+ QI ++A++KLK 
Sbjct: 216 LKISESRVSQIHSEAVKKLKR 236


>gi|229917800|ref|YP_002886446.1| RNA polymerase sigma factor SigB [Exiguobacterium sp. AT1b]
 gi|229469229|gb|ACQ71001.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Exiguobacterium sp. AT1b]
          Length = 266

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 48/217 (22%), Positives = 110/217 (50%), Gaps = 10/217 (4%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV ++A+K++       DL+Q G IGL+ A  +FD   G  F ++A+  +   I R I D
Sbjct: 42  LVEALARKFSRGRAIHDDLVQVGMIGLLAALRRFDPEFGRSFESFAVPTIIGEIKRFIRD 101

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--E 572
           ++ ++ +P  +++   K+ +T   ++ +++R P  +EIA  L +  E + + L++ K  +
Sbjct: 102 KTWSVHVPRRIKELGPKIKKTVEELTTELQRSPRIDEIADHLGVSDEEILETLEMGKSYQ 161

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMR 631
            +S+++ I   +  + G  +   + V   +   ++ + R    +    L  RE  +L   
Sbjct: 162 ALSVDSSI---EADNEGSTVTLLDLVGSQERGYESVDQRLILEKAFNVLNERERAILECA 218

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   M+     +E G+   +++  + +++ +A+ KL+
Sbjct: 219 YYKNMSQ----KETGELLGISQMHVSRLQRRALEKLR 251


>gi|228906737|ref|ZP_04070609.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
 gi|228964059|ref|ZP_04125186.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228795629|gb|EEM43109.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228852914|gb|EEM97696.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
          Length = 203

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    +T  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEQTERRLVLEDIFNVLNDTEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|153938998|ref|YP_001391838.1| sporulation sigma factor SigK [Clostridium botulinum F str.
           Langeland]
 gi|168180573|ref|ZP_02615237.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|152934894|gb|ABS40392.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           Langeland]
 gi|182668432|gb|EDT80411.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|295319864|gb|ADG00242.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           230613]
          Length = 234

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 106/242 (43%), Gaps = 52/242 (21%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E ++ +  ++KG+   ++AK  +VE NLRLV  + KKY+  G    DLI  G +GL+KA 
Sbjct: 35  EEKYYLDRLKKGD---ALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGLIKAI 91

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD   G + +TYA   ++  I   I +   T +  V+++D I                
Sbjct: 92  DSFDNSKGTRLATYAARCIENEILMLIRNNKKT-KGEVYLQDPI---------------- 134

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                           GV K        ISL   +  ++ S + + +  K  V  L   I
Sbjct: 135 ----------------GVDK----EGNEISLMDILSSDEDSII-EIVSTKIEVKKLYGKI 173

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LR            RE++V++MR+G+      T  E+     ++R  + +IE KA++
Sbjct: 174 DTCLR-----------GREKKVIQMRYGLKDGRPRTQREIAGILDISRSYVSRIEKKALK 222

Query: 666 KL 667
           KL
Sbjct: 223 KL 224


>gi|323341369|ref|ZP_08081613.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
 gi|323091246|gb|EFZ33874.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
          Length = 250

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 113/242 (46%), Gaps = 15/242 (6%)

Query: 435 RKGECE--ASIAKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDW 490
           RKG+C     + +++ +   L LV  VA + +  N   ++ DL   G IGL+ A +KFD 
Sbjct: 7   RKGQCRFMYEVDREQEILKYLPLVERVANRISIKNTEYEYDDLYNIGVIGLIDAMQKFDS 66

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F  YA   ++ AI   +   S   +I  +    ++   +  + +  ++KRE T +
Sbjct: 67  SKKVPFENYAAIRIRGAIIDEVRRHS---KISRYKMGNVNSFYQAKQELEQEMKREVTDK 123

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           EI KK+ +    +  +    +    +SLE+ +   +++T  + D + D  A S     ++
Sbjct: 124 EIMKKMGITSSQLGDIYDSIQYLSSVSLESTLYSNNDETVMVQDTLRDSKAPSGEKELMK 183

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              ++     +  L+ RE+ VL + +      D TL+E+     V+  R+ QI  +AI K
Sbjct: 184 QERKKELIEAIKRLSEREQLVLSLYY----EEDATLKEIAAILDVSIARVSQIHGRAIAK 239

Query: 667 LK 668
           ++
Sbjct: 240 IR 241


>gi|317121712|ref|YP_004101715.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
 gi|315591692|gb|ADU50988.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
          Length = 245

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 61/231 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 63  VRHTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                ++ I ++     I +H+R       RT+R                          
Sbjct: 120 -----SKCIENE-----ILMHLR-------RTSR-------------------------- 136

Query: 564 RKVLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVL 617
                 T+  +SL+ P+     G+E    L D I   +    +   ++A + R    R L
Sbjct: 137 ------TRYEVSLDEPLNVDWEGNELL--LSDVIPATDG-DVIYRDLEAKVDRHLLYRAL 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A L+PRE  ++ +RFG+    + T ++V  +  +++  I ++E + I +L+
Sbjct: 188 ARLSPRERLIMELRFGLVDGIERTQKQVADRLGISQSYISRLEKRIINRLR 238


>gi|302538372|ref|ZP_07290714.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302447267|gb|EFL19083.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 323

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 56/246 (22%), Positives = 111/246 (45%), Gaps = 24/246 (9%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWC 491
           +G  E    +  ++E N  LV    +++  R         DL+Q G IGL+KA ++FD  
Sbjct: 69  EGTAERQYVRNTLIEMNASLVQYAVRRFRGRAEGAAGDVDDLVQVGTIGLIKAIDRFDPA 128

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +F+T AM ++   I R   D +  + +P  +++    + +    ++ ++ R PT  +
Sbjct: 129 RENEFATLAMPYITGEIKRHFRDTAWAVHVPRRLQELRIDIAKAKEELTIRLDRSPTVRD 188

Query: 552 IAKKLAMP----VEGVRKVLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLD 602
           +A  L +     +EG+      T    SL+ P      G  +   L + + ++     L 
Sbjct: 189 LAAYLDLTEEQVIEGLVAANGHTSG--SLDAPHAEHGDGPAEGHTLAEVLGEEEPALELV 246

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             IQ     T   +L  L+ RE  +LRMRFG     + T  ++G    +++ ++ ++ ++
Sbjct: 247 EDIQ-----TLAPLLERLSERERTMLRMRFG----EELTQAQMGAALGISQMQVSRLLSR 297

Query: 663 AIRKLK 668
            +  L+
Sbjct: 298 LLAHLR 303


>gi|324999864|ref|ZP_08120976.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 271

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 112/230 (48%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD--WCLGYKFSTYAMW 502
           +  ++ A L L  +++++Y        D+ Q   +GL+KA +++D     G     Y + 
Sbjct: 50  RDRVICAFLPLARNLSRRYVTGVHSADDVEQAATLGLIKAVDRYDPDVATGGPLG-YLVP 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+  + R + D S  +R+P  ++++   + R A  ++ ++ R P P E+A +L +    
Sbjct: 109 CVRGELMRYLRDHSWALRVPRDLKERSVGLNRAAVTLTQRLGRAPRPSELASELDVDTSE 168

Query: 563 VRKVLKI--TKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLAS 619
           V + L    +   +SL+ P  D +T+ LG+ + ED  A+    + ++  LRE     +  
Sbjct: 169 VVEALGAMESYNAVSLDEPGPDGETT-LGERLGEDDGALE--GAPVRTELRER----IGE 221

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE R+L +RF      + T  E+ +   V++  + ++  + +  L+H
Sbjct: 222 LPERERRILLLRF----YGNRTQSEIAEDIGVSQMHVSRLLTRTVATLRH 267


>gi|291548178|emb|CBL21286.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. SR1/5]
          Length = 241

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 106/227 (46%), Gaps = 52/227 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   FD     K +TYA   
Sbjct: 58  GKSVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFDPVKNIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             ++K K E + +E    L +  +G 
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NSKTKMEVSIDE---PLNVDWDGN 149

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L          + I   D   +   +ED+  ++ L  AI            + LT R
Sbjct: 150 ELLL----------SDILGTDDDVISRRLEDEVEIALLGKAI------------SKLTKR 187

Query: 624 EERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++R+RFGIG    ++ T +EV     +++  I ++E + +++L+
Sbjct: 188 EQMIIRLRFGIGNREGSEKTQKEVADLLGISQSYISRLEKRIMKRLR 234


>gi|154684976|ref|YP_001420137.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens FZB42]
 gi|126363073|emb|CAM35801.1| RNA polymerase sigma-B factor [Bacillus amyloliquefaciens FZB42]
 gi|154350827|gb|ABS72906.1| SigB [Bacillus amyloliquefaciens FZB42]
          Length = 262

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ +VE    LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQETLVEVYTNLVEMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPEVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++     +++ + +R P  EEIA  L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAAFLDVSEEE 148

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      +   + N +     VL
Sbjct: 149 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----EGYERVNQQMMIKSVL 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + F      + + +E G    +++  + +++ KA++KL+
Sbjct: 204 HVLSDREKQIIDLTF----VQNKSQKETGDILGISQMHVSRLQRKAVKKLR 250


>gi|119503682|ref|ZP_01625765.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2080]
 gi|119460744|gb|EAW41836.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2080]
          Length = 237

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 56/239 (23%), Positives = 111/239 (46%), Gaps = 28/239 (11%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           G C  +     +V A+L LV  +A++   R    ++  DLIQ G IGL+KA++      G
Sbjct: 13  GACGGASQGDALVRAHLPLVKRIAQQLLVRLPAHIEMDDLIQVGLIGLLKASDDHQADSG 72

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +FSTYA   ++ A+   +  +     +P  ++  + +V     R   ++ R  T +EIA
Sbjct: 73  AQFSTYAAIRIRGAMLDELRSRDW---LPRSVQRDLGRVAAAIERAEQRVGRPATDQEIA 129

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS----AIQANL 609
            +L M ++  +++              G+   + +G  +E+ +  + +D+       +  
Sbjct: 130 DQLEMDLDSYQQL-------------SGELACARIGQ-LEELDVPTEVDATTSIVFDSAR 175

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE     +  L  +E  +L + +  G+N    L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 176 REAVVEAIGRLPEKEGLMLSLYYTEGLN----LKEIGMVLNVSESRVSQIHGQAVARLR 230


>gi|308172341|ref|YP_003919046.1| RNA polymerase sigma-37 factor sigma B [Bacillus amyloliquefaciens
           DSM 7]
 gi|307605205|emb|CBI41576.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328552153|gb|AEB22645.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens TA208]
 gi|328910426|gb|AEB62022.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens LL3]
          Length = 262

 Score = 61.2 bits (147), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ +VE    LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQETLVEVYTNLVEMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPEVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++     +++ + +R P  EEIA  L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAAFLDVSEEE 148

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      +   + N +     VL
Sbjct: 149 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----EGYERVNQQMMIKSVL 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + F      + + +E G    +++  + +++ KA++KL+
Sbjct: 204 HVLSDREKQIIDLTF----VQNKSQKETGDILGISQMHVSRLQRKAVKKLR 250


>gi|289754805|ref|ZP_06514183.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695392|gb|EFD62821.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 473

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 27/46 (58%), Positives = 37/46 (80%), Gaps = 1/46 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ-EGNIGLMKAAEKF 488
           AK  ++EANLRLV+S+AK+YT RG+ FLDLI  +  +GL++A EKF
Sbjct: 293 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIPGKATLGLIRAVEKF 338



 Score = 44.7 bits (104), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 211 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 270


>gi|229074589|ref|ZP_04207614.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
 gi|229095607|ref|ZP_04226590.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|229114558|ref|ZP_04243973.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228668908|gb|EEL24335.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228687817|gb|EEL41712.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|228708547|gb|EEL60695.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
          Length = 203

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    +T  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEQTERRLVLEDIFNVLNETEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|256371428|ref|YP_003109252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008012|gb|ACU53579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 254

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 66/210 (31%), Positives = 97/210 (46%), Gaps = 29/210 (13%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL+ A EKF+   G KF TYA+  +K AI   I +      +P  +R K   
Sbjct: 53  DLASYGTFGLIDALEKFEPERGIKFETYAITRIKGAI---IDELRAIDWVPRSVRAKAKS 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DE------- 583
           V +    +  ++ R PT  E+A +L M  +   ++L I  + IS    +G DE       
Sbjct: 110 VEQAYAALEARLHRPPTDAEVASELGMSED---ELLAIYSK-ISFLGLVGLDEVVMSGER 165

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMNT 638
            +   LGD + D+       SA  A   +   R+LA     L  RE+ VL + +  G   
Sbjct: 166 GEGMTLGDTLADRR-----QSAGGAFEEQERRRMLADSINQLADREKTVLVLYYYEGF-- 218

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+G+   VT  RI QI +KA+  L+
Sbjct: 219 --TLAEIGRILGVTESRICQIHSKAVLALR 246


>gi|126175111|ref|YP_001051260.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|153001435|ref|YP_001367116.1| flagellar biosynthesis sigma factor [Shewanella baltica OS185]
 gi|160876160|ref|YP_001555476.1| flagellar biosynthesis sigma factor [Shewanella baltica OS195]
 gi|217972633|ref|YP_002357384.1| flagellar biosynthesis sigma factor [Shewanella baltica OS223]
 gi|304409942|ref|ZP_07391561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|307302345|ref|ZP_07582103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|125998316|gb|ABN62391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|151366053|gb|ABS09053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS185]
 gi|160861682|gb|ABX50216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS195]
 gi|217497768|gb|ACK45961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS223]
 gi|304351351|gb|EFM15750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|306914383|gb|EFN44804.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|315268356|gb|ADT95209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS678]
          Length = 237

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH  ++  KV      +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDWVPR-SVHRNNR--KVAHAIDELEQALGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D   + D++     ++  +          +  
Sbjct: 130 EYHHILN----DVSVGKIIGIEDLGVSQDILTVSDRSDDDSFEALAENQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|289829788|ref|ZP_06547303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 158

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 38/50 (76%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A+       G
Sbjct: 90  SRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRASRSLTRNAG 139


>gi|171320641|ref|ZP_02909660.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MEX-5]
 gi|172059263|ref|YP_001806915.1| flagellar biosynthesis sigma factor [Burkholderia ambifaria MC40-6]
 gi|171094127|gb|EDT39215.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MEX-5]
 gi|171991780|gb|ACB62699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MC40-6]
          Length = 244

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 95/202 (47%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 98  VEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 153

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRVDHADPLSALLDDHLREALVDAIDRLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|89068737|ref|ZP_01156123.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
 gi|89045700|gb|EAR51762.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
          Length = 241

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ ++ R   + A ++T+      DL+ EG I LM+AAE+FD     +FSTYA WW++ A
Sbjct: 38  LLRSHARQAYAQATRWTDNPSYIEDLVAEGMIALMRAAERFDLTREVRFSTYAAWWLRTA 97

Query: 508 ITRSIADQSCTIRIPV 523
           +  +    S  I +PV
Sbjct: 98  MAEAYGRISAVIDVPV 113


>gi|117919807|ref|YP_868999.1| flagellar biosynthesis sigma factor [Shewanella sp. ANA-3]
 gi|117612139|gb|ABK47593.1| RNA polymerase, sigma 28 subunit [Shewanella sp. ANA-3]
          Length = 237

 Score = 60.8 bits (146), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 104/230 (45%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A
Sbjct: 12  SKTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  +V +    +   + R+    EIA+KL M +
Sbjct: 72  GIRIRGAMLDEIRRGDWVPR-SVHRNNR--RVAQAIDELEQVLGRDARDTEIAEKLDMTL 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLA 618
           +    +L      +S+   IG ED     D +   + VS    ++  +          + 
Sbjct: 129 DEYHHILN----DVSVGKIIGIEDLGVSQDILTSSDNVSDGTYEALAETQFHSALVEAIK 184

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 185 LLPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|317499143|ref|ZP_07957420.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316893556|gb|EFV15761.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 231

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 103/234 (44%), Gaps = 52/234 (22%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G      A+  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K 
Sbjct: 39  GTVNEETARSMLIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPAKKIKL 98

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +TYA        +R I ++                ++   RR +NK K E + +      
Sbjct: 99  ATYA--------SRCIENE----------------ILMYLRR-NNKTKMEVSID------ 127

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                          EP++++    D +   L D +     +   D   + + ++  TR 
Sbjct: 128 ---------------EPLNVDW---DGNELLLSDILGTDEDIIYKDLEHEVD-KKLLTRA 168

Query: 617 LASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  LT RE+ ++ +RFGI      + T +EV     +++  I ++E K I++LK
Sbjct: 169 MTILTDREKMIIELRFGINQKEGKEKTQKEVADMLGISQSYISRLEKKIIKRLK 222


>gi|266621294|ref|ZP_06114229.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
           DSM 13479]
 gi|288867054|gb|EFC99352.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
           DSM 13479]
          Length = 188

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 34/140 (24%), Positives = 70/140 (50%), Gaps = 1/140 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG-YKFSTYAMW 502
           AKK ++E NL   +  AK+Y  +G+   DL+ E N+ L  A  +F    G   F  +   
Sbjct: 29  AKKRLIEGNLEAALKCAKEYDGKGVLLTDLVAEANMALTMAVTEFLTDAGDGDFEGFLAA 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +K A+  ++ +Q    +    +  +++ +   ++ ++ ++ RE T EE+A K+ M    
Sbjct: 89  RMKAALDLAVEEQQSAKQTGEELAARVNVLQTVSQMLAKELGREATVEELADKMKMTAGE 148

Query: 563 VRKVLKITKEPISLETPIGD 582
           V+ ++K+  + +S+     D
Sbjct: 149 VKDIMKMAMDAMSMNAENAD 168


>gi|225568655|ref|ZP_03777680.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
 gi|225162583|gb|EEG75202.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
          Length = 246

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPEKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                 +    R +NK K E                 
Sbjct: 120 -----SRCIENE-----------------ILMYLRRNNKTKME----------------- 140

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                     +S++ P+    D +   L D +  E+      L++ ++  L     + ++
Sbjct: 141 ----------VSIDEPLNVDWDGNELLLSDILGTEEDTIYKDLENEVEQKL---LLKAIS 187

Query: 619 SLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ RE  +++MRFG+G     + T +EV     +++  I ++E K +++L+
Sbjct: 188 RLSGRERTIIQMRFGLGTPDGEEKTQKEVADMLGISQSYISRLEKKIMQRLR 239


>gi|115350241|ref|YP_772080.1| flagellar biosynthesis sigma factor [Burkholderia ambifaria AMMD]
 gi|115280229|gb|ABI85746.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           ambifaria AMMD]
          Length = 243

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 95/202 (47%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 97  VEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 152

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYRVDHADPLSALLDDHLREALVDAIDRLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVLEVSESRVCQLHSQAVARLR 230


>gi|239939493|ref|ZP_04691430.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239985982|ref|ZP_04706646.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
          Length = 262

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 101/225 (44%), Gaps = 18/225 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + + L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F TYA+  V
Sbjct: 36  RDETIRSWLPMAHRIATRFRNRGEAMDDLRQVAAMGLVKAVDRYDPERGKAFETYAVPTV 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
              + R   D +  + +P  ++D +   VR ARR          PT  EIA    +  E 
Sbjct: 96  TGELKRHFRDHTWDVHVPRRVQD-LRNRVRVARRELAQTSGGGSPTCAEIASATGLGEED 154

Query: 563 VRKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   L+   +   +SL+  P G E  S L D +   +A   LD+A+    RE     L  
Sbjct: 155 VLLGLEALESYSALSLDAEPAGVEGGSPLVDRLGSCDAA--LDTAVD---REAVKPELRG 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR------ERIR 657
           L  RE  +L +R+   M      E +G  Q  V+R      ER+R
Sbjct: 210 LPERERTILYLRYFQDMTQVRIAERLGISQMHVSRLLSRSCERVR 254


>gi|150016004|ref|YP_001308258.1| sporulation sigma factor SigE [Clostridium beijerinckii NCIMB 8052]
 gi|149902469|gb|ABR33302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 235

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 103/222 (46%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVYVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S KIK E +  E    L +  +G     
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KIKAEISFYE---PLNIDWDG----- 144

Query: 568 KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G E DT +  + IED+     +D       ++     L SL  RE+ 
Sbjct: 145 ----NELLLSDILGTENDTVY--NLIEDE-----VD-------KQLLVMALKSLNDREKE 186

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++R+RFG+    + T +EV     +++  I ++E K I++LK
Sbjct: 187 IVRLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIIKRLK 228


>gi|299534757|ref|ZP_07048087.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
 gi|298729845|gb|EFI70390.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
          Length = 256

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 51/190 (26%), Positives = 86/190 (45%), Gaps = 9/190 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G +GL  A  KFD     KF TYA + V+ AI   +  +     +P   R+K  K
Sbjct: 55  DLTSLGMVGLFDALNKFDINRDLKFDTYASFRVRGAIIDGLRKEDW---LPRSAREKAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +     ++  K  R  TPEE+A+ + + VE V + ++       +S+      E+T    
Sbjct: 112 LDAQIEQLEQKYMRHVTPEELAEHMEVSVEDVYQTVQEHFFSNVLSINEQQDQEETDGKT 171

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D    +P  + I++ L +     +  L  +E+ VL + +      + TL E+G+  
Sbjct: 172 FVIRDDTTKTPEQAIIKSELLDDLAENIQKLNEKEQLVLSLFY----TEELTLTEIGEML 227

Query: 650 CVTRERIRQI 659
            ++  RI QI
Sbjct: 228 ELSTSRISQI 237


>gi|221308296|ref|ZP_03590143.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221312618|ref|ZP_03594423.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221317541|ref|ZP_03598835.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221321817|ref|ZP_03603111.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767137|ref|NP_388354.2| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|321314147|ref|YP_004206434.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
 gi|133469|sp|P06574|RPSB_BACSU RecName: Full=RNA polymerase sigma-B factor; AltName: Full=General
           stress protein 84; Short=GSP84; AltName: Full=Sigma-37
 gi|143538|gb|AAA22754.1| sigma-37 RNA polymerase [Bacillus subtilis]
 gi|225184764|emb|CAB12280.2| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291482882|dbj|BAI83957.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. natto
           BEST195]
 gi|320020421|gb|ADV95407.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
          Length = 262

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ +V     LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQETLVRVYTNLVDMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPVVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++     +++ + +R P  EEIA+ L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAEFLDVSEEE 148

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      D   + N +     VL
Sbjct: 149 VLETMEMGKSYQALSVDHSIEADSDGSTVTILDIVGSQE-----DGYERVNQQLMLQSVL 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 204 HVLSDREKQIIDLTY----IQNKSQKETGDILGISQMHVSRLQRKAVKKLR 250


>gi|307328384|ref|ZP_07607560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885957|gb|EFN16967.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 261

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 106/215 (49%), Gaps = 13/215 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++ A L +   +A ++ N+G    DL Q  ++ L+KA ++++  LG+ F +YA+  +
Sbjct: 37  RETIICAWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVDRYNPDLGHAFPSYAIPVI 96

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKI-KREPTPEEIAKKLAMPVEG 562
              + R   D   T+ IP ++++ +    R+AR  +  ++  R PT  EI  +  MP E 
Sbjct: 97  TGELKRHFRDYLWTLHIPRNIQE-VRSRTRSARDALEQELGGRTPTIHEICLRTGMPQED 155

Query: 563 VRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-AS 619
           V   L+ +    P+SL   +   +   L +       V   D+AI+  +     RVL A 
Sbjct: 156 VMAGLEASASCTPLSLNAAVQGAEERLLAE------TVGADDAAIERVVNREALRVLIAE 209

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L+ ++  VL +RF  G++     E +G  Q  ++R
Sbjct: 210 LSEQDRYVLYLRFFAGLSQSQIGEILGFSQMHISR 244


>gi|167767678|ref|ZP_02439731.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|167710695|gb|EDS21274.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|291560812|emb|CBL39612.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SSC/2]
          Length = 240

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 104/234 (44%), Gaps = 52/234 (22%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G      A+  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K 
Sbjct: 48  GTVNEETARSMLIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPAKKIKL 107

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +TYA        +R I ++     I +++R             +NK K E + +      
Sbjct: 108 ATYA--------SRCIENE-----ILMYLRR------------NNKTKMEVSID------ 136

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                          EP++++    D +   L D +     +   D   + + ++  TR 
Sbjct: 137 ---------------EPLNVD---WDGNELLLSDILGTDEDIIYKDLEHEVD-KKLLTRA 177

Query: 617 LASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  LT RE+ ++ +RFGI      + T +EV     +++  I ++E K I++LK
Sbjct: 178 MTILTDREKMIIELRFGINQKEGKEKTQKEVADMLGISQSYISRLEKKIIKRLK 231


>gi|291060074|gb|ADD72809.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 262

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 109/211 (51%), Gaps = 22/211 (10%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMR 526
           ++F DL+  G  GL  A +K+D     +F+TYA+  ++ AI     D+  +I  +P  +R
Sbjct: 53  VEFDDLVSYGIFGLFDAIDKYDPEKNIRFNTYAVTRIRGAIF----DELRSIDWVPRSVR 108

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKIT-KEPISL-ETPIGDE 583
            +  ++      +  ++ R  T  EIA  L + +E   + +LK++    ISL ++  G +
Sbjct: 109 QQTRQIEEAIADLEARLGRAATDTEIACALNIELEEYHQLLLKVSGTSVISLADSKFGGD 168

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMN 637
           +  H  +GD IE   +++P D  ++   RE   R++A     L+ RE++VL + +     
Sbjct: 169 ERDHVSVGDSIEAPASLNP-DVIVE---REEIKRIIAEAIRELSQREQQVLILYY----Y 220

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + TL+E+GK   VT  RI QI   A  KLK
Sbjct: 221 EEMTLKEIGKVLKVTESRISQIHTSANLKLK 251


>gi|170701719|ref|ZP_02892658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           IOP40-10]
 gi|170133382|gb|EDT01771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           IOP40-10]
          Length = 244

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 95/202 (47%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 98  VEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 153

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRVDLADPLSALLDDHLREALVDAIDRLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|15639696|ref|NP_219146.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025934|ref|YP_001933706.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum SS14]
 gi|3323011|gb|AAC65675.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018509|gb|ACD71127.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 262

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 64/213 (30%), Positives = 108/213 (50%), Gaps = 26/213 (12%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI---TRSIADQSCTIRIPVH 524
           ++F DL+  G  GL  A +K+D     +F+TYA+  ++ AI    RSI        +P  
Sbjct: 53  VEFDDLVSYGIFGLFDAIDKYDPEKNIRFNTYAVTRIRGAIFDELRSID------WVPRS 106

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKIT-KEPISL-ETPIG 581
           +R +  ++      +  ++ R  T  EIA  L + +E   + +LK++    ISL ++  G
Sbjct: 107 VRQQTRQIEEAIADLEARLGRXATDTEIACALNIELEEYHQLLLKVSGTSVISLADSKFG 166

Query: 582 DEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIG 635
            ++  H  +GD IE   +++P D  ++   RE   R++A     L+ RE++VL + +   
Sbjct: 167 GDERDHVSVGDSIEAPASLNP-DVIVE---REEIKRIIAEAIRELSQREQQVLILYY--- 219

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + TL+E+GK   VT  RI QI   A  KLK
Sbjct: 220 -YEEMTLKEIGKVLKVTESRISQIHTSANLKLK 251


>gi|146293655|ref|YP_001184079.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|145565345|gb|ABP76280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
 gi|319427054|gb|ADV55128.1| RNA polymerase sigma-28 factor for flagellar operon, FliA
           [Shewanella putrefaciens 200]
          Length = 237

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH  ++  +V +    +  ++ R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDWVPR-SVHRNNR--RVAQAIDELEQELGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D   + D++     ++  +          +  
Sbjct: 130 EYHHILN----DVSVGKIIGIEDLGVSQDILTLSDRSDDGSFEALAETQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|239934588|emb|CAR94608.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 220

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 37/52 (71%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G    M ++   P + Q ++
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIVIAKRIEEGVREFMHAVAYWPGSVQKIL 52


>gi|295399723|ref|ZP_06809704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111758|ref|YP_003990074.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
 gi|294978126|gb|EFG53723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216859|gb|ADP75463.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
          Length = 239

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK++ E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKVRAEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  ED      L++ +  NL     R    L+
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTEDDVITKDLEADVDRNLLFNALR---QLS 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232


>gi|21104384|dbj|BAB93462.1| rpoS like gene [Variovorax sp. WFF52]
          Length = 47

 Score = 60.8 bits (146), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 27/46 (58%), Positives = 36/46 (78%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           LV+++AK Y NRG+ F DLI+EGN+GLM A  KF+   G++FSTYA
Sbjct: 1   LVVNIAKAYLNRGVPFSDLIEEGNLGLMHAITKFEPERGFRFSTYA 46


>gi|292493580|ref|YP_003529019.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus
           halophilus Nc4]
 gi|291582175|gb|ADE16632.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus
           halophilus Nc4]
          Length = 241

 Score = 60.5 bits (145), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 89/203 (43%), Gaps = 14/203 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++AA  ++   G  F TYA   ++ AI   I         P  +  
Sbjct: 43  VQLDDLIQAGMIGLLEAARNYNASQGASFETYAGIRIRGAILDEIRRNDWA---PRSVHR 99

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDT 585
           K  +V    R + N+  R+    E+AK+L + +    ++L+        SL+     E+T
Sbjct: 100 KARQVAEVMREIENREGRDARDHEVAKELGLSLNDYHRLLQDAGGYRVFSLDEFNEGEET 159

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L   ++      P D     + R      +  L  RE  V+ + +      D  L E+
Sbjct: 160 EPLTTPLQ-----GPFDGLQDQSFRSALVGAIDGLPERERLVMSLYY----VEDLNLREI 210

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+   V+  R+ QI ++A+ +L+
Sbjct: 211 GEVLGVSESRVSQIHSQAVLRLR 233


>gi|213027409|ref|ZP_03341856.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 185

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 47/189 (24%), Positives = 91/189 (48%), Gaps = 14/189 (7%)

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++
Sbjct: 1   AVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQEL 57

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI----EDKNAVS 599
            R  T  E+A++L +PV   R++L  T           DE     GD I    E+    +
Sbjct: 58  GRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSY---DEWREEHGDSIELVTEEHQQEN 114

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           PL   ++ +LR+     + SL  RE+ VL + +   +N    L+E+G    V   R+ Q+
Sbjct: 115 PLHQLLEGDLRQRVMDAIESLPEREQLVLTLYYQEELN----LKEIGAVLEVGESRVSQL 170

Query: 660 EAKAIRKLK 668
            ++AI++L+
Sbjct: 171 HSQAIKRLR 179


>gi|325662349|ref|ZP_08150958.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331086152|ref|ZP_08335234.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471351|gb|EGC74574.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330406311|gb|EGG85825.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 247

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 106/233 (45%), Gaps = 64/233 (27%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKKVLIEHNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPTKKIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK K E                 
Sbjct: 120 -----SRCIENE-----ILMYLRR------------NNKTKLE----------------- 140

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI--EDKNAVSPLDS-AIQANLRETTTRVL 617
                     +S++ P+    D +   L D +  E+      L++ A Q  LR    + +
Sbjct: 141 ----------VSIDEPLNVDWDGNELLLSDILGTEEDTIYRDLETEAEQKMLR----KAI 186

Query: 618 ASLTPREERVLRMRFGIGMN--TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+PRE+ ++ MRFGI  +   + T +EV     +++  I ++E K +++LK
Sbjct: 187 EKLSPREKTIVEMRFGINRSEGEEKTQKEVADLLGISQSYISRLEKKIMQRLK 239


>gi|1378114|gb|AAB41955.1| whiG [Streptomyces sp.]
          Length = 209

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 84/185 (45%), Gaps = 21/185 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D +  G  GL+ A EKFD     KF TYA+  ++ A+   I +      IP  +R K   
Sbjct: 33  DFVSSGVFGLIDAIEKFDVDREIKFETYAITRIRGAM---IDELRALDWIPRSVRQKARN 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-- 589
           V R    +  + +R P+  E+A ++ + +E +  V       +SL   +  E+  H G  
Sbjct: 90  VERAYATLEAQFRRTPSEAEVASEMGIALEELHAVFS----QLSLANVVALEELLHAGGE 145

Query: 590 --------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                   D +ED  A +P++ A    LR    R + +L  RE+ V+ + +  G+    T
Sbjct: 146 GGGRLSLMDTLEDTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEGL----T 201

Query: 642 LEEVG 646
           L E+G
Sbjct: 202 LAEIG 206


>gi|113969642|ref|YP_733435.1| flagellar biosynthesis sigma factor [Shewanella sp. MR-4]
 gi|114046872|ref|YP_737422.1| flagellar biosynthesis sigma factor [Shewanella sp. MR-7]
 gi|113884326|gb|ABI38378.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888314|gb|ABI42365.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
          Length = 237

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 104/230 (45%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A
Sbjct: 12  SKTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFA 71

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  +V +    +   + R+    EIA+KL M +
Sbjct: 72  GIRIRGAMLDEIRRGDWVPR-SVHRNNR--RVAQAIDELEQVLGRDARDTEIAEKLDMTL 128

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLA 618
           +    +L      +S+   IG ED     D +   + VS    ++  +          + 
Sbjct: 129 DEYHHILN----DVSVGKIIGIEDLGVSQDILTPSDNVSDGTFEALAETQFHSALVEAIK 184

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 185 LLPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|121596110|ref|YP_988006.1| FliA/WhiG family RNA polymerase sigma factor [Acidovorax sp. JS42]
 gi|222112265|ref|YP_002554529.1| RNA polymerase, sigma 28 subunit, flia/whig [Acidovorax ebreus
           TPSY]
 gi|120608190|gb|ABM43930.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidovorax sp.
           JS42]
 gi|221731709|gb|ACM34529.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax ebreus
           TPSY]
          Length = 237

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 91/200 (45%), Gaps = 11/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL  A  +++   G +F T+A   ++ A+   + +     R     R     
Sbjct: 40  DLIQVGMIGLNDALSRYEVAQGVQFETFASQRIRGAMLDELREGDWMSRSS---RKSQKD 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE-TPIGDEDTSHL 588
           +     R+  ++ R P   EIA +L M +E  + +L   +  + + LE     DED   L
Sbjct: 97  IEHALHRVEQRLGRSPIESEIAAELGMSLEDYQALLSKVRGTQLVYLEDFHHDDEDEGFL 156

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              + D+ A  P+       LR +    + +L  RE+ ++ M +   MN    L+E+   
Sbjct: 157 DRHVADEGA-DPMAVLRDQRLRASLVEAIKALPEREQYIMGMYYEHDMN----LKEIAAV 211

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             VT  R+ Q+ ++AI +L+
Sbjct: 212 LGVTESRVCQLHSQAIARLR 231


>gi|228899672|ref|ZP_04063925.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
 gi|228859981|gb|EEN04388.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
          Length = 203

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 99/210 (47%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    +T  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEQTERRLVLEDIFNVLNDMEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            E +G    +++  + +I+ +AI KLK  +
Sbjct: 174 RERLG----ISQMHVSRIKRQAISKLKQAA 199


>gi|332799203|ref|YP_004460702.1| RNA polymerase sigma-28 subunit FliA/WhiG [Tepidanaerobacter sp.
           Re1]
 gi|332696938|gb|AEE91395.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Tepidanaerobacter sp.
           Re1]
          Length = 246

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 97/210 (46%), Gaps = 17/210 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L++ DLI  G  GLM+A E++D   G KF TYA   +K +I   I +   T  IP  +R 
Sbjct: 48  LEYEDLISYGVFGLMQAIERYDTKKGIKFETYAYTRIKGSI---IDELRKTDMIPQDIRK 104

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           KI  +      M   +      ++I+  L +  + + K+ K       +    G      
Sbjct: 105 KIKMLQNAFSEMEQILGHSANDDDISNYLGISKKDLYKIYK------EISAAYGVLSFDE 158

Query: 588 LGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L ++ ED    S  P   A +  ++E     +  L P+E+ V+ + +  G+N     +E+
Sbjct: 159 LIEY-EDVGQASGQPDIQAEKEEVKEILGNAINQLPPQEKLVITLYYYEGLN----FKEI 213

Query: 646 GKQFCVTRERIRQIEAKAIRKLK-HPSRSK 674
            +   +++ RI QI  KAI +L+ H SR K
Sbjct: 214 AEVLELSQGRISQIHTKAILRLRGHLSRKK 243


>gi|225018358|ref|ZP_03707550.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
 gi|224948875|gb|EEG30084.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
          Length = 245

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 101/226 (44%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++  NLRLV+ +AKK+ + G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 63  ARDQLIVHNLRLVVYIAKKFESTGIGVEDLISIGTIGLIKAVNTFSPEKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R                 K  P   EI+          
Sbjct: 120 -----SRCIENE-----ILMHLR-----------------KSNPIKSEIS---------- 142

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP+ ++    D +   L D +  +N    ++  I+  + R+     +  L  
Sbjct: 143 ------IDEPLKIDW---DGNELLLSDVLGTENDC--VNRGIEDQVERDLIVSCVNKLGD 191

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  +++MRFG+    +HT +EV  +  +++  I ++E + I++LK
Sbjct: 192 RERSIMQMRFGMIDGKEHTQKEVADKIGISQSYISRLEKRIIKRLK 237


>gi|153835421|ref|ZP_01988088.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156975413|ref|YP_001446320.1| flagellar biosynthesis sigma factor [Vibrio harveyi ATCC BAA-1116]
 gi|148868042|gb|EDL67225.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156527007|gb|ABU72093.1| hypothetical protein VIBHAR_03144 [Vibrio harveyi ATCC BAA-1116]
          Length = 244

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  ++ +    +   + R+P+  E+A  L M +
Sbjct: 75  GIRIRGAMLDDIRKGDWVPR-SVHKNNR--EINQAIAELEGVLNRDPSDSEVAAHLGMTL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P       + ++     +
Sbjct: 132 DQYHSALT----DINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVADESFKKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G    V+  R+ QI ++A+++L+
Sbjct: 188 KQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQAMQRLR 234


>gi|143460|gb|AAA22713.1| 37 kd minor sigma factor (rpoF, sigB; ttg start codon) [Bacillus
           subtilis]
 gi|143463|gb|AAA22715.1| 37 kd minor sigma factor (ttg start codon) [Bacillus subtilis]
 gi|1881283|dbj|BAA19310.1| RNA POLYMERASE SIGMA-B FACTOR (SIGMA-37) [Bacillus subtilis]
          Length = 264

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 119/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ +V     LV  +AKKY+ +G  F  DL Q G IGL+ A +++D  +G  F  +A+ 
Sbjct: 32  AQETLVRVYTNLVDMLAKKYS-KGKSFHEDLRQVGMIGLLGAIKRYDPVVGKSFEAFAIP 90

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++     +++ + +R P  EEIA+ L +  E 
Sbjct: 91  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAEFLDVSEEE 150

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      D   + N +     VL
Sbjct: 151 VLETMEMGKSYQALSVDHSIEADSDGSTVTILDIVGSQE-----DGYERVNQQLMLQSVL 205

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 206 HVLSDREKQIIDLTY----IQNKSQKETGDILGISQMHVSRLQRKAVKKLR 252


>gi|120598267|ref|YP_962841.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|120558360|gb|ABM24287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
          Length = 237

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH  ++  +V +    +  ++ R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDWVPR-SVHRNNR--RVAQAIDELEKELGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D   + D++     ++  +          +  
Sbjct: 130 EYHHILN----DVSVGKIIGIEDLGVSQDILTLSDRSDDGSFEALAETQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|289578255|ref|YP_003476882.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
 gi|289527968|gb|ADD02320.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
          Length = 231

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 94/224 (41%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   
Sbjct: 51  ARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  S                     VR  ++M  ++            L  P+ GV
Sbjct: 111 IENEILMS---------------------VRAEKKMKGEV-----------FLQDPI-GV 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E+ + + + +E K  +  L + +   L+            R
Sbjct: 138 DK----EGNEISLMDVLGTEE-NEISEQVEKKIQIKKLYNKMNNVLKN-----------R 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  ++ MR+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 182 ERLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|78045111|ref|YP_359473.1| sporulation sigma factor SigK [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77997226|gb|ABB16125.1| RNA polymerase sigma-K factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 234

 Score = 60.5 bits (145), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 91/227 (40%), Gaps = 56/227 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E NLRLV  + KK+   G    DLI  G IGL+KA + F    G K +TYA   
Sbjct: 50  ARDVLAERNLRLVAHIVKKFEGTGEATEDLISIGTIGLIKAIDTFRPDKGTKLATYAAKC 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  I              +H+R                                     
Sbjct: 110 VENEIL-------------MHLR------------------------------------- 119

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
               K  +  +SL  PIG +   +   L D +  +  +  L+  ++    ET  + L  L
Sbjct: 120 --ATKKNRGEVSLYDPIGFDKEGNEITLLDILGTRGDIV-LEQVVRMLDAETIEKNLKKL 176

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           TPRE +V+  RFG+      T  E+ K+  ++R  + +IE +AI KL
Sbjct: 177 TPRERKVIEERFGLSQTPRKTQREIAKKMGISRSYVSRIEKRAILKL 223


>gi|121533733|ref|ZP_01665560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121307724|gb|EAX48639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 252

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 111/231 (48%), Gaps = 24/231 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++E  L LV  VA +      Q +D   LI  G  GL+ A E+FD     KF TYA+
Sbjct: 28  REKLIEKYLPLVKMVAGRVAIGLPQHIDKEDLISYGFFGLLDAIERFDPSRNIKFETYAV 87

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ +I  +I  Q     +P  +R K   + RT   + N + R  T  EIA+ +   VE
Sbjct: 88  ARIRGSIFDAIRVQDW---LPASLRQKGRLLERTVAELENSLGRSATDAEIAQAMNFTVE 144

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK--NAVSP-LDSAI-QANLRETTTRVL 617
            + ++  I +   S   P        L +F++++  N  SP L   I Q  +++T  + +
Sbjct: 145 QLHQL--INQLNASTLIP--------LEEFVQNETVNQASPNLAQEIEQEEVKKTLAKAI 194

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  +E  V+ + +  G+    TL+E+     ++  RI Q+  KAI +L+
Sbjct: 195 DRLPEKERLVISLYYYEGL----TLKEISLILKLSEARISQLHTKAIFRLR 241


>gi|323493327|ref|ZP_08098450.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
 gi|323312413|gb|EGA65554.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
          Length = 244

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/204 (25%), Positives = 98/204 (48%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R  VH  +
Sbjct: 42  VQVEDLIQAGMIGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHN 100

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +  +V +    +  ++ R+P+  E+A+ + + +E    +L      I+    +G ED   
Sbjct: 101 R--EVSQAISELEGQLNRDPSDAEVAQHMGISLEQYHTILT----DINCSRLVGIEDLGV 154

Query: 588 LGDFI--EDKNAVS-PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D I  +D++  + P         R+     + SL  RE  VL + +   +N    L+E
Sbjct: 155 SEDVISPDDRDEENLPFQGVADEYFRKALIDSIKSLPEREALVLSLYYDEELN----LKE 210

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+   V+  R+ QI ++++++L+
Sbjct: 211 IGEVIGVSESRVSQILSQSMQRLR 234


>gi|317970154|ref|ZP_07971544.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 253

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/194 (28%), Positives = 92/194 (47%), Gaps = 10/194 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V ANL LV  VA++ + R G  F DL QEG  GL+KA E+FD  LGY  ST A+ W
Sbjct: 23  RNAVVAANLPLVWKVARRESERSGHSFEDLAQEGVRGLIKAVERFDPSLGYTLSTAAVPW 82

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPV 560
           ++ A+   + D+    R+    R+ I  + R A     + ++  +P     +A+ L    
Sbjct: 83  IRGAMRHYLRDR---CRVFSGARNVIELLQRGAALQRRREQQGLSPMNDSSLARALGCSQ 139

Query: 561 EGVR--KVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  +  + L+      SL+ P G  D  + L + + D+ A        +  LR    R L
Sbjct: 140 QRWQEAQALQTCLRVASLDQPGGGSDPETPLVEQLSDQQAPGQYGWLERCELRRQLWRGL 199

Query: 618 ASLTPREERVLRMR 631
            +L   + R++  R
Sbjct: 200 KTLQASQRRLVLAR 213


>gi|291442923|ref|ZP_06582313.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291345870|gb|EFE72774.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 265

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 101/225 (44%), Gaps = 18/225 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + + L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F TYA+  V
Sbjct: 39  RDETIRSWLPMAHRIATRFRNRGEAMDDLRQVAAMGLVKAVDRYDPERGKAFETYAVPTV 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
              + R   D +  + +P  ++D +   VR ARR          PT  EIA    +  E 
Sbjct: 99  TGELKRHFRDHTWDVHVPRRVQD-LRNRVRVARRELAQTSGGGSPTCAEIASATGLGEED 157

Query: 563 VRKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   L+   +   +SL+  P G E  S L D +   +A   LD+A+    RE     L  
Sbjct: 158 VLLGLEALESYSALSLDAEPAGVEGGSPLVDRLGSCDAA--LDTAVD---REAVKPELRG 212

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR------ERIR 657
           L  RE  +L +R+   M      E +G  Q  V+R      ER+R
Sbjct: 213 LPERERTILYLRYFQDMTQVRIAERLGISQMHVSRLLSRSCERVR 257


>gi|225850277|ref|YP_002730511.1| RNA polymerase sigma factor for flagellar operon [Persephonella
           marina EX-H1]
 gi|225646527|gb|ACO04713.1| RNA polymerase sigma factor for flagellar operon [Persephonella
           marina EX-H1]
          Length = 209

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 112/229 (48%), Gaps = 39/229 (17%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           K+++V  NL LV  VA K  +R     ++F DL+    IGLMKA +++D     KFSTYA
Sbjct: 10  KEQIVLENLSLVKKVASKIYSRLPKGDIEFDDLVNTWIIGLMKAIDRYDKDKA-KFSTYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +  +S  I +P  +RD+I K    A R       EP P           
Sbjct: 69  YIKIRGEILDYL--RSLDI-VPRTVRDRIKK--EKAER------EEPMP----------- 106

Query: 561 EGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                 L  +   +S+E  +  +D S  L D +  K   +P +  I+ +L++   +V+  
Sbjct: 107 ------LSTSAVMVSIEKALSTKDESLKLIDTLVSKKE-TPEEEVIKDDLKDRLIKVIDM 159

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E+RVL+M +   ++     + V  +  ++  R+ QI+++A+RKLK
Sbjct: 160 LNEKEKRVLQMLYFEELD----FKTVASELNISVSRVSQIKSEALRKLK 204


>gi|2660755|gb|AAC29510.1| sigma-B general stress transcription factor [Bacillus
           licheniformis]
          Length = 265

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/231 (22%), Positives = 120/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +V+    LV ++AKKY+ +G  F  DL Q G +GL+ A +++D  +G  F  +A+ 
Sbjct: 32  AQLTLVQTYKNLVETLAKKYS-KGKSFHEDLCQVGMLGLLGAIKRYDPDVGKSFEAFAIP 90

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++      ++N+ +R P  +EIA+ L +  E 
Sbjct: 91  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDHLTNETQRSPKVDEIAEFLDVTEEE 150

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      +   + N +     VL
Sbjct: 151 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----EGYEKVNQKLMLESVL 205

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G    +++  + +++ KA++KL+
Sbjct: 206 HVLSDREKQIIELTY----IQNKSQKETGDMLGISQMHVSRLQRKAVKKLR 252


>gi|225871941|ref|YP_002753395.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
 gi|225792596|gb|ACO32686.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
          Length = 336

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 50/203 (24%), Positives = 93/203 (45%), Gaps = 17/203 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL+ A  KFD     +F +YA + ++ AI  S+     +   P  +R K   
Sbjct: 107 DLVSAGVVGLLDAMRKFDPAKKVQFRSYAQFRIRGAILDSLRMLDWS---PRELRRKGRA 163

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVE------GVRKVLKITKEPISLETPIGDEDT 585
           V    R ++ ++ R P   E+A ++ +P+       G  K L+I    +      G+E+ 
Sbjct: 164 VEEAIRAVTARLGRAPQESEVAGEMGLPLHEYQQLLGELKGLEIGTLHVERSEDSGEEEL 223

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           + L +  ED     PL   ++  +RE     + +L  RE  V+ + +      + T++E+
Sbjct: 224 AFLPNDPED----DPLFRCLKGEMRERLMAAIDALPERERLVMTLYY----YEEMTMKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G    V   R+ Q+ + A+  L+
Sbjct: 276 GLTLGVVESRVSQMHSSAVLHLR 298


>gi|237732926|ref|ZP_04563407.1| sporulation sigma factor sigK [Mollicutes bacterium D7]
 gi|229383995|gb|EEO34086.1| sporulation sigma factor sigK [Coprobacillus sp. D7]
          Length = 223

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 68/255 (26%), Positives = 106/255 (41%), Gaps = 59/255 (23%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IKS S E  ++  E    +     G+ EA   +  ++E NLRLV  +AKKY N      D
Sbjct: 18  IKSKSFELPLTAKEEERYLEQFFNGDKEA---RNVLIERNLRLVAHIAKKYENNKDMQED 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA + +      K +TYA        +R I ++     I +H+R      
Sbjct: 75  LISIGTIGLIKAVDSYKQNHKTKLATYA--------SRCIENE-----ILMHLRTN---- 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSH--LG 589
                                              K T   ISL   IG D+D S   LG
Sbjct: 118 -----------------------------------KKTNLDISLNETIGIDKDGSEIVLG 142

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I  K     +D   + +  +  T   + L PRE+  L MR+G+     +T +++ K+ 
Sbjct: 143 DIIAAKQE-EFIDIVDKKDTLDKFTTYFSVLEPREKDTLIMRYGLNNTKKYTQKDIAKKL 201

Query: 650 CVTRERIRQIEAKAI 664
            ++R  + ++E +A+
Sbjct: 202 NISRSYVSRLEKRAL 216


>gi|155061095|gb|ABS90485.1| RNA polymerase sigma factor [Streptomyces albus]
          Length = 282

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 108/237 (45%), Gaps = 18/237 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EF  + S+    E EA  A  E+VEA L +   +A ++ N+G    DL Q   +GL+KA 
Sbjct: 29  EFARLASLGSGPEREALCA--EIVEAWLPMAHRIAGRFRNKGESLEDLQQVAAMGLVKAV 86

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR----MSN 541
            +++   G  F +YA+  +   + R   D+   +R+P  +++  +K VR ARR       
Sbjct: 87  NRYEPGRG-AFESYAVPTITGELRRHFRDRMWDVRVPRRVQELRNK-VRAARRELLDRPG 144

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNA 597
              REPT  EI ++  +    VR  ++  +    +SL+  +   + D   L D +    A
Sbjct: 145 GSGREPTLAEIGEQAELTEAEVRDGMEAMEGYSALSLDAEVSSAEPDGFSLADTL---GA 201

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             P    I  N RE     L  L  RE  +L +R+   M      EE+G  Q  V+R
Sbjct: 202 PDPAYDHI--NDREAAKAGLRRLPERERTILYLRYFEDMTQSRIAEELGISQMHVSR 256


>gi|158337871|ref|YP_001519047.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308112|gb|ABW29729.1| RNA polymerase sigma factor, group 3 [Acaryochloris marina
           MBIC11017]
          Length = 265

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 83/159 (52%), Gaps = 9/159 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V  N+ LV  VA +  ++  + + DL Q G +GL+ A E+FD   GY FS++A+ +
Sbjct: 27  RNRLVRLNMGLVRKVAHRLAHQCAEPYEDLEQCGFLGLITAIERFDPTQGYAFSSFAVPY 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D++ T+RIP   +       +  + ++ ++ R P+ +EIA +L + ++  
Sbjct: 87  IRGEILHFLRDRANTVRIPRRWQQLSRDGAKVRQALTMELGRHPSDQEIADELDLSMQEW 146

Query: 564 R--KVLKITKEPISLETPI--GDEDTS----HLGDFIED 594
           R  K+    + P+SL   +  G    S     LGD + D
Sbjct: 147 RAVKLAASNRVPLSLNARVSSGHHQQSDSMMTLGDTLMD 185


>gi|289208354|ref|YP_003460420.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
 gi|288943985|gb|ADC71684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
          Length = 253

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 106/236 (44%), Gaps = 15/236 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           E  A+   ++ V  ++ LV  +A     R    +Q  DLIQ G IGL++AA +F+   G 
Sbjct: 12  ESVAATGHEQRVAEHIELVHRIAHHLMARLPSSVQVDDLIQAGMIGLLEAARQFEGGQGA 71

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F+TYA   ++ A+   +     T R  VH   +  K+    + +  +  R     E+A+
Sbjct: 72  TFATYAGIRIRGAMIDELRRSDWTPR-SVHRNSR--KIAEAIQTVEAREGRAARGVEVAE 128

Query: 555 KLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           +L +P++    +L+        +L+  +G  D     D + +    SP  +      RE 
Sbjct: 129 ELEVPIDEYYSMLQDHAGAHLFALDD-LGGTDGD--ADRVIEGQEASPSRTIEAGEFREE 185

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  L  RE  VL + +   +N    L E+G    VT  R+ QI ++A+ +L+
Sbjct: 186 LAAALGDLPERERLVLSLYYIEELN----LREIGAVLGVTESRVSQIRSQAVIRLR 237


>gi|88798984|ref|ZP_01114565.1| flagellar biosynthesis sigma factor FliA [Reinekea sp. MED297]
 gi|88778211|gb|EAR09405.1| flagellar biosynthesis sigma factor FliA [Reinekea sp. MED297]
          Length = 238

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/213 (25%), Positives = 94/213 (44%), Gaps = 37/213 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +AA  +D   G  F TYA                  IRI   M D+I K
Sbjct: 40  DLIQSGMIGLFEAAANYDQSKGASFETYA-----------------GIRIRGSMLDEIRK 82

Query: 532 -------VVRTARRMSNKIK-------REPTPEEIAKKLAMPVEGVRKVLKITKEP--IS 575
                  V R +RR+S+ I        R+    E+A++L + ++    ++K T+     S
Sbjct: 83  GDWIPRSVHRNSRRISDAIHTVEMREGRDAQDHEVAQELGVSLDEYYTLMKDTQGSRLFS 142

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            E  + +  + H  +  +    ++P      + + +     + +L  RE+ VL + +   
Sbjct: 143 FEELVDNSPSDHHENRPDASEGMAPHSGHQSSQMNDQLVEAIKALPEREQIVLSLYYEEE 202

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +N    L+E+G    V+  R+ QI ++A  +L+
Sbjct: 203 LN----LKEIGAVLGVSESRVSQIHSQATLRLR 231


>gi|163801862|ref|ZP_02195759.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
 gi|159174370|gb|EDP59174.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
          Length = 244

 Score = 60.5 bits (145), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAKQNYDGSKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  ++ +    +   + R+P   E+A+ L M +
Sbjct: 75  GIRIRGAMLDDIRKGDWVPR-SVHKNNR--QINQAIAELEGALNRDPFDSEVAEHLGMTL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P       + ++     +
Sbjct: 132 DQYHSALT----DINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVADDSFKKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G    V+  R+ QI ++A+++L+
Sbjct: 188 KQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQAMQRLR 234


>gi|124268265|ref|YP_001022269.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
 gi|124261040|gb|ABM96034.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
          Length = 237

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/214 (25%), Positives = 96/214 (44%), Gaps = 31/214 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA----------ITRSIADQSCTIRI 521
           DLIQ G IGL  A  +FD   G +F T+A   ++ A          ++R    Q   I +
Sbjct: 40  DLIQVGLIGLTDAMSRFDSAQGVQFETFATQRIRGAMLDELRGSDWMSRGNRKQQREIEV 99

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP 579
            VH             ++  ++ R P   EIAK++ + +   +++L   +  + + LE  
Sbjct: 100 AVH-------------KLQQQLGRAPAESEIAKQMGLSLADYQELLGKVRGTQLVYLEDM 146

Query: 580 IGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            GD+ D   L   + D+N  +P+       +R      + +L  RE+ V+ M +   MN 
Sbjct: 147 SGDDGDNDFLDRHVADENE-NPVALLQDHRMRLALIEAIKTLPEREQFVMGMYYEQDMN- 204

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              L+E+     VT  R+ Q+ +++I +L+   R
Sbjct: 205 ---LKEIAAVLGVTESRVCQLHSQSIARLRAKLR 235


>gi|332670026|ref|YP_004453034.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Cellulomonas
           fimi ATCC 484]
 gi|332339064|gb|AEE45647.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cellulomonas
           fimi ATCC 484]
          Length = 296

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 102/234 (43%), Gaps = 16/234 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++ ++     LV +VA +   R    ++  DL+  G  GL+ A EK++     KF +YA
Sbjct: 61  AREHLILHYAPLVAAVAGRVGMRLPSTVEQADLVSYGMFGLIDAIEKYETDRAVKFESYA 120

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ AI   I +      +P  +R K   V R    +   + R PT  E+A+ L + V
Sbjct: 121 SSRIRGAI---IDELRAMDWVPRSVRTKARSVDRAYAELEATLHRAPTEAEVARHLEISV 177

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLG----DFIEDKNAVSPLDSAIQANLRETTT 614
             +R       T    +L+  +G  +    G    D + D+    P  S   A  +    
Sbjct: 178 GELRATFSQLSTVNIAALDELLGGGEDRQAGVCLVDTLGDERTQDPAGSLDAAETKYLLA 237

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R +  L  RE  V+ + +  GM    TL E+G+   VT  RI Q+   A+ +L+
Sbjct: 238 RAIEQLGDRERMVVVLYYYEGM----TLAEIGRVLGVTESRISQMHTAAMLRLR 287


>gi|15894966|ref|NP_348315.1| sporulation sigma factor SigK [Clostridium acetobutylicum ATCC 824]
 gi|15024653|gb|AAK79655.1|AE007679_1 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|528974|gb|AAB94775.1| SigK [Clostridium acetobutylicum]
 gi|325509103|gb|ADZ20739.1| sporulation sigma factor SigK [Clostridium acetobutylicum EA 2018]
          Length = 234

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 62/252 (24%), Positives = 113/252 (44%), Gaps = 64/252 (25%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S SE ++ +  +++G+    +AK  ++E NLRLV  + KKY+  G +  DLI  G IGL
Sbjct: 31  LSESEEKYYLKKLKEGD---PLAKNILIERNLRLVAHIVKKYSYSGKEVDDLISIGTIGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + ++   G + +TYA                                   AR + N
Sbjct: 88  IKAIDSYNVSKGTRLATYA-----------------------------------ARCIEN 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFI--EDKN 596
           +I              M +   +K    +K  + L+ PIG +   +   L D +  +D +
Sbjct: 113 EI-------------LMLIRNNKK----SKNEVYLQDPIGVDKEGNEISLIDILSSDDDS 155

Query: 597 AVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            +  +++ IQ   L     RVL     RE+ +++MR+G+G        E+ +   ++R  
Sbjct: 156 VIEIVENRIQIGKLYVEINRVLKG---REKAIIKMRYGLGDGKPRNQREIAQILGISRSY 212

Query: 656 IRQIEAKAIRKL 667
           + +IE +A++KL
Sbjct: 213 VSRIEKRALKKL 224


>gi|266626024|ref|ZP_06118959.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288862073|gb|EFC94371.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 246

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 102/232 (43%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKSELIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPGKNIKLATYASRC 122

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                         R +NK K E                 
Sbjct: 123 IENEILMYL-------------------------RRNNKTKME----------------- 140

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSP-LDSAIQANLRETTTRVLA 618
                     +S++ P+    D +   L D +  D++ +   L++ ++ NL  +    ++
Sbjct: 141 ----------VSIDEPLNVDWDGNELLLSDILGTDEDVIYKDLETEVERNLLNSA---IS 187

Query: 619 SLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+PRE +++ +RFG+      + T +EV     +++  I ++E K +++LK
Sbjct: 188 RLSPRERKIVELRFGLSDEEGEEMTQKEVADLLGISQSYISRLEKKIMKRLK 239


>gi|283798349|ref|ZP_06347502.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291073934|gb|EFE11298.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|295092808|emb|CBK78915.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium cf.
           saccharolyticum K10]
          Length = 246

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 105/228 (46%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKSRLIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNTGKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++            R +NK K E + +E    L +  +G 
Sbjct: 120 -----SRCIENE-----ILMYL------------RRNNKTKLEVSIDE---PLNVDWDG- 153

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DED  +             L+  I+ NL  T    ++ L P
Sbjct: 154 --------NELLLSDILGTDEDVIY-----------RDLEDEIERNLLNTA---ISRLNP 191

Query: 623 REERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+      + T +EV     +++  I ++E K +++LK
Sbjct: 192 REKKIVELRFGLNSENGEEMTQKEVADLLGISQSYISRLEKKIMKRLK 239


>gi|209522287|ref|ZP_03270915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp. H160]
 gi|209497281|gb|EDZ97508.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp. H160]
          Length = 244

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     R+   + R  +  EIA+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHRVEQNLGRSASEAEIAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDDSLRSAVVDAIDRLPEREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|317129289|ref|YP_004095571.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474237|gb|ADU30840.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 106/222 (47%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD     K +TYA       
Sbjct: 61  LIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVSTFDPEKKIKLATYA------- 113

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR +NKI+ E + +E    L +  +G     
Sbjct: 114 -SRCIENE----------------ILMYLRR-NNKIRSEVSFDE---PLNIDWDG----- 147

Query: 568 KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G +ED    G  IEDK     +D       R+   + L +L  RE++
Sbjct: 148 ----NELLLSDVLGTEEDIITKG--IEDK-----VD-------RKLLVKALEALNDREKQ 189

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +RFG+  + + T ++V     +++  I ++E + I++L+
Sbjct: 190 IMELRFGLAGDEEKTQKDVADMLGISQSYISRLEKRIIKRLQ 231


>gi|312135825|ref|YP_004003163.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775876|gb|ADQ05363.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 246

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 115/230 (50%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 19  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +  Q     +P  +R K  ++ +    +  +  R PT  E+AK+L + + 
Sbjct: 79  TRIRGAIIDCVRSQDF---LPRSIRQKAKEIEKAYIEIERE-GRTPTDYEVAKRLGISIS 134

Query: 562 GVRKVL-KITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVLA 618
            ++K+  KI+   I SLE+ +     S +G     ++ VS  +  I+   L+    + + 
Sbjct: 135 ELQKLQEKISSGMIVSLESFLEQSYESKIGGL---EDFVSQPEHFIENEELKNVLRQQID 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   E  V+ + +      + +++E+ K   ++  R+ Q+  +A+ KL+
Sbjct: 192 NLMENERMVIMLYY----YEELSIKEIAKILGISESRVSQLHTRALLKLR 237


>gi|327399094|ref|YP_004339963.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hippea maritima DSM
           10411]
 gi|327181723|gb|AEA33904.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hippea maritima DSM
           10411]
          Length = 238

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 115/235 (48%), Gaps = 18/235 (7%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY-KFST 498
           I K+E++++   +V  + KK   R   G    D +Q G +GL+KA E +D      +F +
Sbjct: 2   IDKEEIIQSYYPIVRRIVKKTVVRMPEGYDEEDFVQIGMMGLLKAIENWDENKSLSEFKS 61

Query: 499 YAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           YA       I   I D+  +I  PV  + RDK+ K+    R++ ++    PT +EIA++ 
Sbjct: 62  YA----NTKIRGYILDKLRSID-PVSRYARDKLKKINMAYRQLMSEGNFNPTDDEIAERA 116

Query: 557 AMPVEGVRKVL--KITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETT 613
            M ++   ++L  +     +S++  +  +D    L + IE+K++ SPL    +  L++  
Sbjct: 117 DMSIDEFNELLYKQSNSTMLSIDEAVSSDDGDMVLLEVIENKSSKSPLAILEEEELKDIV 176

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L +L   E  VL + +      D  ++E+      T  RI QI+ KA+ K++
Sbjct: 177 KEALKALNETEITVLSLYY----YEDFNMKEIASLIGKTESRISQIKTKALLKIR 227


>gi|254425398|ref|ZP_05039116.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196192887|gb|EDX87851.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 246

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 109/222 (49%), Gaps = 9/222 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V  N  LV  +A + +++  + + DL Q G IGL+++ E+FD   G  FS++A+ +
Sbjct: 12  RNQLVRLNAGLVRKIAHRVSHQCAEPYEDLEQIGYIGLIRSIERFDPGQGCAFSSFAVPY 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+  T++IP   +D   +  +    +  +  R+P+  E+A+ L + V+  
Sbjct: 72  IRGEMLHFLRDRGTTVKIPRRWQDLQKEGQKRQSELIRRYGRQPSDIEMAEALTVSVQEW 131

Query: 564 RKVLKITKE--PISLETPIGDE-DTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R+V    K   P+SL+  +  + D+S  LGD + D   V    + I    R+   R ++ 
Sbjct: 132 RQVKLANKNRMPLSLDATVCHQIDSSITLGDTLPD---VHYQLTQILEEDRQQIQRAMSQ 188

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIE 660
           L  +    +   F  G++     E +G     VTR   R +E
Sbjct: 189 LEEKTRSAIEFVFFKGLSRKEVAERIGVSPMTVTRRIQRGVE 230


>gi|23098930|ref|NP_692396.1| sporulation sigma factor SigE [Oceanobacillus iheyensis HTE831]
 gi|22777158|dbj|BAC13431.1| stage II sporulation protein GB (RNA polymerase
           sporulation-specific sigma E factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 239

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 105/227 (46%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAMLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK+K E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKLKSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  E+      L+S +   L ++    L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVMGTEEDIITKNLESTVDKTLLKSA---LEKLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E K IR+LK
Sbjct: 186 AREKQIMELRFGLIGEEEKTQKDVADMLGISQSYISRLEKKIIRRLK 232


>gi|284043529|ref|YP_003393869.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947750|gb|ADB50494.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 261

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 106/225 (47%), Gaps = 12/225 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +   +E+ + LV  +A++Y        DL+Q   +GL+KA ++FD   G +F+++A+  +
Sbjct: 42  RTRAIESFMPLVHKLARRYHPGPEPLDDLVQVACVGLVKAIDRFDPDAGPRFASFAIPTI 101

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D + ++ +P  +++   ++      +S +  R PT  E++    +  E + 
Sbjct: 102 TGELRRHFRDTTWSVHVPRRVQEDALRLRHAMTELSERPGRSPTIHELSAATGLDDEQIT 161

Query: 565 KVLKIT--KEPISLETPIGDED--TSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLAS 619
           + L  T  K   SL+ P+  +D  ++ +GD +  D+   +       A  R T    L +
Sbjct: 162 EALHATTAKAASSLDRPVPGQDDGSATIGDTLGCDEYGFA------LAEHRTTIGPRLRA 215

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKA 663
           L  R+  +L +RF   M      + +G  Q  V+R   R ++A A
Sbjct: 216 LPLRDREILYLRFAEDMTQHEIAQRIGCSQMQVSRLLRRALDALA 260


>gi|1588993|prf||2209422A fliA gene
          Length = 237

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 92/198 (46%), Gaps = 10/198 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+    Q I   + +       P  +R    +
Sbjct: 42  DLLQAGGIGLLNAVERYDALQGTAFTTYAV----QRIAPMLDELRQRDWAPRRIRRNARE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDEDTSHLGD 590
           V    +++  ++    T +E+A+ L + +   R++L  T            +E    +  
Sbjct: 98  VASAMQKVEQRLGAPATEQEVAQNLDIDLTEYRQILLDTNNSQLFSYDEWREEHGRTVEP 157

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     +PL   ++ NLR+      A L  RE+ VL + +   +N    L+E+G    
Sbjct: 158 MLEGHEDANPLQHLLEGNLRQRVIEAEA-LPEREKMVLTLYYQEELN----LKEIGAVLE 212

Query: 651 VTRERIRQIEAKAIRKLK 668
           V   R+ Q+ ++AI++L+
Sbjct: 213 VGESRVSQLHSQAIKRLR 230


>gi|294501014|ref|YP_003564714.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|295706363|ref|YP_003599438.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
 gi|294350951|gb|ADE71280.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|294804022|gb|ADF41088.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
          Length = 239

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 107/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NKI+ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +  +   D  ++AN+ R+   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVMGTEEDIITKD--LEANVDRKLLLKALHQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|149188102|ref|ZP_01866397.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
 gi|148838090|gb|EDL55032.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
          Length = 243

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 90/200 (45%), Gaps = 15/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMRDKIH 530
           DLIQ G IGL++A + +D   G  F TYA   ++ A+   I       R +  H RD   
Sbjct: 46  DLIQAGMIGLIEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPRSVHKHSRD--- 102

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
            + +    +  ++ R+PT  E+A  L + +    K L      I+    +G ED     D
Sbjct: 103 -ISQAISVLEVELNRDPTDSEVANYLGLSLAQYHKALT----DINCSKLVGIEDLGVSED 157

Query: 591 --FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              + D+   +P         RE     + SL  RE   L + +   +N    L+E+G+ 
Sbjct: 158 SVSVSDEEDNTPFQGVADDAFREALIESIKSLPEREALTLSLYYDEELN----LKEIGEV 213

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++++++L+
Sbjct: 214 LGVSESRVSQILSQSMQRLR 233


>gi|325662152|ref|ZP_08150770.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471601|gb|EGC74821.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 211

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 69/258 (26%), Positives = 111/258 (43%), Gaps = 64/258 (24%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T ++ +E ++ +    +G+ EA   K  ++E NLRLV  + KKY        DLI  
Sbjct: 6   SFPTPLTSAEEQYYMQKYTEGDLEA---KHILIEHNLRLVAHIVKKYQRPEEDNEDLISI 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA   F+   G + STYA                                   A
Sbjct: 63  GTVGLIKAVITFNPEKGNRLSTYA-----------------------------------A 87

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R + N+I            L M    +R   K ++E ISL  PIG   T   G+ I+  +
Sbjct: 88  RCIENEI------------LMM----LRSRKKSSRE-ISLYEPIG---TDREGNEIQLFD 127

Query: 597 AVSPLDSAIQA------NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +   D  I        ++R    +V + L+ RE  VL+MR+G+    ++T  E+ K+  
Sbjct: 128 VMETTDEDIHEKINLKDDVRTLYEKVESELSDRERLVLKMRYGLYNEEEYTQREIAKRLG 187

Query: 651 VTRERIRQIEAKAIRKLK 668
           ++R  + +IE  A+ KL+
Sbjct: 188 ISRSYVSRIEKSAVEKLR 205


>gi|167838290|ref|ZP_02465149.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           MSMB43]
          Length = 244

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/202 (24%), Positives = 93/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R     EIA  L MP++  + +L    + +     +  ED     D 
Sbjct: 98  VEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSML----QDLHGSQLVYYEDFDRSADD 153

Query: 591 --FIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++   A    PL + +  +LR+     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRADHSDPLSALLDEHLRDALVDAIEHLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|67922879|ref|ZP_00516377.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
 gi|67855303|gb|EAM50564.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
          Length = 260

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 69/118 (58%), Gaps = 1/118 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE NL LV  VA + +N+  + + DL Q G +G ++A E+F+   G  FS++ + +
Sbjct: 31  RNQLVECNLGLVRQVAHRISNQCSEPYEDLEQIGYLGFIRAIERFNPQQGCAFSSFDIPY 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  +   + D+   +RIP   ++  +K  +  ++++  +KR P   EIA+ L +P+E
Sbjct: 91  IRGEMLHYLRDKGSVMRIPRRWQELHNKGKKIRKQLTASLKRSPFDWEIAEALMIPLE 148


>gi|296272949|ref|YP_003655580.1| RpoD subfamily RNA polymerase sigma-70 factor subunit [Arcobacter
           nitrofigilis DSM 7299]
 gi|296097123|gb|ADG93073.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcobacter
           nitrofigilis DSM 7299]
          Length = 626

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 70/130 (53%), Gaps = 8/130 (6%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE------DEEGSEDSLDLASSASNSSVF- 105
           L P   SS+ ++  +A++    +N++   +        + +  ED  +        SV+ 
Sbjct: 30  LFPKAPSSQNIKKLIALMQLYNVNMMTSQEQAKVMNAVEAKKREDQRNKMIDGGEDSVYD 89

Query: 106 LQKRKDSADRS-TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           L K K+  + S +D PVRMYLREMG I LL++E EI I+K+IE G  +++ ++C  P   
Sbjct: 90  LLKNKELLEWSRSDSPVRMYLREMGQIPLLTKEEEIEISKKIEMGEDIILDAICFVPYLV 149

Query: 165 QALIIWRDEL 174
             ++ +++ L
Sbjct: 150 DFILEYKEPL 159


>gi|166031185|ref|ZP_02234014.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
 gi|166029032|gb|EDR47789.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
          Length = 246

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 102/227 (44%), Gaps = 52/227 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  ARKLLIEHNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPTKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NK K E + +E    L +  +G 
Sbjct: 120 -----SRCIENE----------------ILMYLRR-NNKTKLEVSIDE---PLNVDWDG- 153

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G E+ +   D  ++               R+   + L  L+ R
Sbjct: 154 --------NELLLSDILGTEEDTIYKDLEQEAE-------------RKILIKALNLLSAR 192

Query: 624 EERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  +++MRFGIG     + T +EV     +++  I ++E K + +L+
Sbjct: 193 ERSIIQMRFGIGTVDGEEKTQKEVADLLGISQSYISRLEKKIMVRLR 239


>gi|157363480|ref|YP_001470247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
 gi|157314084|gb|ABV33183.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
          Length = 236

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 96/199 (48%), Gaps = 12/199 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG + L+ A  ++D   G    ++ +  +K A+   +        +P ++R  + +
Sbjct: 36  DLIQEGVLALLSAIRRYDPKKGVSMYSFVVKRIKGAMYDYLRKIDW---MPRNLRKNVKE 92

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLG 589
           V +    + N + + P+ EEIA    +    V++ L   + K+ + L+  I  E      
Sbjct: 93  VEKAIHELENHLNKHPSIEEIALHTGLSTNEVKRALDETVRKQLLRLDEFIY-EGLDSFS 151

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I+  +   P ++A +  + E     + +L+ RE+ VL +RF      D +L+E+G   
Sbjct: 152 DIIKADD--EPSENAFREIILEKVAEAIRTLSKREQLVLSLRF----EQDLSLKEIGTVI 205

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ QI + ++ K+K
Sbjct: 206 GVSESRVSQILSSSLIKIK 224


>gi|260762514|ref|ZP_05874851.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672940|gb|EEX59761.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 131

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 43/70 (61%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 62  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 121

Query: 494 YKFSTYAMWW 503
            +FSTYA WW
Sbjct: 122 VRFSTYASWW 131


>gi|297544535|ref|YP_003676837.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842310|gb|ADH60826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 231

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 95/224 (42%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   
Sbjct: 51  ARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  SI                         R   K+K E   ++       P+ GV
Sbjct: 111 IENEILMSI-------------------------RAEKKMKGEVFLQD-------PI-GV 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E+ + + + +E K  +  L + +   L+            R
Sbjct: 138 DK----EGNEISLMDVLGTEE-NEISEQVEKKIQIKKLYNKMNNVLKN-----------R 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E+ ++ MR+G+      T  E+ K   ++R  + +IE +A+ KL
Sbjct: 182 EKLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRIEKRALNKL 225


>gi|167630135|ref|YP_001680634.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
 gi|167592875|gb|ABZ84623.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
          Length = 235

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 106/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 54  VKSILIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPLKKIKLATYA--- 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK + E + +             
Sbjct: 111 -----SRCIENE-----ILMYLRR------------NNKTRSEVSFD------------- 135

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +N +  +  +I+  + R+     ++ LT 
Sbjct: 136 --------EPLNID---WDGNELLLSDVLGTENDI--IYKSIEEEVDRKLLQAAMSKLTS 182

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE R++ +RFG+  + + T +EV     +++  I ++E + I++L+
Sbjct: 183 RERRIVELRFGLRDSREKTQKEVADMLGISQSYISRLEKRIIKRLR 228


>gi|160933251|ref|ZP_02080640.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
 gi|156868325|gb|EDO61697.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
          Length = 230

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/241 (23%), Positives = 107/241 (44%), Gaps = 57/241 (23%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  VR+GE  A   ++ ++  NLRLV+ +AKK+ + G    DLI  G IGL+KA   F 
Sbjct: 38  VMERVRRGEKNA---REPLITHNLRLVVYIAKKFDSNGASVEDLISIGTIGLIKAVNTFC 94

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                K +TYA        +R I ++             I   +R + ++ N+I      
Sbjct: 95  PERNIKLATYA--------SRCIENE-------------ILMFLRKSSQLKNEIS----- 128

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQA 607
                                 EP++++    D +   L D +   N +    ++  ++ 
Sbjct: 129 --------------------IDEPLNVD---WDGNELLLSDILGSDNDIVNRDIEKEVEC 165

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L     + ++ L PRE +++ +RFG+    +HT ++V     +++  I ++E + I +L
Sbjct: 166 SL---VLQAVSRLAPRERQIMELRFGLCGQKEHTQKQVADVLGISQSYISRLEKRIIERL 222

Query: 668 K 668
           K
Sbjct: 223 K 223


>gi|312794093|ref|YP_004027016.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181233|gb|ADQ41403.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 244

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 100/232 (43%), Gaps = 66/232 (28%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK ++E NLRLV+ +AK++ N  +   DL+  G IGL+KA   ++     K +TYA    
Sbjct: 64  KKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGLIKAINTYNPNKNIKLATYA---- 119

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
               ++ I ++                ++   RR SN            KKL M ++   
Sbjct: 120 ----SKCIENE----------------ILMFLRRNSN------------KKLEMSID--- 144

Query: 565 KVLKITKEPIS--------LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                  EP++        L + +   DT  + + IE+      L  AIQ          
Sbjct: 145 -------EPLNVDWDGNELLLSEVLGTDTEEIYNRIENNVEKEALLQAIQ---------- 187

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  RE++++ +RFG G + + T +EV     +++  I ++E K I +LK
Sbjct: 188 --KLPSREKKIVELRFGFGDDGEKTQKEVADMLGISQSYISRLEKKIITRLK 237


>gi|255505283|ref|ZP_05345211.3| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255268593|gb|EET61798.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 249

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 101/237 (42%), Gaps = 58/237 (24%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  E+  AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K 
Sbjct: 59  GGRESGEAKSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPGKNIKL 118

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +TYA        +R I ++     I +++R       RT++                   
Sbjct: 119 ATYA--------SRCIENE-----ILMYLR-------RTSK------------------- 139

Query: 557 AMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                        TK  +S + P+    D +   L D +     V   D   +   +   
Sbjct: 140 -------------TKMEVSFDEPLNVDWDGNELLLSDILGTDEDVIYRDMETEVEYK-LL 185

Query: 614 TRVLASLTPREERVLRMRFGIGMN--TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L+ RE  ++++RFGIG N   + T +EV     +++  I ++E K I +LK
Sbjct: 186 MHAIDKLSDRERMIIQLRFGIGRNDGEEKTQKEVADMLGISQSYISRLEKKIIGRLK 242


>gi|302746276|gb|ADL62728.1| RpoD [Morganella morganii subsp. morganii]
          Length = 274

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVR 60

Query: 181 LREII 185
           L ++I
Sbjct: 61  LSDLI 65


>gi|297196315|ref|ZP_06913713.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722893|gb|EDY66801.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 272

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 98/217 (45%), Gaps = 17/217 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+V A L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F ++A+  V
Sbjct: 37  RQEIVSAWLPMAERIAGRFRNRGESIEDLQQVAALGLVKAVDRYDPSRG-AFESFAVPTV 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVE- 561
              + R   D    + +P  ++D +   VR AR+  +     R PT  EIA++  +  E 
Sbjct: 96  VGEVKRHFRDHMWALHVPRRVQD-LRNRVRFARQDLVQTVSGRAPTVAEIAERAGVSEED 154

Query: 562 ---GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVL 617
              G+  +   T   +  E P G +D   L D       +   D AI   + RE     L
Sbjct: 155 ALVGLEALESFTALSLDAELP-GADDGYSLSD------TLGSADPAIDVLVDREAVKPGL 207

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             L  RE+ +L MRF   M      + +G  Q  V+R
Sbjct: 208 RKLPEREQNILYMRFFRDMTQSSIAQTLGISQMHVSR 244


>gi|295092950|emb|CBK82041.1| DNA-directed RNA polymerase specialized sigma subunit [Coprococcus
           sp. ART55/1]
          Length = 128

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 46/75 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V  N+ LV+SVA++Y  RG +  DLIQ G IGL+KA ++FD     K STYA+  
Sbjct: 18  ARDKLVTDNMGLVVSVARRYVGRGQELEDLIQIGLIGLVKAIDRFDMDYEVKLSTYAVPL 77

Query: 504 VKQAITRSIADQSCT 518
           ++  I R + D    
Sbjct: 78  IQGEIRRFLRDDGMV 92


>gi|218289913|ref|ZP_03494103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240053|gb|EED07239.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 102/223 (45%), Gaps = 52/223 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 2   LIERNLRLVVYIARKFENTGVNIEDLVSIGTIGLIKAVNTFDPSKKIKLATYA------- 54

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NK++ E + +E    L +  +G     
Sbjct: 55  -SRCIENE-----ILMYLRR------------NNKLRAEVSLDE---PLNVDWDG----- 88

Query: 568 KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G D DT +       +N    +D       RE     L  L+ RE  
Sbjct: 89  ----NELLLSDVLGTDSDTIY-------RNLEDEVD-------RELLYDALDKLSERERT 130

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++ +RFG+G   + T ++V     +++  I ++E + +++L+ 
Sbjct: 131 IMELRFGLGTGQEMTQKDVADLLGISQSYISRLEKRILKRLQR 173


>gi|331269717|ref|YP_004396209.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
 gi|329126267|gb|AEB76212.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
          Length = 226

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 101/231 (43%), Gaps = 59/231 (25%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++AK  ++E NLRLV  + KKY+       DLI  G +GL+KA + FD   G + +TYA 
Sbjct: 39  TLAKGILIERNLRLVAHIVKKYSYPNKDIDDLISIGTVGLIKAIDSFDISKGTRLATYA- 97

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
                                             AR + N+I              M + 
Sbjct: 98  ----------------------------------ARCIENEI-------------LMLIR 110

Query: 562 GVRKVLKITKEPISLETPIG----DEDTSHLGDFIEDKNAV-SPLDSAIQANLRETTTRV 616
             +K+    K  + L+ PIG      + S +     D+N+V   +++ +Q  +++   ++
Sbjct: 111 NTKKI----KSEVYLQDPIGVDKEGNEISLMDVLSSDENSVIEVVENRMQ--VKKLYDKI 164

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              LT RE+ +++MR+G+      T  E+     ++R  + +IE +A++K+
Sbjct: 165 NECLTDREKIIIKMRYGLNDGKPKTQREIAAFLNISRSYVSRIEKRALKKM 215


>gi|226944861|ref|YP_002799934.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
 gi|226719788|gb|ACO78959.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
          Length = 231

 Score = 60.1 bits (144), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/237 (23%), Positives = 109/237 (45%), Gaps = 19/237 (8%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            +  I +++++E  L LV   A     R    ++  DLIQ G IGL+ A  ++D   G  
Sbjct: 4   AQGKIRQRDLLEEYLPLVRRQALNLQTRLPASVELDDLIQAGTIGLLDALSRYDAAQGAS 63

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+T+A   V+ A+   +  +     +P  +R     +  T R++  ++ R     EIA  
Sbjct: 64  FATFASQRVRGAMLDELRSRDW---VPRSVRRNARALEDTLRQLEQRLGRPAEEREIATS 120

Query: 556 LAMPVEGVRKVLKITK--EPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + + +   R++L  +   + ++++    DE D   +G +       SP     +    E 
Sbjct: 121 MGLDLAEYRQLLLDSNGSQLVAIDDLGEDEVDAMSVGHY------ASPFVELAEGRDLER 174

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + + +L  RE+ VL    G+    D  L+E+G    V+  R+ Q+ ++A+ +L++
Sbjct: 175 LVKAIEALPEREKLVL----GLYYQEDLNLKEIGAVLGVSESRVCQLHSQAVARLRN 227


>gi|326385162|ref|ZP_08206830.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196127|gb|EGD53333.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 250

 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/157 (28%), Positives = 78/157 (49%), Gaps = 8/157 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+   +I + E + A L L   +A++Y  RG  F DL Q   +GL+ A ++FD   G  F
Sbjct: 22  GDPRRTILRDEAIVACLPLARHIAQRYRERGEPFDDLEQVARLGLVHAVDRFDPTQGNDF 81

Query: 497 STYAMWWVKQAITRSIADQSCTIRIP---VHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            ++A+  +   + R   D++ +IR+P   + +R +I +      ++     R P  +EIA
Sbjct: 82  LSFAVPTIIGEVRRHFRDRTASIRLPRSAIELRGRIRE---AEEQLEQTHGRTPDDDEIA 138

Query: 554 KKLA-MPVEGVR-KVLKITKEPISLETPIGDEDTSHL 588
             L   P   VR +   I +  +SL+   GD++ + L
Sbjct: 139 AFLGESPDAIVRARAADIAQSAVSLDAGAGDDERALL 175


>gi|253996640|ref|YP_003048704.1| flagellar biosynthesis sigma factor [Methylotenera mobilis JLW8]
 gi|253983319|gb|ACT48177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylotenera mobilis
           JLW8]
          Length = 244

 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 46/205 (22%), Positives = 94/205 (45%), Gaps = 9/205 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+ A  +++   G +F TYA   ++ A+   +        +P  +R  +  
Sbjct: 41  DLIQAGMMGLLDAVNRYEDTHGAQFETYAAQRIRGAMLDELRSSDW---LPRSIRKNMRD 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++  ++ + PT  ++AKKL M +    ++L      + I  E     +   H  
Sbjct: 98  VENAISQLEQQLGQSPTENDVAKKLNMSLAEYHEMLGDCSGHQLIYYEDFHEADSGEHFL 157

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D  +  +   P+   +  + ++     + SL  RE+ +L + +   +N    L+E+G   
Sbjct: 158 DRFQTDHDNDPIKGLLIGDFKDALIGAIDSLPEREKILLGLYYEQELN----LKEIGAVM 213

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSK 674
            V+  R+ Q+ ++A+ +L+   R K
Sbjct: 214 SVSESRVCQLHSQAVARLRANLREK 238


>gi|225181965|ref|ZP_03735398.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
 gi|225167327|gb|EEG76145.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
          Length = 234

 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 73/287 (25%), Positives = 123/287 (42%), Gaps = 65/287 (22%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           +   VA  V  I+ + + + + S    +   E +  ++++ KG+ EA   +  ++E NLR
Sbjct: 4   FITIVAAVVKEIVLLVSYLNNNSFPQPLKPQEEKKYLALMAKGDEEA---RSILIERNLR 60

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV  V KK+ N G    DLI  G +GL+KA + F+   G + +TYA         R I +
Sbjct: 61  LVAHVIKKFENTGEDQEDLISIGTVGLIKAIDSFNNNKGTRLATYA--------ARCIEN 112

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           +     I +H+R      V T R                                 K  +
Sbjct: 113 E-----ILMHIR------VITKR---------------------------------KAEV 128

Query: 575 SLETPIGDEDTSH---LGDFI--EDKNAVSPLD-SAIQANLRETTTRVLASLTPREERVL 628
            L  PIG +   +   L D +  +++  ++ +D   ++A L E   +    L  RE  VL
Sbjct: 129 LLHDPIGTDKEGNEITLLDVLGSDEELVLNEVDRKMLEAKLYEVIKK----LKLRERTVL 184

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            MRFG+ M    T +E+ K   ++R  + +IE K I K+    R ++
Sbjct: 185 AMRFGLPMGRRKTQKEIAKSLGISRSYVSRIEKKVIAKIAEEFRQER 231


>gi|212634384|ref|YP_002310909.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212555868|gb|ACJ28322.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 239

 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 103/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+    EIA++L M ++
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RVAQVIDELEQELGRDARDPEIAERLEMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +  ED +     +S  +          +  
Sbjct: 130 EYYSILN----DVSVGKVVGIEDLGVAVDVVNHEDNHDDVAYESLAEVEFHSALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|171058305|ref|YP_001790654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptothrix cholodnii
           SP-6]
 gi|170775750|gb|ACB33889.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptothrix cholodnii
           SP-6]
          Length = 238

 Score = 59.7 bits (143), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 91/206 (44%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP-VHMRDKIH 530
           DLIQ G IGL  A  +FD   G  F T+A   ++ A+   +       R    H RD   
Sbjct: 40  DLIQVGMIGLTDALSRFDIGQGVMFETFATQRIRGAMLDELRGSDWMSRGNRKHQRD--- 96

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIG-DEDTSH 587
            +     R+  K+ R P   EIAK++ + +   + +L   +  + I LE   G D D  +
Sbjct: 97  -IEGAVHRLEQKLGRTPQESEIAKEMGITLLEYQDLLNRVRGTQLIYLEDMGGADGDNDY 155

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   +       PL       +R+     + +L  RE+ V+ M +   MN    L+E+  
Sbjct: 156 LDRHVAADTGGDPLARLNDHRMRQALVDAIKNLPEREQYVMSMYYEEDMN----LKEIAA 211

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  R+ Q+ +++I +L+   R+
Sbjct: 212 VLGVTESRVCQLHSQSIARLRAKLRT 237


>gi|225848018|ref|YP_002728181.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225644246|gb|ACN99296.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 240

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 96/203 (47%), Gaps = 13/203 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL  A EK+D   G K STYA   ++  I   +        +P  +R KI  
Sbjct: 39  DLIQVGVLGLYDALEKYDPSKGIKLSTYAEIRIRGYIIDHLRQLDW---VPRSVRSKIKN 95

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG--DEDTSH 587
           +     ++  ++ R+   EEIA  L M VE      ++   K  ISL++ +   D+++ H
Sbjct: 96  LENKIAQLEAQLGRQAKTEEIANYLGMTVEEYMTYAEVLANKVLISLDSDVSKDDDESLH 155

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           L + I   N  +P     +  L+E  +  +L  L  RE  ++ + +   +N    ++E+ 
Sbjct: 156 LWEVI-SSNDDTPDKVVEEKQLKEILSDIILNHLDERERLLISLYYYEELN----MKEIA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +T  R+ Q+  K + KLK+
Sbjct: 211 DILGITESRVSQLHTKIMLKLKN 233


>gi|194368262|gb|ACF58023.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 47/75 (62%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + ++  
Sbjct: 5   DEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEEGEKEVLRALLACKVAVEEILDI 64

Query: 171 RDELNDGTTLLREII 185
            ++L      +R++I
Sbjct: 65  GNKLKTAKLRVRDVI 79


>gi|312126848|ref|YP_003991722.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311776867|gb|ADQ06353.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 248

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 116/230 (50%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD   G KF TYA 
Sbjct: 21  KEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKFETYAY 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K AI   +  Q     +P  +R K  K +  A     K  + PT +E+AK++ + V+
Sbjct: 81  TRIKGAIIDCVRSQDF---LPRSIRQK-AKEIEKAYIEIEKEGKTPTDQEVAKRIGISVD 136

Query: 562 GVRKVL-KITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLA 618
            ++K+  +I+    ISL++ +     S +G     ++ VS  +  I+    +T  R  + 
Sbjct: 137 ELQKLQDRISSGMIISLDSFLEQNYESKIGGL---EDFVSQPEHFIENEELKTVLRQQID 193

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 194 NLMENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLR 239


>gi|261405539|ref|YP_003241780.1| sporulation sigma factor SigK [Paenibacillus sp. Y412MC10]
 gi|315645904|ref|ZP_07899025.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|329925929|ref|ZP_08280639.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
 gi|261282002|gb|ACX63973.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. Y412MC10]
 gi|315278665|gb|EFU41979.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|328939580|gb|EGG35929.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
          Length = 233

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 100/244 (40%), Gaps = 73/244 (29%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++ +++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +T+A   
Sbjct: 50  SRNKLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFRPNKGTKLATFAARC 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +H+R                                     
Sbjct: 110 IENEIL-------------MHLRS------------------------------------ 120

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD----------SAIQANLRET- 612
              LK T++ +SL  PIG +         ++ N ++ +D           A+Q  + ++ 
Sbjct: 121 ---LKKTRKDVSLHDPIGTD---------KEGNEITLIDILGTEADDIVDAVQLKIEKSK 168

Query: 613 TTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             R L  L  RE+ V+  RFG+     + T  E+ K+  ++R  + +IE +A+ KL H  
Sbjct: 169 IYRNLDILDDREKEVVIGRFGLEAGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEF 228

Query: 672 RSKK 675
             +K
Sbjct: 229 YKQK 232


>gi|187932801|ref|YP_001885388.1| sporulation sigma factor SigE [Clostridium botulinum B str. Eklund
           17B]
 gi|187720954|gb|ACD22175.1| RNA polymerase sigma-E factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 235

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 101/223 (45%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVHVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++KIK E +                   
Sbjct: 111 -SRCIENE-----ILMYLRR------------NSKIKAEIS------------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
               EP++++    D +   L D +  E+    + ++  +   L     R+   L  RE+
Sbjct: 134 --FYEPLNID---WDGNELLLSDILGTENDEVYNLIEDEVDKQLLLMALRI---LNDREK 185

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++R+RFG+    + T +EV     +++  I ++E K IR+LK
Sbjct: 186 EIVRLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIIRRLK 228


>gi|188587739|ref|YP_001920535.1| sporulation sigma factor SigE [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251779018|ref|ZP_04821938.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498020|gb|ACD51156.1| RNA polymerase sigma-E factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083333|gb|EES49223.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 235

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 101/223 (45%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVHVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++KIK E +                   
Sbjct: 111 -SRCIENE-----ILMYLRR------------NSKIKAEIS------------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
               EP++++    D +   L D +  E+    + ++  +   L     R+   L  RE+
Sbjct: 134 --FYEPLNID---WDGNELLLSDILGTENDEVYNLIEDEVDKQLLLMALRI---LNDREK 185

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++R+RFG+    + T +EV     +++  I ++E K IR+LK
Sbjct: 186 EIVRLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIIRRLK 228


>gi|302746282|gb|ADL62731.1| RpoD [Morganella morganii subsp. morganii]
          Length = 277

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVR 60

Query: 181 LREII 185
           L ++I
Sbjct: 61  LSDLI 65


>gi|229171759|ref|ZP_04299331.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
 gi|228611656|gb|EEK68906.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
          Length = 203

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 98/210 (46%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D  +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDCSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|220917697|ref|YP_002493001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955551|gb|ACL65935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 232

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/205 (23%), Positives = 92/205 (44%), Gaps = 19/205 (9%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T   ++  DL   G +GL++AA ++D     +F T+A   V+ A+   +        +P 
Sbjct: 41  TGHAVEPGDLWSAGAMGLLEAARRYDPAHDVRFETFAEHRVRGAMLDELRRMD---HLPR 97

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            +R    +V+    R+   + REP P E+A+   +P E V ++L +   P+ +E      
Sbjct: 98  RLRADADRVLAARARLEQSLGREPDPVEVAEAAELPAEQVGELLLLASPPVPVE------ 151

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
                 D +    A+ P D A+ A  R      + +  P   +VL     +  +   T  
Sbjct: 152 ------DDLAPTPAL-PADEALGAAERRRALARMVAALPERLQVL---LALYYDEALTYR 201

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ K   V+  R+ Q+ A+A+++L+
Sbjct: 202 EIAKVLGVSEPRVCQLHAEAVKRLR 226


>gi|114765238|ref|ZP_01444370.1| RNA polymerase sigma factor protein (sigma-70) [Pelagibaca
           bermudensis HTCC2601]
 gi|114542373|gb|EAU45401.1| RNA polymerase sigma factor protein (sigma-70) [Roseovarius sp.
           HTCC2601]
          Length = 249

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 100/225 (44%), Gaps = 32/225 (14%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++ ++ R   S A ++T+  +   DL  EG +GL++AA+ FD     +F+TYA WWV+ A
Sbjct: 39  LLRSHARQAWSHAARFTDNPVHLEDLAAEGVMGLLRAADSFDRAQDVRFATYAAWWVRNA 98

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ++ +++     I IP                      R     ++ K   +  E V  V 
Sbjct: 99  VSSALSRIKAVIDIP---------------------SRTYLDAQMGK---LSDEDVFIVQ 134

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV----LASLTPR 623
             T+  ++L+T    ED       +   +   P + A   + R    R+    LA + P 
Sbjct: 135 LATRGTLALDT--HQEDAGRDPAQLLVSSEPDPEEHASLQSQRRMLLRLIDDALARMEPE 192

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  V+R R         TL ++     +T++R+RQ+E +A+ +L+
Sbjct: 193 EVAVIRRRRLA--PEPETLADIAADLGITQDRLRQVERRAMMRLR 235


>gi|134294347|ref|YP_001118082.1| flagellar biosynthesis sigma factor [Burkholderia vietnamiensis G4]
 gi|134137504|gb|ABO53247.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           vietnamiensis G4]
          Length = 244

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 95/202 (47%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R  +  EIA+ L MP++  +++L    + +     I  ED     D 
Sbjct: 98  VEHAVHQVEQQLGRSASEAEIAQHLKMPLDEYQEML----QDLHGSQLIYYEDFDRAADD 153

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRVDHADPLSALLDDHLRGALVDAIDRLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|270057069|gb|ACZ59656.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 296

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 42/66 (63%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+      
Sbjct: 1   PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQL 60

Query: 180 LLREII 185
            L +II
Sbjct: 61  RLSDII 66


>gi|269795656|ref|YP_003315111.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269097841|gb|ACZ22277.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 345

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 105/238 (44%), Gaps = 15/238 (6%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           C  +  ++ ++     LV SVA +   +    ++  DL+  G  GL+ A EKF+     K
Sbjct: 106 CADAPTRERLILHYAPLVTSVASRVGMKLPSTVEHADLVSYGMFGLIDAIEKFELDREIK 165

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F TYA   ++ AI   +        +P  +R K   V R    +  ++ R PT  EIA+ 
Sbjct: 166 FETYATSRIRGAILDELRANDW---VPRSVRSKARAVDRAHAELEARLHRAPTDPEIAEH 222

Query: 556 LAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET- 612
           + + +  +R +  L  T   ++L+   G  D       ++  +     D A     +ET 
Sbjct: 223 MEIALSELRSIRHLVSTVNLVALDEVFGAGDQVEPVGHLDTGHGARSTDPARTFESKETK 282

Query: 613 --TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++ +  L  RE+ +L + +  GM    TL E+G    VT  RI Q+   A+ +L+
Sbjct: 283 FLLSQAMDQLGEREKIMLVLYYYEGM----TLAEIGAVLGVTESRISQMHTAAMGRLR 336


>gi|254698074|ref|ZP_05159902.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 118

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 43/70 (61%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD    
Sbjct: 49  IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRD 108

Query: 494 YKFSTYAMWW 503
            +FSTYA WW
Sbjct: 109 VRFSTYASWW 118


>gi|254411015|ref|ZP_05024793.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196182370|gb|EDX77356.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 85/156 (54%), Gaps = 7/156 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V  N  LV  +A + + +  + + DL+Q G +GL++A E+F    GY FS++A+ +
Sbjct: 26  RNQLVRLNSGLVKKIAYRVSQQCSEPYDDLVQLGYLGLIRAIERFKPDQGYAFSSFAVPF 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+   ++IP   ++   +  R ++R++  + R P   EIA+ L + ++  
Sbjct: 86  IRGEMLHFLRDKGNIVKIPRRWQELQQEGQRVSKRLTATLGRPPKEAEIAQALNISMQEW 145

Query: 564 R--KVLKITKEPISLETPIGDEDTSH---LGDFIED 594
           +  K+    + P+SL+  +G  +  H   LGD + D
Sbjct: 146 QESKLASKNRLPLSLDLTVG-HNVDHPVTLGDMLPD 180


>gi|85859187|ref|YP_461389.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
 gi|85722278|gb|ABC77221.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
          Length = 261

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 93/200 (46%), Gaps = 10/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGLM A EK+D     +F TYA   ++ A+   +  +     +P  +R + ++
Sbjct: 61  DLIHVGIIGLMSAIEKYDTRRNVRFETYAGIRIRGAVLDELRARDW---VPRAVRSRDNE 117

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDE-DTSHL 588
           + +    +   ++R P   EI++ L + +E   K+L  ++    IS E   GD  D    
Sbjct: 118 ITKAISSLQKILRRAPDDHEISEYLGLSIEEYFKLLDDSRCISLISSEDLPGDYLDRYSC 177

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I      S LD       R    + +  L  +E  VL + +      + T++E+GK 
Sbjct: 178 SDVIRAVEQGSALDLITDHEFRMQLKKAMELLPDKERLVLTLYY----YEELTMKEIGKV 233

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +T  R+ Q+ ++AI +L+
Sbjct: 234 LDLTESRVCQLHSQAIFRLR 253


>gi|56962590|ref|YP_174316.1| RNA polymerase sigma factor SigB [Bacillus clausii KSM-K16]
 gi|56908828|dbj|BAD63355.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Bacillus clausii KSM-K16]
          Length = 261

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/246 (23%), Positives = 128/246 (52%), Gaps = 23/246 (9%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAAEKFDWCLG 493
           + G  EA I      EA   LV S+++K++ +G ++  DL Q G +GL+ A ++++   G
Sbjct: 24  KTGSEEAQIKLVNHFEA---LVRSLSRKFS-KGREYDEDLYQVGMVGLLAAMKRYNEDYG 79

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F ++A+  V   I R I D++ ++ +P  +++   K+ + A  ++ +++R P   EIA
Sbjct: 80  RSFESFAVPTVVGEIKRFIRDKTWSVHVPRRIKELGPKIKKAADTLTIELQRSPYVHEIA 139

Query: 554 KKLAMPVEGVRKVLKITK--EPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           + L +  E V + ++++K  + +S+  P+     G E T  L D + ++ A        Q
Sbjct: 140 EYLQVTEEEVLETMEMSKSYQALSVNRPLEADQEGGEVT--LLDLVGNEEA-----GYEQ 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A+ +    +    L  RE+ +L+  +   ++   T E++G    +++  + +++ +A++K
Sbjct: 193 ADQKLLLEKAFEVLNEREKDILQCTYYENLSQKETGEKLG----ISQMHVSRLQRRALQK 248

Query: 667 LKHPSR 672
           L+   R
Sbjct: 249 LRDSIR 254


>gi|239934558|emb|CAR94593.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 208

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 44/69 (63%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IA+RIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAERIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREII 185
            T  L +II
Sbjct: 61  QTVRLADII 69


>gi|260589068|ref|ZP_05854981.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|331082498|ref|ZP_08331623.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540488|gb|EEX21057.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|330400476|gb|EGG80106.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 208

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 95/232 (40%), Gaps = 63/232 (27%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY     +  DLI  G IGL+KA   FD     + STYA   
Sbjct: 27  AKNILIERNLRLVAHIVKKYQGAPEEMDDLISIGTIGLIKAIHTFDAQKASRLSTYA--- 83

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                                           AR + N             +L M +   
Sbjct: 84  --------------------------------ARCIDN-------------ELLMLLRSK 98

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLA-- 618
           +K    +   +SL  PIG +   +   L D IE +    P+D     +L++   R+    
Sbjct: 99  KK----SNREVSLYDPIGTDKEGNEISLLDIIETE----PVDVVKNYSLKQDIARLYQLL 150

Query: 619 --SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              LT RE  ++++R+G+    + T  E+ K+  ++R  + +IE  AI KL+
Sbjct: 151 PKVLTTREREIIKLRYGLYGEQELTQREIAKRLNISRSYVSRIEKNAILKLR 202


>gi|149376625|ref|ZP_01894385.1| flagellar biosynthesis sigma factor FliA [Marinobacter algicola
           DG893]
 gi|149359143|gb|EDM47607.1| flagellar biosynthesis sigma factor FliA [Marinobacter algicola
           DG893]
          Length = 207

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/210 (24%), Positives = 99/210 (47%), Gaps = 27/210 (12%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DL+Q G IGL++AA+++    G  F TYA   ++ A+   I        +P  +  
Sbjct: 8   VQLDDLMQAGMIGLLEAAQRYSSDKGATFETYAGIRIRGAMVDEIRKGDW---VPRSVHR 64

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE---------GVRKVLKITKEPISLET 578
              ++ +  + + +++ RE    E+A++L + ++            ++  + +   S E 
Sbjct: 65  NSRRIAKAIKAVEDRLGREAQDSEVAEELGLDLDEYYSSLSDANSGRLFSLDELNESGEL 124

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PI  E+T       ED +  +PLD     N R++    +  L  RE+ VL + +   +N 
Sbjct: 125 PI--EET-------EDSD--NPLDGLASDNFRKSLATAIGDLPEREKLVLSLYYQEELN- 172

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L+E+G    V+  R+ QI ++A  +L+
Sbjct: 173 ---LKEIGAVLGVSESRVSQIHSQAALRLR 199


>gi|302389895|ref|YP_003825716.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
 gi|302200523|gb|ADL08093.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
          Length = 239

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/235 (24%), Positives = 97/235 (41%), Gaps = 62/235 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA   F+   G + +TYA   
Sbjct: 55  ARNILIERNLRLVAHIVKKFANTGEDMDDLISIGTIGLIKAITTFNKTKGNRLATYAARC 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  ++                         R + KIK E                 
Sbjct: 115 IENEILMNL-------------------------RTTKKIKAE----------------- 132

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                     +SL+ PIG +   +   L D +  E    +  + +  Q   ++   ++  
Sbjct: 133 ----------VSLQDPIGVDKEGNEISLMDILGTESDAIIEEISNKFQQ--KKLYDKIRT 180

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL---KHP 670
            L  RE++V+ +R+G+      T  E+ K   ++R  + +IE +AI+KL    HP
Sbjct: 181 VLKGREKKVIELRYGLLNGKARTQREIAKLLGISRSYVSRIEKRAIKKLFDELHP 235


>gi|330815163|ref|YP_004358868.1| FliA [Burkholderia gladioli BSR3]
 gi|327367556|gb|AEA58912.1| FliA [Burkholderia gladioli BSR3]
          Length = 254

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 93/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 51  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V +   R+  ++ R     EIA  L MP+   + +L+     + I  E    D D S   
Sbjct: 108 VEQAVHRVEQQLGRSANESEIASHLEMPLPDYQAMLQDLHGSQLIYYE----DFDRSADD 163

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 164 EPFLDRYRVDHSDPLSALLDDHLRAALVEAIERLPEREKLLMSLYYERGLN----LREIG 219

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 220 AVLEVSESRVCQLHSQAVARLR 241


>gi|303248004|ref|ZP_07334270.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
 gi|302490561|gb|EFL50466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
          Length = 225

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/222 (22%), Positives = 107/222 (48%), Gaps = 10/222 (4%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +++V +  K    + ++  +L+  G +GL++A  +F   LG KF TYA   +K A+   +
Sbjct: 8   IKIVATRLKAKLPQSVELGELLSAGAMGLLEALGRFRPELGIKFETYAESRIKGAMLDDL 67

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                  R     R ++  +   +RR+ +   R P+ E++A+   +    V + L+  + 
Sbjct: 68  RRMDWFSR---GQRHRVRTLEEASRRIESDSGRTPSVEQLAEATGLSEREVTQGLEALQN 124

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            + L     D  T ++  + +++    P  SA    L +    ++  LTPRE+ VL + +
Sbjct: 125 QLCLSL---DAITENISSYQKNQLENEPYKSAEFKELVDKLASLIDDLTPREKLVLSLYY 181

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G  +N   T E +G    +T  R+ Q+ ++A+ +L+   +++
Sbjct: 182 GEELNMRETSEVMG----ITEGRVSQLHSQALARLRQKFKAQ 219


>gi|154503852|ref|ZP_02040912.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
 gi|153795451|gb|EDN77871.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
          Length = 246

 Score = 59.7 bits (143), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 100/231 (43%), Gaps = 60/231 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKKMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR S                       
Sbjct: 120 -----SRCIENE----------------ILMYLRRNSK---------------------- 136

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                 TK  +S++ P+    D +   L D +  +      D   +A  R+   R +  L
Sbjct: 137 ------TKMEVSIDEPLNVDWDGNELLLSDILGTEEDTIYRDLETEAE-RKLLVRAINQL 189

Query: 621 TPREERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + RE+ +++MRFG+  N D    T +EV     +++  I ++E K +++LK
Sbjct: 190 SSREKLIVKMRFGLD-NPDGIEKTQKEVADLLGISQSYISRLEKKIMQRLK 239


>gi|306820145|ref|ZP_07453793.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551923|gb|EFM39866.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 247

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 108/229 (47%), Gaps = 15/229 (6%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E++   + LV  V+ K   Y  + +++ DL+  G IGL+ A +KFD+    KF TYA 
Sbjct: 25  KEEIITKYVSLVKIVSGKLFNYYAQKIEYDDLMGYGIIGLIDAIDKFDYSKNIKFETYAS 84

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I  Q     +P  +R K+  +      + NK+ RE T  E+++ L + ++
Sbjct: 85  IRIRGAIIDEIRSQDW---VPRGIRKKMKTLNTAMEELENKLGREATRHELSEHLGISLK 141

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V ++     T   +S+E  + +     + D    K   SP    I  +      + + +
Sbjct: 142 EVDELFDETATFNIVSIEDELSENVKIQIPD---TKVENSPEQQLIYTDTVNDLAKAIDT 198

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E+ ++ + +   +    T +E+ +   ++  RI QI +  + KL+
Sbjct: 199 LKEKEKIIINLYYYENL----TYKEISEIIGISESRISQIISACLTKLR 243


>gi|89276143|gb|ABD66430.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276145|gb|ABD66431.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276147|gb|ABD66432.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276149|gb|ABD66433.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276151|gb|ABD66434.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276155|gb|ABD66436.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276157|gb|ABD66437.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276161|gb|ABD66439.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276163|gb|ABD66440.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276165|gb|ABD66441.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276167|gb|ABD66442.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276169|gb|ABD66443.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276171|gb|ABD66444.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276173|gb|ABD66445.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276175|gb|ABD66446.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276177|gb|ABD66447.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276179|gb|ABD66448.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276181|gb|ABD66449.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368248|gb|ACF58016.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368250|gb|ACF58017.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368252|gb|ACF58018.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368254|gb|ACF58019.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368256|gb|ACF58020.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368258|gb|ACF58021.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368260|gb|ACF58022.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368264|gb|ACF58024.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368268|gb|ACF58026.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368270|gb|ACF58027.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368274|gb|ACF58029.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368276|gb|ACF58030.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368278|gb|ACF58031.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368280|gb|ACF58032.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368282|gb|ACF58033.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 47/75 (62%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + ++  
Sbjct: 5   DEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEEILDI 64

Query: 171 RDELNDGTTLLREII 185
            ++L      +R++I
Sbjct: 65  GNKLKTAKLRVRDVI 79


>gi|256391118|ref|YP_003112682.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256357344|gb|ACU70841.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 366

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 97/221 (43%), Gaps = 15/221 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++  ++     VA +++       DL Q   + L+KA + FD   G  F  Y    V
Sbjct: 129 RDELIAEHMNYARYVASRFSVPADTAEDLEQVAYLALIKAVDNFDPARGTAFLGYLTPMV 188

Query: 505 KQAITRSIADQSCTIRIPVHMRD---KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
              I R   D +  + +P  M++    +H     A ++  ++ R PT  E+A+ L    E
Sbjct: 189 AGEIKRYFRDSTWDVHVPRRMQELSLALHGA--PAEQLERRLGRSPTIAELAEHLGAQPE 246

Query: 562 GVRKVLKITK--EPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + +    +      SLE P+  GDE  + LG+ +   +     D+      RE    +L
Sbjct: 247 EIVEAFDASAAYSATSLERPLVPGDEQGASLGETLGGDD-----DAYEWVVDREALKPLL 301

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIR 657
           A+L  +++R+L MRF  GM       E+G  Q  V+R   R
Sbjct: 302 AALPEKDKRILLMRFFRGMTQSQIGTELGVSQMQVSRYLTR 342


>gi|207743817|ref|YP_002260209.1| rna polymerase sigma d (sigma-70) factor (partial sequence n
           terminus) protein [Ralstonia solanacearum IPO1609]
 gi|206595217|emb|CAQ62144.1| probable rna polymerase sigma d (sigma-70) factor (partial sequence
           n terminus) protein [Ralstonia solanacearum IPO1609]
          Length = 39

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/38 (71%), Positives = 34/38 (89%)

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +GK F VTRE IRQ++AKA+RKL+HPSRS KL+SFL+G
Sbjct: 1   MGKHFDVTRESIRQMKAKAVRKLRHPSRSDKLKSFLEG 38


>gi|294140220|ref|YP_003556198.1| RNA polymerase sigma-27 factor [Shewanella violacea DSS12]
 gi|293326689|dbj|BAJ01420.1| RNA polymerase sigma-27 factor [Shewanella violacea DSS12]
          Length = 239

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KALIVEQYAPLVKKIAHHLLARLPASVQIDDLLQAGMMGLLEASSKFDGNKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+    EIA++L M + 
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RVAQVIDELEQELGRDAKDAEIAQRLDMTLN 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D I   N V+    +S  +          +  
Sbjct: 130 EYHHILN----DVSVGKVIGIEDLGVSVDVISHDNGVNDDTFESIAEGEFHLALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|302541605|ref|ZP_07293947.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459223|gb|EFL22316.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 292

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 102/216 (47%), Gaps = 15/216 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + ++FR I S+      EA   ++++V A + +   +A ++ NRG    DL Q   +GL+
Sbjct: 46  TTADFRRIASLPEGAPKEA--LRQDVVRAWMPMAERLAGQFRNRGESAEDLRQVAMLGLV 103

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP---VHMRDKIHKVVRTARRM 539
           KA  ++D   G  F +YA+  V   + R   D    + +P     +R+++   V+   R 
Sbjct: 104 KAVNRYDPDRGTAFESYAVPTVVGEVKRHFRDHLWGLHVPRRVQELRNRVRTAVQDLTRT 163

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKN 596
            +   R P+  ++A+   +  E VR  ++   +   +SL+  + G +D   L D +    
Sbjct: 164 PD--GRTPSVADVAEHTGLSEEEVRSGMEALESYSTLSLDAELRGADDGYALVDTLG--- 218

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             SP  S  +   RE     LA+L  RE R+L +RF
Sbjct: 219 --SPEPSYDRVVQREALKPCLAALPERERRILYLRF 252


>gi|238924921|ref|YP_002938437.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
 gi|238876596|gb|ACR76303.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
          Length = 224

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 46/82 (56%), Gaps = 5/82 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  N+ L+  V K++ NRG+   DL Q G +GL KAA++FD   G+ FSTYA+  +   
Sbjct: 9   LVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKI 529
           I R + D        VH+  KI
Sbjct: 69  IQRFLRDDGM-----VHISRKI 85


>gi|197122905|ref|YP_002134856.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter sp.
           K]
 gi|196172754|gb|ACG73727.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter sp.
           K]
          Length = 232

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/205 (24%), Positives = 91/205 (44%), Gaps = 19/205 (9%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T   ++  DL   G +GL++AA ++D     +F T+A   V+ A+   +        +P 
Sbjct: 41  TGHAVEPGDLWSAGAMGLLEAARRYDPAHDVRFETFAEHRVRGAMLDELRRMD---HLPR 97

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            +R    +V+    R+   + REP P E+A+   +P E V ++L +   P+ +E      
Sbjct: 98  RLRADADRVLAARARLEQSLGREPDPVEVAEAAELPAEQVGELLLLASPPVPVE------ 151

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
                 D +    AV P D A+ A  R        +  P   +VL     +  +   T  
Sbjct: 152 ------DDLAPAPAV-PADEALGAAERRRALARTVAALPERLQVL---LALYYDEALTYR 201

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ K   V+  R+ Q+ A+A+++L+
Sbjct: 202 EIAKVLGVSEPRVCQLHAEAVKRLR 226


>gi|89902470|ref|YP_524941.1| sigma 28 (flagella/sporulation) [Rhodoferax ferrireducens T118]
 gi|89347207|gb|ABD71410.1| sigma 28 (Flagella/Sporulation) [Rhodoferax ferrireducens T118]
          Length = 238

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 53/206 (25%), Positives = 97/206 (47%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +++   G +F T+A   ++ A+   +       R     +  I +
Sbjct: 40  DLIQVGLIGLSEALTRYEAAQGVQFETFATQRIRGAMLDELRGNDWMSRGSRKSQKDIEQ 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSH 587
            +   RR+ +K+ R P   EIA  L + +   + +L   +  + + LE      DE+ S 
Sbjct: 100 AL---RRLEHKLGRTPLESEIAADLGLSLVDYQTLLGKVRGTQLVYLEDMARGNDEEDSF 156

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D +A  P++      LR+     + +L  RE+ ++ M +   MN    L+E+  
Sbjct: 157 LDRHVGDSDA-DPMNVLRDQRLRQALVAAIKNLPEREQFIMSMYYEQDMN----LKEIAA 211

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  RI Q+ +++I +L+   R+
Sbjct: 212 VLDVTESRICQLHSQSIARLRAKMRA 237


>gi|325527508|gb|EGD04836.1| flagellar biosynthesis sigma factor [Burkholderia sp. TJI49]
          Length = 243

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 97  VEHAVHQVEQQLGRAASEAEIAQHLNMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 152

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYRVDHADPLSALLDDHLRGALVEAIERLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVLEVSESRVCQLHSQAVARLR 230


>gi|253682196|ref|ZP_04862993.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
 gi|253561908|gb|EES91360.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 101/231 (43%), Gaps = 59/231 (25%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++AK  ++E NLRLV  + KKY+       DLI  G +GL+KA + FD   G + +TYA 
Sbjct: 48  ALAKGILIERNLRLVAHIVKKYSYPNKDIDDLISIGTVGLIKAIDSFDISKGTRLATYA- 106

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
                                             AR + N+I              M + 
Sbjct: 107 ----------------------------------ARCIENEI-------------LMLIR 119

Query: 562 GVRKVLKITKEPISLETPIG----DEDTSHLGDFIEDKNAV-SPLDSAIQANLRETTTRV 616
             +K+    K  + L+ PIG      + S +     D+N+V   +++ +Q  +++   ++
Sbjct: 120 NTKKI----KSEVYLQDPIGVDKEGNEISLMDVLSSDENSVIEVVENRMQ--IKKLYDKI 173

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              LT RE+ +++MR+G+      T  E+     ++R  + +IE +A++K+
Sbjct: 174 NECLTEREKIIIKMRYGLNDGKPKTQREIAAFLNISRSYVSRIEKRALKKM 224


>gi|89276159|gb|ABD66438.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368272|gb|ACF58028.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 46/69 (66%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + ++   ++L  
Sbjct: 11  SNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEEILDIGNKLKT 70

Query: 177 GTTLLREII 185
               +R++I
Sbjct: 71  AKLRVRDVI 79


>gi|269103161|ref|ZP_06155858.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163059|gb|EEZ41555.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 240

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/200 (23%), Positives = 91/200 (45%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A + +D   G  F T+A   ++ A+   I        +P  +     +
Sbjct: 44  DLIQAGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRR 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +     ++ +++ R+P   E+A+ L M +E   + L      ++    +G +D     D 
Sbjct: 101 ISEAMAQLEHELGRDPNDHEVAEHLEMSLEQYHQALN----DVNCGRLVGIDDLGISEDA 156

Query: 592 IEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           + +   +    P    +  + R+     + +L  RE  VL + +   +N    L+E+G  
Sbjct: 157 VANDELLEENLPFQGVVDDSFRQALAEAIKTLPEREALVLSLYYDEELN----LKEIGAV 212

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  RI QI  +A+++LK
Sbjct: 213 IGVSESRICQIHTQAMQRLK 232


>gi|300113620|ref|YP_003760195.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Nitrosococcus
           watsonii C-113]
 gi|299539557|gb|ADJ27874.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Nitrosococcus watsonii C-113]
          Length = 241

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/233 (24%), Positives = 97/233 (41%), Gaps = 29/233 (12%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E+V     LV  +A     R    +Q  DLIQ G IGL++A   ++   G  F TYA   
Sbjct: 19  ELVTQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAVRNYNASQGASFETYAGIR 78

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   I         P  +  K  +V    R + N+  R+    E+ ++L +P+   
Sbjct: 79  IRGAILDEIRRNDWA---PRSVHRKARQVAEVMREVENREGRDARDYEVVEELGLPLNEY 135

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA--------NLRETTTR 615
            ++L+            G      L +F E + A  PL + ++         N R     
Sbjct: 136 HRLLQDA----------GGYRVFSLDEFNEGEEA-EPLSAPLKGPYEGLQDQNFRGALVE 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L  RE  V+ + +      D  L E+G+   V+  R+ QI ++A+ +L+
Sbjct: 185 AIEGLPERERLVMSLYY----VEDLNLREIGEVLGVSESRVSQIHSQAVLRLR 233


>gi|83719422|ref|YP_443660.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           E264]
 gi|167582695|ref|ZP_02375569.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           TXDOH]
 gi|167620811|ref|ZP_02389442.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           Bt4]
 gi|83653247|gb|ABC37310.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 243

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/202 (24%), Positives = 92/202 (45%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R     EIA  L MP++  + +L    + +     +  ED     D 
Sbjct: 97  VEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSML----QDLHGSQLVYYEDFDRSADD 152

Query: 591 --FIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++   A    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYRADHSDPLSALLDEHLRSALVDAIEHLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVLEVSESRVCQLHSQAVARLR 230


>gi|57505389|ref|ZP_00371317.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
 gi|57016214|gb|EAL53000.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
          Length = 619

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/152 (28%), Positives = 81/152 (53%), Gaps = 22/152 (14%)

Query: 30  SWKKMIK-LARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE- 87
           +++K++K L +Q     I+++ + +   +V       + A ++ M  NV D   LE+E+ 
Sbjct: 23  TYEKLVKYLNKQPNLTAIKKIRSLMKKYKVELY----SAAQIAQMQ-NVADAKRLEEEKQ 77

Query: 88  -----GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
                G E+  +LA    N +  L+  +      +D PVRMYLREMG I LL+++ E+ I
Sbjct: 78  KLQDTGLENEFNLA----NENELLEWSR------SDSPVRMYLREMGQIALLNKDEEVEI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +K+IE G  +++ + C  P     ++ +++ L
Sbjct: 128 SKKIELGEDIIIDAFCSVPYLIDFILDYQEPL 159


>gi|269961637|ref|ZP_06175999.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
 gi|269833678|gb|EEZ87775.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
          Length = 244

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +++  +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA
Sbjct: 15  SQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYA 74

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   I       R  VH  ++  ++ +    +   + R+P+  E+A  L M +
Sbjct: 75  GIRIRGAMLDDIRKGDWVPR-SVHKNNR--EINQAIAELEGVLNRDPSDSEVAAHLGMTL 131

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVL 617
           +     L      I+    +G ED     D I   ++ +  +P       + ++     +
Sbjct: 132 DQYHSALT----DINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVADESFKKALVESI 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL + +   +N    L+E+G    V+  R+ QI ++++++L+
Sbjct: 188 KQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQILSQSMQRLR 234


>gi|253795563|ref|YP_003038659.1| putative RNA polymerase sigma factor [Candidatus Hodgkinia
           cicadicola Dsem]
 gi|253739871|gb|ACT34206.1| putative RNA polymerase sigma factor [Candidatus Hodgkinia
           cicadicola Dsem]
          Length = 373

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 93/240 (38%), Gaps = 41/240 (17%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ +V ++  ++  V K Y +   Q   L   G  GLM +A +FD   GY+F+ Y+ WW
Sbjct: 168 AKRSLVGSSASVIADVIKAYPSCDAQDPALASAGRDGLMASANRFDLVSGYRFAAYSKWW 227

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           VK                     + I  V+  A+  +            AK+LA   +  
Sbjct: 228 VKH--------------------NVIAHVLAGAKGWA---------AASAKQLAGAAKLK 258

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLA 618
           R  L       SL   +  E  S L   +     + P     Q          T    L 
Sbjct: 259 RLSLDYCGGGASLHEAV--EGGSALAGGV-----LKPAARGAQPRFEARCDDYTLISSLM 311

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L PREERV+R+R         +L  +G    +TRER+RQ+   A  KL   + S  L S
Sbjct: 312 LLAPREERVVRLRGRARAPFSWSLRRIGLDVGLTRERVRQLALSASTKLASAALSCSLAS 371


>gi|166154282|ref|YP_001654400.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 434/Bu]
 gi|166155157|ref|YP_001653412.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335533|ref|ZP_07223777.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis L2tet1]
 gi|165930270|emb|CAP03756.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931145|emb|CAP06710.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 253

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 109/241 (45%), Gaps = 39/241 (16%)

Query: 448 MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+ L LV +VA +  +     ++  DL   G  GL++A E+FD     +F +YA++ +
Sbjct: 25  LIESYLPLVKNVAHRLASGMPSHVKMEDLYALGVEGLIRAVERFDPEKSKRFESYALFII 84

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           K AI   +  Q     +P  +  + +++      +   + +EPT  E+ + L +  + + 
Sbjct: 85  KAAIIDGLRKQDW---VPRSVYQRANRLADAMDSLRQTLGKEPTDGELCEYLNISQQELS 141

Query: 564 ------RKVLKIT----------KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
                 R  L ++           E ++LE  I DE      D I  K A+S L      
Sbjct: 142 HWFSSSRPALVLSLNDDFSCQDDDEGLALEERIADERAETGYDVIRKKEAISIL------ 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 T  L +L  +E +V+ + +      D  L+E+GK   V+  R+ QI +KA+ KL
Sbjct: 196 ------TEALLALDEKERQVMALYY----YDDLVLKEIGKILGVSESRVSQIHSKALLKL 245

Query: 668 K 668
           +
Sbjct: 246 R 246


>gi|291527309|emb|CBK92895.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 224

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 46/82 (56%), Gaps = 5/82 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  N+ L+  V K++ NRG+   DL Q G +GL KAA++FD   G+ FSTYA+  +   
Sbjct: 9   LVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKI 529
           I R + D        VH+  KI
Sbjct: 69  IQRFLRDDGM-----VHISRKI 85


>gi|325677679|ref|ZP_08157331.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
 gi|324110647|gb|EGC04811.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
          Length = 231

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 93/230 (40%), Gaps = 60/230 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  NLRLV  + KKY        DLI  G IGL+KA + FD+  G +F+TY    
Sbjct: 53  ARDRLISHNLRLVAHIIKKYYAAASDQDDLISIGTIGLIKAVQTFDYTKGTRFATYGSRC 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  I              +H R                                     
Sbjct: 113 VENEIL-------------MHFR------------------------------------- 122

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLR-ETTTRVLA- 618
              LK +   +S+E P     D ++  L D + D   V+     I+  +R E    +L  
Sbjct: 123 --ALKKSASDVSIEEPAQSDKDGNSLCLMDLLTDGEDVA---DRIELLMRAEQLYGILGD 177

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE  V+ MR+G+   +  T  EV ++ C++R  + +IE +A+ KL+
Sbjct: 178 CLDDREREVVVMRYGLYGGSALTQREVSEKLCISRSYVSRIEKRALEKLR 227


>gi|291558216|emb|CBL35333.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum V10Sc8a]
          Length = 251

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/213 (26%), Positives = 102/213 (47%), Gaps = 18/213 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+I EG I LM A + FD     KF TYA   +K A+   +       R+P  +R    +
Sbjct: 55  DIINEGVIALMAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRKLD---RVPRTLRKLSKQ 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +     R+++++ R PT EE+A+ + M    + K++  T   I+L      E+  +  + 
Sbjct: 112 LDDNFARLNSELCRTPTDEELAESMNMTTAQLSKLMANTAGMITLSF----EELLYEDNL 167

Query: 592 IEDKNAVSPLDSA--IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            E  +A S    A   +   ++     +A+L  +E++V+ M +   +       E+ K  
Sbjct: 168 DESISASSETADAKMYEREKKQVIANAVATLPEKEKQVVTMYYYERLK----YSEIAKVM 223

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +T+ R+ QI +KA+  LK+     KL S+++G
Sbjct: 224 SITQSRVCQIHSKAMLTLKN-----KLESYING 251


>gi|332976341|gb|EGK13197.1| DNA-directed RNA polymerase sigma subunit SigE [Desmospora sp.
           8437]
          Length = 240

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 111/237 (46%), Gaps = 53/237 (22%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R    +A++ +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 49  LIRLPSGDAAV-RAMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFDPSK 107

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++                ++   RR +NKI+ E + +E 
Sbjct: 108 KIKLATYA--------SRCIENE----------------ILMFLRR-NNKIRSEVSFDE- 141

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
              L M  +G           + L   +G D DT +       +N    +D  I   LR 
Sbjct: 142 --PLNMDWDG---------NELLLSDVMGTDNDTIY-------RNIEEQVDRKI---LRT 180

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +R    L+ RE +++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 181 ALSR----LSERERKIMELRFGLNGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 233


>gi|323527722|ref|YP_004229875.1| RNA polymerase sigma-28 subunit FliA/WhiG [Burkholderia sp.
           CCGE1001]
 gi|323384724|gb|ADX56815.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           CCGE1001]
          Length = 244

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  EIA+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDESLRSALVEAIDRLPEREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|161523359|ref|YP_001578371.1| flagellar biosynthesis sigma factor [Burkholderia multivorans ATCC
           17616]
 gi|189351868|ref|YP_001947496.1| flagellar biosynthesis sigma factor [Burkholderia multivorans ATCC
           17616]
 gi|221202383|ref|ZP_03575416.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2M]
 gi|221208978|ref|ZP_03581974.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2]
 gi|221214209|ref|ZP_03587181.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD1]
 gi|160340788|gb|ABX13874.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           multivorans ATCC 17616]
 gi|189335890|dbj|BAG44960.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans ATCC 17616]
 gi|221165864|gb|EED98338.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD1]
 gi|221171100|gb|EEE03551.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2]
 gi|221177797|gb|EEE10211.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2M]
          Length = 244

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 98  VELAVHQVEQRLGRAASEAEIAQHLNMPLDEYQAML----QDLHGSQLIYYEDFDRAADD 153

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRVDHADPLSALLDEHLRGALVEAIERLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|37781598|gb|AAP42804.1| SigB [Staphylococcus aureus]
          Length = 256

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 53/232 (22%), Positives = 117/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD  L  KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSLERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIANRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|15604780|ref|NP_219564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D/UW-3/CX]
 gi|76788774|ref|YP_327860.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           A/HAR-13]
 gi|237802495|ref|YP_002887689.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/Jali20/OT]
 gi|237804410|ref|YP_002888564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/TZ1A828/OT]
 gi|255310863|ref|ZP_05353433.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276]
 gi|255317163|ref|ZP_05358409.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276s]
 gi|255348424|ref|ZP_05380431.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70]
 gi|255502966|ref|ZP_05381356.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70s]
 gi|255506635|ref|ZP_05382274.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D(s)2923]
 gi|3328455|gb|AAC67652.1| Sigma-28/WhiG Family [Chlamydia trachomatis D/UW-3/CX]
 gi|76167304|gb|AAX50312.1| FliA [Chlamydia trachomatis A/HAR-13]
 gi|231272710|emb|CAX09614.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273729|emb|CAX10508.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|289525106|emb|CBJ14577.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296434648|gb|ADH16826.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis E/150]
 gi|296435578|gb|ADH17752.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9768]
 gi|296436502|gb|ADH18672.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11222]
 gi|296437438|gb|ADH19599.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11074]
 gi|296438365|gb|ADH20518.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           E/11023]
 gi|297139937|gb|ADH96695.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9301]
 gi|297748191|gb|ADI50737.1| FliA [Chlamydia trachomatis D-EC]
 gi|297749071|gb|ADI51749.1| FliA [Chlamydia trachomatis D-LC]
          Length = 253

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 109/241 (45%), Gaps = 39/241 (16%)

Query: 448 MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+ L LV +VA +  +     ++  DL   G  GL++A E+FD     +F +YA++ +
Sbjct: 25  LIESYLPLVKNVAHRLASGMPSHVKMEDLYALGVEGLIRAVERFDPEKSKRFESYALFII 84

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           K AI   +  Q     +P  +  + +++      +   + +EPT  E+ + L +  + + 
Sbjct: 85  KAAIIDGLRKQDW---VPRSVYQRANRLADAMDSLRQTLGKEPTDGELCEYLNISQQELS 141

Query: 564 ------RKVLKIT----------KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
                 R  L ++           E ++LE  I DE      D I  K A+S L      
Sbjct: 142 HWFSSSRPALVLSLHDDFSCQDDDEGLALEERIADERAETGYDVIRKKEAISIL------ 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 T  L +L  +E +V+ + +      D  L+E+GK   V+  R+ QI +KA+ KL
Sbjct: 196 ------TEALLALDEKERQVMALYY----YDDLVLKEIGKILGVSESRVSQIHSKALLKL 245

Query: 668 K 668
           +
Sbjct: 246 R 246


>gi|182440239|ref|YP_001827958.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178468755|dbj|BAG23275.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 264

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 101/225 (44%), Gaps = 18/225 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + A L +   +A ++ +RG    DL Q   +GL+KA +++D   G  F +YA+  V
Sbjct: 38  RDETICAWLPMAHRIATRFRDRGEAMDDLRQVAAMGLVKAVDRYDPDRGKAFESYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
              + R   D +  + +P  ++D +   VR ARR    +     PT  +IA    +  E 
Sbjct: 98  TGELKRHFRDHTWDVHVPRRVQD-LRNRVRVARRELAQSSGGAAPTCADIASATGLGEED 156

Query: 563 VRKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   L+   +   +SL+  P G E  S L D +   +    LD AI    RE     L  
Sbjct: 157 VLLGLEALESYSALSLDAGPAGVEGGSPLADRLGSCDGA--LDVAID---REAVKPGLRG 211

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR------ERIR 657
           L  RE  +L +R+   M      E++G  Q  V+R      ER+R
Sbjct: 212 LPERERTILYLRYFRDMTQSRIAEQLGISQMHVSRLLSQSCERVR 256


>gi|146164121|gb|ABQ08728.1| RNA polymerase sigma-70 factor [Aeromonas sharmana]
          Length = 292

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 42/65 (64%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+   G   
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLDQYDKHEAGQIR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LGDII 65



 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 83/173 (47%), Gaps = 11/173 (6%)

Query: 289 EVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E + ELR+  D         G++DE++ ++     +KL  +     L   + D LV  + 
Sbjct: 125 EKFGELRAQSDVTRDSIKAYGREDERTQLEI----QKLADVFRQFRLVPKQFDRLVNNMR 180

Query: 344 DISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D+ +R+   E  +++   +   + +  F+     +E D  W   A+   +  W   +   
Sbjct: 181 DMMERVRVQERIIMKGCVERAKMPKKNFVALFTNKESDLSWFLAARAAGKS-WSVALEDV 239

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            + + +   +++ +  ETG+SI++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 240 AEDVERAVTKLQQVEDETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRL 292


>gi|331085949|ref|ZP_08335032.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406872|gb|EGG86377.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 192

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 98/231 (42%), Gaps = 61/231 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY        DLI  G +GL+KA   F+   G + STYA   
Sbjct: 11  AKHILIEHNLRLVAHIVKKYQRPEEDNEDLISIGTVGLIKAVITFNPEKGNRLSTYA--- 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                                           AR + N+I            L M    +
Sbjct: 68  --------------------------------ARCIENEI------------LMM----L 79

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA------NLRETTTRVL 617
           R   K ++E ISL  PIG   T   G+ I+  + +   D  I        ++R    +V 
Sbjct: 80  RSRKKSSRE-ISLYEPIG---TDREGNEIQLFDVMETTDEDIHEKINLKDDVRTLYEKVE 135

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L+ RE  VL+MR+G+    ++T  E+ K+  ++R  + +IE  A+ KL+
Sbjct: 136 SELSDRERLVLKMRYGLYNEEEYTQREIAKRLGISRSYVSRIEKSAVEKLR 186


>gi|157961206|ref|YP_001501240.1| flagellar biosynthesis sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846206|gb|ABV86705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella pealeana
           ATCC 700345]
          Length = 239

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+  FD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSNFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+    EIA++L + +E
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RVAQVIDELEQELGRDARDGEIAERLEVSLE 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D I  ED +     +S  +          +  
Sbjct: 130 EYHAILN----DVSVGKVVGIEDLGVAADGINPEDGHEDDAYESLAEVEFHSALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|89276153|gb|ABD66435.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368266|gb|ACF58025.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 47/75 (62%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + ++  
Sbjct: 5   DEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEEILDI 64

Query: 171 RDELNDGTTLLREII 185
            ++L      +R++I
Sbjct: 65  GNKLKTAKLRVRDVI 79


>gi|121534479|ref|ZP_01666302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306972|gb|EAX47891.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 94/226 (41%), Gaps = 54/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KK+ N G    DLI  G IGL+KA   FD     + +TYA   
Sbjct: 51  AKNVLIERNLRLVAHIVKKFDNTGEDVDDLISIGTIGLIKAINTFDQAKKIRLATYA--- 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+        R+ RR+                        
Sbjct: 108 -----ARCIENE-----ILMHL--------RSTRRI------------------------ 125

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLT 621
                  +  +SL  PIG +   +    I+       + +    N  ET   ++ +  L+
Sbjct: 126 -------RSEVSLYDPIGVDKEGNEITLIDVLGTAPDVVAEAVENQCETERLSKEIHRLS 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE+ VL MRFG+   +  T  ++ K   ++R  + +IE +AI KL
Sbjct: 179 KREKWVLEMRFGMPDGSRKTQRDIAKLLGISRSYVSRIEKRAISKL 224


>gi|225175485|ref|ZP_03729479.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168814|gb|EEG77614.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
          Length = 243

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/230 (24%), Positives = 100/230 (43%), Gaps = 52/230 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 62  VKAVLIERNLRLVVYIARKFENTGILIDDLVSIGTIGLIKAVNTFDPHKNIKLATYA--- 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                        C           I   +    R +NK+K E + +             
Sbjct: 119 -----------SKC-----------IENEILMFLRRNNKVKAEVSFD------------- 143

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +N +  +   I+A + R+     +  L  
Sbjct: 144 --------EPLNVD---WDGNELLLSDVLGTENDL--VIKGIEAEVERKLLYNAIEKLNR 190

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE+R++ +RFG+    + T +EV     +++  I ++E + I++L+   R
Sbjct: 191 REKRIMELRFGLLGQEEKTQKEVAVMLGISQSYISRLEKRIIKRLQKEIR 240


>gi|91785643|ref|YP_560849.1| flagellar biosynthesis sigma factor [Burkholderia xenovorans LB400]
 gi|296157465|ref|ZP_06840300.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           Ch1-1]
 gi|91689597|gb|ABE32797.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           xenovorans LB400]
 gi|295892237|gb|EFG72020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           Ch1-1]
          Length = 244

 Score = 59.3 bits (142), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  EIA+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDDSLRSALVEAIDRLPEREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|322504100|emb|CBX46975.1| RNA polymerase subunit D, sigma factor [Pseudomonas sp. C2(2009)]
          Length = 290

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 37/49 (75%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           PVRMY+REMG++ELL+REGEI IAKRIE G   +M+++   P T   ++
Sbjct: 2   PVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGIL 50



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 69/139 (49%), Gaps = 8/139 (5%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++ D   R+   E  +++L  +   + R  FL    G E+
Sbjct: 156 LAELFMPIKLVPKQYDALVTRVRDALDRLRTQERAIMQLCVRDARMPRADFLRLFPGNEI 215

Query: 380 DPHWVSYAKDFPEGEWKNFVAC---EVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           D  W   A D  +G+ K   A    + D I + + ++  +  E  ++++E + I   +  
Sbjct: 216 DMDW---AADLAKGKAKYAEALGNLQAD-IQRCQQKLADLEAECSLTLAEIKDINRRMSI 271

Query: 437 GECEASIAKKEMVEANLRL 455
           GE +A  AKKEMVEANLRL
Sbjct: 272 GEAKARRAKKEMVEANLRL 290


>gi|322504098|emb|CBX46974.1| RNA polymerase subunit D, sigma factor [Pseudomonas sp. C2(2009)]
          Length = 289

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 37/49 (75%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           PVRMY+REMG++ELL+REGEI IAKRIE G   +M+++   P T   ++
Sbjct: 1   PVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGIL 49



 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 69/139 (49%), Gaps = 8/139 (5%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++ D   R+   E  +++L  +   + R  FL    G E+
Sbjct: 155 LAELFMPIKLVPKQYDALVTRVRDALDRLRTQERAIMQLCVRDARMPRADFLRLFPGNEI 214

Query: 380 DPHWVSYAKDFPEGEWKNFVAC---EVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           D  W   A D  +G+ K   A    + D I + + ++  +  E  ++++E + I   +  
Sbjct: 215 DMDW---AADLAKGKAKYAEALGNLQAD-IQRCQQKLADLEAECSLTLAEIKDINRRMSI 270

Query: 437 GECEASIAKKEMVEANLRL 455
           GE +A  AKKEMVEANLRL
Sbjct: 271 GEAKARRAKKEMVEANLRL 289


>gi|291542064|emb|CBL15174.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 219

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 67/144 (46%), Gaps = 1/144 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K ++ + N+ LV +  K+++ +G+++ +L   G +GL KA   FD     +FSTYA   +
Sbjct: 4   KNKLADKNMGLVHACCKRFSGKGIEYEELFASGCLGLAKAINNFDESRNLQFSTYAFPVI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D    IR+   +++    + R       K  RE T  E+A++L    E + 
Sbjct: 64  MGEIKRLFRDGG-AIRVSRTLKELSLAISRLNNESKLKNGRELTVSELAERLDTSEEKII 122

Query: 565 KVLKITKEPISLETPIGDEDTSHL 588
             L  T+ P+SL      E    L
Sbjct: 123 DALNSTRVPLSLTAEYDSEGNPQL 146


>gi|332799103|ref|YP_004460602.1| RNA polymerase sigma-28 subunit SigE [Tepidanaerobacter sp. Re1]
 gi|332696838|gb|AEE91295.1| RNA polymerase, sigma 28 subunit, SigE [Tepidanaerobacter sp. Re1]
          Length = 239

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 103/238 (43%), Gaps = 50/238 (21%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  ++K +      K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD 
Sbjct: 45  VFYLKKLQMGDQTVKTVLIERNLRLVVYIARKFENTGICIEDLISIGTIGLIKAINTFDP 104

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               K +TYA   ++  I   +                         R +NK + E + +
Sbjct: 105 NKKIKLATYASKCIENEILMYL-------------------------RRNNKTRMEVSFD 139

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E    L +  +G   +L          + I   D   +  +IED+     +D       R
Sbjct: 140 E---PLNIDWDGNELLL----------SDILGTDNDMIYKYIEDE-----VD-------R 174

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E     +  L+ RE  ++++RFG+    + T +EV     +++  I ++E K I++LK
Sbjct: 175 ELLYTAMKRLSQRERCIIKLRFGLNGGVEKTQKEVADLLGISQSYISRLEKKIIKRLK 232


>gi|15894509|ref|NP_347858.1| RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|15024150|gb|AAK79198.1|AE007635_12 RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
          Length = 227

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 108/230 (46%), Gaps = 31/230 (13%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++VE  + LV S+A+KY NR   L+  D++Q G I ++ A E FD+  G KFSTYA  
Sbjct: 17  RNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFSTYARH 76

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMP 559
            V+  +        C     +H+ +   K +R  +++ ++ + E       EI+ +L + 
Sbjct: 77  CVEGGMK-----NYCKKNELIHLSEYQRKDLRRIKKLFDEKQLENKDIDITEISAELGIE 131

Query: 560 VE-GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            E  +  +  + K+      PI D +  +   F  +K  V  +              ++ 
Sbjct: 132 KEKAINLICFLNKDKY---IPIDDYEYKYGKSF--EKEIVDNI----------LIRSLIE 176

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   ++ ++R R       D +  ++GK++ +TR+ ++Q   + I K+K
Sbjct: 177 NLPKNQQNLIRERL-----KDMSFTDIGKKYNITRQAVQQSVKRIINKMK 221


>gi|251772425|gb|EES52992.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptospirillum
           ferrodiazotrophum]
          Length = 250

 Score = 58.9 bits (141), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/216 (25%), Positives = 100/216 (46%), Gaps = 14/216 (6%)

Query: 460 AKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           A +Y +R    L   DLI  G   L+++A +FD   G KF T A   ++ A+   I    
Sbjct: 21  AMRYAHRLPPELGVEDLISVGLHSLVESARRFDPSRGLKFKTMAEHRIRGAMLDEIRSMD 80

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPI- 574
               +P  +R+K   V      +  ++ R P   E+A +L + +E +  +L +I   P+ 
Sbjct: 81  W---VPRSVREKQADVQMARESLERELGRHPEDAELAARLGLSLEDLETLLWEIDPHPVL 137

Query: 575 SLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           SL+   G +++    LGD +       PL   +Q    +     L +L  ++  VL + +
Sbjct: 138 SLDEVFGPDESEGESLGDHLPGPKGEDPLSRLLQGEALDALAGALDALPEKQRLVLTLYY 197

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 + T++EV +   V+  R+ QI ++A+R ++
Sbjct: 198 ----YEELTMKEVAQVLDVSESRVSQIHSQALRGIR 229


>gi|332799375|ref|YP_004460874.1| RNA polymerase sigma-28 subunit SigK [Tepidanaerobacter sp. Re1]
 gi|332697110|gb|AEE91567.1| RNA polymerase, sigma 28 subunit, SigK [Tepidanaerobacter sp. Re1]
          Length = 240

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/224 (26%), Positives = 95/224 (42%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ + G    DLI  G IGL+KA   F++  G + +TYA   
Sbjct: 55  ARNILIEHNLRLVAHIVKKFASTGEDMDDLISIGTIGLIKAISTFNYSKGSRLATYAARC 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  ++                         R + KIK E   +E       P+ GV
Sbjct: 115 IENEILMNL-------------------------RSTKKIKSEVYLQE-------PI-GV 141

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K        ISL   +G E    + D I  K     L   I  +L+            +
Sbjct: 142 DK----EGNEISLIDVLGTE-VDAVTDEITKKFQNEKLYEKISTSLK-----------SQ 185

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E +V+ +R+G+      T  E+ K   ++R  + +IE +AI+KL
Sbjct: 186 ERKVIELRYGLFNGVTKTQREIAKILGISRSYVSRIEKRAIKKL 229


>gi|325508641|gb|ADZ20277.1| RNA polymerase sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 219

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 108/230 (46%), Gaps = 31/230 (13%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++VE  + LV S+A+KY NR   L+  D++Q G I ++ A E FD+  G KFSTYA  
Sbjct: 9   RNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFSTYARH 68

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP---EEIAKKLAMP 559
            V+  +        C     +H+ +   K +R  +++ ++ + E       EI+ +L + 
Sbjct: 69  CVEGGMK-----NYCKKNELIHLSEYQRKDLRRIKKLFDEKQLENKDIDITEISAELGIE 123

Query: 560 VE-GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            E  +  +  + K+      PI D +  +   F  +K  V  +              ++ 
Sbjct: 124 KEKAINLICFLNKDKY---IPIDDYEYKYGKSF--EKEIVDNI----------LIRSLIE 168

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L   ++ ++R R       D +  ++GK++ +TR+ ++Q   + I K+K
Sbjct: 169 NLPKNQQNLIRERL-----KDMSFTDIGKKYNITRQAVQQSVKRIINKMK 213


>gi|326780902|ref|ZP_08240167.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326661235|gb|EGE46081.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 264

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 101/225 (44%), Gaps = 18/225 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + A L +   +A ++ +RG    DL Q   +GL+KA +++D   G  F +YA+  V
Sbjct: 38  RDETICAWLPMAHRIATRFRDRGEAMDDLRQVAAMGLVKAVDRYDPDRGKAFESYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
              + R   D +  + +P  ++D +   VR ARR    +     PT  +IA    +  E 
Sbjct: 98  TGELKRHFRDHTWDVHVPRRVQD-LRNRVRVARRELAQSSGGAAPTCADIASATGLGEED 156

Query: 563 VRKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   L+   +   +SL+  P G E  S L D +   +    LD AI    RE     L  
Sbjct: 157 VLLGLEALESYSALSLDAGPAGVEGGSPLADRLGSCDGA--LDVAID---REAVKPGLRG 211

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR------ERIR 657
           L  RE  +L +R+   M      E++G  Q  V+R      ER+R
Sbjct: 212 LPERERTILYLRYFRDMTQSRIAEQLGISQMHVSRLLSQSCERVR 256


>gi|302874723|ref|YP_003843356.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
 gi|307690664|ref|ZP_07633110.1| sporulation sigma factor SigE [Clostridium cellulovorans 743B]
 gi|302577580|gb|ADL51592.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
          Length = 235

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 103/223 (46%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIKAVNTFDPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++K+K E +                   
Sbjct: 111 -SRCIENE-----ILMYLRR------------NSKVKAEIS------------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
               EP++++    D +   L D +  E+ N  + L+  +    R+  +  L  L  RE+
Sbjct: 134 --FYEPLNID---WDGNELLLSDILGSENDNIYNLLEDEVD---RQLLSIALRKLNEREK 185

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +R+G+    + T +EV     +++  I ++E + IR+LK
Sbjct: 186 QIVELRYGLNGCNEKTQKEVADMLGISQSYISRLEKRIIRRLK 228


>gi|167623396|ref|YP_001673690.1| flagellar biosynthesis sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353418|gb|ABZ76031.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella
           halifaxensis HAW-EB4]
          Length = 239

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+  FD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSNFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+    EIA++L MP++
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RVAQVIDELEQELGRDARDGEIAERLEMPLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIE-----DKNAVSPLDSAIQANLRETTTRV 616
               +L      +S+   +G ED   LG  +E     D +     +S  +          
Sbjct: 130 EYYSILN----DVSVGKVVGIED---LGVAVEGLNQDDGHEDDAYESLAEVEFHSALVAA 182

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 183 IKLLPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|53724308|ref|YP_104354.1| flagellar biosynthesis sigma factor [Burkholderia mallei ATCC
           23344]
 gi|67639807|ref|ZP_00438640.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Burkholderia mallei GB8
           horse 4]
 gi|121601051|ref|YP_994697.1| flagellar biosynthesis sigma factor [Burkholderia mallei SAVP1]
 gi|124385599|ref|YP_001027679.1| flagellar biosynthesis sigma factor [Burkholderia mallei NCTC
           10229]
 gi|126442044|ref|YP_001060834.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 668]
 gi|126450811|ref|YP_001082651.1| flagellar biosynthesis sigma factor [Burkholderia mallei NCTC
           10247]
 gi|126454531|ref|YP_001068141.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           1106a]
 gi|134281398|ref|ZP_01768106.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 305]
 gi|167002947|ref|ZP_02268737.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei PRL-20]
 gi|167721669|ref|ZP_02404905.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           DM98]
 gi|167740651|ref|ZP_02413425.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 14]
 gi|167817858|ref|ZP_02449538.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 91]
 gi|167826237|ref|ZP_02457708.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 9]
 gi|167847745|ref|ZP_02473253.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           B7210]
 gi|167896335|ref|ZP_02483737.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           7894]
 gi|167904709|ref|ZP_02491914.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei NCTC
           13177]
 gi|167912987|ref|ZP_02500078.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 112]
 gi|167920926|ref|ZP_02508017.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           BCC215]
 gi|217423992|ref|ZP_03455492.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 576]
 gi|226193247|ref|ZP_03788857.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pakistan 9]
 gi|237814231|ref|YP_002898682.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Burkholderia pseudomallei MSHR346]
 gi|242316800|ref|ZP_04815816.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106b]
 gi|254174808|ref|ZP_04881469.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei ATCC 10399]
 gi|254183872|ref|ZP_04890463.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|254186350|ref|ZP_04892867.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254194761|ref|ZP_04901192.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei S13]
 gi|254201430|ref|ZP_04907794.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei FMH]
 gi|254206772|ref|ZP_04913123.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei JHU]
 gi|254261523|ref|ZP_04952577.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1710a]
 gi|254298806|ref|ZP_04966257.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|254357205|ref|ZP_04973479.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei 2002721280]
 gi|52427731|gb|AAU48324.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           mallei ATCC 23344]
 gi|121229861|gb|ABM52379.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei SAVP1]
 gi|124293619|gb|ABN02888.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           mallei NCTC 10229]
 gi|126221537|gb|ABN85043.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 668]
 gi|126228173|gb|ABN91713.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106a]
 gi|126243681|gb|ABO06774.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei NCTC 10247]
 gi|134247065|gb|EBA47151.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 305]
 gi|147747324|gb|EDK54400.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei FMH]
 gi|147752314|gb|EDK59380.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei JHU]
 gi|148026269|gb|EDK84354.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei 2002721280]
 gi|157808491|gb|EDO85661.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|157934035|gb|EDO89705.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160695853|gb|EDP85823.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei ATCC 10399]
 gi|169651511|gb|EDS84204.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei S13]
 gi|184214404|gb|EDU11447.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|217393055|gb|EEC33077.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 576]
 gi|225934847|gb|EEH30824.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pakistan 9]
 gi|237506113|gb|ACQ98431.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Burkholderia pseudomallei MSHR346]
 gi|238520417|gb|EEP83877.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Burkholderia mallei GB8
           horse 4]
 gi|242140039|gb|EES26441.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106b]
 gi|243061438|gb|EES43624.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei PRL-20]
 gi|254220212|gb|EET09596.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1710a]
          Length = 244

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/202 (24%), Positives = 92/202 (45%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R     EIA  L MP++  + +L    + +     +  ED     D 
Sbjct: 98  VEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSML----QDLHGSQLVYYEDFDRSADD 153

Query: 591 --FIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++   A    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRADHSDPLSALLDEHLRSALVDAIERLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|228992639|ref|ZP_04152565.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
 gi|228998685|ref|ZP_04158272.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|229006188|ref|ZP_04163874.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228755029|gb|EEM04388.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228761153|gb|EEM10112.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|228766971|gb|EEM15608.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
          Length = 239

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 105/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+            R +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHL------------RRNNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  ++AN+ R    + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKD--LEANVDRHLLKKALHQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|163750532|ref|ZP_02157770.1| flagellar biosynthesis sigma factor FliA [Shewanella benthica KT99]
 gi|161329687|gb|EDQ00676.1| flagellar biosynthesis sigma factor FliA [Shewanella benthica KT99]
          Length = 246

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 103/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KALIVEQYASLVKKIAHHLLARLPASVQLDDLLQAGMMGLLEASAKFDANKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+   +EIA++L M ++
Sbjct: 73  IRIRGSMLDDIRRGDWVPR-SVHRNQR--RVAQVIDELEQELGRDAKDDEIAQRLEMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D I   + V     +S  +          +  
Sbjct: 130 EYHHILN----NVSVGKIIGIEDLGVSVDVISHDDGVKDDTYESIAEDKFHAALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|89094438|ref|ZP_01167378.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
 gi|89081330|gb|EAR60562.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
          Length = 236

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/199 (26%), Positives = 92/199 (46%), Gaps = 11/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++AA K+D   G  F TYA   ++ +I   +     T R  VH   +  +
Sbjct: 40  DLIQAGMIGLLEAASKYDASKGASFETYAGIRIRGSIIDEVRRGDWTPR-SVHRNSR--R 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V    +++  +  R+ +  E+AK+L + V+    +LK  +     S E  +  E      
Sbjct: 97  VTEAIQQIEARTGRDASDSEVAKELGISVDEYHNLLKDSLDSRLFSFEEMLNPEHEGPGE 156

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F  D     P     +    +  +  + +L  RE+ VL + +   +N    L+E+G+  
Sbjct: 157 SFANDDPG--PNKHIEREAFLKALSEAINNLPEREKLVLALYYDEELN----LKEIGQVL 210

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ QI ++A  +L+
Sbjct: 211 GVSESRVSQIHSQAALRLR 229


>gi|327441149|dbj|BAK17514.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 236

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 97/228 (42%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+++ N      DLI  G+IGL+KA E F+     K +TYA   
Sbjct: 54  ARDMLIERNLRLVVYIARRFDNTSTPIEDLISIGSIGLIKAIETFNLDKNIKLATYA--- 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R       +T+R                          
Sbjct: 111 -----SRCIENE-----ILMHLR-------KTSR-------------------------- 127

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                  K  +S + P+    D +   L D +  +  +  LD   +   R+     +  L
Sbjct: 128 ------MKGEVSFDEPLNADADGNELLLSDILGTEEHIITLDVERKIE-RQHMFNAINQL 180

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TPRE+ ++  RFG+    + T +EV     +++  I ++E K I  L+
Sbjct: 181 TPREKYIMECRFGLNGKEEMTQKEVADHLGISQSYISRLEKKIIMDLR 228


>gi|319787083|ref|YP_004146558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317465595|gb|ADV27327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 248

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 91/199 (45%), Gaps = 14/199 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 46  DLIQAGMIGLIEASRSYDPEQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
                R +     R   P+E+A KL MP+    ++L+     + +SL++ + D      G
Sbjct: 103 AAAAVREIEQATGRAAAPQEVAAKLDMPLPEYLRLLEDASRGQVLSLDSHVEDH-----G 157

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D   + N+ +P     + +        ++ L  RE+ VL + +   +N    L+E+G   
Sbjct: 158 DVQVNSNSPTPQQVLERGDFGRELATAISGLPEREQLVLSLYYEQELN----LKEIGAVL 213

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ QI  +A+ +L+
Sbjct: 214 GVSESRVCQIHGQAVLRLR 232


>gi|251779245|ref|ZP_04822165.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243083560|gb|EES49450.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 234

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 96/239 (40%), Gaps = 63/239 (26%)

Query: 447 EMVEANLRLVISVAKK-YTN--RGLQFLDLIQEGNIGLMKAAEKFDWCL--GYKFSTYAM 501
           +++E N +L+  +  K Y N    +   DL QEG IGLM AAEK+ + +    KFSTYA+
Sbjct: 20  QLIENNKKLIYKIVNKFYVNETNSIDIEDLEQEGMIGLMIAAEKYKFNIENKAKFSTYAI 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           +W+   IT  I  ++                                             
Sbjct: 80  YWIYGRITEFINKRN--------------------------------------------- 94

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLAS 619
                   T    SL TPI +E    L D IE  D    +  +      LR     V+  
Sbjct: 95  --------TNYETSLNTPITEEGEKELKDIIEYIDYEFENVEERIYIKELRRELEEVMKE 146

Query: 620 -LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            LT RE ++L   +G     + T   +G+ F +T  R+RQI  +A+ K++  S+  K+R
Sbjct: 147 ILTLRERQILMFYYG-WHTKECTFNYIGEIFNITSSRVRQIHLRALSKIR-KSKWGKMR 203


>gi|304407606|ref|ZP_07389258.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343557|gb|EFM09399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 232

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 95/228 (41%), Gaps = 61/228 (26%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +T+A       
Sbjct: 53  LIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQVGKGTKLATFA------- 105

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
             R I ++     I +H+R                                        L
Sbjct: 106 -ARCIENE-----ILMHLRS---------------------------------------L 120

Query: 568 KITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           K T++ +SL  PIG +   +   L D +  E  + V  +   I+   +    R L  L  
Sbjct: 121 KKTRKDVSLHDPIGTDKEGNEITLIDILGSEADDIVEKVQLKIE---KSKIYRNLDILDD 177

Query: 623 REERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+ V+  RFG+     + T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 178 REKEVVVGRFGLEHGGEERTQREIAKELGISRSYVSRIEKRALMKLYH 225


>gi|261416067|ref|YP_003249750.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|261372523|gb|ACX75268.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|302327561|gb|ADL26762.1| sigma-70 factor family protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 376

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 106/241 (43%), Gaps = 34/241 (14%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK----- 495
           A+K  +E NLR+ + +A + +   N+ +  +D I E  + L+ A      C  YK     
Sbjct: 121 ARKRAIEGNLRIAVILAYRESVAYNKNI--VDCIGEACLALVSA------CNSYKPDEHQ 172

Query: 496 -FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F++Y    V   + R+I        IPV+       +V   R++   IK     ++ A 
Sbjct: 173 TFASYISIAVFDYLARTIGVP--FFSIPVN-------IVNLCRKLYKDIKYNRLGKKDAL 223

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETT 613
                  G+ +        I L     DED   ++ D +  ++      + ++ ++    
Sbjct: 224 LYVCSCYGLEEYWSNVLYDI-LHVFFLDEDVLDNVLDNVYSESCYENFLTDVENDIERKN 282

Query: 614 TRVLAS------LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            ++L +      LT RE  V+  R+G+     H+L E+G    V+RERIRQIE KA+ KL
Sbjct: 283 VQILINRCLNECLTDREYNVVEHRYGLNGKDSHSLVELGSHQVVSRERIRQIEKKALTKL 342

Query: 668 K 668
           +
Sbjct: 343 E 343


>gi|307731372|ref|YP_003908596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1003]
 gi|307585907|gb|ADN59305.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1003]
          Length = 244

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  EIA+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDESLRSALVDAIDRLPEREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|53720901|ref|YP_109887.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           K96243]
 gi|76811948|ref|YP_331475.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           1710b]
 gi|52211315|emb|CAH37304.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia pseudomallei K96243]
 gi|76581401|gb|ABA50876.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 1710b]
          Length = 243

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/202 (24%), Positives = 92/202 (45%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R     EIA  L MP++  + +L    + +     +  ED     D 
Sbjct: 97  VEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSML----QDLHGSQLVYYEDFDRSADD 152

Query: 591 --FIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++   A    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYRADHSDPLSALLDEHLRSALVDAIERLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVLEVSESRVCQLHSQAVARLR 230


>gi|326204596|ref|ZP_08194452.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
 gi|325985163|gb|EGD46003.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
          Length = 254

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 109/235 (46%), Gaps = 11/235 (4%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           E + + AK++++     L+  VA +   Y    ++F DL+  G  GL+ A EK+D   G 
Sbjct: 15  ENKEAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEKYDLAKGV 74

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KF TYA   ++ +I  SI D      +P  +R K  ++ +    + N+     T +E+A+
Sbjct: 75  KFETYASLRIRGSIIDSIRDMDW---VPRSLRQKNKELEKVYAEIENEKGHTATDKEVAE 131

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETT 613
           K+ + ++   K+L        +      E     G  I  ++     +++++ N +++  
Sbjct: 132 KMGLGMDDFYKLLNDVNVSSMMSLDEFMEQNYERGLEIFSESTEDKPEASLEFNEMKQLL 191

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  +E+ V+   +      + TL+E+     VT  RI Q+  KA+ ++K
Sbjct: 192 ADSIDKLPEKEKAVITFYYF----EELTLKEISAIMSVTESRISQLHTKALLRMK 242


>gi|24374722|ref|NP_718765.1| flagellar biosynthesis sigma factor [Shewanella oneidensis MR-1]
 gi|24349382|gb|AAN56209.1|AE015759_1 RNA polymerase sigma-27 factor [Shewanella oneidensis MR-1]
          Length = 237

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I       R  VH  ++  ++ +    +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDWVPR-SVHRNNR--RIAQAIDELEQVLGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +   + VS    +   +          +  
Sbjct: 130 EYHHILN----DVSVGKIIGIEDLGVSEDILTTSDNVSDGTFEVLAETQFHSALVEAIKI 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|313115572|ref|ZP_07801031.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622087|gb|EFQ05583.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 234

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 98/222 (44%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++  NLRLV+ +AKKY + G+   D+I  G IGL+KA   F      K +TYA       
Sbjct: 58  LITHNLRLVVYLAKKYESSGVPAEDMISIGTIGLIKAVNTFTPERSIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   R+ SN+ ++E +                   
Sbjct: 111 -SRCIGNE----------------ILMYLRKSSNR-RQEAS------------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
               EP++++   GD +   L D +  D+N +S      Q   R    R + SL+PRE +
Sbjct: 134 --IDEPLNVD---GDGNELLLSDILGSDENQIS--QRLEQDAERAVLRRAVDSLSPRERQ 186

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +RFG+    + T +E      +++  I ++E + I  LK
Sbjct: 187 IMELRFGLADGIERTQKEAADALGISQSYISRLEKRIIHTLK 228


>gi|220929479|ref|YP_002506388.1| sporulation sigma factor SigE [Clostridium cellulolyticum H10]
 gi|219999807|gb|ACL76408.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulolyticum
           H10]
          Length = 243

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 105/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 62  VKSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGLIKAINTFNPSKNIKLATYA--- 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +N++K E + +             
Sbjct: 119 -----SRCIENE-----ILMYLRR------------NNRVKAEISID------------- 143

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +N +  +  +I+  + +E     +  L+ 
Sbjct: 144 --------EPLNID---WDGNELLLSDILGTENDM--IHRSIEDEVDKELLATAMKKLSV 190

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T +EV     +++  I ++E + I +LK
Sbjct: 191 REKKIMELRFGLSNGVEKTQKEVADMLGISQSYISRLEKRIISRLK 236


>gi|320107038|ref|YP_004182628.1| RNA polymerase sigma 28 subunit FliA/WhiG [Terriglobus saanensis
           SP1PR4]
 gi|319925559|gb|ADV82634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Terriglobus saanensis
           SP1PR4]
          Length = 294

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 96/215 (44%), Gaps = 12/215 (5%)

Query: 459 VAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VA++   R  Q +   DLI  G IGL+ A  KFD     +F +YA + ++ AI  S+   
Sbjct: 73  VARRIHERLPQHMELDDLIAAGMIGLIDAFSKFDHSKKVQFKSYAQFRIRGAILDSLRTL 132

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EP 573
             +   P  +R K   V    R ++ +    P  +EIA+++ + +   + +L   K  E 
Sbjct: 133 DWS---PRELRRKGRAVEEAIRAVTQRFGCVPAEQEIAREMNLSLSEYQGLLGELKGLEI 189

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            SL    G++       ++       PL   ++  L++     +  L  RE  VL + + 
Sbjct: 190 GSLHAERGEDSGEEELAYVPGSPEDGPLFRCLKGELKQHLMEAIDDLPERERMVLTLYY- 248

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + T++EVG    V   R+ QI + A+ +L+
Sbjct: 249 ---YEELTMKEVGLTLGVVESRVSQIHSSAVARLR 280


>gi|295109522|emb|CBL23475.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus obeum A2-162]
          Length = 243

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 103/232 (44%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 60  ARSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNIKLATYA--- 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR S                       
Sbjct: 117 -----SRCIENE----------------ILMYLRRNSK---------------------- 133

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVS-PLDSAIQANLRETTTRVLA 618
                 TK  +S++ P+    D +   L D +  D++ +S  ++  ++  L     + + 
Sbjct: 134 ------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDVISRRMEDEVEITL---LAKAIN 184

Query: 619 SLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+PRE+ ++R+RFG+      + T +EV     +++  I ++E + +++LK
Sbjct: 185 KLSPREQTIIRLRFGLNNAEGKEKTQKEVADLLGISQSYISRLEKRIMKRLK 236


>gi|182418945|ref|ZP_02950202.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237668989|ref|ZP_04528973.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377228|gb|EDT74796.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237657337|gb|EEP54893.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 235

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 103/222 (46%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVYVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +  E    L +  +G     
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEISFYE---PLNIDWDG----- 144

Query: 568 KITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G E DT +  + IED+     +D       ++     L SL  RE+ 
Sbjct: 145 ----NELLLSDILGTENDTVY--NLIEDE-----VD-------KQLLFMALKSLNDREKE 186

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++R+RFG+    + T +EV     +++  I ++E K I++LK
Sbjct: 187 IVRLRFGLNGAREKTQKEVADMLGISQSYISRLEKKIIKRLK 228


>gi|157692207|ref|YP_001486669.1| sporulation sigma factor SigE [Bacillus pumilus SAFR-032]
 gi|157680965|gb|ABV62109.1| DNA-directed RNA polymerase sigma subunit SigE [Bacillus pumilus
           SAFR-032]
          Length = 239

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 106/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITRD--IEANVDKKLLKKALEQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLVGGEEKTQKDVADMLGISQSYISRLEKRIIKRLQ 232


>gi|295798118|emb|CAX68947.1| RNA polymerase sigma factor 70 [uncultured bacterium]
          Length = 259

 Score = 58.9 bits (141), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 107/235 (45%), Gaps = 17/235 (7%)

Query: 443 IAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + ++E+V   + LV  VA +        ++F DL+  G +GL  A EK+D   G KF TY
Sbjct: 19  LLREEIVRKYMYLVKYVAGRVAIGLPSNVEFNDLVSYGLLGLFDAIEKYDVMQGNKFETY 78

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  ++ AI   +       R+   +R +  ++ + +R + ++  R  T +E+A+ L M 
Sbjct: 79  AVSRIRGAIMDELRKLDWAPRL---LRKRAREIEKKSRELEDQFGRMATDDELAQSLGMS 135

Query: 560 VEGVRKVLKITKEPISL------ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           VE +  +         L      +   G++  S L   +ED    +  +   Q  +++  
Sbjct: 136 VEDLNGIYSELNSTTFLSLDEVWQNDDGNKPISRLQT-VEDSLITNQFNYVNQNEVKQLL 194

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  +E+ V+ + +      + TL E+G    V+  R+ QI  K + +L+
Sbjct: 195 AESIDLLPEKEKLVVVLYY----YENLTLREIGDVLNVSESRVCQIHTKVVSRLR 245


>gi|291562040|emb|CBL40856.1| RNA polymerase sigma factor, sigma-70 family [butyrate-producing
           bacterium SS3/4]
          Length = 265

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/234 (25%), Positives = 109/234 (46%), Gaps = 20/234 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           KKE+    L +  + A K  +     +Q  D + EG + ++K  + +D     KFSTY  
Sbjct: 25  KKEITMQYLYIARTTATKLYDLYSTTMQMEDAVNEGVVAIIKGIDMYDPDKNIKFSTYIT 84

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+ A+   +  Q     +P     ++  +      M  ++ R PT +E+AK L +  +
Sbjct: 85  TRVRGAMLDYVRKQEW---MPRGFYKQLGIIESACEDMKRELGRTPTVDELAKHLGIEKK 141

Query: 562 GVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-- 617
             +++  +K  +   SL+  + +++TS+      +   V P +    A L E   RVL  
Sbjct: 142 RCQRIISMKNRRNIQSLDFLLENQNTSNGLQITNNDTQVQPEE----ACLWEEDMRVLAE 197

Query: 618 --ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             A L  +E++ L + +  G+     +E+VG+   V++ R  QI   A+RKL+H
Sbjct: 198 GIAQLNEKEQKTLALHYMEGLK----MEQVGRVIGVSQPRASQIHTIALRKLRH 247


>gi|254246774|ref|ZP_04940095.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
 gi|124871550|gb|EAY63266.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
          Length = 306

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 103 DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 159

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++   + R  +  EIA+ L MP++  + +L    + +     I  ED     D 
Sbjct: 160 VEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGML----QDLHGSQLIYYEDFDRAADD 215

Query: 591 --FIEDK--NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++    +   PL + +  +LRE     +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 216 EPFLDRYRVDHADPLSALLDDHLREALVEAIERLPEREKLLMSLYYERGLN----LREIG 271

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 272 AVLEVSESRVCQLHSQAVARLR 293


>gi|332982149|ref|YP_004463590.1| RNA polymerase sigma-29 subunit SigE [Mahella australiensis 50-1
           BON]
 gi|332699827|gb|AEE96768.1| RNA polymerase, sigma 29 subunit, SigE [Mahella australiensis 50-1
           BON]
          Length = 239

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 102/225 (45%), Gaps = 49/225 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+++ N G+   DLI  G IGL+KA   FD     K +TYA   
Sbjct: 57  VKSILIERNLRLVVYIARRFENTGIPVEDLISIGTIGLIKAVNTFDPDKKIKLATYA--- 113

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R       R  R   NK     T   I + L    +G 
Sbjct: 114 -----SRCIENE-----ILMYLR-------RNCR--FNK-----TEVSIDEPLNTDWDG- 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G E    + + IED+     L+ A+              L+ R
Sbjct: 149 --------NELLLSDVLGTE-VDLVYNIIEDEVDKQLLNIALN------------KLSSR 187

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+R++++RFG+    + T +EV     +++  I ++E + I++LK
Sbjct: 188 EQRIMQLRFGLDDGVEKTQKEVADMLGISQSYISRLEKRIIKRLK 232


>gi|152976265|ref|YP_001375782.1| sporulation sigma factor SigE [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025017|gb|ABS22787.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 239

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 105/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  ++AN+ R    + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKD--LEANVDRYLLMKALHQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|302391540|ref|YP_003827360.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
 gi|302203617|gb|ADL12295.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
          Length = 247

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 114/242 (47%), Gaps = 54/242 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +++S +++G+      +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F
Sbjct: 51  YLLSKLKEGD---KAVRSVLIERNLRLVVYIARKFENTGIDIEDLVSIGTIGLIKAVNTF 107

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA        +R I ++     I +++R             +NK K E +
Sbjct: 108 DVSKRIKLATYA--------SRCIENE-----ILMYLRR------------NNKKKSEIS 142

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            +E    L +  +G           + L   +G  D   +  +IE+      +D      
Sbjct: 143 FDE---PLNIDWDG---------NELKLSDVLGT-DMDLIYQYIEE-----DVD------ 178

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE   + +  LT RE +++ +RFG+G + +  T +EV     +++  I ++E + I+KL
Sbjct: 179 -RELLLQAMEVLTDRERKIMILRFGLGEDREEMTQKEVADILGISQSYISRLEKRIIKKL 237

Query: 668 KH 669
           + 
Sbjct: 238 QQ 239


>gi|262276378|ref|ZP_06054187.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
 gi|262220186|gb|EEY71502.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
          Length = 224

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 102/225 (45%), Gaps = 13/225 (5%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           M E    LV  +A     R    +Q  DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 1   MFEQYATLVKRIAHHLVARLPPNVQVEDLIQAGMVGLLEAQQNYDASKGASFETYAGIRI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I       R  VH  ++  ++     ++  ++ R+P  +EIAK+L M +E   
Sbjct: 61  RGAMLDDIRKGDWVPR-SVHKNNR--QISEVIAQLEGELGRDPKDKEIAKRLGMSLEQYH 117

Query: 565 KVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +    I    +     +G  + + + +   D+N   P +     + +      +  L  R
Sbjct: 118 QAQNDINAGRLIGIVDLGVSEDAFVTESHRDENL--PFEEVAGDSFKSHLANAIRGLPER 175

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  VL + +   +N    L+E+G    V+  R+ QI+ +A+++L+
Sbjct: 176 EALVLSLYYDEELN----LKEIGAIIGVSESRVCQIQNQAMQRLR 216


>gi|258511273|ref|YP_003184707.1| sporulation sigma factor SigE [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257477999|gb|ACV58318.1| RNA polymerase, sigma 28 subunit, SigE [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 249

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 96/229 (41%), Gaps = 64/229 (27%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   ++  
Sbjct: 72  LIERNLRLVVYIARKFENTGVNIEDLVSIGTIGLIKAVNTFDPSKKIKLATYASRCIENE 131

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I   +                         R +NK++ E                     
Sbjct: 132 ILMYL-------------------------RRNNKLRAE--------------------- 145

Query: 568 KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDS-AIQANL-----RETTTRVLASL 620
                 +SL+ P+  D D + L   + D   V   DS  I  NL     RE     L  L
Sbjct: 146 ------VSLDEPLNVDWDGNEL--LLSD---VLGTDSDTIYRNLEDEVDRELLYDALDKL 194

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + RE  ++ +RFG+G   + T ++V     +++  I ++E + +++L+ 
Sbjct: 195 SERERTIMELRFGLGTGQEMTQKDVADLLGISQSYISRLEKRILKRLQR 243


>gi|238927435|ref|ZP_04659195.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
 gi|238884717|gb|EEQ48355.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
          Length = 252

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/201 (23%), Positives = 93/201 (46%), Gaps = 21/201 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A E+++   G KF TYA   V+ A+   +  +     +PV +R  I K
Sbjct: 59  DLLSSGFFGLLDAIERYELARGNKFETYAGVRVRGAMLDHLRAKDW---VPVSVRQNIKK 115

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             +T  ++  ++ R  T +E+A++L + +E +            LE+ +       L ++
Sbjct: 116 YEKTVAQLEGELGRAATDKELAEELNLSIEELHH----------LESQVSAATVIPLEEY 165

Query: 592 IEDKNAVS----PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +      S    P++ A    ++ET    +  L  +E  V+ + +   M    TL+E+  
Sbjct: 166 LRADTQASLEDGPVEHAEWTEVKETLAAAIEKLPEKERTVIALYYYDEM----TLKEIAA 221

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+  KAI +++
Sbjct: 222 ILHLSEARISQLHTKAIFRMR 242


>gi|112981044|gb|ABI29246.1| DNA-dependent RNA polymerase sigma factor D subunit [Brachymonas
           denitrificans]
          Length = 270

 Score = 58.5 bits (140), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 41/62 (66%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   MM ++  SP T   ++   DE+ +   ++  +
Sbjct: 1   MREMGTVELLTREGEIEIAKRIEGGMMDMMEAISGSPATIDEILAMADEIREDKVVITTV 60

Query: 185 ID 186
           +D
Sbjct: 61  VD 62


>gi|118442872|ref|YP_878340.1| sporulation sigma factor SigK [Clostridium novyi NT]
 gi|118133328|gb|ABK60372.1| DNA-dependent RNA polymerase sigma subunit [Clostridium novyi NT]
          Length = 225

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 96/234 (41%), Gaps = 65/234 (27%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++AK  ++E NLRLV  + KKY+       DLI  G +GL+KA + FD   G + +TYA 
Sbjct: 39  ALAKGILIERNLRLVAHIVKKYSYPNKDVDDLISIGTVGLIKAIDSFDVDKGTRLATYAA 98

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   I                         R S KIK E               
Sbjct: 99  RCIENEILMLI-------------------------RNSKKIKSE--------------- 118

Query: 562 GVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQA-----NLRETT 613
                       + L+ PIG +   +   L D +      S  DS I+       +R+  
Sbjct: 119 ------------VYLQDPIGVDKEGNEISLMDILS-----SDEDSVIEVVENRMEVRKLY 161

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            ++   LT RE+ +++MR+G+      T  E+     ++R  + +IE +A++K+
Sbjct: 162 DKIEKCLTEREKIIIKMRYGLVDGKSKTQREIASLLNISRSYVSRIEKRALKKI 215


>gi|304311117|ref|YP_003810715.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
 gi|301796850|emb|CBL45062.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
          Length = 244

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 106/238 (44%), Gaps = 22/238 (9%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +A  +   +VE +L LV  +A     R    +   DLIQ G IGL+ A +K+D   G  F
Sbjct: 13  QAHASLDTLVEQHLPLVRRIAHHMIGRLPSNVIVDDLIQAGVIGLIDALQKYDTGKGASF 72

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR----TARRMSNKIKREPTPEEI 552
            TYA   ++ A+   I       R        +H+  R      R +  +++R+ T  E+
Sbjct: 73  ETYAGIRIRGAMIDEIRRGEWAPR-------SVHRNARAIQDAIRNVEARVQRDATDREV 125

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++L +P++    + +  +     S+E     E     GD  +  +  +P     +  + 
Sbjct: 126 AEELGVPLDAYHAMAQDSMATRLFSMEELTAPESIIDRGDLQQAHD--NPASHFQRDMML 183

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    +  L  RE+ VL + +   +N    L+E+G+   V+  R+ QI ++A  +L+
Sbjct: 184 TSMANAIKDLPEREQLVLSLYYDEELN----LKEIGEVLGVSESRVCQIHSQATHRLR 237


>gi|260221743|emb|CBA30612.1| hypothetical protein Csp_C24420 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 264

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 110/231 (47%), Gaps = 19/231 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC---LGYKFSTY 499
           +++VE +  +V SVA     R    +   DL+Q+G +GLM+A     W     G  F  Y
Sbjct: 13  RKLVEDHQPVVRSVANHVGRRLPPNVDRADLVQDGMLGLMEAL--LRWTKESSGTHFENY 70

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
                + A+   +       R    +R  + +V    +++S+++ R PT  E+AK+L MP
Sbjct: 71  IALRAQGAMIDGLRAADPVSR---QVRKDMRRVEVALQQLSHRLGRPPTEGELAKQLDMP 127

Query: 560 VEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +   +++L+  +    ISL+   GD    +L   +ED NA  PL    +A LR+     +
Sbjct: 128 LADYQRLLQDAQGYVLISLQDLTGDSVDQYLKRCLED-NA-DPLALLERAALRQALAESI 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L PR+ ++L     +    +  + E+ K   ++  RI Q+  ++I +L+
Sbjct: 186 -QLLPRKSQIL---LTLYYEHEMRMHEIAKHLGLSEARISQMHTQSIAQLR 232


>gi|229918653|ref|YP_002887299.1| RNA polymerase sigma factor SigD [Exiguobacterium sp. AT1b]
 gi|229470082|gb|ACQ71854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium sp.
           AT1b]
          Length = 256

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 51/219 (23%), Positives = 102/219 (46%), Gaps = 15/219 (6%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           R+++++ K      L+ L     G +GL  A  K+D     KF TYA + ++ AI   + 
Sbjct: 38  RMIVTLPKSVERDELKSL-----GYMGLYDALMKYDPEHNNKFDTYAAFRIRGAIIDGLR 92

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITK 571
                  +P  +R+K+ K+   A ++   + R PT  E+A    +P+  + + +      
Sbjct: 93  KVDW---LPRSVREKVKKIDHVAEQLEQSLHRAPTKSELASACDLPISEIERTMAEGYFA 149

Query: 572 EPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             +S++  +   E+   +     D ++  P D+ +Q  L +     +  L+ +E  V+ +
Sbjct: 150 NMLSIDEAVTLQEEGKVMSVTYFDPDSEKPEDTLLQRELIDVLAAEVDHLSEKERLVVSL 209

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +   +    TL E+G+   ++  RI QI +KA++ LKH
Sbjct: 210 FYFDEL----TLTEIGEVLELSTSRISQIHSKALKTLKH 244


>gi|221309406|ref|ZP_03591253.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313731|ref|ZP_03595536.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318655|ref|ZP_03599949.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322928|ref|ZP_03604222.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767354|ref|NP_389415.2| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296331108|ref|ZP_06873582.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674263|ref|YP_003865935.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315297|ref|YP_004207584.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|133472|sp|P06222|RPSE_BACSU RecName: Full=RNA polymerase sigma-E factor; AltName: Full=P31;
           AltName: Full=Sigma-29; AltName: Full=Stage II
           sporulation protein GB; Flags: Precursor
 gi|40169|emb|CAA25620.1| unnamed protein product [Bacillus subtilis]
 gi|225184981|emb|CAB13406.2| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484083|dbj|BAI85158.1| sporulation sigma factor SigE [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151752|gb|EFG92627.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412507|gb|ADM37626.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021571|gb|ADV96557.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|224259|prf||1012299A spoIIG gene
          Length = 239

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 106/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKD--IEANVDKKLLKKALEQLNE 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLR 232


>gi|257458803|ref|ZP_05623926.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
 gi|257443791|gb|EEV18911.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
          Length = 626

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 74/155 (47%), Gaps = 33/155 (21%)

Query: 40  QRGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDG------DDLED------ 85
           Q+ Y+T E L  F    P   + +++E   A+     + ++         +LED      
Sbjct: 19  QKSYITYERLIKFFDKAPTATAVKKVE---ALTKKFDVELISAAEISKIKNLEDAKLKEA 75

Query: 86  ------EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                 +EG ++  DL+S        L+  +      +D PVRMYLREMG I LL++E E
Sbjct: 76  TQKKLLDEGWDEEFDLSSDVE----LLEWSR------SDSPVRMYLREMGQIPLLTKEEE 125

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           I I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 126 IEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 160


>gi|310643126|ref|YP_003947884.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248076|gb|ADO57643.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 233

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 98/243 (40%), Gaps = 71/243 (29%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +T+A   
Sbjct: 50  SRNTLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLRS------------------------------------ 120

Query: 564 RKVLKITKEPISLETPIGDEDTSH-------LG---DFIEDKNAVSPLDSAIQANLRETT 613
              LK T++ +SL  PIG +   +       LG   D I DK  +    S I  N     
Sbjct: 121 ---LKKTRKDVSLHDPIGTDKEGNEITLIDILGSEADDIVDKVQLKIEKSKIYRN----- 172

Query: 614 TRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              L  L  RE+ V+  RFG+     + T  E+ ++  ++R  + +IE +A+ KL H   
Sbjct: 173 ---LDILDEREKEVVIGRFGLEAGGEERTQREIARELGISRSYVSRIEKRALMKLYHEFY 229

Query: 673 SKK 675
            +K
Sbjct: 230 KQK 232


>gi|170694383|ref|ZP_02885537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia graminis
           C4D1M]
 gi|170140806|gb|EDT08980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia graminis
           C4D1M]
          Length = 244

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  E+A+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHKVEQNLGRSASETEVAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDDSLRSALVEAIDRLPEREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|320178177|gb|EFW53154.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           ATCC 9905]
 gi|320182764|gb|EFW57648.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           ATCC 9905]
          Length = 196

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 42/157 (26%), Positives = 74/157 (47%), Gaps = 10/157 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 43  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++  ++ R  T  E+A++L + +   R++L  T           DE     GD 
Sbjct: 100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY---DEWREEHGDS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           IE    D    +PL   + +NLR+     + +L  RE
Sbjct: 157 IELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPERE 193


>gi|228950124|ref|ZP_04112308.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229120608|ref|ZP_04249853.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228662893|gb|EEL18488.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228809547|gb|EEM55984.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 203

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 98/210 (46%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   F   +N   T
Sbjct: 114 VENASDGSSVARIESVGEVEKGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|194014382|ref|ZP_03052999.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
 gi|194013408|gb|EDW22973.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
          Length = 239

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 106/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITRD--IEANVDKKLLKKALEQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLIGGEEKTQKDVADMLGISQSYISRLEKRIIKRLQ 232


>gi|312128105|ref|YP_003992979.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778124|gb|ADQ07610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 244

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 53/226 (23%), Positives = 105/226 (46%), Gaps = 54/226 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK ++E NLRLV+ +AK++ N  +   DL+  G IGL+KA   ++     K +TYA    
Sbjct: 64  KKLLIERNLRLVVYIAKRFENTKINLEDLVSIGTIGLIKAINTYNPNKNIKLATYA---- 119

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
               ++ I ++                ++   RR SN            +KL + ++   
Sbjct: 120 ----SKCIENE----------------ILMFLRRNSN------------RKLELSID--- 144

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                  EP++++    D +   L D +  + +   + ++S+++   +E   + +  L  
Sbjct: 145 -------EPLNVD---WDGNELLLSDVLGTDTEEIYNKIESSVE---KEALLQAIQKLPS 191

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG G   + T +EV     +++  I ++E K I +LK
Sbjct: 192 REKKIVELRFGFGDGGEKTQKEVADMLGISQSYISRLEKKIITRLK 237


>gi|207092651|ref|ZP_03240438.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 367

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 44/69 (63%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L +
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALIN 224

Query: 177 GTTLLREII 185
               ++E+ 
Sbjct: 225 RERKVKELF 233


>gi|318040084|ref|ZP_07972040.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 58/117 (49%), Gaps = 4/117 (3%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A++++V  NL LV     ++            D +QE  + L++AAEKFD   GY+FSTY
Sbjct: 61  AREQLVRHNLGLVAHTWGRHRCSLPAHDDTTADALQEAALNLVRAAEKFDPAKGYRFSTY 120

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           A +WV++  T         IR P      + K +R +++       EP+ E +A +L
Sbjct: 121 ATFWVRRGFTEFEQRAKRAIRFPAEKAAVVLKALRLSQQHQASTGDEPSLEWLAAQL 177


>gi|332531601|ref|ZP_08407498.1| RNA polymerase sigma-28 subunit FliA/WhiG [Hylemonella gracilis
           ATCC 19624]
 gi|332038964|gb|EGI75393.1| RNA polymerase sigma-28 subunit FliA/WhiG [Hylemonella gracilis
           ATCC 19624]
          Length = 245

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 52/208 (25%), Positives = 96/208 (46%), Gaps = 9/208 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL +A  +++   G +F T+A   ++ A+   + +     R     + 
Sbjct: 44  IQVDDLIQVGLIGLSEALTRYEATQGVQFETFATQRIRGAMIDELRENDWMSRGSRKSQK 103

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDT 585
           +I   +    R+ +++ R P+  EIA++L M +   + +L   K  + + LE   G +D 
Sbjct: 104 EIESAL---TRLEHQLGRSPSESEIAEELGMELAEYQALLYKVKGTQLVYLEDMSGGDDE 160

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D         P+       LR +    + +L  RE+ V+ M +   MN    L+E+
Sbjct: 161 EGFLDRHMVDGESDPMALLRNQRLRASLVDAIKALPEREQYVMSMYYEQDMN----LKEI 216

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                VT  R+ Q+ +++I +L+   RS
Sbjct: 217 AAVLGVTESRVCQLHSQSIARLRAKMRS 244


>gi|311068053|ref|YP_003972976.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
 gi|310868570|gb|ADP32045.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
          Length = 239

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 107/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NKI+ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKD--IEANVDKKLLKKALEQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLR 232


>gi|154685948|ref|YP_001421109.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens FZB42]
 gi|154351799|gb|ABS73878.1| SigE [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 107/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NKI+ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKD--IEANVDKKLLKKALEQLNE 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLR 232


>gi|153803628|ref|ZP_01958214.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
 gi|124120837|gb|EAY39580.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
          Length = 193

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 91/193 (47%), Gaps = 14/193 (7%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  ++ +    
Sbjct: 2   VGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHNR--EISQAIAV 58

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDK 595
           +  ++ R+PT  E+AK L M +E    VL      I+    +G ED     D I   E+ 
Sbjct: 59  LEGELNRDPTDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVSDDAISPFEEG 114

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              SP     + + R+     + SL  RE  VL + +   +N    L+E+G+   V+  R
Sbjct: 115 EDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEELN----LKEIGEVLGVSESR 170

Query: 656 IRQIEAKAIRKLK 668
           + QI ++++++L+
Sbjct: 171 VSQILSQSMQRLR 183


>gi|85058037|ref|YP_453739.1| flagellar biosynthesis sigma factor [Sodalis glossinidius str.
           'morsitans']
 gi|84778557|dbj|BAE73334.1| RNA polymerase sigma factor for flagellar operon FliA [Sodalis
           glossinidius str. 'morsitans']
          Length = 241

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 52/230 (22%), Positives = 102/230 (44%), Gaps = 19/230 (8%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A I + E +   +RL  SV         +  DLIQ G IGL+ A + FD   G  F+TYA
Sbjct: 22  APIIRHEALRLQVRLPASV---------ELEDLIQAGMIGLLAAIDSFDAAQGASFTTYA 72

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  +   + ++     +P  +R    ++    +R+  ++    + ++IA +L + +
Sbjct: 73  RSRIRWGMLDELRERDW---VPRSVRRNAREIAAAIQRLEQRLGANTSEQQIADELGVSL 129

Query: 561 EGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              + +L  T   +  SL+  +  E     G  +       P    +   LR+     + 
Sbjct: 130 TAYQTMLHETNCSQLFSLDELMAQE-AQGTGPALPADAGQDPFQLLMAGGLRKQVKDEIG 188

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ +L + +   +N    L+E+G+   V   R+ Q+ + AI++L+
Sbjct: 189 RLPEREQLLLNLYYHQELN----LKEIGEVLGVGESRVSQLHSLAIKRLR 234


>gi|308070013|ref|YP_003871618.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859292|gb|ADM71080.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 233

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 98/243 (40%), Gaps = 71/243 (29%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E F    G K +T+A   
Sbjct: 50  SRNTLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 107 -----ARCIENE-----ILMHLRS------------------------------------ 120

Query: 564 RKVLKITKEPISLETPIGDEDTSH-------LG---DFIEDKNAVSPLDSAIQANLRETT 613
              LK T++ +SL  PIG +   +       LG   D I DK  +    S I  N     
Sbjct: 121 ---LKKTRKDVSLHDPIGTDKEGNEITLIDILGTEADDIVDKVQLKIEKSKIYRN----- 172

Query: 614 TRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              L  L  RE+ V+  RFG+     + T  E+ ++  ++R  + +IE +A+ KL H   
Sbjct: 173 ---LDILDEREKEVVIGRFGLEAGGEERTQREIARELGISRSYVSRIEKRALMKLYHEFY 229

Query: 673 SKK 675
            +K
Sbjct: 230 KQK 232


>gi|289758831|ref|ZP_06518209.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714395|gb|EFD78407.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 330

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 31/37 (83%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEG  G
Sbjct: 293 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGLPG 329



 Score = 45.1 bits (105), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 211 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 270


>gi|226361251|ref|YP_002779029.1| RNA polymerase sigma factor SigF [Rhodococcus opacus B4]
 gi|226239736|dbj|BAH50084.1| RNA polymerase sigma factor SigF [Rhodococcus opacus B4]
          Length = 265

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 51/217 (23%), Positives = 96/217 (44%), Gaps = 8/217 (3%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L L   +A+++  RG    DL+Q   +GL+ + ++FD   G  F ++A+  +   + R  
Sbjct: 50  LPLAEHIARRFDGRGEAHDDLVQVARLGLVNSVDRFDVERGSDFVSFAVPTIMGEVRRHF 109

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            D    +R+P  M++    + +    +S  +   PT  E+A+ L +  E V + L     
Sbjct: 110 RDTGWAVRVPRRMKELHLALSQAVAELSQSLGHAPTVSELAEHLDLEQEEVAQGLLAGN- 168

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMR 631
             + +T   D  +S     +     +   D+A+      ET   +L SL  RE  VL +R
Sbjct: 169 --AYQTVSVDNTSSDRAGELSMVETLGDYDAAMDDVENHETLRPLLQSLPERERTVLMLR 226

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           F   M      + VG    +++  + ++ AK +  L+
Sbjct: 227 FFGNMTQTQIADRVG----ISQMHVSRLLAKTLASLR 259


>gi|187925770|ref|YP_001897412.1| flagellar biosynthesis sigma factor [Burkholderia phytofirmans
           PsJN]
 gi|187716964|gb|ACD18188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           phytofirmans PsJN]
          Length = 244

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  EIA+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDDSLRSALVEAIDRLPDREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|302746280|gb|ADL62730.1| RpoD [Morganella morganii subsp. morganii]
          Length = 274

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/64 (46%), Positives = 40/64 (62%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRL 60

Query: 182 REII 185
            ++I
Sbjct: 61  SDLI 64


>gi|319937135|ref|ZP_08011542.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807501|gb|EFW04094.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 230

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 63/233 (27%)

Query: 444 AKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  ++E NLRLV+ VAKKY    N  ++  DLI  G IGL+KA   F      K +TYA
Sbjct: 48  ARDLLIEHNLRLVVYVAKKYDSVQNGSIE--DLISIGTIGLVKAVNTFKMDKNIKLATYA 105

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
                   +R I ++                 +    R +NK+++E              
Sbjct: 106 --------SRCIENE-----------------ILMFLRKNNKLRQE-------------- 126

Query: 561 EGVRKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRV 616
                        ISL+ P+    D +   L D I  DK+ V   D     + +E   R 
Sbjct: 127 -------------ISLDEPLNVDYDGNELLLSDIIGTDKDIVQ--DEIEHNDQKEKFYRA 171

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L  RE+ +L MR+G+  + + T ++V +   +++  I ++E K I+KL++
Sbjct: 172 LHHLNEREQEILMMRYGLVGHDELTQKDVAEVLGISQSYISRLEKKIIKKLRN 224


>gi|226323679|ref|ZP_03799197.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
 gi|225207863|gb|EEG90217.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
          Length = 247

 Score = 58.5 bits (140), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 54/242 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +S++  G+ E    KK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F
Sbjct: 50  HAISLLGGGQDEE--GKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTF 107

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +     K +TYA        +R I ++                ++   RR +NK K E +
Sbjct: 108 NPEKNIKLATYA--------SRCIENE----------------ILMYLRR-NNKTKLEVS 142

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            +                     EP++++    D +   L D +  +      D   +A 
Sbjct: 143 ID---------------------EPLNVDW---DGNELLLSDILGTEEDTIYRDMETEAE 178

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +   + +  L+ RE  +++MRFG+G     + T +EV     +++  I ++E K +++
Sbjct: 179 -HKLLGKAIGRLSNRERVIVQMRFGLGTPDGEEKTQKEVADLLGISQSYISRLEKKIMQR 237

Query: 667 LK 668
           L+
Sbjct: 238 LR 239


>gi|310826431|ref|YP_003958788.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
 gi|308738165|gb|ADO35825.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
          Length = 250

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 103/229 (44%), Gaps = 20/229 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L +   + KKY  R     D+ Q   +GLM A E++D   G++F T+A   +   
Sbjct: 31  LIENFLYIPKLLVKKYAYRSNDVEDIYQVACLGLMYAVERYDPDRGFEFDTFASPTIIGE 90

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D+   IR+P  +++   ++ R    + +K+ + PT  EIA  L +  E V + +
Sbjct: 91  IKKYYRDKQWIIRVPRRIQELNREINRAKTTLEHKLMKTPTISEIADYLEVTEEAVIEAM 150

Query: 568 KITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQ--ANLRETTTRVLASL 620
           +      P SL T      D   + L D I ++      D  I+   N+ +   R L SL
Sbjct: 151 EGNNVFYPKSLSTEFESNADGQEATLLDLIGEE------DERIENIGNVEDLRQR-LESL 203

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGK-QFCVTRERIRQIEAKAIRKLK 668
            P E  ++  R+  G         +GK Q  V+R     +E K + KL+
Sbjct: 204 NPVERMIIEERYYNGKTQKEVAAIIGKSQMTVSR-----LEKKVMEKLR 247


>gi|229108567|ref|ZP_04238180.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
 gi|228674898|gb|EEL30129.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
          Length = 203

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 98/210 (46%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   F   +N   T
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFRENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|119511138|ref|ZP_01630256.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119464233|gb|EAW45152.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 261

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 36/137 (26%), Positives = 77/137 (56%), Gaps = 3/137 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ +  LV  +A K++++  + + DL Q G  GL++A E+FD   GY FS++A+ +
Sbjct: 28  RNQLVQLHTGLVRKIAHKFSHQCHEPYEDLEQIGYFGLIRAIERFDPSQGYAFSSFAVPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+S  ++IP   ++  +   +  + ++  + R P   EIA+KL + V   
Sbjct: 88  IRGEMLHFLRDRSSLLKIPRRWQELYNDGQKVRKELAVSLGRSPRDAEIAQKLQVSVHEW 147

Query: 564 R--KVLKITKEPISLET 578
           +  K+    + P+SL+ 
Sbjct: 148 QETKLAAQNRMPLSLDA 164


>gi|254459646|ref|ZP_05073062.1| flagellar-specific RNA polymerase sigma factor [Rhodobacterales
           bacterium HTCC2083]
 gi|206676235|gb|EDZ40722.1| flagellar-specific RNA polymerase sigma factor [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 219

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 56/203 (27%), Positives = 99/203 (48%), Gaps = 15/203 (7%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++F DL+Q G +GL++AA+++    G  F +YA+  V+ AI   +   S   R  +    
Sbjct: 17  VEFDDLLQIGLMGLIEAAQRYTRQEGISFESYAVIRVRGAINDFLRKNSALSRKSM---- 72

Query: 528 KIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           KI+K V  AR ++ + + R P   E+AK + + ++      +      S    I DE   
Sbjct: 73  KINKEVNEARNKLVHDLGRAPEGHEVAKAVGLSLDEFTAWEQTLNS--SYHNSIQDEYDE 130

Query: 587 HLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           H   F     A +P++  + +A L+E     L +L  RE  VL++ +   +N    L E+
Sbjct: 131 HSMWF---ATADAPIEQELDRARLKEALLYALKTLPEREALVLQLYYVEELN----LFEI 183

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
                VT  R+ QI++ A +K++
Sbjct: 184 AAVLDVTSGRVSQIKSSAFKKMQ 206


>gi|238782801|ref|ZP_04626830.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238716224|gb|EEQ08207.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 241

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 95/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A + FD   G   STY    V+ A+   + ++     +P  +R    +
Sbjct: 43  DLIQAGAIGLLTAIDHFDPKKGIGLSTYITQRVRWAMIDELRERDW---VPRRVRSNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    +R+  +     T  ++A  + + +   +K+L  T    S +    DE    L D 
Sbjct: 100 IAVIIQRIEQESGHVATEADVANSMGVTLPEYQKMLADTN---SSQLYSLDELQEELADG 156

Query: 592 IEDKNA----VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E  +     ++PL   ++ NL +  +R + +L  RE+ +L + +   +N    ++E+  
Sbjct: 157 FEQSDTQHEMLNPLHEIMKGNLTKQISREIKALPEREQLLLNLYYQQELN----MKEISV 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  R+ Q+ ++AI++L+
Sbjct: 213 LLNVTETRVSQLHSQAIKRLR 233


>gi|228932399|ref|ZP_04095281.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228984185|ref|ZP_04144367.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229183301|ref|ZP_04310530.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228600171|gb|EEK57762.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228775472|gb|EEM23856.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228827335|gb|EEM73087.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 203

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 98/210 (46%), Gaps = 24/210 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +      +++ ++R P   EIA  L +  E V +++              +   S L D 
Sbjct: 64  IKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDV 113

Query: 592 IE---DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHT 641
           +E   D ++V+ ++S   ++    ET  R     +   L   E+ V+   F   +N   T
Sbjct: 114 VENASDGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDT 173

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               G++  +++  + +I+ +AI KLK  +
Sbjct: 174 ----GERLGISQMHVSRIKRQAISKLKQAA 199


>gi|94264039|ref|ZP_01287839.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|94266375|ref|ZP_01290074.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93453027|gb|EAT03515.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93455550|gb|EAT05737.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 256

 Score = 58.2 bits (139), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 99/204 (48%), Gaps = 17/204 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A  KFD     +F TYA + +K A+   + +      +P  +R KI +
Sbjct: 54  DLISCGIVGLIDAINKFDPAKNVQFKTYAEFRIKGAM---LDELRALDWVPRSVRRKITE 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-----TPIGDEDTS 586
           + + +  + +K+ R P  EE A  L + +    ++L  TK    L+     + + DE   
Sbjct: 111 LEKISGELESKLGRPPDDEETAAALGIELADFHRLLDETKSVTFLDIDYLRSKVPDEIEG 170

Query: 587 HLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            +G+    +DK+  + L+     NL     + +  L  +E+  + + +    + + T++E
Sbjct: 171 DVGEIFARDDKDPFTALNLGETRNL---LAKAIGELPEKEKLTVALYY----HEELTMKE 223

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+    T  RI Q+ +KA+ +L+
Sbjct: 224 IGEVLGYTESRISQMHSKAMLRLR 247


>gi|240144184|ref|ZP_04742785.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257203788|gb|EEV02073.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|291536439|emb|CBL09551.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           M50/1]
 gi|291538693|emb|CBL11804.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           XB6B4]
          Length = 243

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 45/78 (57%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
             +A+K+++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA
Sbjct: 57  GQLARKQLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPGKNIKLATYA 116

Query: 501 MWWVKQAITRSIADQSCT 518
              ++  I   +   S T
Sbjct: 117 SRCIENEILMYLRRNSKT 134


>gi|207108883|ref|ZP_03243045.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 228

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D L
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDAL 222


>gi|258592481|emb|CBE68790.1| RNA polymerase sigma factor whiG (modular protein) [NC10 bacterium
           'Dutch sediment']
          Length = 459

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 111/232 (47%), Gaps = 15/232 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  ++ AN+ LV  VA + + +    ++  DL   G +GL+ A E +D     +F+TYA 
Sbjct: 20  RDRLITANISLVRQVAGRLSLQLPSCVELDDLESAGAVGLVSAVEHYDPDQPSEFATYAQ 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + ++ AI   +  Q      P  +R K  ++ +T  R+   + REP+ +E+A  L M  E
Sbjct: 80  YRIRGAILDDLRAQDFA---PRSLRAKAREIQQTLVRLEVDLGREPSDDEVAAALGMDRE 136

Query: 562 GVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              + L   +    +SL+ P  + D +     I +    +  D + +A  RE   R+L  
Sbjct: 137 TYWRTLGEIRGMVLVSLDEPGVEADGTESDRLIWELPDRAGRDPSTEAARRE-RVRLLGG 195

Query: 620 LT---PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    P +ER++   +      + T++E+G+   V+  R+ QI   AI +++
Sbjct: 196 IIEALPAQERLVLTLY---YFEELTMKEIGRVLEVSESRVSQIHTSAILRMR 244


>gi|326204637|ref|ZP_08194493.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
 gi|325985204|gb|EGD46044.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
          Length = 243

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 104/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 62  VKSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGLIKAINTFNPSKNIKLATYA--- 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +N++K E + +             
Sbjct: 119 -----SRCIENE-----ILMYLRR------------NNRVKAEISID------------- 143

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   N +  +  +I+  + +E     +  L+ 
Sbjct: 144 --------EPLNID---WDGNELLLSDILGTDNDM--IHRSIEDEVDKELLAAAMKKLSV 190

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T +EV     +++  I ++E + I +LK
Sbjct: 191 REKKIMELRFGLSNGVEKTQKEVADMLGISQSYISRLEKRIISRLK 236


>gi|317969500|ref|ZP_07970890.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 315

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 58/117 (49%), Gaps = 4/117 (3%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A++++V  NL LV     ++            D +QE  + L++AAEKFD   GY+FSTY
Sbjct: 66  AREQLVRHNLGLVAHTWGRHRCSLPAHDDTTADALQEAALNLVRAAEKFDPAKGYRFSTY 125

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           A +WV++  T         IR P      + K +R +++       EP+ E +A +L
Sbjct: 126 ATFWVRRGFTEFEQRAKRAIRFPAEKAAVVLKALRLSQQQQATTGDEPSLEWLAAQL 182


>gi|308173494|ref|YP_003920199.1| RNA polymerase sporulation-specific sigma-29 factor sigma-E
           [Bacillus amyloliquefaciens DSM 7]
 gi|307606358|emb|CBI42729.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553576|gb|AEB24068.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens TA208]
 gi|328911631|gb|AEB63227.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens LL3]
          Length = 239

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 107/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NKI+ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKD--IEANVDKKLLKKALEQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLIGEEEKTQKDVADMMGISQSYISRLEKRIIKRLR 232


>gi|238025872|ref|YP_002910103.1| flagellar biosynthesis sigma factor [Burkholderia glumae BGR1]
 gi|124695885|gb|ABN14279.1| FliA [Burkholderia glumae BGR1]
 gi|237875066|gb|ACR27399.1| FliA [Burkholderia glumae BGR1]
          Length = 241

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 38  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 94

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V +   ++  ++ R     E+A  L MP++  + +L+     + I  E    D D S   
Sbjct: 95  VEQAIHQVEQRLGRSANESEVATHLEMPLDDYQAMLQDLHGSQLIYYE----DFDRSADD 150

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 151 EPFLDRYRVDHSDPLSALLDEHLRAALVEAIDRLPEREKLLMSLYYERGLN----LREIG 206

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 207 AVLEVSESRVCQLHSQAVARLR 228


>gi|91978893|gb|ABE66422.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 289

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/137 (29%), Positives = 68/137 (49%), Gaps = 2/137 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E
Sbjct: 154 QLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVAAFTNNE 213

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            D  W  Y K   +      V  + D +L+   +++ I VETG+SI++ + I   +  GE
Sbjct: 214 CDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVETGLSIAQIKDINRRMSIGE 272

Query: 439 CEASIAKKEMVEANLRL 455
            +A  AKKEMVEANLRL
Sbjct: 273 AKARRAKKEMVEANLRL 289


>gi|167750707|ref|ZP_02422834.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
 gi|167656386|gb|EDS00516.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
          Length = 251

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 56/213 (26%), Positives = 102/213 (47%), Gaps = 18/213 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+I EG I LM A + FD     KF TYA   +K A+   +       R+P  +R    +
Sbjct: 55  DIINEGVIALMAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRKLD---RVPRTLRKLSKQ 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +     R+++++ R PT EE+A+ + M    + K++  T   I+L      E+  +  + 
Sbjct: 112 LDDNFARLNSELCRTPTDEELAESMNMTTAQLSKLMANTAGMITLSF----EELLYEDNL 167

Query: 592 IEDKNAVSPLDSA--IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            E+ +A S    A   +   ++     +A+L  +E++V+ M +   +       E+ K  
Sbjct: 168 DENISASSETADAKMYEREKKQVIADAVATLPEKEKQVVTMYYYERLK----YSEIAKVM 223

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +T+ R+ QI +KA+  LK+     KL S++ G
Sbjct: 224 SITQSRVCQIHSKAMLTLKN-----KLESYIKG 251


>gi|111019111|ref|YP_702083.1| RNA polymerase sigma factor SigF [Rhodococcus jostii RHA1]
 gi|110818641|gb|ABG93925.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 98/224 (43%), Gaps = 22/224 (9%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L L   +A+++  RG    DL+Q   +GL+ + ++FD   G  F ++A+  +   + R  
Sbjct: 50  LPLAEHIARRFDGRGEAHDDLVQVARLGLVNSVDRFDVERGSDFVSFAVPTIMGEVRRHF 109

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--T 570
            D    +R+P  M++    + +    +S  +   PT  E+A+ L +  E V + L     
Sbjct: 110 RDTGWAVRVPRRMKELHLALSQAVAELSQSLGHAPTVSELAEHLDLEQEEVAQGLLAGNA 169

Query: 571 KEPISLETPIGDED-----TSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPRE 624
            + +S++    D          LGD+          D+A+      ET   +L SL  RE
Sbjct: 170 YQTVSVDNTSSDRTGELSMVETLGDY----------DAAMDDVENHETLRPLLQSLPERE 219

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL +RF   M      + VG    +++  + ++ AK +  L+
Sbjct: 220 RTVLMLRFFGNMTQTQIADRVG----ISQMHVSRLLAKTLASLR 259


>gi|331090017|ref|ZP_08338907.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
 gi|330402931|gb|EGG82497.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 245

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 46/84 (54%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R G   A  AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     
Sbjct: 53  RLGTEYAEDAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKI 112

Query: 495 KFSTYAMWWVKQAITRSIADQSCT 518
           K +TYA   ++  I   +   S T
Sbjct: 113 KLATYASRCIENEILMYLRRNSKT 136


>gi|311741871|ref|ZP_07715682.1| DNA-directed RNA polymerase sigma subunit SigF [Aeromicrobium
           marinum DSM 15272]
 gi|311314877|gb|EFQ84783.1| DNA-directed RNA polymerase sigma subunit SigF [Aeromicrobium
           marinum DSM 15272]
          Length = 258

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 109/234 (46%), Gaps = 33/234 (14%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++L    S+A +Y NRGL+  DL Q  N+ L+KA  +F    G  F+++A   +  
Sbjct: 35  DVVRSHLGFANSLASRYRNRGLELDDLRQVANLALVKAVRRFRADRG-DFASFAAVTISG 93

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            + R   D   TIR P  ++     + +     +++   EPT +E+A +L +P E V + 
Sbjct: 94  ELKRHFRDHGWTIRPPRSIQQLQVDLRKAKEEAAHESSVEPTLDELAARLHVPREAVAEA 153

Query: 567 ------LKITK--EPISL-ETPIGDEDTSHLGD---FIEDKNAVSPLDSAIQANLRETTT 614
                  + T   EP    E P+ D   + +GD   F+E+    +P              
Sbjct: 154 SAANGCFRTTSLDEPRGASEAPLADR-LAAVGDDMEFVEEWCDFTP-------------- 198

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                LT  ++ ++++RF  G+    T  E+G+   V++ +I +  ++ ++ L+
Sbjct: 199 -AWEGLTDEDKELIKLRFFEGL----TQREIGEAVGVSQMQISRRLSRVLQSLR 247


>gi|225574871|ref|ZP_03783481.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037945|gb|EEG48191.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
          Length = 230

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 59/255 (23%), Positives = 108/255 (42%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           + +  +++ E R+ +   ++G+ +A   K  ++E NLRLV  V KKY        DLI  
Sbjct: 25  TFQKPLTVEEERYYLKKFQEGDLKA---KDILIERNLRLVAHVVKKYQGLEEDLDDLISI 81

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   FD     + STYA         R I ++   +             +R  
Sbjct: 82  GTIGLIKAVSTFDSKKSNRLSTYA--------ARCIDNELLMM-------------LRAR 120

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIE 593
           ++ S  +                               SL  PIG +   +  +L D IE
Sbjct: 121 KKYSRDV-------------------------------SLYEPIGTDKEGNEINLLDIIE 149

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                   + +++ ++++    +   L+ +E  V+R+RFG+    ++T  E+ K+  ++R
Sbjct: 150 SPPEDVVENYSVKQDIQKAMHLLSTCLSHKEYEVIRLRFGLFGEKEYTQREIAKRLNISR 209

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE  A+ KL+
Sbjct: 210 SYVSRIEKNALLKLR 224


>gi|126697577|ref|YP_001086474.1| RNA polymerase sigma-B factor [Clostridium difficile 630]
 gi|254977353|ref|ZP_05273825.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-66c26]
 gi|255102910|ref|ZP_05331887.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-63q42]
 gi|255308730|ref|ZP_05352901.1| RNA polymerase sigma-B factor [Clostridium difficile ATCC 43255]
 gi|255316437|ref|ZP_05358020.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-76w55]
 gi|255519098|ref|ZP_05386774.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-97b34]
 gi|255652280|ref|ZP_05399182.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-37x79]
 gi|260681780|ref|YP_003213065.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260685377|ref|YP_003216510.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296452670|ref|ZP_06894361.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296880077|ref|ZP_06904046.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
 gi|306521994|ref|ZP_07408341.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-32g58]
 gi|115249014|emb|CAJ66825.1| RNA polymerase sigma-B factor (Sigma-37) [Clostridium difficile]
 gi|260207943|emb|CBA60060.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260211393|emb|CBE01463.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296258452|gb|EFH05356.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296428944|gb|EFH14822.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
          Length = 257

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/116 (26%), Positives = 65/116 (56%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L L   +AKKY N+G+ F D+ Q  ++ L+ A +++D   G++FS++A   +   
Sbjct: 34  LIERHLYLARLLAKKYINKGVDFEDIYQVASLALIYAIDRYDVEKGFEFSSFATPTIVGE 93

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           I +   D+  T+R+P  +++   K+     ++  + K+ P  ++IA  + +  E V
Sbjct: 94  IKKYFRDKVWTLRVPRRIQELSKKISDAKIKLEQENKKHPKVKDIADYIGVSEEDV 149


>gi|172057862|ref|YP_001814322.1| RNA polymerase sigma factor SigD [Exiguobacterium sibiricum 255-15]
 gi|171990383|gb|ACB61305.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium
           sibiricum 255-15]
          Length = 257

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 52/204 (25%), Positives = 95/204 (46%), Gaps = 12/204 (5%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL  A +KFD     KF TYA + ++ AI   +        +P  +R+K  +V    
Sbjct: 56  GMMGLYDALQKFDQNHNNKFDTYAAFRIRGAILDGLRKIDW---LPRSLREKSKRVEAAV 112

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLE--TPIGDEDTSHLGDFI 592
             +   ++R PT +E++  + M  E V+  L        +S++    + DE  +    ++
Sbjct: 113 EILEQSLQRTPTIDEVSSIVDMSPEEVKTALAESYFANILSIDEAVTLQDEGKAMAVSYL 172

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +  +P D+ +   L       +  L+ +E+ V+ + +      + TL E+G+   ++
Sbjct: 173 -DPDTATPEDTLLMRELISKLAEEVEQLSEKEQYVVSLFYF----EELTLTEIGEVLGLS 227

Query: 653 RERIRQIEAKAIRKLKHPSRSKKL 676
             RI QI +KA+RKLK    S  L
Sbjct: 228 TSRISQIHSKALRKLKQALGSAYL 251


>gi|239623611|ref|ZP_04666642.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521642|gb|EEQ61508.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 197

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 32/133 (24%), Positives = 75/133 (56%), Gaps = 2/133 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE +LR V+++A +Y  R L   D++QE N  LM AA ++D     ++ +     
Sbjct: 38  ARNRLVEGSLRHVLNLAAEYEGRELPMSDIVQEANTALMLAAIEYDGS--EEWDSLLARR 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V++A+  ++ +Q     I   M  +++ +   ++ ++ ++ RE T +E+A K+ M  + +
Sbjct: 96  VREAVELALEEQKAEAEIEETMAARVNVLQTVSQMLARELGREATLQELAAKMKMTEDEI 155

Query: 564 RKVLKITKEPISL 576
           + ++K+  + +++
Sbjct: 156 KDIMKLALDALTV 168


>gi|217967265|ref|YP_002352771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
 gi|217336364|gb|ACK42157.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
          Length = 235

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 102/217 (47%), Gaps = 28/217 (12%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A K+T+ G    DLIQ G +G +KA E +D   G + STY   +V   I   + D+   I
Sbjct: 36  ASKFTSYGEPLEDLIQIGYLGFLKAIENYDPKKG-ELSTYISHYVLGEIRHHLRDKIDKI 94

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS---- 575
           +IP  ++  I+K+    + +  K  R P+ EEIAK L + VE V ++ KI +  ++    
Sbjct: 95  KIPRSVKILINKMDNFIKEVWEKENRSPSCEEIAKHLNITVESVDELFKIKEAMMTVSIE 154

Query: 576 -LETPIGDEDTSHLGDF---IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            LE  +    T  L  F   IE+K A   L+ AI + L E   +++  +           
Sbjct: 155 DLEIEVDRIRTERLESFKLPIEEKIA---LEQAI-SKLPEIQKKIIEYI----------- 199

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  D T  EV K   +++ ++ ++   A+ KL+
Sbjct: 200 ----FYQDLTQTEVAKILKISQTQVSRLLKSALEKLR 232


>gi|311029937|ref|ZP_07708027.1| sporulation sigma factor SigE [Bacillus sp. m3-13]
          Length = 239

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 107/226 (47%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK++ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKVRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +  +   D  ++AN+ R+   + L  L  
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTEEDIITKD--LEANVDRKLLLKALEQLND 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLIGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|255094683|ref|ZP_05324161.1| RNA polymerase sigma-B factor [Clostridium difficile CIP 107932]
          Length = 252

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/116 (26%), Positives = 65/116 (56%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E +L L   +AKKY N+G+ F D+ Q  ++ L+ A +++D   G++FS++A   +   
Sbjct: 34  LIERHLYLARLLAKKYINKGVDFEDIYQVASLALIYAIDRYDVEKGFEFSSFATPTIVGE 93

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           I +   D+  T+R+P  +++   K+     ++  + K+ P  ++IA  + +  E V
Sbjct: 94  IKKYFRDKVWTLRVPRRIQELSKKISDAKIKLEQENKKHPKVKDIADYIGVSEEDV 149


>gi|220929439|ref|YP_002506348.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
 gi|219999767|gb|ACL76368.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
          Length = 254

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 108/235 (45%), Gaps = 11/235 (4%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           E + + AK++++     L+  VA +   Y    ++F DL+  G  GL+ A EK+D   G 
Sbjct: 15  ETKDAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEKYDLAKGV 74

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KF TYA   ++ +I  SI D      +P  +R K  ++ +    + N+     T +E+A+
Sbjct: 75  KFETYASLRIRGSIIDSIRDMDW---VPRSLRQKNKELEKVYVEIENEKGHTATDKEVAE 131

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETT 613
           K+ + +    K+L        +      E     G  I  ++     +++++ N +++  
Sbjct: 132 KMGLSMSDFYKLLNDVNVSSMMSLDEFMEQNYERGLEIFSESTEDKPEASLEFNEMKQLL 191

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  +E+ V+   +      + TL+E+     VT  RI Q+  KA+ ++K
Sbjct: 192 ADCIDKLPEKEKAVITFYYF----EELTLKEISAIMNVTESRISQLHTKALLRMK 242


>gi|153814605|ref|ZP_01967273.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|317501234|ref|ZP_07959439.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|145848099|gb|EDK25017.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|316897410|gb|EFV19476.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 246

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 46/84 (54%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R G   A  AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     
Sbjct: 54  RLGTEYAEDAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKI 113

Query: 495 KFSTYAMWWVKQAITRSIADQSCT 518
           K +TYA   ++  I   +   S T
Sbjct: 114 KLATYASRCIENEILMYLRRNSKT 137


>gi|168186818|ref|ZP_02621453.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
 gi|169295229|gb|EDS77362.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score = 58.2 bits (139), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 99/226 (43%), Gaps = 49/226 (21%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++AK  ++E NLRLV  + KKY+       DLI  G +GL+KA + FD   G + +TYA 
Sbjct: 48  ALAKGILIERNLRLVAHIVKKYSYPNKDIDDLISIGTVGLIKAIDSFDVDKGTRLATYAA 107

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   I                         R S KIK E   ++       P+ 
Sbjct: 108 RCIENEILMLI-------------------------RNSKKIKSEVYLQD-------PI- 134

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           GV K        ISL   +  ++ S + + +E++  V  L   I+             LT
Sbjct: 135 GVDK----EGNEISLMDVLSSDEDSVI-EVVENRMEVRKLYDKIE-----------KCLT 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE+ +++MR+G+      T  E+     ++R  + +IE +A++K+
Sbjct: 179 EREKIIIKMRYGLVDGKSKTQREIASFLNISRSYVSRIEKRALKKI 224


>gi|21104382|dbj|BAB93461.1| unnamed protein product [Roseateles depolymerans]
          Length = 47

 Score = 57.8 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/46 (58%), Positives = 34/46 (73%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           LV+S+AK Y  RGL   DLI+EGN+GLM A  KF+   G++FSTYA
Sbjct: 1   LVVSIAKNYLGRGLPMSDLIEEGNLGLMHAIGKFEPERGFRFSTYA 46


>gi|15927639|ref|NP_375172.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus N315]
 gi|148268516|ref|YP_001247459.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394579|ref|YP_001317254.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JH1]
 gi|253315694|ref|ZP_04838907.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|257794514|ref|ZP_05643493.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9781]
 gi|258411256|ref|ZP_05681534.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9763]
 gi|258419772|ref|ZP_05682738.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9719]
 gi|258438079|ref|ZP_05689458.1| sigma factor B [Staphylococcus aureus A9299]
 gi|258441327|ref|ZP_05690812.1| sigma factor B [Staphylococcus aureus A8115]
 gi|258446979|ref|ZP_05695131.1| sigma factor B [Staphylococcus aureus A6300]
 gi|258449788|ref|ZP_05697888.1| sigma factor B [Staphylococcus aureus A6224]
 gi|258453474|ref|ZP_05701453.1| sigma factor B [Staphylococcus aureus A5937]
 gi|269203699|ref|YP_003282968.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282895212|ref|ZP_06303428.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8117]
 gi|295407610|ref|ZP_06817401.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8819]
 gi|296275695|ref|ZP_06858202.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297246607|ref|ZP_06930438.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8796]
 gi|13701859|dbj|BAB43151.1| sigma factor B [Staphylococcus aureus subsp. aureus N315]
 gi|147741585|gb|ABQ49883.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149947031|gb|ABR52967.1| RNA polymerase sigma-B type [Staphylococcus aureus subsp. aureus
           JH1]
 gi|257788486|gb|EEV26826.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9781]
 gi|257840011|gb|EEV64477.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9763]
 gi|257844254|gb|EEV68637.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9719]
 gi|257848496|gb|EEV72486.1| sigma factor B [Staphylococcus aureus A9299]
 gi|257852371|gb|EEV76296.1| sigma factor B [Staphylococcus aureus A8115]
 gi|257854212|gb|EEV77163.1| sigma factor B [Staphylococcus aureus A6300]
 gi|257856962|gb|EEV79863.1| sigma factor B [Staphylococcus aureus A6224]
 gi|257864346|gb|EEV87095.1| sigma factor B [Staphylococcus aureus A5937]
 gi|262075989|gb|ACY11962.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282762402|gb|EFC02546.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8117]
 gi|285817729|gb|ADC38216.1| RNA polymerase sigma factor SigB [Staphylococcus aureus 04-02981]
 gi|294967508|gb|EFG43546.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8819]
 gi|297176507|gb|EFH35773.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8796]
 gi|312830416|emb|CBX35258.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315128403|gb|EFT84412.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|329727790|gb|EGG64242.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21172]
          Length = 256

 Score = 57.8 bits (138), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIANRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|295696453|ref|YP_003589691.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412055|gb|ADG06547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score = 57.8 bits (138), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 57/241 (23%), Positives = 106/241 (43%), Gaps = 61/241 (25%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +VR  E + S+ +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 51  LVRLIEGDESV-RSTLIERNLRLVVYIARKFENTGIYIEDLVSIGTIGLIKAVNTFDPQK 109

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++                 +    R +NK++ E + +  
Sbjct: 110 RIKLATYA--------SRCIENE-----------------ILMFLRRNNKVRAEVSFD-- 142

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                              EP++++    D +   L D +  +N        I  N+ E 
Sbjct: 143 -------------------EPLNVDW---DGNELLLSDVLGTEN------DTIYRNIEEQ 174

Query: 613 TTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +      L  LT RE +++ +RFG+    + T ++V     +++  I ++E + I++L
Sbjct: 175 IDKHLLYDALGKLTERERKIMELRFGLAGGQEMTQKDVADLLGISQSYISRLEKRIIKRL 234

Query: 668 K 668
           +
Sbjct: 235 R 235


>gi|317132580|ref|YP_004091894.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
 gi|315470559|gb|ADU27163.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
          Length = 242

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 48/87 (55%), Gaps = 5/87 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N G+   DL+  G IGL+KA   F    G K +TYA   
Sbjct: 61  AKNRLIEHNLRLVVYIAKKFENTGVGVEDLVSIGTIGLIKAVNTFCPSRGIKLATYASRC 120

Query: 504 VKQAI---TRSIADQSCTIRI--PVHM 525
           ++  I    R   +Q   + I  P+H+
Sbjct: 121 IENEILMFLRKTQNQKNEVSIDEPLHV 147


>gi|307152337|ref|YP_003887721.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306982565|gb|ADN14446.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 257

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 34/115 (29%), Positives = 65/115 (56%), Gaps = 1/115 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE N  LV  VA + + +  + + DL Q G +GL++A E+F+   G  FS++A+ +
Sbjct: 28  RNQLVELNAGLVRQVAHRISRQCCEPYEDLEQVGYLGLIRAIERFNPQQGCAFSSFAIPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           V+  I   + D+   +RIP   +D   K  +  ++++  + R+P   EIA+ L +
Sbjct: 88  VRGEILHYLRDRGSVMRIPRRWQDLYTKGKKLRKQLAQTLGRQPKESEIAQALGV 142


>gi|325288800|ref|YP_004264981.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964201|gb|ADY54980.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 254

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 100/217 (46%), Gaps = 27/217 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GL+ A +K++   G KF TYA   ++ A+   +        +P   R K+ K
Sbjct: 49  DLIGYGVFGLIDALQKYEPSRGVKFETYASLRIRGAMIDGLRSMDW---VPHSARQKVKK 105

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +    + N   R P+ EE+A  L + +E +   L +  + ++L   +      H GD 
Sbjct: 106 VRQAYIDLENLQGRTPSIEEVAGFLEIQLEELHTTL-LHGQYMTL-VSMDQLLDGHSGD- 162

Query: 592 IEDKNAVSPLDSAIQANLRET------------TTRVLASLTPREERVLRMRFGIGMNTD 639
               + +SP+D  I A  +E+              R +  L+ +E+ V+ M +      +
Sbjct: 163 ----SGISPVDLIIDAEAQESFNNIEKEEQKQILAREIEKLSEKEKLVIAMYY----REE 214

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
            TL+E+     ++  RI QI ++AI +L+ +  R KK
Sbjct: 215 MTLKEIAAVMNLSESRISQIHSQAILRLRGYLGRQKK 251


>gi|293375494|ref|ZP_06621773.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325844950|ref|ZP_08168315.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
 gi|292645894|gb|EFF63925.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325489000|gb|EGC91389.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
          Length = 236

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 108/226 (47%), Gaps = 13/226 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I  ++ K +     A+  +V  ++ LV SV  K+ +  ++  DL Q G +GL+K+  +
Sbjct: 4   KQIHELIAKAQSGDEEARLTLVTNHMDLVWSVVHKFGHIEVEKDDLFQIGCMGLLKSINQ 63

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD       STYA+  +   I   I +QS  I+I   ++  IHK+      ++  ++REP
Sbjct: 64  FDSSYDTTLSTYAIPLIIGEIKAFIREQS-PIKISRSIKSNIHKIQEVKDHLNKVLEREP 122

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T +EIA++  +  E +   L       SL+    + +   L + I +      L+  I  
Sbjct: 123 TIKEIAQETELSEEQIILALNAPINVTSLDN--YEREDMPLIERIPNHQEGMGLEQKI-- 178

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                  +++++L P E+ ++ +RF +G    +T  EV K+  + +
Sbjct: 179 ----VLKQLVSNLDPIEKLLIYLRFDLG----YTQSEVAKRLEINQ 216


>gi|57650736|ref|YP_186870.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus COL]
 gi|87160164|ref|YP_494668.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195964|ref|YP_500776.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|151222182|ref|YP_001333004.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|161510276|ref|YP_001575935.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221141586|ref|ZP_03566079.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|258453225|ref|ZP_05701216.1| RNA polymerase sigma-B factor [Staphylococcus aureus A5948]
 gi|262049235|ref|ZP_06022110.1| sigma factor B [Staphylococcus aureus D30]
 gi|262052481|ref|ZP_06024679.1| sigma factor B [Staphylococcus aureus 930918-3]
 gi|282923053|ref|ZP_06330738.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9765]
 gi|284025100|ref|ZP_06379498.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus 132]
 gi|294850549|ref|ZP_06791276.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9754]
 gi|304379245|ref|ZP_07361984.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|1729797|emb|CAA71068.1| sigma-B [Staphylococcus aureus subsp. aureus COL]
 gi|1934991|emb|CAA68932.1| sigma factor B [Staphylococcus aureus]
 gi|37781588|gb|AAP42796.1| SigB [Staphylococcus aureus]
 gi|57284922|gb|AAW37016.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           COL]
 gi|87126138|gb|ABD20652.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87203522|gb|ABD31332.1| sigma factor B, putative [Staphylococcus aureus subsp. aureus NCTC
           8325]
 gi|150374982|dbj|BAF68242.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160369085|gb|ABX30056.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|257859171|gb|EEV82028.1| RNA polymerase sigma-B factor [Staphylococcus aureus A5948]
 gi|259159602|gb|EEW44648.1| sigma factor B [Staphylococcus aureus 930918-3]
 gi|259162600|gb|EEW47167.1| sigma factor B [Staphylococcus aureus D30]
 gi|269941665|emb|CBI50072.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282593244|gb|EFB98241.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9765]
 gi|294822569|gb|EFG39011.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9754]
 gi|302751946|gb|ADL66123.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304342104|gb|EFM08004.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|315197004|gb|EFU27346.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140765|gb|EFW32617.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320143740|gb|EFW35517.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329314750|gb|AEB89163.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           T0131]
 gi|329724065|gb|EGG60589.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21189]
          Length = 256

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|332095502|gb|EGJ00518.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 155-74]
          Length = 186

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 46/186 (24%), Positives = 85/186 (45%), Gaps = 19/186 (10%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + + E +   +RL+ SV         +  DL+Q G IGL+ A E++D   G  F+TYA+ 
Sbjct: 13  LVRHEALRLQVRLLASV---------ELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQ 63

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + +  
Sbjct: 64  RIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIAD 120

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRVLA 618
            R++L+ T           DE     GD IE    D    +PL   + +NL +     + 
Sbjct: 121 YRQMLRDTNNSQLFSY---DEWREEHGDSIELVTDDHQRENPLQQLLDSNLCQRVMEAIE 177

Query: 619 SLTPRE 624
           +L  RE
Sbjct: 178 TLPERE 183


>gi|282856209|ref|ZP_06265492.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
 gi|282585968|gb|EFB91253.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
          Length = 196

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 49/80 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++ A   LV  VAKK+   G +F DL+QEG + L++A +KFD  LG++F+TYA + 
Sbjct: 26  AREQLILAYRPLVYWVAKKFRVNGQRFSDLVQEGTLALIRAVDKFDVSLGHRFTTYACYR 85

Query: 504 VKQAITRSIADQSCTIRIPV 523
           ++  +   +        IPV
Sbjct: 86  IRGQMLNFLQRVEGKAPIPV 105


>gi|146295966|ref|YP_001179737.1| sporulation sigma factor SigE [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409542|gb|ABP66546.1| RNA polymerase, sigma 29 subunit, SigE [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 246

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 103/226 (45%), Gaps = 54/226 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK +VE NLRLV+ +A+K+ N  +   DL+  G IGL+KA   ++     K +TYA    
Sbjct: 66  KKVLVERNLRLVVYIARKFENTKINLEDLVSIGTIGLIKAINTYNPDKNIKLATYA---- 121

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
               ++ I ++     I + +R   H                       +KL + ++   
Sbjct: 122 ----SKCIENE-----ILMFLRRNSH-----------------------RKLELSID--- 146

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                  EP++++    D +   L D +  + +   S ++S+++   +E   + +  L  
Sbjct: 147 -------EPLNVD---WDGNELLLSDVLGTDSEGVYSSIESSVE---KEALLKAIQKLPK 193

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+R++ +RFG     + T +EV     +++  I ++E K I +LK
Sbjct: 194 REKRIVELRFGFSDEGEKTQKEVADMLGISQSYISRLEKKIITRLK 239


>gi|73532520|dbj|BAE19818.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda]
          Length = 168

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 42/160 (26%), Positives = 75/160 (46%), Gaps = 10/160 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R     
Sbjct: 15  DLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDELRSRDW---VPRSVRRNARG 71

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V    +R   ++ R P   EIA+++ +P+E  +++L  T           DE     GD 
Sbjct: 72  VSAAMQRAEQRLGRTPGDSEIAQEMGIPLEEYQQILLDTNTSQLFSY---DEWREDHGDS 128

Query: 591 ---FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
               +E     +PL   ++++LR      + +L  RE+ V
Sbjct: 129 AEPVLEQSEEANPLRQLLESDLRGRVIAAIEALPEREKLV 168


>gi|253731099|ref|ZP_04865264.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733102|ref|ZP_04867267.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|253725174|gb|EES93903.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728935|gb|EES97664.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus TCH130]
          Length = 256

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|229061510|ref|ZP_04198854.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
 gi|229134714|ref|ZP_04263523.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|229168645|ref|ZP_04296367.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228614801|gb|EEK71904.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228648760|gb|EEL04786.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|228717744|gb|EEL69394.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
          Length = 232

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 51  ARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 108 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 132

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 133 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 179 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 225


>gi|226939710|ref|YP_002794783.1| FliA1 [Laribacter hongkongensis HLHK9]
 gi|226714636|gb|ACO73774.1| FliA1 [Laribacter hongkongensis HLHK9]
          Length = 247

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 56/247 (22%), Positives = 116/247 (46%), Gaps = 17/247 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +S +R  +  A+      +  +L LV  +A    +R    ++  DL+Q G IGL++AA++
Sbjct: 1   MSKLRAYQSAATTNSSVDITEHLTLVRKLASMMISRLPASVELDDLVQVGMIGLIEAAQQ 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVHMRDKIHKVVRTARRMSNKIKRE 546
           FD   G  F T+A     Q I  ++ D+   +  +P   R    ++     ++   +   
Sbjct: 61  FDPAQGVLFETFA----SQRIRGAMLDELRRLDWLPRQARRNAKQIEEAMAQLEQSLGHP 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED---TSHLGDFIEDKNAVSPL 601
           P   EIA +L + V+  + +L   K  + +  E    D+D   ++ + + + D+  V+P 
Sbjct: 117 PGEGEIAARLGLSVDEYQTMLFECKGHQLVYFEDFGHDDDEGSSTRMVEQVADQGMVNPF 176

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +   ++  R      +  L  R++ V+ + +   +N    L+E+G    VT  R+ Q+ +
Sbjct: 177 EILGESRFRSHLVAAIKELPERDQLVMSLYYEQELN----LKEIGAVLNVTESRVCQLHS 232

Query: 662 KAIRKLK 668
           +A+ +L+
Sbjct: 233 QAVARLR 239


>gi|153812463|ref|ZP_01965131.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
 gi|149831388|gb|EDM86476.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
          Length = 243

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 99/228 (43%), Gaps = 54/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 60  ARSLLIEHNLRLVVYIARKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNIKLATYASRC 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +   S T                   RM   I  EP        L +  +G 
Sbjct: 120 IENEILMYLRRNSKT-------------------RMEVSID-EP--------LNVDWDGN 151

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             +L          + I   D   +   +ED+  ++ L  AI              L+PR
Sbjct: 152 ELLL----------SDILGTDDDVISRKLEDEVEITLLGKAIN------------KLSPR 189

Query: 624 EERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++R+RFG+  N D    T +EV     +++  I ++E + +++LK
Sbjct: 190 EQTIIRLRFGLN-NADGKEKTQKEVADLLGISQSYISRLEKRIMKRLK 236


>gi|301055830|ref|YP_003794041.1| RNA polymerase sigma-28 factor [Bacillus anthracis CI]
 gi|300377999|gb|ADK06903.1| RNA polymerase sigma-28 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 181

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 88/212 (41%), Gaps = 54/212 (25%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            KK+ N G    DLI  G IGL+KA E +    G K +TYA         R I ++    
Sbjct: 9   VKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYA--------ARCIENE---- 56

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
            I +H+R                                       VLK TK+ +SL  P
Sbjct: 57  -ILMHLR---------------------------------------VLKKTKKDVSLHDP 76

Query: 580 IGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMN 637
           IG +   +    I+  K+    +   IQ ++  E     +  L  RE+ V+  RFG+G++
Sbjct: 77  IGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLD 136

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 137 KEKTQREIAKALGISRSYVSRIEKRALMKMFH 168


>gi|295678067|ref|YP_003606591.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1002]
 gi|295437910|gb|ADG17080.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1002]
          Length = 244

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  E+A+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VETAVHKVEQNLGRSASEAEVAEHLQMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  GMN    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDDSLRSALIEAIDRLPEREKLLMSLYYERGMN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|21283717|ref|NP_646805.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49486858|ref|YP_044079.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|297210116|ref|ZP_06926509.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC 51811]
 gi|300910479|ref|ZP_07127931.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|21205159|dbj|BAB95853.1| sigma factor B [Staphylococcus aureus subsp. aureus MW2]
 gi|49245301|emb|CAG43776.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|296885316|gb|EFH24256.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC 51811]
 gi|300888321|gb|EFK83512.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH70]
          Length = 256

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|169827282|ref|YP_001697440.1| RNA polymerase sigma-F factor [Lysinibacillus sphaericus C3-41]
 gi|168991770|gb|ACA39310.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Lysinibacillus sphaericus
           C3-41]
          Length = 195

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 94/200 (47%), Gaps = 36/200 (18%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK+ +KFD     KFSTYA+  +   I R + D            D + KV R+ R ++ 
Sbjct: 1   MKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD------------DGMVKVSRSIRELNF 48

Query: 542 KIK-----------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           KI+             PT +E+A+ L +  E +       ++P SL   + +   D+  L
Sbjct: 49  KIRHATDEFIKRNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITL 108

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D ++D+ +  P D      L+E  TR    L PRE+ ++ +R+     +D T  E+  +
Sbjct: 109 MDQMKDEKSEQPFDY---IPLKEVLTR----LEPREQSIIYLRYF----SDCTQTEIANR 157

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ ++ ++E K + +LK
Sbjct: 158 LGISQVQVSRLEKKILAQLK 177


>gi|49484290|ref|YP_041514.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|82751667|ref|YP_417408.1| RNA polymerase sigma factor SigB [Staphylococcus aureus RF122]
 gi|257426202|ref|ZP_05602617.1| SigB protein [Staphylococcus aureus subsp. aureus 55/2053]
 gi|257428861|ref|ZP_05605255.1| SigB protein [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257431471|ref|ZP_05607844.1| SigB protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257434181|ref|ZP_05610531.1| SigB protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257437094|ref|ZP_05613134.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M876]
 gi|258422934|ref|ZP_05685834.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9635]
 gi|282904730|ref|ZP_06312604.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C160]
 gi|282906409|ref|ZP_06314260.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282909377|ref|ZP_06317192.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911631|ref|ZP_06319430.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914909|ref|ZP_06322689.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M899]
 gi|282917412|ref|ZP_06325165.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           D139]
 gi|282920240|ref|ZP_06327964.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C427]
 gi|282925452|ref|ZP_06333106.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C101]
 gi|283771232|ref|ZP_06344121.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           H19]
 gi|283958843|ref|ZP_06376288.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|293508983|ref|ZP_06667770.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510895|ref|ZP_06669594.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M809]
 gi|293547495|ref|ZP_06672170.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M1015]
 gi|295428651|ref|ZP_06821277.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589872|ref|ZP_06948512.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MN8]
 gi|49242419|emb|CAG41133.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|61889366|emb|CAI72514.1| SigB protein [Staphylococcus aureus]
 gi|82657198|emb|CAI81638.1| RNA polymerase sigma factor B [Staphylococcus aureus RF122]
 gi|257270907|gb|EEV03080.1| SigB protein [Staphylococcus aureus subsp. aureus 55/2053]
 gi|257274203|gb|EEV05720.1| SigB protein [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257277712|gb|EEV08382.1| SigB protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257280820|gb|EEV10965.1| SigB protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257283487|gb|EEV13614.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M876]
 gi|257846958|gb|EEV70972.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9635]
 gi|282312853|gb|EFB43254.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C101]
 gi|282316100|gb|EFB46481.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C427]
 gi|282318614|gb|EFB48971.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           D139]
 gi|282321112|gb|EFB51443.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M899]
 gi|282324396|gb|EFB54709.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326647|gb|EFB56945.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282330359|gb|EFB59877.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282594763|gb|EFB99740.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C160]
 gi|283459437|gb|EFC06530.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           H19]
 gi|283471280|emb|CAQ50491.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ST398]
 gi|283789561|gb|EFC28384.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|290919615|gb|EFD96688.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291094687|gb|EFE24959.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466180|gb|EFF08707.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127321|gb|EFG56961.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297577000|gb|EFH95714.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MN8]
 gi|298695339|gb|ADI98561.1| RNA polymerase sigma factor B [Staphylococcus aureus subsp. aureus
           ED133]
 gi|302333711|gb|ADL23904.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|312437522|gb|ADQ76593.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|315193223|gb|EFU23621.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|323439220|gb|EGA96947.1| RNA polymerase sigma factor SigB [Staphylococcus aureus O11]
 gi|323442402|gb|EGB00031.1| RNA polymerase sigma factor SigB [Staphylococcus aureus O46]
 gi|329729290|gb|EGG65698.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21193]
          Length = 256

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|318040135|ref|ZP_07972091.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 57.8 bits (138), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 57/117 (48%), Gaps = 4/117 (3%)

Query: 444 AKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A++++V  NL LV     ++            D +QE  + L++AAEKFD   GY+FSTY
Sbjct: 61  AREQLVRHNLGLVAHTWGRHRCSLPAHDDTTADALQEAALNLVRAAEKFDPAKGYRFSTY 120

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           A +WV++  T         IR P      + K +R +++       EP  E +A +L
Sbjct: 121 ATFWVRRGFTEFEQRAKRAIRFPAEKAAVVLKALRLSQQHQATTGDEPALEWLAAQL 177


>gi|293376227|ref|ZP_06622470.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325845158|ref|ZP_08168467.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
 gi|292645119|gb|EFF63186.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325488823|gb|EGC91223.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
          Length = 236

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 99/225 (44%), Gaps = 50/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++E NLRLV+ +AKK+ + G+   DLI  G +GL+K  + F      K +TYA   
Sbjct: 55  ARQTLIEHNLRLVVYIAKKFESSGVNLEDLISIGTLGLIKGVQTFKMDKNIKLATYA--- 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +N+I+ E + +E    L +  +G 
Sbjct: 112 -----SRCIENE-----ILMHLRK------------TNRIRNEVSLDE---PLNVDWDG- 145

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G E+     D  ED               R+     +  L  R
Sbjct: 146 --------NELLLSDILGTEENEVYKDIEEDVE-------------RQLVFDAINRLKRR 184

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  ++ MRFG+      T +EV ++  +++  I ++E K I K++
Sbjct: 185 EREIMYMRFGLCGEDPLTQKEVAQKLDISQSYISRLEKKIIDKIR 229


>gi|167571638|ref|ZP_02364512.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           C6786]
          Length = 244

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/202 (23%), Positives = 91/202 (45%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R     E+A  L MP+   + +L    + +     +  ED     D 
Sbjct: 98  VEHAVHQVEQRLGRSANETEVAAHLQMPLGEYQSML----QDLHGSQLVYYEDFDRSADD 153

Query: 591 --FIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++   A    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRADHADPLSALLDDHLRSALVDAIEHLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|229157483|ref|ZP_04285560.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
 gi|228625933|gb|EEK82683.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
          Length = 223

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 42  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+            R +NK + E + +             
Sbjct: 99  -----SRCIENE-----ILMHL------------RRNNKNRSEVSFD------------- 123

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 124 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 169

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 170 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 216


>gi|149183912|ref|ZP_01862300.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
 gi|148848376|gb|EDL62638.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
          Length = 239

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NKI+ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKIRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  E+      L++ +    R+     L  L+
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTEEDIITKDLEATVD---RKLLFNALTELS 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++LK
Sbjct: 186 DREKQIMELRFGLMGGEEKTQKDVADMLGISQSYISRLEKRIIKRLK 232


>gi|15615119|ref|NP_243422.1| sporulation sigma factor SigE [Bacillus halodurans C-125]
 gi|10175176|dbj|BAB06275.1| RNA polymerase sporulation mother cell-specific (early) sigma-29
           factor [Bacillus halodurans C-125]
          Length = 237

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 105/222 (47%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 60  LIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA------- 112

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NKI+ E + +                 
Sbjct: 113 -SRCIENE-----ILMYLRR------------NNKIRSEVSFD----------------- 137

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPREER 626
               EP++++    D +   L D +   + +  +   I+  + R+   + L +LT RE++
Sbjct: 138 ----EPLNID---WDGNELLLSDVLGTDDDI--ITRGIEEKVDRKLLMKALHTLTDREKQ 188

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 189 IMELRFGLAGGEEKTQKDVADLLGISQSYISRLEKRIIKRLQ 230


>gi|188585936|ref|YP_001917481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350623|gb|ACB84893.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 239

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 95/222 (42%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD     K +TYA       
Sbjct: 62  LIERNLRLVVYIARKFENTGVNIEDLISIGTIGLIKAVNTFDPQKKIKLATYA------- 114

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
                    C           I   +    R +NK+K E + +E    L +  +G     
Sbjct: 115 -------SKC-----------IENEILMYLRRNNKLKNEVSIDE---PLNIDWDG----- 148

Query: 568 KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G D D  H             ++  +  NL +     L  L+ RE+ 
Sbjct: 149 ----NELLLSDVLGTDIDIIH-----------QNIEQKVNKNLLKMA---LEKLSQREKT 190

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++RFG+G     T +EV     +++  I ++E + I +++
Sbjct: 191 IMKLRFGLGRQEGKTQKEVADILGISQSYISRLEKRIINRMR 232


>gi|108762696|ref|YP_629049.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
 gi|108466576|gb|ABF91761.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
          Length = 273

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 111/234 (47%), Gaps = 26/234 (11%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V  +L+LV  +A KY   GL   +L+ EGN+GLM+AA +F+   G  F+ YA  W++  I
Sbjct: 35  VREHLKLVRRLAWKYRWTGLSMEELVAEGNVGLMEAAGRFE-ERGVPFAAYASQWIRARI 93

Query: 509 TRSIADQSCTI---RIPVHMRDKIHKVVRTARRMSNKIKR---EPTPE---EIAKKLAMP 559
            R+   ++ ++   R P         VV   RR  ++++    E  PE    +A+ L   
Sbjct: 94  -RAYVGRNWSMAGGRAPW--------VVFQLRRERSRLEARWGEGHPEVEKRLAEALGKR 144

Query: 560 VEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVS-PLDSAIQA-NLRETTTRV 616
            + V   ++     +SL+ P+  D + + L   + D ++    +D A  A  LR +    
Sbjct: 145 EDEVALAMEALSRDVSLDAPVSPDSEATRLEGLMADADSQEDQVDRAKWARRLRASVDAA 204

Query: 617 LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              L  RE  ++  R    +  D  + E + ++F VT  RIRQIE     KL+H
Sbjct: 205 WPELDARERALVEERM---LAEDGVSAELLARRFGVTAVRIRQIEQGLRVKLRH 255


>gi|270157125|ref|ZP_06185782.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|289164470|ref|YP_003454608.1| sigma factor 28 [Legionella longbeachae NSW150]
 gi|269989150|gb|EEZ95404.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|288857643|emb|CBJ11483.1| sigma factor 28 [Legionella longbeachae NSW150]
          Length = 238

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 107/230 (46%), Gaps = 17/230 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +V+ +  LV  +A     R   G+Q  DLIQ G +GL++AA  +D   G  F TYA 
Sbjct: 15  QETLVKNHALLVKRIAHHLLGRLPQGIQLDDLIQAGMLGLLEAARHYDSSKGASFETYAG 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  +   +       R  VH   ++  +    + + +++ RE    EIA +L + + 
Sbjct: 75  IRIRGYMLDEVRRNDWVPR-SVHRNSRL--ISEAVKYVEHRLGREAKDSEIAAELGVSLA 131

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLA 618
              ++L   ++ +S     G +D     D ++  N   +  P  +   ++L    + V+ 
Sbjct: 132 EYHEML---QDSVSSHL-YGFDDLGVTDDALQTDNQSASTEPHVNVFHSDLMRRLSEVIR 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  +E  VL + +   +N    L+E+G+   V+  R+ QI ++A  ++K
Sbjct: 188 GLPHKERMVLSLYYEHDLN----LKEIGEVIGVSESRVSQILSQATHRIK 233


>gi|118418349|gb|ABK86768.1| RNA polymerase, sigma 29 subunit, SigE [Bacillus thuringiensis str.
           Al Hakam]
          Length = 248

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 67  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 123

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 124 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 149 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 194

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 195 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 241


>gi|163941644|ref|YP_001646528.1| sporulation sigma factor SigE [Bacillus weihenstephanensis KBAB4]
 gi|229013089|ref|ZP_04170254.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|163863841|gb|ABY44900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228748343|gb|EEL98203.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|322510149|gb|ADX05463.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|169827019|ref|YP_001697177.1| RNA polymerase sigma-35 factor [Lysinibacillus sphaericus C3-41]
 gi|168991507|gb|ACA39047.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 204

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 98/228 (42%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+++ N G    DLI  G+IGL+KA E F+     K +TYA   
Sbjct: 22  ARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLIKAIETFNTDKNIKLATYA--- 78

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R       +T+R                          
Sbjct: 79  -----SRCIENE-----ILMHLR-------KTSR-------------------------- 95

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                  K  +SL+ P+    D +   L D +  +  +  LD+  +   R+     +  L
Sbjct: 96  ------MKGEVSLDEPLNSDADGNELLLSDILGTEEHI-ILDNVEKKIERQHMFHAINLL 148

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++  RFG+    + T +EV     +++  I ++E K I+ L+
Sbjct: 149 GARERYIMECRFGLNGKVEMTQKEVADHLGISQSYISRLEKKIIQDLR 196


>gi|284027885|gb|ADB66757.1| RNA polymerase sigma-70 factor [Aeromonas sp. CECT 5178]
          Length = 295

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 74/154 (48%), Gaps = 6/154 (3%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQ 361
           NG+  E++         +L  +     L   + D LV  + ++ +R+   E  +L++  +
Sbjct: 147 NGRAHEETQAAIA----QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVE 202

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +A   D +L+   +++ I  ETG
Sbjct: 203 QAKMPKKTFVSAFTNNECETAWFEYQKQAGKA-WSAPLAAMEDEVLRSIGKLQQIEEETG 261

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +SI++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 262 LSIAQIKDINRRMSIGEAKARRAKKEMVEANLRL 295


>gi|150019798|ref|YP_001312052.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium beijerinckii
           NCIMB 8052]
 gi|149906263|gb|ABR37096.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium beijerinckii
           NCIMB 8052]
          Length = 250

 Score = 57.8 bits (138), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 108/245 (44%), Gaps = 52/245 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK--FSTY 499
           A + ++EAN  +V  +A K+   N+ ++F DL+Q G IGL+ AA K++  L  K  F TY
Sbjct: 17  ALESLIEANEGIVKKLANKFNGINKMIEFDDLVQAGIIGLINAANKYNNELENKASFITY 76

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A  ++K+ I   +                     R+ + +SN                  
Sbjct: 77  AFQYIKREIFSCVNG-------------------RSEKEISNN----------------- 100

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTT-RV 616
                   K+    +SL+ PI +++   L D IE  D    +  +      LRE     +
Sbjct: 101 --------KLYNSCVSLDVPIQEDNDIQLKDTIESIDYGFENVEEKIYIKQLREELEDAM 152

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK-K 675
           L + T +E  +L++ +G       T +EV +   ++   I QIE  A+RKL++ +  K K
Sbjct: 153 LDNNTLKEREILQLCYGWNYQKIFTYKEVAETLNISINSIPQIEFNALRKLRNSTWGKEK 212

Query: 676 LRSFL 680
           ++ ++
Sbjct: 213 VKEYM 217


>gi|158320420|ref|YP_001512927.1| sporulation sigma factor SigE [Alkaliphilus oremlandii OhILAs]
 gi|158140619|gb|ABW18931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 244

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 108/241 (44%), Gaps = 60/241 (24%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K + + S  +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 52  LISKLKSDESTVRTILIERNLRLVVYIARKFENTGIGIEDLISIGTIGLIKAVNTFNPEK 111

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++     I +++R             ++K+K E + +  
Sbjct: 112 NIKLATYA--------SRCIENE-----ILMYLRR------------NSKVKMEVSFD-- 144

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                              EP++++    D +   L D +  +N V      I   L E 
Sbjct: 145 -------------------EPLNID---WDGNELLLSDILGTENDV------IHKFLEEE 176

Query: 613 TTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R      L  L+ RE++++ +RFG+    + T +EV     +++  I ++E + I +L
Sbjct: 177 VDRDLLKIALEKLSKREKKIMELRFGLNTGQEKTQKEVADILGISQSYISRLEKRIITRL 236

Query: 668 K 668
           +
Sbjct: 237 Q 237


>gi|307824496|ref|ZP_07654721.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
 gi|307734480|gb|EFO05332.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
          Length = 237

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 92/204 (45%), Gaps = 14/204 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G +GL++A + +D   G  F TYA   ++ ++   +     T R  VH + 
Sbjct: 36  VQVDDLIQAGMLGLLEAIKNYDASQGASFDTYAGIRIRGSMLDEVRRSDWTPR-SVHKKS 94

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++  V    R + NK  RE    ++AK L + ++    +L+ +            E+ + 
Sbjct: 95  RM--VSDAIRTIENKTGREARDVDVAKYLGIAIDEYNHILQDSSSCRVFSV----EELAQ 148

Query: 588 LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            GD   D+       P+D   +   ++     +  L  RE  V+ + +    + +  L E
Sbjct: 149 DGDHYMDETLSHEEGPVDGLSREGFQQALANAIMGLPERERLVISLYY----DEEFNLRE 204

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+   ++  R+ QI  +A+ +L+
Sbjct: 205 IGEVLNISESRVSQICTQAVLRLR 228


>gi|220903606|ref|YP_002478918.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219867905|gb|ACL48240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 260

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/217 (24%), Positives = 98/217 (45%), Gaps = 11/217 (5%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
            +R +    K    R ++  +LI  G +GLM+A  KF   LG +F TYA   ++ A+   
Sbjct: 42  KIRFLALRLKAKLPRSVELGELISSGTLGLMEALGKFRPQLGIRFETYAESRIRGAMLDE 101

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +         P  +R ++  +    R++ ++  R+ T EE+     +P+  VR+ L+  +
Sbjct: 102 LRRLDW---FPRSLRQRVRTLDEAIRKVEHEHGRQATEEELQAITGLPLRDVRQGLEALQ 158

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             + L      +  S  GD  E      P        L E    ++  LTPRE+ VL + 
Sbjct: 159 NQLWLSLDAIQDTIS--GDAQEPGG--EPYRKTAFRELVERVAPLIDRLTPREKLVLSLY 214

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +N   T E +G    +T  R+ Q+ ++A+ +L+
Sbjct: 215 YTDELNMRETAEVMG----ITEGRVSQLHSQALSRLR 247


>gi|229019107|ref|ZP_04175942.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
 gi|229025351|ref|ZP_04181769.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228735936|gb|EEL86513.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228742207|gb|EEL92372.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
          Length = 232

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 51  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 107

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 108 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 132

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 133 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 179 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 225


>gi|167641125|ref|ZP_02399380.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
 gi|167510905|gb|EDR86296.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
          Length = 239

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|160896045|ref|YP_001561627.1| RNA polymerase sigma 28 subunit FliA/WhiG [Delftia acidovorans
           SPH-1]
 gi|160361629|gb|ABX33242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Delftia acidovorans
           SPH-1]
          Length = 237

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 91/205 (44%), Gaps = 11/205 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +F+   G +F T+A   ++ A+   + +     R     R     
Sbjct: 40  DLIQVGMIGLAEALSRFESEQGVQFETFASQRIRGAMLDELREGDWMSRSS---RKSQKD 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE-TPIGDEDTSHL 588
           +     R+  ++ R P   EIA +L M ++  + +L   +  + + LE    GDE    L
Sbjct: 97  IEHALHRLEQRLGRTPLESEIADELGMDLDDYQSLLGKVRGTQLVYLEDMSGGDEGEDFL 156

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              + D  A  P        LR      + +L  RE+ ++ M +   MN    L+E+   
Sbjct: 157 ERHVADSGA-DPFALLRDHRLRVALVEAIKALPEREQYIMGMYYEHDMN----LKEIAAV 211

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             VT  R+ Q+ ++AI +L+   R+
Sbjct: 212 LGVTESRVCQLHSQAIARLRTKMRA 236


>gi|75764483|ref|ZP_00743968.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488030|gb|EAO51761.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 224

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 43  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+            R +NK + E + +             
Sbjct: 100 -----SRCIENE-----ILMHL------------RRNNKNRSEVSFD------------- 124

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 125 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 170

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 171 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 217


>gi|299535876|ref|ZP_07049196.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728628|gb|EFI69183.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 206

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 98/228 (42%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+++ N G    DLI  G+IGL+KA E F+     K +TYA   
Sbjct: 24  ARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLIKAIETFNTDKNIKLATYA--- 80

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R       +T+R                          
Sbjct: 81  -----SRCIENE-----ILMHLR-------KTSR-------------------------- 97

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                  K  +SL+ P+    D +   L D +  +  +  LD+  +   R+     +  L
Sbjct: 98  ------MKGEVSLDEPLNSDADGNELLLSDILGTEEHII-LDNVEKKIERQHMFHAINLL 150

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++  RFG+    + T +EV     +++  I ++E K I+ L+
Sbjct: 151 GARERYIMECRFGLNGKVEMTQKEVADHLGISQSYISRLEKKIIQDLR 198


>gi|61889360|emb|CAI72509.1| SigB protein [Staphylococcus aureus]
          Length = 256

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSNREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|323099955|gb|ADX23555.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|218887101|ref|YP_002436422.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218758055|gb|ACL08954.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 265

 Score = 57.4 bits (137), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 50/208 (24%), Positives = 93/208 (44%), Gaps = 10/208 (4%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           R ++  +LI  G +GLM+A  KF   LG +F TYA   ++ A+   +         P  +
Sbjct: 60  RNVELNELISAGTLGLMEALGKFRPQLGIRFETYAESRIRGAMLDELRRLDW---FPRSL 116

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           R ++ ++    +R+ ++  R PT  E+     +  + VR  L+  +  + L     D   
Sbjct: 117 RQRVRQLDEAIQRIEHEKGRHPTEAELQDATGLDQKDVRLGLEALQNQLCLSL---DAIQ 173

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L      +    P  +     L E    ++  LTPRE+ VL + +   +N   T E +
Sbjct: 174 DSLAPDTGVQGEGEPFQTTATQELIERVAGLIDELTPREKLVLSLYYSDELNMRETAEVM 233

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           G    +T  R+ Q+ ++A+ +L+   R+
Sbjct: 234 G----ITEGRVSQLHSQALNRLRKEFRN 257


>gi|254387242|ref|ZP_05002505.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346050|gb|EDX27016.1| sigma factor [Streptomyces sp. Mg1]
          Length = 272

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 112/250 (44%), Gaps = 23/250 (9%)

Query: 433 MVRKGECEASIAKKEMVEANLRLV----ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++ +G  E   A+  ++E NL LV         +    G+   D++Q G IGL+KA +++
Sbjct: 25  VLEEGTREYQYARNTLIEMNLSLVQFAARRFRARAFGGGIDMDDIVQVGTIGLIKAIDRY 84

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FST A+ ++   I R   D +  + +P  +++   ++ +    +++ + R PT
Sbjct: 85  DPEREVEFSTLALPYITGEIKRHFRDTTWAVHVPRRLQELRTELAKAQESLTDVLGRAPT 144

Query: 549 PEEIAKK----LAMPVEGVRKVLKITKEPISLETPIGDED------TSHLGDFIEDKNAV 598
            +EIA+         +EG+      T   +      GD        T  L + I D +  
Sbjct: 145 VKEIAQHLELPEEEIIEGLVAANGYTSGSLDTAGSEGDNQSTSSRGTRPLAEKIGDNDPA 204

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             L          T   +L  L  R+  +LRMRFG     + T  E+G +  +++ ++ +
Sbjct: 205 MELFEEFH-----TLAPLLEKLDERDLLILRMRFG----EEKTQAEIGAELGISQMQVSR 255

Query: 659 IEAKAIRKLK 668
           I ++ + +L+
Sbjct: 256 ILSRTLTRLR 265


>gi|30021993|ref|NP_833624.1| sporulation sigma factor SigE [Bacillus cereus ATCC 14579]
 gi|30263906|ref|NP_846283.1| sporulation sigma factor SigE [Bacillus anthracis str. Ames]
 gi|42782997|ref|NP_980244.1| sporulation sigma factor SigE [Bacillus cereus ATCC 10987]
 gi|47529336|ref|YP_020685.1| sporulation sigma factor SigE [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49186754|ref|YP_030006.1| sporulation sigma factor SigE [Bacillus anthracis str. Sterne]
 gi|49478442|ref|YP_037966.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141583|ref|YP_085245.1| sporulation sigma factor SigE [Bacillus cereus E33L]
 gi|162382776|ref|YP_896275.2| sporulation sigma factor SigE [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872323|ref|ZP_02216960.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|167636583|ref|ZP_02394877.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170688850|ref|ZP_02880053.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|170708793|ref|ZP_02899229.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|177654897|ref|ZP_02936614.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190566146|ref|ZP_03019065.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035954|ref|ZP_03103356.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196038626|ref|ZP_03105934.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|196045866|ref|ZP_03113095.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|206971306|ref|ZP_03232257.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206976716|ref|ZP_03237620.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217961326|ref|YP_002339894.1| sporulation sigma factor SigE [Bacillus cereus AH187]
 gi|218234749|ref|YP_002368704.1| sporulation sigma factor SigE [Bacillus cereus B4264]
 gi|218899058|ref|YP_002447469.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|218905035|ref|YP_002452869.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|222097350|ref|YP_002531407.1| sporulation sigma factor sige [Bacillus cereus Q1]
 gi|225865886|ref|YP_002751264.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227813186|ref|YP_002813195.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228902410|ref|ZP_04066564.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|228909730|ref|ZP_04073553.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228916542|ref|ZP_04080108.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922657|ref|ZP_04085957.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228928953|ref|ZP_04091985.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935220|ref|ZP_04098046.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228940993|ref|ZP_04103551.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947624|ref|ZP_04109914.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954181|ref|ZP_04116209.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960122|ref|ZP_04121786.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966858|ref|ZP_04127902.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228973924|ref|ZP_04134499.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980513|ref|ZP_04140823.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228987049|ref|ZP_04147174.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229047589|ref|ZP_04193179.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|229071404|ref|ZP_04204626.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|229081157|ref|ZP_04213667.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|229092951|ref|ZP_04224084.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|229111374|ref|ZP_04240927.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|229123418|ref|ZP_04252622.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|229129182|ref|ZP_04258155.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|229140553|ref|ZP_04269108.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|229146476|ref|ZP_04274847.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|229152102|ref|ZP_04280297.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|229180180|ref|ZP_04307524.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|229186145|ref|ZP_04313314.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|229192074|ref|ZP_04319043.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|229198016|ref|ZP_04324730.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|229601447|ref|YP_002868140.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|254683386|ref|ZP_05147246.1| sporulation sigma factor SigE [Bacillus anthracis str. CNEVA-9066]
 gi|254721438|ref|ZP_05183227.1| sporulation sigma factor SigE [Bacillus anthracis str. A1055]
 gi|254735943|ref|ZP_05193649.1| sporulation sigma factor SigE [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739808|ref|ZP_05197501.1| sporulation sigma factor SigE [Bacillus anthracis str. Kruger B]
 gi|254750998|ref|ZP_05203037.1| sporulation sigma factor SigE [Bacillus anthracis str. Vollum]
 gi|254757944|ref|ZP_05209971.1| sporulation sigma factor SigE [Bacillus anthracis str. Australia
           94]
 gi|296504398|ref|YP_003666098.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|49065841|sp|P62177|RP35_BACAN RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065842|sp|P62178|RP35_BACCR RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065843|sp|P62179|RP35_BACTK RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|40335|emb|CAA40026.1| sigma factor 35 [Bacillus thuringiensis serovar kurstaki]
 gi|19918914|gb|AAL99378.1| sigma factor 35 [Bacillus thuringiensis serovar israelensis]
 gi|29897549|gb|AAP10825.1| RNA polymerase sigma-E factor [Bacillus cereus ATCC 14579]
 gi|30258550|gb|AAP27769.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Ames]
 gi|42738924|gb|AAS42852.1| RNA polymerase sigma-29 factor [Bacillus cereus ATCC 10987]
 gi|47504484|gb|AAT33160.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49180681|gb|AAT56057.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Sterne]
 gi|49329998|gb|AAT60644.1| RNA polymerase sporulation-specific sigma E factor [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51975052|gb|AAU16602.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           E33L]
 gi|164711999|gb|EDR17539.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|165973128|gb|ABY76243.1| sigma factor [Bacillus thuringiensis]
 gi|167528006|gb|EDR90812.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170126278|gb|EDS95169.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|170667205|gb|EDT17965.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|172080408|gb|EDT65495.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190563065|gb|EDV17031.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991603|gb|EDX55569.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196023306|gb|EDX61984.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|196030349|gb|EDX68948.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|206734078|gb|EDZ51249.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206745026|gb|EDZ56429.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217065302|gb|ACJ79552.1| RNA polymerase sigma-29 factor [Bacillus cereus AH187]
 gi|218162706|gb|ACK62698.1| RNA polymerase sigma-29 factor [Bacillus cereus B4264]
 gi|218537297|gb|ACK89695.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|218544009|gb|ACK96403.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|221241408|gb|ACM14118.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           Q1]
 gi|225791008|gb|ACO31225.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227003693|gb|ACP13436.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228585495|gb|EEK43599.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|228591400|gb|EEK49250.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|228597321|gb|EEK54972.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|228603389|gb|EEK60866.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|228631451|gb|EEK88085.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|228637109|gb|EEK93568.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|228643114|gb|EEK99390.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|228654419|gb|EEL10284.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|228660194|gb|EEL15830.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|228672150|gb|EEL27441.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|228690455|gb|EEL44239.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|228702201|gb|EEL54677.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|228711695|gb|EEL63648.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|228723836|gb|EEL75191.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|228772643|gb|EEM21084.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228779333|gb|EEM27590.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228785790|gb|EEM33794.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792957|gb|EEM40515.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228799638|gb|EEM46591.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805501|gb|EEM52092.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228812144|gb|EEM58475.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818672|gb|EEM64739.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824385|gb|EEM70191.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830760|gb|EEM76365.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228837086|gb|EEM82427.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228843121|gb|EEM88203.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228850019|gb|EEM94850.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228857154|gb|EEN01660.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|229265855|gb|ACQ47492.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|296325450|gb|ADH08378.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|308154178|gb|ADA55132.3| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|308154180|gb|ADA55133.2| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|324327803|gb|ADY23063.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941674|gb|AEA17570.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 239

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|302547278|ref|ZP_07299620.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302464896|gb|EFL27989.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 264

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 108/236 (45%), Gaps = 16/236 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +EFR I ++    E EA   ++++V A + +   +A+++ NRG    DL Q   +GL+KA
Sbjct: 20  AEFRRIATLPEGAEKEA--LRQDVVRAWMPMAERLARQFRNRGESAEDLRQVAMLGLVKA 77

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI- 543
            ++++   G  F+++A+  V   I R   D    + +P  +++  ++V   A+ ++    
Sbjct: 78  VKRYEPDRGSAFASFAVPTVVGEIKRHFRDHMWGVHVPRRVQELRNRVRAAAQELTRTPD 137

Query: 544 KREPTPEEIAKKLAMPVE----GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            R P+   I +   M  E    G+  +   +   +  E P G ED   L D +    A  
Sbjct: 138 DRSPSVSAIVEHTGMSEEDVLLGMEAMESFSALSLDAELP-GAEDGYSLADTL---GAPE 193

Query: 600 P-LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           P  D  IQ   RE     L +L  RE  +L +RF          E++G  Q  V+R
Sbjct: 194 PSYDRVIQ---REALKPRLRALPERERHILYLRFFREETQGRIAEQLGISQMHVSR 246


>gi|110803132|ref|YP_699053.1| sporulation sigma factor SigK [Clostridium perfringens SM101]
 gi|6715486|gb|AAF26431.1|AF218835_2 RNA polymerase sigma factor SigK [Clostridium perfringens]
 gi|110683633|gb|ABG87003.1| RNA polymerase sigma-70 factor family [Clostridium perfringens
           SM101]
          Length = 233

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 101/232 (43%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 50  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 109

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
                                              A+ + N+I              M  
Sbjct: 110 -----------------------------------AKCIDNEI-------------LMFF 121

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-----NLRETTTR 615
              +K    TK  + L+ PIG +   +    I+  ++ S  DS ++A      ++E   +
Sbjct: 122 RNTKK----TKGEVFLQDPIGVDKEGNEICLIDILSSDS--DSVLEAVENSLQVKELYKK 175

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +   L+PRE+ +++MR+G+      T  E+     ++R  + +IE KA++KL
Sbjct: 176 MSDILSPREKEIIKMRYGLLDGDIKTQREIAAILGISRSYVSRIEKKALKKL 227


>gi|220907105|ref|YP_002482416.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219863716|gb|ACL44055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 263

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 37/142 (26%), Positives = 76/142 (53%), Gaps = 5/142 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V  +L LV  VA +   +  + + DL+Q G +GL+ A E+FD   GY FS++A+ +
Sbjct: 27  RNQLVRLHLGLVRKVAHRLARQCKEPYEDLVQCGCLGLIAAIERFDPSQGYAFSSFAVPY 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE-- 561
           ++  I   + D++  ++IP   +       +  + ++  + R PT E++A +L +  E  
Sbjct: 87  IRGEILHFLRDRAYMLKIPRRWQQLNQDGQKVRQELAKVLDRPPTEEQVASQLQVSPEEW 146

Query: 562 -GVRKVLKITKEPISLETPIGD 582
             VR  ++  + P+S+ T +  
Sbjct: 147 RSVRLAMR-NRTPLSINTTLSS 167


>gi|301055395|ref|YP_003793606.1| sporulation sigma factor SigE [Bacillus anthracis CI]
 gi|300377564|gb|ADK06468.1| sporulation sigma factor SigE [Bacillus cereus biovar anthracis
           str. CI]
          Length = 238

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 57  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 113

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 114 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 138

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 139 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 184

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 185 DREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLR 231


>gi|254250894|ref|ZP_04944212.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
 gi|124893503|gb|EAY67383.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
          Length = 369

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 93/204 (45%), Gaps = 20/204 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 166 DLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 222

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-------ITKEPISLETPIGDED 584
           V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E          +D
Sbjct: 223 VEHAVHQVEQQLGRAASEAEIAQHLNMPLDEYQAMLQDLHGSQLIYYEDFDRAA----DD 278

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L  F  D     PL + +  +LR+     +  L  RE+ ++ + +  G+N    L E
Sbjct: 279 EPFLDRFRVDH--ADPLSALLDEHLRDALVEAIERLPEREKLLMSLYYERGLN----LRE 332

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    V+  R+ Q+ ++A+ +L+
Sbjct: 333 IGAVLEVSESRVCQLHSQAVARLR 356


>gi|83589646|ref|YP_429655.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83572560|gb|ABC19112.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Moorella
           thermoacetica ATCC 39073]
          Length = 255

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 47/203 (23%), Positives = 99/203 (48%), Gaps = 14/203 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL++A +++D   G  F T+A   ++ AI  ++         P  + +K+ +
Sbjct: 51  DLLGYGIVGLLEAVDRYDPSRGVNFETFASQRIRGAILDALRRAHWA---PRSLIEKLRR 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPI----GDEDT 585
             +  R++  +   E +   +A+ L +    +R++++   +   +SLE  +    G+E T
Sbjct: 108 ASQVYRQLEQEQGGEVSDGAVARALGITEAELRELMERGSQMAILSLEDFLLDQEGEEGT 167

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           +  G+ + D  +  P+    Q  LR      L +L  ++  VL + +  G+    TL+E+
Sbjct: 168 TR-GELLADPGSPDPVGIYEQGELRRALAAALENLKEKDRLVLTLYYYEGL----TLKEI 222

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           GK   ++  R+ Q+  +AI  L+
Sbjct: 223 GKVLGISESRVCQLHGRAILNLR 245


>gi|283850718|ref|ZP_06368005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
 gi|283573961|gb|EFC21934.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
          Length = 264

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 51/222 (22%), Positives = 106/222 (47%), Gaps = 10/222 (4%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +++V S  K    + ++  +L+  G +GL++A  +F   LG KF TYA   +K ++   +
Sbjct: 47  IKIVASRLKAKLPQSVEMGELLSAGAMGLIEALGRFRPELGIKFETYAESRIKGSMLDDL 106

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                  R     R ++  +   +RR+ N   +  T E++A+   +    V + L+  + 
Sbjct: 107 RRMDWFSR---GQRHRVRTLEEASRRIENDSGKAATVEQLAEATGLTEREVTQGLEALQN 163

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            + L     D  T ++  + +++    P  SA    L +    ++  LTPRE+ VL + +
Sbjct: 164 QLCLSL---DAITENISSYQKNQLENEPYKSAEFKELVDKLASLIDDLTPREKLVLSLYY 220

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G  +N   T E +G    +T  R+ Q+ ++A+ +L+   +++
Sbjct: 221 GEELNMRETSEVMG----ITEGRVSQLHSQALARLRQKFKAQ 258


>gi|206895926|ref|YP_002247112.1| RNA polymerase sigma-37 factor [Coprothermobacter proteolyticus DSM
           5265]
 gi|206738543|gb|ACI17621.1| RNA polymerase sigma-37 factor [Coprothermobacter proteolyticus DSM
           5265]
          Length = 243

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 99/216 (45%), Gaps = 20/216 (9%)

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SV  ++    +   DL QE    L+ A ++F+   G  F T+A+  +   + R + D   
Sbjct: 38  SVVNRFAPYQIDKDDLRQEAYRALVDAIDRFNPSYGNLFETFAIPTIVGNLKRYLRDYGW 97

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPIS 575
            I +P  M D  + + +    ++ K+  EPT +EIA++L +  E V +VL I   K   S
Sbjct: 98  AISVPRSMVDMAYSIQKKLPEIAEKLGHEPTIKEIAEELELDEEQVSEVLAIMAVKNTSS 157

Query: 576 LETPIGDE-DTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           +++ I DE DT+   L   + D++              E    +  S  P  ER +  + 
Sbjct: 158 IDSKITDESDTTGEELLGLLSDRDLED-----------EALLEIAVSELPEPERFIIEKR 206

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             G++      E+ K   +++ ++ + E KAI KLK
Sbjct: 207 LEGLSQS----EIAKLLNISQAQVSRFERKAITKLK 238


>gi|126435251|ref|YP_001070942.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           JLS]
 gi|126235051|gb|ABN98451.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 284

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 34/138 (24%), Positives = 72/138 (52%), Gaps = 3/138 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++ A + +   +A ++  RG    D+IQ   IGL+K  +++D   G+ F  +A+  +
Sbjct: 46  RRHIITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVDRYDPDKGH-FLAFAVPTI 104

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE--G 562
           +  I R   D + T+R+P  +++   ++      +S ++ R PT  E+A++L +  E  G
Sbjct: 105 RGEIRRHFRDNTWTVRVPRKVQETQLRMRDAVNTLSQRLNRTPTGVELAEELDVGSEELG 164

Query: 563 VRKVLKITKEPISLETPI 580
             +       P+SL+ P+
Sbjct: 165 DCQAATTAYRPVSLDAPL 182


>gi|160895354|ref|ZP_02076125.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
 gi|156863047|gb|EDO56478.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
          Length = 226

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 98/231 (42%), Gaps = 62/231 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K ++E N+RLV  +AKKY N   +  DLI  G IGL+KA + +D   G +  TYA   
Sbjct: 47  ARKTLIEYNMRLVAHIAKKY-NGSHENDDLISAGTIGLIKAIDTYDSKKGKRLVTYA--- 102

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++   +                  R + K  RE                 
Sbjct: 103 -----SRCIENELLML-----------------LRQNRKHARE----------------- 123

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP-----LDSAIQ-ANLRETTTRVL 617
                     +SL  PIG   T   G+ I   + +SP     LDS +   NL++    +L
Sbjct: 124 ----------VSLFEPIG---TDKEGNEISLMDIISPDTPSILDSMVHDYNLKQLPDCML 170

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             LT +E  +L  R+G+      T +E+     ++R  + +IE +A+ KL+
Sbjct: 171 HHLTKQEMVLLSRRYGLSGEAPCTQKEIASAMGISRSYVSRIEKRALLKLR 221


>gi|229140635|ref|ZP_04269187.1| Prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus cereus
           BDRD-ST26]
 gi|228642831|gb|EEK99110.1| Prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus cereus
           BDRD-ST26]
          Length = 314

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 107/236 (45%), Gaps = 28/236 (11%)

Query: 454 RLVISVAKKYTNR---------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           RLV     KY +           L   DLIQ G +GL+ A   F   LG+KF+T+A+  +
Sbjct: 28  RLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPII 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +++ D S  IRI     ++++++     RM  K+  E   E IAK L + V  V+
Sbjct: 88  LGYIRKAVRD-SQKIRIT----NEVYEIKGKISRM--KLHDEEV-ESIAKLLEVSVRDVK 139

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              +     ISL+TP+  E   +   L + + DK     LD+ I+   +   T  L++L 
Sbjct: 140 TAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTLDNVIK---KMIITAFLSTLC 196

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +E+ V  +        + T   +GK+  VT+ +I +I     +K +       LR
Sbjct: 197 SKEKFVWELH-----AKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNKHSLR 247


>gi|312134671|ref|YP_004002009.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774722|gb|ADQ04209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 244

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 102/225 (45%), Gaps = 52/225 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK ++E NLRLV+ +A+++ N  +   DL+  G IGL+KA   ++     K +TYA   +
Sbjct: 64  KKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGLIKAINTYNPNKNIKLATYASKCI 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +                        ++++   RR SN            KKL + ++   
Sbjct: 124 E------------------------NEILMFLRRNSN------------KKLELSID--- 144

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPR 623
                  EP++++    D +   L D +        + + I++N+ +E   + +  L  R
Sbjct: 145 -------EPLNVD---WDGNELLLSDVL--GTDTEEIYNRIESNVEKEALLQAIQKLPSR 192

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E++++ +RFG G   + T +EV     +++  I ++E K I +LK
Sbjct: 193 EKKIVELRFGFGDEGEKTQKEVADMLGISQSYISRLEKKIITRLK 237


>gi|311695193|gb|ADP98066.1| flagellar biosynthesis sigma factor FliA [marine bacterium HP15]
          Length = 247

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 103/248 (41%), Gaps = 58/248 (23%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++E +  LV  +A     R    +Q  DL+Q G IGL++AA+++    G  F TYA   
Sbjct: 20  QLIEQHAPLVKKIALHLMARLPASVQLEDLMQAGMIGLLEAAQRYSSTKGATFETYA--- 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------REPTP 549
                          IRI   M D+I K       V R ARR+S  IK       RE   
Sbjct: 77  --------------GIRIRGAMVDEIRKGDWVPRSVHRNARRISQAIKAVEDRLGREAHD 122

Query: 550 EEIAKKLAMPVEGVRKVLKITKEP--ISL-------ETPIGDEDTSHLGDFIEDKNAVSP 600
           +E+A++L M +      L  +      SL       E PI   +T             +P
Sbjct: 123 QEVAEELGMGLPEYHSYLSDSNSGRLFSLDELNESGELPIEQTETQD-----------NP 171

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           L+       R +    +  L  RE+ VL + +   +N    L+E+G    V+  R+ QI 
Sbjct: 172 LEGLSSDAFRRSLAEAIEDLPEREKLVLSLYYQEELN----LKEIGAVLGVSESRVSQIH 227

Query: 661 AKAIRKLK 668
           ++A  +L+
Sbjct: 228 SQAALRLR 235


>gi|261419324|ref|YP_003253006.1| sporulation sigma factor SigE [Geobacillus sp. Y412MC61]
 gi|297530706|ref|YP_003671981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766140|ref|YP_004131641.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
 gi|261375781|gb|ACX78524.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC61]
 gi|297253958|gb|ADI27404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111006|gb|ADU93498.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
          Length = 239

 Score = 57.4 bits (137), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 101/225 (44%), Gaps = 50/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK++ E + +E    L +  +G 
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKVRAEVSFDE---PLNIDWDG- 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G ED     D   D +             R      L  L+ R
Sbjct: 149 --------NELLLSDVLGTEDDVITKDLEADVD-------------RRLLLNALRQLSDR 187

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 188 EKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232


>gi|229073720|ref|ZP_04206833.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus cereus
           F65185]
 gi|228709429|gb|EEL61490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus cereus
           F65185]
          Length = 236

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 42/117 (35%), Positives = 58/117 (49%), Gaps = 16/117 (13%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +N GL+  DLIQ G IGL+KA + FD   GYKFST A+  +    TR+I +         
Sbjct: 34  SNTGLEIEDLIQCGMIGLLKARKDFDPAYGYKFSTLAIPKMHGETTRAIINNQKV----- 88

Query: 524 HMRDKIHKVVRTARRMSNKIKREPT----PEEIAKKLAMPVEGVRKVLKITKEPISL 576
                  KV R    +  +I RE      PE I++ L + VE V + L+  + P SL
Sbjct: 89  -------KVTREIFYLKGRIIREKLAEEKPEVISQLLGVTVEDVEEALRYQQIPSSL 138


>gi|167564488|ref|ZP_02357404.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           EO147]
          Length = 244

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 48/202 (23%), Positives = 91/202 (45%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 41  DLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSRE 97

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V     ++  ++ R     E+A  L MP+   + +L    + +     +  ED     D 
Sbjct: 98  VEHAIHQVEQRLGRSANETEVAAHLQMPLGEYQSML----QDLHGSQLVYYEDFDRSADD 153

Query: 591 --FIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F++   A    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 154 EPFLDRYRADHADPLSALLDDHLRSALVDAIEHLPEREKLLMSLYYERGLN----LREIG 209

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 210 AVLEVSESRVCQLHSQAVARLR 231


>gi|229031536|ref|ZP_04187536.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
 gi|229075661|ref|ZP_04208643.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|229098375|ref|ZP_04229320.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|229104467|ref|ZP_04235134.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|229117401|ref|ZP_04246777.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|229162840|ref|ZP_04290797.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|229174571|ref|ZP_04302101.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228608876|gb|EEK66168.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228620722|gb|EEK77591.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|228666011|gb|EEL21477.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|228678909|gb|EEL33119.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|228684992|gb|EEL38925.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|228707437|gb|EEL59628.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|228729825|gb|EEL80805.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
          Length = 239

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 103/227 (45%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  +D      L++ +    R    + L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITKDLEATVD---RHLLMKALHQLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLAGEEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|126649719|ref|ZP_01721955.1| sporulation sigma factor SigE [Bacillus sp. B14905]
 gi|126593438|gb|EAZ87383.1| sporulation sigma factor SigE [Bacillus sp. B14905]
          Length = 227

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 98/228 (42%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+++ N G    DLI  G+IGL+KA E F+     K +TYA   
Sbjct: 45  ARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLIKAIETFNTDKNIKLATYA--- 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R       +T+R                          
Sbjct: 102 -----SRCIENE-----ILMHLR-------KTSR-------------------------- 118

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                  K  +SL+ P+    D +   L D +  +  +  LD+  +   R+     +  L
Sbjct: 119 ------MKGEVSLDEPLNSDADGNELLLSDILGTEEHI-ILDNVEKKIERQHMFHAINLL 171

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  ++  RFG+    + T +EV     +++  I ++E K I+ L+
Sbjct: 172 GARERYIMECRFGLNGKVEMTQKEVADHLGISQSYISRLEKKIIQDLR 219


>gi|110799358|ref|YP_696454.1| sporulation sigma factor SigK [Clostridium perfringens ATCC 13124]
 gi|110674005|gb|ABG82992.1| RNA polymerase sigma-70 factor family [Clostridium perfringens ATCC
           13124]
          Length = 233

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 101/232 (43%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 50  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 109

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
                                              A+ + N+I              M  
Sbjct: 110 -----------------------------------AKCIDNEI-------------LMFF 121

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-----NLRETTTR 615
              +K    TK  + L+ PIG +   +    I+  ++ S  DS ++A      ++E   +
Sbjct: 122 RNTKK----TKGEVFLQDPIGVDKEGNEICLIDILSSDS--DSVLEAVENSLQVKELYKK 175

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +   L+PRE+ +++MR+G+      T  E+     ++R  + +IE KA++KL
Sbjct: 176 MSDILSPREKEIIKMRYGLLDGDIKTQREIAAILGISRSYVSRIEKKALKKL 227


>gi|222824021|ref|YP_002575595.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
 gi|222539243|gb|ACM64344.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
          Length = 625

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 42/151 (27%), Positives = 79/151 (52%), Gaps = 27/151 (17%)

Query: 41  RGYVTIEELNAFLP--PDEVSSEQMED-----TVAMLSNMGI----NVVDGDDLEDEEGS 89
           + Y+T E+L  +    P+  S++++ D      V ++S+  I    N+ +   L++E+  
Sbjct: 17  KDYITYEKLVKYFAKLPNVTSAKKIRDLMDKHKVELISSAEIAKKRNLEEAKKLQEEKQK 76

Query: 90  ------EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                 E+  DLA    N +  L+  +      +D PVRMYLREMG I LL+++ E+ I+
Sbjct: 77  LQDTSLENEFDLA----NENDLLEWSR------SDSPVRMYLREMGQIALLNKDEEVEIS 126

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           K+IE G  +++ + C  P     ++ +++ L
Sbjct: 127 KKIELGEDIIIDAFCSVPYLIDFILDYKEPL 157


>gi|157376181|ref|YP_001474781.1| flagellar biosynthesis sigma factor [Shewanella sediminis HAW-EB3]
 gi|157318555|gb|ABV37653.1| Phosphatidylserine decarboxylase [Shewanella sediminis HAW-EB3]
          Length = 239

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KASIVEQYAPLVKKIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+    EIA++L M ++
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RVAQVIDELGQELGRDAVDSEIAQRLDMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +  E+       +S       +     +  
Sbjct: 130 EYHHILN----DVSVGKVVGIEDLGVSVDVVSHEEVQQDDIFESIADVEFHKALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYYDEALN----LKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|186477706|ref|YP_001859176.1| flagellar biosynthesis sigma factor [Burkholderia phymatum STM815]
 gi|184194165|gb|ACC72130.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia phymatum
           STM815]
          Length = 244

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R    +
Sbjct: 40  DLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRRTSRE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V     ++   + R  +  EIA+ L MP++  + +L+     + I  E    D D S   
Sbjct: 97  VESAVHQVEQSLGRSASETEIAEHLKMPLDEYQSMLQDLHGSQLIYYE----DFDRSADD 152

Query: 590 DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +   D+  V    PL + +  +LR      +  L  RE+ ++ + +  G+N    L E+G
Sbjct: 153 EPFLDRYCVDHSDPLSALLDESLRGALVEAIDRLPEREKLLMSLYYERGLN----LREIG 208

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ ++A+ +L+
Sbjct: 209 AVMEVSESRVCQLHSQAVARLR 230


>gi|239826532|ref|YP_002949156.1| sporulation sigma factor SigE [Geobacillus sp. WCH70]
 gi|239806825|gb|ACS23890.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. WCH70]
          Length = 239

 Score = 57.4 bits (137), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 105/236 (44%), Gaps = 50/236 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LIKKLSSGDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++     I +++R             +NK++ E + +E 
Sbjct: 107 KIKLATYA--------SRCIENE-----ILMYLRR------------NNKVRAEVSFDE- 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
              L +  +G           + L   +G ED     D   D +             R  
Sbjct: 141 --PLNIDWDG---------NELLLSDVLGTEDDVITKDLEADVD-------------RRL 176

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  L+ RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 177 LFNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232


>gi|91978901|gb|ABE66426.1| RNA polymerase sigma-70 factor [Aeromonas simiae]
 gi|91978903|gb|ABE66427.1| RNA polymerase sigma-70 factor [Aeromonas simiae]
          Length = 282

 Score = 57.0 bits (136), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/137 (29%), Positives = 68/137 (49%), Gaps = 2/137 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E
Sbjct: 147 KLADIFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVSAFTNNE 206

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      VA E + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 207 CETAWFEYQKQAGKAWSAPLVAME-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 265

Query: 439 CEASIAKKEMVEANLRL 455
            +A  AKKEMVEANLRL
Sbjct: 266 AKARRAKKEMVEANLRL 282


>gi|325264805|ref|ZP_08131534.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
 gi|324030097|gb|EGB91383.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
          Length = 246

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 43/75 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRC 122

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 123 IENEILMYLRRNSKT 137


>gi|182625388|ref|ZP_02953161.1| sigma factor [Clostridium perfringens D str. JGS1721]
 gi|177909385|gb|EDT71837.1| sigma factor [Clostridium perfringens D str. JGS1721]
          Length = 232

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 105/242 (43%), Gaps = 64/242 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD--WCLGYKFST 498
           A  +++E N +L+  VA K+ +     ++F DL+QEG IG + A  K+D  +    KF T
Sbjct: 22  ALDKLLENNDKLIYKVASKFYSDKTSSIEFDDLLQEGRIGFILACSKYDIEYIKKTKFIT 81

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA +W+ Q                     KIH+ + T            T EE       
Sbjct: 82  YAFYWIYQ---------------------KIHRFITT----------HNTNEE------- 103

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQ-ANLRETTTRV 616
                          ISL TP+ +E+   L + IE   N +   +  +  + LR     V
Sbjct: 104 ---------------ISLNTPVSEENQDELINSIESHSNEIKDREEELYLSELRLELEAV 148

Query: 617 LASLTPREER-VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +       ER +L++ +  G +TD  +++++   F  +   ++ I+A+AIRKL++    K
Sbjct: 149 MDKHNTLNEREILKLYY--GWDTDELSIDQIADIFETSSSEVKNIKARAIRKLRNSMWFK 206

Query: 675 KL 676
           K+
Sbjct: 207 KV 208


>gi|146164092|gb|ABQ08723.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164097|gb|ABQ08724.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164102|gb|ABQ08725.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164105|gb|ABQ08726.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164119|gb|ABQ08727.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 293

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LSDII 65


>gi|153952229|ref|YP_001397920.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
 gi|152939675|gb|ABS44416.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
          Length = 622

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|312126664|ref|YP_003991538.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311776683|gb|ADQ06169.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 206

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 63/103 (61%), Gaps = 5/103 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + +V  +++G+ +A+   +E++ A   L+IS A KY N+   F DL QEG   +
Sbjct: 4   LSFDEQKELVCRIKQGDKKAA---EELICAYEPLIISFAAKY-NKPEIFEDLKQEGYCAI 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           ++AA KF+  LG  F T A++++K+ + R + ++  TIR P +
Sbjct: 60  LQAARKFNVSLGVSFITLAVYYIKRNMDRCV-NRDRTIRPPFN 101


>gi|257470879|ref|ZP_05634969.1| RNA polymerase sigma factor [Fusobacterium ulcerans ATCC 49185]
 gi|317065081|ref|ZP_07929566.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690757|gb|EFS27592.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 284

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 44/76 (57%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++++  NL  V S+A  Y   G+ ++D++QEG +GL+KA + FD      F  Y+ +W+
Sbjct: 88  KEKVIVKNLNEVASIAFNYVKNGIAYMDVVQEGTVGLIKAVDYFDPDRNGDFKNYSKYWI 147

Query: 505 KQAITRSIADQSCTIR 520
            + I   I ++   IR
Sbjct: 148 AREIVLYIENKVADIR 163


>gi|108799609|ref|YP_639806.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119868720|ref|YP_938672.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           KMS]
 gi|108770028|gb|ABG08750.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694809|gb|ABL91882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
          Length = 284

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/138 (24%), Positives = 71/138 (51%), Gaps = 3/138 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++ A + +   +A ++  RG    D+IQ   IGL+K  +++D   G+ F  +A+  +
Sbjct: 46  RRHIITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVDRYDPDKGH-FLAFAVPTI 104

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE--G 562
           +  I R   D + T+R+P  +++   ++      +S ++ R PT  E+A +L +  E  G
Sbjct: 105 RGEIRRHFRDNTWTVRVPRKVQETQLRMRDAVNTLSQRLNRTPTGVELADELDVGSEELG 164

Query: 563 VRKVLKITKEPISLETPI 580
             +       P+SL+ P+
Sbjct: 165 DCQAATTAYRPVSLDAPL 182


>gi|86150479|ref|ZP_01068704.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88596833|ref|ZP_01100070.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|148926089|ref|ZP_01809775.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|218562617|ref|YP_002344396.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|85839074|gb|EAQ56338.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88191674|gb|EAQ95646.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|112360323|emb|CAL35119.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|145845568|gb|EDK22660.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|284926231|gb|ADC28583.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni IA3902]
 gi|315058444|gb|ADT72773.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni S3]
 gi|315928360|gb|EFV07675.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni DFVF1099]
          Length = 622

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|2764713|emb|CAA05353.1| sigma 70 [Campylobacter jejuni]
          Length = 622

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|315929035|gb|EFV08275.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           305]
          Length = 622

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|309775717|ref|ZP_07670714.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916522|gb|EFP62265.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 249

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 93/224 (41%), Gaps = 49/224 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E NLRLV  + KKY  +  Q  DLI  G IGL+K  + F    G+K +TYA   
Sbjct: 47  ARNKLIEHNLRLVAHIVKKYDIKKEQTEDLISIGTIGLIKGVDSFKPEKGHKLTTYASKC 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +++R        +     N    EP        +A   +G 
Sbjct: 107 IENEIL-------------MYLRS-------SKNYFQNVSLNEP--------IATDKDGS 138

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L        ++     EDTS + D I + N          A L+    R +  L  R
Sbjct: 139 EITL--------IDAIASPEDTSIIDDMIVEDNI---------ARLK----RFIHVLDAR 177

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  ++  RFG+    + T  E+ +Q  ++R  + +IE +A  K+
Sbjct: 178 ELEIITKRFGLYGQEEETQREIARQLHISRSYVSRIEKRAFMKI 221


>gi|57237826|ref|YP_179074.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|86150708|ref|ZP_01068924.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|86152585|ref|ZP_01070790.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612947|ref|YP_001000680.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157415258|ref|YP_001482514.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|167005602|ref|ZP_02271360.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|205356712|ref|ZP_03223473.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315124489|ref|YP_004066493.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|57166630|gb|AAW35409.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|85841878|gb|EAQ59124.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|85843470|gb|EAQ60680.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249244|gb|EAQ72205.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157386222|gb|ABV52537.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|205345450|gb|EDZ32092.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315018211|gb|ADT66304.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315932129|gb|EFV11072.1| Phosphatidylserine decarboxylase [Campylobacter jejuni subsp.
           jejuni 327]
          Length = 622

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|315654569|ref|ZP_07907475.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           ATCC 51333]
 gi|315491033|gb|EFU80652.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           ATCC 51333]
          Length = 433

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/228 (23%), Positives = 105/228 (46%), Gaps = 18/228 (7%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + E++E NL LV     +   R   F+   DL   G++ L++AA  +D   G  F  Y
Sbjct: 8   VNRNELIENNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAANSYDSATGVPFHRY 67

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A++ ++ A+   +       R       ++ ++  T   ++    R PT EE+A  L + 
Sbjct: 68  AIYRIRGAMLDELRSMDWATRGARQRTKQLEEMTST---LTAAAGRAPTKEELASALGVD 124

Query: 560 VEGVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           VE V    +   +  +S++ P+G ED   L   + D++  SP D+ +  + R    R   
Sbjct: 125 VESVESAQQDAARRVVSMDAPVGSEDERSL--ELPDESP-SPEDTLLD-DERLVYLRASV 180

Query: 619 SLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              P+     R+R+ +      +  +++V  +  VT+ R+ Q+ ++A+
Sbjct: 181 RALPQ-----RLRYVVEQVFFEERPIQDVADELGVTQSRVSQLRSEAL 223


>gi|197302589|ref|ZP_03167644.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
 gi|197298487|gb|EDY33032.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
          Length = 248

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 43/75 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 65  AKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRC 124

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 125 IENEILMYLRRNSKT 139


>gi|138894662|ref|YP_001125115.1| sporulation sigma factor SigE [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247723|ref|ZP_03146425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134266175|gb|ABO66370.1| RNA polymerase sigma-E factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196212507|gb|EDY07264.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 239

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 101/225 (44%), Gaps = 50/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK++ E + +E    L +  +G 
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKVRAEVSFDE---PLNIDWDG- 148

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G ED     D   D +             R      L  L+ R
Sbjct: 149 --------NELLLSDVLGTEDDVITKDLEADVD-------------RRLLLNALRQLSDR 187

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 188 EKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232


>gi|18310750|ref|NP_562684.1| sporulation sigma factor SigK [Clostridium perfringens str. 13]
 gi|168214245|ref|ZP_02639870.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|169343581|ref|ZP_02864580.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170764185|ref|ZP_02633869.2| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|182420555|ref|ZP_02643878.2| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
 gi|182625679|ref|ZP_02953448.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|18145431|dbj|BAB81474.1| probable transcription initiation factor sigma K [Clostridium
           perfringens str. 13]
 gi|169298141|gb|EDS80231.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170660828|gb|EDT13511.1| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|170714308|gb|EDT26490.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|177909081|gb|EDT71556.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|182379749|gb|EDT77228.1| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
          Length = 233

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 101/232 (43%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 50  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 109

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
                                              A+ + N+I              M  
Sbjct: 110 -----------------------------------AKCIDNEI-------------LMFF 121

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-----NLRETTTR 615
              +K    TK  + L+ PIG +   +    I+  ++ S  DS ++A      ++E   +
Sbjct: 122 RNTKK----TKGEVFLQDPIGVDKEGNEICLIDILSSDS--DSVLEAVENSLQVKELYKK 175

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +   L+PRE+ +++MR+G+      T  E+     ++R  + +IE KA++KL
Sbjct: 176 MSDVLSPREKEIIQMRYGLLDGDIKTQREIAGILGISRSYVSRIEKKALKKL 227


>gi|283956399|ref|ZP_06373879.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
 gi|283792119|gb|EFC30908.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
          Length = 622

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|291522682|emb|CBK80975.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus catus GD/7]
          Length = 245

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 109/235 (46%), Gaps = 56/235 (23%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E    +  ++E NLRLV+ +A+K+ N G    DLI  G IGL+KA   ++     K +
Sbjct: 54  EAEREHGRNILIEHNLRLVVYIARKFDNTGAGMEDLISIGTIGLIKAINSYNPDKNIKLA 113

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA        +R I ++     I +++R             S+K+K E + +       
Sbjct: 114 TYA--------SRCIENE-----ILMYLRR------------SSKLKMEVSID------- 141

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAV-SPLDSAIQANLRETTTR 615
                         EP++++    D +   L D +  D+N + + ++  +  +L     +
Sbjct: 142 --------------EPLNVDW---DGNELLLSDILGTDENVIYNKMEEEVNYHL---LYK 181

Query: 616 VLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LA L+PRE+ ++++RFGI      + T +EV     +++  I ++E K I +LK
Sbjct: 182 ALAKLSPREKTIIQLRFGIRTADGEEKTQKEVADFLGISQSYISRLEKKIIGRLK 236


>gi|291326349|ref|ZP_06124166.2| motility sigma factor FliA [Providencia rettgeri DSM 1131]
 gi|291314661|gb|EFE55114.1| motility sigma factor FliA [Providencia rettgeri DSM 1131]
          Length = 241

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 95/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A E+FD   G  F+TYA+  ++ ++   +  +     +P  +R +  +
Sbjct: 47  DLIQAGGIGLLHALERFDVTQGASFATYAVQRIRGSMLDELRSRDW---VPRSVRRQARE 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +   + R  T  EIAK L + +   R+ L  T           DE     G+ 
Sbjct: 104 MTKAIGALEQSLGRSATEPEIAKALDIDLAEYRQALLDTNNSQLFSY---DEWHEIHGES 160

Query: 592 IEDK----NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E +    +  +PL   + ++LR+     +  L  RE+ VL + +   +N    L+E+G 
Sbjct: 161 CEPQMDEDDGGNPLSLLLDSSLRDQIAAAIEQLPEREKMVLTLYYQEELN----LKEIGA 216

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V   R+ Q+ ++AI++L+
Sbjct: 217 VLEVGESRVSQLHSQAIKRLR 237


>gi|154485092|ref|ZP_02027540.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
 gi|149734045|gb|EDM50164.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
          Length = 244

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 112/246 (45%), Gaps = 65/246 (26%)

Query: 435 RKGECEASI-------AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R+GEC  ++       AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+K    
Sbjct: 45  REGECIKNLIENNDEEAKSMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKGINT 104

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F      K +TYA        +R I ++     I +++R             +NK K E 
Sbjct: 105 FKPDKNIKLATYA--------SRCIENE-----ILMYLRK------------NNKTKLEV 139

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSP-LDSAI 605
           + +                     EP++++    D +   L D +  D++ +S  ++S +
Sbjct: 140 SID---------------------EPLNVDW---DGNELLLSDILGTDEDVISKGIESEV 175

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAK 662
           +  L     + +  L  RE+ ++ MR+G+  N D    T +EV     +++  I ++E K
Sbjct: 176 EKKL---LYKAIEKLNHREKVIVEMRYGLN-NKDGEEMTQKEVADSLGISQSYISRLEKK 231

Query: 663 AIRKLK 668
            I++LK
Sbjct: 232 IIKRLK 237


>gi|146164086|gb|ABQ08722.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
          Length = 293

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LSDII 65


>gi|152997431|ref|YP_001342266.1| RNA polymerase sigma-28 subunit FliA/WhiG [Marinomonas sp. MWYL1]
 gi|150838355|gb|ABR72331.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas sp. MWYL1]
          Length = 245

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/199 (24%), Positives = 95/199 (47%), Gaps = 11/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A ++F+   G  F TYA   ++ +I   +         P  +R     
Sbjct: 48  DLIQAGMMGLIEAYKRFESTKGASFETYAGIRIRGSIMDEVRKTDWA---PRSVRRNGRA 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLG 589
           V    + +  K+ RE +  E+A  + + ++   +++   ++ +  S E  + D DT++L 
Sbjct: 105 VATAIKELEAKLGREVSDMEVASHMNISMDEYHEMIHSSMSTQLFSYEEML-DSDTNNL- 162

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D IE +   +P     +   +    + +  L  RE+ VL + +    N +  L+E+G   
Sbjct: 163 DSIESEVENAPYSLVEEGGFQNQLAKEIDDLPEREKLVLSLYY----NEELNLKEIGAVL 218

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ QI ++A  +L+
Sbjct: 219 GVSESRVSQIHSQAAMRLR 237


>gi|260893401|ref|YP_003239498.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
 gi|260865542|gb|ACX52648.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
          Length = 242

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 45/77 (58%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +  +VE NLRLV+ +A+KY + G+   DL+  G+IGL+KA   F+     K +TYA   
Sbjct: 59  VRNTLVERNLRLVVYIARKYESTGINLEDLVSIGSIGLIKAVNTFNPQRKVKLATYASRC 118

Query: 504 VKQAITRSIADQSCTIR 520
           ++  I   +  QS T+R
Sbjct: 119 IENEILMFLRRQSRTLR 135


>gi|33863056|ref|NP_894616.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9313]
 gi|33634973|emb|CAE20959.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9313]
          Length = 269

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/117 (35%), Positives = 62/117 (52%), Gaps = 2/117 (1%)

Query: 442 SIAKK-EMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           SI K+ E V  +L L    A +   RG + LD LIQE  +GL+ A E FD  LG+K S+Y
Sbjct: 35  SIQKRNEAVVEHLGLAHLAATRQATRGGEELDDLIQEARLGLIMAMENFDANLGFKASSY 94

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           AM      I     D+S  +R+P  +RD   + +R  ++  N   +  T E++A +L
Sbjct: 95  AMARANGQILHFRRDRSQIVRVPWRLRDLYTRGMRLKQKQQNDGLKPFTEEQLAAQL 151


>gi|218439022|ref|YP_002377351.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218171750|gb|ACK70483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 257

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/115 (28%), Positives = 64/115 (55%), Gaps = 1/115 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE N  LV  VA + + +  + + DL Q G +GL++A E+F+   G  FS++A+ +
Sbjct: 28  RNQLVELNAGLVRQVAHRISRQCCEPYEDLEQVGYLGLIRAIERFNPQQGSAFSSFAIPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           ++  I   + D+   +RIP   +D   K  +  + ++  + R+P   EIA+ L +
Sbjct: 88  IRGEILHYLRDRGSVMRIPRRWQDLYTKGKKLRKELAQTLGRQPRESEIAQALGI 142


>gi|154498128|ref|ZP_02036506.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
 gi|150273118|gb|EDN00275.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
          Length = 240

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 91/230 (39%), Gaps = 60/230 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K +++E NLRLV+ +A+++ N G+   DLI  G IGL+KA   +      K +TYA   
Sbjct: 59  VKSQLIERNLRLVVYIARRFENTGVGIEDLISIGTIGLIKAINTYKPAKNIKLATYASRC 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +   SC                                              
Sbjct: 119 IENEILMHLRKTSC---------------------------------------------- 132

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLA 618
                  K  +S + P+    D +   L D +  +N V   P++  +    R+     + 
Sbjct: 133 ------LKSEVSFDEPLNTDWDGNELLLSDILGTENDVVMKPIEDDVD---RQLLLEAME 183

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE++++ MRFG+    + T +EV     +++  I ++E + I +LK
Sbjct: 184 KLDGREKQIITMRFGLDGRPERTQKEVADLLGISQSYISRLEKRIISRLK 233


>gi|146164076|gb|ABQ08721.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
          Length = 293

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LSDII 65


>gi|239933011|ref|ZP_04689964.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441364|ref|ZP_06580754.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344259|gb|EFE71215.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 287

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 100/215 (46%), Gaps = 13/215 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 50  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPGRG-AFESYAVPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
              + R   D+   +R+P  +++  +K VR ARR    N    EP+  +IA    +  E 
Sbjct: 109 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARRELTQNPGSPEPSVADIAAHTGLTEEE 167

Query: 563 VRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   ++  +    +SL+  +  D+D   L D +   +A    D  I    RE+    L  
Sbjct: 168 VGAGMEALESFSTLSLDAELSADDDGYSLADTLGASDAS--YDIVID---RESAKEGLRR 222

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  RE  +L MRF   M      + +G  Q  V+R
Sbjct: 223 LPERERAILYMRFFEDMTQSRIADRLGISQMHVSR 257


>gi|189426332|ref|YP_001953509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter lovleyi SZ]
 gi|189422591|gb|ACD96989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter lovleyi SZ]
          Length = 250

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 113/254 (44%), Gaps = 43/254 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ M+ ++L LV  +  ++T +    +D   L     IGL+ AA+++D   G +F T+A 
Sbjct: 19  RETMITSHLPLVRYLVNRFTAQLPSHIDPQDLASAAVIGLIHAADRYDPGRGVQFKTFAE 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +  ++C   +   MRDK   V R   R  +++ R PT  E+A+ L + ++
Sbjct: 79  QHIRGAILDEL--RACD-PLSRTMRDKCKMVEREMHRQEHQLGRNPTGREMAEALQISLD 135

Query: 562 GVRKVLKITKE----------------PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
               +L    E                P+SL   +GD++       +    A   L SAI
Sbjct: 136 DYYGLLDEIHEFSFISIDDSWDDDEGHPLSLADILGDDENKGPQCQVMAGQAAQALGSAI 195

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +            SL  +E   + + +   +N    L+E+G    +T  RI QI ++A+ 
Sbjct: 196 E------------SLPEKERLAVTLYYYEELN----LKEIGAVLGLTESRICQILSQAMI 239

Query: 666 KLKHPSRSKKLRSF 679
           +LK      KL+ F
Sbjct: 240 RLK-----GKLKPF 248


>gi|317472443|ref|ZP_07931767.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
 gi|316900087|gb|EFV22077.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
          Length = 238

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 107/239 (44%), Gaps = 53/239 (22%)

Query: 433 MVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           M+ K G  E   A+ +++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+  
Sbjct: 41  MIHKLGTAEEPEARAKLIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPA 100

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              K +TYA        +R I ++     I +++R             +NK K E + + 
Sbjct: 101 KKIKLATYA--------SRCIENE-----ILMYLRR------------NNKTKMEVSID- 134

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                               EP++++    D +   L D +     +   D   + + R+
Sbjct: 135 --------------------EPLNVD---WDGNELLLSDILGTDEDIIYRDLEHEVD-RK 170

Query: 612 TTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L+ RE +++ +RFGI      + T +EV     +++  I ++E K I++LK
Sbjct: 171 LLLNAMKILSDRERKIIELRFGINQKDGEEKTQKEVADLMGISQSYISRLEKKIIKRLK 229


>gi|313901033|ref|ZP_07834521.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
 gi|312953991|gb|EFR35671.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
          Length = 242

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 101/240 (42%), Gaps = 56/240 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E NLRLV  + KKY  +  Q  DLI  G IGL+KA + F    G+K +TYA   
Sbjct: 47  ARNKLIEHNLRLVAHIVKKYDIKKEQTEDLISIGTIGLIKAVDSFKPEKGHKLTTYASKC 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +++R        +     N    EP        +A   +G 
Sbjct: 107 IENEIL-------------MYLRS-------SKNYFQNVSLNEP--------IATDKDG- 137

Query: 564 RKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     I+L   I   ED+S + D I + N          A L+    R +  L  
Sbjct: 138 --------SEITLIDAISSPEDSSIIDDMIVEDNI---------ARLK----RYIHVLDA 176

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL-----KHPSRSKKLR 677
           RE  ++  RFG+    + T  E+ +Q  ++R  + +IE +A  K+     K   R ++LR
Sbjct: 177 RELEIITKRFGLYGQEEETQREIARQLHISRSYVSRIEKRAFMKIYREFQKEEKRKERLR 236


>gi|224005495|ref|XP_002291708.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220972227|gb|EED90559.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 541

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 96/232 (41%), Gaps = 49/232 (21%)

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ--AITRSIADQSCTIRIPVHMRDKIHK 531
           +QEG +GL +A +K+D   G +FSTYA  W+    A  + I D       P         
Sbjct: 323 VQEGMLGLARAVDKYDPERGLRFSTYATHWITSYAAYKKIIKDHLQLGTTP--------- 373

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-----GDEDTS 586
                          P  + IAK+L +  + +   ++ T   +S++ P+     G    S
Sbjct: 374 ---------------PEQKSIAKELGISEQRLTTAIRATGSLVSVDAPVISPGSGSYKGS 418

Query: 587 HLGDFIEDKNAVSPLDSAIQAN-----------LRETTTRVLAS-LTPREERVLRMRFGI 634
             G    +   +  LD+   A            LR+     +A+ LTP E  VLR+R G+
Sbjct: 419 AAGGDGSNSQELLILDTLRCAEPKPEDQVEISFLRQCLENAMATELTPYERDVLRLRLGL 478

Query: 635 GMNTDHTLEEVGKQFC---VTRERIRQIEAKAIRKLKHPS--RSKKLRSFLD 681
                 T+ EV  + C   VT   +R  E +A +KL+ P+   +  L  +LD
Sbjct: 479 DSGEGKTVREV-VEICGGSVTMSDVRSAERRAFKKLRSPTSVHTHNLLEYLD 529


>gi|325961902|ref|YP_004239808.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323467989|gb|ADX71674.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 316

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/112 (27%), Positives = 57/112 (50%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V   L L  ++A ++  RG +  DL Q   +GL+KAA  FD   G  F  YA   +
Sbjct: 40  ENDLVLGYLDLAEALAARFEARGRERADLNQVAYLGLVKAARGFDQSKGESFPAYAAPTI 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
              + R + D++  +R P +++D   ++ R    ++  + R P+  E+A  L
Sbjct: 100 TGELKRYLRDRTWVVRPPRYIQDLRTRMFRAEPELTQSLGRNPSVAELAGAL 151


>gi|298345983|ref|YP_003718670.1| putative DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           curtisii ATCC 43063]
 gi|304390259|ref|ZP_07372213.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315657524|ref|ZP_07910406.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|298236044|gb|ADI67176.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           curtisii ATCC 43063]
 gi|304326741|gb|EFL93985.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315491996|gb|EFU81605.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 433

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 69/150 (46%), Gaps = 7/150 (4%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + E++E NL LV     +   R   F+   DL   G++ L++AA  +D   G  F  Y
Sbjct: 8   VNRNELIENNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAANSYDSATGVPFHRY 67

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A++ ++ A+   +       R       ++ ++  T   ++    R PT EE+A  L + 
Sbjct: 68  AIYRIRGAMLDELRSMDWATRGARQRTKQLEEMTST---LTAAAGRAPTKEELASALGVD 124

Query: 560 VEGVRKVLK-ITKEPISLETPIGDEDTSHL 588
           VE V    +   +  +S++ P+G ED   L
Sbjct: 125 VESVESAQQDAARRVVSMDAPVGSEDERSL 154


>gi|291532045|emb|CBK97630.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 251

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/213 (25%), Positives = 102/213 (47%), Gaps = 18/213 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+I EG I LM A + FD     KF TYA   +K A+   +       R+P  +R    +
Sbjct: 55  DIINEGVIALMAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRKLD---RVPRTLRKLSKQ 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +     R+++++ R PT EE+A+ + M    + K++  T   I+L      E+  +  + 
Sbjct: 112 LDDNFARLNSELCRTPTDEELAESMNMTTAQLSKLMANTAGMITLSF----EELLYEDNL 167

Query: 592 IEDKNAVSPLDSA--IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            E+ +A S    A   +   ++     +A+L  +E++V+ M +   +       E+ K  
Sbjct: 168 DENISASSETADAKMYEREKKQVIADAVATLPEKEKQVVTMYYYERLK----YSEIAKVM 223

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +T+ R+ QI +KA+  LK+     KL S+++ 
Sbjct: 224 SITQSRVCQIHSKAMLTLKN-----KLESYINS 251


>gi|229137791|ref|ZP_04266393.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST26]
 gi|228645648|gb|EEL01880.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST26]
          Length = 196

 Score = 57.0 bits (136), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 46/205 (22%), Positives = 96/205 (46%), Gaps = 24/205 (11%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+    
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAI 61

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--- 593
             ++++++R P   EIA  L +  E V +++              +   S L D +E   
Sbjct: 62  EELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENAS 111

Query: 594 DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           D ++V+ ++S   ++    ET  R     +   L   E+ V+   FG  +N   T    G
Sbjct: 112 DGSSVARIESVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQKDT----G 167

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 168 ERLGISQMHVSRIKRQAISKLKQAA 192


>gi|295097196|emb|CBK86286.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 259

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/208 (23%), Positives = 102/208 (49%), Gaps = 12/208 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ-SCTIRIPVHMRDKIH 530
           DLIQ G++G + A + FD   G   +     W+ Q +  ++ D+   +  +P  +R    
Sbjct: 60  DLIQAGSMGFLSAIDSFDPKKGVALNA----WISQRVKWALMDELRESDWVPRRVRSHSR 115

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++V   +++  +   E T  +IA+++ + ++  +++L               E+ S   +
Sbjct: 116 EIVSLIQQIEQEKGGEATEADIAERMGVSLKEFQQMLADNNSSQMYSIDELQENYSDSWE 175

Query: 591 FIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             + +NA ++PL+ AIQ NL       +  +  RE+++L+  +      D  ++E+G   
Sbjct: 176 SNDGENAQLNPLNEAIQENLIANIAEHIRMIPRREQQILQFYY----QQDLNMKEIGLIL 231

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            VT  R+ Q+ + AI++L+  SR  +LR
Sbjct: 232 GVTETRVSQLHSLAIKRLR--SRMDRLR 257


>gi|153854402|ref|ZP_01995680.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
 gi|149752928|gb|EDM62859.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
          Length = 230

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 109/247 (44%), Gaps = 52/247 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E ++ V    +G+ EA   K  ++E NLRLV  + KKY     +  DL+  G IGL
Sbjct: 31  LTAAEEKYYVQKYTEGDLEA---KHILIERNLRLVAHIVKKYQPPPEEMEDLLSIGTIGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA   FD     + +TYA         R I ++     + +H R K        ++ S 
Sbjct: 88  MKAVVTFDPEKSARLATYA--------ARCIENE-----LLMHFRGK--------KKSSK 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++            L  P+   R+  +I    +     +G+ED  H    +E K  V  L
Sbjct: 127 EV-----------SLYEPIGTDREGNEIQLFDV---IEMGEEDVHHR---LEKKEDVIRL 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +++            L+ RE  VL++R+G+    ++T  E+ K   ++R  + +IE 
Sbjct: 170 YQKVESE-----------LSARERIVLKLRYGLYNEEEYTQREIAKMLGISRSYVSRIEK 218

Query: 662 KAIRKLK 668
            AI KL+
Sbjct: 219 SAIEKLR 225


>gi|166031221|ref|ZP_02234050.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
 gi|166029068|gb|EDR47825.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
          Length = 227

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 96/230 (41%), Gaps = 59/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY     +  DL+  G IGL+KA   F+     +  TYA   
Sbjct: 49  AKHILIEHNLRLVAHIVKKYQANVEEAEDLLSIGTIGLIKAVVTFNPGKNVRLGTYA--- 105

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R +                                   
Sbjct: 106 -----ARCIENE-----ILMHLRAR----------------------------------- 120

Query: 564 RKVLKITKEPISLETPIGDE---DTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLA 618
               K T   +SL  PIG +   +   L D IE  D+ A   ++   + ++ +    V +
Sbjct: 121 ----KKTSREVSLYEPIGTDREGNEIQLFDVIETDDQEAHRKIEE--KDDILKLYQHVES 174

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ RE  VL+MR+G+    ++T  E+ K   ++R  + +IE  AI KL+
Sbjct: 175 KLSTRERLVLKMRYGLYNEEEYTQREIAKLLGISRSYVSRIEKSAIEKLR 224


>gi|106895878|gb|ABF82642.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 278

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 67/136 (49%), Gaps = 2/136 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            D  W  Y K   +      V  + D +L+   +++ I VETG+SI++ + I   +  GE
Sbjct: 204 CDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEMVEANLR 454
            +A  AKKEMVEANLR
Sbjct: 263 AKARRAKKEMVEANLR 278


>gi|52080250|ref|YP_079041.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|52785627|ref|YP_091456.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|319645970|ref|ZP_08000200.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52003461|gb|AAU23403.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus licheniformis
           ATCC 14580]
 gi|52348129|gb|AAU40763.1| SigD [Bacillus licheniformis ATCC 14580]
 gi|317391720|gb|EFV72517.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 254

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 88/193 (45%), Gaps = 10/193 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL  A EKFD     KF TYA + ++ AI   +  +     +P   R+K  K
Sbjct: 54  DLVSLGMLGLYDALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGD-EDTSHL 588
           V     ++  +  R  +P EIA +L M  + V   +        +S++  + D ED  ++
Sbjct: 111 VEAAIEKLEQRYLRNVSPSEIAAELGMSEQDVVTTINEGFFANLLSIDEKLHDHEDGENV 170

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I D    +P +  ++  L       +  L+ +E+ V+ + +      + TL E+G+ 
Sbjct: 171 QVMIRDDKTSTPEEKMLKDELISQLAEKINELSEKEQLVISLFY----KEELTLTEIGQV 226

Query: 649 FCVTRERIRQIEA 661
             ++  RI QI +
Sbjct: 227 LNLSTSRISQIHS 239


>gi|259907643|ref|YP_002647999.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963265|emb|CAX54749.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|283477486|emb|CAY73402.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
          Length = 243

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/201 (21%), Positives = 93/201 (46%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G++G + A + FD   G   S +    ++ A+   + ++     +P  +R    +
Sbjct: 43  DLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDW---VPRRVRKHARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V    +++      E +  +IA ++ + V  ++++L  T    S +    DE      D 
Sbjct: 100 VTAVIQQLEQNKGGEASEADIATEMGVSVGELQQMLADTN---SSQIYSLDELQEQFADS 156

Query: 592 IE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            E       A++P+  A+Q NL       ++ +  RE+R+L++ +      D  + E+G 
Sbjct: 157 YETIDEGNEALNPVHQAVQENLVGKIAEHISVIPEREQRILQLYY----QQDLNMREIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  R+ Q+ + AI++++
Sbjct: 213 VLSLTETRVSQLHSLAIKRIR 233


>gi|52079008|ref|YP_077799.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|319648688|ref|ZP_08002899.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52002219|gb|AAU22161.1| RNA polymerase sigma-37 factor (sigma-B) [Bacillus licheniformis
           ATCC 14580]
 gi|317389107|gb|EFV69923.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 263

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/231 (21%), Positives = 120/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +V+    LV ++AKKY+ +G  F  DL Q G +GL+ A +++D  +G  F  +A+ 
Sbjct: 30  AQLTLVQTYKNLVETLAKKYS-KGKSFHEDLCQVGMLGLLGAIKRYDPDVGKSFEAFAIP 88

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++      ++ + +R P  +EIA+ L +  E 
Sbjct: 89  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDHLTTETQRSPRVDEIAEFLDVTEEE 148

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      +   + N +     VL
Sbjct: 149 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----EGYEKVNQKLMLESVL 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G+   +++  + +++ KA+++L+
Sbjct: 204 HVLSDREKQIIELTY----IQNKSQKETGEMLGISQMHVSRLQRKAVKRLR 250


>gi|283954552|ref|ZP_06372071.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283793956|gb|EFC32706.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 622

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 39/58 (67%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D PVRMYLREMG I LL+++ E+ I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPVRMYLREMGQIALLNKDEEVEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|56419662|ref|YP_146980.1| sporulation sigma factor SigE [Geobacillus kaustophilus HTA426]
 gi|56379504|dbj|BAD75412.1| DNA-directed RNA polymerase sigma-29 factor precursor (sigma-E)
           (stage II sporulation protein GB) [Geobacillus
           kaustophilus HTA426]
          Length = 239

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 106/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK++ E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRR------------NNKVRAEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + V   D  ++A++ R      L  L+ 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDVITKD--LEADVDRRLLLNALRQLSD 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232


>gi|254785490|ref|YP_003072919.1| RNA polymerase sigma factor for flagellar operon [Teredinibacter
           turnerae T7901]
 gi|237687129|gb|ACR14393.1| RNA polymerase sigma factor for flagellar operon [Teredinibacter
           turnerae T7901]
          Length = 235

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 112/249 (44%), Gaps = 33/249 (13%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFD 489
           MV +   EA++A +  VE  + LV  +A     R    +   DL+Q G IGL++AA+K+D
Sbjct: 1   MVYEQAQEAAVAIR--VEDYVPLVKRIAHHMMARMPSHVLVDDLMQAGMIGLLEAAQKYD 58

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI------ 543
              G  F TYA   ++ AI   +       R  VH         R ARR+S  I      
Sbjct: 59  AGKGASFETYAGIRIRGAIVDEMRRGDWAPR-SVH---------RNARRVSEAIGNVEAR 108

Query: 544 -KREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI-GDEDTSHLGDFIEDKNAVS 599
             R+    EIA++L M ++    +L+   +    SLE     +E+   LG    D+    
Sbjct: 109 LGRDARDGEIAEELQMSLDEYHDILRDSTSTRLYSLEETFEENENQFSLGTEGLDE---- 164

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +      +R+     +  L  RE+ VL + +   MN    L+E+G    V+  RI QI
Sbjct: 165 PAEKVQIDAMRKALAGAIEGLPEREQLVLSLYYEQEMN----LKEIGLVLGVSESRISQI 220

Query: 660 EAKAIRKLK 668
            ++A  +LK
Sbjct: 221 HSQAALRLK 229


>gi|169831890|ref|YP_001717872.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638734|gb|ACA60240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 104/234 (44%), Gaps = 20/234 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++  +L LV  +A +   R   F+   DL   G  GL++A EK+D   G  F T+A 
Sbjct: 18  REQLIVEHLPLVRLIAGRLAVRPPSFIAQEDLEGWGIFGLIEAVEKYDPNHGTDFRTFAY 77

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-- 559
             ++ AI   +  QS    +P  +  K+ ++     R+  +     T  E+A  L M   
Sbjct: 78  HRIRGAILDEVRRQSW---LPRSLWHKLQEINEARARLERETGASVTDAEVAASLGMTDL 134

Query: 560 -----VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
                    R V  ++ + +       + +    G  IED  +  PL+  ++    +T  
Sbjct: 135 EFHRLANHFRSVSVMSLDDVRTTR---NGEAVPWGSLIEDTGSPDPLEQVLEEEDHQTLV 191

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  ++  VL + +  G+    TL+E+G+   VT  R  Q+ A+AI +L+
Sbjct: 192 AAITQLEEKDRLVLALYYQEGL----TLKELGRVLEVTESRACQLHARAIARLR 241


>gi|302548084|ref|ZP_07300426.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302465702|gb|EFL28795.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 264

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 108/236 (45%), Gaps = 16/236 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +EFR I ++    E EA   ++++V A + +   +A+++ NRG    DL Q   +GL+KA
Sbjct: 20  AEFRRIATLPEGPEREA--LRQDVVRAWMPMAERLARQFRNRGESAEDLRQVAMLGLVKA 77

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI- 543
            ++++   G  F+++A+  V   I R   D    + +P  +++  ++V   A+ ++    
Sbjct: 78  VKRYEPDRGSAFASFAVPTVVGEIKRHFRDHMWGVHVPRRVQELRNRVRAAAQELTRTPD 137

Query: 544 KREPTPEEIAKKLAMPVE----GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            R P+   I +   M  E    G+  +   +   +  E P G ED   L D +    A  
Sbjct: 138 DRSPSVSAIVEHTGMSEEDVLLGMEAMESFSALSLDAELP-GAEDGYSLADTL---GAPE 193

Query: 600 P-LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           P  D  IQ   RE     L +L  RE  +L +RF          E++G  Q  V+R
Sbjct: 194 PSYDRVIQ---REALKPRLRALPERERHILYLRFFREETQGRIAEQLGISQMHVSR 246


>gi|52784380|ref|YP_090209.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|52346882|gb|AAU39516.1| SigB [Bacillus licheniformis ATCC 14580]
          Length = 264

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/231 (21%), Positives = 120/231 (51%), Gaps = 16/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +V+    LV ++AKKY+ +G  F  DL Q G +GL+ A +++D  +G  F  +A+ 
Sbjct: 31  AQLTLVQTYKNLVETLAKKYS-KGKSFHEDLCQVGMLGLLGAIKRYDPDVGKSFEAFAIP 89

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D++ ++ +P  +++   ++      ++ + +R P  +EIA+ L +  E 
Sbjct: 90  TIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDHLTTETQRSPRVDEIAEFLDVTEEE 149

Query: 563 VRKVLKITK--EPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V + +++ K  + +S++  I    D  T  + D +  +      +   + N +     VL
Sbjct: 150 VLETMEMGKSYQALSVDHSIEADADGSTVTILDIVGSQE-----EGYEKVNQKLMLESVL 204

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE++++ + +      + + +E G+   +++  + +++ KA+++L+
Sbjct: 205 HVLSDREKQIIELTY----IQNKSQKETGEMLGISQMHVSRLQRKAVKRLR 251


>gi|167745312|ref|ZP_02417439.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
 gi|167655033|gb|EDR99162.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
          Length = 243

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 107/239 (44%), Gaps = 53/239 (22%)

Query: 433 MVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           M+ K G  E   A+ +++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+  
Sbjct: 46  MIHKLGTAEEPEARAKLIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPA 105

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              K +TYA        +R I ++     I +++R             +NK K E + + 
Sbjct: 106 KKIKLATYA--------SRCIENE-----ILMYLRR------------NNKTKMEVSID- 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                               EP++++    D +   L D +     +   D   + + R+
Sbjct: 140 --------------------EPLNVDW---DGNELLLSDILGTDEDIIYRDLEHEVD-RK 175

Query: 612 TTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L+ RE +++ +RFGI      + T +EV     +++  I ++E K I++LK
Sbjct: 176 LLLNAMKILSDRERKIIELRFGINQKDGEEKTQKEVADLMGISQSYISRLEKKIIKRLK 234


>gi|49186821|ref|YP_030073.1| prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus
           anthracis str. Sterne]
 gi|65321304|ref|ZP_00394263.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165872143|ref|ZP_02216782.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0488]
 gi|167641041|ref|ZP_02399298.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0193]
 gi|170688784|ref|ZP_02879988.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0465]
 gi|170705857|ref|ZP_02896320.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0389]
 gi|177654265|ref|ZP_02936194.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0174]
 gi|190565820|ref|ZP_03018739.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis Tsiankovskii-I]
 gi|227813117|ref|YP_002813126.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CDC 684]
 gi|229600567|ref|YP_002868208.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0248]
 gi|254683672|ref|ZP_05147532.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CNEVA-9066]
 gi|254721508|ref|ZP_05183297.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A1055]
 gi|254736016|ref|ZP_05193722.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Western North America USA6153]
 gi|254754314|ref|ZP_05206349.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Vollum]
 gi|254757995|ref|ZP_05210022.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Australia 94]
 gi|49180748|gb|AAT56124.1| prophage LambdaBa02, RNA polymerase sigma-F factor, putative
           [Bacillus anthracis str. Sterne]
 gi|164712090|gb|EDR17628.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0488]
 gi|167511091|gb|EDR86480.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0193]
 gi|170129397|gb|EDS98261.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0389]
 gi|170667300|gb|EDT18059.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0465]
 gi|172080755|gb|EDT65836.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0174]
 gi|190562739|gb|EDV16705.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis Tsiankovskii-I]
 gi|227006745|gb|ACP16488.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CDC 684]
 gi|229264975|gb|ACQ46612.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0248]
          Length = 314

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 106/236 (44%), Gaps = 28/236 (11%)

Query: 454 RLVISVAKKYTNR---------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           RLV     KY +           L   DLIQ G +GL+ A   F   LG+KF+T+A+  +
Sbjct: 28  RLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRI 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +++ D S  IRI     ++++++     RM  K+  E   E IAK L + V  V+
Sbjct: 88  LGYIRKAVRD-SQKIRIT----NEVYEIKGKISRM--KLHDEEV-ESIAKLLEVSVRDVK 139

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              +     ISL+TP+  E   +   L + + DK     LD  I+   +   T  L++L 
Sbjct: 140 TAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTLDDVIK---KMIITAFLSTLC 196

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +E+ V  +        + T   +GK+  VT+ +I +I     +K +       LR
Sbjct: 197 SKEKFVWELH-----AKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNKHSLR 247


>gi|284431201|gb|ADB84362.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 292

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LSDII 65


>gi|224120616|ref|XP_002318375.1| predicted protein [Populus trichocarpa]
 gi|222859048|gb|EEE96595.1| predicted protein [Populus trichocarpa]
          Length = 97

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 40/64 (62%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKHP+R   L
Sbjct: 33  LDSLKPKESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHPTRVDYL 92

Query: 677 RSFL 680
           R ++
Sbjct: 93  RRYV 96


>gi|75909293|ref|YP_323589.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75703018|gb|ABA22694.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anabaena
           variabilis ATCC 29413]
          Length = 261

 Score = 56.6 bits (135), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/137 (27%), Positives = 78/137 (56%), Gaps = 3/137 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ +  LV  +A K++++  + + DL Q G  GL++A E+FD   GY FS++A+ +
Sbjct: 28  RNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGYAFSSFAVPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+S  ++IP   ++  ++  +  + +S  + R P   EIAK L + V+  
Sbjct: 88  IRGEMLHFLRDRSTLLKIPRRWQELYNEGQKIRKELSISLGRPPKDAEIAKHLKVSVQEW 147

Query: 564 R--KVLKITKEPISLET 578
           +  K+    + P+SL+ 
Sbjct: 148 QETKLAAQNRMPLSLDA 164


>gi|293401517|ref|ZP_06645660.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305155|gb|EFE46401.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 238

 Score = 56.6 bits (135), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 101/225 (44%), Gaps = 51/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E NLRLV+ +AK+Y    +   DLI  G+IGL+KA   F      K  TYA   
Sbjct: 54  ARNKLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIKAVNTFKRDKNIKLVTYA--- 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I + +R K                                   
Sbjct: 111 -----SRCIENE-----ILMFLRKK---------------------------------SR 127

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV     EP++++    D +   L D +   + +   +   Q N RE     +A+L  R
Sbjct: 128 RKVEVSFDEPLNIDY---DGNELLLSDILGTDDDIVTKEFEKQENKRELLA-AMATLKDR 183

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E ++L+MR+GI  + + T +++ K+  +++  I ++E + I+KLK
Sbjct: 184 ERQILQMRYGIE-HEELTQKDIAKRLGISQSYISRLEKRIIQKLK 227


>gi|225375611|ref|ZP_03752832.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
 gi|225212590|gb|EEG94944.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score = 56.6 bits (135), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 43/75 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+KE++E NLRLV+ +AKK+ N G+   DLI  G IGL+K    F+     K +TYA   
Sbjct: 61  ARKELIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKGINTFNPDKNIKLATYASRC 120

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 121 IENEILMYLRRNSKT 135


>gi|77918763|ref|YP_356578.1| flagellar biosynthesis protein, alternative sigma factor 28
           [Pelobacter carbinolicus DSM 2380]
 gi|77544846|gb|ABA88408.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pelobacter
           carbinolicus DSM 2380]
          Length = 255

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 111/230 (48%), Gaps = 13/230 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +++++L +V  +A++  ++   F+   D+     +GL+ AA +F   +G  F T+A 
Sbjct: 15  KDRLIKSHLHMVSFLAERMVSQVPAFMTREDISSAAMVGLVDAANRFKPSMGVLFKTFAE 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +       R    +R K  ++ +T   +  ++ R P   E+A +L M +E
Sbjct: 75  KRMRGAVLDEVRRMDWFSR---SLRQKQSRIAKTMEALEKRLGRPPEEHEMAAELEMDLE 131

Query: 562 GVRKVLKITKE--PISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             R+ L        +SL   I D  D   + D IED+N+ S ++    + L +   R + 
Sbjct: 132 SYRQALGEVSYLGCVSLHETIEDTPDGPTMLDNIEDQNSPSAVEMLENSELTQELARQID 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            LT +E  V+ + +      + + +E+ +   ++  R+ Q+ ++A+ KLK
Sbjct: 192 RLTDKERLVVSLYY----YEELSQKEIAEVLELSEGRVSQLHSQALIKLK 237


>gi|229086469|ref|ZP_04218641.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
 gi|228696786|gb|EEL49599.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
          Length = 239

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 106/227 (46%), Gaps = 54/227 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H+R             +NK + E + +             
Sbjct: 115 -----SRCIENE-----ILMHLRR------------NNKNRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSP-LDSAIQANLRETTTRVLASLT 621
                   EP++++    D +   L D +  D++ ++  L++ +    R    + L  L 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDEDIITKDLEATVD---RHLLMKALHQLN 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 186 DREKQIMELRFGLAGEEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|146164080|gb|ABQ08720.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp.
           dhakensis]
 gi|284431199|gb|ADB84361.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 293

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLR 60

Query: 181 LREII 185
           L +II
Sbjct: 61  LSDII 65


>gi|51893096|ref|YP_075787.1| sporulation sigma factor SigK [Symbiobacterium thermophilum IAM
           14863]
 gi|51856785|dbj|BAD40943.1| RNA polymerase sigma factor similar to B. subtilis SigK
           [Symbiobacterium thermophilum IAM 14863]
          Length = 236

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 89/228 (39%), Gaps = 58/228 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G +GL+KA   F    G + +TYA   
Sbjct: 52  ARAVLIERNLRLVAHIVKKFDNTGEDVDDLISIGTVGLIKAIGTFKPERGTRLATYAARC 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +H+R                                     
Sbjct: 112 IENEIL-------------MHLRS------------------------------------ 122

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLAS 619
              LK  +  +SL  PIG   + +   L D +     V P    +   L E+  R  L  
Sbjct: 123 ---LKRVRGEVSLYDPIGVDREGNEITLIDVLGSDPDVVP--DLVGKRLDESKLREKLKK 177

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  +E +VL +R+GI      T  E+ +   ++R  + +IE KA+ KL
Sbjct: 178 LGGKERQVLELRYGIAGGPRKTQREIARMLGISRSYVSRIEKKAVMKL 225


>gi|239907027|ref|YP_002953768.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
 gi|239796893|dbj|BAH75882.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
          Length = 264

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 50/203 (24%), Positives = 95/203 (46%), Gaps = 10/203 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G +GL++A  +F   LG KF TYA   +K A+   +       R     R ++  
Sbjct: 66  ELISAGAMGLLEALGRFRPELGIKFETYAESRIKGAMLDDLRRMDWFSR---GQRQRVRT 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +   +RR+ N      + E++A+   +    V   L+  +  + L     D  T ++  +
Sbjct: 123 LEEASRRIENDSGGPASLEQLAEATGLTEREVSMGLEALQNQLCLSL---DAITENISSY 179

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            +++    P  SA    L +    ++  LTPRE+ VL + +G  +N   T E +G    +
Sbjct: 180 QKNQLENEPYKSAEFKELVDKLASLIDDLTPREKLVLSLYYGEELNMRETSEVMG----I 235

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           T  R+ Q+ ++A+ +L+   +S+
Sbjct: 236 TEGRVSQLHSQALARLRQKFKSQ 258


>gi|282929291|ref|ZP_06336862.1| RNA polymerase sigma-B factor [Staphylococcus aureus A10102]
 gi|282589101|gb|EFB94200.1| RNA polymerase sigma-B factor [Staphylococcus aureus A10102]
          Length = 256

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 115/232 (49%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ +  +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSAHVPRRIKEIGPRIKKVSDELTAELERSPSISEIANRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|47168808|pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168810|pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168812|pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168814|pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47169132|pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
          Length = 239

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 111/234 (47%), Gaps = 21/234 (8%)

Query: 443 IAKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           I ++E++   L LV ++A   KK+    +   DLI  G IGL+KA +        +   Y
Sbjct: 12  IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
               +K AI   +       R    +R+K  ++     ++  K+ REPT EE+AK+L + 
Sbjct: 72  IKLRIKGAIYDYLRSLDFGSR---QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIS 128

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTTRV- 616
            E + K L    + I+    +  E+     DF  D + + P  + ++  +  RE T +V 
Sbjct: 129 TEELFKTL----DKINFSYILSLEEV--FRDFARDYSELIPSSTNVEEEVIKRELTEKVK 182

Query: 617 --LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ L  RE+ V+++ F      +   +EV K    +  R+ Q++AKA+ +L+
Sbjct: 183 EAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLR 232


>gi|157959887|ref|YP_001499921.1| flagellar biosynthesis sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157844887|gb|ABV85386.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella pealeana
           ATCC 700345]
          Length = 240

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 112/232 (48%), Gaps = 23/232 (9%)

Query: 443 IAKKEMVEANLRLV---ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A+ ++++  L LV   +S  + +    L   D+ Q G + L+++A ++       F ++
Sbjct: 20  LAESQVMKQYLPLVKRSVSQLRSHCGIALAIEDMEQIGMMALLESARRYPGEYDNGFLSF 79

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++ AI   +  Q    R PV  R + H++    R+++  +KREPT  E+A+ + + 
Sbjct: 80  AGQRIRGAILDELRRQDWRPR-PV--RQQAHELNDMVRKLTRSLKREPTDLEVAQSMGLS 136

Query: 560 -VEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            VE   ++     E + SL+  IGD      G   EDK+     D   Q + +ET  + +
Sbjct: 137 QVEYRERLFASQSESMRSLDELIGD------GGHFEDKS-----DMLEQFSTKETLFQAI 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             L  RE+ +L + +   +N    L+E+     +T  RI Q+   A+++L+ 
Sbjct: 186 LKLNKREQIILSLYYQHELN----LKEIAATLGLTETRICQLHKHAVKQLQQ 233


>gi|160880422|ref|YP_001559390.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160429088|gb|ABX42651.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 207

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 101/230 (43%), Gaps = 61/230 (26%)

Query: 438 ECEAS--IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +C+A   +A+  ++E NLRLV  + KKY     +  DLI  G IGL+K+ + FD   G +
Sbjct: 19  QCKAGNKVARDTLIERNLRLVAHIVKKYNTPDRETDDLISIGTIGLIKSIDTFDSTKGIR 78

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            +TYA        +R I ++             +  ++R+ ++ + +             
Sbjct: 79  LATYA--------SRCIDNE-------------LLMMLRSGKKQARE------------- 104

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIE--DKNAVSPLDSAIQANLR 610
                             + L  PIG +   +  +L D IE  D++ V   +  IQ N++
Sbjct: 105 ------------------VYLYEPIGSDKEGNEINLLDVIESTDEDIVDIFE--IQENIK 144

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
              T +  +L  RE+ ++ MR+G+    + T  E+  +  ++R  + +IE
Sbjct: 145 RLYTFLNTALNEREQEIIIMRYGLSGEKEITQREIADKLGISRSYVSRIE 194


>gi|146296307|ref|YP_001180078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409883|gb|ABP66887.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 245

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 107/232 (46%), Gaps = 40/232 (17%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           ++L+      Y    +++ DL+  G++GL+ A EK+D   G KF TYA   ++ AI   +
Sbjct: 30  VKLIAGRMAMYFGGNVEYDDLVSYGSLGLLDAIEKYDSQKGVKFETYAYTRIRGAIIDCV 89

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
             Q     +P  +R K  +V +    +  + K  PT EE+AK+  + +   +K+    KE
Sbjct: 90  RSQDW---VPRSIRQKAKEVEKAYIEIEKEGKI-PTDEEVAKRTGLTLSEFQKL----KE 141

Query: 573 PIS--------------LETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            IS               E  IG  ++  SH   FIE++             L+E   + 
Sbjct: 142 KISSGMILSLEGFLEQNYEIKIGGLEDFVSHPEVFIENE------------ELKEVLRQE 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L+  E+ V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 190 IENLSENEKMVILLYY----FEELSIKEIAKILGVSESRVSQLHTRALLKLR 237


>gi|225574950|ref|ZP_03783560.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037797|gb|EEG48043.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
          Length = 225

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 103/232 (44%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 42  AKALLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPVKKIKLATYA--- 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR S                       
Sbjct: 99  -----SRCIENE----------------ILMYLRRNSK---------------------- 115

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVS-PLDSAIQANLRETTTRVLA 618
                 TK  +S++ P+    D +   L D +  D++ +S  ++  ++   R+     ++
Sbjct: 116 ------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDVISRGIEDEVE---RDLLGNAIS 166

Query: 619 SLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+PRE+ ++ +RFG+      + T +EV     +++  I ++E + +++LK
Sbjct: 167 KLSPREQTIVTLRFGLHSVDGKEKTQKEVADLLGISQSYISRLEKRIMKRLK 218


>gi|304438454|ref|ZP_07398394.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368537|gb|EFM22222.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 256

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/201 (23%), Positives = 91/201 (45%), Gaps = 21/201 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A E+++   G KF TYA   V+ AI   +  +     IPV +R  I +
Sbjct: 63  DLLSSGFFGLLDAIERYELTRGNKFETYAGVRVRGAILDHLRAKDW---IPVSVRQNIKR 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             +    +   + R  T +E+A+++ + +E + +          LE+ +       L ++
Sbjct: 120 YEKAVAHLEGTLGRTATDQELAEEMDLSIEELHR----------LESQVSAATVIPLEEY 169

Query: 592 IEDKNAVS----PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +      S    P++ A    ++ET    +  L  +E  V+ + +   M    TL+E+  
Sbjct: 170 LRTDAQASLEDGPVEHAEWTEIKETLAAAIEKLPEKERTVVALYYYDEM----TLKEIAA 225

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+  KAI +++
Sbjct: 226 VLHLSEARISQLHTKAIFRMR 246


>gi|62550939|emb|CAI79314.1| putative RNA polymerase sigma-32 [Aeromonas caviae]
          Length = 100

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/83 (39%), Positives = 51/83 (61%), Gaps = 8/83 (9%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N I  +S E    ++E      + + G+ EA+   +++V ++LR V+ VAK Y+  GL  
Sbjct: 25  NSIPVLSAEEKRELAE-----RLQQDGDLEAA---RQLVMSHLRFVVHVAKSYSGYGLPQ 76

Query: 471 LDLIQEGNIGLMKAAEKFDWCLG 493
            DL+QEGNIGLMKA ++FD  +G
Sbjct: 77  ADLVQEGNIGLMKAVKRFDPSVG 99


>gi|238924602|ref|YP_002938118.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
 gi|238876277|gb|ACR75984.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
          Length = 244

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 104/232 (44%), Gaps = 62/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK+++E NLRLV+ +AKK+ N G+   DLI  G IGL+K    F+     K +TYA   
Sbjct: 61  AKKQLIEHNLRLVVYLAKKFENTGVCVEDLISIGTIGLIKGINTFNPEKKIKLATYA--- 117

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                 +    R +N++K E                 
Sbjct: 118 -----SRCIENE-----------------ILMYLRRNNRVKLE----------------- 138

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSP-LDSAIQANLRETTTRVLA 618
                     +S + P+    D +   L D +  D++ +   L++ ++ +L +   + + 
Sbjct: 139 ----------VSFDEPLNTDWDGNELLLSDILGTDEDVIYKDLETEVEISLLK---KAML 185

Query: 619 SLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SL  RE +++ +RFG+    N + T +EV     +++  I ++E K + +LK
Sbjct: 186 SLNERERQIIELRFGVNRVENKELTQKEVADILGISQSYISRLEKKIMERLK 237


>gi|312876364|ref|ZP_07736349.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796858|gb|EFR13202.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 244

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 98/232 (42%), Gaps = 66/232 (28%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK ++E NLRLV+ +AK++ N  +   DL+  G IGL+KA   ++     K +TYA   +
Sbjct: 64  KKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGLIKAINTYNPNKNIKLATYASKCI 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +                        ++++   RR SN            KKL M ++   
Sbjct: 124 E------------------------NEILMFLRRNSN------------KKLEMSID--- 144

Query: 565 KVLKITKEPIS--------LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                  EP++        L + +   DT  + + IE+      L  AIQ          
Sbjct: 145 -------EPLNVDWDGNELLLSEVLGTDTEEIYNRIENNVEKEALLQAIQ---------- 187

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  RE++++ +R G G + + T +EV     +++  I ++E K I +LK
Sbjct: 188 --KLPSREKKIVELRSGFGDDGEKTQKEVADMLGISQSYISRLEKKIITRLK 237


>gi|255021389|ref|ZP_05293437.1| RNA polymerase sigma factor for flagellar operon [Acidithiobacillus
           caldus ATCC 51756]
 gi|254969252|gb|EET26766.1| RNA polymerase sigma factor for flagellar operon [Acidithiobacillus
           caldus ATCC 51756]
          Length = 241

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 114/237 (48%), Gaps = 30/237 (12%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF------DWCLGYK 495
           +  +V   + LV  +A++   R    +   DLIQ G IGL+   E++      D      
Sbjct: 13  RSALVARYVPLVQRIAQRLRARLPANVDLGDLIQAGLIGLLDVLEQYPEPDDSD-----A 67

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  YA   ++ ++   + +Q     +P   R K  +V R   ++  ++ R P+ +E+AK 
Sbjct: 68  FLRYATLRIRGSMIDELREQDW---LPRRARAKEQQVSRAMAQLEQQLGRPPSDQEVAKH 124

Query: 556 LAMPVEGVRKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQA--NLRE 611
           L   ++  +K +  +  + + LE    D D S +G ++ D++A +S +  +++   +L+E
Sbjct: 125 LGWDLDDYQKAIADSGGQLVYLEDLAADND-SFVGQYLRDRHADISEVLGSLEFDRHLQE 183

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TR    L  RE  VL + +      + TL E+G+   VT  R+ QI  +A+ +L+
Sbjct: 184 AITR----LPERERLVLSLYY----REELTLREIGEVLEVTESRVSQIVRQAVLRLR 232


>gi|120554892|ref|YP_959243.1| FliA/WhiG family RNA polymerase sigma factor [Marinobacter
           aquaeolei VT8]
 gi|120324741|gb|ABM19056.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Marinobacter
           aquaeolei VT8]
          Length = 247

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 105/247 (42%), Gaps = 58/247 (23%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E +  LV  +A     R    +Q  DL+Q G IGL++AA+++    G  F TYA    
Sbjct: 21  LIEEHAPLVKKIALHLMARLPPSVQLEDLMQAGMIGLLEAAQRYSSGKGATFETYA---- 76

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------REPTPE 550
                         IRI   M D+I K       V R ARR+++ IK       RE    
Sbjct: 77  -------------GIRIRGAMVDEIRKGDWVPRSVHRNARRIASAIKQVEDRTGREAQDA 123

Query: 551 EIAKKLAMPVEGVR---------KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           E+A++L + ++            ++  + +   S E PI + + S            +PL
Sbjct: 124 EVAEELGIGLDEYHASLADANSGRIFSLDELNESGELPIEEAEASD-----------NPL 172

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D       + +    +  L  RE+ VL + +   +N    L+E+G    V+  R+ QI +
Sbjct: 173 DGIASGAFQRSLADAIEQLPEREKLVLSLYYQEELN----LKEIGAVLGVSESRVSQIHS 228

Query: 662 KAIRKLK 668
           +A  +L+
Sbjct: 229 QAALRLR 235


>gi|150021309|ref|YP_001306663.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
 gi|149793830|gb|ABR31278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
          Length = 226

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 115/235 (48%), Gaps = 24/235 (10%)

Query: 443 IAKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           I K+++++  L  +  +A   KK     ++  DLIQEG IGL++A E+++   G K  +Y
Sbjct: 2   IDKEKIIQEYLPYIKRIAYDLKKNLPHNIEIDDLIQEGLIGLLQAIERYNPKKGAKLRSY 61

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            +  VK A+   +        +P ++R  +  V     +M N  K      EI+K   +P
Sbjct: 62  ILTRVKGAMYDYLRKIDW---MPKNLRHDVKVVEDAISKMENSGKI-IDFNEISKITNLP 117

Query: 560 VEGVRKVLK--ITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +E V++     + K+ + L+  + ++    +T    D+       +P ++A +  ++E  
Sbjct: 118 LENVKRAYNEMVRKQFLMLDDYLTEDLEINETISSSDY-------TPEETAFKEIIKEEL 170

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +  L  +E+ +L +RF      + +L+E+GK   +T  R+ QI +  I KLK
Sbjct: 171 KKAINKLDEKEKIILNLRF----EHELSLKEIGKILNLTESRVSQILSSIILKLK 221


>gi|83589703|ref|YP_429712.1| sporulation sigma factor SigE [Moorella thermoacetica ATCC 39073]
 gi|83572617|gb|ABC19169.1| RNA polymerase, sigma 29 subunit, SigE [Moorella thermoacetica ATCC
           39073]
          Length = 243

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 110/238 (46%), Gaps = 55/238 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R  + +A++ KK ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 52  LLRLEDGDAAV-KKVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPKK 110

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++     I +++R             +NK + E + +  
Sbjct: 111 RIKLATYA--------SRCIENE-----ILMYLRR------------NNKTRAEVSFD-- 143

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLR 610
                              EP++++    D +   L D +   N +    ++  +   L 
Sbjct: 144 -------------------EPLNID---WDGNELLLSDVLGTDNDIIYKSIEEEVDHKLL 181

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   R L+S   RE +++  RFG+    + T +EV     +++  I ++E + I++L+
Sbjct: 182 QLAMRKLSS---RERKIMEFRFGLLDGVEKTQKEVADILGISQSYISRLEKRIIKRLR 236


>gi|258514023|ref|YP_003190245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777728|gb|ACV61622.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 249

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/233 (23%), Positives = 105/233 (45%), Gaps = 14/233 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+++++   L LV  ++ +   R   G+ + DL   G +GL+++ EKF+   G  F T+A
Sbjct: 18  AREKLILMYLPLVKHLSGRLAVRLPIGISYEDLEGYGVVGLIESIEKFNPAKGVSFETFA 77

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ AI   I +      +P  +  K   V     R+        T E++A  L + +
Sbjct: 78  YRRIRGAI---IDEVRKLYWVPRTLWQKFQAVNAERERLRRINGDNVTDEQVAASLNISI 134

Query: 561 EGVRKVL----KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             + K      ++    +       D D+  LG+ I D N+  PLD   + + R      
Sbjct: 135 AELHKTSNCYNQLNMNSLDEVLTSSDGDSVRLGNLIPDPNSPDPLDVVEEQDGRRILAEA 194

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + SL  ++  V+ + +        TL+E+G+   V+  R+ Q+ A+A+ +L+ 
Sbjct: 195 VNSLNEKDRLVMALYY----QERLTLKEIGQVLEVSESRVCQLHARAMSRLRQ 243


>gi|302670750|ref|YP_003830710.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
 gi|302395223|gb|ADL34128.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
          Length = 257

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 100/224 (44%), Gaps = 21/224 (9%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           ++LV      Y    +++ DL+  G  GL+ A +KFD     KF TYA   ++ AI   I
Sbjct: 33  VKLVAGRLSMYLGFNVEYDDLVGYGIFGLIDAIDKFDLMKDVKFETYASLRIRGAILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---VEGVRKVLKI 569
                  R     + KI   +R   R    +    T  EIA K+ +        +  +K+
Sbjct: 93  RKMDWIPRTIRQRQKKIEAAIREIERDGGHV---ATDAEIAAKMQISEDEYANWQNQMKV 149

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKN-----AVSPLDSAIQANLRETTTRVLASLTPRE 624
           T   +SL     +E      D  ED N      V P ++  +  L++   + L SLT +E
Sbjct: 150 TG-VVSL-----NEFMDQGADIPEDSNNRSSGFVKPEEAIEKEELKKMLAQSLESLTDKE 203

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++V+ + +      + TL+E+ +   V+  R+ Q+  KA++K++
Sbjct: 204 KKVILLYY----YEELTLKEISQVLEVSESRVSQLHTKALQKMR 243


>gi|15606452|ref|NP_213832.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
 gi|2983663|gb|AAC07229.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
          Length = 236

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 111/235 (47%), Gaps = 21/235 (8%)

Query: 443 IAKKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           I ++E++   L LV ++A   KK+    +   DLI  G IGL+KA +        +   Y
Sbjct: 9   IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 68

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
               +K AI   +       R    +R+K  ++     ++  K+ REPT EE+AK+L + 
Sbjct: 69  IKLRIKGAIYDYLRSLDFGSR---QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIS 125

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTTRV- 616
            E + K L    + I+    +  E+     DF  D + + P  + ++  +  RE T +V 
Sbjct: 126 TEELFKTL----DKINFSYILSLEEV--FRDFARDYSELIPSSTNVEEEVIKRELTEKVK 179

Query: 617 --LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ L  RE+ V+++ F      +   +EV K    +  R+ Q++AKA+ +L+ 
Sbjct: 180 EAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLRE 230


>gi|17227773|ref|NP_484321.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17135255|dbj|BAB77801.1| RNA polymerase sigma-37 factor [Nostoc sp. PCC 7120]
          Length = 261

 Score = 56.2 bits (134), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/137 (27%), Positives = 77/137 (56%), Gaps = 3/137 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +V+ +  LV  +A K++++  + + DL Q G  GL++A E+FD   GY FS++A+ +
Sbjct: 28  RNRLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGYAFSSFAVPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+S  ++IP   ++  ++  +  + +S  + R P   EIAK L + V+  
Sbjct: 88  IRGEMLHFLRDRSTLLKIPRRWQELYNEGQKVRKELSISLGRPPKDAEIAKYLKVSVQEW 147

Query: 564 R--KVLKITKEPISLET 578
           +  K+    + P+SL+ 
Sbjct: 148 QETKLAAQNRMPLSLDA 164


>gi|150390631|ref|YP_001320680.1| sporulation sigma factor SigE [Alkaliphilus metalliredigens QYMF]
 gi|149950493|gb|ABR49021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 244

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 109/236 (46%), Gaps = 50/236 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K + + S  +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 52  LINKLKNDESTVRTILIERNLRLVVYIARKFENTGIGVEDLISIGTIGLIKAVNTFNPDK 111

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++     I +++R             ++K+K E + +E 
Sbjct: 112 NIKLATYA--------SRCIENE-----ILMYLRR------------NSKVKMEVSFDE- 145

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
              L +  +G   +L          + I   D   +  F+E++     +D       +E 
Sbjct: 146 --PLNIDWDGNELLL----------SDILGTDNDIIYKFLEEE-----VD-------KEL 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  L+ RE +++ +RFG+    + T +EV     +++  I ++E + I +LK
Sbjct: 182 LKFALKKLSKRERKIMELRFGLQTGKERTQKEVADLLGISQSYISRLEKRIIIRLK 237


>gi|255525679|ref|ZP_05392612.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296185437|ref|ZP_06853847.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
 gi|255510665|gb|EET86972.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296050271|gb|EFG89695.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
          Length = 235

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 98/221 (44%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVNVEDLVSVGTIGLIKAVNTFDPSKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +  E    L +  +G   +L
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEISFYE---PLNIDWDGNELLL 149

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   D   + + IED+     L  A++             L  RE+ +
Sbjct: 150 ----------SDILGTDNDVVYNLIEDEVDKQLLMVAMK------------KLNDREKEI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T +EV     +++  I ++E + I++LK
Sbjct: 188 VNLRFGLNGQGEKTQKEVADMLGISQSYISRLEKRIIKRLK 228


>gi|229541193|ref|ZP_04430253.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
 gi|229325613|gb|EEN91288.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
          Length = 239

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/226 (23%), Positives = 106/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NK++ E + +             
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKLRSEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  ++AN+ ++     L  L+ 
Sbjct: 140 --------EPLNID---WDGNELLLSDVLGTDDDIITRD--LEANVDKKLLYSALHRLSD 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLKGQEEKTQKDVADMLGISQSYISRLEKRIIKRLR 232


>gi|37781579|gb|AAP42789.1| SigB [Staphylococcus aureus]
          Length = 256

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 51/232 (21%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  ++ + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKEGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|117926317|ref|YP_866934.1| FliA/WhiG family RNA polymerase sigma factor [Magnetococcus sp.
           MC-1]
 gi|117610073|gb|ABK45528.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Magnetococcus sp.
           MC-1]
          Length = 260

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/255 (22%), Positives = 116/255 (45%), Gaps = 25/255 (9%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL---IQEGNIGLMKAAEKFDWCLG 493
            E   S++++E++     LV  VA + + +  Q +DL    Q G +GL+ A  KFD   G
Sbjct: 18  AEAWKSLSREEIILKYAPLVRYVAGRISMKLPQSVDLDDLYQVGVMGLIDAVSKFDPDRG 77

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF TYA + ++ AI   +        +P  +R    ++     ++  K  R     E+A
Sbjct: 78  IKFQTYAEFRIRGAILDEL---RAIDWVPRQLRQNASQMQEAYNQLEAKFGRPAEDVEVA 134

Query: 554 KKLAMP-------VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           + L +        ++ VR +  ++ E I    P  D++   + + + D +   P+++   
Sbjct: 135 EHLGISLNEYHEQIDQVRGISIVSFEDIR---PNNDDEEWDVLEVLADPSVQDPVEAIGL 191

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR      + +L  +E  V+ + +      + T+ E+G+   +T  RI Q+ +KA  +
Sbjct: 192 MELRHAMADAIETLPEKERLVVTLYYF----EELTMSEIGEVLGLTESRISQLHSKAALR 247

Query: 667 LKHPSRSKKLRSFLD 681
           ++      +++ FL+
Sbjct: 248 MR-----ARIKRFLN 257


>gi|322432980|ref|YP_004210229.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidobacterium sp.
           MP5ACTX9]
 gi|321165207|gb|ADW70911.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidobacterium sp.
           MP5ACTX9]
          Length = 278

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 108/235 (45%), Gaps = 23/235 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++   L  V  +A +   R  Q +   DL+  G IGL++A   FD     +F T+A 
Sbjct: 21  RNELILQELPQVHYIASRMMERLPQHVELGDLVHAGVIGLLEAYRTFDNTKNAQFKTFAK 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + +K AI  S+       R    +R K  ++     ++   + R P+ EEI+ +L + + 
Sbjct: 81  FRIKGAILDSLRALDWGSR---GIRRKAREIAEATLKLEGALGRSPSKEEISAELGLTIA 137

Query: 562 GVRKV------LKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETT 613
            + ++      L +  + +   T   + +T+H  D IE   +   +P +   +A  +   
Sbjct: 138 DLNEIQTQLNGLHLVGQEV---TSSFEGETAH--DLIESAPSSWDNPFEMYAKAESKAHL 192

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R ++ L+ RE+ +L + +      + T++EV +   +   R+ QI +  + KLK
Sbjct: 193 IRAISELSEREQLILSLYY----REELTMKEVAEVVGLAVSRVSQIHSAVLAKLK 243


>gi|326796449|ref|YP_004314269.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas
           mediterranea MMB-1]
 gi|326547213|gb|ADZ92433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas
           mediterranea MMB-1]
          Length = 228

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/199 (23%), Positives = 92/199 (46%), Gaps = 11/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL++A ++F+   G  F TYA   ++ AI   +         P  +R     
Sbjct: 31  DLTQAGMIGLIEAYKRFESTKGASFETYAGIRIRGAIMDEMRKSDWA---PRSVRRNGRA 87

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V    + +  K+ R+ T  E+++ + + V+   ++++  ++ +  S E  +  E  S+  
Sbjct: 88  VTEAIKELEGKLGRDVTDNEVSEHMGISVDEYHEIMRSSMSTQLFSYEEMLESEHGSNEI 147

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           +   D +   P D   +   ++     +  L  RE+ VL + +    N +  L+E+G   
Sbjct: 148 NIESDDS--QPYDVVEEGGFQKQLAVEIDKLPEREKLVLSLYY----NEELNLKEIGAVL 201

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+  R+ QI ++A  +L+
Sbjct: 202 GVSESRVSQIHSQAAMRLR 220


>gi|307109683|gb|EFN57920.1| hypothetical protein CHLNCDRAFT_141990 [Chlorella variabilis]
          Length = 357

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/223 (24%), Positives = 105/223 (47%), Gaps = 22/223 (9%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S +E R +      G+  A  A   +V+AN  LV  +A+++  +GL   DL+ EG + L 
Sbjct: 124 SAAEQRELARAAGAGDERAVAA---LVDANRALVHFLARRFLGKGLAREDLVSEGMLALE 180

Query: 483 KAAEKFDWCLG--YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           +AA ++    G    F T+A   +   ++R++  QS  +R+PVH    + +V +    ++
Sbjct: 181 RAARRYRPQPGRDASFGTFAAATILNGMSRALHTQSRDVRLPVHHFRDMARVRQATLELA 240

Query: 541 NKIKREP-TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD--------F 591
            +  R+P     + + +   V G   ++++  +   +  P+ D+D +  G          
Sbjct: 241 TEQLRQPDYTLHLLRAMGSQV-GQSPLMQVLDQ--EMAAPM-DQDPTQQGGVSLDGLEVL 296

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           +ED+ A       I+A LR      LA L P++  V+ +R G+
Sbjct: 297 LEDEVAAEERSQLIEAELRS----CLARLEPQQVSVVELRHGL 335


>gi|254437394|ref|ZP_05050888.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198252840|gb|EDY77154.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 207

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 95/200 (47%), Gaps = 12/200 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL++AA+++    G  F +YA+  ++ AI   +   +   R  +     +  
Sbjct: 9   DLLQVGLIGLIEAAQRYTRQEGVSFESYAVLRIRGAIYDYLRKNTNLGRKAILTSKAVKA 68

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            + +   +S K+ REPT  E+A+ L+M ++ + K  +      S    + DE   H   F
Sbjct: 69  ALAS---LSQKLGREPTQPELAEALSMSLQELSKWAQNVNS--SYHNSLQDEYDEHSLWF 123

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             ++     L    +  L++     L SL  RE  VL++ +   +N    L E+     V
Sbjct: 124 SSNEPTTEHLVD--RGRLKDALLAALVSLPKREALVLQLYYVEELN----LYEIAAVLEV 177

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           T  R+ Q+++ A +K++ PS
Sbjct: 178 TPGRVSQLKSAAFKKMQ-PS 196


>gi|153932837|ref|YP_001384784.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|170755199|ref|YP_001782157.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
 gi|152928881|gb|ABS34381.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|169120411|gb|ACA44247.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
          Length = 144

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/108 (34%), Positives = 61/108 (56%), Gaps = 4/108 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E ++ +  ++KG+   ++AK  +VE NLRLV  + KKY+  G    DLI  G +GL
Sbjct: 31  LSDEEEKYYLDRLKKGD---ALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           +KA + FD   G + +TYA   ++  I   I +   T +  V+++D I
Sbjct: 88  IKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT-KGEVYLQDPI 134


>gi|114566372|ref|YP_753526.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337307|gb|ABI68155.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 240

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/234 (22%), Positives = 103/234 (44%), Gaps = 60/234 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +AKK+ N G+   DL+  G IGL+KA   F+     K +TYA   
Sbjct: 59  VKATLIEHNLRLVVYIAKKFENTGINIEDLVSIGTIGLIKAVNTFEPKKNIKLATYA--- 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R          R + N+++                   
Sbjct: 116 -----SRCIENE-----ILMYLR----------RNIKNRVE------------------- 136

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKN--AVSPLDSAIQANLRETTTRVLA 618
                     ISL+ P+    D +   L D +  +N      ++  ++ +L     + + 
Sbjct: 137 ----------ISLDEPLNVDWDGNELLLSDVLGTENDMIYKQIEGEVEKSL---LWKAMH 183

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  RE+ ++++RFG+    + T +EV     +++  I ++E + +++L+   R
Sbjct: 184 KLNNREKTIIQLRFGLADGDEKTQKEVADILGISQSYISRLEKRILKRLQREIR 237


>gi|169831144|ref|YP_001717126.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169637988|gb|ACA59494.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 256

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 98/229 (42%), Gaps = 60/229 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E NLRLV  + KKY + G    DLI  G IGL+KA   F+   G + +TYA   
Sbjct: 73  ARNILTERNLRLVAHIIKKYDSTGEDTDDLISIGTIGLIKAINTFNPHKGARLATYAARC 132

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +H+R                                     
Sbjct: 133 IENEIL-------------MHLR------------------------------------- 142

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP--LDSAIQANLRETTTRVL---A 618
              +K T+  +SL+ PIG +   +    I D    +P  ++  ++ +  +   R+L    
Sbjct: 143 --TVKKTRFEVSLQDPIGVDKEGNEITLI-DILGTNPEVVEDKVETHFEQR--RLLEKMH 197

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+ RE++VL +RFG+  +T  T +E+ +   ++R  + +IE +A+ KL
Sbjct: 198 KLSRREKKVLALRFGLVDDTRQTQQEIAQDLGISRSYVSRIEKRALNKL 246


>gi|168213645|ref|ZP_02639270.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|170714810|gb|EDT26992.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
          Length = 227

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 105/249 (42%), Gaps = 78/249 (31%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD--WCLGYKFST 498
           A  +++E N +L+  +A K+ +     ++F DL+QEG IGL+ A  K+D  +    KF T
Sbjct: 17  ALDKLLENNDKLIYKIANKFYSDKTSSIEFDDLLQEGRIGLILACSKYDIEYIKRTKFIT 76

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA +W+ Q I R I   S                               T EE       
Sbjct: 77  YAFYWIYQKIHRFITKYS-------------------------------TNEE------- 98

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI----------EDKNAVSPLDSAIQAN 608
                          ISL TP+ +E+T  L + I          E+K  +S L   ++A 
Sbjct: 99  ---------------ISLNTPVSEENTDELINSIESHSDEINDREEKLYLSELRLELEAV 143

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + +  T     L  RE  +L++ +    +TD   +E++   F  +   I+  +A+AIRKL
Sbjct: 144 MDKHNT-----LNERE--ILKLYY--CWDTDELNIEQIADIFETSSSDIKNTKARAIRKL 194

Query: 668 KHPSRSKKL 676
           ++    KK+
Sbjct: 195 RNSMWFKKV 203


>gi|78044685|ref|YP_360875.1| sporulation sigma factor SigE [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996800|gb|ABB15699.1| RNA polymerase sigma-E factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 237

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 104/225 (46%), Gaps = 50/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F+     K +TYA   
Sbjct: 56  AKSTLIERNLRLVVYIARKFENTGVNIEDLVSIGTIGLIKAVNTFNPEKKIKLATYA--- 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             ++KI+ E + +E    L +  +G 
Sbjct: 113 -----SRCIENE-----ILMYLRR------------NSKIRLEVSFDE---PLNVDWDG- 146

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G E     GD I        ++  ++  L +     L+ L  R
Sbjct: 147 --------NELLLSDVLGTE-----GDII-----YKVMEDEVEKKLLKVA---LSKLNQR 185

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E +++ +RFG+    + T +EV     +++  I ++E K +++LK
Sbjct: 186 ERKIMELRFGLTDGYERTQKEVADLLGISQSYISRLEKKILKRLK 230


>gi|325528539|gb|EGD05649.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. TJI49]
          Length = 115

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/114 (29%), Positives = 61/114 (53%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           M+ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D         +  + 
Sbjct: 1   MLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDEPVASQPFAAAPAA 60

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           D+   A +    L         ++ DP+ +Y+R M ++ LL+RE EI +A+ IE
Sbjct: 61  DVDRDALDEGRTLLGDLARGASASTDPLALYMRRMHAVPLLTREDEIVLAREIE 114


>gi|169351192|ref|ZP_02868130.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
 gi|169292254|gb|EDS74387.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
          Length = 231

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 99/232 (42%), Gaps = 61/232 (26%)

Query: 444 AKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV+ VAK+Y TN+     DLI  G IGL+KA   F      K +TYA  
Sbjct: 47  ARDLLIEHNLRLVVYVAKRYDTNQNGGIEDLISIGTIGLVKAINTFKTDKNIKLATYASR 106

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++  I   +                         R +NK++ E                
Sbjct: 107 CIENEILMFL-------------------------RKNNKLRHE---------------- 125

Query: 563 VRKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLA 618
                      ISL+ P+    D +   L D I  D + V   +   Q++ R        
Sbjct: 126 -----------ISLDEPLNIDYDGNELLLSDIIGTDSDIVK--NELEQSDQRTMFYEAFK 172

Query: 619 SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L+ RE+ +L +R+G+ MN D  T ++V K   +++  I ++E K I+KL++
Sbjct: 173 DLSKREKEILMLRYGL-MNYDELTQKDVAKMMGISQSYISRLEKKIIKKLRN 223


>gi|160880817|ref|YP_001559785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
 gi|160429483|gb|ABX43046.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
          Length = 254

 Score = 55.8 bits (133), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 103/222 (46%), Gaps = 12/222 (5%)

Query: 451 ANL-RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           ANL ++V      Y    +++ DL+  G  GL+ A +KFD   G KF TYA   ++ AI 
Sbjct: 30  ANLVKIVAGRLSIYLGYNVEYDDLVGYGTFGLIDAIDKFDCEKGAKFETYASLRIRGAIL 89

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
             I        IP  +R K  ++    +++     R+ T EE+AK+L +  E +      
Sbjct: 90  DQIRKMDW---IPRTLRQKQKRLDAAYQKLETMYGRQATDEEVAKELEITTEELETWQNQ 146

Query: 570 TK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           TK    +SL+  +  E      + I  ++   P     +  L+    + L  LT +E++V
Sbjct: 147 TKISNLVSLDEYM--EQGEVKVESIASEDYAQPEKVMEKQELKAMLVKALEYLTEKEKKV 204

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + + +      D TL+E+     V+  RI Q+  KA++K++ 
Sbjct: 205 IVLYY----YEDLTLKEISAVLEVSESRISQLHTKALQKMRQ 242


>gi|326384337|ref|ZP_08206018.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196935|gb|EGD54128.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 215

 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 82/184 (44%), Gaps = 8/184 (4%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A L L   +A++Y  RG  F DL Q   +GL+ A ++FD   G  F ++A+  V   + R
Sbjct: 2   ACLPLAKHIAQRYRERGEAFDDLEQVARLGLVHAVDRFDPTQGTDFLSFAIPTVMGEVKR 61

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPV-EGVRKVLK 568
              D S +IR+P    +   ++     +   K  R P   E+AK L   P      +   
Sbjct: 62  HFRDHSASIRMPRSAGELRSRIRLAEEQFEQKHGRSPDDTEVAKILGETPTAVSRARAAA 121

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I +  +SL+    D++ + L     D    + +D A+   LR    R    L  R+ ++L
Sbjct: 122 IAQASVSLDGSGSDDERALLDVLGSDDPGYAHVDRAL--ALRPAVRR----LPERDRKIL 175

Query: 629 RMRF 632
            MRF
Sbjct: 176 GMRF 179


>gi|158339684|ref|YP_001520691.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158309925|gb|ABW31541.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 400

 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 14/140 (10%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++RK +     +   ++  ++RLV  +AK+Y        DLIQEG +G+  A  KFD   
Sbjct: 38  LIRKAKLGHETSLSWLMIGHVRLVSKLAKQYAWTLDDAQDLIQEGMLGIRHAVRKFDSTK 97

Query: 493 GYKFSTYAMWWVKQAITR-SIADQSCTIRIP----VHMRDKIHKVVRTARRMSNKIKREP 547
           G KFSTYA  W++  I R    ++   +R+P    VH+ D+++       R+ N+   + 
Sbjct: 98  GCKFSTYARGWIRGYIRRFCYKNRPKQLRLPEKKQVHL-DRVY-------RLQNQFP-DA 148

Query: 548 TPEEIAKKLAMPVEGVRKVL 567
             EEIA+K  + +E +  +L
Sbjct: 149 NLEEIAQKANLKLEYIEDLL 168


>gi|87310296|ref|ZP_01092427.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87287045|gb|EAQ78948.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 287

 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 47/73 (64%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A+  ++++  ANLRLV S+++K +    +F + + E N  L+ A +KFD+  GY+FSTY
Sbjct: 103 DAAETREQIACANLRLVTSISQKLSLSRDEFEEFLAESNAILLNAIDKFDYARGYRFSTY 162

Query: 500 AMWWVKQAITRSI 512
           A   V++ + R I
Sbjct: 163 ATHAVQRNLFRVI 175



 Score = 38.9 bits (89), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 614 TRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +R+   L  RE+ ++R RFG+ G+    +L E+G++  +++ER RQ+  ++I KL
Sbjct: 219 SRIDQVLDSREQFIVRERFGLDGIGKGKSLREIGEELGISKERTRQLFQRSIEKL 273


>gi|147678403|ref|YP_001212618.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146274500|dbj|BAF60249.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 256

 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 14/231 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E+V + L LV  +A +   +    +   DL   G +GL++A EK++   G  F  YA 
Sbjct: 20  KHEIVMSYLPLVKYLAGRLAVKLPACIGQEDLESFGILGLLEAVEKYNPDYGVSFKAYAY 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI       +    IP  M  KI  +  T  R+  +     T E +A  + + + 
Sbjct: 80  NRIRGAIIDEFRKLNW---IPRTMWQKIQSLNNTRERLQGEAGETVTSETLAGAMGISLP 136

Query: 562 GVRKVL----KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + K+     +++   +     + D +    GD I+D  +  PLD   +   R    + +
Sbjct: 137 ELHKLAWHASRLSLSSLDETVALADGELVRWGDMIQDPESPDPLDIIEKEEGRRLLVQAI 196

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  ++  VL + +  G+    TL+E+G    V+  R+ Q+  +AI +L+
Sbjct: 197 EELPEKDRLVLSLYYQEGL----TLKEIGAVMEVSESRVCQLHTRAINRLR 243


>gi|260438830|ref|ZP_05792646.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292808820|gb|EFF68025.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 246

 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 36/57 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   FD     K +TYA
Sbjct: 63  AKTMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINSFDINKKIKLATYA 119


>gi|239628979|ref|ZP_04672010.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47_FAA]
 gi|239519125|gb|EEQ58991.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47FAA]
          Length = 244

 Score = 55.8 bits (133), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 86/200 (43%), Gaps = 10/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL  +G + LM+  +++D   G +F TYA   V+ A+   I  Q     +P   R+   K
Sbjct: 43  DLTDQGVLALMECLDRYDPGKGARFETYAFVRVRGAMIDYIRSQDW---VPHRARNFQKK 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--- 588
           V      +S++   EP  +++A  L MPVE V   +K       L      +D + +   
Sbjct: 100 VDEAFSILSHEKMGEPDVKDVAGYLDMPVEKVENHIKYMNHASVLSFEAALQDMTAIFAK 159

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+         P +S     + E  T  +  L  +E  V+ + +      +    E+ + 
Sbjct: 160 GELEAGDMDGKPEESLFYREMMEMLTAAIDGLGEKERLVITLYY----YEELKYSEIAEV 215

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             + + R+ QI  KAIRKLK
Sbjct: 216 MGIGQSRVCQIHTKAIRKLK 235


>gi|253682372|ref|ZP_04863169.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
 gi|253562084|gb|EES91536.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/245 (23%), Positives = 107/245 (43%), Gaps = 63/245 (25%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++V+ +R G+      +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F
Sbjct: 42  NLVAKIRAGDDSV---RTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGLIKAVNTF 98

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA        +R I ++     I +++R             +NK+K E  
Sbjct: 99  DPEKKIKLATYA--------SRCIENE-----ILMYLRR------------NNKVKAE-- 131

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKN--AVSPLDS 603
                                    IS   P+    D +   L D +  +N    + ++ 
Sbjct: 132 -------------------------ISFYEPLNTDWDGNKLLLSDILGTENDMVYNLIED 166

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L     R    L+ RE+ ++++RFG+    + T ++V     +++  I ++E + 
Sbjct: 167 EVDKQLLFIAMR---KLSEREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISRLEKRI 223

Query: 664 IRKLK 668
           I++LK
Sbjct: 224 IKRLK 228


>gi|153812846|ref|ZP_01965514.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
 gi|149831058|gb|EDM86147.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
          Length = 107

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 41/71 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +   N  L+ SVA ++  RG +  DL Q G+IGL+KA +KFD     KFSTYA+  
Sbjct: 19  ARDILFHENTGLIYSVAHRFLGRGAEMEDLFQIGSIGLLKAVDKFDLSYDVKFSTYAVPM 78

Query: 504 VKQAITRSIAD 514
           +   I R + D
Sbjct: 79  IAGEIKRFLRD 89


>gi|291288738|ref|YP_003505554.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290885898|gb|ADD69598.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 245

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/194 (23%), Positives = 96/194 (49%), Gaps = 10/194 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL     +GL+++ E+FD      F T+    +K AI  ++ +      +P ++R ++ +
Sbjct: 48  DLYSSACLGLIESLERFDKDRNVNFYTFGERRIKGAILDTLRNLDY---LPRNVRTRLKQ 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           + R           +PT EEI +      + V ++L++ +  + +SL+  +G E  + L 
Sbjct: 105 LERHIGNHYRTAGEKPTVEEIIENSDFSEQEVYRLLELMENDKILSLDESVGPEGDTSLV 164

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFI+    ++P D A++  L +T    + +L+ +E+ V+ + +      + T++E+    
Sbjct: 165 DFIK-STGLTPEDEALKTRLVDTLGEEIENLSEKEKYVVSLYY----YEELTMKEIAMVL 219

Query: 650 CVTRERIRQIEAKA 663
            +T  R+ QI + A
Sbjct: 220 GITESRVSQIHSAA 233


>gi|162139704|ref|YP_878335.2| sporulation sigma factor SigE [Clostridium novyi NT]
          Length = 235

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/245 (23%), Positives = 107/245 (43%), Gaps = 63/245 (25%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++V+ +R G+      +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F
Sbjct: 42  NLVNKIRAGDDSV---RTILIERNLRLVVYIARKFENSGILVEDLISVGTIGLIKAVNTF 98

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA        +R I ++     I +++R             +NK+K E  
Sbjct: 99  DPEKKIKLATYA--------SRCIENE-----ILMYLRR------------NNKVKAE-- 131

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKN--AVSPLDS 603
                                    IS   P+    D +   L D +  +N    + ++ 
Sbjct: 132 -------------------------ISFYEPLNTDWDGNKLLLSDILGTENDMVYNLIED 166

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L     R    L+ RE+ ++++RFG+    + T ++V     +++  I ++E + 
Sbjct: 167 EVDKQLLFIAMR---KLSDREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISRLEKRI 223

Query: 664 IRKLK 668
           I++LK
Sbjct: 224 IKRLK 228


>gi|291464748|gb|ADE05832.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 300

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 75/155 (48%), Gaps = 2/155 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 147 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 206

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 207 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 265

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           I++ + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 266 IAQIKDINRRMSIGEAKARRAKKEMVEANLRLVIS 300


>gi|118134194|gb|ABK61238.1| RNA polymerase sigma-E factor [Clostridium novyi NT]
          Length = 230

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/245 (23%), Positives = 107/245 (43%), Gaps = 63/245 (25%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++V+ +R G+      +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F
Sbjct: 37  NLVNKIRAGDDSV---RTILIERNLRLVVYIARKFENSGILVEDLISVGTIGLIKAVNTF 93

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA        +R I ++     I +++R             +NK+K E  
Sbjct: 94  DPEKKIKLATYA--------SRCIENE-----ILMYLRR------------NNKVKAE-- 126

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKN--AVSPLDS 603
                                    IS   P+    D +   L D +  +N    + ++ 
Sbjct: 127 -------------------------ISFYEPLNTDWDGNKLLLSDILGTENDMVYNLIED 161

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L     R    L+ RE+ ++++RFG+    + T ++V     +++  I ++E + 
Sbjct: 162 EVDKQLLFIAMR---KLSDREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISRLEKRI 218

Query: 664 IRKLK 668
           I++LK
Sbjct: 219 IKRLK 223


>gi|223700510|gb|ACN20374.1| truncated RNA polymerase sigma factor SigB [Listeria monocytogenes]
          Length = 188

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/128 (25%), Positives = 66/128 (51%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  
Sbjct: 30  AQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPT 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  + +  E V
Sbjct: 90  IVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEV 149

Query: 564 RKVLKITK 571
            + +++ K
Sbjct: 150 LEAMEMGK 157


>gi|212637801|ref|YP_002314326.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212559285|gb|ACJ31739.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 240

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 53/215 (24%), Positives = 104/215 (48%), Gaps = 20/215 (9%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S  + +    L   D+ Q G + L+++A ++       F +YA   ++ AI   +  Q 
Sbjct: 37  VSQLRSHCGAVLAIEDMEQIGMMALLESARRYPGEYDNGFISYAGQRIRGAILDELRRQD 96

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPI 574
              R PV  R + H++  T R+++  ++R P+  E+A+ + +  +  RK L   +++   
Sbjct: 97  WRPR-PV--RQQAHELNDTVRKLTKMLERAPSDNEVAQAMGLSQDDYRKRLHASLSESMR 153

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL+  I D      G   EDK  V    SA     +ET  + ++ L  RE+ +L + +  
Sbjct: 154 SLDELISD------GGHFEDKQDVFEQISA-----KETLFQAISKLNKREQVILSLYYQH 202

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +N    L+E+     +T  RI Q+  +A+++L++
Sbjct: 203 ELN----LKEIAATLGLTETRICQLHKQAVKQLQN 233


>gi|254497491|ref|ZP_05110284.1| flagellar biosynthesis sigma factor FliA [Legionella drancourtii
           LLAP12]
 gi|254353306|gb|EET12048.1| flagellar biosynthesis sigma factor FliA [Legionella drancourtii
           LLAP12]
          Length = 238

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 59/253 (23%), Positives = 106/253 (41%), Gaps = 63/253 (24%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++A   +D   G  F TYA 
Sbjct: 15  QETLVKNHALLVKRIAHHLLGRLPQSVQLDDLIQAGMLGLLEATRHYDSSKGASFETYA- 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK-------REP 547
                            IRI  +M D++ +       V R +R +S  +K       RE 
Sbjct: 74  ----------------GIRIRGYMLDEVRRNDWVPRSVYRNSRMISEAVKHVEHRLGREA 117

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF------------IEDK 595
              EIA ++ + +    ++L+             D  +SHL  F             E +
Sbjct: 118 KDFEIAAEIGISLTEYHEMLQ-------------DSASSHLYGFEDLGVTDDALHGEEGQ 164

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           ++  P  +   ++L      V+  L  +E+ VL + +   +N    L+E+G+   V+  R
Sbjct: 165 SSTEPHANVFHSDLMNRLAEVIKGLPHKEQMVLSLYYEHDLN----LKEIGEVLGVSESR 220

Query: 656 IRQIEAKAIRKLK 668
           + QI ++A  ++K
Sbjct: 221 VSQILSQATHRIK 233


>gi|291464746|gb|ADE05831.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 300

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 75/155 (48%), Gaps = 2/155 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 147 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMVERVRVQERIIMKLCVEQA 206

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 207 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 265

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           I++ + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 266 IAQIKDINRRMSIGEAKARRAKKEMVEANLRLVIS 300


>gi|322806877|emb|CBZ04447.1| RNA polymerase sporulation specific sigma factor SigK [Clostridium
           botulinum H04402 065]
          Length = 144

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/108 (34%), Positives = 61/108 (56%), Gaps = 4/108 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E ++ +  ++KG+   ++AK  +VE NLRLV  + KKY+  G    DLI  G +GL
Sbjct: 31  LSDEEEKYYLDRLKKGD---ALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           +KA + FD   G + +TYA   ++  I   I +   T +  V+++D I
Sbjct: 88  IKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT-KGEVYLQDPI 134


>gi|30263977|ref|NP_846354.1| prophage LambdaBa02, RNA polymerase sigma-F factor, putative
           [Bacillus anthracis str. Ames]
 gi|47529410|ref|YP_020759.1| prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|30258621|gb|AAP27840.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Ames]
 gi|47504558|gb|AAT33234.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. 'Ames Ancestor']
          Length = 299

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 106/236 (44%), Gaps = 28/236 (11%)

Query: 454 RLVISVAKKYTNR---------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           RLV     KY +           L   DLIQ G +GL+ A   F   LG+KF+T+A+  +
Sbjct: 13  RLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRI 72

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +++ D S  IRI     ++++++     RM  K+  E   E IAK L + V  V+
Sbjct: 73  LGYIRKAVRD-SQKIRIT----NEVYEIKGKISRM--KLHDEEV-ESIAKLLEVSVRDVK 124

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              +     ISL+TP+  E   +   L + + DK     LD  I+   +   T  L++L 
Sbjct: 125 TAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTLDDVIK---KMIITAFLSTLC 181

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +E+ V  +        + T   +GK+  VT+ +I +I     +K +       LR
Sbjct: 182 SKEKFVWELH-----AKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNKHSLR 232


>gi|294634080|ref|ZP_06712635.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829894|gb|EFF88248.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 311

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 96/214 (44%), Gaps = 9/214 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  
Sbjct: 73  ARDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPDRG-AFESYAVPT 131

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVE 561
           +   + R   D+   +R+P  +++  +K VR ARR    N    EP+   +A    +  +
Sbjct: 132 ITGEVKRHFRDRMWALRVPRRVQELRNK-VRVARRELTQNPGSPEPSVAAVAAHTGLTED 190

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASL 620
            V   ++      S  T   D + S   D     + +   DS+    + RE+    L  L
Sbjct: 191 EVNTGMEALD---SFSTLSLDAEMSTGADGYSLADTLGAADSSYDVVVDRESAKEGLRRL 247

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             RE  +L MRF   M      + +G  Q  V+R
Sbjct: 248 PERERAILYMRFFEDMTQSRIADRLGISQMHVSR 281


>gi|283797733|ref|ZP_06346886.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291074630|gb|EFE11994.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
          Length = 205

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 103/249 (41%), Gaps = 52/249 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R  +   R+G+ EA   K  ++E NLRLV  V KKY     +  DL+  G IGL
Sbjct: 8   LTAEEEREYLKRCREGDEEA---KAVLIERNLRLVAHVIKKYQYTDYETEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F    G + +TYA   V+                     ++I  + R  ++ + 
Sbjct: 65  IKAVNTFKAEKGSRLATYAAKCVE---------------------NEILMLFRAGKKRAR 103

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +        +   + +  +G         E +SL   +  E+T  L   I         
Sbjct: 104 DVS-------LYDSIGVDKDG---------ETVSLMDVLEAEETQVLDTII--------- 138

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              ++ ++RE        L   E++V+ MR+G+    +HT  E+     ++R  + +IE 
Sbjct: 139 ---MEQDVRELYEAYAKCLKDMEKKVVCMRYGLFGTKEHTQREIAAVLGISRSYVSRIEK 195

Query: 662 KAIRKLKHP 670
           KAI KL+  
Sbjct: 196 KAIEKLREA 204


>gi|167767366|ref|ZP_02439419.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|317497448|ref|ZP_07955768.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
 gi|167711341|gb|EDS21920.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|316895234|gb|EFV17396.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
          Length = 207

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 66/250 (26%), Positives = 101/250 (40%), Gaps = 66/250 (26%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E RH + + R+G+  A   +  +VE NLRLV  + KKY N   +  D+I  G IGL+KA 
Sbjct: 12  EERHYLILSRQGDMNA---RNLLVEHNLRLVAHIVKKYHNLDREKEDMISIGVIGLIKAI 68

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
             +D   G++  TYA                                   AR + N    
Sbjct: 69  NTYDISKGHRLVTYA-----------------------------------ARCIEN---- 89

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLD 602
                    +L M +   +K  K T    SL  PIG   + +  HL D +         D
Sbjct: 90  ---------ELLMMLRQEKKTSKNT----SLYEPIGIDKEGNEIHLLDIL----GTQETD 132

Query: 603 SAIQANLRETTTRVLASL----TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +   +E   R+   L      +E++ L MR+G+      T +EV K+  ++R  + +
Sbjct: 133 LIKKIEQKENIKRIYEELEKMEMNKEKKTLIMRYGLYGREPMTQKEVAKKLHISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE KA+  LK
Sbjct: 193 IEKKALMLLK 202


>gi|160939653|ref|ZP_02087001.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437444|gb|EDP15208.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI +G + L++  E++D   G +F T+A   V+ A+   I  Q     +P   R+   K
Sbjct: 57  ELIDQGVLALIECLERYDPDRGARFETFAFMRVRGAMIDYIRSQDW---VPHRARNFQKK 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGD------E 583
           V      +S+K  REP   E+A  L +PVE V   +K       +S E+ + D      +
Sbjct: 114 VEEACSILSHKQMREPDVNEVADYLDLPVEKVENHIKYMNHANLLSFESVLQDMTAIVAK 173

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
                GD IE K    P ++     L  T T  +  L  +E  V+ + +      +    
Sbjct: 174 GELESGD-IEGK----PEENLFYKELMGTLTSAIDGLGEKERLVITLYY----YEELKYS 224

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ +   + + R+ QI  +AI+KLK
Sbjct: 225 EIAQVMGIGQSRVCQIHTRAIQKLK 249


>gi|2224777|emb|CAA80617.1| putative pro-sigma factor E [Clostridium acetobutylicum ATCC 824]
          Length = 235

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 99/223 (44%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD     K +TY        
Sbjct: 58  LIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIKAVNTFDPTKKIKLATYG------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +                   
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEIS------------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANL-RETTTRVLASLTPREE 625
               EP++++    D +   L D +  D + V  L   I+  + ++     L  L  RE+
Sbjct: 134 --FYEPLNIDW---DGNKPLLSDILGTDNDCVYNL---IEGEVDKQLLLFALKKLNEREK 185

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R++ +R+G+    + T +EV     +++  I ++E + I++LK
Sbjct: 186 RIVELRYGLTGVGEKTQKEVADMLGISQSYISRLEKRIIKRLK 228


>gi|331269712|ref|YP_004396204.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126262|gb|AEB76207.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 249

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/245 (23%), Positives = 107/245 (43%), Gaps = 63/245 (25%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++V+ +R G+      +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F
Sbjct: 56  NLVAKIRAGDDSV---RTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGLIKAVNTF 112

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA        +R I ++     I +++R             +NK+K E  
Sbjct: 113 DPEKKIKLATYA--------SRCIENE-----ILMYLRR------------NNKVKAE-- 145

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKN--AVSPLDS 603
                                    IS   P+    D +   L D +  +N    + ++ 
Sbjct: 146 -------------------------ISFYEPLNTDWDGNKLLLSDILGTENDMVYNLIED 180

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   L     R    L+ RE+ ++++RFG+    + T ++V     +++  I ++E + 
Sbjct: 181 EVDKQLLFIAMR---KLSEREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISRLEKRI 237

Query: 664 IRKLK 668
           I++LK
Sbjct: 238 IKRLK 242


>gi|83944156|ref|ZP_00956612.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
 gi|83955144|ref|ZP_00963800.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83840473|gb|EAP79646.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83845023|gb|EAP82904.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
          Length = 223

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 97/231 (41%), Gaps = 57/231 (24%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A + +V ++ R+V   A+K ++   +  DLI EG +GL+ AA+ FD     +FSTYA W
Sbjct: 33  FALESLVLSHARIVFYWARKLSDDQAEREDLISEGILGLIHAADLFDLDRDVRFSTYAKW 92

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WVK A                           TAR     I   P              G
Sbjct: 93  WVKNATM-------------------------TARNHLRAIVETPA-------------G 114

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI----QANLRETTTRVLA 618
           V+K         +++  I D+D+  L    ED N   P ++ I    Q  +R      + 
Sbjct: 115 VQK---------TVQHSIDDDDSFALLAS-EDPN---PEEAVIAQSSQTLIRARLLEAME 161

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L P +  VLR R         +++++  +  VT  ++RQIE +A+ +LK+
Sbjct: 162 RLQPMDREVLRAR--TLQQPPESIQDLATRMEVTPAKLRQIERRAMSRLKY 210


>gi|220931758|ref|YP_002508666.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
 gi|219993068|gb|ACL69671.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
          Length = 245

 Score = 55.5 bits (132), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 108/228 (47%), Gaps = 53/228 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            ++ +++ NLRLV+ +A+K++N G+   DL+  G IGL+KA + FD     K +TYA   
Sbjct: 63  VRQLLIKHNLRLVVYIARKFSNTGIDIEDLVSIGTIGLIKAVKTFDVNKNIKLATYA--- 119

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R       + +R+ +     +P        L +  +G 
Sbjct: 120 -----SRCIENE-----ILMYLR-------KNSRKKAEISFDDP--------LNIDWDG- 153

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     + L   +G E     GD I  +N  S +D        E     + +L+ R
Sbjct: 154 --------NELKLSDVMGTE-----GDIIY-RNIESEIDW-------ELLKDAMKTLSDR 192

Query: 624 EERVLRMRFGIGMNTDH--TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+++L +RFG+ +N+    T ++V     +++  I ++E + IRKLK 
Sbjct: 193 EKKILILRFGL-LNSGETKTQKDVADLLGISQSYISRLEKRIIRKLKR 239


>gi|169350469|ref|ZP_02867407.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
 gi|169292789|gb|EDS74922.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
          Length = 228

 Score = 55.1 bits (131), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 73/261 (27%), Positives = 110/261 (42%), Gaps = 65/261 (24%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFL 471
           IKS S E  ++  E    +     G+ EA   +  ++E NLRLV  +AKKY  N+ LQ  
Sbjct: 18  IKSKSFEIPLTPKEEAKYLERFFNGDQEA---RNVLIERNLRLVAHIAKKYENNKDLQ-E 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+KA + +      K +TYA        +R I ++     I +H+R     
Sbjct: 74  DLISIGTIGLIKAVDSYKQNHKTKLATYA--------SRCIENE-----ILMHLRAN--- 117

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSH--L 588
                                               K T   +SL   IG D+D S   L
Sbjct: 118 ------------------------------------KKTNLDVSLNETIGIDKDGSEIVL 141

Query: 589 GDFIEDKN--AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           GD I  K    +  +D     N R TT      L PRE+  L M +G+     ++ +E+ 
Sbjct: 142 GDTIAIKQDEFIDIIDKKDTLN-RLTT--YFNILDPREKETLIMHYGLNNTKKYSQKEIA 198

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           K+  ++R  + ++E +A+ KL
Sbjct: 199 KKLNISRSYVSRLEKRALIKL 219


>gi|168186813|ref|ZP_02621448.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
 gi|169295137|gb|EDS77270.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score = 55.1 bits (131), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 98/226 (43%), Gaps = 60/226 (26%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENSGVLVEDLISVGTIGLIKAVNTFDPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NK+K E                     
Sbjct: 111 -SRCIENE-----ILMYLRR------------NNKVKAE--------------------- 131

Query: 568 KITKEPISLETPIG---DEDTSHLGDFIEDKN--AVSPLDSAIQANLRETTTRVLASLTP 622
                 IS   P+    D +   L D +  +N    + ++  +   L     R    L+ 
Sbjct: 132 ------ISFYEPLNTDWDGNKLLLSDILGTENDMVYNLIEDEVDKQLLFIAMR---KLSD 182

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++++RFG+    + T ++V     +++  I ++E + I++LK
Sbjct: 183 REKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISRLEKRIIKRLK 228


>gi|291542453|emb|CBL15563.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Ruminococcus bromii
           L2-63]
          Length = 231

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 100/229 (43%), Gaps = 58/229 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE NLRLV  + KKY     +  DL+  G IGL+KA   FD     K S+YA   
Sbjct: 48  ARNMLVEHNLRLVAHIIKKYYGTQSEQDDLVSIGTIGLIKAINTFDMNKNIKLSSYA--- 104

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +H R+                         AKK A      
Sbjct: 105 -----SRCIENE-----ILMHFRN-------------------------AKKSA------ 123

Query: 564 RKVLKITKEPISL-ETPIGDEDTSHLG--DFIE-DKNAVSPLDSAIQANLRETTTRVLAS 619
                   + ISL ET   D+D + L   D +  D N +  LD  ++ N ++    +   
Sbjct: 124 --------QDISLNETIDTDKDGNPLTLLDIMSVDDNIIDNLD--LKLNSKKLGQFIKEE 173

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE++++ +R+G+      T + V K   ++R  + +IE KA+++L+
Sbjct: 174 LNEREQKIIVLRYGLDGKEALTQKSVAKMLGISRSYVSRIETKALKQLR 222


>gi|258645545|ref|ZP_05733014.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
 gi|260402901|gb|EEW96448.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
          Length = 205

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 42/69 (60%), Gaps = 3/69 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           GE EA   +++++E    LV   A KY  +    LDLIQEG +GLM+AAEKFD   G  F
Sbjct: 31  GELEA---RQKLIEHYQLLVFKEATKYPVQETVLLDLIQEGTVGLMEAAEKFDIEQGVAF 87

Query: 497 STYAMWWVK 505
           S YA+  ++
Sbjct: 88  SLYAIHRIR 96


>gi|121997280|ref|YP_001002067.1| FliA/WhiG family RNA polymerase sigma factor [Halorhodospira
           halophila SL1]
 gi|121588685|gb|ABM61265.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Halorhodospira
           halophila SL1]
          Length = 247

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 102/239 (42%), Gaps = 28/239 (11%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A    +++V  +  LV  +A    +R    +Q  DLIQ G IGL++AA ++D   G  F 
Sbjct: 11  AQQGDEDLVTRHASLVKRIAHHLASRLPPSVQLEDLIQAGMIGLLEAARQYDSSQGASFQ 70

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   ++ A+   +     T R  VH + +  +V    R + ++  R+    E+A+ L 
Sbjct: 71  TYAGIRIRGAMLDEMRRLDWTPR-SVHRKGR--EVAEAIRTIEHQTGRDARDHEVAEALG 127

Query: 558 MPVEGVRKVLKITKEP----ISLETPIGDEDTSHLGDFIEDKNAVSPL----DSAIQANL 609
           + V     +L+         I  E P   E     G      +   PL    D A Q  L
Sbjct: 128 ISVAEYHNILQDVSSAKVFSIDQEDPGTGEPHEPAG------HEPGPLAMLQDEAFQGEL 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            E     +  L  RE  V+ + +   +N    L E+G+   V+  R+ QI  + + KL+
Sbjct: 182 AEA----IRELPERERLVMALYYDEELN----LREIGEVLGVSESRVSQIHGRIMLKLR 232


>gi|294500913|ref|YP_003564613.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
 gi|294350850|gb|ADE71179.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
          Length = 253

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 86/194 (44%), Gaps = 9/194 (4%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL  A EKFD+    KF TYA + ++ AI   +  +    R     R+K  ++ +  
Sbjct: 60  GLIGLYDALEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDWLSR---SAREKTKRIEQAT 116

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIED 594
             +  +  R   P E+AK++ M    V   +        +S+E    + +       I+D
Sbjct: 117 EALEQRYLRRVAPSEVAKEVGMTEADVVHTMNEGFLANVLSMEEQPKEYEDGEQKYTIKD 176

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +  +SP +  I     +    V+  L  +E+ V+ + +      + T  E+ +   ++  
Sbjct: 177 EKTLSPEEELINDERYQELAEVIEQLNEKEQLVVSLFY----KEELTFTEIAQLLGLSTS 232

Query: 655 RIRQIEAKAIRKLK 668
           RI QI +KA+ K++
Sbjct: 233 RISQIHSKALFKMR 246


>gi|238916673|ref|YP_002930190.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872033|gb|ACR71743.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 250

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 39/65 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   +D     K +TYA   
Sbjct: 67  AKHTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINSYDKDKNIKLATYASRC 126

Query: 504 VKQAI 508
           ++  I
Sbjct: 127 IENEI 131


>gi|291464750|gb|ADE05833.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 300

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 75/155 (48%), Gaps = 2/155 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 147 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 206

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 207 KMPKKTFVGAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 265

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           I++ + I   +  GE +A  AKKEMVEANLRLVIS
Sbjct: 266 IAQIKDINRRMSIGEAKARRAKKEMVEANLRLVIS 300


>gi|291550014|emb|CBL26276.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus torques L2-14]
          Length = 264

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 43/75 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 81  ARKILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPSKKIKLATYASRC 140

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 141 IENEILMYLRRNSKT 155


>gi|291535996|emb|CBL09108.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Roseburia
           intestinalis M50/1]
          Length = 192

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 98/240 (40%), Gaps = 62/240 (25%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG  EA   + E+   N+RLV  VAKKY N      DLI  G IGLMKA   +    G
Sbjct: 5   IKKGSLEA---RNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGLMKAIATYKEDYG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            + +TYA         R I ++     + ++ R K             K+ RE       
Sbjct: 62  SRLATYA--------ARCIDNE-----LLMYFRAK------------KKVSRE------- 89

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFI--EDKNAVSPLDSAIQAN 608
                               +SL  PIG   + +  HL D +  E+ + V  ++   Q  
Sbjct: 90  --------------------VSLYEPIGMDKEGNQIHLLDIVESEEPDVVEMMERTRQ-- 127

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +    V   L  RE  ++  R+G+  N   T  E+     ++R  + +IE KA+ KLK
Sbjct: 128 IEKLLGLVPKVLQERELYIIVHRYGLFGNKAMTQREIASAVGISRSYVSRIEKKALDKLK 187


>gi|327188541|gb|EGE55752.1| RNA polymerase sigma factor RpoD [Rhizobium etli CNPAF512]
          Length = 764

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 39/65 (60%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L     R+  V+  RFG+G N   TLEE+G  + VTRERIRQIE +A+ +++   R   
Sbjct: 147 LLGQCNARDRLVIERRFGLGSNARETLEEIGSDYGVTRERIRQIEKRALTRMRVRMRHVP 206

Query: 676 LRSFL 680
           L  F+
Sbjct: 207 LADFV 211


>gi|306841478|ref|ZP_07474178.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
 gi|306288442|gb|EFM59798.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
          Length = 198

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 92/188 (48%), Gaps = 19/188 (10%)

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-------KREP 547
           +FSTYA WW++ ++   I      +R       K   +    RR+ +K+        +  
Sbjct: 2   RFSTYASWWIRASMQDYILRNWSIVRGGTSSAQK--ALFFNLRRLRSKLAQTDDNMTKAE 59

Query: 548 TPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP--LD 602
              EI+ +L +    V  +  +++    SL  P+  E+T  S   DF+ D + +     +
Sbjct: 60  IYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAE 119

Query: 603 SAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIE 660
           S+I    R    TR L +L  RE  ++R R    ++ D  TLE +G++  +++ER+RQIE
Sbjct: 120 SSIDMERRNRWLTRALDTLNERELHIIRER---RLDDDGVTLEALGEKLGISKERVRQIE 176

Query: 661 AKAIRKLK 668
           ++A+ KLK
Sbjct: 177 SRAMEKLK 184


>gi|90577362|ref|ZP_01233173.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio angustum S14]
 gi|90440448|gb|EAS65628.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio angustum S14]
          Length = 242

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 53/220 (24%), Positives = 98/220 (44%), Gaps = 26/220 (11%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V++  + +T+    + D+ Q G IGL++AA ++      +F  +A+  ++ AI   +   
Sbjct: 39  VVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGDVEDPQFPAFAICRIRGAILDELRRL 98

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               R   H R + H++    R +  ++ R+PT  EI   L +  E  +         + 
Sbjct: 99  DWRSR---HTRQQAHELNDITRDLMKQLGRQPTEAEITSALGIDSENYQ---------LR 146

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN------LRETTTRVLASLTPREERVLR 629
           L+  +  E  S L   +E   A   LDS ++ N      +R T    L  L+ RE+ +L 
Sbjct: 147 LQASMASEMQS-LDQLLE---AGKELDSPLEYNGVEHEHMRRTLEYALTQLSKREQLLLT 202

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +   +N    L E+     +T  RI Q+  +A++ L H
Sbjct: 203 LFYQHELN----LHEIALVLNLTPPRICQLHKQALKSLNH 238


>gi|253581342|ref|ZP_04858568.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836706|gb|EES65240.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 286

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 44/76 (57%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++++  NL  V S+A  Y   G+ ++D++QEG +GL+KA + FD      F  Y+ +W+
Sbjct: 88  KEKIIVKNLNEVASIAFYYVKTGIAYMDIVQEGTVGLIKAVDYFDPDKNGDFKNYSKYWI 147

Query: 505 KQAITRSIADQSCTIR 520
            + I   I ++   +R
Sbjct: 148 VREIVLYIENKVADLR 163


>gi|222833283|gb|EEE71760.1| predicted protein [Populus trichocarpa]
          Length = 152

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 42/141 (29%), Positives = 68/141 (48%), Gaps = 16/141 (11%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           R+ + +A K     +Q  DLIQ G IGL+ AA++++   G +F TYA   ++ A+   + 
Sbjct: 23  RIALQLAAKLPA-SVQIDDLIQAGMIGLLDAAKRYEDNHGARFETYASQRIRGAMLDEVR 81

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
                 R    +R    K+ RT R++  K+ R P   E+AK+L M +E          E 
Sbjct: 82  ANDWQSR---SLRQFTRKIERTQRQLEQKLGRSPIDSEVAKELEMGLE----------ER 128

Query: 574 ISLETPIGD--EDTSHLGDFI 592
           +    P GD   +++H  D I
Sbjct: 129 LPGSAPWGDRRSESAHGADGI 149


>gi|158320682|ref|YP_001513189.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158140881|gb|ABW19193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 176

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 46/86 (53%), Gaps = 1/86 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE NLRLV  + KKY+N G    DLI  G IGL+K    FD   G + +TYA   
Sbjct: 51  ARNILVERNLRLVAHIVKKYSNIGRDMDDLISIGTIGLIKGITTFDRSKGTRLATYAARC 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKI 529
           ++  I  +I      I+  V ++D I
Sbjct: 111 IENEILMTIRSNK-KIKTEVSLQDPI 135


>gi|238796912|ref|ZP_04640416.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238719172|gb|EEQ10984.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 241

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 96/201 (47%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A E FD   G   S Y    V+ A+   + ++     +P  +R    +
Sbjct: 43  DLIQAGAIGLLTAIEHFDPKKGIAISIYITQKVRWAMIDELRERDW---VPRRVRSNARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V    +R+  +     T  ++A  + + +   +++L  T    S +    DE    L D 
Sbjct: 100 VAAVIQRVEQESGTVATEADVAAAMGVTLREYQQMLADTN---SSQLYSLDELQEELSDS 156

Query: 592 IEDKN----AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           IE  +     ++PL   ++ NL +  ++ + +L  R++ +L + +   +N    ++EVG 
Sbjct: 157 IEQPDIQHEMLNPLHELMKENLTKHISQEIKALPERDQLLLNLYYQQDLN----MKEVGI 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  R+ Q+ ++AI++L+
Sbjct: 213 LLEITETRVSQLHSQAIKRLR 233


>gi|225375310|ref|ZP_03752531.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
 gi|225212799|gb|EEG95153.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
          Length = 196

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 96/229 (41%), Gaps = 55/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E++E N+RLV  VAKKY N   +  DLI  G IGL+KA E +    G + +TYA   
Sbjct: 18  ARNELIERNMRLVAHVAKKYQNPEDEMEDLISIGTIGLIKAVETYKEDYGSRLATYA--- 74

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     + +H R K                                   
Sbjct: 75  -----ARCIDNE-----LLMHFRAK----------------------------------- 89

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASL 620
               K T + +SL  PIG D++ + +       +    +   ++ +  +R     +  +L
Sbjct: 90  ----KKTSKEVSLYEPIGTDKEGNQIQLLDVVVSEDEDVVELLEQDRKVRRLNEIIPQTL 145

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + RE  ++  R+G+      T  E+ ++  ++R  + +IE +AI KL+ 
Sbjct: 146 SGRELFIIINRYGLYGKKTMTQREIARKLGISRSYVSRIEKRAIEKLRQ 194


>gi|167770714|ref|ZP_02442767.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
 gi|167667309|gb|EDS11439.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
          Length = 243

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 106/239 (44%), Gaps = 56/239 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + RK E     AK+ +   NLRLV+ +AKK+ + G+   DLI  G IGL+KA   F    
Sbjct: 51  VFRKLEEHDEAAKETLTVHNLRLVVYIAKKFESTGICVEDLISIGTIGLIKAVNTFCPQK 110

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR-DKIHKVVRTARRMSNKIKREPTPEE 551
             K +TYA        +R I ++     I +H+R ++ HK         N+I        
Sbjct: 111 NIKLATYA--------SRCIENE-----ILMHLRKNQSHK---------NEIS------- 141

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           I + L +  +G   +L   +  +P S+  PI DE   +L        A+  LD       
Sbjct: 142 IDEPLNIDWDGNELLLSDILGTDPDSINRPIEDEAEKNLL-----LGAIDRLDG------ 190

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                        RE  ++++RFG+    + T +EV     +++  I ++E + I+KLK
Sbjct: 191 -------------RERMIMQLRFGLLGAEEKTQKEVADIIGISQSYISRLEKRIIKKLK 236


>gi|254519267|ref|ZP_05131323.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
 gi|226913016|gb|EEH98217.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
          Length = 235

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 100/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVCVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +  E    L +  +G     
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEISFYE---PLNIDWDG----- 144

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                 + L   +G E+   + + IED+     +D       R+     L  L  RE+ +
Sbjct: 145 ----NELLLSDILGTEN-DIVYNLIEDE-----VD-------RQLLFLALKHLNDREKEI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++RFG+    + T +EV     +++  I ++E K I +LK
Sbjct: 188 VKLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIINRLK 228


>gi|218245540|ref|YP_002370911.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|257058577|ref|YP_003136465.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|218166018|gb|ACK64755.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
 gi|256588743|gb|ACU99629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 255

 Score = 55.1 bits (131), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/118 (26%), Positives = 67/118 (56%), Gaps = 1/118 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE +  LV  VA + +N+  + + DL Q G +GL+ A E+F+   G  FS++A+ +
Sbjct: 26  RNQLVELHTGLVRQVAHRISNQCTEPYEDLEQIGYLGLINAIERFNPHQGCAFSSFAIPY 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  +   + D+   +RIP   ++  +K  +  ++++  + R P  +E+A  L + +E
Sbjct: 86  IRGEMLHYLRDKGSVMRIPRRWQELYNKGKKVRKQLTTSLGRTPKDQELADALQVSLE 143


>gi|220931430|ref|YP_002508338.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
 gi|219992740|gb|ACL69343.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
          Length = 232

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 53/237 (22%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +R+G+ EA   +  ++E NLRLV  + KKY +      DLI  G IGL+K    +D 
Sbjct: 38  IKRMRQGDEEA---RNILIEHNLRLVAHIVKKYNSVYTDNEDLISIGTIGLIKGINTYDE 94

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               K +TYA         R I ++     I +H+        R+ +++SN+        
Sbjct: 95  TKKTKLATYA--------ARCIENE-----ILMHL--------RSVKKLSNE-------- 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
                             + +E I  +    D     + D  ED + ++ ++ +I     
Sbjct: 126 -----------------TLLQESIGSDKDGNDITLMDVLDTRED-SVINKVEKSID---E 164

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E     L  L+PRE++VL +R+G+      T +EV     ++R  + +IE KAI++L
Sbjct: 165 EQLYNKLGELSPREKKVLELRYGLLDGKRLTQKEVASILGISRSYVSRIEKKAIQEL 221


>gi|295094809|emb|CBK83900.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus sp. ART55/1]
          Length = 245

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/65 (44%), Positives = 39/65 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 62  AKKMLIERNLRLVVYIAKKFDNTGVGIEDLISIGTIGLIKAINTFKNDKNIKLATYASRC 121

Query: 504 VKQAI 508
           ++  I
Sbjct: 122 IENEI 126


>gi|326791410|ref|YP_004309231.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
 gi|326542174|gb|ADZ84033.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
          Length = 251

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 37/63 (58%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E    K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+K+   F  C   K +
Sbjct: 63  EEEIKAIKTTLIERNLRLVVYIARKFENTGIYMEDLISIGTIGLIKSINTFKPCKKIKLA 122

Query: 498 TYA 500
           TYA
Sbjct: 123 TYA 125


>gi|26991031|ref|NP_746456.1| flagellar biosynthesis sigma factor [Pseudomonas putida KT2440]
 gi|148546765|ref|YP_001266867.1| flagellar biosynthesis sigma factor [Pseudomonas putida F1]
 gi|24986061|gb|AAN69920.1|AE016630_11 flagellar biosynthesis sigma factor FliA [Pseudomonas putida
           KT2440]
 gi|148510823|gb|ABQ77683.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida F1]
 gi|313497816|gb|ADR59182.1| FliA [Pseudomonas putida BIRD-1]
          Length = 246

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 102/232 (43%), Gaps = 17/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ A K+D   G  F TYA
Sbjct: 16  AQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAMRAVEARTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTRV 616
           +    +L  T      S +  +  +D  H G   ED     V P     +   +   T  
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG-LHEDGASGQVEPARGLEEERFQAALTEA 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 190 IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|15894972|ref|NP_348321.1| sporulation sigma factor SigE [Clostridium acetobutylicum ATCC 824]
 gi|585930|sp|P33657|RPSE_CLOAB RecName: Full=RNA polymerase sigma-E factor
 gi|15024659|gb|AAK79661.1|AE007679_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|460971|gb|AAC43309.1| putative sigma factor E [Clostridium acetobutylicum ATCC 824]
 gi|325509109|gb|ADZ20745.1| sporulation sigma factor SigE [Clostridium acetobutylicum EA 2018]
          Length = 235

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 99/223 (44%), Gaps = 54/223 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   FD     K +TY        
Sbjct: 58  LIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIKAVNTFDPTKKIKLATYG------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +                   
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEIS------------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANL-RETTTRVLASLTPREE 625
               EP++++    D +   L D +  D + V  L   I+  + ++     L  L  RE+
Sbjct: 134 --FYEPLNIDW---DGNKLLLSDILGTDNDCVYNL---IEGEVDKQLLLFALKKLNEREK 185

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R++ +R+G+    + T +EV     +++  I ++E + I++LK
Sbjct: 186 RIVELRYGLTGVGEKTQKEVADMLGISQSYISRLEKRIIKRLK 228


>gi|251780405|ref|ZP_04823325.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243084720|gb|EES50610.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 232

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 98/230 (42%), Gaps = 59/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY+       +LI  G +GL+KA + FD   G + +TYA   
Sbjct: 50  AKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIKAIDSFDSGKGTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++             I  + R  ++                         
Sbjct: 107 -----SRCIENE-------------ILMLFRNNKKQ------------------------ 124

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                  K  + L+ PIG +   +   L D +  +  + +  ++S +Q  +++   ++  
Sbjct: 125 -------KSEVYLQDPIGVDKEGNEICLIDILSSDSDSVLEKVESNLQ--IKDLYIKIKD 175

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SLT RE  +L MR+G+      T  E+     ++R  + +IE KA++KL+
Sbjct: 176 SLTKRESTILIMRYGLIDGNRKTQREIAGTLGISRSYVSRIEKKALKKLR 225


>gi|120597321|ref|YP_961895.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|146294534|ref|YP_001184958.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|120557414|gb|ABM23341.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
 gi|145566224|gb|ABP77159.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
          Length = 238

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 52/213 (24%), Positives = 102/213 (47%), Gaps = 16/213 (7%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           ++S  + +    L   D+ Q G + L++++ ++   L   F ++A   ++ AI   +  Q
Sbjct: 37  IVSQMRSHCGVMLSLEDMEQIGMMALLESSRRYPGELDNGFISFAGQRIRGAILDELRRQ 96

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               R PV  R + H++    RR+S ++ REP+  E+A  L +  E  R+ L  T+    
Sbjct: 97  DWRPR-PV--RQQAHELNDVVRRLSREMGREPSDLEVASALGLSAEDYRERLYSTQA--- 150

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            E+    ++   +G+   D+      +   Q  L++T  +V++ L  RE+ +L + +   
Sbjct: 151 -ESMKSLDELLLVGEHPVDRG-----NDVEQLMLKQTLIKVISKLNEREQLILSLYYHHE 204

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +N    L+E+     +T  RI Q+   AI +LK
Sbjct: 205 LN----LKEIAMALGLTETRICQLHKSAISQLK 233


>gi|188588587|ref|YP_001920530.1| sporulation sigma factor SigK [Clostridium botulinum E3 str. Alaska
           E43]
 gi|188498868|gb|ACD52004.1| RNA polymerase sigma-K factor [Clostridium botulinum E3 str. Alaska
           E43]
          Length = 232

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 98/230 (42%), Gaps = 59/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY+       +LI  G +GL+KA + FD   G + +TYA   
Sbjct: 50  AKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIKAIDSFDSGKGTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++             I  + R  ++                         
Sbjct: 107 -----SRCIENE-------------ILMLFRNNKKQ------------------------ 124

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                  K  + L+ PIG +   +   L D +  +  + +  ++S +Q  +++   ++  
Sbjct: 125 -------KSEVYLQDPIGVDKEGNEICLIDILSSDSDSVLEKVESNLQ--IKDLYIKIKD 175

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SLT RE  +L MR+G+      T  E+     ++R  + +IE KA++KL+
Sbjct: 176 SLTKRESTILIMRYGLIDGNRKTQREIAGALGISRSYVSRIEKKALKKLR 225


>gi|295706259|ref|YP_003599334.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
 gi|294803918|gb|ADF40984.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
          Length = 253

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 86/194 (44%), Gaps = 9/194 (4%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL  A EKFD+    KF TYA + ++ AI   +  +    R     R+K  ++ +  
Sbjct: 60  GLIGLYDALEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDWLSR---SAREKTKRIEQAT 116

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIED 594
             +  +  R   P E+AK++ M    V   +        +S+E    + +       I+D
Sbjct: 117 EALEQRYLRRVAPSEVAKEVGMTEADVVHTMNEGFLANVLSMEEQPKEYEDGEQKYTIKD 176

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +  +SP +  I     +    V+  L  +E+ V+ + +      + T  E+ +   ++  
Sbjct: 177 EKTLSPEEELINDERYQELAEVIEQLNEKEQLVVSLFY----KEELTFTEIAQLLGLSTS 232

Query: 655 RIRQIEAKAIRKLK 668
           RI QI +KA+ K++
Sbjct: 233 RISQIHSKALFKMR 246


>gi|167515040|gb|ABZ81804.1| RpoD [Aeromonas aquariorum]
          Length = 285

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/64 (46%), Positives = 40/64 (62%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REII 185
            +II
Sbjct: 61  SDII 64


>gi|167515036|gb|ABZ81802.1| RpoD [Aeromonas aquariorum]
          Length = 285

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/64 (46%), Positives = 40/64 (62%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REII 185
            +II
Sbjct: 61  SDII 64


>gi|167515034|gb|ABZ81801.1| RpoD [Aeromonas aquariorum]
          Length = 292

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/64 (46%), Positives = 40/64 (62%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REII 185
            +II
Sbjct: 61  SDII 64


>gi|37781593|gb|AAP42800.1| SigB [Staphylococcus aureus]
          Length = 256

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 50/232 (21%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L          H  +  ++ + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNAL-------SVDHSIEADKEGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++     +E G +  +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQ----KETGGRIGLSQMHVSRLQRTAIKKLQ 251


>gi|18310744|ref|NP_562678.1| sporulation sigma factor SigE [Clostridium perfringens str. 13]
 gi|110798939|ref|YP_696448.1| sporulation sigma factor SigE [Clostridium perfringens ATCC 13124]
 gi|110801836|ref|YP_699048.1| sporulation sigma factor SigE [Clostridium perfringens SM101]
 gi|168207289|ref|ZP_02633294.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210605|ref|ZP_02636230.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168217049|ref|ZP_02642674.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
 gi|169342673|ref|ZP_02863714.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625822|ref|ZP_02953588.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145425|dbj|BAB81468.1| probable transcription initiation factor sigma E [Clostridium
           perfringens str. 13]
 gi|110673586|gb|ABG82573.1| RNA polymerase sigma-E factor [Clostridium perfringens ATCC 13124]
 gi|110682337|gb|ABG85707.1| RNA polymerase sigma-E factor [Clostridium perfringens SM101]
 gi|169299179|gb|EDS81249.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661363|gb|EDT14046.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711254|gb|EDT23436.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|177908856|gb|EDT71348.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380960|gb|EDT78439.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
          Length = 235

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 103/222 (46%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +  E    L +  +G     
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEISFYE---PLNIDWDG----- 144

Query: 568 KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G D+D  +  + IED+     L +A++            +L+ RE+ 
Sbjct: 145 ----NELLLSDILGTDDDIVY--NLIEDEVDKELLFTAMK------------NLSNREKE 186

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +RFG+    + T +EV     +++  I ++E K I++LK
Sbjct: 187 IVELRFGLCGYKEKTQKEVADMLGISQSYISRLEKKIIKRLK 228


>gi|302549077|ref|ZP_07301419.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466695|gb|EFL29788.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 287

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 99/215 (46%), Gaps = 13/215 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 50  RDELVALWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAVDRFDPSRG-AFESYAVPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEG 562
              + R   D+   +R+P  +++  +K VR ARR    N    EP+   +A    +  E 
Sbjct: 109 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARRELTQNPGSPEPSVPALAAHTGLTEEE 167

Query: 563 VRKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   L+   +   +SL+  +  D+D   L D +   +  +  D  +    RE+    L  
Sbjct: 168 VNAGLEALDSFSTLSLDAELSADDDGYSLADTLGASD--TSYDVVVD---RESAKEGLRR 222

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  RE  +L MRF   M      +++G  Q  V+R
Sbjct: 223 LPERERAILYMRFFEDMTQSRIADQLGISQMHVSR 257


>gi|295091014|emb|CBK77121.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 292

 Score = 54.7 bits (130), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/224 (24%), Positives = 98/224 (43%), Gaps = 28/224 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYK-----FSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           DL QEG + L      +D   GY+     F  YA +W++  I R I   SC + IP   +
Sbjct: 46  DLEQEGFLAL------YDAVRGYQPDKGAFLAYAAYWIEARIRRFIQKDSC-LHIPAGRQ 98

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDED 584
            +  ++ +       +  + P        L + +E    RK   +T   +SL+ PI D++
Sbjct: 99  GQAKELQQFQEAYEKEYGQTPPDAVSCCFLGLTLEEYQERKKTALTGRCLSLDAPITDQE 158

Query: 585 TSHL--GDFIE-----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
              L  GD +      +++ +  +D      L+     ++ SL   +  ++R R+  G +
Sbjct: 159 GEGLTLGDTVAASGSLEEDIIGQIDCQ---ELKRLLWGMVNSLPGMQPAIIRARYQEGKS 215

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                 E G     + E +R  +AKAIR L++P    +LR +L+
Sbjct: 216 IREIAAEQGN----SPEEVRGQQAKAIRTLRNPKNLNRLRCYLE 255


>gi|13446369|gb|AAK20925.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 237

 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 96/198 (48%), Gaps = 18/198 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q G +GL++A  ++D     +F  YA   ++ A+   +  +    R+P  +R ++H 
Sbjct: 51  DMEQVGMMGLLEAWRRYDSEPDPQFERYAFKRIRGAMLDEL--RRLDWRLPT-LRQQVHS 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             +  R + N++ R PT +E+A  L   VE VR++   ++           E    L ++
Sbjct: 108 HNQAQRELYNRLGRSPTEQELAVSLNCTVEEVRQLAYASQA----------EALQSLEEW 157

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +E+    +P   +   ++  T ++VL SL  RE+ +L + +   +N    ++E+     +
Sbjct: 158 LEN-GGKAPATESDDVDMAMTISKVLTSLDKREQLLLSLYYQQELN----MKEIALVLGL 212

Query: 652 TRERIRQIEAKAIRKLKH 669
           T  R+ Q+  + + +LK 
Sbjct: 213 TESRVCQLHKQCVLQLKQ 230


>gi|260438776|ref|ZP_05792592.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
 gi|292808765|gb|EFF67970.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
          Length = 255

 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 102/223 (45%), Gaps = 20/223 (8%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           ++LV      Y    +++ DL+  G  GL+ A +KFD+    KF TYA   ++  I   I
Sbjct: 33  VKLVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDYGKNVKFETYASLRIRGEILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK- 571
                   IP  +R+K  K+     R+  +  +  T EE+A  L + ++ +      TK 
Sbjct: 93  RKMDW---IPRSVREKQKKIDSARTRLETENGKNATDEELAAALDLSLDELNNWQGQTKV 149

Query: 572 -EPISLETPI--GDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
              +SL+  +  G E   +T+    F + +  V   + A++       +  L+ LT +E+
Sbjct: 150 SNLVSLDEFVEQGSELSMETAGNSHFEQPERVVEKEELAVK------ISEALSHLTEKEK 203

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            V+ + +   M    TL+E+     V+  R+ Q+  KA+ KLK
Sbjct: 204 MVVTLYYYEEM----TLKEISNVMEVSESRVSQLHTKALVKLK 242


>gi|49082218|gb|AAT50509.1| PA1455 [synthetic construct]
          Length = 248

 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 59/251 (23%), Positives = 109/251 (43%), Gaps = 32/251 (12%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           V M  K + + S  ++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K
Sbjct: 7   VRMYSKAQAQNS--QEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKK 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F TYA   ++ A+   +       R  VH   ++  V    R +  +  R+ 
Sbjct: 65  YDAGKGASFETYAGIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VTDAIRAIEARTGRDA 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              E+A +L + +E    +L  T+         G    S   D ++D     P D+++  
Sbjct: 122 KDHEVAAELQLSLEDYYGILSDTQ---------GSRLYS-FDDLLQDGEHGLPEDTSLSH 171

Query: 608 N----------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           N           +      +A L  RE  VL + +   +N    L+E+G+   V+  R+ 
Sbjct: 172 NEPIHGLLDERFQAALADAIAKLPERERLVLALYYDEELN----LKEIGEVLGVSESRVS 227

Query: 658 QIEAKAIRKLK 668
           Q+ ++   +L+
Sbjct: 228 QLHSQCAARLR 238


>gi|324328848|gb|ADY24108.1| FliA/WhiG family RNA polymerase sigma factor [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 248

 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 74/172 (43%), Gaps = 24/172 (13%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DL Q G IGL+KA + F+   G KFSTYA+  +   I R+I D            
Sbjct: 50  GLDIEDLTQFGMIGLIKARDNFNLEYGCKFSTYAVPKILGEIGRAIRDHQKV-------- 101

Query: 527 DKIHKVVRTARRMSNKIKRE----PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-- 580
               KV R    +  KI R+     TPEEIA  L   V  V   L       SL   +  
Sbjct: 102 ----KVQRNVYSIKGKILRQNLEDETPEEIASILQEDVSVVSNALHYQPGAQSLNKVVHQ 157

Query: 581 --GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             G+E+ + L   +EDK A +  D +I    R       + L+ +E  VL M
Sbjct: 158 SNGNEELT-LESMLEDKKAENVEDVSIN---RMVIQAFKSQLSHKEHIVLDM 205


>gi|77020162|ref|YP_338218.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
 gi|85701416|ref|YP_460001.1| putative RNA polymerase sigma subunit [Bacillus phage WBeta]
 gi|89152515|ref|YP_512346.1| sigma70 factor [Bacillus phage Fah]
 gi|196033415|ref|ZP_03100827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus cereus
           W]
 gi|76445738|gb|ABA42728.1| sigma70 factor [Bacillus phage Fah]
 gi|76564064|gb|ABA46452.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
 gi|83658652|gb|ABC40436.1| putative RNA polymerase sigma subunit [Bacillus phage WBeta]
 gi|83658705|gb|ABC40488.1| putative RNA polymerase sigma subunit [Bacillus phage Gamma isolate
           d'Herelle]
 gi|195993849|gb|EDX57805.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus cereus
           W]
          Length = 248

 Score = 54.7 bits (130), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 102/230 (44%), Gaps = 32/230 (13%)

Query: 447 EMVEANLRLVI-SVAKKYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +E   RLV   V K+Y  +        GL   DL Q G IGL+KA + FD   G  FS
Sbjct: 21  EFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFGMIGLIKARDNFDLEFGCAFS 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKL 556
           TYA+  +   I R+I D         + + K+ + V   + ++ N+   +  PEEIA  L
Sbjct: 81  TYAVPKIIGEIGRAIRD---------NQKIKVQRTVYGVKGKILNQQLADKEPEEIADIL 131

Query: 557 AMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAI-QANLRET 612
              V  V+  L+      SL   +   G  +   L   IED       ++ I +A +RE 
Sbjct: 132 DESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTEDIEETTINRAVIREF 191

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                A+L P+E  VL MR       + T + +  Q   ++ +I +I AK
Sbjct: 192 K----AALPPKEYIVLDMRL-----QNMTQQNIANQMGYSQVQISRILAK 232


>gi|254239804|ref|ZP_04933126.1| sigma factor FliA [Pseudomonas aeruginosa 2192]
 gi|126193182|gb|EAZ57245.1| sigma factor FliA [Pseudomonas aeruginosa 2192]
          Length = 247

 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 112/249 (44%), Gaps = 28/249 (11%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           V M  K + + S  ++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K
Sbjct: 7   VRMYSKAQAQNS--QEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKK 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F TYA   ++ A+   +       R  VH   ++  V    R +  +  R+ 
Sbjct: 65  YDAGKGASFETYAGIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VTDAIRTIEARTGRDA 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGD------EDTSHLGDFIEDKNAVS 599
              E+A +L + +E    +L  T+     S +  + D      EDTS       ++    
Sbjct: 122 KDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTS----LSHNEPIHG 177

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            LD   QA L +     +A L  RE  VL + +   +N    L+E+G+   V+  R+ Q+
Sbjct: 178 LLDERFQAALADA----IAKLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQL 229

Query: 660 EAKAIRKLK 668
            ++   +L+
Sbjct: 230 HSQCAARLR 238


>gi|15596652|ref|NP_250146.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PAO1]
 gi|116049400|ref|YP_791797.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218892672|ref|YP_002441541.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa LESB58]
 gi|254234554|ref|ZP_04927877.1| sigma factor FliA [Pseudomonas aeruginosa C3719]
 gi|296390178|ref|ZP_06879653.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PAb1]
 gi|120310|sp|P29248|FLIA_PSEAE RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-28; AltName: Full=Sigma-F factor
 gi|9947407|gb|AAG04844.1|AE004575_3 sigma factor FliA [Pseudomonas aeruginosa PAO1]
 gi|45322|emb|CAA43548.1| sigma-28 class sigma factor [Pseudomonas aeruginosa]
 gi|115584621|gb|ABJ10636.1| motility sigma factor FliA [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126166485|gb|EAZ51996.1| sigma factor FliA [Pseudomonas aeruginosa C3719]
 gi|218772900|emb|CAW28712.1| sigma factor FliA [Pseudomonas aeruginosa LESB58]
          Length = 247

 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 59/251 (23%), Positives = 109/251 (43%), Gaps = 32/251 (12%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           V M  K + + S  ++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K
Sbjct: 7   VRMYSKAQAQNS--QEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKK 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F TYA   ++ A+   +       R  VH   ++  V    R +  +  R+ 
Sbjct: 65  YDAGKGASFETYAGIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VTDAIRAIEARTGRDA 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              E+A +L + +E    +L  T+         G    S   D ++D     P D+++  
Sbjct: 122 KDHEVAAELQLSLEDYYGILSDTQ---------GSRLYS-FDDLLQDGEHGLPEDTSLSH 171

Query: 608 N----------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           N           +      +A L  RE  VL + +   +N    L+E+G+   V+  R+ 
Sbjct: 172 NEPIHGLLDERFQAALADAIAKLPERERLVLALYYDEELN----LKEIGEVLGVSESRVS 227

Query: 658 QIEAKAIRKLK 668
           Q+ ++   +L+
Sbjct: 228 QLHSQCAARLR 238


>gi|291563180|emb|CBL41996.1| Sigma-70 region 3 [butyrate-producing bacterium SS3/4]
          Length = 203

 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 33/133 (24%), Positives = 68/133 (51%), Gaps = 3/133 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++E NL+  +   + Y N+G+   DLIQE ++ LM  A   D      F       
Sbjct: 65  ARERLIEGNLKNALFFVQDYINKGVPMADLIQEASLELMMLA---DEGFEGSFEKLLESR 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   I DQ     I   M  +++ +   ++ M+ ++ RE    E+A+++ M  + V
Sbjct: 122 IRVRMEEIINDQKKEADIEEEMLARVNVLQEVSKSMAEELGREAKLSELAERMKMTEDEV 181

Query: 564 RKVLKITKEPISL 576
           R+++K+T + +S+
Sbjct: 182 REIMKVTMDALSM 194


>gi|153818374|ref|ZP_01971041.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
 gi|126511064|gb|EAZ73658.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
          Length = 232

 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 74/164 (45%), Gaps = 10/164 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A + +D   G  F TYA   ++ A+   I       R  VH  ++  +
Sbjct: 46  DLIQAGMVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDWVPR-SVHKHNR--E 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +  ++ R+PT  E+AK L M +E    VL      I+    +G ED     D 
Sbjct: 103 ISQAIAVLEGELNRDPTDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVSDDA 158

Query: 592 I---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           I   E+    SP     + + R+     + SL  RE  VL + +
Sbjct: 159 ISPFEEGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYY 202


>gi|68164561|gb|AAY87290.1| predicted flagellar-specific RNA polymerase sigma factor FliA
           [uncultured bacterium BAC17H8]
          Length = 240

 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 109/229 (47%), Gaps = 18/229 (7%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +E++ +++ LV  +A     R    ++  DLIQ G  GL+ AA+ +    G  F++YA  
Sbjct: 13  EELITSHMELVRQIAWHMHGRLHSSIEIEDLIQIGYFGLVTAAQNYTLREGATFASYAGI 72

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   +   S   R  + M+ K +      R + N++ REPT  E+A+ + +  + 
Sbjct: 73  RIRGAIVDHLRKSSNLCRTTIEMQKKANV---AGRELRNRLGREPTSAEMAEHMCISEDE 129

Query: 563 VRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +       +  +  SL++ + DE +     F   +N  +P ++  +  LR      L +L
Sbjct: 130 MHNWEHAFQANVHQSLDS-VYDEFSIW---FESPEN--TPEENINEEELRNLLKEALRTL 183

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE  V+++ +   +N    + E+ +   VT  R+ QI+  AI  L+H
Sbjct: 184 PEREALVIQLYYVEELN----VYEIAEVLEVTTGRVSQIKKSAIGSLRH 228


>gi|283781321|ref|YP_003372076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
 gi|283439774|gb|ADB18216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
          Length = 261

 Score = 54.3 bits (129), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 102/229 (44%), Gaps = 18/229 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE  L LV    ++   R   G++  DLI  G  GLM A + FD   G KF TY +  +
Sbjct: 31  LVEHYLPLVKYNGERIWARLPEGVELDDLISAGIFGLMDAIDAFDMTRGVKFETYCVPRI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +        +P  +R K  K+    + +  ++ R PT  E+A ++ M V  V 
Sbjct: 91  RGAMLDELRTMDW---VPRLVRSKASKLGEATKTLEARLGRHPTTVELAAQMEMSVPEVE 147

Query: 565 KVLKITKEP--ISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           K++        ISL     + D+       D +EDK    P     + +L    T+ L  
Sbjct: 148 KMVSEASAVGLISLNKKWYETDSYKDVREIDILEDKKGEDPTRRIQKNDLMRLVTKGLN- 206

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R ER++ + +      + T++E+G    ++  R+ Q+ +  + +L+
Sbjct: 207 ---RNERLIIILY---YYEELTMKEIGATLDLSESRVSQMHSSIVSRLQ 249


>gi|291280645|ref|YP_003497479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Deferribacter
           desulfuricans SSM1]
 gi|290755347|dbj|BAI81723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Deferribacter
           desulfuricans SSM1]
          Length = 255

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 95/193 (49%), Gaps = 12/193 (6%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G ++A  ++D      F  +    VK AI   +       R     R K+  +    + +
Sbjct: 63  GFVEALNRYDPSQNIDFKYFVEKRVKGAILDVLRRLDLLSRTK---RTKLKDLENKIQTL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPI-GDEDTSH-LGDFIEDK 595
           S ++ R+PTPEEIA+K  +  E +  +L+++ +   ISL T +  D++  H L DFI+  
Sbjct: 120 SKELGRQPTPEEIAEKYGIDTEEIYNLLELSDKTHIISLNTLLDKDDNEGHSLIDFIKS- 178

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           + ++P +   +  L +   + + +L  +E  V+ + +      + T++E+G+   VT  R
Sbjct: 179 DLLTPEEQVSKQELIDILQKEIENLKEKERLVITLYYY----EELTMKEIGEILGVTEAR 234

Query: 656 IRQIEAKAIRKLK 668
           + QI  K + +LK
Sbjct: 235 VCQIHNKVVEQLK 247


>gi|186681796|ref|YP_001864992.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186464248|gb|ACC80049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 261

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 35/137 (25%), Positives = 79/137 (57%), Gaps = 3/137 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ +  LV  +A K++++  + + DL Q G  GL++A E+FD   GY FS++A+ +
Sbjct: 28  RNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGYAFSSFAVPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+S  ++IP   ++  ++  +  + ++  + R+P   EIA +L + V+  
Sbjct: 88  IRGEMLHFLRDRSTLLKIPRRWQELYNEGQKIRKDLAMSLGRQPKDAEIASELRVSVQEW 147

Query: 564 R--KVLKITKEPISLET 578
           +  K+    + P+SL+ 
Sbjct: 148 QETKLAAQNRMPLSLDA 164


>gi|317471864|ref|ZP_07931199.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|316900637|gb|EFV22616.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 207

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 67/252 (26%), Positives = 106/252 (42%), Gaps = 62/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E ++ +   R G+ EA   +  +VE NLRLV  + KKY N      DLI  G IGL
Sbjct: 8   LSQEEEQYYLKKSRLGDMEA---RNILVEHNLRLVAHIVKKYNNFDRDKDDLISVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++   G++  TYA        +R I ++                          
Sbjct: 65  IKAINTYNMEKGHRLVTYA--------SRCIENE-------------------------- 90

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFI--EDKN 596
                         L M +   RK  K T    SL  PIG   + +  +L D +  ++ +
Sbjct: 91  --------------LLMMLRQERKSAKDT----SLYEPIGIDKEGNEINLLDVLGADEND 132

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            V  LD  ++  +R+    V      RE+  L MR+G+      T +EV K+  ++R  +
Sbjct: 133 IVDELD--LKEKIRDLYKMVDEMEPSREKTTLIMRYGLYGKKPMTQKEVAKELHISRSYV 190

Query: 657 RQIEAKAIRKLK 668
            +IE KA+ K+K
Sbjct: 191 SRIEKKAVEKIK 202


>gi|225375354|ref|ZP_03752575.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
 gi|225212843|gb|EEG95197.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
          Length = 256

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 107/231 (46%), Gaps = 17/231 (7%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           ++LV      Y    +++ DL+  G  GL+ A +KFD     KF TYA   ++  I   I
Sbjct: 33  VKLVAGRLSMYLGYNVEYDDLVSYGIFGLIDAIDKFDLGKEVKFETYASLRIRGTILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---VEGVRKVLKI 569
                   IP  +R K  K+    +++  +  +  + EEIA++L +    +   +  LK+
Sbjct: 93  RKMDW---IPRTVRQKQKKIDEAIKQVEMRTGKNASDEEIAQELGLSEDELTTWQSQLKV 149

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T   +SL   + ++    + D   + + + P D   +  L++     L  LT +E +V+ 
Sbjct: 150 TN-IVSLNEYL-EQGAEPVMDARRNSHFIQPEDKVEEEELKQKLEESLEVLTEKERKVIL 207

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +      D TL+E+     V+  RI Q+  KA+ K++     KKL ++L
Sbjct: 208 LYY----YEDLTLKEISSILEVSESRISQLHTKALLKMR-----KKLGNYL 249


>gi|239817113|ref|YP_002946023.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Variovorax paradoxus
           S110]
 gi|239803690|gb|ACS20757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Variovorax paradoxus
           S110]
          Length = 243

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 95/204 (46%), Gaps = 14/204 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL+ A+ ++    G +F T+A   ++ A+   +       R    +R    K
Sbjct: 40  DLIQAGMIGLLDASTRYQDNRGAQFETFASQRIRGAMLDELRASDWGSR---GLRQSARK 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +  + + +++ R  +  EIA++L M ++  + +L+  +    L      +D      +
Sbjct: 97  VEQAIQALEHRLGRSASEGEIARELKMELDDYQSLLQDIQGCQLLYVEDFAQDGEAENPW 156

Query: 592 IEDKNAV-------SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           +E +           PL   ++A  R      +A+L  R++ +L + +   +N    L E
Sbjct: 157 LERQAQADARLGGDDPLAQLLEAGFRHELVDAIAALPERDQLLLNLYYEEELN----LRE 212

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G    VT+ R+ Q+ ++AI +L+
Sbjct: 213 IGAILEVTQSRVCQLHSQAISRLR 236


>gi|163814130|ref|ZP_02205522.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
 gi|158450579|gb|EDP27574.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
          Length = 245

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 39/65 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 62  AKKMLIERNLRLVVYIARKFDNTGVGIEDLISIGTIGLIKAINTFKNDKNIKLATYASRC 121

Query: 504 VKQAI 508
           ++  I
Sbjct: 122 IENEI 126


>gi|15925054|ref|NP_372588.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|156980380|ref|YP_001442639.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|255006853|ref|ZP_05145454.2| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|14247837|dbj|BAB58226.1| sigma factor B [Staphylococcus aureus subsp. aureus Mu50]
 gi|156722515|dbj|BAF78932.1| sigma factor B [Staphylococcus aureus subsp. aureus Mu3]
          Length = 256

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 53/232 (22%), Positives = 116/232 (50%), Gaps = 18/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V   I R + D++ ++ +   +++   ++ + +  ++ +++R P+  EIA +L +  E V
Sbjct: 91  VIGEIKRYLRDKTWSVHVARRIKEIGPRIKKVSDELTAELERSPSISEIANRLEVSEEEV 150

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-------LRETTTRV 616
            + +++ +   +L       D S   D  +D + V+ LD   Q +        R    ++
Sbjct: 151 LEAMEMGQSYNALSV-----DHSIEAD--KDGSTVTLLDIMGQQDDHYDLTEKRMILEKI 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L+ RE  +++  F  G++   T E +G    +++  + +++  AI+KL+
Sbjct: 204 LPILSDREREIIQCTFIEGLSQKETGERIG----LSQMHVSRLQRTAIKKLQ 251


>gi|310764851|gb|ADP09801.1| RNA polymerase sigma factor for flagellar operon [Erwinia sp.
           Ejp617]
          Length = 243

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 43/201 (21%), Positives = 93/201 (46%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G++G + A + FD   G   S +    ++ A+   + ++     +P  +R    +
Sbjct: 43  DLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDW---VPRRVRKHARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V    +++      E +  +IA ++ + V  ++++L  T    S +    DE      D 
Sbjct: 100 VTAVIQQLEQNKGGEASEADIATEMGVSVGELQQMLADTN---SSQIYSLDELQEQFADS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E+  A++P+  A+Q NL       ++ +  RE+ +L++ +      D  + E+G 
Sbjct: 157 YETIDEENEALNPVHQAVQENLVGKIAEHISVIPEREQVILQLYY----QQDLNMREIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  R+ Q+ + AI++++
Sbjct: 213 VLSLTETRVSQLHSLAIKRIR 233


>gi|160880601|ref|YP_001559569.1| sporulation sigma factor SigE [Clostridium phytofermentans ISDg]
 gi|160429267|gb|ABX42830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 246

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 42/75 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  +VE NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 63  AKSLLVEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPDKNIKLATYASRC 122

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 123 IENEILMYLRRNSKT 137


>gi|153854689|ref|ZP_01995939.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
 gi|149752793|gb|EDM62724.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
          Length = 246

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 37/57 (64%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+K ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA
Sbjct: 63  ARKILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPDKNIKLATYA 119


>gi|143621|gb|AAA22794.1| sporulation protein [Bacillus subtilis]
          Length = 239

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 104/226 (46%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E  LRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 58  ARAILIERILRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +NKI+ E +               
Sbjct: 115 -----SRCIENE----------------ILMYLRR-NNKIRSEVS--------------- 137

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +   + +   D  I+AN+ ++   + L  L  
Sbjct: 138 ------FYEPLNID---WDGNELLLSDVLGTDDDIITKD--IEANVDKKLLKKALEQLNE 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 187 REKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLR 232


>gi|107100889|ref|ZP_01364807.1| hypothetical protein PaerPA_01001919 [Pseudomonas aeruginosa PACS2]
 gi|152986686|ref|YP_001349226.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PA7]
 gi|313106454|ref|ZP_07792685.1| motility sigma factor FliA [Pseudomonas aeruginosa 39016]
 gi|150961844|gb|ABR83869.1| sigma factor FliA [Pseudomonas aeruginosa PA7]
 gi|310879187|gb|EFQ37781.1| motility sigma factor FliA [Pseudomonas aeruginosa 39016]
          Length = 239

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 56/244 (22%), Positives = 107/244 (43%), Gaps = 30/244 (12%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + +A  +++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K+D   G 
Sbjct: 4   KAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGKGA 63

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F TYA   ++ A+   +       R  VH   ++  V    R +  +  R+    E+A 
Sbjct: 64  SFETYAGIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VTDAIRAIEARTGRDAKDHEVAA 120

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN------ 608
           +L + +E    +L  T+         G    S   D ++D     P D+++  N      
Sbjct: 121 ELQLSLEDYYGILSDTQ---------GSRLYS-FDDLLQDGEHGLPEDTSLSHNEPIHGL 170

Query: 609 ----LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                +      +A L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++  
Sbjct: 171 LDERFQAALADAIAKLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCA 226

Query: 665 RKLK 668
            +L+
Sbjct: 227 ARLR 230


>gi|319937328|ref|ZP_08011735.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807694|gb|EFW04287.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 227

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 101/228 (44%), Gaps = 58/228 (25%)

Query: 444 AKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+ +++E NLRLV  +AKKY + + LQ  DLI  G IGL+KA + +      K  TYA  
Sbjct: 46  ARNQLIEHNLRLVAHIAKKYESTKDLQ-EDLISIGTIGLIKAVDSYKPTKATKLGTYAAK 104

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++  I              +HMR                           KK A+ V  
Sbjct: 105 CIENEIL-------------MHMRGN-------------------------KKTALDV-S 125

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQA-NLRETTTRVLAS 619
           + ++L + K+        G E T  L D +  + K  +  +D+  Q   L+E        
Sbjct: 126 LNEILGVDKD--------GGEMT--LLDILPSDQKEIIDQIDTEDQIKKLQE----YFLL 171

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           LTPRE+ +L  R+G+  +  +T +E+     ++R  + ++E +A+ KL
Sbjct: 172 LTPREQEILIYRYGLNKHKVYTQKEIASTMHISRSYVSRLEKRALIKL 219


>gi|331083018|ref|ZP_08332137.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330399755|gb|EGG79416.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 241

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 42/75 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   FD     K +TYA   
Sbjct: 58  ARACLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFDPVKKIKLATYASRC 117

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 118 IENEILMYLRRNSKT 132



 Score = 38.1 bits (87), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           R+   + +  LT RE+ ++R+RFGI M    + T +EV     +++  I ++E K +++L
Sbjct: 174 RKLLGKAIGKLTKREQTIVRLRFGINMPDGGEKTQKEVADLLGISQSYISRLEKKIMKRL 233

Query: 668 K 668
           K
Sbjct: 234 K 234


>gi|168214239|ref|ZP_02639864.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
 gi|170714290|gb|EDT26472.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
          Length = 235

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 103/222 (46%), Gaps = 52/222 (23%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S K+K E +  E    L +  +G     
Sbjct: 111 -SRCIENE----------------ILMYLRRNS-KVKAEISFYE---PLNIDWDG----- 144

Query: 568 KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 + L   +G D+D  +  + IED+     L +A++            +L+ RE+ 
Sbjct: 145 ----NELLLSDILGTDDDIVY--NMIEDEVDKELLFTAMK------------NLSNREKE 186

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ +RFG+    + T +EV     +++  I ++E K I++LK
Sbjct: 187 IVELRFGLCGYKEKTQKEVADMLGISQSYISRLEKKIIKRLK 228


>gi|303238907|ref|ZP_07325438.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593540|gb|EFL63257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 244

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 106/229 (46%), Gaps = 57/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 62  VKTILIERNLRLVVYIARKFENTGVGVEDLISIGTIGLIKAINTFNPSKNIKLATYA--- 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +N++K E + +             
Sbjct: 119 -----SRCIENE----------------ILMYLRR-NNRMKTEISID------------- 143

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTP 622
                   EP++++    D +   L D +  +N +  +  +I+  + +E     +  L+ 
Sbjct: 144 --------EPLNID---WDGNELLLSDILGTENDL--IHRSIEDEVDKELLNTAMKKLSM 190

Query: 623 REERVLRMRFGI---GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE++++ +RFG+   GM  + T +EV     +++  I ++E K I +LK
Sbjct: 191 REKKIMELRFGLSNGGM--EKTQKEVADMLGISQSYISRLEKKIICRLK 237


>gi|323698081|ref|ZP_08109993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           ND132]
 gi|323458013|gb|EGB13878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans ND132]
          Length = 261

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/203 (23%), Positives = 93/203 (45%), Gaps = 11/203 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G++GL+ A  KF+  LG KF TY+   +K A+   +       R    +R K+  
Sbjct: 66  ELISAGSLGLLDALGKFNPELGIKFDTYSENRIKGAMLDELRRMDWFSR---GLRQKVKV 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +  + R++ ++     T E++     M    V++ L+     + L      E+       
Sbjct: 123 LEDSMRQIEHETGSPATTEQLCAHTGMSDREVQQGLEALNNQVCLSLDSFQENLVGQKKM 182

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            +++    P  SA    + +    ++  LTPRE+ V+ + +G  +N   T E +     +
Sbjct: 183 TDNE----PFQSAAFQEIVDKVANLIEELTPREKLVISLYYGEELNMKETAEVMD----I 234

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           T  R+ Q+ ++A+ KL+   R++
Sbjct: 235 TEGRVSQLHSQALNKLRKTFRAR 257


>gi|260589594|ref|ZP_05855507.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|260540162|gb|EEX20731.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
          Length = 252

 Score = 54.3 bits (129), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 42/75 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   FD     K +TYA   
Sbjct: 69  ARACLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFDPVKKIKLATYASRC 128

Query: 504 VKQAITRSIADQSCT 518
           ++  I   +   S T
Sbjct: 129 IENEILMYLRRNSKT 143



 Score = 38.1 bits (87), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           R+   + +  LT RE+ ++R+RFGI M    + T +EV     +++  I ++E K +++L
Sbjct: 185 RKLLGKAIGKLTKREQTIVRLRFGINMPDGGEKTQKEVADLLGISQSYISRLEKKIMKRL 244

Query: 668 K 668
           K
Sbjct: 245 K 245


>gi|87119467|ref|ZP_01075364.1| flagellar biosynthesis sigma factor FliA [Marinomonas sp. MED121]
 gi|86164943|gb|EAQ66211.1| flagellar biosynthesis sigma factor FliA [Marinomonas sp. MED121]
          Length = 244

 Score = 54.3 bits (129), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 93/200 (46%), Gaps = 14/200 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL++A ++F+   G  F TYA   ++ +I   +         P  +R     
Sbjct: 48  DLIQAGMMGLIEAFKRFESTKGASFETYAGIRIRGSIMDEVRKSDWA---PRSVRRNGRA 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           +    + +  K+ RE +  EI++ + + +    ++L+  ++ +  S E  +  E  +   
Sbjct: 105 IASAIKELEAKLGREASDLEISQAMDISLNEYHEMLQSSMSTQLFSFEELLDSEGLNIET 164

Query: 590 DFIEDKNAVSPL-DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D  ED    S + D   Q  L +     + SL  RE+ VL + +    N +  L+E+G  
Sbjct: 165 DSEEDSAPYSFVEDLGFQTQLAQE----IDSLPEREKLVLSLYY----NDELNLKEIGSV 216

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++A  +LK
Sbjct: 217 LGVSESRVSQIHSQAAMRLK 236


>gi|125972968|ref|YP_001036878.1| sporulation sigma factor SigE [Clostridium thermocellum ATCC 27405]
 gi|256004765|ref|ZP_05429740.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281417179|ref|ZP_06248199.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|125713193|gb|ABN51685.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium thermocellum
           ATCC 27405]
 gi|255991215|gb|EEU01322.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281408581|gb|EFB38839.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|316940796|gb|ADU74830.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 1313]
          Length = 244

 Score = 54.3 bits (129), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 59/230 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   
Sbjct: 62  VKSILIERNLRLVVYIARKFENTGVGVEDLVSIGTIGLIKAINTFDPNKNIKLATYA--- 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++                ++   RR +N++K E                 
Sbjct: 119 -----SRCIENE----------------ILMYLRR-NNRMKTE----------------- 139

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLAS 619
                     IS++ P+    D +   L D +  +N +  +  +I+  + +E     +  
Sbjct: 140 ----------ISIDEPLNVDWDGNELLLSDILGTENDL--IHRSIEDEIDKELLAMAMKK 187

Query: 620 LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ RE++++ +RFG+     + T +EV     +++  I ++E K I +L+
Sbjct: 188 LSVREKKIMELRFGLTNGGVEKTQKEVADMLGISQSYISRLEKKIISRLR 237


>gi|238916778|ref|YP_002930295.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
 gi|238872138|gb|ACR71848.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
          Length = 252

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 52/228 (22%), Positives = 100/228 (43%), Gaps = 30/228 (13%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           ++LV      Y    +++ DL+  G  GL+ A +KFD+    KF TYA   ++ AI   I
Sbjct: 33  VKLVAGRLNMYLGYNVEYDDLVGYGIFGLIDAIDKFDYGKNVKFETYASLRIRGAILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                   IP  +R K  ++     ++ ++     + EE+A +L            IT++
Sbjct: 93  RKMDW---IPRSLRQKQKRIEAAMTKIESETGHIASDEELAAELG-----------ITQD 138

Query: 573 PIS-LETPIGDEDTSHLGDFIEDKNAV-----------SPLDSAIQANLRETTTRVLASL 620
            +S  +  +   +   L ++ E  + V            P D+  +  L++   + + SL
Sbjct: 139 ELSDWQGKMKASNLISLDEYTEAGSEVKMESVGNSHFDQPEDAMEKEELKKMMVKAIDSL 198

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T +E  V+ + +      + TL+E+     V+  R+ Q+  KA+ K+K
Sbjct: 199 TEKERSVVVLYY----YEEMTLKEISLTLEVSESRVSQLHTKALNKMK 242


>gi|163816759|ref|ZP_02208122.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
 gi|158448016|gb|EDP25011.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
          Length = 207

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 94/229 (41%), Gaps = 57/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++E NLRLV  + KKY++      DL+  G IGL+KA + +    G K + YA   
Sbjct: 27  ARRVLIEYNLRLVAHIVKKYSSSVRDPEDLLSIGTIGLIKAIDSYKPEKGCKLAGYAAKC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +  ++                         R   K  RE                 
Sbjct: 87  IENELLMNL-------------------------RQEKKKSRE----------------- 104

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI-QANLRETTTRVLAS 619
                     +S+  PIG +   +   + D I    +  PL+  I + +L    + +   
Sbjct: 105 ----------VSMYEPIGTDKEGNEIVIMDIISTSESC-PLEKLITEDHLNHLPSCMNQI 153

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LTPRE  +++MR+GI      T +E  K   ++R  + +IE +A+ KL+
Sbjct: 154 LTPREYHIIQMRYGILGEAPLTQKETAKILGISRSYVSRIEKRALSKLR 202


>gi|153953966|ref|YP_001394731.1| sporulation sigma factor SigE [Clostridium kluyveri DSM 555]
 gi|219854580|ref|YP_002471702.1| hypothetical protein CKR_1237 [Clostridium kluyveri NBRC 12016]
 gi|146346847|gb|EDK33383.1| SigE2 [Clostridium kluyveri DSM 555]
 gi|219568304|dbj|BAH06288.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 235

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 101/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F+     K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGVNVEDLVSVGTIGLIKAVNTFNPEKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++K+K E +  E    L +  +G   +L
Sbjct: 111 -SRCIENE-----ILMYLRR------------NSKVKAEISFYE---PLNVDWDGNELLL 149

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   D   +  FIED+     L  A++             L+ RE+ +
Sbjct: 150 ----------SDILGTDNDVVYSFIEDEVDKQLLVIAMK------------KLSDREKEI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T +EV     +++  I ++E + IR+L+
Sbjct: 188 VNLRFGLNGKKEKTQKEVADLLGISQSYISRLEKRIIRRLR 228


>gi|95929871|ref|ZP_01312612.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95134167|gb|EAT15825.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 243

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 110/234 (47%), Gaps = 22/234 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E+V++++ LV  V  +   +   F+   D+     +GLM AA +FD   G  F T+A 
Sbjct: 15  KNELVKSHMSLVHLVVDRMRAQVPGFVTKDDMTSAAMMGLMDAATRFDPSRGIMFKTFAE 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I       R    +R+K  ++ +T  +M +++ R P  EE+A+ + M ++
Sbjct: 75  RRIRGAIYDEIRKMDWFSR---SLREKQGRIGKTITQMEHRLGRTPEEEEVAEAMDMTLD 131

Query: 562 GVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-----TT 614
             R +L        +SL   + D D     +F++     SP   ++Q  + E+       
Sbjct: 132 EYRHMLGQVCHLGCVSLNETLDDRDDGR--NFLDLLTDDSP---SVQQRIEESELASELA 186

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  L+ +E  V+ + +      + T +E+ +   +T  RI Q+ ++A+ KLK
Sbjct: 187 GQLDKLSEKERLVISLYY----YEELTQKEIAEVLDLTEGRISQLHSQALVKLK 236


>gi|167465670|ref|ZP_02330759.1| sporulation sigma factor SigE [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 196

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 53/221 (23%), Positives = 101/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 19  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 71

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++            R ++KI+ E + +                 
Sbjct: 72  -SRCIENE-----ILMYL------------RRNSKIRTEVSFD----------------- 96

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
               EP++++    D +   L D +  +N     +   Q + R+   + L  LT RE  +
Sbjct: 97  ----EPLNID---WDGNELLLSDVLGTENDTIYRNIEEQVD-RKLLHKALDKLTERERVI 148

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 149 MELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 189


>gi|167630813|ref|YP_001681312.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
 gi|167593553|gb|ABZ85301.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
          Length = 252

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 61/270 (22%), Positives = 109/270 (40%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F+A  +     +   + S S    +S  E    ++    G+ EA   +++++  NLRLV 
Sbjct: 9   FLAFLLKGFAALFGGLNSNSFPKPLSAEEEAEYIARTTGGDAEA---REKLITHNLRLVA 65

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KKY +   +  DLI  G IGL+KA   F      + STYA        +R I ++  
Sbjct: 66  HICKKYYSNDEEIEDLISIGTIGLIKAINTFKAEKQVRLSTYA--------SRCIENE-- 115

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
              I +H+R+K               KR+       + + +  +G R             
Sbjct: 116 ---ILMHLRNK---------------KRDSRVVSFEESVGIDKDGNRMTY---------- 147

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           + I   D   + + +E  + +  L +           +V   L  +E  +L +R+G+   
Sbjct: 148 SDILGTDGDTVAELVERSSEIEDLQN-----------KVRRRLNKKEREILTLRYGLSDG 196

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           T  T + V     ++R  + +IE + IRKL
Sbjct: 197 TPKTQQTVADLLNISRSYVSRIEGRGIRKL 226


>gi|227873530|ref|ZP_03991775.1| possible DNA-directed RNA polymerase sigma subunit D [Oribacterium
           sinus F0268]
 gi|227840620|gb|EEJ51005.1| possible DNA-directed RNA polymerase sigma subunit D [Oribacterium
           sinus F0268]
          Length = 259

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 107/230 (46%), Gaps = 13/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+    + +V S+A +       F+   D++ EG I +M+A E++D     KF T+ 
Sbjct: 29  VKQELTMRYVYIVRSIAYQMREMYHDFMQTDDIVNEGVIEIMRAIERYDESKDNKFETFI 88

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  +   +        +P +       +      ++N++ R PT EE+A  L M V
Sbjct: 89  SRRIRGMVIDMMRKNDW---LPRNFHKDSRSIETATVELNNRLGRAPTDEELADYLNMNV 145

Query: 561 EGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           + ++K+ +++     +SL+    DE    L     + ++  P  S +Q       T  + 
Sbjct: 146 KKLQKIQRMSNMVNVLSLDMTY-DEGNETLLQIPSEDHSTQPEFSFMQKENVRALTEAIE 204

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SL  +E+ V+ + +   +N    + ++ +   V++ R+ Q+ + AIRKL+
Sbjct: 205 SLQEKEKLVISLYYVEELN----MNQIAEVMEVSQPRVSQLHSIAIRKLR 250


>gi|146282908|ref|YP_001173061.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri A1501]
 gi|145571113|gb|ABP80219.1| flagellar biosynthesis sigma factor FliA [Pseudomonas stutzeri
           A1501]
          Length = 241

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + +A  A+  +++    LV  +A     R    +Q  DLIQ G IGL++AA+K+D   G 
Sbjct: 5   KAQAKDAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDAGKGA 64

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F TYA   ++  +   +       R  VH   ++  V    R +  K  R+    E+A 
Sbjct: 65  SFETYAGIRIRGTMLDEVRKGDWAPR-SVHRNSRM--VSEAIRAIEAKTGRDAKDHEVAA 121

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLR 610
           +L + ++    +L   +     S +  +  ++  H GD  ED  +    P         +
Sbjct: 122 ELKLSLDEYYGILGDTLGSRLFSFDDLL--QEGEH-GDLQEDAGSTHPEPFRDLEDERFQ 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     +A+L  RE+ VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 179 QALADAIANLPEREKLVLSLYYDEELN----LKEIGQVLGVSESRVSQLHSQCAARLR 232


>gi|238762342|ref|ZP_04623313.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Yersinia
           kristensenii ATCC 33638]
 gi|238699327|gb|EEP92073.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Yersinia
           kristensenii ATCC 33638]
          Length = 231

 Score = 53.9 bits (128), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 50/205 (24%), Positives = 95/205 (46%), Gaps = 31/205 (15%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q   +GL++A  ++    G +F+ YA+  ++ A+   + +       P  +R K HK
Sbjct: 47  DMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGAVLDQLREHDWR---PRRLRQKTHK 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--------EPISLETPIGDE 583
                R+++ K+  EP+ EEIA  L +  E  ++ L +          E +SL+TP    
Sbjct: 103 TNEAIRQLAKKLGHEPSFEEIATALQLTAEEYQEYLLLESASGMESLDEILSLDTPTDAL 162

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +  L + I            I+ NL       +ASL  RE+ +L + +      + +++
Sbjct: 163 QSRELEESI-----------IIEDNL----NHAIASLEKREQMILHLYY----QQEMSMK 203

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ +   +T  RI Q+  K ++K+K
Sbjct: 204 EIAQVLDLTEARICQLNKKLVQKIK 228


>gi|254433106|ref|ZP_05046614.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus oceani
           AFC27]
 gi|207089439|gb|EDZ66710.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus oceani
           AFC27]
          Length = 189

 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 85/198 (42%), Gaps = 26/198 (13%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL++AA  ++   G  F TYA   ++ AI   I         P  +  K  +V    R 
Sbjct: 2   IGLLEAARNYNASQGASFETYAGIRIRGAILDEIRRNDWA---PRSVHRKARQVAEVMRE 58

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + N+  R+    E+A++L +P+    ++L+            G      L +F E + + 
Sbjct: 59  VENREGRDARDHEVAEELGLPLNEYHRLLQ----------DAGGYRVFSLDEFNEGEES- 107

Query: 599 SPLDSAIQA--------NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            PL ++++         N R      +  L  RE  V+ + +      D  L E+G+   
Sbjct: 108 EPLSASLKGPYEGLQDQNFRGALVEAIEGLPERERLVMSLYY----VEDLNLREIGEVLG 163

Query: 651 VTRERIRQIEAKAIRKLK 668
           V+  R+ QI ++A+ +L+
Sbjct: 164 VSESRVSQIHSQAVLRLR 181


>gi|213419681|ref|ZP_03352747.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 174

 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 44/177 (24%), Positives = 85/177 (48%), Gaps = 14/177 (7%)

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++
Sbjct: 2   FTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVAER 58

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI----EDKNAVSPLDSAIQANLRE 611
           L +PV   R++L  T           DE     GD I    E+    +PL   ++ +LR+
Sbjct: 59  LGIPVAEYRQMLLDTNNSQLFSY---DEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQ 115

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + SL  RE+ VL + +   +N    L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 116 RVMDAIESLPEREQLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIKRLR 168


>gi|160892593|ref|ZP_02073383.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
 gi|156865634|gb|EDO59065.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
          Length = 245

 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 38/64 (59%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F      K +TYA   +
Sbjct: 63  KKILIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFKCDKNIKLATYASRCI 122

Query: 505 KQAI 508
           +  I
Sbjct: 123 ENEI 126


>gi|228912145|ref|ZP_04075860.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228847482|gb|EEM92421.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 232

 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 77/172 (44%), Gaps = 24/172 (13%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DL Q G IGL+KA + FD   G KFSTYA+  +   I R+I D         H +
Sbjct: 34  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAIRD---------HQK 84

Query: 527 DKIHKVVRTARRMSNKIKRE----PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-- 580
            K+ + V + +    KI R+      PEEIA  L   V  V   L       SL   +  
Sbjct: 85  VKVQRSVYSVK---GKILRQNLGDEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVHQ 141

Query: 581 --GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             G+E+ + L   +EDK A +  D +I    R       + L+ +E  VL M
Sbjct: 142 SNGNEELT-LESMLEDKKAENVEDVSIN---RMVIQSFKSQLSHKEHIVLDM 189


>gi|158340491|ref|YP_001521485.1| RNA polymerase sigma-2 subunit [Acaryochloris marina MBIC11017]
 gi|158310732|gb|ABW32346.1| RNA polymerase sigma-2 subunit domain protein [Acaryochloris marina
           MBIC11017]
          Length = 697

 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 14/140 (10%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++RK +     +   ++  ++RLV  +AK+Y        DLIQEG +G+  A  KFD   
Sbjct: 38  LIRKAKRGHETSLSWLMIGHVRLVAKLAKQYAWTLDDAQDLIQEGMLGIRHAVGKFDSTK 97

Query: 493 GYKFSTYAMWWVKQAITR-SIADQSCTIRIP----VHMRDKIHKVVRTARRMSNKIKREP 547
           G KFSTYA  W++  I R    ++   +R+P    VH+ D+++       R+ N+   + 
Sbjct: 98  GCKFSTYARGWIRGYIRRFCYKNRPKQLRLPEKKQVHL-DRVY-------RLQNEFP-DA 148

Query: 548 TPEEIAKKLAMPVEGVRKVL 567
             EEIA+K  + +E +  +L
Sbjct: 149 NLEEIARKANLKLEYIEDLL 168


>gi|325273563|ref|ZP_08139791.1| flagellar biosynthesis sigma factor [Pseudomonas sp. TJI-51]
 gi|324101302|gb|EGB98920.1| flagellar biosynthesis sigma factor [Pseudomonas sp. TJI-51]
          Length = 246

 Score = 53.9 bits (128), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 102/232 (43%), Gaps = 17/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ A K+D   G  F TYA
Sbjct: 16  AQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAMRAVEARTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTRV 616
           +    +L  T      S +  +  +D  H G   ED     V P     +   +   T  
Sbjct: 133 DDYYAILNDTLGSRLFSFDDLL--QDGEHEG-LHEDGASGQVEPARGLEEERFQLALTEA 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 190 IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|228943596|ref|ZP_04106021.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976443|ref|ZP_04136903.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981654|ref|ZP_04141950.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228778139|gb|EEM26410.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228783244|gb|EEM31363.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228816045|gb|EEM62245.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 232

 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 74/172 (43%), Gaps = 24/172 (13%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DL Q G IGL+KA + FD   G KFSTYA+  +   I R+I D            
Sbjct: 34  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAIRDHQKV-------- 85

Query: 527 DKIHKVVRTARRMSNKIKRE----PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-- 580
               KV R+   +  KI R+      PEEIA  L   V  V   L       SL   +  
Sbjct: 86  ----KVQRSVYSIKGKILRQNLEYEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVHQ 141

Query: 581 --GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             G+E+ + L   +EDK A +  D +I    R       + L+ +E  VL M
Sbjct: 142 SNGNEELT-LESMLEDKKAENVEDVSIN---RMVIQAFKSQLSHKEHIVLDM 189


>gi|307747900|gb|ADN91170.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni M1]
          Length = 622

 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 38/58 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +D P RMYLREMG I LL+++ EI I+K+IE G  +++ + C  P     ++ +++ L
Sbjct: 102 SDSPDRMYLREMGQIALLNKDEEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPL 159


>gi|240145516|ref|ZP_04744117.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257202333|gb|EEV00618.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
          Length = 207

 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 95/243 (39%), Gaps = 68/243 (27%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++KG  EA   + E+   N+RLV  VAKKY N      DLI  G IGLMKA   +    G
Sbjct: 20  LKKGSLEA---RNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGLMKAIATYKEDYG 76

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            + +TYA         R I ++     + ++ R K             K+ RE       
Sbjct: 77  SRLATYA--------ARCIDNE-----LLMYFRAK------------KKVSRE------- 104

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
                               +SL  PIG   + +  HL D +E +         ++   R
Sbjct: 105 --------------------VSLYEPIGMDKEGNQIHLLDIVESEEP-----DVVEMMER 139

Query: 611 ETTTRVLASLTP-----REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                 L  L P     RE  ++  R+G+  N   T  E+     ++R  + +IE KA+ 
Sbjct: 140 TRQIEKLLGLVPKVLQERELYIVVHRYGLFGNKAMTQREIASAVGISRSYVSRIEKKALD 199

Query: 666 KLK 668
           KLK
Sbjct: 200 KLK 202


>gi|331696199|ref|YP_004332438.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950888|gb|AEA24585.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 303

 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/239 (21%), Positives = 111/239 (46%), Gaps = 36/239 (15%)

Query: 445 KKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKFDWCLGY-KFSTYAM 501
           ++++V + L +V  +A++Y N  R   + DL+Q G +GL+ A +++D      +F  Y +
Sbjct: 73  REQLVLSFLPVVEHLARRYGNGYRVAAYDDLVQTGTVGLITAIDRWDPERAKGEFLGYLI 132

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+  I R   D++ ++R+P  ++D    + + +  ++ ++ R P P E+A  L +  E
Sbjct: 133 PCVRGEILRYFRDRTWSMRVPRRLKDLGVAIGKASGPLTQELGRAPRPSELAAHLGVDRE 192

Query: 562 GV------------RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            V              +  +T +  + E  +G  + ++  D +E   A+ PL        
Sbjct: 193 EVIEALAAAADRRATPLFPVTHDDDAPEERVGTVEKAY--DHVEYAIALKPL-------- 242

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L  RE  +L +RF      D T  ++  +  V++  + ++ A+ + +L+
Sbjct: 243 -------IEQLPERERLILTLRF----FGDQTQSQIAARVGVSQMHVSRLLARTLERLR 290


>gi|302556940|ref|ZP_07309282.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474558|gb|EFL37651.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 285

 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 99/215 (46%), Gaps = 13/215 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 48  RDELVTAWLPMAHRIAGRFRDRGEAVEDLRQVAALGLVKAIDRFDPSRG-AFESYAVPTI 106

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEG 562
              + R   D+   +R+P  +++  +K VR ARR   +    P P    IA    +  + 
Sbjct: 107 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARRELTQSPGSPEPSVAAIAAHTGLTEDE 165

Query: 563 VRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   ++  +    +SL+  +  D+D   L D +   +  S  D  +    RE+    L  
Sbjct: 166 VGAGMEALESFSTLSLDAELSSDDDGYSLADTLGASD--SSYDVVVD---RESAKEGLRR 220

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           L  RE  +L MRF   M      +++G  Q  V+R
Sbjct: 221 LPERERAILYMRFFEDMTQSRIADQLGISQMHVSR 255


>gi|296133648|ref|YP_003640895.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032226|gb|ADG82994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 242

 Score = 53.9 bits (128), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 3/79 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E  +++S +  G+      +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 42  LSNAEENYLISKLATGDAAV---RSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 98

Query: 482 MKAAEKFDWCLGYKFSTYA 500
           +KA   FD     K +TYA
Sbjct: 99  IKAVNTFDPAKKIKLATYA 117


>gi|293400805|ref|ZP_06644950.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305831|gb|EFE47075.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 247

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 91/227 (40%), Gaps = 55/227 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            + +++E NLRLV  + KKY  +  Q  DLI  G IGL+KA + F    G+K +TYA   
Sbjct: 50  CRNKLIEHNLRLVAHIVKKYDIKKEQTEDLISIGTIGLIKAIDSFKPEKGHKLTTYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++             I   +R+++     +                    
Sbjct: 107 -----SRCIENE-------------ILMYLRSSKNYFQNV-------------------- 128

Query: 564 RKVLKITKEPISLETPIG-DEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                      SL  PI  D+D S   L D I      S ++  +  +      + L  L
Sbjct: 129 -----------SLNDPIATDKDGSEITLIDAISSPQETSIIEDMVVEDNISKLKQFLHVL 177

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE  ++  RFG+    + T  E+ KQ  ++R  + +IE +A  KL
Sbjct: 178 DSRELEIITKRFGLYGVEEETQREIAKQLHISRSYVSRIEKRAFMKL 224


>gi|82702442|ref|YP_412008.1| sigma 28 (flagella/sporulation) [Nitrosospira multiformis ATCC
           25196]
 gi|82410507|gb|ABB74616.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosospira
           multiformis ATCC 25196]
          Length = 242

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 98/200 (49%), Gaps = 12/200 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI-RIPVHMRDKIH 530
           DL+Q G IGLM+A  +++   G +F TYA    +Q I  ++ D+   +  +P   R  + 
Sbjct: 40  DLVQVGMIGLMEALNRYEEMPGAQFETYA----QQRIRGAMLDELRQLDWLPRGARRVMR 95

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHL 588
           ++      + +++ R P+  +IA++L + +E  +++L   K  + I  E    DED   L
Sbjct: 96  QIESAINVLQHRLGRSPSERQIAEELGVSIESYQQMLFEAKGTQLIHYEDFSDDEDDDFL 155

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
                D N   PL + +  +LR      +  L  RE+ ++    G+    +   +E+G  
Sbjct: 156 ERNCAD-NTADPLAALLDGDLRRILINAIEILPEREKTLM----GLYYEQELNFKEIGAV 210

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  RI Q+ ++AI +L+
Sbjct: 211 LGVSESRICQMHSQAIARLR 230


>gi|168704991|ref|ZP_02737268.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 169

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/152 (26%), Positives = 66/152 (43%), Gaps = 34/152 (22%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G++  DLI  G  GL+ A + FD   G KF TY +  ++ A+   +        +P  +R
Sbjct: 18  GVELDDLISAGVFGLLDAIDAFDLTRGVKFETYCVPRIRGAMLDELRTMDW---VPRLVR 74

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            K  K+    +++   + R P PEE+++KL +P+E              LE+ +GD    
Sbjct: 75  SKASKMEAARKQLEAALGRPPKPEELSEKLGIPLE-------------QLESYVGDATAV 121

Query: 587 HLG------------------DFIEDKNAVSP 600
           +L                   D +EDK A SP
Sbjct: 122 NLVSLNKKWYETDSYKDVREIDILEDKKAESP 153


>gi|326942736|gb|AEA18632.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 248

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 74/172 (43%), Gaps = 24/172 (13%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DL Q G IGL+KA + FD   G KFSTYA+  +   I R+I D            
Sbjct: 50  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAIRDHQKV-------- 101

Query: 527 DKIHKVVRTARRMSNKIKRE----PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-- 580
               KV R+   +  KI R+      PEEIA  L   V  V   L       SL   +  
Sbjct: 102 ----KVQRSVYSIKGKILRQNLEYEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVHQ 157

Query: 581 --GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             G+E+ + L   +EDK A +  D +I    R       + L+ +E  VL M
Sbjct: 158 SNGNEELT-LESMLEDKKAENVEDVSIN---RMVIQAFKSQLSHKEHIVLDM 205


>gi|218133693|ref|ZP_03462497.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991068|gb|EEC57074.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
          Length = 254

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 95/218 (43%), Gaps = 9/218 (4%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           ++LV      Y    +++ DL   G  GL+ A +KFD     KF TYA   ++ AI   I
Sbjct: 33  VKLVAGRLGMYLGYSVEYDDLCGYGIFGLIDAIDKFDCNKNVKFETYASLRIRGAILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                   IP  +R K  K+     ++  +     T EE+A++L + ++        TK 
Sbjct: 93  RKMDW---IPRSLRQKQKKIDAAMSKIEAQKGSVATDEELAQELGITLDEFNDWQGKTKA 149

Query: 573 P--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
              ISL+     + T    D + +     P D   +  L++     ++ LT +E  V+ +
Sbjct: 150 TNLISLDEYTETQGTEAKMDSVTNARFDQPEDVVEKEELKKMIVEAISLLTDKERSVVTL 209

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      + TL+E+     V+  R+ Q+  KA+ K+K
Sbjct: 210 YY----YEEMTLKEISLVLDVSESRVSQLHTKALLKMK 243


>gi|28210822|ref|NP_781766.1| RNA polymerase sigma-G factor [Clostridium tetani E88]
 gi|28203260|gb|AAO35703.1| RNA polymerase sigma-G factor [Clostridium tetani E88]
          Length = 161

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 47/164 (28%), Positives = 86/164 (52%), Gaps = 14/164 (8%)

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R + D + +IR+   +RD  +K ++   ++  K  +EPT  EIAK+L +P E V   L
Sbjct: 6   IRRYLRDNN-SIRVSRSLRDIAYKALQVRDKLIAKNDKEPTVSEIAKELDIPREDVVFAL 64

Query: 568 KITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              ++P+SL  PI  +  D+ ++ D I D KN    LD +   N+       + +L  RE
Sbjct: 65  DAIQDPLSLFEPIYQDGGDSIYVMDQISDTKN----LDDSWIENI--AIKEAMRNLNKRE 118

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++
Sbjct: 119 KLILSLRFFDG----RTQMEVADEIGISQAQVSRLEKTALKHMR 158


>gi|298243769|ref|ZP_06967576.1| RNA polymerase sigma factor, sigma-70 family [Ktedonobacter
           racemifer DSM 44963]
 gi|297556823|gb|EFH90687.1| RNA polymerase sigma factor, sigma-70 family [Ktedonobacter
           racemifer DSM 44963]
          Length = 453

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 105/243 (43%), Gaps = 55/243 (22%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTN--RGL-------QFLDLIQEGNIGLMKAAEKF-- 488
           EA    ++++E +LRLVI VA ++    R L         +DLIQ GN+ L++ A ++  
Sbjct: 55  EARAIVQQLIEGSLRLVIFVAARFYRYYRALDGGRFRVPLMDLIQTGNMALVECAHRYLD 114

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
                  FS YA  +++ A+ +S            ++R  + KV              P 
Sbjct: 115 REAEHTDFSAYAASYIRFALRKS------------YIRASLFKV--------------PQ 148

Query: 549 PE--EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E  E A++           L    E  SL+ P  DE T  L D +E      PL    Q
Sbjct: 149 AEWDEAAEQ---------GRLFQFYEVSSLDQPFSDESTRSLLDCLETPE---PLSENTQ 196

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           A  R  T  +LA +  RE++V+R+R+G+       HT +E+  +   + +    IE + +
Sbjct: 197 ACERAET--LLARVPEREQQVVRLRYGLDPLDQRTHTYQEIADKIGASVQTCLNIEQRVL 254

Query: 665 RKL 667
           + L
Sbjct: 255 QAL 257


>gi|297616993|ref|YP_003702152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144830|gb|ADI01587.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 241

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 35/57 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K  ++E NLRLV+ +AKK+ N G+   DL+  G IGL+KA   F+     K +TYA
Sbjct: 60  VKSTLIEHNLRLVVYIAKKFENTGINIEDLVSIGTIGLIKAVNTFEPRKNIKLATYA 116


>gi|296121398|ref|YP_003629176.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
 gi|296013738|gb|ADG66977.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
          Length = 259

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 95/211 (45%), Gaps = 21/211 (9%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLI  G  GLM A E FD   G KF TY +  ++ A+   +        +P  +R
Sbjct: 51  GVDINDLISAGVFGLMDAIEAFDMERGVKFETYCVPRIRGAMLDELRTMDW---VPRLVR 107

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL--------ET 578
            K  K+    ++   ++ R P   E+A K+ +P++   K LK     ++L        ET
Sbjct: 108 SKASKLESARKQAEAELGRPPADNEVAAKMGVPLDEYEK-LKSEASAVNLVSLNKKWYET 166

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
               +D   + D IED     P  S  + +L +  T+ L     R ER++ + +      
Sbjct: 167 D-SYKDVREI-DIIEDTKGEDPTLSIQKRDLMKLVTKGLN----RNERLIIILY---YYE 217

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + T++E+G    ++  R+ Q+ +  + +LK 
Sbjct: 218 ELTMKEIGSTLGLSESRVSQMHSSIVNRLKE 248


>gi|226225717|ref|YP_002759823.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
 gi|226088908|dbj|BAH37353.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
          Length = 251

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 107/246 (43%), Gaps = 42/246 (17%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A+  ++E +L LV  VA++  +R L     F +L+  G IGLM A E FD   G  FST+
Sbjct: 16  ARDRLLEEHLGLVHHVARQ-VSRTLAVRADFDELVSAGTIGLMTALEGFDASRGLAFSTF 74

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM- 558
           A   ++ AI   +  Q     +P  +R K  ++            R P   E+A++L + 
Sbjct: 75  AAPRIRGAILDELRKQD---HVPRSIRRKTREITAAREAFQRASGRAPEDRELAEQLNVD 131

Query: 559 ---------PVEGVRKVLKITKEPISLE--TPIGDE-----DTSHLGDFIEDKNAVSPLD 602
                     VEG   +  + + P   E  TP+  E     + S + D +  +  VS L 
Sbjct: 132 LETLWRWQADVEGAHHI-PLDRAPGERENTTPVPAEVLTSGEESGVEDSLTHEQEVSHLK 190

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            AI   L+E   R++ SL   EE                L E+ K   +T  R+ QI +K
Sbjct: 191 DAI-LRLKE-QERIVLSLYYFEEL--------------KLHEIAKVLELTESRVSQIRSK 234

Query: 663 AIRKLK 668
           A+ KL+
Sbjct: 235 ALSKLR 240


>gi|300854418|ref|YP_003779402.1| RNA polymerase sigma-E factor [Clostridium ljungdahlii DSM 13528]
 gi|300434533|gb|ADK14300.1| RNA polymerase sigma-E factor precursor [Clostridium ljungdahlii
           DSM 13528]
          Length = 241

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 52/233 (22%), Positives = 102/233 (43%), Gaps = 66/233 (28%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F+     K +TYA   
Sbjct: 60  VRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGLIKAVNTFNPEKKIKLATYA--- 116

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R                 +   T  EI+          
Sbjct: 117 -----SRCIENE-----ILMYLR-----------------RNSKTKAEIS---------- 139

Query: 564 RKVLKITKEPISLE--------TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                   EP++++        + I   D   + +FIED+     +D       ++    
Sbjct: 140 ------FYEPLNIDWDGNELLLSDILGTDNDVVYNFIEDE-----VD-------KQLLML 181

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L+ RE+ ++ +RFG+   ++ T +EV     +++  I ++E + I++L+
Sbjct: 182 AMKKLSDREKEIVNLRFGLNGKSEKTQKEVADLLGISQSYISRLEKRIIKRLR 234


>gi|124023131|ref|YP_001017438.1| type III sigma factor [Prochlorococcus marinus str. MIT 9303]
 gi|123963417|gb|ABM78173.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9303]
          Length = 269

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/100 (33%), Positives = 52/100 (52%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++  ++ T  G +  DLIQE  +GL+ A EKFD   G+K S+YAM      I     D+S
Sbjct: 52  LAATRQATRGGEELDDLIQEARLGLIMAMEKFDANRGFKVSSYAMARANGQILHFRRDRS 111

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
             +R+P  +RD   + +R  +   N      T E++A +L
Sbjct: 112 QIVRVPWRLRDLYTRGMRLQQMQQNDGLNPLTEEQLAAQL 151


>gi|294084434|ref|YP_003551192.1| RNA polymerase sigma 28 subunit FliA/WhiG [Candidatus
           Puniceispirillum marinum IMCC1322]
 gi|292664007|gb|ADE39108.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Puniceispirillum marinum IMCC1322]
          Length = 241

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 52/199 (26%), Positives = 98/199 (49%), Gaps = 15/199 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G  GL+ AA+ +    G  FS+YA   ++ +I   +   S   R  + M+ K  +
Sbjct: 42  DLVQIGYYGLVMAAQNYTVQEGATFSSYASIRIRGSIVDHLRKNSNLCRTTIQMQKKARQ 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLG 589
                R+   K+ R+P+ +E+A  L +  E +R+  +  +  +  SL+  + DE +    
Sbjct: 102 SEEILRQ---KLGRDPSIDEVASDLDIAPEEMREWEQAFQANVHQSLDN-VYDEFSIW-- 155

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F+ ++N  +P D+     LR+     L +L  RE  V+++ +   +N    + E+ +  
Sbjct: 156 -FVSNEN--TPEDNISDNELRDVLKDALTTLPEREALVIQLYYVEELN----VYEIAEIL 208

Query: 650 CVTRERIRQIEAKAIRKLK 668
            VT  R+ QI+  AI +L+
Sbjct: 209 DVTTGRVSQIKKAAIARLR 227


>gi|303326430|ref|ZP_07356873.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
 gi|302864346|gb|EFL87277.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
          Length = 260

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/217 (24%), Positives = 101/217 (46%), Gaps = 13/217 (5%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +R +    K    R ++  ++I  G +GLM+A  KF   LG +F TYA    +  I  ++
Sbjct: 43  IRFLALRLKSKLPRSVELGEMISSGTLGLMEALGKFRPQLGIRFETYA----ENRIRGAM 98

Query: 513 ADQSCTI-RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
            D+   +   P  +R ++  +    R++ ++  R+ T EE+     + +  VR+ L+  +
Sbjct: 99  LDELRRLDWFPRSLRQRVRVLDEAMRKVEHEQGRQATEEELQDITGLELRDVRQGLEALQ 158

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             + L      +DT   GD  E      P  +     L E    ++  LTPRE+ VL + 
Sbjct: 159 NQLWLSLD-AIQDTLA-GDGPESGG--EPYSNTALRELVERVAPLIERLTPREKLVLSLY 214

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +N   T E +G    +T  R+ Q+ ++A+ +L+
Sbjct: 215 YTDELNMRETAEIMG----ITEGRVSQLHSQALGRLR 247


>gi|126700257|ref|YP_001089154.1| sporulation sigma factor SigE [Clostridium difficile 630]
 gi|254976236|ref|ZP_05272708.1| sporulation sigma factor SigE [Clostridium difficile QCD-66c26]
 gi|255093623|ref|ZP_05323101.1| sporulation sigma factor SigE [Clostridium difficile CIP 107932]
 gi|255101811|ref|ZP_05330788.1| sporulation sigma factor SigE [Clostridium difficile QCD-63q42]
 gi|255307678|ref|ZP_05351849.1| sporulation sigma factor SigE [Clostridium difficile ATCC 43255]
 gi|255518036|ref|ZP_05385712.1| sporulation sigma factor SigE [Clostridium difficile QCD-97b34]
 gi|255651152|ref|ZP_05398054.1| sporulation sigma factor SigE [Clostridium difficile QCD-37x79]
 gi|255656620|ref|ZP_05402029.1| sporulation sigma factor SigE [Clostridium difficile QCD-23m63]
 gi|260684218|ref|YP_003215503.1| sporulation sigma factor SigE [Clostridium difficile CD196]
 gi|260687877|ref|YP_003219011.1| sporulation sigma factor SigE [Clostridium difficile R20291]
 gi|296449924|ref|ZP_06891688.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296878306|ref|ZP_06902314.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|306521002|ref|ZP_07407349.1| sporulation sigma factor SigE [Clostridium difficile QCD-32g58]
 gi|115251694|emb|CAJ69529.1| RNA polymerase sigma-E factor [Clostridium difficile]
 gi|260210381|emb|CBA64762.1| RNA polymerase sigma-E factor [Clostridium difficile CD196]
 gi|260213894|emb|CBE05927.1| RNA polymerase sigma-E factor [Clostridium difficile R20291]
 gi|296261194|gb|EFH08025.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296430604|gb|EFH16443.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 240

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 107/237 (45%), Gaps = 52/237 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K E + S+ K  ++E NLRLV+ +++K+ N G+   DLI  G IGL+KA   F    
Sbjct: 48  LLQKLETDESV-KSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGLIKAVNTFKLNK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA        +R I ++     I +++R             +NK K E + +  
Sbjct: 107 NIKLATYA--------SRCIENE-----ILMYLRK------------NNKKKTEVSFD-- 139

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                              EP++++    D +   L D +  +N         + + R+ 
Sbjct: 140 -------------------EPLNIDL---DGNELLLSDVLGTENDEIYKIIEEEID-RDL 176

Query: 613 TTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               L  L+ RE++++ +RFG I    + T +EV     +++  I ++E K I +L+
Sbjct: 177 LVMALDRLSDREKQIMELRFGLIDKGIEKTQKEVAGMLGISQSYISRLEKKIISRLQ 233


>gi|126664990|ref|ZP_01735973.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
 gi|126630360|gb|EBA00975.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
          Length = 246

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 107/260 (41%), Gaps = 62/260 (23%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           R G  +AS     ++E +  LV  +A     R    +Q  DL+Q G IGL++A++++   
Sbjct: 12  RSGASDASW----LIEEHAPLVKKIALHLLARLPSSVQLEDLMQAGMIGLLEASQRYTTG 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK 544
            G  F TYA                  IRI   M D+I K       V R +RR+S+ IK
Sbjct: 68  KGATFETYA-----------------GIRIRGAMVDEIRKGDWVPRSVHRNSRRISSAIK 110

Query: 545 -------REPTPEEIAKKLAMPVEGVRKVLKITKEP--ISL-------ETPIGDEDTSHL 588
                  RE    E+A +L M +      L  +      SL       E PI   +T   
Sbjct: 111 AVEGREGRESHDVEVAAELDMTLSEYHSCLADSNSGRLFSLDELNDSGELPIEQSET--- 167

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
                D N   PL    +   R +    + +L  RE+ VL + +   +N    L E+G  
Sbjct: 168 -----DDN---PLHGVSEFAFRNSLAAAIETLPEREKLVLSLYYQEELN----LREIGAV 215

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+  R+ QI ++A  +L+
Sbjct: 216 LDVSESRVSQIHSQAALRLR 235


>gi|268611133|ref|ZP_06144860.1| sporulation sigma factor SigE [Ruminococcus flavefaciens FD-1]
          Length = 232

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 39/65 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K ++E NLRLV+ +AKK+ + G+   DL+  G IGL+KA   F      K +TYA   
Sbjct: 51  ARKYLIEHNLRLVVYIAKKFESSGVGIEDLVSIGTIGLIKAVNTFCPTKNIKLATYASRC 110

Query: 504 VKQAI 508
           ++  I
Sbjct: 111 IENEI 115


>gi|207743453|ref|YP_002259845.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
 gi|206594850|emb|CAQ61777.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
          Length = 184

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 48/74 (64%), Gaps = 3/74 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE  A   ++ M+E NLRLV+S+AK Y  +G+
Sbjct: 109 VQHYLNRISIKPLLTPAEELHFSTRAKAGEFAA---RQVMIERNLRLVVSIAKGYLKQGV 165

Query: 469 QFLDLIQEGNIGLM 482
           + +++I EGN G+M
Sbjct: 166 RLMEMISEGNRGVM 179


>gi|168206182|ref|ZP_02632187.1| sigma factor [Clostridium perfringens E str. JGS1987]
 gi|170662325|gb|EDT15008.1| sigma factor [Clostridium perfringens E str. JGS1987]
          Length = 227

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 101/234 (43%), Gaps = 64/234 (27%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD--WCLGYKFST 498
           A  +++E N +L+  +A K+ +     ++F DL+QEG IG + A  K+D  +    KF T
Sbjct: 17  ALDKLLENNDKLIYKIASKFYSEKINAIEFDDLLQEGRIGFILACNKYDCEYIKKTKFIT 76

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA +W+ Q I R I   +                               T +EI      
Sbjct: 77  YAFYWIYQKIHRFITGNN-------------------------------TNDEI------ 99

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQ-ANLRETTTRV 616
                           SL TP+ +E+   L + IE ++N ++  +  +  + LR     V
Sbjct: 100 ----------------SLNTPVSEENKDELINGIESNRNEINDREEELYLSELRLELEAV 143

Query: 617 LASLTPREER-VLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +       ER +L++ +  G +TD  ++E++   F  +   I+  +A+AIRKL+
Sbjct: 144 MDKHNTLNEREILKLYY--GWDTDELSIEQIADIFETSSSDIKNTKARAIRKLR 195


>gi|218132856|ref|ZP_03461660.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991729|gb|EEC57733.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
          Length = 205

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 100/229 (43%), Gaps = 52/229 (22%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+G+ EA   + +++E N+RLV  + KKY        DL+  G IGL+KA   FD     
Sbjct: 28  REGDLEA---RNKLIEKNMRLVAHIVKKYACADRDTEDLLSVGTIGLIKAVNTFDMNKSI 84

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + +TYA                C       + +++  ++R+ RR S +I        I +
Sbjct: 85  RLATYA--------------AKC-------IDNELLMLLRSDRRKSREI-------SIYE 116

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            +    EG           I+L   IG  + + + D+ E +  V  L SA++        
Sbjct: 117 PVGKDKEG---------NEINLIEIIGTSEDTVVEDY-ELRQDVKKLYSAVEKK------ 160

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                LT RE  ++ MR+G+    + T  E+ ++  ++R  + +IE K+
Sbjct: 161 -----LTDREREIIIMRYGLYGTQEITQREIAQKMNISRSYVSRIEKKS 204


>gi|32490948|ref|NP_871202.1| flagellar biosynthesis sigma factor [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166154|dbj|BAC24345.1| fliA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 246

 Score = 53.5 bits (127), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 47/199 (23%), Positives = 95/199 (47%), Gaps = 9/199 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IG + A + FD   G  F TYA   V+ ++   + ++     +P  +R     
Sbjct: 48  DLIQAGMIGFLSAIDNFDINQGASFPTYARSRVRWSMLDELRERDW---VPRSVRRNARD 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           +    +R+  ++    + ++IAK+L + +   +K+L+ T   +  SL+     E     G
Sbjct: 105 IASAIQRLEQRLGSSASEKQIAKELKISLCEYQKMLQETNCGQIFSLDELNNQEIIGSFG 164

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I   ++  P    +  +L++   + +  L  RE+ +L + +   +N    L+E+G+  
Sbjct: 165 MNIPIDHSKDPCQLLLINSLKKKIIKEIQKLPKREKILLNLYYQQELN----LKEIGEVL 220

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V   R+ Q+ + AI++L+
Sbjct: 221 GVGESRVSQLHSLAIKRLR 239


>gi|307323818|ref|ZP_07603027.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306890267|gb|EFN21244.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 268

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 97/212 (45%), Gaps = 15/212 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR I  +    E EA   ++E+V A + +   +A +Y NRG    DL Q   +GL+KA +
Sbjct: 26  FRRIAELPDGSEKEA--LREEVVRAWMPMAERIASQYRNRGETHEDLRQVAMVGLVKAVK 83

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH---MRDKIHKVVRTARRMSNKI 543
           +++   G  F +YA+  V   + R   D    + +P     +R+++   V+   R  +  
Sbjct: 84  RYEPDRGSAFESYAVPTVVGEVKRHFRDHMWGLHVPRRVQELRNRVRTAVQELTRSPD-- 141

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSP 600
            R P+  +IA+   M  E V   ++  +    +SL+  + G +D   L D +      S 
Sbjct: 142 DRSPSVRDIARHTGMAEEDVLLGMEALESFRTLSLDAALRGADDGYALVDTLGSTE--SS 199

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +  +Q   RE+    L  L  RE  +L +RF
Sbjct: 200 YERVVQ---RESLKPCLRRLPEREREILYLRF 228


>gi|167628365|ref|YP_001678864.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591105|gb|ABZ82853.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 233

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 91/236 (38%), Gaps = 60/236 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E NLRLV  + KK+   G    DLI  G IGL+KA   FD   G K +TYA   
Sbjct: 52  ARNKLIEHNLRLVAHLVKKFDGTGENNDDLISIGTIGLIKAINTFDASKGTKLATYAARC 111

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I              +H+R                                     
Sbjct: 112 IENEIL-------------MHLR------------------------------------- 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRVLAS 619
              +K  +  +SL  PIG +   +    I+    D  AVS +   ++  L +        
Sbjct: 122 --AMKKMRGEVSLYDPIGVDKEGNEITLIDILGTDPEAVSDI---VENALEQARLLSKLK 176

Query: 620 LTPREER-VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
              + ER V+ +R+G+      T  E+ K   ++R  + +IE +AI KL     SK
Sbjct: 177 KLSKRERYVIELRYGLLSGCRQTQREIAKNLGISRSYVSRIEKRAIMKLMSDLASK 232


>gi|330808235|ref|YP_004352697.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327376343|gb|AEA67693.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 247

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 106/237 (44%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 17  AQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSNKYDASKGASFETYA 76

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 77  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 133

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  +  +D  H G  + + NA + +       D   Q+ L E
Sbjct: 134 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG--LHEDNASAHMEPSRDLEDERFQSALAE 189

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 190 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 238


>gi|146295930|ref|YP_001179701.1| sporulation sigma factor SigK [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409506|gb|ABP66510.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 220

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 93/231 (40%), Gaps = 62/231 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A+  ++E NLRLV  +AKKYT   L F     D+I  G IGL+KA E +      + STY
Sbjct: 33  ARNILIEKNLRLVAHIAKKYT---LSFPNLTDDIISVGTIGLIKAIETYSQEKNTRLSTY 89

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A                                   A+ + N+I              M 
Sbjct: 90  A-----------------------------------AKCIENEI-------------LMY 101

Query: 560 VEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           +   +K L      ISLE PIG   D +   L D ++           ++  ++    ++
Sbjct: 102 LRQNKKFL----SQISLENPIGSDKDGNEITLIDVLQSDQDDIDDQVNVKIQIKNLLRKL 157

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              L  RE+ ++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 158 DKILKGREKHIIELRYGLKNGKERTQMEVANLLGISRSYVSRIEKKALKKL 208


>gi|125973016|ref|YP_001036926.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125713241|gb|ABN51733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Clostridium
           thermocellum ATCC 27405]
          Length = 218

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 82/181 (45%), Gaps = 24/181 (13%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y    +++ DLI  G  GL+ A EKFD   G KF TYA   ++ +I  SI +      +P
Sbjct: 45  YFGSNVEYDDLIGYGIFGLIDAIEKFDINKGVKFETYASLRIRGSIIDSIRELDW---VP 101

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +R K  ++ +    + N++ R  + +E+A KL + V+ + K+L      ++L + I  
Sbjct: 102 RSLRQKNKELEKVYAEIENELGRSASDKEVADKLGITVDELNKLLN----EVNLSSMI-- 155

Query: 583 EDTSHLGDFIEDKNAVS-----------PLDSAIQANLRETTTRVLASLTPREERVLRMR 631
                L +F+E    +            P      A LRE     ++ L  +E+ V+ + 
Sbjct: 156 ----SLEEFLEQNYEIGVTTAPESRDEKPEGYIEMAELREILADAISKLPEKEKMVITLY 211

Query: 632 F 632
           +
Sbjct: 212 Y 212


>gi|298528406|ref|ZP_07015810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298512058|gb|EFI35960.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 261

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/197 (24%), Positives = 90/197 (45%), Gaps = 11/197 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G++GL++A   FD   G K  T+A   +K A+   +       R    +R K+ K
Sbjct: 66  DLISAGSLGLIEALGNFDPTQGIKLETFADNRIKGAMLDELRRMDWFSR---GLRKKVKK 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + ++ R         P+  E+ +      E V + L   +  I L      E+ S  G  
Sbjct: 123 LEQSMREFEQNTGHSPSHSELKEITGYSREEVEEGLLALQNQICLSLEAIQENFSATG-- 180

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
              +++  P  S +  +L +    ++  L+ +E+ VL + +      + T++EV +   V
Sbjct: 181 --TQDSDEPQLSVVFHDLVDKVAAIIEKLSNKEQLVLSLYY----TEELTMKEVAQVLDV 234

Query: 652 TRERIRQIEAKAIRKLK 668
           T  R+ Q+ ++AI+K+K
Sbjct: 235 TEGRVSQLHSQAIKKVK 251


>gi|51892359|ref|YP_075050.1| sporulation sigma factor SigE [Symbiobacterium thermophilum IAM
           14863]
 gi|51856048|dbj|BAD40206.1| RNA polymerase sigma factor similar to B. subtilis SigE
           [Symbiobacterium thermophilum IAM 14863]
          Length = 251

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA + FD     K +TYA
Sbjct: 70  VKNTLIERNLRLVVYIARKFDNTGIWVEDLVSIGTIGLIKAVKTFDPSKRIKLATYA 126


>gi|167034905|ref|YP_001670136.1| flagellar biosynthesis sigma factor [Pseudomonas putida GB-1]
 gi|166861393|gb|ABY99800.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida
           GB-1]
          Length = 246

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 101/232 (43%), Gaps = 17/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ A K+D   G  F TYA
Sbjct: 16  AQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAMRAVEARTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTRV 616
           +    +L  T      S +  +  +D  H G   ED     V P         +   T  
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG-LHEDGASGQVEPARGLEDERFQVALTEA 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 190 IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|297746561|emb|CAZ60998.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 271

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 71/150 (47%), Gaps = 2/150 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +  
Sbjct: 123 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQA 182

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E D  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 183 KMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLS 241

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           I++ + I   +  GE +A  AKKEMVEANL
Sbjct: 242 IAQIKDINRRMSIGEAKARRAKKEMVEANL 271


>gi|317051537|ref|YP_004112653.1| FliA/WhiG family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946621|gb|ADU66097.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfurispirillum
           indicum S5]
          Length = 250

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 93/202 (46%), Gaps = 12/202 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A +KFD   G  F TYA   ++  I   +        +P  +R K   
Sbjct: 50  DLISIGALGLIDAIDKFDMNRGVLFKTYAESRIRGKILDELRKLDW---LPRGLRQKNKA 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH-- 587
           + R   ++     RE +  E+A +L +    V++ +        +SL+  + D D S   
Sbjct: 107 LDRAYSKLGINEGREVSDGELAAELGIDEAEVQQYISQAGGYTMLSLDEQMYDRDGSESG 166

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D I D+    P +       +E   + +  L+ +E+++L + +      + T++E+G
Sbjct: 167 TLSDLIPDRENAGPEEHLEITQNQEFLKKHIRLLSEKEQQMLALYY----YEELTMKEIG 222

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               +T  R+ QI ++A+ KLK
Sbjct: 223 TVLGITESRVSQIHSQALFKLK 244


>gi|224005601|ref|XP_002291761.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220972280|gb|EED90612.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 217

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 102/216 (47%), Gaps = 20/216 (9%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYK--------FSTYAMWWVKQAITRSIADQSCTI 519
           + + DL+QEG I L+ A   ++    YK        F  YA   ++ ++   +A  S  I
Sbjct: 5   ISYPDLVQEGMIALLHAISSYN---SYKTHNKNDQSFEKYAQQTIQSSLLHFLAHSSRPI 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P  ++  +      A ++ + + REPT  ++AK++ +    +      T+E    E  
Sbjct: 62  RLPFSLQTTLQSANEAAAKLRSALGREPTLTQVAKEVNIDAHQLALYPGATEED-DWEIN 120

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMN 637
             +   + L D + D   ++   S  Q  L  +E    +  +LT  E  V+++RFG+ ++
Sbjct: 121 NPERTVAPLRDILTDTEEINNPLSYTQHYLLTQELDQFLYETLTHDELEVIQLRFGL-LD 179

Query: 638 TDH-----TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +     +  ++G++  + +E + +I + A+ KL+
Sbjct: 180 SKYGGKGWSAGQIGERMNMDKEEVVKIASSALEKLR 215


>gi|253576138|ref|ZP_04853470.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844481|gb|EES72497.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 240

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 53/221 (23%), Positives = 101/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 63  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 115

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++KI+ E + +                 
Sbjct: 116 -SRCIENE-----ILMYLRR------------NSKIRTEVSFD----------------- 140

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
               EP++++    D +   L D +  +N     +   Q + R+   + L  LT RE  +
Sbjct: 141 ----EPLNID---WDGNELLLSDVLGTENDTIYRNIEEQVD-RKLLHKALDKLTERERMI 192

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 193 MELRFGLVDGDEKTQKDVADLLGISQSYISRLEKRIIKRLR 233


>gi|160915288|ref|ZP_02077501.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
 gi|158433087|gb|EDP11376.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
          Length = 239

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 100/245 (40%), Gaps = 57/245 (23%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SE ++I ++ +  +     A+ +++E NLRLV  + KKY  +     DLI  G IGL+KA
Sbjct: 34  SETKYIAALAKGNQT----ARDKLIEHNLRLVAHIVKKYDFKKEATEDLISIGTIGLIKA 89

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + F    G+K +TYA                C       + ++I   +R+++     + 
Sbjct: 90  VDSFKPEKGHKLTTYA--------------SKC-------IENEILMYLRSSKNYFQNVS 128

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLD 602
                                      EPI+      D+D S   L D I      S +D
Sbjct: 129 -------------------------LNEPIA-----TDKDGSEIMLIDAIASPCDTSIID 158

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             + A+      + +  L  RE  ++  RFG+    + T  E+ KQ  ++R  + +IE +
Sbjct: 159 DMLVADNIVKLKQYMHVLDARELEIITKRFGLFGQKEATQREIAKQLHISRSYVSRIEKR 218

Query: 663 AIRKL 667
           A  KL
Sbjct: 219 AFMKL 223


>gi|126348076|emb|CAJ89797.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 289

 Score = 53.1 bits (126), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 97/216 (44%), Gaps = 15/216 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 53  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVPTI 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVE- 561
              + R   D+   +R+P  +++  +K VR ARR    N    EP+   +A    +  + 
Sbjct: 112 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARRELTQNPGSPEPSVAALAAHTGLTEDE 170

Query: 562 ---GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              G+  +   +   +  E   GD+  S L D +    A    D+ I    RE+    L 
Sbjct: 171 VSAGMEALESFSTLSLDAELSAGDDGYS-LADTL--GAADGSYDTVID---RESAKEGLR 224

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            L  RE  +L MRF   M      + +G  Q  V+R
Sbjct: 225 RLPERERAILYMRFFEDMTQSRIADRLGISQMHVSR 260


>gi|228937937|ref|ZP_04100564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228821728|gb|EEM67729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
          Length = 210

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 69/144 (47%), Gaps = 21/144 (14%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I + S  I++P 
Sbjct: 7   ANTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMN-SHKIKVP- 64

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVLKITKEPISLETP 579
                     R   ++  K+ R+   EE    I K+L + +  V++ L+      SL+  
Sbjct: 65  ----------RALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDV 114

Query: 580 I-----GDEDTSHLGDFIEDKNAV 598
           +     G  +   L D +ED   +
Sbjct: 115 MYTSAGGGSEEILLEDMLEDTQVI 138


>gi|318061849|ref|ZP_07980570.1| sigma factor [Streptomyces sp. SA3_actG]
          Length = 295

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 89/191 (46%), Gaps = 14/191 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VEA L +   +A +Y  RG    DL Q   +GL++A ++FD  +   F TYA+  ++  
Sbjct: 41  LVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAVPTMQGE 100

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEGVRK 565
           + R   D +  + +P  +++ +   VR A +        R P+  E+A+   +    VR+
Sbjct: 101 LKRHFRDNTWGVHVPRRVQE-LRSAVRAALQELAPRPALRAPSVGELARCAKLSEAEVRQ 159

Query: 566 VLKI--TKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            L+   +   +SL++    E    L D +  ED    + +D       RE+    LA L 
Sbjct: 160 GLEALDSYRSVSLDSAAPSEGEHPLRDRLGAEDPAYETVVD-------RESVRPALAELP 212

Query: 622 PREERVLRMRF 632
            RE  +L +RF
Sbjct: 213 ERERYILYLRF 223


>gi|329937662|ref|ZP_08287181.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329303061|gb|EGG46949.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 327

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/138 (28%), Positives = 72/138 (52%), Gaps = 6/138 (4%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + S+F  + ++    E EA   + E+V A L +   +A ++ +RG    DL Q   +GL+
Sbjct: 70  TASDFARLAALEDGPEREA--LRDELVTAWLPMAHRIAGRFRDRGESLEDLRQVAALGLV 127

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MS 540
           KA +++D C    F +YA+  +   I R   D+   +R+P  +++  +K VR ARR  M 
Sbjct: 128 KAIDRYD-CERGAFESYAVPTITGEIKRHFRDRMWALRVPRRVQELRNK-VRVARRELMQ 185

Query: 541 NKIKREPTPEEIAKKLAM 558
           +    EP+  ++A+   +
Sbjct: 186 SPGSPEPSAADVARHTGL 203


>gi|121535239|ref|ZP_01667053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306124|gb|EAX47052.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 3/90 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            ++S ++KG+      K   +E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F
Sbjct: 40  FLLSRLQKGD---KAVKSIFIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTF 96

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           D     K +TYA   ++  I   +   S T
Sbjct: 97  DPIKRIKLATYASRCIENEILMYLRRNSKT 126


>gi|323706112|ref|ZP_08117681.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534556|gb|EGB24338.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 241

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/116 (32%), Positives = 61/116 (52%), Gaps = 7/116 (6%)

Query: 407 LKIRNEIKSI----SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           LKIR+ I  +    ++   +S  E   +++ +  G+ EA   K  ++E NLRLV+ +AKK
Sbjct: 22  LKIRDSIFYVGGSEALPPPLSAEEEMFLIAKMESGDNEA---KSMLIERNLRLVVYIAKK 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           + N G+   DLI  G IGL+K+   F+     K +TYA   ++  I   +   S T
Sbjct: 79  FENTGVGIEDLISIGTIGLIKSINTFNPRKKIKLATYASRCIENEILMYLRRNSKT 134



 Score = 38.5 bits (88), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 36/59 (61%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  T  L  L+ RE+R++ +RFG+   T+ T +EV     +++  I ++E + +++LK
Sbjct: 176 KQLLTNALKKLSDREKRIIGLRFGLSGGTEMTQKEVADLLGISQSYISRLEKRILKRLK 234


>gi|257438884|ref|ZP_05614639.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
 gi|257198699|gb|EEU96983.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
          Length = 153

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/71 (45%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++  NLRLV  VAKKY  +     DLI  G IGLMKA + FD     +F+TYA   
Sbjct: 51  AREKIIRHNLRLVAHVAKKYYAQPGDQEDLISIGTIGLMKAVDTFDITRKARFATYASRC 110

Query: 504 VKQAI-TRSIA 513
           ++ AI TR+ A
Sbjct: 111 IENAILTRANA 121


>gi|221069309|ref|ZP_03545414.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
 gi|220714332|gb|EED69700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
          Length = 239

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 94/206 (45%), Gaps = 11/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +F+   G +F T+A   ++ A+   + +     R     + +I +
Sbjct: 40  DLIQVGMIGLAEALSRFESEQGVQFDTFASQRIRGAMLDELREGDWMSRSSRKSQKEIEQ 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGD 590
            +    R+  ++ R P   EIA +L M ++  + +L K+    +     IG  D     D
Sbjct: 100 AL---NRLEQRLGRPPLESEIAAELGMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDD 156

Query: 591 FIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           ++E   A S   P        +R      + +L  RE+ V+ M +   MN    L+E+  
Sbjct: 157 YLERHVADSGADPFALLRDQRMRSALVEAIKALPEREQYVMGMYYEHDMN----LKEIAA 212

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  R+ Q+ ++AI +L+   RS
Sbjct: 213 VLGVTESRVCQLHSQAIARLRTKMRS 238


>gi|51246530|ref|YP_066414.1| RNA polymerase sigma factor (FliA) [Desulfotalea psychrophila
           LSv54]
 gi|50877567|emb|CAG37407.1| related to RNA polymerase sigma factor (FliA) [Desulfotalea
           psychrophila LSv54]
          Length = 245

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 104/229 (45%), Gaps = 14/229 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++V+ +L LV  +  +  ++   F+   D+   G  GL  A++KFD      F T+A + 
Sbjct: 16  QLVDDHLYLVDILVSRMVSQVPSFMSRDDMRSAGMFGLFDASKKFDASKNILFKTFAEYR 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   +       R    +RDK +K+ R    +  K+ R+P   EIA+ L M ++  
Sbjct: 76  IRGAIFDEMRKLDWFSR---SLRDKHNKIGRAILALELKLGRDPEEFEIAQSLNMNLDAY 132

Query: 564 RKVLKITKEP--ISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +L        +SL   + +  E  S L   ++ +   +P     Q  L      +L  
Sbjct: 133 HNLLGQVSHLGCVSLNEVLDNSQEGRSFLDSLVDKRKNNTPTAFIEQQELNIKIAEILDQ 192

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ +E+ V+ + +   ++     E +G    V+  RI Q+ ++++ KLK
Sbjct: 193 LSEKEKLVISLYYYEELSQKEIAEVIG----VSEGRISQLHSQSLIKLK 237


>gi|160935680|ref|ZP_02083055.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441424|gb|EDP19134.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
          Length = 246

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 101/229 (44%), Gaps = 56/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F      K +TYA   
Sbjct: 63  ARAALIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFKPDKNIKLATYASRC 122

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                         R +NK + E + +E    L +  +G 
Sbjct: 123 IENEILMYL-------------------------RRNNKTRLEVSIDE---PLNVDWDG- 153

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DED  +    IED+   S L++AI            + L P
Sbjct: 154 --------NELLLSDILGTDEDVIYHD--IEDEIEKSLLNNAI------------SRLNP 191

Query: 623 REERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +++ +R+G+  N D    T +EV     +++  I ++E K +++LK
Sbjct: 192 RERKIVELRYGL-TNEDGEEMTQKEVADLLGISQSYISRLEKKIMKRLK 239


>gi|120613052|ref|YP_972730.1| FliA/WhiG family RNA polymerase sigma factor [Acidovorax citrulli
           AAC00-1]
 gi|120591516|gb|ABM34956.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidovorax
           citrulli AAC00-1]
          Length = 238

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 97/206 (47%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +++   G +F T+A   ++ A+   + +     R     + +I  
Sbjct: 40  DLIQVGMIGLNEALSRYEVTQGVQFETFASQRIRGAMLDELREGDWMSRSSRKSQKEIEH 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE--TPIGDEDTSH 587
            V    R+  K+ R P   EIA +L + +   + +L   +  + + LE  T   D+D   
Sbjct: 100 AV---TRLEQKLGRSPHESEIATELELSLAEYQSLLSKVRGTQLVYLEDMTRGDDDDDGF 156

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D +A  P+       LR +    + +L  RE++++ M +   MN    L+E+  
Sbjct: 157 LDRHVAD-SAADPMAMLRDQRLRASLVAAIKALPEREQQIMGMYYEHDMN----LKEIAA 211

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  RI Q+ +++I +L+   RS
Sbjct: 212 VLGVTESRICQLHSQSIARLRAKMRS 237


>gi|288554854|ref|YP_003426789.1| RNA polymerase sigma factor SigB [Bacillus pseudofirmus OF4]
 gi|288546014|gb|ADC49897.1| RNA polymerase sigma factor SigB [Bacillus pseudofirmus OF4]
          Length = 261

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/240 (24%), Positives = 126/240 (52%), Gaps = 23/240 (9%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAAEKFDWCLGYK 495
           GE E  +   +  EA   LV S+A+K++ +G ++  DL Q G +GL+ A  +FD   G  
Sbjct: 26  GEEEVQVKLVKHYEA---LVRSLARKFS-KGREYDEDLYQVGMVGLLAALTRFDSEFGRS 81

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F ++A+  +   I R I D++ ++ +P  +++   K+ +    ++ ++ R P   EIA  
Sbjct: 82  FESFAVPTIVGEIKRFIRDKTWSVHVPRRIKELGPKIKKAVESLTVELNRSPLVHEIAAY 141

Query: 556 LAMPVEGVRKVLKITK--EPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           L +  E V + ++++K  + +S++  +     G E T  L D + +++  S  +   Q  
Sbjct: 142 LEVSEEEVLETMEMSKSYQALSVDRSLEADQEGGEVT--LLDLVGNED--SGFEKTDQKM 197

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +   +V   L  RE+++L + +   ++   T E++G    +++  + +++ +A++KL+
Sbjct: 198 LLQKAFQV---LNEREKQILMLTYYDNLSQKETGEKLG----ISQMHVSRLQRRALQKLR 250


>gi|264676583|ref|YP_003276489.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
 gi|262207095|gb|ACY31193.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
          Length = 239

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 94/206 (45%), Gaps = 11/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +F+   G +F T+A   ++ A+   + +     R     + +I +
Sbjct: 40  DLIQVGMIGLAEALSRFESEQGVQFDTFASQRIRGAMLDELREGDWMSRSSRKSQKEIEQ 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGD 590
            +    R+  ++ R P   EIA +L M ++  + +L K+    +     IG  D     D
Sbjct: 100 AL---NRLEQRLGRPPLESEIAAELGMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDD 156

Query: 591 FIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           ++E   A S   P        +R      + +L  RE+ V+ M +   MN    L+E+  
Sbjct: 157 YLERHVADSGADPFALLRDQRMRSALVEAIKTLPEREQYVMGMYYEHDMN----LKEIAA 212

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  R+ Q+ ++AI +L+   RS
Sbjct: 213 VLGVTESRVCQLHSQAIARLRTKMRS 238


>gi|299531273|ref|ZP_07044683.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
 gi|298720680|gb|EFI61627.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
          Length = 239

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 94/206 (45%), Gaps = 11/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A  +F+   G +F T+A   ++ A+   + +     R     + +I +
Sbjct: 40  DLIQVGMIGLAEALSRFESEQGVQFDTFASQRIRGAMLDELREGDWMSRSSRKSQKEIEQ 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGD 590
            +    R+  ++ R P   EIA +L M ++  + +L K+    +     IG  D     D
Sbjct: 100 AL---NRLEQRLGRPPLESEIAAELGMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDD 156

Query: 591 FIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           ++E   A S   P        +R      + +L  RE+ V+ M +   MN    L+E+  
Sbjct: 157 YLERHVADSGADPFALLRDHRMRSALVEAIKALPEREQYVMGMYYEHDMN----LKEIAA 212

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  R+ Q+ ++AI +L+   RS
Sbjct: 213 VLGVTESRVCQLHSQAIARLRTKMRS 238


>gi|255039934|gb|ACT99724.1| putative sporulation sigma factor [Bacillus phage Wip4]
          Length = 248

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/195 (28%), Positives = 86/195 (44%), Gaps = 21/195 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+KA + F+   G  FSTYA+  +   I R+I D         + + K+ +
Sbjct: 55  DLTQFGMIGLIKARDNFNPEFGCAFSTYAVPKIIGEIGRAIRD---------NQKVKVQR 105

Query: 532 VVRTAR-RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSH 587
            V + + ++ N+   +  PEEIA  L  PV  V+  LK      SL   +   G  +   
Sbjct: 106 SVYSVKGKILNQQLSDKGPEEIADILNEPVTLVKMALKYQPSTDSLNKVVYASGSNEDVT 165

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   +ED       ++ I    R       A+L P+E  VL M        + T + +  
Sbjct: 166 LEKMLEDTKVEDIEETTIN---RAVIREFKAALAPKEYIVLDMHL-----QNMTQQNIAN 217

Query: 648 QFCVTRERIRQIEAK 662
           Q   ++ +I +I AK
Sbjct: 218 QMGYSQVQISRILAK 232


>gi|239827399|ref|YP_002950023.1| RNA polymerase, sigma 70 family subunit [Geobacillus sp. WCH70]
 gi|239807692|gb|ACS24757.1| putative RNA polymerase, sigma 70 family subunit [Geobacillus sp.
           WCH70]
          Length = 831

 Score = 53.1 bits (126), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 34/48 (70%)

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PR+ +++  RFG     + TL+E+G+ F V+RERIRQIE KA++ LK
Sbjct: 774 NPRDWKIILYRFGFMTGEEMTLQEIGELFGVSRERIRQIENKALKHLK 821



 Score = 38.1 bits (87), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 32/69 (46%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           +   AKK++   +   DL QE    L KA EK++  LG  F  Y    +   + R  +D 
Sbjct: 583 IYQYAKKFSCETVPMEDLYQEAYFALHKAYEKYNPELGGSFYHYFRRHLFARLQRYKSDN 642

Query: 516 SCTIRIPVH 524
              IRIP H
Sbjct: 643 LSLIRIPTH 651


>gi|294673099|ref|YP_003573715.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
 gi|294472548|gb|ADE81937.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
          Length = 240

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 47/81 (58%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + A+ +++EANLR V++ A       +   +LI  GN GL  AA +++      F +YA+
Sbjct: 42  TTARNKLIEANLRFVLTCAIDMATPFVPIEELIAAGNYGLTIAAARYNPSFDNHFCSYAV 101

Query: 502 WWVKQAITRSIADQSCTIRIP 522
             +++AI+ +I   +C+++ P
Sbjct: 102 HHIRRAISEAIRTWTCSVKTP 122


>gi|239934570|emb|CAR94599.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 34/47 (72%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           RMY+ EMG++ELL+REGEI IAKRIE G   +M ++   P + Q ++
Sbjct: 1   RMYMSEMGTVELLTREGEIVIAKRIEEGVRELMHAVAYWPGSVQKIL 47


>gi|288573001|ref|ZP_06391358.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288568742|gb|EFC90299.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 248

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 105/231 (45%), Gaps = 17/231 (7%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E+V   + LV  V  + T     GL + DLI  G +GL+ A ++F+   G+ F T+A+
Sbjct: 21  KDEIVSRYIPLVKYVVARMTVTPPPGLDYEDLISFGLMGLLDAIDRFEIERGFSFQTFAV 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR-TARRMSNKIKREPTPEEIAKKLAMPV 560
             ++ A+   +       R     R+K+ ++ R T R M   I   P  E + +++ +  
Sbjct: 81  PRIRGAVLDELRKCDWFSRTG---REKLQRLERATERLMIQGIT--PDDESLKREMDVDD 135

Query: 561 EGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  R++L +      +SL+  +  DE     GD +    A S  +       R+     L
Sbjct: 136 KTYREMLSLASRGYVVSLDEVMSLDEGDVQKGDLLSYTGA-SAQEFLENREERDLVVGAL 194

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+ RE  VL M +      + TL+E+G    VT  R+ QI  KAI  LK
Sbjct: 195 NRLSERERLVLSMYY----LEEMTLKEIGLVLGVTESRVSQIHGKAIVSLK 241


>gi|170722830|ref|YP_001750518.1| flagellar biosynthesis sigma factor [Pseudomonas putida W619]
 gi|169760833|gb|ACA74149.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida
           W619]
          Length = 246

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 101/231 (43%), Gaps = 15/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ ++VE    LV  +A     R    +Q  DLIQ G IGL++ A K+D   G  F TYA
Sbjct: 16  AQYDLVERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAMRAVEARTGRDAKDHEVAAELKLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVL 617
           +    +L  T      S +  +  +D  H G   E  +  V P         +   T  +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEGLHEEGASGQVEPSRDLEDERFQAALTDAI 190

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 191 ANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|85859095|ref|YP_461297.1| putative cytoplasmic protein [Syntrophus aciditrophicus SB]
 gi|85722186|gb|ABC77129.1| hypothetical cytosolic protein [Syntrophus aciditrophicus SB]
          Length = 94

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/39 (64%), Positives = 30/39 (76%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TLEEVG    VTRERIRQIEAKA++KL+H  R  +L+ F
Sbjct: 46  TLEEVGDMMGVTRERIRQIEAKALKKLQHKKRRDQLKDF 84


>gi|313905149|ref|ZP_07838518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Eubacterium
           cellulosolvens 6]
 gi|313470052|gb|EFR65385.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Eubacterium
           cellulosolvens 6]
          Length = 258

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 113/235 (48%), Gaps = 21/235 (8%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           I ++E+    L +V ++A +  +  + F    D+I EG + +MK  +++D     KF T+
Sbjct: 29  ILRQELTMRYLYIVKAIAYQMRDMYIGFAQPDDIINEGVLEIMKGIDRYDPDRDNKFDTF 88

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
               ++  +   +        +P +       +  T + +S K+ R PT EE A KL + 
Sbjct: 89  ISRRIRGMVIDLMRKNDW---MPRNFHRDRRTIEDTVQELSEKLGRTPTDEETAHKLGIE 145

Query: 560 VEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V+ ++KV  +T     +SL+    + D + L    ED  +V P  +     +R  T R+L
Sbjct: 146 VKKLQKVRTMTTMVNVLSLDMTYDENDEAVLQVPTEDI-SVQPERNF----MRGETVRIL 200

Query: 618 A----SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A    SL  +E+ ++ + +   +N    + ++     +++ R+ Q+ A+A++KL+
Sbjct: 201 ADAINSLQEKEKMIISLYYVDNLN----MSQIASVMDISQPRVSQLHAQAVKKLR 251


>gi|168182610|ref|ZP_02617274.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|170759960|ref|YP_001787849.1| sporulation sigma factor SigE [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237795972|ref|YP_002863524.1| sporulation sigma factor SigE [Clostridium botulinum Ba4 str. 657]
 gi|169406949|gb|ACA55360.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182674165|gb|EDT86126.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|229261167|gb|ACQ52200.1| RNA polymerase sigma-E factor [Clostridium botulinum Ba4 str. 657]
          Length = 235

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 100/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F      K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGICIEDLVSVGTIGLIKAVNTFKPDKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++K+K E +  E    L +  +G   +L
Sbjct: 111 -SRCIENE-----ILMYLRR------------NSKVKAEISFYE---PLNIDWDGNELLL 149

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   D   + + IED+     +D       ++     +  L  RE+ +
Sbjct: 150 ----------SDILGTDNDEVYNLIEDE-----VD-------KQLLLLAMKKLNEREKEI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R+RFG+    + T +EV     +++  I ++E + I+ LK
Sbjct: 188 VRLRFGLNGKREKTQKEVADMLGISQSYISRLEKRIIKTLK 228


>gi|2853597|gb|AAC08061.1| FliA [Pseudomonas putida]
          Length = 246

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 17/232 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  AQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVSSKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAMRAVEARTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQANLRETTTRV 616
           +    +L  T      S +  +  +D  H G   ED  +  V P         +   T  
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG-LHEDGASGHVEPARGLEDERFQAALTEA 189

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 190 IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|291531057|emb|CBK96642.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum 70/3]
          Length = 239

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 97/225 (43%), Gaps = 50/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++  NLRLV+ +AKK+ + G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 57  ARETLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIGLIKAVNTFSVEKNIKLATYA--- 113

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R                 K  P   E++          
Sbjct: 114 -----SRCIENE-----ILMYLR-----------------KTNPQKMEVS---------- 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   EP++++    D +   L D +   +    +D   +A  R      +  L  R
Sbjct: 137 ------IDEPLNVD---WDGNELLLSDILGTDDDTVSVDIESEAEKR-MLLEAVEKLDER 186

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++ +RFG+    + T +EV     +++  I ++E + I++LK
Sbjct: 187 EKLIMELRFGLNNRPEKTQKEVADMIGISQSYISRLEKRIIKRLK 231


>gi|148380490|ref|YP_001255031.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153932419|ref|YP_001384713.1| sporulation sigma factor SigE [Clostridium botulinum A str. ATCC
           19397]
 gi|153937804|ref|YP_001388234.1| sporulation sigma factor SigE [Clostridium botulinum A str. Hall]
 gi|153940530|ref|YP_001391830.1| sporulation sigma factor SigE [Clostridium botulinum F str.
           Langeland]
 gi|168180581|ref|ZP_02615245.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|170756639|ref|YP_001782077.1| sporulation sigma factor SigE [Clostridium botulinum B1 str. Okra]
 gi|187778871|ref|ZP_02995344.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226949888|ref|YP_002804979.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|148289974|emb|CAL84087.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152928463|gb|ABS33963.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152933718|gb|ABS39217.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. Hall]
 gi|152936426|gb|ABS41924.1| RNA polymerase sigma-E factor [Clostridium botulinum F str.
           Langeland]
 gi|169121851|gb|ACA45687.1| RNA polymerase sigma-E factor [Clostridium botulinum B1 str. Okra]
 gi|182668430|gb|EDT80409.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|187772496|gb|EDU36298.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226843077|gb|ACO85743.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|295319856|gb|ADG00234.1| RNA polymerase sigma-E factor [Clostridium botulinum F str. 230613]
 gi|322806803|emb|CBZ04372.1| RNA polymerase sporulation specific sigma factor SigE [Clostridium
           botulinum H04402 065]
          Length = 235

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 100/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F      K +TYA       
Sbjct: 58  LIERNLRLVVYIARKFENTGICIEDLVSVGTIGLIKAVNTFKPDKKIKLATYA------- 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++K+K E +  E    L +  +G   +L
Sbjct: 111 -SRCIENE-----ILMYLRR------------NSKVKAEISFYE---PLNIDWDGNELLL 149

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   D   + + IED+     +D       ++     +  L  RE+ +
Sbjct: 150 ----------SDILGTDNDEVYNLIEDE-----VD-------KQLLLLAMKKLNEREKEI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R+RFG+    + T +EV     +++  I ++E + I+ LK
Sbjct: 188 VRLRFGLNGKREKTQKEVADMLGISQSYISRLEKRIIKTLK 228


>gi|167749813|ref|ZP_02421940.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|167657125|gb|EDS01255.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|291557474|emb|CBL34591.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum
           V10Sc8a]
          Length = 239

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 98/230 (42%), Gaps = 50/230 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++  NLRLV+ +AKK+ + G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 57  ARETLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIGLIKAVNTFSVEKNIKLATYA--- 113

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R                 K  P   E++          
Sbjct: 114 -----SRCIENE-----ILMYLR-----------------KTNPQKMEVS---------- 136

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   EP++++    D +   L D +   +    +D   +A  R      +  L  R
Sbjct: 137 ------IDEPLNVD---WDGNELLLSDILGTDDDTVSVDIESEAEKR-MLLEAVEKLDER 186

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+ ++ +RFG+    + T +EV     +++  I ++E + I++LK    S
Sbjct: 187 EKLIMELRFGLNNRPEKTQKEVADMIGISQSYISRLEKRIIKRLKKEMES 236


>gi|322384113|ref|ZP_08057831.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151193|gb|EFX44502.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 233

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 100/226 (44%), Gaps = 60/226 (26%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 56  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 108

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             ++KI+ E + +                 
Sbjct: 109 -SRCIENE-----ILMYLRR------------NSKIRTEVSFD----------------- 133

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASLTP 622
               EP++++    D +   L D +  +N        I  N+ E   R      L  LT 
Sbjct: 134 ----EPLNIDW---DGNELLLSDVLGTEN------DTIYRNIEEQVDRKLLHKALDKLTE 180

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 181 RERVIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 226


>gi|304404017|ref|ZP_07385679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304346995|gb|EFM12827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 240

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 93/229 (40%), Gaps = 66/229 (28%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 63  LIERNLRLVVYIARKFENTGIHIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 115

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S                           
Sbjct: 116 -SRCIENE----------------ILMYLRRNSK-------------------------- 132

Query: 568 KITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLAS 619
             T+  +S + P+    D +   L D +  +N        I  N+ E   R      L  
Sbjct: 133 --TRTEVSFDEPLNIDWDGNELLLSDVLGTEN------DTIYRNIEEQVDRKLLHKALDK 184

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LT RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 185 LTERERIIMELRFGLADGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 233


>gi|326938416|gb|AEA14312.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 243

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 69/144 (47%), Gaps = 21/144 (14%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I + S  I++P 
Sbjct: 40  ANTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMN-SHKIKVP- 97

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVLKITKEPISLETP 579
                     R   ++  K+ R+   EE    I K+L + +  V++ L+      SL+  
Sbjct: 98  ----------RALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDV 147

Query: 580 I-----GDEDTSHLGDFIEDKNAV 598
           +     G  +   L D +ED   +
Sbjct: 148 MYTSAGGGSEEILLEDMLEDTQVI 171


>gi|318075206|ref|ZP_07982538.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 293

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 89/191 (46%), Gaps = 14/191 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VEA L +   +A +Y  RG    DL Q   +GL++A ++FD  +   F TYA+  ++  
Sbjct: 41  LVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAVPTMQGE 100

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEGVRK 565
           + R   D +  + +P  +++ +   VR A +        R P+  E+A+   +    VR+
Sbjct: 101 LKRHFRDNTWGVHVPRRVQE-LRSAVRAALQELAPRPALRAPSVGELARCAKLSEAEVRQ 159

Query: 566 VLKI--TKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            L+   +   +SL++    E    L D +  ED    + +D       RE+    LA L 
Sbjct: 160 GLEALDSYRSVSLDSAAPSEGEHPLRDRLGAEDPAYETVVD-------RESVRPALAELP 212

Query: 622 PREERVLRMRF 632
            RE  +L +RF
Sbjct: 213 ERERYILYLRF 223


>gi|313682837|ref|YP_004060575.1| sigma-70 region 4 domain protein [Sulfuricurvum kujiense DSM 16994]
 gi|313155697|gb|ADR34375.1| sigma-70 region 4 domain protein [Sulfuricurvum kujiense DSM 16994]
          Length = 83

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 36/51 (70%), Gaps = 1/51 (1%)

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           R G+    D TL E+G+   VTRER+RQIEA AI+KLKHP   + ++++++
Sbjct: 33  RLGL-HGCDFTLSEIGEVLHVTRERVRQIEASAIKKLKHPKMGRVIKAYME 82


>gi|187935479|ref|YP_001884301.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723632|gb|ACD24853.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 233

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 113/247 (45%), Gaps = 65/247 (26%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAE 486
           +V + ++G+ +A     +++E N +LV  +  K+       +   DL QEG +GL+ AA+
Sbjct: 6   LVELYQEGDKQAL---NKLIENNKKLVFKIVNKFYINATNSIDIEDLEQEGYMGLIMAAK 62

Query: 487 KFDWCLGYK--FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           K++  + Y   FSTY+ +W+ Q I                               ++ IK
Sbjct: 63  KYNSNMDYHASFSTYSFYWIYQKI-------------------------------NSFIK 91

Query: 545 REPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
           ++ T +E +  L +P+ EG        KE + L   I  G E+       IE+K  +  L
Sbjct: 92  QKNTNDETS--LNIPLNEGEE------KEKVDLIEYIDNGYEN-------IEEKLYLEQL 136

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            S ++ NL E  T      T RE  +L++ +G     + T+  +     ++++R+RQIE 
Sbjct: 137 RSDLE-NLMEHNT------TLRERSILKLHYGWDC-RECTMTYIAGMLEISQQRVRQIEK 188

Query: 662 KAIRKLK 668
             +RKL+
Sbjct: 189 STLRKLR 195


>gi|229544420|ref|ZP_04433478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
 gi|229324905|gb|EEN90582.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
          Length = 257

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 90/202 (44%), Gaps = 11/202 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL+ +  KFD     +F TYA + ++ AI   +  +    R     R+K  K
Sbjct: 56  DLKSLGMFGLLDSLNKFDPSRELRFDTYASFRIRGAILDGLRKEDWLSR---GTREKAKK 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLG 589
           +      +  K  R  +P+E+A +L M    V   +  +     +S+E    D D     
Sbjct: 113 IESAIESLEQKYLRTVSPKEVALELGMEETEVCTTMNEQFFANVLSIEETGTDNDEPEAA 172

Query: 590 D-FIE-DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             F+  D+NA  P     +    +     + +L+ +E+ VL + +      + TL E+G+
Sbjct: 173 SRFVSGDRNAGQPESELEKKETVKELAEAIRALSEKEQLVLSLFY----QEECTLTEIGE 228

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++  RI QI +KAI KL++
Sbjct: 229 VMGLSTSRISQIHSKAIYKLRN 250


>gi|77165620|ref|YP_344145.1| Sigma28 (flagella) [Nitrosococcus oceani ATCC 19707]
 gi|76883934|gb|ABA58615.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosococcus
           oceani ATCC 19707]
          Length = 234

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 90/220 (40%), Gaps = 29/220 (13%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E+V     LV  +A     R    +Q  DLIQ G IGL++AA  ++   G  F TYA   
Sbjct: 19  ELVAQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAARNYNASQGASFETYAGIR 78

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   I         P  +  K  +V    R + N+  R+    E+A++L +P+   
Sbjct: 79  IRGAILDEIRRNDWA---PRSVHRKARQVAEVMREVENREGRDARDHEVAEELGLPLNEY 135

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA--------NLRETTTR 615
            ++L+            G      L +F E + +  PL ++++         N R     
Sbjct: 136 HRLLQDA----------GGYRVFSLDEFNEGEES-EPLSASLKGPYEGLQDQNFRGALVE 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            +  L  RE  V+ + +      D  L E+G+   V+  R
Sbjct: 185 AIEGLPERERLVMSLYY----VEDLNLREIGEVLGVSESR 220


>gi|88813218|ref|ZP_01128458.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
 gi|88789540|gb|EAR20667.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
          Length = 240

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/203 (24%), Positives = 92/203 (45%), Gaps = 21/203 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++AA ++D   G  F TYA   ++ A+   I     T   P  +  K  +
Sbjct: 46  DLIQAGMIGLLEAARQYDATQGASFQTYAAIRIRGAMLDEIRRLDWT---PRSVHRKARE 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
           V      + ++  RE    E+ ++L + +    ++L+   T    S+     D+    LG
Sbjct: 103 VASAVAEIEHRTGREAKDWEVVQQLGLDLNDYHQILQDAATARIFSI-----DDQDPELG 157

Query: 590 DFIE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           +  E    +  A+  L+   Q + +      +  L  RE+ V+++ +    N +  L+E+
Sbjct: 158 EPHEIAGHEPTAMEILE---QQDFQAALIAAIRELPEREQLVMQLYY----NEELNLKEI 210

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+   V+  R+ QI  +   KL+
Sbjct: 211 GQVLGVSESRVSQIHGRIALKLR 233


>gi|261855330|ref|YP_003262613.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothiobacillus
           neapolitanus c2]
 gi|261835799|gb|ACX95566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothiobacillus
           neapolitanus c2]
          Length = 239

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 57/244 (23%), Positives = 105/244 (43%), Gaps = 18/244 (7%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKA 484
           R + + V++G  EA +A+      +  LV  +A    NR    +Q  DLIQ G IGL++A
Sbjct: 4   RAMYTDVQRGGAEAVVAE------HAGLVKRIAFHLMNRLPDHIQAEDLIQAGMIGLLEA 57

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           +  +D   G  F TYA   ++ A+   +       R  VH R +  ++ +    +  +  
Sbjct: 58  SNHYDAAQGASFETYAGIRIRGAMLDEVRRNDWAPR-SVHRRHR--EISQAVHEIETRTG 114

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            E    ++   L + ++   + L  + +        G ED +   D  + ++   P    
Sbjct: 115 CEAKDADVCALLGISLDDYYEALNDSVQVRLAPLDAGGEDHNETIDVADHRD--QPDQYL 172

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                 E     +++L  RE  V+ + +   +N     +E+G    V+  R+ QI+ KAI
Sbjct: 173 SHERFHEDLAEHISALPERERLVMSLYYVDELNQ----KEIGAVLGVSESRVCQIQNKAI 228

Query: 665 RKLK 668
            +LK
Sbjct: 229 LRLK 232


>gi|242280062|ref|YP_002992191.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
 gi|242122956|gb|ACS80652.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
          Length = 263

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/217 (21%), Positives = 103/217 (47%), Gaps = 12/217 (5%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +R++    K    + ++  +LI  G++GL+++  KF   L  KF TYA   +K A+   +
Sbjct: 47  IRIIALRMKAKLPQNVELGELISAGSLGLVESLGKFRPELKIKFETYAENRIKGAMLDEL 106

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                  R    +R K+  +    R + ++   +PT  ++ +      + V++ L+  + 
Sbjct: 107 RRMDWFSR---GLRQKVKTIENCIREIEHETGEKPTSAQLEEATGFSAKEVQQGLEALQN 163

Query: 573 PISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            + +      D   S+    ++D+    P  SA+     +    ++ +LTPRE+ VL + 
Sbjct: 164 QLCVNLDAFNDNIPSNKDSQLDDE----PFQSAVFQETVDKVADLIDNLTPREKLVLSLY 219

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +G  +N    ++E  +   +T  R+ Q+ ++A++KL+
Sbjct: 220 YGEELN----MKETSEVMEITEGRVSQLHSQALKKLR 252


>gi|308069873|ref|YP_003871478.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859152|gb|ADM70940.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 246

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 94/224 (41%), Gaps = 56/224 (25%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 69  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 121

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S                           
Sbjct: 122 -SRCIENE----------------ILMYLRRNSK-------------------------- 138

Query: 568 KITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             T+  +S + P+    D +   L D +  +N     +   Q + R+   + L  LT RE
Sbjct: 139 --TRTEVSFDEPLNIDWDGNELLLSDVMGTENDTIYRNIEEQVD-RKLLHKALDKLTDRE 195

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 196 RLIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 239


>gi|228970817|ref|ZP_04131457.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228977391|ref|ZP_04137786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228782368|gb|EEM30551.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228788942|gb|EEM36881.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
          Length = 234

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 69/144 (47%), Gaps = 21/144 (14%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I + S  I++P 
Sbjct: 31  ANTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMN-SHKIKVP- 88

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVLKITKEPISLETP 579
                     R   ++  K+ R+   EE    I K+L + +  V++ L+      SL+  
Sbjct: 89  ----------RALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDV 138

Query: 580 I-----GDEDTSHLGDFIEDKNAV 598
           +     G  +   L D +ED   +
Sbjct: 139 MYTSAGGGSEEILLEDMLEDTQVI 162


>gi|310642979|ref|YP_003947737.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247929|gb|ADO57496.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 246

 Score = 52.8 bits (125), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 94/224 (41%), Gaps = 56/224 (25%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 69  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 121

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S                           
Sbjct: 122 -SRCIENE----------------ILMYLRRNSK-------------------------- 138

Query: 568 KITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             T+  +S + P+    D +   L D +  +N     +   Q + R+   + L  LT RE
Sbjct: 139 --TRTEVSFDEPLNIDWDGNELLLSDVMGTENDTIYRNIEEQVD-RKLLHKALDKLTDRE 195

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 196 RLIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 239


>gi|239934590|emb|CAR94609.1| DNA-directed RNA polymerase subunit D [uncultured Acidobacteria
           bacterium]
          Length = 219

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 1/66 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E  N V  ++  + +++ EI+   +  G S+S+ +H + ++R GE EA  AK+EMVEAN
Sbjct: 155 AEASNSVNAQI-RVRELKREIRKKEMMAGASLSDLKHTLQVIRFGEIEAERAKREMVEAN 213

Query: 453 LRLVIS 458
           LRLVIS
Sbjct: 214 LRLVIS 219


>gi|228902053|ref|ZP_04066217.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
 gi|228857479|gb|EEN01975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
          Length = 237

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 69/144 (47%), Gaps = 21/144 (14%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I + S  I++P 
Sbjct: 34  ANTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMN-SHKIKVP- 91

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVLKITKEPISLETP 579
                     R   ++  K+ R+   EE    I K+L + +  V++ L+      SL+  
Sbjct: 92  ----------RALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDV 141

Query: 580 I-----GDEDTSHLGDFIEDKNAV 598
           +     G  +   L D +ED   +
Sbjct: 142 MYTSAGGGSEEILLEDMLEDTQVI 165


>gi|145297471|ref|YP_001140312.1| LafS [Aeromonas salmonicida subsp. salmonicida A449]
 gi|22758825|gb|AAN04223.1| LafS [Aeromonas salmonicida]
 gi|142850243|gb|ABO88564.1| LafS [Aeromonas salmonicida subsp. salmonicida A449]
          Length = 235

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/198 (22%), Positives = 94/198 (47%), Gaps = 18/198 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q G +GL++A  ++D     +F +YA   ++ A+   +         P  +R ++H 
Sbjct: 49  DMEQVGMMGLLEAWRRYDSEPDPQFESYAFKRIRGAMLDELRRLDWR---PRQLRQQVHS 105

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             +  R + N++ R PT +E+A  L   VE VR++   ++           E    L ++
Sbjct: 106 HNQAQRELYNRLGRAPTEQELAVSLNCTVEEVRQLAYASQA----------EALQSLEEW 155

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +E+    +P   +   ++  T ++VL SL  RE+ +L + +   +N    ++E+     +
Sbjct: 156 LEN-GGKAPATESDDVDMAMTISKVLTSLDKREQLLLSLYYQQELN----MKEIALVLGL 210

Query: 652 TRERIRQIEAKAIRKLKH 669
           T  R+ Q+  + + +LK 
Sbjct: 211 TESRVCQLHKQCVLQLKQ 228


>gi|89072296|ref|ZP_01158875.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium sp. SKA34]
 gi|89051828|gb|EAR57280.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium sp. SKA34]
          Length = 242

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/220 (23%), Positives = 98/220 (44%), Gaps = 26/220 (11%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V++  + +T+    + D+ Q G IGL++AA ++      +F  +A+  ++ AI   +   
Sbjct: 39  VVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGNVEDPQFPAFAVCRIRGAILDELRRL 98

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               R   H R + H++    R +  ++ R+PT  EI   L +  E  +         + 
Sbjct: 99  DWRSR---HTRQQAHELNDITRDLMKQLGRQPTEAEITSALGIDSENYQ---------LR 146

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN------LRETTTRVLASLTPREERVLR 629
           L+  +  E  S L   +E   A   LD+ ++ N      +R T    L  L+ RE+ +L 
Sbjct: 147 LQACMASEMQS-LDQLLE---AGKELDAPLEYNGVEHEHMRRTLEYALTQLSRREQLLLT 202

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +   +N    L E+     +T  RI Q+  +A++ L H
Sbjct: 203 LFYQHELN----LHEIALVLDLTPPRICQLHKQALKSLNH 238


>gi|61966525|emb|CAI72582.1| SigB protein [Staphylococcus aureus]
          Length = 186

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/110 (25%), Positives = 61/110 (55%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 31  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA
Sbjct: 91  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIA 140


>gi|126176138|ref|YP_001052287.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|304412490|ref|ZP_07394096.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS183]
 gi|307307149|ref|ZP_07586887.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           BA175]
 gi|125999343|gb|ABN63418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|304349132|gb|EFM13544.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS183]
 gi|306910388|gb|EFN40819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           BA175]
          Length = 238

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 102/216 (47%), Gaps = 22/216 (10%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           ++S  + +    L   D+ Q G + L++++ ++   L   F ++A   ++ AI   +  Q
Sbjct: 37  IVSQMRSHCGVMLSLEDMEQIGMMALLESSRRYPGELDNGFISFAGQRIRGAILDELRRQ 96

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI- 574
               R PV  R + H++    RR+S ++ REP+  E+A  L +  E  R+ L  T+    
Sbjct: 97  DWRPR-PV--RQQAHELNDVVRRLSREMGREPSDLEVASALGLSAEDYRERLYSTQAESM 153

Query: 575 -SL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            SL E  +G E        ++  N V  L       L++T  +V++ L  RE+ +L + +
Sbjct: 154 KSLDELLLGGEQP------VDRSNDVERL------MLKQTLIKVISKLNEREQLILSLYY 201

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +N    L+E+     +T  RI Q+   AI +LK
Sbjct: 202 HHELN----LKEIAMALGLTETRICQLHKSAISQLK 233


>gi|11466545|ref|NP_044794.1| transcription initiation factor sigma [Reclinomonas americana]
 gi|2258375|gb|AAD11909.1| transcription initiation factor sigma [Reclinomonas americana]
          Length = 532

 Score = 52.4 bits (124), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 60/120 (50%), Gaps = 11/120 (9%)

Query: 411 NEIKSIS-VETGISISEFRHIVSMVRKGECEASI---AKKEMVEANLRLVISVAKKYTNR 466
           N+IK+ S ++ G++     HI  M+       +I    K  ++   +  + +++K+Y   
Sbjct: 320 NKIKNNSLIKYGLT-----HIYDMILISILRENIKVTLKNRIIFNYMPYITTISKQYVKI 374

Query: 467 GLQ--FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           G Q  F DLIQEG  G+  AAEKF    G +F TYA WW+   + ++   +   +R   H
Sbjct: 375 GYQAQFSDLIQEGISGVSDAAEKFQLGRGVRFLTYAYWWMHNYMMKATIKKKKKLRFNEH 434


>gi|302874716|ref|YP_003843349.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
 gi|307690671|ref|ZP_07633117.1| sporulation sigma factor SigK [Clostridium cellulovorans 743B]
 gi|302577573|gb|ADL51585.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
          Length = 233

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/225 (24%), Positives = 98/225 (43%), Gaps = 49/225 (21%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++K  +VE NLRLV  + KKY+  G    +LI  G +GL+KA + F+   G + +TYA  
Sbjct: 48  LSKSILVERNLRLVAHIVKKYSGVGKDSDELISIGTVGLIKAIDSFNVDKGTRLATYAAR 107

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++  +   I +   T +  V+++D I                                G
Sbjct: 108 CIENELLMLIRNSKKT-KGEVYLQDPI--------------------------------G 134

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V K        ISL   +  E+ S + + +E+   ++ L   I+  L+            
Sbjct: 135 VDK----EGNEISLMDVLSSEEDSVI-EIVENNMQIAKLYEEIEKCLK-----------G 178

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE+ +++MR+G+      T  E+     ++R  + +IE +A++KL
Sbjct: 179 REKTIIQMRYGLINGKPKTQREIALLLGISRSYVSRIEKRALKKL 223


>gi|315646039|ref|ZP_07899160.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
 gi|315278800|gb|EFU42114.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
          Length = 240

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 100/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 63  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 115

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NK + E + +                 
Sbjct: 116 -SRCIENE-----ILMYLRR------------NNKTRSEVSFD----------------- 140

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
               EP++++    D +   L D +  +N     +   Q + R+   + L  L+ RE  +
Sbjct: 141 ----EPLNID---WDGNELLLSDVLGTENDTIYRNIEEQVD-RKLLQKALDKLSDRERMI 192

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 193 MELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 233


>gi|320102910|ref|YP_004178501.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Isosphaera pallida
           ATCC 43644]
 gi|319750192|gb|ADV61952.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Isosphaera
           pallida ATCC 43644]
          Length = 273

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 20/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE  L LV   A++   R   G+   DLI  G  GLM A + FD   G KF TY +
Sbjct: 40  RNRLVERYLPLVKYNAERIWQRLPDGVDLDDLISAGTFGLMDAIDAFDLSRGVKFETYCV 99

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPV 560
             ++ A+   +        +P  +R K H  +  AR+    I  R PT  EIA++L +  
Sbjct: 100 PRIRGAMLDELRTMDW---VPRLVRSK-HSRMEEARKALEAIHGRPPTDAEIAERLGVTP 155

Query: 561 EGVRKVLKITKEP--ISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           E   K+   +     +SL     + D+       D +EDK    P     + +L    TR
Sbjct: 156 EEFEKMALESNAVGLVSLNKKWYETDSYKDVREIDILEDKKGEDPTRRLQRKDLMRMVTR 215

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L     R ER++ + +      + T++E+G    ++  R+ Q+ +  I++L+
Sbjct: 216 GLN----RNERLIIILY---YYEELTMKEIGATLDLSESRVSQMHSSIIQRLQ 261


>gi|332653441|ref|ZP_08419186.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332518587|gb|EGJ48190.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++ ++E NLRLV+ +A+++ N G+   DLI  G IGL+KA   +      K +TYA
Sbjct: 58  ARQTLIEHNLRLVVYIARRFENTGINIEDLISIGTIGLIKAVGTYQPARSIKLATYA 114


>gi|332297782|ref|YP_004439704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
 gi|332180885|gb|AEE16573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
          Length = 262

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 48/206 (23%), Positives = 98/206 (47%), Gaps = 12/206 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++F DL+  G  GL+ A  K+D     KF TYA+  ++ +I   +        +P  +R 
Sbjct: 53  VEFDDLVGFGQFGLLDAINKYDPDKNVKFKTYAVTRIRGSIFDELRQLDW---VPRSVRQ 109

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-VEGVRKVLKITKEPI-SL-ETPIGDED 584
           K  ++      + +++ R  +  E+A  + +   E  + V++++   + SL +     +D
Sbjct: 110 KAREIEDAIVALESRLGRPASDAEVAGSMGISEAEFQQTVMRVSGTSVLSLNDVWYSGDD 169

Query: 585 TSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           + H  +GD IE   +++P     +  +R      +  L  +E+ VL + +    + D T 
Sbjct: 170 SDHVSIGDSIESPASLNPDVIVEREEIRRVIAEAITELPEKEKMVLVLYY----HEDLTF 225

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+G+   V+  RI Q+  KA  +L+
Sbjct: 226 KEIGQVLNVSESRISQLHTKANMRLR 251


>gi|302871379|ref|YP_003840015.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574238|gb|ADL42029.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 262

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 50/222 (22%), Positives = 101/222 (45%), Gaps = 52/222 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KK ++E NLRLV+ +A+++ N  +   DL+  G IGL+KA   ++     K +TYA    
Sbjct: 64  KKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGLIKAINTYNPNKNIKLATYA---- 119

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
               ++ I ++                ++   RR SN            KKL + ++   
Sbjct: 120 ----SKCIENE----------------ILMFLRRNSN------------KKLELSID--- 144

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASLTPR 623
                  EP++++    D +   L D +        + + I++N+ +E   + +  L  R
Sbjct: 145 -------EPLNVD---WDGNELLLSDVL--GTDTEEIYNRIESNVEKEALLQAIQKLPSR 192

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           E++++ +RFG G   + T +EV     +++  I ++E + ++
Sbjct: 193 EKKIVELRFGFGDEGEKTQKEVADMLGISQSYISRLEKRLLQ 234


>gi|238924140|ref|YP_002937656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|238875815|gb|ACR75522.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|291524873|emb|CBK90460.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale DSM 17629]
 gi|291529014|emb|CBK94600.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale M104/1]
          Length = 255

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/219 (23%), Positives = 99/219 (45%), Gaps = 12/219 (5%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +RLV      Y    +++ DL+  G  GL+ A +KF+     KF TYA   ++ AI   I
Sbjct: 33  VRLVAGRLSMYLGHNVEYDDLVSYGIFGLIDAIDKFNLEKNVKFETYASLRIRGAILDQI 92

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV---RKVLKI 569
                   IP  +R +  K+    + +  +  +     ++AK+L++  + +   +  LK+
Sbjct: 93  RKMDW---IPRTVRQRQRKIDEAIKNIELRTGKTANDADLAKELSISEDELCSWQSQLKV 149

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T   +SL+    +     + D   + +   P +   Q  L+    + L +LT +E RV+ 
Sbjct: 150 TN-VVSLD-EFDESGPEPVMDAAHNSHYAQPEEIVTQEELKTMLVKSLDNLTEKERRVIE 207

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +      D TL+E+     V+  R+ Q+  K + K++
Sbjct: 208 LYY----YEDLTLKEISNILEVSESRVSQLHTKGLIKMR 242


>gi|255315371|ref|ZP_05356954.1| sporulation sigma factor SigE [Clostridium difficile QCD-76w55]
          Length = 240

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 99/226 (43%), Gaps = 51/226 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +++K+ N G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 58  VKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGLIKAVNTFKLNKNIKLATYA--- 114

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I +++R             +NK K E + +             
Sbjct: 115 -----SRCIENE-----ILMYLRK------------NNKKKTEVSFD------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   EP++++    D +   L D +  +N         + + R+     L  L+ R
Sbjct: 140 --------EPLNIDL---DGNELLLSDVLGTENDEIYKIIEEEID-RDLLVMALDRLSDR 187

Query: 624 EERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E++++ +RFG I    + T +EV     +++  I ++E K I +L+
Sbjct: 188 EKQIMELRFGLIDKGIEKTQKEVAGMLGISQSYISRLEKKIISRLQ 233


>gi|302389525|ref|YP_003825346.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
 gi|302200153|gb|ADL07723.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
          Length = 239

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 102/221 (46%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G    DLI  G IGL+KA   FD     K +TYA       
Sbjct: 62  LIERNLRLVVYIARKFENTGAGIEDLISIGTIGLIKAINTFDPHKKIKLATYA------- 114

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +N+ + E + +E    L +  +G   +L
Sbjct: 115 -SRCIENE-----ILMYLRR------------NNRNRAEVSFDE---PLNIDWDGNELLL 153

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                     + I   D+  +   IE++     LD+A++             L+ RE  +
Sbjct: 154 ----------SDILGTDSDMIYKCIEEEVEKELLDTAMK------------RLSKRERCI 191

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T +EV +   +++  I ++E + I++L+
Sbjct: 192 MELRFGLNDGKEKTQKEVAELLGISQSYISRLEKRIIKRLR 232


>gi|268316324|ref|YP_003290043.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodothermus marinus
           DSM 4252]
 gi|262333858|gb|ACY47655.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodothermus marinus
           DSM 4252]
          Length = 253

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 97/202 (48%), Gaps = 15/202 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT---RSIADQSCTIRIPVHMRDK 528
           DL   G +GL++A + +D   G  F +YA   ++ A+    RSI        +P   R K
Sbjct: 51  DLENVGLMGLLQALDSYDPERGTPFVSYAYGRIRGALVDYLRSIDA------LPRERRRK 104

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS 586
           + ++ +    +   +  EP  +++A  L + ++    +L   +    +SL+  +G++   
Sbjct: 105 LAELQQAIETLRQTLGGEPEDQDVADYLGISLQEYYTLLTDAQRRFALSLQETVGEDGDQ 164

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + + I +++A   L+   +A+L E  T+++  L  RE+ +L + +      + TL E+ 
Sbjct: 165 SVLETIPNEDAEKQLEDIDRASLIEYVTKLIQRLPEREQNILALYY----YENLTLREIA 220

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   +T  RI QI  K +  L+
Sbjct: 221 QLLGLTEARISQILGKTLLTLR 242


>gi|221319748|ref|ZP_03601042.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
          Length = 160

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/96 (33%), Positives = 51/96 (53%), Gaps = 3/96 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+ +    +S SE +  + ++ KG+     A+  ++E NLRLV  + KK+ N G    D
Sbjct: 27  VKNNAFPQPLSSSEEKKYLELMAKGD---EHARNMLIEHNLRLVAHIVKKFENTGEDAED 83

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LI  G IGL+K  E +    G K +TYA   ++  I
Sbjct: 84  LISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI 119


>gi|221310502|ref|ZP_03592349.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314826|ref|ZP_03596631.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221324026|ref|ZP_03605320.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321312063|ref|YP_004204350.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|143642|gb|AAA22804.1| spoIVCB peptide precursor [Bacillus subtilis]
 gi|320018337|gb|ADV93323.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 155

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/96 (33%), Positives = 51/96 (53%), Gaps = 3/96 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+ +    +S SE +  + ++ KG+     A+  ++E NLRLV  + KK+ N G    D
Sbjct: 22  VKNNAFPQPLSSSEEKKYLELMAKGD---EHARNMLIEHNLRLVAHIVKKFENTGEDAED 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LI  G IGL+K  E +    G K +TYA   ++  I
Sbjct: 79  LISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI 114


>gi|312173282|emb|CBX81537.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 243

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 42/201 (20%), Positives = 93/201 (46%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G++G + A + FD   G   S +    ++ A+   + ++     +P  +R    +
Sbjct: 43  DLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDW---VPRRVRKHARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    +++      E +  +IA ++ + V  ++++L  T    S +    DE      D 
Sbjct: 100 MTAVIQQLEQNKGGEASEADIATEMGVSVCELQQMLADTN---SSQIYSLDELQEQFADS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E+  A++P+  A+Q NL       ++ +  RE+ +L++ +      D  + E+G 
Sbjct: 157 YETIDEENEALNPVHQAVQENLVGKIAEHISVIPEREQVILQLYY----QQDLNMREIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  R+ Q+ + AI++++
Sbjct: 213 VLSLTETRVSQLHSLAIKRIR 233


>gi|215270887|emb|CAR48121.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
          Length = 291

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 33/45 (73%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           Y+REMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 45



 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 76/173 (43%), Gaps = 11/173 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    +  S K  V  E ++ +     L   + D LV +L   
Sbjct: 124 EKFNQLRSTYQNLQLAINEYGYD--SPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTA 181

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  ++     YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 182 MDRVRTQERLIMNSVVEYGKMPKKSFIALFTGNESSDAWLDEILASDKPYAEK---IKRN 238

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRL
Sbjct: 239 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRL 291


>gi|215270885|emb|CAR48120.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
 gi|215270889|emb|CAR48122.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
 gi|215270891|emb|CAR48123.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
          Length = 291

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 33/45 (73%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           Y+REMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 45



 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 77/173 (44%), Gaps = 11/173 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    +  S K  V  E ++ +     L   + D LV +L   
Sbjct: 124 EKFNQLRSTYQNLQLAINEYGYD--SPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTA 181

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++    YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 182 MDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSDAWLDEILASDKPYAEK---IKRN 238

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMVEANLRL
Sbjct: 239 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRL 291


>gi|295092920|emb|CBK82011.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus sp.
           ART55/1]
          Length = 206

 Score = 52.4 bits (124), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 95/229 (41%), Gaps = 57/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  +++KY +      DL+  G IGL+KA + +    G K S YA   
Sbjct: 27  ARSILIEYNLRLVAHISRKYNSAVRDPEDLLSIGTIGLIKAIDSYKPDKGCKLSGYAAKC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +  ++                         R   K  RE                 
Sbjct: 87  IENELLMTL-------------------------RHEKKKARE----------------- 104

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
                     +S+  PIG +   +   + D I  +N V+ LD  IQ +        ++S 
Sbjct: 105 ----------VSIYDPIGTDKEGNEIVILDIIGSEN-VNVLDKMIQDDHLCLLPSCISSL 153

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ RE  ++ MR+G+   +  T +EV +   ++R  + +IE KA+ KL+
Sbjct: 154 LSSREREIICMRYGLDGQSPLTQKEVARMLGISRSYVSRIEKKALGKLR 202


>gi|126698826|ref|YP_001087723.1| sporulation sigma factor SigK [Clostridium difficile 630]
 gi|26000675|gb|AAN75197.1| sigma K [Clostridium difficile]
 gi|26000677|gb|AAN75198.1| sigma K [Clostridium difficile]
          Length = 213

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 91/216 (42%), Gaps = 49/216 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E N+RLV  +AKKY N      DLI  G IGL+KA E ++   G + +TYA   
Sbjct: 31  AKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIKAIETYNIDKGTRLATYASRC 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I  +I                           SN  K+  T   +   +    EG 
Sbjct: 91  IENEILMNIR--------------------------SN--KKNKTQVSLQDPIGTDKEG- 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                     ISL   +G E  +++ D +E K  V          L E   ++   LTPR
Sbjct: 122 --------NEISLLDILGTE-ANYVLDEVELKVQV--------GKLYEQLNKI---LTPR 161

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           E  ++++R+G+      T  E+ ++  ++R  + +I
Sbjct: 162 EREIVQLRYGLTPYGYKTQREIAQKLDISRSYVSRI 197


>gi|261405673|ref|YP_003241914.1| sporulation sigma factor SigE [Paenibacillus sp. Y412MC10]
 gi|329922715|ref|ZP_08278267.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
 gi|261282136|gb|ACX64107.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. Y412MC10]
 gi|328942057|gb|EGG38340.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
          Length = 240

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 100/221 (45%), Gaps = 50/221 (22%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 63  LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 115

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++     I +++R             +NK + E + +                 
Sbjct: 116 -SRCIENE-----ILMYLRR------------NNKTRSEVSFD----------------- 140

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
               EP++++    D +   L D +  +N     +   Q + R+   + L  L+ RE  +
Sbjct: 141 ----EPLNID---WDGNELLLSDVLGTENDTIYRNIEEQVD-RKLLQKALDKLSDRERMI 192

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 193 MELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 233


>gi|251797867|ref|YP_003012598.1| sporulation sigma factor SigE [Paenibacillus sp. JDR-2]
 gi|247545493|gb|ACT02512.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. JDR-2]
          Length = 240

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 93/229 (40%), Gaps = 66/229 (28%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA       
Sbjct: 63  LIERNLRLVVYIARKFENTGIHIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA------- 115

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
            +R I ++                ++   RR S                           
Sbjct: 116 -SRCIENE----------------ILMYLRRNSK-------------------------- 132

Query: 568 KITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLAS 619
             T+  +S + P+    D +   L D +  +N        I  N+ E   R      L  
Sbjct: 133 --TRTEVSFDEPLNIDWDGNELLLSDVLGTEN------DTIYRNIEEQVDRKLLHKALDK 184

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 185 LSERERIIMELRFGLADGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 233


>gi|317153074|ref|YP_004121122.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316943325|gb|ADU62376.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 261

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 47/203 (23%), Positives = 91/203 (44%), Gaps = 11/203 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G++GL+ A  K++   G KF TY+   +K A+   +       R    +R K+  
Sbjct: 66  ELISAGSLGLLDALGKYNAQRGIKFDTYSENRIKGAMLDELRRMDWFSR---GLRQKVKA 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    R++ ++     T E++     M  + VR+ L+     + L      E+       
Sbjct: 123 LEDAQRQVEHETGGPATTEQLQALTGMSEKDVRQGLEALHNQMCLSLDSFHENVIGRKAM 182

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            ED+    P  S     + +    ++  LTPRE+ V+ + +G  +N   T E +     +
Sbjct: 183 TEDE----PFQSTAFQEIVDKVASLIEELTPREKLVISLYYGEELNMKETAEVMD----I 234

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           T  R+ Q+ ++A+ KL+   R++
Sbjct: 235 TEGRVSQLHSQALTKLRKTFRAR 257


>gi|226313414|ref|YP_002773308.1| sporulation sigma factor SigE [Brevibacillus brevis NBRC 100599]
 gi|226096362|dbj|BAH44804.1| RNA polymerase sigma-E factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 240

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA
Sbjct: 63  LIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFDPDKNIKLATYA 115


>gi|62185044|ref|YP_219829.1| RNA polymerase sigma factor sigma-28 [Chlamydophila abortus S26/3]
 gi|62148111|emb|CAH63868.1| putative RNA polymerase sigma factor [Chlamydophila abortus S26/3]
          Length = 257

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 95/215 (44%), Gaps = 37/215 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL++A E+F+     +F  YA++ +K AI   +  Q     +P  +  K +K
Sbjct: 55  DLYASGVEGLVRAVERFNPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANK 111

Query: 532 VVRTARRMSNKIKREPTPEEIA-------KKLAMPVEGVRKVLKIT-----------KEP 573
           +      +   + REPT  ++        ++L+      R  L I+           +  
Sbjct: 112 LADAMDALRLSLGREPTDGDLCEYFQISQQELSGWFASARPALIISLNEERPSLSDGESG 171

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ++LE  I DE      D ++ K   S L SAI+ +L E   +V+A L   EE VL+    
Sbjct: 172 VALEERIADERAETGYDIVDKKEFSSFLASAIE-SLEEKERKVMA-LYYYEELVLK---- 225

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                     E+GK   V+  R+ QI +KA+ KL+
Sbjct: 226 ----------EIGKILGVSESRVSQIHSKALIKLR 250


>gi|87311163|ref|ZP_01093286.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
 gi|87286071|gb|EAQ77982.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
          Length = 261

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/232 (23%), Positives = 104/232 (44%), Gaps = 18/232 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE  L LV    ++   R   G++  DLI  G  GLM A + FD   G KF TY +
Sbjct: 27  RNRLVERYLPLVKYNGERIWARLPEGVELDDLISAGVFGLMDAIDAFDMSRGVKFETYCV 86

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  K+    +++  K  R+PT  E++  + M V+
Sbjct: 87  PRIRGAMLDELRTMDW---VPRLVRSKASKLNEANKQLEAKFGRQPTEIELSAHMGMSVK 143

Query: 562 GVRKVLKITKEP--ISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + K++        ISL     + D+       D +ED     P     + +L    T+ 
Sbjct: 144 ELEKMISDANAVGLISLNKKWYETDSYKDVREIDILEDIKGEDPTRRIQKNDLMRLVTKG 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L     R ER++ + +      + T++E+G    ++  R+ Q+ +  +++L+
Sbjct: 204 LN----RNERLIIILY---YYEELTMKEIGATLDLSESRVSQMHSSIVQRLQ 248


>gi|292489124|ref|YP_003532011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292900243|ref|YP_003539612.1| RNA polymerase sigma factor for flagellar operon [Erwinia amylovora
           ATCC 49946]
 gi|291200091|emb|CBJ47217.1| RNA polymerase sigma factor for flagellar operon [Erwinia amylovora
           ATCC 49946]
 gi|291554558|emb|CBA22163.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
          Length = 243

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 42/201 (20%), Positives = 93/201 (46%), Gaps = 14/201 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G++G + A + FD   G   S +    ++ A+   + ++     +P  +R    +
Sbjct: 43  DLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDW---VPRRVRKHARE 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    +++      E +  +IA ++ + V  ++++L  T    S +    DE      D 
Sbjct: 100 MTAVIQQLEQNKGGEASEADIATEMGVSVCELQQMLADTN---SSQIYSLDELQEQFADS 156

Query: 592 I----EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                E+  A++P+  A+Q NL       ++ +  RE+ +L++ +      D  + E+G 
Sbjct: 157 YETIDEENEALNPVHQAVQENLVGKIAEHISVIPEREQVILQLYY----QQDLNMREIGA 212

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  R+ Q+ + AI++++
Sbjct: 213 VLSLTETRVSQLHSLAIKRIR 233


>gi|269792906|ref|YP_003317810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269100541|gb|ACZ19528.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 187

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 49/80 (61%), Gaps = 2/80 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++ A   +V  +A++  NR  Q  D++QEG +GL++A + FD   G++FSTYA + 
Sbjct: 27  AREELILAYRPMVFWLARRLGNRAYQ--DVVQEGMLGLLEAVDNFDPSRGHRFSTYAYYR 84

Query: 504 VKQAITRSIADQSCTIRIPV 523
           ++  +   ++    +  IPV
Sbjct: 85  IRGRMINFLSRVEGSSPIPV 104


>gi|212638647|ref|YP_002315167.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
 gi|212560127|gb|ACJ33182.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
          Length = 129

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 3/77 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNKLIEHNLRLVAHIVKKFENTGEDPEDLISIGTIGLIKAIESYSTGKGTKLATYAARC 109

Query: 504 VKQAITRSIADQSCTIR 520
           ++  I  +I    C I+
Sbjct: 110 IENEIFMTIV---CVIK 123


>gi|332707787|ref|ZP_08427814.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
 gi|332353490|gb|EGJ33003.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
          Length = 260

 Score = 52.0 bits (123), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/218 (25%), Positives = 99/218 (45%), Gaps = 25/218 (11%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V  N  LV  +A   + +  + + DL Q G IGL++A E+FD   G  FS+ A+ +
Sbjct: 26  RNQIVRLNAGLVRKIAHIVSQKCAEPYEDLEQMGYIGLIRAIERFDPHQGCAFSSLAVPY 85

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK--------- 554
           ++  +   + D+   ++IP   ++      R +++++  + R P  EEIAK         
Sbjct: 86  IRGEMLHFLRDRGSLVKIPRRWQELQQAGKRVSKKLATNLGRFPRDEEIAKALDVSLQEW 145

Query: 555 ---KLA----MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK----NAVSPLDS 603
              KLA    +P+     V +   +P++L   + D    +L  + ED+     A+S L+ 
Sbjct: 146 QESKLAVQNRLPLSLDATVSQKVDQPMTLGETLPDYYEENLHYWEEDRQQLQGALSQLED 205

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             QA +     R L    PR+E   R+       T H 
Sbjct: 206 KTQAAIEFVFLREL----PRKEAAKRIGVSPMTVTRHV 239


>gi|167461547|ref|ZP_02326636.1| RNA polymerase sigma factor [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 361

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 105/235 (44%), Gaps = 29/235 (12%)

Query: 447 EMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK----FSTY 499
           EM+ A  ++V SVA+KY      GL + DL+  G IGL++A   +D     +    FSTY
Sbjct: 14  EMIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRFNRKVSSFSTY 73

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   +K +I R +AD+  ++R+P  +++K+  + +           + + E IA+K    
Sbjct: 74  AFNMIKWSIQRFLADKRFSVRVPRSIQNKLTVIWKQGW-------DQESAESIAEKTGWK 126

Query: 560 VEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  +R+V +        SL+  +  + T      ++   A++   S    +        L
Sbjct: 127 LAEIREVKRHLAGWSVASLDQALSSDKTDEEATMLDVLPAMTDFTSVHVQDF-------L 179

Query: 618 ASLTPREERVLRMRFG------IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +L P E  VL +R        I M+   T   V +     +++  Q +A  +++
Sbjct: 180 CALKPLERAVLELRLQDQTQKEIAMHIGKTQMYVSRILKKIKDKYTQFQAGTLKR 234


>gi|220932500|ref|YP_002509408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
 gi|219993810|gb|ACL70413.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
          Length = 254

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 115/237 (48%), Gaps = 30/237 (12%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL--DLIQE------GNIGLMKAAEKFDWCLGYK 495
           A+KE++   L LV     KY    ++ +  D I+E      G IGL+ A EK+D+ LG K
Sbjct: 25  ARKELILNYLPLV-----KYQVERVKMIIPDFIEEDDLESYGIIGLIDAIEKYDYRLGIK 79

Query: 496 FSTYAMWWVKQAITRSIADQSCTI-RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           F+TYA     + I  SI D    +  +P  +R +  ++ + A +++ ++ R+PT  E+A 
Sbjct: 80  FNTYA----SRRIRGSIIDHLRKLDWLPHSLRREGKELQKVADKLAKELGRKPTVAELAN 135

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR-E 611
           K  +  E V K+     + + +SL    G+   S + +FI  K    P D  +    R +
Sbjct: 136 KTNISREKVTKIYSKLNSAKWVSLYEDWGE---STVFNFI--KGDCLPPDRILDKKERIK 190

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R +  L+  E  V+ + +      + T +E+ +   ++  RI QI  +A+ +L+
Sbjct: 191 LLARAIDRLSESERTVISLYY----YEELTQKEIAEVMGLSPARISQIHKRAVYRLR 243


>gi|319764532|ref|YP_004128469.1| RNA polymerase sigma factor, flia/whig family [Alicycliphilus
           denitrificans BC]
 gi|330826748|ref|YP_004390051.1| RNA polymerase sigma 28 subunit FliA/WhiG [Alicycliphilus
           denitrificans K601]
 gi|317119093|gb|ADV01582.1| RNA polymerase sigma factor, FliA/WhiG family [Alicycliphilus
           denitrificans BC]
 gi|329312120|gb|AEB86535.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alicycliphilus
           denitrificans K601]
          Length = 238

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 49/206 (23%), Positives = 91/206 (44%), Gaps = 12/206 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL  A  +++   G +F T+A   ++ A+   + D     R     R    +
Sbjct: 40  DLVQVGMIGLTDALSRYEAAQGVQFETFASQRIRGAMLDELRDGDWMSRGA---RKSQKE 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE--TPIGDEDTSH 587
           + +   R+  ++ R P   EIA +L M +   + +L   +  + + LE      + +   
Sbjct: 97  IEQALHRVEQRLGRSPMESEIAAELGMDLADYQALLGKVRGTQLVYLEDMGGGEEGEEGF 156

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + D+ A  P+       LR +    +  L  RE+ ++ M +   MN    L+E+  
Sbjct: 157 LDRHVADEGA-DPMAVLRDQRLRTSLVAAIKQLPEREQHIMGMYYEHDMN----LKEIAA 211

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
              VT  R+ Q+ ++AI +L+   R 
Sbjct: 212 VLGVTESRVCQLHSQAIARLRTKMRG 237


>gi|309778066|ref|ZP_07673005.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|313901138|ref|ZP_07834626.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
 gi|308914160|gb|EFP59961.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|312954096|gb|EFR35776.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
          Length = 234

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 99/225 (44%), Gaps = 51/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AK+Y    +   DLI  G+IGL+KA   F      K  TYA   
Sbjct: 54  ARNTLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIKAVNTFKRDKNIKLVTYA--- 110

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I + +R K                                   
Sbjct: 111 -----SRCIENE-----ILMFLRKK---------------------------------SR 127

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV     EP++++    D +   L D +   + V   +   + N RE     +++L  R
Sbjct: 128 RKVEVSFDEPLNIDY---DGNELLLSDILGTDDDVVTKEFEKKENKRE-LLEAMSTLKER 183

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E ++L+MR+GI  + + T +++ K+  +++  I ++E + I KLK
Sbjct: 184 ERQILQMRYGIQ-HEELTQKDIAKRLGISQSYISRLEKRIIAKLK 227


>gi|146164074|gb|ABQ08719.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp. ranae]
          Length = 293

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 67/137 (48%), Gaps = 2/137 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 158 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 217

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 218 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 276

Query: 439 CEASIAKKEMVEANLRL 455
            +A  AKKEMVEANLRL
Sbjct: 277 AKARRAKKEMVEANLRL 293


>gi|160936421|ref|ZP_02083790.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440704|gb|EDP18442.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
           BAA-613]
          Length = 199

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/133 (24%), Positives = 72/133 (54%), Gaps = 2/133 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE  L  V+ + ++Y +  L   DL+QE N  LM AA ++D      ++      
Sbjct: 39  ARSRLVEGCLGEVLEMVREYGDSELPLSDLVQEANTALMLAAIEYDGS--EPWNELMTRR 96

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           VK+++  ++ +Q    +I   M  +++ +   ++ ++ ++ RE T EE++ K+ M  + V
Sbjct: 97  VKESVELALEEQRTENQIEETMAARVNVLQTVSQVLAKELGREATLEELSAKMKMSEDEV 156

Query: 564 RKVLKITKEPISL 576
           R ++K+  + +++
Sbjct: 157 RDIMKLALDALTV 169


>gi|237757202|ref|ZP_04585618.1| RNA polymerase sigma-D factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690638|gb|EEP59830.1| RNA polymerase sigma-D factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 242

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 100/220 (45%), Gaps = 26/220 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G +GL  A EKFD   G KFSTYA   V+  I   +        +P ++R+K+  
Sbjct: 39  DLFQVGVLGLYDALEKFDPSKGVKFSTYAEIRVRGYILDHLRQLDW---VPRNIRNKVKN 95

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVE--------GVRKVLKITKEPISLETPIGDE 583
           +      +  K+ RE   EEIA+ L M +E         V K+L      IS +     +
Sbjct: 96  LENKIVELETKLGREAKLEEIAEYLGMSLEEYMIYAEKAVNKILISIDSDISKDD----D 151

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTL 642
           ++ HL + I   +  +P     +  L+E  + ++ + L  RE  ++ + +   +N    +
Sbjct: 152 ESLHLWEVISTDDD-TPEKYVEEKQLKEILSDIIMNKLDERERLIVTLYYYEDLN----M 206

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +E+ +    T  R+ Q+  K + K++     K +  +L G
Sbjct: 207 KEIAEILGYTESRVSQLHTKIMLKIR-----KLIEKYLGG 241


>gi|167755748|ref|ZP_02427875.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|237734714|ref|ZP_04565195.1| sporulation sigma factor sigE [Mollicutes bacterium D7]
 gi|167704687|gb|EDS19266.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|229382042|gb|EEO32133.1| sporulation sigma factor sigE [Coprobacillus sp. D7]
          Length = 231

 Score = 52.0 bits (123), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 101/234 (43%), Gaps = 65/234 (27%)

Query: 444 AKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  ++E NLRLV+ VAK+Y    N G++  DLI  G IGL+KA   F      K +TYA
Sbjct: 47  ARDLLIEHNLRLVVYVAKRYDTTQNGGIE--DLISIGTIGLVKAINTFKPDKNIKLATYA 104

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
                   +R I ++                 +    R +NK++ E              
Sbjct: 105 --------SRCIENE-----------------ILMFLRKNNKLRHE-------------- 125

Query: 561 EGVRKVLKITKEPISLETPIG---DEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRV 616
                        ISL+ P+    D +   L D I  D + V   +   Q++ +      
Sbjct: 126 -------------ISLDEPLNIDYDGNELLLSDIIGTDSDIVK--NELEQSDQKAMFYEA 170

Query: 617 LASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              L+ RE+ +L  R+G+ MN D  T ++V K   +++  I ++E K I+KL++
Sbjct: 171 FKDLSKREKEILMFRYGL-MNYDELTQKDVAKMMGISQSYISRLEKKIIKKLRN 223


>gi|329942781|ref|ZP_08291560.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Chlamydophila psittaci Cal10]
 gi|332287373|ref|YP_004422274.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313847955|emb|CBY16951.1| putative RNA polymerase sigma factor [Chlamydophila psittaci RD1]
 gi|325507072|gb|ADZ18710.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328815041|gb|EGF85030.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Chlamydophila psittaci Cal10]
 gi|328914621|gb|AEB55454.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           psittaci 6BC]
          Length = 257

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 94/215 (43%), Gaps = 37/215 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL++A E+F+     +F  YA++ +K AI   +  Q     +P  +  K +K
Sbjct: 55  DLYASGVEGLVRAVERFNPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANK 111

Query: 532 VVRTARRMSNKIKREPTPEEIA-------KKLAMPVEGVRKVLKIT-----------KEP 573
           +      +   + REPT  ++        ++L+      R  L I+           +  
Sbjct: 112 LADAMDALRLSLGREPTDGDLCEYFQISQQELSGWFASARPALIISLNEERPSLSDGESG 171

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ++LE  I DE      D ++ K   S L SAI+  L E   +V+A L   EE VL+    
Sbjct: 172 VALEERIADERAETGYDIVDKKEFSSFLASAIE-GLEEKERKVMA-LYYYEELVLK---- 225

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                     E+GK   V+  R+ QI +KA+ KL+
Sbjct: 226 ----------EIGKILGVSESRVSQIHSKALIKLR 250


>gi|239623450|ref|ZP_04666481.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521481|gb|EEQ61347.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 246

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 101/229 (44%), Gaps = 56/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F      K +TYA   
Sbjct: 63  ARSTLIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFKPDKNIKLATYASRC 122

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                         R +NK + E + +E    L +  +G 
Sbjct: 123 IENEILMYL-------------------------RRNNKTRLEVSIDE---PLNVDWDG- 153

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DED  +    IED+   + L++AI            + L P
Sbjct: 154 --------NELLLSDILGTDEDVIY--HDIEDEIEKNLLNNAI------------SRLNP 191

Query: 623 REERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +++ +R+G+  N D    T +EV     +++  I ++E K +++LK
Sbjct: 192 RERKIVELRYGL-TNEDGEEMTQKEVADLLGISQSYISRLEKKIMKRLK 239


>gi|251798274|ref|YP_003013005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
 gi|247545900|gb|ACT02919.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
          Length = 184

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 87/216 (40%), Gaps = 61/216 (28%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            KK+ N G    DLI  G IGL+KA E F    G K +T+A         R I ++    
Sbjct: 17  VKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFA--------ARCIENE---- 64

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
            I +H+R                                        LK T++ +SL  P
Sbjct: 65  -ILMHLRS---------------------------------------LKKTRKDVSLHDP 84

Query: 580 IGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           IG +   +   L D +  E  + V  +   I+   +    R L  L  RE+ V+R RFG+
Sbjct: 85  IGTDKEGNEITLIDILGTEADDVVDRVQLKIE---KSKIYRNLDILDEREQEVIRGRFGL 141

Query: 635 GMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               D  T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 142 DHGGDERTQREIAKELGISRSYVSRIEKRALMKLYH 177


>gi|455127|gb|AAA22315.1| RNA polymerase sigma-K subunit (cisB) [Bacillus subtilis]
 gi|1303780|dbj|BAA12436.1| SpoIVCB [Bacillus subtilis]
          Length = 156

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/96 (33%), Positives = 51/96 (53%), Gaps = 3/96 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+ +    +S SE +  + ++ KG+     A+  ++E NLRLV  + KK+ N G    D
Sbjct: 23  VKNNAFPQPLSSSEEKKYLELMAKGD---EHARNMLIEHNLRLVAHIVKKFENTGEDAED 79

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LI  G IGL+K  E +    G K +TYA   ++  I
Sbjct: 80  LISIGTIGLIKGIESYSAGKGTKVATYAARCIENEI 115


>gi|160914280|ref|ZP_02076501.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
 gi|158433907|gb|EDP12196.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
          Length = 233

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 101/225 (44%), Gaps = 51/225 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AK+Y    +   DLI  G+IGL+KA   F      K  TYA   
Sbjct: 52  ARNTLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIKAVNTFKRNKNIKLVTYA--- 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I + +R K       +RR                KL +  +  
Sbjct: 109 -----SRCIENE-----ILMFLRKK-------SRR----------------KLEVSFD-- 133

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                   EP++++    D +   L D +   + V       + N RE   + +  L  R
Sbjct: 134 --------EPLNIDY---DGNELLLSDILGTDDDVVTKQFEREENKRE-LLKAMRGLKDR 181

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E ++L+MR+GI  + + T +++ K+  +++  I ++E + I KLK
Sbjct: 182 ERQILQMRYGIE-HEELTQKDIAKRLGISQSYISRLEKRIIHKLK 225


>gi|218459714|ref|ZP_03499805.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 198

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 54/190 (28%), Positives = 88/190 (46%), Gaps = 18/190 (9%)

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----EPTPE---EI 552
           AMWW+K +I   I      +++      K  ++    RR+  +I+     +  PE   EI
Sbjct: 1   AMWWIKASIQEYILRSWSLVKMGTTANQK--RLFFNLRRLKGRIQAIDDGDLKPEHVSEI 58

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A KL +  E V  + +      SL  PI   + D+    D++ D +  S  D  I+ +  
Sbjct: 59  ATKLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHD-SQEDVLIEQDEL 117

Query: 611 ETTTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           ET  R+L+     L  RE R+   R         TLE++  +F ++RER+RQIE +A  K
Sbjct: 118 ETRRRMLSKAMSVLNERERRIFEARRL--AEEPVTLEDLSAEFDISRERVRQIEVRAFEK 175

Query: 667 LKHPSRSKKL 676
           ++   R + L
Sbjct: 176 VQDAVRKEAL 185


>gi|152990367|ref|YP_001356089.1| RNA polymerase sigma factor for flagellar operon [Nitratiruptor sp.
           SB155-2]
 gi|151422228|dbj|BAF69732.1| RNA polymerase sigma factor for flagellar operon [Nitratiruptor sp.
           SB155-2]
          Length = 211

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 109/230 (47%), Gaps = 40/230 (17%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           K+++V  NL LV  VA K   +      ++F +L+  G IGL KA EK++     +FSTY
Sbjct: 8   KQQIVLDNLALVKKVASKIYFKLPKDANIEFDELVNTGTIGLYKAIEKYNRDKA-QFSTY 66

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A  ++K  I   I D         ++R  +H V RT R    K K          +  +P
Sbjct: 67  A--YIK--IRGEILD---------YLRS-LHIVPRTMREKIKKEKE-------EGQKEIP 105

Query: 560 VEGVRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  +  ++       S+E  +G+ E+   L D +   N  SP D AI + + +     L 
Sbjct: 106 LSNLAIMM-------SMEKALGESENGPRLMDIL-ISNEKSPEDYAISSEIHDKIVEALD 157

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           SL+  E + L+M +      +   +E+ +   +++ R+ QI++KAI KLK
Sbjct: 158 SLSESERKTLQMLYF----EEREPKEISQILGISQSRVSQIKSKAIVKLK 203


>gi|89476477|gb|ABD73739.1| SigB [Staphylococcus aureus]
 gi|89476479|gb|ABD73740.1| SigB [Staphylococcus aureus]
 gi|89476485|gb|ABD73743.1| SigB [Staphylococcus aureus]
          Length = 147

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/112 (25%), Positives = 62/112 (55%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 20  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 79

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA +
Sbjct: 80  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIANR 131


>gi|110084474|gb|ABG49394.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 285

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 39/152 (25%), Positives = 74/152 (48%), Gaps = 2/152 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++  + +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 135 QKNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 194

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 195 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEDVLRAIGKLQQIEEETGLS 253

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           I++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 254 IAQIKDINRRMSIGEAKARRAKKEMVEANLRL 285


>gi|163782183|ref|ZP_02177182.1| RNA polymerase sigma factor FliA [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882715|gb|EDP76220.1| RNA polymerase sigma factor FliA [Hydrogenivirga sp. 128-5-R1-1]
          Length = 235

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 112/229 (48%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++E+V   L LV S+A   K+     +   DLI  G IGLMKA EK D     +  +Y  
Sbjct: 12  REELVLKYLPLVKSIAFTIKRQIPPTIDVRDLIGHGIIGLMKALEKLDTQKNPE--SYLK 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +       R    +R+K  K+    R ++ K+ REPT EEIA+ L   + 
Sbjct: 70  IRIRGAIYDYLRSLDFGSR---RIREKERKIREALRELTEKLGREPTDEEIAEYLGEDLG 126

Query: 562 GVRKVL-KITKEPI-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            ++  L +I+   I +LE    +E  S+  + I  K  V   D  ++ +L E     + +
Sbjct: 127 TLQHDLSRISFSYILNLEDIFTEERRSY-EEVIGSKR-VDVEDEIVKKDLIEKLKEAIEA 184

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+ V+++ F      +  L+E+ +    +  R+ QI+A+AI KLK
Sbjct: 185 LDEREKLVIQLIF----YEELPLKEIAQILNCSISRVSQIKAEAIEKLK 229


>gi|77457790|ref|YP_347295.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens Pf0-1]
 gi|77381793|gb|ABA73306.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           fluorescens Pf0-1]
          Length = 246

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 105/237 (44%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  AQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRSIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  +  +D  H G  + +  A + L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG--LHEDGASAHLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|167626171|ref|YP_001676465.1| flagellar biosynthesis sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167356193|gb|ABZ78806.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella
           halifaxensis HAW-EB4]
          Length = 240

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 50/215 (23%), Positives = 107/215 (49%), Gaps = 20/215 (9%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S  + +    L   D+ Q G + L++AA ++       F ++A   ++ AI   +  Q 
Sbjct: 37  VSQLRSHCGSVLAIEDMEQIGMMALLEAARRYPGEYDNGFLSFAGQRIRGAILDELRRQD 96

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLKITKEPI- 574
              R PV  R + H++  T R+++  ++REP+ +E+A+ + +  VE   ++     E + 
Sbjct: 97  WRPR-PV--RQQAHELNDTIRKLTRLLEREPSDKEVAEAMGLNEVEYRERLFASQSESMR 153

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL     DE  S  G+F+++ + +       Q + +E   + ++ L  RE+ +L + +  
Sbjct: 154 SL-----DELISEGGNFVDNNDMLE------QFSAKECLFQAISKLNKREQLILSLYYQH 202

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +N    L+E+     +T  RI Q+  +A+++L++
Sbjct: 203 ELN----LKEIAATLGLTETRICQLHKQAVKQLQN 233


>gi|89476431|gb|ABD73716.1| SigB [Staphylococcus aureus]
 gi|89476433|gb|ABD73717.1| SigB [Staphylococcus aureus]
 gi|89476435|gb|ABD73718.1| SigB [Staphylococcus aureus]
 gi|89476437|gb|ABD73719.1| SigB [Staphylococcus aureus]
 gi|89476439|gb|ABD73720.1| SigB [Staphylococcus aureus]
 gi|89476441|gb|ABD73721.1| SigB [Staphylococcus aureus]
 gi|89476443|gb|ABD73722.1| SigB [Staphylococcus aureus]
 gi|89476445|gb|ABD73723.1| SigB [Staphylococcus aureus]
 gi|89476447|gb|ABD73724.1| SigB [Staphylococcus aureus]
 gi|89476449|gb|ABD73725.1| SigB [Staphylococcus aureus]
 gi|89476451|gb|ABD73726.1| SigB [Staphylococcus aureus]
 gi|89476453|gb|ABD73727.1| SigB [Staphylococcus aureus]
 gi|89476455|gb|ABD73728.1| SigB [Staphylococcus aureus]
 gi|89476457|gb|ABD73729.1| SigB [Staphylococcus aureus]
 gi|89476459|gb|ABD73730.1| SigB [Staphylococcus aureus]
 gi|89476461|gb|ABD73731.1| SigB [Staphylococcus aureus]
 gi|89476463|gb|ABD73732.1| SigB [Staphylococcus aureus]
 gi|89476465|gb|ABD73733.1| SigB [Staphylococcus aureus]
 gi|89476467|gb|ABD73734.1| SigB [Staphylococcus aureus]
 gi|89476469|gb|ABD73735.1| SigB [Staphylococcus aureus]
 gi|89476471|gb|ABD73736.1| SigB [Staphylococcus aureus]
 gi|89476473|gb|ABD73737.1| SigB [Staphylococcus aureus]
 gi|89476475|gb|ABD73738.1| SigB [Staphylococcus aureus]
 gi|89476481|gb|ABD73741.1| SigB [Staphylococcus aureus]
 gi|89476483|gb|ABD73742.1| SigB [Staphylococcus aureus]
 gi|89476487|gb|ABD73744.1| SigB [Staphylococcus aureus]
          Length = 147

 Score = 51.6 bits (122), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/110 (25%), Positives = 61/110 (55%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +FD     KF  + +  
Sbjct: 20  AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPT 79

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P+  EIA
Sbjct: 80  VIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIA 129


>gi|29840191|ref|NP_829297.1| RNA polymerase sigma factor sigma-28 [Chlamydophila caviae GPIC]
 gi|29834539|gb|AAP05175.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 257

 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 93/215 (43%), Gaps = 37/215 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL++A E+FD     +F  YA++ +K AI   +  Q     +P  +  K +K
Sbjct: 55  DLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVE-------GVRKVLKIT-----------KEP 573
           +      +   + REPT  ++ +   +  +         R  L I+           +  
Sbjct: 112 LSEAMDTLRQSLGREPTDGDLCEYFQISQQELSGWFISARPALIISLNEERPSLSDGESG 171

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ++LE  I DE      D ++ K   S L +AI+  L E   +V+A L   EE VL+    
Sbjct: 172 VALEERIPDERAETGYDIVDKKEFSSFLANAIEG-LEEKERKVMA-LYYYEELVLK---- 225

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                     E+GK   V+  R+ QI +KA+ KL+
Sbjct: 226 ----------EIGKILGVSESRVSQIHSKALIKLR 250


>gi|73662123|ref|YP_300904.1| RNA polymerase sigma-B factor [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494638|dbj|BAE17959.1| truncated RNA polymerase sigma-B factor [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 192

 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 44/200 (22%), Positives = 99/200 (49%), Gaps = 18/200 (9%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL+ A  +FD     KF  + +  V   I R + D++ ++ +P  +++   ++ +    
Sbjct: 2   VGLIGAINRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVTDE 61

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           ++N+++R P+  EIA +L +  E V + +++ +   +L       D S   D  +D + V
Sbjct: 62  LTNELERSPSITEIADRLEVNEEDVLEAMEMGQSYNALSV-----DHSIEAD--KDGSTV 114

Query: 599 SPLDSAIQAN-------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + LD   Q +        R    ++L  L+ RE ++++  F  G++   T E +G    +
Sbjct: 115 TLLDIMGQQDDNYDLTEKRMILEKILPILSERERQIIQCTFIEGLSQKETGERIG----L 170

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           ++  + +++  AI+KL+  +
Sbjct: 171 SQMHVSRLQRTAIKKLQEAA 190


>gi|225575508|ref|ZP_03784118.1| hypothetical protein RUMHYD_03600 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037258|gb|EEG47504.1| hypothetical protein RUMHYD_03600 [Blautia hydrogenotrophica DSM
           10507]
          Length = 286

 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 96/202 (47%), Gaps = 9/202 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL QEG + L +A   +D      F +YA +W+K  + R + DQ+  +R+P ++ D++ +
Sbjct: 46  DLKQEGYLALCEAVRGYDVTREVPFLSYASFWLKTRMRRYV-DQNKPVRLPSYLGDEVRQ 104

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISL-ETPIGDEDTSHL 588
             +T      +   E +  E+   L +  + +RK+ +     +  SL E   G ED +  
Sbjct: 105 YQKTKSDFLKRYGYEASDRELCGLLGVNEKKIRKLKRAASMGQIQSLNELLPGTEDFTLE 164

Query: 589 GDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                +++      + + +  ++E   R +  L  R   V+RMR+      + TL EVG+
Sbjct: 165 ESIASEEDLEEEAAARLDRERMKEELWRSVDELPDRLPVVVRMRY----QEETTLNEVGE 220

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  V+  R  Q+  +A+R L+ 
Sbjct: 221 RLGVSLSRAAQMNKQAMRTLRQ 242


>gi|312622956|ref|YP_004024569.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203423|gb|ADQ46750.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 219

 Score = 51.6 bits (122), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 97/230 (42%), Gaps = 60/230 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV  +AKKYT        D+I  G IGL+KA E +      K STYA  
Sbjct: 33  ARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSSAKCTKLSTYA-- 90

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                                            A+ + N+I              M +  
Sbjct: 91  ---------------------------------AKCIENEI-------------LMYLRQ 104

Query: 563 VRKVLKITKEPISLETPIG---DEDTSHLGDFIE-DKNAV-SPLDSAIQANLRETTTRVL 617
            +K L      +SLE PIG   D +   L D ++ D+N +   +D  IQ   +    ++ 
Sbjct: 105 NKKFL----SQLSLENPIGSDKDGNEITLMDVLQNDQNDIDEQVDLKIQI--KNLLKKLD 158

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L  RE++++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 159 KILKGREKKIIELRYGLKNGIERTQMEVANLLGISRSYVSRIEKKALQKL 208


>gi|289678962|ref|ZP_06499852.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae FF5]
          Length = 239

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRSIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|312794136|ref|YP_004027059.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181276|gb|ADQ41446.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 219

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 95/230 (41%), Gaps = 60/230 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV  +AKKYT       D +I  G IGL+KA E +      K STYA  
Sbjct: 33  ARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSKAKSTKLSTYA-- 90

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                                            A+ + N+I              M +  
Sbjct: 91  ---------------------------------AKCIENEI-------------LMYLRQ 104

Query: 563 VRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVL 617
            +K L      +SLE PIG D+D + +      +N    +D   Q NL+        ++ 
Sbjct: 105 NKKFL----SQLSLENPIGSDKDGNEITLMDVLQNDQDDIDE--QVNLKIQIKNLLKKLD 158

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L  RE++++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 159 KILKGREKKIIELRYGLKNGIERTQMEVANLLGISRSYVSRIEKKALQKL 208


>gi|254974785|ref|ZP_05271257.1| sporulation sigma factor SigK [Clostridium difficile QCD-66c26]
 gi|255100257|ref|ZP_05329234.1| sporulation sigma factor SigK [Clostridium difficile QCD-63q42]
 gi|255306197|ref|ZP_05350369.1| sporulation sigma factor SigK [Clostridium difficile ATCC 43255]
 gi|255313912|ref|ZP_05355495.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
 gi|255516591|ref|ZP_05384267.1| sporulation sigma factor SigK [Clostridium difficile QCD-97b34]
 gi|306519807|ref|ZP_07406154.1| sporulation sigma factor SigK [Clostridium difficile QCD-32g58]
          Length = 130

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 40/69 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E N+RLV  +AKKY N      DLI  G IGL+KA E ++   G + +TYA   
Sbjct: 31  AKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIKAIETYNIDKGTRLATYASRC 90

Query: 504 VKQAITRSI 512
           ++  I  +I
Sbjct: 91  IENEILMNI 99


>gi|225389924|ref|ZP_03759648.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
 gi|225044004|gb|EEG54250.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
          Length = 223

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 101/229 (44%), Gaps = 56/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F      K +TYA   
Sbjct: 40  ARAALIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFKPDKNIKLATYASRC 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                         R +NK + E + +E    L +  +G 
Sbjct: 100 IENEILMYL-------------------------RRNNKTRMEVSIDE---PLNVDWDG- 130

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DED  +    IED+   + L++AI            + L P
Sbjct: 131 --------NELLLSDILGTDEDVIYHD--IEDEIEKNLLNNAI------------SRLNP 168

Query: 623 REERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE +++ +R+G+  N D    T +EV     +++  I ++E K +++L+
Sbjct: 169 RERKIVELRYGL-TNEDGEEMTQKEVADLLGISQSYISRLEKKIMKRLR 216


>gi|157962130|ref|YP_001502164.1| sigma-70 region 4 domain-containing protein [Shewanella pealeana
           ATCC 700345]
 gi|157847130|gb|ABV87629.1| sigma-70 region 4 domain protein [Shewanella pealeana ATCC 700345]
          Length = 930

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 51/96 (53%), Gaps = 8/96 (8%)

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           +PI+ E P G  D      F    N     + A    L+E  T+ L+ L  RE+ ++ +R
Sbjct: 360 KPITAE-PFGKMD------FTAQSNNEFKYNLASNIPLKEHFTQALSLLKDREKEIIELR 412

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            G   +   TLEEVG +F VTRERIRQI+ K + ++
Sbjct: 413 MGFHGHI-LTLEEVGTKFGVTRERIRQIQKKHVARI 447


>gi|91978897|gb|ABE66424.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 289

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 38/62 (61%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSD 60

Query: 184 II 185
           II
Sbjct: 61  II 62


>gi|218905533|ref|YP_002453367.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218535778|gb|ACK88176.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 149

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 3/81 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R  + ++ +G+ +A   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E 
Sbjct: 36  RKYLELMEQGDAQA---RNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIES 92

Query: 488 FDWCLGYKFSTYAMWWVKQAI 508
           +    G K +TYA   ++  I
Sbjct: 93  YSAGKGTKLATYAARCIENEI 113


>gi|291334306|gb|ADD93967.1| sigma factor FliA sigma 28 group flagellar [uncultured marine
           bacterium MedDCM-OCT-S09-C247]
          Length = 225

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 102/226 (45%), Gaps = 18/226 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K +++  NL +V  +A  Y  R  + +   DL+Q G +GL++AA  +       F  YA 
Sbjct: 12  KAQLINDNLDIVKKIAFFYVGRVGKVVEVDDLLQLGMVGLIEAAHNYTPQDDVSFVNYAR 71

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             VK AI   +   S   R  +  +       R  R++  ++ R+P   EIAK+L + V 
Sbjct: 72  LRVKGAIVDYLRKSSNLCRGTIRRKQDYE---RAKRKLEKELFRQPETHEIAKELKVEVS 128

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L    +  + +    +E +   GDF+   DK   S  +      L++     L  
Sbjct: 129 ---DLLSWQHDFAASQHQSLEEASDAYGDFLFATDK---SVEEKIFNGELKDILRTKLED 182

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L  ++  VL++ +   +N    + E+G+   V+  R+ QI++ AI+
Sbjct: 183 LNEQQLMVLQLYYVEELN----VYEIGEILSVSTGRVSQIKSAAIK 224


>gi|291543210|emb|CBL16319.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. 18P13]
          Length = 232

 Score = 51.2 bits (121), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 40/69 (57%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  R G  +A  A++ ++  NLRLV+ +AKK+ + G+   DLI  G IGL+KA   F   
Sbjct: 40  AFARLGTGDAESARQTLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIGLIKAVNTFCPE 99

Query: 492 LGYKFSTYA 500
              K +TYA
Sbjct: 100 KNIKLATYA 108



 Score = 41.6 bits (96), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 601 LDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           ++  I+A   ++  R  +  L PRE+R+++MRFG+    + T +EV  +  +++  I ++
Sbjct: 158 VNRGIEAEAEKSVLRQAVDGLEPREKRIMQMRFGLLGGREKTQKEVADEIGISQSYISRL 217

Query: 660 EAKAIRKLK 668
           E K IR+LK
Sbjct: 218 EKKIIRRLK 226


>gi|104782801|ref|YP_609299.1| flagellar biosynthesis sigma factor [Pseudomonas entomophila L48]
 gi|95111788|emb|CAK16512.1| sigma factor FliA [Pseudomonas entomophila L48]
          Length = 246

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E+VE    LV  +A     R    +Q  DLIQ G IGL++ A K+D   G  F TYA
Sbjct: 16  AQYELVERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRSVEARTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  +  +D  H G  + +  A   L       D   Q+ L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG--LHEDGASGQLEPSRDLEDERFQSALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|74055051|gb|AAZ95856.1| FliA [Aeromonas hydrophila]
          Length = 239

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 98/241 (40%), Gaps = 45/241 (18%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA    
Sbjct: 16  LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYA---- 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHK---VVRTARRMSNKIK-----------REPTPE 550
                         IRI   M D+I +   V R+  R S  I            R+    
Sbjct: 72  -------------GIRIRGSMLDEIRRGDWVPRSVHRNSRSIAEAIENVEQAHGRDARDT 118

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQA 607
           E+A ++ + +     +L    + +S    IG ED     D I   +D  + S  D     
Sbjct: 119 EVAAQMGVSLGEYHTML----QDVSCGKIIGIEDLGVSEDVIGHPDDAASNSGFDELAAE 174

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +      +  L  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ +L
Sbjct: 175 RFQGALAEHIGRLPEREALVLSLYYDEELN----LREIGEVLNVSESRVSQIHSQAMHRL 230

Query: 668 K 668
           +
Sbjct: 231 R 231


>gi|332971253|gb|EGK10216.1| hypothetical protein HMPREF9374_2566 [Desmospora sp. 8437]
          Length = 188

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 97/228 (42%), Gaps = 62/228 (27%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG-YKFSTYAMWW 503
           ++E+VE + RLV  VA ++    +++ DL+Q G IGL+KA ++++  +   KFST+A  +
Sbjct: 14  REELVEQHQRLVYFVANQFRQSKMEWDDLVQIGFIGLIKAVDRYNPGIKKVKFSTFAFHY 73

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                                +R +I   +R  +R +      P  E             
Sbjct: 74  ---------------------IRGEILHELRALKRHN------PAME------------- 93

Query: 564 RKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                     +S+E  +   G++D   L D +       P +     + R      +A L
Sbjct: 94  ----------VSVENVVEGGGEDDEIRLMDTL----GTDPDEVETTVSNRVALEESMADL 139

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T +E  V+  RFG       T  E+ + F V  +RIR IE KAIRKL+
Sbjct: 140 TDQEREVISFRFG----KQWTQGEIAELFDVPEKRIRVIEQKAIRKLR 183


>gi|330828816|ref|YP_004391768.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803952|gb|AEB49151.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 225

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 96/227 (42%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA   +
Sbjct: 2   LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIRI 61

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I       R  VH   +   +      +     R+    E+A ++ + +    
Sbjct: 62  RGAMLDEIRRGDWVPR-SVHRNSR--AIAEAIENVEQTHGRDARDTEVAAEMGVSIADYH 118

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +L    + +S    IG ED     D I   +D  + S  D       +   +  +  L 
Sbjct: 119 AML----QDVSCGKIIGIEDLGVSEDVIGHPDDAPSGSGFDELAAERFQIQLSEQIGRLP 174

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ +L+
Sbjct: 175 EREALVLSLYYDEELN----LREIGEVLNVSESRVSQIHSQAMHRLR 217


>gi|77020206|ref|YP_338165.1| RNA polymerase sigma factor, putative [Bacillus phage Cherry]
 gi|76563996|gb|ABA46386.1| RNA polymerase sigma factor, putative [Bacillus phage Cherry]
          Length = 248

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 101/230 (43%), Gaps = 32/230 (13%)

Query: 447 EMVEANLRLVI-SVAKKYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +E   RLV   V K+Y  +        GL   DL Q   IGL+KA + FD   G  FS
Sbjct: 21  EFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFXMIGLIKARDNFDLEFGCAFS 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKL 556
           TYA+  +   I R+I D         + + K+ + V   + ++ N+   +  PEEIA  L
Sbjct: 81  TYAVPKIIGEIGRAIRD---------NQKIKVQRTVYGVKGKILNQQLADKEPEEIADIL 131

Query: 557 AMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAI-QANLRET 612
              V  V+  L+      SL   +   G  +   L   IED       ++ I +A +RE 
Sbjct: 132 DESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTEDIEETTINRAVIREF 191

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                A+L P+E  VL MR       + T + +  Q   ++ +I +I AK
Sbjct: 192 K----AALPPKEYIVLDMRL-----QNMTQQNIANQMGYSQVQISRILAK 232


>gi|215270901|emb|CAR48128.1| RNA polymerase sigma factor [Vibrio cholerae]
 gi|223635919|emb|CAQ03761.1| RNA polymerase sigma factor [Vibrio cholerae]
          Length = 292

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 33/45 (73%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           Y+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYIL 45


>gi|296103602|ref|YP_003613748.1| RNA polymerase sigma factor for flagellar operon FliA [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058061|gb|ADF62799.1| RNA polymerase sigma factor for flagellar operon FliA [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
          Length = 241

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 44/199 (22%), Positives = 100/199 (50%), Gaps = 10/199 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ-SCTIRIPVHMRDKIH 530
           DLIQ G+IG + A E FD   G   +     W+ Q +  ++ D+   +  +P  +R    
Sbjct: 43  DLIQAGSIGFLSAVESFDPKKGVTLTA----WISQRVKWALLDELRESDWVPRRVRTHTR 98

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++V   +++  +   E T  EIA+++ + ++  +++L               E+ +   +
Sbjct: 99  EIVALIQQIEQEKGGEATEAEIAERMGVSLQEFQQMLADNNASQMYSVDELQENYADSWE 158

Query: 591 FIEDKN-AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             +++N  ++PL+ A++ NL E  T  +  +  RE+ +L++ +   +N    ++E+G   
Sbjct: 159 TSDEENEQLNPLNDAVRQNLMERITEHIQVIPEREQVLLQLYYLQDLN----MKEIGLIL 214

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +T  R+ Q+ + A+++L+
Sbjct: 215 GITETRVSQLHSLAVKRLR 233


>gi|218289804|ref|ZP_03494004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240095|gb|EED07280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 54/222 (24%), Positives = 91/222 (40%), Gaps = 60/222 (27%)

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KK+   G+   DLI  G +GL+KA + +    G KF+TYA                    
Sbjct: 2   KKFDTSGIDQDDLISIGTVGLIKAVDTYQPSKGTKFATYA-------------------- 41

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
                          AR + N+I              M +   RK    +++ +SL +PI
Sbjct: 42  ---------------ARCIQNEI-------------LMQLRAQRK----SRKDVSLYSPI 69

Query: 581 GDEDTSH---LGD--FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           G +   +   +GD  F E  +    +   ++ N   T  ++L  L  RE +V+ +RFG+ 
Sbjct: 70  GTDKEGNEITIGDILFSESDSTEDEVSRRMELN---TMRQLLDVLDERERKVIELRFGLA 126

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
              + T  EV     ++R  + ++E +A+ K+ H S   K R
Sbjct: 127 DGREWTQNEVADSLEISRSYVSRLEKRALLKMFHQSHVAKER 168


>gi|228913674|ref|ZP_04077301.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229090035|ref|ZP_04221286.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228693265|gb|EEL46975.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228845962|gb|EEM90986.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 196

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 44/205 (21%), Positives = 94/205 (45%), Gaps = 24/205 (11%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+    
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAI 61

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--- 593
             +++ ++R P   EIA  L +  E V +++              +   S L D +E   
Sbjct: 62  EELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENAS 111

Query: 594 DKNAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           D ++V+ ++S   ++    +T  R     +   L   E+ V+   F   +N   T    G
Sbjct: 112 DGSSVARIESVGEVEQGYEQTERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDT----G 167

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 168 ERLGISQMHVSRIKRQAISKLKQAA 192


>gi|167747049|ref|ZP_02419176.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
 gi|167654009|gb|EDR98138.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
          Length = 200

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 104/250 (41%), Gaps = 62/250 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E ++ +   R G+ EA   +  +VE NLRLV  + KKY N      DLI  G IGL
Sbjct: 8   LSQEEEQYYLKKSRLGDMEA---RNILVEHNLRLVAHIVKKYNNFDRDKDDLISVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++   G++  TYA        +R I ++                          
Sbjct: 65  IKAINTYNLEKGHRLVTYA--------SRCIENE-------------------------- 90

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFI--EDKN 596
                         L M +   RK  K T    SL  PIG   + +  +L D +  ++ +
Sbjct: 91  --------------LLMMLRQERKSAKDT----SLYEPIGIDKEGNEINLLDVLGADEND 132

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            V  LD  ++  +R+    V      RE+  L MR+G+      T +EV K+  ++R  +
Sbjct: 133 IVDELD--LKEKIRDLYKMVDEMEPSREKTTLIMRYGLYGKKPMTQKEVAKELHISRSYV 190

Query: 657 RQIEAKAIRK 666
            +IE K +R+
Sbjct: 191 SRIEKKLLRR 200


>gi|288553151|ref|YP_003425086.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
 gi|288544311|gb|ADC48194.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
          Length = 237

 Score = 51.2 bits (121), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA
Sbjct: 60  LIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 112


>gi|327439575|dbj|BAK15940.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 233

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 99/228 (43%), Gaps = 58/228 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E++E N+RLV  V KK+        D I  G IGLMKA   F      + +TYA   
Sbjct: 50  ARVELIERNMRLVAHVVKKFHPSHDLLDDYISIGTIGLMKAVSSFTPEKKTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG- 562
                 R I ++     I +H+R +             K++++ +   + + + +  +G 
Sbjct: 107 -----ARCIENE-----ILMHLRAQ------------KKVQKDVS---LFEPIGIDKDGQ 141

Query: 563 ---VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              +R +L++  EP ++E     ED + L                          R L +
Sbjct: 142 SLQIRDLLQLD-EPSTIEKIERQEDFAQL-------------------------YRYLDT 175

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L PRE  ++  R+G+     HT +E+ K+  ++R  + +IE +A+ KL
Sbjct: 176 LDPRELEIISYRYGLQNFDPHTQKEIAKRLNISRSYVSRIEKRALIKL 223


>gi|260886663|ref|ZP_05897926.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|330839507|ref|YP_004414087.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
 gi|260863515|gb|EEX78015.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|329747271|gb|AEC00628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
          Length = 252

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 48/199 (24%), Positives = 89/199 (44%), Gaps = 17/199 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ A E++D   G KF TY    ++ A+   +        IPV  R KI +
Sbjct: 57  DLVSSGFFGLLDAIERYDVERGNKFETYGGVRIRGAMLDYLRTMDW---IPVSKRQKIRR 113

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
             +    +  ++ R  T +E+A +L +  + +  ++  T     I LE  +  E  S   
Sbjct: 114 YEQAVTTLEGRLGRSATDDELAAELKISKKELHDLVSQTNIATVIPLEEYVRTESPS--- 170

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                   + P ++A +  LR+T    +  L  +E  V+ + +      + TL+E+    
Sbjct: 171 -----SQTIDPEENAEKNELRDTLAEAIDQLPEKERTVVSLYY----YEELTLKEISLIL 221

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++  RI Q+  KA+ +L+
Sbjct: 222 HLSEARISQLHTKAVFRLR 240


>gi|164686361|ref|ZP_02210391.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
 gi|164601963|gb|EDQ95428.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
          Length = 231

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 38/65 (58%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K  ++E NLRLV+ +++K+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 49  VKTILIERNLRLVVYISRKFENTGIDMEDLISIGTIGLIKAVNTFNLDKNIKLATYASRC 108

Query: 504 VKQAI 508
           ++  I
Sbjct: 109 IENEI 113


>gi|226311507|ref|YP_002771401.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
 gi|226094455|dbj|BAH42897.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 119

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNKLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYQVDKGTKLATYAARC 109

Query: 504 VKQAITRS 511
           ++  I  S
Sbjct: 110 IENEIVMS 117


>gi|90021809|ref|YP_527636.1| flagellar protein FliS [Saccharophagus degradans 2-40]
 gi|89951409|gb|ABD81424.1| RNA polymerase sigma factor, FliA/WhiG [Saccharophagus degradans
           2-40]
          Length = 250

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 95/221 (42%), Gaps = 26/221 (11%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G +GL++AA+K+D   G  F TY+   ++ AI   +       R       
Sbjct: 46  VQIEDLIQAGMLGLLEAAQKYDASKGASFETYSGIRIRGAIVDEMRRGDWAPR------- 98

Query: 528 KIHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLET 578
               V R +RR++  I        R+    EIA+++ + ++    + +   +    S E 
Sbjct: 99  ---SVHRNSRRVAEAIATVEARHGRDARDHEIAEEMGLSLDEYYAMARDSASTRLFSYEE 155

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
              + D S   ++        P +   +  L       +  L  RE  VL + +   MN 
Sbjct: 156 TY-ENDESRFDEYEPSDGLRGPSEQVHRNALYTDLVAAIGKLPERERLVLSLYYEQEMN- 213

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              L+E+G    V+  R+ QI ++A  +LK  SR +  +S+
Sbjct: 214 ---LKEIGLVLGVSESRVSQIHSQAALRLK--SRMQDWQSY 249


>gi|332162882|ref|YP_004299459.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318604274|emb|CBY25772.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325667112|gb|ADZ43756.1| Putative RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330863330|emb|CBX73453.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 228

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 109/232 (46%), Gaps = 36/232 (15%)

Query: 449 VEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EA L LV  + ++ + +    +   D+ Q   +GL++A  ++    G +F+ YA+  ++
Sbjct: 18  LEAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIR 76

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   + +       P  +R K HK   + R+++ K+  EP+ EEIA +L +  E  ++
Sbjct: 77  GAVLDQLREHDWR---PRRLRQKTHKTNESIRQLAKKLGHEPSFEEIAAELQLTAEEYQE 133

Query: 566 VLKITK--------EPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRV 616
            L +          E +SL+TP     +  L +  I + N    L+ AI           
Sbjct: 134 YLLLESAGAMESLDEILSLDTPTDALQSRELEESIITEDN----LNHAI----------- 178

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ASL  RE+ +L + +   M    +++E+ +   +T  RI Q+    ++K+K
Sbjct: 179 -ASLEKREQMILHLYYQQEM----SMKEIAEVLDLTEARICQLNKILVQKIK 225


>gi|256783387|ref|ZP_05521818.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767263|ref|ZP_06526641.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289697462|gb|EFD64891.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 287

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 111/247 (44%), Gaps = 30/247 (12%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 53  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVPTI 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP-TPEEIAKKLAMPV--- 560
              + R   D+   +R+P  +++  +K VR ARR   ++ + P +PE     LA      
Sbjct: 112 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARR---ELAQSPGSPEPSVAALAAHTGLS 167

Query: 561 -----EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                 G+  +   +   +  E   GD+  S L D +    A +  D+ I    RE+   
Sbjct: 168 EDEVGAGMEALESFSTLSLDAELSAGDDGYS-LADTL--GAADTSYDTVID---RESAKE 221

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR------ERIRQIEAKAIRKLK 668
            L  L  RE  +L MRF   M      + +G  Q  V+R       R+R  EA   R  +
Sbjct: 222 GLRRLPERERAILYMRFFEDMTQSRIADCLGISQMHVSRLISRSCARVRD-EAMGQRTAR 280

Query: 669 --HPSRS 673
             HP+R+
Sbjct: 281 PGHPART 287


>gi|212639538|ref|YP_002316058.1| RNA polymerase sigma factor SigD [Anoxybacillus flavithermus WK1]
 gi|212561018|gb|ACJ34073.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anoxybacillus flavithermus WK1]
          Length = 243

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 92/199 (46%), Gaps = 9/199 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL     +GL  A EKFD     KF TYA + ++ AI   +  +     +P  +R+K  K
Sbjct: 45  DLKSLALLGLYDALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSVREKAKK 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLG 589
           +  T  R+     R+ + +E+A  L +  + V  V+  +     +SL+    D+D     
Sbjct: 102 IEATIERLQQMHMRDVSAKEVADALNISEDEVYAVMNEQFFANVLSLDERPFDDDDDQPS 161

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             I D ++ SP +  ++        +V+  L  +E+ V+ + +      + T  E+G   
Sbjct: 162 FTIRDDHSPSPEEHMLREEQIAQLAQVIQQLNEKEQLVISLFY----KEELTFTEIGHIM 217

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++  RI QI AKA+ K++
Sbjct: 218 GLSTSRISQIHAKALFKMR 236


>gi|121607918|ref|YP_995725.1| FliA/WhiG family RNA polymerase sigma factor [Verminephrobacter
           eiseniae EF01-2]
 gi|121552558|gb|ABM56707.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Verminephrobacter eiseniae EF01-2]
          Length = 241

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 48/209 (22%), Positives = 96/209 (45%), Gaps = 15/209 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL  A  ++    G +F T+A   ++ A+   + +     R     + +I +
Sbjct: 40  DLIQVGMMGLADALSRYQVAQGVQFETFASQRIRGAMLDQLREGDWMSRSARKSQKEIEQ 99

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG---DEDTSH 587
            V    R+  ++ R P   EIA ++ + +   + +L K+    +     +G   DE  + 
Sbjct: 100 AV---HRLEQRLGRSPLESEIASEMGLHLASYQSLLGKVRGTQLVYLEDMGQGRDEREAE 156

Query: 588 LGDFIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            G F+E     +A  P++      L+ +    + SL  RE+ ++ M +   MN    L+E
Sbjct: 157 DG-FLERHIVDSAADPVELLRDQRLKTSLVAAIQSLPEREQHIMGMYYEHDMN----LKE 211

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +     +T  R+ Q+ +++I +L+   R+
Sbjct: 212 IAAVLGITESRVCQLHSQSIVRLRAKMRA 240


>gi|213967540|ref|ZP_03395688.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato T1]
 gi|301382877|ref|ZP_07231295.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato Max13]
 gi|302062797|ref|ZP_07254338.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato K40]
 gi|302131296|ref|ZP_07257286.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato NCPPB 1108]
 gi|213927841|gb|EEB61388.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato T1]
          Length = 246

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSEAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|68304088|gb|AAY89702.1| FliA [Escherichia coli LW1655F+]
          Length = 157

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 52/96 (54%), Gaps = 3/96 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 33  DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 89

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           V +   ++  ++ R  T  E+A++L + +   R++L
Sbjct: 90  VAQAIGQLEQELGRNATETEVAERLGIDIADYRQML 125


>gi|320325134|gb|EFW81203.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. B076]
          Length = 246

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVQDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|297569692|ref|YP_003691036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
 gi|296925607|gb|ADH86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
          Length = 262

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 56/220 (25%), Positives = 101/220 (45%), Gaps = 26/220 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A  KFD     +F TYA + +K A+   + +      +P  +R K+ +
Sbjct: 60  DLISCGIVGLIDAINKFDPAKNVQFKTYAEFRIKGAM---LDELRALDWVPRSIRRKVTE 116

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-------EPISLETPIGDED 584
           + +    +  K+ R  T EE A  L + +E   ++L  TK       E +  + P   E 
Sbjct: 117 LEQVCSELEVKLGRPATDEETATALGIGLEEYHRLLDETKSVSFLDIEYLRRQAPA--EV 174

Query: 585 TSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
             +L +    +DK+  + L      NL ET   +  ++    E+  ++   +  + + T+
Sbjct: 175 EGNLAEVFASDDKDPFAAL------NLGETKALLAKAINELPEKE-KLTVALYYHEELTM 227

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            E+G+    T  RI Q+ +KA+ +L+      KL+  LD 
Sbjct: 228 REIGEVLGYTESRISQMHSKAMLRLRG-----KLKKSLDA 262


>gi|56964116|ref|YP_175847.1| sporulation sigma factor SigE [Bacillus clausii KSM-K16]
 gi|56910359|dbj|BAD64886.1| DNA-directed RNA polymerase sigma-29 factor sigma-E [Bacillus
           clausii KSM-K16]
          Length = 237

 Score = 50.8 bits (120), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA
Sbjct: 60  LIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 112


>gi|330899448|gb|EGH30867.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           japonica str. M301072PT]
 gi|330940686|gb|EGH43699.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv. pisi
           str. 1704B]
 gi|330976015|gb|EGH76081.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aptata str. DSM 50252]
          Length = 246

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRSIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|26000679|gb|AAN75199.1| sigma K [Clostridium difficile]
 gi|26000681|gb|AAN75200.1| sigma K [Clostridium difficile CD196]
 gi|26000696|gb|AAN75201.1| sigma K [Clostridium difficile]
 gi|26000698|gb|AAN75202.1| sigma K [Clostridium difficile]
 gi|26000700|gb|AAN75203.1| sigma K [Clostridium difficile]
          Length = 108

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 40/69 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E N+RLV  +AKKY N      DLI  G IGL+KA E ++   G + +TYA   
Sbjct: 31  AKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIKAIETYNIDKGTRLATYASRC 90

Query: 504 VKQAITRSI 512
           ++  I  +I
Sbjct: 91  IENEILMNI 99


>gi|225569957|ref|ZP_03778982.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
 gi|225161427|gb|EEG74046.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
          Length = 274

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 99/231 (42%), Gaps = 13/231 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTN--RGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            K+E+    L +V S+A +  N   G  Q  D++ EG I LMKA +K++     KF TY 
Sbjct: 31  VKQEIALRYLYIVKSIAVQMRNVYAGFSQVEDIVNEGVIMLMKAIDKYEADKNAKFETYV 90

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I      Q     IP  +R     +   +    ++  REP  EE+++ L M +
Sbjct: 91  SKRIRGMIIDIARKQDW---IPRTVRKSYRDIKEASAVFYSEHGREPEAEELSELLHMDI 147

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSAIQANLRETTTRVL 617
           E  R ++        L   +  E+T      I+   DK    P    +    R      +
Sbjct: 148 EKFRDIMGKASLFSVLSLDMVLEETKEQYRSIQIPSDKKEEQPEAHLMDKEFRHMLADGI 207

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            SL   E+ V+ + +   +N    ++E+     V+  RI QI A AIRKL+
Sbjct: 208 RSLKENEQTVISLYYMEELN----MKEIAGILHVSEPRISQIHAGAIRKLR 254


>gi|330876038|gb|EGH10187.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 246

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|228926137|ref|ZP_04089213.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228833502|gb|EEM79063.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 194

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 44/203 (21%), Positives = 93/203 (45%), Gaps = 24/203 (11%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+      
Sbjct: 2   LGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEE 61

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---DK 595
           +++ ++R P   EIA  L +  E V +++              +   S L D +E   D 
Sbjct: 62  LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKN----------NYRVSSLDDVVENASDG 111

Query: 596 NAVSPLDSA--IQANLRETTTR-----VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           ++V+ ++S   ++    ET  R     +   L   E+ V+   F   +N   T    G++
Sbjct: 112 SSVARIESVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFEENLNQKDT----GER 167

Query: 649 FCVTRERIRQIEAKAIRKLKHPS 671
             +++  + +I+ +AI KLK  +
Sbjct: 168 LGISQMHVSRIKRQAISKLKQAA 190


>gi|327481248|gb|AEA84558.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 54/238 (22%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + +A  A+  +++    LV  +A     R    +Q  DLIQ G IGL++AA+K+D   G 
Sbjct: 5   KAQAKDAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDAGKGA 64

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F TYA   ++  +   +       R  VH   ++  V    R +  K  R+    E+A 
Sbjct: 65  SFETYAGIRIRGTMLDEVRKGDWAPR-SVHRNSRM--VSEAIRAIEAKTGRDAKDHEVAA 121

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVS--PLDSAIQANLR 610
           +L + ++    +L   +     S +  +  ++  H G+  ED ++    P         +
Sbjct: 122 ELKLSLDEYYAILGDTLGSRLFSFDDLL--QEGEH-GELQEDASSTHPEPFRDLEDERFQ 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     + +L  RE+ VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 179 QALADAIGNLPEREKLVLSLYYDEELN----LKEIGQVLGVSESRVSQLHSQCAARLR 232


>gi|158327335|emb|CAM82841.1| sigma factor FliA [Yersinia enterocolitica W22703]
          Length = 231

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 55/232 (23%), Positives = 109/232 (46%), Gaps = 36/232 (15%)

Query: 449 VEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EA L LV  + ++ + +    +   D+ Q   +GL++A  ++    G +F+ YA+  ++
Sbjct: 21  LEAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIR 79

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   + +       P  +R K HK   + R+++ K+  EP+ EEIA +L +  E  ++
Sbjct: 80  GAVLDQLREHDWR---PRRLRQKTHKTNESIRQLAKKLGHEPSFEEIAAELQLTAEEYQE 136

Query: 566 VLKITK--------EPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRV 616
            L +          E +SL+TP     +  L +  I + N    L+ AI           
Sbjct: 137 YLLLESAGAMESLDEILSLDTPTDALQSRELEESIITEDN----LNHAI----------- 181

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ASL  RE+ +L + +      + +++E+ +   +T  RI Q+    ++K+K
Sbjct: 182 -ASLEKREQMILHLYY----QQEMSMKEIAEVLDLTEARICQLNKILVQKIK 228


>gi|269792915|ref|YP_003317819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100550|gb|ACZ19537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 245

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 93/204 (45%), Gaps = 10/204 (4%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL + D++  G +GL+ A ++FD   G+ F T+A+  ++ AI   +       R     R
Sbjct: 46  GLDYDDILSFGVMGLLDAMDRFDPSRGFCFQTFAVPRIRGAILDELRRYDWISRTG---R 102

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDED 584
           DK+ ++   A   +         E + ++L M  +  R++L+I      +SL+  +G ED
Sbjct: 103 DKLQRLE-RAMEEAAAEGTLLDDEALMERLGMNEKSYRELLEIASRSYVVSLDEVLGLED 161

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
                D + +  + SP +   +        R L  L  RE  +L + +  G+    TL+E
Sbjct: 162 GEVKRDGLLEDPSPSPQEEVERREELALVRRALEELPERERLLLSLYYQEGL----TLKE 217

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           VG    VT  R  Q+  +AI  L+
Sbjct: 218 VGAVLGVTESRASQLHGRAIAMLR 241


>gi|157373192|ref|YP_001471792.1| flagellar biosynthesis sigma factor [Shewanella sediminis HAW-EB3]
 gi|157315566|gb|ABV34664.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           sediminis HAW-EB3]
          Length = 240

 Score = 50.8 bits (120), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 49/212 (23%), Positives = 102/212 (48%), Gaps = 16/212 (7%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS  + +    L   D+ Q G + L++++ ++       F +YA   ++ AI   +  Q 
Sbjct: 37  ISQLRSHCGTVLAIEDMEQIGMMALLESSRRYPGEYDNGFISYAGQRIRGAILDELRRQD 96

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
              R PV  R + H++  T R+++  + REP+  E+A+ + +  E  R+ L  ++     
Sbjct: 97  WRPR-PV--RQQAHELNDTVRKLTRLLGREPSDIEVAEAMGLNREEYRERLYASQS---- 149

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           E+    +D   +G    DK  V       Q ++++T  + ++ L+ RE+ +L + +   +
Sbjct: 150 ESMKSLDDMLSVGAHFPDKTNVIE-----QFSVQKTLIKAISKLSKREQLILSLYYQHEL 204

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           N    L+E+     +T  RI Q+  +A++ L+
Sbjct: 205 N----LKEIAGTLGLTETRICQLHKQAVKHLQ 232


>gi|330961240|gb|EGH61500.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 246

 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|71736085|ref|YP_275521.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71556638|gb|AAZ35849.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           syringae pv. phaseolicola 1448A]
          Length = 239

 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 9   SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 68

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 69  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 125

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 126 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 181

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 230


>gi|168335365|ref|ZP_02693459.1| sporulation sigma factor SigE [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 246

 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 99/227 (43%), Gaps = 55/227 (24%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           KK ++E NLRLV+ +AKK+  TN+G++  DLI  G+IGL+KA   F      K +TYA  
Sbjct: 65  KKILIERNLRLVVYIAKKFENTNKGME--DLISIGSIGLIKAINTFKPDKKIKLATYASR 122

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++  I   I                         R +NK+K E + +E    L    +G
Sbjct: 123 CIENEILMDI-------------------------RRTNKLKVEVSIDE---PLNTDWDG 154

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              +L          + I   D   +   IED+   + L++A            L  L+ 
Sbjct: 155 NELLL----------SDILGTDFDSVYRNIEDEVDKALLNTA------------LGQLST 192

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  ++ +R+G      + T +EV     +++  I ++E K I +LK
Sbjct: 193 REREIVELRYGFKNEGKEKTQKEVADMLGISQSYISRLEKKIIGRLK 239


>gi|255092173|ref|ZP_05321651.1| sporulation sigma factor SigK [Clostridium difficile CIP 107932]
 gi|255649691|ref|ZP_05396593.1| sporulation sigma factor SigK [Clostridium difficile QCD-37x79]
          Length = 105

 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 40/69 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E N+RLV  +AKKY N      DLI  G IGL+KA E ++   G + +TYA   
Sbjct: 31  AKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIKAIETYNIDKGTRLATYASRC 90

Query: 504 VKQAITRSI 512
           ++  I  +I
Sbjct: 91  IENEILMNI 99


>gi|21225590|ref|NP_631369.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|8347047|emb|CAB93752.1| probable RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 299

 Score = 50.4 bits (119), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 91/197 (46%), Gaps = 20/197 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 53  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVPTI 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP-TPEEIAKKLAMPV--- 560
              + R   D+   +R+P  +++  +K VR ARR   ++ + P +PE     LA      
Sbjct: 112 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARR---ELAQSPGSPEPSVAALAAHTGLS 167

Query: 561 -----EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                 G+  +   +   +  E   GD+  S L D +    A +  D+ I    RE+   
Sbjct: 168 EDEVGAGMEALESFSTLSLDAELSAGDDGYS-LADTL--GAADTSYDTVID---RESAKE 221

Query: 616 VLASLTPREERVLRMRF 632
            L  L  RE  +L MRF
Sbjct: 222 GLRRLPERERAILYMRF 238


>gi|237736225|ref|ZP_04566706.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
 gi|229421778|gb|EEO36825.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
          Length = 232

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 41/75 (54%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++ +  NL LV S+A  Y   G+ +LD++QEG +GL+K  E ++      F  Y  +W+ 
Sbjct: 38  EDFIVQNLPLVASIAFNYLREGVAYLDVVQEGTMGLIKGIENYNGEKHGDFENYKKYWII 97

Query: 506 QAITRSIADQSCTIR 520
           + I   I ++   I+
Sbjct: 98  REIVLFINNKITDIK 112


>gi|145298363|ref|YP_001141204.1| flagellar biosynthesis sigma factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142851135|gb|ABO89456.1| RNA polymerase sigma-27 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 239

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 97/241 (40%), Gaps = 45/241 (18%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA    
Sbjct: 16  LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYA---- 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHK---VVRTARRMSNKIK-----------REPTPE 550
                         IRI   M D+I +   V R+  R S  I            R+    
Sbjct: 72  -------------GIRIRGSMLDEIRRGDWVPRSVHRNSRAIAEAIENVEQAHGRDARDT 118

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQA 607
           E+A ++ + +     +L    + +S    IG ED     D I   +D    S  D     
Sbjct: 119 EVAVQMGVSLGEYHTML----QDVSCGKIIGIEDLGVSEDVIGHPDDAGGNSGFDELAAE 174

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +      +  L  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ +L
Sbjct: 175 RFQGALAEHIGRLPEREALVLSLYYDEELN----LREIGEVLNVSESRVSQIHSQAMHRL 230

Query: 668 K 668
           +
Sbjct: 231 R 231


>gi|88856926|ref|ZP_01131577.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
 gi|88813802|gb|EAR23673.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
          Length = 244

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 101/242 (41%), Gaps = 27/242 (11%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + + +  GE EA     E+  +      S++ K+T RG+   DL  E   GL++AA+ FD
Sbjct: 21  LAARISNGEMEAV---HELAMSGYAWAKSLSHKFTGRGVDLDDLNSEAYFGLVEAAKTFD 77

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +F+ Y+  +V+ AI ++I     ++ IP H  D   ++V    R+S +       
Sbjct: 78  PTRG-RFAGYSTAFVQGAIWKAIRLSGRSVSIPKHAFDA--ELVGNRDRISERYAANAAL 134

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
              A     P +           P+S + P    D       I D   V       Q  +
Sbjct: 135 ASEASAWHFPTQ--------LDAPLSSDAPGTAADV-----LISDARGVE------QTVV 175

Query: 610 RETTTRVLASLTPREER-VLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +     + S  PR ER VL  RF + G  +      +     + + RI +IE KA+ +L
Sbjct: 176 EQIFLDGMLSEIPRIEREVLLARFELPGACSAPGQAAISAALNIDQRRISEIEKKALARL 235

Query: 668 KH 669
           ++
Sbjct: 236 RN 237


>gi|28869183|ref|NP_791802.1| motility sigma factor FliA [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|66046666|ref|YP_236507.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae B728a]
 gi|237799256|ref|ZP_04587717.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           oryzae str. 1_6]
 gi|28852423|gb|AAO55497.1| motility sigma factor FliA [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|63257373|gb|AAY38469.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas
           syringae pv. syringae B728a]
 gi|330964675|gb|EGH64935.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           actinidiae str. M302091]
 gi|330972456|gb|EGH72522.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aceris str. M302273PT]
 gi|331016985|gb|EGH97041.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
 gi|331022111|gb|EGI02168.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           oryzae str. 1_6]
          Length = 246

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|257484896|ref|ZP_05638937.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289629013|ref|ZP_06461967.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289647088|ref|ZP_06478431.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|298487813|ref|ZP_07005854.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|302185382|ref|ZP_07262055.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae 642]
 gi|298157905|gb|EFH98984.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320329393|gb|EFW85386.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. race 4]
 gi|330866465|gb|EGH01174.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330880595|gb|EGH14744.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. race 4]
 gi|330889039|gb|EGH21700.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv. mori
           str. 301020]
 gi|330953768|gb|EGH54028.1| flagellar biosynthesis sigma factor [Pseudomonas syringae Cit 7]
 gi|330986509|gb|EGH84612.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 246

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  + D D  H G  + +  A   L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLLQDGD--HEG--LHEDGASGSLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|255655251|ref|ZP_05400660.1| sporulation sigma factor SigK [Clostridium difficile QCD-23m63]
 gi|296451236|ref|ZP_06892976.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296880412|ref|ZP_06904375.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|296259842|gb|EFH06697.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296428653|gb|EFH14537.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 138

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 40/69 (57%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E N+RLV  +AKKY N      DLI  G IGL+KA E ++   G + +TYA   
Sbjct: 31  AKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIKAIETYNIDKGTRLATYASRC 90

Query: 504 VKQAITRSI 512
           ++  I  +I
Sbjct: 91  IENEILMNI 99


>gi|91978899|gb|ABE66425.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 279

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 72/152 (47%), Gaps = 2/152 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           I++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEMVEANLRL 279


>gi|91978905|gb|ABE66428.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 286

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 72/152 (47%), Gaps = 2/152 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 136 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 195

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 196 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 254

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           I++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 255 IAQIKDINRRMSIGEAKARRAKKEMVEANLRL 286


>gi|148747769|ref|YP_001285848.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Geobacillus virus E2]
 gi|113715711|gb|ABI36860.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Geobacillus virus E2]
          Length = 232

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/234 (25%), Positives = 106/234 (45%), Gaps = 40/234 (17%)

Query: 447 EMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + +E ++RLV  V ++Y        +++ D I  G I L +A +KFD   GY+FSTYA+ 
Sbjct: 16  QAIEKHIRLVHYVVRRYFRSLHEIRIEYDDAISVGVIALARAYQKFDDSHGYRFSTYAVP 75

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   IT  + + S     P+H   +I  +   A+   NK      P + +K+L + V+ 
Sbjct: 76  RIWGEITNCVKNSS-----PIHFATRIKNLYLKAK---NKQIDLSNPTKASKELGVTVDV 127

Query: 563 VRKVLKITKEPISLETPIGD-------EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           V +V K         T + D       E  + + DF+  +   S       A +R+    
Sbjct: 128 VMEVKKYVDS--FYMTSLSDVVFENEREKKTTIEDFLSTEEDFS------SAYVRD---- 175

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L +L  R + VL M     +   +T  ++G++  V   R+ QI    +++++H
Sbjct: 176 FLDTLPNRHKMVLLM-----VMAGYTHVQIGREIGVGSSRVGQI----VKEIRH 220


>gi|319788967|ref|YP_004090282.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
 gi|315450834|gb|ADU24396.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 234

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 102/226 (45%), Gaps = 52/226 (23%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++  NLRLV+ ++KK+ + G    DLI  G+IGL+KA   F      K +TYA   
Sbjct: 53  ARELLIVHNLRLVVYISKKFESTGAGIEDLISIGSIGLIKAVNTFRPDKNIKLATYA--- 109

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++     I + +R       + ++R S     EP        L    +G 
Sbjct: 110 -----SRCIENE-----ILMFLR-------KASQRRSEISIDEP--------LNTDWDG- 143

Query: 564 RKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     + L   +G DEDT H G           ++S ++  L     R +  L  
Sbjct: 144 --------NELLLSDILGTDEDTVHKG-----------IESEVEKTL---LRREIDKLGE 181

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++ MRFG+   ++ T +EV +   +++  I ++E K ++ ++
Sbjct: 182 REKMIMEMRFGLNGKSEMTQKEVAQTVGISQSYISRLEKKTLKAIR 227


>gi|313113343|ref|ZP_07798935.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310624319|gb|EFQ07682.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 167

 Score = 50.4 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 35/96 (36%), Positives = 50/96 (52%), Gaps = 3/96 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++S S    +S  E     S +R G+     A+++++  NLRLV  + KKY        D
Sbjct: 28  LESGSFPRPLSAREETEAFSALRAGD---PAAREKLIRHNLRLVAHIVKKYYALPGDQDD 84

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LI  G IGLMKA + FD     +FSTYA   ++ AI
Sbjct: 85  LISIGTIGLMKAVDTFDSDRRARFSTYASRCIENAI 120


>gi|106895880|gb|ABE66433.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC78]
          Length = 288

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 72/152 (47%), Gaps = 2/152 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 138 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 197

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 198 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 256

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           I++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 257 IAQIKDINRRMSIGEAKARRAKKEMVEANLRL 288


>gi|317055222|ref|YP_004103689.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447491|gb|ADU21055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 127

 Score = 50.4 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  NLRLV  + KKY        DLI  G IGL+KA + FD+  G +F+TY    
Sbjct: 52  ARDTLIRHNLRLVAHIIKKYYANSSDQDDLISIGTIGLIKAVQTFDYTKGTRFATYGSRC 111

Query: 504 VKQAITRSIADQSCTI 519
           V+ A T+S    SC +
Sbjct: 112 VENA-TQSQRTFSCQM 126


>gi|325679376|ref|ZP_08158961.1| putative RNA polymerase sigma-G factor [Ruminococcus albus 8]
 gi|324108973|gb|EGC03204.1| putative RNA polymerase sigma-G factor [Ruminococcus albus 8]
          Length = 162

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 45/153 (29%), Positives = 78/153 (50%), Gaps = 14/153 (9%)

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+   MRD  +K ++       K +REP+ +EIA+        +   L+   +P+S+  
Sbjct: 18  IRVSRSMRDLAYKAMQAKESFIAKHQREPSIDEIAELTGEKRADIVTALESITDPVSIYE 77

Query: 579 PIGDE--DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           P+  E  D  ++ D I D N   S L+   + NL+E     L +L  RE+ +L +RF  G
Sbjct: 78  PVYTEGGDALYIVDQICDSNDDKSWLE---ELNLKEA----LKTLKDREKNILFLRFYKG 130

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               HT  EV K+  +++ ++ ++E  A+ K+K
Sbjct: 131 ----HTQMEVAKEIGISQAQVSRLEKNALDKIK 159


>gi|218133504|ref|ZP_03462308.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990879|gb|EEC56885.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
          Length = 238

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  ++E NLRLV+ +AK++ N G+   DLI  G IGL+KA   ++     K +TYA
Sbjct: 63  ARSVLIEHNLRLVVYIAKRFDNTGIGVEDLISIGTIGLIKAIHSYNPDKSIKLATYA 119


>gi|168069803|ref|XP_001786584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162660945|gb|EDQ48604.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 406

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 52/229 (22%), Positives = 104/229 (45%), Gaps = 35/229 (15%)

Query: 448 MVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKF-DWCLGYKFSTYAMWWVK 505
            +  NLRLV   AK+Y  NRG  + D++ EG IGL+ A +++ D  +   FST+A  +++
Sbjct: 17  FITQNLRLVHMCAKRYAYNRG--YDDVVSEGTIGLILAYDRYSDATVA--FSTFAATYIR 72

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             I         T+ +P        + +  +RR++     +  PE +A+ L + V+    
Sbjct: 73  GYIRNYFRSLRGTVSVP-------RRTLDNSRRIAEAGLEDKAPETVAEALGIAVKHAED 125

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            L       S      DE+ +       D + V  +++ I+  +            P+ +
Sbjct: 126 ALYYLAVTESGSRDY-DEEINAKSVHTFDDDTVPDVNAFIERQV------------PKNQ 172

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           R+LR+     +  ++T  E  ++  V+    RQ  ++A+++++ P  +K
Sbjct: 173 RLLRL-----LMDEYTQTEAAEKLGVS----RQAASQALKRMRAPDGTK 212


>gi|106895864|gb|ABF82640.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|106895884|gb|ABF82644.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC285]
 gi|106895888|gb|ABF82646.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 292

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 72/152 (47%), Gaps = 2/152 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 142 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 201

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 202 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 260

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           I++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 261 IAQIKDINRRMSIGEAKARRAKKEMVEANLRL 292


>gi|76564105|gb|ABA46492.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
          Length = 255

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 101/230 (43%), Gaps = 32/230 (13%)

Query: 447 EMVEANLRLVI-SVAKKYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +E   RLV   V K+Y  +        GL   DL Q   IGL+KA + FD   G  FS
Sbjct: 28  EFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFVMIGLIKARDNFDLEFGCAFS 87

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR-RMSNKIKREPTPEEIAKKL 556
           TYA+  +   I R+I D         + + K+ + V   + ++ N+   +  PEEIA  L
Sbjct: 88  TYAVPKIIGEIGRAIRD---------NQKIKVQRTVYGVKGKILNQQLADKEPEEIADIL 138

Query: 557 AMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAI-QANLRET 612
              V  V+  L+      SL   +   G  +   L   IED       ++ I +A +RE 
Sbjct: 139 DESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTEDIEETTINRAVIREF 198

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                A+L P+E  VL MR       + T + +  Q   ++ +I +I AK
Sbjct: 199 K----AALPPKEYIVLDMRL-----QNMTQQNIANQMGYSQVQISRILAK 239


>gi|70729057|ref|YP_258793.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens Pf-5]
 gi|68343356|gb|AAY90962.1| motility sigma factor FliA [Pseudomonas fluorescens Pf-5]
          Length = 246

 Score = 50.4 bits (119), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 105/237 (44%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  +  +D  H G  + +  A + L       D   QA L +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG--LHEDGASAHLEPSRDLEDERFQAALAD 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|237734715|ref|ZP_04565196.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382043|gb|EEO32134.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 97

 Score = 50.1 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/57 (45%), Positives = 36/57 (63%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +V  N +LV+S+A+++  R     DL Q G IGL+KA E F+   G KFSTYA+
Sbjct: 39  KDRLVNDNTKLVLSMARRFYGREDSMDDLFQVGMIGLIKAIENFNTSFGLKFSTYAV 95


>gi|106895882|gb|ABF82643.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 291

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 72/152 (47%), Gaps = 2/152 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 141 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 200

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 201 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 259

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           I++ + I   +  GE +A  AKKEMVEANLRL
Sbjct: 260 IAQIKDINRRMSIGEAKARRAKKEMVEANLRL 291


>gi|22596849|gb|AAN03367.1|AF481091_4 FliA [Pseudomonas fluorescens]
          Length = 246

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 105/237 (44%), Gaps = 27/237 (11%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQGELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPL-------DSAIQANLRE 611
           +    +L  T      S +  +  +D  H G  + +  A + L       D   Q+ L E
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEG--LHEDGASAHLEPSRDLEDERFQSALAE 188

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 189 A----IANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|225174918|ref|ZP_03728915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169558|gb|EEG78355.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 231

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 37/121 (30%), Positives = 59/121 (48%), Gaps = 3/121 (2%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +VEA   L+   A+ YT    +  D +Q G  GLMKA ++++   G  F+TYA   V   
Sbjct: 26  VVEAGRSLIHHFARLYTGGFGE--DAVQAGMEGLMKAVQRYEVGKGTAFATYAAHCVMGE 83

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I   +  +S   R P  ++D   +V R    +  +    P   EIAK+L +  EGV + +
Sbjct: 84  IRHYVRKESSYYR-PGSIKDLQFRVARLVDEVLKETGEPPGVSEIAKRLNVKEEGVVQAM 142

Query: 568 K 568
           +
Sbjct: 143 R 143


>gi|312128148|ref|YP_003993022.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778167|gb|ADQ07653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 219

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 91/228 (39%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV  +AKKYT       D +I  G IGL+KA E +      K STYA  
Sbjct: 33  ARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSTAKCTKLSTYA-- 90

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                                            A+ + N+I              M +  
Sbjct: 91  ---------------------------------AKCIENEI-------------LMYLRQ 104

Query: 563 VRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +K L      +SLE PIG D+D + +      +N    +D  +   ++           
Sbjct: 105 NKKFL----SQLSLENPIGSDKDGNEITLMDVLQNDQDDIDEQVDLKIQIKNLLKKLDKI 160

Query: 622 P--REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              RE++++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 161 LKGREKKIIELRYGLKNGIERTQMEVANLLGISRSYVSRIEKKALQKL 208


>gi|295399263|ref|ZP_06809245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978729|gb|EFG54325.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 155

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 37/65 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNILIEHNLRLVAHIVKKFENTGEDVEDLISIGTIGLIKAIESYSSNKGTKLATYAARC 109

Query: 504 VKQAI 508
           ++  I
Sbjct: 110 IENEI 114


>gi|291563982|emb|CBL42798.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SS3/4]
          Length = 246

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 33/53 (62%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F+     K +TYA
Sbjct: 67  LIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPTKNIKLATYA 119


>gi|117619369|ref|YP_855921.1| flagellar biosynthesis sigma factor [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560776|gb|ABK37724.1| RNA polymerase sigma factor for flagellar operon [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 239

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 98/241 (40%), Gaps = 45/241 (18%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA    
Sbjct: 16  LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYA---- 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHK---VVRTARRMSNKIK-----------REPTPE 550
                         IRI   M D+I +   V R+  R S  I            R+    
Sbjct: 72  -------------GIRIRGSMLDEIRRGDWVPRSVHRNSRTIAEAIENVEQAHGRDARDS 118

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQA 607
           E+A ++ + +     +L    + +S    IG ED     D I   +D+   +  D     
Sbjct: 119 EVAAQMGVSLGEYHTML----QDVSCGKIIGIEDLGVSEDVIGHPDDEPGSNGFDELAAE 174

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +      +  L  RE  VL + +   +N    L E+G+   V+  R+ QI ++A+ +L
Sbjct: 175 RFQGALAEHIGRLPEREALVLSLYYDEELN----LREIGEVLNVSESRVSQIHSQAMHRL 230

Query: 668 K 668
           +
Sbjct: 231 R 231


>gi|242089065|ref|XP_002440365.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
 gi|241945650|gb|EES18795.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
          Length = 182

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           L   +A+ YT  G     L+Q G IG++  +EKFD   G +FSTY  +W+++ +   +A+
Sbjct: 8   LFSYIARTYTGMGTALDKLLQAGKIGVLDGSEKFDNRKGCRFSTYVKYWIRKGMLALLAE 67

Query: 515 QSCTI 519
            S  I
Sbjct: 68  NSGVI 72


>gi|222528742|ref|YP_002572624.1| sporulation sigma factor SigK [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455589|gb|ACM59851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 219

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 91/228 (39%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV  +AKKYT       D +I  G IGL+KA E +      K STYA  
Sbjct: 33  ARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSSAKCTKLSTYA-- 90

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                                            A+ + N+I              M +  
Sbjct: 91  ---------------------------------AKCIENEI-------------LMYLRQ 104

Query: 563 VRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +K L      +SLE PIG D+D + +      +N    +D  +   ++           
Sbjct: 105 NKKFL----SQLSLENPIGSDKDGNEITLMDVMQNDQEDIDEQVDLKIQIKNLLKKLDKI 160

Query: 622 P--REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              RE++++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 161 LKGREKKIIELRYGLKNGIERTQMEVANLLGISRSYVSRIEKKALQKL 208


>gi|213621148|ref|ZP_03373931.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 150

 Score = 50.1 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/96 (28%), Positives = 53/96 (55%), Gaps = 3/96 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +
Sbjct: 39  DLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNARE 95

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           V +   ++  ++ R  T  E+A++L +PV   R++L
Sbjct: 96  VAQAMGQLEQELGRNATETEVAERLGIPVAEYRQML 131


>gi|325679635|ref|ZP_08159210.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
 gi|324108665|gb|EGC02906.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
          Length = 235

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 39/65 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++  NLRLV+ +++K+ N G+   DLI  G+IGL+KA   F      K +TYA   
Sbjct: 54  AKELLIVHNLRLVVYISRKFENAGVGLEDLISIGSIGLIKAVNTFRPDKNIKLATYASRC 113

Query: 504 VKQAI 508
           ++  I
Sbjct: 114 IENEI 118


>gi|294339807|emb|CAZ88170.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Thiomonas sp. 3As]
          Length = 250

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 52/238 (21%), Positives = 103/238 (43%), Gaps = 10/238 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ G   A   ++E +  +L +V  +A +   +    + F DL Q G IGL  A ++ + 
Sbjct: 1   MKPGLYPAPETREERLSKHLPMVRRIAGQMAAQLPASVDFSDLEQAGMIGLWDALDRGEM 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +F+TYA   ++ AI   +        +P   R K  ++ R  + ++ ++ R P   
Sbjct: 61  QSPAQFATYAAIRIRGAIYDELRKLDW---LPRRSRAKERQIERAEQLLTQRLGRHPEDG 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  L   +      L  T   +     +  +D     D   D+ ++ P +    A L 
Sbjct: 118 ELAAHLGWELAEYYDALAETSMQLVYLEDLTHDDGGDYADRKADEASLLPEELLQDAQLE 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A L  RE+ VL + +      D  L+++G+   V+  R+ Q+  +A+ +L+
Sbjct: 178 RDLQAAIADLPEREKLVLSLYY----QEDLQLKDIGRVLEVSESRVSQLMKQAVMRLR 231


>gi|296135638|ref|YP_003642880.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thiomonas
           intermedia K12]
 gi|295795760|gb|ADG30550.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thiomonas
           intermedia K12]
          Length = 250

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 52/238 (21%), Positives = 103/238 (43%), Gaps = 10/238 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ G   A   ++E +  +L +V  +A +   +    + F DL Q G IGL  A ++ + 
Sbjct: 1   MKPGLYPAPETREERLSKHLPMVRRIAGQMAAQLPASVDFSDLEQAGMIGLWDALDRGEM 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +F+TYA   ++ AI   +        +P   R K  ++ R  + ++ ++ R P   
Sbjct: 61  QSPAQFATYAAIRIRGAIYDELRKLDW---LPRRSRAKERQIERAEQLLTQRLGRHPEDG 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  L   +      L  T   +     +  +D     D   D+ ++ P +    A L 
Sbjct: 118 ELAAHLGWELAEYYDALAETSMQLVYLEDLTHDDGGDYADRKADEASLLPEELLQDAQLE 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A L  RE+ VL + +      D  L+++G+   V+  R+ Q+  +A+ +L+
Sbjct: 178 RDLQAAIADLPEREKLVLSLYY----QEDLQLKDIGRVLEVSESRVSQLMKQAVMRLR 231


>gi|110678161|ref|YP_681168.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
 gi|109454277|gb|ABG30482.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
          Length = 1005

 Score = 50.1 bits (118), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 41/60 (68%), Gaps = 1/60 (1%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +++L  R++ +L+ R+GI      TLE+V   + VTRERIRQIE KA +KL+   R+KK+
Sbjct: 467 ISTLNDRQQDILQRRYGINRGQTETLEQVASDYDVTRERIRQIEKKAKQKLET-KRTKKV 525


>gi|84514822|ref|ZP_01002185.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
 gi|84510981|gb|EAQ07435.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
          Length = 239

 Score = 49.7 bits (117), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/217 (27%), Positives = 103/217 (47%), Gaps = 20/217 (9%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++F DL+Q G IGL++AA+++    G  F  YA+  V+ AI   +   S   R  +    
Sbjct: 37  VEFDDLLQVGLIGLIEAAQRYTRREGVSFENYAVLRVRGAIYDYLRKNSNLGRKTI---- 92

Query: 528 KIHKVVRTAR-RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DT 585
              KVV+ A+  +S K+ R PT  E+A+ ++M +  +    +      S +  + DE D 
Sbjct: 93  ATTKVVKFAQAELSQKLGRAPTRVELAEAVSMTIGELNAWEQSLNS--SYQNSLQDEYDE 150

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             +    E+  A   LD   +  L++     L SL  RE  VL++ +   +N    + E+
Sbjct: 151 YSMWFSAEEPPAEQLLD---RGRLKDALLIALKSLPQREALVLQLYYVEELN----IYEI 203

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
                VT  R+ Q+++ A +K++       LR F +G
Sbjct: 204 AAILEVTPGRVSQLKSMAFKKMQ-----PLLRDFAEG 235


>gi|325509467|gb|ADZ21103.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum EA 2018]
          Length = 246

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 5/99 (5%)

Query: 444 AKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           AK  +++++++ +  +A  +   N+ L   DL+QEG I ++KA   +D     KFSTY  
Sbjct: 20  AKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVIKAINSYDLDKNVKFSTYVY 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
             +   +   I  +    +IP H   ++ K+V+  RR S
Sbjct: 80  SMINFTLISEIKKKYSYFKIPEH---QVSKIVKFKRRAS 115


>gi|226310246|ref|YP_002770140.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226093194|dbj|BAH41636.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 268

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 54/232 (23%), Positives = 101/232 (43%), Gaps = 41/232 (17%)

Query: 447 EMVEANLRLVISVAKKYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           E++ AN  L+     KY  +         L+  D++Q G +G++KA + FD   G KFS+
Sbjct: 39  EVILANEELIWHSVHKYIGKPETLVKQYCLEKADILQLGRMGIIKAIKAFDIARGVKFSS 98

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A+  + + I   + D    +R        +H +     ++   +   PT EE++  L  
Sbjct: 99  FAVITIVREINCFLRDSGNIVRPTRTATTILHHI----SKIEADLGYLPTIEELSLLLGE 154

Query: 559 PVEGVRKVLKITKEPISLETP-IGDEDTSH---------------LGDFIEDKNAVSPLD 602
            VE ++K L + +    L+ P +    +SH               + +++ DK  V+ L 
Sbjct: 155 NVEQIKKALDVGRPVKYLQEPFLKASASSHEAATAMDVLKDEGRDVEEYVLDKLYVTALL 214

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           + +Q             ++ +E +VL++R   G N   T E +   Q CV+R
Sbjct: 215 AQLQNQ-----------ISLKEWQVLQLRMA-GYNQTQTAEFLNVSQMCVSR 254


>gi|149927789|ref|ZP_01916040.1| sigma 28 (Flagella/Sporulation) [Limnobacter sp. MED105]
 gi|149823411|gb|EDM82642.1| sigma 28 (Flagella/Sporulation) [Limnobacter sp. MED105]
          Length = 238

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 53/240 (22%), Positives = 99/240 (41%), Gaps = 13/240 (5%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            + ++ K + V+  + LV  +A     +    +Q  DLIQ G IGLM A  +F+   G +
Sbjct: 4   AQGTLDKSKQVDQYIPLVRRLAHHLIAKLPASVQIDDLIQAGLIGLMDAITRFEEGQGAQ 63

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F TYA   ++ A+   +        +P  +R    K+     R   K+ R  + +EIA  
Sbjct: 64  FETYASQRIRGAMLDELRSADW---MPRGVRQAQRKIETATLRAEQKLGRSASEKEIADV 120

Query: 556 LAMPVEGVRKVLKITKEP---ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + + ++  + +L  ++        +     +   +L   I      +PL+       RE 
Sbjct: 121 MGVSLDEYQDMLFDSRGASLVFYDDYADDGDGEGYLDRQIGGDEEANPLEMLGDQRFREN 180

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + +  L  RE    +M  G+    +    E+     VT  R+ Q+  +A+ +LK   R
Sbjct: 181 LIQAIEDLPERE----KMLMGLYYEQELNFREIAAVLGVTESRVCQLHTQAVSRLKAKLR 236


>gi|312134632|ref|YP_004001970.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774683|gb|ADQ04170.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 242

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 91/228 (39%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV  +AKKYT       D +I  G IGL+KA E +      K STYA  
Sbjct: 56  ARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSTAKCTKLSTYA-- 113

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                                            A+ + N+I              M +  
Sbjct: 114 ---------------------------------AKCIENEI-------------LMYLRQ 127

Query: 563 VRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +K L      +SLE PIG D+D + +      +N    +D  +   ++           
Sbjct: 128 NKKFL----SQLSLENPIGSDKDGNEITLMDVLQNNQDDIDEQVDLKIQIKNLLKKLDKI 183

Query: 622 P--REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              RE++++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 184 LKGREKKIIELRYGLKNGIERTQMEVANLLGISRSYVSRIEKKALQKL 231


>gi|297197375|ref|ZP_06914772.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|297146698|gb|EDY58861.2| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 294

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 34/116 (29%), Positives = 60/116 (51%), Gaps = 4/116 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++F+   G  F +YA+  +
Sbjct: 50  RDELVSAWLPMAHRIAGRFRDRGESLEDLRQVAALGLVKAIDRFEPERG-AFESYAVPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAM 558
              + R   D+   +R+P  +++  +K VR ARR    N    EPT  ++A    +
Sbjct: 109 TGEVKRHFRDRMWALRVPRRVQELRNK-VRVARRELTQNPGSPEPTTADLAAHTGL 163


>gi|89898386|ref|YP_515496.1| RNA polymerase sigma factor sigma-28 [Chlamydophila felis Fe/C-56]
 gi|89331758|dbj|BAE81351.1| DNA-directed RNA polymerase sigma 28 [Chlamydophila felis Fe/C-56]
          Length = 257

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 93/215 (43%), Gaps = 37/215 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL++A E+F+     +F  YA++ +K AI   +  Q     +P  +  K +K
Sbjct: 55  DLYASGVEGLVRAVERFNPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAK------------------KLAMPVEGVRKVLKITKEP 573
           +      +   + REPT  ++ +                   L + +   R +L   +  
Sbjct: 112 LSDAMDTLRQSLGREPTDGDLCEYFQISQQELSGWFVSARPALIISLNEERPLLSDGESG 171

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ++LE  I DE      D ++ K   S L +AI+  L E   +V+A L   EE VL+    
Sbjct: 172 VALEERIPDERAETGYDIVDRKEFSSFLANAIEG-LEEKERKVMA-LYYYEELVLK---- 225

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                     E+GK   V+  R+ QI +KA+ KL+
Sbjct: 226 ----------EIGKILGVSESRVSQIHSKALIKLR 250


>gi|56964615|ref|YP_176346.1| DNA-directed RNA polymerase sigma factor [Bacillus clausii KSM-K16]
 gi|56910858|dbj|BAD65385.1| DNA-directed RNA polymerase sigma factor [Bacillus clausii KSM-K16]
          Length = 220

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 50/212 (23%), Positives = 99/212 (46%), Gaps = 29/212 (13%)

Query: 445 KKEMVEANLRLVISVAK--KYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           + EM+ +N+ LV  +AK  K++ R     + DLI  G IGL+ A E ++   G  F+ YA
Sbjct: 7   QNEMILSNMGLVHKIAKDLKWSIRSSWFHYSDLISVGTIGLINAVENYENKKGITFAAYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +++++ +++  Q   + +P    D I ++V   + + N      + EE+A  L +P 
Sbjct: 67  VPVIRRSMLKALNKQMAGLSVP----DYIIELVPRLKSLEN--WGNLSVEEVASILGIPT 120

Query: 561 EGVRKVLKITKEP--ISLETPI-------------GDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  R +L     P  IS+++ +              D    ++ DF+   N +   D  I
Sbjct: 121 KKARNLLIAVNRPDLISMDSEVKEDRDYNEVFGARTDYGMIYVNDFL---NTLKERDKEI 177

Query: 606 -QANLRETTTRVLASLTPREERVLRMRFGIGM 636
            +A L   + + +AS+     + +  RF + +
Sbjct: 178 LEAKLAGYSQQEIASMYGTSPQAISQRFKLNI 209


>gi|288572993|ref|ZP_06391350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
 gi|288568734|gb|EFC90291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
          Length = 189

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 45/80 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+++++ A   LV  +AKK+   G  + DLIQEG + L+K  + FD   G++F+TY  + 
Sbjct: 25  AREDLILAYRPLVFWIAKKFNVGGDIYPDLIQEGMMALIKGIDSFDPSRGFRFTTYGYYR 84

Query: 504 VKQAITRSIADQSCTIRIPV 523
           ++  +   +  +     +P+
Sbjct: 85  IRGQMLNYLQRKEAKAPLPM 104


>gi|260653773|dbj|BAI44426.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
           [Monochamus alternatus]
          Length = 56

 Score = 49.7 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +++ ++L LV  +A K+ N GL F+DL+ EGN+GLM   +KF+  LG+
Sbjct: 9   KLITSHLNLVXKIAMKFKNYGLLFMDLVMEGNMGLMHPVKKFNPDLGF 56


>gi|31747734|gb|AAO38358.1| Lfe160p1 [Leptospirillum ferrooxidans]
          Length = 218

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 88/211 (41%), Gaps = 31/211 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G  GL+ AA++FD   G KF T A   ++ A+   I        +P  +R+K   
Sbjct: 15  DLVSVGMTGLIDAAKRFDPSRGIKFKTMAEHRIRGAMLDEIRSADW---VPRSVREKASS 71

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V      +   + REP   E+AK L+M ++          E ++LE  I       + D 
Sbjct: 72  VHAVREGLRAALLREPDDMEMAKALSMSLD----------EYLTLENEIEPHHLYSIEDL 121

Query: 592 IE----------DKNAVS----PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            E          D+  V     PL   +++       + L SL  ++  VL + +     
Sbjct: 122 FEMEEGAGSSILDRMVVPGEADPLSEFLKSEEASLLEKALDSLPEKQRLVLSLYY----Y 177

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +++EV     V+  R+ QI   AI+ LK
Sbjct: 178 EELSMKEVAAVLEVSESRVSQIHTLAIKNLK 208


>gi|312962254|ref|ZP_07776746.1| RNA polymerase sigma factor for flagellar operon FliA [Pseudomonas
           fluorescens WH6]
 gi|311283591|gb|EFQ62180.1| RNA polymerase sigma factor for flagellar operon FliA [Pseudomonas
           fluorescens WH6]
          Length = 246

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 101/231 (43%), Gaps = 15/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQGELIERYAPLVKRIAYHLLGRLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVL 617
           +    +L  T      S +  +  +D  H G   +  +A + P         +      +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEGLHEDGASAHMEPSRDLEDQRFQGALADAI 190

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 191 ANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|253681618|ref|ZP_04862415.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum D
           str. 1873]
 gi|253561330|gb|EES90782.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum D
           str. 1873]
          Length = 236

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 80/204 (39%), Gaps = 58/204 (28%)

Query: 472 DLIQEGNIGLMKAAEKFDWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           DL QEG IGL+ AA K+D+      KF TYA+ W+   I R I  ++             
Sbjct: 48  DLEQEGTIGLIIAARKYDFNNEKKAKFITYAIHWIYSKINRYINQRN------------- 94

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
                                                   T +  SL   IG+++ + L 
Sbjct: 95  ----------------------------------------TNDETSLNIHIGEDEENELI 114

Query: 590 DFIEDKN-AVSPLDSAIQAN-LRETTTRVLASLTPREER-VLRMRFGIGMNTDHTLEEVG 646
           D I+D + +   ++  I    LR+    V+      EER +L++R G   N    L ++G
Sbjct: 115 DTIKDIDYSYENVEEKIYMKELRQEIEEVMKEYNTLEEREILKLRHGWDSNNIMALSDIG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHP 670
           +   +   R+R IE +A RKL+  
Sbjct: 175 ELLNINVGRVRTIEDRAYRKLRRT 198


>gi|188586385|ref|YP_001917930.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351072|gb|ACB85342.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 114

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++ ++E NLRLV  V KK+ N G    DLI  G IGL+KA   +++  G + +TYA
Sbjct: 50  AREVLIERNLRLVAHVIKKFENSGEDPEDLISIGTIGLIKAINTYNYRKGTRLATYA 106


>gi|215270833|emb|CAR48094.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270835|emb|CAR48095.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 291

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 32/45 (71%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           Y+ EMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   YMSEMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 45



 Score = 46.2 bits (108), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 77/173 (44%), Gaps = 11/173 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    E  S K  V  E ++ +     L   + D LV +L   
Sbjct: 124 EKFNQLRSTYQNLQLAINEHGYE--SPKATVANELMLDVFKEFRLTPKQFDHLVNELRTA 181

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++ A  YG + +  F+    G E    W+    + D P  E    +   
Sbjct: 182 MDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEK---IKRN 238

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            + I +   ++K I  ET +++   + I   +  GE +A  AK EMVEA+LRL
Sbjct: 239 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKNEMVEAHLRL 291


>gi|215270831|emb|CAR48093.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270837|emb|CAR48096.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 291

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 32/45 (71%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           Y+ EMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   YMSEMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 45


>gi|331696172|ref|YP_004332411.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950861|gb|AEA24558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 270

 Score = 49.7 bits (117), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 100/210 (47%), Gaps = 33/210 (15%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYK-FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           DL Q  +  +++A +++D       F  Y +  V+  + R   DQS ++R+P  +++ + 
Sbjct: 71  DLRQAASEAVVRAVDRWDPERAQGDFLGYLVPCVRGEVLRWFRDQSWSVRVPRRLKE-LS 129

Query: 531 KVVRTAR-RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPI-GDE--D 584
             +R+A   M+ ++   P P E+A++L + +E V + L         +L+ P  GDE   
Sbjct: 130 VAIRSAHGPMAQRLGSAPRPSELARELGVDIEEVLEALHAEENHRAATLDAPAPGDERLP 189

Query: 585 TSHLG------DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
              LG      + +ED   + PL               +A+L  RE R+L +RF  G   
Sbjct: 190 GEQLGEIDRQLELVEDAETLRPL---------------IAALPERERRILLLRFYGG--- 231

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             T  ++G++  V++  + ++ ++ + +L+
Sbjct: 232 -RTQSQIGEELGVSQMHVSRLLSRTLARLR 260


>gi|302391432|ref|YP_003827252.1| sigma-70 region 4 domain protein [Acetohalobium arabaticum DSM
           5501]
 gi|302203509|gb|ADL12187.1| sigma-70 region 4 domain protein [Acetohalobium arabaticum DSM
           5501]
          Length = 1154

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/223 (26%), Positives = 104/223 (46%), Gaps = 22/223 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDKIH 530
           DL+ +G + L+    K +    + F  ++       I  +   + C T  +   +R  I+
Sbjct: 302 DLLNDGPLCLVDLKMKLELEDNWYFCLFSALKKINNIGLNKKRKICLTNNLNARIRFCIN 361

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPV--EGVRKVLKITKEPISLETPIGDEDTSHL 588
             +   +R+ NK K +   + +   L  P+  + ++K L      +SLE    DE   + 
Sbjct: 362 SALTKIKRLKNK-KIDNLIKNLFINLETPLLLKEIKKYLMFLNIDLSLEEI--DELLRNN 418

Query: 589 GDF-IEDKNAVSPLDS-----AIQANLRETTTRVLASLTPREER-----VLRMRFGIGMN 637
            DF + D N  S LDS           + T  ++L+S  P E R     +L  R     +
Sbjct: 419 ADFKLIDVNKWS-LDSWDEYPEFNEEFKSTWEQILSSF-PEENRERDIDILNKRI---FS 473

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            D+TLE++G++  ++R+R+RQ+E   +RKL H +R K ++ FL
Sbjct: 474 NDYTLEKLGEEHSISRQRVRQLEESGMRKLVHYTRIKYIKPFL 516


>gi|302871341|ref|YP_003839977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574200|gb|ADL41991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 242

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 57/228 (25%), Positives = 91/228 (39%), Gaps = 56/228 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  +VE NLRLV  +AKKYT        D+I  G IGL+KA E +      K STYA  
Sbjct: 56  ARNILVEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSKDKSTKLSTYA-- 113

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
                                            A+ + N+I              M +  
Sbjct: 114 ---------------------------------AKCIENEI-------------LMYLRQ 127

Query: 563 VRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +K L      +SLE PIG D+D + +      +N    +D  +   ++           
Sbjct: 128 NKKFL----SQLSLENPIGSDKDGNEITLMDVLQNDQDDIDEQVDLKIQIKNLLKKLDKI 183

Query: 622 P--REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              RE++++ +R+G+    + T  EV     ++R  + +IE KA++KL
Sbjct: 184 LKGREKKIIELRYGLKNGIERTQMEVASLLGISRSYVSRIEKKALKKL 231


>gi|225569539|ref|ZP_03778564.1| hypothetical protein CLOHYLEM_05633 [Clostridium hylemonae DSM
           15053]
 gi|225161747|gb|EEG74366.1| hypothetical protein CLOHYLEM_05633 [Clostridium hylemonae DSM
           15053]
          Length = 236

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 60/118 (50%), Gaps = 2/118 (1%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           L LV   A +   + L   D+IQEGN+ LM A  +F+  +  +     M  V+  +   I
Sbjct: 110 LPLVADAALQMHRKELFIGDMIQEGNLSLMAALRRFEGAVDSEQEI--MEEVRAGLQAFI 167

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
             Q+ T R    M  ++ ++  T R MS  + R+ + +E+A++L+M  E V  +LK+ 
Sbjct: 168 ESQTETRRQDKKMVSQVAELDETIRHMSEDMGRKVSVDEVAQQLSMETEQVEALLKLA 225


>gi|158340672|ref|YP_001521840.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158310913|gb|ABW32526.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 440

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 50/239 (20%), Positives = 119/239 (49%), Gaps = 24/239 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ +NL  + S   +++ +G+   +LI EG  GL +A +++D   G    TY+   
Sbjct: 42  ARQTVIYSNLAWICSRGGQFSRKGIDDGELINEGYWGLNRAIDQWDPTKGANLRTYSERK 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + +  + +I  Q   IR+P    +++ K+    ++ +  +  + T  ++A++  +  + +
Sbjct: 102 IYKFQSEAIR-QKNHIRLPKSTYEQLSKL----KKATESLGEDATVAQLAEETEIKEKRI 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RK+ +I+ +P+SL +  G+ +   L D   D +++  LD A+ + L +    ++  L PR
Sbjct: 157 RKLQEIS-QPVSLNSVTGERENLELLDQQAD-DSLGSLDPALSSELLD----LVDKLHPR 210

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +L +        + + +++     +  +++R++  KA+           LR FL G
Sbjct: 211 QREILHLYHW----EELSFQKISDYLGLPAKQVRKLYKKAL---------DLLRKFLQG 256


>gi|224771357|dbj|BAH28620.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTSKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|170725990|ref|YP_001760016.1| flagellar biosynthesis sigma factor [Shewanella woodyi ATCC 51908]
 gi|169811337|gb|ACA85921.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella woodyi ATCC
           51908]
          Length = 242

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 99/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+  FD   G KF T+A 
Sbjct: 13  KASIVEQYAPLVKKIAHHLLARLPASVQIDDLLQAGMMGLLEASTNFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I       R  VH   +  +V +    +  ++ R+    EIA++L + + 
Sbjct: 73  IRIRGSMLDEIRRGDWVPR-SVHRNQR--RVAQVIDELEQELGRDAKDTEIAQRLDISLN 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +   ++      +S             +  
Sbjct: 130 EYHHILN----DVSVGKVVGIEDLGVSLDVVGQAEERKDDTFESIADVEFHTALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +   +N    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYYDEALN----LKEIGSILEVSESRVSQILSQAMLRLK 230


>gi|15895322|ref|NP_348671.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|15025038|gb|AAK80011.1|AE007708_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
          Length = 237

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 5/99 (5%)

Query: 444 AKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           AK  +++++++ +  +A  +   N+ L   DL+QEG I ++KA   +D     KFSTY  
Sbjct: 22  AKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVIKAINSYDLDKNVKFSTYVY 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
             +   +   I  +    +IP H   ++ K+V+  RR S
Sbjct: 82  SMINFTLISEIKKKYSYFKIPEH---QVSKIVKFKRRAS 117


>gi|291542628|emb|CBL15738.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus bromii L2-63]
          Length = 233

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 55/106 (51%), Gaps = 7/106 (6%)

Query: 407 LKIRNEIKSI----SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           L I NEI  I    ++   ++  E +HI+  + KG+   S A++ ++  NLRLV+ +AKK
Sbjct: 14  LVIENEIFYINGSETLPPPLTREEEQHIMENIAKGD---SKAREPLIVHNLRLVVYIAKK 70

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +        DLI  G IGL+KA   F      K +TYA   ++  I
Sbjct: 71  FETPNASAEDLISIGTIGLIKAVNTFSPEKNIKLATYASRCIENEI 116


>gi|257463359|ref|ZP_05627755.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. D12]
          Length = 155

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 32/108 (29%), Positives = 54/108 (50%), Gaps = 9/108 (8%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++ + + G+ EA   + E++E N+ LV  + + Y +      D  QEG +    A +KFD
Sbjct: 1   LIRLAKLGDIEA---RNELIEKNINLVHKINRMYGSSE----DGFQEGILAFCHAIDKFD 53

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
                K S+YA  W++Q I R    +    R+P H+ +K+ K  R  R
Sbjct: 54  ETKNVKLSSYAFHWIRQKIKRYREREK--YRLPAHVIEKMSKEERKIR 99


>gi|88809560|ref|ZP_01125067.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786310|gb|EAR17470.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 131

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 51/88 (57%), Gaps = 4/88 (4%)

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTPREERVLRMRFGI-GMNTDH 640
           D S L D +  +  + PL+ A  A    +  ++L  ++LTP+E  V+ +RFG+ G N   
Sbjct: 32  DPSELVDVLPSEE-IPPLERAEIAERTASAWKLLDKSNLTPKERTVVMLRFGLDGSNEWR 90

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 91  TLAEVARQMNCSREYCRQVVQRALRKLR 118


>gi|28210768|ref|NP_781712.1| RNA polymerase sigma factor [Clostridium tetani E88]
 gi|28203206|gb|AAO35649.1| RNA polymerase sigma factor [Clostridium tetani E88]
          Length = 182

 Score = 49.3 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/104 (33%), Positives = 55/104 (52%), Gaps = 4/104 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E ++ +  + KG+  A   K  ++E NLRLV  + KKY+  G    DLI  G IGL+KA 
Sbjct: 65  EEKYYLKQLEKGDISA---KGVLIERNLRLVAHIVKKYSFPGKDMDDLISIGTIGLIKAI 121

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           + F    G + +TYA   ++  I   I +   T +  V+++D I
Sbjct: 122 DSFKIDRGTRLATYAAKCIENEILMLIRNNKKT-KGEVYLQDPI 164


>gi|326204040|ref|ZP_08193901.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985807|gb|EGD46642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 138

 Score = 49.3 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 38/65 (58%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KKY + G    DLI  G IGL+KA   F+   G + +TYA   
Sbjct: 52  ARNILIERNLRLVAHIVKKYGSCGSDSDDLISIGTIGLIKAISTFNMDKGTRLATYAARC 111

Query: 504 VKQAI 508
           ++ AI
Sbjct: 112 IENAI 116


>gi|323356683|ref|YP_004223079.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323273054|dbj|BAJ73199.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 538

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 36/53 (67%), Gaps = 1/53 (1%)

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           PRE+++LRMR G       TL E+ ++F ++RERIRQIE++A   L H +R+ 
Sbjct: 177 PREQKILRMRVGF-EGAPRTLAEIAREFDLSRERIRQIESRARNILVHQARTP 228


>gi|330502783|ref|YP_004379652.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina NK-01]
 gi|328917069|gb|AEB57900.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina NK-01]
          Length = 240

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 64/256 (25%), Positives = 110/256 (42%), Gaps = 53/256 (20%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + +A  ++ +++E    LV  +A     R    +Q  DLIQ G IGL++A+ K+D   G 
Sbjct: 4   KAQAQDSQHQLIERYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEASRKYDSGKGA 63

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK-------VVRTARRMSNKIK--- 544
            F T+A                  IRI   M D++ K       V R +R +S+ I+   
Sbjct: 64  SFETFA-----------------GIRIRGSMLDEVRKGDWAPRSVHRNSRMVSDAIRTVE 106

Query: 545 ----REPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIED--KN 596
               R+    E+A +L + +E    +L   +     S +  +  +D  H G   ED    
Sbjct: 107 ARTGRDAKDHEVAAELQLSLEDYYGILGDTLGSRLFSFDDLL--QDGEH-GGLHEDAGHT 163

Query: 597 AVSPL----DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + P     D   QA L +     +A L  RE  VL + +   +N    L+E+G+   V+
Sbjct: 164 HLEPSRDLEDERFQAALADA----IAGLPERERLVLALYYDEELN----LKEIGEVLGVS 215

Query: 653 RERIRQIEAKAIRKLK 668
             R+ Q+ ++   +L+
Sbjct: 216 ESRVSQLHSQCAARLR 231


>gi|325674464|ref|ZP_08154152.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
 gi|325554724|gb|EGD24398.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
          Length = 269

 Score = 49.3 bits (116), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 94/210 (44%), Gaps = 17/210 (8%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A L +   VA +Y NRG+   +L Q   + L+ AA +FD   G  F  YA+  V+  I +
Sbjct: 50  AALPMAYRVAGRYRNRGVPTAELRQVAALALVGAARRFDPSRGTDFIPYAVTSVRGEIRK 109

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
              D + +  +P  +++    V      +S ++ R    +E+A  L MPVE   +  ++ 
Sbjct: 110 YFRDFTWSTHVPRRLQESHLAVRNRMESLSTELGRTVRLDEVAHSLGMPVEEAEEAERV- 168

Query: 571 KEPISLE----TPI-GDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            E  S E    TP+ G     H  GD   D + V           R    R++A+L  R+
Sbjct: 169 GELYSCESLDATPVDGSVPRLHTTGDVDADLSRVEH---------RHLLRRLMATLDERQ 219

Query: 625 ERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             +L +R+   M+     E+VG  Q  V+R
Sbjct: 220 RTLLWLRYFHQMSQSEIAEQVGLSQMHVSR 249


>gi|317060933|ref|ZP_07925418.1| predicted protein [Fusobacterium sp. D12]
 gi|313686609|gb|EFS23444.1| predicted protein [Fusobacterium sp. D12]
          Length = 149

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E++E N+ LV  + + Y +      D  QEG +    A +KFD     K S+YA  W
Sbjct: 6   ARNELIEKNINLVHKINRMYGSSE----DGFQEGILAFCHAIDKFDETKNVKLSSYAFHW 61

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           ++Q I R    +    R+P H+ +K+ K  R  R
Sbjct: 62  IRQKIKRYREREK--YRLPAHVIEKMSKEERKIR 93


>gi|150390238|ref|YP_001320287.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950100|gb|ABR48628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 149

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 39/65 (60%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE NLRLV  V KKY+N      DLI  G IGL+KA   F+   G + +TYA   
Sbjct: 52  ARNILVERNLRLVAHVVKKYSNVNRDADDLISIGTIGLIKAITTFNRGKGTRLATYAARC 111

Query: 504 VKQAI 508
           +++A+
Sbjct: 112 IEKAM 116


>gi|148242553|ref|YP_001227710.1| putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
 gi|147850863|emb|CAK28357.1| Putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
          Length = 259

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 50/98 (51%), Gaps = 1/98 (1%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           R G+      +  +VEA+L LV   A +++      + DL Q+G  GL+ A +++    G
Sbjct: 17  RYGQSRCLKLRNRLVEAHLNLVRQQAARFSQASSACYDDLFQQGCFGLLDAVQRYQPQRG 76

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           Y FSTYA+  ++  +   + D+   IR P  +R  + +
Sbjct: 77  YAFSTYAVTLIRGQMQHYLRDRHHLIRSPWRLRQLLSR 114


>gi|146307827|ref|YP_001188292.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina ymp]
 gi|145576028|gb|ABP85560.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           mendocina ymp]
          Length = 248

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 107/242 (44%), Gaps = 25/242 (10%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           + +A  ++ +++E    LV  +A     R    +Q  DLIQ G IGL++A+ K+D   G 
Sbjct: 12  KAQAQDSQHQLIERYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEASRKYDSGKGA 71

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F T+A   ++ A+   +       R  VH   ++  V    R +  +  R+    E+A 
Sbjct: 72  SFETFAGIRIRGAMLDEVRKGDWAPR-SVHRNSRM--VSDAIRVVEARTGRDAKDHEVAA 128

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKN--AVSPL----DSAIQ 606
           +L + +E    +L   +     S +  +  +D  H G   ED     + P     D   Q
Sbjct: 129 ELQLSLEDYYGILGDTLGSRLFSFDDLL--QDGEH-GGLHEDAGHTHLEPSRDLEDERFQ 185

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A L +     +A L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +
Sbjct: 186 AALADA----IAGLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAAR 237

Query: 667 LK 668
           L+
Sbjct: 238 LR 239


>gi|146164070|gb|ABQ08718.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
          Length = 292

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 65/136 (47%), Gaps = 2/136 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E 
Sbjct: 158 LADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNEC 217

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W  Y K   +      V  + D + +   +++ I  ETG+SI++ + I   +  GE 
Sbjct: 218 ETAWFEYQKQAGKAWSPRLVEMDED-VQRAIGKLQQIEEETGLSIAQIKDINRRMSIGEA 276

Query: 440 EASIAKKEMVEANLRL 455
           +A  AKKEMVEANLRL
Sbjct: 277 KARRAKKEMVEANLRL 292


>gi|148554202|ref|YP_001261784.1| RNA polymerase sigma 28 subunit FliA/WhiG [Sphingomonas wittichii
           RW1]
 gi|148499392|gb|ABQ67646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphingomonas wittichii
           RW1]
          Length = 242

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 103/231 (44%), Gaps = 25/231 (10%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +++V A+++LV  +A     R    +   DLIQ G I L++AA  ++   G+ FSTYA  
Sbjct: 22  EDLVRAHMQLVRKIAWHVHGRVSTAIDVEDLIQIGMIALVEAANGYE-DRGHAFSTYASM 80

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR-MSNKIKREPTPEEIAKKLAMPVE 561
            V+ A+   +  Q+   R  +  R    + + TA+     K  R P+  E+A+ L +   
Sbjct: 81  RVRGAMIDHLRRQAALTRSAMAKR----RALLTAKADFEKKHGRSPSESELAQALGLDGA 136

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-- 619
               +L  T             D S     +E++     +D  I+   RE     LA   
Sbjct: 137 AFHALLDETAATYHESIDEVYSDQSMWFADVEER-----VDQTIE---REELAGALAEHI 188

Query: 620 --LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  RE  VL++ F   MN    LEE+G+   +   R+ QI+  A+ KL+
Sbjct: 189 SELPEREAMVLQLYFVEEMN----LEEIGQTLGIGAARVCQIKKAALDKLR 235


>gi|325567514|ref|ZP_08144181.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158947|gb|EGC71093.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
          Length = 235

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 88/201 (43%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGLM A  KFD      F +YA   +K AI   +   +   +I  +    +++
Sbjct: 35  DLYNIGVIGLMDALRKFDPSKKVPFESYAAIRIKGAIIDEVRKHA---KISRYKMAAVNQ 91

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSH 587
             +  + +   +KRE T  EI K+L +    +  + +       +SLE  +    E+   
Sbjct: 92  FYQARQELEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEGMT 151

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D  A +  D+ +    R      +  L  RE+ +L + +      + TL+E+ +
Sbjct: 152 LKDMVRDP-AENVEDTLVAEEKRTALVACIKKLGEREQLILSLYY----TEELTLKEIAE 206

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI  K I KL+
Sbjct: 207 ILEVSIPRVSQIHGKTIAKLR 227


>gi|229591832|ref|YP_002873951.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens SBW25]
 gi|229363698|emb|CAY51076.1| RNA polymerase sigma factor for flagellar regulon FliA [Pseudomonas
           fluorescens SBW25]
          Length = 246

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 101/231 (43%), Gaps = 15/231 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQGELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVL 617
           +    +L  T      S +  +  +D  H G   +  +A + P         +      +
Sbjct: 133 DDYYGILNDTLGSRLFSFDDLL--QDGEHEGLHEDGASAHMEPSRDLEDERFQGALADAI 190

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 191 ANLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|332294870|ref|YP_004436793.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermodesulfobium
           narugense DSM 14796]
 gi|332177973|gb|AEE13662.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermodesulfobium
           narugense DSM 14796]
          Length = 223

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 95/211 (45%), Gaps = 32/211 (15%)

Query: 460 AKKYTN-RG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           AK YT  +G ++F +L+  G  GL+ + E+F+     KF T+A   ++ AI   +     
Sbjct: 36  AKIYTTIQGKVEFEELLNYGIFGLLTSIERFEESRNLKFETFATHRIRGAILDGLRQIDP 95

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
             R     R K+ K+ R    + + + ++P+ +++A             L ITKE +   
Sbjct: 96  LKR---GTRSKVKKIDRAINELKSSLGKDPSDKDVA-----------DYLNITKEELLNW 141

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
               D  ++   DF + + +   L  AI+             L  RE++V+ + +     
Sbjct: 142 YAEIDALSTFQSDFSDSEKSYIDLSMAIE------------KLEEREKQVIDLYY----Y 185

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            D +L+E+ K   ++  R+ QI  KA+ KLK
Sbjct: 186 EDLSLDEIAKILNISVSRVSQIHGKALIKLK 216


>gi|257876008|ref|ZP_05655661.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
 gi|257810174|gb|EEV38994.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
          Length = 235

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 88/201 (43%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGLM A  KFD      F +YA   +K AI   +   +   +I  +    +++
Sbjct: 35  DLYNIGVIGLMDALRKFDPSKKVPFESYAAIRIKGAIIDEVRKHA---KISRYKMAAVNQ 91

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSH 587
             +  + +   +KRE T  EI K+L +    +  + +       +SLE  +    E+   
Sbjct: 92  FYQARQELEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEGMT 151

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D  A +  D+ +    R      +  L  RE+ +L + +      + TL+E+ +
Sbjct: 152 LKDMVRDP-AENVEDTLVAEEKRTALVACIKKLGEREQLILSLYY----TEELTLKEIAE 206

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI  K I KL+
Sbjct: 207 ILEVSIPRVSQIHGKTIAKLR 227


>gi|262273680|ref|ZP_06051493.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
 gi|262222095|gb|EEY73407.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
          Length = 78

 Score = 48.9 bits (115), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 40/60 (66%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++    L  L P++  VL  RFG+  +   TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 1   MKKSIVHWLQELNPKQREVLARRFGLLGHEASTLEDVGREIGLTRERVRQIQVEGLRRLR 60


>gi|224771371|dbj|BAH28627.1| sporulation sigma factor SigK [Clostridium perfringens NCTC 8239]
 gi|224771377|dbj|BAH28630.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771385|dbj|BAH28634.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771387|dbj|BAH28635.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771389|dbj|BAH28636.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771391|dbj|BAH28637.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771407|dbj|BAH28645.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771409|dbj|BAH28646.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771411|dbj|BAH28647.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|91978907|gb|ABE66429.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 291

 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 71/151 (47%), Gaps = 2/151 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 142 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 201

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 202 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 260

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           I++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 261 IAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|224771349|dbj|BAH28616.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSSYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|224771331|dbj|BAH28607.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771333|dbj|BAH28608.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771337|dbj|BAH28610.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSSYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|224771307|dbj|BAH28595.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771319|dbj|BAH28601.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771321|dbj|BAH28602.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|224771305|dbj|BAH28594.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771309|dbj|BAH28596.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771311|dbj|BAH28597.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771313|dbj|BAH28598.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771315|dbj|BAH28599.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771317|dbj|BAH28600.1| sporulation sigma factor SigK [Clostridium perfringens CPE str.
           F4969]
 gi|224771323|dbj|BAH28603.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771325|dbj|BAH28604.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771327|dbj|BAH28605.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771329|dbj|BAH28606.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771335|dbj|BAH28609.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771339|dbj|BAH28611.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771341|dbj|BAH28612.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771343|dbj|BAH28613.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771345|dbj|BAH28614.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771347|dbj|BAH28615.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771351|dbj|BAH28617.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771353|dbj|BAH28618.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771355|dbj|BAH28619.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771359|dbj|BAH28621.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771361|dbj|BAH28622.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771365|dbj|BAH28624.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771369|dbj|BAH28626.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771373|dbj|BAH28628.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771375|dbj|BAH28629.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771379|dbj|BAH28631.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771381|dbj|BAH28632.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771383|dbj|BAH28633.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771393|dbj|BAH28638.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771395|dbj|BAH28639.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771397|dbj|BAH28640.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771399|dbj|BAH28641.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771401|dbj|BAH28642.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771403|dbj|BAH28643.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771405|dbj|BAH28644.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|224771363|dbj|BAH28623.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|332653851|ref|ZP_08419595.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332516937|gb|EGJ46542.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 231

 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 89/229 (38%), Gaps = 56/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  +VE NLRLV  + KKY  +     DLI  G IGL+K    F      + +TYA   
Sbjct: 49  ARNILVEHNLRLVAHIVKKYYAQTGDQDDLISIGTIGLIKGISTFKADKNVRLATYA--- 105

Query: 504 VKQAITRSIADQSCTIRIPVHMR--DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
                +R I ++     I +H R   K+   V  +  M N                    
Sbjct: 106 -----SRCIENE-----ILMHFRAQKKLQGEVSLSDTMENG------------------- 136

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASL 620
                              GD ++  L D I  D N +  LD+  +   R     V   L
Sbjct: 137 -------------------GDGNSLSLMDVIAVDDNMLEDLDT--RDACRRVRQCVGECL 175

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE  ++ +R+G+      T  EV  +  ++R  + +IE +A+ KL+ 
Sbjct: 176 NPRERAIITLRYGLDDQPPRTQREVAARCGISRSYVSRIEKRALAKLEQ 224


>gi|238684475|gb|ACR54289.1| RNA polymerase sigma 70 factor [Aeromonas tecta]
          Length = 283

 Score = 48.5 bits (114), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +I
Sbjct: 1   LREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61


>gi|224771367|dbj|BAH28625.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 48.1 bits (113), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD   G + +TYA
Sbjct: 37  AKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYA 96

Query: 501 MWWVKQAI 508
              +   I
Sbjct: 97  AKCIDNEI 104


>gi|163785214|ref|ZP_02179892.1| RNA polymerase sigma factor for flagellar operon [Hydrogenivirga
           sp. 128-5-R1-1]
 gi|159879519|gb|EDP73345.1| RNA polymerase sigma factor for flagellar operon [Hydrogenivirga
           sp. 128-5-R1-1]
          Length = 177

 Score = 48.1 bits (113), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 54/192 (28%), Positives = 87/192 (45%), Gaps = 32/192 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           K ++V  NL L+  VA K   R     + F +L+  G IGL+KA + ++  L  KFSTYA
Sbjct: 9   KNKVVLDNLNLIKKVASKIYYRLPKGEIDFDELVNIGVIGLLKALDNYNEDLA-KFSTYA 67

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
                             IRI   + D +  +    R + +KIK+E  P  + +++ +P+
Sbjct: 68  Y-----------------IRIRGEILDYLRSLDIVPRGIRDKIKKEEKP--VDEQMEIPL 108

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                 L       S+E  IG  +     D ++ +   SP + A +  LRE     L  L
Sbjct: 109 SSSAIFL-------SIEKAIGGTEDLKFIDTLKSRME-SPEEYAYKVELREKIEEKLNLL 160

Query: 621 TPREERVLRMRF 632
           T  E++V++M F
Sbjct: 161 TENEKKVIQMIF 172


>gi|167464009|ref|ZP_02329098.1| RNA polymerase, sigma 28 subunit [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 175

 Score = 48.1 bits (113), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 54/90 (60%), Gaps = 7/90 (7%)

Query: 447 EMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDW-CLGYK---FSTY 499
           +++ A  ++V SVA+KY      GL + DL+  G IGL++A   +D   L  K   FSTY
Sbjct: 14  QIIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFSTY 73

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           A   +K +I R +AD+  ++R+P  +++K+
Sbjct: 74  AFNMIKWSIQRFLADKRFSVRVPRSIQNKL 103


>gi|237756227|ref|ZP_04584790.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237691619|gb|EEP60664.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 78

 Score = 48.1 bits (113), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 49/76 (64%)

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I+  + E    +L  L  RE+ +++MR+G+      TLEEVG++  ++RER+RQ+E +A+
Sbjct: 2   IEETIHEELESMLDVLDEREKEIIKMRYGLNGEESRTLEEVGEKLGISRERVRQLEQRAL 61

Query: 665 RKLKHPSRSKKLRSFL 680
           +KLK  +  K L+ FL
Sbjct: 62  KKLKAVALKKHLKDFL 77


>gi|257451779|ref|ZP_05617078.1| RpoS [Fusobacterium sp. 3_1_5R]
 gi|317058336|ref|ZP_07922821.1| predicted protein [Fusobacterium sp. 3_1_5R]
 gi|313684012|gb|EFS20847.1| predicted protein [Fusobacterium sp. 3_1_5R]
          Length = 201

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 6/94 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ E++E N+ L+  + ++Y +      D  QEG +    A +KFD     K S+YA  W
Sbjct: 20  ARNELIEKNINLIHKINRRYGSSE----DGFQEGVLAFCHAIDKFDETKKVKLSSYAFHW 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           ++Q I R    +    R+P H+ +K+ K  R  R
Sbjct: 76  IRQRIKRYRDREK--YRLPAHVIEKMTKEERKIR 107


>gi|207111845|ref|ZP_03246007.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 37

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 31/37 (83%)

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +  ++ REP PEEIAK+L MPVE VR++LKI++EP+S
Sbjct: 1   LLQELGREPLPEEIAKELDMPVERVREILKISQEPVS 37


>gi|169334386|ref|ZP_02861579.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259103|gb|EDS73069.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
          Length = 233

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 37/69 (53%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  K  ++E NLRLV+ +AKK+        DLI  G IGL+KA + F      K +TY
Sbjct: 47  ETNTTKTILIERNLRLVVYIAKKFDTSSASVEDLISIGTIGLIKAVKTFKVEKNIKLATY 106

Query: 500 AMWWVKQAI 508
           A   ++  I
Sbjct: 107 ASKCIENEI 115


>gi|124514599|gb|EAY56111.1| putative RNA polymerase sigma-70 factor family [Leptospirillum
           rubarum]
          Length = 99

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 39/63 (61%)

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           R+L  L  R  +++ +R+GIG     TL+E+G +F +TRER+RQI   ++ KL    R K
Sbjct: 34  RILQDLPDRSRKMVLLRYGIGTGISWTLQEIGLEFGLTRERVRQILRTSLEKLVKRQRRK 93

Query: 675 KLR 677
           + R
Sbjct: 94  ESR 96


>gi|313650139|gb|EFS14552.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           2a str. 2457T]
 gi|332757220|gb|EGJ87557.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           2747-71]
 gi|332766654|gb|EGJ96858.1| RNA polymerase sigma factor, sigma-70 family protein [Shigella
           flexneri 2930-71]
          Length = 161

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 38/152 (25%), Positives = 72/152 (47%), Gaps = 11/152 (7%)

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P  +R    +V +   ++  ++ R  T  E+A++L + +   R++L  T          
Sbjct: 11  VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY-- 68

Query: 581 GDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
            DE     GD IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +
Sbjct: 69  -DEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEEL 127

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           N    L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 128 N----LKEIGAVLEVGESRVSQLHSQAIKRLR 155


>gi|169831583|ref|YP_001717565.1| sporulation sigma factor SigE [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638427|gb|ACA59933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 241

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            +  ++E NLRLV+ +A+K+ + G+   D++  G IGL+KA   FD     K +TYA
Sbjct: 60  VRSTLIERNLRLVVYIARKFESTGVGIEDMVSIGTIGLIKAVNTFDPRKRIKLATYA 116


>gi|149176711|ref|ZP_01855322.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
 gi|148844352|gb|EDL58704.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
          Length = 258

 Score = 48.1 bits (113), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 50/207 (24%), Positives = 88/207 (42%), Gaps = 15/207 (7%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLI  G  GLM A   FD   G KF TY +  ++ A+   +        +P  +R
Sbjct: 51  GVDLNDLISAGVFGLMDAINAFDLERGVKFETYCVPRIRGAMLDELRTMDW---VPRLVR 107

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDED 584
            K  K+    +    +  R P  EEIA+K+ +  +   K+         +SL     + D
Sbjct: 108 SKASKLEAARKAAEAEFGRPPADEEIARKMQLSRKEFEKLKNEANAVGLVSLNKKWYETD 167

Query: 585 TS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +       D +ED     P  S  + +L    T+ L     R ER++ + +      + T
Sbjct: 168 SYKDVREVDILEDAKGEDPTKSIQKRDLMRLVTKGLN----RNERLIIILY---YYEELT 220

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++E+G    ++  R+ Q+ +  + +LK
Sbjct: 221 MKEIGSTLGLSESRVSQMHSSIVNRLK 247


>gi|330444437|ref|YP_004377423.1| RNA polymerase sigma factor [Chlamydophila pecorum E58]
 gi|328807547|gb|AEB41720.1| RNA polymerase sigma factor [Chlamydophila pecorum E58]
          Length = 256

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 94/215 (43%), Gaps = 38/215 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL++A E+++     +F  +A++ +K AI   +  Q     +P  +  K +K
Sbjct: 55  DLYASGVEGLVRAVERYN-PERSRFEGFAIFLIKAAIIDDLRKQDW---VPRSVYQKANK 110

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-------RKVLKIT-----------KEP 573
           +      +   + +EPT  E+ + L + +  +       R  L I+            E 
Sbjct: 111 LTEAMDTLRQSLGKEPTDLELCEYLNISLHELSQWFASSRPALIISLNTDWPSHSCEGEG 170

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           I+LE  I DE      D ++ K   S L  AIQ             L  +E +V+ + + 
Sbjct: 171 IALEERIPDERAETGYDVVDKKEFCSFLALAIQG------------LEEKERQVMALYYY 218

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            G+     L+E+GK   V+  R+ QI +KA+ KL+
Sbjct: 219 EGL----VLKEIGKILGVSESRVSQIHSKALIKLR 249


>gi|289523542|ref|ZP_06440396.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503234|gb|EFD24398.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 251

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 103/233 (44%), Gaps = 21/233 (9%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V   L LV  V  + +     GL   DL+  G +GL+ A +++D   G  F+T+A 
Sbjct: 26  KEEIVGLFLPLVRYVVGRMSIVIPPGLSQDDLLSFGAMGLLDAIDRYDPSRGVSFNTFAF 85

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +       R     RDKI ++ +    M N+   +   E + +KL M   
Sbjct: 86  SRIRGAILDELRRYDWLSR---GARDKIQRLEKAIAEM-NEQGLKANDEMLMEKLQMD-- 139

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE------TTTR 615
              K L+   E +S    +  ++   L +   +++A+ P  S       E      T   
Sbjct: 140 --EKELRWLYELMSRSYVVSLDEVISLDEGDVERSALVPDTSPNPEEYMEAMEDCDTLKG 197

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  L  RE+ VL + +  G+    T +E+G+   VT  R+ QI  KA+  LK
Sbjct: 198 ALEKLEEREQLVLSLYYYEGL----TFKEIGEVLGVTESRVSQIHGKALAMLK 246


>gi|32475302|ref|NP_868296.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|32445843|emb|CAD78574.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|327540927|gb|EGF27485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodopirellula baltica
           WH47]
          Length = 272

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 52/244 (21%), Positives = 109/244 (44%), Gaps = 26/244 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + ++VE  ++LV    ++   R   G++  DLI  G  GLM A + +D   G KF T+ +
Sbjct: 39  RNQLVERYMQLVRYNGERIWQRLPDGVELDDLISAGMFGLMDAIDAYDTERGVKFETFCV 98

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  K+    + +  +  R PT +E++  + + V+
Sbjct: 99  PRIRGAMLDELRKMDW---VPRLVRSKASKLATATKTLEARFGRAPTVQELSAHMEIDVK 155

Query: 562 GVRK---------VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            V K         V+ + K+    ++    +D   + D +EDK    P     + +L   
Sbjct: 156 EVEKMQSEANAVGVVSLNKKWYETDSY---KDVREI-DILEDKKGEDPTRRVQKNDLMRL 211

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            T+ L     R ER++ + +      + T++E+G    ++  R+ Q+    + +L+    
Sbjct: 212 VTKGLN----RNERLIIILY---YYEELTMKEIGATLDLSESRVSQMHTAIVNRLQQQLG 264

Query: 673 SKKL 676
            ++L
Sbjct: 265 VRRL 268


>gi|224004150|ref|XP_002295726.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209585758|gb|ACI64443.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 395

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 15/83 (18%)

Query: 472 DLIQEGNIGLMKAAEKFDWCL---------------GYKFSTYAMWWVKQAITRSIADQS 516
           DL+ EG IGL +A +K+D+                 G +  TYA +W++  I R+I  + 
Sbjct: 70  DLLHEGTIGLAEALDKYDFSYSDLSVTEHTSSTAPKGARLGTYATYWIRGRILRAIQSRE 129

Query: 517 CTIRIPVHMRDKIHKVVRTARRM 539
              R P  +    H++V+ A+ +
Sbjct: 130 HAFRFPERVLQASHRLVKAAKEL 152


>gi|158334762|ref|YP_001515934.1| hypothetical protein AM1_1596 [Acaryochloris marina MBIC11017]
 gi|158305003|gb|ABW26620.1| hypothetical protein AM1_1596 [Acaryochloris marina MBIC11017]
          Length = 51

 Score = 47.8 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 22/33 (66%), Positives = 26/33 (78%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           L+FL LIQEG IGL ++ EKFD   GY+FSTYA
Sbjct: 18  LEFLVLIQEGTIGLRRSVEKFDPTKGYRFSTYA 50


>gi|134298861|ref|YP_001112357.1| sigma-70 region 2 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051561|gb|ABO49532.1| sigma-70 region 2 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 47.8 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 33/116 (28%), Positives = 58/116 (50%), Gaps = 3/116 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           G W   V   V+ ++ + + I + +    +   E    ++++ +G+    +A+  + E N
Sbjct: 4   GLWTVTVLSVVNGVMALVSYIANNTFPQPLKEVEEARYLALLAEGD---EMARNILTERN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LRLV  + KK+ + G    DLI  G IGL+KA   F    G + +TYA   ++ AI
Sbjct: 61  LRLVAHIVKKFDSTGEDVDDLISIGTIGLIKAINTFKADKGTRLATYAARCIENAI 116


>gi|312140062|ref|YP_004007398.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311889401|emb|CBH48717.1| sigma-70 factor [Rhodococcus equi 103S]
          Length = 289

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 58/213 (27%), Positives = 95/213 (44%), Gaps = 17/213 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +  A L +   VA +Y NRG+   +L Q   + L+ AA +FD   G  F  YA+  V+  
Sbjct: 67  LCVAALPMAYRVAGRYRNRGVPTAELRQVAALALVGAARRFDPSRGTDFIPYAVTSVRGE 126

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D + +  +P  +++    V      +S ++ R    +E+A  L MPVE   +  
Sbjct: 127 IRKYFRDFTWSTHVPRRLQESHLAVRNRMESLSTELGRTVRLDEVAHSLGMPVEEAEEAE 186

Query: 568 KITKEPISLE----TPI-GDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           ++  E  S E    TP+ G     H  GD   D + V           R    R++A+L 
Sbjct: 187 RV-GELYSCESLDATPVDGSVPRLHTTGDVDADLSRV---------EHRHLLRRLMATLD 236

Query: 622 PREERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
            R+  +L +R+   M+     E+VG  Q  V+R
Sbjct: 237 ERQRTLLWLRYFHQMSQSEIAEQVGLSQMHVSR 269


>gi|81300593|ref|YP_400801.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|81169474|gb|ABB57814.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 260

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 40/161 (24%), Positives = 81/161 (50%), Gaps = 8/161 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWC 491
           +V   E  +   + ++V+ NL LV  +A + + +  + + DL Q G +GL++A E+F   
Sbjct: 15  LVAYAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQPH 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D   +IRIP   ++   +  +    + ++  R PT +E
Sbjct: 75  QGCAFSSFAVPYIRGEILHFLRDSCHSIRIPRRWQELQRQGQQLREVLRHEWGRAPTEQE 134

Query: 552 IAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGD 590
           +A  L + +   +++   +  + P+SL     D   S  GD
Sbjct: 135 LAFALNLSMTEWQEIHLARRNRMPMSL-----DATLSQAGD 170


>gi|291544363|emb|CBL17472.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           sp. 18P13]
          Length = 118

 Score = 47.8 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/66 (40%), Positives = 38/66 (57%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A+  ++E NLRLV  + KKY        +LI  G +GL+KA   FD   G KF+TYA 
Sbjct: 47  SQARAMLIEHNLRLVAHMIKKYYANSKDQDELISIGTMGLIKAVNTFDAAKGSKFATYAG 106

Query: 502 WWVKQA 507
             +++A
Sbjct: 107 RCIEKA 112


>gi|56752318|ref|YP_173019.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|56687277|dbj|BAD80499.1| group3 RNA polymerase sigma factor SigF2 [Synechococcus elongatus
           PCC 6301]
          Length = 275

 Score = 47.8 bits (112), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 40/161 (24%), Positives = 81/161 (50%), Gaps = 8/161 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWC 491
           +V   E  +   + ++V+ NL LV  +A + + +  + + DL Q G +GL++A E+F   
Sbjct: 30  LVAYAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQPH 89

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D   +IRIP   ++   +  +    + ++  R PT +E
Sbjct: 90  QGCAFSSFAVPYIRGEILHFLRDSCHSIRIPRRWQELQRQGQQLREVLRHEWGRAPTEQE 149

Query: 552 IAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGD 590
           +A  L + +   +++   +  + P+SL     D   S  GD
Sbjct: 150 LAFALNLSMTEWQEIHLARRNRMPMSL-----DATLSQAGD 185


>gi|226949740|ref|YP_002804831.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
 gi|226840763|gb|ACO83429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
          Length = 183

 Score = 47.8 bits (112), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 450 EANLRLVISVA-KKYTN--RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E +L LV S+A K+Y+       + +L QEG +GLMKA  +FD   G KFSTYA  +V  
Sbjct: 5   EEHLNLVHSIASKRYSQFKHKYTYEELFQEGCLGLMKAVNRFDTSRGIKFSTYAYPYVDG 64

Query: 507 AI 508
           AI
Sbjct: 65  AI 66


>gi|220932606|ref|YP_002509514.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
 gi|219993916|gb|ACL70519.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
          Length = 209

 Score = 47.8 bits (112), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 47/84 (55%), Gaps = 3/84 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ +   LV  + ++Y       +DLIQEG +GL+ A + +D   G  FS+YA+++
Sbjct: 35  ARQRLITSYQPLVFKIVRQYARDNEVVMDLIQEGTLGLIDAIDSYDHKRGKSFSSYALYY 94

Query: 504 VKQAITRSIADQ-SCTIRIPVHMR 526
           ++  +   +    +C+  IP  +R
Sbjct: 95  IRGRVINYLKKAPACS--IPAELR 116


>gi|295092257|emb|CBK78364.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 220

 Score = 47.8 bits (112), Expect = 0.007,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 96/235 (40%), Gaps = 47/235 (20%)

Query: 442 SIAKKEMVEANLRLVISVA-KKYTNRGLQ-------FLDLIQEGNIGLMKAAEKFDWCLG 493
           + A+  ++E NL  +  +A ++Y + GL          DL+QEG+IGL+ A   FD   G
Sbjct: 18  TAARDILLENNLGFIRKIALEQYRSMGLDENDIGIDLDDLVQEGSIGLLNAIPLFDAGRG 77

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF TYA   ++ A+T  I                   + +  +RM +K K  P      
Sbjct: 78  MKFLTYAAPAIRNAMTDCIR----------------AALAQFEQRMVDK-KNGP------ 114

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                   G ++V         L+  + D++     + I D +  +P    IQ       
Sbjct: 115 --------GFQRVY--------LDDILSDDERMLRIEAIADPHTQTPEQIYIQKEQLTEL 158

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  LT RE+  L  R+G     +H L      F ++  R +++E +A+  L+
Sbjct: 159 YAALDKLTAREQTYLLYRYGFTDGIEHPLIGAALHFHLSESRTKKVEGEAMDSLR 213


>gi|238753169|ref|ZP_04614612.1| Lateral flagellar motor protein A (MotA-like) [Yersinia rohdei ATCC
           43380]
 gi|238708608|gb|EEQ00883.1| Lateral flagellar motor protein A (MotA-like) [Yersinia rohdei ATCC
           43380]
          Length = 525

 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 49/208 (23%), Positives = 97/208 (46%), Gaps = 37/208 (17%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGY---KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           D+ Q   +GL++A  ++    G+   +F+ YA+  ++ A+   + +       P  +R K
Sbjct: 47  DMQQIALMGLLEALRRY----GHPDVQFAAYAVHRIRGAVLDQLREHDWR---PRRLRQK 99

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--------EPISLETPI 580
            HK+    R +  K+  EP+ EEI  +L +  E  ++ L +          + +SLETP 
Sbjct: 100 THKINEAIRAIMRKLGHEPSFEEITAELKLTAEEYQEYLLLESASAMESLDDILSLETPT 159

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
               + +L D I            ++ NL +     +ASL  RE+ +L + +      + 
Sbjct: 160 DALQSRNLEDSI-----------IVEDNLNQA----IASLEEREQMILHLYY----QKEM 200

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++E+ +   +T  RI Q+  K ++K+K
Sbjct: 201 SMKEIAEVLDLTEARICQLNKKIVQKIK 228


>gi|163785765|ref|ZP_02180266.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159878964|gb|EDP72967.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 64

 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 40/62 (64%)

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE  +++ R+G+      TL EVG+   ++RER+RQ+E +A++KL+  +  + L+ 
Sbjct: 2   ALDEREREIIKHRYGLEGEEPKTLNEVGEMLGISRERVRQLENRALKKLRALAMKRHLKD 61

Query: 679 FL 680
           FL
Sbjct: 62  FL 63


>gi|148793340|gb|ABR12734.1| RNA polymerase sigma factor [Photobacterium iliopiscarium]
          Length = 281

 Score = 47.4 bits (111), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61



 Score = 37.4 bits (85), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 43/165 (26%), Positives = 73/165 (44%), Gaps = 11/165 (6%)

Query: 289 EVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR S +  A+    + +     ++  E+L ++     L   + D LV  L D   
Sbjct: 122 EKFLELRHSYEKMALAINTNGRQHATTEIAVEELSEIFKQFRLIPKQFDRLVSSLRDSMD 181

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYA----KDFPEGEWKNFVACE 402
           ++  NE  ++R+   +  + +  F+    G E +  W+  A    K + E   KN+    
Sbjct: 182 KVRTNERLIMRMCVDNSKMPKKTFISLFAGNESNSDWIDTALNSGKPYAE-RLKNYEEDL 240

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
             S LK+R     +  ETG+SI   + I   +  GE +A  AKKE
Sbjct: 241 RRSTLKLR----ILEQETGLSIERIKDISRRMSIGEAKARRAKKE 281


>gi|167515030|gb|ABZ81799.1| RpoD [Aeromonas aquariorum]
          Length = 282

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61


>gi|148793344|gb|ABR12736.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 284

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61



 Score = 44.7 bits (104), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 77/169 (45%), Gaps = 11/169 (6%)

Query: 289 EVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR S +  A+   +  +     +V  E+L ++     L   + D LV  L D   
Sbjct: 121 EKFLELRQSYEKMALAINQHGRQHATTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMD 180

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYA----KDFPEGEWKNFVACE 402
           ++  NE  ++R+   +  + +  F+    G E +  W+  A    K + E   KN+    
Sbjct: 181 KVRTNERLIMRMCVDNSKMPKKTFISLFAGNESNSDWIDTALNSGKPYAE-RLKNYEEDL 239

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             S LK+R     +  ETG+SI   + I   +  GE +A  AKKEMVEA
Sbjct: 240 RRSTLKLR----ILEQETGLSIERIKDISRRMSIGEAKARRAKKEMVEA 284


>gi|157826498|ref|YP_001495562.1| RNA polymerase sigma factor [Rickettsia bellii OSU 85-389]
 gi|157801802|gb|ABV78525.1| RNA polymerase sigma factor [Rickettsia bellii OSU 85-389]
          Length = 36

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/30 (73%), Positives = 26/30 (86%), Gaps = 1/30 (3%)

Query: 567 LKITKEPISLETPIGD-EDTSHLGDFIEDK 595
           +KI KEPISLE P+GD +D S+LGDFIEDK
Sbjct: 1   MKIAKEPISLENPVGDGDDNSYLGDFIEDK 30


>gi|154482592|ref|ZP_02025040.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
 gi|149736617|gb|EDM52503.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
          Length = 192

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 53/226 (23%), Positives = 96/226 (42%), Gaps = 51/226 (22%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  V KKY +   +  DLI  G +GL+KA   ++   G +  TYA   
Sbjct: 8   AKDILIERNLRLVAHVVKKYYDENRENQDLISIGIVGLIKAVNTYNPDKGNRLVTYA--- 64

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                        C       + +++  ++R  ++ S  +                    
Sbjct: 65  -----------AKC-------IENELLMMLRAEKKRSKDVS------------------- 87

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTP 622
                   EPI  +    + +T  L D +E+ + +  L+   +A N+      V   L  
Sbjct: 88  ------LNEPIGTDK---EGNTISLIDVVEN-DEMDTLEQIEKAENISLVQKYVAQILNE 137

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ ++  R+G+      T ++VG++  ++R  + +IE +A+ KLK
Sbjct: 138 REKEIIVWRYGLDGKKPMTQKKVGEKLGISRSYVSRIEKRALEKLK 183


>gi|87201086|ref|YP_498343.1| sigma 28 (flagella/sporulation) [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87136767|gb|ABD27509.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 244

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 90/202 (44%), Gaps = 11/202 (5%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G++  DLIQ G + L + A++ D      F+ YA   V+ A+   +   +   R     R
Sbjct: 44  GIEIEDLIQAGLVALTECAQRHDGPTEDGFAAYAKLRVRGAMVDLVRRSTPLSRSATERR 103

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + +   T   ++ ++ R P+  E+A+ + +  E      +   EP+  E  I D  + 
Sbjct: 104 RVLREKTAT---LATELGRPPSEAELARAVGL-TERELADQRAADEPLRFEA-IDDAYSD 158

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
               F +D+      D    A +R      +A L  R + ++++ F   +N    L E+ 
Sbjct: 159 SNSAFADDRP--DSFDMLADAEMRGAVAAAIAGLPERLQLIIQLYFVEELN----LAEIA 212

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   V+  R+ Q++A+AI KL+
Sbjct: 213 EVLGVSIPRVHQLKAQAIDKLR 234


>gi|148793342|gb|ABR12735.1| RNA polymerase sigma factor [Photobacterium iliopiscarium]
          Length = 285

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61



 Score = 44.7 bits (104), Expect = 0.059,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 77/169 (45%), Gaps = 11/169 (6%)

Query: 289 EVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR S +  A+    + +     ++  E+L ++     L   + D LV  L D   
Sbjct: 122 EKFLELRHSYEKMALAINTNGRQHATTEIAVEELSEIFKQFRLIPKQFDRLVSSLRDSMD 181

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYA----KDFPEGEWKNFVACE 402
           ++  NE  ++R+   +  + +  F+    G E +  W+  A    K + E   KN+    
Sbjct: 182 KVRTNERLIMRMCVDNSKMPKKTFISLFAGNESNSDWIDTALNSGKPYAE-RLKNYEEDL 240

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             S LK+R     +  ETG+SI   + I   +  GE +A  AKKEMVEA
Sbjct: 241 RRSTLKLR----ILEQETGLSIERIKDISRRMSIGEAKARRAKKEMVEA 285


>gi|239934582|emb|CAR94605.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 220

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 59/184 (32%), Positives = 84/184 (45%), Gaps = 24/184 (13%)

Query: 289 EVYRELRSLQDNAVNGQKD--EKSSVKCKVLK--EKLVKLVGSLSLNQSRIDLLVEQLYD 344
           E  R   SL    V  QK   EK +   KV+K  +KL      L L+    D+L+ Q+  
Sbjct: 47  EAARRFDSLSKTFVQVQKGMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLITQIRR 106

Query: 345 ISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
               I + E +++ L  +  G+ R  F+      E +  W+           K+  A   
Sbjct: 107 SLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLD----------KHIRAKRK 156

Query: 404 DS--ILKIRNEI-----KSISVE--TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            S  + K+R EI     K + VE  T +SI+  + I   +  GE +A  AKKEMVEANLR
Sbjct: 157 HSAHLAKLREEIEAQQKKLMGVEELTHLSIAGIKEINREIAVGEAKARRAKKEMVEANLR 216

Query: 455 LVIS 458
           LVIS
Sbjct: 217 LVIS 220


>gi|148793324|gb|ABR12726.1| RNA polymerase sigma factor [Photobacterium angustum]
 gi|148793326|gb|ABR12727.1| RNA polymerase sigma factor [Photobacterium angustum]
          Length = 284

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 76/168 (45%), Gaps = 9/168 (5%)

Query: 289 EVYRELRSLQDN-AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR   D  A+  + + + +   +V  E+L ++     L   + D LV  L D   
Sbjct: 121 EKFLELRQAYDKMALAIETNGRQNATTEVAVEELSEVFKQFRLIPKQFDRLVSSLRDSMD 180

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD-- 404
           ++  NE  ++R+   +  + +  F+    G E    W+  A +  +   +     E D  
Sbjct: 181 KVRTNERLIMRMCVDNSKMPKKTFVSLFAGNESSQDWIDEALNSGKPYAERLKVYEEDLR 240

Query: 405 -SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            S LK+R     +  ETG+SI   + I   +  GE +A  AKKEMVEA
Sbjct: 241 RSSLKLR----MLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEA 284


>gi|148793336|gb|ABR12732.1| RNA polymerase sigma factor [Photobacterium phosphoreum]
 gi|148793338|gb|ABR12733.1| RNA polymerase sigma factor [Photobacterium phosphoreum]
          Length = 285

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61



 Score = 43.5 bits (101), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 77/169 (45%), Gaps = 11/169 (6%)

Query: 289 EVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR S +  A+    + +     +V  E+L ++     L   + D LV  L D   
Sbjct: 122 EKFLELRHSYEKMALAINTNGRQHATTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMD 181

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYA----KDFPEGEWKNFVACE 402
           ++  NE  ++R+   +  + +  F+    G E +  W+  A    K + E   KN+    
Sbjct: 182 KVRTNERLIMRMCVDNSKMPKKTFISLFGGNESNSDWIDTALNSGKPYAE-RLKNYEEDL 240

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             + LK+R     +  ETG+SI   + I   +  GE +A  AKKEMVEA
Sbjct: 241 RRATLKLR----ILEQETGLSIERIKDISRRMSIGEAKARRAKKEMVEA 285


>gi|148793350|gb|ABR12739.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 271

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61


>gi|148793320|gb|ABR12724.1| RNA polymerase sigma factor [Aliivibrio fischeri]
          Length = 279

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 37/61 (60%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDI 60

Query: 185 I 185
           I
Sbjct: 61  I 61



 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 36/135 (26%), Positives = 61/135 (45%), Gaps = 6/135 (4%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRE 378
           +L  +     L   + D LV+++ D   R+   E  ++R+   YG + +  F+    G E
Sbjct: 148 ELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMPKKSFIALFTGNE 207

Query: 379 LDPHWVS--YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
               W +   A D P   +   +    + I +   ++ SI  ETG+ +   + I   +  
Sbjct: 208 SSDEWFNEIMASDKP---YVERLQRYEEDIRRSIAKLDSIEKETGLPVENIKDISRRMSI 264

Query: 437 GECEASIAKKEMVEA 451
           GE +A  AKKEMVEA
Sbjct: 265 GEAKARRAKKEMVEA 279


>gi|258516390|ref|YP_003192612.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
 gi|257780095|gb|ACV63989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
          Length = 239

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 104/225 (46%), Gaps = 25/225 (11%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++++ +  RLV   AK Y + G Q  DL+Q G  GL+KA  +FD   G  FSTYA   + 
Sbjct: 32  RQVMMSGSRLVRHFAKLYAS-GRQTEDLMQSGYEGLLKALGRFDSSRGVLFSTYAAHCIM 90

Query: 506 QAITRSI---ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
             I   I   A  +C   +   ++ +I++ V    + + +I   P+  +IA+ + +  EG
Sbjct: 91  GEIRHHIRKEASYACPAAVA-ELQARINRFVDDYMKENGQI---PSLSQIAEFVNVCEEG 146

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V + ++     +SL     DE   H    ++ ++   P++  I         + L  LT 
Sbjct: 147 VVQAMRAGF--VSL-----DEIELHKIQSLKYESFCLPIEDRI------VLEQALYKLTE 193

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            ++RV+ + F      D T  E   Q  +++  + +I  K++  L
Sbjct: 194 LQQRVIHLLF----YKDMTQTEAASQLGISQRSVSRILRKSLNLL 234


>gi|160942608|ref|ZP_02089853.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446087|gb|EDP23090.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
          Length = 234

 Score = 47.4 bits (111), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 35/59 (59%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           + A+++++  NLRLV  + KKY        DL+  G IGLMKA + FD     +FSTYA
Sbjct: 53  AAAREKLIRHNLRLVAHIVKKYYALPGDQEDLVSIGTIGLMKAVDTFDATRKARFSTYA 111


>gi|322384374|ref|ZP_08058069.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150809|gb|EFX44249.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 340

 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 101/227 (44%), Gaps = 29/227 (12%)

Query: 455 LVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDW-CLGYK---FSTYAMWWVKQA 507
           +V SVA+KY      GL + DL+  G IGL++A   +D   L  K   FSTYA   +K +
Sbjct: 1   MVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFSTYAFNMIKWS 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R +AD+  ++R+P  +++K+  + +           + + E IA+K    +  +R+V 
Sbjct: 61  IQRFLADKRFSVRVPRSIQNKLTVIWKQGW-------DQESAESIAEKTGWKLAEIREVK 113

Query: 568 K--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +        SL+  +  + T      ++   A++   S    +        L +L P E 
Sbjct: 114 RHLAGWSVASLDQALSSDKTDEEATMLDVLPAMTDFTSVHVQDF-------LCALKPLER 166

Query: 626 RVLRMRFG------IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            VL +R        I M+   T   V +     +++  Q +A  +++
Sbjct: 167 AVLELRLQDQTQKEIAMHIGKTQMYVSRILKKIKDKYTQFQAGTLKR 213


>gi|226324647|ref|ZP_03800165.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
 gi|225207095|gb|EEG89449.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
          Length = 222

 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 52/220 (23%), Positives = 92/220 (41%), Gaps = 55/220 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  V KKY +      DL+  G IGL+KA   F+     + +TYA   
Sbjct: 27  ARHILIERNLRLVAHVIKKYQHLEDDTEDLLSIGTIGLIKAVSTFNPDKKARLATYACRC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++                     +++  ++RT R+ SN+                     
Sbjct: 87  IE---------------------NELLMMLRTKRK-SNR--------------------- 103

Query: 564 RKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                      SL  PIG +   +   L D IE     + +  A++ ++     ++ + L
Sbjct: 104 ---------ETSLYEPIGTDREGNEIRLYDVIESDEEDACMQLALKNDISLLYEKLESVL 154

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           T RE+ VL+ R+G+    ++T +EV     ++R  + +IE
Sbjct: 155 TDREQLVLKKRYGLYGEKEYTQKEVAASLGISRSYVSRIE 194


>gi|296132610|ref|YP_003639857.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031188|gb|ADG81956.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 245

 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 99/237 (41%), Gaps = 53/237 (22%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ KG+ EA   +  ++E NLRLV  + KK+        DLI  G IGL+KA   F+ 
Sbjct: 52  LELLEKGDEEA---RNVLIERNLRLVAHIVKKFDGALDDNDDLISIGTIGLIKAINTFNR 108

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G + +TYA         R I ++     I +H+R                 K+     
Sbjct: 109 YKGTRLATYA--------ARCIENE-----ILMHLR---------------ATKKNRVEV 140

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +   + +  EG           I+L   +G E    L       + V  L    Q  L 
Sbjct: 141 SLYDSIGVDKEG---------NEITLIDVLGTESEIVL-------DTVESLFE--QRRLL 182

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E   +    L+ RE+ VL++RFG+      T  E+ ++  ++R  + +IE +A+ KL
Sbjct: 183 EKVKK----LSYREKNVLQLRFGLVNGIRKTQREIARKLGISRSYVSRIEKRALNKL 235


>gi|170764001|ref|ZP_02637018.2| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170710658|gb|EDT22840.1| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
          Length = 152

 Score = 47.4 bits (111), Expect = 0.009,   Method: Composition-based stats.
 Identities = 29/70 (41%), Positives = 42/70 (60%), Gaps = 6/70 (8%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ G+ EA   K+ +VE NLRLV  + KKY++      +  DLI  G IGL+KA + FD 
Sbjct: 43  LKDGDVEA---KRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGTIGLIKAIDSFDT 99

Query: 491 CLGYKFSTYA 500
             G + +TYA
Sbjct: 100 NKGIRLATYA 109


>gi|291277483|ref|YP_003517255.1| putative flagellar operon RNA polymerase sigma factor [Helicobacter
           mustelae 12198]
 gi|290964677|emb|CBG40532.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter mustelae 12198]
          Length = 231

 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 93/197 (47%), Gaps = 17/197 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G   L+K A K+D  L   F  YA   V  A+   +  +S  I I    R  I  
Sbjct: 44  DLISIGTEELIKLARKYDSKLNDSFWGYAKTRVNGALLDYL--RSLDI-ISRANRKLIKS 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   R  N+ + EP+   +A+ L    E +R+  +I  + I L  PI ++  +     
Sbjct: 101 IDQEITRYYNQHQEEPSDAYLAQVLGEDEEKIREA-RIASD-IYLLVPIDEQYNA----- 153

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE  + V  L+   +  L +   ++L+ L+ RE+ +++M F   MN    L E+ +   +
Sbjct: 154 IESDDIVEKLE---KEELVQKIKKILSGLSQREQMIMQMYFFEEMN----LNEIKEVLDI 206

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI QI  + I+K++
Sbjct: 207 TESRISQITKEVIKKIR 223


>gi|257871306|ref|ZP_05650959.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
 gi|257805470|gb|EEV34292.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
          Length = 235

 Score = 47.4 bits (111), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 89/201 (44%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGLM A  KFD      F +YA+  +K AI   +   +   +I  +    +++
Sbjct: 35  DLYNIGVIGLMDALRKFDPSKKVPFESYAVIRIKGAIIDEVRKHA---KISRYKMAAVNQ 91

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSH 587
             +  + +   +KRE T  EI K+L +    +  + +       +SLE  +    E+   
Sbjct: 92  FYQARQELEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEGMT 151

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D  A +  D+ +    R      +  L  RE+ +L + +      + TL+E+ +
Sbjct: 152 IKDMVRDP-AENVEDTLVAEEKRTALVACIKKLGEREQIILSLYY----TEELTLKEIAE 206

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  R+ QI  K I KL+
Sbjct: 207 ILEISIPRVSQIHGKTIAKLR 227


>gi|7677125|gb|AAF67044.1|AF183382_4 motility sigma factor FliA [Pseudomonas putida]
          Length = 245

 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 56/230 (24%), Positives = 98/230 (42%), Gaps = 14/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  AQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVSSKYDASKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  +  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAMRAVEARTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQANLRETTTRVLA 618
           +    +L  T    S      D   +      ED  +  V P         +   T  +A
Sbjct: 133 DDYYGILNDTLG--SRLFSFDDLLQTRARRLHEDGASGHVEPARGLEDERFQAALTEAIA 190

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L  RE  VL + +   +N    L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 191 NLPERERLVLALYYDEELN----LKEIGEVLGVSESRVSQLHSQCAARLR 236


>gi|285018163|ref|YP_003375874.1| RNA polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Xanthomonas albilineans GPE PC73]
 gi|283473381|emb|CBA15886.1| probable rna polymerase sigma factor for flagellar operon (sigma-f
           factor) protein [Xanthomonas albilineans]
          Length = 249

 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 55/210 (26%), Positives = 95/210 (45%), Gaps = 18/210 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I       R  VH R +   
Sbjct: 45  DLIQAGMIGLIEASRSYDADQGASFETYASIRIRGSMIDEIRRGDWVPR-SVHRRAR--D 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLG 589
                R++     R     E+A  + MP+    ++++     + +SLE+ I  ED   L 
Sbjct: 102 AASAIRKIEQNTGRAAAANEVAAAMEMPLPEYMRLMEDAARGQVLSLESRI--EDHGEL- 158

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I  K   +P     ++       + +A L  RE+ VL + +   +N    L+E+G   
Sbjct: 159 DTIA-KGGPNPQQMLERSEFGRELGKAIAQLPEREQLVLSLYYEQELN----LKEIGAVL 213

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            V+  R+ QI  +A  +L+      +L++F
Sbjct: 214 GVSESRVCQIHGQATVRLR-----GRLKAF 238


>gi|148793330|gb|ABR12729.1| RNA polymerase sigma factor [Photobacterium leiognathi]
 gi|148793332|gb|ABR12730.1| RNA polymerase sigma factor [Photobacterium leiognathi subsp.
           mandapamensis]
 gi|148793334|gb|ABR12731.1| RNA polymerase sigma factor [Photobacterium leiognathi subsp.
           mandapamensis]
          Length = 284

 Score = 47.0 bits (110), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 30/44 (68%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLL 44



 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 79/172 (45%), Gaps = 17/172 (9%)

Query: 289 EVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E + ELR+  D        NG++D+++ +      E+L ++     L   + D LV  L 
Sbjct: 121 EKFLELRNAYDKMALAIDTNGRQDKQTEIAV----EELSEVFKQFRLIPKQFDRLVSSLR 176

Query: 344 DISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   ++  NE  ++R+   +  + +  F+    G E +  W+  A +  +   +     E
Sbjct: 177 DAMDKVRTNERLIMRMCVDNSKMPKKTFVTLFAGNEANQDWIDEALNSGKPYAERLKTYE 236

Query: 403 VD---SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            D   S +K+R     +  ETG+SI   + I   +  GE +A  AKKEMVEA
Sbjct: 237 EDLRRSAIKLR----MLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEA 284


>gi|254519270|ref|ZP_05131326.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
 gi|226913019|gb|EEH98220.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
          Length = 231

 Score = 47.0 bits (110), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 49/221 (22%), Positives = 91/221 (41%), Gaps = 59/221 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY        +LI  G +GL+KA + FD   G + +TYA   
Sbjct: 50  AKSILIERNLRLVAHIVKKYNFPNKDIDELISIGTVGLIKAIDSFDASKGTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++             I  + R  ++  N+                     
Sbjct: 107 -----SRCIENE-------------ILMLFRNNKKQKNE--------------------- 127

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                     + L+ PIG +   +   L D +  E  + +  ++S +Q  +++   ++  
Sbjct: 128 ----------VYLQDPIGVDKEGNEICLIDVLSSEKDSVLEKVESNLQ--IKQLYNKICV 175

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           SL+ RE  +++MR+G+      T  E+     ++R  + +I
Sbjct: 176 SLSEREGEIVKMRYGLIDGRCRTQREIAALLGISRSYVSRI 216


>gi|296282290|ref|ZP_06860288.1| sigma 28 (flagella/sporulation) [Citromicrobium bathyomarinum
           JL354]
          Length = 240

 Score = 47.0 bits (110), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 103/232 (44%), Gaps = 27/232 (11%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +E V   L LV  +A  Y   G   +D   L+Q G + L +AA++ D      F+ YA  
Sbjct: 19  QEKVTQFLPLVRKLAWYYEGHGSATVDVDDLMQVGMMALTEAAQRHDRPSDDGFAAYAKM 78

Query: 503 WVKQAITRSIADQSCTIRIPV---HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
            V+ A+   +  QS   R        RD   + +RT      ++ R P   E+A+ + MP
Sbjct: 79  RVRGAMVDLLRGQSHRPRSAAAWTRKRDVAEQTLRT------ELGRAPNAAEMAQAMEMP 132

Query: 560 VEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTRV 616
           ++    + L  +    S++    D DT+   D   D   N ++  DS + A       + 
Sbjct: 133 LDRYESMRLAASTSATSIDECYSDSDTA-FSDNRPDPEANLLASEDSGVLA-------QA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L  R + VL++ F   +N    L E+     V+  R+ Q++A A++K +
Sbjct: 185 IGALPERLQLVLKLYFIEELN----LNEIAAVLGVSVPRVHQLKADALKKAR 232


>gi|310772144|emb|CBX46976.1| RNA polymerase subunit D, sigma factor [Pseudomonas
           cuatrocienegasensis]
          Length = 254

 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 38/137 (27%), Positives = 67/137 (48%), Gaps = 4/137 (2%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           L +L   + L   + D LV ++    +R+   E  +++L  +   + R  FL    G E 
Sbjct: 120 LAELFMPIKLVPKQYDALVVRVRGALERLRAQERAIMQLCVRDARMPRADFLRLFPGNET 179

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           DP W    AK   +G++   +      I + + ++ ++  E  ++++E + I   +  GE
Sbjct: 180 DPTWAEGLAKG--KGKYAEAIGNLQADIQRCQQKLTALEAECDLTLAEIKDINRRMSIGE 237

Query: 439 CEASIAKKEMVEANLRL 455
            +A  AK EMVEANLRL
Sbjct: 238 AKARRAKNEMVEANLRL 254


>gi|321312139|ref|YP_004204426.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|320018413|gb|ADV93399.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 126

 Score = 47.0 bits (110), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 58/109 (53%), Gaps = 6/109 (5%)

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASL 620
           + LK TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E   + +  L
Sbjct: 4   RALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEKVKQYIDIL 61

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 62  DDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 110


>gi|210611678|ref|ZP_03288975.1| hypothetical protein CLONEX_01165 [Clostridium nexile DSM 1787]
 gi|210151925|gb|EEA82932.1| hypothetical protein CLONEX_01165 [Clostridium nexile DSM 1787]
          Length = 254

 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 67/129 (51%), Gaps = 2/129 (1%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++AK  +VE  L  V+ +AK+  +  +   DL+QEGN+GL+   +  D     K      
Sbjct: 120 ALAKSRLVEIYLPEVVEIAKQLYHPEVFLGDLVQEGNVGLILGVDMIDDL--DKAHDVIR 177

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++QAI   I +Q+        M +K++ +  + + ++ ++ R+ T EE+A  + M  E
Sbjct: 178 REIRQAIQMLIEEQTELKNRDKKMVEKVNTLDESIQALTEELGRKVTIEELAVYMGMSEE 237

Query: 562 GVRKVLKIT 570
            V  +L++T
Sbjct: 238 EVEDILRLT 246


>gi|295696140|ref|YP_003589378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411742|gb|ADG06234.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 88/200 (44%), Gaps = 22/200 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL++AA ++D      F  +A   ++ A+   +  +    R      +++ K
Sbjct: 38  DLVSFGMLGLLEAARRYDPGQETPFEVFARLRIRGAMIDGVRAEGPASR---RRWERVKK 94

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT-------KEPISLETPIGDED 584
           V     R+ +K K   + EE+ K+L     GV +   I          PISL+  I  ED
Sbjct: 95  VQEAYERLFSKGK-SGSDEEMCKEL-----GVDRGTFIGWLEEFERFHPISLDRVIHTED 148

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
             +  + D I D   V P  +  +  +R+     + +L  RE+ VL + +  G+    + 
Sbjct: 149 GESFRIADAIPDPEGVDPAQTVSRQAVRQMLAEAITALPEREKYVLSLHYIEGL----SF 204

Query: 643 EEVGKQFCVTRERIRQIEAK 662
            EV     VT  R+ Q+ +K
Sbjct: 205 REVAAVLGVTPARVSQLHSK 224


>gi|307690662|ref|ZP_07633108.1| sporulation sigma factor SigG [Clostridium cellulovorans 743B]
          Length = 139

 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 41/146 (28%), Positives = 74/146 (50%), Gaps = 13/146 (8%)

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  ++ ++   ++  +  +EPT  +IAK+L +  E V   L   +EP+SL  PI  +  
Sbjct: 1   RDIAYRALQVRDKLLTENNKEPTVYQIAKELDVAKEEVIFALDAIQEPVSLFEPIYHDGG 60

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D I D KN    LD +   N+       +  L+ RE+ +L MRF  G     T 
Sbjct: 61  DAIYVMDQISDSKN----LDESWLENI--AIKEAMKRLSDREKLILNMRFFDG----RTQ 110

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            EV  +  +++ ++ ++E  A+R ++
Sbjct: 111 MEVADEIGISQAQVSRLEKNALRHMR 136


>gi|298492777|ref|YP_003722954.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298234695|gb|ADI65831.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 263

 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 29/118 (24%), Positives = 66/118 (55%), Gaps = 1/118 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE +  LV  +A K+ ++  + + DL Q G +GL++A E+F+    Y FS++A+ +
Sbjct: 28  RNQLVEVHKGLVRKMAYKFIHQCNEPYEDLEQIGYLGLIRAIERFNPHQRYAFSSFAIPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           ++  +   + D S  ++IP   ++  +   +  ++ +  + R P   +IA KL + ++
Sbjct: 88  IRGEMLHFLRDHSTLLKIPRRWQELYNAGQKIRKQFTLSLGRPPREIDIATKLNISLQ 145


>gi|221310570|ref|ZP_03592417.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314894|ref|ZP_03596699.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319816|ref|ZP_03601110.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221324095|ref|ZP_03605389.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
          Length = 132

 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 58/109 (53%), Gaps = 6/109 (5%)

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASL 620
           + LK TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E   + +  L
Sbjct: 10  RALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEKVKQYIDIL 67

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 68  DDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 116


>gi|269796407|ref|YP_003315862.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269098592|gb|ACZ23028.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 300

 Score = 46.6 bits (109), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 54/198 (27%), Positives = 87/198 (43%), Gaps = 14/198 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G + L++AA  +D   G  F+ YA   +K A+   +       R     R +  K
Sbjct: 35  DLASAGALALVQAARAYDATTGVPFNRYAAIRIKGAMVDELRSMDWVSR---GARQRARK 91

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGD 590
           +   A  ++  + R PT EEIA  L + V  V    +     + SLE   G      L +
Sbjct: 92  LTTVADELTADLGRAPTREEIAHALGVDVSEVDTAREAAATRVLSLEGYDGA-----LAE 146

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +  +  V P +S I   L E  T + A+++   ER LR         D T+ ++ K   
Sbjct: 147 VLPARE-VGPEESVI---LDERLTYLHAAVSTLPER-LRTVVEQVFFHDRTVTDIAKDMG 201

Query: 651 VTRERIRQIEAKAIRKLK 668
           VT+ R+ Q+ A+A+  L+
Sbjct: 202 VTQSRVSQLRAEAMVLLR 219


>gi|257866395|ref|ZP_05646048.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257873089|ref|ZP_05652742.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
 gi|257800353|gb|EEV29381.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257807253|gb|EEV36075.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
          Length = 235

 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 50/201 (24%), Positives = 88/201 (43%), Gaps = 12/201 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGLM A  KFD      F +YA   +K AI   +   +   +I  +    +++
Sbjct: 35  DLYNIGVIGLMDALRKFDPSKKVPFESYAAIRIKGAIIDEVRKHA---KISRYKMAAVNQ 91

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPI--GDEDTSH 587
             +  + +   +KRE T  EI K+L +    +  + +       +SLE  +    E+   
Sbjct: 92  FYQARQELEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEGMT 151

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D  A +  ++ +    R      +  L  RE+ +L + +      + TL+E+ +
Sbjct: 152 LKDMVRDP-AENVEETLVAEEKRTALVACIKKLGEREQLILSLYY----TEELTLKEIAE 206

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI  K I KL+
Sbjct: 207 ILEVSIPRVSQIHGKTIAKLR 227


>gi|261368117|ref|ZP_05981000.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
 gi|282569875|gb|EFB75410.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
          Length = 147

 Score = 46.6 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 27/61 (44%), Positives = 34/61 (55%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++  NLRLV  V KKY        DLI  G IGL+KA + FD     KFS+YA   ++ A
Sbjct: 58  LIRHNLRLVAHVTKKYFAATASQDDLISIGTIGLIKAVDTFDPVRASKFSSYASRCIENA 117

Query: 508 I 508
           I
Sbjct: 118 I 118


>gi|194365639|ref|YP_002028249.1| RNA polymerase sigma-28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
 gi|194348443|gb|ACF51566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
          Length = 247

 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 103/230 (44%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  E++  +  LV  +A     R    ++  DLIQ G +GL++A+  +D   G  F TYA
Sbjct: 14  AANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYDADQGASFETYA 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ ++   I       R  VH R +      T RR+     R  +  E+A  + MP+
Sbjct: 74  SIRIRGSMIDEIRRGDWVPR-SVHRRAR--DAAATIRRLEQSSGRAASATEVAAAMEMPL 130

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               ++++     + +SLE+ I  ED   L D +  +   +P     +        + + 
Sbjct: 131 PEYLRLMEDAARGQVLSLESRI--EDQGEL-DTV-TQGGPTPQQVLERGEFGRELGKAIG 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ VL + +   +N    L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 HLPEREQLVLSLYYEQELN----LKEIGAVLGVSESRVCQIHGQAVLRLR 232


>gi|314918186|gb|EFS82017.1| sigma-70, region 4 [Propionibacterium acnes HL050PA1]
          Length = 270

 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 91/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGQDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|149908440|ref|ZP_01897103.1| flagellar biosynthesis sigma factor FliA [Moritella sp. PE36]
 gi|149808603|gb|EDM68538.1| flagellar biosynthesis sigma factor FliA [Moritella sp. PE36]
          Length = 241

 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 50/221 (22%), Positives = 96/221 (43%), Gaps = 27/221 (12%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL+ AA  FD   G  F TYA   ++ ++   +       R       
Sbjct: 40  VQLDDLIQSGMIGLLDAARNFDGSKGASFETYAGIRIRGSMIDEMRRGDWVPR------- 92

Query: 528 KIHKVVRTARRMSNKIKREPTPE----EIAKKLAMPVEGVRKVLKITKEPISL---ETPI 580
            +HK  R      ++I+++   +    +IA +L + +     +L        L   +  +
Sbjct: 93  SVHKNGRNIAAAIDRIEKQTGTDAKDTDIAGELGVSLADYHSMLMDVNSGHILAVEDLTV 152

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            +ED        E K++ +P     +   ++     + +L  RE  VL + +   +N   
Sbjct: 153 SNEDAY---SAYEGKSS-TPCAEFSEQRFQQALADCIKTLPERESLVLSLYYDEELN--- 205

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            L E+G+   V+  R+ QI ++A+ ++K      ++ ++LD
Sbjct: 206 -LREIGEVLSVSESRVSQIHSQAMHRVK-----ARMHAWLD 240


>gi|187935345|ref|YP_001885383.1| sporulation sigma factor SigK [Clostridium botulinum B str. Eklund
           17B]
 gi|187723498|gb|ACD24719.1| RNA polymerase sigma-K factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 232

 Score = 46.6 bits (109), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 37/65 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY+       +LI  G +GL+KA + FD   G + +TYA   
Sbjct: 50  AKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIKAIDSFDSGKGTRLATYASRC 109

Query: 504 VKQAI 508
           ++  I
Sbjct: 110 IENEI 114


>gi|206890966|ref|YP_002249859.1| RNA polymerase sigma factor for flagellar operon
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206742904|gb|ACI21961.1| RNA polymerase sigma factor for flagellar operon
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 236

 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 49/206 (23%), Positives = 98/206 (47%), Gaps = 14/206 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L+  DLI  G  GL++A  K++  L      +  + ++ AI   I       +     R 
Sbjct: 34  LELEDLISAGIKGLLEALNKYNPSLNVPLVAFIDYRIRGAILDEIRSVDVFSK---EFRK 90

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITKEPI-SLETPIGDE-- 583
           K+  V +T + +     ++PT EE+A  L +  E +++V + IT   I SL++ +  E  
Sbjct: 91  KVENVKKTYKNLKQS-GKDPTDEELANYLNITQEELQEVYQSITASDIVSLDSFVVGENG 149

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  +L + I D+  +   +      L+E  T  + +L+  E+ ++ + +   +N    ++
Sbjct: 150 DKLNLLEVISDEKNI--FEDIKFRELKEKLTSAIENLSETEKLIISLYYYEELN----MK 203

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+ +   ++  R+ QI  K + KLK+
Sbjct: 204 EIAQVLGISLSRVSQIHGKTLLKLKN 229


>gi|229073422|ref|ZP_04206558.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228709729|gb|EEL61767.1| RNA polymerase sigma factor [Bacillus cereus F65185]
          Length = 301

 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 29/107 (27%), Positives = 53/107 (49%), Gaps = 4/107 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+Q   I ++ A   FD+  G KF+TY    +   I + + + S  +R+     D    
Sbjct: 48  ELLQHAYIAVITAIRDFDFNKGIKFTTYIYRPIIWEINQLLYNDSRLVRLSRSAVD---- 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +++   ++ N++   P  EE+AK L + VE +  VL+   E  SL +
Sbjct: 104 LLKQMEKVENELGYFPKAEELAKLLDVTVERIENVLRFASELTSLNS 150


>gi|182418995|ref|ZP_02950251.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
 gi|182377278|gb|EDT74846.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
          Length = 232

 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 37/65 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY+       +LI  G +GL+KA + FD   G + +TYA   
Sbjct: 50  AKSILIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIKAIDSFDSSKGTRLATYASRC 109

Query: 504 VKQAI 508
           ++  I
Sbjct: 110 IENEI 114


>gi|147677461|ref|YP_001211676.1| hypothetical protein PTH_1126 [Pelotomaculum thermopropionicum SI]
 gi|146273558|dbj|BAF59307.1| hypothetical protein [Pelotomaculum thermopropionicum SI]
          Length = 127

 Score = 46.6 bits (109), Expect = 0.015,   Method: Composition-based stats.
 Identities = 34/108 (31%), Positives = 53/108 (49%), Gaps = 3/108 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           G W   V   V+ +L + + I + +    +S  E    + ++  G  EA   +  + E N
Sbjct: 4   GLWTLTVVSLVNGLLLLVSYIANNTFPQPLSEEEEAKYLKLLNMGNEEA---RNILTERN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           LRLV  + KK+ + G    DLI  G IGL+KA   F+   G + +TYA
Sbjct: 61  LRLVAHIVKKFDSTGEDSDDLISIGTIGLIKAINTFNPGKGTRLATYA 108


>gi|87125785|ref|ZP_01081628.1| putative type III sigma factor [Synechococcus sp. RS9917]
 gi|86166594|gb|EAQ67858.1| putative type III sigma factor [Synechococcus sp. RS9917]
          Length = 262

 Score = 46.6 bits (109), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 451 ANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           ++L L   VA + + RG   + DL+QE ++GL+ A E FD   G++ S+YA+      I 
Sbjct: 36  SHLGLAHHVAGRQSTRGHGDWDDLVQEASLGLIAAVEGFDSSRGHQLSSYAVSRAHGQIL 95

Query: 510 RSIADQSCTIRIPVHMRD 527
               D+  TIRIP  +R 
Sbjct: 96  HFRRDRQSTIRIPWRLRS 113


>gi|148793328|gb|ABR12728.1| RNA polymerase sigma factor [Photobacterium leiognathi]
          Length = 283

 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 79/172 (45%), Gaps = 17/172 (9%)

Query: 289 EVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E + ELR+  D        NG++D+++ +      E+L ++     L   + D LV  L 
Sbjct: 120 EKFLELRNAYDKMALAIDTNGRQDKQTEIAV----EELSEVFKQFRLIPKQFDRLVSSLR 175

Query: 344 DISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   ++  NE  ++R+   +  + +  F+    G E +  W+  A +  +   +     E
Sbjct: 176 DAMDKVRTNERLIMRMCVDNSKMPKKTFVTLFAGNEANQDWIDEALNSGKPYAERLKTYE 235

Query: 403 VD---SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            D   S +K+R     +  ETG+SI   + I   +  GE +A  AKKEMVEA
Sbjct: 236 EDLRRSAIKLR----MLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEA 283



 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 29/43 (67%)

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+
Sbjct: 1   REMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLL 43


>gi|149184196|ref|ZP_01862514.1| sigma 28 (Flagella/Sporulation) [Erythrobacter sp. SD-21]
 gi|148831516|gb|EDL49949.1| sigma 28 (Flagella/Sporulation) [Erythrobacter sp. SD-21]
          Length = 241

 Score = 46.6 bits (109), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 91/198 (45%), Gaps = 14/198 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G I L + A++ +      F+ YA   V+ A+   +   S  +R    +R K+  
Sbjct: 48  DLLQAGMIALTECAQRHERPSEDGFAAYAKMRVRGAMIDLLRSNSHHVRGAAALRRKMDA 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGD 590
                RR   +  R+P+ +E+A  L M  E  +K   ++    + L+    D D +    
Sbjct: 108 ATDELRR---QFGRDPSGDEVALFLGMTPEDYQKARNRVATRMVDLQDCYSDSDPAFA-- 162

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             E+ +A   L    QA+ +    + +A+L  R + V+++ F   +N    L E+     
Sbjct: 163 -TEEPDAEEQL--VAQAD-KTALAQAIANLPERLQLVIQLHFLEELN----LTEIAAVLE 214

Query: 651 VTRERIRQIEAKAIRKLK 668
           V+  R+ Q++A A+ KLK
Sbjct: 215 VSVPRVHQLKANALDKLK 232


>gi|258655075|ref|YP_003204231.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258558300|gb|ACV81242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 308

 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 91/212 (42%), Gaps = 10/212 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++++V   + +  S+A +Y+ RG++  DL Q   +GL+KA +++       F  +A+  +
Sbjct: 89  QQQVVTEYIPVARSLAARYSGRGVERSDLEQLAYMGLIKAVQRWRPGRSDDFLQFAVPTI 148

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
              I R   D S  +R P  +++    +    +   ++  R P+  E+AK     V  + 
Sbjct: 149 VGEIKRYFRDHSWLVRPPRRIQELRAAISEAEQSQRHQDGRAPSDAELAKATGATVTDID 208

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +       P SL+   G      L    ED       D       R T  R+L +LT 
Sbjct: 209 EARAAAACCRPRSLDEEQGPGLALALSWGEEDAELRRVED-------RATVERLLDALTD 261

Query: 623 REERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
           RE  V+ MRF  G +      E+G  Q  V+R
Sbjct: 262 RERDVVHMRFDNGWSQSRIGREIGVSQMQVSR 293


>gi|228962768|ref|ZP_04124034.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228796921|gb|EEM44265.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 225

 Score = 46.2 bits (108), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 24/99 (24%), Positives = 53/99 (53%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV S+A +Y+       D +Q G +GL+ A  ++D  L  +F  + +  +   + + + D
Sbjct: 6   LVHSLAYRYSKGNASHEDFVQIGMLGLLGAIRRYDTSLKKEFEAFLIPTIMGEMKKYLRD 65

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++  + +P  ++DK   + +T   +++ ++R P  +EIA
Sbjct: 66  KTWDVHVPRRIKDKSSTLKKTIEILTSTLQRSPQIQEIA 104


>gi|223984440|ref|ZP_03634576.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
 gi|223963596|gb|EEF67972.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
          Length = 232

 Score = 46.2 bits (108), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 32/57 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  ++E NLRLV+ +AK+Y    +   DLI  G IGL+KA   F      K  TYA
Sbjct: 52  ARDTLIEHNLRLVVYIAKRYETNPIFMEDLISIGTIGLIKAVNTFKRDKNIKLVTYA 108


>gi|150015999|ref|YP_001308253.1| sporulation sigma factor SigK [Clostridium beijerinckii NCIMB 8052]
 gi|149902464|gb|ABR33297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 232

 Score = 46.2 bits (108), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 51/221 (23%), Positives = 91/221 (41%), Gaps = 59/221 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV  + KKY+       +LI  G +GL+KA + FD   G + +TYA   
Sbjct: 50  AKSILIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIKAIDSFDAGKGTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                +R I ++             I  + R +++                         
Sbjct: 107 -----SRCIENE-------------ILMLFRNSKK------------------------- 123

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLA 618
                  K  + L+ PIG +   +   L D +  E  + +  ++S +Q  +R    +++ 
Sbjct: 124 ------QKSEVYLQDPIGVDKEGNEFCLMDILSSEKDSVLEKVESNLQ--VRALYKKLIE 175

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           SLT RE  ++ MR+G+      T  E+     ++R  + +I
Sbjct: 176 SLTKRESAIIIMRYGLIDGKCKTQREIAVNLGISRSYVSRI 216


>gi|317970333|ref|ZP_07971723.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 202

 Score = 46.2 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQ-----FLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           A+ ++V  NL LV    +K  + GL        D +QE  + L++AAEKFD    Y+FST
Sbjct: 54  ARDQLVRHNLALVGFTWRK-QHSGLSPEDAATADALQEAALNLLRAAEKFDPTRSYRFST 112

Query: 499 YAMWWVKQAITR 510
           YA +W+++ + R
Sbjct: 113 YASFWIRRGLLR 124


>gi|190574220|ref|YP_001972065.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
 gi|190012142|emb|CAQ45765.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
          Length = 247

 Score = 46.2 bits (108), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 103/230 (44%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  E++  +  LV  +A     R    ++  DLIQ G +GL++A+  +D   G  F TYA
Sbjct: 14  AANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYDADQGASFETYA 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ ++   I       R  VH R +      T RR+     R  +  E+A  + MP+
Sbjct: 74  SIRIRGSMIDEIRRGDWVPR-SVHRRAR--DAAATIRRLEQSSGRAASATEVAAAMEMPL 130

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               ++++     + +SLE+ I  ED   L D +  +   +P     +        + + 
Sbjct: 131 PEYLRLMEDAARGQVLSLESRI--EDQGEL-DTVA-QGGPTPQQVLERGEFGRELGKAIG 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ VL + +   +N    L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 HLPEREQLVLSLYYEQELN----LKEIGAVLGVSESRVCQIHGQAVLRLR 232


>gi|108756900|ref|YP_630657.1| FliA/WhiG family RNA polymerase sigma factor [Myxococcus xanthus DK
           1622]
 gi|108460780|gb|ABF85965.1| RNA polymerase sigma factor, FliA/WhiG/SigD family [Myxococcus
           xanthus DK 1622]
          Length = 278

 Score = 46.2 bits (108), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 55/216 (25%), Positives = 90/216 (41%), Gaps = 22/216 (10%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +R + +  +K  N  L+  +L+  G IGL++AAE+FD  +G  F T+A + +K AI   +
Sbjct: 18  VRSLAATVRKQFNAQLELDELLAYGQIGLLEAAERFDPKVGANFLTFAHYRIKGAIFDGL 77

Query: 513 ADQSCTIRIPVHMRDKIHKVV--RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
                     +   D  +  V  R A  + N   RE             V  +     +T
Sbjct: 78  RKMGV-----LRGSDARNAYVGERAAAYLGNLSDREAGAGNRGSSFDDDVNDISDA--VT 130

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL--TPREERVL 628
              +   T I   DT+   D         P+D  I+    +  TRV A++   P +ER L
Sbjct: 131 GLAMVFATSIEGADTAGYTD------ESLPVD--IRMEQEQLKTRVRAAIEKLPEKERKL 182

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            M +        TLEE G +   ++    ++ A+AI
Sbjct: 183 LMGY---YFQGRTLEEAGAEIGQSKSWASRLHARAI 215


>gi|225568718|ref|ZP_03777743.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
 gi|225162217|gb|EEG74836.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
          Length = 189

 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 3/98 (3%)

Query: 574 ISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +SL  PIG +   +   L D IE     +    A++ ++R    +V   L+ RE  VL+M
Sbjct: 89  VSLYEPIGTDREGNEIQLFDIIETDEDDAHRKVALKDDIRLLYEKVEGELSQRERLVLKM 148

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+G+    ++T  E+ ++  ++R  + +IE  AI KL+
Sbjct: 149 RYGLYNEEEYTQREIARRLGISRSYVSRIEKSAIEKLR 186



 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 4/67 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF--DWCLGYKFSTYAM 501
           AK  ++E NLRLV  + KKY +      DL+  G IGL+KA   F  D C+  +  TYA 
Sbjct: 11  AKHVLIERNLRLVAHIVKKYQSLEEDNEDLLSIGTIGLIKAVVTFNPDKCV--RLGTYAA 68

Query: 502 WWVKQAI 508
             ++  I
Sbjct: 69  RCIENEI 75


>gi|160934631|ref|ZP_02082017.1| hypothetical protein CLOLEP_03504 [Clostridium leptum DSM 753]
 gi|156866084|gb|EDO59456.1| hypothetical protein CLOLEP_03504 [Clostridium leptum DSM 753]
          Length = 251

 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 57/244 (23%), Positives = 102/244 (41%), Gaps = 52/244 (21%)

Query: 444 AKKEMVEANLRLVISVAK-KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           AKK ++E   + V  + K K+ +    + DL Q G  GL+KA E +D     K +TY  +
Sbjct: 24  AKKAVIEDYSKFVSYIIKEKFYSYRKHWEDLFQCGICGLLKALENYDPHFS-KPTTYFYY 82

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVR-TARRMSNKIKR--------------EP 547
           ++ Q I                  D I K +  T R  S K+K               EP
Sbjct: 83  FIVQEIN-----------------DFISKYIEGTNRYYSRKVKSLDESILKLKRSGIPEP 125

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISL----ETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  E+AK + +     R +++I    +PISL    E+ +  ++ +++   +E +      
Sbjct: 126 SARELAKVMNLKETSARNLIRIKHISQPISLDYLIESNLLKDNQTYVEVLVEKRM----- 180

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  L+E   + + SL   E++V+  +FG+  +T  T +E+     +    I     
Sbjct: 181 -------LKEILEKAVFSLPKNEKKVIERKFGLFGHTKMTNQEISVDTGIPSNMINYYFK 233

Query: 662 KAIR 665
           K +R
Sbjct: 234 KGVR 237


>gi|88808533|ref|ZP_01124043.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88787521|gb|EAR18678.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 198

 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V+ +L+LV  +A+ Y  R G+   DL Q G +GL++AAE F+      F  +A   
Sbjct: 8   RNQRVKDHLQLVTPIARHYAQRCGIDADDLRQVGLMGLLRAAENFNTERCTPFKAFARPH 67

Query: 504 VKQAITRSIADQSCTIRIP 522
           ++ AI   + D +  +R P
Sbjct: 68  IRGAILHYLRDNASVVRFP 86


>gi|218132995|ref|ZP_03461799.1| hypothetical protein BACPEC_00856 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991868|gb|EEC57872.1| hypothetical protein BACPEC_00856 [Bacteroides pectinophilus ATCC
           43243]
          Length = 306

 Score = 46.2 bits (108), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 37/167 (22%), Positives = 72/167 (43%), Gaps = 20/167 (11%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRL-VISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           R   +++ +  C+  +  + ++  N  L V+   K Y  +G+  +DLIQE N+ +M    
Sbjct: 133 RTTQAVILQDVCDKDVESRGVIINNYFLQVVEWVKAYAGKGVAMMDLIQEANVIVMDELG 192

Query: 487 KFDWC-------------------LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + DW                    L  +   Y +  VK+ I + I +Q+        +  
Sbjct: 193 RRDWMKRLDAFDVMDSDDINAWTDLSERLDAYLIDRVKEGIGKLIEEQTDEKMAGNKILA 252

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           K++ V   A     +  R+ T EE+A+ + +P E V + L+++   I
Sbjct: 253 KVNAVNDAAEAAHKEYGRKVTVEELAQFMHVPAEDVSEALRLSANRI 299


>gi|333024157|ref|ZP_08452221.1| putative RNA polymerase sigma factor WhiG [Streptomyces sp. Tu6071]
 gi|332744009|gb|EGJ74450.1| putative RNA polymerase sigma factor WhiG [Streptomyces sp. Tu6071]
          Length = 123

 Score = 46.2 bits (108), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 52/102 (50%), Gaps = 11/102 (10%)

Query: 580 IGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +G E    L   D +ED  A +P++ A    LR+  +R + SL  RE+ V+ + +  G+ 
Sbjct: 29  VGSEGGGRLSIMDTLEDTGADNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYYEGL- 87

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              TL E+G    VT  R+ QI  K++ +L+      KL SF
Sbjct: 88  ---TLAEIGHVLGVTESRVSQIHTKSVLQLR-----AKLSSF 121


>gi|260886518|ref|ZP_05897781.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|330839639|ref|YP_004414219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863661|gb|EEX78161.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|329747403|gb|AEC00760.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 208

 Score = 45.8 bits (107), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A++ ++E+   LV   A  +       +D+IQEG +GL++AAE FDW  G  FS +A+
Sbjct: 36  ARQRLIESYQPLVFKTALPW-RMSESIMDIIQEGTVGLIEAAENFDWKRGVAFSLFAV 92


>gi|289425371|ref|ZP_06427148.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289427143|ref|ZP_06428859.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|295130519|ref|YP_003581182.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|289154349|gb|EFD03037.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289159612|gb|EFD07800.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|291375175|gb|ADD99029.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|313764535|gb|EFS35899.1| sigma-70, region 4 [Propionibacterium acnes HL013PA1]
 gi|313772426|gb|EFS38392.1| sigma-70, region 4 [Propionibacterium acnes HL074PA1]
 gi|313792224|gb|EFS40325.1| sigma-70, region 4 [Propionibacterium acnes HL110PA1]
 gi|313801827|gb|EFS43061.1| sigma-70, region 4 [Propionibacterium acnes HL110PA2]
 gi|313807437|gb|EFS45924.1| sigma-70, region 4 [Propionibacterium acnes HL087PA2]
 gi|313809944|gb|EFS47665.1| sigma-70, region 4 [Propionibacterium acnes HL083PA1]
 gi|313813018|gb|EFS50732.1| sigma-70, region 4 [Propionibacterium acnes HL025PA1]
 gi|313816077|gb|EFS53791.1| sigma-70, region 4 [Propionibacterium acnes HL059PA1]
 gi|313818482|gb|EFS56196.1| sigma-70, region 4 [Propionibacterium acnes HL046PA2]
 gi|313825126|gb|EFS62840.1| sigma-70, region 4 [Propionibacterium acnes HL063PA1]
 gi|313827695|gb|EFS65409.1| sigma-70, region 4 [Propionibacterium acnes HL063PA2]
 gi|313830275|gb|EFS67989.1| sigma-70, region 4 [Propionibacterium acnes HL007PA1]
 gi|313834076|gb|EFS71790.1| sigma-70, region 4 [Propionibacterium acnes HL056PA1]
 gi|313838653|gb|EFS76367.1| sigma-70, region 4 [Propionibacterium acnes HL086PA1]
 gi|314915531|gb|EFS79362.1| sigma-70, region 4 [Propionibacterium acnes HL005PA4]
 gi|314920001|gb|EFS83832.1| sigma-70, region 4 [Propionibacterium acnes HL050PA3]
 gi|314932014|gb|EFS95845.1| sigma-70, region 4 [Propionibacterium acnes HL067PA1]
 gi|314955884|gb|EFT00284.1| sigma-70, region 4 [Propionibacterium acnes HL027PA1]
 gi|314958197|gb|EFT02300.1| sigma-70, region 4 [Propionibacterium acnes HL002PA1]
 gi|314960081|gb|EFT04183.1| sigma-70, region 4 [Propionibacterium acnes HL002PA2]
 gi|314962882|gb|EFT06982.1| sigma-70, region 4 [Propionibacterium acnes HL082PA1]
 gi|314967752|gb|EFT11851.1| sigma-70, region 4 [Propionibacterium acnes HL037PA1]
 gi|314973281|gb|EFT17377.1| sigma-70, region 4 [Propionibacterium acnes HL053PA1]
 gi|314975956|gb|EFT20051.1| sigma-70, region 4 [Propionibacterium acnes HL045PA1]
 gi|314978286|gb|EFT22380.1| sigma-70, region 4 [Propionibacterium acnes HL072PA2]
 gi|314984025|gb|EFT28117.1| sigma-70, region 4 [Propionibacterium acnes HL005PA1]
 gi|314988208|gb|EFT32299.1| sigma-70, region 4 [Propionibacterium acnes HL005PA2]
 gi|314990010|gb|EFT34101.1| sigma-70, region 4 [Propionibacterium acnes HL005PA3]
 gi|315078096|gb|EFT50147.1| sigma-70, region 4 [Propionibacterium acnes HL053PA2]
 gi|315080726|gb|EFT52702.1| sigma-70, region 4 [Propionibacterium acnes HL078PA1]
 gi|315084397|gb|EFT56373.1| sigma-70, region 4 [Propionibacterium acnes HL027PA2]
 gi|315085736|gb|EFT57712.1| sigma-70, region 4 [Propionibacterium acnes HL002PA3]
 gi|315088845|gb|EFT60821.1| sigma-70, region 4 [Propionibacterium acnes HL072PA1]
 gi|315096194|gb|EFT68170.1| sigma-70, region 4 [Propionibacterium acnes HL038PA1]
 gi|315098455|gb|EFT70431.1| sigma-70, region 4 [Propionibacterium acnes HL059PA2]
 gi|327326110|gb|EGE67900.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA2]
 gi|327332019|gb|EGE73756.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA3]
 gi|327443222|gb|EGE89876.1| sigma-70, region 4 [Propionibacterium acnes HL013PA2]
 gi|327446006|gb|EGE92660.1| sigma-70, region 4 [Propionibacterium acnes HL043PA2]
 gi|327448014|gb|EGE94668.1| sigma-70, region 4 [Propionibacterium acnes HL043PA1]
 gi|327450862|gb|EGE97516.1| sigma-70, region 4 [Propionibacterium acnes HL087PA3]
 gi|327453061|gb|EGE99715.1| sigma-70, region 4 [Propionibacterium acnes HL092PA1]
 gi|327453790|gb|EGF00445.1| sigma-70, region 4 [Propionibacterium acnes HL083PA2]
 gi|328753549|gb|EGF67165.1| sigma-70, region 4 [Propionibacterium acnes HL020PA1]
 gi|328754281|gb|EGF67897.1| sigma-70, region 4 [Propionibacterium acnes HL087PA1]
 gi|328754466|gb|EGF68082.1| sigma-70, region 4 [Propionibacterium acnes HL025PA2]
 gi|328760671|gb|EGF74238.1| RNA polymerase sigma factor [Propionibacterium acnes HL099PA1]
          Length = 270

 Score = 45.8 bits (107), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 91/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|169834851|ref|YP_001715950.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
 gi|169408958|gb|ACA57368.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
          Length = 271

 Score = 45.8 bits (107), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 56/253 (22%), Positives = 110/253 (43%), Gaps = 33/253 (13%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN----RGLQFLDLIQEGNIGLMK 483
           R ++   +K   E+   K+E+++    L++    KY      +G++F DL+ +  +G +K
Sbjct: 21  RDLIIGSQKNNKESEKYKEELLKRYEGLIVQWTNKYFKILNVQGMEFDDLLIDAKLGFLK 80

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G   STYA   ++  I  SI   +  I++             ++R ++ +I
Sbjct: 81  ALEKFDINKGNALSTYATHCMRNYILNSIRVNNNMIKL-------------SSREVNKRI 127

Query: 544 KREPTPEEIAKKLAMPV--EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA---V 598
           K       ++KK    +  +G  K        I  +  +   DT     ++++ +    +
Sbjct: 128 K-------LSKKFKANILNKGNYKFNYNIYNKIFSQHNVRLIDTHEYQSYLDNSSIEQEI 180

Query: 599 SPLDSAIQANLRETTTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           S  +  ++   +   TR + S    L   E  ++   FG+      TL E+ K+  +  E
Sbjct: 181 SSEEMFMEKEQKRFNTRQIISALKILDKTELFIIVHYFGLFNKKKRTLRELSKRLNIGYE 240

Query: 655 RIRQIEAKAIRKL 667
             R+I+ KA+ K+
Sbjct: 241 NTRKIKGKALSKI 253


>gi|315108409|gb|EFT80385.1| sigma-70, region 4 [Propionibacterium acnes HL030PA2]
          Length = 270

 Score = 45.8 bits (107), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 91/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|134298777|ref|YP_001112273.1| sigma-70 region 4 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051477|gb|ABO49448.1| sigma-70 region 4 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 10/109 (9%)

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT---TRVL---A 618
           + +K  K  +SL  PIG +   +    I+    +   D  + A+  E+T    R+L    
Sbjct: 4   RFIKKVKAEVSLYDPIGVDKEGNEISLID----ILGTDPEVVADTVESTFEKNRLLEKIT 59

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LT RE+RVL MRFG+G     T  E+ +   ++R  + +IE +A+ KL
Sbjct: 60  KLTTREKRVLEMRFGLGTTARKTQREIARTLGISRSYVSRIEKRALNKL 108


>gi|50842442|ref|YP_055669.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|50840044|gb|AAT82711.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|315105463|gb|EFT77439.1| sigma-70, region 4 [Propionibacterium acnes HL030PA1]
          Length = 270

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 91/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|143644|gb|AAA22805.1| spoIIIC peptide [Bacillus subtilis]
 gi|1303719|dbj|BAA12375.1| SpoIIIC [Bacillus subtilis]
          Length = 138

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 58/109 (53%), Gaps = 6/109 (5%)

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASL 620
           + LK TK+ +SL  PIG +   +   L D ++ +N    +   IQ N+  E   + +  L
Sbjct: 16  RALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSEN--EDVIDTIQLNMELEKVKQYIDIL 73

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 74  DDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 122


>gi|149194332|ref|ZP_01871429.1| flagellar biosynthesis sigma factor [Caminibacter mediatlanticus
           TB-2]
 gi|149135507|gb|EDM23986.1| flagellar biosynthesis sigma factor [Caminibacter mediatlanticus
           TB-2]
          Length = 228

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 55/202 (27%), Positives = 91/202 (45%), Gaps = 19/202 (9%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            + F DL+  G   L+K A+++D  +   F  YA   +  A+   +       R    + 
Sbjct: 40  SVDFNDLVSIGYEELVKLAKRYDSSINDNFWGYAQKRINGAMLDFLRSLDTVSRGDRKLI 99

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            +I K++   R MSN    EP  EEIA  L + V  V+K  + + E  S+  PI D+   
Sbjct: 100 KEIDKIIE--RYMSNH-GYEPDDEEIATILDVDVSKVKKA-RQSNEIYSV-MPIEDQ--- 151

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L  F +    V       Q  L E    +L  L  +E+ ++++ +   M    +L+E+ 
Sbjct: 152 -LNYFDDVSKKVE------QDELIEKIEEILNDLGEKEQLIIQLYYFEEM----SLKEIS 200

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   VT  R+ QI  K I+KL+
Sbjct: 201 EILGVTESRVSQIHKKVIKKLR 222


>gi|91794980|ref|YP_564631.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91716982|gb|ABE56908.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 236

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 47/197 (23%), Positives = 92/197 (46%), Gaps = 16/197 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q G + L++++ ++       F ++A   ++ AI   +  Q    R PV  R + H 
Sbjct: 53  DMEQIGMMALIESSRRYPGEFDNGFISFAGQRIRGAILDELRRQDWRPR-PV--RQQAHI 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    R +S  + REPT  E+A  L +  E  R+ L  T+     E+    ++   +G+ 
Sbjct: 110 LNDKVRELSRTLGREPTDTEVATGLGLSPEAYRESLYATQA----ESMKSLDEMLTIGEQ 165

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             DK+     +   +  L++T  + +  L  RE+ +L + +   +N    L+E+     +
Sbjct: 166 PADKH-----NEVERFMLKKTLIKAMTKLNEREQLILSLYYHHELN----LKEIALTLGL 216

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI Q+  +A+ KL+
Sbjct: 217 TETRICQLHKQAVAKLQ 233


>gi|158340150|ref|YP_001521320.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158310391|gb|ABW32006.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 508

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 36/145 (24%), Positives = 74/145 (51%), Gaps = 7/145 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A +++++     +++ +++Y +R +    L+  G   +  AA+K+D   G++F TY  W 
Sbjct: 94  ALRQLIKEYKGFIVTASQRY-DRSIDRQALVCSGEAAVDIAAKKYDESKGHRFITYFSWV 152

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I +    ++   R    +   +  V   A  ++N + REP+ EEIA++  + V+ V
Sbjct: 153 LRTEIQKRYCSEAGISR---EVSRNVSAVNEAAAFLTNALGREPSVEEIAEQSNLTVQTV 209

Query: 564 RKVL--KITKEPISLETPIGDEDTS 586
              L  K   + +SL   I DED++
Sbjct: 210 LNALMAKNFTQSLSLSGLI-DEDST 233


>gi|94495423|ref|ZP_01302003.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
 gi|94424811|gb|EAT09832.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
          Length = 243

 Score = 45.8 bits (107), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G + L++AA  F+   G  F+ YA   V+ A+   +  Q+   R  +  R +I  
Sbjct: 51  DLLQIGMVALVEAANSFE-DRGLGFAAYAQLRVRGAMIDHLRRQATLCRSAMARRKEIAG 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V     R+  ++ R PT  E++ ++ +     R+     +    ++    DE  S    +
Sbjct: 110 V---RNRLEQQLGRLPTEAEMSSEMGLEPAAYREAADSVE---MVQHTSMDEVYSDQSMW 163

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D       D A Q   RE+  + +A+    L  RE  VL++ F   MN    LEE+G+
Sbjct: 164 FADVE-----DRADQVLERESLKKAMAACISELPQREAMVLQLYFVEEMN----LEEIGQ 214

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSR 672
              +   R+ QI+  A+ KL+   R
Sbjct: 215 TLDIGAARVCQIKKAALDKLREKLR 239


>gi|261366886|ref|ZP_05979769.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282571000|gb|EFB76535.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 237

 Score = 45.8 bits (107), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 35/65 (53%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  NLRLV+ +AKK+        D+I  G IGL+KA   F+     K +TYA   
Sbjct: 56  ARDLLITHNLRLVVYIAKKFETPSAGIEDMISIGTIGLIKAVNTFEPSKNIKLATYASRC 115

Query: 504 VKQAI 508
           ++  I
Sbjct: 116 IENEI 120



 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SA +A LR    R    L PRE R++ +RFG+   ++HT +EV     +++  I ++E +
Sbjct: 169 SAERAALRLAVGR----LAPRERRIMELRFGLNHESEHTQKEVADALGISQSYISRLEKR 224

Query: 663 AIRKLK 668
            I++L+
Sbjct: 225 IIKRLR 230


>gi|169835541|ref|ZP_02868729.1| hypothetical protein cdivTM_00208 [candidate division TM7
           single-cell isolate TM7a]
          Length = 45

 Score = 45.8 bits (107), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 26/32 (81%)

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           N  HTL+E+G+Q  +TRER+RQIE KAI KLK
Sbjct: 4   NKIHTLKEIGEQMGITRERVRQIEKKAITKLK 35


>gi|228969112|ref|ZP_04130026.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228790601|gb|EEM38288.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
          Length = 301

 Score = 45.8 bits (107), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 28/107 (26%), Positives = 53/107 (49%), Gaps = 4/107 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+Q   I ++ A   FD+  G KF+TY    +   + + + + S  +R+     D    
Sbjct: 48  ELLQHAYIAVITAIRDFDFNKGIKFTTYIYRPIIWEVNQLLYNDSRLVRLSRSAVD---- 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +++   ++ N++   P  EE+AK L + VE +  VL+   E  SL +
Sbjct: 104 LLKQMEKVENELGYFPKAEELAKLLDVTVERIENVLRFASELTSLNS 150


>gi|323702293|ref|ZP_08113959.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532783|gb|EGB22656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 121

 Score = 45.8 bits (107), Expect = 0.024,   Method: Composition-based stats.
 Identities = 34/108 (31%), Positives = 52/108 (48%), Gaps = 3/108 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           G W   V   V+  L + + I + +    ++  E  + +  + KG+     A+  +VE N
Sbjct: 4   GLWTVTVLSVVNGALALVSYITNNTFPQPLTEEEEAYYLEQLAKGD---ESARNVLVERN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           LRLV  + KK+   G    DLI  G IGL+KA   F    G + +TYA
Sbjct: 61  LRLVAHIVKKFDQTGEDVDDLISIGAIGLIKAINTFKTDKGTRLATYA 108


>gi|113954672|ref|YP_730552.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113882023|gb|ABI46981.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 218

 Score = 45.8 bits (107), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 49/93 (52%), Gaps = 1/93 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + +E +L+LV  +A  Y  R GL   DL Q G +GL++AAE ++      F  YA   
Sbjct: 8   RNQRIERHLKLVDPIAGHYAKRSGLDRDDLKQVGMLGLLRAAEGYEQGQEKPFEVYARPH 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           ++ AI   + D    +R+P  ++++    ++ +
Sbjct: 68  IRGAILHYLRDSVGLVRLPRRLQEQAQNTIKNS 100


>gi|327330175|gb|EGE71924.1| RNA polymerase sigma factor [Propionibacterium acnes HL097PA1]
          Length = 270

 Score = 45.8 bits (107), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 91/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|153955577|ref|YP_001396342.1| RNA polymerase sigma factor-related protein [Clostridium kluyveri
           DSM 555]
 gi|146348435|gb|EDK34971.1| RNA polymerase sigma factor-related protein [Clostridium kluyveri
           DSM 555]
          Length = 235

 Score = 45.8 bits (107), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 54/233 (23%), Positives = 93/233 (39%), Gaps = 61/233 (26%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDW-----CLGYKFST 498
           +++E N  +V   A ++       +D   L QEG +GLM AA+K+ +     C   KFST
Sbjct: 20  KLIELNKGIVYKFANRFYTEKTNSIDKEDLKQEGFMGLMVAADKYKFNIEKPC---KFST 76

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA++W+   + R I  ++      +++                     P   +   +   
Sbjct: 77  YAVYWIYHKMNRFIKSKNTNEETSLNI---------------------PNSSDGDIEFMD 115

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +EGV                 G E+       +EDK      +  +   L E   R   
Sbjct: 116 CIEGV---------------DYGFEN-------VEDK----IYNEQLHRELEEVMAR-YN 148

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +L  RE  +L+ R+G       T  ++G+ + VTR +I  IE  A+ K++  S
Sbjct: 149 TLKERE--ILKFRYGWDNYKCMTCGQIGEIYNVTRSKINNIEHTALGKIRRSS 199


>gi|254431663|ref|ZP_05045366.1| group3 RNA polymerase sigma factor SigF1 [Cyanobium sp. PCC 7001]
 gi|197626116|gb|EDY38675.1| group3 RNA polymerase sigma factor SigF1 [Cyanobium sp. PCC 7001]
          Length = 257

 Score = 45.8 bits (107), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 47/196 (23%), Positives = 86/196 (43%), Gaps = 20/196 (10%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKF 496
           +C A  A+   VE    LV  +A  Y +R  + LD LIQ G +GL++AAE +       F
Sbjct: 14  DCRAIQARNRRVEQYKALVRPIALHYHHRCSEPLDDLIQVGLMGLLRAAELYRPSTATPF 73

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
             +A   V+ A+   + D +  IR+P  + ++  ++ R          R  T +E+ + L
Sbjct: 74  EAFARPHVRGALLHYLRDVALPIRLPRRLDEQRLQLARLRSSWLAAHHRPATEQELRQLL 133

Query: 557 AM------PVEGVRKVLKITK---------EPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +       ++   +++++           EP   ET  G  D        E+ +A + L
Sbjct: 134 GLDQSHWNRLQAAEQLVRVQSLDFWLDDGGEPPCAETETGPADPCR----GEEASAPAAL 189

Query: 602 DSAIQANLRETTTRVL 617
            + ++  LR+   RV+
Sbjct: 190 LAGLEEPLRQVVERVI 205


>gi|295094135|emb|CBK83226.1| RNA polymerase sigma factor, sigma-70 family [Coprococcus sp.
           ART55/1]
          Length = 220

 Score = 45.8 bits (107), Expect = 0.026,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 105/248 (42%), Gaps = 50/248 (20%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVA-KKYTNRGLQ-------FLDLIQEGNIG 480
            +  + +KG+   + A+  ++E NL  +  +A ++Y N GL          DL+QEG+IG
Sbjct: 8   QLCRLAQKGD---TAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIG 64

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+ A   FD   G KF TYA   ++ A+T       C IR  + + ++         RM 
Sbjct: 65  LLNAIPLFDAGRGMKFLTYAAPALRNAMT------DC-IRAALGLFEQ---------RMV 108

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           +K K  P              G ++V         L+  + +++     + I D +  +P
Sbjct: 109 DK-KDAP--------------GFQRVY--------LDDVLSEDERMLRIEAIADPHTQTP 145

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               IQ          L  LT RE+  L  R+G     +H L      F ++  R +++E
Sbjct: 146 EQIYIQKEQLIELYAALDKLTAREQTYLLYRYGFTDGIEHPLIGAALHFHLSESRTKKVE 205

Query: 661 AKAIRKLK 668
            +A+  L+
Sbjct: 206 GEAMDSLR 213


>gi|87303692|ref|ZP_01086467.1| group3 RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87281797|gb|EAQ73762.1| group3 RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 267

 Score = 45.8 bits (107), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V  +L LV  +A  Y++   +  D L Q G +GL++AAE F    G  F  +A   
Sbjct: 23  RNDRVARHLELVRPIAHHYSSLCREGRDDLTQVGLLGLLRAAELFQSDQGTPFEAFARHH 82

Query: 504 VKQAITRSIADQSCTIRIPVHMRD 527
           ++ AI   + DQ+  IR+P   R+
Sbjct: 83  IRGAILHYLRDQAPVIRLPRRQRE 106


>gi|229587513|ref|YP_002860551.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
 gi|229260138|gb|ACQ51175.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
          Length = 271

 Score = 45.8 bits (107), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 56/253 (22%), Positives = 110/253 (43%), Gaps = 33/253 (13%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN----RGLQFLDLIQEGNIGLMK 483
           R ++   +K   E+   K+E+++    L++    KY      +G++F DL+ +  +G +K
Sbjct: 21  RDLIIGSQKNNKESEKYKEELLKRYEGLIVQWTNKYFKILNVQGMEFDDLLIDAKLGFLK 80

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G   STYA   ++  I  SI   +  I++             ++R ++ +I
Sbjct: 81  ALEKFDINKGNALSTYATHCMRNYILNSIRVNNNMIKL-------------SSREVNKRI 127

Query: 544 KREPTPEEIAKKLAMPV--EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA---V 598
           K       ++KK    +  +G  K        I  +  +   DT     ++++ +    +
Sbjct: 128 K-------LSKKFKANILNKGNYKFNYNIYNKIFSQHNVRLIDTHEYQSYLDNSSIEQEI 180

Query: 599 SPLDSAIQANLRETTTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           S  +  ++   +   TR + S    L   E  ++   FG+      TL E+ K+  +  E
Sbjct: 181 SSEEMFMEKEQKRFNTRQIISALKILDKTELFIIVHYFGLFNKKKRTLRELSKRLNIGYE 240

Query: 655 RIRQIEAKAIRKL 667
             R+I+ KA+ K+
Sbjct: 241 NTRKIKGKALSKI 253


>gi|153815652|ref|ZP_01968320.1| hypothetical protein RUMTOR_01888 [Ruminococcus torques ATCC 27756]
 gi|145847083|gb|EDK24001.1| hypothetical protein RUMTOR_01888 [Ruminococcus torques ATCC 27756]
          Length = 114

 Score = 45.8 bits (107), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 50/98 (51%), Gaps = 3/98 (3%)

Query: 574 ISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           ISL  PIG +   +   L D IE           ++ N++    +V   L+ RE  +L+M
Sbjct: 13  ISLYEPIGTDREGNEIKLYDIIETDEEEVAEKIHLKENIQTLYEKVEKELSQRERIILKM 72

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+G+    ++T  E+ +Q  ++R  + +IE  A+ KL+
Sbjct: 73  RYGLYNGEEYTQREIARQLGISRSYVSRIEKGAVEKLR 110


>gi|303239104|ref|ZP_07325634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593442|gb|EFL63160.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score = 45.8 bits (107), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 41/144 (28%), Positives = 64/144 (44%), Gaps = 11/144 (7%)

Query: 447 EMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E +  N RLV  V +K   Y     ++ D  Q G IGL+ AA++F    G  FSTYA+  
Sbjct: 16  EFIRENQRLVSMVIRKQFSYVYNTAEYEDYFQSGCIGLVNAAKRFKPEYGTAFSTYAVSL 75

Query: 504 VKQAITRSIADQSCT-IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           +   I R   D   + I    +++DK ++    A R      R     E  ++L +    
Sbjct: 76  IAGEIMRYRRDYCASGIHSSRNIKDKYYRY--QALR-----NRGVAEAEACRELGVDSAE 128

Query: 563 VRKVLKITKEPISLETPIGDEDTS 586
           + KV+   +   SL+  I D D+ 
Sbjct: 129 LNKVINAMEPGYSLDAVIYDNDSG 152


>gi|238019186|ref|ZP_04599612.1| hypothetical protein VEIDISOL_01050 [Veillonella dispar ATCC 17748]
 gi|237863885|gb|EEP65175.1| hypothetical protein VEIDISOL_01050 [Veillonella dispar ATCC 17748]
          Length = 261

 Score = 45.4 bits (106), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 55/236 (23%), Positives = 119/236 (50%), Gaps = 22/236 (9%)

Query: 442 SIAKKEMVEANLRL-----VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           S+ +K+ ++ +L L     +IS+A  Y N      DL QEG I ++++ E +D+     F
Sbjct: 30  SLRRKKQIKEDLVLNQCGQIISIASIYKNVD-DIEDLFQEGMIAVLESFENYDYTHEASF 88

Query: 497 STYAMWWVKQAITRSIAD---QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +TY    +++ I R I D   ++ TI +P    +K+ K+ + A+ +  ++ +  T E I+
Sbjct: 89  TTY----MRRGIFRQICDYLRRNKTIGLPQAAIEKLKKINK-AKELLERLNKPITTEAIS 143

Query: 554 KKLAMPVEGVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
               +    V ++L  ++ E +      G+ + S L + +EDK A    D  +  ++ E 
Sbjct: 144 DITNIKEHNVIEILNTLSVEELDRLCNDGEGEVSIL-EHVEDKQASKAFDDVLD-DMTEP 201

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T   ++ L+ RE+ V+ + +   +    +L ++ ++  +    I   +++A++KL+
Sbjct: 202 TID-MSCLSDREKEVIILLYYKNL----SLHQIARRLHLKITLISDAKSRALKKLR 252


>gi|332757481|gb|EGJ87816.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-671]
 gi|333017677|gb|EGK36989.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-304]
          Length = 161

 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 37/152 (24%), Positives = 71/152 (46%), Gaps = 11/152 (7%)

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P  +R    +V +   ++  ++ R  T  E+A++L + +   R++L  T          
Sbjct: 11  VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSY-- 68

Query: 581 GDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
            DE     GD IE    D    +PL   + +NLR+     + +L  RE+ VL + +   +
Sbjct: 69  -DEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEEL 127

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           N    L+E+G    V   R+ Q+ ++ I++L+
Sbjct: 128 N----LKEIGAVLEVGESRVSQLHSQDIKRLR 155


>gi|294146897|ref|YP_003559563.1| ECF-type sigma factor [Sphingobium japonicum UT26S]
 gi|292677314|dbj|BAI98831.1| ECF-type sigma factor [Sphingobium japonicum UT26S]
          Length = 244

 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T  R++A L P E++V+R+R G+G +   TL    K   V+  RI QIE KA R+++
Sbjct: 33  TVERLIAMLEPHEQQVVRLRIGLGPSPALTLAATAKIVGVSPSRIGQIEDKAFRRIR 89


>gi|258515964|ref|YP_003192186.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779669|gb|ACV63563.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 234

 Score = 45.4 bits (106), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 91/227 (40%), Gaps = 56/227 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E NLRLV  + KK+        DLI  G IGL+KA   ++   G K +TYA   
Sbjct: 52  ARNVLTERNLRLVAHIVKKFDKTVGDTDDLISIGTIGLIKAVNTYNPEKGTKLATYA--- 108

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R                                     
Sbjct: 109 -----ARCIENE-----ILMHLR------------------------------------- 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV---LASL 620
              +K  +  +SL  PIG +   +    I+     S + + I  N  E   R+   +  L
Sbjct: 122 --FMKKVRAEVSLYDPIGVDKEGNEITLIDILGTHSEVVAEIVENSFE-QKRLGDKVKLL 178

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + RE++VL +RFG+      T  E+ K   ++R  + +IE +A+ KL
Sbjct: 179 SRREKKVLELRFGLEGRQRKTQREIAKFLGISRSYVSRIEKRALTKL 225


>gi|219855964|ref|YP_002473086.1| hypothetical protein CKR_2621 [Clostridium kluyveri NBRC 12016]
 gi|219569688|dbj|BAH07672.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 238

 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 54/233 (23%), Positives = 93/233 (39%), Gaps = 61/233 (26%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDW-----CLGYKFST 498
           +++E N  +V   A ++       +D   L QEG +GLM AA+K+ +     C   KFST
Sbjct: 23  KLIELNKGIVYKFANRFYTEKTNSIDKEDLKQEGFMGLMVAADKYKFNIEKPC---KFST 79

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA++W+   + R I  ++      +++                     P   +   +   
Sbjct: 80  YAVYWIYHKMNRFIKSKNTNEETSLNI---------------------PNSSDGDIEFMD 118

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +EGV                 G E+       +EDK      +  +   L E   R   
Sbjct: 119 CIEGV---------------DYGFEN-------VEDK----IYNEQLHRELEEVMAR-YN 151

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +L  RE  +L+ R+G       T  ++G+ + VTR +I  IE  A+ K++  S
Sbjct: 152 TLKERE--ILKFRYGWDNYKCMTCGQIGEIYNVTRSKINNIEHTALGKIRRSS 202


>gi|91978913|gb|ABE66432.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|106895876|gb|ABF82641.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 272

 Score = 45.4 bits (106), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 34/130 (26%), Positives = 61/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            D  W  Y K   +      V  + D +L+   +++ I VETG+SI++ + I   +  GE
Sbjct: 204 CDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|317133668|ref|YP_004092982.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
 gi|315471647|gb|ADU28251.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
          Length = 228

 Score = 45.4 bits (106), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 53/251 (21%), Positives = 103/251 (41%), Gaps = 62/251 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E R  ++ ++ G+ +A   +  ++E NLRLV+ + KKY        DL+  G IGL
Sbjct: 30  LTAAEERECLARMQAGDTKA---QDMLIEHNLRLVMHIIKKYYANARDQEDLLSVGTIGL 86

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K    F    G + +TYA   ++  I              +H R +             
Sbjct: 87  IKGVITFKPEKGTRLATYAARCIENEIL-------------MHFRSQ------------- 120

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                                     K + + + +  PI   DT   G+ +   + VS  
Sbjct: 121 --------------------------KKSAQDVYISDPI---DTDKDGNQLTLMDVVSCE 151

Query: 602 DSAI-QANLRETTTRVLASLT---PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           D+ +   +L+  + ++ A +    PRE  ++ MR+G+      T  EV  +  ++R  + 
Sbjct: 152 DTILDDVDLKMKSEKLRAYIVKLPPRERAIIEMRYGLHGAKPQTQREVAGKLNISRSYVS 211

Query: 658 QIEAKAIRKLK 668
           +IE +A+ +L+
Sbjct: 212 RIEKRALGELR 222


>gi|313647806|gb|EFS12252.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2a str. 2457T]
          Length = 76

 Score = 45.4 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 43/68 (63%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++  + L  L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 1   MKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 60

Query: 669 HPSRSKKL 676
              +++ L
Sbjct: 61  EILQTQGL 68


>gi|147677483|ref|YP_001211698.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273580|dbj|BAF59329.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 45.4 bits (106), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 105/251 (41%), Gaps = 41/251 (16%)

Query: 434 VRKGECEASIAK----------KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           V+ G  EA++A           +++VEA  RLV      Y   G    DL+Q G  GL+K
Sbjct: 13  VQAGNIEAAMAAYLQDGSAESLQKVVEAGTRLVHYFVGLYAP-GHSREDLVQSGFEGLLK 71

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AA+++D   G  FSTYA   +   +   I  ++   R P        +V R      N+ 
Sbjct: 72  AAKRYDPGRGVSFSTYASHCIMGEVRHFIRKEASFSR-PGWAAGLQERVNRFLEEYLNEK 130

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
              PT ++IA  + +  EG+ +V+++                   G    D+  VS + S
Sbjct: 131 GELPTLDQIAGAVNIRKEGLLQVMRV-------------------GWVAPDEIDVSKIRS 171

Query: 604 AIQANL------RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
               +       R    + +  LT  + RV+ M F   M      EE+G    +T+ ++ 
Sbjct: 172 QRYESFQLPVEDRIVLRQAVEKLTELQRRVIAMLFFKNMTQGEAAEELG----ITQRKVS 227

Query: 658 QIEAKAIRKLK 668
           ++  K+++ L+
Sbjct: 228 RVLHKSLKLLR 238


>gi|89895713|ref|YP_519200.1| hypothetical protein DSY2967 [Desulfitobacterium hafniense Y51]
 gi|89335161|dbj|BAE84756.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score = 45.4 bits (106), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 52/210 (24%), Positives = 89/210 (42%), Gaps = 14/210 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GL+ A E+FD   G KF TYA   ++ AI   +        +P   R KI +
Sbjct: 44  DLIGYGVFGLLDALERFDPVRGVKFETYATLRIRGAIIDGLRTMDW---VPHSARQKIKR 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL----ETPIGDEDTSH 587
           +      +  +  R  + EE+A  L M    +   L    + ++L    E  +G+E  + 
Sbjct: 101 IQDAFAEVEARHGRPASNEEVAVLLQMEPRDLEAALH-QGQMLTLTSLDEVAVGEEGEA- 158

Query: 588 LGDFIEDKNAVSPL-DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              +        P+   A Q    +   ++LA    +     ++   +    D TL+E+ 
Sbjct: 159 ---YTPRTQLADPIAQEAFQEVELDEQKKILADAIEKLPEKEKLVVALYYQEDLTLKEIA 215

Query: 647 KQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
               ++  RI Q+ ++AI +L+   SR KK
Sbjct: 216 VIMKLSESRISQLHSQAILRLRGRLSRQKK 245


>gi|87124483|ref|ZP_01080332.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168055|gb|EAQ69313.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 213

 Score = 45.4 bits (106), Expect = 0.033,   Method: Composition-based stats.
 Identities = 28/91 (30%), Positives = 49/91 (53%), Gaps = 1/91 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +   VE +LRLV  +A+ Y  R G    DL+Q G +GL++AA  +D   G  F  +A   
Sbjct: 8   RNRRVEQHLRLVQPIARHYAQRSGEDRDDLLQVGCLGLIRAAGLYDGAKGVPFEAFARPH 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           V+ AI   + D    +++P  ++++  ++ R
Sbjct: 68  VRGAILHYLRDSRGLVKLPRRLQERAQRLNR 98


>gi|215404667|ref|ZP_03416848.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|289746504|ref|ZP_06505882.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687032|gb|EFD54520.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|326904317|gb|EGE51250.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor [Mycobacterium
           tuberculosis W-148]
          Length = 316

 Score = 45.4 bits (106), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCE 159
           S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +M  L E
Sbjct: 211 SEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSE 270



 Score = 39.3 bits (90), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 16/24 (66%), Positives = 21/24 (87%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRG 467
           AK  ++EANLRLV+S+AK+YT RG
Sbjct: 293 AKNHLLEANLRLVVSLAKRYTGRG 316


>gi|237668235|ref|ZP_04528219.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237656583|gb|EEP54139.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 146

 Score = 45.4 bits (106), Expect = 0.034,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 34/57 (59%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           AK  ++E NLRLV  + KKY+       +LI  G +GL+KA + FD   G + +TYA
Sbjct: 50  AKSILIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIKAIDSFDSSKGTRLATYA 106


>gi|237734716|ref|ZP_04565197.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382044|gb|EEO32135.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 128

 Score = 45.4 bits (106), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 64/131 (48%), Gaps = 13/131 (9%)

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNAV 598
           K+ REPT  E+A +L +    V + L  T    SL+  + ++D ++L       +DK  V
Sbjct: 5   KLNREPTINELANELEVEPSAVIEALLSTNSVSSLQEEVKNDDGNNLKMIDSITDDKTVV 64

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           S  +  I           L SL  +E RV++ R+  G++      E+ K+  +++ ++ +
Sbjct: 65  SRTNETIDL------YDALKSLNQKEHRVIKQRYFEGLSQS----EIAKELFISQAQVSR 114

Query: 659 IEAKAIRKLKH 669
           IE KA+  L +
Sbjct: 115 IERKALDNLHN 125


>gi|116074935|ref|ZP_01472196.1| putative type III sigma factor [Synechococcus sp. RS9916]
 gi|116068157|gb|EAU73910.1| putative type III sigma factor [Synechococcus sp. RS9916]
          Length = 248

 Score = 45.4 bits (106), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 32/111 (28%), Positives = 56/111 (50%), Gaps = 4/111 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+QE  +GL++ +E+F+   G +FS+YAM      I     D+   +RIP  + D +H 
Sbjct: 34  DLLQEAYLGLIQGSERFEASRGNRFSSYAMRLATGRIQHFRRDRVRCLRIPWRL-DALHT 92

Query: 532 VVRTARRMSNKIKREP-TPEEIAKKLAMPVEGVRKVLKITKEP--ISLETP 579
                +      +R P +  ++A  L + +E  R+ L   ++   ISL+ P
Sbjct: 93  QAIRLQEQRAHAQRPPFSDHQLASTLGVSLERWRQALIGHQQHHLISLDQP 143


>gi|99034132|ref|ZP_01314232.1| hypothetical protein Wendoof_01000979 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 148

 Score = 45.4 bits (106), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 36/102 (35%), Positives = 55/102 (53%), Gaps = 7/102 (6%)

Query: 580 IGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETT-TRVLASLTPREERVLRMRFGIG 635
           IGD+    L D I   N VS      +  +  L+ET     LASL  R   +   R+ + 
Sbjct: 45  IGDDSKRELQDMI-PCNLVSQEVTYQNHEEKELKETILNNALASLNERARDIFISRY-LS 102

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            N   TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 103 ENI-QTLDELSKKYCVSRERIRQLAEQAMAKVKQYIQSESLK 143


>gi|332975582|gb|EGK12472.1| DNA-directed RNA polymerase sigma subunit SigK [Desmospora sp.
           8437]
          Length = 160

 Score = 45.1 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 36/65 (55%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N      DLI  G IGL+KA E +    G K +TYA   
Sbjct: 50  ARNILIEHNLRLVAHIVKKFENTSEDNEDLISIGTIGLIKAIESYQPNKGTKLATYAARC 109

Query: 504 VKQAI 508
           ++  I
Sbjct: 110 IENEI 114


>gi|301060344|ref|ZP_07201207.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
 gi|300445540|gb|EFK09442.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
          Length = 772

 Score = 45.1 bits (105), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 28/39 (71%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TLEE+G+ F +TRER+RQI  KAI++ KH +   ++  F
Sbjct: 254 TLEEIGQAFGITRERVRQIVKKAIKQFKHTANISQIEKF 292


>gi|219670137|ref|YP_002460572.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
 gi|219540397|gb|ACL22136.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
          Length = 248

 Score = 45.1 bits (105), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 52/210 (24%), Positives = 89/210 (42%), Gaps = 14/210 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G  GL+ A E+FD   G KF TYA   ++ AI   +        +P   R KI +
Sbjct: 44  DLIGYGVFGLLDALERFDPVRGVKFETYATLRIRGAIIDGLRTMDW---VPHSARQKIKR 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL----ETPIGDEDTSH 587
           +      +  +  R  + EE+A  L M    +   L    + ++L    E  +G+E  + 
Sbjct: 101 IQDAFAEVEARHGRPASNEEVAVLLEMEPRDLEAALH-QGQMLTLTSLDEVAVGEEGEA- 158

Query: 588 LGDFIEDKNAVSPL-DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              +        P+   A Q    +   ++LA    +     ++   +    D TL+E+ 
Sbjct: 159 ---YTPRTQLTDPIAQEAFQEVELDEQKKILADAIEKLPEKEKLVVALYYQEDLTLKEIA 215

Query: 647 KQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
               ++  RI Q+ ++AI +L+   SR KK
Sbjct: 216 VIMKLSESRISQLHSQAILRLRGRLSRQKK 245


>gi|224825766|ref|ZP_03698870.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601990|gb|EEG08169.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 230

 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 91/204 (44%), Gaps = 31/204 (15%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q G + L++A  ++      +F+ YA+  V+ AI   +         P  +R   H+
Sbjct: 45  DMEQIGLMALLEALRRYGEP-DARFAGYAVLRVRGAILDELRRLDWR---PRALRQDAHR 100

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    R ++ ++ REP+  E   +L +  E  R +L               E+   +  F
Sbjct: 101 LRDGLRELTRRLGREPSEAEAVAQLGLSAEDYRALLVA-------------ENAEAMASF 147

Query: 592 IEDKNA-VSPLD------SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            E   A + P+D      S +Q   R T    L++L  RE+RV+++ +   +    +L+E
Sbjct: 148 DELVAAGIEPIDDNTPEASVLQ---RRTLAAALSALDEREQRVIQLYYEFEL----SLKE 200

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +     +T  R+ QI   A++K+K
Sbjct: 201 IAAVLDLTEARVCQINKSALKKMK 224


>gi|116626504|ref|YP_828660.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116229666|gb|ABJ88375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 251

 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 86/198 (43%), Gaps = 8/198 (4%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G +GL+ A + FD     K  TYA + ++ AI  S+         P   R K  +
Sbjct: 45  DLVSTGVLGLISAIDNFDASHNVKLKTYAEYKIRGAILDSLRGLDWA---PRQKRRKSKQ 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKITKEPISLETPIGDEDTSHLGD 590
           +         ++   P  EEIA +L + V+   + +++I    ++     G+E    L  
Sbjct: 102 IEAAIAVAEQRLHASPGEEEIAGELGITVDEYHEWLVEIRGLNVASLEYAGNEQGRDLLH 161

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +I D +   P     ++ L       +  +   E  VL + F    + + TL E+ +   
Sbjct: 162 YIPDGSDNLPSTLLERSELERLLASSIDGIPAIERTVLSLYF----HEELTLREIAQVVN 217

Query: 651 VTRERIRQIEAKAIRKLK 668
           +   RI Q++++AI +L+
Sbjct: 218 LHESRISQLKSQAILRLR 235


>gi|220932485|ref|YP_002509393.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halothermothrix
           orenii H 168]
 gi|219993795|gb|ACL70398.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halothermothrix
           orenii H 168]
          Length = 207

 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 26/101 (25%), Positives = 51/101 (50%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R+ +     A + ++ +N+ +V + AK +  +GL   D+IQEG +GL KA   F +  
Sbjct: 10  IIRQAQNRNRRAIEYLINSNMDIVYAKAKYFFIKGLDKDDVIQEGMVGLFKAIRDFKFEK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           G  F  +A   V + +  +I   +    IP++    I + +
Sbjct: 70  GASFRGFAQLCVHRQLVSAIKRANRQKHIPLNTSTSIDRSI 110


>gi|14646833|dbj|BAB62001.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 79

 Score = 45.1 bits (105), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 40/61 (65%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L
Sbjct: 4   DLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRL 63

Query: 668 K 668
           +
Sbjct: 64  R 64


>gi|229817514|ref|ZP_04447796.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
 gi|229785303|gb|EEP21417.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
          Length = 621

 Score = 45.1 bits (105), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 49/87 (56%), Gaps = 12/87 (13%)

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           N  +P++SA   +L E+ T +L S   RE  +   R  +      TL+E+GK+F +TRER
Sbjct: 123 NEFTPIESA-PPSLAESLTMLLFSFDEREYAIATQR--LMAEQPSTLDEIGKEFNITRER 179

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +RQIE KA+R         ++ + LDG
Sbjct: 180 VRQIE-KALR--------NEITTLLDG 197


>gi|153812706|ref|ZP_01965374.1| hypothetical protein RUMOBE_03113 [Ruminococcus obeum ATCC 29174]
 gi|149831222|gb|EDM86311.1| hypothetical protein RUMOBE_03113 [Ruminococcus obeum ATCC 29174]
          Length = 114

 Score = 45.1 bits (105), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 31/102 (30%), Positives = 53/102 (51%), Gaps = 11/102 (10%)

Query: 574 ISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS----LTPREER 626
           +SL  PIG +   +   L D IE      P+D   + + R+    + +S    LTP+E +
Sbjct: 13  VSLYEPIGTDKEGNEISLLDIIES----PPVDIVEEYSTRQDIRFLFSSMKDILTPKEYQ 68

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+  R+G+  N + T  E+  Q  ++R  + +IE  A++KLK
Sbjct: 69  VICCRYGLFENNEMTQREIADQLHISRSYVSRIEKNALKKLK 110


>gi|169829306|ref|YP_001699464.1| RNA polymerase sigma-28 factor [Lysinibacillus sphaericus C3-41]
 gi|168993794|gb|ACA41334.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 228

 Score = 45.1 bits (105), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 93/236 (39%), Gaps = 74/236 (31%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E N+RLV  V KK+  +  Q  D I  G IGLMKA E +      + +TYA   
Sbjct: 43  ARLDLIERNMRLVAHVVKKFHPKHEQLDDYISIGTIGLMKAVESYTPDKKTRLATYA--- 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R +                                   
Sbjct: 100 -----ARCIENE-----ILMHLRTQ----------------------------------- 114

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV------- 616
               K  ++ +SL  PIG +         +D NA+   D  +Q +    T ++       
Sbjct: 115 ----KKVQKDVSLFEPIGTD---------KDGNALQIRD-LLQCDEESATEKIEHKEHVA 160

Query: 617 -----LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                L  L  RE  ++ +R+G+      T +E+  +  ++R  + +IE +A+ KL
Sbjct: 161 QLYHYLHMLDERELEIVTLRYGLNQQDALTQKEIAARLNISRSYVSRIEKRALIKL 216


>gi|289811768|ref|ZP_06542397.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
          enterica serovar Typhi str. AG3]
          Length = 63

 Score = 45.1 bits (105), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 34/49 (69%)

Query: 31 WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++
Sbjct: 9  LKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVME 57


>gi|310658943|ref|YP_003936664.1| RNA polymerase subunit alpha domain-containing protein [Clostridium
           sticklandii DSM 519]
 gi|308825721|emb|CBH21759.1| RNA polymerase, alpha subunit domain protein [Clostridium
           sticklandii]
          Length = 911

 Score = 45.1 bits (105), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 30/48 (62%), Gaps = 5/48 (10%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE  VL  R         TLE+VG +  VTRERIRQIEAKAI+KL
Sbjct: 302 LNEREYNVLLQRI-----QGKTLEDVGLEMNVTRERIRQIEAKAIKKL 344


>gi|106895886|gb|ABF82645.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC364]
          Length = 284

 Score = 45.1 bits (105), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 37/149 (24%), Positives = 69/149 (46%), Gaps = 2/149 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 137 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 196

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 197 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 255

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           I++ + I   +  GE +A  AKKEMVEAN
Sbjct: 256 IAQIKDINRRMSIGEAKARRAKKEMVEAN 284


>gi|114566052|ref|YP_753206.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114336987|gb|ABI67835.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 126

 Score = 45.1 bits (105), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 34/57 (59%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A+  ++E NLRLV  V KKY + G    DLI  G IG +KA   +++  G + +TYA
Sbjct: 52  ARNILIEHNLRLVAHVVKKYESSGEDLEDLISIGTIGPIKAIRTYNFERGVRLATYA 108


>gi|299535719|ref|ZP_07049040.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728919|gb|EFI69473.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 235

 Score = 45.1 bits (105), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 52/229 (22%), Positives = 92/229 (40%), Gaps = 60/229 (26%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E N+RLV  V KK+  +  Q  D I  G IGLMKA E +      + +TYA   
Sbjct: 50  ARLDLIERNMRLVAHVVKKFHPKHEQLDDYISIGTIGLMKAVESYTPDKKTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R +                                   
Sbjct: 107 -----ARCIENE-----ILMHLRTQ----------------------------------- 121

Query: 564 RKVLKITKEPISLETPIG---DEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLA 618
               K  ++ +SL  PIG   D +   + D ++  +++A   L+              L 
Sbjct: 122 ----KKVQKDVSLFEPIGTDKDGNALQIRDLLQCDEESATEKLEHKEHVA---QLYHYLH 174

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L  RE  ++ +R+G+      T +E+  +  ++R  + +IE +A+ KL
Sbjct: 175 MLDERELEIVTLRYGLNQQDALTQKEIAARLNISRSYVSRIEKRALIKL 223


>gi|237755445|ref|ZP_04584070.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692409|gb|EEP61392.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 98

 Score = 45.1 bits (105), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 49/89 (55%), Gaps = 8/89 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           KKE+VE ++ LV  VA K   R     ++F DL+Q G +GL+KA E ++   G KFSTYA
Sbjct: 8   KKEIVEEHIGLVKKVASKIFYRLPDCEIEFDDLVQTGIVGLLKALENYNEDKG-KFSTYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKI 529
              ++  I   +  Q     +P   +DKI
Sbjct: 67  YIRIRGEILDFLRQQDI---MPKTEKDKI 92


>gi|126653890|ref|ZP_01725737.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
 gi|126589615|gb|EAZ83754.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
          Length = 235

 Score = 45.1 bits (105), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 93/236 (39%), Gaps = 74/236 (31%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +++E N+RLV  V KK+  +  Q  D I  G IGLMKA E +      + +TYA   
Sbjct: 50  ARLDLIERNMRLVAHVVKKFHPKHEQLDDYISIGTIGLMKAVESYTPDKKTRLATYA--- 106

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
                 R I ++     I +H+R +                                   
Sbjct: 107 -----ARCIENE-----ILMHLRTQ----------------------------------- 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV------- 616
               K  ++ +SL  PIG +         +D NA+   D  +Q +    T ++       
Sbjct: 122 ----KKVQKDVSLFEPIGTD---------KDGNALQIRD-LLQCDEESATEKIEHKEHVA 167

Query: 617 -----LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                L  L  RE  ++ +R+G+      T +E+  +  ++R  + +IE +A+ KL
Sbjct: 168 QLYHYLHMLDERELEIVTLRYGLNQQDALTQKEIAARLNISRSYVSRIEKRALIKL 223


>gi|37784446|gb|AAO13116.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
          Length = 274

 Score = 45.1 bits (105), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 35/147 (23%), Positives = 67/147 (45%), Gaps = 6/147 (4%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           NG+  E++         +L  +     L   + D LV  + ++ +R+   E  +L++  +
Sbjct: 133 NGRAHEETQAAIA----QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVE 188

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +A   D +L+   +++ I  ETG
Sbjct: 189 QAKMPKKTFVSAFTNNECETAWFEYQKQAGKA-WSAPLAAMEDEVLRSIGKLQQIEEETG 247

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEM 448
           +SI++ + I   +  GE +A  AKKEM
Sbjct: 248 LSIAQIKDINRRMSIGEAKARRAKKEM 274


>gi|302389688|ref|YP_003825509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
 gi|302200316|gb|ADL07886.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
          Length = 245

 Score = 44.7 bits (104), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 47/208 (22%), Positives = 96/208 (46%), Gaps = 16/208 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G IGL++A E++D   G +F T+A   ++ A+   +   +    IP    +K   
Sbjct: 53  DLVSAGIIGLLQAIERYDVGKGVRFETFAYTRIRGAMLDELRRLNW---IPQKTMEKAKL 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +     +M  ++      E+IA+KL + +  + +    T + ++    +  E+   +   
Sbjct: 110 LQDAYSQMEQELNGNVKDEDIARKLNITIAELHQ----TYKELAATNLVSLEEIFSVA-- 163

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +ED     P+    +  ++      +  L P+E+ V+ + +  G+N    L+E+     +
Sbjct: 164 VEDNG--EPVSHVEKEEIKRILGEAIDRLPPKEKLVIALYYYEGLN----LKEISVVLNL 217

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +  RI Q+  KAI +L+  S S+K   F
Sbjct: 218 SPARISQLHTKAILRLRG-SLSRKRAYF 244


>gi|254255074|ref|ZP_04948391.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
 gi|124899719|gb|EAY71562.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
          Length = 241

 Score = 44.7 bits (104), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 64/259 (24%), Positives = 110/259 (42%), Gaps = 35/259 (13%)

Query: 420 TGISISEF----RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           T I+ +E+    R    M+ +GE         +V    + V+     +   G+   DL Q
Sbjct: 2   TSITFTEYENVQRACNGMLPRGEAHWIAEYAPLV----KRVVGKLAGHGAAGIDRDDLEQ 57

Query: 476 EGNIGLMKAAEKF----DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
            G +GL++A  ++    D      F+ YA+  ++ A+   +  Q      P   R   H+
Sbjct: 58  IGIMGLLEALRRYGEPDD-----AFANYAVVRIRGAVLDELRRQDWR---PRTARQGAHR 109

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVL-KITKEPISLETPIGDEDTSHLG 589
           +    R + +K+ REP  ++I   L +  VE  R +L     E +SL     DE  +  G
Sbjct: 110 LRSCERALRSKLGREPGKDDICAALGIDGVEYDRIMLDDSANELMSL-----DELINAHG 164

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D   +  A        Q   R    + L  L  RE+RV+++ +      D TL E+G   
Sbjct: 165 DVPGEAQA----GPEAQVLARRGIEQALLVLDEREQRVIQLYY----EFDLTLPEIGAVL 216

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +T  RI Q+   A++K++
Sbjct: 217 NLTTARICQLHRGALKKMR 235


>gi|282882222|ref|ZP_06290861.1| putative sporulation sigma factor SigK [Peptoniphilus lacrimalis
           315-B]
 gi|281297987|gb|EFA90444.1| putative sporulation sigma factor SigK [Peptoniphilus lacrimalis
           315-B]
          Length = 256

 Score = 44.7 bits (104), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 38/55 (69%), Gaps = 3/55 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS--CTIRIPVH 524
           +++Q+G I L+KA E FD+ LG+KFS+YA+  +  ++TR+  D +   ++  P++
Sbjct: 51  EMLQDGYIALIKAVESFDYRLGFKFSSYAIKCI-LSLTRTRIDYNKDLSLNTPIN 104


>gi|303326435|ref|ZP_07356878.1| flagellar biosynthesis protein FlhG [Desulfovibrio sp. 3_1_syn3]
 gi|302864351|gb|EFL87282.1| flagellar biosynthesis protein FlhG [Desulfovibrio sp. 3_1_syn3]
          Length = 555

 Score = 44.7 bits (104), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 52/207 (25%), Positives = 93/207 (44%), Gaps = 31/207 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+  G +GL++A   F    G  F  YA   ++ A+   +  Q     +P  +R  + +
Sbjct: 354 ELLGAGALGLVEALCNFRPERGVCFERYAENRIRGAMLDELRRQDW---LPRSLRRAMRR 410

Query: 532 VVRTARRMSNKIK-REPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHL 588
           +   ARRM  + + R+ T EE+     +    +R  ++    ++  SL            
Sbjct: 411 L-DEARRMVERGRGRQATEEELLSMTGLEPRTLRYAMEALEARQFFSL------------ 457

Query: 589 GDFIEDKNAV-------SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            D I+D  A         P  +A+   L E   R+LA LTPRE+ VL + +  G+    T
Sbjct: 458 -DAIQDSLAADGPGGADEPCHTAVMRELAEHMERLLARLTPREKMVLSLYYTDGL----T 512

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + E  +   +T  R+ Q+ A+A+ +L+
Sbjct: 513 MREAAEVMSITECRVSQLHAQALARLR 539


>gi|237751751|ref|ZP_04582231.1| flagellar biosynthesis sigma factor [Helicobacter bilis ATCC 43879]
 gi|229373117|gb|EEO23508.1| flagellar biosynthesis sigma factor [Helicobacter bilis ATCC 43879]
          Length = 240

 Score = 44.7 bits (104), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 83/211 (39%), Gaps = 45/211 (21%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+  G   L+K A ++D      F  YA    K  +  ++ D   T+ I      K+ K
Sbjct: 53  DLVSIGTEELIKLARRYDSNKNDSFWGYA----KTRVNGAMLDYLRTLDIVSRSSRKLIK 108

Query: 532 VVRT-ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
            +     R  N+ + EP+ E +AK L   +E +                       H   
Sbjct: 109 AIEAEVSRYFNEFEEEPSNEYLAKVLNEDIEKI-----------------------HQAR 145

Query: 591 FIEDKNAVSPLDSAI-------------QANLRETTTRVLASLTPREERVLRMRFGIGMN 637
              D  AV PLD                Q  L E   +VLA LT RE+ ++++ +     
Sbjct: 146 LASDIYAVVPLDEQFNALEDGDILQYCEQKELMEIIQKVLAKLTEREQLIIQLYYL---- 201

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L E+ +   +T  RI QI  + I+K++
Sbjct: 202 EELSLSEISEVLDITESRISQISKEVIKKIR 232


>gi|239934514|emb|CAR94571.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 255

 Score = 44.7 bits (104), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 70/319 (21%), Positives = 130/319 (40%), Gaps = 74/319 (23%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGE+ IAKRIE G   ++A+L + P T   +      L+ G   L +++         
Sbjct: 4   TREGELEIAKRIEDGLNQVLAALSQYPRTMHIVHQAGARLSVGELRLGDVLS-------- 55

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF                     D   ET                   +PP   +N+
Sbjct: 56  ---GFI--------------------DPASET-------------------APPVPHQNN 73

Query: 255 ERNLD-EDEDDSAHTLSAMEDQLRPKVMCA-LDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
             N + +D +++  T   +E+      +CA +  + E+++  R+L      G+  + +  
Sbjct: 74  GENRNGDDSEEAVDTGPDLEE------VCARIAALVELHK--RALAAVKRYGRDHKTARR 125

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
           + + L E++V+            DLLV  L  + +RI   E  ++ +  +   + R  F+
Sbjct: 126 RYEELAEQIVQF----KFVPRFFDLLVGNLRQVIQRIRSKERAIMEICVRQTQMPRREFV 181

Query: 372 ERHQGRELDPHWV----SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                RE DP W+    +  + +  G  ++     +D I +++ ++ SI  E  +SI E 
Sbjct: 182 STFPKRETDPQWLQDQLNAGRAYSAGLREH-----IDEITRLQQKLVSIEKEACLSIGEI 236

Query: 428 RHIVSMVRKGECEASIAKK 446
           + I   +  GE +A  AKK
Sbjct: 237 KEINRRMSIGEAKARRAKK 255


>gi|15618277|ref|NP_224562.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           CWL029]
 gi|15835895|ref|NP_300419.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           J138]
 gi|16752677|ref|NP_444944.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           AR39]
 gi|33241705|ref|NP_876646.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           TW-183]
 gi|4376638|gb|AAD18506.1| Sigma-28/WhiG Family [Chlamydophila pneumoniae CWL029]
 gi|7189319|gb|AAF38240.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
 gi|8978734|dbj|BAA98570.1| sigma-28/WhiG family [Chlamydophila pneumoniae J138]
 gi|33236214|gb|AAP98303.1| transcription initiation factor sigmaD protein [Chlamydophila
           pneumoniae TW-183]
 gi|269303237|gb|ACZ33337.1| RNA polymerase sigma factor, FliA [Chlamydophila pneumoniae LPCoLN]
          Length = 257

 Score = 44.7 bits (104), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 52/231 (22%), Positives = 105/231 (45%), Gaps = 18/231 (7%)

Query: 448 MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E  L LV SV  +  +     ++  DL   G  GL++A E+++     +F  YA++ +
Sbjct: 28  LIEFYLPLVKSVVHRLISGMPSHVKTEDLYASGVEGLVRAVERYNPERSRRFEGYAVFLI 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           K AI   +  Q     +P  +  K +K+      +   + +EPT  E+ + L +  + + 
Sbjct: 88  KAAIIDDLRKQDW---VPRSVHQKANKLSGAMDSLRQSLGKEPTDLELCEYLNISQQELS 144

Query: 565 KVLKITKEP---ISL--ETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVL 617
               ++  P   +SL  E P   ++ + +   + I D+ A +  D   +          +
Sbjct: 145 GWF-VSARPALIVSLNEEWPSQSDEGAGMALEERIPDERAETGYDVVDKQEFSLCLANAI 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  +E +V+ + +      +  L+E+GK   V+  R+ QI +KA+ KL+
Sbjct: 204 QELEEKERKVMALYY----YEELVLKEIGKVLGVSESRVSQIHSKALLKLR 250


>gi|222528749|ref|YP_002572631.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222530717|ref|YP_002574606.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455596|gb|ACM59858.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457564|gb|ACM61825.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 310

 Score = 44.7 bits (104), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 48/87 (55%), Gaps = 7/87 (8%)

Query: 441 ASIAKKEMVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAEKFDWCLGYKF 496
           A +  + ++  NL+LV  VA K+    +G  +   DL+ EG IGL+ AA+ +D   G  F
Sbjct: 10  AKVQSQLLIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKG-SF 68

Query: 497 STYAMWWVKQAITRSIA--DQSCTIRI 521
           STYA   ++  I RS+   + SC I +
Sbjct: 69  STYACKVIESKIKRSLPKYELSCAISL 95


>gi|294102492|ref|YP_003554350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
 gi|293617472|gb|ADE57626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
          Length = 196

 Score = 44.7 bits (104), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 48/85 (56%), Gaps = 2/85 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++ +   LV  +A+K+      + DLIQEG + L+K+ +KF+     KF+TYA + 
Sbjct: 32  AREELIISYRPLVFWLAQKFYVSPSLYPDLIQEGMVALIKSVDKFEPERQLKFTTYAFYR 91

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK 528
           +K  +   +  Q    + P+ M D+
Sbjct: 92  IKGQMVNFL--QRSEAKAPIPMDDE 114


>gi|239934516|emb|CAR94572.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 266

 Score = 44.7 bits (104), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 50/163 (30%), Positives = 79/163 (48%), Gaps = 24/163 (14%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           +G +DEK++     L+++L      L L     DLLVE L     +I   E ++++   +
Sbjct: 118 HGSQDEKTTK----LRKQLSSEFMELKLAPKMFDLLVETLRGNIGKIRALERQVMQFCIR 173

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS--ILKIRNEI-----K 414
             G+ R  F+      E +  W++          K+  A    S  + K+R++I     K
Sbjct: 174 QAGMPRKEFISSFPENETNLDWIN----------KHIRAKRKHSSQLSKLRDDITCAQRK 223

Query: 415 SISVE--TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            I +E  T +SISE + I   +  GE +A  AKKEMV+ANLRL
Sbjct: 224 LIEIEHSTSLSISEIKEINRQMSIGEAKARRAKKEMVDANLRL 266



 Score = 43.1 bits (100), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           ++ELL+REGEI IAKRIE G   +  +L   P T+ AL+   + ++ G   L++II
Sbjct: 1   TVELLTREGEIRIAKRIEDGLNQVRGALGVFPGTYGALLGIYEPVSRGEGRLQDII 56


>gi|289523531|ref|ZP_06440385.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503223|gb|EFD24387.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 189

 Score = 44.3 bits (103), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 47/87 (54%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++E++ +   +V  +AKK+      + DLIQEG + L++A +++D   G KF TYA + 
Sbjct: 30  AREEVIISYRPMVFWLAKKFHVPSDSYQDLIQEGMVALIEAVDRYDAKRGTKFITYAYYR 89

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIH 530
           +K  +   +         PV + D ++
Sbjct: 90  IKGRMVNFLERSEARAPEPVDIDDHLY 116


>gi|215270851|emb|CAR48103.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score = 44.3 bits (103), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 41


>gi|215270845|emb|CAR48100.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270849|emb|CAR48102.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score = 44.3 bits (103), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 41



 Score = 38.5 bits (88), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 71/166 (42%), Gaps = 11/166 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    E  S K  V  E ++ +     L   + D LV +L   
Sbjct: 120 EKFNQLRSTYQNLQLAINEHGYE--SPKATVANELMLDVFKEFRLTPKQFDHLVNELRTA 177

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++ A  YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 178 MDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEK---IKRN 234

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEM
Sbjct: 235 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEM 280


>gi|254446671|ref|ZP_05060147.1| RNA polymerase sigma factor, FliA/WhiG family [Verrucomicrobiae
           bacterium DG1235]
 gi|198260979|gb|EDY85287.1| RNA polymerase sigma factor, FliA/WhiG family [Verrucomicrobiae
           bacterium DG1235]
          Length = 269

 Score = 44.3 bits (103), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 98/210 (46%), Gaps = 28/210 (13%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G  GL+ A +K+D      F +YA   ++ +I   +        +P + R    K
Sbjct: 66  DLHSVGITGLIAALKKYDPAQKKSFGSYAAMRIRGSILDELRRMDW---MPRNARTNFKK 122

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI------GDE-D 584
           +  T   +  ++ R  T EEI  +L +  +   +++  T+ P+S   P+      GD+ +
Sbjct: 123 LRATIEEVEQRLGRPATEEEIRAELGLNRKEYDQLMAETR-PVSF-LPLDNAAAGGDDGE 180

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL------TPREERVLRMRFGIGMNT 638
            + L + I D N V P+ S ++   ++  TR++A        TPR  +VL M +      
Sbjct: 181 GADLYEVIPDDNVV-PVTSKME---KDEVTRLVAERINQLPETPR--KVLAMYYF----Q 230

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           D  L E+ + F +T  RI QI ++AI  L+
Sbjct: 231 DMRLAEIAEVFGLTESRICQIHSQAIISLR 260


>gi|11078919|dbj|BAB17464.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 44.3 bits (103), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 70/313 (22%), Positives = 133/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+  +V+S P  
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAAKAEGTDDDEEESADAS-DEEDEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+     G++D+ +
Sbjct: 107 ----------DPVIAAQRFGAVSDQM------------EITR--KALKK---FGREDKHA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
             +   L E    L   + L   + + LVE++     R+   E  +++L  +   + R  
Sbjct: 140 IAEMVALAE----LFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   +G++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|215270839|emb|CAR48097.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score = 44.3 bits (103), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 41


>gi|218669756|gb|ACL00355.1| Bcp25 [Bacillus phage Bcp1]
          Length = 250

 Score = 44.3 bits (103), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 59/103 (57%), Gaps = 2/103 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +V++    +  AK++++     +V ++AK+++ ++  +F D+ QEG   L++  +KFD
Sbjct: 17  IELVKEARAGSEEAKEKIILGYKGMVYTLAKRFSRSKQHEFEDMFQEGLTILLEVVDKFD 76

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
              GY FSTYA  +V   +  ++  +   I+I  H+ D I ++
Sbjct: 77  IDSGYAFSTYAYPFVFGKMN-NVRKRYNPIKISAHITDIISRI 118


>gi|289422613|ref|ZP_06424455.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
 gi|289156964|gb|EFD05587.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
          Length = 289

 Score = 44.3 bits (103), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 45/93 (48%), Gaps = 9/93 (9%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK------YTNRGLQFLDLIQEGNIGL 481
           R +V   ++G+    +A  +++E   + V  + K       Y  RGL   DL Q G IGL
Sbjct: 43  RKLVKSAKEGDL---VALNKVIEKKSKYVKGIIKNDYEIMAYKKRGLDQEDLFQSGMIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           + A +KFD+  G KF TY    VK +I     D
Sbjct: 100 LNAVKKFDFRDGIKFDTYLAHNVKYSIKNDFRD 132


>gi|309388843|gb|ADO76723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Halanaerobium praevalens DSM 2228]
          Length = 251

 Score = 44.3 bits (103), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 97/201 (48%), Gaps = 17/201 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G IGL++A E F++  G KFST+A+  +K  I   +  +     +P +MR ++ K
Sbjct: 50  DLESYGIIGLIEAIENFNYQRGVKFSTFALPRIKGEIYDYLRSKDW---LPDNMRRELKK 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           V    R    K  ++P  +E++K   +    + K+ + ++    ISL     D D + L 
Sbjct: 107 VDEQKRSYKAKTGKKPDQKELSKLTGIKKSRLEKIERHSQLANWISLSH---DFDGTELI 163

Query: 590 DFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + +  + K AV   D   +    +   + +  L+ +E+ VL + +      + T  E+ +
Sbjct: 164 ELVAADFKQAV---DRLTEKEAVDFLAKKIDLLSEKEKLVLSLYY----YEELTQVEIAE 216

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  R+ QI  +AIR+L+
Sbjct: 217 IIELSAARVSQIHGRAIRRLR 237


>gi|257437879|ref|ZP_05613634.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
 gi|257199539|gb|EEU97823.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
          Length = 221

 Score = 44.3 bits (103), Expect = 0.069,   Method: Composition-based stats.
 Identities = 49/196 (25%), Positives = 73/196 (37%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+GL KA  KFD   G KF TYA   ++ A+   + D        +   DK   
Sbjct: 55  DLKQAGNMGLWKAVPKFDAARGMKFLTYAAPAIRNAMMDMVRDAFTAFEQRMVTEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +G      I  + +SL+  +  E+     + 
Sbjct: 112 -----------------------------DG------ICCQRVSLDDVLPGEEQLRRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P     +  LR      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADPYAMQPQTIMEEQELRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
           T+ R ++ E +A+  L
Sbjct: 197 TKGRAQKTEEQAMDNL 212


>gi|282854097|ref|ZP_06263434.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|282583550|gb|EFB88930.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|314923070|gb|EFS86901.1| sigma-70, region 4 [Propionibacterium acnes HL001PA1]
 gi|314966840|gb|EFT10939.1| sigma-70, region 4 [Propionibacterium acnes HL082PA2]
 gi|314981182|gb|EFT25276.1| sigma-70, region 4 [Propionibacterium acnes HL110PA3]
 gi|315092002|gb|EFT63978.1| sigma-70, region 4 [Propionibacterium acnes HL110PA4]
 gi|315093239|gb|EFT65215.1| sigma-70, region 4 [Propionibacterium acnes HL060PA1]
 gi|315103504|gb|EFT75480.1| sigma-70, region 4 [Propionibacterium acnes HL050PA2]
 gi|327327666|gb|EGE69442.1| RNA polymerase sigma factor [Propionibacterium acnes HL103PA1]
          Length = 270

 Score = 44.3 bits (103), Expect = 0.070,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 90/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCVGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ +    P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWHSVPSSDAIAAQMGKDVMWVEKRRV-----ERWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|254523268|ref|ZP_05135323.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
 gi|219720859|gb|EED39384.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
          Length = 247

 Score = 44.3 bits (103), Expect = 0.070,   Method: Compositional matrix adjust.
 Identities = 56/230 (24%), Positives = 102/230 (44%), Gaps = 16/230 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  E++  +  LV  +A     R    ++  DLIQ G +GL++A+  +D   G  F TY 
Sbjct: 14  AANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYDADQGASFETYT 73

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ ++   I       R  VH R +      T RR+     R  +  E+A  + MP+
Sbjct: 74  SIRIRGSMIDEIRRGDWVPR-SVHRRAR--DAAATIRRLEQSSGRAASATEVAAAMEMPL 130

Query: 561 EGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               ++++     + +SLE+ I  ED   L D +  +   +P     +        + + 
Sbjct: 131 PEYLRLMEDAARGQVLSLESRI--EDQGEL-DTVA-QGGPTPQQVLERGEFGRELGKAIG 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE+ VL + +   +N    L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 HLPEREQLVLSLYYEQELN----LKEIGAVLGVSESRVCQIHGQAVLRLR 232


>gi|222529010|ref|YP_002572892.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455857|gb|ACM60119.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 310

 Score = 44.3 bits (103), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 7/87 (8%)

Query: 441 ASIAKKEMVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAEKFDWCLGYKF 496
           A +  + ++  NL+LV  VA K+    +G  +   DL+ EG IGL+ AA+ +D   G  F
Sbjct: 10  AKVQSQLLIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKG-SF 68

Query: 497 STYAMWWVKQAITRSIADQ--SCTIRI 521
           STYA   ++  I RS+     SC I +
Sbjct: 69  STYACKVIESKIKRSLPKYKLSCAISL 95


>gi|15643664|ref|NP_228710.1| RNA polymerase sigma-28 factor, putative [Thermotoga maritima MSB8]
 gi|4981438|gb|AAD35983.1|AE001755_6 RNA polymerase sigma-28 factor, putative [Thermotoga maritima MSB8]
          Length = 220

 Score = 44.3 bits (103), Expect = 0.074,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 98/200 (49%), Gaps = 24/200 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG +  + + E++D      F+T+ M  VK A+   +        +P ++R    K
Sbjct: 34  DLIQEGIVAALSSLERYDPSKA-SFTTFIMKRVKGAMYDYLRKIDW---MPRNLR----K 85

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHLG 589
            V+   R+  + +  P+ EEIA+K  +    +++V++   E +  +  + D  ED   L 
Sbjct: 86  NVKMIERVIYESEEFPSDEEIARKTGLE---LKEVVRARNEMMRKQLLMIDAMEDEIVLK 142

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
               D+NA   L       L E   + +  L+ +E+ VL +RF  G+    +L+E+ +  
Sbjct: 143 TEGPDENAYREL-------LVEEMKKAIEKLSDKEKLVLSLRFEKGL----SLKEIARVL 191

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            V+  R+ QI +K++ K+K 
Sbjct: 192 GVSESRVSQIISKSLLKIKK 211


>gi|170287832|ref|YP_001738070.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga sp. RQ2]
 gi|281411468|ref|YP_003345547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermotoga
           naphthophila RKU-10]
 gi|170175335|gb|ACB08387.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga sp. RQ2]
 gi|281372571|gb|ADA66133.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 220

 Score = 44.3 bits (103), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 96/200 (48%), Gaps = 24/200 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG +  + + E++D      F+T+ M  VK A+   +        +P ++R    K
Sbjct: 34  DLIQEGIVAALSSLERYDPSKA-SFTTFIMKRVKGAMYDYLRKIDW---MPRNLR----K 85

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHLG 589
            V+   R   + +  P+ EEIA+K  +    +++V++   E +  +  + D  ED   L 
Sbjct: 86  NVKMIERAIYESEEFPSDEEIARKTGLE---LKEVVRARNEMMRKQLLMIDAMEDEIVLK 142

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
               D+NA   L       L E   + +  L+ +E+ VL +RF      D +L+E+ K  
Sbjct: 143 TEGPDENAYREL-------LVEEMKKAIEKLSDKEKLVLSLRF----EKDLSLKEIAKVL 191

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            V+  R+ QI +K++ K+K 
Sbjct: 192 DVSESRVSQIISKSLLKIKK 211


>gi|317447069|emb|CBX24518.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
          Length = 269

 Score = 44.3 bits (103), Expect = 0.076,   Method: Compositional matrix adjust.
 Identities = 69/313 (22%), Positives = 133/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S DD  +V+S P+ 
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEGSADAS-DDEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|315101187|gb|EFT73163.1| sigma-70, region 4 [Propionibacterium acnes HL046PA1]
          Length = 270

 Score = 44.3 bits (103), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 90/199 (45%), Gaps = 28/199 (14%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +  E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGETIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  + ++  LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPESGLIGLLTGQERRIVELRHGF-EGEPMTITAVAHEL 242

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 243 GLSASNVRRIEQRALGRLR 261


>gi|37784436|gb|AAO13111.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|37955130|gb|AAP76217.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 272

 Score = 44.3 bits (103), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 34/145 (23%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E D  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|295102717|emb|CBL00262.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 44.3 bits (103), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 72/196 (36%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+GL KA  KFD   G KF TYA   ++ A+   + D        +   DK   
Sbjct: 55  DLKQAGNLGLWKAVSKFDAACGMKFLTYAAPAIRNAMMDMVRDAFAAFEQRMVTEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +GV        + +SL+  +  E+     + 
Sbjct: 112 -----------------------------DGV------CYQRVSLDEVLPGEEQLRRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P     +   R      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADPYAMQPQSIMEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
           T+ R ++ E +A+  L
Sbjct: 197 TKGRAKKTEEQAMDNL 212


>gi|302670826|ref|YP_003830786.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395299|gb|ADL34204.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 258

 Score = 43.9 bits (102), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 33/139 (23%), Positives = 62/139 (44%), Gaps = 15/139 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC--------LGYK 495
           A+ +++E  L LV+ VA+ YT +G+   DLI EGN  L K     D            YK
Sbjct: 113 AQSKLIECFLPLVVDVARMYTEQGVYLEDLIGEGNFALTKGVTMLDAVGEPEEVEGFLYK 172

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
               AM  V ++     A +   +++       + +V   A  ++  ++R+ T +E+  +
Sbjct: 173 LMLDAMEAVIESNLAEDAGEQKVLKL-------VQEVADKASELAQDLRRKVTVKELMDE 225

Query: 556 LAMPVEGVRKVLKITKEPI 574
                + +R  +K + + I
Sbjct: 226 TGWDEDKIRSAIKFSGDNI 244


>gi|308050008|ref|YP_003913574.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
 gi|307632198|gb|ADN76500.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
          Length = 242

 Score = 43.9 bits (102), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 48/201 (23%), Positives = 88/201 (43%), Gaps = 24/201 (11%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q G + L+ A  ++       F  +A   ++ AI   +  Q      P  +R + H+
Sbjct: 52  DMEQIGLMALLDALRRYPGEPDNGFIAFASLRIRGAILDELRRQDWR---PRQLRQQSHE 108

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +  T RR++ ++ R P  +E+A  L++ +E  R+ L  ++           E    L + 
Sbjct: 109 LNDTVRRLTRELGRPPHDQEVADALSLSLEQYRERLYASQA----------ESLQSLDEL 158

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS----LTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +    A + L+       R    R LAS    L  RE+ VL + +   +N    L+E+  
Sbjct: 159 L---GAGASLEQEGNETERFQRHRTLASALGKLNQREQLVLSLYYQHELN----LKEIAL 211

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              +T  RI Q+   A+++LK
Sbjct: 212 TLGLTESRICQLHKHAVKQLK 232


>gi|302746284|gb|ADL62732.1| RpoD [Morganella morganii subsp. sibonii]
          Length = 267

 Score = 43.9 bits (102), Expect = 0.083,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 1   GTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLI 57


>gi|148269170|ref|YP_001243630.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga petrophila
           RKU-1]
 gi|147734714|gb|ABQ46054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga petrophila
           RKU-1]
          Length = 214

 Score = 43.9 bits (102), Expect = 0.086,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 96/200 (48%), Gaps = 24/200 (12%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG +  + + E++D      F+T+ M  VK A+   +        +P ++R    K
Sbjct: 28  DLIQEGIVAALSSLERYDPSKA-SFTTFIMKRVKGAMYDYLRKIDW---MPRNLR----K 79

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHLG 589
            V+   R   + +  P+ EEIA+K  +    +++V++   E +  +  + D  ED   L 
Sbjct: 80  NVKMIERAIYESEEFPSDEEIARKTGL---ELKEVVRARNEMMRKQLLMIDAMEDEIVLK 136

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
               D+NA   L       L E   + +  L+ +E+ VL +RF      D +L+E+ K  
Sbjct: 137 TEGPDENAYREL-------LVEEMKKAIEKLSDKEKLVLSLRF----EKDLSLKEIAKVL 185

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            V+  R+ QI +K++ K+K 
Sbjct: 186 DVSESRVSQIISKSLLKIKK 205


>gi|153938326|ref|YP_001391685.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           F str. Langeland]
 gi|152934222|gb|ABS39720.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. Langeland]
 gi|295319714|gb|ADG00092.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. 230613]
          Length = 183

 Score = 43.9 bits (102), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 26/41 (63%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           DL QEG +GLMKAA +FD     KFSTYA  +V   I R I
Sbjct: 30  DLFQEGCLGLMKAANRFDSSRRIKFSTYAYPYVDGQILRMI 70


>gi|319790426|ref|YP_004152059.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114928|gb|ADU97418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 203

 Score = 43.9 bits (102), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 101/229 (44%), Gaps = 41/229 (17%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +KE+V  +L LV  VA +   R     ++F +L+  G IGL+KA E++D     KFSTY
Sbjct: 5   TRKELVLEHLPLVKKVANRIYRRIPEGAVEFEELVNTGVIGLIKAIERYDENRA-KFSTY 63

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A                  I+I   + D + K+    R +  K+K           L   
Sbjct: 64  AY-----------------IKIRGEILDYLRKLDFLPRSVREKVKN--------GDLDDL 98

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            EGV   + I       E    D D   + D +   +   P +  +  + +E  T  +  
Sbjct: 99  KEGVASFISIE------EKLFADSDRFTVKDTLASPDD-GPEERMLLEDAKEKLTEAIKK 151

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ +E+ VL++ F   ++    L+ +G+   ++  R+ QI++ A++KL+
Sbjct: 152 LSEKEQLVLQLIFVEELD----LKSIGEILGISVSRVSQIKSSALKKLR 196


>gi|170737028|ref|YP_001778288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
 gi|169819216|gb|ACA93798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 242

 Score = 43.9 bits (102), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 52/227 (22%), Positives = 103/227 (45%), Gaps = 35/227 (15%)

Query: 455 LVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGY---KFSTYAMWWVKQAI 508
           LV  + +K  ++    ++  DL Q G +GL++A  ++    G    +F  +A++ V+ AI
Sbjct: 34  LVKRIVRKLASQAGGAMEACDLEQLGLMGLLEALRRY----GEPDDEFEHFALFRVRGAI 89

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL- 567
              +  Q      P   R   H++  T R +  ++ R+PT EE+   L +  +   ++  
Sbjct: 90  LDELRRQDWR---PRSARQGAHRLRGTERALRRELGRDPTKEEVCNALEIGDDEYEQLQL 146

Query: 568 -KITKEPISLETPIGDEDTSHL----GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
               +E +S +  + +ED         D IE +           A LR +  + L  L  
Sbjct: 147 DDCAQEFVSFDALL-EEDAERYECDSSDGIEHR-----------AMLRHSLEQALGVLDA 194

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE++++++ +      D +  E+G    +TR R+ QI   A+ K+++
Sbjct: 195 REQQIIQLYY----EFDLSQAEIGAVLGLTRARVCQINKSALVKMRN 237


>gi|225389367|ref|ZP_03759091.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
           DSM 15981]
 gi|225044546|gb|EEG54792.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
           DSM 15981]
          Length = 384

 Score = 43.9 bits (102), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 3/68 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   I+     GE +A   +K +VE NL+ V+S+AK+Y    L   D++QE N  L
Sbjct: 19  MSAEEEARILERTAAGEVQA---RKRLVEGNLQKVLSIAKEYEGSRLPMADIVQEANTAL 75

Query: 482 MKAAEKFD 489
             AA ++D
Sbjct: 76  TLAAVEYD 83


>gi|188997549|ref|YP_001931800.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932616|gb|ACD67246.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 213

 Score = 43.9 bits (102), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 48/89 (53%), Gaps = 8/89 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           KK++VE  + LV  VA K   R     ++F DL+Q G +GL+KA E ++   G KFSTYA
Sbjct: 8   KKQIVEEYIGLVKKVASKIFYRLPDCEIEFDDLVQTGIVGLLKALENYNEDKG-KFSTYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKI 529
              ++  I   +  Q     +P   +DKI
Sbjct: 67  YIRIRGEILDFLRQQDI---MPKTEKDKI 92


>gi|11078917|dbj|BAB17463.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078921|dbj|BAB17465.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078927|dbj|BAB17468.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078935|dbj|BAB17472.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078941|dbj|BAB17475.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078943|dbj|BAB17476.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|11078947|dbj|BAB17478.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|11078949|dbj|BAB17479.1| DNA-directed RNA polymerase subunit D [Pseudomonas amygdali]
 gi|11078951|dbj|BAB17480.1| DNA-directed RNA polymerase subunit D [Pseudomonas amygdali]
 gi|11078953|dbj|BAB17481.1| DNA-directed RNA polymerase subunit D [Pseudomonas amygdali]
 gi|11078955|dbj|BAB17482.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|11078959|dbj|BAB17484.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|146150873|gb|ABQ02693.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
 gi|315064861|emb|CBX20966.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
 gi|315064865|emb|CBX20968.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
 gi|317447071|emb|CBX24519.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
          Length = 269

 Score = 43.9 bits (102), Expect = 0.094,   Method: Compositional matrix adjust.
 Identities = 69/313 (22%), Positives = 133/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S DD  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADAS-DDEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|160943408|ref|ZP_02090642.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445268|gb|EDP22271.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 43.9 bits (102), Expect = 0.096,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 72/196 (36%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+GL KA  KFD   G KF TYA   ++ A+   + D        +   DK   
Sbjct: 55  DLKQAGNLGLWKAVPKFDAAQGMKFLTYAAPAIRNAMVDMVRDAFAAFEQRMVTEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +G      I  + +SL+  +  E+     + 
Sbjct: 112 -----------------------------DG------ICYQRVSLDDVLPGEEQLRRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P     +   R      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADPYAMQPQSIMEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
           T+ R ++ E +A+  L
Sbjct: 197 TKGRAKKTEEQAMDNL 212


>gi|11078999|dbj|BAB17504.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score = 43.9 bits (102), Expect = 0.099,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 135/313 (43%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P  
Sbjct: 57  -------GYIDPDDGITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDEEEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+    +G+  +++
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------ELAR--KALKK---HGRGSKQA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
           + +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 140 TAELLALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|11079125|dbj|BAB17567.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 268

 Score = 43.9 bits (102), Expect = 0.099,   Method: Compositional matrix adjust.
 Identities = 74/315 (23%), Positives = 129/315 (40%), Gaps = 54/315 (17%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T  +++     +      L E+  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDSILSEYTRVTTEGGRLAEV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+   G     E      ++ ++ E E +D +E +GD E                   
Sbjct: 59  IDPDD--GIAAPAEVPVPVIKDGAAAEPETED-EEADGDSE------------------- 96

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                   DE+E D            R +     D++ +  + L+    ++  G  +   
Sbjct: 97  --------DEEEGDGGPDPEVA----RVRFGAVADQLEKAKKVLKKHGRDSKQGMAE--- 141

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
                 L E L  L   + L   + D LV ++ D   R+   E  +++L  +   + R  
Sbjct: 142 ------LAE-LASLFMPIKLVPKQFDALVTRVRDALDRLRAQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVAC---EVDSILKIRNEIKSISVETGISISE 426
           FL +    E+D  W   A+   +G+ K   A    + D IL+ + ++ ++  ETG+ +SE
Sbjct: 195 FLRQFPSHEIDESW---AEQLSKGKSKYAEAIGRLQAD-ILRCQQKLVALEAETGLKLSE 250

Query: 427 FRHIVSMVRKGECEA 441
            + I   +  GE +A
Sbjct: 251 IKDINRRMSIGEAKA 265


>gi|188586354|ref|YP_001917899.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|179351041|gb|ACB85311.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 113

 Score = 43.9 bits (102), Expect = 0.100,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 50/96 (52%), Gaps = 6/96 (6%)

Query: 576 LETPIG----DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           L+ PIG      + + L     D N V  +D    +  ++   RV+ +L PREE++LR R
Sbjct: 15  LQDPIGVDKEGNEITLLDILGSDSNMV--IDQVTLSIDKDKLRRVIKTLKPREEKILRWR 72

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           FG+      T +EV ++  ++R  + +IE + + K+
Sbjct: 73  FGLSNEKALTQKEVAEKLGISRSYVSRIEKRILNKM 108


>gi|54654477|gb|AAV37115.1| RpoD [Vibrio lentus]
          Length = 176

 Score = 43.5 bits (101), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 45/174 (25%), Positives = 77/174 (44%), Gaps = 15/174 (8%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+++   ++++    +     L   + D LV +L 
Sbjct: 10  EKFTALRTSYQNRQLAINEYGHESPKATLATTMMQD----VFKEFRLTPKQFDYLVNELR 65

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
               R+   E  ++R    YG + +  F+    G E    W+    A D P  E    + 
Sbjct: 66  TSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEK---IK 122

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
              + I +   ++  I  ET +++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 123 RNENDIRRSIQKLDMIEKETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLR 176


>gi|295104322|emb|CBL01866.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 221

 Score = 43.5 bits (101), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 72/196 (36%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+GL KA  KFD   G KF TYA   +  A+   + D   T    + + DK   
Sbjct: 55  DLKQAGNLGLWKAVPKFDAARGMKFLTYAAPAICNAMMDMVRDAFATFEQRMQIEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +G      I  + +SL+  +  E+     + 
Sbjct: 112 -----------------------------DG------ICYQRVSLDDVLPGEEQLRRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P     +   R      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADLYAMQPQSIIEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
            + R ++ E +A+  L
Sbjct: 197 AKSRAKKTEEQAMDNL 212


>gi|228907496|ref|ZP_04071353.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228851988|gb|EEM96785.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 324

 Score = 43.5 bits (101), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 28/107 (26%), Positives = 52/107 (48%), Gaps = 4/107 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+Q   I ++ A   FD+  G KF+TY    +   I + + + S  +R+     D    
Sbjct: 68  ELLQHAYIAVITAIRDFDFNKGIKFTTYIYRPIIWEINQLLYNDSRLVRLSRSAVD---- 123

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +++   ++ N++   P  EE+A  L + VE +  VL+   E  SL +
Sbjct: 124 LLKQMEKVENELGYFPKAEELAILLDVTVERIENVLRFASELTSLNS 170


>gi|167760166|ref|ZP_02432293.1| hypothetical protein CLOSCI_02538 [Clostridium scindens ATCC 35704]
 gi|167662291|gb|EDS06421.1| hypothetical protein CLOSCI_02538 [Clostridium scindens ATCC 35704]
          Length = 233

 Score = 43.5 bits (101), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 30/104 (28%), Positives = 53/104 (50%), Gaps = 4/104 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCL-GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           D+IQEGNI LM A    D C  G +     M  V+  +   +  Q+ T R    M +++ 
Sbjct: 129 DMIQEGNISLMMA---LDECKEGQEDEEAVMEAVRAGMQALLESQTETRRQDKKMVERVS 185

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           ++  T + MS ++ R+ + EE+A +L +    +  +LK+  E +
Sbjct: 186 ELDETIKGMSEELGRKVSVEEVADRLGITEAEIEDILKLAGEEV 229


>gi|11078937|dbj|BAB17473.1| DNA-directed RNA polymerase subunit D [Pseudomonas caricapapayae]
 gi|11078945|dbj|BAB17477.1| DNA-directed RNA polymerase subunit D [Pseudomonas caricapapayae]
          Length = 269

 Score = 43.5 bits (101), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 69/313 (22%), Positives = 133/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S DD  +V+S P+ 
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADGS-DDEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   +G++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|54654479|gb|AAV37116.1| RpoD [Vibrio cyclitrophicus]
          Length = 176

 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 48/177 (27%), Positives = 78/177 (44%), Gaps = 21/177 (11%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+++   ++++    +     L   + D LV +L 
Sbjct: 10  EKFTALRTSYQNRQLAINEYGHESPKATIATTMMQD----VFKEFRLTPKQFDYLVNELR 65

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
               R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 66  TSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 123

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            E D    IR  I+ + +   ET +++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 124 NEHD----IRRSIQKLDMIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLR 176


>gi|306031830|gb|ADM83576.1| RNA polymerase sigma-70 factor [Pseudomonas sp. M1(2010b)]
          Length = 275

 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 36/132 (27%), Positives = 66/132 (50%), Gaps = 2/132 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGREL 379
           L +L   + L   + + LVE++    +R+   E  +++L  +   + R  FL    G E+
Sbjct: 145 LAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRLFPGNEV 204

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W S A    + ++   +      I++ + ++ ++  ETG+ I+E + I   +  GE 
Sbjct: 205 DESW-SDALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEIKDINRRMSIGEA 263

Query: 440 EASIAKKEMVEA 451
           +A  AKKEMVEA
Sbjct: 264 KARRAKKEMVEA 275


>gi|11078995|dbj|BAB17502.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 135/313 (43%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P  
Sbjct: 57  -------GYIDPDDGITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDEEEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+    +G+  +++
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------ELAR--KALKK---HGRGSKQA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
           + +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 140 TAELLALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|146295621|ref|YP_001179392.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409197|gb|ABP66201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 310

 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 7/80 (8%)

Query: 448 MVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++  NL+LV  VA K+    +G  +   DL+ EG IGL+ AA+ +D   G  FSTYA   
Sbjct: 17  LIVDNLKLVYHVANKFMPCPKGYYYEVEDLVSEGYIGLVVAAKNYDPTKG-SFSTYACKV 75

Query: 504 VKQAITRSIADQ--SCTIRI 521
           ++  I RS+     SC I +
Sbjct: 76  IESKIKRSLPKYKLSCAISL 95


>gi|11079035|dbj|BAB17522.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score = 43.5 bits (101), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 135/313 (43%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P  
Sbjct: 57  -------GYIDPDDGITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDDEEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+    +G+  +++
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------ELAR--KALKK---HGRGSKQA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
           + +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 140 TAELLALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRFQPDIVRCQQKLTALQTETGLTIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|213958518|gb|ACJ54680.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm3R]
          Length = 260

 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 29/42 (69%)

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           EMG++ELL+REGEI IAKRIE G   +M ++   P T   ++
Sbjct: 1   EMGTVELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHIL 42


>gi|83816261|ref|YP_446679.1| RNA polymerase sigma-28 factor [Salinibacter ruber DSM 13855]
 gi|294508614|ref|YP_003572673.1| RNA polymerase sigma factor for flagellar operon [Salinibacter
           ruber M8]
 gi|83757655|gb|ABC45768.1| RNA polymerase sigma-28 factor [Salinibacter ruber DSM 13855]
 gi|294344943|emb|CBH25721.1| RNA polymerase sigma factor for flagellar operon [Salinibacter
           ruber M8]
          Length = 248

 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 44/193 (22%), Positives = 88/193 (45%), Gaps = 11/193 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G +GL++A + +D     +F+T+A   ++  I   +       R     R K+  
Sbjct: 51  DLESVGIVGLLEALDNYDPEQA-QFATHAYRRIRGNIIDYLRSIDVLSR---EKRKKMGA 106

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLG 589
           V      +   +  EP+ E++A  + M VE    +L+    +  +SL  P  D+D + L 
Sbjct: 107 VQEALSSLRQMLGEEPSDEDVADYMGMAVEEYHDLLRDAQCRFSLSLSRPSEDDDHTML- 165

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +   +     +   +A+ ++    ++ +L  R++ +L    G+    D TL+E+G+  
Sbjct: 166 DVLPSDDGTEGFEQFEKASTQKHLEDLIQTLPERQQTIL----GLYYTEDLTLQEIGEVL 221

Query: 650 CVTRERIRQIEAK 662
            ++  RI Q+  K
Sbjct: 222 DLSAARISQLLGK 234


>gi|124265243|ref|YP_001019247.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
 gi|124258018|gb|ABM93012.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
          Length = 265

 Score = 43.5 bits (101), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 107/245 (43%), Gaps = 30/245 (12%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A+  + E +  +  LV  +AK+   R    ++  +L+Q G IGL +A  +F+   G  F 
Sbjct: 28  AATVRNEQLHQHGALVRRIAKRMRARLPANVEMDELLQAGLIGLNEAITRFEESFGASFD 87

Query: 498 TYAMWWVKQAITRSI-ADQSCTIRIPVHMRDKIHKVVRTA-RRMSNKIKREPTPEEIAKK 555
           TYA   ++ A+  S+ A  + +     H R      +R A + + +++ R P   E+A +
Sbjct: 88  TYASRRIEGAMLDSLRAADTLSRDARAHQR-----AIRAAVQALEHRLLRPPRAMEVASE 142

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-----------VSPLDSA 604
           L   +  + + L    E  +     GD     L D    + A             PL +A
Sbjct: 143 LGWSLARLHQRL---VEAGAAGQRAGDAPLDGLADEASARGAEDDLHATADDHADPL-AA 198

Query: 605 IQANLRETT-TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +Q   R T       +L  RE+ +++M +  G++     E +G    V+  R+ Q+ A  
Sbjct: 199 LQRRQRTTALNAAFDTLEEREQLMMKMIYERGLDHQDAAESLG----VSPSRVSQMHAVV 254

Query: 664 IRKLK 668
           ++KLK
Sbjct: 255 VQKLK 259


>gi|253574829|ref|ZP_04852169.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251845875|gb|EES73883.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 110

 Score = 43.5 bits (101), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +H+  M  +G+ E+   +  ++E NLRLV  + KK+ N G    DLI  G IGL+KA 
Sbjct: 44  ETKHLQRMA-EGDSES---RNILIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAI 99

Query: 486 EKFDWCLGYKF 496
           E F    G K 
Sbjct: 100 ESFRPNKGTKL 110


>gi|11078931|dbj|BAB17470.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078961|dbj|BAB17485.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 72/313 (23%), Positives = 135/313 (43%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   +      L++ T +  E   L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHI------LSEYTCVTSEGGRLSDV 54

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +      G+    +G +         + +    + T+ D E +A  S DD  +V+S P+ 
Sbjct: 55  LS-----GYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADAS-DDEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|331002428|ref|ZP_08325946.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330410244|gb|EGG89678.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 172

 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 28/137 (20%), Positives = 69/137 (50%), Gaps = 3/137 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EA++     + + +   G + +DLI E ++ L  A  ++               
Sbjct: 39  AKNRLIEAHMMYATELVQPFMGCGQEVMDLISESHLALTMAVTEYK---SGDLKAQIRQA 95

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V++ +   I +Q+        + +++++++  +  ++N+  RE T +E++ +L +P + V
Sbjct: 96  VEKRLNEIIDEQNRAKHDSNELTNRLNELMEISSALANEYGREATAKELSDRLLIPQDEV 155

Query: 564 RKVLKITKEPISLETPI 580
            ++LKI+   I+L+  I
Sbjct: 156 EELLKISLNAINLDKNI 172


>gi|68171972|ref|ZP_00545278.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998602|gb|EAM85349.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
          Length = 205

 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 48/205 (23%), Positives = 88/205 (42%), Gaps = 45/205 (21%)

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPE 550
           LG++ STYA+WW+K  I   I      I+I     + K+   +R  ++   K     T E
Sbjct: 3   LGFRLSTYAIWWIKAFIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLFKYNHNITKE 62

Query: 551 EI---AKKLAMPVEGVRKVLKI----------------------TKEPISLETPIGDEDT 585
           +I   A K +   + V ++ +                        +E I  +TP   EDT
Sbjct: 63  DIKLIANKCSTSEQEVEQMNRYFLYRDRSLNELVFSNDNQNGVELQEIIKCDTP-NQEDT 121

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV-LRMRFGIGMNTDHTLEE 644
             L + +  K A+               ++ L++L  R   + +R R    +    TL++
Sbjct: 122 YLLNEELNIKKAL--------------ISQALSTLNERYRDIFIRRRL---IEEPDTLDK 164

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           + +++ +++ER+RQIE  A  K+K+
Sbjct: 165 LSQEYNISKERVRQIEMHAFTKVKN 189


>gi|115377816|ref|ZP_01465004.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|310820297|ref|YP_003952655.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
 gi|115365148|gb|EAU64195.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393369|gb|ADO70828.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
          Length = 260

 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 35/56 (62%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +R + +  +K  N  L+  +L+  G IGL++AA++FD  +G  F T+A + +K AI
Sbjct: 1   MRSLAATVRKQFNAQLELDELVSYGQIGLLEAADRFDPKVGANFLTFAHYRIKGAI 56


>gi|307293798|ref|ZP_07573642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
 gi|306879949|gb|EFN11166.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
          Length = 245

 Score = 43.1 bits (100), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 48/203 (23%), Positives = 91/203 (44%), Gaps = 16/203 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G + L++AA  F+   G  F++YA   V+ A+   +   +   R  +  R ++  
Sbjct: 54  DLLQIGMVALVEAANGFE-DRGLGFASYAQMRVRGAMIDHLRRHATMTRSAMAQRKQLAG 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           +     R+  K+ R P   E++ ++ +     R+V    +  +  S++    D+ +    
Sbjct: 113 I---RNRLEQKLGRIPLESEMSAEMGLDPAAYREVADGCEMVQHTSMDEVYSDQ-SMWFA 168

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D  E  + V   +S     L+    + +  L  RE  VL++ F   +N    LEE+G   
Sbjct: 169 DVEERADDVMERES-----LKAALAKCIGDLPQREALVLQLYFVEELN----LEEIGATL 219

Query: 650 CVTRERIRQIEAKAIRKLKHPSR 672
            +   R+ QI+  A+ KL+   R
Sbjct: 220 DIGAARVCQIKKAALDKLREKLR 242


>gi|294013075|ref|YP_003546535.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
 gi|292676405|dbj|BAI97923.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
          Length = 245

 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 47/203 (23%), Positives = 93/203 (45%), Gaps = 16/203 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G + L++AA  F+   G  F++YA   V+ A+   +   +   R  +  R ++  
Sbjct: 54  DLLQIGMVALVEAANGFE-DRGLGFASYAQMRVRGAMIDHLRRHATMTRSAMSQRKQLAA 112

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG 589
           +     R+  ++ R P   E++ ++ +     R+V    +  +  S++    D+ +    
Sbjct: 113 I---RNRLEQRLGRAPLEAEMSAEMGLDAAAYREVADGCEMVQHTSMDEVYSDQ-SMWFA 168

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +ED+      D   + +L+    + +  L  RE  VL++ F   +N    LEE+G   
Sbjct: 169 D-VEDRAD----DIMERESLKGALAQYIGELPQREALVLQLYFVEELN----LEEIGATL 219

Query: 650 CVTRERIRQIEAKAIRKLKHPSR 672
            +   R+ QI+  A+ KL+   R
Sbjct: 220 DIGAARVCQIKKAALDKLREKLR 242


>gi|160902849|ref|YP_001568430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
 gi|160360493|gb|ABX32107.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
          Length = 231

 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 98/212 (46%), Gaps = 27/212 (12%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           + ++  DLIQEG IGL+++ ++++   G  F TYA+    + I  S+ D    I      
Sbjct: 31  KNIELEDLIQEGIIGLLQSYKRYNPEKGTSFYTYAL----KRIKGSMYDYLRRI------ 80

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEE------IAKKLAMPVEGVRKV-LKITKEPISL-- 576
            D + K VR+  +    +  E    E      +A+KL +    V K+   ++K  I    
Sbjct: 81  -DWLPKDVRSLVKKYEDLIYECKDNEYIDDNSVAEKLHIEKNDVDKIKFSLSKRQILQLD 139

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           E  + +E+ + L D  E+ +   P   A +  L +  T  +  L  RE+ +L + +  G+
Sbjct: 140 EYFLNNEEDTWLEDIQEEND---PEILAYKDMLHDKLTESIEKLEEREKLILSLYYNEGL 196

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T +E+G    ++  R+ Q+ +  + KLK
Sbjct: 197 ----TFKEIGSVLEISESRVSQLHSVILVKLK 224


>gi|182412226|ref|YP_001817292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
 gi|177839440|gb|ACB73692.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
          Length = 262

 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 56/240 (23%), Positives = 106/240 (44%), Gaps = 14/240 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCL 492
           +G   +++ +K+++E +L LV +V  +        +D   L   G  GL+ A  KFD   
Sbjct: 21  QGVSPSNVDEKDLIERHLYLVRNVVDRIKLNLPTHIDADDLYSVGVTGLIAAVRKFDPEQ 80

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F++YA   ++ A+   +         P   R +  K+  T   +  K+ R  + EEI
Sbjct: 81  GCTFASYAAMRIRGAVLDELRRMDWC---PRRARARSRKLKETIIEVEQKLGRAASDEEI 137

Query: 553 AKKLAMPVEGVRKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
              L +  +   K ++    +T   I       D + + L + ++D+  V+  ++  +  
Sbjct: 138 CSALGLTQKDYAKWVEDARPVTFLAIDHRNENEDGEGASLHELLKDETDVTGRENLEKRE 197

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E  T+ ++ L    +++L M +   M     L E+   F +T  RI QI A+ I  L+
Sbjct: 198 LLELLTQRISELPDIPKKILAMYYFENMR----LAEIAAVFNLTESRICQIHAQTILGLR 253


>gi|167574693|ref|ZP_02367567.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           C6786]
          Length = 236

 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 53/218 (24%), Positives = 93/218 (42%), Gaps = 23/218 (10%)

Query: 455 LVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  VA++     N  +   D+ Q G +GL++A  ++       F+ YA   V+ AI   
Sbjct: 32  LVKRVARQLGSQANGAIALEDMEQIGLMGLLEALRRYG-SPDEAFAGYAALRVRGAILDE 90

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKIT 570
           +         P  +R+  H+     R +   + R PT  E++  L + ++  R+ V+   
Sbjct: 91  LRRHDWR---PRAVRNAAHRARDCERALCRTLGRVPTAGEVSASLGIGIDEYRENVMANR 147

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            E ++    + D D         D N         Q  LR    + L SL  RE+RV+++
Sbjct: 148 AEAMASFDEMLDADW-----LAHDDNPER------QVVLRRCLEQALTSLDEREQRVIQL 196

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      D +L E+     +T  R+ QI   A+RK++
Sbjct: 197 YY----EFDLSLREIAAVLELTEARVCQINKAALRKMR 230


>gi|27383248|ref|NP_774777.1| sigma-70 subunit [Bradyrhizobium japonicum USDA 110]
 gi|27356422|dbj|BAC53402.1| bsr8137 [Bradyrhizobium japonicum USDA 110]
          Length = 65

 Score = 43.1 bits (100), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 30/47 (63%)

Query: 35 IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
          I L R++G+VT E+LN  LP   +  + +E  +  LS+ GIN++D D
Sbjct: 17 IGLGRRKGFVTFEQLNQLLPAATIEPKDIEAIMQALSDEGINLIDDD 63


>gi|239934592|emb|CAR94610.1| DNA-directed RNA polymerase subunit D [uncultured Acidobacteria
           bacterium]
          Length = 226

 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           ++  I++I  ET  +  E R  +  + +G+  A IAK EMVEANLRLVIS
Sbjct: 177 VKVRIEAIEAETKSTALELRRTLQSMVQGQITAEIAKNEMVEANLRLVIS 226


>gi|215270843|emb|CAR48099.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270853|emb|CAR48104.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           MG++ELL+REGEI IA+RIE G   + +S+ E P T   ++
Sbjct: 1   MGTVELLTREGEIDIAQRIEEGINQVQSSVAEYPGTIPYIL 41


>gi|215270841|emb|CAR48098.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270847|emb|CAR48101.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           MG++ELL+REGEI IA+RIE G   + +S+ E P T   ++
Sbjct: 1   MGTVELLTREGEIDIAQRIEEGINQVQSSVAEYPGTIPYIL 41



 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 71/166 (42%), Gaps = 11/166 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    E  S K  V  E ++ +     L   + D LV +L   
Sbjct: 120 EKFNQLRSTYQNLQLAINEHGYE--SPKATVANELMLDVFKEFRLTPKQFDHLVNELRTA 177

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++ A  YG + +  F+    G E    W+    A D P  E    +   
Sbjct: 178 MDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEK---IKRN 234

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEM
Sbjct: 235 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEM 280


>gi|293375374|ref|ZP_06621655.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325844422|ref|ZP_08168149.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
 gi|292645927|gb|EFF63956.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325489096|gb|EGC91480.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
          Length = 200

 Score = 43.1 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 32/64 (50%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E    L+  +A  Y   G  + D  QEG +  +KA   FD    Y F +YAM  V+ A
Sbjct: 25  IIEKYSPLIGKIASSYYGIGYDYQDFFQEGRMAFIKAIYSFDENSNYSFYSYAMTCVRNA 84

Query: 508 ITRS 511
           IT S
Sbjct: 85  ITTS 88


>gi|11078971|dbj|BAB17490.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 43.1 bits (100), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 70/314 (22%), Positives = 132/314 (42%), Gaps = 51/314 (16%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+  +V+S P  
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAAKAEGTDDDEEESADAS-DEEDEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE-LRSLQDNAVNGQKDEK 309
                     D   +A    A+ DQ+            E+ R+ L+ L      G++D+ 
Sbjct: 107 ----------DPVIAAQRFGAVSDQM------------EITRKALKKL------GREDKH 138

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRD 368
           +  +   L E    L   + L   + + LVE++     R+   E  +++L  +   + R 
Sbjct: 139 AIAEMVALAE----LFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRA 194

Query: 369 VFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E 
Sbjct: 195 DFLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEI 252

Query: 428 RHIVSMVRKGECEA 441
           + I   +  GE +A
Sbjct: 253 KDINRRMSIGEAKA 266


>gi|332669182|ref|YP_004452190.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Cellulomonas
           fimi ATCC 484]
 gi|332338220|gb|AEE44803.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cellulomonas
           fimi ATCC 484]
          Length = 296

 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 44/205 (21%), Positives = 91/205 (44%), Gaps = 28/205 (13%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L   G++ L+ AA+ +D   G  F+ YA   ++ A+   +       R     R ++ +
Sbjct: 38  ELASAGSLALVLAAQAYDPTTGVPFARYASLRIRGALVDELRSMDWASR---GARQRVRE 94

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--------RKVLKITKEPISLETPIGDE 583
           +  T  R++  ++R+PT +E+A+ + + V  V        R+VL +            D 
Sbjct: 95  LAATTERLTAVLRRKPTRDELAEAMGVDVRAVDDAARDAERRVLSM------------DA 142

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               + D + D    +P +S +  + R    R      P  +R+  +  G+ +  D ++ 
Sbjct: 143 TEGTVADLVVDAEP-TPEESLLN-DERHRWLRAAVETLP--DRLRTVVVGLFL-LDRSVA 197

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  +  VT+ RI Q+  +A+  L+
Sbjct: 198 ELAAELGVTQSRISQLRTEALGLLR 222


>gi|295104067|emb|CBL01611.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 220

 Score = 43.1 bits (100), Expect = 0.17,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 105/248 (42%), Gaps = 50/248 (20%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVA-KKYTNRGLQ-------FLDLIQEGNIG 480
            +  + +KG+   + A+  ++E NL  +  +A ++Y N GL          DL+QEG+IG
Sbjct: 8   QLCRLAQKGD---TAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIG 64

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+ A   FD   G KF TYA   ++ A+T       C IR  + + ++         RM 
Sbjct: 65  LLNAIPLFDAGRGMKFLTYAAPALRNAMT------DC-IRAALGLFEQ---------RMV 108

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           +K K  P              G ++V         L+  + +++     + I D +  +P
Sbjct: 109 DK-KDGP--------------GFQRVY--------LDDVLSEDERMLRIEAIADPHTQTP 145

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               IQ          L +LT RE+  L  R+G     +H L      F ++    +++E
Sbjct: 146 EQIYIQKEQLIELYAALDNLTAREQTYLLYRYGFTDGIEHPLIGAALHFHLSESWTKKVE 205

Query: 661 AKAIRKLK 668
            +A+  L+
Sbjct: 206 GEAMDSLR 213


>gi|325107978|ref|YP_004269046.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
 gi|324968246|gb|ADY59024.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
          Length = 259

 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 58/264 (21%), Positives = 115/264 (43%), Gaps = 19/264 (7%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQE 476
           T +S  E   I    +K +    + +  ++E  L LV   A++   +   G+   DL+  
Sbjct: 3   TKLSPEEVLEIWEAYKKDQTNQHL-RNRLIERYLPLVRYNAERVWAKLPDGVDLNDLMSA 61

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G  GLM A + FD   G KF TY +  ++ A+   +        +P  +R K  K+   +
Sbjct: 62  GVFGLMDAIDAFDMERGVKFETYCVPRIRGAMLDELRTMDW---VPRLVRSKASKLAAAS 118

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS---HLGDF 591
           + +  +  R PT  E+A K+ + +E   K+         +SL     + D+       D 
Sbjct: 119 KAVEAETGRPPTDVEVAAKMELSLEEFEKLKSEAAAVGLVSLNKKWYETDSYKDVREVDI 178

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +ED     P +   + ++ +  T+ L     R ER++ + +      + T++E+G    +
Sbjct: 179 LEDGKGEDPTNGIQKRDIMKLVTKGLN----RNERLIMILY---YYEELTMKEIGMTLGL 231

Query: 652 TRERIRQIEAKAIRKLKHPSRSKK 675
           +  R+ Q+ +  + +LK   R ++
Sbjct: 232 SESRVSQMHSSIVNRLKDQLRKRR 255


>gi|148239620|ref|YP_001225007.1| DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. WH 7803]
 gi|147848159|emb|CAK23710.1| Possible DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. WH 7803]
          Length = 210

 Score = 43.1 bits (100), Expect = 0.17,   Method: Composition-based stats.
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V  +L+LV  +A+ Y NR G++  DL Q G +GL++AAE F+      F  +A   
Sbjct: 21  RNQRVNDHLQLVSPIARHYANRCGVECDDLNQVGLMGLLRAAENFNADRCIPFHAFARPH 80

Query: 504 VKQAITRSIADQSCTIRIP 522
           ++ AI   + D +  +R+P
Sbjct: 81  IRGAILHYLRDNASMVRMP 99


>gi|254698073|ref|ZP_05159901.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 188

 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 57/100 (57%), Gaps = 9/100 (9%)

Query: 575 SLETPIGDEDT--SHLGDFIEDKNAVSP--LDSAIQANLRET-TTRVLASLTPREERVLR 629
           SL  P+  E+T  S   DF+ D + +     +S+I    R    TR L +L  RE  ++R
Sbjct: 78  SLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIR 137

Query: 630 MRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    ++ D  TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 138 ER---RLDDDGVTLEALGEKLGISKERVRQIESRAMEKLK 174


>gi|37784428|gb|AAO13107.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
          Length = 274

 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 34/147 (23%), Positives = 67/147 (45%), Gaps = 6/147 (4%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           NG+  E++         +L  +     L   + D LV  + ++ +R+   E  +L++  +
Sbjct: 133 NGRAHEETQAAIA----QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVE 188

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +A   + +L+   +++ I  ETG
Sbjct: 189 QAKMPKKTFVSAFTNNECETAWFEYQKQAGKA-WSAPLAAMEEEVLRSIGKLQQIEEETG 247

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEM 448
           +SI++ + I   +  GE +A  AKKEM
Sbjct: 248 LSIAQIKDINRRMSIGEAKARRAKKEM 274


>gi|45442811|ref|NP_994350.1| flagellar biosynthesis sigma factor [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108809036|ref|YP_652952.1| flagellar biosynthesis sigma factor [Yersinia pestis Antiqua]
 gi|150260230|ref|ZP_01916958.1| lateral flagellar sigma factor 28 protein [Yersinia pestis
           CA88-4125]
 gi|162420360|ref|YP_001604825.1| flagellar biosynthesis sigma factor [Yersinia pestis Angola]
 gi|165925029|ref|ZP_02220861.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165939031|ref|ZP_02227583.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|166008912|ref|ZP_02229810.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166212025|ref|ZP_02238060.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167398583|ref|ZP_02304107.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167418724|ref|ZP_02310477.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167466317|ref|ZP_02331021.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis FV-1]
 gi|218927931|ref|YP_002345806.1| flagellar biosynthesis sigma factor [Yersinia pestis CO92]
 gi|229837430|ref|ZP_04457593.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides A]
 gi|229840642|ref|ZP_04460801.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229842806|ref|ZP_04462958.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|294502807|ref|YP_003566869.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|45437677|gb|AAS63227.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis biovar Microtus str. 91001]
 gi|108780949|gb|ABG15007.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis Antiqua]
 gi|115346542|emb|CAL19419.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis CO92]
 gi|149289638|gb|EDM39715.1| lateral flagellar sigma factor 28 protein [Yersinia pestis
           CA88-4125]
 gi|162353175|gb|ABX87123.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis Angola]
 gi|165912987|gb|EDR31612.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|165923229|gb|EDR40380.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165992251|gb|EDR44552.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166206771|gb|EDR51251.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|166962718|gb|EDR58739.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167051087|gb|EDR62495.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|229690073|gb|EEO82130.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229697008|gb|EEO87055.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229705553|gb|EEO91563.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides A]
 gi|262360839|gb|ACY57560.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D106004]
 gi|262364784|gb|ACY61341.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D182038]
 gi|294353266|gb|ADE63607.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
          Length = 231

 Score = 43.1 bits (100), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 43/199 (21%), Positives = 99/199 (49%), Gaps = 19/199 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q   +GL++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK
Sbjct: 47  DMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDWR---PRRLRQKTHK 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLG 589
                R+++ ++  EP  EEI+ +L +  +  ++ L +       SL+  +  E  +H  
Sbjct: 103 TNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALE--AH-N 159

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D ++ ++    +   I+ NL++     +++L  RE+ +L + +      + +++E+ +  
Sbjct: 160 DILQSRDLEENI--IIEDNLKQA----ISTLDEREQMILHLYY----QQELSMKEIAQVL 209

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +T  RI Q+  K ++K+K
Sbjct: 210 DLTEARICQLNKKLVQKIK 228


>gi|113954054|ref|YP_730869.1| type III sigma factor [Synechococcus sp. CC9311]
 gi|113881405|gb|ABI46363.1| putative type III sigma factor [Synechococcus sp. CC9311]
          Length = 271

 Score = 43.1 bits (100), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+QEG +GL+     FD   G++ STY +  V   I     D+   +RIP  ++D   +
Sbjct: 51  DLVQEGCLGLINGMANFDPQRGFRISTYVLARVNGQILHFRRDRQHALRIPWRLKDLHSR 110

Query: 532 VVR-TARRMSNKI 543
            VR  A+R+   +
Sbjct: 111 GVRLQAQRLQQSL 123


>gi|312877884|ref|ZP_07737830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795347|gb|EFR11730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 114

 Score = 42.7 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 27/66 (40%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+  ++E NLRLV  +AKKYT       D +I  G IGL+KA E +      K STYA  
Sbjct: 33  ARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIGLIKAIETYSKAKSTKLSTYAAK 92

Query: 503 WVKQAI 508
            ++  I
Sbjct: 93  CIENEI 98


>gi|260762513|ref|ZP_05874850.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672939|gb|EEX59760.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 184

 Score = 42.7 bits (99), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 35/100 (35%), Positives = 57/100 (57%), Gaps = 9/100 (9%)

Query: 575 SLETPIGDEDT--SHLGDFIEDKNAVSP--LDSAIQANLRET-TTRVLASLTPREERVLR 629
           SL  P+  E+T  S   DF+ D + +     +S+I    R    TR L +L  RE  ++R
Sbjct: 74  SLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIR 133

Query: 630 MRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    ++ D  TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 134 ER---RLDDDGVTLEALGEKLGISKERVRQIESRAMEKLK 170


>gi|330984347|gb|EGH82450.1| putative alternative sigma factor RpoH [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 263

 Score = 42.7 bits (99), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 70/275 (25%), Positives = 112/275 (40%), Gaps = 32/275 (11%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           DS   I N+I+  S++      E  + + + +   C    A    V A L +V  +A   
Sbjct: 8   DSFFAILNKIQIPSIQ------EMDNNIRIFKSTGCRK--AHDACVTALLPMVYGLAVAN 59

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             R  +  D+ Q+G + +M A  KFD        ++   +V +AI       +  IR+P 
Sbjct: 60  AGRA-EVDDMFQQGALAVMDALRKFDPDDELNILSWTKLYVSRAINSLCVFGTKLIRVPD 118

Query: 524 HMRDKIHKVVRTA-RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPI- 580
                  K +R   RRM   +K  P  E  +K LA  +    +  KI ++   S   P+ 
Sbjct: 119 ------TKTIRLCYRRMGLFLKDGPINEARSKILANELGVSLEDFKIARDLYSSCYEPVL 172

Query: 581 --GDEDTSHLGDFIEDKNAVSPLDSAI-----QANLRETTTRVLASLTPREERVLRMRFG 633
             GDE          D      L+ AI      A++     R++  L P+E  V+R+R  
Sbjct: 173 SCGDEPWQG-----HDIKTSETLEEAIIVEDEAAHVTRVVGRLMTVLNPKEAEVIRLR-- 225

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                   L  VG+Q   + ER RQ+E  A  K++
Sbjct: 226 CLQEEPVQLRLVGEQLGFSTERARQVENIAKDKMR 260


>gi|239934532|emb|CAR94580.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 238

 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG----TTLLREIIDLE 188
           LL+REGEI IAKRIE G   + A+LC  P TF  L I  + +  G    T LL   +D  
Sbjct: 2   LLTREGEIRIAKRIEEGLNQVKAALCLFPPTFDHLRISYEIIRAGEARLTDLLTGFVDPN 61

Query: 189 A 189
           A
Sbjct: 62  A 62


>gi|225075400|ref|ZP_03718599.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
 gi|224953218|gb|EEG34427.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
          Length = 113

 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 4/90 (4%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           DED     D++ D +A      + QA+     E     LA L  R  R++  R+ +  + 
Sbjct: 15  DEDNFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSHRIVESRW-LQDDG 73

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 74  GLTLHELAAEYGVSAERIRQIEAKAMQKLR 103


>gi|150390243|ref|YP_001320292.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Alkaliphilus
           metalliredigens QYMF]
 gi|149950105|gb|ABR48633.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alkaliphilus metalliredigens QYMF]
          Length = 117

 Score = 42.7 bits (99), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 7/105 (6%)

Query: 568 KITKEPISLETPIGDEDTSH---LGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           K TK  +SL+ PIG +   +   L D +  E    V  ++  IQ  +R+   ++   L  
Sbjct: 7   KKTKAEVSLQDPIGVDKEGNEISLLDILGTESDGVVDEVELKIQ--IRKLYQKMSKVLKS 64

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           RE+ V+ +R+GI      T  E+ K   ++R  + +IE +AI KL
Sbjct: 65  REKMVIELRYGIAGCGSKTQREIAKMLGISRSYVSRIEKRAINKL 109


>gi|11078933|dbj|BAB17471.1| DNA-directed RNA polymerase subunit D [Pseudomonas ficuserectae]
          Length = 269

 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 133/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S DD  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADAS-DDEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + L+E++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLLERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|266706197|gb|ACY78403.1| sigma factor [Streptomyces chattanoogensis]
          Length = 269

 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 8/70 (11%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKD--------SADRSTDDPVRMYLREMGSIELLSREGE 139
           G  D+ + A  A N+   L    +        +A  +T DPV+ YL+++G +  L+ E E
Sbjct: 179 GKGDAPEAAEGAENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPFLNAEQE 238

Query: 140 IAIAKRIEAG 149
           + +AKRIEAG
Sbjct: 239 VELAKRIEAG 248


>gi|312621865|ref|YP_004023478.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202332|gb|ADQ45659.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 302

 Score = 42.7 bits (99), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 5/86 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAEKFDWCLG 493
           E   S+ ++ ++  N++LV  VA K+    +G  +   DLI EG IGL+ AA+ +D   G
Sbjct: 3   ESLTSVQRQMLIADNIKLVYHVANKFMPCPKGYCYEVDDLISEGYIGLVVAAKNYDPAKG 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTI 519
             FS+YA   ++  I RS+     T+
Sbjct: 63  -SFSSYACKVIESRIKRSLPKYRLTL 87


>gi|301312525|ref|ZP_07218422.1| RNA polymerase sigma factor RpoD [Bacteroides sp. 20_3]
 gi|300829491|gb|EFK60164.1| RNA polymerase sigma factor RpoD [Bacteroides sp. 20_3]
          Length = 84

 Score = 42.7 bits (99), Expect = 0.21,   Method: Composition-based stats.
 Identities = 20/46 (43%), Positives = 30/46 (65%)

Query: 32 KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
          K +I    ++GY+T  E+N  LP D V +EQ+ED + M++ MGI V
Sbjct: 17 KLLISKGLEQGYLTYAEVNDHLPDDLVDAEQIEDIIGMINGMGIEV 62


>gi|58699678|ref|ZP_00374352.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533807|gb|EAL58132.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 93

 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 40/66 (60%), Gaps = 2/66 (3%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LASL  R   +   R+ +  N   TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ L
Sbjct: 30  LASLNERARDIFISRY-LSENIQ-TLDELSKKYCVSRERIRQLAEQAMAKVKQYIQSESL 87

Query: 677 RSFLDG 682
           +  L  
Sbjct: 88  KFCLHA 93


>gi|317969864|ref|ZP_07971254.1| DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. CB0205]
          Length = 227

 Score = 42.7 bits (99), Expect = 0.22,   Method: Composition-based stats.
 Identities = 25/89 (28%), Positives = 47/89 (52%), Gaps = 1/89 (1%)

Query: 455 LVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           LV+  A+ Y  R  + +D LIQ G +G ++A+ +F          YA  +V+ AI R + 
Sbjct: 17  LVLGTARHYAQRCREPIDDLIQAGWVGFLRASARFQPGPDRSLGAYAKPFVRGAILRHLR 76

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           D S  +R+P  ++D++ ++ +      N+
Sbjct: 77  DNSRLVRLPRSVQDRLAQLNKIEAATGNQ 105


>gi|260893856|ref|YP_003239953.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
 gi|260865997|gb|ACX53103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
          Length = 252

 Score = 42.7 bits (99), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 49/232 (21%), Positives = 101/232 (43%), Gaps = 12/232 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           + +K+E+V   L LV  +  +   R    +   D+   G +GL+ A E++D   G +F +
Sbjct: 16  TTSKEELVRRYLPLVKYLVGRLAVRLPPWVSLEDIEGAGILGLLAAMERYDPSQGVEFES 75

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA + +  A+   +   +   R       ++  V++   R   +    P  E++A++L  
Sbjct: 76  YARYRIWGAMLDEVRRWA---RFSRRTWQQMQAVLKVQERWEREKGCRPKVEDVAQELGW 132

Query: 559 PVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               V ++ +        SLE     E  S   +F+ D     PL+  ++          
Sbjct: 133 EPAQVDRLGRYFAAFNSFSLEEVRSAEGRSPWEEFLADPKGQDPLEELLEKEDLGRLAEA 192

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  R + +L + +  G+    TL E+G+   ++  R+ Q+ ++A+ KL+
Sbjct: 193 IGRLEERLQLILALYYQEGL----TLREIGEVLGISESRVCQLHSRALTKLR 240


>gi|152976319|ref|YP_001375836.1| FliA/WhiG family RNA polymerase sigma factor [Bacillus cereus
           subsp. cytotoxis NVH 391-98]
 gi|152025071|gb|ABS22841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 242

 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 9/69 (13%)

Query: 442 SIAKKEMVEANLRLVIS-VAKKYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++ +E ++   + V   + KKY +R        GL+F DL+Q G I L+KA E+F   +
Sbjct: 9   ALSDEEFIQKYEKFVFHFIHKKYGHRLQAIKDDTGLEFEDLVQCGMIALIKAREQFKPEM 68

Query: 493 GYKFSTYAM 501
           G+KF T+A+
Sbjct: 69  GFKFLTFAV 77


>gi|46204564|ref|ZP_00049813.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 132

 Score = 42.7 bits (99), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 49/102 (48%), Gaps = 13/102 (12%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV------LASLTPREERVL 628
           SL  P+ +E      D++ D    SP    + A   E   R+      L  L PRE R+ 
Sbjct: 18  SLNAPLREEGEGEWQDWLVDN---SPSQETVLAREEEGRNRLSALRDALGVLNPRERRIF 74

Query: 629 RMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             R    +  D  TLE++  +F V+RER+RQIE +A  K++ 
Sbjct: 75  EARR---LADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQE 113


>gi|255658878|ref|ZP_05404287.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
 gi|260848826|gb|EEX68833.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
          Length = 208

 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A++ ++E+   LV   A  +       LDLIQEG +GL++AAE++D   G  FS +A+
Sbjct: 36  ARQRLIESYQPLVFKQAAPFAQLDCA-LDLIQEGTVGLIEAAERYDHTRGVAFSLFAV 92


>gi|21231354|ref|NP_637271.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66768593|ref|YP_243355.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|188991595|ref|YP_001903605.1| RNA polymerase sigma factor rpoD (Sigma-70). [Xanthomonas
           campestris pv. campestris str. B100]
 gi|21113015|gb|AAM41195.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573925|gb|AAY49335.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|167733355|emb|CAP51556.1| RNA polymerase sigma factor rpoD (Sigma-70) [Xanthomonas campestris
           pv. campestris]
          Length = 255

 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 88/202 (43%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 51  DLIQAGMIGLIEASRSYDSDQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 108 AAAAVRKIEQNTGRAAAATEVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTT 167

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     +        + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 168 -------AKGGPNPQQMMERGEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 216

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 217 AVLGVSESRVCQIHGQAVVRLR 238


>gi|302872420|ref|YP_003841056.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302575279|gb|ADL43070.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 310

 Score = 42.4 bits (98), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAEKFDWCLGYKFS 497
           ++ ++ ++  NL+LV  VA K+    +G  +   DLI EG  GL+ AA  +   LG  FS
Sbjct: 11  NLHRQLLIANNLKLVYHVANKFMPCPKGYMYEVDDLISEGYFGLVVAANNYKPELGTPFS 70

Query: 498 TYAMWWVKQAITRSI 512
           +YA   ++  I RS+
Sbjct: 71  SYACKVIESKIKRSL 85


>gi|186896753|ref|YP_001873865.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|186699779|gb|ACC90408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 231

 Score = 42.4 bits (98), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 39/197 (19%), Positives = 89/197 (45%), Gaps = 15/197 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q   +GL++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK
Sbjct: 47  DMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDWR---PRRLRQKTHK 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                R+++ ++  EP  EEI+ +L +  +         +E + LE     E    +   
Sbjct: 103 TNEAIRQIAKRLGHEPNFEEISAELNLTADEY-------QEYLLLENAGAMESLDEILAL 155

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
               + +   D      + +   + +++L  RE+ +L + +      + +++E+ +   +
Sbjct: 156 DAHNDILQSCDLEENIIIEDNLKQAISALDEREQMILHLYY----QQELSMKEIAQVLDL 211

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI Q+  K ++K+K
Sbjct: 212 TEARICQLNKKLVQKIK 228


>gi|325917849|ref|ZP_08180027.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535933|gb|EGD07751.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 255

 Score = 42.4 bits (98), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 88/202 (43%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 51  DLIQAGMIGLIEASRSYDSDQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 108 AAAAVRKIEQNTGRAAAATEVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTT 167

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     +        + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 168 -------AKGGPNPQQMMERGEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 216

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 217 AVLGVSESRVCQIHGQAVVRLR 238


>gi|317134088|ref|YP_004089999.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
 gi|315450550|gb|ADU24113.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 330

 Score = 42.4 bits (98), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           E  +A   ++E N+ L+ S  K +T N+   + +L+Q G  G+  AA+++ +  G +F T
Sbjct: 30  EKELAATVLIEKNIGLITSTLKHFTTNKRTSWDELMQAGRYGIFYAAKRYKFNEGTQFHT 89

Query: 499 YAMWWVKQAI 508
           +A+  +K AI
Sbjct: 90  FAVSQIKAAI 99


>gi|54654457|gb|AAV37105.1| RpoD [Vibrio gigantis]
 gi|54654481|gb|AAV37117.1| RpoD [Vibrio crassostreae]
          Length = 176

 Score = 42.4 bits (98), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 48/177 (27%), Positives = 78/177 (44%), Gaps = 21/177 (11%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+ +   ++++    +     L   + D LV +L 
Sbjct: 10  EKFTALRTSYQNRQLAINEYGHESPKAMLATTMMQD----VFKEFRLTPKQFDYLVNELR 65

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
           +   R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 66  NSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 123

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            E D    IR  I+ + +   ET +++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 124 NEHD----IRRSIQKLDMIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLR 176


>gi|256831228|ref|YP_003159956.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
 gi|256580404|gb|ACU91540.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
          Length = 267

 Score = 42.4 bits (98), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 44/197 (22%), Positives = 82/197 (41%), Gaps = 10/197 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GLM+A  KF   L  +F T+A   ++ A+   +       R    +R +I K
Sbjct: 70  DLISAGTLGLMEALGKFQPELNIRFETFADSRIRGAMLDELRRMDWYSR---GLRQRIKK 126

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  R    +    PT  E+ +      + +   L+     I L      +  +  GD 
Sbjct: 127 LEQVIRGFEQENGHAPTRSELLELTGQDRQELEATLEAVNSQIILSLDAIQDQWNQPGD- 185

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
               N   P  +    ++ +    ++  L  RE+ VL + +      +  ++EV     +
Sbjct: 186 --GGNHREPFAAVAFHDIIDKLGHLIDRLNEREKLVLSLYY----TEEFNMKEVALALDI 239

Query: 652 TRERIRQIEAKAIRKLK 668
           T  R+ Q+ ++A+ KLK
Sbjct: 240 TEGRVSQLHSQALGKLK 256


>gi|237808347|ref|YP_002892787.1| sigma-70 region 4 domain-containing protein [Tolumonas auensis DSM
           9187]
 gi|237500608|gb|ACQ93201.1| sigma-70 region 4 domain protein [Tolumonas auensis DSM 9187]
          Length = 913

 Score = 42.4 bits (98), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 35/55 (63%), Gaps = 1/55 (1%)

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK-LKHPS 671
           AS+   E+ +  +   +  N   TLEE+G  + VTRERIRQ+E+ AI K LK+PS
Sbjct: 398 ASIVKNEKELATIVCRLLSNNKKTLEELGAIYGVTRERIRQLESLAIAKLLKNPS 452


>gi|327485473|gb|AEA79879.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 185

 Score = 42.4 bits (98), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 8/83 (9%)

Query: 591 FIEDKNAVSPLDSAIQANLRE--TTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEV 645
           ++EDK+  S L   ++A   E  TT R+   LASL  R + ++R R+ +  +   TL+++
Sbjct: 100 YLEDKH--SDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNKTTLQDL 156

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
            + + V+ ERIRQ+E  A+RKLK
Sbjct: 157 AEMYGVSAERIRQLEKNAMRKLK 179


>gi|313837242|gb|EFS74956.1| sigma-70, region 4 [Propionibacterium acnes HL037PA2]
 gi|314927738|gb|EFS91569.1| sigma-70, region 4 [Propionibacterium acnes HL044PA1]
 gi|314972014|gb|EFT16112.1| sigma-70, region 4 [Propionibacterium acnes HL037PA3]
 gi|328907208|gb|EGG26974.1| sigma-70, region 4 [Propionibacterium sp. P08]
          Length = 270

 Score = 42.4 bits (98), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 49/94 (52%), Gaps = 2/94 (2%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQSGCVGLGEAIERYDERRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           V R    ++ + +R P+ + IA ++   V  V K
Sbjct: 147 VARIEEELTARWQRVPSSDAIAAQMGKDVMWVEK 180


>gi|295101345|emb|CBK98890.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 42.4 bits (98), Expect = 0.29,   Method: Composition-based stats.
 Identities = 48/196 (24%), Positives = 71/196 (36%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+GL KA  KFD   G KF TYA   ++ A+   + D        +   DK   
Sbjct: 55  DLKQAGNLGLWKAVPKFDAARGMKFLTYAAPAIRNAMMDMVRDAFAAFEQRMVTEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +G      I  + +SL+  +  E+     + 
Sbjct: 112 -----------------------------DG------ICYQRVSLDDVLPGEEQLQRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P         R      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADPYAMQPQSIMEDQESRRELYDGLKRLTQREQTYLLYRYGFTDGKEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
           T+ R ++ E +A+  L
Sbjct: 197 TKGRAQKTEEQAMDNL 212


>gi|66474715|gb|AAY46927.1| RpoD [Aeromonas veronii]
          Length = 275

 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 60/129 (46%), Gaps = 2/129 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           KL  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E
Sbjct: 148 KLADIFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVSAFTNNE 207

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      VA E + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 208 CETAWFEYQKQAGKAWSAPLVAME-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 266

Query: 439 CEASIAKKE 447
            +A  AKKE
Sbjct: 267 AQARRAKKE 275


>gi|312898376|ref|ZP_07757766.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
 gi|310620295|gb|EFQ03865.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
          Length = 205

 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 16/30 (53%), Positives = 25/30 (83%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           D++QEGN+GL++A E++D+ LG  FS YA+
Sbjct: 58  DVLQEGNLGLIEAVERYDYKLGVAFSIYAV 87


>gi|148239819|ref|YP_001225206.1| putative group 3 RNA polymerase sigma factor [Synechococcus sp. WH
           7803]
 gi|147848358|emb|CAK23909.1| Putative group 3 RNA polymerase sigma factor [Synechococcus sp. WH
           7803]
          Length = 286

 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 49/89 (55%), Gaps = 2/89 (2%)

Query: 441 ASIAKKE-MVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           ASI K+  +V  +L L    A +   RG  ++ DL QE  +GL+K+ ++F+   G++ S+
Sbjct: 28  ASIQKRNGLVLQHLGLAHHAANQQLPRGGGEYDDLCQEARLGLVKSLDRFEPSRGHQVSS 87

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           YA+      I     D+  T+RIP  ++D
Sbjct: 88  YAIPKATGQILHYRRDRLHTLRIPWRIKD 116


>gi|284097320|ref|ZP_06385455.1| hypothetical protein POR_0044 [Candidatus Poribacteria sp. WGA-A3]
 gi|283831170|gb|EFC35145.1| hypothetical protein POR_0044 [Candidatus Poribacteria sp. WGA-A3]
          Length = 119

 Score = 42.4 bits (98), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 17/20 (85%), Positives = 19/20 (95%)

Query: 117 TDDPVRMYLREMGSIELLSR 136
           TDDPVR+YLREMGS+ LLSR
Sbjct: 100 TDDPVRLYLREMGSVSLLSR 119


>gi|197250155|ref|YP_002147819.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197213858|gb|ACH51255.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 68

 Score = 42.4 bits (98), Expect = 0.29,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 37/57 (64%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 4   LNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 60


>gi|11078967|dbj|BAB17488.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078973|dbj|BAB17491.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 72/313 (23%), Positives = 131/313 (41%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEKGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+   G     E       +    E   DD +E+          S D+  +V+S P+ 
Sbjct: 59  IDPDD--GIAPPAEVPPPVDPKAVKAEGADDDEEESAD--------SSDEEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W    AK   +G++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGHEVDESWTDGLAKG--KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|21242677|ref|NP_642259.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|294664736|ref|ZP_06730065.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|21108148|gb|AAM36795.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|292605490|gb|EFF48812.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 255

 Score = 42.4 bits (98), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 88/202 (43%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 51  DLIQAGMIGLIEASRSYDSEQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 108 AAAAVRKIEQNTGRAAAATEVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTT 167

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     +        + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 168 -------AKGGPNPQQMMERGEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 216

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 217 AVLGVSESRVCQIHGQAVVRLR 238


>gi|331005480|ref|ZP_08328859.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330420756|gb|EGG95043.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 225

 Score = 42.0 bits (97), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 50/220 (22%), Positives = 88/220 (40%), Gaps = 37/220 (16%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           ++  S+ KK  +  L+F D    G IGL++A +K+    G  F TYA + +K AI   I 
Sbjct: 25  KIAASLYKKRFDNSLEFDDYKHYGFIGLLEAKKKYTSDQGASFDTYATYRIKGAILNGIV 84

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK----LAMPVEGVRKVLKI 569
             S          +K+      +RR  ++++    PE   +     L + + G   V   
Sbjct: 85  KNS----------EKMQLYAYNSRREKDRLRSLKAPEPTNRMDLFDLFIELTGNLAV--- 131

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQANLRETTTRVLASLTPREERVL 628
                           S L D  E + +V    ++  Q+ +       +  L   E+ V+
Sbjct: 132 ---------------ASLLDDMSESEISVDECSETYYQSQMSSDLLLGVEHLNGNEKLVV 176

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  G++     +EV     VT+ RI Q+   A+ KL+
Sbjct: 177 TYHYFGGLD----FQEVADILEVTKGRISQLHKSALEKLR 212


>gi|149182533|ref|ZP_01861006.1| sigma factor SigD [Bacillus sp. SG-1]
 gi|148849793|gb|EDL63970.1| sigma factor SigD [Bacillus sp. SG-1]
          Length = 161

 Score = 42.0 bits (97), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 3/87 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G +GL+ A EKFD     KF TYA + V+ +I   +  +     +P   R++  K
Sbjct: 55  DLKSLGLMGLLDALEKFDPSRDLKFDTYASFRVRGSIIDGLRKEDW---LPRSTRERAKK 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAM 558
           +      +  ++ R  TPEEIA+++ M
Sbjct: 112 IEAKIESLEQELLRHVTPEEIAQEMQM 138


>gi|78047533|ref|YP_363708.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325928018|ref|ZP_08189235.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
 gi|78035963|emb|CAJ23654.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325541614|gb|EGD13139.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
          Length = 255

 Score = 42.0 bits (97), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 88/202 (43%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 51  DLIQAGMIGLIEASRSYDSEQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 108 AAAAVRKIEQNTGRAAAATEVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTT 167

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     +        + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 168 -------AKGGPNPQQMMERGEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 216

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 217 AVLGVSESRVCQIHGQAVVRLR 238


>gi|166712012|ref|ZP_02243219.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola
           BLS256]
 gi|289666124|ref|ZP_06487705.1| RNA polymerase sigma factor [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 255

 Score = 42.0 bits (97), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 88/202 (43%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 51  DLIQAGMIGLIEASRSYDSEQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 108 AAAAVRKIEQNTGRAAAATEVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTT 167

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     +        + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 168 -------AKGGPNPQQMMERGEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 216

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 217 AVLGVSESRVCQIHGQAVVRLR 238


>gi|23429449|gb|AAM94472.1| RNA polymerase sigma factor D [Aeromonas veronii]
          Length = 281

 Score = 42.0 bits (97), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 II 185
           II
Sbjct: 60  II 61


>gi|167567742|ref|ZP_02360658.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           EO147]
          Length = 236

 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 53/218 (24%), Positives = 93/218 (42%), Gaps = 23/218 (10%)

Query: 455 LVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  VA++     N  +   D+ Q G +GL++A  ++       F+ YA   V+ AI   
Sbjct: 32  LVKRVARQLGSQANGVIALEDMEQIGLMGLLEALRRYG-SPDEAFAGYAALRVRGAILDE 90

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKIT 570
           +         P  +R+  H+     R +   + R PT  E++  L + ++  R+ V+   
Sbjct: 91  LRRHDWR---PRAVRNAAHRARDCERALCRTLGRVPTAGEVSASLGIGIDEYRENVMANR 147

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            E ++    + D D         D N         Q  LR    + L SL  RE+RV+++
Sbjct: 148 AEAMASFDEMLDADW-----LAHDDNPER------QVVLRRCLEQALTSLDEREQRVIQL 196

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      D +L E+     +T  R+ QI   A+RK++
Sbjct: 197 YY----EFDLSLREIAAVLELTEARVCQINKAALRKMR 230


>gi|239934594|emb|CAR94611.1| DNA-directed RNA polymerase subunit D [uncultured Acidobacteria
           bacterium]
          Length = 231

 Score = 42.0 bits (97), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 33/51 (64%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +REGE+ IA+RIE G+  ++ S+  +PL  + +I   D L+ G   +RE++
Sbjct: 1   TREGEVEIARRIERGKLSVIKSISRTPLVSRKVIQLGDALHTGDRTIRELV 51


>gi|90406802|ref|ZP_01214994.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
 gi|90312039|gb|EAS40132.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
          Length = 235

 Score = 42.0 bits (97), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 98/220 (44%), Gaps = 44/220 (20%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G IGL++AA  FD   G  F T++                  IRI   M D++ +
Sbjct: 41  DLLQSGMIGLLEAARNFDGSKGASFETFS-----------------GIRIRGAMLDEMRR 83

Query: 532 -------VVRTARRMSNKI----KR---EPTPEEIAKKLAMPVEGVRKVLKITK--EPIS 575
                  V + +R +SN I    KR   +    EIA +L + +   +++L+     + ++
Sbjct: 84  GDWVPRSVHKNSREISNAISAVEKRNAGDAKESEIASQLGVTLAKYQQMLRDVNCAKLVN 143

Query: 576 LETPIGDEDTSHLGDFIEDKNA-VSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFG 633
            E   G E T     F    N+ V P  + + ++   E    ++  L  RE  VL + + 
Sbjct: 144 YEDLGGAEAT-----FSSSVNSEVDPTFNCVSESEYSEQLLLMIKQLPEREALVLSLYYD 198

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +N    L+E+G    +   R+ QI ++A+ +LK  +++
Sbjct: 199 EELN----LKEIGLVLELGESRVSQILSQALHRLKAKAQT 234


>gi|326386918|ref|ZP_08208532.1| sigma 28 (flagella/sporulation) [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208598|gb|EGD59401.1| sigma 28 (flagella/sporulation) [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 243

 Score = 42.0 bits (97), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 54/214 (25%), Positives = 94/214 (43%), Gaps = 35/214 (16%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA----------ITRSIADQS 516
           G+   DLIQ G + L + ++K        F+ YA   V+ A          ++RS AD+ 
Sbjct: 43  GIDLEDLIQAGLVALTECSQKHTGQTEDGFAAYAKLRVRGAMVDLIRRTAPMSRSAADRR 102

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            T      +RD           +S  + R+PT  E+A+ + +        L+   EP+  
Sbjct: 103 RT------LRDHTES-------LSCALGRQPTEGELAEAMGL-TLADLADLRAAAEPLRF 148

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGI 634
           ET I D  +     F +D+    P   A+ A+   R      +A+L  R + V+++ F  
Sbjct: 149 ET-IDDAYSESSMAFADDR----PDSFALLADEETRHVVGAAIAALPERLQMVIQLYFVE 203

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +N    L E+     V+  R+ Q++A+A+ KL+
Sbjct: 204 ELN----LAEIAAVLEVSVPRVHQLKAQALDKLR 233


>gi|323490161|ref|ZP_08095381.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
 gi|323396209|gb|EGA89035.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
          Length = 252

 Score = 42.0 bits (97), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 41/188 (21%), Positives = 84/188 (44%), Gaps = 10/188 (5%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A  KF+     KF TYA W +K AI   +        +P  +RDK+ K+ +    +
Sbjct: 64  GLLDALSKFNIERDLKFETYASWRIKGAIIDGLRQSDW---LPRSVRDKVKKIEKAFLLL 120

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +     + EE++  L +    + K   +++  +S    + D++    G  + + +  S
Sbjct: 121 EQQSGVSVSDEEVSSYLGITKAELNKT--VSEAALSTMISMDDDNFEEQGKLV-NYHVDS 177

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P     +   +E+  R +  L  +E+  + + +   M     L E+ +   V+  R+ Q+
Sbjct: 178 PERHLSEQMRKESLVRAIERLPEKEKITVSLCYFEEMK----LTEIAEILNVSVSRVSQL 233

Query: 660 EAKAIRKL 667
            +KA+ +L
Sbjct: 234 HSKAMLRL 241


>gi|23429441|gb|AAM94468.1| RNA polymerase sigma factor D [Aeromonas sobria]
          Length = 281

 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 II 185
           II
Sbjct: 60  II 61


>gi|3021678|dbj|BAA25359.1| RNA polymerase sigma-70 factor [Pseudomonas fluorescens]
 gi|11079001|dbj|BAB17505.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
 gi|11079013|dbj|BAB17511.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score = 42.0 bits (97), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 134/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P  
Sbjct: 57  -------GYIDPDDGIAPPAAEVPPPVDPK-AVKADDDAEDDDAEASTDDEDEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+    +G+ ++ +
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------EITR--KALKK---HGRSNKLA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
             +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 140 IAELVALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KAKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|51597620|ref|YP_071811.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|51590902|emb|CAH22558.1| Putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
          Length = 231

 Score = 42.0 bits (97), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 39/197 (19%), Positives = 89/197 (45%), Gaps = 15/197 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q   +GL++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK
Sbjct: 47  DMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDWR---PRRLRQKTHK 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                R+++ ++  EP  EEI+ +L +  +         +E + LE     E    +   
Sbjct: 103 TNEAIRQIAKRLGHEPNFEEISAELNLTADEY-------QEYLLLENAGAMESLDEILAL 155

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
               + +   D      + +   + +++L  RE+ +L + +      + +++E+ +   +
Sbjct: 156 DAHNDILQSRDLEENIIIEDNLKQAISALDEREQMILHLYY----QQELSMKEIAQVLDL 211

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI Q+  K ++K+K
Sbjct: 212 TEARICQLNKKLVQKIK 228


>gi|224419054|ref|ZP_03657060.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
 gi|253827994|ref|ZP_04870879.1| flagellar biosynthesis sigma factor FliA [Helicobacter canadensis
           MIT 98-5491]
 gi|313142562|ref|ZP_07804755.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
 gi|253511400|gb|EES90059.1| flagellar biosynthesis sigma factor FliA [Helicobacter canadensis
           MIT 98-5491]
 gi|313131593|gb|EFR49210.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
          Length = 235

 Score = 42.0 bits (97), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 46/202 (22%), Positives = 87/202 (43%), Gaps = 17/202 (8%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++F DL+  G   L+K A K+D  L   F  YA   V  A+   +    C  R   H R
Sbjct: 41  NVEFADLVSIGTEELIKLARKYDQNLNDSFWGYAKSRVYGAMLDYLRGLDCMSR---HTR 97

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I  + +   +  N+ + EP    ++K L   +E +++    ++  I    P+ +E ++
Sbjct: 98  TLIKSINKEISKYYNEYQEEPDNAYLSKVLNEDIEKIKEARNASE--IYGILPLDEELSA 155

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              D   +K     L   IQ         +L S +  E+ V+++ +      + + +E+ 
Sbjct: 156 AQEDKTYNKIEKQELIGIIQ--------NILESASKNEQLVIQLYY----YEELSFKEIS 203

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   ++  RI QI    IRK++
Sbjct: 204 EILEISESRISQIHKSVIRKIR 225


>gi|225629823|ref|ZP_03787747.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225591324|gb|EEH12440.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 95

 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 3/70 (4%)

Query: 609 LRETT-TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+ET     LASL  R   +   R+ +  N   TL+E+ K++CV+RERIRQ+  +A+ K+
Sbjct: 23  LKETILNNALASLNERARDIFISRY-LSENI-QTLDELSKKYCVSRERIRQLAEQAMAKV 80

Query: 668 KHPSRSKKLR 677
           K   +S+ L+
Sbjct: 81  KPYIQSESLK 90


>gi|11078965|dbj|BAB17487.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078969|dbj|BAB17489.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 72/313 (23%), Positives = 131/313 (41%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+   G     E       +    E   DD +E+          S D+  +V+S P+ 
Sbjct: 59  IDPDD--GIAPPAEVPPPVDPKAVKAEGADDDEEESAD--------SSDEEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W    AK   +G++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGHEVDESWTDGLAKG--KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|11078987|dbj|BAB17498.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 268

 Score = 42.0 bits (97), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 72/314 (22%), Positives = 132/314 (42%), Gaps = 52/314 (16%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K    + + E DD +E   D       + D+  +V+S P+ 
Sbjct: 59  IDPDDGIAPPAEVPPPVDPK----AAKAEGDDEEEESAD-------ASDEEDEVESGPDP 107

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE-LRSLQDNAVNGQKDEK 309
               +R              A+ DQ+            E+ R+ L+ L        +D+K
Sbjct: 108 VIAQQR------------FGAVSDQM------------EITRKALKKLG-------RDDK 136

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R 
Sbjct: 137 HAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRA 193

Query: 369 VFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            FL +  G E+D  W  + AK   + ++   +A     I + + ++ ++  ETG+ I+E 
Sbjct: 194 DFLRQFPGNEVDESWTDALAKG--KSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEI 251

Query: 428 RHIVSMVRKGECEA 441
           + I   +  GE +A
Sbjct: 252 KDINRRMSIGEAKA 265


>gi|23429439|gb|AAM94467.1| RNA polymerase sigma factor D [Aeromonas media]
          Length = 280

 Score = 41.6 bits (96), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 II 185
           II
Sbjct: 60  II 61


>gi|46371299|gb|AAS90415.1| stationary phase sigma factor [Azomonas macrocytogenes]
          Length = 55

 Score = 41.6 bits (96), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 30/38 (78%)

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+
Sbjct: 3   RFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLR 40


>gi|23429453|gb|AAM94474.1| RNA polymerase sigma factor D [Aeromonas sp. 'CDC 2478-85']
          Length = 281

 Score = 41.6 bits (96), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 II 185
           II
Sbjct: 60  II 61


>gi|153947529|ref|YP_001399652.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|152959024|gb|ABS46485.1| flagellar operon sigma factor , sigma-28 [Yersinia
           pseudotuberculosis IP 31758]
          Length = 231

 Score = 41.6 bits (96), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 39/197 (19%), Positives = 89/197 (45%), Gaps = 15/197 (7%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q   +GL++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK
Sbjct: 47  DMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDWR---PRRLRQKTHK 102

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                R+++ ++  EP  EEI+ +L +  +         +E + LE     E    +   
Sbjct: 103 TNEAIRQIAKRLGHEPNFEEISAELNLTADEY-------QEYLLLENAGAMESLDEILAL 155

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
               + +   D      + +   + +++L  RE+ +L + +      + +++E+ +   +
Sbjct: 156 DAHNDILQSRDLEENIIIEDNLKQAISALDEREQMILHLYY----QQELSMKEIAQVLDL 211

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI Q+  K ++K+K
Sbjct: 212 TEARICQLNKKLVQKIK 228


>gi|197294375|ref|YP_001798916.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853702|emb|CAM11593.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 151

 Score = 41.6 bits (96), Expect = 0.43,   Method: Composition-based stats.
 Identities = 35/110 (31%), Positives = 54/110 (49%), Gaps = 11/110 (10%)

Query: 445 KKEMVEANLRLVISVAKK--YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++++ +  LV  +A K  Y  + LQ  DL QEG +GL+K+ + ++  LGY F  YA  
Sbjct: 20  RDQLIKMHFPLVKKIANKFKYFPKSLQREDLYQEGILGLIKSLDNYE-DLGYDFIAYATP 78

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
            +K  IT  I     T   P+       KV R  ++ SN    E  P+ I
Sbjct: 79  TIKGEITELIRGLQ-TTSTPI-------KVFRKEKQTSNIPFEENQPQSI 120


>gi|54654469|gb|AAV37111.1| RpoD [Vibrio tasmaniensis]
          Length = 175

 Score = 41.6 bits (96), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 77/176 (43%), Gaps = 21/176 (11%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+++   ++++    +     L   + D LV +L 
Sbjct: 10  EKFTALRTSYQNRQLAINEYGHESPKATLATTMMQD----VFKEFRLTPKQFDYLVNELR 65

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
               R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 66  TSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 123

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            E D    IR  I+ + +   ET +++   + I   +  GE +A  AKKEMVEANL
Sbjct: 124 NEHD----IRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANL 175


>gi|37784470|gb|AAO13128.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score = 41.6 bits (96), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    KL  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAKLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLVMDEEVLRSIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|167730889|emb|CAJ29295.2| DNA-directed RNA polymerase subunit D [Pseudomonas
           frederiksbergensis]
          Length = 272

 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 65/130 (50%), Gaps = 4/130 (3%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           L +L   + L   + + LVE++     R+   E  +++L  +   + R  FL +  G E+
Sbjct: 145 LAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 204

Query: 380 DPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE
Sbjct: 205 DESWTDALAKG--KSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|302746278|gb|ADL62729.1| RpoD [Morganella morganii subsp. morganii]
          Length = 267

 Score = 41.6 bits (96), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 32/56 (57%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           ++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I
Sbjct: 2   TVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLI 57


>gi|310779951|ref|YP_003968283.1| RNA polymerase, sigma 30 subunit, SigH [Ilyobacter polytropus DSM
           2926]
 gi|309749274|gb|ADO83935.1| RNA polymerase, sigma 30 subunit, SigH [Ilyobacter polytropus DSM
           2926]
          Length = 203

 Score = 41.6 bits (96), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 3/88 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           ++V M ++G+ EA     E+      LV+  +K Y   G    DL+QEG IGL+KA   +
Sbjct: 4   NLVKMAQEGDQEAVT---EIFNKYRGLVLMKSKNYFLNGADRDDLLQEGMIGLLKAIRAY 60

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQS 516
           D      F+T+A   +K+ I  +I + +
Sbjct: 61  DEGKNTSFNTFASLCIKRQIITAIKNSN 88


>gi|23429481|gb|AAM97308.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 281

 Score = 41.6 bits (96), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 II 185
           II
Sbjct: 60  II 61


>gi|320529893|ref|ZP_08030970.1| sigma-70 region 2 [Selenomonas artemidis F0399]
 gi|320137911|gb|EFW29816.1| sigma-70 region 2 [Selenomonas artemidis F0399]
          Length = 208

 Score = 41.6 bits (96), Expect = 0.51,   Method: Composition-based stats.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 10/117 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ ++EA   LV      Y  R L   +D +QEG IGL++A E++D   G  FS YA+ 
Sbjct: 35  ARRRIIEAYQPLVFREVMPY--RALPAVMDAVQEGTIGLIEAVERYDPARGVAFSLYAVH 92

Query: 503 WVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
            V+  I   +  +  T+ +P +   D++H+   TA+ +   +  +P+  E+A+  A+
Sbjct: 93  RVRGCILDFLRREG-TVDLPCLEASDEMHE---TAKELIAAV--QPSVPELAEHHAL 143


>gi|289670573|ref|ZP_06491648.1| RNA polymerase sigma factor [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 255

 Score = 41.6 bits (96), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 88/202 (43%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 51  DLIQAGMIGLIEASRSYDSEQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 108 AAAAVRKIEQNTGRAAAATEVAAAMEMPLLDYLRLMEDAARGQVLSLESRIEDHGELDTT 167

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     +        + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 168 -------AKGGPNPQQMMERGEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 216

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 217 AVLGVSESRVCQIHGQAVVRLR 238


>gi|228982422|ref|ZP_04142681.1| sporulation sigma factor SigK [Bacillus thuringiensis Bt407]
 gi|228776605|gb|EEM24913.1| sporulation sigma factor SigK [Bacillus thuringiensis Bt407]
          Length = 203

 Score = 41.6 bits (96), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 48/231 (20%), Positives = 92/231 (39%), Gaps = 57/231 (24%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           N RLV  V K + N  +   +L+  G +G  KA   FD     KFSTYA+  +K  I   
Sbjct: 23  NERLVYYVVKMFENSQIDPDELVNAGMVGYAKALNAFDTTREVKFSTYAINCIKNEILFF 82

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +             ++K H       R++N                              
Sbjct: 83  LR------------KEKKH-------RLNN------------------------------ 93

Query: 572 EPISLETPIG---DEDTSHLGDFIEDKNA--VSPLDSAIQANLRETTTRVLASLTPREER 626
             +SL T +    + +  HL D + +KN    S  D  ++ + +      +  L P E+ 
Sbjct: 94  --VSLNTVLSVDKNGNGFHLEDIVAEKNNGEKSLEDRVVEDDHKRLIREAIKMLNPEEQY 151

Query: 627 VLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++  R+G+  N T+ T +++ +   +++  + +I+   + K+K   + +K+
Sbjct: 152 IMTFRYGLDKNGTEKTQKQIAEDINMSQANVSKIQKHCLLKIKRLIKEEKV 202


>gi|52546486|dbj|BAD51626.1| DNA-directed RNA polymerase subunit D [Burkholderia caryophylli]
 gi|52546488|dbj|BAD51627.1| DNA-directed RNA polymerase subunit D [Burkholderia caryophylli]
          Length = 274

 Score = 41.6 bits (96), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   +++  + + +    + E++D    I
Sbjct: 1   ELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILVMAERVANDDLRIDELVD--GLI 58

Query: 192 GPESKGGFFHGTEGHSYQKRE 212
            P ++      T+G S Q+ E
Sbjct: 59  DPNAE-----DTDGFSAQEAE 74


>gi|254729465|ref|YP_003084147.1| type III RNAP sigma factor [Cyanophage PSS2]
 gi|254211617|gb|ACT65565.1| type III RNAP sigma factor [Cyanophage PSS2]
 gi|265524818|gb|ACY75710.1| predicted protein [Cyanophage PSS2]
          Length = 213

 Score = 41.2 bits (95), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 39/125 (31%), Positives = 58/125 (46%), Gaps = 12/125 (9%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRG-----LQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           S A++   E NL L    A +   R      L + DL     IGLMKA  +FD   G KF
Sbjct: 9   SKAQQLKTEENLNLARKEAWRAFKRQSPRSRLPYDDLEAAAFIGLMKACFRFDEEFGCKF 68

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA+  ++  I   I D +  +++   MR+   +  R   + ++ I       EIAK L
Sbjct: 69  STYAVPKIRGEILHFIRDHTYLLKLTHRMRETWQRGKRLLDQGNSDI-------EIAKAL 121

Query: 557 AMPVE 561
            + +E
Sbjct: 122 EIELE 126


>gi|224437149|ref|ZP_03658130.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
 gi|313143612|ref|ZP_07805805.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
 gi|313128643|gb|EFR46260.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
          Length = 235

 Score = 41.2 bits (95), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 46/204 (22%), Positives = 92/204 (45%), Gaps = 19/204 (9%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++  DL+  G   L+K A ++D  L   F  YA    K  +  ++ D   ++ +     
Sbjct: 43  SIEMADLVSIGTEELIKLARRYDSSLNDSFWGYA----KTRVNGAMLDYLRSLDVLSRAS 98

Query: 527 DKIHKVV-RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            K+ K +     +  N  + EP+ E +AK L   V  +++  ++  +  +L  PI ++  
Sbjct: 99  RKLVKAIDYEISKYFNDYQEEPSDEYLAKILNEDVAKIKEA-RVASDVYAL-VPIDEQYN 156

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           +  G+ I        L+   +  L E    VL  L  RE+ ++++ +   +N    L+E+
Sbjct: 157 AICGENI--------LEDVQKDELMEIVHNVLKKLGKREQMIIQLYYFEELN----LKEI 204

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            +   +T  RI QI  + I+K++ 
Sbjct: 205 SEILEITESRISQITKEVIKKIRQ 228


>gi|160944734|ref|ZP_02091961.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443918|gb|EDP20922.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 41.2 bits (95), Expect = 0.52,   Method: Composition-based stats.
 Identities = 48/196 (24%), Positives = 71/196 (36%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+GL KA  KFD   G KF TYA   +  A+   + D        +   DK   
Sbjct: 55  DLKQAGNMGLWKAVPKFDAARGMKFLTYAAPAIHNAMMDMVRDAFTAFEQRMVTEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +G      I  + +SL+  +  E+     + 
Sbjct: 112 -----------------------------DG------ICYQRVSLDDVLPGEEQLRRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P     +   R      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADPYAMQPQTIMEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
           T+ R ++ E +A+  L
Sbjct: 197 TKGRAKKTEEQAMDNL 212


>gi|332675354|gb|AEE72170.1| RNA polymerase sigma factor [Propionibacterium acnes 266]
          Length = 266

 Score = 41.2 bits (95), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 89/199 (44%), Gaps = 32/199 (16%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREA-AE 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLG 589
           V R    ++ + +  P+ + IA ++   V  V  R+V     E   +ET           
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDVMWVEKRRV-----ECWEVET----------- 190

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            F E         + +Q +  +  +     LT +E R++ +R G       T+  V  + 
Sbjct: 191 SFFEQV-------AVVQKSCDDPES----GLTGQERRIVELRHGF-EGEPMTITAVAHEL 238

Query: 650 CVTRERIRQIEAKAIRKLK 668
            ++   +R+IE +A+ +L+
Sbjct: 239 GLSASNVRRIEQRALGRLR 257


>gi|292905274|ref|YP_003541145.1| sigma-70 region 2-containing protein [Anabaena variabilis ATCC
           29413]
 gi|75705012|gb|ABA24687.1| Sigma-70 region 2 [Anabaena variabilis ATCC 29413]
          Length = 240

 Score = 41.2 bits (95), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 31/51 (60%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           DLIQ   +G++ A E+FD      FS++A  ++K  I   + D++ T++IP
Sbjct: 46  DLIQLAGVGMLTAIERFDPSRSNAFSSFACPYIKGEIRHYLRDKASTVKIP 96


>gi|315064845|emb|CBX20958.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|315064849|emb|CBX20960.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|315064853|emb|CBX20962.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|315064857|emb|CBX20964.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 269

 Score = 41.2 bits (95), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 72/313 (23%), Positives = 131/313 (41%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+   G     E       +    E   DD +E+          S D+  +V+S P+ 
Sbjct: 59  IDPDD--GIAPPAEVPPPVDPKAVKAEGADDDEEESAD--------SSDEEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 IIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W    AK   +G++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGHEVDESWTDGLAKG--KGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|90415333|ref|ZP_01223267.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2207]
 gi|90332656|gb|EAS47826.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2207]
          Length = 240

 Score = 41.2 bits (95), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 53/220 (24%), Positives = 94/220 (42%), Gaps = 20/220 (9%)

Query: 455 LVISVAKKYTNRGLQFLDL---IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  VA     R   F++L   IQ G IGL++A + FD   G  F  +A   ++ AI   
Sbjct: 26  LVKRVALHLKGRLPNFMELDELIQVGMIGLIEADKSFDSTKGVDFEVFAKNRIRGAILDQ 85

Query: 512 IADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +   S   R   V +RD  H     A  ++ ++ R P+  E+A  +    +  +K     
Sbjct: 86  VRKMSYLPRSAIVSIRD--HNEASAA--LTGELGRAPSQAELADFMGKDADTFQKERTHA 141

Query: 571 K--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
              + +SLE       TS   D +   N+ +P    ++    +     +  L  R+  ++
Sbjct: 142 HRFQTVSLEA-----QTSESVD-LPTGNSSNPEKELVEEQFMDALAASIGELPERDRTIV 195

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +   MN    L+E+G    V+  R+ QI +  ++ L+
Sbjct: 196 SLYYVEEMN----LKEIGAVLDVSESRVSQILSACVKTLR 231


>gi|313895463|ref|ZP_07829020.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|312976358|gb|EFR41816.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
          Length = 208

 Score = 41.2 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 35/117 (29%), Positives = 63/117 (53%), Gaps = 10/117 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A++ ++EA   LV      Y  R L   +D +QEG IGL++A E++D   G  FS YA+ 
Sbjct: 35  ARRRIIEAYQPLVFREVMPY--RALPAVMDAVQEGTIGLIEAVERYDPARGVAFSLYAVH 92

Query: 503 WVKQAITRSIADQSCTIRIP-VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
            V+  I   +  +  T+ +P +   D++H+   TA+ +   +  +P+  E+A+  A+
Sbjct: 93  RVRGCILDFLRREG-TVDLPCLEASDEMHE---TAKELIAAV--QPSVPELAEHHAL 143


>gi|133722029|gb|ABO37133.1| SigF [Mycobacterium asiaticum]
          Length = 142

 Score = 41.2 bits (95), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 69/150 (46%), Gaps = 20/150 (13%)

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----VEGVRKVLKI 569
           D S ++++P  +++   ++      +S ++ R PT  E+A +L M     VEG+  V   
Sbjct: 2   DNSWSVKVPRRLKELHLRLGTATAELSQRLGRAPTATELAAELGMDRAEVVEGL--VAGS 59

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-----RETTTRVLASLTPRE 624
           +   +S+++  G+ED        +D  A++     + A L     RE    +L +L  RE
Sbjct: 60  SYNTLSIDSGGGNED--------DDARAIADTLGDVDAGLDRIENREALRPLLEALPERE 111

Query: 625 ERVLRMRFGIGMNTDHTLEEVG-KQFCVTR 653
             VL +RF   M      E VG  Q  V+R
Sbjct: 112 RMVLVLRFFESMTQTQIAERVGISQMHVSR 141


>gi|292492344|ref|YP_003527783.1| sigma-70 region 4 domain protein [Nitrosococcus halophilus Nc4]
 gi|291580939|gb|ADE15396.1| sigma-70 region 4 domain protein [Nitrosococcus halophilus Nc4]
          Length = 192

 Score = 41.2 bits (95), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 30/45 (66%)

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           R + +L  RF +    ++TLE++G  + +TRER+RQIEAK I  L
Sbjct: 132 RNKDILCKRFNLEGEGEYTLEDIGIYYDLTRERVRQIEAKTISDL 176


>gi|167813608|ref|ZP_02445288.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
          Length = 182

 Score = 41.2 bits (95), Expect = 0.61,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  M+ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQMLQALAEA 150


>gi|304413523|ref|ZP_07394996.1| flagellar biosynthesis sigma factor [Candidatus Regiella
           insecticola LSR1]
 gi|304284366|gb|EFL92759.1| flagellar biosynthesis sigma factor [Candidatus Regiella
           insecticola LSR1]
          Length = 246

 Score = 41.2 bits (95), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 51/234 (21%), Positives = 106/234 (45%), Gaps = 26/234 (11%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGY---K 495
           S+ + + ++A L LV  V ++ + +    L   D+ Q   +GL++A  ++    G+   +
Sbjct: 27  SLDEGKYLDAYLPLVKRVVRQLSFQADSVLEREDMQQIALMGLLEALRRY----GHPDQQ 82

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+ YA+  ++ AI   + +       P  +R K HK     R +  ++  EP  +EIA +
Sbjct: 83  FAAYAVHRIRGAILDQLREHDWR---PRRLRQKTHKTNEAIRELGKRLGHEPNYDEIAAE 139

Query: 556 LAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           L++ P E         +E + LE     E    L       +A+   +   Q  ++++  
Sbjct: 140 LSITPQE--------YQEYLLLENAKAMESLDDLLSLETHNDALQSRELEEQMIIQDSLR 191

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + + +L  RE+ +L + +      + +L+E+     +T  R+ Q+  K   K+K
Sbjct: 192 QAIGTLDDREKLILSLYY----QQELSLKEIALVLELTEARVCQLNKKIAEKIK 241


>gi|295091495|emb|CBK77602.1| DNA-directed RNA polymerase specialized sigma subunit [Clostridium
           cf. saccharolyticum K10]
          Length = 121

 Score = 41.2 bits (95), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 33/56 (58%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++E++E N+ L    AKK+    L+  D+     +GL+KAAE+FD      FST+A
Sbjct: 6   QRELIENNIGLAKYTAKKFHTMPLEMDDIYSAAYLGLVKAAERFDEGRAVSFSTFA 61


>gi|23429487|gb|AAM97311.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 281

 Score = 41.2 bits (95), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II
Sbjct: 5   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII 61


>gi|11079198|dbj|BAB17590.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 41.2 bits (95), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 69/313 (22%), Positives = 132/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+  +V+S P  
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADAS-DEEDEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+     G++D+ +
Sbjct: 107 ----------DPVIAAQRFGAVSDQM------------EITR--KALKK---FGREDKHA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
             +   L E    L   + L   + + LVE++     R+   E  +++L  +   + R  
Sbjct: 140 IAEMVALAE----LFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|4514517|dbj|BAA75457.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 279

 Score = 41.2 bits (95), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEA 189
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    E ND  T  R + D L  
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVL---QEYNDFLTGERRLADILSG 57

Query: 190 CIGPES 195
            + PES
Sbjct: 58  YLDPES 63


>gi|87302171|ref|ZP_01084996.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
 gi|87283096|gb|EAQ75052.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
          Length = 318

 Score = 41.2 bits (95), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 2/88 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  +VE NL LV  VA + +      LD L+Q G +GL++A E FD       S++A+ +
Sbjct: 34  RNRLVELNLPLVRQVAVRQSGSTRVPLDDLVQLGCLGLIRAIEAFDPSRHTALSSFAVLY 93

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHK 531
           ++  +   + D    +R    +R+ +H+
Sbjct: 94  IRGEMQHHLRDHEQPLRCSRQLRE-LHR 120


>gi|282857702|ref|ZP_06266911.1| RNA polymerase sigma factor [Pyramidobacter piscolens W5455]
 gi|282584372|gb|EFB89731.1| RNA polymerase sigma factor [Pyramidobacter piscolens W5455]
          Length = 168

 Score = 41.2 bits (95), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 4/56 (7%)

Query: 438 ECEASIAKKEMV-EANLR---LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ECE   A KE + E  LR   L   +A +YT RG ++ DL+QEG I L +   ++D
Sbjct: 2   ECERCAASKEQLNETALRFLPLAKKIAWQYTRRGAEYEDLVQEGMIALFELVRRYD 57


>gi|23429483|gb|AAM97309.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 281

 Score = 41.2 bits (95), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II
Sbjct: 5   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII 61


>gi|4514521|dbj|BAA75459.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 279

 Score = 41.2 bits (95), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEA 189
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    E ND  T  R + D L  
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVL---QEYNDFLTGERRLADILSG 57

Query: 190 CIGPES 195
            + PES
Sbjct: 58  YLDPES 63


>gi|150389709|ref|YP_001319758.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|150392068|ref|YP_001322117.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949571|gb|ABR48099.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
 gi|149951930|gb|ABR50458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 215

 Score = 41.2 bits (95), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +K ++E NLRLV   A KY N+  +  D+   G IGL+KA + +D     +F TYA   +
Sbjct: 32  RKHLIERNLRLVAYEAYKYKNQDSE--DIFSVGCIGLIKAIDSYDPSKQTRFDTYANRCI 89

Query: 505 KQAI 508
           +  I
Sbjct: 90  QNEI 93


>gi|150388236|ref|YP_001318285.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149948098|gb|ABR46626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 218

 Score = 40.8 bits (94), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +K ++E NLRLV   A KY N+  +  D+   G IGL+KA + +D     +F TYA   +
Sbjct: 35  RKHLIERNLRLVAYEAYKYKNQDSE--DIFSVGCIGLIKAIDSYDPSKQTRFDTYANRCI 92

Query: 505 KQAI 508
           +  I
Sbjct: 93  QNEI 96


>gi|119490024|ref|ZP_01622648.1| hypothetical protein L8106_20630 [Lyngbya sp. PCC 8106]
 gi|119454176|gb|EAW35328.1| hypothetical protein L8106_20630 [Lyngbya sp. PCC 8106]
          Length = 40

 Score = 40.8 bits (94), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 25/29 (86%)

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQIEAKA++KL+ P RS ++R +L+
Sbjct: 5   RERVRQIEAKALQKLRQPKRSNRVRHYLE 33


>gi|311826277|emb|CBX60046.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 279

 Score = 40.8 bits (94), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           G++ELL+REG+I IAKRIE G   + +S+ E P T   ++
Sbjct: 1   GTVELLTREGDIDIAKRIEEGINQVQSSVAEYPGTIPYIL 40


>gi|11078929|dbj|BAB17469.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078963|dbj|BAB17486.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 40.8 bits (94), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 67/313 (21%), Positives = 132/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEKGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S D+  +V+S P+ 
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAAKAEGADDDEEESADAS-DEEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|11078939|dbj|BAB17474.1| DNA-directed RNA polymerase subunit D [Pseudomonas caricapapayae]
          Length = 269

 Score = 40.8 bits (94), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 132/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S DD  +V+S P+ 
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADGS-DDEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|269925713|ref|YP_003322336.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269789373|gb|ACZ41514.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 785

 Score = 40.8 bits (94), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E T  +    +PR  RVL  RFG+      TL+E+G +  +++ER+RQ+E + +R ++
Sbjct: 324 KEITKLIQTIKSPRVRRVLEARFGVSGKI-LTLQEIGAELKLSKERVRQLEERGLRLIR 381


>gi|314055297|ref|YP_004063635.1| RNA-polymerase sigma factor-possible host origin [Ostreococcus
           tauri virus 2]
 gi|313575188|emb|CBI70201.1| RNA-polymerase sigma factor-possible host origin [Ostreococcus
           tauri virus 2]
          Length = 172

 Score = 40.8 bits (94), Expect = 0.80,   Method: Composition-based stats.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 13/90 (14%)

Query: 442 SIAKKEMVEANLRLVISVA-----KKYT-NRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           ++ KKE++  +++L   V+     K Y   RG+    D+   G  GL++AA+KF+  LG+
Sbjct: 22  NLYKKELIANHVKLAYKVSNDVYFKTYPRQRGIHTRKDINSVGLHGLVRAAQKFNPELGF 81

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           KFSTYA  W+  +       ++C  R  +H
Sbjct: 82  KFSTYAYPWIYWSC------KNCLRRTTIH 105


>gi|313844183|ref|YP_004061846.1| hypothetical protein OlV1_214 [Ostreococcus lucimarinus virus OlV1]
 gi|312599568|gb|ADQ91590.1| hypothetical protein OlV1_214 [Ostreococcus lucimarinus virus OlV1]
          Length = 171

 Score = 40.8 bits (94), Expect = 0.80,   Method: Composition-based stats.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 13/90 (14%)

Query: 442 SIAKKEMVEANLRLVISVA-----KKYT-NRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
           ++ KKE++  +++L   V+     K Y   RG+    D+   G  GL++AA+KF+  LG+
Sbjct: 22  NLYKKELIANHVKLAYKVSNDVYFKTYPRQRGIHTRKDINSVGLHGLVRAAQKFNPELGF 81

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           KFSTYA  W+  +       ++C  R  +H
Sbjct: 82  KFSTYAYPWIYWSC------KNCLRRTTIH 105


>gi|89885916|ref|YP_516114.1| XRE family transcriptional regulator [Rhodoferax ferrireducens
           T118]
 gi|89347914|gb|ABD72116.1| transcriptional regulator, XRE family [Rhodoferax ferrireducens
           T118]
          Length = 887

 Score = 40.8 bits (94), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 606 QANLRETTTRVLASLTPREE---RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A LR TT   L  LTP E+    +  +R+G+      TLE  GK+  VTRERIRQI  K
Sbjct: 403 KAILRRTTEWGL--LTPTEKSWAEIFSVRYGVQGEGQSTLESGGKRVGVTRERIRQIVKK 460

Query: 663 AIRK---LKHPS 671
              +   LK P+
Sbjct: 461 MTERADGLKMPT 472


>gi|323704017|ref|ZP_08115638.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531020|gb|EGB20938.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 85

 Score = 40.8 bits (94), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 18/48 (37%), Positives = 31/48 (64%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+ RE++VL MRFG+G +   T  E+ +   ++R  + +IE +A+ KL
Sbjct: 28  LSRREKKVLEMRFGLGTSARKTQREIARALGISRSYVSRIEKRALNKL 75


>gi|152965591|ref|YP_001361375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
 gi|151360108|gb|ABS03111.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 286

 Score = 40.8 bits (94), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 54/117 (46%), Gaps = 6/117 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE NL LV  +  ++  R    +   DL   G + L +A+  +D   G  F+ YA 
Sbjct: 9   RHALVEKNLPLVGYITSEFIGRLPSHVSRDDLTSAGLMALFQASRGYDPNTGVPFNRYAN 68

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
             ++ AI   +       R    +R +  ++ RT  +++ ++ R PT  E+A  L +
Sbjct: 69  TRIRGAILDDLRGADWASR---GVRSRQRQLSRTEDQLTTELGRTPTSAELAASLGV 122


>gi|313116074|ref|ZP_07801498.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310621671|gb|EFQ05202.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 221

 Score = 40.8 bits (94), Expect = 0.85,   Method: Composition-based stats.
 Identities = 47/196 (23%), Positives = 70/196 (35%), Gaps = 38/196 (19%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q GN+G  KA  KFD   G KF TYA   ++ A+   + D        +   DK   
Sbjct: 55  DLKQAGNLGFWKAVPKFDAARGMKFLTYAAPAIRNAMMDMVRDAFAAFEQRMVTEDK--- 111

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                        +G      I  + +SL   +  E+     + 
Sbjct: 112 -----------------------------DG------ICYQRVSLNDVLPGEEQLRRIEA 136

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  A+ P     +   R      L  LT RE+  L  R+G     +H L      F +
Sbjct: 137 IADPYAMQPQSIMEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHL 196

Query: 652 TRERIRQIEAKAIRKL 667
           T+ R ++ E +A+  L
Sbjct: 197 TKGRAQKTEEQAMDNL 212


>gi|167515038|gb|ABZ81803.1| RpoD [Aeromonas aquariorum]
          Length = 285

 Score = 40.8 bits (94), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II
Sbjct: 8   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII 64


>gi|57908870|gb|AAW59363.1| stationary phase sigma factor [Azotobacter salinestris]
          Length = 55

 Score = 40.8 bits (94), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 29/38 (76%)

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RFG+  +   TLEEVG++  +TRER+RQI+ +A++ L+
Sbjct: 3   RFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKPLR 40


>gi|168207186|ref|ZP_02633191.1| RNA polymerase sigma-B factor [Clostridium perfringens E str.
           JGS1987]
 gi|170661420|gb|EDT14103.1| RNA polymerase sigma-B factor [Clostridium perfringens E str.
           JGS1987]
          Length = 184

 Score = 40.8 bits (94), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           N  + F +++    +GL+KAA +FD   G+KFSTYAM  ++  I
Sbjct: 22  NSSMNFEEVLSAAMLGLVKAANRFDEKKGFKFSTYAMSTMRGQI 65


>gi|331011084|gb|EGH91140.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 160

 Score = 40.8 bits (94), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 35/130 (26%), Positives = 59/130 (45%), Gaps = 6/130 (4%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G  F TYA
Sbjct: 16  SQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFETYA 75

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++ A+   +       R  VH   ++  V    R +  K  R+    E+A +L + +
Sbjct: 76  GIRIRGAMLDEVRKGDWAPR-SVHRNTRM--VSDAIRAIEAKTGRDAKDHEVAAELQLSL 132

Query: 561 EGVRKVLKIT 570
           +    +L  T
Sbjct: 133 DDYYGILNDT 142


>gi|114777586|ref|ZP_01452567.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
 gi|114552057|gb|EAU54574.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
          Length = 243

 Score = 40.4 bits (93), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 59/234 (25%), Positives = 105/234 (44%), Gaps = 23/234 (9%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E++E  L LV   A +   R    ++F DLI  G +GL+  A++FD     +F T+  + 
Sbjct: 15  ELLEEYLPLVRYHADQLMRRTPDSIEFDDLINAGVLGLLDGAQRFDHSRDVQFKTFVSYR 74

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE-EIAKKLAMPVEG 562
           V+ A+   +        +P  +RD   K ++TA +   ++   P  E EIAK L + ++ 
Sbjct: 75  VRGAMIDYLRAFDW---MPRGLRDHA-KEMQTAFQQLEQVYGRPAEETEIAKHLNISLDE 130

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDF-----IEDKNAVSPLDSAIQANLRETTTRVL 617
            R  L   +  +S+   I  +D     DF     I +  A  P D+    N      + L
Sbjct: 131 YRTRLTNVRS-MSI---IHFDDLPVNNDFDDEISILETLAGDPADTPEAQNSLMQFVQQL 186

Query: 618 A---SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A   S  P  E+VL     +    + T++E+     +T  R+ Q+ ++ + +L+
Sbjct: 187 ADGISRLPAREQVL---VTLYYYEELTMKEIALILGLTESRVSQLHSQMVVRLR 237


>gi|11078923|dbj|BAB17466.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score = 40.4 bits (93), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 67/313 (21%), Positives = 132/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S D+  +V+S P+ 
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAAKTEGADDDEEESADAS-DEEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|4514519|dbj|BAA75458.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 278

 Score = 40.4 bits (93), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEA 189
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    E ND  T  R + D L  
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVL---QEYNDFLTGERRLADILSG 57

Query: 190 CIGPES 195
            + PE+
Sbjct: 58  YLDPET 63


>gi|4514511|dbj|BAA75454.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 278

 Score = 40.4 bits (93), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEA 189
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    E ND  T  R + D L  
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVL---QEYNDFLTGERRLADILSG 57

Query: 190 CIGPES 195
            + PE+
Sbjct: 58  YLDPET 63


>gi|325662599|ref|ZP_08151199.1| hypothetical protein HMPREF0490_01939 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471096|gb|EGC74322.1| hypothetical protein HMPREF0490_01939 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 246

 Score = 40.4 bits (93), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 31/128 (24%), Positives = 63/128 (49%), Gaps = 2/128 (1%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++A+  ++E  L  V+  AK+  ++ +   DLIQEGN+ LM A ++ +     +     M
Sbjct: 118 ALARGRLIELYLEKVVEAAKEMYHKEVFLGDLIQEGNVSLMLALDELESV--EEAHGKIM 175

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+  +   I +Q+   R    + +K   +    +++  +  R+ T EE++  L MP E
Sbjct: 176 EEVRAGMQMLIEEQTEVKRRDHTLLEKYTDLDDNIKKLKEETGRDVTIEEVSAFLDMPEE 235

Query: 562 GVRKVLKI 569
            +  +L +
Sbjct: 236 EINDILNL 243


>gi|4514513|dbj|BAA75455.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
 gi|4514515|dbj|BAA75456.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 278

 Score = 40.4 bits (93), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEA 189
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    E ND  T  R + D L  
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVL---QEYNDFLTGERRLADILSG 57

Query: 190 CIGPES 195
            + PE+
Sbjct: 58  YLDPET 63


>gi|160893355|ref|ZP_02074142.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
 gi|156865047|gb|EDO58478.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
          Length = 200

 Score = 40.4 bits (93), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 26/41 (63%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           D+IQEG IGL+KA   FD   G  FST+A   +K+ +  ++
Sbjct: 52  DIIQEGMIGLIKAIRSFDGSKGASFSTFANLCIKRQLITAV 92


>gi|23429451|gb|AAM94473.1| RNA polymerase sigma factor D [Aeromonas schubertii]
          Length = 283

 Score = 40.4 bits (93), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 33/146 (22%), Positives = 66/146 (45%), Gaps = 6/146 (4%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           NG+  E++         +L  +     L   + D LV  + ++ +R+   E  +L++  +
Sbjct: 143 NGRAHEETQAAIA----QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVE 198

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +A   + +L+   +++ I  ETG
Sbjct: 199 QAKMPKKTFVSAFTNNECETAWFEYQKQAGKA-WSAPLAAMEEEVLRSIGKLQQIEEETG 257

Query: 422 ISISEFRHIVSMVRKGECEASIAKKE 447
           +SI++ + I   +  GE +A  AKKE
Sbjct: 258 LSIAQIKDINRRMSIGEAKARRAKKE 283


>gi|118595065|ref|ZP_01552412.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
 gi|118440843|gb|EAV47470.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
          Length = 808

 Score = 40.4 bits (93), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 18/25 (72%), Positives = 22/25 (88%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIR 665
           TLEE+G++  VTRERIRQIEAK I+
Sbjct: 251 TLEEIGEKLGVTRERIRQIEAKVIK 275


>gi|238789522|ref|ZP_04633307.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
 gi|238722472|gb|EEQ14127.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
          Length = 531

 Score = 40.4 bits (93), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           R+  +L MR G+  +  HTL E+  +  ++RER+RQI+ +A R+L   SR
Sbjct: 172 RDRDILLMRLGMDEH-PHTLAEIAIKLGISRERVRQIQERAFRRLAAKSR 220


>gi|242309557|ref|ZP_04808712.1| flagellar biosynthesis sigma factor [Helicobacter pullorum MIT
           98-5489]
 gi|239524128|gb|EEQ63994.1| flagellar biosynthesis sigma factor [Helicobacter pullorum MIT
           98-5489]
          Length = 235

 Score = 40.4 bits (93), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 46/202 (22%), Positives = 86/202 (42%), Gaps = 17/202 (8%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++F DL+  G   L+K A K+D  L   F  YA   V  A+   +    C  R   + R
Sbjct: 41  NVEFADLVSIGTEELIKLARKYDSTLNDSFWGYAKSRVHGAMLDYLRGLDCMSR---YSR 97

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + R   +  N+ + EP    +++ L   +E ++     ++  I    P+ +E ++
Sbjct: 98  TLTKNIDREISKYYNEHQEEPDNAYLSQVLNEDIEKIKDARNASE--IYGILPLDEELSA 155

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              D   +K     L   IQ        ++L +    E+ V+++ +   +N     +E+G
Sbjct: 156 SQDDKTYNKVEKEELIEIIQ--------KILETSPQNEQLVIQLYYYEELN----FKEIG 203

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           +   +T  R+ QI    IRK+K
Sbjct: 204 EILEITESRVSQIHKAVIRKIK 225


>gi|284989337|ref|YP_003407891.1| sigma-70 region 4 domain-containing protein [Geodermatophilus
           obscurus DSM 43160]
 gi|284062582|gb|ADB73520.1| sigma-70 region 4 domain protein [Geodermatophilus obscurus DSM
           43160]
          Length = 896

 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 25/36 (69%)

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           L  R+G+      TL+EVG+   VTRER+RQ+++KA
Sbjct: 444 LGSRYGLAGADPQTLDEVGRTLGVTRERVRQVQSKA 479


>gi|292398068|gb|ADE27982.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 272

 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 33/146 (22%), Positives = 67/146 (45%), Gaps = 2/146 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 127 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 186

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 187 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 245

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMV 449
           I++ + I   +  GE +A  AKKEMV
Sbjct: 246 IAQIKDINRRMSIGEAKARRAKKEMV 271


>gi|23429459|gb|AAM94477.1| RNA polymerase sigma factor D [Aeromonas popoffii]
          Length = 281

 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++E L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVEFLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 II 185
           II
Sbjct: 60  II 61


>gi|315652062|ref|ZP_07905063.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
           3986]
 gi|315485709|gb|EFU76090.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
           3986]
          Length = 171

 Score = 40.4 bits (93), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 32/135 (23%), Positives = 71/135 (52%), Gaps = 5/135 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E ++   + + K +   G +  DLI E ++ L  A    ++  G   S      
Sbjct: 39  ARNRLIEGHMMYAVKLIKPFIGCGEEMSDLISESHLALTMAV--MEYSHGDLKSQIKSRV 96

Query: 504 VKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            K+     IAD+  + +   + + D+I++++  +  +++ I +E T EE++++L +P + 
Sbjct: 97  EKR--LNEIADEEKSKKDASNKLADRINELMDVSSALASDIGKEATLEELSERLQIPKDE 154

Query: 563 VRKVLKITKEPISLE 577
           V ++LKI+   I+LE
Sbjct: 155 VEELLKISLNAINLE 169


>gi|195441551|ref|XP_002068571.1| GK20351 [Drosophila willistoni]
 gi|194164656|gb|EDW79557.1| GK20351 [Drosophila willistoni]
          Length = 2052

 Score = 40.4 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 28/112 (25%), Positives = 59/112 (52%), Gaps = 10/112 (8%)

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN---LDEDEDDSAH 267
           ++D+  +K+R + +  E ++E  A + K+ R + DSP E+  +D R    LD+ E ++  
Sbjct: 360 KQDTPNKKKRTEQEANEPNVEETATI-KEKRKRPDSPVESMNSDSRPDSVLDDGESNTTD 418

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           T +A +   +        EI    +E R +  + ++ + +EK+S+K ++  E
Sbjct: 419 TTTAEQQSNKDS-----KEIISC-KEEREIIASDLDIKSEEKTSIKAEIAAE 464


>gi|332982726|ref|YP_004464167.1| RNA polymerase sigma-30 subunit SigH [Mahella australiensis 50-1
           BON]
 gi|332700404|gb|AEE97345.1| RNA polymerase, sigma 30 subunit, SigH [Mahella australiensis 50-1
           BON]
          Length = 216

 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 64/131 (48%), Gaps = 8/131 (6%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +VS  +KG+    +A + ++E    ++ + AK Y  +G    D+IQEG IGL KA + 
Sbjct: 18  RELVSRAKKGD---DVALECLIERYKSIIHNRAKTYFLKGSDREDIIQEGLIGLYKAIKN 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV---RTARRMSNKIK 544
           +       F ++A   + + I  ++   +    IP++    ++K +      R++ + I 
Sbjct: 75  YREDKAVSFRSFADMCITRQIITAVKAATRQKHIPLNSYVSLNKTIYEDEAERQLMDVIA 134

Query: 545 REPT--PEEIA 553
            EP   PEE+ 
Sbjct: 135 LEPQGDPEEMV 145


>gi|291461239|ref|ZP_06027789.2| RNA polymerase sigma factor [Fusobacterium periodonticum ATCC
           33693]
 gi|291378120|gb|EFE85638.1| RNA polymerase sigma factor [Fusobacterium periodonticum ATCC
           33693]
          Length = 259

 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VE NL+ V  +A      G+ + DL QEG IGLMKA E F+      F  Y  +++ +A+
Sbjct: 69  VEKNLKKVYQIALYMLRDGILYQDLTQEGVIGLMKAHELFED--DKDFKLYKDYYIARAM 126

Query: 509 TRSI 512
              I
Sbjct: 127 FNYI 130


>gi|46370560|gb|AAS90114.1| RNA polymerase sigma-G factor [Pasteuria penetrans]
          Length = 92

 Score = 40.4 bits (93), Expect = 1.1,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 7/71 (9%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +RN+++   V+T     +   E R + + ++ GE     A++++V  NLRLV+SV +++ 
Sbjct: 24  VRNKVEICGVDTSMLPVLKNQEMRLLFTQLQSGEI---WARQKLVHGNLRLVLSVIQRFH 80

Query: 465 NRGLQFLDLIQ 475
           NRG    DL Q
Sbjct: 81  NRGESVDDLFQ 91


>gi|37784442|gb|AAO13114.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|37784448|gb|AAO13117.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|37955128|gb|AAP76216.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|37955134|gb|AAP76219.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 272

 Score = 40.4 bits (93), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|253584124|ref|ZP_04861322.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
 gi|251834696|gb|EES63259.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
          Length = 197

 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 48/88 (54%), Gaps = 3/88 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +   ++G+ +A    +++ E+  +L+I   KKY   G    D++QE  IGL+KA   +
Sbjct: 5   HTIHAAQEGDEDAI---QQIFESFKQLIIFKTKKYFFHGGDRDDVMQEAMIGLLKAINAY 61

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQS 516
           D      F+T+A+  +K+ I  ++ + +
Sbjct: 62  DENKNASFTTFALLCIKRQIITALKNSN 89


>gi|151413326|gb|ABS11159.1| RpoD [Pseudomonas oleovorans subsp. lubricantis]
          Length = 271

 Score = 40.0 bits (92), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           G++ELL+REGEI IAKRIE G   +M+++   P T   ++
Sbjct: 1   GTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGIL 40


>gi|85710152|ref|ZP_01041217.1| flagellar-specific RNA polymerase sigma factor [Erythrobacter sp.
           NAP1]
 gi|85688862|gb|EAQ28866.1| flagellar-specific RNA polymerase sigma factor [Erythrobacter sp.
           NAP1]
          Length = 242

 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 86/202 (42%), Gaps = 13/202 (6%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL+  DL+Q G + L + A++ +      F+ YA   V+ A+   I       R     R
Sbjct: 47  GLEIEDLMQAGVVALTECAQRHEGPGEDGFAAYAKIRVRGAMFDQIRKLMNDTRTARKKR 106

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            ++ +VV    R+ N+   EP+   I + L +      ++L+I    +++ T I DE   
Sbjct: 107 AQLGEVV---ERLRNETGEEPSRARICETLGISDA---ELLEIEASSVTV-TSIADEYDE 159

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
               F  D     P         RE     +  L  R + VL++ F   +N    L E+ 
Sbjct: 160 TSTAFASDDP--DPFQVLAGNEDRERLIAAMVKLPDRLKLVLQLFFVEELN----LTEIA 213

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ Q+ AKA++ L+
Sbjct: 214 TVLEVSVPRVHQLRAKALKDLR 235


>gi|54307284|ref|YP_128304.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium profundum SS9]
 gi|46911704|emb|CAG18502.1| Hypothetical flagellar-specific transcription initiation factor
           sigma, LafS [Photobacterium profundum SS9]
          Length = 251

 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 35/143 (24%), Positives = 69/143 (48%), Gaps = 12/143 (8%)

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED 584
           R K H++  T R +  ++ R PT +E+A +L + +  V+ + +    E ++    + ++ 
Sbjct: 109 RQKSHELRDTERALGRQLGRMPTDQEVAAELDIELGDVKQRRVDTQAESLTSMDALQEDG 168

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
               G   +        +S  +  L++   + LA L+ RE+ +L   +   MN    L+E
Sbjct: 169 EQFFGLSFQ-------CNSYERVALKKAMAQALARLSKREQVMLSFYYEHEMN----LKE 217

Query: 645 VGKQFCVTRERIRQIEAKAIRKL 667
           +G  F +T  R+ QI  KA++ L
Sbjct: 218 IGLVFELTEARVSQIHKKALKSL 240


>gi|312135662|ref|YP_004003000.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           owensensis OL]
 gi|311775713|gb|ADQ05200.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           owensensis OL]
          Length = 302

 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 5/85 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFL--DLIQEGNIGLMKAAEKFDWCLG 493
           E   S+  +++V  N++LV  VA K+    +G  +   DL+ EG IGL+ AA  +D   G
Sbjct: 3   ETLTSVQTQKLVADNIKLVYHVANKFMPCPKGYCYEVDDLVSEGYIGLVVAARNYDPEKG 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCT 518
             FSTYA   ++  I +S+     T
Sbjct: 63  -SFSTYACKVIESKIRKSLPKYRLT 86


>gi|311826275|emb|CBX60045.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 278

 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|269121539|ref|YP_003309716.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268615417|gb|ACZ09785.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 309

 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 47/225 (20%), Positives = 94/225 (41%), Gaps = 34/225 (15%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V  +L++VI  + +Y   G  FLDL+QE  IG++   EK          +   +W+K 
Sbjct: 98  QLVNKHLKIVIRESLQYVKLGFSFLDLVQEATIGVINGIEKLKNS-----ESDIEFWLKN 152

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE----PTPEEIAKKLAMPVEG 562
              + I +    I     ++D   K    A  +  K++ E     + EEI+K++ + +  
Sbjct: 153 FAIKYILEYQKKI-----LKD--FKASELAYILYLKVQLELNNGLSLEEISKQMNIELNY 205

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  +                E  + + D  E  N+ S ++       +   + +   L  
Sbjct: 206 LNAL---------------QELFTKMDDMPE--NSYSIVEKVSHLTRKYVLSNIPKKLNY 248

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +ER+L M +G+  +  +  +E+ K   +    I  +  KA+ KL
Sbjct: 249 LDERILMMHYGLD-DKFYKTKEISKILNIEESNINVLREKALTKL 292


>gi|121534953|ref|ZP_01666772.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
 gi|121306552|gb|EAX47475.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
          Length = 215

 Score = 40.0 bits (92), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ ++E    LV   A ++       +DLIQEG +GL++A E FD   G  FS YA
Sbjct: 37  RRRLIEHYQPLVFKEAMRWRAHEGVVMDLIQEGTVGLIEAVENFDPERGVAFSLYA 92


>gi|11078925|dbj|BAB17467.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11079200|dbj|BAB17591.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|146150865|gb|ABQ02689.1| sigma factor 70 [Pseudomonas avellanae]
 gi|146150867|gb|ABQ02690.1| sigma factor 70 [Pseudomonas avellanae]
 gi|315064841|emb|CBX20956.1| sigma factor 70 [Pseudomonas syringae pv. syringae]
          Length = 269

 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 67/313 (21%), Positives = 132/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S D+  +V+S P+ 
Sbjct: 57  -------GYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADAS-DEEDEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +R              A+ DQ+            E+ R  ++L+       +D+K 
Sbjct: 109 VIAQQR------------FGAVSDQM------------EITR--KALKKFG----RDDKH 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           ++   V    L +L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 139 AIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I + + ++ ++  ETG+ I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|313820245|gb|EFS57959.1| sigma-70 region 2 [Propionibacterium acnes HL036PA1]
 gi|313822945|gb|EFS60659.1| sigma-70 region 2 [Propionibacterium acnes HL036PA2]
 gi|314925132|gb|EFS88963.1| sigma-70 region 2 [Propionibacterium acnes HL036PA3]
          Length = 228

 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 2/89 (2%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL +A E++D   G +FST A  W+++ I   +   S   R    MR+   +
Sbjct: 89  DLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVRLSGA-RSRSVMREAA-E 146

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           V R    ++ + +  P+ + IA ++   V
Sbjct: 147 VARIEEELTARWQSVPSSDAIAARMGKDV 175


>gi|148243883|ref|YP_001220122.1| sigma-70 region 4 domain-containing protein [Acidiphilium cryptum
           JF-5]
 gi|146400446|gb|ABQ28980.1| sigma-70 region 4 domain protein [Acidiphilium cryptum JF-5]
          Length = 894

 Score = 40.0 bits (92), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 2/53 (3%)

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL-KHPSRSK 674
           ++ ++L MR+G   +   TL+ V     +T+ER+RQIE +A++ L + PSR K
Sbjct: 291 KQAQILAMRYGF-FDKPATLDVVSNTVGITKERVRQIEVEAVKHLGREPSRQK 342


>gi|157119736|ref|XP_001659481.1| laminin A chain, putative [Aedes aegypti]
 gi|108875197|gb|EAT39422.1| laminin A chain, putative [Aedes aegypti]
          Length = 3701

 Score = 40.0 bits (92), Expect = 1.5,   Method: Composition-based stats.
 Identities = 30/143 (20%), Positives = 67/143 (46%), Gaps = 2/143 (1%)

Query: 214  SSQEKE-RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
            ++Q KE +D+++  +  ++ ++K+S D  +   +  ++A ++ + L+   D         
Sbjct: 2353 AAQHKEAKDNIENAKNLLDDSSKISLDIFT-THTELDHANSELKQLNSKVDQELPENDRE 2411

Query: 273  EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
               L PK+  A D  A +  E   L  N  N   + ++++K      K+V  V    +N 
Sbjct: 2412 YQDLVPKIDTAKDYAANLKDEASRLTANYSNVTANSETALKAATAYSKIVDAVNEAKVNA 2471

Query: 333  SRIDLLVEQLYDISKRIMHNEGE 355
             + D+L + + +++K +    GE
Sbjct: 2472 DQADVLAQNVTELTKGVDERAGE 2494


>gi|11079077|dbj|BAB17543.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score = 40.0 bits (92), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 68/312 (21%), Positives = 133/312 (42%), Gaps = 47/312 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +   +  +   E  A+ S DD  +V+S P  
Sbjct: 57  -------GYIDPDDGIAPPAAEVPPPVDPKAP-KADDDTDEDEAEASTDDEEEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+    +G+ ++++
Sbjct: 107 ----------DPVVAAQRFGAVSDQM------------EITR--KALKK---HGRGNKQA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
             +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 140 IAELLALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W S A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDETW-SDALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLTIAEIKD 254

Query: 430 IVSMVRKGECEA 441
           I   +  GE +A
Sbjct: 255 INRRMSIGEAKA 266


>gi|329897641|ref|ZP_08272165.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC3088]
 gi|328921090|gb|EGG28499.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC3088]
          Length = 204

 Score = 39.7 bits (91), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 48/202 (23%), Positives = 95/202 (47%), Gaps = 22/202 (10%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L+Q G IGL++A + FD   G   +++A   ++ AI   +  +S     P+  +D IH 
Sbjct: 15  ELVQIGMIGLLEAFKSFDESQGDDLASFATKRIRGAILDEVRRRS-----PLSRQDNIHA 69

Query: 532 VVRTARRMSN--KIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHL 588
             R A    +  +  R P+  EI+ ++ + +E   R  +K     +S    + +      
Sbjct: 70  KTREAIIDDHLARTGRRPSAVEISSEMGVTLEDYHRSEMKTHTYQLSSYEVLTE------ 123

Query: 589 GDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             F +  +A SP D  I+ +  L    TR+   L  R++ +L + +   +N    L+E+G
Sbjct: 124 NGFEQAHDADSP-DEEIEHSQTLGILETRI-GQLEQRDQLILSLYYEKELN----LKEIG 177

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               ++  R+ Q+ +K + +L+
Sbjct: 178 SILNISESRVSQLLSKIVTQLR 199


>gi|255606356|ref|XP_002538551.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
 gi|223511619|gb|EEF23833.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
          Length = 123

 Score = 39.7 bits (91), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 3/87 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G +GL+ A  +++   G +F TYA+  ++ A+   +        +P   R  + K
Sbjct: 40  DLVQAGMMGLLDAINRYEENHGAQFETYAVLRIRGAMLDELRSSDW---MPRSTRANMRK 96

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAM 558
           V      +  ++ R P+  E+AK L +
Sbjct: 97  VESAMAALQQQLGRPPSESEVAKSLKL 123


>gi|167628189|ref|YP_001678688.1| hypothetical protein HM1_0052 [Heliobacterium modesticaldum Ice1]
 gi|167590929|gb|ABZ82677.1| hypothetical protein HM1_0052 [Heliobacterium modesticaldum Ice1]
          Length = 238

 Score = 39.7 bits (91), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 41/129 (31%), Positives = 64/129 (49%), Gaps = 11/129 (8%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN- 608
           E  ++L +  +   KVL    E ISLETPI  DE+   L D I D +A +   S  + N 
Sbjct: 86  ECWRELGISFQTGGKVLNREVETISLETPISDDEEGLTLEDIISDPDADT--YSFCELND 143

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R    R +  L+PRE+ V+   +GI  N + T+E + ++F      +  +   A   L+
Sbjct: 144 MRLIVRREIERLSPREQCVI---YGIFYN-NKTIEGLAQEFGCELGTVLSVRDTAFNSLR 199

Query: 669 HPSRSKKLR 677
              RSK +R
Sbjct: 200 ---RSKGIR 205


>gi|57168743|ref|ZP_00367874.1| probable RNA polymerase sigma factor for flagellar operon Cj0061c
           [Campylobacter coli RM2228]
 gi|305432515|ref|ZP_07401677.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter coli
           JV20]
 gi|57019790|gb|EAL56473.1| probable RNA polymerase sigma factor for flagellar operon Cj0061c
           [Campylobacter coli RM2228]
 gi|304444554|gb|EFM37205.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter coli
           JV20]
          Length = 230

 Score = 39.7 bits (91), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 14/123 (11%)

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  E +AKKL + VE +++V   T   IS   PI D+        +E  N    L+   
Sbjct: 118 EPDDEYLAKKLDLDVEKIKEVR--TAHAISYTLPIDDQ--------LELYNEDDTLEKLE 167

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L E    VL  L  R++ ++++ +      + +L+E+ +   ++  RI QI  K ++
Sbjct: 168 KEQLLEKIHEVLEDLKERDQLIIQLYYY----EELSLKEISEILEISESRISQIHKKLLK 223

Query: 666 KLK 668
           KL+
Sbjct: 224 KLR 226


>gi|331085692|ref|ZP_08334775.1| hypothetical protein HMPREF0987_01078 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406615|gb|EGG86120.1| hypothetical protein HMPREF0987_01078 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 207

 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 46/96 (47%), Gaps = 3/96 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +++ +RKGE E       ++E    LV   AK     G +  DLIQEG IGL KA   +
Sbjct: 11  QLIAALRKGESEIM---DFIMEKYKYLVRKKAKAMFLLGGENDDLIQEGMIGLFKAVRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           D  L   F+++A   + + +  +I        IP++
Sbjct: 68  DLALETSFASFAELCISRQMYSAIEASKRKKHIPLN 103


>gi|182412871|ref|YP_001817937.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Opitutus terrae
           PB90-1]
 gi|177840085|gb|ACB74337.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Opitutus terrae PB90-1]
          Length = 240

 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 48/200 (24%), Positives = 86/200 (43%), Gaps = 16/200 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL   G + L++A  +FD     +   Y    V+ A+   +       R   H R ++  
Sbjct: 38  DLASAGKLALVEAMLRFDGP-AEQLRGYCFARVRGALLDELRRLDPLSR---HTRSQVTF 93

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD- 590
           V R    +  ++ R PT +EI        E + ++ ++ +   +       ++T   GD 
Sbjct: 94  VRRATAALEKELHRAPTRDEIVTATGYSHETLTQLERLAEAAQACSI----DETDAYGDD 149

Query: 591 --FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              IED+ A  P  +A   +   +    LA L      VLR R+ +    D TL+ +  +
Sbjct: 150 LHVIEDE-AACPARTAESLDAHSSVHVALARLPANHAHVLR-RYYLD---DATLDVIAGE 204

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V++ER+RQ+   A +KL+
Sbjct: 205 LGVSKERVRQLREAAEKKLR 224


>gi|162451917|ref|YP_001614284.1| hypothetical protein sce3644 [Sorangium cellulosum 'So ce 56']
 gi|161162499|emb|CAN93804.1| hypothetical protein predicted by Glimmer/Critica [Sorangium
           cellulosum 'So ce 56']
          Length = 258

 Score = 39.7 bits (91), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 27/41 (65%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLE+VG    +TRERIRQ+E KA+ KL+       LR ++D
Sbjct: 154 TLEDVGAIMNLTRERIRQVEVKALAKLEALKDMMALRDYVD 194


>gi|325661897|ref|ZP_08150518.1| hypothetical protein HMPREF0490_01256 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471875|gb|EGC75092.1| hypothetical protein HMPREF0490_01256 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 207

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 46/96 (47%), Gaps = 3/96 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +++ +RKGE E       ++E    LV   AK     G +  DLIQEG IGL KA   +
Sbjct: 11  QLIAALRKGESEIM---DFIMEKYKYLVRKKAKAMFLLGGENDDLIQEGMIGLFKAVRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           D  L   F+++A   + + +  +I        IP++
Sbjct: 68  DLALETSFASFAELCISRQMYSAIEASKRKKHIPLN 103


>gi|295399303|ref|ZP_06809285.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geobacillus thermoglucosidasius C56-YS93]
 gi|294978769|gb|EFG54365.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geobacillus thermoglucosidasius C56-YS93]
          Length = 99

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 605 IQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           IQ N+  E   + +  L  RE+ V+  RFG+ M  + T  E+ K+  ++R  + +IE +A
Sbjct: 23  IQLNMELEQVKKYIDVLDEREKEVIINRFGLDMQQEKTQREIAKELGISRSYVSRIEKRA 82

Query: 664 IRKLKH 669
           + K+ H
Sbjct: 83  LMKMFH 88


>gi|260222952|emb|CBA33033.1| hypothetical protein Csp_B17010 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 161

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 31/49 (63%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
            K +I L + RGY+T  E++  LP   V +E +E  ++ML++MG+ V +
Sbjct: 62  LKALITLGKTRGYLTHGEISDHLPDKLVDAETLEVVISMLNDMGVAVYE 110


>gi|311826285|emb|CBX60050.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 271

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|311826287|emb|CBX60051.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 279

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39



 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 72/167 (43%), Gaps = 11/167 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    E  S K  V  E ++ +     L   + D LV +L   
Sbjct: 118 EKFNQLRSTYQNLQLAINEHGYE--SPKATVANELMLDVFKEFRLTPKQFDHLVNELRTA 175

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++ A  YG + +  F+    G E    W+    + D P  E    +   
Sbjct: 176 MDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEK---IKRN 232

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEMV
Sbjct: 233 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEMV 279


>gi|311826271|emb|CBX60043.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|311826279|emb|CBX60047.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|311826283|emb|CBX60049.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 279

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|311826267|emb|CBX60041.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 275

 Score = 39.7 bits (91), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|311826263|emb|CBX60039.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 275

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|257469667|ref|ZP_05633759.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
 gi|317063900|ref|ZP_07928385.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
 gi|313689576|gb|EFS26411.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
          Length = 197

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 48/88 (54%), Gaps = 3/88 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +   ++G+ +A    +++ E+  +L+I   KKY   G    D++QE  IGL+KA   +
Sbjct: 5   HTIHAAQEGDEDAI---QQIFESFKQLMIFKTKKYFFHGGDREDVMQEAMIGLLKAINAY 61

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQS 516
           D      F+T+A+  +K+ I  ++ + +
Sbjct: 62  DENKNASFTTFALLCIKRQIITALKNSN 89


>gi|261368103|ref|ZP_05980986.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282569861|gb|EFB75396.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 118

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 32/98 (32%), Positives = 52/98 (53%), Gaps = 9/98 (9%)

Query: 574 ISLETPI-GDEDTSHLGDFIEDKNAVSPLDS---AIQANLRETTTRVLASLTPREERVLR 629
           +SL+ P+ G E    L D + D  AV   D    A  A LR    ++L +L PRE++VL 
Sbjct: 13  LSLQEPLEGSEGQLTLADTLPDP-AVMEDDCERRADAARLR----KLLETLPPREQQVLT 67

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R+G+      T +E+  Q  ++R  I ++E +A++ L
Sbjct: 68  RRYGLDGRPPCTQQEIAGQMGISRSYISRLEKRALQAL 105


>gi|311826281|emb|CBX60048.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 279

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|326682080|emb|CBL30931.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682090|emb|CBL30936.1| RNA polymerase sigma factor [Aeromonas aquariorum]
          Length = 272

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|311826273|emb|CBX60044.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 278

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39



 Score = 37.4 bits (85), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 71/166 (42%), Gaps = 11/166 (6%)

Query: 289 EVYRELRSLQDN---AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E + +LRS   N   A+N    E  S K  V  E ++ +     L   + D LV +L   
Sbjct: 118 EKFNQLRSTYQNLQLAINEHGYE--SPKATVANELMLDVFKEFRLTPKQFDHLVNELRTA 175

Query: 346 SKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVACE 402
             R+   E  +++ A  YG + +  F+    G E    W+    + D P  E    +   
Sbjct: 176 MDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEK---IKRN 232

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I +   ++K I  ET +++   + I   +  GE +A  AKKEM
Sbjct: 233 EEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEM 278


>gi|311826269|emb|CBX60042.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 278

 Score = 39.7 bits (91), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|37784406|gb|AAO13096.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784468|gb|AAO13127.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784484|gb|AAO13135.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784486|gb|AAO13136.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784488|gb|AAO13137.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|259479057|dbj|BAI40076.1| RNA polymerase sigma-70 factor [Aeromonas sp. GV16]
 gi|264685604|dbj|BAI49151.1| RNA polymerase beta subunit [Aeromonas sp. A10]
 gi|264685608|dbj|BAI49153.1| RNA polymerase beta subunit [Aeromonas sp. Y62]
 gi|264685614|dbj|BAI49156.1| RNA polymerase beta subunit [Aeromonas sp. GF1]
 gi|264685618|dbj|BAI49158.1| RNA polymerase beta subunit [Aeromonas sp. ATCC 19570]
 gi|264685620|dbj|BAI49159.1| RNA polymerase beta subunit [Aeromonas sp. ATCC 14715]
          Length = 272

 Score = 39.7 bits (91), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|11079053|dbj|BAB17531.1| DNA-directed RNA polymerase subunit D [Pseudomonas tolaasii NCPPB
           2192]
 gi|11079061|dbj|BAB17535.1| DNA-directed RNA polymerase subunit D [Pseudomonas tolaasii]
          Length = 269

 Score = 39.7 bits (91), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 73/314 (23%), Positives = 134/314 (42%), Gaps = 51/314 (16%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-LEA 189
           +ELL+REGEI IAKRIE G   +M ++   P T   ++    E N  TT    + D L  
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHIL---SEYNRVTTEGGRLSDVLSG 57

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P+                +   + +   DD  E+ G          DD  +V+S P 
Sbjct: 58  YIDPDDGIAPPAAEVPPPVDAKAAKADDDSEDDDAESSG----------DDEDEVESGP- 106

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                      D   +A    A+ DQ+            E+ R  ++L+    +G+ +++
Sbjct: 107 -----------DPIIAAQRFGAVSDQM------------EITR--KALKK---HGRTNKQ 138

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRD 368
           +  +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R 
Sbjct: 139 AIAELIALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRA 194

Query: 369 VFLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            FL +  G E+D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 DFLRQFPGNEVDESWTDALAKG--KAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 252

Query: 428 RHIVSMVRKGECEA 441
           + I   +  GE +A
Sbjct: 253 KDINRRMSIGEAKA 266


>gi|11078993|dbj|BAB17501.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score = 39.7 bits (91), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 68/313 (21%), Positives = 134/313 (42%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLS---- 56

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + E   +  A+ S DD  +V+S P  
Sbjct: 57  -------GYIDPDDGIAPPAAEIPPPVDPKAAKADDE-TDDDEAEASTDDEEEVESGP-- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R  ++L+    +G+  +++
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------ELAR--KALKK---HGRGSKQA 139

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDV 369
           + +   L E    L   + L   + + LVE++    +R+   E  +++L  +   + R  
Sbjct: 140 TAELLALAE----LFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWV-SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           FL +  G E+D  W  + AK   + ++   +      I++ + ++ ++  ETG++I+E +
Sbjct: 196 FLRQFPGNEVDESWTDALAKG--KSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIK 253

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 254 DINRRMSIGEAKA 266


>gi|264685606|dbj|BAI49152.1| RNA polymerase beta subunit [Aeromonas sp. 67P24]
          Length = 272

 Score = 39.3 bits (90), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|167470529|ref|ZP_02335233.1| alternative sigma factor RpoH [Yersinia pestis FV-1]
          Length = 127

 Score = 39.3 bits (90), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 9/84 (10%)

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           TS   D IE+ N  S        +  +  +  L  L  R + ++R R+    N   TL+E
Sbjct: 48  TSDFADGIEEDNWDS--------HAADKLSYALEGLDERSQHIIRARWLDDENK-STLQE 98

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 99  LADQYGVSAERVRQLEKNAMKKLR 122


>gi|124809465|ref|XP_001348581.1| guanine nucleotide exchange factor, putative [Plasmodium falciparum
            3D7]
 gi|23497477|gb|AAN37020.1| guanine nucleotide exchange factor, putative [Plasmodium falciparum
            3D7]
          Length = 3384

 Score = 39.3 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 212  EDSSQEKE---RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            +DS+QEKE   +D  QE E +I+ + + +KDD + + +  E  E  +   +E ++D AH+
Sbjct: 3316 KDSTQEKEDNIKDSTQEVEDNIKDSIEGNKDDNANISNDDEEHEKTQELKEEGKEDDAHS 3375


>gi|259479061|dbj|BAI40078.1| RNA polymerase sigma-70 factor [Aeromonas sp. Kochi]
 gi|326682074|emb|CBL30928.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682076|emb|CBL30929.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682078|emb|CBL30930.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682082|emb|CBL30932.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682084|emb|CBL30933.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682086|emb|CBL30934.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682088|emb|CBL30935.1| RNA polymerase sigma factor [Aeromonas aquariorum]
          Length = 272

 Score = 39.3 bits (90), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|264685610|dbj|BAI49154.1| RNA polymerase beta subunit [Aeromonas sp. AC9804]
 gi|264685612|dbj|BAI49155.1| RNA polymerase beta subunit [Aeromonas sp. AC0202]
          Length = 272

 Score = 39.3 bits (90), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|58699437|ref|ZP_00374184.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534044|gb|EAL58296.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 57

 Score = 39.3 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 14/27 (51%), Positives = 22/27 (81%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           M A +KF+  LG++FSTYA+WW++ +I
Sbjct: 1   MHAVKKFNPDLGFRFSTYAVWWIEASI 27


>gi|260896280|ref|ZP_05904776.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio parahaemolyticus Peru-466]
 gi|308088782|gb|EFO38477.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio parahaemolyticus Peru-466]
          Length = 146

 Score = 39.3 bits (90), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 31/129 (24%), Positives = 58/129 (44%), Gaps = 11/129 (8%)

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVS 599
           + R+PT  E+A  L M ++     L      I+    +G ED     D I   ++ +  +
Sbjct: 16  LNRDPTDSEVAAHLGMSLDQYHSALT----DINCSRLVGIEDLGVSDDVISPADETDDSN 71

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P       + R+     +  L  RE  VL + +   +N    L+E+G    V+  R+ QI
Sbjct: 72  PFKGVADESFRKALVESIKQLPEREALVLSLYYDEELN----LKEIGDVLGVSESRVSQI 127

Query: 660 EAKAIRKLK 668
            ++A+++L+
Sbjct: 128 LSQAMQRLR 136


>gi|213958522|gb|ACJ54682.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm5R]
          Length = 252

 Score = 39.3 bits (90), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 27/42 (64%)

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           EMG++ELL+ EGEI IA RIE G   +M ++   P T   ++
Sbjct: 1   EMGTVELLTLEGEIEIANRIEEGIREVMGAIAHFPGTVDPIL 42


>gi|261341477|ref|ZP_05969335.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288316273|gb|EFC55211.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 233

 Score = 39.3 bits (90), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 102/229 (44%), Gaps = 30/229 (13%)

Query: 449 VEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY---KFSTYAMW 502
           V A L LV  V K+    T+  +   D+ Q   +GL+ A  ++    G+   +F  YA  
Sbjct: 21  VSAWLPLVHRVVKQLAWQTSSVMDREDMEQIALMGLLTALRRY----GHPDEQFGAYAAQ 76

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ A+   + +       P  +R K HK+    R ++ K+ R P+ E+++  L++  E 
Sbjct: 77  RIRGAVLDELRELDWR---PRRLRQKSHKLNDAIREVTRKLGRTPSFEDLSTHLSITAEE 133

Query: 563 VRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLAS 619
             + L +   K   SL+  +G       GD +    N  S  D  + +    T    LAS
Sbjct: 134 YHEYLLLDCAKTLESLDELLG-------GDALNGTLNTCSLEDEMVTSG---TLRAALAS 183

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE+ +L + +   M    +L+E+     +T  R+ Q+  K  +K++
Sbjct: 184 LDEREQLILSLYYQHEM----SLKEIALVLDLTEARVCQLNKKIAQKIQ 228


>gi|167717487|ref|ZP_02400723.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 163

 Score = 39.3 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++ DP+ +++R M ++ LL+   EIA+A  IEAGR  ++ +L E+
Sbjct: 106 ASTDPLALFVRRMHAVPLLTHAQEIALAAEIEAGREQVLQALAEA 150


>gi|156101057|ref|XP_001616222.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148805096|gb|EDL46495.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 659

 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 40/190 (21%), Positives = 82/190 (43%), Gaps = 15/190 (7%)

Query: 492 LGYK-FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
           LG K  + Y   W K +           + +  H     + V +       K +R+P+ +
Sbjct: 413 LGIKNLTKYVYIWAKNSTYNYYQKHKSFVSVSPHTYKDYNNVKKFEESFEEKHERKPSIK 472

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSH-----LGDFIEDKNAVSPLDS 603
           EI+  L M +E V+K L      I  E PI   + +++H       D I + + +  ++ 
Sbjct: 473 EISDGLHMTMERVQKALSSAVNVIDAEKPIVYQNSNSAHPEKNTYTDLIVNSDDIHSMNE 532

Query: 604 AIQANLRETTTRVLASLTPRE---ERVLRMRFGIGMNTD-HTLEEVGKQFCVTR---ERI 656
            +  ++     R     + R+   + ++ M+FG+ +    +T EE+ +   +T+   +R+
Sbjct: 533 IVYNDIVIKGLRKFICKSLRKKINKLIIFMKFGLFLRKKIYTDEEICRALQITQNKLQRL 592

Query: 657 RQIEAKAIRK 666
            Q+  K I+K
Sbjct: 593 FQLSLKEIKK 602


>gi|317062458|ref|ZP_07926943.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
 gi|313688134|gb|EFS24969.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
          Length = 244

 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 40/173 (23%), Positives = 78/173 (45%), Gaps = 21/173 (12%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +K RN  +     T + + E   ++ + ++G+ EA   + +++   LR +  +  +Y N 
Sbjct: 1   MKTRNMYREYPAITEVEVQE---LLPLAQEGDIEA---RNKIIVGYLRYITHLNNRYGN- 53

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G +  D  Q    G+++    +    G KFSTY  +W+KQ I R+   ++          
Sbjct: 54  GSE--DCFQSAIFGVIEGIRNYK-NNGIKFSTYCYFWIKQRINRTRDKENY--------- 101

Query: 527 DKIHKVVRTARRMSNKIKREPT--PEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           D     +   ++    IK +P    +E+ KKL +    +R + + T   ISL+
Sbjct: 102 DGNTSFIERRKKYEKLIKNDPLLPKKEVLKKLQISESTLRGIERSTYAKISLQ 154


>gi|239934518|emb|CAR94573.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 257

 Score = 39.3 bits (90), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REGEI IAKRIE G   +M ++   P T + ++
Sbjct: 1   TVELLTREGEIVIAKRIEEGLRELMKAMALFPGTVEHIL 39



 Score = 37.4 bits (85), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 63/131 (48%), Gaps = 8/131 (6%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           EKL +L  S  L   + + L++ +  +  R+  +E  ++ LA +   + R  F+    G 
Sbjct: 131 EKLGELFKSFKLTPRQFEPLLQHIRAVLTRLRRHEKTVMSLAVRGAKMPRKEFITSFPGN 190

Query: 378 ELDPHWVS---YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           E +  W+     AK  P  E    V  EV   ++ + +IK +  ETG++++E + I   +
Sbjct: 191 ETNEKWIDKHIRAKK-PYSELLVNVKTEV---IRAQKKIKLLEEETGLTVTEIKDINRQM 246

Query: 435 RKGECEASIAK 445
             GE ++  AK
Sbjct: 247 SIGEAKSRRAK 257


>gi|37784434|gb|AAO13110.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
 gi|37955126|gb|AAP76215.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 272

 Score = 39.3 bits (90), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 67/145 (46%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++  + +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEDVLRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|39938997|ref|NP_950763.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722106|dbj|BAD04596.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 201

 Score = 39.3 bits (90), Expect = 2.5,   Method: Composition-based stats.
 Identities = 33/89 (37%), Positives = 48/89 (53%), Gaps = 6/89 (6%)

Query: 445 KKEMVEANLRLVISVAK--KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++++ +L LV  + K  KY  R LQ  DL QEG +GL+KA   +   LGY F  YA  
Sbjct: 20  RNQLIDLHLPLVNKLVKQFKYYPRVLQKEDLYQEGVLGLIKALNHYQ-DLGYDFIAYATP 78

Query: 503 WVKQAITRSIADQSCTIRIPV--HMRDKI 529
            +K  I R I  +S +  IP   H +D +
Sbjct: 79  TIKSEI-REIIRKSHSPSIPQKNHKKDNL 106


>gi|87311655|ref|ZP_01093772.1| RNA polymerase ECF-type sigma factor [Blastopirellula marina DSM
           3645]
 gi|87285658|gb|EAQ77575.1| RNA polymerase ECF-type sigma factor [Blastopirellula marina DSM
           3645]
          Length = 201

 Score = 39.3 bits (90), Expect = 2.5,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           ET +GD   S +  F  D  A  PL + I A   E   R+L  LTP +   +R+RF   M
Sbjct: 98  ETEVGD---SPVIQFQADDAAAEPLAAMITAERHEHVRRLLTELTPSQAEAVRLRFFGQM 154

Query: 637 NTDHTLEEVGKQFCVTRERIRQ 658
                 + +G      + R+R+
Sbjct: 155 KFQEIADSLGCTLPAAKARVRK 176


>gi|226329392|ref|ZP_03804910.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
 gi|225202578|gb|EEG84932.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
          Length = 131

 Score = 39.3 bits (90), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 31/128 (24%), Positives = 68/128 (53%), Gaps = 12/128 (9%)

Query: 550 EEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD---FIEDKNAVSPLDSAI 605
           E +A++L +    VR++  +++ + ++ +    D D SH      F+EDK+  S     I
Sbjct: 2   ELVARELGVSESDVREMESRMSAQDMAFDMTADDSDDSHPIAPVLFLEDKS--SDFADGI 59

Query: 606 QAN-----LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           + +       +  T  + +L  R + ++R R+ +  +   TL+++  ++ V+ ER+RQ+E
Sbjct: 60  EEDNWDNHAADKLTSAIETLDERSQDIIRARW-LDDDNKSTLQDLATKYGVSAERVRQLE 118

Query: 661 AKAIRKLK 668
             A++KL+
Sbjct: 119 KNAMKKLR 126


>gi|323140910|ref|ZP_08075823.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
 gi|322414648|gb|EFY05454.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
          Length = 211

 Score = 38.9 bits (89), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 37/66 (56%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + ++ A   LV  +A  +       ++LIQEG +GL++AAE +D+     FS +A + 
Sbjct: 34  AHQRLMTAYQPLVFKIASSFRLPEADTMELIQEGMVGLLEAAESYDYKRQVAFSLFASYR 93

Query: 504 VKQAIT 509
           ++ ++ 
Sbjct: 94  IRGSMV 99


>gi|218905476|ref|YP_002453310.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218536250|gb|ACK88648.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 100

 Score = 38.9 bits (89), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 38  LDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 87


>gi|116074869|ref|ZP_01472130.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116068091|gb|EAU73844.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 203

 Score = 38.9 bits (89), Expect = 2.7,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 44/81 (54%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G +GL+KAA  +       FS +A   ++ AI   + D    +R+P  ++++  +
Sbjct: 19  DLIQVGRLGLIKAAGLYQNAFQVPFSAFARPHIRGAILHYLRDSVGLVRLPRRVQERAQR 78

Query: 532 VVRTARRMSNKIKREPTPEEI 552
           +++   + +  ++ + +P ++
Sbjct: 79  LLKQQGQTAQFLQHQVSPSDL 99


>gi|149174254|ref|ZP_01852881.1| RNA polymerase ECF-type sigma factor [Planctomyces maris DSM 8797]
 gi|148846799|gb|EDL61135.1| RNA polymerase ECF-type sigma factor [Planctomyces maris DSM 8797]
          Length = 217

 Score = 38.9 bits (89), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 4/52 (7%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            A LT +E++VLR+ F  GM T     E+ ++   T   IRQI+++A+RK++
Sbjct: 163 FAGLTDKEKQVLRLFFLSGMTT----REIAEELQTTTANIRQIQSRALRKIR 210


>gi|37784420|gb|AAO13103.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 270

 Score = 38.9 bits (89), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 127 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 186

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 187 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 245

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 246 IAQIKDINRRMSIGEAKARRAKKEM 270


>gi|37784462|gb|AAO13124.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score = 38.9 bits (89), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|315001918|emb|CBI75445.1| RNA polymerase sigma factor [Aeromonas sobria]
          Length = 242

 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 34/155 (21%), Positives = 70/155 (45%), Gaps = 3/155 (1%)

Query: 289 EVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV  + ++ +
Sbjct: 89  EKFGELRAQYEVTRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMME 148

Query: 348 RIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +L+L  +   + +  F+      E D  W  Y K   +  W   +    D +
Sbjct: 149 RVRVQERIILKLCVEQAKMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WSPRLVEMADDV 207

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 208 LRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|37784418|gb|AAO13102.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           smithia]
          Length = 270

 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 127 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 186

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 187 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 245

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 246 IAQIKDINRRMSIGEAKARRAKKEM 270


>gi|37784480|gb|AAO13133.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 274

 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 131 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 190

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 191 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 249

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 250 IAQIKDINRRMSIGEAKARRAKKEM 274


>gi|37784424|gb|AAO13105.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784426|gb|AAO13106.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784456|gb|AAO13121.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784458|gb|AAO13122.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784466|gb|AAO13126.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784472|gb|AAO13129.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784474|gb|AAO13130.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784476|gb|AAO13131.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37784478|gb|AAO13132.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784482|gb|AAO13134.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784492|gb|AAO13139.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|37784404|gb|AAO13095.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           pectinolytica]
 gi|37784412|gb|AAO13099.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784414|gb|AAO13100.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           achromogenes]
 gi|242117652|dbj|BAH80098.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 270

 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 127 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 186

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 187 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 245

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 246 IAQIKDINRRMSIGEAKARRAKKEM 270


>gi|296329094|ref|ZP_06871599.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153813|gb|EFG94626.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 979

 Score = 38.9 bits (89), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 17/27 (62%), Positives = 21/27 (77%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKL 667
           TLEE+G+   VTRERIRQIE +  +KL
Sbjct: 388 TLEEIGEALNVTRERIRQIETRGFKKL 414


>gi|37784460|gb|AAO13123.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score = 38.9 bits (89), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 32/145 (22%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|222112349|ref|YP_002554613.1| sigma-70 region 4 domain-containing protein [Acidovorax ebreus
           TPSY]
 gi|221731793|gb|ACM34613.1| sigma-70 region 4 domain protein [Acidovorax ebreus TPSY]
          Length = 893

 Score = 38.9 bits (89), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L   E  +   R G      HTL+++  Q  V+RER+RQIE K  +K++     + L   
Sbjct: 348 LNENERGIFAARLGFRCEP-HTLQQISDQIGVSRERVRQIEVKIFKKIRRHLFWESLAER 406

Query: 680 LDG 682
           LDG
Sbjct: 407 LDG 409


>gi|300856821|ref|YP_003781805.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300436936|gb|ADK16703.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 187

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 82/198 (41%), Gaps = 55/198 (27%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+ Q G +GLM+AA+ F+   G KFSTYA  +V+  I     + S  +            
Sbjct: 39  DMFQAGCVGLMRAAKNFNESKGRKFSTYAYKYVEGHIINLARNDSWYV------------ 86

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGD 590
                   +N++ R+ T E  A                   P+SL+  +G  EDT  +  
Sbjct: 87  --------ANRV-RDRTKESYA-------------------PVSLDQLVGYQEDTPMVDL 118

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            + D +  S LD      LR    ++  +L    ++++ MR+      D T  E+ K   
Sbjct: 119 IMGDVSEYSNLD------LRMALGKLPGTL----KKIIEMRYFY----DFTWREISKSIN 164

Query: 651 VTRERIRQIEAKAIRKLK 668
           + +  + + + +A+  L+
Sbjct: 165 MPQSTLYKYKKEALETLR 182


>gi|148793322|gb|ABR12725.1| RNA polymerase sigma factor [Photobacterium indicum]
          Length = 271

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 73/322 (22%), Positives = 128/322 (39%), Gaps = 57/322 (17%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDII----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDS-SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                  GF    E  +          E    D+ + + ++E+     +++ + +D  PE
Sbjct: 56  ------SGFIDPNEEQTAAPTATHIGSELSETDLADEDKNLETDEDDEEEEDTGID--PE 107

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A      L    +  A  ++    +       A+ E++E++++ R              
Sbjct: 108 LAREKFLELRHSYEKMALAINT-HGRHNATTEVAVGELSEIFKQFR-------------- 152

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRD 368
                 ++ ++  KLV SL               D   ++  NE  ++R+   +  + + 
Sbjct: 153 ------LIPKQFDKLVRSLR--------------DSMDKVRTNERLIMRMCVDNSKMPKK 192

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD---SILKIRNEIKSISVETGISIS 425
            F++   G E  P W+  A +  +   +     E D   S LK+R     +  ETG+SI 
Sbjct: 193 TFIKFFAGNESSPDWIDEALNSGKPYAERLKIYEEDLRRSSLKLR----ILEKETGLSIE 248

Query: 426 EFRHIVSMVRKGECEASIAKKE 447
             + I   +  GE +A  AKKE
Sbjct: 249 RIKDISRRMSIGEAKARRAKKE 270


>gi|331091821|ref|ZP_08340653.1| hypothetical protein HMPREF9477_01296 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330402720|gb|EGG82287.1| hypothetical protein HMPREF9477_01296 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 230

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 56/115 (48%), Gaps = 5/115 (4%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +AK+         DLIQEGN+GLM A EK +           +  ++Q +   + +Q
Sbjct: 112 VVEIAKELHTPEFFIGDLIQEGNVGLMLALEKEEAE-----EQEILEGIRQMMQLLVEEQ 166

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
                    M +K+  +  + + ++  + R+PT EE+A  + M  E V  +L++T
Sbjct: 167 EEVKHQDNKMVEKVIFLDESLKNLTEDLNRKPTLEELADYMEMTEEEVNDILRLT 221


>gi|261414353|gb|ACX83585.1| RNA polymerase sigma-70 factor [Aeromonas sanarellii]
          Length = 272

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + IL+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEILRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|284156787|gb|ACM45450.2| RNA polymerase sigma-70 factor [Aeromonas fluvialis]
          Length = 271

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 34/145 (23%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +  
Sbjct: 128 QKNGRAHQDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQA 187

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 188 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 246

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 247 IAQIKDINRRMSIGEAKARRAKKEM 271


>gi|86148201|ref|ZP_01066499.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|85834048|gb|EAQ52208.1| RNA polymerase sigma factor [Vibrio sp. MED222]
          Length = 83

 Score = 38.9 bits (89), Expect = 3.3,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 8/76 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +DS ++  N    ++ +    ++E  H      KGE +A+   K ++ ++LR V+ VA+ 
Sbjct: 16  LDSYIRSANSYPMLTPDEERGLAERLHY-----KGEIDAA---KGLILSHLRFVVHVARG 67

Query: 463 YTNRGLQFLDLIQEGN 478
           Y+  GL   DL+QEGN
Sbjct: 68  YSGYGLPMADLVQEGN 83


>gi|209407278|emb|CAP72524.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 272

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   D +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYDRVTSEGGRLSDI--LSGY 58

Query: 191 IGPESKGG 198
           I P+  G 
Sbjct: 59  IDPDDDGA 66


>gi|149916583|ref|ZP_01905097.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149809510|gb|EDM69370.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 189

 Score = 38.9 bits (89), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 50/103 (48%), Gaps = 7/103 (6%)

Query: 575 SLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLR 629
           SL   IG   E +    D++ED++A    D   +  L   RE     +  L  RE  +L 
Sbjct: 77  SLNAQIGSDGEGSMEWQDWLEDEDADQASDYERRDELEARREMLALAMDVLNERERDILT 136

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            R     +   TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 137 QRRL--SDETVTLEDLSTQYDVSRERIRQIEVRAFEKLQDRMR 177


>gi|37784432|gb|AAO13109.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|37955122|gb|AAP76213.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|37955124|gb|AAP76214.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763298|gb|ACD35526.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 272

 Score = 38.5 bits (88), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLVEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|54654463|gb|AAV37108.1| RpoD [Vibrio crassostreae]
          Length = 175

 Score = 38.5 bits (88), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 76/176 (43%), Gaps = 21/176 (11%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+ +   ++++    +     L   + D LV +L 
Sbjct: 10  EKFTALRTSYQNRQLAINEYGHESPKAMLATTMMQD----VFKEFRLTPKQFDYLVNELR 65

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
           +   R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 66  NSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 123

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            E D    IR  I+ + +   ET +++   + I   +  GE +A   KKEMVEANL
Sbjct: 124 NEHD----IRRSIQKLDMIERETSLTVQSIKDISRRMSIGEAKARRGKKEMVEANL 175


>gi|317010689|gb|ADU84436.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           SouthAfrica7]
          Length = 255

 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 88/204 (43%), Gaps = 19/204 (9%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            + F DL+  G   L+K A +++  L   F  YA   V  A+   +       R     R
Sbjct: 63  SIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLDVISR---SNR 119

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I  +     +  N+  +EP+ E +AK L   +E +R+    T   I    PI ++  +
Sbjct: 120 KLIKSIDFEITKYLNEHGKEPSDEYLAKALGENIEKIREAK--TASDIYALVPIDEQFNA 177

Query: 587 HLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
              D I  K         I+A  L E   +VL  ++ RE+ ++++ +   +N    L E+
Sbjct: 178 IEQDEITKK---------IEAEELLEHVQKVLNQMSEREQMLIQLYYFEELN----LSEI 224

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            +   +T  RI QI  + I+K++ 
Sbjct: 225 KEILGITESRISQIIKEVIKKVRQ 248


>gi|261414351|gb|ACX83584.1| RNA polymerase sigma-70 factor [Aeromonas taiwanensis]
          Length = 272

 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + IL+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEILRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|322378964|ref|ZP_08053378.1| flagellar biosynthesis sigma factor [Helicobacter suis HS1]
 gi|322379818|ref|ZP_08054115.1| flagellar biosynthesis sigma factor [Helicobacter suis HS5]
 gi|321147786|gb|EFX42389.1| flagellar biosynthesis sigma factor [Helicobacter suis HS5]
 gi|321148640|gb|EFX43126.1| flagellar biosynthesis sigma factor [Helicobacter suis HS1]
          Length = 236

 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 47/199 (23%), Positives = 84/199 (42%), Gaps = 17/199 (8%)

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           F DL+  G   L+K + ++D  L   F  YA   V  A+   +       R     R  I
Sbjct: 47  FNDLVSAGTEELIKLSRRYDVALNDSFWGYAKTRVNGAMLDYLRSLDVVSR---SSRKLI 103

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
             +     +  N   +EP    +A+ L   +  +R   K+  + I +  PI ++  +   
Sbjct: 104 KNIDHEISKYYNVHGQEPDDAYLAEVLGEDISKIRDA-KVASD-IYVHVPIDEQFNA--- 158

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             IE       L+      L E T  +L +++ RE+ V+++ F   +N    L E+ +  
Sbjct: 159 --IEQDTMTKKLEF---EELVEATQMILKTMSDREQLVIQLYFFEELN----LSEIREIL 209

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +T  RI QI  + I+K++
Sbjct: 210 GITESRISQIIKEVIKKIR 228


>gi|39939186|ref|NP_950952.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722295|dbj|BAD04785.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 228

 Score = 38.5 bits (88), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 447 EMVEANLRLV--ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++E +L LV  IS   KY  + L   DL QEG +GL+KA + +   LGY F  YA   +
Sbjct: 46  QLIELHLPLVKKISSKFKYYPKLLTKEDLYQEGVLGLIKALDNYQ-DLGYDFIAYATPTI 104

Query: 505 KQAITRSI 512
           K  I   I
Sbjct: 105 KSTINELI 112


>gi|11079147|dbj|BAB17578.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
          Length = 270

 Score = 38.5 bits (88), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 28/38 (73%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M+++ + P T  +++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAQFPGTVDSIL 38


>gi|283834438|ref|ZP_06354179.1| RNA polymerase sigma factor [Citrobacter youngae ATCC 29220]
 gi|291069985|gb|EFE08094.1| RNA polymerase sigma factor [Citrobacter youngae ATCC 29220]
          Length = 238

 Score = 38.5 bits (88), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 51/226 (22%), Positives = 100/226 (44%), Gaps = 25/226 (11%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++A L LV  V ++   +    +D   + Q   +GL+ A  ++       F+ YA+  ++
Sbjct: 26  LQAYLPLVRKVVRQLAPQCTCVMDRQDMEQTALMGLLNAIRRYGQP-DEGFAGYAVHRIR 84

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            AI   +  +S   R P  +R K H++    R    ++  EP+ EE++ +L +  E  ++
Sbjct: 85  GAILDEL--RSLDWR-PRQLRQKYHQIKDLIRDARTQLGHEPSWEELS-RLGLSSEDYQE 140

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI---QANLRETTTRVLASLTP 622
             ++           G E  + L + +     ++PL+      Q   +E  +  L+ L+ 
Sbjct: 141 YQQLE----------GAETLASLDELLNGDMPIAPLEGRGLEEQFVTQEMLSYALSQLSE 190

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E  VL M +   MN    L+E+     +T  RI Q+  K   K++
Sbjct: 191 KEGLVLSMYYQHDMN----LKEIALVLGLTEARICQMNKKITHKIR 232


>gi|39939022|ref|NP_950788.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722131|dbj|BAD04621.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 228

 Score = 38.5 bits (88), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 447 EMVEANLRLV--ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++E +L LV  IS   KY  + L   DL QEG +GL+KA + +   LGY F  YA   +
Sbjct: 46  QLIELHLPLVKKISSKFKYYPKLLTKEDLYQEGILGLIKALDNYQ-DLGYDFIAYATPTI 104

Query: 505 KQAITRSI 512
           K  I   I
Sbjct: 105 KSTINELI 112


>gi|296061206|emb|CBJ55914.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
          Length = 199

 Score = 38.5 bits (88), Expect = 4.0,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REGEIAIAKRIE G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 1   REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 50


>gi|262198088|ref|YP_003269297.1| hypothetical protein Hoch_4915 [Haliangium ochraceum DSM 14365]
 gi|262081435|gb|ACY17404.1| hypothetical protein Hoch_4915 [Haliangium ochraceum DSM 14365]
          Length = 246

 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 26/35 (74%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           TLEEVG+   +TRERIRQ+E + +RKL+  S S +
Sbjct: 201 TLEEVGEIMNLTRERIRQVEVRGLRKLRARSPSPE 235


>gi|302391036|ref|YP_003826856.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302203113|gb|ADL11791.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 222

 Score = 38.5 bits (88), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 23/110 (20%), Positives = 56/110 (50%), Gaps = 3/110 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + ++ + + G+    +A++ +++ N+ +V + +K +  +GL   D+IQEG +GL KA   
Sbjct: 18  QEVIDLAQNGD---KLAEEYLLDNNIDIVYAKSKLFYIKGLDKDDVIQEGLVGLYKAIRD 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           +       F  +A   V + +  +I   +    +P++    I K ++ ++
Sbjct: 75  YKEQRAASFRGFAHLCVSRQLISAIKTANRQKHMPLNTSTSIDKKLKYSK 124


>gi|58582244|ref|YP_201260.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84624137|ref|YP_451509.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188576807|ref|YP_001913736.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188577000|ref|YP_001913929.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|6969595|gb|AAF33832.1|AF226282_6 RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae]
 gi|58426838|gb|AAW75875.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84368077|dbj|BAE69235.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188521259|gb|ACD59204.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188521452|gb|ACD59397.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 251

 Score = 38.5 bits (88), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 47/202 (23%), Positives = 89/202 (44%), Gaps = 19/202 (9%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQ G IGL++A+  +D   G  F TYA   ++ ++   I        +P  +  +   
Sbjct: 47  DLIQAGMIGLIEASRSYDSEQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARD 103

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI---GDEDTS 586
                R++     R     E+A  + MP+    ++++     + +SLE+ I   G+ DT+
Sbjct: 104 AAAAVRKIEQNTGRAAAAAEVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTT 163

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                   K   +P     ++       + +  L  RE+ VL + +   +N    L+E+G
Sbjct: 164 -------AKGGPNPQQMMERSEFGRELGKAIGQLPEREQLVLSLYYEQELN----LKEIG 212

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI  +A+ +L+
Sbjct: 213 AVLGVSESRVCQIHGQAVVRLR 234


>gi|315453792|ref|YP_004074062.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter felis ATCC 49179]
 gi|315132844|emb|CBY83472.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter felis ATCC 49179]
          Length = 232

 Score = 38.5 bits (88), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 86/199 (43%), Gaps = 17/199 (8%)

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           F DLI  G   L+K A ++D  L   F  YA   V  A+   +       R     R  I
Sbjct: 43  FNDLISVGTEELIKLARRYDTSLNDSFWGYAKTRVNGAMLDYLRSLDVVSRAS---RKLI 99

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+     +  N+  +EP    +A+ L   +  +R   K+  + I    PI ++  +   
Sbjct: 100 KKIDHEVSKYYNEHGQEPDDAYLAEVLGEDISKIRDA-KMASD-IYASVPIDEQFNA--- 154

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             IE +N  + L+      L      +L +++ RE+ ++++ F   +N    L E+ +  
Sbjct: 155 --IEQRNINAKLEF---EELIAHIHAILKTMSEREQLIIQLYFFEELN----LSEIREIL 205

Query: 650 CVTRERIRQIEAKAIRKLK 668
            VT  RI QI  + I+K++
Sbjct: 206 GVTESRISQIIKEVIKKIR 224


>gi|11079145|dbj|BAB17577.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
 gi|11079149|dbj|BAB17579.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
 gi|11079151|dbj|BAB17580.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
 gi|11079153|dbj|BAB17581.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
          Length = 270

 Score = 38.5 bits (88), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 28/38 (73%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M+++ + P T  +++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAQFPGTVDSIL 38


>gi|189219201|ref|YP_001939842.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186059|gb|ACD83244.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 401

 Score = 38.5 bits (88), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 49/205 (23%), Positives = 89/205 (43%), Gaps = 15/205 (7%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q+ D    G  G++ A EK+D  +  +F  YA+  VK  +         T+R P      
Sbjct: 171 QWPDAENVGWFGILDALEKWDEQMQIRFFDYAIHHVKNRVRNYANACRTTVRRP------ 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            + V R  R++   +++  T EEI          + K+L++    ISL     DE  +T 
Sbjct: 225 -NSVYREYRKIEKFLEQGLTLEEITALYGYSPYQLEKILQVYSLDISLHFTAFDEESETC 283

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT---DHTLE 643
            L   +  +N    L+   +  LR+  T VL+ L     +++   FGI   T        
Sbjct: 284 FLDLLVYPENPDDSLER--EERLRKLFT-VLSHLDEISRKIVFFFFGIEEGTGAKGKPTA 340

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
            +  +  + R+++ Q+  +A+++LK
Sbjct: 341 WIAHKLKIPRQKVMQMLEEALKQLK 365


>gi|154500630|ref|ZP_02038668.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
 gi|150270519|gb|EDM97828.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
          Length = 221

 Score = 38.5 bits (88), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 33/65 (50%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KKY  +     DLI  G IGL+K    F      + +TYA   
Sbjct: 55  ARNILIEHNLRLVAHIIKKYYTQTDDQDDLISIGTIGLIKGISTFKPDKNVRLATYASRC 114

Query: 504 VKQAI 508
           ++  I
Sbjct: 115 IENEI 119


>gi|167745714|ref|ZP_02417841.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|317472694|ref|ZP_07932009.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655026|gb|EDR99155.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|316899871|gb|EFV21870.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
          Length = 192

 Score = 38.5 bits (88), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 32/59 (54%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           LV   ++K+   G    DLIQEG IGL KA + +D      FST+A   VK+ I  ++ 
Sbjct: 34  LVRRESRKFFLAGADEEDLIQEGMIGLFKAVKNYDDEKNASFSTFASLCVKRQIYTTVT 92


>gi|145952318|gb|ABP98982.1| sigma factor F [Mycobacterium gilvum]
          Length = 139

 Score = 38.5 bits (88), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 69/144 (47%), Gaps = 13/144 (9%)

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM----PVEGVRKVLKITK 571
           S ++++P  +++   ++      +S ++ R PT  E+A +L M     +EG+  V   + 
Sbjct: 2   SWSVKVPRRLKELHLRLGAATAELSQRLGRAPTATELAAELEMDRDEVIEGL--VAGSSY 59

Query: 572 EPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             +S+++   G+ED   + D + D +    LD   Q   RE    +LA+L  RE  VL +
Sbjct: 60  NTLSIDSGRHGNEDAPAIADTLGDVDLT--LD---QIENREALRPLLAALPERERTVLVL 114

Query: 631 RFGIGMNTDHTLEEVG-KQFCVTR 653
           RF   M      E VG  Q  V+R
Sbjct: 115 RFFESMTQTQIAERVGISQMHVSR 138


>gi|296061192|emb|CBJ55907.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061194|emb|CBJ55908.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061196|emb|CBJ55909.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061198|emb|CBJ55910.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061200|emb|CBJ55911.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061202|emb|CBJ55912.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061204|emb|CBJ55913.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061208|emb|CBJ55915.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061210|emb|CBJ55916.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
          Length = 199

 Score = 38.1 bits (87), Expect = 4.4,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REGEIAIAKRIE G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 1   REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 50


>gi|268610544|ref|ZP_06144271.1| RNA polymerase factor sigma-70 [Ruminococcus flavefaciens FD-1]
          Length = 208

 Score = 38.1 bits (87), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +VS+ +  +  AS+    ++    +L++  +K Y N      DL QEG + L+KA   +D
Sbjct: 22  LVSLAKTDKAAASV----ILSRYSKLILIKSKIYANSDTDSEDLHQEGLMSLLKAINAYD 77

Query: 490 WCLGYKFSTYA 500
             +G KFST+A
Sbjct: 78  PSMGAKFSTFA 88


>gi|257468173|ref|ZP_05632269.1| sporulation sigma factor SigG [Fusobacterium ulcerans ATCC 49185]
          Length = 239

 Score = 38.1 bits (87), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 73/159 (45%), Gaps = 18/159 (11%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            I+  E + ++ + ++G+ EA   + +++   LR +  +  +Y N G +  D  Q    G
Sbjct: 7   AITEVEVQELLPLAQEGDIEA---RNKIIVGYLRYITHLNNRYGN-GSE--DCFQSAIFG 60

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           +++    +    G KFSTY  +W+KQ I R+   ++          D     +   ++  
Sbjct: 61  VIEGIRNYK-NNGIKFSTYCYFWIKQRINRTRDKENY---------DGNTSFIERRKKYE 110

Query: 541 NKIKREPT--PEEIAKKLAMPVEGVRKVLKITKEPISLE 577
             IK +P    +E+ KKL +    +R + + T   ISL+
Sbjct: 111 KLIKNDPLLPKKEVLKKLQISESTLRGIERSTYAKISLQ 149


>gi|67920929|ref|ZP_00514448.1| Sigma-70 region 2 [Crocosphaera watsonii WH 8501]
 gi|67857046|gb|EAM52286.1| Sigma-70 region 2 [Crocosphaera watsonii WH 8501]
          Length = 110

 Score = 38.1 bits (87), Expect = 4.4,   Method: Composition-based stats.
 Identities = 20/79 (25%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++  + + DL+Q G++GL++A E+F    G+ FS++A+ +
Sbjct: 29  RNKILELNFGLVRREAHHWVHQCPESYEDLVQVGSLGLIRAIERFSIGKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIP 522
           ++  I   + +++     P
Sbjct: 89  IRGEIQHYLREKNIQFVFP 107


>gi|158341129|ref|YP_001522296.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158311370|gb|ABW32982.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 476

 Score = 38.1 bits (87), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 50/239 (20%), Positives = 111/239 (46%), Gaps = 24/239 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++ +NL  + S+    + +G++  +LI EG  GL KA +++    G    T++   
Sbjct: 42  ARQTVIYSNLAWICSMGGSLSRKGIEDGELISEGYFGLNKAIDQWSSEKGANIRTFSRDK 101

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           + +  + ++  Q   IR+P    +++ K+    ++ +  +  + T  ++A+   +  + +
Sbjct: 102 IYKFQSEAV-HQKNHIRLPKSTYEQLSKL----KKATAVLGEDATVAQLAEGTEIKEKRI 156

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + +I+ +P+SL +  G  +   L D   D +    LD A+ + L +    ++  L PR
Sbjct: 157 RTLQEIS-QPVSLNSVTGTRENLELLDQQAD-DCQGSLDPALSSELLD----LVDKLHPR 210

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +L +     ++     + +G            + AK +RKL +      LR FL G
Sbjct: 211 QREILHLYHWEELSFQKISDYLG------------LPAKKVRKL-YKQALDLLRKFLQG 256


>gi|37956271|gb|AAO73806.1| RNA polymerase sigma-70 factor [Aeromonas sp. 117P]
 gi|37956275|gb|AAO73808.1| RNA polymerase sigma-70 factor [Aeromonas sp. 40]
          Length = 272

 Score = 38.1 bits (87), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 33/147 (22%), Positives = 66/147 (44%), Gaps = 6/147 (4%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQ 361
           NG+  E +     +L +    +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 131 NGRAHEDTQAAIALLAD----VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 186

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG
Sbjct: 187 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLVEMDEEVLRSIGKLQQIEEETG 245

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEM 448
           +SI++ + I   +  GE +A  AKKEM
Sbjct: 246 LSIAQIKDINRRMSIGEAKARRAKKEM 272


>gi|37784408|gb|AAO13097.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37956249|gb|AAO73795.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37956265|gb|AAO73803.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37956267|gb|AAO73804.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37956269|gb|AAO73805.1| RNA polymerase sigma-70 factor [Aeromonas sp. LMG 13662]
          Length = 272

 Score = 38.1 bits (87), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 33/147 (22%), Positives = 66/147 (44%), Gaps = 6/147 (4%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQ 361
           NG+  E +     +L +    +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 131 NGRAHEDTQAAIALLAD----VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 186

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I  ETG
Sbjct: 187 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLVEMDEEVLRSIGKLQQIEEETG 245

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEM 448
           +SI++ + I   +  GE +A  AKKEM
Sbjct: 246 LSIAQIKDINRRMSIGEAKARRAKKEM 272


>gi|256833253|ref|YP_003161980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686784|gb|ACV09677.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 348

 Score = 38.1 bits (87), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 3/89 (3%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L   G   L++AA  FD   G  F+ +A   +K A+   +       R    +R KI  
Sbjct: 88  ELSSAGQFALVQAARNFDPSSGVPFARFAAIRIKGALVDELRSMDWVSR---GVRKKIRD 144

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           + + +  ++  + R PT +E+A  L +P+
Sbjct: 145 LNQVSDTLTATLGRTPTRQELATALGVPL 173


>gi|237749638|ref|ZP_04580118.1| RNA polymerase sigma-K factor [Helicobacter bilis ATCC 43879]
 gi|229374766|gb|EEO25157.1| RNA polymerase sigma-K factor [Helicobacter bilis ATCC 43879]
          Length = 104

 Score = 38.1 bits (87), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 604 AIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            IQ N+  E   + +  L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +
Sbjct: 22  TIQLNMELEKVKKYIDILDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKR 81

Query: 663 AIRKLKH 669
           A+ K+ H
Sbjct: 82  ALMKMFH 88


>gi|262038185|ref|ZP_06011579.1| hypothetical protein HMPREF0554_1929 [Leptotrichia goodfellowii
           F0264]
 gi|261747766|gb|EEY35211.1| hypothetical protein HMPREF0554_1929 [Leptotrichia goodfellowii
           F0264]
          Length = 314

 Score = 38.1 bits (87), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 45/228 (19%), Positives = 100/228 (43%), Gaps = 34/228 (14%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E+++  L++ +  +  Y+  G  FLD +QE  +G++     +D     + S    +++K
Sbjct: 94  RELIDEYLKVAVRESLLYSKFGFSFLDTVQEATLGVLSGINYYDRIK--EISKDPEFFIK 151

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
               + I +    +     ++D   K    +  +  K+K       + K++   ++ + K
Sbjct: 152 SFAVKYILEFQKNL-----LKD--IKASELSYVLYLKVK-------VDKEMGHSIDEISK 197

Query: 566 VLKITKEPISLETPIGDEDTSHLGD------FIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +T E I        ED   L D       I+++  +   D   Q  + E   + L+ 
Sbjct: 198 QMNVTPEYI--------EDLEKLFDGVEPEELIQNEQILEKADKITQLYILENIPKKLSY 249

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L   +E++L M +G+  +  +T +E+ K   ++   +  ++ KAI KL
Sbjct: 250 L---DEKILVMAYGLD-DKVYTGKEIAKTLNISLHNVNILKEKAINKL 293


>gi|219849677|ref|YP_002464110.1| tetratricopeptide repeat-containing protein [Chloroflexus aggregans
            DSM 9485]
 gi|219543936|gb|ACL25674.1| Tetratricopeptide TPR_2 repeat protein [Chloroflexus aggregans DSM
            9485]
          Length = 1838

 Score = 38.1 bits (87), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 19   DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D+  + D  D    ++I+L  ++GYV I ++ A +   E  +E++E     L   GI + 
Sbjct: 1200 DEEPMIDTGDPVLNRLIQLGHRQGYVDITDIIAVVQDPEREAERIEQIGWSLHRAGIQIR 1259

Query: 79   DGD---DLEDEEGSEDS 92
            DGD   D+E E G ED+
Sbjct: 1260 DGDEIIDMEAELGEEDT 1276


>gi|311826289|emb|CBX60052.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 278

 Score = 38.1 bits (87), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ++ELL+REG+I IAKRIE G   + +S+ E P T   ++
Sbjct: 1   TVELLTREGDIDIAKRIEEGINQVQSSVAEYPGTIPYIL 39


>gi|187763324|gb|ACD35539.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score = 38.1 bits (87), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|223635917|emb|CAQ03760.1| RNA polymerase sigma factor [Enterovibrio coralii]
          Length = 242

 Score = 38.1 bits (87), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII 55


>gi|34822013|gb|AAQ82815.1| RNA polymerase sigma-70 factor [Aeromonas sp. 239]
 gi|34822032|gb|AAQ82816.1| RNA polymerase sigma-70 factor [Aeromonas sp. 480]
 gi|34822063|gb|AAQ82817.1| RNA polymerase sigma-70 factor [Aeromonas sp. 57]
 gi|34822087|gb|AAQ82818.1| RNA polymerase sigma-70 factor [Aeromonas sp. 280]
 gi|34822107|gb|AAQ82819.1| RNA polymerase sigma-70 factor [Aeromonas sp. 610]
 gi|187763294|gb|ACD35524.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763296|gb|ACD35525.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763318|gb|ACD35536.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763362|gb|ACD35558.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|264685616|dbj|BAI49157.1| RNA polymerase beta subunit [Aeromonas sp. GMA0361]
          Length = 272

 Score = 38.1 bits (87), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|311826265|emb|CBX60040.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 276

 Score = 38.1 bits (87), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 25/37 (67%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           ELL+REGEI IAKRIE G   + +S+ E P T   ++
Sbjct: 1   ELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYIL 37


>gi|296061190|emb|CBJ55906.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
          Length = 198

 Score = 38.1 bits (87), Expect = 5.2,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REGEIAIAKRIE G + + A+L   PL+ + L+   +   +G   L EI+
Sbjct: 1   REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV 50


>gi|322421804|ref|YP_004201027.1| hypothetical protein GM18_4340 [Geobacter sp. M18]
 gi|320128191|gb|ADW15751.1| hypothetical protein GM18_4340 [Geobacter sp. M18]
          Length = 1030

 Score = 38.1 bits (87), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 32/118 (27%), Positives = 58/118 (49%), Gaps = 3/118 (2%)

Query: 560 VEGVRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  +R + ++ +  +S+ E+      T   GDF  D+   + L+ A+Q  +     R   
Sbjct: 257 LRAIRYLWQLQERAVSIAESAQAGLPTKAYGDF--DRLTDAYLEWALQLAVARKCGRPDQ 314

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               +  +VLR R  +   +   L E+G+++ VT ERIRQ+E+K +  LK P   + L
Sbjct: 315 ERVNQYRQVLRSRLRLVDGSKCQLRELGRRYGVTGERIRQMESKVMAVLKSPKGLRHL 372


>gi|37784430|gb|AAO13108.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|37955142|gb|AAP76221.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|37956263|gb|AAO73802.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763276|gb|ACD35515.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763278|gb|ACD35516.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763280|gb|ACD35517.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763282|gb|ACD35518.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763288|gb|ACD35521.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763290|gb|ACD35522.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763300|gb|ACD35527.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763320|gb|ACD35537.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763326|gb|ACD35540.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763332|gb|ACD35543.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763334|gb|ACD35544.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763336|gb|ACD35545.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763338|gb|ACD35546.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763340|gb|ACD35547.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763342|gb|ACD35548.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763344|gb|ACD35549.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763352|gb|ACD35553.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763356|gb|ACD35555.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763358|gb|ACD35556.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score = 38.1 bits (87), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|187763322|gb|ACD35538.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score = 38.1 bits (87), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|213584001|ref|ZP_03365827.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 148

 Score = 38.1 bits (87), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 17/88 (19%)

Query: 585 TSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +S+  D IED N    A + L  A+Q             L  R + ++R R+ +  +   
Sbjct: 69  SSNFADGIEDDNWEEQAANRLTDAMQG------------LDERSQDIIRARW-LDEDNKS 115

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 116 TLQELADRYGVSAERVRQLEKNAMKKLR 143


>gi|309390163|gb|ADO78043.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 208

 Score = 38.1 bits (87), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 28/122 (22%), Positives = 55/122 (45%), Gaps = 4/122 (3%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+ M + G      A + ++  N+ +V + ++ +  +GL   D+IQEG +GL KA   F 
Sbjct: 10  IIQMAQAGN---DFAIEYLINQNMDIVYAKSRFFFIKGLDHDDVIQEGRVGLYKAIRDFR 66

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  ++   V + +  +I   +    +P++    + K +      S +   E  P
Sbjct: 67  AEKGASFRGFSQLCVHRQLISAIKKANRQKHVPLNTSASLDKSLDYGSE-SGRTFNEILP 125

Query: 550 EE 551
           +E
Sbjct: 126 DE 127


>gi|187763348|gb|ACD35551.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score = 38.1 bits (87), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|187763306|gb|ACD35530.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 272

 Score = 38.1 bits (87), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 144 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVRERIIMKLCVEQAKMPKKTFVAAFTNNE 203

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 204 CETAWFEYQKQAGKA-WSPRLLEMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGE 262

Query: 439 CEASIAKKEM 448
            +A  AKKEM
Sbjct: 263 AKARRAKKEM 272


>gi|326332685|ref|ZP_08198948.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
 gi|325949513|gb|EGD41590.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
          Length = 176

 Score = 37.7 bits (86), Expect = 6.0,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++++V  +L +  S+A +Y+ RG++  DL Q   +GL+KAA ++D   G  F +YA+   
Sbjct: 15  QEDLVVRHLPVARSLAARYSGRGIEVEDLRQAARMGLVKAARRYDPEQG-AFLSYAVPMA 73

Query: 505 KQAITRSIADQSCTIR 520
           K  + R   D +  +R
Sbjct: 74  KGEMRRCFRDLARCVR 89


>gi|223635903|emb|CAQ03753.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635905|emb|CAQ03754.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635907|emb|CAQ03755.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635909|emb|CAQ03756.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635911|emb|CAQ03757.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635913|emb|CAQ03758.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635915|emb|CAQ03759.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|226484295|emb|CAQ03752.1| RNA polymerase sigma factor [Enterovibrio coralii]
          Length = 267

 Score = 37.7 bits (86), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII 55


>gi|187763302|gb|ACD35528.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score = 37.7 bits (86), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 37/162 (22%), Positives = 74/162 (45%), Gaps = 3/162 (1%)

Query: 289 EVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV  + ++ +
Sbjct: 112 EKFGELRAQYEVTRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMME 171

Query: 348 RIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +++L  +   + +  F+      E +  W  Y K   +      V  + D I
Sbjct: 172 RVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-I 230

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            +   +++ I  ETG+SI++ + I   +  GE +A  AKKEM
Sbjct: 231 QRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRAKKEM 272


>gi|11079194|dbj|BAB17588.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score = 37.7 bits (86), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGY 58

Query: 191 IGPESKGG 198
           I P+  G 
Sbjct: 59  IDPDDDGA 66


>gi|11079161|dbj|BAB17585.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 270

 Score = 37.7 bits (86), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGY 58

Query: 191 IGPESKGG 198
           I P+  G 
Sbjct: 59  IDPDDDGA 66


>gi|11079117|dbj|BAB17563.1| DNA-directed RNA polymerase subunit D [Pseudomonas asplenii]
 gi|11079119|dbj|BAB17564.1| DNA-directed RNA polymerase subunit D [Pseudomonas asplenii]
          Length = 268

 Score = 37.7 bits (86), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 3/49 (6%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   DE N  T+
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYIL---DEYNRVTS 46


>gi|52546578|dbj|BAD51672.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546582|dbj|BAD51674.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546586|dbj|BAD51676.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546588|dbj|BAD51677.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546590|dbj|BAD51678.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546592|dbj|BAD51679.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546594|dbj|BAD51680.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546600|dbj|BAD51683.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546604|dbj|BAD51685.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546606|dbj|BAD51686.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546608|dbj|BAD51687.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546610|dbj|BAD51688.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546614|dbj|BAD51690.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546616|dbj|BAD51691.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546620|dbj|BAD51693.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546622|dbj|BAD51694.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042248|dbj|BAE46943.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042250|dbj|BAE46944.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042252|dbj|BAE46945.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
          Length = 275

 Score = 37.7 bits (86), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRIDELVD 55


>gi|52546576|dbj|BAD51671.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546580|dbj|BAD51673.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546584|dbj|BAD51675.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546596|dbj|BAD51681.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546598|dbj|BAD51682.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546602|dbj|BAD51684.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546612|dbj|BAD51689.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546618|dbj|BAD51692.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546624|dbj|BAD51695.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546626|dbj|BAD51696.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040326|dbj|BAE16160.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040328|dbj|BAE16161.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040330|dbj|BAE16162.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040332|dbj|BAE16163.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040334|dbj|BAE16164.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040336|dbj|BAE16165.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040338|dbj|BAE16166.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040340|dbj|BAE16167.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040342|dbj|BAE16168.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli pv.
           cocovenerans]
 gi|71040344|dbj|BAE16169.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli pv.
           agaricicola]
 gi|78042254|dbj|BAE46946.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042256|dbj|BAE46947.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042258|dbj|BAE46948.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
          Length = 275

 Score = 37.7 bits (86), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRIDELVD 55


>gi|221057916|ref|XP_002261466.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
 gi|194247471|emb|CAQ40871.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
          Length = 792

 Score = 37.7 bits (86), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 37/179 (20%), Positives = 77/179 (43%), Gaps = 12/179 (6%)

Query: 492 LGYK-FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
           LG K  + Y   W K +           + +  H     +K+ +       K +R+P+ +
Sbjct: 564 LGIKNLTKYVYIWAKNSTYNYYQKHKSFVSVSPHTYKDYNKIKKFEESFEEKHERKPSIK 623

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSH-----LGDFIEDKNAVSPLDS 603
           EIA  L+M +E V+K L      I  E PI   + ++ H       D I + + +  ++ 
Sbjct: 624 EIADGLSMTMERVQKALSSAVNVIDAEKPIMYQNNNSDHPEKNTYTDLIVNADDIHSMNE 683

Query: 604 AIQANLRETTTR--VLASLTPREER-VLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQ 658
            +  +L     R  +  SL  +  + ++ M+FG+ +     T +E+     +T+ ++++
Sbjct: 684 IVYNDLVIKGLRKFICKSLKKKINKLIIFMKFGLFLRKKIFTDDEICHTLQITKNKLQK 742


>gi|187763286|gb|ACD35520.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score = 37.7 bits (86), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|187763308|gb|ACD35531.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 271

 Score = 37.7 bits (86), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 128 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 187

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 188 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 246

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 247 IAQIKDINRRMSIGEAKARRAKKEM 271


>gi|187763292|gb|ACD35523.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score = 37.7 bits (86), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|37784422|gb|AAO13104.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
 gi|37784440|gb|AAO13113.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. veronii]
 gi|37784452|gb|AAO13119.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|37784464|gb|AAO13125.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. veronii]
 gi|37956259|gb|AAO73800.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|37956261|gb|AAO73801.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|91978895|gb|ABE66423.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|91978909|gb|ABE66430.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|91978911|gb|ABE66431.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763270|gb|ACD35512.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763272|gb|ACD35513.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763284|gb|ACD35519.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763312|gb|ACD35533.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763328|gb|ACD35541.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763330|gb|ACD35542.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763350|gb|ACD35552.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763360|gb|ACD35557.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score = 37.7 bits (86), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|37784450|gb|AAO13118.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37784454|gb|AAO13120.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37784490|gb|AAO13138.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956251|gb|AAO73796.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956253|gb|AAO73797.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956255|gb|AAO73798.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956257|gb|AAO73799.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
          Length = 272

 Score = 37.7 bits (86), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 34/147 (23%), Positives = 65/147 (44%), Gaps = 6/147 (4%)

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQ 361
           NG+  E +     +L +    +     L   + D LV  +  + +R+   E  +++L  +
Sbjct: 131 NGRAHEDTQAAIALLAD----VFRQFRLMPKQFDRLVNNMRGMMERVRVQERIIMKLCVE 186

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  ETG
Sbjct: 187 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRSIGKLQQIEEETG 245

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEM 448
           +SI++ + I   +  GE +A  AKKEM
Sbjct: 246 LSIAQIKDINRRMSIGEAKARRAKKEM 272


>gi|187933785|ref|YP_001886205.1| protein NdvB [Clostridium botulinum B str. Eklund 17B]
 gi|187721938|gb|ACD23159.1| glycosyl transferase, group 36 family protein [Clostridium
           botulinum B str. Eklund 17B]
          Length = 3072

 Score = 37.7 bits (86), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 61/151 (40%), Gaps = 30/151 (19%)

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISV 418
            SYG++R++  E +QG         Y K   +G  K   A E  +D+I  I  E K+I  
Sbjct: 5   NSYGLRRNILRELNQGFSCIHENFKYFKKLSKGRNKVLGAAEWLLDNIYLIEKEYKAIKK 64

Query: 419 ETGI-------SISEFRHIVSMVRKGECEASIAKKEM-------------VEANLRLVIS 458
           E  I       SI+EF   V   +      S   K               VE  L  +  
Sbjct: 65  EMPIDYFKSLPSITEFNDNVDHNKAHRINNSFKSKNFYDERGYEKKGYNEVENELPRIFV 124

Query: 459 VAKKYTNRG--------LQFLDLIQEGNIGL 481
           VAK Y + G        +++++ IQE N+G+
Sbjct: 125 VAKMYVDMGGDIDYESFIKYINKIQEENLGI 155


>gi|331084310|ref|ZP_08333415.1| hypothetical protein HMPREF0992_02339 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330401845|gb|EGG81422.1| hypothetical protein HMPREF0992_02339 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 247

 Score = 37.7 bits (86), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 16/122 (13%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF-------DWCLGYKFSTYAMWWVKQAI 508
           ++  AKK     + F DL+QEGN+GL+ A E+        +W +    ST  ++  +Q  
Sbjct: 131 IVKAAKKLNREDIFFGDLLQEGNMGLLTALERLSEQENPDEWIVREIESTMKLFIEEQ-- 188

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
               A Q     I V   +K+  + +  + ++     + + EE+A  L M +E +  VL+
Sbjct: 189 ----AQQKKEDNILV---EKVRDLEKKVKELTEDEDVKYSVEELAAFLDMDLEEMESVLR 241

Query: 569 IT 570
           +T
Sbjct: 242 LT 243


>gi|226484289|emb|CAQ03749.1| RNA polymerase sigma factor [Enterovibrio nigricans]
 gi|226484291|emb|CAQ03750.1| RNA polymerase sigma factor [Enterovibrio nigricans]
          Length = 265

 Score = 37.7 bits (86), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII 55


>gi|37595578|gb|AAQ94633.1| FliA [Phytoplasma sp. AY1]
 gi|47717362|gb|AAT37711.1| DNA-directed RNA polymerase sigma subunit [New Jersey aster yellows
           phytoplasma]
          Length = 150

 Score = 37.7 bits (86), Expect = 7.1,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 445 KKEMVEANLRLVISVAK--KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + +++E +L LV  +A   KY  + L   DL QEG +GL+KA   +   LGY F TYA  
Sbjct: 20  RNQLIELHLPLVKKLAYHFKYYPKVLTKEDLYQEGILGLIKALNNYQ-DLGYDFVTYATP 78

Query: 503 WVKQAITRSI 512
            +K AI   I
Sbjct: 79  KIKFAINELI 88


>gi|238058450|gb|ACR39376.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 274

 Score = 37.7 bits (86), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 31/55 (56%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII 55


>gi|226484293|emb|CAQ03751.1| RNA polymerase sigma factor [Enterovibrio nigricans]
          Length = 265

 Score = 37.7 bits (86), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII 55


>gi|59859799|gb|AAX09621.1| DNA-directed RNA polymerase subunit D [Pseudomonas entomophila L48]
          Length = 269

 Score = 37.7 bits (86), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 25/38 (65%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M ++   P T   +I
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYII 38


>gi|168704081|ref|ZP_02736358.1| RNA polymerase sigma factor for flagellar operon [Gemmata
           obscuriglobus UQM 2246]
          Length = 247

 Score = 37.7 bits (86), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 50/105 (47%), Gaps = 6/105 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++ ++L LV  V  +       G+   +L   G +GL++AA KFD     +F T+A 
Sbjct: 22  RDELIVSHLPLVKHVIGRLIGDVPPGVDVENLESAGVLGLVEAAAKFDPARNAQFKTFAY 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
             ++ AI   +   S    +P H+  ++  V R  R + + I  E
Sbjct: 82  LRIRGAIVDEMRRNSP---LPQHVHARLALVRRACRTLPHPITVE 123


>gi|52546480|dbj|BAD51623.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|52546482|dbj|BAD51624.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|52546484|dbj|BAD51625.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
          Length = 281

 Score = 37.7 bits (86), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 30/56 (53%), Gaps = 10/56 (17%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI----------IWRDELNDG 177
           ELL+REGEI IAKRIE G   M+ ++   P T   ++          I  DEL DG
Sbjct: 1   ELLTREGEIEIAKRIEEGLKHMVQAISACPTTIADILGMAERVANDEIRVDELVDG 56


>gi|289169247|emb|CAX46383.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 271

 Score = 37.7 bits (86), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 31/55 (56%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII 55


>gi|259479067|dbj|BAI40081.1| RNA polymerase sigma-70 factor [Aeromonas sp. TT2]
 gi|259479069|dbj|BAI40082.1| RNA polymerase sigma-70 factor [Aeromonas sp. TT5]
          Length = 272

 Score = 37.7 bits (86), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|187763304|gb|ACD35529.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score = 37.7 bits (86), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|259479059|dbj|BAI40077.1| RNA polymerase sigma-70 factor [Aeromonas sp. GV20]
          Length = 272

 Score = 37.4 bits (85), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE +A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEAKARRAKKEM 272


>gi|315638331|ref|ZP_07893511.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter
           upsaliensis JV21]
 gi|315481598|gb|EFU72222.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter
           upsaliensis JV21]
          Length = 231

 Score = 37.4 bits (85), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 33/123 (26%), Positives = 60/123 (48%), Gaps = 14/123 (11%)

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  E +AKKL + VE VR+V       IS   P+ ++        IE  +    L+   
Sbjct: 119 EPDDEYLAKKLEIDVERVREVR--AAHAISYTLPLDEQ--------IEMYSEDETLEKIE 168

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L E    +L +L  R++ ++++ +      + +L+E+ +   V+  RI QI  K ++
Sbjct: 169 RGELLEHINEILDTLKERDQLIIQLYYY----EELSLKEISEILNVSESRISQIHKKLLK 224

Query: 666 KLK 668
           KL+
Sbjct: 225 KLR 227


>gi|11078979|dbj|BAB17494.1| DNA-directed RNA polymerase subunit D [Pseudomonas cichorii]
 gi|11078981|dbj|BAB17495.1| DNA-directed RNA polymerase subunit D [Pseudomonas cichorii]
          Length = 269

 Score = 37.4 bits (85), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL-NDGTTL---LREIID 186
           +ELL+REGEI IAKRIE G   +M+++   P T + ++   D + ++G  L   L   ID
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVEHILSEYDRVTSEGGRLSDVLSGYID 60

Query: 187 LEACIGPESK 196
            +  I P ++
Sbjct: 61  PDDGIAPPAE 70


>gi|54025688|ref|YP_119930.1| hypothetical protein nfa37180 [Nocardia farcinica IFM 10152]
 gi|54017196|dbj|BAD58566.1| hypothetical protein [Nocardia farcinica IFM 10152]
          Length = 417

 Score = 37.4 bits (85), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 11/90 (12%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            +E+  GD+    +   +E+ N V     A+ A  R            R+  +L  R GI
Sbjct: 25  GVESAFGDDVAGEVAFGLEEVNEVIAGLVAVHAERRR-----------RDAEILAARLGI 73

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           G     TL  +G +F + R+R+RQ+  + +
Sbjct: 74  GGEPPQTLAAIGARFDLARDRVRQLHTRTV 103


>gi|11079157|dbj|BAB17583.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score = 37.4 bits (85), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 27/38 (71%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M+++   P T  +++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSIL 38


>gi|54654465|gb|AAV37109.1| RpoD [Vibrio kanaloae]
 gi|54654471|gb|AAV37112.1| RpoD [Vibrio splendidus]
          Length = 173

 Score = 37.4 bits (85), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 45/174 (25%), Positives = 75/174 (43%), Gaps = 21/174 (12%)

Query: 289 EVYRELRSLQDN---AVN--GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           E +  LR+   N   A+N  G +  K+++   ++++    +     L   + D LV +L 
Sbjct: 10  EKFTALRTSYQNRQLAINEYGHESPKATLATTMMQD----VFKEFRLTPKQFDYLVNELR 65

Query: 344 DISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--YAKDFPEGEWKNFVA 400
               R+   E  ++R    YG + +  F+    G E    W+    A D P  E      
Sbjct: 66  TSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAE--KIKR 123

Query: 401 CEVDSILKIRNEIKSISV---ETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E D    IR  I+ + +   ET +++   + I   +  GE +A  AKKEMVEA
Sbjct: 124 NEHD----IRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEA 173


>gi|85057474|ref|YP_456390.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789579|gb|ABC65311.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 208

 Score = 37.4 bits (85), Expect = 8.0,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 445 KKEMVEANLRLVISVAK--KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + +++E +L LV  +A   KY  + L   DL QEG +GL+KA   +   LGY F TYA  
Sbjct: 20  RNQLIELHLPLVKKLAYHFKYYPKVLTKEDLYQEGILGLIKALNNYQ-DLGYDFVTYATP 78

Query: 503 WVKQAITRSI 512
            +K AI   I
Sbjct: 79  KIKFAINELI 88


>gi|254517801|ref|ZP_05129857.1| sigma-70 family RNA polymerase sigma factor [Clostridium sp.
           7_2_43FAA]
 gi|226911550|gb|EEH96751.1| sigma-70 family RNA polymerase sigma factor [Clostridium sp.
           7_2_43FAA]
          Length = 187

 Score = 37.4 bits (85), Expect = 8.2,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+ K +   S +K+E+++    L+I  AK    +   F D++Q G I L+   + FD   
Sbjct: 1   MLLKAKNNDSSSKEEIIKMYYPLIIKEAKTIYLKNKSFEDIVQIGVINLLHVIDVFDLSK 60

Query: 493 GY-KFSTYAMWWVKQA 507
              KF +YA+W +K  
Sbjct: 61  NVDKFPSYALWAIKNG 76


>gi|149908744|ref|ZP_01897405.1| RNA polymerase sigma factor for flagellar operon [Moritella sp.
           PE36]
 gi|149808286|gb|EDM68225.1| RNA polymerase sigma factor for flagellar operon [Moritella sp.
           PE36]
          Length = 238

 Score = 37.4 bits (85), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 44/196 (22%), Positives = 90/196 (45%), Gaps = 16/196 (8%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+Q G +GL++A  ++     Y F +YA   ++  I   +  Q      P   R + H 
Sbjct: 51  DLVQIGTMGLLEAIRRYGSEPDYGFESYAFQRIRGEILDELRRQDWR---PRQARQQGHS 107

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    R +S  + RE   +E+   L +  E ++ ++    + +S E    DE      D 
Sbjct: 108 LNHARRTLSRTLGREANEKELMAFLEIDAEQLQDMI---FDSVSEEMQSLDELLQAGTDI 164

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            ++ + +   D  I+ +L++T    L+ L  R++ +L + +   +N    ++E+     +
Sbjct: 165 TDENSDIQKFD--IKRSLKQT----LSLLDQRDQLLLTLYYQYELN----MKEISLTLKI 214

Query: 652 TRERIRQIEAKAIRKL 667
           T  R+ Q+   A++KL
Sbjct: 215 TESRVCQLHQLALKKL 230


>gi|187763316|gb|ACD35535.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score = 37.4 bits (85), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 64/145 (44%), Gaps = 2/145 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 129 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 188

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+S
Sbjct: 189 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLS 247

Query: 424 ISEFRHIVSMVRKGECEASIAKKEM 448
           I++ + I   +  GE  A  AKKEM
Sbjct: 248 IAQIKDINRRMSIGEARARRAKKEM 272


>gi|292670483|ref|ZP_06603909.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
 gi|292647893|gb|EFF65865.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
          Length = 205

 Score = 37.4 bits (85), Expect = 8.4,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E  H +    K E + S A++ ++EA   LV      Y    +  +D +QEG IGL++A 
Sbjct: 13  EEEHALWRAYKEEGDES-ARRRIIEAYQPLVFREVMPYRTMPV-VMDAVQEGTIGLIEAV 70

Query: 486 EKFDWCLGYKFSTYAMWWVKQAI 508
           E++D   G  FS YA+  V+  I
Sbjct: 71  ERYDPTRGVAFSLYAVHRVRGRI 93


>gi|11079192|dbj|BAB17587.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|11079196|dbj|BAB17589.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score = 37.4 bits (85), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 27/38 (71%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M+++   P T  +++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSIL 38


>gi|11079051|dbj|BAB17530.1| DNA-directed RNA polymerase subunit D [Pseudomonas agarici]
          Length = 268

 Score = 37.4 bits (85), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 26/38 (68%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M ++   P T + ++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHIL 38


>gi|78184762|ref|YP_377197.1| putative type III sigma factor [Synechococcus sp. CC9902]
 gi|78169056|gb|ABB26153.1| putative type III sigma factor [Synechococcus sp. CC9902]
          Length = 124

 Score = 37.4 bits (85), Expect = 8.5,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLD-LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V  +L L   VA +  +RG +  D L+QE  +GL++  +KFD   G + S+Y M  
Sbjct: 22  RNQKVLQHLGLAHCVAMRQRHRGPEERDDLLQEACLGLIQGLQKFDPSRGLRPSSYLMSR 81

Query: 504 VKQAITRSIADQSCTIRIPVHMRD 527
               +     D+S  +RIP  ++D
Sbjct: 82  ANGQVLHYRRDRSRMVRIPWRLQD 105


>gi|11079067|dbj|BAB17538.1| DNA-directed RNA polymerase subunit D [Pseudomonas agarici]
          Length = 268

 Score = 37.4 bits (85), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 26/38 (68%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M ++   P T + ++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHIL 38


>gi|52546628|dbj|BAD51697.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546630|dbj|BAD51698.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546632|dbj|BAD51699.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546636|dbj|BAD51701.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546638|dbj|BAD51702.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546640|dbj|BAD51703.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546642|dbj|BAD51704.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546644|dbj|BAD51705.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546646|dbj|BAD51706.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546648|dbj|BAD51707.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546650|dbj|BAD51708.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546652|dbj|BAD51709.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546656|dbj|BAD51714.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546658|dbj|BAD51715.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546662|dbj|BAD51717.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546672|dbj|BAD51731.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|71040346|dbj|BAE16170.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
          Length = 275

 Score = 37.4 bits (85), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVD 55


>gi|52546634|dbj|BAD51700.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546654|dbj|BAD51712.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546660|dbj|BAD51716.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546664|dbj|BAD51720.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546666|dbj|BAD51721.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546668|dbj|BAD51724.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546670|dbj|BAD51726.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
          Length = 275

 Score = 37.4 bits (85), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVD 55


>gi|52546494|dbj|BAD51630.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546496|dbj|BAD51631.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546498|dbj|BAD51632.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546500|dbj|BAD51633.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546502|dbj|BAD51634.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546504|dbj|BAD51635.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546506|dbj|BAD51636.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546508|dbj|BAD51637.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546510|dbj|BAD51638.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546512|dbj|BAD51639.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546514|dbj|BAD51640.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546516|dbj|BAD51641.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546518|dbj|BAD51642.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546520|dbj|BAD51643.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546522|dbj|BAD51644.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546524|dbj|BAD51645.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546526|dbj|BAD51646.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546528|dbj|BAD51647.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546530|dbj|BAD51648.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546532|dbj|BAD51649.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546534|dbj|BAD51650.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546536|dbj|BAD51651.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546538|dbj|BAD51652.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546540|dbj|BAD51653.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546542|dbj|BAD51654.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546544|dbj|BAD51655.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546546|dbj|BAD51656.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546548|dbj|BAD51657.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546550|dbj|BAD51658.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546552|dbj|BAD51659.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546554|dbj|BAD51660.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546556|dbj|BAD51661.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546558|dbj|BAD51662.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546560|dbj|BAD51663.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546562|dbj|BAD51664.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546564|dbj|BAD51665.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546566|dbj|BAD51666.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546568|dbj|BAD51667.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546570|dbj|BAD51668.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546572|dbj|BAD51669.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546574|dbj|BAD51670.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506775|dbj|BAD91134.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506778|dbj|BAD91135.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506781|dbj|BAD91136.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506784|dbj|BAD91137.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506788|dbj|BAD91138.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506791|dbj|BAD91139.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506795|dbj|BAD91140.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506798|dbj|BAD91141.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506801|dbj|BAD91142.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506804|dbj|BAD91143.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506807|dbj|BAD91144.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506810|dbj|BAD91145.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506813|dbj|BAD91146.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506816|dbj|BAD91147.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506819|dbj|BAD91148.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506822|dbj|BAD91149.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506825|dbj|BAD91150.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506828|dbj|BAD91151.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506831|dbj|BAD91152.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506834|dbj|BAD91153.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506838|dbj|BAD91154.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506841|dbj|BAD91155.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506844|dbj|BAD91156.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506847|dbj|BAD91157.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506850|dbj|BAD91158.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506853|dbj|BAD91159.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
          Length = 275

 Score = 37.4 bits (85), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVD 55


>gi|11079057|dbj|BAB17533.1| DNA-directed RNA polymerase subunit D [Pseudomonas agarici]
          Length = 268

 Score = 37.4 bits (85), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 26/38 (68%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +ELL+REGEI IAKRIE G   +M ++   P T + ++
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHIL 38


>gi|66474703|gb|AAY46921.1| RpoD [Aeromonas sp. 13m]
          Length = 272

 Score = 37.4 bits (85), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 30/129 (23%), Positives = 59/129 (45%), Gaps = 2/129 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE 378
           +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E
Sbjct: 145 QLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNE 204

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE
Sbjct: 205 CETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGE 263

Query: 439 CEASIAKKE 447
            +A  AKKE
Sbjct: 264 AKARRAKKE 272


>gi|66474653|gb|AAY46896.1| RpoD [Aeromonas sp. AN-46]
          Length = 269

 Score = 37.4 bits (85), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 32/144 (22%), Positives = 65/144 (45%), Gaps = 2/144 (1%)

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 127 QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 186

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  ETG+S
Sbjct: 187 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLS 245

Query: 424 ISEFRHIVSMVRKGECEASIAKKE 447
           I++ + I   +  GE +A  AKKE
Sbjct: 246 IAQIKDINRRMSIGEAKARRAKKE 269


>gi|332975577|gb|EGK12467.1| RNA polymerase sigma-K factor [Desmospora sp. 8437]
          Length = 86

 Score = 37.4 bits (85), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 31/53 (58%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L  RE+ V+R RFG+    + T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 26  LHILDEREQDVIRNRFGLSGGKEKTQREIAKELGISRSYVSRIEKRALIKLFH 78


>gi|270659580|ref|ZP_06222335.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270316998|gb|EFA28670.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 147

 Score = 37.4 bits (85), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 31/123 (25%), Positives = 63/123 (51%), Gaps = 8/123 (6%)

Query: 552 IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGD--FIEDK--NAVSPLDS-AI 605
           +A +L +  E V ++  +++   +  + P  D +T       ++EDK  N  + L++   
Sbjct: 22  VANELGVSKEDVIEMESRMSGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENF 81

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           ++   E     L SL  R + +++ R+    +   TL ++  ++ V+ ERIRQ+E  A++
Sbjct: 82  ESQATEQLGAALQSLDARSQDIIKARWLD--DNKATLHDLAAKYNVSAERIRQLETNALK 139

Query: 666 KLK 668
           KLK
Sbjct: 140 KLK 142


>gi|224533308|ref|ZP_03673902.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
 gi|224513473|gb|EEF83830.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
          Length = 373

 Score = 37.0 bits (84), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 36/56 (64%), Gaps = 5/56 (8%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           D  ++DP+++YL+E+G   LL+   E+ +AK++++G      S+ E+ L  + L+I
Sbjct: 134 DSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQMDSG-----ESIIENILKNEGLVI 184


>gi|54654467|gb|AAV37110.1| RpoD [Vibrio pomeroyi]
          Length = 173

 Score = 37.0 bits (84), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 34/125 (27%), Positives = 55/125 (44%), Gaps = 6/125 (4%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS--Y 386
           L   + D LV +L +   R+   E  ++R    YG + +  F+    G E    W+    
Sbjct: 52  LTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVL 111

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A D P  E    +    + I +   ++  I  ET +++   + I   +  GE +A  AKK
Sbjct: 112 ASDKPYAEK---IKRNENDIRRSIQKLDMIEKETSLTVQSIKDISRRMSIGEAKARRAKK 168

Query: 447 EMVEA 451
           EMVEA
Sbjct: 169 EMVEA 173


>gi|157313272|gb|ABV32529.1| RNA polymerase sigma factor [Xanthomonas campestris]
 gi|157313274|gb|ABV32530.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 37.0 bits (84), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 45/173 (26%), Positives = 79/173 (45%), Gaps = 12/173 (6%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +   A NG  + K  VK +   E +  +  +L L     D LV
Sbjct: 69  VATRMENLANEYAKFKKIY--AKNGA-EHKLVVKAR---EDMAAIFTTLKLPLPLTDALV 122

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W + 
Sbjct: 123 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQ-KWSSA 181

Query: 399 VACEVDSILKIRNEIKSISVETG--ISISEFRHIVSMVRKGECEASIAKKEMV 449
           +    D I  +  +  SI +E    +++ E + I   +  GE +A  AKKEMV
Sbjct: 182 LRDVKDQI--VSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMV 232


Searching..................................................done


Results from round 2




>gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254039966|gb|ACT56762.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 682

 Score =  710 bits (1832), Expect = 0.0,   Method: Composition-based stats.
 Identities = 682/682 (100%), Positives = 682/682 (100%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS
Sbjct: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP
Sbjct: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL
Sbjct: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD
Sbjct: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN
Sbjct: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA
Sbjct: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET
Sbjct: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG
Sbjct: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS
Sbjct: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP
Sbjct: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE
Sbjct: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKAIRKLKHPSRSKKLRSFLDG
Sbjct: 661 AKAIRKLKHPSRSKKLRSFLDG 682


>gi|315122849|ref|YP_004063338.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313496251|gb|ADR52850.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 683

 Score =  622 bits (1604), Expect = e-176,   Method: Composition-based stats.
 Identities = 544/684 (79%), Positives = 595/684 (86%), Gaps = 3/684 (0%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M  G+K+NRDSDSEHE+S+D+LVFDFSDDSWKKM+K A+QRGYVT+EELN   P +E S 
Sbjct: 1   MIKGRKKNRDSDSEHENSEDTLVFDFSDDSWKKMLKAAKQRGYVTVEELNTVFPSEEASV 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED-EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           EQ+E+T+AMLSNMGINVVD DDLED EEGSEDSLDL  S  N++V  QKRKD ADRSTDD
Sbjct: 61  EQIEETMAMLSNMGINVVDSDDLEDLEEGSEDSLDLTHSNGNTAVLSQKRKDLADRSTDD 120

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT
Sbjct: 121 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 180

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LLREIIDLEACIGP SK  FF G+E  S   +E+ + +++ D     +   +++   S  
Sbjct: 181 LLREIIDLEACIGPGSKATFFQGSEADSCVNQEEGAPQEKADGEDGIKSVSKNSKVESDH 240

Query: 240 DRSKVD-SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
             S  D S  EN + +E  LDEDEDDS HTLSAMEDQLRP+VM AL+EIAE Y++LR LQ
Sbjct: 241 VSSLSDNSAAENGDGEENGLDEDEDDSRHTLSAMEDQLRPQVMSALNEIAESYQKLRLLQ 300

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           ++      DEK  VK + LK +LV+LVGSLSLNQSRIDLLVEQLYDISKRIM NEGELLR
Sbjct: 301 ESTRRQN-DEKYLVKYRELKGRLVELVGSLSLNQSRIDLLVEQLYDISKRIMKNEGELLR 359

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           LAQSYGIKRDVFL+R+QG ELDP W S AK F E +WKNFV CE+DSIL+IR++IK I+ 
Sbjct: 360 LAQSYGIKRDVFLDRYQGHELDPEWTSSAKGFSEKKWKNFVDCEMDSILRIRDDIKGIAS 419

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN
Sbjct: 420 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 479

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA EKFDWCLGYKFSTY MWWVKQA+TRSIADQS TIRIPVHM + I+KVVRTARR
Sbjct: 480 IGLMKAVEKFDWCLGYKFSTYGMWWVKQAVTRSIADQSRTIRIPVHMIETINKVVRTARR 539

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           MSN IKREPTP+EIAKKLAMP+E V+KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV
Sbjct: 540 MSNTIKREPTPDEIAKKLAMPLERVQKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 599

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP+DSAIQANLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ
Sbjct: 600 SPVDSAIQANLRENTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 659

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKAIRKLKHPSRSKKLRSFLD 
Sbjct: 660 IEAKAIRKLKHPSRSKKLRSFLDS 683


>gi|312113102|ref|YP_004010698.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
 gi|311218231|gb|ADP69599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
          Length = 697

 Score =  581 bits (1497), Expect = e-163,   Method: Composition-based stats.
 Identities = 389/701 (55%), Positives = 498/701 (71%), Gaps = 23/701 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     +N D +++  +S DS V D  D + K++IK A+ RGYVT +E+N  +PP++VS 
Sbjct: 1   MATATTKNEDQETQASESTDSPVLDLLDAAVKRLIKTAKARGYVTYDEINEVMPPEDVSP 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSE-DSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +Q+ED + M S++GINVVD +++E+      D  +   +A  +    Q+R       TDD
Sbjct: 61  DQIEDIMTMFSDLGINVVDAEEVEEASAEHLDDEEDDRAAPANLPVKQERSTEVGERTDD 120

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+IIWRDELN+G  
Sbjct: 121 PVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIGGLCESPLTFQAIIIWRDELNEGKI 180

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV--- 236
           LLR+IIDLEA       G F    EG   ++  D   + +   V      + +       
Sbjct: 181 LLRDIIDLEATYS----GPFSRPEEGDGSEEEYDPEPQPQLQPVSGPRPVVTNGGGATNG 236

Query: 237 ----------SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                     ++ + +    P           D+D+ +++ +L+AME +L+PKV+   D 
Sbjct: 237 VTGLNGANGHARPEGTDAVGPEGETAEFRGEEDDDDLENSLSLAAMEAELKPKVLETFDR 296

Query: 287 IAEVYRELRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA  Y++LR LQD  V     +     +   + + L++ +++ V SLSLN +RI+ LVEQ
Sbjct: 297 IATEYKKLRKLQDQHVERKLADDALSPQQEKRSRRLRDAVIQDVKSLSLNPARIESLVEQ 356

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           LYDI+KR++  EG LLRLA  +G++RD FL  +QG ELDP+W+          W+ FV  
Sbjct: 357 LYDINKRLIGYEGRLLRLADGFGVRRDEFLSYYQGSELDPNWIDRIGTLKGKGWQKFVEK 416

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E   I +IR EI +++ ETG+ I+EFR IV +V+KGE EA  AKKEMVEANLRLVIS+AK
Sbjct: 417 ERQRIDEIRQEIYALATETGLDIAEFRRIVKIVQKGEREARQAKKEMVEANLRLVISIAK 476

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 477 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 536

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+VRT+R+M ++I REPTPEE+A+KL+MP+E VRKVLKI KEPISLETPIG
Sbjct: 537 PVHMIETINKIVRTSRQMMHEIGREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIG 596

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+ SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHT
Sbjct: 597 DEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 656

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 657 LEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 697


>gi|118591038|ref|ZP_01548438.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118436560|gb|EAV43201.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 662

 Score =  577 bits (1486), Expect = e-162,   Method: Composition-based stats.
 Identities = 410/688 (59%), Positives = 508/688 (73%), Gaps = 32/688 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     +  D+  +  D  D  + D SD + KKMIK A++RGYVT +ELN  LP ++VSS
Sbjct: 1   MVAKATQADDTQEQSTDGPDGPLLDLSDAAVKKMIKAAKKRGYVTYDELNEVLPSEQVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           E++EDT++MLS+MGINV+D D+ E+     D  DL   A++++   +         TDDP
Sbjct: 61  EKIEDTMSMLSDMGINVIDSDEAEEGPEEVDGGDLV--AASTTALAKSTTKEPADRTDDP 118

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   L
Sbjct: 119 VRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEAQVL 178

Query: 181 LREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LR+IIDLEA   GP++K G                      DDV   EG+ E++   S+D
Sbjct: 179 LRDIIDLEATYAGPDAKAGPAVAN-----------------DDVAPGEGNSENSGGASED 221

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
             S+           + + D+DE +S  +LSAME +L+P V+   D IA+ Y++LR LQD
Sbjct: 222 TESED-------GEGDGDDDDDEFESNVSLSAMEAELKPGVLETFDNIADNYKKLRRLQD 274

Query: 300 NAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             V     N         + K LKE ++  V SLSLNQ+RID LV QLYDI+KR+M  EG
Sbjct: 275 QLVENKLANKTLSPSQERRYKKLKEDIIVDVKSLSLNQNRIDALVAQLYDINKRLMGYEG 334

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
            LLRLA SY + R  FL+++QG ELDP+W+    +     WKNF+A E +++ ++R +I+
Sbjct: 335 RLLRLADSYNVDRTDFLKQYQGAELDPNWLRKVANLSTRGWKNFIAKEKETVRELRQDIQ 394

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +++ ETG+ I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 395 TLATETGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 454

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 455 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 514

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIED
Sbjct: 515 TSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIED 574

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 575 KNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 634

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 635 RIRQIEAKALRKLKHPSRSRKLRSFLDS 662


>gi|325293528|ref|YP_004279392.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
 gi|325061381|gb|ADY65072.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
          Length = 684

 Score =  576 bits (1483), Expect = e-162,   Method: Composition-based stats.
 Identities = 419/696 (60%), Positives = 514/696 (73%), Gaps = 26/696 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS--------VFLQKRKDS 112
           EQ+EDT+AMLS+MGINV++ +D E+  G  +S D  +  S                +K  
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDAEEAPGEAESDDSDNEESEGGELAPSGGTALATAKKKE 120

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWRD
Sbjct: 121 PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWRD 180

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+GTTLLREIIDLE                   +Q  E    +++  + +E    + +
Sbjct: 181 ELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRA 234

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            +          D  P   E ++ +       S  +L+AME +LRP+VM  LD IA+ Y+
Sbjct: 235 PSGDEDVTDVGGDGLPPEEEEEDDDE------SNLSLAAMEAELRPQVMETLDTIADTYK 288

Query: 293 ELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +LR LQD       A  G        + K LK++L+  V SLSLNQ+R+D LVEQLYDIS
Sbjct: 289 KLRKLQDQQVEARLACTGTLSSGQERRYKDLKDQLITAVKSLSLNQNRVDSLVEQLYDIS 348

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F   E ++I
Sbjct: 349 KRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSIANLAARGWKEFAREESNTI 408

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 409 REIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNR 468

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 469 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S
Sbjct: 529 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDS 588

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 589 HLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 648

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 684


>gi|209884282|ref|YP_002288139.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209872478|gb|ACI92274.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 708

 Score =  575 bits (1481), Expect = e-162,   Method: Composition-based stats.
 Identities = 397/696 (57%), Positives = 499/696 (71%), Gaps = 17/696 (2%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K  + +++  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S E
Sbjct: 13  KEKEQKAAETPEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRST 117
           Q+ED +AMLS+MGINV + D+ ++EE  +D  D  +        S    + +K      T
Sbjct: 73  QIEDIMAMLSDMGINVSESDEADNEEEEKDEADDDTDNELVEVTSKAVTETKKSEPGERT 132

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G
Sbjct: 133 DDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEG 192

Query: 178 TTLLREIIDLEACI-GPESKGG----FFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
              LR+IIDLEA   GPE KGG       G  G   Q             V   +     
Sbjct: 193 KIFLRDIIDLEATYAGPEGKGGVNTAMIAGPSGPDGQPTNAIVNGDGTVQVMPAQAAAAQ 252

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDED-DSAHTLSAMEDQLRPKVMCALDEIAEVY 291
            A  +        +  ++A   E   DED++ ++  +L+A+E +L+P+V+   D+IA  Y
Sbjct: 253 TAPQTATPFRPAPAAGDDASASEGEGDEDDEFENQMSLAAIEAELKPRVVETFDKIASEY 312

Query: 292 RELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           ++LR LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLYDI+
Sbjct: 313 KKLRRLQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDIN 372

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR++  EG L RL  S+G+ R+ FL+ + G ELDP W++         WKNFVA E D I
Sbjct: 373 KRLVSYEGRLFRLGDSHGVSREDFLKNYVGSELDPRWLNRVSKLSAKGWKNFVAHEKDKI 432

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +R+E++ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNR
Sbjct: 433 KDLRHEVQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTNR 492

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 493 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 552

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ S
Sbjct: 553 ETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDS 612

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 613 HLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 672

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 708


>gi|328542886|ref|YP_004302995.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326412632|gb|ADZ69695.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 666

 Score =  574 bits (1480), Expect = e-161,   Method: Composition-based stats.
 Identities = 400/688 (58%), Positives = 499/688 (72%), Gaps = 28/688 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     +  ++     +  D  + D SD + K+MIK A++RGYVT +ELN  LP ++VSS
Sbjct: 1   MVAKATQAEETQEPAAEGQDGPLLDLSDAAVKRMIKAAKKRGYVTYDELNEVLPSEQVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSE-DSLDLASSASNSSVFLQKRKDSADRSTDD 119
           EQ+EDT++MLS+MGINV+D D++++    + D       +  ++V            TDD
Sbjct: 61  EQIEDTMSMLSDMGINVIDSDEVDEAAIDDGDDGSDLVPSGGTAVAKTTTTREPTDRTDD 120

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  
Sbjct: 121 PVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKV 180

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LLR+IIDLEA                        +  + +         + E      + 
Sbjct: 181 LLRDIIDLEATY----------------------AGPDAKAGPAGGDGEEDEEGETEKRA 218

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
             +  D     AE +    +EDE ++  +LSAME +L+P+V+   D +A+ Y++LR LQD
Sbjct: 219 PAASGDDSERGAEGEGEEDEEDEFETNVSLSAMEAELKPQVLETFDRVADSYKKLRRLQD 278

Query: 300 NAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             V     N         + K LK+++V  V SLSLNQ+RID LVEQLYDI+KR+M  EG
Sbjct: 279 QLVENKLANRTLSPSQERRYKKLKDEIVVDVKSLSLNQNRIDALVEQLYDINKRLMGYEG 338

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
            LLRLA S+G+ R  FL+++QG ELDP+W+    +     WKNFVA E D+I ++R EI+
Sbjct: 339 RLLRLADSHGVDRTDFLKQYQGAELDPNWLRKVANLATRGWKNFVAKEKDTIRELRQEIQ 398

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +++ ETG+ I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 399 TLATETGLEITEFRKIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 458

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 459 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 518

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIED
Sbjct: 519 TSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIED 578

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 579 KNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 639 RIRQIEAKALRKLKHPSRSRKLRSFLDS 666


>gi|92118365|ref|YP_578094.1| RNA polymerase sigma factor RpoD [Nitrobacter hamburgensis X14]
 gi|91801259|gb|ABE63634.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter hamburgensis
           X14]
          Length = 717

 Score =  573 bits (1476), Expect = e-161,   Method: Composition-based stats.
 Identities = 392/705 (55%), Positives = 496/705 (70%), Gaps = 26/705 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K ++ +D+  +D+ D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S E
Sbjct: 13  KEKDDKAADAPEKDAADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDE----EGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           Q+ED ++MLS+MGINV + D+ + E    E +ED  D            + +K      T
Sbjct: 73  QIEDIMSMLSDMGINVSESDEADSEDENKEEAEDETDNELVEVTQKAVTEVKKSEPGERT 132

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G
Sbjct: 133 DDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEG 192

Query: 178 TTLLREIIDLEACI-GPESKG-------GFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
              LR+IIDL+A   GP++K        G   G +G      + ++   E D        
Sbjct: 193 KIFLRDIIDLDATYAGPDAKNNMNPALLGAPTGPDGQPLPAGDAAAASGEGDLGATVTAP 252

Query: 230 IESAAKV-------SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
             +                +      +     E  ++ED+ D+  +L+A+E +L+PKV+ 
Sbjct: 253 PAAPPSPTPFRAVRGAPAGAGDRDEKDQTGAAEGEMEEDDFDNQMSLAAIEAELKPKVVE 312

Query: 283 ALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
             D+IA+ Y++LR LQ+        +         + + LK+++V  V SL LNQ+RID 
Sbjct: 313 TFDKIADNYKKLRRLQEADISNQLQSETLSPNQERRYRKLKDEIVVEVKSLRLNQARIDS 372

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           LVEQLYDI+KR++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKN
Sbjct: 373 LVEQLYDINKRLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPKWINRVSKLSAKGWKN 432

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           FV  E D I ++R EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVI
Sbjct: 433 FVHHEKDRIKELRGEIQQLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVI 492

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 493 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 552

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLE
Sbjct: 553 TIRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLE 612

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMN
Sbjct: 613 TPVGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMN 672

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 TDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 717


>gi|148257986|ref|YP_001242571.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. BTAi1]
 gi|146410159|gb|ABQ38665.1| RNA polymerase, sigma 70 subunit, RpoD [Bradyrhizobium sp. BTAi1]
          Length = 702

 Score =  572 bits (1474), Expect = e-161,   Method: Composition-based stats.
 Identities = 393/690 (56%), Positives = 502/690 (72%), Gaps = 11/690 (1%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K ++ +D+  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S E
Sbjct: 13  KEKDDKAADAPEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS---SVFLQKRKDSADRSTD 118
           Q+ED ++MLS+MGINV + ++ ++ E  +D  D   +           + +K      TD
Sbjct: 73  QIEDIMSMLSDMGINVTEAEEADESEEKDDGDDETDNELVEITQKAVTEVKKSEPGERTD 132

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G 
Sbjct: 133 DPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGK 192

Query: 179 TLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LR+IIDLEA   GPESKGG        +  + E +   + +  V       +     +
Sbjct: 193 IFLRDIIDLEATYAGPESKGGMNPQIAAPANGEGEAADGGEIQAAVAPPAAPQQPTPFRA 252

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             + + V+         E ++D+DE ++  +L+A+E +L+PKV+   D+IA  Y++LR L
Sbjct: 253 APNGAPVEEKDPGEAAAEADMDDDEFENQMSLAAIEAELKPKVVETFDKIASEYKKLRRL 312

Query: 298 QDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           Q+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  
Sbjct: 313 QEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSF 372

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
           E  L+RLA S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I  +R E
Sbjct: 373 ESRLMRLADSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHYEKDRIKDLRQE 432

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 433 VQSLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 492

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 493 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 552

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFI
Sbjct: 553 VRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFI 612

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VT
Sbjct: 613 EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 672

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 RERIRQIEAKALRKLKHPSRSRKLRSFLDN 702


>gi|115523078|ref|YP_779989.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisA53]
 gi|115517025|gb|ABJ05009.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           BisA53]
          Length = 704

 Score =  572 bits (1474), Expect = e-161,   Method: Composition-based stats.
 Identities = 394/695 (56%), Positives = 495/695 (71%), Gaps = 14/695 (2%)

Query: 2   TIGKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           T   K ++  D+  +++ D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S
Sbjct: 10  TKDSKDDKAVDAPEKEAADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTS 69

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN-----SSVFLQKRKDSAD 114
            EQ+ED ++MLS+MGINV + DD ++EE            ++     +    + +K    
Sbjct: 70  PEQIEDIMSMLSDMGINVSESDDTDNEEEETKEEADDEPDTDLVEVTAKAVTETKKSEPG 129

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 130 ERTDDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 189

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           N+G   LR+IIDLEA   GP++K            +  ED                  + 
Sbjct: 190 NEGKIFLRDIIDLEATYAGPDAKNNMNPALAAPEGETSEDPDAVAAPPAAPPQPTPFRAG 249

Query: 234 AKVSKDDRSKVDSPPENAE-NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
           A       +  +   + AE   E ++D+DE ++  +L+A+E +L+PKV+   D+IAE Y+
Sbjct: 250 APRPAPAATPGEEGKDPAESAAEGDMDDDEFENQMSLAAIEAELKPKVVETFDKIAENYK 309

Query: 293 ELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           +LR LQ+        N         K K LK++++  V SL LNQ+RID LVEQLYDI+K
Sbjct: 310 KLRRLQEQDISNQLQNETLSPAQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINK 369

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           +++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I 
Sbjct: 370 KLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIK 429

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           ++R EI+S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 430 ELRQEIQSLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRG 489

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 490 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 549

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SH
Sbjct: 550 TINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSH 609

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 610 LGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQ 669

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 670 QFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 704


>gi|15889446|ref|NP_355127.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
 gi|20141718|sp|P33452|RPOD_AGRT5 RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15157308|gb|AAK87912.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
          Length = 684

 Score =  572 bits (1473), Expect = e-161,   Method: Composition-based stats.
 Identities = 420/696 (60%), Positives = 513/696 (73%), Gaps = 26/696 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS--------VFLQKRKDS 112
           EQ+EDT+AMLS+MGINV++ +D E+   +ED  D  +  S                +K  
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKE 120

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWRD
Sbjct: 121 PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWRD 180

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+GTTLLREIIDLE                   +Q  E    +++  + +E    + +
Sbjct: 181 ELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRA 234

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                       D  P   E ++ +       S  +L+AME +LRP+VM  LD IA+ Y+
Sbjct: 235 PTGDEDVTDVGGDGLPPEEEEEDDDE------SNLSLAAMEAELRPQVMETLDTIADTYK 288

Query: 293 ELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +LR LQD       A  G        + K LK++L+  V SLSLNQ+RID LVEQLYDIS
Sbjct: 289 KLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDIS 348

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F   E ++I
Sbjct: 349 KRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEFAREESNTI 408

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 409 REIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNR 468

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 469 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S
Sbjct: 529 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDS 588

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 589 HLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 648

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 684


>gi|307944279|ref|ZP_07659620.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
 gi|307772625|gb|EFO31845.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
          Length = 669

 Score =  570 bits (1469), Expect = e-160,   Method: Composition-based stats.
 Identities = 397/687 (57%), Positives = 496/687 (72%), Gaps = 23/687 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     +  ++     D  D  + D SD + KKMIK A++RG+VT +ELN  LP ++VSS
Sbjct: 1   MVAKATQADETQDNAADGPDGPLLDLSDAAVKKMIKAAKKRGFVTYDELNEVLPSEQVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           E++ED ++MLS+MGINV++ D+ E+  G ++      + + ++   +         TDDP
Sbjct: 61  EKIEDIMSMLSDMGINVIEADEAEEG-GPDEVDGGELTTTKTTAVAKTTTKEPTDRTDDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G  L
Sbjct: 120 VRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGNVL 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDLEA            G                  +D           A+    D
Sbjct: 180 LRDIIDLEATYAGPDAKAGPTG-----------------ANDDDPDGESGNDNAEARSPD 222

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            +  +   +    +  + D+DE +S  +LSAME +L+P+V+   D IA+ Y++LR LQD 
Sbjct: 223 AANSERGEDQEGAEGDDEDDDEFESNVSLSAMEAELKPQVLETFDNIADNYKKLRRLQDQ 282

Query: 301 AV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            V     N         + K LKE +V  V SLSLNQ+RID LV QLYDI+KR+M  EG 
Sbjct: 283 LVENKLANKTLSPSQERRYKKLKEDIVVDVKSLSLNQNRIDALVTQLYDINKRLMGYEGR 342

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           LLRLA SY + R  FL+++QG ELDP+W+    +     WKNF+A E +++ ++R EI++
Sbjct: 343 LLRLADSYNVDRSDFLKQYQGAELDPNWLRKVANLSSRGWKNFIAKEKETVRELRQEIQT 402

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ ETG+ I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 403 LATETGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 462

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 463 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRT 522

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 523 SRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 582

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 583 NAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 642

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           IRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 643 IRQIEAKALRKLKHPSRSRKLRSFLDS 669


>gi|90422490|ref|YP_530860.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisB18]
 gi|90104504|gb|ABD86541.1| sigma 70 (RpoD) [Rhodopseudomonas palustris BisB18]
          Length = 702

 Score =  570 bits (1469), Expect = e-160,   Method: Composition-based stats.
 Identities = 389/693 (56%), Positives = 491/693 (70%), Gaps = 12/693 (1%)

Query: 2   TIGKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           T   K ++  D+  +D+ D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S
Sbjct: 10  TKDTKDDKVVDAPEKDAPDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTS 69

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN-----SSVFLQKRKDSAD 114
            EQ+ED ++MLS+MGINV + DD + +E            +      +    + +K    
Sbjct: 70  PEQIEDIMSMLSDMGINVSEADDADSDEEDAKEEAEEEPDNELVEVTAKAVTETKKSEPG 129

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 130 ERTDDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDEL 189

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           N+G   LR+IIDLEA           +          +  + +              +  
Sbjct: 190 NEGKIFLRDIIDLEATYAGPDAKNNMNPALIAPPAAADGEAADGAEAVAAPPAAPPSATP 249

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             +       D P E++E+ + + D+DE ++  +L+A+E +L+PKV+   D+IAE Y++L
Sbjct: 250 FRAAPPPRPADEPKESSESADGDADDDEFENQMSLAAIEAELKPKVVETFDKIAENYKKL 309

Query: 295 RSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           R LQ+        N         K K LK++++  V SL LNQ+RID LVEQLYDI+K++
Sbjct: 310 RRLQEQDISNQLQNETLSPAQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKL 369

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNFVA E D I ++
Sbjct: 370 VSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVAHEKDRIKEL 429

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R EI+S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 430 RGEIQSLAALTGLEIGEFRKIVHGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQ 489

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 490 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 549

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLG
Sbjct: 550 NKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLG 609

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 610 DFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 669

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 670 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 702


>gi|222149282|ref|YP_002550239.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
 gi|221736266|gb|ACM37229.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
          Length = 681

 Score =  570 bits (1468), Expect = e-160,   Method: Composition-based stats.
 Identities = 426/695 (61%), Positives = 518/695 (74%), Gaps = 27/695 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSA 113
           EQ+EDT+AMLS+MGINVV+ +D ED    E   D  + +                +K   
Sbjct: 61  EQIEDTMAMLSDMGINVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEP 120

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDE
Sbjct: 121 TDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDE 180

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           LN+GTTLLREIIDLE                    +    +++EKE+             
Sbjct: 181 LNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRR 230

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            + S+DD + V    +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++
Sbjct: 231 VRSSEDDITNVGGDMQMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKK 286

Query: 294 LRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           LR LQD       A  G        + K LK++L+  V SLSLNQ+RID LVEQLYDISK
Sbjct: 287 LRKLQDQQVEARLACAGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISK 346

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           R+M NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK+F   E ++I 
Sbjct: 347 RLMQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSVGNLAARGWKDFAREENNTIR 406

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 407 EIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRG 466

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 467 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 526

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SH
Sbjct: 527 TINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSH 586

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 587 LGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQ 646

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 QFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 681


>gi|27382460|ref|NP_773989.1| RNA polymerase sigma factor RpoD [Bradyrhizobium japonicum USDA
           110]
 gi|1742976|emb|CAA67902.1| primary sigma factor [Bradyrhizobium japonicum]
 gi|27355631|dbj|BAC52614.1| primary sigma factor [Bradyrhizobium japonicum USDA 110]
          Length = 719

 Score =  569 bits (1467), Expect = e-160,   Method: Composition-based stats.
 Identities = 397/707 (56%), Positives = 503/707 (71%), Gaps = 28/707 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K ++ +D+  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D+ S E
Sbjct: 13  KEKDDKAADAPEKDSQDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDQTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEE----GSEDSLDLASSASNSSVFLQKRKDSADRST 117
           Q+ED ++MLS+MGINV + DD E EE    G ED  D            + +K      T
Sbjct: 73  QIEDIMSMLSDMGINVTEADDSEGEEDKDEGGEDETDNELVEVTQKAVTEVKKSEPGERT 132

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRDELN+G
Sbjct: 133 DDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLSFQAIIIWRDELNEG 192

Query: 178 TTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQE------------KERDDVQ 224
              LR+IIDLEA   GPE+KGG      G    +  +++ E                   
Sbjct: 193 KIFLRDIIDLEATYAGPEAKGGMNTAMIGGPTGENGEATAEGGEAVAVTGAAPAHVAPPA 252

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                    A  +  + ++ +  P  A  +    ++DE ++  +L+A+E +L+PKV+   
Sbjct: 253 APPAPTPFRAAPAAGNGAEAEKDPGEAAAEADMDEDDEFENQMSLAAIEAELKPKVVEIF 312

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSS---------VKCKVLKEKLVKLVGSLSLNQSRI 335
           D+IAE Y++LR LQ+  +  Q +  S           K + LK++++  V SL LNQ+RI
Sbjct: 313 DKIAESYKKLRKLQEQDIQNQLESTSHGPSLSPHQERKYRKLKDEIIVEVKSLRLNQARI 372

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           D LVEQLYDI+KR++ +EG L+RLA S+G+ R+ FL  + G ELDP W++         W
Sbjct: 373 DSLVEQLYDINKRLVSHEGRLMRLADSHGVAREDFLRNYTGSELDPRWLNRVSKLSAKGW 432

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           KNFV  E D I  +R+E+  ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRL
Sbjct: 433 KNFVHHEKDRIKDLRHEVHQLAALTGLEIVEFRKIVHSVQKGEREARQAKKEMVEANLRL 492

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ
Sbjct: 493 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 552

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+S
Sbjct: 553 ARTIRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLS 612

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETP+GDE+ SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIG
Sbjct: 613 LETPVGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIG 672

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 719


>gi|146338438|ref|YP_001203486.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. ORS278]
 gi|146191244|emb|CAL75249.1| sigma D (sigma 70) factor of RNA polymerase [Bradyrhizobium sp.
           ORS278]
          Length = 703

 Score =  569 bits (1466), Expect = e-160,   Method: Composition-based stats.
 Identities = 391/691 (56%), Positives = 501/691 (72%), Gaps = 12/691 (1%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K ++ +D+  +D+ D+   + D SD + KKMIK A++RG+VT ++LN  LPPD  S E
Sbjct: 13  KEKDDKAADAPEKDAADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPPDTTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS---SVFLQKRKDSADRSTD 118
           Q+ED ++MLS+MGINV + ++ ++ E  +D  D   +           + +K      TD
Sbjct: 73  QIEDIMSMLSDMGINVTEAEETDEAEDKDDGDDETDNELVEITQKAVTEVKKSEPGERTD 132

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G 
Sbjct: 133 DPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGK 192

Query: 179 TLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEK-ERDDVQETEGDIESAAKV 236
             LR+IIDLEA   GPESKGG      G +  +       + +           ++    
Sbjct: 193 IFLRDIIDLEATYAGPESKGGMNPQIAGPANGEAAAGEGGEIQAAVAAPPAAPQQATPFR 252

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +  + +  +         E ++D+DE ++  +L+A+E +L+PKV+   D+IA  Y++LR 
Sbjct: 253 AAPNGAPAEEKDPGEAAAEADMDDDEFENQMSLAAIEAELKPKVVETFDKIASEYKKLRR 312

Query: 297 LQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLYDI+K+++ 
Sbjct: 313 LQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVS 372

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E  L+RLA S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I  +R 
Sbjct: 373 FESRLMRLADSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHYEKDRIKDLRQ 432

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E++S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 433 EVQSLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFL 492

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 493 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 552

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDF
Sbjct: 553 IVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDF 612

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF V
Sbjct: 613 IEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 672

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 TRERIRQIEAKALRKLKHPSRSRKLRSFLDN 703


>gi|227822807|ref|YP_002826779.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
 gi|227341808|gb|ACP26026.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
          Length = 684

 Score =  569 bits (1465), Expect = e-160,   Method: Composition-based stats.
 Identities = 428/696 (61%), Positives = 516/696 (74%), Gaps = 26/696 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++D E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEADVEREGTPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS--------NSSVFLQKRKDS 112
           EQ+EDT+AMLS+MGINV++ ++ E+  G +D        S        + +     +K  
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEEAEEAAGGDDEDSSDDGESEGGELATVSGTALATGKKKE 120

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRD
Sbjct: 121 PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRD 180

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+G TLLREIIDLE                  + Q +     E +R   +E E   +S
Sbjct: 181 ELNEGQTLLREIIDLETTYSG--------PEAKAAPQFQSPEKIEADRKAAEEKEKTRKS 232

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
               + DD + V    +  E +E + DE    S  +L+AME +LRP+VM  LD IAE Y+
Sbjct: 233 RVAANDDDITNVGGEGQPVEEEEEDDDE----SNLSLAAMEAELRPQVMETLDIIAETYK 288

Query: 293 ELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDIS
Sbjct: 289 KLRKLQDQQVEARLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDIS 348

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F   E  +I
Sbjct: 349 KRLMQNEGRLLRLAESYGVKRDSFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTI 408

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 409 RDIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNR 468

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 469 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S
Sbjct: 529 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDS 588

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 589 HLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 648

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 684


>gi|209550278|ref|YP_002282195.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536034|gb|ACI55969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM2304]
          Length = 685

 Score =  568 bits (1464), Expect = e-159,   Method: Composition-based stats.
 Identities = 421/699 (60%), Positives = 515/699 (73%), Gaps = 31/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGS-----------EDSLDLASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S           E+S     + S+ +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGSDEESEGGELAPSSGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+II
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P E  E+++         S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPPEEEEEDEDE--------SNLSLAAMEAELRPQVMETLDTIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       + +G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E 
Sbjct: 347 DINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFARGEN 406

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 407 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 466

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 467 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 526

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 527 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 586

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 587 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 646

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 685


>gi|190892699|ref|YP_001979241.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190697978|gb|ACE92063.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|327189666|gb|EGE56814.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 685

 Score =  568 bits (1463), Expect = e-159,   Method: Composition-based stats.
 Identities = 421/699 (60%), Positives = 512/699 (73%), Gaps = 31/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S    D              + S  +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGELAPSGGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P E  E+++         S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPPEEEEEDEDE--------SNLSLAAMEAELRPQVMETLDTIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       + +G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E 
Sbjct: 347 DINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFAKGEN 406

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 407 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 466

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 467 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 526

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 527 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 586

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 587 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 646

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 685


>gi|116253144|ref|YP_768982.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           viciae 3841]
 gi|115257792|emb|CAK08890.1| putative RNA polymerase sigma factor RpoD [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 685

 Score =  568 bits (1463), Expect = e-159,   Method: Composition-based stats.
 Identities = 422/699 (60%), Positives = 515/699 (73%), Gaps = 31/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS-----------SASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S  S D  +           + S+ +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGSSDDDDAGGDEESEGGELAPSSGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKLAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P E  E+++         S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPPEEEEEDEDE--------SNLSLAAMEAELRPQVMETLDTIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       + +G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E 
Sbjct: 347 DINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFARGEN 406

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 407 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 466

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 467 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 526

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 527 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 586

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 587 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 646

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 685


>gi|150397423|ref|YP_001327890.1| RNA polymerase sigma factor RpoD [Sinorhizobium medicae WSM419]
 gi|150028938|gb|ABR61055.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium medicae
           WSM419]
          Length = 684

 Score =  568 bits (1463), Expect = e-159,   Method: Composition-based stats.
 Identities = 426/696 (61%), Positives = 519/696 (74%), Gaps = 26/696 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++D E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEADVEREGAPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGS--------EDSLDLASSASNSSVFLQKRKDS 112
           EQ+EDT++MLS+MGINV++ ++ E+  GS         +S     + ++ +     +K  
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGGSDDDDSSDDAESEGGELAPASGTALATSKKKE 120

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRD
Sbjct: 121 PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRD 180

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+G TLLREIIDLE                  + Q +     E +R   +E E   ++
Sbjct: 181 ELNEGQTLLREIIDLETTYSG--------PEAKAAPQFQSPEKIEADRKAAEEKEKVRKT 232

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            A  + DD + V    + AE +E + DE    S  +L+AME +LRP+VM  LD IAE Y+
Sbjct: 233 RAAANDDDITNVGGEGQPAEEEEDDDDE----SNLSLAAMEAELRPQVMETLDVIAETYK 288

Query: 293 ELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDIS
Sbjct: 289 KLRKLQDQQVEARLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDIS 348

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR+  NEG LLRLA+SYG+KR+ FLE++ G ELDP+W+    +     WK F   E  +I
Sbjct: 349 KRLTQNEGRLLRLAESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTI 408

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 409 RDIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNR 468

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 469 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S
Sbjct: 529 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDS 588

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 589 HLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 648

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 684


>gi|254504180|ref|ZP_05116331.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
 gi|222440251|gb|EEE46930.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
          Length = 671

 Score =  567 bits (1462), Expect = e-159,   Method: Composition-based stats.
 Identities = 404/688 (58%), Positives = 500/688 (72%), Gaps = 27/688 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     +  D+  +  D+ D  + D SD + KKMIK A++RGYVT +ELN  LP D+ SS
Sbjct: 5   MVAKATQADDNQEQGADNADGPLLDLSDAAVKKMIKAAKKRGYVTYDELNEVLPSDQNSS 64

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           E++ED ++M S+MGINV++ ++ ED     D  +L  +A +S+V            TDDP
Sbjct: 65  EKIEDIMSMFSDMGINVIEAEEAEDAPEEVDGGEL-VAAKSSAVAKTTTGKEPADRTDDP 123

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+   L
Sbjct: 124 VRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEAQVL 183

Query: 181 LREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LR+IIDLEA   GP++K G     +     +  +S  + + D   E   + +S      D
Sbjct: 184 LRDIIDLEATYAGPDAKAGPTGDNDDEPESENGESGSQNQTDGPSENTENEDSEGDGEDD 243

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           D                        S  +LSAME +L+P+V+   D IA+ Y++LR LQD
Sbjct: 244 DDEFE--------------------SNVSLSAMEAELKPQVLETFDRIADDYKKLRRLQD 283

Query: 300 NAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             V     N         + K LKE +V  V SLSLNQ+RID LV QLYDI+KR+M  EG
Sbjct: 284 QLVENKLANKTLSPSQERRYKKLKEDIVVDVKSLSLNQNRIDALVAQLYDINKRLMGYEG 343

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
            LLRLA SY + R  FL+++QG ELDP+W+    +     WKNF+A E +++ ++R+EI+
Sbjct: 344 RLLRLADSYNVDRQDFLKQYQGAELDPNWLRKVANLSTRGWKNFIAKEKENVRELRHEIQ 403

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +++ ETG+ I+EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 404 TLATETGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 463

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 464 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 523

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIED
Sbjct: 524 TSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIED 583

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 584 KNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 643

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 644 RIRQIEAKALRKLKHPSRSRKLRSFLDS 671


>gi|299131999|ref|ZP_07025194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
 gi|298592136|gb|EFI52336.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
          Length = 709

 Score =  567 bits (1461), Expect = e-159,   Method: Composition-based stats.
 Identities = 394/697 (56%), Positives = 498/697 (71%), Gaps = 18/697 (2%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K  + +++  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D+ S E
Sbjct: 13  KEKEAKAAETPEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDQTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRST 117
           Q+ED +AMLS+MGINV + DD  DE+  +D  D  +        S    + +K      T
Sbjct: 73  QIEDIMAMLSDMGINVSEADDANDEDEEKDEADDDTDNELVEVTSKAVTETKKSEPGERT 132

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G
Sbjct: 133 DDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEG 192

Query: 178 TTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDD------VQETEGDI 230
              LR+IIDLEA   GPE K G                +      D        +     
Sbjct: 193 KIFLRDIIDLEATYAGPEGKNGVNPAMIAGPVGPDGQPTAAVVNGDGTVQVIAAQQAAPA 252

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           ++A + +   R    +  + A  +    ++DE ++  +L+A+E +L+P+V+   D+IA  
Sbjct: 253 QTAPQTATPFRPAPAAGDDAAAPEGDGDEDDEFENQMSLAAIEAELKPRVVETFDKIASE 312

Query: 291 YRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           Y++LR LQ+  +  Q   +S       K K LK++++  V SL LNQ+RID LVEQLYDI
Sbjct: 313 YKKLRRLQEQDIANQLQSESLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDI 372

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
           +KR++  EG L RL  S+G+ R+ FL+ + G ELDP W++         WKNFVA E D 
Sbjct: 373 NKRLVSYEGRLFRLGDSHGVGREDFLKNYVGSELDPRWLNRVSKLAAKGWKNFVAHEKDK 432

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I  +R+EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 433 IKDLRHEIQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTN 492

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 493 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 552

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ 
Sbjct: 553 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEED 612

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV
Sbjct: 613 SHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 672

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 GQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 709


>gi|192289891|ref|YP_001990496.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris TIE-1]
 gi|192283640|gb|ACF00021.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodopseudomonas
           palustris TIE-1]
          Length = 698

 Score =  567 bits (1460), Expect = e-159,   Method: Composition-based stats.
 Identities = 389/682 (57%), Positives = 485/682 (71%), Gaps = 16/682 (2%)

Query: 13  SEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++ML
Sbjct: 21  APEKDSVDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSML 80

Query: 71  SNMGINV-----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           S+MGINV      + ++ E +E +++ LD       +    + +K      TDDPVRMYL
Sbjct: 81  SDMGINVSEAEDTEAEEEEAKEEADEELDNDLVEVTAKAVTETKKSEPGERTDDPVRMYL 140

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+II
Sbjct: 141 REMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDII 200

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           DLEA       G       G   ++            V        +        R    
Sbjct: 201 DLEATYA----GPEGKNNIGEPGEEAAAEGDGGAPAHVAPPAAPPSATPFRPAQQRGAAP 256

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA---- 301
           +  E     E + D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+      
Sbjct: 257 AEAEGEGAPEGDGDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQDIANQ 316

Query: 302 -VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
             N Q       K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  E  L+RLA
Sbjct: 317 LQNEQLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFESRLMRLA 376

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            S+G+ RD FL  +QG ELDP W++         WKNFV  E D I  +R E++S++  T
Sbjct: 377 DSHGVARDDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKDLRQEVQSMAALT 436

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 437 GLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 496

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M 
Sbjct: 497 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQML 556

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV P
Sbjct: 557 NEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVLP 616

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 617 IDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 676

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKLKHPSRS+KLRSFLD 
Sbjct: 677 AKALRKLKHPSRSRKLRSFLDN 698


>gi|182680201|ref|YP_001834347.1| RNA polymerase sigma factor RpoD [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182636084|gb|ACB96858.1| RNA polymerase, sigma 70 subunit, RpoD family [Beijerinckia indica
           subsp. indica ATCC 9039]
          Length = 685

 Score =  566 bits (1459), Expect = e-159,   Method: Composition-based stats.
 Identities = 397/693 (57%), Positives = 494/693 (71%), Gaps = 19/693 (2%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D +    ++ DS + D SD + K+MIK+A++RG+VT  ELNA LP +EV+S
Sbjct: 1   MAKKDTDKTDGEGGGVETVDSPLLDLSDAAVKRMIKVAKKRGFVTYSELNAVLPSEEVNS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSADR 115
           EQ+ED +AML+ MGINVV+ ++ + EE  + + +  S       ++ S  +  R      
Sbjct: 61  EQIEDILAMLNEMGINVVESEEQDTEESEDSNEEEESEGGDLVEASQSKAVTTRSSEPSD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELN 180

Query: 176 DGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           D   LLR+IIDLEA   GPE +       +         + +E   +             
Sbjct: 181 DSKVLLRDIIDLEATYAGPEGRSSPKLDLDA--------TDEEDPDNPDAPEAPSTAPLN 232

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
              +   ++ D   +    +E   +ED+ +++ +LSAME +L+PKV+   D +A+ Y++L
Sbjct: 233 PPGRLRPAREDGDIDPPPMEEMFDEEDDMENSVSLSAMEAELKPKVLETFDRVADAYKKL 292

Query: 295 RSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           R LQD        N         K K LK+++V  V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 293 RRLQDQNVENKLKNETLTPAQERKYKTLKKEIVADVKSLSLNQNRIEALVEQLYDINKRL 352

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +  E  LLRLA+ YG+ R+ FL  +Q  ELDP W+          WK+FVA   D+I  +
Sbjct: 353 IGQETRLLRLAEGYGVAREDFLRNYQNSELDPKWLLRVSKLGSRGWKDFVAKAKDTIKDL 412

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             EI  ++ ETG+ I EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 413 LGEIHGLATETGLEIQEFRKIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQ 472

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 473 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 532

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLG
Sbjct: 533 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLG 592

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 593 DFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 652

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 653 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 685


>gi|15966067|ref|NP_386420.1| RNA polymerase sigma factor RpoD [Sinorhizobium meliloti 1021]
 gi|307305622|ref|ZP_07585369.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
 gi|307317625|ref|ZP_07597064.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|7388096|sp|Q59753|RPOD_RHIME RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|1050336|gb|AAA88524.1| sigma factor [Sinorhizobium meliloti]
 gi|15075337|emb|CAC46893.1| RNA polymerase sigma factor transcription regulation protein
           [Sinorhizobium meliloti 1021]
 gi|306896783|gb|EFN27530.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|306902325|gb|EFN32921.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
          Length = 684

 Score =  566 bits (1459), Expect = e-159,   Method: Composition-based stats.
 Identities = 420/696 (60%), Positives = 511/696 (73%), Gaps = 26/696 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++D E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEADVEREGAPDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS--------VFLQKRKDS 112
           EQ+EDT++MLS+MGINV++ ++ E+   S+D        S                +K  
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAAASDDDDGADEGESEGGELAPASGTALAASKKKE 120

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRD
Sbjct: 121 PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRD 180

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+G TLLREIIDLE                    +    +++EKE+     T  + + 
Sbjct: 181 ELNEGQTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKVRRTRTAANDDD 240

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
              V  + ++                +ED+D+S  +L+AME +LRP+VM  LD IAE Y+
Sbjct: 241 ITNVGGEGQAPE------------EEEEDDDESNLSLAAMEAELRPQVMETLDVIAETYK 288

Query: 293 ELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDIS
Sbjct: 289 KLRKLQDQQVEARLAATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDIS 348

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR+  NEG LLRLA+SYG+KR+ FLE++ G ELDP+W+    +     WK F   E  +I
Sbjct: 349 KRLTQNEGRLLRLAESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTI 408

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             IR EI++++ ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 409 RDIRQEIQNLATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNR 468

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 469 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S
Sbjct: 529 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDS 588

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 589 HLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 648

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 684


>gi|254470295|ref|ZP_05083699.1| sigma 70 [Pseudovibrio sp. JE062]
 gi|211960606|gb|EEA95802.1| sigma 70 [Pseudovibrio sp. JE062]
          Length = 701

 Score =  566 bits (1458), Expect = e-159,   Method: Composition-based stats.
 Identities = 394/701 (56%), Positives = 492/701 (70%), Gaps = 19/701 (2%)

Query: 1   MTIGKKRNRDS-DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           M     +  D+ +    +  D  + D S  + KKMIK A++RGY+T +ELN  LPPD+VS
Sbjct: 1   MATKATQAEDTQEPAGAEGQDGPLLDLSVAAVKKMIKTAKKRGYITYDELNEVLPPDQVS 60

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSAD 114
           SEQ+EDT+++LS MGINVV+ +D E+ +  ED+           AS+++V          
Sbjct: 61  SEQIEDTMSLLSEMGINVVEAEDAEEGKEEEDAPAAVDGGELVVASSTAVTKTSTAKEPT 120

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+IIW +EL
Sbjct: 121 DRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMISGLCESPLTFQAIIIWGEEL 180

Query: 175 NDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            +G  LLR+IIDL+A   GP   GG          +  E    E  R   +E     +  
Sbjct: 181 AEGKVLLRDIIDLDATYSGPGDAGGPSDDDLSEQEEAGEGEVPEAVRQKEKEEARKRKEE 240

Query: 234 AKVSKDDRSKVD-------SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +  +                  +  + D+DE ++  +LS ME +L+P V+   D+
Sbjct: 241 EARKANGAAAPAPAADGAQGEQTGEGGESTDDDDDEYEANVSLSVMEAELKPMVVEIFDK 300

Query: 287 IAEVYRELRSLQDNAV-----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           I E Y++LR LQD  V     N         + K LKE ++  V SL LN +RI+ LV+Q
Sbjct: 301 ITEDYKKLRKLQDQLVENKLANKTLSPSQERRYKKLKEDIIAEVKSLHLNANRIETLVQQ 360

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           LY I+K +M  EG LLRLA S G+ R  F++ +QG ELDP+W+    +     WK FV  
Sbjct: 361 LYSINKMLMGYEGRLLRLADSNGVNRADFIKHYQGSELDPNWIRKVANLSGRGWKKFVTN 420

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           + D I ++R EI+S++ ETG+ I+EFR +VSMV+KGE EA IAKKEMVEANLRLVIS+AK
Sbjct: 421 DGDMIRELRGEIQSLATETGLEITEFRTLVSMVQKGEREARIAKKEMVEANLRLVISIAK 480

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 481 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 540

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+VRT+R+M ++I REPTPEE+++KL MP+E VRKVLKI KEPISLETPIG
Sbjct: 541 PVHMIETINKIVRTSRQMLHEIGREPTPEELSEKLQMPLEKVRKVLKIAKEPISLETPIG 600

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+ SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT
Sbjct: 601 DEEDSHLGDFIEDKNAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 660

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 661 LEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 701


>gi|86358552|ref|YP_470444.1| RNA polymerase sigma factor RpoD [Rhizobium etli CFN 42]
 gi|86282654|gb|ABC91717.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 685

 Score =  566 bits (1457), Expect = e-159,   Method: Composition-based stats.
 Identities = 422/699 (60%), Positives = 511/699 (73%), Gaps = 31/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S    D              + S  +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGELAPSAGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P E  E+++         S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPPEEEEEDEDE--------SNLSLAAMEAELRPQVMETLDIIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLAATGTLSSAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E 
Sbjct: 347 DINKRLVQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFAKAEN 406

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 407 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 466

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 467 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 526

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 527 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 586

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 587 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 646

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 685


>gi|241205658|ref|YP_002976754.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859548|gb|ACS57215.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM1325]
          Length = 685

 Score =  566 bits (1457), Expect = e-159,   Method: Composition-based stats.
 Identities = 426/699 (60%), Positives = 517/699 (73%), Gaps = 31/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGS-----------EDSLDLASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S           E+S     + S+ +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGSSDDDDAGSDEESEGGELAPSSGTALAAAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                    +     ++EKE+         
Sbjct: 181 WRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKLAEEKEK--------- 231

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
               A+   DD + V      AE +E + DE    S  +L+AME +LRP+VM  LD IAE
Sbjct: 232 -TRRARSGDDDITDVGGEGLPAEEEEEDEDE----SNLSLAAMEAELRPQVMETLDTIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       + +G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E 
Sbjct: 347 DINKRLVSNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFARGEN 406

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 407 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 466

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 467 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 526

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 527 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 586

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 587 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 646

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 685


>gi|85715949|ref|ZP_01046926.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85697147|gb|EAQ35028.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 716

 Score =  565 bits (1456), Expect = e-159,   Method: Composition-based stats.
 Identities = 391/704 (55%), Positives = 496/704 (70%), Gaps = 25/704 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K ++ +D+  +D  D+   + D SD + KKMIK A++RG+VT ++LN  LP +  S E
Sbjct: 13  KEKDDKAADAPEKDIADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSETTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRST 117
           Q+ED ++MLS+MGINV + +D + E+ +++  D  +             + +K      T
Sbjct: 73  QIEDIMSMLSDMGINVSESEDADSEDENKEEADEETDNELVEVTQKAVTEVKKSEPGERT 132

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G
Sbjct: 133 DDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEG 192

Query: 178 TTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
              LR+IIDLEA   GPE+K              +  S+   + D  +   G   +A   
Sbjct: 193 KIFLRDIIDLEATYAGPEAKSNQALLGSPAGPDGQPLSADASDADSGESDVGSTVTAPPA 252

Query: 237 SKDDRS-------------KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +    +               D         E  ++ED+ D+  +L+A+E +L+PKV+  
Sbjct: 253 APPSPTPFRAARAAPAGSADPDDKDPGVAAAEGEMEEDDFDNQMSLAAIEAELKPKVVET 312

Query: 284 LDEIAEVYRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            D+IA+ Y++LR LQ+        N         + K LK++++  V SL LNQ+RID L
Sbjct: 313 FDKIADNYKKLRRLQEADISNQLQNESLSPNQERRYKKLKDEIIVEVKSLRLNQARIDSL 372

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           VEQLYDI+KR++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNF
Sbjct: 373 VEQLYDINKRLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNF 432

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V  E D I ++R EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS
Sbjct: 433 VHHEKDRIKELRGEIQQLAALTGLEIGEFRKIVQGVQKGEREARQAKKEMVEANLRLVIS 492

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 493 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 552

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLET
Sbjct: 553 IRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLET 612

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNT
Sbjct: 613 PVGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 672

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           DHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 716


>gi|91978433|ref|YP_571092.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris BisB5]
 gi|91684889|gb|ABE41191.1| RNA polymerase sigma factor RpoD-like [Rhodopseudomonas palustris
           BisB5]
          Length = 711

 Score =  565 bits (1455), Expect = e-159,   Method: Composition-based stats.
 Identities = 388/690 (56%), Positives = 490/690 (71%), Gaps = 21/690 (3%)

Query: 14  EHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
             +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS
Sbjct: 22  PEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLS 81

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASN-----SSVFLQKRKDSADRSTDDPVRMYLR 126
           +MGINV + ++ + E+            ++          + +K      TDDPVRMYLR
Sbjct: 82  DMGINVSEAEESDSEDEESKDEAEEEPDNDLVEVTQKAVTETKKSEPGERTDDPVRMYLR 141

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IID
Sbjct: 142 EMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIID 201

Query: 187 LEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           LEA   GP++K        G + ++     +      +        +        R+   
Sbjct: 202 LEATYAGPDAKNNMNPAMAGETGEEASAEGEGGAPAHLAPPAAPPSATPFRPAQQRAAPS 261

Query: 246 SPPENAENDER----NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             P      E     ++D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+  
Sbjct: 262 QAPAGEGGGEGAAEGDMDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQD 321

Query: 302 VNGQKDEKS---------SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           +  Q +  S           K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  
Sbjct: 322 IANQLESASQGPSLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSF 381

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
           EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I ++R E
Sbjct: 382 EGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKELRQE 441

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 442 IQSMAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 501

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 502 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 561

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFI
Sbjct: 562 VRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFI 621

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VT
Sbjct: 622 EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 681

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 682 RERIRQIEAKALRKLKHPSRSRKLRSFLDN 711


>gi|222086540|ref|YP_002545074.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
 gi|221723988|gb|ACM27144.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
          Length = 687

 Score =  565 bits (1455), Expect = e-158,   Method: Composition-based stats.
 Identities = 423/699 (60%), Positives = 513/699 (73%), Gaps = 29/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVERDGTSDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT+AMLS+MGINV++ +D+E+   +  S D              + S  S     +
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDVEEAGAATSSDDDDSSDDDNGEGGELAPSTGSALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIGGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                    +    +++EKE+     +   
Sbjct: 181 WRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKARRGRSPSG 240

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
            +    V                      +EDED+S+ +L+AME +LRP+VM  LD IAE
Sbjct: 241 DDDITDVGG------------EGLPGEEEEEDEDESSLSLAAMEAELRPQVMTTLDTIAE 288

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       + +G        + K LK++LVK V SLSLNQ+RID LVEQLY
Sbjct: 289 TYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELKDELVKSVKSLSLNQNRIDALVEQLY 348

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E 
Sbjct: 349 DINKRLVQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFAKSEN 408

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 409 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 468

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 469 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 528

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 529 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 588

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 589 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 648

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 687


>gi|39934363|ref|NP_946639.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           CGA009]
 gi|39648212|emb|CAE26731.1| RNA polymerase sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           CGA009]
          Length = 698

 Score =  562 bits (1449), Expect = e-158,   Method: Composition-based stats.
 Identities = 392/683 (57%), Positives = 490/683 (71%), Gaps = 18/683 (2%)

Query: 13  SEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++ML
Sbjct: 21  APEKDSVDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSML 80

Query: 71  SNMGINV-----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           S+MGINV      + ++ E +E +++ LD       +    + +K      TDDPVRMYL
Sbjct: 81  SDMGINVSEAEDTEAEEEEAKEEADEELDNDLVEVTAKAVTETKKSEPGERTDDPVRMYL 140

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+II
Sbjct: 141 REMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDII 200

Query: 186 DLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           DLEA   GPE K       E  + +    +           +      A +     R   
Sbjct: 201 DLEATYAGPEGKNNIGEPGEEAAAEGEGGAPAHVAPPAAPPSATPFRPAQQ-----RGAA 255

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA--- 301
            +  E     E + D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+     
Sbjct: 256 PAEAEGEGAPEGDGDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQDIAN 315

Query: 302 --VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              N Q       K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  E  L+RL
Sbjct: 316 QLQNEQLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFESRLMRL 375

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A S+G+ RD FL  +QG ELDP W++         WKNFV  E D I  +R E++S++  
Sbjct: 376 ADSHGVARDDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKDLRQEVQSMAAL 435

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 436 TGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 495

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M
Sbjct: 496 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQM 555

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV 
Sbjct: 556 LNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVL 615

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 616 PIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 675

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 676 EAKALRKLKHPSRSRKLRSFLDN 698


>gi|75676624|ref|YP_319045.1| RNA polymerase sigma factor RpoD [Nitrobacter winogradskyi Nb-255]
 gi|74421494|gb|ABA05693.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter winogradskyi
           Nb-255]
          Length = 717

 Score =  561 bits (1446), Expect = e-157,   Method: Composition-based stats.
 Identities = 391/705 (55%), Positives = 492/705 (69%), Gaps = 26/705 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +K ++ +D+  +D+ D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S E
Sbjct: 13  KEKDDKAADAPEKDTADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPE 72

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRST 117
           Q+ED ++MLS+MGINV + +D + E+ +++  D  +             + +K      T
Sbjct: 73  QIEDIMSMLSDMGINVSESEDADSEDENKEEADEETDNELVEVTQKAVTEVKKSEPGERT 132

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G
Sbjct: 133 DDPVRMYLREMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEG 192

Query: 178 TTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES---- 232
              LR+IIDLEA   GPE+K        G               D      G   +    
Sbjct: 193 KIFLRDIIDLEATYAGPEAKSSMNPALLGAPGGPGGQPLSADASDGASGEGGAEATVNAP 252

Query: 233 ----------AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                      A  +    +            E  ++ED+ D+  +L+A+E +L+PKV+ 
Sbjct: 253 PSAPPSPTPFRAARAAPAGAADREEKIPGAAAEGEMEEDDFDNQMSLAAIEAELKPKVVE 312

Query: 283 ALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
             D+IA+ Y++LR LQ+        N         + K LK++++  V SL LNQ+RID 
Sbjct: 313 TFDKIADSYKKLRRLQEADISNQLQNESLSPNQERRYKKLKDEIIVEVKSLRLNQARIDS 372

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           LVEQLYDI+KR++  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKN
Sbjct: 373 LVEQLYDINKRLVSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKN 432

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           FV  E D I ++R EI+ ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVI
Sbjct: 433 FVHHEKDRIKELRGEIQQLAALTGLEIGEFRKIVQGVQKGEREARQAKKEMVEANLRLVI 492

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 493 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 552

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLE
Sbjct: 553 TIRIPVHMIETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLE 612

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMN
Sbjct: 613 TPVGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMN 672

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 673 TDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 717


>gi|39132|emb|CAA49185.1| vegetative sigma factor [Agrobacterium tumefaciens str. C58]
          Length = 684

 Score =  561 bits (1445), Expect = e-157,   Method: Composition-based stats.
 Identities = 410/696 (58%), Positives = 506/696 (72%), Gaps = 26/696 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N ++++E + + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+S
Sbjct: 1   MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS--------VFLQKRKDS 112
           EQ+EDT+AMLS+MGINV++ +D E+   +ED  D  +  S                +K  
Sbjct: 61  EQIEDTMAMLSDMGINVIEDEDAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKE 120

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               TDDPVRMYLREMGS+ELLSREG+IAIAKRIEAGR  M++ LCESPLTFQALIIWRD
Sbjct: 121 PTDRTDDPVRMYLREMGSVELLSREGQIAIAKRIEAGRETMISGLCESPLTFQALIIWRD 180

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           ELN+GTTL+REIIDLE                   +Q  E    +++  + +E    +  
Sbjct: 181 ELNEGTTLVREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRG 234

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                       D  P   E ++ +       S  +L+AME +LRP+VM  LD IA+ Y+
Sbjct: 235 PTGDEDVTDVGGDGLPPEEEEEDDDE------SNLSLAAMEAELRPQVMETLDTIADTYK 288

Query: 293 ELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            +R LQD       A  G        + K LK++L+  V SLSLNQ+RID LVEQLYDIS
Sbjct: 289 NVRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDIS 348

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           KR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +     WK F   E ++I
Sbjct: 349 KRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEFAREESNTI 408

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNR
Sbjct: 409 REIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNR 468

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 469 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S
Sbjct: 529 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDS 588

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNA+ P+D+AIQ  LRETTTRVLASLTP EERVLRM FGIGMNTDHTLEEVG
Sbjct: 589 HLGDFIEDKNALLPIDAAIQGFLRETTTRVLASLTPSEERVLRMPFGIGMNTDHTLEEVG 648

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+R +KHPSRS+KLR+FLD 
Sbjct: 649 QQFSVTRERIRQIEAKALRNVKHPSRSRKLRTFLDS 684


>gi|114704974|ref|ZP_01437882.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
 gi|114539759|gb|EAU42879.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
          Length = 682

 Score =  560 bits (1442), Expect = e-157,   Method: Composition-based stats.
 Identities = 397/694 (57%), Positives = 501/694 (72%), Gaps = 24/694 (3%)

Query: 1   MTIGKKRNRD-SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           M    K     +D   E + D  + D SDD+ KKMIK A++RG+VT+++LN+ L  D V+
Sbjct: 1   MATKVKEKEAPADERAEAATDGPLLDLSDDAVKKMIKAAKKRGFVTMDKLNSMLSSDGVT 60

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF-----LQKRKDSAD 114
           S+Q+ED +AML++MGINVV+ D+  + +   D+ D +S++++ +           K S+ 
Sbjct: 61  SDQVEDLMAMLNDMGINVVEDDEEGEADNDNDNDDNSSNSTDVAETGKTQIATTEKKSSG 120

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL
Sbjct: 121 DRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDEL 180

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           N+G  LLR+I+DLEA            G E  +       S+    +   +  G   SA 
Sbjct: 181 NEGNILLRDIVDLEATYA---------GPEAKAPAAVAAPSEANGSEAGSDANGRTSSAN 231

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             + +     ++ P   E ++ + D++   +  +L+AME ++ P+VM   D IA+ Y  L
Sbjct: 232 GATAEQTRPGEARPIGTEEEDEDEDDE---NNLSLAAMEAEILPQVMETFDLIADTYLRL 288

Query: 295 RSLQDNAVN------GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           R LQD  V       G          + LKE L+  V  LSLNQ+RID LVEQLYDI+KR
Sbjct: 289 RKLQDQQVENRLQATGALSPSQEKSYRKLKEDLIAAVKGLSLNQNRIDALVEQLYDINKR 348

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++ NEG+LLRL +S+G++RD FL  +QG ELDP+W     +     W +FV  +   I +
Sbjct: 349 LVGNEGKLLRLGESHGVRRDEFLNEYQGSELDPNWTRRVANLSGKGWLDFVQKDKVKIQR 408

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R EI++++ ETG+ I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGL
Sbjct: 409 LRGEIQNLATETGLEITEFRRIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGL 468

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 469 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 528

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHL
Sbjct: 529 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHL 588

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKNAV P+D+AIQ NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 589 GDFIEDKNAVLPIDAAIQGNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 648

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 649 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 682


>gi|86751238|ref|YP_487734.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris HaA2]
 gi|86574266|gb|ABD08823.1| sigma 70 (RpoD) [Rhodopseudomonas palustris HaA2]
          Length = 714

 Score =  559 bits (1440), Expect = e-157,   Method: Composition-based stats.
 Identities = 386/693 (55%), Positives = 485/693 (69%), Gaps = 24/693 (3%)

Query: 14  EHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
             +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++MLS
Sbjct: 22  PEKDSADAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSMLS 81

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASN-----SSVFLQKRKDSADRSTDDPVRMYLR 126
           +MGINV + ++ + E+            ++          + +K      TDDPVRMYLR
Sbjct: 82  DMGINVSEAEESDSEDEDAKDEAEEEPDNDLVEVTQKAVTETKKSEPGERTDDPVRMYLR 141

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+IID
Sbjct: 142 EMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDIID 201

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKER--------DDVQETEGDIESAAKVSK 238
           LEA           +        +   +  E +              T      A + S 
Sbjct: 202 LEATYAGPDAKANMNPAMAEGAGEEASAEGEADAGAPAHVAPPAAPPTATPFRPAQQRSA 261

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
              +            E ++D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ
Sbjct: 262 PAAAPAAGEGGGEGAAEGDMDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQ 321

Query: 299 DNAVNGQKDEKS---------SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           +  +  Q +  S           K K LK++++  V SL LNQ+RID LVEQLYDI+K++
Sbjct: 322 EQDIANQLESASQGPSLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKL 381

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +  EG LLRL  S+G+ R+ FL  +QG ELDP W++         WKNFV  E D I ++
Sbjct: 382 VSFEGRLLRLGDSHGVAREDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHFEKDRIREL 441

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R EI+S++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 442 RQEIQSMAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQ 501

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 502 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 561

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLG
Sbjct: 562 NKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLG 621

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 622 DFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 681

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 682 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 714


>gi|1765926|emb|CAA70052.1| RNA polymerase sigma-70 subunit [Rhizobium etli]
          Length = 685

 Score =  559 bits (1440), Expect = e-157,   Method: Composition-based stats.
 Identities = 421/699 (60%), Positives = 509/699 (72%), Gaps = 31/699 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S    D              + S  +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGELAPSAGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P E  E+++         S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPPEEEEEDEDE--------SNLSLAAMEAELRPQVMETLDIIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       A  G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLAATGTLSSAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           DI+KR++ NEG LLRLA+SY +KRD FLE+ QG ELDP+W+    +     WK F   E 
Sbjct: 347 DINKRLVQNEGRLLRLAESYAVKRDSFLEQDQGAELDPNWMKSIGNLAARGWKEFAKAEN 406

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            +I  IR EI++++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKY
Sbjct: 407 TTIRDIRQEIQNLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKY 466

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 467 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 526

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE
Sbjct: 527 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDE 586

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE
Sbjct: 587 EDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 646

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 647 EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 685


>gi|316935466|ref|YP_004110448.1| RpoD subfamily RNA polymerase sigma 70 subunit [Rhodopseudomonas
           palustris DX-1]
 gi|315603180|gb|ADU45715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopseudomonas
           palustris DX-1]
          Length = 698

 Score =  559 bits (1439), Expect = e-157,   Method: Composition-based stats.
 Identities = 390/682 (57%), Positives = 487/682 (71%), Gaps = 16/682 (2%)

Query: 13  SEHEDSDDSL--VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +  +DS D+   + D SD + KKMIK A++RG+VT ++LN  LP D  S EQ+ED ++ML
Sbjct: 21  APEKDSVDAPSPLLDLSDAAVKKMIKQAKKRGFVTFDQLNEVLPSDTTSPEQIEDIMSML 80

Query: 71  SNMGINV-----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           S+MGINV      + ++ E +E +++ LD       +    + +K      TDDPVRMYL
Sbjct: 81  SDMGINVSEAEDTEAEEEEAKEEADEELDNDLVEVTAKAVTETKKSEPGERTDDPVRMYL 140

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+G   LR+II
Sbjct: 141 REMGTVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNEGKIFLRDII 200

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           DLEA       G       G S ++     +      V        +        R    
Sbjct: 201 DLEATYA----GPEGKNNIGDSGEEAAAEGEGGAPAHVAPPAAPPSATPFRPAQQRGAAP 256

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA---- 301
           +  E     E + D+DE ++  +L+A+E +L+PKV+   D+IA+ Y++LR LQ+      
Sbjct: 257 AEGEGEGAPEGDGDDDEFENQMSLAAIEAELKPKVVETFDKIADNYKKLRKLQEQDIANQ 316

Query: 302 -VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
             N Q       K K LK++++  V SL LNQ+RID LVEQLYDI+K+++  E  L+RLA
Sbjct: 317 LQNEQLSPSQERKYKKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKKLVSFESRLMRLA 376

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            S+G+ RD FL  +QG ELDP W++         WKNFV  E D I  +R E++S++  T
Sbjct: 377 DSHGVARDDFLRNYQGSELDPRWLNRVSKLSAKGWKNFVHHEKDRIKDLRQEVQSMAALT 436

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 437 GLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 496

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M 
Sbjct: 497 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQML 556

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           N+I REPTPEE+A+KL MP+E VRKVLKI KEP+SLETP+GDE+ SHLGDFIEDKNAV P
Sbjct: 557 NEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPVGDEEDSHLGDFIEDKNAVLP 616

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 617 IDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 676

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKLKHPSRS+KLRSFLD 
Sbjct: 677 AKALRKLKHPSRSRKLRSFLDN 698


>gi|90418027|ref|ZP_01225939.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337699|gb|EAS51350.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 668

 Score =  559 bits (1439), Expect = e-157,   Method: Composition-based stats.
 Identities = 403/691 (58%), Positives = 498/691 (72%), Gaps = 35/691 (5%)

Query: 1   MTIGKKRNRDS-DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           M I  K +    +  +E + D  + D SDD+ KKMIK A++RG+VT+++LN+ L  ++V+
Sbjct: 4   MAIKAKESEAPIEERNEGAPDGPLLDLSDDAVKKMIKAAKKRGFVTMDKLNSMLSAEDVT 63

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV-FLQKRKDSADRSTD 118
           SEQ+ED +  L++MGINVV+ D+  + E   +S +    A           K  A   TD
Sbjct: 64  SEQIEDMMTNLNDMGINVVESDEEGENEEQSESSESTEVAETGRTQVATTTKKEAGDRTD 123

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRDELN+G 
Sbjct: 124 DPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDELNEGN 183

Query: 179 TLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
            +LREI+DLEA   GPE+K       EG                          S   VS
Sbjct: 184 IMLREIVDLEATYAGPEAKTPTPPAVEG--------------------------SNGSVS 217

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                   S    A  +E + ++D+ ++  +L+AME ++RP+VM   D+IA+ YR LR L
Sbjct: 218 GVPNGPPHSTGARAPGEEEDEEDDDLENNLSLAAMEAEIRPQVMETFDQIADAYRRLRKL 277

Query: 298 QDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           QD       A  G          K LKE+L+  V SLSLNQ+RID LV QLYDI+KR++ 
Sbjct: 278 QDQQVENRLAAQGTLSPSQERSYKKLKEELITAVKSLSLNQNRIDALVAQLYDINKRLVG 337

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           NEG LLRLA+S+G+KRD FL  +QG ELDP+W  +  +     W  FV  E + I ++R 
Sbjct: 338 NEGRLLRLAESHGVKRDEFLNEYQGTELDPNWTRHIANLSGKGWLKFVQAEKEQIKRLRQ 397

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           EI++++ ETG+ I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 398 EIQNLATETGLEITEFRRIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFL 457

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 458 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 517

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDF
Sbjct: 518 IVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDF 577

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IEDKNA+ P+D+AIQ NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF V
Sbjct: 578 IEDKNAILPIDAAIQGNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 637

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 638 TRERIRQIEAKALRKLKHPSRSRKLRSFLDS 668


>gi|217977790|ref|YP_002361937.1| RNA polymerase sigma factor RpoD [Methylocella silvestris BL2]
 gi|217503166|gb|ACK50575.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocella silvestris
           BL2]
          Length = 683

 Score =  558 bits (1437), Expect = e-156,   Method: Composition-based stats.
 Identities = 393/692 (56%), Positives = 495/692 (71%), Gaps = 21/692 (3%)

Query: 3   IGKKRNRDSDSEHE--DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           + KK N  +++E    ++ DS + D SD + K+MIK A++RG+VT  ELNA LP +EV+S
Sbjct: 1   MAKKDNEKTEAEGGVVETADSPLLDLSDAAVKRMIKAAKKRGFVTYAELNAVLPSEEVNS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSADR 115
           EQ+ED +AML+ MGINVV+ ++ E+ E  E + +  +       +++   +  R      
Sbjct: 61  EQIEDILAMLNEMGINVVETEEQEEGEAEEAAEEEEAEGGDLVEASTVKAVTVRSSEPAD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           D   LLR+IIDLEA            G +G +  K + ++         +      +   
Sbjct: 181 DSKVLLRDIIDLEATYA---------GPDGRNTPKIDMTAPGAAEALAAQQAAPATAPLT 231

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                R   +   +    ++   +ED+ +++ +LSAME +L+PKV+   D +A+ Y++LR
Sbjct: 232 PPARLRPAGEDGVDPPIPEDVFDEEDDMENSVSLSAMEAELKPKVLDTFDRVADAYKKLR 291

Query: 296 SLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
            LQD        N         K K LK+++V  V SLSLN +RI+ LVEQLYDI+KR++
Sbjct: 292 RLQDQNVENKLKNESLSPSQERKYKTLKKEVVTDVKSLSLNPNRIEALVEQLYDINKRLI 351

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             E  LLRLA+  G+ R+ FL  +Q  ELDP W+          W++FVA   D I  + 
Sbjct: 352 GLETRLLRLAEGSGVTREDFLRNYQNSELDPKWLLRVSKLGGRGWRDFVATAKDQIKDLL 411

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            EI +++ ETG+ I EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 412 AEIHALATETGLEIQEFRKIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 471

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 472 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 531

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGD
Sbjct: 532 KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 591

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 592 FIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 651

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 652 VTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 683


>gi|83594214|ref|YP_427966.1| RNA polymerase sigma factor RpoD [Rhodospirillum rubrum ATCC 11170]
 gi|83577128|gb|ABC23679.1| Sigma 70 (RpoD) [Rhodospirillum rubrum ATCC 11170]
          Length = 696

 Score =  556 bits (1433), Expect = e-156,   Method: Composition-based stats.
 Identities = 369/696 (53%), Positives = 465/696 (66%), Gaps = 14/696 (2%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++ +  E+  DS + D  + + KK++   + RGY+T +ELN  LPPD+VSS
Sbjct: 1   MATKATNTAEAVNTQEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT+AMLS+MGINVV+ ++  +   +  +                  +     TDDP
Sbjct: 61  EQIEDTMAMLSDMGINVVEDEEEGEASAAPPAEAGEEEPGREVAATGNVSEDDIGRTDDP 120

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +AL+ W D L DG  L
Sbjct: 121 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTIRALLQWHDALVDGRML 180

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSY---------QKREDSSQEKERDDVQETEGDIE 231
           LR+IIDL+A  G  +           S            R    +  E ++      D +
Sbjct: 181 LRDIIDLDATYGSGAGPDVVAEGLEDSVVPLSPLALSPARALPKEADEAEEAVTPGRDDD 240

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
           S  +   DD    D   +         + D  ++  +L+AME +L P+V+   + IA  Y
Sbjct: 241 SEDEDEGDDAKPADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLETFEHIATTY 300

Query: 292 RELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            +L+  QD  +   +  +        K   LK +LV L+  + LN +RI+ LVEQL  ++
Sbjct: 301 GKLKKAQDQRIAALQKGEEPGAALERKYDKLKLELVGLMEDVHLNNARIEQLVEQLNALN 360

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           K ++  EG+LLRLA+   I+RD FL+ + GRE+DP W       P   W++F     D I
Sbjct: 361 KGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWREDVAALPGKGWRDFTTRFADEI 420

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             IR  I  I+  + + I EFR IVS V+KGE EAS AKKEM+EANLRLVIS+AKKYTNR
Sbjct: 421 KDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVISIAKKYTNR 480

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 481 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 540

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ S
Sbjct: 541 ETINKLVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDS 600

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKNAV PLD+AI +NLRET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 601 HLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 660

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 661 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 696


>gi|163761137|ref|ZP_02168214.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
 gi|162281688|gb|EDQ31982.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
          Length = 680

 Score =  556 bits (1433), Expect = e-156,   Method: Composition-based stats.
 Identities = 411/695 (59%), Positives = 502/695 (72%), Gaps = 28/695 (4%)

Query: 1   MTIGKKRNRD--SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEV 58
           M    K   D   +       D  + D SDD+ KKMIK +++RGYVT++ELNA LP +EV
Sbjct: 1   MASKVKEAADDTENEREAGGPDGPLLDLSDDAVKKMIKTSKKRGYVTMDELNAVLPSEEV 60

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----RKDSA 113
           +SEQ+ED ++MLS+MGINVV+ D+  +++ S+D     S     +          +K   
Sbjct: 61  TSEQIEDILSMLSDMGINVVEEDEASEDKDSDDDSAETSEGGEVATAGGTAVAATKKKEP 120

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR+E
Sbjct: 121 TDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWREE 180

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           LN+G TLLREIIDLE                     + + + Q +  + ++      E  
Sbjct: 181 LNEGATLLREIIDLETTYS---------------GPEAKAAPQFQSPEKIEADRKVAEEK 225

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            K   +     D      E      D+D+D++  +L+AME +LRP+VM  LD IA+ Y++
Sbjct: 226 EKARAEKAKSDDITNVGGEGQYEEDDDDDDENNLSLAAMEAELRPQVMETLDTIADTYKK 285

Query: 294 LRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           LR LQD       A  G        + K LKE L+  V SLSLNQ+RID LVEQLYDI+K
Sbjct: 286 LRKLQDQQVEARLAATGTLSPAQERRYKELKEALITAVKSLSLNQNRIDSLVEQLYDINK 345

Query: 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
           R++ NEG LLRLA+SYG+KRD FL ++ G ELDP+W+    +     WK+F   E  +I 
Sbjct: 346 RLVSNEGRLLRLAESYGVKRDDFLAQYSGAELDPNWMKSIANLSAKGWKDFAKSESTNIR 405

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +R EI+ ++ ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRG
Sbjct: 406 DLRAEIQYLAQETGISISEFRRIVQMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRG 465

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 466 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 525

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SH
Sbjct: 526 TINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSH 585

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDKNA+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+
Sbjct: 586 LGDFIEDKNAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQ 645

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 646 QFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 680


>gi|296445787|ref|ZP_06887740.1| RNA polymerase, sigma 70 subunit, RpoD [Methylosinus trichosporium
           OB3b]
 gi|296256767|gb|EFH03841.1| RNA polymerase, sigma 70 subunit, RpoD [Methylosinus trichosporium
           OB3b]
          Length = 669

 Score =  555 bits (1429), Expect = e-155,   Method: Composition-based stats.
 Identities = 393/694 (56%), Positives = 495/694 (71%), Gaps = 39/694 (5%)

Query: 3   IGKKRNRDSDSEHE---DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           + KK +   ++E     ++ D  + D +D + K+MIKLA++RG+VT  ELNA LP +EVS
Sbjct: 1   MAKKDDEKVETEGAVAVETADGPLLDLNDAAVKRMIKLAKKRGFVTYTELNAVLPSEEVS 60

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS------ASNSSVFLQKRKDSA 113
           S+Q+ED  AML  MGI V +GDD +D EG E   +  +        S  +  +  R    
Sbjct: 61  SDQIEDVYAMLQEMGITVSEGDDPDDAEGEEQQEEEEAETGGEVVESARATAVATRSSEP 120

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR+E
Sbjct: 121 ADRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWREE 180

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           L  G  LLR+IIDLEA                 +  + +++     +DD+          
Sbjct: 181 LEAGKVLLRDIIDLEATY---------------AGPEGKNAKPPAPQDDLAPATAPRSPP 225

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           A         +D P   AE      +ED+ +++ +LSAME +L+P+V+     +A+ Y++
Sbjct: 226 AA--------LDEPGAPAEESFE--EEDDLENSVSLSAMEAELKPRVLETFARVADAYKK 275

Query: 294 LRSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQD        N         K K LK+++V  V SLSLNQ+RI+ LVEQLYDI+KR
Sbjct: 276 LRRLQDQNVENKLKNETLTPAQERKYKQLKKEIVTDVKSLSLNQNRIEALVEQLYDINKR 335

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++  E +L  LA + G++R+ F+++ QG ELDP W++         WK FVA E D I +
Sbjct: 336 LVGYERKLFMLADAQGVQREDFIDKFQGSELDPKWINRVSKLGSRGWKEFVANEKDRIRE 395

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R EI +++ ETG+ I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGL
Sbjct: 396 LRGEIHALATETGLEIAEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGL 455

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 456 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 515

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+++KLAMP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 516 INKIVRTSRQMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 575

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKNA+ P+++AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 576 GDFIEDKNAILPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 635

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 636 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 669


>gi|163843732|ref|YP_001628136.1| RNA polymerase sigma factor RpoD [Brucella suis ATCC 23445]
 gi|163674455|gb|ABY38566.1| RNA polymerase sigma factor RpoD [Brucella suis ATCC 23445]
          Length = 666

 Score =  553 bits (1425), Expect = e-155,   Method: Composition-based stats.
 Identities = 414/688 (60%), Positives = 512/688 (74%), Gaps = 28/688 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT++MLS+MGINVV+ DD +D +  E + D A     ++V     K      TDDP
Sbjct: 61  EQIEDTMSMLSDMGINVVE-DDEQDNDREEGNDDEAEEGGGTAVATTTTKKEPTDRTDDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN+   L
Sbjct: 120 VRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNIL 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LREIIDLE                    + R++  Q + RDD   T    +   +   DD
Sbjct: 180 LREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDD 239

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             +                     +  +L+AME +LRP+VM  LD IA+ Y++LR LQD 
Sbjct: 240 EDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLRKLQDQ 278

Query: 301 ------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                 A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG
Sbjct: 279 QVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEG 338

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
           +LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++R+EI+
Sbjct: 339 KLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRLRSEIQ 398

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 399 NLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 458

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 459 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 518

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIED
Sbjct: 519 TSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIED 578

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 579 KNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 639 RIRQIEAKALRKLKHPSRSRKLRSFLDS 666


>gi|298292324|ref|YP_003694263.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
 gi|296928835|gb|ADH89644.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
          Length = 666

 Score =  552 bits (1423), Expect = e-155,   Method: Composition-based stats.
 Identities = 396/698 (56%), Positives = 497/698 (71%), Gaps = 48/698 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++  +  D+ DS + D SD   +KMIKLA++RGYVT +ELN  LP D+ +S
Sbjct: 1   MAKQAAEATEAPEKDGDTPDSPLLDLSDAGVRKMIKLAKKRGYVTYDELNEVLPSDQNTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDE-----------EGSEDSLDLASSASNSSVFLQKR 109
           +Q+ED  AML+ MGINVV+ ++ E E           +  E+S    + ++  +V   + 
Sbjct: 61  DQIEDIYAMLNEMGINVVEAEEAEAEAEAEESGPEAADEEEESGGELTESAPRAVVRSET 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+II
Sbjct: 121 KSEPGERTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDEL +G  LLR+IIDLEA                +S      S   +  ++ + T G+
Sbjct: 181 WRDELVEGKVLLRDIIDLEATYAG--------PEAKNSPIVEGGSLAPEAEEEREPTLGE 232

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             ++                         D+D+ +++ +L+AME +++PKV+   D IA+
Sbjct: 233 TIASD------------------------DDDDMENSLSLAAMEAEIKPKVLETFDNIAD 268

Query: 290 VYRELRSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            Y++LR LQD        N         K K LK+ L+  V SLSLNQ+RID LVEQLYD
Sbjct: 269 AYKKLRRLQDQNVESKLRNESLSPSQDRKYKSLKDALIADVKSLSLNQARIDNLVEQLYD 328

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           I+KR++  EG L+RLA+S+G+ R+ FL+++QG ELDP W+   K+     WK FV  E+D
Sbjct: 329 INKRLVSLEGRLMRLAESFGVAREDFLKQYQGSELDPKWIIRVKNLTSRGWKGFVGQELD 388

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I  +R+EI +++ ETG+ I EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYT
Sbjct: 389 AIRDLRSEIHALATETGLEIQEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYT 448

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 449 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 508

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+
Sbjct: 509 MIETINKIVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEE 568

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE
Sbjct: 569 DSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 628

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 629 VGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 666


>gi|154245186|ref|YP_001416144.1| RNA polymerase sigma factor RpoD [Xanthobacter autotrophicus Py2]
 gi|154159271|gb|ABS66487.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthobacter autotrophicus
           Py2]
          Length = 666

 Score =  551 bits (1420), Expect = e-154,   Method: Composition-based stats.
 Identities = 400/697 (57%), Positives = 493/697 (70%), Gaps = 46/697 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++  +  D+ D  + D SD + +KMIK A++RGYVT E+LN  +P +EV+S
Sbjct: 1   MAKQSSEATEAPEKETDAPDGPLLDLSDAAVRKMIKNAKRRGYVTYEQLNEVMPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----------ASNSSVFLQKRK 110
           EQ+EDT+AML++MGINV++ ++ E EEG+E++                 +  +V   + K
Sbjct: 61  EQIEDTLAMLNDMGINVIEAEEAEAEEGAEETETAEEPEEAEGGELAEPAPRAVARSETK 120

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
                 TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIW
Sbjct: 121 SEPAERTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIW 180

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           RDEL +G  LLR+IIDLEA                             E  +     G+ 
Sbjct: 181 RDELTEGRVLLRDIIDLEATY------------------------AGPEGKNPPAALGEE 216

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
            + A  + +D    D+P    E       +D+ +++ +L+AME +++PKV+   D IA  
Sbjct: 217 AALAPEAGEDGLLGDAPGPEGE-------DDDMENSMSLAAMEAEIKPKVLETFDRIASS 269

Query: 291 YRELRSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           Y +LR LQD        N         K K LKE LV  V SLSLNQ+RID LVEQLY+I
Sbjct: 270 YTKLRRLQDQNVESKLKNETLSPAQERKAKKLKEDLVGDVKSLSLNQARIDALVEQLYEI 329

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
           +KR++  EG LLRLA SYG+ RD FL+ + G ELDP W+          WK FV  E D+
Sbjct: 330 NKRLVGLEGRLLRLADSYGVTRDDFLKNYMGAELDPKWLLRVSKLGTKGWKGFVGHEKDT 389

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I +IR +I +++ ETG+ I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 390 IHEIRGDIHALATETGLEIAEFRKIVQMVQKGEKEARQAKKEMVEANLRLVISIAKKYTN 449

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 450 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 509

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ 
Sbjct: 510 IETINKIVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEED 569

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV
Sbjct: 570 SHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 629

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 630 GQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 666


>gi|62290370|ref|YP_222163.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 1 str.
           9-941]
 gi|254708148|ref|ZP_05169976.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 gi|261315652|ref|ZP_05954849.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 gi|62196502|gb|AAX74802.1| RpoD, RNA polymerase sigma-70 factor [Brucella abortus bv. 1 str.
           9-941]
 gi|261304678|gb|EEY08175.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
          Length = 672

 Score =  551 bits (1419), Expect = e-154,   Method: Composition-based stats.
 Identities = 414/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDCEEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|110633818|ref|YP_674026.1| RNA polymerase sigma factor RpoD [Mesorhizobium sp. BNC1]
 gi|110284802|gb|ABG62861.1| RNA polymerase, sigma 38 subunit, RpoS [Chelativorans sp. BNC1]
          Length = 668

 Score =  550 bits (1418), Expect = e-154,   Method: Composition-based stats.
 Identities = 417/690 (60%), Positives = 510/690 (73%), Gaps = 32/690 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   + + E  D  D  + D SDD+ KKMIKLA++RGYVT++ELNA LP  EVSSEQ
Sbjct: 1   MATKEKEEVEIER-DGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQ 59

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS--ASNSSVFLQKRKDSADRSTDDP 120
           +EDT+AMLS+MGINVV+ ++  +E  ++ + +  S   A   S      K      TDDP
Sbjct: 60  IEDTMAMLSDMGINVVEDEEAGEEAEADSAPEEESGELAETGSAVATVAKKEPTDRTDDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+ELNDG  L
Sbjct: 120 VRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELNDGKIL 179

Query: 181 LREIIDLEACI-GPESKGGFFHG-TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           LREIIDLEA   GPE K        E  +    E+    + RDD   T            
Sbjct: 180 LREIIDLEATYAGPEGKQAPVIARPEDVARPAPEEKLMRRARDDDDITNV---------- 229

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
                        E+     DE+ED++  +L+AME +L+P  M  LD IA+ Y +LR LQ
Sbjct: 230 -----------GGESRPEEDDEEEDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQ 278

Query: 299 DNAVNGQKDEK------SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           D  V  +  +          + K LK++L+K V SLSLN  RI+ LVEQLYDI+KR++ N
Sbjct: 279 DQEVESRLGDSDKLSAGQERRSKELKDELIKAVKSLSLNNQRIETLVEQLYDINKRLVQN 338

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
           E +L RLA+SYG++R+ FL+ +QG ELDP+W S     P+  W++FV  E D+I  +R+E
Sbjct: 339 ELKLFRLAESYGVRREDFLKAYQGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSE 398

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I++++ ETGISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 399 IQNLAQETGISIGEFRRIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLD 458

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 459 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 518

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFI
Sbjct: 519 VRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFI 578

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           EDK+A+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VT
Sbjct: 579 EDKSAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 638

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 639 RERIRQIEAKALRKLKHPSRSRKLRSFLDS 668


>gi|306844486|ref|ZP_07477075.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
 gi|306275097|gb|EFM56853.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
          Length = 672

 Score =  550 bits (1418), Expect = e-154,   Method: Composition-based stats.
 Identities = 415/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R+D  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDDRPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|163868737|ref|YP_001609951.1| RNA polymerase sigma factor RpoD [Bartonella tribocorum CIP 105476]
 gi|161018398|emb|CAK01956.1| RNA polymerase sigma factor [Bartonella tribocorum CIP 105476]
          Length = 671

 Score =  550 bits (1418), Expect = e-154,   Method: Composition-based stats.
 Identities = 401/694 (57%), Positives = 500/694 (72%), Gaps = 35/694 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++   + S D  + DFSDD+ KKMIKLA++ GYVT++ELNA LP DEV+S
Sbjct: 1   MATKVKQKDNAEVTSQASLDGPLLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA----SSASNSSVFLQKRKDSADRS 116
           EQ+ED +AM S MG+NVVD ++  + E  E+ + +       AS+ ++     K      
Sbjct: 61  EQIEDILAMFSEMGVNVVDDENEVESENYEEEITVEGGDLVEASSHAIATTTNKREVTDR 120

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDEL +
Sbjct: 121 TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELKE 180

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
              LLREIIDLE                          +   ER +V + +G+  S+   
Sbjct: 181 QRILLREIIDLETTYA----------------GPEAKQAPVIERSEVDKIKGEDISSGIR 224

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +  +        E+ E D+ ++         +L+AME++L P+VM  LD IA+ Y +LR 
Sbjct: 225 NIGEDIGERGIEEDDEEDDDDV-------NLSLAAMENELCPQVMETLDFIAQTYVKLRK 277

Query: 297 LQDNAVNGQKDEKSS--------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LQD  V     E+           K   LK +L++ V SLSLNQ+RI+ LVEQLYDI+KR
Sbjct: 278 LQDQHVESSLAERKEGALTASQKKKYIQLKGELIQAVKSLSLNQNRIEALVEQLYDINKR 337

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++HNEG+L R+A SYGI  D FL  +QGRELD  W++Y    P   WK F   E   I K
Sbjct: 338 LIHNEGKLKRIANSYGIGHDDFLREYQGRELDADWMNYIATLPAPGWKEFSMREAKEIQK 397

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+EI++++  T ISI EFR IV  V+KGE E++IAKKEMVE+NLRLVIS+AKKYTNRGL
Sbjct: 398 LRSEIQNLAQATAISIGEFRRIVMQVQKGERESTIAKKEMVESNLRLVISIAKKYTNRGL 457

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 458 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 517

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHL
Sbjct: 518 INKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHL 577

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 578 GDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 637

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 638 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 671


>gi|225627926|ref|ZP_03785962.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|256160209|ref|ZP_05457903.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|256255415|ref|ZP_05460951.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|260169148|ref|ZP_05755959.1| RNA polymerase sigma factor RpoD [Brucella sp. F5/99]
 gi|261222619|ref|ZP_05936900.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|261758658|ref|ZP_06002367.1| RNA polymerase sigma factor [Brucella sp. F5/99]
 gi|265998584|ref|ZP_06111141.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|225617089|gb|EEH14135.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|260921203|gb|EEX87856.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|261738642|gb|EEY26638.1| RNA polymerase sigma factor [Brucella sp. F5/99]
 gi|262553208|gb|EEZ09042.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
          Length = 672

 Score =  550 bits (1418), Expect = e-154,   Method: Composition-based stats.
 Identities = 414/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKKLKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|323137010|ref|ZP_08072090.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocystis sp. ATCC
           49242]
 gi|322397771|gb|EFY00293.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocystis sp. ATCC
           49242]
          Length = 670

 Score =  550 bits (1416), Expect = e-154,   Method: Composition-based stats.
 Identities = 394/693 (56%), Positives = 484/693 (69%), Gaps = 36/693 (5%)

Query: 3   IGKKRNRDSDSEHE---DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           + KK     ++E     D+ D  + D +D + K+MIKLA++RG+VT  ELNA LP +EVS
Sbjct: 1   MAKKDEEKVENEAGAAVDTADGPLLDLNDAAVKRMIKLAKKRGFVTYAELNAVLPSEEVS 60

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLED-----EEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           S+Q+ED  AMLS MGI V +GDD +D     +   E+        S  S  +  R     
Sbjct: 61  SDQIEDVYAMLSEMGITVSEGDDPDDVEAEEQAEEEEGEGGDLVESPRSTAVATRTSEPA 120

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR+EL
Sbjct: 121 DRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWREEL 180

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
             G  LLR+IIDLEA             +     +    ++       + E     E A 
Sbjct: 181 EAGKVLLRDIIDLEATYAGPDGKAAGKTSGETEGEMAPATAPRTPPAGLSEEAAPPEEAF 240

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +  +D                        +++ +LSAME +L+PKV+     +A+ Y++L
Sbjct: 241 EEEED-----------------------MENSVSLSAMEAELKPKVLETFARVADAYKKL 277

Query: 295 RSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           R LQD        N         K K +K+++V  V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 278 RRLQDQNVENKLKNETLTPAQERKYKTIKKEIVTDVKSLSLNQNRIEALVEQLYDINKRL 337

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +  E +LLRLA S+G+ R+ F+++  G ELDP WV          WK FVA E D I  +
Sbjct: 338 IGYETKLLRLADSHGVAREDFIDKFHGSELDPKWVMRVAQLRSRGWKEFVAEEKDRIKDL 397

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R EI +++ ETG+ ISEFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 398 RAEIHALATETGLEISEFRKIVHMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQ 457

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 458 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 517

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+++KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLG
Sbjct: 518 NKIVRTSRQMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLG 577

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNAV P+++AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 578 DFIEDKNAVLPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 637

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 638 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 670


>gi|170744799|ref|YP_001773454.1| RNA polymerase sigma factor RpoD [Methylobacterium sp. 4-46]
 gi|168199073|gb|ACA21020.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium sp. 4-46]
          Length = 666

 Score =  550 bits (1416), Expect = e-154,   Method: Composition-based stats.
 Identities = 395/702 (56%), Positives = 484/702 (68%), Gaps = 56/702 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++++  E   D  + D +D S K+MIKLA++RGYVT +ELN  LP +E +S
Sbjct: 1   MATKATEREETEAAPEQQTDGPLLDLTDASVKRMIKLAKKRGYVTYDELNEVLPQEEFTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDE--------------EGSEDSLDLASSASNSSVFL 106
           EQ+ED +  LS +G+NVV+ ++ +D               E SE +     + +  +V  
Sbjct: 61  EQIEDVLGQLSELGVNVVEAEEADDNQAEGAAAEGGGDDEEASEGTEVAEVAPNRPAVLR 120

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            +        TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 121 TETTKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQA 180

Query: 167 LIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +IIWRDEL DG  LLR+IIDLEA   GP+ + G   G         E      E D    
Sbjct: 181 IIIWRDELVDGRVLLRDIIDLEATYAGPDGRAGPAEGEVEAEGDGPEGEVAAPEGDG--- 237

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
                                            DED+ ++  +LSAME +L+P+V+   D
Sbjct: 238 ---------------------------------DEDDLENNVSLSAMEAELKPRVLETFD 264

Query: 286 EIAEVYRELRSLQDNAVNGQK-----DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
            IAE YR+LR +Q      +      +E  S +   LK ++V  V SLSLN +RI+ LVE
Sbjct: 265 AIAENYRKLRQVQAQQAETRLQGAGANEGQSRQYAELKSRIVADVKSLSLNANRIEALVE 324

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
           QLYDI+KR++  EG L+RLA+S+G+ RD FL  +QG+ELDPHWV          WKNF  
Sbjct: 325 QLYDINKRLISQEGRLMRLAESHGVARDEFLRHYQGQELDPHWVERVGKLGGKGWKNFTE 384

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              D I  +R +I S++ ETG+ I E+R IV MV+KGE EA  AKKEM+EANLRLVIS+A
Sbjct: 385 RGQDGIKTLREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIA 444

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 445 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 504

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPI
Sbjct: 505 IPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI 564

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GDE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDH
Sbjct: 565 GDEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 624

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 625 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 666


>gi|17986815|ref|NP_539449.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           16M]
 gi|23502348|ref|NP_698475.1| RNA polymerase sigma factor RpoD [Brucella suis 1330]
 gi|82700292|ref|YP_414866.1| RNA polymerase sigma factor RpoD [Brucella melitensis biovar
           Abortus 2308]
 gi|161619426|ref|YP_001593313.1| RNA polymerase sigma factor RpoD [Brucella canis ATCC 23365]
 gi|189024598|ref|YP_001935366.1| RNA polymerase sigma factor RpoD [Brucella abortus S19]
 gi|237815873|ref|ZP_04594870.1| RNA polymerase sigma factor RpoD [Brucella abortus str. 2308 A]
 gi|254689668|ref|ZP_05152922.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|254694158|ref|ZP_05155986.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697811|ref|ZP_05159639.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254702196|ref|ZP_05164024.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|254714701|ref|ZP_05176512.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|254717762|ref|ZP_05179573.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|254730700|ref|ZP_05189278.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|256045103|ref|ZP_05448004.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114033|ref|ZP_05454810.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|256257919|ref|ZP_05463455.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|256369896|ref|YP_003107407.1| RNA polymerase sigma factor [Brucella microti CCM 4915]
 gi|260546908|ref|ZP_05822647.1| RNA polymerase sigma factor [Brucella abortus NCTC 8038]
 gi|260565297|ref|ZP_05835781.1| RNA polymerase sigma factor [Brucella melitensis bv. 1 str. 16M]
 gi|260566021|ref|ZP_05836491.1| RNA polymerase sigma factor [Brucella suis bv. 4 str. 40]
 gi|260755199|ref|ZP_05867547.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|260758418|ref|ZP_05870766.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|260762244|ref|ZP_05874587.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884215|ref|ZP_05895829.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|261214461|ref|ZP_05928742.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|261219607|ref|ZP_05933888.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|261322495|ref|ZP_05961692.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|261752768|ref|ZP_05996477.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|265991536|ref|ZP_06104093.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995374|ref|ZP_06107931.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|294852799|ref|ZP_06793472.1| RNA polymerase primary sigma factor [Brucella sp. NVSL 07-0026]
 gi|297248755|ref|ZP_06932473.1| RNA polymerase primary sigma factor [Brucella abortus bv. 5 str.
           B3196]
 gi|306843169|ref|ZP_07475787.1| RNA polymerase sigma factor RpoD [Brucella sp. BO2]
 gi|17982448|gb|AAL51713.1| RNA polymerase sigma factor rpod [Brucella melitensis bv. 1 str.
           16M]
 gi|23348329|gb|AAN30390.1| RNA polymerase sigma-70 factor [Brucella suis 1330]
 gi|82616393|emb|CAJ11454.1| Sigma-70 factor family:Sigma-70 factor, region 1.1:Sigma-70 region
           3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70,
           non-essent [Brucella melitensis biovar Abortus 2308]
 gi|161336237|gb|ABX62542.1| RNA polymerase sigma factor rpoD [Brucella canis ATCC 23365]
 gi|189020170|gb|ACD72892.1| RNA polymerase sigma factor [Brucella abortus S19]
 gi|237789171|gb|EEP63382.1| RNA polymerase sigma factor RpoD [Brucella abortus str. 2308 A]
 gi|256000059|gb|ACU48458.1| RNA polymerase sigma factor [Brucella microti CCM 4915]
 gi|260095958|gb|EEW79835.1| RNA polymerase sigma factor [Brucella abortus NCTC 8038]
 gi|260151365|gb|EEW86459.1| RNA polymerase sigma factor [Brucella melitensis bv. 1 str. 16M]
 gi|260155539|gb|EEW90619.1| RNA polymerase sigma factor [Brucella suis bv. 4 str. 40]
 gi|260668736|gb|EEX55676.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|260672676|gb|EEX59497.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675307|gb|EEX62128.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|260873743|gb|EEX80812.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|260916068|gb|EEX82929.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|260924696|gb|EEX91264.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|261295185|gb|EEX98681.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|261742521|gb|EEY30447.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|262766487|gb|EEZ12276.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|263002320|gb|EEZ14895.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|294821388|gb|EFG38387.1| RNA polymerase primary sigma factor [Brucella sp. NVSL 07-0026]
 gi|297175924|gb|EFH35271.1| RNA polymerase primary sigma factor [Brucella abortus bv. 5 str.
           B3196]
 gi|306286647|gb|EFM58210.1| RNA polymerase sigma factor RpoD [Brucella sp. BO2]
          Length = 672

 Score =  549 bits (1415), Expect = e-154,   Method: Composition-based stats.
 Identities = 414/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|225852960|ref|YP_002733193.1| RNA polymerase sigma factor RpoD [Brucella melitensis ATCC 23457]
 gi|256263561|ref|ZP_05466093.1| RNA polymerase sigma factor [Brucella melitensis bv. 2 str. 63/9]
 gi|225641325|gb|ACO01239.1| RNA polymerase sigma factor RpoD [Brucella melitensis ATCC 23457]
 gi|263093589|gb|EEZ17614.1| RNA polymerase sigma factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409500|gb|ADZ66565.1| RNA polymerase sigma factor RpoD [Brucella melitensis M28]
 gi|326539207|gb|ADZ87422.1| RNA polymerase sigma factor RpoD [Brucella melitensis M5-90]
          Length = 672

 Score =  549 bits (1414), Expect = e-154,   Method: Composition-based stats.
 Identities = 414/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNVLLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|148559099|ref|YP_001259363.1| RNA polymerase sigma factor RpoD [Brucella ovis ATCC 25840]
 gi|148370356|gb|ABQ60335.1| RNA polymerase sigma-70 factor [Brucella ovis ATCC 25840]
          Length = 672

 Score =  549 bits (1413), Expect = e-154,   Method: Composition-based stats.
 Identities = 413/693 (59%), Positives = 514/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLTMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|254719520|ref|ZP_05181331.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|265984525|ref|ZP_06097260.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|306837542|ref|ZP_07470416.1| RNA polymerase sigma factor RpoD [Brucella sp. NF 2653]
 gi|264663117|gb|EEZ33378.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|306407378|gb|EFM63583.1| RNA polymerase sigma factor RpoD [Brucella sp. NF 2653]
          Length = 672

 Score =  548 bits (1412), Expect = e-153,   Method: Composition-based stats.
 Identities = 413/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E +SI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEANSISRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|256061534|ref|ZP_05451676.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 gi|261325543|ref|ZP_05964740.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 gi|261301523|gb|EEY05020.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
          Length = 672

 Score =  548 bits (1411), Expect = e-153,   Method: Composition-based stats.
 Identities = 413/693 (59%), Positives = 515/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ L+EQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLIEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|188579854|ref|YP_001923299.1| RNA polymerase sigma factor RpoD [Methylobacterium populi BJ001]
 gi|179343352|gb|ACB78764.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium populi
           BJ001]
          Length = 667

 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 383/701 (54%), Positives = 477/701 (68%), Gaps = 53/701 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  
Sbjct: 1   MATKATERDDADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDG 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--------------ASSASNSSVFL 106
           +Q+ED +A L +MGI VV+ ++ E+      +                  ++ S +    
Sbjct: 61  DQIEDVLAQLDDMGIRVVEAEESEETATEAKANGEAAEEEESAEGGEVAETAGSRAVAVA 120

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
                     TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 121 TPTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQA 180

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           +IIWRDEL DG  LLR+IIDLEA        G   G E    ++ E              
Sbjct: 181 IIIWRDELVDGKVLLRDIIDLEATYAGPDARGAPQGGEAEEGEESE-------------- 226

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                               PPE  +      DED+ ++  +L+AME +++P+V+   D 
Sbjct: 227 --------------DGDGAVPPEGGD------DEDDMENNVSLAAMEAEIKPRVLETFDN 266

Query: 287 IAEVYRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA  YR+LR LQ+      A  G      + K   LK+ +V  V SLSLN +RI+ LVEQ
Sbjct: 267 IASNYRKLRKLQNEETDLKAGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQ 326

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           LYDI+KR++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV  
Sbjct: 327 LYDINKRLISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVER 386

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +  +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AK
Sbjct: 387 GGRQVADLREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAK 446

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 447 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 506

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIG
Sbjct: 507 PVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIG 566

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHT
Sbjct: 567 DEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 626

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 627 LEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 667


>gi|154252764|ref|YP_001413588.1| RNA polymerase sigma factor RpoD [Parvibaculum lavamentivorans
           DS-1]
 gi|154156714|gb|ABS63931.1| RNA polymerase, sigma 70 subunit, RpoD [Parvibaculum
           lavamentivorans DS-1]
          Length = 656

 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 393/692 (56%), Positives = 481/692 (69%), Gaps = 46/692 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    ++    ++  E   D  + D SD + KKMIK A+ RG+VT +ELN  LP +E SS
Sbjct: 1   MAKTAEQTEAPEAAPEAPQDGPLLDMSDAAVKKMIKAAKARGFVTYDELNKVLPSEEFSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSED-----SLDLASSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS MGINVV+ D+ ED     D       D   + +  +V       S+  
Sbjct: 61  EQIEDTLSMLSEMGINVVENDEAEDNAEGADGEADEDRDDEEAPTGKAVATTTTTSSSLD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +G  LLR+IIDL+A           H     + +       E+E  D    +        
Sbjct: 181 EGKILLRDIIDLDATFAGPDAKKVDHSQAALAGEAPPRIEPEEEEVDEDGED-------- 232

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                                       D++ +L+AME +L+PKV+   D IA  Y++LR
Sbjct: 233 ----------------------------DNSMSLAAMEAELKPKVLETFDTIAADYKKLR 264

Query: 296 SLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
            LQD  V      ++       K + L   L++ V SLSLN +RI+ LVEQLY I+KR+M
Sbjct: 265 KLQDQKVELALQGEALSSAQEKKYQKLTSDLIEEVKSLSLNNNRIESLVEQLYAINKRLM 324

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             EG LLRLA+S+GI RD FL+++ G ELDP+W+          W NF   E D +  +R
Sbjct: 325 GLEGRLLRLAESHGIPRDEFLKQYFGNELDPNWIRRVSRLKGKGWVNFTKDERDQVKDLR 384

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            EI++++ ETG+ I E+R IVS V+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 385 QEIQTLASETGLDIQEYRRIVSGVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQF 444

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 445 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 504

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGD
Sbjct: 505 KLVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 564

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 565 FIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 624

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 625 VTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 656


>gi|254710518|ref|ZP_05172329.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|256032011|ref|ZP_05445625.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261318089|ref|ZP_05957286.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|265989123|ref|ZP_06101680.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261297312|gb|EEY00809.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|264661320|gb|EEZ31581.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
          Length = 672

 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 413/693 (59%), Positives = 514/693 (74%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ S LG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSLLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|254559198|ref|YP_003066293.1| sigma D factor of RNA polymerase [Methylobacterium extorquens DM4]
 gi|254266476|emb|CAX22240.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens DM4]
          Length = 666

 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 383/701 (54%), Positives = 474/701 (67%), Gaps = 54/701 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  
Sbjct: 1   MATKATERDDADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDG 60

Query: 61  EQMEDTVAMLSNMGINVV--------------DGDDLEDEEGSEDSLDLASSASNSSVFL 106
           +Q+ED +A L +MGI VV              +G+  E+EE +E      +S + +    
Sbjct: 61  DQIEDVLAQLDDMGIRVVEAEESEEAAPEAKANGEASEEEESTEGGEVAETSGTRAVAVA 120

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
                     TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 121 TPTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQA 180

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           +IIWRDEL DG  LLR+IIDLEA        G     E    +  E              
Sbjct: 181 IIIWRDELVDGKVLLRDIIDLEATYAGPDARGAPQEAEAEGEESEEAEGAVPP------- 233

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                                       E   DED+ ++  +L+AME +++P+V+   D 
Sbjct: 234 ----------------------------EGGDDEDDMENNVSLAAMEAEIKPRVLETFDN 265

Query: 287 IAEVYRELRSLQDNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA  YR+LR LQ+         G      + K   LK+ +V  V SLSLN +RI+ LVEQ
Sbjct: 266 IASNYRKLRKLQNEETELKTGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQ 325

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           LYDI+KR++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV  
Sbjct: 326 LYDINKRLISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVER 385

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +  +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AK
Sbjct: 386 GGRQVADLREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAK 445

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 446 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 505

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIG
Sbjct: 506 PVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIG 565

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHT
Sbjct: 566 DEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 625

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 626 LEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 666


>gi|240850913|ref|YP_002972313.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
 gi|240268036|gb|ACS51624.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
          Length = 671

 Score =  547 bits (1409), Expect = e-153,   Method: Composition-based stats.
 Identities = 409/694 (58%), Positives = 506/694 (72%), Gaps = 35/694 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++   + S D  + DFSDD+ KKMIKLA++ GYVT++ELNA LP DEV+S
Sbjct: 1   MATRVKQKDNAEVTSQASLDGPLLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA----SSASNSSVFLQKRKDSADRS 116
           EQ+ED +AM S MG+NVVD +D  + E  E+ + +       AS+ ++     K      
Sbjct: 61  EQIEDILAMFSEMGVNVVDDEDEVESENYEEEVTVEGGDLVEASSHAIATTTNKREVTDR 120

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDEL +
Sbjct: 121 TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELKE 180

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
              LLREIIDLE             G E       E S   K  ++            K+
Sbjct: 181 QRILLREIIDLETTYA---------GPEAKQAPVIERSEVNKTEEE------------KM 219

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           S   R+  +S  E   N E + +ED+DD   +L+AME++L P+VM  LD IA+ Y +LR 
Sbjct: 220 SSGIRNMGESAGE--RNIEDDEEEDDDDVNLSLAAMENELCPQVMETLDFIAQTYVKLRK 277

Query: 297 LQDNAVNGQKDEKSS--------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LQD  V     E+           K   LK +L++ V SLSLNQ+RI+ LVEQLYDI+KR
Sbjct: 278 LQDQHVESSLAERKEGALTSSQKKKYIQLKGELIQAVKSLSLNQNRIEALVEQLYDINKR 337

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++HNEG+L R+A SYGI  + FL+ +QGRELD  W++Y    P   W+ F   E   I K
Sbjct: 338 LIHNEGKLKRIANSYGIGHEDFLKEYQGRELDADWMNYIAALPTPGWREFSMREAKEIQK 397

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+EI++++ ET ISI EFR IV  V+KGE E++IAKKEMVE+NLRLVIS+AKKYTNRGL
Sbjct: 398 LRSEIQNLAQETAISIGEFRRIVMQVQKGERESTIAKKEMVESNLRLVISIAKKYTNRGL 457

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 458 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 517

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHL
Sbjct: 518 INKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHL 577

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 578 GDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 637

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 638 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 671


>gi|163850052|ref|YP_001638095.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
 gi|163661657|gb|ABY29024.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
          Length = 718

 Score =  547 bits (1409), Expect = e-153,   Method: Composition-based stats.
 Identities = 383/701 (54%), Positives = 474/701 (67%), Gaps = 54/701 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  
Sbjct: 53  MATKATERDDADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDG 112

Query: 61  EQMEDTVAMLSNMGINVV--------------DGDDLEDEEGSEDSLDLASSASNSSVFL 106
           +Q+ED +A L +MGI VV              +G+  E+EE +E      +S + +    
Sbjct: 113 DQIEDVLAQLDDMGIRVVEAEESEEAAPEAKANGEASEEEESTEGGEVAETSGTRAVAVA 172

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
                     TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 173 TPTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQA 232

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           +IIWRDEL DG  LLR+IIDLEA        G     E    +  E              
Sbjct: 233 IIIWRDELVDGKVLLRDIIDLEATYAGPDARGAPQEAEAEGEESEEAEGAVPP------- 285

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                                       E   DED+ ++  +L+AME +++P+V+   D 
Sbjct: 286 ----------------------------EGGDDEDDMENNVSLAAMEAEIKPRVLETFDN 317

Query: 287 IAEVYRELRSLQDNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA  YR+LR LQ+         G      + K   LK+ +V  V SLSLN +RI+ LVEQ
Sbjct: 318 IASNYRKLRKLQNEETELKTGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQ 377

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           LYDI+KR++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV  
Sbjct: 378 LYDINKRLISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVER 437

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +  +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AK
Sbjct: 438 GGRQVADLREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAK 497

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 498 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 557

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIG
Sbjct: 558 PVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIG 617

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHT
Sbjct: 618 DEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 677

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 678 LEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 718


>gi|218528655|ref|YP_002419471.1| RNA polymerase sigma factor RpoD [Methylobacterium chloromethanicum
           CM4]
 gi|240137186|ref|YP_002961655.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
 gi|218520958|gb|ACK81543.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
           chloromethanicum CM4]
 gi|240007152|gb|ACS38378.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
          Length = 666

 Score =  547 bits (1408), Expect = e-153,   Method: Composition-based stats.
 Identities = 386/701 (55%), Positives = 478/701 (68%), Gaps = 54/701 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+D+  +   D  + D +D + K+M+KLA++RGYVT EE+N  LP  +V  
Sbjct: 1   MATKATERDDADAAQDQPTDGPLLDLTDAAVKRMVKLAKKRGYVTYEEINEVLPDGQVDG 60

Query: 61  EQMEDTVAMLSNMGINVV--------------DGDDLEDEEGSEDSLDLASSASNSSVFL 106
           +Q+ED +A L +MGI VV              +G+  E+EE +E      +S + +    
Sbjct: 61  DQIEDVLAQLDDMGIRVVEAEESEEAAPEAKANGEASEEEESTEGGEVAETSGTRAVAVA 120

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
                     TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA
Sbjct: 121 TPTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQA 180

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           +IIWRDEL DG  LLR+IIDLEA        G     E    +  E              
Sbjct: 181 IIIWRDELVDGKVLLRDIIDLEATYAGPDARGAPQEAEAEGEESEEAEGA---------- 230

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                               PPE A+      DED+ ++  +L+AME +++P+V+   D 
Sbjct: 231 -------------------VPPEGAD------DEDDMENNVSLAAMEAEIKPRVLETFDN 265

Query: 287 IAEVYRELRSLQDNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA  YR+LR LQ+         G      + K   LK+ +V  V SLSLN +RI+ LVEQ
Sbjct: 266 IASNYRKLRKLQNEETELKTGGGTVTSAQTKKQAELKDIVVTDVKSLSLNANRIEALVEQ 325

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           LYDI+KR++ +EG L+R A+ +G+ RD FL  +QG ELDP+W+          WKNFV  
Sbjct: 326 LYDINKRLISHEGRLMRAAEHHGVARDEFLRHYQGYELDPNWMDRVATLGGKGWKNFVER 385

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +  +R +I +++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AK
Sbjct: 386 GGRQVADLREQILTLASETGLQIGEYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAK 445

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRI
Sbjct: 446 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 505

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIG
Sbjct: 506 PVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIG 565

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHT
Sbjct: 566 DEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 625

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 626 LEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 666


>gi|158425267|ref|YP_001526559.1| RNA polymerase sigma factor RpoD [Azorhizobium caulinodans ORS 571]
 gi|158332156|dbj|BAF89641.1| sigma-70 [Azorhizobium caulinodans ORS 571]
          Length = 690

 Score =  547 bits (1408), Expect = e-153,   Method: Composition-based stats.
 Identities = 406/700 (58%), Positives = 501/700 (71%), Gaps = 51/700 (7%)

Query: 1   MTIGKKRNRDSDSEHE--DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEV 58
           M++ K+    +++  +  D+ D  + D SD + +KMIK A++RGYVT E+LN  +P +EV
Sbjct: 24  MSMAKQATETTEAPEKEVDAPDGPLLDLSDAAVRKMIKSAKRRGYVTYEQLNEVMPSEEV 83

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR--------- 109
           +SEQ+EDT+AML++MGINV++ ++ E EE SE+           S  L ++         
Sbjct: 84  TSEQIEDTLAMLNDMGINVIEAEEAEAEEASEEGETADEPEEVDSGELAEQSPRAVVRSE 143

Query: 110 -KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+I
Sbjct: 144 TKSEPGERTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAII 203

Query: 169 IWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           IWRDEL +G  LLR+IIDLEA   GPE K G                            E
Sbjct: 204 IWRDELTEGRVLLRDIIDLEATYAGPEGKAGPV-------------------------IE 238

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
           G+   A +  +D      + P +        DED+ +++ +L+AME +++PKV+   + I
Sbjct: 239 GETALAPEAGEDGLLNDSAAPGD--------DEDDMENSLSLAAMETEIKPKVLETFERI 290

Query: 288 AEVYRELRSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           A+ Y++LR LQD        N         K K LKE LV  + SLSLNQ+RID LVEQL
Sbjct: 291 ADNYKKLRRLQDQNVESKLKNETLSPAQERKAKKLKEDLVLDMKSLSLNQARIDSLVEQL 350

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           Y+I+KR++  EG LLRLA+SYG+ RD FL ++QG ELDP W+          WK FVA E
Sbjct: 351 YEINKRLVSLEGRLLRLAESYGVARDDFLRQYQGYELDPKWLLRVSKLGSKGWKEFVAHE 410

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            D I  +R +I +++ ET + I+EFR IV MV+KGE EA  AKKEMVEANLRLVIS+AKK
Sbjct: 411 KDGIHTLRGDIHALATETALEIAEFRKIVQMVQKGEKEARQAKKEMVEANLRLVISIAKK 470

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 471 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 530

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+VRT+R+M ++I REPTPEE+A+KL MP+E VRKVLKI KEPISLETPIGD
Sbjct: 531 VHMIETINKIVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGD 590

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL
Sbjct: 591 EEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 650

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 651 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 690


>gi|304391338|ref|ZP_07373282.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
 gi|303296694|gb|EFL91050.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
          Length = 692

 Score =  546 bits (1406), Expect = e-153,   Method: Composition-based stats.
 Identities = 391/697 (56%), Positives = 499/697 (71%), Gaps = 20/697 (2%)

Query: 1   MTIGKKRNRDS-DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           M       + +  +  + + D  + D +DD  KKMIK A++RG+VT++ELNA +P DEVS
Sbjct: 1   MAKAATAKKPTPQTPEQAAADRPLLDLNDDKVKKMIKAAKKRGFVTVDELNAVMPSDEVS 60

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            +Q+EDT++MLS MGI   +  + E+ E + + +      +         K      TDD
Sbjct: 61  PDQIEDTMSMLSEMGI---NVVEEEESEEAPEEVSTEIVEAGKKAVATVAKKEPTDRTDD 117

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDEL +   
Sbjct: 118 PVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELLEENI 177

Query: 180 LLREIIDLEACI-GPESKGGFFHGTEGHSYQKR--------EDSSQEKERDDVQETEGDI 230
           LLR+IIDLEA   GP++K          +            E S +   R   ++   D 
Sbjct: 178 LLRDIIDLEATYAGPDAKQNVPVNPNAPASVAEAVRQGSGGEHSPEAIARRKAEKDGTDP 237

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           E+A +  K   +  D+  EN    + + D+++D++A +L+AME +L+PKV+   D IA  
Sbjct: 238 EAAVEALKGPEAGDDTSSEN--KTDDDDDDEDDEAALSLAAMEAELKPKVLEIFDSIAGN 295

Query: 291 YRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           Y++LR LQD       +N +       +   LKE++V  V SL LN +RI+ LVEQLYDI
Sbjct: 296 YKKLRKLQDTYVEKRMLNEKLSPSQEKRLVALKEEIVVSVKSLELNLNRIEALVEQLYDI 355

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
           +KR++ +EG L+RLA+ +G+ R++FLE ++G ELDP+W+    +     WK F A E   
Sbjct: 356 NKRLVQSEGRLMRLAEKHGVARELFLEEYRGAELDPNWIRRIANLGAKGWKEFCANEKPE 415

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I ++R +I+ +S ETG+   EFR IV  V+KGE E+ IAKKEMVEANLRLVIS+AKKYTN
Sbjct: 416 IKELRADIQMLSHETGLDTGEFRRIVHQVQKGERESRIAKKEMVEANLRLVISIAKKYTN 475

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 476 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 535

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+VRT+R+M ++I REPTPEE++ KLAMP+E VRKVLKI KEPISLETPIGDE+ 
Sbjct: 536 IETINKIVRTSRQMLHEIGREPTPEELSTKLAMPLEKVRKVLKIAKEPISLETPIGDEED 595

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDKNA+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV
Sbjct: 596 SHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 655

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 656 GQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 692


>gi|153009018|ref|YP_001370233.1| RNA polymerase sigma factor RpoD [Ochrobactrum anthropi ATCC 49188]
 gi|151560906|gb|ABS14404.1| RNA polymerase, sigma 70 subunit, RpoD [Ochrobactrum anthropi ATCC
           49188]
          Length = 671

 Score =  545 bits (1403), Expect = e-152,   Method: Composition-based stats.
 Identities = 410/694 (59%), Positives = 512/694 (73%), Gaps = 35/694 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS-----SASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ +++    +  D         +  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREENNDDDSEEGGDLVESGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           D   LLREIIDLE    GPE+K             + +   + ++ DD+    GD+ +  
Sbjct: 181 DSNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDDKPQRRRDDDDITNVGGDMPTEE 240

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +   +D                        +  +L+AME +LRP+VM  LD IA+ Y++L
Sbjct: 241 EEEDEDE-----------------------ANLSLAAMEAELRPQVMETLDLIADTYKKL 277

Query: 295 RSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           R LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR
Sbjct: 278 RKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKR 337

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++ NEG+LLRLA+S+G++R+ FL+ +QG ELDP WV          WK F A E  +I +
Sbjct: 338 LVQNEGKLLRLAESFGVRREEFLKEYQGHELDPKWVERVSTLSARGWKEFAAKEERAIDR 397

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+EI+ ++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGL
Sbjct: 398 LRSEIQMLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGL 457

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 458 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 517

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHL
Sbjct: 518 INKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHL 577

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 578 GDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 637

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 638 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 671


>gi|239832356|ref|ZP_04680685.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
 gi|239824623|gb|EEQ96191.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
          Length = 672

 Score =  544 bits (1402), Expect = e-152,   Method: Composition-based stats.
 Identities = 414/693 (59%), Positives = 509/693 (73%), Gaps = 32/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS-----SASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ +++       D         +  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREDNSDDDSEEGGDLVESGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           D   LLREIIDLE             G E       E   +EK RDD  +     +    
Sbjct: 181 DSNILLREIIDLETTYA---------GPEAKQAPVIERVEEEKPRDDKPQRRSRDDDDIT 231

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
               D                  +EDED++  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 232 NVGGDMPVE------------EEEEDEDEANLSLAAMEAELRPQVMETLDLIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP WV          WK F A E  +I ++
Sbjct: 340 VQNEGKLLRLAESFGVRREEFLKEYQGHELDPKWVERVSTLSARGWKEFAAKEERTIDRL 399

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI+ ++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 400 RSEIQMLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQ 459

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 460 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 519

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 520 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 579

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 580 DFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 639

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 640 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 672


>gi|220927258|ref|YP_002502560.1| RNA polymerase sigma factor RpoD [Methylobacterium nodulans ORS
           2060]
 gi|219951865|gb|ACL62257.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium nodulans
           ORS 2060]
          Length = 665

 Score =  544 bits (1401), Expect = e-152,   Method: Composition-based stats.
 Identities = 392/700 (56%), Positives = 484/700 (69%), Gaps = 53/700 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++++  E   D  + D +D S K+MIKLA++RGYVT +ELN  LP +E +S
Sbjct: 1   MATKATEREETEAAPEQQTDGPLLDLTDASVKRMIKLAKKRGYVTYDELNEVLPQEEFTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEG-------------SEDSLDLASSASNSSVFLQ 107
           EQ+ED +  LS +G+NVV+ ++ +D +              SE +     + +  +V   
Sbjct: 61  EQIEDVLGQLSELGVNVVEAEEADDNQAEGAGEGGAEDEEVSEGTEVAEVAQNRPAVLRT 120

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           +        TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+
Sbjct: 121 ETTKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAI 180

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           IIWRDEL DG  LLR+IIDLEA                                   +  
Sbjct: 181 IIWRDELVDGRVLLRDIIDLEATYA------------------------------GPDGR 210

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
           G      +  + +  + + PP   E DE +L     ++  +LSAME +L+P+V+   D I
Sbjct: 211 GGPAEGEEEGEGEAPEGEVPPPEGEGDEDDL-----ENNVSLSAMEAELKPRVLETFDAI 265

Query: 288 AEVYRELRSLQ-----DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           AE YR+LR++Q          G   E    +   LK ++V  V SLSLN +RI+ LVEQL
Sbjct: 266 AENYRKLRNVQAEQAETRLQGGGASEAQGRQYSELKSRIVADVKSLSLNANRIEALVEQL 325

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           YDI+KR++  EG L+RLA+S+G+ RD FL  +QG ELDPHWV          WKNFV   
Sbjct: 326 YDINKRLISQEGRLMRLAESHGVARDEFLRHYQGYELDPHWVERVGKLGGKGWKNFVERG 385

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            D I  +R +I S++ ETG+ I E+R IV MV+KGE EA  AKKEM+EANLRLVIS+AKK
Sbjct: 386 ADGIQSLREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKK 445

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 446 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 505

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGD
Sbjct: 506 VHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGD 565

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL
Sbjct: 566 EEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 625

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 626 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 665


>gi|170747007|ref|YP_001753267.1| RNA polymerase sigma factor RpoD [Methylobacterium radiotolerans
           JCM 2831]
 gi|170653529|gb|ACB22584.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
           radiotolerans JCM 2831]
          Length = 659

 Score =  543 bits (1399), Expect = e-152,   Method: Composition-based stats.
 Identities = 377/696 (54%), Positives = 469/696 (67%), Gaps = 51/696 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++D+  E   D  + D +D S K+M+KLA++RGYVT EE+N  LP  +   
Sbjct: 1   MATKATERDETDAAPEQQTDGPLLDLTDASVKRMVKLAKKRGYVTYEEVNEVLPEGQSDP 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK---------D 111
           +Q+ED ++ LS MGINVV+ ++ ++  G + +      A    V                
Sbjct: 61  DQLEDVLSQLSEMGINVVEAEETDEAAGEKAADGEEEEAEGGEVAEVAPARAVAVATTTK 120

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWR
Sbjct: 121 EPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWR 180

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
           DEL +G  LLR+IIDLEA              EG   +  E  +  +  DD         
Sbjct: 181 DELVEGKVLLRDIIDLEATYAGPDGKNAPQLAEGEESEDGEPPAPPEGGDD--------- 231

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                                       ED+ ++  +L+AME +++P+V+   D IA  Y
Sbjct: 232 ----------------------------EDDLENNVSLAAMEAEIKPRVLETFDAIAANY 263

Query: 292 RELRSLQ-----DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           R+LR  Q       A   Q       K   LK+ +V  V SLSLN +RI+ LV QLY I+
Sbjct: 264 RKLRKFQIEGTERKAAGEQNTPAQDQKQAELKDIVVADVKSLSLNNNRIEALVGQLYSIN 323

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           K+++ +EG L+R A+S+G+ RD FL  +QG ELDP+W+          WKN V      +
Sbjct: 324 KQLIGHEGRLMRFAESHGVARDEFLRHYQGYELDPNWMERVGTLGGKGWKNLVERGSKQV 383

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            ++R +I  ++ ETG+ I E+R IV+MV+KGE EA  AKKEM+EANLRLVIS+AKKYTNR
Sbjct: 384 AELRAQILDLASETGLEIGEYRRIVNMVQKGEREARQAKKEMIEANLRLVISIAKKYTNR 443

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 444 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 503

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ S
Sbjct: 504 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDS 563

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIEDKN V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
Sbjct: 564 HLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 623

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 624 QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 659


>gi|49474476|ref|YP_032518.1| RNA polymerase sigma factor RpoD [Bartonella quintana str.
           Toulouse]
 gi|49239980|emb|CAF26393.1| RNA polymerase sigma factor rpod [Bartonella quintana str.
           Toulouse]
          Length = 670

 Score =  542 bits (1396), Expect = e-152,   Method: Composition-based stats.
 Identities = 401/693 (57%), Positives = 494/693 (71%), Gaps = 34/693 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++ + + S DS + DFSDD+ KKM+KLA++ GYVT++ELNA LPPDEV+S
Sbjct: 1   MATKVKQKDNTEVKGQASVDSPLLDFSDDAIKKMVKLAKKNGYVTMDELNAVLPPDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRST 117
           EQ+EDT+AM S MGINVVD +D  + E  E+ + +                 K      T
Sbjct: 61  EQIEDTLAMFSEMGINVVDDEDEGESEHYEEEVTVEGGDLVEVTRNAIATTTKREVTDRT 120

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+EL + 
Sbjct: 121 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELKEQ 180

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LLREIIDLE                    + +E+ S    RD  +    DI       
Sbjct: 181 RILLREIIDLEMTYAGPEAKQAPVIERSEIGKIKEEKSFSGTRDMEENITRDIGVEDDEE 240

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           +DD                           +L+AME++L P+VM  LD IAE Y +LR L
Sbjct: 241 EDDDV-----------------------NLSLAAMENELCPQVMETLDFIAEAYIKLRKL 277

Query: 298 QDNAVNGQKDEKSS--------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           QD  V     E+           K   LK +L++ V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 278 QDQHVESSLAERKEGTLSLSQKKKYIQLKSELIQAVKSLSLNQNRIEALVEQLYDINKRL 337

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +HNEG+L R+A +YG+  + FL+ +QGRELD  W++Y        WK F   EV  I  +
Sbjct: 338 IHNEGKLKRIANNYGVSHEEFLKEYQGRELDADWINYIATLSGRGWKEFSMREVKEIQSL 397

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE E++IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 398 RSEIQNLAQETAISIGEFRRIVTQVQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQ 457

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 458 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 517

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLG
Sbjct: 518 NKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLG 577

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 578 DFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 637

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 638 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 670


>gi|13472238|ref|NP_103805.1| RNA polymerase sigma factor RpoD [Mesorhizobium loti MAFF303099]
 gi|14022983|dbj|BAB49591.1| RNA polymerase sigma subunit [Mesorhizobium loti MAFF303099]
          Length = 674

 Score =  540 bits (1390), Expect = e-151,   Method: Composition-based stats.
 Identities = 410/693 (59%), Positives = 508/693 (73%), Gaps = 32/693 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   + ++E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+SEQ
Sbjct: 1   MATKEKEEVETEREGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF-------LQKRKDSADR 115
           +EDT+AMLS+MGINVV+ D+  +E  + D+   A   +N               K     
Sbjct: 61  IEDTMAMLSDMGINVVEDDEQGEEAEAGDTAADAEEDANELAEQTGTAVAATTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLEA            G E       E   +  + ++            +
Sbjct: 181 ESKILLREIIDLEATYA---------GPEAKQAPVVERIEEAPKAEEK----------PR 221

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
             +DD   V +   +      + +EDED+++ +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 222 RGRDDEDDVTNVGADTRGIGDDDEEDEDEASLSLAAMEAELRPQVMETLDVIADTYKKLR 281

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR+
Sbjct: 282 KLQDQQVENRLAAAGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRL 341

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+SYG++R+ FL+ +QG ELDP+W     +     WK F   E D+I  +
Sbjct: 342 VQNEGKLLRLAESYGVRREEFLKEYQGSELDPNWTRAIGNLTSRGWKEFTKNEKDAIKDL 401

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R EI+ ++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 402 RAEIQHLATETAISILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQ 461

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 462 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 521

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 522 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 581

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDK A+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 582 DFIEDKMAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 641

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 642 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 674


>gi|319408880|emb|CBI82537.1| RNA polymerase sigma factor [Bartonella schoenbuchensis R1]
          Length = 667

 Score =  539 bits (1388), Expect = e-151,   Method: Composition-based stats.
 Identities = 406/693 (58%), Positives = 499/693 (72%), Gaps = 37/693 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+        + S DS + DFSDD+ KKMIKLA++ GYVT++ELNA LP + V+S
Sbjct: 1   MATKAKQKDSVAETGQVSLDSPLLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSESVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF---LQKRKDSADRST 117
           EQ+EDT+AMLS MGINVVD +D  D E  E+ + +       +         K      T
Sbjct: 61  EQIEDTLAMLSEMGINVVDDEDEVDSEPYEEEITIEGGDLVEATSRSIATISKCDTTDRT 120

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+ELN+ 
Sbjct: 121 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELNEK 180

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LLREIIDLE             G E       E S  EK ++++      +     ++
Sbjct: 181 RILLREIIDLEMTYA---------GPEAKQAPAIERSEVEKIKEEMP--CSSMHDVDDLA 229

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           +D   +               D++ED+   +L+AME++L P+VM  LD IAE Y +LR L
Sbjct: 230 EDIGVE---------------DDEEDEVNLSLAAMENELCPQVMETLDFIAETYVKLRKL 274

Query: 298 QDNAVNGQKDEKSS--------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           QD  V     +            KC  LK  LV+ V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 275 QDQHVESSLADCKEDALSSSQKKKCTQLKADLVQAVKSLSLNQNRIEALVEQLYDINKRL 334

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +H+EG+L RLA +YG+  + FL+ +QGRELD  W++Y    P   WK F   E   I  +
Sbjct: 335 VHSEGKLKRLANNYGVGHEDFLKEYQGRELDADWINYIATLPGSGWKEFSTREAKVIQSL 394

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI+S++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AK+YTNRGLQ
Sbjct: 395 RSEIQSLAQETAISIGEFRRIVTQVQKGEREATIAKKEMVEANLRLVISIAKRYTNRGLQ 454

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 455 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 514

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLG
Sbjct: 515 NKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLG 574

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 575 DFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 634

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 635 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 667


>gi|49475878|ref|YP_033919.1| RNA polymerase sigma factor RpoD [Bartonella henselae str.
           Houston-1]
 gi|49238686|emb|CAF27936.1| RNA polymerase sigma factor rpod [Bartonella henselae str.
           Houston-1]
          Length = 667

 Score =  539 bits (1387), Expect = e-151,   Method: Composition-based stats.
 Identities = 403/692 (58%), Positives = 499/692 (72%), Gaps = 35/692 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  +++   + S DS + DFSDD+ KKM+K+A++ GYVT++ELNA LPPDEV+S
Sbjct: 1   MATKVKQKDNTEVTTQASVDSPLLDFSDDAIKKMVKIAKKNGYVTMDELNAVLPPDEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS-SASNSSVFLQKRKDSADRSTDD 119
           EQ+EDT+AM S MGINVVD +   +    E  ++      + S+  +   K      TDD
Sbjct: 61  EQIEDTLAMFSEMGINVVDDEGEAENYEEEVRVEGGDLVEATSNALVTTAKRELTDRTDD 120

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWR+EL +   
Sbjct: 121 PVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELKEQRI 180

Query: 180 LLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           LLREIIDLE    GPE+K       E    QK ++        D++    DI       +
Sbjct: 181 LLREIIDLEMTYAGPEAKQAPV--IERSEVQKVKEEKSSSAMRDMENIARDIGVEEDDEE 238

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           DD                           +L+AME++L P+VM  LD IAE Y +LR LQ
Sbjct: 239 DDDV-----------------------NLSLAAMENELCPQVMGTLDFIAETYVKLRKLQ 275

Query: 299 DNAVNGQKDEKSS--------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           D  V     E+           KC  LK +LV+ V SLSLNQ+RI+ LVEQLYDI+KR++
Sbjct: 276 DQHVESSLAERKEGALSPSQRKKCIQLKSELVQAVKSLSLNQNRIESLVEQLYDINKRLI 335

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
           HNEG+L R+A +YG+  + FL+ +QGRELD  W++Y        WK F   E   I  +R
Sbjct: 336 HNEGKLKRIANNYGVGHEEFLKEYQGRELDADWINYIATLSGRGWKEFSKREAKEIKTLR 395

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +EI++++ ET ISI EFR IV+ V+KGE E++IAKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 396 SEIQNLAQETAISIGEFRRIVTQVQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQF 455

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 456 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 515

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R++ ++I R+PTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLGD
Sbjct: 516 KIVRTSRQILHEIGRDPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGD 575

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 576 FIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 635

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 636 VTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 667


>gi|254461643|ref|ZP_05075059.1| RNA polymerase sigma-70 factor RpoD [Rhodobacterales bacterium
           HTCC2083]
 gi|206678232|gb|EDZ42719.1| RNA polymerase sigma-70 factor RpoD [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 660

 Score =  538 bits (1385), Expect = e-150,   Method: Composition-based stats.
 Identities = 373/685 (54%), Positives = 478/685 (69%), Gaps = 32/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D   + +D D +   D S  + KKMI  AR+RG++T ++LNA LPPD+VSS+Q
Sbjct: 1   MAAKDNDDR--KSDDQDSAHTLDMSQTAVKKMIADARERGFITYDQLNAVLPPDQVSSDQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGI V   +D + EE  + + DL ++ +N  V +          TDDPVR
Sbjct: 59  IEDVMSMLSEMGIQVT-EEDEDAEEEDKGTTDLVAAGTNKEVAVSTAASEKLDRTDDPVR 117

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR
Sbjct: 118 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLR 177

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G                    D   E+E   V  T  +  +A K       
Sbjct: 178 DVIDLEATFG--------------------DQMGEEETTPVVPTAANSTTAPKAEGMAEL 217

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
             D  P  +++D+ + DE    +  +L+AME  L+P+V+ +L+ IA +Y +L  +QD+ +
Sbjct: 218 DADGNPITSDDDDDDEDEQ---ANMSLAAMEAALKPQVLESLEVIAGLYEQLSQMQDSRI 274

Query: 303 NGQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E      K     + L+ ++V LV  + L+ +RI+ L++QLY I++R+M  +  +
Sbjct: 275 SATLNEDDSFSDKQEANYQKLRSEIVVLVNEMHLHNNRIEALIDQLYGINRRVMSIDSSI 334

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F+E ++GRELDP+W+          W+ F+    D + ++R ++  +
Sbjct: 335 VKLADQARINRREFVEAYRGRELDPNWLEEMAGKAGRGWQMFIERSTDKVEELRADMAQV 394

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 395 GQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 454

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 455 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 514

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 515 RQMLHEIGREPTPEELAAKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 574

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 575 AVLPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 634

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 635 RQIEAKALRKLKHPSRSRKLRSFLD 659


>gi|126727888|ref|ZP_01743716.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126702829|gb|EBA01934.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 661

 Score =  537 bits (1384), Expect = e-150,   Method: Composition-based stats.
 Identities = 372/685 (54%), Positives = 475/685 (69%), Gaps = 31/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N DS  +  D D+  + D S  + KKMI  AR +GY+T ++LNA LPP++VSSEQ
Sbjct: 1   MAAKDNDDS--KQNDQDNDGMTDTSQTAVKKMIAEARVKGYITYDQLNAVLPPEQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGI   +  + E+ E    S D+ ++     + L          TDDPVR
Sbjct: 59  IEDVMSMLSEMGI---NIIEDEEAEDEVKSTDVVTTDQERGLVLAGADKEKLDRTDDPVR 115

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR
Sbjct: 116 MYLREMGSVELLSREGEIAIAKRIEAGRKTMILGLCESPLTFQAITIWRDELLSEDILLR 175

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLE   G                    ++  E+  D V    G   +  K S +  +
Sbjct: 176 DVIDLETTFG--------------------NTMGEEGEDGVTAVPGAATAETKPSGETAA 215

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           +      N  +++ + D++++ +  +L+AME  L+P+V+  L+EIA+ Y EL  +QD  +
Sbjct: 216 QELDADGNPISNDDDDDDEDEQANLSLAAMEAVLKPRVLETLEEIADYYAELSDMQDVRI 275

Query: 303 NGQKDEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E  S         + L+ K+V LV S+ L+ +RI+ L++QLY I++RIM  +  +
Sbjct: 276 SATLNESESYSSKEEDAYQALRTKIVDLVTSMHLHNNRIEALIDQLYGINRRIMQIDSSM 335

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F++ ++G ELDP W+    + P   W  F+    D + ++R E+  +
Sbjct: 336 VKLADQARINRKEFIDAYRGHELDPTWLETIAELPGRGWAAFLERSADKVSELRTEMAQV 395

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 396 GTYVGLDISEFRRIVQQVQKGEKEARAAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 455

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 456 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 515

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+AKKL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 516 RQMLHEIGREPTPEELAKKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 575

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 576 AVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 635

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 RQIEAKALRKLKHPSRSRKLRSFLD 660


>gi|319782038|ref|YP_004141514.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167926|gb|ADV11464.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 673

 Score =  537 bits (1384), Expect = e-150,   Method: Composition-based stats.
 Identities = 413/693 (59%), Positives = 509/693 (73%), Gaps = 33/693 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   + ++E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+SEQ
Sbjct: 1   MATKEKEEVETEREGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF-------LQKRKDSADR 115
           +EDT+AMLS+MGINVV+ D+  +E  + D+   A   +N               K     
Sbjct: 61  IEDTMAMLSDMGINVVEDDEQGEEPEAADTAADAEEDANELAEQTGTAVAATTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLEA            G E       E   + K  D             +
Sbjct: 181 ESKILLREIIDLEATYA---------GPEAKQAPVVERVEEAKVEDK-----------PR 220

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
            S+DD   + +   +      + DEDED+++ +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 221 RSRDDEDDITNVGADTRGLTDDDDEDEDEASLSLAAMEAELRPQVMETLDVIADTYKKLR 280

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR+
Sbjct: 281 KLQDQQVENRLAAAGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRL 340

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+SYG++R+ FL+ +QG ELDP+W     +     WK F   E D+I  +
Sbjct: 341 VQNEGKLLRLAESYGVRREEFLKEYQGSELDPNWTRSIGNLTSRGWKEFTKNEKDAIKDL 400

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 401 RAEIQNLATETAISILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQ 460

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 461 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 520

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 521 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 580

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDK A+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 581 DFIEDKMAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 640

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 641 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 673


>gi|260464077|ref|ZP_05812272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
 gi|259030248|gb|EEW31529.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
          Length = 674

 Score =  537 bits (1383), Expect = e-150,   Method: Composition-based stats.
 Identities = 408/693 (58%), Positives = 509/693 (73%), Gaps = 32/693 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   + ++E E + D  + D SDD+ KKMIK A++RGYVT++ELN+ LP +EV+SEQ
Sbjct: 1   MATKEKEEVETEREGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF-------LQKRKDSADR 115
           +EDT+AMLS+MGINVV+ D+  +E  + D+   A   +N               K     
Sbjct: 61  IEDTMAMLSDMGINVVEDDEQGEEAEAGDTAADAEEDANELAEQTGTAVAATTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLEA            G E       E   +  + ++            +
Sbjct: 181 ESKILLREIIDLEATYA---------GPEAKQAPVVERIEEAPKAEEK----------PR 221

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
             +D+   + +   +      + +EDED+++ +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 222 RGRDEEEDITNVGADTRGLTDDDEEDEDEASLSLAAMEAELRPQVMETLDVIADTYKKLR 281

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR+
Sbjct: 282 KLQDQQVENRLAAAGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRL 341

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+SYG++R+ FL+ +QG ELDP+W     +     WK F   E D+I ++
Sbjct: 342 VQNEGKLLRLAESYGVRREEFLKEYQGSELDPNWTRAIGNLTSRGWKEFTKNEKDAIKEL 401

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R EI+ ++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 402 RAEIQHLATETAISILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQ 461

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 462 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 521

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLG
Sbjct: 522 NKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG 581

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDK A+ P+D+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 582 DFIEDKMAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 641

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 642 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 674


>gi|300023333|ref|YP_003755944.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525154|gb|ADJ23623.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 666

 Score =  536 bits (1381), Expect = e-150,   Method: Composition-based stats.
 Identities = 380/691 (54%), Positives = 485/691 (70%), Gaps = 41/691 (5%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
              K   ++  +      DS + D SD + K+++K A+ +GYVT+++LN+ LP +EVSS+
Sbjct: 7   AAQKTEEKEQPAADAPERDSPLLDLSDQAVKRLLKSAKAKGYVTLDQLNSVLPSEEVSSD 66

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSADRS 116
           Q+ED  A LS+MGI VV+ +D E+     +            A N+++   + K      
Sbjct: 67  QIEDLYATLSDMGITVVENEDGEEAAEGSEESGDEEEGRALVAQNNALVKSETKSEPAER 126

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRDELN+
Sbjct: 127 TDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELNE 186

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G  LLR+IIDLEA              EG   ++ ++++ E   +  Q       S A  
Sbjct: 187 GKILLRDIIDLEATY------------EGPEAKEVQEAASEDSPEPEQPAANQRPSGAPE 234

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            + D                  D+DE ++A +L+AME +L+PKV+   D+IA  Y++LR 
Sbjct: 235 GEGD------------------DDDEFENAMSLAAMEAELKPKVLETFDQIAATYKKLRK 276

Query: 297 LQDNAVNGQK-----DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            QD  +  Q        +     + ++++++  V SLSLN +RI+ LVEQLY I+KR++ 
Sbjct: 277 QQDKKLEQQLVGDQGSRQQQKAYEKIRDEIIVDVKSLSLNNNRIESLVEQLYAINKRLIG 336

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            EG L+RLA SYG+ R  F++ + G ELD  W+       +  W  FV  E   ++ IR 
Sbjct: 337 LEGRLMRLADSYGVPRQHFIDEYYGNELDQTWLDRVAGNGKK-WGQFVKTERTQVVDIRT 395

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           EI  ++ ETG+ I E+R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 396 EIHQLATETGLEIPEYRRIVKAVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFL 455

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 456 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 515

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDF
Sbjct: 516 IVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 575

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IED+NAV P+++AIQ+NLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF V
Sbjct: 576 IEDRNAVLPIEAAIQSNLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 635

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 636 TRERIRQIEAKALRKLKHPSRSRKLRSFLDN 666


>gi|83941156|ref|ZP_00953618.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83955715|ref|ZP_00964295.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83840009|gb|EAP79185.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83846976|gb|EAP84851.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 660

 Score =  535 bits (1379), Expect = e-150,   Method: Composition-based stats.
 Identities = 366/684 (53%), Positives = 480/684 (70%), Gaps = 31/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + D++ +D D     D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 1   MAAKDTNEDAKSDDQDAGHSLDMSQAAVKKMIGEAREKGYITYDQLNTVLPPDQVSSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGINV+  D+  +EE ++   ++A++ SN  V L          TDDPVRM
Sbjct: 61  EDVMSMLSEMGINVI-EDEEAEEEDAKGGTEIATTESNRDVALSSGTSEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +                          D+ + T     +  +    + + 
Sbjct: 180 VIDLEATFGTQMG------------------------DEEETTPVVPTAGTETKPAESTS 215

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
                 N  +++ + ++D++ +  +L+AME  L+P+V+ ALD IA+ Y +L  +QD+ ++
Sbjct: 216 EVDADGNPISNDDDDEDDDEQANMSLAAMEAALKPQVLEALDIIADDYVKLSQIQDSRIS 275

Query: 304 GQKDEK------SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E          + + ++ ++V LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 276 ATLNEDGTFSKTDEEEYQRVRSEIVALVNDLHLHNNRIEALIDQLYGINRRIMQIDSAMV 335

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++  + 
Sbjct: 336 KLADQARINRKEFVDAYRGYELDPNWMERMAEKSGRGWQMFIERSSDKVDELRADMAQVG 395

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 396 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 455

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 456 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 515

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 516 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 575

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 576 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 635

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 QIEAKALRKLKHPSRSRKLRSFLD 659


>gi|84687692|ref|ZP_01015565.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664275|gb|EAQ10766.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 670

 Score =  535 bits (1377), Expect = e-149,   Method: Composition-based stats.
 Identities = 368/686 (53%), Positives = 481/686 (70%), Gaps = 27/686 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K  N D + + +D   + + D    + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 3   AKDANDDQNKDEQDDGSNPMGDMDQAAVKKMIAEAREKGYITYDQLNNVLPPDQVSSEQI 62

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSED-SLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ED ++MLS MGIN+++ ++ ED+      S ++ +     +V +          TDDPVR
Sbjct: 63  EDVMSMLSEMGINIIEDEEAEDDNDDAKGSTEVVAKNQGGAVAVSSGDTEKLDRTDDPVR 122

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL +   LLR
Sbjct: 123 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLNEDILLR 182

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS-KDDR 241
           ++IDL+A  G +                     ++ E +DV +  G+  +    S K D 
Sbjct: 183 DVIDLDATFGRQM-------------------GEDGEDEDVVQGLGEAAATNTESQKKDD 223

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                   N    + + ++++D +  +L+AME  L+P+V+  L+ IA  Y +L  +QD  
Sbjct: 224 GPELDADGNPIAKDDDDEDEDDQANMSLAAMEAALKPRVLETLELIARDYTKLSEMQDLR 283

Query: 302 VNGQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           ++   +E      K+  + + L+ ++V LV  L L+ +RI+ LV+QLY I++RIM  +  
Sbjct: 284 MSATLNEDGSFSDKAEAEYQKLRSEIVLLVNELHLHNNRIEALVDQLYGINRRIMSIDSA 343

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F++ ++G ELDP+W+    + P   W+ F+    D + ++R ++  
Sbjct: 344 MVKLADQARINRREFVDAYRGEELDPNWLERMAEKPGRGWQAFIERSSDKVAELRGDMAQ 403

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ ISEFR IVS V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 404 VGQYVGVDISEFRRIVSQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 463

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 464 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 523

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 524 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 583

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 584 NAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 643

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 644 IRQIEAKALRKLKHPSRSRKLRSFLD 669


>gi|295690890|ref|YP_003594583.1| RNA polymerase sigma 70 factor subunit RpoD [Caulobacter segnis
           ATCC 21756]
 gi|295432793|gb|ADG11965.1| RNA polymerase, sigma 70 subunit, RpoD [Caulobacter segnis ATCC
           21756]
          Length = 652

 Score =  534 bits (1376), Expect = e-149,   Method: Composition-based stats.
 Identities = 376/685 (54%), Positives = 467/685 (68%), Gaps = 38/685 (5%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +    + ++++      D  + D +D   KK IK A+ RGYVT++ELN  LP +EVS + 
Sbjct: 1   MSNNSSAETEAPEATGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDA 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +EDT+AMLS MG+NVV      +E+         ++   ++  +   K +A   TDDPVR
Sbjct: 61  IEDTLAMLSEMGVNVV----EAEEDAEGGEGGEVATRDENTTVITSDKPAAYDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGSGRILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E+IDLE            +G       + E+   E   D+  E                 
Sbjct: 177 EVIDLEGTY------AAINGVAAQPAAEDEEGPAEPIDDEAGE----------------- 213

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA- 301
              + PE AE ++ +  +D   +  T+SAME +LR  VM  LD IA  +   R LQD   
Sbjct: 214 ---AKPEGAEGEDDDDFDD--GAGPTVSAMEGELREGVMAILDAIASEFESFRKLQDKLV 268

Query: 302 ----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                     E      + L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LL
Sbjct: 269 GSRLKGEDLSEADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLL 328

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA SYGI R  FL+ + G EL+P W    K      W  FV  +  SI  IR EI +++
Sbjct: 329 RLADSYGISRAEFLKAYFGSELNPTWGEQVKAMGVR-WTKFVENDNSSISDIRQEIAALA 387

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETG+ I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 388 TETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 447

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R
Sbjct: 448 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 507

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA
Sbjct: 508 QMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 567

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 568 VLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 627

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 628 QIEAKALRKLKHPSRSRKLRSFLDS 652


>gi|83309796|ref|YP_420060.1| RNA polymerase sigma factor RpoD [Magnetospirillum magneticum
           AMB-1]
 gi|82944637|dbj|BAE49501.1| DNA-directed RNA polymerase [Magnetospirillum magneticum AMB-1]
          Length = 679

 Score =  534 bits (1376), Expect = e-149,   Method: Composition-based stats.
 Identities = 372/686 (54%), Positives = 475/686 (69%), Gaps = 13/686 (1%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        +     +++ D  + D    + KKM+   ++RGYVT +ELNA +PP+EVSS
Sbjct: 1   MATKSTNTAEVSENQDEAMDGPLLDTLGVAVKKMVAKGKERGYVTYDELNAAMPPEEVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT+AMLS +GINVV+ ++ ED        +   +   S       +D     TDDP
Sbjct: 61  EQIEDTMAMLSELGINVVESEEGEDNTPEAAEEETTETEGYSGAGNVDEEDL--GRTDDP 118

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +A++ W D L +G  L
Sbjct: 119 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTLRAVVDWHDALVEGKML 178

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDL+A  G +         E    +      +E       E + + E+  K   ++
Sbjct: 179 LRDIIDLDATYGAD-----PEPEELAEVEAEGVIVEEAAPAGAAEAKPEGEAEPKAEGEE 233

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             K +      E +     E+ ++++ +L+AME +L P V+   + IA  + +L  +QD 
Sbjct: 234 GEKEEGAEGEPEVEGEGEAEEGEENSISLAAMETELLPIVLETFEVIAATHHKLEKVQDQ 293

Query: 301 AVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +      ++       K   LK +LV+L+  + LN +RI+ LVEQL  +++R+M  EG 
Sbjct: 294 RLAALNKGEAVTPAMEKKYDKLKLELVRLMDGIHLNNARIEQLVEQLNGLNRRLMMQEGR 353

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           LLRLA+S  +KR  FL+ + G ELDP+W+       + +WK+F A        IR  I  
Sbjct: 354 LLRLAESCRVKRQDFLDAYYGSELDPNWIEQVTQRSK-QWKDFGARHGKDAADIRATIAD 412

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           IS E G+ ISE+R IV  V++GE EAS AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 413 ISAEAGLPISEYRRIVQTVQRGEREASRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQ 472

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 473 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 532

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REPTPEE+A+KL+MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 533 SRQMLHEIGREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 592

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLD+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 593 NAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 652

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 653 IRQIEAKALRKLKHPSRSRKLRSFLD 678


>gi|259416365|ref|ZP_05740285.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
 gi|259347804|gb|EEW59581.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
          Length = 664

 Score =  534 bits (1375), Expect = e-149,   Method: Composition-based stats.
 Identities = 369/677 (54%), Positives = 481/677 (71%), Gaps = 26/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +D D  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDRKPDDQDAEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN+++ +D E+EE  + + +L ++ SN  V +          TDDPVRMYLREMGS
Sbjct: 67  SEMGINIIEDEDAEEEEN-KGTTELVTTESNREVAVAGTGTEKLDRTDDPVRMYLREMGS 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW DEL     LLR++IDLEA 
Sbjct: 126 VELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHDELLSEDILLRDVIDLEAT 185

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +                     +E +  +       +  AAK  KD   ++D+    
Sbjct: 186 FGNQMD-------------------EEGDVAEPVVDPSAVSGAAKPEKDSGPELDADGNP 226

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             N++ + D+D+D +  +L+AME  L+ +V+  L+ I+  +  L  +QD  ++   +E  
Sbjct: 227 ILNNDDDDDDDDDQANMSLAAMEAALKDRVLETLERISNDFVTLSEMQDLRISATLNEDG 286

Query: 311 S------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S       + + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA    
Sbjct: 287 SFSKDDEARYQQLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSAMVKLADQAR 346

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++GRELDP+W++   + P   W+ F+    D + ++R+++  +    G+ I
Sbjct: 347 INRKEFVEAYRGRELDPNWLAEMGEKPGRGWQMFIERSTDKVEELRSDMAQVGQYVGLDI 406

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 407 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 466

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 467 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 526

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 527 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 586

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 587 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 646

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 647 RKLKHPSRSRKLRSFLD 663


>gi|144900406|emb|CAM77270.1| RNA polymerase sigma factor rpod [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 664

 Score =  534 bits (1374), Expect = e-149,   Method: Composition-based stats.
 Identities = 371/686 (54%), Positives = 472/686 (68%), Gaps = 28/686 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    +   + +   E++ D  + D    + KKM+   R+RGYVT +ELNA LPPDEVSS
Sbjct: 1   MATKTQNTAEVNESQEENLDGPLLDALGVAVKKMVTRGRERGYVTYDELNAALPPDEVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT+AMLS MGINVV+ ++ ++    E   + A  +S +        +     TDDP
Sbjct: 61  EQIEDTMAMLSEMGINVVESEETDEAAAVETEEEEAEPSSGAG----NVDEEDLGRTDDP 116

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +A+I W D L +G  L
Sbjct: 117 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTIRAIIEWHDALQNGRML 176

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDL+A  G    G                     E +       +  +AA    ++
Sbjct: 177 LRDIIDLDATYGSGPGGEL------------------SEEEMEAGPAEEEPAAAPAEGEE 218

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            ++   P       E   D + +D++ +L+AME QL P+V+   + IA  +  +  LQ +
Sbjct: 219 GAEPRDPNAPEGEVEGEGDGEGEDNSISLAAMEAQLMPQVLETFEAIAANFLRMEKLQKD 278

Query: 301 AVNG-----QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +            +  K   LK ++V+L+  + LN +RI+ LV+ +  ++KR+M  EG 
Sbjct: 279 RMAALSKGDTVSAATEKKYDKLKAEMVRLMEDVHLNNARIEQLVDHMNGLNKRLMGFEGR 338

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           LLRLA+S  +KR  FL+ + G ELDP+W+          WK+F       +  IR +I  
Sbjct: 339 LLRLAESCKVKRQDFLDSYFGSELDPNWLETVA-VKSKHWKDFSEKHRRDVGDIRTQIGV 397

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +S E G+ I+EFR I+  V++GE EAS AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 398 VSGEAGLPITEFRRIIQTVQRGEREASKAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQ 457

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 458 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 517

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REPTPEE+A+KL+MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 518 SRQMLHEIGREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 577

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLD+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 578 NAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 637

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 IRQIEAKALRKLKHPSRSRKLRSFLD 663


>gi|163747450|ref|ZP_02154802.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
 gi|161379303|gb|EDQ03720.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
          Length = 671

 Score =  534 bits (1374), Expect = e-149,   Method: Composition-based stats.
 Identities = 371/684 (54%), Positives = 485/684 (70%), Gaps = 31/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + D++ +DSD     D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 12  MAAKDTNDDAKTDDSDSGHSLDMSQAAVKKMIGEAREKGYITYDQLNTVLPPDQVSSEQI 71

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN++  D+  +EE ++ S ++A++ SN  V L          TDDPVRM
Sbjct: 72  EDVMSMLSEMGINII-EDEEAEEEEAKGSTEVATTESNRDVALSSGTSEKLDRTDDPVRM 130

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 131 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRD 190

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +                          D+ + T     +A   +K D  K
Sbjct: 191 VIDLEATFGTQMG------------------------DEEETTPVVAPTATSDTKSDEGK 226

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +   +       + D++++ +  +L+AME+ L+P+V+ ALD IA+ Y +L ++QD+ ++
Sbjct: 227 TELDADGHPISSDDDDDEDEQANMSLAAMEEALKPQVLEALDIIADDYEKLSAMQDSRIS 286

Query: 304 GQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S         + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 287 ATLNEDGSFTKDEEAMYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSAMV 346

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++G ELDP+W+    +     W+ F+    + + ++RN++  + 
Sbjct: 347 KLADQARINRKEFVDNYRGYELDPNWMERMAEKSGRGWQMFIERSSEKVDELRNDMAQVG 406

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 407 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 466

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 467 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 526

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 527 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 586

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 587 VLPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 646

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 647 QIEAKALRKLKHPSRSRKLRSFLD 670


>gi|99081981|ref|YP_614135.1| RNA polymerase sigma factor RpoD [Ruegeria sp. TM1040]
 gi|99038261|gb|ABF64873.1| RNA polymerase, sigma 38 subunit, RpoS [Ruegeria sp. TM1040]
          Length = 664

 Score =  533 bits (1373), Expect = e-149,   Method: Composition-based stats.
 Identities = 368/677 (54%), Positives = 476/677 (70%), Gaps = 26/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +D D  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDRKPDDQDAEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN+++ ++ E+EE  + + +L ++ SN  V +          TDDPVRMYLREMGS
Sbjct: 67  SEMGINIIEDEEAEEEEN-KGTTELVTTESNREVAVAGAATEKLDRTDDPVRMYLREMGS 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW DEL     LLR++IDLEA 
Sbjct: 126 VELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHDELLSEDILLRDVIDLEAT 185

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +                                   +  AAK  KD   ++D+    
Sbjct: 186 FGNQMDEDGDVAEPVVDPSA-------------------VSGAAKPEKDSGPELDADGNP 226

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             N++ + D+D+D +  +L+AME  L+ +V+  L+ I+  +  L  +QD  ++   +E  
Sbjct: 227 ILNNDDDDDDDDDQANMSLAAMEAALKDRVLETLERISSDFAMLSEMQDLRISATLNEDG 286

Query: 311 S------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S       K + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA    
Sbjct: 287 SFSADDEAKYQQLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSAMVKLADQAR 346

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++GRELDP+W+S   + P   W+ F+    + + ++R ++  +    G+ I
Sbjct: 347 INRKEFVEAYRGRELDPNWLSEMSEKPGRGWQMFIERSTEKVEELRADMAQVGQYVGLDI 406

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 407 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 466

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 467 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 526

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 527 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 586

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 587 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 646

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 647 RKLKHPSRSRKLRSFLD 663


>gi|163733984|ref|ZP_02141425.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
 gi|161392520|gb|EDQ16848.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
          Length = 660

 Score =  532 bits (1369), Expect = e-149,   Method: Composition-based stats.
 Identities = 370/684 (54%), Positives = 479/684 (70%), Gaps = 31/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + D++ +D D     D S  + KKMI  AR++GY+T ++LN  LPPD+V+SEQ+
Sbjct: 1   MAAKDTNDDAKPDDQDAGHSLDMSQTAVKKMIAEAREKGYITYDQLNTVLPPDQVNSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN +  D+  +EE ++ S +LA++     V L          TDDPVRM
Sbjct: 61  EDVMSMLSEMGIN-IIEDEDAEEEEAKGSTELATTEGTREVTLGSGTSEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMISGLCESPLTFQAITIWRDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +                        E   V E     E AA   ++   +
Sbjct: 180 VIDLEATFGNQL----------------------DEDVSVGEPVVATEGAAPQKEEASPE 217

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +D+      ND+ + +++   +  +L+AME  L+P+V+ ALD IA+ Y +L  +QD+ ++
Sbjct: 218 LDADGNPIANDDDDDEDE--QANMSLAAMEAALKPQVLEALDIIADDYTKLSEMQDSRIS 275

Query: 304 GQKDEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S         + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 276 ATLNEDGSFNAGDEALYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSAMV 335

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++  + 
Sbjct: 336 KLADQARINRREFVDEYRGYELDPNWMERMAEKSGRGWQMFIERSSDKVEELRTDMAQVG 395

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 396 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 455

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 456 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 515

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 516 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 575

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 576 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 635

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 QIEAKALRKLKHPSRSRKLRSFLD 659


>gi|254476970|ref|ZP_05090356.1| Sigma-70, region 3 family [Ruegeria sp. R11]
 gi|214031213|gb|EEB72048.1| Sigma-70, region 3 family [Ruegeria sp. R11]
          Length = 661

 Score =  532 bits (1369), Expect = e-148,   Method: Composition-based stats.
 Identities = 370/677 (54%), Positives = 476/677 (70%), Gaps = 29/677 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDRKPDDQEPEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN++  D+  +EE  + S DL ++ SN  V +   +      TDDPVRMYLREMGS
Sbjct: 67  SEMGINII-EDEEAEEEEQKGSTDLVTTDSNREVAVAGAQTEKLDRTDDPVRMYLREMGS 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA 
Sbjct: 126 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEAT 185

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G                      +Q  E  DV E   D  + A       +  +   + 
Sbjct: 186 FG----------------------NQMDEDGDVAEPVVDTSAVAANKPAKDTGPELDADG 223

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                 + D+D++ +  +L+AME  L+ KV+  L++I+  Y +L  +QD+ ++   +E  
Sbjct: 224 NPIASDDDDDDDEQANMSLAAMEAALKDKVLTTLEQISSDYSQLSEMQDSRISATLNEDG 283

Query: 311 SVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S         + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA    
Sbjct: 284 SFSDNDEQIYQSLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSSMVKLADQAR 343

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++GRELDP+W++   + P   W+ F+    D + ++R ++  +    G+ I
Sbjct: 344 INRREFVEAYRGRELDPNWLADMGEKPGRGWQMFIERSTDKVEELRADMAQVGQYVGLDI 403

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 404 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 463

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 464 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 523

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 524 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 583

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 584 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 643

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 644 RKLKHPSRSRKLRSFLD 660


>gi|254464472|ref|ZP_05077883.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
 gi|206685380|gb|EDZ45862.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
          Length = 662

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 363/677 (53%), Positives = 474/677 (70%), Gaps = 28/677 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +D D  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDRKPDDQDAEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN+++ ++ E+EE  + + DL ++     V L   +      TDDPVRMYLREMGS
Sbjct: 67  SEMGINIIEDEEAEEEEN-KGATDLVTTEGPREVALAGAQTEKLDRTDDPVRMYLREMGS 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA 
Sbjct: 126 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEAT 185

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +                      +++ +D           A          +   + 
Sbjct: 186 FGNQL---------------------DEDGEDAAPVVDPSAVQAAAKPSREEGPELDADG 224

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                 + ++++D +  +L+AME  L+ +V+  L+ I+  + EL  +QD+ ++   +E  
Sbjct: 225 NPISADDDEDEDDQANMSLAAMEAALKDRVLTTLERISTDFAELSEMQDSRISATLNEDG 284

Query: 311 S------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S      V+ + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +++LA    
Sbjct: 285 SFSEQDEVRYQSLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSSMVKLADQAR 344

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F++ ++GRELDP+W+S   + P   W+ F+    D + ++R+++  +    G+ I
Sbjct: 345 INRREFVDAYRGRELDPNWLSEMGEKPGRGWQMFIERSTDKVEELRSDMAQVGQYVGLDI 404

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 405 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 464

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 465 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 524

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 525 REPTPEELADKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 584

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 585 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 644

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 645 RKLKHPSRSRKLRSFLD 661


>gi|254511749|ref|ZP_05123816.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
 gi|221535460|gb|EEE38448.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
          Length = 662

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 365/684 (53%), Positives = 475/684 (69%), Gaps = 29/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + D + ++ +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 1   MAAKDTNEDRKSDEQEQEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN+++ ++ E+EE  + S DL ++     V L   +      TDDPVRM
Sbjct: 61  EDVMSMLSEMGINIIEDEEAEEEEN-KGSTDLVTTEGPREVALAGAQTEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLE   G +                        E  DVQE   D  S      +  + 
Sbjct: 180 VIDLETTFGNQL----------------------DEDGDVQEPVVDTSSVQAAKPEKDTG 217

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +   +       + D+D+D +  +L+AME  L+ +V+  L+ I+  +  L  +QD+ ++
Sbjct: 218 PELDADGNPIASDDDDDDDDQANMSLAAMEAALKDQVLTTLERISNDFAMLSEMQDSRIS 277

Query: 304 GQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E      K     + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 278 ATLNEDGSFSEKDEETYQKLRAEIVELVNGLHLHNNRIEALIDQLYGINRRIMSLDSSMV 337

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++GRELDP+W++   + P   W+ F+      + ++RN++  + 
Sbjct: 338 KLADQARINRREFIDAYRGRELDPNWLAEMAEKPGRGWQMFIERSTAKVEELRNDMAQVG 397

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 398 QYVGLDIPEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 457

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 458 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 517

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 518 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 577

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 578 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 637

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 QIEAKALRKLKHPSRSRKLRSFLD 661


>gi|260434101|ref|ZP_05788072.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417929|gb|EEX11188.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 662

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 368/684 (53%), Positives = 475/684 (69%), Gaps = 29/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + + + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 1   MAAKDTNEERKSDDQEQEISLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN++  D+  +EE  + S DL ++ SN  V L   +      TDDPVRM
Sbjct: 61  EDVMSMLSEMGINII-EDEEAEEEEQKGSTDLVTADSNREVALAGSQAEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAISIWHDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +                        E  DV+E   D            + 
Sbjct: 180 VIDLEATFGNQL----------------------DEDGDVEEPVVDTSKVQAAKPAKDTG 217

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +   +       + D++++ +  +L+AME  L+ +V+  L+ I+  +  L  +QD+ ++
Sbjct: 218 PELDADGNPIASDDDDDEDEQANMSLAAMEAALKDQVLTTLERISNDFAMLSEMQDSRIS 277

Query: 304 GQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I+KR+M  +  ++
Sbjct: 278 ATLNEDGSFSAEDEATYQKLRSEIVELVNGLHLHNNRIEALIDQLYGINKRVMALDSAMV 337

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++GRELDP+W+S     P   W+ F+    D + ++RN++  I 
Sbjct: 338 KLADQARINRREFIDEYRGRELDPNWLSDMAQKPGRGWQMFIERSSDKVEELRNDMAQIG 397

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 398 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 457

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 458 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 517

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 518 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 577

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 578 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 637

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 QIEAKALRKLKHPSRSRKLRSFLD 661


>gi|16127277|ref|NP_421841.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1710678|sp|P52324|RPOD_CAUCR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1079588|gb|AAA82054.1| RNA polymerase principal sigma factor [Caulobacter crescentus CB15]
 gi|13424691|gb|AAK25009.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1585612|prf||2201399A sigma73 factor
          Length = 652

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 367/685 (53%), Positives = 462/685 (67%), Gaps = 38/685 (5%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +    + ++++      D  + D +D   KK IK A+ RGYVT++ELN  LP +EVS + 
Sbjct: 1   MSNNSSAETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDA 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +EDT+AMLS MG+NVV+ ++  +     +     ++   ++  +   K +A   TDDPVR
Sbjct: 61  IEDTLAMLSEMGVNVVEAEEDAENAEGGE----VATRDENTTVIASDKPAAYDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E+IDLE            +G       + ++   E   D+  E + +          D  
Sbjct: 177 EVIDLEGTY------AAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDG 230

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA- 301
                                    T+SAME +LR  VM  LD IA  +   R LQD   
Sbjct: 231 AGP----------------------TVSAMEGELREGVMAILDAIASEFEAFRKLQDKLV 268

Query: 302 ----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                     +      + L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LL
Sbjct: 269 GSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLL 328

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA SYGI R  FL+ + G EL+P W    K      W  FV  +  S+  IR+EI +++
Sbjct: 329 RLADSYGISRGEFLKAYFGSELNPTWSEQVKAMGVR-WTKFVENDSQSVTDIRSEIAALA 387

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETG+ I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 388 TETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 447

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R
Sbjct: 448 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 507

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA
Sbjct: 508 QMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 567

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 568 ILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 627

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 628 QIEAKALRKLKHPSRSRKLRSFLDS 652


>gi|288957899|ref|YP_003448240.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
 gi|288910207|dbj|BAI71696.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
          Length = 670

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 370/686 (53%), Positives = 466/686 (67%), Gaps = 22/686 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M      + +     E+S D  + D    + KKMI   ++RGYVT +ELNA LP D  SS
Sbjct: 1   MATKAANSVEVSETREESADGPLMDGMGLAVKKMIARGKERGYVTYDELNAALPQDSSSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT+AMLS MGIN+V+ ++ + E   E + D                D     TDDP
Sbjct: 61  EQIEDTMAMLSEMGINIVESEEQDSENSGEGASDG------EGRSSGNLDDDDIGRTDDP 114

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+ ++CESPLT +A++ W D L +G  L
Sbjct: 115 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGAICESPLTIRAILEWHDSLMEGKML 174

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDL+A  G            G   ++  +   E               AA    D+
Sbjct: 175 LRDIIDLDATYGG-----------GPDGEEMPEGLAEVVEAAGAAGPAGAAPAADAPADE 223

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                 PP      E   + +E ++A +LSAME  L+P+V+   + I   Y +L  L ++
Sbjct: 224 EGDEPRPPRAEGEGEEGEEGEEGENALSLSAMEAALKPQVIETFENIKATYDKLHKLHES 283

Query: 301 AVNGQKD-----EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +   +      +++  K   LK ++V+L+ ++ LN  RI+ LVEQLY +++++   EG 
Sbjct: 284 RMAAMQRGEDLGKQTDRKYDKLKTEMVELMNTVRLNNQRIEQLVEQLYGLNRKLTGFEGR 343

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           LLR+A    +KR+ FL ++ G ELDP+W+   +      W  F       I K R  I +
Sbjct: 344 LLRMATECRVKREDFLNQYFGHELDPNWLERIRGLNPKTWGKFAEKYDGDIRKTREAISN 403

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ E  + I+EFR IVS V+KGE EAS AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 404 VAEEARLPINEFRRIVSTVQKGEKEASRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 463

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 464 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 523

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REPTPEE+A++L MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 524 SRQMLHEIGREPTPEELAERLMMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 583

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLD+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 584 NAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRER 643

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 644 IRQIEAKALRKLKHPSRSRKLRSFLD 669


>gi|221236078|ref|YP_002518515.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus NA1000]
 gi|220965251|gb|ACL96607.1| RNA polymerase sigma factor rpoD [Caulobacter crescentus NA1000]
          Length = 653

 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 367/685 (53%), Positives = 462/685 (67%), Gaps = 38/685 (5%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +    + ++++      D  + D +D   KK IK A+ RGYVT++ELN  LP +EVS + 
Sbjct: 2   MSNNSSAETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDA 61

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +EDT+AMLS MG+NVV+ ++  +     +     ++   ++  +   K +A   TDDPVR
Sbjct: 62  IEDTLAMLSEMGVNVVEAEEDAENAEGGE----VATRDENTTVIASDKPAAYDRTDDPVR 117

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLR
Sbjct: 118 MYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLR 177

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E+IDLE            +G       + ++   E   D+  E + +          D  
Sbjct: 178 EVIDLEGTY------AAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDG 231

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA- 301
                                    T+SAME +LR  VM  LD IA  +   R LQD   
Sbjct: 232 AGP----------------------TVSAMEGELREGVMAILDAIASEFEAFRKLQDKLV 269

Query: 302 ----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                     +      + L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LL
Sbjct: 270 GSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLL 329

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA SYGI R  FL+ + G EL+P W    K      W  FV  +  S+  IR+EI +++
Sbjct: 330 RLADSYGISRGEFLKAYFGSELNPTWSEQVKAMGVR-WTKFVENDSQSVTDIRSEIAALA 388

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETG+ I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 389 TETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 448

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R
Sbjct: 449 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 508

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA
Sbjct: 509 QMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 568

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 569 ILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 628

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 629 QIEAKALRKLKHPSRSRKLRSFLDS 653


>gi|121601699|ref|YP_989245.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
 gi|120613876|gb|ABM44477.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
          Length = 666

 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 400/691 (57%), Positives = 495/691 (71%), Gaps = 39/691 (5%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
             K+  + +   + S D+   DFSDD+ KKMIKLA++ GYVT++ELNA LP DEV+SEQ+
Sbjct: 3   KVKKKDNLEVMGQGSLDNAPLDFSDDAIKKMIKLAKKNGYVTMDELNAVLPSDEVTSEQI 62

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS---ASNSSVFLQKRKDSADRSTDDP 120
           ED + M S MG+NVVD +D  + E  E  + +       + S       K  A   TDDP
Sbjct: 63  EDILMMFSEMGVNVVDDEDEIEAEHYEGEITVEGGDLVEATSREVATIPKREATDRTDDP 122

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMG++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL +   L
Sbjct: 123 VRMYLREMGAVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELREQRIL 182

Query: 181 LREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LREIIDLE    GPE+K             K+E S  +K+  D+                
Sbjct: 183 LREIIDLEMTYAGPEAKQAPIIERSEVEKIKKEASPSDKDDVDI---------------- 226

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                         D    D+++D+   + +AME++L P++M  L+ IAE Y +LR LQ+
Sbjct: 227 -----------IAEDIGAEDDEDDEVNLSFAAMENELYPQIMETLNFIAETYVKLRKLQN 275

Query: 300 NAVNG--------QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
             V                  K   LK  L++ V SLSLNQ+RI+ LVEQLYDI+KR++H
Sbjct: 276 QHVESSLAACKASDLSSAQKKKSTQLKSDLIQAVKSLSLNQNRIEALVEQLYDINKRLVH 335

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           NEG+L R+A SYGI  + FL+ +QGRELD  WV+Y    P   WK F   EV+ I  +R+
Sbjct: 336 NEGKLKRIANSYGIGHEDFLKEYQGRELDSDWVNYIATLPGSGWKEFSTREVEVIRNLRS 395

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 396 EIQNLAQETAISIGEFRRIVTQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFL 455

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 456 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 515

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +VRT+R++ ++I REPTPEE++ KL+MP+E V+KVLKI KEPISLETP+GDED SHLGDF
Sbjct: 516 IVRTSRQILHEIGREPTPEELSSKLSMPLEKVQKVLKIAKEPISLETPVGDEDDSHLGDF 575

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF V
Sbjct: 576 IEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 635

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 636 TRERIRQIEAKALRKLKHPSRSRKLRSFLDS 666


>gi|110679091|ref|YP_682098.1| RNA polymerase sigma factor RpoD [Roseobacter denitrificans OCh
           114]
 gi|109455207|gb|ABG31412.1| RNA polymerase sigma-70 factor RpoD [Roseobacter denitrificans OCh
           114]
          Length = 661

 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 363/684 (53%), Positives = 471/684 (68%), Gaps = 30/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + D++ +D D     D S  + KKMI  AR++GY+T ++LN  LPPD+V+SEQ+
Sbjct: 1   MAAKDTNDDAKPDDQDAGHSLDMSQAAVKKMIAEAREKGYITYDQLNTVLPPDQVNSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN +  D+  +EE ++ S ++A++     V L          TDDPVRM
Sbjct: 61  EDVMSMLSEMGIN-IIEDEDAEEEEAKGSTEIATTEGTREVTLGSGTSEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMISGLCESPLTFQAITIWRDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +       G    +        +E+   ++      I +     +     
Sbjct: 180 VIDLEATFGNQLDEDVSVGEPVVAADGATAPQKEESSPELDADGNPIANDDDDDE----- 234

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
                             ++ +  +L+AME  L+P+V+ ALD IA  Y +L  +QD+ ++
Sbjct: 235 ------------------DEQANMSLAAMEAALKPQVLEALDIIASDYTKLSEMQDSRIS 276

Query: 304 GQKDEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S         + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 277 ATLNEDGSFDEGDEALYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSAMV 336

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++  + 
Sbjct: 337 KLADQARINRREFVDEYRGYELDPNWMERMTEKSGRGWQMFIERSSDKVEELRADMAQVG 396

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 397 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 456

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 457 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 516

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 517 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 576

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 577 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 636

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 QIEAKALRKLKHPSRSRKLRSFLD 660


>gi|85705219|ref|ZP_01036318.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670092|gb|EAQ24954.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 661

 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 365/677 (53%), Positives = 474/677 (70%), Gaps = 29/677 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + ++SD  +  D S  + K+MI  AR++G++T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDQKPDESDTEVSLDMSQAAVKRMIAEAREKGFITYDQLNEVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN+++ +D E+EEG   S  +A       + L   K+     TDDPVRMYLREMGS
Sbjct: 67  SEMGINIIEAEDAEEEEGR--STAVAEIGRRGEITLGSGKEEKLDRTDDPVRMYLREMGS 124

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA 
Sbjct: 125 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLGEDILLRDVIDLEAT 184

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +          G                       ++ SA      D ++ D   + 
Sbjct: 185 FGTQLGDEDAEPVVG---------------------AANVTSAPGNLGRDDNEPDLDADG 223

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                 + DE+++ +  +L+AME  L+P+V+  LD IA+ Y +L  +QD+ ++   +E  
Sbjct: 224 NPIHSDDDDEEDEQANMSLAAMEAALKPRVLETLDRIADDYAKLSEMQDSRISATLNEDG 283

Query: 311 SVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S         + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +++LA    
Sbjct: 284 SFSREQEQTYQTLRSEIVELVNELHLHNNRIEALIDQLYGINRRIMQIDSAMVKLADQAR 343

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F++ ++GRELDP+W+          W+ F+    + + ++R ++  +    G+ I
Sbjct: 344 INRSEFIDEYRGRELDPNWLDDMARKAGRGWQMFIERSPEKVSELRADMAQVGQYVGLDI 403

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 404 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 463

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 464 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 523

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN + PLDSA
Sbjct: 524 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNVILPLDSA 583

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 584 IQDNLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 643

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 644 RKLKHPSRSRKLRSFLD 660


>gi|254488657|ref|ZP_05101862.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
 gi|214045526|gb|EEB86164.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
          Length = 671

 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 369/684 (53%), Positives = 481/684 (70%), Gaps = 31/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++ + D++ +D +     D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 12  MAAKDTNEDTKSDDQEAGHSLDMSQAAVKKMIGDAREKGYITYDQLNTVLPPDQVSSEQI 71

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN +  D+  +EE ++   DL ++ SN  V L          TDDPVRM
Sbjct: 72  EDVMSMLSEMGIN-IIEDEDAEEEEAKGGTDLTTTDSNRDVTLSSGTSEKLDRTDDPVRM 130

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR+
Sbjct: 131 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRD 190

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +                        + D+       +      + +D S+
Sbjct: 191 VIDLEATFGTQMG----------------------DEDETTPVVPVVSGTEAKTNEDTSE 228

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           VD+      ND+ + +++   +  +L+AME  L+P+V+ ALD IA+ Y +L  +QD+ ++
Sbjct: 229 VDADGNPIANDDDDDEDE--QANMSLAAMEAALKPQVLEALDIIADDYVKLSEIQDSRIS 286

Query: 304 GQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E      K   + + ++ ++V LV  L L+ +RI+ L++QLY I++RIM  +  ++
Sbjct: 287 ATLNEDGSFSKKDEEEYQKVRSEIVLLVNELHLHNNRIEALIDQLYGINRRIMQIDSAMV 346

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R+++  + 
Sbjct: 347 KLADQARINRKEFVDNYRGYELDPNWMERMAEKSGRGWQMFIERSADKVEELRSDMAQVG 406

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 407 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 466

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 467 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 526

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 527 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 586

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 587 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 646

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 647 QIEAKALRKLKHPSRSRKLRSFLD 670


>gi|167648221|ref|YP_001685884.1| RNA polymerase sigma factor RpoD [Caulobacter sp. K31]
 gi|167350651|gb|ABZ73386.1| RNA polymerase, sigma 70 subunit, RpoD [Caulobacter sp. K31]
          Length = 649

 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 369/685 (53%), Positives = 461/685 (67%), Gaps = 41/685 (5%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +       ++       D  + D +D   KK IK A+ RGYVT++ELN  LP +EV+SE 
Sbjct: 1   MSTTTTDGAEPPETGGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVTSEA 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +EDT+AMLS MG+NVV+     +E+          +  ++   +   K +A   TDDPVR
Sbjct: 61  IEDTLAMLSEMGVNVVEA----EEDAETSEGGEVVAREDNQQVITSDKPAAYDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E+IDLE                  +      ++ ++  +   E  G    A     +D  
Sbjct: 177 EVIDLEGTY------------AAINGVAAAPAADDEPAEPSDEEPGSEPKAEGEEDEDDF 224

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA- 301
              + P                   T+SAME +LR  VM  LD IA  +   R LQD   
Sbjct: 225 DDGAGP-------------------TVSAMEGELREGVMAILDAIASEFETFRKLQDKLV 265

Query: 302 ----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                     +      + L   +++ + +L LN +RI+ LVEQLY I+KR++  EG LL
Sbjct: 266 GSRLKGADLSDADRKAYEGLSNTIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLL 325

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA SYGI R  FL+ + G EL+P+W+   K      W  FV  + +S+  IR EI +++
Sbjct: 326 RLADSYGISRSEFLKAYFGSELNPNWIDQVKAMGVR-WTKFVENDTNSVGDIRQEIAALA 384

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETG+ I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 385 TETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 444

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R
Sbjct: 445 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 504

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA
Sbjct: 505 QMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 564

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 565 ILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 624

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 625 QIEAKALRKLKHPSRSRKLRSFLDS 649


>gi|83859451|ref|ZP_00952972.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852898|gb|EAP90751.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 678

 Score =  529 bits (1363), Expect = e-148,   Method: Composition-based stats.
 Identities = 374/697 (53%), Positives = 487/697 (69%), Gaps = 34/697 (4%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M+     N ++ SE++   D  + D +D + K MIK A++RGYVT +ELN  LP +E SS
Sbjct: 1   MSKAAAENAEATSENQ---DGPLLDLTDQTVKAMIKTAKKRGYVTHDELNKVLPSEEFSS 57

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA----------SSASNSSVFLQKRK 110
           EQ+ED +A LS MGI VVD ++  D E S    +            +  + S V   +  
Sbjct: 58  EQIEDILAQLSEMGITVVDSEEDVDNEASSSDDEEDDEDEEKSTAVAKKAKSEVAAGQNT 117

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
            SA   TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+++W
Sbjct: 118 TSAQDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRNAMIRGLCESPLTFEAIMVW 177

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           RDEL +G  LLR+IIDL+A  G                 + + ++   + ++ +  E   
Sbjct: 178 RDELQEGQVLLRDIIDLDATYG---------------GVREDATAVSDDEEEGEGDEAKA 222

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           + A   S D+ S  +   ++    + + D+++D +  +L+AME +LR  VM  LD IA  
Sbjct: 223 DDAEAKSDDESSDSEDGEKSEGESDEDGDDEDDGANMSLAAMEAELRDGVMETLDAIATD 282

Query: 291 YRELRSLQDNAVNG-----QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           +   R LQD  V+         +K       + E++V  + SL LN +RI+ LVEQL  I
Sbjct: 283 FDVFRQLQDRLVSSRLSGKHLSDKDQAAYDDVFERIVANLNSLHLNNARIEALVEQLDAI 342

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
           +K++M  EG+LLR+A+++G+ R  FL+ +QG ELDP+W+       +  W  FV  E   
Sbjct: 343 NKKLMGLEGKLLRMAEAHGVPRTDFLKSYQGHELDPNWLKDMAGKSKA-WGRFVEREEKE 401

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
             ++R +I +++ E+G+ I ++R IV+ V+KG  EA +AKKEMVEANLRLVIS+AKKYTN
Sbjct: 402 AGELREQIATLAQESGVPIDDYRRIVATVQKGAREARVAKKEMVEANLRLVISIAKKYTN 461

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 462 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 521

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+VRT+R+M ++I REPTPEE+A+KL+MP+E VRKV+KI KEPISLETPIGDE+ 
Sbjct: 522 IETINKIVRTSRQMLHEIGREPTPEELAEKLSMPLEKVRKVMKIAKEPISLETPIGDEED 581

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIEDKNAV P+D+AI +NLRETTT VLASLTPREERVLRMRFGIGMNTDHTLEEV
Sbjct: 582 SHLGDFIEDKNAVLPIDAAIHSNLRETTTLVLASLTPREERVLRMRFGIGMNTDHTLEEV 641

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 642 GQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 678


>gi|149914287|ref|ZP_01902818.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
 gi|149811806|gb|EDM71639.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
          Length = 662

 Score =  529 bits (1363), Expect = e-148,   Method: Composition-based stats.
 Identities = 372/685 (54%), Positives = 476/685 (69%), Gaps = 30/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D   + ED +  L  D S  + KKMI  AR++G++T ++LN  LPPD+VSSEQ
Sbjct: 1   MAAKDNDD--QKPEDQEAELSLDMSQAAVKKMIGEAREKGFITYDQLNKVLPPDQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN++  ++ + E+  + S  +A       + L   KD     TDDPVR
Sbjct: 59  IEDVMSMLSEMGINII--EEEDAEDEEQKSTAVAEIGRRGELALGSGKDEKLDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLGEDILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G +            +       + E+  D   E + D    A    DD  
Sbjct: 177 DVIDLEATFGTQMGEDGEAEAVVEAANVTTAPASERRDDGQPELDADGNPIASEDDDDED 236

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           +                     +  +L+AME  L+P+V+  LD IA+ Y +L  +QD+ +
Sbjct: 237 E--------------------QANMSLAAMEAALKPRVLETLDRIADDYEKLSEMQDSRI 276

Query: 303 NGQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E      K     + L+ ++V+LV SL L+ +RI+ L++QLY I++RIM  +G +
Sbjct: 277 SATLNEDGSFSAKQEQTYQTLRSEIVQLVNSLHLHNNRIEALIDQLYGINRRIMQIDGAM 336

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F++ ++GRELDP+W+    +     WK F+   +D + ++R ++  +
Sbjct: 337 VKLADQARINRREFIDEYRGRELDPNWLDDMAEKDGRGWKMFMERSLDKVSELRADMAQV 396

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV+ V+KGE EA +AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 397 GQYVGLDISEFRRIVAQVQKGEKEARLAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 456

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 457 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 516

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 517 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 576

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            V PLDSAIQ NLRETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 577 VVLPLDSAIQDNLRETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 636

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 RQIEAKALRKLKHPSRSRKLRSFLD 661


>gi|84515379|ref|ZP_01002741.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510662|gb|EAQ07117.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 659

 Score =  529 bits (1361), Expect = e-148,   Method: Composition-based stats.
 Identities = 362/680 (53%), Positives = 475/680 (69%), Gaps = 32/680 (4%)

Query: 9   RDSDSEHEDSDDS-LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +D+D   ++  D  +  D S  + K+MI  AR+RGY+T ++LNA LPP++VSS+Q+ED +
Sbjct: 4   KDTDDRKDNDQDGDISLDMSQAAVKRMIADARERGYITYDQLNAVLPPEQVSSDQIEDVM 63

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +MLS MGI V + ++ E+ +      D+A+ + +  V +   +      TDDPVRMYLRE
Sbjct: 64  SMLSEMGIQVTEEEESEESDDGAGGTDIATVSGSRDVTIGGAEAEKLDRTDDPVRMYLRE 123

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDL
Sbjct: 124 MGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDL 183

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           E   G +                           +  E E  + +A+     +    +  
Sbjct: 184 ETTFGNQLG-------------------------EEGEVETVVTAASVSDTKEDGGSELD 218

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +     + + D+D+D +  +L+AME  L+P+V+  L+ IA  + +L  +QD  ++   +
Sbjct: 219 ADGNPISKDDDDDDDDQANMSLAAMEAALKPRVLETLEIIARGFADLSDMQDARMSATLN 278

Query: 308 EKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
           E SS       + + L+ ++V LV SL L+ +RI+ L++QLY I++RIM  +  +++LA 
Sbjct: 279 EDSSFSVKEEERYQTLRSEIVVLVNSLHLHNNRIEALIDQLYGINRRIMSIDSAMVKLAD 338

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              I R  F++ ++GRELDP+W+    +     W+  V    D I ++RN++  +    G
Sbjct: 339 QARINRREFIDEYRGRELDPNWLEQMAEKSGRGWQALVEKSTDKIEELRNDMAQVGQYVG 398

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I+EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 399 VDITEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 458

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M +
Sbjct: 459 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLH 518

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PL
Sbjct: 519 EIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPL 578

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 579 DSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 638

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+KLRSFLD
Sbjct: 639 KALRKLKHPSRSRKLRSFLD 658


>gi|149202116|ref|ZP_01879089.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
 gi|149144214|gb|EDM32245.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
          Length = 661

 Score =  527 bits (1358), Expect = e-147,   Method: Composition-based stats.
 Identities = 367/677 (54%), Positives = 473/677 (69%), Gaps = 29/677 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + E+++  +  D S  + K+MI  AR++G++T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDDKPEEAEAEVSLDMSQAAVKRMIAEAREKGFITYDQLNEVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN+++ +D E+EEG   S  +A       + L   K+     TDDPVRMYLREMGS
Sbjct: 67  SEMGINIIEAEDAEEEEGR--STAVAEIGRRGEITLGSGKEEKLDRTDDPVRMYLREMGS 124

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA 
Sbjct: 125 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLGEDILLRDVIDLEAT 184

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +          G                       ++ SA      D S+ D   + 
Sbjct: 185 FGTQLGDEDAEPVVG---------------------AANVTSAPGGMGRDDSEPDLDADG 223

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                 + DED++ +  +L+AME  L+P+V+  LD IA  Y +L  +QD+ ++   +E  
Sbjct: 224 NPIHSDDDDEDDEQANMSLAAMEAALKPRVLDTLDRIAADYAKLSEMQDSRISATLNEDG 283

Query: 311 S------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S         + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +++LA    
Sbjct: 284 SFSREQEATYQTLRSEIVELVNELHLHNNRIEALIDQLYGINRRIMQIDSAMVKLADQAR 343

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++GRELDP+W+          W+ F+    + + ++R ++  +    G+ I
Sbjct: 344 INRSEFIEEYRGRELDPNWLDDMARKAGRGWQMFIERSPEKVAELRADMAQVGQYVGLDI 403

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 404 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 463

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 464 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 523

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN + PLDSA
Sbjct: 524 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNVILPLDSA 583

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 584 IQDNLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 643

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 644 RKLKHPSRSRKLRSFLD 660


>gi|254293486|ref|YP_003059509.1| RNA polymerase sigma factor RpoD [Hirschia baltica ATCC 49814]
 gi|254042017|gb|ACT58812.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hirschia baltica
           ATCC 49814]
          Length = 683

 Score =  527 bits (1357), Expect = e-147,   Method: Composition-based stats.
 Identities = 370/685 (54%), Positives = 486/685 (70%), Gaps = 15/685 (2%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           + +  + E  ++ D  V D S+ S KK I   + RG++T +ELN  LP DEV+ +Q+ED 
Sbjct: 3   KTKADNEEVAENQDGPVLDLSNASVKKFIAAGKARGFITHDELNKVLPSDEVNPDQIEDV 62

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA-----SNSSVFLQKRKDSADRSTDDPV 121
           ++ LS MGINVVD D+  + +G E S D  +++     + S+      +      TDDPV
Sbjct: 63  MSALSEMGINVVDSDEEGEGDGDEASSDGENASGAVTKAKSTAAATGGRSDRYDRTDDPV 122

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+++WR EL D   LL
Sbjct: 123 RMYLREMGTVELLSREGEIAIAKRIEAGRDAMIRGLCESPLTFEAIMVWRQELEDERVLL 182

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           R+IIDLEA     + G   +     + +K E   +  E+ + +E         +++K  R
Sbjct: 183 RDIIDLEATYAAANGGVPDNSAAAVALEKGEPLEKTPEQLEAEEK----AKQDEIAKKKR 238

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
            +   PPE    ++ + D+ +D  A ++SAME +LR  V   LD +A  ++  R LQ+  
Sbjct: 239 IEEGLPPEEEGKEDDDDDDFDDGGAMSMSAMEAELREGVTDILDNVASEFQAYRRLQEKL 298

Query: 302 VNGQ-----KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           VN          K S +   L++ +++ +  L LN +RI+ LVEQLY I+KR+M  EG L
Sbjct: 299 VNRHMEGKELSPKDSEEYVKLQDDIIENLKKLHLNNARIETLVEQLYAINKRLMGLEGGL 358

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           +RLA ++G+ R  FL+ + G EL+P W +         WK F+A E + + ++R+EI S+
Sbjct: 359 MRLADAHGVPRKSFLDNYFGTELEPDWGTRVSLISAK-WKKFIAAETNKVEEMRSEISSL 417

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           + E G+ I +FR IV+ V+KGE EA +AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 418 AQEMGVPIEDFRRIVATVQKGEREARVAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 477

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 478 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTQ 537

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL +P+E +RKVLKI KEPISLETPIGD++ S+LGDFIEDK 
Sbjct: 538 RQMLHEIGREPTPEELAEKLGLPLEKIRKVLKIAKEPISLETPIGDDEDSNLGDFIEDKM 597

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 598 ALLPVDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 657

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 658 RQIEAKALRKLKHPSRSRKLRSFLD 682


>gi|56696627|ref|YP_166988.1| RNA polymerase sigma factor RpoD [Ruegeria pomeroyi DSS-3]
 gi|56678364|gb|AAV95030.1| RNA polymerase sigma-70 factor RpoD [Ruegeria pomeroyi DSS-3]
          Length = 660

 Score =  527 bits (1356), Expect = e-147,   Method: Composition-based stats.
 Identities = 368/684 (53%), Positives = 473/684 (69%), Gaps = 31/684 (4%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              ++   D + ED +D +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+
Sbjct: 1   MAAKDTAEDQKPEDQEDEVSLDMSQAQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED ++MLS MGIN++  D+  +EE  + S DL ++ SN  V L   +      TDDPVRM
Sbjct: 61  EDVMSMLSEMGINII-EDEEAEEEEQKGSTDLITTESNREVALAGAQAEKLDRTDDPVRM 119

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR+
Sbjct: 120 YLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRD 179

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDLEA  G +                          D+  E      +   V       
Sbjct: 180 VIDLEATFGNQL------------------------DDEDDEPVVATSAVQAVKPQREET 215

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +   +       + ++++D +  +L+AME  L+ KV+  L+ I+  Y +L  +QD+ ++
Sbjct: 216 PEYDADGNPIVTEDDEDEDDQANMSLAAMEAALKDKVLITLERISSDYAQLSEMQDSRIS 275

Query: 304 GQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
              +E  S         + L+ ++V LV  L L+ +RI+ L++QLY I+KR+M  +  ++
Sbjct: 276 ATLNEDGSFSAHDEATYQSLRSEIVLLVNELHLHNNRIEALIDQLYGINKRVMSIDSSMV 335

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +LA    I R  F++ ++GRELDP+W++   + P   W+ F+    D + ++R ++  + 
Sbjct: 336 KLADQARINRREFIDAYRGRELDPNWLAEMAEKPGRGWQMFIERSSDKVEELRADMAQVG 395

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
              G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 396 QYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 455

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R
Sbjct: 456 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGR 515

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA
Sbjct: 516 QMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNA 575

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIR
Sbjct: 576 VLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 635

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 QIEAKALRKLKHPSRSRKLRSFLD 659


>gi|126730240|ref|ZP_01746051.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
 gi|126708973|gb|EBA08028.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
          Length = 667

 Score =  526 bits (1355), Expect = e-147,   Method: Composition-based stats.
 Identities = 369/686 (53%), Positives = 474/686 (69%), Gaps = 27/686 (3%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D+ SE  D ++ +  D S  + KKMI  AR+RGY+T ++LN  LPPD+VSS+Q
Sbjct: 1   MAAKDNEDAKSE--DQEEEISLDMSQAAVKKMIAEARERGYITYDQLNQVLPPDQVSSDQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSED-SLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +ED ++MLS MGI V + D+  +EE +   S DL  +     V L          TDDPV
Sbjct: 59  IEDVMSMLSEMGIQVTEDDEESEEEDANKGSTDLVETKRGGEVALGSGTTEKLDRTDDPV 118

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW +EL     LL
Sbjct: 119 RMYLREMGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHEELLSEDILL 178

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           R++IDLE     +                 +    E   D   ET        K S +  
Sbjct: 179 RDVIDLETTFSGQ--------------MGEDGELDEPVVDASVETSNGEAGTQKKSDEPE 224

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
              D  P + ++DE + ++    +  +L+AME  L+P+V+  LD IA  Y +L  +QD+ 
Sbjct: 225 YDADGNPISRDDDEDDDEQ----ANMSLAAMETALKPRVLETLDRIARDYEQLAEMQDSR 280

Query: 302 VNGQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           ++   +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I+KRIM  +  
Sbjct: 281 ISATLNEDGSFDSDDEATYQKLRGEIVELVNGLHLHNNRIEALIDQLYGINKRIMSIDSA 340

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +++LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R+++  
Sbjct: 341 MVKLADQARINRREFVDEYRGHELDPNWLERMAEKSGRGWQMFIERSADKVEELRSDMAQ 400

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 401 VGQYVGLDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 460

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 461 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 520

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDK
Sbjct: 521 GRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDK 580

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NA+ PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 581 NAILPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 640

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 641 IRQIEAKALRKLKHPSRSRKLRSFLD 666


>gi|83951483|ref|ZP_00960215.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83836489|gb|EAP75786.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 660

 Score =  526 bits (1355), Expect = e-147,   Method: Composition-based stats.
 Identities = 366/685 (53%), Positives = 473/685 (69%), Gaps = 32/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D   + +D D  +  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ
Sbjct: 1   MAAKDNDD--QKPDDQDAEISLDLSQTAIKKMIAEAREKGYITYDQLNQALPPDQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN++  +  + EE  +    LA       V L   K+     TDDPVR
Sbjct: 59  IEDVMSMLSEMGINII--EAEDVEEEEQRVTALAEVGKRGEVTLGSGKEEKLDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLTEDILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G +                      + E ++      ++  A     +   
Sbjct: 177 DVIDLEATFGNQLG--------------------DDEDEEAPVVAANVGEAPGKKSETTQ 216

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           ++D+      +D+   ++D   +  +L+AME  L+P+V+  LD IA  Y +L  +QD+ +
Sbjct: 217 ELDADGNPISSDDDEDEDD--QANMSLAAMEAALKPRVLETLDRIANDYEKLSEMQDSRI 274

Query: 303 NGQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E      K     + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +
Sbjct: 275 SATLNEDGSFSAKQEATYQKLRSEIVELVNELHLHNNRIEALIDQLYGINQRIMSIDSAM 334

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F++ ++GRELDP+W+          W+ F+    + + ++R ++  +
Sbjct: 335 VKLADQARINRREFIDAYRGRELDPNWLDDMASKSGRGWQMFMERSPEKVAELRADMAQV 394

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 395 GQYVGLDISEFRRIVGQVQKGEQEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 454

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 455 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 514

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 515 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 574

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 575 AVLPLDSAIQDNLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 634

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 635 RQIEAKALRKLKHPSRSRKLRSFLD 659


>gi|86137897|ref|ZP_01056473.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
 gi|85825489|gb|EAQ45688.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
          Length = 663

 Score =  526 bits (1355), Expect = e-147,   Method: Composition-based stats.
 Identities = 368/685 (53%), Positives = 471/685 (68%), Gaps = 29/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D   + +D D  +  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ
Sbjct: 1   MAAKDNDDR--KPDDQDAEISLDMSQAAVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN++  D+  +EE  + S +L S+ S   V +          TDDPVR
Sbjct: 59  IEDVMSMLSEMGINII-EDEEVEEEEQKGSTELVSADSPREVAVAGAASEKLDRTDDPVR 117

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMG++ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR
Sbjct: 118 MYLREMGTVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLR 177

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G +                    +    ++  QE + D    A    DD  
Sbjct: 178 DVIDLEATFGNQLDEDGEAEDPVVPVVPGAAPAAPAAKEQTQELDADGNPIASDDDDDED 237

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           +                     +  +L+AME  L+ +V+  L+ I+  + +L  +QD+ +
Sbjct: 238 E--------------------QANMSLAAMEAALKDRVLTTLERISTDFSQLSEMQDSRI 277

Query: 303 NGQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E      K     + L+ ++V+LV  L L+ +RID L++QLY I++R+M  +  +
Sbjct: 278 SATLNEDGSFSKKDEATYQSLRSEIVELVNGLHLHNNRIDALIDQLYGINRRVMQIDSSM 337

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F+E ++GRELDP+W+S   + P   W+ F+    D + ++R ++  +
Sbjct: 338 VKLADQARINRREFVEAYRGRELDPNWLSDMGEKPGRGWQMFIERSTDKVEELRADMAQV 397

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 398 GQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 457

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 458 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 517

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 518 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 577

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 578 AVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 637

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 RQIEAKALRKLKHPSRSRKLRSFLD 662


>gi|163738642|ref|ZP_02146056.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
 gi|161387970|gb|EDQ12325.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
          Length = 662

 Score =  526 bits (1354), Expect = e-147,   Method: Composition-based stats.
 Identities = 368/677 (54%), Positives = 474/677 (70%), Gaps = 28/677 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDRKPDDQEPEISLDMSQTQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN++  D+  +EE  + S +L ++ SN  V +          TDDPVRMYLREMGS
Sbjct: 67  SEMGINII-EDEEAEEEEQKGSTELVTTESNREVAVAGAAAEKLDRTDDPVRMYLREMGS 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA 
Sbjct: 126 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEAT 185

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +                      +++ +  +        AA       +  +   + 
Sbjct: 186 FGNQL---------------------DEDGEVSEPVVDTSAVAANKPAAKETGPELDADG 224

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               + + D+++D +  +L+AME  L+ KV+  L++I+  Y +L  +QD+ ++   +E  
Sbjct: 225 NPIAQDDDDDEDDQANMSLAAMEAALKDKVLTTLEQISSDYAQLSEMQDSRISATLNEDG 284

Query: 311 SVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S         + L+ ++V LV  L L+ +RI+ L++QLY I++R+M  +  +++LA    
Sbjct: 285 SFSARDEQVYQSLRAEIVLLVNELHLHNNRIEALIDQLYGINRRVMSIDSSMVKLADQAR 344

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++GRELDP+W+S   D P   W+ FV    D I ++R ++  +    G+ I
Sbjct: 345 INRREFVEAYRGRELDPNWLSDMGDKPGRGWQMFVERSTDKIEELRADMAQVGQYVGLDI 404

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 405 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 464

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 465 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 524

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 525 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 584

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 585 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 644

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 645 RKLKHPSRSRKLRSFLD 661


>gi|56552519|ref|YP_163358.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241762241|ref|ZP_04760323.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|56544093|gb|AAV90247.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241373288|gb|EER62907.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
          Length = 671

 Score =  526 bits (1354), Expect = e-147,   Method: Composition-based stats.
 Identities = 358/682 (52%), Positives = 476/682 (69%), Gaps = 22/682 (3%)

Query: 8   NRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
              +    +++ D+ + D ++ S +K I  A++RGYVT ++LN  LP D++SSEQ+ED +
Sbjct: 3   ETTTAEAKKNAGDAPLIDLNETSIRKFITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIM 62

Query: 68  AMLSNMGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           + LS MGIN+V+ +D  ++   E  + + +L      S       K      TDDPVRMY
Sbjct: 63  SALSEMGINIVENEDSGEDGQQEEEDAAEELQGDGGTSPAPAITTKKETSDRTDDPVRMY 122

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF  +I W + LN+GT  LREI
Sbjct: 123 LREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREI 182

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           IDL+A +           T+G S  + E+   + + +  +   G          DD    
Sbjct: 183 IDLDAML-----------TQGPSPDQFEEDGDDNDNEISERNAGPTFKEDDDEDDDSEGE 231

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-- 302
               EN +  +R   ++ED++  +L+ ME+QL+P  +    +IA++YR+   LQ+  +  
Sbjct: 232 LD--ENGQRIQRENMDEEDENTLSLAQMEEQLKPASLEKFAKIADLYRQFSVLQNARMRA 289

Query: 303 ---NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              N +  E      + L+E+L   V S+  + +RI+ LVEQLY+ + R+    G++LRL
Sbjct: 290 LGANEEFPEDQENAYQQLREELTAEVESVKFHNARIEFLVEQLYNYNSRLRTLNGQMLRL 349

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A+ Y + RD FL  + G E++  WV       +  W NF   E +SI +IR+E+  I+  
Sbjct: 350 AERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKK-WANFTTSEAESIERIRSEVAEIAQV 408

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+++ E R IV+MV+KGE EA IAK EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 409 TGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 468

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++
Sbjct: 469 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQI 528

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ 
Sbjct: 529 LHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAII 588

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 589 PVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 648

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+K+RSFLD
Sbjct: 649 EAKALRKLKHPSRSRKMRSFLD 670


>gi|260576520|ref|ZP_05844509.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
 gi|259021243|gb|EEW24550.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
          Length = 668

 Score =  526 bits (1354), Expect = e-147,   Method: Composition-based stats.
 Identities = 365/685 (53%), Positives = 473/685 (69%), Gaps = 24/685 (3%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   D   + +++D S   D S  + K+MI  AR+RGY+T ++LNA LPP++ SSEQ
Sbjct: 1   MAVKDTDDGKPDEQEADTS--LDMSQAAVKRMIADARERGYITYDQLNAVLPPEQASSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGINV++ D++++ E +    +L  ++++  + +      A   TDDPVR
Sbjct: 59  IEDVMSMLSEMGINVIENDEIDEGEPA---GELVETSTSREIAVSGASAEALDRTDDPVR 115

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR
Sbjct: 116 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLR 175

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G    G       G                 ++    ++  AA        
Sbjct: 176 DVIDLEATFGRSLDGDDDMVGPGLET-------------GIEAGLDEVGVAAPRRNGADE 222

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
                  N  +   + DED++ SA +L+AME  L+P+V+  L+ IA  Y  L  +QD  +
Sbjct: 223 PELDADGNPISRADDDDEDDEASAMSLAAMEAALKPRVLETLEVIARDYATLAEMQDRRM 282

Query: 303 NGQKDEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   ++ S          + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +
Sbjct: 283 HATMNDASRFSANDEAIYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMAINSGM 342

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA +  I R  F++ +QG ELDP W           W++ +    D + ++R ++  +
Sbjct: 343 VKLADAARINRREFIDEYQGYELDPTWGDRMAAKAGRGWQSLMEKSRDKVEELRADMAQV 402

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 403 GQYIGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 462

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 463 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 522

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 523 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 582

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 583 AILPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 642

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 643 RQIEAKALRKLKHPSRSRKLRSFLD 667


>gi|260753821|ref|YP_003226714.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|258553184|gb|ACV76130.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 671

 Score =  526 bits (1354), Expect = e-147,   Method: Composition-based stats.
 Identities = 358/682 (52%), Positives = 476/682 (69%), Gaps = 22/682 (3%)

Query: 8   NRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
              +    +++ D+ + D ++ S +K I  A++RGYVT ++LN  LP D++SSEQ+ED +
Sbjct: 3   ETTTAEAKKNAGDAPLIDLNETSIRKFITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIM 62

Query: 68  AMLSNMGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           + LS MGIN+V+ +D  ++   E  + + +L      S       K      TDDPVRMY
Sbjct: 63  SALSEMGINIVENEDSGEDGQQEEEDAAEELQGDGGTSPAPAITTKKETSDRTDDPVRMY 122

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF  +I W + LN+GT  LREI
Sbjct: 123 LREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREI 182

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           IDL+A +           T+G S  + E+   + + +  +   G          DD    
Sbjct: 183 IDLDAML-----------TQGPSPDQFEEEGDDNDNEISERNAGPTFKEDDDEDDDSEGE 231

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-- 302
               EN +  +R   ++ED++  +L+ ME+QL+P  +    +IA++YR+   LQ+  +  
Sbjct: 232 LD--ENGQRIQRENMDEEDENTLSLAQMEEQLKPASLEKFAKIADLYRQFSVLQNARMRA 289

Query: 303 ---NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              N +  E      + L+E+L   V S+  + +RI+ LVEQLY+ + R+    G++LRL
Sbjct: 290 LGANEEFPEDQENAYQQLREELTAEVESVKFHNARIEFLVEQLYNYNSRLRTLNGQMLRL 349

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A+ Y + RD FL  + G E++  WV       +  W NF   E +SI +IR+E+  I+  
Sbjct: 350 AERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKK-WANFTTSEAESIERIRSEVAEIAQV 408

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+++ E R IV+MV+KGE EA IAK EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 409 TGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 468

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++
Sbjct: 469 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQI 528

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++I REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ 
Sbjct: 529 LHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAII 588

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 589 PVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 648

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+K+RSFLD
Sbjct: 649 EAKALRKLKHPSRSRKMRSFLD 670


>gi|319406862|emb|CBI80497.1| RNA polymerase sigma factor [Bartonella sp. 1-1C]
          Length = 669

 Score =  525 bits (1353), Expect = e-147,   Method: Composition-based stats.
 Identities = 393/693 (56%), Positives = 488/693 (70%), Gaps = 35/693 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  + +   + S D  + DFSDD+ KKM+KLA++ GYV ++ELNA L  +E +S
Sbjct: 1   MATKVKQKDNVEEMGKVSSDGPLLDFSDDAIKKMMKLAKKNGYVLMDELNAALSSEEFTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRST 117
           EQ+ED +AM S MGI+V+D +D  + E  E+ + +       +         K      T
Sbjct: 61  EQIEDILAMFSEMGISVIDDEDEIEAEQYEEEITVEGGDLVEATNYAVATTSKREVADRT 120

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL + 
Sbjct: 121 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELQEQ 180

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LLREIIDLE               E    + +E++S    RD                
Sbjct: 181 RILLREIIDLEMTYSGPEAKQAPIIDESEVKKIKEETSSSNMRD---------------- 224

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                         E    + DE++D+   +L+AME +L P+V+  LD IAE Y +LR L
Sbjct: 225 --------MDDLEEEIGGEDDDEEDDEVNLSLAAMEHELCPQVVDTLDFIAETYVKLREL 276

Query: 298 QDNAVNGQKDEK--------SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           QD  V      +           +   LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 277 QDQQVESSLSHRKAEPISSEQRKQYTELKDALIQAVKSLSLNQNRIEALVEQLYDINKRL 336

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + +EG+L RLA +YGI  + FL  +QGRELD  WV+Y        WK F  CE   I  +
Sbjct: 337 IQSEGKLKRLASNYGIGHEDFLREYQGRELDADWVNYIATLSGRGWKEFSTCEAKVIQSL 396

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           RNEI++++ ET ISISEFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 397 RNEIQNLAQETAISISEFRRIVTQVQKGEREANIAKKEMVEANLRLVISIAKKYTNRGLQ 456

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 457 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 516

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLG
Sbjct: 517 NKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLG 576

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 577 DFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 636

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 637 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 669


>gi|126738765|ref|ZP_01754461.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
 gi|126719946|gb|EBA16653.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
          Length = 663

 Score =  525 bits (1352), Expect = e-147,   Method: Composition-based stats.
 Identities = 367/685 (53%), Positives = 475/685 (69%), Gaps = 29/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D   + ED +  +  D S  + KKMI  AR++GY+T ++LN  LPPD+VSSEQ
Sbjct: 1   MAAKDNDDR--KPEDQEAEISLDMSQAAVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN+++ +++E+EE  + + DL ++     V L   +      TDDPVR
Sbjct: 59  IEDVMSMLSEMGINIIEDEEVEEEEN-KGATDLVTTEGPREVALAGAQAEKLDRTDDPVR 117

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR
Sbjct: 118 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLR 177

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLE   G +            +       + + E+D+  E + D    A    DD  
Sbjct: 178 DVIDLETTFGNQMDEDGEVDEPVVAPGAAAAPAAKSEKDEGPELDADGNPIASDDDDDED 237

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           +                     +  +L+AME  L+ +V+  L+ I+  + +L  +QD+ +
Sbjct: 238 E--------------------QANMSLAAMEAALKDRVLVTLERISTDFAQLSEMQDSRI 277

Query: 303 NGQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I++R+M  +  +
Sbjct: 278 SATLNEDGSFSSQDEKTYQSLRSEIVELVNGLHLHNNRIEALIDQLYGINRRVMQIDSNM 337

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F+E ++GRELDP+W+S   + P   W+ F+    + +  +R E+  +
Sbjct: 338 VKLADQARINRREFVEAYRGRELDPNWLSEMSEKPGRGWQMFIERSTEKVEDLRAEMAQV 397

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 398 GQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 457

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 458 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 517

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 518 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 577

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 578 AVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 637

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 RQIEAKALRKLKHPSRSRKLRSFLD 662


>gi|159044804|ref|YP_001533598.1| RNA polymerase sigma factor RpoD [Dinoroseobacter shibae DFL 12]
 gi|157912564|gb|ABV93997.1| RNA polymerase sigma factor [Dinoroseobacter shibae DFL 12]
          Length = 664

 Score =  525 bits (1352), Expect = e-147,   Method: Composition-based stats.
 Identities = 370/668 (55%), Positives = 466/668 (69%), Gaps = 28/668 (4%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
             + D S  + KKMI  AR RGY+T ++LN  LPPD+VSSEQ+ED ++MLS MGIN+++ 
Sbjct: 17  EAMLDMSQAAVKKMIAEARTRGYITYDQLNQVLPPDQVSSEQIEDVMSMLSEMGINIIEE 76

Query: 81  DDLEDEEGSED-SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           D+ ED +   + S  +  S+S+  V +          TDDPVRMYLREMGS+ELLSREGE
Sbjct: 77  DEAEDGDAPANASTQVVESSSSREVAVSTSSSETLDRTDDPVRMYLREMGSVELLSREGE 136

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA +G       
Sbjct: 137 IAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEATMG------- 189

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                         +  E E             AA   K D  ++D+          + D
Sbjct: 190 -------------GAMDEDEESSSVVEMAANSPAAPSEKSDEPELDADGNPI-AKTDDED 235

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK------ 313
           +++D +  +L+AME  L+PKV+  LD IA  Y +L  +QD  ++   +E  S        
Sbjct: 236 DEDDQANMSLAAMEAALKPKVLETLDLIARDYAQLSEMQDLRISATLNEDESFSVEDESN 295

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            + L+ ++V LV  L L+ +RI+ L++QLY I++RIM  +  +++LA    I R  F+E 
Sbjct: 296 YQKLRAEIVLLVNELHLHNNRIEALIDQLYGINRRIMAIDSSMVKLADQARINRREFVEA 355

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           ++G ELDP W+    + P   W+ F+      I ++R+++  +    G+ I+EFR IV  
Sbjct: 356 YRGYELDPTWLERMAEKPGRGWQAFIERSTTKIEELRSDMAQVGTYVGVDITEFRRIVQQ 415

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 416 VQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 475

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A
Sbjct: 476 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELA 535

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSAIQ NL+ETT
Sbjct: 536 EKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETT 595

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS
Sbjct: 596 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 655

Query: 674 KKLRSFLD 681
           +KLRSFLD
Sbjct: 656 RKLRSFLD 663


>gi|89070863|ref|ZP_01158102.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89043551|gb|EAR49761.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 657

 Score =  525 bits (1352), Expect = e-147,   Method: Composition-based stats.
 Identities = 366/680 (53%), Positives = 469/680 (68%), Gaps = 34/680 (5%)

Query: 9   RDSDSEHEDSDDS-LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
           +D+D   ED  D  +  D S  + KKMI  AR+RGY+T ++LN+ LPPD+VSS+Q+ED +
Sbjct: 4   KDTDERKEDEQDGAMSLDMSQTAVKKMIADARERGYITYDQLNSVLPPDQVSSDQIEDVM 63

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +MLS MGI V   ++  +E     S DL ++  +  V +   +      TDDPVRMYLRE
Sbjct: 64  SMLSEMGIQVT-EEEESEETEETKSTDLVTTGGSRDVAVSSGETEKLDRTDDPVRMYLRE 122

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL +   LLR++IDL
Sbjct: 123 MGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLNEDILLRDVIDL 182

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           EA  G +                           + +     +E  A          +  
Sbjct: 183 EATFGNQL--------------------------EEEGDTPVVEPGAADGAKKEEGPELD 216

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +     + + ++++D +  +L+AME  L+P+V+  LD IA  +  L  +QD  ++ Q +
Sbjct: 217 ADGNPIAKDDDEDEDDAANMSLAAMEAALKPRVLETLDTIAADFGNLSEMQDARISAQLN 276

Query: 308 EKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
           E SS         + L+ ++V+LV SL L+ +RI+ L++QLY I++RIM  +  +++LA 
Sbjct: 277 EDSSFTEKDEETYQKLRGEIVELVNSLHLHNNRIEALIDQLYGINRRIMSIDSSMVKLAD 336

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              I R  F++ ++G ELDP W+      P   W+ F+      + ++R E+  +    G
Sbjct: 337 QARINRREFIDAYRGYELDPTWLDRMGQNPGRAWQAFIERSTGKVEELRAEMAQVGQYVG 396

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 397 VDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 456

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M +
Sbjct: 457 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLH 516

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PL
Sbjct: 517 EIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPL 576

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEA
Sbjct: 577 DSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 636

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKLKHPSRS+KLRSFLD
Sbjct: 637 KALRKLKHPSRSRKLRSFLD 656


>gi|114570679|ref|YP_757359.1| RNA polymerase sigma factor RpoD [Maricaulis maris MCS10]
 gi|114341141|gb|ABI66421.1| RNA polymerase, sigma 70 subunit, RpoD [Maricaulis maris MCS10]
          Length = 710

 Score =  525 bits (1352), Expect = e-147,   Method: Composition-based stats.
 Identities = 377/716 (52%), Positives = 479/716 (66%), Gaps = 40/716 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M+   + N  ++     + D  + D +D S K M+K A++RGYVT +ELNA LP +E SS
Sbjct: 1   MSKSAEANDATE-----NSDGPLLDLTDQSVKNMVKTAKKRGYVTHDELNAVLPSEEFSS 55

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD--------- 111
           EQ+ED +A LS MGINVVD D   D++ +E       +AS ++      ++         
Sbjct: 56  EQIEDVLAQLSEMGINVVDNDSDVDDDSAETPKPAKGAASAATTSSDDDEEDSDDEEESD 115

Query: 112 ------------------SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                             S+   TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M
Sbjct: 116 SRAVAGASKTAVTGLNTPSSADRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRNAM 175

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           +  LCESPLTF+A+++WRDEL +G  LLR+IIDL+A  G +         E        +
Sbjct: 176 IRGLCESPLTFEAIMVWRDELQEGQVLLRDIIDLDATYGGQQAEAAEDDDENADGTGEGE 235

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS--AHTLSA 271
           +         +    D +      K      D   E+ E    + D+D+D+   + +LSA
Sbjct: 236 TPTPAGGTTPKPESDDEDDGEDGEKKSEKSGDDDEEDGETSSSDDDDDDDEDGVSLSLSA 295

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
           ME +LR  VM  LD IA  +   R LQD  V  + + K     S  K +  +  +V  + 
Sbjct: 296 MEAELRDGVMETLDSIATDFAAFRKLQDKLVAARIEGKDLTKQSREKYEGFQNAIVTNLN 355

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           ++ LN +RI+ LVEQLY I+K  M  EG+LLR+A ++G+ R  F++ + G EL+P W + 
Sbjct: 356 TMHLNNARIEALVEQLYAINKERMALEGKLLRMADAHGVPRAQFMDSYFGNELNPEWPTS 415

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  W  F+  E     KIR+++  ++   G+ I + R IV  V+KGE EA +AKK
Sbjct: 416 MASTSKA-WARFIDREGVDAGKIRDDLADLTQRAGVPIEDLRRIVRTVQKGEREARVAKK 474

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 475 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 534

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKV
Sbjct: 535 AITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKV 594

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQANLRETTTRVLASLTPREER
Sbjct: 595 MKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAIQANLRETTTRVLASLTPREER 654

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 655 VLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN 710


>gi|114764808|ref|ZP_01443990.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114542694|gb|EAU45717.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 661

 Score =  525 bits (1352), Expect = e-147,   Method: Composition-based stats.
 Identities = 365/685 (53%), Positives = 476/685 (69%), Gaps = 31/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D+  E +D  D+   D S  + KKMI  AR+RGY+T ++LN  LPPD+VSS+Q
Sbjct: 1   MAAKDNDDAKPETQD--DAHSLDMSQAAVKKMIAEARERGYITYDQLNQVLPPDQVSSDQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGI V + D+  +E+ ++ S +L  ++    V L    +     TDDPVR
Sbjct: 59  IEDVMSMLSEMGIQVTEEDEEAEEDANKGSTELVDASKGRDVALSSGANEKLDRTDDPVR 118

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IW  EL +   LLR
Sbjct: 119 MYLREMGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWHQELLEEEILLR 178

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLE   G +                      ++E    +       + A+  K D  
Sbjct: 179 DVIDLETTFGNQ---------------------MDEEGGLEEPVVDATAATAEKPKKDEP 217

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           + D+       D+ + DE  + +  +L+AME  L+P+V+  L+ IA  Y +L ++QD  +
Sbjct: 218 EYDADGNPIARDDDDDDE--EQANMSLAAMEAALKPRVLETLERIAGDYEQLAAMQDARI 275

Query: 303 NGQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E  S       + + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +
Sbjct: 276 SATLNEDGSFSQADEAQYQQLRSEIVELVNGLHLHNNRIEALIDQLYGINRRIMSIDSSM 335

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F++ ++G ELDP+W+    + P   W+  +    D I  +R+++  +
Sbjct: 336 VKLADQARINRREFIDEYRGHELDPNWIERMSEKPGRGWQMLIERFEDKIEGLRSDMAQV 395

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 396 GQYVGLDISEFRRIVGQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 455

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 456 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 515

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 516 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 575

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 576 AILPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 635

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 636 RQIEAKALRKLKHPSRSRKLRSFLD 660


>gi|254441274|ref|ZP_05054767.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
 gi|198251352|gb|EDY75667.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
          Length = 655

 Score =  525 bits (1352), Expect = e-147,   Method: Composition-based stats.
 Identities = 367/679 (54%), Positives = 476/679 (70%), Gaps = 34/679 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           +D++ + +D+D S   D S  + KKMI  AR+RG +T ++LNA LPPD+VSS+Q+ED ++
Sbjct: 4   KDTNVQRDDADHS--LDMSQAAVKKMIAEARERGTITYDQLNAVLPPDQVSSDQIEDVMS 61

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           ML+ MGI V + ++ E+ +    S +LA+ A    V L   +      TDDPVRMYLREM
Sbjct: 62  MLNEMGIQVTEEEESEEVDDDGTSKELATVAGGRDVVLGGAEAEKLDRTDDPVRMYLREM 121

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE
Sbjct: 122 GSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLE 181

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              G +                          ++ +ET      +     D++ ++D+  
Sbjct: 182 TTFGDQL------------------------AEETEETAVVSAVSVGEKSDEKPELDADG 217

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
               ND+ + +E+   +  +L+AME QL+P+V+  L+ IA+ + +L  +QD  ++   +E
Sbjct: 218 NPIANDDDDDEEEA--ANLSLAAMEAQLKPQVLDTLEVIAKGFAKLSDMQDLRMSATLNE 275

Query: 309 ------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
                 K   K + L+ ++V+LV SL L+ +RI+ L++QLY I++RIM  +  +++LA  
Sbjct: 276 DDSFSGKEEKKYQKLRSEIVQLVNSLHLHNNRIEALIDQLYGINRRIMQIDSNMVKLADQ 335

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             I R  F++ ++GRELDP W+          W+  +      I ++R E+  +    G+
Sbjct: 336 SRINRREFIDAYRGRELDPSWLDEMGQKAGRGWQMLIERSTTKIEELRAEMAQVGQYVGV 395

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 396 DISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 455

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++
Sbjct: 456 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHE 515

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           I REPTPEE+A KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLD
Sbjct: 516 IGREPTPEELAAKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLD 575

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 576 SAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 635

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS++LRSFLD
Sbjct: 636 ALRKLKHPSRSRRLRSFLD 654


>gi|319405291|emb|CBI78905.1| RNA polymerase sigma factor [Bartonella sp. AR 15-3]
          Length = 669

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 395/694 (56%), Positives = 496/694 (71%), Gaps = 37/694 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  + +   + S D  + DFSDD+ KKMIKLA++ GYV ++ELNA L  +E++S
Sbjct: 1   MATKVKQKDNVEEMGKVSSDGSLLDFSDDAIKKMIKLAQKNGYVMMDELNAALSAEEITS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRST 117
           EQ+ED +AM S MGI+V+D +D  + E  E+ + +       +         K      T
Sbjct: 61  EQIEDILAMFSEMGISVIDDEDEIEAEQYEEEITIEGGDLVEATNYAVATTSKREVADRT 120

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL + 
Sbjct: 121 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELQEQ 180

Query: 178 TTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
             LLREIIDLE    GPE+K       +G   +K ++ +      DV + + DI S    
Sbjct: 181 RILLREIIDLEMTYSGPEAKQAPI--IDGSEVKKIKEETPSSSMHDVNDLKEDIRSEDDD 238

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +DD                           +L+AME +L P+++  LD IAE Y +LR 
Sbjct: 239 EEDDEV-----------------------NLSLAAMEHELCPQIVETLDFIAETYVKLRK 275

Query: 297 LQDNAVNGQKDEKSSV--------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LQD  V      +           +   LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR
Sbjct: 276 LQDQQVESSLSHRKEKLLSSAQRKQYTQLKDALIQAVKSLSLNQNRIEALVEQLYDINKR 335

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           ++H+EG+L RLA +YGI  + FL  +QGRELD  W++Y        WK F  CE  +I  
Sbjct: 336 LIHSEGKLKRLASNYGIGHEDFLREYQGRELDVDWINYITTLSGRGWKEFSTCEAKAIQS 395

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+EI++++ ET ISISEFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGL
Sbjct: 396 LRSEIQNLAQETAISISEFRRIVTQVQKGEREANIAKKEMVEANLRLVISIAKKYTNRGL 455

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 456 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 515

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHL
Sbjct: 516 INKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHL 575

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+NA+ P+D+AIQANLR+TTTR+LASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 576 GDFIEDRNALLPIDAAIQANLRDTTTRILASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 635

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 636 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 669


>gi|319898528|ref|YP_004158621.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
 gi|319402492|emb|CBI76035.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
          Length = 669

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 391/693 (56%), Positives = 481/693 (69%), Gaps = 35/693 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+    +   + S D  + DFSDD+ KKMIKLA++ GYV ++ELNA L  DE +S
Sbjct: 1   MATKVKQKDSVEEMGKVSSDGPLLDFSDDAIKKMIKLAKKNGYVIMDELNAALSADEFTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRST 117
           EQ+EDT+AM S MGINV+D +D  + E  E+ + +       +         K      T
Sbjct: 61  EQIEDTLAMFSEMGINVIDDEDEIESEQYEEEIAIEGGDLVEATNYAVATTSKREVADRT 120

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL + 
Sbjct: 121 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELKEQ 180

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LLREIIDLE               E    + +E++     RD     E          
Sbjct: 181 RILLREIIDLEMTYAGPEAKQAPIIEESEVKKIKEETLSSSMRDMDDIEEDIGGEDDDED 240

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
            D+                           +L+AME++L P+V+  LD IA+ Y +LR L
Sbjct: 241 DDE------------------------VNLSLAAMENELCPQVVETLDFIADTYVKLRKL 276

Query: 298 QDN--------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           QD                     +   LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 277 QDQQVESSLSYRKEEPLSSAQRKQYNQLKDDLIQAVKSLSLNQNRIEALVEQLYDINKRL 336

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           +H+EG+L RLA +YGI  + FL  +QGRELD  WV+Y        WK F  CE   I  +
Sbjct: 337 IHSEGKLKRLASNYGIGHEDFLREYQGRELDADWVNYIAALSGRGWKEFSTCEAKVIQNL 396

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+EI++++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 397 RSEIQNLAQETAISIGEFRRIVTQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQ 456

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 457 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 516

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLG
Sbjct: 517 NKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLG 576

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 577 DFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 636

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 637 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 669


>gi|126733203|ref|ZP_01748950.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
 gi|126716069|gb|EBA12933.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
          Length = 660

 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 362/666 (54%), Positives = 466/666 (69%), Gaps = 29/666 (4%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +  D S  + KKMI  AR+RGY+T ++LNA LPP++VSS+Q+ED ++MLS MGI V + +
Sbjct: 17  ISLDMSQTAVKKMIADARERGYITYDQLNAVLPPEQVSSDQIEDVMSMLSEMGIQVTEEE 76

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           + E+ E ++ +  +A+ A +  V L   +      TDDPVRMYLREMGS+ELLSREGEIA
Sbjct: 77  ESEETEENQGNTAVATVAGSREVTLGGAEAEKLDRTDDPVRMYLREMGSVELLSREGEIA 136

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE   G +       
Sbjct: 137 IAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLETTFGNQLG----- 191

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                              D  +ET     +AA          +   +     + + D++
Sbjct: 192 ------------------EDGEEETVVAAPAAAGTETKKEETQELDADGNPIAKDDDDDE 233

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE------KSSVKCK 315
           ED +  +L+AME  L+P+V+  L+ IA  +  L  +QD  ++   +E      K   K +
Sbjct: 234 EDQANMSLAAMEAALKPRVLETLELIARDFAALSDMQDARMSATLNEDSSFSDKQEKKYQ 293

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
            L+ ++V+LV SL L+ +RI+ L++QLY I++RIM  +  +++LA    I R  F+E ++
Sbjct: 294 KLRSEIVELVNSLHLHNNRIEALIDQLYGINRRIMSIDSSMVKLADQARINRREFIEAYR 353

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           GRELDP+W+    +     W+  +      I ++R ++  +    G+ I+EFR IV  V+
Sbjct: 354 GRELDPNWLDDMGEKSGRGWQMMIEKSTGKIEELRGDMAQVGQYVGVDITEFRRIVQQVQ 413

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 414 KGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 473

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A+K
Sbjct: 474 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAEK 533

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSAIQ NL+ETTTR
Sbjct: 534 LQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSAIQENLKETTTR 593

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+K
Sbjct: 594 VLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRK 653

Query: 676 LRSFLD 681
           LRSFLD
Sbjct: 654 LRSFLD 659


>gi|329114160|ref|ZP_08242922.1| RNA polymerase sigma factor RpoD [Acetobacter pomorum DM001]
 gi|326696236|gb|EGE47915.1| RNA polymerase sigma factor RpoD [Acetobacter pomorum DM001]
          Length = 672

 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 356/693 (51%), Positives = 465/693 (67%), Gaps = 47/693 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              +   +++  E   D+ + D    + KK+I   R+RG +T +ELNA LP D++SSEQ+
Sbjct: 10  MATKTASTNAAQEQDGDTTLLDTRSSAVKKLIAKGRERGCITFDELNAVLPQDKMSSEQI 69

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK----------DSA 113
           ED +A+LS MGI VV+ +D ++EE         S  +++    +               +
Sbjct: 70  EDIMAVLSEMGIQVVENEDNDNEEAEPKKAAAESEDADAEEEAETEAEAESPTGNVNAES 129

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + 
Sbjct: 130 VGRTDDPVRMYLREMGTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEM 189

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           + +   LLR+I+DLEA            G +G   +   DS  E+  +   E EGDIES 
Sbjct: 190 IRNNEMLLRDIVDLEAM--QSGGNPLEEGGDGTFNEAESDSDSEEAEEPETEGEGDIES- 246

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                                        + S  +LSA+E++L+P+++   DEI  +Y  
Sbjct: 247 -----------------------------EGSGLSLSALEEKLKPEILAHFDEIEPLYAA 277

Query: 294 LRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ   +      +            L+EKLV  V  + L+ +RI+ LV QL  + ++
Sbjct: 278 LRKLQVQRIEALTSGEDVDGNFEENYVALREKLVGKVEQVHLHNNRIEDLVAQLKQMFQK 337

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           +   EG +LRLA+S  + R+ FL +++GRELDP W+          WKNFVA   ++++ 
Sbjct: 338 LNMLEGRMLRLAESCRVSREDFLLKYRGRELDPGWMDMVSALSGRSWKNFVAKHANTVVD 397

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+++  ++ ETG+ I EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 398 LRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEANLRLVISIAKKYTNRGL 457

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 458 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 517

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 518 INKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 577

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK A+ PLD+AIQ NLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 578 GDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 637

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 FNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670


>gi|58038783|ref|YP_190747.1| RNA polymerase sigma factor RpoD [Gluconobacter oxydans 621H]
 gi|58001197|gb|AAW60091.1| RNA polymerase sigma factor RpoD [Gluconobacter oxydans 621H]
          Length = 652

 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 348/686 (50%), Positives = 457/686 (66%), Gaps = 41/686 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D +++ ++  D+ + D    + K++I   R+RG++T +ELNA LP D++SS
Sbjct: 1   MATKTASGTDRNAQEQE-GDTTLLDTQSAAVKRLIAKGRERGHITFDELNAVLPQDQMSS 59

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+ED +A LS MGI V++ +D ++ E   +                     A   TDDP
Sbjct: 60  EQIEDVMAALSEMGIQVIENEDQDEAEAPAEKEAEGDGEEAEGPQGGNVDAEAASRTDDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLT +A+I W + L DG  L
Sbjct: 120 VRMYLREMGSVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTIRAIISWHERLKDGEML 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+I+DLEA  G                                   G  +  A   ++ 
Sbjct: 180 LRDIVDLEASQG-----------------------------------GGPDPEAVEGEEG 204

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               +      + +E    + ++ S  +LSA+E++L+P+++   + I  +Y +LR LQ  
Sbjct: 205 DEASEEDDTAEDENEEGEGDQQEGSGLSLSALEEKLKPEILARFEAIEPLYHKLRKLQIK 264

Query: 301 AVNGQK-----DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +          +KS    + L+ +LV LV  + L+ +RI+ LV Q+    +++ + EG 
Sbjct: 265 RIEALTGGEDHSDKSEQTYEKLRHELVSLVEQVHLHNNRIEELVAQIKMQVQKLNNVEGR 324

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           ++RLA+S  I RD FL +++ RELDP W+      P   WKN     +D +  +R EI +
Sbjct: 325 MMRLAESCKISRDDFLIKYRSRELDPTWLDSISALPGKGWKNLTTKHMDQLRNLRGEIAA 384

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +S ETG+ + EFR + + + +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 385 LSHETGLPVGEFRRVYATISRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQ 444

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 445 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAKTIRIPVHMIETINKLVRT 504

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 505 SRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 564

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            AV PLD+AIQ NLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 565 TAVIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRER 624

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 625 IRQIEAKALRKLKHPSRSRKLRSFLD 650


>gi|162149105|ref|YP_001603566.1| RNA polymerase sigma factor RpoD [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161787682|emb|CAP57278.1| RNA polymerase sigma factor rpoD (Sigma-A) [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 656

 Score =  524 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 358/688 (52%), Positives = 473/688 (68%), Gaps = 47/688 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++ +  +D +D+ + D    + K++I   ++RGY+T +ELNA LP D++SS
Sbjct: 7   MATKTAAGSEATAGDQD-NDTTLLDTQSGAVKRLIARGKERGYITFDELNAVLPQDQMSS 65

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           EQ+ED +A+LS MGI VV+ +D +D E    E + +  +    +          +   TD
Sbjct: 66  EQIEDVMAVLSEMGIQVVENEDNDDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTD 125

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L  G 
Sbjct: 126 DPVRMYLREMGSVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGE 185

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR+I+DLEA                                  Q    + E+ A+  +
Sbjct: 186 MLLRDIVDLEAM---------------------------------QSGGAEAEAGAEGGE 212

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            +    D+ PE+ + +E       D +  +LSA+E++L+P+++   +EI E+Y  L+ LQ
Sbjct: 213 QEDGSFDAAPESEDGEEG------DSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQ 266

Query: 299 DNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
              +       +  +KS    + L+E+LV  V  + L+ +RI++LV+ L +I +R+   E
Sbjct: 267 SKRLETLTSGAEMSDKSEKSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLE 326

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           G +LRLA+S  + R+ FL +++G ELDP W+      P   WKNFVA    S+L +R ++
Sbjct: 327 GRMLRLAESTKVSREDFLIKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQV 386

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
            S+S ETG+ + EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 387 ASLSQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 446

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 447 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 506

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIE
Sbjct: 507 RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 566

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK AV PLD+AIQ NLRE TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 567 DKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 626

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 627 ERIRQIEAKALRKLKHPSRSRKLRSFLD 654


>gi|209545152|ref|YP_002277381.1| RNA polymerase sigma factor RpoD [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209532829|gb|ACI52766.1| RNA polymerase, sigma 70 subunit, RpoD [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 650

 Score =  524 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 358/688 (52%), Positives = 473/688 (68%), Gaps = 47/688 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        ++ +  +D +D+ + D    + K++I   ++RGY+T +ELNA LP D++SS
Sbjct: 1   MATKTAAGSEATAGDQD-NDTTLLDTQSGAVKRLIARGKERGYITFDELNAVLPQDQMSS 59

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEG--SEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           EQ+ED +A+LS MGI VV+ +D +D E    E + +  +    +          +   TD
Sbjct: 60  EQIEDVMAVLSEMGIQVVENEDNDDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTD 119

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L  G 
Sbjct: 120 DPVRMYLREMGSVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGE 179

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR+I+DLEA                                  Q    + E+ A+  +
Sbjct: 180 MLLRDIVDLEAM---------------------------------QSGGAEAEAGAEGGE 206

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            +    D+ PE+ + +E       D +  +LSA+E++L+P+++   +EI E+Y  L+ LQ
Sbjct: 207 QEDGSFDAAPESEDGEEG------DSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQ 260

Query: 299 DNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
              +       +  +KS    + L+E+LV  V  + L+ +RI++LV+ L +I +R+   E
Sbjct: 261 SKRLETLTSGAEMSDKSEKSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLE 320

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           G +LRLA+S  + R+ FL +++G ELDP W+      P   WKNFVA    S+L +R ++
Sbjct: 321 GRMLRLAESTKVSREDFLIKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQV 380

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
            S+S ETG+ + EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 381 ASLSQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 440

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 441 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 500

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIE
Sbjct: 501 RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 560

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK AV PLD+AIQ NLRE TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 561 DKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 620

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 621 ERIRQIEAKALRKLKHPSRSRKLRSFLD 648


>gi|94498543|ref|ZP_01305098.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
 gi|94421986|gb|EAT07032.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
          Length = 682

 Score =  523 bits (1346), Expect = e-146,   Method: Composition-based stats.
 Identities = 352/691 (50%), Positives = 469/691 (67%), Gaps = 22/691 (3%)

Query: 3   IGKKRNRDS-DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           +  K N  +  +E ED  D+ + D ++ S KK+I  A++RGY+T +ELN  LP D++SSE
Sbjct: 1   MATKANSKTGVAEGEDGGDAPLLDLNEASVKKLIARAKKRGYITYDELNDALPQDQMSSE 60

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDE------EGSEDSLDLASSASNSSVFLQKRKDSADR 115
           Q+ED +A L+ MG+N+V+ ++  ++          +  +  SS  +    + ++K     
Sbjct: 61  QIEDIMAALNEMGVNIVENEEASEDGDEQREREDAEDAEDESSDDDGPKLVTEKKKETVD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP TF A+I W   LN
Sbjct: 121 RTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDTMIFGLCESPTTFNAIIEWSTALN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +G   LREI+DL+A +  +               +  + +      + +E E +     +
Sbjct: 181 NGEMQLREILDLDAMLSKDPAPESLEEGAEDEDGEISEKTAGPSFKEEEEPEEESADGDE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                    D          RN +E+E+D+  +L+ ME+ L+P  +     I +++R   
Sbjct: 241 ---------DEDGLTERRARRNEEEEEEDNTLSLAQMEETLKPMALEKFATITDIFRNFS 291

Query: 296 SLQDNAVNGQKDE-----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
             Q+  +    +      K+    + L+E L   V S+  +Q +I+ LV+QLY  ++R+ 
Sbjct: 292 QAQEARMQAMANGDALSQKAEDDYQALRESLTAEVESVQFHQQKIEYLVDQLYAYNRRLT 351

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
              G++LRLA+ + + R  FL+R+   ELD  W+       +  W  F A E  S+ +IR
Sbjct: 352 ALGGQMLRLAERHKVSRKDFLDRYVNHELDDGWLDKVSGLDKK-WTAFAAAEGRSVDRIR 410

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           NEI  I+  TG+S+ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 411 NEIAEIAQATGMSLGEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQF 470

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 471 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 530

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+  ++  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGD
Sbjct: 531 KLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGD 590

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDKNA+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 591 FIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 650

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 651 VTRERIRQIEAKALRKLKHPSRSRKMRSFLD 681


>gi|163742972|ref|ZP_02150355.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383655|gb|EDQ08041.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 662

 Score =  522 bits (1344), Expect = e-146,   Method: Composition-based stats.
 Identities = 364/677 (53%), Positives = 474/677 (70%), Gaps = 28/677 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +D +  +  D S    KKMI  AR++GY+T ++LN  LPPD+VSSEQ+ED ++ML
Sbjct: 7   DDRKPDDQEPEISLDMSQTQVKKMIAEAREKGYITYDQLNQVLPPDQVSSEQIEDVMSML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN++  D+  +EE  + S +L ++ SN  V +          TDDPVRMYLREMGS
Sbjct: 67  SEMGINII-EDEEAEEEEQKGSTELVTTESNREVAVAGAAAEKLDRTDDPVRMYLREMGS 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW DEL     LLR++IDLEA 
Sbjct: 126 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHDELLSEDILLRDVIDLEAT 185

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G +                      +++ +  +        AA       +  +   + 
Sbjct: 186 FGNQL---------------------DEDGEVSEPVVDTSAVAANKPAAKETGPELDADG 224

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               + + D+++D +  +L+AME  L+ KV+  L++I+  Y +L  +QD+ ++   +E  
Sbjct: 225 NPIAQDDDDDEDDQANMSLAAMEAALKDKVLTTLEQISSDYAQLSEMQDSRISATLNEDG 284

Query: 311 SVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S         + L+ ++V LV  L L+ +RI+ L++QLY I++R+M  +  +++LA    
Sbjct: 285 SFSARDEQVYQSLRSEIVLLVNELHLHNNRIEALIDQLYGINRRVMSIDSSMVKLADQAR 344

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++GRELDP+W++   + P   W+ FV    + + ++R ++  +    G+ I
Sbjct: 345 INRREFVEAYRGRELDPNWLAEMGEKPGRGWQMFVERSTEKVEELRADMAQVGQYVGLDI 404

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 405 SEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 464

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 465 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 524

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 525 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 584

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 585 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 644

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 645 RKLKHPSRSRKLRSFLD 661


>gi|260425299|ref|ZP_05779279.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
 gi|260423239|gb|EEX16489.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
          Length = 665

 Score =  522 bits (1344), Expect = e-146,   Method: Composition-based stats.
 Identities = 364/688 (52%), Positives = 477/688 (69%), Gaps = 33/688 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D+  + +  DD    D S  + KKMI  AR+RGY+T ++LN  LPPD+VSS+Q
Sbjct: 1   MAAKDNDDA--KPDSQDDGHSLDMSQAAVKKMIAEARERGYITYDQLNQVLPPDQVSSDQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEG---SEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +ED ++MLS MGI V + D+  + +    ++ S +L  ++    V L   ++     TDD
Sbjct: 59  IEDVMSMLSEMGIQVTEDDEEGESDDDKDNKGSTELVDASRGRDVALSSGQNEKLDRTDD 118

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IW  EL +   
Sbjct: 119 PVRMYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWHQELLEEEI 178

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LLR++IDLE   G                      +Q  E  D++ T  D  S +   K 
Sbjct: 179 LLRDVIDLETTFG----------------------NQMDEEGDLEGTVVDTGSGSVSEKP 216

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
            R + +   +       + ++D++ +  +L+AME  L+P+V+  L+ I+  Y EL  +QD
Sbjct: 217 RRDEPELDADGNPIAREDDEDDDEQANMSLAAMETALKPRVLETLERISRDYEELAEMQD 276

Query: 300 NAVNGQKDEKSSVK------CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
             ++   +E  S         + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +
Sbjct: 277 ARISATLNEDGSFSQSDEALYQKLRSEIVELVNGLHLHNNRIEALIDQLYGINRRIMSID 336

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
             +++LA    I R  F++ ++G ELDP+W+    +     W+ F+    D + ++R ++
Sbjct: 337 SSMVKLADQARINRREFVDEYRGNELDPNWMERMNEKSGRGWQMFIERFSDKVEELRADM 396

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +    G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 397 AQVGQYVGLDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDL 456

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 457 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 516

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIE
Sbjct: 517 RTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIE 576

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DKNA+ PLDSAIQ NL+ETTTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 577 DKNAILPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTR 636

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 637 ERIRQIEAKALRKLKHPSRSRKLRSFLD 664


>gi|296116667|ref|ZP_06835277.1| RNA polymerase sigma factor RpoD [Gluconacetobacter hansenii ATCC
           23769]
 gi|295976879|gb|EFG83647.1| RNA polymerase sigma factor RpoD [Gluconacetobacter hansenii ATCC
           23769]
          Length = 659

 Score =  522 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 348/691 (50%), Positives = 459/691 (66%), Gaps = 44/691 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+ S  +D +D+ + D    + K++I   ++RGY+T +ELNA LP D++SS
Sbjct: 1   MATKTAAGTDAASGDQD-NDTTLLDTQSGAVKRLIARGKERGYITFDELNAVLPQDQMSS 59

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----RKDSADR 115
           EQ+ED +A LS MG+ VV+ +D + E     +   A S   +    ++            
Sbjct: 60  EQIEDVMAALSEMGMQVVENEDNDSESDDAAAEPEAKSEEPAEGDSEEPAAGNVDSENLG 119

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L 
Sbjct: 120 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLK 179

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
            G  LLR+I+DLEA     +  G           +    S     +  +           
Sbjct: 180 AGEMLLRDIVDLEAMQSGNAGPGEETEEGEEPASEDSFDSATDNEESEEGEGEGEG---- 235

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                                        +  +LSA+E++L+P+++   +E+  +Y  L 
Sbjct: 236 -----------------------------AGLSLSALEEKLKPEILEQFEEVEALYARLH 266

Query: 296 SLQDNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
            LQ   +      G+   ++    + L+ +LV  V  + L+ +RI++LVE L  I +R+ 
Sbjct: 267 ELQATRLEKLTSGGEISAEAEAAYEQLRCELVGKVQQVHLHNTRIEVLVEHLKAIFQRLN 326

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             EG +LRLA+S  + R+ FL +++GRELDP WV      P   WKNFVA  +++++++R
Sbjct: 327 GLEGRMLRLAESTKVSREDFLLKYRGRELDPGWVDVVSALPGKAWKNFVAKHMETVIRLR 386

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            ++  ++ ETG+ + EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQF
Sbjct: 387 GQVAELTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQF 446

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 447 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 506

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGD
Sbjct: 507 KLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 566

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK AV PLD+AIQ NLRE TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 567 FIEDKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 626

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 627 VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|103486468|ref|YP_616029.1| RNA polymerase sigma factor RpoD [Sphingopyxis alaskensis RB2256]
 gi|98976545|gb|ABF52696.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingopyxis alaskensis
           RB2256]
          Length = 669

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 348/676 (51%), Positives = 470/676 (69%), Gaps = 19/676 (2%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           ++E   D+ + D ++   KK+I   ++RGY+T +ELNA LP DE+SSEQ+ED ++ +S+M
Sbjct: 4   KNEADTDAPLIDLNEADVKKLIARGKKRGYLTYDELNAALPQDEMSSEQIEDIMSAISDM 63

Query: 74  GINVVDGDDLEDEEGS---EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           GIN+V+ D+   EE     +D +D+++   + S    ++K      TDDPVRMYLREMG+
Sbjct: 64  GINIVESDEDVQEEAEQEVDDEVDVSAGTGSVSNPAIEKKKETVDRTDDPVRMYLREMGA 123

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+  LCESPLTF A+I W + LN+G   LREI+DLEA 
Sbjct: 124 VELLSREGEIAIAKRIEAGRDTMILGLCESPLTFNAIIEWSNALNNGDMQLREIVDLEAM 183

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +  +              +  E ++    +D+ +  E                 D   E 
Sbjct: 184 LSKDPAPENLDEEGAEDGEISEKTAGVSFKDEDEVEEEPAADGD----------DEDGEG 233

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK- 309
                 + D+D++D+  +L+AME+ L+P  +     I + ++  + LQ+  +      + 
Sbjct: 234 TSGKRESFDDDDEDNTLSLAAMEELLKPDALEKFANITKSFKAFQKLQEARLEALSSGEE 293

Query: 310 ----SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
               S  K   L+E+L   V S+  + ++I+ LV+QLY  ++R+    G++LRLA+ + +
Sbjct: 294 FPAASEKKYHKLREELTAQVESVQFHGTKIEYLVDQLYSYNRRLTALGGQMLRLAERHKV 353

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL+ + GREL+ +W+       +  W  F   E  ++ +IR EI  I+   G+S++
Sbjct: 354 PRKSFLDHYVGRELEENWLEEVAGIDKK-WAAFAENEAAAVDRIRVEISEIAQAAGMSLT 412

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR +V+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 413 EFRRVVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 472

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR +R+  ++  R
Sbjct: 473 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRCSRQFLHESGR 532

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+A+
Sbjct: 533 EPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVIPVDAAV 592

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 593 QSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 652

Query: 666 KLKHPSRSKKLRSFLD 681
           KLKHPSRS+K+RSFLD
Sbjct: 653 KLKHPSRSRKMRSFLD 668


>gi|330993917|ref|ZP_08317847.1| RNA polymerase sigma factor rpoD [Gluconacetobacter sp. SXCC-1]
 gi|329758863|gb|EGG75377.1| RNA polymerase sigma factor rpoD [Gluconacetobacter sp. SXCC-1]
          Length = 659

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 352/691 (50%), Positives = 463/691 (67%), Gaps = 44/691 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+ S  +D +D+ + D    + KK+I   ++RGY+T +ELNA LP D++SS
Sbjct: 1   MATKTATGTDTASGDQD-NDTTLLDTRSGAVKKLIARGKERGYITFDELNAVLPQDQMSS 59

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV-----FLQKRKDSADR 115
           EQ+ED +A LS MG+ VV+ +D +D E +  +       +                 +  
Sbjct: 60  EQIEDVMAALSEMGMQVVENEDNDDTEAAATADTKGDDTAEEESESEEPAAGNVDTESLG 119

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + L 
Sbjct: 120 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLK 179

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
            G  LLR+I+DLEA                                  Q    D   A +
Sbjct: 180 AGEMLLRDIVDLEAM---------------------------------QSGGNDPAEAVE 206

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                     +  E AE  E   + + + +  +LSA+E++L+P+++    E+  +Y  L 
Sbjct: 207 GEDAFAENDGNEAEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFKEVEALYEALH 266

Query: 296 SLQDNAVNGQK-----DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
            +Q   +           +   + + L+ +LV  V  + L+ +RI++LVE L +I +R+ 
Sbjct: 267 RVQAERLEKFTAGSDISAEEESRYEQLRLELVGKVQQVHLHNARIEVLVEHLKEIFQRLN 326

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
             EG +LRLA+S  + RD FL +++GRELDP W+  A   P   WKNF+A   ++++++R
Sbjct: 327 GLEGRMLRLAESTRVSRDDFLLKYRGRELDPGWMDMAAALPGKSWKNFIAKHGETVIRLR 386

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N++  ++ ETG+ + EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQF
Sbjct: 387 NQVADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQF 446

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 447 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 506

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VRT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGD
Sbjct: 507 KLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 566

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK AV PLD+AIQ NLRE TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF 
Sbjct: 567 FIEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 626

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 627 VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|146276891|ref|YP_001167050.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555132|gb|ABP69745.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 667

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 363/677 (53%), Positives = 461/677 (68%), Gaps = 23/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + ED D     D S  + K+MI  AR+RGY+T ++LN  LP D+VSSEQ+ED +AML
Sbjct: 7   DDGKPEDQDAETSLDMSQAAVKRMIAEARERGYITYDQLNTVLPQDQVSSEQIEDVMAML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGINV+  ++ E EEG      +   + +  + +   +      TDDPVRMYLREMGS
Sbjct: 67  SEMGINVI--ENEEAEEGEPAGELVEQGSGSREIAVAGTQGETLDRTDDPVRMYLREMGS 124

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA 
Sbjct: 125 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEAT 184

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G    G            +   ++          +E ++++                 N
Sbjct: 185 FGRSLDGDDDLDGPEIEEVEVTAAAPSPAPRRTNASEPELDADG---------------N 229

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-- 308
             +     DED++ SA +L+AME  L+P+V+  L+ IA  Y  L  +Q   ++   ++  
Sbjct: 230 PISRAEEEDEDDEASAMSLAAMEAALKPRVLETLELIARDYATLAEMQTKRMSATLNDNI 289

Query: 309 ----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
               +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA +  
Sbjct: 290 RFNPEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLADAAR 349

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E +QG ELDP W           W+  +    D +  +R ++  +    G+ I
Sbjct: 350 INRREFIEEYQGYELDPTWAERMAQKSGRGWQTLMEKSRDKVEDLRGDMAQVGQYVGVDI 409

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 410 SEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 469

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 470 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 529

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSA
Sbjct: 530 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSA 589

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 590 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 649

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 650 RKLKHPSRSRKLRSFLD 666


>gi|258542087|ref|YP_003187520.1| RNA polymerase sigma factor RpoD [Acetobacter pasteurianus IFO
           3283-01]
 gi|256633165|dbj|BAH99140.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-01]
 gi|256636222|dbj|BAI02191.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-03]
 gi|256639277|dbj|BAI05239.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-07]
 gi|256642331|dbj|BAI08286.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-22]
 gi|256645386|dbj|BAI11334.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-26]
 gi|256648441|dbj|BAI14382.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-32]
 gi|256651494|dbj|BAI17428.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-01-42C]
 gi|256654485|dbj|BAI20412.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
           pasteurianus IFO 3283-12]
          Length = 672

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 357/693 (51%), Positives = 464/693 (66%), Gaps = 47/693 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
              +   +++  E   D+ + D    + KK+I   R+RG +T +ELNA LP D++SSEQ+
Sbjct: 10  MATKTASTNAAQEQDGDTTLLDTRSSAVKKLIAKGRERGCITFDELNAVLPQDKMSSEQI 69

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK----------DSA 113
           ED +A+LS MGI VV+ +D ++EE         S  +      +               +
Sbjct: 70  EDIMAVLSEMGIQVVENEDNDNEEAEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAES 129

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+I W + 
Sbjct: 130 VGRTDDPVRMYLREMGTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEM 189

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           + +   LLR+I+DLEA            G +G   +   DS  E+  +   E EGDIES 
Sbjct: 190 IRNNEMLLRDIVDLEAM--QSGGNPLEEGGDGTFNEAESDSESEEAEEPEAEGEGDIES- 246

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                                        + S  +LSA+E++L+P+++   DEI  +Y E
Sbjct: 247 -----------------------------EGSGLSLSALEEKLKPEILAHFDEIEPLYAE 277

Query: 294 LRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           LR LQ   +      +            L+EKLV  V  + L+ +RI+ LV QL  + ++
Sbjct: 278 LRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNNRIEDLVAQLKQMFQK 337

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           +   EG +LRLA+S  + R+ FL +++GRELDP W+          WKNFVA   ++++ 
Sbjct: 338 LNMLEGRMLRLAESCRVSREDFLLKYRGRELDPGWMDMVSGLSGRSWKNFVAKHANTVVG 397

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R+++  ++ ETG+ I EFR + + V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 398 LRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEANLRLVISIAKKYTNRGL 457

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 458 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 517

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 518 INKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 577

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK A+ PLD+AIQ NLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 578 GDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 637

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 FNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670


>gi|254452739|ref|ZP_05066176.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
 gi|198267145|gb|EDY91415.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
          Length = 637

 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 359/662 (54%), Positives = 456/662 (68%), Gaps = 32/662 (4%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S  + KKMI  AR+RG +T ++LNA LPPD+VSS+Q+ED ++ML+ MGI V + ++ E+
Sbjct: 1   MSQAAVKKMIAEARERGTITYDQLNAVLPPDQVSSDQIEDVMSMLNEMGIQVTEEEESEE 60

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +    S +LA+ A    V L   +      TDDPVRMYLREMGS+ELLSREGEIAIAKR
Sbjct: 61  VDDDGTSKELATVAGRRDVILGGAEAEKLDRTDDPVRMYLREMGSVELLSREGEIAIAKR 120

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IEAGR  M+  LCESPLTFQA+ IWRDEL     LLR++IDLE   G +           
Sbjct: 121 IEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLRDVIDLETTFGDQLAEETGESAVV 180

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E S ++++ D   +     +   +                             +
Sbjct: 181 SAAPSAEKSEEKQDLDADGKPIAKDDDDDEEEA--------------------------A 214

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE------KSSVKCKVLKE 319
             +L+AME QL+P+V+  L+ IA+ + +L  +QD+ ++   +E      K   K + L+ 
Sbjct: 215 NLSLAAMEAQLKPQVLDTLEVIAKGFAKLSDMQDSRMSATLNEDDSFSGKEEKKYQKLRS 274

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
           ++V LV SL L+ +RID L++QLY I++RIM  +  +++LA    I R  F++ ++GREL
Sbjct: 275 EVVALVVSLHLHNNRIDALIDQLYGINRRIMQIDSNMVKLADQSRINRREFVDAYRGREL 334

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           DP W+          W+  +      I ++R E+  +    G+ ISEFR IV  V+KGE 
Sbjct: 335 DPTWLEEMGQKAGRGWQMLIERSTTKIEELRAEMAQVGQYVGVDISEFRRIVQQVQKGEK 394

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 395 EARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 454

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A KL MP
Sbjct: 455 ATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAAKLQMP 514

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSAIQ NL+ETTTRVLAS
Sbjct: 515 LEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRVLAS 574

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS++LRSF
Sbjct: 575 LTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRRLRSF 634

Query: 680 LD 681
           LD
Sbjct: 635 LD 636


>gi|302382122|ref|YP_003817945.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302192750|gb|ADL00322.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 652

 Score =  520 bits (1338), Expect = e-145,   Method: Composition-based stats.
 Identities = 367/678 (54%), Positives = 454/678 (66%), Gaps = 33/678 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+    E + D  + D +D   KK IK A+ RGYVT+EELN  LP +EV+ + +EDT+AM
Sbjct: 3   DTQEAPEATTDGPLLDLTDAGVKKFIKQAKARGYVTMEELNKVLPSEEVTPDAIEDTLAM 62

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           LS MG+NVV+      EE + +S     +    +   +         TDDPVRMYLREMG
Sbjct: 63  LSEMGVNVVEA-----EEDAAESTGGELAEKAETSVTEGDAKPTYDRTDDPVRMYLREMG 117

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M++ LCES LTF+A+++WRDEL +   LLRE+IDL+A
Sbjct: 118 SVELLSREGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWRDELANNRILLREVIDLDA 177

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
             G  +     H         +    + +     +      E   +    D         
Sbjct: 178 TYGVLNPSSLPHNQPQPPIPGQPIPPKPEPEPGAEAEADKAEQDEEDEDFDDGGG----- 232

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK--- 306
                             ++SA+E +LR  VM  LD IA  +   R LQ+  V  +    
Sbjct: 233 -----------------MSISALEAELRDGVMETLDAIAGDFDAFRKLQEKLVESRLKGE 275

Query: 307 --DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
               K       L   +   + +L LN +RI+ LVEQLY I+KR++  EG LLRLA SYG
Sbjct: 276 ELSAKDRKAYDTLSAAISGRLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYG 335

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  FL+ +   ELDP W +  KD     W  F   E   I  IR+++ +++VE G+ I
Sbjct: 336 ISRPEFLKAYFTAELDPTWSTRVKDMGVR-WTKFSDNEATQIATIRHDVAAVAVEAGLPI 394

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 395 DDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 454

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I 
Sbjct: 455 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIG 514

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+A
Sbjct: 515 REPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAA 574

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 575 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 634

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKLKHPSRS+KLRSFLD 
Sbjct: 635 RKLKHPSRSRKLRSFLDS 652


>gi|209965297|ref|YP_002298212.1| RNA polymerase sigma factor RpoD [Rhodospirillum centenum SW]
 gi|209958763|gb|ACI99399.1| DNA-directed RNA polymerase, sigma subunit RpoD [Rhodospirillum
           centenum SW]
          Length = 648

 Score =  519 bits (1335), Expect = e-145,   Method: Composition-based stats.
 Identities = 369/686 (53%), Positives = 467/686 (68%), Gaps = 44/686 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M     ++ +     ED  +  + D    + KKMI+  ++RGYVT +ELNA LPPD+ SS
Sbjct: 1   MATKATQSAEVTDTREDEANGPLMDNMAIAVKKMIQRGKERGYVTYDELNAALPPDQSSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT+A LS MGINVV+G++ ED +         +S            D     TDDP
Sbjct: 61  EQIEDTMAQLSEMGINVVEGEEPEDGQ--------DASGDGEGRVSGNLDDDDIGRTDDP 112

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+ ++CESPLT +A+I W   L +G  L
Sbjct: 113 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGAICESPLTIRAIIEWHQSLMEGKML 172

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDL+A  G + + G   G +  + +   +  +  ER                    
Sbjct: 173 LRDIIDLDATYGIDPESGEPTGEDLSAVEAESEEEETPER-------------------- 212

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                      E  E   +  +++   +LSAME +L+PKV+     I E Y +L  +Q+ 
Sbjct: 213 ----------PEGAEGEPEGGDEEGNISLSAMEAELKPKVIETFARIEETYEKLHKVQEQ 262

Query: 301 AVNGQKDEK-----SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +   +  +     S  K   LK +L  LV S+ LN +RI+ LVEQLY ++++++  EG+
Sbjct: 263 RLAVLQRGEELPKGSDKKYDKLKAELTDLVNSVRLNNARIEQLVEQLYGLNRKLLGYEGK 322

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           LLRLA    IKR+ FL  + G ELDP+W+   +   +  W  F       + ++R  I  
Sbjct: 323 LLRLATDCKIKREDFLHHYYGSELDPNWLERCRGLSKS-WGRFADKSSVEVGRVREAISE 381

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ +  + I EFR IVS V+KGE EAS AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 382 VADQVRLPIGEFRRIVSTVQKGEKEASRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 441

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 442 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 501

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REPTPEE+A++L MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 502 SRQMLHEIGREPTPEELAERLMMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 561

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLD+AIQANLRETTTR+LA+LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 562 NAVLPLDAAIQANLRETTTRILATLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 621

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 622 IRQIEAKALRKLKHPSRSRKLRSFLD 647


>gi|148553355|ref|YP_001260937.1| RNA polymerase sigma factor RpoD [Sphingomonas wittichii RW1]
 gi|148498545|gb|ABQ66799.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingomonas wittichii RW1]
          Length = 674

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 349/685 (50%), Positives = 475/685 (69%), Gaps = 24/685 (3%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           +   S+       D+ + D ++ S KK+I  A+++GY+T E+LN  LP D+++S+Q+ED 
Sbjct: 3   KTNGSEGGDRIDGDAPLIDLNEGSLKKLIARAKRKGYITYEQLNEALPQDQMTSDQLEDV 62

Query: 67  VAMLSNMGINVVDGDDL-EDEEGSEDSLDLASSASNSS---VFLQKRKDSADRSTDDPVR 122
           ++ L+ MG+N+V+ +D  EDE+  ED +D  + +             K      TDDPVR
Sbjct: 63  MSALNEMGVNIVENEDAGEDEQPEEDGIDEVAGSEEGDTGPALTTTAKKETVDRTDDPVR 122

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF A+I W + LN+GT  LR
Sbjct: 123 MYLREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPITFNAIIEWSNALNEGTMQLR 182

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           EI+DL+A +                    +  +++ + +   ET G      +  +++ S
Sbjct: 183 EILDLDAMLS-------------KGPTAEQVENEDADAEISAETAGPTFKEEEEPEEEAS 229

Query: 243 KVDSPPENAENDE-RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             +      E    R  ++D++D+  +L+ ME+QL+P  +     I ++Y+    +Q   
Sbjct: 230 ADEDEDSMTERRAPRPQEDDDEDNTLSLAQMEEQLKPMALERFAAITDLYKTFSQVQSAR 289

Query: 302 VNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           V               + + L+E+L   V S+  + ++I+ LV+QLY  ++R+    G++
Sbjct: 290 VAALGVGDDFPAAEEERYQGLREQLTAEVESVQFHGAKIEYLVDQLYSFNRRLTTLGGQM 349

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           LRLA+ + + R  FLE +   E++  W+       +  W NF A E D++ +IRNEI  I
Sbjct: 350 LRLAERHKVPRRDFLEAYVNHEMEDGWLDRVGRIDKK-WANFAANEADAVDRIRNEIGEI 408

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +  TG+++SEFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 409 AQATGMALSEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 468

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+
Sbjct: 469 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTS 528

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++ ++I REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKN
Sbjct: 529 RQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKN 588

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ P+D+AIQ+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 589 AIIPVDAAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 648

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 649 RQIEAKALRKLKHPSRSRKMRSFLD 673


>gi|1237088|emb|CAA92648.1| major sigma factor [Rhodobacter capsulatus]
          Length = 674

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 360/685 (52%), Positives = 463/685 (67%), Gaps = 18/685 (2%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   D+  +    +D+  FD S  + K+MI  A++RGY+TI++LNA +PP+ VS EQ
Sbjct: 1   MAAKDIDDTKPDTAADEDA-SFDMSQAAVKRMIGEAKERGYITIDQLNAVMPPETVSGEQ 59

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGI   +  + E+ E SE    + + + +  + +          TDDPVR
Sbjct: 60  IEDVMSMLSEMGI---NVVEGEEVEESEGGEVVETGSGSREIAVAGAAGETLDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEEILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G         G EG    +  +    +  D          +    S +   
Sbjct: 177 DVIDLEATFGRS-----LDGDEGLEGMEGIEGPVVEGLDLEAAEGAAPAARRPASDEPEY 231

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
             D  P +        ++D+D S  +L+AME  L+PKV+  L+ IA  Y +L  +QD  +
Sbjct: 232 DADGNPIS---RIDEEEDDDDSSNMSLAAMEAALKPKVLETLELIARDYAKLAEMQDLRM 288

Query: 303 NGQKDEKS------SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E            + L+ ++V LV  L L+ +RI+ L++QLY I+++IM  +  +
Sbjct: 289 SATLNEDGTFTVAEEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSIDSGM 348

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA +  I R  F++ ++G ELDP W+      P   W          +  +R+E+  +
Sbjct: 349 VKLADAARINRREFIDEYRGYELDPTWMDRMSAKPARAWVTLFEKSRHKVEDLRHEMAQV 408

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 409 GQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 468

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 469 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 528

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIG E+ S LGDFIEDKN
Sbjct: 529 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGHEEDSQLGDFIEDKN 588

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLDSAIQ NL+ETTTRVL SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 589 AILPLDSAIQENLKETTTRVLPSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 648

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KL SFLD
Sbjct: 649 RQIEAKALRKLKHPSRSRKLPSFLD 673


>gi|319403851|emb|CBI77437.1| RNA polymerase sigma factor [Bartonella rochalimae ATCC BAA-1498]
          Length = 669

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 391/693 (56%), Positives = 486/693 (70%), Gaps = 35/693 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K+  + +   + S D  + DFSDD+ KKM+KLA++  YV ++ELNA L  +E +S
Sbjct: 1   MATKVKQKDNVEEMGKVSSDGSLLDFSDDAIKKMMKLAKKNSYVLMDELNAALSSEEFTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRST 117
           EQ+ED +AM S MGI+V+D +D  +    E+ + +       +         K      T
Sbjct: 61  EQIEDILAMFSEMGISVIDDEDEIESGQYEEEITVEGGDLVEATNYAVATTSKREVADRT 120

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQALIIWR+EL + 
Sbjct: 121 DDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWREELQEQ 180

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             LLREIIDLE               E    + +E++S    RD                
Sbjct: 181 RILLREIIDLEMTYSGPEAKQAPIIDESEVKKIKEETSSSSMRD---------------- 224

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                         E    + DE++D+   +L+AME +L P+V+  LD IAE Y +LR L
Sbjct: 225 --------MNDLGEEIGGEDDDEEDDEVNLSLAAMEHELCPQVVETLDFIAETYVKLREL 276

Query: 298 QDNAVNGQKDEK--------SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           QD  V      +           +   LK+ L++ V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 277 QDQQVESSLSHRKAEPLSSEQRKQYTELKDALIQAVKSLSLNQNRIEALVEQLYDINKRL 336

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + +EG+L RLA +YGI  + FL  +QGRELD  WV+Y        WK F  CE   I  +
Sbjct: 337 IQSEGKLKRLASNYGIGHEDFLREYQGRELDADWVNYIATLSGRGWKEFSTCEAKVIQSL 396

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           RNEI++++ ET ISISEFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 397 RNEIQNLAQETAISISEFRRIVTQVQKGEREANIAKKEMVEANLRLVISIAKKYTNRGLQ 456

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 457 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 516

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R++ ++I REPTPEE++ KL+MP+E VRKVLKI KEPISLETP+GDED SHLG
Sbjct: 517 NKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDASHLG 576

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 577 DFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 636

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 637 SVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 669


>gi|294678570|ref|YP_003579185.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
 gi|1173126|sp|P46400|RPOD_RHOCA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|881516|gb|AAA70413.1| RpoD [Rhodobacter capsulatus SB 1003]
 gi|294477390|gb|ADE86778.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
          Length = 674

 Score =  517 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 364/685 (53%), Positives = 467/685 (68%), Gaps = 18/685 (2%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   D+  +    +D+  FD S  + K+MI  A++RGY+TI++LNA +PP+ VS EQ
Sbjct: 1   MAAKDIDDTKPDTAADEDA-SFDMSQAAVKRMIGEAKERGYITIDQLNAVMPPETVSGEQ 59

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGI   +  + E+ E SE    + + + +  + +          TDDPVR
Sbjct: 60  IEDVMSMLSEMGI---NVVEGEEVEESEGGEVVETGSGSREIAVAGAAGETLDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEEILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G         G EG    +  +    +  D          +    S +   
Sbjct: 177 DVIDLEATFGRS-----LDGDEGMEGMEGIEGPVVEGLDLETAEGAAPAARRPASDEPEY 231

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
             D  P +        ++D+D S  +L+AME  L+PKV+  L+ IA  Y +L  +QD  +
Sbjct: 232 DADGNPIS---RIDEEEDDDDSSNMSLAAMEAALKPKVLETLELIARDYAKLAEMQDLRM 288

Query: 303 NGQKDEKS------SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E            + L+ ++V LV  L L+ +RI+ L++QLY I+++IM  +  +
Sbjct: 289 SATLNEDGTFSVAEEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSIDSGM 348

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA +  I R  F++ ++G ELDP W+      P   W        D +  +R+E+  +
Sbjct: 349 VKLADAARINRREFIDEYRGYELDPTWMDRMSAKPARAWVTLFEKSRDKVEDLRHEMAQV 408

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 409 GQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 468

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 469 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 528

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 529 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 588

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 589 AILPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 648

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 649 RQIEAKALRKLKHPSRSRKLRSFLD 673


>gi|255261823|ref|ZP_05341165.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
 gi|255104158|gb|EET46832.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
          Length = 658

 Score =  517 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 365/685 (53%), Positives = 476/685 (69%), Gaps = 34/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N D  S++ D+D  +  D S  + KKMI  AR+RGY+T ++LN  LPP++VSSEQ
Sbjct: 1   MAAKDNDDRKSDNSDAD--ISLDMSQAAVKKMIGEARERGYITYDQLNQVLPPEQVSSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN++  ++  ++E  +   D+ ++  N  V +   +      TDDPVR
Sbjct: 59  IEDVMSMLSEMGINII--EEETEDEEQKGGTDVTTTGGNREVAVSSGETEKLDRTDDPVR 116

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL     LLR
Sbjct: 117 MYLREMGSVELLSREGEIAIAKRIEAGRNTMILGLCESPLTFQAITIWRDELLSEDILLR 176

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLE   G                       Q  E ++          AA   K++  
Sbjct: 177 DVIDLETTFG----------------------DQMGEDEEEAPVVDTTAGAAAPKKEEAQ 214

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           ++D+        + + D++++ +  +L+AME  L+P+V+  LD IA  + +L  +QD  +
Sbjct: 215 ELDADGNPIA--KEDDDDEDEQANMSLAAMEAALKPRVLETLDLIANDFAKLSEMQDARI 272

Query: 303 NGQKDE------KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E      K+    + L+ ++V+LV S+ L+ +RI+ L++QLY I++RIM  +  +
Sbjct: 273 SATLNEDESFSDKAEKSYQKLRSEIVELVNSMHLHNNRIEALIDQLYGINRRIMSIDSSM 332

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F++ ++G ELDP W+    + P   W+  +      I  +R ++  +
Sbjct: 333 VKLADQARINRREFIDAYRGHELDPTWLEQMGEKPGRGWQALIEKSTGKIEDLRADMAQV 392

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 393 GQYIGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 452

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 453 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 512

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 513 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 572

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AV PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 573 AVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 632

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 633 RQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|294011419|ref|YP_003544879.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
 gi|292674749|dbj|BAI96267.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
          Length = 681

 Score =  516 bits (1328), Expect = e-144,   Method: Composition-based stats.
 Identities = 350/692 (50%), Positives = 480/692 (69%), Gaps = 25/692 (3%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N     E +D+ D+ + D ++ S KK+I  A++RGY+T +ELN  LP D++SSEQ
Sbjct: 1   MASKANGKGAGEDQDTGDAPLLDLNEASVKKLIARAKKRGYITYDELNDALPQDQMSSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF------LQKRKDSADRS 116
           +ED ++ L+ MG+N+V+ ++  ++   +       SA +S+        + ++K      
Sbjct: 61  IEDIMSALNEMGVNIVENEEAGEDGDDQRDDGDDDSADDSADDDGSPRPVTEKKKETVDR 120

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP TF A+I W   LN+
Sbjct: 121 TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPTTFNAIIEWSTALNN 180

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   LREI+DL+A +  +            + +  E+ +++ + +  ++T G      + 
Sbjct: 181 GEMQLREILDLDAMLSKD-----------PAPENLEEGAEDDDGEISEKTAGPSFKEEEE 229

Query: 237 SKDDRSKVDSPPEN--AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
            +++ +  D   +        R  +E+E+D+  +L+ ME+ L+P  +     I E++R  
Sbjct: 230 PEEESADTDEDEDGLTERRARRMEEEEEEDNTLSLAQMEETLKPMALEKFATITEIFRTF 289

Query: 295 RSLQDNAVNGQKDE-----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
              Q++ +    +      K+    + L+E+L   V S+  +Q +I+ LV+QLY  ++R+
Sbjct: 290 SKAQESRMAAMANGETLSQKAEDDYQELREQLTAEVESVQFHQQKIEYLVDQLYAYNRRL 349

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
               G++LRLA+ + + R  FL+R+   ELD  W+       +  W  F A E  ++ +I
Sbjct: 350 TALGGQMLRLAERHKVSRKDFLDRYVNHELDDGWLDKVSGLDKK-WAAFAAAEGRAVERI 408

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R E+  I+  TG+S+SEFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 409 RVEVSEIAQATGMSLSEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQ 468

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 469 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 528

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+  ++  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLG
Sbjct: 529 NKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLG 588

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 589 DFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 648

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 649 SVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 680


>gi|197106036|ref|YP_002131413.1| RNA polymerase sigma factor RpoD [Phenylobacterium zucineum HLK1]
 gi|196479456|gb|ACG78984.1| RNA polymerase sigma factor RpoD [Phenylobacterium zucineum HLK1]
          Length = 638

 Score =  516 bits (1328), Expect = e-144,   Method: Composition-based stats.
 Identities = 374/679 (55%), Positives = 463/679 (68%), Gaps = 51/679 (7%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            ++++      D  + D +D + KK IK A+ RGYVT++ELN  +P +EV+SE +EDT+A
Sbjct: 6   AEAETPETTQGDGPLLDLTDAAVKKFIKQAKARGYVTMDELNKVMPSEEVTSEAIEDTLA 65

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           ML+ MG+NVV+ +        ED+     +    S  ++  K+ A   TDDPVRMYLREM
Sbjct: 66  MLNEMGVNVVESE--------EDAEGGEVAVREESAVVETTKEPAYDRTDDPVRMYLREM 117

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLRE+IDLE
Sbjct: 118 GSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELEGGRILLREVIDLE 177

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              G +++G            + E +  E E DD                          
Sbjct: 178 QTYGGQNQGEAPAEAAEAEEPEAEGAEGEGESDD-------------------------- 211

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG---- 304
                      + +D +  T+SAME +LR  VM  LD IA  +   R LQ+  V      
Sbjct: 212 -----------DFDDGAGPTISAMEAELREGVMATLDAIAAEFESFRLLQEKLVAAKLKG 260

Query: 305 -QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
               E      +     +V+ + +L LN +RI+ LVEQLY I+KR+M  EG LLRLA SY
Sbjct: 261 EDLSEGDRKAYQAATGAIVQHLKTLKLNNNRIEALVEQLYAINKRLMVLEGRLLRLADSY 320

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           GI R  FL+ + G E+ P W    K      W  F   +   I +IRNEI +++ ETG+ 
Sbjct: 321 GISRQEFLKAYFGNEMRPDWTDMVKPLGVR-WTKFAENDASQIGEIRNEIAALAQETGVP 379

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 380 IDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 439

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I
Sbjct: 440 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEI 499

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+
Sbjct: 500 GREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDA 559

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 560 AIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 619

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKLKHPSRS+KLRSFLD 
Sbjct: 620 LRKLKHPSRSRKLRSFLDS 638


>gi|315499353|ref|YP_004088157.1| RNA polymerase, sigma 70 subunit, rpod [Asticcacaulis excentricus
           CB 48]
 gi|315417365|gb|ADU14006.1| RNA polymerase, sigma 70 subunit, RpoD [Asticcacaulis excentricus
           CB 48]
          Length = 696

 Score =  516 bits (1328), Expect = e-144,   Method: Composition-based stats.
 Identities = 374/698 (53%), Positives = 464/698 (66%), Gaps = 33/698 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
              E +   D  + D +D   KK IK A+ RGYVT++ELN  LP +E +SEQ+EDT+AML
Sbjct: 6   DKPEADTPSDGPLLDLTDAGVKKFIKNAKARGYVTMDELNKVLPSEEFTSEQIEDTLAML 65

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           + MG+NVVD ++   E G        +    +   +   K SA   TDDPVRMYLREMGS
Sbjct: 66  TEMGVNVVDSEEEATEGGE------IAVREETGGVVVAEKTSAYDRTDDPVRMYLREMGS 119

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A++IWR+EL  G  LLREIIDLE  
Sbjct: 120 VELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMIWREELESGRILLREIIDLEGT 179

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS-------- 242
            G     G   G      ++ +  +    R      +          +            
Sbjct: 180 YGGGPSEGPPPGALDDEAEEEDADAPIAMRAPEPVVKAPELKPEPKPEPQPEAKKPEPKK 239

Query: 243 -------------KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
                         +D   +  + +E   D+ +D +  ++SAME +LR  VM  LD IA 
Sbjct: 240 KADGGDEDEDDYVPMDEEEKKPQPEEEEEDDFDDGAGPSVSAMESELREGVMSTLDAIAG 299

Query: 290 VYRELRSLQDNAVNGQK-----DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            +   R LQ+  +  +      D    V    +   + + + +L LN  RI+ LVEQLY 
Sbjct: 300 EFETYRGLQERILGARLEGLPVDPADKVAYDEVTSAITRHLKTLKLNNQRIEALVEQLYT 359

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           I+KR+M  EG LLRLA SYGI R  FL+ +  RELDP W    +      W+ F   E  
Sbjct: 360 INKRLMSLEGRLLRLADSYGISRQEFLQNYYHRELDPQWTDKVRALGVR-WQKFADNEAG 418

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI +IR +I  ++ + G+++ ++R IV  V+KGE EA  AK EMVEANLRLVIS+AKKYT
Sbjct: 419 SIGRIRADIIQLATDMGVAVDDYRRIVQTVQKGEREARQAKTEMVEANLRLVISIAKKYT 478

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 479 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 538

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+
Sbjct: 539 MIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEE 598

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE
Sbjct: 599 DSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 658

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 659 VGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 696


>gi|114771658|ref|ZP_01449062.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114547730|gb|EAU50620.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 656

 Score =  516 bits (1328), Expect = e-144,   Method: Composition-based stats.
 Identities = 362/678 (53%), Positives = 474/678 (69%), Gaps = 34/678 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            DS  +   +  + D S  + KKMI +AR+RGY+T +ELN  +PPD+V+SEQ+ED ++ML
Sbjct: 5   EDSSKKGEVNEGMGDMSQAAVKKMIAVARERGYITYDELNDVMPPDQVASEQIEDVMSML 64

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN+++ D++EDE  ++ ++    +     V L          TDDPVRMYLREMGS
Sbjct: 65  SEMGINIIEADEVEDEGPTDVTV---VANDAKEVTLAATGKETLDRTDDPVRMYLREMGS 121

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+  LCESPLTFQA+ IWRDEL +   LLR++IDLE  
Sbjct: 122 VELLSREGEIAIAKRIEAGRKTMIEGLCESPLTFQAITIWRDELLEEEILLRDVIDLETT 181

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                                     +   DD     G +  A K S     ++D+    
Sbjct: 182 F------------------------SDTLDDDEDPMVGPLTGAPKPSSSPAHELDADGNR 217

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-- 308
             +DE   ++++D +  +L+AME+ L+P V+  L +IA+ Y +L S+QD  ++   +E  
Sbjct: 218 LNDDEDEDEDEDDAANISLAAMEETLKPDVLATLAKIAKDYNKLASMQDERISATINEDD 277

Query: 309 ----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
               KS    + L+  LV+ V +L  + +RID L++QLY I+++IM  +  ++++A    
Sbjct: 278 TFSDKSEKSYQKLRNSLVEQVNALHFHNNRIDALIDQLYGINRKIMSIDSGMVKIADQSR 337

Query: 365 IKRDVFLERHQGRELDPHWVSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           I R  F+++++G+ELDP W+   A++     WK F+    +   ++R ++  +    G+ 
Sbjct: 338 INRREFVDKYRGQELDPMWLDKIAENEDGRGWKTFIEKHREKAEELRADMAQVGHYVGVD 397

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I EFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 398 IPEFRRIVNQVQKGEKEARSAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 457

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I
Sbjct: 458 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEI 517

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A KL MP++ VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PL+S
Sbjct: 518 GREPTPEELASKLQMPLDKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLES 577

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 578 AIQGNLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 637

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+KLRSFLD
Sbjct: 638 LRKLKHPSRSRKLRSFLD 655


>gi|87200249|ref|YP_497506.1| RNA polymerase sigma factor RpoD [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87135930|gb|ABD26672.1| RNA polymerase, sigma 70 subunit, RpoD [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 667

 Score =  516 bits (1328), Expect = e-144,   Method: Composition-based stats.
 Identities = 355/677 (52%), Positives = 468/677 (69%), Gaps = 18/677 (2%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           + ++  DS D+ + D +D S KK+I  A++RG +T +ELN  LP D++SSEQ+ED +A +
Sbjct: 2   ASNDKTDSGDAPLIDLNDASIKKLIARAKRRGIITYDELNEALPQDQMSSEQIEDIMAAI 61

Query: 71  SNMGINVVDGD-DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           S MG+N+V+ D D  D E      +L  + +        ++      TDDPVRMYLREMG
Sbjct: 62  SEMGVNIVESDEDAVDPEERAQDDELDEAETVEDRPDVIKRKETVERTDDPVRMYLREMG 121

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF A+I W + LN G   LREI+DL+A
Sbjct: 122 AVELLSREGEIAIAKRIEAGRDTMIMGLCESPITFHAIIQWSEALNAGEMQLREILDLDA 181

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            +  E +            +   +  +E E +  + T G      +  +++ +  D   E
Sbjct: 182 MLSKEPQ-----------PENLSEDGEEAEPEISEATAGPTFKEEEDIEEEETADDEDDE 230

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK--- 306
             E   R  +E+E+D+  +L+ ME QL+P  +    EI  ++R+   +Q   +N      
Sbjct: 231 LRERRARPAEEEEEDNTLSLAQMEAQLKPAALERFAEITSLFRQFEKIQAERLNALGMGN 290

Query: 307 --DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
                   + + L+E L   V S+  + S+I+ LV+ LY  ++R+    G++LRLA+ + 
Sbjct: 291 DFPAARETQYQKLREDLTAQVESVQFHASKIEYLVDNLYAFNRRLTTLGGQMLRLAERHK 350

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL+ + GRELD  W+       +  W  F A E   + +IR EI  I+  TG+S+
Sbjct: 351 VPRKDFLDMYVGRELDDGWLQGLAGRDKR-WAAFAANEATPVERIRAEISDIASATGMSL 409

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 410 GEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 469

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++  
Sbjct: 470 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQG 529

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+A
Sbjct: 530 REPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAA 589

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 590 IQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 649

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+K+RSFLD
Sbjct: 650 RKLKHPSRSRKMRSFLD 666


>gi|332185826|ref|ZP_08387573.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
 gi|332014184|gb|EGI56242.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
          Length = 671

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 347/669 (51%), Positives = 473/669 (70%), Gaps = 22/669 (3%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
            + D ++ S KK+I  A++RGY+T ++LN  LP D++SS+Q+ED +A L+ MG+N+V+ +
Sbjct: 15  PLIDLNEASIKKLIARAKKRGYITYDQLNEALPQDQMSSDQLEDIMAALNEMGVNIVENE 74

Query: 82  DLEDEEGSEDSLDLA----SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +  ++   E+  D A       S+S    + +K      TDDPVRMYLREMG++ELLSRE
Sbjct: 75  EQGEDGEGEEEADDAADSVDGDSDSGPQPEAKKKETVDRTDDPVRMYLREMGAVELLSRE 134

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIAIAKRIEAGR  M+  LCESP+TF A+I W   LN+GT  LREI+DL+A +  ++  
Sbjct: 135 GEIAIAKRIEAGRDTMILGLCESPITFNAIIDWSTALNEGTMQLREILDLDAMLSKDAG- 193

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       +     ++ +  ++       +   +   ++ S  D   E  E     
Sbjct: 194 -----------PENLGEDEDDDNGEISAKNAGPQFKEEEEPEEPSVDDEDGEGGERRGPR 242

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN-----AVNGQKDEKSSV 312
            +++E+D+  +L+ ME+ L+P+ +     I  +Y++   +Q       A+ G+       
Sbjct: 243 AEDEEEDNTLSLAQMEETLKPQALEKFANITSIYKKFSKIQQQRLESMALGGELSAADER 302

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           K   L+E+L   V S+  + ++I+ LV+QLY  ++R+    G++LRLA+ + + R  FL+
Sbjct: 303 KYHKLREELTAEVESVQFHNAKIEFLVDQLYAFNRRLTALGGQMLRLAERHKVNRKDFLD 362

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           R+ G ELD +W+   +   +  W NF + E  ++ +IR+EI  IS +TG++++EFR IV+
Sbjct: 363 RYLGHELDENWLDTVRGLDKK-WGNFASNEAATVDRIRSEIAEISQQTGMALTEFRRIVN 421

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 422 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 481

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++  REPTPEE+
Sbjct: 482 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEM 541

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AIQANL+ET
Sbjct: 542 AERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVIPVDAAIQANLKET 601

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 602 VTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 661

Query: 673 SKKLRSFLD 681
           S+K+RSFLD
Sbjct: 662 SRKMRSFLD 670


>gi|77463967|ref|YP_353471.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126462810|ref|YP_001043924.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17029]
 gi|77388385|gb|ABA79570.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126104474|gb|ABN77152.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 668

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 365/677 (53%), Positives = 462/677 (68%), Gaps = 22/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + ED D     D S  + K+MI  AR+RGY+T ++LN  LP D+VSSEQ+ED +AML
Sbjct: 7   DDGKPEDQDAETSLDMSQAAVKRMIAEARERGYITYDQLNTVLPQDQVSSEQIEDVMAML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGINV+  ++ E EEG      +   + +  + +   +      TDDPVRMYLREMGS
Sbjct: 67  SEMGINVI--ENEEAEEGEPAGELVEQGSGSREIAVAGTQGETLDRTDDPVRMYLREMGS 124

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA 
Sbjct: 125 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEAT 184

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G    G      +G    + E ++          +      A                N
Sbjct: 185 FGRSLDGDGDDEIDGPEIDEVEVAAAPAPAPRRSTSSEPELDADG--------------N 230

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-- 308
             +     DED++ SA +L+AME  L+P+V+  L+ IA  Y +L  +Q+  ++   ++  
Sbjct: 231 PISRAEEEDEDDEASAMSLAAMEAALKPRVLETLELIARDYGKLAEMQNRRMSATLNDHI 290

Query: 309 ----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
               +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA +  
Sbjct: 291 RFTTEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLADAAR 350

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F++ +QG ELDP W           W+  +    D +  +R E+  +    G+ I
Sbjct: 351 INRREFIDEYQGYELDPMWAERMAAKSGRGWQTLMEKSRDRVEDLRGEMAQVGQYVGVDI 410

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 411 SEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 470

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 471 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 530

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSA
Sbjct: 531 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSA 590

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 591 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 650

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 651 RKLKHPSRSRKLRSFLD 667


>gi|221639823|ref|YP_002526085.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides KD131]
 gi|332558839|ref|ZP_08413161.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
 gi|221160604|gb|ACM01584.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332276551|gb|EGJ21866.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
          Length = 668

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 365/677 (53%), Positives = 462/677 (68%), Gaps = 22/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + ED D     D S  + K+MI  AR+RGY+T ++LN  LP D+VSSEQ+ED +AML
Sbjct: 7   DDGKPEDQDAETSLDMSQAAVKRMIAEARERGYITYDQLNTVLPQDQVSSEQIEDVMAML 66

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGINV+  ++ E EEG      +   + +  + +   +      TDDPVRMYLREMGS
Sbjct: 67  SEMGINVI--ENEEAEEGEPAGELVEQGSGSREIAVAGTQGETLDRTDDPVRMYLREMGS 124

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA 
Sbjct: 125 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEAT 184

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G    G      +G    + E ++          +      A                N
Sbjct: 185 FGRSLDGDGDDEIDGPEIDEVEVAAAPAPAPRRSASSEPELDADG--------------N 230

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-- 308
             +     DED++ SA +L+AME  L+P+V+  L+ IA  Y +L  +Q+  ++   ++  
Sbjct: 231 PISRAEEEDEDDEASAMSLAAMEAALKPRVLETLELIARDYGKLAEMQNRRMSATLNDHI 290

Query: 309 ----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
               +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA +  
Sbjct: 291 RFTTEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLADAAR 350

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F++ +QG ELDP W           W+  +    D +  +R E+  +    G+ I
Sbjct: 351 INRREFIDEYQGYELDPMWAERMAAKSGRGWQTLMEKSRDRVEDLRGEMAQVGQYVGVDI 410

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 411 SEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 470

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 471 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 530

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSA
Sbjct: 531 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSA 590

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 591 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 650

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 651 RKLKHPSRSRKLRSFLD 667


>gi|329848685|ref|ZP_08263713.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
 gi|328843748|gb|EGF93317.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
          Length = 699

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 372/702 (52%), Positives = 463/702 (65%), Gaps = 36/702 (5%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
               E E S D  + D +D + KK IK A+ RGYVT++ELN  LP +E +SEQ+EDT+AM
Sbjct: 5   AEKPESEASSDGPLLDLTDSAVKKFIKAAKARGYVTMDELNKVLPSEEFTSEQIEDTLAM 64

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L+ MG+NV++ ++              +    S   ++  K SA   TDDPVRMYLREMG
Sbjct: 65  LTEMGVNVIESEE------EAGETTEVAVREESGSLVETAKTSAYDRTDDPVRMYLREMG 118

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+  LCES LTF+A+++WR+EL  G  LLREIIDLE 
Sbjct: 119 SVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGSGRILLREIIDLEG 178

Query: 190 CIGPESK------------------GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
             G                       G            +     +       +   + +
Sbjct: 179 TYGGGPSEGPPPGALGEDGEEEEVDAGVIAMRAPAPVVVKAPEPPKPPEPPKPQAVVEAK 238

Query: 232 SAAKVSKDDRS------KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
                 K D         +D   +  E +E   D+ +D +  ++SAME +LR  VM  LD
Sbjct: 239 PVEAKKKSDDDEDDDYVPMDEQEKKPEPEEEEEDDFDDGAGPSVSAMESELRDGVMATLD 298

Query: 286 EIAEVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
            IA  +   R  Q+            D         +   + + + +L LN  RI+ LVE
Sbjct: 299 AIAGEFETYRRTQEKMLTAKLEGSPLDPADRAAYDEVTATITRHLKTLKLNNQRIEALVE 358

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
           QLY I+KR+M  EG LLRLA SYGI R  FL  +  RELDP W S  +D     W+ F+ 
Sbjct: 359 QLYGINKRLMQLEGRLLRLADSYGISRTEFLGAYYSRELDPQWESKVRDMGVR-WQKFID 417

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E  +I +IR +I +++ + G+++ ++R IV  V+KGE EA  AK EMVEANLRLVIS+A
Sbjct: 418 NEGGAISRIRTDIITLATDMGVAVDDYRRIVQTVQKGEREARQAKTEMVEANLRLVISIA 477

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 478 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 537

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETPI
Sbjct: 538 IPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI 597

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GDE+ SHLGDFIEDKNAV P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDH
Sbjct: 598 GDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 657

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 658 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 699


>gi|84502758|ref|ZP_01000877.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84389153|gb|EAQ01951.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 663

 Score =  514 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 364/685 (53%), Positives = 470/685 (68%), Gaps = 29/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K   +   + ++ +  +  D S    KKMI  AR+RG++T ++LN  LP D+VSSEQ
Sbjct: 1   MAPKDTDEDQRQDDEQEQDVSLDLSQAQIKKMIAEARERGFITYDQLNQVLPQDQVSSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGIN++  +D E EE    S  +  + SN  V L          TDDPVR
Sbjct: 61  IEDVMSMLSEMGINII--EDEEAEEEESKSTAVVETTSNREVALGSGSQEKLDRTDDPVR 118

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR
Sbjct: 119 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLR 178

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLE   G +                      E + D           AA  +K    
Sbjct: 179 DVIDLETTFGDQ---------------------MEGDEDAPVVDPAQAAPAAPAAKPQEE 217

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           + +   +     +   +++++ +  +L+AME  L+P+V+  LD IA  +  L  +QDN +
Sbjct: 218 QPEYDADGNPIAKDEDEDEDEQANMSLAAMETALKPRVLETLDTIARDFAVLSEIQDNRI 277

Query: 303 NGQKDEKSS------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           +   +E  S       + + L+ ++V+LV  L L+ +RI+ L++QLY I++RIM  +  +
Sbjct: 278 SATLNEDDSFNASDEAEYQKLRAEIVELVNGLHLHNNRIEALIDQLYGINRRIMQIDSAM 337

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F+E ++G ELDP+W+    +     W+ F+    D +  +R+++  +
Sbjct: 338 VKLADQARINRREFIEEYRGHELDPNWMERMSEKSGRGWQMFIDRFSDKVEDLRSDMAQV 397

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ ISEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 398 GQYVGLDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 457

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT 
Sbjct: 458 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTG 517

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 518 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 577

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 578 AILPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 637

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 638 RQIEAKALRKLKHPSRSRKLRSFLD 662


>gi|89055941|ref|YP_511392.1| RNA polymerase sigma factor RpoD [Jannaschia sp. CCS1]
 gi|88865490|gb|ABD56367.1| RNA polymerase, sigma 70 subunit, RpoD [Jannaschia sp. CCS1]
          Length = 668

 Score =  514 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 357/677 (52%), Positives = 463/677 (68%), Gaps = 21/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + +  +  +  D S  + KKMI  AR RGY+T ++LN  LPP++VSSEQ+ED ++ML
Sbjct: 6   DDRKQDGDETEMGLDMSQAAVKKMIAEARVRGYITYDQLNTVLPPEQVSSEQIEDVMSML 65

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGIN++  DD  +E   + + +L ++  +  V +   +      TDDPVRMYLREMGS
Sbjct: 66  SEMGINII-EDDEAEEGDDKPAGELVTTEGSREVAVAATETEKLDRTDDPVRMYLREMGS 124

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL +   LLR++IDL+  
Sbjct: 125 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLEEDILLRDVIDLDTT 184

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G   G E  +                       +       D      +    
Sbjct: 185 F------GRTMGDENDTPVVPAGVGSTPPSATPAPPPEPKKEEPTQELDADGNPIA---- 234

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               + + +++++ +  +L+AME  L+P+V+  LD+IA  Y  L  +QD+ ++   +E  
Sbjct: 235 ----KDDDEDEDEQANMSLAAMELALKPQVLATLDQIANDYIRLSEMQDSRISATLNEDD 290

Query: 311 S------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           S       + + L+ ++V+LV  L L+ +RI+ LV+QLY I++RIM  +  +++LA    
Sbjct: 291 SFSKAEEAEYQHLRSEIVELVNELHLHNNRIEALVDQLYGINRRIMSIDSSMVKLADQAR 350

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F+E ++ +ELDP W+          W+  +      I ++R ++  +    G+ I
Sbjct: 351 INRREFIEEYRNQELDPTWMERMTQKSGRGWQALMERSSGKIEELRGDMAQVGQYVGLDI 410

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 411 PEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 470

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 471 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 530

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSA
Sbjct: 531 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSA 590

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 591 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 650

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 651 RKLKHPSRSRKLRSFLD 667


>gi|119386779|ref|YP_917834.1| RNA polymerase sigma factor RpoD [Paracoccus denitrificans PD1222]
 gi|119377374|gb|ABL72138.1| RNA polymerase, sigma 70 subunit, RpoD [Paracoccus denitrificans
           PD1222]
          Length = 664

 Score =  512 bits (1318), Expect = e-143,   Method: Composition-based stats.
 Identities = 355/664 (53%), Positives = 456/664 (68%), Gaps = 25/664 (3%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D S  + K+MI   R+RG++T ++LNA LPP++VSS+Q+ED ++MLS M I VV+ D+ 
Sbjct: 19  LDMSQAAVKRMIAEGRERGFITYDQLNAVLPPEQVSSDQIEDVMSMLSEMDIRVVESDEE 78

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            DE      L   +++++  + +   +      TDDPVRMYLREMGS+ELLSREGEIAIA
Sbjct: 79  ADEAEPGGELA-TTASTSRELTVATTETEKLDRTDDPVRMYLREMGSVELLSREGEIAIA 137

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIEAGR  M+A LCESPLTF+A+ +WR EL D   LLR++IDLE   G           
Sbjct: 138 KRIEAGRNTMIAGLCESPLTFKAITMWRQELLDEDILLRDVIDLETTFG----------- 186

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                  R      +E + +        + A  +   R + +   +         +ED+D
Sbjct: 187 -------RAMDEDGEEEEVLPTETRPAANTAGAAGTAREEEEFDADGNPMGREEDEEDDD 239

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV------KCKVL 317
               +L+AME  L+PKV+  L+ IA  Y EL  +QDN ++   +E  +         +VL
Sbjct: 240 GQNLSLAAMEASLKPKVLETLEAIARGYEELSHMQDNRMSATLNEDGTFSAAQESAYQVL 299

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           +  +V LV  L L+ +RI+ LV+Q+Y I++RI+  +  +++LA +  I R  F++ ++G 
Sbjct: 300 RSHIVALVNELHLHNNRIEALVDQIYGINRRIVTIDSNVVKLADAARINRREFIDAYRGS 359

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           ELDP WV          W+         +  +R E+  +    G+ I EFR IVS V++G
Sbjct: 360 ELDPTWVERMMQNKGRGWQALFEKSRPQVENLRAEMAMVGQHVGVDIEEFRRIVSQVQRG 419

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E E+  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 420 EKESRQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 479

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I REPTPEE+A+KL 
Sbjct: 480 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAEKLQ 539

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNAV PLDSAIQ NL+ETTTRVL
Sbjct: 540 MPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRVL 599

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLR
Sbjct: 600 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLR 659

Query: 678 SFLD 681
           SFLD
Sbjct: 660 SFLD 663


>gi|307295455|ref|ZP_07575291.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
 gi|306878494|gb|EFN09714.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
          Length = 681

 Score =  512 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 350/692 (50%), Positives = 479/692 (69%), Gaps = 25/692 (3%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K N     E +D+ D+ + D ++ S KK+I  A++RGY+T +ELN  LP D++SSEQ
Sbjct: 1   MASKANGKGAGEDQDTGDAPLLDLNEASIKKLIARAKKRGYITYDELNDALPQDQMSSEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF------LQKRKDSADRS 116
           +ED ++ L+ MG+N+V+ ++  ++   +       S  +S+        + ++K      
Sbjct: 61  IEDIMSALNEMGVNIVENEEAGEDGDDQRDDSDDDSTDDSADDDGSPRPVAEKKKETVDR 120

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           TDDPVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESP TF A+I W   LN+
Sbjct: 121 TDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDTMILGLCESPTTFNAIIEWSTALNN 180

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   LREI+DL+A +  +            + +  E+ +++ + +  ++T G      + 
Sbjct: 181 GEMQLREILDLDAMLSKD-----------PAPENLEEGAEDDDGEISEKTAGPSFKEEEE 229

Query: 237 SKDDRSKVDSPPEN--AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
            +++ +  D   +        R  +E+E+D+  +L+ ME+ L+P  +     I E++R  
Sbjct: 230 PEEESADADEDEDGLTERRTRRVEEEEEEDNTLSLAQMEETLKPMALEKFATITEIFRTF 289

Query: 295 RSLQDN-----AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            + Q++     A+     +K     + L+E+L   V S+  +Q +I+ LV+QLY  ++R+
Sbjct: 290 SNAQESRMIAMAIGETLSQKDEDDYQELREQLTAEVESVQFHQQKIEYLVDQLYAYNRRL 349

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
               G++LRLA+ + + R  FL+R+   ELD  W+       +  W  F A E  ++ +I
Sbjct: 350 TALGGQMLRLAERHKVSRKDFLDRYVNHELDDGWLDRISGLDKK-WAAFAAAEGRAVERI 408

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R E+  I+  TG+S+SEFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 409 RTEVSEIAQATGMSLSEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQ 468

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 469 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 528

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+VRT+R+  ++  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLG
Sbjct: 529 NKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLG 588

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDKNA+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF
Sbjct: 589 DFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 648

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKLKHPSRS K+RSFLD
Sbjct: 649 SVTRERIRQIEAKALRKLKHPSRSHKMRSFLD 680


>gi|114328948|ref|YP_746105.1| RNA polymerase sigma factor RpoD [Granulibacter bethesdensis
           CGDNIH1]
 gi|114317122|gb|ABI63182.1| RNA polymerase sigma factor rpoD [Granulibacter bethesdensis
           CGDNIH1]
          Length = 654

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 350/685 (51%), Positives = 458/685 (66%), Gaps = 38/685 (5%)

Query: 3   IGKKRNRDSDSEHEDSD-DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           +  K+   ++S   + D ++ + D    S K++I   ++RGY+T +ELNA LP ++ SSE
Sbjct: 1   MATKQAATAESASSEQDVETTLLDTQSASVKRLIARGKERGYITFDELNAVLPSEQNSSE 60

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q+ED +A LS MGI VV   +  +E G   +    +  +          + +   TDDPV
Sbjct: 61  QIEDVMANLSEMGIQVV-ESEETEESGEPAARAERAEETEDEERSGNVDEESLGRTDDPV 119

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  LCESPLTF+A+I W + L  G  LL
Sbjct: 120 RMYLREMGSVELLSREGEIAIAKRIEAGRDMMIGGLCESPLTFRAIITWHERLKAGEMLL 179

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           R+IIDLEA  G    G    G EG    + +  +        +  +GD            
Sbjct: 180 RDIIDLEATQGGPPPGVVEGGEEGAEEGEADAEAFTPPPPPEESEDGD------------ 227

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                              D D    +LSA+E++L+P+ +   +EI  +Y++L  +Q   
Sbjct: 228 -------------------DADGIGMSLSALEEKLKPETLQRFEEIEAIYKKLSKMQSKR 268

Query: 302 VNGQKDE-----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           ++          +S    + ++++LV  V  + L+  R++ LV QL  +++R+   EG+L
Sbjct: 269 LDSFTSGEEVTARSEKTYEKMRDELVAKVSEVRLHNGRVEELVLQLKQLNQRLTGLEGQL 328

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           LRLA+S  + RD FLE+H+  EL+P+W+      P   WKNF A     + +IR  I  +
Sbjct: 329 LRLAESCKVPRDSFLEQHRNHELEPNWLERVSTLPGKAWKNFSARYPQEVGQIRGRIGEV 388

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           + + G+ I EF  +   V +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 389 AADAGLPIPEFLRVYKTVNRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQE 448

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+
Sbjct: 449 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTS 508

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK 
Sbjct: 509 RQMLHEIGREPQPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKA 568

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLD+AIQANLRE TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 569 AIIPLDAAIQANLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERI 628

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 629 RQIEAKALRKLKHPSRSRKLRSFLD 653


>gi|148259873|ref|YP_001234000.1| RNA polymerase sigma factor RpoD [Acidiphilium cryptum JF-5]
 gi|326403199|ref|YP_004283280.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
 gi|146401554|gb|ABQ30081.1| RNA polymerase, sigma 70 subunit, RpoD [Acidiphilium cryptum JF-5]
 gi|325050060|dbj|BAJ80398.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
          Length = 638

 Score =  510 bits (1312), Expect = e-142,   Method: Composition-based stats.
 Identities = 349/667 (52%), Positives = 453/667 (67%), Gaps = 53/667 (7%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D+   D    S K++I   ++RGY+T +ELNA LP ++ SSEQ+ED ++MLS MGI VV+
Sbjct: 19  DTATLDIQSASVKRLIARGKERGYITFDELNAVLPSEQNSSEQIEDVMSMLSEMGIQVVE 78

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G++ E+ E +  +     +A +         +S+   TDDPVRMYLREMG++ELLSREGE
Sbjct: 79  GEEGEEAETAGRAEKDEEAAEDEEAASGNISESSGSRTDDPVRMYLREMGTVELLSREGE 138

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR MM+  LCESPLTF+A+I W + L DG  LLR++IDLEA  G       
Sbjct: 139 IAIAKRIEAGRDMMIGGLCESPLTFRAIISWHESLKDGKMLLRDVIDLEATQG------- 191

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                                                           P  A  +E   D
Sbjct: 192 -----------------------------------------GGDGGFNPSAAVPEEPEED 210

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-----KSSVKC 314
           E+ + S  +LSA+E++L+P+V     E+ ++Y +   LQ   +           +S    
Sbjct: 211 EEGESSGLSLSAVEEKLKPEVFETFTEVEKLYEKFMKLQHKRLEALNAGEEMASRSEKTY 270

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
           + L+++LV  V  +SL+ +RI+ LV QL ++++R+   EG++LRLA+   I RD FL+ +
Sbjct: 271 EKLRDELVAKVEQVSLHNNRIEELVIQLKELNQRLNGLEGQMLRLAEGCKITRDDFLDAY 330

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           +GRE+DP W+      P   WK FV      + ++R +I  I+ E  + I EFR + S V
Sbjct: 331 RGREMDPTWLDDVAKRPGKGWKVFVERYGTQVTELRAQIGRIAAEAQLPIEEFRRVYSTV 390

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +++ AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 391 SRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 450

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+
Sbjct: 451 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAE 510

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNA+ PLD+A+ ANLRE  T
Sbjct: 511 KLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPLDAAVHANLREAAT 570

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           RVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+
Sbjct: 571 RVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSR 630

Query: 675 KLRSFLD 681
           KLRSFL+
Sbjct: 631 KLRSFLE 637


>gi|326387391|ref|ZP_08209000.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208047|gb|EGD58855.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 667

 Score =  509 bits (1310), Expect = e-142,   Method: Composition-based stats.
 Identities = 349/678 (51%), Positives = 466/678 (68%), Gaps = 20/678 (2%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           + ++  DS D+ + D +D S KK+I  A++RG +T +ELN  LP D++SSEQ+ED +A +
Sbjct: 2   ASNDKTDSGDAPLIDLNDASIKKLIARAKRRGIITYDELNEALPQDQMSSEQIEDIMAAI 61

Query: 71  SNMGINVVDGD-DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           S MG+N+V+ D D  D E  +      +        + +++      TDDPVRMYLREMG
Sbjct: 62  SEMGVNIVESDEDAVDPEERDVEETEDTDTGMDDRPVVEKRKETIERTDDPVRMYLREMG 121

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF A+I W + LN G   LREI+DL+A
Sbjct: 122 AVELLSREGEIAIAKRIEAGRDTMIMGLCESPITFHAIIQWSEALNAGEMQLREILDLDA 181

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI-ESAAKVSKDDRSKVDSPP 248
            +  E +             +      E + +  + T G   +    + ++   + +   
Sbjct: 182 MLSKEPQ------------PENLSEDGEGDGEISEATAGPTFKEEEDIEEEASEEDEDDE 229

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
                  R  +EDE+D+  +L+ ME  L+P+ +    EI   +R    +Q   ++     
Sbjct: 230 LRERRTPRPAEEDEEDNTLSLAQMEAALKPQALEKFAEITASFRAFERVQAERLDAIGLG 289

Query: 309 -----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
                        L+E+L   V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ +
Sbjct: 290 IDFPADKEALYHKLREELTAHVESVQFHATKIEYLVDNLYTFNRRLTTLGGQMLRLAERH 349

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + R  FL+ + GRELD +W+       +  W  F A E D++ +IR+EI  I+  TG+S
Sbjct: 350 KVSRKDFLDGYLGRELDENWLQSMSGKDKR-WGAFAANEADAVERIRSEISDIASATGMS 408

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           +SEFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 409 LSEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 468

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++ 
Sbjct: 469 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQ 528

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+
Sbjct: 529 GREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDA 588

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQ+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 589 AIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 648

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+K+RSFLD
Sbjct: 649 LRKLKHPSRSRKMRSFLD 666


>gi|254419911|ref|ZP_05033635.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
 gi|196186088|gb|EDX81064.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
          Length = 648

 Score =  509 bits (1310), Expect = e-142,   Method: Composition-based stats.
 Identities = 372/677 (54%), Positives = 469/677 (69%), Gaps = 39/677 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
              + E + D  + D +D   KK IK A+ RGYVT+EELN  LP +EV+ + +EDT+AML
Sbjct: 6   ETQDAEVTTDGPLLDLTDAGVKKFIKQAKARGYVTMEELNKVLPSEEVTPDAIEDTLAML 65

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MG+NVV+ ++   E+ S D      +A+  +   +    +A   TDDPVRMYLREMGS
Sbjct: 66  SEMGVNVVEAEEDAQEQQSTD-----VAAAAGTAVAEAPAKAAYDRTDDPVRMYLREMGS 120

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M++ LCES LTF+A+++WRDEL +   LLRE+IDL+A 
Sbjct: 121 VELLSREGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWRDELENNRILLREVIDLDAT 180

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G  +        +  + ++ E   +                                E 
Sbjct: 181 YGVLNPSSLPGAVQPEAEEEEEAEEKPAAE----------------------------EK 212

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK---- 306
            E+D+ + D+ +D    ++SA+E +LR  VM  L+ IA  + E R LQD  V  +     
Sbjct: 213 PESDDDDDDDFDDGGGMSVSALEAELRDGVMEVLNLIAADFSEFRGLQDKLVQTRLKGEV 272

Query: 307 -DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
              K S   + L + +   + ++ LN +RI+ LVEQLY I+KR++  EG LLRLA SYGI
Sbjct: 273 LSAKDSKAYQTLTKSISDRLKTMKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYGI 332

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL+ + G ELDP W    K+     W  F   E   I  IR ++ ++++E G+ I 
Sbjct: 333 SRPEFLKAYFGAELDPTWTERIKEQGVR-WTKFSDNEASQIATIRADVAAVALEAGLPID 391

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           ++R IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 392 DYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 451

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 452 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 511

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AI
Sbjct: 512 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAI 571

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 572 QSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 631

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHPSRS+KLRSFLD 
Sbjct: 632 KLKHPSRSRKLRSFLDS 648


>gi|1519634|gb|AAC44891.1| sigma 70-type sigma factor SigA [Rhodobacter sphaeroides]
          Length = 666

 Score =  509 bits (1310), Expect = e-142,   Method: Composition-based stats.
 Identities = 366/677 (54%), Positives = 462/677 (68%), Gaps = 24/677 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
            D + ED D     D S  + K+MI  A +RGY+T ++LN  LP D+VSSEQ+ED +AML
Sbjct: 7   DDGKPEDQDAETSLDMSQAAVKRMIAEA-ERGYITYDQLNTVLPQDQVSSEQIEDVMAML 65

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MGINV+  ++ E EEG      +   + +  + +   +      TDDPVRMYLREMGS
Sbjct: 66  SEMGINVI--ENEEAEEGEPAGELVEQGSGSREIAVAGTQGETLDRTDDPVRMYLREMGS 123

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+ IWRDEL     LLR++IDLEA 
Sbjct: 124 VELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFQAITIWRDELLSEDILLRDVIDLEAT 183

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G    G              +D     E D+V+            S +     D  P +
Sbjct: 184 FGRSLDG------------DGDDEIDGPEIDEVEVAAARAAPRRSTSSEPELDADGNPIS 231

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-- 308
              +E   DE    SA +L+AME  L+P+V+  L+ IA  Y +L  +Q+  ++   ++  
Sbjct: 232 RAEEEDEDDEA---SAMSLAAMEAALKPRVLETLELIARDYGKLAEMQNRRMSATLNDHI 288

Query: 309 ----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
               +     + L+ ++V LV  L L+ +RI+ L++QLY I+++IM     +++LA +  
Sbjct: 289 RFTTEDEAAYQKLRSEIVLLVNELHLHNNRIEALIDQLYGINRKIMSINSAMVKLADAAR 348

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           I R  F++ +QG ELDP W           W+  +    D +  +R E+  +    G+ I
Sbjct: 349 INRREFIDEYQGYELDPMWAERMAAKVGRGWQTLMEKSRDRVEDLRGEMAQVGQYVGVDI 408

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           SEFR IV+ V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 409 SEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 468

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I 
Sbjct: 469 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIG 528

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKNA+ PLDSA
Sbjct: 529 REPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSA 588

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           IQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER+RQIEAKA+
Sbjct: 589 IQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERLRQIEAKAL 648

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRS+KLRSFLD
Sbjct: 649 RKLKHPSRSRKLRSFLD 665


>gi|310816221|ref|YP_003964185.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
 gi|308754956|gb|ADO42885.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
          Length = 658

 Score =  508 bits (1309), Expect = e-142,   Method: Composition-based stats.
 Identities = 369/685 (53%), Positives = 477/685 (69%), Gaps = 34/685 (4%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K + D     +DSD  + FD S  + K+MI  AR+RGY+T ++LN+ LPPD+VSS+Q
Sbjct: 1   MAVKDSDDVKDNEQDSD--ISFDMSQAAVKRMIADARERGYITYDQLNSVLPPDQVSSDQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED ++MLS MGI V D ++ E+      S ++A+  +   + L   +      TDDPVR
Sbjct: 59  IEDVMSMLSEMGIQVTDEEETEEVADDGTSREVATVGARE-LTLAGPEVEKTDRTDDPVR 117

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTF A+ IWRDEL D   LLR
Sbjct: 118 MYLREMGSVELLSREGEIAIAKRIEAGRNTMIAGLCESPLTFNAITIWRDELMDEAVLLR 177

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++IDLEA  G +                          DD          +    ++  +
Sbjct: 178 DVIDLEATFGNQMG-----------------------EDDDAPVVDAAGGSEPKMRERGA 214

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           ++D+       D+ + D+D   ++ +L+AME  LRP+V+ ALD IAE    L  LQ+  +
Sbjct: 215 ELDADGNPISRDDDDEDDD--QNSMSLAAMEATLRPRVLEALDTIAEQAMALEELQEARM 272

Query: 303 NGQKDEKSSV------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
             + +E +        + +VL++K+V++V SL L+ +RID L++QLY I++RIM  +  +
Sbjct: 273 RAKMEEGADFSVAEEGQYQVLRQKIVEVVNSLHLHSNRIDALIDQLYGINRRIMSIDSSM 332

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++LA    I R  F++ ++G ELDP W+      P   W   +    + + ++R E+  +
Sbjct: 333 VKLADQARINRKEFIDEYRGSELDPSWLERMGQKPGRGWAMLIERSREKVEELRAEMAQV 392

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G+ I+EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 393 GQYVGVDINEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 452

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+
Sbjct: 453 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTS 512

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M ++I REPTPEE+A+KL MP+E VRKV+KI KEPISLETPIGDE+ S LGDFIEDKN
Sbjct: 513 RQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKN 572

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ PLDSAIQ NL+ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 573 AILPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 632

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 633 RQIEAKALRKLKHPSRSRKLRSFLD 657


>gi|329890710|ref|ZP_08269053.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
 gi|328846011|gb|EGF95575.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
          Length = 640

 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 364/677 (53%), Positives = 452/677 (66%), Gaps = 47/677 (6%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
              + E + D  + D +D   KK I+ A+ RGYVT+EELN  LP +EV+ +Q+ED +AML
Sbjct: 6   ETQDAETNADGPLLDLTDAGVKKFIRQAKTRGYVTMEELNKVLPSEEVTPDQIEDILAML 65

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           S MG+NVV+ ++   E    D      +A+  +   +    +A   TDDPVRMYLREMG+
Sbjct: 66  SEMGVNVVEAEEDAAEATGTD-----VAAAAETSVAEAPAKAAYDRTDDPVRMYLREMGT 120

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELLSREGEIAIAKRIEAGR  M++ LCES LTF+A+++WR+EL +   LLRE+IDL+A 
Sbjct: 121 VELLSREGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWREELANNRILLREVIDLDAT 180

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
            G  +     H     +    E     +E DD    +G   S + +              
Sbjct: 181 YGILNPSSLPHNQPAPAQPTGEPDGDGEEDDDEDFDDGGAMSISALE------------- 227

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-- 308
                                   +LR  VM  LD IA  + E R LQD  V  +     
Sbjct: 228 -----------------------AELRDGVMEVLDAIAVDFGEFRKLQDKLVEARLKGEV 264

Query: 309 ---KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
              K     + L   +   + ++ LN +RI+ LVEQLY I+KR++  EG LLRLA  YGI
Sbjct: 265 LTAKDQKTYEALTASISDRLKTMKLNNARIEALVEQLYAINKRLIGQEGRLLRLADGYGI 324

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL+ + G E+DP W    K+     W  F   E   I  IR +I +++ E G+ I 
Sbjct: 325 SRPEFLKAYFGSEMDPTWAERIKEMGVR-WTKFSENEAAQIDTIRTQIAAVATEAGVPID 383

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           ++R IV MV+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 384 DYRRIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 443

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++I R
Sbjct: 444 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTQRQMLHEIGR 503

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           E TPEE+A++LAMP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV P+D+AI
Sbjct: 504 EATPEELAERLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVLPIDAAI 563

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 564 QSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 623

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHPSRS+KLRSFLD 
Sbjct: 624 KLKHPSRSRKLRSFLDS 640


>gi|304322159|ref|YP_003855802.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303301061|gb|ADM10660.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 650

 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 364/682 (53%), Positives = 464/682 (68%), Gaps = 45/682 (6%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++    +  D  V D +  S KKMI  A++RGYVT ++LNA LP  E +SEQ+ED +  L
Sbjct: 4   TNQAVTEEADRPVLDLNLASVKKMIDAAKKRGYVTYDQLNAALPESEYTSEQIEDIMTKL 63

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSAS-----NSSVFLQKRKDSADRSTDDPVRMYL 125
           S+MGINV + D+   +  +++     + +S      SS  +     +    TDDPVRMYL
Sbjct: 64  SDMGINVTEDDEDGGDGDADEEGGEKAQSSAVVKKESSATVATNTKADSDRTDDPVRMYL 123

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG++ELLSREGEIAIAKRIEAGR  M+ +LCES LTF+A+ +WR+EL +G  LLR+II
Sbjct: 124 REMGAVELLSREGEIAIAKRIEAGRESMIRALCESSLTFEAITVWREELEEGRVLLRDII 183

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           DL+A                                      G  ES   ++K + ++  
Sbjct: 184 DLDATYD-----------------------------------GGPESKPDMTKPEVAEAV 208

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-----N 300
              +     +   DED D+   +LSA E +LR  VM    EIAE +++LR LQD      
Sbjct: 209 QREQEERAAQGLDDEDIDEGDLSLSAKEAELREGVMDTFSEIAEDFKKLRRLQDIQIEQQ 268

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                  +    + + L++ +V+ V S+ L+  RI+ LVEQLY+I++ +M  EG L+RLA
Sbjct: 269 LSGEDLSDSQLKRLRKLQKDIVERVRSVRLHNHRIEALVEQLYEINRSLMALEGRLVRLA 328

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            SYG+ R  FL  + G ELDP W+          W  F     D I+ +R  I  ++ ET
Sbjct: 329 DSYGVNRQDFLTSYLGYELDPEWLDRVSAMDGRGWTQFTTKGRDQIVDLRENIGQLAQET 388

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+++ +FR IV  V+KGE EA IAKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 389 GLTVKDFRRIVQTVQKGEREARIAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 448

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R++ 
Sbjct: 449 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQIL 508

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           N+I REPTPEE+A KL+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P
Sbjct: 509 NEIGREPTPEELAAKLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAILP 568

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 569 IDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIE 628

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKLKHPSRS+KLRSFLD 
Sbjct: 629 AKALRKLKHPSRSRKLRSFLDN 650


>gi|163796954|ref|ZP_02190910.1| RNA polymerase sigma factor rpoD [alpha proteobacterium BAL199]
 gi|159177701|gb|EDP62252.1| RNA polymerase sigma factor rpoD [alpha proteobacterium BAL199]
          Length = 639

 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 353/668 (52%), Positives = 450/668 (67%), Gaps = 57/668 (8%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D  + D  + + K +IK  ++RG++T +E+NA LP +E+SSEQ+ED ++ L+ MG+NVV
Sbjct: 23  PDGPLMDNINQAVKNLIKKGKERGFLTYDEVNAALPQEEMSSEQIEDIMSALNEMGVNVV 82

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + +D        D    A      +       D     TDDPVRMYLREMGS+ELLSREG
Sbjct: 83  ENED--------DGDQSAEKEDTEAKLAGNVSDDDVGRTDDPVRMYLREMGSVELLSREG 134

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EIAIAKRIEAGR MM+  +CESPLT +AL+ WRD+L +GT LLR+IIDLEA  G E    
Sbjct: 135 EIAIAKRIEAGREMMIGGICESPLTLRALVNWRDQLKEGTVLLRDIIDLEATYGAEV--- 191

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                                                   +      +        E + 
Sbjct: 192 ----------------------------------------ETNDTSTTTEGEETEGENDD 211

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVK 313
           D D++++  +LSAME QL P+V+   D+IA+ Y ++  +Q    +  K  +     +  K
Sbjct: 212 DSDDEENNPSLSAMEQQLLPQVLETFDKIADTYGKMVRMQKRRFDKLKGGEELARTTERK 271

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            + LK +L++ + S+ L+ +RI+ LVEQLY +++R+   +  L + A   G+ R  F+E 
Sbjct: 272 YEKLKGELIEGMESVRLHNARIEALVEQLYTLNRRLSQVDIRLWKQADRVGVSRKSFMEE 331

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
           H G EL+P W+       +  W+ F     + + + R  +  IS + G++I EFR IV  
Sbjct: 332 HFGNELEPDWLERVATV-DARWRKFAETAAEEVSEAREHLAMISADAGLTIGEFRRIVQT 390

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 391 VQKGEREAGRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A
Sbjct: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELA 510

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKNAV PLD+AI ANLRETT
Sbjct: 511 EKLVMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAIHANLRETT 570

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS
Sbjct: 571 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 630

Query: 674 KKLRSFLD 681
           +KLRSFLD
Sbjct: 631 RKLRSFLD 638


>gi|296284010|ref|ZP_06862008.1| RNA polymerase sigma factor RpoD [Citromicrobium bathyomarinum
           JL354]
          Length = 667

 Score =  502 bits (1293), Expect = e-140,   Method: Composition-based stats.
 Identities = 353/679 (51%), Positives = 477/679 (70%), Gaps = 21/679 (3%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
            S+++ ++++D+ + D ++ S KK+I  A++RGYVT +ELN  LP  E+SS+Q+ED  A 
Sbjct: 2   ASEAKTKETEDAPLIDLNEASIKKLISKAKKRGYVTYDELNEALPQGEMSSDQIEDIQAA 61

Query: 70  LSNMGINVVDGDDLEDEEGSE--DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           +S MG+ +V+ DD  + E  E  +    + +  ++       K + D  TDDPVRMYLRE
Sbjct: 62  ISEMGVQIVESDDEVESEKDEVEEIAPDSGAKKDTKSAAAAPKKTVDARTDDPVRMYLRE 121

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELLSREGEIAIAKRIEAGR  M+  LCESP+TF A+I W D LN+G   LREI+DL
Sbjct: 122 MGAVELLSREGEIAIAKRIEAGRDTMIIGLCESPITFHAIIQWSDALNEGEMQLREILDL 181

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           +A +  E               K E+ +++   +  +ET G          DD +     
Sbjct: 182 DAMLSKE-----------PPVDKMEEENEDDSGEISEETAGPTIREDDDDDDDETAEGDE 230

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
             + E+  R+ D++E D+  +L+ ME  L+P  +     I +++++   LQ   V+    
Sbjct: 231 DGDGESKRRDDDDEE-DNTMSLAQMEAALKPDALERFARITDLFKKFEKLQAERVDVLGR 289

Query: 308 EKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             +       K + L+E+L   V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ 
Sbjct: 290 GDAFPAAKEKKYEDLREQLTAEVESVQFHATKIEFLVDNLYAFNRRLTALGGQMLRLAER 349

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + IKR  FL+ + G E+D  W++      + +W  F   E +SI +IR EI  I+ +TG+
Sbjct: 350 HKIKRIDFLDAYLGNEMDDEWLT--SRTKDKKWAAFAEKEAESIERIRTEISDIASQTGM 407

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           ++ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 408 ALEEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 467

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+  ++
Sbjct: 468 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHE 527

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D
Sbjct: 528 QGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVD 587

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +AIQ+NL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAK
Sbjct: 588 AAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 647

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKLKHPSRS+K+RSFLD
Sbjct: 648 ALRKLKHPSRSRKMRSFLD 666


>gi|296532787|ref|ZP_06895466.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
 gi|296266895|gb|EFH12841.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
          Length = 639

 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 343/689 (49%), Positives = 450/689 (65%), Gaps = 57/689 (8%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        D+    +++ +  + D    + KK+I   ++RGYVT +ELN  LP +EVSS
Sbjct: 1   MASKVANGTDTVENRDEAVEGALLDILSAAVKKLIARGKERGYVTYDELNQALPSEEVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--RSTD 118
           E +EDT+AMLS +GINVV+ ++ E+ EG+      A  A              +    TD
Sbjct: 61  ELIEDTMAMLSELGINVVEAEETEEAEGAAKPAAKAEGAEEDEEEEGGGNVDEESLGRTD 120

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  LCESPLTFQA++ W + + +G 
Sbjct: 121 DPVRMYLREMGSVELLSREGEIAIAKRIEAGRDMMIGGLCESPLTFQAILTWHNAVKEGR 180

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR++IDLEA    E+        E     +  +                         
Sbjct: 181 MLLRDVIDLEATAAAENPEAAPAPDEEFEEGEEGEGM----------------------- 217

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
                                        +LSA+E++L+P+ +   + I E+Y +L+ L 
Sbjct: 218 ---------------------------GLSLSALEEKLKPEALATFEAIEELYGKLQKLS 250

Query: 299 DNAVNGQKDE-----KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
              +           ++    +  + +LV LV  + L+ +RI+ LV+QL  +++RI   E
Sbjct: 251 LKRMEAYTAGEEFASRTEKTYEKQRLELVALVEKVQLHNNRIEELVDQLKGLNRRITSLE 310

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           G++LRLA+   +KR+ FL+  +G E+DP W       P+  WKNF+      + +IR ++
Sbjct: 311 GQVLRLAEGSRVKREDFLQYWRGAEIDPAWFERISALPQKSWKNFIERSRQDVEQIRTQL 370

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
            + +  TG+ + EF+ + + V +GE + + AKKEM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 371 SNTAALTGLPVDEFKRVYATVSRGERDMTQAKKEMIEANLRLVISIAKKYTNRGLQFLDL 430

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+V
Sbjct: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 490

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT+R+M ++I REP PEE+A+KL MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIE
Sbjct: 491 RTSRQMLHEIGREPQPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 550

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK A+ PLD+AIQ+NLRE TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTR
Sbjct: 551 DKAAIIPLDAAIQSNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 610

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 611 ERIRQIEAKALRKLKHPSRSRKLRSFLDN 639


>gi|114797662|ref|YP_761566.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
 gi|114737836|gb|ABI75961.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
          Length = 666

 Score =  493 bits (1268), Expect = e-137,   Method: Composition-based stats.
 Identities = 359/687 (52%), Positives = 471/687 (68%), Gaps = 32/687 (4%)

Query: 2   TIGKKRNRDSDSEHEDS--DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
              KK+N   D E ED    +S + DF+    KK++K A++RG++T +E+N  LP  ++S
Sbjct: 4   ATKKKKNTAGDGEGEDDKETESGLVDFNATDVKKVLKRAQKRGFITHDEINQLLPDSDMS 63

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           S+Q+ED ++ +S MGI VV+ ++  +E+G        +   +  V  +K        TDD
Sbjct: 64  SDQIEDVMSQISEMGIAVVETEEEAEEQGKA-----LTKIEDKKVVAKKGNARGSDRTDD 118

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYLREMG++ELLSREGEIAIAKRIEAGR  M+  LCESPLTF+A+++WRDEL +   
Sbjct: 119 PVRMYLREMGAVELLSREGEIAIAKRIEAGRDAMIRGLCESPLTFEAMMVWRDELMNERI 178

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LLR++IDLEA  G E+        E    +       +K                   + 
Sbjct: 179 LLRDLIDLEATYGAENPPPEPKPVEERPPEPAAPVKGKK-------------------RS 219

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                +   E     ++  +E++D  A ++SAME +LR  V+  LDEIA+ +   R LQD
Sbjct: 220 AEEVDEVEAERMRQQQQEEEEEDDAVAMSMSAMEGELREGVLAKLDEIADAFSRFRKLQD 279

Query: 300 NA-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         K+  +   L  ++V  + ++ +N +RI+ LVEQLY I+K++M  EG
Sbjct: 280 RLLVRRIEGKDLTPKAQGEYDDLSLQIVDNLKTIHINNARIEALVEQLYAINKKLMGLEG 339

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
           +L+RLA ++G+ R  FL  + G EL+P W    ++     WK  V  + + +  +R+EI 
Sbjct: 340 KLMRLADAHGVPRKEFLHNYIGSELEPDWAERVREISAK-WKRLVDGKGEEVQVVRDEIS 398

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I+ E GI I +FR IV  V+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 399 EIAQEIGIPIDDFRRIVQTVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 458

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K++R
Sbjct: 459 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIIR 518

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T R+M ++I REPTPEE+A+KL +P+E +RKVLKI KEPISLETPIGD++ S+LGDFIED
Sbjct: 519 TQRQMLHEIGREPTPEELAEKLGLPLEKIRKVLKIAKEPISLETPIGDDEDSNLGDFIED 578

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K A+ P+D+AIQ+NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 579 KMALLPVDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 639 RIRQIEAKALRKLKHPSRSRKLRSFLD 665


>gi|294085800|ref|YP_003552560.1| sigma-70 factor RpoD [Candidatus Puniceispirillum marinum IMCC1322]
 gi|292665375|gb|ADE40476.1| Sigma 70 (RpoD) [Candidatus Puniceispirillum marinum IMCC1322]
          Length = 674

 Score =  493 bits (1268), Expect = e-137,   Method: Composition-based stats.
 Identities = 349/687 (50%), Positives = 462/687 (67%), Gaps = 18/687 (2%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M +  K+  + ++   D+  +   D +  + K +IK+ ++RG+VT +ELNA LP ++ +S
Sbjct: 1   MAVKAKKQVEPETNSPDASQASSADAAQQTIKTLIKIGKERGFVTHDELNAALPAEDYTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ++D ++ LS MG++VVD  + ++              +          DS    TDDP
Sbjct: 61  EQIDDVMSSLSEMGVSVVDSAETDENN--------EEEQAEGGKAAGNLSDSDVSGTDDP 112

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +AL+ WRD++ DG   
Sbjct: 113 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTIRALMHWRDQIADGVVP 172

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDLE+     +K      T+ +      D   +++ +D +E   + E      +D+
Sbjct: 173 LRDIIDLEST---HTKLNGGPITDQNVINAMNDEISDEDLEDDEEELEEEELDDDDEEDE 229

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             +      +    + + DED +D   +L+AMED +R  VM   DEIA V++     QD 
Sbjct: 230 DDESGDSDTDTSTRDSHDDEDSEDINMSLAAMEDAVRDDVMAMFDEIATVFKAFTKSQDR 289

Query: 301 A-----VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                        KS V    LK KL +L+  +  N  RI+ L EQL+ +++ +   EG 
Sbjct: 290 RLVRMSKGEALVPKSEVAHLELKIKLCELMEGVIFNTGRIEALSEQLFTLNRHVTGIEGR 349

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           L+RLA   GI R   LE    RE+   W     DF    W+       + I +++++I+ 
Sbjct: 350 LMRLAIDSGIPRAQVLEAWSWREVIEGW--PGSDFSTKAWQKLDKNHSEEITELQDKIRL 407

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +  +  ++I EFR ++  +++G+ EA+ AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 408 VVDDVSLAIPEFREVIQTIQRGQREAARAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 467

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 468 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 527

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+M ++I REPTPEE+A+KL+MP++ VRKVLKI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 528 SRQMLHEIGREPTPEELAEKLSMPIDKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDK 587

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV PLD+AI ANLRETTTRVLASLT REERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 588 NAVQPLDAAIHANLRETTTRVLASLTAREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 647

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           IRQIEAKA+RKLKHPSRS+KLRSFL+ 
Sbjct: 648 IRQIEAKALRKLKHPSRSRKLRSFLEN 674


>gi|85373960|ref|YP_458022.1| RNA polymerase sigma factor RpoD [Erythrobacter litoralis HTCC2594]
 gi|84787043|gb|ABC63225.1| RNA polymerase sigma-70 factor [Erythrobacter litoralis HTCC2594]
          Length = 675

 Score =  487 bits (1252), Expect = e-135,   Method: Composition-based stats.
 Identities = 340/682 (49%), Positives = 453/682 (66%), Gaps = 26/682 (3%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
            +   ++D+ + D ++ S KKMI  A+++GYVT +ELN  LP  E+S +Q+ED    LS 
Sbjct: 6   KKKTQAEDAPLIDLNEASIKKMITKAKRKGYVTYDELNEALPSGEMSPDQIEDIQTSLSE 65

Query: 73  MGINVVDGDDLEDE--------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           MG+ +V+ D+  +         E                     +K +    TDDPVRMY
Sbjct: 66  MGVQIVESDEEAEAEQEQANEVEEIAPGAAKDEKKDAKKPAAAVKKTTTGDRTDDPVRMY 125

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMG++ELLSREGEIAIAKRIEAGR  M+  LC+SP+TF A+I W + LN     LREI
Sbjct: 126 LREMGAVELLSREGEIAIAKRIEAGRDTMIIGLCQSPITFHAIIQWSEALNAEEMQLREI 185

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           +DL+A +  E               ++ +   E + D     E    +      D   + 
Sbjct: 186 LDLDAMLSKE------------PPAEKLEEGAEDDDDGEISEENAGPTIVDDDDDTDDED 233

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-----D 299
               +  E   ++ D++++D+  +L+ ME  L+P  +     I  ++++   LQ      
Sbjct: 234 SDDEDGEEGSSKSDDDEDEDNTMSLAQMEAALKPDAIERFARITSLFKKFEKLQLERVDT 293

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            A      +    + + L E+L   V S+  + ++I+ LV+ LY  ++R+    G++LRL
Sbjct: 294 IARGEVLPKAKENRYEKLGEELTAEVESMQFHATKIEFLVDNLYAFNRRLTALGGQMLRL 353

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           A+ + IKR  FL+ + G ELD  ++       +  W  F   E D+I +IR EI  I+ +
Sbjct: 354 AERHKIKRADFLQAYIGNELDEDFLKDRVKKDKK-WAAFADKEADAIDRIRTEIADIASQ 412

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           TG+++ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 413 TGMALPEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 472

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+ 
Sbjct: 473 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQF 532

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            ++  REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ 
Sbjct: 533 LHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAII 592

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQI
Sbjct: 593 PVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 652

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKLKHPSRS+K+RSFLD
Sbjct: 653 EAKALRKLKHPSRSRKMRSFLD 674


>gi|149184445|ref|ZP_01862763.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
 gi|148831765|gb|EDL50198.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
          Length = 668

 Score =  486 bits (1251), Expect = e-135,   Method: Composition-based stats.
 Identities = 351/678 (51%), Positives = 465/678 (68%), Gaps = 18/678 (2%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
            + S+  D DD+ + D ++ S KK+I  A+++GYVT +ELN  LP  E+SS+Q+ED  + 
Sbjct: 2   ATKSKSGDKDDAPLIDLNEASIKKLITKAKKKGYVTYDELNDALPQGEMSSDQIEDIQSA 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREM 128
           LS MG+ +V+ D+  + E   + +  A SA    V     K +A    TDDPVRMYLREM
Sbjct: 62  LSEMGVQIVEHDEDAEPEDEVEEIAPAPSAKEKDVKKAPAKKAATEGRTDDPVRMYLREM 121

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELLSREGEIAIAKRIEAGR MM+  LC+SP+TF A+I W + LN+    LREI+DL+
Sbjct: 122 GAVELLSREGEIAIAKRIEAGRDMMIMGLCQSPITFHAIIQWSEALNNEEMQLREILDLD 181

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
           A +  E               K  D +++ + D     E    +      DD  +     
Sbjct: 182 AMLSKE-----------PPADKLNDDAEDDDDDGEISEETAGPTIRDDDDDDSDEDSEGE 230

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +  E   ++ D++++D+  +L+ ME  L+P  +     I +++ +   LQ   V      
Sbjct: 231 DGEEGSSKSDDDEDEDNTMSLAQMEAALKPDAIERFARIKDLFGKFEKLQKERVEVLGRG 290

Query: 309 KS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           ++       K + L ++L   V S+  + ++I+ LV+ LY  ++R+    G++LRLA+ +
Sbjct: 291 EAFPPAKEKKYEALSDQLTAEVESVQFHATKIEFLVDNLYAFNRRLTALGGQMLRLAERH 350

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            +KR  FL+ + G ELD  W+       +  W  F   E D+I +IR EI  I+  TG++
Sbjct: 351 KVKRIDFLDAYIGNELDDSWMDDRVKKDKK-WAAFAEKEADAIDRIRTEISDIASATGMA 409

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 410 LPEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 469

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR +R+  +  
Sbjct: 470 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRCSRQFLHDQ 529

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+KL+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKNA+ P+D+
Sbjct: 530 GREPTPEEMAEKLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDA 589

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA
Sbjct: 590 AIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKA 649

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKLKHPSRS+K+RSFLD
Sbjct: 650 LRKLKHPSRSRKMRSFLD 667


>gi|329906288|ref|ZP_08274384.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327547308|gb|EGF32147.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 827

 Score =  477 bits (1228), Expect = e-132,   Method: Composition-based stats.
 Identities = 254/672 (37%), Positives = 374/672 (55%), Gaps = 43/672 (6%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            +        +      K +IKL + RG++T  E+N  LP + V  E +E  +   ++MG
Sbjct: 194 SDTEATEEELERRRQKLKTLIKLGKDRGFLTYAEINDHLPENIVDPEAIEGIIGTFNDMG 253

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSI 131
           I V +     +     D++   +S   +    +      DS    T DPVRMY+REMGS+
Sbjct: 254 IAVYEHAPDAESMLLTDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSV 313

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +G T + EI+D    +
Sbjct: 314 ELLTREGEIEIAKRIEDGLKDMIQAISACPTTISEILAAAERITNGETKIDEIVDGLVDM 373

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                             + E+  + +E +   E E +   AA  + +            
Sbjct: 374 LVIEVVVVPPPKVVSEDDEEEEEEEAEEEESGAEEETNASGAAGFTAEQI---------- 423

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                 +QL+ + +     I+  + ++R   +      K+  +S
Sbjct: 424 ----------------------EQLKRESLVKFQAISTQFDKMRKAYE------KEGYNS 455

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
                 +E +   + ++      ++ L + L    + + H E ++L +A     + R  F
Sbjct: 456 KPYVKAQEAISSELLAIRFTAKVVEKLCDTLRGQVEEVRHIERQILDVAVNKCRMPRSHF 515

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           ++   G E +  WV   +      +   +   V ++ +++ ++  +     + + + R I
Sbjct: 516 IKVFPGNETNLDWVD-GEVSGNHPYSVILGRNVPTVKELQQKLLDLQSRVVLPLPDLRAI 574

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 575 NRRMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 634

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P 
Sbjct: 635 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 694

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A K+ MP E +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R
Sbjct: 695 TLAIKMEMPEEKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMR 754

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP
Sbjct: 755 GVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 814

Query: 671 SRSKKLRSFLDG 682
           SRS +L+SFL+G
Sbjct: 815 SRSDRLKSFLEG 826


>gi|163856346|ref|YP_001630644.1| RNA polymerase sigma factor RpoD [Bordetella petrii DSM 12804]
 gi|163260074|emb|CAP42375.1| RNA polymerase sigma-70 factor [Bordetella petrii]
          Length = 806

 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 253/664 (38%), Positives = 372/664 (56%), Gaps = 66/664 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI+V D     
Sbjct: 202 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYDQAPDA 261

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 262 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 321

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 322 IAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD-----------GLVD 370

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ D+    D P     + +      
Sbjct: 371 PEDGEEY-----------------------AGAGVAADEDENDDGPAGGMSSKQL----- 402

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+ + + ++R   +      +D   S      +E +
Sbjct: 403 ------------EDLRVKALAKFDEVTKQFEKMRQSYE------RDGYKSEAYIKAQEAI 444

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
           +  +  +      ++ L + L    + +   E  +L       G+ R  F++   G E +
Sbjct: 445 LNELMGIRFTAKMVEKLADTLRSQVEEVRQLERAVLHTCVDRAGMPRSHFIKVFPGNETN 504

Query: 381 PHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
             WV    A   P  E    +  ++ ++ +++ ++  +     + + + + +   +  GE
Sbjct: 505 LDWVLQEVAAGHPYAE---TLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGE 561

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 562 AKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 621

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ M
Sbjct: 622 YATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDM 681

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+    VL 
Sbjct: 682 PEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDVVKEVLD 741

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+S
Sbjct: 742 SLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKS 801

Query: 679 FLDG 682
           FL+G
Sbjct: 802 FLEG 805


>gi|297180868|gb|ADI17073.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured alpha proteobacterium HF0010_30A23]
          Length = 668

 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 330/683 (48%), Positives = 447/683 (65%), Gaps = 25/683 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            +   + +D++          D    + +K+ + A+  G VT +++N FLP D+VSS+Q+
Sbjct: 5   ARAAEKPTDTDAAKDAAGGAQDTVLIAVRKLTERAKANGSVTYDDINEFLPEDQVSSDQI 64

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           ED +A LS  G+ V + ++ + E+           +++ +      KD     TDDPVRM
Sbjct: 65  EDVMAQLSEAGVTVTESENADAEK---------EESTDLANPTGNIKDEDVGRTDDPVRM 115

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLREMGS+ELLSREGEIAIAKRIEAGR  M+A +CESPLTF AL+ WR  L +   LLR+
Sbjct: 116 YLREMGSVELLSREGEIAIAKRIEAGREDMIAGICESPLTFSALMSWRQSLQEEVVLLRD 175

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +IDL+A      +          S    ++   +   D         E     ++D    
Sbjct: 176 VIDLDATYAAYMR----------SIAGDDEDPNDPALDVSASESLQDEEDEDEAEDGEES 225

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
                E A     + D+D++D++ +LSAME  LR  VM ALD IA  Y  L  +Q + + 
Sbjct: 226 EKEGEEGAAAASDDDDDDDEDNSVSLSAMEGILREDVMEALDVIAGAYGGLHKVQKDRMT 285

Query: 304 GQKD-----EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
             +      E      +  ++ +++ +  + LN + ID LV+Q+  I+K I+ +E +L++
Sbjct: 286 LLQTGEDVPEDIEAAYEEGRDTVIRAMKLIRLNNNLIDQLVDQMKSINKAIIGHEIKLMK 345

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           L+    I RD F++ +   E+DP W+    +  +  WK           +IR +I  I  
Sbjct: 346 LSDRCKIPRDEFIDEYFENEIDPSWLERMAE-ADASWKMLYERYGSMAKEIREDIADIIH 404

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +  + +SEF+ IV  V+KGE +++ AK EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 405 QVDLPVSEFKRIVEKVQKGERDSNRAKAEMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 464

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+
Sbjct: 465 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQ 524

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M ++I RE TPEE+A +L MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFI+D+NA+
Sbjct: 525 MLHEIGREATPEELAARLGMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIKDENAI 584

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P+++AI  NLRE+TTRVL+SLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQ
Sbjct: 585 IPVEAAINNNLRESTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 644

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 645 IEAKALRKLKHPSRSRKLRSFLD 667


>gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma factor [Janthinobacterium sp.
           Marseille]
 gi|151280838|gb|ABR89248.1| RNA polymerase primary sigma factor [Janthinobacterium sp.
           Marseille]
          Length = 826

 Score =  475 bits (1222), Expect = e-131,   Method: Composition-based stats.
 Identities = 255/672 (37%), Positives = 376/672 (55%), Gaps = 44/672 (6%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            +        +      K +IK  ++RG++T  E+N  LP + +  E +E  +   ++MG
Sbjct: 194 SDTEASEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMG 253

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSI 131
           I V +     +     D++   +S   +    +      DS    T DPVRMY+REMGS+
Sbjct: 254 IAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSV 313

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   +I   + ++     + EI+D    +
Sbjct: 314 ELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIIAAAERISKDEAKIDEIVDGLVDM 373

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                          S  + ++  +E+E ++ +ET     +A   S+             
Sbjct: 374 DAAEPVVAPPAPAASSDDEEDEEEEEEEEEEEEETTAASGAAGFSSEQLE---------- 423

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                  QL+   +     IA+ + ++R   +      K+  +S
Sbjct: 424 -----------------------QLKRDSLAKFSTIAQQFDKMRKAFE------KEGYNS 454

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
                 +E +   + S+      ++ L + L      + H E ++L +A    G+ R  F
Sbjct: 455 KPYVKAQEIISNELLSIRFTAKVVEKLCDTLRGQVDEVRHIEKQILDVAVNRCGMPRGHF 514

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           ++   G E +  WV    +  +  +   +A  V ++ +++ ++  +     + + + R I
Sbjct: 515 IKVFPGNETNLDWVDGEVN-GKHAYSVVLARNVPTVKELQQKLIDLQARVVLPLPDLRAI 573

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 574 NKKMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 633

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P 
Sbjct: 634 RRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 693

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R
Sbjct: 694 TLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMR 753

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP
Sbjct: 754 GVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 813

Query: 671 SRSKKLRSFLDG 682
           SRS KL+SFL+G
Sbjct: 814 SRSDKLKSFLEG 825


>gi|85708548|ref|ZP_01039614.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85690082|gb|EAQ30085.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 674

 Score =  475 bits (1222), Expect = e-131,   Method: Composition-based stats.
 Identities = 349/686 (50%), Positives = 460/686 (67%), Gaps = 28/686 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
            S ++  D DD+ + D ++ S KK++  A+++GY+T +ELNA LP  E+S +Q+ED    
Sbjct: 2   ASTAKAADKDDAPLIDLNEASVKKLMTKAKKKGYITYDELNAALPSGEMSPDQIEDIQTA 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS---------ADRSTDDP 120
           LS MG+ +V+ D+  + E  +++     S    +   +  K +             TDDP
Sbjct: 62  LSEMGVQIVENDEEAEAEAEQEAEVEEMSVEGEAEKKKDTKAAAKPAAKKTGTGERTDDP 121

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMG++ELLSREGEIAIAKRIEAGR MM+  LCESP+TF A+I W + LN     
Sbjct: 122 VRMYLREMGAVELLSREGEIAIAKRIEAGRDMMIMGLCESPITFHAIIQWSEALNSEDMQ 181

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LREI+DL+A +  E               +  + +      D  E + D     +  ++ 
Sbjct: 182 LREILDLDAMLSKEPPPDKMEEENEDDDGEISEETAGPTIRDDDEDDSDESEDGEDGEEG 241

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            SK D             DE+E+D+  +L+ ME  L+P  +     I ++++    LQ  
Sbjct: 242 ASKKD-------------DEEEEDNTLSLAQMEAALKPDAIERFARITKLFKTFEKLQAE 288

Query: 301 AVNGQKD-----EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            V          +    K + L E+L   V S+  + ++I+ LV+ LY  ++R+    G+
Sbjct: 289 RVETLAAGNEFPKAKENKYEKLSEELTAEVESVQFHATKIEFLVDNLYAFNRRLTALGGQ 348

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           +LRLA+ + IKR  FL+ + G ELD  W++      +  W  F   E  +I +IR EI  
Sbjct: 349 MLRLAERHKIKRIDFLKSYVGNELDDSWIAANAKKDKK-WAAFAEKEEAAIERIRTEITD 407

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I+ +TG+++ EFR IV+MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 408 IAAQTGMALPEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 467

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT
Sbjct: 468 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRT 527

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R+  ++  REPTPEE+A +L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDK
Sbjct: 528 SRQFLHEEGREPTPEEMAARLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDK 587

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRER
Sbjct: 588 NAVIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 647

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKLKHPSRS+K+RSFLD
Sbjct: 648 IRQIEAKALRKLKHPSRSRKMRSFLD 673


>gi|253991033|ref|YP_003042389.1| RNA polymerase sigma factor RpoD [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782483|emb|CAQ85647.1| rna polymerase, sigma(70) factor; regulation of proteins induced a
           high temperatures (rna polymerase sigma 70 factor rpod)
           [Photorhabdus asymbiotica]
          Length = 651

 Score =  473 bits (1217), Expect = e-131,   Method: Composition-based stats.
 Identities = 271/675 (40%), Positives = 379/675 (56%), Gaps = 48/675 (7%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D++         L+        K ++   +++GY+T  E+N  LP D V S+Q+ED + 
Sbjct: 22  TDTNPNTLKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQ 81

Query: 69  MLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           M+++MGI V++   D +D   +E + D    A  ++  +    +S    T DPVRMY+RE
Sbjct: 82  MINDMGIQVMEEAPDADDLMLAETTNDTDEDAVEAAAQVLSSVESEIGRTTDPVRMYMRE 141

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I  
Sbjct: 142 MGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT- 200

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              + P +        E            E  ++++ + + + +       D        
Sbjct: 201 -GFVDPNA--------EEDLAPTATHVGSELPQEELDDDDDEDDEDNDDDSDGDDDNSID 251

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE A    + L E  + +   +                                   +K+
Sbjct: 252 PELARQKFQELHEQYEITRQEI-----------------------------------KKN 276

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIK 366
            +          KL ++     L   + D LV  +  +  R+   E ++++   +   + 
Sbjct: 277 GRDHANTTAEILKLSEIFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMP 336

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W + AK   +   +  +  E + I +    ++ I  ETG++I +
Sbjct: 337 KKNFITLFSGNETSDIWFTAAKAMNKPWSEKLLEVE-EEIQRSLQRLRQIEEETGLTIEQ 395

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 396 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 455

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 456 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 515

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA  
Sbjct: 516 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATS 575

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 576 ESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 635

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 636 LRHPSRSEVLRSFLD 650


>gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA polymerase [Herminiimonas
           arsenicoxydans]
          Length = 858

 Score =  473 bits (1216), Expect = e-131,   Method: Composition-based stats.
 Identities = 251/672 (37%), Positives = 372/672 (55%), Gaps = 45/672 (6%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           ++        +      K +IK  ++RG++T  E+N  LP + +  E +E  +   ++MG
Sbjct: 227 NDTEASEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMG 286

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSI 131
           I V +     +     D++   +S   +    +      DS    T DPVRMY+REMGS+
Sbjct: 287 IAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSV 346

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + ++     + EI+D    +
Sbjct: 347 ELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIVD--GLV 404

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
              +           +    E+  +E+E  + +E       AA  S +            
Sbjct: 405 DMNASEPVIAPPAPAAASDEEEEEEEEEEAEEEEETPAASGAAGFSSEQL---------- 454

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                 +QL+   +     IA  + ++R   +      K+  +S
Sbjct: 455 ----------------------EQLKRDSLAKFSTIAMQFDKMRKAFE------KEGYNS 486

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
                 +E +   +  +      ++ L + L      +   E ++L +A     + R+ F
Sbjct: 487 KPYVKAQEIISNELLGIRFTAKVVEKLCDTLRGQVDEVRQIEKQILDIAVNRCEMPRNHF 546

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           ++   G E +  WV    +     +   +A  V ++ +++ ++  +     + + + R I
Sbjct: 547 IKVFPGNETNLDWVDGEVE-GNHPYSIVLARNVPAVKELQQKLIDLQARVVLPLPDLRAI 605

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 606 NRKMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 665

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P 
Sbjct: 666 RRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 725

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R
Sbjct: 726 TLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMR 785

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP
Sbjct: 786 GVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 845

Query: 671 SRSKKLRSFLDG 682
           SRS KL+SFL+G
Sbjct: 846 SRSDKLKSFLEG 857


>gi|293394293|ref|ZP_06638593.1| DNA-directed RNA polymerase sigma subunit RpoD [Serratia odorifera
           DSM 4582]
 gi|291423271|gb|EFE96500.1| DNA-directed RNA polymerase sigma subunit RpoD [Serratia odorifera
           DSM 4582]
          Length = 647

 Score =  472 bits (1215), Expect = e-131,   Method: Composition-based stats.
 Identities = 271/683 (39%), Positives = 371/683 (54%), Gaps = 53/683 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M +      D++         L+        K ++   +++GY+T  E+N  LP D V S
Sbjct: 15  MLLLAVSPTDTNPNTLKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDS 74

Query: 61  EQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +Q+ED + M+++MGI V++   D +D   +E+S      A  ++  +    +S    T D
Sbjct: 75  DQIEDIIQMINDMGIQVMEEAPDADDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTD 134

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G +
Sbjct: 135 PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGES 194

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L ++I            GF               +      ++   E   +       D
Sbjct: 195 RLSDLI-----------TGFVDPNAEEDI----APTATHIGSELSTEEQSDDEEEDDDDD 239

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                   PE A      L E  + +   +                              
Sbjct: 240 AEDDNSIDPELARQKFTELREQYEATRQVIKT---------------------------- 271

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  + +S         KL  +     L   + D LV  +  +  R+   E  +++L
Sbjct: 272 -------NGRSHASAAEEILKLSDVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKL 324

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+    G E    W   A    +  W   +    + + +   +++ I  
Sbjct: 325 CVEQCKMPKKNFVTLFAGNETSDSWFEAALAMAKP-WSEKLKDVAEDVQRSLQKLRQIEE 383

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 384 ETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 443

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 444 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 503

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    
Sbjct: 504 MLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE 563

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 564 LPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 623

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 624 IEAKALRKLRHPSRSEVLRSFLD 646


>gi|270263179|ref|ZP_06191449.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
 gi|270042867|gb|EFA15961.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
          Length = 648

 Score =  472 bits (1215), Expect = e-131,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 370/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 42  QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 101

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 102 LLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 161

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I            GF       
Sbjct: 162 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI-----------TGFVDPNAEE 210

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  ++     +   E + D E       D        PE A     +L +  + + 
Sbjct: 211 DI---APTATHVGSELSTEEQNDDEEDEDEDDDAEDDNSIDPELARQKFTDLRDQYEATR 267

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 268 LVI-----------------------------------KKNGRSHASAAEEILKLSEVFK 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W  
Sbjct: 293 QFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFAGNETSNSWFE 352

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 353 AALAMAKP-WSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 411

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 412 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 471

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 472 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 531

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 532 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 591

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 592 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 647


>gi|284008589|emb|CBA75169.1| RNA polymerase sigma-70 factor [Arsenophonus nasoniae]
          Length = 622

 Score =  470 bits (1208), Expect = e-130,   Method: Composition-based stats.
 Identities = 274/656 (41%), Positives = 378/656 (57%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 13  QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 72

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 73  ILAETATDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 132

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+     +  G T L +II            GF       
Sbjct: 133 EDGINQVQCSVAEYPEAIAYLLDQYQRVEKGETRLSDII-----------IGFVDPNAEE 181

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                         ++    + D +       DD  + +  PE A      L E  + ++
Sbjct: 182 DLAPTATHIGSVLPEEALNDDEDEDKDEDEDSDDSDENNVDPELARQKFSELREQYERTS 241

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   QK  ++        E+L ++  
Sbjct: 242 LEI-----------------------------------QKSGRNHANSIAEIEQLSEIFK 266

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + D+ +R+   E  +++L  +   + +  F+    G E + +W++
Sbjct: 267 QFRLIPKQFDYLVNNMRDMMERVRSQERLIMKLCIEQCKMPKKNFITLFSGNETNVNWLA 326

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +   +  V  E + I +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 327 AAKAMNKPWSEKLVEVE-EEIQRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 385

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 386 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 445

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 446 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 505

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 506 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHEVLAGLTTREA 565

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 566 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 621


>gi|300690868|ref|YP_003751863.1| RNA polymerase sigma70 factor [Ralstonia solanacearum PSI07]
 gi|299077928|emb|CBJ50567.2| RNA polymerase sigma70 factor [Ralstonia solanacearum PSI07]
          Length = 876

 Score =  469 bits (1207), Expect = e-130,   Method: Composition-based stats.
 Identities = 253/674 (37%), Positives = 374/674 (55%), Gaps = 45/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 243 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 302

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 303 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 362

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 363 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 420

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +             ++ ED   E+  D+ ++ + +    A  S            
Sbjct: 421 LIDPNADAEAAAQAAADEDEEFEDEEAEEVGDEEEDEDDEGAGGAAAS------------ 468

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                               +   ++L+   +     I + + ++R   +      K+  
Sbjct: 469 --------------------ARQLEELKQAALVRFSVIGDQFDKMRRAFE------KEGY 502

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 503 KSKPYLKAQESIQNELMAIRFTARTVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRG 562

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W+       +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 563 DFVSRFPGNETNLKWIDSVVADGKP-YSAIVERNIPAVHELQQKLIDLQARVVLPLTELK 621

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 622 DVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 681

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 682 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 741

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 742 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 801

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 802 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 861

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 862 HPSRSDKLKSFLEG 875


>gi|317403353|gb|EFV83866.1| RNA polymerase sigma-70 factor [Achromobacter xylosoxidans C54]
          Length = 813

 Score =  469 bits (1207), Expect = e-130,   Method: Composition-based stats.
 Identities = 259/687 (37%), Positives = 380/687 (55%), Gaps = 68/687 (9%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            + +    D        +  ++   +  K++IKL + RGY+T  E+N  LP D V +E +
Sbjct: 186 KRGKADPKDLIARGPVSAEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAI 245

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK-----DSADRSTD 118
           +  ++  S+MGI V D     +     ++  +AS+  +  V  +        DS    T 
Sbjct: 246 DGIISTFSDMGIAVYDQAPDAETLLMSENAPVASNDDDDDVEDEAEAALTTVDSDFGRTT 305

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+REMGS+ELL+REGEI IAKRIE G   M+ ++   P T   ++     + +G 
Sbjct: 306 DPVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHVLRVREGQ 365

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
             + E++D           G     +G  Y                       + A VS 
Sbjct: 366 AQIDEVVD-----------GLVDPEDGEEY-----------------------AGAGVSA 391

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           D+    D P     + +                  + LR K +   DE+ + + ++R   
Sbjct: 392 DEDESDDGPAGGMSSKQL-----------------EDLRVKALAKFDEVGKQFDKMRLSY 434

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL- 357
           +      KD   S      +E +   +  +      ++ L + L +  + +   E  +L 
Sbjct: 435 E------KDGYKSDIYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLH 488

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                 G+ R  F++   G E +  WV    A   P  E    +  ++ ++ +++ ++  
Sbjct: 489 TCVDRAGMPRTHFIKVFPGNETNLQWVVDEVAAGHPYAE---TLERQIPAVQELQQKLID 545

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     + + + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQ
Sbjct: 546 LQTRVVLPLKDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQ 605

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R 
Sbjct: 606 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRI 665

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R++  +   EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED 
Sbjct: 666 SRQILQETGAEPDPATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDT 725

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           + ++P D+A+  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRER
Sbjct: 726 STLAPSDAALHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRER 785

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           IRQIEAKA+RKL+HPSR+ KL+SFL+G
Sbjct: 786 IRQIEAKALRKLRHPSRADKLKSFLEG 812


>gi|237729995|ref|ZP_04560476.1| RNA polymerase sigma-70 factor [Citrobacter sp. 30_2]
 gi|226908601|gb|EEH94519.1| RNA polymerase sigma-70 factor [Citrobacter sp. 30_2]
          Length = 660

 Score =  469 bits (1207), Expect = e-130,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E S      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 219

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A      L    + + 
Sbjct: 220 DMAPTATHVGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFGELRTQYEITR 279

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +   +KL ++  
Sbjct: 280 DTIKAK-----------------------------------GRSHAAAQEEIQKLSEVFK 304

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 305 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 365 AAIAMNKP-WSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 423

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 424 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 483

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 484 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 543

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 544 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 603

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 604 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659


>gi|237809411|ref|YP_002893851.1| RNA polymerase, sigma 70 subunit, RpoD [Tolumonas auensis DSM 9187]
 gi|237501672|gb|ACQ94265.1| RNA polymerase, sigma 70 subunit, RpoD [Tolumonas auensis DSM 9187]
          Length = 617

 Score =  468 bits (1204), Expect = e-129,   Method: Composition-based stats.
 Identities = 268/655 (40%), Positives = 366/655 (55%), Gaps = 48/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     D+ 
Sbjct: 9   QSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENVPDADDL 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++      A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  LLTENNAADDDAAEAAAQVLASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     L+   D    G   L +II            GF    +   
Sbjct: 129 DGINQVQSSVAEYPEAITYLLDQFDRFEAGHIRLGDII-----------SGFVSEDDDLP 177

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S   E     +   D +       D        PE A      L    + +  
Sbjct: 178 PTATNIGSALDEETLKADDTDDEDEDEDGDDDAEEDTGPDPEVAREKFSALRTQYEITRD 237

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A                                   + + S   KV   +L  +   
Sbjct: 238 AIKA-----------------------------------NGRDSDLAKVQILELANVFKE 262

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  + ++ +R+   E  +LR    Y  + +  F+      E    W  +
Sbjct: 263 FRLVPKQFDRLVNSMREMMERVRVQERLILRYCVEYAKMPKKNFVTAFTNNESSNGWFEF 322

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           AK   +  W   +A   + + +   +++ +  ETG+SI++ + I   +  GE +A  AKK
Sbjct: 323 AKSSGKP-WSTALANMDEDVQRSIQKLQQVEQETGLSIAQIKDINRRMSIGEAKARRAKK 381

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 382 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 441

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 442 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMGMPEDKIRKV 501

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P D+A   +L+  T  VL+ LT RE +
Sbjct: 502 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLKAATRDVLSGLTAREAK 561

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 616


>gi|161506225|ref|YP_001573337.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160867572|gb|ABX24195.1| hypothetical protein SARI_04418 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 660

 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 219

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 220 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 268

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 269 -------AELRAQYIVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 304

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 305 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 365 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 423

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 424 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 483

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 484 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 543

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 544 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 603

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 604 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659


>gi|16761985|ref|NP_457602.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29143472|ref|NP_806814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|25288442|pir||AB0893 RNA polymerase sigma-70 factor [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16504288|emb|CAD07736.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139106|gb|AAO70674.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
          Length = 660

 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 219

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 220 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 268

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 269 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 304

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 305 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 365 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 423

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 424 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 483

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 484 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 543

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 544 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 603

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 604 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659


>gi|193222233|emb|CAL60659.2| putative RNA polymerase sigma factor rpoD (Sigma-70) [Herminiimonas
           arsenicoxydans]
          Length = 800

 Score =  467 bits (1202), Expect = e-129,   Method: Composition-based stats.
 Identities = 251/672 (37%), Positives = 372/672 (55%), Gaps = 45/672 (6%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           ++        +      K +IK  ++RG++T  E+N  LP + +  E +E  +   ++MG
Sbjct: 169 NDTEASEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIGTFNDMG 228

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSI 131
           I V +     +     D++   +S   +    +      DS    T DPVRMY+REMGS+
Sbjct: 229 IAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSV 288

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + ++     + EI+D    +
Sbjct: 289 ELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIVD--GLV 346

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
              +           +    E+  +E+E  + +E       AA  S +            
Sbjct: 347 DMNASEPVIAPPAPAAASDEEEEEEEEEEAEEEEETPAASGAAGFSSEQL---------- 396

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                 +QL+   +     IA  + ++R   +      K+  +S
Sbjct: 397 ----------------------EQLKRDSLAKFSTIAMQFDKMRKAFE------KEGYNS 428

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
                 +E +   +  +      ++ L + L      +   E ++L +A     + R+ F
Sbjct: 429 KPYVKAQEIISNELLGIRFTAKVVEKLCDTLRGQVDEVRQIEKQILDIAVNRCEMPRNHF 488

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           ++   G E +  WV    +     +   +A  V ++ +++ ++  +     + + + R I
Sbjct: 489 IKVFPGNETNLDWVDGEVE-GNHPYSIVLARNVPAVKELQQKLIDLQARVVLPLPDLRAI 547

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 548 NRKMAAGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 607

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P 
Sbjct: 608 RRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 667

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R
Sbjct: 668 TLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMR 727

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP
Sbjct: 728 GVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 787

Query: 671 SRSKKLRSFLDG 682
           SRS KL+SFL+G
Sbjct: 788 SRSDKLKSFLEG 799


>gi|187929499|ref|YP_001899986.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12J]
 gi|187726389|gb|ACD27554.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12J]
          Length = 829

 Score =  467 bits (1202), Expect = e-129,   Method: Composition-based stats.
 Identities = 255/674 (37%), Positives = 377/674 (55%), Gaps = 47/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V  E +E  VA L++
Sbjct: 198 AASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLND 257

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +G+ V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 258 IGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 317

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 318 TVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 375

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P ++       E     + E++ +E + ++ ++ EG   +AA               
Sbjct: 376 LIDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGAAAAS-------------- 421

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                               +   ++L+   +     I E + ++R   +      K+  
Sbjct: 422 --------------------ARQLEELKQAALLKFGVIGEQFDKMRRAFE------KEGY 455

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 456 KSKPYVKAQEAIQAELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRS 515

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W+       +  +   V   V ++ +++ ++  +     + ++E +
Sbjct: 516 DFVARFPGNETNLKWIETVVADGKP-YSTIVERNVPAVHELQQKLIDLQARVVLPLTELK 574

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 575 DVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 634

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 635 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 694

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 695 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 754

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 755 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 814

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 815 HPSRSDKLKSFLEG 828


>gi|94311542|ref|YP_584752.1| RNA polymerase sigma factor RpoD [Cupriavidus metallidurans CH34]
 gi|93355394|gb|ABF09483.1| RNA polymerase sigma D factor (housekeeping sigma factor)
           [Cupriavidus metallidurans CH34]
          Length = 855

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 258/670 (38%), Positives = 377/670 (56%), Gaps = 45/670 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
            +      +      K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI 
Sbjct: 226 QAGSEEELEIRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 285

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIEL 133
           V +     +     D+   A+S   +    +      DS    T DPVRMY+REMG++EL
Sbjct: 286 VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 345

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E +D    I P
Sbjct: 346 LTREGEIEIAKRIEAGLKDMVMAISACPVTISEILASAERVANEEIKIDEFVD--GLIDP 403

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
            ++    +          ED   +++ DD +E + +    A  S                
Sbjct: 404 NAEEVQDNSPAQAVAADDEDEDSDEDGDDGEEEDDESGGGAGAS---------------- 447

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
                           +   ++L+   +     IAE + ++R   +      K+   S  
Sbjct: 448 ----------------ARQLEELKVAALEKFRVIAEQFDKMRRAFE------KEGYKSKP 485

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
               +E +   + S+      ++ L + L      +   E  +L +     G+ R  F+ 
Sbjct: 486 YVKAQEAIQAELMSIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRADFVA 545

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           R  G E +  W+       +  +   V   V ++ +++ ++  +     + + E + +  
Sbjct: 546 RFPGNETNLDWIQTIVADNKS-YSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKDVNR 604

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 605 KMSEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 664

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +
Sbjct: 665 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATL 724

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  ++R+ 
Sbjct: 725 AEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALDGSMRDV 784

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR
Sbjct: 785 VKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 844

Query: 673 SKKLRSFLDG 682
           S KL+SFL+G
Sbjct: 845 SDKLKSFLEG 854


>gi|56415151|ref|YP_152226.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197364081|ref|YP_002143718.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|205358509|ref|ZP_02656872.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205359720|ref|ZP_02831723.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|16421768|gb|AAL22085.1| sigma D factor of RNA polymerase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56129408|gb|AAV78914.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095558|emb|CAR61123.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|205333914|gb|EDZ20678.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205343355|gb|EDZ30119.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|261248341|emb|CBG26178.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995406|gb|ACY90291.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|320087665|emb|CBY97429.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|323131572|gb|ADX19002.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326624968|gb|EGE31313.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332990077|gb|AEF09060.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 660

 Score =  467 bits (1200), Expect = e-129,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 219

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 220 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 268

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 269 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 304

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 305 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 365 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 423

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 424 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 483

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 484 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 543

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 544 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 603

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 604 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659


>gi|146313109|ref|YP_001178183.1| RNA polymerase sigma factor RpoD [Enterobacter sp. 638]
 gi|145319985|gb|ABP62132.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter sp. 638]
          Length = 631

 Score =  466 bits (1199), Expect = e-129,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 376/656 (57%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 25  QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 84

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S +    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 85  LLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 144

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L +II     + P ++          
Sbjct: 145 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDIIT--GFVDPNAE---------- 192

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             ++   ++     +  +E   + E   +  +++       PE A      L    + + 
Sbjct: 193 --EEVAPTATHVGSELTKEEREENEEEDEEDEEEEDDNSIDPELAREKFGELRTQYELAR 250

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    K   +KL  +  
Sbjct: 251 DTIKAK-----------------------------------GRSHAAAKEEIQKLSDVFK 275

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 276 QFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFN 335

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 336 AAIAMNKP-WSEKLHDVSDDVQRGLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 394

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 395 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 454

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 455 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 514

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 515 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 574

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 575 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 630


>gi|157372533|ref|YP_001480522.1| RNA polymerase sigma factor RpoD [Serratia proteamaculans 568]
 gi|157324297|gb|ABV43394.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia proteamaculans
           568]
          Length = 647

 Score =  466 bits (1199), Expect = e-129,   Method: Composition-based stats.
 Identities = 274/683 (40%), Positives = 380/683 (55%), Gaps = 53/683 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M +      D++         L+        K ++   +++GY+T  E+N  LP D V S
Sbjct: 15  MLLLAVSPTDTNPNTLKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDS 74

Query: 61  EQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +Q+ED + M+++MGI V++   D +D   +E++ D    A+ ++  +    +S    T D
Sbjct: 75  DQIEDIIQMINDMGIQVLEEAPDADDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTD 134

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G  
Sbjct: 135 PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEA 194

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L ++I        E          G      E    E+E D+ +E + +          
Sbjct: 195 RLSDLITGFVDPNAEEDIAPTATHVGSELSTEEQKDDEEEDDEDEEEDDN---------- 244

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                   PE A     +L +  + +   +                              
Sbjct: 245 -----SIDPELARQKFADLRDQYEATRVVI------------------------------ 269

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                +K+ +S         KL ++     L   + D LV  +  +  R+   E  +++L
Sbjct: 270 -----KKNGRSHASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKL 324

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+      E    W + A    +  W   +    D + +   +++ I  
Sbjct: 325 CVEQCKMPKKNFVTLFSSNETSDTWFAAALAMAKP-WSEKLKDVADDVQRSLQKLRQIEE 383

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 384 ETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 443

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 444 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 503

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    
Sbjct: 504 MLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE 563

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 564 LPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 623

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 624 IEAKALRKLRHPSRSEVLRSFLD 646


>gi|326629245|gb|EGE35588.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 660

 Score =  466 bits (1198), Expect = e-129,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 365/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 219

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 220 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 268

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 269 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 304

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 305 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 365 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 423

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 424 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 483

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 484 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 543

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+E PIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 544 VLKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 603

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 604 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659


>gi|304312382|ref|YP_003811980.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) [gamma
           proteobacterium HdN1]
 gi|301798115|emb|CBL46337.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) [gamma
           proteobacterium HdN1]
          Length = 627

 Score =  465 bits (1197), Expect = e-129,   Method: Composition-based stats.
 Identities = 272/659 (41%), Positives = 383/659 (58%), Gaps = 41/659 (6%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++G++T  ++N  LPPD    EQ+ED +AM+++MGI V +     
Sbjct: 5   EQQKSQLKQLIARGKEQGFLTFADVNDHLPPDITDPEQVEDIIAMINDMGIPVHEAAPGA 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +      +      AS+         D+    T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 65  EGLLRGGANPSNEDASDEESPANAVIDAEPGRTTDPVRMYMREMGSVELLTREGEIVIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M++L   P     ++    +++     L +II                   
Sbjct: 125 RIEEGIREVMSALAFWPDAVDVVLDEYSKVDSQERRLNDII------------------- 165

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       +    +V+E++    + AK +      +    E  E++  + D  E++
Sbjct: 166 --------SGYLDLAECEVEESDFQANAPAKEATLKDKDLSDDDEEEESEGESGDSSEEE 217

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            A +L   E ++R   +            L +L       ++  + S      +E+L   
Sbjct: 218 DAGSLDPEEARVRFGAL------------LDALNAAKTTREEKGRKSKPFTNAQEELANQ 265

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELDPHW 383
             +  L     + LV  + +  +R+  NE  ++ R  +   + R  F+++  G E +  W
Sbjct: 266 FITFKLVPRLFEQLVGGVRETLERVRENERAIMTRCIRIAKMPRKDFVKQFPGNETNIEW 325

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V       +  +   V    D I+K++  +  +     +SI+E + I   +  GE +A+ 
Sbjct: 326 VDKIAG-GKTAYAERVGALKDDIIKLQQNLLGLESTLSLSIAEIKEINRRISIGEAKAAR 384

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + V
Sbjct: 445 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGERMDMPEDKV 504

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D+A   +LRE T  VLASLT R
Sbjct: 505 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTMQSPVDAATAESLREATRDVLASLTAR 564

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E +VL MRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLDG
Sbjct: 565 EAKVLAMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLDG 623


>gi|62181728|ref|YP_218145.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62129361|gb|AAX67064.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|322716214|gb|EFZ07785.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 658

 Score =  465 bits (1197), Expect = e-129,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 369/656 (56%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I        E +        G 
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGS 230

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +    E E D   +   D  S               PE A               
Sbjct: 231 ELSQEDLDDDEDEEDGDDDAADDDNSID-------------PELAREKF----------- 266

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 267 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQKEILKLSEVFK 302

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 303 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 362

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 363 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 421

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 422 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 481

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 482 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 541

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 542 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 601

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 602 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 657


>gi|238796946|ref|ZP_04640450.1| RNA polymerase sigma factor rpoD [Yersinia mollaretii ATCC 43969]
 gi|238719206|gb|EEQ11018.1| RNA polymerase sigma factor rpoD [Yersinia mollaretii ATCC 43969]
          Length = 634

 Score =  465 bits (1197), Expect = e-129,   Method: Composition-based stats.
 Identities = 271/675 (40%), Positives = 376/675 (55%), Gaps = 52/675 (7%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D++         L+        K ++   +++GY+T  E+N  LP D V S+Q+ED + 
Sbjct: 9   TDTNPNTLKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQ 68

Query: 69  MLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           M+++MGI V++   D +D   +E++ D    A+ ++  +    +S    T DPVRMY+RE
Sbjct: 69  MINDMGIQVLEEAPDADDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMRE 128

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I+ 
Sbjct: 129 MGTVELLTREGEIDIAKRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLING 188

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 E          G      E    +KE               +  +++       
Sbjct: 189 FVDPNAEEDIAPTATHVGSELSTEEMDDDDKEE--------------EDEEEEEDDNSID 234

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE A      L E  +++   +                                   +K+
Sbjct: 235 PELARQKFSELREQYENTRMAI-----------------------------------KKN 259

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            +S          L ++     L   + D LV  +  +  R+   E  +++L  +   + 
Sbjct: 260 GRSHATAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMP 319

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E    W + A    +  W   +    D + +   +++ I  ETG++I +
Sbjct: 320 KKNFVTLFASNETSDTWFAAAVAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQ 378

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 379 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 438

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 439 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 498

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA  
Sbjct: 499 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATS 558

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 559 ESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 618

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 619 LRHPSRSEVLRSFLD 633


>gi|290474860|ref|YP_003467740.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus bovienii
           SS-2004]
 gi|289174173|emb|CBJ80960.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus bovienii
           SS-2004]
          Length = 616

 Score =  465 bits (1197), Expect = e-129,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 380/656 (57%), Gaps = 48/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTNDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I     + P +        E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGECRLSDLIT--GFVDPNA--------EED 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E  + ++ +++ D +  ++   D        PE A    + L +  + + 
Sbjct: 176 LSPTATHIGSELPQAELDDSDDDDDEESEDDADSEDDNSIDPELARQKFQELRDQYETTR 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            ++ +                                     +S          L ++  
Sbjct: 236 QSIKSY-----------------------------------GRSHPNTAAEILTLSEVFK 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E +++++      + +  F+    G E    W +
Sbjct: 261 QFRLIPKQFDYLVNNMRSMMDRVRLQERQIMKMCVELCKMPKKNFITLFSGNETTDTWFT 320

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +  W + ++   D +++   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 321 AAKAMNKP-WSDKLSEVEDDVMRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 379

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 380 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 439

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 440 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 499

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETP+GD+D SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 500 VLKIAKEPISMETPVGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 559

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 615


>gi|300703499|ref|YP_003745101.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CFBP2957]
 gi|299071162|emb|CBJ42476.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CFBP2957]
          Length = 873

 Score =  465 bits (1196), Expect = e-128,   Method: Composition-based stats.
 Identities = 254/674 (37%), Positives = 378/674 (56%), Gaps = 48/674 (7%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 243 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 302

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 303 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 362

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 363 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 420

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +                                   E+ A+ + +D    D   +
Sbjct: 421 LIDPNA-----------------------------------EAEAQSADEDEDFEDEEAD 445

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             + +E + D+D    +   +   ++L+   +     I + + ++R   +      K+  
Sbjct: 446 EGDEEEEDEDDDGAGGSAASARQLEELKQAALEKFSIIGDQFEKMRRAFE------KEGY 499

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 500 KSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 559

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 560 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELK 618

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 619 DVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 678

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 679 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 738

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 739 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 798

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 799 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 858

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 859 HPSRSDKLKSFLEG 872


>gi|259907100|ref|YP_002647456.1| RNA polymerase sigma factor RpoD [Erwinia pyrifoliae Ep1/96]
 gi|224962722|emb|CAX54177.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia pyrifoliae
           Ep1/96]
 gi|283476901|emb|CAY72757.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia pyrifoliae DSM
           12163]
 gi|310766301|gb|ADP11251.1| RNA polymerase sigma factor RpoD [Erwinia sp. Ejp617]
          Length = 613

 Score =  465 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 369/656 (56%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E   ++++ +   ++  D  S               PE A     +L    + + 
Sbjct: 186 ELSAEEREDEDEDEESDDDSSDDDNSID-------------PELAREKFGDLRIQYETTR 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A                                     +S        + L  +  
Sbjct: 233 TVIKAK-----------------------------------SRSHADAIAEIQNLSDVFK 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W  
Sbjct: 258 QFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETWFK 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 318 AALAMNKP-WSEKLNDVSDDVNRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|224585014|ref|YP_002638813.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|224469542|gb|ACN47372.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
          Length = 658

 Score =  464 bits (1194), Expect = e-128,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 369/656 (56%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 51  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 110

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 111 LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 170

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I        E +        G 
Sbjct: 171 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGS 230

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +    E E D   +   D  S               PE A               
Sbjct: 231 ELSQEDLDDDEDEEDGDDDAADDDNSID-------------PELAREKF----------- 266

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 267 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 302

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 303 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 362

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 363 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 421

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 422 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 481

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 482 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 541

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 542 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 601

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 602 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 657


>gi|309781724|ref|ZP_07676457.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_7_47FAA]
 gi|308919365|gb|EFP65029.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_7_47FAA]
          Length = 821

 Score =  464 bits (1194), Expect = e-128,   Method: Composition-based stats.
 Identities = 255/674 (37%), Positives = 377/674 (55%), Gaps = 47/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V  E +E  VA L++
Sbjct: 190 AASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLND 249

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +G+ V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 250 IGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 309

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 310 TVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 367

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P ++       E     + E++ +E + ++ ++ EG   +AA               
Sbjct: 368 LIDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGAAAAS-------------- 413

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                               +   ++L+   +     I E + ++R   +      K+  
Sbjct: 414 --------------------ARQLEELKQAALLKFGVIGEQFDKMRRAFE------KEGY 447

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 448 KSKPYVKAQEAIQAELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRS 507

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W+       +  +   V   V ++ +++ ++  +     + ++E +
Sbjct: 508 DFVARFPGNETNLKWIETVVADGKP-YSTIVERNVPAVHELQQKLIDLQARVVLPLTELK 566

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 567 DVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 626

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 627 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 686

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 687 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 746

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 747 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 806

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 807 HPSRSDKLKSFLEG 820


>gi|22127411|ref|NP_670834.1| RNA polymerase sigma factor RpoD [Yersinia pestis KIM 10]
 gi|21960500|gb|AAM87085.1|AE013956_10 RNA polymerase, sigma(70) factor [Yersinia pestis KIM 10]
          Length = 632

 Score =  464 bits (1194), Expect = e-128,   Method: Composition-based stats.
 Identities = 270/675 (40%), Positives = 377/675 (55%), Gaps = 52/675 (7%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D++         L+        K ++   +++GY+T  E+N  LP D V S+Q+ED + 
Sbjct: 7   TDTNPNTLKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQ 66

Query: 69  MLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           M+++MGI V++   D +D   +E++ D    A+ ++  +    +S    T DPVRMY+RE
Sbjct: 67  MINDMGIQVLEEAPDADDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMRE 126

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G + L ++I  
Sbjct: 127 MGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-- 184

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                     GF              ++     +   E   D +       D        
Sbjct: 185 ---------TGFVDPNAEEDI---APTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSID 232

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE A     +L E  +++   +                                   +K+
Sbjct: 233 PELARQKFSDLREQYENARMEI-----------------------------------KKN 257

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            ++         KL ++     L   + D LV  +  +  R+   E  +++L  +   + 
Sbjct: 258 GRNHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMP 317

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E    W + A    +  W   +    + + +   +++ I  ETG++I +
Sbjct: 318 KKNFVTLFSSNETSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQ 376

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 377 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 436

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 437 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 496

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA  
Sbjct: 497 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATS 556

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 557 ESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 616

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 617 LRHPSRSEVLRSFLD 631


>gi|71891846|ref|YP_277575.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|71795952|gb|AAZ40703.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 611

 Score =  464 bits (1194), Expect = e-128,   Method: Composition-based stats.
 Identities = 270/658 (41%), Positives = 371/658 (56%), Gaps = 57/658 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++ L +++GY+T  E+N  LP D V   Q+E+ + M+++MGI V++     DE 
Sbjct: 6   QSQLKLLVTLGKEQGYLTFSEVNDHLPEDIVDPGQIENIIQMMNDMGIQVMEEAPNSDEF 65

Query: 88  GSED---SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
              +   S +    A+ ++V      DS    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  LLIEHTHSTNDEEDATEAAVQALTNVDSELGRTTDPVRMYMREMGTVELLTREGEIDIAK 125

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+     +  G T L ++I     + P+          
Sbjct: 126 RIEDGINQVQCSVSEYPEAITYLLEQYKRVETGETRLSDLIT--GFVDPDIN-------- 175

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                  E+ S     + +         +    +++  + +  PE A      L    D 
Sbjct: 176 -------ENISIHTNINHITAEVTTESISDDDEEENNDENNIDPEIAYVKFTALRNQYDI 228

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +  T+                                 NG+   KSS +   L E    +
Sbjct: 229 TRKTI-------------------------------KYNGRNHIKSSKEILKLSE----I 253

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  + +R+   E  +++L      + +  F+    G + +  W
Sbjct: 254 FKQFRLVPKQFDYLVNNMRSMMERVRKQERLIMKLCVEISKMPKKNFIALFSGNQTNKTW 313

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            + A       W   +    + +    +++  I  ETG++I + + I   +  GE +A  
Sbjct: 314 FNTALSMHTS-WSEKLYKVDEDVQNSLSKLHQIEKETGLTIEQVKDINRRMSIGEAKARR 372

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I  EPTPEE+A+++ M  + +
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEIGHEPTPEELAERMLMSEDKI 492

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETP+GD++ SHLGDFIED N   PLDSA   NLR  T  +L+ LTPR
Sbjct: 493 RKVLKIAKEPISMETPVGDDEDSHLGDFIEDTNHDLPLDSATSDNLRTATHDILSGLTPR 552

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 553 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILRSFLD 610


>gi|307129360|ref|YP_003881376.1| RNA polymerase sigma-70 (sigma D) factor [Dickeya dadantii 3937]
 gi|306526889|gb|ADM96819.1| RNA polymerase, sigma 70 (sigma D) factor [Dickeya dadantii 3937]
          Length = 611

 Score =  464 bits (1193), Expect = e-128,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 372/655 (56%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +  G + L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   D  + + + E   +   DD + +D  PE A      L +  + +  
Sbjct: 174 LAPSTTPENAELAGDGMDDDDENEEDEEDDTDDDNSID--PELARQKFTELRDQYEATRV 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           ++ A                                     +S         KL ++   
Sbjct: 232 SIKA-----------------------------------HGRSHPTAIDEINKLSEVFKQ 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + DLLV  +  +  R+   E ++++L      + +  F+    G E +  W   
Sbjct: 257 FRLVPKQFDLLVNNMRAMMDRVRAQERQIMKLCVELCKMPKKNFVTLFTGNETNRKWFDA 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 317 ALSMGKP-WCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|241663618|ref|YP_002981978.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12D]
 gi|240865645|gb|ACS63306.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12D]
          Length = 821

 Score =  464 bits (1193), Expect = e-128,   Method: Composition-based stats.
 Identities = 255/674 (37%), Positives = 377/674 (55%), Gaps = 47/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V  E +E  VA L++
Sbjct: 190 AASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLND 249

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +G+ V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 250 IGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 309

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 310 TVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 367

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P ++       E     + E++ +E + ++ ++ EG   +AA               
Sbjct: 368 LIDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGAAAAS-------------- 413

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                               +   ++L+   +     I E + ++R   +      K+  
Sbjct: 414 --------------------ARQLEELKQAALVKFGVIGEQFDKMRRAFE------KEGY 447

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 448 KSKPYVKAQEAIQAELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRS 507

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W+       +  +   V   V ++ +++ ++  +     + ++E +
Sbjct: 508 DFVARFPGNETNLKWIETVVADGKP-YSTIVERNVPAVHELQQKLIDLQARVVLPLAELK 566

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 567 DVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 626

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 627 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 686

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 687 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 746

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 747 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 806

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 807 HPSRSDKLKSFLEG 820


>gi|45442721|ref|NP_994260.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus
           str. 91001]
 gi|45437587|gb|AAS63137.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus
           str. 91001]
          Length = 631

 Score =  463 bits (1192), Expect = e-128,   Method: Composition-based stats.
 Identities = 269/675 (39%), Positives = 376/675 (55%), Gaps = 52/675 (7%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D++         L+        K ++   +++GY+T  E+N  LP D V S+Q+ED + 
Sbjct: 6   TDTNPNTLKCGYCLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQ 65

Query: 69  MLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           M+++MGI V++   D +D   +E++ D    A+ ++  +    +S    T DPVRMY+RE
Sbjct: 66  MINDMGIQVLEEAPDADDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMRE 125

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G + L ++I  
Sbjct: 126 MGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-- 183

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                     GF              ++     +   E   D +       D        
Sbjct: 184 ---------TGFVDPNAEEDI---APTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSID 231

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE A     +L E  +++   +                                   +K+
Sbjct: 232 PELARQKFSDLREQYENARMEI-----------------------------------KKN 256

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            ++         KL ++     L   + D LV  +  +  R+   E  +++L  +   + 
Sbjct: 257 GRNHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMP 316

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E    W + A    +  W   +    + + +   +++ I  ETG++I +
Sbjct: 317 KKNFVTLFSSNETSDTWFNAAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQ 375

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 376 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 435

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+   +R+M  ++ RE
Sbjct: 436 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNGISRQMLQEMGRE 495

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA  
Sbjct: 496 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATS 555

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 556 ESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 615

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 616 LRHPSRSEVLRSFLD 630


>gi|188532569|ref|YP_001906366.1| RNA polymerase sigma factor RpoD [Erwinia tasmaniensis Et1/99]
 gi|188027611|emb|CAO95461.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia tasmaniensis
           Et1/99]
          Length = 613

 Score =  463 bits (1192), Expect = e-128,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 369/656 (56%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAINYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    +++ +   ++  D  S               PE A     +L    + + 
Sbjct: 186 ELSAEEREDDDEDEESDDDSSDDDNSID-------------PELAREKFSDLRIQYETTR 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A                                     +S     V  + L  +  
Sbjct: 233 TVIKAK-----------------------------------SRSHADAIVEIQNLSDVFK 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W  
Sbjct: 258 QFRLVPKQFDFLVNSMRVMMDRVRTQERLIMKLCVELCKMPKKNFITLFTGNETNETWFK 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 318 AALAMNKP-WSEKLNDVSEDVTRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|332288976|ref|YP_004419828.1| RNA polymerase sigma factor RpoD [Gallibacterium anatis UMN179]
 gi|330431872|gb|AEC16931.1| RNA polymerase sigma factor RpoD [Gallibacterium anatis UMN179]
          Length = 624

 Score =  463 bits (1190), Expect = e-128,   Method: Composition-based stats.
 Identities = 277/655 (42%), Positives = 377/655 (57%), Gaps = 38/655 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K++I   +++GY+T  E+N  LP D V ++Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKQLIAQGKEQGYLTYAEVNDSLPEDLVDADQIEDIIQMINDMGIQVLESAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A   +  +    +S    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLNENVT-DEDAVEEATQVLSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  ++ E P     L+   D +  G   L ++I             +       S
Sbjct: 125 EGINEVQCAVAEYPQALDHLLAQYDLVEKGEVRLSDLITGFVDPNAVDTEDYSKFMSDDS 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +  +D +   +  D  + + D +S +  S D+ S     PE A      L E    +  
Sbjct: 185 GEGEDDDNISSDDLDESDDDEDSDSESNNSADNDSDNSIDPEMAREKFSALKEQHHKTVA 244

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                    K  + + K K     L ++   
Sbjct: 245 AID-----------------------------------KYGRGNKKAKDQINALSEIFQQ 269

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSY 386
             L   + D+LV  + D+ KRI   E ++ RLA  Y  + +  F +   G E +  W+  
Sbjct: 270 FRLVPKQFDILVLSMRDMMKRIRTQERQIQRLAVEYAKMPKGTFQKAFIGHETNDAWIEK 329

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A       W   +    D I +    +K I  E+G++I++ R I   + +GE +A  AKK
Sbjct: 330 ALA-AGKNWSEKLKDYEDGIRQAIALLKVIEQESGLTITQIRQIGEKISQGELKARRAKK 388

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 389 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 448

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 449 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 508

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 509 LKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLKVATHEVLEGLTPREAK 568

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 569 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 623


>gi|332284638|ref|YP_004416549.1| RNA polymerase sigma factor RpoD [Pusillimonas sp. T7-7]
 gi|330428591|gb|AEC19925.1| RNA polymerase sigma factor RpoD [Pusillimonas sp. T7-7]
          Length = 749

 Score =  463 bits (1190), Expect = e-128,   Method: Composition-based stats.
 Identities = 256/683 (37%), Positives = 377/683 (55%), Gaps = 63/683 (9%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           GK+   D D    +       +   +  K +IKL + RGY+T  E+N  LP D V +E +
Sbjct: 125 GKRGKADKDVPARNQMTPEEQEARRNRLKVLIKLGKDRGYLTYGEINDHLPDDLVDAEAI 184

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDP 120
           +  ++  S+MGI+V D     D     D+  +        + +       DS    T DP
Sbjct: 185 DGIISTFSDMGISVYDQAPDADALLMSDNAPVASSDDDVEDEAEAALTTVDSDFGRTTDP 244

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   M+ ++   P T   ++ +   + DG   
Sbjct: 245 VRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAIAACPTTVNEILQYIQRVRDGAAQ 304

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++                                   D + + EG+  + A VS D+
Sbjct: 305 IDEVV-----------------------------------DGLIDQEGEEYAGAGVSVDN 329

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               D P     + +                  + LR K +   + I+  + ++R+  + 
Sbjct: 330 DENEDGPAGGMSSKQL-----------------EHLRTKSLKKFENISVWFSKMRTAFE- 371

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RL 359
                +D   + +    +E ++  +  +      ++ L + L +   ++   E  +L   
Sbjct: 372 -----RDGYQAQEYAEAQEAILNELMGVRFTAKMVEKLADTLREQVAQVRKLERTVLHTC 426

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ R  F++   G E + +WV   +      +   +   + ++ +I+ ++  +   
Sbjct: 427 VDRAGMPRAYFIKVFPGNETNLNWV-LEEVAAGHPYSETLERHIPAVQEIQQKLIDLQTS 485

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             + + + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 486 VVLPLKDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 545

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R  R++
Sbjct: 546 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQI 605

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP P  +A+K+ MP + VRK+LKI KEPIS+ETPIGD+D SHLGDFIED   +S
Sbjct: 606 LQETGAEPDPATLAQKMDMPEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDTGTLS 665

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P + A+  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQI
Sbjct: 666 PSEWALHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQI 725

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HPSR+ KL+SFL+G
Sbjct: 726 EAKALRKLRHPSRADKLKSFLEG 748


>gi|261344812|ref|ZP_05972456.1| RNA polymerase sigma factor RpoD [Providencia rustigianii DSM 4541]
 gi|282567259|gb|EFB72794.1| RNA polymerase sigma factor RpoD [Providencia rustigianii DSM 4541]
          Length = 616

 Score =  462 bits (1189), Expect = e-128,   Method: Composition-based stats.
 Identities = 272/656 (41%), Positives = 379/656 (57%), Gaps = 48/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I     + P +        E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIT--GFVDPNA--------EED 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E  ++++   E + E       D        PE A     +L E  +   
Sbjct: 176 LAPTATHVGSELPQEELNNDEEEEEDEDSEDSDTDDDNSIDPELARQKFSDLREQYE--- 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                               + ++  +S  K      +L  +  
Sbjct: 233 --------------------------------KTRSHIKQYGRSDAKTVAAINQLSDVFK 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++ +R+   E  +++L  +   + +  F+    G E    W++
Sbjct: 261 EFRLVPKQFDYLVNNMREMMERVRQQERTIMKLCVEQCKMPKKNFITLFGGNETSETWLT 320

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +   +  +  E D +L+    ++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 321 AAKAMNKPWSEKLLDVEED-VLRCLQRLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 379

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 380 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 439

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 440 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 499

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 500 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHEVLAGLTAREA 559

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 615


>gi|212711167|ref|ZP_03319295.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
 gi|212686335|gb|EEB45863.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
          Length = 615

 Score =  462 bits (1189), Expect = e-128,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 375/656 (57%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + + E       D        PE A     +L E  +   
Sbjct: 175 DLAPTATHVGSELPQEELDDDEEEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYE--- 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                               + ++  +S  K     E+L ++  
Sbjct: 232 --------------------------------KTRTHIKQYGRSDAKTVAAIEQLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++  R+   E  +++L  +   + +  F+    G E    W++
Sbjct: 260 EFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPKKNFITLFSGNETSETWLT 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +  W   +    + +L+    ++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAKAMNKP-WSEKLLEVEEEVLRCLQRLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHEVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|260599325|ref|YP_003211896.1| RNA polymerase sigma factor RpoD [Cronobacter turicensis z3032]
 gi|260218502|emb|CBA33681.1| RNA polymerase sigma factor rpoD [Cronobacter turicensis z3032]
          Length = 614

 Score =  462 bits (1189), Expect = e-128,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 371/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E    E E ++  +   D +++              PE A      L    + + 
Sbjct: 186 ELSQEEMDDDEDEDEESDDDSSDDDNSI------------DPELAREKFGELRTQYEVTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S+   +    KL ++  
Sbjct: 234 DTIKAK-----------------------------------GRSNAASQEEILKLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++   +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKMCVEQCKMPKKNFITLFTGNETSETWFN 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAIAMNKP-WSEKLHDVADDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|291618943|ref|YP_003521685.1| RpoD [Pantoea ananatis LMG 20103]
 gi|291153973|gb|ADD78557.1| RpoD [Pantoea ananatis LMG 20103]
 gi|327395293|dbj|BAK12715.1| RNA polymerase sigma factor RpoD [Pantoea ananatis AJ13355]
          Length = 614

 Score =  462 bits (1189), Expect = e-128,   Method: Composition-based stats.
 Identities = 276/656 (42%), Positives = 377/656 (57%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I     + P +        E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLIT--GFVDPNA--------EED 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E    D  + E D E +   S DD + +D  PE A     +L    + + 
Sbjct: 176 LAPTATHVGSELSEADRNDDEDDDEESDDDSSDDDNSID--PELAREKFSDLRTQYETTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + +                                     +S        + L  +  
Sbjct: 234 DVIKSK-----------------------------------GRSHAASVAEIQNLSDVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++ +R+   E  +++L      + +  F+    G E +  W  
Sbjct: 259 QFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIEVCKMPKKNFITLFTGNETNESWFK 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D +++   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AALAMNKP-WSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|156932573|ref|YP_001436489.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156530827|gb|ABU75653.1| hypothetical protein ESA_00355 [Cronobacter sakazakii ATCC BAA-894]
          Length = 614

 Score =  462 bits (1189), Expect = e-128,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 371/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E    E E ++  +   D +++              PE A      L    + + 
Sbjct: 186 ELSQEEMDDDEDEDEESDDDSSDDDNSI------------DPELAREKFGELRTQYEVTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S+   +    KL ++  
Sbjct: 234 DTIKAK-----------------------------------GRSNAASQEEILKLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++   +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKNFITLFTGNETSETWFN 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAIAMNKP-WSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|304396867|ref|ZP_07378747.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
 gi|304355663|gb|EFM20030.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
          Length = 613

 Score =  462 bits (1189), Expect = e-128,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 375/656 (57%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++  G + L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + + +  E+E ++  ++  D  S               PE A     +L +  + + 
Sbjct: 186 ELSEADRNDDEEEDEEDDDSSDDDNSID-------------PELAREKFSDLRKQYEATR 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + +                                     +S        + L  +  
Sbjct: 233 SVIKSK-----------------------------------GRSHAAAVAEIQNLSDVFK 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + +R+   E  +++L      + +  F+    G E +  W  
Sbjct: 258 QFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPKKNFITLFTGNETNESWFK 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D +++   ++  +  ETG++I + + I   +  GE +A  AK
Sbjct: 318 AALAMNKP-WSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVKDINRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|251791058|ref|YP_003005779.1| RNA polymerase sigma factor RpoD [Dickeya zeae Ech1591]
 gi|247539679|gb|ACT08300.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya zeae Ech1591]
          Length = 611

 Score =  462 bits (1188), Expect = e-127,   Method: Composition-based stats.
 Identities = 268/655 (40%), Positives = 368/655 (56%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +  G + L ++I        E         E   
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPNVAPENAE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    + E ++ ++   D  S               PE A      L +  + +  
Sbjct: 185 LADDGIDDDDDENEEDEDDTDDDNSID-------------PELARQKFTELRDQYEATRV 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           ++ A                                     +S         KL ++   
Sbjct: 232 SIKA-----------------------------------HGRSHPSAIEEINKLSEVFKQ 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + DLLV  +  +  R+   E ++++L      + +  F+    G E +  W   
Sbjct: 257 FRLVPKQFDLLVNNMRSMMDRVRTQERQIMKLCVELCKMPKKNFVTLFTGNETNSKWFEA 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 317 ALSMGKP-WCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|271499150|ref|YP_003332175.1| RNA polymerase sigma-70 subunit RpoD [Dickeya dadantii Ech586]
 gi|270342705|gb|ACZ75470.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya dadantii Ech586]
          Length = 611

 Score =  462 bits (1188), Expect = e-127,   Method: Composition-based stats.
 Identities = 271/655 (41%), Positives = 372/655 (56%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +  G + L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +  DD  + + D     +   DD + +D  PE A      L +  + +  
Sbjct: 174 LAPNAAPENAELADDGIDDDDDENEEDEDDTDDDNSID--PELARQKFTELRDQYEATRV 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           ++ A                                     +S         KL ++   
Sbjct: 232 SIKA-----------------------------------HGRSHPSAIEEINKLSEVFKQ 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + DLLV  +  +  R+   E ++++L      + +  F+    G E +  W   
Sbjct: 257 FRLVPKQFDLLVNNMRSMMDRVRAQERQIMKLCVELCKMPKKNFVTLFTGNETNSKWFEA 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 317 AVSMGKP-WCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
 gi|300072989|gb|ADJ62388.1| RNA polymerase sigma-70 factor transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 850

 Score =  462 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 257/672 (38%), Positives = 375/672 (55%), Gaps = 45/672 (6%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            +        +      K +IKL ++RG++T  E+N  LP + V  E +E  +   S+MG
Sbjct: 219 SDTEASEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIGTFSDMG 278

Query: 75  INVVDGDDLEDEEGSEDSLD---LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           I+V +     +     D++        A  ++       DS    T DPVRMY+REMGS+
Sbjct: 279 ISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSV 338

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + ++     + EI+D    +
Sbjct: 339 ELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAAERISKDEIKVDEIVD--GLV 396

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P             S +  ED  +E+E ++ +E+E     AA  S +            
Sbjct: 397 DPNESEQQVEAASSDSDEDDEDEEEEEEDEEEEESESTGSGAAGFSAEQL---------- 446

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                 +QL+   +     I   +  +R   +      K+  +S
Sbjct: 447 ----------------------EQLKRDALGKFAVIGTQFENMRKAFE------KEGYNS 478

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
                 +E +   +  +      ++ L + L      +   E ++L +A     + R  F
Sbjct: 479 KPYVKAQEIISNELLGIRFTAKIVEKLCDTLRAQVDEVRTVERQILDVAVNKCNMPRAHF 538

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           ++   G E++  WV         ++   ++  V +I +++ ++  +     + + + R I
Sbjct: 539 IKVFPGNEVNLDWVDGEVA-ANHDYSAVLSRNVPAIKELQQKLIDLQARVVLPLQDLRAI 597

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +  GE +A +AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 598 NKKMGAGEKKARMAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 657

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P 
Sbjct: 658 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 717

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R
Sbjct: 718 TLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMR 777

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP
Sbjct: 778 NVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 837

Query: 671 SRSKKLRSFLDG 682
           SRS KL+SFL+G
Sbjct: 838 SRSDKLKSFLEG 849


>gi|322613615|gb|EFY10556.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621208|gb|EFY18066.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624271|gb|EFY21105.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627991|gb|EFY24780.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633109|gb|EFY29851.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636314|gb|EFY33022.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322643488|gb|EFY40050.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322644793|gb|EFY41328.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322648602|gb|EFY45049.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322653654|gb|EFY49980.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657762|gb|EFY54030.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663863|gb|EFY60062.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322669126|gb|EFY65277.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672881|gb|EFY68988.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322678129|gb|EFY74192.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681305|gb|EFY77338.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322687765|gb|EFY83732.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195577|gb|EFZ80754.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199742|gb|EFZ84832.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202510|gb|EFZ87550.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323208002|gb|EFZ92948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323212446|gb|EFZ97263.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215072|gb|EFZ99820.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222802|gb|EGA07167.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323224117|gb|EGA08410.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230441|gb|EGA14559.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235207|gb|EGA19293.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323239248|gb|EGA23298.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323244394|gb|EGA28400.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323247011|gb|EGA30977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323253507|gb|EGA37336.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323256187|gb|EGA39923.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262637|gb|EGA46193.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323267267|gb|EGA50751.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269331|gb|EGA52786.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 615

 Score =  462 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 175 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 224 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVSEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|283836397|ref|ZP_06356138.1| RNA polymerase sigma factor RpoD [Citrobacter youngae ATCC 29220]
 gi|291067770|gb|EFE05879.1| RNA polymerase sigma factor RpoD [Citrobacter youngae ATCC 29220]
          Length = 615

 Score =  462 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E S      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A      L    + + 
Sbjct: 175 DMAPTATHVGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFAELRTQYEITR 234

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +   +KL ++  
Sbjct: 235 DTIKAK-----------------------------------GRSHAAAQEEIQKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|292486903|ref|YP_003529773.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
           CFBP1430]
 gi|292900702|ref|YP_003540071.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 gi|291200550|emb|CBJ47679.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 gi|291552320|emb|CBA19364.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
           CFBP1430]
 gi|312170973|emb|CBX79232.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora ATCC
           BAA-2158]
          Length = 614

 Score =  462 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 368/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    E E ++  +   D +++              PE A     +L    + + 
Sbjct: 186 ELSAEERDDDEDEDEESDDDSSDDDNSI------------DPELAREKFNDLRIQYETTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A                                     +S        + L  +  
Sbjct: 234 TVIKAK-----------------------------------SRSHADAIAEIQNLSDVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L      + +  F+    G E    W  
Sbjct: 259 QFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETSETWFK 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AALAMNKP-WSEKLNDVSEDVNRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|39546362|ref|NP_462126.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161616204|ref|YP_001590169.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167551873|ref|ZP_02345626.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|167990234|ref|ZP_02571334.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|168237909|ref|ZP_02662967.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|168243042|ref|ZP_02667974.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168262827|ref|ZP_02684800.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168463576|ref|ZP_02697493.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|194445988|ref|YP_002042478.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451693|ref|YP_002047209.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194472915|ref|ZP_03078899.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194736124|ref|YP_002116168.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197251872|ref|YP_002148141.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197264102|ref|ZP_03164176.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|198242489|ref|YP_002217192.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200389116|ref|ZP_03215728.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204928094|ref|ZP_03219294.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|207858469|ref|YP_002245120.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213425630|ref|ZP_03358380.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213586893|ref|ZP_03368719.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646106|ref|ZP_03376159.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213865054|ref|ZP_03387173.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|238910014|ref|ZP_04653851.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|61234163|sp|P0A2E3|RPOD_SALTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|61234169|sp|P0A2E4|RPOD_SALTI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|154406|gb|AAA27242.1| rpoD protein [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|161365568|gb|ABX69336.1| hypothetical protein SPAB_04007 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194404651|gb|ACF64873.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194409997|gb|ACF70216.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194459279|gb|EDX48118.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194711626|gb|ACF90847.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195633147|gb|EDX51561.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197215575|gb|ACH52972.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197242357|gb|EDY24977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197289083|gb|EDY28452.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|197937005|gb|ACH74338.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|199606214|gb|EDZ04759.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204322416|gb|EDZ07613.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205323318|gb|EDZ11157.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205331247|gb|EDZ18011.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205337819|gb|EDZ24583.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205348629|gb|EDZ35260.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|206710272|emb|CAR34630.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|301159764|emb|CBW19283.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312914239|dbj|BAJ38213.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321225894|gb|EFX50948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
          Length = 615

 Score =  462 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 175 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 224 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|308188146|ref|YP_003932277.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pantoea vagans C9-1]
 gi|308058656|gb|ADO10828.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pantoea vagans C9-1]
          Length = 613

 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 375/656 (57%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++  G + L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + + +  ++E ++  ++  D  S               PE A     +L +  + + 
Sbjct: 186 ELSEADRNDDDEEDEEDDDSSDDDNSID-------------PELAREKFSDLRKQYETTR 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + +                                     +S        + L  +  
Sbjct: 233 DVIKSK-----------------------------------GRSHAAAVAEIQNLSDVFK 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + +R+   E  +++L      + +  F+    G E +  W  
Sbjct: 258 QFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPKKNFITLFTGNETNESWFK 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D +++   ++  +  ETG++I + + I   +  GE +A  AK
Sbjct: 318 AALAMNKP-WSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVKDINRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|300718455|ref|YP_003743258.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia billingiae
           Eb661]
 gi|299064291|emb|CAX61411.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia billingiae
           Eb661]
          Length = 612

 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 366/656 (55%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E++        G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDMITGFVDPNAEAEIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E +  ++E               +   D        PE A     +L    + + 
Sbjct: 186 ELSEAERNDNDEEE--------------EDEDDAEDDNSIDPELAREKFNDLRVQYEKAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A                                     +S        + L  +  
Sbjct: 232 TVIKAK-----------------------------------GRSHADAAAEIQNLSDVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++       + +  F+    G E    W  
Sbjct: 257 QFRLVPKQFDFLVNSMRIMMDRVRTQERLIMKFCVEICKMPKKNFITLFTGNETSETWFK 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AALAMNKP-WSEKLKDVADDVQRGLMKLGQIEQETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|268590608|ref|ZP_06124829.1| RNA polymerase sigma factor RpoD [Providencia rettgeri DSM 1131]
 gi|291314000|gb|EFE54453.1| RNA polymerase sigma factor RpoD [Providencia rettgeri DSM 1131]
          Length = 617

 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 273/656 (41%), Positives = 382/656 (58%), Gaps = 47/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I     + P       +  E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIT--GFVDP-------NAEEDL 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +       S+  + +  ++ + D E       D        PE A     +L E  +   
Sbjct: 177 APTATHVGSELPQEELDKDDDEDEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYE--- 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                               + ++  +S  K     E+L ++  
Sbjct: 234 --------------------------------KTRQHIKQYGRSDAKTAAAIEQLSEVFK 261

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++  R+   E  +++L  +   + +  F+    G E    W++
Sbjct: 262 EFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPKKNFITLFSGNETSETWLT 321

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +   +  +  E + IL+    ++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 322 AAKAMNKPWSEKLLEVE-EEILRCLQRLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 380

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 381 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 440

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 441 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 500

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 501 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHEVLAGLTAREA 560

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 616


>gi|113868683|ref|YP_727172.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha H16]
 gi|113527459|emb|CAJ93804.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia
           eutropha H16]
          Length = 827

 Score =  461 bits (1185), Expect = e-127,   Method: Composition-based stats.
 Identities = 258/684 (37%), Positives = 378/684 (55%), Gaps = 45/684 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K++    +            +      K +IKL + RGY+T  E+N  LP D V SE 
Sbjct: 184 KAKEKALLKEFASTQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSET 243

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDD 119
           ++  VA L+++GI V +     +     D+   A+S   +    +      DS    T D
Sbjct: 244 IDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTD 303

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +   
Sbjct: 304 PVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAHAERVANDEI 363

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + E +D    I P +           +    ED   + E +  ++ + +  + A  S  
Sbjct: 364 KIDEFVD--GLIDPNADEAPEAPAAPAAAADDEDIESDDEEEGDEDDDDEGGAGAGASAR 421

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                                             ++L+   +     IAE + ++R   +
Sbjct: 422 QL--------------------------------EELKQNALEKFRVIAEQFDKMRRAFE 449

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 K+  +S      +E +   +  +      ++ L + L      +   E  +L +
Sbjct: 450 ------KEGYNSKPYVKAQEAIQAELMGIRFTARNVERLCDTLRGQVDEVRKLERSILNI 503

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                G+ R  F+ R  G E +  WV       +G +   V   V ++ +++ ++  +  
Sbjct: 504 VVDKCGMPRSEFVARFPGNETNLEWVHTIVADGKG-YSTIVERNVPAVHELQQKLIDLQS 562

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 563 RVVLPLKELKGVNRKMAEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 622

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 623 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 682

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N +
Sbjct: 683 ILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTL 742

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQ
Sbjct: 743 APAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQ 802

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 803 IEAKALRKLRHPSRSDKLKSFLEG 826


>gi|33519536|ref|NP_878368.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus]
 gi|33517199|emb|CAD83581.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus]
          Length = 617

 Score =  461 bits (1185), Expect = e-127,   Method: Composition-based stats.
 Identities = 265/659 (40%), Positives = 367/659 (55%), Gaps = 54/659 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE- 86
               K ++   +++GY+T  E+N  LP D + S+Q+ + + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTFSEVNDHLPEDIIDSDQLNNIIQMMNDMGIQVMEEAPDSDDF 65

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
              E    S +    A+ ++V      D+    T DPVRMY++EMG++ELL+REGEI IA
Sbjct: 66  LLTENCGTSNNDEEDATEAAVQALSHVDTDLGRTTDPVRMYMKEMGAVELLTREGEIDIA 125

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +  S+ E P     L+     +  G   L +++            GF    
Sbjct: 126 KRIEDGIHQVQCSVAEYPEAITYLLEQYKRVKTGEVRLSDLV-----------TGFVELN 174

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
             H     +         ++  +   I+       DD + VD  PE A     +L +  +
Sbjct: 175 LEHDTLSTKTIHDGYITPEIINSPIIIDDEENTENDDDNNVD--PELARKKFTDLQKQYE 232

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +  T+          ++  L                                   KL +
Sbjct: 233 KTRITIKYNGRDHHQSLLEIL-----------------------------------KLSE 257

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPH 382
           +     L   + D LV  +  +  RI   E  +++L      + +  F+    G E    
Sbjct: 258 VFKQFRLVPKQFDYLVNNMRSMMDRIRLQERLIMKLCVDVSQMPKKKFINLFSGNETSKD 317

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W++ A       W   +      I +   ++  I  ETG++I + ++I   +  GE +A 
Sbjct: 318 WLNKALSLNTS-WSQKLHNVDSKIQQSLYQLHQIEKETGLTIEQIKNINKRMAIGEAKAK 376

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 377 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 436

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EPTPEE+A+++ M  + 
Sbjct: 437 WIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQILQETGCEPTPEELAERMFMSEDK 496

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEP+S+ETPIGD++ SHLGDFIED N   PLDSA   NLR  T  VL+ LTP
Sbjct: 497 IRKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPLDSATSDNLRAATNDVLSGLTP 556

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 557 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|115358008|ref|YP_775146.1| RNA polymerase sigma factor RpoD [Burkholderia ambifaria AMMD]
 gi|115283296|gb|ABI88812.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           AMMD]
          Length = 805

 Score =  461 bits (1185), Expect = e-127,   Method: Composition-based stats.
 Identities = 253/663 (38%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 345

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E +E +   
Sbjct: 346 -------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAA 392

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 393 QASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +A  + +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLDWAEKITAEGHS-YSAVLARNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|205354126|ref|YP_002227927.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273907|emb|CAR38909.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
          Length = 615

 Score =  460 bits (1184), Expect = e-127,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 365/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 175 EMAPTATHVGYELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 224 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+E PIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|300724881|ref|YP_003714206.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297631423|emb|CBJ92120.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
          Length = 616

 Score =  460 bits (1184), Expect = e-127,   Method: Composition-based stats.
 Identities = 264/656 (40%), Positives = 375/656 (57%), Gaps = 48/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTNDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I     + P +        E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIT--GFVDPNA--------EED 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E  ++++ + + + +       D  +     PE A    + L    + + 
Sbjct: 176 LAPTATHVGSELPKEELDDDDDEEDEDRDDDSDSENDNSIDPELARQKFQELRTQYEITR 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + +            L                                    L ++  
Sbjct: 236 QAIKSYGRSNPNTAAEILT-----------------------------------LSEVFK 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E ++++   +   + +  F+    G E    W +
Sbjct: 261 QFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPKKNFITLFSGNETTDTWFT 320

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +      +  E + +++   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 321 AAKAMNKPWSNKLLEIE-EEVMRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 379

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 380 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 439

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 440 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRK 499

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETP+GD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 500 VLKIAKEPISMETPVGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 559

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 615


>gi|83648911|ref|YP_437346.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
 gi|83636954|gb|ABC32921.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
          Length = 639

 Score =  460 bits (1184), Expect = e-127,   Method: Composition-based stats.
 Identities = 270/659 (40%), Positives = 383/659 (58%), Gaps = 26/659 (3%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +     
Sbjct: 4   NSRKSRLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIMVCEEAPDA 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D     D      S +  +       ++    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 64  DTLLITDGDSTDESVAAEAAAALASVENDVGRTTDPVRMYMREMGTVELLTREGEIQIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELN-DGTTLLREIIDLEACIGPESKGGFFHGT 203
           RIE G   +MA+L   P T   ++   D    +    + ++I     + P   G      
Sbjct: 124 RIEEGLRDVMATLVYYPGTVSNILAAFDATQGEDGGRVSDVIT--GFLDPVEDGVIPEAN 181

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +       ++   E E  +    + D ++   + +D+  + +    +  +D+ +   D +
Sbjct: 182 DEIESDDVDEDEDEDEEAEESSGKDDAKAKKDLDEDEDEESEGDDNSDSDDDNDSGPDPE 241

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +                    E+ E +  L +  D      K  ++S + +   +++ +
Sbjct: 242 IARG---------------RFAELREAFNTLNAAID------KHGRASREAQECFDEVSR 280

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           +     L Q + D ++  +   +  +   E E+L +      + R  F++   G E +  
Sbjct: 281 IFAPFKLAQKQFDEIINTIRVTNDSVRKYEREILNICTRDCKMPRKNFIKMFPGNETNLE 340

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       E EW      + + I +++  I SI  E  + +++ + I   +  GE +A 
Sbjct: 341 WVKGLGARSE-EWAKTAQTKEEEITRLQRRIVSIQNEVDLPVADIKEIHRRISIGEAKAR 399

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 400 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R M  ++ RE TPEE+AKK+ MP + 
Sbjct: 460 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRHMLQEMGREATPEELAKKMDMPEDK 519

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPIS+ETPIGD++ SHLGDFIED +A SP+DSA    L+E+T RVLA LT 
Sbjct: 520 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSHAESPIDSATTEGLKESTRRVLAGLTA 579

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSF+D
Sbjct: 580 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFID 638


>gi|289207448|ref|YP_003459514.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           K90mix]
 gi|288943079|gb|ADC70778.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           K90mix]
          Length = 629

 Score =  460 bits (1184), Expect = e-127,   Method: Composition-based stats.
 Identities = 268/659 (40%), Positives = 386/659 (58%), Gaps = 35/659 (5%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++GY+T  E+N  LP   + S+Q+ED +AM+++MGI V +     
Sbjct: 4   EEQQSQLKELIAKGKEQGYLTYTEVNDHLPDSIIDSDQVEDIIAMINDMGIAVHEQAPDA 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D     D    A   +  +V      DS    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 64  DSLLLSDGSVSADEDAEDAVAALASADSDFGRTTDPVRMYMREMGTVELLTREGEIRIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ +L   P   + LI   D++ +    L +++   + I P++         
Sbjct: 124 RIEEGLMQVLFALAHHPGAIEHLIREYDQIVENNGRLTDLV--VSFIDPKNPLDGEAVAR 181

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +    ++E ++    E   ++++  +  +D   +   P +   + E         
Sbjct: 182 GLVSPEDAQKAEEAQKAAAAEASPELDAIVEEVEDAEEEDAEPVDTGPDPE--------- 232

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                                E  E + +LR L   A    + +         +E   K 
Sbjct: 233 ---------------------EARERFNKLRKLHAKAHKAFE-KGDRKAYATAREATAKY 270

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L    +D L  +L+    RI  +E  ++ LA     + R  F++     E +  W
Sbjct: 271 FMEFKLVPRMVDQLTTKLHGTIDRIRSHERRIMELAVNQAQMPRKSFIDSFPKNETNLDW 330

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +  A    +G++   +A   D I++++ ++  I  E  ++ISE + I   +  GE +A  
Sbjct: 331 IKQACK-AKGKYTTALAEHEDEIVRLQKKLAEIEHEASLNISEIKEINRRMSIGEAKARR 389

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + +
Sbjct: 450 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERMEMPEDKI 509

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI+KEPIS+ETPIGD++ SHLGDFIED+   SP DSA + +L E T  +L++LTPR
Sbjct: 510 RKVLKISKEPISMETPIGDDEDSHLGDFIEDEKVASPSDSAARESLSEATREILSTLTPR 569

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+R++ LR++ D 
Sbjct: 570 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRAELLRTYTDA 628


>gi|11993459|gb|AAG42748.1|AF299295_2 RNA polymerase sigma factor [Zymomonas mobilis]
          Length = 763

 Score =  460 bits (1184), Expect = e-127,   Method: Composition-based stats.
 Identities = 294/683 (43%), Positives = 417/683 (61%), Gaps = 26/683 (3%)

Query: 8   NRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMED 65
              +    +++ D+ + D ++ S +K I   ++  YVT ++LN  LP D     +++  +
Sbjct: 3   ETTTAEAKKNAGDAPLIDLNETSIRKFITQPKKTEYVTYDQLNEALPQDQDVFGTDRKYN 62

Query: 66  TVAMLSNMGINVVDG---DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
               ++       +    D  ++EE +   L       + S    +RK          V 
Sbjct: 63  VCPFVNGHQYRKNEDSGQDGQQEEENAAKKLQGQRWHFSGSGHYDQRKKHPTEQMIRCVC 122

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +  + + S    SREGEIAIAKRIEAGR  M+  LCESP+TF  +I W + LN+GT  LR
Sbjct: 123 ISAKWVRS-SFWSREGEIAIAKRIEAGRDTMILGLCESPITFDNIIEWSNALNEGTLQLR 181

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           EIIDL+A +           T+G S  + E+   + + +  +   G          DD  
Sbjct: 182 EIIDLDAML-----------TQGPSPDQFEEDGDDNDNEISERNAGPTFKEDDDEDDDSE 230

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
                 EN +  +R   ++ED++  +L+ ME+QL+P  +    +IA++YR+   LQ+  +
Sbjct: 231 GELD--ENGQRIQRENMDEEDENTLSLAQMEEQLKPASLEKFAKIADLYRQFSVLQNARM 288

Query: 303 -----NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                N +  E      + L+E+L   V S+  + +RI+ LVEQLY+ + R+    G++L
Sbjct: 289 RALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIEFLVEQLYNYNSRLRTLNGQML 348

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA+ Y + RD FL  + G E++  WV       +    NF   E +SI +IR+E+  I+
Sbjct: 349 RLAERYKVPRDSFLNAYLGNEMEEGWVERVFKNRQK-MGNFTTSEAESIERIRSEVAEIA 407

Query: 418 VETGISISEFRHIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             TG+++ E R IV+MV+KG   +  + K E ++     +  + K         L L + 
Sbjct: 408 QVTGMTVKELRRIVTMVQKGRKRSPHSLKPEWLKPICVWLSLLPKNIPIAVCSSLXLFRX 467

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
              GLMKA  KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+
Sbjct: 468 AISGLMKAVGKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTS 527

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++ ++I REPTPEE+A++L+MP+E VRKV+KI KEPISLETPIGDE+ SHLGDFIEDKN
Sbjct: 528 RQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKN 587

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ P+D+AIQANL+ET TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERI
Sbjct: 588 AIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 647

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAKA+RKLKHPSRS+K+RSF
Sbjct: 648 RQIEAKALRKLKHPSRSRKMRSF 670


>gi|322831339|ref|YP_004211366.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
 gi|321166540|gb|ADW72239.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
          Length = 612

 Score =  460 bits (1182), Expect = e-127,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 371/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+  D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENRPDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I     + P ++          
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEVRLSDLIT--GFVDPNAE---------- 173

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             ++   ++     +   E + D +       D        PE A      L E  + + 
Sbjct: 174 --EEIAPTATHVGSELTTEEQDDDDEDEDEDDDAEDDNSIDPELARQKFTELREQHEATR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL  +  
Sbjct: 232 LVI-----------------------------------KKNGRSHKSAAEEILKLSDVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++   +   + +  F+    G E    W  
Sbjct: 257 QFRLVPKQFDFLVNSMRSMMDRVRAQERLIMKVCVEQCKMPKKNFVNLFAGNETSDTWFD 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AALAMGKP-WSEKLKEVTEDVQRGLMKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|283787203|ref|YP_003367068.1| RNA polymerase sigma-70 factor [Citrobacter rodentium ICC168]
 gi|282950657|emb|CBG90329.1| RNA polymerase sigma-70 factor [Citrobacter rodentium ICC168]
          Length = 614

 Score =  460 bits (1182), Expect = e-127,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 369/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +    E E ++  +   D +++              PE A      L    + + 
Sbjct: 186 ELSQEDLDDDEDEDEEEDDDSADDDNSI------------DPELAREKFAELRTQYEVTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +    KL ++  
Sbjct: 234 DTIKAK-----------------------------------GRSHADAQAEILKLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAIAMNKP-WSEKLHDVADEVHRGLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|238897855|ref|YP_002923534.1| RNA polymerase, sigma 70 (sigma D) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229465612|gb|ACQ67386.1| RNA polymerase, sigma 70 (sigma D) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 610

 Score =  460 bits (1182), Expect = e-127,   Method: Composition-based stats.
 Identities = 274/656 (41%), Positives = 370/656 (56%), Gaps = 54/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLIARGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEQAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ +    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTGETHDDAVEAATQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I+    + P  +     G    
Sbjct: 126 EEGIHQVQCSVAEYPEAITYLLEQYDRVELGALRLSDLIN--GFVDPNIQENVLPGAIHV 183

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  +    ++E  D  E E D                  PE A+     L    + + 
Sbjct: 184 GSELSDAEIDDEEDSDTSEVEDDNSI--------------DPELAQQKFSELRAQYESTR 229

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +              L                                   KL ++  
Sbjct: 230 TAIKQKGRHHLTTATEIL-----------------------------------KLAEIFK 254

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
             SL   + D LV  +  +  R+   E  +L+L  +   + +  F+E     E +  W+ 
Sbjct: 255 QFSLVPKQFDYLVSSMRSMMDRVRVQERLILKLCVEQCKMPKKNFIELFLNNETNNSWLK 314

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +   ++ +     +++ I  ETG+SI + + I   +  GE +A  AK
Sbjct: 315 TALAM-KKPWVEKLNDVLEDVQSNVQKLRQIEEETGLSIEQVKDINRRMAIGEAKARRAK 373

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 374 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 433

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP E +RK
Sbjct: 434 QAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPAPEELAERMLMPEEKIRK 493

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 494 VLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRLATNDVLAGLTAREA 553

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD
Sbjct: 554 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLKSFLD 609


>gi|289827081|ref|ZP_06545870.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 615

 Score =  460 bits (1182), Expect = e-127,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 175 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 224 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFIMLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|238762467|ref|ZP_04623438.1| RNA polymerase sigma factor rpoD [Yersinia kristensenii ATCC 33638]
 gi|238699452|gb|EEP92198.1| RNA polymerase sigma factor rpoD [Yersinia kristensenii ATCC 33638]
          Length = 613

 Score =  460 bits (1182), Expect = e-127,   Method: Composition-based stats.
 Identities = 272/656 (41%), Positives = 373/656 (56%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I+       E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    + + D+ +E E D  S               PE A      L E  +++ 
Sbjct: 186 ELSTEERDDDDDKEDEDEEEEEDDNSID-------------PELARQKFSELREQYENTR 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S          L ++  
Sbjct: 233 MAI-----------------------------------KKNGRSHASAAAEILNLSEVFK 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 258 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 318 AAVAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|183597880|ref|ZP_02959373.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
 gi|188022641|gb|EDU60681.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
          Length = 617

 Score =  459 bits (1181), Expect = e-127,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 379/656 (57%), Gaps = 47/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I     + P       +  E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDHVEAGESRLSDLIT--GFVDP-------NAEEDL 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +       S+  + +  ++ + D +       D        PE A      L    +   
Sbjct: 177 APTATHVGSELPQEELDKDDDEDEDDEDGDDSDSDDDNSIDPELAREKFSELRAQYE--- 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                               + ++  +++ +     E+L ++  
Sbjct: 234 --------------------------------KTRQHIKQFGRNNAQTAQAIEELSEVFK 261

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++  R+   E  +++L  +   + +  F+    G E    W++
Sbjct: 262 QFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPKKNFITLFSGNETSETWLT 321

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +  W   +    + IL+    ++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 322 AAKAMNKP-WCEKLVEVEEEILRCLQRLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 380

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 381 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 440

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 441 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRK 500

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 501 VLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATSESLRSATHEVLAGLTAREA 560

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 616


>gi|293604556|ref|ZP_06686961.1| DNA-directed RNA polymerase sigma subunit RpoD [Achromobacter
           piechaudii ATCC 43553]
 gi|292817137|gb|EFF76213.1| DNA-directed RNA polymerase sigma subunit RpoD [Achromobacter
           piechaudii ATCC 43553]
          Length = 770

 Score =  459 bits (1181), Expect = e-127,   Method: Composition-based stats.
 Identities = 254/664 (38%), Positives = 371/664 (55%), Gaps = 66/664 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D     
Sbjct: 166 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDA 225

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 226 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 285

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 286 IAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVD-----------GLVD 334

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ D+    D P     + +      
Sbjct: 335 PEDGEEY-----------------------AGAGVTADEDESDDGPAGGMSSKQL----- 366

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+ + + ++R   +      KD   S      +E +
Sbjct: 367 ------------EDLRVKALAKFDEVGKQFDKMRLSYE------KDGYKSDIYVRAQESI 408

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
              +  +      ++ L + L +  + +   E  +L       G+ R  F++   G E +
Sbjct: 409 QNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTHFIKVFPGNETN 468

Query: 381 PHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
             WV    A   P  E    +  ++ ++ +++ ++  +     + + + + +   +  GE
Sbjct: 469 LQWVVDEVAAGHPYAE---TLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGE 525

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 526 AKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 585

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ M
Sbjct: 586 YATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDM 645

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+    VL 
Sbjct: 646 PEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDVVKEVLD 705

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+S
Sbjct: 706 SLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKS 765

Query: 679 FLDG 682
           FL+G
Sbjct: 766 FLEG 769


>gi|226946707|ref|YP_002801780.1| RNA polymerase sigma factor RpoD [Azotobacter vinelandii DJ]
 gi|226721634|gb|ACO80805.1| RNA polymerase sigma factor, sigma70; RpoD [Azotobacter vinelandii
           DJ]
          Length = 620

 Score =  459 bits (1181), Expect = e-127,   Method: Composition-based stats.
 Identities = 271/657 (41%), Positives = 381/657 (57%), Gaps = 44/657 (6%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDTD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T   ++     +      L +I  L   I P+         E 
Sbjct: 125 IEEGIREVMSAIAHFPGTVDGILAEYQRVTSEGGRLSDI--LSGYIDPDDDSAVPAEAEV 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               K +                   +A   + +D  + +S   +++++E +   D + +
Sbjct: 183 PVDLKSK------------------SAATPAASEDEDEDESEESDSDDEEGDGGPDPEIA 224

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                A+ +QL    +                       ++  + SV+     + L  L 
Sbjct: 225 RQRFGAVAEQLGRTRVAL---------------------ERHGRHSVEGLEALQALASLF 263

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LVEQ+ D   R+   E  +++L      + R  FL +  G E D  WV
Sbjct: 264 MPIKLVPKQYDTLVEQVRDALTRVRAQERAIMQLCVRDARMPRADFLRQFPGNETDQDWV 323

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  + ++   +    D I + + ++  +  + G++I+E + I   +  GE +A  A
Sbjct: 324 DLLAK-GKAKYAEALGNLADDIKQCQQKLIDLEQKVGLTIAEIKDINRQMSIGEAKARRA 382

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 383 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 442

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 443 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKIR 502

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E T  VLA LT RE
Sbjct: 503 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVATVESLKEATREVLAGLTARE 562

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 563 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 619


>gi|238756616|ref|ZP_04617911.1| RNA polymerase sigma factor rpoD [Yersinia ruckeri ATCC 29473]
 gi|238705164|gb|EEP97586.1| RNA polymerase sigma factor rpoD [Yersinia ruckeri ATCC 29473]
          Length = 613

 Score =  459 bits (1181), Expect = e-127,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 368/656 (56%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTNDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIIGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                             E   D         D        PE A     +L E  +++ 
Sbjct: 186 ELS-------------TAEMGDDENEDEDEDDDSEDDNSIDPELARQKFSDLREQYENAR 232

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S +       KL ++  
Sbjct: 233 KEI-----------------------------------KKNGRSHISAAAEILKLSEVFK 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 258 QFRLVPKQFDYLVNNMRTMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 318 AALAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|222034799|emb|CAP77541.1| RNA polymerase sigma factor rpoD [Escherichia coli LF82]
          Length = 613

 Score =  459 bits (1180), Expect = e-127,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 363/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYIVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIA Q+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIAVQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|261342495|ref|ZP_05970353.1| RNA polymerase sigma factor RpoD [Enterobacter cancerogenus ATCC
           35316]
 gi|288315137|gb|EFC54075.1| RNA polymerase sigma factor RpoD [Enterobacter cancerogenus ATCC
           35316]
          Length = 614

 Score =  459 bits (1180), Expect = e-127,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 371/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E S +    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E    E E ++  +   D +++              PE A      L    + + 
Sbjct: 186 ELSQEEMDDDEDEDEEEDDDSSDDDNSI------------DPELAREKFAELRTQYELAR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +    KL ++  
Sbjct: 234 DTIKAK-----------------------------------GRSHAAAQEQILKLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFN 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAIAMNKP-WSEKLHDVKDDVHRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|149910043|ref|ZP_01898691.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149806911|gb|EDM66872.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 609

 Score =  459 bits (1180), Expect = e-127,   Method: Composition-based stats.
 Identities = 266/660 (40%), Positives = 375/660 (56%), Gaps = 54/660 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDD 82
            +      K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D
Sbjct: 1   MESPQSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQVEDIIQMINDMGIQVLETAPD 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            +D   +E++      A+ ++       +S    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 61  ADDLLMAENTTAPDDDAAEAAAAALASVESEIGRTTDPVRMYMREMGTVELLTREGEIVI 120

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  ++ E P    +L+   D+     + L +II            GF   
Sbjct: 121 AKRIEEGIYAVQTAVAEYPEAINSLLAEYDKFLAEESRLSDII-----------TGFIDP 169

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                         E     V + + + +S     +++       PE A           
Sbjct: 170 NADDVAPTATHIGSE-----VTKKQNESDSTDDDEEEEEGNKGPDPEEAAEKF------- 217

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                       +LR      L  I +                       K ++  E L 
Sbjct: 218 -----------AELRKHHTALLKGIKD-----------------HGLDHPKTRLHVEMLS 249

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
           ++  +  L   + D +V  + D+   +   E  +++   +   + +  F+E   G E D 
Sbjct: 250 EVFRTFRLIPKQFDRIVNSMRDMMDHVRVQERLVIKMCVEQCKMPKAAFVEAFAGNETDF 309

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W   A+             + D + +  N++K +   TG++IS+ ++I   +  GE +A
Sbjct: 310 TWFEKAQQSAAPYAPALQRIDFD-VRRCINKLKLVENTTGLTISQIKNINRRMSIGEAKA 368

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 369 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 428

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP +
Sbjct: 429 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMMMPED 488

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A + +L+  T  VLA LT
Sbjct: 489 RIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLSLPVDAATKDSLKGATDDVLAGLT 548

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 549 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 608


>gi|296104731|ref|YP_003614877.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059190|gb|ADF63928.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 615

 Score =  459 bits (1180), Expect = e-127,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 366/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E S +    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A      L    + + 
Sbjct: 175 DMAPTATHVGSELSQEEMDDDEDEDEEESDDDSADDDNSIDPELAREKFAELRTQYEVTR 234

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +    KL ++  
Sbjct: 235 DTIKAK-----------------------------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVKEDVHRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|157148639|ref|YP_001455958.1| RNA polymerase sigma factor RpoD [Citrobacter koseri ATCC BAA-895]
 gi|157085844|gb|ABV15522.1| hypothetical protein CKO_04466 [Citrobacter koseri ATCC BAA-895]
          Length = 614

 Score =  459 bits (1180), Expect = e-127,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 371/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ +    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E    + E ++  +   D +++              PE A      L    + + 
Sbjct: 186 ELSQEEMDDDDDEDEEEDDDSSDDDNSI------------DPELAREKFAELRTQYEVTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +    KL ++  
Sbjct: 234 DTIKAK-----------------------------------GRSHADAQTEILKLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAIAMNKP-WSEKLHDVTEDVQRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|37678745|ref|NP_933354.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus YJ016]
 gi|37197486|dbj|BAC93325.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus YJ016]
          Length = 643

 Score =  458 bits (1179), Expect = e-127,   Method: Composition-based stats.
 Identities = 265/656 (40%), Positives = 372/656 (56%), Gaps = 40/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 25  QSQLKLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 84

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 85  ALSDETNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 144

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I     + P +           
Sbjct: 145 EDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPNADETAAPTATHI 202

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  E   ++++  D+ + + D +     S D    V   PE A      L        
Sbjct: 203 GSELAESDLEDEDNTDIDDEDEDEDEDGDSSSDSEEDVGIDPEMALEKFTQLRNSY---- 258

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          Q+  +   +  + S +     E ++ +  
Sbjct: 259 -------------------------------QNLQLAVNEHGRESAQTAQAHELMLDVFK 287

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++ A     + +  F+    G E +  W+ 
Sbjct: 288 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGNESNEEWLD 347

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++++I  ET +S++  + I   +  GE +A  AK
Sbjct: 348 QILA-SDKPYVEKIKLHEEDIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAK 406

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 407 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 466

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 467 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 526

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 527 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREA 586

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 587 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 642


>gi|301325578|ref|ZP_07219046.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 78-1]
 gi|300847629|gb|EFK75389.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 78-1]
          Length = 613

 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDPTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|319760203|ref|YP_004124141.1| RNA polymerase sigma factor [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318038917|gb|ADV33467.1| RNA polymerase sigma factor [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 620

 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/660 (40%), Positives = 382/660 (57%), Gaps = 53/660 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  L  D + S+Q+ + + M+++MGI V++     DE 
Sbjct: 6   QSQLKLLVTRGKEQGYLTFSEVNDHLSEDIIDSDQLHNIIQMMNDMGIQVMEEAPDSDEF 65

Query: 88  GSEDSLD-----LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
               + D         A+ ++V      D     T DPVRMY++EMG++ELL+REGEI I
Sbjct: 66  LLTKNCDTVVNNDEEDATEAAVQALSNTDPDLGRTTDPVRMYMKEMGAVELLTREGEIDI 125

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  S+ E P     L+     +  G T L ++I                 
Sbjct: 126 AKRIEDGINQVQCSVAEYPEAITYLLEQYQRVETGETRLSDLITGFV------------- 172

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                              D+     ++E+   +++ +   + S      +DE N + ++
Sbjct: 173 -------------------DLDNFNQNVETIPNITQQNIHHLSSNILTVTDDEENTENED 213

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           DD++     ++ +L  K   AL +  E  R     Q    NG+  +KSS +   L E   
Sbjct: 214 DDNS-----IDPELARKKFIALRKQYETTR-----QTIKYNGRNHDKSSSEILKLSE--- 260

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +     L   + D LV  +  +  RI  +E  +++L      + +  F++   G E + 
Sbjct: 261 -IFKQFRLVPKQFDYLVNNMRSMMDRIRFHERLIMKLCVDISKMPKKKFIDLFSGNETNK 319

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W+  A     G W   +      + +   ++  I  ETG++I + ++I   +  GE +A
Sbjct: 320 AWLIQALSMNAG-WAKKLDTVNAEVQQNIWQLYQIEKETGLTIEQVKNINRRMSIGEAKA 378

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EPTPEE++K++ +  +
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGCEPTPEELSKRMLISED 498

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEP+S+ETPIGD++ SHLGDFIED N   PLDSA   NL+  T  VL+ LT
Sbjct: 499 KIRKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPLDSATSDNLKAATNDVLSGLT 558

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 PREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRSEILRSFLD 618


>gi|172062815|ref|YP_001810466.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
 gi|171995332|gb|ACB66250.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
          Length = 805

 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 345

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E ++ +   
Sbjct: 346 -------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAA 392

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 393 QATANAAQLEA----LKRASLDKFSQISEWFDKMRRAFE------KEGYKSKSYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLDWAEKIAAEGHS-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|238024932|ref|YP_002909164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
 gi|237879597|gb|ACR31929.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
          Length = 805

 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 250/663 (37%), Positives = 369/663 (55%), Gaps = 45/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 183 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 242

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 243 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 302

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 303 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDPNAEDTDGFN 362

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                 + +  E+  +  E ++ ++ +G  ++ A  ++ +                    
Sbjct: 363 AKEAEEAEEAEEEEEEANEDEEEEDDDGAAQATANAAQLEA------------------- 403

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 404 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLTWAEKVAAESHS-YSAILVRNIPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|238896571|ref|YP_002921314.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae NTUH-K2044]
 gi|238548896|dbj|BAH65247.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 632

 Score =  458 bits (1178), Expect = e-126,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 365/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 25  QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 84

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 85  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 143

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 144 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 192

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +       +        PE A      L    + +  
Sbjct: 193 MAPTATHVGSELSQEEMDDDEDEDEDEDADDNSDDDNSIDPELAREKFAELRTQYELTRD 252

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 253 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 277

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 278 FRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNA 337

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 338 AVAMNKP-WSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 396

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 397 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 456

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 457 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 516

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 517 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 576

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 577 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 631


>gi|37527834|ref|NP_931179.1| RNA polymerase sigma factor RpoD [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787270|emb|CAE16351.1| RNA polymerase sigma factor rpoD (Sigma-70) [Photorhabdus
           luminescens subsp. laumondii TTO1]
          Length = 614

 Score =  458 bits (1178), Expect = e-126,   Method: Composition-based stats.
 Identities = 275/656 (41%), Positives = 382/656 (58%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAETANDTDEDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I     + P +        E  
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--GFVDPNA--------EEE 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E  ++++ + E D +  +    DD + +D  PE A    + L +  D + 
Sbjct: 176 LAPTATHVGSELPQEELDDDEDDDDEDSDDDSDDDNSID--PELARQKFQELRQQYDITR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          Q+   NG+    ++ +   L E    +  
Sbjct: 234 -------------------------------QEIKENGRNHPNTAAEILKLSE----VFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E ++++   +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPKKNFITLFSGNETSDIWFT 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            AK   +   +  +  E D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAKAMNKPWSEKLLEVE-DEVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|91212497|ref|YP_542483.1| RNA polymerase sigma factor RpoD [Escherichia coli UTI89]
 gi|117625379|ref|YP_855524.1| RNA polymerase sigma factor RpoD [Escherichia coli APEC O1]
 gi|218560154|ref|YP_002393067.1| RNA polymerase sigma factor RpoD [Escherichia coli S88]
 gi|218691372|ref|YP_002399584.1| RNA polymerase sigma factor RpoD [Escherichia coli ED1a]
 gi|227887792|ref|ZP_04005597.1| RNA polymerase sigma factor RpoD [Escherichia coli 83972]
 gi|237706170|ref|ZP_04536651.1| RNA polymerase sigma factor RpoD [Escherichia sp. 3_2_53FAA]
 gi|300973231|ref|ZP_07172070.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 45-1]
 gi|301048094|ref|ZP_07195132.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 185-1]
 gi|306816579|ref|ZP_07450711.1| RNA polymerase sigma factor RpoD [Escherichia coli NC101]
 gi|331648869|ref|ZP_08349957.1| RNA polymerase sigma factor RpoD [Escherichia coli M605]
 gi|331659358|ref|ZP_08360300.1| RNA polymerase sigma factor RpoD (Sigma-70) [Escherichia coli
           TA206]
 gi|91074071|gb|ABE08952.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
           high temperatures [Escherichia coli UTI89]
 gi|115514503|gb|ABJ02578.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
           high temperatures [Escherichia coli APEC O1]
 gi|218366923|emb|CAR04694.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli S88]
 gi|218428936|emb|CAR09739.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli ED1a]
 gi|226899210|gb|EEH85469.1| RNA polymerase sigma factor RpoD [Escherichia sp. 3_2_53FAA]
 gi|227835188|gb|EEJ45654.1| RNA polymerase sigma factor RpoD [Escherichia coli 83972]
 gi|281180121|dbj|BAI56451.1| RNA polymerase sigma factor RpoD [Escherichia coli SE15]
 gi|294493374|gb|ADE92130.1| RNA polymerase sigma factor RpoD [Escherichia coli IHE3034]
 gi|300300014|gb|EFJ56399.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 185-1]
 gi|300410811|gb|EFJ94349.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 45-1]
 gi|305850144|gb|EFM50603.1| RNA polymerase sigma factor RpoD [Escherichia coli NC101]
 gi|307555174|gb|ADN47949.1| hypothetical protein ECABU_c34860 [Escherichia coli ABU 83972]
 gi|307625318|gb|ADN69622.1| RNA polymerase sigma factor RpoD [Escherichia coli UM146]
 gi|312947638|gb|ADR28465.1| RNA polymerase sigma factor RpoD [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315288818|gb|EFU48216.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 110-3]
 gi|315295035|gb|EFU54372.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 153-1]
 gi|315297744|gb|EFU57021.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 16-3]
 gi|320195230|gb|EFW69859.1| RNA polymerase sigma factor RpoD [Escherichia coli WV_060327]
 gi|323951399|gb|EGB47274.1| RNA polymerase sigma proteinRpoD [Escherichia coli H252]
 gi|323957772|gb|EGB53486.1| RNA polymerase sigma proteinRpoD [Escherichia coli H263]
 gi|324008872|gb|EGB78091.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 57-2]
 gi|330909133|gb|EGH37647.1| RNA polymerase sigma factor RpoD [Escherichia coli AA86]
 gi|331042616|gb|EGI14758.1| RNA polymerase sigma factor RpoD [Escherichia coli M605]
 gi|331053940|gb|EGI25969.1| RNA polymerase sigma factor RpoD (Sigma-70) [Escherichia coli
           TA206]
          Length = 613

 Score =  458 bits (1178), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYIVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|197286218|ref|YP_002152090.1| RNA polymerase sigma factor RpoD [Proteus mirabilis HI4320]
 gi|227357334|ref|ZP_03841691.1| RNA polymerase sigma-70 factor [Proteus mirabilis ATCC 29906]
 gi|194683705|emb|CAR44685.1| RNA polymerase sigma-70 factor [Proteus mirabilis HI4320]
 gi|227162597|gb|EEI47586.1| RNA polymerase sigma-70 factor [Proteus mirabilis ATCC 29906]
          Length = 618

 Score =  458 bits (1178), Expect = e-126,   Method: Composition-based stats.
 Identities = 272/656 (41%), Positives = 378/656 (57%), Gaps = 46/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENSNDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I   A I P ++          
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--AFIDPNAE------EVAE 177

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           S         ++  +   + + D +  +    D        PE A      L E  + + 
Sbjct: 178 SDDVNLGKDDDEIDNSADDEDEDEDEDSDTDSDSDDDNSIDPELARQKFTELREQYEKTR 237

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            ++ A     +   +  L                                   +L ++  
Sbjct: 238 QSIKAKGRNHKDTELEIL-----------------------------------QLSEIFK 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++  R+   E  ++RL      + +  F+    G E +  W +
Sbjct: 263 QFRLVPKQFDYLVNNMREMMDRVRAQERHIMRLCVDQVKMPKKNFITLFTGNETNDTWFT 322

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A+   +  W   +A   + + +   +++ I VETG++I + + I   +  GE +A  AK
Sbjct: 323 AARAMNKP-WSEKLAGIEEEVQRSLQKLQQIEVETGLTIEQVKDINRRMSIGEAKARRAK 381

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 382 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 441

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 442 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRK 501

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL  LT RE 
Sbjct: 502 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHEVLGGLTLREA 561

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 617


>gi|104779687|ref|YP_606185.1| RNA polymerase sigma factor RpoD [Pseudomonas entomophila L48]
 gi|95108674|emb|CAK13368.1| sigma D (sigma 70) factor of RNA polymerase [Pseudomonas
           entomophila L48]
          Length = 616

 Score =  458 bits (1178), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/657 (40%), Positives = 373/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   +I   D +      L +++            G+    + 
Sbjct: 125 IEEGIREVMGAIAHFPGTVDYIISEYDRVTAEGGRLSDVL-----------SGYIDPDDN 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E      +    +E E + +  A+ S D+      P             D   +
Sbjct: 174 IAAPTEEVPIPGAKAAAAKEEEDEDDENAESSDDEEEAESGP-------------DPVVA 220

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A    A+ DQL    +  L  +                  K  ++  +     + L  L 
Sbjct: 221 AQRFGAVNDQL----VITLKVLK-----------------KHGRTHAESIGAMQALADLF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LVE++     R+   E  +++L      + R  FL      E D  W 
Sbjct: 260 MPIKLVPKQFDALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLFPSNETDQTWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     W   +  +  +I+  + ++  +  ETG++++E + I   +  GE +A  A
Sbjct: 320 GDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|227113748|ref|ZP_03827404.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 611

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 375/656 (57%), Gaps = 53/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                   +      ++   E D +   +  +++       PE A      L E  + + 
Sbjct: 175 DI----APTATHVGSELSSEEMDDDDEEEEDEEEEDDNSIDPELAREKFTELREQYETTR 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A     R   + A + +                                 L ++  
Sbjct: 231 QVIKA---HGRSHALAAQEILN--------------------------------LSEVFK 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E +  W +
Sbjct: 256 QFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNETNSTWFA 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 316 AAVAMGKP-WSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|170723972|ref|YP_001751660.1| RNA polymerase sigma factor RpoD [Pseudomonas putida W619]
 gi|169761975|gb|ACA75291.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida W619]
          Length = 616

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 370/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++   D +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIA------- 175

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +  +       K     +E + + ES      ++ ++    P  A      + +    +
Sbjct: 176 -APTEEVPIPGAKAAAAKEEADDEEESDDSSDDEEETESGPDPVVAAQRFGAVSDQLAIT 234

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  +S  +     + L  L 
Sbjct: 235 LKVL-----------------------------------KKHGRSHAESIGAMQALADLF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D+LVE++ D   R+   E  +++L      + R  FL      E D  W 
Sbjct: 260 MPIKLVPKQFDVLVERVRDALARLRQQERAIMQLCVRDARMPRADFLRLFPSNETDQTWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     W   +  +  +I+  + ++  +  ETG++++E + I   +  GE +A  A
Sbjct: 320 GDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|187733221|ref|YP_001881829.1| RNA polymerase sigma factor RpoD [Shigella boydii CDC 3083-94]
 gi|187430213|gb|ACD09487.1| RNA polymerase sigma factor RpoD [Shigella boydii CDC 3083-94]
          Length = 613

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSTDDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|15803609|ref|NP_289642.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 EDL933]
 gi|15833204|ref|NP_311977.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           Sakai]
 gi|24114367|ref|NP_708877.1| RNA polymerase sigma factor RpoD [Shigella flexneri 2a str. 301]
 gi|74313602|ref|YP_312021.1| RNA polymerase sigma factor RpoD [Shigella sonnei Ss046]
 gi|82545322|ref|YP_409269.1| RNA polymerase sigma factor RpoD [Shigella boydii Sb227]
 gi|110643311|ref|YP_671041.1| RNA polymerase sigma factor RpoD [Escherichia coli 536]
 gi|110806954|ref|YP_690474.1| RNA polymerase sigma factor RpoD [Shigella flexneri 5 str. 8401]
 gi|157155497|ref|YP_001464528.1| RNA polymerase sigma factor RpoD [Escherichia coli E24377A]
 gi|168749343|ref|ZP_02774365.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4113]
 gi|168754040|ref|ZP_02779047.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4401]
 gi|168762022|ref|ZP_02787029.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4501]
 gi|168769477|ref|ZP_02794484.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4486]
 gi|168781203|ref|ZP_02806210.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4076]
 gi|168785943|ref|ZP_02810950.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC869]
 gi|168797660|ref|ZP_02822667.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC508]
 gi|170683578|ref|YP_001745339.1| RNA polymerase sigma factor RpoD [Escherichia coli SMS-3-5]
 gi|188493368|ref|ZP_03000638.1| RNA polymerase sigma factor RpoD [Escherichia coli 53638]
 gi|191166845|ref|ZP_03028670.1| RNA polymerase sigma factor RpoD [Escherichia coli B7A]
 gi|191172227|ref|ZP_03033770.1| RNA polymerase sigma factor RpoD [Escherichia coli F11]
 gi|193062048|ref|ZP_03043144.1| RNA polymerase sigma factor RpoD [Escherichia coli E22]
 gi|193067502|ref|ZP_03048470.1| RNA polymerase sigma factor RpoD [Escherichia coli E110019]
 gi|194427683|ref|ZP_03060230.1| RNA polymerase sigma factor RpoD [Escherichia coli B171]
 gi|194431653|ref|ZP_03063944.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae 1012]
 gi|195937213|ref|ZP_03082595.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4024]
 gi|208809700|ref|ZP_03252037.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813639|ref|ZP_03254968.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4045]
 gi|208820039|ref|ZP_03260359.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4042]
 gi|209399452|ref|YP_002272540.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920540|ref|YP_002294624.1| RNA polymerase sigma factor RpoD [Escherichia coli SE11]
 gi|215488398|ref|YP_002330829.1| RNA polymerase sigma factor RpoD [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217326836|ref|ZP_03442919.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           TW14588]
 gi|218555637|ref|YP_002388550.1| RNA polymerase sigma factor RpoD [Escherichia coli IAI1]
 gi|218696772|ref|YP_002404439.1| RNA polymerase sigma factor RpoD [Escherichia coli 55989]
 gi|218701838|ref|YP_002409467.1| RNA polymerase sigma factor RpoD [Escherichia coli IAI39]
 gi|218706692|ref|YP_002414211.1| RNA polymerase sigma factor RpoD [Escherichia coli UMN026]
 gi|254795019|ref|YP_003079856.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           TW14359]
 gi|256019017|ref|ZP_05432882.1| RNA polymerase sigma factor RpoD [Shigella sp. D9]
 gi|260845821|ref|YP_003223599.1| RNA polymerase, sigma 70 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260857197|ref|YP_003231088.1| RNA polymerase, sigma 70 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260869819|ref|YP_003236221.1| RNA polymerase, sigma 70 factor [Escherichia coli O111:H- str.
           11128]
 gi|261228080|ref|ZP_05942361.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261254936|ref|ZP_05947469.1| RNA polymerase, sigma 70 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284446|ref|YP_003501264.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
           CB9615]
 gi|293406680|ref|ZP_06650606.1| RNA polymerase sigma factor RpoD [Escherichia coli FVEC1412]
 gi|293412444|ref|ZP_06655167.1| RNA polymerase sigma factor rpoD [Escherichia coli B354]
 gi|293416506|ref|ZP_06659145.1| RNA polymerase primary sigma factor [Escherichia coli B185]
 gi|293449405|ref|ZP_06663826.1| RNA polymerase primary sigma factor [Escherichia coli B088]
 gi|298382421|ref|ZP_06992018.1| RNA polymerase sigma factor rpoD [Escherichia coli FVEC1302]
 gi|300818835|ref|ZP_07099041.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 107-1]
 gi|300821663|ref|ZP_07101809.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 119-7]
 gi|300901451|ref|ZP_07119536.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 198-1]
 gi|300917392|ref|ZP_07134058.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 115-1]
 gi|300923730|ref|ZP_07139755.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 182-1]
 gi|300937447|ref|ZP_07152273.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 21-1]
 gi|300977468|ref|ZP_07173931.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 200-1]
 gi|301021861|ref|ZP_07185824.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 69-1]
 gi|307310308|ref|ZP_07589956.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W]
 gi|309793633|ref|ZP_07688059.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 145-7]
 gi|312968589|ref|ZP_07782798.1| RNA polymerase sigma factor rpoD [Escherichia coli 2362-75]
 gi|331654667|ref|ZP_08355667.1| RNA polymerase sigma factor RpoD [Escherichia coli M718]
 gi|331664680|ref|ZP_08365586.1| RNA polymerase sigma factor RpoD [Escherichia coli TA143]
 gi|331669908|ref|ZP_08370753.1| RNA polymerase sigma factor RpoD [Escherichia coli TA271]
 gi|331679143|ref|ZP_08379815.1| RNA polymerase sigma factor RpoD [Escherichia coli H591]
 gi|331684720|ref|ZP_08385312.1| RNA polymerase sigma factor RpoD [Escherichia coli H299]
 gi|332280114|ref|ZP_08392527.1| RNA polymerase sigma 70 (sigma D) factor [Shigella sp. D9]
 gi|12517649|gb|AAG58201.1|AE005536_2 RNA polymerase, sigma(70) factor; regulation of proteins induced at
           high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|13363423|dbj|BAB37373.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli O157:H7 str.
           Sakai]
 gi|24053533|gb|AAN44584.1| sigmaD(70) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|73857079|gb|AAZ89786.1| RNA polymerase, sigma(70) factor [Shigella sonnei Ss046]
 gi|81246733|gb|ABB67441.1| RNA polymerase sigma(70) factor [Shigella boydii Sb227]
 gi|110344903|gb|ABG71140.1| RNA polymerase sigma factor RpoD [Escherichia coli 536]
 gi|110616502|gb|ABF05169.1| RpoD protein [Shigella flexneri 5 str. 8401]
 gi|157077527|gb|ABV17235.1| RNA polymerase sigma factor RpoD [Escherichia coli E24377A]
 gi|170521296|gb|ACB19474.1| RNA polymerase sigma factor RpoD [Escherichia coli SMS-3-5]
 gi|188016365|gb|EDU54487.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4113]
 gi|188488567|gb|EDU63670.1| RNA polymerase sigma factor RpoD [Escherichia coli 53638]
 gi|189000977|gb|EDU69963.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4076]
 gi|189358698|gb|EDU77117.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4401]
 gi|189361403|gb|EDU79822.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4486]
 gi|189367616|gb|EDU86032.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4501]
 gi|189374126|gb|EDU92542.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC869]
 gi|189379773|gb|EDU98189.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC508]
 gi|190903087|gb|EDV62811.1| RNA polymerase sigma factor RpoD [Escherichia coli B7A]
 gi|190907537|gb|EDV67133.1| RNA polymerase sigma factor RpoD [Escherichia coli F11]
 gi|192932268|gb|EDV84866.1| RNA polymerase sigma factor RpoD [Escherichia coli E22]
 gi|192959459|gb|EDV89894.1| RNA polymerase sigma factor RpoD [Escherichia coli E110019]
 gi|194414191|gb|EDX30466.1| RNA polymerase sigma factor RpoD [Escherichia coli B171]
 gi|194420009|gb|EDX36087.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae 1012]
 gi|195183229|dbj|BAG66772.1| RNA polymerase, sigma(70) factor [Escherichia coli O111:H-]
 gi|208729501|gb|EDZ79102.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4206]
 gi|208734916|gb|EDZ83603.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4045]
 gi|208740162|gb|EDZ87844.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4042]
 gi|209160852|gb|ACI38285.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC4115]
 gi|209759228|gb|ACI77926.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759230|gb|ACI77927.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759232|gb|ACI77928.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759234|gb|ACI77929.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759236|gb|ACI77930.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209913799|dbj|BAG78873.1| RNA polymerase sigma factor RpoD [Escherichia coli SE11]
 gi|215266470|emb|CAS10908.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|217319203|gb|EEC27628.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353504|emb|CAU99623.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli 55989]
 gi|218362405|emb|CAR00029.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli IAI1]
 gi|218371824|emb|CAR19679.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli IAI39]
 gi|218433789|emb|CAR14706.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli UMN026]
 gi|254594419|gb|ACT73780.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257755846|dbj|BAI27348.1| RNA polymerase, sigma 70 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257760968|dbj|BAI32465.1| RNA polymerase, sigma 70 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257766175|dbj|BAI37670.1| RNA polymerase, sigma 70 factor [Escherichia coli O111:H- str.
           11128]
 gi|281602456|gb|ADA75440.1| putative DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Shigella flexneri 2002017]
 gi|284923096|emb|CBG36189.1| RNA polymerase sigma-70 factor [Escherichia coli 042]
 gi|290764319|gb|ADD58280.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
           CB9615]
 gi|291322495|gb|EFE61924.1| RNA polymerase primary sigma factor [Escherichia coli B088]
 gi|291426686|gb|EFE99718.1| RNA polymerase sigma factor RpoD [Escherichia coli FVEC1412]
 gi|291431862|gb|EFF04845.1| RNA polymerase primary sigma factor [Escherichia coli B185]
 gi|291469215|gb|EFF11706.1| RNA polymerase sigma factor rpoD [Escherichia coli B354]
 gi|298277561|gb|EFI19077.1| RNA polymerase sigma factor rpoD [Escherichia coli FVEC1302]
 gi|300308326|gb|EFJ62846.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 200-1]
 gi|300355153|gb|EFJ71023.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 198-1]
 gi|300397877|gb|EFJ81415.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 69-1]
 gi|300415349|gb|EFJ98659.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 115-1]
 gi|300420000|gb|EFK03311.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 182-1]
 gi|300457482|gb|EFK20975.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 21-1]
 gi|300525801|gb|EFK46870.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 119-7]
 gi|300528620|gb|EFK49682.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 107-1]
 gi|306909203|gb|EFN39698.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W]
 gi|308122590|gb|EFO59852.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 145-7]
 gi|312286807|gb|EFR14718.1| RNA polymerase sigma factor rpoD [Escherichia coli 2362-75]
 gi|313648184|gb|EFS12630.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2a str. 2457T]
 gi|315062375|gb|ADT76702.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli W]
 gi|320176471|gb|EFW51521.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae CDC 74-1112]
 gi|320179315|gb|EFW54273.1| RNA polymerase sigma factor RpoD [Shigella boydii ATCC 9905]
 gi|320182888|gb|EFW57762.1| RNA polymerase sigma factor RpoD [Shigella flexneri CDC 796-83]
 gi|320189419|gb|EFW64078.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           EC1212]
 gi|320201978|gb|EFW76553.1| RNA polymerase sigma factor RpoD [Escherichia coli EC4100B]
 gi|320640141|gb|EFX09713.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           G5101]
 gi|320645439|gb|EFX14448.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str.
           493-89]
 gi|320650750|gb|EFX19207.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str. H
           2687]
 gi|320656128|gb|EFX24040.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320661818|gb|EFX29226.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320666969|gb|EFX33945.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154524|gb|EFZ40724.1| RNA polymerase sigma factor rpoD [Escherichia coli EPECa14]
 gi|323163118|gb|EFZ48951.1| RNA polymerase sigma factor rpoD [Escherichia coli E128010]
 gi|323168088|gb|EFZ53775.1| RNA polymerase sigma factor rpoD [Shigella sonnei 53G]
 gi|323173687|gb|EFZ59316.1| RNA polymerase sigma factor rpoD [Escherichia coli LT-68]
 gi|323178773|gb|EFZ64349.1| RNA polymerase sigma factor rpoD [Escherichia coli 1180]
 gi|323183651|gb|EFZ69048.1| RNA polymerase sigma factor rpoD [Escherichia coli 1357]
 gi|323188489|gb|EFZ73774.1| RNA polymerase sigma factor rpoD [Escherichia coli RN587/1]
 gi|323377037|gb|ADX49305.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli KO11]
 gi|323946863|gb|EGB42881.1| RNA polymerase sigma protein RpoD [Escherichia coli H120]
 gi|323966596|gb|EGB62029.1| RNA polymerase sigma proteinRpoD [Escherichia coli M863]
 gi|323978859|gb|EGB73939.1| RNA polymerase sigma proteinRpoD [Escherichia coli TW10509]
 gi|324011983|gb|EGB81202.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 60-1]
 gi|324018214|gb|EGB87433.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 117-3]
 gi|324119675|gb|EGC13556.1| RNA polymerase sigma proteinRpoD [Escherichia coli E1167]
 gi|326337771|gb|EGD61605.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           1125]
 gi|326347336|gb|EGD71061.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
           1044]
 gi|327251853|gb|EGE63539.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_7v]
 gi|331048049|gb|EGI20126.1| RNA polymerase sigma factor RpoD [Escherichia coli M718]
 gi|331058611|gb|EGI30592.1| RNA polymerase sigma factor RpoD [Escherichia coli TA143]
 gi|331062821|gb|EGI34735.1| RNA polymerase sigma factor RpoD [Escherichia coli TA271]
 gi|331073208|gb|EGI44531.1| RNA polymerase sigma factor RpoD [Escherichia coli H591]
 gi|331078335|gb|EGI49541.1| RNA polymerase sigma factor RpoD [Escherichia coli H299]
 gi|332086727|gb|EGI91867.1| RNA polymerase sigma factor rpoD [Shigella boydii 5216-82]
 gi|332086765|gb|EGI91902.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|332086940|gb|EGI92075.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|332092163|gb|EGI97241.1| RNA polymerase sigma factor rpoD [Shigella boydii 3594-74]
 gi|332102466|gb|EGJ05812.1| RNA polymerase sigma 70 (sigma D) factor [Shigella sp. D9]
 gi|332752740|gb|EGJ83125.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-671]
 gi|332753124|gb|EGJ83508.1| RNA polymerase sigma factor rpoD [Shigella flexneri 4343-70]
 gi|332754402|gb|EGJ84768.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2747-71]
 gi|332765316|gb|EGJ95540.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
           flexneri 2930-71]
 gi|332998670|gb|EGK18266.1| RNA polymerase sigma factor rpoD [Shigella flexneri VA-6]
 gi|332999827|gb|EGK19411.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-272]
 gi|332999919|gb|EGK19502.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-218]
 gi|333014798|gb|EGK34143.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-304]
 gi|333015695|gb|EGK35034.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-227]
          Length = 613

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|167031434|ref|YP_001666665.1| RNA polymerase sigma factor RpoD [Pseudomonas putida GB-1]
 gi|166857922|gb|ABY96329.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida GB-1]
          Length = 616

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/657 (40%), Positives = 374/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++   D +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               K   + +E + ++ +   GD E  A+   D                         +
Sbjct: 183 IPGTKAAAAKEESDDEEEESESGDDEEEAESGPDPVV----------------------A 220

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A    A+ DQ                     LQ  +   +K+ +   +     + L  L 
Sbjct: 221 AQRFGAVSDQ---------------------LQATSKVLKKNGRGHKESIEALQALADLF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + ++LVE++ D   R+   E  +++L      + R  FL      E D  W 
Sbjct: 260 MPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     W   +  +  +I+  + ++  +  ETG++++E + I   +  GE +A  A
Sbjct: 320 GDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|85058229|ref|YP_453931.1| RNA polymerase sigma factor RpoD [Sodalis glossinidius str.
           'morsitans']
 gi|84778749|dbj|BAE73526.1| RNA polymerase sigma-70 factor RpoD [Sodalis glossinidius str.
           'morsitans']
          Length = 615

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 363/656 (55%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTFAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   D    + D +                PE A      L E  + + 
Sbjct: 175 DMAPTATHIGSELSADEIADDDDEDEEDGDDDSTDDDNSIDPELARQKFVELREQYEITR 234

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           + +                                     + +S  K       L  +  
Sbjct: 235 NVIKT-----------------------------------NGRSHAKSASEILNLSDVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L      + +  F+    G E    W  
Sbjct: 260 QFRLVPKQFDYLVNNMRAMMDRVRTQERLIMKLCVEISKMPKKNFVTLFAGNETSESWFK 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AALAMNKP-WSEKLHEVDDDVYRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 499 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 558

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|238760057|ref|ZP_04621208.1| RNA polymerase sigma factor rpoD [Yersinia aldovae ATCC 35236]
 gi|238701744|gb|EEP94310.1| RNA polymerase sigma factor rpoD [Yersinia aldovae ATCC 35236]
          Length = 611

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 373/656 (56%), Gaps = 53/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I+       E          G 
Sbjct: 126 EEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    +KE D+ +E + +                  PE A      L +  +++ 
Sbjct: 186 ELSTEEMDEDDKEEDEEEEEDDN---------------SIDPELARQKFSELRDQYENTR 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S          L ++  
Sbjct: 231 MAI-----------------------------------KKNGRSHASAAAEILNLSEVFK 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 256 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 316 AAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|71282406|ref|YP_270983.1| RNA polymerase sigma-70 factor [Colwellia psychrerythraea 34H]
 gi|71148146|gb|AAZ28619.1| RNA polymerase sigma-70 factor [Colwellia psychrerythraea 34H]
          Length = 616

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 366/655 (55%), Gaps = 45/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  ++N  LP D + S+Q+ED V+M+++MGI V +    +D  
Sbjct: 6   QSRLKDLITKGKEQGYLTFAQVNDHLPQDIIDSDQVEDIVSMINDMGIQVFENAPDQDTL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++ +    A+ ++       +S    T DPVRMY+REMG++ELL+R+GEI IAKRIE
Sbjct: 66  MMAEA-NTDEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTRKGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D        L +II        E        T   S
Sbjct: 125 EGIKEVQRSVSEYPPAINYLLDMWDNFEAEEVRLTDIIIGFLDPDAEDDDVAAAATHVGS 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
              +ED + E       + E + E       D        PE A      L E  +++  
Sbjct: 185 ELSKEDLANEDSEKKEGDAEEEDEEEEDTGPD--------PELAREKFTLLREAHENATK 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                   +K  +     +   + + ++   
Sbjct: 237 VV-----------------------------------KKKGRGHKDAQEAIDAVAEVFKE 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
             L     D LV+ +  +  R+   E  +++   S G+ +  F++   G E    W    
Sbjct: 262 FRLIPKLFDKLVKNMRGMMDRLRVQERLIMKHCVSAGMPKTTFIKIFPGNETSKEWFEAE 321

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           K      +   +      + +   ++  I  ET ++I   + I   +  GE +A  AKKE
Sbjct: 322 KA-AGNPYSTKLGDIEHDVERCIYKLNQIEEETHLNIHGIKDINRRMSIGEAKARRAKKE 380

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 381 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 440

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVL
Sbjct: 441 ITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELAERMVMPEDKIRKVL 500

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD++ SHLGDFIED +   P+DSA   NL+  T  VLA LT RE +V
Sbjct: 501 KIAKEPISMETPIGDDEDSHLGDFIEDGSGELPVDSATSENLKGATHEVLAGLTAREAKV 560

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++L+SFLDG
Sbjct: 561 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLKSFLDG 615


>gi|119473196|ref|ZP_01614893.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
 gi|119444560|gb|EAW25875.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
          Length = 614

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 373/656 (56%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE 
Sbjct: 6   QSQLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +++     +A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMQETTTDEDAAEAAAAALATVEK-EIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D+       L +II            GF    E  +
Sbjct: 125 EGINQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------VGFIDPNEDEA 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                +   E     + + + D + +     ++       PE A     NL +  + +  
Sbjct: 174 PISATNIGSELSEKQLDDDDEDDDKSDDDEDEEEVDTGPDPEEARIHFENLRDLYNKARD 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T  A + +  P    A+ EI E++                                   +
Sbjct: 234 TFEA-KGRSHPDSQAAIFEIGELF----------------------------------RT 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D +V  + ++  R+   E  +++ A     + +  F++     E DP WV  
Sbjct: 259 FKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQIAKLPKKAFVKHFANNETDPSWVDL 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                E  +   +      I++  N++  I   TG+SI   + I   +  GE +A  AKK
Sbjct: 319 EISNNEK-YSAKLEEVKPEIIRCINKLSIIEQTTGLSIERIKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 613


>gi|266618720|pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
          Length = 613

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   + +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHATAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|317049603|ref|YP_004117251.1| RNA polymerase,sigma 70 subunit,RpoD [Pantoea sp. At-9b]
 gi|316951220|gb|ADU70695.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. At-9b]
          Length = 614

 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 367/656 (55%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSADTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  +    E  +    + D +                PE A      L    + + 
Sbjct: 175 DL-APTATHVGSELSEEDRDDDDEDDEESDDDSSDDDNSIDPELAREKFVELRTQYETTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A                                     +S        + L ++  
Sbjct: 234 TVIKAK-----------------------------------GRSHADAVAEIQNLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++ +R+   E  +++L      + +  F+    G E    W  
Sbjct: 259 QFRLVPKQFDYLVNNMREMMERVRTQERIIMKLCVELCKMPKKNFITLFTGNETSESWFK 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D +++   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AALAMNKP-WSEKLLEVQDDVMRCLQKLLQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|157162543|ref|YP_001459861.1| RNA polymerase sigma factor RpoD [Escherichia coli HS]
 gi|170018681|ref|YP_001723635.1| RNA polymerase sigma factor RpoD [Escherichia coli ATCC 8739]
 gi|194439798|ref|ZP_03071864.1| RNA polymerase sigma factor RpoD [Escherichia coli 101-1]
 gi|253772097|ref|YP_003034928.1| RNA polymerase sigma factor RpoD [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038237|ref|ZP_04872295.1| RNA polymerase sigma factor RpoD [Escherichia sp. 1_1_43]
 gi|254163014|ref|YP_003046122.1| RNA polymerase sigma factor RpoD [Escherichia coli B str. REL606]
 gi|256024353|ref|ZP_05438218.1| RNA polymerase sigma factor RpoD [Escherichia sp. 4_1_40B]
 gi|300905790|ref|ZP_07123524.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 84-1]
 gi|300931954|ref|ZP_07147251.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 187-1]
 gi|300950721|ref|ZP_07164609.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 116-1]
 gi|300958456|ref|ZP_07170595.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 175-1]
 gi|301021226|ref|ZP_07185258.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 196-1]
 gi|301301890|ref|ZP_07208024.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 124-1]
 gi|301644765|ref|ZP_07244740.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 146-1]
 gi|307139755|ref|ZP_07499111.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|312972668|ref|ZP_07786841.1| RNA polymerase sigma factor rpoD [Escherichia coli 1827-70]
 gi|331643766|ref|ZP_08344897.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|157068223|gb|ABV07478.1| RNA polymerase sigma factor RpoD [Escherichia coli HS]
 gi|169753609|gb|ACA76308.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli ATCC 8739]
 gi|194421246|gb|EDX37267.1| RNA polymerase sigma factor RpoD [Escherichia coli 101-1]
 gi|226839861|gb|EEH71882.1| RNA polymerase sigma factor RpoD [Escherichia sp. 1_1_43]
 gi|242378617|emb|CAQ33404.1| RNA polymerase, sigma 70 (sigma D) factor, subunit of RNA
           polymerase sigma 70 [Escherichia coli BL21(DE3)]
 gi|253323141|gb|ACT27743.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974915|gb|ACT40586.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979071|gb|ACT44741.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|299881584|gb|EFI89795.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 196-1]
 gi|300314897|gb|EFJ64681.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 175-1]
 gi|300402389|gb|EFJ85927.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 84-1]
 gi|300449958|gb|EFK13578.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 116-1]
 gi|300460377|gb|EFK23870.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 187-1]
 gi|300842871|gb|EFK70631.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 124-1]
 gi|301076919|gb|EFK91725.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 146-1]
 gi|309703498|emb|CBJ02838.1| RNA polymerase sigma-70 factor [Escherichia coli ETEC H10407]
 gi|310332610|gb|EFP99823.1| RNA polymerase sigma factor rpoD [Escherichia coli 1827-70]
 gi|315256981|gb|EFU36949.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 85-1]
 gi|315617141|gb|EFU97750.1| RNA polymerase sigma factor rpoD [Escherichia coli 3431]
 gi|323935931|gb|EGB32226.1| RNA polymerase sigma protein RpoD [Escherichia coli E1520]
 gi|323941835|gb|EGB38014.1| RNA polymerase sigma proteinRpoD [Escherichia coli E482]
 gi|323960998|gb|EGB56615.1| RNA polymerase sigma proteinRpoD [Escherichia coli H489]
 gi|323971810|gb|EGB67035.1| RNA polymerase sigma proteinRpoD [Escherichia coli TA007]
 gi|331037237|gb|EGI09461.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|332345022|gb|AEE58356.1| RNA polymerase sigma factor protein RpoD [Escherichia coli UMNK88]
          Length = 613

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHATAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|324115354|gb|EGC09318.1| RNA polymerase sigma proteinRpoD [Escherichia fergusonii B253]
          Length = 613

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 362/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEEE 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A      L    + +  
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFSELRAQYEVTRD 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 234 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    D + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVADEVHRSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|227329605|ref|ZP_03833629.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 611

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 375/656 (57%), Gaps = 53/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                   +      ++   E D +   +  +++       PE A      L E  + + 
Sbjct: 175 DI----APTATHVGSELSTEEMDDDDEEEDDEEEEDDNSIDPELAREKFTELREQYETTR 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A     R   + A + +                                 L ++  
Sbjct: 231 QVIKA---HGRSHALAAQEILN--------------------------------LSEVFK 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E +  W +
Sbjct: 256 QFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNETNNTWFA 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 316 AAVAMGKP-WSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|123443868|ref|YP_001007839.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090829|emb|CAL13711.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 612

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 370/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    + E               +  +++       PE A      L E  +++ 
Sbjct: 186 ELSTEEMDDDDDED--------------EDDEEEEDDNSIDPELARQKFSELREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 232 LEI-----------------------------------KKNGRSHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFTSNETSDTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|162420372|ref|YP_001604920.1| RNA polymerase sigma factor RpoD [Yersinia pestis Angola]
 gi|162353187|gb|ABX87135.1| RNA polymerase sigma factor RpoD [Yersinia pestis Angola]
          Length = 612

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 371/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E   ++++                   D        PE A     +L E  +++ 
Sbjct: 186 ELSTEEMDDEDEDE--------------DEDDDAEDDNSIDPELARQKFSDLREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ ++         KL ++  
Sbjct: 232 MEI-----------------------------------KKNGRNHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFN 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   NLR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSENLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|152999721|ref|YP_001365402.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS185]
 gi|160874340|ref|YP_001553656.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS195]
 gi|151364339|gb|ABS07339.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS185]
 gi|160859862|gb|ABX48396.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS195]
          Length = 627

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 273/655 (41%), Positives = 379/655 (57%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 22  QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 81

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 82  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 140

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E  +
Sbjct: 141 EGINTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEDVA 189

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S+  E     E E D E       ++       PE A      L    + +  
Sbjct: 190 PTATHIGSELSEE--ELEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALK 247

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 248 IIEA-KGREHPESVKALFEIGEIFKE---------------------------------- 272

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W + 
Sbjct: 273 FRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGNETNLDWFNT 332

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   +  +   +    D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 333 EKASTKP-YAEGLRMVEDDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 391

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 392 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 451

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 452 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 511

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 512 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAK 571

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 572 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 626


>gi|145300336|ref|YP_001143177.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853108|gb|ABO91429.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 616

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 372/655 (56%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  IMAEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     L+   D+       L +II     I P          +  +
Sbjct: 126 DGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE-------ADDVA 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S+  E D   E E + E     S DD       PE A     +L    + +  
Sbjct: 177 PTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDSGPDPEVAREKFGDLRAQYEVTRL 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           ++                                   QK+ ++    +    +L  +   
Sbjct: 237 SI-----------------------------------QKNGRAHEDTQAAIAQLADVFRQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y
Sbjct: 262 FRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEY 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   +      +  + + +L+   +++ I  ETG+SI++ + I   +  GE +A  AKK
Sbjct: 322 QKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A ++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P D+A   +LR  T  VLA LT RE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLRNATREVLAGLTAREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 615


>gi|170765503|ref|ZP_02900314.1| RNA polymerase sigma factor RpoD [Escherichia albertii TW07627]
 gi|170124649|gb|EDS93580.1| RNA polymerase sigma factor RpoD [Escherichia albertii TW07627]
          Length = 613

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 365/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEEE 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I E                   +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKEK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|238794325|ref|ZP_04637937.1| RNA polymerase sigma factor rpoD [Yersinia intermedia ATCC 29909]
 gi|238726319|gb|EEQ17861.1| RNA polymerase sigma factor rpoD [Yersinia intermedia ATCC 29909]
          Length = 612

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 371/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I+       E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E                D +   +   ++       PE A     +L E  +++ 
Sbjct: 186 ELSTAE--------------MDDDDDEDEDEDEEEDDNSIDPELARQKFSDLREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 232 MEI-----------------------------------KKNGRSHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRTMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|126173383|ref|YP_001049532.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125996588|gb|ABN60663.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS155]
          Length = 627

 Score =  457 bits (1176), Expect = e-126,   Method: Composition-based stats.
 Identities = 273/655 (41%), Positives = 379/655 (57%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 22  QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 81

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 82  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 140

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E  +
Sbjct: 141 EGINTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEDVA 189

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S+  E     E E D E       ++       PE A      L    + +  
Sbjct: 190 PTATHIGSELSEE--ELEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALK 247

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 248 IIEA-KGREHPESVKALFEIGEIFKE---------------------------------- 272

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W + 
Sbjct: 273 FRLVPKQFDRLVKSIRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGNETNLDWFNT 332

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   +  +   +    D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 333 EKASTKP-YAEGLRMVEDDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 391

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 392 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 451

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 452 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 511

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 512 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAK 571

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 572 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 626


>gi|218550316|ref|YP_002384107.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ATCC
           35469]
 gi|218357857|emb|CAQ90501.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia fergusonii
           ATCC 35469]
 gi|325498620|gb|EGC96479.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ECD227]
          Length = 613

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 362/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEEE 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A      L    + +  
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYEVTRD 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 234 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    D + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVADEVHRSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|187478819|ref|YP_786843.1| RNA polymerase sigma factor RpoD [Bordetella avium 197N]
 gi|115423405|emb|CAJ49939.1| RNA polymerase sigma factor 70 [Bordetella avium 197N]
          Length = 726

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 257/685 (37%), Positives = 377/685 (55%), Gaps = 66/685 (9%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            + +    D           ++   +  K++IKL + RGY+T  E+N  LP D V +E +
Sbjct: 101 KRGKGDPKDLIARGPVSPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAI 160

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDP 120
           +  ++  S+MGI+V D     +     ++  +        + +       DS    T DP
Sbjct: 161 DGIISTFSDMGISVYDQAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDP 220

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMGS+ELL+REGEI IAKRIE G   M+ ++   P T   ++     + +G   
Sbjct: 221 VRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHATRVREGQNQ 280

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++D           G     +G  Y                       + A VS D+
Sbjct: 281 IDEVVD-----------GLVDPEDGEEY-----------------------AGAGVSADE 306

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               D P     + +                  + LR K +   DE++  + ++R+  + 
Sbjct: 307 EEGDDGPAGGMSSKQL-----------------EDLRVKALAKFDEVSRQFDKMRNSYE- 348

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RL 359
                KD   S      +E +   +  +      ++ L + L +  + +   E  +L   
Sbjct: 349 -----KDGYRSDIYISAQETIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTC 403

Query: 360 AQSYGIKRDVFLERHQGRELDPHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
               G+ R  FL+   G E +  WV    A   P  E    +  ++ ++ +++ ++  + 
Sbjct: 404 VDRAGMPRSHFLKVFPGNETNLQWVVEEVAAGHPYAE---TLERQIPAVQELQQKLIDLQ 460

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + + + + +   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 461 TRVVLPLKDLKDVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEG 520

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R
Sbjct: 521 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISR 580

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +   EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + 
Sbjct: 581 QILQETGAEPDPATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTST 640

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           ++P D+A+  ++R+    VL SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIR
Sbjct: 641 LAPSDAALHGSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIR 700

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKL+HPSR+ KL+SFL+G
Sbjct: 701 QIEAKALRKLRHPSRADKLKSFLEG 725


>gi|33593188|ref|NP_880832.1| RNA polymerase sigma factor RpoD [Bordetella pertussis Tohama I]
 gi|33563563|emb|CAE42462.1| RNA polymerase sigma factor 70 [Bordetella pertussis Tohama I]
 gi|332382599|gb|AEE67446.1| RNA polymerase sigma factor RpoD [Bordetella pertussis CS]
          Length = 760

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 250/662 (37%), Positives = 368/662 (55%), Gaps = 62/662 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D     
Sbjct: 156 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDA 215

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 216 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 275

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 276 IAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD-----------GLVD 324

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ D+    D P     + +      
Sbjct: 325 PEDGEEY-----------------------AGAGVTADEDEGDDGPAGGMSSKQL----- 356

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+++ + ++R   +      K+   S      ++ +
Sbjct: 357 ------------EDLRVKALAKFDEVSKQFEKMRQSYE------KEGYKSDAYLKAQDII 398

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
              +  +      ++ L + L    + +   E  +L       G+ R  FL+   G E +
Sbjct: 399 QTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSHFLKAFPGNETN 458

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV          +   +  ++ ++ +++ ++  +     + + + + +   +  GE +
Sbjct: 459 LQWVLDEVA-AAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGEAK 517

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 518 ARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 577

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP 
Sbjct: 578 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDMPE 637

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+  ++R+    VL SL
Sbjct: 638 DKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMRDVVKEVLDSL 697

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL
Sbjct: 698 TPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFL 757

Query: 681 DG 682
           +G
Sbjct: 758 EG 759


>gi|26987129|ref|NP_742554.1| RNA polymerase sigma factor RpoD [Pseudomonas putida KT2440]
 gi|148545673|ref|YP_001265775.1| RNA polymerase sigma factor RpoD [Pseudomonas putida F1]
 gi|24981760|gb|AAN66018.1|AE016231_1 RNA polymerase sigma factor RpoD [Pseudomonas putida KT2440]
 gi|2654492|gb|AAB87749.1| DNA-directed RNA polymerase sigma subunit [Pseudomonas putida]
 gi|2731762|gb|AAC38073.1| sigma-70 [Pseudomonas putida]
 gi|148509731|gb|ABQ76591.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida F1]
 gi|313496752|gb|ADR58118.1| RpoD [Pseudomonas putida BIRD-1]
          Length = 616

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/657 (41%), Positives = 375/657 (57%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++   D +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               K   + +E + D+ +   GD E  A+   D                         +
Sbjct: 183 IPGAKAAAAKEESDDDEEESESGDDEEEAESGPDPVV----------------------A 220

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A    A+ DQ                     LQ  +   +K+ ++  +     + L  L 
Sbjct: 221 AQRFGAVSDQ---------------------LQATSKVLKKNGRNHKESIEALQALADLF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + ++LVE++ D   R+   E  +++L      + R  FL      E D  W 
Sbjct: 260 MPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     W   +  +  +I+  + ++  +  ETG++++E + I   +  GE +A  A
Sbjct: 320 GDLAKRNTK-WAAALGEKNAAIVACQQKLIDLETETGLTVAEIKEINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|238782836|ref|ZP_04626865.1| RNA polymerase sigma factor rpoD [Yersinia bercovieri ATCC 43970]
 gi|238716259|gb|EEQ08242.1| RNA polymerase sigma factor rpoD [Yersinia bercovieri ATCC 43970]
          Length = 612

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 370/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I+       E          G 
Sbjct: 126 EEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    +KE               +  +++       PE A      L E  + + 
Sbjct: 186 ELSTEEMDDDDKEE--------------EDEEEEEDDNSIDPELARQKFSELREQYETTR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S          L ++  
Sbjct: 232 MAI-----------------------------------KKNGRSHATAAAEILNLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAVAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|161521349|ref|YP_001584776.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
           17616]
 gi|189352484|ref|YP_001948111.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
           17616]
 gi|160345399|gb|ABX18484.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia multivorans
           ATCC 17616]
 gi|189336506|dbj|BAG45575.1| RNA polymerase primary sigma factor [Burkholderia multivorans ATCC
           17616]
          Length = 804

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 250/665 (37%), Positives = 372/665 (55%), Gaps = 47/665 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID--LEACIGPESKGG 198
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D  L+         G
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDPNASDTDTDG 359

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           F          + E+  +E+E ++ ++ +G  ++ A  ++ +                  
Sbjct: 360 FSAKEAEEIENEDEEVEEEEEEEEEEDDDGAAQATANAAQLEA----------------- 402

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                            L+   +     I+E + ++R   +      K+   S      +
Sbjct: 403 -----------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQ 439

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           E +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G 
Sbjct: 440 ETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGN 499

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W           +   ++  + +I + +  +  +     + + + +     +  G
Sbjct: 500 ETDLDWAEKIAAEGHS-YSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAG 558

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 559 ELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 618

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ 
Sbjct: 619 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKME 678

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL
Sbjct: 679 MPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVL 738

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+
Sbjct: 739 DSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLK 798

Query: 678 SFLDG 682
           SFL+G
Sbjct: 799 SFLEG 803


>gi|147756|gb|AAA24601.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 613

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 264/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   + +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHATAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|329298675|ref|ZP_08256011.1| RNA polymerase sigma factor RpoD [Plautia stali symbiont]
          Length = 610

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 370/656 (56%), Gaps = 54/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   + +GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTRGKVQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLNENSTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEENLAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +    E+E ++  + +  I                 PE A     +L    + + 
Sbjct: 186 ELSEEDRDDDEEEDEESDDDDNSI----------------DPELAREKFNDLRTQYETTR 229

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A                                     +S          L ++  
Sbjct: 230 TVIKAK-----------------------------------GRSHADAVAEINNLSEVFK 254

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++ +R+   E  +++L      + +  F+    G E    W  
Sbjct: 255 QFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCVELCKMPKKNFITLFTGNETSESWFK 314

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +   +     E D +++   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 315 TALAMNKPWSEKLQEVEKD-VMRSLQKLLQIEEETGLTIEQVKDINRRMSIGEAKARRAK 373

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 374 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 433

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 434 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 493

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 494 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 553

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 554 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 609


>gi|51597716|ref|YP_071907.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           32953]
 gi|108809138|ref|YP_653054.1| RNA polymerase sigma factor RpoD [Yersinia pestis Antiqua]
 gi|108810668|ref|YP_646435.1| RNA polymerase sigma factor RpoD [Yersinia pestis Nepal516]
 gi|150260325|ref|ZP_01917053.1| RNA polymerase sigma factor RpoD [Yersinia pestis CA88-4125]
 gi|153950753|ref|YP_001399546.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           31758]
 gi|165924959|ref|ZP_02220791.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165937882|ref|ZP_02226443.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166008817|ref|ZP_02229715.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166212040|ref|ZP_02238075.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|167399605|ref|ZP_02305129.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167419320|ref|ZP_02311073.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167425120|ref|ZP_02316873.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|170022885|ref|YP_001719390.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis
           YPIII]
 gi|186896860|ref|YP_001873972.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis
           PB1/+]
 gi|218927836|ref|YP_002345711.1| RNA polymerase sigma factor RpoD [Yersinia pestis CO92]
 gi|229837321|ref|ZP_04457484.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Pestoides A]
 gi|229840533|ref|ZP_04460692.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229842919|ref|ZP_04463070.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229900861|ref|ZP_04515985.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Nepal516]
 gi|294502714|ref|YP_003566776.1| RNA polymerase sigma factor RpoD [Yersinia pestis Z176003]
 gi|51590998|emb|CAH22656.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           32953]
 gi|108774316|gb|ABG16835.1| RNA polymerase sigma factor RpoD [Yersinia pestis Nepal516]
 gi|108781051|gb|ABG15109.1| RNA polymerase sigma factor RpoD [Yersinia pestis Antiqua]
 gi|115346447|emb|CAL19320.1| RNA polymerase sigma factor RpoD [Yersinia pestis CO92]
 gi|149289733|gb|EDM39810.1| RNA polymerase sigma factor RpoD [Yersinia pestis CA88-4125]
 gi|152962248|gb|ABS49709.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
           31758]
 gi|165914294|gb|EDR32910.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165923159|gb|EDR40310.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165992156|gb|EDR44457.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166206786|gb|EDR51266.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|166963314|gb|EDR59335.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167052109|gb|EDR63517.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167055883|gb|EDR65664.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|169749419|gb|ACA66937.1| RNA polymerase, sigma 70 subunit, RpoD [Yersinia pseudotuberculosis
           YPIII]
 gi|186699886|gb|ACC90515.1| RNA polymerase, sigma 70 subunit, RpoD [Yersinia pseudotuberculosis
           PB1/+]
 gi|229682200|gb|EEO78292.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Nepal516]
 gi|229689985|gb|EEO82043.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229696899|gb|EEO86946.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229705444|gb|EEO91454.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis
           Pestoides A]
 gi|262360743|gb|ACY57464.1| RNA polymerase sigma factor RpoD [Yersinia pestis D106004]
 gi|294353173|gb|ADE63514.1| RNA polymerase sigma factor RpoD [Yersinia pestis Z176003]
 gi|320016798|gb|ADW00370.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 612

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 371/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E   ++++                   D        PE A     +L E  +++ 
Sbjct: 186 ELSTEEMDDEDEDE--------------DEDDDAEDDNSIDPELARQKFSDLREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ ++         KL ++  
Sbjct: 232 MEI-----------------------------------KKNGRNHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFN 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|145597737|ref|YP_001161813.1| RNA polymerase sigma factor RpoD [Yersinia pestis Pestoides F]
 gi|145209433|gb|ABP38840.1| RNA polymerase sigma factor RpoD [Yersinia pestis Pestoides F]
          Length = 608

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 369/656 (56%), Gaps = 56/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I                   G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIT------------------GF 167

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E+           E   +         D        PE A     +L E  +++ 
Sbjct: 168 VDPNAEEDIAPTATHVGSELSTEEMDDEDEDDDAEDDNSIDPELARQKFSDLREQYENAR 227

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ ++         KL ++  
Sbjct: 228 MEI-----------------------------------KKNGRNHANAAAEILKLSEVFK 252

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 253 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFN 312

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 313 AAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 371

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 372 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 431

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 432 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 491

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 492 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLKLPLDSATSESLRSATHDVLAGLTAREA 551

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 552 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 607


>gi|238789198|ref|ZP_04632986.1| RNA polymerase sigma factor rpoD [Yersinia frederiksenii ATCC
           33641]
 gi|238722730|gb|EEQ14382.1| RNA polymerase sigma factor rpoD [Yersinia frederiksenii ATCC
           33641]
          Length = 612

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 370/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    + E               +   ++       PE A      L E  +++ 
Sbjct: 186 ELSTEEMDDDDDED--------------EDDDEEEDDNSIDPELARQKFSELREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 232 LEI-----------------------------------KKNGRSHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|332163001|ref|YP_004299578.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318604173|emb|CBY25671.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325667231|gb|ADZ43875.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 612

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 370/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    + E               +  +++       PE A      L E  +++ 
Sbjct: 186 ELSTEEMDDDDDED--------------EDDEEEEDDNSIDPELARQKFSELREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 232 LEI-----------------------------------KKNGRSHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|16130963|ref|NP_417539.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|89109837|ref|AP_003617.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|170082610|ref|YP_001731930.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238902178|ref|YP_002927974.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|1710680|sp|P00579|RPOD_ECOLI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|882590|gb|AAA89147.1| CG Site No. 231; alternate gene name alt [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1789448|gb|AAC76103.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|73671318|gb|AAZ80070.1| RpoD [Escherichia coli LW1655F+]
 gi|85675868|dbj|BAE77118.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|169890445|gb|ACB04152.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238863501|gb|ACR65499.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|260447898|gb|ACX38320.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli DH1]
 gi|315137660|dbj|BAJ44819.1| RNA polymerase sigma factor RpoD [Escherichia coli DH1]
          Length = 613

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 364/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHATAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|307726543|ref|YP_003909756.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
 gi|307587068|gb|ADN60465.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
          Length = 803

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 250/663 (37%), Positives = 366/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 182 LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 241

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 242 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 301

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 302 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEVRIDELVDGLIDADAEDADGFS 361

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E+  +E+E D+ ++      +A     +                     
Sbjct: 362 VQEAEAIESEDEEEEEEEEGDEEEDDGTAQATANAAQMEA-------------------- 401

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 402 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 440

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 441 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 500

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 501 DLEWADKIVSEGHS-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 559

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 560 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 619

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 620 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 679

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 680 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 739

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 740 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 799

Query: 680 LDG 682
           L+G
Sbjct: 800 LEG 802


>gi|33597397|ref|NP_885040.1| RNA polymerase sigma factor RpoD [Bordetella parapertussis 12822]
 gi|33573824|emb|CAE38132.1| RNA polymerase sigma factor 70 [Bordetella parapertussis]
          Length = 760

 Score =  456 bits (1174), Expect = e-126,   Method: Composition-based stats.
 Identities = 250/662 (37%), Positives = 368/662 (55%), Gaps = 62/662 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D     
Sbjct: 156 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDA 215

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 216 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 275

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 276 IAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD-----------GLVD 324

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ D+    D P     + +      
Sbjct: 325 PEDGEEY-----------------------AGAGVTADEDEADDGPAGGMSSKQL----- 356

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+++ + ++R   +      K+   S      ++ +
Sbjct: 357 ------------EDLRVKALAKFDEVSKQFEKMRQSYE------KEGYKSDAYLKAQDII 398

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
              +  +      ++ L + L    + +   E  +L       G+ R  FL+   G E +
Sbjct: 399 QTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSHFLKAFPGNETN 458

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV          +   +  ++ ++ +++ ++  +     + + + + +   +  GE +
Sbjct: 459 LQWVLDEVA-AAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGEAK 517

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 518 ARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 577

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP 
Sbjct: 578 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDMPE 637

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+  ++R+    VL SL
Sbjct: 638 DKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMRDVVKEVLDSL 697

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL
Sbjct: 698 TPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFL 757

Query: 681 DG 682
           +G
Sbjct: 758 EG 759


>gi|21672345|ref|NP_660412.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|401010|sp|P32001|RPOD_BUCAP RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|144139|gb|AAA73234.1| sigma factor [Buchnera aphidicola]
 gi|21622948|gb|AAM67623.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 617

 Score =  456 bits (1173), Expect = e-126,   Method: Composition-based stats.
 Identities = 273/653 (41%), Positives = 384/653 (58%), Gaps = 47/653 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
            K ++   +++GY+T  E+N  LP + + SEQ++D + M+++MGI VV+   D +D   +
Sbjct: 9   LKLLVTHGKEQGYLTYAEVNDHLPEEIIDSEQIDDIIQMINDMGIQVVEEAPDADDLILN 68

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  EINTDTDEDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +S+ E P     L+   D +  G   L +II     + P ++  F H T      
Sbjct: 129 INQVQSSVSEYPEAITYLLEQYDRIKTGQIRLSDIIT--GFVDPNAEEIFSHSTSAIHIG 186

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                   +  D++     + E   +   +D  +    PE A    R L +   ++++T+
Sbjct: 187 S-------EILDNITNDSNENEDENEDENEDEDENSIDPELANEKFRELRKQYTNTSNTI 239

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                  +  ++   +                                   L ++     
Sbjct: 240 KNKNRNHQDSLLEIYN-----------------------------------LSEIFKQFR 264

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L   + D LV  + ++  R+   E ++++L  +   I + +FL+   G+E D +W    +
Sbjct: 265 LVPKQFDHLVNNMRNMMNRVRKQERKIMKLCIEECKIPKKIFLKIFSGKETDQNWFKKEQ 324

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              +  W   +    + +     ++K I  ETG++I + + I   +  GE +A  AKKEM
Sbjct: 325 SSNQS-WSKKLEEIKEKVFSSMKKLKQIEKETGLTIEQVKDINKRMSIGEAKAKRAKKEM 383

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 384 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 443

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +RKVLK
Sbjct: 444 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLK 503

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ LT RE +VL
Sbjct: 504 IAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVL 563

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 616


>gi|116691983|ref|YP_837516.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia HI2424]
 gi|116649983|gb|ABK10623.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           HI2424]
          Length = 805

 Score =  456 bits (1173), Expect = e-126,   Method: Composition-based stats.
 Identities = 253/663 (38%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 345

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E +E +   
Sbjct: 346 -------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAA 392

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 393 QASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  V +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLDWAEKITAEGHP-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|295097580|emb|CBK86670.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 614

 Score =  456 bits (1173), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 371/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E S +    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E    E E ++ ++   D +++              PE A      L    + + 
Sbjct: 186 ELSQEEMDDDEDEDEEEEDDSSDDDNSI------------DPELAREKFAELRTQYEVTR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A                                     +S    +    KL ++  
Sbjct: 234 DTIKAK-----------------------------------GRSHAAAQEEILKLSEVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 259 QFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFN 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 319 AAIAMNKP-WSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|134292973|ref|YP_001116709.1| RNA polymerase sigma factor RpoD [Burkholderia vietnamiensis G4]
 gi|134136130|gb|ABO57244.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia vietnamiensis
           G4]
          Length = 809

 Score =  456 bits (1173), Expect = e-126,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 184 LEERRVKLRALIKLGKERGFLTYGEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 243

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 244 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 303

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 304 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 349

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E ++ +   
Sbjct: 350 -------------GLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAA 396

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 397 QATANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKSYLKAQET 446

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 447 IQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 506

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 507 DLDWAEKIAAEGHS-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 565

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 566 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 625

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 626 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 685

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 686 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 745

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 746 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 805

Query: 680 LDG 682
           L+G
Sbjct: 806 LEG 808


>gi|229526927|ref|ZP_04416329.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
 gi|229336054|gb|EEO01074.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
          Length = 547

 Score =  456 bits (1173), Expect = e-126,   Method: Composition-based stats.
 Identities = 360/568 (63%), Positives = 432/568 (76%), Gaps = 27/568 (4%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +RMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQA+IIWRD+LND   L
Sbjct: 1   MRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLNDSNIL 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LREIIDLE             G E       E   +EK RDD  +     +        D
Sbjct: 61  LREIIDLETTYA---------GPEAKQAPVIERVEEEKPRDDKPQRRSRDDDDITNVGGD 111

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                             +EDED++  +L+AME +LRP+VM  LD IA+ Y++LR LQD 
Sbjct: 112 MPV------------EEEEEDEDEANLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQ 159

Query: 301 ------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                 A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR++ NEG
Sbjct: 160 QVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRLVQNEG 219

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
           +LLRLA+S+G++R+ FL+ +QG ELDP WV          WK F A E  +I ++R+EI+
Sbjct: 220 KLLRLAESFGVRREEFLKEYQGHELDPKWVERVSTLSARGWKEFAAKEERTIDRLRSEIQ 279

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++ ET ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 280 MLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 339

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VR
Sbjct: 340 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVR 399

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T+R+M ++I REPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIED
Sbjct: 400 TSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIED 459

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNA+ P+D+AIQANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRE
Sbjct: 460 KNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 519

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 520 RIRQIEAKALRKLKHPSRSRKLRSFLDS 547


>gi|238750950|ref|ZP_04612447.1| RNA polymerase sigma factor rpoD [Yersinia rohdei ATCC 43380]
 gi|238710864|gb|EEQ03085.1| RNA polymerase sigma factor rpoD [Yersinia rohdei ATCC 43380]
          Length = 612

 Score =  456 bits (1173), Expect = e-126,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 370/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I        E          G 
Sbjct: 126 EEGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E    + E               +  +++       PE A      L E  + + 
Sbjct: 186 ELSTEEMDDDDDEE--------------EDEEEEEDDNSIDPELARQKFSELREQYESTR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 232 MEI-----------------------------------KKNGRSHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|82778397|ref|YP_404746.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae Sd197]
 gi|309785377|ref|ZP_07680008.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 1617]
 gi|81242545|gb|ABB63255.1| RNA polymerase, sigma(70) factor [Shigella dysenteriae Sd197]
 gi|308926497|gb|EFP71973.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 1617]
          Length = 613

 Score =  456 bits (1172), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 363/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQENLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 ATAMNKP-WSEKLHDVSEEVHRALQKLLQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|325273045|ref|ZP_08139355.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. TJI-51]
 gi|324101818|gb|EGB99354.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. TJI-51]
          Length = 616

 Score =  456 bits (1172), Expect = e-126,   Method: Composition-based stats.
 Identities = 266/657 (40%), Positives = 370/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++   D +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDYILGEYDRVTAEGGRLSDV--LSGYIDPDDNIAAP----- 177

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                              E       A    ++   + +    + + +E     D   +
Sbjct: 178 -----------------TDEVPVIGAKAPAAKEESDEEDEESEGSDDEEETESGPDPVVA 220

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A    A+ DQ                     LQ      +K  ++  +     + L  L 
Sbjct: 221 AQRFGAVNDQ---------------------LQVTNKVLKKHGRNHKESIEALQALADLF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + ++LVE++ D   R+   E  +++L      + R  FL      E D  W 
Sbjct: 260 MPIKLVPKQFEVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     W   +  +  +I+  + ++  +  ETG++++E + I   +  GE +A  A
Sbjct: 320 GDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|226939395|ref|YP_002794468.1| RNA polymerase sigma factor RpoD [Laribacter hongkongensis HLHK9]
 gi|226714321|gb|ACO73459.1| RpoD [Laribacter hongkongensis HLHK9]
          Length = 649

 Score =  456 bits (1172), Expect = e-126,   Method: Composition-based stats.
 Identities = 259/682 (37%), Positives = 388/682 (56%), Gaps = 46/682 (6%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDS---WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            N +SD   E    +   D +++     K++I   ++RG++T  E+N  LP D + +EQ+
Sbjct: 3   DNSNSDKAAESKAQAAPLDNTEERRKRLKQLIVQGKERGFLTYAEINDSLPEDVLDAEQI 62

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPV 121
           E  + M+++MGI V D     ++    D+  +     A   +       DS    T DPV
Sbjct: 63  ESIIGMITDMGIQVYDEAPDAEQLLMSDATPVVADEDAVEEAESALSSVDSEFGRTTDPV 122

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   M+ ++   P   + ++   +++ +    +
Sbjct: 123 RMYMREMGTVELLTREGEIEIAKRIEDGLRHMVQAISACPGIVKDVLDQIEKVENDELRI 182

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E+ID           G            R ++      +   E +   +   +    + 
Sbjct: 183 DEVID-----------GIIDPNAPDEADARAEAELAAVNEQDAEADEADDDGEEEENAEE 231

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
               +P  N E                      +L+ + +     + ++Y ++       
Sbjct: 232 GTPAAPGTNLE----------------------ELKAQALEHFANVRKLYEKMVK----- 264

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LA 360
               K    S +   ++ ++ +    +  +  +++ L ++L  +   I  NE E+     
Sbjct: 265 -ALVKHGPQSKQYLEVQAEITETFLLVRFSARQVEALSDRLRSVVDDIRRNEREIQDICV 323

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           Q   + RDVFL      E +  WV  A    +  + + +     +I + ++ + ++   +
Sbjct: 324 QKCKMPRDVFLHTFVNNETNLEWVDAAMSLGKA-FASAIERYQHAIREKQSNLIALQDSS 382

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            + I E + I   +  GE +A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 383 MLPIRELKEISRQMATGEAKARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 442

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++ 
Sbjct: 443 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQIL 502

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP P E+A+++ MP + +RK++KI+KEPIS+ETPIGD+D SHLGDFIED   ++P
Sbjct: 503 QETGAEPDPAELARRMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDLATMAP 562

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+ A+L+E T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 563 SDAAMYASLKEATKEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIE 622

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS++LRSFLD 
Sbjct: 623 AKALRKLRHPTRSERLRSFLDA 644


>gi|114564160|ref|YP_751674.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella frigidimarina
           NCIMB 400]
 gi|114335453|gb|ABI72835.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella frigidimarina
           NCIMB 400]
          Length = 614

 Score =  456 bits (1172), Expect = e-126,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 380/655 (58%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  +   
Sbjct: 128 EGINTVQSSVSEYPQAIAMILEQFDKYEAEELRLSDII-----------SGFINPDDDDV 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                +   E    D +  + D +      +++       PE A+     L E  + S  
Sbjct: 177 APTATNVGSELA--DSKNDDDDDDDDDDDEEEEEGNKGPDPEEAKEKFTQLREAYEKSLG 234

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + +L  I E+++E                                  
Sbjct: 235 II-AEKGRDHPEAIGSLFVIGELFKE---------------------------------- 259

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ + ++  R+   E  +++L   +  + +  F++   G E +  W + 
Sbjct: 260 FRLVPKQFDRLVKSMRNMMDRVRIQERLVIKLCVEHAKMPKKNFIKAFTGNETNLDWFNK 319

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K+  +  +   +    D + +   ++ +I VET ++I+  + I   +  GE +A  AKK
Sbjct: 320 EKESTKP-YAEGLRLITDDVTRCVTKLGAIEVETDLTIAGIKDINRRMSIGEAKARRAKK 378

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 379 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 438

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 439 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 498

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 499 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAK 558

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 559 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 613


>gi|117618585|ref|YP_855378.1| RNA polymerase sigma factor RpoD [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559992|gb|ABK36940.1| RNA polymerase sigma factor RpoD [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 618

 Score =  455 bits (1171), Expect = e-126,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 376/656 (57%), Gaps = 46/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  IMAEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     L+   D+       L +II     I P              
Sbjct: 126 DGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------- 170

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                      E DDV  T   I S            D   +   + + + D+ +     
Sbjct: 171 -----------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDP 219

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            ++                  E + +LR+  +   ++ Q++ ++    +    +L  +  
Sbjct: 220 EVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLADVFR 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  
Sbjct: 263 QFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFE 322

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
           Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   +  GE +A  AK
Sbjct: 323 YQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRAK 381

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 382 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 441

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A ++ MP + +RK
Sbjct: 442 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGMPEDKIRK 501

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P D+A   +LR  T  VLA LT RE 
Sbjct: 502 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLRNATREVLAGLTAREA 561

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 617


>gi|50119628|ref|YP_048795.1| RNA polymerase sigma factor RpoD [Pectobacterium atrosepticum
           SCRI1043]
 gi|49610154|emb|CAG73594.1| RNA polymerase sigma-70 factor [Pectobacterium atrosepticum
           SCRI1043]
          Length = 611

 Score =  455 bits (1171), Expect = e-126,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 371/656 (56%), Gaps = 53/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------IGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                   +      ++   E       +   ++       PE A      L E  + + 
Sbjct: 175 DI----APTATHVGSELSSEEISDNDEEEDEDEEEDDNSIDPELAREKFTELREQYETTR 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A     R   + A + +                                 L ++  
Sbjct: 231 KVIKA---HGRSHALAAQEILN--------------------------------LSEVFK 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E +  W +
Sbjct: 256 QFRLVPKQFDFLVNSMRTMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTSNETNNSWFA 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   ++K I  ETG++I + + I   +  GE +A  AK
Sbjct: 316 AAVAMGKP-WSEKLNDVAEDVTRSLQKLKQIEEETGLTIEQVKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|107026824|ref|YP_624335.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia AU 1054]
 gi|105896198|gb|ABF79362.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia AU
           1054]
          Length = 805

 Score =  455 bits (1171), Expect = e-125,   Method: Composition-based stats.
 Identities = 253/663 (38%), Positives = 371/663 (55%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 345

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E +E +   
Sbjct: 346 -------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAA 392

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 393 QASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  V +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLDWAEKITAEGHP-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A  A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAAPHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|261820103|ref|YP_003258209.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae WPP163]
 gi|261604116|gb|ACX86602.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium wasabiae
           WPP163]
          Length = 611

 Score =  455 bits (1171), Expect = e-125,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 373/656 (56%), Gaps = 53/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------IGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                   +      ++   E   +   +   ++       PE A      L E  + + 
Sbjct: 175 DI----APTATHVGSELSSEEISDDDEEEDEDEEEDDNSIDPELAREKFTELREQYETTR 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A     R   + A + +                                 L ++  
Sbjct: 231 QVIKA---HGRSHALAAQEILN--------------------------------LSEVFK 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E +  W +
Sbjct: 256 QFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNETNNSWFA 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 316 AAVAMGKP-WSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|254248772|ref|ZP_04942092.1| Sigma-70 region 1.1 [Burkholderia cenocepacia PC184]
 gi|124875273|gb|EAY65263.1| Sigma-70 region 1.1 [Burkholderia cenocepacia PC184]
          Length = 805

 Score =  455 bits (1171), Expect = e-125,   Method: Composition-based stats.
 Identities = 252/663 (38%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 345

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E +E +   
Sbjct: 346 -------------GLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAA 392

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 393 QASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  V +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLDWAEKITAEGHP-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EA+LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEAHLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|220936192|ref|YP_002515091.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997502|gb|ACL74104.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 619

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 274/657 (41%), Positives = 382/657 (58%), Gaps = 47/657 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K++I   +++G++T  E+N  LP   V  EQ+ED +AM+++MGI V +     D 
Sbjct: 6   QQSRLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIAMINDMGIAVHEQAPDSDS 65

Query: 87  EGSEDS-LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
               DS +     A+  +       DS    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  LILSDSTVSTDEDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGEIKIAKR 125

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   ++ +L   P +   L+   D++  G   L +++   + I P       +  + 
Sbjct: 126 IEDGLGQVLFALAHYPQSISTLLAEFDKVEAGEMKLTDLV--VSFIDP-------NADDV 176

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E  S + +     +                   D+ P+  E  ER         
Sbjct: 177 PAVAANEADSADTDASASDDDSDSDSDDEDDDDTASEPEDTGPDPEEARER--------- 227

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                    + +LR++ + A+ G   +K + K + ++E++    
Sbjct: 228 -------------------------FTKLRAMYEEAM-GFAAKKHTAKYRKVREEMASYF 261

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWV 384
               L    +D L   L+++ +RI   E  ++        + R  F+      E +  W+
Sbjct: 262 MEFKLLPRFVDQLTADLHEMVERIRMQERTVMDICVNRCNMPRKEFITAFPENETNLKWL 321

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                      K  +A   D IL+I+ ++ +I  E+ ++ISE + I   +  GE +A  A
Sbjct: 322 DTQTKGKSKHAK-LLAEHKDEILRIQKKLVAIEDESNLTISEIKDINRRMSIGEAKARRA 380

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 381 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 440

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+++++ MP + VR
Sbjct: 441 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELSERMEMPEDKVR 500

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED N +SP+++A +  L E T  VLASLTPRE
Sbjct: 501 KVLKIAKEPISMETPIGDDEDSHLGDFIEDVNVMSPIEAATREGLSEATRDVLASLTPRE 560

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEMLRSFLD 617


>gi|54307643|ref|YP_128663.1| RNA polymerase sigma factor RpoD [Photobacterium profundum SS9]
 gi|46912066|emb|CAG18861.1| putative DNA-directed RNA polymerase, sigmasubunit [Photobacterium
           profundum SS9]
          Length = 612

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 374/655 (57%), Gaps = 50/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEI 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  +    A  ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTED-NTDDDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      L +II     I P          E  +
Sbjct: 125 DGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDII--SGFIDPN--------EEQTA 174

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E    D+ + + ++E+     +++ + +D  PE A      L    +  A 
Sbjct: 175 APTATHIGSELSETDLADEDKNLETDDDDEEEEDTGID--PELAREKFLELRHSYEKMAL 232

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            ++                                      + +   +V   +L ++   
Sbjct: 233 AINT-----------------------------------HGRHNATTEVAVGELSEIFKQ 257

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  L D   ++  NE  ++R+      + +  F++   G E  P W+  
Sbjct: 258 FRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCIDNSKMPKKTFIKFFAGNESSPDWIDE 317

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A +  +  +   +    + + +   +++ +  ETG+SI   + I   +  GE +A  AKK
Sbjct: 318 ALNSGKP-YAERLKNYEEDLRRSSLKLRILEKETGLSIERIKDISRRMSIGEAKARRAKK 376

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 377 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 436

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 437 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEELAERMQMPEDKIRKV 496

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +
Sbjct: 497 LKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAATNDVLAGLTPREAK 556

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 557 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 611


>gi|311278024|ref|YP_003940255.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae SCF1]
 gi|308747219|gb|ADO46971.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae SCF1]
          Length = 614

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 370/655 (56%), Gaps = 48/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I     + P +        E   
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAAEARLSDLIT--GFVDPNA--------EEDM 174

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E  ++++ + + + E     S          PE A      L    + +  
Sbjct: 175 APTATHVGSELSQEEMDDDDEEDEDEDSDSDSSDDDNSIDPELAREKFGELRAQYEVTRD 234

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 235 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 259

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  + +R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 260 FRLVPKQFDYLVNSMRTMMERVRIQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNA 319

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 320 AIAMNKP-WSEKLHDVTEDVQRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 378

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 379 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 438

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 439 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 498

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 499 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 558

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 613


>gi|149376143|ref|ZP_01893908.1| sigma factor RpoD [Marinobacter algicola DG893]
 gi|149359548|gb|EDM48007.1| sigma factor RpoD [Marinobacter algicola DG893]
          Length = 616

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 260/659 (39%), Positives = 364/659 (55%), Gaps = 53/659 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDL 83
           +      K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D 
Sbjct: 4   NSQKSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDA 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +    ++       +A+  +       +S    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 64  DTLLMTDGDSTADEAAAAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +MA++   P     +I   D + +    L +I+     + P+    F    
Sbjct: 124 KRIEEGIRDVMAAVAHFPGITGTVIQAYDRIIENEGRLSDIV--SGFLDPDGAEPFME-- 179

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                                  +   +       ++ ++    PE        L E  D
Sbjct: 180 -----------EDTTPDTSSTSDDSSDDDDDDDDSEEETESGPDPEETRLRFELLKEKLD 228

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +  +L+                                   K  +   K +    +L +
Sbjct: 229 AADASLA-----------------------------------KHGRGHKKTQEALNELGQ 253

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           +     L     D LV  +   +  +  NE  ++++      + R  F++   G E    
Sbjct: 254 VFAPFKLGNKAFDELVNVVRSTNDLVRENERAIMKICVRECKMPRKDFIKSFPGNETSLD 313

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W        +  +   +A  +D +++++  I +I  E  + +S+ + I   V  GE +A 
Sbjct: 314 WAEKMSK-GKKPYAPLIAERIDEVVRLQKRIANIQTEVDLDVSDIKEINRRVSIGEAKAR 372

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 373 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 432

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + 
Sbjct: 433 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDK 492

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A+SP+DSA    LRE T  VL+ LT 
Sbjct: 493 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSVLSGLTA 552

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR F+D
Sbjct: 553 RESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFID 611


>gi|149927883|ref|ZP_01916133.1| RNA polymerase sigma factor RpoD [Limnobacter sp. MED105]
 gi|149823322|gb|EDM82555.1| RNA polymerase sigma factor RpoD [Limnobacter sp. MED105]
          Length = 878

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 260/685 (37%), Positives = 391/685 (57%), Gaps = 54/685 (7%)

Query: 4   GKKRNRDSDSEHEDSDDSLV--FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
             K     +S +  S ++ V   +   +  K +IK+ ++RGY+T  E+N  LP D    E
Sbjct: 241 KAKDKALINSAYLSSANATVEELELRRNQLKTLIKMGKERGYLTFAEINDHLPDDVTDGE 300

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR---KDSADRSTD 118
            +E  V+   +MGI V +     +     D+  + +SA ++    +      DS    T 
Sbjct: 301 VIEAMVSTFHDMGITVYEQAPDAEALLMNDNAPVGTSAEDAEEEAEAALSNVDSEFGRTT 360

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+REMG++ELL+REGEI IAKRIEAG   M+ ++   P   + ++     + +G 
Sbjct: 361 DPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVQAISACPAIVEDVVGLGQRIAEGL 420

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           + + E++D                                         G I+ +     
Sbjct: 421 STVDEVVD-----------------------------------------GIIDDSITEEM 439

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            + +  +   ++ +N++     D   ++   +   ++L+   +    EI + + +L+ ++
Sbjct: 440 VEAAAPEETNDDDDNEDEEEGNDGGTTSGMSARQLEELKKNSLAVFAEIEKQFAKLKKVR 499

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                      ++   K  KE + +    +     +++ L   L +    +   E E+  
Sbjct: 500 ------ADGGYNTPAYKKAKEAIAEQFMKIRFTAKQVERLCSILREQVDSVRKIEREIYD 553

Query: 359 LA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +A    G+ R+ FL++ +G E++  WV          W    A  V +I +++ ++ +I 
Sbjct: 554 IAVNRVGVPREQFLDKFRGHEVEAAWVDTFSA-SNAAWAETWARNVPAINELQQKLVAIQ 612

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + +++ R I   +  GE  A +AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 613 DTVSLPLNDLRAINKQMVSGENRARLAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEG 672

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R
Sbjct: 673 NVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISR 732

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +   EP P  +A+++ MP E +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + 
Sbjct: 733 QILQETGIEPDPATLAERMEMPEEKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDNHT 792

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           ++P D+A  ++LR  T  VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIR
Sbjct: 793 LAPQDAAQYSSLRFVTKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIR 852

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 853 QIEAKALRKLRHPSRSDKLKSFLEG 877


>gi|242240773|ref|YP_002988954.1| RNA polymerase sigma factor RpoD [Dickeya dadantii Ech703]
 gi|242132830|gb|ACS87132.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya dadantii Ech703]
          Length = 612

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 367/655 (56%), Gaps = 50/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +  G + L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  E E + E     + D        PE A      L E  + +  
Sbjct: 174 L-AAAAPESTELEGEEIEDEEEDEEEDGDNSDSDDDNSIDPELARQKFTELREQYEATRL 232

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           ++ A                                     +S         KL ++   
Sbjct: 233 SIKA-----------------------------------HGRSHQSAIDEINKLSEVFKQ 257

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + DLLV  +  +  R+   E  +++L  +   + +  F+    G E    W   
Sbjct: 258 FRLVPKQFDLLVNSMRSMMDRVRTQERLIMKLCVEQCKMPKKNFMTMFTGNETSIKWFEA 317

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 318 ALAMGKP-WSEKLREVTDDVERSLLKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 376

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 377 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 436

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 437 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 496

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 497 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAK 556

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|254229773|ref|ZP_04923181.1| sigma-70, non-essential region family [Vibrio sp. Ex25]
 gi|269968567|ref|ZP_06182570.1| RNA polymerase sigma factor [Vibrio alginolyticus 40B]
 gi|151937740|gb|EDN56590.1| sigma-70, non-essential region family [Vibrio sp. Ex25]
 gi|269826825|gb|EEZ81156.1| RNA polymerase sigma factor [Vibrio alginolyticus 40B]
          Length = 639

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 263/656 (40%), Positives = 369/656 (56%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 25  QSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 84

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 85  ALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 144

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I        +          G 
Sbjct: 145 EEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTATHIGS 204

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +   ++ E  D  E   D    ++       ++                      
Sbjct: 205 ELTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPEL---------------------- 242

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +   +++   Y+ L+      +   +   +S K  V  E ++ +  
Sbjct: 243 -------------ALEKFNQLRSTYQNLQ------LAINEYGYNSPKATVANEMMLDVFR 283

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++    YG + +  F+    G E    W+ 
Sbjct: 284 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEAWLD 343

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 344 EVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAK 402

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 403 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 463 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 522

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 523 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREA 582

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 583 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 638


>gi|269960187|ref|ZP_06174562.1| RNA polymerase sigma factor [Vibrio harveyi 1DA3]
 gi|269834994|gb|EEZ89078.1| RNA polymerase sigma factor [Vibrio harveyi 1DA3]
          Length = 639

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 265/663 (39%), Positives = 372/663 (56%), Gaps = 45/663 (6%)

Query: 22  LVFDFS-DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
              D +     K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+ 
Sbjct: 18  PSMDQNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVET 77

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
               D+    D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGE
Sbjct: 78  APDADDLALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 137

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I IAKRIE G   + +S+ E P T   ++   D++      L ++I        +     
Sbjct: 138 IDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAP 197

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                G    + +   +++E  D  E   D    ++       ++               
Sbjct: 198 TATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL--------------- 242

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
                                +   +++   Y+ L+      +   +    S K  V  E
Sbjct: 243 --------------------ALEKFNQLRSTYQNLQ------LAINEHGYESPKATVANE 276

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRE 378
            ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+    G E
Sbjct: 277 LMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKAAVEYGKMPKKSFIALFTGNE 336

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
               W+       +  +   +    + I +   ++K I  ET +++   + I   +  GE
Sbjct: 337 SSEAWLDEILS-SDKPYAEKIKRSEEEIRRSITKLKMIEEETSLNVQNIKDISRRMSIGE 395

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 396 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ M
Sbjct: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQM 515

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA
Sbjct: 516 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKMATKDVLA 575

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRS
Sbjct: 576 GLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 635

Query: 679 FLD 681
           FLD
Sbjct: 636 FLD 638


>gi|78063051|ref|YP_372959.1| RNA polymerase sigma factor RpoD [Burkholderia sp. 383]
 gi|77970936|gb|ABB12315.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. 383]
          Length = 808

 Score =  455 bits (1169), Expect = e-125,   Method: Composition-based stats.
 Identities = 253/663 (38%), Positives = 372/663 (56%), Gaps = 40/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 181 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 240

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 241 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 300

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D    + P +     
Sbjct: 301 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD--GLLDPNASDS-- 356

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                                     + D  SA +    +    ++  E  E +E   ++
Sbjct: 357 -------------------------ADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEEED 391

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D    A   +A  + L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 392 DGAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQET 445

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 446 IQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 505

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  V +I + +  +  +     + + + +     +  GE 
Sbjct: 506 DLDWSEKIMAEGHS-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 564

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 565 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 624

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 625 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 684

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 685 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 744

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 745 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 804

Query: 680 LDG 682
           L+G
Sbjct: 805 LEG 807


>gi|157960786|ref|YP_001500820.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella pealeana ATCC
           700345]
 gi|157845786|gb|ABV86285.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella pealeana ATCC
           700345]
          Length = 616

 Score =  455 bits (1169), Expect = e-125,   Method: Composition-based stats.
 Identities = 268/655 (40%), Positives = 373/655 (56%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEI 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSED-STDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P     ++   D        L +II            GF        
Sbjct: 128 EGINTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDII-----------SGFVDPNAEDV 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E   D++ + + D +      +++       PE A+     L    + +A 
Sbjct: 177 APTATHVGSELSDDELDDEDDDDDDDDDDDEEEEGPKGPDPEEAKEKFTTLRLAHE-NAL 235

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+   AL EI E+++E                                  
Sbjct: 236 RIIADKGRGHPESTVALFEIGEIFKE---------------------------------- 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   E    W + 
Sbjct: 262 FRLMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFND 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +   +     E D + + R ++ +I VETG++I   + I   +  GE +A  AKK
Sbjct: 322 ELASGKPYVEGLQMVEFD-VQRCRAKLDAIEVETGLAIGAIKDINRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|77359315|ref|YP_338890.1| RNA polymerase sigma factor [Pseudoalteromonas haloplanktis TAC125]
 gi|76874226|emb|CAI85447.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 615

 Score =  455 bits (1169), Expect = e-125,   Method: Composition-based stats.
 Identities = 272/657 (41%), Positives = 376/657 (57%), Gaps = 50/657 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE 
Sbjct: 6   QSQLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +++     +A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMQETTTDEDAAEAAAAALATVEK-EIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D+       L +II            GF    E  +
Sbjct: 125 EGINQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------VGFIDPNEDTA 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP-PENAENDERNLDEDEDDSA 266
                +   E     + + + D + + +  +D+      P PE A     NL +  + + 
Sbjct: 174 PISATNIGSELSAKQLNDDDKDDDDSDEDDEDEEEVDTGPDPEEARVHFENLRDLYNKAR 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T  A + +  P  + A+ EI E++                                   
Sbjct: 234 ETFEA-KGRSHPDSLAAIFEIGELF----------------------------------K 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           +  L   + D +V  + ++  R+   E  +++ A     + +  F++     E D  WV 
Sbjct: 259 TFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQIAKLPKKTFVKHFANNETDATWVD 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 E  +   +      I++  N+++ I   TG++I   + I   +  GE +A  AK
Sbjct: 319 LEIAANEK-YSAKLEEVKPEIIRSLNKLRVIESSTGLNIERIKDINRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + VRK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKVRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 614


>gi|253686949|ref|YP_003016139.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251753527|gb|ACT11603.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 612

 Score =  454 bits (1168), Expect = e-125,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 374/656 (57%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  ++     +   E   D +  ++   D        PE A      L +  + + 
Sbjct: 175 DI---APTATHVGSELSSEEMDDDDEESEDDDDSEDDNSIDPELAREKFTELRDQYETTR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +   ++  R   +   + +                                 L ++  
Sbjct: 232 KVI---KEHGRSHALAVQEILN--------------------------------LSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E +  W +
Sbjct: 257 QFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNETNSTWFA 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAVAMGKP-WSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|90411915|ref|ZP_01219923.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90327173|gb|EAS43545.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 612

 Score =  454 bits (1168), Expect = e-125,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 374/655 (57%), Gaps = 50/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEI 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  +    A  ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTED-NTDEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      L +II     I P          E  +
Sbjct: 125 DGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDII--SGFIDPN--------EEQTA 174

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E    D+ + + ++E+     +++ + +D  PE A      L    +  A 
Sbjct: 175 APTATHIGSELSETDLADEDKNLETDEDDEEEEDTGID--PELAREKFLELRHSYEKMAL 232

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            ++                                      + +   +V   +L ++   
Sbjct: 233 AINT-----------------------------------HGRHNATTEVAVGELSEIFKQ 257

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  L D   ++  NE  ++R+      + +  F++   G E  P W+  
Sbjct: 258 FRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFIKFFAGNESSPDWIDE 317

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A +  +  +   +    + + +   +++ +  ETG+SI   + I   +  GE +A  AKK
Sbjct: 318 ALNSGKP-YAERLKIYEEDLRRSSLKLRILEKETGLSIERIKDISRRMSIGEAKARRAKK 376

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 377 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 436

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 437 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEELAERMQMPEDKIRKV 496

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +
Sbjct: 497 LKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAATNDVLAGLTPREAK 556

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 557 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 611


>gi|91788957|ref|YP_549909.1| sigma 70 (RpoD) [Polaromonas sp. JS666]
 gi|91698182|gb|ABE45011.1| RNA polymerase, sigma 70 subunit, RpoD [Polaromonas sp. JS666]
          Length = 784

 Score =  454 bits (1167), Expect = e-125,   Method: Composition-based stats.
 Identities = 260/655 (39%), Positives = 372/655 (56%), Gaps = 57/655 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE--- 86
             K +IKL + RGY+T  E++  LP   V +E +E  V ML++MG+ V +     +    
Sbjct: 182 RLKTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVVNMLNDMGVAVYEQAPDAETLLL 241

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +  ++     A   +       DS    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 242 NNTGPTVATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 301

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   MM ++ ESP T   ++   +E+ +G  ++  ++D           GF +  E  
Sbjct: 302 EGGLMKMMEAISESPATIAEIMRLGEEIREGKIVISTVVD-----------GFSNPNEAD 350

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y   ED  +  E DD     G                                     +
Sbjct: 351 DYVAEEDFDEFDEEDDDDGKGG-------------------------------------S 373

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L+   ++L+ + +   D+IA ++ ++    D    G          K L ++L+ +  
Sbjct: 374 KALTKKLEELKKEALSRFDKIASLFEKVHKTYDK--EGYGTPTYVKAQKALSDELMTVRF 431

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +    +   D+L  Q+ D+ K+       +    +  G+ ++ F++      L+  WV  
Sbjct: 432 TAKTIEKLCDMLRGQVLDVRKKERELRRII---VEKCGMPQETFIKDFPPNLLNLKWVEK 488

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  W   +A  +  I +++ ++  +     + + + + I   + +GE  +  AKK
Sbjct: 489 QVASGKP-WSTVMARNIPPIQELQTKLAELQARVVVPLGQLKDINKRMNEGESNSRDAKK 547

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 548 EMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 607

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + +RK+
Sbjct: 608 AITRSIADQARTIRIPVHMIETINKMNRLSRQHLQEFGFEPDASILAAKMEIPEDKIRKI 667

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD+D SHLGDFIED    +PL++A+QA LR+    +L SLTPRE +
Sbjct: 668 MKIAKEPISMETPIGDDDDSHLGDFIEDSANTAPLEAAMQAGLRDVVKDILDSLTPREAK 727

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 728 VLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 782


>gi|23428541|gb|AAL11450.1| RNA polymerase sigma-70 subunit [Serratia plymuthica]
          Length = 612

 Score =  454 bits (1167), Expect = e-125,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 368/656 (56%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHVGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E +  E++               +   D        PE A     +L +  + + 
Sbjct: 186 ELSTEEQNDDEEDE--------------EDDDDAEDDNSIDPELARQKFTDLRDQYEATR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 232 LVI-----------------------------------KKNGRSHASAAEEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W  
Sbjct: 257 QFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFAGNETSDSWFE 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    D + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AALAMAKP-WSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLI++GNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIRKGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF V RERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVIRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|311105374|ref|YP_003978227.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans A8]
 gi|310760063|gb|ADP15512.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans A8]
          Length = 750

 Score =  454 bits (1167), Expect = e-125,   Method: Composition-based stats.
 Identities = 253/664 (38%), Positives = 370/664 (55%), Gaps = 66/664 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D     
Sbjct: 146 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDA 205

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 206 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 265

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 266 IAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVD-----------GLVD 314

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ ++    D P     + +      
Sbjct: 315 PEDGEEY-----------------------AGAGVTAEEDEGDDGPAGGMSSKQL----- 346

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+ + + ++R   +      KD   S      +E +
Sbjct: 347 ------------EDLRVKALAKFDEVGKQFEKMRHSYE------KDGYKSDVYVRAQESI 388

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
              +  +      ++ L + L    + +   E  +L       G+ R  F++   G E +
Sbjct: 389 QNELMGIRFTAKMVEKLADTLRQQVEEVRQLERAVLHTCVDRAGMPRTHFIKVFPGNETN 448

Query: 381 PHWV--SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
             WV    A   P  E    +  ++ ++ +++ ++  +     + + + + +   +  GE
Sbjct: 449 MQWVVDEVAAGHPYAE---TLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGE 505

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 506 AKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 565

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ M
Sbjct: 566 YATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDM 625

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED + ++P D+A+  ++R+    VL 
Sbjct: 626 PEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDVVKEVLD 685

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLTPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+S
Sbjct: 686 SLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKS 745

Query: 679 FLDG 682
           FL+G
Sbjct: 746 FLEG 749


>gi|311693206|gb|ADP96079.1| RNA polymerase, sigma 70 subunit, RpoD [marine bacterium HP15]
          Length = 615

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 262/659 (39%), Positives = 369/659 (55%), Gaps = 55/659 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-DDL 83
           +      K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D 
Sbjct: 4   NSQKSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDA 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +    +E       +A+  +       ++    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 64  DTLLMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +MA++   P T   +I   D + +    + +I+            GF    
Sbjct: 124 KRIEEGIRDVMAAVAHFPGTAGTVIQAYDRILENEGRISDIV-----------TGFLDPD 172

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +       E    E    +  +           S ++ +     PE        L+E  +
Sbjct: 173 DA------EPFMGEDTTPESSDDSDSDSDDDDDSSEEETDNGPDPEETRLRFELLNEKLE 226

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +   L+                                   K  +S  K +    +L +
Sbjct: 227 AANKALA-----------------------------------KHGRSDKKTQEALNELGQ 251

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           +     L     D LV  +   +  +  NE  ++++      + R  F++   G E +  
Sbjct: 252 VFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRECKMPRKDFIKSFPGNETNLD 311

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W        +  +   +A  +D +++++  I+++  E  + +++ + I   V  GE +A 
Sbjct: 312 WADKIAK-SKKPYAAPLAERIDEVVRLQKRIQNVQTEVDLDVADIKEINRRVSIGEAKAR 370

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 371 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 430

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + 
Sbjct: 431 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDK 490

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A+SP+DSA    LRE T  VLA LT 
Sbjct: 491 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSVLAGLTA 550

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR F+D
Sbjct: 551 RESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFID 609


>gi|217974326|ref|YP_002359077.1| RNA polymerase sigma 70 subunit RpoD [Shewanella baltica OS223]
 gi|217499461|gb|ACK47654.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS223]
          Length = 611

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 273/655 (41%), Positives = 379/655 (57%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E  +
Sbjct: 125 EGINTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEDVA 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S+  E     E E D E       ++       PE A      L    + +  
Sbjct: 174 PTATHIGSELSEE--ELEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALK 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 232 IIDA-KGREHPESVKALFEIGEIFKE---------------------------------- 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W + 
Sbjct: 257 FRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKFFTGNETNLDWFNT 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   +  +   +    D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 317 EKASTKP-YAEGLRMVEDDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 610


>gi|206576865|ref|YP_002236518.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae 342]
 gi|288933503|ref|YP_003437562.1| RNA polymerase, sigma 70 subunit, RpoD [Klebsiella variicola At-22]
 gi|290511438|ref|ZP_06550807.1| RNA polymerase primary sigma factor [Klebsiella sp. 1_1_55]
 gi|206565923|gb|ACI07699.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae 342]
 gi|288888232|gb|ADC56550.1| RNA polymerase, sigma 70 subunit, RpoD [Klebsiella variicola At-22]
 gi|289776431|gb|EFD84430.1| RNA polymerase primary sigma factor [Klebsiella sp. 1_1_55]
          Length = 613

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 365/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +       +        PE A      L    + +  
Sbjct: 174 MAPTATHVGSELSQEEMDDDEDEDEDDDADDNSDDDNSIDPELAREKFAELRTQYELTRD 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 234 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AVAMNKP-WSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|152971991|ref|YP_001337100.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|330003818|ref|ZP_08304768.1| RNA polymerase sigma factor RpoD [Klebsiella sp. MS 92-3]
 gi|150956840|gb|ABR78870.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|328536802|gb|EGF63114.1| RNA polymerase sigma factor RpoD [Klebsiella sp. MS 92-3]
          Length = 613

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 365/655 (55%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +       +        PE A      L    + +  
Sbjct: 174 MAPTATHVGSELSQEEMDDDEDEDEDEDADDNSDDDNSIDPELAREKFAELRTQYELTRD 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 234 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AVAMNKP-WSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|320539899|ref|ZP_08039558.1| putative RNA polymerase, sigma 70 (sigma D) factor [Serratia
           symbiotica str. Tucson]
 gi|320030085|gb|EFW12105.1| putative RNA polymerase, sigma 70 (sigma D) factor [Serratia
           symbiotica str. Tucson]
          Length = 607

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 369/656 (56%), Gaps = 57/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I        E          G 
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPDAEEDIAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E   ++ +  +   +                     PE A     +L +  + + 
Sbjct: 186 ELSTEEQDDEDDDDAEDDNSI-------------------DPELARQKFADLRDQYETTR 226

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ +S         KL ++  
Sbjct: 227 LVI-----------------------------------RKNSRSHASAAEEILKLSEVFK 251

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+  +E  +++L  +   + +  F+    G E    W  
Sbjct: 252 QFRLVPKQFDFLVNSMRAMMDRVHTHERTIMKLCVEQCKMPKKNFVTLFAGNETSDVWFE 311

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A+   +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 312 KAQAMTKP-WSEKLKDVAEDVQRSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAK 370

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 371 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 430

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 431 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPMPEELAERMLMPEDKIRK 490

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE 
Sbjct: 491 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTFELPLDSATSESLRSATHDVLAGLTAREA 550

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 551 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 606


>gi|262275021|ref|ZP_06052832.1| RNA polymerase sigma factor RpoD [Grimontia hollisae CIP 101886]
 gi|262221584|gb|EEY72898.1| RNA polymerase sigma factor RpoD [Grimontia hollisae CIP 101886]
          Length = 615

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 269/657 (40%), Positives = 376/657 (57%), Gaps = 51/657 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVETAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++    +   ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSETVADEDAVEAAAAALSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P +  +L+   D++      L +II            GF    +   
Sbjct: 125 DGINQVQVSVAEYPGSISSLLDQFDKVEAEELRLTDII-----------SGFVDPNQDDI 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS--PPENAENDERNLDEDEDDS 265
                    E   + + + + D++       +D ++ D+   PE A      L    +  
Sbjct: 174 APTATHIGSELTDEQLDDEDDDVDDDDDEDSEDEAEEDTGIDPELAREKFNELRVAYEGM 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
             ++                                   QK  +   +  V   +L ++ 
Sbjct: 234 QQSI-----------------------------------QKYGRFHEQTTVAIAELSEVF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV 384
               L   + D LV ++ D   R+   E  ++RL      + +  F++   G E    W+
Sbjct: 259 KQFRLVPKQFDRLVNEMRDTMDRVRTQERIIMRLCVDQAKMPKKTFVQLFAGNESSDAWL 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    +  +   +    + + +   ++K +  ETG+S+   + I   +  GE +A  A
Sbjct: 319 DKALA-SDKPYAERLKQHEEDLRRCIQKLKIVEDETGLSVERVKDISRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   NL+  T+ VLA LTPRE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPMDSATMNNLKMATSEVLAGLTPRE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614


>gi|330831100|ref|YP_004394052.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806236|gb|AEB51435.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 618

 Score =  453 bits (1165), Expect = e-125,   Method: Composition-based stats.
 Identities = 272/655 (41%), Positives = 371/655 (56%), Gaps = 44/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  IMAEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     L+   D+       L +II            GF    E   
Sbjct: 126 DGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE--- 171

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                                  E  A  +    S++       E++E   DEDED  + 
Sbjct: 172 ----------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDGDSS 209

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                             E+   Y          ++ QK+ ++    +    +L  +   
Sbjct: 210 DDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADVFRQ 263

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y
Sbjct: 264 FRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEY 323

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   +      V  + D I +   +++ I  ETG+SI++ + I   +  GE +A  AKK
Sbjct: 324 QKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRAKK 382

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 383 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 442

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A ++ MP + +RKV
Sbjct: 443 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGMPEDKIRKV 502

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P D+A   +LR  T  VLA LT RE +
Sbjct: 503 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLRNATREVLAGLTAREAK 562

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 563 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 617


>gi|294634612|ref|ZP_06713146.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|291091942|gb|EFE24503.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
          Length = 613

 Score =  453 bits (1165), Expect = e-125,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 367/655 (56%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A+ ++V +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENI-ADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +  ++    + D +   +   D        PE A      L E  + +  
Sbjct: 174 MAPTATHVGSELPEEELNDDDDEDDDDEDGDDSDDDNSIDPELARQKFIELREQYEKTRL 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A                                   + +SS K +     L ++   
Sbjct: 234 AIKA-----------------------------------EGRSSAKAQEEILNLSEIFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W   
Sbjct: 259 FRLVPKQFDYLVNNMRAMMDRVRGQERLIMKLCVEQSKMPKKNFITLFTGNETSITWFEA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 ALAMGKP-WGEKLKDMREEVERSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATRDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|1905967|gb|AAC45085.1| RNA polymerase sigma 80 subunit [Bordetella pertussis 18323]
          Length = 733

 Score =  453 bits (1165), Expect = e-125,   Method: Composition-based stats.
 Identities = 250/662 (37%), Positives = 368/662 (55%), Gaps = 62/662 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D     
Sbjct: 129 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDA 188

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 189 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 248

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 249 IAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD-----------GLVD 297

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ D+    D P     + +      
Sbjct: 298 PEDGEEY-----------------------AGAGVTADEDEGDDGPAGGMSSKQL----- 329

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+++ + ++R   +      K+   S      ++ +
Sbjct: 330 ------------EDLRVKALAKFDEVSKQFEKMRQSYE------KEGYKSDAYLKAQDII 371

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
              +  +      ++ L + L    + +   E  +L       G+ R  FL+   G E +
Sbjct: 372 QTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSHFLKAFPGNETN 431

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV          +   +  ++ ++ +++ ++  +     + + + + +   +  GE +
Sbjct: 432 LQWVLDEVA-AAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGEAK 490

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 491 ARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 550

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP 
Sbjct: 551 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDMPE 610

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+  ++R+    VL SL
Sbjct: 611 DKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMRDVVKEVLDSL 670

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL
Sbjct: 671 TPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFL 730

Query: 681 DG 682
           +G
Sbjct: 731 EG 732


>gi|327479259|gb|AEA82569.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 4166]
          Length = 617

 Score =  453 bits (1165), Expect = e-125,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 379/657 (57%), Gaps = 47/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I+  R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T  +++   + + +    L +I  L   I P+  G        
Sbjct: 125 IEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPDDDGAA------ 176

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            + Q+ E  + +     V + + D E     ++++       PE A      + E  + +
Sbjct: 177 -APQEVEPETPQTTAKPVVDDKDDDEEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKA 235

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  ++S +     E L  L 
Sbjct: 236 NKAL-----------------------------------KKHGRASQQATEELEALAILF 260

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LVE++ D   +I   E  +++L      + R  FL +    E +  W 
Sbjct: 261 MPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQFPSNETNLDWA 320

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  + ++   +    + I + + ++  +  +  ++I++ + I   +  GE +A  A
Sbjct: 321 EQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRMSIGEAKARRA 379

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 380 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 439

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 440 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 499

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 500 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATREVLSGLTARE 559

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 560 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 616


>gi|229525180|ref|ZP_04414585.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
 gi|229338761|gb|EEO03778.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
          Length = 642

 Score =  453 bits (1165), Expect = e-125,   Method: Composition-based stats.
 Identities = 269/664 (40%), Positives = 370/664 (55%), Gaps = 42/664 (6%)

Query: 22  LVFDFS-DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
              D +     K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+ 
Sbjct: 16  PSMDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVET 75

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
               D+    D   +    +  +        +S    T DPVRMY+REMG++ELL+REGE
Sbjct: 76  APDADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 135

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGG 198
           I IAKRIE G   + +++ E P T   ++   D +      L ++I     + P   +  
Sbjct: 136 IDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETE 193

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
               T   S     D + E +     E E + E     S D   +V   PE A      L
Sbjct: 194 APTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNEL 253

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                                                  Q+  +   +  + S +     
Sbjct: 254 R-----------------------------------GKFQNLQLAVNEFGRDSHQASEAS 278

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGR 377
           + ++ +     L   + D LVE L     R+   E  +++       + +  F+    G 
Sbjct: 279 DLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGN 338

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+       +  +   V  + + I +   +++ I  ET +S+   + I   +  G
Sbjct: 339 ESNEEWLDKVLA-SDKPYVAKVRAQQEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIG 397

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 398 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 457

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ 
Sbjct: 458 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQ 517

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VL
Sbjct: 518 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVL 577

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 578 AGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 637

Query: 678 SFLD 681
           SFLD
Sbjct: 638 SFLD 641


>gi|114321663|ref|YP_743346.1| RNA polymerase, sigma 70 subunit, RpoD [Alkalilimnicola ehrlichii
           MLHE-1]
 gi|114228057|gb|ABI57856.1| RNA polymerase, sigma 70 subunit, RpoD [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 598

 Score =  453 bits (1164), Expect = e-125,   Method: Composition-based stats.
 Identities = 277/656 (42%), Positives = 377/656 (57%), Gaps = 64/656 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLED 85
                K++I   +++G++T  E+N  LP D V  EQ+ED + M+++MGINV +   D ++
Sbjct: 5   QQSQIKQLIAKGKEQGFLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGINVHEVAPDADE 64

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              S+ ++      +  +       D+    T DPVRMY+REMG++ELL+REGEI +AKR
Sbjct: 65  LLLSDAAVSTDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGTVELLTREGEIELAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   ++A+L   P     L+    ++ DG   L E++           GGF +  E 
Sbjct: 125 IEEGLDQVLAALSAYPGAAAKLLDLYRKVQDGEMRLNELM-----------GGFRNPDEE 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            S    +   +E E  +                         PE A    R L E +   
Sbjct: 174 LSAYSADAGKEEDEDGEEAVV----------------DNGPDPEMAAELFRRLAEADQRM 217

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   ++    S +C  L+E+L ++ 
Sbjct: 218 QEVL-----------------------------------RRQGSDSPECAELREQLAEIF 242

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
            +       ID LV+ L      +  NE  +L+     G+ R  F+     RE DP W+ 
Sbjct: 243 LTFKFPPKIIDQLVDGLRRDVNVLRRNERHILKACTKAGMPRKTFVRSFISRETDPGWLD 302

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  W   +A   D I + +  +     + G++I E + I   +  GE +A  AK
Sbjct: 303 EMLA-SKEPWAQRLAEHEDDIRRAQQVLIDAERKVGMTIGEIKDINRRMSIGEAKARRAK 361

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 362 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 421

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+P+E+A+++ MP + VRK
Sbjct: 422 QAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPDELAERMEMPEDKVRK 481

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED NA+SP+DSA +  LRE+   VL+ LTPRE 
Sbjct: 482 VLKIAKEPISMETPIGDDEDSHLGDFIEDINAMSPVDSATREGLRESVKGVLSGLTPREA 541

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 542 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEGLRSFLD 597


>gi|120599857|ref|YP_964431.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146292207|ref|YP_001182631.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
           CN-32]
 gi|120559950|gb|ABM25877.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. W3-18-1]
 gi|145563897|gb|ABP74832.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
           CN-32]
          Length = 616

 Score =  453 bits (1164), Expect = e-125,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 382/655 (58%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E   
Sbjct: 128 EGINTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEEDV 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E   +D+ + + + E      ++D +     PE A      L    +++  
Sbjct: 177 APTATHIGSELSDEDLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALK 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 237 IIEA-KGREHPESVKALFEIGEIFKE---------------------------------- 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E   ++L  +   + +  F++   G E +  W  +
Sbjct: 262 FRLVPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFTGNETNLDWF-H 320

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A+      +   +    + +L+ R+++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 321 AEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|319425507|gb|ADV53581.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
           200]
          Length = 613

 Score =  453 bits (1164), Expect = e-125,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 382/655 (58%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E   
Sbjct: 125 EGINTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEEDV 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E   +D+ + + + E      ++D +     PE A      L    +++  
Sbjct: 174 APTATHIGSELSDEDLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALK 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 234 IIEA-KGREHPESVKALFEIGEIFKE---------------------------------- 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E   ++L  +   + +  F++   G E +  W  +
Sbjct: 259 FRLVPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFTGNETNLDWF-H 317

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A+      +   +    + +L+ R+++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 318 AEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 612


>gi|260767412|ref|ZP_05876349.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|260617524|gb|EEX42706.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|315181195|gb|ADT88109.1| RNA polymerase sigma factor RpoD [Vibrio furnissii NCTC 11218]
          Length = 628

 Score =  453 bits (1164), Expect = e-125,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 380/656 (57%), Gaps = 36/656 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDNAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P T   ++   D++      L ++I     + P          E  
Sbjct: 126 EDGINQVQSAVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPN--------EEET 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           S         E    D+++ E + +  +   +D+    D   ++   +E  +D +     
Sbjct: 176 SAPTATHIGSELSGADLEDEEEEKDVDSDDDEDEDEDGDDNSDDDSEEEVGIDPE----- 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           AL +  E+  + ++LQ   +   +    S K +   + ++ +  
Sbjct: 231 ---------------LALQKFTELRNKFQNLQ---LAINEHGNESSKAQQATDLVLDVFR 272

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV+ L     R+   E  +++ + +   + +  F+    G E    W+ 
Sbjct: 273 EFRLTPKQFDHLVDTLRTSMDRVRTQERLIMKSVVEVAKMPKKSFIAVFTGNESSEAWLD 332

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  + + +    D I +   +++ I  ET +++   + I   +  GE +A  AK
Sbjct: 333 QVLA-SDKPYVDKIRQYEDDIRRSIQKLQIIEQETSLTVERIKDISRRMSIGEAKARRAK 391

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 392 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 451

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 452 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 511

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 512 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREA 571

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 572 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 627


>gi|114048481|ref|YP_739031.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-7]
 gi|113889923|gb|ABI43974.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-7]
          Length = 619

 Score =  453 bits (1164), Expect = e-125,   Method: Composition-based stats.
 Identities = 271/658 (41%), Positives = 379/658 (57%), Gaps = 52/658 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E   
Sbjct: 128 EGINTVQSSVAEYPQAIAMILEQYDQYEADELRLSDII-----------SGFVNPDEEDL 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV---DSPPENAENDERNLDEDEDD 264
                    E   +D+ + + D E   +    D          PE A      L    ++
Sbjct: 177 GPTATHIGSELSEEDLDDEDDDEEDEDEDGDGDGDDDGNKGPDPEEARERFGQLRTAYEN 236

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A + +  P+ + AL EI E+++E                               
Sbjct: 237 ALKIIEA-KGREHPESIKALFEIGEIFKE------------------------------- 264

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV+ +  +  R+   E  L++L  +   + +  F++   G E +  W
Sbjct: 265 ---FRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDW 321

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K+  +  +   +    + + + R+++ +I  ETG+ I+  + I   +  GE +A  
Sbjct: 322 FDAEKNSTKP-YAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARR 380

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +
Sbjct: 441 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKI 500

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT R
Sbjct: 501 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAR 560

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 618


>gi|117921525|ref|YP_870717.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. ANA-3]
 gi|117613857|gb|ABK49311.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. ANA-3]
          Length = 619

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 269/658 (40%), Positives = 379/658 (57%), Gaps = 52/658 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E   
Sbjct: 128 EGINTVQSSVAEYPQAIAMILEQYDQYEADELRLSDII-----------SGFVNPDEEDL 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV---DSPPENAENDERNLDEDEDD 264
                    E   +D+ + + D +   +    +          PE A      L    ++
Sbjct: 177 GPTATHIGSELSEEDLDDEDDDEDDEDEDGDGEGDDDGNKGPDPEEARERFSQLRTAYEN 236

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A + +  P+ + AL EI E+++E                               
Sbjct: 237 ALKIIDA-KGREHPESIQALFEIGEIFKE------------------------------- 264

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV+ +  +  R+   E  L++L  +   + +  F++   G E +  W
Sbjct: 265 ---FRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDW 321

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K+  +  +   +    + + + R+++ +I  ETG+ I+  + I   +  GE +A  
Sbjct: 322 FDAEKNSTKP-YAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARR 380

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +
Sbjct: 441 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKI 500

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT R
Sbjct: 501 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAR 560

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 618


>gi|304409306|ref|ZP_07390926.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|307303664|ref|ZP_07583417.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|304351824|gb|EFM16222.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|306912562|gb|EFN42985.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|315266575|gb|ADT93428.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS678]
          Length = 611

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 273/655 (41%), Positives = 379/655 (57%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E  +
Sbjct: 125 EGINTVQSSVAEYPQAIAMILEQFDQFEADELRLSDII-----------SGFVNPDEDVA 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S+  E     E E D E       ++       PE A      L    + +  
Sbjct: 174 PTATHIGSELSEE--ELEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALK 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 232 IIEA-KGREHPESVKALFEIGEIFKE---------------------------------- 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E  +L+L  +   + +  F++   G E +  W + 
Sbjct: 257 FRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGNETNLDWFNT 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            K   +  +   +    D +++ R ++ ++  ETG++IS  + I   +  GE +A  AKK
Sbjct: 317 EKASTKP-YAEGLRMVEDDVIRCRTKLAAVEEETGLAISAIKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 610


>gi|87119778|ref|ZP_01075675.1| RNA polymerase sigma factor [Marinomonas sp. MED121]
 gi|86165254|gb|EAQ66522.1| RNA polymerase sigma factor [Marinomonas sp. MED121]
          Length = 614

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 270/660 (40%), Positives = 375/660 (56%), Gaps = 48/660 (7%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + D      K++I   +++GY+T  E+N  LP D    EQ+E  +AM+++MGI V +   
Sbjct: 1   MSDNQQSRLKELIAKGKEQGYLTFAEVNDHLPDDLSDPEQVEQIIAMINDMGIVVGEYAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ++    E+      +A+  +       +     T DPVRMY+REMG++ELL+R GEIAI
Sbjct: 61  DKENLLMEEGDSTDEAAAEEAAAALAAVEGDVARTTDPVRMYMREMGTVELLTRAGEIAI 120

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +MA++   P   Q L+   ++  +    L +I             GF  G
Sbjct: 121 AKRIEEGTREVMAAVSYYPGAVQTLLDAYEKSKEEEGRLSDIF-----------SGFIDG 169

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  +     +E   +++ ++  + E       ++ +     PE             
Sbjct: 170 DGEEPVFEDAPLVEEVSEEELDKSTEESEDGDDDEDEEETDNGPDPEETARR-------- 221

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                                  EI   + EL +L +N        +     K  +E+L 
Sbjct: 222 ---------------------FGEIERNHTELLALLEN------HSRQDSIVKEKQEELS 254

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
                + L     D LV+++     ++   E  +++   +  G+ R  FL+R    E + 
Sbjct: 255 ICFAPIKLVPKIFDDLVDRVRSRMDKVREQERIIMQVCVRKAGMPRTEFLKRFPNNETNI 314

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W         G        E +  ++ + ++++IS +TG++I E + I   +  GE  A
Sbjct: 315 QWFPDQIASGAGYAAALQENEAE-FMRSQRKLRNISKDTGLTIVELKEINRRISIGETRA 373

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 374 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A ++ MP +
Sbjct: 434 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAVRMDMPED 493

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A SP+D+A    LRE TT VL+ LT
Sbjct: 494 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDTATIEGLREATTSVLSGLT 553

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 554 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 613


>gi|296932701|gb|ADH93504.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. In5]
          Length = 616

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 264/657 (40%), Positives = 372/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D
Sbjct: 6   QQQSRIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  SLMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E       +    + + D E A   + D+      P             D+ + 
Sbjct: 174 IAPPAAEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  L  +AE++                                  
Sbjct: 234 TRKALKKHGRGNKAAIAELVLLAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +G++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 320 D-GLARGKGKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|119899516|ref|YP_934729.1| RNA polymerase sigma factor RpoD [Azoarcus sp. BH72]
 gi|119671929|emb|CAL95843.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 662

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 261/683 (38%), Positives = 382/683 (55%), Gaps = 46/683 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K +++ +          L  +      K +I L ++RGY+T  E++  LP D   +EQ+
Sbjct: 20  SKAKDKAAQVVDSPEVAPLDAEVRRTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQI 79

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK---RKDSADRSTDDP 120
           E  +A  +NMGI V D     ++    D++  +     +    ++     DS    T DP
Sbjct: 80  EGIIATFNNMGIQVFDEAPAAEDLLMSDNVATSVDEDVAEEEAEQALSSVDSEFGRTTDP 139

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   M+ ++   P T   ++   D +      
Sbjct: 140 VRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVQAISACPTTITEMLDTADRVARDEVR 199

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++D    I P +                                   + AA    D+
Sbjct: 200 IDELVD--GLIDPNAAS---------------------------------DEAALSEADE 224

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                +  +   +DE   D D D      +A   QL+   +     I E Y  + +    
Sbjct: 225 EVTAAADEDADGDDEEEADGDGDGGESANAASLLQLKTDALARFAVIREHYERMMA---- 280

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                K     +     ++++   + ++      I+ L + +  + +++  +E ++L+L 
Sbjct: 281 --ALAKSGSQDIAYLAAQQQISDELLNIRFTAKAIERLCDSVRHMVEQVRTHERQILQLC 338

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ R  F++   G+E    W+       +   +  +     ++L+++ ++  +   
Sbjct: 339 VDRAGMPRQHFIKVFPGQETSIDWLKDEIASGKSYAEGLMRIH-PAVLEVQQKLIDLQDR 397

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            GI + E + I   +  GE +   AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 398 IGIPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 457

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++
Sbjct: 458 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 517

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP P  +A+K+ MP E +RK++KI+KEPIS+ETPIGD+D SHLGDFIED   ++
Sbjct: 518 LQETGAEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDTATLA 577

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+ + LR+ T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 578 PAEAAMYSGLRDATAEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 637

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HPSRS+KLRSFLD 
Sbjct: 638 EAKALRKLRHPSRSEKLRSFLDS 660


>gi|332531768|ref|ZP_08407653.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038744|gb|EGI75186.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 616

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 269/658 (40%), Positives = 372/658 (56%), Gaps = 51/658 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE 
Sbjct: 6   QSQLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +++     +A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMQETTTDEDAAEAAAAALATVEK-EIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D+       L +II            GF    E  +
Sbjct: 125 EGINQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------VGFIDPNEDTA 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK--VDSPPENAENDERNLDEDEDDS 265
                +   E     +++ + D +  A    +D  +      PE A     NL +  + +
Sbjct: 174 PISATNIGSELSAKQLEDDDKDDKDDADSDDEDEEEIDTGPDPEEARIHFENLRDLYNKA 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
             T  A                                     +S  + +    ++ +L 
Sbjct: 234 RDTFEAK-----------------------------------GRSHPESQAAIFEIGELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
            +  L   + D +V  + ++  R+   E  +++ A     + +  F++     E D  WV
Sbjct: 259 RTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQIAKLPKKTFVKHFANNETDASWV 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  E  +   +      I++  N++  I   TG+SI   + I   +  GE +A  A
Sbjct: 319 DLEISGNEK-YSAKLEEVKPEIIRSINKLSVIEQTTGLSIERIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 615


>gi|167622943|ref|YP_001673237.1| RNA polymerase sigma 70 subunit RpoD [Shewanella halifaxensis
           HAW-EB4]
 gi|167352965|gb|ABZ75578.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella halifaxensis
           HAW-EB4]
          Length = 615

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 372/655 (56%), Gaps = 50/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEI 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSED-STDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P     ++   D        L +II     + P ++      T   S
Sbjct: 128 EGINTVQASVAEYPQAIAMILEQFDRYEAEEVRLSDII--SGFVDPNAEDVAPTATHVGS 185

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               +D   E +           +      +++       PE A+     L    + +A 
Sbjct: 186 DLSDDDLDDEDDD----------DDDDDDDEEEEGPKGPDPEEAKEKFTTLRVAHE-NAL 234

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+   AL EI E+++E                                  
Sbjct: 235 RIIADKGRGHPESTVALFEIGEIFKE---------------------------------- 260

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   E    W + 
Sbjct: 261 FRLMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNE 320

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +   +       D + + R ++ +I  ETG++I   + I   +  GE +A  AKK
Sbjct: 321 ELASGKPYAEGLKVVSFD-VQRCRAKLDAIETETGLAIGAIKDINRRMSIGEAKARRAKK 379

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 380 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 439

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 440 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKV 499

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 500 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAK 559

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 560 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 614


>gi|120553592|ref|YP_957943.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei
           VT8]
 gi|120323441|gb|ABM17756.1| RNA polymerase, sigma 70 subunit, RpoD [Marinobacter aquaeolei VT8]
          Length = 618

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 267/659 (40%), Positives = 373/659 (56%), Gaps = 51/659 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-DDL 83
           +      K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D 
Sbjct: 4   NSQKSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDA 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +    +E       +A+  +       ++    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 64  DTLLMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +MA++   P T   +I   D + +    + +I+            GF    
Sbjct: 124 KRIEEGIRDVMAAVAHFPGTAGTVIQAYDRIIENEGRISDIV-----------TGFLDPD 172

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +   +   + S+++   DD   +  D +       D+ +  D  PE        L E  D
Sbjct: 173 DAEPFMGEDTSTEDTSADDSDTSSDDDDDDTSSEDDNDNGPD--PEETRLRFELLKEKLD 230

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +   L+                                   K  +   K +    +L +
Sbjct: 231 AAEKALA-----------------------------------KHGRGHKKTQEALNELGQ 255

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           +     L     D LV  +   +  +  NE  ++++      + R  F++   G E D  
Sbjct: 256 VFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRDCKMPRKDFIKWFPGNETDLE 315

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W        +  +   +   VD I++++  I+++  E  + +++ + I   V  GE +A 
Sbjct: 316 WAGEIAA-TKKPYAAAIGERVDEIVRLQKRIQNVQTEVDLDVADIKEINRRVSIGEAKAR 374

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 375 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 434

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + 
Sbjct: 435 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDK 494

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A+SP+DSA    LRE T  VLA LT 
Sbjct: 495 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSVLAGLTA 554

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR F+D
Sbjct: 555 RESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFID 613


>gi|229592968|ref|YP_002875087.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens SBW25]
 gi|229364834|emb|CAY52873.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas fluorescens
           SBW25]
          Length = 616

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 376/657 (57%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D
Sbjct: 6   QQQSRIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  SLMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEVP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                +   + +   DD  E  GD         +D  +    P  A      + +  + +
Sbjct: 183 PPVDAKAAKADDDTEDDDAEASGD--------DEDEVESGPDPVIAAQRFGAVSDQMEIT 234

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  +S+ +       L +L 
Sbjct: 235 RKAL-----------------------------------KKHGRSNKQAIAELLALAELF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|269137812|ref|YP_003294512.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Edwardsiella tarda EIB202]
 gi|267983472|gb|ACY83301.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Edwardsiella tarda EIB202]
 gi|304557867|gb|ADM40531.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda FL6-60]
          Length = 611

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 271/655 (41%), Positives = 370/655 (56%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A+ ++V +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENI-ADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I        E          G  
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + E    E E +D  +   D  S               PE A      L E  + +  
Sbjct: 185 LPEEELDDDEDEDEDEDDDSDDDNSID-------------PELARQKFVELREQYEKTRL 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A                                   + +SS K +   + L ++   
Sbjct: 232 AIKA-----------------------------------EGRSSGKAQEEIQNLSEIFKQ 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  + ++  R+   E  +++L  +   + +  F+    G E    W   
Sbjct: 257 FRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPKKNFITLFTGNETSITWFDA 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 317 ALAMGKP-WGEKLKDMREDVERSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATRDVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|317493716|ref|ZP_07952133.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918043|gb|EFV39385.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 610

 Score =  452 bits (1163), Expect = e-125,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 362/655 (55%), Gaps = 52/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A+ ++V +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENI-ADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L +II        E          G  
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDIITGFVDPNAEEDLAPTATNVGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               + +  ++E                   D        PE A      L E  + +  
Sbjct: 185 LSSEDLNDDDEEE--------------DEDDDSEDDNSIDPELARQKFSELREQYEKTRV 230

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                       +S  K       L ++   
Sbjct: 231 AIKT-----------------------------------HGRSHAKAAEEILNLSEVFKQ 255

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E +  W   
Sbjct: 256 FRLVPKQFDYLVNNMRQMMDRVRTQERLIMKLCVEQSKMPKKNFITLFTGNETNTTWFDA 315

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 316 ALAMAKP-WGEKLKDVREDVERSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 374

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 375 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 434

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 435 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPEDKIRKV 494

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VL+ LT RE +
Sbjct: 495 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATRDVLSGLTAREAK 554

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 609


>gi|27364091|ref|NP_759619.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus CMCP6]
 gi|320157475|ref|YP_004189854.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus MO6-24/O]
 gi|27360209|gb|AAO09146.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus CMCP6]
 gi|319932787|gb|ADV87651.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus MO6-24/O]
          Length = 624

 Score =  452 bits (1162), Expect = e-125,   Method: Composition-based stats.
 Identities = 265/656 (40%), Positives = 372/656 (56%), Gaps = 40/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDETNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I     + P +           
Sbjct: 126 EDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPNADETAAPTATHI 183

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  E   ++++  D+ + + D +     S D    V   PE A      L        
Sbjct: 184 GSELAESDLEDEDNTDIDDEDEDEDEDGDSSSDSEEDVGIDPEMALEKFTQLRNSY---- 239

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          Q+  +   +  + S +     E ++ +  
Sbjct: 240 -------------------------------QNLQLAVNEHGRESAQTAQAHELMLDVFK 268

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++ A     + +  F+    G E +  W+ 
Sbjct: 269 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEIAKMPKKSFIALFTGNESNEEWLD 328

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++++I  ET +S++  + I   +  GE +A  AK
Sbjct: 329 QILA-SDKPYVEKIKLHEEDIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAK 387

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 388 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 447

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 448 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 507

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 508 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREA 567

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 623


>gi|238918478|ref|YP_002931992.1| RNA polymerase sigma factor RpoD [Edwardsiella ictaluri 93-146]
 gi|238868046|gb|ACR67757.1| RNA polymerase sigma factor RpoD, putative [Edwardsiella ictaluri
           93-146]
          Length = 611

 Score =  452 bits (1162), Expect = e-124,   Method: Composition-based stats.
 Identities = 269/655 (41%), Positives = 369/655 (56%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A+ ++V +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENI-ADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I        E          G  
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + E      E +D  +   D  S               PE A      L +  + +  
Sbjct: 185 LPEEELDDDGDENEDEDDDSDDDNSID-------------PELARQKFVELRQQYEKTRL 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A                                   + +SS K +   + L ++   
Sbjct: 232 AIKA-----------------------------------EGRSSGKAQEEIQNLSEIFKQ 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  + ++  R+   E  +++L  +   + +  F+    G E    W   
Sbjct: 257 FRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPKKNFITLFTGNETSITWFDA 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   ++  I  ETG++I + + I   +  GE +A  AKK
Sbjct: 317 ALAMGKP-WGEKLKDMREEVERSLQKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATRDVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|113971243|ref|YP_735036.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-4]
 gi|113885927|gb|ABI39979.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-4]
          Length = 619

 Score =  452 bits (1162), Expect = e-124,   Method: Composition-based stats.
 Identities = 271/658 (41%), Positives = 379/658 (57%), Gaps = 52/658 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E   
Sbjct: 128 EGINTVQSSVAEYPQAIAMILEQYDQYEADELRLSDII-----------SGFVNPDEEDL 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV---DSPPENAENDERNLDEDEDD 264
                    E   +D+ + + D E   +    D          PE A      L    ++
Sbjct: 177 GPTATHIGSELSEEDLDDEDDDEEDEDEDGDGDGDDDGNKGPDPEEARERFGQLRTAYEN 236

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A + +  P+ + AL EI E+++E                               
Sbjct: 237 ALKIIEA-KGREHPESIKALFEIGEIFKE------------------------------- 264

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV+ +  +  R+   E  L++L  +   + +  F++   G E +  W
Sbjct: 265 ---FRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDW 321

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K+  +  +   +    + + + R+++ +I  ETG+ I+  + I   +  GE +A  
Sbjct: 322 FDAEKNSNKP-YAEGLKMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARR 380

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +
Sbjct: 441 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKI 500

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT R
Sbjct: 501 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAR 560

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 618


>gi|209696105|ref|YP_002264035.1| RNA polymerase sigma factor RpoD [Aliivibrio salmonicida LFI1238]
 gi|208010058|emb|CAQ80381.1| RNA polymerase sigma factor RpoD (sigma-70) [Aliivibrio salmonicida
           LFI1238]
          Length = 610

 Score =  452 bits (1162), Expect = e-124,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 365/656 (55%), Gaps = 54/656 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDM 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++D       A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  SLNDDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++      L +II     + P          +G 
Sbjct: 126 EEGINEVQCSVAEFPGAISYLLEQFDKVQAEEIRLTDII--SGFVDPND--------DGS 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +         E    D+ +         +   D+   V   PE A      L     +  
Sbjct: 176 AAPTATHIGSELSESDLAD------EDKEAKDDEEEDVGIDPELALEKFTQLRTSYHNMQ 229

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                                  +  + + K +    +L  +  
Sbjct: 230 LAFE-----------------------------------EHGRDNGKAREAIGELTDVFR 254

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV ++     R+   E  ++R+   YG + +  F+    G E    W +
Sbjct: 255 EFKLIPKQFDFLVREMRGSMDRVRTQERLIMRMCVEYGKMPKKSFIALFSGNEASDEWFN 314

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   +I SI  ETG+ +   + I   +  GE +A  AK
Sbjct: 315 EILA-SDKPYVERLKRYEEDIRRSIKKINSIVKETGLPVVNIKDISRRMSIGEAKARRAK 373

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 374 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 433

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 434 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 493

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  VLA LTPRE 
Sbjct: 494 VLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPVDSATSTSLKFATNDVLAGLTPREA 553

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 554 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 609


>gi|3646419|emb|CAA07705.1| sigma-70 factor [Pseudomonas tolaasii]
          Length = 616

 Score =  452 bits (1162), Expect = e-124,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 378/657 (57%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D
Sbjct: 6   QQQSRIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   K      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  SLMLADADTDEAAAEEAAAALAAVKTDI-GRTTDPVRMYMREMGTVELLTREGEIGIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++   + +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDRILSEYNRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEVP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                +   + +   DD  E+ GD         +D  +    P  A      + +  + +
Sbjct: 183 PPVDAKAAKADDDSEDDDAESSGD--------DEDEVESGPDPIIAAQRFGAVSDQMEIT 234

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  +++ +       L +L 
Sbjct: 235 RKAL-----------------------------------KKHGRTNKQAIAELIALAELF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|221134905|ref|ZP_03561208.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola sp. HTCC2999]
          Length = 607

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 263/659 (39%), Positives = 365/659 (55%), Gaps = 54/659 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                   K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +    
Sbjct: 1   MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVFESAPD 60

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            DE    ++      A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 61  SDELLMAETTTDEEVAEAAAQALATVE-SEIGRTTDPVRMYMREMGTVELLTREGEIEIA 119

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +  S+ E P     L+   D        L +II            GF    
Sbjct: 120 KRIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDII-----------IGFVDPN 168

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E  +          +        E   +     ++++       PE A      L +  +
Sbjct: 169 EDENLAPTATHIGSELS-----EEELEDEDDDDAEEEEVDTGVDPELAREKFDALRKQYN 223

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +   + A                                     +S+   K    KL  
Sbjct: 224 KTRDVIEAK-----------------------------------GRSNAAAKKQIAKLSD 248

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPH 382
           +     L   + D +V+ +  +  R+   E  +++       + +  F++   G E    
Sbjct: 249 VFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLIMKHCVAQAKMPKKDFIKAFAGNETSTD 308

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W        +  +   +    + I +  +++ ++  ETG+ I++ + I   +  GE +A 
Sbjct: 309 WYYKILKTSKP-YVLVLETFQEDIERSVSKMNAVEAETGLCIADIKDINRRMSIGEAKAR 367

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 368 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 427

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+++++ MP + 
Sbjct: 428 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMIMPEDK 487

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   + PLDSA   +L++ T  VLA LT 
Sbjct: 488 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIIQPLDSATGGSLKDATQDVLAGLTQ 547

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 548 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 606


>gi|77461370|ref|YP_350877.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf0-1]
 gi|77385373|gb|ABA76886.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas fluorescens
           Pf0-1]
          Length = 615

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 261/657 (39%), Positives = 374/657 (56%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                  ++IKL R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIIELIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E       +    + + + + A     ++ ++    P  A      + +  + +
Sbjct: 174 ITPPAAEVPPPIDAKAAKADDDSEDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEIT 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  + +         L +L 
Sbjct: 234 RKAL-----------------------------------KKHGRHNKAAIAELLALAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 259 MPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWS 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +A     I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 319 D-ALAKGKSKYAEAIARVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|91794185|ref|YP_563836.1| RNA polymerase sigma factor RpoD-like protein [Shewanella
           denitrificans OS217]
 gi|91716187|gb|ABE56113.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella denitrificans
           OS217]
          Length = 617

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 377/656 (57%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II            GF +  E   
Sbjct: 128 EGINTVQSSVSEYPQAIAMILEQFDQYEADELRLTDII-----------AGFINPDEDDV 176

Query: 208 YQKREDSSQE-KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                +   E  E     +   D +  +   +++       PE A+     L E  +   
Sbjct: 177 APTATNIGSELSEAQQNDDDNDDDDDDSDDEEEEEGNKGPDPEQAKEKFTELREVYEKGL 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             + A + +  P+ + AL  I E+++E                                 
Sbjct: 237 AVI-AEKGRDHPEAIGALFVIGELFKE--------------------------------- 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV+ +  +  R+   E  +L+L  +   + +  F++     E +  W +
Sbjct: 263 -FRLVPKQFDRLVKSMRTMMDRVRVQERLILKLCVEQAKMPKKNFVKAFTSNETNLDWFN 321

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
              +  +  + + +      + +  +++ +I +ET ++IS  + I   +  GE +A  AK
Sbjct: 322 KEMNSNKP-YADALKAVAHDVNRCSSKLTAIELETDLTISSIKDINRRMSIGEAKARRAK 380

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 381 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 440

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RK
Sbjct: 441 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRK 500

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE 
Sbjct: 501 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEVLAGLTAREA 560

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 616


>gi|33602137|ref|NP_889697.1| RNA polymerase sigma factor RpoD [Bordetella bronchiseptica RB50]
 gi|33576575|emb|CAE33653.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica RB50]
          Length = 722

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 250/662 (37%), Positives = 368/662 (55%), Gaps = 62/662 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +  K++IKL + RGY+T  E+N  LP D V +E ++  ++  S+MGI V D     
Sbjct: 118 EARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQAPDA 177

Query: 85  DEEGSEDSLDL---ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     ++  +        + +       DS    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 178 ETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREGEIE 237

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++     + +G   + E++D           G   
Sbjct: 238 IAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVD-----------GLVD 286

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G  Y                       + A V+ D+    D P     + +      
Sbjct: 287 PEDGEEY-----------------------AGAGVTADEDEADDGPAGGMSSKQL----- 318

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       + LR K +   DE+++ + ++R   +      K+   S      ++ +
Sbjct: 319 ------------EDLRVKALAKFDEVSKQFEKMRQSYE------KEGYKSDAYLKAQDII 360

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELD 380
              +  +      ++ L + L    + +   E  +L       G+ R  FL+   G E +
Sbjct: 361 QTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSHFLKAFPGNETN 420

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV          +   +  ++ ++ +++ ++  +     + + + + +   +  GE +
Sbjct: 421 LQWVLDEVA-AAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNKRMATGEAK 479

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 480 ARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 539

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP 
Sbjct: 540 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAQKMDMPE 599

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+  ++R+    VL SL
Sbjct: 600 DKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMRDVVKEVLDSL 659

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI M+TD TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL
Sbjct: 660 TPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFL 719

Query: 681 DG 682
           +G
Sbjct: 720 EG 721


>gi|73540591|ref|YP_295111.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha JMP134]
 gi|72118004|gb|AAZ60267.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 783

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 259/684 (37%), Positives = 375/684 (54%), Gaps = 46/684 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K++    +            +      K +IKL + RGY+T  E+N  LP D V SE 
Sbjct: 141 KAKEKALLKEFASTQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSET 200

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDD 119
           ++  VA L+++GI V +     +     D+   A+S   +    +      DS    T D
Sbjct: 201 IDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTD 260

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + +     
Sbjct: 261 PVRMYMREMGTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILANAERVASDEI 320

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + E +D    I P +           +  + +  S E E  D  E + D   A   ++ 
Sbjct: 321 KIDEFVD--GLIDPNADEMAQEAAGASAADEEDLESDEDEESDEDEEDDDAAGAGASARQ 378

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                                              +L+   +     IAE + ++R   +
Sbjct: 379 LE---------------------------------ELKLSALEKFRVIAEQFDKMRRAFE 405

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 K+  +S      +E +   +  +      ++ L + L      +   E  +L +
Sbjct: 406 ------KEGYNSKPYVKAQEAIQAELMGIRFTARSVERLCDTLRGQVDEVRKLERSILNI 459

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                G+ R  F+ R  G E +  WV       +  +   V   V ++ +++ ++  +  
Sbjct: 460 VVDKCGMPRSDFVARFPGNETNLDWVGTIVADGKP-YSTIVERNVPAVHELQQKLIDLQS 518

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 519 RVVLPLKELKGVNRKMAEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 578

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 579 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 638

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N +
Sbjct: 639 ILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTL 698

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQ
Sbjct: 699 APAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQ 758

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 759 IEAKALRKLRHPSRSDKLKSFLEG 782


>gi|332994458|gb|AEF04513.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 608

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 264/660 (40%), Positives = 376/660 (56%), Gaps = 54/660 (8%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +        K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   
Sbjct: 1   MAQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             DE   +++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 61  DSDELLMQEATADEDAAEAAAQALATVE-SEIGRTTDPVRMYMREMGTVELLTREGEIEI 119

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  S+ E P     L+   D        + +II     + P         
Sbjct: 120 AKRIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRISDII--SGFVDPNDDQDLAPT 177

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                 +  E+  ++++                  ++D  +    PE A           
Sbjct: 178 ATHIGSELSEEELEDEDD--------------DDDEEDEDEGGVDPELARAKF------- 216

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                        LR + + A D I                 +K  +S    +     L 
Sbjct: 217 -----------GALRDQYIKARDVI-----------------EKKGRSHAAAREQINALS 248

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
           ++     L   + D +V+ +  +  ++   E  +++    +  + +  F++   G E   
Sbjct: 249 EVFKEFRLVPKQFDRMVKNMRSMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGNETSS 308

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W++ A       + + +A   + I +  +++  +  ETG+ I++ + I   +  GE +A
Sbjct: 309 AWLTKAIK-ANAAYSDALAVNKEEIERCISKMNQVEQETGLVIADIKDINRRMSIGEAKA 367

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 368 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 427

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+++++ MP +
Sbjct: 428 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED 487

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   + PLDSA   +L++ T  VLA LT
Sbjct: 488 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEVLAGLT 547

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 548 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 607


>gi|312883925|ref|ZP_07743642.1| RNA polymerase sigma factor RpoD [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309368383|gb|EFP95918.1| RNA polymerase sigma factor RpoD [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 618

 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 260/656 (39%), Positives = 368/656 (56%), Gaps = 46/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        ++    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P T   ++   D++      L ++I        +          G 
Sbjct: 126 EDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPNADETTAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E   ++   D+ +E     +   +   D                           
Sbjct: 186 ELTESELDDEDDVDDEDEEDGEGTDDEEESGIDPEL------------------------ 221

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +     +   ++  +      +   +    S K ++  E ++ +  
Sbjct: 222 -------------ALEKFTSLRNTFQNFQ------LACNEYGSESPKAQIAHELVLDVFR 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LVE+L    +R+   E  +++ +  YG + +  F+    G E    W+ 
Sbjct: 263 EFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMPKKSFITLFTGNESSDAWLD 322

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    D I +   ++K+I  ET +++   + I   +  GE +A  AK
Sbjct: 323 EILA-SDKPYAEKIRRSEDDIRRSIAKLKTIEEETSLTVQSIKDISRRMSIGEAKARRAK 381

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 382 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 441

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 442 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 501

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 502 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAGSLKVATKDVLAGLTPREA 561

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 617


>gi|299066184|emb|CBJ37368.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CMR15]
          Length = 777

 Score =  451 bits (1160), Expect = e-124,   Method: Composition-based stats.
 Identities = 255/674 (37%), Positives = 378/674 (56%), Gaps = 47/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 146 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 205

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 206 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 265

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 266 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 323

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +                                    + A+   +D    D   +
Sbjct: 324 LIDPNADA----------------------------------AEAQAGDEDEDFEDEDAD 349

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             +++E + D+D    A   +   ++L+   +     IA+ + ++R   +      K+  
Sbjct: 350 EGDDEEEDEDDDGAGGAAASARQLEELKQAALAKFAIIADQFEKMRRAFE------KEGY 403

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 404 KSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 463

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 464 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQARVVLPLAELK 522

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 523 DVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 582

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 583 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 642

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 643 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 702

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 703 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 762

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 763 HPSRSDKLKSFLEG 776


>gi|91776674|ref|YP_546430.1| sigma 70 (RpoD) [Methylobacillus flagellatus KT]
 gi|91710661|gb|ABE50589.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacillus flagellatus
           KT]
          Length = 644

 Score =  451 bits (1160), Expect = e-124,   Method: Composition-based stats.
 Identities = 258/683 (37%), Positives = 386/683 (56%), Gaps = 48/683 (7%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           +   K  ++ +   +        D      K +I L ++RGY+T  E+N  LP D   SE
Sbjct: 3   SSMAKEQQNDNVNDKADITLNDADIRRTRLKSLIILGKERGYLTYAEINDHLPDDVQDSE 62

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSED--SLDLASSASNSSVFLQKRKDSADRSTDD 119
           Q++  + M+++MGI V +     +     D  +      A   +       DS    T D
Sbjct: 63  QIDSIIGMINDMGIQVYEEAPDAEALLMSDVPAPVADEDAVEEAEQALSTVDSEFGRTTD 122

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG+++LL+REGEI IAKRIE G   M+ ++   P T   L+   D++  G  
Sbjct: 123 PVRMYMREMGTVDLLTREGEIEIAKRIEDGLKHMVQAIAACPSTIAELLAMVDQVEKGEL 182

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + +++D           G     +G   +   + + +                      
Sbjct: 183 GVDDLVD-----------GLIDADDGLGAEIVAEEAAD---------------------- 209

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                        ++E   D+D   +A   +    +LR +V+     I   + ++  L  
Sbjct: 210 -----AGDVAEDADEEDEEDDDGAKAAAISAEALARLREEVLTRFAVIRSAHEKMTVLLA 264

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR- 358
           +  +  K      +   L+  +++ + +   +  +++ L +++  + + I  +E +++  
Sbjct: 265 SKGSQDK------EYLKLQATIIEELMAFRFSAKQVEALCDRVRGMVEEIRSHERKIMDF 318

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +  G+ R  F++   G E +P W++      +  +   +     SI   + ++ +I  
Sbjct: 319 CVEKAGMPRAHFIKSFPGNEGNPEWLAAELAVNKP-YVERLERFRHSIDDQQQQLLAIQE 377

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
             GI I E + I   +  GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 378 RVGIPIRELKEINKQMSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 437

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 438 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 497

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A+K+ MP + +RK+LKI+KEPIS+ETPIGD+D SHLGDFIED   +
Sbjct: 498 ILQETGLEPDPATLAEKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDVATL 557

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P+D+A+ A+LR+ T  VL SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQ
Sbjct: 558 APVDAAVYASLRDATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQ 617

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HP+RS++LRSFL+
Sbjct: 618 IEAKALRKLRHPTRSERLRSFLE 640


>gi|296136130|ref|YP_003643372.1| RNA polymerase, sigma 70 subunit, RpoD [Thiomonas intermedia K12]
 gi|295796252|gb|ADG31042.1| RNA polymerase, sigma 70 subunit, RpoD [Thiomonas intermedia K12]
          Length = 778

 Score =  451 bits (1159), Expect = e-124,   Method: Composition-based stats.
 Identities = 260/659 (39%), Positives = 363/659 (55%), Gaps = 58/659 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IK+ + RG++T  E+N  +P +    E ME  V+ML+++GI V +       
Sbjct: 172 RRARLKSLIKMGKTRGFLTYGEINDHIPDNLADPELMETIVSMLNDVGIAVYETTPDAQT 231

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                   +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 232 LLLNQHGPTASSEEEAEEEAEAALSNVDSEFGRTTDPVRMYMREMGTVELLTREGEIVIA 291

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++     ++ G   + E++D           G     
Sbjct: 292 KRIEDGLRQMMLAISASPSTVAEILAMAARIHHGELPVDEVVD-----------GMVSDD 340

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED                                         + + +EDED
Sbjct: 341 ESDDYVAEEDVDYSL------------------------------------DESGEEDED 364

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             A   S   ++L+ K + A  ++ + + ++R   D      KD   S      +E +  
Sbjct: 365 GGAGATSMKLEELKGKALEAFADVHDAFMKMRRAYD------KDGYRSASYLKAQEAISA 418

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
            +  +      ++ L   L      +   E E+ R A    G+ ++ F++   G +LD  
Sbjct: 419 ALMEVRFTARTVEKLCNLLRAQVDEVRRYEREIRRYAVDRCGMPQEEFIKSFPGHQLDLK 478

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  +   ++  V +I +++  +  I     + + + + I + +  GE  A 
Sbjct: 479 WVDKHVASGKP-YSVILSRNVPAIKELQQRLIDIQTRVVVPLDDLKEINTQMSLGEQAAR 537

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA W
Sbjct: 538 EAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATW 597

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+KV R +R+   +   EP    +A+K+ MP + 
Sbjct: 598 WIRQAITRSIADQARTIRIPVHMIETINKVNRISRQHLQETGTEPDAAVLAEKMEMPEDK 657

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRK+LKI +EPIS+ETPIGD+D SHLGDFIED   ++P ++A+QA LR+    +L SLTP
Sbjct: 658 VRKILKIAREPISMETPIGDDDDSHLGDFIEDSGTLAPTEAAMQAGLRDVVKEILDSLTP 717

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI M  DHTLEEVGKQF VTRERIRQIEAKA+RKLKHP+RS KLRSFLD
Sbjct: 718 REAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPTRSDKLRSFLD 776


>gi|254509368|ref|ZP_05121455.1| RNA polymerase sigma factor [Vibrio parahaemolyticus 16]
 gi|219547710|gb|EED24748.1| RNA polymerase sigma factor [Vibrio parahaemolyticus 16]
          Length = 620

 Score =  451 bits (1159), Expect = e-124,   Method: Composition-based stats.
 Identities = 261/656 (39%), Positives = 370/656 (56%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        ++    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDETITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P T   ++   D++      L ++I        +          G 
Sbjct: 126 EDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +   ++ E  D ++ E + E + +       +                       
Sbjct: 186 ELAESDLEDEDAEDADEEDEESEDEESEEEDTGIDPE----------------------- 222

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +     +   +      Q+  +   +    S K  V  E ++ +  
Sbjct: 223 ------------FALEKFTALRNTF------QNYQLACNEYGSESPKATVAHEMVIDVFK 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV++L    +R+   E  +++ +  YG + +  F+    G E    W+ 
Sbjct: 265 EFRLTPKQFDYLVDELRTSMERVRTQERLIMKASVEYGKMPKKSFIALFSGNESSDAWLD 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  + + +    D I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 325 EILA-SDKPYADKIRRSEDDIRRSIAKLKIIEEETSLTVQNIKDISRRMSIGEAKARRAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 504 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAGSLKVATKDVLAGLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619


>gi|229507128|ref|ZP_04396634.1| RNA polymerase sigma factor RpoD [Vibrio cholerae BX 330286]
 gi|229509009|ref|ZP_04398497.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|229512571|ref|ZP_04402042.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TMA 21]
 gi|229519677|ref|ZP_04409120.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC9]
 gi|229520813|ref|ZP_04410235.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TM 11079-80]
 gi|229530331|ref|ZP_04419719.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 12129(1)]
 gi|229606193|ref|YP_002876841.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MJ-1236]
 gi|229332104|gb|EEN97592.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 12129(1)]
 gi|229342046|gb|EEO07042.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TM 11079-80]
 gi|229344366|gb|EEO09341.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC9]
 gi|229350464|gb|EEO15413.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TMA 21]
 gi|229353934|gb|EEO18868.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|229355873|gb|EEO20793.1| RNA polymerase sigma factor RpoD [Vibrio cholerae BX 330286]
 gi|229368848|gb|ACQ59271.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MJ-1236]
          Length = 642

 Score =  451 bits (1159), Expect = e-124,   Method: Composition-based stats.
 Identities = 269/664 (40%), Positives = 370/664 (55%), Gaps = 42/664 (6%)

Query: 22  LVFDFS-DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
              D +     K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+ 
Sbjct: 16  PSMDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVET 75

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
               D+    D   +    +  +        +S    T DPVRMY+REMG++ELL+REGE
Sbjct: 76  APDADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 135

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGG 198
           I IAKRIE G   + +++ E P T   ++   D +      L ++I     + P   +  
Sbjct: 136 IDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETE 193

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
               T   S     D + E +     E E + E     S D   +V   PE A      L
Sbjct: 194 APTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNEL 253

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                                                  Q+  +   +  + S +     
Sbjct: 254 R-----------------------------------GKFQNLQLAVNEFGRDSHQASEAS 278

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGR 377
           + ++ +     L   + D LVE L     R+   E  +++       + +  F+    G 
Sbjct: 279 DLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGN 338

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+       +  +   V  + + I +   +++ I  ET +S+   + I   +  G
Sbjct: 339 ESNEEWLDKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIG 397

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 398 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 457

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ 
Sbjct: 458 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQ 517

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VL
Sbjct: 518 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVL 577

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR
Sbjct: 578 AGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 637

Query: 678 SFLD 681
           SFLD
Sbjct: 638 SFLD 641


>gi|237746700|ref|ZP_04577180.1| RNA polymerase primary sigma factor [Oxalobacter formigenes HOxBLS]
 gi|229378051|gb|EEO28142.1| RNA polymerase primary sigma factor [Oxalobacter formigenes HOxBLS]
          Length = 827

 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 257/655 (39%), Positives = 370/655 (56%), Gaps = 38/655 (5%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSE 90
           K +IKL ++R ++T  E+N  LP + +  + +E  ++  ++MGI+V +   D ED   ++
Sbjct: 206 KMLIKLGKERSFLTYAEINDHLPDNVIDPDAIEGIISTFNDMGISVYEHAPDAEDLLLTD 265

Query: 91  DSLDLASSASNSSVFLQKRK--DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + + + S     +         DS    T DPVRMY+REMGS+ELL+REGEI IAKRIE 
Sbjct: 266 NVVTVTSDEEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEE 325

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   M+ ++   P T   +I   +++ +    + E++D     G   + G        S 
Sbjct: 326 GLKDMIQAISSCPTTILEIIGQAEKIRNDEIRIDEVVD-----GLADEAGESQVLAAASD 380

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
             +++S ++    D  + E   E  +       +      E  E                
Sbjct: 381 NDQDESDEDDSDADENDGEEAEEEESDGGSAGGAAAGFSAEQLE---------------- 424

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
                 +L+   +     I   ++E++   +      KD  +S         +   +  +
Sbjct: 425 ------KLKEDALARFALIETYFKEMQQAFE------KDGYNSPAYVKAHNSISDELLGM 472

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYA 387
                 I+ L + L      +   E E+L +A    G+ R  F++   G E +  WV   
Sbjct: 473 RFTARFIEKLCDTLRTQMDDVRQIEREILNVAVNKCGVPRAHFIKTFPGNETNMEWVDEE 532

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                  +   ++  V  I +++  +  I    G+ +++ R I   +  GE  A  AKKE
Sbjct: 533 VH-AGHPYSEILSRNVPMIKELQQNLVDIEKRIGMPLADLREINRKMVAGEMRARKAKKE 591

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 592 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 651

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A K+ MP + +RK++
Sbjct: 652 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAVKMDMPEDKIRKIM 711

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R     VL SLTPRE +V
Sbjct: 712 KIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDVLDSLTPREAKV 771

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LRMRFG+ M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+ 
Sbjct: 772 LRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLES 826


>gi|119773960|ref|YP_926700.1| RNA polymerase sigma-70 factor [Shewanella amazonensis SB2B]
 gi|119766460|gb|ABL99030.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella amazonensis
           SB2B]
          Length = 620

 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 273/655 (41%), Positives = 385/655 (58%), Gaps = 45/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE 
Sbjct: 9   QSQLKMLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEEAPDADEM 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II     + P  +      T   S
Sbjct: 128 EGINTVQSSVAEYPQAISMILEQFDQFEADAIRLSDII--SGFVDPNEEDVGPTATHIGS 185

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               E+   E + D+ +E + D +S+              PE A      L    D++  
Sbjct: 186 ELSEEELEDEDDMDEDEEEDEDGDSSDDDGAK-----GPDPEVARERFAALRAAYDNALK 240

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +  ++ +  P+   AL E+ E+++E                                  
Sbjct: 241 VIE-VKGRAHPESTRALFELGEIFKE---------------------------------- 265

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ + ++  ++   E  +++L  +   + +  F++   G E D  W + 
Sbjct: 266 FRLVPKQFDRLVKSMREMMDKVRVQERLIMKLCVEQAKMPKKNFVKLFTGNETDLTWFNK 325

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             +     +   +    + + + R ++++I VETG+SI   + I   +  GE +A  AKK
Sbjct: 326 EIE-AGRPYSADLKLVDEDVQRCRAKLEAIEVETGLSIESIKDINRRMSIGEAKARRAKK 384

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 385 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 444

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++AMP + +RKV
Sbjct: 445 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMAMPEDKIRKV 504

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L++ T  VLA LT RE +
Sbjct: 505 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKQATHEVLAGLTAREAK 564

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 565 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 619


>gi|312795733|ref|YP_004028655.1| RNA polymerase sigma factor rpoD [Burkholderia rhizoxinica HKI 454]
 gi|312167508|emb|CBW74511.1| RNA polymerase sigma factor rpoD [Burkholderia rhizoxinica HKI 454]
          Length = 778

 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 246/673 (36%), Positives = 366/673 (54%), Gaps = 46/673 (6%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
                  +   +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++M
Sbjct: 147 ASHQPGTAEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFAETEAIESIISTFNDM 206

Query: 74  GINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           G+ V +     +      +  S+         +       DS    T DPVRMY+REMG+
Sbjct: 207 GVAVYEQAPDAETLLLNDNAPSVSSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGT 266

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D    
Sbjct: 267 VELLTREGEIEIAKRIEDGLKHMVQAISACPTTIADILAMAERVANDEIRVDELVDGLID 326

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   GF                                     S  D  + ++   +
Sbjct: 327 PNAEDADGF-----------------------------------SASDADEIESEADDAD 351

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             ++E   +++   +A   +A  + L+   +     I E + ++R   +      K+   
Sbjct: 352 EGDEEEEEEDEGAGAAAASAAQLEALKRASLERFALIGEWFDKMRRAYE------KEGYK 405

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           S      +E +   + S+      ++ L + L      +   E ++L +     G+ R  
Sbjct: 406 SKSYLKAQEAIQAELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRAE 465

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F+ R    E +  W           +   +   + +I + +  +  +     + + + + 
Sbjct: 466 FIARFPSNETNLDWAEQIVAEGHP-YSAVLERNIPAIREQQQRLIDLQARVVLPLKDLKE 524

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
               +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 525 TNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 584

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P
Sbjct: 585 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDP 644

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++
Sbjct: 645 ATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASM 704

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+H
Sbjct: 705 RDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 764

Query: 670 PSRSKKLRSFLDG 682
           PSRS KL+SFL+G
Sbjct: 765 PSRSDKLKSFLEG 777


>gi|1072030|gb|AAB60181.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 603

 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 361/655 (55%), Gaps = 59/655 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SQIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I        E          G  
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + +    +                              PE A                
Sbjct: 185 LSQEDLGDDDSAD---------------------DDNSIDPELAREKF------------ 211

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 212 ------AELRAQYVVTRDTIKAK-----------------GRSHATAQEEILKLSEVFKQ 248

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 249 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 308

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 309 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 367

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 368 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 427

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 428 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 487

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 488 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 547

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 548 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 602


>gi|167855425|ref|ZP_02478190.1| RNA polymerase sigma factor 70 [Haemophilus parasuis 29755]
 gi|219871370|ref|YP_002475745.1| RNA polymerase sigma factor RpoD [Haemophilus parasuis SH0165]
 gi|167853419|gb|EDS24668.1| RNA polymerase sigma factor 70 [Haemophilus parasuis 29755]
 gi|219691574|gb|ACL32797.1| RNA polymerase sigma factor RpoD [Haemophilus parasuis SH0165]
          Length = 621

 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 280/660 (42%), Positives = 380/660 (57%), Gaps = 48/660 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +I   R++GY+TI E++  LP + V ++Q+ED + M+++MGI V++    
Sbjct: 7   LEEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDADQIEDIIQMINDMGIKVLETAPD 66

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            D+     ++        ++  L   + S    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 67  ADDLMLAGNIADEDVVEEATKVLSTVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIA 125

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +   + E P     LI   D++ +GT  L +++   A + P       +  
Sbjct: 126 KRIEEGINEVQCVIAEYPEALSELIARYDQVEEGTVRLSDLVT--AFVDP-------NAV 176

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E       +    E+   D      D     + S D        PE A      L E   
Sbjct: 177 ESTPVDDLDADLDEESESDTVADIDDESEDGESSGDGGDDNSIDPELAREKFTLLKEQH- 235

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                                             Q      QK  ++S + +   + L  
Sbjct: 236 ----------------------------------QKALQAIQKHGRTSKRSRDQIQALSD 261

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPH 382
           +     L   + DLLVE +  + K++   E ++ R A  Y G+K+  F++  QG EL   
Sbjct: 262 IFREFRLVPKQFDLLVETMQKMMKQVRAEERQIQRYAVEYAGMKKTDFIKVFQGNELSEA 321

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+  A +  +G     +A  VD+I      ++ +   TG++I++ R I   +  GE +A 
Sbjct: 322 WIDKAINAKKGG-VPKLANYVDNIRVNIANLQKLEETTGLTITQIREIGGRIADGELKAR 380

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 381 KAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 440

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+K+ MP + 
Sbjct: 441 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAEKMGMPEDK 500

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LT 621
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED +   PLDSA   +LR  T  VL   LT
Sbjct: 501 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDSSLELPLDSATAESLRIATNAVLEEGLT 560

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 620


>gi|260773557|ref|ZP_05882473.1| RNA polymerase sigma factor RpoD [Vibrio metschnikovii CIP 69.14]
 gi|260612696|gb|EEX37899.1| RNA polymerase sigma factor RpoD [Vibrio metschnikovii CIP 69.14]
          Length = 623

 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 262/656 (39%), Positives = 369/656 (56%), Gaps = 41/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDNTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P T   ++   D++      L ++I     + P          +  
Sbjct: 126 EEGINQVQSAVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPN--------EDET 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +         E    D+ + +       +   +D    D   E+   D            
Sbjct: 176 TAPTATHIGSELTGADLDDEDSKDIDEDEDEDEDGDSTDDAEEDTGIDPE---------- 225

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           AL++  E+  + ++LQ   +   +    S   +   E ++ +  
Sbjct: 226 ---------------LALEKFTELRNKYQNLQ---LAINEHGNDSSTTQQASELVLDIFR 267

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  L +  +R+   E  +++       + +  F+    G E    W+ 
Sbjct: 268 EFRLTPKQFDHLVTTLRNSMERVRTQERLIMKTVVEVAKMPKKSFIALFTGNESSEAWLD 327

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   +++ I  ET + ++  + I   +  GE +A  AK
Sbjct: 328 QVLATDKP-YVEKIRANEEMIRRSIQKLRIIEQETSLDVNRIKDISRRMSIGEAKARRAK 386

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 387 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 446

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 447 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 506

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T   LA LTPRE 
Sbjct: 507 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLRAATRDALAGLTPREA 566

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 567 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|33340521|gb|AAQ14856.1| RpoD [Pseudomonas fluorescens]
          Length = 616

 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 263/657 (40%), Positives = 374/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D
Sbjct: 6   QQQSRIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  SLMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E       +    + + D + A   S D+      P             D+ + 
Sbjct: 174 IAPPAAEVPPPVGAKTAKADDDTDDDEAEASSDDEEEVESGPDPIIAAQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +   + +  L  +AE++                                  
Sbjct: 234 TRKALKKHGRGNKQAIAELIALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  F+ +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFVRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|24372864|ref|NP_716906.1| RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
 gi|24346976|gb|AAN54351.1|AE015572_6 RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
          Length = 616

 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 273/655 (41%), Positives = 383/655 (58%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     D+ 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSEDNTDEDAAEEAAAALATVE-SELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +S+ E P     ++   D+       L +II     + P+ +      T   S
Sbjct: 125 EGINTVQSSVAEYPQAIAMILEQYDQYEADELRLSDII--SGFVNPDEEDLGPTATHIGS 182

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               ED   E + +D ++ +GD +     +K         PE A      L    + +  
Sbjct: 183 ELSEEDLEDEDDEEDDEDEDGDGDGDDDGNK------GPDPEEARERFSQLRTAYESALK 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+ + AL EI E+++E                                  
Sbjct: 237 IIDA-KGREHPESIQALFEIGEIFKE---------------------------------- 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E  L++L  +   + +  F++   G E +  W   
Sbjct: 262 FRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVKFFTGNETNLDWFE- 320

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A+      +   +    + + + R+++ +I  ETG+ I+  + I   +  GE +A  AKK
Sbjct: 321 AEKTSNKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEVLAGLTAREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|262042263|ref|ZP_06015428.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259040327|gb|EEW41433.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 611

 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 363/655 (55%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +++  +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I        E          G  
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + E    E E                   +        PE A      L    + +  
Sbjct: 185 LSQEEMDDDEDED-------------EDADDNSDDDNSIDPELAREKFAELRTQYELTRD 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T+ A                                     +S    +    KL ++   
Sbjct: 232 TIKAK-----------------------------------GRSHAAAQEEILKLSEVFKQ 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 257 FRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNA 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 317 AVAMNKP-WSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 610


>gi|30064415|ref|NP_838586.1| RNA polymerase sigma factor RpoD [Shigella flexneri 2a str. 2457T]
 gi|30042672|gb|AAP18396.1| sigmaD(70) factor of RNA polymerase [Shigella flexneri 2a str.
           2457T]
          Length = 608

 Score =  450 bits (1156), Expect = e-124,   Method: Composition-based stats.
 Identities = 261/651 (40%), Positives = 360/651 (55%), Gaps = 49/651 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D +      L ++I            GF        
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEED 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                     +   +  + + D +                PE A                
Sbjct: 174 LAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF------------ 221

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +LR + +   D I                     +S    +    KL ++   
Sbjct: 222 ------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQ 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + 
Sbjct: 259 FRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNA 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKK
Sbjct: 319 AIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLQ 608


>gi|323493625|ref|ZP_08098746.1| RNA polymerase sigma factor RpoD [Vibrio brasiliensis LMG 20546]
 gi|323312148|gb|EGA65291.1| RNA polymerase sigma factor RpoD [Vibrio brasiliensis LMG 20546]
          Length = 617

 Score =  450 bits (1156), Expect = e-124,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 373/656 (56%), Gaps = 47/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        ++    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P T   ++   D++      L ++I     + P+         E  
Sbjct: 126 EDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLIT--GFVDPD-------ADETA 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +       S+  E +   E   D E  +  S+++       PE A      L        
Sbjct: 177 APTATHIGSELAESELEDEDAEDEEEDSDDSEEEEEDTGIDPELALEKFTALR------- 229

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                        + Q+  +   +    S K ++  E ++ +  
Sbjct: 230 ----------------------------NTFQNFQLACNEYGNESPKAQIAHELVLDVFK 261

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LVE+L    +R+   E  +++ +  YG + +  F+    G E    W+ 
Sbjct: 262 EFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMPKKSFITLFTGNESSDAWLD 321

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    D I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 322 EILA-SDKPYAEKIRRSEDDIRRSIAKLKVIEEETSLTVQNIKDISRRMSIGEAKARRAK 380

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 381 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 440

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 441 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 500

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 501 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREA 560

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 616


>gi|262392398|ref|YP_003284252.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
 gi|262335992|gb|ACY49787.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
          Length = 620

 Score =  450 bits (1156), Expect = e-124,   Method: Composition-based stats.
 Identities = 263/656 (40%), Positives = 369/656 (56%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I        +          G 
Sbjct: 126 EEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +   ++ E  D  E   D    ++       ++                      
Sbjct: 186 ELTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPEL---------------------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +   +++   Y+ L+      +   +   +S K  V  E ++ +  
Sbjct: 224 -------------ALEKFNQLRSTYQNLQ------LAINEYGYNSPKATVANEMMLDVFR 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++    YG + +  F+    G E    W+ 
Sbjct: 265 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEAWLD 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 325 EVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 504 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619


>gi|269103529|ref|ZP_06156226.1| RNA polymerase sigma factor RpoD [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163427|gb|EEZ41923.1| RNA polymerase sigma factor RpoD [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 619

 Score =  450 bits (1156), Expect = e-124,   Method: Composition-based stats.
 Identities = 272/655 (41%), Positives = 373/655 (56%), Gaps = 43/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +   ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTEDNADEDAIEAAAQALSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      L +II     + P  +          +
Sbjct: 125 DGINQVQCSVAEYPKAISQLLDMFDKVEADELRLTDII--SGFVDPNEEE---TAAPTAT 179

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           +   E S  + E +D    E + E     S DD    +  PE A      L +  +  A 
Sbjct: 180 HIGSELSESDLEDEDRDLDEDEDEDEDGDSSDDSDDNNIDPEVAREKFTELRQSYEKMAL 239

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                       ++    ++  ++L ++   
Sbjct: 240 AIDT-----------------------------------HGRNHPTAELAVDELSEIFKQ 264

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D L+  L D   R+  NE  ++R+      + +  F+    G E    W+  
Sbjct: 265 FRLVPKQFDKLIGSLRDSMDRVRTNERLIMRMCVDNSKMPKKTFINLFAGNEASSEWIDE 324

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A +  +  +   +    + + +   +++ +  ETG+SI   + I   +  GE +A  AKK
Sbjct: 325 ALNSGKP-YAERLKTYEEELRRCSTKLRLLEEETGLSIERIKDISRRMSIGEAKARRAKK 383

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 384 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 443

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 444 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKV 503

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A Q NLR  T  VLA LTPRE +
Sbjct: 504 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATQTNLRAATNEVLAGLTPREAK 563

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 564 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 618


>gi|330812146|ref|YP_004356608.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|327380254|gb|AEA71604.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 615

 Score =  450 bits (1156), Expect = e-124,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 378/657 (57%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +    +D
Sbjct: 6   QQQSRIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E       +    + + D + A     ++ ++    P  A      + +  + +
Sbjct: 174 IAPPAAEVPPPIDAKAVKADDDTDDDEAEASDDEEEAESGPDPVIAAQRFGAVADQMEIT 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  +++ +       L +L 
Sbjct: 234 RKAL-----------------------------------KKHGRNNKQAIAELLALAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 259 MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +A     I++ + ++ ++  ETG+SI+E + I   +  GE +A  A
Sbjct: 319 D-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|114330327|ref|YP_746549.1| RNA polymerase sigma factor RpoD [Nitrosomonas eutropha C91]
 gi|114307341|gb|ABI58584.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas eutropha C91]
          Length = 749

 Score =  450 bits (1156), Expect = e-124,   Method: Composition-based stats.
 Identities = 260/662 (39%), Positives = 382/662 (57%), Gaps = 54/662 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      KK+I   ++RGY+T  E+N  LP D + ++Q+E  ++M+++MGI+V D    
Sbjct: 136 VELRRMRLKKLIMQGKERGYLTYSEINDHLPDDMLDADQIESIISMINDMGISVHDEAPD 195

Query: 84  EDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +     D+         +  +       DS    T DPVRMY+REMGS+ LL+RE EI 
Sbjct: 196 AEALLMSDTATAVADEDVAEETEAALSSVDSEFGRTTDPVRMYMREMGSVGLLTRESEIE 255

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P   + ++    ++  G     E++D               
Sbjct: 256 IAKRIEDGLRHMIQAISACPTIIENILGLAADVESGQLRADELVDGFL------------ 303

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                              DD +E  G                   PE + + + + DE 
Sbjct: 304 ------------------DDDTEEIIGK----------------GMPEESLDQDFDSDET 329

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           E++   + +A   +++ +V+     I + Y +++ + D    G++D     K K L+EK+
Sbjct: 330 EEEQIASANADMLKMKNEVLERFAMIRQTYDDMKKIIDKKGGGRQD----KKYKQLQEKI 385

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQGRELD 380
              + ++  +   ++ L +    I   I   E ++  L      + R+ F++   G E +
Sbjct: 386 SAELMAMRFSAKMVERLCDTQRAIVNDIRSCERKIAELCVVRAKMPRNHFIKAFPGNETN 445

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W++   D  +  +   +     ++++ + ++ ++  + GI I E + I   +  GE +
Sbjct: 446 IDWINSEVDANQP-YSQSLEHYRPAVMEQQQKMLTLQEQAGIPIKELKEINRRMTTGEAK 504

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 505 ARSAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 564

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  +EP P  +A+K+ M  
Sbjct: 565 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQEPEPAVLAEKMEMTE 624

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED + + P D+AI A LR  T  VL SL
Sbjct: 625 EKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVSTMEPADAAIYAGLRTVTKDVLDSL 684

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HP+RS +LRSFL
Sbjct: 685 TPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPARSDRLRSFL 744

Query: 681 DG 682
           D 
Sbjct: 745 DS 746


>gi|119944095|ref|YP_941775.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
 gi|119862699|gb|ABM02176.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
          Length = 617

 Score =  449 bits (1155), Expect = e-124,   Method: Composition-based stats.
 Identities = 259/663 (39%), Positives = 372/663 (56%), Gaps = 51/663 (7%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +        K++I   +++G++T  E+N  LP D V SEQ+ED + M+ +MGI VV+   
Sbjct: 1   MAQTPQSQLKELIIKGKEKGFLTYAEVNDHLPQDIVESEQIEDIIQMIGDMGIRVVETAP 60

Query: 83  LEDEE--GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             D+   G++DS      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI
Sbjct: 61  DADDMLIGADDSETPDEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEI 120

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   +  ++ E P T   L+   D        L ++I     + P       
Sbjct: 121 VIAKRIEEGIKEVQTAVSEYPATISGLLDNWDSYEAEEMKLTDLI--SGFVDPNDDM--- 175

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           E  +  +++ +   +  +    ++       PE A         
Sbjct: 176 -----TQAVSATHIGSELSKKQLEDEDKADKDDSDEDDEEEGPKGPDPEEA--------- 221

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL-QDNAVNGQKDEKSSVKCKVLKE 319
                                      AE + ELR L Q    +  K+ ++  + +    
Sbjct: 222 ---------------------------AEKFAELRKLNQVVEDSITKNGRAHAETRAAIN 254

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRE 378
           +  +      L   + D +V+ +      +   E   L+   +   + +  F++  +G E
Sbjct: 255 EQAEFFQQFKLIPKQFDRMVKAIRFAMNAVRVQERLALKICVEQCKMPKKEFIKLFKGNE 314

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +P W+         ++   ++   + + +   ++ ++ V++ ++I+  + I   +  GE
Sbjct: 315 TNPAWLEVILSNGT-DYATRISEFEEDLRRCLRKMLAVEVQSVLTITNMKGISRNMSIGE 373

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 374 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 433

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ M
Sbjct: 434 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPQPEELAERMMM 493

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED     P + A   +L+  T  VL 
Sbjct: 494 PEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIALPANCATSESLKNATNDVLE 553

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRS
Sbjct: 554 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRS 613

Query: 679 FLD 681
           FLD
Sbjct: 614 FLD 616


>gi|311086952|gb|ADP67032.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  449 bits (1155), Expect = e-124,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 376/656 (57%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILNEINTDTDEDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L +II            GF       
Sbjct: 126 EEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDII-----------TGFVDPNAEQ 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            +         +  D+ Q  E D E+  +  +DD S     PE A      L    +++ 
Sbjct: 175 IFPPTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSI---DPELANEKFSELRIQYNNTN 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           +T+       +  ++   +                                   L ++  
Sbjct: 232 NTIKNKNRTHKDSLLEIYN-----------------------------------LSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + +R+   E  +++L      + +  F++    ++++  W  
Sbjct: 257 QFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKINYLWFI 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             ++  +  W   +    + +     ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 REQNTNQP-WSENLKKVKEDVFISVKKLIKIEEETGLTIEQVKDINKRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|260775520|ref|ZP_05884417.1| RNA polymerase sigma factor RpoD [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608701|gb|EEX34866.1| RNA polymerase sigma factor RpoD [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 617

 Score =  449 bits (1155), Expect = e-124,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 370/656 (56%), Gaps = 47/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        ++    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P T   ++   D++      L ++I     + P+         E  
Sbjct: 126 EDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLIT--GFVDPD-------ADETA 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +       S+  E D   E   + ++      ++       PE A      L        
Sbjct: 177 APTATHIGSELAESDLEDEDAEEEDAEESEDDEEEEDTGIDPELALEKFTALR------- 229

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                        + Q+  +   +    S K  +  E ++ +  
Sbjct: 230 ----------------------------NTFQNYQLACNEYGNESPKATLAHEMVIDVFK 261

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LVE+L    +R+   E  +++ +  YG + +  F+    G E    W+ 
Sbjct: 262 EFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMPKKSFITLFTGNESSEAWLD 321

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    D I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 322 EILS-SDKPYAEKIRRSEDDIRRSIMKLKVIEEETSLTVQNIKDISRRMSIGEAKARRAK 380

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 381 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 440

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 441 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 500

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 501 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSTSLKVATKDVLAGLTPREA 560

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 616


>gi|261868195|ref|YP_003256117.1| RNA polymerase sigma factor RpoD [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413527|gb|ACX82898.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 616

 Score =  449 bits (1155), Expect = e-124,   Method: Composition-based stats.
 Identities = 269/655 (41%), Positives = 374/655 (57%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLIVQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++         +  +    ++    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLNENIT-DEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++   P     LI   D + +G   L ++I     + P         TE  +
Sbjct: 125 EGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLIT--GFVDPNVL------TESET 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               ED + E+  D   E+E + ++    S D  S     PE A      L +    +  
Sbjct: 177 EGLAEDFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLE 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           +++                                   K  +++ K K   + L  +   
Sbjct: 237 SIA-----------------------------------KHGRTAKKAKDEIQVLSDIFTQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D+LV  +  I KR+   E  + R+      + +  F +   G E    W+  
Sbjct: 262 FRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMPKSGFQKSFIGHETTDTWLVK 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +    +  I  +T ++I + R I   + +GE +A  AKK
Sbjct: 322 ALSAGKS-WSEKLVQYENQLRQAITNLVQIEQDTHLTIPQIREIGERITQGELKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 501 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQSLKAATHEVLEGLTPREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 615


>gi|237748836|ref|ZP_04579316.1| RNA polymerase primary sigma factor [Oxalobacter formigenes OXCC13]
 gi|229380198|gb|EEO30289.1| RNA polymerase primary sigma factor [Oxalobacter formigenes OXCC13]
          Length = 819

 Score =  449 bits (1155), Expect = e-124,   Method: Composition-based stats.
 Identities = 250/653 (38%), Positives = 370/653 (56%), Gaps = 39/653 (5%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +IKL ++R ++T  E+N  LP + +  + +E  ++  ++MGI+V +     +E    D++
Sbjct: 201 LIKLGKERSFLTYAEINDHLPDNVIDPDAIEGIISTFNDMGISVYEQAPDAEELLLTDNV 260

Query: 94  ---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                   A  ++       DS    T DPVRMY+REMGS+ELL+REGEI IAKRIE G 
Sbjct: 261 VTVTSDEEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEEGL 320

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             M++++   P T   +I   +++      + E++D                        
Sbjct: 321 RDMISAISSCPTTILEIIDQAEKIRADEVKIDEVVD------------------------ 356

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                   + +  +    +  ++      D    D    + E D+         +A   +
Sbjct: 357 ----GLADDEEGSENAALNASASDSDEDSDEEDSDEEDSDDEEDDEESGSAGGAAAGFSA 412

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
              ++L+ + +     I   ++E++       + +KD  +S       E +   + ++  
Sbjct: 413 EQLEKLKDEALGKFAVIGAHFKEMQ------QSFEKDGYNSPAYLQAHESISAELLTMRF 466

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKD 389
               I+ L + L      +   E E+L +     G+ R  F++   G E D  W+    +
Sbjct: 467 TARFIEKLCDTLRAQMDEVRQIEREILNVVVNKCGVPRAHFIKTFPGNETDLTWIDEEVE 526

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +  +   +   V  + +++ ++  I    G+ +++ R I   +  GE  A  AKKEM 
Sbjct: 527 -ADHPYSAILERNVPMVKELQQKLVDIQNRIGMPLADLREINRKMVAGEMRARKAKKEMT 585

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 586 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 645

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A K+ MP + +RK++KI
Sbjct: 646 RSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAVKMEMPEDKIRKIMKI 705

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD+D SHLGDFIED N ++P D+A+ A++R     VL SLTPRE +VLR
Sbjct: 706 AKEPISMETPIGDDDDSHLGDFIEDNNTLAPSDAALHASMRNVVKDVLDSLTPREAKVLR 765

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFG+ M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+ 
Sbjct: 766 MRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLES 818


>gi|293391709|ref|ZP_06636043.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952243|gb|EFE02362.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 616

 Score =  449 bits (1155), Expect = e-124,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 376/655 (57%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++        ++  L   + +    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLNENITDEDVVEEATQVLSSVE-AELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++   P     LI   D + +G   L ++I     + P         TE  +
Sbjct: 125 EGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLIT--GFVDPNVL------TESET 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +  ED + E+  D   E+E + ++    S D  S     PE A      L +    +  
Sbjct: 177 EELAEDFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLE 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           +++                                   K  +++ K K   + L  +   
Sbjct: 237 SIA-----------------------------------KHGRTAKKAKDEIQVLSDIFTQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D+LV  +  I KR+   E  + R+      + +  F +   G E    W+  
Sbjct: 262 FRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMPKSGFQKSFIGHETTDTWLVK 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +    + + +    +  I  +T ++I + R I   + +GE +A  AKK
Sbjct: 322 ALSAGKS-WSEKLVQYENQLRQAITNLVQIEQDTHLTIPQIREIGERITQGELKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 501 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQSLKAATHEVLEGLTPREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 615


>gi|70732951|ref|YP_262722.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
 gi|1710687|sp|P52326|RPOD_PSEFL RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|929808|emb|CAA59134.1| sigma 70 [Pseudomonas fluorescens]
 gi|68347250|gb|AAY94856.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
          Length = 615

 Score =  449 bits (1154), Expect = e-124,   Method: Composition-based stats.
 Identities = 263/657 (40%), Positives = 375/657 (57%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E       +    + + + E A     ++ ++    P  A      + +  + +
Sbjct: 174 ITPPAAEVPPPVDTKTAKADDDSEDEEAEATEDEEEAESGPDPVIAAQRFGAVADQMEVT 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  + + +       L +L 
Sbjct: 234 RKAL-----------------------------------KKHGRENKQAIAEMLALAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 259 MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +A     I++ + ++ ++ VETG+ I+E + I   +  GE +A  A
Sbjct: 319 D-ALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKIAEIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|217969610|ref|YP_002354844.1| RNA polymerase sigma factor RpoD [Thauera sp. MZ1T]
 gi|217506937|gb|ACK53948.1| RNA polymerase, sigma 70 subunit, RpoD [Thauera sp. MZ1T]
          Length = 666

 Score =  449 bits (1154), Expect = e-124,   Method: Composition-based stats.
 Identities = 260/683 (38%), Positives = 389/683 (56%), Gaps = 42/683 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K +++ +      +   L  +      K +I L ++RGY+T  E++  LP D   +EQ+
Sbjct: 20  AKAKDKAAPVVESPAATPLDAEVRRTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQI 79

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK---RKDSADRSTDDP 120
           E  +A  +NMGI V D     ++    DS+        +    ++     DS    T DP
Sbjct: 80  EGIIATFNNMGIQVYDEAPAAEDLLMSDSVATNVDEDVAEEEAEQALSSVDSEFGRTTDP 139

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   M+ ++   P T   ++   D +      
Sbjct: 140 VRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVQAISACPTTIAEMLGIVDRIAADDAK 199

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++D    I P +        E  S  +  ++ +++  +D  E + + +SA       
Sbjct: 200 IDELVD--GLIDPNAGSAEEAAAEEESADEDTEAEEDEGAEDEDEGDDEEDSA------- 250

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                                 + +    +A   QL+   +   D I  +Y +       
Sbjct: 251 ----------------------ESAERANAASLLQLKNDALARFDVIRGLYEK------K 282

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               +K     +    L++++   + ++      I+ L + +  + +++  +E ++L+L 
Sbjct: 283 MQALEKRGSQDLSYLALQQQISDELLNIRFTAKAIEKLCDSVRHMVEQVRSHERQILQLC 342

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ R  F++   G+E++  W+       +      +     ++L+ + ++  +   
Sbjct: 343 VDRAGMPRQHFIKVFPGQEVNLDWLKDEIAAGKNYADGLMRIH-PAVLEEQQKLIDLQDR 401

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            GI + E + I   +  GE +   AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 402 IGIPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 461

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++
Sbjct: 462 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 521

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  +EP P  +A+K+ MP E +RK++KI+KEPIS+ETPIGD+D SHLGDFIED   ++
Sbjct: 522 LQETGQEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDTATLA 581

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+ + LR+ T  VL SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 582 PAEAAMYSGLRDATCEVLDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 641

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HPSRS+KLRSFLD 
Sbjct: 642 EAKALRKLRHPSRSEKLRSFLDS 664


>gi|261250212|ref|ZP_05942788.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
 gi|260939328|gb|EEX95314.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
          Length = 618

 Score =  449 bits (1154), Expect = e-124,   Method: Composition-based stats.
 Identities = 265/656 (40%), Positives = 365/656 (55%), Gaps = 46/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        ++    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P T   ++   D +      L ++I        +          G 
Sbjct: 126 EDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E   ++ E  +  +   D E       D                           
Sbjct: 186 ELAESELEDEDAEEKEESDDSDDEEEEEDTGIDPEL------------------------ 221

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +     +   ++        A N   +E  S K  +  E ++ +  
Sbjct: 222 -------------ALEKFTALRNTFQN----YQLACNEYGNE--SPKATLAHEMVIDVFK 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LVE+L    +R+   E  +++    YG + +  F+    G E    W+ 
Sbjct: 263 EFRLTPKQFDYLVEELRTSMERVRTQERLIMKATVEYGKMPKKSFITLFTGNESTDAWLD 322

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   V    D I +  +++K I  ET +++   + I   +  GE +A  AK
Sbjct: 323 EILA-SDKPYAEKVRRSEDDIRRSISKLKIIEEETSLTVQNIKDISRRMSIGEAKARRAK 381

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 382 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 441

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 442 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 501

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 502 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAGSLKVATKDVLAGLTPREA 561

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 617


>gi|15616680|ref|NP_239892.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681437|ref|YP_002467822.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|257471112|ref|ZP_05635111.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|11134512|sp|P57163|RPOD_BUCAI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|25288437|pir||B84936 RNA polymerase sigma factor rpoD [imported] - Buchnera sp.  (strain
           APS)
 gi|10038743|dbj|BAB12778.1| RNA polymerase sigma factor rpoD [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219624280|gb|ACL30435.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  449 bits (1154), Expect = e-124,   Method: Composition-based stats.
 Identities = 270/656 (41%), Positives = 376/656 (57%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILNEINTDTDEDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L +II            GF       
Sbjct: 126 EEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDII-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            +         +  D+ Q  E D E+  +  +DD S     PE A      L    +++ 
Sbjct: 175 IFPPTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSI---DPELANEKFSELRIQYNNTN 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           +T+       +  ++   +                                   L ++  
Sbjct: 232 NTIKNKNRTHKDSLLEIYN-----------------------------------LSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + +R+   E  +++L      + +  F++    ++++  W  
Sbjct: 257 QFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKINYLWFI 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             ++  +  W   +    + +     ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 REQNTNQP-WSENLKKVKEDVFISVKKLIKIEEETGLTIEQVKDINKRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|294139649|ref|YP_003555627.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
 gi|7388082|sp|O24744|RPOD_SHEVD RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1912047|dbj|BAA19475.1| RNA polymerase sigma factor [Shewanella violacea]
 gi|293326118|dbj|BAJ00849.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
          Length = 614

 Score =  449 bits (1154), Expect = e-124,   Method: Composition-based stats.
 Identities = 261/655 (39%), Positives = 365/655 (55%), Gaps = 48/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +     DE 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEI 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTED-STDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P    +++   D        L +II            GF        
Sbjct: 125 EGIYTVQASVAEYPPAIASILDQFDRYEAEEVRLSDII-----------SGFIDPNAADI 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    +  + +  + +   +S      ++      P      +      +  ++  
Sbjct: 174 APTATHIGSDLSQSERDKDDSKDDSKDDDEDEEEEGPKGPDPEESKERFTQLREVHENTL 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+   AL EI E+++E                                  
Sbjct: 234 KIIADKGRGHPEATVALFEIGELFKE---------------------------------- 259

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +     ++   E  +++L  +   + +  F++ +   E    W   
Sbjct: 260 FRLMPKQFDRLVKNMRATMDKVRVQERLIMKLCVEQAKMPKKNFVKGYTADESSIAWFDT 319

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  +   +      + + R ++  I  ETG++I+  + I   +  GE +A  AKK
Sbjct: 320 ELA-SKKPYAEGLKMIEPDVRRCRFKLDIIEKETGLAIASIKDINRRMSIGEAKARRAKK 378

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 379 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 438

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 439 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 498

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 499 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGLTAREAK 558

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 559 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 613


>gi|28897178|ref|NP_796783.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153839257|ref|ZP_01991924.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ3810]
 gi|260361470|ref|ZP_05774529.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus K5030]
 gi|260878083|ref|ZP_05890438.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AN-5034]
 gi|260896978|ref|ZP_05905474.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio
           parahaemolyticus Peru-466]
 gi|260902497|ref|ZP_05910892.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ4037]
 gi|28805387|dbj|BAC58667.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus RIMD
           2210633]
 gi|149747222|gb|EDM58210.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ3810]
 gi|308088714|gb|EFO38409.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio
           parahaemolyticus Peru-466]
 gi|308089726|gb|EFO39421.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AN-5034]
 gi|308109810|gb|EFO47350.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ4037]
 gi|308110993|gb|EFO48533.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus K5030]
 gi|328471947|gb|EGF42824.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus 10329]
          Length = 620

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 376/656 (57%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I     + P++           
Sbjct: 126 EEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPDAD----DTAAPT 179

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +     + S+ +  ++ +E   D E +   S D    V   PE A               
Sbjct: 180 ATHIGSELSETQLEEEDEEDLEDDEESDDDSDDSEEDVGIDPELA--------------- 224

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +   +++   Y+ L+      +   +    S K  V  E ++ +  
Sbjct: 225 --------------LEKFNQLRSTYQNLQ------LAINEYGYDSPKATVANEMMLDVFK 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++    YG + +  F+    G E    W+ 
Sbjct: 265 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSDAWLD 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 325 EILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 504 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKMATKDVLAGLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619


>gi|323495834|ref|ZP_08100902.1| RNA polymerase sigma factor RpoD [Vibrio sinaloensis DSM 21326]
 gi|323319050|gb|EGA71993.1| RNA polymerase sigma factor RpoD [Vibrio sinaloensis DSM 21326]
          Length = 620

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 259/656 (39%), Positives = 370/656 (56%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVLKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        ++    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDETITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P T   ++   D++      L ++I        +          G 
Sbjct: 126 EDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + E   ++ E  + +E +G+ +  ++       +                       
Sbjct: 186 ELAESELKDEDAEDVEDEEEDGEDDDDSEEDTGIDPE----------------------- 222

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +     +   ++  +      +   +    S K ++  E ++ +  
Sbjct: 223 ------------FALEKFTSLRNTFQNFQ------LACNEYGNESPKAQIAHELVLDVFK 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L    +R+   E  +++ +  YG + +  F+    G E    W+ 
Sbjct: 265 EFRLTPKQFDYLVNELRTSMERVRTQERLIMKASVEYGKMPKKSFISLFSGNESSDAWLD 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  + + +    D I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 325 EILA-SDKPYADKIRRSEDDIRRSIMKLKMIEEETSLTVQSIKDISRRMSIGEAKARRAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 504 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619


>gi|30248253|ref|NP_840323.1| RNA polymerase sigma factor RpoD [Nitrosomonas europaea ATCC 19718]
 gi|30180138|emb|CAD84140.1| DNA-dependent RNA polymerase sigma subunits (sigma70/32)
           [Nitrosomonas europaea ATCC 19718]
          Length = 751

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/662 (39%), Positives = 382/662 (57%), Gaps = 55/662 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      KK+I   ++RGY+T  E+N  LP D + ++Q+E  ++M+++MGI+V D    
Sbjct: 139 IELRRMRLKKLIMQGKERGYLTYSEINDHLPDDMLDADQIESIISMINDMGISVHDEAPD 198

Query: 84  EDEEGSEDSLDLASSAS--NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +     D+    +       +       DS    T DPVRMY+REMGS+ELL+RE EI 
Sbjct: 199 AEALLMSDAATAVTDEDVVEEAEAALSSVDSEFGRTTDPVRMYMREMGSVELLTRESEIE 258

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P   + ++    ++ +G     E++D               
Sbjct: 259 IAKRIEDGLRHMIQAISACPTIIENILELAADVENGRLRADELVDGFL------------ 306

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                              DD  E  G   S   + +D  S                ++ 
Sbjct: 307 ------------------DDDTDEIMGKEMSEESLDQDFDS----------------EDG 332

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           ED+     SA   +++ +V+     I + Y  ++ + +      KD +   K K L+EK+
Sbjct: 333 EDEQVAAASADMLKMKAEVLERFAVIRQTYDGMKKIINK-----KDGRQDKKYKQLQEKI 387

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
              + ++  +   ++ L +   DI   I + E ++  L     G+ R+ F++   G E D
Sbjct: 388 STELMAMRFSAKMVEKLCDTQRDIVNDIRNCERKIAELCVTRAGMPRNYFIKAFPGNETD 447

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+S   +  +  +   +     ++++ + ++  +  + GI I E + I   +  GE +
Sbjct: 448 IDWISSEVESGQP-YSQSLEHFRPAVMEQQQKMLELQKQAGIPIKELKEINRRMTTGEAK 506

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 507 ARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 566

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  +EP P  +A+K+ MP 
Sbjct: 567 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQEPEPAVLAEKMEMPE 626

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED + + P D+A+ A LR  T  VL SL
Sbjct: 627 EKIRKILKISKEPISMETPIGDDEDSHLGDFIEDASTMEPADAAVYAGLRTVTKDVLDSL 686

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HP+RS +LRSFL
Sbjct: 687 TPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPARSDRLRSFL 746

Query: 681 DG 682
           D 
Sbjct: 747 DS 748


>gi|76817579|ref|YP_335991.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710b]
 gi|76582052|gb|ABA51526.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710b]
          Length = 800

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 247/663 (37%), Positives = 364/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 179 LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 238

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 239 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 298

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 299 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADTDGFS 358

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    +  ++ ++ E ++  +      +A     +                     
Sbjct: 359 EKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 398

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 399 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 437

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 438 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 497

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 498 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 556

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 557 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 616

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 617 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 676

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 677 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 736

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 737 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 796

Query: 680 LDG 682
           L+G
Sbjct: 797 LEG 799


>gi|83716798|ref|YP_438821.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|83650623|gb|ABC34687.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 800

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 248/663 (37%), Positives = 364/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 179 LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 238

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 239 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 298

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D           GF 
Sbjct: 299 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLIDPNAADTDGFS 358

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E++ ++ E ++  +      +A     +                     
Sbjct: 359 EKDAEEIENEDEEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 398

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 399 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 437

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 438 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 497

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 498 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 556

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 557 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 616

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 617 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 676

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 677 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 736

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 737 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 796

Query: 680 LDG 682
           L+G
Sbjct: 797 LEG 799


>gi|294340365|emb|CAZ88746.1| RNA polymerase sigma factor rpoD (Sigma-70) [Thiomonas sp. 3As]
          Length = 778

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 260/659 (39%), Positives = 364/659 (55%), Gaps = 58/659 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IK+ + RG++T  E+N  +P +    E ME  V+ML+++GI V +       
Sbjct: 172 RRARLKSLIKMGKTRGFLTYGEINDHIPDNLADPELMETIVSMLNDVGIAVYETTPDAQT 231

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                   +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 232 LLLNQHGPTASSEEEAEEEAEAALSNVDSEFGRTTDPVRMYMREMGTVELLTREGEIVIA 291

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++     ++ G   + E++D           G     
Sbjct: 292 KRIEDGLRQMMLAISASPSTVAEILAMAARIHHGELPVDEVVD-----------GMVSDD 340

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED                                         + + +EDED
Sbjct: 341 ESDDYVAEEDVDYSL------------------------------------DESGEEDED 364

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             A   S   ++L+ K + A  ++ + + ++R   D      KD   S      +E +  
Sbjct: 365 GGAGATSMKLEELKGKALEAFADVHDAFMKMRRAYD------KDGYRSASYLKAQEAISA 418

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
            +  +      ++ L   L      +   E E+ R A    G+ ++ F++   G +LD  
Sbjct: 419 ALMEVRFTARTVEKLCNLLRAQVDEVRRYEREIRRYAVDRCGMPQEEFIKSFPGHQLDLK 478

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  +   ++  V +I +++ ++  I     + + + + I + +  GE  A 
Sbjct: 479 WVDKHVASGKP-YSVILSRNVPAIKELQQKLIDIQTRVVVPLDDLKEINTQMSLGEQAAR 537

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA W
Sbjct: 538 EAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATW 597

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+KV R +R+   +   EP    +A+K+ MP + 
Sbjct: 598 WIRQAITRSIADQARTIRIPVHMIETINKVNRISRQHLQETGTEPDAAVLAEKMEMPEDK 657

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRK+LKI +EPIS+ETPIGD+D SHLGDFIED   ++P ++A+QA LR+    +L SLTP
Sbjct: 658 VRKILKIAREPISMETPIGDDDDSHLGDFIEDSGTLAPTEAAMQAGLRDVVKEILDSLTP 717

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI M  DHTLEEVGKQF VTRERIRQIEAKA+RKLKHP+RS KLRSFLD
Sbjct: 718 REAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPTRSDKLRSFLD 776


>gi|109897363|ref|YP_660618.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoalteromonas atlantica
           T6c]
 gi|109699644|gb|ABG39564.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoalteromonas atlantica
           T6c]
          Length = 613

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/660 (40%), Positives = 372/660 (56%), Gaps = 49/660 (7%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +        K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   
Sbjct: 1   MVQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             DE   +++      A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 61  DSDELLMQETTTDEEVAEAAAQALATVE-SEIGRTTDPVRMYMREMGTVELLTREGEIVI 119

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  S+ E P     L+   D        L +II            GF   
Sbjct: 120 AKRIEEGINQVQCSVAEYPEAITYLLDQWDMFEAEEIRLSDII-----------VGFVDP 168

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E  +          +  ++  E E D    +    ++       PE A      L    
Sbjct: 169 NEADNIAPTATHIGSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQY 228

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           + +   +++                                   + +S  K +   ++L 
Sbjct: 229 EKTRDVIAS-----------------------------------EGRSHAKSRKEIDELS 253

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
           ++     L   + D +V+ +  +  RI   E  +++    +  + +  F++   G E   
Sbjct: 254 EIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKDFIKAFSGNETST 313

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W+       +  +   +    + + +   ++ ++  ETG+ I++ + I   +  GE +A
Sbjct: 314 DWLFEILA-SDAPYVEELKVHQEELERSIGKMNAVEDETGLIIADIKDINRRMSIGEAKA 372

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 373 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+++++ MP +
Sbjct: 433 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED 492

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   V PLDSA   +L+  T  VLA LT
Sbjct: 493 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQPLDSATGGSLKNATQEVLAGLT 552

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 553 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 612


>gi|152995072|ref|YP_001339907.1| RNA polymerase sigma-70 subunit RpoD [Marinomonas sp. MWYL1]
 gi|150835996|gb|ABR69972.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas sp. MWYL1]
          Length = 612

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 270/658 (41%), Positives = 381/658 (57%), Gaps = 50/658 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D      K++I   +++GY+T  E+N  LP D    EQ+E+ +AM+++MGI V +    +
Sbjct: 3   DTQQSRLKELISKGKEQGYLTYAEVNDHLPDDLSDPEQVEEIIAMINDMGITVSEVAPDK 62

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D    E+      +A+  +       +     T DPVRMY+REMG++ELL+R GEIAIAK
Sbjct: 63  DSLLMEEGDATDEAAAEEAAAALAAVEGDITRTTDPVRMYMREMGTVELLTRAGEIAIAK 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +MA++   P     L+    ++ +    L +I             GF  G +
Sbjct: 123 RIEEGTREVMAAISYFPGAVDVLLDAYAKVQEEEGRLSDIF-----------SGFIDG-D 170

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      + +++E   D+      + +  +  ++++      P E A             
Sbjct: 171 GEEPVFEDVATEEPIIDEDTVDSDEDDDDSDTAEEETDNGPDPEETA------------- 217

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               ++I  +Y EL+ L +         +     +  +E+L   
Sbjct: 218 -----------------LRFNDITRIYTELKELLETRN------RQDPAVQSKQEELSIS 254

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHW 383
              + L     D LV+++    +++   E  +++   +  G+ R  FL+R    E +  W
Sbjct: 255 FAPIKLVPKLFDDLVDRVRSRMEKVREQERLIMQVCVRKSGMPRTEFLKRFPSNETNSDW 314

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +                 E +  ++ + +++++S ETG++I+E + I   +  GE  A  
Sbjct: 315 LKEQIASGADYAATLEENEAE-FMRSQRKLRAVSKETGLTIAELKEINRRISIGETRARR 373

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A ++ MP + +
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAARMDMPEDKI 493

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A SP+D A    LRE+TT VLA LT R
Sbjct: 494 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDIATIEGLRESTTMVLAGLTAR 553

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 554 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 611


>gi|152978401|ref|YP_001344030.1| RNA polymerase sigma factor RpoD [Actinobacillus succinogenes 130Z]
 gi|150840124|gb|ABR74095.1| RNA polymerase, sigma 70 subunit, RpoD [Actinobacillus succinogenes
           130Z]
          Length = 623

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 277/657 (42%), Positives = 388/657 (59%), Gaps = 43/657 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K +I   +++GY+T  E+N  LP D V ++Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLIAQGKEQGYLTFAEVNDHLPEDLVDTDQIEDIIQMINDMGIQVLETAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+  D    A   +  +    +S    T DPVRMY+REMGS+ELL REGEI IAKRI
Sbjct: 66  LLNENITDTDEDAVEEATQVLSSVESELGRTTDPVRMYMREMGSVELLDREGEIGIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P     L+    ++ +G   L ++I     + P  +      ++  
Sbjct: 126 EDGINEVQSAIAEYPEGITYLLDQYAQVEEGGIRLADLIT--GFVDPTVEESADEFSDDL 183

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +  +  D   + + DD  E E D    +  S D+ + +D  PE A      L +  D + 
Sbjct: 184 ADDEDADVEVDADLDDENEDEEDNNDNSSSSDDNDNSID--PEVAREKFYALRDQHDKTI 241

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T++                                   K  + S K +   + L ++  
Sbjct: 242 ATIA-----------------------------------KHGRGSAKAREQMKALSEIFT 266

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERH-QGRELDPHWV 384
              L   + D+LV  +  + KRI   E ++ R A  Y  + +D F++    G+E +  W+
Sbjct: 267 QFRLVPRQFDVLVIPMRKMMKRIRAEERQIQRWAVDYARMPKDEFVKVFSTGKETNDAWL 326

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +  +   +A   D+I      ++++  E  ++I + R+I   + +GE +A  A
Sbjct: 327 TKLLG-GKKPYAEKLAKYADNIRASIARLQNLEQEAHLTIEQIRNIGDRISQGELKARRA 385

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 386 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 445

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +R
Sbjct: 446 RQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIR 505

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE
Sbjct: 506 KVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPRE 565

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 566 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|163751572|ref|ZP_02158794.1| RNA polymerase sigma-70 factor [Shewanella benthica KT99]
 gi|161328580|gb|EDP99733.1| RNA polymerase sigma-70 factor [Shewanella benthica KT99]
          Length = 609

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 369/655 (56%), Gaps = 53/655 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +     DE 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEI 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSED-STDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P    A++   D        L +II            GF        
Sbjct: 125 EGINTVQASVAEYPQAIAAILDQFDRYEAEEVRLSDII-----------SGFIDPNADDI 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    +  + ++ +      S     +++       PE ++     L E  +++  
Sbjct: 174 APTATHVGSDLSQSELDKDN----SKDDEDEEEEGPKGPDPEESKERFTQLREVHENTLR 229

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A + +  P+   AL EI E+++E                                  
Sbjct: 230 II-ADKGRGHPEATVALFEIGELFKE---------------------------------- 254

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +     ++   E  +++L  +   + +  F++ +   E    W   
Sbjct: 255 FRLMPKQFDRLVKGMRATMDKVRVQERLIMKLCVEQAKMPKKNFVKCYTADESSIAWFDA 314

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +         E D + + R ++  I  ETG++I+  + I   +  GE +A  AKK
Sbjct: 315 ELASKKPYVAGLQMVETD-VRRCRFKLDIIEKETGLAIASIKDINRRMSIGEAKARRAKK 373

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 374 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 433

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 434 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPEDKIRKV 493

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 494 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGLTAREAK 553

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 554 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 608


>gi|262401783|ref|ZP_06078349.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC586]
 gi|262352200|gb|EEZ01330.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC586]
          Length = 627

 Score =  448 bits (1151), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/656 (40%), Positives = 375/656 (57%), Gaps = 37/656 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P T   ++   D +      L ++I            GF    +  
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI-----------AGFVDPND-- 172

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E E         ++  A    +DD    +   +  E+ E N +  + +  
Sbjct: 173 ---------METEAPTATHIGSELTEADLADEDDEIAAEEDEDEDEDGEGNSESSDSEEE 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +     +         ++  E+  + ++LQ   +   +  + S +       ++ +  
Sbjct: 224 VGIDPELAR---------EKFNELRGKFQNLQ---LAVNEFGRDSNQASEASGLVLDIFR 271

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LVE L     R+   E  +++       + +  F+    G E +  W+ 
Sbjct: 272 EFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLD 331

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  AK
Sbjct: 332 KVLA-SDKPYVQKVREQEEDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAK 390

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 391 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 450

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 451 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 510

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 511 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREA 570

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 626


>gi|260912696|ref|ZP_05919182.1| DNA-directed RNA polymerase sigma subunit RpoD [Pasteurella
           dagmatis ATCC 43325]
 gi|260633074|gb|EEX51239.1| DNA-directed RNA polymerase sigma subunit RpoD [Pasteurella
           dagmatis ATCC 43325]
          Length = 623

 Score =  448 bits (1151), Expect = e-123,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 370/655 (56%), Gaps = 39/655 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V +EQ+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A   +  +    +S    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLSETIT-DEDAVEEATQVLSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++   P     L+     + DG   L ++I            GF        
Sbjct: 125 EGINEVQSAVAFYPEALNYLLEQYSLVEDGGVRLADLI-----------TGFVDPNAITE 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               E      E +D     G        +K D ++ +      EN   + D D      
Sbjct: 174 EDVAEIDESFDEDEDSDTVVG--------AKLDDTEEEEEESEEENTSDDNDSDNSIDPE 225

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
              A   +L+ + +  L+ I                  K  ++S K K   + L  +   
Sbjct: 226 LAHAKFLELKTQHVKTLETI-----------------VKHGRASKKSKDQIQALADVFTQ 268

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D+LV  +  + K +   E  + ++      + ++ F +   G E    W+  
Sbjct: 269 FRLVPKQFDMLVNLMSGMMKSVRLQERNIQKIVVDKAKMPKEQFQKVFIGHENQDTWLVK 328

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A       W   +A     I    + I  I  +T +++ + R +   +  GE +A  AKK
Sbjct: 329 ALS-AGKTWSEKLAKHEAEIRASIDNILEIERQTNLTVQQIREVCERISAGELKARRAKK 387

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 388 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 447

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 448 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 507

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 508 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKAATHEVLEGLTPREAK 567

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|90580773|ref|ZP_01236576.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90438041|gb|EAS63229.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 616

 Score =  448 bits (1151), Expect = e-123,   Method: Composition-based stats.
 Identities = 275/655 (41%), Positives = 373/655 (56%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +   ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTEDNADEDAIEAAAQALSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      L +II        E+         G  
Sbjct: 125 DGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPNEEATAAPTATHIGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + +   ++K+ +D ++ E   E     S D        PE A      L +  D  A 
Sbjct: 185 LSESDLEDEDKDLEDDEDAEDSDEEEDDGSID--------PELAREKFLELRQAYDKMAL 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                     + + +   +V  E+L ++   
Sbjct: 237 AIET-----------------------------------NGRQNATTEVAVEELSEVFKQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  L D   ++  NE  ++R+      + +  F+    G E    W+  
Sbjct: 262 FRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFVSLFAGNESSQDWIDE 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A +  +   +   A E D + +   +++ +  ETG+SI   + I   +  GE +A  AKK
Sbjct: 322 ALNSGKPYAERLKAYEED-LRRSSLKLRMLEEETGLSIERIKDISRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATATNLRAATNDVLAGLTPREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 615


>gi|146309042|ref|YP_001189507.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina ymp]
 gi|145577243|gb|ABP86775.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas mendocina ymp]
          Length = 615

 Score =  448 bits (1151), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 374/657 (56%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T + ++   + +      L E++            G+    +G
Sbjct: 125 IEEGIREVMSAIAHFPGTVEGILAEYNRVTTEGGRLAEVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               +       KE    +E++ + +  +   +++       PE A      + E ++  
Sbjct: 174 SVPDEAAAPVPVKEGAAAEESDDEEDEESGDDEEEEGDGGPDPEEAARRFSAVAEQQEKV 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  + S +       L +L 
Sbjct: 234 QKAL-----------------------------------KKHGRGSKQATEELAALAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LV Q+ D   R+   E  +++L      + R  FL    G E+D  W 
Sbjct: 259 MPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRADFLRLFPGNEIDMDWA 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      + ++   +      I + + ++  +  E  +S++E + I   +  GE +A  A
Sbjct: 319 ADLAK-GKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VLA LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLAGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|315634867|ref|ZP_07890149.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           segnis ATCC 33393]
 gi|315476419|gb|EFU67169.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           segnis ATCC 33393]
          Length = 621

 Score =  448 bits (1151), Expect = e-123,   Method: Composition-based stats.
 Identities = 271/655 (41%), Positives = 371/655 (56%), Gaps = 41/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++         +  +    ++    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLNENIT-DEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++   P     LI   D +  G   L ++I            GF        
Sbjct: 125 EGINEVQSAIAAYPEAITYLIEQYDLVESGGVRLADLI-----------TGFVDP----- 168

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                +   E E  ++ E   +       + +   + +   ++ E+   + D D      
Sbjct: 169 -----NVLSESETAELDEFHSEEGEENVAAAEIDDESEDEEDSEESASDDSDSDNSIDPE 223

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                   LR +    L+ IA                 K  ++  K K   + L  +   
Sbjct: 224 VAREKFTALRQQHQKTLEIIA-----------------KHGRTGKKAKDEIQALSDIFTQ 266

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV    D+ KR+ H E  + RL      + +  F +   G E    W+  
Sbjct: 267 FRLVPKQFDTLVLSTRDMMKRVRHQERLIQRLVVDNAKMPKSSFQKSFIGHETSDVWLVK 326

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +  W   +A   D + +    +  I  +T ++I + R I   + +GE +A  AKK
Sbjct: 327 ALAAGKS-WSEKLAQYEDELRQAIAHLVQIEQDTNLTIGQIREIGERISQGELKARRAKK 385

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 386 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 445

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + +RKV
Sbjct: 446 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKV 505

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 506 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKAATHEVLEGLTPREAK 565

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 566 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 620


>gi|156973168|ref|YP_001444075.1| RNA polymerase sigma factor RpoD [Vibrio harveyi ATCC BAA-1116]
 gi|156524762|gb|ABU69848.1| hypothetical protein VIBHAR_00848 [Vibrio harveyi ATCC BAA-1116]
          Length = 620

 Score =  448 bits (1151), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/656 (40%), Positives = 370/656 (56%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I        +          G 
Sbjct: 126 EEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +   +++E  D  E   D    ++       ++                      
Sbjct: 186 ELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL---------------------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +   +++   Y+ L+      +   +    S K  V  E ++ +  
Sbjct: 224 -------------ALEKFNQLRSTYQNLQ------LAINEHGYESPKATVANELMLDVFK 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++ A  YG + +  F+    G E    W+ 
Sbjct: 265 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNESSEAWLD 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 325 EILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 504 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKMATKDVLAGLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619


>gi|332307721|ref|YP_004435572.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175050|gb|AEE24304.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 613

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/660 (40%), Positives = 373/660 (56%), Gaps = 49/660 (7%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +        K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   
Sbjct: 1   MVQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             DE   +++      A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 61  DSDELLMQETTTDEEVAEAAAQALATVE-SEIGRTTDPVRMYMREMGTVELLTREGEIVI 119

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  S+ E P     L+   D        L +II            GF   
Sbjct: 120 AKRIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDII-----------VGFVDP 168

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E  +          +  ++  E E D    +    ++       PE A      L    
Sbjct: 169 NEADNIAPTATHIGSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQY 228

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           + +   +++                                   + +S  K +   ++L 
Sbjct: 229 EKTRDVIAS-----------------------------------EGRSHAKSRKEIDELS 253

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
           ++     L   + D +V+ +  +  RI   E  +++    +  + +  F++   G E   
Sbjct: 254 EIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKDFIKAFSGNETST 313

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W+ Y     +  +   +    + + +   ++ ++  ETG+ I++ + I   +  GE +A
Sbjct: 314 DWL-YELMASDAPYVEELKVHQEELERSIGKMNAVEEETGLIIADIKDINRRMSIGEAKA 372

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 373 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+++++ MP +
Sbjct: 433 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED 492

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   V PLDSA   +L+  T  VLA LT
Sbjct: 493 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQPLDSATGGSLKNATQEVLAGLT 552

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 553 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 612


>gi|17546934|ref|NP_520336.1| RNA polymerase sigma factor RpoD [Ralstonia solanacearum GMI1000]
 gi|17429234|emb|CAD15922.1| probable rna polymerase sigma d (sigma-70) factor transcription
           regulator protein [Ralstonia solanacearum GMI1000]
          Length = 755

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 251/674 (37%), Positives = 372/674 (55%), Gaps = 46/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 123 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 182

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 183 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 242

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 243 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 300

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +                ++ + E   ++  E +    S+A  ++           
Sbjct: 301 LIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAASARQLE-------- 352

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                    +L+   +     I + + ++R   +      K+  
Sbjct: 353 -------------------------ELKQAALAKFAIIGDQFEKMRRAFE------KEGY 381

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 382 KSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 441

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 442 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQARVVLPLAELK 500

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 501 DVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 560

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 561 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 620

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 621 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 680

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 681 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 740

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 741 HPSRSDKLKSFLEG 754


>gi|330505280|ref|YP_004382149.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina NK-01]
 gi|328919566|gb|AEB60397.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina NK-01]
          Length = 615

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 266/657 (40%), Positives = 373/657 (56%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T   ++   + +      L E++            G+    +G
Sbjct: 125 IEEGIREVMSAIAHFPGTVDGILAEYNRVTTEGGRLAEVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               +       KE    +E++ + E  +   +++       PE A      + E ++  
Sbjct: 174 SVPDEAAAPVPVKEGAAAEESDDEEEDESGDDEEEEGDGGPDPEEAARRFTAVAEQQEKV 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  + S +       L +L 
Sbjct: 234 QKAL-----------------------------------KKHGRGSKQAIEELATLAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LV Q+ D   R+   E  +++L      + R  FL    G E+D  W 
Sbjct: 259 MPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRADFLRLFPGNEIDMDWA 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      + ++   +      I + + ++  +  E  +S++E + I   +  GE +A  A
Sbjct: 319 ADLAK-GKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VLA LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLAGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|254429850|ref|ZP_05043557.1| Sigma-70, non-essential region family [Alcanivorax sp. DG881]
 gi|196196019|gb|EDX90978.1| Sigma-70, non-essential region family [Alcanivorax sp. DG881]
          Length = 633

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/652 (40%), Positives = 363/652 (55%), Gaps = 40/652 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSL 93
           I L +++GY+T  E+N  LP     ++Q+ED + M+++MGI VV+   D +     E + 
Sbjct: 16  IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDESAD 75

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                A+  +  +    ++    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +
Sbjct: 76  STDEVAAEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + +L   P     +I     + +    L +II     + P   G              + 
Sbjct: 136 LHALAFWPGAVDMVIDEYARVENEERKLTDII--AGYLDPNDDGAAATNVNRDPAFAEKA 193

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
               +E+   +E   +  +  K S DD  + +   +                        
Sbjct: 194 KKAAEEKAKAKEKAKEEGTDDKDSDDDEEEDEGGLDPVLA-------------------- 233

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQ 332
                         AE +  L+ L + A    K + +         E L +      L  
Sbjct: 234 --------------AERFETLKKLHEKAERSLKRNGRDHASSAKALEALAEHFTLFKLVP 279

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFP 391
              D ++    D    +   E +++      G + R  F++   G E +  W+       
Sbjct: 280 RIFDGMLVGARDNLDLVRKFERQIMSATIRRGGMDRKDFIKVFPGNETNMDWIDGQLKTK 339

Query: 392 EGEW-KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           +G+   + +    + + + + +I +I    G+ + + + I   +  GE +A  AKKEMVE
Sbjct: 340 KGKAIADKLGAVKEDVQRAQRKIGTIEDIIGLPVGDIKEINRRISIGEAKARRAKKEMVE 399

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 400 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 459

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R  R+M  ++ REPTPEE+  +L MP + VRKVLKI 
Sbjct: 460 SIADQARTIRIPVHMIETINKINRVQRQMLQEMGREPTPEELGVRLEMPEDKVRKVLKIA 519

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ S LGDFIED N  SP+DSA    L E T  VLA+LT RE +VLRM
Sbjct: 520 KEPISMETPIGDDEDSSLGDFIEDGNMESPVDSATSLGLEEATRDVLANLTAREAKVLRM 579

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLDG
Sbjct: 580 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLDG 631


>gi|219681993|ref|YP_002468377.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219621726|gb|ACL29882.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/656 (40%), Positives = 375/656 (57%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILNEINTDTDEDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L +II     + P ++  F       
Sbjct: 126 EEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIIT--GFVDPNAEEIFL------ 177

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  ++     + + E + + E      +D        PE A      L    +++ 
Sbjct: 178 ------PTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRIQYNNTN 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           +T+       +  ++   +                                   L ++  
Sbjct: 232 NTIKNKNRTHKDSLLEIYN-----------------------------------LSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + +R+   E  +++L      + +  F++    ++++  W  
Sbjct: 257 QFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKINYLWFI 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             ++  +  W   +    + +     ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 REQNTNQP-WSENLKKVKEDVFVSVKKLIKIEEETGLTIEQVKDINKRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|212633971|ref|YP_002310496.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
 gi|212555455|gb|ACJ27909.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
          Length = 612

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 266/655 (40%), Positives = 370/655 (56%), Gaps = 53/655 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEI 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSED-STDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P     ++   D        L +II     I P ++      T   S
Sbjct: 128 EGINTVQASVAEYPQAIAMILEQFDRFEAEEVRLSDII--SGFIDPNAEDVAPTATHVGS 185

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               E+                 +       ++       PE A+     L    + +  
Sbjct: 186 ELSDEELDD-------------EDDDEDDEDEEEGPKGPDPEEAKEKFTTLRVAHERALE 232

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +S ++ +  P+   AL EI E+++E                                  
Sbjct: 233 IIS-IKGRGHPESTVALFEIGEIFKE---------------------------------- 257

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   E    W + 
Sbjct: 258 FRLMPKQFDRLVKSMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNE 317

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +   +     + D + + R ++ +I  ETG++I   + I   +  GE +A  AKK
Sbjct: 318 ELASGKPYAEGLKMVDYD-VQRCRAKLDAIETETGLAIGAIKDINRRMSIGEAKARRAKK 376

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 377 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 436

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 437 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKV 496

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +
Sbjct: 497 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGLTAREAK 556

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 557 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 611


>gi|152984199|ref|YP_001346113.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PA7]
 gi|150959357|gb|ABR81382.1| sigma factor RpoD [Pseudomonas aeruginosa PA7]
          Length = 617

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 380/657 (57%), Gaps = 47/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVE-SDIGRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++ + P T  +++   + +      L +++            G+    +G
Sbjct: 125 IEEGIREVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               +  +    K+     + + D E  +  + D   + D  P            D +++
Sbjct: 174 SLPAEEVEPVNLKDDSADSKEKDDEEEESDDNSDSDDEGDGGP------------DPEEA 221

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
               +A+ +QL                            +K  + S +       L +L 
Sbjct: 222 RLRFTAVSEQLDKA---------------------KKALKKHGRGSKQATAELTGLAELF 260

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LV ++    + +   E  +++L      + R  FL      E D  WV
Sbjct: 261 MPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHETDEKWV 320

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  + ++   +    D IL+ + ++ ++  E  ++++E + I   +  GE +A  A
Sbjct: 321 DSVLK-SKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGEAKARRA 379

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 380 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 439

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 440 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKIR 499

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA LT RE
Sbjct: 500 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLAGLTARE 559

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 616


>gi|254517369|ref|ZP_05129426.1| RNA polymerase sigma factor RpoD [gamma proteobacterium NOR5-3]
 gi|219674207|gb|EED30576.1| RNA polymerase sigma factor RpoD [gamma proteobacterium NOR5-3]
          Length = 607

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/658 (40%), Positives = 368/658 (55%), Gaps = 61/658 (9%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLE 84
                 K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D +
Sbjct: 6   TQQSRLKSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDAD 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D   ++        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DLILTDGDGSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAK 125

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +MA+L   P   ++++     +      L +I+            G+ +  +
Sbjct: 126 RIEEGIRELMAALAFYPGAVKSVLDDYALVAKEEKKLADIL-----------VGYLNPAD 174

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                ++    Q                                  A     N+DED++D
Sbjct: 175 HVPSAQQIAEQQ----------------------------------AAKAAGNVDEDDND 200

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           S      +E +           +   + +   +        +  +         EKL ++
Sbjct: 201 SPAGPDPVEAK------KRFTALKRQFNKTEKI------LLEKGRQDKAAIKEMEKLGEI 248

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                      D L ++       +   E E++RLA +   + R  F+   QG E +  W
Sbjct: 249 FKFFKFTPKVFDPLNDEARSALAGVREQEREIMRLAVRRCQMPRKDFITSFQGNESNAKW 308

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +S      + ++   +    + IL+ + +I  I   TG++++E + I   +  GE  A  
Sbjct: 309 LSR--HTRKKDYGPKLNAYKEEILRAQRQIGQIEAATGLTVTEIKEINRRMSMGEARARR 366

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 367 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + V
Sbjct: 427 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKV 486

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED+   SP+D+A    L E T  VLA LT R
Sbjct: 487 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTINSPIDAATGQGLMEATKDVLAGLTAR 546

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 547 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 604


>gi|258623542|ref|ZP_05718543.1| RNA polymerase sigma factor [Vibrio mimicus VM573]
 gi|258623776|ref|ZP_05718733.1| RNA polymerase sigma factor [Vibrio mimicus VM603]
 gi|262172395|ref|ZP_06040073.1| RNA polymerase sigma factor RpoD [Vibrio mimicus MB-451]
 gi|258583899|gb|EEW08691.1| RNA polymerase sigma factor [Vibrio mimicus VM603]
 gi|258584204|gb|EEW08952.1| RNA polymerase sigma factor [Vibrio mimicus VM573]
 gi|261893471|gb|EEY39457.1| RNA polymerase sigma factor RpoD [Vibrio mimicus MB-451]
          Length = 625

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 269/657 (40%), Positives = 368/657 (56%), Gaps = 41/657 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEG 205
           E G   + +++ E P T   ++   D++      L ++I     + P   +      T  
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPNDMETEAPTATHI 183

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            S     D + E +     E E + E     S D   +V   PE A      L       
Sbjct: 184 GSELSEADLADEDDEVAEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------ 237

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                           Q+  +   +  + S +       ++ + 
Sbjct: 238 -----------------------------GKFQNLQLAVNEFGRDSNQASEASSLVLDIF 268

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L   + D LVE L     R+   E  +++       + +  F+    G E +  W+
Sbjct: 269 REFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWL 328

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +  +   V  + D I +   +++ I  ET +S+   + I   +  GE +A  A
Sbjct: 329 DKVLA-SDKPYVQKVREQEDDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRA 387

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 388 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 447

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +R
Sbjct: 448 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIR 507

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE
Sbjct: 508 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPRE 567

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624


>gi|261210089|ref|ZP_05924387.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC341]
 gi|260840854|gb|EEX67396.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC341]
          Length = 628

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 263/656 (40%), Positives = 373/656 (56%), Gaps = 36/656 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P T   ++   D +      L ++I     + P             
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDM--------ET 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E    D+ + + +I +      +D  +      +   +E  +D +     
Sbjct: 176 EAPTATHIGSELSEADLADEDDEIAAEEDDEDEDEDENGEGESSDSEEEVGIDPE----- 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           A ++  E+  + ++LQ   +   +  + S +       ++ +  
Sbjct: 231 ---------------LAREKFNELRGKFQNLQ---LAVNEFGRDSNQASEASGLILDIFR 272

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LVE L     R+   E  +++       + +  F+    G E +  W+ 
Sbjct: 273 EFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEIAKMPKKSFIALFTGNESNEEWLD 332

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  AK
Sbjct: 333 KVLA-SDKPYVQKVRDQEEDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAK 391

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 392 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 451

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 452 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 511

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 512 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREA 571

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 572 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 627


>gi|149191850|ref|ZP_01870086.1| RNA polymerase sigma factor RpoD [Vibrio shilonii AK1]
 gi|148834326|gb|EDL51327.1| RNA polymerase sigma factor RpoD [Vibrio shilonii AK1]
          Length = 616

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 366/656 (55%), Gaps = 48/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDNNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I     + P          E  
Sbjct: 126 EDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDVIT--GFVDPN--------EEET 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +         E    D+++ + +       S+++       PE A      L        
Sbjct: 176 TAPTATHIGSELSEADLEDEDDEDVDEDDDSEEEEEDTGIDPELALEKFTALRNSY---- 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          QD  +   +    S +     E + ++  
Sbjct: 232 -------------------------------QDLQLVINEYGYDSPQVAKSHELVQEVFK 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  ++R A  YG + +  F+    G E    W+ 
Sbjct: 261 EFRLTPKQFDHLVNELRTSMDRVRTQERLIMRQAVEYGKMPKKSFIAVFTGNESSEAWLD 320

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    D I +   ++  I  ET +S+   + I   +  GE +A  AK
Sbjct: 321 EVLA-SDKPYAEKIKRYEDDIRRSIQKLDIIEEETSLSVQNIKDISRRMSIGEAKARRAK 379

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 380 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 439

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 440 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 499

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +LR  T  VLA LTPRE 
Sbjct: 500 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPVDSATMTSLRVATKDVLAGLTPREA 559

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 615


>gi|311085799|gb|ADP65881.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086374|gb|ADP66455.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. TLW03
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/656 (40%), Positives = 375/656 (57%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D + SEQ++D + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ILNEINTDTDEDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L +II     + P ++  F       
Sbjct: 126 EEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIIT--GFVDPNAEEIFL------ 177

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  ++     + + E + + E      +D        PE A      L    +++ 
Sbjct: 178 ------PTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRIQYNNTN 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
           +T+       +  ++   +                                   L ++  
Sbjct: 232 NTIKNKNRTHKDSLLEIYN-----------------------------------LSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + +R+   E  +++L      + +  F++    ++++  W  
Sbjct: 257 QFRLVPKQFDHLVNNMRHMMERVRKQERIIIKLCVEICKMPKKNFIKIFPIKKINYLWFI 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             ++  +  W   +    + +     ++  I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 REQNTNQP-WSENLKKVKEDVFISVKKLIKIEEETGLTIEQVKDINKRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 376 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +RK
Sbjct: 436 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL+ LT RE 
Sbjct: 496 VLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|254784701|ref|YP_003072129.1| RNA polymerase sigma factor RpoD [Teredinibacter turnerae T7901]
 gi|237686864|gb|ACR14128.1| RNA polymerase sigma factor RpoD [Teredinibacter turnerae T7901]
          Length = 619

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 273/661 (41%), Positives = 380/661 (57%), Gaps = 45/661 (6%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GD 81
           + +      K++I   R++GY+T +E+N  LP D    +Q+ED + M+++MGI V +   
Sbjct: 1   MSEQQQSRIKELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAP 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D ++   ++        A+  +       ++    T DPVRMY+REMG++ELL+REGEIA
Sbjct: 61  DADELLMTDGEASPDEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIA 120

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +M +L   P   Q ++   D +      L ++I     + P        
Sbjct: 121 IAKRIEEGLRELMHALAFWPNAVQQIMDEYDLVEKEERRLNDVI--SGWLDPAE-----E 173

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                     +++++    D+    + + E     S +D +     PE A          
Sbjct: 174 VEAATPVDSTDNNTKNDADDEDDSDDDEDEDDDSSSDEDENNSGIDPEYARERF------ 227

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                       D+LR +++ A D IA                 K    S +  V  E L
Sbjct: 228 ------------DELRVQLVAANDAIA-----------------KHGLDSKETGVALEAL 258

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELD 380
            ++     L   + D +   + D+  RI   E E++RL     G+ R  F++   G E++
Sbjct: 259 GEVFKFFKLAPRQFDPIYNYVRDVLARIRAEEKEIMRLCVRMAGMPRKTFVKEFPGNEIN 318

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+       + ++ + +      IL+ + +++ I  ETG+ ++  + I   +  GE  
Sbjct: 319 EDWIPEII-RKKRDYSDSLRPVEGDILRSQRKLQQIEEETGLELTAIKEINRRMSIGEAR 377

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 378 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 437

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP 
Sbjct: 438 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 497

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++SA    L E T  VLA L
Sbjct: 498 DKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTITSPVESATSQGLMEATKAVLAGL 557

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR FL
Sbjct: 558 TAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFL 617

Query: 681 D 681
           D
Sbjct: 618 D 618


>gi|88810991|ref|ZP_01126247.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88791530|gb|EAR22641.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 609

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 278/663 (41%), Positives = 387/663 (58%), Gaps = 59/663 (8%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-G 80
           +         +++I   +++GY+T  E+N  LP D V  EQ+ED + M+++MGI+V +  
Sbjct: 1   MTIQDQQSQIRELIARGKEQGYLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGISVHETA 60

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D +    S+ ++      +  +       D+    T DPVRMY+REMG++ELL+REGEI
Sbjct: 61  PDSDTLLLSDAAVATDEDEAEEAAAALASVDAEFGRTTDPVRMYMREMGTVELLTREGEI 120

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            +AKRIE G   ++ +L   P + + L      +  G   L+EI+     +  E  GG  
Sbjct: 121 ELAKRIEEGLDQVLRALSAYPESARTLCSLHRHVEAGRLRLQEILAGFRGLEDELDGGAD 180

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                                                                   + D+
Sbjct: 181 AVDVSVGI------------------------------------------------DGDD 192

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL-RSLQDNAVNGQKDEKSSVKCKVLKE 319
           ++++SA   +A       + +   + I E++  L  +LQ+           S +C+ L+E
Sbjct: 193 EDEESASNAAADSGPNPEQAVQLFNRIRELHEALLIALQER-------GSGSEQCRELRE 245

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRE 378
           ++  L  S+ L    ID + E L    +RI   E E+ R   +  G+ R  F+    GRE
Sbjct: 246 EMGNLFLSMKLAPKVIDGMAENLRKAVERIRRAEREVTRICVKQAGMPRKEFITLFPGRE 305

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            DP WV       +  +   VA     +L+ +  + +I   TG+++SE + I   +  GE
Sbjct: 306 TDPSWVDE-LIRADKPYSEAVAERRQMLLEAQVGLAAIQEATGLAVSEVKEINRRMSIGE 364

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 365 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 424

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ RT+R+M  ++ REP P+E+A+++ M
Sbjct: 425 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRTSRQMLQEMGREPQPDELAERMEM 484

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED   +SP+DSA +  L+E+   VLA
Sbjct: 485 PEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDAAVMSPVDSATREGLKESVREVLA 544

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRS
Sbjct: 545 GLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSESLRS 604

Query: 679 FLD 681
           FLD
Sbjct: 605 FLD 607


>gi|315127802|ref|YP_004069805.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315016316|gb|ADT69654.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 614

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 368/656 (56%), Gaps = 49/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE 
Sbjct: 6   QSQLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +++     +A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMQETTTDEDAAEAAAAALATVEK-EIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D+       L +II            GFF      +
Sbjct: 125 EGINQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDII-----------SGFFDPDAEEA 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                 +   +  +   +   D +  +    ++       PE A     NL +       
Sbjct: 174 PPIAATNIGSELSEKQLDDSDDDDDDSDDEDEEEVDTGPDPEEARVHFENLRD------- 226

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                   L  K     D                       +S  + +    ++ +L  +
Sbjct: 227 --------LYTKARETFDN--------------------KGRSHPESQAAILEIGELFRT 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D +V  + ++  R+   E  +++ A     + +  F++     E D  W+  
Sbjct: 259 FKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFANNETDTAWLDI 318

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                E      +      IL+  +++ S+   TG+SI   + I   +  GE +A  AKK
Sbjct: 319 EIAANEKH-SAKLEEVKPEILRCISKLTSMEESTGLSIERIKDINRRMSIGEAKARRAKK 377

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 378 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 437

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIRKV 497

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +LR  T  VLA LT RE +
Sbjct: 498 LKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVLAGLTAREAK 557

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD 
Sbjct: 558 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLDA 613


>gi|71274854|ref|ZP_00651142.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Dixon]
 gi|71902125|ref|ZP_00684157.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
 gi|170729898|ref|YP_001775331.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa M12]
 gi|71164586|gb|EAO14300.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Dixon]
 gi|71728114|gb|EAO30313.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
 gi|167964691|gb|ACA11701.1| RNA polymerase sigma-70 factor [Xylella fastidiosa M12]
          Length = 623

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 388/660 (58%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + 
Sbjct: 13  QQSDIKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAET 72

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   EG+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 73  LLLNEGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAI 132

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L E++                 
Sbjct: 133 AKRIEEGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVVVGF-------------- 178

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             +D+ E +  + S+  V+ +   +VD   +++  ++ +     
Sbjct: 179 ------------------NDLIEDDNSVTSSVDVTDESIVEVDEEDDDSVGNDED----- 215

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                  + M      +V   ++ ++  Y + + L        K          ++E + 
Sbjct: 216 -------APMIGPDPAEVASRIESLSTEYAKFKKLY------AKHGPEHKAVIKVREDMA 262

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +  L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + + 
Sbjct: 263 AIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNL 322

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I   +     +     +++++ + I  M+  GE +A
Sbjct: 323 EWVEDAIKR-KQKWSSALRDIKDQITAEQQSSIDLEKVNSLTLADIKEINRMMVYGEAKA 381

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA 
Sbjct: 382 SKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYAT 441

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 442 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 501

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 502 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLT 561

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 562 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 621


>gi|157374211|ref|YP_001472811.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
           HAW-EB3]
 gi|157316585|gb|ABV35683.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
           HAW-EB3]
          Length = 612

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/655 (40%), Positives = 372/655 (56%), Gaps = 53/655 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +     DE 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEI 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSED-STDEDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P     ++   D        L +II     + P +       T   S
Sbjct: 128 EGINTVQASVAEYPQAISMILEQFDRYEAEEVRLSDII--SGFVDPNADDVAPTATHVGS 185

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               E+                 +      +++       PE A+     L E  +++  
Sbjct: 186 ELSDEELDD-------------EDDEEDDDEEEEGPKGPDPEEAKERFTQLREVHENTLK 232

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            + A++ +  P+   AL EI E+++E                                  
Sbjct: 233 VI-ALKGRGHPESTLALFEIGELFKEF--------------------------------- 258

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  ++   E  +++L  +   + +  F++ +   E    W + 
Sbjct: 259 -RLMPKQFDRLVKNMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNE 317

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  +   +      + + R ++ +I  ETG++I+  + I   +  GE +A  AKK
Sbjct: 318 ELA-SKKPYVEGLEMVDPDVRRCRAKLDAIEKETGLAIASIKDINRRMSIGEAKARRAKK 376

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 377 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 436

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 437 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKV 496

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 497 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAK 556

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 557 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 611


>gi|308050979|ref|YP_003914545.1| RNA polymerase, sigma 70 subunit, RpoD [Ferrimonas balearica DSM
           9799]
 gi|307633169|gb|ADN77471.1| RNA polymerase, sigma 70 subunit, RpoD [Ferrimonas balearica DSM
           9799]
          Length = 610

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 369/655 (56%), Gaps = 52/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +    +DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIQVFESAPDQDEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                      A+ ++       +     T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MM-SEDATDEDAAEAAAQALASVEGELGRTTDPVRMYMREMGTVELLTREGEILIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D        L EII        E+      G+E   
Sbjct: 125 DGINQVQCSIAEYPEAISFLLDQWDRFEAEEIRLAEIISGFVTEEEEAPTATHVGSELPK 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +  ++   E+E                   DD +     PE A     +L E  +    
Sbjct: 185 EELDDEDEDEEED--------------DDDSDDDTSNGPDPEQAREKFTSLREHYELVQK 230

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             +                                   +  + S++  +L  +L +L   
Sbjct: 231 AFA-----------------------------------EHGRDSLEAAMLITRLSELFKE 255

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D+LV  +  +  R+   E  +++   +   + +  FL+   G E +  W+  
Sbjct: 256 FRLVPKQFDVLVNNMRSMMDRVRVQERLIMKMCVEQAKMPKKNFLKLFAGHESETAWL-Q 314

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A+      +   +    + + +   ++  I  ETG+SI++ + I   +  GE +A  AKK
Sbjct: 315 AEIDAGKSYSAALGEHQEELHRCIQKLAQIQEETGLSIAKIKDINRRMSIGEAKARRAKK 374

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 375 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 434

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKV
Sbjct: 435 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPEDKIRKV 494

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  VLA LT RE +
Sbjct: 495 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLAQPVDSATAESLKAATAEVLAGLTAREAK 554

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 555 VLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 609


>gi|197335189|ref|YP_002157048.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
 gi|197316679|gb|ACH66126.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
          Length = 613

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 273/656 (41%), Positives = 377/656 (57%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDM 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++D       A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  SLNDDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++      L +II     + P    G    T  H
Sbjct: 126 EEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDII--SGFVDPNDD-GSSAPTATH 182

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              +  ++  + E D+  E E + E  A +  +                           
Sbjct: 183 IGSELSEAELDDEDDEDDEGETEEEEDAGIDPE--------------------------- 215

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           AL++  E+     ++Q       +D+    K +    +L  +  
Sbjct: 216 ---------------LALEKFTELRTSYHNMQLAFEEFGRDD---AKSREAIGELTDIFR 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV+++ D   R+   E  ++R+   YG + +  F+    G E    W +
Sbjct: 258 EFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMPKKSFIALFTGNESSDEWFN 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++ SI  ETG+ +   + I   +  GE +A  AK
Sbjct: 318 EIMA-SDKPYVERLQRYEEDIRRSIAKLDSIEKETGLPVENIKDISRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  VLA LTPRE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPVDSATSTSLKFATNDVLAGLTPREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|206562773|ref|YP_002233536.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia J2315]
 gi|198038813|emb|CAR54775.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia J2315]
          Length = 621

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 253/657 (38%), Positives = 371/657 (56%), Gaps = 42/657 (6%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +    
Sbjct: 2   KLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLL 61

Query: 90  EDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 62  NDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 121

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   M+ ++   P T   ++   + + +    + E++D                    
Sbjct: 122 EDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------------- 161

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     +    D  +T+G     A+  +++  + +   E  E +E +       +A
Sbjct: 162 -------GLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANA 214

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L A    L+   +    +I+E + ++R   +      K+   S      +E +   + 
Sbjct: 215 AQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQETIQSELM 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
           ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E D  W  
Sbjct: 265 TIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAE 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                    +   ++  V +I + +  +  +     + + + +     +  GE +A  AK
Sbjct: 325 KITAEGHS-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 REMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE 
Sbjct: 504 IMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 564 KVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 620


>gi|307546061|ref|YP_003898540.1| RNA polymerase sigma factor RpoD [Halomonas elongata DSM 2581]
 gi|307218085|emb|CBV43355.1| RNA polymerase sigma factor RpoD [Halomonas elongata DSM 2581]
          Length = 615

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 368/657 (56%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   +++G++T  E+N  LP D    +Q+ED + M+++MGINVV+    ED
Sbjct: 6   QQQSRLKELIARGKEQGFLTYAEVNDHLPEDIADPDQVEDIIGMINDMGINVVEEAPDED 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D     S+A  +   L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  TLMMADQSTDESAAEEAVAALAAVESDV-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M++L   P    +++   D   D     R + DL +        GF    EG
Sbjct: 125 IEEGTREVMSALAYLPGAVDSILEAYDATQDEEAPGR-LSDLFS--------GFIDPDEG 175

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                  D  + +      +  G+       ++++ S     PE A      + E  + +
Sbjct: 176 IPGVAEADVPEPEPEQSAAD--GEASDEDDDAEEEESGGGPDPEEARARFEQIREQNEAA 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              +                                    +  + + + +    +L +L 
Sbjct: 234 RRAIE-----------------------------------EHGRGAKQAQDELARLAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV 384
             + L     + LV Q+    +++   E  +++L  +   + R  F++   G E    W+
Sbjct: 259 SPIKLVPKHFERLVGQVRISVEQVRAQEKAIMQLCVKKAKVPRKTFIKSFPGNESRQDWL 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                    ++ + +A     I + + +I        + +++ + +   +  GE +A  A
Sbjct: 319 DSFMAE-NAKYADRLAPLKGDIQRAQRKIAFEEEMVALVVTDLKEVNRKLSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ ++L MP + VR
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGERLEMPEDKVR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD+D SHLGDFIED   V P+DSA    L E T  VL  LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMVLPIDSATGEGLIEATRNVLGGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEPLRSFLD 614


>gi|254480921|ref|ZP_05094167.1| Sigma-70, non-essential region family [marine gamma proteobacterium
           HTCC2148]
 gi|214038716|gb|EEB79377.1| Sigma-70, non-essential region family [marine gamma proteobacterium
           HTCC2148]
          Length = 605

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 266/657 (40%), Positives = 371/657 (56%), Gaps = 61/657 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLED 85
                K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D ++
Sbjct: 7   QQSRLKALIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDMGIQVFEQAPDADE 66

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +E        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 67  LLMTEGDRSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   ++++L   P   ++++   + +      L +I+            G+    + 
Sbjct: 127 IEEGIRELLSALALYPGAVKSILDEYELVTKEERKLADIM-----------VGYLDPAQH 175

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                    + + + D             K   D+  + D+ P+  E  +R         
Sbjct: 176 VPTAAELAEAAQAKAD-------------KAGTDEEEETDNGPDPVEAKKR--------- 213

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                +   Y +   +        +  ++        EKL +L 
Sbjct: 214 ------------------FTALKRQYNKTEKV------IAEKGRTDAAAIKEMEKLGELF 249

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L     D + +   +I   +   E E++R+A    G+ R  F+   QG E D  W+
Sbjct: 250 KFFKLTPRVFDPISDTPRNILAAVRDQEREIMRIAIKVCGMPRKDFISTFQGSESDLKWL 309

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           S      + ++   +  E + I +++  I++I  + G+ ISE + I   +  GE  A  A
Sbjct: 310 SRQAR--KKDYGPKLNAEKEIIHRLQRRIQAIEGQCGLQISEIKEINRRMSMGEARARRA 367

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 368 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 427

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VR
Sbjct: 428 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKVR 487

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA    L+E T  VLA LT RE
Sbjct: 488 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTISSPVDSATGQGLQEATKDVLAGLTARE 547

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 548 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 604


>gi|330821204|ref|YP_004350066.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
 gi|327373199|gb|AEA64554.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
          Length = 805

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 253/663 (38%), Positives = 368/663 (55%), Gaps = 45/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL + RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 183 LEERRVKLRALIKLGKDRGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 242

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 243 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 302

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 303 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRIDELVDGLNDPNAEDADGFN 362

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                 + Q  ED  +  E ++ ++ +G  ++ A  ++ +                    
Sbjct: 363 AKEAEEAEQADEDEEEAAEDEEEEDDDGAAQATANAAQLEA------------------- 403

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 404 ---------------LKRTSLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 442

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 443 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFISRFPGSET 502

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   V +I + +  +  +     + + + +     +  GE 
Sbjct: 503 DLAWAEKIATESHS-YSAILQRNVPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 561

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 562 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 621

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 622 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 681

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 682 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDS 741

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 742 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 801

Query: 680 LDG 682
           L+G
Sbjct: 802 LEG 804


>gi|330448778|ref|ZP_08312425.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492969|dbj|GAA06922.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 616

 Score =  446 bits (1148), Expect = e-123,   Method: Composition-based stats.
 Identities = 270/655 (41%), Positives = 372/655 (56%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +   ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTEDNADEDAIEAAAQALSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      + +II        E+         G  
Sbjct: 125 DGINQVQCSVAEYPSAIAHLLEQFDKVEADELRITDIISGFVDPNEEATAAPTATHIGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + +   ++K+ +D  + + D E     S D        PE A      L    D  A 
Sbjct: 185 LSETDLEDEDKDLEDDDDEDADSEDEDDGSID--------PELAREKFLELRNAYDKMAL 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                     + +   + ++  E+L ++   
Sbjct: 237 AIDT-----------------------------------NGRQDKQTEIAVEELSEVFKQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  L D   ++  NE  ++R+      + +  F+    G E +  W+  
Sbjct: 262 FRLIPKQFDRLVSSLRDAMDKVRTNERLIMRMCVDNSKMPKKTFVTLFAGNEANQDWIDE 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A +  +  +   +    + + +   +++ +  ETG+SI   + I   +  GE +A  AKK
Sbjct: 322 ALNSGKP-YAERLKTYEEDLRRSAIKLRMLEEETGLSIERIKDISRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATATNLRAATNDVLAGLTPREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 615


>gi|89075585|ref|ZP_01161990.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048725|gb|EAR54297.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 616

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 271/655 (41%), Positives = 371/655 (56%), Gaps = 46/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI VV+     DE 
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +      +   ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMTEDNADEDAIEAAAQALSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D++      L +II        E+         G  
Sbjct: 125 DGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPNEEATAAPTATHIGSE 184

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             + +   ++K+ +D + +E   E     S D        PE A      L    D  A 
Sbjct: 185 LSESDLEDEDKDLEDDENSEDSDEEEDDGSID--------PELAREKFLELRNAYDKMAL 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                     + + +   ++  E+L ++   
Sbjct: 237 AIDT-----------------------------------NGRQNATTEIAVEELSEVFKQ 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  L D   ++  NE  ++R+      + +  F+    G E    W+  
Sbjct: 262 FRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFVSLFAGNESKQDWIDE 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A +  +  +   +    + + +   +++ +  ETG+SI   + I   +  GE +A  AKK
Sbjct: 322 ALNSGKP-YAERLKVYEEDLRRASIKLRMLEEETGLSIERIKDISRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     P+D+A   NLR  T  VLA LTPRE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATATNLRAATNDVLAGLTPREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLRSFLD 615


>gi|163802687|ref|ZP_02196578.1| RNA polymerase sigma factor RpoD [Vibrio sp. AND4]
 gi|159173575|gb|EDP58395.1| RNA polymerase sigma factor RpoD [Vibrio sp. AND4]
          Length = 620

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 264/656 (40%), Positives = 371/656 (56%), Gaps = 44/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +S+ E P T   ++   D++      L ++I        +          G 
Sbjct: 126 EEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTATHIGS 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +   ++ E  D  E   D    ++       ++                      
Sbjct: 186 ELTETQLKEEDSEDVDDDEESDDDSDDSEEDAGIDPEL---------------------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           AL++ +++    ++LQ   +   +    S K  +  E ++ +  
Sbjct: 224 ----------------ALEKFSQLRNTYQNLQ---LAINEHGYESPKATLANELMLDVFR 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  +++    YG + +  F+    G E    W+ 
Sbjct: 265 EFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSTVEYGKMPKKSFIALFTGNESSEAWLD 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++K I  ET +++   + I   +  GE +A  AK
Sbjct: 325 EILA-SDKPYAEKIKRSEEDIRRSITKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 504 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKMATKDVLAGLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 619


>gi|84622216|ref|YP_449588.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188574947|ref|YP_001911876.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|84366156|dbj|BAE67314.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188519399|gb|ACD57344.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 624

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 379/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +     +  +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDALDEDDDEDGDDAAAEEEVGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   +  +A  Y + + +        K+          +E + 
Sbjct: 227 -----------------VATRMQNLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +   + +++ E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|297539657|ref|YP_003675426.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera sp. 301]
 gi|297259004|gb|ADI30849.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera sp. 301]
          Length = 645

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 257/688 (37%), Positives = 388/688 (56%), Gaps = 54/688 (7%)

Query: 1   MTIGKKRNRDSDSEHED----SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPD 56
           M   KK ++ ++    +           +      K +I L ++RGY+T  E+N  LP D
Sbjct: 1   MARPKKSDQLAEKNKMEFVSPELQEASAEERRSRLKSLIVLGKERGYLTYAEINDHLPDD 60

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED--SLDLASSASNSSVFLQKRKDSAD 114
             +SEQ++  + M+++MGI V +     +     D         A   +       DS  
Sbjct: 61  VQNSEQIDGIIGMINDMGIQVYEEAPDAEVLLMSDAPPAVTDEDAVEEAEQALATVDSDF 120

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG+++LL+RE EI IA+RIE G   M+ ++   P T  AL+   D++
Sbjct: 121 GRTTDPVRMYMREMGTVDLLTRESEIEIARRIEDGLKHMVQAIAACPTTIAALLALVDKV 180

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            +    + +++D           G      G       +++++++  D    EG+ E  A
Sbjct: 181 ENDELSVDDLVD-----------GLIDSDVGAVADVVIEAAEDEDEVDEDIDEGEDEDGA 229

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           K +      +                              +L+ +V+     +    +++
Sbjct: 230 KAAAISAEAL-----------------------------AKLKEEVVNRFTVVRAANKKM 260

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             +               + + L  +++  + +   +  +++ L +Q+ D+ + I  +E 
Sbjct: 261 TEI------LPLRGSQDPQYQALLSEILVELTAFRFSPKQVEGLCDQVRDLVETIRSHER 314

Query: 355 ELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           ++L    +  G+ R  F++   G E +  W++      +   +  +     SIL  +  +
Sbjct: 315 KVLDFCVEKSGMPRLHFIKSFPGNESNLGWLAEELKADKPYIEKLIRYN-HSILDQQQRL 373

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +    GI I E + I   +  GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 374 IDLEKNVGIPIKELKEINKQMTTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDL 433

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ 
Sbjct: 434 IQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 493

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R +R++  +   EP P  +A+K+ MP + +RK+LKI+KEPIS+ETPIGD++ SHLGDFIE
Sbjct: 494 RISRQILQETGVEPDPALLAEKMEMPEDKIRKILKISKEPISMETPIGDDEDSHLGDFIE 553

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D   ++P+D+AI A+LR+ T+ VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTR
Sbjct: 554 DGQTLAPVDAAIYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTR 613

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKL+HP+RS++LRSFL+
Sbjct: 614 ERIRQIEAKALRKLRHPTRSERLRSFLE 641


>gi|28198503|ref|NP_778817.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa Temecula1]
 gi|182681181|ref|YP_001829341.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa M23]
 gi|28056587|gb|AAO28466.1| RNA polymerase sigma-70 factor [Xylella fastidiosa Temecula1]
 gi|182631291|gb|ACB92067.1| RNA polymerase, sigma 70 subunit, RpoD [Xylella fastidiosa M23]
          Length = 623

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 388/660 (58%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + 
Sbjct: 13  QQSDIKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAET 72

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   EG+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 73  LLLNEGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAI 132

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L E++                 
Sbjct: 133 AKRIEEGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVVVGF-------------- 178

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             +D+ E +  + S+  V+ +   +VD   +++  ++ +     
Sbjct: 179 ------------------NDLIEEDNSVTSSVDVTDESIVEVDEEDDDSVGNDED----- 215

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                  + M      +V   ++ ++  Y + + L        K          ++E + 
Sbjct: 216 -------APMIGPDPAEVASRIESLSTEYAKFKKLY------AKHGPEHKAVIKVREDVA 262

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +  L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + + 
Sbjct: 263 AIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNL 322

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I   +     +     +++++ + I  M+  GE +A
Sbjct: 323 EWVEDAIKR-KQKWSSALRDIKDQITAEQQASIDLEKVNSLTLADIKEINRMMVYGEAKA 381

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA 
Sbjct: 382 SKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYAT 441

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 442 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 501

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 502 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLT 561

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 562 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 621


>gi|251793982|ref|YP_003008714.1| RNA polymerase sigma factor RpoD [Aggregatibacter aphrophilus
           NJ8700]
 gi|247535381|gb|ACS98627.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
           aphrophilus NJ8700]
          Length = 623

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 377/655 (57%), Gaps = 39/655 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++        ++  L   + +    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLNETITDEDVVEEATQVLSSVE-AELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++   P     LI   + + +G   L ++I            GF        
Sbjct: 125 EGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLI-----------TGFVDPNVLSE 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                        ++ +E  GD      +  +   + D    ++++ + +   D + +  
Sbjct: 174 SDNTHLDENFDSDEENEEDVGD----NGLDDESEDEEDGEENSSDDGDSDNSIDPEVARE 229

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             +A+++Q                      Q    + +K  ++S K K   + L  +   
Sbjct: 230 KFTALKEQH---------------------QKTLASIEKHGRTSKKTKDEIQALSDIFTQ 268

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D+LV  + D+ KR+   E  + R+      + +  F +   G E    W+  
Sbjct: 269 FRLVPKQFDILVLSMRDMMKRVRAQERFIQRIVVDNAKMPKSGFQKSFIGHETTDTWLIK 328

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A    +   +  V  E D + +    +  I  +T ++I + R I   + +GE +A  AKK
Sbjct: 329 ALGADKAWSEKLVQYEND-LRQAIANLVQIEQDTHLTIQQIREICERIAQGELKARRAKK 387

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 388 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 447

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 448 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 507

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LT RE +
Sbjct: 508 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKAATHEVLEGLTSREAK 567

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|71899844|ref|ZP_00681993.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
 gi|71730361|gb|EAO32443.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Xylella fastidiosa Ann-1]
          Length = 623

 Score =  446 bits (1147), Expect = e-123,   Method: Composition-based stats.
 Identities = 272/660 (41%), Positives = 387/660 (58%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + 
Sbjct: 13  QQSDIKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAET 72

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   EG+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 73  LLLNEGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAI 132

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L E++                 
Sbjct: 133 AKRIEEGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVVVGF-------------- 178

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             +D+ E +  + SA  V+ +   +VD   +++  ++ +     
Sbjct: 179 ------------------NDLIEEDNSVTSAVDVTDESIVEVDEEDDDSVGNDED----- 215

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                  + M      +V   ++ ++  Y + + L        K          ++E + 
Sbjct: 216 -------APMIGPDPAEVASRIESLSTEYAKFKKLY------AKHGPEHKAVIKVREDVA 262

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +  L+    DLLV+QL +    +  +E ++L LA +   + R  F+   +  + + 
Sbjct: 263 AIFVTFKLSLPLTDLLVQQLQNTVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNL 322

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I   +     +     +++++ + I  M+  GE +A
Sbjct: 323 EWVEDAIKR-KQKWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMMVYGEAKA 381

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA 
Sbjct: 382 SKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYAT 441

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 442 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 501

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 502 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLT 561

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 562 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 621


>gi|88704608|ref|ZP_01102321.1| RNA polymerase sigma factor rpoD [Congregibacter litoralis KT71]
 gi|88700929|gb|EAQ98035.1| RNA polymerase sigma factor rpoD [Congregibacter litoralis KT71]
          Length = 607

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 261/658 (39%), Positives = 363/658 (55%), Gaps = 61/658 (9%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLE 84
                 K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D +
Sbjct: 6   TQQSRLKSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDAD 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D   ++        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DLILTDGDGSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAK 125

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +MA+L   P   ++++     +      L +I+                   
Sbjct: 126 RIEEGIRELMAALAFYPGAVKSVLDDYALVAKEEKKLADIL------------------- 166

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                    +        + E +    +     +DD +     P  A+     L      
Sbjct: 167 ---VGYLNPADHVPSAQQIAEQQAAKAAGNTDDEDDNAPTGPDPVEAKKRFTALK----- 218

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                                      R+    +       + +K+S+K     EKL ++
Sbjct: 219 ---------------------------RQFNKTEKVLAEKGRQDKASIKE---MEKLGEI 248

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                      D L ++       +   E E++R+  +   + R  F+   QG E +  W
Sbjct: 249 FKFFKFTPKVFDPLNDEARSALAGVREQEREIMRIVVRRCQMPRKEFITSFQGNESNAKW 308

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +S      + ++   +    + I + + +I  I   TG++++E + I   +  GE  A  
Sbjct: 309 LSRHAR--KKDYGPKLNAHKEEIHRAQRQIGQIEEATGLTVTEIKEINRRMSMGEARARR 366

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 367 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + V
Sbjct: 427 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKV 486

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED+   SP+DSA    L+E T  VL  LT R
Sbjct: 487 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTIHSPIDSATGQGLQEATKDVLGGLTAR 546

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 547 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 604


>gi|312963434|ref|ZP_07777916.1| sigma-70 [Pseudomonas fluorescens WH6]
 gi|311282240|gb|EFQ60839.1| sigma-70 [Pseudomonas fluorescens WH6]
          Length = 616

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 379/657 (57%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E       +    + + D + A   + D+      P             D   +
Sbjct: 174 IAPPAAEVPPPVDAKAAKADDDSDDDEAEASTDDEEEAESGP-------------DPIIA 220

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A    A+ DQ+            E+ R+            K  +S+ +       L +L 
Sbjct: 221 AQRFGAVSDQM------------EITRKALK---------KHGRSNKQAIAELLALAELF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESWS 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALENETGLTIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|117924113|ref|YP_864730.1| RpoD family RNA polymerase sigma factor [Magnetococcus sp. MC-1]
 gi|117607869|gb|ABK43324.1| RNA polymerase, sigma 70 subunit, RpoD [Magnetococcus sp. MC-1]
          Length = 683

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 296/699 (42%), Positives = 417/699 (59%), Gaps = 50/699 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D   ++  D   +  KK+I   ++RG++T +E+N  LP D  S+E MED V +L NMGI+
Sbjct: 2   DGKSNMAEDTKREDMKKLIARGKERGFLTYDEVNDVLPNDMTSAEDMEDVVGLLDNMGID 61

Query: 77  VVDGDDLE---------DEEGSEDSLDLASSASNSSVFLQKR-----------------K 110
           ++D +  E            G+ DSLD         +                      +
Sbjct: 62  LIDDEREEGARPKSRPAAGIGNLDSLDDDVDEEILGISDFDSEDDESDDEDGLRSDGAIE 121

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D     TDDPVRMYLREMGS+ELL+REGEIAIAKRIE G   ++A++C++P TF  +++ 
Sbjct: 122 DIDLGKTDDPVRMYLREMGSVELLTREGEIAIAKRIEEGCNEVIATICDAPSTFNEVMML 181

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
            + L  G   LRE++D+       S+    +  +       E   ++ + DD+      +
Sbjct: 182 AERLRAGEISLREVLDISTPQDEGSEDEDLNNDDDEVEASTESDDEDVDEDDIVNGPVKV 241

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
            +            + PP   E +     E +++          +L    +   DEI   
Sbjct: 242 RNPVP---------EPPPVKTEEEIAAQREADNEQFR-------ELYEATLAIFDEITRE 285

Query: 291 YRELRSLQDNAVNGQKD-------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
              L  L+D   +  ++       ++   + +  K ++V++V  +  +  + D LVE++ 
Sbjct: 286 NEVLVELRDPLNDALQNDPEGETCKRLLAEYQAHKARIVEIVAGIKFSPKQRDRLVERIK 345

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
                +   E +++ +     +K+  F+E+  G E D  W+          WK     + 
Sbjct: 346 SYVAAVRAQEQKIITIVTQCNVKKPEFIEQFTGNESDTTWIQNFAKTRSAPWKRLYE-QS 404

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           + I + +  I+SI  E G ++++ +     +  GE  A+ AKKEMVEANLRLVIS+AKKY
Sbjct: 405 ELICEAQLVIRSIEEEAGQTVADLKKCNKKLMDGERRANQAKKEMVEANLRLVISIAKKY 464

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF+W  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 465 TNRGLQFLDLIQEGNIGLMKAVDKFEWRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 524

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+VRT+R+M  ++ REPTPEEIA++++M +E VRKVLKI KEPISLETP+GDE
Sbjct: 525 HMIETINKLVRTSRQMVQEMGREPTPEEIAERMSMSLEKVRKVLKIAKEPISLETPVGDE 584

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFIEDK+ +SP + AI +NLR+TT RVL +LT REE VLRMRFGIG+ TDHTLE
Sbjct: 585 EDSHLGDFIEDKSMLSPSEHAIMSNLRDTTGRVLQTLTSREEHVLRMRFGIGLPTDHTLE 644

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EVGKQF VTRERIRQIEAKA+RKL+HP+RS+KLRSFL+ 
Sbjct: 645 EVGKQFNVTRERIRQIEAKALRKLRHPTRSRKLRSFLES 683


>gi|156563504|dbj|BAF76047.1| Sigma70 [Ralstonia solanacearum]
          Length = 755

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 250/674 (37%), Positives = 371/674 (55%), Gaps = 46/674 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 123 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 182

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 183 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 242

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 243 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 300

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +                ++ + E   ++  E +    S+A  ++           
Sbjct: 301 LIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAASARQLE-------- 352

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                    +L+   +     I + + ++R   +      K+  
Sbjct: 353 -------------------------ELKQAALAKFAIIGDQFEKMRRAFE------KEGY 381

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 382 KSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 441

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 442 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQARVVLPLAELK 500

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 501 DVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 560

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 561 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 620

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 621 PATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 680

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SL PRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+
Sbjct: 681 MRGVVKDVLDSLAPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 740

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS KL+SFL+G
Sbjct: 741 HPSRSDKLKSFLEG 754


>gi|253997427|ref|YP_003049491.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera mobilis JLW8]
 gi|253984106|gb|ACT48964.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera mobilis JLW8]
          Length = 646

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 263/689 (38%), Positives = 390/689 (56%), Gaps = 55/689 (7%)

Query: 1   MTIGKKRNRDSDSEHED-----SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPP 55
           M   KK ++ ++   ED         +  +      K +I L ++RGY+T  E+N  LP 
Sbjct: 1   MARPKKSDQQAEKNAEDYVHTEQLQEVSAEERRIRLKSLIVLGKERGYLTYAEINDHLPD 60

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED--SLDLASSASNSSVFLQKRKDSA 113
           D   SEQ++  + M+++MGI V +     +     D         A   +       DS 
Sbjct: 61  DVQGSEQIDGIIGMINDMGIQVYEETPDAEALLMSDAPPAVTDDDAVEEAEQALATVDSE 120

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG+++LL+RE EI IA+RIE G   M+ ++   P T  AL+   D+
Sbjct: 121 FGRTTDPVRMYMREMGTVDLLTRESEIEIARRIEDGLKHMVQAIAACPTTIAALLEMVDK 180

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +      + +++D           G      G      ED+  ++E +  ++ +   E  
Sbjct: 181 VERDELSVDDLVD-----------GLIDSDIGLDDAMTEDTQDDEEPEVDEDEDEGDEDG 229

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           AK +      +                              +L+ +++   + +   +++
Sbjct: 230 AKAAAISAEAL-----------------------------AKLKEELLKRFEVVRAAHQK 260

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           +  +        K  +  V   +L E LV+L      +  +++ L +Q+  + + +  +E
Sbjct: 261 MTVI-----LPVKGSQDPVYLALLSEILVELTA-FRFSPKQVETLCDQVRGLVETVRGHE 314

Query: 354 GELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
            ++L    +  G+ R  F++   G E +  W+          +   +A    SIL  +  
Sbjct: 315 RKVLDFCVEKAGMPRPYFIKSFPGNESNLAWLDDELKLDNP-YNEKLARFNHSILDQQQR 373

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I  +  + GIS  E + I   +  GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLD
Sbjct: 374 IIDLETKVGISAKELKEINKQMTTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLD 433

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+
Sbjct: 434 LIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 493

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R +R++  +   EP P  +A+K+ MP + +RK+LKI+KEPIS+ETPIGD++ SHLGDFI
Sbjct: 494 NRISRQILQETGIEPDPALLAEKMEMPEDKIRKILKISKEPISMETPIGDDEDSHLGDFI 553

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED   ++P+D+A+ A+LR+ T+ VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VT
Sbjct: 554 EDSTTLAPVDAAVYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVT 613

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKL+HP+RS++LRSFL+
Sbjct: 614 RERIRQIEAKALRKLRHPTRSERLRSFLE 642


>gi|92113104|ref|YP_573032.1| sigma 70 (RpoD) [Chromohalobacter salexigens DSM 3043]
 gi|91796194|gb|ABE58333.1| RNA polymerase, sigma 70 subunit, RpoD [Chromohalobacter salexigens
           DSM 3043]
          Length = 614

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 261/658 (39%), Positives = 363/658 (55%), Gaps = 49/658 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++G++T  E+N  LP D    +Q+ED +AM+++MGI+VV+    E
Sbjct: 4   NTQQSRLKELIAQGKEQGFLTYAEVNDHLPEDIADPDQVEDIIAMINDMGISVVEEAPDE 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D     D     S+A  +   L   +      T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 64  DTLMMSDQSADESAAEEAVAALAAVESDV-GRTTDPVRMYMREMGTVELLTREGEIEIAK 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+SL   P    +++   D   D     R        I P+          
Sbjct: 123 RIEEGTREVMSSLAYLPGAVDSILSAYDATQDEEAPGRLSDLFSGFIDPD---------- 172

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   ++   +   +    +GD+      ++++ +     PE A      + E  + 
Sbjct: 173 -EGIPGVAEAEVPEPEPEPSAADGDVSEDDDEAEEEETGGGPDPEEARARFEQIREQNER 231

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   +                                    +    S +    + +L +L
Sbjct: 232 AKAAIE-----------------------------------EHGLGSKEASAEQARLAEL 256

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW 383
              + L     + LV Q+    ++I   E  ++++  +   + R  F+    G E D  W
Sbjct: 257 FSPIKLVPKHFERLVGQVRISVEQIRGQEKAIMQIFVKQAKVPRKTFIGSFPGAESDLEW 316

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +          + + +      I + + +I        + +S  + +   +  GE +A  
Sbjct: 317 LDRFMAKHTK-FADRLEPFRADIQRAQRKIGFEEEMVLLPVSHIKEVNRRLSIGEAKARR 375

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ ++L MP + V
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGERLEMPEDKV 495

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD+D SHLGDFIED   + P+DSA    L E T  VL  LT R
Sbjct: 496 RKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDSATGEGLIEATRNVLGGLTAR 555

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR+FLD
Sbjct: 556 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEPLRTFLD 613


>gi|58580221|ref|YP_199237.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58424815|gb|AAW73852.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 629

 Score =  446 bits (1146), Expect = e-123,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 379/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 13  QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 72

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 73  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 132

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 133 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 181

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +     +  +     + P+  E          
Sbjct: 182 IEEADAAAAALAAAGPVAVDEDALDEDDDEDGDDAAAEEEVGPTGPDPVE---------- 231

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   +  +A  Y + + +        K+          +E + 
Sbjct: 232 -----------------VATRMQNLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 268

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 269 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 328

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +   + +++ E + I   +  GE +A
Sbjct: 329 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEISRAMAYGEAKA 387

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 388 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 447

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 448 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 507

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 508 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 567

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 568 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 627


>gi|119474865|ref|ZP_01615218.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451068|gb|EAW32301.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 600

 Score =  445 bits (1145), Expect = e-123,   Method: Composition-based stats.
 Identities = 265/658 (40%), Positives = 365/658 (55%), Gaps = 64/658 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K +I   +++GY+T  E+N  LP D    +Q+ED + M++++GI V +     
Sbjct: 5   EQQQSRLKTLIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDLGIQVFETAPDA 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE    +       A+  +       ++    T DPVRMY+REMG++ELL+REGEIAIAK
Sbjct: 65  DEILLTEEDSTDDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +MA++   P   Q +I   D++      L +I+            G+ + T+
Sbjct: 125 RIEEGIRDIMAAVAYYPGAVQDVIDDYDKVATEERRLADIL-----------VGYLNPTD 173

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 ++ ++     DD                DD +     PE A+     L +  + 
Sbjct: 174 VVPPAAQQAAAAVSTDDD----------------DDETPSGPDPEEAKKRFTALRKQHNK 217

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               +                                    K  + S +     +KL ++
Sbjct: 218 LDKAIE-----------------------------------KHGRYSKESAKELQKLGEV 242

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELDPHW 383
                L     + L  ++      I  NE  ++    +   + R  F++  QG+E +  W
Sbjct: 243 FKFFKLTPKVFEPLSIRVRSKLNVIRSNERLIMNTCVRQAKMTRRDFVKSFQGQETNLDW 302

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +       E +    +    + IL+ + +I  I  +TG++I + + I   +  GE  A  
Sbjct: 303 IEQQIKAHE-DVAPVLEANKEEILRAQRKIAQIETQTGLTILDIKEINRRMSIGEARARR 361

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 362 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 421

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + V
Sbjct: 422 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKV 481

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA    L+E T  VL  LT R
Sbjct: 482 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIAQPVDSATGQGLQEATKDVLGGLTAR 541

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 542 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFLD 599


>gi|32130003|sp|Q87DT7|RPOD_XYLFT RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|307579626|gb|ADN63595.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 618

 Score =  445 bits (1145), Expect = e-123,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 388/660 (58%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + 
Sbjct: 8   QQSDIKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   EG+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNEGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L E++                 
Sbjct: 128 AKRIEEGLSEVQAALGAFPLSTELLLSEYELHKEGKRRLTEVVVGF-------------- 173

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             +D+ E +  + S+  V+ +   +VD   +++  ++ +     
Sbjct: 174 ------------------NDLIEEDNSVTSSVDVTDESIVEVDEEDDDSVGNDED----- 210

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                  + M      +V   ++ ++  Y + + L        K          ++E + 
Sbjct: 211 -------APMIGPDPAEVASRIESLSTEYAKFKKLY------AKHGPEHKAVIKVREDVA 257

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +  L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + + 
Sbjct: 258 AIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNL 317

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I   +     +     +++++ + I  M+  GE +A
Sbjct: 318 EWVEDAIKR-KQKWSSALRDIKDQITAEQQASIDLEKVNSLTLADIKEINRMMVYGEAKA 376

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA 
Sbjct: 377 SKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYAT 436

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 437 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 496

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 497 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLT 556

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 557 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|241764884|ref|ZP_04762887.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax delafieldii 2AN]
 gi|241365587|gb|EER60323.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax delafieldii 2AN]
          Length = 788

 Score =  445 bits (1145), Expect = e-123,   Method: Composition-based stats.
 Identities = 254/660 (38%), Positives = 367/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IKL + RGY+T  E++  LP   V +E +E  +  L+++G+ V +     + 
Sbjct: 183 RRSRLKTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLNDLGVAVYEQTPDAEA 242

Query: 87  EGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
               D+         A  ++       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 243 LIITDNAPSGATEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 302

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  
Sbjct: 303 KRIEGGLMAMMEAISASPATIAEILNMGEEIREGKVVISTIVD-----------GFSNPN 351

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 352 EADDYVAEEDFDEFDEADDDDGKGG----------------------------------- 376

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D++ E++ ++  + D    G      +      +  L +
Sbjct: 377 --SKALTKKLEELKKQALERFDKLRELFEKVHKVYDKEGYG------TPAYVKAQTALSE 428

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 429 ELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLK 488

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +A  +  I  ++ ++  +     + ++E + I   + +GE  + 
Sbjct: 489 WVEKQAAAGKP-WSAVMARNIPPIQDLQQKLADLQSRVVVPLAELKGINKRMNEGEATSR 547

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 548 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 607

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 608 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 667

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+++A+QA LR+    +L  LTP
Sbjct: 668 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTP 727

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 728 REAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 787


>gi|325913856|ref|ZP_08176215.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325539931|gb|EGD11568.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 624

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 378/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +        +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 227 -----------------VATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDIA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|148979373|ref|ZP_01815479.1| RNA polymerase sigma factor RpoD [Vibrionales bacterium SWAT-3]
 gi|145961809|gb|EDK27102.1| RNA polymerase sigma factor RpoD [Vibrionales bacterium SWAT-3]
          Length = 614

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 264/656 (40%), Positives = 372/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++D  ++   A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P T   ++   D +      L ++I+    + P+         +G 
Sbjct: 126 EDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLIN--GFVDPDD--------DGT 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +         E    D+ + + +     +  +++ + +D                     
Sbjct: 176 AAPTATHIGSELAETDLDDEDAEDVDDDEEEEEEDTGIDP-------------------- 215

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +     +   Y      Q+  +   +    S K  +    +  +  
Sbjct: 216 -----------ELALEKFTALRTSY------QNRQLAINEYGHESPKAMLATTMMQDVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L +   R+   E  ++R    YG + +  F+    G E    W+ 
Sbjct: 259 EFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLD 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++  I  ET +++   + I   +  GE +A  AK
Sbjct: 319 EVLA-SDKPYAEKIKRHENDIRRSIQKLDMIEKETSLTVQSIKDISRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LTPRE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 613


>gi|59712861|ref|YP_205637.1| RNA polymerase sigma factor RpoD [Vibrio fischeri ES114]
 gi|59480962|gb|AAW86749.1| RNA polymerase, sigma-70 (sigma-D) factor [Vibrio fischeri ES114]
          Length = 613

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 269/656 (41%), Positives = 376/656 (57%), Gaps = 51/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDADDM 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++D       A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  SLNDDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D++      L +II            GF    +  
Sbjct: 126 EEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDII-----------SGFVDPNDDG 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           S          +  +   + E D ++  +  +++ + +D                     
Sbjct: 175 SSAPTATHIGSELSESELDDEDDEDAEGETEEEEDAGIDPE------------------- 215

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           AL++  E+     ++Q       +D+    K +    +L  +  
Sbjct: 216 ---------------LALEKFTELRTSYHNMQLAFEEFGRDD---AKSREAIGELTDIFR 257

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV+++ D   R+   E  ++R+   YG + +  F+    G E    W +
Sbjct: 258 EFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMPKKSFIALFTGNESSDEWFN 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +    + I +   ++ SI  ETG+ +   + I   +  GE +A  AK
Sbjct: 318 EIMA-SDKPYVERLQRYEEDIRRSIAKLDSIEKETGLPVENIKDISRRMSIGEAKARRAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 377 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +L+  T  VLA LTPRE 
Sbjct: 497 VLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPVDSATSTSLKFATNDVLAGLTPREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612


>gi|86148095|ref|ZP_01066395.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|218708434|ref|YP_002416055.1| RNA polymerase sigma factor RpoD [Vibrio splendidus LGP32]
 gi|85834082|gb|EAQ52240.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|218321453|emb|CAV17405.1| RNA polymerase sigma factor rpoD (Sigma-70) [Vibrio splendidus
           LGP32]
          Length = 614

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 264/656 (40%), Positives = 372/656 (56%), Gaps = 50/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+   D +D 
Sbjct: 6   QSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             ++D  ++   A+ ++       +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P T   ++   D +      L ++I+    + P+         +G 
Sbjct: 126 EDGINTVQLSVAEYPGTIPYILEQFDRVLAEEIRLTDLIN--GFVDPDD--------DGT 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +         E  + D+++ + +     +  +++ + +D                     
Sbjct: 176 AAPTATHIGSELAKTDLEDEDKEEAEDDEEEEEEDTGIDP-------------------- 215

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                         +     +   Y      Q+  +   +    S K  +    +  +  
Sbjct: 216 -----------ELALEKFTALRTSY------QNRQLAINEYGHESPKATLATTMMQDVFK 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV +L     R+   E  ++R    YG + +  F+    G E    W+ 
Sbjct: 259 EFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLD 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   +      I +   ++  I  ET +++   + I   +  GE +A  AK
Sbjct: 319 EVLA-SDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LTPRE 
Sbjct: 498 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREA 557

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 558 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 613


>gi|192362484|ref|YP_001981272.1| transcription initiation factor sigma 70 [Cellvibrio japonicus
           Ueda107]
 gi|190688649|gb|ACE86327.1| transcription initiation factor sigma 70 [Cellvibrio japonicus
           Ueda107]
          Length = 633

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 258/658 (39%), Positives = 363/658 (55%), Gaps = 46/658 (6%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLE 84
                 K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D +
Sbjct: 19  QQQSRIKELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIRVYETAPDAD 78

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               ++        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 79  TLLMTDGDAAADEIAAAEAAAALVAVETETGRTTDPVRMYMREMGTVELLTREGEIVIAK 138

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M +L   P   + ++     +      L ++I            G+    E
Sbjct: 139 RIEEGVRELMHALAYWPGAVEHVLNEYALVAKEERRLADVI-----------IGWLDPIE 187

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                        +  S DD     +   N +  E   +++E  
Sbjct: 188 DIP--------------------------SATSDDDTELPVAANGNKKAGEEEDEDEEGG 221

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           S     A+      +     +E+ + Y +            K    S + +     L  L
Sbjct: 222 SEDEEEAITGVDPEEARARFEELQKQYEKTTK------ALAKHGYGSKQAEKELNALGDL 275

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D +     +   ++  +E  ++ L      ++R  F++   G E +  W
Sbjct: 276 FKFFKLPARQFDPIYNNAREALDKVRKHERRVMDLCTRKAQMQRKTFIKEFPGNETNADW 335

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +       + E  + +   + ++   + ++  I  E+ +S++  + I   +  GE  A  
Sbjct: 336 LPDLLK-GKIEGADKLQVVLPNVQAEQQQLAQIEAESSLSLASIKDINRRMSIGEARARR 394

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 395 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 454

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + V
Sbjct: 455 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGERMDMPEDKV 514

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED   +SP++SA    L E T  VLA LT R
Sbjct: 515 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIISPVESATMEGLMEATREVLAGLTAR 574

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 575 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFLD 632


>gi|153801472|ref|ZP_01956058.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-3]
 gi|124122963|gb|EAY41706.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-3]
          Length = 625

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 368/657 (56%), Gaps = 41/657 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEG 205
           E G   + +++ E P T   ++   D +      L ++I     + P   +      T  
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETEAPTATHI 183

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            S     D + E +     E E + E     S D   +V   PE A      L       
Sbjct: 184 GSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------ 237

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                           Q+  +   +  + S +     + ++ + 
Sbjct: 238 -----------------------------GKFQNLQLAVNEFGRDSHQASEASDLVLDIF 268

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L   + D LVE L     R+   E  +++       + +  F+    G E +  W+
Sbjct: 269 REFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWL 328

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  A
Sbjct: 329 DKVLA-SDKPYAAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRA 387

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 388 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 447

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +R
Sbjct: 448 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIR 507

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE
Sbjct: 508 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPRE 567

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624


>gi|294666254|ref|ZP_06731505.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292603963|gb|EFF47363.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 625

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 273/660 (41%), Positives = 380/660 (57%), Gaps = 49/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+     +  E+       
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAAL 187

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    +D + +++ D+  + +   E A     D                       
Sbjct: 188 AAAGPVAVSDDEAVDEDDDEDGDDDAAEEEAGPTGPDPVE-------------------- 227

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 228 -----------------VATRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 264

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 265 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 324

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 325 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 383

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 384 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 443

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 444 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 503

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 504 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 563

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 564 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623


>gi|21244512|ref|NP_644094.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|32130007|sp|Q8PG33|RPOD_XANAC RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|21110182|gb|AAM38630.1| RNA polymerase sigma-70 factor [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 625

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 380/660 (57%), Gaps = 49/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+     +  E+       
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAAL 187

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    +D + +++ D+  + E   E A     D                       
Sbjct: 188 AAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVE-------------------- 227

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 228 -----------------VATRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 264

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 265 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 324

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 325 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 383

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 384 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 443

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 444 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 503

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 504 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 563

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 564 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623


>gi|326794299|ref|YP_004312119.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas mediterranea
           MMB-1]
 gi|326545063|gb|ADZ90283.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas mediterranea
           MMB-1]
          Length = 610

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 270/660 (40%), Positives = 381/660 (57%), Gaps = 52/660 (7%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + D      K++I   +++GY+T  E+N  LP D    EQ+E+ VAM+++MGI V +   
Sbjct: 1   MSDTQQSRLKELIAKGKEQGYLTFTEVNDHLPDDLSDPEQVEEIVAMINDMGIVVSEYAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ++    E+       A+  +       +     T DPVRMY+REMG++ELL+R GEIAI
Sbjct: 61  DKESLLMEEGDSTDEEAAEEAAAALAAVEGDVARTTDPVRMYMREMGTVELLTRAGEIAI 120

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +MASL   P     L+       +    L +I              F   
Sbjct: 121 AKRIEEGTREVMASLSYFPGAVDVLLDTYARTVEEEGRLSDI--------------FSGF 166

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +G   +   +   E+  ++ ++   + ES+    +++      P E A           
Sbjct: 167 IDGDGEEPIFEEVIEEVVEEEEDESDEEESSDDDEEEETESGPDPEETAR---------- 216

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                                 +EI  ++ E+ +L +N       ++     +  +E+L 
Sbjct: 217 --------------------RFNEIKRIHHEVLALLEN------SDRQDPAVRAKQEELS 250

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
                + L     D L++++     ++   E  +++   +  G+ R  FL+R    E +P
Sbjct: 251 ISFAPIKLVPKLFDDLIDRVRSRMDKVREQERLIMQVCVRKAGMPRTEFLKRFPSNETNP 310

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W+    D     +   +        + + ++++IS +TG+SI++ + I   +  GE  A
Sbjct: 311 GWLQEQIDLSAS-YSAALEENEAEFSRSQRKLRAISKDTGLSIAQLKEINRRISIGETRA 369

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 370 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 429

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A ++ MP +
Sbjct: 430 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAVRMDMPED 489

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A SP+D+A    L+E+TT VLA LT
Sbjct: 490 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPVDTATIEGLKESTTTVLAGLT 549

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 550 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 609


>gi|194290318|ref|YP_002006225.1| RNA polymerase sigma factor rpod [Cupriavidus taiwanensis LMG
           19424]
 gi|193224153|emb|CAQ70162.1| RNA POLYMERASE SIGMA D (SIGMA-70) FACTOR TRANSCRIPTION REGULATOR
           PROTEIN [Cupriavidus taiwanensis LMG 19424]
          Length = 683

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 256/684 (37%), Positives = 379/684 (55%), Gaps = 45/684 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K++    +            +      K +IKL + RGY+T  E+N  LP D V SE 
Sbjct: 40  KAKEKALLKEFASTQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSET 99

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDD 119
           ++  VA L+++GI V +     +     D+   A+S   +    +      DS    T D
Sbjct: 100 IDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTD 159

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +   
Sbjct: 160 PVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAHAERVANDEI 219

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + E +D    I P ++      +   +    ED   + + +  ++ + +  + A  S  
Sbjct: 220 KIDEFVD--GLIDPNAEEAPEAPSAPAAAADDEDLESDDDEEGDEDEDDEGGAGAGASAR 277

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                                             ++L+   +     IAE + ++R   +
Sbjct: 278 QL--------------------------------EELKQNALEKFRVIAEQFDKMRRAFE 305

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 K+   S      +E +   +  +      ++ L + L      +   E  +L +
Sbjct: 306 ------KEGYKSKPYVKAQEAIQAELMGIRFTARNVERLCDTLRGQVDEVRKLERAILNI 359

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                G+ R  F+ R  G E +  W+       +G +   V   V ++ +++ ++  +  
Sbjct: 360 VVDKCGMPRADFVARFPGNETNLEWIHTVVADGKG-YSTIVERNVPAVHELQQKLIDLQA 418

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 419 RVVLPLKELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 478

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 479 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 538

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N +
Sbjct: 539 ILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTL 598

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A+  ++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQ
Sbjct: 599 APAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQ 658

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 659 IEAKALRKLRHPSRSDKLKSFLEG 682


>gi|15640541|ref|NP_230168.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121728933|ref|ZP_01681939.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V52]
 gi|153819447|ref|ZP_01972114.1| RNA polymerase sigma factor RpoD [Vibrio cholerae NCTC 8457]
 gi|153822185|ref|ZP_01974852.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|227080700|ref|YP_002809251.1| RNA polymerase sigma factor RpoD [Vibrio cholerae M66-2]
 gi|254291201|ref|ZP_04961997.1| RNA polymerase sigma factor RpoD [Vibrio cholerae AM-19226]
 gi|254850756|ref|ZP_05240106.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MO10]
 gi|255744255|ref|ZP_05418208.1| RNA polymerase sigma factor RpoD [Vibrio cholera CIRS 101]
 gi|9654945|gb|AAF93687.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121628781|gb|EAX61245.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V52]
 gi|126510018|gb|EAZ72612.1| RNA polymerase sigma factor RpoD [Vibrio cholerae NCTC 8457]
 gi|126520320|gb|EAZ77543.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|150422895|gb|EDN14846.1| RNA polymerase sigma factor RpoD [Vibrio cholerae AM-19226]
 gi|220897845|dbj|BAH11107.1| RNA polymerase sigma factor [Vibrio cholerae O1 biovar El tor]
 gi|227008588|gb|ACP04800.1| RNA polymerase sigma factor RpoD [Vibrio cholerae M66-2]
 gi|254846461|gb|EET24875.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MO10]
 gi|255738195|gb|EET93587.1| RNA polymerase sigma factor RpoD [Vibrio cholera CIRS 101]
          Length = 625

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 368/657 (56%), Gaps = 41/657 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEG 205
           E G   + +++ E P T   ++   D +      L ++I     + P   +      T  
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETEAPTATHI 183

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            S     D + E +     E E + E     S D   +V   PE A      L       
Sbjct: 184 GSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------ 237

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                           Q+  +   +  + S +     + ++ + 
Sbjct: 238 -----------------------------GKFQNLQLAVNEFGRDSHQASEASDLVLDIF 268

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L   + D LVE L     R+   E  +++       + +  F+    G E +  W+
Sbjct: 269 REFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWL 328

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  A
Sbjct: 329 DKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRA 387

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 388 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 447

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +R
Sbjct: 448 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIR 507

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE
Sbjct: 508 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPRE 567

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624


>gi|257092101|ref|YP_003165742.1| RNA polymerase sigma factor RpoD [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257044625|gb|ACV33813.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 648

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 256/663 (38%), Positives = 364/663 (54%), Gaps = 56/663 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K +IKL ++RG++T  E+N  LP D V +EQ+E  +   ++MGI V D     
Sbjct: 34  ETRKMRLKTLIKLGKERGFLTYAEINDHLPDDVVDAEQIESIINTFNDMGIQVYDEAPDA 93

Query: 85  DE----EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +     + +  +    +     +       DS    T DPVRMY+REMGS+ELL+REGEI
Sbjct: 94  ETLLMSDAAPAAGADDADVEEQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEI 153

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   D +      + E+ID    I PE+ G   
Sbjct: 154 EIAKRIEDGLKHMIQAISACPTTIAEILNCADRIARDEMRIDELID--GLIDPETSGSLE 211

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E    +  ++  +  E  +       +                              
Sbjct: 212 ELAEELESEAEDEDEEAAEAVEGAAAAASLL----------------------------- 242

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                         +LR + +  L+ I   Y +  +L        +           +++
Sbjct: 243 --------------RLRTEGLERLERIRAGYTKAHAL------LLRKGSQDKGYLQFQQE 282

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGREL 379
           + + +  +      I+ L + +  + +     E ++ R+      + R  F++   G EL
Sbjct: 283 ISEEMMGMRFTSKTIERLCDSVRAMVEEARACERKIQRICVDTVRMPRVHFIKVFPGNEL 342

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV          +   +     +I + + ++ ++    GI + E + I   +  GE 
Sbjct: 343 NIDWVDVEIAAAGKTYGAVLLRNAPNIKEEQKKLLALQDRIGIPLRELKDINKQMSTGEA 402

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 403 KARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 462

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E  P  +AKK+ MP
Sbjct: 463 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEADPATLAKKMEMP 522

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E +RK+LKI+KEPIS+ETPIGD+D SHLGDFIED   ++P ++A+ ++LR  T  VL +
Sbjct: 523 EEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDHATLAPTEAALYSSLRFITKDVLDT 582

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KLRSF
Sbjct: 583 LTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLRSF 642

Query: 680 LDG 682
           LD 
Sbjct: 643 LDS 645


>gi|289667862|ref|ZP_06488937.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 624

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 379/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +        +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 227 -----------------VATRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +   + +++ E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSMEMEKSSYLTLGEIKEISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|289664793|ref|ZP_06486374.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 624

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 379/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +        +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDEAAEEEAGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 227 -----------------VATRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +   + +++ E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSMEMEKSSYLTLGEIKEISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|304415465|ref|ZP_07396113.1| RNA polymerase sigma 70 (sigma D) subunit [Candidatus Regiella
           insecticola LSR1]
 gi|304282694|gb|EFL91209.1| RNA polymerase sigma 70 (sigma D) subunit [Candidatus Regiella
           insecticola LSR1]
          Length = 612

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 263/656 (40%), Positives = 360/656 (54%), Gaps = 52/656 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I     +  +        +   
Sbjct: 126 EEGINQVQCSVAEYPEAITYLLEQYDRVEAEEVRLSDLITGFVDLNAKENEEDITLSASA 185

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           ++   E S++E    D                DD +     P  A      L E  +++ 
Sbjct: 186 THIGSELSTEELIDSD----------GDTADSDDENNNSIDPLLAREKFSELREQYENTK 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +KD ++ +  K     L  +  
Sbjct: 236 KAI-----------------------------------KKDGRNRLNAKNEILALSNIFK 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  + K+I   E  +++L  +   + + +FL      E D  W  
Sbjct: 261 LFRLVPKQFDYLVNNMRLMMKQIRAQERIIIKLCVEQCKMPKKIFLTLFTRHETDDKWFE 320

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + +   R ++  I  +TG+++ + + I   +  GE +A  AK
Sbjct: 321 EALSANKP-WSEKLKEVAEDVGCCRKKLIQIEEKTGLTVEQIKDINRRMSIGEAKARRAK 379

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 380 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 439

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R AR+M  +               MP + +RK
Sbjct: 440 QAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEXXXXXXX----XXXXMPEDKIRK 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PL SA   +LR  T  VLA LTPRE 
Sbjct: 496 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLGSATSESLRSATHEVLAGLTPREA 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 556 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|285019606|ref|YP_003377317.1| RNA polymerase sigma-70 factor, rpod protein [Xanthomonas
           albilineans GPE PC73]
 gi|283474824|emb|CBA17323.1| probable rna polymerase sigma-70 factor, rpod protein [Xanthomonas
           albilineans]
          Length = 620

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 276/660 (41%), Positives = 380/660 (57%), Gaps = 54/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K++I    ++GY+T  E+N  LP D V  EQ+ED + M++ MGI+V     D + 
Sbjct: 8   QQSDIKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL  + L+   ++  +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E                    +  GD +  A V   +     + P+ AE          
Sbjct: 177 IEEEPAPVVVAEDDSA----AADAAGDEDEDADVDASEEDAGPTGPDPAE---------- 222

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ ++  Y + +          K+         L+  + 
Sbjct: 223 -----------------VARRMEVLSAEYAKFKKAY------AKNGAEHKLVAKLRNDIA 259

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
           ++  +L L     D LV +L D   ++  +E  +L LA     + R  F+   +G + + 
Sbjct: 260 EVFVTLKLPLPLTDALVRKLRDAMAQVKEHERRVLHLATHVARMPRKDFIRSWEGNQTNV 319

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +   T +S++E + I   +  GE +A
Sbjct: 320 VWVDDALKR-KQKWSSALRDVKDQIIAEQEATVGVEQSTYLSLTELKEISRAMAYGEAKA 378

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 379 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKEMDMPED 498

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+++    NL ET   VLA LT
Sbjct: 499 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRDVLAGLT 558

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 618


>gi|224823888|ref|ZP_03696997.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
 gi|224604343|gb|EEG10517.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
          Length = 640

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 260/677 (38%), Positives = 384/677 (56%), Gaps = 50/677 (7%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            +     ++  +S+  +      + +I L ++RGY+T  E+N  LP D   +EQ+E+ V 
Sbjct: 6   ENQKDMQDNEQESMSLEDQRKRLRLLIALGKERGYLTYAEINDHLPEDVSDTEQIENIVT 65

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           M++ +GI V D     D     D+        A   +       DS    T DPVRMY+R
Sbjct: 66  MITGLGIQVYDEAPDADTLLMSDATPAVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMR 125

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELL+REGEI IAKRIE G   M+ ++   P T   ++   + +  G   + E++D
Sbjct: 126 EMGSVELLTREGEIEIAKRIEDGLKHMIEAISACPGTISEVLALLERVEAGDIRVDEVVD 185

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
               I P                                       A    +   ++   
Sbjct: 186 --GFIDPN--------------------------------------AEVEEEVPFAEPVD 205

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
           P E  + +E   + +E+D+    +A  ++L+ + +     +  ++ EL  +       +K
Sbjct: 206 PDEVLDEEEEEEEAEEEDAEAISNANLEELKLQSLEHFALVRALFEELVVV------LRK 259

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGI 365
               S + + L+  + +    +     +I+ L E L      I   E ++         +
Sbjct: 260 QGNQSEEYRQLQGAITESFMKVRFATRQIESLCESLRSRVNEIRSYERDIQDICVTRVRM 319

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  F++   G E++  WV       +  W   +     +I++ + ++  +     +SI 
Sbjct: 320 DRAHFIKYFPGNEINTDWVEDEISSGKP-WSEALTRFKYAIIEKQTKLAELQDRAMLSIK 378

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I   +  GE +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 379 DLKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 438

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   
Sbjct: 439 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGH 498

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP P E+A+++ MP + +RK++KI+KEPIS+ETPIGD+D SHLGDFIED+N ++P D+A+
Sbjct: 499 EPDPAELAERMEMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQNNLAPSDAAM 558

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++L++ T  VL +LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 559 YSSLKDATKEVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 618

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+HP+RS++LRSFLD 
Sbjct: 619 KLRHPTRSERLRSFLDN 635


>gi|166713725|ref|ZP_02244932.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 624

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 380/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +     +  +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDAAAEEEAGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 227 -----------------VATRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +   + +++ E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|21233164|ref|NP_639081.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770104|ref|YP_244866.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|32130006|sp|Q8P4H2|RPOD_XANCP RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|21115012|gb|AAM42993.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575436|gb|AAY50846.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           campestris str. 8004]
          Length = 624

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 378/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +        +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDAVDEDADEDGDDDAAEEEAGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + +          K+          +E + 
Sbjct: 227 -----------------VATRMENLANEYAKFKKAYVKYGAEHKNVA------KAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     ++++E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLAEIKDISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|126666520|ref|ZP_01737498.1| RNA polymerase sigma factor RpoD [Marinobacter sp. ELB17]
 gi|126628908|gb|EAZ99527.1| RNA polymerase sigma factor RpoD [Marinobacter sp. ELB17]
          Length = 616

 Score =  445 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 265/659 (40%), Positives = 374/659 (56%), Gaps = 53/659 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDL 83
           +      K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   D 
Sbjct: 4   NSQKSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDA 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +    ++       +A+  +       +S    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 64  DTLIMTDGDSTADEAATAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +MA++   P T   +I   D + +    L +I+     + P+    F    
Sbjct: 124 KRIEEGIRDVMAAVAHFPGTTGTVIQGYDRIVENEGRLSDIV--AGFLDPDDAEPFMPEE 181

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
              +     + S   +              A  ++++ ++    PE        L E   
Sbjct: 182 PAPAAPASAEESDSDDD-------------ADDAEEEETESGPDPEETRLRFGLLKEK-- 226

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                  A+ D+L                             +  +S  + +    +L  
Sbjct: 227 ------LAVADELLE---------------------------QHGRSDKRTQKALNELGA 253

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           +     L     D LV  +   +  I  NE  ++R+      + R  F++   G E++  
Sbjct: 254 VFAPFKLGNKAFDGLVNVVRSTNDMIRQNERTIMRICIRESKMDRKEFIKSFPGNEINLD 313

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W        +  + + ++  +D I++++  IK++ +E  + + + + I   V  GE +A 
Sbjct: 314 WAEKIA-RSKKPYASAISERLDEIVRLQKRIKNVQLEVALDVVDIKEINRRVSIGEAKAR 372

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 373 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 432

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + 
Sbjct: 433 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDK 492

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED  A+SP+DSA    LRE T  VLA LT 
Sbjct: 493 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSVLAGLTA 552

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR F+D
Sbjct: 553 RESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFID 611


>gi|147674012|ref|YP_001216017.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|146315895|gb|ABQ20434.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|227012343|gb|ACP08553.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
          Length = 621

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 367/656 (55%), Gaps = 43/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P T   ++   D +      L ++I     + P             
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPND---METEAPTA 180

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           ++   E S  +   +D    E + E     S D   +V   PE A      L        
Sbjct: 181 THIGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------- 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          Q+  +   +  + S +     + ++ +  
Sbjct: 234 ----------------------------GKFQNLQLAVNEFGRDSHQASEASDLVLDIFR 265

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LVE L     R+   E  +++       + +  F+    G E +  W+ 
Sbjct: 266 EFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLD 325

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  AK
Sbjct: 326 KVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISHRMSIGEAKARRAK 384

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 385 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 444

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 445 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 504

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 505 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREA 564

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 565 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 620


>gi|262167116|ref|ZP_06034830.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC27]
 gi|262024416|gb|EEY43103.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC27]
          Length = 621

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 367/656 (55%), Gaps = 43/656 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++ E P T   ++   D +      L ++I     + P             
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPND---METEAPTA 180

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           ++   E S  +   +D    E + E     S D   +V   PE A      L        
Sbjct: 181 THIGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------- 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          Q+  +   +  + S +     + ++ +  
Sbjct: 234 ----------------------------GKFQNLQLAVNEFGRDSHQASEASDLVLDIFR 265

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LVE L     R+   E  +++       + +  F+    G E +  W+ 
Sbjct: 266 EFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLD 325

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  AK
Sbjct: 326 KVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAK 384

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 385 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 444

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 445 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRK 504

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE 
Sbjct: 505 VLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREA 564

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 565 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 620


>gi|188993312|ref|YP_001905322.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           campestris str. B100]
 gi|167735072|emb|CAP53284.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           campestris]
          Length = 624

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 378/660 (57%), Gaps = 50/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTELLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++      D    + D +        +     + P+  E          
Sbjct: 177 IEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------- 226

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 227 -----------------VATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 323

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 324 EWVEDALKR-KQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 382

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 383 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 502

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 503 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 562

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 563 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 622


>gi|78049468|ref|YP_365643.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325926137|ref|ZP_08187498.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas perforans
           91-118]
 gi|78037898|emb|CAJ25643.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|325543482|gb|EGD14904.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas perforans
           91-118]
          Length = 625

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 274/660 (41%), Positives = 379/660 (57%), Gaps = 49/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+     +  E+       
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAAL 187

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    +D + +++ D+  + E   E A     D                       
Sbjct: 188 AAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVE-------------------- 227

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + +          K+          +E + 
Sbjct: 228 -----------------VATRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDMA 264

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 265 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 324

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 325 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 383

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 384 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 443

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 444 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 503

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 504 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 563

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 564 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623


>gi|254226294|ref|ZP_04919885.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V51]
 gi|125621156|gb|EAZ49499.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V51]
          Length = 625

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 368/657 (56%), Gaps = 41/657 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEG 205
           E G   + +++ E P T   ++   D +      L ++I     + P   +      T  
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETEAPTATHI 183

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            S     D + E +     E E + E     S D   +V   PE A      L       
Sbjct: 184 GSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------ 237

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                           Q+  +   +  + S +     + ++ + 
Sbjct: 238 -----------------------------GKFQNLQLAVNEFGRESHQASEASDLVLDIF 268

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L   + D LVE L     R+   E  +++       + +  F+    G E +  W+
Sbjct: 269 REFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWL 328

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +  +   V  + + I +   +++ I  ET +S+   + I   +  GE +A  A
Sbjct: 329 DKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRA 387

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 388 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 447

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +R
Sbjct: 448 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIR 507

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE
Sbjct: 508 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPRE 567

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 568 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 624


>gi|4128212|gb|AAD03549.1| principal sigma factor [Burkholderia cepacia]
          Length = 621

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 251/657 (38%), Positives = 371/657 (56%), Gaps = 42/657 (6%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +     +    
Sbjct: 2   KLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLL 61

Query: 90  EDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 62  NDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 121

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   M+ ++   P T   ++   + + +    + E++D                    
Sbjct: 122 EDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------------- 161

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     +    D  +T+G     A+  +++  + +   E  E ++ +       +A
Sbjct: 162 -------GLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAAQATANA 214

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L A    L+   +    +I+E + ++R   +      K+   S      +E +   + 
Sbjct: 215 AQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKSYLKAQETIQTELM 264

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
           ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E D  W  
Sbjct: 265 TIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAE 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                    +   ++  + +I + +  +  +     + + + +     +  GE +A  AK
Sbjct: 325 KIAAEGHS-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAK 383

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 384 REMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 443

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK
Sbjct: 444 QAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRK 503

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE 
Sbjct: 504 IMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREA 563

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 564 KVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 620


>gi|94676896|ref|YP_589041.1| RNA polymerase, sigma 70 factor [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94220046|gb|ABF14205.1| RNA polymerase, sigma 70 factor [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 612

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 268/653 (41%), Positives = 368/653 (56%), Gaps = 52/653 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
            K ++   +++GY+T+ E+N  LP D V S+Q+ED + M+++MGI V++   D +D    
Sbjct: 9   LKLLVTRGKEQGYLTVAEVNDLLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDILLD 68

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E + D    A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  ETNSDTDEDAVEAAAQVLSSVESEIVRTTDPVRMYMREMGTVELLTREGEINIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              +  S+ E P     L+   D +  G   L ++I               +  + H   
Sbjct: 129 MTQVQCSVAEYPEAITYLLKQYDRVELGEARLSDLI--------------INFVDTHMEV 174

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
               S+      ++     D E      ++        PE A      L E  + + + +
Sbjct: 175 PDIISTTSNISTELASDISDDEDEEVNDENTNEDSSIDPEIAHQKFVELREQYEITRNII 234

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                                  +S  K      KL ++     
Sbjct: 235 DTK-----------------------------------GRSHAKAIEEILKLSEIFKQFH 259

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAK 388
           L   + D LV+ +  +  RI   E  +++L      + +  F++   G E    W   A 
Sbjct: 260 LAPKQFDYLVKNMRAVMDRIRLQERLVMKLCVDISKMPKKDFIKLFAGNETSETWFKTAL 319

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              +  W   +     ++     +++ I  ETG+SI + + I   +  GE +A  AKKEM
Sbjct: 320 AMNQP-WSEKLYNVDKNVHNSLQKLRQIEEETGLSIEQIKDINRRMSIGEAKARRAKKEM 378

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 379 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 438

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+A+++ MP + +RKVLK
Sbjct: 439 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERMFMPEDKIRKVLK 498

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEP+S+ETPIGD++ +HLGDFIED     PL+SA   +LR  T  +LA LT RE +VL
Sbjct: 499 IAKEPLSMETPIGDDEDTHLGDFIEDTTLELPLESATSESLRSATHEILAGLTAREAKVL 558

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 559 RMRFGIDMNTDHTLEEVGKQFAVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 611


>gi|294625247|ref|ZP_06703887.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292600475|gb|EFF44572.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 621

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 273/660 (41%), Positives = 376/660 (56%), Gaps = 53/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+            GF   
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDL 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         ++         E   + +      ++       P E             
Sbjct: 177 IEEADAAAAALAAAGPVAVSDDEAVDEDDDDDAAEEEAGPTGPDPVE------------- 223

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 224 -----------------VATRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMA 260

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 261 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 320

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 321 EWVEDALKR-KQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 379

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 380 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 439

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 440 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 499

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 500 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 559

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 560 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 619


>gi|71906166|ref|YP_283753.1| RNA polymerase sigma factor RpoD [Dechloromonas aromatica RCB]
 gi|71845787|gb|AAZ45283.1| RNA polymerase, sigma 70 subunit, RpoD [Dechloromonas aromatica
           RCB]
          Length = 657

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 244/674 (36%), Positives = 362/674 (53%), Gaps = 54/674 (8%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
             +  ++ + L  +      K +IKL ++RGY+T  E+N  LP D V +E +E  ++  S
Sbjct: 30  QGQMAETPEPLDAEARKMRLKALIKLGKERGYLTYAEINDHLPDDVVDAESIEAIISTFS 89

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR---KDSADRSTDDPVRMYLREM 128
            M I V D     ++    D+  +A+         ++     DS    T DPVRMY+REM
Sbjct: 90  EMSIQVFDEAPAAEDLLMSDTAAVAADDEEVEAQAEQALSTVDSEFGRTTDPVRMYMREM 149

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELL+REGEI IAKRIE G   M+ ++   P T   ++    ++      + E++D  
Sbjct: 150 GSVELLTREGEIEIAKRIEEGLKHMIQAIAACPTTISDILELAAKVESDEMRIDELVD-- 207

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P +           + +  E+   +                               
Sbjct: 208 GLIDPNAVEEAPAAEMPEAEEDEEEDGDDDGEGAGGGAAAASLL---------------- 251

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
                                     QL+   +     I  ++ +++ +           
Sbjct: 252 --------------------------QLKTDALERFKNIKGIHAKMQKM------LPTKG 279

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKR 367
                   L +++   + ++      I+ L + +  + +++   E ++ +       + R
Sbjct: 280 SHDKVYIKLLQQVSDELMNIRFTSRSIERLCDSVRGMVEQVRGCERKIQQICVDRVKMPR 339

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F++   G E++  W           +   +      I + + ++ ++    GI + + 
Sbjct: 340 PHFIQSFPGNEINLDWADAEVAAAPKTYVAILTRNAPDIKEEQKKLLALQDRIGIPLKDL 399

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 400 KDINKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 459

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP
Sbjct: 460 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEP 519

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P  +AKK+ MP + +RK++KI+KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+ +
Sbjct: 520 DPATLAKKMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDSGTLAPADAAMYS 579

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR  T  +L +LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 580 SLRGVTKEILDTLTTREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 639

Query: 668 KHPSRSKKLRSFLD 681
           +HP+RS KLRSF+D
Sbjct: 640 RHPTRSDKLRSFVD 653


>gi|257483092|ref|ZP_05637133.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289627702|ref|ZP_06460656.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289649021|ref|ZP_06480364.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298485287|ref|ZP_07003379.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298160137|gb|EFI01166.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320325995|gb|EFW82053.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320332070|gb|EFW88006.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330868477|gb|EGH03186.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330881700|gb|EGH15849.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891182|gb|EGH23843.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. mori
           str. 301020]
 gi|330985810|gb|EGH83913.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331011674|gb|EGH91730.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 616

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 262/657 (39%), Positives = 370/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    + T+ D E +A  S D+      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  +  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAEMVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|15837951|ref|NP_298639.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa 9a5c]
 gi|20140311|sp|Q9PDM9|RPOD_XYLFA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|9106350|gb|AAF84159.1|AE003967_3 RNA polymerase sigma-70 factor [Xylella fastidiosa 9a5c]
          Length = 618

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 273/660 (41%), Positives = 387/660 (58%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K++I    ++GY+T  E+N  LP D V  +Q+ED + M++ MGI V     D + 
Sbjct: 8   QQSDIKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   EG+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNEGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L E++                 
Sbjct: 128 AKRIEEGLSEVQAALGVFPLSTELLLSEYELHKEGKRRLTEVVVGF-------------- 173

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             +D+ E +  + S+  V+ +   +VD   +++  ++ +     
Sbjct: 174 ------------------NDLIEEDNSVTSSVDVTDESIVEVDEEDDDSVGNDEDAPTIG 215

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            D A   S +E             ++  Y + + L        K          ++E + 
Sbjct: 216 PDPAEVASRIES------------LSTEYAKFKKLY------AKHGPEHKAVIKVREDVA 257

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +  L+    DLLV+QL ++   +  +E ++L LA +   + R  F+   +  + + 
Sbjct: 258 AIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRSWENNQTNL 317

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I   +     +     +++++ + I  M+  GE +A
Sbjct: 318 EWVEDAIKR-KQKWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMMVYGEAKA 376

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA  KF+   G+KFSTYA 
Sbjct: 377 SKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFKFSTYAT 436

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 437 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 496

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 497 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLT 556

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 557 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|56477911|ref|YP_159500.1| RNA polymerase sigma factor RpoD [Aromatoleum aromaticum EbN1]
 gi|56313954|emb|CAI08599.1| DNA-dependent RNA polymerase sigma subunits (Sigma70/32)
           [Aromatoleum aromaticum EbN1]
          Length = 663

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 264/683 (38%), Positives = 385/683 (56%), Gaps = 44/683 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            + +++            L  +      K +I L ++RGY+T  E++  LP D   +EQ+
Sbjct: 19  SRAKDKGVLVAEGPQVAPLDAEVRRTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQI 78

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDP 120
           E  +A  +NMGI V D     ++    D++        A   +       DS    T DP
Sbjct: 79  EGIIATFNNMGIRVFDEAPAAEDLLMSDAVPSSVDEDVAEEEAEQALSSVDSEFGRTTDP 138

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   M+ ++   P T   ++   D++      
Sbjct: 139 VRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVQAISACPTTIAEMLEITDKVARDEMR 198

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E+ID    I P +                                   E++A  + DD
Sbjct: 199 IDELID--GLIDPNAAQ-------------------------------AAEASAAETADD 225

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               D   E+ +  + + + DED  A   +A   QL+   +     I E++         
Sbjct: 226 ERAADDEVESEDGGDDDDESDEDKEAAANAATLLQLKNDALVRFAIIRELHER------K 279

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                           L++++   + ++      I+ L + +  + +++  +E  +L+L 
Sbjct: 280 MAALATVGSQDRSYLDLQQQISGELLNIRFTAKAIERLCDSVRHMVEQVRGHERHILQLC 339

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ R  F++   GRE+D  W+       +   +  +     ++L+ + ++  +   
Sbjct: 340 VDRAGMPRQHFIKVFPGREIDLDWLKDEIGAGKNYAEGLMRVH-PAVLEEQQKLIDLQTR 398

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            GI + E + I   +  GE +   AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 399 IGIPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 458

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++
Sbjct: 459 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 518

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  +EP P  +A+K+ MP E +RK++KI+KEPIS+ETPIGD+D SHLGDFIED+  ++
Sbjct: 519 LQETGQEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQATLA 578

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D+A+ ++LR+ T  VL SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 579 PADAAMYSSLRDATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 638

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HPSRS++LRSFLD 
Sbjct: 639 EAKALRKLRHPSRSERLRSFLDS 661


>gi|52425815|ref|YP_088952.1| RNA polymerase sigma factor RpoD [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307867|gb|AAU38367.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 628

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 269/655 (41%), Positives = 378/655 (57%), Gaps = 42/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V ++Q+ED + M+++MGI V++     D+ 
Sbjct: 14  QSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDTDQIEDIIQMINDMGIQVLESAPDADDL 73

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A   +  +    ++    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 74  MLSETIA-DEDAVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++ E P     L+   +++ +G+  L ++I     +  E         E   
Sbjct: 133 DGINEVQSAVAEYPEALDYLLKQYEQVEEGSVRLADLITGFVDLNAEEASEEISDLE--- 189

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +  +D   +   D + + E D ES    +  D S     PE A                
Sbjct: 190 -EVLDDEDGDIPADALNDEEEDEESDEGDTSTDDSDNSIDPEVAREKFSA---------- 238

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                   L+ + +  L+ I                 +K  ++  K K   + L  +   
Sbjct: 239 --------LKDQCVKTLEFI-----------------EKYGRTDNKVKEQIQVLSDIFTQ 273

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  +  + K++   E ++ RLA  Y  + +D F +   G E    W+  
Sbjct: 274 FRLVPRQFDTLVLSMRSMMKQVRAEERQIQRLAVDYAKVPKDDFQKAFIGNETSEQWLES 333

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  +   +      I K    ++ +  +T +++ + R I   + +GE +A  AKK
Sbjct: 334 LLQ-SKKTYVEKLQQRAPEISKSIVRLQQVETDTKLTVQQIRDIGERIAQGELKARRAKK 392

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 393 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 452

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 453 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 512

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 513 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAK 572

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 573 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 627


>gi|121597172|ref|YP_991115.1| RNA polymerase sigma factor RpoD [Burkholderia mallei SAVP1]
 gi|126456327|ref|YP_001076416.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|121224970|gb|ABM48501.1| RNA polymerase sigma factor RpoD [Burkholderia mallei SAVP1]
 gi|126230095|gb|ABN93508.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
          Length = 736

 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 247/663 (37%), Positives = 364/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 115 LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 174

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 175 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 234

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 235 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADTDGFS 294

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    +  ++ ++ E ++  +      +A     +                     
Sbjct: 295 EKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 334

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 335 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 373

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 374 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 433

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 434 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 492

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 493 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 552

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 553 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 612

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 613 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 672

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 673 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 732

Query: 680 LDG 682
           L+G
Sbjct: 733 LEG 735


>gi|50085952|ref|YP_047462.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter sp. ADP1]
 gi|49531928|emb|CAG69640.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter sp. ADP1]
          Length = 629

 Score =  443 bits (1140), Expect = e-122,   Method: Composition-based stats.
 Identities = 268/653 (41%), Positives = 373/653 (57%), Gaps = 36/653 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +     D+    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DS +    A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G 
Sbjct: 71  DSTEADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGI 130

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             ++ S+   P   + ++   ++   G   L +I  L   + PE+        E  +  +
Sbjct: 131 RDVLHSIAYWPNAVEVVLQEYNDYVTGERRLADI--LSGYLDPETDDDIPEVLEEEAELE 188

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            +D S  K      + + D E   +   DD S+ DS P+                     
Sbjct: 189 EDDESTSKTTTKDVKLDDDDEEEEESEGDDDSEGDSGPDP-------------------- 228

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                         +E+   ++  +++ +      K  ++S +     E L  +      
Sbjct: 229 -------EIAKVRFEELEAAWKNTKTVIE------KHGRNSEEANAALESLATVFMMFKF 275

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKD 389
                D++ E +    + I  NE E++R A   G + R  F     G+E +P W+     
Sbjct: 276 TPRLFDIISEMIRGTHENIRSNEREVMRYAVRRGRMDRTQFRTSFPGQESNPAWLEEQIA 335

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
               E K ++      I   + +I  I  +  +++ E + I   +  GE +A  AKKEMV
Sbjct: 336 KAPNESKAYLEKVRPDIQAFQQKIAEIEQDLNLNVREIKEIAKRMAVGEAKARRAKKEMV 395

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 396 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 455

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLKI
Sbjct: 456 RSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKI 515

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL+
Sbjct: 516 AKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVLK 575

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 576 MRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 628


>gi|127511929|ref|YP_001093126.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637224|gb|ABO22867.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella loihica PV-4]
          Length = 616

 Score =  443 bits (1140), Expect = e-122,   Method: Composition-based stats.
 Identities = 264/655 (40%), Positives = 373/655 (56%), Gaps = 49/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +     DE 
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEI 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 69  MMSED-STDEDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P     ++   D        L +II            GF        
Sbjct: 128 EGINTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDII-----------SGFVDPNAEDM 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    E   DD+ + + + +       ++ S     PE A      L E  + +  
Sbjct: 177 APTATHIGSELSDDDLDDEDDEGDDEDDDGDEEDSPKGPDPEEARERFTQLREAHEKALK 236

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +  ++ +  P+   AL +I E+++E                                  
Sbjct: 237 VIE-LKGREHPEATAALFDIGEIFKE---------------------------------- 261

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ + ++  ++   E  +++L  +   + +  F++ +   E    W + 
Sbjct: 262 FRLVPKQFDRLVKNMREMMDKVRIQERLIMKLCVEQAKMPKKNFVKVYTSNESSIEWFNE 321

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  +   +    + + + R ++ +I  ETG++I+  + I   +  GE +A  AKK
Sbjct: 322 EIA-AKKPYAEGLEMVAEDVQRCRAKLDAIENETGLAIAAIKDINRRMSIGEAKARRAKK 380

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 381 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 440

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 441 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKV 500

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 501 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAK 560

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 561 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 615


>gi|302877609|ref|YP_003846173.1| RNA polymerase, sigma 70 subunit, RpoD [Gallionella
           capsiferriformans ES-2]
 gi|302580398|gb|ADL54409.1| RNA polymerase, sigma 70 subunit, RpoD [Gallionella
           capsiferriformans ES-2]
          Length = 655

 Score =  443 bits (1140), Expect = e-122,   Method: Composition-based stats.
 Identities = 251/662 (37%), Positives = 372/662 (56%), Gaps = 40/662 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D    S K +I L ++RGY+T  E+N  LP D +  EQ+E   +M+++MGI V D    
Sbjct: 29  IDARRTSLKALIVLGKERGYLTYAEINDHLP-DMLEVEQIESVASMINDMGIRVCDVAPD 87

Query: 84  EDEEGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +     DS        A+  +       DS    T DPVRMY+REMG+++LL+RE EI 
Sbjct: 88  AEALIMTDSAPTAADEDAAEEAEAALSTVDSEFGRTTDPVRMYMREMGTVDLLTREKEIE 147

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G+  M+ ++   P+T   ++    ++      + E+ID    I  E + G   
Sbjct: 148 IAKRIEEGQRNMIQAISACPVTIAEILSLAAKIEIDEIRVNELIDGFVDIELEDESGLTA 207

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +       E+ S E+   +  + E +   AA  +    + +                 
Sbjct: 208 SDDQEQDDAEEEESSEESSSEDGDEEDEEAMAAASAAAAAADL----------------- 250

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                        QL+   +     IA+++ ++    +      K    S +  V +  +
Sbjct: 251 ------------AQLKADALARFAVIADLFSKMGKAYE------KYGYLSAQYNVHQAGI 292

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELD 380
            + + +      ++D L   +  + + I  NE  +         + R  F++   G E+D
Sbjct: 293 TEELMAFRFTAKQVDALCNTMRGLVEEIRTNERGIQDICVTKSKMPRPHFIKSFVGHEVD 352

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W++      +  +   +     +I++ +  + ++    G+ I++ + I   +  GE  
Sbjct: 353 MDWLAQEIKAAKP-YSELLVRYQHAIVEKQQNLINMQKRVGLPITDLKEINRRMTNGEAR 411

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +  AK++M+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 412 SHRAKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 471

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  +E     +A+K+ M  
Sbjct: 472 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQEADAATLAEKMEMTE 531

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + + K+LKI KEPIS+ETP+GD+D SHLGDFIED N   P+++A+  +LR  T+ +L SL
Sbjct: 532 DKIHKILKIAKEPISMETPVGDDDDSHLGDFIEDSNTTVPIEAAVYESLRSATSDILDSL 591

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KL+SFL
Sbjct: 592 TQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLKSFL 651

Query: 681 DG 682
           D 
Sbjct: 652 DS 653


>gi|160900477|ref|YP_001566059.1| RNA polymerase sigma 70 subunit RpoD [Delftia acidovorans SPH-1]
 gi|160366061|gb|ABX37674.1| RNA polymerase, sigma 70 subunit, RpoD [Delftia acidovorans SPH-1]
          Length = 808

 Score =  443 bits (1140), Expect = e-122,   Method: Composition-based stats.
 Identities = 258/663 (38%), Positives = 368/663 (55%), Gaps = 59/663 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                   K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V +    
Sbjct: 200 MSTRRQRLKALIKLGKTRGYLTHSEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPD 259

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  S      A   +       DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 260 AETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 319

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF 
Sbjct: 320 EIAKRIEGGLMDMMEAISASPATIAEILAMSEEIREGKVVISTIVD-----------GFV 368

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
           +  E   Y   ED  +  E DD     G                                
Sbjct: 369 NANENDDYVAEEDFDEYDEEDDDDGKGG-------------------------------- 396

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                +  L+   ++L+ + +   D + E + ++  + D    G      +     +++ 
Sbjct: 397 -----SKALTKKLEELKNEALRRFDAMRENFDKMHKVYDKEGYG------TPTYIKVQKA 445

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           L + + ++      I+ L + +      +   E EL + +    G+ ++ F+ +     L
Sbjct: 446 LTEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVDKCGMPQETFIAQFPPNLL 505

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV   +      W N +   +  + +++  +  +     + + E + I   +  GE 
Sbjct: 506 NLQWV-VQQVAAGKPWSNVLERNIPPVQELQQNLIDLQSRVVVPLDELKRINKRMNDGER 564

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 565 ASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 624

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P
Sbjct: 625 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIP 684

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  
Sbjct: 685 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPVDAAMQAGLRDVVKDILDG 744

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF
Sbjct: 745 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSF 804

Query: 680 LDG 682
           +D 
Sbjct: 805 IDS 807


>gi|126443442|ref|YP_001063518.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126222933|gb|ABN86438.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 736

 Score =  443 bits (1140), Expect = e-122,   Method: Composition-based stats.
 Identities = 247/663 (37%), Positives = 364/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 115 LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 174

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 175 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 234

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 235 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADTDGFS 294

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    +  ++ ++ E ++  +      +A     +                     
Sbjct: 295 EKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 334

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 335 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 373

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 374 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 433

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 434 DLDWAEKIAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 492

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 493 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 552

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 553 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 612

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 613 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 672

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 673 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 732

Query: 680 LDG 682
           L+G
Sbjct: 733 LEG 735


>gi|170725515|ref|YP_001759541.1| RNA polymerase sigma 70 subunit RpoD [Shewanella woodyi ATCC 51908]
 gi|169810862|gb|ACA85446.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella woodyi ATCC
           51908]
          Length = 611

 Score =  443 bits (1140), Expect = e-122,   Method: Composition-based stats.
 Identities = 267/655 (40%), Positives = 373/655 (56%), Gaps = 51/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V ++Q+ED V M+++MGI V +     DE 
Sbjct: 6   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEM 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +       A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMSED-STDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + AS+ E P     ++   D        L +II     + P ++      T   S
Sbjct: 125 EGINTVQASVAEYPQAIAMILEQYDRYEAEEIRLSDII--SGFVDPNAEDVAPTATHVGS 182

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               ED   E             E +     ++       PE A+     L E  +++  
Sbjct: 183 ELSDEDLDDED-----------DEDSEDDEDEEEGPKGPDPEEAKERFTQLREAHENTLR 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            ++ ++ +  P+   AL EI E+++E                                  
Sbjct: 232 VIN-LKGRGHPESTLALFEIGEIFKE---------------------------------- 256

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV+ +  +  R+   E  +++L  +   + +  F++ +   E    W   
Sbjct: 257 FRLMPKQFDRLVKSMRAMMDRVRVQERLIMKLCVEQAKMPKKNFVKGYTSDESSIAWFDE 316

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  +   +      + + R ++ +I  ETG++I+  + I   +  GE +A  AKK
Sbjct: 317 ELA-SKKPYVEGLEMVEPDVRRCRAKLDAIEKETGLAIAAIKDINRRMSIGEAKARRAKK 375

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 376 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 435

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +RKV
Sbjct: 436 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPEDKIRKV 495

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA LT RE +
Sbjct: 496 LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGLTAREAK 555

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD
Sbjct: 556 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLD 610


>gi|325924346|ref|ZP_08185890.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas gardneri ATCC
           19865]
 gi|325545211|gb|EGD16521.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas gardneri ATCC
           19865]
          Length = 625

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 273/660 (41%), Positives = 378/660 (57%), Gaps = 49/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 68  LLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L   PL+ + L+   +   +G   L EI+     +  E+       
Sbjct: 128 AKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAAL 187

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    ED + + +  +  + +   E A     D                       
Sbjct: 188 AAAGPVAVSEDDAADDDDAEDGDDDAAEEEAGPTGPDPVE-------------------- 227

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   ++ +A  Y + + +        K+          +E + 
Sbjct: 228 -----------------VATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMA 264

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 265 AIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATAVARMPRKDFIRSWEGNQTNL 324

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     +++ E + I   +  GE +A
Sbjct: 325 EWVEDALKR-KQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKA 383

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 384 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 443

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 444 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPED 503

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 504 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 563

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 564 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 623


>gi|331017645|gb|EGH97701.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 616

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 262/657 (39%), Positives = 370/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + D E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  L  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAELVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +G++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 DGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKITKEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKITKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|221212356|ref|ZP_03585333.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
 gi|221167455|gb|EED99924.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
          Length = 682

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 250/665 (37%), Positives = 372/665 (55%), Gaps = 47/665 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 58  LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 117

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 118 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 177

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID--LEACIGPESKGG 198
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D  L+         G
Sbjct: 178 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDPNASDTDTDG 237

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           F          + E+  +E+E ++ ++ +G  ++ A  ++ +                  
Sbjct: 238 FSAKEAEEIENEDEEVEEEEEEEEEEDDDGAAQATANAAQLEA----------------- 280

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                            L+   +     I+E + ++R   +      K+   S      +
Sbjct: 281 -----------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQ 317

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           E +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G 
Sbjct: 318 ETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGN 377

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W           +   ++  + +I + +  +  +     + + + +     +  G
Sbjct: 378 ETDLDWAEKIAAEGHS-YSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAG 436

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 437 ELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 496

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ 
Sbjct: 497 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKME 556

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL
Sbjct: 557 MPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVL 616

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+
Sbjct: 617 DSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLK 676

Query: 678 SFLDG 682
           SFL+G
Sbjct: 677 SFLEG 681


>gi|71736970|ref|YP_272918.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557523|gb|AAZ36734.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 616

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 262/657 (39%), Positives = 370/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTCVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    + T+ D E +A  S D+      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  +  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAEMVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|254000081|ref|YP_003052144.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. SIP3-4]
 gi|313202040|ref|YP_004040698.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. MP688]
 gi|253986760|gb|ACT51617.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. SIP3-4]
 gi|312441356|gb|ADQ85462.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. MP688]
          Length = 638

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 254/682 (37%), Positives = 386/682 (56%), Gaps = 51/682 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  ++N   + + E        D      K +I L ++RGY+T  E+N  LP D   SEQ
Sbjct: 1   MANEQNDKVNDKVETQISD--ADIRRTRLKSLIVLGKERGYLTYAEINDHLPDDVQDSEQ 58

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD--LASSASNSSVFLQKRKDSADRSTDDP 120
           ++  + M+++MGI V +     +     D+        A   +       DS    T DP
Sbjct: 59  IDGIIGMINDMGIQVYEETPDAEALLMSDAPPPVADEDAVEEAEQALSTVDSEFGRTTDP 118

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG+++LL+REGEI IAKRIE G   M+ ++   P T   L+   +++      
Sbjct: 119 VRMYMREMGTVDLLTREGEIEIAKRIEDGLKHMVQAIAACPTTIAELLAMVEKVEKDELS 178

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + +++D           G      G       ++++ +E +   + E D +     +   
Sbjct: 179 VDDLVD-----------GLIDSDVGLEEDIPVEAAEAEEEEPEDDEEDDGDEDGAKAAAI 227

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            ++                               +L+ +V+     I + ++++  +   
Sbjct: 228 SAEAL----------------------------AKLKEEVLTRFAVIRQSHQKMTVI--- 256

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-L 359
               Q+      + + L+  +++ + +   +  +++ L +Q+ ++ + I  +E +++   
Sbjct: 257 ---LQERGSQDKEYQALQNAILEELTAFRFSAKQVEALCDQVRNMVEEIRGHERKIMEFC 313

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ R  F++   G E +  W++      +  +   +     SI+  +  +  +   
Sbjct: 314 VDKSGMPRAHFIKVFPGNEGNLDWLAGELTVNKP-YVERLERFKHSIVDQQQRLLDLQDR 372

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            GI I E + I   +  GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 373 VGIPIKELKEINKQMSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 432

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++
Sbjct: 433 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 492

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP P  +A+K+ MP + +RK+LKI+KEPIS+ETPIGD+D SHLGDFIED   ++
Sbjct: 493 LQETGLEPDPATLAEKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDMTTLA 552

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+A+ A+LRE T  VL SLT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 553 PVDAAVYASLREATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 612

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HP+RS++LRSFL+
Sbjct: 613 EAKALRKLRHPTRSERLRSFLE 634


>gi|170736023|ref|YP_001777283.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
 gi|169818211|gb|ACA92793.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
          Length = 683

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 253/663 (38%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 58  LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 117

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 118 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 177

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 178 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 223

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E +E +   
Sbjct: 224 -------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAA 270

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 271 QASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKSKAYLKAQET 320

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 321 IQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 380

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  V +I + +  +  +     + + + +     +  GE 
Sbjct: 381 DLDWAEKITAEGHP-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 439

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 440 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 499

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 500 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 559

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 560 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 619

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 620 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 679

Query: 680 LDG 682
           L+G
Sbjct: 680 LEG 682


>gi|256823391|ref|YP_003147354.1| RNA polymerase sigma-70 subunit RpoD [Kangiella koreensis DSM
           16069]
 gi|256796930|gb|ACV27586.1| RNA polymerase, sigma 70 subunit, RpoD [Kangiella koreensis DSM
           16069]
          Length = 616

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 271/658 (41%), Positives = 365/658 (55%), Gaps = 47/658 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K +I   +++GY+T  E+N  LPPD V  EQ+ED + M+++MGI V +     
Sbjct: 4   NSQQSQLKLLIARGKEQGYLTYAEVNDHLPPDIVDPEQIEDIIRMINDMGIQVYETTPDA 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE    D       A+  +       DS    T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 64  DELLMNDESVTDEEAAEEAAAALASVDSEFGRTTDPVRMYMREMGSVELLTREGEIDIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ ++   P T + L+       +    L EI+            GF  G E
Sbjct: 124 RIEEGIRQVLGAIANYPDTIRILLEEFALYQEEQVRLTEIV-----------TGFSDGEE 172

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
               Q+  +++Q       +    D        +++      P                 
Sbjct: 173 AEFVQEESEAAQIAASASEELDSDDDADDDDDDEEETEVDTGPDPEEAA----------- 221

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                                E+ + Y +     D      K  ++        E + +L
Sbjct: 222 -----------------ARFAELKKQYDKTVKAVD------KYGRTHKSTIKQLEAMKEL 258

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHW 383
              L L     D LV  L      I   E  ++ L      + R  F+    G E DP W
Sbjct: 259 FMQLRLAPRMFDFLVTNLRQKMDGIREQERYIMMLSVNGARMPRKTFISTFSGSETDPSW 318

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +       + ++   +A   + ILK + +++ I     +S+ E +     +  GE +A  
Sbjct: 319 IEQHV-TKKSKYSEPLAEHAEEILKAQRKLQIIEESCSLSVMEIKEANREMSIGEAKARR 377

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +
Sbjct: 438 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPQPEELAERMEMPEDKI 497

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D+A   +L+E T  +LA LT R
Sbjct: 498 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIDSPVDAATGESLKEVTDEILAGLTAR 557

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLR++LD
Sbjct: 558 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRTYLD 615


>gi|28867765|ref|NP_790384.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213967690|ref|ZP_03395837.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382750|ref|ZP_07231168.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
           Max13]
 gi|302064027|ref|ZP_07255568.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
           K40]
 gi|302130708|ref|ZP_07256698.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|28851000|gb|AAO54079.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213927466|gb|EEB61014.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato T1]
 gi|330878419|gb|EGH12568.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 616

 Score =  443 bits (1139), Expect = e-122,   Method: Composition-based stats.
 Identities = 261/657 (39%), Positives = 369/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + D E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  L  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAELVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +G++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 DGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|221197050|ref|ZP_03570097.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD2M]
 gi|221203722|ref|ZP_03576740.1| sigma-70, non-essential region family [Burkholderia multivorans
           CGD2]
 gi|221175888|gb|EEE08317.1| sigma-70, non-essential region family [Burkholderia multivorans
           CGD2]
 gi|221183604|gb|EEE16004.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD2M]
          Length = 682

 Score =  443 bits (1138), Expect = e-122,   Method: Composition-based stats.
 Identities = 250/665 (37%), Positives = 372/665 (55%), Gaps = 47/665 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 58  LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 117

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 118 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 177

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID--LEACIGPESKGG 198
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D  L+         G
Sbjct: 178 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDPNASDTDTDG 237

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           F          + E+  +E+E ++ ++ +G  ++ A  ++ +                  
Sbjct: 238 FSAKEAEEIENEDEEVEEEEEEEEEEDDDGAAQATANAAQLEA----------------- 280

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                            L+   +     I+E + ++R   +      K+   S      +
Sbjct: 281 -----------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQ 317

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           E +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G 
Sbjct: 318 ETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGN 377

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W           +   ++  + +I + +  +  +     + + + +     +  G
Sbjct: 378 ETDLDWAEKIAAEGHS-YSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAG 436

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 437 ELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 496

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ 
Sbjct: 497 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKME 556

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL
Sbjct: 557 MPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVL 616

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+
Sbjct: 617 DSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLK 676

Query: 678 SFLDG 682
           SFL+G
Sbjct: 677 SFLEG 681


>gi|330826139|ref|YP_004389442.1| RNA polymerase sigma-710 subunit RpoD [Alicycliphilus denitrificans
           K601]
 gi|329311511|gb|AEB85926.1| RNA polymerase, sigma 70 subunit, RpoD [Alicycliphilus
           denitrificans K601]
          Length = 802

 Score =  443 bits (1138), Expect = e-122,   Method: Composition-based stats.
 Identities = 258/660 (39%), Positives = 369/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
                KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V +     + 
Sbjct: 197 RRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAET 256

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +     +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 257 LFQNNVAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 316

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  
Sbjct: 317 KRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPE 365

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 366 EADDYVAEEDFDEYDEEDDDDGKGG----------------------------------- 390

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  ++ + ++L+ + +   DE+  ++ ++  + D    G      S     ++ ++  
Sbjct: 391 --SKAMTRLLEKLKTEALDRFDELRSLFEKMHKIYDKEGYG------SPAYMKVQHEISA 442

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 443 KLMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVDKCGMPQETFIKEFPPNLLNLQ 502

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +   +  I +++  +  +     + ++E + I   + +GE  + 
Sbjct: 503 WVEKQAAAGKP-WSAVMQRNIPPIQELQQHLIDLQSRVVVPLAELKAINKRMNQGEANSR 561

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 562 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 621

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 622 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 681

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTP
Sbjct: 682 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPIDAAMQAGLRDVVKDILDGLTP 741

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 742 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 801


>gi|170699447|ref|ZP_02890491.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           IOP40-10]
 gi|170135647|gb|EDT03931.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           IOP40-10]
          Length = 683

 Score =  443 bits (1138), Expect = e-122,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 372/663 (56%), Gaps = 42/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 58  LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 117

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 118 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 177

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D              
Sbjct: 178 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD-------------- 223

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           +    D  +T+G     A+  +++  + +   E  E ++ +   
Sbjct: 224 -------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAA 270

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 271 QATANAAQLEA----LKRASLDKFSQISEWFDKMRRAFE------KEGYKSKSYLKAQET 320

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 321 IQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 380

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 381 DLDWAEKIAAEGHS-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 439

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 440 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 499

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 500 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 559

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 560 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 619

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 620 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 679

Query: 680 LDG 682
           L+G
Sbjct: 680 LEG 682


>gi|15603106|ref|NP_246178.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|12721597|gb|AAK03325.1| RpoD [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 622

 Score =  443 bits (1138), Expect = e-122,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 368/655 (56%), Gaps = 40/655 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I   +++GY+T  E+N  LP + V +EQ+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +++     A   +  +    ++    T DPVRMY+REMGS+ELL+REGEI IAKRIE
Sbjct: 66  MLNETIA-DEDAVEEATQVLSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + +++   P     L+     + +G   L ++I     + P +           +
Sbjct: 125 EGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLIT--GFVDPNAMTESDVAEIEDT 182

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           + + EDS       + +E E +       + D  S     PE A      L      +  
Sbjct: 183 FDEDEDSDSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHAKAVA 242

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +                                    K  ++S K K   + L  +   
Sbjct: 243 MIE-----------------------------------KHGRTSKKSKDQIQALADVFTQ 267

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
             L   + D LV  + ++ K +   E  + ++      + ++ F +   G E    W+  
Sbjct: 268 FRLVPKQFDTLVNLMSNMMKSVRLQERSIQKIVVDKAKMPKEQFQKVFIGHENKDTWLVK 327

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A       W   +A   + I    + I  I  +T +++S+ R +   +  GE +A  AKK
Sbjct: 328 ALS-SGKTWSEKLAKHEEEIRYYIDNILEIERQTNLTVSQIREVCERISAGELKARRAKK 386

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 387 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 446

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE +PEE+A+++ MP + +RKV
Sbjct: 447 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 506

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  LTPRE +
Sbjct: 507 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAK 566

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 567 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 621


>gi|121609019|ref|YP_996826.1| RpoD family RNA polymerase sigma factor [Verminephrobacter eiseniae
           EF01-2]
 gi|121553659|gb|ABM57808.1| RNA polymerase, sigma 70 subunit, RpoD family [Verminephrobacter
           eiseniae EF01-2]
          Length = 635

 Score =  442 bits (1137), Expect = e-122,   Method: Composition-based stats.
 Identities = 254/660 (38%), Positives = 370/660 (56%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IKL + RGY+T  E++  LP   V +E +E  +  L+++G+ V +     + 
Sbjct: 30  RRSRLKTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLNDLGVAVYEQTPDAEA 89

Query: 87  EGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
               D+         A  ++       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 90  LIITDNAPTGASEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 149

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+  G  ++  I+D           GF +  
Sbjct: 150 KRIEGGLMAMMEAISASPATIAEILNMGEEIRAGKVVISTIVD-----------GFSNPN 198

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 199 EADDYVAEEDFDEFDEADDDDGKGG----------------------------------- 223

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D++ +++ ++  + D      KD   ++     ++ L  
Sbjct: 224 --SKALTKKLEELKKQALERFDKLRDLFEKMHKVYD------KDGYGTLAYVQAQQALSA 275

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 276 ELMTIRFTAKTIEKLCDMVRGQVDDVRRKERELRRIIVDKCGMPQETFIKDFPPNLLNLQ 335

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W + +A  +  I  ++ ++  +     + ++E + I   + +GE  + 
Sbjct: 336 WVEKQAAMGKP-WSSIIARNIPPIQDLQQKLMDLQSRVVVPLTELKVINKRMNEGEATSR 394

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 395 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 454

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 455 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASLLAAKMEIPEDK 514

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED +  +P+++A+QA LR+    +L  LTP
Sbjct: 515 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDASNTAPIEAAMQAGLRDVVKDILDGLTP 574

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 575 REAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 634


>gi|330963831|gb|EGH64091.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 616

 Score =  442 bits (1137), Expect = e-122,   Method: Composition-based stats.
 Identities = 261/657 (39%), Positives = 369/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + D E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  L  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAELVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  +G++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 DGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|302185957|ref|ZP_07262630.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           642]
          Length = 616

 Score =  442 bits (1137), Expect = e-122,   Method: Composition-based stats.
 Identities = 259/657 (39%), Positives = 369/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + + E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  +  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAEMVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|1710688|sp|P52327|RPOD_PSEPU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|762877|dbj|BAA06281.1| principal sigma factor [Pseudomonas putida]
 gi|1586519|prf||2204230A sigma factor
          Length = 614

 Score =  442 bits (1137), Expect = e-122,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 372/657 (56%), Gaps = 50/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   +    R T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVETDI-RRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++   D +N G   L +++            G+    + 
Sbjct: 125 IEEGIREVMGAIAHFPGTVDYILGEYDRVNRG-CRLSDVL-----------SGYIDPDDN 172

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +    E      +    +E   D E  ++   D+                         
Sbjct: 173 IAAPTEEVPIPGTKAAAAKEEADDDEEESEGGDDEEEPK--------------------- 211

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
               +A+    +P V               S  D+    +K      K + L + L  L 
Sbjct: 212 ----AALTRSSQPSVSVRYP---------SSFSDHQGPEEKRSYPQGKRRAL-QALADLF 257

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + ++LVE++ D   R+   E  +++L      + R  FL      E D  W 
Sbjct: 258 MPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWS 317

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     W   +  +  +I+  + ++  +  ETG++++E + I   +  GE +A  A
Sbjct: 318 GDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMSIGEAKARRA 376

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 377 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 436

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 437 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 496

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+  A   +L+E T  VL+ LT RE
Sbjct: 497 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIYVATVESLKEATRDVLSGLTARE 556

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA RKL+HP+RS+ LRSFLD
Sbjct: 557 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAWRKLRHPTRSEHLRSFLD 613


>gi|209517800|ref|ZP_03266635.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
 gi|209501746|gb|EEA01767.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
          Length = 680

 Score =  442 bits (1137), Expect = e-122,   Method: Composition-based stats.
 Identities = 252/663 (38%), Positives = 367/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 59  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 179 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANDEVRIDELVDGLIDADAEDADGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E++ +E E D+ ++                                   
Sbjct: 239 AQEAEAIENEDEEAEEEDEEDEEEDDGSA------------------------------- 267

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                A   +A  + LR   +     I+E + ++R   +      K+   S      +E 
Sbjct: 268 ----QATANAAQLEALRRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 318 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLEWADKIVAEGHV-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|237803341|ref|ZP_04590926.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331025322|gb|EGI05378.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 615

 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 262/657 (39%), Positives = 374/657 (56%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + + ESA    ++D  +    P  A+     + +  + +
Sbjct: 174 IAPPAEVPPPVDPKAAKAEGDDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEIT 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L  +    +  +   +                                    L +L 
Sbjct: 234 RKALKKLGRDDKHAIAEMV-----------------------------------ALAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 259 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +A     I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 319 D-ALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 558 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 614


>gi|295700835|ref|YP_003608728.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295440048|gb|ADG19217.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 680

 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 252/663 (38%), Positives = 367/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 59  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 179 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANDENRIDELVDGLIDADAEDADGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E++ +E E D+ ++                                   
Sbjct: 239 AQEAEAIENEDEEAEEEDEEDEEEDDGSA------------------------------- 267

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                A   +A  + LR   +     I+E + ++R   +      K+   S      +E 
Sbjct: 268 ----QATANAAQLEALRRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 318 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLEWADKIVAEGHA-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|88858406|ref|ZP_01133048.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
           tunicata D2]
 gi|88820023|gb|EAR29836.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
           tunicata D2]
          Length = 615

 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 265/655 (40%), Positives = 374/655 (57%), Gaps = 48/655 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K +I+  +++GY+T  E+N  LP D + S+Q+ED ++M+++MGI V +     DE 
Sbjct: 6   QSQLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVCESAPDADEL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +++     +A  ++  L    D     T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MMQETTTDEDAAEAAAAALATV-DKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +  S+ E P     L+   D+       L +II            GFF   E   
Sbjct: 125 EGINQVQISVAEYPEAITYLLEQWDKYEAEEIRLSDII-----------SGFFDSDEEQF 173

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    +   + +++ + D++       ++      P      +      D  + A 
Sbjct: 174 PIAATHIGSDLNDEQLKDEDVDLDDDDDDDSNEEEVDLGPDPELARENFEKLRDLYNKAR 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +   + +  P    A+ EI E++R                                  +
Sbjct: 234 LIFEEKGRSHPDAKEAITEIGELFR----------------------------------T 259

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
             L   + D +V  + D+  R+   E  +++ A     + +  F++     E +  W+  
Sbjct: 260 FKLMPKQFDRMVNNMRDMMDRVRVQERLIMKQACQIAKLPKKTFIKHFANNESNGEWLDI 319

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             +  E  + + +A     I +  N+++++   TG+S+   + I   +  GE +A  AKK
Sbjct: 320 EINAGEK-YSDKLAECRPEIERSLNKLRNMEQTTGLSVERIKDINRRMSIGEAKARRAKK 378

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 379 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 438

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKV
Sbjct: 439 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPEDKIRKV 498

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA   +L+  T  VLA LT RE +
Sbjct: 499 LKIAKEPISMETPIGDDEDSHLGDFIEDSTIESPIDSATMESLKGATHEVLAGLTAREAK 558

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFLD
Sbjct: 559 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLKSFLD 613


>gi|170719016|ref|YP_001784175.1| RNA polymerase sigma factor RpoD [Haemophilus somnus 2336]
 gi|168827145|gb|ACA32516.1| RNA polymerase, sigma 70 subunit, RpoD [Haemophilus somnus 2336]
          Length = 621

 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 268/656 (40%), Positives = 368/656 (56%), Gaps = 41/656 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   +++GY+T  E+N  LP D V ++Q+ED + M+++MGI V++     D+
Sbjct: 5   KQSQLKLLIARGKEQGYLTYAEVNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDADD 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               +++     A   +  +    ++    T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 65  LMLNENIT-DEDAVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + +++   P     L+     + +G   L ++I          +       +  
Sbjct: 124 EEGINEVQSAVAAYPKALNYLLEQYTLVEEGGMRLADLITGFVDPNAVVEEEIIEADDIL 183

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +    E      + +D +E E   +++   S  D +     PE A      L        
Sbjct: 184 TEDDEEHVESNVDVNDEEEEEDSEDNSNVDSDSDNTIA---PEVAREKFEALRIQH---- 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                                          Q      +K  +S  + K   + L  +  
Sbjct: 237 -------------------------------QKTLAAIEKYGRSRKQAKDHIQALADIFT 265

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + D+ K +  +E ++ +L      + ++ F +   G E    W+ 
Sbjct: 266 QFRLVPKQFDALVNYMRDMMKSVRQHERQIQKLVVDLAKMPKENFQKLFIGNESSEGWLD 325

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                    W   +     ++ +  N++  I  ET ++IS+ R I   V +GE +A  AK
Sbjct: 326 KLL-LARKPWSERLIQHESAVRQSINQLLKIEQETNLTISQIREICDKVAQGELKARRAK 384

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 385 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 444

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  K+ RE T EE+A+++ MP + +RK
Sbjct: 445 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQKMGREATSEELAERMGMPEDKIRK 504

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +LR  T  VL  LTPRE 
Sbjct: 505 VLKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLRAATHEVLEGLTPREA 564

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 565 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 620


>gi|254362696|ref|ZP_04978782.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
 gi|153094317|gb|EDN75178.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
          Length = 623

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 275/648 (42%), Positives = 387/648 (59%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+T+ E++  LP + V +EQ+ED + M+++MGI V++     D+    +++ 
Sbjct: 19  ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDADDLLLAENIA 78

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 79  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 137

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     L+    ++  G   L +++   A + P                     
Sbjct: 138 CAIAEYPEALSGLLACYAQVETGEMRLSDLVT--AFVDPN-------------------I 176

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E   +D++   G+ E ++ V   D    D   +++ +   +   D + +     A+  
Sbjct: 177 LEEAPLEDIEAALGEDEESSDVPDVDDENEDENGDSSSDSSDDSSIDPELAREKFEALRS 236

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           Q    ++                       QK  ++S K K   E L  +     L   +
Sbjct: 237 QHEKVLLVI---------------------QKHGRTSKKSKEQIEILSHIFREFRLVPKQ 275

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLV  +  + K++   E ++ R A  Y G+K+  FL+  QG EL   W+  A +  + 
Sbjct: 276 FDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQGHELSEAWIEKAIN-AKK 334

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  VD+I      ++++   +G++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 335 NAAPKLANYVDNIRVNIANLQNLEQTSGLTIAQIREIGGRISNGELKARRAKKEMVEANL 394

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 395 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 454

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 455 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 514

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 515 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEVLEGLTPREAKVLRMRFG 574

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 575 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|330898880|gb|EGH30299.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330980978|gb|EGH79081.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 616

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 264/657 (40%), Positives = 370/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               K   +    + ++        ESA    ++D  +    P  A+     + +  + +
Sbjct: 183 PVDPKAAKAEGADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEIT 234

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  +           L +L 
Sbjct: 235 RKAL-----------------------------------KKFGRDDKHAIAEMVALAELF 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|325518128|gb|EGC97914.1| RNA polymerase sigma factor RpoD [Burkholderia sp. TJI49]
          Length = 682

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 251/665 (37%), Positives = 374/665 (56%), Gaps = 47/665 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 58  LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 117

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 118 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 177

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID--LEACIGPESKGG 198
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D  L+         G
Sbjct: 178 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLLDPNASDTDTDG 237

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           F          + ED+ +E+E ++ ++ +G  ++ A  ++ +                  
Sbjct: 238 FSAKEAEEIENEDEDAEEEEEEEEEEDDDGAAQATANAAQLEA----------------- 280

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                            L+   +    +I+E + ++R   +      K+   S      +
Sbjct: 281 -----------------LKRASLEKFAQISEWFDKMRRAFE------KEGYKSKSYLKAQ 317

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
           E +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G 
Sbjct: 318 ETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGS 377

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W           +   ++  + +I + +  +  +     + + + +     +  G
Sbjct: 378 ETDLDWAEKIAAEGHS-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAG 436

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 437 ELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 496

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ 
Sbjct: 497 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKME 556

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL
Sbjct: 557 MPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVL 616

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+
Sbjct: 617 DSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLK 676

Query: 678 SFLDG 682
           SFL+G
Sbjct: 677 SFLEG 681


>gi|66047868|ref|YP_237709.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63258575|gb|AAY39671.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Pseudomonas syringae pv. syringae B728a]
          Length = 616

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 260/657 (39%), Positives = 369/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + D E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  +  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAEMVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|262376664|ref|ZP_06069892.1| RNA polymerase sigma factor rpoD [Acinetobacter lwoffii SH145]
 gi|262308374|gb|EEY89509.1| RNA polymerase sigma factor rpoD [Acinetobacter lwoffii SH145]
          Length = 628

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 265/654 (40%), Positives = 369/654 (56%), Gaps = 39/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I   +++GY+T  E+N  LP     SEQ+ED + ML+++GI V D     D+   E
Sbjct: 11  VAALISRGKEQGYLTFAEVNDHLPDSITESEQIEDIIQMLNDVGIPVHDRAPESDDTMFE 70

Query: 91  DSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D+ + A   +           ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  DTAEAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++    +   G   L ++  L   + PES        E  +  
Sbjct: 131 IRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADL--LSGYLDPESDEEIPEVLEEEAVL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
             +++  +K   DV+  + + E  A    +  +     PE A+     L+    ++  T+
Sbjct: 189 AEDETDSKKSTKDVKLDDDEEEEEADSDDESEADSGPDPEIAKARFTELENAWLNTKATI 248

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  + S + +   + L  +     
Sbjct: 249 E-----------------------------------KHGRDSKQAEEALQALATVFMMFK 273

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +     +I   E E++R A   G + R  F     G+E +P W+    
Sbjct: 274 FTPRLFDIISEMIRGTHDQIRGAEREVMRYAVRRGRMDRTQFRTSFPGQESNPAWLDEQI 333

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                + K ++      +L  + +I  I  E G+ +   + I   +  GE +A  AKKEM
Sbjct: 334 AKTPADQKAYLEKVRPDVLAFQQKIADIEKELGLDVKGIKDIAKRMAVGEAKARRAKKEM 393

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 394 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 453

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 454 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 513

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 514 IAKEPISMETPIGDDEDSHLGDFIEDSNITSPIDAATSEGLKEATREVLENLTEREAKVL 573

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 574 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 627


>gi|89094383|ref|ZP_01167323.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081275|gb|EAR60507.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 616

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 263/657 (40%), Positives = 370/657 (56%), Gaps = 50/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI+V +     +
Sbjct: 7   QQQSRLKELIARGKEQGYLTYSEVNDHLPQDIADPDQVEDIIRMINDMGISVSEEAPDAE 66

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                +      +   +   L   +  A   T DPVRMY+REMG++ELL+REGEI+IAKR
Sbjct: 67  TLLMTEGDSAEEADEEAVAALAAVESDA-GRTTDPVRMYMREMGTVELLTREGEISIAKR 125

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T ++++       +    L +I             G+    + 
Sbjct: 126 IEEGLREVMSAVACFPGTVESILEAYKLTLEEEGRLSDIF-----------SGYIDADDD 174

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                      E++  D  + E +        +D++ K    PE A      L ++ D  
Sbjct: 175 EEIPAAVIPGSEEDLSDEDDDEDEDSDDDDDEEDEKEK-GPDPEEAARRFGLLSDNYDAL 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                    K  + S +    + +L +  
Sbjct: 234 LIALD-----------------------------------KHGRDSKEFGAAQVELSESF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV 384
             + L     + LV Q+    + I + E  ++R+  Q   + R  F++   G E++  W 
Sbjct: 259 APIKLAPRYYEALVNQVRSTIENIRNQERTIMRICTQRAKMPRKTFIKEFPGNEVNADWF 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +   +  E  +   +   +  + + + ++    +ETGIS++E + +   +  GE  A  A
Sbjct: 319 NQVIESGES-YSRAIKTNLIELKRAQKKLIQAEIETGISLAEIKEVNRRMSIGEARARRA 377

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 378 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 437

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + VR
Sbjct: 438 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMEMPEDKVR 497

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ S LGDFIED    SP+DSA    LRE T  VLA LT RE
Sbjct: 498 KVLKIAKEPISMETPIGDDEDSSLGDFIEDTTISSPVDSATGEGLREATREVLAGLTVRE 557

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LR FLD
Sbjct: 558 SKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRGFLD 614


>gi|319944403|ref|ZP_08018677.1| DNA-directed RNA polymerase sigma subunit RpoD [Lautropia mirabilis
           ATCC 51599]
 gi|319742364|gb|EFV94777.1| DNA-directed RNA polymerase sigma subunit RpoD [Lautropia mirabilis
           ATCC 51599]
          Length = 785

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 250/677 (36%), Positives = 367/677 (54%), Gaps = 60/677 (8%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           +++ +  +        +      +++IKL ++RG++T  E+N  LP      E ++  + 
Sbjct: 165 KEALASVKQGVTEEEMEARRSRLRQLIKLGKERGFLTYAEINDHLPEGLTEVEAIDQMIG 224

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
             S+MGI+V +     D     D             +       DS    T DPVRMY+R
Sbjct: 225 TFSDMGISVYEQAPDTDSLLLNDRTVTSSDDDTEEEAEAALSSVDSEFGRTTDPVRMYMR 284

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELL+REGEI IAK+IE G   MM ++   P T   ++   D++      + EI+ 
Sbjct: 285 EMGSVELLTREGEIVIAKKIEEGLKDMMHAISACPTTIAEVLEQADKVRAAQLRVDEIV- 343

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                                     D   + + DD + + G   S              
Sbjct: 344 --------------------------DGLLDPDADDEEMSFGPARSDGD----------- 366

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
                       D+DE   A   +A  ++L+ + +   D I   + ++          + 
Sbjct: 367 ------------DDDEASVAAMNNAKLEELKEEALSRFDSIGAAFEQM------RQALET 408

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGI 365
           D   S      +E + + + S+      ++ L + L      +   E  +L       G+
Sbjct: 409 DGYKSPAYLAAQESVQRQLMSIRFTAKVVEKLCDMLRAQVDEVRTVERTILDICVNRVGM 468

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R+ F++   G E +  WV          + + +A  +  I  ++ ++  + V   + + 
Sbjct: 469 SREHFIKSFPGNETNLAWVENELA-GNPPYADVLARSIPDIQDLQQKLIDLQVRVVLPLP 527

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           + + I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA 
Sbjct: 528 DLKEINKRMAMGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAV 587

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   
Sbjct: 588 DKFEFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGV 647

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP P  +A+K+ MP + +RK+LKI KEPIS+ETPIGD+D SHLGDFIED   ++P D+A+
Sbjct: 648 EPDPATLAEKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTTTLAPSDAAL 707

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             ++RE    VL SLTPRE +VLRMRFG+ M+TDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 708 HDSMREVVKEVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALR 767

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+HPSR+ KL+SFL+G
Sbjct: 768 KLRHPSRADKLKSFLEG 784


>gi|167583913|ref|ZP_02376301.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ubonensis Bu]
          Length = 681

 Score =  441 bits (1134), Expect = e-121,   Method: Composition-based stats.
 Identities = 252/663 (38%), Positives = 375/663 (56%), Gaps = 43/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 57  LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 116

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 117 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 176

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D    + P +     
Sbjct: 177 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRIDELVD--GLLDPNAS---- 230

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                                   +T+G    AA+  +++  + +   E  E ++ +   
Sbjct: 231 ----------------------DTDTDGFSAKAAEEIENEDDEAEEEEEEEEEEDDDGAA 268

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +A  L A    L+   +    +I+E + ++R   +      K+   S      +E 
Sbjct: 269 QATANAAQLEA----LKRASLEKFAQISEWFDKMRRAFE------KEGYKSKSYLKAQET 318

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 319 IQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 378

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 379 DLDWAEKVAAEGHS-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 437

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 438 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 497

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 498 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 557

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 558 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 617

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 618 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 677

Query: 680 LDG 682
           L+G
Sbjct: 678 LEG 680


>gi|121595443|ref|YP_987339.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. JS42]
 gi|120607523|gb|ABM43263.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax sp. JS42]
          Length = 797

 Score =  441 bits (1134), Expect = e-121,   Method: Composition-based stats.
 Identities = 259/660 (39%), Positives = 366/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
                KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V +     + 
Sbjct: 192 RRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAET 251

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +     +      A   +       DS    T DPVRMY+REMG +ELL+REGEI IA
Sbjct: 252 LFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGKVELLTREGEIEIA 311

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  
Sbjct: 312 KRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPN 360

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 361 EADDYVAEEDFDEFDEEDDDDGKGG----------------------------------- 385

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D +  ++ ++  + D      KD         ++ ++  
Sbjct: 386 --SKALTKKLEELKNEALRRFDTLRALFEKMHKIYD------KDGYGGPAYMKVQHEISA 437

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 438 ELMTIRFTAKTIEKLCDMVRAQVDDVRKMERELRRIIVDKCGMPQETFIKEFPANLLNLQ 497

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +   +  I +++ ++  +     + +SE + I   +  GE  + 
Sbjct: 498 WVEKQAAAGKP-WSAVMQRNIPPIQELQQKLIDLQARVVVPLSELKEINKRMNAGEASSR 556

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 557 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 616

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 617 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 676

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTP
Sbjct: 677 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPVDAAMQAGLRDVVKDILDGLTP 736

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 737 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 796


>gi|190575994|ref|YP_001973839.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
           K279a]
 gi|190013916|emb|CAQ47556.1| putative RNA polymerase sigma factor RpoD [Stenotrophomonas
           maltophilia K279a]
          Length = 617

 Score =  441 bits (1134), Expect = e-121,   Method: Composition-based stats.
 Identities = 272/660 (41%), Positives = 380/660 (57%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
           +    K++I    ++GY+T  E+N  LP D V  EQ+ED + M++ MGI+V +     + 
Sbjct: 7   AQSEIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVET 66

Query: 86  ---EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
               +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 67  LLLNDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 126

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L + P++ ++L+   +   +G   L E+I     +G          
Sbjct: 127 AKRIEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVI-----VGFNDLVDEEPA 181

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +     D+  E + D+  + +G  E AA    D                       
Sbjct: 182 PPAVAADDSADADAEGDEDEDDDVDGGDEEAAPTGPDPEE-------------------- 221

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   +  +++ +   +                     L+E++ 
Sbjct: 222 -----------------VAARMQALSDAFNAFKKAATKGDK--------KNLPRLREEMS 256

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQGRELDP 381
            +  +L L     D+L +QL D    I  +E  +L LA  +  + R  F+   +G + + 
Sbjct: 257 AVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIRSWEGNQTNL 316

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     I   T + + E + I   +  GE +A
Sbjct: 317 EWVEDALKR-KQKWSSALREVKDQIIAEQQATIDIETLTQLDLEELKEISRAMAYGEAKA 375

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 376 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 435

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 436 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKEMDMPED 495

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+++    NL ET   VLA LT
Sbjct: 496 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRDVLAGLT 555

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 556 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 615


>gi|330970856|gb|EGH70922.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 616

 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 259/657 (39%), Positives = 369/657 (56%), Gaps = 48/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + D E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  +  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAEMVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 379 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 439 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIR 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE
Sbjct: 499 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTARE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNT+HTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 559 AKVLRMRFGIDMNTNHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 615


>gi|326316262|ref|YP_004233934.1| RNA polymerase sigma-70 subunit RpoD [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323373098|gb|ADX45367.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 780

 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 256/660 (38%), Positives = 364/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
                K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V +     + 
Sbjct: 175 RRSRLKALITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAET 234

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +     +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 235 LFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 294

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  
Sbjct: 295 KRIEGGLQAMMEAISASPATIAEILAMGEEIREGKVVISTIVD-----------GFSNPN 343

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 344 EADDYVAEEDFDEFDEEDDDDGKGG----------------------------------- 368

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D +  ++ ++  + D    G      +      +  +  
Sbjct: 369 --SKALTKKLEELKNEALRRFDNLRGLFEKMHKIYDKEGYG------TPAYMKAQHAISA 420

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 421 ELMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQ 480

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +A  +  + +++  +  +     + +SE + I   + +GE  + 
Sbjct: 481 WVEKQAAAGKP-WSAVLARNIPPVQELQQRLMDLQSRVVVPLSELKDINKRMNEGESASR 539

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 540 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 599

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 600 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 659

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+D+A+QA LR+    +L  LTP
Sbjct: 660 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTP 719

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 720 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 779


>gi|165976903|ref|YP_001652496.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|303252483|ref|ZP_07338647.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307248518|ref|ZP_07530536.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307250749|ref|ZP_07532682.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307261955|ref|ZP_07543613.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|165877004|gb|ABY70052.1| RNA polymerase sigma factor [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|302648684|gb|EFL78876.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854994|gb|EFM87179.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306857217|gb|EFM89340.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306868366|gb|EFN00185.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 619

 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 276/648 (42%), Positives = 379/648 (58%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P          E       +  
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPN-----IQADEALEDLDVDLD 186

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E+  D     +   E  +  + D        PE A      L E  + +   +     
Sbjct: 187 DEEEAEDVADVDDESEEEESDGNADTGDDNSIDPELAREKFYALREQHEKALQAI----- 241

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +S  K +   + L  +     L   +
Sbjct: 242 ------------------------------QKHGRSHKKSREQIQALSDIFREFRLVPKQ 271

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  + 
Sbjct: 272 FDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAIN-AKK 330

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  +D I    + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 331 GAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANL 390

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 451 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 510

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 511 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFG 570

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|120610093|ref|YP_969771.1| RpoD family RNA polymerase sigma factor [Acidovorax citrulli
           AAC00-1]
 gi|120588557|gb|ABM31997.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax citrulli
           AAC00-1]
          Length = 781

 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 256/660 (38%), Positives = 364/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
                K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V +     + 
Sbjct: 176 RRSRLKALITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAET 235

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +     +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 236 LFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 295

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  
Sbjct: 296 KRIEGGLQAMMEAISASPATIAEILAMGEEIREGKVVISTIVD-----------GFSNPN 344

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 345 EADDYVAEEDFDEFDEEDDDDGKGG----------------------------------- 369

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D +  ++ ++  + D    G      +      +  +  
Sbjct: 370 --SKALTKKLEELKNEALRRFDNLRGLFEKMHKIYDKEGYG------TPAYMKAQHAISA 421

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 422 ELMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQ 481

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +A  +  + +++  +  +     + +SE + I   + +GE  + 
Sbjct: 482 WVEKQAAAGKP-WSAVLARNIPPVQELQQRLMDLQSRVVVPLSELKDINKRMNEGESASR 540

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 541 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 600

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 601 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 660

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+D+A+QA LR+    +L  LTP
Sbjct: 661 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTP 720

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 721 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 780


>gi|110834924|ref|YP_693783.1| RNA polymerase sigma factor RpoD [Alcanivorax borkumensis SK2]
 gi|110648035|emb|CAL17511.1| RNA polymerase sigma factor RpoD [Alcanivorax borkumensis SK2]
          Length = 633

 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 265/652 (40%), Positives = 366/652 (56%), Gaps = 40/652 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSL 93
           I L +++GY+T  E+N  LP     ++Q+ED + M+++MGI VV+   D +     E + 
Sbjct: 16  IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDESAD 75

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                A+  +  +    ++    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +
Sbjct: 76  STDEVAAEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + +L   P     +I     + +    L +II     + P   G              + 
Sbjct: 136 LHALAFWPGAVDMVIEEYARVENEERKLTDII--AGYLDPNDDGAAATNANRDPAFAEKA 193

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
               +E+   +E   +  S  K S D+  + +   +                        
Sbjct: 194 KKAAEEKAKAKEKAKEEGSDDKDSDDEDEEDEGGLDPVLA-------------------- 233

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQ 332
                         AE +  L+ LQ+ A    K + +         E L +      L  
Sbjct: 234 --------------AERFETLKKLQEKAERSLKRNGRDHASTAKALEALAEHFTLFKLVP 279

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFP 391
              D ++    D    +   E +++      G + R  F++   G E +  W+       
Sbjct: 280 RIFDSMLVGARDNLDLVRKFERQIMSATIRRGGMDRKDFIKAFPGNETNMEWIDSQLKTK 339

Query: 392 EGEW-KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           +G+   + ++   + + + + +I +I    G+ +++ + I   +  GE +A  AKKEMVE
Sbjct: 340 KGKAIADKLSVVKEDVQRAQRKISTIEDIIGLPVADIKEINRRISIGEAKARRAKKEMVE 399

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 400 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 459

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R  R+M  ++ REPTPEE+  +L MP + VRKVLKI 
Sbjct: 460 SIADQARTIRIPVHMIETINKINRVQRQMLQEMGREPTPEELGVRLEMPEDKVRKVLKIA 519

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ S LGDFIED N  SP+DSA    L E T  VLA+LT RE +VLRM
Sbjct: 520 KEPISMETPIGDDEDSSLGDFIEDGNMESPVDSATSLGLEEATRDVLANLTAREAKVLRM 579

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLDG
Sbjct: 580 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLDG 631


>gi|190150752|ref|YP_001969277.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|189915883|gb|ACE62135.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
          Length = 619

 Score =  440 bits (1132), Expect = e-121,   Method: Composition-based stats.
 Identities = 277/648 (42%), Positives = 379/648 (58%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P          E       +  
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPN-----IQADEALEDLDVDLD 186

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E+  D     +   E  +  S D        PE A      L E  + +   +     
Sbjct: 187 DEEEAEDVADVDDESEEEESDGSADTGDDNSIDPELAREKFYALREQHEKALQAI----- 241

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +S  K +   + L  +     L   +
Sbjct: 242 ------------------------------QKHGRSHKKSREQIQALSDIFREFRLVPKQ 271

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  + 
Sbjct: 272 FDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAIN-AKK 330

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  +D I    + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 331 GAAPKLANYIDQIRVNIDNLQHMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANL 390

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 451 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 510

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 511 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFG 570

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|291614899|ref|YP_003525056.1| RNA polymerase, sigma 70 subunit, RpoD [Sideroxydans lithotrophicus
           ES-1]
 gi|291585011|gb|ADE12669.1| RNA polymerase, sigma 70 subunit, RpoD [Sideroxydans lithotrophicus
           ES-1]
          Length = 654

 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 250/662 (37%), Positives = 367/662 (55%), Gaps = 54/662 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +I L ++RGY+T  E+N  LP D +  EQ+E  V+M+++MGI V D    
Sbjct: 42  IEARRTRLKALILLGKERGYLTFAEINDHLP-DMLEVEQVEGVVSMINDMGITVCDVAPD 100

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ--KRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +     ++    +    +          DS    T DPVRMY+REMG + LL+R+ EI 
Sbjct: 101 TESLVMNETAPPVADEDAAEEAEAAISTVDSEFGRTTDPVRMYMREMGVVNLLTRQDEIE 160

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P T   ++   D++      + E+ID       E+      
Sbjct: 161 IAKRIEDGLKHMIQAISACPATIAEILALADKVAKEELRIDELIDGFIDTQDEAMVSEVA 220

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E    ++ ED  +E E D       ++                               
Sbjct: 221 EEEETEEEEEEDEEEESEEDGEAAAAANL------------------------------- 249

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                        QL+   +     I++++ +L    +      K    S +   L++++
Sbjct: 250 ------------AQLKEDALVRFALISDLFTKLGKAYE------KYGYRSKQYDKLQQQI 291

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
              +     +  ++D L E +  + + +   E  +  L      + R  F++     E +
Sbjct: 292 SDELMQFRFSAKQVDALCETMRGLVEEVRSCERSIQELCVTKAHMPRTHFIKVFPLNEGN 351

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV +     +  +   ++    +I+  + ++ ++    GI I + + I   +  GE +
Sbjct: 352 LEWVKHEMA-SKKAYSETLSRYEAAIVDQQKKMLALQQRVGIPILDLKEINKQMTNGEAK 410

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK++M+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 411 ARRAKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 470

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   E     +A K+ MP 
Sbjct: 471 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGMEADAATLAIKMEMPE 530

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RK+LKI KEPIS+ETP+GD+D SHLGDFIED N+++P+++A+  +LR  T  +L SL
Sbjct: 531 DKIRKILKIAKEPISMETPVGDDDDSHLGDFIEDANSLAPIEAAVYDSLRNVTKDILDSL 590

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KL+SFL
Sbjct: 591 TPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLKSFL 650

Query: 681 DG 682
           DG
Sbjct: 651 DG 652


>gi|171059243|ref|YP_001791592.1| RNA polymerase sigma-70 subunit RpoD [Leptothrix cholodnii SP-6]
 gi|170776688|gb|ACB34827.1| RNA polymerase, sigma 70 subunit, RpoD [Leptothrix cholodnii SP-6]
          Length = 754

 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 257/660 (38%), Positives = 369/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IK+ + RG++T +E+N  LP   V +E +E  V+ML++MGI V +       
Sbjct: 149 RRSELKTLIKMGKTRGFLTHQEINDHLPEKLVEAEILEAIVSMLNDMGIAVYEQAPDAAT 208

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
               G   +      A  ++       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 209 LLIAGGGTTTSTEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 268

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +++  GT  +  ++D           GF    
Sbjct: 269 KRIEGGLQAMMLAISASPATIAEVLEMANKIRAGTDPISSVVD-----------GFVAAD 317

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E +D     G                                   
Sbjct: 318 EADDYVAEEDFDEFDEEEDDDGNGG----------------------------------- 342

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D +   + ++R   D      KD   S      +E +  
Sbjct: 343 --SKALTKKLEELKNQALVKFDALQLDFDKMRKAYD------KDGYKSPAYNKAQEAISG 394

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + L      I   E EL ++     G+ ++ F++      L+  
Sbjct: 395 QLMTVRFTVKTIEKLCDLLRSQVDDIRRFERELRKIVVDRCGMPQEYFIKSFPPNILNLE 454

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W           +   ++  + +I +++ ++  +  +  + I + + I   + +GE  + 
Sbjct: 455 WAENEIA-ANKPYSAVMSRNLPAIQELQQKLTDLQTKAVVPIDDLKQINRRMNEGEASSR 513

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 514 EAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 573

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A+K+ MP + 
Sbjct: 574 WIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQEFGFEPDAPSLAEKMEMPEDK 633

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+++A+Q+ LR+    +L SLTP
Sbjct: 634 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPIEAAMQSGLRDVVRDILDSLTP 693

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKAIRKLKHPSRS KLR++LD 
Sbjct: 694 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRSDKLRTYLDN 753


>gi|303250977|ref|ZP_07337166.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253124|ref|ZP_07535005.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302650194|gb|EFL80361.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859418|gb|EFM91450.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 619

 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 275/648 (42%), Positives = 378/648 (58%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P          E       +  
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPN-----IQADEALEDLDVDLD 186

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E+  D     +   E  +  + D        PE A      L E  + +   +     
Sbjct: 187 DEEEAEDVADVDDESEEEESDGNADTGDDNSIDPELAREKFYALREQHEKALQAI----- 241

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +S  K +   + L  +     L   +
Sbjct: 242 ------------------------------QKHGRSHKKSREQIQALSDIFREFRLVPKQ 271

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  + 
Sbjct: 272 FDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAIN-AKK 330

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +   +D I    + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 331 GAAPKLTNYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANL 390

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 451 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 510

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 511 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFG 570

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|307264154|ref|ZP_07545748.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|306870528|gb|EFN02278.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 619

 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 276/648 (42%), Positives = 379/648 (58%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P          E       +  
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPN-----IQADEALEDLDVDLD 186

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E+  D     +   E  +  S D        PE A      L E  + +   +     
Sbjct: 187 DEEEAEDVADVDDESEEEESDGSADTGDDNSIDPELAREKFYALREQHEKALQAI----- 241

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +S  K +   + L  +     L   +
Sbjct: 242 ------------------------------QKHGRSHKKSREQIQALSDIFREFRLVPKQ 271

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  +G E    W+  A +  + 
Sbjct: 272 FDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFRGNETSEEWIEKAIN-AKK 330

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  +D I    + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 331 GAAPKLANYIDQIRVNIDNLQHMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANL 390

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 451 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 510

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 511 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFG 570

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|27904560|ref|NP_777686.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340403|sp|Q89B10|RPOD_BUCBP RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|27903957|gb|AAO26791.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
          Length = 609

 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 257/658 (39%), Positives = 366/658 (55%), Gaps = 59/658 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  L  + ++S+Q+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKLLVTYGKEQGYLTYSEINDHLSDNIINSDQIEDIIQMINDMGIQVVEKAPDSDDL 65

Query: 88  GSED---SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
              +   + +       ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  ILHEIKRNNETDEDIVEATAQVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAK 125

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   + +  G   L E+I     + P ++      T 
Sbjct: 126 RIEDGINQVQCSVAEYPEAITHLLEQYNRVELGELRLSELI--HGFVDPNAEAVHTSITN 183

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +    E    +   ++  +                      PE A      L      
Sbjct: 184 HINTNSEEHHHNDNTEENNDDDHLV-----------------DPELAREKFIALKNQYHI 226

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           + + +       +  ++                                       L ++
Sbjct: 227 TNYAIKTKNRNHQDTLIEI-----------------------------------NNLSEI 251

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHW 383
                L   + D LV  +  + ++I   E  + +L   YG I +   L     ++ +  W
Sbjct: 252 FKQFRLVPKQFDHLVINMRKMMQKIRIQERNIAKLCIEYGNIPKKALLNFFSLQKTNQIW 311

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               ++  +  W +        I  I  +++ +  ETG++I + ++I   +  GE +A  
Sbjct: 312 SKIVQNI-KKPWIDKFNTIKPDIQMILKKLQKVEEETGLTIHQVKNINKRISLGEAKAKR 370

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 371 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 430

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +I REPTPEE+++++ +P + +
Sbjct: 431 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQEIGREPTPEELSERMLIPEDKI 490

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPIS+ETPIG++D SHLGDF+ED N   PLDSA  A+LR  T  VL+ LT R
Sbjct: 491 RKVLKIAKEPISMETPIGEDDDSHLGDFLEDTNIELPLDSATSASLRSATKNVLSGLTTR 550

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 551 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILRSFLD 608


>gi|319792617|ref|YP_004154257.1| RNA polymerase, sigma 70 subunit, rpod [Variovorax paradoxus EPS]
 gi|315595080|gb|ADU36146.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus EPS]
          Length = 778

 Score =  440 bits (1130), Expect = e-121,   Method: Composition-based stats.
 Identities = 261/669 (39%), Positives = 368/669 (55%), Gaps = 69/669 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V +     + 
Sbjct: 163 RRSRLKTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAET 222

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 223 LLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 282

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF +  
Sbjct: 283 KRIEGGLMAMMEAISASPATIAEILRLANEIREGKVVISTIVD-----------GFSNPN 331

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 332 EADDYVAEEDFDEFDEEDDDDGKGG----------------------------------- 356

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+   +   D IA ++ ++  + D      K+   +      +E L +
Sbjct: 357 --SKALTKKLEELKRDALERFDRIAGMFEKVHKIYD------KEGYGTPAYVKAQEALSE 408

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQG------ 376
            + ++      I+ L + +      +   E EL R +    G  +D F+    G      
Sbjct: 409 ELMTIRFTAKTIEKLCDLVRTQVDDVRKKERELRRIIVDKCGFPQDEFIRDFSGYDKNGN 468

Query: 377 ----RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                 L+  WV       +  W   +A  +  + +++  +  I     + +++ + I  
Sbjct: 469 RIASNLLNLKWVEKQAAAGKP-WSAVLARNIPPVQELQQRLADIQSRVVVPLTQLKDINK 527

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 528 RMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 587

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +
Sbjct: 588 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGIL 647

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A K+ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED +  +P+++A+QA LR+ 
Sbjct: 648 AAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDV 707

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 708 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSR 767

Query: 673 SKKLRSFLD 681
           S KLRSF+D
Sbjct: 768 SDKLRSFID 776


>gi|32034495|ref|ZP_00134667.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|126208939|ref|YP_001054164.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
           L20]
 gi|307257544|ref|ZP_07539308.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|126097731|gb|ABN74559.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
 gi|306863980|gb|EFM95899.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 619

 Score =  440 bits (1130), Expect = e-121,   Method: Composition-based stats.
 Identities = 277/648 (42%), Positives = 379/648 (58%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P          E       +  
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPN-----IQADEALEDLDVDLD 186

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E+  D     +   E  +  S D        PE A      L E  + +   +     
Sbjct: 187 DEEEAEDVADVDDESEEEESDGSTDTGDDNSIDPELAREKFYALREQHEKALQAI----- 241

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +S  K +   + L  +     L   +
Sbjct: 242 ------------------------------QKHGRSHKKSREQIQALSDIFREFRLVPKQ 271

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  + 
Sbjct: 272 FDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAIN-AKK 330

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  +D I    + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 331 GAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANL 390

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 451 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 510

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 511 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPREAKVLRMRFG 570

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|34499217|ref|NP_903432.1| RNA polymerase sigma factor RpoD [Chromobacterium violaceum ATCC
           12472]
 gi|34105068|gb|AAQ61424.1| RNA polymerase sigma factor RpoD [Chromobacterium violaceum ATCC
           12472]
          Length = 643

 Score =  440 bits (1130), Expect = e-121,   Method: Composition-based stats.
 Identities = 253/677 (37%), Positives = 378/677 (55%), Gaps = 47/677 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            +     +   + +  +      +++I L ++RGY+T  E+N  LP D   +EQ+E+ V 
Sbjct: 6   ENQKDVKDSQQEVMSLEEQRKRLRQLIALGKERGYLTYAEINDHLPEDVSDAEQIENIVT 65

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSL--DLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           M++ +GI V +     +     D+        A   +       DS    T DPVRMY+R
Sbjct: 66  MIAGLGIQVCEEAPDAETLLMSDATPSVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMR 125

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMGS+ELL+REGEI IAKRIE G   M+ ++   P T   ++   + +      + E++D
Sbjct: 126 EMGSVELLTREGEIEIAKRIEDGLKYMIQAISACPGTIAEVLELMERVARDEIRVDEVVD 185

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
               +                       +  ++     E E   +   +  +++  +  +
Sbjct: 186 GFIDLN----------------------APTEDEAQFAEPEDSDDLLDEEEEEEEDEDGA 223

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
           P +   +   NL+E               L+ + +     +  ++ ++            
Sbjct: 224 PVDADADAAANLEE---------------LKQQALEHFAGVRMLFDKMVK------ALNA 262

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGI 365
             + S +   L++ +      +     +++ L E L      I   E ++         +
Sbjct: 263 KGQQSKEYLELQDAITTEFMLVRFATRQVESLCESLRGRVNEIRTYERDIQDICVSRVRM 322

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  F++   G E +  WV    D  +  W   +     +I++ +  +  +  +  +SI 
Sbjct: 323 DRAHFIKVFPGNETNLDWVENEIDSGKA-WSEALTRFKHAIIEKQTRLSDLQDKAMLSIK 381

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
             + I   +  GE +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 382 ALKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 441

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  R
Sbjct: 442 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQESGR 501

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP P E+A+K+ MP E +RK++KI+KEPIS+ETPIGD+D SHLGDFIED+N ++P D+A+
Sbjct: 502 EPDPAELAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQNNLAPSDAAM 561

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++L++ T  VL +LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 562 YSSLKDATKEVLDTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 621

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+HP+RS++LRSFLD 
Sbjct: 622 KLRHPTRSERLRSFLDS 638


>gi|330721841|gb|EGG99811.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC2047]
          Length = 614

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 270/660 (40%), Positives = 371/660 (56%), Gaps = 51/660 (7%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
             +      K++I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +   
Sbjct: 4   TSEQQRSRLKELIARGKEQGYLTYAEVNDHLPQDISDPDQVEDIIRMINDMGITVDEVAP 63

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            +D     ++      A   +       ++    T DPVRMY+REMGS+ELL+REGEI I
Sbjct: 64  DQDTLQLNENT--DDDAVEEAAAALAAVETEVGRTTDPVRMYMREMGSVELLTREGEIVI 121

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +M +L   P     ++    +  +    + +I+            GF   
Sbjct: 122 AKRIEEGIREVMCALASFPGAVDVILEAYAQTIEEEGRISDIL-----------SGFLED 170

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  + + + Q  E  DV   E D + +    +D+  +   P E AE          
Sbjct: 171 EVEEPVIQGQQAPQPVEETDVTVDETDTDDSDDEDEDEVERGPDPVETAER--------- 221

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                             M AL +  E+  +            K  + S +    +E+L 
Sbjct: 222 ------------------MSALKKQFEIVNKAIE---------KHGRGSKQVLEAQEELG 254

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDP 381
           ++   + L     D LV+ + +  + I   E  +L        + R  F++   G E DP
Sbjct: 255 EIFCPIKLTPRYFDRLVQNVRETLEFIRAQERLILHTCTRTVRMPRKAFIKEFMGSETDP 314

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W+  A +    ++   +A   + I++ + ++K+        I E + I   +  GE +A
Sbjct: 315 AWLDRAIE-GGHDYSEGLAEHREDIVRAQRKLKTTEESIDAPIHEIKEINRHMSIGEAKA 373

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 374 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP +
Sbjct: 434 WWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGERMDMPED 493

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VRKVLKI KEPIS+ETPIGD++ SHLGDFIED N  SP+DSA    L E T  VL+ LT
Sbjct: 494 KVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNIDSPIDSATAEGLSEATRGVLSGLT 553

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR FLD
Sbjct: 554 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFLD 613


>gi|90020363|ref|YP_526190.1| Fis family transcriptional regulator [Saccharophagus degradans
           2-40]
 gi|89949963|gb|ABD79978.1| RNA polymerase sigma factor RpoD-like protein [Saccharophagus
           degradans 2-40]
          Length = 613

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 269/657 (40%), Positives = 369/657 (56%), Gaps = 53/657 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLED 85
                K++I   R++GY+T +E+N  LP D    +Q+ED + M+++MGI V +   D ++
Sbjct: 7   KQSRIKELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAPDADE 66

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              ++        A+  +       ++    T DPVRMY+REMG++ELL+REGEIAIAKR
Sbjct: 67  LLMTDGDSSADEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +  ++   P   Q  +   D +      L ++I            G+    E 
Sbjct: 127 IEEGLRELNHAIALWPEAVQQYVNEYDLVEKEERRLADVI-----------SGWLDPAED 175

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +       + E         + D +     ++D+       PE A              
Sbjct: 176 VAPPVVAAETAEDTD----SDDDDDDDDDTDTEDEEESTGIDPEYARERF---------- 221

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                   D+L+  ++     IA                 K    S       E L ++ 
Sbjct: 222 --------DELKAALLKVEKAIA-----------------KHGFESKAAGKEMEALGEIF 256

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV 384
               L   + D + + +  I  R+   E E++RL    G + R  F++   G+E D  W+
Sbjct: 257 KYFKLPPRQFDPIYQGIRQILTRVRAEEREIMRLCTRLGGMPRKTFMKEFPGQETDEDWI 316

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A      ++ + +    + I++ + ++K I  E+G+S+   + I   +  GE  A  A
Sbjct: 317 P-ATIGKGRDYSDSLKPYAEDIIRAQRKLKQIQEESGLSLGHIKEINRRMSIGEARARRA 375

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 376 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 435

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VR
Sbjct: 436 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKVR 495

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA    L E T  VLA LT RE
Sbjct: 496 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPVDSATIQGLTEATRSVLAGLTARE 555

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LR FLD
Sbjct: 556 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRGFLD 612


>gi|260548994|ref|ZP_05823216.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
 gi|260408162|gb|EEX01633.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
          Length = 628

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 268/654 (40%), Positives = 368/654 (56%), Gaps = 39/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E     
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEEL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED S  K   +V+  + D E  ++   D        PE A+     L+     +   +
Sbjct: 189 EEEDESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVI 248

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  ++S +     E L  +     
Sbjct: 249 E-----------------------------------KHGRNSPEANEALESLATVFMMFK 273

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  NE E++R A   G + R  F       E +P W+    
Sbjct: 274 FTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKHESNPAWLDEQI 333

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E  +S++E + I   +  GE +A  AKKEM
Sbjct: 334 AKAPAEIKVHLEKVRPDVLAFQQKIADIEKELNLSVAEIKDISKRMAIGEAKARRAKKEM 393

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 394 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 453

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 454 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 513

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 514 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVL 573

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 574 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 627


>gi|222111657|ref|YP_002553921.1| RNA polymerase sigma-70 subunit RpoD [Acidovorax ebreus TPSY]
 gi|221731101|gb|ACM33921.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax ebreus TPSY]
          Length = 801

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 258/660 (39%), Positives = 367/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
                KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V +     + 
Sbjct: 196 RRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAET 255

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +     +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 256 LFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 315

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  
Sbjct: 316 KRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPN 364

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 365 EADDYVAEEDFDEFDEEDDDDGKGG----------------------------------- 389

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D +  ++ ++  + D      KD         ++ ++  
Sbjct: 390 --SKALTKKLEELKNEALRRFDTLRALFEKMHKIYD------KDGYGGPAYMKVQHEISA 441

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F++      L+  
Sbjct: 442 ELMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVDKCGMPQETFIKDFPANLLNLQ 501

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +   +  I +++ ++  +     + +SE + I   +  GE  + 
Sbjct: 502 WVEKQAAAGKP-WSAVMQRNIPPIQELQQKLMDLQARVVVPLSELKEINKRMNAGEASSR 560

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 561 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 620

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 621 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 680

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED +  +P+D+A+QA LR+    +L  LTP
Sbjct: 681 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPVDAAMQAGLRDVVKDILDGLTP 740

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 741 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 800


>gi|295700891|ref|YP_003608784.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295440104|gb|ADG19273.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 665

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 231/662 (34%), Positives = 353/662 (53%), Gaps = 47/662 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +I+L +++GY+T  ++N  LP +  ++  ++  V+  S+MG+ V +    
Sbjct: 46  AEERQRLMRALIQLGKEQGYLTHAQINDHLPDNFTATAAIDSIVSAFSDMGVQVYEQAPD 105

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  ++     A   +       DS    T DPVRMY+REMG+ ELL+R GEI
Sbjct: 106 AETLLLNSNSPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGEI 165

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           AIAKRIE G   M+ ++   PL   A++    ++ DG   + E++D              
Sbjct: 166 AIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVD-------------G 212

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E  + ++ E +  + E D V + + D E        D S  D               
Sbjct: 213 LNEETGAAEEVESADADAEEDGVADEDSDDEEEDDDGPADSSAADE-------------- 258

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                     A   QL    +    ++  +Y E+ +         + + +S      +E+
Sbjct: 259 ----------ARLKQLTSDCLEIFAQVGILYDEMNA------AHTRGDVTSKGYLRAREE 302

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           + + +  +      ID L   +     ++   E  +L++     G+ R+ F+E   G E 
Sbjct: 303 IQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVSKAGMPREKFIETFAGNEA 362

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W   A       +   +   + +I   + ++  I     + +   + I   +   E 
Sbjct: 363 DLGWTERAARTGASTYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRKMVAAES 422

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTY
Sbjct: 423 KMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTY 482

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +A+++ + 
Sbjct: 483 ATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAERMELS 542

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR +LKI K+P+SLETP+GD+  + LGD IED    SP D+A+QA+LR      L S
Sbjct: 543 EEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVSSPADAAMQADLRAAIDDALDS 602

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ +L+SF
Sbjct: 603 LSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLKSF 662

Query: 680 LD 681
           LD
Sbjct: 663 LD 664


>gi|319762043|ref|YP_004125980.1| RNA polymerase sigma factor rpod [Alicycliphilus denitrificans BC]
 gi|317116604|gb|ADU99092.1| RNA polymerase sigma factor RpoD [Alicycliphilus denitrificans BC]
          Length = 802

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 258/660 (39%), Positives = 368/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
                KK+I L + RGY+T  E++  LP   V +E ME  VAML +MG+ V +     + 
Sbjct: 197 RRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLGDMGVAVYEQTPDAET 256

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +     +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 257 LFQNNVAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 316

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF +  
Sbjct: 317 KRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVD-----------GFSNPE 365

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 366 EADDYVAEEDFDEYDEEDDDDGKGG----------------------------------- 390

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  ++ + ++L+ + +   DE+  ++ ++  + D    G      S     ++ ++  
Sbjct: 391 --SKAMTRLLEKLKTEALDRFDELRSLFEKMHKIYDKEGYG------SPAYMKVQHEISA 442

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + +      +   E EL R+     G+ ++ F +      L+  
Sbjct: 443 KLMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVDKCGMPQETFSKEFPSNLLNLQ 502

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           WV       +  W   +   +  I +++  +  +     + ++E + I   + +GE  + 
Sbjct: 503 WVEKQAAAGKP-WSAVMQRNIPPIQELQQHLIDLQSRVVVPLAELKAINKRMNQGEANSR 561

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 562 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 621

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P + 
Sbjct: 622 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDK 681

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  LTP
Sbjct: 682 IRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPIDAAMQAGLRDVVKDILDGLTP 741

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D 
Sbjct: 742 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFIDS 801


>gi|15595773|ref|NP_249267.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAO1]
 gi|116054304|ref|YP_788749.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218889317|ref|YP_002438181.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa LESB58]
 gi|254243670|ref|ZP_04936992.1| sigma factor RpoD [Pseudomonas aeruginosa 2192]
 gi|296387081|ref|ZP_06876580.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAb1]
 gi|313111780|ref|ZP_07797573.1| sigma factor RpoD [Pseudomonas aeruginosa 39016]
 gi|133310|sp|P26480|RPOD_PSEAE RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|9946447|gb|AAG03965.1|AE004494_1 sigma factor RpoD [Pseudomonas aeruginosa PAO1]
 gi|216913|dbj|BAA14146.1| principal sigma factor [Pseudomonas aeruginosa]
 gi|30060254|gb|AAP13091.1| RpoD [Pseudomonas sp. M18]
 gi|115589525|gb|ABJ15540.1| sigma factor RpoD [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126197048|gb|EAZ61111.1| sigma factor RpoD [Pseudomonas aeruginosa 2192]
 gi|218769540|emb|CAW25300.1| sigma factor RpoD [Pseudomonas aeruginosa LESB58]
 gi|310884075|gb|EFQ42669.1| sigma factor RpoD [Pseudomonas aeruginosa 39016]
          Length = 617

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 266/657 (40%), Positives = 381/657 (57%), Gaps = 47/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVE-SDIGRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++ + P T  +++   + +      L ++  L   I P+         E 
Sbjct: 125 IEEGIREVMSAIAQFPGTVDSILADYNRIVAEGGRLSDV--LSGYIDPDDGSLPAEEVEP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            + +                     + +A   + D  + +S   +  +DE +   D +++
Sbjct: 183 VNLK---------------------DDSADSKEKDDEEEESDDSSDSDDEGDGGPDPEEA 221

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
               +A+ +QL                            +K  + S +       L +L 
Sbjct: 222 RLRFTAVSEQLDKA---------------------KKALKKHGRGSKQATAELTGLAELF 260

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LV ++    + +   E  +++L      + R  FL      E D  WV
Sbjct: 261 MPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHETDEKWV 320

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  + ++   +    D IL+ + ++ ++  E  ++++E + I   +  GE +A  A
Sbjct: 321 DSVLK-SKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGEAKARRA 379

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 380 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 439

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +R
Sbjct: 440 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKIR 499

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA LT RE
Sbjct: 500 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLAGLTARE 559

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 616


>gi|74318406|ref|YP_316146.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thiobacillus
           denitrificans ATCC 25259]
 gi|74057901|gb|AAZ98341.1| Carbamoyl-phosphate synthase L chain, ATP-binding [Thiobacillus
           denitrificans ATCC 25259]
          Length = 656

 Score =  439 bits (1129), Expect = e-121,   Method: Composition-based stats.
 Identities = 248/660 (37%), Positives = 373/660 (56%), Gaps = 59/660 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +I L ++RG++T  E+N  LP + + ++Q+E  ++M+++MGI V D    
Sbjct: 48  AEARRTQLKNLIILGKERGFLTYAEINDHLPDEVLDADQIEGVISMINDMGIQVYDEAPD 107

Query: 84  EDEEGSEDSLDLASSAS--NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +    +++    +       +       DS    T DPVRMY+REMGS++LL+REGEI 
Sbjct: 108 AETLLMQEAAPAVADEDVVAEAEQALTTVDSEFGRTTDPVRMYMREMGSVDLLTREGEIE 167

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   PLT Q ++    ++             +     E   GF  
Sbjct: 168 IAKRIEEGLRHMVQAISSCPLTIQQILDMAAQVEK-----------DELRIDELIDGFVE 216

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                + ++   +  ++  +D ++    + +A                            
Sbjct: 217 AETEAAAEEETAAGDDETDEDDEDASAAVAAANLA------------------------- 251

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                        QL+ + +   D I + Y++ +          K    S +    + ++
Sbjct: 252 -------------QLKAEALAQFDYIRKAYKKAQ------NAHVKYGLGSAQHMKAQAEV 292

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELD 380
            +L+ ++  +  ++D L EQ+    + +  +E +++       G+ R  F++   G E +
Sbjct: 293 TELLMAIRFSVRQVDNLCEQIRSAVEEVRSHERKIMEFCVNRSGMPRAHFIKAFPGNETN 352

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+       +  + + ++     +   +  + ++    G+ I   + I   +  GE +
Sbjct: 353 LAWLDREIA-AKKAYCSTLSKVQYEVKAHQEALIAMQDRVGLPIKNLKDINKQMSTGEAK 411

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 412 ARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 471

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A K+ MP 
Sbjct: 472 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGIEPDPATLAIKMEMPE 531

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RK++KI KEPIS+ETPIGD++ SHLGDFIED + +SP DSAI ANLR+ T  VL SL
Sbjct: 532 DKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDASTLSPDDSAIYANLRDATREVLDSL 591

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+KL+SF+
Sbjct: 592 TSREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEKLKSFV 651


>gi|167577173|ref|ZP_02370047.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
 gi|167615343|ref|ZP_02383978.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
          Length = 680

 Score =  439 bits (1128), Expect = e-121,   Method: Composition-based stats.
 Identities = 248/663 (37%), Positives = 364/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 59  LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D           GF 
Sbjct: 179 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLIDPNAADTDGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E++ ++ E ++  +      +A     +                     
Sbjct: 239 EKDAEEIENEDEEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 318 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|186472768|ref|YP_001860110.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
 gi|184195100|gb|ACC73064.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
          Length = 685

 Score =  439 bits (1128), Expect = e-121,   Method: Composition-based stats.
 Identities = 249/663 (37%), Positives = 366/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 64  LEERRSKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 123

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 124 AETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 183

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D    +  E   GF 
Sbjct: 184 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDVNAEDTDGFS 243

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E+  +  E ++  +      +A     +                     
Sbjct: 244 EQEAEAIESEDEEEEEADEEEEEDDDGAAQATANAAQLE--------------------- 282

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                         +L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 283 --------------ELKRLSLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 322

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           + + +  +      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 323 IQEELMMIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGNET 382

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  V +I + +  +  +     + + + +     +  GE 
Sbjct: 383 DLEWADKIVSENHA-YSAILSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 441

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 442 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 501

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 502 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 561

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 562 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDS 621

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 622 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 681

Query: 680 LDG 682
           L+G
Sbjct: 682 LEG 684


>gi|169794936|ref|YP_001712729.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter baumannii AYE]
 gi|184159289|ref|YP_001847628.1| DNA-directed RNA polymerase, sigma subunit [Acinetobacter baumannii
           ACICU]
 gi|213157659|ref|YP_002320457.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii
           AB0057]
 gi|215482482|ref|YP_002324668.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB307-0294]
 gi|239502295|ref|ZP_04661605.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB900]
 gi|260557301|ref|ZP_05829517.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii ATCC
           19606]
 gi|301346958|ref|ZP_07227699.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB056]
 gi|301513036|ref|ZP_07238273.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB058]
 gi|301596278|ref|ZP_07241286.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB059]
 gi|332854224|ref|ZP_08435244.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013150]
 gi|332866334|ref|ZP_08436939.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013113]
 gi|332872549|ref|ZP_08440518.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6014059]
 gi|169147863|emb|CAM85726.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter baumannii AYE]
 gi|183210883|gb|ACC58281.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii ACICU]
 gi|193078173|gb|ABO13119.2| sigma D (sigma 70) factor of RNA polymerase major sigma factor
           during exponential growth [Acinetobacter baumannii ATCC
           17978]
 gi|213056819|gb|ACJ41721.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii
           AB0057]
 gi|213988184|gb|ACJ58483.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter
           baumannii AB307-0294]
 gi|260409407|gb|EEX02709.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii ATCC
           19606]
 gi|322509200|gb|ADX04654.1| rpoD [Acinetobacter baumannii 1656-2]
 gi|323519229|gb|ADX93610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii TCDC-AB0715]
 gi|332728149|gb|EGJ59537.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013150]
 gi|332734682|gb|EGJ65786.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013113]
 gi|332739235|gb|EGJ70093.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6014059]
          Length = 628

 Score =  439 bits (1128), Expect = e-121,   Method: Composition-based stats.
 Identities = 269/654 (41%), Positives = 371/654 (56%), Gaps = 39/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E     
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEDVEEL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED S  K   +V+  + D E  ++   D        PE A+     L+     +   +
Sbjct: 189 EEEDESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVI 248

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  ++S +     E L  +     
Sbjct: 249 E-----------------------------------KHGRNSPEANEALESLATVFMMFK 273

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  NE E++R A   G + R+ F      +E +P W+    
Sbjct: 274 FTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRNQFRTSFPKQESNPAWLDEQI 333

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E G+++SE + I   +  GE +A  AKKEM
Sbjct: 334 AKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEM 393

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 394 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 453

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 454 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 513

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 514 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVL 573

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 574 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 627


>gi|332528540|ref|ZP_08404528.1| RNA polymerase, sigma 70 subunit, rpod [Hylemonella gracilis ATCC
           19624]
 gi|332042051|gb|EGI78389.1| RNA polymerase, sigma 70 subunit, rpod [Hylemonella gracilis ATCC
           19624]
          Length = 784

 Score =  439 bits (1128), Expect = e-121,   Method: Composition-based stats.
 Identities = 264/670 (39%), Positives = 368/670 (54%), Gaps = 69/670 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
             +  K +IKL + RGY+T  E++  LP     +E +E  VAMLS+MG+ V +     + 
Sbjct: 169 RRERLKLLIKLGKTRGYLTHGEISDHLPDKLADAETLEVVVAMLSDMGVTVFEQTPDAET 228

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 229 LLINNTAPTAASEEEAEEEAEAAVSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 288

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T  AL+   +E+ +G  ++  ++D           GF +  
Sbjct: 289 KRIEGGLMDMMEAISASPTTIAALLAMAEEIREGKVVISTVVD-----------GFVNAE 337

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 338 ESDDYVAEEDFDEYDEADDDDGKGG----------------------------------- 362

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D I  ++ ++    D    G      +      ++ L  
Sbjct: 363 --SKALTKKLEELKNQALERFDRIRSMFEKVHKAYDKEGYG------TPAYVKAQKALSD 414

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE---- 378
            + ++      I+ L + +      + H E EL R+     G  +D F+    GR+    
Sbjct: 415 ELMTIRFTAKTIEKLCDLVRGQVADVRHKERELRRIIVDRCGYPQDQFVLEFGGRDKNGN 474

Query: 379 ------LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                 LD  WV    +  +  W   ++  V  I  I+ ++  +     + + + + I  
Sbjct: 475 PSKSHLLDLKWVEKQANAGKP-WSGIISRNVPPIQDIQQKLIDLQARVVVPLEQLKDINK 533

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 534 RMNQGEAASRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 593

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +
Sbjct: 594 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASLL 653

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+++A+QA LRE 
Sbjct: 654 AQKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTANTAPVEAAMQAGLREV 713

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +L  LTPRE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 714 VKEILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSR 773

Query: 673 SKKLRSFLDG 682
           S KLRSF D 
Sbjct: 774 SDKLRSFTDN 783


>gi|257454210|ref|ZP_05619480.1| RNA polymerase sigma factor RpoD [Enhydrobacter aerosaccus SK60]
 gi|257448383|gb|EEV23356.1| RNA polymerase sigma factor RpoD [Enhydrobacter aerosaccus SK60]
          Length = 634

 Score =  439 bits (1128), Expect = e-120,   Method: Composition-based stats.
 Identities = 264/661 (39%), Positives = 387/661 (58%), Gaps = 29/661 (4%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + + S      +I+L +++GY+T  E+N  LP     S+Q++D + ML+++GI + +   
Sbjct: 1   MSEHSTSQLATLIQLGKEQGYLTYAEINDQLPESVTESDQIDDIIQMLTDVGIKIFETAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ED+    D  D    A + +  +    +S    T DPVRMY+REMG+++LL+REGEIAI
Sbjct: 61  DEDDIMLSDDADDDEIAVDEAAAVLASVESEPGRTTDPVRMYMREMGTVDLLTREGEIAI 120

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  ++   P T   LI    +  +G   + +II            GF   
Sbjct: 121 AKRIEDGIRDVQHAMTFWPGTVAMLINEYRQTFEGEKKISDII-----------TGFLDP 169

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    +D   E     ++    D  +  ++  +  +      E  E D    ++ +
Sbjct: 170 EAADVIPLADDEEVEIALPIIKPKVKDDTAEDELDDEAENA----DEIEEADGEVSEDAD 225

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            + A  L   E +LR       +E+ +++ +++ L          ++ S   K    +L 
Sbjct: 226 TEEASGLDPEEVRLR------FEELEQLFTKVKDL------LATHDRDSEVVKTAMNELA 273

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDP 381
                  LN    D +++ + ++ + +  NE  +++L    G + +D F +     E + 
Sbjct: 274 NCFMLFKLNSRVSDNIMDMMREVYEDVRKNERHIMKLVIRRGKMPKDEFRKTFPHNETNL 333

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W+   +   +  + + +   +D +L+ +  I+      G+SI + + +   +  GE +A
Sbjct: 334 DWLP-NRIAGKPAFADTLERVLDEVLQYQGRIQQHEQNLGMSIDQMKVVARNMSVGEAKA 392

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 393 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 452

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M   
Sbjct: 453 WWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 512

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VRKVLKI KEPIS+ETPIGD++ SHLGDFIED +  SP+D A    L+E T  VLA+LT
Sbjct: 513 KVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSISSPVDEATAQGLKEATREVLANLT 572

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VL+MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+
Sbjct: 573 EREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 632

Query: 682 G 682
            
Sbjct: 633 N 633


>gi|53716429|ref|YP_105146.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|53722776|ref|YP_111761.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei K96243]
 gi|67643221|ref|ZP_00441969.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|124381664|ref|YP_001025512.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10229]
 gi|126447609|ref|YP_001077577.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|134278673|ref|ZP_01765387.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167000270|ref|ZP_02266089.1| RNA polymerase sigma factor RpoD [Burkholderia mallei PRL-20]
 gi|167743532|ref|ZP_02416306.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|167820721|ref|ZP_02452401.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
 gi|167850557|ref|ZP_02476065.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|167899150|ref|ZP_02486551.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 7894]
 gi|167907493|ref|ZP_02494698.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei NCTC
           13177]
 gi|167915832|ref|ZP_02502923.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 112]
 gi|167923671|ref|ZP_02510762.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei BCC215]
 gi|217422551|ref|ZP_03454054.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|226195650|ref|ZP_03791237.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|237508723|ref|ZP_04521438.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           MSHR346]
 gi|242312268|ref|ZP_04811285.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254177429|ref|ZP_04884085.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254186160|ref|ZP_04892678.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|254194055|ref|ZP_04900487.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|254203084|ref|ZP_04909446.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208417|ref|ZP_04914766.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254265453|ref|ZP_04956318.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|254301213|ref|ZP_04968657.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|254359397|ref|ZP_04975669.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|52213190|emb|CAH39230.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei K96243]
 gi|52422399|gb|AAU45969.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|126240463|gb|ABO03575.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|134250457|gb|EBA50537.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|147746129|gb|EDK53207.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147751104|gb|EDK58172.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148028584|gb|EDK86544.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|157811356|gb|EDO88526.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157933846|gb|EDO89516.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|160698469|gb|EDP88439.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|169650806|gb|EDS83499.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|217394782|gb|EEC34801.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|225932135|gb|EEH28135.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|235000928|gb|EEP50352.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           MSHR346]
 gi|238524506|gb|EEP87939.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|242135507|gb|EES21910.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|243063759|gb|EES45945.1| RNA polymerase sigma factor RpoD [Burkholderia mallei PRL-20]
 gi|254216455|gb|EET05840.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|261826434|gb|ABM99450.2| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10229]
          Length = 680

 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 247/663 (37%), Positives = 364/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 59  LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 179 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADTDGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    +  ++ ++ E ++  +      +A     +                     
Sbjct: 239 EKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 318 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|254522302|ref|ZP_05134357.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
 gi|219719893|gb|EED38418.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
          Length = 617

 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 272/660 (41%), Positives = 381/660 (57%), Gaps = 56/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
           +    K++I    ++GY+T  E+N  LP D V  EQ+ED + M++ MGI+V +     + 
Sbjct: 7   AQSEIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVET 66

Query: 86  ---EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
               +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 67  LLLNDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 126

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L + P++ ++L+   +   +G   L E+I     +G          
Sbjct: 127 AKRIEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVI-----VGFNDLTDEAPA 181

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +    +D+  + + D+  + EG  E AA    D                       
Sbjct: 182 PAAAAADDSDDADADGDEDEDDDVEGGEEEAAPTGPDPEE-------------------- 221

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   +  +++ +   +                     L+E++ 
Sbjct: 222 -----------------VAARMQALSDAFTAFKKAATKGDK--------KNLPRLREEMS 256

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQGRELDP 381
            +  +L L     D+L +QL D    I  +E  +L LA  +  + R  F+   +G + + 
Sbjct: 257 AVFVTLKLPLPLTDVLTKQLRDTMADIKSHERRVLNLATVTARMPRKDFIRSWEGNQTNL 316

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     I   T + + E + I   +  GE +A
Sbjct: 317 EWVEDALKR-KQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRAMAYGEAKA 375

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 376 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 435

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 436 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKEMDMPED 495

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+++    NL ET   VLA LT
Sbjct: 496 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRDVLAGLT 555

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 556 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 615


>gi|194367344|ref|YP_002029954.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
           R551-3]
 gi|194350148|gb|ACF53271.1| RNA polymerase, sigma 70 subunit, RpoD [Stenotrophomonas
           maltophilia R551-3]
          Length = 618

 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 265/660 (40%), Positives = 379/660 (57%), Gaps = 55/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
           +    K++I    ++GY+T  E+N  LP D V  EQ+ED + M++ MGI+V +     + 
Sbjct: 7   AQSEIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVET 66

Query: 86  ---EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
               +G+  + ++  +A+  +       D+    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 67  LLLNDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAI 126

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G + + A+L + P++ ++L+   +   +G   L E+I              F+ 
Sbjct: 127 AKRIEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVI------------VGFND 174

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                      ++ +   D   + + + +       ++ +     PE             
Sbjct: 175 LAEEVAAPAAPAASDDGDDAGADADEEEDDDVDGGDEEAAPTGPDPEE------------ 222

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                            V   +  +++ +   +                     L+E++ 
Sbjct: 223 -----------------VAARMQALSDAFNAFKKAVAKGDK--------KSLLKLREEMS 257

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQGRELDP 381
            +  +L L     D+L +QL D    I  +E  +L LA  +  + R  F+   +G + + 
Sbjct: 258 AVFVTLKLPLPLTDVLTKQLRDTMAGIKSHERRVLNLATVTARMPRKDFIRSWEGNQTNL 317

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     I   T + + + + +   +  GE +A
Sbjct: 318 EWVEDALKR-KQKWSSALREVKDQIIAEQQATIDIEKLTQLDLDDLKELSRAMAYGEAKA 376

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 377 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 436

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 437 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKEMDMPED 496

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+++    NL ET   VLA LT
Sbjct: 497 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRDVLAGLT 556

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 557 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|160872802|ref|ZP_02062934.1| RNA polymerase sigma factor RpoD (Sigma-70) [Rickettsiella grylli]
 gi|159121601|gb|EDP46939.1| RNA polymerase sigma factor RpoD (Sigma-70) [Rickettsiella grylli]
          Length = 642

 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 265/670 (39%), Positives = 381/670 (56%), Gaps = 44/670 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE-----QMEDTVAMLSNMGINVV 78
           F+      +++I   +++G+VT  E+N  L  D +S       Q+++ + ML+++GI V 
Sbjct: 3   FEQQQSRLRELITHGKKQGFVTYAEINDHLLEDIISEAEQEQLQLDEIILMLNDIGIPVY 62

Query: 79  DGDDLEDEEGSEDSLDLASSASNSS-VFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +     +   S   ++ A   ++S  V +     +    T DPVRMY+REMG++ELL+RE
Sbjct: 63  EVPPDMETLLSSSIVNNAEEENSSENVTILGNITTELGRTTDPVRMYMREMGTVELLTRE 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGP 193
           GEI +AKRIE G   ++A+L + P+    ++            L +II    DLE    P
Sbjct: 123 GEIKLAKRIEDGLQAILAALAQYPVNISHILNEYTRYEQQEIRLNDIISGFLDLEELSIP 182

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                  + T   +  +R + S ++  D   +   D +S    + DD    +        
Sbjct: 183 LELPSGKNITSTETPDERFNRSDKRTDDKDNDEGDDAKSKISATDDDEGFGELDGGPDPE 242

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
                                           E+   Y    + Q       + +K ++K
Sbjct: 243 LAH-------------------------TRFAELKAHYEAYIAAQKKWG---RHDKKTIK 274

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
             VL   L        L   ++D L   +  + ++I   E  ++RL      + R +F+ 
Sbjct: 275 QAVL---LADAFTKFKLIPRQLDKLTRNMRGLLEKIRLQERIIMRLCVNEAKMPRLLFIN 331

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E + +++       +  + + +   +  I   +N++  +    G++I+E + I  
Sbjct: 332 TFPKNETNENFLKKHIH-AKKSYSSRLKELLAPITAAQNKLHELEKTIGMTITEIKEINR 390

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 391 QMSAGETKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 450

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++     +EP+PE++
Sbjct: 451 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQATGKEPSPEDL 510

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +KK+ +P + +RK+LKI KEPIS+ETPIGDED  SHLGDFIED  A+SP+D+A    LRE
Sbjct: 511 SKKMGLPEDKIRKILKIAKEPISMETPIGDEDGDSHLGDFIEDAAALSPIDAATIEGLRE 570

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           T  RVLASLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+
Sbjct: 571 TAQRVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPT 630

Query: 672 RSKKLRSFLD 681
           RS+ LRSFLD
Sbjct: 631 RSEPLRSFLD 640


>gi|167842198|ref|ZP_02468882.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 680

 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 248/663 (37%), Positives = 365/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 59  LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 179 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADSDGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E++ +  E ++ ++      +A     +                     
Sbjct: 239 EKDAEEIENEDEEAEEGDEEEEDEDDGAAQATANAAQLEA-------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 318 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLDWAEKVAAEGHS-YSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|262371919|ref|ZP_06065198.1| RNA polymerase sigma factor sigma-70 [Acinetobacter junii SH205]
 gi|262311944|gb|EEY93029.1| RNA polymerase sigma factor sigma-70 [Acinetobacter junii SH205]
          Length = 627

 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 267/654 (40%), Positives = 370/654 (56%), Gaps = 40/654 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    +S    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESTEAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E  +  
Sbjct: 131 IRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGYLDPETDDDIPEVLEEEAVL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           +  ++     +D V+  + D +  ++   D        PE A+     L+   +D+   +
Sbjct: 189 EDAETPAAPAKD-VKLDDDDEDEDSEGDDDSEGDSGPDPEVAKVRFTELESAWNDTKAII 247

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  +SS + K   E L  +     
Sbjct: 248 E-----------------------------------KHGRSSEEAKAALESLAAVFMMFK 272

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +     +I  NE E++R A   G + R+ F      +E +P W+    
Sbjct: 273 FTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRNQFRTTFPEQESNPAWLDEQI 332

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E  +++ E + I   +  GE +A  AKKEM
Sbjct: 333 AKAPAEIKPHLEKVRPDVLAFQQKIADIEKELDLNVKEIKDISKRMAVGEAKARRAKKEM 392

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 393 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 452

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 453 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 512

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 513 IAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVL 572

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 573 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 626


>gi|261492895|ref|ZP_05989441.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. BOVINE]
 gi|261496755|ref|ZP_05993130.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261307594|gb|EEY08922.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261311436|gb|EEY12593.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica serotype A2 str. BOVINE]
          Length = 623

 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 275/648 (42%), Positives = 387/648 (59%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+T+ E++  LP + V +EQ+ED + M+++MGI V++     D+    +++ 
Sbjct: 19  ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDTDDLLLAENIA 78

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 79  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 137

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     L+    ++  G   L +++   A + P                     
Sbjct: 138 CAIAEYPEALSGLLACYAQVETGEMRLSDLVT--AFVDPN-------------------I 176

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E   +D++   G+ E ++ V   D    D   +++ +   +   D + +     A+  
Sbjct: 177 LEEAPLEDIEAALGEDEESSDVPDVDDENEDEDGDSSSDSSDDSSIDPELAREKFEALRS 236

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           Q    ++                       QK  ++S K K   E L  +     L   +
Sbjct: 237 QHEKVLLVI---------------------QKHGRTSKKSKEQIEILSHIFREFRLVSKQ 275

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLV  +  + K++   E ++ R A  Y G+K+  FL+  QG EL   W+  A +  + 
Sbjct: 276 FDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQGHELSEAWIEKAIN-AKK 334

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  VD+I      ++++   +G++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 335 NAVPKLANYVDNIRVNIANLQNLEQTSGLTIAQIREIGGRISNGELKARRAKKEMVEANL 394

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 395 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 454

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 455 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 514

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE +VLRMRFG
Sbjct: 515 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEVLEGLTPREAKVLRMRFG 574

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 575 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 622


>gi|32491217|ref|NP_871471.1| hypothetical protein WGLp468 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166424|dbj|BAC24614.1| rpoD [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 601

 Score =  438 bits (1125), Expect = e-120,   Method: Composition-based stats.
 Identities = 260/657 (39%), Positives = 370/657 (56%), Gaps = 63/657 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K ++   +++GY+T  E+N FLP + + S Q+ED + M+++MGI V+D     + 
Sbjct: 5   QQSQLKLLVTRGKEQGYLTFSEVNDFLPENIIDSHQIEDIIQMINDMGIQVMDEAPNSEN 64

Query: 87  EGSEDSLD-LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
               DS +      + ++  +    +S    T DPVRMY+REMGS++LL+REGEI +AKR
Sbjct: 65  LLLPDSNNNSDEDVAEAAAQVLSNVESEFGKTTDPVRMYMREMGSVQLLTREGEIDLAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +  ++ E P     L+    +   G + L E+I            GF      
Sbjct: 125 IEYGINQIQCAIVEYPKAIIYLLDQYKKTTTGESKLSELI-----------TGFVDPNIV 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                            V  +  D+ +    S+++ +  +    + E   +   E ++  
Sbjct: 174 -----------------VDSSNIDLNTEDISSEEENNTSEEIDIDKELANKRFIELQEQY 216

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
             + + +++  R       + I                                 L  + 
Sbjct: 217 KISFNTIKEYGRMHEFSIKEII--------------------------------YLADIF 244

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L   + D LV  +    ++I   E  ++R+  +   + +  F+    G E +  W+
Sbjct: 245 KQFRLVPKQFDYLVFIIRSEIEKIRFYERRIMRICVNICKMPKKFFISLFSGNETNDVWL 304

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    +  W   +      I  I N++K I + +GI+I + + I   +  GE +A  A
Sbjct: 305 KKALSLDKP-WSRKLYKLNKPICLILNKLKIIEINSGITIEQAKDINKRMSIGEAKAKRA 363

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 364 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 423

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +P + +R
Sbjct: 424 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIR 483

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDF+ED +   PLDSA   +LR  T  VL+ LT RE
Sbjct: 484 KVLKIAKEPISMETPIGDDEDSHLGDFLEDTSLDLPLDSATSESLRSATHDVLSGLTARE 543

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VL+MRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 544 AKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILRSFLD 600


>gi|254237208|ref|ZP_04930531.1| sigma factor RpoD [Pseudomonas aeruginosa C3719]
 gi|126169139|gb|EAZ54650.1| sigma factor RpoD [Pseudomonas aeruginosa C3719]
          Length = 617

 Score =  438 bits (1125), Expect = e-120,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 380/657 (57%), Gaps = 47/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D
Sbjct: 6   QQQSRLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                ++    ++A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALLLAEADTDEAAAEEAAAALAAVE-SDIGRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++ + P T  +++   + +      L ++  L   I P+         E 
Sbjct: 125 IEEGIREVMSAIAQFPGTVDSILADYNRIVAEGGRLSDV--LSGYIDPDDGSLPAEEVEP 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            + +                     + +A   + D  + +S   +  +DE +   D +++
Sbjct: 183 VNLK---------------------DDSADSKEKDDEEEESDDSSDSDDEGDGGPDPEEA 221

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
               +A+ +QL                            +K  + S +       L +L 
Sbjct: 222 RLRFTAVSEQLDKA---------------------KKALKKHGRGSKQATAELTGLAELF 260

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LV ++    + +   E  +++L      + R  FL      E D  WV
Sbjct: 261 MPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHETDEKWV 320

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  + ++   +    D IL+ + ++ ++  E  ++++E + I   +  GE +A  A
Sbjct: 321 DSVLK-SKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGEAKARRA 379

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 380 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 439

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+ +++ MP + +R
Sbjct: 440 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELGERMDMPEDKIR 499

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA LT RE
Sbjct: 500 KVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLAGLTARE 559

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 560 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 616


>gi|307246390|ref|ZP_07528466.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307255376|ref|ZP_07537186.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307259826|ref|ZP_07541544.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306852723|gb|EFM84952.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306861685|gb|EFM93669.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306866124|gb|EFM97994.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 619

 Score =  438 bits (1125), Expect = e-120,   Method: Composition-based stats.
 Identities = 275/648 (42%), Positives = 378/648 (58%), Gaps = 45/648 (6%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P          E       +  
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPN-----IQADEALEDLDVDLD 186

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +E+  D     +   E  +  + D        PE A      L E  + +   +     
Sbjct: 187 DEEEAEDVADVDDESEEEESDGNADTGDDNSIDPELAREKFYALREQHEKALQAI----- 241

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +S  K +   + L  +     L   +
Sbjct: 242 ------------------------------QKHGRSHKKSREQIQALSDIFREFRLVPKQ 271

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  + 
Sbjct: 272 FDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAIN-AKK 330

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  +D I    + ++ +   TG++I++ R I   +  GE +A  AKKEMVEANL
Sbjct: 331 GAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANL 390

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 451 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 510

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LT RE +VLRMRFG
Sbjct: 511 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTLREAKVLRMRFG 570

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 571 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 618


>gi|322513554|ref|ZP_08066654.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinobacillus
           ureae ATCC 25976]
 gi|322120625|gb|EFX92519.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinobacillus
           ureae ATCC 25976]
          Length = 618

 Score =  437 bits (1124), Expect = e-120,   Method: Composition-based stats.
 Identities = 275/648 (42%), Positives = 376/648 (58%), Gaps = 46/648 (7%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE    +++ 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + 
Sbjct: 75  DEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            ++ E P     LI +  ++ +GT  L +++   A + P ++       E          
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPNAQ------EEATVEDLEAVL 185

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
             E         +   E  +  S D        PE A      L E  + +   +     
Sbjct: 186 DDEDAEAVADVDDESEEEGSDSSADTGDDNSIDPELAREKFYALREQHEKALQAI----- 240

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         QK  +   K +   + L  +     L   +
Sbjct: 241 ------------------------------QKHGRGHKKSREQIQALSDIFREFRLVPKQ 270

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+  A +  + 
Sbjct: 271 FDLLVESMQKMMKQVRAEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWIEKAIN-AKK 329

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                +A  VD I      ++ +   TG+++++ R I   +  GE +A  AKKEM+EANL
Sbjct: 330 GAAPKLANYVDQIRVNIANLQRMEQSTGLTVAQIREIGGRIANGELKARRAKKEMIEANL 389

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIA
Sbjct: 390 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 449

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RKVLKI KEP
Sbjct: 450 DQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRKVLKIAKEP 509

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           IS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPREE+VLRMRFG
Sbjct: 510 ISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRIATNEVLEGLTPREEKVLRMRFG 569

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           I MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 570 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 617


>gi|187921407|ref|YP_001890439.1| RNA polymerase sigma factor RpoD [Burkholderia phytofirmans PsJN]
 gi|187719845|gb|ACD21068.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
           PsJN]
          Length = 681

 Score =  437 bits (1124), Expect = e-120,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 371/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 60  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 119

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 120 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 179

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 180 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGF- 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E  + +  ++  +E   +D +E +G  ++ A  ++ +                    
Sbjct: 239 SAQEAEAIESEDEEVEEDSEEDEEEDDGTAQATANAAQMEA------------------- 279

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 280 ---------------LKRASLEKFAMISEWFDKMRRAFE------KEGYKSKSYLKAQET 318

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 319 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 378

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 379 DLEWADKIVGEGHA-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 437

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 438 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 497

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 498 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 557

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 558 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 617

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 618 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 677

Query: 680 LDG 682
           L+G
Sbjct: 678 LEG 680


>gi|323529251|ref|YP_004231403.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1001]
 gi|323386253|gb|ADX58343.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1001]
          Length = 680

 Score =  437 bits (1123), Expect = e-120,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 373/663 (56%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 59  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 179 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDADAEDADGF- 237

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E  + +  ++  +E++ +D +E +G  ++ A  ++ +                    
Sbjct: 238 SVQEAEAIESEDEDEEEEDEEDEEEDDGTAQATANAAQMEA------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 318 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLEWADKIVAEGHS-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|296159636|ref|ZP_06842459.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295890080|gb|EFG69875.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 680

 Score =  437 bits (1123), Expect = e-120,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 371/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 59  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 179 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGF- 237

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E  + +  ++  +E   +D +E +G  ++ A  ++ +                    
Sbjct: 238 SAQEAEAIESEDEEVEEDAEEDEEEDDGTAQATANAAQMEA------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFAMISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 318 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLEWADKIVGEGHA-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|91777317|ref|YP_552525.1| RNA polymerase sigma factor RpoD [Burkholderia xenovorans LB400]
 gi|91689977|gb|ABE33175.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 680

 Score =  437 bits (1123), Expect = e-120,   Method: Composition-based stats.
 Identities = 251/663 (37%), Positives = 371/663 (55%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 59  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 179 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDANAEDADGF- 237

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E  + +  ++  +E   +D +E +G  ++ A  ++ +                    
Sbjct: 238 SAQEAEAIESEDEEVEEDSEEDEEEDDGTAQATANAAQMEA------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFAMISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 318 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLEWADKIVGEGHA-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|209519886|ref|ZP_03268669.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
 gi|209499704|gb|EDZ99776.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
          Length = 665

 Score =  437 bits (1123), Expect = e-120,   Method: Composition-based stats.
 Identities = 230/663 (34%), Positives = 350/663 (52%), Gaps = 49/663 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +I+L +++GY+T  ++N  LP +   +  ++  V+  S+MG+ V +    
Sbjct: 46  AEERQRLMRALIQLGKEQGYLTHAQINDHLPDNFTQTAAIDSIVSAFSDMGVQVYEQAPD 105

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  ++     A   +       DS    T DPVRMY+REMG+ ELL+R GEI
Sbjct: 106 AETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGEI 165

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           AIAKRIE G   M+ ++   PL   A++    ++ DG   + E++D              
Sbjct: 166 AIAKRIEDGLHEMVQAIAACPLAISAILASAQQIADGELRIDELVD-------------- 211

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                                       + E+AA               + + D  + +E
Sbjct: 212 --------------------------GLNEETAAAEEVASADADADEDTDTDEDSEDEEE 245

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKE 319
           D+   A + +A E +L+      L    E++ ++  L D           +S      +E
Sbjct: 246 DDVGPADSSAADEARLKQLTSDCL----EIFAQVGILYDQMNASHTRGDVTSKAYLRARE 301

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
            + + +  +      ID L   +     ++   E  +L++     G+ R+ F+E   G E
Sbjct: 302 DIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVSKAGMPREKFIETFAGTE 361

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            D  W   A       +   +   + +I   + ++  I     + +   + I   +   E
Sbjct: 362 TDLGWTERAARTGASTYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRQMVAAE 421

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFST
Sbjct: 422 SKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFST 481

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +A+++ +
Sbjct: 482 YATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAERMEL 541

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E VR +LKI K+P+SLETP+GD+  + LGD IED    SP D+A+QA+LR      L 
Sbjct: 542 SEEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVSSPADAAMQADLRAAIDDALD 601

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SL+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ +L+S
Sbjct: 602 SLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLKS 661

Query: 679 FLD 681
           FLD
Sbjct: 662 FLD 664


>gi|239814768|ref|YP_002943678.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus S110]
 gi|239801345|gb|ACS18412.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus S110]
          Length = 754

 Score =  436 bits (1122), Expect = e-120,   Method: Composition-based stats.
 Identities = 258/669 (38%), Positives = 368/669 (55%), Gaps = 69/669 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I L + RGY+T  E++  LP   V +E ME  V ML++MG+ V +     + 
Sbjct: 139 RRSRLKTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLNDMGVAVYEQTPDAET 198

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 199 LLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 258

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++    ++ +G  ++  ++D           GF +  
Sbjct: 259 KRIEGGLMAMMEAISASPATIAEILRLAADIREGKVVISTVVD-----------GFSNPN 307

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 308 EADDYVAEEDFDEFDEEDDDDGKGG----------------------------------- 332

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+   +   D IA ++ ++  + D      K+   +   +  ++ L  
Sbjct: 333 --SKALTKKLEELKRDALERFDRIASMFEKVHKIYD------KEGYGTPAYEKAQQALSD 384

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQG------ 376
            + ++      I+ L + +      +   E EL R +    G  +D F+    G      
Sbjct: 385 ELMTIRFTAKTIEKLCDLVRTQVDDVRKKERELRRIIVDKCGFPQDEFIRDFSGYDKNGN 444

Query: 377 ----RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                 L+  WV       +  W   +A  +  + +++ ++  I     + +++ + I  
Sbjct: 445 RVPSNLLNQKWVEKQAAAGKP-WSAVLARNIPPVQELQQKLADIQSRVVVPLTQLKEINK 503

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 504 RMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 563

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +
Sbjct: 564 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGIL 623

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A K+ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED +  +P+++A+QA LR+ 
Sbjct: 624 AAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDV 683

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 684 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSR 743

Query: 673 SKKLRSFLD 681
           S KLRSF+D
Sbjct: 744 SDKLRSFID 752


>gi|254184931|ref|ZP_04891520.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184215523|gb|EDU12504.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 680

 Score =  436 bits (1122), Expect = e-120,   Method: Composition-based stats.
 Identities = 246/663 (37%), Positives = 363/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 59  LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 179 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADTDGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    +  ++ ++ E ++  +      +A     +                     
Sbjct: 239 EKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 318 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAK +RKL+HPSRS KL+SF
Sbjct: 617 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKTLRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|167724581|ref|ZP_02407817.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 680

 Score =  436 bits (1121), Expect = e-120,   Method: Composition-based stats.
 Identities = 246/663 (37%), Positives = 363/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 59  LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 179 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADTDGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    +  ++ ++ E ++  +      +A     +                     
Sbjct: 239 EKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEA-------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 318 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLDWAEKVAAEGHS-YGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 496

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 497 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 556

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 557 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 616

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTP E +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 617 LTPSEAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 676

Query: 680 LDG 682
           L+G
Sbjct: 677 LEG 679


>gi|167566502|ref|ZP_02359418.1| RNA polymerase sigma factor RpoD [Burkholderia oklahomensis EO147]
 gi|167573583|ref|ZP_02366457.1| RNA polymerase sigma factor RpoD [Burkholderia oklahomensis C6786]
          Length = 681

 Score =  436 bits (1120), Expect = e-120,   Method: Composition-based stats.
 Identities = 248/663 (37%), Positives = 363/663 (54%), Gaps = 46/663 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 60  LEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 119

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 120 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 179

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +  + + E++D           GF 
Sbjct: 180 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELVDGLIDPNAADADGFS 239

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E++ + +E +   +      SA     +                     
Sbjct: 240 EKDAEEIENEDEEAEENEEEEAEDDDGAAQASANAAQLEA-------------------- 279

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 280 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 318

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + S+      ++ L + L      +   E ++L +     G+ R  F+ R    E 
Sbjct: 319 IQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPSNET 378

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 379 DLDWAEKIAAEGHS-YSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 437

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 438 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 497

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 498 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 557

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ A++R+    VL S
Sbjct: 558 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDS 617

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SF
Sbjct: 618 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSF 677

Query: 680 LDG 682
           L+G
Sbjct: 678 LEG 680


>gi|90407543|ref|ZP_01215725.1| RNA polymerase sigma factor RpoD [Psychromonas sp. CNPT3]
 gi|90311353|gb|EAS39456.1| RNA polymerase sigma factor RpoD [Psychromonas sp. CNPT3]
          Length = 610

 Score =  436 bits (1120), Expect = e-120,   Method: Composition-based stats.
 Identities = 260/663 (39%), Positives = 364/663 (54%), Gaps = 58/663 (8%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +        K++I   +++G++T  E+N  LP D   +EQ+ED + M+ +MGI V +   
Sbjct: 1   MAQTPQSQLKELIIKGKEKGFLTYAEVNDHLPQDIFEAEQIEDIIQMIGDMGIKVYETAP 60

Query: 83  LEDE--EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             DE   G E +      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI
Sbjct: 61  DADEISLGEESNDTADEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEI 120

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   +  S+ E P T   L+   D        L ++I     I P       
Sbjct: 121 VIAKRIEEGIKEVQTSVSEYPGTITGLLDNWDSYEAEEMKLTDMI--SGFIDPND----- 173

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                       D +Q     +V     D +      +D+  +    P   E+       
Sbjct: 174 ------------DMTQAPTATNVGSELTDAQKKDNEEEDEEEEGPKGPCPEES------- 214

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCKVLKE 319
                                      AE + ELR L     +   K  ++  K +    
Sbjct: 215 ---------------------------AEKFTELRRLNTIVEDMIAKHGRAHAKTRTAIN 247

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRE 378
              +      L   + D +V+ +      +   E  +L++      + +  F+   +G E
Sbjct: 248 AQAEFFQQFKLIPKQFDRMVKTIRASMNMVRTQERLVLKICVEQNKMPKKAFISLFKGNE 307

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +  W+       E E+   +    + +++   ++  +  +T ++I   + I   +  GE
Sbjct: 308 TNKAWLDAIYA-TEKEYAKRIKEFDEDLVRCIRKMALVETQTALTIINLKEISRKMSIGE 366

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 367 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 426

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ R+P P+E+A+++ M
Sbjct: 427 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRDPHPDELAERMMM 486

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     P+D A   +L+  T  VL 
Sbjct: 487 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIALPVDCATSESLKNATNEVLE 546

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRS
Sbjct: 547 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRS 606

Query: 679 FLD 681
           FLD
Sbjct: 607 FLD 609


>gi|299533869|ref|ZP_07047236.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni S44]
 gi|298718153|gb|EFI59143.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni S44]
          Length = 815

 Score =  435 bits (1119), Expect = e-120,   Method: Composition-based stats.
 Identities = 255/663 (38%), Positives = 369/663 (55%), Gaps = 59/663 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V +    
Sbjct: 207 MNTRRQRLKMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPD 266

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  S      A   +       DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 267 AETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 326

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF 
Sbjct: 327 EIAKRIEGGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVD-----------GFV 375

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
           +  E   Y   ED  +  E DD     G                                
Sbjct: 376 NANENDDYVAEEDFDEYDEEDDDDGKGG-------------------------------- 403

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                +  L+   ++L+ + +   D + E++ ++  + D    G      +     +++ 
Sbjct: 404 -----SKALTKKLEELKNEALGRFDSMRELFDKMHKVYDKEGYG------TEAYMKVQKA 452

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           + + + ++      I+ L + +      +   E EL + +    G+ ++ F++      L
Sbjct: 453 ITEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVDKCGMPQEQFIKDFPPNLL 512

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV          +   +   +  + +++  +  +     + + E +HI   +  GE 
Sbjct: 513 NLDWVIKQVA-AGKNYSAVLERNIPPVQELQQNLIDLQARVVVPLEELKHINKRMNSGER 571

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 572 ASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 631

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P
Sbjct: 632 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIP 691

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  
Sbjct: 692 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDG 751

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF
Sbjct: 752 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSF 811

Query: 680 LDG 682
           +D 
Sbjct: 812 IDS 814


>gi|254447663|ref|ZP_05061129.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium
           HTCC5015]
 gi|198263006|gb|EDY87285.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium
           HTCC5015]
          Length = 602

 Score =  435 bits (1119), Expect = e-120,   Method: Composition-based stats.
 Identities = 264/670 (39%), Positives = 381/670 (56%), Gaps = 72/670 (10%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
            + E    + V        K +I   +++GY+T  E+N  LP + V  EQ+ED + M+++
Sbjct: 3   DKDETQQGNKVTKEQQSQIKLLIAKGKEQGYLTFAEVNDHLPNEIVDPEQVEDIIQMIND 62

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           MGI V++     +E    +        ++ +V      DS    T DPVRMY+REMG++E
Sbjct: 63  MGIKVLESAPDAEELLMMEGDTSNDEDADEAVANLANNDSDFGRTTDPVRMYMREMGTVE 122

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   ++ +L   P    AL    D + +    + ++I       
Sbjct: 123 LLTREGEIEIAKRIEDGLRQVVTALSTYPHAVNALFETYDGIIEREGRITDLI------- 175

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
               GGF    +          +                      +D+ ++ D+ P+  E
Sbjct: 176 ----GGFIDPDDDEVQNPNAPKN----------------------EDEEAEEDTGPDLEE 209

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                      V   ++++ + Y +    +D             
Sbjct: 210 ---------------------------VAKHINQMRKQYEKATKKKDGIYQ--------- 233

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFL 371
           +     EKL +L   L L+ + I+  ++ + D+  R+   E +++       G+ R  F+
Sbjct: 234 REAKASEKLSELFMQLKLDNNFINREIQLVRDVVGRVRQLERDVMTICVHRCGMPRKTFI 293

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           +     E +P+WV         ++   +A   + + +++  +  I  E+G+SIS+ + I 
Sbjct: 294 DSFPENETNPNWVKDHSK--SKKFGEKIAAHANDLNELQQHLIRIEQESGLSISDLKEIN 351

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +  G+ +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 352 RKMSIGQAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 411

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE
Sbjct: 412 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEE 471

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+++ MP + VRKVLKI KEPIS+ETP+GD++ S LGDF++D NA SP+++A+   L E
Sbjct: 472 LAERMEMPEDKVRKVLKIAKEPISMETPVGDDEDSSLGDFLQDVNAESPIEAAVGEGLSE 531

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +T  +LA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+
Sbjct: 532 STRDILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPT 591

Query: 672 RSKKLRSFLD 681
           RS  LRSFLD
Sbjct: 592 RSDSLRSFLD 601


>gi|169632612|ref|YP_001706348.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter baumannii SDF]
 gi|169151404|emb|CAP00133.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter baumannii]
          Length = 630

 Score =  435 bits (1119), Expect = e-119,   Method: Composition-based stats.
 Identities = 267/654 (40%), Positives = 369/654 (56%), Gaps = 37/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I+        E+        E     
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETETDEDIPEVLEDVEEL 190

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED S  K   +V+  + D E  ++   D        PE A+     L+     +   +
Sbjct: 191 EEEDESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVI 250

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  ++S +     E L  +     
Sbjct: 251 E-----------------------------------KHGRNSPEANEALESLATVFMMFK 275

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  NE E++R A   G + R+ F      +E +P W+    
Sbjct: 276 FTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRNQFRTSFPKQESNPAWLDEQI 335

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E G+++SE + I   +  GE +A  AKKEM
Sbjct: 336 AKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEM 395

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 396 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 455

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 456 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 515

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 516 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSKGLKEATREVLENLTEREAKVL 575

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 576 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 629


>gi|56461300|ref|YP_156581.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina loihiensis
           L2TR]
 gi|56180310|gb|AAV83032.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina loihiensis
           L2TR]
          Length = 609

 Score =  435 bits (1119), Expect = e-119,   Method: Composition-based stats.
 Identities = 263/656 (40%), Positives = 367/656 (55%), Gaps = 53/656 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   +++G++T  E+N  LP + V S+Q+ED + M+++MGI V +     D+
Sbjct: 5   RQSQLKVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQVEDIIRMINDMGIRVFESAPDADD 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               +S     +A  ++  L    D     T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 65  LMMAESAADEDAAEEAAQALASV-DGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D        L +II            GF    E  
Sbjct: 124 EEGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTDII-----------SGFIDPDEVD 172

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  +       ++   E +         ++ +     PE A +    L E  + + 
Sbjct: 173 EAPVAATNV----GSELPSEELEKSDDDDDEDEEEADTGIDPEFARSKFNALREQYEATR 228

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             ++                                   K  +     +V  +KL  L  
Sbjct: 229 QAIA-----------------------------------KHGRDGAGARVEIDKLSDLFK 253

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + D LV+ +  + +R+   E  +++++   G + +  F++     E +  WV 
Sbjct: 254 QFRLVPKQFDRLVKDMRAMMQRVRVQERIIMKISVEQGEMPKRNFMKAFATHENNMAWVD 313

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
              D     + + +      I +  N++  +  ETG++I + + I   +  GE +A  AK
Sbjct: 314 KEID-SGASYSDTLKEVRGEIERCVNKLVDVERETGLTIGKVKEINRRMSIGEAKARRAK 372

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 373 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 432

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RK
Sbjct: 433 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMMMPEDKIRK 492

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +LR +   VL  LT RE 
Sbjct: 493 VLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSATSESLRNSVRDVLGGLTAREA 552

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++L+SFLD
Sbjct: 553 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLKSFLD 608


>gi|299768976|ref|YP_003731002.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
 gi|298699064|gb|ADI89629.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
          Length = 627

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 264/654 (40%), Positives = 370/654 (56%), Gaps = 40/654 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +     D+    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 91  DSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +S D A   +           ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESTDTADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E  +  
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEETEL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + +D+     ++ V+  + + +  ++   D   +    PE A+     L+     +   +
Sbjct: 189 EEDDAPATPAKE-VKLDDDEEDEESESDDDSEGESGPDPEVAKIRFNELESAWTKTKGII 247

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  ++S +     E L  +     
Sbjct: 248 E-----------------------------------KHGRNSPEADEALEALATVFMMFK 272

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  NE E++R A   G + R  F      +E +P W+    
Sbjct: 273 FTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKQESNPAWLDEQI 332

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E  +S++E + I   +  GE +A  AKKEM
Sbjct: 333 AKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAKKEM 392

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 393 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 452

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 453 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 512

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 513 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVL 572

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 573 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 626


>gi|264677331|ref|YP_003277237.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
 gi|262207843|gb|ACY31941.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
          Length = 815

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 255/663 (38%), Positives = 370/663 (55%), Gaps = 59/663 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V +    
Sbjct: 207 MNTRRQRLKMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPD 266

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  S      A   +       DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 267 AETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 326

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF 
Sbjct: 327 EIAKRIEGGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVD-----------GFV 375

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
           +  E   Y   ED  +  E DD     G                                
Sbjct: 376 NANENDDYVAEEDFDEYDEEDDDDGKGG-------------------------------- 403

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                +  L+   ++L+ + +   D + E++ ++  + D      K+   +     +++ 
Sbjct: 404 -----SKALTKKLEELKNEALGRFDSMRELFDKMHKVYD------KEGYGTEAYMKVQKA 452

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           + + + ++      I+ L + +      +   E EL + +    G+ ++ F++      L
Sbjct: 453 ITEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVDKCGMPQEQFIKDFPPNLL 512

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV          +   +   +  + +++  +  +     + + E +HI   +  GE 
Sbjct: 513 NLDWVIKQVA-AGKNYSAVLERNIPPVQELQQNLIDLQARVVVPLEELKHINKRMNSGER 571

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 572 ASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 631

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P
Sbjct: 632 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIP 691

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  
Sbjct: 692 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDG 751

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF
Sbjct: 752 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSF 811

Query: 680 LDG 682
           +D 
Sbjct: 812 IDS 814


>gi|262369385|ref|ZP_06062713.1| DNA-directed RNA polymerase [Acinetobacter johnsonii SH046]
 gi|262315453|gb|EEY96492.1| DNA-directed RNA polymerase [Acinetobacter johnsonii SH046]
          Length = 628

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 266/654 (40%), Positives = 371/654 (56%), Gaps = 39/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFE 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  GGNEAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++    +   G   L +I  L   + PE+        E  S  
Sbjct: 131 IRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADI--LSGYLDPETDEAIPEVLEEESEI 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
             ED S  K   DV+  + + E  ++   D   +    PE A+                 
Sbjct: 189 DEEDDSSTKSTKDVKLDDDEEEEESESDDDSEGESGPDPEIAK----------------- 231

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                          DE+   ++  R++ +      K  +SS + +   E L  +     
Sbjct: 232 ------------ARFDELTAAWKNTRTIIE------KHGRSSKEAEDALESLATVFMMFK 273

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  +E E++R A   G + R  F     G+E +  W+    
Sbjct: 274 FTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMDRTQFRTSFPGQESNFAWLDEQI 333

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                + K ++      +L  + +I  I  +  + +   + I   +  GE +A  AKKEM
Sbjct: 334 AKASPDQKGYLEKVRPDVLAFQQKIADIEKDLDLDVKGIKEISKRMAVGEAKARRAKKEM 393

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 394 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 453

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 454 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 513

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 514 IAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVL 573

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 574 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 627


>gi|293610908|ref|ZP_06693207.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292826560|gb|EFF84926.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 628

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 268/654 (40%), Positives = 374/654 (57%), Gaps = 39/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E     
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEEL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED S  K   +V+  + D E  ++   D        PE A+                 
Sbjct: 189 EEEDESSSKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAK----------------- 231

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                           E+   + + +++ +      K  ++S + +   E L  +     
Sbjct: 232 ------------VRFTELEAAWAKTKAVVE------KHGRNSPEAEEALEALATVFMMFK 273

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  NE E++R A   G + R  F      +E +P W+    
Sbjct: 274 FTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKQESNPAWLDEQI 333

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E  +S++E + I   +  GE +A  AKKEM
Sbjct: 334 AKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAKKEM 393

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 394 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 453

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 454 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 513

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 514 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVL 573

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 574 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 627


>gi|85711761|ref|ZP_01042817.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina baltica
           OS145]
 gi|85694376|gb|EAQ32318.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina baltica
           OS145]
          Length = 611

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 271/656 (41%), Positives = 370/656 (56%), Gaps = 51/656 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   +++G++T  E+N  LP + V S+Q+ED + M+++MGI V +     D+
Sbjct: 5   RQSQLKVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQIEDIIRMINDMGIRVFESAPDADD 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               +S     +A  ++  L    D     T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 65  LMMSESAADEDAAEEAAQALATV-DGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D        L EII            GF    E  
Sbjct: 124 EDGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTEII-----------VGFIDPDEVD 172

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +  +D  E E D +      +++ S +D  PE A      L E  + + 
Sbjct: 173 EAPVSATHVGSELSEDELEDEDDDDEDDDDEEENDSGID--PEFARQKFTELREQYEATR 230

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             ++                                   +  +     +V  +KL  L  
Sbjct: 231 QAIT-----------------------------------QFGREHPDARVEIDKLSDLFK 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV+ +  + +R+   E  +++ A +  G+ +  F++   G E    WV 
Sbjct: 256 QFRLVPKQFDRLVQDMRAMMQRVRVQERLVMKAAVEQAGMPKRAFMKAFAGNENSLAWVD 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                            V+ I +   ++  I  ETG++I++ + I   +  GE +A  AK
Sbjct: 316 EQISAGVDYATTLQEARVE-IERCVTKLNEIEKETGLTIAKVKDINRRMSIGEAKARRAK 374

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 375 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 434

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++AMP + +RK
Sbjct: 435 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMAMPEDKIRK 494

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED     P+DSA   +LR +   VL  LT RE 
Sbjct: 495 VLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSATSESLRNSVRDVLGGLTAREA 554

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++L+SFLD
Sbjct: 555 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLKSFLD 610


>gi|82703177|ref|YP_412743.1| RNA polymerase sigma factor RpoD [Nitrosospira multiformis ATCC
           25196]
 gi|82411242|gb|ABB75351.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosospira multiformis
           ATCC 25196]
          Length = 707

 Score =  435 bits (1117), Expect = e-119,   Method: Composition-based stats.
 Identities = 254/682 (37%), Positives = 387/682 (56%), Gaps = 57/682 (8%)

Query: 4   GKKRNRDSDSE-HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             +  ++S ++  E +  S   +      K +I   ++RGY+T  E+N  LP D + +EQ
Sbjct: 76  AAREGKNSHAKDPEKAAASQELEARRMRLKNLIVQGKERGYLTYAEINDHLPDDMLDAEQ 135

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS--NSSVFLQKRKDSADRSTDDP 120
           +E+ ++M++++GI+V D     +     ++    +       +       DS    T DP
Sbjct: 136 IENIISMINDVGISVYDEAPDAETLLMSETAPTVADEDVVEEAEAALSTVDSEFGRTTDP 195

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMGS+ELL+RE EI IAKRIE G   M+ ++   P T   ++ + D ++     
Sbjct: 196 VRMYMREMGSVELLTRESEIEIAKRIEDGLKHMIQAISACPTTIAGILEFADRVSKDEMR 255

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++D                                                     +
Sbjct: 256 VDELVD----------------------------------------------GLLDPSTE 269

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               +   + +   E N D +++D     +A   +L+   +     + + Y E++ + + 
Sbjct: 270 EIISEEISDESLEQELNSDAEDEDVTAVANANLLKLKNDALERFAVVQKAYDEMQKVLEK 329

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
             +G K        K ++E++   + ++  +   ++ L +    +   +   E +++ L 
Sbjct: 330 KGSGNK------AYKDIQEQISSELMAIRFSAKMVERLCDTQRALVDEMRGYERKIMELC 383

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ R+ F++   G E + +WV       +  +   +      I++ +  + ++  +
Sbjct: 384 VSKVGMSRNHFIKTFPGNESNLNWVDEEIALGKP-YSAALERYRPEIVEQQQNLLALQKQ 442

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            GI + E + I   +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 443 VGIPLKELKEINRRMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 502

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++
Sbjct: 503 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 562

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  +EP P  +A+K+ MP E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++
Sbjct: 563 LQETGQEPEPAVLAQKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSATMA 622

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D+A+ A+LR+ T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 623 PADAAVYASLRDVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 682

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HPSRS++LRSFLD
Sbjct: 683 EAKALRKLRHPSRSERLRSFLD 704


>gi|295701329|ref|YP_003610330.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295441652|gb|ADG20819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 663

 Score =  435 bits (1117), Expect = e-119,   Method: Composition-based stats.
 Identities = 237/661 (35%), Positives = 356/661 (53%), Gaps = 46/661 (6%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      + +I+L ++RGY+T  E+N  LP +   +  +E  V+  ++MG+ V +     
Sbjct: 44  EEQQRQMRALIQLGKERGYLTHAEINDHLPDNFAQTAAIETIVSTFNDMGVAVYEQAPSA 103

Query: 85  DEEGSEDSLD---LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +     D+     L   A   +       DS    T DP RMY+REMG+  LL+R GEI 
Sbjct: 104 EVLLMNDATPATMLDDQADEEAEVALSSVDSEFGRTTDPFRMYMREMGATGLLTRAGEIE 163

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++  SP T  A+++   ++  G   + E++D               
Sbjct: 164 IAKRIEGGLHEMVQAIAVSPATVSAILLSAKQIEAGELRIDELVD--------------- 208

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                            E + V+++  D        +          E++E ++R     
Sbjct: 209 -------------GINAETESVEQSSTDFAEEPDTEQATADDDGGGDEHSEIEDR----- 250

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
             D+A +  A   QL    +     + E++ ++   Q          K  V    L+E +
Sbjct: 251 --DTARSNEARLKQLTSDSLVIFARVRELFEQISGSQAAQ------GKGRVARADLREAI 302

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
            + +  +      ID L   +     ++   E  +L++A    G+ R+ F+E  QGRE D
Sbjct: 303 QRELAPIRFTARTIDRLCNAVQQQVAQVRAVERHILQIAVDRCGMPREKFVESFQGRETD 362

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W          E+   +   + +I   + ++  I  + G+ + + + I   +   E +
Sbjct: 363 LAWSESTAA-ASREYGAALERSLPAIQAEQRKLLDIETKVGLPLQQLKKINRQMMAAESK 421

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTYA
Sbjct: 422 MLQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYA 481

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WWV+QA+TRS+ADQ+ TIRIPVHM + I+K+ R +R +  +  RE  P  +A+++ +P 
Sbjct: 482 TWWVRQAVTRSLADQARTIRIPVHMMESINKLNRISREILQQTGREAHPAVLAQRMEVPE 541

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VR +LKI ++P+SLETP+GDE  + L D IED  A SP D+A+QANLR      L +L
Sbjct: 542 EKVRAMLKIGRQPLSLETPVGDEADTTLSDVIEDPMATSPADAAVQANLRAAINTALDAL 601

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE +VLRMRFGI   +D TLEE+GKQF +TRERIRQIE+KA+RKL HP+R+ KLR FL
Sbjct: 602 SPREAKVLRMRFGIDTASDCTLEELGKQFDLTRERIRQIESKAMRKLMHPNRTAKLRPFL 661

Query: 681 D 681
           D
Sbjct: 662 D 662


>gi|329898803|ref|ZP_08272472.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC3088]
 gi|328920738|gb|EGG28203.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC3088]
          Length = 600

 Score =  435 bits (1117), Expect = e-119,   Method: Composition-based stats.
 Identities = 264/657 (40%), Positives = 364/657 (55%), Gaps = 66/657 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +     DE
Sbjct: 7   QQSRLKSLIAKGKEQGYLTYSEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEEAPDADE 66

Query: 87  E-GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +E        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 67  LLMTEGDSSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +MA+L   P   + ++    ++      L +++                    
Sbjct: 127 IEEGIRELMAALAHYPGAVEHVLNEYAQVTQEERRLGDVM-------------------- 166

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                          D+V        +      D+       P  A    + L +  + +
Sbjct: 167 --------VGYLDPADEVPTAAEVAAANEASGDDEEGDSGPDPVEAAKRFKELRKQWEKT 218

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L+                                   K  +S V  K L +KL ++ 
Sbjct: 219 EKALAE----------------------------------KGRQSKVTLKEL-DKLGEVF 243

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L     D L++   D+ + +   E E++ +      + R  F++   G E +  W+
Sbjct: 244 KFFKLTPRVFDPLLDMARDVLQEVRTQEREIMTICVRHCSVPRKAFIDSFVGNETNEAWL 303

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                    E    +  + D++++++  I +   ++G+S+SE + I   +  GE  A  A
Sbjct: 304 DDLIK-KAPERAAKLEADRDTLMRLQRRIIATEEKSGLSVSEIKEINRRMSMGEARARRA 362

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 363 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 422

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VR
Sbjct: 423 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKVR 482

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA    L+E TT VLA LT RE
Sbjct: 483 KVLKIAKEPISMETPIGDDEDSHLGDFIEDVTIASPVDSATGQGLQEATTEVLAGLTARE 542

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 543 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 599


>gi|255019635|ref|ZP_05291715.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus ATCC
           51756]
 gi|254970938|gb|EET28420.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus ATCC
           51756]
          Length = 625

 Score =  435 bits (1117), Expect = e-119,   Method: Composition-based stats.
 Identities = 270/663 (40%), Positives = 389/663 (58%), Gaps = 52/663 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++GY+T  E+N  LP D    EQME+ + M+++MGI V +    +
Sbjct: 4   ESQRSELKRLIARGKEQGYLTYREINDLLPEDVFDPEQMENVITMINDMGIEVFEEAPDD 63

Query: 85  DE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +    +   + +  A  A  ++       ++    T DPVRMY+REMG++ELL+REGEI 
Sbjct: 64  ETLLMDNEGNPIVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGTVELLTREGEIE 123

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IA+RIE G   ++ ++   P T   L+    ++  G   L E++D  A I P        
Sbjct: 124 IARRIEDGLLQVLRAVSTCPTTIALLLEAAQKVEQGELRLDEVVD--AFIDPN------- 174

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                                         +  + + +D     +   +  +D    +++
Sbjct: 175 ------------------------------AINEAAAEDEDLGLAAEADEADDGDEDEDE 204

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           ED +  +++    QL  + +     I   Y  L +L          +  S + +  ++ L
Sbjct: 205 EDGAGLSVADKGPQL-EEALERFAAIRAGYEHLLALHKA------GKVRSPEYQEQRQLL 257

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
                 + LN  +IDL+ + L ++++ +   E EL+ L     G  R  F+  + G E D
Sbjct: 258 ADRFMEMKLNVRQIDLMADALRNLTEEVRLAERELMALCIDRAGFPRKEFVRSYPGHESD 317

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV  A+      +   +    D I+ +  ++  I    G+ I+E +    ++  GE +
Sbjct: 318 IAWVD-AQIAAGRPYSPMMLVLRDEIVAVMTQLADIEERAGLPIAEIKEASRLMSIGEAK 376

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 377 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 436

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A ++ MP 
Sbjct: 437 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAARMEMPE 496

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  +P D+A+ A +RE    +L + 
Sbjct: 497 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVAAPTDAAVNAAIREVVEELLDTG 556

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSF
Sbjct: 557 LTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRSF 616

Query: 680 LDG 682
           +DG
Sbjct: 617 VDG 619


>gi|124267677|ref|YP_001021681.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Methylibium petroleiphilum PM1]
 gi|124260452|gb|ABM95446.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Methylibium petroleiphilum PM1]
          Length = 746

 Score =  435 bits (1117), Expect = e-119,   Method: Composition-based stats.
 Identities = 268/689 (38%), Positives = 375/689 (54%), Gaps = 62/689 (8%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDF---SDDSWKKMIKLARQRGYVTIEELNAFLPPDE 57
           M + + + R    E    + +L  D         K +IK+ + RG++T +E+N  LP   
Sbjct: 112 MKVSRAKERALMREFGLDETALTEDEVAKRRQELKTLIKMGKTRGFLTHQEINDHLPEKL 171

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSAD 114
           + +E +E  V+ML++MGI V +           G   +      A   +       DS  
Sbjct: 172 IEAEILEAIVSMLNDMGIAVYEQAPDAATLLIAGGSTATSTDEEAEEEAEAALSTVDSEF 231

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   MM ++ ESP T   +++  D++
Sbjct: 232 GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLQAMMLAISESPTTIAEILVLADKI 291

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
             G   + E +D           GF    E   Y   ED  +  E DD     G      
Sbjct: 292 RVGEMQISEAVD-----------GFVSNEEADDYVAEEDFDEFDEEDDDDGNGG------ 334

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                                          +  L+   ++L+ + +   DE+   +  +
Sbjct: 335 -------------------------------SKALTKKLEELKTQALVRFDELRTHFDRM 363

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
           R   +      K+   S      +  +   + SL      I+ L + L      I   E 
Sbjct: 364 RKAYE------KEGYKSPAYNRAQMGVSSEIMSLRFTVKTIERLCQILRSQVDDIRRYER 417

Query: 355 ELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           EL ++     G+ +D F++      L+  W           +   +A  +  I  ++ ++
Sbjct: 418 ELRKIVVDKCGMPQDHFIKTFPPNSLNLKWAEKEIA-ANKSYSAVMARNLPPIQDLQQKL 476

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     + I + + I   + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 477 IDLQSRAVVPIDDLKLINKKMNQGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDL 536

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ 
Sbjct: 537 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 596

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R +R+   +   EP    +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIE
Sbjct: 597 RLSRQHLQEFGFEPDAPTLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIE 656

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D N  +P+++A+QA LR+    +L SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTR
Sbjct: 657 DTNNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTR 716

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ERIRQIEAKAIRKLKHPSRS KLR++LD 
Sbjct: 717 ERIRQIEAKAIRKLKHPSRSDKLRTYLDN 745


>gi|323529380|ref|YP_004231532.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1001]
 gi|323386382|gb|ADX58472.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1001]
          Length = 664

 Score =  434 bits (1115), Expect = e-119,   Method: Composition-based stats.
 Identities = 227/662 (34%), Positives = 354/662 (53%), Gaps = 47/662 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V +    
Sbjct: 45  AEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQAPD 104

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  ++     A   +       DS    T DPVRMY+REMG+ ELL+R GEI
Sbjct: 105 AETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGEI 164

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           AIAKRIE G   M+ ++   PL   A++    ++ DG   + E++D              
Sbjct: 165 AIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVD-------------- 210

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                      ++ + E+E      +  +   A      D      P +++  DE     
Sbjct: 211 -------GLNEDNVAAEEENVSADASADEDTDAEDDEDSDGDDDVGPADSSAADE----- 258

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                     A   QL    +    ++  +Y ++ +      +  + + SS   +  +E+
Sbjct: 259 ----------ARLKQLTSDCLEIFAQVGILYDQMNA------SHTRGDVSSKAYQKAREE 302

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           + + +  +      ID L   +     ++   E  +L++     G+ R+ F+E   G E 
Sbjct: 303 IQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVTKSGMPREKFIESFSGHEA 362

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W   A       +   +   + +I   + ++  I     + +   + I   +   E 
Sbjct: 363 DLGWTERAARGNTS-YGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRQMVAAES 421

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTY
Sbjct: 422 KMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTY 481

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +A+++ + 
Sbjct: 482 ATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPSVLAERMDLS 541

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR +LKI K+P+S+ETP+GD+  + LGD IED  A SP D+A+QA+LR      L S
Sbjct: 542 EEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAMQADLRAAIDDALDS 601

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ +L+SF
Sbjct: 602 LSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLKSF 661

Query: 680 LD 681
           LD
Sbjct: 662 LD 663


>gi|33151868|ref|NP_873221.1| RNA polymerase sigma factor RpoD [Haemophilus ducreyi 35000HP]
 gi|33148089|gb|AAP95610.1| RNA polymerase sigma factor [Haemophilus ducreyi 35000HP]
          Length = 613

 Score =  434 bits (1115), Expect = e-119,   Method: Composition-based stats.
 Identities = 274/656 (41%), Positives = 380/656 (57%), Gaps = 47/656 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                + +I   R++GY+TI E++  LP + V +EQ+ED + M+++MGI V++     DE
Sbjct: 3   QQSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDE 62

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               +++        ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 63  LMLAENIADEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 121

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P     LI +  ++ +GT  L +++   A + P  +       E  
Sbjct: 122 EEGINEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVT--AFVDPNIQA------EED 173

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +   D  +E         + + +  +  S D+       PE A      L E  + + 
Sbjct: 174 VVELDSDLDEEASDVVADVDDENEDEESDGSADNTDDNSIDPELAREKFYALREQHEKAL 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   QK  +S  K K   + L  +  
Sbjct: 234 QAI-----------------------------------QKHGRSHKKSKQHIQALSDIFR 258

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
              L   + DLLVE +  + K++   E ++ R A  Y  +K+  FL+  QG E    W+ 
Sbjct: 259 EFRLVPKQFDLLVESMQRMMKQVRAEERQIQRYAVEYAQMKKADFLKLFQGNETSEEWID 318

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A +         +A  V+ I    + ++ +  +T +++++ R I   +  GE +A  AK
Sbjct: 319 KAIN-ARKGAAPKLANYVEQIRINISNLQRMEQDTDLTVAQIREIGGRIASGELKARRAK 377

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 378 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 437

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RK
Sbjct: 438 QAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMGMPEDKIRK 497

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPI  +D SHLGDFI+D+N   PLDSA   +LR  T  VL  LTPRE 
Sbjct: 498 VLKIAKEPISMETPI-GDDDSHLGDFIQDENLELPLDSATAESLRLATNEVLEGLTPREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 557 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 612


>gi|121997892|ref|YP_001002679.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
           SL1]
 gi|121589297|gb|ABM61877.1| RNA polymerase, sigma 70 subunit, RpoD [Halorhodospira halophila
           SL1]
          Length = 602

 Score =  433 bits (1114), Expect = e-119,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 375/657 (57%), Gaps = 62/657 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K++I   +++G++T  E+N  LP D V  +Q++D + M+++MGINV +     DE
Sbjct: 5   QQSQIKQLIAKGKEQGFLTYAEVNDHLPDDIVDPDQIDDIIGMINDMGINVHETAPDSDE 64

Query: 87  EG-SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +E ++      +  +       D+    T DPVRMY+REMGS+ELL+REGEI +AKR
Sbjct: 65  LLLAETTVATDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGSVELLTREGEIQLAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G    +A+L   P   + LI+  D   +G   L +I+                    
Sbjct: 125 IEDGLDRALAALSSYPEAARQLIMLYDRAQEGEARLTDIV-------------------- 164

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                     ++      +       +A +  +   ++    PE        L    ++ 
Sbjct: 165 ----AGFRDREDDSEQPPEAPAAPEAAADEDEEATSAETGPDPEAVAELFERLRAAYNEM 220

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L+                                    +  +S +   L+ +L ++ 
Sbjct: 221 QEVLAT-----------------------------------EGSASPRIAELRGELEEVF 245

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV 384
            S+      +D + ++L      I   E E++ L    G + R  F++  Q RE DP W+
Sbjct: 246 LSIKFTPKVVDAVADRLRGTVDTIRAREREIMNLCTREGRMARKEFVKSFQDRETDPTWL 305

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                  E E    +    ++I K ++E+K I+ + G+S++E + I   +  GE +A  A
Sbjct: 306 DDLLAEGE-ERAERLQPHAEAIRKAQSELKEIADKNGLSVAEIKEINRRMSIGEAKARRA 364

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 365 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 424

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + VR
Sbjct: 425 RQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERMEMPEDKVR 484

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED +  SP+DSA    LRE+   VL+ LTPRE
Sbjct: 485 KVLKIAKEPISMETPIGDDEDSHLGDFIEDTSVTSPVDSATSEGLRESVREVLSGLTPRE 544

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFL+
Sbjct: 545 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDGLRSFLE 601


>gi|89900350|ref|YP_522821.1| sigma 70 (RpoD) [Rhodoferax ferrireducens T118]
 gi|89345087|gb|ABD69290.1| sigma 70 (RpoD) [Rhodoferax ferrireducens T118]
          Length = 783

 Score =  433 bits (1114), Expect = e-119,   Method: Composition-based stats.
 Identities = 252/670 (37%), Positives = 369/670 (55%), Gaps = 69/670 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IKL + RGY+T  E++  LP   V +E +E  ++ML++MG+ V +     + 
Sbjct: 168 RRQRLKALIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAET 227

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  +      A   +       DS    T DPVRMY+REMG++ELL+REGEI IA
Sbjct: 228 LLLNNNVSTAATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIA 287

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   +++ +G  ++  I+D           GF +  
Sbjct: 288 KRIEGGLMAMMEAISASPATIAEILRLSEDIREGKVVITTIVD-----------GFSNPN 336

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +    DD     G                                   
Sbjct: 337 EADDYVAEEDFDEFDAADDDDGKGG----------------------------------- 361

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D + E++ ++ ++        K+   +      ++ L +
Sbjct: 362 --SKALTKKLEELKNEALSRFDRLRELFEKIHTIY------NKEGYGTPSYIKTQKALSE 413

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRE---- 378
            + S+      I+ L + +      +   E EL R+     G  ++ F+    GR+    
Sbjct: 414 ELMSIRFTAKTIEKLCDLVRSQVDDVRKKERELRRIIVDKCGYPQENFIADFSGRDKHGN 473

Query: 379 ------LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                 L+  W+          W   +A  +  +  ++ ++  +  +  + + + + I  
Sbjct: 474 KVASQLLNLKWIEKQAA-SGKHWGPIMARNIPPVQDLQQKLTDLQSKVVVPLDQLKDINK 532

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 533 RMNEGEYSSRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 592

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +
Sbjct: 593 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASVL 652

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+++ +P + +RK++KI KEPIS+ETPIGD+D SHLGDFIED    +P+++A+QA LR+ 
Sbjct: 653 AERMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAANTAPMEAAMQAGLRDV 712

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +L SLTPRE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 713 VKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSR 772

Query: 673 SKKLRSFLDG 682
           S KLRSF D 
Sbjct: 773 SDKLRSFTDN 782


>gi|296112900|ref|YP_003626838.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|295920594|gb|ADG60945.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|326561129|gb|EGE11494.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 7169]
 gi|326564438|gb|EGE14665.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 103P14B1]
 gi|326564864|gb|EGE15069.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 46P47B1]
 gi|326567590|gb|EGE17705.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC1]
 gi|326569439|gb|EGE19499.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC8]
 gi|326571363|gb|EGE21378.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC7]
 gi|326575352|gb|EGE25280.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis CO72]
 gi|326576561|gb|EGE26468.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 101P30B1]
 gi|326577423|gb|EGE27307.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis O35E]
          Length = 626

 Score =  433 bits (1113), Expect = e-119,   Method: Composition-based stats.
 Identities = 256/660 (38%), Positives = 378/660 (57%), Gaps = 48/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D S      +I+L +++GY+T  E+N  LP     S+Q+ED + ML+++GI V +    +
Sbjct: 12  DTSSSQLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDD 71

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D+    D+      A++ +  +    ++    T DPVRMY+REMG+++LL+REGEI IAK
Sbjct: 72  DDILLSDTGSDDDIATDEAAAVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIGIAK 131

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +   +   P T + ++    ++  G   + +I+            GF +G +
Sbjct: 132 RIEEGTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIV-----------SGFLNGDD 180

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      E+   +          G  ++  K   ++  + D    +  +D     E    
Sbjct: 181 GDFILNEEEIELD---------LGSPKTTDKDDAEEDGESDGTELDDTDDSSLDPE---- 227

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVK 323
                                E+   + E++ L D A     K  + S   KV  ++L  
Sbjct: 228 ---------------------EVRVRFEEIQRLYDVAQEALAKHGRGSEAVKVAYDELAN 266

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPH 382
               + LN    D ++  + ++ + +  NE  +++L   +G +  D F +     E +  
Sbjct: 267 HFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEFKKTFPSNETNLE 326

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+S+ +      +   +A     ++ ++ ++ +      + I + + +   +  GE +A 
Sbjct: 327 WLSH-RIKGGPAFAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVARQMAIGEAKAR 385

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKK+MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 386 RAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 445

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    
Sbjct: 446 WIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLDMDEAK 505

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+++A    LRE T  VL +LT 
Sbjct: 506 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLREATREVLDNLTE 565

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VL+MRFGI M +DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 566 REAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 625


>gi|107099562|ref|ZP_01363480.1| hypothetical protein PaerPA_01000575 [Pseudomonas aeruginosa PACS2]
          Length = 604

 Score =  433 bits (1113), Expect = e-119,   Method: Composition-based stats.
 Identities = 266/649 (40%), Positives = 379/649 (58%), Gaps = 47/649 (7%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           MI   R++GY+T  E+N  LP D    EQ+ED + M+++MGINV +     D     ++ 
Sbjct: 1   MIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLLAEAD 60

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
              ++A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +
Sbjct: 61  TDEAAAEEAAAALAAVE-SDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREV 119

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           M+++ + P T  +++   + +      L ++  L   I P+         E  + +    
Sbjct: 120 MSAIAQFPGTVDSILADYNRIVAEGGRLSDV--LSGYIDPDDGSLPAEEVEPVNLK---- 173

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                            + +A   + D  + +S   +  +DE +   D +++    +A+ 
Sbjct: 174 -----------------DDSADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVS 216

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           +QL                            +K  + S +       L +L   + L   
Sbjct: 217 EQLDKA---------------------KKALKKHGRGSKQATAELTGLAELFMPIKLVPK 255

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           + D LV ++    + +   E  +++L      + R  FL      E D  WV       +
Sbjct: 256 QFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNHETDEKWVDSVLK-SK 314

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            ++   +    D IL+ + ++ ++  E  ++++E + I   +  GE +A  AKKEMVEAN
Sbjct: 315 PKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGEAKARRAKKEMVEAN 374

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 375 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 434

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI KE
Sbjct: 435 ADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKIRKVLKIAKE 494

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PIS+ETPIGD++ SHLGDFIED    SP++ A   +L+E+T  VLA LT RE +VLRMRF
Sbjct: 495 PISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLAGLTAREAKVLRMRF 554

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 555 GIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLD 603


>gi|332527902|ref|ZP_08403939.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Rubrivivax benzoatilyticus JA2]
 gi|332112479|gb|EGJ12272.1| putative RNA polymerase sigma(sigma-70) factor transcription
           regulator protein [Rubrivivax benzoatilyticus JA2]
          Length = 734

 Score =  433 bits (1112), Expect = e-119,   Method: Composition-based stats.
 Identities = 259/660 (39%), Positives = 368/660 (55%), Gaps = 59/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +IK+ + RG++T +E+N  LP   V +E +E  V+ML++MGI V +       
Sbjct: 129 RRQELKTLIKMGKTRGFLTHQEINDHLPEKLVDNEILEAIVSMLNDMGIAVYEQAPDAAT 188

Query: 87  ---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
               GS  +      A  ++       DS    T DPVRMY+REMGS+ELL+REGEI IA
Sbjct: 189 LLINGSNTATATDEEAEEAAEAALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEIEIA 248

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   MM ++  SP T   ++   D++  G   + E++D           GF    
Sbjct: 249 KRIEGGLQAMMLAISASPTTIAEILAMADKIAAGEMQISEVVD-----------GFVSDD 297

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E   Y   ED  +  E DD     G                                   
Sbjct: 298 EADDYVAEEDFDEFDEDDDDDGAGG----------------------------------- 322

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             +  L+   ++L+ + +   D +   +  +R   +      KD   S      +E + +
Sbjct: 323 --SKALTKKLEELKKQALEKFDLLRSHFDRMRKAYE------KDGYKSPAYNKAQEAISQ 374

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
            + ++      I+ L + L      +   E E+ ++     G+ ++ F++      L+  
Sbjct: 375 DLMTIRFTVKTIEKLCQILRAQVDDVRRYEREIRKIVVDKCGMPQEQFIKTFPPNVLNLK 434

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W        +  +   +   + ++ +++ ++  +     + + + + I   +  GE  + 
Sbjct: 435 WAEKEAAAGKP-YSAVLGRNLPAVQELQQKLIDLQGRAVVPLDDLKEINRHMNAGEKASR 493

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 494 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 553

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A+K+ +P + 
Sbjct: 554 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAPTLAEKMEIPEDK 613

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RK++ I KEPIS+ETPIGD+D SHLGDFIED N V+P+D+A+QA LRE    +L SLTP
Sbjct: 614 IRKIMMIAKEPISMETPIGDDDDSHLGDFIEDTNNVAPVDAAMQAGLREVVKDILDSLTP 673

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKAIRKLKHPSRS KLR++LD 
Sbjct: 674 REAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRSDKLRTYLDN 733


>gi|222475070|ref|YP_002563485.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
 gi|255003048|ref|ZP_05278012.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str. Puerto
           Rico]
 gi|255004170|ref|ZP_05278971.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Virginia]
 gi|222419206|gb|ACM49229.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
          Length = 646

 Score =  432 bits (1111), Expect = e-119,   Method: Composition-based stats.
 Identities = 279/658 (42%), Positives = 402/658 (61%), Gaps = 46/658 (6%)

Query: 26  FSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDL 83
              +  K +I    +Q G +T ++++  L  D+V SSE +++T+++L + GI V++  D 
Sbjct: 32  MDKELVKNLITKGIKQGGVITFDDISDALSDDDVVSSESIDETISLLQDSGIGVLEQSDE 91

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ +      + A    + +      +      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 92  EEADAVVSEENAAKDEEDEAG----MRSLDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 147

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRI++ +  M+ SL E+PL  +  + WRD+L +   +LR++IDL+A      +GG     
Sbjct: 148 KRIKSEKINMLRSLIEAPLVLRTFMSWRDDLVNQQVMLRDLIDLDANY----RGGAPRQE 203

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                +  E    E    DV     D E                            ED  
Sbjct: 204 FEEGGEYGEQEMAEPGDSDVGGDGADDEDEG-------------------------EDSS 238

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME  L PKV+  LD   E   ++  ++    +  K +K       L E + +
Sbjct: 239 AGNASILEMESALLPKVISILDATIESAEKILEMKKQKRDSGKYDK--KAYNALHENIWE 296

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           LV  + L+   +  + +Q+Y++SK I   E  L+ L +SYG+ R  FLE +    +    
Sbjct: 297 LVSQMKLSDPAVLSVTQQIYNLSKAIAAEEAALMSLVESYGVDRKSFLEAYNNNTV---- 352

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             + +     EWKN +  E  ++  I+N+++ +S E   S   F+ +V+ ++K E  A+ 
Sbjct: 353 --FEQANASPEWKNLLEKEKKTLTDIQNKVRLLSGED--SPGNFKALVAKIQKHERTANK 408

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 409 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 468

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L M VE +
Sbjct: 469 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSTRLGMNVEKI 528

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+
Sbjct: 529 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPK 588

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 589 EERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 646


>gi|307726409|ref|YP_003909622.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
 gi|307586934|gb|ADN60331.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
          Length = 664

 Score =  432 bits (1111), Expect = e-119,   Method: Composition-based stats.
 Identities = 227/662 (34%), Positives = 352/662 (53%), Gaps = 47/662 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +I+L +++GY+T  ++N  LP +   +  ++  V+  ++MG+ V +    
Sbjct: 45  AEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFTQTAAIDSIVSAFNDMGVQVYEQAPD 104

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  ++     A   +       DS    T DPVRMY+REMG+ ELL+R GEI
Sbjct: 105 AETLLLNSNTPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGEI 164

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           AIAKRIE G   M+ ++   PL   A++    ++ DG   + E++D    +  E+     
Sbjct: 165 AIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVD---GLNEENVAAEE 221

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                 S    +  + E E  D  +  G  +S+A                          
Sbjct: 222 ETVSADSAADDDADADEDEDSDSDDDVGPADSSAADE----------------------- 258

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                     A   QL    +    ++  +Y  + +      +  + + +S   +  +E+
Sbjct: 259 ----------ARLKQLTSDCLEIFAQVGILYDRMNA------SHTRGDVTSKAYQKAREE 302

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           + + +  +      ID L   +     ++   E  +L++     G+ R+ F+E   G E 
Sbjct: 303 IQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVTKSGMPREKFIESFSGHEA 362

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W   A       +   +   + +I   + ++  I     + +   + I   +   E 
Sbjct: 363 DLGWTERAA-RGNTSYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRQMVAAES 421

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTY
Sbjct: 422 KMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTY 481

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +A+++ + 
Sbjct: 482 ATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPSVLAERMDLS 541

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR +LKI K+P+S+ETP+GD+  + LGD IED  A SP D+A+QA+LR      L S
Sbjct: 542 EEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAMQADLRAAIDDALDS 601

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ +L+SF
Sbjct: 602 LSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRLKSF 661

Query: 680 LD 681
           LD
Sbjct: 662 LD 663


>gi|167584375|ref|ZP_02376763.1| sigma 70 (RpoD) [Burkholderia ubonensis Bu]
          Length = 611

 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 230/654 (35%), Positives = 352/654 (53%), Gaps = 49/654 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE---EG 88
           + +I L R+RGY+T  ++N  LP +   +  ME  V+  S+MG+ V +     +      
Sbjct: 2   RALIALGRERGYLTHADINDHLPDNFAQTAAMETIVSTFSDMGVAVYEQAPDAETLLLND 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  ++     A   +       DS    T DPVRMY+REMG+ ELL+R GEI IAKRIE+
Sbjct: 62  ATAAVASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEIEIAKRIES 121

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   M+ ++   P     ++   D +  G   + E++D                      
Sbjct: 122 GLQDMIQAIAACPTVVSTILADADRIAAGELRIDELVD---------------------- 159

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                               D + +    + D  +V++   + + D  + + D  DS   
Sbjct: 160 ----------------GISDDTDESDMTLESDEVEVEADASDDDPDGDDDEADAGDSEKA 203

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
            +A  ++L    +     +  ++ +L  +         D+  S     ++ ++ + +  +
Sbjct: 204 NTARLEELTNDSLAIFARVRALFEQLPDVP------ATDKTRSAAAVQVRAEIQRELAPI 257

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYA 387
                 ID L   ++D    +   E  +L +A    G+ RD F+E   G E D  W S  
Sbjct: 258 RFTAKTIDRLCASVHDQVTEVRAIERSILEIAVDRCGMPRDAFVESFPGHETDLEWTSRT 317

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
               + ++   +   + +I   + ++  I     + + + + I   +   E +   AK++
Sbjct: 318 AATSK-QFGAALERHLPAIQAGQQKLIDIESRVLLPLQQLKQINRQMSAAESKMRQAKRQ 376

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLVIS+AKKY NRG+QFLDLIQEGNIGLMKA +KF++  G+KFSTYA WWV+QA
Sbjct: 377 MIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQA 436

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +TR++ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +AK++ M  E VR +L
Sbjct: 437 VTRALADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAKRMEMSEEKVRSIL 496

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI K+P+SLETP+GD+  + LGD IED +A SP ++AI AN+R      L  L+PRE +V
Sbjct: 497 KIAKQPVSLETPVGDDADATLGDMIEDVSASSPAEAAIHANMRAAIDEALDGLSPREAKV 556

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFG+   +DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ KLR FL+
Sbjct: 557 LRMRFGLDTTSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADKLRPFLE 610


>gi|254497834|ref|ZP_05110600.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
 gi|254352912|gb|EET11681.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
          Length = 628

 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 272/660 (41%), Positives = 375/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    +
Sbjct: 14  EQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPGD 72

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 73  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 131

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   +        L EII   A               
Sbjct: 132 RIEEGIYQVLKSLAHYPETVQLVLDDYERFIAQEIRLNEIISGFA--------------- 176

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         + D+      +I S    S+ D   + +  E+ + +    + D+  
Sbjct: 177 --------------DSDEEMAPAANIGSMLDESQQDELILANDDEDEDGEGGIAEVDDGP 222

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +     A  D+LR     A+  + E                   ++  K     E +   
Sbjct: 223 NPEQAKAYFDELRECFNAAMVVLKE-----------------HGRTHAKTNKSLEAMSDS 265

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 266 FLKLKLTSRQVDRLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLEW 325

Query: 384 VS-YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           ++       +    + ++   + IL+I++ + S  VE G++I E + I   +  GE +A 
Sbjct: 326 LNNIIAKHAKKLDMSRISEYTEEILRIQSRLVSFEVEYGLTIGEIKDINRKMSIGEAKAR 385

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 386 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 445

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 446 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 505

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 506 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 565

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 566 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 625


>gi|226951573|ref|ZP_03822037.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter sp. ATCC 27244]
 gi|226837676|gb|EEH70059.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
           during exponential growth [Acinetobacter sp. ATCC 27244]
          Length = 626

 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 266/654 (40%), Positives = 369/654 (56%), Gaps = 41/654 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    +S    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESTEAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E  +  
Sbjct: 131 IRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGYLDPETDEEIPEVLEDEAEI 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + E S     ++   + + D E  ++   D        PE A+     L+   +D+   +
Sbjct: 189 EEEKSPTSTTKE--VKLDDDDEEESESDDDSEGDSGPDPEVAKIRFTELETAWNDTKAII 246

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  ++S + +   E L  +     
Sbjct: 247 E-----------------------------------KHGRNSKEAEAALEALAAVFMMFK 271

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +     +I  NE E++R A   G + R  F      +E +P W+    
Sbjct: 272 FTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTFRTTFPEQESNPAWLDEQI 331

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEM
Sbjct: 332 AKAPAEIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDISKRMAVGEAKARRAKKEM 391

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 392 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 451

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 452 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 511

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 512 IAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVL 571

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 572 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 625


>gi|294651232|ref|ZP_06728560.1| RNA polymerase sigma factor RpoD [Acinetobacter haemolyticus ATCC
           19194]
 gi|292822885|gb|EFF81760.1| RNA polymerase sigma factor RpoD [Acinetobacter haemolyticus ATCC
           19194]
          Length = 626

 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 266/654 (40%), Positives = 370/654 (56%), Gaps = 41/654 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    +S    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESTEAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E  +  
Sbjct: 131 IRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGYLDPETDEEIPEVLEDEAEI 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + E+S     ++   + + D E  ++   D        PE A+     L+   +D+   +
Sbjct: 189 EEEESPTSTTKE--VKLDDDDEEESESDDDSEGDSGPDPEVAKIRFTELETAWNDTKAII 246

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                                               K  ++S + +   E L  +     
Sbjct: 247 E-----------------------------------KHGRNSKEAEAALEALAAVFMMFK 271

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +     +I  NE E++R A   G + R  F      +E +P W+    
Sbjct: 272 FTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTFRTTFPEQESNPAWLDEQI 331

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEM
Sbjct: 332 AKAPAEIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDISKRMAVGEAKARRAKKEM 391

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 392 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 451

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 452 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 511

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 512 IAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLKEATREVLENLTEREAKVL 571

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 572 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 625


>gi|262281266|ref|ZP_06059048.1| RNA polymerase sigma factor rpoD [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257497|gb|EEY76233.1| RNA polymerase sigma factor rpoD [Acinetobacter calcoaceticus
           RUH2202]
          Length = 627

 Score =  431 bits (1108), Expect = e-118,   Method: Composition-based stats.
 Identities = 261/654 (39%), Positives = 370/654 (56%), Gaps = 40/654 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESTDTTDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E  +  
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEETEL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + E++     ++   + + + E +      +      P                      
Sbjct: 189 EEEEAPAVPAKEVKLDDDEEDEESESDDDSEGESGPDP---------------------- 226

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                          +E+   + + +++ +      K  ++S +     E L  +     
Sbjct: 227 --------EVAKVRFNELEAAWTKTKAIIE------KHGRNSPEADDALEALATVFMMFK 272

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  NE E++R A   G + R  F      +E +P W+    
Sbjct: 273 FTPRLFDIISEMIRGTHEQIRANEREVMRYAVRRGRMDRTQFRTSFPKQESNPAWLDEQI 332

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E K  +      IL  + +I  I  E  +S++E + I   +  GE +A  AKKEM
Sbjct: 333 AKAPAEIKAHLEKVRPDILAFQQKIADIEKELNLSVAEIKDISKRMAIGEAKARRAKKEM 392

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 393 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 452

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 453 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 512

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 513 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVL 572

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 573 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 626


>gi|319788464|ref|YP_004147939.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466976|gb|ADV28708.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 618

 Score =  431 bits (1108), Expect = e-118,   Method: Composition-based stats.
 Identities = 273/660 (41%), Positives = 373/660 (56%), Gaps = 55/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
           +    K++I    ++GY+T  E+N  LP D V  EQ+ED + M++ MGI+V +     + 
Sbjct: 7   AQSEIKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDVET 66

Query: 86  ---EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
               +G+  + ++  +A+  +       DS    T DPVRMY+REMG++ELL+REGEIAI
Sbjct: 67  LLLNDGNTGNREIDDTAAEEAAAALTALDSEGGRTTDPVRMYMREMGTVELLTREGEIAI 126

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   + A+L   P + +AL+   +    G   L E++                 
Sbjct: 127 AKRIEEGLGQVQAALGSVPASVEALLEEYELHKAGKKRLAEVV----------------- 169

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                             D+  E    +E  A    +   + +   E+ E +      D 
Sbjct: 170 -----------VGFNDLLDETPEPPAPVEDTADADAEGEDEEEDVAEDDEAEAGPTGPDP 218

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            + A  +  +   L                             K      K   L+ ++ 
Sbjct: 219 AEVARRMEQLAADLAKF---------------------KKAHAKAGAQDKKVIKLRAEMA 257

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
           +   +  L     D+LV +L D+   I   E  +L LA +   + R  F+   +G +++ 
Sbjct: 258 EQFVTFKLPLPLTDVLVRKLRDVLTEIKDRERRVLHLATNVARMPRKDFIRAWEGNQVNL 317

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV       + +W + +    D I+  +    +I     + +S+ R I   +  GE +A
Sbjct: 318 EWVDEVLKR-KQKWSSALRDVKDQIIAEQQATIAIEQAMCLDLSDIREIGRQLAYGEAKA 376

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 377 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 436

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP +
Sbjct: 437 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKEMDMPED 496

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+DS    NL ET   VLA LT
Sbjct: 497 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDSTTNTNLMETVRDVLAGLT 556

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 557 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 616


>gi|93005952|ref|YP_580389.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
 gi|92393630|gb|ABE74905.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
          Length = 648

 Score =  431 bits (1108), Expect = e-118,   Method: Composition-based stats.
 Identities = 267/657 (40%), Positives = 390/657 (59%), Gaps = 28/657 (4%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S      +I++ +++GY+T  E+N  LP     S+Q+ED V ML+++GI + +     D+
Sbjct: 18  STSQLATLIQMGKEQGYLTYAEVNDQLPDSITESDQIEDIVQMLTDVGIKIFESAPDADD 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D       A++ +  +    ++    T DPVRMY+REMG+++LL+REGEIAIAKRI
Sbjct: 78  ILMNDDSSDDDMAADEAAAVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIAIAKRI 137

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++   P T Q ++    ++ DG   L ++I     + PE++       E  
Sbjct: 138 EEGIRDVQHAMSYWPGTVQFVLDEYQKVQDGEKKLSDVIT--GFLDPETEEDKIAAQEAK 195

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              K E    ++E+++    +            +++KV S  ++ E D+  ++ED ++  
Sbjct: 196 EAAKEERERIKEEKENPPIIK------------EKAKVKSGLDDDEEDDEEVEEDAEEET 243

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +   E +LR      L+EI  ++ +               + S +     E+L     
Sbjct: 244 SGIDPEEVRLR------LEEIEHLFIK------AKQALLDYGRGSAQANEAYEQLASRFM 291

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
            L LN    D ++  ++D+   +  +E +++RL    G + R+ F +     E +  W+ 
Sbjct: 292 MLKLNNRLSDQVMAIMHDVYDDVRKHERQIMRLVIRRGRMPREEFRKTFPSNETNVDWL- 350

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             +   +  +   +    D ++ ++  I+    +  + I + + +   +  GE +A  AK
Sbjct: 351 IERIKGKPAFAATLEKVADDVILLQRAIRDYEHKLEMEIHDMKDVARRMAIGEAKARRAK 410

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 411 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 470

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRK
Sbjct: 471 QAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEAKVRK 530

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A  A LRE T  VL +LT RE 
Sbjct: 531 VLKIAKEPISMETPIGDDEDSHLGDFIEDGTISSPVDDATAAGLREATRDVLGNLTEREA 590

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RVL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 591 RVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 647


>gi|90416498|ref|ZP_01224429.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
 gi|90331697|gb|EAS46925.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
          Length = 612

 Score =  431 bits (1107), Expect = e-118,   Method: Composition-based stats.
 Identities = 262/657 (39%), Positives = 371/657 (56%), Gaps = 55/657 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D 
Sbjct: 8   QQSGIKDLIAKGREQRYLTYAEVNDHLPEDIADPEQVEDIIQMINDMGITVFETAPDADT 67

Query: 87  EGS-EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
             S          A+  +       +S    T DPVRMY+REMGS+ELL+REGEI IAKR
Sbjct: 68  LSSLASDNTPDEVAAAEAAAALASVESEQHRTTDPVRMYMREMGSVELLTREGEIEIAKR 127

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++ + P T   ++   +++  G   L +II            G+ +  E 
Sbjct: 128 IEEGTRELMSAVADWPTTVATIVAEYEKVEAGEKKLTDII-----------SGYLNPMEH 176

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                 +  + E  +        + E   +  ++++ +    PE A              
Sbjct: 177 VPSALAQQQAAEALK------LENGEEEEEEEEEEQHEGGLDPEVA-------------- 216

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                              D I +       L+       +  +     +   E+L +L 
Sbjct: 217 ---------------FERFDTIRKQ------LKKTDTCIARYGRGGEASQKNLEELAELF 255

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV 384
             L L   + D L+ ++    +R+   E +++RL    G + R  F++   G E +  W 
Sbjct: 256 KYLKLTPRQFDPLIAKVRLAVERVRAEERKIMRLCIRLGKMPRKDFIKMFPGNESNMQWT 315

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      E   +   A EV+ IL+ + ++  +     ++I++ + I   +  GE  A  A
Sbjct: 316 AELAKSKESWAERVSAQEVE-ILRSQRKLAQVEKLADMNIAQIKDINRRMTMGEAMARRA 374

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 375 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 434

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP + +R
Sbjct: 435 RQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPEELAERMEMPEDKIR 494

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIG+++ + +GD IED     PLD A + NL E+T  VL+SLT RE
Sbjct: 495 KVLKIAKEPISMETPIGEDEDASIGDLIEDTTIALPLDEATKNNLTESTRGVLSSLTARE 554

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSF+D
Sbjct: 555 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDHLRSFID 611


>gi|72383848|ref|YP_293202.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72123191|gb|AAZ65345.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 624

 Score =  431 bits (1107), Expect = e-118,   Method: Composition-based stats.
 Identities = 223/661 (33%), Positives = 342/661 (51%), Gaps = 49/661 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      + +I L R+RGY+T  ++N  LP +   +  ME  V+  S+MG+ V +     
Sbjct: 8   EERQRQMRALIALGRERGYLTHADINDHLPDNFTQTAAMETIVSTFSDMGVTVYEQAPDA 67

Query: 85  DEEGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D     D+         A   +       DS    T DPVR+Y+REMG+ ELL+R GEI 
Sbjct: 68  DTLLLSDTAPAGASDDQADEEAEAALSTVDSEFGRTTDPVRLYMREMGASELLTRAGEIE 127

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P     ++   D +  G   + E++                
Sbjct: 128 IAKRIEGGLQGMIQAIAACPSVVSTMLADVDRIVAGELRIDELV---------------- 171

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                                      D+  +      D   V++   + +    +++ D
Sbjct: 172 ----------------------YGISDDVNDSEIALASDDVHVEADASDDDPVGDDVEPD 209

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
             DS    +A  +QL    +     +  ++ +L             +  S   + L+ K+
Sbjct: 210 AGDSEKANAARLEQLTLDSLAIFARVRALFEQL------PDAPVTGKARSAAVEQLRSKI 263

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
              +  +      ID L   +++    +   E  +L +A    G+ R VF+E   G E D
Sbjct: 264 QSELAPIRFTAKTIDRLCASVHEQLTEVRAIERSILEIAVDRCGMPRKVFVESFPGNETD 323

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W S        ++   +   + +I   + ++  I  +  + + +F+ I   +   E +
Sbjct: 324 LKWTSKMAA-TSRQFGAALKRHLPAIQAGQQKLIDIEAKVTLPLQQFKQINRQMSAAELK 382

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+E++EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++  G+KFSTYA
Sbjct: 383 MRQAKRELIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYA 442

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WWV+QA+TR++ADQ+ TIR+PVHM + I+K+ R +R    +  RE  P  +A+++ M  
Sbjct: 443 TWWVRQAVTRALADQARTIRVPVHMVEMINKLNRISRDFRQQTGREAHPAVLAERMEMSE 502

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VR +L+  ++P+SLETP+GD+  + LGD IED +A SP ++AI A++R      L  L
Sbjct: 503 EKVRSILRSARQPVSLETPVGDDADATLGDMIEDVSASSPAEAAIHADMRAAIDEALDGL 562

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE +VLRMRFG+   +D TLEEV KQF VTRERIRQIE++A+RKL HPSR+ KLR FL
Sbjct: 563 SPREAKVLRMRFGLDTTSDRTLEEVSKQFDVTRERIRQIESQAMRKLLHPSRADKLRPFL 622

Query: 681 D 681
           +
Sbjct: 623 E 623


>gi|325983602|ref|YP_004296004.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. AL212]
 gi|325533121|gb|ADZ27842.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. AL212]
          Length = 740

 Score =  430 bits (1106), Expect = e-118,   Method: Composition-based stats.
 Identities = 256/661 (38%), Positives = 379/661 (57%), Gaps = 48/661 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +I L ++RGY+T  E+N  LP D + +EQ+E  ++M+++MGI+V D    
Sbjct: 121 IEARRMRLKILIGLGKERGYLTYAEINDHLPDDMLDAEQIEGIISMINDMGISVHDEAPD 180

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRK--DSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +     D+    +    +          DS    T DPVRMY+REMGS+ LL+RE EI 
Sbjct: 181 VETLLMSDAATTVADEDVAEEAEAALSTVDSEFGRTTDPVRMYMREMGSVGLLTRESEIE 240

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P     +I    E+   T  + E++D     G         
Sbjct: 241 IAKRIEGGLRHMIQAISACPPIIAKIIDLAVEVEKETMRIDEVVD-----GLLDANAQDI 295

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E  S +  E      +    ++ + D + AA  S D                      
Sbjct: 296 INEELSEEAIEQELSSNDLAGDEDEDEDSDGAAIASADLL-------------------- 335

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                        +L+   +     I +++ E+++L ++      D         L++K+
Sbjct: 336 -------------KLKADALERFAVIRQMHNEMQALLES------DGPYHQGYIELQDKI 376

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
              + ++  +   ++ L +   ++   + + E +++ L      + R+ F++   G E +
Sbjct: 377 SSELMAIRFSAKMMEKLCDTQRELVGDVRNYERKIMDLCVSKAKMPRNHFIKTFPGNETN 436

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W++      +  +   +     +IL+ ++ + ++  + GI I + + I   +  GE +
Sbjct: 437 LDWIAQEIKVGKP-YSQALEHYKPAILEEQHNLLALRSKIGIPIKDLKEINRKMSTGEAK 495

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 496 ARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 555

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  +EP P  +A+K+ MP 
Sbjct: 556 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQEPEPAVLAQKMEMPE 615

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++P D+A+ A+LR  T  +L SL
Sbjct: 616 EKIRKILKISKEPISMETPIGDDEDSHLGDFIEDAATMAPADAAVYASLRGVTKDILDSL 675

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS++LRSFL
Sbjct: 676 TPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPARSERLRSFL 735

Query: 681 D 681
           D
Sbjct: 736 D 736


>gi|325123225|gb|ADY82748.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
           during exponential growth [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 636

 Score =  430 bits (1106), Expect = e-118,   Method: Composition-based stats.
 Identities = 268/662 (40%), Positives = 373/662 (56%), Gaps = 47/662 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGS 89
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +   + +D    
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFG 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +      A   +  +    ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  ESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++   ++   G   L +I  L   + PE+        E     
Sbjct: 131 IRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEEL 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED S  K   +V+  + D E  ++   D        PE A+                 
Sbjct: 189 EEEDESSSKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAK----------------- 231

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                           E+   + + +++ +      K  ++S + +   E L  +     
Sbjct: 232 ------------VRFTELEAAWAKTKAVVE------KHGRNSPEAEEALEALATVFMMFK 273

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL--------D 380
                 D++ E +    ++I  NE E++R A   G + R  F       E         +
Sbjct: 274 FTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRTQFRTSFPKHESTSFPKQESN 333

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           P W+         E K  +      +L  + +I  I  E  +S++E + I   +  GE +
Sbjct: 334 PAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIKDISKRMAIGEAK 393

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 394 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 453

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M  
Sbjct: 454 TWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDE 513

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +L
Sbjct: 514 VKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGLKEATREVLENL 573

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 574 TEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFL 633

Query: 681 DG 682
           + 
Sbjct: 634 EN 635


>gi|71065817|ref|YP_264544.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
 gi|71038802|gb|AAZ19110.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
          Length = 647

 Score =  430 bits (1106), Expect = e-118,   Method: Composition-based stats.
 Identities = 260/657 (39%), Positives = 379/657 (57%), Gaps = 29/657 (4%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S      +I++ +++GY+T  E+N  LP     S+Q+ED + ML+++GI + +     D+
Sbjct: 18  STSQLATLIQMGKEQGYLTYAEVNDQLPDSITESDQIEDIIQMLTDVGIKIFESAPDADD 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D       A++ +  +    ++    T DPVRMY+REMG+++LL+REGEIAIAKRI
Sbjct: 78  ILMNDDSSDDDMAADEAAAVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIAIAKRI 137

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++   P T Q ++    ++ DG   L ++I     + PE++       E  
Sbjct: 138 EEGIRDVQHAMSYWPGTVQFVLDEYQKVQDGEKKLSDVIT--GFLDPETEEDKIAAQEAK 195

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              K E    ++E+++    +   ++ + +  D+           E    + +E      
Sbjct: 196 EAAKEERERIKEEKENPPIIKEKAKAKSGLDDDEDEDDVEEDAEEETSGIDPEE------ 249

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                        V   L+EI  ++ +               + S +     E+L     
Sbjct: 250 -------------VRLRLEEIEHLFIK------AKQALLDYGRGSAQANEAYEQLASRFM 290

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVS 385
            L LN    D ++  ++D+   +  +E +++RL    G + R+ F +     E +  W+ 
Sbjct: 291 MLKLNNRLSDQVMAIMHDVYDDVRKHERQIMRLVIRRGRMPREEFRKTFPSNETNVDWL- 349

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             +   +  +   +    D ++ ++  I+    +  + I + + +   +  GE +A  AK
Sbjct: 350 IERIKGKPAFAATLEKVTDDVILLQRAIRDYEHKLEMEIHDMKDVARRMAIGEAKARRAK 409

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 410 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 469

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRK
Sbjct: 470 QAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRK 529

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A  A LRE T  VL +LT RE 
Sbjct: 530 VLKIAKEPISMETPIGDDEDSHLGDFIEDGTISSPVDDATAAGLREATRDVLGNLTEREA 589

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RVL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 590 RVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 646


>gi|255318840|ref|ZP_05360066.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens
           SK82]
 gi|255304096|gb|EET83287.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens
           SK82]
          Length = 626

 Score =  430 bits (1105), Expect = e-118,   Method: Composition-based stats.
 Identities = 270/654 (41%), Positives = 374/654 (57%), Gaps = 38/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +     D+   E
Sbjct: 8   VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFE 67

Query: 91  DSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D+ + A   +           ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 68  DNAEAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++    +  +G   L +I  L   + PES        E    +
Sbjct: 128 IRDVLHSIAYWPNAVEVVLKEYKDYQEGERRLADI--LSGYLDPESDEEIPEVIEDAVLE 185

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED +  K   +V+  + + E     S DD      P                      
Sbjct: 186 EDEDETASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAK---------------- 229

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                           E+  V++E +S+ +      K  + S + K   E L  +     
Sbjct: 230 ------------VRFTELETVWQETKSVIE------KHGRDSAEAKAALEALASVFMMFK 271

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  +E E++R A   G + R  F     G+E +P W+    
Sbjct: 272 FTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDRTQFRTSFPGQESNPGWLDEQM 331

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                + K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEM
Sbjct: 332 AKASPDIKGHLEKVRPDVLAFQQKIADIEKELGLNVIDIKDISKRMAIGEAKARRAKKEM 391

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 392 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 451

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 452 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 511

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 512 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSEGLKEATREVLENLTEREAKVL 571

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 572 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 625


>gi|288941560|ref|YP_003443800.1| RNA polymerase sigma-70 subunit RpoD [Allochromatium vinosum DSM
           180]
 gi|288896932|gb|ADC62768.1| RNA polymerase, sigma 70 subunit, RpoD [Allochromatium vinosum DSM
           180]
          Length = 623

 Score =  430 bits (1104), Expect = e-118,   Method: Composition-based stats.
 Identities = 267/650 (41%), Positives = 360/650 (55%), Gaps = 41/650 (6%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++GY+T  E+N  LPP  V ++Q+ED V M+++MGI V +      +    DS 
Sbjct: 13  LIAKGKEQGYLTYTEVNDHLPPGIVETDQIEDIVRMINDMGIMVQETAPDVVDHTLSDSA 72

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                A+ ++       DS    T DPVRMY+REMG++ELL+REGE+ IAKRIE G   +
Sbjct: 73  VSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELQIAKRIEDGLNQV 132

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + +L   P + + LI   D ++     L ++I        E+        +       E 
Sbjct: 133 LNALSVYPRSIEKLIEIFDRVDREEARLTDVISGFNDEATETDETLATDVQA----ASET 188

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
            +   + D   E           S          PE+A      L E             
Sbjct: 189 DADADKTDLDVEAADLDSDDDDDSATVEVDTGPDPEDAARRANLLRE------------- 235

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                   Q      ++  +   + +   + + ++     L   
Sbjct: 236 ----------------------RYQTLKAALEEYGRDDERSREAMQAVSEVFLQFKLVSP 273

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
               L E L    +RI   E  ++ L  +  G+ R  F+E     E +P W+        
Sbjct: 274 VFQELAEILRATIERIRAQERAIMSLCVEQAGMGRKEFIETFPSNETNPEWLDGLIARGR 333

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             +   +      I + + +++ I  E  ++I E + +   +  GE +A  AKKEMVEAN
Sbjct: 334 P-FSVRLQELAPDIQRAQRKLQDIERENILTIGEIKEVNRKMSIGEAKARRAKKEMVEAN 392

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSI
Sbjct: 393 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 452

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A ++ MP + VRKVLKI KE
Sbjct: 453 ADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAARMDMPEDKVRKVLKIAKE 512

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PIS+ETPIGD++ SHLGDFIED   +SPLDSA    LRE T  +LASLT RE +VLRMRF
Sbjct: 513 PISMETPIGDDEDSHLGDFIEDSGVISPLDSATAEGLREATQNMLASLTSREAKVLRMRF 572

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS KLRSFLD 
Sbjct: 573 GIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKLRSFLDN 622


>gi|301155442|emb|CBW14908.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 629

 Score =  430 bits (1104), Expect = e-118,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 369/667 (55%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS-NMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L  + GI
Sbjct: 2   EQNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDLIDPEYYDKLLQTLQHDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     DE    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDEMMLNDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  ++   P     L+   D++  G   L ++I     + P  
Sbjct: 121 REDEISIAKRIEEGIDEVQTAIAAYPEALTELLDNYDQVEAGNYRLADLIT--GFVDPNI 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   + +   +        + DD  + E + +S++     D       PE A    
Sbjct: 179 AAEEVVNVDENFADEEVSVGAAADVDDESDEEDESDSSSSSDDSDSDN-SIDPEVARERF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L E    +  T++                                   K  +S  + K
Sbjct: 238 SALREQHTKTLATIA-----------------------------------KHGRSGKRAK 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ KR+   E +L + L    G+ +D F    
Sbjct: 263 DQIAQLADIFKQFRLVPKQFDTLVLSMKNMMKRVRAEERQLQKVLVDIAGMPKDEFEALI 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                   WV+ A    +  W   +    + I    + + +I   T ++I + R I   V
Sbjct: 323 VANGSSDAWVAKALKSTKA-WAKRLPKYEERIRLSLDNLANIEQHTNLTIQQMREICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 SRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|221068481|ref|ZP_03544586.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           KF-1]
 gi|220713504|gb|EED68872.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           KF-1]
          Length = 815

 Score =  429 bits (1103), Expect = e-118,   Method: Composition-based stats.
 Identities = 255/663 (38%), Positives = 369/663 (55%), Gaps = 59/663 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V +    
Sbjct: 207 MNTRRQRLKMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPD 266

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  S      A   +       DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 267 AETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 326

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           GF 
Sbjct: 327 EIAKRIEGGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVD-----------GFV 375

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
           +  E   Y   ED  +  E DD     G                                
Sbjct: 376 NANENDDYVAEEDFDEYDEEDDDDGKGG-------------------------------- 403

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                +  L+   ++L+ + +   D + E++ ++  + D    G      +     +++ 
Sbjct: 404 -----SKALTKKLEELKNEALGRFDSMRELFDKMHKVYDKEGYG------TEAYMKVQKA 452

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGREL 379
           + + + ++      I+ L + +      +   E EL + +    G+ ++ F++      L
Sbjct: 453 ITEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVDKCGMPQEQFIKDFPPNLL 512

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  WV          +   +   +  + +++  +  +     + + E +HI   +  GE 
Sbjct: 513 NLDWVIKQVA-AGKNYSAVLERNIPPVQELQQNLIDLQARVVVPLEELKHINKRMNSGER 571

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 572 ASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 631

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A K+ +P
Sbjct: 632 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAAKMEIP 691

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N  +P+D+A+QA LR+    +L  
Sbjct: 692 EDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDG 751

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF
Sbjct: 752 LTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSF 811

Query: 680 LDG 682
           +D 
Sbjct: 812 IDS 814


>gi|119504971|ref|ZP_01627048.1| putative transcriptional regulator, Fis family protein [marine
           gamma proteobacterium HTCC2080]
 gi|119459257|gb|EAW40355.1| putative transcriptional regulator, Fis family protein [marine
           gamma proteobacterium HTCC2080]
          Length = 606

 Score =  429 bits (1103), Expect = e-118,   Method: Composition-based stats.
 Identities = 265/657 (40%), Positives = 360/657 (54%), Gaps = 60/657 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +     DE
Sbjct: 7   QQSRLKALIAKGKEQGYLTYAEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADE 66

Query: 87  EG-SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +E        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 67  LILTEGDRSADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +MA++   P   + L    D +      L +I  L   + P            
Sbjct: 127 IEEGIRELMAAMAHYPGVARKLSNAYDMVAKEERKLSDI--LIGYLDPAEHVPSAQEMAE 184

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +      ++ + +  +V+     +E+                                 
Sbjct: 185 AAEAAAATATDDDDDTEVETGPDPVEAK-------------------------------- 212

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                +     +          G K   + +      +KL +L 
Sbjct: 213 ----------------KRFTALKRQCTKTEKAIATHGYGHKTATAEM------DKLGELF 250

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L     D L+++  +    I   E  ++R+A     + R  F++   G E D  W+
Sbjct: 251 KFFKLTPRVFDPLIDEPRESLYIIRKQERAIMRIAVRECRMDRKEFIKSFSGSESDSRWI 310

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           S      + +    +A   D I +++  I  +   TG+S++E + I   +  GE  A  A
Sbjct: 311 SRVAR--KKDIGARLALHKDDIQRMQRRISEVEQATGLSVAEIKEINRRMSMGEARARRA 368

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 369 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 428

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VR
Sbjct: 429 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKVR 488

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+DSA +  L E T  VLA LT RE
Sbjct: 489 KVLKIAKEPISMETPIGDDEDSHLGDFIEDVTISSPVDSATEEGLTEATQDVLAGLTARE 548

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 549 AKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 605


>gi|262378901|ref|ZP_06072058.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
 gi|262300186|gb|EEY88098.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
          Length = 629

 Score =  429 bits (1103), Expect = e-118,   Method: Composition-based stats.
 Identities = 270/654 (41%), Positives = 374/654 (57%), Gaps = 38/654 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I   +++GY+T  E+N  LP     SEQ+ED + ML ++GI V +     D+   E
Sbjct: 11  VAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFE 70

Query: 91  DSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D+ + A   +           ++    T DPVRMY+REMG++ELL+REGEI+IAKRIE G
Sbjct: 71  DNAEAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEG 130

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              ++ S+   P   + ++    +  +G   L +I  L   + PES        E    +
Sbjct: 131 IRDVLHSIAYWPNAVEVVLKEYKDYQEGERRLADI--LSGYLDPESDEEIPEVIEDAVLE 188

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + ED +  K   +V+  + + E     S DD      P                      
Sbjct: 189 EDEDETASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAK---------------- 232

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                           E+  V++E +S+ +      K  + S + K   E L  +     
Sbjct: 233 ------------VRFTELETVWQETKSVIE------KHGRDSAEAKAALEALASVFMMFK 274

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
                 D++ E +    ++I  +E E++R A   G + R  F     G+E +P W+    
Sbjct: 275 FTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDRTQFRTSFPGQESNPGWLDEQM 334

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                + K  +      +L  + +I  I  E G+++ + + I   +  GE +A  AKKEM
Sbjct: 335 AKASPDIKGHLEKVRPDVLAFQQKIADIEKELGLNVIDIKDISKRMAIGEAKARRAKKEM 394

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 395 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 454

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VRKVLK
Sbjct: 455 TRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLK 514

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A    L+E T  VL +LT RE +VL
Sbjct: 515 IAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSEGLKEATREVLENLTEREAKVL 574

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 575 KMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 628


>gi|53802939|ref|YP_115383.1| RNA polymerase sigma-70 factor [Methylococcus capsulatus str. Bath]
 gi|53756700|gb|AAU90991.1| RNA polymerase sigma-70 factor [Methylococcus capsulatus str. Bath]
          Length = 599

 Score =  429 bits (1103), Expect = e-118,   Method: Composition-based stats.
 Identities = 266/664 (40%), Positives = 366/664 (55%), Gaps = 71/664 (10%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +  +      K++I   + +GY+T  E+N  LP D V  EQMED + M+++MGI V +  
Sbjct: 1   MTPEQQQHQLKELIAKGKMQGYLTFSEVNDHLPSDIVDPEQMEDIICMINDMGIEVHEDV 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREG 138
              ++   + ++   S    ++          D+    T DPVRMY+REMG++ELL+REG
Sbjct: 61  PDNEDLIQDTAVVAESDEDEAAEVAAALASSVDTELGRTTDPVRMYMREMGTVELLTREG 120

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E++IAKRIE G  +    L   P   +  +   + +++G   L ++I             
Sbjct: 121 ELSIAKRIEEGLNIAANELVRFPAAMEHFLKAFETVDNGELRLSDLI-----------SD 169

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           FF      +    +D+  E                                    DE + 
Sbjct: 170 FFDPAAADTVATEDDAEAEI----------------------------------IDEGDT 195

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
             D +     L+A                   +R+L           K      K +   
Sbjct: 196 GPDPELVKEKLAA-------------------FRKLHKA--AVTAHHKYGYGHEKTQKSF 234

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGR 377
           + L                L + L D   +I   E  L  +  + G + +  F+E   G 
Sbjct: 235 DALATAFMEFKKTPQFFKELTDTLRDTVAKIREQERALTDICVTKGKMPKAEFIESFSGS 294

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W+    D P   +   +    + I +I+ ++  I  E  + I+  + I   V  G
Sbjct: 295 ETDEGWLDRVCD-PAKPYAAAIKAHAEEIRRIQAKLAQIEKENRLDIALIKDIHRRVSAG 353

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A +AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 354 ENQARLAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 413

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP+E+A ++ 
Sbjct: 414 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPDELAARMD 473

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP + VRKV+KI KEPIS+ETPIGD+D SHLGDFIED   +SP++ A  A+LRETT +VL
Sbjct: 474 MPEDKVRKVMKIAKEPISMETPIGDDDDSHLGDFIEDSRVLSPVEHATVASLRETTQQVL 533

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LR
Sbjct: 534 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLR 593

Query: 678 SFLD 681
           SFLD
Sbjct: 594 SFLD 597


>gi|198284073|ref|YP_002220394.1| RNA polymerase sigma-70 subunit RpoD [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|198248594|gb|ACH84187.1| RNA polymerase, sigma 70 subunit, RpoD [Acidithiobacillus
           ferrooxidans ATCC 53993]
          Length = 631

 Score =  429 bits (1103), Expect = e-118,   Method: Composition-based stats.
 Identities = 262/663 (39%), Positives = 375/663 (56%), Gaps = 53/663 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++GY+T  E+N  LP +    EQME+ ++M+++MGI V +    +
Sbjct: 11  ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 70

Query: 85  DE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D    +G   ++  A  A  ++       ++    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 71  DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 130

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IA+RIE G   ++ ++   P T   L+     +  G T L E++D    +          
Sbjct: 131 IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETVSE 190

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E    +  +    E E +        ++   ++                         
Sbjct: 191 AEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLED----------------------- 227

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                              +     I   Y  L +      +  + E      +  + +L
Sbjct: 228 ------------------ALERFAVIRAAYTALLA------SHAEGEMHGESYQRQRREL 263

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
            +    + LN  +ID++ + L  +++ +   E EL+ L  +     R  F+  + G E D
Sbjct: 264 AERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMELCIERARFPRKEFVRSYPGHEGD 323

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+          +   +    D I+ I   + +I    G+ I+E +    ++  GE +
Sbjct: 324 IGWIDQQIA-AGHAYSTRLVEFRDDIVAIMKRLANIEKRAGLPIAEIKEASRLMSIGEAK 382

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 383 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 442

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP 
Sbjct: 443 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMEMPE 502

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  +P DSA+ A +RE    +L + 
Sbjct: 503 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTAPADSAVNAAIREVVEELLDNG 562

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSF
Sbjct: 563 LTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRSF 622

Query: 680 LDG 682
           +DG
Sbjct: 623 VDG 625


>gi|254491243|ref|ZP_05104424.1| Sigma-70, non-essential region family [Methylophaga thiooxidans
           DMS010]
 gi|224463756|gb|EEF80024.1| Sigma-70, non-essential region family [Methylophaga thiooxydans
           DMS010]
          Length = 610

 Score =  429 bits (1103), Expect = e-118,   Method: Composition-based stats.
 Identities = 272/659 (41%), Positives = 372/659 (56%), Gaps = 58/659 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLE 84
                K++I L ++RGY+T  E+N  LP D V ++Q+ED V+M S++GI V +   D  E
Sbjct: 4   QQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMDTDE 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            E  +E        +   +  +    D     T DPVRMY+REMGS+ELL+REGEI IAK
Sbjct: 64  MERLAEAISSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIVIAK 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIEAG    +  L   P    + +   D +  G   L E+I            GF    E
Sbjct: 124 RIEAGLRESLQMLSTYPDCIASFLELFDAVEAGEMRLNELI-----------KGFIVAEE 172

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             + ++ ++    +E D   + + D        ++   ++D     A             
Sbjct: 173 EVAEEEAKEEVSVEESDSESDDDDDDSDDVSDDEEGSGEIDPEEAKAR------------ 220

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               D + + ++                 +    +  +E+   L
Sbjct: 221 -------------------FDALRDSFKAYNK------------AAGDAAEEAREQTSNL 249

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L    +  L + + D    I   E  ++ +      + R  F++  QG E + +W
Sbjct: 250 FMEFKLTPKTLIYLNDLMADTIDEIRKQERTIMSIVVDQARMNRRDFIDSFQGNESNVNW 309

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
                   +  + + +    D ++  ++++  IS + G+SISE + I   +   E +A  
Sbjct: 310 ADKHI-RAKKHYSSTIKKHHDEVVAAQSKLAEISEDRGLSISEIKEIARQMSISEAKARR 368

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 428

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+ R AR+M  ++ REPTP+E+A+++ MP + V
Sbjct: 429 IRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREPTPDELAERVEMPEDKV 488

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI+KEPIS+ETPIGD++ SHLGDF+ED N +SP DSAI   LRE T  VL  LT R
Sbjct: 489 RKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVISPSDSAIIEGLREATQGVLNGLTER 548

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS +LRSFLD 
Sbjct: 549 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDQLRSFLDS 607


>gi|218665974|ref|YP_002426728.1| RNA polymerase sigma factor RpoD [Acidithiobacillus ferrooxidans
           ATCC 23270]
 gi|218518187|gb|ACK78773.1| RNA polymerase sigma factor RpoD [Acidithiobacillus ferrooxidans
           ATCC 23270]
          Length = 624

 Score =  429 bits (1102), Expect = e-118,   Method: Composition-based stats.
 Identities = 262/663 (39%), Positives = 375/663 (56%), Gaps = 53/663 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +++GY+T  E+N  LP +    EQME+ ++M+++MGI V +    +
Sbjct: 4   ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 63

Query: 85  DE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D    +G   ++  A  A  ++       ++    T DPVRMY+REMGS+ELL+REGEI 
Sbjct: 64  DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 123

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IA+RIE G   ++ ++   P T   L+     +  G T L E++D    +          
Sbjct: 124 IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETVSE 183

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E    +  +    E E +        ++   ++                         
Sbjct: 184 AEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLED----------------------- 220

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                              +     I   Y  L +      +  + E      +  + +L
Sbjct: 221 ------------------ALERFAVIRAAYTALLA------SHAEGEMHGESYQRQRREL 256

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
            +    + LN  +ID++ + L  +++ +   E EL+ L  +     R  F+  + G E D
Sbjct: 257 AERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMELCIERARFPRKEFVRSYPGHEGD 316

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+          +   +    D I+ I   + +I    G+ I+E +    ++  GE +
Sbjct: 317 IGWIDQQIA-AGHAYSTRLVEFRDDIVAIMKRLANIEKRAGLPIAEIKEASRLMSIGEAK 375

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 376 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 435

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP+PEE+A+++ MP 
Sbjct: 436 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMEMPE 495

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
           + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  +P DSA+ A +RE    +L + 
Sbjct: 496 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTAPADSAVNAAIREVVEELLDNG 555

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE +VLRMRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSF
Sbjct: 556 LTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRSF 615

Query: 680 LDG 682
           +DG
Sbjct: 616 VDG 618


>gi|91777566|ref|YP_552774.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91690226|gb|ABE33424.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 665

 Score =  429 bits (1102), Expect = e-118,   Method: Composition-based stats.
 Identities = 231/684 (33%), Positives = 358/684 (52%), Gaps = 49/684 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K +                 +      + +I+L +++GY+T  ++N  LP +   +  
Sbjct: 25  TAKGKGAGKAIPVAAELPPQQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAA 84

Query: 63  MEDTVAMLSNMGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           ++  V+  ++MG+ V +     +      +  ++     A   +       DS    T D
Sbjct: 85  IDSIVSAFNDMGVQVYEQAPDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTD 144

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG+ ELL+R GEIAIAKRIE G   M+ ++   PL   A++    ++ DG  
Sbjct: 145 PVRMYMREMGATELLTRAGEIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGEL 204

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + E++D                         ED+   +E     E   ++++     +D
Sbjct: 205 RIDELVD----------------------GLNEDTIAAEEDSASAEASAEVDADTDGDED 242

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           + S  D  P +                 + +A E +L+      L    E++ ++  L D
Sbjct: 243 EDSDDDVGPAD-----------------SSAADEARLKQLTSDCL----EIFAQVGMLSD 281

Query: 300 NAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                      +S   +  +E++ + +  +      ID L   +     ++   E  +L+
Sbjct: 282 QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 359 LA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +     G+ R+ F+E   G E D  W   A       +   +   + +I   + ++  I 
Sbjct: 342 IVVSKSGMPREKFIESFAGHEADLGWTERAA-RGASAYGAALERHLPAIQSEQQKLIEIE 400

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + +   + I   +   E +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEG
Sbjct: 401 ATVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEG 460

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  G+KFSTYA WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R
Sbjct: 461 NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISR 520

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +  +  +E  P  +A+++ +  E VR +LKI K+P+S+ETP+GD+  + LGD IED  A
Sbjct: 521 EILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAA 580

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP D+A+QA+LR      L SL+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIR
Sbjct: 581 SSPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIR 640

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIE+KA+RKL HPSR+ +L+SFLD
Sbjct: 641 QIESKAMRKLMHPSRADRLKSFLD 664


>gi|330813718|ref|YP_004357957.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486813|gb|AEA81218.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 621

 Score =  429 bits (1102), Expect = e-117,   Method: Composition-based stats.
 Identities = 302/659 (45%), Positives = 428/659 (64%), Gaps = 49/659 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            S++++++    RG++T EEL   L     + E +E +V  + +  I  V        + 
Sbjct: 7   KSFERLMEKGLSRGFITYEELQKSLGKRNANVESLEKSVLHIFDQAICFVKKKSDFKVKK 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E                  ++      +DDP+RMYLREMG +ELLSREGEIAIAKRIE+
Sbjct: 67  LESE--------------TSKQPKNQDRSDDPIRMYLREMGGVELLSREGEIAIAKRIES 112

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G+ +M++SL ESP+T + +  W + L +   L+R+IIDL+     + K       +    
Sbjct: 113 GKYVMVSSLSESPVTAKKIFEWEERLINNEMLVRDIIDLDTNFLDDDKLKKSIKEKKEKE 172

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           +K +    +++ ++   T  DI                             +D+D+   +
Sbjct: 173 EKLKKKESKEKGEETNTTTADIV----------------------------DDDDEFNIS 204

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVK 323
           L+++E +L+PK++   + I++ YR+L + Q+ ++      +          + +K+++++
Sbjct: 205 LASLEIELKPKILKTFENISKNYRKLIAYQEESLQCILSSQKFSDSKKKNYEKIKKEIME 264

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
            +  L  NQ   + LV   Y+ +K+ ++ +G+L+R A  YGI RD F++ + G EL+P++
Sbjct: 265 EMLGLQFNQVTQEDLVALNYNENKKAINLDGDLMRAALKYGISRDDFIKFYVGNELNPNF 324

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            S+     +  W  F   E       R ++  +S   GISIS+F+ +V+ ++KGE E+ I
Sbjct: 325 ESFLS--GDKNWSKFFKNEQKLFKISREKLTDLSKNIGISISDFKILVNKIKKGERESRI 382

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 383 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++  REPTPEE++KKLAMP+E V
Sbjct: 443 IRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMMSEYGREPTPEELSKKLAMPLEKV 502

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPISLETP+GDED S LGDFIED NA+ P+D+AIQ  L+ +TT+VLASLTPR
Sbjct: 503 RKVLKIAKEPISLETPVGDEDDSSLGDFIEDTNALIPVDAAIQTGLKNSTTKVLASLTPR 562

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS++L+SFLD 
Sbjct: 563 EERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRQLKSFLDN 621


>gi|148825193|ref|YP_001289946.1| aspartate ammonia-lyase [Haemophilus influenzae PittEE]
 gi|148715353|gb|ABQ97563.1| aspartate ammonia-lyase [Haemophilus influenzae PittEE]
          Length = 645

 Score =  429 bits (1102), Expect = e-117,   Method: Composition-based stats.
 Identities = 275/680 (40%), Positives = 380/680 (55%), Gaps = 56/680 (8%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           K+N   + +++ S      +   +  +++++L R +GY+T  E+N  LP D +  E  + 
Sbjct: 17  KQNEYKNGKNQQS----TAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDK 72

Query: 66  TVAML-SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
            +  L ++ GI V+D     D+    D++     A   +  +    +S    T DPVRMY
Sbjct: 73  LLQTLQNDAGIPVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMY 131

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG+++LL+RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++
Sbjct: 132 MREMGTVDLLTREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDL 191

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I            GF             D     E D+ + +  D+E     S  D S  
Sbjct: 192 I-----------TGFVDPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDS 240

Query: 245 DS--PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           D+   PE A    + L E    +   +                                 
Sbjct: 241 DNSIDPEVAREKFQQLREQHSKTLAVIE-------------------------------- 268

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQ 361
              K  +S  + +     L ++     L   + DLLV  + ++ KR+ + E +L + L  
Sbjct: 269 ---KHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVD 325

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
             G+ +D F +       +  WV+ A    +   K  +  E D I +  N +      T 
Sbjct: 326 IAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTK 384

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I++ R I   V +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 385 LTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 444

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 445 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQ 504

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE TPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PL
Sbjct: 505 EMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPL 564

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSA   +L+  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEA
Sbjct: 565 DSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 624

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS+ LRSFLD
Sbjct: 625 KALRKLRHPSRSETLRSFLD 644


>gi|319775546|ref|YP_004138034.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           F3047]
 gi|317450137|emb|CBY86351.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           F3047]
          Length = 629

 Score =  428 bits (1101), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/661 (40%), Positives = 373/661 (56%), Gaps = 42/661 (6%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGINVVDGD 81
             +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI V+D  
Sbjct: 8   TAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEA 67

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+RE EI+
Sbjct: 68  PESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLTREDEIS 126

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P ++    +
Sbjct: 127 IAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNAEIEEHN 184

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
           G +   +   +D  +    D     + +   +   S    S     PE A    + L E 
Sbjct: 185 GLD-EDFSDEDDEEESSNADVENNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQLREQ 243

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
              +   +                                    K  +S  + +     L
Sbjct: 244 HSKTLAVIE-----------------------------------KHGRSGKRAQDQIALL 268

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELD 380
            ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       +
Sbjct: 269 GEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSN 328

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE +
Sbjct: 329 SEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQK 387

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 388 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 447

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP 
Sbjct: 448 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMPE 507

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  L
Sbjct: 508 DKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGL 567

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 568 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFL 627

Query: 681 D 681
           D
Sbjct: 628 D 628


>gi|319897950|ref|YP_004136147.1| RNA polymerase, sigma 70 (sigma d) factor [Haemophilus influenzae
           F3031]
 gi|329122411|ref|ZP_08250998.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           aegyptius ATCC 11116]
 gi|317433456|emb|CBY81839.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           F3031]
 gi|327473693|gb|EGF19112.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           aegyptius ATCC 11116]
          Length = 629

 Score =  428 bits (1101), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/661 (40%), Positives = 373/661 (56%), Gaps = 42/661 (6%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGINVVDGD 81
             +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI V+D  
Sbjct: 8   TAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEA 67

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+RE EI+
Sbjct: 68  PESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLTREDEIS 126

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P ++    +
Sbjct: 127 IAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNAEIEEHN 184

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
           G +   +   +D  +    D     + +   +   S    S     PE A    + L E 
Sbjct: 185 GLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQLREQ 243

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
              +   +                                    K  +S  + +     L
Sbjct: 244 HSKTLAVIE-----------------------------------KHGRSGKRAQDQIALL 268

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELD 380
            ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       +
Sbjct: 269 GEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSN 328

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE +
Sbjct: 329 SEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQK 387

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 388 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 447

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP 
Sbjct: 448 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMPE 507

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  L
Sbjct: 508 DKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGL 567

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 568 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFL 627

Query: 681 D 681
           D
Sbjct: 628 D 628


>gi|193884351|dbj|BAG54997.1| Sigma70 [Ralstonia solanacearum]
          Length = 758

 Score =  428 bits (1100), Expect = e-117,   Method: Composition-based stats.
 Identities = 243/668 (36%), Positives = 361/668 (54%), Gaps = 46/668 (6%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 123 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 182

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 183 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 242

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 243 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 300

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +                ++ + E   ++  E +    S+A  ++           
Sbjct: 301 LIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAASARQLE-------- 352

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                    +L+   +     I + + ++R   +      K+  
Sbjct: 353 -------------------------ELKQAALAKFAIIGDQFEKMRRAFE------KEGY 381

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 382 KSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 441

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 442 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQARVVLPLAELK 500

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 501 DVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 560

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 561 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 620

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P  +A+K+ MP + +RK+ KI KEPIS+ETPIGD+D SHLGDFIED N ++P ++A+  +
Sbjct: 621 PATLAEKMEMPEDKIRKIRKIAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGS 680

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL 
Sbjct: 681 MRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLC 740

Query: 669 HPSRSKKL 676
              RS +L
Sbjct: 741 LLIRSGRL 748


>gi|52842571|ref|YP_096370.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52629682|gb|AAU28423.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 623

 Score =  428 bits (1100), Expect = e-117,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 374/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 9   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 67

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 68  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 126

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 127 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 176

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 177 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKIY-------- 225

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 226 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 260

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 261 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGW 320

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +      +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 321 LETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 380

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 381 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 440

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 441 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 500

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 501 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 560

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 561 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 620


>gi|300112780|ref|YP_003759355.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299538717|gb|ADJ27034.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii
           C-113]
          Length = 602

 Score =  428 bits (1100), Expect = e-117,   Method: Composition-based stats.
 Identities = 273/656 (41%), Positives = 373/656 (56%), Gaps = 68/656 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   + RGY++  E+N  LP + +  EQ+ED + M ++MGI+V +     D 
Sbjct: 9   RQSQLKLLIARGKDRGYLSYSEVNDHLPEEVIDPEQIEDIITMFNDMGISVHEDMAEADA 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D+      A+  +       D     T DPVRMY+REMGS+ELL+REGEI+IAKRI
Sbjct: 69  LAIMDTAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  +L   P +   L+   +++  G   L ++I            GF    E  
Sbjct: 129 EEGMRQVYTALSRFPGSVAELLRQYEKVEVGEIRLVDVI-----------SGFQESEEA- 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                                       + + ++   V S     E ++  LD       
Sbjct: 177 -------------------------DLKESAAEEEVSVSSEGNAEEENDNGLD------- 204

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                            LD + E + +LR L +                   E+L +   
Sbjct: 205 -----------------LDRVQEYFAQLRKLYERCQAADHKGNDGA-----LEELSEYFL 242

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
            L L       L+E L  +   I   E  ++++A  S  + R  FL   Q +E + +WV 
Sbjct: 243 QLKLMPRLSQRLIENLRRVVAEIRVLERSIMKIAVNSAQMPRKDFLSSFQKQETNLNWVE 302

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  + + +  + D+I K + ++ ++    G+SI++ + I   +  GE  A  AK
Sbjct: 303 KHI-RAKKHYSSVLRKQGDAIQKAQEKLIALEQRAGMSITQIKEINRSLSIGEARARRAK 361

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 362 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 421

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP+E+A+++ MP + VRK
Sbjct: 422 QAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAERVEMPKDKVRK 481

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI +EPIS+ETPIGD++ SHLGDF+ED   +SP DSAI + LRETT  +LA LTPRE 
Sbjct: 482 VLKIAREPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQLILAGLTPREA 541

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 542 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 597


>gi|296107953|ref|YP_003619654.1| RNA polymerase primary sigma factor [Legionella pneumophila 2300/99
           Alcoy]
 gi|295649855|gb|ADG25702.1| RNA polymerase primary sigma factor [Legionella pneumophila 2300/99
           Alcoy]
          Length = 621

 Score =  428 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 374/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 7   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 125 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 174

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 175 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKVY-------- 223

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 224 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 258

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 259 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLSW 318

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +      +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 319 LETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 378

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 379 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 438

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 439 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 498

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 499 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 558

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 559 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 618


>gi|257464575|ref|ZP_05628946.1| RNA polymerase sigma factor RpoD [Actinobacillus minor 202]
 gi|257450235|gb|EEV24278.1| RNA polymerase sigma factor RpoD [Actinobacillus minor 202]
          Length = 621

 Score =  428 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 384/656 (58%), Gaps = 47/656 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                + +I   R++GY+ + E++  LP + V +EQ+ED + M+++MGI V++     DE
Sbjct: 11  QQSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDE 70

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               +++        ++  L   + S    T DPVRMY+REMG++ELL+RE EI I+KRI
Sbjct: 71  LMLAENITDEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREDEIQISKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P     ++    ++  G   L ++I                     
Sbjct: 130 EEGINEVQCAVAEYPEALVGVLECYAQVEAGEMRLVDLI--------------------- 168

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                 D + ++E    ++   D E +  V+  D    D   +++ ++  +   D + + 
Sbjct: 169 --TAFVDPNAQEETPIDEDAHLDDEESDIVADVDDESEDEDGDSSSDNGDDSSIDPELAR 226

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              +A++ Q    ++                       QK  ++  K +     L  +  
Sbjct: 227 EKFAALKAQHEKALLAI---------------------QKHGRTHAKAREQINALSDIFR 265

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVS 385
              L   + DLLV  +  + K++   E ++ R A  Y G+K+  FL+  Q  E    W+ 
Sbjct: 266 EFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYAGMKKADFLKAFQNNETTEAWIE 325

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A +  +G     +A  V+ I      ++++  ++G++I++ R I   +  GE +A  AK
Sbjct: 326 KAINAKKGG-APKLANYVEKIRINIVNLQNLEQQSGLTIAQIREIGGRIANGELKARRAK 384

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 385 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 444

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RK
Sbjct: 445 QAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMNMPEDKIRK 504

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE 
Sbjct: 505 VLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRIATNEVLEGLTPREA 564

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 565 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 620


>gi|292490206|ref|YP_003525645.1| RNA polymerase sigma factor RpoD [Nitrosococcus halophilus Nc4]
 gi|291578801|gb|ADE13258.1| RNA polymerase sigma factor RpoD [Nitrosococcus halophilus Nc4]
          Length = 602

 Score =  428 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/656 (40%), Positives = 368/656 (56%), Gaps = 63/656 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   + RGY++  E+N  LP D +  EQ+ED + M ++MGI+V +     D 
Sbjct: 5   RQSQLKLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEADA 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D+      A+  +       D     T DPVRMY+REMGS+ELL+REGEI IAKRI
Sbjct: 65  LAIMDTAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEIRIAKRI 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  +L   P +   L+   + +  G   L ++I                     
Sbjct: 125 EEGMRQVHTALSLFPGSVAELLRQYERVEAGDARLADMI--------------------- 163

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                    +E++  +    E  +  +A+ S+++ +     PE A      L E      
Sbjct: 164 ---SGFHEPEEEDIKEAVAEEEAVADSAEDSEEEENGGGPDPERAREQFVQLRELYRLRQ 220

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              S  +                                           L E + +   
Sbjct: 221 EAASKDDG-------------------------------------KALAELSEAMSECFL 243

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L       L+E L  +   I   E  ++++A     + R  FL   QG+E + +WV 
Sbjct: 244 RFKLVPRLSLQLIEGLRAVVAGIRVLERTIMQIAVNEAHMPRQDFLSSFQGQETNLNWVE 303

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  + + +  + ++I + + ++ ++    G+S++E +     +  GE  A  AK
Sbjct: 304 KHI-RAKKHYSSVLRKKGEAIRQAQEKLIALEQGAGMSVAEIKEANRSLSIGEARARRAK 362

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 363 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 422

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP+E+A+++ MP + VRK
Sbjct: 423 QAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAERVDMPKDKVRK 482

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD++ SHLGDF+ED   VSP D+AI + LRETT ++LA LTPRE 
Sbjct: 483 VLKIAKEPISMETPIGDDEDSHLGDFVEDAEVVSPPDAAIFSGLRETTQQILAGLTPREA 542

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 543 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 598


>gi|148359903|ref|YP_001251110.1| RNA polymerase sigma 70 factor RpoD [Legionella pneumophila str.
           Corby]
 gi|148281676|gb|ABQ55764.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila str.
           Corby]
          Length = 619

 Score =  428 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 374/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 5   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 64  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 123 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 172

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 173 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKVY-------- 221

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 222 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 256

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 257 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLSW 316

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +      +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 317 LETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 376

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 377 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 436

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 437 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 496

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 497 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 556

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 557 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 616


>gi|331006388|ref|ZP_08329697.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC1989]
 gi|330419812|gb|EGG94169.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC1989]
          Length = 601

 Score =  428 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 270/659 (40%), Positives = 371/659 (56%), Gaps = 64/659 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDL 83
           +  +   K +I   +++GY+T  ++N  LP D    +Q+ED + M+++MGI V +   D 
Sbjct: 4   NKQESRIKLLIARGKEQGYLTYADVNDHLPQDISDPDQVEDIIQMINDMGIRVYENAPDA 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+   ++        AS  +       ++    T DPVRMY+REMG++ELL+REGEIAIA
Sbjct: 64  EELLMTDGDSSADEIASAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +M +L   P   Q LI              +++  E    P+   G+    
Sbjct: 124 KRIEEGTRDLMHALACWPNVVQILIDEF-----------DLLVKEERRIPDLIAGWLDP- 171

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                            DDV       +       +D  +VD+  +  E +ER       
Sbjct: 172 ----------------ADDVPAAGPAAQKNKTDDDEDEDEVDTGLDPVEVNER------- 208

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                  A++ QL        D+I +                K  + S + +    +L  
Sbjct: 209 -----FGALKKQL-----AKTDKIIK----------------KHGRESKEAEAELSELGD 242

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           ++    L   + D + ++   + + +   E  +L L      + R  F++   G E DP 
Sbjct: 243 IIKFFKLPPRQFDPMYKKARGVLESVRREERRILSLCVRTAKMPRKTFIKEFPGNETDPT 302

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+    +  + ++        + IL+ + ++  I    GI +S  + I   +  GE  A 
Sbjct: 303 WIPGVIE-KKRDYSANFEEVKEEILRAQRKLDQIQNTVGIELSMIKEINRRMSIGEARAR 361

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 362 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 421

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP E 
Sbjct: 422 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEEK 481

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP++SA    L E+T  VL+ LT 
Sbjct: 482 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTITSPVESATDVGLTESTRDVLSGLTA 541

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 542 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFLD 600


>gi|78060207|ref|YP_366782.1| sigma 70 (RpoD) [Burkholderia sp. 383]
 gi|77964757|gb|ABB06138.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. 383]
          Length = 677

 Score =  428 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 229/661 (34%), Positives = 350/661 (52%), Gaps = 49/661 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      + +I L R+RGY+T  ++N  LP +   +  M+  V+  S+MG+ V +     
Sbjct: 61  EERQRQMRALIALGRERGYLTHADINDHLPDNFAQTAAMDTIVSTFSDMGVAVYEQAPDA 120

Query: 85  DE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +      +  ++     A   +       DS    T DPVRMY+REMG+ ELL+R GEI 
Sbjct: 121 EALLLTEAAPAVASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEIE 180

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           +AKRIE G   M+ ++   P     ++   D +  G   + E++D               
Sbjct: 181 VAKRIEDGLQDMIQAIAACPSIVSTILADVDRIVAGELRIDELVD--------------- 225

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                                      D + +    +    + +    + ++DE +++ D
Sbjct: 226 -----------------------GISVDTDESEMTPESQEEEAEVLAADDDSDEDDVETD 262

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
             DS    +A  ++L    +     +  ++ +L  +          E  S     ++  +
Sbjct: 263 AGDSEKVNAARLEELTNDSLVIFARVRALFEQLPDVP------VTGEARSAAAAQVRAAI 316

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELD 380
            + +  +      ID L E ++     +   E  +L +A    G+ RD F+E   G E D
Sbjct: 317 QRELAPIRFTAKTIDRLCEIVHGQVTEVRAIERSVLAIAVDRCGMPRDAFVESFPGHETD 376

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W S      + ++   +     +I   + ++  I     + + + + I   +   E +
Sbjct: 377 LDWTSRTAATSQ-QFGAALERHQPAIQAAQQKLVDIESRVSLPLQQLKQINRQMSAAELK 435

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+EM+EANLRLVIS+AKKY NRG+QFLDLIQEGNIGLMKA +KF++  G+KFSTYA
Sbjct: 436 MRQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYA 495

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WWV+QA+TR++ADQ+ TIR+PVHM + I+K+ R +R +  +  +E  P  +AK++ M  
Sbjct: 496 TWWVRQAVTRALADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAKRMEMSE 555

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E VR +LKI K+P+SLETP+GD+  + LGD IED +A SP ++AI AN+R      L  L
Sbjct: 556 EKVRSILKIAKQPVSLETPVGDDADATLGDMIEDVSASSPAEAAIHANMRAAIDEALNGL 615

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE +VLRMRFG+  N+DHTLEEVGKQF VTRERIRQIE+KA+RKL HPSR+ KLR FL
Sbjct: 616 SPREAKVLRMRFGLDTNSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADKLRPFL 675

Query: 681 D 681
           +
Sbjct: 676 E 676


>gi|325576583|ref|ZP_08147301.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325161146|gb|EGC73261.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 629

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 269/667 (40%), Positives = 373/667 (55%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS-NMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L  + GI
Sbjct: 2   EQNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQHDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     DE    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDEMMLNDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  ++   P     L+   D++  G   L ++I     + P  
Sbjct: 121 REDEISIAKRIEEGIDEVQTAIAAYPEALTELLDHYDQVEAGNYRLADLIT--GFVDPNI 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   + H   + E +    + DD  + E + +S++     D       PE A    
Sbjct: 179 AEEETANIDEHFADEDESAESAVDVDDESDEEDESDSSSSSDDSDSDN-SIDPEVARERF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L E    +  T++                                   K  +S  + K
Sbjct: 238 AALREQHTKTLATIA-----------------------------------KHGRSGKRAK 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
               +L  +     L   + D+LV  + ++ KR+   E +L + L    G+ +D F    
Sbjct: 263 DQIAQLADIFKQFRLVPKQFDVLVLSMKNMIKRVRAEERQLQKVLVDIAGMPKDEFEALI 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +  W   +    + I    + + +I   T ++I + R I   V
Sbjct: 323 VANGSNDTWVAKALKSTKA-WAKRLPKYEERIRLSLDNLANIEQHTNLTIQQMREICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 SRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|54295203|ref|YP_127618.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
           str. Lens]
 gi|53755035|emb|CAH16523.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
           str. Lens]
          Length = 621

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 374/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 7   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 125 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 174

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 175 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKIY-------- 223

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 224 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 258

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 259 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGW 318

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +      +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 319 LETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 378

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 379 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 438

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 439 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 498

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 499 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 558

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 559 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 618


>gi|121604510|ref|YP_981839.1| RpoD family RNA polymerase sigma factor [Polaromonas
           naphthalenivorans CJ2]
 gi|120593479|gb|ABM36918.1| RNA polymerase, sigma 70 subunit, RpoD [Polaromonas
           naphthalenivorans CJ2]
          Length = 736

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 261/655 (39%), Positives = 374/655 (57%), Gaps = 57/655 (8%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE--- 86
             K +IKL + RGY+T  E++  LP   V +E +E  + ML++MG+ V +     +    
Sbjct: 134 RLKTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVINMLNDMGVAVYEQAPDAETLLL 193

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +  ++     A   +       DS    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 194 NNTGATVATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 253

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   MM ++ ESP T   ++   D++ +G  ++  ++D           GF +  E  
Sbjct: 254 EGGLMKMMEAISESPATIAEIMRLADDIREGKVVISTVVD-----------GFSNPNEAD 302

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y   ED  +  E DD     G                                     +
Sbjct: 303 DYVAEEDFDEFDEDDDDDGKGG-------------------------------------S 325

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L+   ++L+ + +   +++ E   +++ L +    G          K L ++L+ +  
Sbjct: 326 KALTKKLEELKKEALSRFEKVGEYAEKVKKLYEK--EGYGGPTYLKTQKALSDELMTVRF 383

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +    +   DLL  Q+ D+ K+       +    +  G+ ++VF++      L+  WV  
Sbjct: 384 TAKTIEKLCDLLRGQVLDVRKKERELRRII---VEKCGMPQEVFIKDFPPNLLNLKWVEK 440

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +  W N +A  +  I +++ ++  +     + +   + I   + +GE  +  AKK
Sbjct: 441 QVAAGKP-WSNVMARNIPPIQELQTKLGELQARVVVPLLHLKDINKRMNEGESNSRDAKK 499

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 500 EMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 559

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP    +A+K+ +P E +RK+
Sbjct: 560 AITRSIADQARTIRIPVHMIETINKMNRLSRQHLQEFGFEPDASILAEKMEIPEEKIRKI 619

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +KI KEPIS+ETPIGD+D SHLGDFIED    +PL++A+QA LR+    +L SLTPRE +
Sbjct: 620 MKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPLEAAMQAGLRDVVKDILDSLTPREAK 679

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS KLRSF+D
Sbjct: 680 VLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSFID 734


>gi|187921222|ref|YP_001890254.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
           PsJN]
 gi|187719660|gb|ACD20883.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
           PsJN]
          Length = 665

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 228/684 (33%), Positives = 354/684 (51%), Gaps = 49/684 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K +                 +      + +I+L +++GY+T  ++N  LP +   +  
Sbjct: 25  TAKGKGAGKAIPVAAELPPQQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAA 84

Query: 63  MEDTVAMLSNMGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           ++  V+  ++MG+ V +     +      +  ++     A   +       DS    T D
Sbjct: 85  IDSIVSAFNDMGVQVYEQAPDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTD 144

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG+ ELL+R GEIAIAKRIE G   M+ ++   PL   A++    ++ DG  
Sbjct: 145 PVRMYMREMGATELLTRAGEIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGEL 204

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + E++D                                          +   AA+    
Sbjct: 205 RIDELVD---------------------------------------GLNEDTLAAEEDST 225

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                     + ++D+    +D+   A + +A E +L+      L    E++ ++  L D
Sbjct: 226 GADASADVDADTDSDDDEDSDDDVGPADSSAADEARLKQLTSDCL----EIFAQVGMLSD 281

Query: 300 NAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                      +S   +  +E++ + +  +      ID L   +     ++   E  +L+
Sbjct: 282 QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 359 LA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +     G+ R+ F+E   G E D  W   A       +   +   + +I   + ++  I 
Sbjct: 342 IVVSKSGMPREKFIESFAGHEADLGWTERAA-RGASSYGAALERHLPAIQSEQQKLIEIE 400

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + +   + I   +   E +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEG
Sbjct: 401 ATVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEG 460

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  G+KFSTYA WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R
Sbjct: 461 NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISR 520

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +  +  +E  P  +A+++ +  E VR +LKI K+P+S+ETP+GD+  + LGD IED  A
Sbjct: 521 EILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAA 580

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP D+A+QA+LR      L SL+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIR
Sbjct: 581 SSPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIR 640

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIE+KA+RKL HPSR+ +L+SFLD
Sbjct: 641 QIESKAMRKLMHPSRADRLKSFLD 664


>gi|307611207|emb|CBX00855.1| RNA polymerase sigma factor rpoD [Legionella pneumophila 130b]
          Length = 619

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 374/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 5   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 64  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 123 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 172

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 173 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKIY-------- 221

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 222 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 256

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 257 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGW 316

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +      +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 317 LETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 376

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 377 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 436

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 437 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 496

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 497 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 556

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 557 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 616


>gi|240948851|ref|ZP_04753207.1| RNA polymerase sigma factor RpoD [Actinobacillus minor NM305]
 gi|240296666|gb|EER47277.1| RNA polymerase sigma factor RpoD [Actinobacillus minor NM305]
          Length = 621

 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 266/656 (40%), Positives = 384/656 (58%), Gaps = 47/656 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                + +I   R++GY+ + E++  LP + V +EQ+ED + M+++MGI V++     DE
Sbjct: 11  QQSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDE 70

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               +++        ++  L   + S    T DPVRMY+REMG++ELL+RE EI I+KRI
Sbjct: 71  LMLAENITDEDVVEEATKVLSTVE-SELGRTTDPVRMYMREMGTVELLTREDEIQISKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  ++ E P     ++    ++  G   L ++I                     
Sbjct: 130 EEGINEVQCAVAEYPEALVGVLECYAQVEAGEMRLVDLI--------------------- 168

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                 D + ++E    ++   D E +  V+  D    D   +++ ++  +   D + + 
Sbjct: 169 --TAFVDPNAQEEAPIDEDAHLDDEESDIVADVDDESEDEDGDSSSDNADDSSIDPELAR 226

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              +A++ Q    ++                       QK  ++  K +     L  +  
Sbjct: 227 EKFAALKAQHEKALLAI---------------------QKHGRTHAKAREQINALSDIFR 265

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVS 385
              L   + DLLV  +  + K++   E ++ R A  Y G+K+  FL+  Q  E    W+ 
Sbjct: 266 EFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYAGMKKADFLKAFQNNETTEAWIE 325

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A +  +G     +A  V+ I      ++++  ++G++I++ R I   +  GE +A  AK
Sbjct: 326 KAINAKKGG-VPKLANYVEKIRINIVNLQNLEQQSGLTIAQIREIGGRIANGELKARRAK 384

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 385 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 444

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   ++ RE TPEE+A+++ MP + +RK
Sbjct: 445 QAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERMNMPEDKIRK 504

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPIS+ETPIGD+D SHLGDFI+D++   PLDSA   +LR  T  VL  LTPRE 
Sbjct: 505 VLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRIATNEVLEGLTPREA 564

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 565 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 620


>gi|269958878|ref|YP_003328667.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
 gi|269848709|gb|ACZ49353.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
          Length = 649

 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 275/658 (41%), Positives = 403/658 (61%), Gaps = 46/658 (6%)

Query: 26  FSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDL 83
              +  K +I    +Q G +T ++++  L  D+V SSE +++T+++L + GI V++  D 
Sbjct: 35  MDKELVKNLITKGIKQGGVITFDDISDALSDDDVVSSESIDETISLLQDSGIGVLEQSDE 94

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ + +    + A    + S      +      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 95  EEADAAVSEENAAKDEEDESG----MRSLDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 150

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRI++ +  M+ SL E+P+  +  + WRD+L +   +LR++IDL+A      +GG     
Sbjct: 151 KRIKSEKVNMLRSLIEAPMVLRTFMSWRDDLVNQQVMLRDLIDLDANY----RGGAPQQE 206

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                +  E    + E  DV     D +   + +                          
Sbjct: 207 FEEGEEYGEREMADPEDSDVGHEGSDDDDEGEDASV------------------------ 242

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME  L PKV+  LD   E   ++  ++    +  K +        L E + +
Sbjct: 243 -GNASILEMESALLPKVISILDATIESAEKILEMKKRKRDSGKCD--EKAYNELHENIWE 299

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           LV  + L+   +  + +Q+Y++SK I   E  L+ L +SYG+ R  FLE +    +    
Sbjct: 300 LVSQMKLSDPAVLSVTQQIYNLSKAIAAEEVALMSLVESYGVDRKSFLEAYNNNTV---- 355

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             + +     EWKN +  E  ++  I+N+++ +S E   S   F+ +V+ ++K E  A+ 
Sbjct: 356 --FEQADASPEWKNLLEKEKKTLTDIQNKVRLLSGED--SPGSFKALVAKIQKHERTANK 411

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 412 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 471

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L M VE +
Sbjct: 472 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLGMNVEKI 531

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+
Sbjct: 532 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPK 591

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 592 EERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 649


>gi|145640511|ref|ZP_01796095.1| DNA primase [Haemophilus influenzae R3021]
 gi|145275097|gb|EDK14959.1| DNA primase [Haemophilus influenzae 22.4-21]
          Length = 629

 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 375/667 (56%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +    +G +   +   +D  +    D     + +   +   S    S     PE A    
Sbjct: 179 EIEEHNGLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 238 QQLREQHSKTLAVIE-----------------------------------KHGRSGKRAQ 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 263 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRNQERQLQKILVDIAGMPKDDFEKII 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 323 TTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|296161119|ref|ZP_06843929.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888642|gb|EFG68450.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 705

 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 220/660 (33%), Positives = 352/660 (53%), Gaps = 49/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      + +IKL  +RG+V   E++  LP      + +E+ +   S MGI V +     
Sbjct: 90  ESGRADLRALIKLGTERGFVIRGEISDCLPERLAQPDAIENVIRAFSEMGIAVFEQAPDA 149

Query: 85  DEEGSEDSLDLASSA--SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +     D   +++       +V      D+    T DPVRMY+REMG+ ELL+R+GEIA+
Sbjct: 150 ESMILHDRAAVSADDQIEEEAVTAISSVDAEFGRTTDPVRMYMREMGTTELLTRQGEIAL 209

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           A+RIE GR  M+ ++   P T   ++   D +  G T + E++D    I P + G     
Sbjct: 210 ARRIEEGRNGMIRAISSCPATIAEILAIADGVACGETAIDELVD--GLIDPAATG----- 262

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                               V E   D  S     + D    D+  E A+          
Sbjct: 263 --------------TDGMTAVPEDSLDTASVFDDDQGDEDDDDTETEPADQ--------- 299

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                      + L+   +    ++A+ + +LR   +    G        + +  +  + 
Sbjct: 300 ---------YIETLKHDALAKFAKVADWFGQLRDAYETQGYGC------ARYRAAQAAIE 344

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
             + ++      ID L   L   +  +   E E+ R+  +  G+ RD F+   +G E   
Sbjct: 345 AELMTIRFTARTIDRLCGALRLSADEVRTIEREIARIVVERCGVPRDTFVAHFRGNETHL 404

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            W +         + + +   + +I   + ++ ++     + + EFR +   +   E + 
Sbjct: 405 AW-ARQLVAAGQPFSSVLERNLPAIDLEQEKLLALQQRVVLPLDEFREVCRALSASEAKT 463

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK EM+EANLRLVIS+AK+YTNRGL FLDLIQEGNIGLM+A +KF++  GYKFSTYA 
Sbjct: 464 LRAKGEMIEANLRLVISIAKRYTNRGLLFLDLIQEGNIGLMRAVDKFEYRRGYKFSTYAT 523

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QA++RSIADQ+ TIR+PVHM + ++K+ R +R++  +   EP    +A+++ M  +
Sbjct: 524 WWIRQAVSRSIADQARTIRVPVHMIESLNKLKRISRQILQETGSEPDAALLAQRMEMQEQ 583

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR +L+I +EP+SL+  +G+ D + +GD IED  A+ P D+A+ A++R+  +  L +LT
Sbjct: 584 KVRAMLRIVREPVSLDASVGENDDTSIGDLIEDSTAILPDDAALHASMRDAISEALMTLT 643

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE ++LR+RFGI    DHTLEE+G+QF +TRERIRQIE KA+RKL+HP+RS++L+SFLD
Sbjct: 644 PREAKILRLRFGIESGRDHTLEELGEQFELTRERIRQIEVKALRKLRHPARSERLKSFLD 703


>gi|145630289|ref|ZP_01786070.1| aspartate ammonia-lyase [Haemophilus influenzae R3021]
 gi|260582763|ref|ZP_05850550.1| aspartate ammonia-lyase [Haemophilus influenzae NT127]
 gi|144984024|gb|EDJ91461.1| aspartate ammonia-lyase [Haemophilus influenzae R3021]
 gi|260094213|gb|EEW78114.1| aspartate ammonia-lyase [Haemophilus influenzae NT127]
          Length = 629

 Score =  426 bits (1096), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 375/667 (56%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +    +G +   +   +D  +    D     + +   +   S    S     PE A    
Sbjct: 179 EIEEHNGLD-EDFSNEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 238 QQLREQHSKTLAVIE-----------------------------------KHGRSGKRAQ 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 263 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKII 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 323 TTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|54298252|ref|YP_124621.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
           str. Paris]
 gi|53752037|emb|CAH13463.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
           str. Paris]
          Length = 621

 Score =  426 bits (1096), Expect = e-117,   Method: Composition-based stats.
 Identities = 271/660 (41%), Positives = 375/660 (56%), Gaps = 50/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 7   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 125 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 174

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 175 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKIY-------- 223

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 224 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 258

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 259 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLSW 318

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +    + +    + IL++++++ S  +E G++ISE + I   +  GE +A 
Sbjct: 319 LETIISKHAKKLDLDRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMSIGEAKAR 378

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 379 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 438

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 439 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 498

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 499 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 558

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 559 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 618


>gi|145638551|ref|ZP_01794160.1| aspartate ammonia-lyase [Haemophilus influenzae PittII]
 gi|229844308|ref|ZP_04464448.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 6P18H1]
 gi|229846616|ref|ZP_04466724.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 7P49H1]
 gi|145272146|gb|EDK12054.1| aspartate ammonia-lyase [Haemophilus influenzae PittII]
 gi|229810709|gb|EEP46427.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 7P49H1]
 gi|229812557|gb|EEP48246.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 6P18H1]
 gi|309750056|gb|ADO80040.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2866]
 gi|309972316|gb|ADO95517.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2846]
          Length = 629

 Score =  426 bits (1096), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 375/667 (56%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +    +G +   +   +D  +    D     + +   +   S    S     PE A    
Sbjct: 179 EIEEHNGLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 238 QQLREQHSKTLAVIE-----------------------------------KHGRSGKRAQ 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 263 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKII 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 323 TTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|16272477|ref|NP_438691.1| RNA polymerase sigma-70 factor [Haemophilus influenzae Rd KW20]
 gi|260580980|ref|ZP_05848803.1| transcription initiation factor sigma 70 [Haemophilus influenzae
           RdAW]
 gi|1173125|sp|P43766|RPOD_HAEIN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1573517|gb|AAC22190.1| RNA polymerase sigma-70 factor (rpoD) [Haemophilus influenzae Rd
           KW20]
 gi|260092339|gb|EEW76279.1| transcription initiation factor sigma 70 [Haemophilus influenzae
           RdAW]
          Length = 629

 Score =  426 bits (1095), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 375/667 (56%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +    +G +   +   +D  +    D     + +   +   S    S     PE A    
Sbjct: 179 EIEEHNGLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 238 QQLREQHSKTLAVIE-----------------------------------KHGRSGKRAQ 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 263 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKII 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 323 TTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|148827724|ref|YP_001292477.1| DNA primase [Haemophilus influenzae PittGG]
 gi|148718966|gb|ABR00094.1| DNA primase [Haemophilus influenzae PittGG]
          Length = 629

 Score =  426 bits (1095), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 375/667 (56%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +    +G +   +   +D  +    D     + +   +   S    S     PE A    
Sbjct: 179 EIEEHNGLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 238 QQLREQHSKTLAVIE-----------------------------------KHGRSGKRAQ 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 263 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKII 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 323 TANGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|225025101|ref|ZP_03714293.1| hypothetical protein EIKCOROL_01993 [Eikenella corrodens ATCC
           23834]
 gi|224942062|gb|EEG23271.1| hypothetical protein EIKCOROL_01993 [Eikenella corrodens ATCC
           23834]
          Length = 648

 Score =  426 bits (1095), Expect = e-117,   Method: Composition-based stats.
 Identities = 256/682 (37%), Positives = 380/682 (55%), Gaps = 42/682 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
             ++N  +  E ++S+  L  +      +++I   ++RGY+T  E+N  LP D   +EQ+
Sbjct: 1   MSEQNNPATEEQDESNRPLTPEEQRARLRQLILQGKERGYITYAEINDALPDDMSDAEQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLD--LASSASNSSVFLQKRKDSADRSTDDPV 121
           ++ V M+S +GI V +     +     D+        A   +       DS    T DPV
Sbjct: 61  DNIVNMISGLGIQVTEETPDSETLLMADNTANMTDDDAVAEAEAALSSADSEFGRTTDPV 120

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    +
Sbjct: 121 RMYMREMGQVDLLTREDEIVIAKKIETALRNMIQAISACPGSVAEILELIEKVRNDEIRV 180

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                ++  D  E   D         ++ 
Sbjct: 181 DEVV--------------------------------EDIIDPHEELLDELGIGVDKAEES 208

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +      E+ + D    D DE+D+    +A  ++L+ KV+   ++I   Y+++ +     
Sbjct: 209 APEADLEESEDEDADEEDADEEDAGAISAANLEELKQKVLAHFEDIQATYKKMVA----- 263

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
              QK          L+  +   + ++     +I+ L   L      I   E E+  +  
Sbjct: 264 -ALQKHHSQHKTYLNLRNYIADQLLNVRFTTRQIETLSNNLRTRVDSIRRLEREIRDICL 322

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               + RD F+        D +WV  A+      W   ++    +I++ +N +       
Sbjct: 323 NRVHMDRDYFINNFLPNITDLNWVE-AEIGKNRVWSEALSRFQYAIIEKQNILIEQEQHA 381

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI+E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 382 QISIAELKEISKNMVANEKETAAAKREMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 441

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 442 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 501

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   +P   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P
Sbjct: 502 QETGEDPDAAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNIAP 561

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+ ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 562 ADAAMYSSLREATKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 621

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 622 AKALRKLRHPTRSDRLRSFLDS 643


>gi|270158971|ref|ZP_06187627.1| RNA polymerase sigma factor RpoD [Legionella longbeachae D-4968]
 gi|289166186|ref|YP_003456324.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella longbeachae
           NSW150]
 gi|269987310|gb|EEZ93565.1| RNA polymerase sigma factor RpoD [Legionella longbeachae D-4968]
 gi|288859359|emb|CBJ13295.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella longbeachae
           NSW150]
          Length = 622

 Score =  426 bits (1094), Expect = e-117,   Method: Composition-based stats.
 Identities = 270/660 (40%), Positives = 376/660 (56%), Gaps = 49/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    +
Sbjct: 7   EQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPGD 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   +  N     L EII   A +             
Sbjct: 125 RIEEGIYQVLKSLAHYPETVQLVLDDYERFNAQEIRLNEIISGFADV------------- 171

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                           D++           +  + +   + S  E+ + +   ++ D+  
Sbjct: 172 ---------------EDEIAPASSIGSMLDEDQQQEEEILLSDEEDEDGEGGMVEVDDGP 216

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +        D LR     A+  + E                   ++  K     E + + 
Sbjct: 217 NPEQAKIYFDDLRETYEAAIVALKE-----------------HGRTHAKTTKALEIMSES 259

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I  +E  ++RL  +   I R +F++   G+E D  W
Sbjct: 260 FLKLKLTSRQVDRLTRHFRQLRNHIREHERGIMRLCIEKARIPRKLFIDTFPGQETDLEW 319

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           ++     + +    N +    + IL+I++ + +  +E G+SISE + I   +  GE +A 
Sbjct: 320 LNTIIAKYSKKLDMNRIQENTEEILRIQSRLVAFELEYGLSISEIKEINRKMSIGEAKAR 379

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 439

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 440 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 499

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 500 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 559

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 560 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 619


>gi|145637426|ref|ZP_01793085.1| aspartate ammonia-lyase [Haemophilus influenzae PittHH]
 gi|145269372|gb|EDK09316.1| aspartate ammonia-lyase [Haemophilus influenzae PittHH]
          Length = 629

 Score =  426 bits (1094), Expect = e-117,   Method: Composition-based stats.
 Identities = 267/661 (40%), Positives = 373/661 (56%), Gaps = 42/661 (6%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGINVVDGD 81
             +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI V+D  
Sbjct: 8   TAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEA 67

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+RE EI+
Sbjct: 68  PESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLTREDEIS 126

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P ++    +
Sbjct: 127 IAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNAEIEEHN 184

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
           G +   +   +D  +    D     + +   +   S    S     PE A    + L E 
Sbjct: 185 GLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQLREQ 243

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
              +   +                                    K  +S  + +     L
Sbjct: 244 HSKTLAVIE-----------------------------------KHGRSGKRAQDQIALL 268

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELD 380
            ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +       +
Sbjct: 269 GEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSN 328

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V +GE +
Sbjct: 329 SEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAVARGEQK 387

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 388 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 447

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP 
Sbjct: 448 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAERMGMPE 507

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T  VL  L
Sbjct: 508 DKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGL 567

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL
Sbjct: 568 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFL 627

Query: 681 D 681
           D
Sbjct: 628 D 628


>gi|56416704|ref|YP_153778.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
 gi|56387936|gb|AAV86523.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
          Length = 632

 Score =  426 bits (1094), Expect = e-117,   Method: Composition-based stats.
 Identities = 278/658 (42%), Positives = 403/658 (61%), Gaps = 46/658 (6%)

Query: 26  FSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDL 83
              +  K +I    +Q G +T ++++  L  D+V SSE +++T+++L + GI V++  D 
Sbjct: 18  MDKELVKNLITKGIKQGGVITFDDISDALSDDDVVSSESIDETISLLQDSGIGVLEQSDE 77

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ +      + A    + +      +      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 78  EEADAVVSEENAAKDEEDEAG----MRSLDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 133

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRI++ +  M+ SL E+PL  +  + WRD+L +   +LR++IDL+A      +GG     
Sbjct: 134 KRIKSEKINMLRSLIEAPLVLRTFMSWRDDLVNQQVMLRDLIDLDANY----RGGAPRQE 189

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                +  E    E    DV     D                         + +  ED  
Sbjct: 190 FEEGGEYGEQEMAEPGDSDVGGDGAD-------------------------DEDEGEDSS 224

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME  L PKV+  LD   E   ++  ++    +  K +K       L E + +
Sbjct: 225 AGNASILEMESALLPKVISILDATIESAEKILEMKKQKRDSGKYDK--KAYNALHENIWE 282

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           LV  + L+   +  + +Q+Y++SK I   E  L+ L +SYG+ R  FLE +    +    
Sbjct: 283 LVSQMKLSDPAVLSVTQQIYNLSKAIAAEEAALMSLVESYGVDRKSFLEAYNNNTV---- 338

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             + +     EWKN +  E  ++  I+N+++ +S E   S   F+ +V+ ++K E  A+ 
Sbjct: 339 --FEQANASPEWKNLLEKEKKTLTDIQNKVRLLSGED--SPGNFKALVAKIQKHERTANK 394

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 395 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 454

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L M VE +
Sbjct: 455 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSTRLGMNVEKI 514

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+
Sbjct: 515 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPK 574

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 575 EERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 632


>gi|148653373|ref|YP_001280466.1| RNA polymerase, sigma 70 subunit, RpoD [Psychrobacter sp. PRwf-1]
 gi|148572457|gb|ABQ94516.1| RNA polymerase, sigma 70 subunit, RpoD [Psychrobacter sp. PRwf-1]
          Length = 623

 Score =  426 bits (1094), Expect = e-117,   Method: Composition-based stats.
 Identities = 264/658 (40%), Positives = 379/658 (57%), Gaps = 44/658 (6%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S      +I++ +++GY+T  E+N  LP     S+Q+ED V ML+++GI + +     D
Sbjct: 8   QSTSQLATLIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDAD 67

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +    D  +    A++ +  +    ++    T DPVRMY+REMG+++LL+REGEI IAKR
Sbjct: 68  DILMNDGANDDDMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKR 127

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +  ++   P T Q ++   D +  G   L ++I            GF    E 
Sbjct: 128 IEEGIRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVI-----------TGFLDPEEI 176

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                 ED          +E    I + +K    D    +   E  E  E +   D +  
Sbjct: 177 EPAVVEED----------EEKIPVITTKSKAKDVDDEDDEEEAEEEEEAEESGGLDPE-- 224

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                         V   ++EI E++   +   +         + S + +    +L +  
Sbjct: 225 -------------LVRQRVEEIRELFAVAKQALEQY------GRGSAQAEEAYAQLAERF 265

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV 384
             L LN    D ++  ++D+   +   E +++RL    G + R  F +     E +  W+
Sbjct: 266 MLLKLNNRMADNVMAIMHDVYDDVRKQERQIMRLVIRRGKMPRSEFRKTFPSNETNVDWL 325

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +        ++ + +A  VD ++ ++  I+    +  + I+E + +   +  GE +A  A
Sbjct: 326 TDRLK-GNPKFADSLAKVVDDVVVLQRRIRDHEDKLDMQITEMKEVARRMAIGEAKARRA 384

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 385 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 444

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VR
Sbjct: 445 RQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVR 504

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED+   SP++ A  A L+E T  VL++LT RE
Sbjct: 505 KVLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDATSAGLQEATRDVLSNLTERE 564

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +VLRMRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 565 AKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 622


>gi|332974186|gb|EGK11120.1| DNA-directed RNA polymerase sigma subunit RpoD [Psychrobacter sp.
           1501(2011)]
          Length = 624

 Score =  426 bits (1094), Expect = e-117,   Method: Composition-based stats.
 Identities = 262/658 (39%), Positives = 378/658 (57%), Gaps = 43/658 (6%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S      +I++ +++GY+T  E+N  LP     S+Q+ED V ML+++GI + +     D
Sbjct: 8   QSTSQLATLIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDAD 67

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +    D  +    A++ +  +    ++    T DPVRMY+REMG+++LL+REGEI IAKR
Sbjct: 68  DILMNDGANDDEMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKR 127

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +  ++   P T Q ++   D +  G   L ++I            GF    E 
Sbjct: 128 IEEGIRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVI-----------TGFLDPEEI 176

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                          +D +E    I + +KV + D    +    + E D       + + 
Sbjct: 177 EPPVV----------EDDEEQLPVITTKSKVKELDDEDEEEEETDEEEDAEEAGGLDPEL 226

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                         V   ++EI E++             ++  + S + +    +L    
Sbjct: 227 --------------VRQRVEEIRELFA------TAKQALEEYGRGSPQAEEAYAQLADRF 266

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWV 384
             L LN    D ++  ++D+   +   E +++RL    G + R  F +     E +  W+
Sbjct: 267 MLLKLNNRMSDNVMAIMHDVYDDVRKQERQIMRLVIRRGKMPRAEFRKTFPSNETNVDWL 326

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +        ++ + +A  VD ++ ++  I+    +  + I E + +   +  GE +A  A
Sbjct: 327 TDRLK-GNPKFADSLAKVVDDVVVLQRRIRDHEDKLDMEIGEMKEVARRMAIGEAKARRA 385

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 386 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 445

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    VR
Sbjct: 446 RQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEVKVR 505

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED+   SP++ A  A L+E T  VL++LT RE
Sbjct: 506 KVLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDATSAGLQEATRDVLSNLTERE 565

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            +VLRMRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 566 AKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 623


>gi|254281823|ref|ZP_04956791.1| RNA polymerase, sigma 70 subunit, RpoD family [gamma
           proteobacterium NOR51-B]
 gi|219678026|gb|EED34375.1| RNA polymerase, sigma 70 subunit, RpoD family [gamma
           proteobacterium NOR51-B]
          Length = 603

 Score =  425 bits (1093), Expect = e-116,   Method: Composition-based stats.
 Identities = 275/657 (41%), Positives = 367/657 (55%), Gaps = 63/657 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   +++GY+T  E+N  LP D    +Q+ED + M+++MGI V +     DE
Sbjct: 7   KQSRLKALIAKGKEQGYLTYSEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADE 66

Query: 87  EG-SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +E        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 67  LILTEGDRSADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +MA++   P   + L    D +      L +I  L   + P            
Sbjct: 127 IEEGIRELMAAMAHYPGVARRLTEEYDLVTKEERKLADI--LVGYLDPADHV-------- 176

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                              +   +  +AAK   DD    D+ P+  E  +R         
Sbjct: 177 ----------------PSAQEIAEQTAAAKNKTDDDEAPDTGPDPIEAKKR--------- 211

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                            AL        ++ +          + + S K     +KL +L 
Sbjct: 212 ---------------FTALKRQCTRTEKVLAA---------ESRQSKKAIAEMDKLGELF 247

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L     D LVE      + +   E E++R+      + R  F++  QG E D  WV
Sbjct: 248 KFFKLTPRVFDPLVEAPRTALQIVREQEREIMRIVVRECRMDRKDFIKSFQGSESDSRWV 307

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           S      + E    ++   D I +++  I ++  E G++++E + I   +  GE  A  A
Sbjct: 308 SRV--MRKKELGARISLHKDEIQRLQRRIGAVEDEIGLTVAEIKEINRRMSMGEARARRA 365

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 366 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 425

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + VR
Sbjct: 426 RQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKVR 485

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ S LGDFIED    SP+DSA +  L E TT VLA LT RE
Sbjct: 486 KVLKIAKEPISMETPIGDDEDSSLGDFIEDVTIASPVDSATEEGLTEATTDVLAGLTARE 545

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  LRSFLD
Sbjct: 546 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 602


>gi|254455607|ref|ZP_05069036.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
 gi|207082609|gb|EDZ60035.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
          Length = 608

 Score =  425 bits (1092), Expect = e-116,   Method: Composition-based stats.
 Identities = 295/659 (44%), Positives = 414/659 (62%), Gaps = 62/659 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            S+ +++     RG++T EELN  L    +S E +      + +  I +V+         
Sbjct: 7   KSFARLMGRGTHRGFITYEELNKSLGKRNLSDENLAQAFIHILDENITLVE--------- 57

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +    +      SS    K +      +DDP+RMYLREMG +ELLSREGEIAIAKRIEA
Sbjct: 58  KKSDFKVLRKKEGSS----KEEGKTMEKSDDPIRMYLREMGGVELLSREGEIAIAKRIEA 113

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G+ +M+ +L +SP+T Q    W D+L     L+REIID++     +   G     +    
Sbjct: 114 GKDVMLIALSQSPMTAQQFFEWNDQLQKDEILVREIIDIDTNYMEDETTGPSAKQKNAGE 173

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            ++++ S E + DD   T                                          
Sbjct: 174 TEKDEGSGEGDEDDFNPT------------------------------------------ 191

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVK 323
           L+AME +++PKV+  +  + + Y +L   Q   ++   + ++         + + + +++
Sbjct: 192 LAAMETEIKPKVLKTVSTLTKEYNKLIKYQKEKLDCILNSQNFSPAKEKGYQKIVDDILE 251

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
            + SL L+ S ++ LV++ Y  +K+I+  EG LLRLA  + I R+ F++ + G E++P+ 
Sbjct: 252 NIKSLQLSPSVLEELVQKHYVENKKIISLEGNLLRLAMDHKIPRNEFIKFYIGNEINPNL 311

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             +        WK F +   +    IR  +  IS + GIS+++F+ +VS V+KGE E+ I
Sbjct: 312 KKFL--DTNSIWKQFFSKNKEEFKNIRERLIEISHKLGISVTDFKKLVSRVQKGEKESRI 369

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 370 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 429

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+VRT R + ++  RE TPEE+A+KL MP++ V
Sbjct: 430 IRQAITRSIADQARTIRIPVHMIETINKIVRTQRLILSEFGREATPEELAQKLRMPLDKV 489

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI+KEP+SLE P+GDE+ S LGDFIED  A++PL+ AI++NL E TT++L++LTPR
Sbjct: 490 RKVLKISKEPVSLEKPVGDEEDSSLGDFIEDTKALAPLEQAIKSNLGEATTKILSTLTPR 549

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EERVLRMRFG+GMNTDHTLEEVG QF VTRERIRQIEAKA+RKLKHPSRSK+L+SFL+ 
Sbjct: 550 EERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRSKQLKSFLES 608


>gi|301169248|emb|CBW28845.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           10810]
          Length = 629

 Score =  425 bits (1092), Expect = e-116,   Method: Composition-based stats.
 Identities = 267/667 (40%), Positives = 374/667 (56%), Gaps = 42/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +     G +   +   +D  +    D     + +   +   S    S     PE A    
Sbjct: 179 EIEEHSGLD-EDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 238 QQLREQHSKTLAVIE-----------------------------------KHGRSEKRAQ 262

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 263 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEKII 322

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 323 TTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 381

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 382 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 441

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 442 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 501

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 502 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 561

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 562 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 622 TLRSFLD 628


>gi|145633515|ref|ZP_01789244.1| aspartate ammonia-lyase [Haemophilus influenzae 3655]
 gi|144985884|gb|EDJ92492.1| aspartate ammonia-lyase [Haemophilus influenzae 3655]
          Length = 628

 Score =  425 bits (1091), Expect = e-116,   Method: Composition-based stats.
 Identities = 271/667 (40%), Positives = 380/667 (56%), Gaps = 43/667 (6%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I     + P +
Sbjct: 121 REDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLIT--GFVDPNA 178

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +    +G +     + ED   E+E     + E +   +   S D  + +D  PE A    
Sbjct: 179 EIEEHNGLDEDFSDEDEDEDDEEEGSSNADVEDNESESTSDSSDSDNSID--PEVAREKF 236

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
           + L E    +   +                                    K  +S  + +
Sbjct: 237 QQLREQHSKTLAVIE-----------------------------------KHGRSGKRAQ 261

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +  
Sbjct: 262 DQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYEERQLQKILVDIAGMPKDDFEKII 321

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
                +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I   V
Sbjct: 322 TTNGSNSEWVTKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICDAV 380

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GY
Sbjct: 381 ARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 440

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+
Sbjct: 441 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEELAE 500

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  T 
Sbjct: 501 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATH 560

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 561 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 620

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 621 TLRSFLD 627


>gi|94499953|ref|ZP_01306488.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
 gi|94427811|gb|EAT12786.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
          Length = 606

 Score =  425 bits (1091), Expect = e-116,   Method: Composition-based stats.
 Identities = 268/657 (40%), Positives = 373/657 (56%), Gaps = 56/657 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I   +++GY+T  ++N  LP D  + EQ+ED + M++++GI V +     D
Sbjct: 4   TQQSRLKELIAKGKEQGYLTYAQVNDHLPDDIATPEQVEDIIRMINDIGITVSEVAPDAD 63

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E    + +    +A   +       ++    T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 64  ELNMGE-VTTDEAAIEEAAAALAAVETDVGRTTDPVRMYMREMGTVELLTREGEIVIAKR 122

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +MA+L   P   + ++   +E         EI  L          GF   ++ 
Sbjct: 123 IEEGIREVMAALSYFPGAVRTVLDAVEESMADE----EINRLGDVFN-----GFIDASD- 172

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                                  D E A  VS +  +  DS  ++ ++ +     D ++ 
Sbjct: 173 ----------------------DDPEPATPVSAEAAADKDSDDDDDDSSDAPSGPDPEEV 210

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              ++ +E Q                     L       +K  + S +     EKL +L 
Sbjct: 211 KRRMAEIEKQ---------------------LDKTEKAIEKHGRGSKQADKEGEKLAELF 249

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L+    D LV    D    I   E +++ +      +KR  F++  QG E +  W+
Sbjct: 250 APIKLSPKYFDDLVGTARDNLDFIRVQERQIMVICTRKAKMKRQEFIKSFQGNEGNDSWI 309

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
               +    ++   +      + + + +I+ +    G+ IS+ + I   V  GE  A  A
Sbjct: 310 DDLIN-AGKDYSQIIENHGYDLKRAQKKIRQVKDRVGLEISDIKEINRRVSIGEARARRA 368

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 369 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 428

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ MP + +R
Sbjct: 429 RQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERMDMPEDKIR 488

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+A +  L + T  VL+ LT RE
Sbjct: 489 KVLKIAKEPISMETPIGDDEDSHLGDFIEDVNGHSPIDTATETGLTDATRSVLSGLTARE 548

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSFLD
Sbjct: 549 SKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFLD 605


>gi|145628917|ref|ZP_01784717.1| DNA primase [Haemophilus influenzae 22.1-21]
 gi|145635386|ref|ZP_01791088.1| aspartate ammonia-lyase [Haemophilus influenzae PittAA]
 gi|144979387|gb|EDJ89073.1| DNA primase [Haemophilus influenzae 22.1-21]
 gi|145267392|gb|EDK07394.1| aspartate ammonia-lyase [Haemophilus influenzae PittAA]
          Length = 623

 Score =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 272/669 (40%), Positives = 374/669 (55%), Gaps = 52/669 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I          
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI---------- 170

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS--PPENAEN 253
             GF             D     E D+ + +  D+E     S  D S  D+   PE A  
Sbjct: 171 -TGFVDPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVARE 229

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
             + L E    +   +                                    K  +S  +
Sbjct: 230 KFQQLREQHSKTLAVIE-----------------------------------KHGRSGKR 254

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLE 372
            +     L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +
Sbjct: 255 AQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEK 314

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                  +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I  
Sbjct: 315 IITTNGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICD 373

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            V +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 374 AVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEEL 493

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  
Sbjct: 494 AERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVA 553

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR
Sbjct: 554 THEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 613

Query: 673 SKKLRSFLD 681
           S+ LRSFLD
Sbjct: 614 SETLRSFLD 622


>gi|68249130|ref|YP_248242.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae 86-028NP]
 gi|68057329|gb|AAX87582.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae 86-028NP]
          Length = 623

 Score =  423 bits (1088), Expect = e-116,   Method: Composition-based stats.
 Identities = 272/669 (40%), Positives = 374/669 (55%), Gaps = 52/669 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML-SNMGI 75
           + +     +   +  +++++L R +GY+T  E+N  LP D +  E  +  +  L ++ GI
Sbjct: 2   EKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGI 61

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V+D     D+    D++     A   +  +    +S    T DPVRMY+REMG+++LL+
Sbjct: 62  PVLDEAPESDDMMLSDTI-PDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT 120

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE EI+IAKRIE G   +  S+   P     L+   D++  G   L ++I          
Sbjct: 121 REDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLI---------- 170

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS--PPENAEN 253
             GF             D     E D+ + +  D+E     S  D S  D+   PE A  
Sbjct: 171 -TGFVDPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVARE 229

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
             + L E    +   +                                    K  +S  +
Sbjct: 230 KFQQLREQHSKTLAVIE-----------------------------------KHGRSGKR 254

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLE 372
            +     L ++     L   + DLLV  + ++ KR+ + E +L + L    G+ +D F +
Sbjct: 255 AQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEK 314

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                  +  WV+ A    +   K  +  E D I +  N +      T ++I++ R I  
Sbjct: 315 IITANGSNSEWVAKALKSSKPWAKRLIKYE-DRIYEALNNLAITEENTKLTITQMRDICD 373

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            V +GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 374 AVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQLLQEMGREATPEEL 493

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHLGDFIED     PLDSA   +L+  
Sbjct: 494 AERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVA 553

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR
Sbjct: 554 THEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 613

Query: 673 SKKLRSFLD 681
           S+ LRSFLD
Sbjct: 614 SETLRSFLD 622


>gi|73666941|ref|YP_302957.1| RNA polymerase sigma factor rpoD [Ehrlichia canis str. Jake]
 gi|72394082|gb|AAZ68359.1| RNA polymerase, sigma 70 subunit, RpoD [Ehrlichia canis str. Jake]
          Length = 622

 Score =  423 bits (1087), Expect = e-116,   Method: Composition-based stats.
 Identities = 273/658 (41%), Positives = 408/658 (62%), Gaps = 40/658 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                +  K ++    ++G+VT  ++N       +S++ +++T++ML + GINV++  D 
Sbjct: 4   LQTDKELLKTLVSKGLKQGFVTFNDINDVFSDYVLSADNIDETISMLQDSGINVLEQSDE 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ++     +   +        V     K      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 64  DEANSIVEENRIKEDLDEDDVSDGGIKSWDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+I++ +  M+ SL ESP+  +  + WRD+L +   +LR++IDL+A    E    F    
Sbjct: 124 KKIKSEKVNMLRSLVESPVVLRTFMSWRDDLVNEQIMLRDLIDLDANYRYEFPEKFADAD 183

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E       +D   E + D              +S+DD                  DE+  
Sbjct: 184 EASVLDYDKDLIDESDED------------TDISEDD------------------DEENV 213

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME+ L PKV+  LD +     ++  L+     G+ ++    +   L + + +
Sbjct: 214 SINASILEMENALLPKVVSILDSVIASAEKILELKKQ-YQGKINQDIEKQYNDLHDSIWE 272

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           ++  + L+ S +  + +Q+Y +SK I   E +++ LA+SYGI+R  FL+ +    +    
Sbjct: 273 MIYQIKLSNSAVLSITQQIYSLSKSIAAEEAKIISLAESYGIQRKDFLDAYNTNSV---- 328

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K     +W N +A E  +I+ + ++IK +S E  ++  EF+ +V+ ++K E  A+ 
Sbjct: 329 --LQKKGTSPQWNNLLANEESNIVSMYSKIKLLSGENNLT--EFKALVTKIQKHERAANQ 384

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 385 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 444

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M +++ REPT EE++ KL + V+ +
Sbjct: 445 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTLEELSAKLNINVDKI 504

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P D+A+ A+LRE TT+VL++LTP+
Sbjct: 505 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADLREITTKVLSTLTPK 564

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 565 EERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 622


>gi|319779662|ref|YP_004130575.1| RNA polymerase sigma factor RpoD [Taylorella equigenitalis MCE9]
 gi|317109686|gb|ADU92432.1| RNA polymerase sigma factor RpoD [Taylorella equigenitalis MCE9]
          Length = 840

 Score =  423 bits (1087), Expect = e-116,   Method: Composition-based stats.
 Identities = 244/661 (36%), Positives = 358/661 (54%), Gaps = 62/661 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      + +IK  +  GY+T  E+N  L  D V SE ME  V+ L +MGI V +     
Sbjct: 238 EERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMVSTLESMGIPVYEEAPNA 297

Query: 85  DEE--GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++       +++      + +       DS    T DPVRMY+REMGS+ELL+R  EI I
Sbjct: 298 EDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYMREMGSVELLNRTKEIEI 357

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++  SP T   ++    ++ DG   +                     
Sbjct: 358 AKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQI--------------------- 396

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    E+       DD +E  G   + A    ++           E          
Sbjct: 397 ---------EEIVDGLISDDGEEYAGSGAADADEESEEAQTGGMSSLQIE---------- 437

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                       +LR + +   D + + + ++++  +      K    S       +++ 
Sbjct: 438 ------------KLREESLAKFDRVQKAFDKMKAEYE------KGRFQSQAYNKANQQIH 479

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDP 381
             +  +      ++ L E L    +R+   E  ++       G+ R+ F++   G E + 
Sbjct: 480 DEISGVRFTAKMVEKLAEILRKQIERVRELEKAMISVCVDKVGMPREHFIDSFPGNETNL 539

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV+      + ++   +   +  I +I+ +   +  E  + I E + +   +  GE +A
Sbjct: 540 EWVNDELK-KKPKYAEKLERSIPDIHEIQQKFIDLEKEVILPIKELKDVNKRMVNGEAKA 598

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 599 KKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 658

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+  IRIPVHM + I+K+ R  R++  +   EP    +A+K+ MP+E
Sbjct: 659 WWIRQAITRSIADQARIIRIPVHMIETINKINRITRQILQETGVEPDSAMLAEKMDMPIE 718

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RK+LKI+K+PIS+ETPIGD+D SHLGDFIED + +SP ++A+Q ++ E    V+ SLT
Sbjct: 719 KIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLSPEEAALQRSMSEVFDEVINSLT 778

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE +VLRMRFGIGM++D TLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+
Sbjct: 779 QREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRADKLKSFLE 838

Query: 682 G 682
            
Sbjct: 839 N 839


>gi|296159716|ref|ZP_06842538.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295889930|gb|EFG69726.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 665

 Score =  423 bits (1086), Expect = e-116,   Method: Composition-based stats.
 Identities = 229/684 (33%), Positives = 355/684 (51%), Gaps = 49/684 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K +                 +      + +I+L +++GY+T  ++N  LP +   +  
Sbjct: 25  TAKGKGAGKAIPVAAELPPQQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAA 84

Query: 63  MEDTVAMLSNMGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           ++  V+  ++MG+ V +     +      +  ++     A   +       DS    T D
Sbjct: 85  IDSIVSAFNDMGVQVYEQAPDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTD 144

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG+ ELL+R GEIAIAKRIE G   M+ ++   PL   A++    ++ DG  
Sbjct: 145 PVRMYMREMGATELLTRAGEIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGEL 204

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + E++D                                          +   AA+    
Sbjct: 205 RIDELVD---------------------------------------GLNEDTIAAEEDSA 225

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                     + ++D+    +D+D  A + +A E +L+      L    E++ ++  L D
Sbjct: 226 SADASADVDADTDSDDDEDSDDDDGPADSSAADEARLKQLTSDCL----EIFAQVGMLSD 281

Query: 300 NAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                      +S   +  +E++ + +  +      ID L   +     ++   E  +L+
Sbjct: 282 QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 359 LA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +     G+ R+ F+E   G E D  W   A       +   +   + +I   + ++  I 
Sbjct: 342 IVVSKSGMPREKFIESFAGHEADLGWTERAA-RGASAYGAALERHLPAIQSEQQKLIEIE 400

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + +   + I   +   E +   AK EM+EANLRLVIS+AKKY NRG+ FLDLIQEG
Sbjct: 401 ATVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEG 460

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  G+KFSTYA WWV+QA+TRS+ADQ+ TIR+PVHM + I+K+ R +R
Sbjct: 461 NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISR 520

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +  +  +E  P  +A+++ +  E VR +LKI K+P+S+ETP+GD+  + LGD IED  A
Sbjct: 521 EILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAA 580

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            SP D+A+QA+LR      L SL+PRE +VLRMR+GI   +DHTLEEVGKQF VTRERIR
Sbjct: 581 SSPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIR 640

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIE+KA+RKL HPSR+ +L+SFLD
Sbjct: 641 QIESKAMRKLMHPSRADRLKSFLD 664


>gi|1710686|sp|P52325|RPOD_NEIGO RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|808742|gb|AAA67115.1| sigma 70 [Neisseria gonorrhoeae]
          Length = 642

 Score =  423 bits (1086), Expect = e-116,   Method: Composition-based stats.
 Identities = 257/682 (37%), Positives = 387/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLRNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGCLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E  ++ AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKVSAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|1575485|gb|AAB09543.1| LprpoD [Legionella pneumophila]
          Length = 620

 Score =  422 bits (1085), Expect = e-116,   Method: Composition-based stats.
 Identities = 270/660 (40%), Positives = 372/660 (56%), Gaps = 51/660 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       K+I L +++GY+T  ++N  LP   V +E  +  ++ML  M I V +    E
Sbjct: 7   DQQSSQITKVISLGKEQGYLTYSQINDLLPN-IVDTEHFDVIISMLEGMNIKVFELPPSE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE     + +       +++ L    D     T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  DELALLLNTEEVPDIEEAAMVLASV-DKETGRTTDPVRMYMREMGTVELLTREGEIRIAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   ++ SL   P T Q ++   D        L EII   A +  E          
Sbjct: 125 RIEEGIYQVLKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEE---------- 174

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                   +     + +  +E   D++   +  +   S VD  P   +            
Sbjct: 175 ---IAPATNIGSMLDEEQQEEILLDVDEEDEDGEGGISDVDDGPNPEQAKIY-------- 223

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                               DE+ E + +           ++  +++ K   L + + + 
Sbjct: 224 -------------------FDELREAFEKAMK------ALKEHGRTNKKTVELLDSMSES 258

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
              L L   ++D L      +   I   E  ++RL  +   I R +F++   G+E D  W
Sbjct: 259 FLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQETDLGW 318

Query: 384 VSY-AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           +        +      +    + IL++++++ S  +E G++ISE + I   +     EA 
Sbjct: 319 LETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS-IGDEAR 377

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 378 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 437

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +  RE TPEE+A+K+ +  + 
Sbjct: 438 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKMELSEDK 497

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETP+GD+D SHLGDFIED N  SP+D A    LRE T  +L +LTP
Sbjct: 498 IRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEILETLTP 557

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KLRSFL+G
Sbjct: 558 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLRSFLEG 617


>gi|194098357|ref|YP_002001415.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae NCCP11945]
 gi|239998768|ref|ZP_04718692.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|240112698|ref|ZP_04727188.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae MS11]
 gi|240117739|ref|ZP_04731801.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID1]
 gi|254493553|ref|ZP_05106724.1| RNA polymerase sigma factor rpoD [Neisseria gonorrhoeae 1291]
 gi|268594613|ref|ZP_06128780.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|268598759|ref|ZP_06132926.1| RNA polymerase sigma factor [Neisseria gonorrhoeae MS11]
 gi|268603436|ref|ZP_06137603.1| sigma 70 domain-containing protein [Neisseria gonorrhoeae PID1]
 gi|193933647|gb|ACF29471.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512593|gb|EEH61938.1| RNA polymerase sigma factor rpoD [Neisseria gonorrhoeae 1291]
 gi|268548002|gb|EEZ43420.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|268582890|gb|EEZ47566.1| RNA polymerase sigma factor [Neisseria gonorrhoeae MS11]
 gi|268587567|gb|EEZ52243.1| sigma 70 domain-containing protein [Neisseria gonorrhoeae PID1]
 gi|317164060|gb|ADV07601.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 642

 Score =  422 bits (1084), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/682 (37%), Positives = 387/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEVSAANLAELKQKVIGHFAQIEKDYKKMIGCLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|240127996|ref|ZP_04740657.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-93-1035]
 gi|268686384|ref|ZP_06153246.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-93-1035]
 gi|268626668|gb|EEZ59068.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-93-1035]
          Length = 642

 Score =  421 bits (1083), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/682 (37%), Positives = 387/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENTLKNMVQAISACPGSIAEILELIEKICKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGCLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|57239060|ref|YP_180196.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58579003|ref|YP_197215.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58617062|ref|YP_196261.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|57161139|emb|CAH58052.1| RNA polymerase sigma-70 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58416674|emb|CAI27787.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|58417629|emb|CAI26833.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 622

 Score =  421 bits (1083), Expect = e-115,   Method: Composition-based stats.
 Identities = 267/658 (40%), Positives = 402/658 (61%), Gaps = 40/658 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                +  + ++    ++G+VT  ++N       +S++ +++T+++L + GINV++  D 
Sbjct: 4   LQTDKELIRTLVSKGIKQGFVTFNDINDVFSDYVLSADNIDETISLLQDSGINVLEQSDE 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ++     +S  L     +  V     K      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 64  DEASSIVESGRLKDGIDDDDVSDTSIKSWDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+I++ +  M+ SL ESP+  +  + WRD+L +   +LR++IDL+A    E    F    
Sbjct: 124 KKIKSEKVNMLRSLVESPMVLRTFMSWRDDLVNEQIMLRDLIDLDANYRYEFPEKFSDVD 183

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +                                  D    +    +  +  + + D+D  
Sbjct: 184 DESVL------------------------------DYDKDLMDEDDTDDISDDDDDDDNT 213

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME  L PKV+  LD + E   ++  L+     G+  +    +   L + + +
Sbjct: 214 SINASILEMESALLPKVVSILDAVIESAEKILELKKQ-HKGKLTKDIEKQYNDLHDNIWE 272

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           ++  + L+ S +  + +Q+Y ++K I   E +++ LA+SYGI R  FL+ +    +    
Sbjct: 273 MIYQIKLSNSAVLSITQQIYSLNKSIAAEEAKIISLAESYGIPRKEFLDAYNTNSV---- 328

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K      W N +  E  +I+ + N+IK +S     S++EF+ +V+ ++K E  A+ 
Sbjct: 329 --LEKKGTSPAWNNMIEKEETNIVSMYNKIKLLSG--ENSLAEFKSLVTKIQKHERAATQ 384

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 385 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 444

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L + V+ +
Sbjct: 445 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNINVDKI 504

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P D+A+ A+LRE TT+VL++LTP+
Sbjct: 505 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVRPEDAAVLADLREITTKVLSTLTPK 564

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 565 EERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 622


>gi|59801382|ref|YP_208094.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA 1090]
 gi|240014315|ref|ZP_04721228.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI18]
 gi|240016750|ref|ZP_04723290.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA6140]
 gi|240121878|ref|ZP_04734840.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID24-1]
 gi|240123293|ref|ZP_04736249.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID332]
 gi|240125543|ref|ZP_04738429.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-92-679]
 gi|268681916|ref|ZP_06148778.1| RNA polymerase sigma factor [Neisseria gonorrhoeae PID332]
 gi|268684130|ref|ZP_06150992.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-92-679]
 gi|293399243|ref|ZP_06643408.1| RNA polymerase primary sigma factor [Neisseria gonorrhoeae F62]
 gi|59718277|gb|AAW89682.1| putative RNA polymerase sigma factor [Neisseria gonorrhoeae FA
           1090]
 gi|268622200|gb|EEZ54600.1| RNA polymerase sigma factor [Neisseria gonorrhoeae PID332]
 gi|268624414|gb|EEZ56814.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-92-679]
 gi|291610657|gb|EFF39767.1| RNA polymerase primary sigma factor [Neisseria gonorrhoeae F62]
          Length = 642

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/682 (37%), Positives = 387/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGCLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|240115443|ref|ZP_04729505.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID18]
 gi|260440745|ref|ZP_05794561.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 gi|268601118|ref|ZP_06135285.1| RNA polymerase, sigma 70 subunit [Neisseria gonorrhoeae PID18]
 gi|291044060|ref|ZP_06569776.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 gi|268585249|gb|EEZ49925.1| RNA polymerase, sigma 70 subunit [Neisseria gonorrhoeae PID18]
 gi|291012523|gb|EFE04512.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
          Length = 642

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/682 (37%), Positives = 388/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P ++  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSKDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGCLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|240080942|ref|ZP_04725485.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 gi|268597061|ref|ZP_06131228.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 gi|268550849|gb|EEZ45868.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
          Length = 642

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/682 (37%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGCLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADVAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|254469018|ref|ZP_05082424.1| sigma 70 [beta proteobacterium KB13]
 gi|207087828|gb|EDZ65111.1| sigma 70 [beta proteobacterium KB13]
          Length = 658

 Score =  421 bits (1081), Expect = e-115,   Method: Composition-based stats.
 Identities = 245/670 (36%), Positives = 370/670 (55%), Gaps = 47/670 (7%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           +++ +    +   +  K +I L ++RGY+T  E+N  LP +   ++Q+++ ++++ +MGI
Sbjct: 31  DEASNPKEAENRRNQLKALIILGKERGYLTHAEINDHLPDEISETDQVDEIISIIHDMGI 90

Query: 76  NVVDGDDLEDEEGSEDSLD--LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
              D     +    +D+        A+  +       DS    T DPVRMY+REMG + L
Sbjct: 91  RTYDEAPDAENLLMDDAPAPVTDEEAAEEAEQALATVDSEFGRTTDPVRMYMREMGKVGL 150

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L ++ EI IAKRIE G   M+ ++   P     L+   D++  G   + E +D    +  
Sbjct: 151 LDKKEEIEIAKRIEDGLKHMVQAISACPGIIDDLMQMGDKVKAGELSVDEFVDGLIDLEA 210

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           E +     G         EDS  + +     +    + S                     
Sbjct: 211 EKELNEALGMNDEESSNDEDSDDDDDDSSSSDNGKGMSSEDL------------------ 252

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
                                 L  +V+    +I   +++L  L++             +
Sbjct: 253 --------------------KVLTEEVLKRFKKIKSAHKKLALLREKNKWIDD-----PE 287

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLE 372
            K  ++ + K + +   +   +++L +++     +I  +E  ++        + R  F++
Sbjct: 288 YKKHQDVIQKELLNFRFSAKLVEVLCDKVRQFIVQIRSHERTIMDFCVNQAKMPRTQFIK 347

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
              G E    W+       +  +   +     SIL  + ++K +   +GI I  F+ I  
Sbjct: 348 SFPGNETSNKWLKVEMKEDKP-YIANLEKLKHSILDQQAQLKELEDFSGIPIKNFKEINR 406

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +GE  A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 407 QMTRGESRARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 466

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++     +EP P  +
Sbjct: 467 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQATGQEPEPAVL 526

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ MP + +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++P D+A+ ++LR  
Sbjct: 527 AEKMEMPEDKIRKILKISKEPISMETPIGDDEDSHLGDFIEDLGTLTPDDAAVYSSLRNV 586

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T  +L  LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+R
Sbjct: 587 TNEILEGLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 646

Query: 673 SKKLRSFLDG 682
           S +L+SFL+G
Sbjct: 647 SDRLKSFLEG 656


>gi|186472529|ref|YP_001859871.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
 gi|184194861|gb|ACC72825.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
          Length = 664

 Score =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 223/671 (33%), Positives = 344/671 (51%), Gaps = 45/671 (6%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            + +    + +      + +I L R+RGY+T  ++N  LP +   +  ME  V+    MG
Sbjct: 33  QDSALMESLAEERQRQMRALIALGRERGYLTHADINDHLPDNFTETAAMETIVSTFGEMG 92

Query: 75  INVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           ++V +     +         +      A   +       DS    T DPVRMY+REMG+ 
Sbjct: 93  VSVYETAPDAETLLLNDGPSAAASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMGAS 152

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+R GEI IAKRIE G   M+ ++   P     ++   D +  G   + E++D     
Sbjct: 153 ELLTRAGEIEIAKRIEGGLQDMVQAIAMCPSIIATILADVDRVVAGEIRIDELVD----- 207

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                 G    TE          +  +E  +   ++ D +       DD  +        
Sbjct: 208 ------GISDTTEAAELDDDSAEAAAEEELETSASDDDSDDEDGDLSDDGGE-------- 253

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                             +A  +QL    +   + +  ++  +  +         D++ +
Sbjct: 254 ---------------KANAARLEQLTADSLAIFERVRALFASVPDMP------VTDKRRA 292

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
                L+E + + +  +      ID L  ++     ++   E  +L++A     + R+ F
Sbjct: 293 TAIANLRESIQQELTPIRFTAKTIDRLCAEVQAQVAQVRAIERSILQIAVDRCDMPRETF 352

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +E   G E D  W        +  +   +   + +I   + ++  I     + + + + I
Sbjct: 353 VESFPGNETDLDWTMRVAAKSKT-YGPALERHLPAIQSEQQKLVDIEASIALPLQQLKQI 411

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +   E +   AK+EM+EANLRLVIS+AKKY NRG+ FLDLIQEGNIGLMKA +KF++
Sbjct: 412 NKQLGSAESKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEY 471

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WWV+QAITR+IADQ+ TIR+PVHM + I+K+ R  R +  +  +EP P 
Sbjct: 472 RRGWKFSTYATWWVRQAITRAIADQARTIRVPVHMIESINKLNRIQREIVQQTGQEPHPS 531

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A+++ MP   +R +LKI K P SL++P+G++  + LGD IED +A SP D+A+ AN+R
Sbjct: 532 VLAERMDMPEAKIRSILKIAKNPASLDSPVGEDADTTLGDMIEDTSATSPADAAVHANMR 591

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 L +LTPRE +VLRMR+GI   ++ TLEEVG+QF VTRERIRQIE KAIRKL HP
Sbjct: 592 RAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIEGKAIRKLNHP 651

Query: 671 SRSKKLRSFLD 681
           SR+ KLR FL+
Sbjct: 652 SRADKLRPFLE 662


>gi|118594360|ref|ZP_01551707.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440138|gb|EAV46765.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 654

 Score =  420 bits (1078), Expect = e-115,   Method: Composition-based stats.
 Identities = 252/662 (38%), Positives = 376/662 (56%), Gaps = 49/662 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      K +I + ++RGY+T  E+N  LP +   SEQ+E  + ++++MGI V +    
Sbjct: 37  AENRRLQLKALIIMGKERGYLTYAEINDHLPDEVSESEQVEGIIGIINDMGIMVYEQAPD 96

Query: 84  EDEEGSEDSLD--LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            +     D         A+  +       DS    T DPVRMY+REMG+++LL+REGEI 
Sbjct: 97  AESLLMSDDRAPVTDEEAAEEAEQALATVDSEFGRTTDPVRMYMREMGTVDLLTREGEIE 156

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   M+ ++   P     L+   +++      + E +D           G   
Sbjct: 157 IAKRIEDGLRHMVQAISACPGIIDDLMNMAEKVKKEELGVEEFVD-----------GLID 205

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                   K E +  + + ++  E + D   + K S      +                 
Sbjct: 206 MEAERELAKVEAALAQTDDEESDEDDDDENDSGKASGMSAEDL----------------- 248

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                         L  +V+    +I   +++L  L++       +E      K  ++ +
Sbjct: 249 ------------AILTKEVLSRFGKIKRAHKKLSELREQKKWTDDEE-----YKKHQDII 291

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELD 380
           +K + +   +   +++L +++    K+I  +E  ++    +   + R  F++   G E +
Sbjct: 292 LKELINFRFSSKFVEVLCDKVRTFVKQIRGHERAVMEFCVEESKMPRSHFIKSFPGNETN 351

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             W+       + ++   +     SIL  ++++ ++    GI I  F+ I   +  GE  
Sbjct: 352 LKWLKEEIK-SDKKYVESLEKLKHSILDQQSKLIALEELAGIPIKNFKEINRHMTTGEAR 410

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 411 AKRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 470

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++     +EP P E+A+K+ MP 
Sbjct: 471 TWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQSTGQEPEPSELAEKMEMPE 530

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +RK+LKI+KEPIS+ETPIGD++ SHLGDFIED   ++P D+A+  +LR  T+ +L  L
Sbjct: 531 EKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVGTLTPDDAAVYGSLRSVTSEILEGL 590

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS++L+SFL
Sbjct: 591 TPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSERLKSFL 650

Query: 681 DG 682
           +G
Sbjct: 651 EG 652


>gi|68171251|ref|ZP_00544654.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88657966|ref|YP_507558.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
 gi|67999333|gb|EAM85979.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70, non-essential region:Sigma-70 region
           1.2 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88599423|gb|ABD44892.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 622

 Score =  420 bits (1078), Expect = e-115,   Method: Composition-based stats.
 Identities = 267/658 (40%), Positives = 403/658 (61%), Gaps = 40/658 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                +  + ++    ++G+VT  ++N       +SS+ +++T++ML + GINV++  D 
Sbjct: 4   LQTDKELLRTLVSKGLKQGFVTFNDINDVFSDYVLSSDNIDETISMLQDSGINVLEQSDE 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ++     +   +        V     K      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 64  DEANSIIEENRIKDEMDEDDVSDTSIKSWDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+I++ +  M+ SL ESP+  +  + WRD+L +   +LR++IDL+A    E    F    
Sbjct: 124 KKIKSEKVNMLRSLVESPIVLRTFMSWRDDLVNEQIMLRDLIDLDANYRYEFPEKFSDTD 183

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +       +D   E + D                                   + DE+  
Sbjct: 184 DASVLGYDKDLMDEPDEDPDIP------------------------------EDEDEENI 213

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME+ L PKV+  LD +     ++  L+     G+ ++    +   L + + +
Sbjct: 214 SINASILEMENALLPKVVSILDSVIASAEKILELKKQ-YQGKINQDIEKQYNDLHDSIWE 272

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           ++  + L+ S +  + +Q+Y +SK I   E +++ LA+SYGI+R  FL+ +    +    
Sbjct: 273 MIYQIKLSNSAVLSITQQIYSLSKSIAAEEAKIISLAESYGIQRKDFLDAYNTNSV---- 328

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K     +W N +  E  +I+ + ++IK +S E  ++  EF+ +V+ ++K E  A+ 
Sbjct: 329 --LQKKGTSPQWDNMLLNEESNIVSMYSKIKLLSGENNLT--EFKALVTKIQKHERAANQ 384

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 385 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 444

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M +++ REPT EE++ +L + V+ +
Sbjct: 445 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTLEELSARLNINVDKI 504

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P D+A+ A+LRE TT+VL++LTP+
Sbjct: 505 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADLREITTKVLSTLTPK 564

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVGK F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 565 EERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 622


>gi|121591668|ref|ZP_01678905.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 2740-80]
 gi|121546475|gb|EAX56696.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 2740-80]
          Length = 603

 Score =  420 bits (1078), Expect = e-115,   Method: Composition-based stats.
 Identities = 264/639 (41%), Positives = 357/639 (55%), Gaps = 41/639 (6%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF 105
             E+N  LP + V SEQ+ED + M+++MGI VV+     D+    D   +    +  +  
Sbjct: 2   YAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAA 61

Query: 106 LQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
                 +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T 
Sbjct: 62  AALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTI 121

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEGHSYQKREDSSQEKERDDV 223
             ++   D +      L ++I     + P   +      T   S     D + E +    
Sbjct: 122 PYILEQFDRVQAEELRLTDLI--SGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVE 179

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            E E + E     S D   +V   PE A      L                         
Sbjct: 180 DEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------------------------ 215

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                         Q+  +   +  + S +     + ++ +     L   + D LVE L 
Sbjct: 216 -----------GKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLR 264

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               R+   E  +++       + +  F+    G E +  W+       +  +   V  +
Sbjct: 265 TSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLA-SDKPYVAKVREQ 323

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + I +   +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLVIS+AKK
Sbjct: 324 EEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKK 383

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIP
Sbjct: 384 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 443

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD
Sbjct: 444 VHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGD 503

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 504 DEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 563

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 564 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 602


>gi|91762832|ref|ZP_01264797.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718634|gb|EAS85284.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 607

 Score =  419 bits (1077), Expect = e-115,   Method: Composition-based stats.
 Identities = 300/659 (45%), Positives = 415/659 (62%), Gaps = 63/659 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            S+ +++     RG++T +ELN  L    +S E +E     + +  + +V+         
Sbjct: 7   KSFARLMGRGTHRGFITFDELNKSLGKRNLSDENLEQAFMHILDESVALVE--------- 57

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +    +     NSS    K +      +DDP+RMYLREMG +ELLSREGEIAIAKRIEA
Sbjct: 58  KKSDFKVLRKKENSS----KEEGKTIEKSDDPIRMYLREMGGVELLSREGEIAIAKRIEA 113

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G+ +M+ +L +SP+T Q  + W ++L     L+REIID++     +   G          
Sbjct: 114 GKDVMLIALAQSPITAQQFVEWDEKLQSDEILVREIIDIDTNYMEDENTGP--------- 164

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                     E D  +E  G                                D+D+   T
Sbjct: 165 --SAKQRNSGETDKNEENNG--------------------------------DDDEFNPT 190

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK-----VLKEKLVK 323
           L+AME +++PKV+  ++ + + Y +L   Q   ++   +  S    K      +   +++
Sbjct: 191 LAAMETEIKPKVLKTVNTLTKEYAKLIKYQKEKLDCILNAVSFSAAKEKGHDKIVSDILE 250

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
            + SL L+ S ++ LV++ Y  +K+I+  EG LLRLA    I R+ F++ + G E++P+ 
Sbjct: 251 NIKSLQLSPSVLEELVQKHYVENKKIVSLEGNLLRLAMDQKIPRNEFIKFYIGNEINPNL 310

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             +    P   WK F +   D    IR  +  IS + GIS+++++ IVS V+KGE E+ I
Sbjct: 311 KKFLDTNP--MWKQFFSKNKDEFKNIRERLIEISHKLGISVTDYKKIVSRVQKGEKESRI 368

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 428

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+VRT R + ++  RE TPEE+A+KL MP++ V
Sbjct: 429 IRQAITRSIADQARTIRIPVHMIETINKIVRTQRLILSEFGREATPEELAQKLRMPLDKV 488

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI+KEP+SLE P+GDE+ S LGDFIED  A++PL+ AI++NL E TT++L++LTPR
Sbjct: 489 RKVLKISKEPVSLEKPVGDEEDSSLGDFIEDTKALAPLEQAIKSNLSEATTKILSTLTPR 548

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EERVLRMRFG+GMNTDHTLEEVG QF VTRERIRQIEAKA+RKLKHPSRSK+L+SFL+ 
Sbjct: 549 EERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRSKQLKSFLES 607


>gi|121635207|ref|YP_975452.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis FAM18]
 gi|120866913|emb|CAM10672.1| RNA polymerase sigma factor [Neisseria meningitidis FAM18]
          Length = 658

 Score =  419 bits (1077), Expect = e-115,   Method: Composition-based stats.
 Identities = 254/683 (37%), Positives = 387/683 (56%), Gaps = 47/683 (6%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           T+ K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++
Sbjct: 16  TMSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAD 72

Query: 62  QMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           Q+++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DP
Sbjct: 73  QIDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDP 132

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      
Sbjct: 133 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIR 192

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++                                   + + +    + +   +   +
Sbjct: 193 VDEVV-----------------------------------EAIIDPNEVLLNELGLGHLE 217

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    + 
Sbjct: 218 TTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEK 277

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
             +  KD          ++ +   +  +     +ID L   L    + I   E E+  + 
Sbjct: 278 HHSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDIC 331

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                ++RD F++       +  W+          W + +     +IL+ + E+  +  E
Sbjct: 332 LDRVHMERDYFIQNFLPEITNLEWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKE 390

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 391 TRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 450

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 451 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQH 510

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+
Sbjct: 511 LQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVA 570

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQI
Sbjct: 571 PADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQI 630

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HP+RS +LRSFLD 
Sbjct: 631 EAKALRKLRHPTRSDRLRSFLDS 653


>gi|261400701|ref|ZP_05986826.1| RNA polymerase sigma factor RpoD [Neisseria lactamica ATCC 23970]
 gi|269209456|gb|EEZ75911.1| RNA polymerase sigma factor RpoD [Neisseria lactamica ATCC 23970]
          Length = 642

 Score =  419 bits (1076), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/682 (37%), Positives = 387/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDTRPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                                    + +   +   + 
Sbjct: 178 DEVV--EAIIDPN---------------------------------EVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W N +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSNALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|262276866|ref|ZP_06054659.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
 gi|262223969|gb|EEY74428.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
          Length = 613

 Score =  419 bits (1076), Expect = e-114,   Method: Composition-based stats.
 Identities = 300/659 (45%), Positives = 422/659 (64%), Gaps = 57/659 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            S++++++    RG++T EEL   L     + E ++  +  + +  I +V        + 
Sbjct: 7   KSFERLVEKGLNRGFITYEELQKSLGKRNSNVESLDTALVHIFDQAITLVQNKSDFKVKK 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E      +                   +DDP+RMYLREMG +ELLSREGE AIAKRIE+
Sbjct: 67  QESETAKQTKTVE--------------RSDDPIRMYLREMGGVELLSREGETAIAKRIES 112

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           GR +M++SL ESP+T + +  W ++L +   L+R+IIDL+     + K       +    
Sbjct: 113 GRYVMISSLSESPITAKKIFDWEEKLINNEMLVRDIIDLDTNFIDDEKLAKSIKEKSKKE 172

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            K ++ + + E +D  E                                    +D+   +
Sbjct: 173 AKEKNPNIDTESEDSNE------------------------------------DDEFNIS 196

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA-----VNGQKDEKSSVKCKVLKEKLVK 323
           L+++E +L+PK++ A   I + Y++L S Q +       N    +      + +K+++++
Sbjct: 197 LASLEIELKPKILEAFSRITKNYKKLISYQRDKLECVLKNQALSDSKKKSYEKVKKEIME 256

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
            +  L LNQ   + LV   Y  +K+I+  +GEL+R A  +GI RD F++ + G EL+P++
Sbjct: 257 ELLKLQLNQVTQEDLVALNYAENKKILSYDGELMRAANKHGISRDDFIKFYVGNELNPNF 316

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             +  +  E  W  F   E      +++++  +S   G+SIS+FR +V+ ++KGE E+ I
Sbjct: 317 EKFLSE--EKSWLAFFTKEKKLFANLKDKLIELSDNIGMSISDFRILVNKIKKGERESRI 374

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 375 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSIADQ+ TIRIPVHM + I+K+VRT R+M ++  REPTPEE++KKLAMP+E V
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKIVRTQRQMMSEFGREPTPEELSKKLAMPLEKV 494

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEP+SLETP+GDE+ S LGDFIED NA+ P+D+A+Q  L+ TTT+VLASLTPR
Sbjct: 495 RKVLKIAKEPVSLETPVGDEEDSTLGDFIEDSNALIPVDAAVQTALKNTTTKVLASLTPR 554

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS++L+SFLD 
Sbjct: 555 EERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRQLKSFLDN 613


>gi|254672481|emb|CBA05947.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha275]
          Length = 642

 Score =  418 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 253/682 (37%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDTRPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W + +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLEWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|313668077|ref|YP_004048361.1| RNA polymerase sigma factor [Neisseria lactamica ST-640]
 gi|313005539|emb|CBN86975.1| RNA polymerase sigma factor [Neisseria lactamica 020-06]
          Length = 642

 Score =  418 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 253/682 (37%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W + +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|88607510|ref|YP_505167.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
 gi|88598573|gb|ABD44043.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
          Length = 627

 Score =  418 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 276/658 (41%), Positives = 408/658 (62%), Gaps = 39/658 (5%)

Query: 26  FSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDL 83
              +  + +I    +Q G VT ++LN  L  DEV +S+ +++T++ML + GI+V++  D+
Sbjct: 6   MDKELVRSLITKGIKQGGIVTFDDLNDALSDDEVVTSDSIDETISMLQDSGISVLEQSDV 65

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +D + +     +     + +      +      TDDP+RMYL EM S+ELLSREGEI IA
Sbjct: 66  DDTDDTVTGESVVKDEEDEA----SIRSWDFGQTDDPIRMYLCEMSSVELLSREGEIEIA 121

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRI++ +  M+  + E+PL  +  + WRD+L +   LLR++IDL+A          F   
Sbjct: 122 KRIKSEKVNMLRCMVEAPLVLRTFMSWRDDLVNQQVLLRDLIDLDANYRCGFPQPGFGEG 181

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +G  Y            D                       D  PE++ +DE + D++  
Sbjct: 182 DGEEYGVGRGDVVLPPDD----------------------GDVDPESSLDDEADEDDESS 219

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
               ++  ME  L PKV+  LD   E   ++  ++    +G   E        L + + +
Sbjct: 220 LGNASILEMESALLPKVISILDSTIEAAEKILEMKKKKRDG--GEYDENAYNELHDSIWE 277

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           +V  + L+ S +  + +Q+Y +SK I   E  L+ LA+SYG+ R  FL+ +    +    
Sbjct: 278 MVSQMKLSDSAVASVTQQIYALSKSIAAEESSLISLAESYGVDRKSFLDAYNNNTI---- 333

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               +     EW+N +  E D++L+++N +K +S E       F+ +V+ ++K E  A+ 
Sbjct: 334 --AEQAKTSFEWQNLLDKEGDTLLEMQNRVKLLSGED--CPGSFKALVAKIQKHERTANR 389

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+EM++ANLRLV+S+AKKY+NRGLQFLDL+QEGNIGLMKA +KFD+  GYKFSTYA WW
Sbjct: 390 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 449

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IADQ+ TIRIPVHM + ++K+ RT R+M ++I REPT EE++ +L + VE +
Sbjct: 450 VRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNINVEKI 509

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKV+KI K+P+SLE+PIGD+D+S  GD IEDK AV P ++A+ A+LRE TT+VL++LTP+
Sbjct: 510 RKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLSTLTPK 569

Query: 624 EERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EER+LRMRFGIG    DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR++KLR F 
Sbjct: 570 EERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLRGFF 627


>gi|309378741|emb|CBX22691.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 642

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 253/682 (37%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDAHPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W + +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMERET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|329120411|ref|ZP_08249077.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327462095|gb|EGF08423.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 649

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 253/683 (37%), Positives = 369/683 (54%), Gaps = 41/683 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  + +     E ED +  L  +      + +I   ++RGY+T  E+N  LP D   +EQ
Sbjct: 1   MSNQPDNQDYEEQEDGNRPLTPEEQRQRLRLLILQGKERGYITYAEINDALPDDMSDAEQ 60

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDP 120
           +++ V M+  +GI V +     D     D+        A   +       DS    T DP
Sbjct: 61  IDNIVNMIQGLGIQVTEEAPDADTLLMNDTGTGMTDDDAVEEAEAALSNADSEFGRTTDP 120

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++  G   
Sbjct: 121 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMIQAISACPGSIAEILGLIEQVRSGEIK 180

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++  EA + P        G              ++  ++  + +GD E  A   + D
Sbjct: 181 VDEVV--EAILDPNEVLMHELGVSDLEVIPPGSRPSDRAAEEENDEDGDEEDGASSEEID 238

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           R  +                             ++L+  V+     I+E Y  +      
Sbjct: 239 RINL-----------------------------EELKQDVLAHFAGISENYGLMVEALQA 269

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
             +   D          ++ +   +  +     +I+ L   L      I   E E+  + 
Sbjct: 270 KGSKHPD------YLKHRDAIAHKLLEVRFATRQIENLSGSLRQKVDNIRKLEREIRDIC 323

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                + RD F+ +      D  W+          W + +     +IL+ + E+  +   
Sbjct: 324 LDRVQMDRDYFIAQFLPNITDLGWLEGEIAR-RRVWGDALERFRHAILEKQTEVAEMEKS 382

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             ISI E + I   ++  E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 383 AQISIEELKEINKNMQNSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 442

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 443 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 502

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   +P   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+
Sbjct: 503 LQEHGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVA 562

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+ ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 563 PAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 622

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HP+RS +L+SFLD 
Sbjct: 623 EAKALRKLRHPTRSDRLKSFLDS 645


>gi|261855081|ref|YP_003262364.1| RNA polymerase, sigma 70 subunit, RpoD [Halothiobacillus
           neapolitanus c2]
 gi|261835550|gb|ACX95317.1| RNA polymerase, sigma 70 subunit, RpoD [Halothiobacillus
           neapolitanus c2]
          Length = 608

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 271/663 (40%), Positives = 398/663 (60%), Gaps = 63/663 (9%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +++    S K +I   R++GY+T  E++  LP   V ++Q+ED + M+  MGI+V +   
Sbjct: 1   MYEDQQASIKSLIARGREQGYLTYAEISDHLPEALVDADQIEDIIGMIQEMGISVSEVAP 60

Query: 83  LEDEEGSEDSLDLASSA---SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D+ G  D    AS       +   L  + D+    T DPVRMY+REMG+++LL+R+GE
Sbjct: 61  DGDDLGLADESRAASDEDATEEAVAVLASQVDAEFGRTTDPVRMYMREMGTVDLLNRQGE 120

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I IAKRIE G   +  +L   P T + L+     +  G   ++++I              
Sbjct: 121 IEIAKRIEEGLIDVTRALAFYPPTIETLLEHYARIEAGDLRMQDVI-------------- 166

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                                       G IE   ++ +D   K     E   ++  + D
Sbjct: 167 ---------------------------VGIIEPEVEIPEDAEEKPLDVAEGKASNTDDED 199

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           EDE+D     + +++ L P+++               ++   +    DE+S      L +
Sbjct: 200 EDEEDDTEEEAVVDNTLDPELVRT-----------HLMEIKRLAENLDERSPEYLASLAD 248

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRE 378
           +LV     L LN +  + L+EQ+     RI   E +++ +     G+KR+ F+E  +  E
Sbjct: 249 QLV----QLKLNPAFNEKLLEQIRQAIARIRLLEKQIMHQAVDKGGLKRETFIEAFRSNE 304

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            D  WV  A    +G+     +     I +++  + +++ ++ +++++ R +  ++  GE
Sbjct: 305 SDIGWVKVA---TKGKPTAKFSQVQPEIERLQKRLNTVARDSKLTVAQTREVHRLITLGE 361

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +A  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 362 AKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 421

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE TPEE+A+++ +
Sbjct: 422 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMDL 481

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIG++D S+LGDFIED++A+SP+DSA  A+L E    +LA
Sbjct: 482 PEDKIRKVLKIAKEPISMETPIGEDDDSNLGDFIEDQSAISPMDSATNASLSEIVREILA 541

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLTPRE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRS
Sbjct: 542 SLTPREAKVLMMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSERLRS 601

Query: 679 FLD 681
           F++
Sbjct: 602 FIE 604


>gi|307824736|ref|ZP_07654959.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
 gi|307734094|gb|EFO04948.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
          Length = 602

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 257/652 (39%), Positives = 354/652 (54%), Gaps = 66/652 (10%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   + +GY+T  E+N  LP D V  EQ+ED + M+++MGI V +    ED   ++ + 
Sbjct: 13  LIAKGKVQGYLTYAEVNDHLPSDIVDPEQIEDIIGMINDMGIQVYEVAPDEDSLITDSAA 72

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                     V      DS    T DPVRMY+REMGS+ELL+R  E+ IAKRIE G+  +
Sbjct: 73  VTTDDEDAEEVAALASVDSEFGRTTDPVRMYMREMGSVELLTRADELKIAKRIEEGQQQL 132

Query: 154 MASLCESPLTFQALIIWRDEL--NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           + ++  S +  +  +   D +   +G   L ++I                          
Sbjct: 133 VKAIARSCIVVEDFLQSFDNISGEEGGIRLTDLI-------------------------- 166

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                           G ++ +          V    E    +E     + ++    + A
Sbjct: 167 ---------------SGFVDLSEPEDFVTALPVSEDVEETPAEEEPKGLNYEEVKEKVEA 211

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           +  QL+                           +K   S+ K     E L  L       
Sbjct: 212 LRKQLKTAAAAI---------------------KKHGYSNDKTDKEFEALADLFMEFKWT 250

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVSYAKDF 390
              +  L   + +    +   E  ++ +  +Y  + R  F+      E    W     + 
Sbjct: 251 PQYLKKLTAIIPNGVTAVREQEKLIMDICINYAKMPRKEFIASFPEHETSSEWFDQYLNA 310

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
                +     E + + K +  +  I  E G++IS  + I   +  GE +A  AKKEM+E
Sbjct: 311 GSKYSETLKEREKE-VRKAQKILADIEAEYGLTISGLKDINRRMSIGEAKARRAKKEMIE 369

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 370 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 429

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE TPEE+A+++ MP + VRKVLKI 
Sbjct: 430 SIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAERMEMPEDKVRKVLKIA 489

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ SHLGDFIED   +SP+++A  A LRE+T  VLA LT RE +VLRM
Sbjct: 490 KEPISMETPIGDDEDSHLGDFIEDAKVLSPVEAATIAGLRESTQNVLAGLTAREAKVLRM 549

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LR FLDG
Sbjct: 550 RFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRCFLDG 601


>gi|161870399|ref|YP_001599571.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 053442]
 gi|218768518|ref|YP_002343030.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis Z2491]
 gi|254805303|ref|YP_003083524.1| RNA polymerase sigma factor [Neisseria meningitidis alpha14]
 gi|304387052|ref|ZP_07369304.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           meningitidis ATCC 13091]
 gi|121052526|emb|CAM08865.1| RNA polymerase sigma factor [Neisseria meningitidis Z2491]
 gi|161595952|gb|ABX73612.1| RNA polymerase primary sigma factor [Neisseria meningitidis 053442]
 gi|254668845|emb|CBA06900.1| RNA polymerase sigma factor [Neisseria meningitidis alpha14]
 gi|254669783|emb|CBA04064.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha153]
 gi|304338851|gb|EFM04953.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           meningitidis ATCC 13091]
 gi|308389681|gb|ADO32001.1| RNA polymerase sigma factor [Neisseria meningitidis alpha710]
 gi|319410767|emb|CBY91151.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
           WUE 2594]
 gi|325128589|gb|EGC51459.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis N1568]
 gi|325132679|gb|EGC55363.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M6190]
 gi|325134647|gb|EGC57287.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M13399]
 gi|325136570|gb|EGC59171.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M0579]
 gi|325138535|gb|EGC61098.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis ES14902]
 gi|325204514|gb|ADY99967.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M01-240355]
          Length = 642

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 253/682 (37%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSKNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W + +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLEWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|171464016|ref|YP_001798129.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|171193554|gb|ACB44515.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 900

 Score =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 237/680 (34%), Positives = 369/680 (54%), Gaps = 50/680 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K++    +   +        +      K +IK+   +GY+T  E+N  +  +   ++ 
Sbjct: 268 KAKEKALLKEFAAQQLGTEEQQELRRARLKTLIKMGMSKGYLTQGEMNDVMSDELSDADA 327

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E  +++L+++GI V +     +     D+   A+S   +   L    DS    T DPVR
Sbjct: 328 LETLISLLNDIGITVYEQAPDAETLILSDNTAAAASEEEAEAALSTV-DSEFGRTTDPVR 386

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG+++LL+REGEI IAK+IEAG   M+ +L   P+T   ++   D++  G   + 
Sbjct: 387 MYMREMGTVDLLTREGEIVIAKKIEAGLKDMVMALAACPVTIAEILSNVDKIASGEIEID 446

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           + +D                                         G ++  A+  K    
Sbjct: 447 QFVD-----------------------------------------GLVDPNAEDIKLGPE 465

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           + +  P+  E +E   DE    +A   +   ++L+   +     +    +++R   D   
Sbjct: 466 EPEVDPDAEEGEEDGEDEGGGGAATANAKQLEELKQISLEKFAIVRAQAKKMRRAFD--- 522

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQ 361
              KD  +       ++ +   +    L    ++ L + +     ++   E  ++  L  
Sbjct: 523 ---KDGYNCPAYIKAQDAIRAELLGFRLTAKSVEKLCDTMRSQVDQVWKLERGIVSLLVD 579

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
             G+ R   L+      ++  W        +  +   +   V +I +++ ++  I     
Sbjct: 580 KVGVNRGEVLKDFPKMSMNLAWTDKLLKENKP-YSALLQRNVPAIQELQQKLIDIQKNVV 638

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           I + E + +   +  GE  A  AK+EM  ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 639 IPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 698

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 699 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 758

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP    +A K+ +P + +RK++KI KEP+S+ETPIGD++ SHLGDFIED N ++P 
Sbjct: 759 ETGHEPDAATLALKMEIPEDKIRKIMKIAKEPVSMETPIGDDEDSHLGDFIEDGNTLAPA 818

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++A+  ++R+    VL SLTPRE +VLRMRFG+ M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 819 EAALHNSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEA 878

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RK++HPSRS KL++FL+
Sbjct: 879 KALRKMRHPSRSDKLKTFLE 898


>gi|325130608|gb|EGC53353.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           OX99.30304]
 gi|325142722|gb|EGC65100.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis 961-5945]
 gi|325198658|gb|ADY94114.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis G2136]
 gi|325201773|gb|ADY97227.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M01-240149]
 gi|325208475|gb|ADZ03927.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NZ-05/33]
          Length = 642

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 252/682 (36%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + + +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSRNQNHE---EYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W + +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLEWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|15677390|ref|NP_274545.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 gi|7226783|gb|AAF41893.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 gi|261392218|emb|CAX49733.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
           8013]
 gi|316985995|gb|EFV64932.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|325140674|gb|EGC63190.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis CU385]
 gi|325144806|gb|EGC67096.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M01-240013]
 gi|325199861|gb|ADY95316.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|325205715|gb|ADZ01168.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis
           M04-240196]
          Length = 642

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 252/682 (36%), Positives = 386/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + + +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSRNQNHE---EYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +ID L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  W+          W + +     +IL+ + E+  +  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLEWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|225076460|ref|ZP_03719659.1| hypothetical protein NEIFLAOT_01506 [Neisseria flavescens
           NRL30031/H210]
 gi|224952139|gb|EEG33348.1| hypothetical protein NEIFLAOT_01506 [Neisseria flavescens
           NRL30031/H210]
          Length = 650

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 259/683 (37%), Positives = 382/683 (55%), Gaps = 41/683 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N + + + +D +  L  +      +++I + ++RGY+T  E+N  LP D   +EQ
Sbjct: 1   MSKNQNYE-EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQ 59

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDP 120
           +++ V+M+S +GI V +     ++    D+        A   +       DS    T DP
Sbjct: 60  IDNIVSMISGLGIQVTEQAPDAEDILLSDNAAAMTDDDAVEEAEAALSSADSEFGRTTDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    
Sbjct: 120 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIR 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++  EA I P        G                                + +K D
Sbjct: 180 VDEVV--EAIIDPNEVLLNELGL----------------------------GHLENAKPD 209

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             + ++  ++ + D+ + D+   DS    +A   +L+ KV+     I   Y ++      
Sbjct: 210 DEEGETVSDDEDGDDEDEDDSSSDSDAMSAAHLAELKQKVLEHFAFIESEYGKMIKQ--- 266

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               +K           ++ +   +  +     +I+ L   L    + I   E E+  + 
Sbjct: 267 ---LEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREIRDIC 323

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                + RD F++       D  WV          W N +     +IL+ + E+ ++  E
Sbjct: 324 IDRVRMDRDYFIKNFLPAITDLEWVEEEVA-KGCVWANALDRFRHAILEKQTELANMEAE 382

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ISI E + I   +   E E S AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 383 TRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 442

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 443 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 502

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+
Sbjct: 503 LQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVA 562

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 563 PAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 622

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HP+RS +LRSFLD 
Sbjct: 623 EAKALRKLRHPTRSDRLRSFLDS 645


>gi|71082746|ref|YP_265465.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71061859|gb|AAZ20862.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 595

 Score =  416 bits (1068), Expect = e-114,   Method: Composition-based stats.
 Identities = 299/653 (45%), Positives = 411/653 (62%), Gaps = 63/653 (9%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           +     RG++T +ELN  L    +S E +E     + +  + +V+          +    
Sbjct: 1   MGRGTHRGFITFDELNKSLGKRNLSDENLEQAFMHILDESVALVE---------KKSDFK 51

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           +     NSS    K +      +DDP+RMYLREMG +ELLSREGEIAIAKRIEAG+ +M+
Sbjct: 52  VLRKKENSS----KEEGKTIEKSDDPIRMYLREMGGVELLSREGEIAIAKRIEAGKDVML 107

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            +L +SP+T Q  + W ++L     L+REIID++     +   G                
Sbjct: 108 IALAQSPITAQQFVEWDEKLQSDEILVREIIDIDTNYMEDENTGP-----------SAKQ 156

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
               E D  +E  G                                D+D+   TL+AME 
Sbjct: 157 RNSGETDKNEENNG--------------------------------DDDEFNPTLAAMET 184

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK-----VLKEKLVKLVGSLS 329
           +++PKV+  ++ + + Y +L   Q   ++   +  S    K      +   +++ + SL 
Sbjct: 185 EIKPKVLKTVNTLTKEYAKLIKYQKEKLDCILNAVSFSAAKEKGHDKIVSDILENIKSLQ 244

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           L+ S ++ LV++ Y  +K+I+  EG LLRLA    I R+ F++ + G E++P+   +   
Sbjct: 245 LSPSVLEELVQKHYVENKKIVSLEGNLLRLAMDQKIPRNEFIKFYIGNEINPNLKKFLDT 304

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            P   WK F +   D    IR  +  IS + GIS+++++ IVS V+KGE E+ IAKKEMV
Sbjct: 305 NP--MWKQFFSKNKDEFKNIRERLIEISHKLGISVTDYKKIVSRVQKGEKESRIAKKEMV 362

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 363 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 422

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+VRT R + ++  RE TPEE+A+KL MP++ VRKVLKI
Sbjct: 423 RSIADQARTIRIPVHMIETINKIVRTQRLILSEFGREATPEELAQKLRMPLDKVRKVLKI 482

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +KEP+SLE P+GDE+ S LGDFIED  A++PL+ AI++NL E TT++L++LTPREERVLR
Sbjct: 483 SKEPVSLEKPVGDEEDSSLGDFIEDTKALAPLEQAIKSNLSEATTKILSTLTPREERVLR 542

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFG+GMNTDHTLEEVG QF VTRERIRQIEAKA+RKLKHPSRSK+L+SFL+ 
Sbjct: 543 MRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRSKQLKSFLES 595


>gi|261377614|ref|ZP_05982187.1| RNA polymerase sigma factor RpoD [Neisseria cinerea ATCC 14685]
 gi|269146367|gb|EEZ72785.1| RNA polymerase sigma factor RpoD [Neisseria cinerea ATCC 14685]
          Length = 642

 Score =  416 bits (1068), Expect = e-114,   Method: Composition-based stats.
 Identities = 253/682 (37%), Positives = 387/682 (56%), Gaps = 47/682 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + + +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSRNQNHE---EYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHTPDAEDILLSDNAAVTDDDAVEEAEAALSNADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILGLIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLEN 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  + + + +E E D+    +A   +L+ KV+    +I + Y+++ S  +  
Sbjct: 203 TAHEEPANDDPDADEDDEESEGDADAISAANLAELKQKVIDHFAQIEKDYKKMISRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
            +  KD          ++ +   +  +     +I+ L   L    + I   E E+  +  
Sbjct: 263 HSRHKD------YLAYRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRDICL 316

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  WV          W + +     +IL+ + E+ ++  ET
Sbjct: 317 DRVHMERDYFIQNFLPEITNLQWVEEEVA-KGRVWSDALDRFRHAILEKQTELANMERET 375

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 376 RISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 435

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 436 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHL 495

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P
Sbjct: 496 QETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNIAP 555

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 556 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 615

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 616 AKALRKLRHPTRSDRLRSFLDS 637


>gi|91779751|ref|YP_554959.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692411|gb|ABE35609.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 647

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 226/671 (33%), Positives = 359/671 (53%), Gaps = 50/671 (7%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            ++S      +      K +IKL  +RG+V   E++  LP      + +E+ V   S MG
Sbjct: 21  QDESGKENENESGRADLKALIKLGTERGFVIRGEISDCLPERLAQPDAIENVVRAFSEMG 80

Query: 75  INVVDGDDLEDEEGSED---SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           I V +     +     D   ++         +V      D+    T DPVRMY+REMG+ 
Sbjct: 81  IAVFEQAPDAESMIMNDHPAAVATDEQIEEEAVTAISSVDAEFGRTTDPVRMYMREMGTT 140

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+R+GEIA+A+RIE GR  M+ ++   P T   ++   D +  G T + E +D    +
Sbjct: 141 ELLTRQGEIALAQRIEEGRNGMIRAISSCPATIAEILAIADGVACGETAIDEFVD--GLV 198

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P +                         DD+     D   A  +  DD+   D     A
Sbjct: 199 DPAATA----------------------TDDMIAVPEDSLGATPMFDDDQGDEDDDGAEA 236

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
           E  +++++                L+   +    ++A+ + +LR   +    G      S
Sbjct: 237 EPADQHIET---------------LKHDALAKFAKVADWFSQLRDAYETQGYG------S 275

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
            + +  +  +   + ++      I+ L   L   +  +   E E+ R+A +  G+ RD F
Sbjct: 276 ARYRAAQAAIEAELMTIRFTARTIERLCGALRLSADEVRTIEREIARIAVERCGVPRDTF 335

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +   +G E DP W +         + + +   + +I   + ++ ++     + + EFR +
Sbjct: 336 IAHFRGNETDPAW-ARQLAAAGQPFSSVLERNLPAIGLEQEKLLALQKRVVLPLDEFREV 394

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +   E +   AK EM+EANLRLVIS+AK+YTNRGL FLDLIQEGNIGLM+A +KF++
Sbjct: 395 CRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNRGLLFLDLIQEGNIGLMRAVDKFEY 454

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QA++RSIADQ+ TIR+PVHM + ++K+ R +R++  +   EP   
Sbjct: 455 RRGYKFSTYATWWIRQAVSRSIADQARTIRVPVHMIESLNKLKRISRKILQETGNEPDAA 514

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +A+ + M  + VR +L+I KEP+SL+  +G+ D + +GD IED  A+ P D+A+ A +R
Sbjct: 515 LLAQLMEMQEQKVRAMLRIVKEPVSLDASVGENDDTSIGDLIEDSAAILPDDAALHAGMR 574

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +  +  L +LTPRE ++LR+RFGI  + DHTLEE+G+QF +TRERIRQIE KA+RKL+HP
Sbjct: 575 DAISEALMTLTPREAKILRLRFGIESSRDHTLEELGEQFELTRERIRQIEVKALRKLRHP 634

Query: 671 SRSKKLRSFLD 681
           +RS +L+SFLD
Sbjct: 635 ARSARLKSFLD 645


>gi|261380693|ref|ZP_05985266.1| RNA polymerase sigma factor RpoD [Neisseria subflava NJ9703]
 gi|284796404|gb|EFC51751.1| RNA polymerase sigma factor RpoD [Neisseria subflava NJ9703]
          Length = 650

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 261/683 (38%), Positives = 384/683 (56%), Gaps = 41/683 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N + + + +D +  L  +      +++I + ++RGY+T  E+N  LP D   +EQ
Sbjct: 1   MSKNQNYE-EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQ 59

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDP 120
           +++ V+M+S +GI V +     ++    D+        A   +       DS    T DP
Sbjct: 60  IDNIVSMISGLGIQVTEQAPDAEDILLSDNAAAMTDDDAVEEAEAALSSADSEFGRTTDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    
Sbjct: 120 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIR 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++  EA I P        G                                + +K D
Sbjct: 180 VDEVV--EAIIDPNEVLLNELGL----------------------------GHLENAKPD 209

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             + ++  ++ + DE + D+  +DS    +A   +L+ KV+     I   Y ++      
Sbjct: 210 DEEGETDSDDEDGDEEDEDDSGNDSEAISAAHLAELKQKVLEHFAFIESEYGKMIKQ--- 266

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               +K           ++ +   +  +     +I+ L   L    + I   E E+  + 
Sbjct: 267 ---LEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREIRDIC 323

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                ++RD F+E       D  WV          W N +     +IL+ + E+ ++  E
Sbjct: 324 IDRVRMERDYFIENFLPAITDLEWVEKEVA-KGRVWANALDRFRHAILEKQAELANMETE 382

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ISI E + I   +   E E S AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 383 TRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 442

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 443 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 502

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+
Sbjct: 503 LQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVA 562

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 563 PAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 622

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HP+RS +LRSFLD 
Sbjct: 623 EAKALRKLRHPTRSDRLRSFLDS 645


>gi|323144090|ref|ZP_08078731.1| RNA polymerase sigma factor RpoD [Succinatimonas hippei YIT 12066]
 gi|322416132|gb|EFY06825.1| RNA polymerase sigma factor RpoD [Succinatimonas hippei YIT 12066]
          Length = 648

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 270/664 (40%), Positives = 386/664 (58%), Gaps = 26/664 (3%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + +   +K++I   +++GY+TIEE+N  +PPD +S +Q+   +    +MGINV +     
Sbjct: 4   NSASTEFKQLIARGKEQGYLTIEEINDLIPPDIISGDQLSVFIQTFIDMGINVCETPPDP 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D+    DS   A+     +V  Q         T DPVRMY+REMG++ LL+R+ EI I+K
Sbjct: 64  DDILLSDSSQ-AAEEDVETVANQLDSTVDIGRTTDPVRMYMREMGNVSLLTRKDEIEISK 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELN--DGTTLLREIIDLEACIGPESKGGFFHG 202
           RIE G   +   + E PL  + L    DE    D    L +I+            GF   
Sbjct: 123 RIERGTNDVQMCIVEYPLAMEELFRRYDEALAPDSEIRLGDIV-----------VGFSEP 171

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
           ++       +DS +    +D+++   + ESA     D + +     +  +  +   D D 
Sbjct: 172 SKEEINIDIDDSVE--TEEDIEKLIDEEESAEVQLDDVKEENTGKAKKGKKSKVEDDPDS 229

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN--AVNGQKDEKSSVKCKVLKEK 320
           D+     SA +    P      + + + + ELR   +   A + +K   +  K K   +K
Sbjct: 230 DEDEDEDSASQADSGPDP----ELVKQKFTELRIQYEKVVAAHAKKGSAAVKKYKQELQK 285

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQG--R 377
           L ++  +  L    +D L+ +++D+  R+ + +  +  +A +  G+K D     +     
Sbjct: 286 LSEMFSTFRLVPQVLDSLLRKMHDMMDRVKNQDHRIREVAVNICGMKLDELKAFYTDSEH 345

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D  W   A    +  +   +      I +  N +K +  E+GISI+  R +   V  G
Sbjct: 346 ESDMSWFDKALK-SKRPYVARLKDYRPVIEECVNALKEVETESGISIARLRDLSRRVMMG 404

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 405 DAMAKKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 464

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  REPTPEE+A+K+ 
Sbjct: 465 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEKGREPTPEELAEKMG 524

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P + +RKV+KI KEPISLETP+GD+D SHLGDFIED + V P ++A   +L+     VL
Sbjct: 525 LPEDKIRKVMKIAKEPISLETPVGDDDDSHLGDFIEDSSIVVPAEAATSESLKNAINNVL 584

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             + PRE +VLRMRFGIGM +DHTLEEVG+QF VTRERIRQIEAKA+RKL+HP RS  LR
Sbjct: 585 DEMPPREAQVLRMRFGIGMPSDHTLEEVGRQFGVTRERIRQIEAKALRKLRHPCRSAGLR 644

Query: 678 SFLD 681
            FLD
Sbjct: 645 GFLD 648


>gi|241760450|ref|ZP_04758543.1| RNA polymerase sigma factor RpoD [Neisseria flavescens SK114]
 gi|241318954|gb|EER55456.1| RNA polymerase sigma factor RpoD [Neisseria flavescens SK114]
          Length = 650

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 259/683 (37%), Positives = 382/683 (55%), Gaps = 41/683 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N + + + +D +  L  +      +++I + ++RGY+T  E+N  LP D   +EQ
Sbjct: 1   MSKNQNYE-EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQ 59

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDP 120
           +++ V+M+S +GI V +     ++    D+        A   +       DS    T DP
Sbjct: 60  IDNIVSMISGLGIQVTEQAPDAEDILLSDNAAAMTDDDAVEEAEAALSSADSEFGRTTDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    
Sbjct: 120 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIR 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++  EA I P        G                                + +K D
Sbjct: 180 VDEVV--EAIIDPNEVLLNELGL----------------------------GHLENAKPD 209

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             + ++  ++ + D+ + D    DS    +A   +L+ KV+     I   Y ++      
Sbjct: 210 NEEGETDSDDEDGDDEDEDGSGSDSEAISAAHLAELKQKVLEHFAFIESEYGKMIKQ--- 266

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               +K           ++ +   +  +     +I+ L   L    + I   E E+  + 
Sbjct: 267 ---LEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREIRDIC 323

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                ++RD F++       D  WV          W N +     +IL+ + E+ ++  E
Sbjct: 324 IDRVRMERDYFIKNFLPAITDLKWVEEEVA-KGRVWANALDRFRHAILEKQTELANMEAE 382

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ISI E + I   +   E E S AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 383 TRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 442

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 443 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 502

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+
Sbjct: 503 LQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVA 562

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 563 PAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 622

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HP+RS +LRSFLD 
Sbjct: 623 EAKALRKLRHPTRSDRLRSFLDS 645


>gi|298369314|ref|ZP_06980632.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298283317|gb|EFI24804.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 648

 Score =  415 bits (1065), Expect = e-113,   Method: Composition-based stats.
 Identities = 256/679 (37%), Positives = 374/679 (55%), Gaps = 40/679 (5%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
                +   +D +  L  +      +++I + ++RGY+T  E+N  LP D   ++Q+++ 
Sbjct: 2   SKHTDEYHDQDDNRPLTVEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNI 61

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           V+M+S +GI V +     ++    D+        A   +       DS    T DPVRMY
Sbjct: 62  VSMISGLGIQVTEQAPDAEDILLSDNAATITDDDAVEEAEAALSSADSEFGRTTDPVRMY 121

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    + E+
Sbjct: 122 MREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSVAEILALIEQVRNDEIRVDEV 181

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           +  EA I P        G          D + + +                         
Sbjct: 182 V--EAIIDPNEVLLNELGLGHLENNASADDNNDSDN------------------------ 215

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
               EN +  + + D+  +DS    +A  ++L+ KV+    +I   Y ++          
Sbjct: 216 ----ENDDESDDDEDDGNNDSDALSAANLEELKQKVLEHFVQIETAYTKMIEQ------L 265

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
            K           ++ +   +  +     +I+ L   L +    I   E E+  +     
Sbjct: 266 TKHHSRHAAYLEHRDAIASKLLEVRFATRQIESLSGSLRNRVDNIRKLEREIRDICLDRV 325

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + RD F+        D +W+       E  W   +     +IL+ + E+  +  ET IS
Sbjct: 326 HMDRDYFIRNFLPVITDLNWLENEIA-KENAWSGALDRFRHAILEKQTELAEMEKETRIS 384

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 385 IGELKDINKNMVISEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 444

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 445 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQET 504

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+
Sbjct: 505 GEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDINNVAPADA 564

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+ ++L E T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 565 AMYSSLHEVTKEVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 624

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS +LRSFLD 
Sbjct: 625 LRKLRHPTRSDRLRSFLDS 643


>gi|325266676|ref|ZP_08133353.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella
           denitrificans ATCC 33394]
 gi|324982119|gb|EGC17754.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella
           denitrificans ATCC 33394]
          Length = 671

 Score =  415 bits (1065), Expect = e-113,   Method: Composition-based stats.
 Identities = 253/677 (37%), Positives = 368/677 (54%), Gaps = 41/677 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            +   +  + +  L  +   +  +++I   ++RGY+T  E+N  LP D   +E ++  V 
Sbjct: 29  DNETEDQLNDNRPLSPEEQRERLRRLILQGKERGYITYAEINDALPDDMSDAEHIDGVVN 88

Query: 69  MLSNMGINVVDGDDLEDEEGSED--SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           M+  +GI V +     D     D  S      A   +     + DS    T DPVRMY+R
Sbjct: 89  MIQGLGIQVTEEAPDADTLLMSDNSSAMTDEDAVAEAEAALSQADSEFGRTTDPVRMYMR 148

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG +ELL+RE EI IAK IE     M+ ++   P +   ++   D++      + E++ 
Sbjct: 149 EMGQVELLTREDEIKIAKEIENALKNMIQAISACPGSVGEILALIDQVKKDEIRVDEVV- 207

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
            EA I P        G           + +    +D ++   D E A   S + +  +  
Sbjct: 208 -EAIIDPNEVLLNELGLGHLENNSAHPAEESDGGEDDEDGGEDDEDADSGSLESQQNL-- 264

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
                                      ++L+ +V+     I + Y  +    D   +   
Sbjct: 265 ---------------------------EELKAQVLEHFKHIEKSYGLMVKALDKHHSKHD 297

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGI 365
                      +  + + +  +  +  +I+ L E L    ++I   E E+  +      +
Sbjct: 298 T------YLKHRNNIAQKLLEVRFSTRQIENLSENLRGRVEQIRRLEREIRDICLDRVRM 351

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            RD F+E       +  W+          W   +A     IL+ + ++  +     ISI+
Sbjct: 352 DRDYFIEHFMPNATNLAWLEEEIG-KNRVWSETLARFKHDILEKQAKMAELEAHARISIA 410

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E + I   + K E E + AK++M++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 411 ELKEISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 470

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   
Sbjct: 471 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGE 530

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P ++A+
Sbjct: 531 EPDSAKLAELMDMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAPAEAAM 590

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 591 YSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 650

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+HP+RS KL+SFLD 
Sbjct: 651 KLRHPTRSDKLKSFLDS 667


>gi|319638161|ref|ZP_07992924.1| RNA polymerase sigma factor rpoD [Neisseria mucosa C102]
 gi|317400434|gb|EFV81092.1| RNA polymerase sigma factor rpoD [Neisseria mucosa C102]
          Length = 650

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 266/683 (38%), Positives = 387/683 (56%), Gaps = 41/683 (6%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K +N + + + +D +  L  +      +++I + ++RGY+T  E+N  LP D   +EQ
Sbjct: 1   MSKNQNYE-EYQDQDDNRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQ 59

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDL-ASSASNSSVFLQKRKDSADRSTDDP 120
           +++ V+M+S +GI V +   D ED   S+++  L    A   +       DS    T DP
Sbjct: 60  IDNIVSMISGLGIQVTEQAPDAEDILLSDNAAALTDDDAVEEAEAALSSADSEFGRTTDP 119

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++ +    
Sbjct: 120 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIR 179

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E++  EA I P        G                                + +K D
Sbjct: 180 VDEVV--EAIIDPNEVLLNELGL----------------------------GHLENTKPD 209

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             + ++  E  ++DE + D+   DS    +A   +L+ KV+     I   Y ++      
Sbjct: 210 DEEGETDSEVEDDDEDDEDDSGSDSEAMSAAHLAELKQKVLEHFAFIESEYGKMIKQ--- 266

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               +K           ++ +   +  +     +I+ L   L    + I   E E+  + 
Sbjct: 267 ---LEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREIRDIC 323

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                ++RD F+E       D  WV          W N +     +IL+ + E+ ++  E
Sbjct: 324 IDRVRMERDYFIENFLPAITDLEWVEKEVA-KGRVWANALDRFRHAILEKQAELANMETE 382

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ISI E + I   +   E E S AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNI
Sbjct: 383 TRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 442

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+ 
Sbjct: 443 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 502

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+
Sbjct: 503 LQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVA 562

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 563 PAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 622

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           EAKA+RKL+HP+RS +LRSFLD 
Sbjct: 623 EAKALRKLRHPTRSDRLRSFLDS 645


>gi|88798840|ref|ZP_01114422.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778320|gb|EAR09513.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 614

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 256/659 (38%), Positives = 362/659 (54%), Gaps = 54/659 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLE 84
                 K++I   +++GY+T  E+N  LP +  S +Q+ED +AM++++GI V +   D +
Sbjct: 6   QRQSRLKELIAKGKEQGYLTFAEVNDHLPEEINSPDQVEDIIAMINDIGIEVFEQAPDAD 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               SE        A+  +       ++    T DPVRMY+REMG++ELL+REGEI IAK
Sbjct: 66  QLLLSESDQSTDEDATEEAAAALAAVETDTGRTTDPVRMYMREMGTVELLTREGEIVIAK 125

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDE-LNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           RIE G   +M ++   P    ++I   +  L +    L +I+        +         
Sbjct: 126 RIEEGTREVMQAMAFYPGVIDSMIGAYENTLEEEGGRLSDILTSFQDPDDDDPLPAADSP 185

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +    +  +    + +                   DD       PE A      L E  +
Sbjct: 186 DAIQSEDDKSDDVDDDD--------------DDDSDDEVDNGPDPELARERFTLLKEQLE 231

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +   +                                       + S +       + +
Sbjct: 232 SAKALIEEK-----------------------------------GRYSKEANAALSSMGE 256

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPH 382
                 L     D  +E +    + I   E +++ +      + R  F++   G E +  
Sbjct: 257 TFSCFKLTPKAFDDAIEPIKATVEEIRSQERKVIAICVRTLNMPRKAFIDAFVGHETEDE 316

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W++   + P+   + F       + + + ++++I   TGI+++E + I   +  GE  A 
Sbjct: 317 WLNELLENPKYADEAF--RYEVELRRAQRKLRNIQKNTGITLAEVKDIHRRISIGEARAR 374

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 375 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 434

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + 
Sbjct: 435 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMDMPEDK 494

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI+KEPISLETPIGD++ S LGDFIED   + P++SA    LR+ TT VLA LT 
Sbjct: 495 IRKVLKISKEPISLETPIGDDEDSSLGDFIEDNTMILPVNSATSTGLRDATTEVLAGLTA 554

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  LRSF+D
Sbjct: 555 REAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFID 613


>gi|212212053|ref|YP_002302989.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212010463|gb|ACJ17844.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
          Length = 698

 Score =  414 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 257/678 (37%), Positives = 357/678 (52%), Gaps = 57/678 (8%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
           KK +       +        +     +  +++ A+ +GY+  E+L   LP D     QME
Sbjct: 74  KKPSAPPSETQQPKIGENAAESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQME 133

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
             +  L+ MGI V +     D    E+         N  V       + +  T DPVRMY
Sbjct: 134 GIIGRLTEMGIKVFEIPPDADSLLLEEDTQSDDDEINEDVA---EVLATETRTTDPVRMY 190

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMGS+ELL+REGEI IAKRIE G   +M ++ + P   +  I                
Sbjct: 191 MREMGSVELLTREGEIVIAKRIEEGIRQVMGAVVQYPELIEKFIKEY------------- 237

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                                               D +  TEG +        D+    
Sbjct: 238 ------------------------------------DTIVATEGRLSDLLIGFFDEEEST 261

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
            SP      D+     DEDD     S    +  P  +     + E+ +     Q+     
Sbjct: 262 ASPVAPEARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRY 321

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSY 363
            K   +++K +     L +L  +  L+  + + L  QL  + +     E  ++       
Sbjct: 322 GKKAPATLKHQK---ALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKA 378

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
              R  F+      E +  W+   K+  + + K  +      I + +  +  +  +  ++
Sbjct: 379 KTPRKKFIASFPHNETNMKWLEQYKNENKEQAKR-LEKYSKEIYRAQRNLAQLEEQNNLN 437

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   V  GE ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 438 IQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 497

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  + 
Sbjct: 498 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQET 557

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E TPEE+ +++ MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D 
Sbjct: 558 GIEATPEELGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF 617

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A  A L E T  +L++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 618 ATSAGLMEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 677

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSR++KL SF++
Sbjct: 678 LRKLRHPSRAEKLHSFIE 695


>gi|154705741|ref|YP_001423814.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355027|gb|ABS76489.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 698

 Score =  413 bits (1062), Expect = e-113,   Method: Composition-based stats.
 Identities = 257/678 (37%), Positives = 357/678 (52%), Gaps = 57/678 (8%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
           KK +       +        +     +  +++ A+ +GY+  E+L   LP D     QME
Sbjct: 74  KKPSAPPSETQQPKIGENAAESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQME 133

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
             +  L+ MGI V +     D    E+         N  V       + +  T DPVRMY
Sbjct: 134 GIIGRLTEMGIKVFEIPPDADSLLLEEDTQSDDDEINEDVA---EVLATETRTTDPVRMY 190

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMGS+ELL+REGEI IAKRIE G   +M ++ + P   +  I                
Sbjct: 191 MREMGSVELLTREGEIVIAKRIEEGIRQVMGAVVQYPELIEKFIKEY------------- 237

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                                               D +  TEG +        D+    
Sbjct: 238 ------------------------------------DTIVATEGRLSDLLIGFFDEEEST 261

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
            SP      D+     DEDD     S    +  P  +     + E+ +     Q+     
Sbjct: 262 ASPVAPEARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRY 321

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSY 363
            K   +++K +     L +L  +  L+  + + L  QL  + +     E  ++       
Sbjct: 322 GKKAPATLKHQK---ALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKA 378

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
              R  F+      E +  W+   K+  + + K  +      I + +  +  +  +  ++
Sbjct: 379 KTPRKKFIASFPHNETNMKWLEQYKNENKEQAKR-LEKYSKEIYRAQRNLAQLEEQNNLN 437

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   V  GE ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 438 IQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 497

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  + 
Sbjct: 498 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQET 557

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E TPEE+ +++ MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D 
Sbjct: 558 GIEATPEELGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF 617

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A  A L E T  +L++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 618 ATSAGLMEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 677

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSR++KL SF++
Sbjct: 678 LRKLRHPSRAEKLHSFIE 695


>gi|29654887|ref|NP_820579.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|161831165|ref|YP_001597431.1| RNA polymerase sigma factor RpoD [Coxiella burnetii RSA 331]
 gi|81628631|sp|Q83BB6|RPOD_COXBU RecName: Full=RNA polymerase sigma factor rpoD
 gi|29542156|gb|AAO91093.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|161763032|gb|ABX78674.1| RNA polymerase sigma factor RpoD [Coxiella burnetii RSA 331]
          Length = 698

 Score =  413 bits (1062), Expect = e-113,   Method: Composition-based stats.
 Identities = 257/678 (37%), Positives = 357/678 (52%), Gaps = 57/678 (8%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
           KK +       +        +     +  +++ A+ +GY+  E+L   LP D     QME
Sbjct: 74  KKPSAPPSETQQPKIGENAAESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQME 133

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
             +  L+ MGI V +     D    E+         N  V       + +  T DPVRMY
Sbjct: 134 GIIGRLTEMGIKVFEIPPDADSLLLEEDTQSDDDEINEDVA---EVLATETRTTDPVRMY 190

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMGS+ELL+REGEI IAKRIE G   +M ++ + P   +  I                
Sbjct: 191 MREMGSVELLTREGEIVIAKRIEEGIRQVMGAVVQYPELIEKFIKEY------------- 237

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                                               D +  TEG +        D+    
Sbjct: 238 ------------------------------------DTIVATEGRLSDLLIGFFDEEEST 261

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
            SP      D+     DEDD     S    +  P  +     + E+ +     Q+     
Sbjct: 262 ASPVAPEARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRY 321

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSY 363
            K   +++K +     L +L  +  L+  + + L  QL  + +     E  ++       
Sbjct: 322 GKKAPATLKHQK---ALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKA 378

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
              R  F+      E +  W+   K+  + + K  +      I + +  +  +  +  ++
Sbjct: 379 KTPRKKFIASFPHNETNMKWLEQYKNENKEQAKR-LEKYSKEIYRAQRNLAQLEEQNNLN 437

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   V  GE ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 438 IQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 497

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  + 
Sbjct: 498 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQET 557

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E TPEE+ +++ MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D 
Sbjct: 558 GIEATPEELGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF 617

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A  A L E T  +L++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 618 ATSAGLMEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 677

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSR++KL SF++
Sbjct: 678 LRKLRHPSRAEKLHSFIE 695


>gi|153208748|ref|ZP_01946986.1| RNA polymerase sigma factor RpoD [Coxiella burnetii 'MSU Goat
           Q177']
 gi|212219307|ref|YP_002306094.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120575780|gb|EAX32404.1| RNA polymerase sigma factor RpoD [Coxiella burnetii 'MSU Goat
           Q177']
 gi|212013569|gb|ACJ20949.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 698

 Score =  413 bits (1062), Expect = e-113,   Method: Composition-based stats.
 Identities = 257/678 (37%), Positives = 357/678 (52%), Gaps = 57/678 (8%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
           KK +       +        +     +  +++ A+ +GY+  E+L   LP D     QME
Sbjct: 74  KKPSAPPSETQQPKIGENAAESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQME 133

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
             +  L+ MGI V +     D    E+         N  V       + +  T DPVRMY
Sbjct: 134 GIIGRLTEMGIKVFEIPPDADSLLLEEDTQSDDDEINEDVA---EVLATETRTTDPVRMY 190

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMGS+ELL+REGEI IAKRIE G   +M ++ + P   +  I                
Sbjct: 191 MREMGSVELLTREGEIVIAKRIEEGIRQVMGAVVQYPELIEKFIKEY------------- 237

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                                               D +  TEG +        D+    
Sbjct: 238 ------------------------------------DTIVATEGRLSDLLIGFFDEEEST 261

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
            SP      D+     DEDD     S    +  P  +     + E+ +     Q+     
Sbjct: 262 ASPVAPEARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRY 321

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSY 363
            K   +++K +     L +L  +  L+  + + L  QL  + +     E  ++       
Sbjct: 322 GKKAPATLKHQK---ALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKA 378

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
              R  F+      E +  W+   K+  + + K  +      I + +  +  +  +  ++
Sbjct: 379 KTPRKKFIASFPHNETNMKWLEQYKNENKEQAKR-LEKYSKEIYRAQRNLAQLEEQNNLN 437

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   V  GE ++  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 438 IQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 497

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  + 
Sbjct: 498 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQET 557

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E TPEE+ +++ MP E VRKVLKI KEPIS+ETPIG+++ S+LGDFIED N  SP+D 
Sbjct: 558 GIEATPEELGRRIDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF 617

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A  A L E T  +L++LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 618 ATSAGLMEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 677

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+HPSR++KL SF++
Sbjct: 678 LRKLRHPSRAEKLHSFIE 695


>gi|77163592|ref|YP_342117.1| hypothetical protein Noc_0045 [Nitrosococcus oceani ATCC 19707]
 gi|254436143|ref|ZP_05049650.1| Sigma-70, non-essential region family [Nitrosococcus oceani AFC27]
 gi|76881906|gb|ABA56587.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
           19707]
 gi|207089254|gb|EDZ66526.1| Sigma-70, non-essential region family [Nitrosococcus oceani AFC27]
          Length = 602

 Score =  413 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 272/656 (41%), Positives = 370/656 (56%), Gaps = 68/656 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                K +I   + RGY++  E+N  LP D +  EQ+ED + M ++MGI+V +     D 
Sbjct: 9   RQSQLKLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEADA 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D+       +  +       D     T DPVRMY+REMGS+ELL+REGEI+IAKRI
Sbjct: 69  LAIMDTAVADDEVAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  +L   P +   L      L     +  + I L   I               
Sbjct: 129 EEGMRQVYTALSRFPGSVAEL------LCQYEKVEADEIRLADVIS-------------- 168

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                    QE E  D++E+  +  S +     +  + D+  +                 
Sbjct: 169 -------GFQESEEADLKESAAEEASVSSEGSTEEEESDNGLD----------------- 204

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                            LD + E + +LR L +        +           +L +   
Sbjct: 205 -----------------LDRVREQFTQLRELYERYQAADLKDNDRA-----LAELSECFL 242

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
            L L       L+E L  +   I   E  ++++A  S  + R  FL   Q +E + +WV 
Sbjct: 243 QLKLVPRLSQRLIENLRGVVAEIRVLERSIMKIAVNSAQMPRKDFLSSFQKQETNLNWVE 302

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                 +  + + +  + D+I K + ++  +    G+SI++ + I   +  GE  A  AK
Sbjct: 303 KHI-RAKKHYSSVLRKQGDAIQKAQEKLIVLEQRAGMSITQIKEINRSLSIGEARARRAK 361

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 362 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 421

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTP+E+A+++ MP + VRK
Sbjct: 422 QAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAERVEMPKDKVRK 481

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI +EPIS+ETPIGD++ SHLGDF+ED   +SP DSAI + LRETT  +LA LTPRE 
Sbjct: 482 VLKIAREPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQLILAGLTPREA 541

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 542 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 597


>gi|51474026|ref|YP_067783.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
 gi|81389911|sp|Q68VQ5|RPOD_RICTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|51460338|gb|AAU04301.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
          Length = 635

 Score =  413 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 279/666 (41%), Positives = 411/666 (61%), Gaps = 57/666 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGY-VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGD 81
            D        +++ A+ +   VT +++N  LP     S  Q+E+ +   S+ G+++++ +
Sbjct: 6   IDNDPAKIDSLLRKAKSKKIPVTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESN 65

Query: 82  DLEDEEGSEDSLDLASSASN-SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           + ++ +      +    ++N  +    + ++    STDDPVR+YL++MG ++LL+RE E+
Sbjct: 66  EDDEIKLDIGIDEEFKLSTNVDNESEDEVEEENIGSTDDPVRLYLKDMGGVDLLTRENEV 125

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE GR  M ASLC SP+  +  I+W ++L +   LLR++IDLEA +  +      
Sbjct: 126 EIAKRIEEGRKTMTASLCRSPVAMRCFIVWYEDLVNEKMLLRDLIDLEANMLHDEVH--- 182

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                                                            + E++     E
Sbjct: 183 -----------------------------------------------ENDEEHNSETEVE 195

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVL 317
           + +D+  ++S +E Q+   ++  + +I+ +  EL            D K   +S K    
Sbjct: 196 EHEDNHLSMSRVETQILHNIIDRMKKISFICEELLIEAKKCYEESFDPKVLQNSRKYNNN 255

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            E L+  V  +  N  R + ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G 
Sbjct: 256 LELLIHEVSEIHFNSKRTEEILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGS 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            ++  W        +  WK  +  E D I ++ NE+  I   TG+ +++F+ +V+ ++K 
Sbjct: 316 VINAAWKEKMLKNKKVAWKELITKESDYIDQMINELSVIESNTGLLVNDFKKLVNTIQKS 375

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +   AKK+M+EANLRLVIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLS 495

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           MP++ VRKV+KI KEPISLE P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRV
Sbjct: 496 MPLDKVRKVMKIAKEPISLENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRV 555

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA+LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL
Sbjct: 556 LATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKL 615

Query: 677 RSFLDG 682
            SF +G
Sbjct: 616 NSFRNG 621


>gi|255066480|ref|ZP_05318335.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
 gi|255049360|gb|EET44824.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
          Length = 649

 Score =  412 bits (1058), Expect = e-112,   Method: Composition-based stats.
 Identities = 255/682 (37%), Positives = 377/682 (55%), Gaps = 41/682 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
             K     D + +D +  L  +      +++I + ++RGY+T  E+N  LP D   ++Q+
Sbjct: 1   MSKDQNHEDYQEQDDNRPLTLEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPV 121
           ++ V+M+S +GI V +     ++    D+        A   +       DS    T DPV
Sbjct: 61  DNIVSMISGLGIQVTEQAPDAEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPV 120

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 121 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRV 180

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                              +    ++      S  + 
Sbjct: 181 DEVV--EAIIDPN-----------------------------EVLLNELGLGHLESASND 209

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
               S  E+  +++ + D+   DS    +A   +L+ KV+     I   Y ++       
Sbjct: 210 DDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEHFAFIESEYGKMIK----- 264

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
              +K +         ++ +   +  +     +I+ L   L    + I   E E+  +  
Sbjct: 265 -KLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRDICL 323

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  WV          W + +     +IL+ + E+ ++  ET
Sbjct: 324 DRVHMERDYFIQNFLPEITNLKWVEEEVA-KGRVWSDALDRFRHAILEKQTELANMEKET 382

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 383 RISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 442

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 443 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 502

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 503 QETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 562

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 563 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 622

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 623 AKALRKLRHPTRSDRLRSFLDS 644


>gi|261363710|ref|ZP_05976593.1| RNA polymerase sigma factor RpoD [Neisseria mucosa ATCC 25996]
 gi|288568271|gb|EFC89831.1| RNA polymerase sigma factor RpoD [Neisseria mucosa ATCC 25996]
          Length = 649

 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 256/682 (37%), Positives = 379/682 (55%), Gaps = 41/682 (6%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
             K     D + +D +  L  +      +++I + ++RGY+T  E+N  LP D   ++Q+
Sbjct: 1   MSKDQNHEDYQEQDDNRPLTLEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPV 121
           ++ V+M+S +GI V +     ++    D+        A   +       DS    T DPV
Sbjct: 61  DNIVSMISGLGIQVTEQAPDAEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPV 120

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 121 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRV 180

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++  EA I P                              +    ++      S  + 
Sbjct: 181 DEVV--EAIIDPN-----------------------------EVLLNELGLGHLESASND 209

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
               S  E+ E+++ + D+   D+    +A   +L+ KV+     I   Y ++       
Sbjct: 210 DDSGSSDEDEEDEDEDDDDSGSDAEAMSAAHLAELKQKVLDHFAFIESEYGKMIK----- 264

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
              +K + S       ++ +   +  +     +I+ L   L    + I   E E+  +  
Sbjct: 265 -KLEKHDSSHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRDICL 323

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               ++RD F++       +  WV          W + +     +IL+ + E+ ++  ET
Sbjct: 324 DRAHMERDYFIQNFLPEITNLKWVEEEVA-KGRVWSDALDRFRHAILEKQTELANMEKET 382

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 383 RISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 442

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+  
Sbjct: 443 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 502

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P
Sbjct: 503 QETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAP 562

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A+  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 563 ADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 622

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKL+HP+RS +LRSFLD 
Sbjct: 623 AKALRKLRHPTRSDRLRSFLDS 644


>gi|113461378|ref|YP_719447.1| RNA polymerase sigma factor RpoD [Haemophilus somnus 129PT]
 gi|112823421|gb|ABI25510.1| RNA polymerase, sigma 70 subunit, RpoD [Haemophilus somnus 129PT]
          Length = 595

 Score =  411 bits (1056), Expect = e-112,   Method: Composition-based stats.
 Identities = 265/633 (41%), Positives = 357/633 (56%), Gaps = 41/633 (6%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N  LP D V ++Q+ED + M+++MGI V++     D+    +++     A   +  +   
Sbjct: 2   NDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDADDLMLNENIT-DEDAVEEATQVLSS 60

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
            ++    T DPVRMY+REMGS+ELL+REGEI IAKRIE G   + +++   P     L+ 
Sbjct: 61  VEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEGINEVQSAVAAYPKALNYLLE 120

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
               + +G   L ++I     + P +        E       +D    +   DV + E +
Sbjct: 121 QYTLVEEGGMRLADLIT--GFVDPNAVVEE-EIIETDDILTEDDEEHVESNVDVNDEEEE 177

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
            +S    + D  S     PE A      L                               
Sbjct: 178 EDSEDNSNVDSDSDNTIAPEVAREKFEALRIQH--------------------------- 210

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
                   Q      +K  +S  + K   + L  +     L   + D LV  + D+ K +
Sbjct: 211 --------QKTLAAIEKYGRSRKQAKDHIQALADIFTQFRLVPKQFDALVNYMRDMMKSV 262

Query: 350 MHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
             +E ++ +L      + ++ F +   G E    W+          W   +     ++ +
Sbjct: 263 RQHERQIQKLVVDLAKMPKENFQKLFIGNESSEGWLDKLL-LARKPWSERLIQHESAVRQ 321

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
             N++  I  ET ++IS+ R I   V +GE +A  AKKEMVEANLRLVIS+AKKYTNRGL
Sbjct: 322 SINQLLKIEQETNLTISQIREICDKVAQGELKARRAKKEMVEANLRLVISIAKKYTNRGL 381

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 382 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 441

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R +R+M  K+ RE T EE+A+++ MP + +RKVLKI KEPIS+ETPIGD+D SHL
Sbjct: 442 INKLNRISRQMLQKMGREATSEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHL 501

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED     PLDSA   +LR  T  VL  LTPRE +VLRMRFGI MNTDHTLEEVGKQ
Sbjct: 502 GDFIEDNTLELPLDSATAQSLRAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQ 561

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 562 FDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 594


>gi|262164053|ref|ZP_06031792.1| RNA polymerase sigma factor RpoD [Vibrio mimicus VM223]
 gi|262027581|gb|EEY46247.1| RNA polymerase sigma factor RpoD [Vibrio mimicus VM223]
          Length = 595

 Score =  411 bits (1056), Expect = e-112,   Method: Composition-based stats.
 Identities = 261/632 (41%), Positives = 354/632 (56%), Gaps = 41/632 (6%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKD 111
           +P + V SEQ+ED + M+++MGI VV+     D+    D   +    +  +        +
Sbjct: 1   MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++   
Sbjct: 61  SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAVAEYPGTIPYILEQF 120

Query: 172 DELNDGTTLLREIIDLEACIGPES-KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           D++      L ++I     + P   +      T   S     D + E +     E E + 
Sbjct: 121 DKVQAEELRLTDLI--SGFVDPNDMETEAPTATHIGSELSEADLADEDDEIADDEDEDED 178

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           E     S D   +V   PE A      L                                
Sbjct: 179 EDGDGESSDSEEEVGIDPELAREKFNELR------------------------------- 207

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
                  Q+  +   +  + S +       ++ +     L   + D LVE L     R+ 
Sbjct: 208 ----GKFQNLQLAVNEFGRDSNQASEASSLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 263

Query: 351 HNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
             E  +++       + +  F+    G E +  W+       +  +   +  + D I + 
Sbjct: 264 TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLA-SDKPYVQKIREQEDDIRRS 322

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 323 IQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 382

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 383 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 442

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLG
Sbjct: 443 NKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 502

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF
Sbjct: 503 DFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 562

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 563 DVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 594


>gi|294787697|ref|ZP_06752941.1| RNA polymerase sigma factor RpoD [Simonsiella muelleri ATCC 29453]
 gi|294483990|gb|EFG31673.1| RNA polymerase sigma factor RpoD [Simonsiella muelleri ATCC 29453]
          Length = 652

 Score =  411 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 254/679 (37%), Positives = 374/679 (55%), Gaps = 44/679 (6%)

Query: 8   NRDSDSEHEDSDDSLVF-DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           + DSD+E + SD+  +  +      +++I   ++RGY+T  E+N  LP D   +EQ+++ 
Sbjct: 10  DHDSDNEEQLSDNRPLTPEEQRARLRQLIIFGKERGYITYAEINDTLPDDMSDAEQIDNI 69

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDS--LDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           V M+  +GI V +     +     D+        A   +     + DS    T DPVRMY
Sbjct: 70  VNMIQGLGIQVTEEAPDAETLLMSDNSAAVADEDAVAEAEAALSQADSEFGRTTDPVRMY 129

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG +ELL+R  EI IAK+IE     M+ ++   P +   ++   D++      + E+
Sbjct: 130 MREMGQVELLTRADEIIIAKKIENALKNMIQAISACPGSVGEILALIDQIKKDEIRVDEV 189

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           +  EA I P        G         ED +  +  D   + E + +++    +    + 
Sbjct: 190 V--EAIIDPNEVLLNELGLSHLENGASEDDTSSESDDADDDEEDEEDASGSNLEGQNLE- 246

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
                                         +L+ +V+    +I + Y  +          
Sbjct: 247 ------------------------------ELKAQVIEHFKQIGKSYGLMIK------AL 270

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           +K +    K    ++ +   +  +  +  +I+ L E L      I   E E+  +     
Sbjct: 271 EKYDSKHTKYLEHRDAIASKLLEVRFSTRQIEKLSESLRGRVDLIRKLEREIRDICLDRV 330

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +D F+        + +W+    +     W   +      IL+ + E+ ++     IS
Sbjct: 331 RMDKDYFISSFLPNATNLNWIEDEIN-KNRVWSETLQRFKHDILEKQTEMSNLEAHARIS 389

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMK
Sbjct: 390 IEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 449

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   + 
Sbjct: 450 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQET 509

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD++ SHLGDFIED N V+P D+
Sbjct: 510 GEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDANNVAPSDA 569

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A+ ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA
Sbjct: 570 AMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 629

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+HP+RS KL+SFLD 
Sbjct: 630 LRKLRHPTRSDKLKSFLDS 648


>gi|114778492|ref|ZP_01453336.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114551217|gb|EAU53776.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 660

 Score =  411 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 253/650 (38%), Positives = 378/650 (58%), Gaps = 18/650 (2%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           ++   +Q G++T ++LN  LP   VS++++E  + + + MG+ VVD +       +    
Sbjct: 17  LMAKGKQAGFITYDDLNKHLPGGLVSADRVEQLINVFTEMGVEVVDPERAPTGAYAMRKD 76

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
            L     +S++     +       DDPVRMYLREMG++ELL+REGEI IA+RIE GR  +
Sbjct: 77  RLRK--EDSALRADTSQLGTVIRIDDPVRMYLREMGTVELLTREGEIEIARRIEEGRMQV 134

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
             ++C  P TF+ +++  + +      +R+          E+       +        E 
Sbjct: 135 HEAICLCPSTFREIMLLGERI----IQIRD----------EAMELGEEPSFRDIIDVDEK 180

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                   + +      E       +   K+D          R    D      T+   E
Sbjct: 181 VVNSAAIKEYENRMSRSEEDDDEPVETEPKLDGEQLTEAIKARTATPDGTPMQETVITKE 240

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           +QL  + +    E  +++ +   ++        D+   ++ + + + ++  + S+  +  
Sbjct: 241 EQL-EEALFHFGEAKKLHDDFIEVKKKLAKRPNDKALLLRSREVLDAMLLELVSIPFSPR 299

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV-SYAKDFPE 392
           ++D LV++  +  +++   E  +   A    + R +FLE     E +  W+    K   +
Sbjct: 300 QLDQLVQRFKNAVEKVRRFERSIRDYALEARMPRKLFLETFPVDETNERWIDELMKQNKD 359

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             W   +      I + +  ++ +  ET + + E + +   +  GE +   AK+EM+EAN
Sbjct: 360 AAWVTAIEEVTGKIKENQRRLRRVEQETEMGVVELKDVARKLTMGEAKMRQAKREMIEAN 419

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLVIS+AKKYTNRGL FLDLIQEGNIGLMKA EKF+W  GYKFSTYA WW++QAITRSI
Sbjct: 420 LRLVISIAKKYTNRGLGFLDLIQEGNIGLMKAVEKFEWRRGYKFSTYATWWIRQAITRSI 479

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K++R +R+++ +I REPTPEE+A+ L +PVE V ++L++ KE
Sbjct: 480 ADQARTIRIPVHMIETINKMMRVSRQIAQEIGREPTPEELAEHLELPVEKVLQILEVAKE 539

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+SLETPIGD++ S LGDF+ED NA +PLDS I A L E T  VL +LT RE++VLRMRF
Sbjct: 540 PVSLETPIGDDEDSQLGDFVEDDNAENPLDSTIGAALAEATLEVLENLTDREQKVLRMRF 599

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+KL++F D 
Sbjct: 600 GIGMNTDHTLEEVGKQFGVTRERIRQIEAKALRKLRHPSRSQKLKTFADA 649


>gi|295698766|ref|YP_003603421.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
 gi|291157279|gb|ADD79724.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
          Length = 629

 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 264/656 (40%), Positives = 374/656 (57%), Gaps = 42/656 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++   +++GY+T  E+N  LP D V S+Q+ED +  + +MGI V +    EDE    
Sbjct: 9   LKVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTEEVPDEDELILT 68

Query: 91  DSLDLASSAS-NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D        +  ++  +    +     T DP+RMY+REMG+IELL+REGEI IAKRIE G
Sbjct: 69  DPTSSTDEETVEAATQVLSSVEQEIGRTTDPIRMYMREMGTIELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              +  S+ E P +   ++        G   L +II            G        S +
Sbjct: 129 INQIQRSISEYPKSISYILKQYFLFESGEMKLSDII-----------TGLSSEDTFSSSK 177

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
             + +    + + +     +I S     KD     +S   N E++  ++D          
Sbjct: 178 NVDKNFSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHIDP--------- 228

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL-KEKLVKLVGSL 328
                              + + EL++  +   +  K+        +L  + L ++    
Sbjct: 229 ---------------KIARKKFLELQNQYEKVTHSLKENGIKSSQSILDIQDLCEIFKQF 273

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR--ELDPHWVS 385
            L   ++D L+  +    ++I   E  ++ ++ + Y I +  FL        E D   + 
Sbjct: 274 RLVPKQLDFLISDIRKTIEKIKIQEKLIINISFKEYKIPKKYFLNLFSENPKEYDLKELI 333

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            +  + + + K F      +I++  NE+  I  +TGISIS+ + I   +  GE  A  AK
Sbjct: 334 VSNRYNKKDEKKFKLDS--TIVQALNELNEIEKDTGISISKIKEIGRKISIGETIARRAK 391

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 392 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 451

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+   +R++  +  REP+PEE+++++ +P E +RK
Sbjct: 452 QAITRSIADQARTIRIPVHMIETINKLNHISRQILQETGREPSPEELSERMLIPEEKIRK 511

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI +EPIS+ETPIGD++ SHLGDFIED     PL+SA   +LR  T  VL+ LT RE 
Sbjct: 512 VLKIAREPISMETPIGDDEDSHLGDFIEDTTLELPLESATSESLRSATNEVLSGLTTREA 571

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 572 KVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSELLRSFLD 627


>gi|258545971|ref|ZP_05706205.1| DNA-directed RNA polymerase, sigmasubunit [Cardiobacterium hominis
           ATCC 15826]
 gi|258518776|gb|EEV87635.1| DNA-directed RNA polymerase, sigmasubunit [Cardiobacterium hominis
           ATCC 15826]
          Length = 617

 Score =  409 bits (1052), Expect = e-112,   Method: Composition-based stats.
 Identities = 273/666 (40%), Positives = 388/666 (58%), Gaps = 53/666 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D +         D  K+++   R++G++T EE++  LP   +  ++ ++ +A++  MGI+
Sbjct: 3   DFEQEPEEYDVQDEVKELLARGREQGFLTYEEIHEALPEHALEGDKYDEMIALIVEMGID 62

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           VV+          ED   +A+             ++    T DPVRMY+REMG+++LL+R
Sbjct: 63  VVES-------AQEDGGVIATDDEEEVPSAAALNEAEIGRTTDPVRMYMREMGAVDLLTR 115

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEIAIAKRIEAG   +  +L E P    AL+    ++  G   L +++           
Sbjct: 116 EGEIAIAKRIEAGLNTVQQTLAEFPFAVSALLEEFAKIEAGEGRLSDLV----------- 164

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
               +G       K E++  E   D+  ET       +    D+     +P E A N++ 
Sbjct: 165 ----NGYGDPYANKEEETLLESSDDEDSETL-----ISAGDDDEDDDSAAPLEEAPNNQD 215

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            L E ++                    L E+A ++++L +        +       K + 
Sbjct: 216 ALLEAKE-------------------KLHELAAIHKKLMT-----ALNKGKSLDDKKNQK 251

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
           L  ++ + + + S  Q  IDL+  QL   ++ I   E  L+RL  +  G+ R +F++   
Sbjct: 252 LHGEIKEYIAAFSFPQKTIDLMEAQLNVAAEEIRDIERRLMRLVIERAGMPRKLFIQEFP 311

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G E +P W+         ++   +   +  I   + +   I     +SI + + I   + 
Sbjct: 312 GNETNPDWIVGQSKQ-RRKYAEKLKGMITEIQVEQEKYLEIEKRYHMSILQLKEIQKRLS 370

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G+ +A  AK+EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G+K
Sbjct: 371 MGKNQAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFK 430

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R +  K  REPTPEE+A+ 
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRTLVQKNGREPTPEELAEA 490

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP E +RKVLKI KEPIS+ETPIGD++ SHLGDFIED N +SPL++A    L E T  
Sbjct: 491 MDMPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNVMSPLEAATTRGLSEATNE 550

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLASLTPREERVLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HP+RS+ 
Sbjct: 551 VLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPNRSEL 610

Query: 676 LRSFLD 681
           L+SFL+
Sbjct: 611 LKSFLN 616


>gi|157826344|ref|YP_001494064.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
 gi|157800302|gb|ABV75556.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
          Length = 635

 Score =  409 bits (1052), Expect = e-112,   Method: Composition-based stats.
 Identities = 281/642 (43%), Positives = 406/642 (63%), Gaps = 56/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS-EDSLDLASSASN 101
           VT +++N  LP  +  S  Q+E+ +   S+ G+++++ ++ +D +       +   S + 
Sbjct: 27  VTYDDINKALPLNENPSIRQLEEAILKFSDAGVDILESNEDDDIKLDIGMDEEFKLSTNI 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC SP
Sbjct: 87  DNEPEDEAEEENIGTTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGRKTMTASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA I                     D + E + +
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANI-------------------LHDETPENDEE 187

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              ETEG                               E+ DD+  ++S +E Q+ P ++
Sbjct: 188 HSSETEG-------------------------------EEHDDNHLSMSRVETQILPNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +I+ +  EL            + K   +S K     E L+  V  +  N  R + +
Sbjct: 217 ERMKKISFICEELLIEAKKCYEKSFEPKVLQNSKKYNNNLELLLHEVSEIHFNSKRTEEI 276

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 277 LGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 336

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 337 ITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 396

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 397 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 456

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 457 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 516

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNA++P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 517 PVGDDSDGGQLGDFIEDKNAIAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 576

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 577 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 618


>gi|157965030|ref|YP_001499854.1| RNA polymerase sigma factor RpoD [Rickettsia massiliae MTU5]
 gi|157844806|gb|ABV85307.1| RNA polymerase sigma factor [Rickettsia massiliae MTU5]
          Length = 633

 Score =  409 bits (1050), Expect = e-111,   Method: Composition-based stats.
 Identities = 277/641 (43%), Positives = 403/641 (62%), Gaps = 56/641 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           VT +++N  LP     S  Q+E+ +   S+ GI++++ ++ ++ +      +    ++N 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGIDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
               +   +    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC SP+
Sbjct: 87  DNEPEDEVEENIGATDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGHKTMTASLCRSPI 146

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
             +  I+W ++L +   LLR++IDLEA +  +                            
Sbjct: 147 AMRCFIVWYEDLVNEKMLLRDLIDLEANMLHDE--------------------------- 179

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                                  +P  + E+      E+ +D+  ++S +E Q+ P ++ 
Sbjct: 180 -----------------------TPENDEEHSSETEGEEHEDNHLSISRVETQILPNIIE 216

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
            + +I+ +  EL            + K   +S K   L E L+  V  +  N  R + ++
Sbjct: 217 RMKKISFICEELLIEAKKCYEKSFEPKVLQNSKKYNNL-ELLINEVSEIHFNSKRTEEIL 275

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +G WK  +
Sbjct: 276 GKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKGAWKELM 335

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS+
Sbjct: 336 TKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVISI 395

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TI
Sbjct: 396 AKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTI 455

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE P
Sbjct: 456 RIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLENP 515

Query: 580 IGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMNT
Sbjct: 516 VGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNT 575

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           DHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 576 DHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 616


>gi|238022360|ref|ZP_04602786.1| hypothetical protein GCWU000324_02267 [Kingella oralis ATCC 51147]
 gi|237866974|gb|EEP68016.1| hypothetical protein GCWU000324_02267 [Kingella oralis ATCC 51147]
          Length = 654

 Score =  408 bits (1049), Expect = e-111,   Method: Composition-based stats.
 Identities = 254/685 (37%), Positives = 383/685 (55%), Gaps = 38/685 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M+      ++++    + +  L  +   +  +++I   ++RGY+T  E+N  LP D   +
Sbjct: 1   MSEKHLPEQENEETLSNDNRPLTPEEQRERLRRLIIQGKERGYITYAEINDALPDDMSDA 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTD 118
           EQ+++ V M+  +GI V +     D     D+        A   +     + DS    T 
Sbjct: 61  EQIDNIVNMIQGLGIQVTEEAPDADSLLMNDNSTAITDEDAVAEAEAALSQADSEFGRTT 120

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+REMG ++LL+RE EI IAK IE     M+ ++   P +   ++   +++    
Sbjct: 121 DPVRMYMREMGQVDLLTREDEIKIAKEIENALKNMIQAISACPGSIGEILDLINQIKKDE 180

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
             + E++  EA I P                           + +    G     + ++ 
Sbjct: 181 IKVDEVV--EAIIDPN--------------------------EVLLNELGLGHLESSLNS 212

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
              +  D   E+  ++  + D+ E DSA   S   ++L+ +V+    +I + Y  +    
Sbjct: 213 HQAASGDESDESDGDESGDDDDSEGDSAAIESQNLEELKAQVLDHFKQIEKSYNLMIRAL 272

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           D      K   SS K    +  +   +  +  +  +I+ L + L    ++I   E E+  
Sbjct: 273 D------KSGSSSAKYLEHRGNIANKLLEVRFSTRQIEKLSDSLRSRVEKIRKLEREIRD 326

Query: 359 LA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           +      + RD F+        +  W+       +  W   +     +IL+ + E+  + 
Sbjct: 327 ICLDRVNMDRDHFIAHFLPNATNLDWIEEEIA-KKRAWSETLDRFRHAILEKQTEMAELE 385

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +SI+E + I   + K E E + AK++M++ANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 386 QHARVSIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEG 445

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R
Sbjct: 446 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISR 505

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +   +   +P   ++A+ + MP + +RK++KI KEPIS+E+PIGD+D SHLGDFIED N 
Sbjct: 506 QYLQETGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMESPIGDDDDSHLGDFIEDVNN 565

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V+P ++A+ ++LRE T  VL SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIR
Sbjct: 566 VAPAEAAMYSSLREVTAGVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 625

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKL+HP+RS KL+SFLD 
Sbjct: 626 QIEAKALRKLRHPTRSDKLKSFLDS 650


>gi|157804249|ref|YP_001492798.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
 gi|157785512|gb|ABV74013.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
          Length = 635

 Score =  408 bits (1049), Expect = e-111,   Method: Composition-based stats.
 Identities = 280/644 (43%), Positives = 405/644 (62%), Gaps = 60/644 (9%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED---EEGSEDSLDLASSA 99
           VT +++N  LP     S  Q+E+ +   S+ GI++++ ++ ++   + G ++   L+ + 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGIDILESNEDDEIKLDIGMDEEFKLSINV 86

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            N      + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC 
Sbjct: 87  DNE--PDDEVEEKNIGTTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCR 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           SP+  +  I+W ++L +   LLR++IDLEA +  +                         
Sbjct: 145 SPIAMRCFIVWYEDLVNEKMLLRDLIDLEANMLHD------------------------- 179

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
                                    ++   + E+   N  E+ +D   ++S +E Q+ P 
Sbjct: 180 -------------------------ETSENDEEHSSDNEGEEHEDHHLSMSRVETQILPN 214

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRID 336
           V+  + +IA +  EL            + K   +S K     E L+  V  +  N  + D
Sbjct: 215 VIERMKKIAFICEELLIEAKKCYEKSFEPKVLQNSRKYNNNLELLINEVSEIHFNSKKTD 274

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            ++ ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK
Sbjct: 275 EILGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKIAWK 334

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLV
Sbjct: 335 ELITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLV 394

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           IS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+
Sbjct: 395 ISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQA 454

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISL
Sbjct: 455 RTIRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISL 514

Query: 577 ETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           E P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIG
Sbjct: 515 ENPVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIG 574

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           MNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 575 MNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 618


>gi|153214921|ref|ZP_01949704.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 1587]
 gi|262151177|ref|ZP_06028315.1| RNA polymerase sigma factor RpoD [Vibrio cholerae INDRE 91/1]
 gi|124114994|gb|EAY33814.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 1587]
 gi|262031008|gb|EEY49634.1| RNA polymerase sigma factor RpoD [Vibrio cholerae INDRE 91/1]
          Length = 595

 Score =  408 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 261/632 (41%), Positives = 354/632 (56%), Gaps = 41/632 (6%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKD 111
           +P + V SEQ+ED + M+++MGI VV+     D+    D   +    +  +        +
Sbjct: 1   MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++   
Sbjct: 61  SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQF 120

Query: 172 DELNDGTTLLREIIDLEACIGPES-KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           D +      L ++I     + P   +      T   S     D + E +     E E + 
Sbjct: 121 DRVQAEELRLTDLI--SGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDED 178

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           E     S D   +V   PE A      L                                
Sbjct: 179 EDGDGESSDSEEEVGIDPELAREKFNELR------------------------------- 207

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
                  Q+  +   +  + S +     + ++ +     L   + D LVE L     R+ 
Sbjct: 208 ----GKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 263

Query: 351 HNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
             E  +++       + +  F+    G E +  W+       +  +   V  + + I + 
Sbjct: 264 TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLA-SDKPYVAKVREQEEEIRRS 322

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 323 IQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 382

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 383 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 442

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLG
Sbjct: 443 NKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 502

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF
Sbjct: 503 DFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 562

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 563 DVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 594


>gi|67459749|ref|YP_247373.1| RNA polymerase sigma factor RpoD [Rickettsia felis URRWXCal2]
 gi|75535861|sp|Q4UJT1|RPOD_RICFE RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|67005282|gb|AAY62208.1| RNA polymerase sigma factor [Rickettsia felis URRWXCal2]
          Length = 635

 Score =  408 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 277/642 (43%), Positives = 402/642 (62%), Gaps = 56/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N  LP     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC+SP
Sbjct: 87  DNEPEDEVEEENIGTTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCKSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA +  +                           
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANMLHDE-------------------------- 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                                   +P  + E+      E+ +D+  ++S +E Q+ P ++
Sbjct: 181 ------------------------TPENDEEHSSETEGEEHEDNHLSMSRVETQILPNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +I+ +  EL            + K   +S K     E L+  V  +  N  R + +
Sbjct: 217 ERMKKISFICEELLIEAKKCYEKSFEPKVLQNSKKYNNNLELLINEVSEIHFNSKRTEEI 276

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 277 LGKMYGINRDLINKEIAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 336

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 337 ITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 396

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 397 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 456

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 457 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 516

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 517 PVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 576

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 577 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 618


>gi|15604688|ref|NP_221206.1| RNA polymerase sigma factor RpoD [Rickettsia prowazekii str. Madrid
           E]
 gi|464670|sp|P33451|RPOD_RICPR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|434681|gb|AAB81404.1| major sigma factor of RNA polymerase [Rickettsia prowazekii]
 gi|3861383|emb|CAA15282.1| RNA POLYMERASE SIGMA FACTOR RPOD (rpoD) [Rickettsia prowazekii]
 gi|292572521|gb|ADE30436.1| RNA polymerase sigma factor [Rickettsia prowazekii Rp22]
          Length = 635

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 278/645 (43%), Positives = 402/645 (62%), Gaps = 56/645 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N  LP     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    STDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC SP
Sbjct: 87  DNESEDEVEEENIGSTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA +  +                           
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANMLHDEVH------------------------ 182

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                                       + E++     E+ +D+  ++S +E Q+   ++
Sbjct: 183 --------------------------ENDEEHNSETEVEEHEDNHLSMSRVETQILHNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +I+ +  EL            + K   +S K     E L+  V  +  N  R + +
Sbjct: 217 DRMKKISFICEELLIEAKKCYEESFEPKVLQNSKKYNNNLELLINEVSEIHFNSKRTEEI 276

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 277 LGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 336

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++ NE+  I   TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 337 ITKESDYIDQMINELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 396

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 397 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 456

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 457 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 516

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 517 PVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 576

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF +G
Sbjct: 577 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSFRNG 621


>gi|91204871|ref|YP_537226.1| RNA polymerase sigma factor RpoD [Rickettsia bellii RML369-C]
 gi|122426123|sp|Q1RKH7|RPOD_RICBR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|91068415|gb|ABE04137.1| RNA polymerase sigma factor [Rickettsia bellii RML369-C]
          Length = 641

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 278/645 (43%), Positives = 403/645 (62%), Gaps = 51/645 (7%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDDLEDEEGSEDSLDLASSA 99
           G VT  ++N  LP D  S E+++  +   S   ++++D   DD    +  E       S 
Sbjct: 24  GSVTYNDINRALP-DGTSVEEIDKVMFRFSEAEVDILDTNEDDAIKIDDMEMEEGFKIST 82

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           +       + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  ++A+LC 
Sbjct: 83  NIDHEPEDETEEENIGTTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTLIAALCR 142

Query: 160 SPLTFQALIIWR-DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           SP+       W  D +N+   LLR++IDLE+ +  + +           +++        
Sbjct: 143 SPIAMDKFRKWYADLVNENNMLLRDLIDLESNMMHDDETSESEDDHNSDHEE-------- 194

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                                              +E++ D D +++  ++S +E Q+ P
Sbjct: 195 -----------------------------------EEQDHDHDHEENILSMSKVETQILP 219

Query: 279 KVMCALDEIAEVYREL---RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            ++  + +IA +  EL            G K  ++S K     E L+  V  +  N  R 
Sbjct: 220 NIIERMKKIAFICEELLIETKKSFEKSAGPKILQNSKKYNDNLELLISEVSEIHFNSKRT 279

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           + ++ ++Y I++ +++ E   L+LA+ YGI R  FL+ + G  ++  W        +  W
Sbjct: 280 EEILSEMYRINRDLINKETAFLKLAEKYGITRQNFLDEYIGAVINAAWKEKMLKNKKAGW 339

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K  +  E D I ++  E+ +I + TG+ +++F+ +V+ ++K E +   AKK+M+EANLRL
Sbjct: 340 KELLTKESDYIDQMIAELSAIEINTGLLVNDFKKLVNAIQKSERQTLQAKKDMIEANLRL 399

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ
Sbjct: 400 VISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQ 459

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++RT+R+M N++  EPTP EIA +L+MP++ VRKV+KI KEPIS
Sbjct: 460 ARTIRIPVHMIETINKIIRTSRQMLNELGYEPTPAEIAARLSMPIDKVRKVMKIAKEPIS 519

Query: 576 LETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           LE P+   +D S+LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGI
Sbjct: 520 LENPVGDGDDNSYLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGI 579

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 580 GMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 624


>gi|239948365|ref|ZP_04700118.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922641|gb|EER22665.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 635

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 275/642 (42%), Positives = 400/642 (62%), Gaps = 56/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N  LP     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINKALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSINV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  M ASLC SP
Sbjct: 87  DNEPEDEVEEENIGTTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTMTASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +T +  I+W ++L +   LLR++IDLEA +  +                           
Sbjct: 147 ITMRCFIVWYEDLVNEKMLLRDLIDLEANMLHD--------------------------- 179

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                                  ++P  + E+      E+ +D+  ++  +E Q+ P ++
Sbjct: 180 -----------------------ETPENDEEHSSNTEGEEHEDNHLSMYRVETQILPNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +I+ +  EL            + K   +S K     E L+  V  +  N  R + +
Sbjct: 217 ERMKKISFICEELLIEAKKCYEKSFEPKVLQNSKKYNNNLELLINEVSEIHFNSKRTEEI 276

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 277 LGKMYGINRDLINKETTFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 336

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I   TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 337 ITKESDYIDQMIAELSVIESNTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 396

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 397 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 456

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++R +R+M N++  EPT  EIA +L+MP++ V KV+KI KEPISLE 
Sbjct: 457 IRIPVHMIETINKILRISRQMLNELGYEPTATEIANRLSMPLDKVCKVMKIAKEPISLEN 516

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 517 PVGDDIDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 576

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 577 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 618


>gi|34581080|ref|ZP_00142560.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|229587226|ref|YP_002845727.1| RNA polymerase sigma factor RpoD [Rickettsia africae ESF-5]
 gi|28262465|gb|EAA25969.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|228022276|gb|ACP53984.1| RNA polymerase sigma factor [Rickettsia africae ESF-5]
          Length = 634

 Score =  406 bits (1043), Expect = e-111,   Method: Composition-based stats.
 Identities = 283/642 (44%), Positives = 406/642 (63%), Gaps = 57/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N  LP     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC SP
Sbjct: 87  DNEPEDEVEEENIGTTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMTASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA +                     D + E + +
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANM-------------------LHDETPENDEE 187

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  ETEG                               E+ +D+  ++S +E Q+ P V+
Sbjct: 188 NSSETEG-------------------------------EEHEDNHLSMSRVETQILPNVI 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +IA +  EL            + K   +S K   L E L+  V  +  N  R + +
Sbjct: 217 ERMKKIAFICEELLIEAKKCYEKSFEPKVLQNSKKYNNL-ELLINEVSEIHFNSKRTEEI 275

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 276 LGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 335

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 336 MTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 395

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 396 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 455

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 456 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 515

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 516 PVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 575

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 576 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 617


>gi|15893252|ref|NP_360966.1| RNA polymerase sigma factor RpoD [Rickettsia conorii str. Malish 7]
 gi|47606046|sp|Q92FZ8|RPOD_RICCN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|15620471|gb|AAL03867.1| RNA polymerase sigma factor [Rickettsia conorii str. Malish 7]
          Length = 634

 Score =  405 bits (1041), Expect = e-110,   Method: Composition-based stats.
 Identities = 282/642 (43%), Positives = 407/642 (63%), Gaps = 57/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N  LP     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M+ASLC SP
Sbjct: 87  DNEPEDEVEEENIGTTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMIASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA +                     D + E + +
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANM-------------------LHDETPENDEE 187

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  ETEG                               E+ +D+  ++S +E Q+ P ++
Sbjct: 188 NSSETEG-------------------------------EEHEDNHLSMSRVETQILPNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +IA +  EL            + K   +S K   L E L+  V  +  N  R + +
Sbjct: 217 ERMKKIAFICEELLIEAKKCYEKSFEPKVLQNSKKYNNL-ELLINEVSEIHFNSKRTEEI 275

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 276 LGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 335

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 336 MTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 395

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 396 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 455

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 456 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 515

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 516 PVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 575

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 576 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 617


>gi|146329704|ref|YP_001209965.1| RNA polymerase sigma-70 factor [Dichelobacter nodosus VCS1703A]
 gi|146233174|gb|ABQ14152.1| RNA polymerase sigma-70 factor [Dichelobacter nodosus VCS1703A]
          Length = 623

 Score =  405 bits (1041), Expect = e-110,   Method: Composition-based stats.
 Identities = 271/665 (40%), Positives = 392/665 (58%), Gaps = 47/665 (7%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D + +   D   + +K++ +  R++G++T EE+N  LP   V  E+ ++ +A L+  GI+
Sbjct: 3   DFERNPEDDDVHEEYKELFEQGREQGFLTYEEINETLPESAVEGEKFDELIAFLNENGID 62

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           VV+    E+E  ++D   LA++  +S+       D+    T DPVRMY+REMG+++LL+R
Sbjct: 63  VVETPPEEEEAVTDDEESLANNVLSSA-------DAEVGRTTDPVRMYMREMGAVDLLTR 115

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEIAIAKRIE+G  ++  +L E PL   AL+   + +  G   L ++++       +  
Sbjct: 116 EGEIAIAKRIESGLDLVQQTLAEFPLAIAALVAEFERVEAGEGRLSDLVNGYGDPFAQKT 175

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                  E  S    ED   E     + +   D +     S +    V+   E A     
Sbjct: 176 EEATDDEETESAVSSEDEDDEL----LTQAGDDDDEDGDESTEAEITVNDSLEEAR---- 227

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
                                      L E+++V+++L++  D   +      ++ K + 
Sbjct: 228 -------------------------EKLLELSQVFKKLKTALDKGQS-----LATKKNQK 257

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
           L +++ +   + S  Q  +DL+  QL +  + I   E  L+RL  +  G+ R  F+    
Sbjct: 258 LHDEVKQYFVAFSFPQKTMDLMEAQLEEPMEMIHAIERRLMRLVIEKSGMPRKSFISDFP 317

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G E D  WV         ++   +   ++ +   + +   +    G+SI + + I   + 
Sbjct: 318 GHETDLEWVVKQS-TLRRKYAEKLKLMIEDVQAEQQKFLEVEKTYGMSIQQIKDIYRQLA 376

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            G+  A  AK+EMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G+K
Sbjct: 377 VGKERAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFK 436

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R +  K  R+PTPEE++  
Sbjct: 437 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRMLQQKNGRDPTPEELSVA 496

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RKV KI KEPIS+ETPIGD++ SHLGDF+ED N +SPL++A    L E T  
Sbjct: 497 MDMPEDKIRKVWKIAKEPISMETPIGDDEDSHLGDFLEDSNVISPLEAATTRGLSEATNE 556

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VLASLTPREERVLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HP+RS+ 
Sbjct: 557 VLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPNRSEL 616

Query: 676 LRSFL 680
           L+SFL
Sbjct: 617 LKSFL 621


>gi|157829159|ref|YP_001495401.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165933888|ref|YP_001650677.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str. Iowa]
 gi|157801640|gb|ABV76893.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165908975|gb|ABY73271.1| RNA polymerase sigma factor [Rickettsia rickettsii str. Iowa]
          Length = 634

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 282/642 (43%), Positives = 405/642 (63%), Gaps = 57/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N  LP     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINNALPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC SP
Sbjct: 87  DNEPEDEVEEENIGTTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMTASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA +                     D + E + +
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANM-------------------LHDETPENDEE 187

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              ETEG                               E+ +D+  ++S +E Q+ P ++
Sbjct: 188 HSSETEG-------------------------------EEHEDNHLSMSRVETQILPNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +IA +  EL            + K   +S K   L E L+  V  +  N  R + +
Sbjct: 217 ERMKKIAFICEELLIEAKKCYEKSFEPKVLQNSKKYNNL-ELLINEVSEIHFNSKRTEEI 275

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 276 LGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 335

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 336 MTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 395

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 396 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 455

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 456 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 515

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE TTRVLA+LTPREERVLRMRFGIGMN
Sbjct: 516 PVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTTRVLATLTPREERVLRMRFGIGMN 575

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 576 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 617


>gi|332975259|gb|EGK12159.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella kingae
           ATCC 23330]
          Length = 654

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 255/667 (38%), Positives = 379/667 (56%), Gaps = 38/667 (5%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
              L  +   +  +++I L ++RGY+T  E+N  LP D   +EQ++  V M+ ++GI V 
Sbjct: 19  SRPLTPEEQRERLRRLIMLGKERGYITYAEINDSLPDDMSDAEQIDGIVNMIQSLGIQVT 78

Query: 79  DGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           +     D     D+        A   +     + DS    T DPVRMY+REMG +ELL+R
Sbjct: 79  EEAPDADALLMNDNSTGITDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTR 138

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E EI IAK IE     M+ ++   P +   ++   +++      + E++  EA I P   
Sbjct: 139 EDEIKIAKEIENALKNMIQAISACPGSVGEILELIEQIKKDEIRVDEVV--EAIIDPN-- 194

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                   + +    G     + +  D+ +  DS   + E+DE 
Sbjct: 195 ------------------------EVLLNELGLGHLESSLQSDNDAATDSDDSSDESDED 230

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
           +  +  D  +       ++L+ +V+    +I + Y  +  + D      K++    K   
Sbjct: 231 DDSDSGDAGSMDNQQNLEELKAEVLEHFKQIEKSYGLMIRVLD------KNDSKHAKYLE 284

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
            +  + + +  +  +  +I+ L + L    ++I   E E+  +      + R+ F+E+  
Sbjct: 285 HRNNIAQKLLEVRFSTRQIEKLSDNLRSRVEQIRKLEREIRDICLDRVRMDREYFIEQFM 344

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
                  W+          W   +     +IL+ + E+ ++     ISI+E + I   + 
Sbjct: 345 PNATYLEWIDEEVA-KNRVWSEALGRFKHAILEKQTEMAALEAHARISIAELKDISKNMV 403

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K E E + AK++M++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 404 KSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 463

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +   EP   ++A+ 
Sbjct: 464 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEEPDSAKLAEL 523

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P D+A+ ++LRE T+ 
Sbjct: 524 MEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAPADAAMYSSLREVTSD 583

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L SLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS K
Sbjct: 584 ILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDK 643

Query: 676 LRSFLDG 682
           L+SFLD 
Sbjct: 644 LKSFLDS 650


>gi|238651104|ref|YP_002916962.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
 gi|238625202|gb|ACR47908.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
          Length = 634

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 280/642 (43%), Positives = 403/642 (62%), Gaps = 57/642 (8%)

Query: 44  VTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASN 101
           VT +++N   P     S  Q+E+ +   S+ G+++++  +D E +       +   S + 
Sbjct: 27  VTYDDINNAFPLNKNPSIRQLEEAILKFSDAGVDILESNEDDEIKLDIGMDEEFKLSTNV 86

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +    + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE G   M ASLC SP
Sbjct: 87  DNEPEDEVEEENIGTTDDPVRLYLKDMGGVDLLTREHEVEIAKRIEEGHKTMTASLCRSP 146

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           +  +  I+W ++L +   LLR++IDLEA +                     D + E + +
Sbjct: 147 IAMRCFIVWYEDLVNEKMLLRDLIDLEANM-------------------LHDETPENDEE 187

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              ETEG                               E+ +D+  ++S +E Q+ P ++
Sbjct: 188 HSSETEG-------------------------------EEHEDNHLSMSRVETQILPNII 216

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEK---SSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             + +IA +  EL            + K   +S K   L E L+  V  +  N  R + +
Sbjct: 217 ERMKKIAFICEELLIEAKKCYEKSFEPKVLQNSKKYNNL-ELLINEVSEIHFNSKRTEEI 275

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++Y I++ +++ E   L+LA+ YG+ R  FL+ + G  ++  W        +  WK  
Sbjct: 276 LGKMYGINRDLINKETAFLKLAEKYGVTRQNFLDEYIGSVINAAWKEKMLKNKKVAWKEL 335

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E D I ++  E+  I  +TG+ +++F+ +V+ ++K E +   AKK+M+EANLRLVIS
Sbjct: 336 MTKESDYIDQMIAELSVIESKTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRLVIS 395

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 396 IAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQART 455

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++RT+R+M N++  EPT  EIA +L+MP++ VRKV+KI KEPISLE 
Sbjct: 456 IRIPVHMIETINKILRTSRQMLNELGYEPTATEIANRLSMPLDKVRKVMKIAKEPISLEN 515

Query: 579 PIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+GD+ D   LGDFIEDKNAV+P+D+AIQ+NLRE T RVLA+LTPREERVLRMRFGIGMN
Sbjct: 516 PVGDDSDGGQLGDFIEDKNAVAPIDAAIQSNLREVTIRVLATLTPREERVLRMRFGIGMN 575

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKKL SF
Sbjct: 576 TDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKKLNSF 617


>gi|148244277|ref|YP_001218971.1| DNA-directed RNA polymerase sigma-70 factor [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326104|dbj|BAF61247.1| DNA-directed RNA polymerase sigma-70 factor [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 603

 Score =  402 bits (1032), Expect = e-109,   Method: Composition-based stats.
 Identities = 241/654 (36%), Positives = 356/654 (54%), Gaps = 59/654 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
             + +K+I + +++GY+T  E+N  LP D ++ EQ+E  V +L  + I V D     D  
Sbjct: 9   KQALQKLIMVGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDITVSDTVPDADTL 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E      S+++ +++      DS    T DPVRMY+REMG ++LL +E EI IAK IE
Sbjct: 69  VVESGAKAQSTSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLEQEDEIRIAKEIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           AG   +M S+   P+           L +G   + ++I            G+    E  +
Sbjct: 129 AGVFEIMQSITLYPVITDFFFKAHTRLEEGKCKMTDVI-----------IGYQGDAEDFA 177

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +K    + E                                         D DE+    
Sbjct: 178 NKKVAFDAGE----------------------------------------FDNDEEYEEI 197

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                    + +V    D + +  +      +      K      K    +++L K +  
Sbjct: 198 EEMEYTGPDKNQVYNRFDTVLKYSKTYNKTTEQLGFRHK------KTIKTRQQLSKGLSD 251

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           L L    ++ ++E + +   ++   E  +  +    GI R  F E     E + +W+   
Sbjct: 252 LRLAPKLVNTMIEVICNRVSQVKEQEKIIKNICLDAGINRLHFFELFSNNETNFNWLDTV 311

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           K   + E    +    D I   +  ++    E  ++I E + +  M R+G+  A  AK +
Sbjct: 312 KLDEKIEKN--LKDSKDKIYYAQKNLQQFEEEMQLTIVELKKLNKMYRRGDRRAKKAKSQ 369

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLVIS+AKKY NRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 370 MIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQA 429

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R  R++  K  RE + EE+A ++ +P   + K+L
Sbjct: 430 ITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREASSEELATEMELPEYKIIKIL 489

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEP+S+ETP+GD++ S++GDFIED N  SP++   + +LRETT  +L++L+PRE +V
Sbjct: 490 KIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTKESLRETTGDLLSNLSPREAKV 549

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           L+MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+
Sbjct: 550 LKMRFGINMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLQSFLE 603


>gi|73541439|ref|YP_295959.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72118852|gb|AAZ61115.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 653

 Score =  401 bits (1031), Expect = e-109,   Method: Composition-based stats.
 Identities = 221/655 (33%), Positives = 350/655 (53%), Gaps = 45/655 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              + +I+L RQRGY+T  +++  L  +   +  ME  V   + MG+ + +     +   
Sbjct: 38  QQLRALIQLGRQRGYLTHADISDHLQENFTDTAAMESIVTTFAEMGVKIFEQTPDAETLL 97

Query: 89  SEDSLDLASS--ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             D+  +AS   A   +       DS    T DPVRMY+REM S  LL+R+ E+ +AKRI
Sbjct: 98  LSDNAVVASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMSSATLLTRKEEVELAKRI 157

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   M+ ++   P T   ++     +      + +++D                    
Sbjct: 158 EDGLNNMVHAISACPSTIATILELSGRVASAEMGIDDLVD-------------------- 197

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                           + +  G        + D         +  +++E + D +E  + 
Sbjct: 198 ---------------GLTDESGADAPVTASADDSDDDSADTADEDDSNEDDDDAEEGSTQ 242

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            +  A   +LR + +     ++E +  +R  Q+ A NG            ++++L     
Sbjct: 243 QSAEADLAKLRDECLKRFARVSEQFELMR--QEYAANGSGSAGFVTARDTVRDEL----R 296

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVS 385
           ++      I+ L   +  +   +   E ++++L     G+ R+  + R  G E +  W  
Sbjct: 297 TIRFTAKTIERLCADVQSMVDDVRVVERQVVQLLVDRCGMDREDVIARFPGNETNLSW-G 355

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                    +   VA  +  +   + ++  I     + ++E + +   +   E +   AK
Sbjct: 356 RDLAAASRPYSAAVARALPDLEAHQQKLIDIQARAALPLAELKAVNRKMLAAERQMRQAK 415

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            EM +ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G+KFSTYA WWV+
Sbjct: 416 HEMTQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVR 475

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA+TR+IADQ+ TIR+PVHM ++I+K+ R +R +  +  +EP P  +A+++ MP E VR 
Sbjct: 476 QAVTRAIADQARTIRVPVHMIEQINKLNRLSRELMQQTGKEPDPAVLAERMDMPEEKVRA 535

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++KI +EP+S+ETP+G++  + LGD I D +  +P D+A+QA+LRE    +L  LTPRE 
Sbjct: 536 IMKIAREPVSMETPVGEDGDTSLGDMIADSDTATPADAALQASLREVVREMLDELTPREA 595

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +VLRMRFGI M TD+TLEEVGKQF VTRERIRQIE+KA+RKL+HPSR+ +L ++L
Sbjct: 596 KVLRMRFGIDMATDYTLEEVGKQFDVTRERIRQIESKAMRKLRHPSRADQLITYL 650


>gi|146281106|ref|YP_001171259.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri A1501]
 gi|145569311|gb|ABP78417.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri A1501]
          Length = 569

 Score =  401 bits (1031), Expect = e-109,   Method: Composition-based stats.
 Identities = 249/614 (40%), Positives = 355/614 (57%), Gaps = 47/614 (7%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           M+++MGINV +     D     ++    ++A  ++  L   +      T DPVRMY+REM
Sbjct: 1   MINDMGINVFETAPDADALLLAEADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREM 59

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L 
Sbjct: 60  GTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LS 117

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P+  G         + Q+ E  + +     V + + D +     ++++       P
Sbjct: 118 GYIDPDDDGAA-------APQEVEPETPQTTAKPVVDDKDDDDEEESDTEEEEGDGGPDP 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           E A      + E  + +   L                                   +K  
Sbjct: 171 EVARVRFGAVAEQLEKANKAL-----------------------------------KKHG 195

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKR 367
           ++S +     E L  L   + L   + D LVE++ D   +I   E  +++L      + R
Sbjct: 196 RASQQATEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPR 255

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             FL +    E +  W        + ++   +    + I + + ++  +  +  ++I++ 
Sbjct: 256 ADFLRQFPSNETNLDWAEQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADI 314

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K
Sbjct: 315 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 374

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP
Sbjct: 375 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 434

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   
Sbjct: 435 TPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVE 494

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+E T  VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL
Sbjct: 495 SLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 554

Query: 668 KHPSRSKKLRSFLD 681
           +HP+RS+ LRSFLD
Sbjct: 555 RHPTRSEHLRSFLD 568


>gi|113867637|ref|YP_726126.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia
           eutropha H16]
 gi|113526413|emb|CAJ92758.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia
           eutropha H16]
          Length = 656

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 222/688 (32%), Positives = 357/688 (51%), Gaps = 53/688 (7%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDS------WKKMIKLARQRGYVTIEELNAFLPP 55
              ++     D     +  +   D S ++       + +I+L RQRGY+T  +++  LP 
Sbjct: 10  AKTRETGAIKDPGQTSAGSTAQPDPSTEAAARSQQLRALIQLGRQRGYLTHADISDHLPE 69

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS--LDLASSASNSSVFLQKRKDSA 113
           +   +  ME  V+  + MG+ + +     +     D   +     A   +       DS 
Sbjct: 70  NFTDTAAMESIVSTFAEMGVKIYEQTPDAETLLLSDGPVVASDDQADEEAEVALATVDSE 129

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REM S  LL+R+ E+ IAKRIE G   M+ ++   P T  A++    +
Sbjct: 130 FGRTTDPVRMYMREMSSATLLTRKQEVEIAKRIEEGLNNMVHAISACPFTIAAILELSGK 189

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +      + +++D                                       ++  I  A
Sbjct: 190 VASNEISIDDLVD-------------------------------------GLSDESIAEA 212

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           A  +  D +       +  +D+    +DE  +  +      QLR + +     +   +  
Sbjct: 213 AVAAAADETDDSVDSADEADDDSEDSDDEGSTQQSNEKALAQLREECLKRFARVTAQFEL 272

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           +   Q++A NG            ++E+L     ++      I+ L   +  +   +   E
Sbjct: 273 MC--QESAANGAGSAAFLAARDAVREEL----RTIRFTAKTIERLCANVQAMVDEVRTVE 326

Query: 354 GELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
            ++++L  +  G++R+  + R  G E +  W           +   VA  +  +   + +
Sbjct: 327 RQVVQLLVERCGMEREEVIARFPGNETNLAWGQELVAQSRP-YSAAVARALPDLEAHQQK 385

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     +S+ + + +   +   E +   AK EM +ANLRLVIS+AKKYTNRG+ FLD
Sbjct: 386 LIDIQARAALSLPDLKGVNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMLFLD 445

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF++  G+KFSTYA WWV+QA+TR+IADQ+ TIR+PVHM ++I+K+
Sbjct: 446 LIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKL 505

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R +R +  +  +EP P  +A++L M  + VR ++KI KEP+S+ETP+G++  + LGD I
Sbjct: 506 NRLSREIMQQTGKEPDPAVLAERLDMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMI 565

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +  +P D+A+QA LR     +L  LTPRE +VLRMRFGI M+TD+TLEEVGKQF VT
Sbjct: 566 ADSDTATPADAALQAGLRAVVREMLDELTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVT 625

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RERIRQIE+KA++KL+HPSR+ +L ++L
Sbjct: 626 RERIRQIESKAMKKLRHPSRADQLITYL 653


>gi|269468904|gb|EEZ80491.1| DNA-directed RNA polymerase, sigma subunit [uncultured SUP05
           cluster bacterium]
          Length = 603

 Score =  399 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 235/654 (35%), Positives = 354/654 (54%), Gaps = 59/654 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
             + +K+I + +++GY+T  E+N  LP D ++ EQ+E  V +L  + I V D     D  
Sbjct: 9   KQALQKLIMIGKEQGYLTYAEINDILPEDLLTQEQVEPIVTILEELDIAVSDTVPDADTL 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E      S+++ ++V      DS    T DPVRMY+REMG ++LL +  EI IAK IE
Sbjct: 69  VVESGAKAQSTSAEAAVAALAALDSEFGRTTDPVRMYMREMGVVDLLEQSDEIRIAKEIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           AG   +M S+   P            L +G   + ++I                      
Sbjct: 129 AGVFEIMKSITLYPAITGFFFKAHTRLEEGKCKMTDVI---------------------- 166

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               +  +++  +       G+ +   +  + +  +   P E                  
Sbjct: 167 -IGYQGDAEDFAKKKAAFDAGEFDDDEEYEEMEEMEYTGPDEGQV--------------- 210

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                           + + +E Y++            K      K    +++L + +  
Sbjct: 211 ----------YGRFETVLKCSEAYQKTNE---------KHGFRDKKTIAARQQLSEGLSD 251

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           L L    +  ++E + D    +   E  +       G++R+ F +     E +  W+  A
Sbjct: 252 LRLAPKLVSTMMEVICDRVALVKKQEKTIQSACLYAGMEREQFFKLFNDNETNFDWLKGA 311

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           K   + +    +    D I   +  +     E  +++ E + +  + R+G+  A  AK +
Sbjct: 312 K--LDKKVAEALKVSKDEIYYAQKNLLEFEEEMQLTVPELKALNKLYRRGDRRAKKAKSQ 369

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLVIS+AKKY NRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 370 MIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQA 429

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R  R++  K  RE TPEE+A ++ +P   + K+L
Sbjct: 430 ITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREATPEELAVEMELPEYKINKIL 489

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEP+S+ETP+GD++ S++GDFIED N  SP++   + +L+ETT  +LA+L+PRE +V
Sbjct: 490 KIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTRESLKETTGELLANLSPREAKV 549

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           L+MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+
Sbjct: 550 LKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLQSFLE 603


>gi|84394590|ref|ZP_00993293.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84374781|gb|EAP91725.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 573

 Score =  398 bits (1022), Expect = e-108,   Method: Composition-based stats.
 Identities = 252/620 (40%), Positives = 351/620 (56%), Gaps = 50/620 (8%)

Query: 64  EDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ED + M+++MGI VV+   D +D   ++D  ++   A+ ++       +S    T DPVR
Sbjct: 1   EDIIQMINDMGIKVVETAPDADDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVR 60

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG++ELL+REGEI IAKRIE G   +  S+ E P T   ++   D +      L 
Sbjct: 61  MYMREMGTVELLTREGEIDIAKRIEDGINTVQLSVAEYPGTIPYILEQFDRVLAEEIRLT 120

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++I+    + P+         +G +         E  + D+++ + +     +  +++ +
Sbjct: 121 DLIN--GFVDPDD--------DGTAAPTATHIGSELAKTDLEDEDKEEAEDDEEEEEEDT 170

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
            +D                                   +     +   Y      Q+  +
Sbjct: 171 GIDP-------------------------------ELALEKFTALRTSY------QNRQL 193

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              +    S K  +    +  +     L   + D LV +L     R+   E  ++R    
Sbjct: 194 AINEYGHESPKATLATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVE 253

Query: 363 YG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
           YG + +  F+    G E    W+       +  +   +      I +   ++  I  ET 
Sbjct: 254 YGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDIIERETS 312

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 313 LTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 372

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  
Sbjct: 373 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 432

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PL
Sbjct: 433 EMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL 492

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSA   +LR  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEA
Sbjct: 493 DSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 552

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS+ LRSFLD
Sbjct: 553 KALRKLRHPSRSETLRSFLD 572


>gi|91227144|ref|ZP_01261628.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|91188796|gb|EAS75083.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
          Length = 574

 Score =  397 bits (1020), Expect = e-108,   Method: Composition-based stats.
 Identities = 249/615 (40%), Positives = 345/615 (56%), Gaps = 44/615 (7%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLRE 127
           M+++MGI VV+     D+    D  ++    +  +        +S    T DPVRMY+RE
Sbjct: 1   MINDMGIKVVETAPDADDLALNDDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMRE 60

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I  
Sbjct: 61  MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISG 120

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 +          G    + +   ++ E  D  E   D    ++       ++   
Sbjct: 121 FVDPDADDTAAPTATHIGSELTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPEL--- 177

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
                                            +   +++   Y+ L+      +   + 
Sbjct: 178 --------------------------------ALEKFNQLRSTYQNLQ------LAINEY 199

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
             +S K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + 
Sbjct: 200 GYNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMP 259

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W+       +  +   +    + I +   ++K I  ET +++  
Sbjct: 260 KKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQN 318

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 319 IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 378

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 379 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 438

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA  
Sbjct: 439 PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 498

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 499 TSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 558

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 559 LRHPSRSETLRSFLD 573


>gi|296161690|ref|ZP_06844493.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888004|gb|EFG67819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 628

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 218/665 (32%), Positives = 346/665 (52%), Gaps = 49/665 (7%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           S+  D  +   + ++KL ++RG++T  E+   LP     ++ +E  V   +++GI V D 
Sbjct: 8   SMEQDSREMQLRALMKLGKERGFLTHTEIVDHLPDCVAQADAIEGIVKAFNDVGIAVRDF 67

Query: 81  DDLEDEEGSEDSLD---LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
               D     D+         A + +        S      DP+R YLREMG+  LL+RE
Sbjct: 68  APTGDALLLGDAAQQSAPDDVAEDETATALTIAISEPGPAADPMRAYLREMGATPLLTRE 127

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIA+A+RIEA    M+  +   P T  A++   D +  G   + +++D           
Sbjct: 128 GEIAVARRIEACLREMLEVIALRPATVDAILARADRVAAGELDIDDLVD----------- 176

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                             +++  + +   +G     A  SK D    D  P NA      
Sbjct: 177 ---------------GFLEQQPDEMLPAMQGATAEGAAGSKVD----DGVPSNA------ 211

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
                +DSA  + A E ++  ++    + I    RE  +    AV G    +   +  ++
Sbjct: 212 -----NDSAGAIEADEARI-ARLTAGCNAIFLQVREQLASWRAAVAGTTGRREDAQSTLV 265

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQG 376
              +   +G +  +   I  L   +    + I   E  +LRLA    G+ RD+F+E   G
Sbjct: 266 --LIASTLGQIRFSARTIGELSADVRRAVEEIRGIERNVLRLAVNQGGMVRDMFVETFVG 323

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E DP W++ A           + C   SI   + ++  I    G+S+ E + I   +  
Sbjct: 324 SETDPEWLARAAAAAPACSAALMRC-APSIHGQQEKLAQIEAREGLSLQELKRISRKMNV 382

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            + E   A++ M+EANLRLV+SVAKKY   G+  LDL+QEGNIGLMKA ++F++  G+KF
Sbjct: 383 ADRELQDARRAMIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKF 442

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++Q+++R+IAD   TIR+PVHM D +H+V R A  M  +  R+    E+A +L
Sbjct: 443 STYATWWIRQSVSRAIADYGRTIRVPVHMADAMHRVKRVAGEMRQETGRQARSSELAARL 502

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M  E VR V ++T++P+SL+ PIG++  + LG+ +ED +A++PLD+ +QA+LR      
Sbjct: 503 GMSEEKVRSVQRVTRQPVSLDVPIGEDADTTLGEMVEDPSALAPLDALLQADLRVAIDAA 562

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  LTPRE +V+++RFG+   ++HTLEE+G QF VTRER+RQI+ KA++KL+H      L
Sbjct: 563 LGVLTPREAKVIKLRFGVDAVSEHTLEELGDQFDVTRERVRQIQNKALQKLRHSDGISTL 622

Query: 677 RSFLD 681
           +S+LD
Sbjct: 623 KSYLD 627


>gi|194289649|ref|YP_002005556.1| RNA polymerase sigma 70 (sigma d) factor [Cupriavidus taiwanensis
           LMG 19424]
 gi|193223484|emb|CAQ69489.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus taiwanensis
           LMG 19424]
          Length = 655

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 217/673 (32%), Positives = 353/673 (52%), Gaps = 46/673 (6%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +      +D +          + +I+L RQRGY+T  +++  LP +   +  ME  V   
Sbjct: 23  ATPAAAHTDPTAEAAARSQQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVGTF 82

Query: 71  SNMGINVVDGDDLEDEEGSEDS--LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           + MG+ + +     +     D   +     A   +       DS    T DPVRMY+REM
Sbjct: 83  AEMGVKIYEQTPDAETLLLSDGPVVASDEQAEEEAEVALATVDSEFGRTTDPVRMYMREM 142

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
            S  LL+R+ E+ IAKRIE G   M+ ++   P T   ++    ++      + +++D  
Sbjct: 143 SSATLLTRKQEVEIAKRIEDGLNNMVHAISACPFTIATILELSAKVASNEIGIDDVVDGL 202

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
           +                                     E   E AA  + D         
Sbjct: 203 S------------------------------------DESIAEPAAAAADDADDSSLDSA 226

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +  + D+ +  ++      +  A   +LR + M     +AE +  +R+        +   
Sbjct: 227 DETDEDDDDSADEGSSGQQSAEADLARLREECMKRFARVAEQFERMRA------ESEAGG 280

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKR 367
            ++      ++ + + + ++      I+ L   +  +   +   E ++++L  +  G++R
Sbjct: 281 AATPAFAAARDAVREELRTIRFTARTIERLCANVQGMVDEVRAIERQVVQLLVERCGMER 340

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +  + R  G E +  W        +  +   VA  +  +   + ++  I     +S++E 
Sbjct: 341 EDVIARFPGNETNLAW-GQGLVAEDRPYSAAVARALPDLEAHQQKLIDIQARAALSLAEL 399

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +   +   E +   AK EM +ANLRLVIS+AKKYTNRG+QFLDLIQEGNIGLMKA +K
Sbjct: 400 KAVNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMQFLDLIQEGNIGLMKAVDK 459

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WWV+QA+TR+IADQ+ TIR+PVHM ++I+K+ R +R +  +  +EP
Sbjct: 460 FEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQTGKEP 519

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P  +A++L M  + VR ++KI KEP+S+ETP+G++  + LGD I D +  +P D+A+QA
Sbjct: 520 DPAVLAERLDMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADAALQA 579

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR     +L  L+PRE +VLRMRFGI M+TD+TLEEVGKQF VTRERIRQIE+KA++KL
Sbjct: 580 GLRAVVREMLDELSPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKKL 639

Query: 668 KHPSRSKKLRSFL 680
           +HPSR+ +L ++L
Sbjct: 640 RHPSRADQLITYL 652


>gi|58584650|ref|YP_198223.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58418966|gb|AAW70981.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
          Length = 649

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 252/669 (37%), Positives = 399/669 (59%), Gaps = 40/669 (5%)

Query: 25  DFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           +      + ++  + ++ G++T +++N  L  + +SS+ ++DT+++L + GIN+++  + 
Sbjct: 8   EDKKKIIRDLVTKSIKKGGFITFDDINDKLSDENLSSDFIDDTISLLQDSGINILESSED 67

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+E  S             S              DDPVR+YL++M S++LLSR  EI IA
Sbjct: 68  EEEAPSNSDDSKLDDDDALSNTTTTL-----VQNDDPVRVYLQDMSSVKLLSRTDEIEIA 122

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+IE+ +  M+ ++ E+ +T + +  WRD+L+ G+ LLREIIDL+A    +        +
Sbjct: 123 KKIESEKHNMLRAIIETSVTLKMIKAWRDDLSSGSLLLREIIDLDAIYNSDFNAIPKEES 182

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E      ++  +  +   D +               +  ++DS   N E +  N D +  
Sbjct: 183 EESIEDDKDSENVSEGTKDDEYC-------------EDDEIDSKKGNDEKENSNEDINSA 229

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   ++  ME+ L PKV+ ALDEI        +L D A+  +KD    ++ + L +++  
Sbjct: 230 NLNVSILEMENDLLPKVIVALDEI-------ITLADEALTLRKDPSGGLRYQNLYDQIWS 282

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE-------RHQG 376
           +V  + L+ + +  + ++LY+I++ IM  E  L+  A+ Y I R+ FL+       R++ 
Sbjct: 283 IVLQIKLSDTAVAKITQKLYNINRSIMLEEANLISEAKKYNIDRESFLKVYADVLLRYKL 342

Query: 377 RELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
            E+     S  +    GE KN    F+    + I    N IK        ++ EF+ ++ 
Sbjct: 343 EEISSLKSSENQFCFTGELKNKFVKFIDDNFEHIADTLNNIKQH--IQEDNVQEFKELIK 400

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             +K E E S AK+ M++ANLRLV+S+AKKY+NRGL  LDLIQEGNIGLMKA +KFD+  
Sbjct: 401 RTQKHEREVSEAKQGMIKANLRLVVSIAKKYSNRGLALLDLIQEGNIGLMKAVDKFDYKR 460

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R++++++ REPT EE+
Sbjct: 461 GYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKLTHEMGREPTLEEL 520

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + +L MP+E +RKV+KI ++P+SL+ P G +D+S  GD IEDK    P D+AI  +LR  
Sbjct: 521 SMELGMPLERIRKVMKIARDPVSLDAPTGKDDSSTFGDCIEDKRVSKPEDAAILTDLRCI 580

Query: 613 TTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TT +LA+LTP+EER++RMRFG+G +  +HTLEE+G  F VTRERIRQ+E+KA+RKLKHP 
Sbjct: 581 TTNLLATLTPKEERIIRMRFGLGKDCKEHTLEEIGCIFKVTRERIRQVESKALRKLKHPC 640

Query: 672 RSKKLRSFL 680
           R++KLR F 
Sbjct: 641 RARKLRGFF 649


>gi|91779694|ref|YP_554902.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692354|gb|ABE35552.1| Sigma 70 (RpoD) [Burkholderia xenovorans LB400]
          Length = 628

 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 210/665 (31%), Positives = 340/665 (51%), Gaps = 49/665 (7%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           S+  D  +   + ++KL ++RG++T  E+   LP     ++ +E  V   +++GI V D 
Sbjct: 8   SMEQDSREMQLRALMKLGKERGFLTHTEIVDHLPDCVAQADAIEGIVKAFNDVGIAVRDF 67

Query: 81  DDLEDEEGSEDSLD---LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
               D     D+         A + +        S      DP+R YLREMG+  LL+RE
Sbjct: 68  APTGDALLLGDAAQQSAPDDVAEDETATALTIAISEPGPAADPMRAYLREMGATPLLTRE 127

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIA+A+RIEA    M+  +   P T  A++   D +  G   + +++D           
Sbjct: 128 GEIAVARRIEACLREMLEVIALRPATVDAILSRADRVAAGELDIDDLVD----------- 176

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           GF            + ++ E       ++     ++                        
Sbjct: 177 GFLEQQPDEMLPAMQGATAEGAAGSKADSGVPTSAS------------------------ 212

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
                 +SA  + A E ++  ++    + I    RE  +    AV G+  ++   +  ++
Sbjct: 213 ------ESAGAIEADEARI-ARLTAGCNAIFSQVREQLASWRAAVAGRTGQREEAQSTLV 265

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQG 376
              +   +G +  +   I  L   +    + I   E  +LRLA    G+ RD+F+E   G
Sbjct: 266 --LIASTLGQIRFSARTIGELSADVRRAVEEIRGIERNVLRLAVNQGGMARDMFVETFVG 323

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E DP W++ A           + C   SI   + ++  I    G+S+ E + I   +  
Sbjct: 324 SETDPEWLARAAAAAPACSAALMRC-APSIHSQQEKLAQIEAREGLSLQELKWISRKMNV 382

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            + E   A++ M+EANLRLV+SVAKKY   G+  LDL+QEGNIGLMKA ++F++  G+KF
Sbjct: 383 ADRELQDARRAMIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKF 442

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++Q+++R+IAD   TIR+PVHM D +H+V R A  M  +  R     E+A +L
Sbjct: 443 STYATWWIRQSVSRAIADYGRTIRVPVHMADAMHRVKRVAGEMRQETGRPARSSELAARL 502

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M  E VR V ++T++P+SL+ PIG+E  + LG+ +ED + ++PLD+ +QA+LR      
Sbjct: 503 GMSEEKVRSVQRVTRQPVSLDVPIGEEADTTLGEMVEDSSTLAPLDALLQADLRVAIDAA 562

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  LTPRE +V+++RFG+   ++HTLEE+G QF VTRER+RQI+ KA++KL+H      L
Sbjct: 563 LGVLTPREAKVIKLRFGVDAVSEHTLEELGDQFDVTRERVRQIQNKALQKLRHSDGISTL 622

Query: 677 RSFLD 681
           +++LD
Sbjct: 623 KNYLD 627


>gi|118602160|ref|YP_903375.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
 gi|118567099|gb|ABL01904.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 600

 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 244/654 (37%), Positives = 365/654 (55%), Gaps = 62/654 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
             S +K+I   +++GY+T  E+N  LP D ++ EQ+E  V +L  + I V D     D  
Sbjct: 9   KQSLQKLIMAGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDIAVSDIVPDADTL 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E      S+++ +++      DS    T DPVRMY+REMG ++LL +E EI IAK IE
Sbjct: 69  VVESGAKAQSTSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLEQEDEIRIAKEIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           AG   +M  +   P+           L +G   + ++I            G+   TE  +
Sbjct: 129 AGVFEIMKGITLYPVITDFFFKAHTRLEEGKCKMTDVI-----------IGYQGDTEDFA 177

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +K    + + + D+  E                 +   P EN                 
Sbjct: 178 VKKAAFDAGKFDNDEEHEDM---------------EYTGPDEN----------------- 205

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                      +V    + I++  +      +      K      K   ++++L + +  
Sbjct: 206 -----------QVYNRFETISKCSKTYNETNEKLGFRHK------KTIEMRQQLSQSLSD 248

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           L L    ++ ++E + +  +++   E  +       G+ R  F E     E +  W+S  
Sbjct: 249 LRLAPKLVNTMIEVICNRVEQVKKQEKTIQNKCLDAGMNRLYFFESFSKNETNFDWLSAI 308

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           K   + E K  +    D I   +  ++    E  ++I+E + +  M R+G+  A  AK +
Sbjct: 309 KLDEKTEEK--LKVSKDEIYYAQKNLQQFEEEMQLTITELKTLNKMYRRGDRRAKKAKSQ 366

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLVIS+AKKY NRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 367 MIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQA 426

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+ R  R++  K  RE +PEE+A ++ +P   + K+L
Sbjct: 427 ITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREASPEELATEMELPEYKIIKIL 486

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI+KEP+S+ETP+GD++ S++GDFIED N  SP++   + +LRETT+ +L++L+PRE +V
Sbjct: 487 KISKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTKESLRETTSELLSNLSPREAKV 546

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           L+MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSR+ KL+SFL+
Sbjct: 547 LKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLQSFLE 600


>gi|145589878|ref|YP_001156475.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048284|gb|ABP34911.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 678

 Score =  391 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 235/683 (34%), Positives = 363/683 (53%), Gaps = 49/683 (7%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
             K++    +   +        +      K +IK+   +GY+T  E+N  +  +   ++ 
Sbjct: 39  KAKEKALLKEFAAQQLGTEEQQELRRARLKTLIKMGMSKGYLTHGEMNDVMSDELSDADA 98

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDD 119
           +E  +++L+++GI V +     +     D+ + A+S   +    +      DS    T D
Sbjct: 99  LETLISLLNDIGITVYEQAPDAETLILSDNTEAAASEEEAEEKAEAALSTVDSEFGRTTD 158

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG+++LL+REGEI IAK+IEAG   M+ +L   P+T   ++   D++  G  
Sbjct: 159 PVRMYMREMGTVDLLTREGEIVIAKKIEAGLKDMVMALAACPVTIAEIMSNVDKIASGEM 218

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            + + +D    + P ++       E       E+  +E   D+     G   + AK  + 
Sbjct: 219 EIDQFVD--GLVDPNAEDIKLGPEEPEVDPDAEEGDEEGGEDEGGGGGGAATANAKQLE- 275

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                                              +L+   +     +     ++R   D
Sbjct: 276 -----------------------------------ELKQISLEKFAIVRAQAEKMRRAFD 300

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR- 358
                             +E +   +    L    ++ L + +     ++   E  ++  
Sbjct: 301 KEGYNC------PAYIKAQEAIRAELLGFRLTAKSVEKLCDTMRSQVDQVWKLERGIVNL 354

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           L    G+ R   L+      ++  W        +  +   +   V +I +++ ++  I  
Sbjct: 355 LVDKVGVNRGEVLKDFPKMSMNLTWTEKLLKENKP-YSALLQRNVPAIQELQQKLIDIQT 413

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              I + E + +   +  GE  A  AK+EM  ANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 414 RVVIPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDLIQEGN 473

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 474 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 533

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP    +A K+ +P + +RK++KI KEPIS+ETPIGD++ SHLGDFIED N +
Sbjct: 534 ILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDGNTL 593

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A+  ++R+    VL SLTPRE +VLRMRFG+ M+TDHTLEEVGKQF VTRERIRQ
Sbjct: 594 APAEAALHDSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQ 653

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RK++HPSRS KL++FL+
Sbjct: 654 IEAKALRKMRHPSRSDKLKTFLE 676


>gi|116514979|ref|YP_802608.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256833|gb|ABJ90515.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 613

 Score =  389 bits (999), Expect = e-106,   Method: Composition-based stats.
 Identities = 254/653 (38%), Positives = 359/653 (54%), Gaps = 50/653 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG-S 89
            K ++   +++GY+T  E++  LP D V ++Q+++ + M+ ++GI +V+     +E   +
Sbjct: 9   LKLLVSHGKEQGYLTYSEVHDHLPNDIVDADQIKNIIQMIKDLGIQIVEEVREIEELIIN 68

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E   D       ++  +    ++    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 69  EAPTDTDEDTVEAATQVLSNVETEIGRTTDPVRMYMREMGTVELLTREGEIGIAKRIEEG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +S+ E P +   L+     +  G   L E+I            GF    +    +
Sbjct: 129 INQVQSSVSEYPTSILYLLEQYHHVKLGNIKLSELI-----------IGFIDKKKKPKKK 177

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
              +    K+                              NAE +E  +D+         
Sbjct: 178 IFTEEVITKKL---------------------YNNKKKSLNAEKNEDTIDDYNHIDPILA 216

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                QL+ +       I                 Q   ++         KL K+     
Sbjct: 217 KKKFSQLKKQYYITNHII-----------------QNKPRNHKDSINAIHKLSKIFKQFR 259

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           L   + D LV  + +   +I   E +++ L             +   +    +   Y+  
Sbjct: 260 LAPKQFDYLVTNMRNEIHKITLQEKKIMNLCVHTCKIPKKKFLKFFKKHKKNYKNFYSVI 319

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +  W   +      I+K   ++  I  +T + I++ + I   +  GE +A  AKKEMV
Sbjct: 320 KKKKSWLYKLKFIKKEIIKRIKKLLIIEKKTKLKITQIKDINKRIILGEEKAKRAKKEMV 379

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAIT
Sbjct: 380 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 439

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE+++K+ +  E +RKVLKI
Sbjct: 440 RSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELSEKMLISEEKIRKVLKI 499

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEPIS+ETPIG++D +HLGDFIED N   PL+SA   +L+  T  VL+ LT RE +VLR
Sbjct: 500 AKEPISMETPIGEDDDTHLGDFIEDTNLELPLESATSESLKTITNDVLSGLTDREAKVLR 559

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           MRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+RKL+HPSRS+ L+SFLD 
Sbjct: 560 MRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRSEILKSFLDN 612


>gi|126642737|ref|YP_001085721.1| sigma D (sigma 70) factor of RNA polymerase major sigma factor
           during exponential growth [Acinetobacter baumannii ATCC
           17978]
          Length = 580

 Score =  386 bits (992), Expect = e-105,   Method: Composition-based stats.
 Identities = 256/616 (41%), Positives = 350/616 (56%), Gaps = 39/616 (6%)

Query: 69  MLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           ML ++GI V +   + +D    E +      A   +  +    ++    T DPVRMY+RE
Sbjct: 1   MLQDVGIPVHERAPESDDTMFGESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMRE 60

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI+IAKRIE G   ++ S+   P   + ++   ++   G   L +I  L
Sbjct: 61  MGTVELLTREGEISIAKRIEEGIRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADI--L 118

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              + PE+        E     + ED S  K   +V+  + D E  ++   D        
Sbjct: 119 SGYLDPETDEDIPEVLEDVEELEEEDESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPD 178

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE A+     L+     +   +                                    K 
Sbjct: 179 PEVAKVRFAELEAAWAQTKAVIE-----------------------------------KH 203

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
            ++S +     E L  +           D++ E +    ++I  NE E++R A   G + 
Sbjct: 204 GRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMD 263

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           R+ F      +E +P W+         E K  +      +L  + +I  I  E G+++SE
Sbjct: 264 RNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSE 323

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 324 IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 383

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ RE
Sbjct: 384 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 443

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEE+ ++L M    VRKVLKI KEPIS+ETPIGD++ SHLGDFIED+N  SP+D+A  
Sbjct: 444 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATS 503

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E T  VL +LT RE +VL+MRFGI M TDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 504 EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 563

Query: 667 LKHPSRSKKLRSFLDG 682
           L+HPSRS+ LRSFL+ 
Sbjct: 564 LRHPSRSEHLRSFLEN 579


>gi|225677095|ref|ZP_03788097.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225590854|gb|EEH12079.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 669

 Score =  386 bits (990), Expect = e-105,   Method: Composition-based stats.
 Identities = 264/675 (39%), Positives = 399/675 (59%), Gaps = 31/675 (4%)

Query: 24  FDFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
            +      K ++  + ++ G++T +++N  L  +  SS+ ++D +++L + GINV++  +
Sbjct: 8   AEDKKKIIKDLVTKSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVLESIE 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E     ED    +  +            +     DDPVR+YL++M S++LLSR  EI I
Sbjct: 68  DE-----EDIPSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEI 122

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AK+IE+ +  M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A    +        
Sbjct: 123 AKKIESEKHNMLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAIYNSDFNVVPKEE 182

Query: 203 TEGHSYQKREDSSQEKERDD-----VQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           +E       +    E   +D       E +       K SK    + DS   + E D  N
Sbjct: 183 SEESEESAEDVEDSEDVSEDAEYCSDDEKDSKKSDDEKDSKKSDDEKDSKKSDDEKDGNN 242

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
            D    +   ++  ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L
Sbjct: 243 EDISSVNLNVSILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENL 296

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF------- 370
             ++  +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       
Sbjct: 297 YNQIWSIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDV 356

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISE 426
           L +H+ +++    ++  +    GE KN    F+    + I    N IK    E   ++ E
Sbjct: 357 LLKHELKKISLLKINENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQHIQED--NVQE 414

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F+ ++  ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +
Sbjct: 415 FKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVD 474

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ RE
Sbjct: 475 KFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGRE 534

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI 
Sbjct: 535 PTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAIL 594

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           A+LR  TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+R
Sbjct: 595 ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALR 654

Query: 666 KLKHPSRSKKLRSFL 680
           KLKHPSR++KLR F 
Sbjct: 655 KLKHPSRARKLRGFF 669


>gi|225630998|ref|YP_002727789.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
 gi|225592979|gb|ACN95998.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
          Length = 650

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 266/670 (39%), Positives = 403/670 (60%), Gaps = 39/670 (5%)

Query: 24  FDFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
            +      K ++  + ++ G++T +++N  L  +  SS+ ++D +++L + GINV++  +
Sbjct: 7   AEDKKKIIKDLVTKSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVLESSE 66

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E     ED    +  +            +     DDPVR+YL++M S++LLSR  EI I
Sbjct: 67  DE-----EDIPSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEI 121

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AK+IE+ +  M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A    +        
Sbjct: 122 AKKIESEKHNMLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAIYNSDFN------ 175

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  K E    E+  +DV+++E   E A   S D++   DS   + E D  N D   
Sbjct: 176 ----VVPKEESEESEESAEDVEDSEDVSEDAEYCSDDEK---DSKKSDDEKDGNNEDISS 228

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            +   ++  ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++ 
Sbjct: 229 VNLNVSILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIW 282

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQ 375
            +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+
Sbjct: 283 SIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHE 342

Query: 376 GRELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +++    ++  +    GE KN    F+    + I    N IK        ++ EF+ ++
Sbjct: 343 LKKISLLKINENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQH--IQEDNVQEFKELI 400

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+ 
Sbjct: 401 KRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYK 460

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ REPT EE
Sbjct: 461 RGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGREPTLEE 520

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR 
Sbjct: 521 LSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRG 580

Query: 612 TTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHP
Sbjct: 581 ITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHP 640

Query: 671 SRSKKLRSFL 680
           SR++KLR F 
Sbjct: 641 SRARKLRGFF 650


>gi|153828433|ref|ZP_01981100.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
 gi|148876142|gb|EDL74277.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
          Length = 572

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 241/572 (42%), Positives = 331/572 (57%), Gaps = 36/572 (6%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++  
Sbjct: 35  ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQ 94

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
            D +      L ++I     + P                       E    D+ + +  +
Sbjct: 95  FDRVQAEELRLTDLI--SGFVDPNDM--------ETEAPTATHIGSELSEADLADEDDAV 144

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
                  +D+    D    ++E +     E                      A ++  E+
Sbjct: 145 VEDEDEDEDEDEDGDGESSDSEEEVGIDPEL---------------------AREKFNEL 183

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
             + ++LQ   +   +  + S +     + ++ +     L   + D LVE L     R+ 
Sbjct: 184 RGKFQNLQ---LAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 240

Query: 351 HNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
             E  +++       + +  F+    G E +  W+       +  +   V  + + I + 
Sbjct: 241 TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLA-SDKPYVAKVREQEEEIRRS 299

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             +++ I  ET +S+   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQ
Sbjct: 300 IQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 359

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 360 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 419

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ R +R+M  ++ REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLG
Sbjct: 420 NKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 479

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED     PLDSA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF
Sbjct: 480 DFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 539

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 540 DVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 571


>gi|42521092|ref|NP_967007.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
 gi|42410833|gb|AAS14941.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
          Length = 642

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 265/670 (39%), Positives = 400/670 (59%), Gaps = 48/670 (7%)

Query: 24  FDFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
            +      K ++  + ++ G++T +++N  L  +  SS+ ++D +++L + GINV++  +
Sbjct: 8   AEDKKKIIKDLVTKSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVLESSE 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E     ED    +  +            +     DDPVR+YL++M S++LLSR  EI I
Sbjct: 68  DE-----EDIPSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEI 122

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AK+IE+G+  M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A    +        
Sbjct: 123 AKKIESGKHNMLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAMYNSDFN------ 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  K E    E+  +DV+++E   E A   S D            E D  N D   
Sbjct: 177 ----VVPKEESEESEESAEDVEDSEDVSEDAEYCSDD------------EKDGNNEDISS 220

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            +   ++  ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++ 
Sbjct: 221 VNLNVSILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIW 274

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQ 375
            +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+
Sbjct: 275 SIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHE 334

Query: 376 GRELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +++    ++  +    GE KN    F+  + + I    N IK        ++ EF+ ++
Sbjct: 335 LKKISLLKINENQSSFTGELKNKFLRFIDDKSEHIASTLNGIKQH--IQEDNVQEFKELI 392

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+ 
Sbjct: 393 KRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYK 452

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ REPT EE
Sbjct: 453 RGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGREPTLEE 512

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR 
Sbjct: 513 LSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRG 572

Query: 612 TTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHP
Sbjct: 573 ITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHP 632

Query: 671 SRSKKLRSFL 680
           SR++KLR F 
Sbjct: 633 SRARKLRGFF 642


>gi|295698783|ref|YP_003603438.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
 gi|291157386|gb|ADD79831.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
          Length = 607

 Score =  380 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 248/636 (38%), Positives = 355/636 (55%), Gaps = 42/636 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++   +++GY+T  E+N  LP D V S+Q+ED +  + +MGI V +    EDE    
Sbjct: 9   LKVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTEEVPDEDELILT 68

Query: 91  DSLDLASSAS-NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D        +  ++  +    +     T DP+RMY+REMG+IELL+REGEI IAKRIE G
Sbjct: 69  DPTSSTDEETVEAATQVLSSVEQEIGRTTDPIRMYMREMGTIELLTREGEIDIAKRIEDG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              +  S+ E P +   ++        G   L +II            G        S +
Sbjct: 129 INQIQRSISEYPKSISYILKQYFLFESGEMKLSDII-----------TGLSSEDTFSSSK 177

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
             + +    + + +     +I S     KD     +S   N E++  ++D          
Sbjct: 178 NVDKNFSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHIDP--------- 228

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL-KEKLVKLVGSL 328
                              + + EL++  +   +  K+        +L  + L ++    
Sbjct: 229 ---------------KIARKKFLELQNQYEKVTHSLKENGIKSSQSILDIQDLCEIFKQF 273

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR--ELDPHWVS 385
            L   ++D L+  +    ++I   E  ++ ++ + Y I +  FL        E D   + 
Sbjct: 274 RLVPKQLDFLISDIRKTIEKIKIQEKLIINISFKEYKIPKKYFLNLFSENPKEYDLKELI 333

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            +  + + + K F      +I++  NE+  I  +TGISIS+ + I   +  GE  A  AK
Sbjct: 334 VSNRYNKKDEKKFKLDS--TIVQALNELNEIEKDTGISISKIKEIGRKISIGETIARRAK 391

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 392 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 451

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+   +R++  +  REP+PEE+++++ +P E +RK
Sbjct: 452 QAITRSIADQARTIRIPVHMIETINKLNHISRQILQETGREPSPEELSERMLIPEEKIRK 511

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI +EPIS+ETPIGD++ SHLGDFIED     PL+SA   +LR  T  VL+ LT RE 
Sbjct: 512 VLKIAREPISMETPIGDDEDSHLGDFIEDTTLELPLESATSESLRSATNEVLSGLTTREA 571

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 572 KVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEA 607


>gi|303257749|ref|ZP_07343761.1| RNA polymerase sigma factor RpoD [Burkholderiales bacterium 1_1_47]
 gi|302859719|gb|EFL82798.1| RNA polymerase sigma factor RpoD [Burkholderiales bacterium 1_1_47]
          Length = 814

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 251/684 (36%), Positives = 372/684 (54%), Gaps = 69/684 (10%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
              K   +    H + DD    +   +  K +I++ ++RGY+T  E+N  +P + V  +Q
Sbjct: 192 KAMKEALNRSYAHHEEDDK---ETRLNKLKALIRMGKERGYLTYSEVNDHMPENIVDPDQ 248

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK--DSADRSTDDP 120
           ++  ++ L+++GI V +     D+    DS+  AS  +            DS    T DP
Sbjct: 249 IDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEEAEAALATVDSEFGRTTDP 308

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMGS+ELL+REG                                          
Sbjct: 309 VRMYMREMGSVELLTREG------------------------------------------ 326

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
                  E  I    + G  H     S       +  ++ + V+     I+         
Sbjct: 327 -------EIEIAKRIEDGLKHMVHAISGCPTTIVAILEDAEKVRNGTMQIDQIVD----- 374

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQD 299
              VD   E A       DE  D  A  ++A + D+L+  V+  LD   E+Y++L+   +
Sbjct: 375 -GLVDGLDEEASEQVAEDDESTDIGASGMTAGQIDELKTVVLAKLDHCKELYQDLKHAYE 433

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +   S      ++ + + + SL    + ++ L   L    + +   E  +  +
Sbjct: 434 A------EGYRSPAFIKAQDAIQEELLSLRFTANTVERLCTMLKTQVEEVRKYESRIYDI 487

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                 + R++FL+     E +  W S A    +  +   V  ++  I  ++ ++++I  
Sbjct: 488 VVNRAKMPRELFLKEFLDNETNLAW-SQAIAESDKPYAIDVKRKLPEIQHLQQQLQNIQN 546

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + + + + + +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 547 AVTLPLKDLKDVYNQMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 606

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 607 VGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 666

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P E+A+K+ MP + +RK+LKI KEPIS+ETPIGD++ SHLGDF+ED   V
Sbjct: 667 ILQETGVEPDPAELAEKMDMPEDKIRKILKIAKEPISMETPIGDDEDSHLGDFLEDFGTV 726

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A Q++L E T  VL SLTPRE +VLRMRFGI M+TDHTLEEVG+QF VTRERIRQ
Sbjct: 727 APAEAAQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFDVTRERIRQ 786

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SF++G
Sbjct: 787 IEAKALRKLRHPSRSDKLKSFMEG 810


>gi|331001176|ref|ZP_08324803.1| RNA polymerase sigma factor RpoD [Parasutterella excrementihominis
           YIT 11859]
 gi|329569108|gb|EGG50900.1| RNA polymerase sigma factor RpoD [Parasutterella excrementihominis
           YIT 11859]
          Length = 814

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 251/684 (36%), Positives = 372/684 (54%), Gaps = 69/684 (10%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
              K   +    H + DD    +   +  K +I++ ++RGY+T  E+N  +P + V  +Q
Sbjct: 192 KAMKEALNRSYAHHEEDDK---ETRLNKLKALIRMGKERGYLTYSEVNDHMPENIVDPDQ 248

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK--DSADRSTDDP 120
           ++  ++ L+++GI V +     D+    DS+  AS  +            DS    T DP
Sbjct: 249 IDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEEAEAALATVDSEFGRTTDP 308

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMGS+ELL+REG                                          
Sbjct: 309 VRMYMREMGSVELLTREG------------------------------------------ 326

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
                  E  I    + G  H     S       +  ++ + V+     I+         
Sbjct: 327 -------EIEIAKRIEDGLKHMVHAISGCPTTIVAILEDAEKVRNGTMQIDQIVD----- 374

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAME-DQLRPKVMCALDEIAEVYRELRSLQD 299
              VD   E A       DE  D  A  ++A + D+L+  V+  LD   E+Y++L+   +
Sbjct: 375 -GLVDGLDEEASEQVAEDDESTDIGASGMTAGQIDELKTVVLAKLDHCKELYQDLKHAYE 433

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +   S      ++ + + + SL    + ++ L   L    + +   E  +  +
Sbjct: 434 A------EGYRSPAFIKAQDAIQEELLSLRFTANTVERLCTMLKTQVEEVRKYESRIYDI 487

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                 + R++FL+     E +  W S A    +  +   V  ++  I  ++ ++++I  
Sbjct: 488 VVNRAKMPRELFLKEFLDNETNLAW-SQAIAESDKPYAIDVKRKLPEIQHLQQQLQNIQN 546

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              + + + + + + +  GE +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN
Sbjct: 547 AVTLPLKDLKDVYNQMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGN 606

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+
Sbjct: 607 VGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 666

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +   EP P E+A+K+ MP + +RK+LKI KEPIS+ETPIGD++ SHLGDF+ED   V
Sbjct: 667 ILQETGVEPDPAELAEKMDMPEDKIRKILKIAKEPISMETPIGDDEDSHLGDFLEDFGTV 726

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A Q++L E T  VL SLTPRE +VLRMRFGI M+TDHTLEEVG+QF VTRERIRQ
Sbjct: 727 APAEAAQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFDVTRERIRQ 786

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS KL+SF++G
Sbjct: 787 IEAKALRKLRHPSRSDKLKSFMEG 810


>gi|86157148|ref|YP_463933.1| sigma 70 (RpoD) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773659|gb|ABC80496.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 805

 Score =  378 bits (971), Expect = e-102,   Method: Composition-based stats.
 Identities = 263/670 (39%), Positives = 390/670 (58%), Gaps = 40/670 (5%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D +         K+++   R++G++T +E+N  LP D + S+Q++D ++M     I VV
Sbjct: 170 QDDMSDITERSEVKELMARGREKGFLTYDEVNDALPSD-IGSDQIDDVMSMFGEHDIEVV 228

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DG   E +    D      + + S    ++  D+    ++DPVRMYLR+MGS+ LL+REG
Sbjct: 229 DG--AEKKMKLPDKPPEPEAKAESEEEKEEEDDAGYGKSNDPVRMYLRKMGSVSLLTREG 286

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E+ IAKRIE G   ++A++  S +  + ++   + L  G   +REII          K  
Sbjct: 287 EVEIAKRIEEGEKEILAAVLSSSIAIREILELGERLRKGKIRVREII----------KDA 336

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                      + E     +  +   E E +  +    +          P   + +ER +
Sbjct: 337 GDEQQAEQEEPEEELDEAVEAAEGQGEAEAEAGAEGDGAAAAEGAEPEKPRIPKEEERKV 396

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVK 313
           +                    V+  +D I ++ R++  +++       ++  K ++   +
Sbjct: 397 E-------------------HVLKHIDRIRKLERDVAKVRETLQGGKKLSEVKRKELKGE 437

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            + ++ ++++ + ++ LN+ +ID +V +L    KR+   E E     +  G+        
Sbjct: 438 VRAIEAEMMENLEAIQLNKKQIDRIVLRLKSFIKRVEEAEREFFDCERRTGVPVKDLRRL 497

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVS 432
              RE         K   +         E+D ++     +I  +  E  + + E R    
Sbjct: 498 L--RETREDEAERKKLAKKLRCALDEVEELDRTLRSAGRKILRVQEEAEVPVDELRRTYR 555

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+  GE +A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 556 MIGDGERKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKR 615

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEI
Sbjct: 616 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEI 675

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E 
Sbjct: 676 AEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQ 735

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 736 TRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSR 795

Query: 673 SKKLRSFLDG 682
           SK+L+SF++ 
Sbjct: 796 SKRLKSFVES 805


>gi|153003633|ref|YP_001377958.1| RNA polymerase sigma-70 subunit RpoD [Anaeromyxobacter sp. Fw109-5]
 gi|152027206|gb|ABS24974.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter sp.
           Fw109-5]
          Length = 819

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 261/669 (39%), Positives = 390/669 (58%), Gaps = 40/669 (5%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D +         K +++  R++G++T +E+N  LP D + S+Q++D ++M     I VV
Sbjct: 186 QDDMSDITERSEVKALMQRGREKGFLTYDEVNDALPSD-IGSDQIDDVMSMFGEHDIEVV 244

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DG   E +    D        + +     + +D     ++DPVRMYLR+MGS+ LL+REG
Sbjct: 245 DG--AEKKMKLPDKPPEPEGKAEAEEEKDEDEDPGYGKSNDPVRMYLRKMGSVSLLTREG 302

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E+ IAKRIE G   ++A++  S +  + ++   + L  G   +REII             
Sbjct: 303 EVEIAKRIEEGEKEILAAVLSSSIAIREILELGERLRKGKIRVREII------------- 349

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                            ++   +   E E +      +  +   +  +    AE  E   
Sbjct: 350 -----------------KDAGDEQQAEREEEEIEEESLEAEGAEEASAEAAGAEGPEGGA 392

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD----NAVNGQKDEKSSVKC 314
            E  +     +   E++    V+  +D I ++  ++  +++      V+  K ++   + 
Sbjct: 393 AEGAEPERPKIPKEEERKVEHVLKHIDLIRKLEDDVVKVKETLTTKKVSEPKRKELRSEI 452

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
           K ++ ++++ + ++ LN+ +ID +V +L    KR+   E EL    ++  +         
Sbjct: 453 KTIEGEMMEHLEAIQLNKKQIDRIVLRLKGFIKRVEEAERELADCERATSVPVRELRRLL 512

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSM 433
             RE      +  K   +         E+D ++     ++  +  E  + + E R     
Sbjct: 513 --REAREDEGARKKLGKKLGCSAEEVEELDRTVRSAYRKMLRVQEEAEVPVDELRRTYRT 570

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +  GE +A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 571 ISDGEHKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRG 630

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA
Sbjct: 631 YKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEIA 690

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E T
Sbjct: 691 EKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQT 750

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 751 RKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRS 810

Query: 674 KKLRSFLDG 682
           K+L+SF++ 
Sbjct: 811 KRLKSFVEN 819


>gi|317050370|ref|YP_004111486.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
 gi|316945454|gb|ADU64930.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
          Length = 627

 Score =  378 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 259/670 (38%), Positives = 374/670 (55%), Gaps = 77/670 (11%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++++ +++RG++T +ELN FLP +    + ++  +  L  +GI +V  + L   +G    
Sbjct: 13  QLMEKSKERGFITYDELNDFLPKETTDPDLIDSIIENLGRIGIRLVATNKLSKGKGESSD 72

Query: 93  LDLASSASNSSVFLQKRKDSADR---------------------STDDPVRMYLREMGSI 131
                     +V      ++ D                       TDDPVR+YL+EMGS+
Sbjct: 73  EFAVFLKDQPAVLDGDDIENDDEEESDEEESEESTLDLTPDTSFRTDDPVRLYLKEMGSV 132

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+REGE+ IAK+IEAG   +++SL   P   ++L    ++L  G   L++II L+  +
Sbjct: 133 PLLTREGEVDIAKKIEAGYEKIISSLIAIPKAVESLQELAEKLEAGEIGLKDIIMLDDEV 192

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G     G     +       ED+                                     
Sbjct: 193 GSMGIIGNSTSYDEDEESAEEDAEDPS--------------------------------- 219

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                        SAH  +    ++R  V+   + I ++ ++L SL++    G+KD    
Sbjct: 220 -------------SAHVRAENATEMRDFVI---NSICDIGQQLLSLREYKAKGKKD---- 259

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
            K +   E +  ++  + L    I  +   + +          EL ++ +  G+ RD  L
Sbjct: 260 -KYRKTLESMTAVISEIRLTNETISRISNMIKEQYLESRRAGSELAKIIKVTGLSRDD-L 317

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           +   G E     V  A+       ++F    +    +    ++ I   TG+  +E   IV
Sbjct: 318 QYLCGEESSAEHVESARAKTSLRAEDF-ERLLGKASESIASLREIEESTGVDANELMSIV 376

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             VR+GE E+  AK +++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ 
Sbjct: 377 QQVREGEEESKAAKMQLIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 436

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ REPTPEE
Sbjct: 437 RGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLVRTSRNLVQELGREPTPEE 496

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA K+ +PVE VRKVLKI KEPISLETPIG+E+ S LGDFIEDKN VSP ++ I  NL+E
Sbjct: 497 IADKMDLPVEKVRKVLKIAKEPISLETPIGEEEDSSLGDFIEDKNTVSPAEAVISFNLKE 556

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  VL++RFGI  ++DHTLEEVGK+F VTRERIRQIEAKA+RKL+HP+
Sbjct: 557 QVRSVLHTLSAREAEVLKLRFGIDTDSDHTLEEVGKKFNVTRERIRQIEAKALRKLRHPT 616

Query: 672 RSKKLRSFLD 681
           RSK LR+FL+
Sbjct: 617 RSKILRTFLE 626


>gi|220915874|ref|YP_002491178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219953728|gb|ACL64112.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 802

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 262/670 (39%), Positives = 390/670 (58%), Gaps = 43/670 (6%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D +         K+++   R++G++T +E+N  LP D + S+Q++D ++M     I VV
Sbjct: 170 QDDMSDITERSEVKELMARGREKGFLTYDEVNDALPSD-IGSDQIDDVMSMFGEHDIEVV 228

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DG   E +    D      + +++    ++  D+    ++DPVRMYLR+MGS+ LL+REG
Sbjct: 229 DG--AEKKMKLPDKPPEPEAKADAEEEKEEEDDAGYGKSNDPVRMYLRKMGSVSLLTREG 286

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E+ IAKRIE G   ++ ++  S +  + ++   + L  G   +REII             
Sbjct: 287 EVEIAKRIEEGEKEILGAVLSSSIAIREILELGERLRKGKIRVREII------------- 333

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                              K+  D Q+ E +          +  +     E    D    
Sbjct: 334 -------------------KDAGDEQQAEAEEPEEELDEAAEAPEGQGDAEAEAGDGAAP 374

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVK 313
            E  +     +   E++    V+  +D I ++ R++  +++       ++  K ++   +
Sbjct: 375 AEGAEPEKPRIPKEEERKVEHVLKHIDRIRKLERDVAKVRETLQGGKKLSEVKRKELKGE 434

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            + ++ ++++ + ++ LN+ +ID +V +L    KR+   E E     +  G+        
Sbjct: 435 IRAIEAEMMENLEAIQLNKKQIDRIVLRLKSFIKRVEEAEREFFDCERRTGVPVKDLRRL 494

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVS 432
              RE         K   +         E+D ++     +I  +  E  + + E R    
Sbjct: 495 L--RETREDEAERKKLAKKLRCALDEVEELDRTLRSAGRKILRVQEEAEVPVEELRRTYR 552

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+  GE +A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 553 MIGDGERKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKR 612

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEI
Sbjct: 613 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEI 672

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E 
Sbjct: 673 AEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQ 732

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 733 TRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSR 792

Query: 673 SKKLRSFLDG 682
           SK+L+SF++ 
Sbjct: 793 SKRLKSFVES 802


>gi|108763751|ref|YP_633357.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|133312|sp|P17531|RPOD_MYXXA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-80
 gi|150118|gb|AAA25404.1| sigma factor (rpoD) [Myxococcus xanthus]
 gi|710343|gb|AAB60208.1| major sigma factor [Myxococcus xanthus]
 gi|108467631|gb|ABF92816.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|1586812|prf||2204381D sigma factor
          Length = 708

 Score =  377 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 259/673 (38%), Positives = 392/673 (58%), Gaps = 54/673 (8%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D D+  +D ++  V +      K ++   R++G++T +E+N  LP D VSS+Q++D ++M
Sbjct: 90  DPDAVEDDIEEDPVAE--RKEVKDLLAAGREKGFLTYDEVNDALPADIVSSDQIDDVMSM 147

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
             +  I +VD          + ++ +     ++    +   D     ++DPVR+YLR+MG
Sbjct: 148 FGDNDIEIVDAQKAAQNNEIKPTVTVEEEKEDADEDEKDEDDEPGGKSNDPVRLYLRKMG 207

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ LL+REGE+ IAKRIE G   ++ +L    +  + ++   ++L      +R++I    
Sbjct: 208 SVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEEILDIGNKLKTAKLRVRDVI---- 263

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                              +   + +Q +  ++  E  G+ ++ A++++ + +K++   +
Sbjct: 264 -------------------KDAPEETQSEGAEEAPEEVGEGDAPAQLAQSELNKIEQICK 304

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             E   +   +                        D + E     + L +      K E 
Sbjct: 305 QIERFRKFAQD-----------------------CDVLEEELSSKKKLTEVRKKEVKQE- 340

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                K L+ K+++++  + LN+ ++D +V  L  + +R+   E EL  L + Y      
Sbjct: 341 ----IKDLRTKMMEVLEEMRLNKKQVDRIVINLKALIERVDKAEDELRDLERRYDCSMKE 396

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
              + +    +P+     +       +     + D +     +IK +  E  + +   R 
Sbjct: 397 LRPQLKESRENPNIGKKLQKQLNLTPEQLEVLDRD-VRTAVRKIKKVEEEANLPVESLRR 455

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
               +R GE  A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF+
Sbjct: 456 NYDAIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 515

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I REPTP
Sbjct: 516 YKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEIGREPTP 575

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEIA+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL
Sbjct: 576 EEIAEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPADAVINMNL 635

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+H
Sbjct: 636 AEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRH 695

Query: 670 PSRSKKLRSFLDG 682
           PSRSK+LRSF++ 
Sbjct: 696 PSRSKRLRSFVES 708


>gi|197121174|ref|YP_002133125.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
 gi|196171023|gb|ACG71996.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
          Length = 805

 Score =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 262/670 (39%), Positives = 390/670 (58%), Gaps = 43/670 (6%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D +         K+++   R++G++T +E+N  LP D + S+Q++D ++M     I VV
Sbjct: 173 QDDMSDITERSEVKELMARGREKGFLTYDEVNDALPSD-IGSDQIDDVMSMFGEHDIEVV 231

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           DG   E +    D      + +++    ++  D+    ++DPVRMYLR+MGS+ LL+REG
Sbjct: 232 DG--AEKKMKLPDKPPEPEAKADAEEEKEEEDDAGYGKSNDPVRMYLRKMGSVSLLTREG 289

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E+ IAKRIE G   ++ ++  S +  + ++   + L  G   +REII             
Sbjct: 290 EVEIAKRIEEGEKEILGAVLSSSIAIREILELGERLRKGKIRVREII------------- 336

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                              K+  D Q+ E +          +  +     E    D    
Sbjct: 337 -------------------KDAGDEQQAEAEEPEEELDEAAEAPEGQGDAEAEAGDGAAP 377

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVK 313
            E  +     +   E++    V+  +D I ++ R++  +++       ++  K ++   +
Sbjct: 378 AEGAEPEKPRIPKEEERKVEHVLKHIDRIRKLERDVAKVRETLQGGKKLSEVKRKELKGE 437

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            + ++ ++++ + ++ LN+ +ID +V +L    KR+   E E     +  G+        
Sbjct: 438 IRAIEAEMMENLEAIQLNKKQIDRIVLRLKSFIKRVEEAEREFFDCERRTGVPVKDLRRL 497

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVS 432
              RE         K   +         E+D ++     +I  +  E  + + E R    
Sbjct: 498 L--RETREDEAERKKLAKKLRCALDEVEELDRTLRSAGRKILRVQEEAEVPVEELRRTYR 555

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+  GE +A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 556 MIGDGERKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKR 615

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEI
Sbjct: 616 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPTPEEI 675

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+ +P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E 
Sbjct: 676 AEKMELPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVINMNLAEQ 735

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 736 TRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSR 795

Query: 673 SKKLRSFLDG 682
           SK+L+SF++ 
Sbjct: 796 SKRLKSFVES 805


>gi|1938356|gb|AAC45155.1| RpoD [Xanthomonas campestris pv. campestris]
          Length = 622

 Score =  376 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 253/660 (38%), Positives = 352/660 (53%), Gaps = 52/660 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
                K +I    ++GY+T  E+N  LP D V  EQ+ED ++M++ MGI+V     D + 
Sbjct: 8   QQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAET 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L   +G+  + ++  +A+ ++       D+    T DPVRMY+R                
Sbjct: 68  LLLNDGNTGNREVDDTAAEAAAAALTALDTEGGRTTDPVRMYMR---------------- 111

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
               E G   ++    E        I     + +G         L               
Sbjct: 112 ----EMGTVELLTREAE--------IAIAKRIEEG---------LSQVQAALGTFPLVDR 150

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                 +  +   +   RD      G ++   + S+  R  + +   +     R      
Sbjct: 151 AAAVRLRSAQGRQEAPGRD-----RGRLQRPDRRSRRCRCSLAAAGRSPLTKMRWTKTQT 205

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
             +  TL   +     +    L      +    S   +     K           +E + 
Sbjct: 206 KTAMTTLPRKKSGPTVRTRWKLPRAWRTWP--TSTPSSRRPYVKYGAEHKNVAKAREDMA 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            +  +  LN    D LV QL  +   I  +E ++L LA +   + R  F+   +G + + 
Sbjct: 264 AIFTT--LNVPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNL 321

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV  A    + +W + +    D I+  +     +     ++++E + I   +  GE +A
Sbjct: 322 EWVEDALKR-KQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLAEIKDISRAMAYGEAKA 380

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 381 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 440

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +  REPTPEE+AK++ MP +
Sbjct: 441 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREPTPEELAKEMDMPED 500

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  SP+D+    NL ET   VLA LT
Sbjct: 501 KIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAGLT 560

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 561 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 620


>gi|115375627|ref|ZP_01462884.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823184|ref|YP_003955542.1| RNA polymerase sigma factor rpod [Stigmatella aurantiaca DW4/3-1]
 gi|115367403|gb|EAU66381.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396256|gb|ADO73715.1| RNA polymerase sigma factor RpoD [Stigmatella aurantiaca DW4/3-1]
          Length = 706

 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 250/657 (38%), Positives = 373/657 (56%), Gaps = 55/657 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   R++G++T +E+N  LP D VSS+Q++D ++M  +  I +VD        
Sbjct: 103 RKEVKDLLAAGREKGFLTYDEVNDALPADIVSSDQIDDVMSMFGDNDIEIVDAQKAAQSN 162

Query: 88  GSEDSLDLASSAS-NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             + ++ +   +  ++        D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRI
Sbjct: 163 EIKPTVAVEEESKQDADADDDDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRI 222

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII-DLEACIGPESKGGFFHGTEG 205
           E G   ++ ++    +    ++   ++L  G   +R++I D       E           
Sbjct: 223 EDGEKEVLRAMLACRVAVADILDIGNKLKTGKLRVRDVIKDAPEEAQAEGAEEAPEEGVE 282

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               ++   S+  + + + +        AK  +    ++    +  +  ++ + ++  D 
Sbjct: 283 GEQPQQLAQSELNKIEQINKQIERFRKFAKDCEVLEEELSGKKKLTDVKKKEVKQEVKD- 341

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                                              L+ K+++++
Sbjct: 342 ---------------------------------------------------LRTKMMEVL 350

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             + LN+ ++D +V  L  + +R+   E EL  L +  G+       + +    +P+   
Sbjct: 351 EEMRLNKKQVDRIVLNLKQLIERVDKAEEELRDLERRNGVSMKELRPQLKESRDNPNTAK 410

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             +       +   A + D +     +IK +  E  + +   R     +R GE  A  AK
Sbjct: 411 KLQKQLNFTPEQLEALDRD-VRTAVRKIKRVEEEANLPVDALRRNYDAIRLGERRAERAK 469

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 470 SELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIR 529

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I REPTPEEIA+K+ +P++ VRK
Sbjct: 530 QAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEIGREPTPEEIAEKMELPLDKVRK 589

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL E T +VLA+LTPREE
Sbjct: 590 VLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPADAVINMNLAEQTRKVLATLTPREE 649

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+LRSF++ 
Sbjct: 650 KVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKRLRSFVES 706


>gi|78486147|ref|YP_392072.1| sigma 70 (RpoD) [Thiomicrospira crunogena XCL-2]
 gi|78364433|gb|ABB42398.1| sigma 70 (RpoD) [Thiomicrospira crunogena XCL-2]
          Length = 594

 Score =  373 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 248/656 (37%), Positives = 363/656 (55%), Gaps = 68/656 (10%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                  +I+ A+  GY+T  ++N  LP D +  +Q+   + +L + GI + +     DE
Sbjct: 6   RKQQLIDLIERAKDLGYLTFSDVNDVLPDD-IEEDQLGQVLTILRDFGIQLFESAPDADE 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +++      +A+ +++      D+    T DPVRMY+REMGS+ELL+R+GE+ IAKRI
Sbjct: 65  LLTKEGETFDDAAAEAAILALAEVDAEFGRTTDPVRMYMREMGSVELLTRQGEVEIAKRI 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   M+ ++ + P     L+                               F   E  
Sbjct: 125 EYGIRDMLEAMAKYPQVAMELL-----------------------------ASFSRIEDG 155

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  +         D+ +   +  S    S + +    +P E                 
Sbjct: 156 EGKTADLIQGFIRPADLVDIPIEELSPDNDSGEPKEDGINPEE----------------- 198

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                            LD   +   +L +  D     +K+  S  K    + ++V L+ 
Sbjct: 199 -----------------LDAFLQKLAKLNA--DTLKAEEKNGYSDPKSVKKRAEIVALLA 239

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDPHWVS 385
           ++ L+   ++ +++ +      I   E  ++       G+ R  FL+   G E D   + 
Sbjct: 240 TVKLSPVFVNRMIKGIKLRVSSIREQERNVVNAVMRQVGVPRPSFLKLFVGSETDYDVLD 299

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             K+    +  + +      + + +  +  I     + I++++ I   + K E  A IAK
Sbjct: 300 RLKE-AHPDKADALEEVRADVKRAQKRLAMIEKAEKMPINQYKTIYKDLSKAESIARIAK 358

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKFSTYA WW++
Sbjct: 359 REMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWWIR 418

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R  R++  K+ REPTPEE+A+++ MP + VRK
Sbjct: 419 QAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEMPEDKVRK 478

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V+KI KEPIS+ETP+GD++ S LGDFIED N +SP DSA    + ET   +L++LTPRE 
Sbjct: 479 VMKIAKEPISMETPVGDDEDSSLGDFIEDSNILSPQDSADLEGMGETVREMLSTLTPREA 538

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFG+GMNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSR+++L+SFLD
Sbjct: 539 KVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAERLKSFLD 594


>gi|213018850|ref|ZP_03334658.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995801|gb|EEB56441.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 632

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/667 (39%), Positives = 396/667 (59%), Gaps = 53/667 (7%)

Query: 25  DFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           +      K ++  + R+ G++T +++N  L  +  S++ ++DT+A+L + GIN+++  + 
Sbjct: 8   EDRKKIIKDLVTKSIRKGGFITFDDINDKLSDENFSTDFIDDTIALLQDSGINILESSED 67

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+E  S +  +       S         +     DDPVR+YL++M S++LLSR  EI IA
Sbjct: 68  EEEAPSNNDGNKLDDDETS-----LNTTTTLVQNDDPVRIYLQDMSSVKLLSRADEIKIA 122

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+IE+ +  M+ ++ E+ + F+ +  WRD+L+ GT LLREII+L+A    +         
Sbjct: 123 KKIESEKHNMLRAIIETSVAFKIIKTWRDDLSGGTFLLREIINLDAIYNSDFNM------ 176

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                       +E E +DV++   D E       ++   + S                 
Sbjct: 177 ---------VDKEESEAEDVRDCVNDEEKGNDEKGNESEDISSA---------------- 211

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   ++  ME  L PKV+ ALDEI  +  E   L+ N       +  S + + L  ++  
Sbjct: 212 NLNISVLEMESDLLPKVITALDEIIALTNEALVLKKN------SKDFSNELENLYNQIWS 265

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQG 376
           +   +  + + I  + ++LY+I++ I   E  L+  A+ Y I R+ F       L  H+ 
Sbjct: 266 VALQIQFSDAAITRITQKLYEINRLITFEEANLITEARKYDIDRESFYNVYDDVLLEHEF 325

Query: 377 RELDPHWVSYAKDFPEGEWKN-FVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMV 434
            E+    ++  +    GE KN F+    DS   I + + +I S   G  + EF+ ++  +
Sbjct: 326 SEISFLKINENQSLFTGELKNKFLRFINDSYEYIASALSNIKSYVQGDRVQEFKKVIKRI 385

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GY
Sbjct: 386 QKHEQEVSQAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGY 445

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTY  WWVKQ+ITR+I +QS  +RIPVHM + I K+ +  R+M++++ REPT EE++ 
Sbjct: 446 KFSTYGTWWVKQSITRAIPEQSKVVRIPVHMVEIISKINKALRKMTHEMGREPTLEELSI 505

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +LAMP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT
Sbjct: 506 ELAMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSKPEDAAILADLRGITT 565

Query: 615 RVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR+
Sbjct: 566 NVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRA 625

Query: 674 KKLRSFL 680
           KKLR F 
Sbjct: 626 KKLRGFF 632


>gi|152656|gb|AAA26473.1| sigma factor [Stigmatella aurantiaca]
          Length = 706

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 249/657 (37%), Positives = 372/657 (56%), Gaps = 55/657 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   R++G++T +E+N  LP D VSS+Q++D ++M  +  I +VD        
Sbjct: 103 RKEVKDLLAAGREKGFLTYDEVNDALPADIVSSDQIDDVMSMFGDNDIEIVDAQKAAQSN 162

Query: 88  GSEDSLDLASSAS-NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             + ++ +   +  ++        D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRI
Sbjct: 163 EIKPTVAVEEESKQDADADDDDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRI 222

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII-DLEACIGPESKGGFFHGTEG 205
           E G   ++ ++    +    ++   ++L  G   +R++I D       E           
Sbjct: 223 EDGEKEVLRAMLACRVAVADILDIGNKLKTGKLRVRDVIKDAPEEAQAEGAEEAPEEGVE 282

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               ++   S+  + + + +        AK  +    ++    +  +  ++ + ++  D 
Sbjct: 283 GEQPQQLAQSELNKIEQINKQIERFRKFAKDCEVLEEELSGKKKLTDVKKKEVKQEVKD- 341

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                                              L+ K+++++
Sbjct: 342 ---------------------------------------------------LRTKMMEVL 350

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             + LN+ ++D +V  L  + +R+   E EL  L +  G+       + +    +P+   
Sbjct: 351 EEMRLNKKQVDRIVLNLKQLIERVDKAEEELRDLERRNGVSMKELRPQLKESRDNPNTAK 410

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             +       +   A + D +     +IK +  E  + +   R     +R GE  A  AK
Sbjct: 411 KLQKQLNFTPEQLEALDRD-VRTAVRKIKRVEEEANLPVDALRRNYDAIRLGERRAERAK 469

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 470 SELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIR 529

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +I REPTPEEIA+K+ +P++ VRK
Sbjct: 530 QAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEIGREPTPEEIAEKMELPLDKVRK 589

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPISLETPIG+E+ SHLGDFIEDK+ VSP D+ I  NL   T +VLA+LTPREE
Sbjct: 590 VLKIAKEPISLETPIGEEEDSHLGDFIEDKSLVSPADAVINMNLAARTRKVLATLTPREE 649

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+LRSF++ 
Sbjct: 650 KVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKRLRSFVES 706


>gi|190571452|ref|YP_001975810.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357724|emb|CAQ55173.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 633

 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 263/667 (39%), Positives = 396/667 (59%), Gaps = 53/667 (7%)

Query: 25  DFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           +      K ++  + R+ G++T +++N  L  +  S++ ++DT+A+L + GIN+++  + 
Sbjct: 9   EDRKKIIKDLVTKSIRKGGFITFDDINDKLSDENFSTDFIDDTIALLQDSGINILESSED 68

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+E  S +  +       S         +     DDPVR+YL++M S++LLSR  EI IA
Sbjct: 69  EEEAPSNNDGNKLDDDETS-----LNTTTTLVQNDDPVRIYLQDMSSVKLLSRADEIKIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+IE+ +  M+ ++ E+ + F+ +  WRD+L+ GT LLREII+L+A    +         
Sbjct: 124 KKIESEKHNMLRAIIETSVAFKIIKTWRDDLSGGTFLLREIINLDAIYNSDFNM------ 177

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                       +E E +DV++   D E       ++   + S                 
Sbjct: 178 ---------VDKEESEAEDVRDCVNDEEKGNDEKGNESEDISSA---------------- 212

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   ++  ME  L PKV+ ALDEI  +  E   L+ N       +  S + + L  ++  
Sbjct: 213 NLNISVLEMESDLLPKVITALDEIIALTNEALVLKKN------SKDFSNELENLYNQIWS 266

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQG 376
           +   +  + + I  + ++LY+I++ I   E  L+  A+ Y I R+ F       L  H+ 
Sbjct: 267 VALQIQFSDAAITRITQKLYEINRLITFEEANLITEARKYDIDRESFYNVYDDVLLEHEF 326

Query: 377 RELDPHWVSYAKDFPEGEWKN-FVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMV 434
            E+    ++  +    GE KN F+    DS   I + + +I S   G  + EF+ ++  +
Sbjct: 327 SEISFLKINENQSLFTGELKNKFLRFINDSYEYIASALSNIKSYVQGDRVQEFKKVIKRI 386

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GY
Sbjct: 387 QKHEQEVSQAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGY 446

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTY  WWVKQ+ITR+I +QS  +RIPVHM + I K+ +  R+M++++ REPT EE++ 
Sbjct: 447 KFSTYGTWWVKQSITRAIPEQSKVVRIPVHMVEIISKINKALRKMTHEMGREPTLEELSI 506

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +LAMP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT
Sbjct: 507 ELAMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSKPEDAAILADLRGITT 566

Query: 615 RVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR+
Sbjct: 567 NVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRA 626

Query: 674 KKLRSFL 680
           KKLR F 
Sbjct: 627 KKLRGFF 633


>gi|258593489|emb|CBE69828.1| RNA polymerase sigma factor rpoD (Sigma-80) [NC10 bacterium 'Dutch
           sediment']
          Length = 654

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/681 (37%), Positives = 376/681 (55%), Gaps = 76/681 (11%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
             G + N  S S  + +  ++V     +  K ++ L R++GY+T +E+N+FLP +  S +
Sbjct: 50  AKGARSNAGSKSAKKPT--TVVSAALKEGIKPLVSLGRKKGYLTYDEVNSFLPEEVTSGD 107

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q++  + +   M I VVD  +      S         A      +     S+   TDDPV
Sbjct: 108 QIDKILNLFDEMDIEVVDEAERTKTTRSPAPQQEEEGAEVEPELIP----SSVGRTDDPV 163

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYLREMG   LL+REGEI IAKRIE G   +  ++C++ +  + +    + L      +
Sbjct: 164 RMYLREMGKTPLLTREGEIQIAKRIEDGHKEVAEAVCQAGVAVREITEIGERLLHEKARI 223

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++ L                             E      +E   +     +  +D++
Sbjct: 224 YELLSLNEF-------------------------DEISEQKERELLAEHTPTLEALRDEQ 258

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
            K+DS                             LR +    +  ++E +++        
Sbjct: 259 VKIDS-----------------------------LRRRYQRGVGRLSERWQQ-------- 281

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
                DE +  K          L+  L +NQ  ID +V ++ ++ +RI   E EL  +A+
Sbjct: 282 --RILDELAHRKAAQ-----ATLIRKLHVNQRVIDRVVARIRNLLERIEQGEQELREVAR 334

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
            + +  +  +    G                G  +  +     ++  I+ +I+ +  E  
Sbjct: 335 VHHLSMED-IRIIAGNGRGKTTAIRGILRRTGLDRKGLDECEHAVAAIQRKIRRVEEEAD 393

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
            S  E R ++  +  GE +A +AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGL
Sbjct: 394 ASGKELRSLLHAITTGERKAHLAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 453

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M+A +KF++  GYKFSTYA WWV+QAITR+IADQ+ TIRIPVHM + I+K+ R +R +  
Sbjct: 454 MRAVDKFEYQRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETINKLTRASRYLVQ 513

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPTPEEIA+K+ +PV+ VRKVLKI +EPISLETPIG+E+ SHLGDFIEDK  +SP+
Sbjct: 514 EFGREPTPEEIAQKIDLPVDKVRKVLKIAQEPISLETPIGEEEGSHLGDFIEDKGVISPI 573

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ I  NL   T +VL +LT RE+++L++RFG+G   DHTLEEVG+QF VTRERIRQIEA
Sbjct: 574 EAVIGMNLSGQTEQVLETLTEREQKILKLRFGLGDGRDHTLEEVGQQFDVTRERIRQIEA 633

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           KA+RKL+HP+RS+KL+SF++ 
Sbjct: 634 KALRKLRHPTRSRKLKSFVES 654


>gi|326566650|gb|EGE16791.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 585

 Score =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 213/611 (34%), Positives = 330/611 (54%), Gaps = 48/611 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D S      +I+L +++GY+T  E+N  LP     S+Q+ED + ML+++GI V +    +
Sbjct: 12  DTSSSQLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDD 71

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D+    D+      A++ +  +    ++    T DPVRMY+REMG+++LL+REGEI IAK
Sbjct: 72  DDILLSDTGSDDDIATDEAAAVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIGIAK 131

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +   +   P T + ++    ++  G   + +I+            GF +G +
Sbjct: 132 RIEEGTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIV-----------SGFLNGDD 180

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      E+   +          G  ++  K   ++  + D    +  +D     E    
Sbjct: 181 GDFILNEEEIELD---------LGSPKTTDKDDAEEDGESDGTELDDTDDSSLDPE---- 227

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVK 323
                                E+   + E++ L D A     K  + S   KV  ++L  
Sbjct: 228 ---------------------EVRVRFEEIQRLYDVAQEALAKHGRGSEAVKVAYDELAN 266

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPH 382
               + LN    D ++  + ++ + +  NE  +++L   +G +  D F +     E +  
Sbjct: 267 HFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEFKKTFPSNETNVE 326

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+S+ +      +   +A     ++ ++ ++ +      + I + + +   +  GE +A 
Sbjct: 327 WLSH-RIKGGPAFAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVARQMAIGEAKAR 385

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKK+MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 386 RAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 445

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  ++ REPTPEE+ ++L M    
Sbjct: 446 WIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEELGERLDMDEAK 505

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VRKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+++A    LRE T  VL +LT 
Sbjct: 506 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLREATREVLDNLTE 565

Query: 623 REERVLRMRFG 633
           RE +VL+    
Sbjct: 566 REAKVLKNAIW 576


>gi|330862244|emb|CBX72405.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 553

 Score =  365 bits (937), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 193/571 (33%), Positives = 293/571 (51%), Gaps = 52/571 (9%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D++         L+        K ++   +++GY+T  E+N  LP D V S+Q+ED + 
Sbjct: 30  TDTNPNTLKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQ 89

Query: 69  MLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           M+++MGI V++   D +D   +E++ D    A+ ++  +    +S    T DPVRMY+RE
Sbjct: 90  MINDMGIQVLEEAPDADDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMRE 149

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I  
Sbjct: 150 MGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI-- 207

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                     GF              ++     +   E   D +   +  +++       
Sbjct: 208 ---------TGFVDPNAEEDI---APTATHVGSELSTEEMDDDDDEDEDDEEEEDDNSID 255

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE A      L E  +++   +                                   +K+
Sbjct: 256 PELARQKFSELREQYENARLEI-----------------------------------KKN 280

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            +S         KL ++     L   + D LV  +  +  R+   E  +++L  +   + 
Sbjct: 281 GRSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMP 340

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E    W + A    +  W   +    D + +   +++ I  ETG++I +
Sbjct: 341 KKNFVTLFASNETSDTWFAAAIAMGKP-WSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQ 399

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 400 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 459

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 460 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 519

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           PTPEE+A+++ MP + +RKVLKI KEPIS+E
Sbjct: 520 PTPEELAERMLMPEDKIRKVLKIAKEPISME 550


>gi|297180571|gb|ADI16783.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0010_11B23]
          Length = 605

 Score =  365 bits (936), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 241/656 (36%), Positives = 355/656 (54%), Gaps = 60/656 (9%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
              +   ++I+L R++GY+T  ++   LP     ++  E+   +L +MGI V +    +D
Sbjct: 7   TQKNDIAQLIQLGREQGYLTHADITDTLPDGSTDADNFEEITQVLRDMGIKVFEDTPDQD 66

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E    +  +    A+  +V    + +     T DPVRMY+REMGS++LL++ GEI IAKR
Sbjct: 67  ELMLGEDEETDELAAEDAVAALSQTEIESGRTTDPVRMYMREMGSVDLLTKTGEIGIAKR 126

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IEA    +++   E PL  + ++ + + +  G    +++I       PE +       + 
Sbjct: 127 IEAAMKEVLSLCAEYPLCIEYILDFFNRIKIGEKKTQDLISGFMLEEPEEEIVEQEFEDT 186

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                 +    E+E  +V                                          
Sbjct: 187 EQVPAEDSEDDEEEEANV------------------------------------------ 204

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
             +    E +++         I   Y +             +EK   K +   +KL    
Sbjct: 205 -ISFEECEAKIKV--------IKREYNKYLK-------SLSNEKLDEKGQKALDKLKTEF 248

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWV 384
             +  N    D LV+   +    +   E EL R L +  G+      +  +   ++   +
Sbjct: 249 QVIKFNSKVFDTLVQIPAEKKHLVGGFEKELKRLLVKEIGVPNKEARDLIEDNLINIRLL 308

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +        + K  +     + ++I+ ++  I     + +++   +   + K       A
Sbjct: 309 TKLAKDKRFK-KKKIDEVKPTFVRIQKDLIKIDENNLMPVTQIISLNKRINKAYRGLLRA 367

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 368 KKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 427

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE++K+L +P + +R
Sbjct: 428 RQAITRSIADQARTIRIPVHMIETINKLNRLSRQMMQEIGREPTPEEMSKRLDIPEDKMR 487

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KV+KI KEPIS+ETPIGD++ S+LGDF+ED +  SP+D A    L++ T  +LASLT RE
Sbjct: 488 KVMKIAKEPISMETPIGDDEDSNLGDFLEDTSINSPIDDASIRGLKDATDEILASLTARE 547

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +VLRMRFGIGMN DHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS  L+SFL
Sbjct: 548 AKVLRMRFGIGMNNDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDVLKSFL 603


>gi|262189558|ref|ZP_06047968.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CT 5369-93]
 gi|262034560|gb|EEY52890.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CT 5369-93]
          Length = 522

 Score =  359 bits (920), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 238/559 (42%), Positives = 318/559 (56%), Gaps = 40/559 (7%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++   D +      L ++
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDL 60

Query: 185 IDLEACIGPES-KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           I     + P   +      T   S     D + E +     E E + E     S D   +
Sbjct: 61  I--SGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEE 118

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           V   PE A      L                                       Q+  + 
Sbjct: 119 VGIDPELAREKFNELR-----------------------------------GKFQNLQLA 143

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS- 362
             +  + S +     + ++ +     L   + D LVE L     R+   E  +++     
Sbjct: 144 VNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEV 203

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+    G E +  W+       +  +   V  + + I +   +++ I  ET +
Sbjct: 204 AKMPKKSFIALFTGNESNEEWLDKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSL 262

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S+   + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 263 SVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 322

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +
Sbjct: 323 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 382

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REP PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLD
Sbjct: 383 MGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 442

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           SA   +L+  T  VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAK
Sbjct: 443 SATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 502

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKL+HPSRS+ LRSFLD
Sbjct: 503 ALRKLRHPSRSEVLRSFLD 521


>gi|207723755|ref|YP_002254153.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206588959|emb|CAQ35921.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
          Length = 773

 Score =  359 bits (920), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 191/583 (32%), Positives = 303/583 (51%), Gaps = 48/583 (8%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 186 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 245

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 246 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 305

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 306 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYID--G 363

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P +                                   E+ A+ + +D    D   +
Sbjct: 364 LIDPNA-----------------------------------EAEAQSADEDEDFEDEEAD 388

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             +++E + D+D    A   +   ++L+   +     I + + ++R   +      K+  
Sbjct: 389 EGDDEEEDEDDDGAGGAAASARQLEELKQAALEKFSIIGDQFEKMRRAFE------KEGY 442

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 443 KSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 502

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 503 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELK 561

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 562 DVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 621

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 622 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 681

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           P  +A+K+ MP + +RK++KI KEPIS++TPIGD+D SHLGDF
Sbjct: 682 PATLAEKMEMPEDKIRKIMKIAKEPISMKTPIGDDDDSHLGDF 724


>gi|213616352|ref|ZP_03372178.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 508

 Score =  358 bits (918), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 188/550 (34%), Positives = 279/550 (50%), Gaps = 49/550 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 175 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 224 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 379 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 438

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 439 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 498

Query: 566 VLKITKEPIS 575
           VLKI KEPIS
Sbjct: 499 VLKIAKEPIS 508


>gi|148284623|ref|YP_001248713.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
 gi|146740062|emb|CAM80186.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
          Length = 614

 Score =  354 bits (908), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 242/625 (38%), Positives = 367/625 (58%), Gaps = 59/625 (9%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTD 118
            ++ E   + +S+  IN+    D        D ++   + ++++   +  +D  D   + 
Sbjct: 32  VDESEKLSSKISDSDINLDKDFDYTKLGVCPDKIEEEVALASNATEGEFEEDLDDNIYST 91

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VR YL++M +  LLSREGEI +AK++E G+  ++  +C  P   + LI W ++L    
Sbjct: 92  DIVRAYLKDMSNTTLLSREGEIELAKQMEEGKKTVIHFICHLPYVMKLLIQWYEDLVHSR 151

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            L+R +I+L                                                   
Sbjct: 152 ILVRNLIEL--------------------------------------------------- 160

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            + +  D P ++ + D  +  + E+     L+ +E ++ PK++  +  ++++  +L  + 
Sbjct: 161 -ESNIYDQPEDDNQQDYDSDGDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEVA 219

Query: 299 DNAVNGQKDEKS---SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +     K   S   S K   L ++L+  V ++  N+  I  ++ +LY ++K I+  E  
Sbjct: 220 AHDFKLHKSSCSYQESKKFTELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEIN 279

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           LL+ A+ Y I R  FL ++       +W+   K   + EW  F++ E D I    +    
Sbjct: 280 LLKAAEKYKISRHDFLFQYN---SGSNWLQKVKLLHQDEWNKFLSKEKDLIKSTIDCFGE 336

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I     + +  F+ I+  ++ GE +  +AKK+MVE+N RLV+ VAK Y NRGL FLDLIQ
Sbjct: 337 IEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQ 396

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLMKA +K+++ LGYKFST A WWV+Q+I+R++ADQ+ TIRIPVHM D I K+VR 
Sbjct: 397 EGNIGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMADTISKIVRV 456

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +++M N++  EPT  EIA+KL+MP++ V+KV++I KEP+SLE PIG+ED S L DFIEDK
Sbjct: 457 SKQMHNELGYEPTASEIAEKLSMPIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIEDK 516

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           NAV P++ AI+ +LRETTTR L++LT REERVLR+RFGIG+ TD+TLEEVG +F VTRER
Sbjct: 517 NAVLPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTRER 576

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           +RQIEAKA+RKLKHP RSKKL+SFL
Sbjct: 577 VRQIEAKALRKLKHPVRSKKLKSFL 601


>gi|260222953|emb|CBA33035.1| RNA polymerase sigma factor rpoD [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 519

 Score =  353 bits (906), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 228/572 (39%), Positives = 327/572 (57%), Gaps = 66/572 (11%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +RMY+REMG++ELL+REGEI IAKRIE G   MM ++  SP T   ++   +E+ +G  +
Sbjct: 1   MRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILRLGEEIREGKVV 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           +  I+D           GF +  E   Y   ED  +  E DD     G            
Sbjct: 61  ITTIVD-----------GFSNPNEADDYVAEEDFDEFDEADDDDGKGG------------ 97

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                                    +  L+   ++L+ + +   D++ E++ ++  + D 
Sbjct: 98  -------------------------SKALTKKLEELKKQALERFDKMRELFEKVHKVYDK 132

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL- 359
              G      +      ++ L   + ++      I+ L + +      +   E EL R+ 
Sbjct: 133 EGYG------TPAYVKAQKALSDELMTIRFTAKAIEKLCDMVRAQVDDVRKKERELRRII 186

Query: 360 AQSYGIKRDVFLERHQGRE----------LDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
               G  ++ F+    GR+          L+  W+       +  W   +   +  +  +
Sbjct: 187 VDKCGYPQENFIADFSGRDKAGNKVASNLLNLKWIEKQAASGKS-WAAVMGRNIPPVQDL 245

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           + ++  +  +  + + + + I   + +GE  +  AKKEM+EANLRLVIS+AKKYTNRGLQ
Sbjct: 246 QQKLIDLQAQVVVPLDQLKDINKRMNEGEYASRAAKKEMIEANLRLVISIAKKYTNRGLQ 305

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I
Sbjct: 306 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 365

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ R +R+   +   EP    +A+K+ +P + +RK++KI KEPIS+ETPIGD+D SHLG
Sbjct: 366 NKMNRISRQHLQEFGFEPDASVLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 425

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED    +P+++A+QA LR+    +L SLTPRE +VLRMRFGI M +DHTLEEVGKQF
Sbjct: 426 DFIEDSANTAPMEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQF 485

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+RKLKHPSRS KLRSF D
Sbjct: 486 DVTRERIRQIEAKALRKLKHPSRSDKLRSFTD 517


>gi|189183187|ref|YP_001936972.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
 gi|189179958|dbj|BAG39738.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
          Length = 615

 Score =  352 bits (902), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 241/626 (38%), Positives = 367/626 (58%), Gaps = 60/626 (9%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS--ASNSSVFLQKRKDSADRST 117
            ++ E   + +S+  IN+    D        D ++      ASN++    +     +  +
Sbjct: 32  VDESEKLSSKISDSDINLDKDFDYTKLGVCPDKIEEEEVVLASNATEGEFEEDLDDNIYS 91

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D VR YL++M +  LLSREGEI +AK++E G+  ++  +C  P   + LI W ++L   
Sbjct: 92  TDIVRAYLKDMSNTTLLSREGEIELAKQMEEGKKTVIHFICHLPYVMKLLIQWYEDLVHS 151

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             L+R +I+L                                                  
Sbjct: 152 RILVRNLIEL-------------------------------------------------- 161

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             + +  D P ++ ++D  +  + E+     L+ +E ++ PK++  +  ++++  +L  +
Sbjct: 162 --ESNIYDQPEDDNQHDYDSDGDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEV 219

Query: 298 QDNAVNGQK---DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             +     K   + + S K   L ++L+  V ++  N+  I  ++ +LY ++K I+  E 
Sbjct: 220 AAHDFKLHKSSCNYQESKKFTELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEI 279

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
            LL+ A+ Y I R  FL ++       +W+   K   + EW  F++ E D I    +   
Sbjct: 280 NLLKAAEKYKISRHDFLFQYN---SGSNWLQKVKLLHQDEWNKFLSKEKDLIKSTIDYFS 336

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I     + +  F+ I+  ++ GE +  +AKK+MVE+N RLV+ VAK Y NRGL FLDLI
Sbjct: 337 EIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLI 396

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGLMKA +K+++ LGYKFST A WWV+Q+I+R++ADQ+ TIRIPVHM D I K+VR
Sbjct: 397 QEGNIGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMADTISKIVR 456

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
            +++M N++  EPT  EIA+KL+MP++ V+KV++I KEP+SLE PIG+ED S L DFIED
Sbjct: 457 VSKQMHNELGYEPTASEIAEKLSMPIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIED 516

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           KNA+ P++ AI+ +LRETTTR L++LT REERVLR+RFGIG+ TD+TLEEVG +F VTRE
Sbjct: 517 KNAILPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTRE 576

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+RQIEAKA+RKLKHP RSKKL+SFL
Sbjct: 577 RVRQIEAKALRKLKHPVRSKKLKSFL 602


>gi|298529696|ref|ZP_07017099.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511132|gb|EFI35035.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 588

 Score =  351 bits (900), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 244/657 (37%), Positives = 362/657 (55%), Gaps = 79/657 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +++G++T +E+N  LP D  + EQ+E+ +++   + I +VDG   +    
Sbjct: 8   QQIKALIAEGKKKGFLTFDEINKALPSDVTTPEQVEEIISIFDQLDIAIVDGKAGKTISV 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S +  +  +     ++   +    A   ++DPVR YLREMG++ LL R+GE+ IAK+IE+
Sbjct: 68  SSEDTNSLAETLALNLDRLEDTAEAVSRSNDPVRTYLREMGAVGLLDRDGEVVIAKKIES 127

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   ++ SL E P+  + LI   ++L      L++++                       
Sbjct: 128 GEMEVLYSLVEVPVAIEELIQVGEDLKKEKIKLKDVV----------------------K 165

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
              ED   E+E +  +     +E   +  K  RS  +   E A  D              
Sbjct: 166 TIEEDDPTEEEMNQRERVIALLEEIKQCYKKRRSVYEKLNECARLD-------------- 211

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
                                VY + + + D      +  K     K L + +++ V   
Sbjct: 212 -------------------RRVYGQQKKILDYKYEIVEHLKHIKLEKTLIDSIIERVN-- 250

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV---FLERHQGRELDPHWVS 385
                          D  +++ + + +L     S G+ +D     L +   RE++P   +
Sbjct: 251 ---------------DYVRQMHNCQRDLSAYILSLGMSQDELHSLLNKLHNREINPVAAA 295

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                   E  +F        ++I+  ++   +    ++ E   I+  + KG  EA  AK
Sbjct: 296 DQLGMTVDELFSFKELIYGK-MEIQERLQQRCMH---NVHELEEILWRINKGNEEALRAK 351

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 352 QELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIR 411

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ R+P+PEEIA+++  P+E V+K
Sbjct: 412 QAITRAIADQARTIRIPVHMIETINKLVRTSRYLVQELGRDPSPEEIAERMDYPLEKVKK 471

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPISLETPIGDE+ S LGDFIEDK AV+P D  + + L E  ++VLA LTPREE
Sbjct: 472 VLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPADEVVNSKLSEQISKVLAELTPREE 531

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  L+++ + 
Sbjct: 532 QVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSSSLKTYYES 588


>gi|297181479|gb|ADI17666.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0130_23I23]
          Length = 602

 Score =  350 bits (898), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 247/650 (38%), Positives = 359/650 (55%), Gaps = 66/650 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
             ++I+LA+ +GY+T  ++   LP     ++  E+ V +L +MGI V +    EDE    
Sbjct: 17  IAQLIQLAKDQGYLTHADITDTLPDGSTDADNFEEIVQVLKDMGIKVFEDTPDEDELMLG 76

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +  +    A+  +V    + +     T DPVRMY+REMGS++LL++ GEI IAKRIE+  
Sbjct: 77  EDEETDDVAAEDAVAALSQTEIESGRTTDPVRMYMREMGSVDLLTKTGEIDIAKRIESAM 136

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             ++A   E PL  + ++ + D +  G    +++I            GF          +
Sbjct: 137 KEVLALCAEYPLCIEYVLDFFDRIKIGEKKTQDLI-----------SGFMIDDPVEEVVE 185

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            E    + E ++ + T    E  A   +  + + +   ++  N + +    +      L 
Sbjct: 186 EEFVENDNEEEEEEVTAVSFEECASKIRIIKREYNRYLKSLSNSKLDTKGQKALDRLKLE 245

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +   KV   L EI    R L    +                    +L KL+ S+ +
Sbjct: 246 FQHIKFNSKVFDTLVEIPGEKRFLVGGFER-------------------ELKKLLKSIGV 286

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
               I        ++    + N   L ++A+    K+                       
Sbjct: 287 PNKEI-------RELIDANLINTRLLTKIAKDRRFKKKD--------------------- 318

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
                   V     + ++I+ ++  I     + +++   +   + K       AKKEM+E
Sbjct: 319 --------VEEIKPTFIRIQKDLIKIDENNLMPVTQILSLNKRINKAYRGLLRAKKEMIE 370

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 371 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 430

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R +R+M  +I REPTPEE++K+L +P + +RKV+KI 
Sbjct: 431 SIADQARTIRIPVHMIETINKLNRLSRQMMQEIGREPTPEEMSKRLDIPEDKMRKVMKIA 490

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ S+LGDF+ED +  SP+D A   +L+++T  +LASLT RE +VLRM
Sbjct: 491 KEPISMETPIGDDEDSNLGDFLEDSSINSPIDDASIRSLKDSTDEILASLTAREAKVLRM 550

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RFGIGMN DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS  L+SFL
Sbjct: 551 RFGIGMNNDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDVLKSFL 600


>gi|197120055|ref|YP_002140482.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
 gi|197089415|gb|ACH40686.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
          Length = 584

 Score =  350 bits (898), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 266/662 (40%), Positives = 383/662 (57%), Gaps = 89/662 (13%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T EE+N  LPPD VSS+Q++D ++M  +M I +VD       
Sbjct: 5   SMDEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSDQIDDVMSMFGDMDIEIVDSAQKVKI 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +  L+       S   ++    +    T DPVRMYLREMGS+ LL+REGE+ IAKRI
Sbjct: 65  PKIKMDLEEEEEHEGSEEEVEFEPGTL-GRTSDPVRMYLREMGSVSLLTREGEVEIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + + +  +P+T + ++   + L                       G    ++  
Sbjct: 124 EVGERDVASVILNTPITVREVVSLGERLRKQQI------------------GAIEISKDV 165

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  E+  ++ +   V     +I+       + +  +D+    A+  E           
Sbjct: 166 EEEVLEEGEEDLQALKVLTIIDEIKEIDLRMNEIQGVLDNEKAAAKERE----------- 214

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L A   +L+ K+   L  +    R +             EK + + K L  K+  ++ 
Sbjct: 215 -ALGAEHAELKVKMAETLKSLRLKDRHI-------------EKIAQRLKELSCKVDTVMQ 260

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
                                        +  L +  G +R+ FL   +G          
Sbjct: 261 E----------------------------ITELEKESGAEREPFLAAFEG---------- 282

Query: 387 AKDFPEGEWKNFVACEVDSILKIRN-------EIKSISVETGISISEFRHIVSMVRKGEC 439
           AK   E E++  +   ++   K+          +K I  E+G   SE  + +  + +GE 
Sbjct: 283 AKGGSEAEFQKKLNLTLEEGQKLEKRFRSSEARLKKIEQESGFKASELANALLAIEEGEH 342

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A +AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 343 KAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTY 402

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++A+P
Sbjct: 403 ATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMALP 462

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++
Sbjct: 463 LDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLST 522

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF
Sbjct: 523 LTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSF 582

Query: 680 LD 681
           ++
Sbjct: 583 VE 584


>gi|262199546|ref|YP_003270755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082893|gb|ACY18862.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 697

 Score =  346 bits (888), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 255/661 (38%), Positives = 373/661 (56%), Gaps = 79/661 (11%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S+   KK+I+L R +G+VT +E+N  +P D +SSEQ++  ++ L   GI++VD      +
Sbjct: 109 SETLKKKLIELGRSKGFVTYDEVNDHMPEDVISSEQIDSWLSALGEEGIDIVDSAASARK 168

Query: 87  EGSEDSLD------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +   D  D       + +        ++ +D +   T DPVRMYLR+MGS+ LL+REGE+
Sbjct: 169 KAPADDDDSSGGKVASLNDDKELEKEEEEEDYSYSRTSDPVRMYLRKMGSVSLLTREGEV 228

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+A++  S +  + LI    +L DG    +EII               
Sbjct: 229 EIAKRIEEGERRMLAAVLNSSVAVEELIDLGKQLADGKARAKEII--------------- 273

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           E++ +  ++   D   +       R+  +        D    + 
Sbjct: 274 ------------KDIDEEDSEVDEQWHVDRIQSVIAKVRGRATDNEGIREKLADRTLGEV 321

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            +     ++ A ++ +              + +L  LQ   +N    ++     K +  K
Sbjct: 322 KKKKYRDSIQANKEAM--------------FEDLSELQ---LNKSVVDRMVANLKAIIVK 364

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L +    +   ++R+ +  +++    + +  +  +   + + + +  D F          
Sbjct: 365 LDRAETEIRAVENRLGMPAKEIRKTLRDMKASATKTRSVGKRFALTVDDF---------- 414

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
                         ++  +      I  +  E +S       S+ E R     +  GE  
Sbjct: 415 ------------DAFEAAIKNAQKKIKVLEEECRS-------SVEELRQTFREMSDGERM 455

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 456 AERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYA 515

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ REPTPEEIA+++ +P+
Sbjct: 516 TWWIRQAITRAIADQARTIRIPVHMIETINKLVRTSRYLVQELGREPTPEEIAERMELPL 575

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+  SP D+ I  NL E T +VLA+L
Sbjct: 576 DKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSVTSPSDAVISVNLAEQTRKVLATL 635

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L++F+
Sbjct: 636 TPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKRLKAFV 695

Query: 681 D 681
           +
Sbjct: 696 E 696


>gi|94313583|ref|YP_586792.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
 gi|93357435|gb|ABF11523.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
          Length = 617

 Score =  346 bits (886), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 186/657 (28%), Positives = 330/657 (50%), Gaps = 52/657 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE-- 86
           +S   ++ L  +RG++T  E++  LP  +           +L  +G+ +V+     +   
Sbjct: 7   ESLVALVALGSERGFLTHGEISDALPDSDFG-----QIQRVLEELGVQIVERTLANEPIR 61

Query: 87  -EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E   D+L +  +    +     + D  +  T DPV++YLRE+G+I LL+RE E+AIA+R
Sbjct: 62  LEEHADALVVDEAVIEEAAAAVMQADGREARTTDPVQLYLREIGTIPLLTREDEVAIARR 121

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
            E     M+A +   PL    L+   DE+  G   + ++ID                   
Sbjct: 122 HEIAVTEMVAEMVSCPLVVYELLTMADEIERGEMAVDDLID------------------- 162

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                          D+V     ++ +                   + +E +       +
Sbjct: 163 -------------HWDEVPAAAVNVPAIEMSEAVQDDDPAPGAAGVDLEETDPVSTGAST 209

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           A + +A+E +    V+  L  +   + +       +        + V    ++ +L    
Sbjct: 210 ARSSAALESE----VIARLAIVRARFLDWSR---QSRQQAATSDAFVALNAIRAELAVY- 261

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV 384
                + + +  L + L      I   E  +  +     GI R+ FL+   G E+D  W 
Sbjct: 262 ---HFSAAAVARLGQVLSTHIAAIQQAERRIAGIVIDRCGIAREQFLQTFPGHEIDLGWS 318

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                       + +   +  I  I+ E++ +     +S+ + +++   V K    A  A
Sbjct: 319 EALAAERISGAADALVRAIPEIQAIQREMRVLENRAAMSLGDLKNLGQRVAKARARAQAA 378

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + EM+ +NLRLV+S AKKY +RG+  LDLIQEGN+GLM+A ++FD+  GYKFSTYA WW+
Sbjct: 379 RDEMIRSNLRLVVSNAKKYLHRGMPLLDLIQEGNLGLMRAVDRFDYRRGYKFSTYATWWI 438

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q ITR+IAD+  TIRIP+H+ + + KV R +R + ++    P PE +A +L++ V+ V+
Sbjct: 439 RQGITRAIADKGPTIRIPIHLVEVVGKVNRASRELFHETGEAPAPEALAARLSLSVKKVK 498

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +L + KEP+SLE  +G+   + L D + D+ + SP +SA++ +LR+     LA+L PRE
Sbjct: 499 AILDLVKEPLSLEMSVGESGDALLWDTLTDECSASPDESAMRVSLRKDLDEALATLKPRE 558

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            ++++MR+G+   TD+TLEE+G+Q+ ++RER+RQ+E +A+RKL++P R+ +L++  D
Sbjct: 559 AKIVKMRYGVDAGTDYTLEEIGQQYGLSRERVRQLERQALRKLRNPDRAPRLQAHRD 615


>gi|302036356|ref|YP_003796678.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
 gi|300604420|emb|CBK40752.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
          Length = 601

 Score =  345 bits (885), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 255/658 (38%), Positives = 360/658 (54%), Gaps = 71/658 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             KK+I L +++G++T ++LN+ LP D VSS+Q    + M   M I +V+  + E    +
Sbjct: 9   EVKKLINLGKEKGFLTYDDLNSTLPADVVSSDQFSTIMTMFGEMDIEIVESAETERAPKA 68

Query: 90  EDSLDLASSASNSSVFLQKRKD-----SADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            +  +    +  S       K+      A   TDDPVR+YL+EMGS+ LLSREGEI IAK
Sbjct: 69  AEGEEAIEESEESEASEDNEKEIDLTPGALSRTDDPVRLYLKEMGSVALLSREGEIEIAK 128

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G+  +   +   P+T + ++  RD+L +G   +REI+                 TE
Sbjct: 129 RIEEGKKDIATVVYGLPMTLEFVLNLRDQLKNGKIDVREIV-------------PVVETE 175

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
               ++  +   E+ R    ++   +   +   KD   K      + E  ++   + +  
Sbjct: 176 EDFEEEAVEKDYEELRVKTLDSLNAVRKVSASLKDLYDKARHVGADPEKQKKLRKQIDTV 235

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               +  ME      V                                    LK+++ + 
Sbjct: 236 RGQVVDKMESVNLHGV------------------------------------LKDRMTQR 259

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
           V  L+L   + +    ++    +R+         L +         L   +   L    +
Sbjct: 260 VRDLNLLFRQAER---EVTSCQRRLGVGGEAGAELLRRLCRTHKDLLAVKRRTSLSEEVL 316

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
              K   +         E +  L              IS  E +  V  +   E +    
Sbjct: 317 QDIKKHYQAAKGRIRQLETEEAL--------------ISAEEIKDAVKHLDVAEEKVKRG 362

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 363 KAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWI 422

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  K+ REPTPEEIA+++ +P++ VR
Sbjct: 423 RQAITRAIADQARTIRIPVHMIETINKLIRTSRHLVQKLGREPTPEEIAERMDLPLDKVR 482

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+LKI +EPISLETPIG+E+ SHLGDFIEDK AVSPL++AI+ +L+      L +LTPRE
Sbjct: 483 KILKIAREPISLETPIGEEEDSHLGDFIEDKKAVSPLEAAIRYDLQRQINGALETLTPRE 542

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E+VLR RFGIG  TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKLRSF++ 
Sbjct: 543 EKVLRKRFGIGEATDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKKLRSFVES 600


>gi|256830224|ref|YP_003158952.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579400|gb|ACU90536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfomicrobium
           baculatum DSM 4028]
          Length = 588

 Score =  344 bits (882), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 241/654 (36%), Positives = 354/654 (54%), Gaps = 73/654 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              + +I   +++G++T +ELN  LP +  + EQ+E+ + +   + I++VD       E 
Sbjct: 8   QQIQALIAEGKKKGFLTFDELNKALPSEVNTPEQIEEIIVIFDQLDIDIVDEKLSRGIEI 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +ED  +         +   +        ++DPVRMYLREMG++ LL R+GE+ IAK+IEA
Sbjct: 68  AEDDGEEPKEEEKLELAEDEDGADYSSRSNDPVRMYLREMGAVGLLDRDGEVYIAKKIEA 127

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   +M +L E P+  + L+   ++L  G   L++++                       
Sbjct: 128 GELEVMYALVEVPVAVEELVRVGEDLKKGRMKLKDVV----------------------- 164

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                  +  E DD  E                        N       L ED  +    
Sbjct: 165 -------KTIEEDDPSEE---------------------EMNQRERVIKLLEDVKNIYRK 196

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
              +  +L       LD+   V+   + + D      +  +     K L +++++ VG  
Sbjct: 197 KKPLYTRLDEC--ATLDK--RVFGVQKKIMDYKEGVVQCLRDIKLEKTLIDRIIETVG-- 250

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
                      + +  +          +L L +S      +F ++ + R ++P   +   
Sbjct: 251 -----------DYVRQMHNCRRDLSAYILSLGKSQDEIFGIF-KQLEERTINPVAAADQL 298

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                E  +F       I      +  +       + +   I+  +RKG  +A  AK+E+
Sbjct: 299 GMTMEELFSFKEMVNGKIEI----LGKLQENAMHDVDQLEEILWRIRKGNTDALDAKQEL 354

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 355 IRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAI 414

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ R+P+PEEIA+++  P+E V+KVLK
Sbjct: 415 TRAIADQARTIRIPVHMIETINKLVRTSRYLVQELGRDPSPEEIAERMDYPLEKVKKVLK 474

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPISLETPIGDE+ S LGDFIEDK AV+P D  +   L E   +VL+ LTPREE+VL
Sbjct: 475 IAKEPISLETPIGDEEDSSLGDFIEDKKAVAPADEVVNTKLAEQIAQVLSDLTPREEQVL 534

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           R RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS++LRS+ + 
Sbjct: 535 RKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQQLRSYYES 588


>gi|322421611|ref|YP_004200834.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320127998|gb|ADW15558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 583

 Score =  342 bits (876), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 256/655 (39%), Positives = 376/655 (57%), Gaps = 76/655 (11%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T EE+N  LPPD VSS+Q++D ++M  +M I +VD       
Sbjct: 5   SMDEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSDQIDDVMSMFGDMDIEIVDSAQKVKI 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +  L+           ++    +    T DPVRMYLREMGS+ LL+REGE+ IAKRI
Sbjct: 65  PKIKMDLEEEEEHEGGEEEVEFEPGTL-GRTSDPVRMYLREMGSVSLLTREGEVEIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + + +  +P+T + ++   + L                       G    ++  
Sbjct: 124 EVGERDVASVILNTPITVREVVSLGERLRKQQI------------------GAIEISKDV 165

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +  E+  ++ +   V     +I+   +  +  ++ ++      E+D  N +  E    
Sbjct: 166 EEEVLEEGEEDLQALRVLGIIDEIKEMDQRMEQIQTALEGKVSAKESDALNSEHGELKVK 225

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              +    +L+ +    +++IA+  +EL    D  +      +   +   +K+  +    
Sbjct: 226 MAETLKSLRLKDR---HIEKIAQRLKELSCKVDTVMQEV--AEFEKETSTVKDVFLTAFE 280

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            L               D SK++     E  +L            +R++  E +   +  
Sbjct: 281 GLK---------SASEADFSKKMHMTLEEGQKLE-----------KRYRSSEANLKKIEQ 320

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                                             G   SE  + +  + +GE +A +AK 
Sbjct: 321 ES--------------------------------GFKASELANALLAIEEGEHKAKLAKS 348

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 349 ELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQ 408

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++A+P++ VRKV
Sbjct: 409 AITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMALPLDKVRKV 468

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+
Sbjct: 469 LKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEK 528

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 529 VLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 583


>gi|323697926|ref|ZP_08109838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           ND132]
 gi|323457858|gb|EGB13723.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans ND132]
          Length = 583

 Score =  341 bits (875), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 241/656 (36%), Positives = 353/656 (53%), Gaps = 82/656 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +++G++T EEL+  LP D  S +Q+E+  A+   M I +VD      ++ 
Sbjct: 8   QQIKALIAEGKKKGFLTYEELSKALPSDYNSPDQLEEIHAIFDQMDIALVDS-----DDS 62

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +   D                      + DPVRMYLREMG++ LL REGE+ IAK+IE 
Sbjct: 63  DKKLTDDDDDKELEFDDADDDSSEYASRSTDPVRMYLREMGAVPLLDREGEVVIAKKIEN 122

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   ++ SL E P+  + LI   ++L DG   L++++                       
Sbjct: 123 GEMDVLYSLVEVPVAVEELISVGEDLEDGRIKLKDVV----------------------K 160

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
              ED   E E +  Q     +    K+    +   +     A  D+R     ++  ++ 
Sbjct: 161 TIEEDDPSEDEMNQRQRVIFLLAEVKKLYHKKKKIYEKLDYCACLDKRVYGVQQEILSYK 220

Query: 269 LSAMEDQLRPKVMCA--LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              +  +LR   +    +D I E   +         N Q+D             L   V 
Sbjct: 221 -EEIVTRLRDIKLEKTLIDRIIETVNDYVR---QMHNCQRD-------------LSAYVL 263

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           S+   ++ I+ L +Q       +       +  +   G+  + F      +E+       
Sbjct: 264 SVGKTKAEIEELFQQ-------VDARSINPVAASTQLGMTVEEF---FSFKEM------- 306

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                       +A +++ + +++++          S+ +   ++  ++ G   A  AK+
Sbjct: 307 ------------LAGKLEIMHRLQDKCCH-------SVHDLEEVLWRIKSGNQTAMQAKQ 347

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 348 ELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQ 407

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P+PEEIA+++  P+E V+KV
Sbjct: 408 AITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPSPEEIAERMDYPLEKVKKV 467

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPISLETPIGDE+ S LGDFIEDK A +P +  +   L E    VL+ LTPREE+
Sbjct: 468 LKIAKEPISLETPIGDEEDSSLGDFIEDKKATAPAEEVVSTKLSEQIASVLSDLTPREEQ 527

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  LRS+ + 
Sbjct: 528 VLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSALLRSYFEN 583


>gi|77920269|ref|YP_358084.1| RNA polymerase, sigma(70) factor [Pelobacter carbinolicus DSM 2380]
 gi|77546352|gb|ABA89914.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter carbinolicus DSM
           2380]
          Length = 588

 Score =  341 bits (874), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 252/653 (38%), Positives = 377/653 (57%), Gaps = 74/653 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  +++I + +++GY+T +E+N +LP   VSS+Q++D +++   M I VVD +       
Sbjct: 8   EEVQQLIDMGKEKGYLTYDEVNDYLPESVVSSDQLDDVMSLFGEMDIEVVDSEQKVSVSK 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++   D +SS S       + +      T DPVRMYLREMG + LL+REGE+ IAKRIE 
Sbjct: 68  TQSDSDDSSSDSGEEEEETEYEAGTLGRTSDPVRMYLREMGQVSLLTREGEVEIAKRIEE 127

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G A++   + ++P+ F+ +I   ++L      + EI                   E    
Sbjct: 128 GEALVARVIMKTPIAFREVIRLGEKLAKEQIGVAEI---------------TKEYEEEEG 172

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
              E+  + +  D V++     +    + ++     D    N+                 
Sbjct: 173 ADVEEVQRTRILDLVEKIRQQNDELMVLCQELADCGDRQQRNS----------------- 215

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
                  LR ++      I E+ RE+       +   + +K   + K + +++ K +  +
Sbjct: 216 -------LRDQIAEKKASIGELMREI------RLKDFQVDKIVDRLKDMAQQVKKGLSEV 262

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
              +  +    +++  + +R+  ++ E  R++Q  G+  D  L                 
Sbjct: 263 QACEEELKQPHKEIKRLLRRMRKSDEEAHRISQDLGVPIDTLL----------------- 305

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                            +   + +   +  E+G +  E    +  V KGE  A  AK E+
Sbjct: 306 ------------SVEKRLKSAQRKFNRVEDESGFAPEELLGSLKEVMKGEWRAKAAKSEL 353

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 354 VEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAI 413

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++RT+R++  ++ REP PEEIA+++ +P+E VR+VLK
Sbjct: 414 TRAIADQARTIRIPVHMIETINKLIRTSRQLVQEMGREPVPEEIAERMELPLEKVRRVLK 473

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPISLETPIG+E+ S LGDFIEDK  VSPL++ I+ NL + T+RVLASLTPREE+VL
Sbjct: 474 IAKEPISLETPIGEEEDSSLGDFIEDKGVVSPLEAVIKGNLSDQTSRVLASLTPREEKVL 533

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+++L+SF++
Sbjct: 534 RMRFGIGEKSDHTLEEVGQDFAVTRERIRQIEAKALRKLRHPSRARRLKSFVE 586


>gi|42521867|ref|NP_967247.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
 gi|39574397|emb|CAE77901.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
          Length = 609

 Score =  336 bits (862), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 255/656 (38%), Positives = 376/656 (57%), Gaps = 74/656 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            +  ++ +KLA+++G +TIEE+N  LPP+ V+   ++  +  L   G+ + D  +   EE
Sbjct: 27  KEEIQRFLKLAKEKGALTIEEINELLPPEIVAPSVLDSFMQGLEAGGVVISDLSESSKEE 86

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E +      + +  +  +++ +S D   +DPVR+YLR+MGS+ LL+REGE+ IA+RIE
Sbjct: 87  EGEGAFLENVDSEDEEIDDEEKAESEDVKGNDPVRLYLRKMGSVSLLTREGEVEIARRIE 146

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   ++ ++  SPL    +I     L++G   ++ I               F G E   
Sbjct: 147 KGEREIVRAILLSPLGTYEIIQLGKRLDEGRIKVKSI---------------FRGLEDED 191

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            Q  E        D + E  G +    K               AE     L ++E ++  
Sbjct: 192 TQYDEKEYI----DKIHELIGRVTEYQKA--------------AEKLFMTLRKEETNTPA 233

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             +AM                   +EL ++ D  +   +                    S
Sbjct: 234 RQAAM-------------------KELVAMNDKLMANFE--------------------S 254

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSY 386
           ++ N+  I+ +V +  ++  RI      +   + +++        ER +  + +   ++ 
Sbjct: 255 VNFNRKTINRVVIKFKNLVNRIGTLRRRIKDGVERTFSKDVTAMAERMKLIDANEKELTR 314

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                   ++ F +  + +  +    I  +  ET ++ +  +   + + KGE EA  AK 
Sbjct: 315 MTRDTGLNYQKFKSYVLQA-QEAEKRISRLDSETEMNHNWVKETYTAIWKGEREADAAKS 373

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 374 ELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 433

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K+VRT+R +  ++ REPTPEEIA K+ MPV+ VRKV
Sbjct: 434 AITRAIADQARTIRIPVHMIETINKLVRTSRYLIQELGREPTPEEIADKMDMPVDKVRKV 493

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPISLETP+G+E+ SHLGDFIEDK  ++P ++ +  NL E T RVL++LTPREE+
Sbjct: 494 LKIAKEPISLETPVGEEEDSHLGDFIEDKKVINPAEAIVNLNLAEQTRRVLSTLTPREEK 553

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS KL++F+D 
Sbjct: 554 VLRMRFGIGEESDHTLEEVGQDFNVTRERIRQIEAKALRKLRHPSRSNKLKAFVDS 609


>gi|95928999|ref|ZP_01311744.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134900|gb|EAT16554.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
          Length = 583

 Score =  336 bits (861), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 253/657 (38%), Positives = 370/657 (56%), Gaps = 81/657 (12%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++ ++++I+  +++GY+T +E+N  LP D VSS Q+ED + M   + I +VD +  E+
Sbjct: 5   TKEEEFQQLIETGKEKGYLTYDEVNDALPEDMVSSTQLEDVMTMFGELDIEIVDNETKEE 64

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +   + + D   S           +      T DPVRMYLREMG + LL+REGE+ IAKR
Sbjct: 65  KSKGDSNDDEDDSKEEG----NNFEAGVIGRTSDPVRMYLREMGQVSLLTREGEVEIAKR 120

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G  ++   + ++P+  Q +I   D+L++G   + +I         + + G     + 
Sbjct: 121 IEEGEGLITQVVLKTPIALQEVITLGDQLSEGLIGITDI-----TKDYDEEEGAEAEEKQ 175

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
           +       +   ++ D++ E         +  K    K  +  ++   D       ++ +
Sbjct: 176 YERILGLIAEIRQKNDELIEQRQLSNEGDEAQKKAAQKRIATLKDELCDLMRQIRLKEQT 235

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYREL-RSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
              ++    +L  +V  AL E+    + L  S +D     ++  KS  +   + E+L K 
Sbjct: 236 VSKIAQRLKELSAQVKKALSEVTACEKALGCSHKDIRRYLRRFHKSDDEAAKVVEELGKS 295

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                          ++L    KR+   + +  R+ +  G             EL    V
Sbjct: 296 --------------ADELQVAEKRLKGAQRKFKRVEEETG---------FSPEEL----V 328

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
              K+   GEW+   A                                            
Sbjct: 329 DSLKEVHRGEWRAKAA-------------------------------------------- 344

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 345 KTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWI 404

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  ++ REP PEEIA+++ +P+E VR
Sbjct: 405 RQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQELGREPIPEEIAERMDLPLEKVR 464

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +VLKI KEPISLETPIG+E+ S LGDFIEDK AVSPL++ I+ NL + T  VL++L+PRE
Sbjct: 465 RVLKIAKEPISLETPIGEEEDSSLGDFIEDKGAVSPLEAVIKGNLSDQTAEVLSTLSPRE 524

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+K+LRSF+D
Sbjct: 525 EKVLRMRFGIGERSDHTLEEVGQDFNVTRERIRQIEAKALRKLRHPSRAKRLRSFVD 581


>gi|222053802|ref|YP_002536164.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221563091|gb|ACM19063.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 586

 Score =  334 bits (855), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 255/657 (38%), Positives = 376/657 (57%), Gaps = 81/657 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I L +++G++T EE+N  LPPD VSSEQ++D ++M  +M I +VD    +  + 
Sbjct: 7   DEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSEQIDDVMSMFGDMDIEIVDS--AQKVKI 64

Query: 89  SEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  LDL           +   +      T DPVRMYLREMGS+ LL+REGE+ IAKRIE
Sbjct: 65  PKVKLDLEDEEEMEGEQEEVEFEPGTLGRTSDPVRMYLREMGSVSLLTREGEVEIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   + + +  +P+T + +I   D+L                            ++   
Sbjct: 125 VGERDVASVILNTPITVKEVISLGDKLRKFQI------------------AAIEISKEVE 166

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            ++ E+  ++ + + +  T  +I    +  ++    ++     A+  E  L E  D  A 
Sbjct: 167 EEELEEGEEDVQANRLLATIDEIRDHDRRMEEIFLALEQTTLPAKEREALLAEQRDFKAK 226

Query: 268 TLSAMED-QLRPKVMCAL-DEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKEKLVKL 324
               ++  +L+ + +  +   + E+  ++  +     + +K+   SS     +  K+ K 
Sbjct: 227 LAELLKSLRLKDRHIEKISQRLKELSHKVDKMMHEIADLEKEAGVSSADLAAMLGKMAKG 286

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                    ++ + +E +  + KR    E +L ++ Q  G          +  EL     
Sbjct: 287 PDEEKKVLKKLGISLEDVQKLEKRFKSAERKLKKIEQESG---------FKASELST--- 334

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                                       I+    +  ++ SE                  
Sbjct: 335 ------------------------ALQAIEEGEHKAKLAKSE------------------ 352

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
              +VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 353 ---LVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWI 409

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++++P++ VR
Sbjct: 410 RQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMSLPLDKVR 469

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPRE
Sbjct: 470 KVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPRE 529

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 530 EKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 586


>gi|189424079|ref|YP_001951256.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420338|gb|ACD94736.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 586

 Score =  332 bits (850), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 258/654 (39%), Positives = 360/654 (55%), Gaps = 75/654 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I + +++G++T +E+N  LPPD  + EQ++D + M  +M I +VD         
Sbjct: 7   DEVKQLIDIGKEKGFLTFDEVNDILPPDIAT-EQIDDVMGMFGDMDIEIVDSAQKVKIPK 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  L+     +       + +  A   T DPVRMYLREMGS+ LL+REGE+ I      
Sbjct: 66  IKIDLEEGEEEAEGEAEEVEFEPGAIGRTSDPVRMYLREMGSVSLLTREGEVEI------ 119

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
                                    + DG   +  II L   I  +              
Sbjct: 120 ----------------------AKRIEDGDREVAGII-LNTPITVKEVLALGEKLRKFQI 156

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
              E                       +SKD     D   E  E D + +   E   A  
Sbjct: 157 TPSE-----------------------ISKDIEEDADVDIEEGEEDIQQIRLLETIDAIA 193

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
            S  E                   EL +  ++A    K ++     K  KE L +L+ SL
Sbjct: 194 ASEQE-----------------INELLTALESAKAAAKKKELEKSLKEAKEHLAELLRSL 236

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR-DVFLERHQGRELDPHWVSYA 387
            +    I  + ++L ++S ++   + EL  +       +    LE+ +  E        A
Sbjct: 237 RMKDRHITRVADRLKELSSKVNRVKNELAEVHNVVPPDKLAELLEKFRADEAK----GMA 292

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
              P              +     ++  +  E+G   +E    +  +R+GE +A IAK E
Sbjct: 293 ALKPLKLSDEDFQKVEKRLKNAARKLTKVEQESGFKATELSKAIRAIREGEHKARIAKSE 352

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 353 LIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQA 412

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ+ TIRIPVHM + I+K++RT+R++  +  REP+PEEIA ++ +P++ VRKVL
Sbjct: 413 ITRAIADQARTIRIPVHMIETINKLIRTSRQLVQENGREPSPEEIADRMQLPLDKVRKVL 472

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPISLETPIG+E+ SHLGDFIEDK  V+PL++ I+ANL E T+RVL++LTPREE+V
Sbjct: 473 KIAKEPISLETPIGEEEDSHLGDFIEDKGVVNPLEAVIKANLSEQTSRVLSTLTPREEKV 532

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+SF++
Sbjct: 533 LRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKKLKSFVE 586


>gi|253702377|ref|YP_003023566.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251777227|gb|ACT19808.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 584

 Score =  331 bits (849), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 257/655 (39%), Positives = 371/655 (56%), Gaps = 75/655 (11%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T EE+N  LPPD VSS+Q++D ++M  +M I +VD       
Sbjct: 5   SMDEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSDQIDDVMSMFGDMDIEIVDSAQKVKI 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +  L+       S   ++    +    T DPVRMYLREMGS+ LL+REGE+ IAKRI
Sbjct: 65  PKIKMDLEEEEEHEGSEEEVEFEPGTL-GRTSDPVRMYLREMGSVSLLTREGEVEIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   + + +  +P+T + ++   + L        EI         E         +  
Sbjct: 124 EVGERDVASVILNTPITVREVVSLGERLRKQQIGAIEISKDVEEEVLEEGEEDLQALKVL 183

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +        +++  +     E +  +A +         +   + AE  +    +D     
Sbjct: 184 TIIDEIKEIEQRMSEIQSALEAEKVAAKEREALGAEHAELKVKMAETLKSLRLKDRHI-- 241

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             ++    +L  KV   + EIAE+ +E  + ++  +   +  K   +             
Sbjct: 242 EKIAQRLKELSCKVDTVMQEIAELEKESGAEREPFLTAFEGAKGGSEADF---------- 291

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
                Q ++++ +E+   + KR   +E +L ++ Q  G          +  EL       
Sbjct: 292 -----QKKLNMTLEEGQKLEKRFRSSEAKLKKIEQESG---------FKASEL------- 330

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                                              ++I E  H   +           K 
Sbjct: 331 -------------------------------ANALLAIEEGEHKAKLA----------KS 349

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 350 ELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQ 409

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++A+P++ VRKV
Sbjct: 410 AITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMALPLDKVRKV 469

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+
Sbjct: 470 LKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEK 529

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 530 VLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 584


>gi|162452723|ref|YP_001615090.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
 gi|161163305|emb|CAN94610.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
          Length = 639

 Score =  331 bits (847), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 262/663 (39%), Positives = 376/663 (56%), Gaps = 84/663 (12%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +    + +K+++  + +G++T +E+N  LP D    +Q++D V  L +  I +VDG    
Sbjct: 56  EKDRKTLEKLVETGKSKGFLTYDEVNDALPADVA-PDQLDDVVGALGDEDIEIVDGATQV 114

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKD-SADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                  + + A          ++ +D      ++DPVRMYLR+MGS+ LL+REGE+ IA
Sbjct: 115 KIAPKRIADEEAGEKKLVVTPDREEEDVDYYSKSNDPVRMYLRKMGSVSLLTREGEVEIA 174

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   + A++ +SP+                   REIIDL                
Sbjct: 175 KRIEIGEQKVNAAILDSPIAV-----------------REIIDL---------------- 201

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                            + +++ +  ++   K +++D  + D             +E+ D
Sbjct: 202 ----------------GEKLRKHKIRVKELIKDAENDDQEFD-------------EEEAD 232

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                L     ++  K    L+E  EV  E+R  Q             V+      +LV 
Sbjct: 233 RRIIRLIDKVKRVDKKKAELLEERKEVKTEVRRKQ-----------IDVEVTQATAELVT 281

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
            +  + LN+  ID +V++L  +  ++   E     L +  G+ +         REL    
Sbjct: 282 TLEEMRLNKRTIDKIVQKLKSLISKVEKAEAGATELERRTGLSKGEL-----KRELIKVK 336

Query: 384 VSYAKDFPEGEWKNFVACEVDS----ILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
            + A +    +  N    E++     I   +  +K +  E  I ++  R     +R+GE 
Sbjct: 337 GNRALEGRLAKKLNVQREELNDFESTIKNAQKGLKKVEEELNIDVAAIRDTYENIREGER 396

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            A  AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 397 MAERAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTY 456

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +  REPTPEEIA+K+ +P
Sbjct: 457 ATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEYGREPTPEEIAEKMELP 516

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK+ +SP ++ I  NL E T +VL +
Sbjct: 517 LDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKSVISPAEAVINMNLAEQTRKVLKT 576

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+SF
Sbjct: 577 LTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSKQLKSF 636

Query: 680 LDG 682
           +D 
Sbjct: 637 IDS 639


>gi|251771800|gb|EES52375.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum
           ferrodiazotrophum]
          Length = 590

 Score =  330 bits (846), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 256/659 (38%), Positives = 368/659 (55%), Gaps = 89/659 (13%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL-------- 83
           K +I L ++RGY+T +ELN  LP + V SE+M+  ++   +M I++V+ +          
Sbjct: 11  KDLITLGKERGYLTYDELNHALPSETVDSEEMDSILSYFGDMNIDIVEDEADHVEFTEAE 70

Query: 84  -EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E+EE  E+    A      +  L     +A   TDDPVR+YL+EMGS+ LL+REGEI I
Sbjct: 71  GEEEELFEEIEITALEEEADTEDLSDGIAAAGVRTDDPVRLYLKEMGSVPLLTREGEIKI 130

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           A+RIE G+  + + L   PL+ Q+++  RD++  G   +R+IIDLE     E        
Sbjct: 131 AQRIEEGKTEVFSFLFGVPLSIQSILGLRDKIQTGIIGIRDIIDLEEEETEEEGKSPAAR 190

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               ++ ++    +E                                     + N    +
Sbjct: 191 QATEAFIEQAAKIEEHFA----------------------------------KMNELSQK 216

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
             +     A +  LR KV     E+ EV  E+   Q                 +L EKL 
Sbjct: 217 MKAVLKDPAKKRALREKVKKIRHEVVEVILEMHLQQRQ-------------INILIEKLR 263

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            +VG                          E  L +  +  G+  D  L +         
Sbjct: 264 DVVGQF---------------------EETERTLDQCRRRIGLPVDEILAK--------- 293

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
               ++   + +         +   K    I S+  ET +S SE +  +  + +GE +  
Sbjct: 294 ---LSEKPKKSKLSAEKKELYEQFSKAHERILSLEAETFLSPSEAKESLQQIIRGEEKVR 350

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK E+++ANLRLV+S+AK+YTNRGLQFLDLIQEGNIGLMKA +KF++  G+KFSTYA W
Sbjct: 351 EAKSELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFSTYATW 410

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REP PEE+AK++ MPV+ 
Sbjct: 411 WIRQAITRAIADQARTIRIPVHMIETINKLIRTSRHLVQELGREPLPEELAKEMQMPVDK 470

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK  +SP+++A++ +L     + L++LT 
Sbjct: 471 VRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKTISPIEAAVRYDLVRKIGQSLSTLTD 530

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE+V+R+RFGIG  TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +L+SFLD
Sbjct: 531 REEKVIRLRFGIGELTDHTLEEVGQDFDVTRERIRQIEAKALRKLRHPSRSNQLKSFLD 589


>gi|148266058|ref|YP_001232764.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146399558|gb|ABQ28191.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter uraniireducens
           Rf4]
          Length = 586

 Score =  330 bits (846), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 256/653 (39%), Positives = 369/653 (56%), Gaps = 73/653 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I L +++G++T EE+N  LPPD VSSEQ++D ++M  +M I +VD    + +  
Sbjct: 7   DEVKQLIDLGKEKGFLTYEEVNDLLPPDIVSSEQIDDVMSMFGDMDIEIVDSA-QKVKIP 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                              + +      T DPVRMYLREMGS+ LL+REGE+ IAKRIE 
Sbjct: 66  KVKLDLEDEEELEGEQEEVEFEPGTLGRTSDPVRMYLREMGSVSLLTREGEVEIAKRIEV 125

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   + + +  +P+T + +I   D+L        EI         E        T   + 
Sbjct: 126 GERDVASVILNTPITVKEVISLGDKLRKLQIAAIEISKEVEEEELEEGEEDVQATRLLTV 185

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                        D    +         + +  +   S  EN   +++ L     D   +
Sbjct: 186 I------------DEIRADDTRMEELHAALEQETVTKSERENILAEQQELKAKMADLLKS 233

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
           L  ++D+   K+   L E++    ++  +Q+ A   ++   +      + +K+ K     
Sbjct: 234 LR-LKDRHIEKISQRLKELSWKVDKV--MQEIADLEKEAGVAPADLMPMLDKMHKGADEE 290

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
                ++ + +E+   + KR  + E +L ++ Q  G          Q  EL    ++  +
Sbjct: 291 KKVLKKLGISLEEAQKLEKRFRNAEKKLKKIEQESG---------FQATELSTALLAIEE 341

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              + +                                                +AK E+
Sbjct: 342 GERKAK------------------------------------------------LAKSEL 353

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 354 VEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAI 413

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++++P++ VRKVLK
Sbjct: 414 TRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMSLPLDKVRKVLK 473

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+VL
Sbjct: 474 IAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKVL 533

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 534 RMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 586


>gi|207743818|ref|YP_002260210.1| rna polymerase sigma d (sigma-70) factor (partial sequence c
           terminus) protein [Ralstonia solanacearum IPO1609]
 gi|206595218|emb|CAQ62145.1| rna polymerase sigma d (sigma-70) factor (partial sequence c
           terminus) protein [Ralstonia solanacearum IPO1609]
          Length = 684

 Score =  328 bits (841), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 164/541 (30%), Positives = 265/541 (48%), Gaps = 48/541 (8%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 186 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 245

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 246 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 305

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 306 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGLI 365

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            +  E++       E    ++ ++   E+E +D     G   SA ++             
Sbjct: 366 DLNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAASARQL------------- 412

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                   ++L+   +     I + + ++R   +      K+  
Sbjct: 413 ------------------------EELKQAALEKFSIIGDQFEKMRRAFE------KEGY 442

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
            S      +E +   + ++      ++ L + L      +   E  +L +     G+ R 
Sbjct: 443 KSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRG 502

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+ R  G E +  W++      +  +   V   + ++ +++ ++  +     + ++E +
Sbjct: 503 DFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELK 561

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 562 DVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 621

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP 
Sbjct: 622 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPD 681

Query: 549 P 549
           P
Sbjct: 682 P 682


>gi|254253609|ref|ZP_04946926.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898254|gb|EAY70097.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 773

 Score =  327 bits (838), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 164/541 (30%), Positives = 262/541 (48%), Gaps = 43/541 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  +   ++MG+ V +    
Sbjct: 180 LEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPD 239

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 240 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 299

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D    + P +     
Sbjct: 300 EIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD--GLLDPNAAD--- 354

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                                       D +  +    +     D   E  E +E   D+
Sbjct: 355 ---------------------------TDTDGFSAKEAEAIENEDEDAEEEEEEEEEEDD 387

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D    A   +A  + L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 388 DGAAQATANAAQLEALKRASLEKFALISEWFDKMRRAFE------KEGYKSKAYLKAQET 441

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L +     G+ R  F+ R  G E 
Sbjct: 442 IQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNET 501

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   ++  + +I + +  +  +     + + + +     +  GE 
Sbjct: 502 DLDWAEKIAAEGHP-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 560

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 561 KARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 620

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP
Sbjct: 621 ATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMP 680

Query: 560 V 560
            
Sbjct: 681 E 681


>gi|88608313|ref|YP_506202.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600482|gb|ABD45950.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
          Length = 620

 Score =  327 bits (837), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 217/674 (32%), Positives = 330/674 (48%), Gaps = 88/674 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
              K +I    +RG+VT  EL+     ++  +   +E+ ++ L   GI +++        
Sbjct: 11  QVVKALITKGVKRGFVTYGELSDSFSDEDFENLNCIEEAISKLEESGIGILE-------- 62

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D  D  S         +         TDDPVR+YLREM  ++LLSR+ E+ IAK I 
Sbjct: 63  --KDEEDELSEEVKEEDEEEDEAADILGHTDDPVRLYLREMSYVKLLSRDDEVEIAKAIV 120

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           A +   ++++   P   ++++    +L + T  LRE+I+ ++ +  E             
Sbjct: 121 AEKFESLSAVLLFPSVLKSIVNLGTKLRECTISLREVIESDSGLKSE------------- 167

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                                 +        D    +D  PE            +++   
Sbjct: 168 ----------------------LTEETGKGDDLFEGMDGKPEEGNQM------SDEELME 199

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +  +  +L   +  ALD+  E   ++  + D       +     + + L    V  +  
Sbjct: 200 KVLDIFGELETIITSALDKAKE--GQMVKIVD------GEVILDPEYRELHTLAVNHLNQ 251

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           + LN   +    E     ++ I+  +  LL   + +G+ R V ++  +   LD   +S  
Sbjct: 252 VKLNPKLLAEFFENTRKKNELILEKKKVLLTFLEEHGLDRTVLIKG-KVHILDAVVLSEL 310

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                    +F      S+ +  + I+ +    G+       +   V      A+ AK  
Sbjct: 311 LKEHNICDTHF------SLEEFLSPIRELEKNEGMDYRSISFLTRKVATHLDNANAAKHR 364

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRG+ F DLIQEGNIGLMKA +KFD   G+KFSTYA WW +QA
Sbjct: 365 MVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFSTYATWWCRQA 424

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IAD    +R PVH+ +  +KV+RT RR+ N   REPT EEIA  L +  + V+K L
Sbjct: 425 ITRAIADCGSIVRKPVHIHETANKVMRTRRRLYNLNGREPTVEEIANLLKISPDKVKKSL 484

Query: 568 KITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           K+ ++PISLE+P+GD+  S   GDFIEDKNAVS +D  +  NLR+     LA L+PREE+
Sbjct: 485 KVNQDPISLESPVGDDSNSGSFGDFIEDKNAVSQVDVVLSKNLRKVLDEALAMLSPREEK 544

Query: 627 VLRMRFG--------------------IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +LR RFG                    +   T+ TLE+VG  + VTRERIRQIE+K++RK
Sbjct: 545 ILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTNLTLEQVGILYNVTRERIRQIESKSLRK 604

Query: 667 LKHPSRSKKLRSFL 680
           ++ PSRS KLR+FL
Sbjct: 605 MRSPSRSIKLRTFL 618


>gi|319941927|ref|ZP_08016248.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319804580|gb|EFW01450.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 917

 Score =  326 bits (836), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 225/660 (34%), Positives = 330/660 (50%), Gaps = 66/660 (10%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +       K+I L ++RGYVT  E+N  +P   +  + +E  V +L N+ I V +    E
Sbjct: 317 EDRRSKLIKLISLGKERGYVTYSEINDNIPNTLLDEDAIETIVNILGNLNIAVHEVAPDE 376

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRK--DSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++   +   +  S     +         +S    T DPVR+Y+REMGS+           
Sbjct: 377 EQLLIQGGAEGVSDEDAEAEAEAALSTVESEFGRTTDPVRIYMREMGSV----------- 425

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
                                   L+  +DE+     +             E        
Sbjct: 426 -----------------------ELLSRQDEIEISKRI-------------EDGLKHMVL 449

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                     +  +  ER    ET  D      V+ DD+  V    E         DE +
Sbjct: 450 AIARCPVTVHEILESAERIRSGETPIDEVVDGIVTPDDQKNVVGAVE---------DETD 500

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
             ++       + L+ K +   D +   +R L    D           + + + LK+++ 
Sbjct: 501 MGASAMTVGQLEDLKEKSLAVFDRVEAHFRSLVETFD------GKGPHAPELEGLKDQIQ 554

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGRELDP 381
           + +  +       D L E L      +  +E  +      +  + R+ FL          
Sbjct: 555 RELMEIRFTAKTADRLCESLRRTIGIVRGSERTVYDEYVRHLHLPREWFLANFISNATRI 614

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            WV         +    +     ++ + +  +  +  E+ ++++E       +  GE +A
Sbjct: 615 GWVDEVAA-AYPDKAQVILHMRATVEEEQRRLAQLERESHMTVAELLDTYKQMATGESKA 673

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+EM EANLRLVIS+AKKYTNRGLQFLDLIQEGN+GLMKA +KF++  GYKFSTYA 
Sbjct: 674 RNAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYAT 733

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSIADQ+ TIRIPVHM + I+++ R  R+   +   EP    +A+ + MP +
Sbjct: 734 WWIRQAITRSIADQARTIRIPVHMIETINRMNRITRQELQETGVEPDSRRLAELMEMPED 793

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + K++KI KEPIS+ETPIGD+D SHLGDF+ED   V+P ++   A+L +T  +VL SL+
Sbjct: 794 KILKIMKIAKEPISMETPIGDDDDSHLGDFLEDTQTVAPAEAVQNASLSDTVKQVLDSLS 853

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE +VLRMRFGI M +DHTLEEVGKQF VTRERIRQIE KA+RKL+HPSR+ KL+SFLD
Sbjct: 854 PREAKVLRMRFGIEMQSDHTLEEVGKQFDVTRERIRQIETKALRKLRHPSRADKLKSFLD 913


>gi|242279084|ref|YP_002991213.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
 gi|242121978|gb|ACS79674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
          Length = 585

 Score =  326 bits (836), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 229/654 (35%), Positives = 355/654 (54%), Gaps = 76/654 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            + K +I   +++G++T E+L   LP +   S+Q++D + +   + I +V+  +   +  
Sbjct: 8   QAIKTLISEGKKQGFLTFEQLGKALPAEFNKSDQLDDVIKIFDQLNIAIVNTPEDGKKIM 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                +        S   ++        + DPVRMYLREMG++ LL REGE+ IAK+IE 
Sbjct: 68  DAGVDNDDDIDLTES---EEESVDYVSRSTDPVRMYLREMGAVGLLDREGEVVIAKKIEN 124

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   ++ +L E P+  + LI   ++L++    L++++                       
Sbjct: 125 GEMDVLYALVEIPVAIEELISVGEDLDESRIKLKDVV----------------------K 162

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
              ED   E E +  Q     ++   K+    R       + A  +++   +  +   + 
Sbjct: 163 TIEEDDPSEDEMNQRQRVIFLLDEVKKLYDKKRDLYYKLDDCATLEKKVAKQQNEIVNYK 222

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
              +E +LR   +     I ++   +        N Q+D         L   ++    + 
Sbjct: 223 TEIVE-RLRDIKIEK-TLIDQIIETVGDYVRQMHNCQRD---------LSAYILSTGKTQ 271

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
                      +++ D+ K+I   E   +  +   G+  D                    
Sbjct: 272 -----------QEIKDLFKQIDDREINPVAASDELGMTVDELFS---------------- 304

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                 +K  ++ +++ +++++++          ++ E   ++  ++ G   A  AK+E+
Sbjct: 305 ------FKEMISGKMEILVRLQDKCCH-------NVHELEEVLWRIKHGNRSAMRAKQEL 351

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 352 IRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAI 411

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P+PEEIA+++  P+E V+KVLK
Sbjct: 412 TRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPSPEEIAERMDYPLEKVKKVLK 471

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPISLETPIGDE+ S LGDFIEDK A +P +  +   L E    VL+ LTPREE+VL
Sbjct: 472 IAKEPISLETPIGDEEDSSLGDFIEDKKAAAPAEEVVSTKLGEQIATVLSDLTPREEQVL 531

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           R RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  LRS+ + 
Sbjct: 532 RKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSALLRSYYEN 585


>gi|45128589|gb|AAS55058.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  326 bits (834), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 179/534 (33%), Positives = 275/534 (51%), Gaps = 44/534 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++    ++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    
Sbjct: 1   LKLLVIKGGEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALN 60

Query: 91  DSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 61  DDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 120

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +S+ E P T   ++   D++      L ++I     + P++           +  
Sbjct: 121 INQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPDAD----DTAAPTATH 174

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
              + S+ +  ++ +E   D E +   S D    V   PE A                  
Sbjct: 175 IGSELSETQLEEEDEEDLEDDEESDDDSDDSEEDVGIDPELA------------------ 216

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                      +   +++   Y+ L+      +   +    S K  V  E ++ +     
Sbjct: 217 -----------LEKFNQLRSTYQNLQ------LAINEYGYDSPKATVANEMMLDVFKEFR 259

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           L   + D LV +L     R+   E  +++    YG + +  F+    G E    W+    
Sbjct: 260 LTPKQXDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGXESSDAWLDEIL 319

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              +  +   +    + I +   ++K I  ET +++   + I   +  GE +A  AKKEM
Sbjct: 320 A-SDXPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEM 378

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 379 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 438

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + 
Sbjct: 439 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDK 492


>gi|254796694|ref|YP_003081530.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
 gi|254589929|gb|ACT69291.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
          Length = 620

 Score =  325 bits (833), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 218/674 (32%), Positives = 329/674 (48%), Gaps = 88/674 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
              K +I    +RG+VT  EL+     ++  +   +E+ ++ L   GI +++        
Sbjct: 11  QVVKALITKGVKRGFVTYGELSDSFSDEDFENLNCIEEAISKLEESGIGILE-------- 62

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D  D  S         +         TDDPVR+YLREM  ++LLSR+ E+ IAK I 
Sbjct: 63  --KDEEDELSEEVKEEDEEEDEAADILGHTDDPVRLYLREMSYVKLLSRDDEVEIAKAIV 120

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           A +   ++++   P   + ++    +L +GT  LRE+I+ ++ +  E             
Sbjct: 121 AEKFESLSAVLLFPSVMKGIVDLGTKLREGTISLREVIESDSGLKSE------------- 167

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                                 +        D    +D  PE            +++   
Sbjct: 168 ----------------------LTEETSKGDDLFEGMDGKPEEGNQM------SDEELME 199

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            +  +  +L   +  ALD+  E   ++  + D       +     + + L    V  +  
Sbjct: 200 KVLEIFGELETIITSALDKAKE--GQMVKIVD------GEVILDPEYRELHTLAVNHLNQ 251

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           + LN   +    E     ++ I+  +  LL   +  G+ R V ++  +   LD   +S  
Sbjct: 252 VKLNPKLLAEFFENTRKKNELILEKKKVLLTFLEERGLDRTVLIKG-KVHILDAGVLSEL 310

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                    +F      S+ +  + I+ +    G+       +   V      A+ AK  
Sbjct: 311 LKKHNICDTHF------SLEEFLSPIRELEKNEGMDYESISFLTRKVATHLDNANAAKHR 364

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRG+ F DLIQEGNIGLMKA +KFD   G+KFSTYA WW +QA
Sbjct: 365 MVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFSTYATWWCRQA 424

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IAD    +R PVH+ +  +KV+RT RR+ N   REPT EEIA  L +  + V+K L
Sbjct: 425 ITRAIADCGSIVRKPVHIHETANKVMRTRRRLYNLNGREPTVEEIANLLKISPDKVKKSL 484

Query: 568 KITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           K+ ++PISLE+P+GD+  S   GDFIEDKNAVS +D  +  NLR+     LA L+PREE+
Sbjct: 485 KVNQDPISLESPVGDDSNSGSFGDFIEDKNAVSQVDVVLSKNLRKVLDEALAMLSPREEK 544

Query: 627 VLRMRFG--------------------IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +LR RFG                    +   T+ TLE+VG  + VTRERIRQIE+K++RK
Sbjct: 545 ILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTNLTLEQVGILYNVTRERIRQIESKSLRK 604

Query: 667 LKHPSRSKKLRSFL 680
           ++ PSRS KLR+FL
Sbjct: 605 MRSPSRSIKLRTFL 618


>gi|149923522|ref|ZP_01911923.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149815591|gb|EDM75122.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 589

 Score =  324 bits (831), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 243/659 (36%), Positives = 358/659 (54%), Gaps = 85/659 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   + ++   +++G++T+ EL   LPPD +   ++++  +ML + G+ V+         
Sbjct: 11  DKIKQAIVAFGKKKGHMTVAELRELLPPDVIDHGKLDEWKSMLESEGVKVL--------- 61

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               +  L  S    +   + + +S    T+DPVRMYLR+MGS+ LL+REGE+ IAKRI 
Sbjct: 62  ----AKSLEKSPKRKARTRKAKDESDTSRTNDPVRMYLRKMGSVSLLTREGEVEIAKRI- 116

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                                        G   + EI+       P  +  F        
Sbjct: 117 ---------------------------EQGELQVFEIVLASPVAVPYVQDMFDKIKRSQL 149

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             K   +          +++  +   A                                 
Sbjct: 150 RIKDVVTIATPNDGPQPKSKAPVNQDA--------------------------------- 176

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK---LVKL 324
               M+ QL       +    +   +L + Q    +    E+     + + +    +V  
Sbjct: 177 AFENMQKQL-----EKVRRHHKDIEKLLAAQAATPDKPAKERGKTVEQQVDDHQIAIVDA 231

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
           +  + L++  +D +V++L  I +R+     +L    +  G++          R++     
Sbjct: 232 IREMYLSRRPVDGMVDELNSIVERVQRATQDLTTCERRAGMELSELRGLF--RDVRLSEE 289

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNE-IKSISVETGISISEFRHIVSMVRKGECEASI 443
              K             E+++ +K+  + I+ +  ETG+   +   + + + K   +A  
Sbjct: 290 EEFKLCRRLGLHPSELHEIEARMKLATKRIRQVEQETGMDAPDLIELHTRLMKARRQADR 349

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 350 AKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 409

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REPTPEEIA+K+ +P++ V
Sbjct: 410 IRQAITRAIADQARTIRIPVHMIETINKLIRTSRSLVQELGREPTPEEIAEKMELPLDKV 469

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI KEPISLETPIG+E+ SHLGDFIEDKNAVSP +  I  NL + T RVLA+LTPR
Sbjct: 470 RKVLKIAKEPISLETPIGEEEDSHLGDFIEDKNAVSPAEVVININLADQTRRVLATLTPR 529

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L++F++ 
Sbjct: 530 EEKVLRMRFGIGETSDHTLEEVGQDFSVTRERIRQIEAKALRKLRHPSRSKRLKAFVES 588


>gi|45128597|gb|AAS55059.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  324 bits (830), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 177/534 (33%), Positives = 274/534 (51%), Gaps = 44/534 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    
Sbjct: 1   LKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALN 60

Query: 91  DSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 61  DDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 120

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +S+ E P T   ++   D++      L ++I     + P++           +  
Sbjct: 121 INQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPDAD----DTAAPTATH 174

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
              + S+ +  ++ +E   D E +   S D    V   PE A                  
Sbjct: 175 IGSELSETQLEEEDEEDLEDDEESDDDSDDSEEDVGIDPELA------------------ 216

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                      +   +++   Y+ L+      +   +    S K  V  E ++ +     
Sbjct: 217 -----------LEKFNQLRSTYQNLQ------LAINEYGYDSPKATVANEMMLDVFKEFR 259

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           L   ++  LV +L     R+   E  +++    YG + +  F+    G E    W+    
Sbjct: 260 LTPKQLXHLVXELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGXESSDAWLXEIL 319

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                 +   +    + I +   ++  I  ET +++   + I   +  GE +A  AKKEM
Sbjct: 320 A-SXXPYAEKIKRXEEEIRRSIAKLXMIEEETSLNVQNIKDISRRMSIGEAKAXRAKKEM 378

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 379 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 438

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + 
Sbjct: 439 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDK 492


>gi|297520936|ref|ZP_06939322.1| RNA polymerase sigma factor RpoD [Escherichia coli OP50]
          Length = 436

 Score =  324 bits (829), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 205/396 (51%), Positives = 267/396 (67%), Gaps = 3/396 (0%)

Query: 288 AEVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            E + ELR+      +  K + +S    +    KL ++     L   + D LV  +  + 
Sbjct: 41  REKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMM 100

Query: 347 KRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
            R+   E  +++L  +   + +  F+    G E    W + A    +  W   +    + 
Sbjct: 101 DRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKP-WSEKLHDVSEE 159

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTN
Sbjct: 160 VHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 219

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM
Sbjct: 220 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 279

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ 
Sbjct: 280 IETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED 339

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEV
Sbjct: 340 SHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEV 399

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 400 GKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 435


>gi|188996275|ref|YP_001930526.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188931342|gb|ACD65972.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 590

 Score =  323 bits (828), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 229/656 (34%), Positives = 360/656 (54%), Gaps = 74/656 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLEDE 86
            D  + +I LAR++GYVT  E++ ++  +  SS++ +E  +  L+ + I+V D + ++ E
Sbjct: 7   RDDVRTLINLAREKGYVTYAEISTYVEEEFFSSDENIESLIEYLNELNIDVRDDEKIKSE 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +             +  + +    D      DDPV++YLREMG I LL R+ EI  +  I
Sbjct: 67  D----------EDISEHLGIDLSDDDVWNKADDPVKLYLREMGKIPLLKRDEEIKYSMEI 116

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E GR  +   L  +    + L+    ++ DG   + +I++L+    PE K          
Sbjct: 117 ERGRKKVFRGLLRTSFLTERLLDEWAKVIDGKARVHDILNLDE---PEVKDEEETSESEE 173

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              +   +  +   D +++     +    + + ++  +++     + +        +   
Sbjct: 174 FSLENNGNYDKITADFIKKGLELAKLYRDLIEKEKKYLETGSLEDKKEFVWQHAKLNRFI 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            +L+    +L        DE+ E+Y +LR          K+EK   K   +  K+     
Sbjct: 234 KSLNIKFTKLDKIA----DELKELYTKLR----------KNEKDYEKRIKIISKIHPD-- 277

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
                   IDL++   Y                                  E +P  +  
Sbjct: 278 --------IDLMLSSDY----------------------------------EKNPEILKK 295

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            ++      +  +       LK+++EI+ I  + G   SEF H++ +++ G  E +  K+
Sbjct: 296 LEEHGFSYGRYEILRT--ETLKLKDEIEEIKQKIGTIPSEFDHVLDLIQLGRNEINNVKQ 353

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +V+ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +K+D+  G+KFSTYA WW++Q
Sbjct: 354 VLVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKKGFKFSTYATWWIRQ 413

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++R +R +  ++ REPTPEEIAKK  MP + VRK+
Sbjct: 414 AITRAIADQARTIRIPVHMIETINKLLRISRTLVQELGREPTPEEIAKKAGMPADKVRKI 473

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L+ +++P+SLETPIG ++ SHLGDFIEDK  +SP    ++  LR     VL++L+ REE+
Sbjct: 474 LRTSQDPVSLETPIGSDEESHLGDFIEDKTVLSPEQHMLKQALRLQLDEVLSTLSEREEQ 533

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VLR RFG+  +T+HTLE+VGK+F VTRERIRQIEAKA+RKL+HP R+K L+ F++G
Sbjct: 534 VLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKALRKLRHPHRAKYLKPFIEG 589


>gi|291287657|ref|YP_003504473.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290884817|gb|ADD68517.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 626

 Score =  322 bits (824), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 227/652 (34%), Positives = 366/652 (56%), Gaps = 36/652 (5%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             K +I L +++G++T +E+N  LP D +S+E +++ + +L+ + I+V+D    +    S
Sbjct: 11  EVKSIIALGKEKGFLTFDEINENLPDDILSTELIDEIMMLLAQLKIDVIDSKVDKPGLYS 70

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D  D    + +       ++     STDDPVR+YL+EMG+I LL+RE EI +AK IE G
Sbjct: 71  ADDDDDDEDSIS-----LLKEVEESISTDDPVRLYLKEMGNIALLNREEEIEVAKEIEEG 125

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
           +  ++ ++   P T   ++     + + +  L+                           
Sbjct: 126 QRKVVRAVLLYPNTAMKIMDIARNIRNDSMRLK-------------------------DI 160

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
              D   + E DD+   E + E+    ++    K   P +  E     ++ ++  +    
Sbjct: 161 IDIDDGSDAENDDLDAVENENENEENAAEQPEIKQPEPVKTLEEIAAEVEAEQQLAEERE 220

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q    +    D++ +       +++N  +  +      K     + +   +  + 
Sbjct: 221 EQIKVQFIEILEDIADKLHKNIDLNDKIKENKCSIDEMLNIKFKMHETVDDITDKLLEIK 280

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           +N S+I L+  ++ D  + I     ++ ++ +   I+   + +     E +       + 
Sbjct: 281 VNYSKICLIANEIKDAHQAIYDRSKDIDKICKL--IRYTDYTDAVSVTEDELTRACENRG 338

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
               +++  V     +   +   I S+    G   +E   I   +  GE E   AK +++
Sbjct: 339 MALPDYEIIVKKYKKAKKGLDECINSL----GFDKAELDVIHDSLLMGENETEKAKSKLI 394

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAIT
Sbjct: 395 EANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYKRGYKFSTYATWWIRQAIT 454

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVHM + I+K+++  R++   + REPTPEEI+ K+ +PVE ++KV+KI
Sbjct: 455 RAIADQARTIRIPVHMIETINKMMKITRQLQQDMGREPTPEEISSKMDIPVEKIKKVMKI 514

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            KEP+SLETPIG+++ S LGDFIEDK+A +P +      L+E T ++L +L+ RE  VL+
Sbjct: 515 AKEPVSLETPIGEDEDSSLGDFIEDKSAKNPSEEVTYLKLKEHTKQILETLSHREASVLK 574

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +RFGI  ++DHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ L++F +
Sbjct: 575 LRFGIECDSDHTLEEVGKQFNVTRERIRQIEAKALRKLRHPTRSRILKTFTE 626


>gi|167627930|ref|YP_001678430.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597931|gb|ABZ87929.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 578

 Score =  321 bits (823), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 239/663 (36%), Positives = 344/663 (51%), Gaps = 89/663 (13%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDG 80
           +  +      K ++   ++RGY+T  ++   LP D     ++ E+  A+L + GI+V D 
Sbjct: 1   MTREDLLSDLKDLMVDGKERGYLTRADILDALPGDVSEDPKKYEEIEAILIDAGIDVYDR 60

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
               DE+  E  +  A+             D     T DP+RMY+REMG ++LL ++GE 
Sbjct: 61  TPELDEDDDERKVSEAN------------LDDLKGKTSDPIRMYMREMGIVDLLDKKGET 108

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IA RIE G   + +++   P+  +  I    EL                          
Sbjct: 109 DIAIRIEEGTTEVFSTILSYPIVVKTYIERFRELE------------------------- 143

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                             E+     T  DIE          +++ +   + +  E  + E
Sbjct: 144 ------------------EKAVDYMTSQDIEDEPVAKYIRFNEIMAGFSDEQVTEEKVAE 185

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+ D       ++ Q   +    L+++ E Y+E                     K L  K
Sbjct: 186 DDHDE-----KIDTQRAYEFFVNLEKMFEEYQE------------------KPNKKLYSK 222

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +VK    L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++    
Sbjct: 223 IVKEFECLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYEI--G 280

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+         +   F    V  I  +  +I        + I E + +   + K E 
Sbjct: 281 SIEWL-----PSLTKKYKFTDNTVKEIHNLTKQINQFQNLMMMKIEELKKVNVEISKSEA 335

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTY
Sbjct: 336 KITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTY 395

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AM 558
           A WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M
Sbjct: 396 ATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEYTPNM 455

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ 
Sbjct: 456 TKDKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELID 515

Query: 619 S-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L+
Sbjct: 516 TGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLK 575

Query: 678 SFL 680
           +FL
Sbjct: 576 TFL 578


>gi|241668482|ref|ZP_04756060.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877016|ref|ZP_05249726.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843037|gb|EET21451.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 578

 Score =  321 bits (822), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 238/663 (35%), Positives = 343/663 (51%), Gaps = 89/663 (13%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDG 80
           +  +      K ++   ++RGY+T  ++   LP D     ++ E+  A+L + GI+V D 
Sbjct: 1   MTREDLLSDLKDLMVDGKERGYLTRADILDALPGDVSEDPKKYEEIEAILIDAGIDVYDR 60

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
               DE+  E  +  A+             D     T DP+RMY+REMG ++LL ++GE 
Sbjct: 61  TPELDEDDDERKVSEAN------------LDDLKGKTSDPIRMYMREMGIVDLLDKKGET 108

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IA RIE G   + +++   P+  +  I    EL +                        
Sbjct: 109 DIAIRIEEGTTEVFSTILSYPIVVKTYIERFRELEE------------------------ 144

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              +   Y   +D   E     ++                   +    +    +E+  ++
Sbjct: 145 ---KAVDYMASQDIEDEPVAKYIR---------------FNEIMAGFSDEQVTEEKVAED 186

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D D+   T  A E          L+++ E Y+E                     K L  K
Sbjct: 187 DHDEKIDTQRAYE------FFVNLEKMFEEYQE------------------KPNKKLYSK 222

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           +VK    L L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++    
Sbjct: 223 IVKEFECLRLSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYEI--G 280

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+         +   F    V  I  +  +I        + I E + +   + K E 
Sbjct: 281 SIEWL-----PSLTKKYKFTDNTVKEIHNLTKQINQFQNLMMMKIEELKKVNVEISKSEA 335

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + + AKKEM+EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTY
Sbjct: 336 KITQAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTY 395

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AM 558
           A WW++QAITRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M
Sbjct: 396 ATWWIRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEYTPNM 455

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + ++K+L I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ 
Sbjct: 456 TKDKLKKILNISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELID 515

Query: 619 S-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + LT RE +VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L+
Sbjct: 516 TGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLK 575

Query: 678 SFL 680
           +FL
Sbjct: 576 TFL 578


>gi|15606649|ref|NP_214029.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
 gi|2983864|gb|AAC07417.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
          Length = 575

 Score =  320 bits (820), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 212/653 (32%), Positives = 336/653 (51%), Gaps = 84/653 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            +S K +I++ +++GYVT +E+N  L  D  SSE  E+ + +L  M I          E 
Sbjct: 4   RESVKALIEMGKEKGYVTYDEINEVLEEDVTSSELFEELIDILHRMNI-------QVVES 56

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E   +   +       +     ++     DPV++YLREMG I LL RE EI  A++IE
Sbjct: 57  KEEYEEESEETQEEEEEVVVSGSLTSSSRDGDPVKLYLREMGKIPLLKREEEIYYARQIE 116

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            GR +M   L  +    + ++    +L +G   ++E++DL      +     F   +   
Sbjct: 117 IGRKIMRRGLMRTSFLVEKILDDWAKLCNGKLKIQEVMDLVEYENDDDFEDRFDEFKRFF 176

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                                 IE   +++K  R+ +D   E  +N      +    +  
Sbjct: 177 ----------------------IEKGYELAKAYRNLLDVREEYIKNPSEESRKKYLYAHA 214

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            ++ +  +++       + + E   ++                                 
Sbjct: 215 RMNKIIKEMK-IKYAKFERVTEEIIKIYKEYARKR------------------------- 248

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
                           D++ RI        +L   Y    D F +     E +   +   
Sbjct: 249 ---------------KDLNARIR-------KLKALYKDP-DYFAQNFLTDE-NLQKIVQE 284

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR-HIVSMVRKGECEASIAKK 446
           K+ P  +  N +    +    ++ E++ I    G+   E    ++ ++ +G  +   AK+
Sbjct: 285 KNIPTEKVLNLI----NEYNSLKREVQRIQNLIGVFPEEELPKVMKIIEQGRKKVVQAKQ 340

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+++NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW++Q
Sbjct: 341 VMIQSNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQ 400

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K+++ ++++  +  REPTPEEIA+ L +PVE V+KV
Sbjct: 401 AITRAIADQARTIRIPVHMIETINKIIKASKKLFQENGREPTPEEIAEYLDIPVEKVKKV 460

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K ++EPISLETPIGD+D + L DFIEDK+  +P +   +  LRE   +VL++L+ +E  
Sbjct: 461 MKFSQEPISLETPIGDDDDTFLKDFIEDKSIPNPEEQVTRKLLREQLQKVLSTLSEKERE 520

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +L  R+G+   T++TLE+VGK F VTRERIRQIE KA+RKL+HP+R+K L+ F
Sbjct: 521 ILMYRYGLVDGTEYTLEQVGKMFNVTRERIRQIENKALRKLRHPARAKYLKDF 573


>gi|224370025|ref|YP_002604189.1| RpoD [Desulfobacterium autotrophicum HRM2]
 gi|223692742|gb|ACN16025.1| RpoD [Desulfobacterium autotrophicum HRM2]
          Length = 618

 Score =  319 bits (818), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 241/673 (35%), Positives = 344/673 (51%), Gaps = 86/673 (12%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S +  KK+I+  ++ G ++  E+N  +  +  SS+Q++D +     +GI+++D D  E 
Sbjct: 14  VSKEVLKKLIERGKKEGSLSYAEINEAISENLKSSDQIDDIMVKFKQLGIDLIDTDKGEK 73

Query: 86  EEGSEDSLD-----------------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            +  +                      A     S        D    +  DPV+MYLREM
Sbjct: 74  PKKKKVKKVVKSARLNDGADDGDDDSEAPPGKKSKFGKATAADMEFGTVTDPVKMYLREM 133

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G + LLSREGEI IAK+IE G   ++  L  SP+    L+     +              
Sbjct: 134 GMVTLLSREGEIEIAKKIEVGEREVLKGLLASPIAVDHLLSLGGRMEAQQNR-------- 185

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                                       E  R   +    D++    +  +         
Sbjct: 186 ---------------------------PEDSRLRPKHILRDVDEGDGMVDEVVKLEKFLA 218

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
              E    +L   E  +      +E Q    V    D+I     ++  L           
Sbjct: 219 CLDEIKALHLLNQEKRTQILAGGLEPQ---AVRKMRDDIRSKNEKIYELLKCW------- 268

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
                 +     + K+  S+  N    D + + L               R + S+  +RD
Sbjct: 269 ------RFESGVVDKIEKSIRANIRWFDTMDDLLK--------------RCSASFKARRD 308

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
             ++  +  +    WV    +  E   +         +  I  +I           +  +
Sbjct: 309 DMVDMLEDHDDFVAWVLERSEMDEARARVL----HQDLCAITAQISVRKDNVKGDAATLK 364

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I+  + KG   A  AK E+V ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 365 KIIKGIDKGRMVAKYAKSELVRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ +EP+
Sbjct: 425 EYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEMGKEPS 484

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA+K+ +P++ VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK    P ++AI  N
Sbjct: 485 PEEIAEKMEIPLDKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKFSLPSEAAINLN 544

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E T +VLA+LTPREE+VLRMRFGIG   DHTLEEVG+ F VTRERIRQIEAKA+RKL+
Sbjct: 545 LAEQTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFTVTRERIRQIEAKALRKLR 604

Query: 669 HPSRSKKLRSFLD 681
           HP+RS+KL+SF++
Sbjct: 605 HPTRSRKLKSFIE 617


>gi|45128577|gb|AAS55057.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  319 bits (816), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 174/534 (32%), Positives = 271/534 (50%), Gaps = 44/534 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+    
Sbjct: 1   LKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALN 60

Query: 91  DSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D  ++    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G
Sbjct: 61  DDTNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEG 120

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +S+ E P T   ++   D++      L ++I     + P++           +  
Sbjct: 121 INQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPDAD----DTAAPTATH 174

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
              + S+ +  ++ +E   D E +   S D    V   PE A                  
Sbjct: 175 IGSELSETQLEEEDEEDLEDDEESDDDSDDSEEDVGIDPELA------------------ 216

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                      +   +++   Y+ L+      +   +    S K  V  E ++ +     
Sbjct: 217 -----------LEKFNQLRSTYQNLQ------LAINEYGYDSPKATVANEMMLDVFKEFR 259

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           L   ++   V +      R+   E  +++    YG + +  F+    G E    W+    
Sbjct: 260 LTPKQLXHXVNEXRTAMDRVXTQERLIMKSVVEYGKMPKKSFIALFTGXESSDAWLXEIL 319

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                 +   +    + I +   ++  I  ET +++   + I   +  GE +A  AKKEM
Sbjct: 320 A-SXXPYAEKIKRXEEEIRRSIAKLXMIEEETSLNVQNIKDISRRMSIGEAKARRAKKEM 378

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           VEANLRLVIS+AKKYTNRG QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 379 VEANLRLVISIAKKYTNRGXQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 438

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           TRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP + 
Sbjct: 439 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDK 492


>gi|299135760|ref|ZP_07028944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
 gi|298601884|gb|EFI58038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
          Length = 573

 Score =  319 bits (816), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 225/659 (34%), Positives = 338/659 (51%), Gaps = 94/659 (14%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D  ++   ++I   +++GY+T  E+N  LP D  S ++++D +  ++  GI V+ G+  
Sbjct: 5   LDKYEEDVDRIIDTGKEKGYLTYGEVNDLLPGDITSPDELDDLMTTINTQGIEVLSGEGR 64

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                         S                  T+DPVRMYLREMG++ LL+REGE+   
Sbjct: 65  RAASERAAEDSDNESGEEGDDVELDLSPGTLEKTNDPVRMYLREMGTVPLLTREGEV--- 121

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
                                         +  G   + + I     +  E  G      
Sbjct: 122 -------------------------EIAKRIERGQLRVMKAISRSPIVIREITGLGEDLK 156

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            G    K      E+E  +        ++ A++ +  + +  +    A   E +  + + 
Sbjct: 157 RGVRNIKEVVVFDEEELTEEILAARVKQTVARIDELIKHQKKAADFGARVAEPHGKDAKA 216

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                  +     R  V                                        + +
Sbjct: 217 KEKDKRKSRWLMGREHVF---------------------------------------VNR 237

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           +V  L         L++++      +   E ++  L   +   R   L++          
Sbjct: 238 IVRELKYTNGEKKRLLDKVNKTVDSMRTLERQIRSLEAKFEASRSEELKK---------- 287

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
                                     R +++ +  ++GIS+ + +     + +G+ +A  
Sbjct: 288 -----------------EYKRQQKNCRVDLQRVEADSGISLDDLKRTQREMIQGDMDAEK 330

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW
Sbjct: 331 AKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 390

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  ++ RE + EEIAK++ +PV  V
Sbjct: 391 IRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQELGREASSEEIAKRMDIPVAKV 450

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           RKVLKI +EPISLETPIG+E+ SHLGDFIED+ AVSP D+ I  NL+E T++VL +LTPR
Sbjct: 451 RKVLKIAQEPISLETPIGEEEDSHLGDFIEDRMAVSPSDAVISVNLKEYTSQVLRTLTPR 510

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           EERV++MRFG+   ++HTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS+KL++F+DG
Sbjct: 511 EERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPSRSRKLKAFVDG 569


>gi|172065170|ref|YP_001815882.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171997412|gb|ACB68329.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 621

 Score =  318 bits (815), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 189/653 (28%), Positives = 291/653 (44%), Gaps = 60/653 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I     RG+VT  ++   LP D+ +   ++   A+L  +GI V D  D       E
Sbjct: 25  LHALIATGLSRGFVTHGDIIDGLPDDDANDSGIDAVAAVLDELGIAVCDSADTASGWTLE 84

Query: 91  DSLDLASSASN--SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                A  A             D     T DPVR+YLREMG+  LL+R+ E A A+RIE 
Sbjct: 85  RYFRPAPPARAWADGAGTLAAADLLAPRTTDPVRLYLREMGTTPLLTRDEEFAYARRIER 144

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFFHGTEGHS 207
           GRA   A LC  P    AL+  R E+    T     +I L+                   
Sbjct: 145 GRAASAAVLCGDPDALDALVSIRVEIAQCRTAASTYVIFLDD------------------ 186

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                               G  +       + R+      E A +D+   D   +DSA 
Sbjct: 187 --------------------GPRDDMTVDHAEVRTSATPAGEPARDDDTEADTQTEDSAW 226

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                    R  V+  L  I E+   +R+   +  +     +S V+          L+ +
Sbjct: 227 ---------RGAVVARLARIDELAHGMRAALASGGSACAAYRSHVRDAA------ALLRT 271

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           L L+   ++ + E L   ++R       L R+    G+ R  F   H   +    W++  
Sbjct: 272 LGLSARALERMSEPLRARARRHRALRARLERMLADVGVPR-SF--AHAADDDHAGWLASC 328

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                           + I   R+ I   +  + +       + + +   E     A+  
Sbjct: 329 IAAHPACAPTLKRRAAEFI-DARDAIVRAAPASELPPGATASLDARLGAIERAMQPARTG 387

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D+  G++FSTYA WW++QA
Sbjct: 388 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWWIRQA 447

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           IT ++AD   TIR+P H  D ++K+ R AR    +     TP E+A  +  PV+ VR ++
Sbjct: 448 ITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKVRDLM 507

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            I KEP+S + P+  E      D   D    SP D+A    LR T   V+  L PRE  V
Sbjct: 508 AIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAAGATQLRRTIAAVIDRLPPREAMV 567

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LRSF+
Sbjct: 568 LKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRASDTLGLLRSFI 620


>gi|115360900|ref|YP_778037.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
 gi|115286228|gb|ABI91703.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
          Length = 617

 Score =  318 bits (814), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 186/653 (28%), Positives = 290/653 (44%), Gaps = 64/653 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I     RG+VT  ++   LP D+ +   ++   A+L  +GI V D  D       E
Sbjct: 25  LHALIATGLSRGFVTRGDIIDGLPDDDANDSGVDAVAAVLGELGIAVSDSADTASGWTLE 84

Query: 91  DSLDLASSAS--NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                A  A             D     T DPVR+YLREMG+  LL+R+ E A A+RIE 
Sbjct: 85  RYFRPAPPARAWADGAGALAAADLLAPRTTDPVRLYLREMGTTPLLTRDEEFAYARRIER 144

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFFHGTEGHS 207
           GRA   A LC  P    AL+  R E+    T     +I L+                   
Sbjct: 145 GRAASAAVLCGDPDALDALVSIRVEIAQCRTAASTYVIFLD------------------- 185

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    +  RDD      +  ++A  + +     D+  E++                
Sbjct: 186 ---------DGPRDDTSADHAEAGTSATATGEPARDDDTQTEDSAW-------------- 222

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                    R  V+  L  I  +   +R+   +  +     +S V+          L+ +
Sbjct: 223 ---------RDAVVARLARIDALAHGMRAALASGGSACAAYRSDVRDAA------ALLRT 267

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           L L+   ++ + E L   ++R     G L R+    GI    F   H   +    W++  
Sbjct: 268 LGLSARALERMSEPLRGRARRHRALRGRLERMLADVGIP-PSF--AHAADDDHAGWLASC 324

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                           +  +  R+ I   +  + +       + + +   E     AK  
Sbjct: 325 IAAHPACASTLTRRAAE-FVDARDAILRAAPASELPPGATASLDARLGAIERAMQPAKAG 383

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D   G++FSTYA WW++QA
Sbjct: 384 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDHRRGFRFSTYATWWIRQA 443

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           IT ++AD   TIR+P H  D ++K+ R AR    +     TP E+A  +  PV+ VR+++
Sbjct: 444 ITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKVRELM 503

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            I KEP+S + P+  E      D   D    SP D+A    LR T   V+  L PRE  V
Sbjct: 504 AIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAAGATQLRRTIAAVIDRLPPREAMV 563

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LRSF+
Sbjct: 564 LKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRASDTLGLLRSFV 616


>gi|118581452|ref|YP_902702.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118504162|gb|ABL00645.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter propionicus DSM
           2379]
          Length = 582

 Score =  317 bits (813), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 245/656 (37%), Positives = 353/656 (53%), Gaps = 83/656 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I L +++G++T EE+N  LPPD  + EQ++D + M  ++ I +VD         
Sbjct: 7   DGVKQLIDLGKEKGFLTFEEVNDILPPDIAT-EQIDDVMGMFGDLDIEIVDSAQKVKIPK 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  ++    A   +  ++    S    T DPVRMYLREMGS+ LL+REGE+ IAKRIE 
Sbjct: 66  MKLEMEEEEEAEGEAEEVEFEPGSI-GRTSDPVRMYLREMGSVSLLTREGEVEIAKRIED 124

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G   + + +  +P+T + ++   D+L        EI                   E    
Sbjct: 125 GERDVASVILNTPITIKEVLQLGDKLRKFQLNASEI--------------SKEVEEESLD 170

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            + ED  + +  + +       E    +S++      +  +     +     +       
Sbjct: 171 DEEEDLPKLRILEIIDAISSGDEELTGLSEELEKCAAAAKKKELEKKIQELRESQAKLLI 230

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV---KCKVLKEKLVKLV 325
              ++D+   K+   L E++     L     +  +    EK           +EK    +
Sbjct: 231 SLRLKDRHINKISERLKELSFKVDRLMKELADLEDLIPAEKLRFFMDSYHKDEEKAQAEL 290

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             L L     D        +  R++    +L ++    G          +  EL      
Sbjct: 291 RKLKLGAEEQDR-------VDARLLSTARKLKKIELESG---------FKASELSAA--- 331

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                                               +   E     + + K         
Sbjct: 332 ------------------------------------LQAIEEGECKARIAK--------- 346

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 347 SELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIR 406

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  +  REP PEEIA+++ +P++ VRK
Sbjct: 407 QAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQENGREPAPEEIAERMQLPLDKVRK 466

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEPISLETPIG+E+ SHLGDFIEDK  +SP+++ I+ANL E T+RVL++LTPREE
Sbjct: 467 VLKIAKEPISLETPIGEEEDSHLGDFIEDKAVISPIEAVIKANLSEQTSRVLSTLTPREE 526

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+SF++
Sbjct: 527 KVLRMRFGIGEKSDHTLEEVGQDFAVTRERIRQIEAKALRKLRHPSRSKKLKSFVE 582


>gi|134301933|ref|YP_001121902.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|254369360|ref|ZP_04985372.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
 gi|254372870|ref|ZP_04988359.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. novicida GA99-3549]
 gi|134049710|gb|ABO46781.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151570597|gb|EDN36251.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           novicida GA99-3549]
 gi|157122310|gb|EDO66450.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 577

 Score =  316 bits (810), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 235/654 (35%), Positives = 342/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQVTEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|89256388|ref|YP_513750.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314834|ref|YP_763557.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502477|ref|YP_001428542.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167010407|ref|ZP_02275338.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367725|ref|ZP_04983746.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290953811|ref|ZP_06558432.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312822|ref|ZP_06803554.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144219|emb|CAJ79489.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129733|gb|ABI82920.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. holarctica OSU18]
 gi|134253536|gb|EBA52630.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156253080|gb|ABU61586.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 577

 Score =  316 bits (810), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 235/654 (35%), Positives = 342/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQVTEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMSKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|328676046|gb|AEB28721.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida 3523]
          Length = 577

 Score =  316 bits (809), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 234/654 (35%), Positives = 341/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   ++RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGKERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQLEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE          +++ +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIEDEPVARYIRFNEIMAGFSDEQITEEKIAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y+E                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQE------------------KPNKKLYSKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKIYKV--GSVEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREINNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|187931644|ref|YP_001891628.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712553|gb|ACD30850.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 577

 Score =  316 bits (809), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 234/654 (35%), Positives = 341/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEDNLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAVRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQVTEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LR   +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRVCVERSKTPRQEFIKVYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|118497505|ref|YP_898555.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           novicida U112]
 gi|195536199|ref|ZP_03079206.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208779304|ref|ZP_03246650.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
 gi|118423411|gb|ABK89801.1| RNA polymerase sigma-70 factor [Francisella novicida U112]
 gi|194372676|gb|EDX27387.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208745104|gb|EDZ91402.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
          Length = 577

 Score =  316 bits (809), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 235/654 (35%), Positives = 342/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQITEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|254374325|ref|ZP_04989807.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
 gi|151572045|gb|EDN37699.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
          Length = 577

 Score =  316 bits (809), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 235/654 (35%), Positives = 342/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQVTEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKIYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|56708122|ref|YP_170018.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670593|ref|YP_667150.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|224457213|ref|ZP_03665686.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370608|ref|ZP_04986613.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254874922|ref|ZP_05247632.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604614|emb|CAG45668.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320926|emb|CAL09051.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|151568851|gb|EDN34505.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254840921|gb|EET19357.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159323|gb|ADA78714.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 577

 Score =  316 bits (808), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 234/654 (35%), Positives = 342/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQVTEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK   +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKEFDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDK+  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKSNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|332678201|gb|AEE87330.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida Fx1]
          Length = 577

 Score =  315 bits (807), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 235/654 (35%), Positives = 343/654 (52%), Gaps = 90/654 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
            K ++   R+RGY+T  ++   LP D     +  E+  A+L + GI+V D     +E+  
Sbjct: 10  LKDLMIDGRERGYLTRADILDALPGDVSEDPKIYEEIEAILIDAGIDVYDRTPQIEED-- 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                      +     +   D     T DP+RMY+REMG ++LL ++GE  IA RIE G
Sbjct: 68  -----------DERKVSEANLDDLKGKTSDPIRMYMREMGIVDLLDKKGETDIAIRIEEG 116

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
              + +++   P+  +  I    EL                                   
Sbjct: 117 TTEVFSTILSYPIVIKTYIERFRELE---------------------------------- 142

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                    E+        DIE+         ++V +   + +  E  + ED+ +     
Sbjct: 143 ---------EKAIDYMNSQDIENEPVARYIRFNEVMAGFSDEQVTEEKVAEDDHEE---- 189

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
             ++ Q   +    L+++ E Y++                     K L  K+VK + +L 
Sbjct: 190 -KIDTQRAYEFFTNLEKMFEEYQD------------------KPNKKLYTKIVKELDNLR 230

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L+ S +  LV+ +     R+   E ++LRL  +     R  F++ ++       W+    
Sbjct: 231 LSTSHLQKLVDYIRLPYARVKEFERKILRLCVERSKTPRQEFIKVYKV--GSLEWLE--- 285

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             P  +   F    +  I  +  +I    +   + I E + +   + + E + + AKKEM
Sbjct: 286 --PLTKKYKFTENTIREIKNLTKQINQFQILMMMDIEELKQVNLEISRSEAKITQAKKEM 343

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S AKKYTNRGL FLD+IQEGNIGLMKA +KFD+  G+KFSTYA WW++QAI
Sbjct: 344 IEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWWIRQAI 403

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVL 567
           TRSIADQ+ TIR+PVHM + I+KV R  R++  +  RE T EEI +    M  E ++K+L
Sbjct: 404 TRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEKLKKIL 463

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREER 626
            I+  PIS+E+PIGD++ S +GDFIEDKN  SP+++A   NLRE    ++ + LT RE +
Sbjct: 464 NISHTPISMESPIGDDEDSTVGDFIEDKNNYSPIEAANLENLREAIKELIETGLTEREAK 523

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL MRFGIGMNTDHTLEEVGKQF VTRERIRQIEAKA+RKLKHPSRS  L++FL
Sbjct: 524 VLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPSRSAFLKTFL 577


>gi|46580198|ref|YP_011006.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120602415|ref|YP_966815.1| RpoD family RNA polymerase sigma factor [Desulfovibrio vulgaris
           DP4]
 gi|46449615|gb|AAS96265.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120562644|gb|ABM28388.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio vulgaris DP4]
 gi|311233814|gb|ADP86668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris RCH1]
          Length = 590

 Score =  314 bits (805), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 219/661 (33%), Positives = 331/661 (50%), Gaps = 85/661 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +  G++T +E+N  LP +  + EQ+E+ + +   + I +VD +    +  
Sbjct: 8   QQIKSLIAKGKVSGFLTFDEVNKALPAEVNTPEQIEEIIGIFDQLDIAIVDSEKDGKKIS 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                    + S   + L                              E  +  + R   
Sbjct: 68  MSPGESEEEAPSEGGLDLSDD---------------------------EETVDYSSRSTD 100

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                    D E  I  + + G          
Sbjct: 101 PVRMYLREMGSVPLLDR--------------------DGEVVIAKKIEMGEQDVLYALVE 140

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                       +D+++    ++   K  ++D    D                       
Sbjct: 141 VPVAVEELVNVGEDLKQNRIKLKDVVKTIEEDDPSED----------------------- 177

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV----LKEKLVKL 324
               E   R +V+  L+EI   +++ R +          E+     +      KE +V  
Sbjct: 178 ----EMNQRQRVILLLEEIRTTFKKKRKVYSKLDECCTLERRVASVQREIMNYKEDIVSR 233

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  +        G   RE+ P
Sbjct: 234 LRDIKLEKTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGKTQAEIQALFSGLEAREVSP 293

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              S A +    E  +F    +  I      +  +  +   ++++   ++  +++G   A
Sbjct: 294 VAASAALNMTVEELFSFKEMILGKIEI----LSRLQDKCCHNVNDLEEVLWRIKRGNSIA 349

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P++
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPID 469

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    VLA LT
Sbjct: 470 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLGEQIASVLADLT 529

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 530 PREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQTLRSYYE 589

Query: 682 G 682
            
Sbjct: 590 S 590


>gi|67810071|gb|AAY81984.1| RNase polymerase sigma factor [Wolbachia pipientis]
          Length = 571

 Score =  314 bits (804), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 241/591 (40%), Positives = 353/591 (59%), Gaps = 33/591 (5%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           LE  E  ED    +  +            +     DDPVR+YL++M S++LLSR  EI I
Sbjct: 2   LESSEDEEDIPSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEI 61

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AK+IE+ +  M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A    +        
Sbjct: 62  AKKIESEKHNMLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAIYNSDFN------ 115

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  K E    E+  +DV+++E   E A   S D++   DS   + E D  N D   
Sbjct: 116 ----VVPKEESEESEESAEDVEDSEDVSEDAEYCSDDEK---DSKKSDDEKDGNNEDISS 168

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            +   ++  ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++ 
Sbjct: 169 VNLNVSILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIW 222

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF-------LERHQ 375
            +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F       L +H+
Sbjct: 223 SIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDDVLLKHE 282

Query: 376 GRELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +++    ++  +    GE KN    F+    + I    N IK        ++ EF+ ++
Sbjct: 283 LKKISLLKINENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQH--IQEDNVQEFKELI 340

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA +KFD+ 
Sbjct: 341 KRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYK 400

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  R+M++++ REPT EE
Sbjct: 401 RGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMGREPTLEE 460

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR 
Sbjct: 461 LSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRG 520

Query: 612 TTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEA 661
            TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEA
Sbjct: 521 ITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEA 571


>gi|112702894|emb|CAL34114.1| RNA polymerase sigma factor rpoD [Cronobacter sakazakii]
          Length = 359

 Score =  314 bits (804), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 196/359 (54%), Positives = 251/359 (69%), Gaps = 2/359 (0%)

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  +  +  R+   E  +++   +   + +  F+    G E    
Sbjct: 1   MFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKNFITLFTGNETSET 60

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W + A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A 
Sbjct: 61  WFNAAIAMNKP-WSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDINRRMSIGEAKAR 119

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA W
Sbjct: 120 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 179

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + 
Sbjct: 180 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDK 239

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT 
Sbjct: 240 IRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTA 299

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 300 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 358


>gi|291279867|ref|YP_003496702.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754569|dbj|BAI80946.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 598

 Score =  313 bits (802), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 223/656 (33%), Positives = 355/656 (54%), Gaps = 70/656 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             K++I L +++G++T++E+N  LP + ++ E +++   +L+ + I+V+D +  ++   +
Sbjct: 9   EVKQLIALGKEKGFLTVDEINEILPKEILTPEFLDEIFMLLAQLKIDVIDNN-SKNAVIT 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +  LD      +                DDPVR+YLREMG+I LLSRE E+         
Sbjct: 68  DIDLDEDEDGFDMDDTSSSTASEERIGVDDPVRLYLREMGNIPLLSREEEV--------- 118

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                                   + +G   +   + L                      
Sbjct: 119 -------------------EVAKRIEEGQKKVIRSVLLF--------------------- 138

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
                          E     E   + +   +  +D   E   ++    D D+++     
Sbjct: 139 ----------PSTASEIMSLAEKINEGTLRIKDIIDIGDELDFDEIDYDDLDDEELQVLK 188

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK----EKLVKLV 325
              E+Q+R   +  L++I    +E   L     +      + +  K       +++   +
Sbjct: 189 DEKENQVREDFIVVLNDIVSKLKENIKLTKKLKSNNISIDNILSIKDQINRTVDEITDKL 248

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             + +N  +I  +  ++    + I   E ++ +     GIK    + +    E+      
Sbjct: 249 VEIKINYKKITEIANEIKRSYEEISDCENDIKKFLNLIGIKDISDISQLNNEEIFEMIDK 308

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            + +  +           D   ++++++     + G + +E   I + + +GE EA  AK
Sbjct: 309 SSFNIRDKN------RLKDKYKELKHKLDGFYKKLGFTKNELEVIYNSLLEGEYEAEKAK 362

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKFSTYA WW++
Sbjct: 363 SELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWWIR 422

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q+ITR+IADQ+ TIRIPVHM + I+K++RT R++  ++ +EPTPEEIA+++ +PVE V+K
Sbjct: 423 QSITRAIADQARTIRIPVHMIETINKMIRTIRQLQIELGKEPTPEEIAERMDIPVEKVKK 482

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VLKI KEP+SLETPIG+++ S LGDFIED++A +PLD  +   L+E T  +L +LTPRE 
Sbjct: 483 VLKIAKEPVSLETPIGEDEDSSLGDFIEDQSAKNPLDEVVYEKLKEHTRAILDTLTPREA 542

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VLR+RFGI  ++DHTLEEVG++F VTRERIRQIEAKA+RKL+HP+RS+ L++FL+
Sbjct: 543 SVLRLRFGIDCDSDHTLEEVGRRFNVTRERIRQIEAKALRKLRHPTRSRILKTFLE 598


>gi|289676145|ref|ZP_06497035.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 438

 Score =  311 bits (796), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 209/441 (47%), Positives = 284/441 (64%), Gaps = 5/441 (1%)

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                    A   E   D++E+ +  +    E +  P  + A      V  ++   +   
Sbjct: 1   EAPPPVDPKAAKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 60

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
               +D+K ++   V    L +L   + L   + + LVE++    +R+   E  +++L  
Sbjct: 61  KKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCV 117

Query: 362 S-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               + R  FL +  G E+D  W   A    + ++   +      I + + ++ ++  ET
Sbjct: 118 RDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEET 176

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ I+E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 177 GLKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 236

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M 
Sbjct: 237 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 296

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REPTPEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP
Sbjct: 297 QEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSP 356

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D A   +L+E T  VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 357 IDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 416

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HP+RS+ LRSFLD
Sbjct: 417 AKALRKLRHPTRSEHLRSFLD 437


>gi|225848841|ref|YP_002729005.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644391|gb|ACN99441.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 586

 Score =  310 bits (794), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 231/658 (35%), Positives = 359/658 (54%), Gaps = 78/658 (11%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLE 84
              D  + +I LAR++GYVT  E++ ++  +  SS++ +E  +  L+ + I+V D + ++
Sbjct: 5   QERDDVRTLINLAREKGYVTYSEISTYVDEEFFSSDEHIESLIEYLNELNIDVRDDEKIK 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E+             +         D      DDPV++YLREMG I LL RE EI  A 
Sbjct: 65  EED-------------DDIYLGIDFDDDVWSKADDPVKLYLREMGKIPLLKREEEIKYAM 111

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
            IE GR  +   L  +    + L+    ++ DG   +++++++E       +       E
Sbjct: 112 EIERGRKKVFRGLLRTSFLTERLLDEWAKVVDGKLRVQDLLNVEETEEKVDELSDGESLE 171

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             + +  +  +     D +++     +    + + ++  +++    A+ +        + 
Sbjct: 172 LENNENYDKITS----DFIKKGLELAKLYRDLLEKEKIYLETKTLEAKREFVWQHAKLNK 227

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
              +L+    +L        DE+ E+Y +LR          K+EK   K   +  K+   
Sbjct: 228 FIKSLNIKFTKLDKIA----DELKELYTKLR----------KNEKDYEKRIKIISKIHPD 273

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
           +          DL++   Y+    I+            Y I R   L             
Sbjct: 274 L----------DLMLSTEYEKYPEILKKLESNGFSYGRYEILRTETLRL----------- 312

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                              + I  I+ +I +I         EF H++ ++++G  E +  
Sbjct: 313 ------------------KNEIEDIKAKIGTI-------PEEFDHVLDIIQQGRNEINNV 347

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+ +V+ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +K+D+  G+KFSTYA WW+
Sbjct: 348 KQILVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKRGFKFSTYATWWI 407

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++R AR M  ++ REPTPEEIAKK+ MP E V+
Sbjct: 408 RQAITRAIADQARTIRIPVHMIETINKLIRVARSMVQELGREPTPEEIAKKVGMPAEKVK 467

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+L+ ++EPISLETPIG ++ +HLGDFIEDK+ +SP    ++  LR     VL++L+ RE
Sbjct: 468 KILRTSQEPISLETPIGTDEETHLGDFIEDKSVLSPEAHMLKNALRMQLDEVLSTLSERE 527

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E+VLR RFG+  +T+HTLE+VGK+F VTRERIRQIEAKA+RKL+HP R+K L+ F++G
Sbjct: 528 EQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKALRKLRHPHRAKYLKPFIEG 585


>gi|239996603|ref|ZP_04717127.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 382

 Score =  310 bits (794), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 194/377 (51%), Positives = 262/377 (69%), Gaps = 2/377 (0%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYG 364
           K  ++    +     L  +     L   + D +V+ + ++  ++   E  +++    +  
Sbjct: 6   KKGRAHADSRTQINALSDVFKEFRLVPKQFDRMVKNMREMMDKVRIQERLVMKFCVVNAK 65

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + +  F++   G E    W+  A       +   +A   + I +  +++  +  ETG+ I
Sbjct: 66  MPKKDFIKAFAGNETSNAWLHEAVK-SGAPYAADLAVNQEEIERCISKMNQVEQETGLVI 124

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           ++ + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 125 ADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 184

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ 
Sbjct: 185 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 244

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+++++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   + PLDSA
Sbjct: 245 REPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSA 304

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +L++ T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+
Sbjct: 305 TGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 364

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HPSRS++LRSFLD
Sbjct: 365 RKLRHPSRSEQLRSFLD 381


>gi|332704204|ref|ZP_08424292.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332554353|gb|EGJ51397.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 594

 Score =  310 bits (793), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 228/664 (34%), Positives = 348/664 (52%), Gaps = 87/664 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +Q+G++T +ELN+ LP +  + EQ+E+ +++   + I +VD       E 
Sbjct: 8   QQIKTLIAQGKQKGFLTFKELNSALPSEVNNPEQIEEIISIFDQLEIAIVDS------EK 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               L + S+ S S           + + +D                 E     A R   
Sbjct: 62  EGKKLQILSADSESEEVDVDAASVIEIAGND-----------------EDAADYASRSTD 104

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                      E  I  + + G          
Sbjct: 105 PVRMYLREMGSVPLLDRE--------------------GEVVIAKKIESGELDVLYALVE 144

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                    +   D++++   ++   K  ++D    D                       
Sbjct: 145 VPVAVEELVQVGKDLKDSRIKLKDVVKTIEEDDPSED----------------------- 181

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK----VLKEKLVKL 324
               E   R +V+  LDEI   +++ R +          ++     +      KE++V+ 
Sbjct: 182 ----EMNQRQRVIFLLDEIKASFKKKRKIYTKLDQCATLDRRVFSLQMEIVSFKEEVVQK 237

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ---GRELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  +    +  +    R L+P
Sbjct: 238 LREIKLEKTLIDRVIETVEDYVRQMHNCQRDLAAYIMSTGKTQSEIRDLFRRVDDRTLNP 297

Query: 382 HWVSYAKDFPEGE---WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
              + A      E   +K  +A +++ +++++ +           +SE   ++  +R+G 
Sbjct: 298 LNAAEALGLTVEEFFSYKEMLAGKMEILVRLQEKCCH-------QVSELEEVLWRIRRGN 350

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             AS AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFST
Sbjct: 351 ENASRAKRELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFST 410

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  
Sbjct: 411 YATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDY 470

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E   +VL+
Sbjct: 471 PIEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIGKVLS 530

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS
Sbjct: 531 DLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQILRS 590

Query: 679 FLDG 682
           + + 
Sbjct: 591 YYES 594


>gi|213026208|ref|ZP_03340655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 445

 Score =  309 bits (790), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 180/484 (37%), Positives = 251/484 (51%), Gaps = 48/484 (9%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   
Sbjct: 1   SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQY 60

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
           D +      L ++I            GF                  +   +  + + D +
Sbjct: 61  DRVEAEEARLSDLI-----------TGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDED 109

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                           PE A                       +LR + +   D I    
Sbjct: 110 EEDGDDDAADDDNSIDPELAREKF------------------AELRAQYVVTRDTIKAK- 150

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
                            +S    +    KL ++     L   + D LV  +  +  R+  
Sbjct: 151 ----------------GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRT 194

Query: 352 NEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +++L  +   + +  F+    G E    W + A    +  W   +    + + +  
Sbjct: 195 QERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKP-WSEKLHDVAEEVQRCL 253

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQF
Sbjct: 254 QKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 313

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+
Sbjct: 314 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 373

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGD
Sbjct: 374 KLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 433

Query: 591 FIED 594
           FIED
Sbjct: 434 FIED 437


>gi|297580650|ref|ZP_06942576.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
 gi|297535066|gb|EFH73901.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
          Length = 477

 Score =  307 bits (786), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 153/500 (30%), Positives = 232/500 (46%), Gaps = 42/500 (8%)

Query: 22  LVFDFS-DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
              D +     K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+ 
Sbjct: 16  PSMDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVET 75

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
               D+    D   +    +  +        +S    T DPVRMY+REMG++ELL+REGE
Sbjct: 76  APDADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 135

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGG 198
           I IAKRIE G   + +++ E P T   ++   D +      L ++I     + P   +  
Sbjct: 136 IDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETE 193

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
               T   S     D + E +     E E + E     S D   +V   PE A      L
Sbjct: 194 APTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNEL 253

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                                                  Q+  +   +  + S +     
Sbjct: 254 R-----------------------------------GKFQNLQLAVNEFGRDSHQASEAS 278

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGR 377
           + ++ +     L   + D LVE L     R+   E  +++       + +  F+    G 
Sbjct: 279 DLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGN 338

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+       +  +   V  + + I +   +++ I  ET +S+   + +   +  G
Sbjct: 339 ESNEEWLDKVLA-SDKTYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDLSRRMSIG 397

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E +A  A KEMVEANL LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +K ++  GY FS
Sbjct: 398 EAKARRANKEMVEANLPLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKSEYRRGYNFS 457

Query: 498 TYAMWWVKQAITRSIADQSC 517
           TYA WW++QAITRSIADQS 
Sbjct: 458 TYATWWIRQAITRSIADQSR 477


>gi|134291946|ref|YP_001115715.1| RpoD family RNA polymerase sigma factor [Burkholderia vietnamiensis
           G4]
 gi|134135135|gb|ABO59460.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           vietnamiensis G4]
          Length = 628

 Score =  306 bits (784), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 184/653 (28%), Positives = 290/653 (44%), Gaps = 58/653 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I     RG+VT  ++   LP D+     ++ T AML  +GI V DG         +
Sbjct: 30  LHALISTGLTRGFVTHGDIIDALPDDDAHQGGVDATAAMLRELGIAVSDGAHAA-GWTLD 88

Query: 91  DSLDLASSA--SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                  SA             + +   T DPVR+YLREMG   LL+R+ EI  A+RIE 
Sbjct: 89  RYFQPTPSARAWAEGAGALAAAELSAPRTTDPVRLYLREMGMTPLLTRDEEIMHAQRIER 148

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           GRA  +A LC  P    AL+  R E+ +G T     +   A I   +  G       H+ 
Sbjct: 149 GRAASVAVLCGDPQALDALVAMRIEIAEGRTAASAYVLSIADISDMAPAGGAAAASPHAG 208

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
               D+      DD                                              
Sbjct: 209 DTPADAGASTRDDDAP-------------------------------------------- 224

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A +   R  V+  L  I  +   +R+        + D    +  +    +   L+G+L
Sbjct: 225 --ADDGLCRHTVLARLAPIDALTAAMRA------ALETDGAHGLAYRACVREAAALLGTL 276

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY-A 387
            ++   ++ + E L   ++R     G L R     G+         Q       W++   
Sbjct: 277 RMSMRALERMSEPLRTHARRQRTLHGRLARTLAEAGVPHGAAAACVQRDGDHARWLASCI 336

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
              PE E    +      ++  R+ I   +  + +       + + +   E     A+  
Sbjct: 337 AAHPECE--PALTRRAAELVDARDAIARAARTSPLPPDTIALLDARLDTIERAMQPARMG 394

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW++QA
Sbjct: 395 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQA 454

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           IT ++AD   TIR+P H  D I+K+ R AR    +     TP E+A ++  P++ VR ++
Sbjct: 455 ITHALADLGRTIRVPTHTVDAINKLTRIAREHRQRSGAAATPHELAVQMGEPLDKVRDLM 514

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            I KEP+S + P+  E      D   D +  SP D+A  A LR+T   ++  L  RE  V
Sbjct: 515 SIVKEPMSADAPVSPEGEMTFVDVAPDVSTPSPEDAAGAAQLRDTIAAMIGRLPAREATV 574

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           LR+R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LR+F+
Sbjct: 575 LRLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRASDGLDVLRAFI 627


>gi|206603677|gb|EDZ40157.1| RNA polymerase, sigma 38 subunit, RpoS [Leptospirillum sp. Group II
           '5-way CG']
          Length = 598

 Score =  305 bits (781), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 227/655 (34%), Positives = 361/655 (55%), Gaps = 73/655 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T +ELN  LPP+ + S+Q+++ ++   +M I++VD +  E   G  D
Sbjct: 11  KDLISLGKERGYLTYDELNNVLPPEAIGSDQLDNLMSYFGDMNIDIVDDESREAGYGEMD 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S +    +   SV     ++  +     P        G++             RI+    
Sbjct: 71  SEEEEGFSDLESVRGVDSEEEDEGIDMTP--------GTLS------------RIDDPVR 110

Query: 152 MMMASLCESPLTFQAL-IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           + +  +   PL  +   I     + +G   +  I+            G           +
Sbjct: 111 LYLKEMGAVPLLTREGEIAIAQRIEEGQKEVSGIL-----------FGMPLTVRSILSLR 159

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            +  + +    ++ +   +         D  +  D+                        
Sbjct: 160 EKFQTGQIGIREIVDVMEEETEDEPEEGDSAALRDA------------------------ 195

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV----KCKVLKEKLVKLVG 326
                 R + +   D ++E++ +L ++ +   + QK+         + K +K ++V+L+ 
Sbjct: 196 ------REQFVRQTDSLSELFLKLNAISEKWKDAQKNTSKKKVLREQAKKIKTEIVELIM 249

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            ++L++ +++L++ QL+D+   +  +E  +    +  G  ++  L+           +  
Sbjct: 250 EMNLHRKQVELMIRQLHDVVSVLDESERIIDHSRRRLGANKEDILKA-------IALLKA 302

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            KD  E          + +       +    V   +S SE R  +S++  GE +   AK 
Sbjct: 303 GKDPGERYQDPEKLELLKNYQFALERVHEAEVAALLSSSEIRDSLSLLEAGEQKVREAKA 362

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+++ANLRLV+S+AK+YTNRGLQFLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++Q
Sbjct: 363 ELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFSTYATWWIRQ 422

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++RT R +  ++ REP PEE+AK++ MPVE VR+V
Sbjct: 423 AITRAIADQARTIRIPVHMIETINKLIRTTRHLVQELGREPLPEELAKEMQMPVEKVRRV 482

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI +EPISLETPIG+E+ SHLGDFIEDK ++SP+DSA++ +L     + L+SLT REE+
Sbjct: 483 LKIAREPISLETPIGEEEDSHLGDFIEDKKSISPIDSAVRYDLVRKIGKALSSLTEREEK 542

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+R+RFG+G +TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK L+SF+D
Sbjct: 543 VIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKLRHPSRSKHLKSFVD 597


>gi|23013315|ref|ZP_00053224.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 333

 Score =  305 bits (781), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 241/333 (72%), Positives = 280/333 (84%), Gaps = 1/333 (0%)

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           +M  EG LLRLA+S  +KR  FL+ + G ELDP+W+       + +WK+F A        
Sbjct: 1   MMMQEGRLLRLAESCRVKRQDFLDAYYGSELDPNWLEQVAQRSK-QWKDFAARHGKDAAD 59

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  I  IS E G+ ISE+R IV  V++GE E+S AKKEM+EANLRLVIS+AKKYTNRGL
Sbjct: 60  IRATIAEISGEAGLPISEYRRIVQTVQRGERESSRAKKEMIEANLRLVISIAKKYTNRGL 119

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 120 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 179

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VRT+R+M ++I REPTPEE+A+KL+MP+E VRKVLKI KEPISLETPIGDE+ SHL
Sbjct: 180 INKLVRTSRQMLHEIGREPTPEELAEKLSMPLEKVRKVLKIAKEPISLETPIGDEEDSHL 239

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDKNAV PLD+AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+Q
Sbjct: 240 GDFIEDKNAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQ 299

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD
Sbjct: 300 FSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 332


>gi|83746506|ref|ZP_00943557.1| RpoD [Ralstonia solanacearum UW551]
 gi|83726837|gb|EAP73964.1| RpoD [Ralstonia solanacearum UW551]
          Length = 391

 Score =  305 bits (780), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 184/389 (47%), Positives = 258/389 (66%), Gaps = 2/389 (0%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             L+      +K+   S      +E +   + ++      ++ L + L      +   E 
Sbjct: 3   DRLEKMRSAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLER 62

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +L +     G+ R  F+ R  G E +  W++      +  +   V   + ++ +++ ++
Sbjct: 63  AILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKP-YSAIVERNIPAVHELQQKL 121

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     + ++E + +   + +GE  A  AK+EM EANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 122 IDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDL 181

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ 
Sbjct: 182 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 241

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIE
Sbjct: 242 RISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIE 301

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D N ++P ++A+  ++R     VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTR
Sbjct: 302 DTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTR 361

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 362 ERIRQIEAKALRKLRHPSRSDKLKSFLEG 390


>gi|239906706|ref|YP_002953447.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
 gi|239796572|dbj|BAH75561.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
          Length = 588

 Score =  305 bits (780), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 218/662 (32%), Positives = 340/662 (51%), Gaps = 89/662 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +Q+G++T +E+N  LP +  + EQ+E+ +A+   + IN+VD D       
Sbjct: 8   QQIKSLIIKGKQKGFLTFDEVNKALPSEVNNPEQLEEVIAIFDQLDINLVDTDK------ 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +++A++  + +                           +EL   E  +  + R   
Sbjct: 62  DGRKIEVAAAEPDDAPDAD-----------------------LELTESEDSLDYSSRSTD 98

Query: 149 GRAMMMASLCESPLTFQAL-IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
              M +  +   PL  +   ++   ++ +G                E             
Sbjct: 99  PVRMYLREMGAVPLLDREGEVVIAKKIENGEM--------------EVLYALVEVPVAVE 144

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
              +     +  R  +++    IE       +                            
Sbjct: 145 ELIQVGEDLKIGRIKLKDVVKTIEEDDPSEDEMNQ------------------------- 179

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVK 323
                    R +V+  L+E+   +R+ R +          +K       +  V K+++V 
Sbjct: 180 ---------RQRVIFLLEEVKTSFRKKRKVYSKFDQCACVDKRVAGIQKEIMVFKDEIVT 230

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH---QGRELD 380
            +  + L ++ ID ++E + D  +++ + + +L     S G  +    E       RE++
Sbjct: 231 RLRDIKLEKTLIDRIIEIVEDYVRQMHNCQRDLSAYILSVGKSQSEIQEMFAQLDAREIN 290

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           P   + +      E  +F       +  +      +  +   ++ E   ++  +++G   
Sbjct: 291 PMIAAESLGLTVEELFSFKEMLSAKMEILVR----LQDKCCHNVHELEEVLWRIKRGNNA 346

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 347 AQRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYA 406

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P+
Sbjct: 407 TWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPL 466

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A++P +  +   L E   +VL+ L
Sbjct: 467 EKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKALAPAEEVVNTKLGEQIGKVLSDL 526

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREE+VLR RFG+G  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ 
Sbjct: 527 TPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQHLRSYY 586

Query: 681 DG 682
           +G
Sbjct: 587 EG 588


>gi|124515193|gb|EAY56704.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum rubarum]
          Length = 598

 Score =  305 bits (780), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 227/655 (34%), Positives = 361/655 (55%), Gaps = 73/655 (11%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +I L ++RGY+T +ELN  LPP+ + S+Q+++ ++   +M I++VD +  E   G  D
Sbjct: 11  KDLISLGKERGYLTYDELNNVLPPEAIGSDQLDNLMSYFGDMNIDIVDDESREAGYGEMD 70

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S +    +   SV     ++  +     P        G++             RI+    
Sbjct: 71  SEEEEGFSDLESVRGVDSEEEDEGIDMTP--------GTLS------------RIDDPVR 110

Query: 152 MMMASLCESPLTFQAL-IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           + +  +   PL  +   I     + +G   +  I+            G           +
Sbjct: 111 LYLKEMGAVPLLTREGEIAIAQRIEEGQKEVSGIL-----------FGMPLTVRSILSLR 159

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            +  + +    ++ +   +         D  +  D+                        
Sbjct: 160 EKFQTGQIGIREIVDVMEEETEDEPEEGDSAALRDA------------------------ 195

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV----KCKVLKEKLVKLVG 326
                 R + +   D ++E++ +L ++ +   + QK+         + K +K ++V+L+ 
Sbjct: 196 ------REQFVRQTDSLSELFLKLNAISEKWKDAQKNTSKKKILREQAKKIKTEIVELIM 249

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            ++L++ +++L++ QL+D+   +  +E  +    +  G  ++  L+           +  
Sbjct: 250 EMNLHRRQVELMIRQLHDVVSVLDESERTIDHSRRRLGANKEEILKA-------IALLKA 302

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            KD  E          + +       +    V   +S SE R  +S++  GE +   AK 
Sbjct: 303 GKDPGERYQDPEKLELLKNYQFALERVHEAEVAALLSSSEIRDSLSLLEAGEQKVREAKA 362

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+++ANLRLV+S+AK+YTNRGLQFLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++Q
Sbjct: 363 ELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFSTYATWWIRQ 422

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++RT R +  ++ REP PEE+AK++ MPVE VR+V
Sbjct: 423 AITRAIADQARTIRIPVHMIETINKLIRTTRHLVQELGREPLPEELAKEMQMPVEKVRRV 482

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI +EPISLETPIG+E+ SHLGDFIEDK ++SP+DSA++ +L     + L+SLT REE+
Sbjct: 483 LKIAREPISLETPIGEEEDSHLGDFIEDKKSISPIDSAVRYDLVRKIGKALSSLTEREEK 542

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+R+RFG+G +TDHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK L+SF+D
Sbjct: 543 VIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKLRHPSRSKHLKSFVD 597


>gi|308270755|emb|CBX27365.1| RNA polymerase sigma factor rpoD [uncultured Desulfobacterium sp.]
          Length = 568

 Score =  304 bits (779), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 223/648 (34%), Positives = 346/648 (53%), Gaps = 83/648 (12%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++GY+T ++LN  +  + +S +++++T  +L +  I ++D         +    
Sbjct: 3   LISKGKKQGYITYDDLNEEMSDNIISIDKLDETFEVLDSNDIEIIDD--------NGKKA 54

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           D   +A        +   +   +  DPV+MYL EM  + LLSREGE+ IAK+IE G   +
Sbjct: 55  DDDKTADEKKANQSELAAANFGTVTDPVKMYLHEMSLVTLLSREGEVDIAKKIEDGEQEV 114

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + ++  +P+  + +I    ++  G+   + ++        +    +           +  
Sbjct: 115 LKAMVSTPIGMECIIDLGIQIECGSLRPKHVLK-----DFDESDSYVDEMVQIDNFVKMI 169

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
            S +       E    + S     K +  ++        N+  NL ++    +  L  +E
Sbjct: 170 YSIKDIHQKNNELFEQLYSLKPDKKSEIRQIKKLISANNNEIFNLLKEWRLESGVLDRIE 229

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
             ++  +                                      +    +V ++    +
Sbjct: 230 SLMKGHI--------------------------------------DWFESVVKNIMDCAA 251

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           +I++ V +L       ++    L     S  + +D  L  +   E++             
Sbjct: 252 KINMSVTELKSNINSRINF---LKCARSSCKLGKDDILSIYD--EIN------------- 293

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           ++ + +      I      +K +     +S      + + + K          E+  ANL
Sbjct: 294 KYSSMIDENEKKIRTDCQALKKV-----MSSVAEGRLNAKIAK---------SELTRANL 339

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IA
Sbjct: 340 RLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIA 399

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K++RT+R +  +  REP+PEEIA+K+ +P+E VRKVLKI +EP
Sbjct: 400 DQARTIRIPVHMIETINKLIRTSRYLVQEQGREPSPEEIAEKMEIPLEKVRKVLKIAREP 459

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLETPIG+E+ SHLGDFIEDK  + P D+AI  NL E T +VLA+LTPREE+VLRMRFG
Sbjct: 460 ISLETPIGEEEDSHLGDFIEDKKFMLPSDAAINQNLAEQTRKVLATLTPREEKVLRMRFG 519

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IG   DHTLEEVG+ F VTRERIRQIEAKA+RKL+HP+RS+KL++F++
Sbjct: 520 IGERADHTLEEVGQDFQVTRERIRQIEAKALRKLRHPTRSRKLKNFIE 567


>gi|221212018|ref|ZP_03584996.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
 gi|221168103|gb|EEE00572.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
          Length = 625

 Score =  304 bits (777), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 174/675 (25%), Positives = 292/675 (43%), Gaps = 70/675 (10%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           ++      +        +   +  +I L   RG+VT  ++   LP D+     ++   A+
Sbjct: 16  NARQPAPAAGHDDALASASAPFAGLIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAV 75

Query: 70  LSNMGINVVDGDDLEDEEGSED---SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           L+ +GI V D    E +   +       L+ +A+  +       D     T DPVR+YLR
Sbjct: 76  LAELGIAVSDAAHAETDWSLDRYFRPPPLSRAAAERNGAFAAF-DLLAPRTTDPVRLYLR 134

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ LL+ + EIA A+RIE GRA  +A LC  P    AL   R E+ +G         
Sbjct: 135 EMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGR-------- 186

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                               +Y    D  +  +     +  GD +       D      +
Sbjct: 187 ----------------AAASAYLMFVDEGRHADAAAAVDPHGDAQHDDMRPGDPHVCDAA 230

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
                                             + +LD +A   R   +          
Sbjct: 231 LAR-------------------------------LSSLDALARDMRAALT---------S 250

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
              +S   +        L+  L L+   ++ +   L   ++R       + R+    GI 
Sbjct: 251 GGTASPAYRAAVHDAAALLRPLRLSARAVERIGAPLRGRARRHREQRARMTRVLHHAGIP 310

Query: 367 RDVFLERHQGRELD-PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
                  H   + D   W++ A      E +  +      +   R  I + +  + +   
Sbjct: 311 SQTTWRCHDAHDDDHARWLA-AGIAAHPECERALIRSAPVLFDAREAIAADARASVLPPR 369

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
               + + +   E     AK  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA 
Sbjct: 370 TVALLDARLDAIERATHAAKMALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAI 429

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +++D   G++FSTYA WW++Q+IT ++AD   TIR+P H  D I+K+ R AR    +   
Sbjct: 430 DRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGA 489

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             TP+E+A ++  PV+ VR+++ I KEP+S++ PI  +      D + D +  SP D+A 
Sbjct: 490 AATPDELAAQMGEPVDKVRELMAIVKEPVSVDLPIAPDGDMTFVDVVPDASTPSPEDAAD 549

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A  R      +  L PRE  ++R+R+G+      +L ++G++  ++ ER+RQIEA A+ 
Sbjct: 550 AAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALA 609

Query: 666 KLKHPSRSKKLRSFL 680
           +L+       LR F+
Sbjct: 610 RLRASDALAVLRPFV 624


>gi|218885598|ref|YP_002434919.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
 gi|218756552|gb|ACL07451.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 590

 Score =  304 bits (777), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 222/661 (33%), Positives = 336/661 (50%), Gaps = 85/661 (12%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +  G++T +E+N  LP +  + EQ+E+         I + D  ++   + 
Sbjct: 8   QQIKSLIAKGKVSGFLTFDEVNKALPAEVNTPEQIEEI--------IGIFDQLEIAIVDT 59

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +D   ++ S   S                            ++L+  E     + R   
Sbjct: 60  EKDGKKISVSPGESEEEPSGEPG-------------------LDLVEDEESADYSSRSTD 100

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +          DG   + + I+L       +        E    
Sbjct: 101 PVRMYLREMGAVPLLDR----------DGEVQIAKKIELGEQDVLYALVEVPVAVEELIN 150

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
              +      +  DV +T  + + +                                   
Sbjct: 151 VGEDLKQNRIKLKDVVKTIEEDDPSEDEMNQ----------------------------- 181

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV----LKEKLVKL 324
                   R +V+  LDEI   Y++ R +     +    E+     +      KE +V  
Sbjct: 182 --------RSRVILLLDEIKHTYKKKRKVYAKLDDCCTLERRVTAIQKEILGFKEDIVNR 233

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG---IKRDVFLERHQGRELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G   ++        + RE++P
Sbjct: 234 LRDIKLEKTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGKTQVEIQDIFRMLEAREMNP 293

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              S A      E  +F    +  I +I N ++        ++++   ++  +++G   A
Sbjct: 294 VAASAALGMTVEELFSFKEMIIGKI-EILNRLQDKCCH---NVTDLEEVLWRIKRGNTHA 349

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P++
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPID 469

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    VLA LT
Sbjct: 470 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIASVLADLT 529

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 530 PREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQMLRSYYE 589

Query: 682 G 682
            
Sbjct: 590 S 590


>gi|262364690|gb|ACY61247.1| RNA polymerase sigma factor RpoD [Yersinia pestis D182038]
          Length = 352

 Score =  303 bits (776), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 195/351 (55%), Positives = 249/351 (70%), Gaps = 2/351 (0%)

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
             + D LV  +  +  R+   E  +++L  +   + +  F+      E    W + A   
Sbjct: 2   PKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAM 61

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVE
Sbjct: 62  GKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 120

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR
Sbjct: 121 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 180

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           SIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI 
Sbjct: 181 SIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 240

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRM
Sbjct: 241 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRM 300

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 301 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 351


>gi|283851053|ref|ZP_06368337.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
 gi|283573449|gb|EFC21425.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
          Length = 588

 Score =  303 bits (776), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 223/661 (33%), Positives = 344/661 (52%), Gaps = 87/661 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +Q+G++T +E+N  LP +  + EQ+E+ +A+   + IN+VD D       
Sbjct: 8   QQIKSLIVKGKQKGFLTFDEVNKALPSEVNNPEQLEEVIAIFDQLDINLVDTDK------ 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               +++AS+    +                           +EL   E  +  + R   
Sbjct: 62  DGRKIEVASTEPEETPDAD-----------------------LELTESEDTLDYSSRSTD 98

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                      E  I  + + G          
Sbjct: 99  PVRMYLREMGAVPLLDRE--------------------GEVVIAKKIENGEMDVLYALVE 138

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                    +  +D++     ++   K  ++D    D                       
Sbjct: 139 VPVAVEELIQVGEDLKIGRIKLKDVVKTIEEDDPSED----------------------- 175

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVKL 324
               E   R +V+  LDE+   +R+ R +          ++       +  V KE++V  
Sbjct: 176 ----EMNQRQRVIFLLDEVKASFRKKRKIYSKLDQCACLDRRVAGIQKEIMVFKEEIVVR 231

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH---QGRELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  +    E       R+++P
Sbjct: 232 LRDIKLEKTLIDRIIEIVEDYVRQMHNCQRDLSAYILSVGKSQSEIQEMFAQLDSRDINP 291

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              + +      E  +F    + + ++I + ++         + E   ++  +++G   A
Sbjct: 292 VVAAESLGLTVEELFSFKEM-LSAKMEILDRLQEKCCH---HVHELEEVLWRIKRGNTAA 347

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 348 QRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 407

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P+E
Sbjct: 408 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPLE 467

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A++P +  +   L E   +VL+ LT
Sbjct: 468 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKALAPAEEVVNTKLGEQIGKVLSDLT 527

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFG+G  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 528 PREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQHLRSYYE 587

Query: 682 G 682
           G
Sbjct: 588 G 588


>gi|78221616|ref|YP_383363.1| RNA polymerase sigma factor RpoD-like [Geobacter metallireducens
           GS-15]
 gi|78192871|gb|ABB30638.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter metallireducens
           GS-15]
          Length = 579

 Score =  303 bits (775), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 244/655 (37%), Positives = 352/655 (53%), Gaps = 81/655 (12%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           SD+  ++++ + +++G++T +E+N  LPPD  S+EQ++D ++M   M I++VD       
Sbjct: 6   SDEVKQQLVDIGKEKGFLTYDEVNDVLPPD-FSTEQIDDVMSMFGEMDIDLVDSSQKVKI 64

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +  L+           ++         T DPVRMYLREMGS+ LL+REGE+ IAKRI
Sbjct: 65  PKMKLDLEEEEEMEGEQEEMEYEP-GVLGRTSDPVRMYLREMGSVSLLTREGEVEIAKRI 123

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +   +  +P+T + +I   D+L        EI         E            
Sbjct: 124 EEGERDIARVILTTPITVKEIIALGDKLRKFQISAAEISKEVEEEELEEDEEDVQANRVL 183

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           S    E    +   + + E      +AAK  K+  ++     E   +  ++L   +D   
Sbjct: 184 SIID-EIRDLDVRMEAIAEELDAEGAAAKRQKELHAEQHEIREKFADLVKSLR-LKDRHI 241

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             ++    +L  KV   L EIA V               +   +  + K +  K  +   
Sbjct: 242 TKIAQRLKELSGKVEAILTEIAAV-------------ETEAGINGERLKEIVAKGDEKAK 288

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            L +N       +E    + K+I   E +L +L    G          + +EL      +
Sbjct: 289 GLKVN-------LEDAQKLDKKIRAAEKKLKKLEHESG---------FKAQELSDAL--H 330

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A D  E + K   +  V++ L++   I       G+                        
Sbjct: 331 AIDRGEAKAKLAKSELVEANLRLVVSIAKKYTNRGL------------------------ 366

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
                                 QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++Q
Sbjct: 367 ----------------------QFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQ 404

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++ +P++ VRKV
Sbjct: 405 AITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMNLPLDKVRKV 464

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           LKI KEPISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T+RVL++LTPREE+
Sbjct: 465 LKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEK 524

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKL+SF++
Sbjct: 525 VLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLKSFVE 579


>gi|317484461|ref|ZP_07943373.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
 gi|316924285|gb|EFV45459.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
          Length = 590

 Score =  302 bits (773), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 220/661 (33%), Positives = 338/661 (51%), Gaps = 86/661 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   ++ G++T EE+N  +P +  + EQ E+ + +   + I +V      D E 
Sbjct: 9   QQIKSLIAKGKEMGFLTFEEVNKAVPLEMNTPEQFEEIIGIFDQLEIAIV------DLEK 62

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               + + S+ ++     +                       +EL+  E     + R   
Sbjct: 63  DGKKIPVTSAETDGEQSEE----------------------RLELVDNEDAADFSSRSTD 100

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                    D E  I  + + G          
Sbjct: 101 PVRMYLREMGAVPLLDR--------------------DGEVTIAKKIEQGEQDVLYALVE 140

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                       +D++     ++   K  ++D    D                       
Sbjct: 141 VPVAVEELINVGEDLKLNRIKLKDVVKTIEEDDPTED----------------------- 177

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVKL 324
               E   R +V+  L+EI + +++ R +          E+       +    KE++V  
Sbjct: 178 ----EMNQRTRVILLLEEIRQTFKKKRKIYAKLDECCTLERRVTAIQKEIMAFKEEIVTR 233

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ---GRELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  ++   +  +    R++ P
Sbjct: 234 LRDIKLEKTLIDRIIETVEDYVRQMRNCQRDLSAYLLSTGKNQEEIKDLFRKLDSRDISP 293

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              +   +    E  ++    +  I  ++     +  +   ++S+   ++  +++G   A
Sbjct: 294 VLAAKELNMSVDELFSYKEMILGKIEILQR----LQEKCCHNVSDLEEVLWRIKRGNNAA 349

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA ++  PV+
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIADRMEYPVD 469

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    VLA LT
Sbjct: 470 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIASVLADLT 529

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRSF D
Sbjct: 530 PREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQVLRSFYD 589

Query: 682 G 682
            
Sbjct: 590 S 590


>gi|322433717|ref|YP_004215929.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
 gi|321161444|gb|ADW67149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
          Length = 566

 Score =  302 bits (773), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 223/650 (34%), Positives = 340/650 (52%), Gaps = 98/650 (15%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           +++++ +++GY+T  E+N  LP D  S + ++D +  ++  GI +       DE+     
Sbjct: 11  EIVEVGKEKGYLTFGEVNDLLPGDITSPDDLDDLLTTINTQGIEL-----GGDEDRRGRD 65

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                +   S              T+DPVRMYLREMG++ LL+REGE+            
Sbjct: 66  KYEPEAGEESEDVELDLSPGTLEKTNDPVRMYLREMGTVPLLTREGEV------------ 113

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
                                +  G   + + I     +                     
Sbjct: 114 ----------------EIAKRIERGQIRVMKAISRSPIV--------------------- 136

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
                            I     + +D R  V +  E    DE  L E+   +    +  
Sbjct: 137 -----------------IREIVALGEDLRRGVRNIKEIVTFDEEELTEEILQARVRATVG 179

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
              +  K    +  + E   +  +L+D     ++  K           + +++  L    
Sbjct: 180 RIDVIVKHQKKVTALEEKLEQAGALKDAKAKTKEVRKVRWLIGREHVYVNRVIRELKYTN 239

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +    L++++      +   E ++  L   +   +   L++                   
Sbjct: 240 AEKKRLLDKVNKTVDAMRTLERQIKSLEVKFESSKSEELKK------------------- 280

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                            + +++ +  + GISI + +     + +G+ +A  AK+E++EAN
Sbjct: 281 --------EYKRQQKNCKLDLERVEQDAGISIPDLKRTQREMIQGDMDAEKAKRELIEAN 332

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I
Sbjct: 333 LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAI 392

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K++RT+R++  ++ RE + EEIA+++ +PV  VRKVLKI +E
Sbjct: 393 ADQARTIRIPVHMIETINKLIRTSRQLVQELGREASSEEIARRMDIPVAKVRKVLKIAQE 452

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ SHLGDFIED+ AVSP D+ I  NL+E T++VL +LTPREERV++MRF
Sbjct: 453 PISLETPIGEEEDSHLGDFIEDRMAVSPADAVISVNLKEYTSQVLRTLTPREERVIKMRF 512

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+   ++HTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS+KL++F+DG
Sbjct: 513 GLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPSRSRKLKAFVDG 562


>gi|303245332|ref|ZP_07331616.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
 gi|302493181|gb|EFL53043.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
          Length = 588

 Score =  302 bits (773), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 222/661 (33%), Positives = 345/661 (52%), Gaps = 87/661 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +Q+G++T +E+N  LP + +S EQ+E+ +A+   + IN+V      D + 
Sbjct: 8   QQIKSLIVKGKQKGFLTFDEVNKALPSEVISPEQLEEVIAIFDQLDINLV------DTDK 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               ++ +S+  + +                           +EL   E  +  + R   
Sbjct: 62  DGRKVEASSAEPDDAPDAD-----------------------LELTESEDTLDYSSRSTD 98

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                      E  I  + + G          
Sbjct: 99  PVRMYLREMGAVPLLDRE--------------------GEVVIAKKIENGEMDVLYALVE 138

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                    +  +D++     ++   K  ++D    D                       
Sbjct: 139 VPVAVEELIQVGEDLKIGRIKLKDVVKTIEEDDPSED----------------------- 175

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVKL 324
               E   R +V+  LDE+   +R+ R +          ++       +  V KE++V  
Sbjct: 176 ----EMNQRQRVIFLLDEVKVSFRKKRKIYSKLDQCACLDRRVAGIQKEIMVFKEEIVVR 231

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH---QGRELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  +    E       RE++P
Sbjct: 232 LRDIKLEKTLIDRIIEIVEDYVRQMHNCQRDLSAYILSVGKSQSEIQELFAQLDAREVNP 291

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              + +      E  +F    + + ++I + ++         + +   ++  +++G   A
Sbjct: 292 MVAAESLGLTVEELFSFKEM-LTAKMEILDRLQEKCCH---HVHDLEEVLWRIKRGNTAA 347

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 348 QRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 407

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P+E
Sbjct: 408 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPLE 467

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A++P +  +   L E   +VL+ LT
Sbjct: 468 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKALAPAEEVVNTKLGEQIGKVLSDLT 527

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFG+G  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 528 PREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQHLRSYYE 587

Query: 682 G 682
           G
Sbjct: 588 G 588


>gi|157737257|ref|YP_001489940.1| RNA polymerase sigma factor RpoD [Arcobacter butzleri RM4018]
 gi|157699111|gb|ABV67271.1| RNA polymerase sigma 70 factor [Arcobacter butzleri RM4018]
          Length = 626

 Score =  302 bits (772), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 196/663 (29%), Positives = 350/663 (52%), Gaps = 51/663 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + + ++K  +    +T E++    P        ++  +A++    + V+   +     
Sbjct: 7   NKTIELLVKEYKDS-VLTYEKIIKIFPKAPSGP-TIKKLLALIQLYNVTVISSQEQAKRM 64

Query: 88  GSEDSLDLA-------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             E++            +  +    L+ ++      +D PVRMYLREMG I LL++E E+
Sbjct: 65  NDEEAKKKKELREKLIENEDDVFDLLKNKELLEWSRSDSPVRMYLREMGQIPLLTKEEEV 124

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            I+K+IE G  +++ ++C  P     ++ +R+ L +    ++E+               F
Sbjct: 125 EISKKIETGEDIILDAICYVPYLIDFILEYREPLVNRERKVKEL---------------F 169

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              +  + ++ +D   E   ++  E E   +   KVS   + K+D   +      +NL++
Sbjct: 170 KNFDDDTEEEEDDFDSEDLEEEDSEEESFEDDEEKVSGKKQKKLDKRAQTIIEAFKNLEK 229

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                                   + +    +E     + +     +  ++ K ++LKE 
Sbjct: 230 ---------------------AKKEWLKFQAKETSKSDEESDLMTFNLATAFKKRLLKEA 268

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L+ L  +  L    I  +V+ +    K     + EL RL     +  +   + HQ    +
Sbjct: 269 LLDLGPTSKL----ITEIVKAMETALKSDTGFDSELKRLEYKLPLFNETLQKNHQKILDN 324

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +S A+          V+  ++ I K+    ++      ++  E + ++  +++G+  
Sbjct: 325 IVNLSKAQITAMVPEATMVSTYME-IKKLFQTAEASKDGFDLTPEELKAVLEQIKRGKQI 383

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              +K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 384 TDTSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYA 443

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  EEIAK++ +PV
Sbjct: 444 TWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKGVQENGKEPDIEEIAKEVGLPV 503

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V++V+KITKEP+SLE PIG ++    GDF+ D+ A +P+D+ ++ +L+    ++L+ L
Sbjct: 504 DKVKQVIKITKEPVSLEAPIGSDEDGKFGDFVPDEKAPTPIDNIMKEDLQGQIDQILSQL 563

Query: 621 TPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   K L+++
Sbjct: 564 NEREQAVIRMRFGLMEDASDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGKNLKNY 623

Query: 680 LDG 682
           ++ 
Sbjct: 624 VES 626


>gi|315636974|ref|ZP_07892198.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
 gi|315478804|gb|EFU69513.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
          Length = 626

 Score =  301 bits (771), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 197/663 (29%), Positives = 350/663 (52%), Gaps = 51/663 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + + ++K  +    +T E++    P        ++  +A++    + V+   +     
Sbjct: 7   NKTIELLVKEYKDS-VLTYEKIIKIFPKAPSGP-TIKKLLALIQLYNVTVISSQEQAKRM 64

Query: 88  GSEDSLDLA-------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             E++            +  +    L+ ++      +D PVRMYLREMG I LL++E E+
Sbjct: 65  NDEEAKKKKELREKLIENEDDVFDLLKNKELLEWSRSDSPVRMYLREMGQIPLLTKEEEV 124

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            I+K+IE G  +++ ++C  P     ++ +R+ L +    ++E+               F
Sbjct: 125 EISKKIETGEDIILDAICYVPYLIDFILEYREPLVNRERKVKEL---------------F 169

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              +  + ++ +D   E   ++  E E   E   KVS   + K+D   +      +NL++
Sbjct: 170 KNFDDDTEEEEDDFDNEDLEEEDSEEESFEEDEEKVSGKKQKKLDKRAQTIIEAFKNLEK 229

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                                   + +    +E     + +     +  ++ K ++LKE 
Sbjct: 230 ---------------------AKKEWLKFQAKETSKSDEESDLMTFNLATAFKKRLLKEA 268

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L+ L  +  L    I  +V+ +    K     + EL RL     +  +   + HQ    +
Sbjct: 269 LLDLGPTSKL----ITEIVKAMETALKSDTGFDSELKRLEYKLPLFNETLQKNHQKILDN 324

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +S A+          V+  ++ I K+    ++      ++  E + ++  +++G+  
Sbjct: 325 IVNLSKAQITAMVPEATMVSTYME-IKKLFQTAEASKDGFDLTPEELKAVLEQIKRGKQI 383

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              +K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 384 TDTSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYA 443

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  EEIAK++ +PV
Sbjct: 444 TWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKGVQENGKEPDIEEIAKEVGLPV 503

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V++V+KITKEP+SLE PIG ++    GDF+ D+ A +P+D+ ++ +L+    ++L+ L
Sbjct: 504 DKVKQVIKITKEPVSLEAPIGSDEDGKFGDFVPDEKAPTPIDNIMKEDLQGQIDQILSQL 563

Query: 621 TPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   K L+++
Sbjct: 564 NEREQAVIRMRFGLMEDASDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGKNLKNY 623

Query: 680 LDG 682
           ++ 
Sbjct: 624 VES 626


>gi|24214932|ref|NP_712413.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45657567|ref|YP_001653.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|26399555|sp|P59117|RPOD_LEPIN RecName: Full=RNA polymerase sigma factor rpoD
 gi|47605974|sp|P61540|RPOD_LEPIC RecName: Full=RNA polymerase sigma factor rpoD
 gi|24195965|gb|AAN49431.1|AE011394_5 RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45600806|gb|AAS70290.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 585

 Score =  300 bits (768), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 212/657 (32%), Positives = 338/657 (51%), Gaps = 76/657 (11%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S    +K+I L +  G V+ +++N  LP   ++SE+++D   +L  MGI +V+      
Sbjct: 5   QSMPEVQKIISLGKANGEVSYDDINEILPDKILNSEKIDDFFTLLHEMGIEIVEEYTRNT 64

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E +     L     +     +K   ++   ++DP+++YLRE+G + L+S E E+ +AKR
Sbjct: 65  LEPAS---TLVPKDDSKPARKKKESSASTSGSEDPIKLYLREIGKVSLISGETEVFLAKR 121

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G  ++  ++  S +     I    ++      + ++I ++      ++       E 
Sbjct: 122 IEKGEKIIEETILSSSILRANYIKLLPKIRSKKIKVYDLIRVDKMYALNAEEAH-KLEEL 180

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                     QEK   +           +K  K+ + K+D+  E   N  R L   + + 
Sbjct: 181 FFKNILVIQEQEKVLQEAVSKIRKYSETSKKYKEFKEKIDASTEIIHNAIRELGVSQKE- 239

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              +  +  +++  V      I E+ R    ++       +D K+  +     EKL  + 
Sbjct: 240 ---IQKISQKIKSMVF----RIKEIDRHFLKIKAQYGQDVRDIKAFNRFIEKNEKLDDIE 292

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             + +N       ++++ ++ K I +NE +L R+ Q  G                     
Sbjct: 293 VKMGVN-------IDEVREVIKDIRNNERKLRRMEQEAG--------------------- 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                                    + ++ I       I   R I           S AK
Sbjct: 325 -------------------------STVQEIKDWGEKIIKGEREI-----------SQAK 348

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KE+V+ANLRLV+S+AK+Y NRG+ F DLIQEGNIGL+KA +KF++  GYKFSTYA WW++
Sbjct: 349 KELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWWIR 408

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+I+DQ+ TIR+PVHM ++++KV+R  R    +  R+P  EEIA++L  PV+ V+ 
Sbjct: 409 QAITRAISDQARTIRVPVHMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLGWPVQKVKM 468

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V  + +EPISLE P+G E+ S LGDFI D    +P+++A  + L E   +VL +L  RE+
Sbjct: 469 VKNVAREPISLEIPVGSEEDSELGDFIPDTEVETPVNAAASSILAEQIRQVLHTLPAREQ 528

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +V+RMRFG+      TLEEVG QF VTRERIRQIEAKA+R+L+HPSRSKKL+ ++DG
Sbjct: 529 KVIRMRFGLDDGYPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSRSKKLKDYIDG 585


>gi|254704733|ref|ZP_05166561.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261755429|ref|ZP_05999138.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261745182|gb|EEY33108.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 415

 Score =  300 bits (768), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 204/435 (46%), Positives = 276/435 (63%), Gaps = 32/435 (7%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N +++ E E + D  + D SDD+ KKMIKLA++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEEAEVEREGAADGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLED--EEGSEDSLDLA---SSASNSSVFLQKRKDSADR 115
           EQ+EDT++MLS+MGINVV+ D+ ++  EEG++D  +       A  ++V     K     
Sbjct: 61  EQIEDTMSMLSDMGINVVEDDEQDNDREEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTD 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPL+FQA+IIWRD+LN
Sbjct: 121 RTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLSFQAIIIWRDQLN 180

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +   LLREIIDLE                    + R++  Q + RDD   T    +   +
Sbjct: 181 ESNILLREIIDLETTYAGPEAKQAPVIERVEEEKPRDERPQRRSRDDDDITNVGGDMPVE 240

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD  +                     +  +L+AME +LRP+VM  LD IA+ Y++LR
Sbjct: 241 DDDDDEDE---------------------ANLSLAAMEAELRPQVMETLDFIADTYKKLR 279

Query: 296 SLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
            LQD       A  G+       + K LK++L+K V SLSLNQ+RI+ LVEQLYDI+KR+
Sbjct: 280 KLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLYDINKRL 339

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           + NEG+LLRLA+S+G++R+ FL+ +QG ELDP+WV      P   WK F A E DSI ++
Sbjct: 340 VQNEGKLLRLAESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKEADSIGRL 399

Query: 410 RNEIKSISVETGISI 424
           R+EI++++ ET ISI
Sbjct: 400 RSEIQNLATETAISI 414


>gi|303327390|ref|ZP_07357831.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
 gi|302862330|gb|EFL85263.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
          Length = 589

 Score =  300 bits (767), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 224/661 (33%), Positives = 336/661 (50%), Gaps = 86/661 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              + +I   +  G++T EE+N  LP +  + EQ E+ + +   + I +VD +       
Sbjct: 8   QQIQSLIAKGKGTGFLTFEEVNKALPVEMSTPEQFEEIIGIFEQLEIVIVDSEK------ 61

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                D    ++ ++       +     T+D                 E     + R   
Sbjct: 62  -----DGKKISATAAETDDDVSEDTLDLTED-----------------EESADYSSRSTD 99

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                    D E  I  + + G          
Sbjct: 100 PVRMYLREMGAVPLLDR--------------------DGEVVIAKKIEMGEQDVLYALVE 139

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                       +D+++    ++   K  ++D    D                       
Sbjct: 140 VPVAVEELINVGEDLRQNRVKLKDVVKTIEEDDPSED----------------------- 176

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRS----LQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               E   R +V+  LDEI +V+++ R     L D     ++   +  +    KE++V  
Sbjct: 177 ----EMNQRSRVILLLDEIKQVFKKKRKIYKKLDDCCTLERRVTATQKEIISFKEEIVTR 232

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  +        G   RE++P
Sbjct: 233 LRDIKLEKTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGRTQVEIQTMFDGLEKREVNP 292

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              +        E  +F    +  I      +K +  +   ++ +   ++  +++G   A
Sbjct: 293 TEAARDLKLSVDELFSFKEMIIGKIEI----LKRLQEKCCHNVGDLEEVLWRIKRGNTAA 348

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 349 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 408

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  PVE
Sbjct: 409 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYPVE 468

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  I   L E    VLA LT
Sbjct: 469 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVINTKLSEQLAAVLADLT 528

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 529 PREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQPLRSYYE 588

Query: 682 G 682
            
Sbjct: 589 N 589


>gi|237755496|ref|ZP_04584118.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237692360|gb|EEP61346.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 570

 Score =  300 bits (767), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 218/637 (34%), Positives = 340/637 (53%), Gaps = 74/637 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLEDE 86
            D  + +I LAR++GYVT  E++ ++  +  SS++ +E  +  L+ + I+V D + ++ E
Sbjct: 7   RDDVRTLINLAREKGYVTYAEISTYVDEEFFSSDENIESLIEYLNELNIDVRDDEKIKSE 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +             +  + +    D      DDPV++YLREMG I LL R+ EI  +  I
Sbjct: 67  D----------EDISEHLGIDLSDDDVWNKADDPVKLYLREMGKIPLLKRDEEIKYSMEI 116

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E GR  +   L  +    + L+    ++ DG   + +I++L+    PE K          
Sbjct: 117 ERGRKKVFRGLLRTSFLTERLLDEWAKVIDGKARVHDILNLDE---PEVKDEEETSESEE 173

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              +   +  +   D +++     +    + + ++  +++     + +        +   
Sbjct: 174 FSLENNSNYDKTTADFIKKGLELAKLYRDLLEKEKKYLETGSLEDKKEFIWQHAKLNRFI 233

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            +L+             LD+IA+  +EL +                              
Sbjct: 234 KSLN--------IKFTKLDKIADELKELYT------------------------------ 255

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
                      L +   D  KRI               I  D+ L      E +P  +  
Sbjct: 256 ----------KLRKNEKDYEKRIKIIS----------KIHPDIDLMLSPDYEKNPEILKK 295

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            ++      +  +       LK+R+EI+ I  + G   SEF H++ +++ G  E +  K+
Sbjct: 296 LEEHGFSYGRYEILRT--ETLKLRDEIEEIKQKIGTIPSEFDHVLDLIQSGRNEINHVKQ 353

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +V+ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +K+D+  G+KFSTYA WW++Q
Sbjct: 354 ILVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKKGFKFSTYATWWIRQ 413

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K++R +R +  ++ REPTPEEIAKK  MP + VRK+
Sbjct: 414 AITRAIADQARTIRIPVHMIETINKLLRISRTLVQELGREPTPEEIAKKAGMPADKVRKI 473

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L+ +++P+SLETPIG ++ SHLGDFIEDK+ +SP    ++  LR     VL++L+ REE+
Sbjct: 474 LRTSQDPVSLETPIGSDEESHLGDFIEDKSVLSPEQHMLKQALRLQLDEVLSTLSEREEQ 533

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           VLR RFG+  +T+HTLE+VGK+F VTRERIRQIEAKA
Sbjct: 534 VLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKA 570


>gi|212702263|ref|ZP_03310391.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
 gi|212674326|gb|EEB34809.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
          Length = 589

 Score =  299 bits (764), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 224/661 (33%), Positives = 336/661 (50%), Gaps = 86/661 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              + +I   +  GY+T +E+N  LP +  + EQ E+ + +   + I +VD +    +  
Sbjct: 8   QQIQSLIAKGKGMGYLTFDEVNKALPVEMNTPEQFEEIIGIFEQLEIAIVDSEKDGKKIS 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  +     +                              GS+EL   E     + R   
Sbjct: 68  ATPTETDDDAMD----------------------------GSLELAEDEESADYSSRSTD 99

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                    D E  I  + + G          
Sbjct: 100 PVRMYLREMGAVPLLDR--------------------DGEVVIAKKIEMGEQDVLYALVE 139

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                       +D+++    ++   K  ++D    D                       
Sbjct: 140 VPVAVEELINVGEDLRQNRIKLKDVVKTIEEDDPSED----------------------- 176

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRS----LQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               E   R +V+  LDEI +++++ R     L D     +K      +    KE++V  
Sbjct: 177 ----ELNQRSRVILLLDEIKQIFKKKRKIYKKLDDCNTLDRKVTAIQKEIISYKEEIVTR 232

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE---LDP 381
           +  + L ++ ID ++E + D  +++ + + +L     S G  +    E   G E   ++P
Sbjct: 233 LRDIKLEKTLIDRIIETVEDYVRQMHNCQRDLSAYILSTGRTQAEIQEMFTGLEQRTINP 292

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           +  +        E  +F    +  I      +  +  +   ++++   ++  +++G   A
Sbjct: 293 NDAARDLKLSVDELFSFKEMIIGKIEI----LSRLQEKCCHNVNDLEEVLWRIKRGNTAA 348

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 349 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 408

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  PVE
Sbjct: 409 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYPVE 468

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  I   L E    VLA LT
Sbjct: 469 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVINTKLSEQLAAVLADLT 528

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 529 PREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQPLRSYYE 588

Query: 682 G 682
            
Sbjct: 589 N 589


>gi|218962087|ref|YP_001741862.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730744|emb|CAO81656.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
          Length = 579

 Score =  299 bits (764), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 213/661 (32%), Positives = 332/661 (50%), Gaps = 92/661 (13%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++  KK+++L ++ GY+T +++N  LPP     ++++D +  LS  GI ++D      
Sbjct: 3   TYNECLKKLVELGKESGYITFKQINEILPPSPFFLDKVDDIIFDLSQDGIEIID------ 56

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
               E    +  S +        +K  + R  DDPVRMYLREMG + LL REGE+ +AK+
Sbjct: 57  ----ETEKRITKSGAAIRKPSTAKKFKSKRYYDDPVRMYLREMGRVPLLDREGEVRVAKK 112

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI--IDLEACIGPESKGGFFHGT 203
           IE  + M+  ++ +   T + +  +     +    L +I  +D+   I            
Sbjct: 113 IETYQKMINQNVFKCGSTLREMYNFLHRYRERRVRLDQIFKVDISTWIDKNQDAKIIEKF 172

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +    +  E        + V     + E     +   + ++D       N    L  ++ 
Sbjct: 173 KEILKENEEKF------EKVGNILDNCEFDDTGTSSRQEEIDELRSQIVNTFMQLSYND- 225

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKEKLV 322
                   +  ++  ++   ++ I E Y  + +L         +      + K   E   
Sbjct: 226 -------KLIKRMVYRIRSLVERIEESYESINNLTRIKRYTIDEICMYGRRAKKSDEDFQ 278

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +++    ++ +     VE L     +I +   ++ R+     +                 
Sbjct: 279 EVLEETGIDPNVF---VETLR----KIKNARRKIRRVELETKM----------------- 314

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
                     G    F+  E+D   + +                                
Sbjct: 315 ---------TGNKLIFLLREIDRAERNKER------------------------------ 335

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A+ EM+EAN+RLVIS+AK Y NRGL+FLDLIQEGN GLM+A EK+D+  GYKFSTYA W
Sbjct: 336 -AQNEMIEANVRLVISIAKHYNNRGLEFLDLIQEGNTGLMRAVEKYDYRKGYKFSTYATW 394

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K+ RT+RR+  K+ REP PEEI++ L +PVE 
Sbjct: 395 WIRQAITRAIADQARTIRIPVHMIESINKINRTSRRLMQKLGREPYPEEISEVLDIPVEK 454

Query: 563 VRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           ++ ++ I+KEP+SL+ PIG + + S LGDFIED+  +SP   A ++ L++    VL +LT
Sbjct: 455 IKNIMSISKEPVSLDKPIGHDSEDSILGDFIEDRTIISPERLAERSLLKKQVDEVLKTLT 514

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREERV+R+RFGI      TLEEVG  F VTRERIRQIE KA++KL+HPSR+  L+ FLD
Sbjct: 515 PREERVIRLRFGIDDGYHRTLEEVGNIFQVTRERIRQIEDKALKKLRHPSRAAILQQFLD 574

Query: 682 G 682
            
Sbjct: 575 N 575


>gi|319941926|ref|ZP_08016247.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
 gi|319804579|gb|EFW01449.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
          Length = 779

 Score =  297 bits (761), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 182/653 (27%), Positives = 321/653 (49%), Gaps = 65/653 (9%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEV-SSEQMEDTVAMLSNMGINVVDGDDLEDE-EGSE 90
           ++++L R RG+VT+ ++N +LP   + +SE +++    L  +GI V +    ED+   + 
Sbjct: 189 ELVRLGRSRGWVTLADINDYLPESALRTSENLQEVTEQLGRLGIQVFEAPPDEDDILING 248

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              D +         +    + +   + DP+R YLR +GS +LL+R GEI +AK IE   
Sbjct: 249 MGGDNSDDIDEDDAAVMLTPEESVGLSKDPLRAYLRGVGSHKLLTRAGEIEVAKSIEQFT 308

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             ++A++ E P+  + ++   + L D  T +  ++D                        
Sbjct: 309 IKLVATIVEYPIAVEEILRLGEALKDENTAVDTVVDGF---------------------- 346

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                     +D    E    SA +++ D  +   +  + AE                  
Sbjct: 347 ----------NDAAAEENANSSADEIATDIGAAAMTVDQLAE------------------ 378

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                +R +V+   +      + L  +++   + +++++       +   L  +  S+ L
Sbjct: 379 -----MRARVLSLFEL---ARKSLDRVRETYGDPKREKEYRKALADMSAALSPIRFSVKL 430

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR-ELDPHWVSYAKD 389
                D + + + +++  +         LA    + +   +E  +     DP        
Sbjct: 431 VTQMTDHISQHMDEVNNTLKKMRA---TLANQCRMPQVQVVELLKSDGVTDPECFEKISA 487

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +  W + V+  +  + + +  + S   E  + +SE R +   ++  +     AK +M+
Sbjct: 488 AGKP-WSDAVSHSMAVLKEEQAVLISAEREGLLKLSEQRELGRAMKLAQTNLMQAKAKMI 546

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           EANLRLVIS+AK Y NRGL   DLIQEGN+GLMKA +KF++  GYKFSTYA WWV+Q++T
Sbjct: 547 EANLRLVISIAKGYVNRGLAMTDLIQEGNLGLMKAVDKFEYRRGYKFSTYATWWVRQSVT 606

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R++AD   TIRIPVHM +  +K+ R  ++   +  R+PT +E+A+   +P++ V  + + 
Sbjct: 607 RAVADFGNTIRIPVHMTESYNKLRRQKQKFLQQHGRQPTEQELAELADLPLQKVNLLTQA 666

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +   S++ PIGDE+ +   DF+       P  +    ++ +   + L  L PRE +VLR
Sbjct: 667 MRGVESIDAPIGDEEDATKLDFVRGNERDDPGVAFQDRSMIDCIQKSLNELNPREAQVLR 726

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +R+GIG N DHTLEEVG+   +TRER+RQIE+ AIRKL+ P  +++LR +L  
Sbjct: 727 LRYGIGTNQDHTLEEVGRTLGLTRERVRQIESAAIRKLRTPDFTERLRDYLQS 779


>gi|116328273|ref|YP_797993.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116330997|ref|YP_800715.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
 gi|116121017|gb|ABJ79060.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116124686|gb|ABJ75957.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
          Length = 585

 Score =  296 bits (758), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 211/657 (32%), Positives = 338/657 (51%), Gaps = 76/657 (11%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S    +K+I L +  G V+ +++N  LP   ++SE+++D   +L  MGI +V+      
Sbjct: 5   QSMPEVQKIISLGKANGEVSYDDINEILPDKILNSEKIDDFFTLLHEMGIEIVEEYTRNT 64

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E +     L     +     +K   ++   ++DP+++YLRE+G + L+S E E+ +AKR
Sbjct: 65  LEPAS---TLVPKDDSKPARKKKESSASASGSEDPIKLYLREIGKVSLISGETEVFLAKR 121

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G  ++  ++  S +     I    ++      + ++I ++      ++       E 
Sbjct: 122 IEKGEKIIEETILSSSILRANYIKLLPKIRSKKIKVYDLIRVDKMYALNAEEAH-KLEEL 180

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                     QEK   +           +K  K+ + K+D+  E   N  + L   + + 
Sbjct: 181 FFKNILVIQEQEKVLQEAVSKIRKYSETSKKFKEFKEKIDASTEIIHNAIQELGVSQKE- 239

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              +  +  +++  V      I E+ R    ++       +D K+  +     EKL  + 
Sbjct: 240 ---IQKISQKIKSMVF----RIKEIDRHFLKIKAQYGQDVRDIKAFNRFIEKNEKLDDIE 292

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             + +N       ++++ ++ K I +NE +L R+ Q  G                     
Sbjct: 293 VKMGVN-------IDEVREVIKDIRNNERKLRRMEQEAG--------------------- 324

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                                    + ++ I       I   R I           S AK
Sbjct: 325 -------------------------STVQEIKDWGEKIIKGEREI-----------SQAK 348

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           KE+V+ANLRLV+S+AK+Y NRG+ F DLIQEGNIGL+KA +KF++  GYKFSTYA WW++
Sbjct: 349 KELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWWIR 408

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+I+DQ+ TIR+PVHM ++++KV+R  R    +  R+P  EEIA++L  PV+ V+ 
Sbjct: 409 QAITRAISDQARTIRVPVHMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLGWPVQKVKM 468

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V  + +EPISLE P+G E+ S LGDFI D    +P+++A  + L E   +VL +L  RE+
Sbjct: 469 VKNVAREPISLEIPVGSEEDSELGDFIPDTEVETPVNTAASSILAEQIRQVLHTLPAREQ 528

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +V+RMRFG+      TLEEVG QF VTRERIRQIEAKA+R+L+HPSRSKKL+ ++DG
Sbjct: 529 KVIRMRFGLDDGYPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSRSKKLKDYIDG 585


>gi|307721137|ref|YP_003892277.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
 gi|306979230|gb|ADN09265.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
          Length = 615

 Score =  296 bits (757), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 206/669 (30%), Positives = 348/669 (52%), Gaps = 64/669 (9%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +     + + +   +  + +  VT E L  F    + ++ Q ++   +L      +    
Sbjct: 1   MTAKELNKALETFFEEHKSKDCVTYESLIEFF-DKQPTAAQAKNIYKLLQKNKKCIYTSS 59

Query: 82  DLEDEEGSEDSLD--------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +   +   +++          L  + ++    L++ +      +D PVRMYLREMG I L
Sbjct: 60  EHAKKLNDQEAEARRSAQRKMLEDNETDKFDILKEHELLEWSRSDSPVRMYLREMGQIPL 119

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L++E EI I+K+IEAG ++++ ++C  P     ++ +++ L +    ++E+         
Sbjct: 120 LTKEEEIEISKKIEAGESIIIDAICSVPYLIDFILDYKEPLINRERRVKEL-----FKSF 174

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           E +       +       E +   K++  V +     ++  K  KD     +  PEN  +
Sbjct: 175 EDEKDDGDDNDDSDDDSAEKTLSVKDKSRVDKVSTSFKALEKAKKDWVKAAEKVPENLGD 234

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           +   L E       T++  +  L+ K++  L   +++  EL    + A+    DE    +
Sbjct: 235 E---LSEGTVQYYLTVTFKKAVLKEKLLD-LGPTSKLINELVKAMETALKS--DEGYDKE 288

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            K L+ KL     +L  N     +LVE++ D++K  + N      +  +Y        + 
Sbjct: 289 LKRLEYKLPLFNATLKANHK---ILVEKIQDLTKEDIANMVPEATMVSTYM----EIKKL 341

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
            Q +E   +                                       +   +   I+  
Sbjct: 342 VQTKEASKNSFD------------------------------------MEPEKLADILEQ 365

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+  + I+K +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  G
Sbjct: 366 IKRGKNISEISKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKG 425

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  + IA
Sbjct: 426 YKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKHLQENGKEPDVDTIA 485

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K++ + VE V+ V+KITKEPISLE PIG ED    GDFIEDK ++SP D+ ++ +LR   
Sbjct: 486 KEVGLSVEKVKNVIKITKEPISLEAPIGSEDDGRFGDFIEDKTSLSPSDAILKDDLRIQI 545

Query: 614 TRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +VL  L  RE+ V+++RFGI  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP  
Sbjct: 546 EQVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELSVTRERVRQIESSAIKKLKHPKV 605

Query: 673 SKKLRSFLD 681
            +KL+++++
Sbjct: 606 GRKLKNYIE 614


>gi|317153216|ref|YP_004121264.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
 gi|316943467|gb|ADU62518.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
          Length = 581

 Score =  294 bits (753), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 220/662 (33%), Positives = 331/662 (50%), Gaps = 96/662 (14%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +QRG++T EEL+  LP D  + EQ+E+  A+   MGI +V          
Sbjct: 8   QQIKTLIAEGKQRGFLTYEELSKALPSDYNTPEQLEEIHAIFDQMGIALV---------- 57

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                   S   +  +    ++       DD                       A R   
Sbjct: 58  -------DSDEDDKKLETDDKELELTEKDDDSA-------------------DYASRSTD 91

Query: 149 GRAMMMASLCESPLTFQAL-IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
              M +  +   PL  +   ++   ++ +G                E             
Sbjct: 92  PVRMYLREMGAVPLLDREGEVVIAKKIENGEL--------------EVLYSLIEVPVAVE 137

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                    +  R  +++    IE       +                            
Sbjct: 138 ELISVGEDLKDGRVKLKDVVKTIEEDDPSEDEMNQ------------------------- 172

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVK 323
                    R +V+  LDE+ +++++ R + +      + +K          V K+++V 
Sbjct: 173 ---------RQRVIFLLDEVKKLFKKKRKIYEKLDYCAQTDKRVYGVQKDILVYKDEVVT 223

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ---GRELD 380
            +  + L ++ ID ++E + D  +++ + + +L     S G  +    E  +    R ++
Sbjct: 224 RLRDIKLEKTLIDRIIETVNDYVRQMHNCQRDLSAYVLSVGQTKAEIEELFRQVDARTVN 283

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           P   +        E+ +F       + +I N ++        S+ +   ++  +++G   
Sbjct: 284 PVVAADTLGLTVEEFFSFKEMLAGKL-EIMNRLQDKCCH---SVHDLEEVLWRIKRGNLS 339

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 340 AMRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYA 399

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P+PEEIA+++  P+
Sbjct: 400 TWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPSPEEIAERMDYPL 459

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V+KVLKI KEPISLETPIGDE+ S LGDFIEDK A +P +  +   L E    VL+ L
Sbjct: 460 EKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKATAPAEEVVSTKLGEQIASVLSDL 519

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS  LRS+ 
Sbjct: 520 TPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSALLRSYF 579

Query: 681 DG 682
           + 
Sbjct: 580 EN 581


>gi|294669659|ref|ZP_06734726.1| hypothetical protein NEIELOOT_01560 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308572|gb|EFE49815.1| hypothetical protein NEIELOOT_01560 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 496

 Score =  294 bits (751), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 204/531 (38%), Positives = 297/531 (55%), Gaps = 40/531 (7%)

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           M+ ++   P +   ++   +++ +    + E++  EA I P                   
Sbjct: 1   MIQAISACPGSIAEILELIEKIRNDEIKVDEVV--EAIIDPN------------------ 40

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
                       E   +      +               E+++   ++ E D+A   S  
Sbjct: 41  ------------EVLLNELGLGHLETVPPGARPGDNAEEESEDGEDEDGEGDAADMGSVN 88

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
            ++L+ +V+     I + Y  +            ++    +    ++ +   +  +    
Sbjct: 89  LEELKREVLEHFAVIKDSYGLMVE------ALNANDSKHPEYLKHRDAIAHKLLEVRFAT 142

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
            +I+ L   L      I   E E+  +      + RD F+ +      D  W+       
Sbjct: 143 RQIESLSNSLRQKVDNIRKLEREIRDICLDRVQMDRDYFISQFLPNITDLTWLENEIA-K 201

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
              W N +     +IL+ ++E+  +     ISI E + I   ++  E E + AK+EM++A
Sbjct: 202 RRVWANALERFQHAILEKQSELAEMEKTAQISIEELKEINKNMQSSERETARAKEEMIQA 261

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRS
Sbjct: 262 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 321

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIPVHM + I+K+ R +R+   +   +P   ++A+ + MP + +RK++KI K
Sbjct: 322 IADQARTIRIPVHMIETINKMNRISRQYLQETGEDPDSAKLAELMEMPEDKIRKIMKIAK 381

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPIS+ETPIGD+D SHLGDFIED N V+P D+A+ ++LRE T  VL SLTPRE +VLRMR
Sbjct: 382 EPISMETPIGDDDDSHLGDFIEDVNNVAPADAAMYSSLREVTADVLESLTPREAKVLRMR 441

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS +L+SFLD 
Sbjct: 442 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDRLKSFLDS 492


>gi|170704115|ref|ZP_02894732.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170130976|gb|EDS99686.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 575

 Score =  293 bits (750), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 174/630 (27%), Positives = 275/630 (43%), Gaps = 58/630 (9%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN--SSVFLQKRK 110
           +P D+ +   ++   A+L  +GI V D  D       E        A             
Sbjct: 1   MPDDDANDSGVDAVAAVLGELGIAVCDSADTASGWTLERYFRPTPPARAWADGAGTLVAA 60

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D     T DPVR+YLREMG+  LL+R+ E A A+RIE GRA   A LC  P    AL+  
Sbjct: 61  DLLAPRTTDPVRLYLREMGTTPLLTRDEEFAYARRIERGRAASAAVLCGDPDALDALVSI 120

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           R E+    T                           +         +  R+D      + 
Sbjct: 121 RVEIAQCRT---------------------------AASTYAIFLDDGPRNDTSADHAEA 153

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           +++A  + +     D+  +    D                      R  V+  L  I E+
Sbjct: 154 DTSATAAGEPARDDDTQTDTQTEDSAW-------------------RNAVVARLARIDEL 194

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
              +R+              S   +        L+ +L L+   ++ + E L   ++R  
Sbjct: 195 AHGMRA------ALASGGLPSAAYRSHVRDATALLRTLGLSARALERMSEPLRGRARRHR 248

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
              G L R+    G+    F   H   +    W++                  +  +  R
Sbjct: 249 ALRGRLERMLADVGVP-PSF--AHAADDDHAGWLASCIAAHPACAPTLTRRAAE-FVDAR 304

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + I   +  + +       + + +   E     A+  + +ANLRLV+S+AK+Y +RGL F
Sbjct: 305 DAIVRAAPASELPPGATASLDARLGAIERAMQPARTGLFDANLRLVVSIAKRYPDRGLPF 364

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGNIGL+KA E++D+  G++FSTYA WW++QAIT ++AD   TIR+P H  D ++
Sbjct: 365 ADLIQEGNIGLLKAIERYDYRRGFRFSTYATWWIRQAITHALADLGRTIRVPTHTVDALN 424

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R AR    +     TP E+A  +  PV+ VR ++ I KEP+S + P+  E      D
Sbjct: 425 KLSRLAREHRQRAGTAATPAELAVHMGEPVDKVRDLMAIVKEPVSADVPVSPEGDMTFAD 484

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
              D +  SP D+A    LR T   V+  L PRE  VL++R+G+  +   +L ++G+Q  
Sbjct: 485 VAADTSTPSPEDAAGATQLRRTIAAVIDRLPPREAMVLKLRYGLHADEGCSLRDIGRQLN 544

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++ ER+RQIEA A+ +L+       LRSF+
Sbjct: 545 LSAERVRQIEASALARLRASDALGLLRSFI 574


>gi|85860024|ref|YP_462226.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
 gi|85723115|gb|ABC78058.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
          Length = 580

 Score =  293 bits (749), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 217/653 (33%), Positives = 349/653 (53%), Gaps = 78/653 (11%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   + +KK+I L  ++G++T +++N FLP D  SS+Q++D + +     I+++D +  E
Sbjct: 4   NIQSEEFKKLISLGEEKGFLTYDDVNDFLPSDITSSDQIDDIIMLFGEKNIDIIDTEKGE 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                    +  ++     + +     S    T DPV+MYLREMG + LLSR+GE+ IAK
Sbjct: 64  KLLVKSPVEERETAKEGELIDMM----SVAGKTGDPVKMYLREMGYVSLLSRDGEVEIAK 119

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
            IE G    M ++     + + ++   ++L      ++ +ID       E + G+     
Sbjct: 120 IIEEGAQEAMGAVFGVTASVKEVVDIGNKLKSDEIRIKNVID-----NLEDEDGYVE--- 171

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                      ++ +R+ V +    +      +     K+ +             +  +D
Sbjct: 172 -----------EDSQRERVIKLLDKVAMLDGKNDQILQKLRA------------KDLSED 208

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               L    ++ +  ++    ++    +++  L  N       ++   + +  ++++ K 
Sbjct: 209 GRKALKIQMEKNKKAIIKLCRKVRFGKKQIDKLVANI------KRYLAELEKAEDEIQKC 262

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                L+ ++I+           R+     +   +   YGI  +                
Sbjct: 263 KEETGLSLTQIEKACS-------RLKKYPQDEAAILAEYGITME---------------- 299

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                         +      I +   ++K+I+ ETG S++ F+ I+  +  GE +A  A
Sbjct: 300 -------------KLKSVEAMIREANRKLKNITKETGYSVTAFKKILFNIEHGEKKAEEA 346

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 347 KRKLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWI 406

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ REP+P+EIA K+  P+E VR
Sbjct: 407 RQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGREPSPDEIANKMEYPLEKVR 466

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVLKI KEPISLETPIG+E+ SHLGDFIEDK  +SP ++ I  +L E T ++L++LTPRE
Sbjct: 467 KVLKIAKEPISLETPIGEEEDSHLGDFIEDKKIMSPSEATISMDLAEQTRKILSTLTPRE 526

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           E+VLRMRFGI        EE  +Q     E    IE  A RKL++PSR + ++
Sbjct: 527 EKVLRMRFGI-SERIEYGEEELEQGEEEGEFPGPIETGAYRKLRNPSRRRTVK 578


>gi|313682108|ref|YP_004059846.1| RNA polymerase, sigma 70 subunit, rpod [Sulfuricurvum kujiense DSM
           16994]
 gi|313154968|gb|ADR33646.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfuricurvum kujiense DSM
           16994]
          Length = 620

 Score =  293 bits (749), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 200/666 (30%), Positives = 336/666 (50%), Gaps = 71/666 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +    + +  +T E +       + +  Q ++ + +     I +    +       +
Sbjct: 10  LETLFSEHKSKNCLTYETIVDPF-DKQPTLAQAKNILKLAQKHKICLFTSSEHAKMLNQQ 68

Query: 91  DSLD--------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++          +  ++ +    L++ +      +D PVRMYLREMG I LL++E E+ I
Sbjct: 69  EAAAKRAAQLKYIEEASGDEFDILKQHELLEWSRSDSPVRMYLREMGQIPLLTKEEEVEI 128

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           +KR+E G  +++ ++C  P     ++ ++D L +    ++E+         E        
Sbjct: 129 SKRMEMGEGIIIDAICSVPYLIDFILDYKDPLINRERRVKELF-KSFEEENEDDSEDDSD 187

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            EG   +  E +   K++  V++     ++  K  K+     +   E             
Sbjct: 188 DEGDDDESTEKAPSVKDKKRVEKVVTSFKALEKAKKEWVKATEKMLEE------------ 235

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
                ++  M+ +     +                             S K K+LKE L+
Sbjct: 236 ----RSIDEMDAEYVLFFL---------------------------NVSFKKKMLKEALL 264

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ---GREL 379
            L  +  L    I+ LV  +    +     + EL RL     +  D   + H     +  
Sbjct: 265 DLGPTSKL----INELVRSMETALRSDEGFDRELKRLEYKLPLFNDQLKKNHTLILNKIC 320

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG---ISISEFRHIVSMVRK 436
           D      A   PE       A  V + ++I+  I++     G   +   +   I+  +++
Sbjct: 321 DLTKEEIATKVPE-------ATMVSTYMEIKKLIQTKEASKGGFNMEPEKLADILEQIKR 373

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+  + ++K  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 374 GKNISEVSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKF 433

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IA+++
Sbjct: 434 STYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKHLQEHGKEPDVETIAEEV 493

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + VE V+ V+KITKEPISLE PIG+E+    GDFIEDK ++SP D+ ++ +L+     V
Sbjct: 494 GLSVEKVKNVIKITKEPISLEAPIGNEEDGRFGDFIEDKMSLSPSDAILKDDLKVQIESV 553

Query: 617 LASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L  L  RE+ V++MRFGI  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +K
Sbjct: 554 LEQLNEREKAVIKMRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRK 613

Query: 676 LRSFLD 681
           L+++++
Sbjct: 614 LKNYIE 619


>gi|157826499|ref|YP_001495563.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801803|gb|ABV78526.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 514

 Score =  293 bits (749), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 187/535 (34%), Positives = 301/535 (56%), Gaps = 50/535 (9%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD--GDDLEDEEGSEDSLDLASSA 99
           G VT  ++N  LP D  S E+++  +   S   ++++D   DD    +  E       S 
Sbjct: 24  GSVTYNDINRALP-DGTSVEEIDKVMFRFSEAEVDILDTNEDDAIKIDDIEMEEGFKIST 82

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           +       + ++    +TDDPVR+YL++MG ++LL+RE E+ IAKRIE GR  ++A+LC 
Sbjct: 83  NIDHEPEDETEEENIGTTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEGRKTLIAALCR 142

Query: 160 SPLTFQALIIWR-DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           SP+       W  D +N+   LLR++IDLE+ +  + +           +++        
Sbjct: 143 SPIAMDKFRKWYADLVNENNMLLRDLIDLESNMMHDDETSESEDDHNSDHEE-------- 194

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                                              +E++ D D +++  ++S +E Q+ P
Sbjct: 195 -----------------------------------EEQDHDHDHEENILSMSKVETQILP 219

Query: 279 KVMCALDEIAEVYREL---RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            ++  + +IA +  EL            G K  ++S K     E L+  V  +  N  R 
Sbjct: 220 NIIERMKKIAFICEELLIETKKSFEKSAGPKILQNSKKYNDNLELLISEVSEIHFNSKRT 279

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           + ++ ++Y I++ +++ E   L+LA+ YGI R  FL+ + G  ++  W        +  W
Sbjct: 280 EEILSEMYGINRDLINKETAFLKLAEKYGITRQNFLDEYIGAVINAAWKEKMLKNKKAGW 339

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K  +  E D I ++  E+ +I + TG+ +++F+ +V+ ++K E +   AKK+M+EANLRL
Sbjct: 340 KELLTKESDYIDQMIAELSAIEINTGLLVNDFKKLVNTIQKSERQTLQAKKDMIEANLRL 399

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           VIS+AKKY NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ
Sbjct: 400 VISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQ 459

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           + TIRIPVHM + I+K++RT+R+M N++  EPTP EIA +L+MP++ VRKV + +
Sbjct: 460 ARTIRIPVHMIETINKIIRTSRQMLNELGYEPTPAEIAARLSMPIDKVRKVYENS 514


>gi|118475308|ref|YP_891711.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp. fetus
           82-40]
 gi|118414534|gb|ABK82954.1| RNA polymerase sigma factor [Campylobacter fetus subsp. fetus
           82-40]
          Length = 623

 Score =  292 bits (747), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 203/662 (30%), Positives = 337/662 (50%), Gaps = 56/662 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDGDD---- 82
              +++ K    +GYVT E+L       P   + +++E    +     I+ V+       
Sbjct: 9   AQIEELFKEN-SKGYVTFEKLVRLFDKAPTVATIKKVETLAELYKIQLISAVEAAKIKNI 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDS-ADRSTDDPVRMYLREMGSIELLSREGEIA 141
            E ++  ED L +  +A      L    D      +D PVRMYLREMG I LL++E E+ 
Sbjct: 68  QEAKKSEEDKLKIIDTALEEEFDLTSENDLLEWSRSDSPVRMYLREMGQISLLTKEEEVE 127

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           I+K+IE G  +++ + C  P     ++ +++ L +    ++E+         E +     
Sbjct: 128 ISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELFKSFDEEESEEEEEETT 187

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E    +  EDS+  K++    +   +    +                           
Sbjct: 188 EDEFEYDENEEDSATAKKQPKKLDKRAEKVIES--------------------------- 220

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                                AL++  + + ++ + Q+ ++  + D  + +     K+ L
Sbjct: 221 -------------------FKALEKAKKEWMKIVAKQNISIEEEADLVAKLNLTFKKKVL 261

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
              +  L      I+ +V+ +    K     + EL RL     +      + HQG   D 
Sbjct: 262 KDKLMDLGPTSKLINEIVKSMETALKSDDDFDKELKRLEYRLPMFSAELKKNHQGILKDI 321

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +S             V+  V+ I K+    ++      +   E + ++  +++G+  +
Sbjct: 322 TKLSKEDIISRVPEATMVSTYVE-IKKLFQTKEASKTGFNLEPKELKIVLDQIKRGKNIS 380

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 381 DDAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYAT 440

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP    IA+++ + ++
Sbjct: 441 WWIRQAISRAIADQARTIRIPIHMIETINRINKINRKYLQEEGKEPDVSIIAREVGLSID 500

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V++V+KITKEPISLE PIG ED    GDF+EDK  +SP++  ++ +L+E    VL  L 
Sbjct: 501 KVKQVIKITKEPISLEAPIGSEDDGKYGDFVEDKTTLSPMEQILKGDLKEQIDEVLDQLN 560

Query: 622 PREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL++++
Sbjct: 561 DREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYI 620

Query: 681 DG 682
           +G
Sbjct: 621 EG 622


>gi|78777303|ref|YP_393618.1| RNA polymerase sigma factor RpoD [Sulfurimonas denitrificans DSM
           1251]
 gi|78497843|gb|ABB44383.1| sigma 28 (Flagella/Sporulation) [Sulfurimonas denitrificans DSM
           1251]
          Length = 623

 Score =  291 bits (744), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 198/669 (29%), Positives = 337/669 (50%), Gaps = 56/669 (8%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +     + + +      + +   T E L       + ++ Q  +   ++      +    
Sbjct: 1   MTAKELNKAIETFFANQKPKECSTYESLIELF-DKQPTAAQAANIFKLIQKHKACIYTSS 59

Query: 82  DLEDEEGSEDSLD--------LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +       +++          + ++ ++S   L++ +      +D PVRMYLREMG I L
Sbjct: 60  EHAKLLNDKEAEARRSAQRKMIENNETDSFDILKEHELLEWSRSDSPVRMYLREMGQIPL 119

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L++E EI I+K+IE G ++++ ++C  P     ++ +R+ L +    ++E+         
Sbjct: 120 LTKEEEIEISKKIEGGESIIIDAICSVPYLIDFILDYREPLINRERRVKELFKSFEDEKD 179

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           ES        +     +     +     D    E    S   + K  +  +    + AEN
Sbjct: 180 ESDDSEDSDDDVEDSDEENVVEKTLTAKDKSRVEKVTISFKALEKAKKEWIKLAEKLAEN 239

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
            +  L  D      + +  +  L+ +++  L   +++  EL    + A+    DE    +
Sbjct: 240 TDAELTADLVMHYLSATYKKGVLKERLLD-LGPTSKLINELVKAMETALKS--DEGYDKE 296

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            K L+ KL     +L  N     +LV+++ D++K  +        +  +Y   +    + 
Sbjct: 297 LKRLEYKLPLFNATLKANHR---ILVDKICDLTKEDIATMVPEATMVSTYMEIK----KL 349

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
            Q +E   +                                       +   +   I+  
Sbjct: 350 VQTKEASKNSFD------------------------------------MDPEKLADILEQ 373

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++G+  + I+K +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  G
Sbjct: 374 IKRGKNISEISKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKG 433

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IA
Sbjct: 434 YKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKHLQEHGKEPDVEVIA 493

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            ++ + VE V+ V+KITKEPISLE PIG ED    GDFIEDK ++SP D+ ++ +LR   
Sbjct: 494 LEVGLSVEKVKNVIKITKEPISLEAPIGSEDDGRFGDFIEDKTSLSPSDAILKDDLRVQI 553

Query: 614 TRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             VL  L  RE+ V+++RFGI  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP  
Sbjct: 554 ESVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKV 613

Query: 673 SKKLRSFLD 681
            +KL+++++
Sbjct: 614 GRKLKNYIE 622


>gi|329910007|ref|ZP_08275189.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546317|gb|EGF31339.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 452

 Score =  290 bits (742), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 164/436 (37%), Positives = 257/436 (58%), Gaps = 8/436 (1%)

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            E+ E D       + DS    +A    L+   +   + I + +  +       V    D
Sbjct: 23  DESDEADTAADVLSQADSDMLSAAQLANLKRTSLARFETIGQQHARML------VAAAAD 76

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
                     +  +   +  +      +  L E L      +   E ++L L     G+ 
Sbjct: 77  GFHCSAYADAQAIISAEMLRMRFTAKMVQKLSESLRAQMSEMRGIEKQVLELVVNRGGMP 136

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           R +F+    G E+D  W+       +  +   +A ++ +I +++  + ++    G+ + +
Sbjct: 137 RSLFIATFPGNEIDLGWIDLVVAGQQA-YCVTLARQIPAIKELQTRLVALQERVGLPLPQ 195

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R +   +  GE  A  AK++M EANLRLV+S+AKKY NRG+QFLDLIQEGNIGL+KA +
Sbjct: 196 LRRVSKQMSTGELRARQAKRDMTEANLRLVVSIAKKYINRGMQFLDLIQEGNIGLLKAVD 255

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QA++R+IADQ+ TIR+PVHM + ++K+ R ARR+  +   E
Sbjct: 256 KFEYRRGYKFSTYATWWIRQAVSRAIADQARTIRVPVHMLETVNKLNRIARRILQETGVE 315

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
                +A  + +  + VR+++KI +EPIS+E+P+GD+  S LGDFI+D    +PL++A+ 
Sbjct: 316 ADLPTLALHMELTEQKVREIMKIAREPISMESPVGDDGDSQLGDFIQDSTTTAPLEAAVD 375

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A++R     VL +L PRE ++LRMR+G+   +DHTLEEVGKQF VTRERIRQIE+KA+ K
Sbjct: 376 ASMRTAIKEVLDALPPREAKILRMRYGLDTQSDHTLEEVGKQFEVTRERIRQIESKALVK 435

Query: 667 LKHPSRSKKLRSFLDG 682
           L+HPSR+ KL+ F++G
Sbjct: 436 LRHPSRADKLKIFVEG 451


>gi|163781693|ref|ZP_02176693.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882913|gb|EDP76417.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
          Length = 571

 Score =  290 bits (742), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 212/655 (32%), Positives = 323/655 (49%), Gaps = 92/655 (14%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            +S + ++++ +++G+VT +E+N  L  D VSS+  E+ +  L+N  I VV+ ++  +E+
Sbjct: 4   RESLRHLVEIGKEKGFVTYDEVNEVLEEDFVSSDSFEELIDTLANFNIQVVESEEDYEEK 63

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S D L +++ +            +      DPV++YL+EMG I LL+R+ EI  AK+IE
Sbjct: 64  DSLDELVVSTESF-----------TVMGRDGDPVKLYLKEMGKIPLLTRQQEIHYAKQIE 112

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            GR +M   L  S    + L+    +L +G   + +I+DL                    
Sbjct: 113 IGRKIMRRGLLRSSFLVEKLLQDWGKLCNGKLKIGDIMDL-------------------- 152

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                   ++   D  +E     E      +       +  E  E  ER + E   ++  
Sbjct: 153 ------IEEDPNSDCYEENCEKHEK--FFMEKGLELARAYKELLEARERYIKEGTPEAKR 204

Query: 268 TLSAMEDQLRPKV---MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                  Q+   V        +   V  E+  L    V   +D +S  +           
Sbjct: 205 EYLYKHAQMNRIVHQMRIKYSKFERVADEILKLYQRYVRKNRDYESRKRK---------- 254

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
              L      ID L+             + EL    +S G   D F         +    
Sbjct: 255 ---LQAIHPDIDELINNYLG--------DRELQEKVKSAGYSFDRF---------NSLVS 294

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
            Y            +  EV+ +   RNEI  I  E    +         V K +     +
Sbjct: 295 EYVS----------LKREVEKL---RNEIGVIPEEIKRVMGIIEQGRKKVVKAKQVMIQS 341

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
              +V +  +  ++    +       LDLIQEGNIGLMKA +K+D+  GYKFSTYA WW+
Sbjct: 342 NLRLVVSIAKKYVNRGLHF-------LDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWI 394

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+++++ ++R+  ++ REPTPEEIAK L M  + VR
Sbjct: 395 RQAITRAIADQARTIRIPVHMIETINRIIKASKRLFQELGREPTPEEIAKHLGMTPDKVR 454

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           KVL+  +EPISLETPIGD++ + L DFIEDK+  +P +   +  LRE   RVL +L+ +E
Sbjct: 455 KVLRSAQEPISLETPIGDDEDTFLKDFIEDKSVPNPEEYVSRKLLREQLERVLETLSDKE 514

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             +LR R+G+   T++TLE+VGK F VTRERIRQIE+KAIRKL+HPSR+K L+ F
Sbjct: 515 REILRYRYGLVDGTEYTLEQVGKMFNVTRERIRQIESKAIRKLRHPSRAKYLKDF 569


>gi|322379076|ref|ZP_08053479.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
 gi|322379940|ref|ZP_08054217.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321147638|gb|EFX42261.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321148568|gb|EFX43065.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
          Length = 634

 Score =  290 bits (741), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 209/690 (30%), Positives = 359/690 (52%), Gaps = 70/690 (10%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + K  N++ +   ++S  +   +F  +  +K+ +       V+ E +   +     +S Q
Sbjct: 1   MPKMENKNPNKATKNSISTKQ-NFPQEKLEKLFQEPHPT--VSYERIIDVIQKIPTTS-Q 56

Query: 63  MEDTVAMLSNMGINVVDGDD--------LEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           ++    +++     +V   +        LE +   + S  L      +  F+++++    
Sbjct: 57  LKKIKELVAKYHKTLVHSSEYAHTSLSSLEHKNSRKKSKVLEYDIEENLDFIKEKELPEW 116

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             +D PVRMYLREMG I LLS+E E+ ++K+I+ G  +++ ++C  P     +  +++ L
Sbjct: 117 SRSDSPVRMYLREMGEIPLLSKEEEVYLSKQIKLGENIILDAICSVPYLIDFIYNYKEAL 176

Query: 175 NDGTTLLREI---IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
            +    ++E+    D E  +  + +      +E     + + +S +K++  V+E     +
Sbjct: 177 INRERRVKELFRNFDNEGSMAKKDEDVEIEDSEEEDTPEIKRNSSDKDKKRVEEVLESFK 236

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
           +  K  K+    +++P          ++E ED   H L+                     
Sbjct: 237 ALNKAKKEWLKLLNTP----------VEEQEDPLLHALT--------------------- 265

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
                              + KC+VLKEKL  L  +  L    I+ LV+ +    K    
Sbjct: 266 ------------------LAYKCRVLKEKLYDLGPTSKL----INELVKAMETSLKSDDG 303

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E EL RL     +  +  +E H+    +   +S  +          +   ++ I K+  
Sbjct: 304 FEKELKRLEYKLSLFNESLIENHKNILKNITTMSREEIIAMMPEATMIGVYME-IKKLFQ 362

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
             ++      +  S+ + I+S +++G+  +  AK +M  +NLRLV+S+AK+YT+RGL FL
Sbjct: 363 TKEASKDGFNLEPSKLKEILSQIKRGKLISDRAKNKMARSNLRLVVSIAKRYTSRGLPFL 422

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF+    YKFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I++
Sbjct: 423 DLIQEGNIGLMKAVDKFEHEKNYKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINR 482

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  R+   +  +EP  + +AK++ +P++ VR V+KITKEPISLE+P+G++D    GDF
Sbjct: 483 INKVMRKYMQENGKEPDLDLVAKEVGLPLDKVRNVIKITKEPISLESPVGNDDDGKFGDF 542

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFC 650
           +EDKN V  ++  ++ +L+     VL  L  RE+ V+RMRFG+  +  D TLEE+GK+  
Sbjct: 543 VEDKNVVGSMEHIMREDLKAQIDGVLDQLNEREKSVIRMRFGLLEDESDRTLEEIGKELN 602

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VTRER+RQIE+ AI+KL+ P   + LRS+L
Sbjct: 603 VTRERVRQIESSAIKKLRSPQYGRLLRSYL 632


>gi|149921032|ref|ZP_01909492.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149818164|gb|EDM77620.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 547

 Score =  288 bits (737), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 213/561 (37%), Positives = 309/561 (55%), Gaps = 22/561 (3%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII-- 185
           MG+I LL+REGEI +AKRIEAG   ++  +  SP+    +    D +      +++    
Sbjct: 1   MGTISLLTREGEIEVAKRIEAGENKVIDIVLRSPIAIPYVFDLCDRVERSLVRVKDAFVI 60

Query: 186 ----DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
               D +     +   G     E    Q +    Q +E + ++E   ++++ A  + +  
Sbjct: 61  PAKNDEKRPGEADGPTGQEAAVENMKVQLKRLRKQHRELEKIEERVAELDAQATAASEAE 120

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                P     ++     E     A   +A      P    AL E               
Sbjct: 121 RPAAEPVALVVDNGDAPSEAASAGAAPAAAYAAPSTPPAEVALVE-------------GG 167

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
            +     +   K   L+E  V  +    L++  I+ + E+L +  + +     ELL   +
Sbjct: 168 KDDGARAELDKKHHELREATVGTMLDFRLSRKSIEEMSEELSETVETVRRALRELLDCER 227

Query: 362 SYGIKRDVFLERHQGRELDP-HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
             G+  D      +G  L         +      W+  +   +  +      I+ +  ET
Sbjct: 228 RAGVDLDELRSTFEGVRLREQEEFKLCRRLGLHPWE--LHELITRMKVATKRIRQVEQET 285

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+S      +   + K   E   AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 286 GVSADNLVALYDSLTKARREREAAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIG 345

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITR+I+DQ+ TIR+PVHM + I+K++RT R++ 
Sbjct: 346 LMKAVDKFEYQRGYKFSTYATWWIRQAITRAISDQARTIRVPVHMIESINKLIRTTRQLV 405

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  REPT +EIA+K+ MPVE VR +L+I KEPISLETP+G++  S LGD IEDKNA+ P
Sbjct: 406 QEFGREPTHQEIAEKMNMPVEKVRSILRIAKEPISLETPLGEDGDSSLGDLIEDKNALDP 465

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               ++ +L + T R LASLTPREE++LR+RFGIG  +DHTLEEVG+ F VTRERIRQIE
Sbjct: 466 GSGVVERHLGDETRRALASLTPREEKILRLRFGIGEASDHTLEEVGRDFSVTRERIRQIE 525

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+ KL+   R+K+LR F++
Sbjct: 526 AKALSKLRKADRAKQLREFVE 546


>gi|296272949|ref|YP_003655580.1| RpoD subfamily RNA polymerase sigma-70 factor subunit [Arcobacter
           nitrofigilis DSM 7299]
 gi|296097123|gb|ADG93073.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcobacter
           nitrofigilis DSM 7299]
          Length = 626

 Score =  288 bits (737), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 194/664 (29%), Positives = 339/664 (51%), Gaps = 53/664 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   +K+ K  +    +T E++    P    SS+ ++  +A++    +N++   +     
Sbjct: 7   NKEIEKLAKEYKDS-TLTFEKVIKLFPKAP-SSQNIKKLIALMQLYNVNMMTSQEQAKVM 64

Query: 88  GSEDSLDLASS--------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            + ++                +    L+ ++      +D PVRMYLREMG I LL++E E
Sbjct: 65  NAVEAKKREDQRNKMIDGGEDSVYDLLKNKELLEWSRSDSPVRMYLREMGQIPLLTKEEE 124

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I I+K+IE G  +++ ++C  P     ++ +++ L +    ++E+         ++    
Sbjct: 125 IEISKKIEMGEDIILDAICFVPYLVDFILEYKEPLVNRERKVKELFRNFDDEDNDNDSDD 184

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
               +  +    E    E+E                               +   ++ LD
Sbjct: 185 DDTEDTSNDDAEEVEETEEET------------------------------SGKKQKKLD 214

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           +  +        +E   +       D I    +E     +       +  ++ K +VLK+
Sbjct: 215 KRAETIIAAFKILEKAKK-------DWIKFQSKETAKSDEEFDVITFNLATAFKKQVLKQ 267

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            L+ L  +  L    I  +V+ +    K     + EL RL     +  D   + H+    
Sbjct: 268 ALIDLGPTSKL----ITEIVKAMETALKSDTGFDSELKRLEYKLPLFNDTLKKNHEKLLD 323

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +   +S  +          V+  ++ I K+    ++      +   E   ++  +++G+ 
Sbjct: 324 NIINLSKIQITAMVPEATMVSTYME-IKKLFQTAEASKGGFDLEPEELIDVLEQIKRGKK 382

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
               AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 383 ITDEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTY 442

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  +EIAK++ +P
Sbjct: 443 ATWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKGIQENGKEPNVDEIAKEVGLP 502

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ V++V+KITKEP+SLE PIG ++    GDF+ D  A +P+D+ ++ +L+    ++LA 
Sbjct: 503 VDKVKQVIKITKEPVSLEAPIGSDEDGKFGDFVPDDKAPTPVDNIMKEDLQNQIDQILAQ 562

Query: 620 LTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  RE+ V+RMRFG+  + +D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   K L++
Sbjct: 563 LNEREQAVVRMRFGLMDDASDRTLEEIGKELSVTRERVRQIESSAIKKLKHPKVGKNLKN 622

Query: 679 FLDG 682
           +++ 
Sbjct: 623 YVES 626


>gi|268680166|ref|YP_003304597.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
 gi|268618197|gb|ACZ12562.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
          Length = 617

 Score =  287 bits (734), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 198/655 (30%), Positives = 327/655 (49%), Gaps = 67/655 (10%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL---- 95
           ++ YVT E +         +   ++  + +L    + ++   ++      E++       
Sbjct: 18  EKSYVTYENVMELFVKPP-TPANVKKLMGLLEKYKVTLISSAEIAKLRNKEEAKKREEER 76

Query: 96  ----ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                 +  +      +++      +D PVRMYLREMG I LL++E EI I+K+IE G  
Sbjct: 77  QKLQDEALEDEFDLASEKELLEWSRSDSPVRMYLREMGQISLLTKEEEIDISKKIEFGED 136

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           +++ + C  P     ++ +++ L +    ++E+                 G E     + 
Sbjct: 137 IIIDAFCSVPYLIDFILDYKEALINRERRVKELFKTFEDDDDGDDDDSDDGEEFDEEGEE 196

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    +K+    ++     ++  K  KD       PPE   + E  ++ D          
Sbjct: 197 KRPLSKKDNSRTEKVIESFKALEKAKKDWMKSFARPPEENLDAEEMMNYDL--------- 247

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                                                  + K K+LK+ L+ L  +  L 
Sbjct: 248 -------------------------------------ALAYKKKLLKDALMDLGPTSKL- 269

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDPHWVSYAK 388
              I+ LV+ +    K     + EL RL     +  +   E HQ      +D +    A 
Sbjct: 270 ---INELVKSMETALKSDFEFDKELKRLEYRLPLFNETLKENHQNLLKNIIDLNKEDIAT 326

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             PE    +        I K+    ++      +   + + I+  +++G+  A  +K  M
Sbjct: 327 MVPEATMVSTYM----EIKKLFQTKEASKQGFDLDPEKLKEILEQIKRGKKIADESKTRM 382

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 383 AKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWWIRQAI 442

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IA ++ +  + V+ V+K
Sbjct: 443 SRAIADQARTIRIPIHMIETINRINKIIRKHLQEEGKEPDIETIALEVGLSADKVKNVIK 502

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           ITKEPISLE PIG+ED    GDF+EDK +++PL+  ++++L+E    VL  L  RE+ V+
Sbjct: 503 ITKEPISLEAPIGNEDDGKFGDFVEDKTSIAPLEHILKSDLKEQIDDVLDQLNDREKAVI 562

Query: 629 RMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++ 
Sbjct: 563 RMRFGLMHDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIES 617


>gi|157164653|ref|YP_001467098.1| RNA polymerase sigma factor RpoD [Campylobacter concisus 13826]
 gi|112799942|gb|EAT97286.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter concisus 13826]
          Length = 617

 Score =  287 bits (733), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 204/651 (31%), Positives = 333/651 (51%), Gaps = 62/651 (9%)

Query: 41  RGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDGDDL---EDEEGSEDSLDL 95
           +G++T E+L   L   P     +++E          I   +   L    D +  +++   
Sbjct: 20  KGFLTYEKLVKLLDKAPTATIVKKIEQLAKTNKVQLITSAEAAKLRNLADAKKRQENAQK 79

Query: 96  ASSASNSSVFLQKRKDS-ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           +    +  + L    D      +D PVRMYLREMG I LL+++ E+ I+KRIE G  +++
Sbjct: 80  SDQDIDEDLDLSSETDLLEWSRSDSPVRMYLREMGQIALLTKDEEVEISKRIELGEDIII 139

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
            + C  P     ++ +++ L +    ++E+                   +    +  E+ 
Sbjct: 140 DAFCSVPFLIDFILDYKEPLINRERRVKELFKSFEDESENENEDGEEDIDEEDEENEENE 199

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
           + +K   + +  E  IES                                          
Sbjct: 200 APKKSAKNDKRAEKVIES------------------------------------------ 217

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK--SSVKCKVLKEKLVKLVGSLSLNQ 332
                   AL++  + + +  + QD   +     K   + K K+LKEKL+ L  +  L  
Sbjct: 218 ------FKALEKAKKEWLKTANKQDKVESDDTASKMTLAFKKKILKEKLMDLGPTSKL-- 269

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I  +V+ +    K     + EL RL     +  D   + H+    D   +S  +    
Sbjct: 270 --ISEIVKSMETALKSDDEFDRELKRLEYRLPMFSDELKKNHKSILKDIIKLSKEEIAAR 327

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                 V+  V+ I K+    ++      +  +  + I+  +++G+  +  AK  M ++N
Sbjct: 328 VPEATMVSTYVE-IKKLFTTKEASKQGFDLEPARLKEILEQIKRGKKISDEAKARMAKSN 386

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+I
Sbjct: 387 LRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKGYKFSTYATWWIRQAISRAI 446

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIP+HM + I+++ +  R+   +  +EP    IAK++ + V+ V++V+KITKE
Sbjct: 447 ADQARTIRIPIHMIETINRINKINRKYLQEEGKEPDVSVIAKEVGLSVDKVKQVIKITKE 506

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLE PI +E+    GDF+EDK ++SP+D  ++++LRE    VL+ L  RE+ V+ MRF
Sbjct: 507 PISLEAPIANEEDGKFGDFVEDKTSLSPIDQILKSDLREQIDDVLSQLNEREKAVISMRF 566

Query: 633 GIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +  D TLEE+GK   VTRER+RQIE+ AI+KLKHP   +KL+++++G
Sbjct: 567 GLLEDESDRTLEEIGKALNVTRERVRQIESSAIKKLKHPKVGRKLKNYIEG 617


>gi|99035119|ref|ZP_01314904.1| hypothetical protein Wendoof_01000264 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 502

 Score =  286 bits (732), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 218/523 (41%), Positives = 313/523 (59%), Gaps = 33/523 (6%)

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRD+L++G  LLREIIDL+A    +        +E       +    E   +D +    D
Sbjct: 1   WRDDLSNGALLLREIIDLDAIYNSDFNVVPKEESEESEESAEDVEDSEDVSEDAEYCSDD 60

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
            + + K   +                 N D    +   ++  ME  L PKV+ ALDEI  
Sbjct: 61  KKDSKKSDDEKDGN-------------NEDISSVNLNVSILEMESDLLPKVIVALDEIIT 107

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           +  E   L+ N+ N       S + + L  ++  +   + L+ + +  + ++LY I++ I
Sbjct: 108 LTNEALILRKNSKNF------SNELENLYNQIWSIALQIKLSDAAVARITQELYKINRSI 161

Query: 350 MHNEGELLRLAQSYGIKRDVF-------LERHQGRELDPHWVSYAKDFPEGEWKN----F 398
              E  L+  A+ Y I R+ F       L +H+ +++    ++  +    GE KN    F
Sbjct: 162 TLEEANLIAEARKYDIDRESFYKVYDDVLLKHELKKISLLKINENQSSFTGELKNKFLRF 221

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + I    N IK        ++ EF+ ++  ++K E E S AK+EM++ANLRLV+S
Sbjct: 222 IDDNSEHIASTLNGIKQH--IQEDNVQEFKELIKRIQKHEREVSEAKQEMIKANLRLVVS 279

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY+ RGL  LDLIQEGNIGLMKA +KFD+  GYKFSTY  WWV+Q+ITR+I +QS  
Sbjct: 280 IAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKV 339

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +RIPVHM + I K+ R  R+M++++ REPT EE++ +L MP+E +RKV+KI ++P+SLE 
Sbjct: 340 VRIPVHMVEIISKINRALRKMTHEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEA 399

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN- 637
           P G +D+S  GD IEDK    P D+AI A+LR  TT VLA+LTP+EER+LRMRFG+G + 
Sbjct: 400 PTGKDDSSTFGDCIEDKRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDG 459

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR++KLR F 
Sbjct: 460 KEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRARKLRGFF 502


>gi|23008120|ref|ZP_00049697.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 307

 Score =  286 bits (731), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 223/305 (73%), Positives = 261/305 (85%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+W++         WKNFV      +  +R +I +++ ETG+ I E+R IV+MV+KG
Sbjct: 3   EDPPNWMTRVATLGGKGWKNFVERGGRQVADLREQILTLASETGLQIGEYRKIVAMVQKG 62

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E EA  AKKEM+EANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 63  EREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 122

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLA
Sbjct: 123 TYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLA 182

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP+E VRKVLKI KEPISLETPIGDE+ SHLGDFIEDKN V P+D+AIQ+NLRETTTRVL
Sbjct: 183 MPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVL 242

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLR
Sbjct: 243 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLR 302

Query: 678 SFLDG 682
           SFLD 
Sbjct: 303 SFLDN 307


>gi|325295045|ref|YP_004281559.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065493|gb|ADY73500.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 563

 Score =  285 bits (728), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 203/656 (30%), Positives = 326/656 (49%), Gaps = 94/656 (14%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
               +++++I L R +GY+T +EL   L  + ++ E +E+ +  L    I+++       
Sbjct: 1   MERPNFEEIIALGRDKGYITFDELMEHLDEEVLTPELIEELITQLDEFDIHII------- 53

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                          + S             +DDP+R+YLREM  I LL R  EIA+AKR
Sbjct: 54  -------PKEGEDHVDLSKLQITIAPDTMPRSDDPIRLYLREMSGISLLKRHEEIALAKR 106

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           +E GR  ++  L ++      ++   +++ +G   +R+I+                    
Sbjct: 107 VELGRKALLRYLLKTNAVLDYILNVEEKIKNGELKVRDIM-------------------- 146

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                       +  DD  E           +  +R K   P          L +  + +
Sbjct: 147 ------------RSPDDFAEGGEAQRKKKFFAMVERIKELLP------QFEKLQKQYNRN 188

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L     QL+ + +     I  + R+L               S    + + + + +  
Sbjct: 189 KKNL-----QLKREYLKTWARINFLLRQL-------------PLSYSIYETMADDIYRKY 230

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             L  ++  +  L  +L  +   I     +L        I R     ++  RE+      
Sbjct: 231 KILKKSEKNLQKLSGKLSFLGIPIEEICHKLDDDDIREKIDRS----KYTTREI------ 280

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
                     K  +   +D+    R  I S+     +  + F  +   +   + ++  AK
Sbjct: 281 ----------KKMIKKYLDTKETYRQVIDSLQ----MPRNTFYKLAERIYFYKKDSQEAK 326

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + +V +NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 327 QILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 386

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+KV++ +R+M  +  REP PEEIA++L MP   VR 
Sbjct: 387 QAITRAIADQARTIRIPVHMIETINKVIKASRQMFLEKGREPRPEEIAERLRMPASKVRS 446

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++++ +EP+SLETPIGD++ S LG+FIED  +  P    I+ +L+E  +++L++L+ RE 
Sbjct: 447 IIQLAQEPVSLETPIGDDEDSTLGNFIEDSKSPIPEHEVIKKDLQEKVSQLLSTLSEREA 506

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VL++RFG+    +HTLE+VG++  VTRERIRQIE+KA+RKLK+      L  FL+
Sbjct: 507 LVLKLRFGLDGYPEHTLEQVGRELKVTRERIRQIESKALRKLKNCGLDIDLSIFLE 562


>gi|152993293|ref|YP_001359014.1| RNA polymerase sigma factor RpoD [Sulfurovum sp. NBC37-1]
 gi|151425154|dbj|BAF72657.1| RNA polymerase sigma 70 factor [Sulfurovum sp. NBC37-1]
          Length = 612

 Score =  284 bits (727), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 202/662 (30%), Positives = 332/662 (50%), Gaps = 63/662 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD---- 82
           S  + + + K  ++   VT E +       +V++ Q +    +     +N++   +    
Sbjct: 6   SMKNVEALFKSKKKGDVVTFENIAKEFGK-QVTAAQAKKIHKLSEENKVNIISASEYASY 64

Query: 83  --LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
              ++++  ED+     S  +     ++++      +D PVRMYLREMG I LL++E E+
Sbjct: 65  LIAKEKKRREDARKKGGSEEDEFDLHKEKELLEWSRSDSPVRMYLREMGKIPLLTKEEEV 124

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            ++KRIE G  +++ ++C  P     ++ +++ L +    ++E+         +S     
Sbjct: 125 DLSKRIEEGEDIIIDAICSVPYLIGYILNYKEPLLNRERRVKELFKSFEDDKSDSDDDAA 184

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
            G +G            K    V++     +   K  K+                     
Sbjct: 185 EGEDGGDGTP-------KNDKRVKQVVESFKKLEKAKKEW-------------------- 217

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                                       +   +L    +   +  K     +K    KE+
Sbjct: 218 ---------------------------MKAREDLEKFMETETDPVKITHERLKIAFKKEQ 250

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L   +  L      I+ LV+ +    K     + EL RL     +  D   E HQ    +
Sbjct: 251 LKAALLDLGPTSKLINELVKAMETALKSDDSFDKELKRLEYKLPLFNDTLKENHQKILDN 310

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +              V+  V+ I K+    ++      +S  + + I+  +R+G+ +
Sbjct: 311 IINMDKEDIIDAVPETTMVSTYVE-IKKLFETREASKGGFDLSEEKLQAILEQIRQGKAK 369

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           + +AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 370 SEVAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYEKGYKFSTYA 429

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IAK++ + V
Sbjct: 430 TWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKHLQETGKEPDLETIAKEVGLTV 489

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V+ V+KITKEP+SLETP+GDED    GDFIEDK  +SP D+ ++ +L      VL  L
Sbjct: 490 DKVKNVIKITKEPVSLETPVGDEDDGRFGDFIEDKTTLSPTDAVLKDDLNNQIDEVLDQL 549

Query: 621 TPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++
Sbjct: 550 NEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNY 609

Query: 680 LD 681
           ++
Sbjct: 610 IE 611


>gi|34558185|ref|NP_908000.1| RNA polymerase sigma factor RpoD [Wolinella succinogenes DSM 1740]
 gi|34483904|emb|CAE10900.1| RNA POLYMERASE SIGMA FACTOR [Wolinella succinogenes]
          Length = 620

 Score =  284 bits (727), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 202/652 (30%), Positives = 340/652 (52%), Gaps = 60/652 (9%)

Query: 40  QRGYVTIEELNAFLP--PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD--- 94
           +  YV+ E++    P  P    ++++ +       M ++  +   L + E  +   D   
Sbjct: 18  EAKYVSYEKIVQTFPKPPTAAQAKKVHELSVKYDKMLLSASEVAKLLNREEEKKIEDEKK 77

Query: 95  --LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
             L     +   F+++R+      +D PVRMYLREMG I LL+++ EI ++K IE G  +
Sbjct: 78  RLLDEELEDEFDFMKERELLEWSRSDSPVRMYLREMGQIPLLTKDEEIELSKNIELGENI 137

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIID--LEACIGPESKGGFFHGTEGHSYQK 210
           ++ ++C  P     ++ +++ L +    ++E+     +   G E +            ++
Sbjct: 138 ILDAICSVPYLIDFILDYKEALINRERRVKELFKSFEDEEGGEEEEDEEVEEEADEEGEE 197

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            +    +K++  V++     ++  K  KD    ++      E  E               
Sbjct: 198 SKKPISKKDQKRVEKVLVSFKALEKAKKDWLKTLEGGAAQEEEGE--------------- 242

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                               + EL  L   A           K + LKE+L+ L  +  L
Sbjct: 243 --------------------FVELLHLLTLAY----------KKQTLKERLLDLGPTSKL 272

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
               I+ LV+ + +  +     + EL RL     +  +  LE HQ    +   +S     
Sbjct: 273 ----INELVKAMENTLRNDEGFDRELKRLEYKLPLFNETLLENHQKILENITEMSKNDIA 328

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
                   V+  ++ I K+    ++      +   + + I+  +++G+  A  AK +M +
Sbjct: 329 SAVPEATMVSTYME-IKKLFQTKQASEESFDLEPEKLKEILEQIKRGKDIADKAKTKMAK 387

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R
Sbjct: 388 SNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWWIRQAISR 447

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E I++++ +PV+ V+ V+KIT
Sbjct: 448 AIADQARTIRIPIHMIETINRINKIIRKYLQEEGKEPDVETISEEVGLPVDKVKNVIKIT 507

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           KEPISLE PIG ++    GDF+EDK++V P+D  ++ +L+     VL  L  RE+ V+RM
Sbjct: 508 KEPISLEAPIGSDEDGKFGDFVEDKSSVGPMDHILKEDLKTQIDEVLDQLNEREKAVIRM 567

Query: 631 RFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++
Sbjct: 568 RFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIE 619


>gi|32266044|ref|NP_860076.1| RNA polymerase sigma factor RpoD [Helicobacter hepaticus ATCC
           51449]
 gi|32262093|gb|AAP77142.1| RNA polymerase sigma 70 factor [Helicobacter hepaticus ATCC 51449]
          Length = 623

 Score =  284 bits (727), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 198/647 (30%), Positives = 341/647 (52%), Gaps = 62/647 (9%)

Query: 43  YVTIEELNAFL--PPDEVSSEQMEDTV-----AMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           Y+T E++   +   P     ++++D        +LS+  I  +     + +  ++    L
Sbjct: 30  YITYEKIAQIILKAPTAAQVKKIKDLSKKYKKQLLSSSEIAKMLNTQEQIKRQADKKKML 89

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                +   F++ ++      +D PVRMYLREMG I LL++E EI+++K+IE G   ++ 
Sbjct: 90  NEELEDEFDFMKDKELLEWSRSDSPVRMYLREMGQISLLTKEEEISLSKKIELGENTILD 149

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++C  P     +  ++D L +    ++E+         E++            +    S+
Sbjct: 150 AICSVPYLIDFIYDYKDALINRERRVKELFKSFDDEEEENEEEEEEFDMLDDEEASRKSN 209

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            +K++  +++     ++  K  K+    +++P                     +   ED+
Sbjct: 210 SKKDQKRIEKVMESFKALDKAKKEWLKVLETP---------------------IVEGEDE 248

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           L   ++                             S K  +LK KL+ L  +  L    I
Sbjct: 249 LAHILL----------------------------LSHKKHILKMKLLDLGPTSKL----I 276

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
             LV+ + +  K     E EL RL     +  D+ +E HQ    +   +S  +       
Sbjct: 277 GELVKAMENTLKSGDGFERELKRLEYKLPLFNDMLVENHQKILANITTMSRDEIAAMVPE 336

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              V+  V+ + K+    ++      +   + + I+  +++G+  +  AK +M ++NLRL
Sbjct: 337 TTMVSVYVE-LKKLFQTKEASEGGFNLEPEKLKEILEQIKRGKSISDKAKAKMAKSNLRL 395

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++QAI+R+IADQ
Sbjct: 396 VVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGFKFSTYATWWIRQAISRAIADQ 455

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIP+HM + I+++ +  R+   +  +EP  + IAK++ +P++ V+ V+KITKEP+S
Sbjct: 456 ARTIRIPIHMIETINRIHKIMRKHVQETGKEPDIDFIAKEVGLPIDKVKNVIKITKEPVS 515

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+ PIG +D    GDF+EDK++V P+D  ++ +L+     VL  L  RE+ V+RMRFG+ 
Sbjct: 516 LDAPIGSDDDGKFGDFVEDKSSVGPMDYILKEDLKVQIDEVLEQLNDREKAVIRMRFGLL 575

Query: 636 MNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++
Sbjct: 576 DDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIE 622


>gi|257458803|ref|ZP_05623926.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
 gi|257443791|gb|EEV18911.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
          Length = 626

 Score =  284 bits (725), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 198/651 (30%), Positives = 321/651 (49%), Gaps = 51/651 (7%)

Query: 40  QRGYVTIEELNAFL--PPDEVSSEQMEDT-----VAMLSNMGINVVDGDDLEDEEGSEDS 92
           Q+ Y+T E L  F    P   + +++E       V ++S   I+ +   +    + +   
Sbjct: 19  QKSYITYERLIKFFDKAPTATAVKKVEALTKKFDVELISAAEISKIKNLEDAKLKEATQK 78

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
             L              +      +D PVRMYLREMG I LL++E EI I+K+IE G  +
Sbjct: 79  KLLDEGWDEEFDLSSDVELLEWSRSDSPVRMYLREMGQIPLLTKEEEIEISKKIELGEDI 138

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           ++ + C  P     ++ +++ L +    ++E+         E +           Y   E
Sbjct: 139 IIDAFCSVPYLIDFILDYKEPLINRERRVKELFKSFDDSDEEGEEEDEEELPEDDYDDEE 198

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
           D     E    +  + D  +   +                                    
Sbjct: 199 DEESADEAKQRRSKKNDKRALKVIES---------------------------------- 224

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
                     AL++  + + +       A+   K   S +     K+ L + +  L    
Sbjct: 225 --------FKALEKAKKDWMKFAEKNAEAIKESKGILSKLNLAFKKKILKEKLMDLGPTS 276

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I  +V+ +    K     E EL RL     +      E H+    +   +S       
Sbjct: 277 KLITEIVKSMETALKSDEGFEKELKRLEYKLPMFSAELRENHKKILKEITKLSKDDIIAR 336

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                 V+  VD I K+    ++      +     + I+  +++G+  +  AK  M ++N
Sbjct: 337 VPEATMVSTYVD-IKKLFLTKEASKKSFNLEPERLKEILEQIKRGKRISDNAKARMAKSN 395

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+I
Sbjct: 396 LRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAISRAI 455

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIP+HM + I+++ +  R+   +  +EP    IA+++ + V+ V++V+KITKE
Sbjct: 456 ADQARTIRIPIHMIETINRINKITRKYMQEGGKEPDINVIAQEVGLSVDKVKQVIKITKE 515

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLE PIG+ED    GDF+EDK++VSP++  ++++L+E    +L  L  RE  V+RMRF
Sbjct: 516 PISLEAPIGNEDDGKFGDFVEDKSSVSPIEQILKSDLKEQIDDILEQLNDRERTVIRMRF 575

Query: 633 GIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +  D TLEE+GK+  +TRER+RQIE+ AI+KLKHP   +KL+++++ 
Sbjct: 576 GLLDDESDRTLEEIGKELNITRERVRQIESSAIKKLKHPKIGRKLKTYIES 626


>gi|154173683|ref|YP_001408074.1| RNA polymerase sigma factor RpoD [Campylobacter curvus 525.92]
 gi|112802903|gb|EAU00247.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter curvus 525.92]
          Length = 614

 Score =  284 bits (725), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 190/650 (29%), Positives = 331/650 (50%), Gaps = 63/650 (9%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           +G++T E+L   L     ++  ++    +     + ++   ++       D+     +  
Sbjct: 20  KGFLTYEKLVKLL-DKAPTATMIKKIEQLAKTHKVQLMTAAEIAKMRNIADAKKRLENTQ 78

Query: 101 NSSVFLQKRKDS-------ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
            + V +++  D            +D PVRMYLREMG I LL+++ E+ I+K+IE G  ++
Sbjct: 79  KTDVNIEEDLDLTSDNDFLEWSRSDSPVRMYLREMGQISLLTKDEEVEISKKIELGEDII 138

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + + C  P     ++ +++ L +    ++E+                +  +  +  +   
Sbjct: 139 IDAFCSVPFLIDFILDYKEPLINRERRVKELFKSFEDESESEDEDIENDEDEENEDEEAP 198

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
               K     ++     ++  K  K+                             L  + 
Sbjct: 199 KKSLKNDKRAEKVIESFKALEKAKKEW----------------------------LKTVN 230

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
            Q + +V   + ++   +++                     K+LK+KL+ L  +  L   
Sbjct: 231 KQEKVEVEDTMSKLTLAFKK---------------------KILKDKLMDLGPTSKL--- 266

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            I  +V+ +    K     + EL RL     +  D   + H+    D   ++  +     
Sbjct: 267 -ISEIVKSMETALKSDDEFDRELKRLEYRLPMFSDELKKNHKSILKDIIKLNKEEIAARV 325

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                V+  V+ I K+    ++      +  +  + I+  +++G+  +  AK  M ++NL
Sbjct: 326 PEATMVSTYVE-IKKLFTTKEASKQGFDLEPARLKEILEQIKRGKKISDEAKARMAKSNL 384

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+IA
Sbjct: 385 RLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKGYKFSTYATWWIRQAISRAIA 444

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIP+HM + I+++ +  R+   +  +EP    IAK++ + V+ V++V+KITKEP
Sbjct: 445 DQARTIRIPIHMIETINRINKINRKYLQEEGKEPDVSVIAKEVGLSVDKVKQVIKITKEP 504

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLE PI +E+    GDF+EDK+++SP++  ++ +LRE    VL+ L  RE+ V+ MRFG
Sbjct: 505 ISLEAPIANEEDGKFGDFVEDKSSLSPIEQILKGDLREQIDDVLSQLNDREKAVICMRFG 564

Query: 634 IGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +  D TLEE+GK   VTRER+RQIE+ AI+KLKHP   +KL+++++G
Sbjct: 565 LLEDESDRTLEEIGKALNVTRERVRQIESSAIKKLKHPKVGRKLKNYIEG 614


>gi|94986960|ref|YP_594893.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731209|emb|CAJ54571.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 590

 Score =  284 bits (725), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 200/511 (39%), Positives = 294/511 (57%), Gaps = 15/511 (2%)

Query: 183 EIIDLEACIGPESKG----GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           +++D E      S+       +    G       D      +      +  + +  +V  
Sbjct: 84  DLVDTEDVADFSSRSTDPVRMYLREMGAVPLLDRDGEVVIAKKVETGEQDVLYALVEVPV 143

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
                +    +   N  +  D  +       S  E   R +V+  L+EI +++++ R + 
Sbjct: 144 AVEELISVGEDLKLNRIKLKDVVKTIEEDDPSEDEMSQRNRVILLLEEIRQIFKKKRKVY 203

Query: 299 DNAVNGQKDEKS----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                    E+       +    KE++V  +  + L ++ ID ++E + D  +++ + + 
Sbjct: 204 LKLDECCTLERRVAGIQKEILQFKEEIVTRLRDIKLEKTLIDRIIETVEDYVRQMHNCQR 263

Query: 355 ELLRLAQSYGIKRDVFLERHQ---GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           EL     S G  +D   +       REL P   +   +    E  ++    +  I  ++ 
Sbjct: 264 ELSAYLLSTGKTQDEIKDLFTKLDARELSPRDAALLLNMGVDELFSYKEMILGKIEILQR 323

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
               +  +   ++ +   ++  +++G   A  AK+E++ +NLRLV+S+AKKYTNRGLQFL
Sbjct: 324 ----LQEKCCHNVVDLEEVLWRIKRGNNAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFL 379

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 380 DLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINK 439

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           ++RT+R +  +  R+PTPEEIA+++  P++ V+KVLKI KEPISLETPIGDE+ S LGDF
Sbjct: 440 LIRTSRYLVQEFGRDPTPEEIAERMDYPLDKVKKVLKIAKEPISLETPIGDEEDSSLGDF 499

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IEDK AV+P +  +   L E    VLA LTPREE+VLR RFGIG  +DHTLEEVGK F V
Sbjct: 500 IEDKKAVAPSEEVVNTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNV 559

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEAKA+RKL+HP RS+ LRSF D 
Sbjct: 560 TRERIRQIEAKALRKLRHPVRSQVLRSFYDS 590



 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 46/170 (27%), Positives = 84/170 (49%), Gaps = 1/170 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD-DLEDEE 87
              + +I   +  G+VT EE+N  +P D  + EQ E+ + +   + I +VD + + +   
Sbjct: 9   QQIRTLIAKGKAAGFVTFEEVNKAVPIDMNTPEQFEEIIGIFDQLEIVIVDSEKEGKKIT 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    D  +S +   +   +        + DPVRMYLREMG++ LL R+GE+ IAK++E
Sbjct: 69  VTSPETDGDTSENCFDLVDTEDVADFSSRSTDPVRMYLREMGAVPLLDRDGEVVIAKKVE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            G   ++ +L E P+  + LI   ++L      L++++       P    
Sbjct: 129 TGEQDVLYALVEVPVAVEELISVGEDLKLNRIKLKDVVKTIEEDDPSEDE 178


>gi|220904357|ref|YP_002479669.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219868656|gb|ACL48991.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 589

 Score =  284 bits (725), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 220/661 (33%), Positives = 333/661 (50%), Gaps = 86/661 (13%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              + +I   +  G++T EE+N  LP +  + EQ E+         I + +  ++     
Sbjct: 8   QQIQSLIAKGKGAGFLTFEEVNKALPVEMSTPEQFEEI--------IGIFEQLEI----- 54

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                 +   +      +      +D    D          S++L   E     + R   
Sbjct: 55  ------VIVDSEKDGKKISATASESDEEITD---------SSLDLSEDEDTADYSSRSTD 99

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
              M +  +   PL  +                    D E  I  + + G          
Sbjct: 100 PVRMYLREMGAVPLLDR--------------------DGEVVIAKKIEMGEQDVLYALVE 139

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
                       +D+++    ++   K  ++D    D                       
Sbjct: 140 VPVAVEELINVGEDLRQNRIKLKDVVKTIEEDDPSED----------------------- 176

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV----LKEKLVKL 324
               E   R +V+  LDEI + +++ R +          ++     +      KE++V  
Sbjct: 177 ----EMNQRSRVILLLDEIKQTFKKKRKIYKKLDVCTCMDRRVTAVQKEIICFKEEIVTR 232

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDP 381
           +  + L ++ ID ++E + D  +++ + + +L     + G  +        G   RE++P
Sbjct: 233 LRDIKLEKTLIDRIIETVEDYVRQMHNCQRDLSAYILATGRTQAEIQAMFDGLEQREINP 292

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              +        E  +F    +  I +I N ++        ++++   ++  +++G   A
Sbjct: 293 MDAARDLKLSVDELFSFKEMIIGKI-EILNRLQEKCCH---NVTDLEEVLWRIKRGNTAA 348

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 349 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 408

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  PVE
Sbjct: 409 WWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYPVE 468

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P +  I   L E    VLA LT
Sbjct: 469 KVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEVINTKLSEQLAAVLADLT 528

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PREE+VLR RFGI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ +
Sbjct: 529 PREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQPLRSYYE 588

Query: 682 G 682
            
Sbjct: 589 N 589


>gi|9082209|gb|AAF82776.1|AF273254_1 RNA polymerase sigma factor [Coxiella burnetii]
          Length = 410

 Score =  283 bits (723), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 186/395 (47%), Positives = 249/395 (63%), Gaps = 3/395 (0%)

Query: 289 EVYRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           +   EL+ L     N  K   K +      ++ L +L  +  L+  + + L  QL  + +
Sbjct: 14  QHMEELKKLYGRYQNAIKRYGKKAPATLKHQKALAELFSTFKLSIKQFNRLTGQLRRMLR 73

Query: 348 RIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
                E  ++          R  F+      E +  W+   K+  + + K  +      I
Sbjct: 74  AARAQERLIMSYCVVKAKTPRKKFIASFPHNETNMKWLEQYKNENKEQAKR-LEKYSKEI 132

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            + +  +  +  +  ++I E + I   V  GE ++  AKKEM+EANLRLVIS+AKKYTNR
Sbjct: 133 YRAQRNLAQLEEQNNLNIQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNR 192

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 193 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 252

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R++  +   E TPEE+ +++ MP E VRKVLKI KEPIS+ETPIG+++ S
Sbjct: 253 ETINKLNRISRQILQETGIEATPEELGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDS 312

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +LGDFIED N  SP+D A  A L E T R      P   +VLRMRFGI MNTDHTLEEVG
Sbjct: 313 NLGDFIEDINMESPVDFATSAGLMEATRRNFVYAYPARSQVLRMRFGIDMNTDHTLEEVG 372

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               VTRERIRQIEAKA+RKL+HPSR++KL SF++
Sbjct: 373 NNSDVTRERIRQIEAKALRKLRHPSRAEKLHSFIE 407


>gi|291277050|ref|YP_003516822.1| RNA polymerase sigma-70 factor [Helicobacter mustelae 12198]
 gi|290964244|emb|CBG40093.1| RNA polymerase sigma factor (sigma-70) [Helicobacter mustelae
           12198]
          Length = 614

 Score =  283 bits (723), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 197/651 (30%), Positives = 332/651 (50%), Gaps = 64/651 (9%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD----- 94
           ++ +++ E++   L     S+ Q++    +     + +V   +L     ++D +      
Sbjct: 18  EKDFLSFEKIAEILQKMPTSA-QVKKIRELCQKHQVTLVSSSELAKTLNTKDKIKQAEER 76

Query: 95  ---LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
              L    S+    +++R       +D PVRMYLREMG IELL++E E+ ++++I+ G  
Sbjct: 77  KKILNEELSDEFDLMKERDLLEWSRSDSPVRMYLREMGQIELLTKEDEVELSRQIKLGEN 136

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           +++ ++C  P     +  +R+ L +    ++E+         ES        E    ++ 
Sbjct: 137 IILDAICSVPYLIDFIYDYREALINRERRVKELFKSFDD-SEESGDEDLEEEEEGDEEEG 195

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    +K++   ++      +     KD  +                             
Sbjct: 196 KKPISKKDQKRAEKVLKSFRALDTARKDWLN----------------------------- 226

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                              + E  +L+ +          + K +VLKEKL+ L  +  L 
Sbjct: 227 -------------------FLEKGALEQHEDEWMFILGLAHKQQVLKEKLLDLGPTSKL- 266

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
              I  LV+ + +  K     E EL RL     +  +  ++ HQ    +   +S      
Sbjct: 267 ---ITELVKAMENTLKSDDGFERELKRLEYRLPLFNEHLIQNHQNILANITTMSREDILA 323

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
                  V   +D I K+    ++      +   + + I+  +++G+  +  AK +M ++
Sbjct: 324 AVPEATMVNIYMD-IKKLFQTKEASEEGFDLDPEKLKEILEQIKRGKIISDKAKNKMAKS 382

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KFD+   +KFSTYA WW++QAI+R+
Sbjct: 383 NLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFDYKRNFKFSTYATWWIRQAISRA 442

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IA+K+ + V+ V+ V+KITK
Sbjct: 443 IADQARTIRIPIHMIETINRIHKIMRKYIQETGKEPDVEIIAEKVGLSVDKVKHVIKITK 502

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EP+SLE PIG ++    GDF+EDKN+ + +D  ++ +LR     VL  L  RE+ V+RMR
Sbjct: 503 EPVSLEAPIGSDEDGKFGDFVEDKNSTNTMDQIMKEDLRAQIFEVLDQLNEREQAVIRMR 562

Query: 632 FGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KLR++++
Sbjct: 563 FGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLRNYIE 613


>gi|255322395|ref|ZP_05363541.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
 gi|255300768|gb|EET80039.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
          Length = 627

 Score =  282 bits (722), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 203/650 (31%), Positives = 338/650 (52%), Gaps = 51/650 (7%)

Query: 41  RGYVTIEELNAFLPP-------DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +GY+T E+L  FL          ++ S   E+ V ++++  I  +   +   +   E + 
Sbjct: 21  KGYITYEKLVKFLDKAPTAAIAKKIESLAKENKVQLITSAEIAKMRNIEDAKKRREELAK 80

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
               +         +        +D PVRMYLREMG I LL++E E+ I+K+IE G  ++
Sbjct: 81  LADDNLEEEFDLASETDLLEWSRSDSPVRMYLREMGQIALLTKEEEVEISKKIELGEDII 140

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + + C  P     ++ +++ L +    ++E+       G E         E    +   +
Sbjct: 141 IDAFCSVPYLIDFILDYKEPLINRERRVKELFRSFDDEGEEGSEEVEEEEENEEVEDDVE 200

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
             +EKE    +  + D + A KV +  ++   +  E  +   +  + + +D         
Sbjct: 201 EGEEKEAKPKKHNKKDDKRAEKVIESFKALEKAKKEWLKTANKQNEVETED--------- 251

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                     L +I   +++                     K+LK+KL+ L  +  L   
Sbjct: 252 --------EFLAKITLAFKK---------------------KILKDKLMDLGPTSKL--- 279

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            I  +V+ +    K     + EL RL     +  D   + H+    D   +S        
Sbjct: 280 -ITEIVKSMETALKSDDEFDRELKRLEYKLPMFSDELKKNHKSILKDIIKLSKEDIIARV 338

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                V+  V+ I K+    ++      +     + I+  +++G+  +  AK  M ++NL
Sbjct: 339 PEATMVSTYVE-IKKLFATKEASKSGFNLDPILLKEILEQIKRGKKISDEAKARMAKSNL 397

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+IA
Sbjct: 398 RLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWWIRQAISRAIA 457

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIP+HM + I+++ +  R+   +  +EP    IA ++ +  + +++V+KITKEP
Sbjct: 458 DQARTIRIPIHMIETINRINKINRKYLQEEGKEPDINVIAAEVGLSADKIKQVIKITKEP 517

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLE PIG+ED    GDF+ED++++SP+D  ++ +L+E    VL  L  RE+ V+RMRFG
Sbjct: 518 ISLEAPIGNEDDGKFGDFVEDRSSLSPMDHILKNDLKEQIDEVLDQLNEREKAVIRMRFG 577

Query: 634 IGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++G
Sbjct: 578 LLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIEG 627


>gi|254457867|ref|ZP_05071294.1| sigma 28 [Campylobacterales bacterium GD 1]
 gi|207085260|gb|EDZ62545.1| sigma 28 [Campylobacterales bacterium GD 1]
          Length = 623

 Score =  282 bits (722), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 195/646 (30%), Positives = 337/646 (52%), Gaps = 56/646 (8%)

Query: 45  TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD--------LA 96
           T E L       + ++ Q +    ++      +    +   +   +++          LA
Sbjct: 24  TYEALIELF-DKQPTAAQAKTIHKLMIKHKTCLYTASEHAKKLNDKEAEARKDAQRKMLA 82

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           ++ S++   L++ +      +D PVRMYLREMG I LL++E EI I+K+IE G ++++ +
Sbjct: 83  NNESDNFDILKEHELLEWSRSDSPVRMYLREMGQIPLLTKEEEIEISKKIEGGESIIIDA 142

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
           +C  P   + ++ +R+ L +    ++E+         +S+      ++       E+ ++
Sbjct: 143 ICSVPYLIRFILDYREPLINRERRVKELFKSFEDEKEDSEDDSDSDSDTAIEISDEEETK 202

Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
                D    E    S   + K  +  +    +  E+ +  +  D       ++  +  L
Sbjct: 203 TLTAKDKSRVEKVTLSFKALEKAKKEWIKLAEKIPEDIDGEITSDIVQYFLNVTFKKSVL 262

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           + +++  L   +++  EL    + A+    D+    + K L+ KL     +L  N     
Sbjct: 263 KDRLLD-LGPTSKLINELVKAMETALKS--DDGYDKELKRLEYKLPLFNSTLKANHRV-- 317

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            LV ++ +++K  + +      +  +Y        +  Q +E   +              
Sbjct: 318 -LVGKICELTKEDISSMVPEATMVSTYM----EIKKLVQTKEASKNSFD----------- 361

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
                                    +   +   I+  +++G+  + I+K +M ++NLRLV
Sbjct: 362 -------------------------MEPEKLLDILEQIKRGKNISEISKTKMAKSNLRLV 396

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+IADQ+
Sbjct: 397 VSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWWIRQAISRAIADQA 456

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIP+HM + I+++ +  R+   +  +EP  E IA ++ + VE V+ V+KITKEPISL
Sbjct: 457 RTIRIPIHMIETINRINKIMRKHLQEHGKEPDVEVIALEVGLSVEKVKNVIKITKEPISL 516

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           E PIG+ED    GDFIEDK+++SP D+ ++ +LR     VL  L  RE+ V+++RFGI  
Sbjct: 517 EAPIGNEDDGRFGDFIEDKSSISPSDAILKDDLRVQIEGVLEQLNEREKAVIKLRFGIMD 576

Query: 637 NT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +  D TLEE+G++  VTRER+RQIE+ AI+KLKHP   +KL+S+++
Sbjct: 577 DESDRTLEEIGRELNVTRERVRQIESSAIKKLKHPKVGRKLKSYIE 622


>gi|237751866|ref|ZP_04582346.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376742|gb|EEO26833.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 615

 Score =  281 bits (718), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 202/660 (30%), Positives = 342/660 (51%), Gaps = 59/660 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP--PDEVSSEQMEDTVAMLSNMGINVVD-----G 80
           +    ++ K A +  YV+ E++   L   P    ++++ +         +   +      
Sbjct: 7   NQQLDELFKNATK--YVSYEKIAQVLVKLPTAAQAKKVSELAKKYKKQLMAASEVAKILN 64

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D   +   +    L     +   F+++R+      +D PVRMYLREMG I LL+R+ EI
Sbjct: 65  QDDARKIKEDKKRLLDEELEDEFDFMKERELLEWSRSDSPVRMYLREMGQIPLLTRDEEI 124

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            ++K IE G  +++ ++C  P     ++ +++ L +    ++E+         + +    
Sbjct: 125 ELSKNIELGENIILDAICSVPYLIDFILDYKEALINRERRVKELFKSFDDEEDKEEESEE 184

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E    +  E+ S++      Q+    +  + K  +                      
Sbjct: 185 VDEENEEIETEEEDSKKPISKKDQKRVEKVLVSFKALEK--------------------- 223

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                     A +D L+   +   DE ++    L +L             + K + LKEK
Sbjct: 224 ----------AKKDWLKTWELENGDETSKDMLYLLTL-------------AHKKQFLKEK 260

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L+ L  +  L    I+ LV+ + +  K     + EL RL     +  D+ LE H+    +
Sbjct: 261 LLDLGPTSKL----INELVKAMENTIKSDEGFDKELKRLEYRLPLFNDMLLENHKKILEN 316

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              ++  +          V+  ++ I K+     +      +   + + I+  +++G+  
Sbjct: 317 ITEMNKTEITAAVPEATMVSTYME-IKKLFQTKAASEGSFDLEPEKLKQILEQIKRGKDI 375

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GY+FSTYA
Sbjct: 376 ADKAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYRFSTYA 435

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E+IA+++ +P+
Sbjct: 436 TWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKCLQEEGKEPDLEKIAEEVGLPL 495

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V+ V+KITKEPISLE PIG+ +    GDF+EDK+AV P+D  ++ +L+     VL  L
Sbjct: 496 DKVKNVIKITKEPISLEAPIGNGEDGKFGDFVEDKSAVGPMDHILKEDLKSQIDDVLDQL 555

Query: 621 TPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++
Sbjct: 556 NEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNY 615


>gi|78357095|ref|YP_388544.1| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
 gi|78219500|gb|ABB38849.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 589

 Score =  281 bits (718), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 214/590 (36%), Positives = 325/590 (55%), Gaps = 38/590 (6%)

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN----DGTTLL 181
           +E+  I+ L  +G++A     E      + +   +P   + +I   D+L+    D     
Sbjct: 5   KEIQQIKTLIAKGKVAGFLTFEE-VNKALPAEVNTPEQIEEIIGIFDQLDIAIVDSEKDG 63

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK--------------ERDDVQETE 227
           ++I    A    E   G    T+          S +               +RD      
Sbjct: 64  KKISVSPAEADDEGGDGGLELTDEDDPADYSSRSTDPVRMYLREMGAVPLLDRDGEVNIA 123

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL--------RPK 279
             IE+  +       +V    E   +   +L E+       +  +E+          R +
Sbjct: 124 KKIETGEQDVLYALVEVPIAVEELISVGEDLKENRIKLKDVVKTIEEDDPSEDEMNQRQR 183

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVKLVGSLSLNQSRI 335
           V+  LDEI   +++ R +          E+       +    KE++V  +  + L ++ I
Sbjct: 184 VILLLDEIQSTFKKKRKVYQRLDECCTLERRVYGIQKEIIAYKEEIVSRLRDIKLEKTLI 243

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ---GRELDPHWVSYAKDFPE 392
           D ++E + D  +++ + + +L     S G  +    E  +    RE++P   + + +   
Sbjct: 244 DRIIETVEDYVRQMHNCQRDLSAYILSTGKTQTEMRELFRQLDDREINPVVAADSLNLTV 303

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E  +F    +   ++I N ++        ++++   ++  +++G   A  AK+E++ +N
Sbjct: 304 EELFSFKEMIMGK-MEILNRLQEKCCH---NVTDLEEVLWRIKRGNSHAMRAKQELIRSN 359

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I
Sbjct: 360 LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI 419

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K++RT+R +  ++ R+PTPEEIA+++  P++ V+KVLKI KE
Sbjct: 420 ADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYPIDKVKKVLKIAKE 479

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIGDE+ S LGDFIEDK AV+P +  +   L E    VLA LTPREE+VLR RF
Sbjct: 480 PISLETPIGDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQIAAVLADLTPREEQVLRKRF 539

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI   +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LRS+ + 
Sbjct: 540 GINEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQTLRSYYES 589



 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 48/170 (28%), Positives = 83/170 (48%), Gaps = 1/170 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD-DLEDEE 87
              K +I   +  G++T EE+N  LP +  + EQ+E+ + +   + I +VD + D +   
Sbjct: 8   QQIKTLIAKGKVAGFLTFEEVNKALPAEVNTPEQIEEIIGIFDQLDIAIVDSEKDGKKIS 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S    D         +  +         + DPVRMYLREMG++ LL R+GE+ IAK+IE
Sbjct: 68  VSPAEADDEGGDGGLELTDEDDPADYSSRSTDPVRMYLREMGAVPLLDRDGEVNIAKKIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            G   ++ +L E P+  + LI   ++L +    L++++       P    
Sbjct: 128 TGEQDVLYALVEVPIAVEELISVGEDLKENRIKLKDVVKTIEEDDPSEDE 177


>gi|296532040|ref|ZP_06894819.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
 gi|296267655|gb|EFH13501.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
          Length = 640

 Score =  281 bits (718), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 219/571 (38%), Positives = 299/571 (52%), Gaps = 63/571 (11%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           +++   +DDPVRM+LREM   +LLSRE EIA+A+RIEAGR  M+A LCESP+TF  +  W
Sbjct: 131 EASLARSDDPVRMFLREMSGTDLLSREEEIALAQRIEAGRDAMLAGLCESPVTFTHIAAW 190

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           +  L  G   LR++++LEA     +             +         +     E     
Sbjct: 191 KAALEQGQMPLRDVVELEAMAADAAAPAAAGVETEEPEEGEVVPHATLDEKMKPEVLAAF 250

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
            +A +     R+        A    R        +     A  D L  +V      +  +
Sbjct: 251 GAALEAHAALRAL--PVRSEAAQARRQEMVGLFGALRLRPARLDMLVGEVRDIQRRLLAL 308

Query: 291 YRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             +   L   A    +   +         + LV+    +  + +R    V  L D   +I
Sbjct: 309 DGKALRLAVAARVEHEVVLRLWDGSDAAVQALVEAAQKVRSSAARHAQAVRDLRDTLPQI 368

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
                 ++ L QS G+                                            
Sbjct: 369 RA---AIVMLEQSSGLP------------------------------------------- 382

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             E++ +  E G    + R               AK+E+  ANLRLV+ +AK+Y NRGL 
Sbjct: 383 AAELRRVCAEVGRGERDMRK--------------AKEELTRANLRLVVHIAKRYRNRGLM 428

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           F DLIQEGNIGLM+A +KFDW  G+KF+TYA WWV+QAITRS+ADQ+ TIR+PVHM + +
Sbjct: 429 FGDLIQEGNIGLMRAVDKFDWRRGFKFATYATWWVRQAITRSLADQARTIRVPVHMTETV 488

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            KV R +RR + K  REPTPEE+A +L M V+ VR V ++ +EP+SLE PIG++D   LG
Sbjct: 489 GKVARMSRRFAQKAGREPTPEELAGELGMSVDKVRAVQRLAREPVSLENPIGEDDDGRLG 548

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIED+NAV P D+A ++ +R+ T R+L+ LTPREER+LRMRFGIG   DHTLEEVGK F
Sbjct: 549 DFIEDENAVMPFDAASRSAMRDATMRILSDLTPREERILRMRFGIGGENDHTLEEVGKTF 608

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            VTRERIRQIEAKA++KL+   R K LRSFL
Sbjct: 609 NVTRERIRQIEAKALKKLQVSKRGKSLRSFL 639


>gi|171320298|ref|ZP_02909351.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171094445|gb|EDT39506.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 338

 Score =  279 bits (714), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 181/338 (53%), Positives = 238/338 (70%), Gaps = 2/338 (0%)

Query: 346 SKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
              +   E ++L +     G+ R  F+ R  G E D  W           +   ++  + 
Sbjct: 1   MDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHS-YSAVLSRNIP 59

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVIS+AKKYT
Sbjct: 60  AIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYT 119

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVH
Sbjct: 120 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 179

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D
Sbjct: 180 MIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDD 239

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+TDHTLEE
Sbjct: 240 DSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEE 299

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           VGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 300 VGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 337


>gi|152990473|ref|YP_001356195.1| RNA polymerase sigma factor RpoD [Nitratiruptor sp. SB155-2]
 gi|151422334|dbj|BAF69838.1| RNA polymerase sigma 70 factor [Nitratiruptor sp. SB155-2]
          Length = 608

 Score =  279 bits (713), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 195/651 (29%), Positives = 341/651 (52%), Gaps = 70/651 (10%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED--------EEGSED 91
           ++GYVT E+L  F    + +  Q +  + +     ++++   +           ++  E 
Sbjct: 18  EKGYVTYEQLVDFF-DRQPTLAQAKKILVLQKKYKVDIITSGEAAKRLNIEEKEKKEEER 76

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                   +      + ++      +D PVRMYLREMG I LL++E EI ++K+IE G  
Sbjct: 77  KKLSEEELAEEFDLTKDKELLEWSRSDSPVRMYLREMGQIPLLTKEEEIELSKKIELGEN 136

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           +++ ++C  P     ++ +++ L +    ++E   L      E +       +  + +K 
Sbjct: 137 IILDAICSVPYLIDFILDYKEPLINRERRVKE---LFKSFEDEEEVEEDEHLDKEAKKKA 193

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           + S +EK+  ++ +     +     ++D     D+ PE   + E             ++ 
Sbjct: 194 KYSKREKKIIELFKALEKAKKEWLKARDKELPEDATPEQKFHHE-----------LVVAF 242

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
            + Q++ +++  L   +++  EL    + A+    DE    + K L+ KL          
Sbjct: 243 KKKQMKERLLE-LGPTSKLINELVKSMETALKS--DEGFEKELKKLEYKLPLFN------ 293

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                   EQL +  ++++     L +   +  +     +  +    +D   +  AK+  
Sbjct: 294 --------EQLRENHRKLLSEITHLSKEEIAARVPEATMVSTY----MDIKKLFQAKEAS 341

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  +                          +   +   I+  +++G+  +  AK  M ++
Sbjct: 342 KKGF-------------------------NLDPEQLAEILEQIKRGKKISEEAKTRMAKS 376

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+
Sbjct: 377 NLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWWIRQAISRA 436

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IA+++ MPVE V+ V+KITK
Sbjct: 437 IADQARTIRIPIHMIETINRINKIVRKHLQETGKEPDVETIAEEVGMPVEKVKNVIKITK 496

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EP+SLE PIG+E+    GDFIEDKNA +PL+  ++ +++     +L +L  RE+ V+RMR
Sbjct: 497 EPVSLEAPIGNEEDGKFGDFIEDKNAPNPLEVIMKEDMKSKIEEILENLNEREKAVVRMR 556

Query: 632 FGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +K++++++
Sbjct: 557 FGLMPDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKIKNYIE 607


>gi|319957164|ref|YP_004168427.1| RNA polymerase, sigma 70 subunit, rpod [Nitratifractor salsuginis
           DSM 16511]
 gi|319419568|gb|ADV46678.1| RNA polymerase, sigma 70 subunit, RpoD [Nitratifractor salsuginis
           DSM 16511]
          Length = 618

 Score =  278 bits (711), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 213/662 (32%), Positives = 331/662 (50%), Gaps = 66/662 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD------ 82
            + + +    ++   VT E L         ++ Q      M    GI VV   +      
Sbjct: 13  KTLEALFDKTKKGELVTFENLAKEF-DKAPTAAQARKIKKMADEKGIKVVSASEYAKHLT 71

Query: 83  -LEDEEGSEDSLDLASSASNSSVFLQKRKDS-ADRSTDDPVRMYLREMGSIELLSREGEI 140
            +E +E  E    L+         + K K+      +D PVRMYLREMG I LL++E EI
Sbjct: 72  EVEAKERKERLKRLSEGEVEEEFDITKEKELMEWSRSDSPVRMYLREMGKIPLLTKEEEI 131

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            ++K+IE G  +++ ++C  P     ++ +++ L +    ++E+                
Sbjct: 132 ELSKQIEEGEDIIIDAICSVPYLIDYILNYKEPLLNRERRVKEL------FKSFEDSSSD 185

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              EG      +    +K    V E+   +E A K    +R+K+    E  E DE  +  
Sbjct: 186 DEDEGLDEAAGKAKKADKRVKQVVESFKALEKAKKDWLKERNKLLKLQEEGEADEETI-- 243

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                                                        +  K + +   LKE 
Sbjct: 244 -------------------------------------------FHERLKVAFRKHQLKEA 260

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L+ L  +  L    I+ LV+ +    K     E EL RL     +  D   E H+    +
Sbjct: 261 LINLGPTSKL----INELVKAMETALKSDDGFEKELKRLEYRLQLFNDQLRENHRKILEN 316

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +S  +          V+  V  I K+    ++      +   +   I+  +R G+ +
Sbjct: 317 IVNMSKEEIAAAVPETTMVSTYV-QIKKLFETREASKNSFDLPPEKLEEILEQIRIGKAK 375

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 376 SEKAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYA 435

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E IA+++ + V
Sbjct: 436 TWWIRQAISRAIADQARTIRIPIHMIETINRINKIIRKHLQETGKEPDLETIAEEVGLSV 495

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V+ V+KITKEP+SLETP+GDED    GDFIEDKN++SP ++ +  +L +    VL  L
Sbjct: 496 DKVKNVIKITKEPVSLETPVGDEDDGRFGDFIEDKNSISPTEAVLNDDLNQQIDEVLGQL 555

Query: 621 TPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             RE+ V+RMRFG +   +D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++
Sbjct: 556 NEREQAVIRMRFGLLEDMSDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNY 615

Query: 680 LD 681
           ++
Sbjct: 616 IE 617


>gi|153952229|ref|YP_001397920.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
 gi|152939675|gb|ABS44416.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
          Length = 622

 Score =  278 bits (710), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 205/651 (31%), Positives = 339/651 (52%), Gaps = 58/651 (8%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA- 99
           + Y+T E+L  +L   + S+   +   A++    + +    ++   +  ED+  L     
Sbjct: 19  KDYITYEKLVKYLTK-QPSASTAKKVQALMKKHKVQLFSAAEIAQMKNIEDAKRLQEEKQ 77

Query: 100 -------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                   N      +        +D PVRMYLREMG I LL+++ EI I+K+IE G  +
Sbjct: 78  KLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKDEEIEISKKIELGEDI 137

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           ++ + C  P     ++ +++ L +    ++E+                           +
Sbjct: 138 IIDAFCSVPYLIDFILDYKEPLINRERRVKELF--------------------------K 171

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
               E++ DD  +     E     ++ +  + ++   + + DER L   E          
Sbjct: 172 SFDDEEKSDDKLDELDIDEDEKNEAELEVDEENTKKNSKKEDERTLKVIE---------- 221

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
                     AL++  + + +    +++          + K  +LKEKL+ L  +  L  
Sbjct: 222 -------KFKALEKAKKDWLKTSKDKESGNELLDKLSIAFKKNILKEKLMDLGPTSKL-- 272

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I  +V+ +    K     + EL RL     +  D   +RH     D   +S  +    
Sbjct: 273 --ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADILKDITKLSKEEITER 330

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                 V+  ++ I K+    ++      +  S  + I+  +++G+  +  AK  M ++N
Sbjct: 331 ALETTMVSTYME-IKKLFQTKEAGEKSFDLEKSRLKEILEQIKRGKKISDEAKGRMAKSN 389

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+I
Sbjct: 390 LRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAISRAI 449

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ + ++ V++V+KITKE
Sbjct: 450 ADQARTIRIPIHMIETINQINKIIREHLQKDGKEPNVSVIAKEVGLSIDKVKQVIKITKE 509

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL  L  RE+ V+RMRF
Sbjct: 510 PISLEAPIGNEDDGKFGDFVEDRNSLSPIDHILKDDLKEQIDEVLDQLNDREKAVIRMRF 569

Query: 633 GIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++G
Sbjct: 570 GLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIEG 620


>gi|57237826|ref|YP_179074.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|86150708|ref|ZP_01068924.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|86152585|ref|ZP_01070790.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612947|ref|YP_001000680.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157415258|ref|YP_001482514.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|167005602|ref|ZP_02271360.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|205356712|ref|ZP_03223473.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315124489|ref|YP_004066493.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|57166630|gb|AAW35409.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|85841878|gb|EAQ59124.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|85843470|gb|EAQ60680.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249244|gb|EAQ72205.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157386222|gb|ABV52537.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|205345450|gb|EDZ32092.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315018211|gb|ADT66304.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315932129|gb|EFV11072.1| Phosphatidylserine decarboxylase [Campylobacter jejuni subsp.
           jejuni 327]
          Length = 622

 Score =  277 bits (709), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 206/666 (30%), Positives = 344/666 (51%), Gaps = 59/666 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             +   +++ +    + Y+T E+L  +L   + S+   +   A++    + +    ++  
Sbjct: 5   TQEAELEELFQEN-AKDYITYEKLVKYLTK-QPSASTAKKVQALMKKHKVQLFSAAEIAQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D PVRMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +++ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +    E++ DD  +     E     ++ +  + ++   + + DER 
Sbjct: 171 --------------KSFDDEEKSDDKLDELDIDEDEENETELESDEENTKKNSKKEDERT 216

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + +    +++          + K  +L
Sbjct: 217 LKVIE-----------------KFKALEKAKKDWLKTSKDKESGDELLDKLSIAFKKNIL 259

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  D   +RH   
Sbjct: 260 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADI 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +  S  + I+  +++G
Sbjct: 316 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRG 374

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 375 KKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 434

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 435 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 554

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 555 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 614

Query: 677 RSFLDG 682
           +++++G
Sbjct: 615 KNYIEG 620


>gi|86150479|ref|ZP_01068704.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88596833|ref|ZP_01100070.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|148926089|ref|ZP_01809775.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|218562617|ref|YP_002344396.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|85839074|gb|EAQ56338.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88191674|gb|EAQ95646.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|112360323|emb|CAL35119.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|145845568|gb|EDK22660.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|284926231|gb|ADC28583.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni IA3902]
 gi|315058444|gb|ADT72773.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni S3]
 gi|315928360|gb|EFV07675.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni DFVF1099]
          Length = 622

 Score =  277 bits (709), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 206/666 (30%), Positives = 344/666 (51%), Gaps = 59/666 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             +   +++ +    + Y+T E+L  +L   + S+   +   A++    + +    ++  
Sbjct: 5   TQEAELEELFQEN-AKDYITYEKLVKYLTK-QPSASTTKKVQALMKKHKVQLFSAAEIAQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D PVRMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +++ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +    E++ DD  +     E     ++ +  + ++   + + DER 
Sbjct: 171 --------------KSFDDEEKSDDKLDELDIDEDEENETELESDEENTKKNSKKEDERT 216

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + +    +++          + K  +L
Sbjct: 217 LKVIE-----------------KFKALEKAKKDWLKTSKDKESGDELLDKLSIAFKKNIL 259

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  D   +RH   
Sbjct: 260 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADI 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +  S  + I+  +++G
Sbjct: 316 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRG 374

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 375 KKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 434

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 435 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 554

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 555 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 614

Query: 677 RSFLDG 682
           +++++G
Sbjct: 615 KNYIEG 620


>gi|2764713|emb|CAA05353.1| sigma 70 [Campylobacter jejuni]
          Length = 622

 Score =  277 bits (709), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 206/666 (30%), Positives = 344/666 (51%), Gaps = 59/666 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             +   +++ +    + Y+T E+L  +L   + S+   +   A++    + +    ++  
Sbjct: 5   TQEAELEELFQEN-AKDYITYEKLVKYLTK-QPSASTAKKVQALMKKHKVQLFSAAEIGQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D PVRMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +++ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +    E++ DD  +     E     ++ +  + ++   + + DER 
Sbjct: 171 --------------KSFDDEEKSDDKLDELDIDEDEENETELESDEENTKKNSKKEDERT 216

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + +    +++          + K  +L
Sbjct: 217 LKVIE-----------------KFKALEKAKKDWLKTSKDKESGDELLDKLSIAFKKNIL 259

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  D   +RH   
Sbjct: 260 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADI 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +  S  + I+  +++G
Sbjct: 316 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRG 374

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 375 KKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 434

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 435 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 554

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 555 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 614

Query: 677 RSFLDG 682
           +++++G
Sbjct: 615 KNYIEG 620


>gi|332297995|ref|YP_004439917.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181098|gb|AEE16786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 599

 Score =  277 bits (708), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 214/674 (31%), Positives = 339/674 (50%), Gaps = 91/674 (13%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D  D +  K+++  + +  VT +ELN +LPP+ +++++ME+ + +L    + + + D L
Sbjct: 1   MDELDPAITKLLEYGKTKHSVTWDELNEYLPPEILNTDKMENVLMLLEKNHVQIEEEDTL 60

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSA----------------DRSTDDPVRMYLRE 127
           +D + S D      ++++ +       +                  D S DDPVR+YLRE
Sbjct: 61  DDADASADDASADDASADDASDDDDSTEEETKPEEPERKRLVYNDKDSSGDDPVRLYLRE 120

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           +G   LL+ E E+ ++K++E                            DG  +++ +I  
Sbjct: 121 IGKEHLLTAEQEVFLSKKME----------------------------DGENIIKNVIKK 152

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              + PE     F+     ++ + +     + R ++ E   +         +    V + 
Sbjct: 153 SGILIPE-----FYSIGIRAFSRIDIHEPGRNRKEINEEMTEKRRLKTSYSEHIKPVFAD 207

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +     ++ L E +        +   +LR K++ +L  I     E+       +     
Sbjct: 208 MKGYMQLKKQLYEVDQTRQIFEDSNLVELREKILPSLQLIDIQSEEIERFSTRFI----- 262

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +++ +    + +  K    L ++         +L  + KRI   + E  +L    G+  
Sbjct: 263 -EATKRISEYRHRQEKKAKELRISD------YSELRSLGKRI-AIKSERTKLEYDLGMSA 314

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           D   E +                               I KI  +++ +  E    +SE 
Sbjct: 315 DEIREVYT-----------------------------QIQKIDRKLRRLEYEFENDVSEI 345

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   + +G      AK  ++ ANLRLV+S+AKKYTNRGLQF DL+QEGNIGL+KA EK
Sbjct: 346 LSMAKEIDRGRRMMKEAKNRLINANLRLVVSIAKKYTNRGLQFFDLVQEGNIGLIKAVEK 405

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KVVR +R++  +  REP
Sbjct: 406 FEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVVRESRQLMQRFGREP 465

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EEIA +L  PV  V++V  + +EPISLETPIG+E+ S LGDFIEDK   +P       
Sbjct: 466 TDEEIAAQLGWPVNRVKQVKSVAREPISLETPIGEEEDSLLGDFIEDKEVENPAAKTAYT 525

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    +LA+L PRE+ VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R+L
Sbjct: 526 MLQDHLRSILATLPPREQEVLKMRFGLDDGFSLTLEEVGLYFNVTRERIRQIEAKALRRL 585

Query: 668 KHPSRSKKLRSFLD 681
           +HP RS  LR ++D
Sbjct: 586 RHPRRSGGLRDYID 599


>gi|283956399|ref|ZP_06373879.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
 gi|283792119|gb|EFC30908.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
          Length = 622

 Score =  277 bits (708), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 206/666 (30%), Positives = 344/666 (51%), Gaps = 59/666 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             +   +++ +    + Y+T E+L  +L   + S+   +   A++    + +    ++  
Sbjct: 5   TQEAELEELFQEN-AKDYITYEKLVKYLTK-QPSASTAKKVQALVKKHKVQLFSAAEIAQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D PVRMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +++ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +    E++ DD  +     E     ++ +  + ++   + + DER 
Sbjct: 171 --------------KSFDDEEKSDDKLDELDIDEDEENETELETDEENTKKNSKKEDERT 216

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + +    +++          + K  +L
Sbjct: 217 LKVIE-----------------KFKALEKAKKDWLKTSKDKESGDELLDKLSIAFKKNIL 259

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  D   +RH   
Sbjct: 260 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADI 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +  S  + I+  +++G
Sbjct: 316 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRG 374

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 375 KKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 434

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 435 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 554

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 555 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 614

Query: 677 RSFLDG 682
           +++++G
Sbjct: 615 KNYIEG 620


>gi|57168867|ref|ZP_00367997.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|305431982|ref|ZP_07401149.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
 gi|57019703|gb|EAL56389.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|304445066|gb|EFM37712.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
          Length = 621

 Score =  276 bits (706), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 206/666 (30%), Positives = 341/666 (51%), Gaps = 60/666 (9%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             D   +++ K   ++ Y+T E+L  +    + +S   +    ++    + +    ++  
Sbjct: 5   TQDMELEELFKEN-EKDYITYEKLVKYFSK-QPNSATAKKVQTLMKKYKVQLFSAAEIAQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D PVRMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +R+ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYREPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                           S  ++E++D +  E + E      + +  +      + + DER 
Sbjct: 171 ---------------KSFDDEEKNDDKLDELEDEDEENDEELENEEETPKKTSKKEDERT 215

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + ++   +++          + K  +L
Sbjct: 216 LKVIE-----------------KFKALEKAKKDWLKVSKDKESGDEILDKLGIAFKKNIL 258

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  +    RH   
Sbjct: 259 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSEELKNRHANI 314

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +     + I+  +++G
Sbjct: 315 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKERLKEILEQIKRG 373

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 374 KKISDEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 433

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 434 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 493

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 494 LSVDKVKQVIKITKEPISLEAPIGSEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 553

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 554 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 613

Query: 677 RSFLDG 682
           +++++G
Sbjct: 614 KNYIEG 619


>gi|315929035|gb|EFV08275.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           305]
          Length = 622

 Score =  276 bits (705), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 206/666 (30%), Positives = 344/666 (51%), Gaps = 59/666 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             +   +++ +    + Y+T E+L  +L   + S+   +   A++    + +    ++  
Sbjct: 5   TQEAELEELFQEN-AKDYITYEKLVKYLTK-QPSASTAKKVQALMKKHKVQLFSAAEIAQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D PVRMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +++ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +    E++ DD  +     E     ++ +  + ++   + + DER 
Sbjct: 171 --------------KSFDDEEKSDDKLDELDIDEDEENETELESDEENAKKNSKKEDERT 216

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + +    +++          + K  +L
Sbjct: 217 LKVIE-----------------KFKALEKAKKDWLKTSKDKESEDELLDKLSIAFKKNIL 259

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  D   +RH   
Sbjct: 260 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADI 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +  S  + I+  +++G
Sbjct: 316 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRG 374

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 375 KKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 434

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 435 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 554

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 555 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 614

Query: 677 RSFLDG 682
           +++++G
Sbjct: 615 KNYIEG 620


>gi|258406014|ref|YP_003198756.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
 gi|257798241|gb|ACV69178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
          Length = 587

 Score =  276 bits (705), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 199/485 (41%), Positives = 290/485 (59%), Gaps = 11/485 (2%)

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G       +   E  +         + +  +V       V    +  +   +  D  +  
Sbjct: 107 GIVPLLDREGEVEIAKKIEDGELEVLYALIEVPVAVEELVGVGDDLQKGTIKLKDVVKTI 166

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRE----LRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                S  E   R +V+  L+E+ ++Y++       L + A   ++      K    K +
Sbjct: 167 EEDDPSEDEMNQRERVIYLLEELRKLYKKRVNIYYKLDECATLDKRVRGVQNKIIDYKHE 226

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---R 377
           +V+++  + L ++ ID ++E L+D  +++ +   +L     S G  R    E       R
Sbjct: 227 VVQILRDIKLEKTLIDRVIETLHDYVRQMHNCRRDLSAYVLSVGKTRGEIEEIFAELDRR 286

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           EL+P   +        E  +F       +  ++     +  +   S+++   I+  + +G
Sbjct: 287 ELNPVIAADNLGMTVEELFSFKEMLAGKMEILQR----LEEKCCHSVTDLEEILWRINRG 342

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             +A  AK+E++ +NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 343 NYDALRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFS 402

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  ++ R+P PEEIA+++ 
Sbjct: 403 TYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQELGRDPQPEEIAERMD 462

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PVE V+KVLKI KEPISLETPIGDE+ S LGDFIEDK AV+P + A+ + L E  + VL
Sbjct: 463 YPVEKVKKVLKIAKEPISLETPIGDEEDSSLGDFIEDKKAVAPAEEAVNSKLAEQISTVL 522

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + LTPREE+VLR RFGIG  +DHTLEEVGK F VTRERIRQIEAKA+RKL+HP RS+ LR
Sbjct: 523 SELTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQSLR 582

Query: 678 SFLDG 682
           S+ + 
Sbjct: 583 SYYES 587



 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 50/169 (29%), Positives = 84/169 (49%), Gaps = 1/169 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K +I   +++G++T +ELN  LP +    EQ+E+ + +   + I +VD        G
Sbjct: 8   QQIKTLIAEGKKKGFLTFDELNKALPNEVNQPEQIEEIITIFDQLDIAIVDAQTG-KNLG 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                    S     + + + ++     + DPVRMYLREMG + LL REGE+ IAK+IE 
Sbjct: 67  MVAGDSGGDSEEEEELEITETEEVETTRSSDPVRMYLREMGIVPLLDREGEVEIAKKIED 126

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           G   ++ +L E P+  + L+   D+L  GT  L++++       P    
Sbjct: 127 GELEVLYALIEVPVAVEELVGVGDDLQKGTIKLKDVVKTIEEDDPSEDE 175


>gi|183220954|ref|YP_001838950.1| RNA polymerase sigma factor RpoD [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189911049|ref|YP_001962604.1| DNA-directed RNA polymerase sigma sigma70/sigma32 subunit
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167775725|gb|ABZ94026.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167779376|gb|ABZ97674.1| RNA polymerase sigma factor rpoD (Sigma-70) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 590

 Score =  276 bits (705), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 198/655 (30%), Positives = 332/655 (50%), Gaps = 76/655 (11%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             +K+I + +    V+ +E+N  LP   ++SE+++D   +L  MGI +V+    +  E S
Sbjct: 9   EVQKIISIGKANREVSYDEINEILPDKILNSEKIDDVFTLLHEMGIEIVEEYSKKSLEES 68

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRST---DDPVRMYLREMGSIELLSREGEIAIAKRI 146
                     +  +     RK      +   +DP+R+YL+E+G + L+S E E+ +AKRI
Sbjct: 69  SSLTTTKEETTKETKEKPARKKRESSVSSSSEDPIRLYLKEIGKVSLISGETEVFLAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G  ++  ++  S +  Q       ++      + +++ ++       +       +  
Sbjct: 129 EKGEKIIEETILSSSILRQNFAKLIPKIKSKKIKVYDLVKVDKMYALNQE----QADKLE 184

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     +++   + E+   I   ++ SK  +   +    +    +  + +    S 
Sbjct: 185 KVFFENMELIQQDEKVLNESTNRIRKYSENSKKFKELKEKIDLSTGKIDEAIRKI-GVSQ 243

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +  +  +++  V      + E+ +    ++    +  ++ K+  +     E L ++  
Sbjct: 244 KEIQKISQKIKSMVF----RVKEIEKHFLKIKAKYGHDVREIKALNRFIEKNENLDEI-- 297

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
                +  +   ++++ ++ K I +NE +L R+ Q  G                      
Sbjct: 298 -----EKMMGCDIDEVREVIKDIRNNERKLRRMEQEAGSP-------------------- 332

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                                     +  I       I   R I             AK+
Sbjct: 333 --------------------------VGEIKDWGEKIIKGEREIAQ-----------AKR 355

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V ANLRLV+S+AK+Y NRG+ F DLIQEGNIGL++A +KF++  GYKFSTYA WW++Q
Sbjct: 356 ELVRANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIRAVDKFEYKKGYKFSTYATWWIRQ 415

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+I+DQ+ TIR+PVHM ++++KV+R  R    +  R+P+ +EIA++L  PV+ V+ V
Sbjct: 416 AITRAISDQARTIRVPVHMIEQVNKVIRETRLFVQEFGRDPSNDEIAERLGWPVQKVKAV 475

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
             + +EPISLE P+G E+ S LGDFIEDK  +SPL+SA  + L E   +VL +L  RE++
Sbjct: 476 KNVAREPISLEIPVGSEEDSELGDFIEDKEVISPLNSAASSILSEQIRQVLQTLPAREQK 535

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+RMRFG+      TLEEVG QF VTRERIRQIEAKA+R+L+HPSRSKKL+ ++D
Sbjct: 536 VIRMRFGLDDGYAQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSRSKKLKDYID 590


>gi|283954552|ref|ZP_06372071.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283793956|gb|EFC32706.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 622

 Score =  275 bits (703), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 204/651 (31%), Positives = 340/651 (52%), Gaps = 58/651 (8%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA- 99
           + Y+T E+L  +L   + S+   +   A++    + +    ++   +  ED+  L     
Sbjct: 19  KDYITYEKLVKYLTK-QPSASTAKKVQALMKKHKVQLFSAAEIAQMKNIEDAKRLQEEKQ 77

Query: 100 -------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                   N      +        +D PVRMYLREMG I LL+++ E+ I+K+IE G  +
Sbjct: 78  KLQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKDEEVEISKKIELGEDI 137

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           ++ + C  P     ++ +++ L +    ++E+                           +
Sbjct: 138 IIDAFCSVPYLIDFILDYKEPLINRERRVKELF--------------------------K 171

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
               E++ DD  +     E     ++ +  + ++   N + DER +   E          
Sbjct: 172 SFDDEEKSDDKLDELDIDEDTDNETELESDEENTKKNNKKEDERTVKVVE---------- 221

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
                     AL++  + + +    +++          + K  +LKEKL+ L  +  L  
Sbjct: 222 -------KFKALEKAKKDWLKTSKDKESGDELLDKLSIAFKKNILKEKLMDLGPTSKL-- 272

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I  +V+ +    K     + EL RL     +  D   +RH     D   +S  +    
Sbjct: 273 --ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHVDILKDITKLSKEEITER 330

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                 V+  ++ I K+    ++      +  S  + I+  +++G+  +  AK  M ++N
Sbjct: 331 ALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRGKKISDEAKGRMAKSN 389

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+I
Sbjct: 390 LRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAISRAI 449

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++++ ++ V++V+KITKE
Sbjct: 450 ADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVSLSMDKVKQVIKITKE 509

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL  L  RE+ V+RMRF
Sbjct: 510 PISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVLNQLNDREKAVIRMRF 569

Query: 633 GIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++G
Sbjct: 570 GLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIEG 620


>gi|224418172|ref|ZP_03656178.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253827499|ref|ZP_04870384.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313141707|ref|ZP_07803900.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253510905|gb|EES89564.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313130738|gb|EFR48355.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
          Length = 616

 Score =  275 bits (703), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 190/606 (31%), Positives = 319/606 (52%), Gaps = 58/606 (9%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D   +   +    L     +   F+++R+      +D PVRMYLREMG I LL+RE E
Sbjct: 64  NQDEARKIKEDKKRLLDEELEDEFDFMKERELLEWSRSDSPVRMYLREMGQIPLLTREDE 123

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI---IDLEACIGPESK 196
           + ++K IE G  +++ ++C  P     ++ +++ L +    ++E+    D E   G ES 
Sbjct: 124 VELSKNIELGENIILDAICSVPYLIDFILDYKEALINRERRVKELFKSFDDEDEEGNESD 183

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                  +    +  +    +K++  V++     ++  K  KD              ++ 
Sbjct: 184 DEELEEEQEQEEESGKKPISKKDQKRVEKVLVSFKALEKAKKDWLKTW---------EQE 234

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
             +E+ D       A + Q   + +  L   +++  EL    +N +    DE    + K 
Sbjct: 235 QGEENGDMLYLLTLAHKKQFLKEKLLDLGPTSKLITELVKAMENTIKS--DEGFDRELKR 292

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           L+ +L      L  N  +I   ++ + +++K  +        +  +Y   + +F  +   
Sbjct: 293 LEYRLPLFNDILLANHKKI---LDNITEMNKSDIIAAVPEATMVSTYMEIKKLFQTKLAS 349

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
                                                        +   + + I+  +++
Sbjct: 350 ----------------------------------------EGSFDLEPEKLKQILEQIKR 369

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G+  A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 370 GKDIADRAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKF 429

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  ++IA+++
Sbjct: 430 STYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKYLQEEGKEPDIDKIAEEV 489

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +PV+ V+ V+KITKEPISLE PIG+ +    GDF+EDK +V P++S ++ +L+E    V
Sbjct: 490 GLPVDKVKNVIKITKEPISLEAPIGNGEDGKFGDFVEDKGSVGPMESILKEDLKEQIDDV 549

Query: 617 LASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L  L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +K
Sbjct: 550 LDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRK 609

Query: 676 LRSFLD 681
           L+++++
Sbjct: 610 LKNYIE 615


>gi|315638945|ref|ZP_07894116.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
 gi|315480974|gb|EFU71607.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
          Length = 657

 Score =  274 bits (700), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 197/662 (29%), Positives = 334/662 (50%), Gaps = 62/662 (9%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             +++ K  ++  Y+T E+L  +L   + +   ++   +++    + +     +   +  
Sbjct: 47  ELEELFKENKE-DYITYEKLVKYL-NKQPNLTAIKKIRSLMKKYKVELYSAAQIAQMQNV 104

Query: 90  EDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            D+  L             N      + +      +D PVRMYLREMG I LL+++ E+ 
Sbjct: 105 ADAKRLEEEKQKLQDTGLENEFNLANENELLEWSRSDSPVRMYLREMGQIALLNKDEEVE 164

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           I+K+IE G  +++ + C  P     ++ +++ L +    ++E+                 
Sbjct: 165 ISKKIELGEDIIIDAFCSVPYLIDFILDYQEPLINRERRVKELF---------------- 208

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                                              S D+    ++   + E ++   + +
Sbjct: 209 ----------------------------------KSFDEEEDKENDKLDEEENDEEGESE 234

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           ED      +  ED+   KV+     + +  +E   +       + +    +     K  L
Sbjct: 235 EDKKTKKPNKKEDERTLKVIEKFKALEKAKKEWLKVSKETKAKEDELLDKLSIAFKKNIL 294

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
            + +  L      I  +V+ +    K     + EL RL     +  D    RH     + 
Sbjct: 295 KEKLMDLGPTSKLISEIVKSMETALKSDDEFDKELKRLEYRLPMFSDELKARHADILKEI 354

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +S  +   +      V+  ++ I K+    ++      +  S  + I+  +++G+  +
Sbjct: 355 TKLSKDEIAEKAMETTMVSTYME-IKKLFQTKEASKKSFDLEKSRLKEILEQIKRGKKIS 413

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 414 DEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYAT 473

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP   +IAK++ + V+
Sbjct: 474 WWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKNGKEPDVNDIAKEVGLSVD 533

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V++V+KITKEPISLE PIG ED    GDF+EDKN++SP+D+ ++ +L+E    VL  L 
Sbjct: 534 KVKQVIKITKEPISLEAPIGSEDDGKFGDFVEDKNSLSPMDNILKDDLKEQIDEVLDQLN 593

Query: 622 PREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL++++
Sbjct: 594 DREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYI 653

Query: 681 DG 682
           +G
Sbjct: 654 EG 655


>gi|315453594|ref|YP_004073864.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
 gi|315132646|emb|CBY83274.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
          Length = 621

 Score =  274 bits (699), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 194/644 (30%), Positives = 326/644 (50%), Gaps = 62/644 (9%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED------SLDLAS 97
           V+ E++   L     SS Q++    + S    N V   +      S D            
Sbjct: 31  VSYEQILDILQKIPTSS-QLKKIRELASKYEKNFVHSSECALTSLSADRKVVRKKTKTLE 89

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
             ++   F+++++ +    +D PVRMYLREMG I LLS+E E+ ++K+I+ G  +++ ++
Sbjct: 90  EDNDDLDFIKEKELTEWSRSDSPVRMYLREMGEIPLLSKEEEVELSKQIKLGENIILDAI 149

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
           C  P     +  ++D L +    ++E+                                 
Sbjct: 150 CSVPYLIDFIYGYKDALINRERRVKELFKNF----------------------------- 180

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
               D  ET    E  +++ ++D   ++     +E D + + +  +              
Sbjct: 181 ----DDDETNSKKEEESELEEEDEDALEVKKNLSEKDRKRVGKVIES------------- 223

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                ALD+  + + +  +              + K +VLKE+L  L  +  L    I  
Sbjct: 224 ---FKALDKAKKDWLKTLNTPVQEDELLHALTLAYKRRVLKERLYDLGPTSKL----IGE 276

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           LV+ +    K     E EL RL     +  +  +E H+    +   +S  +         
Sbjct: 277 LVKAMETSLKSGDGFEKELKRLEYKLSLFNEALIENHKNILKNITNMSKEEIAAMVPEAT 336

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   ++ I K+    ++      +   + + I+  +++G+  +  AK +M  +NLRLV+
Sbjct: 337 MIGSYME-IKKLFQTKEASEDGFDLEPGKLKEILEQIKRGKLISDKAKNKMARSNLRLVV 395

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT+RGL FLDLIQEGNIGLMKA +KF+    Y+FSTYA WW+KQAI+R+IADQ+ 
Sbjct: 396 SIAKRYTSRGLPFLDLIQEGNIGLMKAVDKFEHEKNYRFSTYATWWIKQAISRAIADQAR 455

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIP+HM D I+++ +  R+   +  +EP  + +AK++ +P++ V+ V+KITKEPISLE
Sbjct: 456 TIRIPIHMIDTINRINKVMRKYMQENGKEPDLDLVAKEVGLPLDKVKNVIKITKEPISLE 515

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +P+G++D    GDF+E+   V  +D  ++ +L+     VL  L  RE+ V+RMRFG+  +
Sbjct: 516 SPVGNDDDGKFGDFVENDKVVGSMDHIMREDLKTQIDGVLDQLNEREKSVIRMRFGLLED 575

Query: 638 T-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LRS+L
Sbjct: 576 ESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRLLRSYL 619


>gi|195953901|ref|YP_002122191.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195933513|gb|ACG58213.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 578

 Score =  273 bits (698), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 203/650 (31%), Positives = 323/650 (49%), Gaps = 88/650 (13%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           ++++ +++GYVT +++N ++  D V S+++E    +LS  GI +++    E E       
Sbjct: 10  LLEIGKEKGYVTYDDINEYVSEDLVESDELESLFDILSEKGIQILED---EAEAAIHHET 66

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           D      +  + +      AD   +D VR YL+EMG I LL R      A  IE      
Sbjct: 67  DNEILEEDDEMIVSASIVEADLKNNDSVRYYLKEMGKIALLGR------ADEIEHA---- 116

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
                      + + + R +L  G      ++D+      +   G     E         
Sbjct: 117 -----------KYIEMGRKQLRRGLLRTSFLVDMVLRYWAKVCDGKMRSQEIL------- 158

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                   D+QE   D +   +    D   ++   E A+  +  ++              
Sbjct: 159 --------DMQEEHTDYDEYEEAEHVDSVFIEKGIELAKKYKTVIE-------------- 196

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                   +       KD+K+  +      ++ K + S+++  S
Sbjct: 197 ------------------------KRTLFLTYKDKKTKAEYLKAHAEMNKTLKSINIKFS 232

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK----D 389
           R + + ++   + K        L        I++  F   H   E    +    K     
Sbjct: 233 RYEKIADEFIKLCKDYKSKLNSLT-------IQKRRFEAVHPNVEELLSYYDKNKELLNK 285

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             +    +       + L ++ EI+ I    G+   E   I++++ +G      +K  MV
Sbjct: 286 IEKHMPFHTFEISRSNYLALQREIEDIERRLGVLPEELNKIINIIEQGRKRVKESKDMMV 345

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           ++NLRLV+S+AKKY NRGL FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW+KQAIT
Sbjct: 346 KSNLRLVVSIAKKYINRGLHFLDLIQEGNMGLMKAVDKYDYKKGFKFSTYATWWIKQAIT 405

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVHM + I+K+ + ++++  +  REP+PEEIAK L M  E VRK+LK 
Sbjct: 406 RAIADQAKTIRIPVHMIETINKISKVSKKLFQEYGREPSPEEIAKALNMSPEKVRKILKS 465

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +EPISLETPIGD++ +HL DFIED +  +P ++  +  LRE   +++ +L+ +E  V+ 
Sbjct: 466 IQEPISLETPIGDDEDTHLKDFIEDSSISNPEEATARRLLREQIEKIINTLSDKEREVIM 525

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            RFG+    +HTLE+VG  F +TRERIRQIE+KAIRK++HPSR+K L+ F
Sbjct: 526 YRFGLVDGIEHTLEQVGTMFNLTRERIRQIESKAIRKIRHPSRAKYLKDF 575


>gi|307747900|gb|ADN91170.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni M1]
          Length = 622

 Score =  273 bits (698), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 205/666 (30%), Positives = 343/666 (51%), Gaps = 59/666 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             +   +++ +    + Y+T E+L  +L   + S+   +   A++    + +    ++  
Sbjct: 5   TQEAELEELFQEN-AKDYITYEKLVKYLTK-QPSASTAKKVQALMKKHKVQLFSAAEIAQ 62

Query: 86  EEGSEDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  ED+  L             N      +        +D P RMYLREMG I LL+++
Sbjct: 63  MKNIEDAKRLQEEKQKLQDTSLENEFDLANENDLLEWSRSDSPDRMYLREMGQIALLNKD 122

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI I+K+IE G  +++ + C  P     ++ +++ L +    ++E+             
Sbjct: 123 EEIEISKKIELGEDIIIDAFCSVPYLIDFILDYKEPLINRERRVKELF------------ 170

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +    E++ DD  +     E     ++ +  + ++   + + DER 
Sbjct: 171 --------------KSFDDEEKSDDKLDELDIDEDEENETELESDEENTKKNSKKEDERT 216

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L   E                    AL++  + + +    +++          + K  +L
Sbjct: 217 LKVIE-----------------KFKALEKAKKDWLKTSKDKESGDELLDKLSIAFKKNIL 259

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KEKL+ L  +  L    I  +V+ +    K     + EL RL     +  D   +RH   
Sbjct: 260 KEKLMDLGPTSKL----ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKKRHADI 315

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D   +S  +          V+  ++ I K+    ++      +  S  + I+  +++G
Sbjct: 316 LKDITKLSKEEITERALETTMVSTYME-IKKLFQTKEASEKSFDLEKSRLKEILEQIKRG 374

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 375 KKISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFS 434

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ 
Sbjct: 435 TYATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + V+ V++V+KITKEPISLE PIG+ED    GDF+ED+N++SP+D  ++ +L+E    VL
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVL 554

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 555 DQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 614

Query: 677 RSFLDG 682
           +++++G
Sbjct: 615 KNYIEG 620


>gi|237751154|ref|ZP_04581634.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
 gi|229373599|gb|EEO23990.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
          Length = 632

 Score =  272 bits (696), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 195/590 (33%), Positives = 309/590 (52%), Gaps = 42/590 (7%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           ++  S S    F ++R+      +D PVRMYLREMG I LLS+E EI ++K +E G  ++
Sbjct: 84  NMEESLSEEFDFQRERELLEWSRSDSPVRMYLREMGQIPLLSKEEEINLSKDMEKGEDII 143

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + ++C  P     +  ++D L +    ++E+         +                 E+
Sbjct: 144 IDAICSVPYLIDFIYDYKDALINRERRVKELFKSFDDPQSDDDSDDIEFDSSEEEFDEEN 203

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
             + ++     E        A++ K   S         +  +   ++ E +S   +   +
Sbjct: 204 KPKARKNTKADE--------ARIEKVLESFQALNDAKNDWLKILQEDSEYESKGLVRKGD 255

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           D+L   ++ A                             K  +LK++L+ L  +  L   
Sbjct: 256 DELLHTLILA----------------------------HKKHILKQRLLSLGPTSKL--- 284

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            I+ L + + +  K     + EL RL     +  D   + HQ    +   ++  +   + 
Sbjct: 285 -INELTKAMENSLKNDDGFDRELKRLEYRLNLFNDTLRQNHQELLKNIANMTREEIVAQV 343

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                VA  V+ I K+    ++      +   + + I+  +++G+  +  AK +M  +NL
Sbjct: 344 PENTMVATYVE-IQKLYRTREASKSGFNLEPEKLKEILEQIKRGKRISDTAKTKMSRSNL 402

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++   YKFSTYA WW+KQAI+R+IA
Sbjct: 403 RLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKQYKFSTYATWWIKQAISRAIA 462

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIP+HM D I+K+    R+ + +   E   E IA ++ + V+ V+ V+KITKEP
Sbjct: 463 DQARTIRIPIHMIDTINKIKNLMRKHAQEKGEELDVESIANQVGLSVDKVKNVIKITKEP 522

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLE PIG++D    GDF+EDK+ +S +D  ++ +LRE    VL  L  RE+ V++MRFG
Sbjct: 523 ISLEAPIGNDDDGKFGDFVEDKSTMSSMDIMLKEDLREQIDNVLDQLNEREKAVIKMRFG 582

Query: 634 IGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +  D TLEE+GK   VTRER+RQIE+ AI+KLKHP   ++LR +L G
Sbjct: 583 LLEDESDRTLEEIGKALNVTRERVRQIESSAIKKLKHPRIGRQLRQYLGG 632


>gi|222824021|ref|YP_002575595.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
 gi|222539243|gb|ACM64344.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
          Length = 625

 Score =  272 bits (695), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 207/650 (31%), Positives = 337/650 (51%), Gaps = 51/650 (7%)

Query: 41  RGYVTIEELNAFLP--PDEVSSEQMEDTV-----AMLSNMGINVVDGDDLEDEEGSEDSL 93
           + Y+T E+L  +    P+  S++++ D +      ++S+  I      +   +   E   
Sbjct: 17  KDYITYEKLVKYFAKLPNVTSAKKIRDLMDKHKVELISSAEIAKKRNLEEAKKLQEEKQK 76

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
              +S  N      +        +D PVRMYLREMG I LL+++ E+ I+K+IE G  ++
Sbjct: 77  LQDTSLENEFDLANENDLLEWSRSDSPVRMYLREMGQIALLNKDEEVEISKKIELGEDII 136

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + + C  P     ++ +++ L +    ++E+               F   E       + 
Sbjct: 137 IDAFCSVPYLIDFILDYKEPLINRERRVKEL---------------FKSFEDDDKNDDDK 181

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
           +  E + ++  E E +  S  K  K    K D          + L++ + +   T+S + 
Sbjct: 182 NDDEIDSEEENENEENENSNDKKIKKTSKKEDERTLKVIESFKALEKAKKEWLKTISTIN 241

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
            +     +     IA                        K  +LKEKL+ L  +  L   
Sbjct: 242 AENNEDELLNKLIIA-----------------------FKKNILKEKLMDLGPTSKL--- 275

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            I  +V+ +    K     + EL RL     +  D   +RH     D   +S  +     
Sbjct: 276 -ISEIVKSMETALKSDEEFDKELKRLEYRLPMFSDELKQRHADILKDITKLSKEEIAERA 334

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                V+  ++ I K+    ++      +   + + I+  +++G+  +  AK  M ++NL
Sbjct: 335 LETTMVSTYME-IKKLIQTKEASQNSFDLEKDQLKEILEQIKRGKKISDEAKTRMAKSNL 393

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI+R+IA
Sbjct: 394 RLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAISRAIA 453

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIP+HM + I+++ +  R    K  +EP    IAK++ + V+ V++V+KITKEP
Sbjct: 454 DQARTIRIPIHMIETINQINKIIREYLQKEGKEPDVSIIAKEVGLSVDKVKQVIKITKEP 513

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLE PI +ED    GDF+ED+ ++SP+D  ++ +L+E    VL  L  RE+ V+RMRFG
Sbjct: 514 ISLEAPISNEDDGKFGDFVEDRTSISPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFG 573

Query: 634 IGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++G
Sbjct: 574 LMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIEG 623


>gi|242310656|ref|ZP_04809811.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
 gi|239523054|gb|EEQ62920.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
          Length = 615

 Score =  272 bits (695), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 189/605 (31%), Positives = 316/605 (52%), Gaps = 57/605 (9%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D       +    L     +   F+++R+      +D PVRMYLREMG I LL+RE E
Sbjct: 64  NQDEARRIKEDKKRLLDEELEDEFDFMKERELLEWSRSDSPVRMYLREMGQIPLLTREDE 123

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID--LEACIGPESKG 197
           + ++K IE G  +++ ++C  P     ++ +++ L +    ++E+     +       + 
Sbjct: 124 VELSKNIELGENIILDAICSVPYLIDFILDYKEALINRERRVKELFKSFDDEEDEESVES 183

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 EG    + +    +K++  V++     ++  K  KD              ++  
Sbjct: 184 EEEELEEGEEESEGKKPISKKDQKRVEKVLVSFKALEKAKKDWLKTW---------EQEK 234

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
            +E+ D       A + Q   + +  L   +++  EL    +N +    DE    + K L
Sbjct: 235 GEENGDMLYLLTLAHKKQFLKEKLLDLGPTSKLITELVKAMENTIKS--DEGFERELKRL 292

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           + +L      L  N  +I   ++ + ++SK  +        +  +Y   + +F  +    
Sbjct: 293 EYRLPLFNDILLANHKKI---LDNIIEMSKSDIVAAVPEATMVSTYMEIKKLFQTKVASE 349

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E                                           +   + + I+  +++G
Sbjct: 350 ES----------------------------------------FDLEPEKLKQILEQIKRG 369

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +  A  AK +M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFS
Sbjct: 370 KDIADRAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFS 429

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP  E+IA+++ 
Sbjct: 430 TYATWWIRQAISRAIADQARTIRIPIHMIETINRINKIMRKYLQEEGKEPDIEKIAEEVG 489

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PV+ V+ V+KITKEPISLE PIG+ +    GDF+EDK ++ P+DS ++ +L+     VL
Sbjct: 490 LPVDKVKNVIKITKEPISLEAPIGNGEDGKFGDFVEDKASLGPMDSILKEDLKAQIDDVL 549

Query: 618 ASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL
Sbjct: 550 DQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKL 609

Query: 677 RSFLD 681
           +++++
Sbjct: 610 KNYIE 614


>gi|154148465|ref|YP_001406295.1| RNA polymerase sigma factor RpoD [Campylobacter hominis ATCC
           BAA-381]
 gi|153804474|gb|ABS51481.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter hominis ATCC BAA-381]
          Length = 624

 Score =  272 bits (694), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 202/658 (30%), Positives = 325/658 (49%), Gaps = 67/658 (10%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
           Q+ YVT E L  F      S+ Q++    +  N  I ++   ++   +  ED   +    
Sbjct: 19  QKNYVTFERLIKFFDKAPTST-QVKKIEDLAKNFKIKLISSAEIAKIKNIEDLKRIKERE 77

Query: 100 SNSSVFLQKRKD---------SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +   L+K  D              +D PVRMYLREMG+++LL +E EI I+K+IE G 
Sbjct: 78  KKAKSELEKNDDFDIASDNELLEWSRSDSPVRMYLREMGAVDLLKKEEEIEISKKIELGE 137

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            +++ + C  P     ++ + + L +    ++E+         E         E +  + 
Sbjct: 138 DIIIDAFCSVPFLIDFILAYEEPLINRERRVKELFKNFDENEEEENEEEIEEDEENEEEN 197

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             +   +  R +                                    D+  +    +  
Sbjct: 198 VANKKAKISRRN------------------------------------DKRAEKVMKSFK 221

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A+E   +  V  A    ++++        N     +    + K K+LKEKL+ L  +  L
Sbjct: 222 ALEKAKKDWVKYADKNKSDIFDM------NKKTLLQKLNLTFKKKILKEKLMDLGPTSKL 275

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
               I  +V+ +    K       EL RL   Y I      +  +  E     +      
Sbjct: 276 ----ITEIVKSIEKALKSDTEFARELKRL--EYKIPLINLPDHRKRHE---EILKDIISL 326

Query: 391 PEGEWKNFVACEVD-----SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            + E    V           I ++    ++      I     + I+  +++G+  +  AK
Sbjct: 327 SKDEISQMVFENTTVSTYMDIKRLFQTREASKQGFNIDPDRLKQILEQIKRGKKISDEAK 386

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++
Sbjct: 387 SLMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKGYKFSTYATWWIR 446

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAI+R+IADQ+ TIRIP+HM + I+++ +  R+   +  +EP    +AK++ + ++ +++
Sbjct: 447 QAISRAIADQARTIRIPIHMIETINRINKINRKYVQENGKEPDITILAKEVGLSIDKIKQ 506

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V+KITKEPISLE P+G+ED    GDF+EDK  +SP+D  ++ +L+E   +VL  L  RE 
Sbjct: 507 VIKITKEPISLEAPVGNEDDGKFGDFVEDKGTISPIDQILKNDLKEQIDKVLDQLNERER 566

Query: 626 RVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            V+RMRFG+  +  D TLEE+GK+  VTRER+RQIEA AI+KLKHP   + L+ +++ 
Sbjct: 567 AVIRMRFGLLDDESDRTLEEIGKELSVTRERVRQIEASAIKKLKHPKVGRDLKKYIES 624


>gi|308061382|gb|ADO03270.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Cuz20]
          Length = 672

 Score =  271 bits (693), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 183/590 (31%), Positives = 311/590 (52%), Gaps = 58/590 (9%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++
Sbjct: 135 LDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIIL 194

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREI---IDLEACIGPESKGGFFHGTEGHSYQKR 211
            ++C  P     +  ++D L +    ++E+    D +               E    ++R
Sbjct: 195 DAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDSKKDDDSEEYEENEER 254

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    EK+R  V++ +   ++  K  K+    +++P +  E         ++       A
Sbjct: 255 KKVVSEKDRKRVEKVQESFKALDKAKKEWLKALEAPVDEKE---------DELVRLLTLA 305

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
            + Q     +  L+  +++  EL    +  +     +    + K L+ KL     +L  N
Sbjct: 306 YKRQTLKDRLYDLEPTSKLINELVKTMETTLKS--GDGFEKELKRLEYKLPLFNDTLIAN 363

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             +I   +  +  ++K  +  +     +   Y   + +FL +    E             
Sbjct: 364 HKKI---LANITSMTKEDIIAQVPEATMVSVYMDLKKLFLTKEASEE------------- 407

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
                                         +  ++ + I+  +++G+  +  AK +M ++
Sbjct: 408 ---------------------------GFDLDPNKLKEILEQIKRGKLISDRAKNKMAKS 440

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+
Sbjct: 441 NLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRA 500

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TK
Sbjct: 501 IADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNVIKVTK 560

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMR
Sbjct: 561 EPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMR 620

Query: 632 FGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           FG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 621 FGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 670


>gi|317013514|gb|ADU80950.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Gambia94/24]
          Length = 681

 Score =  271 bits (692), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 191/598 (31%), Positives = 320/598 (53%), Gaps = 58/598 (9%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 136 NTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 195

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII---DLEACIGPESKGGFFHGT 203
             G  +++ ++C  P     +  ++D L +    ++E+    D +               
Sbjct: 196 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDPKKDDDSE 255

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E    ++R+    EK++  V++ +   ++  K  K+    +++P          +DE ED
Sbjct: 256 EDEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAP----------IDEKED 305

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   +L+                                        + K + LK++L  
Sbjct: 306 ELVRSLT---------------------------------------LAYKRQTLKDRLYD 326

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           L  +  L    I+ LV+ +    K     E EL RL     +  DV +  H+    +   
Sbjct: 327 LEPTSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDVLIANHKKILANITN 382

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++      +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  
Sbjct: 383 MTKEDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDR 441

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW
Sbjct: 442 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 501

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V
Sbjct: 502 IKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKV 561

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  R
Sbjct: 562 KNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNER 621

Query: 624 EERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 622 EKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 679


>gi|15611152|ref|NP_222803.1| RNA polymerase sigma factor RpoD [Helicobacter pylori J99]
 gi|11387124|sp|Q9ZMY3|RPOD_HELPJ RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|4154591|gb|AAD05665.1| RNA POLYMERASE SIGMA FACTOR (SIGMA-70) [Helicobacter pylori J99]
          Length = 681

 Score =  270 bits (691), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 190/598 (31%), Positives = 319/598 (53%), Gaps = 58/598 (9%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 136 NTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 195

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII---DLEACIGPESKGGFFHGT 203
             G  +++ ++C  P     +  ++D L +    ++E+    D +               
Sbjct: 196 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDPKKDDDSE 255

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E    ++R+    EK++  V++ +   ++  K  K+    +++P          +DE ED
Sbjct: 256 EDEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAP----------IDEKED 305

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   +L+                                        + K + LK++L  
Sbjct: 306 ELVRSLT---------------------------------------LAYKRQTLKDRLYD 326

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           L  +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   
Sbjct: 327 LEPTSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITN 382

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++      +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  
Sbjct: 383 MTKEDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDR 441

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW
Sbjct: 442 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 501

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V
Sbjct: 502 IKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKV 561

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  R
Sbjct: 562 KNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNER 621

Query: 624 EERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 622 EKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 679


>gi|328954514|ref|YP_004371848.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454838|gb|AEB10667.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 577

 Score =  270 bits (689), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 215/503 (42%), Positives = 314/503 (62%), Gaps = 7/503 (1%)

Query: 184 IIDLEACIGPE-SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++DLEA            +  E  +        + +    ++E   +I SA   +K    
Sbjct: 76  LVDLEAGASVRLDDPVKMYLREMGTVSLLTREGEIEIAKRIEEGCKEIVSALLETKFGIR 135

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSA--MEDQLRPKVMCALDEIAEVYRELRS-LQD 299
            +       E ++ +  E+  +         ++     +V+  +  + ++ + L+S L  
Sbjct: 136 AILEIAHRLEQEKPSHSEECKELLEDGLEQGIQPDRLQQVIQGIYRLNDLIKRLQSCLAS 195

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             ++ +K  +   + +  ++++V+   SL L Q +++ ++ Q+ D S  +  ++ E+ R 
Sbjct: 196 KTLSEEKRVQLQTRLERYRQRMVEQFKSLKLPQHQLNRIIRQINDYSYAVRASQKEIDRC 255

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF-VACEVDSILKIRNEIKSISV 418
            Q  G+    F  RH  R+L    +S      +GE     +A   +S    +  ++ I  
Sbjct: 256 LQKIGLDAPEF--RHLCRKLQEKLLSGISPELDGELSIVEIAQLAESWRGAQRRLQKIES 313

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           ETG+S  +   I   V++G+ +AS AK E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGN
Sbjct: 314 ETGLSAEKLLEIQKRVQRGDRQASRAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGN 373

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R 
Sbjct: 374 IGLMKAVEKFEYERGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLLRTSRY 433

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  +I REPTPEE+A+K+  P+E VRKVLKI KEPISLETPIG+E+ S+L DFIEDK   
Sbjct: 434 LVQEIGREPTPEELAEKMEYPLEKVRKVLKIAKEPISLETPIGEEEDSYLADFIEDKKIS 493

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP ++    NL E T +VL++LTPREE+V+R+RFGIG  TDHTLEEVGK+F VTRERIRQ
Sbjct: 494 SPTEAVENLNLAEITRKVLSTLTPREEKVIRLRFGIGEKTDHTLEEVGKKFMVTRERIRQ 553

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+H SR K+L+SF +
Sbjct: 554 IEAKALRKLRHASRLKRLQSFAE 576



 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 31/78 (39%), Positives = 45/78 (57%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             +  L   +  A    DDPV+MYLREMG++ LL+REGEI IAKRIE G   ++++L E+
Sbjct: 71  EPAEILVDLEAGASVRLDDPVKMYLREMGTVSLLTREGEIEIAKRIEEGCKEIVSALLET 130

Query: 161 PLTFQALIIWRDELNDGT 178
               +A++     L    
Sbjct: 131 KFGIRAILEIAHRLEQEK 148


>gi|224438138|ref|ZP_03659073.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313144578|ref|ZP_07806771.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313129609|gb|EFR47226.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
          Length = 623

 Score =  269 bits (688), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 202/647 (31%), Positives = 339/647 (52%), Gaps = 62/647 (9%)

Query: 43  YVTIEELNAFL--PPDEVSSEQMEDTV-----AMLSNMGINVVDGDDLEDEEGSEDSLDL 95
           Y+T E++   +   P     ++++D        +LS+  +  +     + +  ++    L
Sbjct: 30  YITYEKIAQIMLKAPTTAQVKKIKDLSKKYKKQLLSSSEVAKMLNTKEQIQRQADRKKLL 89

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                +   F++ ++      +D PVRMYLREMG I LL++E E++++K IE G   ++ 
Sbjct: 90  NEELEDEFDFMKDKELLEWSRSDSPVRMYLREMGQIPLLTKEEEVSLSKNIELGENTILD 149

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++C  P     +  ++D           +I+ E  +    K       EG   ++  D+ 
Sbjct: 150 AICSVPYLIDFIYDYKDA----------LINRERRVKELFKSFDDEEEEGEEEEEEFDAV 199

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
           +E+E      ++ D +   KV +  +    +  +  +  E  + E ED+  H L      
Sbjct: 200 EEEENSRKANSKKDQKRIEKVMESFKVLDKAKKDWLKVLETPISESEDELGHIL------ 253

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                              S K  +LK KL+ L  +  L    I
Sbjct: 254 ---------------------------------LLSHKKHILKMKLLDLGPTSKL----I 276

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           + LV  + +  K     E EL RL     +  D  +E HQ    +   +S  +       
Sbjct: 277 NELVRAMENSLKSGDGFERELKRLEYKLPLFNDTLVENHQKILANITAMSRDEIASMVPE 336

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              V+  ++ + K+    ++      +   + + I+  +++G+  +  AK +M ++NLRL
Sbjct: 337 TTMVSVYME-LKKLFQTKEASEGGFNLEPEKLKEILEQIKRGKSISDKAKAKMAKSNLRL 395

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  G+KFSTYA WW++QAI+R+IADQ
Sbjct: 396 VVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGFKFSTYATWWIRQAISRAIADQ 455

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIP+HM + I+++ +  R+   +  +EP  E IAK++ +P++ V+ V+KITKEP+S
Sbjct: 456 ARTIRIPIHMIETINRIHKIMRKHIQETGKEPDIEYIAKEVGLPIDKVKNVIKITKEPVS 515

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+ PIG +D    GDF+EDK++V P+D  ++ +L+     VL  L  RE+ V+RMRFG+ 
Sbjct: 516 LDAPIGSDDDGKFGDFVEDKSSVGPMDYILKEDLKVQIDDVLEQLNDREKAVIRMRFGLL 575

Query: 636 MNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL+++++
Sbjct: 576 DDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIE 622


>gi|188526895|ref|YP_001909582.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
 gi|188143135|gb|ACD47552.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
          Length = 661

 Score =  269 bits (686), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 183/590 (31%), Positives = 312/590 (52%), Gaps = 58/590 (9%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++
Sbjct: 124 LDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIIL 183

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREI---IDLEACIGPESKGGFFHGTEGHSYQKR 211
            ++C  P     +  ++D L +    ++E+    D +               E    ++R
Sbjct: 184 DAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDSKKDDDSEEDEENEER 243

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
           +    EK+R  V++ +   ++  K  K+    +++P +  E         ++       A
Sbjct: 244 KKVVSEKDRKRVEKVQESFKALDKAKKEWLKALEAPVDEKE---------DELVRLLTLA 294

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
            + Q     +  L+  +++  EL    +  +     +    + K L+ KL     +L  N
Sbjct: 295 YKRQTLKDRLYDLEPTSKLINELVKTMETTLKS--GDGFEKELKRLEYKLPLFNDTLIAN 352

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             +I   +  + +++K  +  +     +   Y   + +FL +    E             
Sbjct: 353 HKKI---LANITNMTKEDIIAQVPEATMVSVYMDLKKLFLTKEASEE------------- 396

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
                                         +  ++ + I+  +++G+  +  AK +M ++
Sbjct: 397 ---------------------------GFDLDPNKLKEILEQIKRGKLISDRAKNKMAKS 429

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+
Sbjct: 430 NLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRA 489

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V+K+TK
Sbjct: 490 IADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNVIKVTK 549

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ V+RMR
Sbjct: 550 EPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKVQIESVLDQLNEREKAVIRMR 609

Query: 632 FGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           FG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 610 FGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 659


>gi|15644718|ref|NP_206888.1| RNA polymerase sigma factor RpoD [Helicobacter pylori 26695]
 gi|2500785|sp|P55993|RPOD_HELPY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2313167|gb|AAD07156.1| RNA polymerase sigma-70 factor (rpoD) [Helicobacter pylori 26695]
          Length = 671

 Score =  268 bits (684), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 190/598 (31%), Positives = 320/598 (53%), Gaps = 58/598 (9%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 126 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 185

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII---DLEACIGPESKGGFFHGT 203
             G  +++ ++C  P     +  ++D L +    ++E+    D +               
Sbjct: 186 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDSKKDEDNE 245

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E    ++R+    EK++  V++ +   ++  K  K+    +++P          +DE ED
Sbjct: 246 EDEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAP----------IDERED 295

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   +L+                                        + K + LK++L  
Sbjct: 296 ELVRSLT---------------------------------------LAYKRQTLKDRLYD 316

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           L  +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   
Sbjct: 317 LEPTSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITN 372

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++      +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  
Sbjct: 373 MTKEDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDR 431

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW
Sbjct: 432 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 491

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V
Sbjct: 492 IKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKV 551

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  R
Sbjct: 552 KNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNER 611

Query: 624 EERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 612 EKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 669


>gi|149194280|ref|ZP_01871377.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
 gi|149135455|gb|EDM23934.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
          Length = 604

 Score =  267 bits (683), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 195/659 (29%), Positives = 334/659 (50%), Gaps = 67/659 (10%)

Query: 32  KKMIKLARQR--GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           K+++KL +    G VT E L  F       ++  E  + +     I ++   ++   +  
Sbjct: 5   KEIVKLFKDNRNGIVTYESLVNFFDKAPTKTDTKE-ILKLAKEYNIRLMTAAEVAKLKNL 63

Query: 90  EDSLDLASSASN-----SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           ED +             +   L+ ++      +D PVRMYLREMG I LL ++ E+ I +
Sbjct: 64  EDVVKSEEERERKKEELAEDILKDKELLEWSRSDSPVRMYLREMGHIPLLDKDEEVEIFR 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RI+ G  +++ ++C  P     ++ +++ L +    ++E+                 G +
Sbjct: 124 RIQLGEEIILDAICSIPFLIDLVLKYKEPLLNRERRVKELFKNFVDEEEVEDEDTKEGKK 183

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 RE    E  ++             + +K +  KV    +    D    +++   
Sbjct: 184 NKKISLREKRINELFKN------------LEKAKKEWEKVIDEYDRILKDTSMPEDERLH 231

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               L+  + +++   +  L   +++  E+    + A+ G KD +  +K +  +  L   
Sbjct: 232 KILQLTFKKKKVKD-ALNELGYTSKLINEIVKTVETALKGDKDFEKELKKREYRLPLFN- 289

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                          EQL ++ K I+    EL +   +  +     +  +          
Sbjct: 290 ---------------EQLRNLHKEILSKITELSKEDIAAMVPEHTMVNVYM--------- 325

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                                I K+    K+     G+   +   I+  +++G+   + A
Sbjct: 326 --------------------DIKKLVEAKKASENMFGMDPKKLEVILEQLKRGKKIVTEA 365

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++M  ANLRLV+S+AKKYTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 366 KEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIGLMKAIDKFEFEKGYKFSTYATWWI 425

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAI+R+IADQ+ T+RIP+HM + I+++ +  R+   +  +EP+ E IAK++ MPVE ++
Sbjct: 426 RQAISRAIADQARTVRIPIHMIENINQINKIIRKYVQEEGKEPSLEVIAKEMKMPVEKIK 485

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++LKI+KEPISLE P+G+E+    GDFIEDK+  +P D  +  +LR+    +L +L  RE
Sbjct: 486 QILKISKEPISLEAPVGEEEDGKFGDFIEDKSFSNPYDEVVLEDLRKHIDEILENLNERE 545

Query: 625 ERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           + V++MRFG+  +  + TLEE+GK   VTRER+RQIE+ AI+KL+HP+  K L+++++ 
Sbjct: 546 KAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQIESSAIKKLRHPNIGKLLKNYIES 604


>gi|297379310|gb|ADI34197.1| RNA polymerase sigma factor RpoD [Helicobacter pylori v225d]
          Length = 677

 Score =  267 bits (682), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 194/595 (32%), Positives = 316/595 (53%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 132 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 191

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 192 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFR------------------SF 233

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                   S  K+ DD +E E + E    VS+ DR +V+   E+ +  ++   E      
Sbjct: 234 DDDDENSVSDSKKDDDSEEYEENEERKKVVSEKDRKRVEKVQESFKALDKAKKEWLKALE 293

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +   ED+L   +  A                             K + LK++L  L  
Sbjct: 294 APVDEKEDELVRLLTLA----------------------------YKRQTLKDRLYDLEP 325

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 326 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 381

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 382 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 440

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 441 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 500

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 501 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 560

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 561 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 620

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 621 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 675


>gi|57505389|ref|ZP_00371317.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
 gi|57016214|gb|EAL53000.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
          Length = 619

 Score =  267 bits (681), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 200/664 (30%), Positives = 336/664 (50%), Gaps = 66/664 (9%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             +++ K  ++  Y+T E+L  +L   + +   ++   +++    + +     +   +  
Sbjct: 9   ELEELFKENKE-DYITYEKLVKYL-NKQPNLTAIKKIRSLMKKYKVELYSAAQIAQMQNV 66

Query: 90  EDSLDLASSA--------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
            D+  L             N      + +      +D PVRMYLREMG I LL+++ E+ 
Sbjct: 67  ADAKRLEEEKQKLQDTGLENEFNLANENELLEWSRSDSPVRMYLREMGQIALLNKDEEVE 126

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           I+K+IE G  +++ + C  P     ++ +++ L +    ++E+                 
Sbjct: 127 ISKKIELGEDIIIDAFCSVPYLIDFILDYQEPLINRERRVKELF---------------- 170

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                           K  D+ ++ E D     +  ++      +   N   DER L   
Sbjct: 171 ----------------KSFDEEEDKENDKLDEEENDEESEEDKKTKKPNKREDERTL--- 211

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL--KE 319
                            KV+     + +  +E   +       + D++   K  +   K 
Sbjct: 212 -----------------KVIEKFKALEKAKKEWLKVSKETKAKESDDELLDKLSIAFKKN 254

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            L + +  L      I  +V+ +    K     + EL RL     +  D    RH     
Sbjct: 255 ILKEKLMDLGPTSKLISEIVKSMETALKSDDEFDKELKRLEYRLPMFSDELKARHADILK 314

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +   +S  +   +      V+  ++ I K+    ++      +  S  + I+  +++G+ 
Sbjct: 315 EITKLSKDEIAEKAMETTMVSTYME-IKKLFQTKEASKKSFDLEKSRLKEILEQIKRGKK 373

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +  AK  M ++NLRLV+S+AK+YTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 374 ISDEAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTY 433

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI+R+IADQ+ TIRIP+HM + I+++ +  R    K  +EP   +IAK++ + 
Sbjct: 434 ATWWIRQAISRAIADQARTIRIPIHMIETINQINKIIREHLQKNGKEPDVNDIAKEVGLS 493

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ V++V+KITKEPISLE PIG E+    GDF+EDKN++SP+D+ ++ +L+E    VL  
Sbjct: 494 VDKVKQVIKITKEPISLEAPIGSEEDGKFGDFVEDKNSLSPMDNILKDDLKEQIDEVLDQ 553

Query: 620 LTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL++
Sbjct: 554 LNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKN 613

Query: 679 FLDG 682
           +++G
Sbjct: 614 YIEG 617


>gi|307636779|gb|ADN79229.1| RNA polymerase sigma factor [Helicobacter pylori 908]
 gi|325995367|gb|ADZ50772.1| RNA polymerase sigma factor [Helicobacter pylori 2018]
 gi|325996964|gb|ADZ49172.1| RNA polymerase sigma factor [Helicobacter pylori 2017]
          Length = 681

 Score =  267 bits (681), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 136 NTEEKQKVLDEELEDGCDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 195

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 196 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 237

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +       ++  + +   +     ++   E   +S 
Sbjct: 238 ---------------DDDDENSVSDPKKDDDSEEDEENEERKKVVSEKDKKRVEKVQESF 282

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 283 KALDKAKKEWLKALEAPIDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 329

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  DV +  H+    +   ++ 
Sbjct: 330 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDVLIANHKKILANITNMTK 385

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 386 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 444

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 445 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 504

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 505 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNV 564

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 565 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 624

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 625 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 679


>gi|224372659|ref|YP_002607031.1| RNA polymerase sigma factor RpoD [Nautilia profundicola AmH]
 gi|223588464|gb|ACM92200.1| rna polymerase sigma factor [Nautilia profundicola AmH]
          Length = 604

 Score =  266 bits (680), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 196/659 (29%), Positives = 321/659 (48%), Gaps = 67/659 (10%)

Query: 32  KKMIKLAR--QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           K++ KL +  + G VT E +   LP     + Q ++ +       I ++   ++   +  
Sbjct: 5   KELEKLFKSNKNGIVTYETIVNLLPKVPTKT-QSKEILKAAKEYNIKLMTAAEVAKLKNL 63

Query: 90  ED-----SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           ED               +   L+ ++      +D PVRMYLREMG I LL ++ EI I +
Sbjct: 64  EDVVKNEEERERKKEELAEDILKDKELLEWSRSDSPVRMYLREMGHIPLLDKDEEIEIFR 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RI+ G  +++ ++C  P     ++ +++ L +    ++E+                 G  
Sbjct: 124 RIQLGEEIILDAICSIPFLIDLVLKYKEPLLNRERRVKELFKNFVEEEEVDDEDSKEGKR 183

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 RE    E             ++  K  K+    +D   +     + +  E    
Sbjct: 184 QKKISIREKRINEL-----------FKNLEKAKKEWEKVLDEYDQVINAKDMDELERLHK 232

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                       + KV  AL+E+    + +  +        K +K   K    KE  + L
Sbjct: 233 ILQLTFK-----KKKVKEALNELGYTSKLINEIVKTVETALKGDKDFEKELKKKEYKLPL 287

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWV 384
                          EQL  + K I+    EL +   +  +     +  +          
Sbjct: 288 FN-------------EQLRKLHKEILSKITELSKEDIAAMVPEHTMVNVYM--------- 325

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                                I K+    K+     G+   +   I+  +++G+   + A
Sbjct: 326 --------------------DIKKLVEAKKASENMFGMEPEKLEVILEQLKRGKKITTEA 365

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++M  ANLRLV+S+AKKYTNRGL FLDLIQEGNIGLMKA +KF++  GYKFSTYA WW+
Sbjct: 366 KEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIGLMKAIDKFEFEKGYKFSTYATWWI 425

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAI+R+IADQ+ T+RIP+HM + I+++ +  R+   +  +EP+ E IAK++ MP+E V+
Sbjct: 426 RQAISRAIADQARTVRIPIHMIENINQINKIVRKYVQEEGKEPSLEVIAKEMKMPIEKVK 485

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++LKI+KEP+SLE P+G+E+    GDFIEDK   +P +  +  +LR+    +L  L  RE
Sbjct: 486 QILKISKEPVSLEAPVGEEEDGKFGDFIEDKTFTNPYEEVVNEDLRKHIEEILEQLNERE 545

Query: 625 ERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             V++MRFG+  +  + TLEE+GK   VTRER+RQIE+ AI+KL+HP+  K L+++++ 
Sbjct: 546 RAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQIESSAIKKLRHPNIGKFLKNYIES 604


>gi|261837545|gb|ACX97311.1| transcription initiation factor sigma-80 [Helicobacter pylori 51]
          Length = 684

 Score =  266 bits (679), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 139 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 198

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 199 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 240

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +       ++  + +   +     +R   E   +S 
Sbjct: 241 ---------------DDDDENSVSDPKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 285

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 286 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 332

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 333 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 388

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 389 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 447

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 448 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 507

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 508 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 567

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 568 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 627

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 628 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 682


>gi|317179895|dbj|BAJ57681.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F32]
          Length = 671

 Score =  265 bits (678), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 126 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 185

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 186 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 227

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +       ++  + +   +     +R   E   +S 
Sbjct: 228 ---------------DDDDENSVSDPKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 272

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 273 KALDKAKKEWLKALEAPIDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 319

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 320 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 375

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 376 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 434

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 435 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 494

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 495 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 554

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 555 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 614

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 615 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 669


>gi|208434051|ref|YP_002265717.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
 gi|208431980|gb|ACI26851.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
          Length = 682

 Score =  265 bits (677), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 184/595 (30%), Positives = 312/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D+PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 137 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDNPVRMYLREMGDIKLLSKDEEIELSKQI 196

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 197 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 238

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +       ++  + +   +     ++   E   +S 
Sbjct: 239 ---------------DDDDENSVSDPKKDDDSEEDEENEERKKVVSEKDKKRVEKVQESF 283

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 284 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 330

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 331 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 386

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 387 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 445

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 446 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 505

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 506 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 565

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 566 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 625

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 626 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 680


>gi|320537364|ref|ZP_08037319.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
 gi|320145829|gb|EFW37490.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
          Length = 604

 Score =  265 bits (677), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 201/665 (30%), Positives = 331/665 (49%), Gaps = 87/665 (13%)

Query: 33  KMIKLARQRGYVTIEELNAFLPP-DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++  A+++  +T +E+  FLP    VS + M++    L+   I ++  ++ E+E   + 
Sbjct: 12  ELLVYAKEKKSITWDEIYKFLPDGMAVSEDLMDEIAEFLTQKKIYILSNNEDENEIDFDQ 71

Query: 92  SLDLASSASNSSVFLQKRKD------------SADRSTDDPVRMYLREMGSIELLSREGE 139
           + +     S       +  +            + D   DDP+++YLR++G   LL+ + E
Sbjct: 72  NEEELDYESEEFENEDESGEEKEETQKRLLVNTKDSLIDDPIKLYLRDIGQERLLTAKQE 131

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           + ++KR+E                            DG  +++++I     + PE    F
Sbjct: 132 VILSKRME----------------------------DGENIIKDVIQNSGILIPE----F 159

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
           +   +  S +        ++    +E   +I    ++ +     + +     +       
Sbjct: 160 YQIGKNISKKAFAVIDPAEQNKPRKELSEEIVDKRRLKQAYGDSLKTVFSEIKQYMAAKK 219

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
             +D     ++ +ED            I +  + L +LQ   +  ++ ++ S K     +
Sbjct: 220 HLDDRGEPIVAFIEDP---------AAIKQRKKLLNNLQKIELQSEELDRFSKKFLDTAK 270

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISK--RIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+ +        + +  L++  L D+ K  R +    +  +L    G+  D   E +   
Sbjct: 271 KIKEFRRKKERCEKQ--LMISDLSDMRKIGRSLAIPRQRAKLEDELGMSSDEIQEIYT-- 326

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                                       I KI   ++ I  +   +I +   +   + +G
Sbjct: 327 ---------------------------QIQKITRRLRKIEYDFENNIDDIIVMAREIHRG 359

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF++  GYKFS
Sbjct: 360 HTMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFS 419

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++  K+ R+PT EEIA +L 
Sbjct: 420 TYATWWIRQAITRSISDQARTIRVPVHMIEQINKVARESRQLLQKLGRDPTDEEIATQLC 479

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             VE V++V  + +EPISLETPIG+E+ S LGDFI D    +P +   +  LRE    VL
Sbjct: 480 WTVEKVKQVKNVAREPISLETPIGEEEDSSLGDFIPDTEIENPSNVTEKILLREEVQSVL 539

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  VL+MRFG+  +   TLEEVG  F VTRERIRQIEAKA+R+L+HP  S++L+
Sbjct: 540 STLPSREHEVLKMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALRRLRHPRHSRRLK 599

Query: 678 SFLDG 682
            FLD 
Sbjct: 600 DFLDN 604


>gi|317179521|dbj|BAJ57309.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F30]
          Length = 666

 Score =  265 bits (677), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 186/595 (31%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 121 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 180

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 181 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 222

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     +R   E   +S 
Sbjct: 223 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 267

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 268 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 314

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 315 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 370

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 371 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 429

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 430 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 489

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 490 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 549

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 550 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 609

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 610 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 664


>gi|308062951|gb|ADO04838.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Sat464]
          Length = 666

 Score =  265 bits (677), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 186/595 (31%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 121 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 180

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 181 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 222

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     +R   E   +S 
Sbjct: 223 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 267

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 268 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 314

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 315 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 370

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 371 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 429

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 430 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 489

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 490 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 549

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 550 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 609

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 610 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 664


>gi|308183886|ref|YP_003928019.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
 gi|308059806|gb|ADO01702.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
          Length = 679

 Score =  265 bits (676), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 191/595 (32%), Positives = 317/595 (53%), Gaps = 49/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 131 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 190

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 191 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFD----------------- 233

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                E+S  + ++DD  E   + E   KV  +   K     E  +   + LD+ + +  
Sbjct: 234 --DDDENSVSDPKKDDDSEEYEENEERKKVISEKDKKR---VEKVQESFKALDKAKKEWL 288

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L A  D+   +    +  +   Y+                      + LK++L  L  
Sbjct: 289 KALEAPIDEKEDEEDELVRSLTLAYKR---------------------QTLKDRLYDLEP 327

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 328 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 383

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 384 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 442

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 443 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 502

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 503 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNV 562

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 563 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 622

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 623 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 677


>gi|5921146|dbj|BAA84590.1| RNA polymerase sigma 70 [Helicobacter pylori]
          Length = 675

 Score =  265 bits (676), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 187/595 (31%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 130 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 189

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 190 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFD----------------- 232

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                +D           +  G+ E   +  K    K     E  +   + LD+ + +  
Sbjct: 233 -----DDDENSVSDSKKDDDSGEYEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWL 287

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L A  D+ + +++  L                          + K + LK++L  L  
Sbjct: 288 KALEAPVDEKKDELVRLL------------------------TLAYKRQTLKDRLYDLEP 323

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 324 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 379

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 380 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 438

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 439 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 498

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 499 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 558

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN  S +D  ++ +L+     VL  L  RE+ 
Sbjct: 559 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIASSIDHIMREDLKAQIESVLDQLNEREKA 618

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 619 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 673


>gi|2267165|gb|AAC64856.1| sigma 80 [Helicobacter pylori]
          Length = 685

 Score =  264 bits (675), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 186/595 (31%), Positives = 312/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 140 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 199

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 200 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 241

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     +R   E   +S 
Sbjct: 242 ---------------DDDDENSVSDSKKDDDNEEDEENEERKKVVSEKDRKRVEKVQESF 286

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 287 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 333

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 334 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 389

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 390 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 448

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 449 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 508

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 509 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNV 568

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 569 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 628

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 629 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 683


>gi|315586085|gb|ADU40466.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           35A]
          Length = 680

 Score =  264 bits (675), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 184/595 (30%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 135 KTEEKQKVLDEELKDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 194

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 195 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELF--------------------- 233

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +  DD  E           S++D    +     +E D + +++ ++   
Sbjct: 234 -----------RSFDDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDRKRVEKVQES-- 280

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                           ALD+  + + +      +   G+     ++  K  ++ L   + 
Sbjct: 281 --------------FKALDKAKKEWLKALEAPVDEKEGELVRLLTLAYK--RQTLKDRLY 324

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            L      I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 325 DLEPTSKLINELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITSMTK 384

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 385 EDIITQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 443

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 444 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 503

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 504 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 563

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 564 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 623

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 624 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 678


>gi|2522316|gb|AAB81010.1| RNA polymerase principal sigma factor RpoD [Helicobacter pylori]
          Length = 680

 Score =  264 bits (675), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 190/598 (31%), Positives = 321/598 (53%), Gaps = 58/598 (9%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 135 NTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 194

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII---DLEACIGPESKGGFFHGT 203
             G  +++ ++C  P     +  ++D L +    ++E+    D +               
Sbjct: 195 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDSKKDDDSE 254

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E    ++R+    EK++  V++ +   ++  K  K+    +++P          +DE ED
Sbjct: 255 EDEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAP----------IDEKED 304

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   +L+                                        + K ++LK++L  
Sbjct: 305 ELVRSLT---------------------------------------LAYKRQILKDRLYD 325

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           L  +  L    I+ LV+ +    K     E EL RL     +  DV +  H+    +   
Sbjct: 326 LEPTSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDVLIANHKKILANITN 381

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++      +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  
Sbjct: 382 MTKEDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDR 440

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW
Sbjct: 441 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 500

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V
Sbjct: 501 IKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKV 560

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  R
Sbjct: 561 KNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNER 620

Query: 624 EERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ V+RMRFG+  +  + TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 621 EKAVIRMRFGLLDDESERTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 678


>gi|317181391|dbj|BAJ59175.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F57]
          Length = 665

 Score =  264 bits (674), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 186/595 (31%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 120 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 179

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 180 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 221

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     +R   E   +S 
Sbjct: 222 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 266

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 267 KALDKAKKEWLKALEAPIDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 313

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 314 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 369

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 370 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 428

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 429 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 488

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 489 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 548

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 549 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKVQIESVLDQLNEREKA 608

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 609 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 663


>gi|317010368|gb|ADU84115.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SouthAfrica7]
          Length = 685

 Score =  264 bits (674), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 187/598 (31%), Positives = 314/598 (52%), Gaps = 58/598 (9%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 140 NTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 199

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI---IDLEACIGPESKGGFFHGT 203
             G  +++ ++C  P     +  ++D L +    ++E+    D +               
Sbjct: 200 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFDDDDENSVSDSKKDDDSE 259

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E    ++R+    EK++  V++ +   ++  K  K+    +++P +  E++   L     
Sbjct: 260 EDEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAPVDEKEDELVRLLTL-- 317

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                                                          + K + LK++L  
Sbjct: 318 -----------------------------------------------AYKRQTLKDRLYD 330

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           L  +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   
Sbjct: 331 LEPTSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDALIANHKKILSNITN 386

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++      +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  
Sbjct: 387 MTKEDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDR 445

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW
Sbjct: 446 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 505

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V
Sbjct: 506 IKQAISRAIADQARTIRIPIHMIDTINRINKVMRKYMQENGKEPDLELVAEEVGLSLDKV 565

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V+K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  R
Sbjct: 566 KNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIDGVLDQLNER 625

Query: 624 EERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 626 EKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 683


>gi|296127158|ref|YP_003634410.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296018974|gb|ADG72211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 587

 Score =  264 bits (673), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 191/665 (28%), Positives = 324/665 (48%), Gaps = 81/665 (12%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
            +D  +   +++  +K+++      Y+T +E+N  +  D + ++ M+    +L+   I +
Sbjct: 4   EEDCDLLIKNNEKIRKLLEKGNANKYLTFKEINGAI--DNMDTDVMDILFQLLNARKIVI 61

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+ D  E E  S++   +  +A    V      +    + DDP+R+YL+E+G + LL+ +
Sbjct: 62  VE-DKREFESLSKNQNKIDDTAKFIHV------EDKVGNNDDPIRLYLKEIGKVSLLTHD 114

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  +K+IE+G + +   +  + L    ++     +  G   + EI++      P    
Sbjct: 115 DEVDYSKKIESGESEIENIILNTHLVVGEVLNTIKNVQTGKVSIHEILE------PPRIY 168

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 +    +K ++  +E      +    D       ++     +    E  + +   
Sbjct: 169 NVSTQEKRKLERKYKNFEKEYTALAEKYLALDKRIKKITTQKTIKALTKEQEEVKENIVK 228

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L      +   +  + ++L+   +  +++I E + +L+      ++  ++    ++    
Sbjct: 229 LLTKVRLNRMEIDRIAEKLK-FYLHRINQIEEYFEKLKKRYYKEISDFENYYKEIESGN- 286

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+  ++LV   ++    I+ ++             +  +  +     I ++  +E     
Sbjct: 287 KDIYIRLVDEFNITPEAIEAVIT-------SFHKAQVRMADIYDEVRIDKETLVE----- 334

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                WV                     I   R +I                        
Sbjct: 335 -----WVRK-------------------IDSARRKIAQ---------------------- 348

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK  +V+ANLRLVI++AKKY NRGL F DL+QEGNIGL+KA +KF++  GYKFS
Sbjct: 349 ------AKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFS 402

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R  R+   +  REP+ +EIAK L 
Sbjct: 403 TYATWWIRQAITRSISDQARTIRVPVHMIEQINKVQRVLRQYMQQHGREPSIQEIAKALG 462

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            P   V+ V  + K+P+SL  PIGDE+ + LG+ IEDK   SP +      LR+    +L
Sbjct: 463 WPESRVKSVRNVAKDPVSLNAPIGDEEDTILGELIEDKEFESPQNITTFKILRKQIDSIL 522

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SL  RE++V+RMRFG+     HTLEEVG  F VTRERIRQIEAKAIR+L+  S+ K+L+
Sbjct: 523 DSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAIRRLRAQSKKKELK 582

Query: 678 SFLDG 682
            FLD 
Sbjct: 583 DFLDS 587


>gi|109948008|ref|YP_665236.1| RNA polymerase sigma factor RpoD [Helicobacter acinonychis str.
           Sheeba]
 gi|109715229|emb|CAK00237.1| RNA polymerase sigma-70 factor [Helicobacter acinonychis str.
           Sheeba]
          Length = 659

 Score =  264 bits (673), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 189/595 (31%), Positives = 314/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              E    L     +   FL++++      +D PVR+YLREMG+I+LL +E EI ++K+I
Sbjct: 114 NTEEKQKVLDGELEDGYDFLKEKEFLEWSRSDSPVRVYLREMGNIDLLKKEEEIELSKQI 173

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 174 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 215

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                         DD + +  D +      +D+ ++      +  N +R      +   
Sbjct: 216 -------------DDDDENSVSDSKKDDDNEEDEENEERKKVVSERNKKRV-----EKVQ 257

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            +  A++   +  +      I E   EL  L   A           K + LK++L  L  
Sbjct: 258 ESFKALDKAKKEWLKALEAPIDEKEDELVRLLTLAH----------KRQTLKDRLYDLEP 307

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  HQ    +   ++ 
Sbjct: 308 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHQKILSNITNMTK 363

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 364 EDIIAQVPETTMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 422

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF++  G+KFSTYA WW+KQ
Sbjct: 423 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEYEKGFKFSTYATWWIKQ 482

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 483 AISRAIADQARTIRIPIHMIDTINRINKVMRKHMQENGKEPDLEVVAEEVGLSLDKVKNV 542

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 543 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKVQIEGVLDQLNEREKA 602

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 603 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 657


>gi|254778811|ref|YP_003056916.1| RNA polymerase sigma factor RpoD [Helicobacter pylori B38]
 gi|254000722|emb|CAX28640.1| RNA polymerase sigma factor rpoD (Sigma-70) [Helicobacter pylori
           B38]
          Length = 679

 Score =  264 bits (673), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 192/689 (27%), Positives = 342/689 (49%), Gaps = 65/689 (9%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFS---DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
             K N+  +S+ +++    V       +++ +++   +     V+ E +   +     + 
Sbjct: 42  KIKENKTKESKVKETAKEPVPVKKLSFNEALEELFANSLS-NCVSYESIIQ-ISAKVPTL 99

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD--------LASSASNSSVFLQKRKDS 112
            Q++    +       +V   +   +  + D +         L     +   FL+++   
Sbjct: 100 AQIKKIKELCQKYQKKLVSSSEYAKKLNAIDKIKNTEEKQKVLDEELEDGYDFLKEKDFL 159

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               +D PVRMYLREMG I+LLS++ EI ++K+I  G  +++ ++C  P     +  ++D
Sbjct: 160 EWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKD 219

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            L +    ++E+                                     D  +     +S
Sbjct: 220 ALINRERRVKELFRSF---------------------------------DDDDENSVSDS 246

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                 ++  + +   +     ++   E   +S   L   + +    +   +DE  +   
Sbjct: 247 KKDDDSEEDEENEERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAPIDEKEDELV 306

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
            L +L             + K + LK++L      L      I+ LV+ +    K     
Sbjct: 307 RLLTL-------------AYKRQTLKDRLYD----LKPTSKLINELVKTMETTLKSGDGF 349

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
           E EL RL     +  D  +  H+    +   ++      +      V+  +D + K+   
Sbjct: 350 EKELKRLEYKLPLFNDTLIANHKKILANITNMTKEDIIAQVPEATMVSVYMD-LKKLFLT 408

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            ++      ++ ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLD
Sbjct: 409 KEASEEGFDLAPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLD 468

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++
Sbjct: 469 LIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRI 528

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +  R+   +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+
Sbjct: 529 NKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFV 588

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCV 651
           EDKN VS +D  ++ +L+     VL  L  RE+ V+RMRFG+  +  D TLEE+GK+  V
Sbjct: 589 EDKNIVSSIDHIMREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNV 648

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 649 TRERVRQIESSAIKKLRSPQYGRILRNYL 677


>gi|217034615|ref|ZP_03440022.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
 gi|216942910|gb|EEC22397.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
          Length = 671

 Score =  263 bits (672), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 126 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 185

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 186 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 227

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +       ++  + +   +     +R   E   +S 
Sbjct: 228 ---------------DDDDENSVSDPKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 272

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 273 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 319

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 320 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 375

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 376 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 434

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 435 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 494

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 495 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVRLSLDKVKNV 554

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 555 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 614

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 615 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 669


>gi|317176909|dbj|BAJ54698.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F16]
          Length = 671

 Score =  263 bits (671), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 184/595 (30%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 126 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 185

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 186 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 227

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     ++   E   +S 
Sbjct: 228 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDKKRVEKVQESF 272

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 273 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLCDLEP 319

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 320 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 375

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 376 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 434

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 435 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 494

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 495 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 554

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+ KEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 555 IKVAKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDRIMREDLKAQIESVLDQLNEREKA 614

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 615 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 669


>gi|332672929|gb|AEE69746.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           83]
          Length = 674

 Score =  263 bits (671), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 310/595 (52%), Gaps = 53/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 130 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 189

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 190 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSFD----------------- 232

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                             +     +S      ++  + +   +     +R   E   +S 
Sbjct: 233 -----------------DDENSVSDSKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 275

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 276 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 322

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 323 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 378

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 379 ENIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 437

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 438 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 497

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 498 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 557

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 558 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 617

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 618 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 672


>gi|261838959|gb|ACX98724.1| sigma 70 (RpoD) [Helicobacter pylori 52]
          Length = 685

 Score =  262 bits (670), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 140 KTEEKQKVLDEELEDGYDFLREKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 199

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 200 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 241

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +       ++  + +   +     +R   E   +S 
Sbjct: 242 ---------------DDDDENSVSDPKKDDDSEEDEENEERKKVVSEKDRKRVEKVQESF 286

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 287 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 333

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 334 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 389

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 390 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 448

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 449 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 508

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 509 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 568

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 569 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 628

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 629 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 683


>gi|257457793|ref|ZP_05622954.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257444843|gb|EEV19925.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 607

 Score =  262 bits (670), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 205/681 (30%), Positives = 327/681 (48%), Gaps = 97/681 (14%)

Query: 23  VFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDG 80
           + D S+D    K+I  A++   +T +EL+  LP    SSE  M++ + +L    I V+D 
Sbjct: 1   MIDISEDPIIIKLIAHAKEHKTLTWDELSDLLPEKMTSSETVMDEILDLLEQEQIQVIDD 60

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--------------------TDDP 120
              E+++   D LD     +   +F +   +S +                       DDP
Sbjct: 61  AVEENDDVFADELDEVELEAEEQLFEEAELESGNEPEFSKPEDTHKKLLNNDREAIVDDP 120

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +++YLR++G   LL+ E E+ ++K +                             DG  +
Sbjct: 121 IKLYLRDIGKENLLTAEQEVILSKAM----------------------------EDGENI 152

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           ++  I     +  E +          S  +     +E   +D ++         +   + 
Sbjct: 153 IKNAIKNSGVLISEVQMIAQKAFAKISSSESNKPRKELSYEDAEKKRLR-----QSYGEQ 207

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
              +    +     ++ L + E  ++        + R K++  L +I     E+  + D+
Sbjct: 208 LKPIYPDIKAYILLKKKLYDKETLASFLDDEDLQKTRKKILNYLQKIEFQTEEIEKISDH 267

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            +   +  +   + +  K++ + +                 L  + KR+     E  +L 
Sbjct: 268 FLEAARKIREYRRRREKKQRQLGVRA------------YSDLRKLGKRL-AIPRERQKLE 314

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           Q  G+  +   + +                               I  +  +++ I  + 
Sbjct: 315 QELGMTANDIRDIYT-----------------------------HIQTLIRKVRKIEYDF 345

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
                +   +   +R G      AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIG
Sbjct: 346 EAPTEDIIALAKEIRHGHAMLKKAKDKLINANLRLVVSIAKKYTNRGLHFFDLVQEGNIG 405

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA EKF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++ 
Sbjct: 406 LIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLM 465

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            K  REPT EEIA +L   VE V++V  + +EPISLETPIG+E+ S LGDFIEDK+  +P
Sbjct: 466 QKFGREPTDEEIAVQLGWNVERVKQVKNVAREPISLETPIGEEEDSSLGDFIEDKDVENP 525

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +      L+E    VL+ L  RE+ VL+MRFG+      TLEEVG  F VTRERIRQIE
Sbjct: 526 SNLTEYILLQEQLRSVLSCLPLREQEVLKMRFGLDEGYALTLEEVGLYFNVTRERIRQIE 585

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+R+L+HP +S KL+ +LD
Sbjct: 586 AKALRRLRHPKQSTKLKDYLD 606


>gi|108562514|ref|YP_626830.1| RNA polymerase sigma factor RpoD [Helicobacter pylori HPAG1]
 gi|107836287|gb|ABF84156.1| RNA polymerase sigma-80 factor [Helicobacter pylori HPAG1]
          Length = 692

 Score =  262 bits (670), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 147 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 206

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 207 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 248

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  +     +     ++   E   +S 
Sbjct: 249 ---------------DDDDENSVSDSKKDDDSEEDEENKERKKVVSEKDKKRVEKVQESF 293

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 294 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 340

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 341 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITHMTK 396

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 397 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 455

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 456 KMAQSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 515

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 516 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNV 575

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 576 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 635

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 636 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 690


>gi|317008763|gb|ADU79343.1| RNA polymerase sigma factor RpoD [Helicobacter pylori India7]
          Length = 676

 Score =  262 bits (670), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 312/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 131 KTEEKQKVLNEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 190

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 191 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 232

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     ++   E   +S 
Sbjct: 233 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDKKRVEKVQESF 277

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 278 KALDKAKKEWLKALEAPIDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 324

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 325 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 380

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 381 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 439

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 440 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 499

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 500 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNV 559

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 560 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 619

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 620 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 674


>gi|210134292|ref|YP_002300731.1| RNA polymerase sigma factor RpoD [Helicobacter pylori P12]
 gi|210132260|gb|ACJ07251.1| RNA polymerase sigma-80 factor [Helicobacter pylori P12]
          Length = 680

 Score =  262 bits (670), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 312/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 135 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 194

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 195 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 236

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     ++   E   +S 
Sbjct: 237 ---------------DDDDENSVSDSKKDEENEEDEENEERKKVVSEKDKKRVEKVQESF 281

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 282 KALDKAKKEWLKALEAPIDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 328

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 329 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 384

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 385 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 443

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 444 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 503

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 504 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 563

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 564 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 623

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 624 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 678


>gi|317011933|gb|ADU82541.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Lithuania75]
          Length = 680

 Score =  262 bits (668), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 311/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 135 KNEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 194

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 195 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 236

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     ++   E   +S 
Sbjct: 237 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDKKRVEKVQESF 281

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 282 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 328

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 329 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 384

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 385 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 443

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 444 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 503

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 504 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 563

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 564 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 623

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 624 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 678


>gi|308182264|ref|YP_003926391.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
 gi|308064449|gb|ADO06341.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
          Length = 682

 Score =  262 bits (668), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 186/595 (31%), Positives = 310/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 137 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 196

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 197 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 238

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +         +R   E   +S 
Sbjct: 239 ---------------DDDDENSVSDSKKDDDSEEDEENEERKRAVSEKDRKRVEKVQESF 283

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 284 KALDKAKKEWLKALEAPVDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 330

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 331 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 386

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      +  ++ + I+  +++G+  +  AK 
Sbjct: 387 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKN 445

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 446 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 505

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 506 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 565

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 566 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 625

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 626 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 680


>gi|158522162|ref|YP_001530032.1| RpoD family RNA polymerase sigma factor [Desulfococcus oleovorans
           Hxd3]
 gi|158510988|gb|ABW67955.1| RNA polymerase, sigma 70 subunit, RpoD family [Desulfococcus
           oleovorans Hxd3]
          Length = 738

 Score =  262 bits (668), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 192/685 (28%), Positives = 325/685 (47%), Gaps = 88/685 (12%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
             GK   +    +   +  S            +I   +++G +T EE+   +  +++ ++
Sbjct: 138 AAGKAGKKAPAGKKRQAAASPPPQNFKQKLSGLIAKGKKQGELTYEEIAKAIEANDIPTD 197

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           QM+D +  L ++ I+VV   D  D+ G + +       S  +       DS   S  D V
Sbjct: 198 QMDDLLVHLDDLDISVVKKADQADDSGEDGAKSTTRGDSPVT------YDSDPGSVTDTV 251

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           +MYLREMG + LLSREGE+ IAK+IEAG    +  + ++ +  +++I + D ++ G    
Sbjct: 252 KMYLREMGLVTLLSREGEVEIAKKIEAGEQEALRGMLDTAVGVESIIAYGDNIDVGNLRP 311

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           + +  L+     ++        +  +   R+  + +     +++    +  +A   K   
Sbjct: 312 KSV--LKDVDEGDAGEEEILRIDAFAATIRQIKALDATIQPLRQKHLSVSLSATERKTVA 369

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
            ++    +           + +     L AME++++ ++        + +  +    D  
Sbjct: 370 EQLTRKTDEIFELLLPWRLESE----VLDAMEERIQDEI--------KWFDTMEQTIDRR 417

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVG----SLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           + G     +    +   +     V      +   +  +    +++  + +++   E  ++
Sbjct: 418 LAGLGAGGAVSTIRSKMKTKTGFVNWAYPRMQTTKVHLAAFYDEIKSLERQMEIRERAIM 477

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                                 D   +       +  +    A + + I           
Sbjct: 478 A---------------------DRRLLRKTMKKIDDGYLRAKASKSELIRANL------- 509

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
                       +V  + K      +   ++++     ++    K+  R           
Sbjct: 510 -----------RLVVSIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYR----------- 547

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
                          GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R
Sbjct: 548 --------------RGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSR 593

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +  +   EP+PEEIA+K+ +P+E VR+VLKI +EPISLETPIG+E+ SHLGDFIEDK  
Sbjct: 594 YLVQERGYEPSPEEIAEKMEIPLEKVRRVLKIAREPISLETPIGEEEDSHLGDFIEDKKF 653

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           + P ++A+  NL E T +VLA+LTPREE+VLRMRFGIG   DHTLEEVG+ F VTRERIR
Sbjct: 654 MIPSEAAVSMNLSEQTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFAVTRERIR 713

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKL+HP+RSK L+ F++ 
Sbjct: 714 QIEAKALRKLRHPTRSKMLKHFIES 738


>gi|206564209|ref|YP_002234972.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
 gi|198040249|emb|CAR56232.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
          Length = 628

 Score =  261 bits (667), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 163/654 (24%), Positives = 282/654 (43%), Gaps = 61/654 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I L   RGYVT  E+   LP D      ++   +ML  +GI+V +          +
Sbjct: 31  LHALIALGIDRGYVTHGEIADALPDDAADGADVDAAASMLRELGIDVREHAGAHTAWTLD 90

Query: 91  DSLDLASSASNSSVFLQK---RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                 +  ++            D     T+DP+R+YLREM +  LL R+ EIA+A R+E
Sbjct: 91  RHFAQVTEVASPLADASTPLAADDLLAGRTNDPIRLYLREMSATPLLERDEEIALALRLE 150

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           +GRA  + +L   P    A+    +++  G                              
Sbjct: 151 SGRAACIDALSRDPAALAAVAAIANDIRAGKV------------------------AASV 186

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y        E           D    +    DD       P                   
Sbjct: 187 YVTGFAGDAESAASVPTTLPDDPSMTSPAPDDDAGLALDSPAW----------------- 229

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                    R  V+ AL+          ++Q        D  +S   + L  +     G 
Sbjct: 230 ---------RDTVVEALERAG---APASAMQ---HALHADGFASTAYRALLREAAASTGR 274

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL-ERHQGRELDPHWVSY 386
           +      I+ + +   + + +    E  L+    + GI  D    E     +    W+  
Sbjct: 275 IRFTSRAIERIRQANGERATQARTLEKRLVDTLVATGIPLDAARHELFAPCDDVRAWLHT 334

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                       +A    +++  R  +  ++ ++ + +     + + + + E     A+ 
Sbjct: 335 CSAAHPDCAAT-LARHAPALIDARGALARLAAQSPLPLDITIALDARLSRIERAMQPART 393

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW++Q
Sbjct: 394 KLFQSNLRLVVSVAKRYADRGLPFADLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 453

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ VR++
Sbjct: 454 AITHALADLGRTIRVPAHTVDSLNKLSRLARIHRQRTGDVADARALSPQMRLPVDKVREL 513

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           + I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  RE  
Sbjct: 514 MSIVREPISADLPVSPDHDLTLCDVTIDADAPTPEEAASAGQLRAAVAELIDSLPVREAW 573

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 574 ILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 627


>gi|217032875|ref|ZP_03438353.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298736968|ref|YP_003729498.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
 gi|216945415|gb|EEC24081.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298356162|emb|CBI67034.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
          Length = 679

 Score =  261 bits (667), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 312/595 (52%), Gaps = 52/595 (8%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 134 KTEEKQKVLNEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 193

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+                      
Sbjct: 194 RLGEDIILDAICSVPYLIDFIYAYKDALINRERRVKELFRSF------------------ 235

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                          D  +     +S      ++  + +   +     ++   E   +S 
Sbjct: 236 ---------------DDDDENSVSDSKKDDDSEEDEENEERKKVVSEKDKKRVEKVQESF 280

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   + +    +   +DE  +    L +L             + K + LK++L  L  
Sbjct: 281 KALDKAKKEWLKALEAPIDEKEDELVRLLTL-------------AYKRQTLKDRLYDLEP 327

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +  L    I+ LV+ +    K     E EL RL     +  D  +  H+    +   ++ 
Sbjct: 328 TSKL----INELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITNMTK 383

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                +      V+  +D + K+    ++      ++ ++ + I+  +++G+  +  AK 
Sbjct: 384 EDIIAQVPEATMVSVYMD-LKKLFLTKEASEEGFDLAPNKLKEILEQIKRGKLISDRAKN 442

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGLMKA +KF+   G+KFSTYA WW+KQ
Sbjct: 443 KMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQ 502

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R+IADQ+ TIRIP+HM D I+++ +  R+   +  +EP  E +A+++ + ++ V+ V
Sbjct: 503 AISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGLSLDKVKNV 562

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +K+TKEPISLETP+G++D    GDF+EDKN VS +D  ++ +L+     VL  L  RE+ 
Sbjct: 563 IKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKA 622

Query: 627 VLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KL+ P   + LR++L
Sbjct: 623 VIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYL 677


>gi|254249954|ref|ZP_04943274.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
 gi|124876455|gb|EAY66445.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
          Length = 662

 Score =  260 bits (663), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 155/654 (23%), Positives = 279/654 (42%), Gaps = 61/654 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I L   RGYVT  E+   LP D      ++   +ML  +GI+V +          +
Sbjct: 65  LHALIALGIDRGYVTHGEIADALPDDATDGADVDTAASMLRELGIDVREHTGAHTAWTLD 124

Query: 91  DSLDLASSASNSSVFLQK---RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                 +  ++            D     T+DP+R+YLREM +  LL R           
Sbjct: 125 RHFAQVTEVASPLADASTPLAADDLLAGRTNDPIRLYLREMSATPLLER----------- 173

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                                                 D E  +    + G     +  S
Sbjct: 174 --------------------------------------DEEIALALRLESGRAACIDALS 195

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                 ++     DD++  +            D     S P    +D        +D A 
Sbjct: 196 RDPAALAAVAAIADDIRAGKVAASVYVTGFAGDAESPASAPATLPDDPATESPAPNDDAD 255

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            LS      R   + AL+ +  +   ++           D  +S   + L  +       
Sbjct: 256 -LSLDSPAWRDTAVDALERVGALAPAMQR------ALHADGFASAAYRTLLREATASTDR 308

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV-FLERHQGRELDPHWVSY 386
           +      I+ + +   + + R    E  L+    + GI+ +    +     +    W+ +
Sbjct: 309 IRFTSRAIERIGQANGERATRARTFEKRLVDTLATAGIRAESAHHDLFTPCDDVRAWL-H 367

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A      +    +A    +++  R  +  ++ ++ + +     + + + + E     A+ 
Sbjct: 368 ACRAAHPDCAAALARHAPALIDARGALARLAGQSALPLDIAIALDARLSRIERAMQPART 427

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW++Q
Sbjct: 428 KLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 487

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ VR++
Sbjct: 488 AITHALADLGRTIRVPAHTVDTLNKLSRLARLHRQRTGDVADARALSTQMRLPVDKVREL 547

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           + I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  RE  
Sbjct: 548 MSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQLRAAVAELIDSLPVREAW 607

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 608 ILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 661


>gi|292491943|ref|YP_003527382.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580538|gb|ADE14995.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 578

 Score =  259 bits (662), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 164/400 (41%), Positives = 261/400 (65%), Gaps = 3/400 (0%)

Query: 284 LDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           L+++++    +R+L  +  +   ++  +S + + L+ +L +  G L L  +R+  L + +
Sbjct: 179 LEKVSQHLSRIRTLHSELEIALTREGVASAQARELRGELAQEFGLLRLVPARLKQLAQPV 238

Query: 343 YDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            +  +++   E  L        G+ ++ F +       +P WV       + + +   A 
Sbjct: 239 QEWIRKVQTQEQVLKSCCIHQGGVSQEDFWQSFSSNATNPQWVEDLLAVGQEDRQPLQA- 297

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           + ++I   +  +  + +E G+ ++E + +   + +G+ +A  AK +MVEANLRLV+SVAK
Sbjct: 298 QAETIRAAQKVLTQVEIEVGLPLAELKTVHRRLTRGQIQAQRAKAQMVEANLRLVVSVAK 357

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY NRGL FLDLIQEGNIGLM+A +KFD+  GYKFSTYA WW++QAITR+I DQS TIRI
Sbjct: 358 KYRNRGLTFLDLIQEGNIGLMRAVDKFDYRRGYKFSTYAHWWIRQAITRAIDDQSRTIRI 417

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVH+ +K+ K+ R + ++  +  RE  PEE+A++LA+  + +  + +I K+PISLETP+G
Sbjct: 418 PVHVMEKLSKLNRASYQLRQEKGREGRPEELAERLALSEQQIHHMHEIAKQPISLETPLG 477

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            ++ S LG+ +ED+   +P++ AI A L+  T ++LA+LTPRE +V+ MRFGIGM+TDHT
Sbjct: 478 KDEDSQLGELMEDEQVPNPMEVAISAGLQAGTQQLLATLTPREAQVVAMRFGIGMDTDHT 537

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           L EV +QF ++RERIRQIEA+A+ KL+    SK LRSFL+
Sbjct: 538 LGEVAQQFDLSRERIRQIEAQALSKLRRLGHSKALRSFLE 577



 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 77/160 (48%), Gaps = 8/160 (5%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           F+   +  K++I   + +G +T EEL  ++  +   S++ E  V +  +         DL
Sbjct: 3   FEMRQEELKRLILKGKAQGLLTEEELQEYIVQEVEDSDEAEAVVNLFHDQ--------DL 54

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ +   D   L  + + S     +   S+D +  D V  Y+REMG+  LL+RE E+A+A
Sbjct: 55  EELDEKIDPALLLKNGTESEEETAEVVLSSDGAISDMVNTYMREMGAHALLAREEEVALA 114

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           K IEAG +    +L   P     L+ W DE + G   L +
Sbjct: 115 KAIEAGLSQSTEALGSCPAIAAELLRWADEADAGEARLTD 154


>gi|291059871|gb|ADD72606.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 610

 Score =  259 bits (661), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 204/676 (30%), Positives = 328/676 (48%), Gaps = 96/676 (14%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEE- 87
           +  ++++ AR++  +T +E+   L    V +E++  D + ML    I V   ++ E E+ 
Sbjct: 8   AVMRLLEYAREKKAITHDEVENILAHYGVETEELLHDVLDMLEQENIKVFSSEEEELEDE 67

Query: 88  -------GSEDSLDLASSASNSSVFLQKRKDSADRS-----------TDDPVRMYLREMG 129
                   + D  D +   S   V  +    S                DDPV++YLR++G
Sbjct: 68  VFAGLKGPAADDGDGSFPLSTERVRDKLCDSSRGARQNLLSNARNIALDDPVKLYLRDIG 127

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
             +LL+ E E+ ++KR+E                            +G  ++++II    
Sbjct: 128 QEKLLTAEQEVMLSKRME----------------------------EGEGIIKDIITQSG 159

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            + PE            +    + +   + R ++ E   D     +   +    +     
Sbjct: 160 LLLPEF-YHIGRSLSKKALAVLDPAESGRTRKEISEEMADRRRLKQAYGEVLRSLYPEMR 218

Query: 250 NAENDERNLDEDEDDSAHTLSAMED-QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +    ++ LDE  +      S  E  + R K++  L ++     E+       ++  +  
Sbjct: 219 HYMAMKKRLDERGEPVTVLSSDEEVCKQRDKLLSCLQKVDLQLEEIDRFSRKFLDTARKI 278

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK--RIMHNEGELLRLAQSYGIK 366
           +   + K   EK                L++  L D+ K  R +    +  +L ++ G+ 
Sbjct: 279 REYKRRKDRHEK---------------QLMIADLCDMRKIGRGLAVPRQRAKLEETLGMS 323

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            D   E +                               I K+   ++ I  +   +I  
Sbjct: 324 ADCIQEIYT-----------------------------QIQKVTRRLRRIEYDFENTIDG 354

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              +   + +G      AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA E
Sbjct: 355 ILSMARAIHRGHVMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVE 414

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++  K  RE
Sbjct: 415 KFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLLQKFGRE 474

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+ EEIA++L   VE V++V  + +EPISLETPIG+E+ S LGDF+ D +  +P     +
Sbjct: 475 PSDEEIAQQLCWTVEKVKQVKSVAREPISLETPIGEEEDSSLGDFVPDADVENPSRVTER 534

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    +L++L  RE  VLRMRFG+  +   TLEEVG  F VTRERIRQIEAKA+++
Sbjct: 535 VLLKEEVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKR 594

Query: 667 LKHPSRSKKLRSFLDG 682
           L+HP  S++L+ FLD 
Sbjct: 595 LRHPRHSRRLKDFLDS 610


>gi|15639484|ref|NP_218934.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025724|ref|YP_001933496.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum SS14]
 gi|6094131|sp|O83506|RPOD_TREPA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|3322782|gb|AAC65480.1| RNA polymerase sigma-70 factor (rpoD) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018299|gb|ACD70917.1| RNA polymerase sigma-70 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 611

 Score =  259 bits (661), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 204/676 (30%), Positives = 328/676 (48%), Gaps = 96/676 (14%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM-EDTVAMLSNMGINVVDGDDLEDEE- 87
           +  ++++ AR++  +T +E+   L    V +E++  D + ML    I V   ++ E E+ 
Sbjct: 9   AVMRLLEYAREKKAITHDEVENILAHYGVETEELLHDVLDMLEQENIKVFSSEEEELEDE 68

Query: 88  -------GSEDSLDLASSASNSSVFLQKRKDSADRS-----------TDDPVRMYLREMG 129
                   + D  D +   S   V  +    S                DDPV++YLR++G
Sbjct: 69  VFAGLKGPAADDGDGSFPLSTERVRDKLCDSSRGARQNLLSNARNIALDDPVKLYLRDIG 128

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
             +LL+ E E+ ++KR+E                            +G  ++++II    
Sbjct: 129 QEKLLTAEQEVMLSKRME----------------------------EGEGIIKDIITQSG 160

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            + PE            +    + +   + R ++ E   D     +   +    +     
Sbjct: 161 LLLPEF-YHIGRSLSKKALAVLDPAESGRTRKEISEEMADRRRLKQAYGEVLRSLYPEMR 219

Query: 250 NAENDERNLDEDEDDSAHTLSAMED-QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +    ++ LDE  +      S  E  + R K++  L ++     E+       ++  +  
Sbjct: 220 HYMAMKKRLDERGEPVTVLSSDEEVCKQRDKLLSCLQKVDLQLEEIDRFSRKFLDTARKI 279

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK--RIMHNEGELLRLAQSYGIK 366
           +   + K   EK                L++  L D+ K  R +    +  +L ++ G+ 
Sbjct: 280 REYKRRKDRHEK---------------QLMIADLCDMRKIGRGLAVPRQRAKLEETLGMS 324

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            D   E +                               I K+   ++ I  +   +I  
Sbjct: 325 ADCIQEIYT-----------------------------QIQKVTRRLRRIEYDFENTIDG 355

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              +   + +G      AK +++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA E
Sbjct: 356 ILSMARAIHRGHVMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVE 415

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R +R++  K  RE
Sbjct: 416 KFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLLQKFGRE 475

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+ EEIA++L   VE V++V  + +EPISLETPIG+E+ S LGDF+ D +  +P     +
Sbjct: 476 PSDEEIAQQLCWTVEKVKQVKSVAREPISLETPIGEEEDSSLGDFVPDADVENPSRVTER 535

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    +L++L  RE  VLRMRFG+  +   TLEEVG  F VTRERIRQIEAKA+++
Sbjct: 536 VLLKEEVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKR 595

Query: 667 LKHPSRSKKLRSFLDG 682
           L+HP  S++L+ FLD 
Sbjct: 596 LRHPRHSRRLKDFLDS 611


>gi|39998179|ref|NP_954130.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|39985125|gb|AAR36480.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|298507117|gb|ADI85840.1| RNA polymerase sigma-70 factor RpoD [Geobacter sulfurreducens
           KN400]
          Length = 577

 Score =  258 bits (659), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 204/409 (49%), Positives = 285/409 (69%), Gaps = 13/409 (3%)

Query: 277 RPKVMCALDEIAEVYRELRSL----QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           + +++  ++EIA V   L +L    ++ +++  + ++   + + LKEKL ++V SL L  
Sbjct: 178 KTRLLAQVEEIAAVDVRLAALNAELEEESLSASRRQELLAERQELKEKLAEMVTSLRLKD 237

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I  + ++L ++S ++     E+  + +  G+  D  L+     E        A     
Sbjct: 238 RHIAKIAQRLKELSAKVDTIMAEIAAIEKEAGVSADT-LKEIAASE--------AVGKGI 288

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                        +     ++K +  E+G    E    +  + +GE ++ +AK E+VEAN
Sbjct: 289 KLSLEDAQKHEKKVRSAEKKLKKVEEESGFKARELSDALRAIDRGEAKSKLAKSELVEAN 348

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+I
Sbjct: 349 LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI 408

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+++ +P++ VRKVLKI KE
Sbjct: 409 ADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMNLPLDKVRKVLKIAKE 468

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ SHLGDFIEDK  VSPL++ I+ANL E T RVLA+LTPREE+VLRMRF
Sbjct: 469 PISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTARVLATLTPREEKVLRMRF 528

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR+KKLRSF++
Sbjct: 529 GIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLRSFVE 577



 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 79/303 (26%), Positives = 131/303 (43%), Gaps = 4/303 (1%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D  K++I L +++G++T +E+N  LPPD +SSEQ++D ++M   M I++VD       
Sbjct: 5   STDEVKQLIDLGKEKGFLTYDEVNDLLPPD-ISSEQIDDVMSMFGEMDIDIVDSAQKVKI 63

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +  L+            +  +  A   T DPVRMYLREMGS+ LL+REGE+ IAKRI
Sbjct: 64  PKMKLDLEEEEEIEGEQEDFE-YEPGALGRTSDPVRMYLREMGSVSLLTREGEVEIAKRI 122

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +   +  +P+T + +I   ++L  G     EI         E        T   
Sbjct: 123 EEGERDIAGVILNTPITVKEIIALGEKLLRGQVSAAEISKEVEEEELEEDEEDVQKTRLL 182

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +  +   +   +      E E +  SA++  +    + +   + AE       +D   + 
Sbjct: 183 AQVEEIAAVDVRLAALNAELEEESLSASRRQELLAERQELKEKLAEMVTSLRLKDRHIA- 241

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             ++    +L  KV   + EIA + +E     D        E      K+  E   K   
Sbjct: 242 -KIAQRLKELSAKVDTIMAEIAAIEKEAGVSADTLKEIAASEAVGKGIKLSLEDAQKHEK 300

Query: 327 SLS 329
            + 
Sbjct: 301 KVR 303


>gi|170737511|ref|YP_001778771.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169819699|gb|ACA94281.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 627

 Score =  258 bits (658), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 158/654 (24%), Positives = 286/654 (43%), Gaps = 61/654 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I L   RGYVT+ E+   LP D      ++   +ML  +GI+V +          +
Sbjct: 30  LHALIALGIDRGYVTLGEIADALPDDATDGADVDAAASMLRELGIDVREHAGAHTTWTLD 89

Query: 91  ---DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                +   +S  + +       D     T+DP+R+YLREM +  LL R           
Sbjct: 90  RHFAQVTEVASPLDDASTPLAADDLLAGRTNDPIRLYLREMSATPLLER----------- 138

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                                                 D E  +    + G     +  S
Sbjct: 139 --------------------------------------DEEIALALRLESGRAACIDALS 160

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                 ++     DD++  +    +       D     S P    +D        +D A 
Sbjct: 161 RDPAALAAVAAIADDIRAGKVAASAYVTGFAGDAESPASAPATLPDDPATESPAPNDDAD 220

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            LS      R  V+ AL+ +  +   ++           D+ +S   + L  +     G 
Sbjct: 221 -LSLDSPAWRDTVVDALERVGALAPAMQR------ALHADDFASAAYRTLLREATASTGR 273

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV-FLERHQGRELDPHWVSY 386
           +      I+ + +   + + R    E  L+    + GI+ +    +     +    W+ +
Sbjct: 274 IRFTSRAIERIGQANGERATRARTFEKRLVDTLAAAGIRAESAHHDLFTPCDDVRAWL-H 332

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A      +    +A    +++  R  +  ++ ++ + +     + + + + E     A+ 
Sbjct: 333 ACRAAHPDCAAALARHAPALIDARGALARLAGQSALPLDIAIALDARLARIERAMQPART 392

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW++Q
Sbjct: 393 KLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 452

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ VR++
Sbjct: 453 AITHALADLGRTIRVPTHTVDTLNKLSRLARLHRQRTGDVADARALSTQMRLPVDKVREL 512

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           + I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  RE  
Sbjct: 513 MSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQLRAVVAELIDSLPVREAW 572

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 573 ILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 626


>gi|313673328|ref|YP_004051439.1| RNA polymerase, sigma 70 subunit, rpod [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312940084|gb|ADR19276.1| RNA polymerase, sigma 70 subunit, RpoD [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 601

 Score =  258 bits (658), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 223/654 (34%), Positives = 340/654 (51%), Gaps = 69/654 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +I L +++G++T +E+N  +P D +  E +E+ +  L  + I+V+      D   S 
Sbjct: 10  LKPLIALGKEKGFLTFDEINEMIPEDVLLPEILEEILVRLKQLKIDVI------DNRNSA 63

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +  A       + L   +                            EI + + +E G 
Sbjct: 64  APVIAAPIIEEEEMELDDVES--------------------------EEIIMDENLEEG- 96

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                            + + D +      LRE+ ++      E          G     
Sbjct: 97  -----------------LSFDDPV---KLYLREMGNIPLLSREEETEVAKEIENGQREVI 136

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
               S     +       DI++     KD    VD    N E++    + DE++      
Sbjct: 137 INTLSFIYAAEKFLTIVEDIKNGNFKLKD---LVDFEDINVEDEIDIDEVDEEELKRLKD 193

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL-- 328
             + ++R + +  LD+      E   +       +K E+     K + E L  +   L  
Sbjct: 194 ERDLKIRDEYLSILDDTCLKISEAIKICKKIRTMKKQERIEATKKQMNEILDDVARQLLK 253

Query: 329 -SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS-- 385
             +N S I  L +++    + +   E +L ++   +  + +     H    LDP  +   
Sbjct: 254 IKVNYSLICNLAKEISTTYEELTQYEKDLKKIVDIFKYREEDIDYIH----LDPKKLEAC 309

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             K   + + +N +A      LK +  IK +    G S SE   +  M+     +    K
Sbjct: 310 EVKHLSQRDIQNLIAKFKSIQLKAQKNIKLL----GYSRSEVDLLHEMLTNNMTKTERYK 365

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            +++++NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA EKF++  GYKFSTYA WW++
Sbjct: 366 TKLIQSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYQRGYKFSTYATWWIR 425

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K+++ +R++   + REPTPEEIA+K+ +PVE V+K
Sbjct: 426 QAITRAIADQARTIRIPVHMIETINKMMKISRQLQVDLGREPTPEEIAEKMDVPVEKVKK 485

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL+I KEP+SLETPIG+++ S LGDFIEDK + +PLD  +   L E T ++L +L+PRE 
Sbjct: 486 VLRIAKEPVSLETPIGEDEDSSLGDFIEDKKSKNPLDEVVYLKLSEHTKQILDTLSPREA 545

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            VLR+RFGI  ++DHTLEEVGK+F VTRERIRQIEAKA+RKL+HP+RS+ L++F
Sbjct: 546 SVLRLRFGIDCSSDHTLEEVGKKFNVTRERIRQIEAKALRKLRHPTRSRILKTF 599


>gi|302342714|ref|YP_003807243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
 gi|301639327|gb|ADK84649.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
          Length = 590

 Score =  257 bits (656), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 201/430 (46%), Positives = 279/430 (64%), Gaps = 8/430 (1%)

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
           +DE +  + E   A  L+ +E       +  LDE      E    +D  ++ +K ++   
Sbjct: 169 DDEESFVQQETRKAEFLALIEK------VRGLDERNTATYERLQHRDPDLDAEKRKRLRD 222

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
           +    + ++ + +  + L++ ++D L E +    + I H EG +       G+ +    +
Sbjct: 223 EMTKNRRQIAEELAQVKLDKRQVDQLGEIIRVRLRTIDHCEGVITSAMMETGLPKGDIGK 282

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
             +    +                  +    +S+   R  I+ + +E  +     R I+ 
Sbjct: 283 LAKKVRANCACDEDMAKC--RCDGQRLLAVDESLRVARGRIREVEMECKMGAPSLRKILD 340

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            V KG+  A  AK+E+VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  
Sbjct: 341 RVGKGQTLAQDAKQELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 400

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +  +  REPTPEEI
Sbjct: 401 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLVQEFGREPTPEEI 460

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+K+  P+E VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK  ++P D+ I  NL E 
Sbjct: 461 AEKMDFPLEKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKKVINPADAVISLNLCEQ 520

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           T +VLA+LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 521 TRKVLATLTPREEKVLRMRFGIGQKSDHTLEEVGRDFDVTRERIRQIEAKALRKLRHPSR 580

Query: 673 SKKLRSFLDG 682
           +KKL++F++ 
Sbjct: 581 AKKLKAFIEN 590



 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 140/319 (43%), Gaps = 10/319 (3%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + +    + +I   R +G++T EE+N  L  +EV+S++M+D + +L  MGI +VD +   
Sbjct: 5   EKTLADIQMLISKGRSKGFLTYEEINDAL-DEEVTSDRMDDMLMVLDEMGIQLVDDEGSL 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREMGSIELLSREGEIAIA 143
             +  + S +  +          + +   D     DPV+MYLREMG + LL+REGE+ IA
Sbjct: 64  KVKAQDSSFEDEAEDEVVEAAEDEAEIPGDEGRVSDPVKMYLREMGQVSLLTREGEVEIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGF 199
           KRIE G    + +L E  L    ++     L +    +R+++    D E+ +  E++   
Sbjct: 124 KRIEKGERQCIDALLECSLCVAEILELGRRLENDELRIRDVVCDIDDEESFVQQETRKAE 183

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN---DER 256
           F           E ++   ER   ++ + D E   ++  +         E       D+R
Sbjct: 184 FLALIEKVRGLDERNTATYERLQHRDPDLDAEKRKRLRDEMTKNRRQIAEELAQVKLDKR 243

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            +D+  +     L  + D     +  A+ E      ++  L          ++   KC+ 
Sbjct: 244 QVDQLGEIIRVRLRTI-DHCEGVITSAMMETGLPKGDIGKLAKKVRANCACDEDMAKCRC 302

Query: 317 LKEKLVKLVGSLSLNQSRI 335
             ++L+ +  SL + + RI
Sbjct: 303 DGQRLLAVDESLRVARGRI 321


>gi|254704732|ref|ZP_05166560.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 257

 Score =  255 bits (652), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 210/257 (81%), Positives = 239/257 (92%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA 
Sbjct: 1   EFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 60

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I R
Sbjct: 61  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGR 120

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTPEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AI
Sbjct: 121 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAI 180

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           QANLR+TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+R
Sbjct: 181 QANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 240

Query: 666 KLKHPSRSKKLRSFLDG 682
           KLKHPSRS+KLRSFLD 
Sbjct: 241 KLKHPSRSRKLRSFLDS 257


>gi|270487763|ref|ZP_06204837.1| putative RNA polymerase sigma factor RpoD [Yersinia pestis KIM D27]
 gi|270336267|gb|EFA47044.1| putative RNA polymerase sigma factor RpoD [Yersinia pestis KIM D27]
          Length = 402

 Score =  255 bits (651), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 109/435 (25%), Positives = 186/435 (42%), Gaps = 52/435 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                  ++     +   E   D +       D        PE A     +L E  +++ 
Sbjct: 175 DI---APTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYENAR 231

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   +K+ ++         KL ++  
Sbjct: 232 MEI-----------------------------------KKNGRNHANAAAEILKLSEVFK 256

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+      E    W +
Sbjct: 257 QFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFN 316

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 317 AAVAMGKP-WSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 375

Query: 446 KEMVEANLRLVISVA 460
           KEMVEANLRLVIS+A
Sbjct: 376 KEMVEANLRLVISIA 390


>gi|116620135|ref|YP_822291.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223297|gb|ABJ82006.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 563

 Score =  254 bits (649), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 188/395 (47%), Positives = 269/395 (68%), Gaps = 13/395 (3%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
              Q+ A + ++  +   K    ++KL+ +   +   Q R      QL+++++ I+    
Sbjct: 170 EKRQEFARHTEEIARYYKKTLQCRQKLMAIPRGMKPKQYR-----RQLWEVARLIVRTAR 224

Query: 355 ELLRLAQSYGIKRDVFLERHQG--RELDPHWVSYAKDFPEGE-WKNFVACEVDSILKIR- 410
               +     + R   ++R +    EL P     AK   + E W    A  +  + K + 
Sbjct: 225 LCRAVKFQSPVIR-HLIDRLRSAVEELRPVENDLAKTQRKLETWPAARAEAIKDLRKEQR 283

Query: 411 ---NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
               +++ +  + G S +E R  + ++ +   EA  AKKE++EANLRLV+S+AK+YTNRG
Sbjct: 284 SYGQKLQQMEEQYGASAAELRRTLEIITQAHQEAETAKKELIEANLRLVVSIAKRYTNRG 343

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WWV+QAITR+IADQ+ TIRIPVHM +
Sbjct: 344 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIE 403

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K++RT+R+M  ++ REP+ EE+AK+L +PV  VRKVL++ +EPISLETPIG+E+ SH
Sbjct: 404 TINKLIRTSRQMVQELGREPSNEELAKRLQLPVSKVRKVLRVAQEPISLETPIGEEEESH 463

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFI D+N +SP D+ I  NLRE T +VL +LTPREE++++MRFG+   ++HTLEEVG+
Sbjct: 464 LGDFIVDQNGISPSDAVINLNLREQTAQVLKTLTPREEKIIKMRFGLEDGSEHTLEEVGQ 523

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            F VTRERIRQIEAKA+RKL+HPSRS +LR+FL+ 
Sbjct: 524 NFAVTRERIRQIEAKALRKLRHPSRSHRLRAFLEN 558



 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 50/174 (28%), Positives = 92/174 (52%), Gaps = 8/174 (4%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +  D   D  ++++++ +++GYV  +E++  LP D      ++D +A L   GI +++  
Sbjct: 1   MALDDKYDGLQRLVQMGKEKGYVLYDEVSEVLPGDINGGNDLDDVLAGLDVAGIEILEEP 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                   +D       +S   + L+          +DPVRMYLREMG++ LL+REGE+ 
Sbjct: 61  --------KDFEKKIEESSEELIDLELPAGLGGEKINDPVRMYLREMGTVPLLTREGEVE 112

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           IA+RIE G+  ++ SL  +PL  Q +I   +E+ + T   R++I +   +  + 
Sbjct: 113 IARRIERGQNTVLKSLFRAPLVVQEIIGMGEEVINDTLSARDVIQIADPMLTDE 166


>gi|77165531|ref|YP_344056.1| hypothetical protein Noc_2066 [Nitrosococcus oceani ATCC 19707]
 gi|76883845|gb|ABA58526.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
           19707]
          Length = 579

 Score =  254 bits (649), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 163/407 (40%), Positives = 250/407 (61%), Gaps = 3/407 (0%)

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLNQSRI 335
           +     +L+  ++    +R+L  N       E  +S + + L+ KL +    L L  SRI
Sbjct: 173 KDGKESSLEATSKHLSRVRTLYGNLEATLAQEGVASPRARELRRKLAREFQFLRLIPSRI 232

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           + L + +     +    E  +       G + ++ F          P W+         +
Sbjct: 233 NQLTQLVQGWISKAQTQEQIIRSCCIHQGEMSQEDFWHNFSSGTTHPQWLDDLLAHSRID 292

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            +  +  +  ++   +  +  + VE G+ + E + I   + + + +A  AK +MVEANLR
Sbjct: 293 RQG-LQTQAKTLRAAQAVLLQVEVEAGLPLDELKAIHQRLVRSQFQAQRAKAQMVEANLR 351

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+SVAKKY NRGL FLDLIQEGNIGLMKA +KFD+  GYKFSTYA WW++QAITR+I D
Sbjct: 352 LVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAHWWIRQAITRAIDD 411

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           QS TIRIPVH+ +K+ K+ R + ++  +  RE  PEE+A++LA+  + + ++ +I K+PI
Sbjct: 412 QSRTIRIPVHVMEKLSKLNRASYQLRQEKGREGRPEELAERLALSEQQIHRMHEIAKQPI 471

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETP+G ++ S LG+ +ED+   +P++ AI A L+    ++LA+L+PRE +V+ MRFGI
Sbjct: 472 SLETPLGKDEDSQLGELMEDEQVPNPMEVAITAGLQTGAQQLLAALSPREAQVVAMRFGI 531

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GM+TDHTL EV +QF ++RERIRQIEA+A+ KL+    SK LR+FL+
Sbjct: 532 GMDTDHTLGEVAQQFDLSRERIRQIEAQALGKLRRLGHSKALRNFLE 578


>gi|218673095|ref|ZP_03522764.1| RNA polymerase sigma factor RpoD [Rhizobium etli GR56]
          Length = 355

 Score =  254 bits (648), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 173/369 (46%), Positives = 224/369 (60%), Gaps = 31/369 (8%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S  S D              + S  +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGSDDDDAGGDEDSEGGELAPSGGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  +  E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEDIEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P           +EDED+S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPP--------EEEEEDEDESNLSLAAMEAELRPQVMETLDTIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            Y++LR LQD       + +G        + K LK++L+K V SLSLNQ+RID LVEQLY
Sbjct: 287 TYKKLRKLQDQQVEQRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLY 346

Query: 344 DISKRIMHN 352
           DI+KR++ N
Sbjct: 347 DINKRLVSN 355


>gi|328948111|ref|YP_004365448.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328448435|gb|AEB14151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 655

 Score =  254 bits (648), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 204/663 (30%), Positives = 323/663 (48%), Gaps = 80/663 (12%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +  D + KK++  A  +  ++ +E+   L P+ V+S +ME+ + +L+   I V++ D L 
Sbjct: 68  EVLDPNVKKLLDYACSKQIISWDEITEILTPEFVNSPKMEEVLQLLTKNNIQVMEEDSLL 127

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRK-----DSADRSTDDPVRMYLREMGSIELLSREGE 139
           D+E +E+  D  + + +        K     +  +   DDP+R+YLRE+G   LL+ E E
Sbjct: 128 DDEENEEEDDEGALSDSEDDSKFDEKHRLVSNDKEYGVDDPIRLYLREIGKENLLTAEQE 187

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           + ++K++E G+ ++   +  S +           +                         
Sbjct: 188 VILSKQMEDGQNIIKNVIRNSGMIIPEFYQICHTI------------------------- 222

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
           +   + H   K      E   +  +     +E    + +     +    +    D     
Sbjct: 223 YKKIDPHEPGKARKEINELMAERRRLRSCYVEYVKPIREQMAEYMVLKKQLHSEDPTINI 282

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
             +++       +++ L    +   +EI     +  +           ++  +K   + +
Sbjct: 283 FSDENLKRVRDFIKESLLNAELQT-EEIETFSAKFITASKKIDEYHLIQERRMKKLRITD 341

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            +                    L  I +R+     E  +L +   +  D     +     
Sbjct: 342 AVG-------------------LRSIGRRL-AIRTESAKLEKELAMSADEIRSDYT---- 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
                    D    E +      VD IL+++ EI+                     +G  
Sbjct: 378 ----EIQKIDRKLRELEYDFENSVDEILEMKKEIE---------------------RGRL 412

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK  ++ ANLRLV+S+AKKYTNRGLQ  DLIQEGNIGL+KA EKF++  GYKFSTY
Sbjct: 413 QLEQAKNRLINANLRLVVSIAKKYTNRGLQLFDLIQEGNIGLIKAVEKFEYRKGYKFSTY 472

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSI+DQ+ TIR+PVHM ++I+KVVR +R++  K  REPT EEIA +L+ P
Sbjct: 473 ATWWIRQAITRSISDQARTIRVPVHMIEQINKVVRESRQLMQKYGREPTDEEIAAQLSWP 532

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  V++V  + +EPISLETPIG+E+ S LGDFIEDK   +P +      L+E    VL++
Sbjct: 533 LARVKQVKNVAREPISLETPIGEEEDSSLGDFIEDKEIENPANQTAYTLLQEQLRSVLST 592

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE+ VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R+L+HP RS  LR +
Sbjct: 593 LPQREQEVLKMRFGLDDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPRRSNGLRDY 652

Query: 680 LDG 682
           +D 
Sbjct: 653 IDS 655


>gi|254434698|ref|ZP_05048206.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|207091031|gb|EDZ68302.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 595

 Score =  253 bits (647), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 163/407 (40%), Positives = 250/407 (61%), Gaps = 3/407 (0%)

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLNQSRI 335
           +     +L+  ++    +R+L  N       E  +S + + L+ KL +    L L  SRI
Sbjct: 189 KDGKESSLEATSKHLSRVRTLYGNLEATLAQEGVASPRARELRRKLAREFQFLRLIPSRI 248

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           + L + +     +    E  +       G + ++ F          P W+         +
Sbjct: 249 NQLTQLVQGWISKAQTQEQIIRSCCIHQGEMSQEDFWHNFSSGTTHPQWLDDLLAHSRID 308

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            +  +  +  ++   +  +  + VE G+ + E + I   + + + +A  AK +MVEANLR
Sbjct: 309 RQG-LQTQAKTLRAAQAVLLQVEVEAGLPLDELKAIHQRLVRSQFQAQRAKAQMVEANLR 367

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+SVAKKY NRGL FLDLIQEGNIGLMKA +KFD+  GYKFSTYA WW++QAITR+I D
Sbjct: 368 LVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAHWWIRQAITRAIDD 427

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           QS TIRIPVH+ +K+ K+ R + ++  +  RE  PEE+A++LA+  + + ++ +I K+PI
Sbjct: 428 QSRTIRIPVHVMEKLSKLNRASYQLRQEKGREGRPEELAERLALSEQQIHRMHEIAKQPI 487

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETP+G ++ S LG+ +ED+   +P++ AI A L+    ++LA+L+PRE +V+ MRFGI
Sbjct: 488 SLETPLGKDEDSQLGELMEDEQVPNPMEVAITAGLQTGAQQLLAALSPREAQVVAMRFGI 547

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GM+TDHTL EV +QF ++RERIRQIEA+A+ KL+    SK LR+FL+
Sbjct: 548 GMDTDHTLGEVAQQFDLSRERIRQIEAQALGKLRRLGHSKALRNFLE 594


>gi|300113721|ref|YP_003760296.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299539658|gb|ADJ27975.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii
           C-113]
          Length = 578

 Score =  252 bits (643), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 163/411 (39%), Positives = 248/411 (60%), Gaps = 3/411 (0%)

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLN 331
           E  +R +    L+E  +    + +L          E  +S + + L+ KL +    L L 
Sbjct: 168 ETGIRDEKESNLEETNKHISRVCALYSKLETTLTQEGIASPRARELRSKLAQEFRFLRLI 227

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
            SRI  L + +     +    E  +        G+ ++   +        P W+      
Sbjct: 228 PSRIKQLTQLVQTWISKAQTQEHIIRNCCIHQGGMSQEDSWQVLSSNTTHPQWLDNLLAH 287

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
              + +  +  +  +I   +  +  +  E G+ ++E + I   + + + +A  AK +MVE
Sbjct: 288 SGID-RQRLQAQAKTIRAAQAVLLQVEAEAGLPLAELKVIHQRLVQSQFQAQRAKAQMVE 346

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+SVAKKY NRGL FLDLIQEGNIGLMKA +KFD+  GYKFSTYA WW++QAITR
Sbjct: 347 ANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAHWWIRQAITR 406

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           +I DQS TIRIPVH+ +K+ K+ R + ++  +  RE  PEE+A++L +  + + ++ +I 
Sbjct: 407 AIDDQSRTIRIPVHVMEKLSKLNRASYQLRQEKGREGRPEELAERLDLSEQQIHRMHEIA 466

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           K+PISLETP+G ++ S LG+ +ED+   +P++ AI A L+    R+LA+L+PRE +V+ M
Sbjct: 467 KQPISLETPLGKDEDSQLGELMEDEQVPNPMEVAITAGLQTGAQRLLAALSPREAQVVAM 526

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RFGIGM+TDHTL EV +QF ++RERIRQIEA+A+ KL+    SK LR+FL+
Sbjct: 527 RFGIGMDTDHTLGEVARQFDLSRERIRQIEAQALGKLRRLGHSKALRNFLE 577



 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 74/188 (39%), Gaps = 6/188 (3%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           F+   +  K++I   + +G +T EEL  ++  +   S++ E    +  + G+      D 
Sbjct: 3   FEVRQEELKRLILKGKAQGLLTEEELQEYIIQEVEDSDEAETMANLFHHQGL------DE 56

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            DE      L    +    +  +   +     +  D V  Y+REMGS  LL+RE EI +A
Sbjct: 57  FDETLDSTLLLKHGAEEEIAEAVPSLEGEGTGTVSDMVYAYMREMGSHALLTREEEITLA 116

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K IE G      +L   P     L+ W DE+  G   L++ +        E  G      
Sbjct: 117 KAIETGLNQSTEALGGCPAAVAELLRWTDEVAAGKGRLKDWLTGFTEAEIEETGIRDEKE 176

Query: 204 EGHSYQKR 211
                  +
Sbjct: 177 SNLEETNK 184


>gi|116748652|ref|YP_845339.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697716|gb|ABK16904.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 599

 Score =  252 bits (643), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 209/501 (41%), Positives = 293/501 (58%), Gaps = 5/501 (0%)

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I+ +           +    G       +   E  +           +  + S   +  +
Sbjct: 99  IEADVTSRVTDPVKMYLREMGQVSLLTREGEVEIAKRIEAGEREIFNAIMESSIGIKEIM 158

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           +   +  +++ R  D   +         E   + +V+  L E+  +    + LQ   ++ 
Sbjct: 159 NLKHKLEDDNARVSDVLREVDDEITVEEETAQKERVVGILREVQSLDESNKILQTRLLSD 218

Query: 305 QKDEKSSV----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                       + +  KE++V L+  L L++  ID ++++L+     I  +E EL    
Sbjct: 219 SLTRDEEFVLKSQVQQNKEQIVSLLKGLQLSKRHIDSIIDKLHLCLDVIERSEDELRNCL 278

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
              G         ++    D        D    E K+F+     +I + +  I+ + +E 
Sbjct: 279 LLSGKPLQELKPLYETAIEDRGKARACADQVNMEEKDFLELANKAI-EAKQRIEELEIEA 337

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +     R I+  V  G   A +AK E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 338 KMDSRSLRLILRRVEDGLIRAKLAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIG 397

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R + 
Sbjct: 398 LMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYLV 457

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REPTPEEIA+K+  PVE VRKVLKI KEPISLETPIG+E+ SHLGDFIEDK   SP
Sbjct: 458 QELGREPTPEEIAEKMEFPVEKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKRVASP 517

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D+ I  NL E T + LA+LTPREE+VLRMRFGIG   DHTLEEVG+ F VTRERIRQIE
Sbjct: 518 VDAVINLNLSEQTRKALATLTPREEKVLRMRFGIGEKADHTLEEVGQDFAVTRERIRQIE 577

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSR K+L+SF++
Sbjct: 578 AKALRKLRHPSRRKELKSFIE 598



 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 76/372 (20%), Positives = 163/372 (43%), Gaps = 14/372 (3%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D E +   D  +     D  K++I + +++GY+T +E+N  LP D VS E+++D + + 
Sbjct: 2   TDKETKQRRDPALSKPEMDDIKRLITVGKEKGYLTYDEVNEALPEDLVSPEKLDDMMMIF 61

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
             M I +VD +  + +   E S   + S         + +        DPV+MYLREMG 
Sbjct: 62  DEMDIEIVDSE-QQVQVVRETSGADSDSLLEEEEDELQIEADVTSRVTDPVKMYLREMGQ 120

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII-DLEA 189
           + LL+REGE+ IAKRIEAG   +  ++ ES +  + ++  + +L D    + +++ +++ 
Sbjct: 121 VSLLTREGEVEIAKRIEAGEREIFNAIMESSIGIKEIMNLKHKLEDDNARVSDVLREVDD 180

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEK-------ERDDVQETEGDIESAAKVSKDDRS 242
            I  E +        G   + +      K            ++ E  ++S  + +K+   
Sbjct: 181 EITVEEETAQKERVVGILREVQSLDESNKILQTRLLSDSLTRDEEFVLKSQVQQNKEQIV 240

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
            +    + ++    ++ +        +   ED+LR  ++ +   +    +EL+ L + A+
Sbjct: 241 SLLKGLQLSKRHIDSIIDKLHLCLDVIERSEDELRNCLLLSGKPL----QELKPLYETAI 296

Query: 303 NGQKDEKSSVKCKVLKEK-LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
             +   ++      ++EK  ++L       + RI+ L  +    S+ +      +     
Sbjct: 297 EDRGKARACADQVNMEEKDFLELANKAIEAKQRIEELEIEAKMDSRSLRLILRRVEDGLI 356

Query: 362 SYGIKRDVFLER 373
              + +   +E 
Sbjct: 357 RAKLAKSELIEA 368


>gi|107025596|ref|YP_623107.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116693222|ref|YP_838755.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
 gi|105894970|gb|ABF78134.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116651222|gb|ABK11862.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
          Length = 628

 Score =  252 bits (643), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 159/654 (24%), Positives = 286/654 (43%), Gaps = 61/654 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
              +I L   RGYVT  E+   LP D       +   +ML  +GI+V +          +
Sbjct: 31  LHALIALGIDRGYVTHGEIADALPDDATDGADADAAASMLRELGIDVREHTGAHTAWTLD 90

Query: 91  DSLDLASSASNSSVFLQK---RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                 +  ++            D     T+DP+R+YLREM +  LL R+ E        
Sbjct: 91  RHFAQVTEVASPLADASTPLPADDLLAGHTNDPIRLYLREMSATPLLERDEE-------- 142

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                               I     L  G           ACI   S+          +
Sbjct: 143 --------------------IALALRLESGRA---------ACIDALSRD--------PA 165

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                 +  +  R         +   A  ++   S   + P+    +    ++D D S  
Sbjct: 166 ALAAVAALADDIRAGKVAASVYVTGFAGDAESPASAPATLPDAPAIESPAPNDDADLSLD 225

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           + +      R  V+ AL+ +  +   ++           D  +S   + L  +     G 
Sbjct: 226 SPA-----WRDTVVDALERVGALAPAMQR------ALHADGFASAAYRTLLREATASTGR 274

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL-ERHQGRELDPHWVSY 386
           +      I+ + +   + + R    E  L+    + GI+ +    +     +    W+ +
Sbjct: 275 IRFTSRAIERIGQANGERATRARTFEQRLVDTLAAAGIRAESARHDLFTPCDDVRAWL-H 333

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           A      +    +A    +++  R  +  +S ++ + +     + + + + E     A+ 
Sbjct: 334 ACRAAHPDCAAALARHAPALIDARGALARLSGQSALPLHIAIALDARLARIERAMQPART 393

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ ++NLRLV+SVAK+Y +RGL F DLIQEGNIGLMKA +++D   G+KFSTYA WW++Q
Sbjct: 394 KLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 453

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AIT ++AD   TIR+P H  D ++K+ R AR    +         ++ ++ +PV+ VR++
Sbjct: 454 AITHALADLGRTIRVPAHTVDTLNKLSRLARLHRQRTGDVADARALSTQMRLPVDKVREL 513

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           + I +EPIS + P+  +    L D   D +A +P ++A    LR     ++ SL  RE  
Sbjct: 514 MSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQLRAAVAELIDSLPVREAW 573

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +LR+R+GI ++ +++L E+G+Q  ++ ER+RQ+E  A+ +++    +  LRS L
Sbjct: 574 ILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQFRHAPALRSLL 627


>gi|225874024|ref|YP_002755483.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
 gi|83356350|gb|ABC16653.1| major sigma factor RpoD [Acidobacterium capsulatum]
 gi|225793569|gb|ACO33659.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
          Length = 597

 Score =  252 bits (642), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 187/422 (44%), Positives = 275/422 (65%), Gaps = 39/422 (9%)

Query: 273 EDQLRPKVMCA--------LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK---- 320
           E+++  +V+ A        +D I +  +++++L++     +   K   K + L  +    
Sbjct: 199 EEEITEEVLAARVRQTANKIDGIVKHQKKIQALEEKMQAAKSKVKEQRKLRWLIAREMVF 258

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + ++V  L         L++++      +   E ++  L Q Y   +   L++       
Sbjct: 259 ITRIVRDLKYTNQERKRLLDKVNKTVDSMRTLERQIRSLDQKYDQSKSEELKK------- 311

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
                                        + +++ +  E G+SI++ +     + +G+ +
Sbjct: 312 --------------------EYRRQQKNCKTDLEKLEEEAGLSIADLKRTQREIIQGDMD 351

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A  AK+E++EANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA
Sbjct: 352 AEQAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 411

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R++  ++ REPT EEIA+++ +PV
Sbjct: 412 TWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQELGREPTSEEIARRMDIPV 471

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             VRKVLKI +EPISLETPIG+E+ SHLGDFIED  AVSP ++ I  NL+E T++VL +L
Sbjct: 472 AKVRKVLKIAQEPISLETPIGEEEDSHLGDFIEDSQAVSPSEAVISVNLKEYTSQVLRTL 531

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREERV++MRFG+   ++HTLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS+KLR+F+
Sbjct: 532 TPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPSRSRKLRAFV 591

Query: 681 DG 682
           D 
Sbjct: 592 DN 593



 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 95/426 (22%), Positives = 175/426 (41%), Gaps = 38/426 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D  ++  +K+I   +++GY+T  E+N  +P D  S E ++D +  +   GI++++G    
Sbjct: 43  DKYEEDLQKLIDAGKEKGYLTYNEVNDLIPGDMTSPEDLDDLMTTIGTQGIDILEGSPKL 102

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             +G +D          +   L+K        T+DPVRMYLREMG++ LL+REGE+ IAK
Sbjct: 103 GNDGFDDEDSDDVELDLTPGTLEK--------TNDPVRMYLREMGTVPLLTREGEVEIAK 154

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G+  +M ++  SP+  + +I   ++L  G   ++E++  +     E          
Sbjct: 155 RIERGQLRVMKAVSRSPIVIREIIALGEDLRRGVRSVKEVVIFDEEEITEEVLA-----A 209

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                  +     K +  +Q  E  +++A    K+ R              R + + +  
Sbjct: 210 RVRQTANKIDGIVKHQKKIQALEEKMQAAKSKVKEQRKLRWLIAREMVFITRIVRDLKYT 269

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK--------- 315
           +         +L  KV   +D +  + R++RSL D   +  K E+   + +         
Sbjct: 270 NQER-----KRLLDKVNKTVDSMRTLERQIRSL-DQKYDQSKSEELKKEYRRQQKNCKTD 323

Query: 316 --VLKEKLVKLVGSLSLNQSRI---DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
              L+E+    +  L   Q  I   D+  EQ     + I  N   ++ +A+ Y  +   F
Sbjct: 324 LEKLEEEAGLSIADLKRTQREIIQGDMDAEQAK--RELIEANLRLVVSIAKKYTNRGLQF 381

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRH 429
           L+  Q  E +   +     F       F       I + I   I   +    I +     
Sbjct: 382 LDLIQ--EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIET 439

Query: 430 IVSMVR 435
           I  ++R
Sbjct: 440 INKLIR 445


>gi|218674803|ref|ZP_03524472.1| RNA polymerase sigma factor RpoD [Rhizobium etli GR56]
          Length = 254

 Score =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 209/254 (82%), Positives = 235/254 (92%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF
Sbjct: 1   RIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 60

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPT
Sbjct: 61  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPT 120

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQAN
Sbjct: 121 PEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQAN 180

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLK
Sbjct: 181 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 240

Query: 669 HPSRSKKLRSFLDG 682
           HPSRS+KLRSFLD 
Sbjct: 241 HPSRSRKLRSFLDS 254


>gi|225851205|ref|YP_002731439.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
 gi|225645895|gb|ACO04081.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
          Length = 577

 Score =  250 bits (639), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 191/430 (44%), Positives = 284/430 (66%), Gaps = 6/430 (1%)

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           N +++E + +++  D A  + A+      K +     +A +YRELR L+   +    D +
Sbjct: 151 NIDSNEYDTEDESYDEAEVMDAITKDFIQKGLT----LAHMYRELRDLEQAIIENPDDVE 206

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
              +      K+ + + SL++  +++D + ++L ++  ++   E +L +  +        
Sbjct: 207 LKKEFIEKHAKVNRFIKSLNIKFTKLDKIADELKELYMKLKRKEKDLNKRIKRLQKIDPD 266

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
             +  +G   DP  +   ++                 LK++ EI+ +    G   +EF H
Sbjct: 267 VEKLLKGDYDDPEILKKIEENGFS--FGRFEILRTETLKLQEEIEELKEMIGTVPTEFDH 324

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++++++G  E +  K+++V++NLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KFD
Sbjct: 325 VINIIQEGRKEVNETKQKIVQSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFD 384

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR AR M  ++ REPTP
Sbjct: 385 YKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLVRVARSMVQELGREPTP 444

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEIAKK+ MP E VRK+L+ ++EPISLETPIGD+D SHLGDFIEDK  +SP    ++  L
Sbjct: 445 EEIAKKVGMPPEKVRKILRTSQEPISLETPIGDDDESHLGDFIEDKTVMSPEQHVLRQAL 504

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    VL++L+ REE+VLR RFG+  +T++TLE+VGK+F VTRERIRQIEAKA+RKL+H
Sbjct: 505 RQQLEEVLSTLSEREEQVLRYRFGLEDDTEYTLEQVGKKFGVTRERIRQIEAKALRKLRH 564

Query: 670 PSRSKKLRSF 679
           P R+K LR F
Sbjct: 565 PHRAKYLRPF 574



 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/354 (20%), Positives = 150/354 (42%), Gaps = 36/354 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            D  +K+I LA+++GYVT +EL+  +  D + S+++E  +  L+ + I+V++    E+  
Sbjct: 5   RDDVRKVIMLAKEKGYVTYKELSEIIDEDLLLSDELEQLIEYLNELNIDVIEEAKPEEFS 64

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G  D L +               D A   TDDPV++YL+EMG I LL+R+ EI +AK IE
Sbjct: 65  GESDYLGI------------NFSDDAWAKTDDPVKLYLKEMGKIPLLTRDEEIKLAKDIE 112

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            GR  +   L  +    + L+    ++ DG   +++II++++         +       +
Sbjct: 113 RGRKKVFRGLLRTSFLAERLLDEWAKVADGRMKVKDIINIDSNEYDTEDESYDEAEVMDA 172

Query: 208 YQKR-----------------------EDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
             K                        E+    + + +  E    +    K      +K+
Sbjct: 173 ITKDFIQKGLTLAHMYRELRDLEQAIIENPDDVELKKEFIEKHAKVNRFIKSLNIKFTKL 232

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           D   +  +     L   E D    +  ++ ++ P V   L    +    L+ +++N  + 
Sbjct: 233 DKIADELKELYMKLKRKEKDLNKRIKRLQ-KIDPDVEKLLKGDYDDPEILKKIEENGFSF 291

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
            + E    +   L+E++ +L   +    +  D ++  + +  K +   + ++++
Sbjct: 292 GRFEILRTETLKLQEEIEELKEMIGTVPTEFDHVINIIQEGRKEVNETKQKIVQ 345


>gi|94971322|ref|YP_593370.1| sigma 38, RpoS [Candidatus Koribacter versatilis Ellin345]
 gi|94553372|gb|ABF43296.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Koribacter
           versatilis Ellin345]
          Length = 574

 Score =  248 bits (634), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 198/504 (39%), Positives = 298/504 (59%), Gaps = 17/504 (3%)

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           + +       E          + EK  D V+    ++ +   ++++   ++    E  + 
Sbjct: 70  DKRYDDVEAGEEEMELDLTPGALEKTNDPVRMYLREMGTVPLLTREGEVEIAKRIERGQL 129

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR------SLQDNAVNGQKD 307
                          + A+ + L+  V    + +     E+        L+D      + 
Sbjct: 130 RVLKAISRSPIVIRDIIAIGEDLKRGVRSIKEIVIFDEEEITDEVLAARLKDTTGRIDEL 189

Query: 308 EKSSVKCKVLKEKLVKL----VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            K   K   L++KL ++    V  +   +   D  V ++     R + +   ++R     
Sbjct: 190 NKHYKKSSQLEQKLEEIAPGGVKEIKDKKKARD--VRKVRWTLGRELVSISRIIRKINFT 247

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE-----IKSISV 418
            ++R   ++R      +   +       E       + E    LK ++      ++ +  
Sbjct: 248 NVERKRLIDRVSKTVENLRILERQVSHLEHRANETRSEETKKELKKQSRTLKGDLERMEQ 307

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           E G+SI+E +     + +G+ +A  AKKE++EANLRLV+S+AKKYTNRGLQFLDLIQEGN
Sbjct: 308 EAGVSIAELKRTQREIIQGDMDAEQAKKELIEANLRLVVSIAKKYTNRGLQFLDLIQEGN 367

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R+
Sbjct: 368 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQ 427

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  ++ REP+ EEIAK++ +PV  VRKVLKI +EPISLETPIG+E+ SHLGDFIED++ V
Sbjct: 428 LVQELGREPSSEEIAKRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLGDFIEDRSMV 487

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP ++ I  NL++ T +VL +LT REE+V++MRFG+   ++HTLEEVG+ F VTRERIRQ
Sbjct: 488 SPAEAVINVNLKDQTAQVLRTLTAREEKVIKMRFGLEDGSEHTLEEVGQSFAVTRERIRQ 547

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS+KLR+FLDG
Sbjct: 548 IEAKALRKLRHPSRSRKLRAFLDG 571



 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 69/309 (22%), Positives = 126/309 (40%), Gaps = 6/309 (1%)

Query: 22  LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
           +  D   D  KK+I   +++GY+T  E+N  +P D  S + ++D +  +   GI+V++G 
Sbjct: 1   MALDDKYDDIKKLIDTGKEKGYLTYSEVNDLIPHDVHSPDDLDDLLTTIGTQGIDVLEGP 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                    D       A    + L      A   T+DPVRMYLREMG++ LL+REGE+ 
Sbjct: 61  GKLPSAAVLDKRYDDVEAGEEEMELDLTP-GALEKTNDPVRMYLREMGTVPLLTREGEVE 119

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII--DLEACIGPESKGGF 199
           IAKRIE G+  ++ ++  SP+  + +I   ++L  G   ++EI+  D E           
Sbjct: 120 IAKRIERGQLRVLKAISRSPIVIRDIIAIGEDLKRGVRSIKEIVIFDEEEITDEVLAARL 179

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
              T       +      +    ++E         K  K  R                  
Sbjct: 180 KDTTGRIDELNKHYKKSSQLEQKLEEIAPGGVKEIKDKKKARDVRKVRWTLGRELVSISR 239

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
                +   +     +L  +V   ++ +  + R++  L ++  N  + E++  + K    
Sbjct: 240 IIRKINFTNVE--RKRLIDRVSKTVENLRILERQVSHL-EHRANETRSEETKKELKKQSR 296

Query: 320 KLVKLVGSL 328
            L   +  +
Sbjct: 297 TLKGDLERM 305


>gi|182416400|ref|YP_001821466.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843614|gb|ACB77866.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 640

 Score =  248 bits (633), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 176/434 (40%), Positives = 252/434 (58%), Gaps = 38/434 (8%)

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +  E  +R + + + DS  +     ++L      A + +A+ ++E    + +A   +   
Sbjct: 180 DRQERFDRVVIDKKIDSRESYFKGLEKLVLSTRKAEEAVADSWQEYLKAKSDAERKKVMA 239

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           K   +   L+    K    L       +  +EQL  + + I   + +L R          
Sbjct: 240 KHKKRETTLRSHFGKFFFKLK----VYEEFLEQLRPVLEEIESLDQQLER---------- 285

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
                                 P+ +    +  +V     I++ +K I     I  +E  
Sbjct: 286 -------------------AKHPKSKKDATIDTKV-----IQHRLKQIETIHRIDPAELL 321

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +V+  R    EA  AK EMVEANLRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA EKF
Sbjct: 322 KVVTQTRVHVREAHQAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKF 381

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + ++KV++  +++  +   EPT
Sbjct: 382 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQLLQEYGHEPT 441

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A ++ +PVE V++++K+ ++PISL++P+GD D +  GDFIEDK+A +P D    + 
Sbjct: 442 PEEVADEMNLPVERVQQIMKMAQQPISLQSPVGDGDDTSFGDFIEDKSAENPYDMTAFSL 501

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    VL SLT RE RVL +RFG+      TLEEVGKQF VTRERIRQIEAKA+RK++
Sbjct: 502 LREKIIDVLDSLTERERRVLSLRFGLIDGYSRTLEEVGKQFKVTRERIRQIEAKALRKMR 561

Query: 669 HPSRSKKLRSFLDG 682
           HP+R ++L  F D 
Sbjct: 562 HPTRIRQLHGFFDA 575



 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 61/339 (17%), Positives = 142/339 (41%), Gaps = 30/339 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  + +I+L++++GY+T +++N  LP    + E++++ +++L N+ I +++ D ++D +
Sbjct: 43  NDKIRHLIRLSKEQGYLTFDDINEALPESVENQEEIDNVLSILQNLEIEILEPDQVDDYK 102

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  +   S S+    L           DDPVRMYL++MG + LL+RE E+ I+KRIE
Sbjct: 103 QRMEEAEEEESRSSQHDIL-----------DDPVRMYLKQMGQVPLLTREQEVEISKRIE 151

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                   +L ++ +    ++    +L D       ++  +     +S+  +F G E   
Sbjct: 152 NAELKAQEALFQATIIGNYIVTLGQKLIDRQERFDRVVIDKKI---DSRESYFKGLEKLV 208

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
              R+                  E+ A   ++               +    E    S  
Sbjct: 209 LSTRKAE----------------EAVADSWQEYLKAKSDAERKKVMAKHKKRETTLRSHF 252

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                + ++  + +  L  + E    L    + A + +  + +++  KV++ +L ++   
Sbjct: 253 GKFFFKLKVYEEFLEQLRPVLEEIESLDQQLERAKHPKSKKDATIDTKVIQHRLKQIETI 312

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
             ++ + +  +V Q     +     + E++       I 
Sbjct: 313 HRIDPAELLKVVTQTRVHVREAHQAKTEMVEANLRLVIS 351


>gi|297250830|ref|ZP_06934304.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
 gi|296837936|gb|EFH21874.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
          Length = 322

 Score =  248 bits (632), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 179/318 (56%), Positives = 233/318 (73%), Gaps = 1/318 (0%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           ++RD F++       +  W+          W + +     +IL+ + E+  +  ET ISI
Sbjct: 1   MERDYFIQNFLPEITNLQWIEEEIA-KGRVWSDALDRFRHAILEKQTELADMEKETRISI 59

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + I   +   E E + AK+EM++ANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA
Sbjct: 60  EELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 119

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+   +  
Sbjct: 120 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQETG 179

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            EP   ++A+ + MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N ++P D+A
Sbjct: 180 EEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNIAPADAA 239

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  +L E T  +L SLTPRE +VLRMRFGI MNTDHTLEEVG+QF VTRERIRQIEAKA+
Sbjct: 240 MYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 299

Query: 665 RKLKHPSRSKKLRSFLDG 682
           RKL+HP+RS +LRSFLD 
Sbjct: 300 RKLRHPTRSDRLRSFLDS 317


>gi|301064644|ref|ZP_07205038.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
 gi|300441264|gb|EFK05635.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
          Length = 590

 Score =  247 bits (630), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 206/509 (40%), Positives = 295/509 (57%), Gaps = 13/509 (2%)

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           D  A     +            Y K         RD   E    IE+  K + +      
Sbjct: 82  DKSAASFDMADSASRISDPVKMYLKEMGRISLLTRDGEVEIAKRIEAGEKEALEALLTCG 141

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMED--------QLRPKVMCALDEIAEV----YRE 293
              E+       L + E      ++ +ED        + R  ++  +D+I E+      +
Sbjct: 142 IGVEHIIKLGDRLKDTEVKLKDVINDLEDDDAFMQMGEKRESLIHLIDQIQELNAGIREK 201

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            R     + + +   + + + +  ++K++ +V S SL + +++ ++E   ++ K +   +
Sbjct: 202 RREKAKRSCSEETRNRLNSQIQEDQQKILSIVSSFSLEKRQLEKMLESFRELLKIVETAD 261

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
             +       G K   +L R    ++           P    K+ +          R  I
Sbjct: 262 KNVAECMLQAGGKPISYLNR-CISQIPDSVTDDEIIEPINLKKSELLMLKTKADASRRVI 320

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + +   T ++  E +  +  V +   +AS AK E+++ANLRLV+S+AKKYTNRGL FLDL
Sbjct: 321 RQVKERTNMTPRELKSELERVERSLEKASRAKSELIQANLRLVVSIAKKYTNRGLMFLDL 380

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++
Sbjct: 381 IQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLM 440

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT+R +  +  REPT EEIA+K+  P++ VRKVLKI KEPISLETPIG+E+ SHLGDFIE
Sbjct: 441 RTSRYLVQEHGREPTSEEIAEKMEFPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIE 500

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DKN +SP D+ +   L E T +VL +LTPREE+VLRMRFGIG   DHTLEEVG+ F VTR
Sbjct: 501 DKNILSPGDAVVNFGLAEQTRKVLTTLTPREEKVLRMRFGIGEKADHTLEEVGRDFSVTR 560

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ERIRQIEAKA+RKL+HPSRS+KL+SF+D 
Sbjct: 561 ERIRQIEAKALRKLRHPSRSRKLKSFMDN 589



 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 81/350 (23%), Positives = 144/350 (41%), Gaps = 7/350 (2%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSE-QMEDTVAMLSNMGINVVDGDDLEDEEG 88
           S KK+I   + +GYVT EELN  L  + +SSE Q++D + M   + I V+D    +  E 
Sbjct: 10  SLKKLINTGKNKGYVTFEELNDDLSEEIISSEEQIDDLMMMFEELDIMVIDESTKKKIEK 69

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + +        + S       DSA     DPV+MYL+EMG I LL+R+GE+ IAKRIEA
Sbjct: 70  RKKAKKDRIKQEDKSAASFDMADSAS-RISDPVKMYLKEMGRISLLTRDGEVEIAKRIEA 128

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII-DLEACIGP----ESKGGFFHGT 203
           G    + +L    +  + +I   D L D    L+++I DLE         E +    H  
Sbjct: 129 GEKEALEALLTCGIGVEHIIKLGDRLKDTEVKLKDVINDLEDDDAFMQMGEKRESLIHLI 188

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +           + +E+     +E          ++D+ K+ S   +   ++R L++  +
Sbjct: 189 DQIQELNAGIREKRREKAKRSCSEETRNRLNSQIQEDQQKILSIVSSFSLEKRQLEKMLE 248

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                L  +E   +    C L    +    L        +   D++      + K +L+ 
Sbjct: 249 SFRELLKIVETADKNVAECMLQAGGKPISYLNRCISQIPDSVTDDEIIEPINLKKSELLM 308

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
           L      ++  I  + E+     + +      + R  +     +   ++ 
Sbjct: 309 LKTKADASRRVIRQVKERTNMTPRELKSELERVERSLEKASRAKSELIQA 358


>gi|213161043|ref|ZP_03346753.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 383

 Score =  246 bits (628), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 99/425 (23%), Positives = 170/425 (40%), Gaps = 49/425 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++      A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  LLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +      L ++I            GF       
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEE 174

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                      +   +  + + D +                PE A               
Sbjct: 175 EMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF----------- 223

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +LR + +   D I                     +S    +    KL ++  
Sbjct: 224 -------AELRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFK 259

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W +
Sbjct: 260 QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 319

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A    +  W   +    + + +   +++ I  ETG++I + + I   +  GE +A  AK
Sbjct: 320 AAIAMNKP-WSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAK 378

Query: 446 KEMVE 450
           KEMVE
Sbjct: 379 KEMVE 383


>gi|170691126|ref|ZP_02882292.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia graminis
           C4D1M]
 gi|170144375|gb|EDT12537.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia graminis
           C4D1M]
          Length = 469

 Score =  246 bits (627), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 109/453 (24%), Positives = 190/453 (41%), Gaps = 46/453 (10%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +      + +IKL ++RG++T  E+N  LP +   +E +E  ++  ++MG+ V +    
Sbjct: 59  LEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIISTFNDMGVAVYEQAPD 118

Query: 84  EDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +     D+   ASS        +      DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 119 AETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 178

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   M+ ++   P T   ++   + + +    + E++D       E   GF 
Sbjct: 179 EIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELVDGLIDADAEDADGFS 238

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                    + E+  +E E D+ ++      +A     +                     
Sbjct: 239 VQEAEAIESEDEEEEEEDEEDEEEDDGTAQATANAAQMEA-------------------- 278

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                          L+   +     I+E + ++R   +      K+   S      +E 
Sbjct: 279 ---------------LKRASLEKFALISEWFDKMRRAFE------KEGYKSKSYLKAQET 317

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGREL 379
           +   + ++      ++ L + L      +   E ++L  +    G+ R  F+ R  G E 
Sbjct: 318 IQNELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSET 377

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W           +   +   + +I + +  +  +     + + + +     +  GE 
Sbjct: 378 DLEWADKIVSEGHP-YSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGEL 436

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +A  AK+EM EANLRLVIS+AKKYTNRGLQFLD
Sbjct: 437 KARQAKREMTEANLRLVISIAKKYTNRGLQFLD 469


>gi|291451171|ref|ZP_06590561.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291354120|gb|EFE81022.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 397

 Score =  245 bits (624), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 126/295 (42%), Positives = 186/295 (63%), Gaps = 23/295 (7%)

Query: 410 RNEIKSISVETGISISEFRHIVSMV-----------------------RKGECEASIAKK 446
           R  ++ I     +S ++   +   V                       R+       AK 
Sbjct: 103 RQYLREIGRIPLLSAADEVELARRVEAGVFAAAKLAGGCADAGLARDLRRLVVLGERAKG 162

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            ++EANLRLV+SVAK+YT RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW++Q
Sbjct: 163 RLIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQ 222

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           A++R++ADQ+ TIR+PVH+ + I++VVRT R +  +  REP  EE+ ++L +  E V +V
Sbjct: 223 AMSRALADQARTIRVPVHVVELINRVVRTQRALLQEAGREPAAEEVGERLGLSAEKVEEV 282

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++  EPISL  P+G ED   LGD IED +A SP +SA    LR+    VLA+L  RE +
Sbjct: 283 LRLAHEPISLHAPVGGEDDVFLGDLIEDADAASPAESAALLLLRQHLDAVLATLGDRERQ 342

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+++R+G       TLEE+G+ F VTRER+RQIE+K +R+L+  + + +LR +L+
Sbjct: 343 VVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLREHTAAGQLRGYLE 397



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            + A  +  D  R YLRE+G I LLS   E+ +A+R+EAG
Sbjct: 91  SEQAGAAAPDLFRQYLREIGRIPLLSAADEVELARRVEAG 130


>gi|153826548|ref|ZP_01979215.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
 gi|149739640|gb|EDM53854.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
          Length = 302

 Score =  245 bits (624), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 185/302 (61%), Positives = 229/302 (75%), Gaps = 1/302 (0%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           +  W+       +  +   V  + + I +   +++ I  ET +S+   + I   +  GE 
Sbjct: 1   NEEWLDKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEA 59

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTY
Sbjct: 60  KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 119

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REP PEE+A+++ MP
Sbjct: 120 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMP 179

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +L+  T  VLA 
Sbjct: 180 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAG 239

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSF
Sbjct: 240 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF 299

Query: 680 LD 681
           LD
Sbjct: 300 LD 301


>gi|325125918|gb|ADY85248.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 373

 Score =  244 bits (623), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 168/358 (46%), Positives = 229/358 (63%), Gaps = 26/358 (7%)

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           L+    +    +D LV++  D    I+ ++GE  +LA                       
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVDDKGEPSKLA----------------------- 78

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++  K+  + E ++  A        +R  +K I   + +S  E    V + ++       
Sbjct: 79  LAKQKNVEKAELEHLSAPGSRMNDPVRQYLKRIGRVSLLSGDEE---VQLAKRIGAGDQE 135

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK E+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA WW
Sbjct: 136 AKDELTNANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWW 195

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ +PV+ V
Sbjct: 196 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKV 255

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ LK+ +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    LR+    VL +LT R
Sbjct: 256 REALKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLRDQLAEVLDTLTDR 315

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS KLR FL+
Sbjct: 316 EENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNKLRDFLE 373



 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 54/288 (18%), Positives = 97/288 (33%), Gaps = 49/288 (17%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD       +G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVDD------KGEPSKLALAKQKNVEKAELEHL-S 94

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           +     +DPVR YL+ +G + LLS + E+ +AKRI AG       L  + L     I  R
Sbjct: 95  APGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIGAGDQEAKDELTNANLRLVVSIAKR 154

Query: 172 ---------DELNDGTTLLREIIDLEAC-------------------------------- 190
                    D + +G   L + +D                                    
Sbjct: 155 YVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIP 214

Query: 191 -IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               E+                 D   E+   ++      +  A KV+++  S      E
Sbjct: 215 VHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREALKVAQEPVSLETPIGE 274

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             ++   +  ED+D ++    A  + LR ++   LD + +    +  L
Sbjct: 275 EDDSHLGDFIEDKDATSPEQHAASEMLRDQLAEVLDTLTDREENVLRL 322


>gi|289548873|ref|YP_003473861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
 gi|289182490|gb|ADC89734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
          Length = 568

 Score =  244 bits (622), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 168/419 (40%), Positives = 255/419 (60%), Gaps = 3/419 (0%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+  +        +QL    M    E+A+ Y+E    +D  +     E    +      +
Sbjct: 151 DDSRTVEEYEESHEQLERYFMQKGLELAKAYKEALQWRDLYLQYGLSE-YKKEYLKRHAR 209

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + +++  + L  SR + + ++L ++  R      EL +             E  +  +L 
Sbjct: 210 MNRVLKDMKLKYSRFEKIADELLNLYNRYSKRIKELEQRKSKLESIHPNIEELIREYDLR 269

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
           P     A+    G  +  +       L +R E++ +  E GI   E   ++ ++++G  +
Sbjct: 270 PDLQEKAEKAGYGFARFQILRN--EYLALRKEVEELRREMGILPEEIGRVIQIIKEGRTK 327

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + AK+ MV+ NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA
Sbjct: 328 VTQAKQVMVKCNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYA 387

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+ + +  ++++ ++ REPT EEIAK L +PV
Sbjct: 388 TWWIRQAITRAIADQARTIRIPVHMIETINDITKAHKKLTQELGREPTAEEIAKYLGIPV 447

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +  RKV+++ +EPISLETPIGD++ +HL DFIEDK+  SP +   +  LRE   +VL++L
Sbjct: 448 DKARKVMRMAQEPISLETPIGDDEDAHLKDFIEDKSVPSPEEQVTRKLLREQLIKVLSTL 507

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             +E  +L  R+G+   T++TLE++G+ F VTRERIRQIE KAIRKL+HP+RSK L+ F
Sbjct: 508 GEKEREILMYRYGLVDGTEYTLEQIGRMFNVTRERIRQIETKAIRKLRHPARSKYLKDF 566



 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 60/349 (17%), Positives = 131/349 (37%), Gaps = 33/349 (9%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           KK++ L  ++GYVT +ELN  L    + +E  E+ +  L   GI +V             
Sbjct: 8   KKLMSLG-EKGYVTYDELNEALGDSLMDTELYEEIMDFLQERGIKLV------------- 53

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             +      +  + +            DPVR+Y+REMG I LL+RE EI  AK+IE GR 
Sbjct: 54  ESEEDREERDEHLMVSADHLLQSSKDGDPVRLYMREMGKIPLLTREEEIKYAKQIEMGRK 113

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIID-------LEACIGPESKGGFFHGTE 204
           +M   L  +      ++     + +G   +++I+D       +E       +   +   +
Sbjct: 114 IMRRGLLRTSFLIDRVLKDWANVCNGKLRVQDIVDTVDDSRTVEEYEESHEQLERYFMQK 173

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    K    + +     +Q    + +          ++V    +   +    + ++  +
Sbjct: 174 GLELAKAYKEALQWRDLYLQYGLSEYKKEYLKRHARMNRVLKDMKLKYSRFEKIADELLN 233

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-----------SVK 313
             +  S    +L  +    L+ I     EL    D   + Q+  +              +
Sbjct: 234 LYNRYSKRIKELEQRK-SKLESIHPNIEELIREYDLRPDLQEKAEKAGYGFARFQILRNE 292

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              L++++ +L   + +    I  +++ + +   ++   +  +++    
Sbjct: 293 YLALRKEVEELRREMGILPEEIGRVIQIIKEGRTKVTQAKQVMVKCNLR 341


>gi|171322946|ref|ZP_02911628.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171091683|gb|EDT37240.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 498

 Score =  243 bits (620), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 163/554 (29%), Positives = 253/554 (45%), Gaps = 58/554 (10%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IID 186
           MG+  LL+R+ E A A+RIE GRA   A LC  P    AL+  R E+    +     +I 
Sbjct: 1   MGTTPLLTRDDEFAYAQRIERGRAASAAVLCGDPDALDALVSIRIEIAQCRSAASTYVIF 60

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           L+   GP       H   G S       + E  RDD  +    IE++A            
Sbjct: 61  LDD--GPRDNTTADHAEAGTSATA----AGEPARDDDTQANTQIEASAW----------- 103

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
                                         R  V+  L  I E+   +R+   +  +   
Sbjct: 104 ------------------------------RNAVVARLARIDELAHGMRAALASGGSAC- 132

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
                   +        L+ +L L+   I+ + E L   ++R     G L R+    G+ 
Sbjct: 133 -----AAYRTYVRDATALLRTLGLSARAIERMSEPLRARARRHRAFRGRLERMLADVGVP 187

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
              F +     +    W++                  +  +  R+ I   +  + +    
Sbjct: 188 -PSFAQA--ADDDHAGWLASCVAAHPACAATLTRRAAE-FVDARDAILRAAPASELPPGA 243

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              + + +   E     A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E
Sbjct: 244 TASLDARLGAIERAMQPARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIE 303

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D+  G++FSTYA WW++QAIT ++AD   TIR+P H  D ++K+ R AR    +    
Sbjct: 304 RYDYRRGFRFSTYATWWIRQAITHALADLGRTIRVPTHTVDALNKLSRLARAHRQRAGTA 363

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            TP E+A  +  PV+ VR ++ I KEP+S + P+  E      D   D    SP D+A  
Sbjct: 364 ATPAELAVHMGEPVDKVRDLMAIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAAGA 423

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A LR T T V+  L PRE  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +
Sbjct: 424 AQLRRTITAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALAR 483

Query: 667 LKHPSRSKKLRSFL 680
           L+ P     LRSF+
Sbjct: 484 LRAPDTLGLLRSFI 497


>gi|261755428|ref|ZP_05999137.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261745181|gb|EEY33107.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 235

 Score =  243 bits (620), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 194/235 (82%), Positives = 220/235 (93%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QA
Sbjct: 1   MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITRSIADQ+ TIRIPVHM + I+K+VRT+R+M ++I REPTPEE+A+KLAMP+E VRKVL
Sbjct: 61  ITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVL 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLR+TTTRVLASLTPREERV
Sbjct: 121 KIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSRS+KLRSFLD 
Sbjct: 181 LRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 235


>gi|218780916|ref|YP_002432234.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
 gi|218762300|gb|ACL04766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
          Length = 595

 Score =  243 bits (619), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 205/502 (40%), Positives = 285/502 (56%), Gaps = 10/502 (1%)

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           DL    G       +    G       D   E  +   +  +  +++  + +      +D
Sbjct: 97  DLLDAGGSSDPVKLYLREMGMVSLLSRDGEIEIAKKIEEGEQEVLKALLETTIGVEHLID 156

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV--- 302
              E AE + R  D   D         E     ++   LD IA +++E    ++      
Sbjct: 157 LRTEMAEGEVRLKDVLRDVDEGENFVDESTQMARISEILDSIAAIHQENMEFREKLFGSG 216

Query: 303 ---NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              + ++  +          ++  L+    L    +  +  ++Y            L   
Sbjct: 217 PPLDPEERRRVRRSVNRRNRRIFALLKDWRLEHQVVSEIESKIYRQIDWFEAQHEGLNCC 276

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
           AQ+ G+            E    W     D  E + K         +++I+  I+   + 
Sbjct: 277 AQNLGVAVSDLRSHCSCLEDFCSWAGECCDLEESQLKVCYY----QVVEIQTSIRDRELA 332

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
              +    + + + +  G  +A  AK E++ ANLRLV+S+AKKYTNRGLQFLDLIQEGNI
Sbjct: 333 LKANSLALKRVRACIWTGRGKAKDAKAELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNI 392

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R +
Sbjct: 393 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRYL 452

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REPTPEEIA+K+  P+E VR+VLKI KEPISLETPIG+E+ SHLGDFIEDK  + 
Sbjct: 453 VQELGREPTPEEIAQKMEFPLEKVRRVLKIAKEPISLETPIGEEEDSHLGDFIEDKKFML 512

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++AI  NL E T +VLA+LTPREE+VLRMRFGIG   DHTLEEVGK F VTRERIRQI
Sbjct: 513 PSEAAISLNLAEQTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGKDFSVTRERIRQI 572

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HPSRS+KL+SF+D
Sbjct: 573 EAKALRKLRHPSRSQKLKSFID 594



 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/173 (32%), Positives = 97/173 (56%), Gaps = 2/173 (1%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           ++ +    S     +    +++I   +++GY+T +ELN  LP D VSS+Q++DT+ M   
Sbjct: 2   AKAKGKAKSEEIKQAQAGLQELISKGKKQGYLTYDELNEALPEDMVSSDQIDDTLMMFDE 61

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           M I ++DG  +   + S+   D     S   V      D+    + DPV++YLREMG + 
Sbjct: 62  MDIEILDGKKITVSDSSKMDDDSKDQDSEPEVPKPDLLDAGG--SSDPVKLYLREMGMVS 119

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           LLSR+GEI IAK+IE G   ++ +L E+ +  + LI  R E+ +G   L++++
Sbjct: 120 LLSRDGEIEIAKKIEEGEQEVLKALLETTIGVEHLIDLRTEMAEGEVRLKDVL 172


>gi|167829080|ref|ZP_02460551.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia pseudomallei
           9]
          Length = 285

 Score =  242 bits (617), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 171/284 (60%), Positives = 221/284 (77%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           ++  + +I + +  +  +     + + + +     +  GE +A  AK+EM EANLRLVIS
Sbjct: 1   MSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 60

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 61  IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 120

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R +R++  +   EP P  +A+K+ MP + +RK++KI KEPIS+ET
Sbjct: 121 IRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMET 180

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD+D SHLGDFIED N V+P D+A+ A++R+    VL SLTPRE +VLRMRFGI M+T
Sbjct: 181 PIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMST 240

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS KL+SFL+G
Sbjct: 241 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 284


>gi|241896072|ref|ZP_04783368.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
 gi|241870672|gb|EER74423.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
          Length = 378

 Score =  242 bits (617), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 185/383 (48%), Positives = 235/383 (61%), Gaps = 23/383 (6%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           D AV     E    K     +    +V  +SLN  +ID L +Q+      ++   GE   
Sbjct: 19  DKAVKSIIKEFKKDKQIKETDLQKAVVKPMSLNADQIDDLYDQIESAGISVVDENGEPTA 78

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
            A      +           L    +  A D P G   N           +R  +K I  
Sbjct: 79  RALENKKTK-----------LSAKELKQAADAPTGMKIN---------DPVRMYLKEIGR 118

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            + ++  E    VS+  + E     AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN
Sbjct: 119 VSLLTGDEE---VSLAERIEAGDETAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGN 175

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R 
Sbjct: 176 MGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRN 235

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +   + REPTPEEI  ++ +  E VR +LKI +EP+SLETPIG+ED SHLGDFIED  AV
Sbjct: 236 LLQDLGREPTPEEIGAEMDVATEKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAV 295

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP DSA    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQ
Sbjct: 296 SPADSAAYQMLKEQLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGKVFGVTRERIRQ 355

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSK+LR FLD
Sbjct: 356 IEAKALRKLRHPSRSKQLRDFLD 378



 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 85/189 (44%), Gaps = 14/189 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +IK  ++   +   +L   +  P  ++++Q++D    + + GI+VVD    E+ 
Sbjct: 19  DKAVKSIIKEFKKDKQIKETDLQKAVVKPMSLNADQIDDLYDQIESAGISVVD----ENG 74

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E +  +L+   +  ++    Q          +DPVRMYL+E+G + LL+ + E+++A+RI
Sbjct: 75  EPTARALENKKTKLSAKELKQAADAPTGMKINDPVRMYLKEIGRVSLLTGDEEVSLAERI 134

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 135 EAGDETAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKF 185

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 186 DYRKGFKFS 194


>gi|300812189|ref|ZP_07092631.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496825|gb|EFK31905.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 373

 Score =  242 bits (616), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 168/364 (46%), Positives = 231/364 (63%), Gaps = 26/364 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    +    +D LV++  D    I+ ++GE  +LA                 
Sbjct: 36  KEFTDRLLKPYQIEGRAVDQLVQEFEDNGISIVDDKGEPSKLA----------------- 78

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                 ++  K+  + E ++  A        +R  +K I   + +S  E   +   +   
Sbjct: 79  ------LAKQKNVEKAELEHLSAPGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIE-- 130

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK E+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFS
Sbjct: 131 -AGDQEAKDELTSANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYQLGFKFS 189

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ 
Sbjct: 190 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMD 249

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PV+ VR+VLK+ +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L++    VL
Sbjct: 250 LPVKKVREVLKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVL 309

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR
Sbjct: 310 DTLTDREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLR 369

Query: 678 SFLD 681
            FL+
Sbjct: 370 DFLE 373



 Score = 77.2 bits (188), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 97/288 (33%), Gaps = 49/288 (17%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD       +G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVDD------KGEPSKLALAKQKNVEKAELEHL-S 94

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           +     +DPVR YL+ +G + LLS + E+ +AKRIEAG       L  + L     I  R
Sbjct: 95  APGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIEAGDQEAKDELTSANLRLVVSIAKR 154

Query: 172 ---------DELNDGTTLLREIIDLEACI------------------------------- 191
                    D + +G   L + +D                                    
Sbjct: 155 YVGRGMSFLDLIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIP 214

Query: 192 --GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               E+                 D   E+   ++      +    KV+++  S      E
Sbjct: 215 VHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPVSLETPIGE 274

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             ++   +  ED+D ++    A  + L+ ++   LD + +    +  L
Sbjct: 275 EDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRL 322


>gi|227513300|ref|ZP_03943349.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
 gi|227083501|gb|EEI18813.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
          Length = 389

 Score =  242 bits (616), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 165/303 (54%), Positives = 213/303 (70%), Gaps = 4/303 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGE 438
           DP  +  AK   + E  +  A     I   +R  +K I   + +S  E  ++   +    
Sbjct: 90  DPRAIDAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIE--- 146

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFST
Sbjct: 147 SGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFST 206

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M
Sbjct: 207 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDM 266

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL 
Sbjct: 267 PTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLD 326

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ 
Sbjct: 327 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKD 386

Query: 679 FLD 681
           FL+
Sbjct: 387 FLE 389



 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 50/184 (27%), Positives = 80/184 (43%), Gaps = 16/184 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +++K  +  G++T +EL   +  P  +  ++ME+ +  + + GI+VVD        G  D
Sbjct: 37  QIVKDNKPIGHITYDELQKKIEEPFSLDKKEMEELLENIEDSGISVVDD------NGDPD 90

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
              + ++   +   L           +DPVRMYL+E+G + LLS + EI +AKRIE+G  
Sbjct: 91  PRAIDAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIESGDE 150

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
                L E+ L     I  R  +  G   L  I         E   G     E   Y+K 
Sbjct: 151 EAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKFDYRKG 201

Query: 212 EDSS 215
              S
Sbjct: 202 FKFS 205


>gi|42526854|ref|NP_971952.1| RNA polymerase sigma factor RpoD [Treponema denticola ATCC 35405]
 gi|41817169|gb|AAS11863.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
          Length = 619

 Score =  242 bits (616), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 184/590 (31%), Positives = 298/590 (50%), Gaps = 79/590 (13%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           +           +  + S +   DDP+++YL+E+G  +LL+ + E++++K +        
Sbjct: 107 IEKEKPRHETAKKLVRTSHEAGVDDPIKLYLQEIGKEDLLTADEEVSLSKSM-------- 158

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
                                DG  +++++I     + PE     F      ++ K + +
Sbjct: 159 --------------------EDGEAIIKKVIKNSGILIPE-----FFVIGQKAFSKLDPA 193

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
              K R ++ E                                             A + 
Sbjct: 194 ESNKPRKELSEEM-------------------------------------------AEKK 210

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK--SSVKCKVLKEKLVKLVGSLSLNQ 332
           +L+     +L  I    ++  SL+ +  + +  E    S + + L++K+   +  + +  
Sbjct: 211 RLKQVYGDSLRNIYSEIKQYMSLKKHCYDRESLESFLESPELQALRKKMFNSLKRIHIES 270

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I+ + ++  + ++++   + +  R  +  GIK    L +   R   P      +    
Sbjct: 271 EEIEKISDRFIEATEKVQDYQHKKERKEKQLGIKSYADLRKLGKRLAIPREREKLEKELN 330

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                        I  +  +I+ I  +   ++ E   + S ++ G+     AK +++ AN
Sbjct: 331 ISANEVKDIYT-QIQVLTRKIRKIEYDFEATVDEVIDLTSEIKNGQRMLKNAKDKLINAN 389

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKY NRGLQF DL+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI
Sbjct: 390 LRLVVSIAKKYINRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSI 449

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           +DQ+ TIR+PVHM ++I+KV R +R++  K+ REP  +EIA +L   +E V++V  + +E
Sbjct: 450 SDQARTIRVPVHMIEQINKVNRESRQLMQKLGREPNDDEIALQLGWSIEKVKQVKNVARE 509

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ + LGD IEDK   +P +      L+E    VL+SL  RE+ VL+MRF
Sbjct: 510 PISLETPIGEEEDTLLGDLIEDKGVENPSNRTELTLLQEQLEMVLSSLPEREQEVLKMRF 569

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI      TLEEVG  F VTRERIRQIEAK +R+L+HP RS+KL+ +LD 
Sbjct: 570 GIEGGYPLTLEEVGLYFDVTRERIRQIEAKGLRRLRHPKRSRKLKDYLDN 619


>gi|229824058|ref|ZP_04450127.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
 gi|229786412|gb|EEP22526.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
          Length = 379

 Score =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 159/273 (58%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E  ++   ++       IAK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 110 VRMYLKEIGNVPLLSAEEEINLAVRIQG---GDDIAKQELAEANLRLVVSIAKRYVGRGM 166

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 167 QFLDLIQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 226

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 227 INKLVRVQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 286

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A+SP      A LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 287 GDFIEDEGAMSPEVFTSSALLREQLEDVLDTLTDREENVLRLRFGLDDGNIRTLEQVGKV 346

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 347 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 379



 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 38/176 (21%), Positives = 80/176 (45%), Gaps = 6/176 (3%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVA 68
             + + + + +  V     ++ + +I   +  G V  +EL   +  P  + ++ ++  + 
Sbjct: 2   AEEKDLKLTPNQDVASPYLEAVQALILAKKSEGQVHYDELTEKIASPYGLDADGIDTLIQ 61

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           ++ + G++VV     +D   ++  +        + +  + +  ++     DPVRMYL+E+
Sbjct: 62  IVEDNGVSVV----GDDGGPTKQQMVREEEQLQADLAAESKTATSKLKVSDPVRMYLKEI 117

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G++ LLS E EI +A RI+ G  +    L E+ L     I  R  +  G   L  I
Sbjct: 118 GNVPLLSAEEEINLAVRIQGGDDIAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI 172


>gi|226327186|ref|ZP_03802704.1| hypothetical protein PROPEN_01051 [Proteus penneri ATCC 35198]
 gi|225204404|gb|EEG86758.1| hypothetical protein PROPEN_01051 [Proteus penneri ATCC 35198]
          Length = 407

 Score =  241 bits (615), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 104/422 (24%), Positives = 180/422 (42%), Gaps = 46/422 (10%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E+S D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENSNDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G   L ++I   A I P ++          
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--AFIDPNAE------EVAE 177

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           S         ++  +D ++ + D +       D        PE A      L E  + + 
Sbjct: 178 SEDVNLGKEDDEVANDAEDEDEDEDEDGDNDSDSDDDNSIDPELARQKFTELREQYEKTR 237

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            T+ A     +   +  L                                    L ++  
Sbjct: 238 QTIKAKGRNHKDTELEIL-----------------------------------LLSEIFK 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV  + ++  R+   E  ++RL      + +  F+    G E +  W +
Sbjct: 263 QFRLVPKQFDYLVNNMREMMDRVRTQERHIMRLCVDQVKMPKKNFITLFTGNETNDTWFT 322

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A+   +  W   +A   + + +   +++ I VETG++I + + I   +  GE +A  AK
Sbjct: 323 AARAMNKP-WSEKLAGIEEEVQRSLQKLQQIEVETGLTIEQVKDINRRMSIGEAKARRAK 381

Query: 446 KE 447
           K 
Sbjct: 382 KR 383


>gi|313123888|ref|YP_004034147.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280451|gb|ADQ61170.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 373

 Score =  241 bits (615), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 168/364 (46%), Positives = 231/364 (63%), Gaps = 26/364 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    +    +D LV++  D    I+ ++GE  +LA                 
Sbjct: 36  KEFTDRLLKPYQIEGRAVDQLVQEFEDNGISIVDDKGEPSKLA----------------- 78

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                 ++  K+  + E ++  A        +R  +K I   + +S  E   +   +   
Sbjct: 79  ------LAKQKNVEKAELEHLSAPGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIE-- 130

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK E+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFS
Sbjct: 131 -AGDQEAKDELTSANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYQLGFKFS 189

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ 
Sbjct: 190 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMD 249

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PV+ VR+VLK+ +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L++    VL
Sbjct: 250 LPVKKVREVLKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVL 309

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR
Sbjct: 310 DTLTDREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLR 369

Query: 678 SFLD 681
            FL+
Sbjct: 370 DFLE 373



 Score = 77.2 bits (188), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 97/288 (33%), Gaps = 49/288 (17%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD       +G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVDD------KGEPSKLALAKQKNVEKAELEHL-S 94

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           +     +DPVR YL+ +G + LLS + E+ +AKRIEAG       L  + L     I  R
Sbjct: 95  APGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIEAGDQEAKDELTSANLRLVVSIAKR 154

Query: 172 ---------DELNDGTTLLREIIDLEACI------------------------------- 191
                    D + +G   L + +D                                    
Sbjct: 155 YVGRGMSFLDLIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIP 214

Query: 192 --GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               E+                 D   E+   ++      +    KV+++  S      E
Sbjct: 215 VHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPVSLETPIGE 274

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             ++   +  ED+D ++    A  + L+ ++   LD + +    +  L
Sbjct: 275 EDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRL 322


>gi|227544906|ref|ZP_03974955.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300910067|ref|ZP_07127527.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
 gi|227185118|gb|EEI65189.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300892715|gb|EFK86075.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
          Length = 380

 Score =  241 bits (614), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 175/385 (45%), Positives = 232/385 (60%), Gaps = 27/385 (7%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV          K     E   K+     LN   ID L++ + D    ++   G+  
Sbjct: 22  YDTAVGKLIRNYKKQKQIEYDELTTKIAKPFELNADGIDNLLQNIEDAGISVVDENGDP- 80

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSI 416
                                 DP  +   + F +   K+  A     I   +R  +K I
Sbjct: 81  ----------------------DPRALKATEKFSQSAMKDTSAPTGVKINDPVRMYLKEI 118

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                ++  E   +   + K      +AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQE
Sbjct: 119 GRVNLLTADEEVQLALRIEK---GDEVAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQE 175

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  
Sbjct: 176 GNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQ 235

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHLGDFIED++
Sbjct: 236 RQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHLGDFIEDQD 295

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK F VTRERI
Sbjct: 296 ATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERI 355

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 356 RQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 88/186 (47%), Gaps = 15/186 (8%)

Query: 1   MTIGKKRNR-DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEV 58
           M   KK++   S+S + D  +       D +  K+I+  +++  +  +EL   +  P E+
Sbjct: 1   MAKSKKKDIVISNSANFDQQE------YDTAVGKLIRNYKKQKQIEYDELTTKIAKPFEL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           +++ +++ +  + + GI+VVD      E G  D   L ++   S   ++          +
Sbjct: 55  NADGIDNLLQNIEDAGISVVD------ENGDPDPRALKATEKFSQSAMKDTSAPTGVKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLTADEEVQLALRIEKGDEVAKQELAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREI 184
             L  I
Sbjct: 168 QFLDLI 173


>gi|227510293|ref|ZP_03940342.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
 gi|227524444|ref|ZP_03954493.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227088403|gb|EEI23715.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227189945|gb|EEI70012.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
          Length = 389

 Score =  241 bits (614), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 165/303 (54%), Positives = 213/303 (70%), Gaps = 4/303 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGE 438
           DP  +  AK   + E  +  A     I   +R  +K I   + +S  E  ++   +    
Sbjct: 90  DPRAIDAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADEEINLAKRIE--- 146

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFST
Sbjct: 147 SGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFST 206

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M
Sbjct: 207 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDM 266

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL 
Sbjct: 267 PTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLD 326

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ 
Sbjct: 327 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKD 386

Query: 679 FLD 681
           FL+
Sbjct: 387 FLE 389



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 55/220 (25%), Positives = 88/220 (40%), Gaps = 20/220 (9%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKK----MIKLARQRGYVTIEELNAFLP-P 55
           M   K  N     +      +     +   +KK    ++K  +  G++T +EL   +  P
Sbjct: 1   MANKKTNNAKVVKKATTKTKAAAAKKTQKPYKKVFDQIVKDNKPIGHITYDELQKKIEEP 60

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
             +  ++ME+ +  + + GI+VVD        G  D   + ++   +   L         
Sbjct: 61  FSLDKKEMEELLENIEDSGISVVDD------NGDPDPRAIDAAKKVTKKELSDVSAPTGV 114

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
             +DPVRMYL+E+G + LLS + EI +AKRIE+G       L E+ L     I  R  + 
Sbjct: 115 KINDPVRMYLKEIGRVSLLSADEEINLAKRIESGDEEAKQELAEANLRLVVSIAKRY-VG 173

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            G   L  I         E   G     E   Y+K    S
Sbjct: 174 RGMQFLDLI--------QEGNMGLMKAVEKFDYRKGFKFS 205


>gi|318066961|emb|CBY89095.1| RNA polymerase sigma70 factor [Halomonas muralis]
          Length = 367

 Score =  241 bits (614), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 126/397 (31%), Positives = 187/397 (47%), Gaps = 52/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEIAIAKRIE G   +M++L   P   ++++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGTREVMSALAYLPGAVESILDAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D  +E+   +  E++G+ + 
Sbjct: 79  QDEELPGRLSDLF-----------SGFIDPDEGIPGVAEADVPEEEPVSEDAESDGEDDD 127

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            A   +   +     PE A      + E    +   +                       
Sbjct: 128 DAAEEE--ETTSGPDPEEARARFEQIREQNAVAKAAID---------------------- 163

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K   +SV+ K  K +L +L   + L     + LV Q+    ++I   
Sbjct: 164 -------------KHGVASVEAKTEKARLAELFSPIKLVPKHFERLVGQVRISVEQIRIQ 210

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +L+   +   + R  F++     E +P W+         ++ + +      I + + 
Sbjct: 211 EKTILQVFVKKGKVPRKTFIKAFPSNESNPQWLDVFLAN-NAKYTDKLEPFRTDIARAQR 269

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + + E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 270 KIAFEEALIQLPVGEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 329

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 330 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|325473907|gb|EGC77095.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           F0402]
          Length = 619

 Score =  241 bits (614), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 184/590 (31%), Positives = 298/590 (50%), Gaps = 79/590 (13%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           +           +  + S +   DDP+++YL+E+G  +LL+ + E++++K +        
Sbjct: 107 IEKEKPRHETAKKLVRTSHEAGVDDPIKLYLQEIGKEDLLTADEEVSLSKSM-------- 158

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
                                DG  +++++I     + PE     F      ++ K + +
Sbjct: 159 --------------------EDGEAIIKKVIKNSGILIPE-----FFVIGQKAFSKLDPA 193

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
              K R ++ E                                             A + 
Sbjct: 194 ESNKPRKELSEEM-------------------------------------------AEKK 210

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK--SSVKCKVLKEKLVKLVGSLSLNQ 332
           +L+     +L  I    ++  SL+ +  + +  E    S + + L++K+   +  + +  
Sbjct: 211 RLKQVYGDSLRNIYSEIKQYMSLKKHCYDRESLESFLESPELQALRKKMFNSLKRIHIES 270

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             I+ + ++  + ++++   + +  R  +  GIK    L +   R   P      +    
Sbjct: 271 EEIEKISDRFIEATEKVQDYQHKKERKEKQLGIKSYADLRKLGKRLAIPREREKLEKELN 330

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                        I  +  +I+ I  +   ++ E   + S ++ G+     AK +++ AN
Sbjct: 331 ISANEVKDIYT-QIQVLTRKIRKIEYDFEATVDEVIDLTSEIKNGQRMLKNAKDKLINAN 389

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKY NRGLQF DL+QEGNIGL+KA EKF++  GYKFSTYA WW++QAITRSI
Sbjct: 390 LRLVVSIAKKYINRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSI 449

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           +DQ+ TIR+PVHM ++I+KV R +R++  K+ REP  +EIA +L   +E V++V  + +E
Sbjct: 450 SDQARTIRVPVHMIEQINKVNRESRQLMQKLGREPNDDEIALQLGWSIEKVKQVKNVARE 509

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETPIG+E+ + LGD IEDK   +P +      L+E    VL+SL  RE+ VL+MRF
Sbjct: 510 PISLETPIGEEEDTLLGDLIEDKGVENPSNRTELTLLQEQLEMVLSSLPEREQEVLKMRF 569

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           GI      TLEEVG  F VTRERIRQIEAK +R+L+HP RS+KL+ +LD 
Sbjct: 570 GIEGGYPLTLEEVGLYFDVTRERIRQIEAKGLRRLRHPKRSRKLKDYLDN 619


>gi|312874241|ref|ZP_07734275.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
 gi|311090311|gb|EFQ48721.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
          Length = 382

 Score =  240 bits (613), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 173/387 (44%), Positives = 236/387 (60%), Gaps = 28/387 (7%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +L     N  K+ K+S + K   + + ++V    L    ID LV++  D    I+ N+  
Sbjct: 23  TLSQVVKNIIKEVKTSKEIKE-DDFVARMVKPYQLEGKAIDQLVQEFEDNGISIVDND-- 79

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
                               G   +   +   KD  + E  +  A     +   +R  +K
Sbjct: 80  --------------------GNPSNLS-LKKQKDVEKAELNDMTAPSSVRMNDPVRMYLK 118

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I     ++  +   +   +         AK+E+ EANLRLV+S+AK+Y  RG+ FLDLI
Sbjct: 119 EIGRVPLLNADQEIDLAKRIE---NNDDDAKQELAEANLRLVVSIAKRYVGRGMSFLDLI 175

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 176 QEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 235

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ M  + VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 236 IQRQLLQDLGREPTPEEIGAEMDMSTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 295

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K+A SP   A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRE
Sbjct: 296 KDATSPEQHASYELLKEQLEEVLDTLTDREENVLRLRFGLNDGRTRTLEEVGRVFGVTRE 355

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 356 RIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 94.1 bits (232), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 68/157 (43%), Gaps = 8/157 (5%)

Query: 29  DSWKKMIKLARQRGYVTIEE-LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
              K +IK  +    +  ++ +   + P ++  + ++  V    + GI++VD D      
Sbjct: 26  QVVKNIIKEVKTSKEIKEDDFVARMVKPYQLEGKAIDQLVQEFEDNGISIVDND------ 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  +L L          L      +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 80  GNPSNLSLKKQKDVEKAELNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                    L E+ L     I  R  +  G + L  I
Sbjct: 140 NNDDDAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI 175


>gi|320104559|ref|YP_004180150.1| RNA polymerase sigma-70 subunit RpoD [Isosphaera pallida ATCC
           43644]
 gi|319751841|gb|ADV63601.1| RNA polymerase, sigma 70 subunit, RpoD [Isosphaera pallida ATCC
           43644]
          Length = 592

 Score =  240 bits (613), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 189/667 (28%), Positives = 312/667 (46%), Gaps = 86/667 (12%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS-SEQMEDTVAMLSNMGINVVDGDD 82
            D  D+  K ++ L +++G++T+ ++N  LP D  S  ++++     L  +G+ V+  D+
Sbjct: 1   MDMLDEGLKALLDLGKRQGFLTMSQINEVLPDDAGSQPDRLDALFNTLEELGVEVLQRDE 60

Query: 83  LEDEEGSEDSLDLA------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
             D   +             +   + +       D    +  DP                
Sbjct: 61  EADGRIAPGDDLDDESDDLMADPEDLAAVHDHELDPESDADGDP---------------- 104

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
                                 E P +   L +  D   +    +   ID    +     
Sbjct: 105 ------------------GLDLEEPGSDLDLDLDGDLAVEDLDDMSRRIDDPVRMYLTQM 146

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
           G     T        E    E  R   +    + + A ++  D   KVDS     +   +
Sbjct: 147 GEIPLLTREQEISLAERI--ESTRKRFRRRVLECDYALRLVVDVLKKVDSGELPFDRTVK 204

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY-RELRSLQDNAVNGQKDEKSSVKCK 315
               +  +    L  M     P  +  L+ + +   R+ R L     + +K  + +    
Sbjct: 205 VSMTENLEKNQILGRM-----PHNLVTLEHLMDCNDRDFRDLLRARGDKEKRRRLARALA 259

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
           + + K VKLV  LS+   ++  L+++L  IS R+     ++  +    G           
Sbjct: 260 IRRRKAVKLVEELSIRTQKVQPLMKRLEQISARMQELLNQIREVRAGRG----------- 308

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
                                      +D    +  E++ + + T  + +     V  + 
Sbjct: 309 --------------------------RLDEHANLEKELRDLMLMTLETPAGLARRVREMN 342

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +   E   AK+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K++W  G+K
Sbjct: 343 ERFKEYEKAKRKLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEWRRGFK 402

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + + K+    +++  +  REPT EE A+ 
Sbjct: 403 FSTYATWWIRQAITRAIADQARTIRIPVHMIETMSKLRNVNKKLLQEKGREPTIEETARA 462

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             + +E  R+V+KI++ PISL+ P+G+ + S+ GDFIED  A +P++SA Q  L++   +
Sbjct: 463 ANISIEETRRVMKISRHPISLDRPVGESEDSYFGDFIEDTTAENPINSATQEMLKDKIDQ 522

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT RE  ++++R+G+G    +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RS++
Sbjct: 523 VLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSRQ 582

Query: 676 LRSFLDG 682
           L  FL+ 
Sbjct: 583 LEGFLES 589


>gi|261367093|ref|ZP_05979976.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
 gi|282571217|gb|EFB76752.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
          Length = 364

 Score =  240 bits (613), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 151/270 (55%), Positives = 203/270 (75%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++  E   +   ++ G  E   AK+ + EANLRLV+S+AK+Y  RG+QFL
Sbjct: 95  YLKEIGRVPLLTPEEEIDLALKIQAGGPEGEKAKQRLSEANLRLVVSIAKRYVGRGMQFL 154

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 155 DLIQEGNLGLIKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 214

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V + + ++ ++   +P+ EEIA++L M V+ VR+++++ +EP+SLETPIG+E+ SHLGDF
Sbjct: 215 VKKVSSQLLHEYGHDPSAEEIAERLDMSVDKVREIMRVAQEPVSLETPIGEEEDSHLGDF 274

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A  P ++A Q  L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+F V
Sbjct: 275 IPDDDAPVPAEAASQTLLKEQLADVLKTLTPREEKVLRLRFGLEDGRPRTLEEVGKEFNV 334

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRSKKLR FLD
Sbjct: 335 TRERIRQIEAKALRKLRHPSRSKKLRDFLD 364



 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 39/163 (23%), Positives = 68/163 (41%), Gaps = 14/163 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             D  + +I+  R+ G +T  E+   +      +  EQME     L + GI        E
Sbjct: 4   KKDPIRSLIENGRRSGKLTNTEIGDAMEESGHVLDVEQMEKLYEELESNGI--------E 55

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             +         +   ++    ++  ++   + DDPV++YL+E+G + LL+ E EI +A 
Sbjct: 56  VVDDDASDAADVALTEDNVDDFEESLNTDGITIDDPVKVYLKEIGRVPLLTPEEEIDLAL 115

Query: 145 RIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +I+AG          L E+ L     I  R  +  G   L  I
Sbjct: 116 KIQAGGPEGEKAKQRLSEANLRLVVSIAKRY-VGRGMQFLDLI 157


>gi|259503187|ref|ZP_05746089.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
 gi|259168844|gb|EEW53339.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
          Length = 380

 Score =  240 bits (613), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +      +AK+++ EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLTADEEVKLALRIEQ---GDEVAKQQLAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 49/186 (26%), Positives = 84/186 (45%), Gaps = 15/186 (8%)

Query: 1   MTIGKKRN-RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEV 58
           M   KK++   S+SE  D          D +  K+I+  +++  +    L   L  P E+
Sbjct: 1   MAKSKKKDLVISNSEDFDQQK------YDTAVGKLIRQYKKQKEIQYGVLTDKLAKPYEL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           ++E +++ +  + + GI+VVD        G  D   L ++   S   ++          +
Sbjct: 55  NAEGIDNLLQNVEDAGISVVDA------NGDPDPRALKATEKLSQNAMKDTSAPTGVKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLTADEEVKLALRIEQGDEVAKQQLAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREI 184
             L  I
Sbjct: 168 QFLDLI 173


>gi|227890913|ref|ZP_04008718.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
 gi|227867322|gb|EEJ74743.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
          Length = 372

 Score =  240 bits (612), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 174/374 (46%), Positives = 230/374 (61%), Gaps = 26/374 (6%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +  V  KVL +KLV       LN  ++D L+  + D    ++   GE    +       
Sbjct: 25  PQKQVNYKVLTDKLVT---PFKLNADQMDQLIGSIEDRGISVVDENGEPSAHSLKA---- 77

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                            +   +  E +        V     +R  +K I     ++  E 
Sbjct: 78  ----------------ATKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEE 121

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              V++  K E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EK
Sbjct: 122 ---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEK 178

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP
Sbjct: 179 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREP 238

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A   
Sbjct: 239 MPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYE 298

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL
Sbjct: 299 LLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 358

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSK+L+ FL+
Sbjct: 359 RHPSRSKQLKDFLE 372



 Score =  104 bits (259), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 85/188 (45%), Gaps = 14/188 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            + + +I+  + +  V  + L   L  P +++++QM+  +  + + GI+VVD    E+ E
Sbjct: 14  KALRDLIREYKPQKQVNYKVLTDKLVTPFKLNADQMDQLIGSIEDRGISVVD----ENGE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S  SL  A+  +  +   +     +    +DPVRMYL+E+G + LL+ + E+A+A +IE
Sbjct: 70  PSAHSLKAATKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G + L  I         E   G     E   
Sbjct: 130 EGDQEAKQRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------QEGNMGLMKAVEKFD 180

Query: 208 YQKREDSS 215
           Y+K    S
Sbjct: 181 YRKGFKFS 188


>gi|199598416|ref|ZP_03211835.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|258508506|ref|YP_003171257.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
 gi|199590735|gb|EDY98822.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|257148433|emb|CAR87406.1| RNA polymerase sigma factor [Lactobacillus rhamnosus GG]
 gi|259649816|dbj|BAI41978.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
          Length = 416

 Score =  240 bits (612), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 178/387 (45%), Positives = 238/387 (61%), Gaps = 27/387 (6%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
              D+AV     +    K     +   KL+    L  + ID L++++ D    I+   GE
Sbjct: 56  KAYDDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVDENGE 115

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
              ++                       +   K   + E  +  A     I   +R  +K
Sbjct: 116 PATIS-----------------------LKKQKKVSKKEMSDMSAPSGVKINDPVRMYLK 152

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+QFLDLI
Sbjct: 153 EIGRVSLLTADEE---VALALKIEQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLI 209

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 210 QEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 269

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 270 IQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 329

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRE
Sbjct: 330 QDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRE 389

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 390 RIRQIEAKALRKLRHPSRSKQLKDFLE 416



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/190 (26%), Positives = 83/190 (43%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      
Sbjct: 58  YDDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVD------ 111

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +
Sbjct: 112 ENGEPATISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALK 171

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 172 IEQGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 222

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 223 FDYRKGFKFS 232


>gi|295397565|ref|ZP_06807644.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
 gi|294974189|gb|EFG49937.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
          Length = 374

 Score =  240 bits (612), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 161/283 (56%), Positives = 208/283 (73%), Gaps = 3/283 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           VA +V     +R  +K I     ++  E    VS+ ++ E    +AK+E+ EANLRLV+S
Sbjct: 95  VASDVKINDPVRMYLKEIGRVELLTADEE---VSLAQRIEQGDPVAKQELAEANLRLVVS 151

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ T
Sbjct: 152 IAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQART 211

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+VR  R++   + REPTPEEI  ++ +P E VR +LKI +EP+SLET
Sbjct: 212 IRIPVHMVETINKLVRIQRQLLQDLGREPTPEEIGAEMDLPTEKVRDILKIAQEPVSLET 271

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+ED SHLGDFIED +A SP D      L+E    VL +LT REE VLR+RFG+    
Sbjct: 272 PIGEEDDSHLGDFIEDHDATSPDDYTSAELLKEQLNEVLDTLTDREENVLRLRFGLEDGQ 331

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLE+VG+QF VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 332 SKTLEQVGQQFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 40/158 (25%), Positives = 74/158 (46%), Gaps = 3/158 (1%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K++I   +  G +   +L+  +  P  +  + M+  +    + GI VVD ++ E  
Sbjct: 12  NQATKQLIAEKKILGTIQYTDLSDKIAQPFALDDKGMDSLIEKFEDQGIAVVD-ENGEPT 70

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D      +       +     ++D   +DPVRMYL+E+G +ELL+ + E+++A+RI
Sbjct: 71  MRQMDKEADKEAEKVKKEEIDPTSVASDVKINDPVRMYLKEIGRVELLTADEEVSLAQRI 130

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G  +    L E+ L     I  R  +  G + L  I
Sbjct: 131 EQGDPVAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI 167


>gi|148543974|ref|YP_001271344.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri DSM 20016]
 gi|184153369|ref|YP_001841710.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri JCM 1112]
 gi|227364887|ref|ZP_03848933.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|325682488|ref|ZP_08162005.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
 gi|148531008|gb|ABQ83007.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus reuteri DSM
           20016]
 gi|183224713|dbj|BAG25230.1| RNA polymerase sigma-43 factor RpoD [Lactobacillus reuteri JCM
           1112]
 gi|227070091|gb|EEI08468.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|324978327|gb|EGC15277.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
          Length = 380

 Score =  240 bits (612), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 175/385 (45%), Positives = 232/385 (60%), Gaps = 27/385 (7%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV          K     E   K+     LN   ID L++ + D    ++   G+  
Sbjct: 22  YDTAVGKLIRNYKKQKQIEYDELTTKIAKPFELNADGIDNLLQNIEDAGISVVDENGDP- 80

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSI 416
                                 DP  +   + F +   K+  A     I   +R  +K I
Sbjct: 81  ----------------------DPRALKATEKFSQSAMKDTSAPTGVKINDPVRMYLKEI 118

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                ++  E   +   + K      +AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQE
Sbjct: 119 GRVNLLTADEEVQLALRIEK---GDEVAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQE 175

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  
Sbjct: 176 GNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQ 235

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHLGDFIED++
Sbjct: 236 RQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHLGDFIEDQD 295

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK F VTRERI
Sbjct: 296 ATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERI 355

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 356 RQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 87/186 (46%), Gaps = 15/186 (8%)

Query: 1   MTIGKKRNR-DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEV 58
           M   KK++   S+S   D  +       D +  K+I+  +++  +  +EL   +  P E+
Sbjct: 1   MAKSKKKDIVISNSADFDQQE------YDTAVGKLIRNYKKQKQIEYDELTTKIAKPFEL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           +++ +++ +  + + GI+VVD      E G  D   L ++   S   ++          +
Sbjct: 55  NADGIDNLLQNIEDAGISVVD------ENGDPDPRALKATEKFSQSAMKDTSAPTGVKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLTADEEVQLALRIEKGDEVAKQELAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREI 184
             L  I
Sbjct: 168 QFLDLI 173


>gi|331701385|ref|YP_004398344.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
 gi|329128728|gb|AEB73281.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
          Length = 414

 Score =  240 bits (612), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 167/303 (55%), Positives = 216/303 (71%), Gaps = 4/303 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGE 438
           DP  +  AK   + E  +  A     I   +R  +K I   + +S  +    +S+ ++ E
Sbjct: 115 DPRAIGAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADQE---ISLAKRIE 171

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KFST
Sbjct: 172 AGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFST 231

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEI  ++ M
Sbjct: 232 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDM 291

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    VL 
Sbjct: 292 PTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESVLD 351

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ 
Sbjct: 352 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKD 411

Query: 679 FLD 681
           FLD
Sbjct: 412 FLD 414



 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 53/190 (27%), Positives = 81/190 (42%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
               +  ++K  +  G++T +EL   +  P  +S + ME  +  + + GI+VVD      
Sbjct: 56  YKKEFDAIVKANKPIGHITYDELEKKIEKPYSLSEKDMEGLLESIEDSGISVVD------ 109

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G  D   + ++   +   L           +DPVRMYL+E+G + LLS + EI++AKR
Sbjct: 110 ENGDPDPRAIGAAKKVTKKELSDVSAPTGVKINDPVRMYLKEIGRVSLLSADQEISLAKR 169

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IEAG       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 170 IEAGDEEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 220

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 221 FDYRKGFKFS 230


>gi|320105405|ref|YP_004180995.1| RpoD subfamily RNA polymerase sigma-70 factor [Terriglobus
           saanensis SP1PR4]
 gi|319923926|gb|ADV81001.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Terriglobus
           saanensis SP1PR4]
          Length = 567

 Score =  240 bits (612), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 187/444 (42%), Positives = 278/444 (62%), Gaps = 44/444 (9%)

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCA--------LDEIAEVYRELRSLQDNAVNGQKD 307
            +L     +    ++  E++L  +V+ A        +D +   Y++  SLQD   N    
Sbjct: 147 EDLKRGVRNVKEVVTFDEEELTEEVLAARVKQTVKRIDLLVTHYKKAESLQDRITNPVGK 206

Query: 308 EKSSVKCKVLKE---------KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           +  +    + K          K+ ++V  L         L++++      +   E ++ +
Sbjct: 207 DAKAKAKDLRKHRWMAGRELVKVTRIVRELKYTNGEKKRLLDKVNKTVDAMRTLERQIKQ 266

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           L   +   +   L++                                    + ++  + V
Sbjct: 267 LDAKFEASKSEELKK---------------------------EYKRQQKNCKVDLDRLEV 299

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           + G+++ + +     + +G+ +A  AK+E++EANLRLV+S+AKKYTNRGLQFLDLIQEGN
Sbjct: 300 DAGLTVEDLKRTQREMIQGDMDAEKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGN 359

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++RT+R+
Sbjct: 360 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQ 419

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  ++ RE + EEIA+++ +PV  VRKVLKI +EPISLETPIG+E+ SHLGDFIED+ AV
Sbjct: 420 LVQELGREASSEEIARRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLGDFIEDRMAV 479

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP D+ I  NL+E T++VL +LTPREERV++MRFG+   ++HTLEEVG+ F VTRERIRQ
Sbjct: 480 SPSDAVISVNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQ 539

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
           IEAKA+RKL+HPSRS+KL++F+DG
Sbjct: 540 IEAKALRKLRHPSRSRKLKAFVDG 563



 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 66/296 (22%), Positives = 128/296 (43%), Gaps = 12/296 (4%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +  ++   +++   +++GY+T  E+N  LP D  + + ++D +  ++  GI+V+ G+D 
Sbjct: 5   IEKYEEDVDRIVDTGKEKGYLTYGEVNDLLPGDITTPDDLDDLLTTINTQGIDVLGGEDK 64

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                  D+ D       S              T+DPVRMYLREMG++ LL+REGE+ IA
Sbjct: 65  F------DARDKYEEQEESDDVELDLTPGQLEKTNDPVRMYLREMGTVPLLTREGEVEIA 118

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G+  +M ++  S +  + ++   ++L  G   ++E++  +     E         
Sbjct: 119 KRIERGQLRVMKAISRSSIVIREIMGLGEDLKRGVRNVKEVVTFDEEELTEEVLAARVKQ 178

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                       ++ E    + T    + A   +KD R              R + E + 
Sbjct: 179 TVKRIDLLVTHYKKAESLQDRITNPVGKDAKAKAKDLRKHRWMAGRELVKVTRIVRELKY 238

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
            +       + +L  KV   +D +  + R+++ L D      K E+   + K  ++
Sbjct: 239 TNGE-----KKRLLDKVNKTVDAMRTLERQIKQL-DAKFEASKSEELKKEYKRQQK 288


>gi|313884259|ref|ZP_07818025.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620706|gb|EFR32129.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 376

 Score =  240 bits (611), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 174/397 (43%), Positives = 238/397 (59%), Gaps = 23/397 (5%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           +E      EL    D A      EK  +      E   K+ G   L+   +D L++++ D
Sbjct: 3   EENKNTKNELTLSYDQARQQLIAEKKLIGQIHYDELTDKIAGPYKLDAEAMDKLIQKVED 62

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
               ++ ++G   +                             K        +  A ++ 
Sbjct: 63  AGIAVVGDDGGPTKQQMVR--------------------AQEVKVDTSTTGNSATASKIK 102

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
               +R  +K I     +S       +S+ ++ E    +AK+E+ EANLRLV+S+AK+Y 
Sbjct: 103 VSDPVRMYLKEIGRVDLLSADAE---ISLAKRIEDGDELAKQELAEANLRLVVSIAKRYV 159

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVH
Sbjct: 160 GRGMSFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 219

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VR  R +   + REPTPEEI  ++ +P E VR++LKI++EP+SLETPIG+ED
Sbjct: 220 MVETINKLVRVQRNLLQDLGREPTPEEIGAEMDLPTEKVREILKISQEPVSLETPIGEED 279

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            SHLGDFIED+ A+SP      + LRE    VL +LT REE VLR+RFG+      TLE+
Sbjct: 280 DSHLGDFIEDEGAMSPESFTSSSLLREQLEDVLDTLTDREENVLRLRFGLDDGNIRTLEQ 339

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 VGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 376



 Score =  101 bits (251), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 51/204 (25%), Positives = 89/204 (43%), Gaps = 15/204 (7%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLS 71
            E++++ + L   + D + +++I   +  G +  +EL   +  P ++ +E M+  +  + 
Sbjct: 3   EENKNTKNELTLSY-DQARQQLIAEKKLIGQIHYDELTDKIAGPYKLDAEAMDKLIQKVE 61

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           + GI VV  D    ++    + ++    S +       K        DPVRMYL+E+G +
Sbjct: 62  DAGIAVVGDDGGPTKQQMVRAQEVKVDTSTTGNSATASK----IKVSDPVRMYLKEIGRV 117

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           +LLS + EI++AKRIE G  +    L E+ L     I  R  +  G + L  I       
Sbjct: 118 DLLSADAEISLAKRIEDGDELAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI------- 169

Query: 192 GPESKGGFFHGTEGHSYQKREDSS 215
             E   G     E   Y K    S
Sbjct: 170 -QEGNMGLMKAVEKFDYTKGFKFS 192


>gi|259500591|ref|ZP_05743493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|302191282|ref|ZP_07267536.1| RNA polymerase sigma factor RpoD [Lactobacillus iners AB-1]
 gi|309805231|ref|ZP_07699283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|309807583|ref|ZP_07701535.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|312871770|ref|ZP_07731858.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|312875648|ref|ZP_07735649.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|325912054|ref|ZP_08174452.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
 gi|259167975|gb|EEW52470.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|308165465|gb|EFO67696.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|308169189|gb|EFO71255.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|311088902|gb|EFQ47345.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|311092712|gb|EFQ51068.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|325476004|gb|EGC79172.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
          Length = 382

 Score =  240 bits (611), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 173/387 (44%), Positives = 236/387 (60%), Gaps = 28/387 (7%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +L     N  K+ K+S + K   + + ++V    L    ID LV++  D    I+ N+  
Sbjct: 23  TLSQVVKNIIKEVKTSKEIKE-DDFVARMVKPYQLEGKAIDQLVQEFEDNGISIVDND-- 79

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
                               G   +   +   KD  + E  +  A     +   +R  +K
Sbjct: 80  --------------------GNPSNLS-LKKQKDVEKAELNDMTAPSSVRMNDPVRMYLK 118

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I     ++  +   +   +         AK+E+ EANLRLV+S+AK+Y  RG+ FLDLI
Sbjct: 119 EIGRVPLLNADQEIDLAKRIE---NNDDEAKQELAEANLRLVVSIAKRYVGRGMSFLDLI 175

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 176 QEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 235

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ M  + VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 236 IQRQLLQDLGREPTPEEIGAEMDMSTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 295

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K+A SP   A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRE
Sbjct: 296 KDATSPEQHASYELLKEQLEEVLDTLTDREENVLRLRFGLNDGRTRTLEEVGRVFGVTRE 355

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 356 RIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 68/157 (43%), Gaps = 8/157 (5%)

Query: 29  DSWKKMIKLARQRGYVTIEE-LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
              K +IK  +    +  ++ +   + P ++  + ++  V    + GI++VD D      
Sbjct: 26  QVVKNIIKEVKTSKEIKEDDFVARMVKPYQLEGKAIDQLVQEFEDNGISIVDND------ 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  +L L          L      +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 80  GNPSNLSLKKQKDVEKAELNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                    L E+ L     I  R  +  G + L  I
Sbjct: 140 NNDDEAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI 175


>gi|296133798|ref|YP_003641045.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola sp.
           JR]
 gi|296032376|gb|ADG83144.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola
           potens JR]
          Length = 366

 Score =  240 bits (611), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         AK+ + EANLRLV+S+AK+Y  RGL
Sbjct: 97  VRMYLKEIGRVPLLTAEEEVELAKRME---TGDEEAKRRLAEANLRLVVSIAKRYVGRGL 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 154 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA ++ +PV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 214 INKLIRVSRQLLQELGREPTPEEIAAEMDIPVDRVREIMKIAQEPVSLETPIGEEEDSHL 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A +P ++A    LRE    VL +LTPREE+VLR+RFG+      TLEEVG++
Sbjct: 274 GDFIEDQDAPAPAEAASFILLREQLEEVLETLTPREEKVLRLRFGLDDGRSRTLEEVGQE 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 334 FGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 366



 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 46/156 (29%), Positives = 76/156 (48%), Gaps = 5/156 (3%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  +++I+  ++RG +T  E+   L   +++ EQ+++    L+NMGI+VV   ++ D E 
Sbjct: 9   EGVQELIENGKKRGILTYTEIMNTLQNVDLNPEQIDEIYEKLANMGIDVV--PEVPDLEP 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +     A +            D      DDPVRMYL+E+G + LL+ E E+ +AKR+E 
Sbjct: 67  LDSEAIEADAEEAEIEVDLTVPD--GIGIDDPVRMYLKEIGRVPLLTAEEEVELAKRMET 124

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  R  +  G   L  I
Sbjct: 125 GDEEAKRRLAEANLRLVVSIAKRY-VGRGLLFLDLI 159


>gi|116629751|ref|YP_814923.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri ATCC 33323]
 gi|238853400|ref|ZP_04643779.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282851794|ref|ZP_06261157.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300361838|ref|ZP_07058015.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311110607|ref|ZP_07712004.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
 gi|116095333|gb|ABJ60485.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus gasseri ATCC
           33323]
 gi|238833972|gb|EEQ26230.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282557036|gb|EFB62635.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300354457|gb|EFJ70328.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311065761|gb|EFQ46101.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
          Length = 373

 Score =  240 bits (611), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 174/365 (47%), Positives = 236/365 (64%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+   +L    +D LV++  D    I+  +GE  +LA                 
Sbjct: 35  KEFTAQLIKPYNLQGKAVDQLVQEFEDNGISIVDEKGEPSKLA----------------- 77

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD  + E K+  A     +   +R  +K I   + ++  +    +++ ++
Sbjct: 78  ------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQE---IALAKR 128

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 129 IEAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 188

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 189 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 248

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 249 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 308

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 309 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 368

Query: 677 RSFLD 681
           + FLD
Sbjct: 369 KDFLD 373



 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 44/142 (30%), Positives = 66/142 (46%), Gaps = 8/142 (5%)

Query: 44  VTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T +E  A L  P  +  + ++  V    + GI++VD      E+G    L L       
Sbjct: 32  ITEKEFTAQLIKPYNLQGKAVDQLVQEFEDNGISIVD------EKGEPSKLALKKQKDVE 85

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIEAG       L E+ L
Sbjct: 86  KAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIEAGDEEAKQELAEANL 145

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  +  G + L  I
Sbjct: 146 RLVVSIAKRY-VGRGMSFLDLI 166


>gi|309803186|ref|ZP_07697283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|309806578|ref|ZP_07700575.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|312872984|ref|ZP_07733044.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315653573|ref|ZP_07906493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325912624|ref|ZP_08175007.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|329920166|ref|ZP_08276997.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
 gi|308164694|gb|EFO66944.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|308166998|gb|EFO69180.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|311091506|gb|EFQ49890.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315488935|gb|EFU78577.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325478045|gb|EGC81174.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|328936620|gb|EGG33064.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
          Length = 382

 Score =  239 bits (610), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 173/387 (44%), Positives = 236/387 (60%), Gaps = 28/387 (7%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +L     N  K+ K+S + K   + + ++V    L    ID LV++  D    I+ N+  
Sbjct: 23  TLSQVVKNIIKEVKTSKEIKE-DDFVARMVKPYQLEGRAIDQLVQEFEDNGISIVDND-- 79

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
                               G   +   +   KD  + E  +  A     +   +R  +K
Sbjct: 80  --------------------GNPSNLS-LKKQKDVEKAELNDMTAPSSVRMNDPVRMYLK 118

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I     ++  +   +   +         AK+E+ EANLRLV+S+AK+Y  RG+ FLDLI
Sbjct: 119 EIGRVPLLNADQEIDLAKRIE---NNDDEAKQELAEANLRLVVSIAKRYVGRGMSFLDLI 175

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 176 QEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 235

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ M  + VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 236 IQRQLLQDLGREPTPEEIGAEMDMSTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 295

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K+A SP   A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRE
Sbjct: 296 KDATSPEQHASYELLKEQLEEVLDTLTDREENVLRLRFGLNDGRTRTLEEVGRVFGVTRE 355

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 356 RIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 67/157 (42%), Gaps = 8/157 (5%)

Query: 29  DSWKKMIKLARQRGYVTIEE-LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
              K +IK  +    +  ++ +   + P ++    ++  V    + GI++VD D      
Sbjct: 26  QVVKNIIKEVKTSKEIKEDDFVARMVKPYQLEGRAIDQLVQEFEDNGISIVDND------ 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  +L L          L      +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 80  GNPSNLSLKKQKDVEKAELNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                    L E+ L     I  R  +  G + L  I
Sbjct: 140 NNDDEAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI 175


>gi|318066911|emb|CBY89070.1| RNA polymerase sigma70 factor [Chromohalobacter nigrandesensis]
          Length = 367

 Score =  239 bits (610), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 122/395 (30%), Positives = 180/395 (45%), Gaps = 48/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+       G  G +  +      E    D     GD+    
Sbjct: 79  QDEEAPGRLSDLFSGFIDPD------EGIPGVAEAEVPGPEPEPSAAD-----GDVSEDD 127

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             ++++ +     PE A+     + E  + +   +                         
Sbjct: 128 DEAEEEETGGGPDPEEAKARFEQIREQNERAKAAID------------------------ 163

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K    S +    +E+L +L   + L     + LV Q+    +++   E 
Sbjct: 164 -----------KHGLGSSEANKEQERLAELFSPIKLVPKHFERLVGQVRISIEQVRSQEK 212

Query: 355 ELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++   +   + R  F+    G E D  W+   K      +   +      IL+ + +I
Sbjct: 213 AIMQVFVKQAKVPRKTFIGSFPGAESDLEWLDRFKAKHAK-YAERLEPFRADILRAQRKI 271

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 272 GFEEEMVRLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 331

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 332 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|227892546|ref|ZP_04010351.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
 gi|227865667|gb|EEJ73088.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
          Length = 370

 Score =  239 bits (610), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 170/365 (46%), Positives = 233/365 (63%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+   +L+   +L    ID LV++  D    I+   G+  +LA                 
Sbjct: 32  KDFTARLIKPYNLQGKAIDQLVQEFEDNGISIVDENGDPSKLA----------------- 74

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD  + E K+  A     +   +R  +K I     ++  +    +++ ++
Sbjct: 75  ------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQE---IALAKR 125

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 126 IEAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 185

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K+++  R++   + REPTPEEI  ++
Sbjct: 186 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIKIQRQLLQDLGREPTPEEIGAEM 245

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +V
Sbjct: 246 NVPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQV 305

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 306 LETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 365

Query: 677 RSFLD 681
           + F+D
Sbjct: 366 KDFMD 370



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/148 (27%), Positives = 63/148 (42%), Gaps = 15/148 (10%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAIDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIEAG       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIEAGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 ---------DELNDGTTLLREIIDLEAC 190
                    D + +G   L + +D    
Sbjct: 152 YVGRGMSFLDLIQEGNMGLMKAVDKFDY 179


>gi|90961886|ref|YP_535802.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius UCC118]
 gi|90821080|gb|ABD99719.1| RNA polymerase sigma factor [Lactobacillus salivarius UCC118]
          Length = 372

 Score =  239 bits (610), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVNLLTADEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R+M   + REP PEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRIQRQMLQDLGREPMPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDATSPAEHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 372



 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 84/188 (44%), Gaps = 14/188 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            + + +I+  + +  V  + L   L  P ++ ++QM+  +  + + GI+VVD    E+ E
Sbjct: 14  KTLRDLIREYKPQKQVNYKVLTDKLVTPFKLDADQMDQLIGSIEDRGISVVD----ENGE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S  SL  A+  +  +   +     +    +DPVRMYL+E+G + LL+ + E+A+A +IE
Sbjct: 70  PSAHSLKAAAKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G + L  I         E   G     E   
Sbjct: 130 EGDQEAKQRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------QEGNMGLMKAVEKFD 180

Query: 208 YQKREDSS 215
           Y+K    S
Sbjct: 181 YRKGFKFS 188


>gi|194467797|ref|ZP_03073783.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
 gi|194452650|gb|EDX41548.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
          Length = 380

 Score =  239 bits (610), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 174/385 (45%), Positives = 231/385 (60%), Gaps = 27/385 (7%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV          K     E   K+     LN   ID L++ + D    ++   G+  
Sbjct: 22  YDTAVGKLIRNYKKQKQIEYDELTTKIAKPFELNADGIDNLLQNIEDAGISVVDENGDP- 80

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSI 416
                                 DP  +   +   +   K+  A     I   +R  +K I
Sbjct: 81  ----------------------DPRALKATEKLSQSAMKDTSAPTGVKINDPVRMYLKEI 118

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                ++  E   +   + K      +AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQE
Sbjct: 119 GRVNLLTADEEVQLALRIEK---GDEVAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQE 175

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  
Sbjct: 176 GNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQ 235

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHLGDFIED++
Sbjct: 236 RQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHLGDFIEDQD 295

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK F VTRERI
Sbjct: 296 ATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERI 355

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 356 RQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 87/186 (46%), Gaps = 15/186 (8%)

Query: 1   MTIGKKRNR-DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEV 58
           M   KK++   S+S   D  +       D +  K+I+  +++  +  +EL   +  P E+
Sbjct: 1   MAKSKKKDIVISNSADFDQQE------YDTAVGKLIRNYKKQKQIEYDELTTKIAKPFEL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           +++ +++ +  + + GI+VVD      E G  D   L ++   S   ++          +
Sbjct: 55  NADGIDNLLQNIEDAGISVVD------ENGDPDPRALKATEKLSQSAMKDTSAPTGVKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLTADEEVQLALRIEKGDEVAKQELAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREI 184
             L  I
Sbjct: 168 QFLDLI 173


>gi|325686025|gb|EGD28083.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 373

 Score =  239 bits (609), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 167/364 (45%), Positives = 229/364 (62%), Gaps = 26/364 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    +    +D LV++  D    I+ ++GE  +LA                 
Sbjct: 36  KEFTDRLLKPYQIEGRAVDQLVQEFEDNGISIVDDKGEPSKLA----------------- 78

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                 ++  K+  + E ++  A        +R  +K I   + +S  E   +   +   
Sbjct: 79  ------LAKQKNVEKAELEHLSAPGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIE-- 130

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK E+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA  KFD+ LG+KFS
Sbjct: 131 -AGDQEAKDELTSANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVGKFDYQLGFKFS 189

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ 
Sbjct: 190 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMD 249

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +PV+ VR+VLK+ +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L++    VL
Sbjct: 250 LPVKKVREVLKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVL 309

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT  EE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR
Sbjct: 310 DTLTDSEENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLR 369

Query: 678 SFLD 681
            FL+
Sbjct: 370 DFLE 373



 Score = 78.0 bits (190), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 8/133 (6%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            L P ++    ++  V    + GI++VD       +G    L LA   +     L+    
Sbjct: 42  LLKPYQIEGRAVDQLVQEFEDNGISIVDD------KGEPSKLALAKQKNVEKAELEHL-S 94

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           +     +DPVR YL+ +G + LLS + E+ +AKRIEAG       L  + L     I  R
Sbjct: 95  APGSRMNDPVRQYLKRIGRVSLLSGDEEVQLAKRIEAGDQEAKDELTSANLRLVVSIAKR 154

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 155 Y-VGRGMSFLDLI 166


>gi|309810147|ref|ZP_07703992.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169419|gb|EFO71467.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
          Length = 382

 Score =  239 bits (609), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 173/387 (44%), Positives = 236/387 (60%), Gaps = 28/387 (7%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           +L     N  K+ K+S + K   + + ++V    L    ID LV++  D    I+ N+  
Sbjct: 23  TLSQVVKNIIKEVKTSKEIKE-DDFVARMVKPYQLEGRAIDQLVQEFEDNGISIVDND-- 79

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
                               G   +   +   KD  + E  +  A     +   +R  +K
Sbjct: 80  --------------------GNPSNLS-LKKQKDIEKAELNDMTAPSSVRMNDPVRMYLK 118

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I     ++  +   +   +         AK+E+ EANLRLV+S+AK+Y  RG+ FLDLI
Sbjct: 119 EIGRVPLLNADQEIDLAKRIE---NNDDEAKQELAEANLRLVVSIAKRYVGRGMSFLDLI 175

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA +KFD+ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 176 QEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 235

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ M  + VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 236 IQRQLLQDLGREPTPEEIGAEMDMSTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 295

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K+A SP   A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ F VTRE
Sbjct: 296 KDATSPEQHASYELLKEQLEEVLDTLTDREENVLRLRFGLNDGRTRTLEEVGRVFGVTRE 355

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 356 RIRQIEAKALRKLRHPSRSNQLKDFLD 382



 Score = 93.7 bits (231), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 67/157 (42%), Gaps = 8/157 (5%)

Query: 29  DSWKKMIKLARQRGYVTIEE-LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
              K +IK  +    +  ++ +   + P ++    ++  V    + GI++VD D      
Sbjct: 26  QVVKNIIKEVKTSKEIKEDDFVARMVKPYQLEGRAIDQLVQEFEDNGISIVDND------ 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+  +L L          L      +    +DPVRMYL+E+G + LL+ + EI +AKRIE
Sbjct: 80  GNPSNLSLKKQKDIEKAELNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRIE 139

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                    L E+ L     I  R  +  G + L  I
Sbjct: 140 NNDDEAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI 175


>gi|58337478|ref|YP_194063.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus NCFM]
 gi|58254795|gb|AAV43032.1| RNA polymerase sigma factor [Lactobacillus acidophilus NCFM]
          Length = 356

 Score =  239 bits (609), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 171/361 (47%), Positives = 231/361 (63%), Gaps = 27/361 (7%)

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
            +L+   +L    +D LV++  D    I+   G+  +LA                     
Sbjct: 22  ARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA--------------------- 60

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             +   KD  + E K+  A     +   +R  +K I     ++  +    +++ ++ E  
Sbjct: 61  --LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQE---IALAKRIESG 115

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA
Sbjct: 116 DEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYA 175

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP 
Sbjct: 176 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPT 235

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +L
Sbjct: 236 NKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETL 295

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+
Sbjct: 296 TDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFM 355

Query: 681 D 681
           D
Sbjct: 356 D 356



 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 42/142 (29%), Positives = 65/142 (45%), Gaps = 8/142 (5%)

Query: 44  VTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T ++  A L  P  +  + ++  V    + GI++VD      E G    L L       
Sbjct: 15  ITEDDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVE 68

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 69  KAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIESGDEEAKQELAEANL 128

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  +  G + L  I
Sbjct: 129 RLVVSIAKRY-VGRGMSFLDLI 149


>gi|258539717|ref|YP_003174216.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus Lc 705]
 gi|257151393|emb|CAR90365.1| RNA polymerase sigma factor [Lactobacillus rhamnosus Lc 705]
          Length = 416

 Score =  239 bits (609), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 178/387 (45%), Positives = 238/387 (61%), Gaps = 27/387 (6%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
              D+AV     +    K     +   KL+    L  + ID L++++ D    I+   GE
Sbjct: 56  KAYDDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVDENGE 115

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
              ++                       +   K   + E  +  A     I   +R  +K
Sbjct: 116 PATIS-----------------------LKKQKKVSKKEMSDMSAPSGVKINDPVRMYLK 152

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+QFLDLI
Sbjct: 153 EIGRVSLLTTDEE---VALALKIEQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLI 209

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 210 QEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 269

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 270 IQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 329

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRE
Sbjct: 330 QDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRE 389

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 390 RIRQIEAKALRKLRHPSRSKQLKDFLE 416



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 50/190 (26%), Positives = 83/190 (43%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      
Sbjct: 58  YDDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVD------ 111

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +
Sbjct: 112 ENGEPATISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTTDEEVALALK 171

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 172 IEQGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 222

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 223 FDYRKGFKFS 232


>gi|229552308|ref|ZP_04441033.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
 gi|229314290|gb|EEN80263.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
          Length = 416

 Score =  239 bits (609), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 178/387 (45%), Positives = 238/387 (61%), Gaps = 27/387 (6%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
              D+AV     +    K     +   KL+    L  + ID L++++ D    I+   GE
Sbjct: 56  KAYDDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVDENGE 115

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIK 414
              ++                       +   K   + E  +  A     I   +R  +K
Sbjct: 116 PATIS-----------------------LKKQKKVSKKEMSDMSAPSGVKINDPVRMYLK 152

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+QFLDLI
Sbjct: 153 EIGRVSLLTADEE---VALALKIEQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLI 209

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 210 QEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 269

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED
Sbjct: 270 IQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIED 329

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRE
Sbjct: 330 QDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRE 389

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 390 RIRQIEAKALRKLRHPSRSKQLKDFLE 416



 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 50/190 (26%), Positives = 83/190 (43%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            DD+ K +IK  +++  +T ++L +  + P E+ S  ++D +  + + GI +VD      
Sbjct: 58  YDDAVKAVIKDYKKKKQITEDDLTSKLIKPFELKSTAIDDLMQKIEDNGIAIVD------ 111

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +
Sbjct: 112 ENGEPATISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALK 171

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 172 IEQGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 222

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 223 FDYRKGFKFS 232


>gi|42519241|ref|NP_965171.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|41583529|gb|AAS09137.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|329667249|gb|AEB93197.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii DPC 6026]
          Length = 372

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 174/365 (47%), Positives = 234/365 (64%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    L    +D LV++  D    I+   GE  +LA                 
Sbjct: 34  KEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVDENGEPSKLA----------------- 76

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD  + E K+  A     +   +R  +K I   + ++  +    +++ ++
Sbjct: 77  ------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQE---IALAKR 127

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 128 IESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 187

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 188 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 247

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 248 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 307

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 308 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 367

Query: 677 RSFLD 681
           + FLD
Sbjct: 368 KDFLD 372



 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/142 (30%), Positives = 66/142 (46%), Gaps = 8/142 (5%)

Query: 44  VTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T +E  A L  P ++  + ++  V    + GI++VD      E G    L L       
Sbjct: 31  ITEKEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVD------ENGEPSKLALKKQKDVE 84

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 85  KAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGDEEAKQELAEANL 144

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  +  G + L  I
Sbjct: 145 RLVVSIAKRY-VGRGMSFLDLI 165


>gi|326693497|ref|ZP_08230502.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc argentinum KCTC 3773]
          Length = 432

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 173/384 (45%), Positives = 230/384 (59%), Gaps = 23/384 (5%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV     E    K         +L     L+   I+ L+E++ D    I+  +GE  
Sbjct: 68  YDKAVKALIAEYKPAKEVTYATLSERLAEPFHLDGENIERLMEKVEDAGVAIVDEKGEPA 127

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                    +                +  A+D P G   N           +R  +K I 
Sbjct: 128 PEVLQAKQNKP-----------SKEELDQAEDTPAGIKIN---------DPVRMYLKEIG 167

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +   E  +I   +         AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEG
Sbjct: 168 RVNLLKGDEEINIAKRIE---AGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEG 224

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 225 NMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQR 284

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++   + REP PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A
Sbjct: 285 QLLQDLGREPLPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEA 344

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +SP DSA    LR+    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIR
Sbjct: 345 ISPADSAAYEMLRDQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIR 404

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 405 QIEAKALRKLRHPSRSKQLKDFMD 428



 Score =  104 bits (259), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 64/337 (18%), Positives = 113/337 (33%), Gaps = 47/337 (13%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQ 62
                R S  +       +     D + K +I   +    VT   L+  L  P  +  E 
Sbjct: 45  AAAAGRASKPKAAKKSGIIKSPEYDKAVKALIAEYKPAKEVTYATLSERLAEPFHLDGEN 104

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E  +  + + G+ +VD    E  E + + L    +  +     Q     A    +DPVR
Sbjct: 105 IERLMEKVEDAGVAIVD----EKGEPAPEVLQAKQNKPSKEELDQAEDTPAGIKINDPVR 160

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR---------DE 173
           MYL+E+G + LL  + EI IAKRIEAG       L E+ L     I  R         D 
Sbjct: 161 MYLKEIGRVNLLKGDEEINIAKRIEAGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 174 LNDGTTLLREIIDLEACIGP---------------------------------ESKGGFF 200
           + +G   L + +D                                        E+     
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 280

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                       +   E+   ++  T   +    K++++  S      E  ++   +  E
Sbjct: 281 RIQRQLLQDLGREPLPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 340

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           D +  +   SA  + LR ++   L+ + +    +  L
Sbjct: 341 DNEAISPADSAAYEMLRDQLESVLETLTDREENVLRL 377


>gi|315038507|ref|YP_004032075.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325956923|ref|YP_004292335.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|312276640|gb|ADQ59280.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325333488|gb|ADZ07396.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|327183703|gb|AEA32150.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1118]
          Length = 370

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 173/371 (46%), Positives = 234/371 (63%), Gaps = 27/371 (7%)

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
            K    K+   +L+   +L    +D LV++  D    I+   G+  +LA           
Sbjct: 26  EKTITEKDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA----------- 74

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHI 430
                       +   KD  + E K+  A     +   +R  +K I     ++  +    
Sbjct: 75  ------------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQE--- 119

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +++ ++ E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+
Sbjct: 120 IALAKRIEAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDY 179

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPE
Sbjct: 180 RLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPE 239

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  ++ MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+
Sbjct: 240 EIGAEMNMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLK 299

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   +VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP
Sbjct: 300 EQLEQVLETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 359

Query: 671 SRSKKLRSFLD 681
           SRS +LR F+D
Sbjct: 360 SRSNQLRDFMD 370



 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 40/133 (30%), Positives = 60/133 (45%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIEAG       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIEAGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 152 Y-VGRGMSFLDLI 163


>gi|161507646|ref|YP_001577600.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus DPC
           4571]
 gi|160348635|gb|ABX27309.1| RNA polymerase sigma factor [Lactobacillus helveticus DPC 4571]
          Length = 356

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 174/365 (47%), Positives = 233/365 (63%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+   +L+   +L    +D LV++  D    I+   G+  +LA                 
Sbjct: 18  KDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA----------------- 60

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD    E K+  A     +   +R  +K I     I+  +    +++ ++
Sbjct: 61  ------LKKQKDVERAELKDMSAPSSVRMNDPVRMYLKEIGRVPLITADQE---IALAKR 111

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+CLG+KF
Sbjct: 112 IEEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKF 171

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 172 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 231

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +V
Sbjct: 232 NMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQV 291

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 292 LETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 351

Query: 677 RSFLD 681
           R F+D
Sbjct: 352 RDFMD 356



 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 38/133 (28%), Positives = 59/133 (44%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 24  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVERAELKDMSA 77

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + L++ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 78  PSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 137

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 138 Y-VGRGMSFLDLI 149


>gi|318066925|emb|CBY89077.1| RNA polymerase sigma70 factor [Halomonas aquamarina]
 gi|318066927|emb|CBY89078.1| RNA polymerase sigma70 factor [Halomonas axialensis]
 gi|318066959|emb|CBY89094.1| RNA polymerase sigma70 factor [Halomonas meridiana]
          Length = 370

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 126/395 (31%), Positives = 186/395 (47%), Gaps = 45/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E        + S + + D   + E D  +A 
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPVVETELSDDDDIDSDDDDEEDDTTA- 137

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                  S+    PE A+     + E        L+                        
Sbjct: 138 -------SEGGPDPEEAKARFEQIREQNAAVEAVLA------------------------ 166

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L +L   + L     + LV Q+    +++   E 
Sbjct: 167 -----------KHGRGSAELKAEQARLAELFSPIKLVPKHFERLVGQIRISVEQVRAQEK 215

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E DP W+  A      ++ + +      I + + +I
Sbjct: 216 AVMQLCVKKAKVPRKTFIKSFPGHESDPTWLD-AFQEAHPKYADRLEPLRADIARAQRKI 274

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 275 AFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 334

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 335 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 369


>gi|227890104|ref|ZP_04007909.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
 gi|227849548|gb|EEJ59634.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
          Length = 372

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 173/365 (47%), Positives = 234/365 (64%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+   +L+    L    +D LV++  D    I+   GE  +LA                 
Sbjct: 34  KKFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVDENGEPSKLA----------------- 76

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD  + E K+  A     +   +R  +K I   + ++  +    +++ ++
Sbjct: 77  ------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQE---IALAKR 127

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 128 IESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 187

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 188 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 247

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 248 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 307

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 308 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 367

Query: 677 RSFLD 681
           + FLD
Sbjct: 368 KDFLD 372



 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 39/133 (29%), Positives = 61/133 (45%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P ++  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 40  LIKPYDLQGKAVDQLVQEFEDNGISIVD------ENGEPSKLALKKQKDVEKAELKDMSA 93

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L     I  R
Sbjct: 94  PSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGDEEAKQELAEANLRLVVSIAKR 153

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 154 Y-VGRGMSFLDLI 165


>gi|296112139|ref|YP_003622521.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
 gi|295833671|gb|ADG41552.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
          Length = 432

 Score =  238 bits (608), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 173/384 (45%), Positives = 232/384 (60%), Gaps = 23/384 (5%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV     E  + K         +L    +L+   I+ L+E++ D    I+  +GE  
Sbjct: 68  YDKAVKALIAEYKAAKAITYVALSQRLAEPFNLDGENIERLMEKIEDAGVAIVDEKGEPA 127

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                    +                +  A++ P G   N           +R  +K I 
Sbjct: 128 PEVLKAKQNKP-----------SKEELEQAQETPAGIKIN---------DPVRMYLKEIG 167

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +   E  +I   +         AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEG
Sbjct: 168 RVNLLKGDEEINIAKRIE---DGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEG 224

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 225 NMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQR 284

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++   + REP PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A
Sbjct: 285 QLLQDLGREPLPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEA 344

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +SP DSA    LRE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIR
Sbjct: 345 ISPADSAAYEMLREQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIR 404

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 405 QIEAKALRKLRHPSRSKQLKDFMD 428



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 73/353 (20%), Positives = 127/353 (35%), Gaps = 30/353 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +I   +    +T   L+  L  P  +  E +E  +  + + G+ +VD    E 
Sbjct: 68  YDKAVKALIAEYKAAKAITYVALSQRLAEPFNLDGENIERLMEKIEDAGVAIVD----EK 123

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E + + L    +  +     Q ++  A    +DPVRMYL+E+G + LL  + EI IAKR
Sbjct: 124 GEPAPEVLKAKQNKPSKEELEQAQETPAGIKINDPVRMYLKEIGRVNLLKGDEEINIAKR 183

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     + 
Sbjct: 184 IEDGDVEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDK 234

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
             Y K    S        Q     I   A+  +     V++  +      + L +   + 
Sbjct: 235 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREP 294

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRS----------LQDNAVNGQKDEKSSVKCK 315
                  E  L P  +  + +IA+    L +                N       S   +
Sbjct: 295 LPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAISPADSAAYE 354

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           +L+E+L  ++ +L+  +  +  L   L D           L  + + +G+ R+
Sbjct: 355 MLREQLESVLETLTDREENVLRLRFGLED------GRTRTLEEVGRVFGVTRE 401


>gi|28378605|ref|NP_785497.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum WCFS1]
 gi|300768133|ref|ZP_07078038.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308180761|ref|YP_003924889.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|28271441|emb|CAD64346.1| DNA-directed RNA polymerase, sigma factor 42 [Lactobacillus
           plantarum WCFS1]
 gi|300494197|gb|EFK29360.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308046252|gb|ADN98795.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 368

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 160/273 (58%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++  + E     AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVDLLTADEE---VALALRIEQGDESAKQELAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQDATSPADAAAYELLKEQLEGVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 52/190 (27%), Positives = 85/190 (44%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +IK  ++ G +  +EL+  L  P ++ +  ++  +  + + GI+VVD      
Sbjct: 10  YDKAVKALIKEYKKTGSIQYDELSDKLAAPYKLDASGIDKLLQKVEDAGISVVD------ 63

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E+G  D+  + S    S   L     ++    +DPVRMYL+E+G ++LL+ + E+A+A R
Sbjct: 64  EKGDPDARAVKSVKKVSKKELSDAGSASGIKINDPVRMYLKEIGRVDLLTADEEVALALR 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 124 IEQGDESAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 174

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 175 FDYRKGFKFS 184


>gi|116492861|ref|YP_804596.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Pediococcus pentosaceus ATCC 25745]
 gi|116103011|gb|ABJ68154.1| RNA polymerase, sigma 70 subunit, RpoD [Pediococcus pentosaceus
           ATCC 25745]
          Length = 379

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 170/389 (43%), Positives = 238/389 (61%), Gaps = 30/389 (7%)

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           E +   +  +  +K EK     ++ K+ + K      L    +D L++++ D    ++  
Sbjct: 21  EFKKAVNQIIKARKSEKKVKYTQLTKDLITK----FKLTDEDVDDLIQRIEDAGISVVDE 76

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
            G+                +  + +E+    +   K     +  + V          R  
Sbjct: 77  NGDPSE-------------KALKAQEISKEELDDTKAPAGVKINDPV----------RMY 113

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K I   + ++  +   +   + K       A++E+ EANLRLV+S+AK+Y  RG+QFLD
Sbjct: 114 LKEIGRVSLLTADQEVELALRIEK---GDPRARQELAEANLRLVVSIAKRYVGRGMQFLD 170

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+
Sbjct: 171 LIQEGNMGLMKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 230

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R  R++   + REP PEEI  ++ MP + VR++LKI +EP+SLETPIG+ED SHLGDFI
Sbjct: 231 IRIQRQLLQDLGREPMPEEIGAEMDMPSDKVREILKIAQEPVSLETPIGEEDDSHLGDFI 290

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VT
Sbjct: 291 EDQEATSPADHAAYELLKEQLEGVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVT 350

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 351 RERIRQIEAKALRKLRHPSRSKQLKDFLD 379



 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 76/189 (40%), Gaps = 17/189 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELN-AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
             +  ++IK  +    V   +L    +   +++ E ++D +  + + GI+VVD       
Sbjct: 23  KKAVNQIIKARKSEKKVKYTQLTKDLITKFKLTDEDVDDLIQRIEDAGISVVD------- 75

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  + S     +   S   L   K  A    +DPVRMYL+E+G + LL+ + E+ +A RI
Sbjct: 76  ENGDPSEKALKAQEISKEELDDTKAPAGVKINDPVRMYLKEIGRVSLLTADQEVELALRI 135

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 136 EKGDPRARQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKF 186

Query: 207 SYQKREDSS 215
            YQK    S
Sbjct: 187 DYQKGFKFS 195


>gi|323466388|gb|ADX70075.1| RNA polymerase sigma factor [Lactobacillus helveticus H10]
          Length = 370

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 172/365 (47%), Positives = 233/365 (63%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+   +L+   +L    +D LV++  D    I+   G+  +LA                 
Sbjct: 32  KDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA----------------- 74

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD  + E K+  A     +   +R  +K I     ++  +    +++ ++
Sbjct: 75  ------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQE---IALAKR 125

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 126 IEEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 185

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 186 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 245

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +V
Sbjct: 246 NMPTNKVRNILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQV 305

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 306 LETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 365

Query: 677 RSFLD 681
           R F+D
Sbjct: 366 RDFMD 370



 Score = 94.1 bits (232), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 39/133 (29%), Positives = 59/133 (44%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVEKAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 152 Y-VGRGMSFLDLI 163


>gi|315640587|ref|ZP_07895693.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
 gi|315483615|gb|EFU74105.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
          Length = 368

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVPLLTAAEEVELALKIE---EGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRIQRQLLQDLGREPTPEEIGAEMDLSTEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFGI      TLEEVGK 
Sbjct: 276 GDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 46/191 (24%), Positives = 78/191 (40%), Gaps = 15/191 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             + + K+ I+  +  G V  ++L   L  P  + ++QM+  +  + + GI+VVD +   
Sbjct: 8   TYEQAVKEFIRKNKPNGQVVYDQLTNQLATPHNLDADQMDQLIQKIEDAGISVVDENGEP 67

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                +++     S    +V  +          +DPVRMYL+E+G + LL+   E+ +A 
Sbjct: 68  SVHSLKNA-----SKQEKTVQQEDLSAPTGVKINDPVRMYLKEIGRVPLLTAAEEVELAL 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +IE G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 123 KIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVE 173

Query: 205 GHSYQKREDSS 215
              Y+K    S
Sbjct: 174 KFDYRKGFKFS 184


>gi|283797719|ref|ZP_06346872.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291074616|gb|EFE11980.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|295092057|emb|CBK78164.1| RNA polymerase, sigma 70 subunit, RpoD [Clostridium cf.
           saccharolyticum K10]
          Length = 372

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 165/342 (48%), Positives = 232/342 (67%), Gaps = 12/342 (3%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           +QL  I   + +N+ ++L   +   I+ D+FLE     E D    +     PEG      
Sbjct: 43  DQLDQIDDFLENNKVDVLTPEEDLDIEPDLFLEEEMTEEEDIDVDNLELSMPEGVSIE-- 100

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                    +R  +K I     ++  E   +   +         AKK + EANLRLV+S+
Sbjct: 101 -------DPVRMYLKEIGKVPLLTPEEEIDLAKRME---MGDESAKKRLAEANLRLVVSI 150

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RG+QFLDLIQEGN+GL+KA EK+D+  G+KFSTYA WW++QAITRSIADQ+ TI
Sbjct: 151 AKRYVGRGMQFLDLIQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTI 210

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I++++RT+R++  ++ REP+ EE+A+KL MPVE VR+++KI+++P+SLETP
Sbjct: 211 RIPVHMVETINRLIRTSRQLLQELGREPSAEELAEKLDMPVERVREIMKISQDPVSLETP 270

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+E+ SHLGDFI+D +   P+D+A    L E    VL +LT RE++VLR+RFG+     
Sbjct: 271 IGEEEDSHLGDFIQDDHVQVPVDAATYTLLHEQLMEVLDTLTDREQKVLRLRFGLDDGRP 330

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            TLEEVG++F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 331 RTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 372



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 37/143 (25%), Positives = 64/143 (44%), Gaps = 1/143 (0%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
             +  +E+  F   + ++ +Q++     L N  ++V+  ++  D E      +  +   +
Sbjct: 24  NVLEQKEIIDFFHGEILNPDQLDQIDDFLENNKVDVLTPEEDLDIEPDLFLEEEMTEEED 83

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
             V   +       S +DPVRMYL+E+G + LL+ E EI +AKR+E G       L E+ 
Sbjct: 84  IDVDNLELSMPEGVSIEDPVRMYLKEIGKVPLLTPEEEIDLAKRMEMGDESAKKRLAEAN 143

Query: 162 LTFQALIIWRDELNDGTTLLREI 184
           L     I  R  +  G   L  I
Sbjct: 144 LRLVVSIAKRY-VGRGMQFLDLI 165


>gi|254556820|ref|YP_003063237.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
 gi|254045747|gb|ACT62540.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
          Length = 368

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 160/273 (58%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++  + E     AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVDLLTADEE---VALALRIEQGDESAKQELAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQDATSPADAAAYELLKEQLEGVLDTLTNREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/190 (27%), Positives = 85/190 (44%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +IK  ++ G +  +EL+  L  P ++ +  ++  +  + + GI+VVD      
Sbjct: 10  YDKAVKALIKEYKKTGSIQYDELSDKLAAPYKLDASGIDKLLQKVEDAGISVVD------ 63

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E+G  D+  + S    S   L     ++    +DPVRMYL+E+G ++LL+ + E+A+A R
Sbjct: 64  EKGDPDARAVKSVKKVSKKELSDAGSASGIKINDPVRMYLKEIGRVDLLTADEEVALALR 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 124 IEQGDESAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 174

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 175 FDYRKGFKFS 184


>gi|260101316|ref|ZP_05751553.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
 gi|260084901|gb|EEW69021.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
          Length = 370

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 174/365 (47%), Positives = 233/365 (63%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+   +L+   +L    +D LV++  D    I+   G+  +LA                 
Sbjct: 32  KDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA----------------- 74

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD    E K+  A     +   +R  +K I     I+  +    +++ ++
Sbjct: 75  ------LKKQKDVERAELKDMSAPSSVRMNDPVRMYLKEIGRVPLITADQE---IALAKR 125

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+CLG+KF
Sbjct: 126 IEEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKF 185

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 186 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 245

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +V
Sbjct: 246 NMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQV 305

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 306 LETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 365

Query: 677 RSFLD 681
           R F+D
Sbjct: 366 RDFMD 370



 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/133 (28%), Positives = 59/133 (44%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVERAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + L++ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 152 Y-VGRGMSFLDLI 163


>gi|32474203|ref|NP_867197.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32444741|emb|CAD74742.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 567

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 176/657 (26%), Positives = 295/657 (44%), Gaps = 94/657 (14%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
               D    ++I    + G++T +E+NA+LP ++V+ E++   +  L N GI ++     
Sbjct: 1   MQLMDQDLSQLIARGTKDGFLTYDEVNAYLPDEDVNPEKLNSLLLALENRGIQLI----- 55

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                         ++   +     R+ S +      V M           + + E    
Sbjct: 56  -------------EASEKKARDAAARRPSPNVRGLRSVDM-----------TADEE---- 87

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
                    ++A                D        +R  +   A I   S+       
Sbjct: 88  -----SPEQILA-----NEAASQSFSSADMPKASEDPIRMYLSQMAEIPLLSREEEIALA 137

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +     +++      E D       D        +    +           +  + +   
Sbjct: 138 KKIEITRKQYRRSLLETDYALRATVDTLQKVHSGELPFDRTIKVSLTERLTKEQISQRMP 197

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +  TL+              D IA+   +   L   + + +   +   +    + K ++
Sbjct: 198 HNLRTLN--------------DLIAKNKADFEILVRRSASPRLKAEVRKQFLRRRRKCLE 243

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           LV  LSL   R+  L+ QL  IS R+      L  L                        
Sbjct: 244 LVEELSLRSRRVTPLLHQLEKISGRMTFIRERLADLGND--------------------- 282

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
                           A   D    +R E++ + + T  S +   + ++ VR+   +   
Sbjct: 283 ----------------AMSRDEAADLRQELRELMLVTQESPTSLHNRMAKVRRHFDQYEA 326

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K+E+   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  G+KFSTYA WW
Sbjct: 327 TKRELSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWW 386

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM D + K+ +  +R++  ++REPT E+IA+   +P+E V
Sbjct: 387 IRQAITRAIADQARTIRIPVHMIDVLSKLRQAQKRLTQTLRREPTYEDIAEATDVPIEEV 446

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V+ I + P+SL+ P+G+ + S  G+F++D    +P+  A    LR     +L +LT R
Sbjct: 447 RRVMDIGRHPVSLDRPVGEGEDSSFGEFVQDSETDNPVRIAASGMLRNKIDELLKTLTFR 506

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++R+R+G+     +TLEE G+ F VTRER+RQIEAKA+ K++ PSR+++L S+L
Sbjct: 507 EREIIRLRYGLVDGYSYTLEECGRIFKVTRERVRQIEAKAVAKMQSPSRAERLSSYL 563


>gi|300173322|ref|YP_003772488.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
 gi|299887701|emb|CBL91669.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
          Length = 432

 Score =  238 bits (607), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 174/384 (45%), Positives = 233/384 (60%), Gaps = 23/384 (5%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV     E  + K     +   +L    +L+   I+ L+E++ D    I+  +GE  
Sbjct: 68  YDKAVKALIAEYKAAKAITYADLAKRLAEPFNLDGENIERLMEKVEDSGVAIVDEKGEPA 127

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                    +                +  A++ P G   N           +R  +K I 
Sbjct: 128 PEVLKAKQNKP-----------SKEELDQAQETPAGIKIN---------DPVRMYLKEIG 167

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +   E  +I   +         AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEG
Sbjct: 168 RVNLLKGDEEINIAKRIE---DGDIEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEG 224

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 225 NMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQR 284

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++   + REP PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A
Sbjct: 285 QLLQDLGREPLPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEA 344

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           VSP DSA    LRE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIR
Sbjct: 345 VSPADSAAYEMLREQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIR 404

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 405 QIEAKALRKLRHPSRSKQLKDFMD 428



 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 73/353 (20%), Positives = 127/353 (35%), Gaps = 30/353 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +I   +    +T  +L   L  P  +  E +E  +  + + G+ +VD    E 
Sbjct: 68  YDKAVKALIAEYKAAKAITYADLAKRLAEPFNLDGENIERLMEKVEDSGVAIVD----EK 123

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E + + L    +  +     Q ++  A    +DPVRMYL+E+G + LL  + EI IAKR
Sbjct: 124 GEPAPEVLKAKQNKPSKEELDQAQETPAGIKINDPVRMYLKEIGRVNLLKGDEEINIAKR 183

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     + 
Sbjct: 184 IEDGDIEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDK 234

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
             Y K    S        Q     I   A+  +     V++  +      + L +   + 
Sbjct: 235 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREP 294

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRS----------LQDNAVNGQKDEKSSVKCK 315
                  E  L P  +  + +IA+    L +                N       S   +
Sbjct: 295 LPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYE 354

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           +L+E+L  ++ +L+  +  +  L   L D           L  + + +G+ R+
Sbjct: 355 MLREQLESVLETLTDREENVLRLRFGLED------GRTRTLEEVGRVFGVTRE 401


>gi|312869100|ref|ZP_07729274.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
 gi|311095346|gb|EFQ53616.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
          Length = 380

 Score =  238 bits (607), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +      +AK+++ EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLTADEEVKLALRIEQ---GDEVAKQQLAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ MP E +R +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKIRNILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 86/186 (46%), Gaps = 15/186 (8%)

Query: 1   MTIGKKRN-RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEV 58
           M   KK++   S+SE  D  +       D +  K+I+  +++  +  + L   L  P E+
Sbjct: 1   MAKSKKKDLVISNSEDFDQQE------YDTAVGKLIRQYKKQKEIQYDVLTDKLAKPYEL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           +++ +++ +  + + GI+VVD        G  D   L ++   S   ++          +
Sbjct: 55  NADGIDNLLQNVEDAGISVVDA------NGDPDPRALKATEKLSQNAMKDTSAPTGVKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ + E+ +A RIE G  +    L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLTADEEVKLALRIEQGDEVAKQQLAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREI 184
             L  I
Sbjct: 168 QFLDLI 173


>gi|227904114|ref|ZP_04021919.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
 gi|227868133|gb|EEJ75554.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
          Length = 370

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 171/361 (47%), Positives = 231/361 (63%), Gaps = 27/361 (7%)

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
            +L+   +L    +D LV++  D    I+   G+  +LA                     
Sbjct: 36  ARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA--------------------- 74

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             +   KD  + E K+  A     +   +R  +K I     ++  +    +++ ++ E  
Sbjct: 75  --LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQE---IALAKRIESG 129

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA
Sbjct: 130 DEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYA 189

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP 
Sbjct: 190 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPT 249

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +L
Sbjct: 250 NKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETL 309

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+
Sbjct: 310 TDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFM 369

Query: 681 D 681
           D
Sbjct: 370 D 370



 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 42/142 (29%), Positives = 65/142 (45%), Gaps = 8/142 (5%)

Query: 44  VTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T ++  A L  P  +  + ++  V    + GI++VD      E G    L L       
Sbjct: 29  ITEDDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVE 82

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 83  KAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIESGDEEAKQELAEANL 142

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  +  G + L  I
Sbjct: 143 RLVVSIAKRY-VGRGMSFLDLI 163


>gi|225619915|ref|YP_002721172.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225214734|gb|ACN83468.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 587

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 172/665 (25%), Positives = 313/665 (47%), Gaps = 81/665 (12%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
            +D  +   +++  +K+++      Y+T +E+N  +  D + ++ M+    +L+   I +
Sbjct: 4   EEDCDLLIKNNEKIRKLLEKGNTNKYLTFKEINGAI--DNMDTDVMDILFQLLAARKIVI 61

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+ D  E E  S++   +  +A    V      +    + DDP+R+YL+E+G + LL+ +
Sbjct: 62  VE-DKREFESLSKNQNKIDDAAKFIHV------EDKVGNNDDPIRLYLKEIGKVSLLTHD 114

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  +K+IE+G + +   +  + L    ++     +  G   + EI++        ++ 
Sbjct: 115 DEVDYSKKIESGESEIENIILNTHLVVGEVLNTIKNVQIGKVSIHEILEPPRIYNVSTQE 174

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 +  +++K   +  EK     +  +         ++     +    E  ++    
Sbjct: 175 KRKLERKYKNFEKEYVALAEKYLSLDKRIKKIT------TQKTIKALTKEQEEVKDSIVK 228

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L      +   +  + ++L+   +  +++I E + +L+      ++  ++    ++    
Sbjct: 229 LLSKVRLNRMEIDRIAEKLK-FYLHRINQIEEYFEKLKKRYYKEISDFENYYKEIESGN- 286

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+  ++LV   ++    I+ ++             +  +  +     I ++  +      
Sbjct: 287 KDIYIRLVDEFNITPEAIEAVIT-------SFHKAQVRMADIYDEVRIDKETLV------ 333

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
                           EW   +      I + ++ I                        
Sbjct: 334 ----------------EWVRKIDSSRRKIAQAKDHI------------------------ 353

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A   +V A  +  ++    +        DL+QEGNIGL+KA +KF++  GYKFS
Sbjct: 354 ----VKANLRLVIAIAKKYVNRGLHF-------FDLVQEGNIGLIKAVDKFEYKKGYKFS 402

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KV R  R+   +  REP+ +EIAK L+
Sbjct: 403 TYATWWIRQAITRSISDQARTIRVPVHMIEQINKVQRVLRQYMQQHGREPSIQEIAKALS 462

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            P   V+ V  + K+P+SL  PIGDE+ + LG+ IEDK   SP +      LR+    +L
Sbjct: 463 WPESRVKSVRNVAKDPVSLNAPIGDEEDTILGELIEDKEFESPQNITTFKILRKQIDSIL 522

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SL  RE++V+RMRFG+     HTLEEVG  F VTRERIRQIEAKAIR+L+  S+ K+L+
Sbjct: 523 DSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAIRRLRAQSKKKELK 582

Query: 678 SFLDG 682
            FLD 
Sbjct: 583 DFLDS 587


>gi|268319377|ref|YP_003293033.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
 gi|262397752|emb|CAX66766.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
          Length = 372

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 174/365 (47%), Positives = 234/365 (64%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           KE   +L+    L    +D LV++  D    I+   GE  +LA                 
Sbjct: 34  KEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVDENGEPSKLA----------------- 76

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD  + E K+  A     +   +R  +K I   + ++  +    +++ ++
Sbjct: 77  ------LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQE---IALAKR 127

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KF
Sbjct: 128 IESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKF 187

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 188 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 247

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + VR++LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E    V
Sbjct: 248 DMPTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYELLKEQLEEV 307

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 308 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 367

Query: 677 RSFLD 681
           + FLD
Sbjct: 368 KDFLD 372



 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/142 (30%), Positives = 66/142 (46%), Gaps = 8/142 (5%)

Query: 44  VTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T +E  A L  P ++  + ++  V    + GI++VD      E G    L L       
Sbjct: 31  ITEKEFTAQLIKPYDLQGKAVDQLVQEFEDNGISIVD------ENGEPSKLALKKQKDVE 84

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 85  KAELKDMSAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRIESGDEEAKQELAEANL 144

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  +  G + L  I
Sbjct: 145 RLVVSIAKRY-VGRGMSFLDLI 165


>gi|116618341|ref|YP_818712.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|116097188|gb|ABJ62339.1| RNA polymerase, sigma 70 subunit, RpoD [Leuconostoc mesenteroides
           subsp. mesenteroides ATCC 8293]
          Length = 432

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 174/384 (45%), Positives = 235/384 (61%), Gaps = 23/384 (5%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D A      E  + K         +L    +L++  I+ L+E++ D            +
Sbjct: 68  YDKATKALIAEYKAAKQITYAALSKRLAEPFNLDEENIERLMEKVEDAG----------I 117

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            +    G      L+  Q +  D   ++ A++ P G   N           +R  +K I 
Sbjct: 118 AIVDDNGDPAPEVLKAKQNKPTDQE-LAEAEETPAGIKIN---------DPVRMYLKEIG 167

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +  +E   I   +         AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEG
Sbjct: 168 RVNLLKGNEEIDIAKRIE---NGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEG 224

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 225 NMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQR 284

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++   + REP PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A
Sbjct: 285 QLLQDLGREPLPEEIGAEMDLTADKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEA 344

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           VSP DSA    LRE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIR
Sbjct: 345 VSPADSAAYEMLREQLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIR 404

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 405 QIEAKALRKLRHPSRSKQLKDFMD 428



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/314 (18%), Positives = 107/314 (34%), Gaps = 47/314 (14%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +I   +    +T   L+  L  P  +  E +E  +  + + GI +VD     +
Sbjct: 68  YDKATKALIAEYKAAKQITYAALSKRLAEPFNLDEENIERLMEKVEDAGIAIVDD----N 123

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            + + + L    +        +  +  A    +DPVRMYL+E+G + LL    EI IAKR
Sbjct: 124 GDPAPEVLKAKQNKPTDQELAEAEETPAGIKINDPVRMYLKEIGRVNLLKGNEEIDIAKR 183

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGP--- 193
           IE G       L E+ L     I  R         D + +G   L + +D          
Sbjct: 184 IENGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYTKGFKF 243

Query: 194 ------------------------------ESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
                                         E+                 +   E+   ++
Sbjct: 244 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEM 303

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
             T   +    K++++  S      E  ++   +  ED +  +   SA  + LR ++   
Sbjct: 304 DLTADKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYEMLREQLESV 363

Query: 284 LDEIAEVYRELRSL 297
           LD + +    +  L
Sbjct: 364 LDTLTDREENVLRL 377


>gi|302338588|ref|YP_003803794.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635773|gb|ADK81200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 612

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 199/657 (30%), Positives = 319/657 (48%), Gaps = 49/657 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            +D S  K+++ A+++  +T +E+N FLP   V+S   E    +++ +  + +  DD +D
Sbjct: 5   QADKSVAKLLEYAKEKKRITYDEVNDFLPDSIVNS---EKIEEVIALLEEHNISLDDEQD 61

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +       D         +         D            E G   L     +I + + 
Sbjct: 62  KNDDMPDDDGELDDDFVDLDDDDDDSDGDMD----------EKGDTSL----EDIPLKRS 107

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
            +  R ++                     +   + + + I L   +    K       + 
Sbjct: 108 PDRTRRVVYN-------------------DKDASAVDDPIRL--YLREIGKESLLTAEQE 146

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
               K+ +  +   +  V+E+   I     + +   SK D    +    E +        
Sbjct: 147 VELSKQMEHGEAIIKRVVKESGMIIPQLFDLMEKTFSKTDPRELDLSKKEISE------- 199

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              +     +L         +I    R    L+   +    D  +  +    + +L  L+
Sbjct: 200 ---ILTERRRLNQFYRDGFKKIGSQLRNYMELKRKVIATGGDVLTDQRLDKKRHELFSLI 256

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             L ++Q  I    E+  D +KRI+H + E  R+ +  G+     L    GR L      
Sbjct: 257 EELDIHQEEIVGFSEKFSDTAKRILHYQREQERIERRLGVTSSKELRN-MGRGLAIPERR 315

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
              +       + +  ++  I      ++SI +E   +I         +  G+     AK
Sbjct: 316 RKIEEELQLSSDQIKEKIRQIQVNEKHLQSIELEFEDAIDSILERSKEISHGQVMMKNAK 375

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             +++ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++
Sbjct: 376 DRLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYSKGFKFSTYATWWIR 435

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITRSI+DQ+ TIR+PVHM ++I+KVVR +R++   + R+PT EE+A++L   V  V+ 
Sbjct: 436 QAITRSISDQARTIRVPVHMIEQINKVVRESRQLMQILGRDPTDEEVAERLGWTVLRVKS 495

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V  + +EPISLETPIG+E+ S LGDFIEDK+  +P +      L+E    V+ +L PRE+
Sbjct: 496 VKNVAREPISLETPIGEEEDSLLGDFIEDKDIENPANQTAFTLLQEQLQEVMKTLPPREQ 555

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R+L+HP RS++L+ ++D 
Sbjct: 556 EVLKMRFGLDDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPKRSRRLKDYIDN 612


>gi|300871651|ref|YP_003786524.1| RNA polymerase sigma-70 factor RpoD [Brachyspira pilosicoli
           95/1000]
 gi|300689352|gb|ADK32023.1| RNA polymerase sigma factor rpoD (Sigma-70) [Brachyspira pilosicoli
           95/1000]
          Length = 568

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 161/396 (40%), Positives = 229/396 (57%)

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +AE Y  L      A   +  +  + +   +KE +VKL+  + LN+  ID + E+L    
Sbjct: 173 LAEKYLALDKRIKKATTQKTIKNLTNEQNEIKENIVKLLSKVKLNRMEIDRIAEKLKFYL 232

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
            RI   E    +L + YG +   F   +   E     +              +   + S 
Sbjct: 233 HRINQIEEYFEKLKKRYGKEISDFENYYNEIESGNKKIYTRLVDEFNITPEAIKAVLTSF 292

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
              +  +  I  E           V  +     + + AK  +V+ANLRLVIS+AKKYTNR
Sbjct: 293 HNSQVRMADIYDEVRTDKETLVEWVRKIDSSRRKIAQAKDHIVKANLRLVISIAKKYTNR 352

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL F DL+QEGNIGL+KA +KF++  GYKFSTYA WW++QAITRSI+DQ+ TIR+PVHM 
Sbjct: 353 GLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMI 412

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           ++I+KV R  R+   +  REP+ +EIA+ L+ P   V+ V  + K+P+SL  PIGDE+ +
Sbjct: 413 EQINKVTRVLRQYMQQYGREPSIQEIARALSWPESRVKSVRNVAKDPVSLNAPIGDEEDT 472

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LG+ IEDK   SP +      LR+    +L +L  RE++V+RMR+G+    +HTLEEVG
Sbjct: 473 ILGELIEDKEFESPQNITTFKILRKHIDSLLDNLPEREQKVIRMRYGLDDGYNHTLEEVG 532

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             F VTRERIRQIEAKAIR+L+  S+ K+L+ FLD 
Sbjct: 533 YVFKVTRERIRQIEAKAIRRLRATSKKKELKEFLDS 568



 Score = 94.1 bits (232), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 57/354 (16%), Positives = 147/354 (41%), Gaps = 31/354 (8%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           M++      Y+T +E+NA +  D + ++ M+    +L+   I +V+ D  E E  S++  
Sbjct: 1   MLEKGNANKYLTFKEINAAI--DNMDTDVMDILFQLLNARKIVIVE-DKREFESLSKNQN 57

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
            +  +A    V      +    + DDP+R+YL+E+G ++LL+ + E+  +K+IE G + +
Sbjct: 58  KIDDAARFIHV------EDKVGNNDDPIRLYLKEIGKVDLLTHDDEVEYSKKIELGESEI 111

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
            + +  + L    ++     ++ G   + EI+        E    +   T+     +R+ 
Sbjct: 112 ESIILNTHLVVGEVLNTIKCVHSGKVSIHEIL--------EPPRIYNVSTQEKRKLERKY 163

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS-AM 272
            + EKE  D+ E    ++   K +   ++  +   E  E  E  +        + +    
Sbjct: 164 KNFEKEYVDLAEKYLALDKRIKKATTQKTIKNLTNEQNEIKENIVKLLSKVKLNRMEIDR 223

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-------------E 319
             +     +  +++I E + +L+      ++  ++  + ++    K             E
Sbjct: 224 IAEKLKFYLHRINQIEEYFEKLKKRYGKEISDFENYYNEIESGNKKIYTRLVDEFNITPE 283

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            +  ++ S   +Q R+  + +++    + ++    ++    +     +D  ++ 
Sbjct: 284 AIKAVLTSFHNSQVRMADIYDEVRTDKETLVEWVRKIDSSRRKIAQAKDHIVKA 337


>gi|327539652|gb|EGF26260.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 567

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 175/657 (26%), Positives = 295/657 (44%), Gaps = 94/657 (14%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
               D    ++I    + G++T +E+NA+LP ++V+ E++   +  L N GI ++     
Sbjct: 1   MQLMDQDLSQLIARGTKDGFLTYDEVNAYLPDEDVNPEKLNSLLLALENRGIQLI----- 55

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                         ++   +     R+ S +      V M           + + E    
Sbjct: 56  -------------EASEKKARDAAARRPSPNVRGLRSVDM-----------TADEE---- 87

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
                    ++A                D        +R  +   A I   S+       
Sbjct: 88  -----SPEQILA-----NEAASQSFSSADMPKASEDPIRMYLSQMAEIPLLSREEEIALA 137

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +     +++      E D       D        +    +           +  + +   
Sbjct: 138 KKIEITRKQYRRSLLETDYALRATVDTLQKVHSGELPFDRTIKVSLTERLTKEQISQRMP 197

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +  TL+              D IA+   +   L   + + +   +   +    + K ++
Sbjct: 198 HNLRTLN--------------DLIAKNKADFEILVRRSASPRLKAEVRKQFLRRRRKCLE 243

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           LV  LSL   R+  L+ QL  +S R+      L  L                        
Sbjct: 244 LVEELSLRSRRVTPLLHQLEKVSGRMTFIRERLADLGND--------------------- 282

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
                           A   D    +R E++ + + T  S +   + ++ VR+   +   
Sbjct: 283 ----------------AMSRDEAADLRQELRELMLVTQESPTSLHNRMAKVRRHFDQYEA 326

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            K+E+   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  G+KFSTYA WW
Sbjct: 327 TKRELSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWW 386

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM D + K+ +  +R++  ++REPT E+IA+   +P+E V
Sbjct: 387 IRQAITRAIADQARTIRIPVHMIDVLSKLRQAQKRLTQTLRREPTYEDIAEATDVPIEEV 446

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V+ I + P+SL+ P+G+ + S  G+F++D    +P+  A    LR     +L +LT R
Sbjct: 447 RRVMDIGRHPVSLDRPVGEGEDSSFGEFVQDSETDNPVRIAASGMLRNKIDELLKTLTFR 506

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  ++R+R+G+     +TLEE G+ F VTRER+RQIEAKA+ K++ PSR+++L S+L
Sbjct: 507 EREIIRLRYGLVDGYSYTLEECGRIFKVTRERVRQIEAKAVAKMQSPSRAERLSSYL 563


>gi|257869538|ref|ZP_05649191.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
 gi|257803702|gb|EEV32524.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
          Length = 368

 Score =  238 bits (606), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 159/273 (58%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVPLLTAEEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFGI      TLEEVGK 
Sbjct: 276 GDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 48/191 (25%), Positives = 77/191 (40%), Gaps = 15/191 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             D +  + IK  + +G V  +EL   L  P  + ++ M+  +  L + GI+VVD +   
Sbjct: 8   TYDKAVAEFIKENKPKGQVVYDELTNHLATPYSLDADAMDKLIQKLEDSGISVVDENGEP 67

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                + +    ++     +             +DPVRMYL+E+G + LL+ E E+A+A 
Sbjct: 68  SVHSLKSNEKQQATQPQEDL-----SAPTGVKINDPVRMYLKEIGRVPLLTAEEEVALAL 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +IE G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 123 KIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVE 173

Query: 205 GHSYQKREDSS 215
              Y+K    S
Sbjct: 174 KFDYRKGFKFS 184


>gi|227529171|ref|ZP_03959220.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350896|gb|EEJ41187.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
          Length = 380

 Score =  237 bits (605), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    V++  + E     AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLSADEE---VALALRIEQGDEEAKQELAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ MP E VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 88/186 (47%), Gaps = 15/186 (8%)

Query: 1   MTIGKKRNR-DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEV 58
           M   KK+    S+S++ D          D +  K+I+  ++R ++  ++L   +  P E+
Sbjct: 1   MAKSKKKEIVISNSDNFDQKK------YDTAVGKLIRTYKKRKHIKYDDLTELVAKPFEL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           +++ +++ +  + + GI+VVD      E G  D   L ++   S   ++          +
Sbjct: 55  NADGIDNLLQNVEDSGISVVD------ENGDPDPRALMATEKLSQKAMKDTSAPTGVKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LLS + E+A+A RIE G       L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLSADEEVALALRIEQGDEEAKQELAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREI 184
             L  I
Sbjct: 168 QFLDLI 173


>gi|301165749|emb|CBW25321.1| RNA polymerase sigma-70 factor [Bacteriovorax marinus SJ]
          Length = 582

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 187/431 (43%), Positives = 276/431 (64%), Gaps = 1/431 (0%)

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD-EKS 310
           E  E   +++E          ++     +    DEI  V   L +L +   N     ++ 
Sbjct: 150 EKVETQENQNEFVKELVRGLDDESSNADIAKVRDEIYSVCDNLETLLNRVENEDGTIKEY 209

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
           + + K   + +   +  L+ N+  I+  VE +     +      +  R+ +   ++    
Sbjct: 210 TQEEKKKMDTIALRLADLTFNRKIINSFVEPVKKYYLQFRELYEQQERIFKFLEVEGQDD 269

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
            +    + L+                  +   + +   +  +++ +S++ G+  ++   +
Sbjct: 270 YKVLYEKVLEDDAFKRRLAKDLYTTDAKIEQLIRNQEDVIRKLRRLSLDAGMEFTDIEDV 329

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            +++ KGE +A +AK ++VEANLRLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++
Sbjct: 330 YNIILKGETKADVAKSQLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 389

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VRT+R++  ++ REPTPE
Sbjct: 390 RRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKMVRTSRQLIQELGREPTPE 449

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+++ +PV+ V+KV KI+KEPISLETPIG+E+ S LGDFIED   +SP D+ +   L 
Sbjct: 450 EIAERMELPVDKVKKVQKISKEPISLETPIGEEEDSSLGDFIEDDKIISPADAVMSVTLS 509

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E T  VL++LTPREE+VLRMRFGIG  +DHTLEEVG+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 510 EQTRSVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFFVTRERIRQIEAKALRKLRHP 569

Query: 671 SRSKKLRSFLD 681
           SR+K L+S++D
Sbjct: 570 SRAKMLKSYVD 580


>gi|319789700|ref|YP_004151333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114202|gb|ADU96692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 563

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 171/442 (38%), Positives = 263/442 (59%), Gaps = 12/442 (2%)

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           + +    N E   R++    DD A      E Q R K    +++I E+  E   LQ    
Sbjct: 130 EAEERIRNGEIKVRDIMRSPDDFAEG---GESQRRKKFFSIVEQIKELLPEFNRLQKQYY 186

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
             +++ +          K+  L+  L L+ S  + L + +Y+  K +  +E  L +L+  
Sbjct: 187 RNKRNAEVKRAYLKTWAKINGLLRQLPLSYSIYERLADDIYNKYKLLKKSERSLQKLSGK 246

Query: 363 Y---GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+  +    R    E+       A  +   E +  V   +D+    R+ ++S+   
Sbjct: 247 LSFLGLPIEEICHRLDDDEIREKI--DASRYTTREIRKMVKKYLDTKETYRSVLESLD-- 302

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             +  + F  +   +   + ++  AK+ +V +NLRLV+S+AKKY NRGL FLDLIQEGNI
Sbjct: 303 --MPRNAFYELAEKIYFYKKDSQEAKQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNI 360

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV++ +R+M
Sbjct: 361 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKVIKISRQM 420

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEEIA++L MP   VR +L++ +EP+SLETPIGD++ S LG+FIED  +  
Sbjct: 421 FQEMGREPKPEEIAERLKMPASKVRSILQLAQEPVSLETPIGDDEDSTLGNFIEDTKSPI 480

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P    I+ +L+E  +++L+ L+ RE  VL++RFG+    +HTLE+VGK+  VTRERIRQI
Sbjct: 481 PEQEVIKKDLQEKVSQLLSQLSEREALVLKLRFGLDGYPEHTLEQVGKELKVTRERIRQI 540

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E+KA+RKL++   +  L  FL+
Sbjct: 541 ESKALRKLRNSGLNIDLSIFLE 562


>gi|294622679|ref|ZP_06701641.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
 gi|291597877|gb|EFF29007.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
          Length = 369

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRVSLLTAEEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 277 GDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 337 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 46/191 (24%), Positives = 78/191 (40%), Gaps = 15/191 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             + +    IK  + +  V  ++L+  L  P  +++++M+  +  + + GI+VVD +   
Sbjct: 9   TYEAAVAAFIKENKPKRQVVYDDLSNQLATPFTLNADEMDKLIQKIDDAGISVVDENGDP 68

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                + +   A  A    +             +DPVRMYL+E+G + LL+ E E+A+A 
Sbjct: 69  SIHSLKSAEKKAEQAKTEDL-----SAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALAL 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +IE G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 124 KIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVE 174

Query: 205 GHSYQKREDSS 215
              Y+K    S
Sbjct: 175 KFDYRKGFKFS 185


>gi|323484375|ref|ZP_08089742.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692387|ref|ZP_08106623.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402369|gb|EGA94700.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503527|gb|EGB19353.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 372

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +  G      AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGKVPLLSPEEEIELAKQMEMGN---EYAKKRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EK+D+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 160 QFLDLIQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I++++RT+R++  ++ REP PEE+A+++ MPVE VR+++KI+++P+SLETPIG+E+ SHL
Sbjct: 220 INRLIRTSRQLLQELGREPHPEEVAERMDMPVERVREIMKISQDPVSLETPIGEEEDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D +   PLD+A    L E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 280 GDFIQDDHVQVPLDAATFTLLHEQLMEVLDTLTDREQKVLRLRFGLDDGRPRTLEEVGKE 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 340 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 372



 Score =  101 bits (252), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 73/158 (46%), Gaps = 2/158 (1%)

Query: 28  DDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++   ++++LA+ ++  +  +E+  F   + ++ +Q++     L +  ++V+  ++  + 
Sbjct: 9   EEKLTQLLELAKSKKNVLENKEILDFFHGEILNPDQLDQIYDFLDSNKVDVLQFEEELEI 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +      +  +      V           + DDPVRMYL+E+G + LLS E EI +AK++
Sbjct: 69  DPDLFIEEELNDEEEIDVESIDLTIPDGVNIDDPVRMYLKEIGKVPLLSPEEEIELAKQM 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EMGNEYAKKRLAEANLRLVVSIAKRY-VGRGMQFLDLI 165


>gi|256847131|ref|ZP_05552577.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
 gi|256715795|gb|EEU30770.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
          Length = 381

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  +   +   + K       AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 112 VRMYLKEIGRVNLLTADQEVELALRIEK---GDETAKQELAEANLRLVVSIAKRYVGRGM 168

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 169 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 228

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ MP + VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 229 INKLIRIQRQLLQDLGREPLPEEIGAEMDMPTKKVRDILKIAQEPVSLETPIGEEDDSHL 288

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 289 GDFIEDHDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 348

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 349 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 381



 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 53/216 (24%), Positives = 92/216 (42%), Gaps = 20/216 (9%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVS 59
           M   KK+   S+ E+ D          D +  K+I+  ++   +  +EL+  L  P +++
Sbjct: 1   MAKAKKQLVISNDENFDQKK------YDQAVGKLIRQYKKAKTIQYDELSKQLAAPFDLN 54

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           ++ +++ +  + + GI+VVD    E+ +    +L      S  +V  +          +D
Sbjct: 55  ADGLDNLMQNIEDAGISVVD----ENGDPDPRALKATEKLSQKAVNDRDTSAPTGVKIND 110

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMYL+E+G + LL+ + E+ +A RIE G       L E+ L     I  R  +  G  
Sbjct: 111 PVRMYLKEIGRVNLLTADQEVELALRIEKGDETAKQELAEANLRLVVSIAKRY-VGRGMQ 169

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            L  I         E   G     E   Y+K    S
Sbjct: 170 FLDLI--------QEGNMGLMKAVEKFDYRKGFKFS 197


>gi|227431669|ref|ZP_03913702.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352572|gb|EEJ42765.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 432

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 174/384 (45%), Positives = 235/384 (61%), Gaps = 23/384 (5%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D A      E  + K         +L    +L++  I+ L+E++ D            +
Sbjct: 68  YDKATKALIAEYKAAKQITYAALSKRLAEPFNLDEENIERLMEKVEDAG----------I 117

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            +    G      L+  Q +  D   ++ A++ P G   N           +R  +K I 
Sbjct: 118 AIVDDNGDPAPEVLKAKQNKPTDQE-LAEAEETPAGIKIN---------DPVRMYLKEIG 167

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +  +E   I   +         AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEG
Sbjct: 168 RVNLLKGNEEIDIAKRIE---NGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEG 224

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 225 NMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQR 284

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++   + REP PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A
Sbjct: 285 QLLQDLGREPLPEEIGAEIDLTADKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEA 344

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           VSP DSA    LRE    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIR
Sbjct: 345 VSPADSAAYEMLREQLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIR 404

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 405 QIEAKALRKLRHPSRSKQLKDFMD 428



 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 59/314 (18%), Positives = 107/314 (34%), Gaps = 47/314 (14%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +I   +    +T   L+  L  P  +  E +E  +  + + GI +VD     +
Sbjct: 68  YDKATKALIAEYKAAKQITYAALSKRLAEPFNLDEENIERLMEKVEDAGIAIVDD----N 123

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            + + + L    +        +  +  A    +DPVRMYL+E+G + LL    EI IAKR
Sbjct: 124 GDPAPEVLKAKQNKPTDQELAEAEETPAGIKINDPVRMYLKEIGRVNLLKGNEEIDIAKR 183

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGP--- 193
           IE G       L E+ L     I  R         D + +G   L + +D          
Sbjct: 184 IENGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYTKGFKF 243

Query: 194 ------------------------------ESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
                                         E+                 +   E+   ++
Sbjct: 244 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEI 303

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
             T   +    K++++  S      E  ++   +  ED +  +   SA  + LR ++   
Sbjct: 304 DLTADKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAVSPADSAAYEMLREQLESV 363

Query: 284 LDEIAEVYRELRSL 297
           LD + +    +  L
Sbjct: 364 LDTLTDREENVLRL 377


>gi|322373396|ref|ZP_08047932.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
 gi|321278438|gb|EFX55507.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
          Length = 369

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVE---NGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMGMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 116/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P  + ++ ++D +  L++ GI++ D D      G+
Sbjct: 14  VADFIRNHKKAGTAIDDEVTEKLVIPFVLDADGIDDLLERLTDGGISITDKD------GN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +  +     +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G
Sbjct: 68  PSSKYVVEAPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMGMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|328465879|gb|EGF37062.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus MTCC
           5463]
          Length = 370

 Score =  237 bits (605), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 174/365 (47%), Positives = 233/365 (63%), Gaps = 27/365 (7%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           K+   +L+   +L    +D LV++  D    I+   G+  +LA                 
Sbjct: 32  KDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA----------------- 74

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
                 +   KD    E K+  A     +   +R  +K I     I+  +    +++ ++
Sbjct: 75  ------LKKQKDVERAELKDMSAPSSVRMNDPVRMYLKEIGRVPLITADQE---IALAKR 125

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+CLG+KF
Sbjct: 126 IEEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKF 185

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 186 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 245

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP   VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +V
Sbjct: 246 NMPTNKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQV 305

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +L
Sbjct: 306 LETLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQL 365

Query: 677 RSFLD 681
           R F+D
Sbjct: 366 RDFMD 370



 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/133 (28%), Positives = 59/133 (44%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      E G    L L          L+    
Sbjct: 38  LIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVERAELKDMSA 91

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + L++ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 92  PSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRIEEGDEEAKQELAEANLRLVVSIAKR 151

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 152 Y-VGRGMSFLDLI 163


>gi|118586868|ref|ZP_01544302.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
 gi|71466858|emb|CAH41003.1| rpoD protein [Oenococcus oeni]
 gi|118432700|gb|EAV39432.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
          Length = 458

 Score =  237 bits (604), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 162/359 (45%), Positives = 225/359 (62%), Gaps = 20/359 (5%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+    +LN  +ID L+E++ D    I+  +G     +                      
Sbjct: 119 KMAKPFALNADQIDKLIEKVEDAGISIVDEDGNPSEKSLKTK-----------SNNPSQE 167

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
            +S A   P+G   N           +R  +K I   + ++  +   I   + KG  +  
Sbjct: 168 ELSQASSAPKGVKIN---------DPVRMYLKEIGRVSLLNADQEVAIAKRIEKGGSDGE 218

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A++E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA W
Sbjct: 219 RARQELAEANLRLVVSIAKRYVGRGMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATW 278

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P PEEI  ++ +  + 
Sbjct: 279 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRTLIQDLGRDPMPEEIGAEMELTADK 338

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI +EP+SLETPIG+ED SHLGDFIED    SP++S     L++    VL +LT 
Sbjct: 339 VREIQKIAQEPVSLETPIGEEDDSHLGDFIEDNEGESPIESTSDQMLKDQLEEVLGTLTE 398

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 399 REENVLRLRFGLEDGKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFME 457



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 62/216 (28%), Positives = 91/216 (42%), Gaps = 19/216 (8%)

Query: 6   KRNRDSDSEHEDSDDSLVFDF--SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQ 62
           K   +S S  + S  +  FD      S K  IK  ++ G V  ++L N    P  ++++Q
Sbjct: 71  KTKDNSKSGEKSSSAATAFDEKAYAKSLKAFIKKNKKSGQVVYDDLENKMAKPFALNADQ 130

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ++  +  + + GI++VD    ED   SE SL   S+  +     Q          +DPVR
Sbjct: 131 IDKLIEKVEDAGISIVD----EDGNPSEKSLKTKSNNPSQEELSQASSAPKGVKINDPVR 186

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTT 179
           MYL+E+G + LL+ + E+AIAKRIE G          L E+ L     I  R  +  G  
Sbjct: 187 MYLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRY-VGRGMH 245

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            L  I         E   G     E   Y K    S
Sbjct: 246 FLDLI--------QEGNMGLMKAVEKFDYTKGFKFS 273


>gi|210620870|ref|ZP_03292287.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
 gi|210155082|gb|EEA86088.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
          Length = 388

 Score =  237 bits (604), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +   E       +        +AK+ +VEANLRLV+S+AK+Y  RG+
Sbjct: 119 VRMYLKEIGKIPLLKPHEEVEYAKRM---HEGDELAKQRLVEANLRLVVSIAKRYVGRGM 175

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 176 LFLDLIQEGNLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 235

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+  PEEIAK++ + VE VR+++KI ++P+SLETPIG+E+ SHL
Sbjct: 236 INKLMRVSRQLLQELGRDAKPEEIAKEMDLSVEKVREIMKIAQDPVSLETPIGEEEDSHL 295

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P  SA  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+
Sbjct: 296 GDFIPDDDAPAPDISAAYSLLKEQIDEVLGSLNEREQKVLKLRFGLEDGRARTLEEVGKE 355

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 356 FDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 388



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 75/350 (21%), Positives = 127/350 (36%), Gaps = 31/350 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-------- 79
            +    +I   ++ G +T EE+       E++ EQM++    L ++GI +VD        
Sbjct: 14  KEKANALILKGKKNGSLTFEEIGDAFETVEMNKEQMDNLYDTLQSVGIELVDEKSKKNNA 73

Query: 80  ----GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
               G++ +      D  D      +              S DDPVRMYL+E+G I LL 
Sbjct: 74  TFAVGNNDDMGFDHIDDPDSDDDDKDGDSEALDLSLPKGISIDDPVRMYLKEIGKIPLLK 133

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
              E+  AKR+  G  +    L E+ L     I  R  +  G   L  I         E 
Sbjct: 134 PHEEVEYAKRMHEGDELAKQRLVEANLRLVVSIAKRY-VGRGMLFLDLI--------QEG 184

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             G     E   Y+K    S        Q     I   A+  +     V++  +      
Sbjct: 185 NLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLMRVSR 244

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE------- 308
           + L E   D+     A E  L  + +  + +IA+    L +      +    +       
Sbjct: 245 QLLQELGRDAKPEEIAKEMDLSVEKVREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDA 304

Query: 309 ---KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                S    +LKE++ +++GSL+  + ++  L   L D   R +   G+
Sbjct: 305 PAPDISAAYSLLKEQIDEVLGSLNEREQKVLKLRFGLEDGRARTLEEVGK 354


>gi|318066969|emb|CBY89099.1| RNA polymerase sigma70 factor [Halomonas salina]
          Length = 366

 Score =  237 bits (604), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 115/397 (28%), Positives = 173/397 (43%), Gaps = 53/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D  +E     V       E 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADVPEEP----VVAEGASDED 123

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                 +D S     PE A      + E  + +   + A                     
Sbjct: 124 DEDAEDEDDSGGGPDPEEARARFEQIREQNESARQAIDA--------------------- 162

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                         + + S + +    +L +L   + L     + LV Q+    ++I   
Sbjct: 163 --------------NGRGSAQAQAELARLAELFSPIKLVPKHFERLVGQVRISVEQIRAQ 208

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   + R  F++   G E    W+                     I + + 
Sbjct: 209 EKAVMQLCVKKAKVPRKTFIKAFPGNESRQDWLDDFMAXXXXXXXXXXXXLKGEIQRSQR 268

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        +S+++ + +   +  G  +A  AKKEMVEA+LRLVIS+A+KY +RGL FL
Sbjct: 269 KIALEEEMVPLSVTDLKEVNRWLSIGRAKARRAKKEMVEAHLRLVISIAQKYPHRGLPFL 328

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DL QEG+IGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 329 DLFQEGHIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 365


>gi|327458597|gb|EGF04945.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1057]
          Length = 370

 Score =  237 bits (604), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 71/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +E+ +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQTGVATDDEINDQLVIPFTLDADGIENLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|227878689|ref|ZP_03996603.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256843283|ref|ZP_05548771.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256850360|ref|ZP_05555788.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|262046492|ref|ZP_06019454.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|293380134|ref|ZP_06626221.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295693058|ref|YP_003601668.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|312978174|ref|ZP_07789918.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
 gi|227861704|gb|EEJ69309.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256614703|gb|EEU19904.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256712757|gb|EEU27750.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|260573363|gb|EEX29921.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|290923304|gb|EFE00220.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295031164|emb|CBL50643.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|310894892|gb|EFQ43962.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
          Length = 370

 Score =  237 bits (604), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 171/361 (47%), Positives = 231/361 (63%), Gaps = 27/361 (7%)

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
            +L+   +L    +D LV++  D    I+   G+  +LA                     
Sbjct: 36  ARLIKPYNLQGKAVDQLVQEFEDNGISIVDENGDPSKLA--------------------- 74

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             +   KD  + E K+  A     +   +R  +K I     ++  +    +++ ++ E  
Sbjct: 75  --LKKQKDVEKAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQE---IALAKRIESG 129

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA
Sbjct: 130 DEEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYA 189

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP 
Sbjct: 190 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPT 249

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             VR +LKI +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L+E   +VL +L
Sbjct: 250 NKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETL 309

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+
Sbjct: 310 TDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFM 369

Query: 681 D 681
           D
Sbjct: 370 D 370



 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 43/142 (30%), Positives = 65/142 (45%), Gaps = 8/142 (5%)

Query: 44  VTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS 102
           +T E+  A L  P  +  + ++  V    + GI++VD      E G    L L       
Sbjct: 29  ITEEDFTARLIKPYNLQGKAVDQLVQEFEDNGISIVD------ENGDPSKLALKKQKDVE 82

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
              L+     +    +DPVRMYL+E+G + LL+ + EIA+AKRIE+G       L E+ L
Sbjct: 83  KAELKDMSAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRIESGDEEAKQELAEANL 142

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  +  G + L  I
Sbjct: 143 RLVVSIAKRY-VGRGMSFLDLI 163


>gi|315303191|ref|ZP_07873849.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
 gi|313628434|gb|EFR96909.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
          Length = 386

 Score =  237 bits (604), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 117 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 173

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 174 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 233

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 234 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 293

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 294 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 353

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 354 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 386



 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 46/170 (27%), Positives = 79/170 (46%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + + +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 16  KTPNTKPVAELNVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 75

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 76  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 130

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 131 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 179


>gi|299822900|ref|ZP_07054786.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
 gi|299816429|gb|EFI83667.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
          Length = 389

 Score =  237 bits (604), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 120 VRMYLKEIGRVNLLTADEE---VALAKRIETGDIEAKGRLAEANLRLVVSIAKRYVGRGM 176

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 177 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 236

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 237 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 296

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 297 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 356

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 357 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 389



 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 44/173 (25%), Positives = 77/173 (44%), Gaps = 6/173 (3%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKM-IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           ++     +    + S D  K++ I+  ++ G +T +++ A L P  + S+QM++ +  L+
Sbjct: 15  AKKTVETNETTVELSIDQVKELLIETGKKSGTLTYDKVAAQLAPFTLDSDQMDEFLVHLT 74

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
             GI        + +E  +             + L           +DPVRMYL+E+G +
Sbjct: 75  QNGIE----VTDDVDEDEDPDEKELIKEETEELDLTDMSVPPGVKINDPVRMYLKEIGRV 130

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ + E+A+AKRIE G       L E+ L     I  R  +  G   L  I
Sbjct: 131 NLLTADEEVALAKRIETGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 182


>gi|69249285|ref|ZP_00604924.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257877975|ref|ZP_05657628.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257881238|ref|ZP_05660891.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257884904|ref|ZP_05664557.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257889826|ref|ZP_05669479.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|258616539|ref|ZP_05714309.1| RNA polymerase sigma factor RpoD [Enterococcus faecium DO]
 gi|260559026|ref|ZP_05831212.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|261207559|ref|ZP_05922244.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289565071|ref|ZP_06445524.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|293556716|ref|ZP_06675279.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|293563374|ref|ZP_06677823.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|293568034|ref|ZP_06679372.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|294614871|ref|ZP_06694766.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|294618226|ref|ZP_06697809.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|314939477|ref|ZP_07846711.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|314941108|ref|ZP_07848006.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|314949892|ref|ZP_07853194.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
 gi|314951693|ref|ZP_07854736.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|314993960|ref|ZP_07859287.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|314996911|ref|ZP_07861912.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|68194219|gb|EAN08744.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257812203|gb|EEV40961.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257816896|gb|EEV44224.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257820742|gb|EEV47890.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257826186|gb|EEV52812.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|260074783|gb|EEW63099.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|260077942|gb|EEW65648.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289163078|gb|EFD10925.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|291589255|gb|EFF21065.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|291592333|gb|EFF23947.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|291595506|gb|EFF26816.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|291601048|gb|EFF31337.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|291604635|gb|EFF34120.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|313588970|gb|EFR67815.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|313591562|gb|EFR70407.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|313596157|gb|EFR75002.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|313600109|gb|EFR78952.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|313641279|gb|EFS05859.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|313643734|gb|EFS08314.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
          Length = 369

 Score =  237 bits (604), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRVSLLTAEEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 277 GDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 337 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 46/191 (24%), Positives = 78/191 (40%), Gaps = 15/191 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             + +    IK  + +  V  ++L+  L  P  +++++M+  +  + + GI+VVD +   
Sbjct: 9   TYEAAVAAFIKENKPKRQVVYDDLSNQLATPFTLNADEMDKLIQKIEDAGISVVDENGDP 68

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                + +   A  A    +             +DPVRMYL+E+G + LL+ E E+A+A 
Sbjct: 69  SIHSLKSAEKKAEQAKTEDL-----SAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALAL 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +IE G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 124 KIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVE 174

Query: 205 GHSYQKREDSS 215
              Y+K    S
Sbjct: 175 KFDYRKGFKFS 185


>gi|332638574|ref|ZP_08417437.1| RNA polymerase sigma factor [Weissella cibaria KACC 11862]
          Length = 377

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 183/383 (47%), Positives = 235/383 (61%), Gaps = 23/383 (6%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           D AV     E  + K          LV  + LN  +ID L E++      I+  +GE   
Sbjct: 18  DKAVKNIIKEFKADKEIKENALQDALVKPMRLNADQIDELYEKIESAGISIVDEKGEPTA 77

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
            A      +           L    +  A D P G   N           +R  +K I  
Sbjct: 78  RALENKKTK-----------LSEKELKQAADAPTGMKIN---------DPVRMYLKEIGR 117

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            + ++  E    V++  + E     AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN
Sbjct: 118 VSLLTGDEE---VALAERIEQGDDTAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGN 174

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R 
Sbjct: 175 MGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRN 234

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +   + REPTPEEI  ++ +  + VR +LKI +EP+SLETPIG+ED SHLGDFIED  A+
Sbjct: 235 LLQDLGREPTPEEIGAEMDIVTDKVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDNEAI 294

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP DSA    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQ
Sbjct: 295 SPADSAAYQMLKEQLESVLDTLTDREENVLRLRFGLEDGRTRTLEEVGKVFGVTRERIRQ 354

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSK+LR FLD
Sbjct: 355 IEAKALRKLRHPSRSKQLRDFLD 377



 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 80/189 (42%), Gaps = 14/189 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +IK  +    +    L   L  P  ++++Q+++    + + GI++VD    E  
Sbjct: 18  DKAVKNIIKEFKADKEIKENALQDALVKPMRLNADQIDELYEKIESAGISIVD----EKG 73

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E +  +L+   +  +     Q          +DPVRMYL+E+G + LL+ + E+A+A+RI
Sbjct: 74  EPTARALENKKTKLSEKELKQAADAPTGMKINDPVRMYLKEIGRVSLLTGDEEVALAERI 133

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 134 EQGDDTAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKF 184

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 185 DYRKGFKFS 193


>gi|318066905|emb|CBY89067.1| RNA polymerase sigma70 factor [Chromohalobacter canadensis]
          Length = 367

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 123/397 (30%), Positives = 180/397 (45%), Gaps = 52/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLEAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D  + +   D  +  GD   
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADVPEPEPERDAVD--GDASE 125

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
               ++++ +     PE A+     + E  + +   +                       
Sbjct: 126 DDDDAEEEETGGGPDPEEAKARFEQIREQNERAKAAID---------------------- 163

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K    S      + +L +L   + L     + LV Q+    ++I   
Sbjct: 164 -------------KHGLGSSNADQEQARLAELFSPIKLVPKHFERLVGQVRISIEQIRGQ 210

Query: 353 EGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   + R  F+    G E D  W+   K      +   +      IL+ + 
Sbjct: 211 EKAIMQLFVKQAKVPRKTFIGSFPGAESDLEWLDRFKAKHSK-YAERIEPFRADILRAQR 269

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 270 KIGFEEEMVCLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 329

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 330 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|330955106|gb|EGH55366.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae Cit 7]
          Length = 393

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 103/433 (23%), Positives = 180/433 (41%), Gaps = 48/433 (11%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + D E +A  S ++      P             D+ + 
Sbjct: 174 IAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEI 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                    +     +  +  +AE++                                  
Sbjct: 234 TRKALKKFGRDDKHAIAEMVALAELF---------------------------------- 259

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 260 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWT 319

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A    + ++   +      I + + ++ ++  ETG+ I+E + I   +  GE +A  A
Sbjct: 320 D-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIGEAKARRA 378

Query: 445 KKEMVEANLRLVI 457
           KKEMVEANLRLVI
Sbjct: 379 KKEMVEANLRLVI 391


>gi|300214611|gb|ADJ79027.1| RNA polymerase sigma factor [Lactobacillus salivarius CECT 5713]
          Length = 372

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 173/374 (46%), Positives = 230/374 (61%), Gaps = 26/374 (6%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +  V  KVL +KLV       L+  ++D L+  + D    ++   GE    +       
Sbjct: 25  PQKQVNYKVLTDKLVT---PFKLDADQMDQLIGSIEDRGISVVDENGEPSAHSLKA---- 77

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                            +   +  E +        V     +R  +K I     ++  E 
Sbjct: 78  ----------------ATKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEE 121

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              V++  K E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EK
Sbjct: 122 ---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEK 178

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP
Sbjct: 179 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREP 238

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A   
Sbjct: 239 MPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYE 298

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL
Sbjct: 299 LLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 358

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSK+L+ FL+
Sbjct: 359 RHPSRSKQLKDFLE 372



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 84/188 (44%), Gaps = 14/188 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            + + +I+  + +  V  + L   L  P ++ ++QM+  +  + + GI+VVD    E+ E
Sbjct: 14  KALRDLIREYKPQKQVNYKVLTDKLVTPFKLDADQMDQLIGSIEDRGISVVD----ENGE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S  SL  A+  +  +   +     +    +DPVRMYL+E+G + LL+ + E+A+A +IE
Sbjct: 70  PSAHSLKAATKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G + L  I         E   G     E   
Sbjct: 130 EGDQEAKQRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------QEGNMGLMKAVEKFD 180

Query: 208 YQKREDSS 215
           Y+K    S
Sbjct: 181 YRKGFKFS 188


>gi|262282856|ref|ZP_06060623.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
 gi|262261108|gb|EEY79807.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
          Length = 370

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +     + AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAILVEQ---GDTEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 69/333 (20%), Positives = 120/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  ++ G    +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQVAEFIRNHKKTGTAIDDEINDKLIIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 66  EGNPSARVLHNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDTEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|157151547|ref|YP_001450555.1| RNA polymerase sigma factor RpoD [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157076341|gb|ABV11024.1| RNA polymerase sigma factor [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 370

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +     + AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAILVEQ---GDTEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.4 bits (238), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  ++ G V  +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQVAEFIRNHKKAGTVIDDEINDKLIIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 66  EGNPSARVLHNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDTEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|163790450|ref|ZP_02184881.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
 gi|159874354|gb|EDP68427.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
          Length = 373

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E    V +  K E     A++ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLTAAEE---VELAIKIEEGDQEARQRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP ++A    L+E    VL +LT REE VLR+RFG+    + TLE+VGK 
Sbjct: 281 GDFIEDHDATSPAENAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRNRTLEDVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 373



 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 72/189 (38%), Gaps = 13/189 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D   KK+IK  +  G +  ++L N    P  +++++M+  +  + + G+        +  
Sbjct: 13  DSEVKKLIKEYKPAGTIHYDDLTNKIATPFSLTAQKMDALIQTIEDAGVG---VVGDDGG 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +         A   +   +          +DPVRMYL+E+G + LL+   E+ +A +I
Sbjct: 70  PTARQLKLKELKAEKDAEKPEDLTAPPGVKINDPVRMYLKEIGRVNLLTAAEEVELAIKI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 130 EEGDQEARQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKF 180

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 181 DYKKGFKFS 189


>gi|332362696|gb|EGJ40494.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK49]
          Length = 370

 Score =  237 bits (603), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|239979292|ref|ZP_04701816.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 357

 Score =  237 bits (603), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 126/295 (42%), Positives = 186/295 (63%), Gaps = 23/295 (7%)

Query: 410 RNEIKSISVETGISISEFRHIVSMV-----------------------RKGECEASIAKK 446
           R  ++ I     +S ++   +   V                       R+       AK 
Sbjct: 63  RQYLREIGRIPLLSAADEVELARRVEAGVFAAAKLAGGCADAGLARDLRRLVVLGERAKG 122

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            ++EANLRLV+SVAK+YT RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW++Q
Sbjct: 123 RLIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQ 182

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           A++R++ADQ+ TIR+PVH+ + I++VVRT R +  +  REP  EE+ ++L +  E V +V
Sbjct: 183 AMSRALADQARTIRVPVHVVELINRVVRTQRALLQEAGREPAAEEVGERLGLSAEKVEEV 242

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++  EPISL  P+G ED   LGD IED +A SP +SA    LR+    VLA+L  RE +
Sbjct: 243 LRLAHEPISLHAPVGGEDDVFLGDLIEDADAASPAESAALLLLRQHLDAVLATLGDRERQ 302

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           V+++R+G       TLEE+G+ F VTRER+RQIE+K +R+L+  + + +LR +L+
Sbjct: 303 VVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLREHTAAGQLRGYLE 357



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            + A  +  D  R YLRE+G I LLS   E+ +A+R+EAG
Sbjct: 51  SEQAGAAAPDLFRQYLREIGRIPLLSAADEVELARRVEAG 90


>gi|260583936|ref|ZP_05851684.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
 gi|260158562|gb|EEW93630.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
          Length = 374

 Score =  237 bits (603), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 161/289 (55%), Positives = 208/289 (71%), Gaps = 4/289 (1%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E +  ++  V     +R  +K I     +S  E  ++   +++       AK+E+ EANL
Sbjct: 89  EDETALSSNVKINDSVRMYLKEIGRVPLLSADEEVNLALRIQQ---GDQEAKQELAEANL 145

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD   G+KFSTYA WW++QAITR+IA
Sbjct: 146 RLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIA 205

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+VR  R++   + REPTPEEI  ++ +P E VR++LKI +EP
Sbjct: 206 DQARTIRIPVHMVETINKLVRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEP 265

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLETPIG+ED SHLGDFIED NA SP +    A L+E    VL  LT REE VLR+RFG
Sbjct: 266 VSLETPIGEEDDSHLGDFIEDDNATSPAEHTAYALLKEQLDEVLEQLTDREENVLRLRFG 325

Query: 634 IGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +  N    TLE+VG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 326 LDKNGEIRTLEQVGQVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLD 374



 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 39/158 (24%), Positives = 72/158 (45%), Gaps = 5/158 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
            ++  K++   +  G +  ++L+A +  P E+ +E M+  +    + G++VVD D     
Sbjct: 13  KEATSKLLAERKLFGQILYDDLSAQIAIPYELDAEGMDKLIQQFEDAGVSVVDADG---G 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             S      ++      +   +   S++   +D VRMYL+E+G + LLS + E+ +A RI
Sbjct: 70  PTSRQLSSESAKEPEVEMTEDETALSSNVKINDSVRMYLKEIGRVPLLSADEEVNLALRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + G       L E+ L     I  R  +  G   L  I
Sbjct: 130 QQGDQEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI 166


>gi|167768032|ref|ZP_02440085.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|317498375|ref|ZP_07956670.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|167710361|gb|EDS20940.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|291561030|emb|CBL39830.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SSC/2]
 gi|316894269|gb|EFV16456.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 363

 Score =  237 bits (603), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 212/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    + + ++ E     AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 94  VRMYLKEIGKVPLLSADEE---IKLAQRMEEGDEAAKKKLAEANLRLVVSIAKRYVGRGM 150

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 151 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 210

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA+++ +PVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 211 INKLIRVSRQLLQELGREPSPEEIAEEMDIPVERVREILKISQEPVSLETPIGEEEDSHL 270

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D+N   P D+A    L+E    VL +LT RE++VLR+RFG+  +   TLEEVGK+
Sbjct: 271 GDFIQDENVPVPADAAAFTLLKEQLDEVLGTLTEREQKVLRLRFGLDDSRARTLEEVGKE 330

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 331 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 363



 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 36/163 (22%), Positives = 69/163 (42%), Gaps = 11/163 (6%)

Query: 23  VFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
             +   +    +++L ++ + ++   +++++    +++S+ ME     L   GI+V+   
Sbjct: 4   TMEQFTEKLAGLVELGKKNKNFLEYAQIDSYFKDMKLNSDMMEAIYDYLEQNGIDVL--- 60

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
                       D      +      +       S +DPVRMYL+E+G + LLS + EI 
Sbjct: 61  ------TLAAVADDDEDLDDPIEDETEIAVPDGVSIEDPVRMYLKEIGKVPLLSADEEIK 114

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +A+R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 115 LAQRMEEGDEAAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 156


>gi|294812504|ref|ZP_06771147.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325103|gb|EFG06746.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 436

 Score =  237 bits (603), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 131/323 (40%), Positives = 194/323 (60%), Gaps = 25/323 (7%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR-------- 435
              +   P             S    R  ++ I     ++ +E   +   V         
Sbjct: 114 AEESAPRPGSARTARSESSGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEK 173

Query: 436 -----------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
                            +      +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN
Sbjct: 174 LAATPDLNSSRLAADLDRLVVMGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGN 233

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A EKFD+  GYKFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR
Sbjct: 234 LGLIRAVEKFDYTRGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRR 293

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  +   EPTPEE+A +L +P E V +VL++ +EP+SL  P+G+E+   LGD IED +A 
Sbjct: 294 MLQEQGSEPTPEEVAAQLDLPPERVSEVLRLAQEPVSLHAPVGEEEDVALGDLIEDGDAA 353

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP++SA    LRE    VL++L  RE +V+++R+G+      TLEE+G+ F VTRERIRQ
Sbjct: 354 SPVESAAFLLLREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQ 413

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IE+K + KL+  + + +LR +LD
Sbjct: 414 IESKTLNKLRDHAFADQLRGYLD 436



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           A  ++      +  +  +   + D  R YLRE+G I LL+   E+ +A+R+EAG      
Sbjct: 114 AEESAPRPGSARTARSESSGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLF-AEE 172

Query: 156 SLCESP 161
            L  +P
Sbjct: 173 KLAATP 178


>gi|221633686|ref|YP_002522912.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
 gi|221156620|gb|ACM05747.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
          Length = 509

 Score =  237 bits (603), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 131/252 (51%), Positives = 193/252 (76%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++  ++   +   A++++ EANLRLV+S+AK+YT RGL  LDLIQEGN+GLM+A +KF 
Sbjct: 258 LIAHWQRLRRDGEAARRKLTEANLRLVVSIAKRYTGRGLTLLDLIQEGNLGLMRAVDKFQ 317

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G+KFSTYA WW++QAITR++AD + TIR+PVH+ + +++V R AR+++ ++ REPT 
Sbjct: 318 THKGFKFSTYATWWIRQAITRALADHARTIRLPVHLVETLNRVSRVARQLTQELGREPTT 377

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            E+A  + MP++ +R++L+  ++P+SLE P+G E+ S LGDF+ED+ AV+PLD+A  + L
Sbjct: 378 SELAAAVNMPLDRLRELLQAAQDPVSLEAPVGQEEESTLGDFLEDERAVAPLDAAALSLL 437

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE    +LA+LT RE RVL MRFG+     +TLEEVG+ F VTRER+RQIEAKA+RKL+H
Sbjct: 438 REQVQSLLATLTERERRVLAMRFGLEDGQTYTLEEVGRAFGVTRERVRQIEAKALRKLRH 497

Query: 670 PSRSKKLRSFLD 681
           P R++ LR FL+
Sbjct: 498 PQRARALRDFLE 509



 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 41/176 (23%), Positives = 66/176 (37%), Gaps = 23/176 (13%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
             KR+R+  +    S D  V   +D     ++  AR  G +T E+  A +  D +  +  
Sbjct: 9   KPKRSREVVTRANGSVDLPVLAGADA----ILATARLHGRLTREQWLALI--DTLGPDAA 62

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           E  +A L   G+ V        EE  E      S                D   +DPVR+
Sbjct: 63  ETALAELQAEGVPV------AIEEALEPDGTSRSWEPEKEAD-------PDLLVEDPVRL 109

Query: 124 YLREMGSIELLSREGEIAI--AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           YL E+G + LL+ E E+ +  A  +      +     + PL    L+   +    G
Sbjct: 110 YLAEIGRVPLLTAEQEVELGRAVELAEYLDELRRCCGDDPLVL--LLAAWERFVTG 163


>gi|318066915|emb|CBY89072.1| RNA polymerase sigma70 factor [Chromohalobacter sarecensis]
          Length = 369

 Score =  236 bits (602), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 118/397 (29%), Positives = 181/397 (45%), Gaps = 50/397 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLDAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  +    +   + +   ++
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEAEVPEPVPEESAADGDASEDA 127

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            A  ++++ +     PE A+     + E  + +   +                       
Sbjct: 128 DADDAEEEETGGGPDPEEAKARFEQIREQNERAKAAID---------------------- 165

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K    S +    + +L +L   + L     + LV Q+    +++   
Sbjct: 166 -------------KHGLGSSEANKEQARLAELFSPIKLVPKHFERLVGQVRISIEQVRSQ 212

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++   +   + R  F+    G E D  W+   K      +   +      IL+ + 
Sbjct: 213 EKAIMQVFVKQAKVPRKTFIGSFPGAESDLEWLDRFKAKHAK-YAERLEPFRADILRAQR 271

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 272 KIGFEEEMVRLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 331

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 332 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 368


>gi|227551146|ref|ZP_03981195.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257887737|ref|ZP_05667390.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257896230|ref|ZP_05675883.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257898868|ref|ZP_05678521.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|293379528|ref|ZP_06625670.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
 gi|293570226|ref|ZP_06681295.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|227179708|gb|EEI60680.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257823791|gb|EEV50723.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257832795|gb|EEV59216.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257836780|gb|EEV61854.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|291609633|gb|EFF38894.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|292641837|gb|EFF60005.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
          Length = 369

 Score =  236 bits (602), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRVSLLTAEEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 277 GDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 337 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 78/190 (41%), Gaps = 15/190 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + +    IK  + +  V  ++L+  L  P  +++++M+  +  + + GI+VVD +    
Sbjct: 10  YEAAVAAFIKENKPKRQVVYDDLSNQLATPFTLNADEMDKLIQKIEDAGISVVDENGDPS 69

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
               + +   A  A    +             +DPVRMYL+E+G + LL+ E E+A+A +
Sbjct: 70  IHSLKSAEKKAEQAKTEDL-----SAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALALK 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 125 IEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 175

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 176 FDYRKGFKFS 185


>gi|301301338|ref|ZP_07207482.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851066|gb|EFK78806.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 372

 Score =  236 bits (602), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 173/374 (46%), Positives = 230/374 (61%), Gaps = 26/374 (6%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +  V  KVL +KLV       L+  ++D L+  + D    ++   GE    +       
Sbjct: 25  PQKQVNYKVLTDKLVT---PFKLDADQMDQLIGSIEDRGISVVDENGEPSAHSLKA---- 77

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                            +   +  E +        V     +R  +K I     ++  E 
Sbjct: 78  ----------------ATKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEE 121

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              V++  K E     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EK
Sbjct: 122 ---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEK 178

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+M   + REP
Sbjct: 179 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQMLQDLGREP 238

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A   
Sbjct: 239 MPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYE 298

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL
Sbjct: 299 LLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 358

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSK+L+ FL+
Sbjct: 359 RHPSRSKQLKDFLE 372



 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 84/188 (44%), Gaps = 14/188 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            + + +I+  + +  V  + L   L  P ++ ++QM+  +  + + GI+VVD    E+ E
Sbjct: 14  KALRDLIREYKPQKQVNYKVLTDKLVTPFKLDADQMDQLIGSIEDRGISVVD----ENGE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S  SL  A+  +  +   +     +    +DPVRMYL+E+G + LL+ + E+A+A +IE
Sbjct: 70  PSAHSLKAATKEAEKAENDKDVSAPSGVKINDPVRMYLKEIGRVNLLTADEEVALALKIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G + L  I         E   G     E   
Sbjct: 130 EGDQEAKQRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------QEGNMGLMKAVEKFD 180

Query: 208 YQKREDSS 215
           Y+K    S
Sbjct: 181 YRKGFKFS 188


>gi|239631415|ref|ZP_04674446.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|239525880|gb|EEQ64881.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
          Length = 352

 Score =  236 bits (602), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 160/273 (58%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 83  VRMYLKEIGRVSLLTADEE---VALALKIEQGDQEAKQRLAEANLRLVVSIAKRYVGRGM 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 140 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 199

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 200 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 259

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 260 GDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 319

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 320 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 352



 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 78/183 (42%), Gaps = 16/183 (8%)

Query: 34  MIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           MIK  +++  +T ++L   L  P E+ S  ++D +  + + GI +VD      E G   +
Sbjct: 1   MIKDYKKKKQITEDDLTDKLVKPFELKSGAIDDLMQKIEDNGIAIVD------ENGEPAA 54

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           + L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +IE G   
Sbjct: 55  ISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQE 114

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
               L E+ L     I  R  +  G   L  I         E   G     E   Y+K  
Sbjct: 115 AKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKFDYRKGF 165

Query: 213 DSS 215
             S
Sbjct: 166 KFS 168


>gi|26249650|ref|NP_755690.1| hypothetical protein c3819 [Escherichia coli CFT073]
 gi|26110078|gb|AAN82264.1|AE016767_24 Putative conserved protein [Escherichia coli CFT073]
          Length = 368

 Score =  236 bits (602), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 88/403 (21%), Positives = 156/403 (38%), Gaps = 49/403 (12%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+    
Sbjct: 9   LKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLA 68

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE G 
Sbjct: 69  ENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +  S+ E P     L+   D +      L ++I            GF           
Sbjct: 128 NQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEEDLAP 176

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                  +   +  + + D +                PE A                   
Sbjct: 177 TATHVGSELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKF--------------- 221

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +LR + +   D I                     +S    +    KL ++     L
Sbjct: 222 ---AELRAQYIVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQFRL 261

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKD 389
              + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W + A  
Sbjct: 262 VPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIA 321

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
             +  W   +    + + +   +++ I  ETG++I + + I  
Sbjct: 322 MNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINR 363


>gi|323480687|gb|ADX80126.1| RNA polymerase sigma factor rpoD (Sigma-42) [Enterococcus faecalis
           62]
          Length = 356

 Score =  236 bits (602), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 164/306 (53%), Positives = 212/306 (69%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI    R  +K I     ++ +E   +   + 
Sbjct: 54  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 113

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 114 ---EGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 170

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 171 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 230

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 231 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 290

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 291 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 350

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 351 LKDFLE 356



 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 46/184 (25%), Positives = 71/184 (38%), Gaps = 15/184 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
             IK  + +G V  ++L   L  P  + +E ME  +  + + GI+VVD +    E   + 
Sbjct: 3   AFIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVDENGDPSEHSLKK 62

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                          +          +DPVRMYL+E+G ++LL+   E+ +A +IE G  
Sbjct: 63  -----DEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEEGDQ 117

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
                L E+ L     I  R  +  G   L  I         E   G     E   Y+K 
Sbjct: 118 EAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKFDYRKG 168

Query: 212 EDSS 215
              S
Sbjct: 169 FKFS 172


>gi|125717671|ref|YP_001034804.1| RNA polymerase sigma factor RpoD [Streptococcus sanguinis SK36]
 gi|125497588|gb|ABN44254.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32),
           putative [Streptococcus sanguinis SK36]
 gi|324990502|gb|EGC22438.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK353]
 gi|324995458|gb|EGC27370.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK678]
 gi|325688386|gb|EGD30405.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK72]
 gi|325690016|gb|EGD32020.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK115]
 gi|325693940|gb|EGD35858.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK150]
 gi|327461509|gb|EGF07840.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1]
 gi|327468857|gb|EGF14329.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK330]
 gi|327489365|gb|EGF21158.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1058]
 gi|332361594|gb|EGJ39398.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1056]
 gi|332363116|gb|EGJ40903.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK355]
 gi|332365901|gb|EGJ43657.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1059]
          Length = 370

 Score =  236 bits (602), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.8 bits (239), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|116494985|ref|YP_806719.1| RNA polymerase sigma factor RpoD [Lactobacillus casei ATCC 334]
 gi|191638497|ref|YP_001987663.1| RNA polymerase sigma factor RpoD [Lactobacillus casei BL23]
 gi|227535009|ref|ZP_03965058.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|301066553|ref|YP_003788576.1| DNA-directed RNA polymerase sigma70/sigma32 subunit [Lactobacillus
           casei str. Zhang]
 gi|116105135|gb|ABJ70277.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei ATCC
           334]
 gi|190712799|emb|CAQ66805.1| RNA polymerase sigma factor [Lactobacillus casei BL23]
 gi|227187324|gb|EEI67391.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|300438960|gb|ADK18726.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus casei str. Zhang]
 gi|327382532|gb|AEA54008.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei LC2W]
 gi|327385729|gb|AEA57203.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei BD-II]
          Length = 422

 Score =  236 bits (602), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 160/273 (58%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 153 VRMYLKEIGRVSLLTADEE---VALALKIEQGDQEAKQRLAEANLRLVVSIAKRYVGRGM 209

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 210 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 269

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 270 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 329

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 330 GDFIEDQDATSPEDHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 389

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 390 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 422



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 82/189 (43%), Gaps = 16/189 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           DD+ K +IK  +++  +T ++L   L  P E+ S  ++D +  + + GI +VD      E
Sbjct: 65  DDAVKAVIKDYKKKKQITEDDLTDKLVKPFELKSGAIDDLMQKIEDNGIAIVD------E 118

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   ++ L      S   +      +    +DPVRMYL+E+G + LL+ + E+A+A +I
Sbjct: 119 NGEPAAISLKKQKKVSKKEMSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI 178

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 179 EQGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKF 229

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 230 DYRKGFKFS 238


>gi|55821465|ref|YP_139907.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMG
           18311]
 gi|55737450|gb|AAV61092.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus LMG 18311]
          Length = 369

 Score =  236 bits (602), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKKLAIAVE---NGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 116/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P  + ++ ++D +  L++ GI++ D D      G+
Sbjct: 14  VADFIRNHKKAGTAIDDEITEKLVIPFVLDADGIDDLLERLTDGGISITDKD------GN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +  +     +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G
Sbjct: 68  PSSKYVVEAPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKKLAIAVENG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|327473233|gb|EGF18653.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK408]
          Length = 370

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V K       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEK---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNTEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EKGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|325478784|gb|EGC81895.1| RNA polymerase sigma factor RpoD [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 604

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 205/654 (31%), Positives = 321/654 (49%), Gaps = 94/654 (14%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD--LEDEEGSED-------- 91
           G +T  ++  F    E+  +  +  +  + ++GI +V+  +  LEDEE +ED        
Sbjct: 30  GLITYSQIYTFENFKEMEDDSKKFVINQVLSLGIEIVEKSETVLEDEEVTEDMKDDLSDD 89

Query: 92  --SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
               +            +          DDPV+MYL+E+G + LL+   E          
Sbjct: 90  EDLEEEIEEDEVEEDLNKNVDIMVGVKVDDPVKMYLKEIGKVSLLTATEE---------- 139

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                             II    +  G                  K       + +  +
Sbjct: 140 ------------------IILARRMEMGEI-------------ARKKLNGVKFNKQNKTK 168

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
              D       + ++    D+++  K+    + ++D      +  ++ +DED D      
Sbjct: 169 LANDIFFGDLANILKLANDDLKNDGKLDDKTQKEIDGLLNMGDLFKQIMDEDLDKKTL-- 226

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
               ++L+ KVM     IAE       L  +  N   D   S                  
Sbjct: 227 ----EELKTKVMIC--NIAENSISEDDLDKSKANSLCDLFDSFDHM-------------- 266

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           LN +  D +V  +Y     I+       ++  +  +  + F+            V+  + 
Sbjct: 267 LNITESDDIVNLVYLSFNDILSKAANKEQIKTNDRMILNDFI------------VTSERA 314

Query: 390 FPEGEWKNFVACEVDSI---LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
                       E+D I   +++R+    I  +  +S +++  +    +K    +  AK+
Sbjct: 315 RAISNKIELSKEELDEIEASIELRDLAYKIITDDDLSEADYYEL----KKAVFISKAAKQ 370

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW++Q
Sbjct: 371 KLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQ 430

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA+++ + VE V+++
Sbjct: 431 AITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKVQEI 490

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            KI++EP+SLETPIG+ED SHLGDFIED  A+ P ++A    LRE    VL+ L  RE+R
Sbjct: 491 RKISQEPVSLETPIGEEDDSHLGDFIEDDTAIDPGEAANYTMLREQLNDVLSCLGAREKR 550

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 551 VLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 604


>gi|257867642|ref|ZP_05647295.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257873971|ref|ZP_05653624.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257876550|ref|ZP_05656203.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325571155|ref|ZP_08146727.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
 gi|257801725|gb|EEV30628.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257808135|gb|EEV36957.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257810716|gb|EEV39536.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325156240|gb|EGC68426.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
          Length = 368

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 159/273 (58%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVPLLTAEEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFGI      TLEEVGK 
Sbjct: 276 GDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 368



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/191 (23%), Positives = 76/191 (39%), Gaps = 15/191 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             D +  + I+  + +G V  +++   L  P  + ++ M+  +  L + GI+VVD +   
Sbjct: 8   TYDKAVAEYIRENKTKGQVVYDDITNRLATPYTLDADAMDKLIQKLEDSGISVVDENGEP 67

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                + +     +     +             +DPVRMYL+E+G + LL+ E E+A+A 
Sbjct: 68  SVHSLKSNEKRQETQPQEDL-----SAPTGVKINDPVRMYLKEIGRVPLLTAEEEVALAL 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +IE G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 123 KIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVE 173

Query: 205 GHSYQKREDSS 215
              Y+K    S
Sbjct: 174 KFDYRKGFKFS 184


>gi|318066941|emb|CBY89085.1| RNA polymerase sigma70 factor [Halomonas eurihalina]
          Length = 367

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 116/397 (29%), Positives = 181/397 (45%), Gaps = 52/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILDAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D  + +      +  G+   
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADVPEPEPERSAAD--GETSD 125

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
               ++++ S     PE A      + +  + +   +                       
Sbjct: 126 EDDDAEEEESGGGPDPEEARARFEQIRQQNEAARRAIE---------------------- 163

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        +  + + + +    +L +L   + L     + LV Q+    +++   
Sbjct: 164 -------------EHGRGAKQAQNELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQ 210

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   + R  F++   G E    W+          + + +A     I + + 
Sbjct: 211 EKAIMQLCVKKAKVPRKTFIKSFPGNESRQDWLDTFMAEHAR-YADRLAALKGDIQRAQR 269

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + + + + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 270 KIAFEEEMVALVVPDLKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 329

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 330 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|104774139|ref|YP_619119.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423220|emb|CAI98048.1| RNA polymerase sigma factor RpoD (Sigma-A) [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC 11842]
          Length = 372

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 169/360 (46%), Positives = 231/360 (64%), Gaps = 27/360 (7%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+  +G+  +LA                      
Sbjct: 39  RLIKPYKLEGKAVDQLVQEFEDNGISIVDEDGKPSKLA---------------------- 76

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            ++  K+  + E  N  A     +   +R  +K I     ++  E    V++ ++ E   
Sbjct: 77  -LTKQKNVEKAELNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEE---VALAKRIEAGD 132

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA 
Sbjct: 133 EEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYAT 192

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ +PV+
Sbjct: 193 WWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVK 252

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR+ LK+ +EP+SLETPIG+ED SHLGDFIEDK+  SP   A    LR+    VL +LT
Sbjct: 253 KVREALKVAQEPVSLETPIGEEDDSHLGDFIEDKDTTSPEQHAASEMLRDQLAEVLDTLT 312

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS KLR FL+
Sbjct: 313 DREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNKLRDFLE 372



 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 61/313 (19%), Positives = 109/313 (34%), Gaps = 49/313 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +++  +    +T       L  P ++  + ++  V    + GI++VD      E
Sbjct: 15  EKAVKLVVEGVKASHQITEAAFEDRLIKPYKLEGKAVDQLVQEFEDNGISIVD------E 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G    L L    +     L           +DPVRMYL+E+G   LL+ E E+A+AKRI
Sbjct: 69  DGKPSKLALTKQKNVEKAELNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA-------- 189
           EAG       L E+ L     I  R         D + +G   L + +D           
Sbjct: 129 EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFS 188

Query: 190 -------------------------CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
                                        E+                 D   E+   ++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMD 248

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                +  A KV+++  S      E  ++   +  ED+D ++    A  + LR ++   L
Sbjct: 249 LPVKKVREALKVAQEPVSLETPIGEEDDSHLGDFIEDKDTTSPEQHAASEMLRDQLAEVL 308

Query: 285 DEIAEVYRELRSL 297
           D + +    +  L
Sbjct: 309 DTLTDREENVLRL 321


>gi|116511352|ref|YP_808568.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|125623388|ref|YP_001031871.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris MG1363]
 gi|116107006|gb|ABJ72146.1| RNA polymerase, sigma 70 subunit, RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|124492196|emb|CAL97125.1| RNA polymerase sigma factor rpoD (Sigma-42) [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070136|gb|ADJ59536.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris NZ9000]
          Length = 447

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 180/413 (43%), Positives = 242/413 (58%), Gaps = 29/413 (7%)

Query: 277 RPKVMCALD--------EIAEVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           +P V+  +D        EI E          + AV G   ++  +   + +E + +L   
Sbjct: 55  KPVVVEKMDSPKTLARVEIKENGDTFNVKAYEKAVKGYITKRKPLGEALDEEIMDELSVK 114

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
             +    ++ L +Q+ D    I+  +G    LA                   D       
Sbjct: 115 FGIVDDALEDLFKQIQDAGISIVDKDGNPSPLALV----------------TDEIEKEEV 158

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            D    E    +   V     +R  +K I     IS+ E   +   +  G   A  AK+ 
Sbjct: 159 SDTAMDE----IVTNVRIDDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQM 214

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + EANLRLV+S+AK+Y+ RG+QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QA
Sbjct: 215 LAEANLRLVVSIAKRYSGRGMQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQA 274

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR+IADQ+ TIRIPVHM + I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VL
Sbjct: 275 ITRAIADQARTIRIPVHMVETINKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVL 334

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           KI +EP+SLETPIG+ED SHLGDFIED    SP+D   +  LRE    V+ +LT REE V
Sbjct: 335 KIAQEPVSLETPIGEEDDSHLGDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENV 394

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           LRMRFG+     HTLE+VGKQF VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 395 LRMRFGLDDGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 447



 Score = 80.7 bits (197), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 72/189 (38%), Gaps = 17/189 (8%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSN 72
           E +++ D+      + + K  I   +  G    EE+   L     +  + +ED    + +
Sbjct: 72  EIKENGDTFNVKAYEKAVKGYITKRKPLGEALDEEIMDELSVKFGIVDDALEDLFKQIQD 131

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            GI++VD    +D   S  +L                +   +   DDPVRMYL+E+G   
Sbjct: 132 AGISIVD----KDGNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDPVRMYLKEIGRYP 187

Query: 133 LLSREGEIAIAKRI---EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTL 180
           L+S + E  +A+ I     G       L E+ L     I  R         D + +G   
Sbjct: 188 LISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFLDLIQEGNMG 247

Query: 181 LREIIDLEA 189
           L + +D   
Sbjct: 248 LMKAVDKFD 256


>gi|324993240|gb|EGC25160.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK405]
          Length = 370

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.4 bits (238), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQIGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNNEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|318066957|emb|CBY89093.1| RNA polymerase sigma70 factor [Halomonas maura]
          Length = 365

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 120/395 (30%), Positives = 178/395 (45%), Gaps = 50/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E     +      +   +  +E         
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEEPEATVGDADDADESAEE--------- 129

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
               +D S     PE A+     + E  + S   + A                       
Sbjct: 130 ----EDDSGGGPDPEEAKARFEQIREQNEASRQAIDA----------------------- 162

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         + S + +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 163 ------------HGRGSAEAQAELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEK 210

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E    W+          + + +A     I + + +I
Sbjct: 211 AVMQLCVKKAKVPRKTFIKAFPGNESRQDWLDDFMGDNAR-YADRLAPLKADIQRAQRKI 269

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 270 AFEEEMVLLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 329

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 330 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 364


>gi|322389216|ref|ZP_08062777.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
 gi|321144121|gb|EFX39538.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
          Length = 369

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 368



 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 69/345 (20%), Positives = 121/345 (35%), Gaps = 31/345 (8%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMG 74
           ++  D    D       + I+  ++ G  T +E+N  L  P  + ++ ++D +  + + G
Sbjct: 3   KEQKDITTLDVQ---IAEFIRSHKKSGTATDDEINDQLVIPFTLDADGIDDLLQRIQDAG 59

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I++ D D          S  + ++     +  ++   S     +DPVRMYL+E+G + LL
Sbjct: 60  ISITDKD-------GNPSARVLTNEEEPELSDEELLGSNSAKVNDPVRMYLKEIGVVPLL 112

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E E  +A  +E G       L E+ L     I  R  +  G   L  I         E
Sbjct: 113 TNEEEQELAILVEQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QE 163

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              G     +   Y K    S        Q     I   A+  +     V++  +     
Sbjct: 164 GNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQ 223

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L E   D      A    + P     + EI ++ +E  SL+                
Sbjct: 224 RNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 280

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             + E  V     +        +L EQL ++   +   E  +LRL
Sbjct: 281 DEVIENPVDYTTRV--------VLREQLDEVLDTLTDREENVLRL 317


>gi|55823393|ref|YP_141834.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus
           CNRZ1066]
 gi|116628187|ref|YP_820806.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMD-9]
 gi|55739378|gb|AAV63019.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus CNRZ1066]
 gi|116101464|gb|ABJ66610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus thermophilus LMD-9]
 gi|312278801|gb|ADQ63458.1| RNA polymerase sigma factor [Streptococcus thermophilus ND03]
          Length = 369

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVE---NGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 116/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P  + ++ ++D +  L++ GI++ D D      G+
Sbjct: 14  VADFIRNHKKAGTAIDDEITEKLVIPFVLDADGIDDLLERLTDGGISITDKD------GN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +  +     +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G
Sbjct: 68  PSSKYVVEAPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|313903305|ref|ZP_07836697.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466393|gb|EFR61915.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
          Length = 432

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 210/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  +   +   + +       AK+++++ANLRLV+S+AK+Y  RG+
Sbjct: 163 VRMYLKEIGRIPLLTPEQEIELAKRIEQ---GDEEAKRKLIQANLRLVVSIAKRYVGRGM 219

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KAAEKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 220 LFLDLIQEGNLGLIKAAEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 279

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REPTPEEIAK++ +  E VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 280 INKLIRVQRQLVQELGREPTPEEIAKEMGIEPEKVREIMKIAQEPVSLETPIGEEEDSHL 339

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P ++A Q  LRE    VL +LT RE++VLR+RFG+      TLEEVG+ 
Sbjct: 340 GDFIEDEDALAPAEAASQLLLREQLEDVLHTLTDREQKVLRLRFGLDDGRQRTLEEVGQI 399

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 400 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 432



 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 48/213 (22%), Positives = 76/213 (35%), Gaps = 58/213 (27%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV---------- 77
           D  K+++   RQRG  +T +E+   L   ++ ++Q+++   +L ++GI V          
Sbjct: 14  DEVKRLVDRGRQRGGVLTEDEVTDALQAVDLDADQVDEVYQLLEDLGIEVETGPRRSRNG 73

Query: 78  ----------------------VDGDDLEDEEGSEDSLDLASSA---------------- 99
                                 +D   L+   G +   DL +                  
Sbjct: 74  ARNGRAARGHRTRSGDAGLDGMMDEAALDGVAGLDRPEDLDADTAGGGEAGDEGDQDAAA 133

Query: 100 --------SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                                   + DDPVRMYL+E+G I LL+ E EI +AKRIE G  
Sbjct: 134 EGTGVDQLGEPVDDEDDLSMPDGVALDDPVRMYLKEIGRIPLLTPEQEIELAKRIEQGDE 193

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                L ++ L     I  R  +  G   L  I
Sbjct: 194 EAKRKLIQANLRLVVSIAKRY-VGRGMLFLDLI 225


>gi|312863004|ref|ZP_07723242.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
 gi|311100540|gb|EFQ58745.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
          Length = 369

 Score =  236 bits (601), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVE---NGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 116/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P  + ++ ++D +  L++ GI++ D D      G+
Sbjct: 14  VADFIRNHKKAGTAIDDEVTEKLVIPFVLDADGIDDLLERLTDGGISITDKD------GN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +  +     +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G
Sbjct: 68  PSSKYVVEAPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|320531403|ref|ZP_08032370.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320136375|gb|EFW28356.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 537

 Score =  235 bits (600), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 285 KLRRELHWVAQDGQRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 344

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 345 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 404

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 405 PEELAVELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 464

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 465 LQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 524

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 525 HPSRSQVLRDYLD 537



 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S+D     + + +       ++     +T DPV+ YL+++G + LL+ E E+ +AKRIEA
Sbjct: 208 SQDKDGSFTVSDSDEGDEPAQRVVTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEA 267

Query: 149 GRAMMMASLCE 159
           G       L E
Sbjct: 268 GLY-AEHRLAE 277


>gi|323352412|ref|ZP_08087547.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|322121844|gb|EFX93585.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|325696737|gb|EGD38625.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK160]
 gi|328945882|gb|EGG40032.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1087]
          Length = 370

 Score =  235 bits (600), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 121/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +    + +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNTEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|228476995|ref|ZP_04061633.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322516348|ref|ZP_08069273.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
 gi|228251014|gb|EEK10185.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322125081|gb|EFX96474.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
          Length = 369

 Score =  235 bits (600), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSNEEEKELAIAVE---NGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368



 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 116/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P  + ++ ++D +  L++ GI++ D D      G+
Sbjct: 14  VADFIRNHKKAGTAIDDEVTEKLVIPFVLDADGIDDLLERLTDGGISITDKD------GN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +  +     +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +E G
Sbjct: 68  PSSKYVVEAPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|259046798|ref|ZP_05737199.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
 gi|259036566|gb|EEW37821.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
          Length = 374

 Score =  235 bits (600), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 161/297 (54%), Positives = 207/297 (69%), Gaps = 4/297 (1%)

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
              +    E    ++        +R  +K I     +S  E    V++  + +   + AK
Sbjct: 81  REAEVGTVEDDTALSSNTKINDSVRMYLKEIGRVPLLSADEE---VALALRIQEGDTEAK 137

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMK  EKFD   G+KFSTYA WW++
Sbjct: 138 QELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKTVEKFDHTKGFKFSTYATWWIR 197

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + REPTPEEI  ++ +P E VR+
Sbjct: 198 QAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGREPTPEEIGAEMDLPTEKVRE 257

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +LKI +EP+SLETPIG+ED SHLGDFIED NA SP D    A L+E    VL  LT REE
Sbjct: 258 ILKIAQEPVSLETPIGEEDDSHLGDFIEDDNATSPADHTAYALLKEQLDEVLEQLTDREE 317

Query: 626 RVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VLR+RFG+  N    TLE+VG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 318 NVLRLRFGLDKNGEIRTLEQVGQVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLD 374



 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 39/152 (25%), Positives = 69/152 (45%), Gaps = 5/152 (3%)

Query: 34  MIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++   +  G +  ++L+A +  P E+ +E M+  +    + G++VVD +    E  S   
Sbjct: 19  LLAERKLFGQILYDDLSAQIAIPFELDAEGMDKLIQKFEDAGVSVVDANG---EPTSHQL 75

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
              +   +           S++   +D VRMYL+E+G + LLS + E+A+A RI+ G   
Sbjct: 76  SVESQREAEVGTVEDDTALSSNTKINDSVRMYLKEIGRVPLLSADEEVALALRIQEGDTE 135

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  R  +  G   L  I
Sbjct: 136 AKQELAEANLRLVVSIAKRY-VGRGMQFLDLI 166


>gi|315029422|gb|EFT41354.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4000]
          Length = 368

 Score =  235 bits (600), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 164/306 (53%), Positives = 212/306 (69%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI    R  +K I     ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 ---EGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDNGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 73/190 (38%), Gaps = 15/190 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + +    IK  + +G V  ++L   L  P  + +E ME  +  + + GI+VVD +    
Sbjct: 9   YEAAVAAFIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVDENGDPS 68

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   +                +          +DPVRMYL+E+G ++LL+   E+ +A +
Sbjct: 69  EHSLKKD-----EKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALK 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 124 IEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 174

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 175 FDYRKGFKFS 184


>gi|253573701|ref|ZP_04851044.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
 gi|251847229|gb|EES75234.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
          Length = 325

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+A++Y  RG+
Sbjct: 56  VRMYLKEIGRVPLLSAEEEIELAQRIE---NGDEEAKRRLAEANLRLVVSIARRYVGRGM 112

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 113 VFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 172

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +I REPTPEEIAK++ +  + VR+++KI +EP+SLETPIG+E+ S+L
Sbjct: 173 INKLIRVSRQLLQEIGREPTPEEIAKEMDLTPDKVREIMKIAQEPVSLETPIGEENDSNL 232

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A +P ++A    L+E    VL +LT REE VLR+RFG+      TLEEVGK+
Sbjct: 233 GDFIEDHDAPAPAEAAAYELLKEQLEEVLDTLTEREENVLRLRFGMDDGRTRTLEEVGKE 292

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 293 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFME 325



 Score = 80.7 bits (197), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 59/271 (21%), Positives = 89/271 (32%), Gaps = 22/271 (8%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
               +N   +            DDPVRMYL+E+G + LLS E EI +A+RIE G      
Sbjct: 31  EDLKNNELDYTDDLTLPPGIKIDDPVRMYLKEIGRVPLLSAEEEIELAQRIENGDEEAKR 90

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            L E+ L     I  R  +  G   L  I         E   G     E   Y K    S
Sbjct: 91  RLAEANLRLVVSIARRY-VGRGMVFLDLI--------QEGNMGLIKAVEKFDYSKGFKFS 141

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
                   Q     I   A+  +     V++  +      + L E   +      A E  
Sbjct: 142 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEIGREPTPEEIAKEMD 201

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           L P  +  + +IA                 +          L + +           +  
Sbjct: 202 LTPDKVREIMKIA-----------QEPVSLETPIGEENDSNLGDFIEDHDAPAPAEAAAY 250

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
           +LL EQL ++   +   E  +LRL   +G+ 
Sbjct: 251 ELLKEQLEEVLDTLTEREENVLRL--RFGMD 279


>gi|146319082|ref|YP_001198794.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05ZYH33]
 gi|146321288|ref|YP_001200999.1| RNA polymerase sigma factor RpoD [Streptococcus suis 98HAH33]
 gi|223932503|ref|ZP_03624504.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|253752138|ref|YP_003025279.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|253753963|ref|YP_003027104.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|253755898|ref|YP_003029038.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|330833083|ref|YP_004401908.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
 gi|145689888|gb|ABP90394.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 05ZYH33]
 gi|145692094|gb|ABP92599.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 98HAH33]
 gi|223898774|gb|EEF65134.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|251816427|emb|CAZ52060.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|251818362|emb|CAZ56188.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|251820209|emb|CAR46610.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|292558723|gb|ADE31724.1| RNA polymerase sigma factor rpoD [Streptococcus suis GZ1]
 gi|319758521|gb|ADV70463.1| RNA polymerase sigma factor RpoD [Streptococcus suis JS14]
 gi|329307306|gb|AEB81722.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
          Length = 372

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGVVPLLTNEEEQELALAVE---AGDPEAKQRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLVREQRNLLQELGQDPTPEQIAERMDMTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 279 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 339 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 371



 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 69/333 (20%), Positives = 118/333 (35%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +++G  T +E+N  L  P  + ++ ++D +  + + GI++VD +     
Sbjct: 15  DVQVAEFIRNHKKQGSATDDEINDQLVIPFTLDADGIDDLLQRIQDAGISIVDKE----- 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S           +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 70  --GNPSARAMQVEEEPELSDEELLGSTSAKVNDPVRMYLKEIGVVPLLTNEEEQELALAV 127

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 128 EAGDPEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 178

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 179 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 238

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 239 PEQIAERMDMTP---EKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 295

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 296 RV--------VLREQLDEVLDTLTDREENVLRL 320


>gi|312867612|ref|ZP_07727818.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
 gi|311096675|gb|EFQ54913.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
          Length = 369

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 368



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 70/345 (20%), Positives = 121/345 (35%), Gaps = 31/345 (8%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMG 74
           ++  D    D       + I+  ++ G  T +E+N  L  P  + ++ +ED +  + + G
Sbjct: 3   KEQKDITTLDVQ---IAEFIRSHKKSGTATDDEINDQLVIPFTLDADGIEDLLQRIQDAG 59

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I++ D D          S  + ++     +  ++   S     +DPVRMYL+E+G + LL
Sbjct: 60  ISITDKD-------GNPSARVLNNEEEPELSDEELLGSNSAKVNDPVRMYLKEIGVVPLL 112

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E E  +A  +E G       L E+ L     I  R  +  G   L  I         E
Sbjct: 113 TNEEEQELAILVEQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QE 163

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              G     +   Y K    S        Q     I   A+  +     V++  +     
Sbjct: 164 GNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQ 223

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L E   D      A    + P     + EI ++ +E  SL+                
Sbjct: 224 RNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 280

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             + E  V     +        +L EQL ++   +   E  +LRL
Sbjct: 281 DEVIENPVDYTTRV--------VLREQLDEVLDTLTDREENVLRL 317


>gi|184155321|ref|YP_001843661.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227514580|ref|ZP_03944629.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260662165|ref|ZP_05863061.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
 gi|183226665|dbj|BAG27181.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227086991|gb|EEI22303.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260553548|gb|EEX26440.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
          Length = 380

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + K       AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLTADEEVALALRIEK---GDETAKQELAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP PEEI  ++ M  + VR +LKI++EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRIQRQLLQDLGREPLPEEIGAEMDMDTQKVRDILKISQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP D A    +++    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 288 GDFIEDHDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 380



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 49/190 (25%), Positives = 82/190 (43%), Gaps = 16/190 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D +   +I+  ++   +  +EL   +  P  ++++ M+  +  + + G++VVD      
Sbjct: 22  YDKAVGALIRNYKKAKNIQYDELTEKIAEPFGLNADGMDALLQNVEDAGVSVVD------ 75

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E G  D   L ++   SS  L+     +    +DPVRMYL+E+G + LL+ + E+A+A R
Sbjct: 76  ENGDPDLRALKATEKLSSKALKDTTAPSSIKINDPVRMYLKEIGRVNLLTADEEVALALR 135

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 136 IEKGDETAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 186

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 187 FDYRKGFKFS 196


>gi|318066951|emb|CBY89090.1| RNA polymerase sigma70 factor [Halomonas hydrothermalis]
          Length = 370

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 122/395 (30%), Positives = 189/395 (47%), Gaps = 45/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   + S + + D   + E +  +A 
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEPETELSDDDDLDSDDDDEDEDSTA- 137

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                  S+    PE A+     + E        L+                        
Sbjct: 138 -------SEGGPDPEEAKARFEQIREQNVAVEAALA------------------------ 166

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L +L   + L     + LV Q+    +++   E 
Sbjct: 167 -----------KYGRGSAELKSEQSRLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEK 215

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E +P W+   ++  + ++ + +      I + + +I
Sbjct: 216 AVMQLCVKKAKVPRKTFIKSFPGYESNPAWLDTFQE-AQPKYADRLEPLRADIARSQRKI 274

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +++++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 275 AFEEDMVQLTVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 334

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 335 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 369


>gi|170017101|ref|YP_001728020.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
 gi|169803958|gb|ACA82576.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
          Length = 432

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 172/384 (44%), Positives = 232/384 (60%), Gaps = 23/384 (5%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D AV     E    K         +L    +L+   I+ L+E++ D    I+  +GE  
Sbjct: 68  YDKAVKALITEYKPAKEVTYAILSKRLAEPFNLDGENIERLMEKVEDAGVAIVDEKGEPA 127

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                    +                ++ A++ P G   N           +R  +K I 
Sbjct: 128 PEVLQAKQNKP-----------SKEELAQAEETPAGIKIN---------DPVRMYLKEIG 167

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +   E  +I   +         AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEG
Sbjct: 168 RVNLLKGDEEINIAKRIE---DGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEG 224

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 225 NMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQR 284

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++   + REP PEEI  ++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED  A
Sbjct: 285 QLLQDLGREPLPEEIGAEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDNEA 344

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +SP DSA    LR+    VL +LT REE VLR+RFG+      TLEEVG+ F VTRERIR
Sbjct: 345 ISPADSAAYEMLRDQLESVLETLTDREENVLRLRFGLEDGRTRTLEEVGRVFGVTRERIR 404

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 405 QIEAKALRKLRHPSRSKQLKDFMD 428



 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/159 (28%), Positives = 69/159 (43%), Gaps = 6/159 (3%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D + K +I   +    VT   L+  L  P  +  E +E  +  + + G+ +VD    E 
Sbjct: 68  YDKAVKALITEYKPAKEVTYAILSKRLAEPFNLDGENIERLMEKVEDAGVAIVD----EK 123

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E + + L    +  +     Q  +  A    +DPVRMYL+E+G + LL  + EI IAKR
Sbjct: 124 GEPAPEVLQAKQNKPSKEELAQAEETPAGIKINDPVRMYLKEIGRVNLLKGDEEINIAKR 183

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           IE G       L E+ L     I  R  +  G   L  I
Sbjct: 184 IEDGDVEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI 221


>gi|322385457|ref|ZP_08059101.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
 gi|321270195|gb|EFX53111.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
          Length = 370

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLSNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 120/333 (36%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + GI++ D      +
Sbjct: 12  DVQIAEFIRNHKQTGVATDDEINDQLVIPFTLDADGIEDLLQRIQDAGISITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+  +  L +      +  ++   S     +DPVRMYL+E+G + LLS E E  +A  +
Sbjct: 66  EGNPSARVLNTEEEEVELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEQELAILV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|289434736|ref|YP_003464608.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|289170980|emb|CBH27522.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|313633237|gb|EFS00106.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL N1-067]
          Length = 374

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVNLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/170 (27%), Positives = 78/170 (45%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + + +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTQNTKPVAELNVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G + LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDLSVPPGVKINDPVRMYLKEIGRVNLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|329733136|gb|EGG69473.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 314

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 158/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 2   DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 61

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 62  EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 118

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 119 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 178

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 179 DPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 238

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 239 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 298

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 299 KLRHPSRSKRLKDFMD 314



 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/122 (30%), Positives = 57/122 (46%), Gaps = 15/122 (12%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           M+D    L++  I++V+  D  D +   +  DL++                    +DPVR
Sbjct: 1   MDDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSA--------------PPGVKINDPVR 46

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL+E+G + LLS + EI +AKRIE G  +  + L E+ L     I  R  +  G   L 
Sbjct: 47  MYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLD 105

Query: 183 EI 184
            I
Sbjct: 106 LI 107


>gi|116514229|ref|YP_813135.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116093544|gb|ABJ58697.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
          Length = 372

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 169/360 (46%), Positives = 231/360 (64%), Gaps = 27/360 (7%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+  +G+  +LA                      
Sbjct: 39  RLIKPYKLEGKAVDQLVQEFEDNGISIVDEDGKPSKLA---------------------- 76

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            ++  K+  + E  N  A     +   +R  +K I     ++  E    V++ ++ E   
Sbjct: 77  -LTKQKNVEKAELNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEE---VALAKRIEAGD 132

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA 
Sbjct: 133 EEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYAT 192

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+    + R+P PEEIA ++ +PV+
Sbjct: 193 WWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQFLQDLGRDPEPEEIAAEMDLPVK 252

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR+ LK+ +EP+SLETPIG+ED SHLGDFIEDK+A SP   A    L++    VL +LT
Sbjct: 253 KVREALKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVLDTLT 312

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS KLR FL+
Sbjct: 313 DREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNKLRDFLE 372



 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 61/313 (19%), Positives = 110/313 (35%), Gaps = 49/313 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +++  +    +T   L   L  P ++  + ++  V    + GI++VD      E
Sbjct: 15  EKAVKLVVEGVKASHQITEAALEDRLIKPYKLEGKAVDQLVQEFEDNGISIVD------E 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G    L L    +     L           +DPVRMYL+E+G   LL+ E E+A+AKRI
Sbjct: 69  DGKPSKLALTKQKNVEKAELNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA-------- 189
           EAG       L E+ L     I  R         D + +G   L + +D           
Sbjct: 129 EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFS 188

Query: 190 -------------------------CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
                                        E+                 D   E+   ++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQFLQDLGRDPEPEEIAAEMD 248

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                +  A KV+++  S      E  ++   +  ED+D ++    A  + L+ ++   L
Sbjct: 249 LPVKKVREALKVAQEPVSLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVL 308

Query: 285 DEIAEVYRELRSL 297
           D + +    +  L
Sbjct: 309 DTLTDREENVLRL 321


>gi|1943995|dbj|BAA19494.1| sigA=sigma70 [Staphylococcus aureus]
          Length = 368

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 157/316 (49%), Positives = 212/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IA Q+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIAHQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 46/156 (29%), Positives = 78/156 (50%), Gaps = 15/156 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D + 
Sbjct: 21  DVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDE 80

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE 
Sbjct: 81  KLNPSDLSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQ 126

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 127 GDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|220932077|ref|YP_002508985.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
 gi|219993387|gb|ACL69990.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
          Length = 358

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 162/358 (45%), Positives = 234/358 (65%), Gaps = 8/358 (2%)

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG-RELDPHWVSYA 387
           + N  ++  + E +    +       E++   +   +  +   + ++   E++   V   
Sbjct: 4   NFNPDKVKEVKELIKKGKEEGYLTYEEIMDSLEEIELSSEDIEKIYELFNEMNIDVVDDV 63

Query: 388 KDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
            +  + +  + +   +   + I    R  +K I     ++  E   +   + +       
Sbjct: 64  DEVDDDKGDDDLELSIPEGVGIDDPVRMYLKEIGKVPLLTAEEEVDLAKRIEQ---GDEQ 120

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+E+VEANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW
Sbjct: 121 AKRELVEANLRLVVSIAKKYVGRGMSFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWW 180

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTPEEI +++ MP E V
Sbjct: 181 IRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEKGREPTPEEIGEEMGMPAEKV 240

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R++LKI +EP+SLETPIG+E+ SHLGDFIED++A +P  +A    LRE    VL +LT R
Sbjct: 241 REILKIAQEPVSLETPIGEEEDSHLGDFIEDEDAPAPASAASFTLLREQLDDVLDTLTDR 300

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+RVL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 301 EKRVLELRFGLEDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 358



 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 51/156 (32%), Positives = 77/156 (49%), Gaps = 15/156 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              K++IK  ++ GY+T EE+   L   E+SSE +E    + + M I+VVD  D  D++ 
Sbjct: 11  KEVKELIKKGKEEGYLTYEEIMDSLEEIELSSEDIEKIYELFNEMNIDVVDDVDEVDDDK 70

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +D L+L+                     DDPVRMYL+E+G + LL+ E E+ +AKRIE 
Sbjct: 71  GDDDLELS--------------IPEGVGIDDPVRMYLKEIGKVPLLTAEEEVDLAKRIEQ 116

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  +  +  G + L  I
Sbjct: 117 GDEQAKRELVEANLRLVVSIAKKY-VGRGMSFLDLI 151


>gi|296876770|ref|ZP_06900818.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
 gi|296432272|gb|EFH18071.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
          Length = 369

 Score =  235 bits (599), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 368



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 71/345 (20%), Positives = 121/345 (35%), Gaps = 31/345 (8%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMG 74
           ++  D    D       + I+  +Q G  T +E+N  L  P  + ++ +ED +  + + G
Sbjct: 3   KEQKDITTLDVQ---IAEFIRSHKQSGAATDDEINDKLVIPFTLDADGIEDLLQRIQDAG 59

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I++ D D          S  + ++     +  ++   S     +DPVRMYL+E+G + LL
Sbjct: 60  ISITDKD-------GNPSARVLNNEEEPELSDEELLGSNSAKVNDPVRMYLKEIGVVPLL 112

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E E  +A  +E G       L E+ L     I  R  +  G   L  I         E
Sbjct: 113 TNEEEQELAILVEQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QE 163

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              G     +   Y K    S        Q     I   A+  +     V++  +     
Sbjct: 164 GNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQ 223

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L E   D      A    + P     + EI ++ +E  SL+                
Sbjct: 224 RNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 280

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             + E  V     +        +L EQL ++   +   E  +LRL
Sbjct: 281 DEVIENPVDYTTRV--------VLREQLDEVLDTLTDREENVLRL 317


>gi|302024138|ref|ZP_07249349.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05HAS68]
          Length = 372

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGVVPLLTNEEEQELALAVE---AGDPEAKQRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLVREQRNLLQELGQDPTPEQIAERMDMTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 279 GDFIEDEIIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 339 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 371



 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 69/333 (20%), Positives = 118/333 (35%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +++G  T +E+N  L  P  + ++ ++D +  + + GI++VD +     
Sbjct: 15  DVQVAEFIRNHKKQGSATDDEINDQLVIPFTLDADGIDDLLQRIQDAGISIVDKE----- 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S           +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 70  --GNPSARAMQVEEEPELSDEELLGSTSAKVNDPVRMYLKEIGVVPLLTNEEEQELALAV 127

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 128 EAGDPEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 178

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 179 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 238

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 239 PEQIAERMDMTP---EKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEIIENPVDYTT 295

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 296 RV--------VLREQLDEVLDTLTDREENVLRL 320


>gi|116491026|ref|YP_810570.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290890507|ref|ZP_06553582.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
 gi|116091751|gb|ABJ56905.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290479903|gb|EFD88552.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
          Length = 458

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 161/359 (44%), Positives = 225/359 (62%), Gaps = 20/359 (5%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+    +LN  +ID L+E++ D    I+  +G     +                      
Sbjct: 119 KMAKPFALNADQIDKLIEKVEDAGISIVDEDGNPSEKSLKTK-----------SNNPSQE 167

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
            +S A   P+G   N           +R  +K I   + ++  +   I   + KG  +  
Sbjct: 168 ELSQASSAPKGVKIN---------DPVRMYLKEIGRVSLLNADQEVAIAKRIEKGGSDGE 218

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A++E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA W
Sbjct: 219 RARQELAEANLRLVVSIAKRYVGRGMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATW 278

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P PEEI  ++ +  + 
Sbjct: 279 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRTLIQDLGRDPMPEEIGAEMELTADK 338

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI +EP+SLETPIG+E+ SHLGDFIED    SP++S     L++    VL +LT 
Sbjct: 339 VREIQKIAQEPVSLETPIGEENDSHLGDFIEDNEGESPIESTSDQMLKDQLEEVLGTLTE 398

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 399 REENVLRLRFGLEDGKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFME 457



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 62/216 (28%), Positives = 91/216 (42%), Gaps = 19/216 (8%)

Query: 6   KRNRDSDSEHEDSDDSLVFDF--SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQ 62
           K   +S S  + S  +  FD      S K  IK  ++ G V  ++L N    P  ++++Q
Sbjct: 71  KSKDNSKSGEKSSSAATAFDEKAYAKSLKAFIKKNKKSGQVVYDDLENKMAKPFALNADQ 130

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ++  +  + + GI++VD    ED   SE SL   S+  +     Q          +DPVR
Sbjct: 131 IDKLIEKVEDAGISIVD----EDGNPSEKSLKTKSNNPSQEELSQASSAPKGVKINDPVR 186

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTT 179
           MYL+E+G + LL+ + E+AIAKRIE G          L E+ L     I  R  +  G  
Sbjct: 187 MYLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRY-VGRGMH 245

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            L  I         E   G     E   Y K    S
Sbjct: 246 FLDLI--------QEGNMGLMKAVEKFDYTKGFKFS 273


>gi|222872026|gb|EEF09157.1| predicted protein [Populus trichocarpa]
          Length = 425

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 103/442 (23%), Positives = 185/442 (41%), Gaps = 45/442 (10%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
            +      +      K +IKL + RGY+T  E+N  LP D V SE ++  VA L+++GI 
Sbjct: 24  QAGSEEELEIRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 83

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQ---KRKDSADRSTDDPVRMYLREMGSIEL 133
           V +     +     D+   A+S   +    +      DS    T DPVRMY+REMG++EL
Sbjct: 84  VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 143

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E +D    I P
Sbjct: 144 LTREGEIEIAKRIEAGLKDMVMAISACPVTISEILASAERVANEEIKIDEFVD--GLIDP 201

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
            ++    +          ED   +++ DD +E + +    A  S                
Sbjct: 202 NAEEVQDNSPAQAVAADDEDEDSDEDGDDGEEEDDESGGGAGAS---------------- 245

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
                           +   ++L+   +     IAE + ++R   +      K+   S  
Sbjct: 246 ----------------ARQLEELKVAALEKFRVIAEQFDKMRRAFE------KEGYKSKP 283

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLE 372
               +E +   + S+      ++ L + L      +   E  +L +     G+ R  F+ 
Sbjct: 284 YVKAQEAIQAELMSIRFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRADFVA 343

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           R  G E +  W+       +  +   V   V ++ +++ ++  +     + + E + +  
Sbjct: 344 RFPGNETNLDWIQTIVADNKS-YSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKDVNR 402

Query: 433 MVRKGECEASIAKKEMVEANLR 454
            + +GE  A  AK+EM EANLR
Sbjct: 403 KMSEGEKRAREAKREMTEANLR 424


>gi|15672535|ref|NP_266709.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281491019|ref|YP_003352999.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           KF147]
 gi|12723439|gb|AAK04651.1|AE006289_2 major RNA polymerase sigma factor [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281374777|gb|ADA64297.1| RNA polymerase sigma factor RpoD (Sigma-42) [Lactococcus lactis
           subsp. lactis KF147]
 gi|326406054|gb|ADZ63125.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           CV56]
          Length = 447

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 176 VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 235

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 236 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 295

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 296 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 355

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 356 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 415

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 416 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 447



 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 72/189 (38%), Gaps = 17/189 (8%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSN 72
           E +++ D+      + + K  I   +  G    EE+   L     +  + +ED    + +
Sbjct: 72  EVKENGDTFNVKAYEKAVKSYITKRKPLGEALDEEIMDELSVKFGIVDDALEDLFKQIQD 131

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            GI++VD    +D   S  +L                +   +   DDPVRMYL+E+G   
Sbjct: 132 AGISIVD----KDGNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDPVRMYLKEIGRYP 187

Query: 133 LLSREGEIAIAKRI---EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTL 180
           L+S + E  +A+ I     G       L E+ L     I  R         D + +G   
Sbjct: 188 LISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFLDLIQEGNMG 247

Query: 181 LREIIDLEA 189
           L + +D   
Sbjct: 248 LMKAVDKFD 256


>gi|22537572|ref|NP_688423.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae 2603V/R]
 gi|25011538|ref|NP_735933.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae NEM316]
 gi|76788342|ref|YP_330069.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77409561|ref|ZP_00786243.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
 gi|77412516|ref|ZP_00788814.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77414847|ref|ZP_00790961.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|22534455|gb|AAN00296.1|AE014257_3 RNA polymerase sigma-70 factor [Streptococcus agalactiae 2603V/R]
 gi|24413077|emb|CAD47155.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           NEM316]
 gi|76563399|gb|ABA45983.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77159097|gb|EAO70294.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|77161430|gb|EAO72443.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77171826|gb|EAO75013.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
          Length = 369

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V        +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELAVAV---AEGDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 368



 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  +++G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VADFIRNHKKQGTAIDDEVTEKLVIPFVLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSTKYVVEGPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|318066963|emb|CBY89096.1| RNA polymerase sigma70 factor [Halomonas neptunia]
          Length = 368

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 122/395 (30%), Positives = 179/395 (45%), Gaps = 47/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   +   + E D   E E    S  
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEPEPEIDDDVESDGDDEDEDSTAS-- 136

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                   +    PE A      + E         +                        
Sbjct: 137 --------EGGPDPEEARARFEQIREQNALVEAAFA------------------------ 164

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L  L   + L     + LV Q+    +++   E 
Sbjct: 165 -----------KHGRGSPELKAEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEK 213

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E    W+   +   + ++ + +      I + + +I
Sbjct: 214 AVMQLCVKKAKVPRKTFIKSFPGNESSKTWLDEFQA-AQSKYADRLEPLRADIARAQRKI 272

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 273 AFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 332

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 333 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|313608766|gb|EFR84582.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-208]
          Length = 374

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 46/170 (27%), Positives = 78/170 (45%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V   + +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTQNTKPVXXXNVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|255972833|ref|ZP_05423419.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
 gi|255963851|gb|EET96327.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
          Length = 368

 Score =  235 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 164/306 (53%), Positives = 212/306 (69%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI    R  +K I     ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 ---EGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 74/190 (38%), Gaps = 15/190 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + +    IK  + +G V  ++L   L  P  + +E ME  +  + ++GI+VVD +    
Sbjct: 9   YEAAVAAFIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDVGISVVDENGDPS 68

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   +                +          +DPVRMYL+E+G ++LL+   E+ +A +
Sbjct: 69  EHSLKKD-----EKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALK 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 124 IEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 174

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 175 FDYRKGFKFS 184


>gi|317122932|ref|YP_004102935.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
 gi|315592912|gb|ADU52208.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
          Length = 433

 Score =  235 bits (598), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 210/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  +   +   + +       AK+++++ANLRLV+S+AK+Y  RG+
Sbjct: 164 VRMYLKEIGRIPLLTPEQEIELAKRIEQ---GDEEAKRKLIQANLRLVVSIAKRYVGRGM 220

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KAAEKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 221 LFLDLIQEGNLGLIKAAEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 280

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REPTPEEIAK++ +  E VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 281 INKLIRVQRQLVQELGREPTPEEIAKEMGIEPEKVREIMKIAQEPVSLETPIGEEEDSHL 340

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P ++A Q  LRE    VL +LT RE++VLR+RFG+      TLEEVG+ 
Sbjct: 341 GDFIEDEDALAPAEAASQLLLREQLEDVLHTLTDREQKVLRLRFGLDDGRQRTLEEVGQV 400

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 401 FGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 433



 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 49/214 (22%), Positives = 80/214 (37%), Gaps = 59/214 (27%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV---------- 77
           D  K+++   RQ+G  ++ +E++  L   ++  +Q+E+   +L +MGI V          
Sbjct: 14  DEVKRLVDRGRQQGGVLSEDEISDALQAVDLDPDQVEEIYQLLEDMGIEVETGPRRSRNR 73

Query: 78  -------------------------VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS 112
                                    VD   L+       + DL +   +     +   ++
Sbjct: 74  TRGNRVNQNHRTRASDRALDGVDGVVDEVSLDGVTALHRADDLEAGDDDEGDESRDGDEA 133

Query: 113 ADR----------------------STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            D                       + DDPVRMYL+E+G I LL+ E EI +AKRIE G 
Sbjct: 134 GDGTGVDQLGEPVDDDDDLSMPDGVALDDPVRMYLKEIGRIPLLTPEQEIELAKRIEQGD 193

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L ++ L     I  R  +  G   L  I
Sbjct: 194 EEAKRKLIQANLRLVVSIAKRY-VGRGMLFLDLI 226


>gi|167772125|ref|ZP_02444178.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
 gi|167665923|gb|EDS10053.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
          Length = 361

 Score =  235 bits (598), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 163/388 (42%), Positives = 238/388 (61%), Gaps = 27/388 (6%)

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           +   +  A+  +  E    K K+  +++   +  L  +  ++D + + L   +  I+ + 
Sbjct: 1   MGVQEKKAILKELLESGKAKGKLTTKEISDALEELDYDVEQVDKMYDLLEQNNIEIIEDM 60

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
              +          + F +  +G +LD    +   +  +                    +
Sbjct: 61  VTPVE---------EDFKDLGKGTDLDVALAAEGINIDDPVKV---------------YL 96

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K I     +S  E   +   + +       A+K + EANLRLV+S+AK+Y  RG+QFLDL
Sbjct: 97  KEIGRVPLLSADEEIDLAVRMAQ---GDIDARKRLSEANLRLVVSIAKRYVGRGMQFLDL 153

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL+KA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV 
Sbjct: 154 IQEGNLGLIKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVK 213

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           + +  + +K   EPT EEI+ +L MPV+ VR+++++ +EP+SLETPIG+E+ SHLGDFI 
Sbjct: 214 KVSSLLLHKNGHEPTAEEISAELDMPVDKVREIMRVAQEPVSLETPIGEEEDSHLGDFIP 273

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D++A +P  +A    LRE  + VL +LTPREE+VLR+RFG+      TLEEVG++F VTR
Sbjct: 274 DEDAPAPDTAASHTLLREQLSEVLQTLTPREEKVLRLRFGLEDGRSRTLEEVGREFNVTR 333

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 334 ERIRQIEAKALRKLRHPSRSKKLKDFLD 361



 Score =  103 bits (257), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 37/154 (24%), Positives = 67/154 (43%), Gaps = 9/154 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K++++  + +G +T +E++  L   +   EQ++    +L    I +++      EE  +
Sbjct: 10  LKELLESGKAKGKLTTKEISDALEELDYDVEQVDKMYDLLEQNNIEIIEDMVTPVEEDFK 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D              L     +   + DDPV++YL+E+G + LLS + EI +A R+  G 
Sbjct: 70  D--------LGKGTDLDVALAAEGINIDDPVKVYLKEIGRVPLLSADEEIDLAVRMAQGD 121

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 122 IDARKRLSEANLRLVVSIAKRY-VGRGMQFLDLI 154


>gi|157273328|gb|ABV27227.1| sigma 38 RpoS [Candidatus Chloracidobacterium thermophilum]
          Length = 549

 Score =  235 bits (598), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 216/624 (34%), Positives = 321/624 (51%), Gaps = 100/624 (16%)

Query: 65  DTVAMLSNMGINVVDGDD----LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           D   +L+ +   V + DD     E EE  E    +  + SN          S    + D 
Sbjct: 16  DLEKLLAEIDSTVPEEDDFLLDTETEEPEEIEEVIEDAESNGIAPPPDLSASESDRSLDA 75

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +YLREM ++ LL+RE E+ IAKRIE GR  +  +   S +  + L    ++L +    
Sbjct: 76  MTLYLREMSNVALLTREDEVNIAKRIERGRRRLYKAHSRSLIVAEQLEELAEQLKERKIS 135

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           +R++ID                         ED + E E   + ET    ++ ++   + 
Sbjct: 136 IRQVIDTSD-------------------SDAEDITLENEERYLSETIERFQAISRALAEI 176

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           R +                          + +E + +     A     E  R+   L   
Sbjct: 177 REEA-------------------------TKIEKERKRNPRKAQQRYREYLRKRVEL--- 208

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                                 +L+ S+  +        +++  + ++I   E ++    
Sbjct: 209 ---------------------SRLIRSVLFSDQIRQRFTDRIRAVVRQIQDAERKIENAQ 247

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           ++   KR   L       +D   V    +  +    +     ++   +I++ ++ I   T
Sbjct: 248 EALKDKRRRAL-------IDVAEVRAQIEQAQKVIADIEKRYLEPARRIKDSLREIFTST 300

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGN 478
                              EA  A++EM+EANLRLV+S+AK Y N  RGLQF DLIQEGN
Sbjct: 301 E------------------EAEKARREMIEANLRLVVSIAKNYINRSRGLQFSDLIQEGN 342

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLM+A EKFD+  GYKFSTYA WW++QA+TR+IADQ  TIR+PVHM + I+K+VRTAR 
Sbjct: 343 IGLMRAVEKFDYRRGYKFSTYATWWIRQAVTRAIADQGRTIRVPVHMVETINKIVRTARL 402

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ REPT EE+A++  +PV  VR+ LKI +EPISLETPIGD+  S+LG FIED+N++
Sbjct: 403 MVQELGREPTHEELAQRTDLPVAKVRQALKIAQEPISLETPIGDDGESNLGSFIEDRNSL 462

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIR 657
           +P +  +   LRE T  VL++LTPREE++L+MRFG+ G   + TLEEVG+ F VTRERIR
Sbjct: 463 NPAEMIVGKGLREATLEVLSTLTPREEQILKMRFGLDGDGQERTLEEVGRYFHVTRERIR 522

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRS+KL++F D
Sbjct: 523 QIEAKALRKLRHPSRSRKLKTFYD 546


>gi|255659373|ref|ZP_05404782.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
 gi|260848459|gb|EEX68466.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
          Length = 373

 Score =  235 bits (598), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 211/273 (77%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++ ++ E     A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVPLLTAEEE---VALAKRMEAGDEEAQKRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ + V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 221 INKLIRVSRQLLQQLGREPTPEEIAKEMEIGVDRVREIMKIAQEPVSLETPIGEEEDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A +P D+A    L+E    VL +LTPREE+VLR+RFG+      TLEEVG+ 
Sbjct: 281 GDFIEDQDAPAPADAASFMLLKEQLEDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGQN 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ FLD
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSRKLKDFLD 373



 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/185 (25%), Positives = 71/185 (38%), Gaps = 16/185 (8%)

Query: 27  SDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           S +  + ++   ++ G  +T  EL   L    +S ++++      S  GI +VD      
Sbjct: 15  SSEIVEGLLAKGKKNGGTLTYGELIDALQKQALSPDEIDTMYDTFSKRGIEIVDDSQDNS 74

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +   D                        S DDPVRMYL+E+G + LL+ E E+A+AKR
Sbjct: 75  SDDDVDIDKSDEDVEID------LSVPEGVSIDDPVRMYLKEIGRVPLLTAEEEVALAKR 128

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           +EAG       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 129 MEAGDEEAQKRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEK 179

Query: 206 HSYQK 210
             Y K
Sbjct: 180 FDYNK 184


>gi|318066979|emb|CBY89104.1| RNA polymerase sigma70 factor [Halomonas venusta]
          Length = 370

 Score =  235 bits (598), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 121/395 (30%), Positives = 189/395 (47%), Gaps = 45/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   + S + + D   + E +  +A+
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEPETELSDDDDLDSDDDDEDEDSTAS 138

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                   +    PE A+     + E        L+                        
Sbjct: 139 --------EGGPDPEEAKARFEQIREQNVAVEAALA------------------------ 166

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L +L   + L     + LV Q+    +++   E 
Sbjct: 167 -----------KYGRGSAELKSEQSRLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEK 215

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E +P W+   ++  + ++ + +      I + + +I
Sbjct: 216 AVMQLCVKKAKVPRKTFIKSFPGYESNPAWLDIFQE-AQPKYADRLEPLRADIARSQRKI 274

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +++++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 275 AFEEDMVQLTVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 334

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 335 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 369


>gi|269794902|ref|YP_003314357.1| RNA polymerase sigma-70 subunit RpoD [Sanguibacter keddieii DSM
           10542]
 gi|269097087|gb|ACZ21523.1| RNA polymerase, sigma 70 subunit, RpoD [Sanguibacter keddieii DSM
           10542]
          Length = 516

 Score =  235 bits (598), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/250 (54%), Positives = 179/250 (71%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 267 RELEWIAGDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 326

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE
Sbjct: 327 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 386

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E
Sbjct: 387 LAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQE 446

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPS
Sbjct: 447 QLHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 506

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 507 RSQVLRDYLD 516



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 18/36 (50%), Positives = 27/36 (75%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 213 GATADPVKDYLKQIGKVALLNAEQEVDLAKRIEAGL 248


>gi|319947289|ref|ZP_08021522.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
 gi|319746531|gb|EFV98791.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
          Length = 370

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAILVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 70/345 (20%), Positives = 123/345 (35%), Gaps = 30/345 (8%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMG 74
           ++  D    D       + I+  ++ G  T +E+N  L  P  + ++ ++D +  + + G
Sbjct: 3   KEQKDITTLDVQ---IAEFIRSHKKSGTATDDEINDQLVIPFTLDADGIDDLLQRIQDAG 59

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I++ D      +EG+  +  L +      +  ++   S     +DPVRMYL+E+G + LL
Sbjct: 60  ISITD------KEGNPSARVLNTEEEEPELTDEELLGSNSAKVNDPVRMYLKEIGVVPLL 113

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E E  +A  +E G       L E+ L     I  R  +  G   L  I         E
Sbjct: 114 TNEEEQELAILVEQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QE 164

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              G     +   Y K    S        Q     I   A+  +     V++  +     
Sbjct: 165 GNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQ 224

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L E   D      A    + P     + EI ++ +E  SL+                
Sbjct: 225 RNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 281

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             + E  V     +        +L EQL ++   +   E  +LRL
Sbjct: 282 DEVIENPVDYTTRV--------VLREQLDEVLDTLTDREENVLRL 318


>gi|89895793|ref|YP_519280.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense Y51]
 gi|89335241|dbj|BAE84836.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 367

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 165/373 (44%), Positives = 237/373 (63%), Gaps = 17/373 (4%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           K   K  +   +++  +  + L   +ID + EQ+  +   I+   GE+  L +      D
Sbjct: 12  KGKKKGSLTYREIMDTLQGIELTAEQIDEVYEQIGRMGIDIIPEAGEVEALEKVTDEIPD 71

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
                          V       E +    +   V     +R  +K I     ++  E  
Sbjct: 72  D--------------VDDPDVEEEVDVDLSIPEGVGIDDPVRMYLKEIGRVPLLTAEEEI 117

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +       AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKF
Sbjct: 118 ELAKRMEQ---GDESAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKF 174

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPT
Sbjct: 175 DYVKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPT 234

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA ++ + VE VR+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    
Sbjct: 235 PEEIAVQMDISVERVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPSEAASFIL 294

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +LTPREE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+
Sbjct: 295 LKEQLEEVLETLTPREEKVLRLRFGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLR 354

Query: 669 HPSRSKKLRSFLD 681
           HPSRSKKL+ +L+
Sbjct: 355 HPSRSKKLKDYLE 367



 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 43/161 (26%), Positives = 75/161 (46%), Gaps = 3/161 (1%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
              D+ K++I+  +++G +T  E+   L   E+++EQ+++    +  MGI+++      +
Sbjct: 1   MKVDAVKELIQKGKKKGSLTYREIMDTLQGIELTAEQIDEVYEQIGRMGIDIIPEAGEVE 60

Query: 86  --EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
             E+ +++  D                       DDPVRMYL+E+G + LL+ E EI +A
Sbjct: 61  ALEKVTDEIPDDVDDPDVEEEVDVDLSIPEGVGIDDPVRMYLKEIGRVPLLTAEEEIELA 120

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           KR+E G       L E+ L     I  R  +  G   L  I
Sbjct: 121 KRMEQGDESAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 160


>gi|77406972|ref|ZP_00783989.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
 gi|77174413|gb|EAO77265.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
          Length = 369

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V        +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELAVAV---AEGDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 368



 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 119/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  +++G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VADFIRNHKKQGTAIDDEVTEKLVIPFVLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +     +  +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSTKYVVEGPKSEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|303238871|ref|ZP_07325402.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593504|gb|EFL63221.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 359

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 209/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + K     S +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 90  VRMYLKEIGKVPLLSADEEIQLAQKMEK---GDSESKRRLAEANLRLVVSIAKRYVGRGM 146

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 147 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 206

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ +EP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 207 INKLIRVSRQLLQELGKEPQPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 266

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 267 GDFIPDDDAPAPSEAAAFTLLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 326

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 327 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 359



 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/160 (30%), Positives = 71/160 (44%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       ++I   +Q+G +T +E+       E+  E +E     L NMGI++V   + E
Sbjct: 6   DTRKAILLELIDKGKQKGMLTYKEIMDAFEEIEIEPEHIEKVYETLENMGIDIVGDIEAE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE      DL  S                 S DDPVRMYL+E+G + LLS + EI +A+
Sbjct: 66  MEEIQLTEEDLDIS------------IPEGISIDDPVRMYLKEIGKVPLLSADEEIQLAQ 113

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           ++E G +     L E+ L     I  R  +  G   L  I
Sbjct: 114 KMEKGDSESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 152


>gi|125973412|ref|YP_001037322.1| RNA polymerase sigma factor RpoD [Clostridium thermocellum ATCC
           27405]
 gi|125713637|gb|ABN52129.1| RNA polymerase, sigma 38 subunit, RpoS [Clostridium thermocellum
           ATCC 27405]
          Length = 358

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 209/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +     + AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 89  VRMYLKEIGKVPLLTAEEEIELAHRIEQ---GDAEAKRRLAEANLRLVVSIAKRYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKLIRVSRQLLQELGREPHPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 266 GDFIPDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 48/152 (31%), Positives = 70/152 (46%), Gaps = 13/152 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I+  +Q+G +T +E+       ++  EQ+E     L NMGI+VV   + E E+     
Sbjct: 13  ELIEKGKQKGMLTYQEIMDAFEEVDIDPEQIEKIYETLENMGIDVVGDIEAEMEDIQLTE 72

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +L                    S DDPVRMYL+E+G + LL+ E EI +A RIE G A 
Sbjct: 73  DNLD------------LSIPEGISIDDPVRMYLKEIGKVPLLTAEEEIELAHRIEQGDAE 120

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  R  +  G   L  I
Sbjct: 121 AKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 151


>gi|318066971|emb|CBY89100.1| RNA polymerase sigma70 factor [Halomonas sulfidaeris]
          Length = 368

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 123/395 (31%), Positives = 179/395 (45%), Gaps = 47/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   D   + E D   E E    S  
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEPEADIDDDIESDGDDEDEDSTAS-- 136

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                   +    PE A      + E         +                        
Sbjct: 137 --------EGGPDPEEARARFEQIREQNALVEAAFA------------------------ 164

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L  L   + L     + LV Q+    +++   E 
Sbjct: 165 -----------KHGRGSPELKAEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEK 213

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E    W+   +   + ++ + +      I + + +I
Sbjct: 214 AVMQLCVKKAKVPRKTFIKSFPGNESSKTWLDEFQA-AQSKYADRLEPLRADIARAQRKI 272

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 273 AFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 332

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 333 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|29376087|ref|NP_815241.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis V583]
 gi|227518714|ref|ZP_03948763.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227553323|ref|ZP_03983372.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229545861|ref|ZP_04434586.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|229550053|ref|ZP_04438778.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|255975889|ref|ZP_05426475.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256619027|ref|ZP_05475873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256762453|ref|ZP_05503033.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256853088|ref|ZP_05558458.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256958944|ref|ZP_05563115.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256961963|ref|ZP_05566134.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256965161|ref|ZP_05569332.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|257078975|ref|ZP_05573336.1| sigma 42 [Enterococcus faecalis JH1]
 gi|257082587|ref|ZP_05576948.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|257085220|ref|ZP_05579581.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|257086781|ref|ZP_05581142.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|257089848|ref|ZP_05584209.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257416057|ref|ZP_05593051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis AR01/DG]
 gi|257419260|ref|ZP_05596254.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257422656|ref|ZP_05599646.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|293383032|ref|ZP_06628950.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|293389479|ref|ZP_06633936.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294779115|ref|ZP_06744526.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|300860473|ref|ZP_07106560.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|307271055|ref|ZP_07552338.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|307273262|ref|ZP_07554508.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|307274998|ref|ZP_07556161.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|307278111|ref|ZP_07559195.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|307289068|ref|ZP_07569024.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|307292033|ref|ZP_07571902.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|312900723|ref|ZP_07760020.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|312903270|ref|ZP_07762450.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|312907497|ref|ZP_07766488.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|312910115|ref|ZP_07768962.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|312951455|ref|ZP_07770352.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|30179886|sp|P52329|RPOD_ENTFA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|29343549|gb|AAO81311.1| RNA polymerase sigma-43 factor [Enterococcus faecalis V583]
 gi|227073834|gb|EEI11797.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227177552|gb|EEI58524.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229304757|gb|EEN70753.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|229309016|gb|EEN75003.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|255968761|gb|EET99383.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256598554|gb|EEU17730.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256683704|gb|EEU23399.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256711547|gb|EEU26585.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256949440|gb|EEU66072.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256952459|gb|EEU69091.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256955657|gb|EEU72289.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|256987005|gb|EEU74307.1| sigma 42 [Enterococcus faecalis JH1]
 gi|256990617|gb|EEU77919.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|256993250|gb|EEU80552.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|256994811|gb|EEU82113.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|256998660|gb|EEU85180.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257157885|gb|EEU87845.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ARO1/DG]
 gi|257161088|gb|EEU91048.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257164480|gb|EEU94440.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|291079697|gb|EFE17061.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|291081096|gb|EFE18059.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294453840|gb|EFG22231.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|295112959|emb|CBL31596.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Enterococcus sp. 7L76]
 gi|300849512|gb|EFK77262.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|306497031|gb|EFM66579.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|306499777|gb|EFM69138.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|306505508|gb|EFM74694.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|306508446|gb|EFM77553.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|306510247|gb|EFM79271.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|306512553|gb|EFM81202.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|310626525|gb|EFQ09808.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|310630611|gb|EFQ13894.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|310633146|gb|EFQ16429.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|311289388|gb|EFQ67944.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|311292204|gb|EFQ70760.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|315027303|gb|EFT39235.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2137]
 gi|315033932|gb|EFT45864.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0017]
 gi|315036941|gb|EFT48873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0027]
 gi|315144454|gb|EFT88470.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2141]
 gi|315147227|gb|EFT91243.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4244]
 gi|315150574|gb|EFT94590.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0012]
 gi|315152521|gb|EFT96537.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0031]
 gi|315155799|gb|EFT99815.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0043]
 gi|315158034|gb|EFU02051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0312]
 gi|315160483|gb|EFU04500.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0645]
 gi|315163977|gb|EFU07994.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1302]
 gi|315169073|gb|EFU13090.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1341]
 gi|315169690|gb|EFU13707.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1342]
 gi|315172348|gb|EFU16365.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1346]
 gi|315575904|gb|EFU88095.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309B]
 gi|315577570|gb|EFU89761.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0630]
 gi|315580556|gb|EFU92747.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309A]
 gi|327535095|gb|AEA93929.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis OG1RF]
 gi|329571347|gb|EGG53034.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1467]
          Length = 368

 Score =  234 bits (597), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 164/306 (53%), Positives = 212/306 (69%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI    R  +K I     ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 ---EGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 73/190 (38%), Gaps = 15/190 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + +    IK  + +G V  ++L   L  P  + +E ME  +  + + GI+VVD +    
Sbjct: 9   YEAAVAAFIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVDENGDPS 68

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   +                +          +DPVRMYL+E+G ++LL+   E+ +A +
Sbjct: 69  EHSLKKD-----EKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALK 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 124 IEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 174

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 175 FDYRKGFKFS 184


>gi|326803636|ref|YP_004321454.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651510|gb|AEA01693.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 401

 Score =  234 bits (597), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 170/407 (41%), Positives = 246/407 (60%), Gaps = 19/407 (4%)

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD-- 344
           +++   +       A     +EK  +   +  E   K+    SLN  ++D L+E+  D  
Sbjct: 1   MSKTTDKQEKTLKQASQELLNEKKILGSILYTELSDKIAQPYSLNDEQMDQLIEKFEDGG 60

Query: 345 ----------ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
                      ++++ +   ++    +      D  L+  +  +          +     
Sbjct: 61  VAVVDEDGGPTNRQLQNEALKMQEDDEESEKDIDQILDEEEKTKKKDKKDKKDTNKSASS 120

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             + V         +R  +K I     ++  E    V++ ++ E    +AK+E+ EANLR
Sbjct: 121 TSSKVKTNDP----VRMYLKEIGRVDLLTADEE---VALAKRIEAGDPVAKQELAEANLR 173

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITRSIAD
Sbjct: 174 LVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRSIAD 233

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K+VR  R++  ++ REPTPEEI  ++ +P E VR ++KI++EP+
Sbjct: 234 QARTIRIPVHMVETINKLVRIQRQLLQELGREPTPEEIGAEMDLPTEKVRNIMKISQEPV 293

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETPIG+ED SHLGDFIED +A+ P +   Q  L+E    VL +LT REE VLR+RFG+
Sbjct: 294 SLETPIGEEDDSHLGDFIEDNDAMQPDEYTNQELLKEQLNEVLDTLTDREENVLRLRFGL 353

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                 TLE+VG+QF VTRERIRQIEAKA+RKL+HPSR K+L+ FL+
Sbjct: 354 EDGQTKTLEQVGQQFGVTRERIRQIEAKALRKLRHPSRLKQLKDFLE 400



 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 79/182 (43%), Gaps = 26/182 (14%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDD---- 82
             + ++++   +  G +   EL+  +  P  ++ EQM+  +    + G+ VVD D     
Sbjct: 13  KQASQELLNEKKILGSILYTELSDKIAQPYSLNDEQMDQLIEKFEDGGVAVVDEDGGPTN 72

Query: 83  ----------LEDEEGSEDSLD----------LASSASNSSVFLQKRKDSADRSTDDPVR 122
                      ED+E SE  +D                           S+   T+DPVR
Sbjct: 73  RQLQNEALKMQEDDEESEKDIDQILDEEEKTKKKDKKDKKDTNKSASSTSSKVKTNDPVR 132

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL+E+G ++LL+ + E+A+AKRIEAG  +    L E+ L     I  R  +  G + L 
Sbjct: 133 MYLKEIGRVDLLTADEEVALAKRIEAGDPVAKQELAEANLRLVVSIAKRY-VGRGMSFLD 191

Query: 183 EI 184
            I
Sbjct: 192 LI 193


>gi|266623970|ref|ZP_06116905.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288864209|gb|EFC96507.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 345

 Score =  234 bits (597), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +        +AK+++ EANLRLV+S+AK+Y  RG+
Sbjct: 75  VRMYLKEIGKVPLLSSDDEIELAKKIE---LGDELAKEKLTEANLRLVVSIAKRYVGRGM 131

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 132 QFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 191

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VR +R++  ++ REP+PEE+A ++ MPVE VR+++K+++EP+SLETPIG+E+ SHL
Sbjct: 192 INRLVRVSRQLLQELGREPSPEEVASRVDMPVERVREIMKVSQEPVSLETPIGEEEDSHL 251

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D     P D+A    L E    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 252 GDFIQDDQVAVPADAATFTMLHEQLMEVLDTLTEREQKVLRLRFGLDDGRPRTLEEVGRE 311

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 312 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 344



 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 59/136 (43%), Gaps = 3/136 (2%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ--K 108
            F     + +++++     L    ++V+  ++ ED E   D            + ++   
Sbjct: 3   DFFAGTVLDADRLDRIYDFLETNKVDVLQINEDEDLELDPDLFIEEELEEEEEIDMEHID 62

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
                  S +DPVRMYL+E+G + LLS + EI +AK+IE G  +    L E+ L     I
Sbjct: 63  LSVPEGISVEDPVRMYLKEIGKVPLLSSDDEIELAKKIELGDELAKEKLTEANLRLVVSI 122

Query: 169 IWRDELNDGTTLLREI 184
             R  +  G   L  I
Sbjct: 123 AKRY-VGRGMQFLDLI 137


>gi|318066943|emb|CBY89086.1| RNA polymerase sigma70 factor [Halomonas halmophila]
          Length = 367

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 117/395 (29%), Positives = 181/395 (45%), Gaps = 48/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M +L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMMALAYLPGAVDSILEVYDGT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E  +    + ++  +                
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEAPASVPEQGAAAGEAE-----------DED 127

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             ++++ S     PE A      + E  + +   + A                       
Sbjct: 128 AEAEEEESGGGPDPEEARARFEQIREQNEAARRAIEA----------------------- 164

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         + S + +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 165 ------------HGRGSKQAQDALARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEK 212

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E +  W+  A     G++   +      I + + +I
Sbjct: 213 AIMQLCVKKAKMPRKTFIKSFPGNESNQEWLD-AFMADNGKYSTRLEPLKGEIQRSQRKI 271

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +++++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 272 AFEEEMVALAVTDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 331

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 332 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|147677242|ref|YP_001211457.1| RNA polymerase sigma factor RpoD [Pelotomaculum thermopropionicum
           SI]
 gi|146273339|dbj|BAF59088.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
          Length = 363

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 168/374 (44%), Positives = 232/374 (62%), Gaps = 25/374 (6%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK   +  +   +++  +    L   +ID + E+L  +   ++    ++  L  S     
Sbjct: 15  EKGKKRGVLTYNEIMDSLQGTDLTPEQIDDIYEKLAGLGIEVVPEIPDIEPLDSSA---- 70

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                     E  P  V      PEG         V     +R  +K I     ++  E 
Sbjct: 71  ---------LENPPDEVEVDLSIPEG---------VGIDDPVRMYLKEIGRVPLLTPEEE 112

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   + K       AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 113 VELAKRMEK---GDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 169

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P
Sbjct: 170 FDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQELGRDP 229

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +PEEIAK++ +  + VR++LKI +EP+SLETPIG+E+ SHLGDFIED  A +P + A   
Sbjct: 230 SPEEIAKEMNITEDKVREILKIAQEPVSLETPIGEEEDSHLGDFIEDHEARAPAEEASFT 289

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE    VL +LT RE+RVLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL
Sbjct: 290 LLREQLDEVLKTLTEREQRVLRLRFGLDDGRARTLEEVGQKFGVTRERIRQIEAKTLRKL 349

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 350 RHPSRSKKLKDYLD 363



 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 76/354 (21%), Positives = 135/354 (38%), Gaps = 31/354 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D  +D  +++I+  ++RG +T  E+   L   +++ EQ++D    L+ +GI VV      
Sbjct: 4   DEKNDGVRELIEKGKKRGVLTYNEIMDSLQGTDLTPEQIDDIYEKLAGLGIEVV------ 57

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            E    + LD ++  +                 DDPVRMYL+E+G + LL+ E E+ +AK
Sbjct: 58  PEIPDIEPLDSSALENPPDEVEVDLSIPEGVGIDDPVRMYLKEIGRVPLLTPEEEVELAK 117

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           R+E G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 118 RMEKGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVE 168

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
              Y+K    S        Q     I   A+  +     V++  +      + L E   D
Sbjct: 169 KFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQELGRD 228

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRS----------LQDNAVNGQKDEKSSVKC 314
            +    A E  +    +  + +IA+    L +                +  +        
Sbjct: 229 PSPEEIAKEMNITEDKVREILKIAQEPVSLETPIGEEEDSHLGDFIEDHEARAPAEEASF 288

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
            +L+E+L +++ +L+  + R+  L   L D           L  + Q +G+ R+
Sbjct: 289 TLLREQLDEVLKTLTEREQRVLRLRFGLDD------GRARTLEEVGQKFGVTRE 336


>gi|16803494|ref|NP_464979.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46907682|ref|YP_014071.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092744|ref|ZP_00230530.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|47095405|ref|ZP_00233015.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499695|ref|ZP_03668044.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Finland
           1988]
 gi|224501605|ref|ZP_03669912.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-561]
 gi|226224055|ref|YP_002758162.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Clip81459]
 gi|254824487|ref|ZP_05229488.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|254827742|ref|ZP_05232429.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|254829787|ref|ZP_05234442.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 10403S]
 gi|254852080|ref|ZP_05241428.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|254898380|ref|ZP_05258304.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes J0161]
 gi|254912128|ref|ZP_05262140.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|254932639|ref|ZP_05265998.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|254936456|ref|ZP_05268153.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|254994146|ref|ZP_05276336.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-064]
 gi|255029176|ref|ZP_05301127.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes LO28]
 gi|255522085|ref|ZP_05389322.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J1-175]
 gi|284801841|ref|YP_003413706.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284994983|ref|YP_003416751.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|315282349|ref|ZP_07870778.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|1710684|sp|P52331|RPOD_LISMO RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|664756|gb|AAC43306.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes]
 gi|16410883|emb|CAC99532.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46880950|gb|AAT04248.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47016226|gb|EAL07149.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47018932|gb|EAL09679.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|225876517|emb|CAS05226.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. CLIP 80459]
 gi|258600121|gb|EEW13446.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|258605378|gb|EEW17986.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|258609048|gb|EEW21656.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|284057403|gb|ADB68344.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284060450|gb|ADB71389.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|293584198|gb|EFF96230.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|293590099|gb|EFF98433.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|293593725|gb|EFG01486.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|313614010|gb|EFR87725.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|328465497|gb|EGF36726.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 1816]
 gi|332311895|gb|EGJ24990.1| RNA polymerase sigma factor rpoD [Listeria monocytogenes str. Scott
           A]
 gi|1093602|prf||2104269C RNA polymerase:SUBUNIT=sigma
          Length = 374

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 47/170 (27%), Positives = 79/170 (46%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + S +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTKNTKPVAELSVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|320547037|ref|ZP_08041336.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
 gi|320448322|gb|EFW89066.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
          Length = 369

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSSEEEKELAVAV---AAGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMSPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRNHKKNGTAVDDEVTEKLVIPFSLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LLS E E  +A  + AG
Sbjct: 68  PSTKYVVEEPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSSEEEKELAVAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLQAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMSP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|16800559|ref|NP_470827.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116872885|ref|YP_849666.1| RNA polymerase sigma factor RpoD [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|217964400|ref|YP_002350078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290894216|ref|ZP_06557185.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|20140102|sp|Q92BQ6|RPOD_LISIN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|16413964|emb|CAC96722.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116741763|emb|CAK20887.1| RNA polymerase sigma factor RpoD (Sigma-A) [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217333670|gb|ACK39464.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290556213|gb|EFD89758.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|307571035|emb|CAR84214.1| RNA polymerase sigma factor [Listeria monocytogenes L99]
 gi|313623755|gb|EFR93895.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL J1-023]
          Length = 374

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/170 (27%), Positives = 79/170 (46%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + + +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTQNTKPVAELNVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|315223009|ref|ZP_07864888.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319939161|ref|ZP_08013525.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
 gi|315187959|gb|EFU21695.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319812211|gb|EFW08477.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
          Length = 370

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +  +V +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGVVPLLTNEEEQELAVLVEQ---GDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 277 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR F++
Sbjct: 337 FNVTRERIRQIEAKALRKLRHPSRSKPLRDFIE 369



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 119/333 (35%), Gaps = 27/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  ++ G  T +E+N  L  P  + ++ +ED +  + + GI + D      +
Sbjct: 12  DVQVAEFIRNHKKTGTATDDEINDRLVIPFTLEADGIEDLLQRIQDAGIAITD------K 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           EG+     L +    + +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 66  EGNPSERVLNTEEEEAELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEQELAVLV 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 126 EQGDLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 176

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 177 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 236

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 237 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 293

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 294 RI--------VLREQLDEVLDTLTDREENVLRL 318


>gi|171779914|ref|ZP_02920818.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281262|gb|EDT46697.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 369

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   +S  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLSSEEEKELAVAV---AAGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRNHKKNGTAVDDEVTEKLVIPFSLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   +     +DPVRMYL+E+G + LLS E E  +A  + AG
Sbjct: 68  PSTKYVVEEPKPEELTDEELLGNNSAKVNDPVRMYLKEIGVVPLLSSEEEKELAVAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLQAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|322391830|ref|ZP_08065295.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
 gi|321145310|gb|EFX40706.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
          Length = 381

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGVVPLLTNEEEKELALAVE---AGDVEAKQRLAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 288 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 348 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 380



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 73/356 (20%), Positives = 125/356 (35%), Gaps = 33/356 (9%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQM 63
           KK+N    ++ ++   +      D    + I+  ++ G  T +E+N  L  P  +  E +
Sbjct: 6   KKKNGVRMAKKQNEVTTF-----DVQVAEFIRNHKKTGTATDDEINNVLVIPFALDVEGI 60

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           E+ +  + + GI + D +    E        + S+     +  +    S     +DPVRM
Sbjct: 61  ENLLQRIQDAGIAITDNEGNPSE-------RVLSTEEEPELSDEDLIGSTSAKVNDPVRM 113

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G + LL+ E E  +A  +EAG       L E+ L     I  R  +  G   L  
Sbjct: 114 YLKEIGVVPLLTNEEEKELALAVEAGDVEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDL 172

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           I         E   G     +   Y K    S        Q     I   A+  +     
Sbjct: 173 I--------QEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 224

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           V++  +        L E   D      A    + P     + EI ++ +E  SL+     
Sbjct: 225 VETINKLVREQRNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEPVSLETPIGE 281

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                        + E  V     +        +L EQL ++   +   E  +LRL
Sbjct: 282 EDDSHLGDFIEDEVIENPVDYTTRI--------VLREQLDEVLDTLTDREENVLRL 329


>gi|229820409|ref|YP_002881935.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
 gi|229566322|gb|ACQ80173.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
          Length = 499

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 140/283 (49%), Positives = 189/283 (66%), Gaps = 1/283 (0%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EV+   +I   + +          EF+ +   +     +   AK  ++EANLRLV+S
Sbjct: 218 AEQEVELAKRIEAGLFAEETLAAGGSMEFK-LRRELEWIAADGRRAKNHLLEANLRLVVS 276

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ T
Sbjct: 277 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 336

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL T
Sbjct: 337 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHT 396

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  AV P D+     L+E    VL +L+ RE  V+ MRFG+    
Sbjct: 397 PLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQ 456

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 457 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 499



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 13/89 (14%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ-------------KRKDSADRSTDDPV 121
           ++V D  +  + + +E      +         +              ++     +T DPV
Sbjct: 144 VDVDDATEATEGDAAEGGAAKTAKTGTDETEDKGFVYSDADDDDAPAQQVVTAGATADPV 203

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 204 KDYLKQIGKVALLNAEQEVELAKRIEAGL 232


>gi|318066977|emb|CBY89103.1| RNA polymerase sigma70 factor [Halomonas ventosae]
          Length = 366

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 125/395 (31%), Positives = 191/395 (48%), Gaps = 49/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R + DL +        GF    EG       +  +E+ RD+ +      ++ A
Sbjct: 79  QDEEAPGR-LSDLFS--------GFIDPDEGIPGVAEAEVPEEEPRDEPRRMPTTEDAEA 129

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           K       +    P ++E      ++  + +A   +A+ED                    
Sbjct: 130 K------EETTGGPPDSEEARARFEQIREQNAAAQAAIED-------------------- 163

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         + S + +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 164 ------------HGRGSKEAQEELARLGQLFLPIKLVPKHFERLVGQVRISVEQVRAQEK 211

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            ++ L  +   + R  F++   G E +P W+         ++   +      I + + +I
Sbjct: 212 AIMHLCVKKAKVSRKTFIKAFPGSESNPEWLDDFSA-ANPKYAARLEPLRGDIQRAQRKI 270

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 271 AFEEEMIQLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 330

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 331 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 365


>gi|160937106|ref|ZP_02084469.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440007|gb|EDP17755.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
          Length = 378

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     + + +    V + +K E     A+K + E+NLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGKIPLLGMEDE---VELAKKMELGDPEARKRLAESNLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 QFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VRT+R++  ++ REPT EEIA +L +PVE V +++K+++EP+SLETPIG+E+ SHL
Sbjct: 225 INRLVRTSRQLLQELGREPTTEEIAARLDLPVERVSEIMKMSQEPVSLETPIGEEEDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N + P D+A    L E    VL +LT RE++VLR+RFG+      TLEEVGKQ
Sbjct: 285 GDFIQDDNVLVPQDAAAFTLLHEQLMEVLLTLTEREQKVLRLRFGLDDGRPRTLEEVGKQ 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 345 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 377



 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 38/163 (23%), Positives = 67/163 (41%), Gaps = 4/163 (2%)

Query: 25  DFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--DGD 81
           D  ++    +++ A+++   +  +E+  +   +   S Q++     L    ++V+    +
Sbjct: 9   DVFEEKLAGLLEEAKKKKNVLEYQEVMNYFGQEPPVSNQLDRLFEFLDQNKVDVIRMGTE 68

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D  D +   +            V           S +DPVRMYL+E+G I LL  E E+ 
Sbjct: 69  DELDPDLFIEEEMELDEEEEIDVEHLDLSVPEGVSLEDPVRMYLKEIGKIPLLGMEDEVE 128

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +AK++E G       L ES L     I  R  +  G   L  I
Sbjct: 129 LAKKMELGDPEARKRLAESNLRLVVSIAKRY-VGRGMQFLDLI 170


>gi|255026189|ref|ZP_05298175.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-003]
          Length = 361

 Score =  234 bits (596), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 92  VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 148

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 149 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 208

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 209 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 268

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 269 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 328

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 329 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 361



 Score =  114 bits (285), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 73/157 (46%), Gaps = 6/157 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   + +I+  +++G +T  ++ A L P  + S+QM++ +  +   GI V      +D +
Sbjct: 4   EQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAGIEV-----SDDAD 58

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            S  L           +DPVRMYL+E+G ++LL+ + EIA+AKRIE
Sbjct: 59  DEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRIE 118

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AG       L E+ L     I  R  +  G   L  I
Sbjct: 119 AGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 154


>gi|291542495|emb|CBL15605.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 367

 Score =  234 bits (596), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 146/270 (54%), Positives = 202/270 (74%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S  E  ++   +         AK+ + EANLRLV+S+AK+Y  RG+QFL
Sbjct: 100 YLKEIGRVPLLSSDEEINLAIRI---ADGDVAAKQRLSEANLRLVVSIAKRYLGRGMQFL 156

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 157 DLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 216

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++ ++   EP+ +EIA ++ MPV+ VR+++++ +EP+SLETPIG+E+ SHLGDF
Sbjct: 217 VKKVQSQLLHQNGHEPSADEIAAEIDMPVDKVREIMRVAQEPVSLETPIGEEEDSHLGDF 276

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A +P D+A    LRE  + VL++LTPRE +VL++RFG+      TLEEVGK+F V
Sbjct: 277 IPDNDAPAPADAASHTMLREQLSDVLSTLTPREAKVLKLRFGLEDGRSRTLEEVGKEFNV 336

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 337 TRERIRQIEAKALRKLRHPSRSRKLKDYLD 366



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 47/185 (25%), Positives = 78/185 (42%), Gaps = 13/185 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            +++++L +Q+G +T +++   +   +   EQ+E     L+ +GI +V+       +   
Sbjct: 11  VRELVELGKQKGQLTNQDILDAIGEIDFDPEQLEKLYDSLAQLGIEIVED----SGDIKI 66

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D +DL            +  ++   S DDPV++YL+E+G + LLS + EI +A RI  G 
Sbjct: 67  DDIDLGFDEGKDGDSHAQIAETGSVSVDDPVKVYLKEIGRVPLLSSDEEINLAIRIADGD 126

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                 L E+ L     I  R  L  G   L  I         E   G     E   Y K
Sbjct: 127 VAAKQRLSEANLRLVVSIAKRY-LGRGMQFLDLI--------QEGNLGLIKAVEKFDYTK 177

Query: 211 REDSS 215
               S
Sbjct: 178 GFKFS 182


>gi|291520418|emb|CBK75639.1| RNA polymerase, sigma 70 subunit, RpoD [Butyrivibrio fibrisolvens
           16/4]
          Length = 376

 Score =  234 bits (596), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    V + +K E     AK ++ EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGKVPLLSAEEE---VELAQKMEDGDQEAKNKLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNLGLMKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +  REPTPEEIA  + + V+ V ++LKI++EP+SLETPIG+E+ SHL
Sbjct: 223 INKLIRVSRQLLQEYGREPTPEEIAAAMGITVDRVHEILKISQEPVSLETPIGEEEDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D+N   P ++A    L+E    VL +LT RE+RVL +RFG+      TLEEVGK+
Sbjct: 283 GDFLPDENVPVPAEAATFTLLKEQLHEVLDTLTEREQRVLILRFGLEDGKARTLEEVGKE 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 343 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 375



 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 44/161 (27%), Positives = 74/161 (45%), Gaps = 10/161 (6%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIE-ELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           D  D    ++IK+A+ +  +  + E++ FL   ++ ++QME  +  L   GI+V      
Sbjct: 17  DELDSKIAELIKIAKSQKNILEDYEISEFLKDYKIDAKQMERILTYLDKKGIDV------ 70

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                S  S  L  ++ +  +           S +DPVRMYL+E+G + LLS E E+ +A
Sbjct: 71  --NFSSGPSDALLLASDDEDLEDIDMSVPDSVSIEDPVRMYLKEIGKVPLLSAEEEVELA 128

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +++E G       L E+ L     I  R  +  G   L  I
Sbjct: 129 QKMEDGDQEAKNKLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|169830688|ref|YP_001716670.1| RNA polymerase sigma factor RpoD [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637532|gb|ACA59038.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 360

 Score =  234 bits (596), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 155/279 (55%), Positives = 209/279 (74%), Gaps = 3/279 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           VD    +R  +K I     ++  E    VS+ R+ E     AK+ ++EANLRLV+S+AK+
Sbjct: 85  VDIDDPVRMYLKEIGRIPLLTPEEE---VSLARRMEAGDDEAKRRLIEANLRLVVSIAKR 141

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIP
Sbjct: 142 YVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIP 201

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K++R +R++  ++ REP PEEIA+++ +  + VR++ KI +EP+SLETPIG+
Sbjct: 202 VHMVETINKLIRISRQLLQELGREPLPEEIAREMDISEDKVREIQKIAQEPVSLETPIGE 261

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ SHLGDFIED++A +P + A    LRE    VL +LT RE+RVLR+RFG+      TL
Sbjct: 262 EEDSHLGDFIEDQDAQAPAEEASFTLLREQLDDVLKTLTEREQRVLRLRFGLDDGRARTL 321

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVG++F VTRERIRQIEAK +RKL+HPSRSKKL+ +LD
Sbjct: 322 EEVGQEFGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLD 360



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 118/329 (35%), Gaps = 28/329 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +++  +QRG +T  E+   L   E++ +Q++D    L+  GI VV            
Sbjct: 9   IQDLVEKGKQRGTLTYNEVMDSLQGFELTPDQIDDVYERLAGEGIEVVPE--------GP 60

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D   L        V   +         DDPVRMYL+E+G I LL+ E E+++A+R+EAG 
Sbjct: 61  DLAALEEETREEDVEEAEIAIPEGVDIDDPVRMYLKEIGRIPLLTPEEEVSLARRMEAGD 120

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                 L E+ L     I  R  +  G   L  I         E   G     E   Y+K
Sbjct: 121 DEAKRRLIEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEKFDYKK 171

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
               S        Q     I   A+  +     V++  +      + L E   +      
Sbjct: 172 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRISRQLLQELGREPLPEEI 231

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A E  +    +  + +IA                 +      +   L + +         
Sbjct: 232 AREMDISEDKVREIQKIA-----------QEPVSLETPIGEEEDSHLGDFIEDQDAQAPA 280

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            ++   LL EQL D+ K +   E  +LRL
Sbjct: 281 EEASFTLLREQLDDVLKTLTEREQRVLRL 309


>gi|291531112|emb|CBK96697.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 358

 Score =  234 bits (596), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 157/343 (45%), Positives = 230/343 (67%), Gaps = 5/343 (1%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +++ D+ + +  +  E+ +L   +       ++     E     + +          + 
Sbjct: 21  TKEITDVLEELDFDADEINKLYDDFESSNIEIVDDFSADEDLDSALDFTDSDDFESSLSS 80

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
               +D  +KI   +K I     ++  E   + + + +       A+K + EANLRLV+S
Sbjct: 81  EGIAIDDPVKI--YLKEIGRVPLLTAEEEIELATRMAQ---GDKYARKRLSEANLRLVVS 135

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 136 IAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQART 195

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I KV + + ++ ++   EPTP+EIA +L + V+ VR++L+I+++P+SLET
Sbjct: 196 IRIPVHMVETITKVKKVSSQLLHENGHEPTPQEIADRLGITVDRVREILRISQDPVSLET 255

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ SHLGDFI D++A +P ++A +  L+E  + +L +LTPREE+VLR+RFG+    
Sbjct: 256 PIGEEEDSHLGDFIPDEDAPAPAEAASRTLLKEQLSEILGTLTPREEKVLRLRFGLEDGR 315

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 316 PRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 358



 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 38/159 (23%), Positives = 67/159 (42%), Gaps = 8/159 (5%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            +D    ++I   +Q G +T +E+   L   +  ++++        +  I +VD      
Sbjct: 1   MADSKINELINHGKQSGKLTTKEITDVLEELDFDADEINKLYDDFESSNIEIVD------ 54

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            + S D    ++     S   +    S   + DDPV++YL+E+G + LL+ E EI +A R
Sbjct: 55  -DFSADEDLDSALDFTDSDDFESSLSSEGIAIDDPVKIYLKEIGRVPLLTAEEEIELATR 113

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  G       L E+ L     I  R  +  G   L  I
Sbjct: 114 MAQGDKYARKRLSEANLRLVVSIAKRY-VGRGMQFLDLI 151


>gi|219670224|ref|YP_002460659.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense
           DCB-2]
 gi|219540484|gb|ACL22223.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfitobacterium hafniense DCB-2]
          Length = 372

 Score =  234 bits (596), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 165/373 (44%), Positives = 237/373 (63%), Gaps = 17/373 (4%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           K   K  +   +++  +  + L   +ID + EQ+  +   I+   GE+  L +      D
Sbjct: 17  KGKKKGSLTYREIMDTLQGIELTAEQIDEVYEQIGRMGIDIIPEAGEVEALEKVTDEIPD 76

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
                          V       E +    +   V     +R  +K I     ++  E  
Sbjct: 77  D--------------VDDPDVEEEVDVDLSIPEGVGIDDPVRMYLKEIGRVPLLTAEEEI 122

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +       AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKF
Sbjct: 123 ELAKRMEQ---GDESAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKF 179

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REPT
Sbjct: 180 DYVKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPT 239

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA ++ + VE VR+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    
Sbjct: 240 PEEIAVQMDISVERVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPSEAASFIL 299

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +LTPREE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL+
Sbjct: 300 LKEQLEEVLETLTPREEKVLRLRFGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLR 359

Query: 669 HPSRSKKLRSFLD 681
           HPSRSKKL+ +L+
Sbjct: 360 HPSRSKKLKDYLE 372



 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 43/158 (27%), Positives = 75/158 (47%), Gaps = 3/158 (1%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED--E 86
           D+ K++I+  +++G +T  E+   L   E+++EQ+++    +  MGI+++      +  E
Sbjct: 9   DAVKELIQKGKKKGSLTYREIMDTLQGIELTAEQIDEVYEQIGRMGIDIIPEAGEVEALE 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + +++  D                       DDPVRMYL+E+G + LL+ E EI +AKR+
Sbjct: 69  KVTDEIPDDVDDPDVEEEVDVDLSIPEGVGIDDPVRMYLKEIGRVPLLTAEEEIELAKRM 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EQGDESAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 165


>gi|288905580|ref|YP_003430802.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|306831670|ref|ZP_07464827.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978609|ref|YP_004288325.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288732306|emb|CBI13876.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|304426095|gb|EFM29210.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178537|emb|CBZ48581.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 369

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAV---AAGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRNHKKNGTAVDDEVTEKLVIPFSLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  + AG
Sbjct: 68  PSTKYVVEEPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLQAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|298500980|ref|ZP_07010781.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MAK 757]
 gi|297540228|gb|EFH76288.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MAK 757]
          Length = 408

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 96/429 (22%), Positives = 170/429 (39%), Gaps = 42/429 (9%)

Query: 22  LVFDFS-DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
              D +     K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+ 
Sbjct: 16  PSMDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVET 75

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
               D+    D   +    +  +        +S    T DPVRMY+REMG++ELL+REGE
Sbjct: 76  APDADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 135

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGG 198
           I IAKRIE G   + +++ E P T   ++   D +      L ++I     + P   +  
Sbjct: 136 IDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETE 193

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
               T   S     D + E +     E E + E     S D   +V   PE A      L
Sbjct: 194 APTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNEL 253

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                                                  Q+  +   +  + S +     
Sbjct: 254 R-----------------------------------GKFQNLQLAVNEFGRDSHQASEAS 278

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGR 377
           + ++ +     L   + D LVE L     R+   E  +++       + +  F+    G 
Sbjct: 279 DLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGN 338

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W+       +  +   V  + + I +   +++ I  ET +S+   + I   +  G
Sbjct: 339 ESNEEWLDKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIG 397

Query: 438 ECEASIAKK 446
           E +A  A++
Sbjct: 398 EAKARRARR 406


>gi|289450258|ref|YP_003475183.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184805|gb|ADC91230.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 353

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 146/273 (53%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E + +   ++     +  AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 84  VRMYLKEIGKVPLLNAEEEKDLARAMK---EGSQEAKDRLCEANLRLVVSIAKRYVGRGM 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 141 QFLDLIQEGNLGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 200

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REP  EE+A+++ +  E VR++ KI++EP+SLE PIG+E+ SHL
Sbjct: 201 INKLIRVQRQLLQELGREPEVEELAQEMGISPEKVREIQKISQEPVSLEKPIGEEEDSHL 260

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A SP D A    L+E    +L+ LTPREE+VLR+RFG+      TLEEVG++
Sbjct: 261 GDFIPDDDAPSPADQAAFTLLKEQLLEILSGLTPREEKVLRLRFGLDDGRSRTLEEVGRE 320

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RK++HPSRSKKL+ +LD
Sbjct: 321 FNVTRERIRQIEAKALRKMRHPSRSKKLKDYLD 353



 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/189 (20%), Positives = 75/189 (39%), Gaps = 29/189 (15%)

Query: 28  DDSWKKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++    ++K+A+     +  +++ + L   +   E  +     L   G+ +++   ++++
Sbjct: 9   EEIVNDLVKIAKSNNNKINGQDILSKLEAIDFDLEASDTIFEQLKQNGVEIIEDATVDED 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +DS D+                    + DDPVRMYL+E+G + LL+ E E  +A+ +
Sbjct: 69  LNIDDSSDV-------------------MNVDDPVRMYLKEIGKVPLLNAEEEKDLARAM 109

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           + G       LCE+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 110 KEGSQEAKDRLCEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNLGLIKAVDKF 160

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 161 DYEKGFKFS 169


>gi|167750934|ref|ZP_02423061.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|167656113|gb|EDS00243.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|291557421|emb|CBL34538.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 358

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 157/343 (45%), Positives = 230/343 (67%), Gaps = 5/343 (1%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +++ D+ + +  +  E+ +L   +       ++     E     + +          + 
Sbjct: 21  TKEITDVLEELDFDADEINKLYDDFESSNIEIVDDFSADEDLDSALDFTDSDDFESSLSS 80

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
               +D  +KI   +K I     ++  E   + + + +       A+K + EANLRLV+S
Sbjct: 81  EGIAIDDPVKI--YLKEIGRVPLLTAEEEIELATRMAQ---GDKYARKRLSEANLRLVVS 135

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  RG+QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITRSIADQ+ T
Sbjct: 136 IAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQART 195

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I KV + + ++ ++   EPTP+EIA +L + V+ VR++L+I+++P+SLET
Sbjct: 196 IRIPVHMVETITKVKKVSSQLLHENGHEPTPQEIADRLGITVDRVREILRISQDPVSLET 255

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ SHLGDFI D++A +P ++A +  L+E  + +L +LTPREE+VLR+RFG+    
Sbjct: 256 PIGEEEDSHLGDFIPDEDAPAPAEAASRTLLKEQLSEILGTLTPREEKVLRLRFGLEDGR 315

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 316 PRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 358



 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 38/159 (23%), Positives = 67/159 (42%), Gaps = 8/159 (5%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            +D    ++I   +Q G +T +E+   L   +  ++++        +  I +VD      
Sbjct: 1   MADSKINELINHGKQNGKLTTKEITDVLEELDFDADEINKLYDDFESSNIEIVD------ 54

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            + S D    ++     S   +    S   + DDPV++YL+E+G + LL+ E EI +A R
Sbjct: 55  -DFSADEDLDSALDFTDSDDFESSLSSEGIAIDDPVKIYLKEIGRVPLLTAEEEIELATR 113

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  G       L E+ L     I  R  +  G   L  I
Sbjct: 114 MAQGDKYARKRLSEANLRLVVSIAKRY-VGRGMQFLDLI 151


>gi|769798|emb|CAA60113.1| sigma 42 [Enterococcus faecalis]
          Length = 368

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 164/306 (53%), Positives = 211/306 (68%), Gaps = 7/306 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVSMVR 435
           DP   S  KD  E E          + +KI    R  +K I     ++ +E   +   + 
Sbjct: 66  DPSEHSLKKDEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALKIE 125

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+K
Sbjct: 126 ---EGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFK 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + REPTPEEI  +
Sbjct: 183 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRMQRNLLQDLGREPTPEEIGAE 242

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    
Sbjct: 243 MDLPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAEHAAYELLKEQLED 302

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 303 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 363 LKDFLE 368



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 73/190 (38%), Gaps = 15/190 (7%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + +    IK  + +G V  ++L   L  P  + +E ME  +  + + GI+VVD +    
Sbjct: 9   YEAAVGTFIKENKPKGTVVYDDLANQLATPYTLDAEAMEKLIQKVEDAGISVVDENGDPS 68

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   +                +          +DPVRMYL+E+G ++LL+   E+ +A +
Sbjct: 69  EHSLKK-----DEKEAEKAQAEDLSAPTGVKINDPVRMYLKEIGRVQLLTAAEEVELALK 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 124 IEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 174

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 175 FDYRKGFKFS 184


>gi|269836760|ref|YP_003318988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786023|gb|ACZ38166.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 538

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 175/518 (33%), Positives = 265/518 (51%), Gaps = 26/518 (5%)

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
                 +R II+     G  S                 D+   +  +         E A 
Sbjct: 36  RADELAIRRIIERAREQGYLSAEELADVASAPGGAAAVDAITSQLAEMNVPVLDPAEDAP 95

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ----LRPKVMCALDEIAEV 290
            +      + D+   + E  + +L     D    +   E      L  +   AL +  E 
Sbjct: 96  DLPDVAAVEADNDLFSTELSDVDLSGVSLDDPVRIYLREIGRVQLLTGEQEVALAQAMER 155

Query: 291 YRELRSLQDNAVNGQKDEKSSV-----KCKVLKEK--LVKLVGSLSLNQSRIDLLVEQLY 343
              +  LQ     G  D  S+        + L+E   L       +            L 
Sbjct: 156 GDYIFRLQQELQGGNGDRPSAAGIGWTVYRTLREGWPLTIAFYRAAFPDQPATTKTRVLA 215

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
            +       E  +  + + +G+ R+   E  + R ++                + +   +
Sbjct: 216 AVLPLTEEMEPAIQAVGEEFGVSREELEESLRRRRIE---------------YDLLPSPI 260

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             +++  +   +      +   +   + +   +      IA+K++ EANLRLV+SVAKKY
Sbjct: 261 QELIRPVDAFPTDEEVWELLRRDEAALQARWEEFVVRGDIARKKLTEANLRLVVSVAKKY 320

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RG+  LDL+QEGN+GL++A EKF    G+KFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 321 GGRGMSMLDLVQEGNLGLIRAVEKFQHHKGFKFSTYATWWIRQAITRAIADQARTIRIPV 380

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM ++I++++RT+RR+  ++ REPT EEIA ++ +P + VR++LKI++EP+SLE PIG+E
Sbjct: 381 HMVEQINRLIRTSRRLQQELGREPTSEEIAAEMGLPPDKVREILKISQEPVSLEMPIGEE 440

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S+LGDFIED  A++P D+A    L+E    VL SL  RE RVL +RFG+      TLE
Sbjct: 441 EDSNLGDFIEDSKALAPSDAASLKLLKEQVDDVLGSLGDRERRVLELRFGLDDGRTRTLE 500

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVG++F VTRERIRQIEAKA+RKL+HPSRSKKLR +L+
Sbjct: 501 EVGREFGVTRERIRQIEAKALRKLRHPSRSKKLRDYLE 538



 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 35/140 (25%), Positives = 73/140 (52%), Gaps = 6/140 (4%)

Query: 17  DSDDSLVFDFSDD--SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  D +  D   D  + +++I+ AR++GY++ EEL          +  ++   + L+ M 
Sbjct: 26  EGADGISGDDRADELAIRRIIERAREQGYLSAEELADV-ASAPGGAAAVDAITSQLAEMN 84

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           + V+D  +   +     +++  +   ++ +      D +  S DDPVR+YLRE+G ++LL
Sbjct: 85  VPVLDPAEDAPDLPDVAAVEADNDLFSTEL---SDVDLSGVSLDDPVRIYLREIGRVQLL 141

Query: 135 SREGEIAIAKRIEAGRAMMM 154
           + E E+A+A+ +E G  +  
Sbjct: 142 TGEQEVALAQAMERGDYIFR 161


>gi|281417615|ref|ZP_06248635.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
 gi|281409017|gb|EFB39275.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
          Length = 358

 Score =  233 bits (595), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 209/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +     + AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 89  VRMYLKEIGKVPLLTAEEEIELAHRIEQ---GDAEAKRRLAEANLRLVVSIAKRYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKLIRVSRQLLQELGREPHPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 266 GDFIPDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 49/152 (32%), Positives = 70/152 (46%), Gaps = 13/152 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I+  +Q+G +T +E+       ++  EQ+E     L NMGI+VV   + E E+     
Sbjct: 13  ELIEKGKQKGMLTYQEIMDAFEEVDIDPEQIEKIYETLENMGIDVVGDIEAEMEDIQLTE 72

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            DL                    S DDPVRMYL+E+G + LL+ E EI +A RIE G A 
Sbjct: 73  DDLD------------LSIPEGISIDDPVRMYLKEIGKVPLLTAEEEIELAHRIEQGDAE 120

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  R  +  G   L  I
Sbjct: 121 AKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 151


>gi|313618909|gb|EFR90770.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL S4-378]
          Length = 374

 Score =  233 bits (595), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEVGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 45/170 (26%), Positives = 78/170 (45%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + + +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTQNTKPVAELNVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIE G       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEVGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|318066909|emb|CBY89069.1| RNA polymerase sigma70 factor [Chromohalobacter marismortui]
          Length = 367

 Score =  233 bits (595), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 121/397 (30%), Positives = 180/397 (45%), Gaps = 52/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLEAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D ++ +   +  +  G+   
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADVAEPEPERNALD--GEASE 125

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
               ++++ +     PE A      + E  + +   +                       
Sbjct: 126 EEDDAEEEETGGGPDPEEARARFEQIREQNERAKAAID---------------------- 163

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K    S +    + +L +L   + L     + LV Q+    ++I   
Sbjct: 164 -------------KHGLGSSEANQEQARLAELFSPIKLVPKHFERLVGQVRISIEQIRGQ 210

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++   +   + R  F+    G E D  W+   K      +   V      IL+ + 
Sbjct: 211 EKAIMQVFVKQAKVPRKTFIGSFPGAESDLEWLDRFKAKHAK-YAERVEPFRADILRAQR 269

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 270 KIGFEEEMVRLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 329

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 330 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|256004390|ref|ZP_05429371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255991674|gb|EEU01775.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|316940353|gb|ADU74387.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 358

 Score =  233 bits (595), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 209/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +     + AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 89  VRMYLKEIGKVPLLTAEEEIELAHRMEQ---GDAEAKRRLAEANLRLVVSIAKRYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKLIRVSRQLLQELGREPHPEEIAKEMNMPVEKVREIMKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 266 GDFIPDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 48/152 (31%), Positives = 70/152 (46%), Gaps = 13/152 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I+  +Q+G +T +E+       ++  EQ+E     L NMGI+VV   + E E+     
Sbjct: 13  ELIEKGKQKGMLTYQEIMDAFEEVDIDPEQIEKIYETLENMGIDVVGDIEAEMEDIQLTE 72

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            DL                    S DDPVRMYL+E+G + LL+ E EI +A R+E G A 
Sbjct: 73  DDLD------------LSIPEGISIDDPVRMYLKEIGKVPLLTAEEEIELAHRMEQGDAE 120

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  R  +  G   L  I
Sbjct: 121 AKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 151


>gi|318066929|emb|CBY89079.1| RNA polymerase sigma70 factor [Halomonas boliviensis]
          Length = 368

 Score =  233 bits (595), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 122/395 (30%), Positives = 180/395 (45%), Gaps = 47/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   +  ++ E D   E E    S  
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEPESELEEDVEGDSDDEDEDSTAS-- 136

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                   +    PE A      + E         +                        
Sbjct: 137 --------EGGPDPEEARARFEQIREQNALVEAAFA------------------------ 164

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L  L   + L     + LV Q+    +++   E 
Sbjct: 165 -----------KHGRGSAELKSEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEK 213

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E    W+   +   + ++ + +      I + + +I
Sbjct: 214 AVMQLCVKKAKVPRKTFIKSFPGNESRKTWLDDFQA-AQSKYADRLEPLRADIARAQRKI 272

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +S+++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 273 AFEEDMVQLSVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 332

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 333 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|152965499|ref|YP_001361283.1| RNA polymerase sigma factor [Kineococcus radiotolerans SRS30216]
 gi|151360016|gb|ABS03019.1| RNA polymerase, sigma 70 subunit, RpoD family [Kineococcus
           radiotolerans SRS30216]
          Length = 502

 Score =  233 bits (595), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 137/297 (46%), Positives = 188/297 (63%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV------------------------RKGECEASIA 444
           +++ +K I     ++  +   +   +                             +   A
Sbjct: 206 VKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEEKLHSGEDIDSIFKRELWWISEDGRRA 265

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW+
Sbjct: 266 KNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 325

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V 
Sbjct: 326 RQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVV 385

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ RE
Sbjct: 386 EVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSERE 445

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 446 AGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 502



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/39 (48%), Positives = 28/39 (71%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           S   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 197 STAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEAGL 235


>gi|167630065|ref|YP_001680564.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
 gi|167592805|gb|ABZ84553.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
          Length = 371

 Score =  233 bits (595), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGRVPLLSAEEEIELAKRME---EGDEAAKRRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +  REP PEEIAK++ +PVE VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 219 INKLIRVSRQLLQEYGREPMPEEIAKEMDIPVERVREIMKIAQEPVSLETPIGEEEDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A +P ++A    L+E    VL +LT RE +VLR+RFG+      TLEEVG++
Sbjct: 279 GDFIEDQDAPAPAEAASFILLKEQLEEVLETLTAREMKVLRLRFGLDDGRSRTLEEVGQE 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 339 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 371



 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 46/151 (30%), Positives = 68/151 (45%), Gaps = 5/151 (3%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +I   +++G +T +E+   L   E++++Q++D    L NMGI+VV     E+ E      
Sbjct: 19  LIAKGKKKGVLTYQEIMDALQGVEMTADQVDDIYEQLGNMGIDVV----PENTESESLDK 74

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                                   DDPVRMYL+E+G + LLS E EI +AKR+E G    
Sbjct: 75  AEEPIIREEEEIEVDLSVPEGVGIDDPVRMYLKEIGRVPLLSAEEEIELAKRMEEGDEAA 134

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREI 184
              L E+ L     I  R  +  G   L  I
Sbjct: 135 KRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 164


>gi|318066955|emb|CBY89092.1| RNA polymerase sigma70 factor [Halomonas magadiensis]
          Length = 370

 Score =  233 bits (594), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 122/395 (30%), Positives = 187/395 (47%), Gaps = 45/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVASILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   + S + + D   + + +  +A 
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAETPEPEVDTELSDDDDIDSDDDDDDEDTTA- 137

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                  S+    PE A+     + E        L+                        
Sbjct: 138 -------SEGGPDPEEAKARFEQIREQNAAVEAALA------------------------ 166

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + K  + +L +L   + L     + LV Q+    +++   E 
Sbjct: 167 -----------KFGRGSSELKAEQARLAELFSPIKLVPKHFERLVGQIRISVEQVRAQEK 215

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E D  W+  A    + ++ + +      I + + +I
Sbjct: 216 AVMQLCVKKAKVPRKTFIKSFPGHESDSSWLD-AFQEAQPKYADRLEPLRADIARSQRKI 274

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +++++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 275 AFEEDMVQLTVADLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 334

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 335 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 369


>gi|239637627|ref|ZP_04678599.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|239596845|gb|EEQ79370.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|330686029|gb|EGG97652.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU121]
          Length = 367

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      IAK  + EANLRLV+S+AK+Y  RG+
Sbjct: 98  VRMYLKEIGRVDLLSAQEEIELAKRIEQ---GDEIAKSRLAEANLRLVVSIAKRYVGRGM 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 155 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 215 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 275 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 335 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 367



 Score =  101 bits (252), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 46/157 (29%), Positives = 78/157 (49%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   E+ S+ M+D    L++  I +V+  D  D +
Sbjct: 19  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFEMDSDMMDDFFDQLNDNDITLVNEKDHSDTD 78

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G ++LLS + EI +AKRIE
Sbjct: 79  AKLNPNDLSA--------------PPGVKINDPVRMYLKEIGRVDLLSAQEEIELAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 125 QGDEIAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 160


>gi|47679387|gb|AAT36674.1| DNA-directed RNA polymerase sigma A subunit [Oenococcus oeni PSU-1]
          Length = 465

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 161/359 (44%), Positives = 225/359 (62%), Gaps = 20/359 (5%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+    +LN  +ID L+E++ D    I+  +G     +                      
Sbjct: 126 KMAKPFALNADQIDKLIEKVEDAGISIVDEDGNPSEKSLKTK-----------SNNPSQE 174

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
            +S A   P+G   N           +R  +K I   + ++  +   I   + KG  +  
Sbjct: 175 ELSQASSAPKGVKIN---------DPVRMYLKEIGRVSLLNADQEVAIAKRIEKGGSDGE 225

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A++E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EKFD+  G+KFSTYA W
Sbjct: 226 RARQELAEANLRLVVSIAKRYVGRGMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATW 285

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R +   + R+P PEEI  ++ +  + 
Sbjct: 286 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRTLIQDLGRDPMPEEIGAEMELTADK 345

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ KI +EP+SLETPIG+E+ SHLGDFIED    SP++S     L++    VL +LT 
Sbjct: 346 VREIQKIAQEPVSLETPIGEENDSHLGDFIEDNEGESPIESTSDQMLKDQLEEVLGTLTE 405

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 406 REENVLRLRFGLEDGKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFME 464



 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 62/216 (28%), Positives = 91/216 (42%), Gaps = 19/216 (8%)

Query: 6   KRNRDSDSEHEDSDDSLVFDF--SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQ 62
           K   +S S  + S  +  FD      S K  IK  ++ G V  ++L N    P  ++++Q
Sbjct: 78  KSKDNSKSGEKSSSAATAFDEKAYAKSLKAFIKKNKKSGQVVYDDLENKMAKPFALNADQ 137

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ++  +  + + GI++VD    ED   SE SL   S+  +     Q          +DPVR
Sbjct: 138 IDKLIEKVEDAGISIVD----EDGNPSEKSLKTKSNNPSQEELSQASSAPKGVKINDPVR 193

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTT 179
           MYL+E+G + LL+ + E+AIAKRIE G          L E+ L     I  R  +  G  
Sbjct: 194 MYLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRY-VGRGMH 252

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            L  I         E   G     E   Y K    S
Sbjct: 253 FLDLI--------QEGNMGLMKAVEKFDYTKGFKFS 280


>gi|328957491|ref|YP_004374877.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
 gi|328673815|gb|AEB29861.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
          Length = 373

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E    V +  K E     A++ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLTAAEE---VELAIKIEEGDQEARQRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP ++A    L+E    VL +LT REE VLR+RFG+    + TLE+VGK 
Sbjct: 281 GDFIEDHDATSPAENAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRNRTLEDVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 373



 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 42/190 (22%), Positives = 70/190 (36%), Gaps = 13/190 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            D   K +IK  +  G +  +EL N    P  +++ +M+  +  + + G+        + 
Sbjct: 12  YDSEVKSLIKEYKAAGTIHYDELTNKIATPFSLNAVKMDQLIQTIEDAGVG---VVGDDG 68

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              +         A   +   +          +DPVRMYL+E+G + LL+   E+ +A +
Sbjct: 69  GPTARQLKLKEMKAEREAEKPEDLTAPPGVKINDPVRMYLKEIGRVNLLTAAEEVELAIK 128

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G       L E+ L     I  R  +  G   L  I         E   G     E 
Sbjct: 129 IEEGDQEARQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEK 179

Query: 206 HSYQKREDSS 215
             Y+K    S
Sbjct: 180 FDYKKGFKFS 189


>gi|306833811|ref|ZP_07466936.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
 gi|304424005|gb|EFM27146.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
          Length = 369

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAV---ATGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 66/330 (20%), Positives = 117/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRNHKKNGTAVDDEVTEKLVIPFSLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSTKYIVEEPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVATG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLQAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|332686632|ref|YP_004456406.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
 gi|332370641|dbj|BAK21597.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
          Length = 369

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRVQLLTAEEEVELALKIE---EGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 277 GDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 337 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 369



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/193 (24%), Positives = 75/193 (38%), Gaps = 15/193 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
            +    +    IK  +Q+G V  ++L N    P  +S+ +ME  +  + + GI++VD   
Sbjct: 7   MEKYKQAVSAFIKENKQKGVVVYDDLANKLATPFTLSAGEMEKLIQQIEDNGISIVDETG 66

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
              E                   L+          +DPVRMYL+E+G ++LL+ E E+ +
Sbjct: 67  EPSEHSL-----KKDEKEAKKAELEDLSAPTGIKINDPVRMYLKEIGRVQLLTAEEEVEL 121

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           A +IE G       L E+ L     I  R  +  G   L  I         E   G    
Sbjct: 122 ALKIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKA 172

Query: 203 TEGHSYQKREDSS 215
            E   Y+K    S
Sbjct: 173 VEKFDYRKGFKFS 185


>gi|225412271|ref|ZP_03761460.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
 gi|225042189|gb|EEG52435.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
          Length = 376

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     + +      + + R+ E     A K + E+NLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGKIPLLDMEAE---IRLARQMEEGDREAAKRLAESNLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 163 QFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVEN 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VRT+R++  ++ REPT EEIA +  M VE V ++LK+++EP+SLETPIG+E+ SHL
Sbjct: 223 INRLVRTSRQLLQELGREPTTEEIAARAEMSVERVSEILKMSQEPVSLETPIGEEEDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L E    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 283 GDFIQDDNVTVPQDAATYTLLHEQLMEVLTTLTEREQKVLRLRFGLDDGRPRTLEEVGRE 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 343 FKVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 375



 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 37/145 (25%), Positives = 59/145 (40%), Gaps = 1/145 (0%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
           ++  +  +E+  FL      ++Q++     L    ++V+  D  +D +      +     
Sbjct: 25  KKNVLEYQEIMDFLGTPPPDADQLDRIFEFLDQNSVDVLRVDGKDDLDPDLFLEEELEEE 84

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               V           S  DPVRMYL+E+G I LL  E EI +A+++E G       L E
Sbjct: 85  EEIDVEHIDLSVPEGISLQDPVRMYLKEIGKIPLLDMEAEIRLARQMEEGDREAAKRLAE 144

Query: 160 SPLTFQALIIWRDELNDGTTLLREI 184
           S L     I  R  +  G   L  I
Sbjct: 145 SNLRLVVSIAKRY-VGRGMQFLDLI 168


>gi|317473637|ref|ZP_07932926.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
 gi|316898927|gb|EFV20952.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
          Length = 364

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 95  VRMYLKEIGKVPLLSADEEIRLAQRME---EGDEEAKKKLAEANLRLVVSIAKRYVGRGM 151

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 152 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 211

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA+++ +PV+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 212 INKLIRVSRQLLQELGREPLPEEIAEEMDIPVDRVREILKISQEPVSLETPIGEEEDSHL 271

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E  + VL +LT RE++VLR+RFG+  +   TLEEVGK+
Sbjct: 272 GDFIQDDNVPVPADAAAFTLLKEQLSEVLGTLTEREQKVLRLRFGLDDSRARTLEEVGKE 331

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 332 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 364



 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 42/166 (25%), Positives = 76/166 (45%), Gaps = 11/166 (6%)

Query: 20  DSLVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           D  +  FS +    +++L ++ + ++   ++  +    +++S+ ME     L   G++V+
Sbjct: 2   DETMLQFS-EKLAGLVELGKKNKNFLEYAQIETYFKDFKLTSDMMEAIFDYLEQNGVDVL 60

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
              + ED+E  E   ++   A                S +DPVRMYL+E+G + LLS + 
Sbjct: 61  TIPEGEDDEDLEIKEEIEEEAD--------LTIPDGVSIEDPVRMYLKEIGKVPLLSADE 112

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI +A+R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 113 EIRLAQRMEEGDEEAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 157


>gi|167747159|ref|ZP_02419286.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
 gi|167654119|gb|EDR98248.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
          Length = 370

 Score =  233 bits (594), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLSADEEIRLAQRME---EGDEEAKKKLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA+++ +PV+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPLPEEIAEEMDIPVDRVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E  + VL +LT RE++VLR+RFG+  +   TLEEVGK+
Sbjct: 278 GDFIQDDNVPVPADAAAFTLLKEQLSEVLGTLTEREQKVLRLRFGLDDSRARTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 338 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 370



 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 43/170 (25%), Positives = 77/170 (45%), Gaps = 11/170 (6%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
             S D  +  FS +    +++L ++ + ++   ++  +    +++S+ ME     L   G
Sbjct: 4   RKSMDETMLQFS-EKLAGLVELGKKNKNFLEYAQIETYFKDFKLTSDMMEAIFDYLEQNG 62

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           ++V+   + ED+E  E   ++   A                S +DPVRMYL+E+G + LL
Sbjct: 63  VDVLTIPEGEDDEDLEIKEEIEEEAD--------LTIPDGVSIEDPVRMYLKEIGKVPLL 114

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           S + EI +A+R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 115 SADEEIRLAQRMEEGDEEAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|318066933|emb|CBY89081.1| RNA polymerase sigma70 factor [Halomonas campisalis]
          Length = 367

 Score =  233 bits (594), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 118/395 (29%), Positives = 181/395 (45%), Gaps = 48/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAWLPGAVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+                  ++   +E    +      E   
Sbjct: 79  QDEEAPGRLSDLFSGFIDPD-----------EGIPGVAEAEVPEEEPRAESEGDGDEDDD 127

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           + + ++ +     PE A      + E  + +   ++A                       
Sbjct: 128 EDAGEEETTGGPDPEEARARFEQIRELNERARAAIAA----------------------- 164

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         + S + +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 165 ------------HGRGSPEARAELTRLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEK 212

Query: 355 ELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E    W+        G++ + ++     I + +  I
Sbjct: 213 AVMQLFVKKAKVPRKTFIKAFPGNESRQEWLDEFIA-AHGKYADRLSAMRGDIQRAQRRI 271

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +++ E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 272 AFEEDMVQLAVPELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 331

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 332 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|239931428|ref|ZP_04688381.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 430

 Score =  233 bits (594), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 131/296 (44%), Positives = 191/296 (64%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 135 RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSRLAHDLDRLVVMGRMAK 194

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 195 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 254

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +  REPTPEE+A  L +P E V +
Sbjct: 255 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGREPTPEEVAAHLDLPPERVGE 314

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 315 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 374

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 375 KVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 430



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 25/55 (45%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +            +      + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 109 DAREPAEPAETPPPRPETGGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGL 163


>gi|216733|dbj|BAA01038.1| RNA polymerase sigma factor [Lactococcus lactis]
          Length = 340

 Score =  233 bits (594), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 189 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 249 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 308

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 309 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 340



 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/141 (24%), Positives = 55/141 (39%), Gaps = 16/141 (11%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           + +ED    + + GI++VD    +D   S  +L                +   +   DDP
Sbjct: 13  DALEDLFKQIQDAGISIVD----KDGNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDP 68

Query: 121 VRMYLREMGSIELLSREGEIAIAKRI---EAGRAMMMASLCESPLTFQALIIWR------ 171
           VRMYL+E+G   L+S + E  +A+ I     G       L E+ L     I  R      
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 128

Query: 172 ---DELNDGTTLLREIIDLEA 189
              D + +G   L + +D   
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFD 149


>gi|319745370|gb|EFV97681.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           agalactiae ATCC 13813]
          Length = 380

 Score =  233 bits (594), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V        +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 110 VRMYLKEIGVVPLLTNEEEKELAVAV---AEGDLMAKQRLAEANLRLVVSIAKRYVGRGM 166

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 167 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 226

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 227 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 286

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 287 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 346

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 347 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 379



 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  +++G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 25  VADFIRNHKKQGTAIDDEVTEKLVIPFVLDADQIDDLLERLTDGGISITD------KEGN 78

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 79  PSTKYVVEGPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEG 138

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 139 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 189

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 190 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 249

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A    + P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 250 IAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 305

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 306 -------VLREQLDEVLDTLTDREENVLRL 328


>gi|70726356|ref|YP_253270.1| RNA polymerase sigma factor RpoD [Staphylococcus haemolyticus
           JCSC1435]
 gi|68447080|dbj|BAE04664.1| RNA polymerase sigma factor [Staphylococcus haemolyticus JCSC1435]
          Length = 368

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 160/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    N ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPNDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      IAK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 82/175 (46%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I   ++ G+++ EE+   L   ++ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIDKGKKEGHLSHEEIAEKLQNFDMDSDQMDDFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I++V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDISLVNEKDSSDTDEKLNPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AKRIE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|297617785|ref|YP_003702944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297145622|gb|ADI02379.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 361

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 164/376 (43%), Positives = 232/376 (61%), Gaps = 27/376 (7%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
             EK   K  +  +++   +  + L   +I+ + E L  +  R+  +             
Sbjct: 13  LTEKGKKKKNLTYDEISDDLQGIKLEADQIEDIYEHLQAMGIRVGDST------------ 60

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
                 +  +  E         +          V   V+    +R  +K I     +S  
Sbjct: 61  ------DEFEVEET------PVEGEAAETEDVLVPEGVEIDDPVRMYLKEIGRVPLLSAE 108

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   +         AK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA 
Sbjct: 109 EEIELAKRIE---NGDEDAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLMKAV 165

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +  K+ R
Sbjct: 166 EKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLSRIQRALLQKLGR 225

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPTP E+A+++ +PVE V +++K+ +EP+SLETPIG+ED SHLGDFI D++A SP +SA 
Sbjct: 226 EPTPAEVAEEMDIPVERVMEIMKVAQEPVSLETPIGEEDDSHLGDFITDEDAESPEESAS 285

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LRE    +L++LT REE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+R
Sbjct: 286 FVLLREHLDGILSTLTDREEKVLRLRFGLDDGRPRTLEEVGQEFGVTRERIRQIEAKALR 345

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSKKL+ +++
Sbjct: 346 KLRHPSRSKKLKDYIE 361



 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 44/156 (28%), Positives = 70/156 (44%), Gaps = 9/156 (5%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           ++   + +  +++  +T +E++  L   ++ ++Q+ED    L  MGI V D  D  + E 
Sbjct: 8   EAISALTEKGKKKKNLTYDEISDDLQGIKLEADQIEDIYEHLQAMGIRVGDSTDEFEVE- 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                   +     +   +          DDPVRMYL+E+G + LLS E EI +AKRIE 
Sbjct: 67  -------ETPVEGEAAETEDVLVPEGVEIDDPVRMYLKEIGRVPLLSAEEEIELAKRIEN 119

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  R  +  G   L  I
Sbjct: 120 GDEDAKRKLVEANLRLVVSIAKRY-VGRGMLFLDLI 154


>gi|253580849|ref|ZP_04858112.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847919|gb|EES75886.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 375

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGKVPLLSAEEEIELAKRME---NGDEAAKKRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ M VE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 223 INKLIRVSRQLLQELGREPTPEEIAKEMDMSVERVREILKISQEPVSLETPIGEEEDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL++LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 283 GDFIQDDNVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGLDDGRARTLEEVGKE 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 343 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 375



 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 43/160 (26%), Positives = 71/160 (44%), Gaps = 5/160 (3%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGDDLE 84
           +   ++++LA+++   +  +E+N F     +  EQME     L   G++V+   D +  +
Sbjct: 10  EKLVELLELAKKKKNVLEYQEINDFFKDQPLGVEQMEKVFDFLEASGVDVLRITDSNADD 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                +D+           +           S +DPVRMYL+E+G + LLS E EI +AK
Sbjct: 70  MILDDDDADIDKLDEEEIELDKIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEEEIELAK 129

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 130 RMENGDEAAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|318066903|emb|CBY89066.1| RNA polymerase sigma70 factor [Chromohalobacter beijerinckii]
          Length = 367

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 120/397 (30%), Positives = 183/397 (46%), Gaps = 52/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ LL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVGLLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSVLDAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  +     + ++  GD   
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEAEIPEPVPEQNAED--GDDSE 125

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            A+ ++++ +     PE A+     + E  + +   +                       
Sbjct: 126 DAEDAEEEETGGGPDPEEAKARFEQIREQNERAKAAID---------------------- 163

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K    S      + +L +L   + L     + LV Q+    ++I   
Sbjct: 164 -------------KHGLGSSNADQEQARLAELFSPIKLVPKHFERLVGQVRISIEQIRGQ 210

Query: 353 EGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  ++++  +   + R  F+    G E D  W+   +     ++   +      IL+ + 
Sbjct: 211 EKAIMQIFVKQAKVPRKTFIGSFPGAESDLEWLDRFQ-TKHSKYAERLEPFRADILRAQR 269

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + ++  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 270 KIGFEEEMVRLPVTNIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 329

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 330 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|293365255|ref|ZP_06611972.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|306829363|ref|ZP_07462553.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
 gi|291316705|gb|EFE57141.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|304428449|gb|EFM31539.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
          Length = 369

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 118/333 (35%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D      I+  ++ G  T +E+N+ L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVADFIRNHKKTGTATDDEINSSLVIPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|318066989|emb|CBY89109.1| RNA polymerase sigma70 factor [Kushneria marisflavi]
          Length = 373

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 130/395 (32%), Positives = 182/395 (46%), Gaps = 42/395 (10%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P +  +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALASLPGSVDSILQAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   D + + + DD  + E   E   
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGVPGVAEVEEPIPEVVADDADDSDSDDDSDEEDSDEEDD 138

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             S+         PE A      + E  + +   + A                       
Sbjct: 139 TASE-----GGPDPELARVRFEQIREQNEQTKAAIEA----------------------- 170

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                          SS + +  + +L +L   + L     + LV QL     +I   E 
Sbjct: 171 ------------HGLSSSQARSEQARLAELFSPIKLVPRHFERLVGQLRLSVGQIREQEK 218

Query: 355 ELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L    G + R  F+    GRE D  W+    +       N +      I + + +I
Sbjct: 219 TIMQLCVKRGKVPRKTFIASFPGRESDSSWIDDFIERNSKHASN-IEPLRADIERAQRKI 277

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + +SE + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 278 AFEEELALLPVSELKDINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 337

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 338 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 372


>gi|19862496|sp|Q04506|RPOD_LACLA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 386

 Score =  233 bits (593), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 115 VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 174

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 175 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 234

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 235 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 294

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 295 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 354

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 355 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 386



 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 72/189 (38%), Gaps = 17/189 (8%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSN 72
           E +++ D+      + + K  I   +  G    EE+   L     +  + +ED    + +
Sbjct: 11  EVKENGDTFNVKAYEKAVKSYITKRKPLGEALDEEIMDELSVKFGIVDDALEDLFKQIQD 70

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            GI++VD    +D   S  +L                +   +   DDPVRMYL+E+G   
Sbjct: 71  AGISIVD----KDGNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDPVRMYLKEIGRYP 126

Query: 133 LLSREGEIAIAKRI---EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTL 180
           L+S + E  +A+ I     G       L E+ L     I  R         D + +G   
Sbjct: 127 LISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFLDLIQEGNMG 186

Query: 181 LREIIDLEA 189
           L + +D   
Sbjct: 187 LMKAVDKFD 195


>gi|309800318|ref|ZP_07694490.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
 gi|308116065|gb|EFO53569.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
          Length = 369

 Score =  233 bits (593), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 117/333 (35%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  ++ G  T +E+N  L  P  +  E +E+ +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKKTGTATDDEINNALVIPFTLDVEGIENLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSTEEEPELTDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|270291312|ref|ZP_06197534.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304385062|ref|ZP_07367408.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
 gi|270280158|gb|EFA25994.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304329256|gb|EFL96476.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
          Length = 379

 Score =  233 bits (593), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 172/389 (44%), Positives = 237/389 (60%), Gaps = 30/389 (7%)

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           E +   +  +  QK E      K+ ++    L+    L    +D L++++ D    ++  
Sbjct: 21  EFKKAVNQIIKAQKSEHKVKYTKLTRD----LIDKFKLTDEDVDDLIQRIEDAGISVVDE 76

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
            G+                +  + +E+    +   K     +  + V          R  
Sbjct: 77  NGDPSE-------------KALKAQEISKEELDDTKAPAGVKINDPV----------RMY 113

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K I   + ++  E   +   + K       AK+E+ EANLRLV+S+AK+Y  RG+QFLD
Sbjct: 114 LKEIGRVSLLTADEEVALALRIEK---GDERAKQELAEANLRLVVSIAKRYVGRGMQFLD 170

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+
Sbjct: 171 LIQEGNMGLMKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 230

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R  R++   + REP PEEI  ++ MP + VR++LKI +EP+SLETPIG+ED SHLGDFI
Sbjct: 231 IRIQRQLLQDLGREPMPEEIGAEMDMPSDKVREILKIAQEPVSLETPIGEEDDSHLGDFI 290

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VT
Sbjct: 291 EDQEATSPADHAAYELLKEQLEGVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVT 350

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 351 RERIRQIEAKALRKLRHPSRSKQLKDFLD 379



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 54/214 (25%), Positives = 85/214 (39%), Gaps = 20/214 (9%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELN-AFLPPDEVSSE 61
           +  K++     + E    S  F     +  ++IK  +    V   +L    +   +++ E
Sbjct: 1   MASKKSEIKRKKSESIISSPEF---KKAVNQIIKAQKSEHKVKYTKLTRDLIDKFKLTDE 57

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            ++D +  + + GI+VVD       E  + S     +   S   L   K  A    +DPV
Sbjct: 58  DVDDLIQRIEDAGISVVD-------ENGDPSEKALKAQEISKEELDDTKAPAGVKINDPV 110

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYL+E+G + LL+ + E+A+A RIE G       L E+ L     I  R  +  G   L
Sbjct: 111 RMYLKEIGRVSLLTADEEVALALRIEKGDERAKQELAEANLRLVVSIAKRY-VGRGMQFL 169

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
             I         E   G     E   YQK    S
Sbjct: 170 DLI--------QEGNMGLMKAVEKFDYQKGFKFS 195


>gi|222152854|ref|YP_002562031.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
 gi|222113667|emb|CAR41594.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
          Length = 369

 Score =  233 bits (593), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKELAIAV---AAGDVDAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  +Q G    +E+   L  P E+ ++Q++D +  L++ GI++ D D      GS
Sbjct: 14  VADFIRNHKQAGTAIDDEVTEKLVIPFELDADQIDDLLERLTDGGISITDKD------GS 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG
Sbjct: 68  PSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKELAIAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DVDAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|83589488|ref|YP_429497.1| RNA polymerase sigma factor RpoD [Moorella thermoacetica ATCC
           39073]
 gi|83572402|gb|ABC18954.1| RNA polymerase, sigma 70 subunit, RpoD [Moorella thermoacetica ATCC
           39073]
          Length = 361

 Score =  233 bits (593), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 171/384 (44%), Positives = 240/384 (62%), Gaps = 27/384 (7%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q   +  +  EK   +  +   +++  +  + L+  +ID + EQL  +   ++    EL 
Sbjct: 5   QQKQMVKELIEKGKSQGSLTYSEIMDALQGIELSPEQIDDIYEQLGHMGIEVVPEAAELE 64

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            L +          E  +  E D                  +   V     +R  +K I 
Sbjct: 65  ALEK----------EDSEAGETDLD--------------LSIPENVAIDDPVRMYLKEIG 100

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               ++  E   +   +         AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEG
Sbjct: 101 RVPLLTPEEEIELAKRME---AGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEG 157

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R
Sbjct: 158 NLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQR 217

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  ++ REPTPEEIA ++ +PVE VR++ KI +EP+SLETPIG+E+ SHLGDFIED++A
Sbjct: 218 QLLQELGREPTPEEIAHEMDIPVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDEDA 277

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            +P ++A    LRE    VL SLTPRE+RVLR+RFG+      TLEEVG++F VTRERIR
Sbjct: 278 QAPAEAASFMLLREQLEEVLNSLTPREKRVLRLRFGLDDGRARTLEEVGQEFGVTRERIR 337

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 338 QIEAKALRKLRHPSRSKKLKDYLE 361



 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 78/354 (22%), Positives = 134/354 (37%), Gaps = 33/354 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I+  + +G +T  E+   L   E+S EQ++D    L +MGI VV      
Sbjct: 4   EQQKQMVKELIEKGKSQGSLTYSEIMDALQGIELSPEQIDDIYEQLGHMGIEVVPE---- 59

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               + +   L    S +           + + DDPVRMYL+E+G + LL+ E EI +AK
Sbjct: 60  ----AAELEALEKEDSEAGETDLDLSIPENVAIDDPVRMYLKEIGRVPLLTPEEEIELAK 115

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           R+EAG       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 116 RMEAGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVE 166

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
              Y+K    S        Q     I   A+  +     V++  +      + L E   +
Sbjct: 167 KFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRE 226

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ----------KDEKSSVKC 314
                 A E  +  + +  + +IA+    L +      +            +    +   
Sbjct: 227 PTPEEIAHEMDIPVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDEDAQAPAEAASF 286

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
            +L+E+L +++ SL+  + R+  L   L D           L  + Q +G+ R+
Sbjct: 287 MLLREQLEEVLNSLTPREKRVLRLRFGLDD------GRARTLEEVGQEFGVTRE 334


>gi|270292885|ref|ZP_06199096.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|306825379|ref|ZP_07458719.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315613017|ref|ZP_07887928.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|322374450|ref|ZP_08048964.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|331266528|ref|YP_004326158.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
 gi|270278864|gb|EFA24710.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|304432317|gb|EFM35293.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315315127|gb|EFU63168.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|321279950|gb|EFX56989.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|326683200|emb|CBZ00818.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
          Length = 369

 Score =  233 bits (593), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 118/333 (35%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D      I+  ++ G  T +E+N+ L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVADFIRNHKKTGTATDDEINSSLVIPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|227495998|ref|ZP_03926309.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
 gi|226834486|gb|EEH66869.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
          Length = 541

 Score =  233 bits (593), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 136/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++ +E   +   +                              +   
Sbjct: 244 VKDYLKQIGKVALLNAAEEVELAKRIEAGMYAEYLLGTEGNELDAKYRRELHWISNDGQR 303

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 304 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 363

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 364 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKV 423

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E    VL +L+ R
Sbjct: 424 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHAVLDTLSER 483

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 484 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 541



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 30/52 (57%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       +K     +T DPV+ YL+++G + LL+   E+ +AKRIEAG 
Sbjct: 222 SDSDEGDEPAQKVVTAGATADPVKDYLKQIGKVALLNAAEEVELAKRIEAGM 273


>gi|228476045|ref|ZP_04060753.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|314936318|ref|ZP_07843665.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
 gi|228269868|gb|EEK11348.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|313654937|gb|EFS18682.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
          Length = 368

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 159/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    N ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPNDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 83/175 (47%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDMDSDQMDDFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I++V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDISLVNEKDSSDTDEKLNPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AKRIE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|4587113|dbj|BAA76622.1| RpoT [Mycobacterium leprae]
          Length = 576

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 188/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM----------------------------VRKGECE 440
           +R  +K I     ++  E   +                               +     +
Sbjct: 276 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGTKLPTAQRRDMMWICRD 335

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 336 GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 395

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 396 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 455

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 456 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 515

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 516 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 575

Query: 681 D 681
           D
Sbjct: 576 D 576



 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D + +E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 234 DEEIVEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 293

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M  L E
Sbjct: 294 EVELAKRIEAGLYATQLMTELSE 316


>gi|296129901|ref|YP_003637151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296021716|gb|ADG74952.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 495

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 139/283 (49%), Positives = 188/283 (66%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EV+   +I   + +         S    +   +     +   AK  ++EANLRLV+S
Sbjct: 213 AEQEVELAKRIEAGLFAEEKLAETRDSLEPKLRRELEWIAQDGRRAKNHLLEANLRLVVS 272

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ T
Sbjct: 273 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 332

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL T
Sbjct: 333 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHT 392

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  AV P D+     L+E   +VL +L+ RE  V+ MRFG+    
Sbjct: 393 PLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHQVLDTLSEREAGVVSMRFGLTDGQ 452

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 453 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 495



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +      ++  E        +         ++     +T DPV+ YL+++G + LL+ E 
Sbjct: 156 ETKPAAAKKEDEPEDTGFVYSDADDDDAPAQQVVTAGATADPVKDYLKQIGKVALLNAEQ 215

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           E+ +AKRIEAG       L E+
Sbjct: 216 EVELAKRIEAGLF-AEEKLAET 236


>gi|27468166|ref|NP_764803.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis ATCC
           12228]
 gi|57867102|ref|YP_188703.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis RP62A]
 gi|251810978|ref|ZP_04825451.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876013|ref|ZP_06284880.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|293366478|ref|ZP_06613155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|47606037|sp|Q8CP24|RPOD_STAES RecName: Full=RNA polymerase sigma factor rpoD
 gi|81674470|sp|Q5HNY7|RPOD_STAEQ RecName: Full=RNA polymerase sigma factor rpoD
 gi|27315712|gb|AAO04847.1|AE016748_81 RNA polymerase sigma factor [Staphylococcus epidermidis ATCC 12228]
 gi|57637760|gb|AAW54548.1| RNA polymerase sigma-70 factor [Staphylococcus epidermidis RP62A]
 gi|251805488|gb|EES58145.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281295038|gb|EFA87565.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|291319247|gb|EFE59616.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319400897|gb|EFV89116.1| RNA polymerase sigma factor rpoD [Staphylococcus epidermidis
           FRI909]
 gi|329725345|gb|EGG61828.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU144]
 gi|329735301|gb|EGG71593.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU045]
 gi|329737328|gb|EGG73582.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU028]
          Length = 368

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      IAK  + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVNLLSAQEEIELAKRIEQ---GDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I +V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDITLVNEKDSSDTDDKINPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AKRIE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|313890499|ref|ZP_07824127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332523157|ref|ZP_08399409.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
 gi|313121016|gb|EFR44127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332314421|gb|EGJ27406.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 369

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTGEEEKELAIAV---AEGDVDAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 94.1 bits (232), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 66/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRNHKKEGTAVDDEVTEKLVIPFVLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSTKYIVEEPKPEELTDEQLIGSNSAKVNDPVRMYLKEIGVVPLLTGEEEKELAIAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DVDAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|257425686|ref|ZP_05602110.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257271380|gb|EEV03526.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
          Length = 368

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 159/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 EPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|257430984|ref|ZP_05607364.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
 gi|257278414|gb|EEV09050.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
          Length = 342

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 158/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 30  DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 89

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 90  EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 146

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 147 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 206

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 207 DPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 266

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 267 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 326

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 327 KLRHPSRSKRLKDFMD 342



 Score =  106 bits (265), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 44/150 (29%), Positives = 75/150 (50%), Gaps = 15/150 (10%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
           +K  +++G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +   +  D
Sbjct: 1   MKKVKKKGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNPSD 60

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           L++                    +DPVRMYL+E+G + LLS + EI +AKRIE G  +  
Sbjct: 61  LSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAK 106

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + L E+ L     I  R  +  G   L  I
Sbjct: 107 SRLAEANLRLVVSIAKRY-VGRGMLFLDLI 135


>gi|19745866|ref|NP_607002.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS8232]
 gi|19748016|gb|AAL97501.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           MGAS8232]
          Length = 369

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V K      +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAK---GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 119/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +++   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRYHKKEGTAIDDDVTEKLVIPFALDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAKG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|15927141|ref|NP_374674.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus N315]
 gi|20178083|sp|Q99TT5|RPOD_STAAN RecName: Full=RNA polymerase sigma factor rpoD
 gi|13701359|dbj|BAB42653.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           N315]
          Length = 368

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 159/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR+VLKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPAEKVREVLKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (291), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|291546785|emb|CBL19893.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus sp. SR1/5]
          Length = 375

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 165/343 (48%), Positives = 233/343 (67%), Gaps = 9/343 (2%)

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           V+Q+  +   +  +  ++LR+  + G       E     ++D   +   ++    +    
Sbjct: 42  VDQMEKVFDFLEASGVDVLRITDNSGD------ELLLDNDMDMDGMEDEEEVELDKIDLS 95

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V   V     +R  +K I   + +S  E   +   + K       AKK + EANLRLV+S
Sbjct: 96  VPEGVSIEDPVRMYLKEIGKVSLLSADEEIELAKRMEK---GDEAAKKRLAEANLRLVVS 152

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ T
Sbjct: 153 IAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 212

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++R +R++  ++ REPTPEEIA+++ MPV+ VR++LKI++EP+SLET
Sbjct: 213 IRIPVHMVETINKLIRVSRQLLQELGREPTPEEIAEEMDMPVDRVREILKISQEPVSLET 272

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ SHLGDFI+D N   P D+A    L+E    VL++LT RE++VLR+RFG+    
Sbjct: 273 PIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGLDDGR 332

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 333 ARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 375



 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 41/160 (25%), Positives = 71/160 (44%), Gaps = 5/160 (3%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DGDDLE 84
           +   ++++LA+++   +  +E++ F     +  +QME     L   G++V+   D    E
Sbjct: 10  EKLVELLELAKKKKNVLEYQEISDFFKDSPLEVDQMEKVFDFLEASGVDVLRITDNSGDE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
               ++  +D         +           S +DPVRMYL+E+G + LLS + EI +AK
Sbjct: 70  LLLDNDMDMDGMEDEEEVELDKIDLSVPEGVSIEDPVRMYLKEIGKVSLLSADEEIELAK 129

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 130 RMEKGDEAAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|300765597|ref|ZP_07075576.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
 gi|300513698|gb|EFK40766.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
          Length = 374

 Score =  232 bits (592), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 374



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 46/170 (27%), Positives = 78/170 (45%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + S +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +    
Sbjct: 4   KTKNTKPVAELSVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAE 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|212638699|ref|YP_002315219.1| RNA polymerase sigma factor RpoD [Anoxybacillus flavithermus WK1]
 gi|212560179|gb|ACJ33234.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Anoxybacillus flavithermus WK1]
          Length = 372

 Score =  232 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSAEEEIELAKRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDLGREPSPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 80/362 (22%), Positives = 139/362 (38%), Gaps = 29/362 (8%)

Query: 18  SDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           ++ S   D + +  K ++++L ++RG +T EE+   L   ++ S+QM++    L+  GI 
Sbjct: 2   AEKSTHSDLTLEQVKEQLVELGKKRGVLTYEEIAERLSSFDLDSDQMDEYYEYLNEQGIE 61

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           VV   DL+D +             +    L           +DPVRMYL+E+G + LLS 
Sbjct: 62  VVGESDLDDTDLD---DPDFDDLKDEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLSA 118

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E EI +AKRIE G       L E+ L     I  R  +  G   L  I         E  
Sbjct: 119 EEEIELAKRIEQGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGN 169

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            G     E   Y+K    S        Q     I   A+  +     V++  +      +
Sbjct: 170 MGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQ 229

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK---------- 306
            L +   + +    A E  L P+ +  + +IA+    L +      +             
Sbjct: 230 LLQDLGREPSPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDAT 289

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
                   ++LKE+L  ++ +L+  +  +  L   L D           L  + + +G+ 
Sbjct: 290 SPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDD------GRTRTLEEVGKVFGVT 343

Query: 367 RD 368
           R+
Sbjct: 344 RE 345


>gi|318066975|emb|CBY89102.1| RNA polymerase sigma70 factor [Halomonas variabilis]
          Length = 368

 Score =  232 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 120/397 (30%), Positives = 181/397 (45%), Gaps = 51/397 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVASILNAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  + +   +V++       
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEAEVPEPEPEPEVKDDVEGDGD 127

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                         P E                                   ++I E   
Sbjct: 128 EEDEDSTASEGGPDPEE------------------------------ARARFEQIREQNA 157

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
            + +         K  + S + K  + +L  L   + L     + LV Q+    +++   
Sbjct: 158 LVEAAY------AKHGRGSAELKAEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQ 211

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   + R  F++   G E    W+   +   + ++ + +      I + + 
Sbjct: 212 EKAVMQLCVKKAKVPRKTFIKSFPGNESRKTWLDDFQA-AQSKYADRLEPLRADIARAQR 270

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        +S+S+ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 271 KIAFEEDMVQLSVSDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 330

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 331 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|312865945|ref|ZP_07726166.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
 gi|311098349|gb|EFQ56572.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
          Length = 338

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I +   ++  E + +            +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 68  VRMYLKEIGIVPLLTNEEEKELAIAA---AEGDLMAKQRLAEANLRLVVSIAKRYVGRGM 124

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 125 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 184

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 185 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 244

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 245 GDFIEDEVIENPVDYTTRIVLREQLNEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 304

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F++
Sbjct: 305 FNVTRERIRQIEAKALRKLRHPSRSKQLKDFME 337



 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 108/305 (35%), Gaps = 26/305 (8%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
           P  + ++Q++D +  L++ GI++ D      +EG+  S  +  +     +  ++   S  
Sbjct: 8   PFVLDADQIDDLLERLTDGGISITD------KEGNPSSKYVVEAPKPEELTDEELLGSNS 61

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
              +DPVRMYL+E+G + LL+ E E  +A     G  M    L E+ L     I  R  +
Sbjct: 62  AKVNDPVRMYLKEIGIVPLLTNEEEKELAIAAAEGDLMAKQRLAEANLRLVVSIAKRY-V 120

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
             G   L  I         E   G     +   Y K    S        Q     I   A
Sbjct: 121 GRGMQFLDLI--------QEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQA 172

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +  +     V++  +        L E   D      A    + P     + EI ++ +E 
Sbjct: 173 RTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEP 229

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
            SL+                  + E  V     +        +L EQL ++   +   E 
Sbjct: 230 VSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRI--------VLREQLNEVLDTLTDREE 281

Query: 355 ELLRL 359
            +LRL
Sbjct: 282 NVLRL 286


>gi|291563082|emb|CBL41898.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SS3/4]
          Length = 374

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK++ E+NLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGKVPLLSPDEEIELAKKIE---LGDEEAKKKLAESNLRLVVSIAKRYAGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q LDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QLLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VRT R++  K+ RE TPEE+AK+L MPVE VR+++KI+++P+SLETPIG+E+ SHL
Sbjct: 221 INRLVRTQRQLVQKLGREATPEELAKELDMPVERVREIMKISQDPVSLETPIGEEEDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L E    VL++LT RE++VLR+RFG+      TLEEVG+Q
Sbjct: 281 GDFIQDNNVEVPADAATYTLLHEQLMDVLSTLTEREQKVLRLRFGLDDGRPRTLEEVGRQ 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK L+ +LD
Sbjct: 341 FNVTRERIRQIEAKALRKLRHPSRSKILKDYLD 373



 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 42/159 (26%), Positives = 70/159 (44%), Gaps = 3/159 (1%)

Query: 28  DDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLED 85
           ++   K+++LA+ ++  +   E+      DE++ E+++     L    ++++   +D E 
Sbjct: 9   EEKLSKLLELAKSKKNVLDETEVLDAFAGDELTPEKLDRIYDFLDKKHVDILKMSNDDEM 68

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +       + A       V             DDPVRMYL+E+G + LLS + EI +AK+
Sbjct: 69  DPDLFSEDEDADPEDEIDVEHIDLSVPEGIGVDDPVRMYLKEIGKVPLLSPDEEIELAKK 128

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           IE G       L ES L     I  R     G  LL  I
Sbjct: 129 IELGDEEAKKKLAESNLRLVVSIAKRYA-GRGMQLLDLI 166


>gi|15674827|ref|NP_269001.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes M1 GAS]
 gi|50913963|ref|YP_059935.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10394]
 gi|71903245|ref|YP_280048.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS6180]
 gi|71910413|ref|YP_281963.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS5005]
 gi|94988285|ref|YP_596386.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS9429]
 gi|94990164|ref|YP_598264.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10270]
 gi|94992161|ref|YP_600260.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS2096]
 gi|94994083|ref|YP_602181.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10750]
 gi|139474032|ref|YP_001128748.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209559154|ref|YP_002285626.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|306827613|ref|ZP_07460893.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
 gi|13621959|gb|AAK33722.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes M1
           GAS]
 gi|50903037|gb|AAT86752.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10394]
 gi|71802340|gb|AAX71693.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS6180]
 gi|71853195|gb|AAZ51218.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS5005]
 gi|94541793|gb|ABF31842.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS9429]
 gi|94543672|gb|ABF33720.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10270]
 gi|94545669|gb|ABF35716.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS2096]
 gi|94547591|gb|ABF37637.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10750]
 gi|134272279|emb|CAM30532.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209540355|gb|ACI60931.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|304430176|gb|EFM33205.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
          Length = 369

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V K      +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAK---GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.8 bits (226), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 119/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +++   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRHHKKEGTAIDDDVTEKLVIPFALDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAKG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|15924551|ref|NP_372085.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|21283242|ref|NP_646330.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49483810|ref|YP_041034.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|49486397|ref|YP_043618.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|57651954|ref|YP_186458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82751164|ref|YP_416905.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus RF122]
 gi|87162254|ref|YP_494216.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195369|ref|YP_500173.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|148268045|ref|YP_001246988.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394113|ref|YP_001316788.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|151221676|ref|YP_001332498.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|156979879|ref|YP_001442138.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|161509790|ref|YP_001575449.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221140019|ref|ZP_03564512.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253314932|ref|ZP_04838145.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253732214|ref|ZP_04866379.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733189|ref|ZP_04867354.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|255006347|ref|ZP_05144948.2| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257428347|ref|ZP_05604745.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257433672|ref|ZP_05610030.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257436586|ref|ZP_05612630.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257793637|ref|ZP_05642616.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|258411063|ref|ZP_05681343.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|258420133|ref|ZP_05683088.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|258423989|ref|ZP_05686871.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|258443599|ref|ZP_05691938.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|258448720|ref|ZP_05696832.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|258450610|ref|ZP_05698672.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|258453537|ref|ZP_05701515.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|262049137|ref|ZP_06022014.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262051223|ref|ZP_06023447.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|269203189|ref|YP_003282458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282893062|ref|ZP_06301296.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|282904143|ref|ZP_06312031.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282905970|ref|ZP_06313825.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282908880|ref|ZP_06316698.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282911199|ref|ZP_06319001.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282914368|ref|ZP_06322154.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282916831|ref|ZP_06324589.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282919337|ref|ZP_06327072.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282920110|ref|ZP_06327835.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282924662|ref|ZP_06332330.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282928194|ref|ZP_06335799.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|283770637|ref|ZP_06343529.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283958325|ref|ZP_06375776.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|284024620|ref|ZP_06379018.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 132]
 gi|293503442|ref|ZP_06667289.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|293510459|ref|ZP_06669165.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|293530999|ref|ZP_06671681.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|294848592|ref|ZP_06789338.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|295406684|ref|ZP_06816489.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295428139|ref|ZP_06820771.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296275817|ref|ZP_06858324.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297207720|ref|ZP_06924155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297245734|ref|ZP_06929599.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297590895|ref|ZP_06949533.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|300911801|ref|ZP_07129244.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|304380850|ref|ZP_07363510.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|60390420|sp|Q6G905|RPOD_STAAS RecName: Full=RNA polymerase sigma factor rpoD
 gi|60390434|sp|Q6GGD8|RPOD_STAAR RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393872|sp|P0A0I8|RPOD_STAAM RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393873|sp|P0A0I9|RPOD_STAAW RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393874|sp|P0A0J0|RPOD_STAA8 RecName: Full=RNA polymerase sigma factor rpoD
 gi|81694388|sp|Q5HFJ9|RPOD_STAAC RecName: Full=RNA polymerase sigma factor rpoD
 gi|153069|gb|AAB59090.1| sigma factor [Staphylococcus aureus]
 gi|14247332|dbj|BAB57723.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204682|dbj|BAB95378.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49241939|emb|CAG40633.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|49244840|emb|CAG43300.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57286140|gb|AAW38234.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82656695|emb|CAI81122.1| RNA polymerase sigma factor [Staphylococcus aureus RF122]
 gi|87128228|gb|ABD22742.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87202927|gb|ABD30737.1| RNA polymerase sigma factor, putative [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|147741114|gb|ABQ49412.1| RNA polymerase, sigma 70 subunit, RpoD family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946565|gb|ABR52501.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|150374476|dbj|BAF67736.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722014|dbj|BAF78431.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368599|gb|ABX29570.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|253724003|gb|EES92732.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728729|gb|EES97458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|257275188|gb|EEV06675.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257281765|gb|EEV11902.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257283937|gb|EEV14060.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257787609|gb|EEV25949.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|257840213|gb|EEV64677.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|257843844|gb|EEV68238.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|257845610|gb|EEV69642.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|257851005|gb|EEV74948.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|257857998|gb|EEV80887.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|257861768|gb|EEV84567.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|257864268|gb|EEV87018.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|259160860|gb|EEW45880.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|259162806|gb|EEW47371.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262075479|gb|ACY11452.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|269941051|emb|CBI49435.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282313497|gb|EFB43892.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282317147|gb|EFB47521.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282319318|gb|EFB49670.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282321549|gb|EFB51874.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282324894|gb|EFB55204.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282327144|gb|EFB57439.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282331262|gb|EFB60776.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282590001|gb|EFB95083.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|282594458|gb|EFB99443.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282595761|gb|EFC00725.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282764380|gb|EFC04506.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|283460784|gb|EFC07874.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283470839|emb|CAQ50050.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790474|gb|EFC29291.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|285817243|gb|ADC37730.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus 04-02981]
 gi|290920267|gb|EFD97333.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|291095108|gb|EFE25373.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|291466823|gb|EFF09343.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|294824618|gb|EFG41041.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|294968431|gb|EFG44455.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295128497|gb|EFG58131.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296887737|gb|EFH26635.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297177385|gb|EFH36637.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297575781|gb|EFH94497.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|298694843|gb|ADI98065.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300886047|gb|EFK81249.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|302333237|gb|ADL23430.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|302751392|gb|ADL65569.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304340577|gb|EFM06511.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312437970|gb|ADQ77041.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|312829949|emb|CBX34791.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315129839|gb|EFT85829.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|315195463|gb|EFU25850.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|315198744|gb|EFU29072.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140554|gb|EFW32408.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320144091|gb|EFW35860.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|323440459|gb|EGA98171.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O11]
 gi|323443233|gb|EGB00851.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O46]
 gi|329314237|gb|AEB88650.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus T0131]
 gi|329727416|gb|EGG63872.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329728458|gb|EGG64895.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 368

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 158/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|403013|emb|CAA50594.1| major sigma factor [Lactococcus lactis]
          Length = 340

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 189 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 249 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 308

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 309 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 340



 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/141 (24%), Positives = 55/141 (39%), Gaps = 16/141 (11%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           + +ED    + + GI++VD    +D   S  +L                +   +   DDP
Sbjct: 13  DALEDLFKQIQDAGISIVD----KDGNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDP 68

Query: 121 VRMYLREMGSIELLSREGEIAIAKRI---EAGRAMMMASLCESPLTFQALIIWR------ 171
           VRMYL+E+G   L+S + E  +A+ I     G       L E+ L     I  R      
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 128

Query: 172 ---DELNDGTTLLREIIDLEA 189
              D + +G   L + +D   
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFD 149


>gi|307705133|ref|ZP_07642010.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
 gi|307621329|gb|EFO00389.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
          Length = 369

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVVPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|307709167|ref|ZP_07645626.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
 gi|307620113|gb|EFN99230.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
          Length = 369

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVVPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|318066967|emb|CBY89098.1| RNA polymerase sigma70 factor [Halomonas pantelleriensis]
          Length = 363

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 125/415 (30%), Positives = 190/415 (45%), Gaps = 56/415 (13%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
             A+  +V      +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++
Sbjct: 1   EQAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSA 60

Query: 157 LCESPLTFQALIIWRDELNDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
           L   P   ++++   D   D      L ++             GF    EG       D 
Sbjct: 61  LAYLPGAVESILEIYDGTQDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADV 109

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
            +      V+E+    +     +++D S     PE A      + E        ++    
Sbjct: 110 PE------VEESASVDDEDDDAAEEDDSGGGPDPEEARARFEQIREQNALVQAAIA---- 159

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                          K  ++S +    + +L +L   + L    
Sbjct: 160 -------------------------------KHGRTSKQAHDEQARLAELFSPIKLVPKH 188

Query: 335 IDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            + LV Q+    +++   E  +++   +   + R  F++   G E    W+         
Sbjct: 189 FERLVGQVRISVEQVREQEKVIMQVFVKRGKVPRKTFIKSFPGNESRKDWMDDFLA-ANA 247

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           ++ + +A     I + + +I        + +SE + +   +  GE +A  AKKEMVEANL
Sbjct: 248 KFSDRLAPFRGDIARAQRKIAFEEEMVQLPVSELKEVNRRLSIGEAKARRAKKEMVEANL 307

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           RLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 308 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 362


>gi|56963455|ref|YP_175186.1| RNA polymerase sigma factor RpoD [Bacillus clausii KSM-K16]
 gi|56909698|dbj|BAD64225.1| DNA-directed RNA polymerase major sigma-43 factor sigma-A [Bacillus
           clausii KSM-K16]
          Length = 373

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 161/309 (52%), Positives = 212/309 (68%), Gaps = 7/309 (2%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVETGISISEFRHIVS 432
            E +    S A+   + E  +     V   +KI    R  +K I     +S  E   +  
Sbjct: 68  NESEDDVPSLAQVAKDEEEFDLNDLSVPPGIKINDPVRMYLKEIGRVPLLSAEEEIDLAK 127

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +       AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  
Sbjct: 128 RIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYDK 184

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++     REPTPEE+
Sbjct: 185 GFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDYGREPTPEEV 244

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            K++ +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A    L+E 
Sbjct: 245 GKEMDLSPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPSDAAAYELLKEQ 304

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSR
Sbjct: 305 LEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSR 364

Query: 673 SKKLRSFLD 681
           SK+L+ FLD
Sbjct: 365 SKRLKDFLD 373



 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 47/188 (25%), Positives = 75/188 (39%), Gaps = 15/188 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++  ++RG +T  E+   +   E  S+QM++    L   G+ +++  + +   
Sbjct: 17  DQVKEQLVETGKKRGTLTYAEITEKMAAFEQDSDQMDEFYEYLGEQGVELLNESEDDVPS 76

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +        +       L           +DPVRMYL+E+G + LLS E EI +AKRIE
Sbjct: 77  LA------QVAKDEEEFDLNDLSVPPGIKINDPVRMYLKEIGRVPLLSAEEEIDLAKRIE 130

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 131 QGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 181

Query: 208 YQKREDSS 215
           Y K    S
Sbjct: 182 YDKGFKFS 189


>gi|318066907|emb|CBY89068.1| RNA polymerase sigma70 factor [Chromohalobacter israelensis]
 gi|318066913|emb|CBY89071.1| RNA polymerase sigma70 factor [Chromohalobacter salexigens]
          Length = 367

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 119/395 (30%), Positives = 180/395 (45%), Gaps = 48/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSSLAYLPGAVDSILSAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+                  ++   +   +    +GD+    
Sbjct: 79  QDEEAPGRLSDLFSGFIDPD-----------EGIPGVAEAEVPEPEPEPSAADGDVSEDD 127

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             ++++ +     PE A      + E  +      +A+E+                    
Sbjct: 128 DEAEEEETGGGPDPEEARARFEQIREQNE---RAKAAIEE-------------------- 164

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                           S +    + +L +L   + L     + LV Q+    ++I   E 
Sbjct: 165 ------------HGLGSKEASAEQARLAELFSPIKLVPKHFERLVGQVRISVEQIRGQEK 212

Query: 355 ELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            ++++  +   + R  F+    G E D  W+          + + +      I + + +I
Sbjct: 213 AIMQIFVKQAKVPRKTFIGSFPGAESDLEWLDRFMAKHTK-FADRLEPFRADIQRAQRKI 271

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + +S  + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 272 GFEEEMVLLPVSHIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 331

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 332 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|260588574|ref|ZP_05854487.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
 gi|260541049|gb|EEX21618.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
          Length = 330

 Score =  232 bits (591), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    +++ ++ E     AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 61  VRMYLKEIGKVPLLSAEEE---ITLAQRMEEGDESAKKRLAEANLRLVVSIAKRYVGRGM 117

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 118 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 177

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA+++ M VE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 178 INKLIRVSRQLLQELGREPHPEEIAEEMNMSVERVREILKISQEPVSLETPIGEEEDSHL 237

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 238 GDFIQDDNVPVPADAAAFTLLKEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKE 297

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 298 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 330



 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 3/124 (2%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS--ADRSTDDP 120
           M+     L   GI+++   D + ++      D  + +    V ++    S     S +DP
Sbjct: 1   MDKVFDFLEANGIDILRIQDNDMDDLIISDDDDLNLSEEDEVDMENIDLSVPEGVSIEDP 60

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G + LLS E EI +A+R+E G       L E+ L     I  R  +  G   
Sbjct: 61  VRMYLKEIGKVPLLSAEEEITLAQRMEEGDESAKKRLAEANLRLVVSIAKRY-VGRGMLF 119

Query: 181 LREI 184
           L  I
Sbjct: 120 LDLI 123


>gi|256851182|ref|ZP_05556571.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260660606|ref|ZP_05861521.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|282934648|ref|ZP_06339891.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297206047|ref|ZP_06923442.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
 gi|256616244|gb|EEU21432.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260548328|gb|EEX24303.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|281301223|gb|EFA93524.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297149173|gb|EFH29471.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
          Length = 364

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 177/388 (45%), Positives = 234/388 (60%), Gaps = 28/388 (7%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
            +L        K+ K S +     +   KL+    L    +D LV++  D    I+   G
Sbjct: 4   MTLDKKVKELVKEVKKSKEITE-TDFTEKLIKPYKLEGKAVDQLVQEFEDNGISIVDANG 62

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA-CEVDSILKIRNEI 413
           E   LA                       +   KD  + E K+  A   V     +R  +
Sbjct: 63  EPSNLA-----------------------LKKQKDVEKEELKDLSAPASVRMNDPVRMYL 99

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K I     ++  E   +   ++        AK+E+ EANLRLV+S+AK+Y  RG+QFLDL
Sbjct: 100 KEIGRVPLLNADEEIALAKRIQ---DGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 156

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GLMKA +KF++ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++
Sbjct: 157 IQEGNMGLMKAVDKFNYKLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 216

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++   + REPTPEEI  ++ M  + VR +LKI +EP+SLETPIG+ED SHLGDFIE
Sbjct: 217 RIQRQLLQDLGREPTPEEIGAEMDMGTDKVRDILKIAQEPVSLETPIGEEDDSHLGDFIE 276

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK+A SP   A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTR
Sbjct: 277 DKDATSPEQHASYEMLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTR 336

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 337 ERIRQIEAKALRKLRHPSRSNQLKDFLD 364



 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 43/158 (27%), Positives = 70/158 (44%), Gaps = 8/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D   K+++K  ++   +T  +    L  P ++  + ++  V    + GI++VD       
Sbjct: 7   DKKVKELVKEVKKSKEITETDFTEKLIKPYKLEGKAVDQLVQEFEDNGISIVDA------ 60

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   +L L          L+     A    +DPVRMYL+E+G + LL+ + EIA+AKRI
Sbjct: 61  NGEPSNLALKKQKDVEKEELKDLSAPASVRMNDPVRMYLKEIGRVPLLNADEEIALAKRI 120

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + G       L E+ L     I  R  +  G   L  I
Sbjct: 121 QDGDEEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI 157


>gi|21910055|ref|NP_664323.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS315]
 gi|28896247|ref|NP_802597.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes SSI-1]
 gi|21904246|gb|AAM79126.1| putative RNA polymerase sigma 42 protein RpoD [Streptococcus
           pyogenes MGAS315]
 gi|28811498|dbj|BAC64430.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           SSI-1]
          Length = 369

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V K      +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKELAVAVAK---GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 119/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +++   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRYHKKEGTAIDDDVTEKLVIPFALDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSSKYIVEELKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKELAVAVAKG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|298246437|ref|ZP_06970243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553918|gb|EFH87783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 422

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 151/286 (52%), Positives = 206/286 (72%), Gaps = 13/286 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECE-------------ASIAKKEMVEANLRL 455
           +R  ++ I     ++  E   +  ++ +G+ E                A+K + EANLRL
Sbjct: 137 VRMYLREIGRVPLLTAHEEIRLAQLMERGKAERLKPAPNYRYISEGEEAQKRLTEANLRL 196

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+SVAKKY  RG+  LDLIQEGNIGL++A EKFD+  G+KFSTYA WW++QAITR+IADQ
Sbjct: 197 VVSVAKKYIGRGMNLLDLIQEGNIGLIRAVEKFDYNKGFKFSTYATWWIRQAITRAIADQ 256

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I++++R +RR+   + REPT EEIA ++ +  E VR+++K+++EP+S
Sbjct: 257 ARTIRIPVHMVETINRLIRISRRLLQDLGREPTSEEIAAQMEISAEKVREIIKVSQEPVS 316

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+ED SHLGDFIED  A++P D+A    L+E    VL SLT RE +VL++RFG+ 
Sbjct: 317 LETPIGEEDDSHLGDFIEDHTALAPADAASHQLLKEQVEDVLDSLTERERKVLQLRFGLD 376

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 377 DGRSRTLEEVGKEFHVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 422



 Score = 60.6 bits (145), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 1/95 (1%)

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA-SNSSVFLQKRKDSADRSTDDP 120
           Q E+++  L        D +   +E    D+  LA     +            + S DDP
Sbjct: 77  QDEESMDALDPNKEPPADWEPSPEEMNDVDAEVLADPKWEDLQDGFGIVVADLESSLDDP 136

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           VRMYLRE+G + LL+   EI +A+ +E G+A  + 
Sbjct: 137 VRMYLREIGRVPLLTAHEEIRLAQLMERGKAERLK 171


>gi|238854653|ref|ZP_04644983.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260664404|ref|ZP_05865256.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|282932956|ref|ZP_06338353.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|238832443|gb|EEQ24750.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260561469|gb|EEX27441.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|281302991|gb|EFA95196.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
          Length = 364

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 176/388 (45%), Positives = 234/388 (60%), Gaps = 28/388 (7%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
            +L        K+ K S +     +   KL+    L    +D LV++  D    I+   G
Sbjct: 4   MTLDKKVKELVKEVKKSKEITE-TDFTEKLIKPYKLEGKAVDQLVQEFEDNGISIVDANG 62

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA-CEVDSILKIRNEI 413
           +   LA                       +   KD  + E K+  A   V     +R  +
Sbjct: 63  DPSNLA-----------------------LKKQKDVEKEELKDLSAPASVRMNDPVRMYL 99

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K I     ++  E   +   ++        AK+E+ EANLRLV+S+AK+Y  RG+QFLDL
Sbjct: 100 KEIGRVPLLNADEEITLAKRIQ---DGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 156

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GLMKA +KF++ LG+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++
Sbjct: 157 IQEGNMGLMKAVDKFNYKLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 216

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++   + REPTPEEI  ++ M  + VR +LKI +EP+SLETPIG+ED SHLGDFIE
Sbjct: 217 RIQRQLLQDLGREPTPEEIGAEMDMGTDKVRDILKIAQEPVSLETPIGEEDDSHLGDFIE 276

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK+A SP   A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTR
Sbjct: 277 DKDATSPEQHASYEMLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTR 336

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 337 ERIRQIEAKALRKLRHPSRSNQLKDFLD 364



 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 42/158 (26%), Positives = 69/158 (43%), Gaps = 8/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D   K+++K  ++   +T  +    L  P ++  + ++  V    + GI++VD       
Sbjct: 7   DKKVKELVKEVKKSKEITETDFTEKLIKPYKLEGKAVDQLVQEFEDNGISIVDA------ 60

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G   +L L          L+     A    +DPVRMYL+E+G + LL+ + EI +AKRI
Sbjct: 61  NGDPSNLALKKQKDVEKEELKDLSAPASVRMNDPVRMYLKEIGRVPLLNADEEITLAKRI 120

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + G       L E+ L     I  R  +  G   L  I
Sbjct: 121 QDGDEEAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI 157


>gi|258446806|ref|ZP_05694960.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
 gi|257854381|gb|EEV77330.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
          Length = 368

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 158/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++V+  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|239626722|ref|ZP_04669753.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516868|gb|EEQ56734.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 374

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S+ E   +   +      +  A+K + E+NLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGKIPLLSMEEEIELAKSME---LGSEDARKRLAESNLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 QFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VRT+R++  ++ REPT EEIA +  +PVE V +++K+ +EP+SLETPIG+E+ SHL
Sbjct: 221 INRLVRTSRQLLQELGREPTTEEIAARADLPVERVSEIMKMAQEPVSLETPIGEEEDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N + P D+A    L E    VL +LT RE++VL++RFG+      TLEEVG+Q
Sbjct: 281 GDFIQDDNVMVPQDAAAFTLLHEQLMEVLLTLTEREQKVLKLRFGLDDGRPRTLEEVGRQ 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 341 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 373



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/160 (24%), Positives = 69/160 (43%), Gaps = 4/160 (2%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--DGDDLE 84
           ++    +++ A+++   +  +E+ ++   ++ +S+QM+     L    ++++  D     
Sbjct: 8   EEKLAGLLEEAKKKKNVLEYQEIISYFGSEQPTSDQMDQLFDFLEQSKVDIIRMDSAQEL 67

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D +   +            V           S +DPVRMYL+E+G I LLS E EI +AK
Sbjct: 68  DPDLFIEEEISLEEEEEIDVEHLDLSVPEGVSLEDPVRMYLKEIGKIPLLSMEEEIELAK 127

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +E G       L ES L     I  R  +  G   L  I
Sbjct: 128 SMELGSEDARKRLAESNLRLVVSIAKRY-VGRGMQFLDLI 166


>gi|322376488|ref|ZP_08050981.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
 gi|321282295|gb|EFX59302.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
          Length = 369

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVVPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|322387734|ref|ZP_08061343.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
 gi|321141601|gb|EFX37097.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
          Length = 369

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDVEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  +  +EPTPE+IA+K+ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQEYGQEPTPEQIAEKMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 69/333 (20%), Positives = 118/333 (35%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  ++ G  T +E+N  L  P  +  E +E+ +  + + GI++ D +    E
Sbjct: 12  DVQVAEFIRNHKKTGTATDDEINNVLVIPFALDVEGIENLLQRIQDAGISITDNEGNPSE 71

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                   + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 72  -------RVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDVEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   +  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQEYGQEPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A +  + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAEKMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|307706485|ref|ZP_07643293.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
 gi|307708623|ref|ZP_07645087.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307615372|gb|EFN94581.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307618125|gb|EFN97284.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
          Length = 369

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|242242833|ref|ZP_04797278.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
 gi|242233734|gb|EES36046.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
          Length = 368

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      IAK  + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVNLLSAQEEIELAKKIEQ---GDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I +V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDITLVNEKDSSDTDDKINPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AK+IE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKKIEQGDEIAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|134300301|ref|YP_001113797.1| RNA polymerase sigma factor RpoD [Desulfotomaculum reducens MI-1]
 gi|134053001|gb|ABO50972.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfotomaculum reducens
           MI-1]
          Length = 367

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 166/374 (44%), Positives = 239/374 (63%), Gaps = 21/374 (5%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK   +  +   +++  +    L+  +ID + E++  +   ++    +L  L        
Sbjct: 15  EKGKKRGVLTYNEIMDTLQGTELSPDQIDDIYEKISAMGIEVVPLASDLEPL-------- 66

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                     E+D    +  ++  E E    +   +     +R  +K I     +S  E 
Sbjct: 67  ----------EVDDSVENSTEEEVEVEVDLSIPEGIGIDDPVRMYLKEIGRVPLLSPEEE 116

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   + +GE     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 117 VDLAKRMEQGE---EEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 173

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP
Sbjct: 174 FDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP 233

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +PEEIAK++ +  E VR++LKI +EP+SLETPIG+E+ SHLGDFIED +A +P + A   
Sbjct: 234 SPEEIAKEMDISGEKVREILKIAQEPVSLETPIGEEEDSHLGDFIEDADARAPAEEASFT 293

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE    VL +LT RE++VLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL
Sbjct: 294 LLREQLDEVLKTLTDREQKVLRLRFGLDDGRARTLEEVGQKFGVTRERIRQIEAKTLRKL 353

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 354 RHPSRSKKLKDYLD 367



 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 77/350 (22%), Positives = 133/350 (38%), Gaps = 27/350 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  K++I+  ++RG +T  E+   L   E+S +Q++D    +S MGI VV      D E 
Sbjct: 8   EQIKELIEKGKKRGVLTYNEIMDTLQGTELSPDQIDDIYEKISAMGIEVV--PLASDLEP 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E    + +S                   DDPVRMYL+E+G + LLS E E+ +AKR+E 
Sbjct: 66  LEVDDSVENSTEEEVEVEVDLSIPEGIGIDDPVRMYLKEIGRVPLLSPEEEVDLAKRMEQ 125

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G       L E+ L     I  R  +  G   L  I         E   G     E   Y
Sbjct: 126 GEEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEKFDY 176

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           +K    S        Q     I   A+  +     V++  +      + L E   + +  
Sbjct: 177 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPE 236

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ----------KDEKSSVKCKVLK 318
             A E  +  + +  + +IA+    L +      +            +         +L+
Sbjct: 237 EIAKEMDISGEKVREILKIAQEPVSLETPIGEEEDSHLGDFIEDADARAPAEEASFTLLR 296

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           E+L +++ +L+  + ++  L   L D           L  + Q +G+ R+
Sbjct: 297 EQLDEVLKTLTDREQKVLRLRFGLDD------GRARTLEEVGQKFGVTRE 340


>gi|444799|prf||1908232B RNA polymerase:SUBUNIT=sigma factor
          Length = 340

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 158/272 (58%), Positives = 200/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG 
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGN 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 189 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 249 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 308

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 309 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 340



 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/141 (24%), Positives = 55/141 (39%), Gaps = 16/141 (11%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           + +ED    + + GI++VD    +D   S  +L                +   +   DDP
Sbjct: 13  DALEDLFKQIQDAGISIVD----KDGNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDP 68

Query: 121 VRMYLREMGSIELLSREGEIAIAKRI---EAGRAMMMASLCESPLTFQALIIWR------ 171
           VRMYL+E+G   L+S + E  +A+ I     G       L E+ L     I  R      
Sbjct: 69  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGN 128

Query: 172 ---DELNDGTTLLREIIDLEA 189
              D + +G   L + +D   
Sbjct: 129 QFLDLIQEGNMGLMKAVDKFD 149


>gi|169334166|ref|ZP_02861359.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258883|gb|EDS72849.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
          Length = 403

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 148/272 (54%), Positives = 196/272 (72%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         A+K++ EANLRLV+S+AK+Y NRG+
Sbjct: 135 VRMYLKEIGKVDLLSAEEELDLAQKIE---SGDVEARKKLCEANLRLVVSIAKRYVNRGM 191

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 192 SFLDLIQEGNLGLLKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 251

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R +   + R+P   EIAK++ +P E VR ++KI+++P+SLETPIG+E+ SHL
Sbjct: 252 INKLKRVQRMLIQDLGRDPNSHEIAKEMGLPEEKVRDIMKISQDPVSLETPIGEEEDSHL 311

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +AV+P ++A    LR     VL +LT RE +VL +RFG+      TLEEVG  
Sbjct: 312 GDFIPDDDAVAPEEAASYMLLRTQLFEVLKTLTDREAKVLILRFGLEDGRPRTLEEVGDI 371

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           FCVTRERIRQIEAKA+RKL+HP+RSKKLR FL
Sbjct: 372 FCVTRERIRQIEAKALRKLRHPTRSKKLRDFL 403



 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 37/156 (23%), Positives = 71/156 (45%), Gaps = 4/156 (2%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            + + +   A++   V+  E+N         S+++++ +      G+ +    D ++ + 
Sbjct: 46  KTVEDIKAWAKKESVVSQREMNQHFTDLNFGSDEIDEVLEFFFKEGVVL---QDDDESDK 102

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             D+L             + +        +DPVRMYL+E+G ++LLS E E+ +A++IE+
Sbjct: 103 DVDALLDEDIKDEDVKKAEAKAYEPSVHINDPVRMYLKEIGKVDLLSAEEELDLAQKIES 162

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       LCE+ L     I  R  +N G + L  I
Sbjct: 163 GDVEARKKLCEANLRLVVSIAKRY-VNRGMSFLDLI 197


>gi|289167835|ref|YP_003446104.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
 gi|288907402|emb|CBJ22239.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
          Length = 369

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  +  +EPTPE+IA+K+ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQEYGQEPTPEQIAEKMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 71/333 (21%), Positives = 121/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVLPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSAEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   +  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQEYGQEPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A +  + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAEKMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL ++   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEVLDTLTDREENVLRL 317


>gi|222151460|ref|YP_002560616.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
 gi|222120585|dbj|BAH17920.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
          Length = 366

 Score =  232 bits (590), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 97  VRMYLKEIGRVNLLSAEEEIELAKRIEQ---GDEEAKARLAEANLRLVVSIAKRYVGRGM 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 154 LFLDLIQEGNMGLIKAVEKFDFTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 214 INKLIRVQRQLLQDLGRDPSPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHL 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 274 GDFIEDQDAQSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 334 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 366



 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D    ++I+  ++ G+++ EE+   L   E+ S+ M++    ++   I +++  D +D  
Sbjct: 18  DQVKAQLIETGKKNGHLSHEEIADKLQNFEMDSDHMDEFFEAIAENDITLINEKDAQD-- 75

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                       ++  + L           +DPVRMYL+E+G + LLS E EI +AKRIE
Sbjct: 76  ------------TDDKINLNDLSAPPGVKINDPVRMYLKEIGRVNLLSAEEEIELAKRIE 123

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G     A L E+ L     I  R  +  G   L  I
Sbjct: 124 QGDEEAKARLAEANLRLVVSIAKRY-VGRGMLFLDLI 159


>gi|258437393|ref|ZP_05689377.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
 gi|257848598|gb|EEV72586.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
          Length = 368

 Score =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 158/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    + ++    V     +R  +K I     +S  
Sbjct: 56  DDFFDQLNDNDISLINEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/157 (28%), Positives = 79/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM+D    L++  I++++  D  D +
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLINEKDSSDTD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 80  EKLNPSDLSA--------------PPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|318066987|emb|CBY89108.1| RNA polymerase sigma70 factor [Kushneria indalinina]
          Length = 372

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 127/395 (32%), Positives = 182/395 (46%), Gaps = 43/395 (10%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P +  +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALSSLPGSVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+       G  G +  +        +  +  + E   E  +
Sbjct: 79  QDEEAPGRLSDLFSGFIDPD------EGVPGVAEVEEPMPEVVADDAEGSDEEDSDEEDS 132

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
               D  S+    PE A      + E  + +   + A                       
Sbjct: 133 DEEDDTASEGGPDPELARVRFEQIREQNEKTKAAIEA----------------------- 169

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                       +  +S + +  + +L +L   + L     + LV QL     +I   E 
Sbjct: 170 ------------NGLTSSEARSEQARLAELFSPIKLVPRHFERLVGQLRLSVGQIREQEK 217

Query: 355 ELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L    G + R  F+    GRE D  W+            + +      I + + +I
Sbjct: 218 TIMQLCVKRGKVPRKAFIASFPGRESDSSWIDDFIARNSKHAGS-IEPLRSDIERAQRKI 276

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + +SE + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 277 AFEEELAMLPVSELKDINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 336

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 337 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 371


>gi|329946883|ref|ZP_08294295.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328526694|gb|EGF53707.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 543

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 291 KLRRELHWVAQDGQRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 350

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 351 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 410

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 411 PEELAVELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 470

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 471 LQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 530

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 531 HPSRSQVLRDYLD 543



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S+D     + + +       ++     +T DPV+ YL+++G + LL+ E E+ +AKRIEA
Sbjct: 214 SQDKDGSFTVSDSDEGDEPAQRVVTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEA 273

Query: 149 GRAMMMASLCE 159
           G       L E
Sbjct: 274 GLY-AEHRLAE 283


>gi|223044379|ref|ZP_03614413.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
 gi|222442248|gb|EEE48359.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
          Length = 368

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVNLLSAQEEIELAKKIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I +V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDITLVNEKDSSDTDEKLNPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AK+IE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKKIEQGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|18202317|sp|P58290|RPOD_LACLC RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 364

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 158/272 (58%), Positives = 201/272 (73%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     IS+ E   +   +  G   A  AK+ + EANLRLV+S+AK+Y+ RG+
Sbjct: 93  VRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGM 152

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 153 QFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 212

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +  ++ R+P+PEEI K+L M  + VR+VLKI +EP+SLETPIG+ED SHL
Sbjct: 213 INKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEEDDSHL 272

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED    SP+D   +  LRE    V+ +LT REE VLRMRFG+     HTLE+VGKQ
Sbjct: 273 GDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLEDVGKQ 332

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKAI+KL+HP RSK LR F+
Sbjct: 333 FKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 364



 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/176 (22%), Positives = 66/176 (37%), Gaps = 17/176 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + + K  I   +  G    EE+   L     +  + +ED    + + GI++VD    +D
Sbjct: 2   YEKAVKGYITKRKPLGEALDEEIMDELSVKFGIVDDALEDLFKQIQDAGISIVD----KD 57

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
              S  +L                +   +   DDPVRMYL+E+G   L+S + E  +A+ 
Sbjct: 58  GNPSPLALVTDEIEKEEVSDTAMDEIVTNVRIDDPVRMYLKEIGRYPLISLDEETKLAEA 117

Query: 146 I---EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA 189
           I     G       L E+ L     I  R         D + +G   L + +D   
Sbjct: 118 IIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFLDLIQEGNMGLMKAVDKFD 173


>gi|297584635|ref|YP_003700415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
 gi|297143092|gb|ADH99849.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
          Length = 371

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +     +   AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGRVPLLSAKEEVELAKRIE---EDDEEAKRRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEE++K++ +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLIRVQRQLLQDLGREPTPEEVSKEMELTPDKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 279 GDFIEDQEALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 339 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 371



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 99/262 (37%), Gaps = 17/262 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++  ++RG +T  E+   L   +  S+QM++    L   G+++++        
Sbjct: 17  DQVKEQLVEAGKKRGSLTYVEITEKLGAFDQDSDQMDEFFEHLGEQGVDIINE------- 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            SE    L       +  L           +DPVRMYL+E+G + LLS + E+ +AKRIE
Sbjct: 70  -SEAVPSLQQVEKEEAFDLNDLSVPPGIKINDPVRMYLKEIGRVPLLSAKEEVELAKRIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                    L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 129 EDDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 179

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y K    S        Q     I   A+  +     V++  +      + L +   +   
Sbjct: 180 YNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTP 239

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              + E +L P  +  + +IA+
Sbjct: 240 EEVSKEMELTPDKVREILKIAQ 261


>gi|73662504|ref|YP_301285.1| RNA polymerase sigma factor RpoD [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
 gi|72495019|dbj|BAE18340.1| RNA polymerase sigma factor A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 368

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVNLLNAQEEIELAKKIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 80/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   E+ S+QM++    L++  I++V+  D  D++
Sbjct: 20  EDVKKQLIEKGKKEGHLSHEEIAEKLQNFEMDSDQMDELFDQLTDNDISLVNEKDSSDKD 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G + LL+ + EI +AK+IE
Sbjct: 80  SKLNPNDLSA--------------PPGVKINDPVRMYLKEIGRVNLLNAQEEIELAKKIE 125

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 126 QGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|318066965|emb|CBY89097.1| RNA polymerase sigma70 factor [Halomonas pacifica]
          Length = 362

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 121/397 (30%), Positives = 185/397 (46%), Gaps = 57/397 (14%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P   ++++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVESILEAYDLT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D  +E       E    ++ 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADVPEE-------EESASVDD 120

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
             + ++++ S     PE A      + E    +A   +A+E                   
Sbjct: 121 EDEDAEEEESGGGPDPEEARARFEQIRE---QNALVKAAVE------------------- 158

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K    S + +  + +L +L   + L     + LV Q+    +++   
Sbjct: 159 -------------KHGYGSAEAQAEQARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQ 205

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++   +   + R  F++   G E    W+         ++ + +      + + + 
Sbjct: 206 EKAIMQVFVKRGKVPRKAFIKSFPGNESRAEWMDEFLA-DNAKYADRLEPFRGDVQRAQR 264

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + + E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 265 KISFEEDMVQLPVGELKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 324

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 325 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 361


>gi|189219555|ref|YP_001940196.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186413|gb|ACD83598.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 623

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 188/548 (34%), Positives = 291/548 (53%), Gaps = 35/548 (6%)

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK-------- 218
           L    DE  D    LR +I L    G  +                E  +           
Sbjct: 73  LAKIWDECPDKQEKLRTLIKLAKEQGYLTYDDINEALPESVNNSEEIEAVYDFLRTLEID 132

Query: 219 --ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL-------DEDEDDSAHTL 269
             +  DV   +      A+  +   SK+D   +      + +        E E + +  +
Sbjct: 133 IIDSSDVDNAKAVTALDAEEIEGKESKLDIVDDPVRMYLKQMGQVPLLTREQEVEISKRI 192

Query: 270 SAMEDQLRPKVMCALDEIAEVY----RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              E  ++   + +   IA+ Y    ++LR  ++      +D++   + + L  KL +L+
Sbjct: 193 EQSEAMVKSC-LHSFHFIAKEYLNLAKKLRQGKERFDRVIQDKQVECREEYL-AKLPELI 250

Query: 326 GSLSLNQSRIDLLVEQL----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
             L L   ++D L  QL            + K +   +G L ++ + +  K+ V  +  Q
Sbjct: 251 ERLELLIEKVDSLYSQLLDCPEKSKERKSLEKELQRQKGCLEKIYEKFYFKQKVIEDFVQ 310

Query: 376 GRELD-PHWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSM 433
             E      +S  ++    E +     E + ++  + ++++ +  +  + +  F+     
Sbjct: 311 TSESYYREIISLEQNLENFEKEEADPQEREKNLKAVHSKLRELEKQIQLPLPVFKEKHQE 370

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++   EA  AK EMVEANLRLVIS+AKKY+NRGL FLDLIQEGN+GLMKA EKF++  G
Sbjct: 371 LKQWLNEAIKAKSEMVEANLRLVISIAKKYSNRGLSFLDLIQEGNMGLMKAVEKFEYRRG 430

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K++R  +++  ++ REPTPEEIA
Sbjct: 431 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLMRVQKQLIQELGREPTPEEIA 490

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +  M V+ +R ++K+ + PISL+  +G+ + +  GDFIEDK A +P +    + LRE  
Sbjct: 491 DETQMSVDRIRTIIKMAQHPISLQAQVGESEDTTFGDFIEDKAAENPSEMTGYSLLREKI 550

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LT RE  V+  RFG+      TLEEVGKQF VTRERIRQIEAKA+RK++HP+R 
Sbjct: 551 KDVLGTLTERERTVIEQRFGLLDGYPRTLEEVGKQFRVTRERIRQIEAKALRKMRHPTRL 610

Query: 674 KKLRSFLD 681
           + L+ FL+
Sbjct: 611 RHLKGFLE 618



 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 85/423 (20%), Positives = 162/423 (38%), Gaps = 48/423 (11%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
             +  + +IKLA+++GY+T +++N  LP    +SE++E     L  + I+++D  D+++ 
Sbjct: 83  KQEKLRTLIKLAKEQGYLTYDDINEALPESVNNSEEIEAVYDFLRTLEIDIIDSSDVDNA 142

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +              S + +           DDPVRMYL++MG + LL+RE E+ I+KRI
Sbjct: 143 KAVTALDAEEIEGKESKLDI----------VDDPVRMYLKQMGQVPLLTREQEVEISKRI 192

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E   AM+ + L       +  +    +L  G      +I                  E  
Sbjct: 193 EQSEAMVKSCLHSFHFIAKEYLNLAKKLRQGKERFDRVI-------------QDKQVECR 239

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                +     +  + + E    + S      +   +  S  +  +  +  L++  +   
Sbjct: 240 EEYLAKLPELIERLELLIEKVDSLYSQLLDCPEKSKERKSLEKELQRQKGCLEKIYEKFY 299

Query: 267 HTLSAMEDQLRPKVMCALDEIAEV-YRELRSLQDNAVNGQKDEKS----SVKCKVLKEKL 321
                     + KV+    + +E  YRE+ SL+ N  N +K+E          K +  KL
Sbjct: 300 ---------FKQKVIEDFVQTSESYYREIISLEQNLENFEKEEADPQEREKNLKAVHSKL 350

Query: 322 VKLVGSLSL--------NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            +L   + L        +Q     L E +   S+ +  N   ++ +A+ Y  +   FL+ 
Sbjct: 351 RELEKQIQLPLPVFKEKHQELKQWLNEAIKAKSEMVEANLRLVISIAKKYSNRGLSFLDL 410

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVS 432
            Q  E +   +   + F       F       I + I   I   +    I +     I  
Sbjct: 411 IQ--EGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 468

Query: 433 MVR 435
           ++R
Sbjct: 469 LMR 471


>gi|318066919|emb|CBY89074.1| RNA polymerase sigma70 factor [Halomonas alimentaria]
          Length = 362

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 121/395 (30%), Positives = 178/395 (45%), Gaps = 53/395 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    + +     +++ +  +ET G      
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEEEPQAAGDDDEDGEAEEETTG------ 132

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                        PE A      + E    +                             
Sbjct: 133 ----------GPDPEEARARFEQIREQNAAA----------------------------- 153

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                     +   + S   +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 154 ------QAAIEAHGRHSKPAQEELARLAELFSPIKLVPKHFERLVNQVRISVEQVRAQEK 207

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   I R  F++   G E DP W+         ++ + +A     I + + +I
Sbjct: 208 AVMQLCVKKARIPRKTFIKAFPGSESDPEWLDAFAGEH-PKYADRLAPLRTDIQRAQRKI 266

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + + E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 267 AFEEAMVRLPVQEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 326

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 327 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 361


>gi|255282119|ref|ZP_05346674.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
 gi|255267438|gb|EET60643.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
          Length = 374

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 154/272 (56%), Positives = 201/272 (73%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   V         AKK ++EANLRLV+S+AKKY  RG+
Sbjct: 105 VRMYLKEIGNVPLLTTEEEVELAKRVE---AGDEEAKKRLIEANLRLVVSIAKKYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR IAD   TIR+PVHM + 
Sbjct: 162 PFLDLIQEGNMGLMKAVDKFDYAKGFKFSTYATWWIRQAITRGIADTGRTIRVPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K +R  R +  ++ REPTPEE+A++L +PV  VR+VLKI+++P+SL+TPIG+ED SHL
Sbjct: 222 INKTLRMTRTLLQELGREPTPEEVAERLNVPVSRVREVLKISRDPVSLDTPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A+SP DSA  + LRE     L SLT RE +V+++RFG+      TLEEVGK+
Sbjct: 282 GDFIEDDSALSPSDSAAFSMLREELGTALESLTDRERQVVQLRFGLIDGRARTLEEVGKE 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL
Sbjct: 342 FNVTRERIRQIEAKALRKLRHPSRSKRLKDFL 373



 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 122/314 (38%), Gaps = 45/314 (14%)

Query: 29  DSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED-- 85
            + + ++  A+ ++  +T +E+N      ++S E+M+     L    I++V  D+ +D  
Sbjct: 10  KTLEGLVAEAKTKKNMLTYKEVNDAFGSMQISEEKMDFVFEYLEKHNIDLVHEDNADDTT 69

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   ++  D+  S       +         ST+DPVRMYL+E+G++ LL+ E E+ +AKR
Sbjct: 70  ELLLDNDDDILLSDEEEVEIIDDADVLEGVSTEDPVRMYLKEIGNVPLLTTEEEVELAKR 129

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGP--- 193
           +EAG       L E+ L     I  +         D + +G   L + +D          
Sbjct: 130 VEAGDEEAKKRLIEANLRLVVSIAKKYVGRGMPFLDLIQEGNMGLMKAVDKFDYAKGFKF 189

Query: 194 ------------------------------ESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
                                         E+       T     +   + + E+  + +
Sbjct: 190 STYATWWIRQAITRGIADTGRTIRVPVHMVETINKTLRMTRTLLQELGREPTPEEVAERL 249

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
                 +    K+S+D  S      E  ++   +  ED+   + + SA    LR ++  A
Sbjct: 250 NVPVSRVREVLKISRDPVSLDTPIGEEDDSHLGDFIEDDSALSPSDSAAFSMLREELGTA 309

Query: 284 LDEIAEVYRELRSL 297
           L+ + +  R++  L
Sbjct: 310 LESLTDRERQVVQL 323


>gi|242373866|ref|ZP_04819440.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
 gi|242348420|gb|EES40022.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
          Length = 368

 Score =  231 bits (589), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      IAK  + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVNLLSAQEEIELAKKIEQ---GDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I +V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDITLVNEKDSSDTDEKLNPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AK+IE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKKIEQGDEIAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|323340800|ref|ZP_08081052.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
 gi|323091923|gb|EFZ34543.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
          Length = 373

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 198/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E + +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLTAEEEKKLALRIE---EGDEEAKQRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R+M   + REP PEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRIQRQMLQDLGREPIPEEIGAEMNLPTEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDHAATSPADHAAYELLKEQIESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 373



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 54/202 (26%), Positives = 85/202 (42%), Gaps = 14/202 (6%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
             E  ++ L       + +++++  +Q G V   EL   + P +++SEQ+ D +A +   
Sbjct: 2   AEEKKNNQLDDVVYKKALREVVQEFKQAGEVRYSELTKHVSPLDLTSEQINDLIADVEKR 61

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           GI+VVD +     E    + +     S S V        +    +DPVRMYL+E+G + L
Sbjct: 62  GISVVDENGDPTAESLNQAKEEEKELSKSDV-----SAPSGVKINDPVRMYLKEIGRVNL 116

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+ E E  +A RIE G       L E+ L     I  R  +  G + L  I         
Sbjct: 117 LTAEEEKKLALRIEEGDEEAKQRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------Q 167

Query: 194 ESKGGFFHGTEGHSYQKREDSS 215
           E   G     E   Y+K    S
Sbjct: 168 EGNMGLMKAVEKFDYRKGFKFS 189


>gi|148272828|ref|YP_001222389.1| RNA polymerase sigma factor [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830758|emb|CAN01698.1| RNA polymerase principal sigma factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 492

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 133/254 (52%), Positives = 182/254 (71%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   +R    +   AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EK
Sbjct: 239 RELERELRWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEK 298

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 299 FDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 358

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE++++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 359 TPEELSRELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDTEAVVPADAVGFT 418

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    +L SL+ RE  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL
Sbjct: 419 MLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKL 478

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +L+
Sbjct: 479 RHPSRSQSLRDYLE 492



 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
                +     +   +T DPV+ YL+++G + LL+   E+ +A RIEAG       L  +
Sbjct: 176 EEDEDVPVYSTTITGATADPVKDYLKQIGKVALLNAAEEVELAMRIEAGLF-AEDKLANT 234

Query: 161 PLTFQAL 167
           P   + L
Sbjct: 235 PGISREL 241


>gi|81428494|ref|YP_395494.1| RNA polymerase sigma factor RpoD [Lactobacillus sakei subsp. sakei
           23K]
 gi|78610136|emb|CAI55185.1| DNA-directed RNA polymerase sigma factor, sigma A (Primary sigma
           factor) [Lactobacillus sakei subsp. sakei 23K]
          Length = 369

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 169/383 (44%), Positives = 229/383 (59%), Gaps = 26/383 (6%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           D AV     E    K     E + K+V   +L    I+ L++Q+ D    I+  +G    
Sbjct: 13  DTAVKALIKEYKPKKEITNDELVAKIVKPFALEADEINELMQQVEDHGIGIVDEDGNP-- 70

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                                    +   K   +          +     +R  +K I  
Sbjct: 71  ---------------------SAATLKKEKVSAKELKDMSAPTGIKINDPVRMYLKEIGR 109

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            + ++  +   +   + +       AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN
Sbjct: 110 VSLLNAQQEVDLALRIEQ---GDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGN 166

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GLMKA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+
Sbjct: 167 MGLMKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQ 226

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +   + REPTPEEI  ++ M  + VR++LKI +EP+SLETPIG+ED SHLGDFIED++A 
Sbjct: 227 LLQDLGREPTPEEIGAEMDMNTDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDAT 286

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQ
Sbjct: 287 SPEEHASYELLKEQLESVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQ 346

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 347 IEAKALRKLRHPSRSKQLKDFLE 369



 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 40/158 (25%), Positives = 70/158 (44%), Gaps = 9/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D + K +IK  + +  +T +EL    + P  + ++++ + +  + + GI +VD D     
Sbjct: 13  DTAVKALIKEYKPKKEITNDELVAKIVKPFALEADEINELMQQVEDHGIGIVDEDGNPSA 72

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +           S+  L+          +DPVRMYL+E+G + LL+ + E+ +A RI
Sbjct: 73  ATLKK-------EKVSAKELKDMSAPTGIKINDPVRMYLKEIGRVSLLNAQQEVDLALRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 126 EQGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI 162


>gi|86739990|ref|YP_480390.1| sigma 38 [Frankia sp. CcI3]
 gi|86566852|gb|ABD10661.1| RNA polymerase, sigma 70 subunit, RpoD [Frankia sp. CcI3]
          Length = 409

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 148/286 (51%), Positives = 214/286 (74%), Gaps = 6/286 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 127 AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 183

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 184 VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 243

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 244 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 303

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 304 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 363

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 364 DGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 409



 Score =  104 bits (259), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 79/399 (19%), Positives = 139/399 (34%), Gaps = 59/399 (14%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           +    SD     S   L  +   D  K +I   ++ G++T E++   +   E+  EQ E 
Sbjct: 7   RSREGSDEIPPMSPTVLPREAQVDEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAET 66

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            + +L++ GI V++      +E              +    ++ + +    T DPVRMYL
Sbjct: 67  VLQVLNDEGIEVLEAGGESPDEAD----------LLARRRREEEELALKAPTSDPVRMYL 116

Query: 126 REMGSIELLSREGEIAIAKRIEAGR----------------------------AMMMASL 157
           +E+G + LL+ E E+ +AKRIEAG                              +    L
Sbjct: 117 KEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKL 176

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E+ L     I  R  +  G   L  I         E   G     E   Y K    S  
Sbjct: 177 VEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTY 227

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
                 Q     I   A+  +     V++  +      + L +   + +    A E  L 
Sbjct: 228 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLT 287

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           P     + EI +V +E  SL+      +         +     +     S  L Q ++D 
Sbjct: 288 P---DKVREILKVSQEPVSLETPIGEEEDSHLGDF-IEDCDAVVPVDAASFILLQEQLDS 343

Query: 338 LVEQLYDISKRIMHNE--------GELLRLAQSYGIKRD 368
           ++  L D  K+++             L  + + +G+ R+
Sbjct: 344 VLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRE 382


>gi|1710683|sp|P52328|RPSD2_BACSP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|149623|gb|AAA25264.1| RNA polymerase sigma-subunit [Leptospira borgpetersenii]
          Length = 377

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSADDEVELAKRI---MNGDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA ++ + VE VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVSRQLLQELGREPTPEEIAAEMELSVEKVREIMKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEALTPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 45/174 (25%), Positives = 79/174 (45%), Gaps = 5/174 (2%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + +     D   D   ++I+  ++R  +  +++   L P +   EQM++    L
Sbjct: 2   ANDQHTELETEFTLDQVKD---QLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMDEFYEHL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            ++GI VV+ +D E+        D   + ++   F            +DPVRMYL+E+G 
Sbjct: 59  GDLGIEVVNEND-EEVSNLRQGEDHDGNDNDDFNFDDDLSLPPGIKINDPVRMYLKEIGR 117

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + E+ +AKRI  G       L E+ L     I  R  +  G   L  I
Sbjct: 118 VPLLSADDEVELAKRIMNGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 170


>gi|329117418|ref|ZP_08246135.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
 gi|326907823|gb|EGE54737.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
          Length = 369

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V   +     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTGEEEKELAVAV---DEGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 118/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VADFIRNHKKEGSAVDDEITEKLVIPFVLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  ++ G
Sbjct: 68  PSSKYVVEEPKPEELTDEQLIGSNSAKVNDPVRMYLKEIGVVPLLTGEEEKELAVAVDEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|224476669|ref|YP_002634275.1| RNA polymerase sigma factor RpoD [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421276|emb|CAL28090.1| RNA polymerase sigma factor SigA [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 369

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 156/316 (49%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    +++      + D  E    + ++    V     +R  +K I     ++  
Sbjct: 57  DEFFDQINDNDINLVNEKDSSDTDEKLNPHDLSAPPGVKINDPVRMYLKEIGRVDLLNAQ 116

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 117 EEIELAKRIEQ---GDEVAKARLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 173

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 174 EKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 233

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+   SP D A 
Sbjct: 234 DPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEVQSPSDHAA 293

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 294 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 353

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 354 KLRHPSRSKRLKDFMD 369



 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 47/178 (26%), Positives = 86/178 (48%), Gaps = 18/178 (10%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
            N+    + +  D +L  +   D  K+++   ++ G+++ EE+   L   ++ S+QM++ 
Sbjct: 3   ENQVKVVKKQTIDPTLTLE---DVKKQLLDKGKKEGHLSHEEIAEKLQNFDMDSDQMDEF 59

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
              +++  IN+V+  D  D +   +  DL++                    +DPVRMYL+
Sbjct: 60  FDQINDNDINLVNEKDSSDTDEKLNPHDLSA--------------PPGVKINDPVRMYLK 105

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+G ++LL+ + EI +AKRIE G  +  A L E+ L     I  R  +  G   L  I
Sbjct: 106 EIGRVDLLNAQEEIELAKRIEQGDEVAKARLAEANLRLVVSIAKRY-VGRGMLFLDLI 162


>gi|111221463|ref|YP_712257.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
 gi|111148995|emb|CAJ60675.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
          Length = 409

 Score =  231 bits (588), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 148/286 (51%), Positives = 214/286 (74%), Gaps = 6/286 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 127 AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 183

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 184 VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 243

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 244 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 303

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 304 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 363

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 364 DGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 409



 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 81/399 (20%), Positives = 139/399 (34%), Gaps = 59/399 (14%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           +    SD     S   L  +   D  K +I   ++ G++T E++   +   E+  EQ E 
Sbjct: 7   RSREGSDEIPPMSPTVLPREAQVDEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAET 66

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            + +L++ GI V++        G E+  +    A       +    +    T DPVRMYL
Sbjct: 67  VLQVLNDEGIEVLEA-------GGENPDEADLLARRRREEEELALKAP---TSDPVRMYL 116

Query: 126 REMGSIELLSREGEIAIAKRIEAGR----------------------------AMMMASL 157
           +E+G + LL+ E E+ +AKRIEAG                              +    L
Sbjct: 117 KEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKL 176

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E+ L     I  R  +  G   L  I         E   G     E   Y K    S  
Sbjct: 177 VEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTY 227

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
                 Q     I   A+  +     V++  +      + L +   + +    A E  L 
Sbjct: 228 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLT 287

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           P     + EI +V +E  SL+      +         +     +     S  L Q ++D 
Sbjct: 288 P---DKVREILKVSQEPVSLETPIGEEEDSHLGDF-IEDCDAVVPVDAASFILLQEQLDS 343

Query: 338 LVEQLYDISKRIMHNE--------GELLRLAQSYGIKRD 368
           ++  L D  K+++             L  + + +G+ R+
Sbjct: 344 VLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRE 382


>gi|239827752|ref|YP_002950376.1| RNA polymerase sigma factor RpoD [Geobacillus sp. WCH70]
 gi|239808045|gb|ACS25110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           WCH70]
          Length = 374

 Score =  231 bits (588), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVPLLSAEEEIELAKRIEQ---GDEEAKRRLTEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQEATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 63/262 (24%), Positives = 105/262 (40%), Gaps = 15/262 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + +++ +L ++RG +T EE+   L   ++ S+QM++    L++ GI V+       E 
Sbjct: 18  EQAKEQLTELGKKRGILTYEEIAERLSGFDLDSDQMDEFYEYLADQGIEVIS------ES 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +   D+   +      L           +DPVRMYL+E+G + LLS E EI +AKRIE
Sbjct: 72  DLDADPDIDDLSKEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRIE 131

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 132 QGDEEAKRRLTEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 182

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y+K    S        Q     I   A+  +     V++  +      + L +   +   
Sbjct: 183 YRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTP 242

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              A E  L P+ +  + +IA+
Sbjct: 243 EEIAEEMDLTPEKVREILKIAQ 264


>gi|15900942|ref|NP_345546.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae TIGR4]
 gi|15903023|ref|NP_358573.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae R6]
 gi|111657922|ref|ZP_01408632.1| hypothetical protein SpneT_02000898 [Streptococcus pneumoniae
           TIGR4]
 gi|116516638|ref|YP_816435.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae D39]
 gi|148985044|ref|ZP_01818287.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|148989116|ref|ZP_01820506.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|148994179|ref|ZP_01823494.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|148998339|ref|ZP_01825781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|149003984|ref|ZP_01828792.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|149006254|ref|ZP_01829966.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|149013172|ref|ZP_01833989.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|149019675|ref|ZP_01834994.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168483147|ref|ZP_02708099.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|168487460|ref|ZP_02711968.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|168488915|ref|ZP_02713114.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|168494506|ref|ZP_02718649.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|168576202|ref|ZP_02722096.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|169833634|ref|YP_001694498.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182684177|ref|YP_001835924.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|221231817|ref|YP_002510969.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225854569|ref|YP_002736081.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae JJA]
 gi|225856717|ref|YP_002738228.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae P1031]
 gi|225858886|ref|YP_002740396.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 70585]
 gi|225861039|ref|YP_002742548.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|237650028|ref|ZP_04524280.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974]
 gi|237821736|ref|ZP_04597581.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298230104|ref|ZP_06963785.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298255542|ref|ZP_06979128.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|298502915|ref|YP_003724855.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|303256088|ref|ZP_07342108.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|303260611|ref|ZP_07346576.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|303263023|ref|ZP_07348956.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|303264870|ref|ZP_07350786.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|303266910|ref|ZP_07352787.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|303269116|ref|ZP_07354896.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|307067745|ref|YP_003876711.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|307127396|ref|YP_003879427.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|61234224|sp|P0A4I9|RPOD_STRPN RecName: Full=RNA polymerase sigma factor rpoD
 gi|61234230|sp|P0A4J0|RPOD_STRR6 RecName: Full=RNA polymerase sigma factor rpoD
 gi|2108331|emb|CAA72252.1| rpoD [Streptococcus pneumoniae]
 gi|14972548|gb|AAK75186.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae TIGR4]
 gi|15458593|gb|AAK99783.1| RNA polymerase sigmA FACTOR 70 [Streptococcus pneumoniae R6]
 gi|116077214|gb|ABJ54934.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae D39]
 gi|147755736|gb|EDK62781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|147758043|gb|EDK65049.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|147762031|gb|EDK68993.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|147763023|gb|EDK69967.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|147922742|gb|EDK73859.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|147925339|gb|EDK76417.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|147927422|gb|EDK78452.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|147931050|gb|EDK82030.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168996136|gb|ACA36748.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043392|gb|EDT51438.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629511|gb|ACB90459.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|183569691|gb|EDT90219.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|183572434|gb|EDT92962.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|183575600|gb|EDT96128.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|183577989|gb|EDT98517.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|220674277|emb|CAR68818.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225720127|gb|ACO15981.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae 70585]
 gi|225722225|gb|ACO18078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae JJA]
 gi|225725305|gb|ACO21157.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae P1031]
 gi|225728137|gb|ACO23988.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238510|gb|ADI69641.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|301794192|emb|CBW36610.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV104]
 gi|301800046|emb|CBW32640.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae OXC141]
 gi|301802035|emb|CBW34765.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV200]
 gi|302596935|gb|EFL64061.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|302635850|gb|EFL66352.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|302638261|gb|EFL68731.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|302641365|gb|EFL71732.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|302643543|gb|EFL73813.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|302645558|gb|EFL75789.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|306409282|gb|ADM84709.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|306484458|gb|ADM91327.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|327389372|gb|EGE87717.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA04375]
 gi|332073431|gb|EGI83910.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17570]
 gi|332075028|gb|EGI85499.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17545]
 gi|332075404|gb|EGI85873.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41301]
 gi|332200548|gb|EGJ14620.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41317]
 gi|332201555|gb|EGJ15625.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47368]
 gi|332202930|gb|EGJ16998.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47901]
          Length = 369

 Score =  231 bits (588), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    +L +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSNEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL +I   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEILDTLTDREENVLRL 317


>gi|84495969|ref|ZP_00994823.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
 gi|84382737|gb|EAP98618.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
          Length = 546

 Score =  231 bits (588), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 134/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 294 KLKRELWWIAQDGKNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 353

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 354 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 413

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 414 PEELAIELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 473

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 474 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 533

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 534 HPSRSQALRDYLD 546



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 79  DGDDLEDEEGSEDSLDLASSAS----NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           +GDD +D++    +  +A+       +       ++     +T DPV+ YL+++G + LL
Sbjct: 204 EGDDADDKKDEPATTAVAAGGFVLRDDDDDDAPVQQVVTAGATADPVKDYLKQIGKVALL 263

Query: 135 SREGEIAIAKRIEAGR 150
           + E E+ +AKRIEAG 
Sbjct: 264 NAEQEVELAKRIEAGL 279


>gi|260886856|ref|ZP_05898119.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|330839344|ref|YP_004413924.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863455|gb|EEX77955.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|329747108|gb|AEC00465.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 375

 Score =  231 bits (588), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 210/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    +++ ++ E     A+KE+ EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVPLLSADEE---IALAKRMEAGDEEAQKELAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA+ + + VE VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 223 INKLIRVSRQLLQQLGREPSPEEIAEAMEISVERVREIMKIAQEPVSLETPIGEEEDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A +P ++A    L+E    VL +LT REERVLR+RFG+      TLEEVG+ 
Sbjct: 283 GDFIEDQDAPAPAEAASFMLLKEQLEEVLDTLTEREERVLRLRFGLDDGRARTLEEVGQN 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ FLD
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSRKLKDFLD 375



 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/177 (29%), Positives = 74/177 (41%), Gaps = 12/177 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTV 67
             ++    D D       S      ++   R  G  +T  EL   L   E++ ++++D  
Sbjct: 3   EKANKAALDVDKKPT--QSSAIVSSLLTKGRGNGGVLTYGELMTALQEQELTPDEIDDLY 60

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
              SN GI +VD  +    E  ED  +       S             S DDPVRMYL+E
Sbjct: 61  ETFSNKGIEIVDDSNRAQAEMDEDKAEEEVDIDLS--------IPEGISIDDPVRMYLKE 112

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G + LLS + EIA+AKR+EAG       L E+ L     I  R  +  G   L  I
Sbjct: 113 IGRVPLLSADEEIALAKRMEAGDEEAQKELAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|319892618|ref|YP_004149493.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162314|gb|ADV05857.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464344|gb|ADX76497.1| RNA polymerase sigma factor SigA [Staphylococcus pseudintermedius
           ED99]
          Length = 369

 Score =  231 bits (588), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRVDLLSAQEEIELAKRIEQ---GDEVAKARLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 277 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 337 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 369



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/157 (28%), Positives = 80/157 (50%), Gaps = 15/157 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  K++I+  ++ G+++ EE+   L   ++ S+QM++   M+++  I +++  D  D +
Sbjct: 21  EDVKKQLIEKGKKEGHLSHEEVADKLQNFDMDSDQMDEFFDMINDNDIQLINEKDSSDTD 80

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              +  DL++                    +DPVRMYL+E+G ++LLS + EI +AKRIE
Sbjct: 81  DKLNPNDLSA--------------PPGVKINDPVRMYLKEIGRVDLLSAQEEIELAKRIE 126

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G  +  A L E+ L     I  R  +  G   L  I
Sbjct: 127 QGDEVAKARLAEANLRLVVSIAKRY-VGRGMLFLDLI 162


>gi|314933733|ref|ZP_07841098.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
 gi|313653883|gb|EFS17640.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
          Length = 368

 Score =  231 bits (588), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +      +AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVNLLSAQEEIELAKKIEQ---GDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ F+D
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD 368



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++I   ++ G+++ EE+   L   E+ S+QM+D    
Sbjct: 3   DNQVKIKKQTIDPTL-TLEDVKKQLIDKGKKEGHLSHEEIAEKLQNFEMDSDQMDDFFEQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I +V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDITLVNEKDSSDTDEKLNPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LLS + EI +AK+IE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLSAQEEIELAKKIEQGDEVAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|331269992|ref|YP_004396484.1| RpoD family RNA polymerase sigma-70 subunit [Clostridium botulinum
           BKT015925]
 gi|329126542|gb|AEB76487.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           botulinum BKT015925]
          Length = 368

 Score =  230 bits (587), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E  ++   +         AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGKVPLLSPDEEINLAQRIE---DGDMYAKKKLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 216 INKLIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 276 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 368



 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 52/184 (28%), Positives = 82/184 (44%), Gaps = 23/184 (12%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M   KK++  + ++ +D+ D +         K +I   +++G +T +E+   L   E++ 
Sbjct: 1   MADNKKKDTTNKNDVKDNKDRMKI------IKNLIDKGKKKGNLTYKEIMDELDNVELTP 54

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+E    +L +M I VV      + E  E  L +                    S DDP
Sbjct: 55  EQIEKVYGVLESMDIEVVGDIKEIETEEEEIDLSV----------------PEGISIDDP 98

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G + LLS + EI +A+RIE G       L E+ L     I  R  +  G   
Sbjct: 99  VRMYLKEIGKVPLLSPDEEINLAQRIEDGDMYAKKKLAEANLRLVVSIAKRY-VGRGMLF 157

Query: 181 LREI 184
           L  I
Sbjct: 158 LDLI 161


>gi|168491966|ref|ZP_02716109.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183573791|gb|EDT94319.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
          Length = 369

 Score =  230 bits (587), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    +L +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 368



 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGIATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSNEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL +I   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEILDTLTDREENVLRL 317


>gi|56421017|ref|YP_148335.1| RNA polymerase sigma factor RpoD [Geobacillus kaustophilus HTA426]
 gi|261417657|ref|YP_003251339.1| RNA polymerase sigma factor RpoD [Geobacillus sp. Y412MC61]
 gi|297529352|ref|YP_003670627.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|319767537|ref|YP_004133038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
 gi|56380859|dbj|BAD76767.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A)
           [Geobacillus kaustophilus HTA426]
 gi|261374114|gb|ACX76857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC61]
 gi|297252604|gb|ADI26050.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|317112403|gb|ADU94895.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
          Length = 375

 Score =  230 bits (587), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 162/304 (53%), Positives = 210/304 (69%), Gaps = 3/304 (0%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E DP     AK+         V   V     +R  +K I     +S  E   +   + + 
Sbjct: 75  EADPDIDDLAKEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRIEQ- 133

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFS
Sbjct: 134 --GDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFS 191

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+++ 
Sbjct: 192 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEEMD 251

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP + A    L+E    VL
Sbjct: 252 LTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSEHAAYELLKEQLEDVL 311

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+
Sbjct: 312 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLK 371

Query: 678 SFLD 681
            FL+
Sbjct: 372 DFLE 375



 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 108/279 (38%), Gaps = 15/279 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++   +        +  +   +++ +L ++RG +T EE+   L   ++ S+QM++    L
Sbjct: 2   AEKPAQSKQAEAAGESLEQVKEQLAELGKKRGILTYEEIAERLSGFDLDSDQMDEYYEYL 61

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +  GI V+   DLE         D+   A      L           +DPVRMYL+E+G 
Sbjct: 62  AEQGIEVISESDLEA------DPDIDDLAKEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 115

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS E EI +AKRIE G       L E+ L     I  R  +  G   L  I      
Sbjct: 116 VPLLSAEEEIELAKRIEQGDEEAKRRLTEANLRLVVSIAKRY-VGRGMLFLDLI------ 168

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   Y+K    S        Q     I   A+  +     V++  + 
Sbjct: 169 --QEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 226

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
                + L +   +      A E  L P+ +  + +IA+
Sbjct: 227 IRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQ 265


>gi|138896056|ref|YP_001126509.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196248949|ref|ZP_03147649.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
 gi|134267569|gb|ABO67764.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211825|gb|EDY06584.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
          Length = 375

 Score =  230 bits (587), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 161/304 (52%), Positives = 208/304 (68%), Gaps = 3/304 (0%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E DP      K+         V   V     +R  +K I     +S  E   +   + + 
Sbjct: 75  ETDPDIDELVKEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRIEQ- 133

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFS
Sbjct: 134 --GDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFS 191

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEIA+++ 
Sbjct: 192 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEEMD 251

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP + A    L+E    VL
Sbjct: 252 LTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSEHAAYELLKEQLEDVL 311

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+
Sbjct: 312 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLK 371

Query: 678 SFLD 681
            FL+
Sbjct: 372 DFLE 375



 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 109/279 (39%), Gaps = 15/279 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++   +        D  + + +++ +L ++RG +T EE+   L   ++ S+QM++    L
Sbjct: 2   AEKPAQSKQAEAAADTLEQAKEQLAELGKKRGILTYEEIAERLSGFDLDSDQMDEYYEYL 61

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           ++ GI V+   D+E         D+          L           +DPVRMYL+E+G 
Sbjct: 62  ADQGIEVISESDIE------TDPDIDELVKEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 115

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS E EI +AKRIE G       L E+ L     I  R  +  G   L  I      
Sbjct: 116 VPLLSAEEEIELAKRIEQGDEEAKRRLTEANLRLVVSIAKRY-VGRGMLFLDLI------ 168

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   Y+K    S        Q     I   A+  +     V++  + 
Sbjct: 169 --QEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 226

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
                + L +   +      A E  L P+ +  + +IA+
Sbjct: 227 IRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQ 265


>gi|32453269|gb|AAP82767.1| sigma 70 [Hydrogenothermus marinus]
          Length = 369

 Score =  230 bits (587), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 117/388 (30%), Positives = 187/388 (48%), Gaps = 20/388 (5%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYLREMG  ELL+REGEI IAKRIE G+  M+ ++   P T   ++   +++ +  
Sbjct: 1   DPVRMYLREMGHSELLTREGEIEIAKRIEDGQRSMVQAIAACPPTIAFMLETVEKIENDK 60

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
             + E++D           G     +       ++    +  DD  +   D         
Sbjct: 61  LRVDEVVD-----------GLIDNLDDIVPPTTDEEDDAESLDDDIDEALDESDDDATDD 109

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            D +  D   +  E +E   +  E+ +A   +     L+   +    +I E Y+ L +  
Sbjct: 110 SDDTFDDVS-DEDEEEEEEEETKEERAARIQAENLATLKKGTLAHFAKIREWYQALDA-- 166

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                  +    + + + L++ +   +  +      I+ + + +    +++  +E ++  
Sbjct: 167 ----ALTQGGTQNPEYQKLRDLIAHELLHIRFTARYIEQVCDIVRGFIEQVRQHERQIQN 222

Query: 359 LAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           L    G + RD FL+     E +  W+    +     W   +     S+L  +  I  I 
Sbjct: 223 LCTQIGTMPRDHFLKTFPPNETNLDWIKNEIE-AGHPWSESLVRVFPSVLDEQQRIIEIV 281

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + + E + I   + +GE +   AK+EMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 282 ERARVPLDELKDIFKRMSQGEAKMRAAKREMVEANLRLVISIAKKYTNRGLQFLDLIQEG 341

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           NIGLMKA +KF++  GYKFSTYA WW+ 
Sbjct: 342 NIGLMKAVDKFEYRRGYKFSTYATWWII 369


>gi|168187756|ref|ZP_02622391.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
 gi|169294399|gb|EDS76532.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
          Length = 368

 Score =  230 bits (587), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 157/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +  GE     AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGKVPLLTPDEEVDLAQRIEAGEMY---AKKKLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 216 INKLIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 276 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 368



 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 49/154 (31%), Positives = 75/154 (48%), Gaps = 16/154 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +I   +++G +T +E+   L   E+S EQ+E    +L +M I V+ GD  + E   E
Sbjct: 24  IKSLIDKGKKKGSLTYKEIMDELDNVELSPEQIEKVYGVLESMDIEVI-GDMKDMESEEE 82

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +DL+                   S DDPVRMYL+E+G + LL+ + E+ +A+RIEAG 
Sbjct: 83  EEIDLSVPE--------------GISIDDPVRMYLKEIGKVPLLTPDEEVDLAQRIEAGE 128

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 129 MYAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|327440913|dbj|BAK17278.1| DNA-directed RNA polymerase, sigma subunit [Solibacillus silvestris
           StLB046]
          Length = 375

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 198/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSADQEIRLAERIEQ---GDEEARKRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDSEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/157 (26%), Positives = 75/157 (47%), Gaps = 7/157 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   K+++  A+Q G ++++E++  L   E+ +E++ +    +    + V   ++ E+E 
Sbjct: 19  EQVKKQLLAKAKQVGEMSMKEISDTLAFFELENEEIFNFADEIEKNDVTVEGKEEFEEEA 78

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S+        +S  +  L           +DPVRMYL+E+G ++LLS + EI +A+RIE
Sbjct: 79  LSK------QESSEEAFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSADQEIRLAERIE 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 133 QGDEEARKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|318066947|emb|CBY89088.1| RNA polymerase sigma70 factor [Halomonas halodenitrificans]
          Length = 360

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 122/397 (30%), Positives = 179/397 (45%), Gaps = 59/397 (14%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVGSILEAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  +E+             +
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEAEVPEEEP---------SAAN 118

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                +++ S     PE A      + E        + A                     
Sbjct: 119 DEDEEEEEESTGGPDPEEARARFEQIREQSGSVDAAVEA--------------------- 157

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                           + S + K    +L +L   + L     + LV Q+    +++   
Sbjct: 158 --------------HGRHSKEAKEELARLAELFSPIKLVPKHFERLVNQVRISVEQVRAQ 203

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   I R  F++   G E +P W+    D    ++   +      I + + 
Sbjct: 204 EKAVMQLCVKKARIPRKTFIKAFPGSESNPEWLDGFSDEH-PKYAERLRPLRTDIQRAQR 262

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + + E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 263 KIAFEEAMVRLPVKEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 322

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 323 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 359


>gi|318066931|emb|CBY89080.1| RNA polymerase sigma70 factor [Halomonas campaniensis]
          Length = 368

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 126/395 (31%), Positives = 185/395 (46%), Gaps = 47/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P   ++++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVESILDAYDTT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R + DL +        GF    EG      E    E E  D  + +GD     
Sbjct: 79  QDEEAPGR-LSDLFS--------GFIDPDEGIPGVA-EAEVPEPEVSDDLDEDGDGSDDE 128

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +      ++    PE A      + E    +                             
Sbjct: 129 EEDDSTSNEGGPDPEEARARFEQIREQNAAAQAA-------------------------- 162

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         + S + +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 163 ---------IAAHGRHSREAQDELARLAELFSPIKLVPKHFERLVNQVRISVEQVRAQEK 213

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   I R  F++   G E DP W++        ++ + +      I + + +I
Sbjct: 214 AVMQLCVKKARIPRKTFIKAFPGSESDPEWLTRFAADH-PKYADRLEPLRADIARAQRKI 272

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 273 AFEEEMVRLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 332

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 333 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|325290508|ref|YP_004266689.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965909|gb|ADY56688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 392

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 163/393 (41%), Positives = 245/393 (62%), Gaps = 14/393 (3%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
             QD   N   +  +S+  +  K + V  +  + L +++ +L  +++ +  ++I  +E +
Sbjct: 7   KKQDIRSNYPTEGGNSLHAEDHKRECVAHL--IELGKTKGNLTYDEIANALQKIDLSEEQ 64

Query: 356 LLRLAQSYGIKRDVFLERHQGRELD-------PHWVSYAKDFPEGEWKNFVACEVDSILK 408
           +  +           ++ H   E D               +  + +        +D    
Sbjct: 65  IEEVYDQISTLGIDVIDEHSEGETDIVIDKETEKLAEEISEETDIDLSIPEGVGIDD--P 122

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +        +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 123 VRMYLKEIGRVPLLTAEEEIELAKSME---AGDEMAKRRLAEANLRLVVSIAKRYVGRGM 179

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 180 LFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 239

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+PTPEE AK + +P E VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 240 INKLIRVNRQLLQELGRDPTPEETAKVMDIPEERVREIMKIAQEPVSLETPIGEEEDSHL 299

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A    L+E    VL +LT REE+VLR+RFG+      TLEEVG++
Sbjct: 300 GDFIPDEDAPAPSEAASFLLLKEQLEEVLETLTSREEKVLRLRFGLDDGRTRTLEEVGQE 359

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 360 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 392



 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 51/180 (28%), Positives = 82/180 (45%), Gaps = 1/180 (0%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
           KK++  S+   E  +     D   +    +I+L + +G +T +E+   L   ++S EQ+E
Sbjct: 7   KKQDIRSNYPTEGGNSLHAEDHKRECVAHLIELGKTKGNLTYDEIANALQKIDLSEEQIE 66

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           +    +S +GI+V+D     + +   D      +   S               DDPVRMY
Sbjct: 67  EVYDQISTLGIDVIDEHSEGETDIVIDKETEKLAEEISEETDIDLSIPEGVGIDDPVRMY 126

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L+E+G + LL+ E EI +AK +EAG  M    L E+ L     I  R  +  G   L  I
Sbjct: 127 LKEIGRVPLLTAEEEIELAKSMEAGDEMAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 185


>gi|158313963|ref|YP_001506471.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158109368|gb|ABW11565.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 409

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 148/286 (51%), Positives = 214/286 (74%), Gaps = 6/286 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 127 AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 183

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 184 VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 243

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 244 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 303

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 304 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 363

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 364 DGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 409



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 81/399 (20%), Positives = 140/399 (35%), Gaps = 59/399 (14%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           +    SD     S   L  +   D  K +I   ++ G++T E++   +   E+  EQ E 
Sbjct: 7   RSREGSDEIPPMSPTVLPREAQVDEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAET 66

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            + +L++ GI V++        G E++ +    A       +    +    T DPVRMYL
Sbjct: 67  VLQVLNDEGIEVLEA-------GGENADEADLLARRRREEEELALKAP---TSDPVRMYL 116

Query: 126 REMGSIELLSREGEIAIAKRIEAGR----------------------------AMMMASL 157
           +E+G + LL+ E E+ +AKRIEAG                              +    L
Sbjct: 117 KEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKL 176

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E+ L     I  R  +  G   L  I         E   G     E   Y K    S  
Sbjct: 177 VEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTY 227

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
                 Q     I   A+  +     V++  +      + L +   + +    A E  L 
Sbjct: 228 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLT 287

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           P     + EI +V +E  SL+      +         +     +     S  L Q ++D 
Sbjct: 288 P---DKVREILKVSQEPVSLETPIGEEEDSHLGDF-IEDCDAVVPVDAASFILLQEQLDS 343

Query: 338 LVEQLYDISKRIMHNE--------GELLRLAQSYGIKRD 368
           ++  L D  K+++             L  + + +G+ R+
Sbjct: 344 VLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRE 382


>gi|1519632|gb|AAC44890.1| sigma 70-type sigma factor SigA [Heliobacillus mobilis]
          Length = 333

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 64  VRMYLKEIGRVPLLSAEEEIELAKRME---DGDEEAKRRLAEANLRLVVSIAKRYVGRGM 120

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 121 LFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 180

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +  REP PEEIAK++ +PV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 181 INKLIRVSRQLLQEFGREPNPEEIAKEMDIPVDRVREIMKIAQEPVSLETPIGEEEDSHL 240

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A +P ++A    L+E    VL +LT RE +VLR+RFG+      TLEEVG++
Sbjct: 241 GDFIEDQDAPAPAEAASFILLKEQLEEVLETLTAREMKVLRLRFGLDDGRSRTLEEVGQE 300

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ ++D
Sbjct: 301 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYVD 333



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/127 (30%), Positives = 56/127 (44%), Gaps = 1/127 (0%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           ++++Q++D    L NMGI+VV      +     +   +  S                   
Sbjct: 1   MTADQVDDVYEQLGNMGIDVVSEPAEAESMEKAEEPIIRESEEEEEEIEVDLSVPEGVGI 60

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DDPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L     I  R  +  G
Sbjct: 61  DDPVRMYLKEIGRVPLLSAEEEIELAKRMEDGDEEAKRRLAEANLRLVVSIAKRY-VGRG 119

Query: 178 TTLLREI 184
              L  I
Sbjct: 120 MLFLDLI 126


>gi|220912379|ref|YP_002487688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219859257|gb|ACL39599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 433

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 139/283 (49%), Positives = 186/283 (65%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EVD  L+I   + +         S        +     +   AK  ++EANLRLV+S
Sbjct: 151 AEQEVDLALRIEAGLFAEEKIAADDGSMEPKYKRELEFIIHDGKRAKNHLLEANLRLVVS 210

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ T
Sbjct: 211 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQART 270

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V +V K  +EPISL T
Sbjct: 271 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDMTPEKVVEVQKYGREPISLHT 330

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  AV P D+     L+E    VL +L+ RE  V+ MRFG+    
Sbjct: 331 PLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQ 390

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 391 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 433



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 30/52 (57%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +         ++  +  +T DPV+ YL+++G + LL+ E E+ +A RIEAG 
Sbjct: 114 SDADDDDAPVQQVMSAGATADPVKDYLKQIGKVALLNAEQEVDLALRIEAGL 165


>gi|229543825|ref|ZP_04432884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
 gi|229324964|gb|EEN90640.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
          Length = 377

 Score =  230 bits (587), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 172/393 (43%), Positives = 241/393 (61%), Gaps = 24/393 (6%)

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVG--------SLSLNQSRIDLLVEQLYDISKR 348
           + + +   ++ E+S    +  KE+LV+           ++S      DL  +Q+ +  + 
Sbjct: 1   MAEKSARSKEVEESEFTVEKAKEQLVERGKKRGFLTYDTISEKLGHFDLTSDQMDEFYES 60

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
           +     ++            + LE+    E D + +S             V   V     
Sbjct: 61  LGEQGIDVTDDTSDEDAPSHLELEKENDEEFDLNDLS-------------VPPGVKINDP 107

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVDLLSADEEIELAKRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 QFLDLIQEGNMGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + REPTPEEIA+++ +  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVQRSLLQDLGREPTPEEIAEEMDISPDKVREIIKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 76/157 (48%), Gaps = 5/157 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + +++++  ++RG++T + ++  L   +++S+QM++    L   GI+V D    ED  
Sbjct: 19  EKAKEQLVERGKKRGFLTYDTISEKLGHFDLTSDQMDEFYESLGEQGIDVTDDTSDED-- 76

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               S       ++    L           +DPVRMYL+E+G ++LLS + EI +AKRIE
Sbjct: 77  --APSHLELEKENDEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSADEEIELAKRIE 134

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 135 QGDEEAKRRLAEANLRLVVSIAKRY-VGRGMQFLDLI 170


>gi|89100479|ref|ZP_01173341.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
 gi|89084822|gb|EAR63961.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
          Length = 374

 Score =  230 bits (586), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    +S+ ++ E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLSAQEE---ISLAKRIEEGDEEAKRRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPDKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 78/176 (44%), Gaps = 10/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            +  +  ++ D  L  +   +   ++ ++ ++ G +  +++   L   E+ S+QM++   
Sbjct: 2   AEKSARSKEVDSELTMEQVKE---QLTEVGKKTGVLAYDDIAERLSNFELDSDQMDEFYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L + G+ +V  +D  D    E       +       L           +DPVRMYL+E+
Sbjct: 59  FLGDQGVELVGDNDDADPNVQE------LAKGEEEFDLNDLSVPPGVKINDPVRMYLKEI 112

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS + EI++AKRIE G       L E+ L     I  R  +  G   L  I
Sbjct: 113 GRVDLLSAQEEISLAKRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|289550668|ref|YP_003471572.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315658163|ref|ZP_07911035.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
 gi|289180200|gb|ADC87445.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315496492|gb|EFU84815.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
          Length = 368

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 159/316 (50%), Positives = 213/316 (67%), Gaps = 5/316 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISIS 425
           D F ++    ++       + D  E    N ++    V     +R  +K I     ++  
Sbjct: 56  DEFFDQLNDNDISLVNEKDSSDTDEKLNPNDLSAPPGVKINDPVRMYLKEIGRVNLLNAQ 115

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   + +      IAK  + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 116 EEIELAKRIEQ---GDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 172

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R
Sbjct: 173 EKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGR 232

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +P PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHLGDFIED+ A SP D A 
Sbjct: 233 DPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAA 292

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+R
Sbjct: 293 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 352

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSK+L+ F+D
Sbjct: 353 KLRHPSRSKRLKDFMD 368



 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 42/175 (24%), Positives = 83/175 (47%), Gaps = 16/175 (9%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+  + +           +D  K++++  ++ G+++ EE+   +   ++ ++QM++    
Sbjct: 3   DNKVKIKKQTIDPTL-TLEDVKKQLLEKGKKEGHLSHEEIAEKMQNFDMDTDQMDEFFDQ 61

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L++  I++V+  D  D +   +  DL++                    +DPVRMYL+E+G
Sbjct: 62  LNDNDISLVNEKDSSDTDEKLNPNDLSA--------------PPGVKINDPVRMYLKEIG 107

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + LL+ + EI +AKRIE G  +  + L E+ L     I  R  +  G   L  I
Sbjct: 108 RVNLLNAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|188585841|ref|YP_001917386.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350528|gb|ACB84798.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 360

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 165/364 (45%), Positives = 228/364 (62%), Gaps = 32/364 (8%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            ++++  +    L+  +ID   E L      ++   G                       
Sbjct: 29  YKEIMDQLSEFQLSSDQIDEFYEVLTQAGIDVVDAIG----------------------- 65

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E+DP       D  + E    +   V+    +R  +K I     +S  +   +   +   
Sbjct: 66  EVDPD------DPTKAELDLSLPEGVEVSDPVRMYLKEIGKIPLLSPDDEIELAKKIE-- 117

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK+++ EANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFS
Sbjct: 118 -EGDEGAKRKLAEANLRLVVSIAKKYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFS 176

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP PEEIA+++ 
Sbjct: 177 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLVQELGREPLPEEIAEQMD 236

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  + VR++LKI +EP+SLETPIG+ED SHLGDFIED++A  P D+A    L+     VL
Sbjct: 237 MSEDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDAKPPADAAAFELLKGQLEEVL 296

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SLTPRE++VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HP RSK+L+
Sbjct: 297 DSLTPREQKVLRLRFGLDDGKTRTLEEVGKHFGVTRERIRQIEAKALRKLRHPMRSKRLK 356

Query: 678 SFLD 681
            +LD
Sbjct: 357 DYLD 360



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 42/152 (27%), Positives = 71/152 (46%), Gaps = 14/152 (9%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           +++K+ ++RG++T +E+   L   ++SS+Q+++   +L+  GI+VVD             
Sbjct: 16  ELLKVGKERGFLTYKEIMDQLSEFQLSSDQIDEFYEVLTQAGIDVVDAI----------- 64

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                   + +               DPVRMYL+E+G I LLS + EI +AK+IE G   
Sbjct: 65  --GEVDPDDPTKAELDLSLPEGVEVSDPVRMYLKEIGKIPLLSPDDEIELAKKIEEGDEG 122

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  +  +  G   L  I
Sbjct: 123 AKRKLAEANLRLVVSIAKKY-VGRGMLFLDLI 153


>gi|293189827|ref|ZP_06608541.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
 gi|292821242|gb|EFF80187.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
          Length = 561

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 140/273 (51%), Positives = 190/273 (69%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +  E K  +    ++  E R +  + +    +   AK  ++EANLRLV+S+AK+YT RG+
Sbjct: 293 LYAEYKLKNQADEMTSRERRELHFLAQ----DGQQAKNHLLEANLRLVVSLAKRYTGRGM 348

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + 
Sbjct: 349 QFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV 408

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL TP+G++  S  
Sbjct: 409 INKLARVQRQMLQDLGREPTPEELAKELDMTAEKVVEVQKYGREPISLHTPLGEDGDSEF 468

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD IED  A+ P D+     L+E    VL +L+ RE  V+ MRFG+G     TL+E+GK 
Sbjct: 469 GDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKV 528

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 529 YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 561



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +A+RIEAG 
Sbjct: 242 SDSDETDEPVQQVTVAGATADPVKDYLKQIGKVSLLNAEQEVDLARRIEAGL 293


>gi|320096194|ref|ZP_08027783.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319976875|gb|EFW08629.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 543

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 140/273 (51%), Positives = 190/273 (69%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +  E K  +    ++  E R +  + +    +   AK  ++EANLRLV+S+AK+YT RG+
Sbjct: 275 LYAEYKLKNRADEMTSKERRELHFLAQ----DGQQAKNHLLEANLRLVVSLAKRYTGRGM 330

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + 
Sbjct: 331 QFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV 390

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL TP+G++  S  
Sbjct: 391 INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF 450

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD IED  A+ P D+     L+E    VL +L+ RE  V+ MRFG+G     TL+E+GK 
Sbjct: 451 GDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKV 510

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 511 YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 543



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 31/52 (59%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       ++ +   +T DPV+ YL+++G + LL+   E+ +A+RIEAG 
Sbjct: 224 SDSDETDEPVQQVTVAGATADPVKDYLKQIGKVSLLNAAQEVDLARRIEAGL 275


>gi|291439801|ref|ZP_06579191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342696|gb|EFE69652.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 390

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 131/296 (44%), Positives = 191/296 (64%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 95  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSRLAHDLDRLVVMGRMAK 154

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 155 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 214

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +  REPTPEE+A  L +P E V +
Sbjct: 215 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGREPTPEEVAAHLDLPPERVGE 274

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 275 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 334

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 335 KVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 390



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 85  ETGGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGL 123


>gi|196229539|ref|ZP_03128404.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196226771|gb|EDY21276.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 671

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 163/405 (40%), Positives = 223/405 (55%), Gaps = 33/405 (8%)

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           PK+   LD  A+                 D KS    K   + + ++       Q   + 
Sbjct: 297 PKLCAQLDAAAQNCANAYKSYVAHGGKNHDTKSYTDFKKAHDAIQRIYPKFFFKQKVTEE 356

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
            V    +  + +                                 W        +    +
Sbjct: 357 FVHLADEAHRLVSQ-------------------------------WTEELNKPKKKAAGS 385

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
                    +    ++K   + T +S  EF+     ++    +A  AK EMVEANLRLVI
Sbjct: 386 HAHHHAP--IDYGAKLKDQQMRTWLSPEEFQEEYKELKVWLKKALKAKTEMVEANLRLVI 443

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKYTNRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ 
Sbjct: 444 SIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQAR 503

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K++R  +++     REPTPEE+A ++ +PVE VR VLK+ ++PISL+
Sbjct: 504 TIRIPVHMIETINKLMRVQKQLVQDYGREPTPEEVADEIQLPVERVRAVLKMAQQPISLQ 563

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +P+G+ D +  GDFIEDK A +  D      L+E    VL +LT RE +VL  RFG+   
Sbjct: 564 SPVGESDDTSFGDFIEDKGAENLSDMTAIVLLKEKIKDVLETLTERERQVLEQRFGLVDG 623

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEEVG+QF VTRERIRQIEAKA+RK++HP+R ++L  FL+ 
Sbjct: 624 YSRTLEEVGRQFKVTRERIRQIEAKALRKMRHPTRIRQLEGFLEA 668



 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 43/158 (27%), Positives = 79/158 (50%), Gaps = 8/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            +  +++IKLA+++GY+T ++LN  LP +    ++ME  +  L +M I +++  D++  +
Sbjct: 132 QEKLRELIKLAKEQGYLTFDDLNEALPDNVNDPDEMETIMNRLRSMEIEIIEASDVDRFK 191

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + + D           L           DDPVRMYL++MG + LL+RE E+ I+KRIE
Sbjct: 192 DGKKADDQEEEEEKPEAKLDIL--------DDPVRMYLKQMGQVPLLTREQEVEISKRIE 243

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
                +   +       +A +    +L +G      +I
Sbjct: 244 DAELNVQKHINRFGFIARAYLDLAHKLQEGRERFDRVI 281


>gi|15827492|ref|NP_301755.1| RNA polymerase sigma factor [Mycobacterium leprae TN]
 gi|221229969|ref|YP_002503385.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
 gi|699190|gb|AAA62955.1| rpoT [Mycobacterium leprae]
 gi|4587111|dbj|BAA76621.1| RpoT [Mycobacterium leprae]
 gi|13093042|emb|CAC31403.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933076|emb|CAR71117.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 574

 Score =  230 bits (586), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 188/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM----------------------------VRKGECE 440
           +R  +K I     ++  E   +                               +     +
Sbjct: 274 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGTKLPTAQRRDMMWICRD 333

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 334 GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 393

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 394 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 453

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 454 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 513

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 514 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 573

Query: 681 D 681
           D
Sbjct: 574 D 574



 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D + +E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 232 DEEIVEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 291

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M  L E
Sbjct: 292 EVELAKRIEAGLYATQLMTELSE 314


>gi|256825489|ref|YP_003149449.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
 gi|256688882|gb|ACV06684.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
          Length = 594

 Score =  230 bits (586), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 134/253 (52%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 342 KLKRELWWVASDGKNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 401

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 402 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 461

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 462 PEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPSDAVSFTL 521

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+G+ + VTRERIRQIE+K + KL+
Sbjct: 522 LQEQLHSVLDTLSEREAGVVSMRFGLADGQPKTLDEIGRVYGVTRERIRQIESKTMSKLR 581

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 582 HPSRSQVLRDYLD 594



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V      +EE SE    +  +        Q+   +   +T D V+ YL+++G + LL+ E
Sbjct: 257 VAPQKAAEEEASESRGFVLRADDEDDAPAQQVVTA--GATADAVKDYLKQIGKVALLNAE 314

Query: 138 GEIAIAKRIEAGR 150
            E+ +AKRIEAG 
Sbjct: 315 QEVDLAKRIEAGL 327


>gi|195977963|ref|YP_002123207.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|195974668|gb|ACG62194.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 369

 Score =  230 bits (586), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKVLAVAV---AAGDMEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 120/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G  T +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRHHKKEGTATDDEVTEKLVIPFTLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG
Sbjct: 68  PSSKYVVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKVLAVAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DMEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|121534199|ref|ZP_01666024.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
 gi|121307302|gb|EAX48219.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
          Length = 368

 Score =  230 bits (586), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 156/302 (51%), Positives = 213/302 (70%), Gaps = 3/302 (0%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           DP          E +    +   +     +R  +K I     ++  E   +   + +   
Sbjct: 70  DPDITEIEAAPEEVDIDLSIPEGISIDDPVRMYLKEIGRVPLLTAEEEIQLAKRMEQ--- 126

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
               AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTY
Sbjct: 127 GDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGYKFSTY 186

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTPEEIA+++ + 
Sbjct: 187 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEKGREPTPEEIAREMDIS 246

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE VR+++KI +EP+SLETPIG+E+ SHLGDFIED++A +P ++A    L+E    VL +
Sbjct: 247 VERVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDQDAPAPAEAASFMLLKEQLEEVLET 306

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPREE+VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSKKL+ F
Sbjct: 307 LTPREEKVLRLRFGLDDGRARTLEEVGQYFGVTRERIRQIEAKALRKLRHPSRSKKLKDF 366

Query: 680 LD 681
           L+
Sbjct: 367 LE 368



 Score =  121 bits (303), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 41/159 (25%), Positives = 77/159 (48%), Gaps = 5/159 (3%)

Query: 27  SDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           +++   +++   ++RG  +T  E+   L  ++++ ++++D   + ++ GI +VD     +
Sbjct: 7   TNEHVNELLHKGKKRGGVLTYSEIMDTLQGEDLTPDEIDDMYEVFNSKGIEIVDEIPDVE 66

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D  ++ ++     + L         S DDPVRMYL+E+G + LL+ E EI +AKR
Sbjct: 67  TLEDPDITEIEAAPEEVDIDLS---IPEGISIDDPVRMYLKEIGRVPLLTAEEEIQLAKR 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +E G       L E+ L     I  R  +  G   L  I
Sbjct: 124 MEQGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|154509177|ref|ZP_02044819.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798811|gb|EDN81231.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
          Length = 561

 Score =  230 bits (586), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 140/273 (51%), Positives = 190/273 (69%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +  E K  +    ++  E R +  + +    +   AK  ++EANLRLV+S+AK+YT RG+
Sbjct: 293 LYAEYKLKNQADEMTSRERRELHFLAQ----DGQQAKNHLLEANLRLVVSLAKRYTGRGM 348

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + 
Sbjct: 349 QFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV 408

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL TP+G++  S  
Sbjct: 409 INKLARVQRQMLQDLGREPTPEELAKELDMTAEKVVEVQKYGREPISLHTPLGEDGDSEF 468

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD IED  A+ P D+     L+E    VL +L+ RE  V+ MRFG+G     TL+E+GK 
Sbjct: 469 GDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKV 528

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 529 YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 561



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +A+RIEAG 
Sbjct: 242 SDSDETDEPVQQVTVAGATADPVKDYLKQIGKVSLLNAEQEVDLARRIEAGL 293


>gi|325068636|ref|ZP_08127309.1| RNA polymerase, sigma 70 subunit, RpoD [Actinomyces oris K20]
          Length = 542

 Score =  230 bits (585), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 290 KLRRELHWVAQDGQRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 349

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 350 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 409

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 410 PEELAVELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 469

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 470 LQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 529

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 530 HPSRSQVLRDYLD 542



 Score = 54.1 bits (128), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S+D     + + +       ++     +T DPV+ YL+++G + LL+ E E+ +AKRIEA
Sbjct: 213 SQDKDGSFTVSDSDEGDEPAQRVVTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEA 272

Query: 149 GRAMMMASLCE 159
           G       L E
Sbjct: 273 GLY-AEHRLAE 282


>gi|318066935|emb|CBY89082.1| RNA polymerase sigma70 factor [Halomonas cupida]
          Length = 365

 Score =  230 bits (585), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 127/397 (31%), Positives = 186/397 (46%), Gaps = 54/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       D  + +E    + T GD E 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEADVPEIEE----EATAGDDED 123

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
               +++D S     PE A      + E    SA   +A+E                   
Sbjct: 124 DDADAEEDDSGGGPDPEEARARFEQIRE---QSALADAAIEA------------------ 162

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                           + S + +    +L +L   + L     + LV Q+    +++   
Sbjct: 163 --------------HGRQSAQAQEELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQ 208

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++ L +   + R  F++   G E    W+          + + +      + + + 
Sbjct: 209 EKSVMQLLVKQAKVPRKSFIKAFPGNESRLDWLDDFMA-ANARYADRLGELRADVQRAQR 267

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + +SE + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 268 KIAFEEEMVRLPVSEIKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 327

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 328 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 364


>gi|302551232|ref|ZP_07303574.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302468850|gb|EFL31943.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 438

 Score =  230 bits (585), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 130/296 (43%), Positives = 190/296 (64%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 143 RQYLREIGRVPLLTAAEEVELARRVEAGLFAEEKLRLAPDLDSQLAVDLDRLVVMGRMAK 202

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 203 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 262

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +P E V +
Sbjct: 263 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLELPPERVGE 322

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 323 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 382

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 383 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 438



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 30/56 (53%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + ++ +  +V     +      + D  R YLRE+G + LL+   E+ +A+R+EAG 
Sbjct: 116 VETAEAPEAVEPPPARPDTSGPSSDLFRQYLREIGRVPLLTAAEEVELARRVEAGL 171


>gi|288555754|ref|YP_003427689.1| RNA polymerase sigma factor RpoD [Bacillus pseudofirmus OF4]
 gi|288546914|gb|ADC50797.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 372

 Score =  230 bits (585), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSAQEEIELAKRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYEKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++     REPTPEE+A+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDFGREPTPEEVAEEMELTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQEALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 102/262 (38%), Gaps = 16/262 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   ++++++ ++RG +T  E+   L   +  S+QM++    L   G+ +++  D     
Sbjct: 17  DQVKEQLVEVGKKRGVLTYTEITEKLAVFDQDSDQMDEFFEYLGEQGVEILNESD----- 71

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +      ++       L           +DPVRMYL+E+G + LLS + EI +AKRIE
Sbjct: 72  --DVPNLQQAAKEEEEFDLNDLSVPPGIKINDPVRMYLKEIGRVPLLSAQEEIELAKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 130 QGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 180

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y+K    S        Q     I   A+  +     V++  +      + L +   +   
Sbjct: 181 YEKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDFGREPTP 240

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              A E +L P+ +  + +IA+
Sbjct: 241 EEVAEEMELTPEKVREILKIAQ 262


>gi|256832655|ref|YP_003161382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686186|gb|ACV09079.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 504

 Score =  230 bits (585), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 137/254 (53%), Positives = 181/254 (71%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +    R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 251 RKLEREYRWIIQDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 310

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 311 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 370

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 371 TPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFT 430

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E   +VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL
Sbjct: 431 LLQEQLHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKL 490

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 491 RHPSRSQVLRDYLD 504



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E+       +         ++     +T DPV+ YL+++G + LL+ E E+ +AKRIE
Sbjct: 174 DEEEEGAGFIYSDADDDDAPAQQVVTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIE 233

Query: 148 AG---RAMMMASLCE 159
           AG      + A + E
Sbjct: 234 AGLYAEERLAAGVAE 248


>gi|225868705|ref|YP_002744653.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701981|emb|CAW99541.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
          Length = 369

 Score =  230 bits (585), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKVLAVAV---AAGDMEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 120/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G  T +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRHHKKEGTATDDEVTEKLVIPFTLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG
Sbjct: 68  PSSKYVVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKVLAVAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DMEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|318066973|emb|CBY89101.1| RNA polymerase sigma70 factor [Halomonas taeanensis]
          Length = 366

 Score =  230 bits (585), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 122/397 (30%), Positives = 188/397 (47%), Gaps = 53/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P   ++++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIKIAKRIEEGTREVMSALAYLPGAVESVLEVYDGT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  +E         + D + 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEAEVVEEPVS---DSADSDGDE 124

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
             + ++++ +     PE A+     + E    +A   +A+E                   
Sbjct: 125 DDEDAEEEETTSGPDPEEAKARFEQIRE---QNAAVQAALE------------------- 162

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K  + S +    + +L +L   + L     + LV Q+    +++ + 
Sbjct: 163 -------------KHGRGSKQANAEQARLAELFSPIKLVPKHFERLVGQVRISVEQVRNQ 209

Query: 353 EGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +L+L  +   + R  F++   G E    W+          +K+ +      + + + 
Sbjct: 210 EKAILQLFVKKGKVPRKTFIKSFPGNESRSEWLDEF-FEANARYKDRLEPFRGDVARAQR 268

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + + E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 269 KIAFEEDMVQLQVPELKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 328

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 329 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 365


>gi|20808174|ref|NP_623345.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516766|gb|AAM24949.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 372

 Score =  230 bits (585), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 165/364 (45%), Positives = 229/364 (62%), Gaps = 31/364 (8%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
             +++  +  + LN  +I+ + +   D+   I+ +E             R   +      
Sbjct: 40  YNEIMDSLEDIDLNPDQIEKVYDTFEDMGIEIVGDE------------PRQEEISEEDLN 87

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
             D                            +R  +K I     ++  E   +   + + 
Sbjct: 88  LDDLSLPEGVSIDDP----------------VRMYLKEIGKIPLLTPEEEIELAKRIEQ- 130

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFS
Sbjct: 131 --GDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFS 188

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEELAKEMG 248

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VR++LKI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL
Sbjct: 249 MPEEKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAYTMLKEQLMDVL 308

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+
Sbjct: 309 DTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLK 368

Query: 678 SFLD 681
            FLD
Sbjct: 369 DFLD 372



 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 49/182 (26%), Positives = 83/182 (45%), Gaps = 17/182 (9%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +G+KR    + +   +++    + + ++  ++I   ++ G +T  E+   L   +++ +Q
Sbjct: 1   MGRKRETHREGKSMSNNE----ELAREAINELINKGKKTGMLTYNEIMDSLEDIDLNPDQ 56

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E       +MGI +V  +  ++E   ED            + L         S DDPVR
Sbjct: 57  IEKVYDTFEDMGIEIVGDEPRQEEISEED------------LNLDDLSLPEGVSIDDPVR 104

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L 
Sbjct: 105 MYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLIEANLRLVVSIAKRY-VGRGMLFLD 163

Query: 183 EI 184
            I
Sbjct: 164 LI 165


>gi|318066917|emb|CBY89073.1| RNA polymerase sigma70 factor [Cobetia marina]
 gi|318066949|emb|CBY89089.1| RNA polymerase sigma70 factor [Halomonas halodurans]
          Length = 364

 Score =  230 bits (585), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 129/396 (32%), Positives = 186/396 (46%), Gaps = 53/396 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD-E 173
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIKIAKRIEEGTREVMSSLAFLPGAVDSILEAYDGT 78

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           L +    L ++             GF    EG       +  + +      E   + E  
Sbjct: 79  LGEDGGRLSDLF-----------SGFIDPDEGVPGVAEVEVEEVE----EVEEGEESEGE 123

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D  S+    PE A      + E  D    T +A+E                    
Sbjct: 124 DDDEDDSASEGGPDPELARVRFEQIREQND---LTKAAIE-------------------- 160

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
                       K    S + K  +E+L +L   + L     + LV Q+    +++   E
Sbjct: 161 ------------KYGSGSPEAKAEQERLAELFSPIKLVPKHFERLVGQVRVSVEQVREQE 208

Query: 354 GELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
             +L++  +   + R  F++   G E D  W        +  + + +      +L+ + +
Sbjct: 209 KVILQIFVKRGKVPRKSFIKAFPGHESDMDWFDGFIGGSKK-YADKLEPFRADVLRAQRK 267

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I        + +SE + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 268 IAFEQDMVQLPVSELKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 327

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 328 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 363


>gi|226311661|ref|YP_002771555.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226094609|dbj|BAH43051.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 376

 Score =  230 bits (585), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 107 VRMYLKEIGRVPLLSAEEEIKLAQRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 164 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 223

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA+K+ +  E VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 224 INKLIRVSRQLLQELGREPMPEEIAEKMDLTPEKVREIMKIAQEPVSLETPIGEEDDSHL 283

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A+ P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 284 GDFIEDQDALEPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 343

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 344 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 376



 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 73/157 (46%), Gaps = 3/157 (1%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   +++++L ++RG ++ +E+ A L   E  S+QM++    L + GI     ++  +++
Sbjct: 16  EQVKEQLVELGKKRGALSYKEITARLAGFEQDSDQMDEFFEYLGDQGIE--INNNENEDD 73

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E    +     N                +DPVRMYL+E+G + LLS E EI +A+RIE
Sbjct: 74  DDEVDQMIIKDEDNEEFDFDDLSVPPGIKINDPVRMYLKEIGRVPLLSAEEEIKLAQRIE 133

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 134 QGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 169


>gi|318066995|emb|CBY89112.1| RNA polymerase sigma70 factor [Salinicola salarius]
          Length = 368

 Score =  230 bits (585), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 122/397 (30%), Positives = 183/397 (46%), Gaps = 51/397 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++   D+ 
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEILIAKRIEEGLREVMSSLAYLPGAVDSILDVYDQT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  +E E  D+   E D + 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEVEMPEEVEA-DISGDEDDEDD 126

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                 D+ S+    PE A      + E  + +   +                       
Sbjct: 127 EDSEDDDNASEGGPDPEEARVRFEQIREQNEAAKAAIE---------------------- 164

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        K  + S +  + + +L +L   + L+    + LV Q+     ++   
Sbjct: 165 -------------KHGRGSEEADIEQARLAELFSPIKLSPKHFERLVGQVRISVDQVRSQ 211

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++   +   + R  F+    G E    W         G++ + +      + + + 
Sbjct: 212 EKAIMQVFVKQGKVPRKTFISSFLGNETAEGWFDEFIA-KNGKYADRLEPFRGDVQRAQR 270

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + + + + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 271 KIGFEQEMVLLDVGQLKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 330

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 331 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|288916958|ref|ZP_06411330.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288351667|gb|EFC85872.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score =  229 bits (584), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 148/286 (51%), Positives = 214/286 (74%), Gaps = 6/286 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 110 AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 166

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 167 VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 226

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 227 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 286

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 287 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 346

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 347 DGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 392



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 77/380 (20%), Positives = 135/380 (35%), Gaps = 59/380 (15%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   D  K +I   ++ G++T E++   +   E+  EQ E  + +L++ GI V++     
Sbjct: 9   EAQVDEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAETVLQVLNDEGIEVLEA---- 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
              G E++ +    A       +    +    T DPVRMYL+E+G + LL+ E E+ +AK
Sbjct: 65  ---GGENADEADLLARRRREEEELALKAP---TSDPVRMYLKEIGKVPLLTAEEEVDLAK 118

Query: 145 RIEAGR----------------------------AMMMASLCESPLTFQALIIWRDELND 176
           RIEAG                              +    L E+ L     I  R  +  
Sbjct: 119 RIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKLVEANLRLVVSIAKRY-VGR 177

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L  I         E   G     E   Y K    S        Q     I   A+ 
Sbjct: 178 GMLFLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQART 229

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +     V++  +      + L +   + +    A E  L P     + EI +V +E  S
Sbjct: 230 IRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTP---DKVREILKVSQEPVS 286

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE--- 353
           L+      +         +     +     S  L Q ++D ++  L D  K+++      
Sbjct: 287 LETPIGEEEDSHLGDF-IEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGL 345

Query: 354 -----GELLRLAQSYGIKRD 368
                  L  + + +G+ R+
Sbjct: 346 TDGHPRTLEEVGREFGVTRE 365


>gi|225870339|ref|YP_002746286.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
 gi|225699743|emb|CAW93506.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
          Length = 369

 Score =  229 bits (584), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSDEEKVLAVAV---AAGDMEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 120/330 (36%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G  T +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  IAEFIRHHKKEGTATDDEVTEKLVIPFTLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ + E  +A  + AG
Sbjct: 68  PSSKYVVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSDEEKVLAVAVAAG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DMEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|117928637|ref|YP_873188.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649100|gb|ABK53202.1| RNA polymerase, sigma 70 subunit, RpoD [Acidothermus cellulolyticus
           11B]
          Length = 495

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 131/253 (51%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 243 ELRKDLEWIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 302

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + R+PT
Sbjct: 303 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGRDPT 362

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     
Sbjct: 363 PEELAVELDMTPEKVMEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPSDAVSFTL 422

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+G+ + VTRERIRQIE+K + KL+
Sbjct: 423 LQEQLHSVLETLSEREAGVVSMRFGLTDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLR 482

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 483 HPSRSQVLRDYLD 495



 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLA-SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V+  D  D + ++++ DLA            + + +   +T DPV+ YL+++G + LL+ 
Sbjct: 155 VELTDGVDVDPADEATDLAVEDELLLDDDEPQAQLTNAGATADPVKDYLKQIGKVPLLNA 214

Query: 137 EGEIAIAKRIEAGR 150
           E E+ +AKRIEAG 
Sbjct: 215 EQEVELAKRIEAGL 228


>gi|288818771|ref|YP_003433119.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|288788171|dbj|BAI69918.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|308752357|gb|ADO45840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 570

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 165/423 (39%), Positives = 252/423 (59%), Gaps = 11/423 (2%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           DE  +        + L    +    E+A+ Y+E   +        +  +   K      K
Sbjct: 153 DESKTVEEYEESHEHLERYFIEKGLELAKAYKEAL-VWRELYLKYQTPEDKRKYLEKHAK 211

Query: 321 LVKLVGSLSLNQSRIDLLVEQL----YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           + +++  + L  S+ + + ++L       +KR+   E    +L   Y    +  ++ +  
Sbjct: 212 MNRVLKDMKLKYSKFEKIADELLNLYKRYTKRLKEYEARRKKLESIYP-NVEELIKFYDQ 270

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           R+        A     G             L +  E+K +  E G+   E   ++ ++++
Sbjct: 271 RQDLQLRAERA-----GYGFARFQVLRSEYLTLEREVKELRKELGVLPEELDRVMHIIKE 325

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           G  + + AK+ MV+ NLRLV+S+AKKY NRGL FLDLIQEGNIGLMKA +K+D+  GYKF
Sbjct: 326 GRTKVTKAKQVMVKCNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKF 385

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+ + +  +++  ++ REP PEEIAK L
Sbjct: 386 STYATWWIRQAITRAIADQARTIRIPVHMIETINDITKAHKKLFQELGREPFPEEIAKYL 445

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + VE  RKV++ ++EPISLETPIGD++ +HL DFIEDK+ +SP +   +  LRE   +V
Sbjct: 446 GISVEKARKVMRTSQEPISLETPIGDDEETHLKDFIEDKSVLSPEEQVSRKLLREQLIKV 505

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L++L  +E+ +L  R+G+   T++TLE++GK F VTRERIRQIE KAIRKL+HP+R+K L
Sbjct: 506 LSTLGEKEKEILMYRYGLVDGTEYTLEQIGKMFNVTRERIRQIETKAIRKLRHPARAKYL 565

Query: 677 RSF 679
           + F
Sbjct: 566 KDF 568



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 69/342 (20%), Positives = 119/342 (34%), Gaps = 16/342 (4%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            S D+ KK+++L  ++GYVT +E+N  L  D V SE  E+ +  L   G+          
Sbjct: 2   LSKDNIKKLMELG-EKGYVTYDEINEALGEDVVDSEAYEEIMDFLQERGVR--------- 51

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
               E               +            DPV++YLREMG I LLSRE EI  AK+
Sbjct: 52  --IIESEEITEELEHGDEFTVSTENLLLTARDGDPVKLYLREMGRIPLLSREEEIMYAKQ 109

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE GR +M   L  +      ++     + +G     +++D       ESK    +    
Sbjct: 110 IEMGRKIMRRGLLRTSFLIDRVLREWGNVCNGKIKATDLMDTMD----ESKTVEEYEESH 165

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
              ++       +     +E     E   K    +  +         N      + +   
Sbjct: 166 EHLERYFIEKGLELAKAYKEALVWRELYLKYQTPEDKRKYLEKHAKMNRVLKDMKLKYSK 225

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              ++     L  +    L E     ++L S+  N     K        ++  E+     
Sbjct: 226 FEKIADELLNLYKRYTKRLKEYEARRKKLESIYPNVEELIKFYDQRQDLQLRAERAGYGF 285

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
               + +S    L  ++ ++ K +     EL R+       R
Sbjct: 286 ARFQVLRSEYLTLEREVKELRKELGVLPEELDRVMHIIKEGR 327


>gi|15613939|ref|NP_242242.1| RNA polymerase sigma factor RpoD [Bacillus halodurans C-125]
 gi|12643264|sp|O66381|RPOD_BACHD RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|10173992|dbj|BAB05095.1| RNA polymerase major sigma factor [Bacillus halodurans C-125]
          Length = 372

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   + + + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLTAEEEIELATRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEE+A+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDLGREPSPEEVAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 99/262 (37%), Gaps = 16/262 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++L ++RG +T  E+   L P +  S+QM++    L   G+ +++       +
Sbjct: 17  DQVKEQLVELGKKRGVLTYAEITEKLAPYDQDSDQMDEFFEYLGEQGVEILN-------D 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E               L           +DPVRMYL+E+G + LL+ E EI +A RIE
Sbjct: 70  NEEVPSLQQVEKEEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELATRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 130 QGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 180

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y K    S        Q     I   A+  +     V++  +      + L +   + + 
Sbjct: 181 YNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSP 240

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              A E  L P+ +  + +IA+
Sbjct: 241 EEVAEEMDLTPEKVREILKIAQ 262


>gi|309388945|gb|ADO76825.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 364

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 148/273 (54%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +GE     AK+++V+ANLRLV+S+AKKY  RG+
Sbjct: 95  VRMYLKEIGKVDLLTAEEEVELAKRMEQGEEW---AKQQLVQANLRLVVSIAKKYVGRGM 151

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + 
Sbjct: 152 LFLDLIQEGNMGLMKAVDKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVET 211

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +  REP  EEI  ++ +  E VR+++KI+++P+SLETPIG+E+ SHL
Sbjct: 212 INKLIRVSRQLLQEKGREPKDEEIGAEMDISAEKVREIMKISQDPVSLETPIGEEEDSHL 271

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED ++ +P  +A    L+E    VL +LT RE+RVL +RFGI      TLEEVGK+
Sbjct: 272 GDFIEDVDSPAPASAASYILLKEQLNDVLDTLTDREKRVLELRFGIEDGRPRTLEEVGKE 331

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKK++ +L+
Sbjct: 332 FGVTRERIRQIEAKALRKLRHPSRSKKIKDYLN 364



 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 41/155 (26%), Positives = 66/155 (42%), Gaps = 10/155 (6%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             KK++   ++ G +T E++   L   ++ SE +E    + S M I VV          S
Sbjct: 13  EVKKLVSRGKKEGELTYEDIMDALEDIDLDSEDIEKIYEIFSEMNIEVV---------NS 63

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +          +              S DDPVRMYL+E+G ++LL+ E E+ +AKR+E G
Sbjct: 64  KLEDSEEDDDEDDQNSGLDLSIPKSASIDDPVRMYLKEIGKVDLLTAEEEVELAKRMEQG 123

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                  L ++ L     I  +  +  G   L  I
Sbjct: 124 EEWAKQQLVQANLRLVVSIAKKY-VGRGMLFLDLI 157


>gi|292670108|ref|ZP_06603534.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648296|gb|EFF66268.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 370

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++ ++ E     A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGHVPLLTAEEE---VALAQRMEAGDEEARHRLEEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ R+P PEE+A+++ + V  V +++KI +EP+SLETPIG+E+ SHL
Sbjct: 218 INKLVRISRQLLQELGRDPHPEEVAREMGISVARVHEIMKIAQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A +P ++A    LRE    VL +LT RE+ VLR+RFG+      TLEEVG+ 
Sbjct: 278 GDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQS 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 338 FGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 370



 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 69/157 (43%), Gaps = 8/157 (5%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D  ++++   ++ G  +T  EL   L   ++S ++M+D     S+ G+ +VD        
Sbjct: 14  DIIERLLAQGKKNGGTLTYGELIDALQKQDMSPDEMDDMYQRFSDEGVEIVDDA------ 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +         A                S DDPVRMYL+E+G + LL+ E E+A+A+R+E
Sbjct: 68  ATAGEPAEEEPAEKEEEVEIDLSVPEGVSLDDPVRMYLKEIGHVPLLTAEEEVALAQRME 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AG       L E+ L     I  R  +  G   L  I
Sbjct: 128 AGDEEARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|164688099|ref|ZP_02212127.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
 gi|164602512|gb|EDQ95977.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
          Length = 385

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 157/362 (43%), Positives = 236/362 (65%), Gaps = 5/362 (1%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
           ++++      L++ +++ L E L ++   I+ ++ +   +  S      +  +   G  +
Sbjct: 29  EIMEAFSETELDKDQVENLYETLGNLGIEIIEDKTQKADVDFSDNDNDLIVDKDFDG--V 86

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
               +    D    +    +   +     +R  +K I     +   E       +     
Sbjct: 87  SDDELKKEDDIEMDKIDLSLPKGISIDDPVRMYLKEIGKIPLLKPHEEIEYAKRM---LE 143

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
              IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTY
Sbjct: 144 GDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYERGFKFSTY 203

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P PEEIAK++ M 
Sbjct: 204 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDPKPEEIAKEMDMS 263

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR+++KI ++P+SLETPIG+E+ SHLGDFI D++A++P ++A  + L++    VL S
Sbjct: 264 EEKVREIMKIAQDPVSLETPIGEEEDSHLGDFIPDEDALAPAEAAAYSLLKDQIEEVLGS 323

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKLR +
Sbjct: 324 LNEREQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLRDY 383

Query: 680 LD 681
           LD
Sbjct: 384 LD 385



 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 46/174 (26%), Positives = 72/174 (41%), Gaps = 15/174 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV------ 78
           D    + K +I   +++G +T+ E+       E+  +Q+E+    L N+GI ++      
Sbjct: 6   DNKRLTAKTLIDKGKKQGSLTLSEIMEAFSETELDKDQVENLYETLGNLGIEIIEDKTQK 65

Query: 79  --------DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                   D D + D++    S D      +  +           S DDPVRMYL+E+G 
Sbjct: 66  ADVDFSDNDNDLIVDKDFDGVSDDELKKEDDIEMDKIDLSLPKGISIDDPVRMYLKEIGK 125

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           I LL    EI  AKR+  G  +    L E+ L     I  R  +  G   L  I
Sbjct: 126 IPLLKPHEEIEYAKRMLEGDEIAKQRLVEANLRLVVSIAKRY-VGRGMLFLDLI 178


>gi|325125919|gb|ADY85249.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 372

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 169/360 (46%), Positives = 234/360 (65%), Gaps = 27/360 (7%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+  +G+  +LA                      
Sbjct: 39  RLIKPYKLEDKAVDQLVQEFEDNGISIVDEDGKPSKLA---------------------- 76

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            ++  K+  + E  N  A     +   +R  +K I     ++  E    V++ ++ E   
Sbjct: 77  -LTKQKNVEKAELNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEE---VALAKRIEAGD 132

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA 
Sbjct: 133 EEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYAT 192

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ +PV+
Sbjct: 193 WWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVK 252

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR++LKI +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+E    VL +L+
Sbjct: 253 KVREILKICQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVLDTLS 312

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR FLD
Sbjct: 313 DREEEVLRLRFGLDDGKSRTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRSSQLRDFLD 372



 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 109/313 (34%), Gaps = 49/313 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +++  +    +T       L  P ++  + ++  V    + GI++VD      E
Sbjct: 15  EKAVKLVVEGVKASHQITEAAFEDRLIKPYKLEDKAVDQLVQEFEDNGISIVD------E 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G    L L    +     L           +DPVRMYL+E+G   LL+ E E+A+AKRI
Sbjct: 69  DGKPSKLALTKQKNVEKAELNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA-------- 189
           EAG       L E+ L     I  R         D + +G   L + +D           
Sbjct: 129 EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFS 188

Query: 190 -------------------------CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
                                        E+                 D   E+   ++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMD 248

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                +    K+ ++  S      E  +++  +  ED+D  +    A  + L+ ++   L
Sbjct: 249 LPVKKVREILKICQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVL 308

Query: 285 DEIAEVYRELRSL 297
           D +++   E+  L
Sbjct: 309 DTLSDREEEVLRL 321


>gi|297544972|ref|YP_003677274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296842747|gb|ADH61263.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 357

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 167/364 (45%), Positives = 234/364 (64%), Gaps = 32/364 (8%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
             +++  +  + LN  +I+ + +   D+   I+  E             R          
Sbjct: 26  YNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIVGEE------------PRQE-------- 65

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E++   +      PEG   +           +R  +K I     ++  E   +   + + 
Sbjct: 66  EINEEDLDLDLSLPEGISID---------DPVRMYLKEIGKIPLLTPEEEIELAKRIEQ- 115

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFS
Sbjct: 116 --GDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFS 173

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ 
Sbjct: 174 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEELAKEMG 233

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VR+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL
Sbjct: 234 MPEEKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFTMLKEQLMDVL 293

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+
Sbjct: 294 DTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLK 353

Query: 678 SFLD 681
            FLD
Sbjct: 354 DFLD 357



 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 47/160 (29%), Positives = 71/160 (44%), Gaps = 14/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S D+  ++I   ++ G +T  E+   L   +++ +Q+E       +MGI +V  +  +
Sbjct: 5   ELSKDAITELINKGKKTGMLTYNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIVGEEPRQ 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E   ED                        S DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 65  EEINEED-------------LDLDLSLPEGISIDDPVRMYLKEIGKIPLLTPEEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 RIEQGDEEAKKRLIEANLRLVVSIAKRY-VGRGMLFLDLI 150


>gi|258516189|ref|YP_003192411.1| RNA polymerase sigma factor RpoD [Desulfotomaculum acetoxidans DSM
           771]
 gi|257779894|gb|ACV63788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 359

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 167/374 (44%), Positives = 236/374 (63%), Gaps = 29/374 (7%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK   +  +   +++ ++ +  L   +ID + EQL  +   ++  E E+   A       
Sbjct: 15  EKGKKQGYLTYHEIMDVLQTTELTPDQIDDVYEQLSGMGIDLLATEPEMDEAAVKPDEDV 74

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +V L   +G  +D                            +R  +K I     +S  E 
Sbjct: 75  EVDLSVPEGIGIDD--------------------------PVRMYLKEIGRVPLLSSEEE 108

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   +  GE     AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 109 VELAKRMEMGE---EEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEK 165

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP
Sbjct: 166 FDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP 225

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEIAK++ +  + VR+++KI +EP+SLETPIG+E+ SHLGDFIED +A +P + A   
Sbjct: 226 MPEEIAKEMNITEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDHDARAPAEEASFT 285

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE    VL +LT RE++VLR+RFG+      TLEEVG++F VTRERIRQIEAK +RKL
Sbjct: 286 LLREQLDDVLKTLTDREQKVLRLRFGLDDGRARTLEEVGQKFGVTRERIRQIEAKTLRKL 345

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 346 RHPSRSKKLKDYLD 359



 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 72/331 (21%), Positives = 124/331 (37%), Gaps = 30/331 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           ++ + +++  +++GY+T  E+   L   E++ +Q++D    LS MGI+++  +   DE  
Sbjct: 8   ENIRSLVEKGKKQGYLTYHEIMDVLQTTELTPDQIDDVYEQLSGMGIDLLATEPEMDEAA 67

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +   D+                      DDPVRMYL+E+G + LLS E E+ +AKR+E 
Sbjct: 68  VKPDEDVEVD----------LSVPEGIGIDDPVRMYLKEIGRVPLLSSEEEVELAKRMEM 117

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G       L E+ L     I  R  +  G   L  I         E   G     E   Y
Sbjct: 118 GEEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDY 168

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           +K    S        Q     I   A+  +     V++  +      + L E   +    
Sbjct: 169 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPMPE 228

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
             A E  +    +  + +IA                 +      +   L + +       
Sbjct: 229 EIAKEMNITEDKVREIMKIA-----------QEPVSLETPIGEEEDSHLGDFIEDHDARA 277

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              ++   LL EQL D+ K +   E ++LRL
Sbjct: 278 PAEEASFTLLREQLDDVLKTLTDREQKVLRL 308


>gi|295424882|ref|ZP_06817597.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
 gi|295065448|gb|EFG56341.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
          Length = 368

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 168/360 (46%), Positives = 228/360 (63%), Gaps = 27/360 (7%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+   +L    +D LV++  D    I+   G+  +LA                      
Sbjct: 35  RLIEPYNLQGKAVDQLVQEFEDNGISIVDKNGDPSKLA---------------------- 72

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            +   KD  + E ++  A     +   +R  +K I     ++  +    +++ ++ E   
Sbjct: 73  -LKKQKDIEKKELEDMSAPSSVRMNDPVRMYLKEIGRVPLLNADKE---IALAKRIENGD 128

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LG+KFSTYA 
Sbjct: 129 EEAKQELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYAT 188

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++ MP  
Sbjct: 189 WWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMDMPTN 248

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR +LKI +EP+SLETPIG+ED SHLGDFIEDK A SP   A    L+E     L +LT
Sbjct: 249 KVRDILKIAQEPVSLETPIGEEDDSHLGDFIEDKEATSPEQHASYEMLKEQLEETLDTLT 308

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +L+ FLD
Sbjct: 309 DREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLKDFLD 368



 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 38/133 (28%), Positives = 59/133 (44%), Gaps = 7/133 (5%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            + P  +  + ++  V    + GI++VD      + G    L L          L+    
Sbjct: 36  LIEPYNLQGKAVDQLVQEFEDNGISIVD------KNGDPSKLALKKQKDIEKKELEDMSA 89

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +    +DPVRMYL+E+G + LL+ + EIA+AKRIE G       L E+ L     I  R
Sbjct: 90  PSSVRMNDPVRMYLKEIGRVPLLNADKEIALAKRIENGDEEAKQELAEANLRLVVSIAKR 149

Query: 172 DELNDGTTLLREI 184
             +  G + L  I
Sbjct: 150 Y-VGRGMSFLDLI 161


>gi|253682266|ref|ZP_04863063.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
 gi|253561978|gb|EES91430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
          Length = 368

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 209/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    +S+ ++ E     AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGKVPLLSPDEE---ISLAQRIEDGDMYAKKKLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 216 INKLIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 276 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 368



 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 46/154 (29%), Positives = 70/154 (45%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +I   +++G +T +E+   L   E++ EQ+E    +L +M I V+      + E  E
Sbjct: 25  IKNLIDKGKKKGNLTYKEIMDELDNVELTPEQIEKVYGVLESMDIEVIGDMKEIETEEEE 84

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             L +                    S DDPVRMYL+E+G + LLS + EI++A+RIE G 
Sbjct: 85  IDLSI----------------PEGISIDDPVRMYLKEIGKVPLLSPDEEISLAQRIEDGD 128

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 129 MYAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|229825330|ref|ZP_04451399.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
 gi|229790702|gb|EEP26816.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
          Length = 409

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 148/268 (55%), Positives = 197/268 (73%), Gaps = 3/268 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S+ E    V + +K       A   + E+NLRLV+S+AKKY  RGL FL
Sbjct: 142 YLKEIGNYPLLSMDEE---VELAKKIAEGDQYATDRLTESNLRLVVSIAKKYVGRGLSFL 198

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAITRSIADQS TIRIPVHM + I+K
Sbjct: 199 DLIQEGNLGLIKAVDKFDYSKGYKFSTYATWWIRQAITRSIADQSRTIRIPVHMSEVINK 258

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R +R +  ++ REPT EEIAK++ +PVE VR+++KI+ +PISL+TPIG+ED SHLGDF
Sbjct: 259 AYRISRSLLQELGREPTEEEIAKEMNLPVEKVREIMKISADPISLDTPIGEEDDSHLGDF 318

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I+D   + P D+A    L++   ++L +L+ RE+RVL +RFG+      TLEEVGK+F V
Sbjct: 319 IKDDTIMGPEDAAAYTMLQDQIQKLLTTLSEREQRVLILRFGLLDGRTRTLEEVGKEFNV 378

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TRERIRQIEAKA+RKL+HP+R++ LR F
Sbjct: 379 TRERIRQIEAKALRKLRHPNRARMLRGF 406



 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 80/179 (44%), Gaps = 12/179 (6%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMED 65
            N  +D+     DD L         + ++++AR+ +  +  ++LN +     + S   E 
Sbjct: 34  ENSKTDNATVPKDDFLT------KLEGLVEIARKNKDVIESDKLNDYFKSLNIDSGHYEK 87

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
               L + GI +++ +D++D+   +   ++   A            +    +DDPV++YL
Sbjct: 88  IYDYLESNGITIMNINDIDDDLFDDTLPEVDDEAD----LEIGDDITLSIMSDDPVKIYL 143

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +E+G+  LLS + E+ +AK+I  G       L ES L     I  +  +  G + L  I
Sbjct: 144 KEIGNYPLLSMDEEVELAKKIAEGDQYATDRLTESNLRLVVSIAKKY-VGRGLSFLDLI 201


>gi|307703796|ref|ZP_07640737.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
 gi|307622631|gb|EFO01627.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
          Length = 318

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 48  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 104

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 105 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 164

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 165 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 224

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 225 GDFIEDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 284

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ PSRSK LR F++
Sbjct: 285 FNVTRERIRQIEAKALRKLRQPSRSKPLRDFIE 317



 Score = 75.6 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 98/293 (33%), Gaps = 27/293 (9%)

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           +  + + GI++ D +          S  + S+     +  +    S     +DPVRMYL+
Sbjct: 1   MQRIQDAGISITDNE-------GNPSARVLSTEEEPELSDEDLIGSTSAKVNDPVRMYLK 53

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E+G + LL+ E E  +A  +EAG       L E+ L     I  R  +  G   L  I  
Sbjct: 54  EIGVVPLLTNEEEKELALAVEAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI-- 110

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                  E   G     +   Y K    S        Q     I   A+  +     V++
Sbjct: 111 ------QEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 164

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
             +        L E   D      A    + P     + EI ++ +E  SL+        
Sbjct: 165 INKLVREQRNLLQELGQDPTPEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDD 221

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                     + E  V     +        +L EQL ++   +   E  +LRL
Sbjct: 222 SHLGDFIEDEVIENPVDYTTRI--------VLREQLDEVLDTLTDREENVLRL 266


>gi|269956779|ref|YP_003326568.1| RpoD subfamily RNA polymerase sigma-70 subunit [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269305460|gb|ACZ31010.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 549

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 137/254 (53%), Positives = 183/254 (72%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +V  ++    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 296 RRLVRDLQWIAHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 355

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 356 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 415

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 416 TPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFT 475

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E   +VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL
Sbjct: 476 LLQEQLHQVLDTLSEREAGVVSMRFGLQDGQPKTLDEIGKVYGVTRERIRQIESKTMSKL 535

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 536 RHPSRSQVLRDYLD 549



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                ++EG ++       + +       ++     +T DPV+ YL+++G + LL+ E E
Sbjct: 203 EAKPAEKEGEKEEDAGFVVSDSDDEDQPVQQVVTAGATADPVKDYLKQIGKVALLNAEQE 262

Query: 140 IAIAKRIEAGR 150
           + +AKRIEAG 
Sbjct: 263 VELAKRIEAGL 273


>gi|317124635|ref|YP_004098747.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
 gi|315588723|gb|ADU48020.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
          Length = 587

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 335 KLKRELWWIAQDGKKAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 394

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 395 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 454

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 455 PEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 514

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 515 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 574

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 575 HPSRSQVLRDYLD 587



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 35/72 (48%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D   + D+    +         +       ++     +T DPV+ YL+++G + LL+ E 
Sbjct: 249 DAAPVTDKAAEAEDESGFVIRDDDEDDAPAQQVVTAGATADPVKDYLKQIGKVALLNAEQ 308

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 309 EVELAKRIEAGL 320


>gi|291444398|ref|ZP_06583788.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
 gi|291347345|gb|EFE74249.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
          Length = 395

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 124/296 (41%), Positives = 187/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +       AK
Sbjct: 100 RQYLREIGRIPLLTAAEEVELARRVEAGLFAEERLTGTPDLDSRLAGDLDRLVVMGRTAK 159

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 160 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 219

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+IA +L +  E V +
Sbjct: 220 QAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIAVELDLTPERVTE 279

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED    GD IED +A SP++SA    LR+    VL++L  RE 
Sbjct: 280 VLRLAQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGERER 339

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR +LD
Sbjct: 340 KVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDHAFADQLRGYLD 395



 Score = 54.1 bits (128), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 18/70 (25%), Positives = 30/70 (42%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +      G      +  +         + +  +   T D  R YLRE+G I LL+   E+
Sbjct: 59  ETAAGPPGHAPEAVMVEATHLPEPPDPRNRADSGGPTSDLFRQYLREIGRIPLLTAAEEV 118

Query: 141 AIAKRIEAGR 150
            +A+R+EAG 
Sbjct: 119 ELARRVEAGL 128


>gi|24379277|ref|NP_721232.1| RNA polymerase sigma factor RpoD [Streptococcus mutans UA159]
 gi|290580718|ref|YP_003485110.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
 gi|18202024|sp|O33662|RPOD_STRMU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|24377195|gb|AAN58538.1|AE014923_2 DNA-dependent RNA polymerase sigma subunit; major sigma factor
           (sigma 70/42) [Streptococcus mutans UA159]
 gi|2258087|dbj|BAA21507.1| sigma 42 protein [Streptococcus mutans]
 gi|254997617|dbj|BAH88218.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
          Length = 371

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGVVPLLTNEEEKELAIAVE---NGDLEAKQRLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 218 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 278 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSKQLRDFVE 370



 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 95/260 (36%), Gaps = 16/260 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  ++ G    +E+   L  P E+ +EQ++D +  L++ GI++ D       EG+
Sbjct: 16  VADFIRNHKKEGVAVDDEVTEKLVIPFELEAEQIDDLLERLTDGGISITDR------EGN 69

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +           +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +E G
Sbjct: 70  PSTKYAVEEIKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAIAVENG 129

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 130 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 180

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 181 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 240

Query: 270 SAMEDQLRPKVMCALDEIAE 289
            A    + P  +  + +IA+
Sbjct: 241 IAERMDMTPDKVREILKIAQ 260


>gi|170782020|ref|YP_001710352.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156588|emb|CAQ01739.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 355

 Score =  229 bits (584), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 133/254 (52%), Positives = 182/254 (71%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   +R    +   AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EK
Sbjct: 102 RELERELRWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEK 161

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 162 FDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 221

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE++++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 222 TPEELSRELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDTEAVVPADAVGFT 281

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    +L SL+ RE  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL
Sbjct: 282 MLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKL 341

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +L+
Sbjct: 342 RHPSRSQSLRDYLE 355



 Score = 54.1 bits (128), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
                +     +   +T DPV+ YL+++G + LL+   E+ +A RIEAG       L  +
Sbjct: 39  EEDEDVPVYSTTITGATADPVKDYLKQIGKVALLNAAEEVELAMRIEAGLF-AEDKLANT 97

Query: 161 PLTFQAL 167
           P   + L
Sbjct: 98  PGISREL 104


>gi|78044024|ref|YP_359316.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996139|gb|ABB15038.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 370

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    + + ++ E     AK+++ EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGRVPLLTPEEE---IELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R +  ++ REPTPEEIAK++ +  + VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRNLLQELGREPTPEEIAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED +A +P++ A    LRE    VL +LT RE++VLR+RFG+      TLEEVG+ 
Sbjct: 278 GDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVLRLRFGLDDGRARTLEEVGQI 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 338 FGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 370



 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 77/160 (48%), Gaps = 2/160 (1%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLE 84
             ++   ++++  ++RG +T  +L   L   +++SEQ+++    L+N GI VV +  +LE
Sbjct: 5   MQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVPEIPELE 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            +  +    D+    S+              + DDPVRMYL+E+G + LL+ E EI +AK
Sbjct: 65  LDSINSLDDDVDFKPSDIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPEEEIELAK 124

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R E G       L E+ L     I  R  +  G   L  I
Sbjct: 125 RKEEGDEEAKRKLAEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|315924365|ref|ZP_07920587.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622244|gb|EFV02203.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 396

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 152/301 (50%), Positives = 208/301 (69%), Gaps = 3/301 (0%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
               +   +   +   K  +   V+    +R  +K I   + ++  E   I   +     
Sbjct: 98  SIAELRSIEKDEKTNKKEDLTENVNVNDPVRLYLKEIGRVSLLTADEEMAIAKRM---AA 154

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
               AKKE+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTY
Sbjct: 155 GDEDAKKELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLIKAVEKFDYTKGFKFSTY 214

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPTP EI K++   
Sbjct: 215 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEYGREPTPAEIGKEMGFS 274

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + VR++ KI ++P+SLETPIG+E+ SHLGDFI D  A +P ++A  A L+E    VL++
Sbjct: 275 EDKVREIQKIAQDPVSLETPIGEEEDSHLGDFIPDDEAPAPSEAASYALLKEQLIDVLST 334

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +
Sbjct: 335 LTDREEKVLRLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSKKLKDY 394

Query: 680 L 680
           L
Sbjct: 395 L 395



 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 38/155 (24%), Positives = 73/155 (47%), Gaps = 2/155 (1%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + +I+  +Q+G +  E++   L   +  S++++     L    I +    D++  +  
Sbjct: 37  EIQSLIERGKQKGILNSEDIEHALSEKDFDSDEIDAVYLYLQKQNIRLT-FKDMDMTDLD 95

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + S+    S        +K   + + + +DPVR+YL+E+G + LL+ + E+AIAKR+ AG
Sbjct: 96  DASIAELRSIEKDEKTNKKEDLTENVNVNDPVRLYLKEIGRVSLLTADEEMAIAKRMAAG 155

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                  L E+ L     I  R  +  G + L  I
Sbjct: 156 DEDAKKELAEANLRLVVSIAKRY-VGRGMSFLDLI 189


>gi|187736115|ref|YP_001878227.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
 gi|187426167|gb|ACD05446.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
          Length = 688

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 153/275 (55%), Positives = 203/275 (73%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +++  +  + +   ++  E       +RK   EA  AK EMVEANLRLVIS+AKKYTNR
Sbjct: 410 KELKEHLAELELRMWMTADEMGDAYQELRKWLREARRAKDEMVEANLRLVISIAKKYTNR 469

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 470 GLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 529

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K++R  +++  +  REPTPEEIA+++ +PVE VR VLK+ ++PISL+ P+GD D +
Sbjct: 530 ETINKLMRVQKQLVQEYGREPTPEEIAEEIHLPVERVRSVLKMAQQPISLQAPVGDSDDT 589

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             GDFIEDK A +P++ A  + L+E    VL +LT RE  V+  RFG+   +  TLEEVG
Sbjct: 590 SFGDFIEDKAAENPMEEASFSFLKEKIKDVLDTLTDREREVIEQRFGLRDGSPRTLEEVG 649

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +QF VTRERIRQIEAKA+RKL+HP+R  K++ FL+
Sbjct: 650 RQFSVTRERIRQIEAKALRKLRHPTRISKIKGFLE 684



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 48/180 (26%), Positives = 87/180 (48%), Gaps = 10/180 (5%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           +R R +  +  +  D+       +  +++IKLA+++GY+T +++N  LP D V  +  E 
Sbjct: 139 ERKRAASRKITNPIDAPEI---QEKIRELIKLAKEQGYLTFDDINDSLPNDIVDQQDYEA 195

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            +  L +M  +++D  D+       DS    +  S      +++ ++     DDPVRMYL
Sbjct: 196 IMDRLRSMAFDIIDASDV-------DSYTDRTRISTEEEDEEEKLEAKMDILDDPVRMYL 248

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           ++MG + LL+RE E+AI+KRIE     +   +        A +     L D       +I
Sbjct: 249 KQMGQVSLLTREEEVAISKRIEDAEQNVQRCVHRFGFIANAYLDVAYRLLDNEERFDRVI 308


>gi|282856776|ref|ZP_06266037.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
 gi|282585399|gb|EFB90706.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
          Length = 642

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 168/482 (34%), Positives = 260/482 (53%), Gaps = 7/482 (1%)

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E        D+  ++  D   E   D +       D     +   ++  ++  NL+ +
Sbjct: 166 APERIKLTSTLDAVPKEPDDPFAEAPADEDLDNFSGPDAEDLAEVGADDGLDENLNLEVE 225

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
            ++     S+  +            ++ +   +   + N     KD +  +       ++
Sbjct: 226 HEEDDSVGSSSGEISESDPDYLRSMMSHIRGLIVQGRKNGYVTHKDIEKYIPADYWSSEI 285

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
           +  V  ++L +  I +L +     SK     + +         I  +       G +   
Sbjct: 286 LDNVF-INLTELGIQVLDDSAQVSSKDGSSAKSKRPSR-SRTKISDERESPDVPGDDDSA 343

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILK--IRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              + +       +   +    D  L   +R  ++ I     +S  + R +     K E 
Sbjct: 344 SDFASSGGDEAPGYGEELGRMEDVPLSDPVRMYLREIGKVPLLSGEKERELA---IKVEA 400

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
             + AK+++++ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 401 GDAEAKQQIIDANLRLVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEKFDYRKGFKFSTY 460

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  K+ REP+ EEIA ++ + 
Sbjct: 461 ATWWIRQAITRAIADQARTIRIPVHMVETINKMVRISRQLVQKLGREPSDEEIAHEMEIE 520

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              V ++ +I + P+SLETPIG+E+ S LGDFIED+N  SP D+A    L E    +L +
Sbjct: 521 SGRVEEIRRIAQLPVSLETPIGEEEDSQLGDFIEDRNMPSPEDAAAGNLLHEQIEEMLDA 580

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+ RE  VLR RFG+     +TLEEVG++F VTRERIRQIEAKA+RKL+HPSRSKKLR F
Sbjct: 581 LSDREREVLRYRFGLEDGRSYTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSKKLRDF 640

Query: 680 LD 681
           L+
Sbjct: 641 LE 642



 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 70/358 (19%), Positives = 128/358 (35%), Gaps = 49/358 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---------- 80
            + +I   R+ GYVT +++  ++P D  SSE +++    L+ +GI V+D           
Sbjct: 254 IRGLIVQGRKNGYVTHKDIEKYIPADYWSSEILDNVFINLTELGIQVLDDSAQVSSKDGS 313

Query: 81  ---------------DDLEDEEGSEDSLDLASSASNSSVFLQKRKDS----ADRSTDDPV 121
                          D+ E  +   D    +  AS+         +      D    DPV
Sbjct: 314 SAKSKRPSRSRTKISDERESPDVPGDDDSASDFASSGGDEAPGYGEELGRMEDVPLSDPV 373

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYLRE+G + LLS E E  +A ++EAG A     + ++ L     I  +  +  G   L
Sbjct: 374 RMYLREIGKVPLLSGEKERELAIKVEAGDAEAKQQIIDANLRLVVSIAKKY-IGRGMLFL 432

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
             I         E   G     E   Y+K    S        Q     I   A+  +   
Sbjct: 433 DLI--------QEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 484

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             V++  +      + + +   + +    A E ++    +  +  IA++           
Sbjct: 485 HMVETINKMVRISRQLVQKLGREPSDEEIAHEMEIESGRVEEIRRIAQL----------- 533

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
               +      +   L + +         + +  +LL EQ+ ++   +   E E+LR 
Sbjct: 534 PVSLETPIGEEEDSQLGDFIEDRNMPSPEDAAAGNLLHEQIEEMLDALSDREREVLRY 591


>gi|171914125|ref|ZP_02929595.1| RNA polymerase sigma factor RpoD [Verrucomicrobium spinosum DSM
           4136]
          Length = 576

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 177/541 (32%), Positives = 276/541 (51%), Gaps = 34/541 (6%)

Query: 170 WRDELNDGTT--LLREIIDLEACIGPESKGGFFHG-TEGHSYQKREDSSQEKERDDVQET 226
             D++N       LR +I L       +   F      G    +  D    + R    E 
Sbjct: 37  QHDDINAPEIQEKLRFLIRLAKEQDYLTFDDFNESLPNGFVTPELMDEILIRLRSLEIEV 96

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
               +     +K      D      E ++  LD  +D     L     Q+    +   D+
Sbjct: 97  IEPTQVDRVKTKRATVAEDEDTVVEEREDGQLDMLDDPVRMYL----KQMGAVPLLTRDQ 152

Query: 287 IAEVYRELRSLQDNAVNGQKDEKS-SVKCKVLKEKLVKLVGSL-SLN-QSRID------- 336
              + + +   + +     ++    + +   L + L         L    +I+       
Sbjct: 153 EIGISKRIEKAESHLQACLQNIGFIATEYLHLGDALASGTERFDKLVLDRQIEDRDSYFK 212

Query: 337 ---LLVEQLYDISKRIMHNEGELLRLAQSYGIK-RDVF-----------LERHQGRELDP 381
               + +Q+ D   +       L+  +       +D F            + +  ++ + 
Sbjct: 213 KLRQVCDQVRDDISKANEQYRALMSASAKQRQSLKDAFEQTKSSLIKLCAKFYFKQKTNE 272

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             ++  +       +  +     +    ++  ++   +   ++  E+R +V+   +   E
Sbjct: 273 DLIAVLRQRLTELDQIEIEASRSATNPDVQKALEDFELHAWVTPEEYRRLVAETIQWSKE 332

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           ++ AK EMVEANLRLVIS+AKKYTNRGL FLDLIQEGN+GLM+A EKF++  GYKFSTYA
Sbjct: 333 STKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMRAVEKFEYKRGYKFSTYA 392

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQ+ TIRIPVHM D I+K++R  +++  ++ R+PTP+EIA+++ +PV
Sbjct: 393 TWWIRQAITRSIADQARTIRIPVHMIDTINKLLRVQKQLVQELGRDPTPDEIAEEIHLPV 452

Query: 561 EGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           E V  VL+++++P+SL+T +GD D  +  GDFIED  +VSP++      LR+    VL S
Sbjct: 453 ERVNAVLRMSQQPVSLQTKVGDSDGDTEFGDFIEDNTSVSPMELTAMNLLRDKLKDVLDS 512

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE  VL  RFG+   +  TLEEVG+QF VTRERIRQIEAKA+RKL+HP+R +KL  F
Sbjct: 513 LTDRERAVLEQRFGLVDGSGRTLEEVGRQFHVTRERIRQIEAKALRKLRHPTRIRKLGGF 572

Query: 680 L 680
            
Sbjct: 573 F 573



 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 56/216 (25%), Positives = 104/216 (48%), Gaps = 9/216 (4%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
            K +R S+      DD    +   +  + +I+LA+++ Y+T ++ N  LP   V+ E M+
Sbjct: 25  PKSSRASEPPPPQHDDINAPEI-QEKLRFLIRLAKEQDYLTFDDFNESLPNGFVTPELMD 83

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           + +  L ++ I V++   ++  +        A+ A +    +++R+D      DDPVRMY
Sbjct: 84  EILIRLRSLEIEVIEPTQVDRVKTKR-----ATVAEDEDTVVEEREDGQLDMLDDPVRMY 138

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L++MG++ LL+R+ EI I+KRIE   + + A L          +   D L  GT    ++
Sbjct: 139 LKQMGAVPLLTRDQEIGISKRIEKAESHLQACLQNIGFIATEYLHLGDALASGTERFDKL 198

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           +        E +  +F        Q R+D S+  E+
Sbjct: 199 VLDRQI---EDRDSYFKKLRQVCDQVRDDISKANEQ 231


>gi|318066921|emb|CBY89075.1| RNA polymerase sigma70 factor [Halomonas almeriensis]
          Length = 366

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 119/395 (30%), Positives = 182/395 (46%), Gaps = 49/395 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M +L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMFALAYLPGAVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R + DL +        GF    EG       +     E   V +T        
Sbjct: 79  QDEEAPGR-LSDLFS--------GFIDPDEGIPGVAEAEV---PEPQPVHKTAEGEGDED 126

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             ++++ +     PE A      + E  + +   + A                       
Sbjct: 127 VEAEEEETGGGPDPEEARARFEQIREQNEAARRAIEA----------------------- 163

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         +++ + +    +L +L   + L     + LV Q+    +++   E 
Sbjct: 164 ------------HGRAAKEAQSELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEK 211

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L  +   + R  F++   G E +  W+              +      I + + +I
Sbjct: 212 AIMQLCVKKAKLPRKTFIKSFPGNESNQEWLDAFMADNSRHAAR-LEPLKGEIQRSQRKI 270

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   +++++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 271 AFEEEMVALAVTDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 330

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 331 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 365


>gi|154498377|ref|ZP_02036755.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
 gi|150272688|gb|EDM99866.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
          Length = 441

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 151/260 (58%), Positives = 204/260 (78%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + +   +R+       AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL
Sbjct: 186 LTPEEEKALKKDIRR----GEAAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGL 241

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV+R +R++  
Sbjct: 242 IKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVIRVSRQLLQ 301

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++  +P+PEEIA+++ MPV+ VR++LKI +EP+SLETPIG+E+ SHLGDFI D++A  P 
Sbjct: 302 ELGHDPSPEEIAEEMNMPVDKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDEDASEPS 361

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++A    L+E    VL +LTPREE+VL++RFGI      TLEEVGK+F VTRERIRQIEA
Sbjct: 362 EAASFTLLKEQLVDVLGTLTPREEKVLKLRFGIEDGRTRTLEEVGKEFNVTRERIRQIEA 421

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRSKKL+ FL+
Sbjct: 422 KALRKLRHPSRSKKLKDFLN 441



 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 34/135 (25%), Positives = 61/135 (45%), Gaps = 1/135 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +   ++++ A+++G ++  EL   L   E+ SEQM+    +L N+GI  V    L + + 
Sbjct: 44  EKLAELVERAKKKGSLSTNELMDVLEGMELESEQMDKIYDVLENLGIETVSEYYLPELDA 103

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                            +           DDPVRMYL+E+G + LL+ + E+ +A+ + A
Sbjct: 104 DIMPPMEELEEIPEEKIVDPNTLVDSFGIDDPVRMYLKEIGKVNLLNPDEEVQLAQDMGA 163

Query: 149 GRAMMMASLCESPLT 163
           G     A + E    
Sbjct: 164 GD-AAKARMAEIEAA 177


>gi|307700837|ref|ZP_07637862.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
 gi|307613832|gb|EFN93076.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
          Length = 614

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 128/251 (50%), Positives = 179/251 (71%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+
Sbjct: 364 ARELHWVVQDGVNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDY 423

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+
Sbjct: 424 SKGYKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLARVQRQMLQDLGREPTPD 483

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+
Sbjct: 484 ELARELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFVMLQ 543

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   RVL +L+ RE  V+ MR+G+      TL+++G ++ VTRERIRQIE+K + KL+HP
Sbjct: 544 EQLQRVLDTLSEREAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMSKLRHP 603

Query: 671 SRSKKLRSFLD 681
           +RS+ LR +L+
Sbjct: 604 ARSQSLRDYLN 614



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +         +K +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 295 SEKDETDEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVNLAKRIEAGL 346


>gi|302560773|ref|ZP_07313115.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302478391|gb|EFL41484.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 404

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 129/296 (43%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 109 RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSGLALDLDRLVVMGRMAK 168

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 169 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 228

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP E+A  L +P E V +
Sbjct: 229 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPGEVAAHLDLPPERVGE 288

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 289 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 348

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 349 KVVQLRYGLVDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 404



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 28/53 (52%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             + S+    + +      + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 85  ETAGSAEPASRIRPETGGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGL 137


>gi|225026959|ref|ZP_03716151.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
 gi|224955724|gb|EEG36933.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
          Length = 422

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK++ EANLRL +S+AK+Y+ RG+
Sbjct: 152 VRMYLKEIGRIPLLSSEEEIELAKRME---EGDEEAKKKLSEANLRLTVSIAKRYSGRGM 208

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++Q+ITR+IADQ+ TIRIPVHM + 
Sbjct: 209 QFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQSITRAIADQARTIRIPVHMVET 268

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           +++V RT+RR+  +  REPTPEEIA+ + +PVE V ++ KI++EP+SLETPIG+E+ SHL
Sbjct: 269 MNRVNRTSRRLLQEYGREPTPEEIAEAMNLPVERVLEISKISQEPVSLETPIGEEEDSHL 328

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D++   P D A    LRE   +V+ +L+ RE++VL +RFG+     HTLEEVG++
Sbjct: 329 GDFIQDEHIPVPADEAAHTLLREQLEKVMDTLSEREQKVLALRFGLEDGKPHTLEEVGRE 388

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HP+RS+KLR FL+
Sbjct: 389 FQVTRERIRQIEAKALRKLRHPTRSRKLRDFLE 421



 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 46/162 (28%), Positives = 78/162 (48%), Gaps = 24/162 (14%)

Query: 34  MIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV-----VDGDDLEDEE 87
           +++ A+++   V ++E+        ++  Q+E  +A L    I+V     ++ DD+ED+ 
Sbjct: 41  LLERAKKQKNVVELQEIRDVFQNSPLTQAQLERIIAYLEEQKIDVLTMPDINADDIEDDV 100

Query: 88  GSEDSLD-------------LASSASNSSVFLQKRKDSADRSTD-----DPVRMYLREMG 129
           G  DSL+             +  +A     + +  ++S +  T+     DPVRMYL+E+G
Sbjct: 101 GEIDSLNDMDVFQKPDRIGNVQVTAEIEKGYEKTAEESENSFTERGNAEDPVRMYLKEIG 160

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            I LLS E EI +AKR+E G       L E+ L     I  R
Sbjct: 161 RIPLLSSEEEIELAKRMEEGDEEAKKKLSEANLRLTVSIAKR 202


>gi|291166412|gb|EFE28458.1| RNA polymerase sigma factor RpoD [Filifactor alocis ATCC 35896]
          Length = 372

 Score =  229 bits (583), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 164/374 (43%), Positives = 244/374 (65%), Gaps = 16/374 (4%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK   K  +   +L +++  +++N+  I+ + E L  +   I+        +     I+ 
Sbjct: 15  EKGKNKGTLTYMELAEILNPIAVNKDDIENIYETLNQLGIEIIDENTPKTHVNLD-DIEE 73

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F +     E             + E    V   +     +R  +K I   + +S  E 
Sbjct: 74  PEFTDEKDLEET------------KVEEDLSVPKGISVDDPVRMYLKEIGKISLLSAEEE 121

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              + + +K +  + +AKK++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 122 ---IELAQKMDQGSELAKKKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 178

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REP
Sbjct: 179 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREP 238

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEI+K + M VE +R++ KI++EP+SLETPIG+E+ SHLGDFI D +A++P ++A  +
Sbjct: 239 RPEEISKVMDMSVEKIREIQKISQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAYS 298

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL++L  RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 299 LLKEQLEEVLSTLNEREQKVLKLRFGLEDGRTRTLEEVGKEFDVTRERIRQIEAKALRKL 358

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +L+
Sbjct: 359 RHPSRSKKLKDYLE 372



 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 41/154 (26%), Positives = 72/154 (46%), Gaps = 4/154 (2%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +++  + +G +T  EL   L P  V+ + +E+    L+ +GI ++D +  +     +D  
Sbjct: 13  LLEKGKNKGTLTYMELAEILNPIAVNKDDIENIYETLNQLGIEIIDENTPKTHVNLDDIE 72

Query: 94  DLASSAS---NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +   +       +   +        S DDPVRMYL+E+G I LLS E EI +A++++ G 
Sbjct: 73  EPEFTDEKDLEETKVEEDLSVPKGISVDDPVRMYLKEIGKISLLSAEEEIELAQKMDQGS 132

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +    L E+ L     I  R  +  G   L  I
Sbjct: 133 ELAKKKLVEANLRLVVSIAKRY-VGRGMLFLDLI 165


>gi|289578734|ref|YP_003477361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528447|gb|ADD02799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 357

 Score =  229 bits (583), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 167/364 (45%), Positives = 234/364 (64%), Gaps = 32/364 (8%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
             +++  +  + LN  +I+ + +   D+   I+  E             R          
Sbjct: 26  YNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIVGEE------------PRQE-------- 65

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E++   +      PEG   +           +R  +K I     ++  E   +   + + 
Sbjct: 66  EINEEDLDLDLSLPEGISID---------DPVRMYLKEIGKIPLLTPEEEIELAKRIEQ- 115

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AKK ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFS
Sbjct: 116 --GDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFS 173

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ REPTPEE+AK++ 
Sbjct: 174 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQELGREPTPEELAKEMG 233

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           MP E VR+++KI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A    L+E    VL
Sbjct: 234 MPEEKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFTMLKEQLMDVL 293

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+
Sbjct: 294 DTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLK 353

Query: 678 SFLD 681
            FLD
Sbjct: 354 DFLD 357



 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 47/160 (29%), Positives = 71/160 (44%), Gaps = 14/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S D+  ++I   ++ G +T  E+   L   +++ +Q+E       +MGI +V  +  +
Sbjct: 5   ELSKDAITELINKGKKTGMLTYNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIVGEEPRQ 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E   ED                        S DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 65  EEINEED-------------LDLDLSLPEGISIDDPVRMYLKEIGKIPLLTPEEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 RIEQGDEEAKKRLIEANLRLVVSIAKRY-VGRGMLFLDLI 150


>gi|150390747|ref|YP_001320796.1| RpoD family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950609|gb|ABR49137.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           metalliredigens QYMF]
          Length = 372

 Score =  229 bits (583), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 209/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   + + +        +AKK++VEANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGKVPLLTGPEEIDLATRME---AGDELAKKKLVEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +  REP PEEIAK++ +P E VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 220 INKLIRVSRQLLQEFGREPKPEEIAKEMDLPEEKVREILKIAQEPVSLETPIGEEEDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A  + L+E    VL +LTPRE++VLR+RFG+      TLEEVGK+
Sbjct: 280 GDFIPDDDAPAPAEAAAFSLLKEQLIEVLDTLTPREQKVLRLRFGLDDGRARTLEEVGKK 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 340 FDVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 372



 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 46/161 (28%), Positives = 77/161 (47%), Gaps = 2/161 (1%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDL 83
           +   +S KK+I+  ++RG +T  E+   L   E+  EQ+E+     + +GI++V D +  
Sbjct: 6   NMKKESIKKLIEKGKKRGIITYAEIVHALEDIELDKEQIEEIYEHFATLGIDIVGDKEAD 65

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           + ++  E  L+     + +               DDPVRMYL+E+G + LL+   EI +A
Sbjct: 66  DVDDVDEAELEDEEEVTVAENIEADINMLKGVIIDDPVRMYLKEIGKVPLLTGPEEIDLA 125

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            R+EAG  +    L E+ L     I  R  +  G   L  I
Sbjct: 126 TRMEAGDELAKKKLVEANLRLVVSIAKRY-VGRGMLFLDLI 165


>gi|317128328|ref|YP_004094610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315473276|gb|ADU29879.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 372

 Score =  229 bits (583), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S SE   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSASEEIDLAKKIE---DGDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEE++K++ +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDLGREPSPEEVSKEMDLTPDKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQEALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 71/183 (38%), Gaps = 16/183 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++  ++RG +T  E+   L   +  S+QM++    L   G+ +++       E
Sbjct: 17  DQVKEQLLEAGKKRGVLTYAEITERLAVFDQDSDQMDEFFEFLGEQGVEILN-------E 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                           + L           +DPVRMYL+E+G + LLS   EI +AK+IE
Sbjct: 70  TEGVPSLQQVEKEEEEIDLNDLSVPPGIKINDPVRMYLKEIGRVPLLSASEEIDLAKKIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 130 DGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 180

Query: 208 YQK 210
           Y K
Sbjct: 181 YNK 183


>gi|328885546|emb|CCA58785.1| RNA polymerase sigma factor RpoD [Streptomyces venezuelae ATCC
           10712]
          Length = 567

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 315 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 374

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 375 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 434

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 435 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 494

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 495 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 554

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 555 HPSRSQVLRDYLD 567



 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           +         ++ +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 249 SDEDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 307

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            S      L    + + +    
Sbjct: 308 NSDKLAPKLKRELEIIAEDGRR 329


>gi|310827637|ref|YP_003959994.1| RNA polymerase [Eubacterium limosum KIST612]
 gi|308739371|gb|ADO37031.1| RNA polymerase [Eubacterium limosum KIST612]
          Length = 395

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 152/272 (55%), Positives = 202/272 (74%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  +   I   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 126 VRLYLKEIGKVPLLTAEQEMGIAKRME---AGDDEAKKELAEANLRLVVSIAKRYVGRGM 182

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 183 SFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 242

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTP EI K++    E VR++ KI ++P+SLETPIG+E+ SHL
Sbjct: 243 INKLIRVSRQLLQELGREPTPAEIGKEMGFSEEKVREIQKIAQDPVSLETPIGEEEDSHL 302

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED NA +P ++A  A L+E    VL +LT REE+VLR+RFG+      TLEEVGK+
Sbjct: 303 GDFIEDDNAPAPSEAASYALLKEQLMEVLNTLTEREEKVLRLRFGLDDGRARTLEEVGKE 362

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L
Sbjct: 363 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYL 394



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 81/189 (42%), Gaps = 6/189 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDF-SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
           M   KK+    D E    +   + D  +    + +IK  +++G +   +    L   ++ 
Sbjct: 1   MAEAKKKKVKPDMEELLDEVDAIADLEAMPEVQTLIKRGKEKGSLNNADFEEVLEKTDLD 60

Query: 60  SEQMEDTVAMLSNMGINV----VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
            E+++    +L   GI++    ++ +  + +   +  +            ++        
Sbjct: 61  PEEIDSIYLLLQKEGIDLTFQDMEIETDDIDLDIDIDVAELEEIEIEEDPVKDIDLGDSV 120

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           S +DPVR+YL+E+G + LL+ E E+ IAKR+EAG       L E+ L     I  R  + 
Sbjct: 121 SVNDPVRLYLKEIGKVPLLTAEQEMGIAKRMEAGDDEAKKELAEANLRLVVSIAKRY-VG 179

Query: 176 DGTTLLREI 184
            G + L  I
Sbjct: 180 RGMSFLDLI 188


>gi|205374117|ref|ZP_03226917.1| RNA polymerase sigma factor RpoD [Bacillus coahuilensis m4-4]
          Length = 337

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 68  VRMYLKEIGRVDLLSAEEEISLAERIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 124

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 125 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 184

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 185 INKLIRVQRQLLQDLGREPSPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHL 244

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 245 GDFIEDSEAQSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 304

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 305 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 337



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 68/165 (41%), Gaps = 14/165 (8%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
             L   ++ S+Q+++    L   GI +V  +D + +  +E       + +     L    
Sbjct: 3   DKLSSFDLDSDQIDEYFEQLGEQGIEIVHENDSDSDPNAE-----QLNKNEEEFDLNDLS 57

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
                  +DPVRMYL+E+G ++LLS E EI++A+RIE G       L E+ L     I  
Sbjct: 58  VPPGVKINDPVRMYLKEIGRVDLLSAEEEISLAERIEQGDEEAKRRLAEANLRLVVSIAK 117

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           R  +  G   L  I         E   G     E   Y+K    S
Sbjct: 118 RY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDYRKGFKFS 153


>gi|323359909|ref|YP_004226305.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323276280|dbj|BAJ76425.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 436

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 137/284 (48%), Positives = 195/284 (68%), Gaps = 1/284 (0%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVI 457
            A EV+  ++I   + +    + +S +E    + + ++    +   AK  ++ ANLRLV+
Sbjct: 153 AAEEVELAMRIEAGLFAEEKLSNMSAAEKTSQLGLDLQWVARDGQRAKSHLLGANLRLVV 212

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 213 SLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQAR 272

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R  R+M   + REPTPEE++++L M  E V +V K  +EPISL 
Sbjct: 273 TIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKVIEVQKYGREPISLH 332

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED  AV P D+     L+     +L SL+ RE  V+RMRFG+G  
Sbjct: 333 TPLGEDGDSEFGDLIEDTEAVVPADAVGFTMLQRQLESLLDSLSEREAGVIRMRFGLGDG 392

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 393 QPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 436



 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +S+    +         +T DPV+ YL+++G + LL+   E+ +A RIEAG 
Sbjct: 116 SSSDEDDVPVYSAQITGATADPVKDYLKQIGKVPLLNAAEEVELAMRIEAGL 167


>gi|260906542|ref|ZP_05914864.1| RNA polymerase principal sigma factor [Brevibacterium linens BL2]
          Length = 473

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 138/297 (46%), Positives = 191/297 (64%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV------------------------RKGECEASIA 444
           +++ +K I     ++ +E   +   +                        +    +  IA
Sbjct: 177 VKDYLKQIGKVALLNAAEEVDLAKRIEAGMYAEHLLDAGGITEPRESMDYKWIIHDGRIA 236

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW+
Sbjct: 237 KNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWI 296

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP+PEE+AK+L M  E V 
Sbjct: 297 RQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPSPEELAKELDMTPERVV 356

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +V K  +EPISL TP+G++  S  GD IED  AV P DS     L+E    VL +L+ RE
Sbjct: 357 EVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPSDSVSFTLLQEQLHSVLDTLSERE 416

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 417 AGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAKLRHPSRSQVLRDYLD 473



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 79  DGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           +  + ++ E  E +  +  +     +         ++  +  +T DPV+ YL+++G + L
Sbjct: 130 EATETKNSEEKEKNAAVTEAGGFIVSDADEEDAPAQQVVSAGATADPVKDYLKQIGKVAL 189

Query: 134 LSREGEIAIAKRIEAGR 150
           L+   E+ +AKRIEAG 
Sbjct: 190 LNAAEEVDLAKRIEAGM 206


>gi|323703334|ref|ZP_08114984.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531697|gb|EGB21586.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 367

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 98  VRMYLKEIGRVPLLSPEEEVELAKRMEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 155 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +  + VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 215 INKLIRVSRQLLQELGREPTPEEIAKEMNISGDKVREIMKIAQEPVSLETPIGEEEDSHL 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A +P + A    LRE    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 275 GDFIEDADARAPAEEASFTLLREQLDEVLKTLTDREQKVLRLRFGLDDGRARTLEEVGQK 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAK +RKL+HPSRSKKL+ +LD
Sbjct: 335 FGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLD 367



 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 48/156 (30%), Positives = 74/156 (47%), Gaps = 6/156 (3%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  K+MI+  ++RG +T  E+   L   E+++EQ++D    L+ MGI VV      +   
Sbjct: 11  EKVKEMIEKGKKRGSLTYGEIMDSLQGAELTAEQIDDIYEQLAAMGIEVVPEVTDLEPLE 70

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +D+ D     + +               DDPVRMYL+E+G + LLS E E+ +AKR+E 
Sbjct: 71  VDDAAD-----TPTEDVEIDLSIPEGIGIDDPVRMYLKEIGRVPLLSPEEEVELAKRMEQ 125

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  R  +  G   L  I
Sbjct: 126 GDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 160


>gi|3062909|dbj|BAA25730.1| SigA [Bacillus sp.]
          Length = 372

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   + + + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLTAEEEIELATRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEE+A+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVQRQLLQDVGREPSPEEVAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIEDQDALAPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 99/262 (37%), Gaps = 16/262 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++L ++RG +T  E+   L P +  S+QM++    L   G+ +++       +
Sbjct: 17  DQVKEQLVELGKKRGVLTYAEITEKLAPYDQDSDQMDEFFEYLGEQGVEILN-------D 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E               L           +DPVRMYL+E+G + LL+ E EI +A RIE
Sbjct: 70  NEEVPSLQQVEKEEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELATRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 130 QGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 180

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y K    S        Q     I   A+  +     V++  +      + L +   + + 
Sbjct: 181 YNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDVGREPSP 240

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              A E  L P+ +  + +IA+
Sbjct: 241 EEVAEEMDLTPEKVREILKIAQ 262


>gi|227875511|ref|ZP_03993651.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269977243|ref|ZP_06184216.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|306818820|ref|ZP_07452542.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
 gi|227843847|gb|EEJ54016.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269934546|gb|EEZ91107.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|304648506|gb|EFM45809.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
          Length = 614

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 128/251 (50%), Positives = 179/251 (71%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+
Sbjct: 364 ARELHWVVQDGVNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDY 423

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+
Sbjct: 424 SKGYKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLARVQRQMLQDLGREPTPD 483

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+
Sbjct: 484 ELARELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFVMLQ 543

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   RVL +L+ RE  V+ MR+G+      TL+++G ++ VTRERIRQIE+K + KL+HP
Sbjct: 544 EQLQRVLDTLSEREAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMSKLRHP 603

Query: 671 SRSKKLRSFLD 681
           +RS+ LR +L+
Sbjct: 604 ARSQSLRDYLN 614



 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +         +K +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 295 SEKDETDEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVNLAKRIEAGL 346


>gi|326791438|ref|YP_004309259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
 gi|326542202|gb|ADZ84061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
          Length = 363

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   ++        AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 94  VRMYLKEIGKVPLLSAEQEIILAQRMQ---DGDQEAKKKLAEANLRLVVSIAKRYVGRGM 150

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 151 LFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 210

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P PEEIAK++ MPV  VR+++KI++EP+SLETPIG+E+ SHL
Sbjct: 211 INKLMRVSRQLLQELGRDPQPEEIAKRMDMPVSKVREIMKISQEPVSLETPIGEEEDSHL 270

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++   P ++A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 271 GDFIPDEDIPVPAEAAAFTLLKEQLIEVLDTLTEREQKVLRLRFGLDDGRARTLEEVGKE 330

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 331 FSVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 363



 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 39/158 (24%), Positives = 65/158 (41%), Gaps = 17/158 (10%)

Query: 28  DDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
                ++I +A+ ++G +  E++N      ++   ++E     L    I+V+        
Sbjct: 15  KAKLDQLINIAKDKKGMLDQEDINDVFSDMDLEPSKIEQIYEYLEAQNIDVIGN------ 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                     + A    V +         S DDPVRMYL+E+G + LLS E EI +A+R+
Sbjct: 69  ---------LNDAEIDDVDIDLSNLPDGISIDDPVRMYLKEIGKVPLLSAEQEIILAQRM 119

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + G       L E+ L     I  R  +  G   L  I
Sbjct: 120 QDGDQEAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 156


>gi|319651585|ref|ZP_08005712.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396652|gb|EFV77363.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 374

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    +++  + E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLSAEEE---IALANRIEEGDEEAKRRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPDKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/207 (25%), Positives = 86/207 (41%), Gaps = 18/207 (8%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            +  +  ++ D  L  +   D   +++++ ++ G +  +++   L   EV S QM++   
Sbjct: 2   AEKSARSKEVDTELTLEQVKD---QLVEIGKKTGVLAYDDIAERLSQFEVDSHQMDEFYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L + G+ +V  ++ ED    E       + +     L           +DPVRMYL+E+
Sbjct: 59  FLGDQGVELVGDNENEDPNVQE------LAKNEEEFDLNDLSVPPGVKINDPVRMYLKEI 112

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G ++LLS E EIA+A RIE G       L E+ L     I  R  +  G   L  I    
Sbjct: 113 GRVDLLSAEEEIALANRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI---- 167

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSS 215
                E   G     E   Y+K    S
Sbjct: 168 ----QEGNMGLIKAVEKFDYRKGFKFS 190


>gi|315604554|ref|ZP_07879617.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315313566|gb|EFU61620.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 516

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 140/273 (51%), Positives = 190/273 (69%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +  E K  +    ++  E R +  + +    +   AK  ++EANLRLV+S+AK+YT RG+
Sbjct: 248 LYAEYKLKNQADEMTSRERRELHFLAQ----DGQQAKNHLLEANLRLVVSLAKRYTGRGM 303

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + 
Sbjct: 304 QFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV 363

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL TP+G++  S  
Sbjct: 364 INKLARVQRQMLQDLGREPTPEELAKELDMTAEKVVEVQKYGREPISLHTPLGEDGDSEF 423

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD IED  A+ P D+     L+E    VL +L+ RE  V+ MRFG+G     TL+E+GK 
Sbjct: 424 GDLIEDSEAIVPADAVSFTLLQEQLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKV 483

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 484 YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 516



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +A+RIEAG 
Sbjct: 197 SDSDETDEPVQQVTVAGATADPVKDYLKQIGKVSLLNAEQEVDLARRIEAGL 248


>gi|331082069|ref|ZP_08331197.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330405664|gb|EGG85194.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 374

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    +++ ++ E     AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGKVPLLSAEEE---ITLAQRMEEGDESAKKRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA+++ M VE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 222 INKLIRVSRQLLQELGREPHPEEIAEEMNMSVERVREILKISQEPVSLETPIGEEEDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 282 GDFIQDDNVPVPADAAAFTLLKEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKE 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 342 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 374



 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 42/159 (26%), Positives = 75/159 (47%), Gaps = 4/159 (2%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   ++++LA+++   +  +E++ F     +  EQM+     L   GI+++   D + ++
Sbjct: 10  EKLGELMELAKKKKNVLEYQEISDFFKDFPLEPEQMDKVFDFLEANGIDILRIQDNDMDD 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                 D  + +    V ++    S     S +DPVRMYL+E+G + LLS E EI +A+R
Sbjct: 70  LIISDDDDLNLSEEDEVDMENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEEEITLAQR 129

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +E G       L E+ L     I  R  +  G   L  I
Sbjct: 130 MEEGDESAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|312195623|ref|YP_004015684.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226959|gb|ADP79814.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 418

 Score =  228 bits (582), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 142/253 (56%), Positives = 196/253 (77%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +   E +  IAK  +VEANLRLV+S+A++Y  RG+ FLDLIQEGN+GL++A EKF
Sbjct: 166 DLRRELVWVERDGEIAKSRLVEANLRLVVSIARRYVGRGMLFLDLIQEGNLGLIRAVEKF 225

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPT
Sbjct: 226 DYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPT 285

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIAK++ +  + VR++ K+ +EPISLETPIG+E+ SHLGDFIED +AV P+D+A    
Sbjct: 286 PEEIAKEMDLTPDKVREIQKVAQEPISLETPIGEEEDSHLGDFIEDSDAVVPVDAASFLL 345

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+
Sbjct: 346 LQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLR 405

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+KLR +L+
Sbjct: 406 HPSRSQKLRDYLE 418



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 37/81 (45%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +D ED E   ++                   +ADR + D VR YL ++G + LL+ E 
Sbjct: 80  DEEDAEDAEFDANAEAETEKEERDDEQPTPAASAADRMSHDSVRQYLSQIGRVRLLTAEE 139

Query: 139 EIAIAKRIEAGRAMMMASLCE 159
           E+ +AKR+EAG         E
Sbjct: 140 EVDLAKRVEAGLFAAEKLAAE 160


>gi|311742667|ref|ZP_07716476.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
 gi|311314295|gb|EFQ84203.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
          Length = 464

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 135/297 (45%), Positives = 189/297 (63%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIA 444
           +++ +K I   + ++  E   +   +                             +   A
Sbjct: 168 VKDYLKQIGKVSLLTAGEEVELAKRIEAGLFAEEKLAKGGRISPKMREELDWIVVDGRRA 227

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW+
Sbjct: 228 KNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWI 287

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTP+E+AK+L M  E V 
Sbjct: 288 RQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAKELDMTPEKVV 347

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ RE
Sbjct: 348 EVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHAVLDTLSERE 407

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 408 SGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 464



 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + D   D    ED     + ++        ++     +T DPV+ YL+++G + LL+
Sbjct: 123 EVFEKDLKTDPTLKEDESSAFTLSAADESDEPVQQVMVAGATADPVKDYLKQIGKVSLLT 182

Query: 136 REGEIAIAKRIEAGR 150
              E+ +AKRIEAG 
Sbjct: 183 AGEEVELAKRIEAGL 197


>gi|312196071|ref|YP_004016132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311227407|gb|ADP80262.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 146/297 (49%), Positives = 207/297 (69%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEAS------------------------IA 444
           +R  +K I     ++ +E   +   +  G   A                         +A
Sbjct: 97  VRMYLKEIGKVPLLTAAEEVDLAKRIEAGLFAAEKLGGGRRLTVALRVDLEAVARDGDVA 156

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW+
Sbjct: 157 KRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 216

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP PEEIAK++ +  + VR
Sbjct: 217 RQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIAKEMDLTPDKVR 276

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++LK+ +EP+SLETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE
Sbjct: 277 EILKVAQEPVSLETPIGEEEDSHLGDFIEDSDAVVPVDAASFLLLQEQLDSVLHTLSDRE 336

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++V+++RFG+      TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 337 KKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 393



 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 43/158 (27%), Positives = 72/158 (45%), Gaps = 10/158 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  K +I   ++ G++T +++   +   E+  EQ E  + +L++ GI V+D       + 
Sbjct: 15  EEIKDLITRGKEAGFLTTDDITVAIQAAELPQEQAEQVLTLLNDEGIEVLDPR----ADS 70

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +E S  LA           K        T DPVRMYL+E+G + LL+   E+ +AKRIEA
Sbjct: 71  AETSDLLARRRREEEALNAKAP------TSDPVRMYLKEIGKVPLLTAAEEVDLAKRIEA 124

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G            LT    +       DG    R++++
Sbjct: 125 GLFAAEKLGGGRRLTVALRVDLEAVARDGDVAKRKLVE 162


>gi|318066983|emb|CBY89106.1| RNA polymerase sigma70 factor [Kushneria aurantia]
          Length = 370

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 128/395 (32%), Positives = 181/395 (45%), Gaps = 45/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAHLPGAVDSILEAYDGT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +     S ++E DD  + + + ++A 
Sbjct: 79  RDEEAPGRLSDLFSGFIDPDEGVPGVAEVEEPEPEPVASDSDDEESDDEDDDDSEDDNA- 137

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                  S+    PE A      + E  D     +                         
Sbjct: 138 -------SEGGPDPELARVRFEQIREQNDHVKAVIE------------------------ 166

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      +    S   +  +++L +L   + L     + LV QL     ++   E 
Sbjct: 167 -----------QHGLQSEMARAEQKRLAELFSPIKLVPRHFERLVGQLRFSVGQVREQEK 215

Query: 355 ELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L    G + R  F+    GRE D  WV            N +      I + + +I
Sbjct: 216 SIMQLCVKRGKVPRKTFIASFPGRESDTTWVDDFMAKNAKHAGN-IEPLRGDIERAQRKI 274

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 275 AFEEELAMLPVAELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 334

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 335 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 369


>gi|118444745|ref|YP_878546.1| RNA polymerase sigma factor RpoD [Clostridium novyi NT]
 gi|118135201|gb|ABK62245.1| RNA polymerase sigma-70 factor [Clostridium novyi NT]
          Length = 368

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 157/273 (57%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +GE     AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGKVPLLTPDEEIDLAQRIEEGEMY---AKKKLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 216 INKLIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 276 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 368



 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/154 (32%), Positives = 75/154 (48%), Gaps = 16/154 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +I   +++G +T +E+   L   E+S EQ+E   A+L +M I V+ GD  + E   E
Sbjct: 24  IKSLIDKGKKKGSLTYKEIMDELDNVELSPEQIEKVYAVLESMDIEVI-GDMKDMETEEE 82

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +DL+                   S DDPVRMYL+E+G + LL+ + EI +A+RIE G 
Sbjct: 83  EEIDLSVPE--------------GISIDDPVRMYLKEIGKVPLLTPDEEIDLAQRIEEGE 128

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 129 MYAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 161


>gi|297160766|gb|ADI10478.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 453

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 130/296 (43%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     +S +E   +   V                         +      +AK
Sbjct: 158 RQYLREIGRIPLLSAAEEVELARRVEAGLFAEEKLSNTPDLDTQLAHDFDQLVVLGRMAK 217

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 218 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 277

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E V +
Sbjct: 278 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAHHLDLLPERVSE 337

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 338 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 397

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 398 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 453



 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           R +++   + D  R YLRE+G I LLS   E+ +A+R+EAG       L  +P     L 
Sbjct: 145 RAETSSGPSSDLFRQYLREIGRIPLLSAAEEVELARRVEAGLF-AEEKLSNTPDLDTQLA 203

Query: 169 IWRDE-LNDGTTLLREIID 186
              D+ +  G    R +I+
Sbjct: 204 HDFDQLVVLGRMAKRRLIE 222


>gi|160878392|ref|YP_001557360.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427058|gb|ABX40621.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 371

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 153/361 (42%), Positives = 225/361 (62%), Gaps = 21/361 (5%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           +K+      L+LN  +ID + E L   +  +++                    +  +  E
Sbjct: 29  DKVNDFFKELNLNVRQIDKIYEYLEANNIVVLNPT------------------DEDEPNE 70

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
                +    D               S   ++  +K I     +S++E   +   +    
Sbjct: 71  DALLELEDDSDMIGDTEDLSAMTSTISDDPVKQYLKEIGSYPLLSVAEEIELAKKIE--- 127

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++AK+ + E+NLRLV+S+AK+Y  RGL FLDLIQEGN+GL+KA +KFD+  GYKFST
Sbjct: 128 AGDNMAKQILAESNLRLVVSIAKRYVGRGLSFLDLIQEGNLGLIKAVDKFDYNKGYKFST 187

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIRIPVHM + I+K  R +R +  ++ REP+ +E+A  + +
Sbjct: 188 YATWWIRQAITRSIADQSRTIRIPVHMSEVINKTYRVSRNLLQELGREPSEQELADAMNL 247

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P+E VR++LK++ +PISL+TPIG+ED SHLGDFI+D   + P D+A  A L++  +++L 
Sbjct: 248 PIEKVREILKVSADPISLDTPIGEEDDSHLGDFIKDDTIMGPEDAASYAVLQDQISKLLD 307

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +LT RE+RVL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSR++ L+ 
Sbjct: 308 TLTEREQRVLILRFGLQDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRARMLKG 367

Query: 679 F 679
           +
Sbjct: 368 Y 368



 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 46/162 (28%), Positives = 76/162 (46%), Gaps = 4/162 (2%)

Query: 24  FDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
            +  +   K++I  A   +G + ++++N F     ++  Q++     L    I V++  D
Sbjct: 5   VNTFEARLKELIAFANDNKGVIEVDKVNDFFKELNLNVRQIDKIYEYLEANNIVVLNPTD 64

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             ++E +ED+L      S+     +         +DDPV+ YL+E+GS  LLS   EI +
Sbjct: 65  --EDEPNEDALLELEDDSDMIGDTEDLSAMTSTISDDPVKQYLKEIGSYPLLSVAEEIEL 122

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AK+IEAG  M    L ES L     I  R  +  G + L  I
Sbjct: 123 AKKIEAGDNMAKQILAESNLRLVVSIAKRY-VGRGLSFLDLI 163


>gi|318066991|emb|CBY89110.1| RNA polymerase sigma70 factor [Modicisalibacter tunisiensis]
          Length = 373

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 118/395 (29%), Positives = 177/395 (44%), Gaps = 42/395 (10%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+RE EI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREAEIEIAKRIEEGTREVMSSLAYLPGAVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   D    +      + +GD + A 
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEEEPVADLDDGE-----SDDDGDADEAD 133

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                  ++    PE A      + +  + +   ++                        
Sbjct: 134 DEDDSSSNEGGPDPEEARARFEQIRDQNERAKAAVA------------------------ 169

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K    S +    + +L +L   + L     + LV Q+    +++   E 
Sbjct: 170 -----------KHGLGSAEANAEQARLAELFSPIKLVPKHFERLVGQVRISVEQVREQEK 218

Query: 355 ELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +L+L  +   + R  F++   G E    W           + + +      + + + +I
Sbjct: 219 SVLQLFVKKGKVPRKTFIKSFPGNESRLEWFDAFLA-DNPRYADRLGPFRGDVQRAQRKI 277

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + +SE + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 278 AFEEELIQLPVSEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 337

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QA+
Sbjct: 338 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAM 372


>gi|28211633|ref|NP_782577.1| RNA polymerase sigma factor RpoD [Clostridium tetani E88]
 gi|28204075|gb|AAO36514.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 366

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         A+K++ EANLRLV+S+AK+Y  RG+
Sbjct: 97  VRMYLKEIGKVPLLTSEEEVDLAQRIE---AGELKARKKLAEANLRLVVSIAKRYVGRGM 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 154 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ + V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 214 INKLIRVSRQLLQELGREPTPEEIAKEMEISVDRVREIMKIAQEPVSLETPIGEEEDSHL 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 274 GDFIPDDDALAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 334 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 366



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 43/154 (27%), Positives = 64/154 (41%), Gaps = 16/154 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +I   ++ G +T +E+   L   E++ EQ+E     L +M I+V+            
Sbjct: 22  LKNLIDKGKKSGSLTYKEIMDELEEIELTPEQIEKVYEALESMNIDVLGA---------- 71

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                                    S DDPVRMYL+E+G + LL+ E E+ +A+RIEAG 
Sbjct: 72  -----DEIKKEEEEEEIDISVPEGISIDDPVRMYLKEIGKVPLLTSEEEVDLAQRIEAGE 126

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 127 LKARKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 159


>gi|160881641|ref|YP_001560609.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160430307|gb|ABX43870.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 372

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGKVPLLSADEEIVLAQRMEQ---GDKNAKKRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 QFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REP PEE+AK++ +PVE VR++ KI++EP+SLETPIG+E+ SHL
Sbjct: 220 INKLIRVQRQLLQELGREPFPEEVAKEMNIPVERVREIQKISQEPVSLETPIGEEEDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 280 GDFIQDDNVPVPAEAAAFTLLKEQLMEVLGTLTDREQKVLRLRFGLDDGRARTLEEVGKE 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 340 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 372



 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 45/157 (28%), Positives = 77/157 (49%), Gaps = 2/157 (1%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +  K++++ A+++   +  EE+N F    E+ ++++E     L    I+V+   +LE+EE
Sbjct: 10  EKLKELLEYAKKKKNVLEYEEINDFFSDMEIDADRIEKIYEYLEAHNIDVLRAPELEEEE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             ++S      A    +           ST+DPVRMYL+E+G + LLS + EI +A+R+E
Sbjct: 70  EIDESDLALIEAEEEEITNIDLTVPEGISTEDPVRMYLKEIGKVPLLSADEEIVLAQRME 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 130 QGDKNAKKRLAEANLRLVVSIAKRY-VGRGMQFLDLI 165


>gi|126699059|ref|YP_001087956.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile 630]
 gi|115250496|emb|CAJ68320.1| RNA polymerase sigma factor SigA1 (sigma-43) [Clostridium
           difficile]
          Length = 390

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 163/383 (42%), Positives = 235/383 (61%), Gaps = 5/383 (1%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                    EK   +  +   ++++      L++ +++ L E L ++   I   +     
Sbjct: 13  KKVTAKTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKAD 72

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +  S            +  E   H  S A +    +        +D    +R  +K I  
Sbjct: 73  IDFSVADDDLSIGHLDEDAEAISHDDSSAIEIETVDLSLPKGISIDD--PVRMYLKEIGK 130

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +   E       +        IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN
Sbjct: 131 IPLLKPHEEVEFARRM---HEGDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGN 187

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R+
Sbjct: 188 LGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQ 247

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  ++ R+P PEEIAK++ M  + VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A 
Sbjct: 248 LLQELGRDPKPEEIAKEMEMTEDKVREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAP 307

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+F VTRERIRQ
Sbjct: 308 APAEAAAYSLLKEQIEDVLGSLNDREQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQ 367

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSKKLR +LD
Sbjct: 368 IEAKALRKLRHPSRSKKLRDYLD 390



 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 63/273 (23%), Positives = 101/273 (36%), Gaps = 23/273 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----------- 80
           K +I+  +++G +T+ E+       E+  +Q+E+    L N+GI + +            
Sbjct: 18  KTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKADIDFSV 77

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKD---SADRSTDDPVRMYLREMGSIELLSRE 137
            D +   G  D    A S  +SS    +  D       S DDPVRMYL+E+G I LL   
Sbjct: 78  ADDDLSIGHLDEDAEAISHDDSSAIEIETVDLSLPKGISIDDPVRMYLKEIGKIPLLKPH 137

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  A+R+  G  +    L E+ L     I  R  +  G   L  I         E   
Sbjct: 138 EEVEFARRMHEGDEIAKQRLVEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNL 188

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           G     E   Y K    S        Q     I   A+  +     V++  +      + 
Sbjct: 189 GLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQL 248

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           L E   D      A E ++    +  + +IA+ 
Sbjct: 249 LQELGRDPKPEEIAKEMEMTEDKVREIMKIAQD 281


>gi|323127013|gb|ADX24310.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 369

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKVLAVAV---AEGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 97/260 (37%), Gaps = 16/260 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +++   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRHHKKEGTAIDDDVTEKLVIPFALDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKVLAVAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAE 289
            A   ++ P  +  + +IA+
Sbjct: 239 IAERMEMTPDKVREILKIAQ 258


>gi|300812183|ref|ZP_07092625.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496819|gb|EFK31899.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 372

 Score =  228 bits (581), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 167/359 (46%), Positives = 230/359 (64%), Gaps = 25/359 (6%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+   G+  +LA +         +  +  EL+  
Sbjct: 39  RLIKPYKLEGKAVDQLVQEFEDNGISIVDEGGKPSKLALTKQ-------KNVEKAELNNM 91

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
                    +                +R  +K I     ++  E    V++ ++ E    
Sbjct: 92  DAPTGMKMNDP---------------VRMYLKEIGRVNLLTSEEE---VALAKRIEAGDE 133

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LGYKFSTYA W
Sbjct: 134 EAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFSTYATW 193

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEI  ++ +PV+ 
Sbjct: 194 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIGAEMDLPVKK 253

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++LKI +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+E    VL +L+ 
Sbjct: 254 VREILKICQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVLDTLSD 313

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR FLD
Sbjct: 314 REEEVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRSSQLRDFLD 372



 Score = 88.0 bits (216), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 109/313 (34%), Gaps = 49/313 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +++  +    +T       L  P ++  + ++  V    + GI++VD      E
Sbjct: 15  EKAVKLVVEGVKASHQITEAAFEDRLIKPYKLEGKAVDQLVQEFEDNGISIVD------E 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            G    L L    +     L           +DPVRMYL+E+G + LL+ E E+A+AKRI
Sbjct: 69  GGKPSKLALTKQKNVEKAELNNMDAPTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA-------- 189
           EAG       L E+ L     I  R         D + +G   L + +D           
Sbjct: 129 EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFS 188

Query: 190 -------------------------CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
                                        E+                 D   E+   ++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIGAEMD 248

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                +    K+ ++  S      E  +++  +  ED+D  +    A  + L+ ++   L
Sbjct: 249 LPVKKVREILKICQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVL 308

Query: 285 DEIAEVYRELRSL 297
           D +++   E+  L
Sbjct: 309 DTLSDREEEVLRL 321


>gi|283457795|ref|YP_003362387.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
 gi|283133802|dbj|BAI64567.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
          Length = 460

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 134/254 (52%), Positives = 180/254 (70%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +   +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 207 KDLKKALRWVVHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 266

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 267 FDYSKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 326

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+ K+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 327 TPEELGKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFT 386

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL
Sbjct: 387 LLQEQLHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKL 446

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 447 RHPSRSQVLRDYLD 460



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           +N       ++     +T DPV+ YL+++G + LL+ + E+ +AKRIEAG       L E
Sbjct: 143 ANDDDDAPAQRVVTPGATADPVKDYLKQIGKVSLLNAQQEVDLAKRIEAGLY-AEHKLAE 201

Query: 160 SP 161
           +P
Sbjct: 202 NP 203


>gi|311898773|dbj|BAJ31181.1| putative RNA polymerase major sigma factor [Kitasatospora setae
           KM-6054]
          Length = 541

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 289 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 348

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 349 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 408

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 409 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 468

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 469 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 528

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 529 HPSRSQVLRDYLD 541



 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 47/99 (47%), Gaps = 1/99 (1%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D+++ E  E++      + +       ++ +   +T DPV+ YL+++G + LL+ E E+ 
Sbjct: 206 DVKEGEAEEETDQGFVLSDDDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVE 265

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +AKRIEAG       L ++      L    + + +    
Sbjct: 266 LAKRIEAGLF-AEDKLSQADKLAPKLKRELEIIAEDGRR 303


>gi|51891726|ref|YP_074417.1| RNA polymerase sigma factor RpoD [Symbiobacterium thermophilum IAM
           14863]
 gi|51855415|dbj|BAD39573.1| RNA polymerase major sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 388

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E       + K       AK+++ EANLRLV+S+AK+Y  RG+
Sbjct: 119 VRMYLKEIGRVPLLTAEEEIMYAERIEK---GDEEAKRKLAEANLRLVVSIAKRYVGRGM 175

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 176 QFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 235

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REPTPEEIA  + +PVE VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 236 INKLIRVTRQLVQELGREPTPEEIAAVMDIPVERVREIQKIAQEPVSLETPIGEEEDSHL 295

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A +P ++A    L+E    VL SLTPREE+VLR+RFG+      TLEEVG+ 
Sbjct: 296 GDFIEDQDAPAPAEAASFTLLKEQLEEVLESLTPREEKVLRLRFGLDDGRARTLEEVGQV 355

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 356 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 388



 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 75/181 (41%), Gaps = 15/181 (8%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
             +      + +  K++I   +++G ++ +E+   L   E+ +EQME     L+  GI +
Sbjct: 2   ESNEAKMQNARELVKQLIAKGKRKGSLSYDEVADSLQELELDAEQMEAIFDTLTEAGIKL 61

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD--------------SADRSTDDPVRM 123
              +  E EE  +   D+ +        +   +                   + DDPVRM
Sbjct: 62  QGDEPDEAEEPVDGDADVEALDVVEPPPVDDAEPDDDAAAGEDDDLSVPEGIAIDDPVRM 121

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G + LL+ E EI  A+RIE G       L E+ L     I  R  +  G   L  
Sbjct: 122 YLKEIGRVPLLTAEEEIMYAERIEKGDEEAKRKLAEANLRLVVSIAKRY-VGRGMQFLDL 180

Query: 184 I 184
           I
Sbjct: 181 I 181


>gi|225174152|ref|ZP_03728151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169937|gb|EEG78732.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 372

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 166/377 (44%), Positives = 244/377 (64%), Gaps = 8/377 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSL-NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           K  + + + K+++++LV+      L     I   ++++   ++ I      L RL    G
Sbjct: 3   KGLEKAEQLKLIQDELVQRGKKRGLLTYKEIIEPLQEMDLSAEEIDEFYDHLSRL----G 58

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           +     +   +  ++D   +   +D PE E    V   +     +R  +K I     +S 
Sbjct: 59  VDVVDDVAELETLDVDEETIKEEEDTPEEEIDLTVPEGIGVNDPVRMYLKEIGKIPLLSS 118

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +++ ++ E     AK+ + EANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA
Sbjct: 119 DEE---IALAKRMEAGDEEAKRRLAEANLRLVVSIAKKYVGRGMLFLDLIQEGNLGLIKA 175

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ 
Sbjct: 176 VEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLVQELG 235

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP P+EIA  + +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED++  +P ++A
Sbjct: 236 REPAPDEIAHVMNISEERVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDVQAPAEAA 295

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L+E    VL +LTPRE++VL +RFG+      TLEEVG+ F VTRERIRQIEAKA+
Sbjct: 296 AFELLKEQLDDVLETLTPREKKVLTLRFGLEDGRSRTLEEVGQVFGVTRERIRQIEAKAL 355

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKL+HP RSK+L+ +L+
Sbjct: 356 RKLRHPMRSKRLKDYLE 372



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 73/346 (21%), Positives = 141/346 (40%), Gaps = 27/346 (7%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++++  ++RG +T +E+   L   ++S+E++++    LS +G++VVD  D+ + E  +  
Sbjct: 17  ELVQRGKKRGLLTYKEIIEPLQEMDLSAEEIDEFYDHLSRLGVDVVD--DVAELETLDVD 74

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +      ++               +DPVRMYL+E+G I LLS + EIA+AKR+EAG   
Sbjct: 75  EETIKEEEDTPEEEIDLTVPEGIGVNDPVRMYLKEIGKIPLLSSDEEIALAKRMEAGDEE 134

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
               L E+ L     I  +  +  G   L  I         E   G     E   Y+K  
Sbjct: 135 AKRRLAEANLRLVVSIAKKY-VGRGMLFLDLI--------QEGNLGLIKAVEKFDYRKGY 185

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE-----NDERNLDEDEDDSAH 267
             S        Q     I   A+  +     V++  +          E   +   D+ AH
Sbjct: 186 KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLVQELGREPAPDEIAH 245

Query: 268 TLSAMEDQLRPKVMCALDEIAEVY-----RELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            ++  E+++R  +  A + ++         +            +    +   ++LKE+L 
Sbjct: 246 VMNISEERVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDVQAPAEAAAFELLKEQLD 305

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
            ++ +L+  + ++  L   L D           L  + Q +G+ R+
Sbjct: 306 DVLETLTPREKKVLTLRFGLED------GRSRTLEEVGQVFGVTRE 345


>gi|322411497|gb|EFY02405.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 369

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKVLAVAV---AEGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 91.4 bits (225), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 97/260 (37%), Gaps = 16/260 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +++   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRHHKKEGIAIDDDVTEKLVIPFALDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKVLAVAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAE 289
            A   ++ P  +  + +IA+
Sbjct: 239 IAERMEMTPDKVREILKIAQ 258


>gi|318066937|emb|CBY89083.1| RNA polymerase sigma70 factor [Halomonas desiderata]
          Length = 375

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 125/395 (31%), Positives = 177/395 (44%), Gaps = 40/395 (10%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAWLPGAVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+       G       +          D   +   D E  A
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEG---IPGVAEAEVPEELVGDDSDADDADADDADDDEDDA 135

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
             S+ + S     PE A      + E  +     L+                        
Sbjct: 136 DASEAEESTGGPDPEEARARFEQIREQNELVREALA------------------------ 171

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + +V  ++L +L   + L     + LV Q+    ++I   E 
Sbjct: 172 -----------KHGRGSEQARVEMDRLAELFSPIKLVPKHFERLVGQVRISVEQIRTQEK 220

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L      + R  F++   G E    W+         ++   +      I + +  I
Sbjct: 221 AVMQLFVKLAKVPRKSFIKAFPGNESRQEWLDEFIAE-NAKFAERLEPLRADIQRAQRRI 279

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + + E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 280 AFEEEMVQLPVPELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 339

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 340 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 374


>gi|255655465|ref|ZP_05400874.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-23m63]
 gi|296451458|ref|ZP_06893195.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296880193|ref|ZP_06904159.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
 gi|296259725|gb|EFH06583.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296428782|gb|EFH14663.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
          Length = 388

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 163/383 (42%), Positives = 235/383 (61%), Gaps = 5/383 (1%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                    EK   +  +   ++++      L++ +++ L E L ++   I   +     
Sbjct: 11  KKVTAKTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKAD 70

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +  S            +  E   H  S A +    +        +D    +R  +K I  
Sbjct: 71  IDFSVADDDLSIGHLDEDAEAISHEDSSAIEIETVDLSLPKGISIDD--PVRMYLKEIGK 128

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +   E       +        IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN
Sbjct: 129 IPLLKPHEEVEFARRM---HEGDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGN 185

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R+
Sbjct: 186 LGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQ 245

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  ++ R+P PEEIAK++ M  + VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A 
Sbjct: 246 LLQELGRDPKPEEIAKEMEMTEDKVREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAP 305

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+F VTRERIRQ
Sbjct: 306 APAEAAAYSLLKEQIEDVLGSLNDREQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQ 365

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSKKLR +LD
Sbjct: 366 IEAKALRKLRHPSRSKKLRDYLD 388



 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 63/273 (23%), Positives = 101/273 (36%), Gaps = 23/273 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----------- 80
           K +I+  +++G +T+ E+       E+  +Q+E+    L N+GI + +            
Sbjct: 16  KTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKADIDFSV 75

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKD---SADRSTDDPVRMYLREMGSIELLSRE 137
            D +   G  D    A S  +SS    +  D       S DDPVRMYL+E+G I LL   
Sbjct: 76  ADDDLSIGHLDEDAEAISHEDSSAIEIETVDLSLPKGISIDDPVRMYLKEIGKIPLLKPH 135

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  A+R+  G  +    L E+ L     I  R  +  G   L  I         E   
Sbjct: 136 EEVEFARRMHEGDEIAKQRLVEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNL 186

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           G     E   Y K    S        Q     I   A+  +     V++  +      + 
Sbjct: 187 GLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQL 246

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           L E   D      A E ++    +  + +IA+ 
Sbjct: 247 LQELGRDPKPEEIAKEMEMTEDKVREIMKIAQD 279


>gi|295399207|ref|ZP_06809189.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110191|ref|YP_003988507.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294978673|gb|EFG54269.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215292|gb|ADP73896.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 377

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSAEEEIELAKRIEQ---GDEEAKRRLTEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVQRQLLQDLGREPTPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 108/262 (41%), Gaps = 12/262 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + +++ +L ++RG +T EE+   L   ++ S+QM++    L++ GI V+   DLE + 
Sbjct: 18  EQAKEQLTELGKKRGILTYEEIAERLSAFDLDSDQMDEFYEYLTDQGIEVISESDLESDL 77

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +  +D     +     L           +DPVRMYL+E+G + LLS E EI +AKRIE
Sbjct: 78  EHDPDID---DLAKEEFDLNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRIE 134

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 135 QGDEEAKRRLTEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 185

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y+K    S        Q     I   A+  +     V++  +      + L +   +   
Sbjct: 186 YRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTP 245

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              A E  L P+ +  + +IA+
Sbjct: 246 EEIAEEMDLTPEKVREILKIAQ 267


>gi|289642669|ref|ZP_06474809.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507499|gb|EFD28458.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 392

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 146/286 (51%), Positives = 213/286 (74%), Gaps = 6/286 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++  T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 110 AEEEVDLAKRIEAGLFASEKLAAATRKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 166

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QA+TR+IADQ
Sbjct: 167 VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAVTRAIADQ 226

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 227 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 286

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 287 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 346

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TLEEVG++F VTRERIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 347 DGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHPSRSQKLRDYLE 392



 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 75/380 (19%), Positives = 135/380 (35%), Gaps = 59/380 (15%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   D  K +I   ++ G++T E++   L   E+  EQ +  + +L++ GI +++    +
Sbjct: 9   EAQVDEVKDLITRGKEIGFLTTEDVTVALQAAELPPEQTDAVLQVLNDEGIEILEAGGED 68

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE              +    ++ + +    T DPVRMYL+E+G + LL+ E E+ +AK
Sbjct: 69  AEEND----------LLARRRREEEELALKAPTSDPVRMYLKEIGKVPLLTAEEEVDLAK 118

Query: 145 RIEAGR----------------------------AMMMASLCESPLTFQALIIWRDELND 176
           RIEAG                              +    L E+ L     I  R  +  
Sbjct: 119 RIEAGLFASEKLAAATRKTSPQMRRDLEAIERDGQIAKRKLVEANLRLVVSIAKRY-VGR 177

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L  I         E   G     E   Y K    S        Q     I   A+ 
Sbjct: 178 GMLFLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAVTRAIADQART 229

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +     V++  +      + L +   + +    A E  L P     + EI +V +E  S
Sbjct: 230 IRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTP---DKVREILKVSQEPVS 286

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE--- 353
           L+      +         +     +     S  L Q ++D ++  L D  K+++      
Sbjct: 287 LETPIGEEEDSHLGDF-IEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGL 345

Query: 354 -----GELLRLAQSYGIKRD 368
                  L  + + +G+ R+
Sbjct: 346 TDGHPRTLEEVGREFGVTRE 365


>gi|153953576|ref|YP_001394341.1| hypothetical protein CKL_0942 [Clostridium kluyveri DSM 555]
 gi|219854198|ref|YP_002471320.1| hypothetical protein CKR_0855 [Clostridium kluyveri NBRC 12016]
 gi|146346457|gb|EDK32993.1| RpoD2 [Clostridium kluyveri DSM 555]
 gi|219567922|dbj|BAH05906.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 354

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 167/374 (44%), Positives = 237/374 (63%), Gaps = 35/374 (9%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK      +  ++++  +  + L+  +I+ + E L  +   +  +               
Sbjct: 16  EKGKKNGTLTYKEIMDELQEVDLSPQQIEKIYEVLESMGIEVNGDM-------------- 61

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                     EL+ +  +     PEG   +           +R  +K I     +   E 
Sbjct: 62  ---------NELELNEKNLDLSVPEGIAID---------DPVRMYLKEIGKVPLLLPEEE 103

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              +S+ +K E    IAKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 104 ---MSLAKKIEEGDQIAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 160

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP
Sbjct: 161 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP 220

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             EE+AK + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A   
Sbjct: 221 HAEEVAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFT 280

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 281 MLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKL 340

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 341 RHPSRSKKLKDYLD 354



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/154 (31%), Positives = 77/154 (50%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            KK+I+  ++ G +T +E+   L   ++S +Q+E    +L +MGI V    D+ + E +E
Sbjct: 11  VKKLIEKGKKNGTLTYKEIMDELQEVDLSPQQIEKIYEVLESMGIEV--NGDMNELELNE 68

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +LDL+                   + DDPVRMYL+E+G + LL  E E+++AK+IE G 
Sbjct: 69  KNLDLSVPE--------------GIAIDDPVRMYLKEIGKVPLLLPEEEMSLAKKIEEGD 114

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +    L E+ L     I  R  +  G   L  I
Sbjct: 115 QIAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 147


>gi|172056869|ref|YP_001813329.1| RpoD family RNA polymerase sigma factor [Exiguobacterium sibiricum
           255-15]
 gi|171989390|gb|ACB60312.1| RNA polymerase, sigma 70 subunit, RpoD family [Exiguobacterium
           sibiricum 255-15]
          Length = 361

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 164/321 (51%), Positives = 217/321 (67%), Gaps = 7/321 (2%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI----RNEIKSISVET 420
           +    F E  Q  E +   V+      + E  +     V   +KI    R  +K I    
Sbjct: 44  MDAQQFEEFLQLLETEGIKVNNDGTGDDKEEADLNDLSVPPGVKINDPVRMYLKEIGRVD 103

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ++  +   +   + +       AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+G
Sbjct: 104 LLNAEDEVELAKRIEQ---NDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMG 160

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++ 
Sbjct: 161 LIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLL 220

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
             + REPTPEEI+K++ +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A +P
Sbjct: 221 QDLGREPTPEEISKEMEITPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATAP 280

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIE
Sbjct: 281 QDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIE 340

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AKA+RKL+HPSRSK+L+ FLD
Sbjct: 341 AKALRKLRHPSRSKRLKDFLD 361



 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 40/153 (26%), Positives = 67/153 (43%), Gaps = 17/153 (11%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDE-VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++I L  + G ++ +++   L   E + ++Q E+ + +L   GI V +    +D+E    
Sbjct: 18  ELIALGHKNGELSHQKIEDKLSSFESMDAQQFEEFLQLLETEGIKVNNDGTGDDKE---- 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                         L           +DPVRMYL+E+G ++LL+ E E+ +AKRIE    
Sbjct: 74  -----------EADLNDLSVPPGVKINDPVRMYLKEIGRVDLLNAEDEVELAKRIEQNDE 122

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                L E+ L     I  R  +  G   L  I
Sbjct: 123 EAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 154


>gi|308069922|ref|YP_003871527.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|310643031|ref|YP_003947789.1| RNA polymerase sigma factor rpod [Paenibacillus polymyxa SC2]
 gi|305859201|gb|ADM70989.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|309247981|gb|ADO57548.1| RNA polymerase sigma factor rpoD [Paenibacillus polymyxa SC2]
          Length = 377

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSADDEVELAKRI---NNGDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEE+A ++ + VE VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVSRQLLQELGREPTPEEVAAEMELSVEKVREIMKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 77/349 (22%), Positives = 135/349 (38%), Gaps = 24/349 (6%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + +  L  D   D   ++I+L ++   +  +++   L P +   EQM++    L
Sbjct: 2   ANDQHTELETELTLDQVKD---QLIELGKKSSSLNYKDIMEKLSPFDQDPEQMDEFYEQL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            ++GI VV+ +D E+      + D  ++  +   F            +DPVRMYL+E+G 
Sbjct: 59  GDLGIEVVNDND-EEVTRLRQNDDPENNDGDDFNFDDDLSLPPGIKINDPVRMYLKEIGR 117

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS + E+ +AKRI  G       L E+ L     I  R  +  G   L  I      
Sbjct: 118 VPLLSADDEVELAKRINNGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI------ 170

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   Y+K    S        Q     I   A+  +     V++  + 
Sbjct: 171 --QEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 228

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                + L E   +      A E +L    +  + EI ++ +E  SL+            
Sbjct: 229 IRVSRQLLQELGREPTPEEVAAEMEL---SVEKVREIMKIAQEPVSLETPIGEEDDSH-- 283

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 L + +         + +  +LL EQL D+   +   E  +LRL
Sbjct: 284 ------LGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRL 326


>gi|21220928|ref|NP_626707.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289771799|ref|ZP_06531177.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
 gi|19856645|sp|P18182|HRDA_STRCO RecName: Full=RNA polymerase principal sigma factor hrdA
 gi|6759560|emb|CAB69753.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701998|gb|EFD69427.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
          Length = 396

 Score =  228 bits (580), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 128/296 (43%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     +S +E   +   V                         +      +AK
Sbjct: 101 RQYLREIGRIPLLSAAEEVDLARRVEAGLFAEEKLRCSPGLDDRLALDLDRLVVLGRLAK 160

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 161 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 220

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E V +
Sbjct: 221 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDLAPERVGE 280

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL++L  RE 
Sbjct: 281 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGERER 340

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 341 KVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLRDHAYADQLRGYLD 396



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +  +   + D  R YLRE+G I LLS   E+ +A+R+EAG 
Sbjct: 89  RTESGGPSSDLFRQYLREIGRIPLLSAAEEVDLARRVEAGL 129


>gi|251782161|ref|YP_002996463.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390790|dbj|BAH81249.1| RNA polymerase sigma factor [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 369

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E +     V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTSEEEKVFAVAV---AEGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    VL +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKLRHPSRSKQLRDFIE 368



 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 66/330 (20%), Positives = 117/330 (35%), Gaps = 27/330 (8%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             + I+  ++ G    +++   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VAEFIRHHKKEGTAIDDDVTEKLVIPFALDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             S  +        +  ++   S     +DPVRMYL+E+G + LL+ E E   A  +  G
Sbjct: 68  PSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKVFAVAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                  L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            A   ++ P     + EI ++ +E  SL+                  + E  V     + 
Sbjct: 239 IAERMEMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRV- 294

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                  +L EQL ++   +   E  +LRL
Sbjct: 295 -------VLREQLDEVLDTLTDREENVLRL 317


>gi|119717187|ref|YP_924152.1| RNA polymerase sigma factor [Nocardioides sp. JS614]
 gi|119537848|gb|ABL82465.1| RNA polymerase, sigma 70 subunit, RpoD [Nocardioides sp. JS614]
          Length = 495

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 134/253 (52%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 243 KVSEELEWIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 302

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 303 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 362

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     
Sbjct: 363 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTL 422

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 423 LQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 482

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 483 HPSRSQVLRDYLD 495



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLA-SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
            + D   D   +ED    +   ++       +++     +T DPV+ YL+++G + LL+ 
Sbjct: 155 FEKDVAADPSIAEDEKQASFVVSAADDTDEPEQQVMVAGATADPVKDYLKQIGKVPLLNA 214

Query: 137 EGEIAIAKRIEAGR 150
           E E+ +AKRIEAG 
Sbjct: 215 EMEVELAKRIEAGL 228


>gi|254975009|ref|ZP_05271481.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-66c26]
 gi|255092397|ref|ZP_05321875.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile CIP
           107932]
 gi|255100481|ref|ZP_05329458.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-63q42]
 gi|255306421|ref|ZP_05350592.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile ATCC
           43255]
 gi|255314137|ref|ZP_05355720.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-76w55]
 gi|255516815|ref|ZP_05384491.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-97b34]
 gi|255649917|ref|ZP_05396819.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-37x79]
 gi|260683071|ref|YP_003214356.1| RNA polymerase factor sigma-43 [Clostridium difficile CD196]
 gi|260686669|ref|YP_003217802.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
 gi|306520001|ref|ZP_07406348.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-32g58]
 gi|260209234|emb|CBA62522.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           CD196]
 gi|260212685|emb|CBE03759.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
          Length = 388

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 163/383 (42%), Positives = 235/383 (61%), Gaps = 5/383 (1%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                    EK   +  +   ++++      L++ +++ L E L ++   I   +     
Sbjct: 11  KKVTAKTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKAD 70

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +  S            +  E   H  S A +    +        +D    +R  +K I  
Sbjct: 71  IDFSVADDDLSIGHLDEDAEAISHDDSSAIEIETVDLSLPKGISIDD--PVRMYLKEIGK 128

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +   E       +        IAK+ +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN
Sbjct: 129 IPLLKPHEEVEFARRM---HEGDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGN 185

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R+
Sbjct: 186 LGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQ 245

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +  ++ R+P PEEIAK++ M  + VR+++KI ++P+SLETPIG+E+ SHLGDFI D +A 
Sbjct: 246 LLQELGRDPKPEEIAKEMEMTEDKVREIMKIAQDPVSLETPIGEEEDSHLGDFIPDDDAP 305

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+F VTRERIRQ
Sbjct: 306 APAEAAAYSLLKEQIEDVLGSLNDREQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQ 365

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEAKA+RKL+HPSRSKKLR +LD
Sbjct: 366 IEAKALRKLRHPSRSKKLRDYLD 388



 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 63/273 (23%), Positives = 101/273 (36%), Gaps = 23/273 (8%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG----------- 80
           K +I+  +++G +T+ E+       E+  +Q+E+    L N+GI + +            
Sbjct: 16  KTLIEKGKKQGSLTLAEIMEAFSETELDKDQVENLYETLGNLGIEITETKNYKADIDFSV 75

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKD---SADRSTDDPVRMYLREMGSIELLSRE 137
            D +   G  D    A S  +SS    +  D       S DDPVRMYL+E+G I LL   
Sbjct: 76  ADDDLSIGHLDEDAEAISHDDSSAIEIETVDLSLPKGISIDDPVRMYLKEIGKIPLLKPH 135

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  A+R+  G  +    L E+ L     I  R  +  G   L  I         E   
Sbjct: 136 EEVEFARRMHEGDEIAKQRLVEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNL 186

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           G     E   Y K    S        Q     I   A+  +     V++  +      + 
Sbjct: 187 GLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQL 246

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           L E   D      A E ++    +  + +IA+ 
Sbjct: 247 LQELGRDPKPEEIAKEMEMTEDKVREIMKIAQD 279


>gi|268610742|ref|ZP_06144469.1| RNA polymerase sigma factor RpoD [Ruminococcus flavefaciens FD-1]
          Length = 360

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 147/270 (54%), Positives = 201/270 (74%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++  E   +   + K       AKK + EANLRLV+S+AKKY  RG+QFL
Sbjct: 94  YLKEIGRVPLLTTEEEIELAQRMAK---GDRYAKKRLSEANLRLVVSIAKKYVGRGMQFL 150

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I K
Sbjct: 151 DLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETITK 210

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V + + ++ ++   +P+PEEIA KL MPV+ VR+++++ ++P+SLETPIG+E+ SHLGDF
Sbjct: 211 VKKVSSQLLHENGHDPSPEEIADKLNMPVDKVREIMRVAQDPVSLETPIGEEEDSHLGDF 270

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A +P ++A    L+E    VL++LT RE +VL++RFG+      TLEEVG++F V
Sbjct: 271 IPDDDAPAPAEAASHTLLKEQLNEVLSTLTDREAKVLKLRFGLEDGKSRTLEEVGQRFDV 330

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRSKK++ FLD
Sbjct: 331 TRERIRQIEAKALRKLRHPSRSKKVKDFLD 360



 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 40/192 (20%), Positives = 75/192 (39%), Gaps = 16/192 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +   ++ + +++  +  G +T +E+   L   +   +Q+        N+ I +V+  +L
Sbjct: 1   MENKKNTIEALMEQGKTNGKLTTKEITDALEELDFDVDQINTFYDNCENLNIEIVEDMNL 60

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           + +        L          L+    +   + DDPV++YL+E+G + LL+ E EI +A
Sbjct: 61  DADLKIGLDSALTDD-------LEMALSTEGIAIDDPVKIYLKEIGRVPLLTTEEEIELA 113

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           +R+  G       L E+ L     I  +  +  G   L  I         E   G     
Sbjct: 114 QRMAKGDRYAKKRLSEANLRLVVSIAKKY-VGRGMQFLDLI--------QEGNLGLIKAV 164

Query: 204 EGHSYQKREDSS 215
           E   Y K    S
Sbjct: 165 EKFDYTKGFKFS 176


>gi|194397936|ref|YP_002037704.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
 gi|194357603|gb|ACF56051.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
          Length = 369

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELALAVE---AGDIEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+   +P+D   +  LRE    +L +LT REE VLR+RFG+      TLE+VGK 
Sbjct: 276 GDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RK + PSRSK LR F++
Sbjct: 336 FNVTRERIRQIEAKALRKXRQPSRSKPLRDFIE 368



 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 120/333 (36%), Gaps = 28/333 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D    + I+  +Q+G  T +E+NA L  P  + ++ +ED +  + + GI++ D +     
Sbjct: 12  DVQVAEFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNE----- 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                S  + S+     +  +    S     +DPVRMYL+E+G + LL+ E E  +A  +
Sbjct: 67  --GNPSARVLSNEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV 124

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       L E+ L     I  R  +  G   L  I         E   G     +  
Sbjct: 125 EAGDIEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKF 175

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     I   A+  +     V++  +        L E   D  
Sbjct: 176 DYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPT 235

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               A    + P     + EI ++ +E  SL+                  + E  V    
Sbjct: 236 PEQIAERMDMTP---DKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTT 292

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +        +L EQL +I   +   E  +LRL
Sbjct: 293 RI--------VLREQLDEILDTLTDREENVLRL 317


>gi|332653408|ref|ZP_08419153.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
 gi|332518554|gb|EGJ48157.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
          Length = 446

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 152/253 (60%), Positives = 204/253 (80%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +++ + K       AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EKF
Sbjct: 194 EVLAELNKAIKRGERAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKF 253

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KV+R +R++  ++  +P+
Sbjct: 254 DYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVIRVSRQLLQELGHDPS 313

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA++++MPVE VR++LKI +EP+SLETPIG+E+ SHLGDFI D++A  P ++A    
Sbjct: 314 PEEIAEEMSMPVERVREILKIAQEPVSLETPIGEEEDSHLGDFIPDEDASEPAEAASFTL 373

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL++LTPREE+VL++RFGI      TLEEVGK+F VTRERIRQIEAKA+RKL+
Sbjct: 374 LKEQLVEVLSTLTPREEKVLKLRFGIEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLR 433

Query: 669 HPSRSKKLRSFLD 681
           HPSRSKKL+ FL+
Sbjct: 434 HPSRSKKLKDFLN 446



 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 38/131 (29%), Positives = 65/131 (49%), Gaps = 1/131 (0%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +   ++I+  +++G ++  EL   L   ++ SEQM+    +L N+GI+ V  D + +   
Sbjct: 54  EKLAELIERGKKKGNLSSTELMDVLEDMDLESEQMDKIYDVLENLGIDTVGEDYIPELPD 113

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +    A    +    +          TDDPVRMYL+E+G + LLS + EI +A+ + A
Sbjct: 114 DAEPPLEAMEEISEEEMVDPNSMVDSFGTDDPVRMYLKEIGKVNLLSSDEEIELAQAMGA 173

Query: 149 GRAMMMASLCE 159
           G A     L E
Sbjct: 174 G-AEAKEQLAE 183


>gi|228993035|ref|ZP_04152958.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
 gi|228999085|ref|ZP_04158667.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|229006633|ref|ZP_04164267.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228754494|gb|EEM03905.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228760702|gb|EEM09666.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|228766683|gb|EEM15323.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
          Length = 373

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/198 (26%), Positives = 82/198 (41%), Gaps = 17/198 (8%)

Query: 19  DDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
              +  D + +  K ++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++
Sbjct: 8   SKQIETDMTLEQVKEQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDL 67

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V        +  E   +   + +     L           +DPVRMYL+E+G ++LLS E
Sbjct: 68  V-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAE 120

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI +A RIE G       L E+ L     I  R  +  G   L  I         E   
Sbjct: 121 EEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNM 171

Query: 198 GFFHGTEGHSYQKREDSS 215
           G     E   Y+K    S
Sbjct: 172 GLIKAVEKFDYRKGFKFS 189


>gi|40353297|gb|AAR84412.1| essential primary sigma 70 factor [Frankia sp. EaI-12]
          Length = 409

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 144/267 (53%), Positives = 207/267 (77%), Gaps = 3/267 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++V T  +  + R  +  + +   +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLI
Sbjct: 146 KLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLI 202

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R
Sbjct: 203 QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 262

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R++   + REP+PEEIAK++ +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED
Sbjct: 263 IQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIED 322

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +AV P+D+A    L+E    VL +L+ RE++V+++RFG+      TLEEVG++F VTRE
Sbjct: 323 CDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRE 382

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE+K + KL+HPSRS+KLR +L+
Sbjct: 383 RIRQIESKTLSKLRHPSRSQKLRDYLE 409



 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 80/399 (20%), Positives = 139/399 (34%), Gaps = 59/399 (14%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           +    SD     S   L  +   D  K +I   ++ G++T E++   +   E+  EQ E 
Sbjct: 7   RSREGSDEIPPMSPTVLPREAQVDEVKDLITRGKEIGFLTTEDVTVAIQAAELPPEQAET 66

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
            + +L++ GI V++       E +++   LA           K        T +PVRMYL
Sbjct: 67  VLQVLNDEGIEVLEAG----GENADEPDLLARRRREKEELALKAP------TSEPVRMYL 116

Query: 126 REMGSIELLSREGEIAIAKRIEAGR----------------------------AMMMASL 157
           +E+G + LL+ E ++ +AKRIEAG                              +    L
Sbjct: 117 KEIGKVPLLTAEEQVDLAKRIEAGLFASDKLAVATKKTSPQMRRDLEAIERDGQIAKRKL 176

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E+ L     I  R  +  G   L  I         E   G     E   Y K    S  
Sbjct: 177 VEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTY 227

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
                 Q     I   A+  +     V++  +      + L +   + +    A E  L 
Sbjct: 228 ATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLT 287

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           P     + EI +V +E  SL+      +         +     +     S  L Q ++D 
Sbjct: 288 P---DKVREILKVSQEPVSLETPIGEEEDSHLGDF-IEDCDAVVPVDAASFILLQEQLDS 343

Query: 338 LVEQLYDISKRIMHNE--------GELLRLAQSYGIKRD 368
           ++  L D  K+++             L  + + +G+ R+
Sbjct: 344 VLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRE 382


>gi|282882556|ref|ZP_06291177.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
 gi|281297698|gb|EFA90173.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
          Length = 361

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   I   +       + AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 92  VRMYLKEIGKIPLLTGDEEVEIAKRME---NGDNSAKKELAEANLRLVVSIAKRYVGRGM 148

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 149 SFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 208

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++  ++ R+P PEEIAK++ + VE VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 209 INKLVRVQRQLVQELGRDPLPEEIAKEMNIEVEKVREIQKIAQEPVSLETPIGEEEDSHL 268

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D+  +SP D+A    LRE  + VL +LT RE++VL +RFG+      TLEEVGK+
Sbjct: 269 GDFIPDEEILSPQDAATFTLLREQLSTVLETLTDREKKVLTLRFGLDDGRARTLEEVGKE 328

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKAIRKL+HPSRSKKL+ FL+
Sbjct: 329 FAVTRERIRQIEAKAIRKLRHPSRSKKLKDFLE 361



 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 42/158 (26%), Positives = 72/158 (45%), Gaps = 13/158 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
            D +   + K  +++G++T +E++  L    + S++++       N GI +++ D  +D 
Sbjct: 10  KDTTINNLKKEGKEKGHLTYDEISFALEDIPMDSQEIDSIYKDFENDGIELLNDDRDKDY 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +                V  +        S DDPVRMYL+E+G I LL+ + E+ IAKR+
Sbjct: 70  K------------EEIDVEKEDLSVPKGISVDDPVRMYLKEIGKIPLLTGDEEVEIAKRM 117

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G + L  I
Sbjct: 118 ENGDNSAKKELAEANLRLVVSIAKRY-VGRGMSFLDLI 154


>gi|163815580|ref|ZP_02206953.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
 gi|158449217|gb|EDP26212.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
          Length = 399

 Score =  227 bits (579), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 144/272 (52%), Positives = 201/272 (73%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +S  E   +   +         AKK++ E+NLRLV+S+AK+Y  RG+
Sbjct: 129 VKMYLKDIGKVPLLSAEEEIELAKRME---AGDEAAKKKLAESNLRLVVSIAKRYVGRGM 185

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 186 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 245

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV R +R +  K+ REP PEE+ + + +P E V++++KI +EP+SLETPIG+E+ SHL
Sbjct: 246 INKVTRVSRDLLQKLGREPLPEEVGEVMGLPKERVQEIMKIAQEPVSLETPIGEEEDSHL 305

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D++  +P+++  Q  L E    V+++LT RE+RV+++RFG       TLEEVGK+
Sbjct: 306 GDFIQDESIPTPVEATNQTLLHEQLDDVVSTLTEREQRVIKLRFGWDDGRPRTLEEVGKE 365

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HP+RS+KL+ FL
Sbjct: 366 FNVTRERIRQIEAKALRKLRHPNRSRKLKDFL 397



 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 47/188 (25%), Positives = 81/188 (43%), Gaps = 6/188 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLA-RQRGYVTIEELNAF---LPPD 56
           M+     N + +   + SDD  +    +   + ++ +A  ++  +   EL      L   
Sbjct: 6   MSTMDTTNTNENEMIKVSDDEAINAKFNAKLQDLLSIAHSKKNVIEDTELIKHFNDLKEV 65

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
            +  + M+     L   G++++   D ++EE + D   +A       +      D    +
Sbjct: 66  ALDLDTMQKIFNFLEQNGVDILQITDTDEEEPALDEDVIAEGEEVEKIDFTDTGD-ISST 124

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPV+MYL+++G + LLS E EI +AKR+EAG       L ES L     I  R  +  
Sbjct: 125 TQDPVKMYLKDIGKVPLLSAEEEIELAKRMEAGDEAAKKKLAESNLRLVVSIAKRY-VGR 183

Query: 177 GTTLLREI 184
           G   L  I
Sbjct: 184 GMLFLDLI 191


>gi|256396128|ref|YP_003117692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256362354|gb|ACU75851.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 390

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 126/267 (47%), Positives = 189/267 (70%), Gaps = 4/267 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++ +T +     R +  +V     E   AK+ ++EANLRLV+S+AK+Y  RG+  LDL
Sbjct: 127 EKLTFQTHLKPQLRRELAILV----LEGQAAKRRLIEANLRLVVSIAKRYLGRGMSILDL 182

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEGN+GL++A EKFD+  GYKFSTYA WW++QA++R++ADQ+ TIR+PVH+ + +++VV
Sbjct: 183 VQEGNLGLIRAVEKFDYTRGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELMNRVV 242

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  RR+  +   EPTP++IA+ L + VE V +VL++ +EP+SL  P+G+ED   LGD IE
Sbjct: 243 RLQRRLLQENGVEPTPDDIAEVLGVAVERVVEVLRLAQEPVSLHAPVGEEDDVALGDLIE 302

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +AVSP DS     LRE    +L++L  RE+RV+++R+G+     HTLEE+G+ F VTR
Sbjct: 303 DADAVSPADSVAVVMLREHLDALLSTLGEREKRVVQLRYGLTDGQPHTLEEIGRTFGVTR 362

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAK + KL+  + + +L  +L
Sbjct: 363 ERIRQIEAKTLAKLRGHTYADQLLDYL 389



 Score = 42.5 bits (98), Expect = 0.24,   Method: Composition-based stats.
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  R YLRE+G + LL+   E+ +A+ +EAG 
Sbjct: 92  DLFRQYLREIGRVPLLNAVLEVELAQAVEAGL 123


>gi|260893571|ref|YP_003239668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
 gi|260865712|gb|ACX52818.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
          Length = 369

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +       AK+ ++EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRIPLLTPEEEIELAKRMEQ---GDEEAKRRLIEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 LFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ REPTPEEIA+K+ +  E VR+++K+ +EP+SLETPIG+E+ SHL
Sbjct: 217 INKLVRVSRQLVQELGREPTPEEIAEKMGISPEKVREIMKVAQEPVSLETPIGEEEDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A +P + A  A LRE    VL SLTPRE++VLR+RFG+      TLEEVG++
Sbjct: 277 GDFIEDQEAQAPAEEASYALLREQLNEVLQSLTPREQKVLRLRFGLDDGRARTLEEVGQK 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAK +RKL+HPSRSKKL+ +L+
Sbjct: 337 FGVTRERIRQIEAKTLRKLRHPSRSKKLKDYLE 369



 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 47/159 (29%), Positives = 74/159 (46%), Gaps = 10/159 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLED 85
             +  +++I+  R+ G +T  E+   L   +++ EQ+++    L+  GI+VV +  DL +
Sbjct: 13  YQNEIEQLIEKGRKTGVLTYAEIMDDLQGMDLTPEQIDEIYERLAAEGIDVVPEAQDLGE 72

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E  E+ L              +         DDPVRMYL+E+G I LL+ E EI +AKR
Sbjct: 73  GELKEERLGGEEE--------TELGIPEGVEIDDPVRMYLKEIGRIPLLTPEEEIELAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +E G       L E+ L     I  R  +  G   L  I
Sbjct: 125 MEQGDEEAKRRLIEANLRLVVSIAKRY-VGRGMLFLDLI 162


>gi|254445278|ref|ZP_05058754.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
 gi|198259586|gb|EDY83894.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
          Length = 576

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 182/500 (36%), Positives = 272/500 (54%), Gaps = 20/500 (4%)

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             + PE    F    E    ++ + +  +   D V+     +     ++++   ++    
Sbjct: 69  DILDPEEVDNFKAKQEEAEEEQTKANQHDILDDPVRMYLKQMGQVPLLTREQEVEISKRI 128

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI---AEVYRELRSLQDNAVNGQ 305
           ENAE   +         A     + ++L  +     D I    ++       Q+  V  +
Sbjct: 129 ENAEQKAQEELFSVGIMAEFTIDLAEKLLNR-EERFDRIVIDKKIENRETFFQELPVYVE 187

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
           K +K+  +     E+L +                E+   I  R    E  L      +  
Sbjct: 188 KSQKTYARMMNSWEELQEESDP------------EKKKKIRSRFRKQENTLRAYFPKFFF 235

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS---ILKIRNEIKSISVETGI 422
           K  VF E +    L          + + +         D+   +  +R E++ +     +
Sbjct: 236 KLKVF-EEYMDETLSKDLTRINAIYRKLDRAKRPKTAADTHIKVEPLREELEIMHNTYRL 294

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
              +   +++ VR+    A  AK EMVEANLRLVIS+AKKYTNRGL FLDLIQEGN+GLM
Sbjct: 295 EPEKLLSLIAEVRRHLKAAHKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLM 354

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + ++KV++  +++  +
Sbjct: 355 KAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQLLQE 414

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EPTPEE+A+++A+PVE V+ ++K+ ++PISL++P+GD D ++ GDFIEDK+A +P D
Sbjct: 415 YGHEPTPEEVAEEMALPVERVQTIMKMAQQPISLQSPVGDGDDTNFGDFIEDKSAENPYD 474

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
               + LRE    VL SLT RE RVL +RFG+      TLEEVGKQF VTRERIRQIEAK
Sbjct: 475 QTAFSLLREKIIDVLDSLTERERRVLSLRFGLVDGYSRTLEEVGKQFKVTRERIRQIEAK 534

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A+RK++HP+R ++L  F + 
Sbjct: 535 ALRKMRHPTRIRQLHGFFEN 554



 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/341 (18%), Positives = 142/341 (41%), Gaps = 29/341 (8%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++  + +I+ ++++GY+T  ++N  LP    S + +++ +++L N+ I+++D +++++
Sbjct: 19  QVNERIRYLIRQSKEQGYLTHGDINEALPEGIDSQDDIDNVISILQNLEIDILDPEEVDN 78

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +  ++  +   + +N    L           DDPVRMYL++MG + LL+RE E+ I+KR
Sbjct: 79  FKAKQEEAEEEQTKANQHDIL-----------DDPVRMYLKQMGQVPLLTREQEVEISKR 127

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE         L    +  +  I   ++L +       I+     I  + +       E 
Sbjct: 128 IENAEQKAQEELFSVGIMAEFTIDLAEKLLNREERFDRIV-----IDKKIENRETFFQEL 182

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
             Y ++   +  +  +  +E + + +   K     R             E  L       
Sbjct: 183 PVYVEKSQKTYARMMNSWEELQEESDPEKKKKIRSRF---------RKQENTLRAYFPKF 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L   E+ +   +   L  I  +YR+L    D A   +    + +K + L+E+L  + 
Sbjct: 234 FFKLKVFEEYMDETLSKDLTRINAIYRKL----DRAKRPKTAADTHIKVEPLREELEIMH 289

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
            +  L   ++  L+ ++    K     + E++       I 
Sbjct: 290 NTYRLEPEKLLSLIAEVRRHLKAAHKAKTEMVEANLRLVIS 330


>gi|313903914|ref|ZP_07837294.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
 gi|313471063|gb|EFR66385.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
          Length = 373

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 169/373 (45%), Positives = 233/373 (62%), Gaps = 18/373 (4%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
               K  +   ++      L+LN         QL  +   +  ++ ++LR+  + G   D
Sbjct: 19  AKKKKNALEISEIADYFKELNLNDK-------QLKSVVSYLEEHDIDVLRINDNDG-PDD 70

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
             L   +  E +        D    E  +           +R  +K I     +S  E  
Sbjct: 71  EMLLISESDEDNEDNDMENIDLSVPEGVSIEDP-------VRMYLKEIGKVPLLSADEEI 123

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +        +AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKF
Sbjct: 124 ELAKRME---EGDEVAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKF 180

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  REPT
Sbjct: 181 DYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQEYGREPT 240

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIAK + M VE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D+N   P D+A    
Sbjct: 241 PEEIAKNMNMSVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDENVPVPADAAAFTM 300

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L  RE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+
Sbjct: 301 LKEQLEEVLGTLAEREQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 360

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+KL+ +LD
Sbjct: 361 HPSRSRKLKDYLD 373



 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 43/159 (27%), Positives = 77/159 (48%), Gaps = 5/159 (3%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDDLED 85
           +  K++I++A+++   + I E+  +     ++ +Q++  V+ L    I+V  ++ +D  D
Sbjct: 10  EKTKELIEVAKKKKNALEISEIADYFKELNLNDKQLKSVVSYLEEHDIDVLRINDNDGPD 69

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +E    S     +  N    +         S +DPVRMYL+E+G + LLS + EI +AKR
Sbjct: 70  DEMLLISESDEDNEDNDMENID-LSVPEGVSIEDPVRMYLKEIGKVPLLSADEEIELAKR 128

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +E G  +    L E+ L     I  R  +  G   L  I
Sbjct: 129 MEEGDEVAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|302874342|ref|YP_003842975.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
 gi|307689391|ref|ZP_07631837.1| RNA polymerase sigma factor RpoD [Clostridium cellulovorans 743B]
 gi|302577199|gb|ADL51211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
          Length = 363

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 94  VRMYLKEIGKVPLLSPETEIELAERIE---AGDPAAKKKLAEANLRLVVSIAKRYVGRGM 150

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 151 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 210

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEE+A+K+ MPV+ V ++ KI +EP+SLETPIG+E+ SHL
Sbjct: 211 INKLLRITRQLVQELGRDPLPEELAEKMEMPVDKVIEIRKIAQEPVSLETPIGEEEDSHL 270

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVG++
Sbjct: 271 GDFIPDDDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGRE 330

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 331 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 363



 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 58/185 (31%), Positives = 83/185 (44%), Gaps = 25/185 (13%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K +I+  ++ G +T  E+   L   E+S EQ+E    +L ++GI V+   D++D E +E
Sbjct: 20  VKSLIETGKKTGSLTYTEIIDELENIELSPEQIEKIYEVLESVGIEVI--GDMKDIEVTE 77

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  DL+                   + DDPVRMYL+E+G + LLS E EI +A+RIEAG 
Sbjct: 78  DEFDLSVPE--------------GIAIDDPVRMYLKEIGKVPLLSPETEIELAERIEAGD 123

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                 L E+ L     I  R  +  G   L  I         E   G     E   Y+K
Sbjct: 124 PAAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEKFDYRK 174

Query: 211 REDSS 215
               S
Sbjct: 175 GFKFS 179


>gi|300813859|ref|ZP_07094164.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300512046|gb|EFK39241.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 361

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   I   +       + AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 92  VRMYLKEIGKIPLLTGDEEVEIAKRME---NGDNSAKKELAEANLRLVVSIAKRYVGRGM 148

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 149 SFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 208

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++  ++ R+P PEEIAK++++ VE VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 209 INKLVRVQRQLVQELGRDPLPEEIAKEMSIDVEKVREIQKIAQEPVSLETPIGEEEDSHL 268

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D+  +SP D+A    LRE  + VL +LT RE++VL +RFG+      TLEEVGK+
Sbjct: 269 GDFIPDEEILSPQDAATFTLLREQLSTVLETLTDREKKVLTLRFGLDDGRARTLEEVGKE 328

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKAIRKL+HPSRSKKL+ FL+
Sbjct: 329 FAVTRERIRQIEAKAIRKLRHPSRSKKLKDFLE 361



 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 41/158 (25%), Positives = 72/158 (45%), Gaps = 13/158 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
            D +   + K  +++G++T +E++  L    + S++++       N GI +++ +  +D 
Sbjct: 10  KDTTINNLKKEGKEKGHLTYDEISFALEDIPMDSQEIDSIYKDFENDGIELLNDERDKDF 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +                V  +        S DDPVRMYL+E+G I LL+ + E+ IAKR+
Sbjct: 70  K------------EEIDVEKEDLSVPKGISVDDPVRMYLKEIGKIPLLTGDEEVEIAKRM 117

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G + L  I
Sbjct: 118 ENGDNSAKKELAEANLRLVVSIAKRY-VGRGMSFLDLI 154


>gi|302391478|ref|YP_003827298.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302203555|gb|ADL12233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 358

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         AK+ +VEANLRLV+S+AKKY  RG+
Sbjct: 89  VRMYLKEIGKVDLLTAEEEVELAKRME---EGDMEAKRMLVEANLRLVVSIAKKYVGRGM 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 146 LFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVET 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV+R +R +  ++ REPTPEEIA+++ +  E VR+VLKI++EP+SLETPIG+E+ SHL
Sbjct: 206 INKVIRVSRHLLQELGREPTPEEIAEEMDLSEEKVREVLKISQEPVSLETPIGEEEDSHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A +P  +A    L+E    VL +L+ RE+RVL +RFG+      TLEEVGK+
Sbjct: 266 GDFIEDDDAPAPSVAASHMMLQEQLDEVLDTLSDREKRVLELRFGVEDGRSRTLEEVGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 326 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 358



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/162 (29%), Positives = 79/162 (48%), Gaps = 15/162 (9%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           V +  ++  +K+I+   Q G +T +E+   L   E++ EQ++D     + + I VVD D+
Sbjct: 5   VRNIVEEKVEKLIEKGNQEGQITYKEVMDTLAKVELTPEQIDDIYQRFAELDIEVVDEDE 64

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E  + +E+ LDL+                     DDPVRMYL+E+G ++LL+ E E+ +
Sbjct: 65  DEVSKDTEEDLDLSVPD--------------GVGIDDPVRMYLKEIGKVDLLTAEEEVEL 110

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AKR+E G       L E+ L     I  +  +  G   L  I
Sbjct: 111 AKRMEEGDMEAKRMLVEANLRLVVSIAKKY-VGRGMLFLDLI 151


>gi|282891123|ref|ZP_06299627.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498940|gb|EFB41255.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 546

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 148/277 (53%), Positives = 205/277 (74%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +   + ++K   +  G S+ +F+  V M+++   ++  AK+EMVE+NLRLVIS+AKKYT
Sbjct: 265 KLNAAKRKLKKRELAAGRSLEDFKKDVRMLQRWMDKSQEAKREMVESNLRLVISIAKKYT 324

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVH
Sbjct: 325 NRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH 384

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+KV+R A+++  +  REP+PEE+A +L +  E VR++ KI + PISL+  +GD  
Sbjct: 385 MIETINKVLRGAKKLMMETGREPSPEELANELGITAERVREIYKIAQHPISLQAEVGDGG 444

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S  GDF+ED  A SP ++   + L++    VLA+LT RE +VL  RFG+      TLEE
Sbjct: 445 ESQFGDFLEDTGADSPAEATGYSILKDKMNEVLATLTDRERKVLIQRFGLLDGKPKTLEE 504

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG +F VTRERIRQIEAKA+RK++HP+RSK+L++FLD
Sbjct: 505 VGVEFNVTRERIRQIEAKALRKMRHPTRSKQLKAFLD 541



 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 55/302 (18%), Positives = 115/302 (38%), Gaps = 11/302 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
                +++ LA+++GY+T EE+N  LP    +++Q++  +  LS M + V++        
Sbjct: 15  QQKVDELVSLAKEQGYITYEEINEILPMTFDNADQIDQVLIFLSGMDVQVLNQA------ 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                ++        +  ++     ++ S DDPVRMYL+EMGS+ LLSRE E+ I+KRIE
Sbjct: 69  ----EVERQKEKKKEAKEMEGLPKRSEGSPDDPVRMYLKEMGSVPLLSREEEVEISKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             +  +   +     +    I     L  G     + I  +  +  +             
Sbjct: 125 KAQIQIERIIMRFRYSTAEAISIASYLIQGKERFDKCITEKEVVNKQEFLHLL-PKLCDL 183

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            +  +   ++     + ET  +     ++      +      N   D   +     D   
Sbjct: 184 LKDEDAILEQLLLKPLSETLEEDIEKCRIRTQAYLRRLHCRHNVIEDFGEVILRAYDRFL 243

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            L    ++L+P+        A++    R L+   +   +  +   K   + ++ +     
Sbjct: 244 ALEKDINELKPRAERNKYAAAKLNAAKRKLKKRELAAGRSLEDFKKDVRMLQRWMDKSQE 303

Query: 328 LS 329
             
Sbjct: 304 AK 305


>gi|319441597|ref|ZP_07990753.1| RNA polymerase sigma factor [Corynebacterium variabile DSM 44702]
          Length = 536

 Score =  227 bits (578), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 135/290 (46%), Positives = 198/290 (68%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L    +++ I      +S  + R +    R+ + +   AK  ++EA
Sbjct: 251 AEQEVSLAKRIEAGLYATYKMEQIKESGEKVSPMQKRDL----REIDRDGRKAKNHLLEA 306

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 307 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRA 366

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  + V ++ +  +
Sbjct: 367 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEDKVLEIQQYAR 426

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+++R
Sbjct: 427 EPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLR 486

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 487 FGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 536



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 213 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 265


>gi|153813734|ref|ZP_01966402.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
 gi|149830174|gb|EDM85267.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
          Length = 330

 Score =  227 bits (578), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 61  VRMYLKEIGKVSLLTADEEIELAKRMEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 117

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 118 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 177

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA+++ MPV+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 178 INKLIRVSRQLLQELGREPTPEEIAEEMKMPVDRVREILKISQEPVSLETPIGEEEDSHL 237

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 238 GDFIQDDNVPVPADAAAFTLLKEQLIEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKE 297

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 298 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 330



 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/124 (30%), Positives = 57/124 (45%), Gaps = 3/124 (2%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS--ADRSTDDP 120
           ME  +  L   G++V+     ++E   +D  D+        + L K   S     S +DP
Sbjct: 1   MEKVLDFLEASGVDVLRISGNDEELILDDDADIEKMDDEEEIELDKIDLSVPEGVSIEDP 60

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G + LL+ + EI +AKR+E G       L E+ L     I  R  +  G   
Sbjct: 61  VRMYLKEIGKVSLLTADEEIELAKRMEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLF 119

Query: 181 LREI 184
           L  I
Sbjct: 120 LDLI 123


>gi|284990384|ref|YP_003408938.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284063629|gb|ADB74567.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 429

 Score =  227 bits (578), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 133/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 129 VRAYLKQIGKVALLNAEEEVDLAKRIEAGLYGAERLRQAEEEGQKLSPQMRRDLNWIVRD 188

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 189 GERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 248

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 249 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 308

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     +++  T VL +L
Sbjct: 309 DKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLMQDQLTSVLQTL 368

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 369 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 428

Query: 681 D 681
           D
Sbjct: 429 D 429



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/54 (40%), Positives = 32/54 (59%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 105 DDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVDLAKRIEAGL 158


>gi|167037157|ref|YP_001664735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167039957|ref|YP_001662942.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter sp. X514]
 gi|256751255|ref|ZP_05492135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300915505|ref|ZP_07132817.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|307266219|ref|ZP_07547761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724719|ref|YP_003904470.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           sp. X513]
 gi|320115576|ref|YP_004185735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326390577|ref|ZP_08212133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
 gi|166854197|gb|ABY92606.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           sp. X514]
 gi|166855991|gb|ABY94399.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256749810|gb|EEU62834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300888457|gb|EFK83607.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|306918749|gb|EFN48981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581780|gb|ADN55179.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928667|gb|ADV79352.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325993402|gb|EGD51838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
          Length = 357

 Score =  227 bits (578), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +       AKK ++EANLRLV+S+AK+Y  RG+
Sbjct: 88  VRMYLKEIGKIPLLTPEEEIELAKRIEQ---GDEEAKKRLIEANLRLVVSIAKRYVGRGM 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 145 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 204

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ REPTPEE+AK++ MP E VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 205 INKLIRVQRQLLQELGREPTPEELAKEMGMPEEKVREIMKIAQEPVSLETPIGEEEDSHL 264

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 265 GDFIPDEDAPAPAEAAAFTMLKEQLMDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 324

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 325 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 71/160 (44%), Gaps = 14/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S ++  ++I   ++ G +T  E+   L   +++ +Q+E       +MGI +V  +  +
Sbjct: 5   ELSKEAITELINKGKKTGMLTYNEIMDSLEDIDLNPDQIEKVYDAFEDMGIEIVGEEPRQ 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E   ED                        S DDPVRMYL+E+G I LL+ E EI +AK
Sbjct: 65  EEITEED-------------LDLDLSLPEGISIDDPVRMYLKEIGKIPLLTPEEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 RIEQGDEEAKKRLIEANLRLVVSIAKRY-VGRGMLFLDLI 150


>gi|72161271|ref|YP_288928.1| sigma-70 factor [Thermobifida fusca YX]
 gi|71915003|gb|AAZ54905.1| sigma-70 factor [Thermobifida fusca YX]
          Length = 388

 Score =  227 bits (578), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 145/325 (44%), Positives = 207/325 (63%), Gaps = 14/325 (4%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR----NEIKSISVET 420
           + RD F E  + R      V                 EV+    I      E K  +  T
Sbjct: 68  VDRDDFAEHPETRTSSGDIVHAYLREIGRVPLLTAEEEVELAKAIEIGLYAEQKLRAART 127

Query: 421 GI-----SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           G      S   F  +  +VR    E  +AK+ ++E+NLRLV+SVAK+Y  RGL  LDLIQ
Sbjct: 128 GPVPAQYSPEWFEDLNELVR----EGKLAKRRLIESNLRLVVSVAKRYLGRGLALLDLIQ 183

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + I+++ RT
Sbjct: 184 EGNLGLIRAVEKFDYTRGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVESINRLART 243

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            RR+  ++ REPT  E++++L +  + V ++ ++++EPISL TPI  E+ S  GDFIED 
Sbjct: 244 RRRLHQELGREPTLHELSRELNVDHDRVVEIHRVSQEPISLHTPI-GEEDSAFGDFIEDT 302

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +AV P+++A    L++   +VL  L+ RE+RV+ +RFG+     HTLEEVG++F VTRER
Sbjct: 303 DAVPPVEAAAFVMLQDQLAQVLGGLSEREQRVITLRFGLEDGKPHTLEEVGRKFGVTRER 362

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIE+K + KL+ PSR++ LR +L
Sbjct: 363 IRQIESKTLAKLRQPSRARILRDYL 387



 Score = 53.7 bits (127), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/101 (25%), Positives = 39/101 (38%), Gaps = 4/101 (3%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIELLSRE 137
                  E S      A       V      +  +  T   D V  YLRE+G + LL+ E
Sbjct: 44  AGPAAAVERSGGPPVEAVGGEPEYVDRDDFAEHPETRTSSGDIVHAYLREIGRVPLLTAE 103

Query: 138 GEIAIAKRIEAGR--AMMMASLCESPLTFQALIIWRDELND 176
            E+ +AK IE G      + +    P+  Q    W ++LN+
Sbjct: 104 EEVELAKAIEIGLYAEQKLRAARTGPVPAQYSPEWFEDLNE 144


>gi|30264362|ref|NP_846739.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Ames]
 gi|47529811|ref|YP_021160.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187190|ref|YP_030442.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Sterne]
 gi|49481307|ref|YP_038350.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141207|ref|YP_085621.1| RNA polymerase sigma factor RpoD [Bacillus cereus E33L]
 gi|65321666|ref|ZP_00394625.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bacillus anthracis str. A2012]
 gi|118479464|ref|YP_896615.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872043|ref|ZP_02216683.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167634513|ref|ZP_02392833.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|167638663|ref|ZP_02396939.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|170687516|ref|ZP_02878733.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|170707362|ref|ZP_02897816.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|196046412|ref|ZP_03113638.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218905429|ref|YP_002453263.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225866273|ref|YP_002751651.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228929335|ref|ZP_04092360.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935612|ref|ZP_04098427.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948006|ref|ZP_04110292.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229093361|ref|ZP_04224468.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|229123831|ref|ZP_04253025.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|229186532|ref|ZP_04313694.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|229601154|ref|YP_002868581.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
 gi|254684050|ref|ZP_05147910.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str.
           CNEVA-9066]
 gi|254736399|ref|ZP_05194105.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741437|ref|ZP_05199124.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Kruger B]
 gi|254757799|ref|ZP_05209826.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Australia
           94]
 gi|30259020|gb|AAP28225.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Ames]
 gi|47504959|gb|AAT33635.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181117|gb|AAT56493.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Sterne]
 gi|49332863|gb|AAT63509.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974676|gb|AAU16226.1| RNA polymerase sigma-43 factor [Bacillus cereus E33L]
 gi|118418689|gb|ABK87108.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis str. Al
           Hakam]
 gi|164712174|gb|EDR17711.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167513511|gb|EDR88881.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|167529965|gb|EDR92700.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|170127606|gb|EDS96479.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|170668711|gb|EDT19457.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|196022882|gb|EDX61563.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218536133|gb|ACK88531.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225787167|gb|ACO27384.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228596963|gb|EEK54621.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|228659652|gb|EEL15298.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|228690017|gb|EEL43818.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|228811696|gb|EEM58031.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824052|gb|EEM69869.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830349|gb|EEM75961.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229265562|gb|ACQ47199.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
          Length = 373

 Score =  227 bits (578), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 77/176 (43%), Gaps = 11/176 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V        +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 111

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|166030947|ref|ZP_02233776.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
 gi|166029214|gb|EDR47971.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
          Length = 382

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 157/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 113 VRMYLKEIGKVPLLSADEEVELAKRM---AEGDEDAKKRLAEANLRLVVSIAKRYVGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 170 LFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA +L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 230 INKLIRVSRQLLQELGREPTPEEIAAELDMPVERVREILKISQEPVSLETPIGEEEDSHL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 290 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMDDGRARTLEEVGKE 349

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 350 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 382



 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 44/161 (27%), Positives = 77/161 (47%), Gaps = 6/161 (3%)

Query: 29  DSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDL 83
           +  K+++   ++ +  + ++E+N F    E+ +EQME     L    I+V+    DGD +
Sbjct: 16  EKLKQLVAHGKKNKSILELQEINDFFSDMELDAEQMEKVYEYLEANHIDVLRVSGDGDGI 75

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E+ +  +DS  + +   +  +           S +DPVRMYL+E+G + LLS + E+ +A
Sbjct: 76  EELDDVDDSDIVLTDEDDVDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSADEEVELA 135

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           KR+  G       L E+ L     I  R  +  G   L  I
Sbjct: 136 KRMAEGDEDAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 175


>gi|229086862|ref|ZP_04219022.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
 gi|228696437|gb|EEL49262.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
          Length = 373

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 46/167 (27%), Positives = 74/167 (44%), Gaps = 9/167 (5%)

Query: 19  DDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
              +  D + +  K ++ +L ++RG +T EE+   +   E+ S+QM++    L   GI++
Sbjct: 8   SKQIETDMTLEQVKEQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYLGEQGIDL 67

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V        +  E       + +     L           +DPVRMYL+E+G ++LLS E
Sbjct: 68  V-------GDNDEGPNRHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAE 120

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 121 EEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|184201082|ref|YP_001855289.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
 gi|183581312|dbj|BAG29783.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
          Length = 572

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 134/250 (53%), Positives = 177/250 (70%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 323 RAYRWVIHDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 382

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE
Sbjct: 383 KGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 442

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E
Sbjct: 443 LANELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQE 502

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPS
Sbjct: 503 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 562

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 563 RSQVLRDYLD 572



 Score = 53.7 bits (127), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/104 (23%), Positives = 45/104 (43%), Gaps = 2/104 (1%)

Query: 49  LNAFLPPDEVSSEQM--EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           ++  L  DE++ E +  +             V+      +   + S       +N     
Sbjct: 201 VDEALAEDELAPEDVQEDTEDEDAQESAQASVEESAQLMKGRQDRSARGFVLTNNDDDDA 260

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             ++     +T DPV+ YL+++G + LL+ E E+ +A RIEAG 
Sbjct: 261 PAQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLALRIEAGL 304


>gi|318066901|emb|CBY89065.1| RNA polymerase sigma70 factor [Carnimonas nigrificans]
          Length = 371

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 130/414 (31%), Positives = 197/414 (47%), Gaps = 46/414 (11%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
            SA+  +V      ++    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++
Sbjct: 1   ESAAEEAVAALAAVETEVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSA 60

Query: 157 LCESPLTFQALIIWRDELNDGTT-LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           L   P     ++   D         L ++      I P+       G  G +  + E   
Sbjct: 61  LAFLPGAVDTILTVFDGTQGEEGGRLSDL--FSGFIDPD------EGVPGVAEVEEEIDL 112

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
             +E D+  + + D E       ++ ++    PE A+     + E  +D    L A   +
Sbjct: 113 SAEESDEESDVDEDDEDDEDDDSNNTNEGGPDPELAKVRFEQIREQ-NDLVKALIAKNGR 171

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
             P V+ A                                  +E+L +L   + L     
Sbjct: 172 DAPDVIVA----------------------------------QERLAELFSPIKLVPKHF 197

Query: 336 DLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           + L+ Q+    +++  NE  ++++  +   + R  F+      E +  W+         +
Sbjct: 198 ERLILQVRITIEQVRANEKRIMQIFVKRARVPRKTFISSFPANESNQQWLDEFIAKH-PK 256

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           +   +      IL+ +  I     E  +S++E + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 YAEGLEIYRPDILRAQRRIAEEQEEVSLSVAELKEINRRLSIGEAKARRAKKEMVEANLR 316

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 317 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 370


>gi|313123889|ref|YP_004034148.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280452|gb|ADQ61171.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 372

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 166/359 (46%), Positives = 230/359 (64%), Gaps = 25/359 (6%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+  +G+  +LA +         +  +  EL+  
Sbjct: 39  RLIKPYKLEGKAVDQLVQEFEDNGISIVDEDGKPSKLALTKQ-------KNVEKAELNNM 91

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
                    +                +R  +K I     ++  E    V++ ++ E    
Sbjct: 92  DAPTGMKMNDP---------------VRMYLKEIGRVNLLTSEEE---VALAKRIEAGDE 133

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LGYKFSTYA W
Sbjct: 134 EAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFSTYATW 193

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEI  ++ +PV  
Sbjct: 194 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIGAEMDLPVNK 253

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++LK+ +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+E    VL +L+ 
Sbjct: 254 VREILKLCQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVLDTLSD 313

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR FLD
Sbjct: 314 REEEVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRSSQLRDFLD 372



 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 110/313 (35%), Gaps = 49/313 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +++  +    +T       L  P ++  + ++  V    + GI++VD      E
Sbjct: 15  EKAVKLVVEGVKASHQITEAAFEDRLIKPYKLEGKAVDQLVQEFEDNGISIVD------E 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G    L L    +     L           +DPVRMYL+E+G + LL+ E E+A+AKRI
Sbjct: 69  DGKPSKLALTKQKNVEKAELNNMDAPTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA-------- 189
           EAG       L E+ L     I  R         D + +G   L + +D           
Sbjct: 129 EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFS 188

Query: 190 -------------------------CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
                                        E+                 D   E+   ++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIGAEMD 248

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                +    K+ ++  S      E  +++  +  ED+D  +    A  + L+ ++   L
Sbjct: 249 LPVNKVREILKLCQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVL 308

Query: 285 DEIAEVYRELRSL 297
           D +++   E+  L
Sbjct: 309 DTLSDREEEVLRL 321


>gi|300854008|ref|YP_003778992.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434123|gb|ADK13890.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 354

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 167/374 (44%), Positives = 238/374 (63%), Gaps = 35/374 (9%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK      +  ++++  +  + L+  +I+ + E L  +   +  +E              
Sbjct: 16  EKGKKNGTLTYKEIMDELEEVDLSPEQIEKIYEALESMGIEVTGDE-------------- 61

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                     E + +  +     P+G   +           +R  +K I     +   E 
Sbjct: 62  ---------HETESNEKNLDLSVPDGIAID---------DPVRMYLKEIGKVPLLLPEEE 103

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              +S+ ++ E    IAKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 104 ---ISLAKRIEEGDQIAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 160

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ REP
Sbjct: 161 FDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQELGREP 220

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEE+A+ + MPV+ VR+++KI +EP+SLETPIG+E+ SHLGDFI D  A +P ++A   
Sbjct: 221 HPEEVAQIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFT 280

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 281 MLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKL 340

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 341 RHPSRSKKLKDYLD 354



 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/154 (33%), Positives = 75/154 (48%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            KK+I+  ++ G +T +E+   L   ++S EQ+E     L +MGI V    D  + E +E
Sbjct: 11  VKKIIEKGKKNGTLTYKEIMDELEEVDLSPEQIEKIYEALESMGIEV--TGDEHETESNE 68

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +LDL+                   + DDPVRMYL+E+G + LL  E EI++AKRIE G 
Sbjct: 69  KNLDLSVPD--------------GIAIDDPVRMYLKEIGKVPLLLPEEEISLAKRIEEGD 114

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +    L E+ L     I  R  +  G   L  I
Sbjct: 115 QIAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 147


>gi|227817068|ref|YP_002817077.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
 gi|227007300|gb|ACP17043.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
          Length = 373

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 77/176 (43%), Gaps = 11/176 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVRE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V        +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 111

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|325686026|gb|EGD28084.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 372

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 166/359 (46%), Positives = 231/359 (64%), Gaps = 25/359 (6%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L+    L    +D LV++  D    I+  +G+  +LA +         +  +  EL+  
Sbjct: 39  RLIKPYKLEGKAVDQLVQEFEDNGISIVDEDGKPSKLALTKQ-------KNVEKAELNNM 91

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
                    +                +R  +K I     ++  E    V++ ++ E    
Sbjct: 92  DAPTGMKMNDP---------------VRMYLKEIGRVNLLTSEEE---VALAKRIEAGDE 133

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK+E+ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA +KFD+ LGYKFSTYA W
Sbjct: 134 EAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFSTYATW 193

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + R+P PEEI  ++ +PV+ 
Sbjct: 194 WIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIGAEMDLPVKK 253

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++LK+ +EP+SLETPIG+ED S+LGDFIEDK+A+SP   A    L+E    VL +L+ 
Sbjct: 254 VREILKLCQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVLDTLSD 313

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           REE VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR FLD
Sbjct: 314 REEEVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRSSQLRDFLD 372



 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 110/313 (35%), Gaps = 49/313 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +++  +    +T       L  P ++  + ++  V    + GI++VD      E
Sbjct: 15  EKAVKLVVEGVKASHQITEAAFEDRLIKPYKLEGKAVDQLVQEFEDNGISIVD------E 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G    L L    +     L           +DPVRMYL+E+G + LL+ E E+A+AKRI
Sbjct: 69  DGKPSKLALTKQKNVEKAELNNMDAPTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRI 128

Query: 147 EAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEA-------- 189
           EAG       L E+ L     I  R         D + +G   L + +D           
Sbjct: 129 EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFS 188

Query: 190 -------------------------CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
                                        E+                 D   E+   ++ 
Sbjct: 189 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIGAEMD 248

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                +    K+ ++  S      E  +++  +  ED+D  +    A  + L+ ++   L
Sbjct: 249 LPVKKVREILKLCQEPVSLETPIGEEDDSNLGDFIEDKDAMSPEQHAANEMLKEQLAEVL 308

Query: 285 DEIAEVYRELRSL 297
           D +++   E+  L
Sbjct: 309 DTLSDREEEVLRL 321


>gi|255525304|ref|ZP_05392244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296188172|ref|ZP_06856564.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
 gi|255510976|gb|EET87276.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296047298|gb|EFG86740.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
          Length = 361

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 157/273 (57%), Positives = 210/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +S+ ++ E    IAKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 92  VRMYLKEIGKVPLLAPEEE---ISLAQRIENGDQIAKKKLAEANLRLVVSIAKRYVGRGM 148

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 149 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 208

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEE+AK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 209 INKLIRVSRQLLQELGREPQPEEVAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 268

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 269 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 328

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 329 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 361



 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 49/154 (31%), Positives = 77/154 (50%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K++I+  ++ G +T +E+   L   ++S EQ+E    +L +MGI V    D+++ E  E
Sbjct: 18  VKRLIEKGKKTGTLTYKEIMDELDEVDLSPEQIEKIYEVLESMGIEV--AGDIQEVEVDE 75

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             LDL+                   + DDPVRMYL+E+G + LL+ E EI++A+RIE G 
Sbjct: 76  KDLDLSVPE--------------GIAIDDPVRMYLKEIGKVPLLAPEEEISLAQRIENGD 121

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +    L E+ L     I  R  +  G   L  I
Sbjct: 122 QIAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 154


>gi|160935059|ref|ZP_02082445.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
 gi|156866512|gb|EDO59884.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
          Length = 365

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 153/270 (56%), Positives = 200/270 (74%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+QFL
Sbjct: 99  YLKEIGRVPLLSPEEEIDLAIRI---SEGDESAKKRLSEANLRLVVSIAKRYLGRGMQFL 155

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 156 DLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 215

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V + + ++ +    EPT +EIA +L MPV+ VR+++++ +EP+SLETPIG+E+ SHLGDF
Sbjct: 216 VKKVSSQLLHTNGHEPTADEIALELDMPVDKVREIMRVAQEPVSLETPIGEEEDSHLGDF 275

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A +P D+A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+F V
Sbjct: 276 IPDDDAPAPADAASHILLKEQLAEVLDTLTPREEKVLRLRFGLEDGRSRTLEEVGKEFNV 335

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 336 TRERIRQIEAKALRKLRHPSRSKKLKDFLD 365



 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/154 (26%), Positives = 70/154 (45%), Gaps = 7/154 (4%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + + + A+ +G ++ +E+   +   +   EQ+E     L  MG+ +V+  D E+    +
Sbjct: 12  IRDLTEQAKAKGQLSNKEILDAIGELDFEPEQLEKFYDTLEAMGVEIVE--DFEEIPLDD 69

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            + DL     + +    +       + DDPV++YL+E+G + LLS E EI +A RI  G 
Sbjct: 70  INFDLVPDDEDDA----EVPAVESVAIDDPVKVYLKEIGRVPLLSPEEEIDLAIRISEGD 125

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  L  G   L  I
Sbjct: 126 ESAKKRLSEANLRLVVSIAKRY-LGRGMQFLDLI 158


>gi|26249652|ref|NP_755692.1| RpoD protein [Escherichia coli CFT073]
 gi|26110080|gb|AAN82266.1|AE016767_26 RpoD protein [Escherichia coli CFT073]
          Length = 246

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 176/245 (71%), Positives = 206/245 (84%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            + +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKF
Sbjct: 1   MKAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 60

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++
Sbjct: 61  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 120

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  V
Sbjct: 121 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 180

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ L
Sbjct: 181 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 240

Query: 677 RSFLD 681
           RSFLD
Sbjct: 241 RSFLD 245


>gi|306820486|ref|ZP_07454120.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551472|gb|EFM39429.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 538

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 145/273 (53%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +++ E   +  ++ K       AK ++VEANLRLV+S+AK+Y  RG+
Sbjct: 269 VRMYLKEIGKIQLLTVEEEHRLSELMVK---GDEYAKMKIVEANLRLVVSIAKRYVGRGM 325

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 326 LFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 385

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEEIA+++ M  + +R+++KI +EP+SLETPIG+E+ SHL
Sbjct: 386 INKLIRINRQLVQELGRDPRPEEIAEQMGMSQDKIREIMKIAQEPVSLETPIGEEEDSHL 445

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A  + LRE   +VL +LT RE RVL++RFG+      TLEEVGK+
Sbjct: 446 GDFIPDDDAQAPSEAAAYSLLREQIEQVLCTLTDRERRVLKLRFGLDDGRPRTLEEVGKE 505

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+ P +S KL+ +LD
Sbjct: 506 FDVTRERIRQIEAKALRKLRGPKKSNKLKDYLD 538



 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 38/170 (22%), Positives = 77/170 (45%), Gaps = 3/170 (1%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           ++D +D L     + + + +I+  R+ GY+  + +   +   ++  E++ED     ++ G
Sbjct: 165 YDDKEDILSVMEYEKAVQGLIEKGRRDGYIDYDTIMNTVDNYDIGKEKIEDMYDRFASFG 224

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I+    DD++ +   +++      +      L         + DDPVRMYL+E+G I+LL
Sbjct: 225 ID--IIDDMDKDTPHDEAKGGEQKSEGDFDLLSLELSLTKNNVDDPVRMYLKEIGKIQLL 282

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + E E  +++ +  G       + E+ L     I  R  +  G   L  I
Sbjct: 283 TVEEEHRLSELMVKGDEYAKMKIVEANLRLVVSIAKRY-VGRGMLFLDLI 331


>gi|256787912|ref|ZP_05526343.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
          Length = 365

 Score =  227 bits (577), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 128/296 (43%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     +S +E   +   V                         +      +AK
Sbjct: 70  RQYLREIGRIPLLSAAEEVDLARRVEAGLFAEEKLRCSPGLDDRLALDLDRLVVLGRLAK 129

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 130 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 189

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E V +
Sbjct: 190 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDLAPERVGE 249

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL++L  RE 
Sbjct: 250 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGERER 309

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 310 KVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLRDHAYADQLRGYLD 365



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +  +   + D  R YLRE+G I LLS   E+ +A+R+EAG 
Sbjct: 58  RTESGGPSSDLFRQYLREIGRIPLLSAAEEVDLARRVEAGL 98


>gi|291541030|emb|CBL14141.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           XB6B4]
          Length = 397

 Score =  227 bits (577), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 128 VRMYLKEIGKVPLLSAEEEIELAKRME---LGDQEAKKRLAEANLRLVVSIAKRYVGRGM 184

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 185 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 244

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA ++ MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 245 INKLIRVSRQLLQELGREPTPEEIAAEMNMPVERVREILKISQEPVSLETPIGEEEDSHL 304

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL +LT RE++VL +RFG+      TLEEVG++
Sbjct: 305 GDFIQDDNVPVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGRE 364

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 365 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 397



 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 47/194 (24%), Positives = 83/194 (42%), Gaps = 14/194 (7%)

Query: 1   MTIGKKRN---------RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQR-GYVTIEELN 50
           M   KK N         +   S   +++     +   +  K+++ LA+++   +  +E++
Sbjct: 1   MATKKKENNENTKVSGKKAETSAVNNAEAEAAREKFQEKLKELLSLAKKKKNMLEYQEIS 60

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
            F    ++ S++ E  +  L    I+V+   D + ++     +D         + L    
Sbjct: 61  DFFADMQLDSDKFEKILDFLEANNIDVLRITDDDADDDILLEVDDDDEIEVEKIDLSVPD 120

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
                S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L     I  
Sbjct: 121 ---GVSIEDPVRMYLKEIGKVPLLSAEEEIELAKRMELGDQEAKKRLAEANLRLVVSIAK 177

Query: 171 RDELNDGTTLLREI 184
           R  +  G   L  I
Sbjct: 178 RY-VGRGMLFLDLI 190


>gi|297562250|ref|YP_003681224.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296846698|gb|ADH68718.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 571

 Score =  227 bits (577), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 135/283 (47%), Positives = 188/283 (66%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EV+   +I   + +       +      +   +     +   AKK ++EANLRLV+S
Sbjct: 289 AEQEVELAKRIEAGLFAEEKLAEEAELLTVELRDELEWIAEDGGRAKKHLLEANLRLVVS 348

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ T
Sbjct: 349 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQART 408

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+A++L M  E V +V K  +EPISL T
Sbjct: 409 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKVVEVQKYGREPISLHT 468

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  A+ P ++     L+E    VL +L+ RE  V+ MRFG+    
Sbjct: 469 PLGEDGDSEFGDLIEDSEAIQPGEAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQ 528

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 529 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 571



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 34/70 (48%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +         + D +    +        +  A  +T DPV+ YL+++G + LL+ E E+
Sbjct: 234 PEAVGAPAKPANEDESFVLYDDDDDAPAAQVVAAGATADPVKDYLKQIGKVPLLNAEQEV 293

Query: 141 AIAKRIEAGR 150
            +AKRIEAG 
Sbjct: 294 ELAKRIEAGL 303



 Score = 37.9 bits (86), Expect = 6.6,   Method: Composition-based stats.
 Identities = 9/53 (16%), Positives = 25/53 (47%)

Query: 26 FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +   +++I+  R +G++  E++       E+   Q +  +  L+  G+ V+
Sbjct: 15 LQEPVIQQLIERGRSQGFLEPEDVRRAFEEAEIPMSQAQSVLRSLAKEGVTVL 67


>gi|288574624|ref|ZP_06392981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570365|gb|EFC91922.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  227 bits (577), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 143/272 (52%), Positives = 194/272 (71%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     ++  +   +   V         AK +++EANLRLV+S+AKKY  RG+
Sbjct: 112 VRMYLREIGTIPLLNQPQEVELAKRVE---MGDDEAKSQLIEANLRLVVSIAKKYMGRGM 168

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 169 LFLDLIQEGNLGLIRAVEKFDYSRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 228

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV+R +R +   + REPT EEIA ++ +    V ++ K+ +EPISLE+P+G+ED S L
Sbjct: 229 INKVMRASRNLVQSLGREPTDEEIAAEMGIEPAKVVQIRKVAQEPISLESPVGEEDDSEL 288

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIEDK+ +SP DS     LR+    VL  LT RE++VLR+RFG      +TLE+VG++
Sbjct: 289 GDFIEDKDMISPDDSTSMEFLRDQLDDVLEGLTDREKQVLRLRFGFDDGQCYTLEDVGRR 348

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HPSRS  LR ++
Sbjct: 349 FGVTRERIRQIEAKALRKLRHPSRSVTLRDYM 380



 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 44/167 (26%), Positives = 71/167 (42%), Gaps = 11/167 (6%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
               +V D   D  K ++   + +G+VT E++   + P  ++   +E     L  +GI++
Sbjct: 19  DHTEIVLDQYLDKIKDILLEGQSKGFVTKEDIKRHMTPQTLNEVLLEKIYDNLRALGIDI 78

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
                        D  D       SS    +   S      DPVRMYLRE+G+I LL++ 
Sbjct: 79  ----------QGIDDEDEKKGDDPSSRISGESVSSDSGGGGDPVRMYLREIGTIPLLNQP 128

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+ +AKR+E G     + L E+ L     I  +  +  G   L  I
Sbjct: 129 QEVELAKRVEMGDDEAKSQLIEANLRLVVSIAKKY-MGRGMLFLDLI 174


>gi|254389040|ref|ZP_05004270.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441042|ref|ZP_08215776.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702757|gb|EDY48569.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
          Length = 385

 Score =  227 bits (577), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 131/323 (40%), Positives = 194/323 (60%), Gaps = 25/323 (7%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR-------- 435
              +   P             S    R  ++ I     ++ +E   +   V         
Sbjct: 63  AEESAPRPGSARTARSESSGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEK 122

Query: 436 -----------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
                            +      +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN
Sbjct: 123 LAATPDLNSSRLAADLDRLVVMGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGN 182

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A EKFD+  GYKFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR
Sbjct: 183 LGLIRAVEKFDYTRGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRR 242

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  +   EPTPEE+A +L +P E V +VL++ +EP+SL  P+G+E+   LGD IED +A 
Sbjct: 243 MLQEQGSEPTPEEVAAQLDLPPERVSEVLRLAQEPVSLHAPVGEEEDVALGDLIEDGDAA 302

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP++SA    LRE    VL++L  RE +V+++R+G+      TLEE+G+ F VTRERIRQ
Sbjct: 303 SPVESAAFLLLREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQ 362

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IE+K + KL+  + + +LR +LD
Sbjct: 363 IESKTLNKLRDHAFADQLRGYLD 385



 Score = 54.8 bits (130), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           A  ++      +  +  +   + D  R YLRE+G I LL+   E+ +A+R+EAG      
Sbjct: 63  AEESAPRPGSARTARSESSGPSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLF-AEE 121

Query: 156 SLCESP 161
            L  +P
Sbjct: 122 KLAATP 127


>gi|260438482|ref|ZP_05792298.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
 gi|292809071|gb|EFF68276.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
          Length = 370

 Score =  227 bits (577), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLSADEEIELAKRME---LGDEEAKKKLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+P+EIA ++ +PVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPSPQEIADEMDIPVERVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A    L+E    VL +LT RE++VL++RFG+      TLEEVGK 
Sbjct: 278 GDFIQDDNVPVPAEAAAFTLLKEQLNEVLGTLTEREQKVLKLRFGLEDGRARTLEEVGKV 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +L+
Sbjct: 338 FNVTRERIRQIEAKALRKLRHPSRSRKLRDYLE 370



 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/166 (24%), Positives = 75/166 (45%), Gaps = 5/166 (3%)

Query: 20  DSLVFDFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           +  + +   +  K+++ +A+++   +   E+        +++EQM+  +  L    I+ +
Sbjct: 2   EENLMEKFQEKLKELLVIAKKKKNVLEYSEITDLFSDMNLTAEQMDSILEYLEKNNIDTL 61

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
              D ++E   E+++          + L         S +DPVRMYL+E+G + LLS + 
Sbjct: 62  RTTDDDEEPDPEEAVLDEEDIDVEKIDLSV---PDGISIEDPVRMYLKEIGKVPLLSADE 118

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI +AKR+E G       L E+ L     I  R  +  G   L  I
Sbjct: 119 EIELAKRMELGDEEAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|152976724|ref|YP_001376241.1| RNA polymerase sigma factor RpoD [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152025476|gb|ABS23246.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus cytotoxicus
           NVH 391-98]
          Length = 373

 Score =  227 bits (577), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIQLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 77/176 (43%), Gaps = 11/176 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ SEQM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESEQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V        +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 111

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 GRVDLLSAEEEIQLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|18310989|ref|NP_562923.1| RNA polymerase sigma factor RpoD [Clostridium perfringens str. 13]
 gi|18145671|dbj|BAB81713.1| transcription initiation factor sigma A [Clostridium perfringens
           str. 13]
          Length = 373

 Score =  226 bits (576), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +      ++ AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGKVPLLSSEDEIELAKKIE---EGSNYAKKKLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEE++K++ MPV+ VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 221 INKLIRIQRQLVQELGRDPLPEELSKQMDMPVDKVREILKIAQEPVSLETPIGEEEDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 281 GDFIPDDDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 341 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 373



 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 42/154 (27%), Positives = 63/154 (40%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K++I   ++ G +T +E+   L   E++ EQ+E    +L +MG                
Sbjct: 30  VKRLIDKGKKSGSLTYKEIMDELDEIELNPEQIEKIYEVLESMG---------------- 73

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +                      + DDPVRMYL+E+G + LLS E EI +AK+IE G 
Sbjct: 74  IEVISEIEQEEEEEEELDLSVPEGIAIDDPVRMYLKEIGKVPLLSSEDEIELAKKIEEGS 133

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 134 NYAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|254721884|ref|ZP_05183673.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. A1055]
          Length = 373

 Score =  226 bits (576), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGI 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 51/207 (24%), Positives = 84/207 (40%), Gaps = 19/207 (9%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V        +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 111

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I    
Sbjct: 112 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGILFLDLI---- 166

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSS 215
                E   G     E   Y+K    S
Sbjct: 167 ----QEGNMGLIKAVEKFDYRKGFKFS 189


>gi|240147091|ref|ZP_04745692.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|257200737|gb|EEU99021.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|291536629|emb|CBL09741.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           M50/1]
          Length = 397

 Score =  226 bits (576), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 128 VRMYLKEIGKVPLLSAEEEIELAKRME---LGDQEAKKRLAEANLRLVVSIAKRYVGRGM 184

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 185 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 244

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA ++ MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 245 INKLIRVSRQLLQELGREPTPEEIAAEMNMPVERVREILKISQEPVSLETPIGEEEDSHL 304

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL +LT RE++VL +RFG+      TLEEVG++
Sbjct: 305 GDFIQDDNVPVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGRE 364

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 365 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 397



 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 47/194 (24%), Positives = 83/194 (42%), Gaps = 14/194 (7%)

Query: 1   MTIGKKRN---------RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQR-GYVTIEELN 50
           M   KK N         +   S   +++     +   +  K+++ LA+++   +  +E++
Sbjct: 1   MATKKKENNENTKVSGKKAEASAVNNAEAEAAREKFQEKLKELLSLAKKKKNMLEYQEIS 60

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
            F    ++ S++ E  +  L    I+V+   D + ++     +D         + L    
Sbjct: 61  DFFADMQLDSDKFEKILDFLEANNIDVLRITDDDADDDILLEVDDDDEIEVEKIDLSVPD 120

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
                S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L     I  
Sbjct: 121 ---GVSIEDPVRMYLKEIGKVPLLSAEEEIELAKRMELGDQEAKKRLAEANLRLVVSIAK 177

Query: 171 RDELNDGTTLLREI 184
           R  +  G   L  I
Sbjct: 178 RY-VGRGMLFLDLI 190


>gi|153853334|ref|ZP_01994743.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
 gi|149754120|gb|EDM64051.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
          Length = 369

 Score =  226 bits (576), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 157/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGKVPLLSAEEEVELAKRM---ADGDEEAKKRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 LFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA +L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 217 INKLIRVSRQLLQELGREPTPEEIAAELDMPVERVREILKISQEPVSLETPIGEEEDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 277 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 337 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 369



 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 49/162 (30%), Positives = 77/162 (47%), Gaps = 13/162 (8%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDD 82
            +  ++++ L +++ G + I+E+N F    E+ S+QME     L    ++V+    D DD
Sbjct: 9   QEKLRELVSLGKKKKGILEIQEINDFFSDMELDSDQMEKVFDYLEANNVDVLRISNDDDD 68

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           + DE    D  D+     + SV           S +DPVRMYL+E+G + LLS E E+ +
Sbjct: 69  IPDEIVMSDEDDIDVEKIDLSV-------PDGISIEDPVRMYLKEIGKVPLLSAEEEVEL 121

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AKR+  G       L E+ L     I  R  +  G   L  I
Sbjct: 122 AKRMADGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 162


>gi|283456279|ref|YP_003360843.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
 gi|283102913|gb|ADB10019.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
          Length = 328

 Score =  226 bits (576), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 201/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T  S  +F+     ++    +   AK  ++EANLRLV+
Sbjct: 45  AEQEVDLSERIEAGLYAQHLLDTEASQMDFKRR-RELKWAANDGKKAKDHLLEANLRLVV 103

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 104 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 163

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 164 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 223

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 224 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 283

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 284 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 327



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 17  KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 59


>gi|116619924|ref|YP_822080.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223086|gb|ABJ81795.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 518

 Score =  226 bits (576), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 183/516 (35%), Positives = 286/516 (55%), Gaps = 12/516 (2%)

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           + + +  + +  D      PE+ G  F         +    +       V+E+    +  
Sbjct: 3   VGEVSLKVDQFEDQFLAENPEALGLSFEDDPKFFDPEAAHEADFLHPAPVEESIYTDDPV 62

Query: 234 AKVSKDDRSKVDSPPENAENDERNLD--EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
               ++  +      E   +  R ++  +     A + SA+  ++   V   L       
Sbjct: 63  RVYLREMGAVPLLTREGEVDLARRMERGKLRMQKAISRSALVQRVVVDVADQLKRANIEI 122

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
             +  L D       D K   +       +V L   L   + +++          KR+  
Sbjct: 123 ESVVDLGDVEEGSPADVKVRNEAAKHFADIVVLHKKLQQLEDKVEATPLASKKPRKRLCA 182

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS------ 405
                 ++  S  I+R  F    + +E     +  A D            EV S      
Sbjct: 183 KLNR-SKVETSLAIRRAPF-RLIKWKEF-AREIERAVDEISHLDSEIKRLEVRSNPTQQL 239

Query: 406 -ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            + +++ EIK   +  G ++ E +H ++++R GE EA  AKK++VEANLRLV+SVAKKY 
Sbjct: 240 RLRELKREIKKREIAAGATLPELKHSLTVIRHGEAEAERAKKDLVEANLRLVVSVAKKYV 299

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLIQEGNIGLM+AA+KF++  GYKFSTYA WW++QAITR+IADQS TIRIPVH
Sbjct: 300 NRGLHLLDLIQEGNIGLMRAADKFEYRRGYKFSTYATWWIRQAITRAIADQSRTIRIPVH 359

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + ++K +R  R +  ++ R PT +EI +++ +PVE V+K+  I+++P+SLETP+G + 
Sbjct: 360 MNESMNKFLRATRELEKELGRTPTNDEIGRRMDIPVEKVQKLKTISRDPVSLETPVGRDG 419

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGD IED+   SP+D+ I++N+R+ T  +L +L+P+EE+V+RMRFGIG   +HTLEE
Sbjct: 420 ESALGDLIEDRWVGSPVDAVIESNVRDETAGILKTLSPKEEKVIRMRFGIGCEREHTLEE 479

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +G++F VTRERIRQIEAKA+R+L+ P R+++LR+ +
Sbjct: 480 IGQEFDVTRERIRQIEAKALRQLRAPERARRLRALM 515



 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 33/112 (29%), Positives = 57/112 (50%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  +       +D       A++ + FL          TDDPVR+YLREMG++ LL+REG
Sbjct: 20  ENPEALGLSFEDDPKFFDPEAAHEADFLHPAPVEESIYTDDPVRVYLREMGAVPLLTREG 79

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           E+ +A+R+E G+  M  ++  S L  + ++   D+L      +  ++DL   
Sbjct: 80  EVDLARRMERGKLRMQKAISRSALVQRVVVDVADQLKRANIEIESVVDLGDV 131


>gi|269125851|ref|YP_003299221.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268310809|gb|ACY97183.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 559

 Score =  226 bits (576), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 135/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  +   +   +                              +   
Sbjct: 262 VKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEERLATMGDQLSEEDKADLEWIAEDGRR 321

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW
Sbjct: 322 AKAHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 381

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 382 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 441

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 442 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHSVLDTLSER 501

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 502 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 559



 Score = 53.3 bits (126), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 33/51 (64%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++       ++ ++  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 241 TDDDDDAPAQQIASAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGL 291


>gi|196034883|ref|ZP_03102290.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
 gi|195992422|gb|EDX56383.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
          Length = 373

 Score =  226 bits (576), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+E  SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEGDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/207 (24%), Positives = 84/207 (40%), Gaps = 19/207 (9%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V        +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 111

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I    
Sbjct: 112 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI---- 166

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSS 215
                E   G     E   Y+K    S
Sbjct: 167 ----QEGNMGLIKAVEKFDYRKGFKFS 189


>gi|156740438|ref|YP_001430567.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231766|gb|ABU56549.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 405

 Score =  226 bits (576), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 132/249 (53%), Positives = 180/249 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +   E   A++ +++ANLRLV+S+AKKY  RG+  LDLIQEGNIGLM+A EKFD+  
Sbjct: 157 QLHRWVQEGQAARERLIQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRK 216

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR IADQS TIR+PVH+ + I++V+RT+ R+     R+PTP+EI
Sbjct: 217 GYKFSTYATWWIRQAITRVIADQSRTIRLPVHVGETINRVMRTSNRIQQTTGRDPTPDEI 276

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L +PVE VR+VL+  ++ ISLETPIG E  S L DFIED    +P++SA    LRE 
Sbjct: 277 ALELGIPVEKVRRVLEAARQTISLETPIGPEGDSVLADFIEDGKGATPMESASSHILREQ 336

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               L  L  RE R++++R+G+      TLEEVG++F +TRERIRQIEA+ +RKL+HP  
Sbjct: 337 IDSALEKLPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLRKLRHPHY 396

Query: 673 SKKLRSFLD 681
            + LR +L+
Sbjct: 397 GRGLRGYLE 405



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            DDPVR+YLRE+G + LL+ + EI +A+++E G       L     T    +     + +
Sbjct: 106 VDDPVRVYLREIGRVNLLTAQEEIMLAQQVERGE-QANERLQNGDYTPVERLQLHRWVQE 164

Query: 177 GTTLLREII 185
           G      +I
Sbjct: 165 GQAARERLI 173


>gi|163942050|ref|YP_001646934.1| RNA polymerase sigma factor RpoD [Bacillus weihenstephanensis
           KBAB4]
 gi|229013514|ref|ZP_04170648.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
 gi|229019517|ref|ZP_04176334.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|229025758|ref|ZP_04182158.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|229061987|ref|ZP_04199313.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|229135118|ref|ZP_04263920.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|229169042|ref|ZP_04296758.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|163864247|gb|ABY45306.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614451|gb|EEK71560.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|228648347|gb|EEL04380.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|228717296|gb|EEL68969.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|228735541|gb|EEL86136.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|228741773|gb|EEL91956.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|228747751|gb|EEL97620.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
          Length = 375

 Score =  226 bits (576), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 78/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V      D +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-----GDNDNDEGPNNRQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|322383680|ref|ZP_08057431.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151892|gb|EFX44835.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 354

 Score =  226 bits (576), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 85  VRMYLKEIGRVPLLSAEDEVELAKRIEQ---GDEEAKRRLTEANLRLVVSIAKRYVGRGM 141

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 142 LFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 201

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 202 INKLIRVSRQLLQELGREPTPEEIAKEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHL 261

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 262 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 321

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 322 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 354



 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 49/151 (32%), Positives = 74/151 (49%), Gaps = 4/151 (2%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           MI+L ++R  +T +E+   L P +  +EQ++D    LS MGI+V + +D +++     + 
Sbjct: 1   MIELGKKRSSLTYKEIMDRLAPYDQDAEQIDDFFEHLSEMGIDVGNENDDDEDNIRPGNT 60

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           D      N   F            +DPVRMYL+E+G + LLS E E+ +AKRIE G    
Sbjct: 61  DNEDEDFN---FEDDLTLPPGIKINDPVRMYLKEIGRVPLLSAEDEVELAKRIEQGDEEA 117

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREI 184
              L E+ L     I  R  +  G   L  I
Sbjct: 118 KRRLTEANLRLVVSIAKRY-VGRGMLFLDLI 147


>gi|225575013|ref|ZP_03783623.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037764|gb|EEG48010.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
          Length = 374

 Score =  226 bits (576), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGKVNLLTAEEEIELAKRME---EGDEDAKKRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ M V+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 222 INKLIRVSRQLLQELGREPTPEEIAKEMEMSVDRVREILKISQEPVSLETPIGEEEDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL++LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 282 GDFIQDDNVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGLDDGRARTLEEVGKE 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 342 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 374



 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 48/159 (30%), Positives = 75/159 (47%), Gaps = 4/159 (2%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   ++++ A+++   +  +E+N F     + +EQ+E     L   GI+V+   D + +E
Sbjct: 10  EKLVELLEFAKKKKNVLEYQEINDFFKDTPLDTEQLEKVFDFLEASGIDVLRISDSDVDE 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                 DL   A    V L K   S     S +DPVRMYL+E+G + LL+ E EI +AKR
Sbjct: 70  ALLLDEDLDKIAEEEDVELDKIDLSVPEGVSIEDPVRMYLKEIGKVNLLTAEEEIELAKR 129

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +E G       L E+ L     I  R  +  G   L  I
Sbjct: 130 MEEGDEDAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|261407775|ref|YP_003244016.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329927238|ref|ZP_08281536.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261284238|gb|ACX66209.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328938638|gb|EGG35021.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 316

 Score =  226 bits (576), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+A++Y  RG+
Sbjct: 47  VRMYLKEIGRVPLLSADEEVELSKRIE---EGDEEAKRRLAEANLRLVVSIARRYAGRGM 103

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 104 QFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVET 163

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ REPTPEEI K++ +  E VR++ K+++EP+SLETP+G+E  S+L
Sbjct: 164 INKLVRVSRQLLQELGREPTPEEIGKEMDISPEKVREIQKVSQEPVSLETPVGEESDSNL 223

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 224 GDFIEDQDALAPADAAAFELLKEQLEEVLDTLTEREENVLRLRFGLEDGRTRTLEEVGQV 283

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 284 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 316



 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 61/280 (21%), Positives = 93/280 (33%), Gaps = 20/280 (7%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D   E    D+   A+S +                  DPVRMYL+E+G + LLS + E
Sbjct: 6   SADFALEREVTDTEKSANSPTEDFSVHDDLSLPPGIKISDPVRMYLKEIGRVPLLSADEE 65

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           + ++KRIE G       L E+ L     I  R     G   L  I         E   G 
Sbjct: 66  VELSKRIEEGDEEAKRRLAEANLRLVVSIARRYA-GRGMQFLDLI--------QEGNMGL 116

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
               E   Y K    S        Q     I   A+  +     V++  +      + L 
Sbjct: 117 IKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLVRVSRQLLQ 176

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           E   +        E  + P     + EI +V +E  SL+                  L +
Sbjct: 177 ELGREPTPEEIGKEMDISP---EKVREIQKVSQEPVSLETPVGEESDS--------NLGD 225

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +         + +  +LL EQL ++   +   E  +LRL
Sbjct: 226 FIEDQDALAPADAAAFELLKEQLEEVLDTLTEREENVLRL 265


>gi|167462413|ref|ZP_02327502.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 367

 Score =  226 bits (576), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  +   +   +         AK+ + EANLRLV+S+A++Y  RG+
Sbjct: 98  VRMYLKEIGRVHLLTADDEIELAKRI---MEGDEEAKQRLAEANLRLVVSIARRYVGRGM 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 155 LFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +  + VR+++KI++EP+SLETPIG+E+ S+L
Sbjct: 215 INKLIRVSRQLLLELGREPTPEEIAKEMELSTDKVREIMKISQEPVSLETPIGEENDSNL 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 275 GDFIEDQDALAPADAASYELLKEQLEHVLDTLTEREENVLRLRFGLEDGRSRTLEEVGKV 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 335 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 367



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 42/157 (26%), Positives = 71/157 (45%), Gaps = 11/157 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + +++I+  +Q   +T +E+   L P +   EQ+++   +L+ +GI V +  D   E 
Sbjct: 15  ERAKEQLIESGKQHSSLTYKEIIEKLAPFDQEPEQIDEFFELLAELGIEVENETDDNPEP 74

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G++    L                    S +D VRMYL+E+G + LL+ + EI +AKRI 
Sbjct: 75  GNQTKGSLDEDD----------LTLPAGSLNDSVRMYLKEIGRVHLLTADDEIELAKRIM 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 125 EGDEEAKQRLAEANLRLVVSIARRY-VGRGMLFLDLI 160


>gi|75761907|ref|ZP_00741832.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490615|gb|EAO53906.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 268

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 152/271 (56%), Positives = 198/271 (73%), Gaps = 3/271 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+ F
Sbjct: 1   MYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGMLF 57

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+
Sbjct: 58  LDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHLGD
Sbjct: 118 KLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHLGD 177

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F 
Sbjct: 178 FIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFG 237

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 238 VTRERIRQIEAKALRKLRHPSRSKRLKDFLE 268



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/93 (32%), Positives = 38/93 (40%), Gaps = 9/93 (9%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL+E+G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L 
Sbjct: 1   MYLKEIGRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLD 59

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            I         E   G     E   Y+K    S
Sbjct: 60  LI--------QEGNMGLIKAVEKFDYRKGFKFS 84


>gi|320530863|ref|ZP_08031900.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136897|gb|EFW28842.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 370

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +  ++         A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGHVPLLTAEEEVELAQLME---AGDEEARHRLEEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ R+P PEEIAK++ + V  V +++KI +EP+SLETPIG+E+ SHL
Sbjct: 218 INKLVRISRQLLQELGRDPRPEEIAKEMGISVARVHEIMKIAQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A +P ++A    LRE    VL +LT RE+ VLR+RFG+      TLEEVG+ 
Sbjct: 278 GDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQS 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 338 FGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 370



 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 42/159 (26%), Positives = 71/159 (44%), Gaps = 8/159 (5%)

Query: 27  SDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           S +  ++++   ++ G  +T  EL   L   ++S ++M+D     ++ G+++VD      
Sbjct: 12  STEIIERLLAKGKKNGGSLTYGELIDALQKQDMSPDEMDDMYQRFTDEGVDIVD------ 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E  + D       A                S DDPVRMYL+E+G + LL+ E E+ +A+ 
Sbjct: 66  EASAADEPAPEEPAEKEEEVEIDLSIPEGVSLDDPVRMYLKEIGHVPLLTAEEEVELAQL 125

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +EAG       L E+ L     I  R  +  G   L  I
Sbjct: 126 MEAGDEEARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|313897089|ref|ZP_07830636.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974536|gb|EFR40004.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 370

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +  ++         A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGHVPLLTAEEEVELAQLME---AGDEEARHRLEEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ R+P PEEIAK++ + V  V +++KI +EP+SLETPIG+E+ SHL
Sbjct: 218 INKLVRISRQLLQELGRDPRPEEIAKEMGISVARVHEIMKIAQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A +P ++A    LRE    VL +LT RE+ VLR+RFG+      TLEEVG+ 
Sbjct: 278 GDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQS 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 338 FGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 370



 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 42/159 (26%), Positives = 71/159 (44%), Gaps = 8/159 (5%)

Query: 27  SDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           S +  ++++   ++ G  +T  EL   L   ++S ++M+D     ++ G+++VD      
Sbjct: 12  STEIIERLLTKGKKNGGSLTYGELIDALQKQDMSPDEMDDMYQRFADEGVDIVD------ 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E  + D       A                S DDPVRMYL+E+G + LL+ E E+ +A+ 
Sbjct: 66  EASAADEPAPEEPAEKEEEVEIDLSIPEGVSLDDPVRMYLKEIGHVPLLTAEEEVELAQL 125

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +EAG       L E+ L     I  R  +  G   L  I
Sbjct: 126 MEAGDEEARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|317132028|ref|YP_004091342.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470007|gb|ADU26611.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 372

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 150/270 (55%), Positives = 199/270 (73%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S  E   +   +         A+K + EANLRLV+S+AK+Y  RG+QFL
Sbjct: 106 YLKEIGRVPLLSGEEEIELAKRM---GEGDVAARKRLSEANLRLVVSIAKRYVGRGMQFL 162

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 163 DLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 222

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           VVR  R++  ++ R+P  EEIA+ + M V+ VR+++K+ +EP+SLETPIG+E+ SHLGDF
Sbjct: 223 VVRVERQLLQELGRQPQAEEIAELMGMSVDKVREIMKVAQEPVSLETPIGEEEDSHLGDF 282

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A +P ++A    L+E    VL +LT RE +VLR+RFG+      TLEEVG++F V
Sbjct: 283 IPDDDAPAPAEAASHTLLKEQLGDVLKTLTQREAKVLRLRFGLDDGRPRTLEEVGREFNV 342

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 343 TRERIRQIEAKALRKLRHPSRSKKLKDFLD 372



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 47/159 (29%), Positives = 75/159 (47%), Gaps = 2/159 (1%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
             D   ++I+  + +G +T+ E+   L   +  +EQ E     L +  I+V+D  +    
Sbjct: 8   KKDRIAELIETGKTKGNLTMTEITDALEEIDFDAEQTEKLYEALEHHNIDVLDDQEEPTP 67

Query: 87  EGSEDSLDL-ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E  E  L+  A  AS  +V L+    +   + DDPV++YL+E+G + LLS E EI +AKR
Sbjct: 68  EELEGDLEEDAEEASKPNVDLESSLSAEGIAIDDPVKVYLKEIGRVPLLSGEEEIELAKR 127

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  G       L E+ L     I  R  +  G   L  I
Sbjct: 128 MGEGDVAARKRLSEANLRLVVSIAKRY-VGRGMQFLDLI 165


>gi|312876451|ref|ZP_07736435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796809|gb|EFR13154.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 419

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 150 VRMYLKEIGKIPLLTPEEEIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 206

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 207 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 266

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  +  REPTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 267 INKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHL 326

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+
Sbjct: 327 GDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGKE 386

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 387 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 419



 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 70/339 (20%), Positives = 130/339 (38%), Gaps = 64/339 (18%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
                 N+    +  +   SL+     +  +++I L + +G++T  E+   L   E+ + 
Sbjct: 51  AKKSTENKSEGKKMSEEKKSLI----REKIRELISLGQSKGFLTYSEIQEILDKVELDAS 106

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q+E+    L +MGI++VD    E+E   +D  +L                    + DDPV
Sbjct: 107 QVENIYDTLESMGIDIVDDRVSEEELLKDDLENL----------------PEGIAIDDPV 150

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L
Sbjct: 151 RMYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFL 209

Query: 182 REIID-----LEACIGPESKGGFFHGT--------------------------------- 203
             I +     L+A    + + G+   T                                 
Sbjct: 210 DLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 269

Query: 204 -----EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                     +K  + + E+   ++      +    K++++  S      E  ++   + 
Sbjct: 270 LVRVSRQLLQEKGREPTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHLGDF 329

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             D+D  A + +A    L+ +++  LD + E  +++  L
Sbjct: 330 IPDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKL 368


>gi|167463432|ref|ZP_02328521.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 375

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVPLLSAEDEVELAKRIEQ---GDEEAKRRLTEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVSRQLLQELGREPTPEEIAKEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 48/152 (31%), Positives = 75/152 (49%), Gaps = 4/152 (2%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++I+L ++R  +T +E+   L P +  +EQ++D    LS MGI+V + +D +++     +
Sbjct: 21  QLIELGKKRSSLTYKEIMDRLAPYDQDAEQIDDFFEHLSEMGIDVGNENDDDEDNIRPGN 80

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            D      N   F            +DPVRMYL+E+G + LLS E E+ +AKRIE G   
Sbjct: 81  TDNEDEDFN---FEDDLTLPPGIKINDPVRMYLKEIGRVPLLSAEDEVELAKRIEQGDEE 137

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  R  +  G   L  I
Sbjct: 138 AKRRLTEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|315647917|ref|ZP_07901018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315276563|gb|EFU39906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 316

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+A++Y  RG+
Sbjct: 47  VRMYLKEIGRVPLLSADEEVELSKRIE---EGDEEAKRRLAEANLRLVVSIARRYAGRGM 103

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 104 QFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVET 163

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ REPTPEEI K++ +  E VR++ K+++EP+SLETP+G+E  S+L
Sbjct: 164 INKLVRVSRQLLQELGREPTPEEIGKEMDITPEKVREIQKVSQEPVSLETPVGEESDSNL 223

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVG+ 
Sbjct: 224 GDFIEDQDALAPADAAAFELLKEQLEEVLDTLTEREENVLRLRFGLEDGRTRTLEEVGQV 283

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 284 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 316



 Score = 75.3 bits (183), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 61/280 (21%), Positives = 93/280 (33%), Gaps = 20/280 (7%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D   E    D+   A+S +                  DPVRMYL+E+G + LLS + E
Sbjct: 6   NADFALEREVTDTEKTANSPAEDFSVHDDLSLPPGIKISDPVRMYLKEIGRVPLLSADEE 65

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           + ++KRIE G       L E+ L     I  R     G   L  I         E   G 
Sbjct: 66  VELSKRIEEGDEEAKRRLAEANLRLVVSIARRYA-GRGMQFLDLI--------QEGNMGL 116

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
               E   Y K    S        Q     I   A+  +     V++  +      + L 
Sbjct: 117 IKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLVRVSRQLLQ 176

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
           E   +        E  + P     + EI +V +E  SL+                  L +
Sbjct: 177 ELGREPTPEEIGKEMDITP---EKVREIQKVSQEPVSLETPVGEESDS--------NLGD 225

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +         + +  +LL EQL ++   +   E  +LRL
Sbjct: 226 FIEDQDALAPADAAAFELLKEQLEEVLDTLTEREENVLRL 265


>gi|229174966|ref|ZP_04302486.1| RNA polymerase sigma factor [Bacillus cereus MM3]
 gi|228608634|gb|EEK65936.1| RNA polymerase sigma factor [Bacillus cereus MM3]
          Length = 375

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 78/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V      D +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-----GDNDNDEGPNNRQITKAEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|229098765|ref|ZP_04229703.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
 gi|229104924|ref|ZP_04235581.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|229117789|ref|ZP_04247154.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228665652|gb|EEL21129.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228678498|gb|EEL32718.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|228684609|gb|EEL38549.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
          Length = 375

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 79/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ ++ ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTEVGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V  +D E+   +        + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLVGDNDNEEGPNNR-----QITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|226324578|ref|ZP_03800096.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
 gi|225207026|gb|EEG89380.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
          Length = 371

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGKVPLLSAEEEIELAKRM---ADGDEEAKKRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNLGLIKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA +L MPV+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 219 INKLIRVSRQLLQELGREPTPEEIAAELDMPVDRVREILKISQEPVSLETPIGEEEDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL++LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 279 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLSTLTEREQKVLRLRFGMSDGRARTLEEVGKE 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 339 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 371



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 78/189 (41%), Gaps = 11/189 (5%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
            +  K ++ LA+++   + I+E+N      E+   QM+     L   GI+V+  +D  + 
Sbjct: 9   QEKLKNLVALAKKKKNILEIQEINDAFRDMELEPTQMDKVFEYLEANGIDVLQMNDDSNV 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  +  + L S      +           S +DPVRMYL+E+G + LLS E EI +AKR+
Sbjct: 69  DDDDLEIML-SDEDEVDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELAKRM 127

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 128 ADGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEKF 178

Query: 207 SYQKREDSS 215
            YQK    S
Sbjct: 179 DYQKGFKFS 187


>gi|260655747|ref|ZP_05861216.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
 gi|260629363|gb|EEX47557.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
          Length = 969

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 148/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I   + +  +E    V++ ++ E     AK E++ ANLRLV+S+AKKY  RG+
Sbjct: 700 VRMYLRDIGKVSLLDAAEE---VALAKRVEAGDETAKDEIINANLRLVVSIAKKYIGRGM 756

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 757 QFLDLIQEGNLGLIRAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 816

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  K+ REP+ EEIA ++ +  E V ++ +I++ P+SLETPIG+E+ S L
Sbjct: 817 INKMVRISRQLVQKLGREPSDEEIAAEMKIEPERVEEIKRISQMPVSLETPIGEEEDSQL 876

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++  SP D A    L+E    +L +L+ RE  VLR RFG+     +TLEEVG++
Sbjct: 877 GDFIEDRSLPSPEDVAADNLLQEQIEEMLNALSDREREVLRYRFGLEDGRSYTLEEVGRR 936

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR FLD
Sbjct: 937 FGVTRERIRQIEAKALRKLRHPSRSKKLRDFLD 969



 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/188 (23%), Positives = 82/188 (43%), Gaps = 13/188 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDS-WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTV 67
            D +S   D +D+ +   S     +++  + + +G+VT +++   +P D  +S+ +E  +
Sbjct: 576 DDEESGEADDEDAALARQSRMKWVRELYTVGKDKGFVTNQDIEETVPADAWNSDVLEFVI 635

Query: 68  AMLSNMGINVVDG-----------DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
             L N+G+++VD                       + D  S   N   + ++     D  
Sbjct: 636 ENLMNLGVDLVDSTGSAAGDVTAGQAAARALAESKNSDADSDEDNDPGYGEELGKMEDVP 695

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
             DPVRMYLR++G + LL    E+A+AKR+EAG       +  + L     I  +  +  
Sbjct: 696 LSDPVRMYLRDIGKVSLLDAAEEVALAKRVEAGDETAKDEIINANLRLVVSIAKKY-IGR 754

Query: 177 GTTLLREI 184
           G   L  I
Sbjct: 755 GMQFLDLI 762


>gi|42783418|ref|NP_980665.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 10987]
 gi|47567855|ref|ZP_00238563.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217961783|ref|YP_002340353.1| RNA polymerase sigma factor RpoD [Bacillus cereus AH187]
 gi|228916924|ref|ZP_04080486.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228987542|ref|ZP_04147661.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229141030|ref|ZP_04269573.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|229157906|ref|ZP_04285980.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|229163237|ref|ZP_04291192.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|229198419|ref|ZP_04325125.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|301055785|ref|YP_003793996.1| RNA polymerase sigma factor [Bacillus anthracis CI]
 gi|42739347|gb|AAS43273.1| RNA polymerase sigma-43 factor [Bacillus cereus ATCC 10987]
 gi|47555532|gb|EAL13875.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217066780|gb|ACJ81030.1| RNA polymerase sigma-43 factor [Bacillus cereus AH187]
 gi|228585119|gb|EEK43231.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|228620300|gb|EEK77171.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|228625565|gb|EEK82318.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|228642463|gb|EEK98751.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|228772274|gb|EEM20721.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228842748|gb|EEM87834.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|300377954|gb|ADK06858.1| RNA polymerase sigma factor [Bacillus cereus biovar anthracis str.
           CI]
 gi|324328197|gb|ADY23457.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 375

 Score =  226 bits (575), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 47/176 (26%), Positives = 78/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V      D +  E   +   + S     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-----GDNDNDEGPNNRQIAKSEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|318066923|emb|CBY89076.1| RNA polymerase sigma70 factor [Halomonas anticariensis]
          Length = 371

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 118/395 (29%), Positives = 184/395 (46%), Gaps = 44/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   +  ++ + +   + E   +++A
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGIPGVAEAEEPEPEPEAELDEDADSEADDDDEDAEDTSA 138

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                  S+    PE A      + E  + +  T+                         
Sbjct: 139 -------SEGGPDPEEARARFEQIREQNELTKATVE------------------------ 167

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                      K  + S + +  + +L +L   + L     + LV Q+    +++   E 
Sbjct: 168 -----------KHGRGSPRAEEEQARLAELFSPIKLVPKHFERLVGQVRISVEQVRDQEK 216

Query: 355 ELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++   +   + R  F++   G E    W+         ++   +    + I + + +I
Sbjct: 217 VIMQVFVKKGKVPRKTFIKSFPGNESRVEWMDEFLA-ANDKFSERLEPFRNDIARAQRKI 275

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 276 AFEEDMVQLPVAELKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 335

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 336 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 370


>gi|110803528|ref|YP_699284.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169343561|ref|ZP_02864560.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170763881|ref|ZP_02634334.2| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170764050|ref|ZP_02630759.2| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170764227|ref|ZP_02638581.2| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|182420445|ref|ZP_02641259.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182624422|ref|ZP_02952206.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|110684029|gb|ABG87399.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169298121|gb|EDS80211.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170663661|gb|EDT16344.1| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170713105|gb|EDT25287.1| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715649|gb|EDT27831.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|177910425|gb|EDT72802.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|182382279|gb|EDT79758.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 366

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +      ++ AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 97  VRMYLKEIGKVPLLSSEDEIELAKKIE---EGSNYAKKKLAEANLRLVVSIAKRYVGRGM 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 154 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEE++K++ MPV+ VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 214 INKLIRIQRQLVQELGRDPLPEELSKQMDMPVDKVREILKIAQEPVSLETPIGEEEDSHL 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 274 GDFIPDDDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 334 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 366



 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 42/154 (27%), Positives = 63/154 (40%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K++I   ++ G +T +E+   L   E++ EQ+E    +L +MG                
Sbjct: 23  VKRLIDKGKKSGSLTYKEIMDELDEIELNPEQIEKIYEVLESMG---------------- 66

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +                      + DDPVRMYL+E+G + LLS E EI +AK+IE G 
Sbjct: 67  IEVISEIEQEEEEEEELDLSVPEGIAIDDPVRMYLKEIGKVPLLSSEDEIELAKKIEEGS 126

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 127 NYAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 159


>gi|229031941|ref|ZP_04187928.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
 gi|228729405|gb|EEL80395.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
          Length = 375

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---DGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/176 (26%), Positives = 79/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V  +D E+   +        S +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLVGDNDNEEGPNNR-----QISKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEDGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|206971344|ref|ZP_03232295.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218899458|ref|YP_002447869.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228902815|ref|ZP_04066960.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|228910126|ref|ZP_04073946.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228941457|ref|ZP_04104008.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954576|ref|ZP_04116601.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228967357|ref|ZP_04128392.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974388|ref|ZP_04134957.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980981|ref|ZP_04141284.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|229071795|ref|ZP_04205010.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|229081552|ref|ZP_04214050.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|229180570|ref|ZP_04307912.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|229192502|ref|ZP_04319465.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|206734116|gb|EDZ51287.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218541635|gb|ACK94029.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228591079|gb|EEK48935.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|228602994|gb|EEK60473.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|228701757|gb|EEL54245.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|228711390|gb|EEL63350.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228778772|gb|EEM27036.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228785438|gb|EEM33448.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792392|gb|EEM39959.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228805233|gb|EEM51827.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818238|gb|EEM64312.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228849643|gb|EEM94477.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228856824|gb|EEN01339.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|326942074|gb|AEA17970.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 375

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 79/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V  +D E+   +        + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLVGDNDNEEGPNNR-----QITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|302386569|ref|YP_003822391.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197197|gb|ADL04768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 401

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 131 VRMYLKEIGKVPLLSSEDEIELAKKIE---LGDDDAKQRLTEANLRLVVSIAKRYVGRGM 187

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 188 QFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 247

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VR +R++  ++ REP PEEIA +  M V+ VR+++K+++EP+SLETPIG+E+ SHL
Sbjct: 248 INRLVRVSRQLLQELGREPVPEEIAARADMQVDRVREIMKVSQEPVSLETPIGEEEDSHL 307

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D+    P D+A    L E    VL +LT RE++VL++RFG+      TLEEVGK+
Sbjct: 308 GDFIQDEQVAVPADAATFTMLHEQLMEVLDTLTEREQKVLKLRFGLDDGRPRTLEEVGKE 367

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 368 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 400



 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/158 (27%), Positives = 72/158 (45%), Gaps = 5/158 (3%)

Query: 30  SWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
              +++ LA++ R  +  +E+  F   + + S++++     L N  ++V+     ED E 
Sbjct: 38  KLNQLLLLAKKKRNVLENQEILDFFVGENLDSDKLDQIFDFLENNKVDVL-QIGGEDLEL 96

Query: 89  SEDSLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            ED            + ++    S     S +DPVRMYL+E+G + LLS E EI +AK+I
Sbjct: 97  DEDLFIEEDIEDEEEIDMESIDLSVPEGISVEDPVRMYLKEIGKVPLLSSEDEIELAKKI 156

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 157 ELGDDDAKQRLTEANLRLVVSIAKRY-VGRGMQFLDLI 193


>gi|30022370|ref|NP_834001.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 14579]
 gi|218232261|ref|YP_002369099.1| RNA polymerase sigma factor RpoD [Bacillus cereus B4264]
 gi|228923044|ref|ZP_04086337.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228960557|ref|ZP_04122206.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229048011|ref|ZP_04193587.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|229111765|ref|ZP_04241313.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|229129569|ref|ZP_04258539.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|229146877|ref|ZP_04275242.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|229152492|ref|ZP_04280684.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|296504786|ref|YP_003666486.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
 gi|29897928|gb|AAP11202.1| RNA polymerase sigma factor rpoD [Bacillus cereus ATCC 14579]
 gi|218160218|gb|ACK60210.1| RNA polymerase sigma-43 factor [Bacillus cereus B4264]
 gi|228631100|gb|EEK87737.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|228636705|gb|EEK93170.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|228653886|gb|EEL09754.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|228671759|gb|EEL27055.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|228723468|gb|EEL74837.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|228799157|gb|EEM46125.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228836677|gb|EEM82025.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296325838|gb|ADH08766.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
          Length = 375

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 47/176 (26%), Positives = 79/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V  +D E+   +        S +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLVGDNDNEEGPNNR-----QISKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|311031650|ref|ZP_07709740.1| RNA polymerase sigma factor RpoD [Bacillus sp. m3-13]
          Length = 374

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 160/306 (52%), Positives = 211/306 (68%), Gaps = 3/306 (0%)

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G + DP+    AK+         V   V     +R  +K I     +S  E   + + + 
Sbjct: 72  GSDDDPNTQQLAKEEEFDLNDLTVPPGVKINDPVRMYLKEIGRVDLLSAEEEISLANRIE 131

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+K
Sbjct: 132 ---EGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFK 188

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP+PEEIA+ 
Sbjct: 189 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIAED 248

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +  + VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    
Sbjct: 249 MDLTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLKEQLED 308

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+
Sbjct: 309 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 368

Query: 676 LRSFLD 681
           L+ FL+
Sbjct: 369 LKDFLE 374



 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 47/173 (27%), Positives = 79/173 (45%), Gaps = 8/173 (4%)

Query: 13  SEHEDSDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           +E       +  + + +  K ++ ++ ++RG +T EE+   +   E+ S+QM++    L 
Sbjct: 2   AEKSAQSKEMETELTIEQVKEQLTEVGKKRGVLTYEEIAEKMAGFEIESDQMDEYYEYLG 61

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
             G+ ++       E GS+D  +    A      L           +DPVRMYL+E+G +
Sbjct: 62  EQGVEII------GEAGSDDDPNTQQLAKEEEFDLNDLTVPPGVKINDPVRMYLKEIGRV 115

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +LLS E EI++A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 116 DLLSAEEEISLANRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|314960003|gb|EFT04105.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA2]
          Length = 511

 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 214 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 273

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 334 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 393

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 394 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 453

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 454 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 511



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 165 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 224

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 225 ALLNAVEEVDLAKRIEAGL 243


>gi|119026029|ref|YP_909874.1| RNA polymerase sigma factor [Bifidobacterium adolescentis ATCC
           15703]
 gi|118765613|dbj|BAF39792.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 479

 Score =  225 bits (574), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 196 AEQEVDLSERIEAGLYAQHLLDTESDKMDFKRR-RELKWAANDGKRAKDHLLEANLRLVV 254

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 255 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 314

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 315 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 374

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 375 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 434

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 435 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 478



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 168 KRRVIAAGATADPVKDYLKQIGRVNLLNAEQEVDLSERIEAGL 210


>gi|160893000|ref|ZP_02073788.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
 gi|156865083|gb|EDO58514.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
          Length = 377

 Score =  225 bits (574), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 151/272 (55%), Positives = 201/272 (73%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+++ EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGKVPLLSAEEEIELAKRME---EGDEQAKQKLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA  + +PVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 225 INKLIRVSRQLLQELGREPQPEEIADVMDIPVERVREILKISQEPVSLETPIGEEEDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D N   P D+A    L+E    VL +LT RE++VL +RFG+      TLEEVGK+
Sbjct: 285 GDFIPDDNMPVPADAAAFTLLKEQLVEVLDTLTEREKKVLTLRFGLEDGRARTLEEVGKE 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HPSRS+KLR ++
Sbjct: 345 FNVTRERIRQIEAKALRKLRHPSRSRKLRDYI 376



 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 42/174 (24%), Positives = 76/174 (43%), Gaps = 9/174 (5%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIE-ELNAFL---PPDEVSSEQMEDTVAML 70
               +   + +      + ++++A+++  V  + E+  +       E++ E+ME   + L
Sbjct: 2   ESKENKEQIEEKFQAKLQGLLEMAKKKKMVIEDTEIIRYFNDAKEIELNLERMEQIFSFL 61

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            +  ++++       EE  ++ L L     +  V           S +DPVRMYL+E+G 
Sbjct: 62  ESHNVDIL----TITEEDDDEELLLDDLEEDVDVDKIDISVPDGVSIEDPVRMYLKEIGK 117

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS E EI +AKR+E G       L E+ L     I  R  +  G   L  I
Sbjct: 118 VPLLSAEEEIELAKRMEEGDEQAKQKLAEANLRLVVSIAKRY-VGRGMLFLDLI 170


>gi|238927758|ref|ZP_04659518.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
 gi|238884474|gb|EEQ48112.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
          Length = 383

 Score =  225 bits (574), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++ ++ E     A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 114 VRMYLKEIGHVPLLTAEEE---VALAQRMEAGDEEARHRLEEANLRLVVSIAKRYVGRGM 170

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 171 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 230

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ R+P PEEIAK++ + V  V +++KI +EP+SLETPIG+E+ SHL
Sbjct: 231 INKLVRISRQLLQELGRDPHPEEIAKEMGITVARVHEIMKIAQEPVSLETPIGEEEDSHL 290

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A +P ++A    LRE    VL +LT RE+ VLR+RFG+      TLEEVG+ 
Sbjct: 291 GDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQS 350

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 351 FGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 383



 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/159 (27%), Positives = 71/159 (44%), Gaps = 9/159 (5%)

Query: 27  SDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           S D  ++++   ++ G  +T  E+   L   ++S ++M+D     S+ G+ +VD      
Sbjct: 26  STDIIERLLAKGKKNGGSLTFGEIIDALQKQDMSPDEMDDMYQRFSDEGVEIVD------ 79

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            + + D                        S DDPVRMYL+E+G + LL+ E E+A+A+R
Sbjct: 80  -DVATDERAEDEKPEKEEEVEIDLTVPEGISLDDPVRMYLKEIGHVPLLTAEEEVALAQR 138

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +EAG       L E+ L     I  R  +  G   L  I
Sbjct: 139 MEAGDEEARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI 176


>gi|225026302|ref|ZP_03715494.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
 gi|224956366|gb|EEG37575.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
          Length = 367

 Score =  225 bits (574), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 148/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + K       A+K+++EANLRLV+S+AKKY  RG+
Sbjct: 98  VRMYLKEIGNIPLLTAEEEVFLAQRIEK---GDEQARKQLIEANLRLVVSIAKKYVGRGM 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G KFSTY+ WW++QAITR IAD + TIR+PVHM + 
Sbjct: 155 SFLDLIQEGNMGLMKAVEKFDYKKGNKFSTYSTWWIRQAITRGIADTAKTIRVPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K +RT+R +  ++ REPT EEIAKK+ MPV  + ++LK +++P+SL+TPIG+E+ S L
Sbjct: 215 INKTLRTSRMLLQELGREPTNEEIAKKMNMPVAKIDEILKTSRDPVSLDTPIGEEEDSQL 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++ +SP+DSA  + L+E     +ASLT RE  V+++RFG+      TLEEVGK+
Sbjct: 275 GDFIEDESLLSPVDSASFSMLKEELEEAMASLTERERNVIKLRFGLDDGKTRTLEEVGKE 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ FL+
Sbjct: 335 FNVTRERIRQIEAKALRKLRHPSRSRKLKDFLE 367



 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 44/185 (23%), Positives = 77/185 (41%), Gaps = 15/185 (8%)

Query: 32  KKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           +K++K A + +  +  +E+N      E++ E+ E  +      G++V++       E  +
Sbjct: 13  EKLLKQAHKNKNVLEYKEINDAFKNIELTPEKFEWILDYFEKQGVDVLNT-----NEEDD 67

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              +     +     +         S +DPVRMYL+E+G+I LL+ E E+ +A+RIE G 
Sbjct: 68  GDDNFIDDDTEEVEIIDDADILEGVSLEDPVRMYLKEIGNIPLLTAEEEVFLAQRIEKGD 127

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                 L E+ L     I  +  +  G + L  I         E   G     E   Y+K
Sbjct: 128 EQARKQLIEANLRLVVSIAKKY-VGRGMSFLDLI--------QEGNMGLMKAVEKFDYKK 178

Query: 211 REDSS 215
               S
Sbjct: 179 GNKFS 183


>gi|322384625|ref|ZP_08058303.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150510|gb|EFX43991.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 371

 Score =  225 bits (574), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  +   +   +         AK+ + EANLRLV+S+A++Y  RG+
Sbjct: 102 VRMYLKEIGRVHLLTADDEIELAKRI---MEGDEEAKQRLAEANLRLVVSIARRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +  + VR+++KI++EP+SLETPIG+E+ S+L
Sbjct: 219 INKLIRVSRQLLLELGREPTPEEIAKEMELSTDKVREIMKISQEPVSLETPIGEENDSNL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 279 GDFIEDQDALAPADAASYELLKEQLEHVLDTLTEREENVLRLRFGLEDGRSRTLEEVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 339 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 371



 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 42/157 (26%), Positives = 71/157 (45%), Gaps = 11/157 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           + + +++I+  +Q   +T +E+   L P +   EQ+++   +L+ +GI V +  D   E 
Sbjct: 19  ERAKEQLIESGKQHSSLTYKEIIEKLAPFDQEPEQIDEFFELLAELGIEVENETDDNPEP 78

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G++    L                    S +D VRMYL+E+G + LL+ + EI +AKRI 
Sbjct: 79  GNQTKGSLDEDD----------LTLPAGSLNDSVRMYLKEIGRVHLLTADDEIELAKRIM 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EGDEEAKQRLAEANLRLVVSIARRY-VGRGMLFLDLI 164


>gi|312880428|ref|ZP_07740228.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
 gi|310783719|gb|EFQ24117.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
          Length = 387

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     ++  E    V + +  E   + +K ++VEANLRLV+S+AKKY  RG+
Sbjct: 118 VRMYLREIGKIPLLTPEEE---VELAKGVEAGHAPSKAKLVEANLRLVVSIAKKYIGRGM 174

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 175 LFLDLIQEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 234

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPT EEIA ++ +P E V ++ +I +EP+SLETPIG+E+ S L
Sbjct: 235 INKLIRVSRQLVQRLGREPTAEEIAGEMEIPAERVEEIQRIAQEPVSLETPIGEEEDSQL 294

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+EDK+  SP ++A    LRE    +L  LT RE  VLR+RFG+     HTLEEVG++
Sbjct: 295 GDFLEDKDLPSPEEAAASQILREQLEEMLEDLTDREREVLRLRFGLEDGHPHTLEEVGRR 354

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR FL+
Sbjct: 355 FGVTRERIRQIEAKALRKLRHPSRSKKLRDFLE 387



 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 73/376 (19%), Positives = 151/376 (40%), Gaps = 32/376 (8%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
            G  + +  ++  ++   +       D+ ++++   R++G+VT E++   LP + +S++ 
Sbjct: 7   KGTAQAQPENAPVQEPVAADDMMDYIDNVRELLHEGREKGFVTYEDIEKHLPKEVLSADV 66

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +++    L  +GI V++     +E  +++ L         + + ++  +  D    DPVR
Sbjct: 67  LDNLYFNLMELGIEVMEEAKTREETPADEPL-------PQATYQEEMGELEDLPLSDPVR 119

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLRE+G I LL+ E E+ +AK +EAG A   A L E+ L     I  +  +  G   L 
Sbjct: 120 MYLREIGKIPLLTPEEEVELAKGVEAGHAPSKAKLVEANLRLVVSIAKKY-IGRGMLFLD 178

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
            I         E   G     E   Y+K    S        Q     I   A+  +    
Sbjct: 179 LI--------QEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 230

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV---------YRE 293
            V++  +      + +     +      A E ++  + +  +  IA+            E
Sbjct: 231 MVETINKLIRVSRQLVQRLGREPTAEEIAGEMEIPAERVEEIQRIAQEPVSLETPIGEEE 290

Query: 294 LRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
              L D   +      + +   ++L+E+L +++  L+  +  +  L   L D       +
Sbjct: 291 DSQLGDFLEDKDLPSPEEAAASQILREQLEEMLEDLTDREREVLRLRFGLED------GH 344

Query: 353 EGELLRLAQSYGIKRD 368
              L  + + +G+ R+
Sbjct: 345 PHTLEEVGRRFGVTRE 360


>gi|256827331|ref|YP_003151290.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
 gi|256583474|gb|ACU94608.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
          Length = 422

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 140/254 (55%), Positives = 194/254 (76%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     + + E     AK++++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EK
Sbjct: 168 RREHRRLTRIEAVGLDAKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEK 227

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP
Sbjct: 228 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGREP 287

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEEIA+++ +  + VR++ KI++EP+SLETPIG+E+ S LGDFIED  AV P D+A  +
Sbjct: 288 TPEEIAEEMDLTPDRVREIQKISQEPVSLETPIGEEEDSQLGDFIEDDAAVVPPDAASFS 347

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E  T+VL  L  RE +V+ +RFG+      TLEEVG++F VTRERIRQIE+K + KL
Sbjct: 348 MLQEQLTKVLDGLAERERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKL 407

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS KL+ +L+
Sbjct: 408 RHPSRSSKLKDYLE 421



 Score = 59.9 bits (143), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/103 (26%), Positives = 44/103 (42%), Gaps = 7/103 (6%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           +  +  D+  +E  ED +         + + +       S   +  + S    S   +  
Sbjct: 56  DDAIAGDKPEAESEEDLLE-------GIPEEELKASSSVSLPKVTASKSRIRQSSRSRAA 108

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
             S    T DPVRMYL+E+G + LL+   EI +A +IEAG   
Sbjct: 109 DTSITMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVEA 151


>gi|318066985|emb|CBY89107.1| RNA polymerase sigma70 factor [Kushneria avicenniae]
          Length = 373

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 125/395 (31%), Positives = 178/395 (45%), Gaps = 42/395 (10%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+ EGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTLEGEIEIAKRIEEGTREVMSALASLPGAVDSILEAYDGT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+         E    +   D + + +       +   +  +
Sbjct: 79  QDEEAPGRLSDLFSGFIDPDEGVPGVAEVEEPMPEIAADDADDSDS-----DDDSDDDDS 133

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
               D  S+    PE A      + E  + +   + A                       
Sbjct: 134 DDEDDTASEGGPDPELARVRFEQIREQNEKAKAAIEA----------------------- 170

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                          +S + +  + +L +L   + L     + LV QL     +I   E 
Sbjct: 171 ------------HGLTSSEARAEQARLAELFSPIKLVPRHFERLVGQLRLSVGQIREQEK 218

Query: 355 ELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L    G + R  F+    GRE D  W+    +       N V      I + + +I
Sbjct: 219 TIMQLCVKRGKVPRKTFIASFPGRESDTTWIDDFIERNSKHAGN-VEPLRSDIERAQRKI 277

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + +SE + I   +  GE +A  AKKEMVEA LRLVIS+AKKYTNRGLQFLDL
Sbjct: 278 AFEEELAMLPVSELKDINRRLSIGEAKARRAKKEMVEAILRLVISIAKKYTNRGLQFLDL 337

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 338 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 372


>gi|229828460|ref|ZP_04454529.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
 gi|229793054|gb|EEP29168.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
          Length = 614

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 148/278 (53%), Positives = 208/278 (74%), Gaps = 1/278 (0%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           + I  +R EI+S    +   +      + +++        AK+++ EANLRLV+S+AK+Y
Sbjct: 338 EQIEILREEIRS-GDLSEEDMMNLEAQIKILKNDSAVGERAKQKLAEANLRLVVSIAKRY 396

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPV
Sbjct: 397 VGRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPV 456

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K++R +R++  ++ REP+PEEIA+++    + VR++LKI++EP+SLETPIG+E
Sbjct: 457 HMVETINKLIRVSRQLLQELGREPSPEEIAREMETTPDRVREILKISQEPVSLETPIGEE 516

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + SHLGDFI+D+NA  P ++A    L+E    VL +LT RE +VL +RFG+      TLE
Sbjct: 517 EDSHLGDFIQDENAPVPAEAATFTLLKEQLNEVLDTLTERERKVLILRFGLEDGRGRTLE 576

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 577 EVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 614



 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/202 (20%), Positives = 79/202 (39%), Gaps = 18/202 (8%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQ 62
             K   D   E E  + +    +S      ++ L + ++  +   EL    P    + ++
Sbjct: 185 SPKAEEDKTGEQESGEVTAAEMYSR--LGDLVDLGKSKKNILDYAELEEAFPEFRENEDK 242

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS----TD 118
           M+     L   G++V+  DD + +   +  +D                     +     D
Sbjct: 243 MDIIQDYLEQSGVDVLKMDDDDLDIDDDLLMDEDEDEDEDKEPEVDIAALTASTDAVNID 302

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ E E+ +A+++E G               + + I R+E+  G 
Sbjct: 303 DPVRMYLKEIGKVHLLTAEEEVDLAQKMEKGLK-----------ADEQIEILREEIRSGD 351

Query: 179 TLLREIIDLEACIGPESKGGFF 200
               ++++LEA I         
Sbjct: 352 LSEEDMMNLEAQIKILKNDSAV 373


>gi|218288616|ref|ZP_03492893.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258511944|ref|YP_003185378.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|218241273|gb|EED08448.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257478670|gb|ACV58989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 368

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGRVPLLSAQEEIELAKRIEQ---GDEEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA ++ +  E VR++ KI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLIRVSRQLLQELGREPTPEEIAAEMDLTPEKVREIQKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 276 GDFIPDDEAPAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 368



 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 77/349 (22%), Positives = 130/349 (37%), Gaps = 35/349 (10%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ E  D D  +      ++ +++I+L +++G +T EE++  L   ++ ++ M+D    L
Sbjct: 4   TNDEIRDEDQGITL---QEAKQQLIELGKKQGSLTYEEISDRLSSFDMDADAMDDFFEQL 60

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           + +GI+VV+  D E                +    L            DPVRMYL+E+G 
Sbjct: 61  AELGIDVVNERDEE------------GGREDDDYDLDDLSVPPGVKISDPVRMYLKEIGR 108

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS + EI +AKRIE G       L E+ L     I  R  +  G   L  I      
Sbjct: 109 VPLLSAQEEIELAKRIEQGDEEAKQRLAEANLRLVVSIAKRY-VGRGMLFLDLI------ 161

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   Y+K    S        Q     I   A+  +     V++  + 
Sbjct: 162 --QEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 219

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                + L E   +      A E  L P+ +  + +IA                 +    
Sbjct: 220 IRVSRQLLQELGREPTPEEIAAEMDLTPEKVREIQKIA-----------QEPVSLETPIG 268

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 L + +         + +  +LL EQL D+   +   E  +LRL
Sbjct: 269 EEDDSHLGDFIPDDEAPAPADAAAYELLKEQLEDVLDTLTEREENVLRL 317


>gi|225163701|ref|ZP_03726004.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224801692|gb|EEG19985.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 631

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 153/276 (55%), Positives = 201/276 (72%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             I   ++ I VE  I  ++   +V        EA  AK EMVEANLRLVIS+AKKYTNR
Sbjct: 295 KAIHARLREIEVEQRIEPAQLIEVVRKTNVHIREAHQAKTEMVEANLRLVISIAKKYTNR 354

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 355 GLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 414

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + ++KV++  +++  +   EPTPEE+A ++ +PVE V++++K+ ++PISL++P+GD D +
Sbjct: 415 ETLNKVMQVQKQLLQEFGHEPTPEEVADEMNLPVERVQQIMKMAQQPISLQSPVGDGDDT 474

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             GDFIEDK+A +P D    + LRE    VL SLT RE +VL +RFG+      TLEEVG
Sbjct: 475 SFGDFIEDKSAENPYDMTAYSLLREKIIDVLDSLTERERKVLSLRFGLVDGYSRTLEEVG 534

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           KQF VTRERIRQIEAKA+RK++HP+R ++L  F D 
Sbjct: 535 KQFKVTRERIRQIEAKALRKMRHPTRIRQLHGFFDA 570



 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 76/428 (17%), Positives = 174/428 (40%), Gaps = 25/428 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
             + ++ +D    L     ++  + +I+L++++GY+T +++N  LP    + E++++ ++
Sbjct: 19  EAAIAQTQDGGVDLPAGGINEKIRNLIRLSKEQGYLTFDDINEALPESVENQEEIDNVLS 78

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           +L N+ I +++ D +ED +  ++  +   S ++++  L           DDPVRMYL++M
Sbjct: 79  ILQNLEIEILEPDQVEDYKQRQEEQEEEESRTSNNDIL-----------DDPVRMYLKQM 127

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G + LL+RE E+ I+KRIE   +    +L E+ +  + +     +L         I+  +
Sbjct: 128 GQVPLLTREQEVEISKRIETAESKAQEALFEASIVGRHIATLGAKLLTREERFDRIVIDK 187

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                ES           + +  E  S   E       E D +      K   + + S  
Sbjct: 188 RIESRESYFKALPKLVETTQKNEESVSDSWEEFQKARNEADRKKILSKHKKRETTLRSNF 247

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
                  +  +E  + +   LS +E      +   LD       +  +  D      +  
Sbjct: 248 SKFFFKLKVYEEWLETNRPVLSEIE-----LLHAQLDRAKTPKTKKDAAIDTKAIHARLR 302

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           +  V+ ++   +L+++V   +++      + E     ++ +  N   ++ +A+ Y  +  
Sbjct: 303 EIEVEQRIEPAQLIEVVRKTNVH------IREAHQAKTEMVEANLRLVISIAKKYTNRGL 356

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEF 427
            FL+  Q  E +   +   + F       F       I + I   I   +    I +   
Sbjct: 357 SFLDLIQ--EGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 414

Query: 428 RHIVSMVR 435
             +  +++
Sbjct: 415 ETLNKVMQ 422


>gi|225018167|ref|ZP_03707359.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
 gi|224949164|gb|EEG30373.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
          Length = 372

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 149/270 (55%), Positives = 202/270 (74%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++  E    + + +K       A+K + EANLRLV+S+AK+Y  RG+QFL
Sbjct: 106 YLKEIGKVPLLTAEEE---IDLAQKMSAGDPYARKRLSEANLRLVVSIAKRYVGRGMQFL 162

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 163 DLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 222

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V + + ++ +K   E + EEIA++L MPV+ VR+++++++EP+SLETPIG+E+ SHL DF
Sbjct: 223 VKKVSSQLLHKNGHEASAEEIAEELDMPVDKVREIMRVSQEPVSLETPIGEEEDSHLSDF 282

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A +P ++A    LRE    VL +LT REE+VLR+RFG+      TLEEVGK+F V
Sbjct: 283 IPDDDAPAPAEAASHTLLREQLGDVLGTLTEREEKVLRLRFGLEDGRSRTLEEVGKEFNV 342

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 343 TRERIRQIEAKALRKLRHPSRSKKLKDFLD 372



 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 40/183 (21%), Positives = 73/183 (39%), Gaps = 16/183 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++++  +++G +T +E+   L   +   +Q+E       +             E+  +D 
Sbjct: 22  ELLERGKRQGKLTSQEIAVALEELDFDVDQVEKLYESFEHFN-------IEVVEDIDDDI 74

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
               +   N +  L+    +   + DDPV++YL+E+G + LL+ E EI +A+++ AG   
Sbjct: 75  DLDFALEVNLNQDLEATIAAEGINIDDPVKVYLKEIGKVPLLTAEEEIDLAQKMSAGDPY 134

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
               L E+ L     I  R  +  G   L  I         E   G     E   Y K  
Sbjct: 135 ARKRLSEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNLGLIKAVEKFDYTKGF 185

Query: 213 DSS 215
             S
Sbjct: 186 KFS 188


>gi|283769573|ref|ZP_06342469.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
 gi|283103841|gb|EFC05227.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
          Length = 413

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 149/274 (54%), Positives = 197/274 (71%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +  SE   I   + +       A+  ++ +NLRLV+S+AKKY  RG+
Sbjct: 142 VKMYLKEIGRVPLLKASEEIEIAKKIEQ---GDEEARNVLISSNLRLVVSIAKKYVGRGM 198

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 199 QFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 258

Query: 529 IHKVVRTARRMSNKIKREPTPEEI-AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R +  ++ REPTPEEI A    +  + VR++ KI  +P+SLETPIG+ED SH
Sbjct: 259 INKLTRVERSLVQELSREPTPEEISACLEGISADKVREIKKIALDPVSLETPIGEEDDSH 318

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK+A+SP   A    L++    VL+ LT REE+VLR+RFG+      TLEEVG+
Sbjct: 319 LGDFIEDKDALSPDQYASNQLLKDEINDVLSGLTEREEKVLRLRFGLYDGRTRTLEEVGR 378

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHP+RSK+L+ F D
Sbjct: 379 EFNVTRERIRQIEAKALRKLKHPNRSKRLKDFFD 412



 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/217 (21%), Positives = 78/217 (35%), Gaps = 29/217 (13%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
             ++     DD  ++     ++ G +  +++ A L   ++S ++M++     +   + V 
Sbjct: 20  GKNVTLKTLDDLKEEYKVAYQKDGGLLQKDVMASLEHLDLSDDEMDELWDWFNEQKMEVT 79

Query: 79  DGDDLEDEEGSEDSLDLAS---------SASNSSVFLQKRKDSADRSTD----------- 118
             ++LE  E  ED   +              + S   ++ KD      +           
Sbjct: 80  SEEELETFEEEEDQDLVVDRDEDSDEDLDDLDKSDDEKEDKDHYFDHVNAIHGDISATSG 139

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D V+MYL+E+G + LL    EI IAK+IE G       L  S L     I  +  +  G 
Sbjct: 140 DSVKMYLKEIGRVPLLKASEEIEIAKKIEQGDEEARNVLISSNLRLVVSIAKKY-VGRGM 198

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
             L  I         E   G     E   Y K    S
Sbjct: 199 QFLDLI--------QEGNMGLVKAVEKFDYTKGFKFS 227


>gi|317056182|ref|YP_004104649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Ruminococcus albus
           7]
 gi|315448451|gb|ADU22015.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ruminococcus
           albus 7]
          Length = 366

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 147/271 (54%), Positives = 204/271 (75%), Gaps = 1/271 (0%)

Query: 412 EIKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +K I     ++  E   +  M+    + EA  A+K + EANLRLV+S+AK+Y  RG+ F
Sbjct: 96  YLKEIGRVPLLTSEEEIQLAEMMSGDNDREAVKARKRLAEANLRLVVSIAKRYVGRGMSF 155

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I 
Sbjct: 156 LDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIT 215

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           KV + + ++ +K   +P+PEEIA++L M VE VR++++I ++P+SLETPIG+E+ SHLGD
Sbjct: 216 KVKKVSSQLLHKNGHDPSPEEIAEELDMSVERVREIMRIAQDPVSLETPIGEEEDSHLGD 275

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FI D +A +P ++A    L+E   +VL++LT REE+VLR+RFG+      TLEEVG++F 
Sbjct: 276 FIPDDDAPAPAEAASLVLLKEQIDQVLSTLTEREEKVLRLRFGLQDGRSRTLEEVGQEFK 335

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+HP+RS K+R +LD
Sbjct: 336 VTRERIRQIEAKALRKLRHPNRSNKVRDYLD 366



 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 77/189 (40%), Gaps = 20/189 (10%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           + +++  +Q G +T +E+   L       EQM++     +++ I ++      D+   +D
Sbjct: 9   ENLMEHGKQTGKLTTKEITDALEKLNFDVEQMDNFYDTCNSLNIEII------DDVVVDD 62

Query: 92  SLDLASSASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAKRI---- 146
           +LD  +              S D  + DDPV++YL+E+G + LL+ E EI +A+ +    
Sbjct: 63  TLDFVNPDDELDQDDVDIALSTDGIAIDDPVKIYLKEIGRVPLLTSEEEIQLAEMMSGDN 122

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           +         L E+ L     I  R  +  G + L  I         E   G     E  
Sbjct: 123 DREAVKARKRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------QEGNMGLIKAVEKF 173

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 174 DYKKGFKFS 182


>gi|16752284|ref|NP_445653.1| RNA polymerase sigma factor [Chlamydophila pneumoniae AR39]
 gi|7190028|gb|AAF38883.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
          Length = 591

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 196/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 309 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 368

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 369 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 428

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED  
Sbjct: 429 KKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGSESSFGDFLEDTA 488

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 489 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERI 548

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 549 RQIEAKALRKMRHPIRSKQLRAFLD 573



 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 87/181 (48%), Gaps = 10/181 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           ++++  + +    + S    ++++ LA+++G++T EE+N  LP    + EQ++  +  L+
Sbjct: 23  NTQNSQATEVSSEEESQKKLEELVALAKEQGFITYEEINEILPMSFDTPEQIDQVLIFLT 82

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            M I V++  D+E                  +  L+      + + DDPVRMYL+EMG++
Sbjct: 83  GMDIQVLNQIDVE----------RQKEKKKEAKELEGLARRTEGTPDDPVRMYLKEMGTV 132

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+RE E+ I+KRIE  +  +   +     + +  I     L  G     +II  +   
Sbjct: 133 PLLTREEEVEISKRIEKAQVQIERIILRFRYSAKEAISIAHYLISGKERFDKIISEKEVE 192

Query: 192 G 192
            
Sbjct: 193 D 193


>gi|302389497|ref|YP_003825318.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
 gi|302200125|gb|ADL07695.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
          Length = 367

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + K       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 98  VRMYLKEIGKIPLLTPEEEIELAKRIEK---GDKEAKRRLAEANLRLVVSIAKRYVGRGM 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 155 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+PTPEEIA+++ +PVE VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 215 INKLIRVSRQLLQELGRDPTPEEIAEEMELPVEKVREIMKIAQEPVSLETPIGEEEDSHL 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D+ A +P D+A    LRE    VL +LTPREE+VLR+RFG+      TLEEVG+ 
Sbjct: 275 GDFIPDEEAQAPADAAAYRLLREQLEDVLETLTPREEKVLRLRFGLDDGKPRTLEEVGQV 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 335 FGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 367



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 73/157 (46%), Gaps = 12/157 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPP-DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            + K++I+  ++ G +T +E+   L   +++ +EQ++       +MGI +++  D   E 
Sbjct: 15  KAVKELIEKGKKTGVLTYKEIMETLGDIEDLDAEQIDKIYESFEDMGIEIINDADDIPES 74

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E+  ++                    + DDPVRMYL+E+G I LL+ E EI +AKRIE
Sbjct: 75  LLEEISEVE----------LDLSIPEGVAIDDPVRMYLKEIGKIPLLTPEEEIELAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 125 KGDKEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 160


>gi|318066945|emb|CBY89087.1| RNA polymerase sigma70 factor [Halomonas halocynthiae]
          Length = 368

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 124/395 (31%), Positives = 180/395 (45%), Gaps = 47/395 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG+++LL+REGEI IAKRIE G   +MA+L   P   ++++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGIREVMAALAYVPGAVESILEAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+                 E    E E     +  GD +   
Sbjct: 79  QDEEAPGRLTDLFSGFIDPDEGT----------PGVAEADESELEISADDDIVGDDDDGE 128

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
               D+       PE        + E            E +L   V+ A           
Sbjct: 129 GDEDDEAPAGGPDPEETRARFEQIRE------------ELKLTQAVIEA----------- 165

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                         + S + +V  E+L +L   + L     + LV Q+    +++   E 
Sbjct: 166 ------------HGRHSKEAQVELERLAELFSPIKLVPKHFERLVGQIRISVEQVRLQER 213

Query: 355 ELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +L++  +   + R  F++   G E    W+           +  +  + D I + + ++
Sbjct: 214 AVLQICTKKARVPRRTFIKAFPGNEARQEWLDEFVAENSRYAERLLPFKAD-IQRAQRKV 272

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                   + + E + I   +  GE ++  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 273 AFEEDMVSLPVGEIKEINRRLSIGEAKSRRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 332

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           IQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 333 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|197301814|ref|ZP_03166884.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
 gi|197299254|gb|EDY33784.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
          Length = 372

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGKVPLLSAEREIELAQRME---EGDEEAKKELAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 220 INKLIRVSRQLLQELGREPLPEEIAKEMDMPVERVREILKISQEPVSLETPIGEEEDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 280 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGRE 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 340 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 372



 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 75/157 (47%), Gaps = 2/157 (1%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +  K+++ L +++   + ++E+N F    E++++QME     L    I+V+   +  +++
Sbjct: 10  ERLKELVALGKKKKSILDVQEINDFFNDMELNADQMEKVFDYLEANNIDVLRISEDTEDD 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D   + S   +  V           S +DPVRMYL+E+G + LLS E EI +A+R+E
Sbjct: 70  VDVDIDIIISDEDDVDVENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAQRME 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 130 EGDEEAKKELAEANLRLVVSIAKRY-VGRGMLFLDLI 165


>gi|310659059|ref|YP_003936780.1| RNA polymerase sigma factor rpod [Clostridium sticklandii DSM 519]
 gi|308825837|emb|CBH21875.1| RNA polymerase sigma factor RpoD [Clostridium sticklandii]
          Length = 376

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 160/386 (41%), Positives = 238/386 (61%), Gaps = 15/386 (3%)

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
             +         +K      +  E++ + +  + L++ +I+ + +    +   I+     
Sbjct: 6   KQEKKIAVKSLIDKGKKDGSLTYEQIGEALSEMELDKEQIENIYDTFAQLGIDILDEN-- 63

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
              +     I    F +       +P   +  +D    +    +   V     +R  +K 
Sbjct: 64  ---IKDDTVIFNKEFNK-------NPDAETEDEDEDASKLDLSIPKGVSIDDPVRMYLKE 113

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I     +S  E   +   +        IAKK++VEANLRLV+S+AK+Y  RG+ FLDLIQ
Sbjct: 114 IGKIPLLSAEEEIDLAEKM---GYGDEIAKKKLVEANLRLVVSIAKRYVGRGMLFLDLIQ 170

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R 
Sbjct: 171 EGNLGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRV 230

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R++  +  R+P PEE+AK++ MP E +R+++KI +EP+SLETPIG+E+ SHLGDFI D 
Sbjct: 231 HRQLLQEYGRDPKPEELAKEMDMPEEKIREIMKIAQEPVSLETPIGEEEDSHLGDFIPDD 290

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +A +P ++A  + L+E    VL +L  RE++VL++RFG+      TLEEVGK+F VTRER
Sbjct: 291 DAPAPAEAAAYSLLKEQLEDVLCTLNEREQKVLKLRFGLEDGRARTLEEVGKEFDVTRER 350

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 351 IRQIEAKALRKLRHPSRSKKLKDYLD 376



 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 43/159 (27%), Positives = 73/159 (45%), Gaps = 5/159 (3%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED---- 85
           + K +I   ++ G +T E++   L   E+  EQ+E+     + +GI+++D +  +D    
Sbjct: 12  AVKSLIDKGKKDGSLTYEQIGEALSEMELDKEQIENIYDTFAQLGIDILDENIKDDTVIF 71

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            +    + D  +   +              S DDPVRMYL+E+G I LLS E EI +A++
Sbjct: 72  NKEFNKNPDAETEDEDEDASKLDLSIPKGVSIDDPVRMYLKEIGKIPLLSAEEEIDLAEK 131

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  G  +    L E+ L     I  R  +  G   L  I
Sbjct: 132 MGYGDEIAKKKLVEANLRLVVSIAKRY-VGRGMLFLDLI 169


>gi|255327076|ref|ZP_05368152.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
 gi|255296293|gb|EET75634.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
          Length = 457

 Score =  225 bits (573), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 134/254 (52%), Positives = 180/254 (70%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +   +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 204 KDLKKALRWVIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 263

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 264 FDYSKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 323

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+ K+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 324 TPEELGKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFT 383

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL
Sbjct: 384 LLQEQLHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKL 443

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 444 RHPSRSQVLRDYLD 457



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           +N       ++     +T DPV+ YL+++G + LL+ + E+ +A RIEAG       L E
Sbjct: 140 ANDDDDAPAQRVVTPGATADPVKDYLKQIGKVSLLNAQQEVDLAMRIEAGLY-AEHKLAE 198

Query: 160 SP 161
           +P
Sbjct: 199 NP 200


>gi|225570457|ref|ZP_03779482.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
 gi|225160654|gb|EEG73273.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
          Length = 370

 Score =  225 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLTADEEVDLAKRM---ADGDEEAKKRLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA +L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPTPEEIAAELDMPVERVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 278 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/158 (26%), Positives = 71/158 (44%), Gaps = 4/158 (2%)

Query: 28  DDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  K+++ L +++   + ++E+N F    E+ SEQME     L    I+V+     +D+
Sbjct: 9   EEKLKELVSLGKKKKSILELQEINDFFSDMELESEQMERVFEHLEANNIDVLRISGDDDD 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                   + S      V           S +DPVRMYL+E+G + LL+ + E+ +AKR+
Sbjct: 69  IDDA--DIIISEEDEVDVEKIDLSVPDGISIEDPVRMYLKEIGKVPLLTADEEVDLAKRM 126

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             G       L E+ L     I  R  +  G   L  I
Sbjct: 127 ADGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|110798581|ref|YP_696687.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
 gi|15186722|dbj|BAB62883.1| RNA polymerase major sigma factor [Clostridium perfringens]
 gi|110673228|gb|ABG82215.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
          Length = 366

 Score =  225 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +      ++ AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 97  VRMYLKEIGKVQLLSSEDEIELAKKIE---EGSNYAKKKLAEANLRLVVSIAKRYVGRGM 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 154 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEE++K++ MPV+ VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 214 INKLIRIQRQLVQELGRDPLPEELSKQMDMPVDKVREILKIAQEPVSLETPIGEEEDSHL 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 274 GDFIPDDDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 334 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 366



 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 42/154 (27%), Positives = 64/154 (41%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K++I   ++ G +T +E+   L   E++ EQ+E    +L +MG                
Sbjct: 23  VKRLIDKGKKSGSLTYKEIMDELDEIELNPEQIEKIYEVLESMG---------------- 66

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +                      + DDPVRMYL+E+G ++LLS E EI +AK+IE G 
Sbjct: 67  IEVISEIEQEEEEEEELDLSVPEGIAIDDPVRMYLKEIGKVQLLSSEDEIELAKKIEEGS 126

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 127 NYAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 159


>gi|299144149|ref|ZP_07037229.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518634|gb|EFI42373.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 383

 Score =  225 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   I   +         AK+E+ EANLRLV+S+AK+Y  RG+
Sbjct: 114 VRMYLKEIGKIPLLTGDEEIDIAQRME---VGDEDAKQELAEANLRLVVSIAKRYVGRGM 170

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 171 SFLDLIQEGNLGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 230

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++  ++ R+P PEEI K++ + VE VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 231 INKLVRVQRQLVQELGRDPLPEEIGKEMNLEVEKVREIQKIAQEPVSLETPIGEEEDSHL 290

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D   +SP D+A    L+E    VL +LT RE++VL +RFG+      TLEEVGK+
Sbjct: 291 GDFIPDDEILSPSDAATFTLLKEQLEDVLQTLTDREKKVLTLRFGLDDGRARTLEEVGKE 350

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 351 FDVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 383



 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/180 (26%), Positives = 80/180 (44%), Gaps = 9/180 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           +D+DS+ ED +        D     +    +++G +T +E+   L    + S+++E    
Sbjct: 2   QDTDSKIEDGN----LQSKDSIIINLKNNGKKKGNLTYDEIINALEEIPMESDEIELLYQ 57

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLA----SSASNSSVFLQKRKDSADRSTDDPVRMY 124
                GI ++  D ++D+   +D LD             +  +        S DDPVRMY
Sbjct: 58  DFEKSGIEILTDDKIDDDILDDDKLDEDILDVRKDDEDDLSKEDLSVPKGISVDDPVRMY 117

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L+E+G I LL+ + EI IA+R+E G       L E+ L     I  R  +  G + L  I
Sbjct: 118 LKEIGKIPLLTGDEEIDIAQRMEVGDEDAKQELAEANLRLVVSIAKRY-VGRGMSFLDLI 176


>gi|581612|emb|CAA37172.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 396

 Score =  225 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 127/296 (42%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     +S +E   +   V                         +      +AK
Sbjct: 101 RQYLREIGRIPLLSAAEEVDLARRVEAGLFAEEKLRCSPGLDDRLALDLDRLVVLGRLAK 160

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 161 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 220

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E V +
Sbjct: 221 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDLAPERVGE 280

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL++L  RE 
Sbjct: 281 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGERER 340

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+   VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 341 KVVQLRYGLADGRPRTLEEIGRLGGVTRERIRQIESKTLSKLRDHAYADQLRGYLD 396



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +  +   + D  R YLRE+G I LLS   E+ +A+R+EAG 
Sbjct: 89  RTESGGPSSDLFRQYLREIGRIPLLSAAEEVDLARRVEAGL 129


>gi|330836587|ref|YP_004411228.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
 gi|329748490|gb|AEC01846.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
          Length = 685

 Score =  225 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 160/431 (37%), Positives = 237/431 (54%), Gaps = 2/431 (0%)

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            E D  +L          L + + +        L +I    +   +L+   ++   D   
Sbjct: 256 DEADPESLPLMTSKDLKDLISEQKRYAQFYKDGLKDIQGAMKAYLALKKEKIDTSGDSIF 315

Query: 311 SVK-CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
           + +     +  L+K +  + L    I    E+  D  ++I   + +   L    G+    
Sbjct: 316 TDENLVKKRHALMKKLSLIELQPEEITAFTEKFMDAERKISSLQAKKSSLEAQLGVSSTR 375

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
            L +  GR+L         +       + +  ++  I     ++  I  +   +      
Sbjct: 376 ELRQ-MGRDLVTPAKRVLLEEKFAMSADVIKEKIRDIQLTEKKLHEIESDFEENTQVILE 434

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
               +++G    + AK  + +ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF+
Sbjct: 435 HAKEIKRGRIMMTAAKDRLTQANLRLVVSIAKKYTNRGLPFNDLVQEGNIGLIKAVEKFE 494

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +   +KFSTYA WW++QAITR+I+DQ  TIR+PVHM ++I+KV +    +   + R PT 
Sbjct: 495 FRKNFKFSTYATWWIRQAITRAISDQGRTIRVPVHMIEQINKVKKEENALIQSLGRNPTD 554

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEIAKKL  P E V+ V  + +EPISLETP+G+E+ S L DFIEDK+A +P        L
Sbjct: 555 EEIAKKLGWPEEKVKGVKNVAREPISLETPVGEEEDSLLSDFIEDKDAENPASQTSYMLL 614

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E   + LA+L PRE+ VL+MRFG+      TLEEVG  F VTRERIRQIEAK++R+++H
Sbjct: 615 QEQLQKELATLPPREKDVLKMRFGLDDGFALTLEEVGLSFKVTRERIRQIEAKSLRRMRH 674

Query: 670 PSRSKKLRSFL 680
           P RS+KLR FL
Sbjct: 675 PKRSRKLRDFL 685


>gi|290960625|ref|YP_003491807.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
 gi|260650151|emb|CBG73267.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
          Length = 387

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 128/296 (43%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++  E   +   V                         +      +AK
Sbjct: 92  RQYLREIGRIPLLTAVEEVELARRVEAGLFAEERLGTASGLDTRLALDLDRLVVMGRMAK 151

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 152 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 211

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +  E V +
Sbjct: 212 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPDEVAAHLDLAPERVSE 271

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 272 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 331

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 332 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 387



 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 42/96 (43%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +++  A  +    V L + +      + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 61  EAVGPADPSEPEPVELPRVRPDTSGPSSDLFRQYLREIGRIPLLTAVEEVELARRVEAGL 120

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
                    S L  +  +     +  G    R +I+
Sbjct: 121 FAEERLGTASGLDTRLALDLDRLVVMGRMAKRRLIE 156


>gi|116670178|ref|YP_831111.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116610287|gb|ABK03011.1| RNA polymerase, sigma 70 subunit, RpoD [Arthrobacter sp. FB24]
          Length = 441

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 189 KLKRELEFVIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 248

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 249 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 308

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 309 PEELALELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 368

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 369 LQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 428

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 429 HPSRSQVLRDYLD 441



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 79  DGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           D  +L +EE +  +   A+      +         ++  +  +T DPV+ YL+++G + L
Sbjct: 97  DPSELTEEEAASKTGAAATGTGFVYSDADDDDAPVQQVMSAGATADPVKDYLKQIGKVAL 156

Query: 134 LSREGEIAIAKRIEAGR 150
           L+ E E+ +A RIEAG 
Sbjct: 157 LNAEQEVDLALRIEAGL 173


>gi|318066981|emb|CBY89105.1| RNA polymerase sigma70 factor [Halotalea alkalilenta]
          Length = 370

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 117/396 (29%), Positives = 184/396 (46%), Gaps = 47/396 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAFLPGAVDSILEAFDGT 78

Query: 175 NDGTT-LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
                  L ++             GF    EG       +       D+  +++ D +  
Sbjct: 79  QGEEGGRLSDLF-----------SGFIDPDEGVPGVAEVEEELNLSDDEGSDSDLDDDDE 127

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                DD +  +  P+      R  ++  + +    +A+E+                   
Sbjct: 128 DGEDGDDSTTNEGGPDPELARVR-FEQIREQNELVKAAIEE------------------- 167

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
                            S +    + +L +L   + L     + L+ Q+     ++   E
Sbjct: 168 -------------HGPGSREAVAQQNRLAELFAPIKLVPKHFERLIGQIRLSVDQVRTQE 214

Query: 354 GELLRL-AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
             ++++  +   + R  F+    G E D  W          ++   ++     +L+ + +
Sbjct: 215 KLVMQIFVKRCKVARKTFISAFPGHETDLEWFDNFVA-THSKYAEALSDYRVEVLRAQRK 273

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I        ++++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLD
Sbjct: 274 IAFEQELVNLTVAELKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 333

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 334 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 369


>gi|304317433|ref|YP_003852578.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778935|gb|ADL69494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 357

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + K       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 88  VRMYLKEIGKIPLLSPDEEIELAKRIEK---GDEEAKKRLTEANLRLVVSIAKRYVGRGM 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 145 QFLDLIQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 204

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P PEEIAK++ M V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 205 INKLIRVSRQLLQELGRDPLPEEIAKEMDMSVDKVREIMKIAQEPVSLETPIGEEEDSHL 264

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 265 GDFIPDEDAPAPAEAAAFTMLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 324

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 325 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 48/160 (30%), Positives = 73/160 (45%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +S K++I   ++ G +T  E+   L   ++ +EQ+E        +GI +V  +  +
Sbjct: 4   EKVKNSIKELIDKGKKNGMLTYNEIMNSLEDIDMDAEQIEKVYDTFEKLGIEIVGEEPQQ 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E   E+ LDL                    + DDPVRMYL+E+G I LLS + EI +AK
Sbjct: 64  EELIPEEDLDLD------------LSIPEGINIDDPVRMYLKEIGKIPLLSPDEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 RIEKGDEEAKKRLTEANLRLVVSIAKRY-VGRGMQFLDLI 150


>gi|312143990|ref|YP_003995436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311904641|gb|ADQ15082.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 360

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V + ++ E     AK+++VEANLRLV+S+AKKY  RG+
Sbjct: 91  VRMYLKEIGKVDLLTADEE---VMLAKRMEQGDEWAKQQLVEANLRLVVSIAKKYVGRGM 147

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + 
Sbjct: 148 LFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVET 207

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  +  REP PEEI +++ +  E VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 208 INKLIRVSRQLLQEKGREPKPEEIGEEMDISAEKVREIMKIAQEPVSLETPIGEEEDSHL 267

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+++ +P  +A    L+E    VL +LT RE+RVL +RFGI      TLEEVGK+
Sbjct: 268 GDFIEDEDSPAPASAASYILLKEQLDGVLDTLTEREKRVLELRFGIEDGRPRTLEEVGKE 327

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 328 FGVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 360



 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 43/156 (27%), Positives = 70/156 (44%), Gaps = 14/156 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           D  + +I   ++ G +T EE+   L   ++ SE +E    + +   IN+V+    +DEE 
Sbjct: 12  DEVQALISRGKKEGELTYEEIMDALEDIDLDSEDIEQIYDLFNEKNINIVNEKLQQDEEE 71

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +DS                         DDPVRMYL+E+G ++LL+ + E+ +AKR+E 
Sbjct: 72  EDDS-------------GLDLSVPKGVGIDDPVRMYLKEIGKVDLLTADEEVMLAKRMEQ 118

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  +  +  G   L  I
Sbjct: 119 GDEWAKQQLVEANLRLVVSIAKKY-VGRGMLFLDLI 153


>gi|183982025|ref|YP_001850316.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
 gi|183175351|gb|ACC40461.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
          Length = 501

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 134/286 (46%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC---EASIAKKEMVEANLRL 455
              EV+   +I   + +  +   ++    +   +  R       +   AK  ++EANLRL
Sbjct: 216 AEEEVELAKRIEAGLYATQLMAELTDRGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 275

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 276 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 335

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 336 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 395

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 396 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 455

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 456 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 501



 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/72 (36%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 159 EEEIAEPSEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 218

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 219 EVELAKRIEAGL 230


>gi|163841160|ref|YP_001625565.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
 gi|1808669|emb|CAA71796.1| RNA polymerase [Renibacterium salmoninarum]
 gi|162954636|gb|ABY24151.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
          Length = 462

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +    +    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 210 KLNREYQWVIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNMGLIRAVEKF 269

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 270 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 329

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 330 PEELALELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 389

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 390 LQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 449

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 450 HPSRSQVLRDYLD 462



 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 48/101 (47%), Gaps = 10/101 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKR 109
           P  + S+E  +D           V D  + E  +  E++ + A S    +         +
Sbjct: 100 PKADDSAESADD------ESTEGVADSAETETADAPEEAEETAGSGFVYSDADDDDAPVQ 153

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +  +  +T DPV+ YL+++G + LL+ E E+ +A RIEAG 
Sbjct: 154 QVMSAGATADPVKDYLKQIGKVALLNAEQEVDLALRIEAGL 194


>gi|167755652|ref|ZP_02427779.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|237734400|ref|ZP_04564881.1| RNA polymerase sigma factor rpoD [Mollicutes bacterium D7]
 gi|167704591|gb|EDS19170.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|229382630|gb|EEO32721.1| RNA polymerase sigma factor rpoD [Coprobacillus sp. D7]
          Length = 417

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 154/274 (56%), Positives = 200/274 (72%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     ++  E   +   +         AKKE+  ANLRLV+S+AK+Y  RG+
Sbjct: 146 VKMYLKEIGRVELLTHDEEIDLAKKI---LEGDEDAKKELAAANLRLVVSIAKRYVGRGM 202

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 203 LFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 262

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++  ++ REP+ EEIA+K+  M  E VR++ KI+ EP+SLETPIG+ED SH
Sbjct: 263 INKLTRIQRQLIQELGREPSAEEIAEKMDGMTPEKVREIQKISLEPVSLETPIGEEDDSH 322

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED+ A+SP D A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 323 LGDFIEDEGAMSPDDYAANELLKDELNEVLLELTDREEKVLRLRFGLDDGRTRTLEEVGK 382

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHPSRSK+L+ FLD
Sbjct: 383 EFSVTRERIRQIEAKALRKLKHPSRSKRLKDFLD 416



 Score = 77.2 bits (188), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 43/217 (19%), Positives = 80/217 (36%), Gaps = 50/217 (23%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS 98
           ++ G +T ++++ +L   +++ +  E+ +  + N  I V+  D L+D +  ++ L     
Sbjct: 25  KEDGVLTQDQIDNYLSTYDLNDDLAEELLEFIGNNDI-VISDDGLDDLDVEDEVLLAGVP 83

Query: 99  AS----------------------------------------NSSVFLQKRKDSADRSTD 118
           A                                         ++   L + +  ++   +
Sbjct: 84  AELDDDLGLDDDLGLDGDTPDLDFAGDFDMMTGDTIHMYQVADADAELDQNQLGSNVKIN 143

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPV+MYL+E+G +ELL+ + EI +AK+I  G       L  + L     I  R  +  G 
Sbjct: 144 DPVKMYLKEIGRVELLTHDEEIDLAKKILEGDEDAKKELAAANLRLVVSIAKRY-VGRGM 202

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
             L  I         E   G     E   Y K    S
Sbjct: 203 LFLDLI--------QEGNMGLIKAVEKFDYTKGFKFS 231


>gi|313838731|gb|EFS76445.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL086PA1]
          Length = 511

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 214 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 273

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 334 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 393

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 394 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 453

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 454 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 511



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 165 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 224

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 225 ALLNAVEEVDLAKRIEAGL 243


>gi|269792833|ref|YP_003317737.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100468|gb|ACZ19455.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 387

 Score =  225 bits (572), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     +S  E    V + +  E     AK+++VEANLRLV+S+AKKY  RG+
Sbjct: 118 VRMYLREIGRIPLLSPEEE---VELAKGVEAGDKRAKEKLVEANLRLVVSIAKKYIGRGM 174

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 175 LFLDLIQEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 234

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R +  ++ REP+ EEIA+++ + V+ V ++ KI +EP+SLETPIG+E+ S L
Sbjct: 235 INKLIRISRVLVQRLGREPSAEEIAQEMGVTVDRVEEIQKIAQEPVSLETPIGEEEDSQL 294

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+EDK+  SP ++A    LRE    +L  LT RE+ VLR+RFG+     HTLEEVG++
Sbjct: 295 GDFLEDKDLPSPDEAAANQILREQLEEMLEDLTDREKEVLRLRFGLEDGHSHTLEEVGRR 354

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR FLD
Sbjct: 355 FGVTRERIRQIEAKALRKLRHPSRSKRLRDFLD 387



 Score =  109 bits (272), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 45/156 (28%), Positives = 78/156 (50%), Gaps = 7/156 (4%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           ++ + ++  AR++G+VT +++   LP + +S++ +++    L  +GI+VVD    +  + 
Sbjct: 32  ENVRDLLHDAREKGFVTYDDIEKHLPKELLSADVLDNLYYNLMELGIDVVDETKAQRGDS 91

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             + +    S ++         D  D    DPVRMYLRE+G I LLS E E+ +AK +EA
Sbjct: 92  IGEEVLPQISPADD------LGDLEDLPLSDPVRMYLREIGRIPLLSPEEEVELAKGVEA 145

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  +  +  G   L  I
Sbjct: 146 GDKRAKEKLVEANLRLVVSIAKKY-IGRGMLFLDLI 180


>gi|154488794|ref|ZP_02029643.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
 gi|154082931|gb|EDN81976.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
          Length = 478

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 195 AEQEVDLSERIEAGLYAQHLLDTESDKMDFKRR-RELKWAANDGKRAKDHLLEANLRLVV 253

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 254 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 313

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 314 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 373

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 374 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 433

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 434 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 477



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 167 KRRVIAAGATADPVKDYLKQIGRVNLLNAEQEVDLSERIEAGL 209


>gi|220927994|ref|YP_002504903.1| RNA polymerase sigma factor RpoD [Clostridium cellulolyticum H10]
 gi|219998322|gb|ACL74923.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulolyticum H10]
          Length = 359

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 160/374 (42%), Positives = 231/374 (61%), Gaps = 31/374 (8%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           ++   K  +  ++++     + L    I+ + E L  +   ++ +    +          
Sbjct: 17  DRGKQKGMLTYKEIMDAFEEIELEPEHIEKIYETLETMGVDVIGDIDSEMEEI------- 69

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                +    ELD                            +R  +K I     ++  E 
Sbjct: 70  -----QLTDEELDISVPEGVSIDDP----------------VRMYLKEIGKVPLLTADEE 108

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   +         AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EK
Sbjct: 109 IDLAHRME---NGDIEAKRRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEK 165

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP
Sbjct: 166 FDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP 225

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P+EIAK++ M V+ VR+++KI++EP+SLETPIG+E+ SHLGDFI D +A +P ++A   
Sbjct: 226 QPDEIAKEIGMSVDKVREIMKISQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFT 285

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 286 LLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKL 345

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 346 RHPSRSKKLKDYLD 359



 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 69/160 (43%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +Q+G +T +E+       E+  E +E     L  MG++V+   D E
Sbjct: 6   ESRKALLKELIDRGKQKGMLTYKEIMDAFEEIELEPEHIEKIYETLETMGVDVIGDIDSE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE      +L  S                 S DDPVRMYL+E+G + LL+ + EI +A 
Sbjct: 66  MEEIQLTDEELDISV------------PEGVSIDDPVRMYLKEIGKVPLLTADEEIDLAH 113

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 114 RMENGDIEAKRRLAEANLRLVVSIAKRY-VGRGMQFLDLI 152


>gi|221195781|ref|ZP_03568834.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
 gi|221184255|gb|EEE16649.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
          Length = 455

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 137/284 (48%), Positives = 205/284 (72%), Gaps = 5/284 (1%)

Query: 399 VACEVDSILKIRNEIKSIS-VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           +A ++++  +   +++     +  +S +E R ++      E     AK++++ ANLRLV+
Sbjct: 175 LAMKIEAGTEATQKLEDFEDEKIELSRAEQRRLMR----IEQVGLDAKQQLISANLRLVV 230

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 231 SIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAIADQAR 290

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K++R  R++   + R+PTPEEI  ++ M  + VR++ KI++EP+SLE
Sbjct: 291 TIRIPVHMVETINKLIRVQRQLLQDLGRDPTPEEIGAEMGMSPDRVREIQKISQEPVSLE 350

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+E+ S LGDFIED  A++P D+A  + LRE   +VL  L  RE +V++ RFG+   
Sbjct: 351 TPIGEEEDSQLGDFIEDSTAIAPPDAASDSMLREQLEQVLDGLADRERKVIKFRFGLEDG 410

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TLEEVG++F VTRERIRQIE+K + KL+HPSRS +L+ +++
Sbjct: 411 RPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSRLKDYME 454



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 37/77 (48%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +   +++   S      +    +S    ++   S    T DPVRMYL+E+G ++LL+   
Sbjct: 112 EARQVKEALRSVPKAKTSKPKRSSRARARRADTSTVMLTGDPVRMYLKEIGKVDLLTASE 171

Query: 139 EIAIAKRIEAGRAMMMA 155
           E+ +A +IEAG      
Sbjct: 172 EVNLAMKIEAGTEATQK 188


>gi|295394756|ref|ZP_06804971.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294972352|gb|EFG48212.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 473

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 139/297 (46%), Positives = 191/297 (64%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV------------------------RKGECEASIA 444
           +++ +K I     ++ +E   +   +                        +    +  IA
Sbjct: 177 VKDYLKQIGKVALLNAAEEVDLAKRIEAGMYAEHLVDEGKVTDARDLRDYKWIIHDGRIA 236

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW+
Sbjct: 237 KNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWI 296

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V 
Sbjct: 297 RQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPERVV 356

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +V K  +EPISL TP+G++  S  GD IED  AV P DS     L+E    VL +L+ RE
Sbjct: 357 EVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADSVSFTLLQEQLHSVLDTLSERE 416

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 417 AGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAKLRHPSRSQVLRDYLD 473



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
             D+V ++++E+      +           E+++           +         ++ + 
Sbjct: 113 ENDKVETDEVEELATTDES---TETRNSQEEEKDAQIKEAGGFVVSDADDEDQPAQQVAT 169

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +T DPV+ YL+++G + LL+   E+ +AKRIEAG
Sbjct: 170 AGATADPVKDYLKQIGKVALLNAAEEVDLAKRIEAG 205


>gi|269837239|ref|YP_003319467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786502|gb|ACZ38645.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 390

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 135/297 (45%), Positives = 195/297 (65%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK------------------------GECEASIA 444
           +R  ++ I   + +++ E   +   + +                         + +   A
Sbjct: 94  VRLYLQEIGETSLLTMEEEVWLAKRMERGKIAEERLANGDYASEAERAELLADKEDGEKA 153

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +++ANLRLV+SVAKKY  RGL FLDLIQEGNIGLMKA +KFD+  G+KFSTYA WW+
Sbjct: 154 RAHLIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATDKFDYKRGFKFSTYATWWI 213

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+I+DQS TIR+PVH+ + I++V +T++R+    +REPT EE+A+ + +P E VR
Sbjct: 214 RQAITRAISDQSRTIRLPVHVGETINRVKKTSQRLQQIFEREPTFEEVARAMDIPEEKVR 273

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +VL  ++ P+SLE P+G E  + LGDFIED     PL+ A Q  L+   +  L+ LT RE
Sbjct: 274 QVLDASRHPVSLEAPVGQEGDAFLGDFIEDDTMPPPLELASQELLKHQISDALSKLTERE 333

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            R++ +RFG+      TLEEVG++F +TRERIRQIEAKA+RKL+HP+ S +LR +LD
Sbjct: 334 RRIIILRFGLEDGQFRTLEEVGREFGITRERIRQIEAKALRKLRHPTYSHRLRGYLD 390



 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 39/119 (32%), Positives = 65/119 (54%), Gaps = 2/119 (1%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-DEEGSEDS 92
           +I   + RGY+  +E+ A  P  E + E +++  + L   GI V+D +    +   +  S
Sbjct: 5   LIARGKDRGYLLSDEIIAAFPNAEENVESLDEFYSTLVEQGIEVLDQEPTNGNGTTASLS 64

Query: 93  LDLASSASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              AS  + +S  +  R+D AD  S  D VR+YL+E+G   LL+ E E+ +AKR+E G+
Sbjct: 65  ERTASQPAPASPTIDTRQDVADAVSVSDSVRLYLQEIGETSLLTMEEEVWLAKRMERGK 123


>gi|261405623|ref|YP_003241864.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329925852|ref|ZP_08280581.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261282086|gb|ACX64057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328939598|gb|EGG35946.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 377

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   + + + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSADDEIELANRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA ++ + VE VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVSRQLLQELGREPSPEEIAAEMELSVEKVREIMKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 80/349 (22%), Positives = 138/349 (39%), Gaps = 25/349 (7%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + +     D   D   ++I+  ++R  ++ +++   L P +  +EQME+    L
Sbjct: 3   ANDQHTELETEFTLDQVKD---QLIEQGKKRSVLSYKDIMEKLSPFDQDTEQMEEFYEQL 59

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +++GI+VV+ +D  +E     S D  S  +    F            +DPVRMYL+E+G 
Sbjct: 60  ADLGIDVVNEND--EEGPHRQSGDSESHDNEDFGFDDDLSLPPGIKINDPVRMYLKEIGR 117

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS + EI +A RIE G       L E+ L     I  R  +  G   L  I      
Sbjct: 118 VPLLSADDEIELANRIEQGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI------ 170

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   Y+K    S        Q     I   A+  +     V++  + 
Sbjct: 171 --QEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 228

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                + L E   + +    A E +L    +  + EI ++ +E  SL+            
Sbjct: 229 IRVSRQLLQELGREPSPEEIAAEMEL---SVEKVREIMKIAQEPVSLETPIGEEDDSH-- 283

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 L + +         + +  +LL EQL D+   +   E  +LRL
Sbjct: 284 ------LGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRL 326


>gi|29840756|ref|NP_829862.1| RNA polymerase sigma factor [Chlamydophila caviae GPIC]
 gi|29835106|gb|AAP05740.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 572

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 146/277 (52%), Positives = 199/277 (71%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +   +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYT
Sbjct: 278 KLDAAKRRLHKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYT 337

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVH
Sbjct: 338 NRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH 397

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+  
Sbjct: 398 MIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGG 457

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RFG+      TLEE
Sbjct: 458 ESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEE 517

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 518 VGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E ++
Sbjct: 20  QKKLEELVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+      + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  I     L +G     +II  +    
Sbjct: 130 KAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVED 174


>gi|323704675|ref|ZP_08116253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323536137|gb|EGB25910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 357

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + K       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 88  VRMYLKEIGKIPLLSPDEEIELAKRIEK---GDEEAKKRLTEANLRLVVSIAKRYVGRGM 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 145 LFLDLIQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 204

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P PEEIAK++ M V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 205 INKLIRVSRQLLQELGRDPLPEEIAKEMDMSVDKVREIMKIAQEPVSLETPIGEEEDSHL 264

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 265 GDFIPDEDAPAPAEAAAFTMLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 324

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FLD
Sbjct: 325 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLD 357



 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 48/160 (30%), Positives = 73/160 (45%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +S K++I   ++ G +T  E+   L   ++ ++Q+E        +GI +V  +  +
Sbjct: 4   EKVKNSIKELIDKGKKNGMLTYNEIMNSLEDIDMDADQIEKVYDTFEKLGIEIVGEEPQQ 63

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE   E+ LDL                    + DDPVRMYL+E+G I LLS + EI +AK
Sbjct: 64  DELIPEEDLDLD------------LTIPEGINIDDPVRMYLKEIGKIPLLSPDEEIELAK 111

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 RIEKGDEEAKKRLTEANLRLVVSIAKRY-VGRGMLFLDLI 150


>gi|294790965|ref|ZP_06756123.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
 gi|294458862|gb|EFG27215.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
          Length = 588

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 132/250 (52%), Positives = 188/250 (75%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW 
Sbjct: 337 RELKWAANDGKKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWK 396

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E
Sbjct: 397 KGFKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDE 456

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L MPVE V++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E
Sbjct: 457 LARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQE 516

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             T+VL +L+PRE  V++MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPS
Sbjct: 517 QFTQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHPS 576

Query: 672 RSKKLRSFLD 681
           RS+ LR FLD
Sbjct: 577 RSQTLRDFLD 586



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/70 (25%), Positives = 37/70 (52%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             +E+     +  +     + +     KR+     +T DPV+ YL+++G + LL+ + E+
Sbjct: 248 QPVEEGAFVVNEKEDDDDENLTPAGNPKRRVVTTGATADPVKDYLKQIGRVNLLNAQQEV 307

Query: 141 AIAKRIEAGR 150
            +++RIEAG 
Sbjct: 308 DLSERIEAGL 317


>gi|294786990|ref|ZP_06752244.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
 gi|294485823|gb|EFG33457.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
          Length = 403

 Score =  224 bits (571), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 130/250 (52%), Positives = 187/250 (74%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW 
Sbjct: 152 RELKWAANDGRKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWK 211

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E
Sbjct: 212 KGFKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDE 271

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L MPVE V++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E
Sbjct: 272 LARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQE 331

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL +L+PRE  V++MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPS
Sbjct: 332 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHPS 391

Query: 672 RSKKLRSFLD 681
           RS+ L+ FLD
Sbjct: 392 RSQTLQDFLD 401



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 30/43 (69%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+     +T DPV+ YL+++G + LL+ + E+ +++RIEAG 
Sbjct: 90  KRRILTTGATSDPVKDYLKQIGRVNLLNAQQEVDLSERIEAGL 132


>gi|332975851|gb|EGK12729.1| DNA-directed RNA polymerase sigma subunit SigA [Desmospora sp.
           8437]
          Length = 372

 Score =  224 bits (571), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGRVPLLSAEEEVELAKRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA+++ +  E VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 220 INKLIRVSRQLLQELGREPSPEEIAEEMDLSPEKVREIMKIAQEPVSLETPIGEEDDSHL 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A +P D+A    L+E    VL +L+ REE VLR+RFG+      TLEEVGK 
Sbjct: 280 GDFIPDDDAQAPADAAAYELLKEQLKDVLDTLSDREENVLRLRFGLDDGRTRTLEEVGKV 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 340 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 372



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 73/349 (20%), Positives = 127/349 (36%), Gaps = 29/349 (8%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ ++ D +  L  +   D   ++  L ++RG +T +E+   +   +   +Q+++    L
Sbjct: 2   ANEQNVDVEHELTLEQVKD---RLTDLGKKRGVLTYKEITEKMSVFDQEPQQVDEFFEAL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +  GI V++ DD   E              N  +             +DPVRMYL+E+G 
Sbjct: 59  NEQGIEVLNEDDEPME------FSDEEEEENDELLEDDLSVPPGVKINDPVRMYLKEIGR 112

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS E E+ +AKRIE G       L E+ L     I  R  +  G   L  I      
Sbjct: 113 VPLLSAEEEVELAKRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI------ 165

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   ++K    S        Q     I   A+  +     V++  + 
Sbjct: 166 --QEGNMGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 223

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                + L E   + +    A E  L P+ +  + +IA                 +    
Sbjct: 224 IRVSRQLLQELGREPSPEEIAEEMDLSPEKVREIMKIA-----------QEPVSLETPIG 272

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 L + +         + +  +LL EQL D+   +   E  +LRL
Sbjct: 273 EEDDSHLGDFIPDDDAQAPADAAAYELLKEQLKDVLDTLSDREENVLRL 321


>gi|297194519|ref|ZP_06911917.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152294|gb|EFH31643.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 366

 Score =  224 bits (571), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 129/296 (43%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 71  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLANTPDPDSQLAVDLDRLVVMGRMAK 130

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 131 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 190

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E V +
Sbjct: 191 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVATHLELTSERVSE 250

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 251 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLDAVLSTLGERER 310

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 311 KVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 366



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
             R       T D  R YLRE+G I LL+   E+ +A+R+EAG       L  +P
Sbjct: 56  TGRGADTGGPTSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLF-AEEKLANTP 109


>gi|312128161|ref|YP_003993035.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312134621|ref|YP_004001959.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|312792985|ref|YP_004025908.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|311774672|gb|ADQ04159.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311778180|gb|ADQ07666.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312180125|gb|ADQ40295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 417

 Score =  224 bits (571), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 182/435 (41%), Positives = 272/435 (62%), Gaps = 21/435 (4%)

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +N EN+E     D++ +  T S  + ++  +++ +     +  +  +   +N   G+K 
Sbjct: 3   EQNMENNEVKNLNDQNINKETGSEQQQEVEKQLLASQKNENQEKQPAKKSTENKSEGKK- 61

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIK 366
             S  K  +++EK+ +L   +SL QS+  L   ++ +I  ++  +  ++  +  +   + 
Sbjct: 62  -MSEEKKSLIREKVREL---ISLGQSKGFLTYSEIQEILDKVELDASQVENIYDTLESMG 117

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            DV  +R    EL    +              +   +     +R  +K I     ++  E
Sbjct: 118 IDVVDDRVSEEELLKDDLEN------------LPEGIAIDDPVRMYLKEIGKIPLLTPEE 165

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              +   + +       AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA E
Sbjct: 166 EIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVE 222

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  RE
Sbjct: 223 KFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGRE 282

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  
Sbjct: 283 PTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAY 342

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + L+E    VL SL  RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RK
Sbjct: 343 SMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRK 402

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRSKKL+ FL+
Sbjct: 403 LRHPSRSKKLKDFLE 417



 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/183 (28%), Positives = 82/183 (44%), Gaps = 21/183 (11%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
                 N+    +  +   SL+     +  +++I L + +G++T  E+   L   E+ + 
Sbjct: 49  AKKSTENKSEGKKMSEEKKSLI----REKVRELISLGQSKGFLTYSEIQEILDKVELDAS 104

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q+E+    L +MGI+VVD    E+E   +D  +L                    + DDPV
Sbjct: 105 QVENIYDTLESMGIDVVDDRVSEEELLKDDLENL----------------PEGIAIDDPV 148

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L
Sbjct: 149 RMYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFL 207

Query: 182 REI 184
             I
Sbjct: 208 DLI 210


>gi|304439790|ref|ZP_07399688.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371777|gb|EFM25385.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 370

 Score =  224 bits (571), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   I   + K       A +E+ EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKIPLLTADEEVVIAKRMEK---GDREAARELAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 SFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++   + R+P+PEEIA+++ + VE VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 218 INKLVRIQRQLVQDLGRDPSPEEIAEEMNIDVERVREIQKIAQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D+   SP D+A    LRE    VL +LT RE++VL +RFG+    + TLEEVGK+
Sbjct: 278 GDFIPDEEIQSPQDAATFTLLREQLGDVLDTLTDREKKVLTLRFGLEDGRNRTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 370



 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 63/323 (19%), Positives = 119/323 (36%), Gaps = 51/323 (15%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           D +D       D     ++K  +++G +T EE+   L    + S++++         GI 
Sbjct: 6   DFEDEDQSMSKDSIVDSLMKTGKKKGNLTYEEIVDALDEIPMESDEIDSLYKEFEKKGIE 65

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           ++D +  +DE+  +D +DL+                   S DDPVRMYL+E+G I LL+ 
Sbjct: 66  LLDEEIGDDEDDDDDKIDLSKE---------DLSVPKGISVDDPVRMYLKEIGKIPLLTA 116

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDL 187
           + E+ IAKR+E G       L E+ L     I  R         D + +G   L + +D 
Sbjct: 117 DEEVVIAKRMEKGDREAARELAEANLRLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDK 176

Query: 188 EACIGP---------------------------------ESKGGFFHGTEGHSYQKREDS 214
                                                  E+                 D 
Sbjct: 177 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDP 236

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
           S E+  +++      +    K++++  S      E  ++   +   DE+  +   +A   
Sbjct: 237 SPEEIAEEMNIDVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIPDEEIQSPQDAATFT 296

Query: 275 QLRPKVMCALDEIAEVYRELRSL 297
            LR ++   LD + +  +++ +L
Sbjct: 297 LLREQLGDVLDTLTDREKKVLTL 319


>gi|331090835|ref|ZP_08339681.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399694|gb|EGG79356.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 370

 Score =  224 bits (571), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLSAEEEIELAKRM---AEGDEDAKKRLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA++L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPSPEEIAEELDMPVERVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 278 GDFIQDDNVPVPAEAAAATLLKEQLGEVLNTLTDREQKVLRLRFGMNDGRARTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 78/189 (41%), Gaps = 12/189 (6%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  K+++ L +++   + I+E+N      E+  EQME     L    I+V+  +   D+
Sbjct: 9   EEKLKELLALGKKKKNILEIQEINEIFADMELEPEQMEKVFEYLEGQNIDVLRINGDVDD 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +   +   + +      V           S +DPVRMYL+E+G + LLS E EI +AKR+
Sbjct: 69  DDDLEV--VITEEDEVDVEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELAKRM 126

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 127 AEGDEDAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEKF 177

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 178 DYEKGFKFS 186


>gi|307243281|ref|ZP_07525452.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
 gi|306493409|gb|EFM65391.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
          Length = 384

 Score =  224 bits (571), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +   E       +         AK+++VEANLRLV+S+AK+Y  RG+
Sbjct: 115 VRMYLKEIGKIPLLKPHEEVEYAKRM---AEGDEFAKQKLVEANLRLVVSIAKRYVGRGM 171

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 172 LFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 231

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P P+EIAK++ M  E VR+++KI ++P+SLETPIG+E+ SHL
Sbjct: 232 INKLIRVSRQLLQELGRDPKPDEIAKEMNMTEEKVREIMKIAQDPVSLETPIGEEEDSHL 291

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A  + L+E    VL +L  RE+ VL++RFG+      TLEEVGK+
Sbjct: 292 GDFIPDEDAPAPAEAAAYSLLKEQIEDVLNTLNDREQNVLKLRFGLEDGRARTLEEVGKE 351

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR FLD
Sbjct: 352 FDVTRERIRQIEAKALRKLRHPSRSKKLRDFLD 384



 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/169 (26%), Positives = 71/169 (42%), Gaps = 11/169 (6%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
            + ++ KK+ +  ++ G VT+ ++      +++     E+    L N+GI VVD  +++ 
Sbjct: 10  INKEAQKKLFEKGKKDGTVTLIDIMEAFQDNDMDKGVAENLYETLGNLGIEVVDDKEVKA 69

Query: 86  EEGSEDSLDLASSASN----------SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           +       DL   A +           S    +       S DDPVRMYL+E+G I LL 
Sbjct: 70  DIDLSKPDDLDIQAIDEEEDKEEIVAESSDPVEIAVPKGISIDDPVRMYLKEIGKIPLLK 129

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              E+  AKR+  G       L E+ L     I  R  +  G   L  I
Sbjct: 130 PHEEVEYAKRMAEGDEFAKQKLVEANLRLVVSIAKRY-VGRGMLFLDLI 177


>gi|222097738|ref|YP_002531795.1| RNA polymerase sigma factor rpod [Bacillus cereus Q1]
 gi|221241796|gb|ACM14506.1| RNA polymerase sigma-43 factor [Bacillus cereus Q1]
          Length = 375

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAGEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 47/176 (26%), Positives = 78/176 (44%), Gaps = 9/176 (5%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V      D +  E   +   + S     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-----GDNDNDEGPNNRQIAKSEEEFDLNDLSVPPGVKINDPVRMYLKEI 113

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|167758408|ref|ZP_02430535.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
 gi|167664305|gb|EDS08435.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
          Length = 371

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGKVPLLTAEEEVDLAKRM---ADGDEEAKKRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA +L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 219 INKLIRVSRQLLQELGREPTPEEIAAQLDMPVERVREILKISQEPVSLETPIGEEEDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 279 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 339 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 371



 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/158 (26%), Positives = 76/158 (48%), Gaps = 3/158 (1%)

Query: 28  DDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  K+++ L +++   + ++E+N F    E+ +EQME     L +  I+V+     ED+
Sbjct: 9   EEKLKELVSLGKKKKSILELQEINDFFSDMELEAEQMERVFEHLESNNIDVLRISGDEDD 68

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  +  + +A    +  +           S +DPVRMYL+E+G + LL+ E E+ +AKR+
Sbjct: 69  DIDDVDIVIAE-EDDVDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLTAEEEVDLAKRM 127

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             G       L E+ L     I  R  +  G   L  I
Sbjct: 128 ADGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 164


>gi|300741779|ref|ZP_07071800.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
 gi|300380964|gb|EFJ77526.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
          Length = 468

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 134/253 (52%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 216 KLKKELRWVIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 275

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 276 DYSKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 335

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+ K+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 336 PEELGKELDMAPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 395

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 396 LQEQLHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 455

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 456 HPSRSQVLRDYLD 468



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 30/51 (58%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++       ++     +T DPV+ YL+++G + LL+ + E+ +A RIEAG 
Sbjct: 151 ASDDDDAPAQRVVTPGATADPVKDYLKQIGKVSLLNAQQEVDLAMRIEAGL 201


>gi|23099399|ref|NP_692865.1| RNA polymerase sigma factor RpoD [Oceanobacillus iheyensis HTE831]
 gi|22777628|dbj|BAC13900.1| RNA polymerase sigma-43(-A) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 380

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S +E   + S +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVNLLSAAEEIDLASSIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + REPTPEEI +++ +  + VR +LKI +EP+SLETPIG+ED SHL
Sbjct: 228 INKLIRVQRSLLQDLGREPTPEEIGEEMELGPDKVRDILKIAQEPVSLETPIGEEDDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A+SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 288 GDFIEDQEAISPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 380



 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 75/187 (40%), Gaps = 17/187 (9%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            +  +++++ ++RG +  EE+   L   E+  EQM++    L   G++V+          
Sbjct: 27  QAKNRLLEIGKKRGSLAYEEVADGLSNFELEPEQMDEFYEYLEEQGVDVIGE-------- 78

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           SED  ++   A      L           +DPVRMYL+E+G + LLS   EI +A  IE 
Sbjct: 79  SEDDPEMQKIAKEEEFNLNDLSVPLGIKINDPVRMYLKEIGRVNLLSAAEEIDLASSIEE 138

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G       L E+ L     I  R  +  G   L  I         E   G     E   Y
Sbjct: 139 GDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDY 189

Query: 209 QKREDSS 215
           +K    S
Sbjct: 190 RKGFKFS 196


>gi|315655467|ref|ZP_07908366.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
 gi|315490122|gb|EFU79748.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
          Length = 553

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 134/260 (51%), Positives = 188/260 (72%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  + R +  +V+    +  +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL
Sbjct: 298 MTPKQIRELHYVVQ----DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGL 353

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M  
Sbjct: 354 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 413

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P 
Sbjct: 414 DLGREPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPA 473

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEA
Sbjct: 474 DAVSFMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEA 533

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HP+RS+ LR +L+
Sbjct: 534 KTMSKLRHPARSQSLRDYLN 553



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR-AMMMASL 157
           +         +K +   +T DPV+ YL+++G + LL+ E E+ ++KRIEAG  A  +   
Sbjct: 234 SEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKT 293

Query: 158 CESPLTFQALIIWRDELNDGTT 179
            +  +T + +      + DG  
Sbjct: 294 KQETMTPKQIRELHYVVQDGQM 315


>gi|58698250|ref|ZP_00373169.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535222|gb|EAL59302.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 270

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 157/265 (59%), Positives = 206/265 (77%), Gaps = 1/265 (0%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                 ++ EF+ ++  ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQE
Sbjct: 6   QHIQEDNVQEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQE 65

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA +KFD+  GYKFSTY  WWV+Q+ITR+I +QS  +RIPVHM + I K+ R  
Sbjct: 66  GNIGLMKAVDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRAL 125

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+M++++ REPT EE++ +L MP+E +RKV+KI ++P+SLE P G +D+S  GD IEDK 
Sbjct: 126 RKMTHEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKR 185

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRER 655
              P D+AI A+LR  TT VLA+LTP+EER+LRMRFG+G +  +HTLEEVGK F VTRER
Sbjct: 186 VSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRER 245

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIEAKA+RKLKHPSR++KLR F 
Sbjct: 246 IRQIEAKALRKLKHPSRARKLRGFF 270


>gi|254519856|ref|ZP_05131912.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
 gi|226913605|gb|EEH98806.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
          Length = 370

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 161/374 (43%), Positives = 236/374 (63%), Gaps = 33/374 (8%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           +K      +  ++++  V  + L+  +I+ + E L  +   ++                 
Sbjct: 30  DKGKKSGTLTYKEIMDEVEHIDLSPEQIEKIYEVLESMGIEVIG---------------- 73

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                       DP+     ++  + +        +D    +R  +K I     +S  E 
Sbjct: 74  ------------DPNEADEVEEELDLDLTIPEGIAIDD--PVRMYLKEIGKVPLLSSEEE 119

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             + + + +       AKK++ EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 120 IELANRIEQ---GDQRAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 176

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P
Sbjct: 177 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDP 236

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEI+K + +PV+ VR++ KI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A   
Sbjct: 237 FPEEISKVMDLPVDKVREIQKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPAEAAAFT 296

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 297 MLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKL 356

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 357 RHPSRSKKLKDYLD 370



 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/184 (28%), Positives = 80/184 (43%), Gaps = 21/184 (11%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M   K + +    E+ED +  +         K ++   ++ G +T +E+   +   ++S 
Sbjct: 1   MVDEKTKAKQGKKENEDKNSKMTI------VKNLLDKGKKSGTLTYKEIMDEVEHIDLSP 54

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+E    +L +MGI V+   +  DE   E  LDL                    + DDP
Sbjct: 55  EQIEKIYEVLESMGIEVIGDPNEADEVEEELDLDLTIPE--------------GIAIDDP 100

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G + LLS E EI +A RIE G       L E+ L     I  R  +  G   
Sbjct: 101 VRMYLKEIGKVPLLSSEEEIELANRIEQGDQRAKKKLAEANLRLVVSIAKRY-VGRGMLF 159

Query: 181 LREI 184
           L  I
Sbjct: 160 LDLI 163


>gi|222528719|ref|YP_002572601.1| RpoD subfamily RNA polymerase sigma-70 factor [Caldicellulosiruptor
           bescii DSM 6725]
 gi|222455566|gb|ACM59828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 417

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 148 VRMYLKEIGKIPLLTPEEEIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 204

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 205 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 264

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  +  REPTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 265 INKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHL 324

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+
Sbjct: 325 GDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGKE 384

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 385 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 417



 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 53/183 (28%), Positives = 82/183 (44%), Gaps = 20/183 (10%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           +  K     SD +    +   +     +  +++I L + +G++T  E+   L   E+ + 
Sbjct: 48  STKKSTESKSDGKKMSEEKKTLI---REKVRELISLGQSKGFLTYSEIQEILDKVELDAS 104

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q+E+    L +MGI+VVD    E+E   +D  +L                    + DDPV
Sbjct: 105 QVENIYDTLESMGIDVVDDRVSEEELLKDDLENL----------------PEGIAIDDPV 148

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L
Sbjct: 149 RMYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFL 207

Query: 182 REI 184
             I
Sbjct: 208 DLI 210


>gi|139436983|ref|ZP_01771143.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
 gi|133776630|gb|EBA40450.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
          Length = 454

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 143/285 (50%), Positives = 201/285 (70%), Gaps = 3/285 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            EVD  +KI   +++          E    R  +  + + E     AK+ ++ ANLRLV+
Sbjct: 170 EEVDLAMKIEAGLEATEKLEAADAGELELTRAEIRRLTRIENVGLEAKQALISANLRLVV 229

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 230 SIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYQKGFKFSTYATWWIRQAITRAIADQAR 289

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ M  + VR++ KI++EP+SLE
Sbjct: 290 TIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMDMSADRVREIQKISQEPVSLE 349

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+E+ S LGDFIED  A+ P D+A  + L+E  T+VL SL  RE +V+ +RFG+   
Sbjct: 350 TPIGEEEDSQLGDFIEDSQAIVPPDAASFSMLQEQLTQVLDSLADRERKVIELRFGLVDG 409

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +++ 
Sbjct: 410 HPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYIES 454



 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 38/164 (23%), Positives = 61/164 (37%), Gaps = 42/164 (25%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG-- 88
             K++     R  VT +E+   L   +VS EQ+    + L N GI ++     +D     
Sbjct: 21  VAKLMGNGSNRTSVTEDEIQVALKDIDVSDEQLTAVYSALRNSGIQIISASGNDDAPMGV 80

Query: 89  -----------------------SEDSLDLASSASNSSVFLQKRKDSADRS--------- 116
                                   +  L +A  A       + +K    R+         
Sbjct: 81  DDDDTDTDTDDFDDDDEHDSGSLDDHELKMARQADAEMGSSKNKKKRTVRTSRSRSRVRG 140

Query: 117 --------TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                   T DPVRMYL+E+G ++LL+   E+ +A +IEAG   
Sbjct: 141 IDASTVMLTGDPVRMYLKEIGKVDLLTASEEVDLAMKIEAGLEA 184


>gi|253576089|ref|ZP_04853421.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251844432|gb|EES72448.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 374

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVPLLSADDEMELAKRIE---NGDEEAKRRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLIKAVEKFDHKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA ++ + VE VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVSRQLLQELGREPAPEEIAAEMDLSVEKVREIMKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 282 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 43/174 (24%), Positives = 76/174 (43%), Gaps = 8/174 (4%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + +  L  D   D   ++I+  ++R  +T +E+   L P +   EQM++    L
Sbjct: 2   TNEQHTELETELTLDQVRD---QLIEQGKKRSSLTYKEIMEKLSPFDQDPEQMDEFFEQL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +++          + ++      D   S  +   +            +DPVRMYL+E+G 
Sbjct: 59  ADL----GIDITGDGDDDHRSRGDGDDSHDDDFNYDDDLSLPPGIKINDPVRMYLKEIGR 114

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + E+ +AKRIE G       L E+ L     I  R  +  G   L  I
Sbjct: 115 VPLLSADDEMELAKRIENGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|94263094|ref|ZP_01286913.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456637|gb|EAT06745.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 540

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 260/502 (51%), Gaps = 14/502 (2%)

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           +  +           T+    +    ++Q++  D     +           D    V   
Sbjct: 44  DEMLPNSPPSRRAQLTDEDGDEHAPAAAQDEASDGAGADDEPYVWPGDSGGDQVDPVKVY 103

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +   +      E+E   A  + A E  ++  ++ A   IA + + +  +   A N Q  
Sbjct: 104 LQEMGSVPLLSTEEEIAVAREIEAGELLIQQALLTAPPAIAYLSKLIDKVM--AGNRQLS 161

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI------MHNEGELLRLAQ 361
           +      +  K+ + +    L    +  D L  +   +++ +       +   +L     
Sbjct: 162 DLLRGLDEADKKTMGETAKRLHWQLTEADRLARENAALNRELLAPATNRNQARQLKTRIT 221

Query: 362 SYGIKRDVFL--ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                R      +R   + L        +       +     E +     +  +++    
Sbjct: 222 RNNKARAQLFAEDRFSSKHLQAMTARLGRFEESLNRQRAALSEAELPAWRQQCLQNH--- 278

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+       I + + +G+  +  AK  +V+ANLRLV+SVAKKY  RGLQ LDLIQEGNI
Sbjct: 279 -GLDQEGLAEIQAGIARGQEVSQEAKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNI 337

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ  TIRIPVHM D I+++++ A+  
Sbjct: 338 GLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQGRTIRIPVHMIDTINRMLKGAKEF 397

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  REPTP+E+A+ L + V  V+ VLKI KEP+SL+TP+G+ + S L DFIED  A S
Sbjct: 398 QRQHGREPTPDEMAQHLGVEVAKVKSVLKIAKEPLSLDTPVGNSNDSFLADFIEDTEAAS 457

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++ I  NL+    RVL +L+PREE VLR+RFG+    D TLEEVG+ F VTRERIRQI
Sbjct: 458 PDEATIYENLQSNLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQI 517

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA++KLKHP+R  +L SF D
Sbjct: 518 EAKALKKLKHPARRNQLSSFYD 539



 Score = 78.0 bits (190), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 33/105 (31%), Positives = 53/105 (50%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D+  DE     + D AS  + +          +     DPV++YL+EMGS+ LLS E EI
Sbjct: 60  DEDGDEHAPAAAQDEASDGAGADDEPYVWPGDSGGDQVDPVKVYLQEMGSVPLLSTEEEI 119

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           A+A+ IEAG  ++  +L  +P     L    D++  G   L +++
Sbjct: 120 AVAREIEAGELLIQQALLTAPPAIAYLSKLIDKVMAGNRQLSDLL 164


>gi|295110289|emb|CBL24242.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus obeum A2-162]
          Length = 376

 Score =  224 bits (570), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 208/273 (76%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 107 VRMYLKEIGKVSLLTADEEIELAKRMEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 164 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 223

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIA+++ MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 224 INKLIRVSRQLLQELGREPTPEEIAEEMKMPVERVREILKISQEPVSLETPIGEEEDSHL 283

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P D+A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 284 GDFIQDDNVPVPADAAAFTLLKEQLIEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKE 343

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 344 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 376



 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 46/161 (28%), Positives = 77/161 (47%), Gaps = 6/161 (3%)

Query: 29  DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDDLED 85
           +   ++++LA+++   +  +E++ F     +  EQME  +  L   G++V  + G+D E 
Sbjct: 10  EKLVELLELAKKKKNVLEYQEISDFFKDQPLEVEQMEKVLDFLEASGVDVLRISGNDEEL 69

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
               +D  D+        + L K   S     S +DPVRMYL+E+G + LL+ + EI +A
Sbjct: 70  ILDVDDDADIEKMDDEEEIELDKIDLSVPEGVSIEDPVRMYLKEIGKVSLLTADEEIELA 129

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           KR+E G       L E+ L     I  R  +  G   L  I
Sbjct: 130 KRMEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 169


>gi|311111671|ref|YP_003982893.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
 gi|310943165|gb|ADP39459.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
          Length = 468

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 134/253 (52%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 216 KLKKELRWVIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 275

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 276 DYSKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 335

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+ K+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 336 PEELGKELDMAPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 395

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 396 LQEQLHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 455

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 456 HPSRSQVLRDYLD 468



 Score = 51.0 bits (120), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 30/51 (58%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++       ++     +T DPV+ YL+++G + LL+ + E+ +A RIEAG 
Sbjct: 151 ASDDDDAPAQRVVTPGATADPVKDYLKQIGKVSLLNAQQEVDLAMRIEAGL 201


>gi|187934045|ref|YP_001885115.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722198|gb|ACD23419.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
          Length = 374

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +       +        +AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGKVPLLSSEQEIDYAKRIE---EGDPVAKKKLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEEI+K + +PV+ VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 222 INKLIRVQRQLLQELGRDPFPEEISKVMELPVDKVREIQKIAQEPVSLETPIGEEEDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 282 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 342 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 374



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/184 (27%), Positives = 76/184 (41%), Gaps = 17/184 (9%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M  G K + +   + +        +      K +I   ++ G +T +E+   +   ++S 
Sbjct: 1   MAEGGKESMEQKVKKKAEKGKEDKNAKMAMVKGLIDKGKKNGSLTYKEIMDEIDHIDLSP 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+E    +L  MGI V+ G     E   E  L +                    + DDP
Sbjct: 61  EQIEKIYEVLEMMGIEVIGGATDAPEVEEEIDLTV----------------LEGIAIDDP 104

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G + LLS E EI  AKRIE G  +    L E+ L     I  R  +  G   
Sbjct: 105 VRMYLKEIGKVPLLSSEQEIDYAKRIEEGDPVAKKKLAEANLRLVVSIAKRY-VGRGMLF 163

Query: 181 LREI 184
           L  I
Sbjct: 164 LDLI 167


>gi|114567027|ref|YP_754181.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|114337962|gb|ABI68810.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 358

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 163/374 (43%), Positives = 230/374 (61%), Gaps = 31/374 (8%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK   K  +  E++ + + S +L   +ID + E L  +   I                  
Sbjct: 16  EKGKKKKNLSYEEITEELQSFNLEADQIDDIFEHLQSLGITIGTE--------------- 60

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                  Q  ELD        +      +  +   ++    +R  +K I     +  ++ 
Sbjct: 61  -------QDAELDEE------NESIETEEVVIPDGIEIDDPVRMYLKEIGRVPLLIAAQE 107

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   +         AK+++VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EK
Sbjct: 108 IDLAQRIE---EGDEEAKRQLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLMKAVEK 164

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 165 FDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLSRVQRSLLQILGREP 224

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A+++ + V+ V +++K+ +EP+SLETPIG+ED SHLGDFI D+ A SP +SA   
Sbjct: 225 TPAEVAEEMDIAVDRVIEIMKVAQEPVSLETPIGEEDDSHLGDFITDEEAESPEESASFV 284

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE    +L +LT REE+VLR+RFG+      TLEEVG++F VTRERIRQIEAKA+RKL
Sbjct: 285 LLREHLDGILNTLTEREEKVLRLRFGLDDGRPRTLEEVGQEFGVTRERIRQIEAKALRKL 344

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +++
Sbjct: 345 RHPSRSKKLKDYIE 358



 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 39/156 (25%), Positives = 67/156 (42%), Gaps = 13/156 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           ++   + +  +++  ++ EE+   L    + ++Q++D    L ++GI +    D E    
Sbjct: 9   EAVVALAEKGKKKKNLSYEEITEELQSFNLEADQIDDIFEHLQSLGITIGTEQDAEL--- 65

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                       N S+  ++         DDPVRMYL+E+G + LL    EI +A+RIE 
Sbjct: 66  ---------DEENESIETEEVVIPDGIEIDDPVRMYLKEIGRVPLLIAAQEIDLAQRIEE 116

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  R  +  G   L  I
Sbjct: 117 GDEEAKRQLVEANLRLVVSIAKRY-VGRGMLFLDLI 151


>gi|304437691|ref|ZP_07397643.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369324|gb|EFM22997.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 370

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V++ ++ E     A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGHVPLLTAEEE---VALAQRMEAGDEEARHRLEEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ R+P PEEIAK++ + V  V +++KI +EP+SLETPIG+E+ SHL
Sbjct: 218 INKLVRISRQLLQELGRDPRPEEIAKEMGISVARVHEIMKIAQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A +P ++A    LRE    VL +LT RE+ VLR+RFG+      TLEEVG+ 
Sbjct: 278 GDFIEDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLEEVGQS 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK LR FL+
Sbjct: 338 FGVTRERIRQIEAKALRKLRHPSRSKVLRDFLE 370



 Score =  101 bits (252), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 41/159 (25%), Positives = 68/159 (42%), Gaps = 8/159 (5%)

Query: 27  SDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           S D  ++++   ++ G  +   EL   L   ++S ++M+D     S+ G+ +       D
Sbjct: 12  STDIIERLLAKGKKNGGSLLFGELIDALQKQDMSPDEMDDMYQRFSDEGVEI------VD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +  +                          S DDPVRMYL+E+G + LL+ E E+A+A+R
Sbjct: 66  DVAAAGDAADDDGPDKEEEVEIDLSVPEGISLDDPVRMYLKEIGHVPLLTAEEEVALAQR 125

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +EAG       L E+ L     I  R  +  G   L  I
Sbjct: 126 MEAGDEEARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|302554625|ref|ZP_07306967.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472243|gb|EFL35336.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 513

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 261 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 320

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 321 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 380

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 381 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 440

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 441 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 500

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 501 HPSRSQVLRDYLD 513



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 1/96 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +E            +         ++ +A  +T DPV+ YL+++G + LL+ E E+ +AK
Sbjct: 181 EEPEGTTENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQEVELAK 240

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           RIEAG       L  S      L    + + +    
Sbjct: 241 RIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 275


>gi|297199501|ref|ZP_06916898.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297147415|gb|EDY56986.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 428

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 129/296 (43%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++  E   +   V                         +      +AK
Sbjct: 133 RQYLREIGRIPLLTAVEEVELARRVEAGLFAEEKLSSTPDLDSQLALDLDRLVVLGRMAK 192

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 193 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 252

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E V +
Sbjct: 253 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLDLAPERVSE 312

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 313 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 372

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 373 KVVQLRYGLADGRARTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 428



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/112 (25%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V    + E +    ++L+   +        + R D+    + D  R YLRE+G I LL+
Sbjct: 88  RVAHHPEAEPDAPPAETLENVETEPVEPPEPRSRVDT-GGPSSDLFRQYLREIGRIPLLT 146

Query: 136 REGEIAIAKRIEAGRAMMMASLCESP-LTFQALIIWRDELNDGTTLLREIID 186
              E+ +A+R+EAG       L  +P L  Q  +     +  G    R +I+
Sbjct: 147 AVEEVELARRVEAGLF-AEEKLSSTPDLDSQLALDLDRLVVLGRMAKRRLIE 197


>gi|332295554|ref|YP_004437477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
 gi|332178657|gb|AEE14346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
          Length = 356

 Score =  224 bits (570), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 146/272 (53%), Positives = 199/272 (73%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +  SE +++             AKK++ EANLRLV+S+AKKYT RGL
Sbjct: 87  VRQYLKEIGKIPLLKHSEEKYLAERA---FHGDEAAKKKLAEANLRLVVSIAKKYTKRGL 143

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + 
Sbjct: 144 LFLDLIQEGNMGLLRAVEKFDYRKGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMVET 203

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K  +T R +S ++ R+PT EEIA+K+ + VE + ++ +I++EPIS+ETPIG ++ SHL
Sbjct: 204 INKYKKTVRNLSQQLSRKPTDEEIAEKMEVNVEKIHEIKRISQEPISIETPIGKDEDSHL 263

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++  SP+++     L+E    V+  L PRE  V+R+RFG+      TLEEVGK+
Sbjct: 264 GDFIADESISSPMEAVTYRLLKEDLEEVIKDLQPRERDVVRLRFGLVDGHARTLEEVGKE 323

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +L
Sbjct: 324 FGVTRERIRQIEAKALRKLRHPSRSRKLRDYL 355



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/130 (20%), Positives = 47/130 (36%), Gaps = 10/130 (7%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
            D      +++ +  +       VD +D +  +       +  +   S+  +    +   
Sbjct: 30  DDLEEPSDLDNIIKSIEAGN---VDDEDQDLLKI------VNDTEPVSAEDVLTMPEERV 80

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
              +DPVR YL+E+G I LL    E  +A+R   G       L E+ L     I  +   
Sbjct: 81  PMVEDPVRQYLKEIGKIPLLKHSEEKYLAERAFHGDEAAKKKLAEANLRLVVSIAKKY-T 139

Query: 175 NDGTTLLREI 184
             G   L  I
Sbjct: 140 KRGLLFLDLI 149


>gi|325662013|ref|ZP_08150632.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331085863|ref|ZP_08334946.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471676|gb|EGC74895.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330406786|gb|EGG86291.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 370

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLSAEEEIELARRME---EGDEDAKKRLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK+L MPV+ VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPLPEEIAKELDMPVDRVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A    L+E    VL++LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 278 GDFIQDDNVPVPAEAAAATLLKEQLDEVLSTLTDREQKVLRLRFGMNDGRARTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 45/157 (28%), Positives = 73/157 (46%), Gaps = 4/157 (2%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +  K++I L +++   + ++E+N F    E+ SEQM+     L    I+V+     E +E
Sbjct: 10  EKVKELIALGKKKKSILELQEINDFFSDMELDSEQMDKVFEALEASNIDVL--RIGEGDE 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +D   + +      +           S +DPVRMYL+E+G + LLS E EI +A+R+E
Sbjct: 68  DDDDIEIMLTEEDEVDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELARRME 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 128 EGDEDAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|302871329|ref|YP_003839965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574188|gb|ADL41979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 417

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 182/435 (41%), Positives = 272/435 (62%), Gaps = 21/435 (4%)

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +N EN+E     D++ +  T S  + ++  +++ +     +  +  +   +N   G+K 
Sbjct: 3   EQNMENNEVKNLNDQNINKETGSEQQQEVEKQLLESQKNENQEKQPAKKSTENKSEGKK- 61

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIK 366
             S  K  +++EK+ +L   +SL QS+  L   ++ +I  ++  +  ++  +  +   + 
Sbjct: 62  -MSEEKKTLIREKVREL---ISLGQSKGFLTYSEIQEILDKVELDASQVESIYDTLESMG 117

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            DV  +R    EL    +              +   +     +R  +K I     ++  E
Sbjct: 118 IDVVDDRVSEEELLKDDLEN------------LPEGIAIDDPVRMYLKEIGKIPLLTPEE 165

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              +   + +       AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA E
Sbjct: 166 EIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVE 222

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  +  RE
Sbjct: 223 KFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQEKGRE 282

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHLGDFI D +A++P ++A  
Sbjct: 283 PTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDDDALAPSEAAAY 342

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + L+E    VL SL  RE++VL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RK
Sbjct: 343 SMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRK 402

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRSKKL+ FL+
Sbjct: 403 LRHPSRSKKLKDFLE 417



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 53/181 (29%), Positives = 81/181 (44%), Gaps = 19/181 (10%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            KK   +     + S++        +  +++I L + +G++T  E+   L   E+ + Q+
Sbjct: 49  AKKSTENKSEGKKMSEEKKTL--IREKVRELISLGQSKGFLTYSEIQEILDKVELDASQV 106

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           E     L +MGI+VVD    E+E   +D  +L                    + DDPVRM
Sbjct: 107 ESIYDTLESMGIDVVDDRVSEEELLKDDLENL----------------PEGIAIDDPVRM 150

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L  
Sbjct: 151 YLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDL 209

Query: 184 I 184
           I
Sbjct: 210 I 210


>gi|291533682|emb|CBL06795.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Megamonas hypermegale
           ART12/1]
          Length = 329

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 148/266 (55%), Positives = 198/266 (74%), Gaps = 3/266 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 66  VRMYLKEIGRVPLLSADEEIKLAKRMED---GDLEAQKRLAEANLRLVVSIAKRYVGRGM 122

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 123 LFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 182

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++   + REP+PEEIAK++ + V+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 183 INKLIRVSRQLLQSLGREPSPEEIAKEMDVSVDRVREIMKIAQEPVSLETPIGEEEDSHL 242

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A +P ++A    L+E    VL +LT REE+VLR+RFG+      TLEEVG+ 
Sbjct: 243 GDFIEDHDAPAPAEAASFVLLKEQLEDVLDTLTEREEKVLRLRFGLDDGRARTLEEVGQN 302

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
           F VTRERIRQIEAKA+RKL+HPSRSK
Sbjct: 303 FGVTRERIRQIEAKALRKLRHPSRSK 328



 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 34/135 (25%), Positives = 57/135 (42%), Gaps = 7/135 (5%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
              L   ++S +++++     +  GI+++D              D ++   +        
Sbjct: 1   MESLQSVDMSPDEIDELYDTFTKRGIDIIDNG------NDIGPDDDSNLKDDEDDIDIDL 54

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
                 + DDPVRMYL+E+G + LLS + EI +AKR+E G       L E+ L     I 
Sbjct: 55  SIPEGINIDDPVRMYLKEIGRVPLLSADEEIKLAKRMEDGDLEAQKRLAEANLRLVVSIA 114

Query: 170 WRDELNDGTTLLREI 184
            R  +  G   L  I
Sbjct: 115 KRY-VGRGMLFLDLI 128


>gi|221310444|ref|ZP_03592291.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314767|ref|ZP_03596572.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319690|ref|ZP_03600984.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323967|ref|ZP_03605261.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767573|ref|NP_390399.2| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296333322|ref|ZP_06875775.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305675173|ref|YP_003866845.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|321312003|ref|YP_004204290.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
 gi|251757327|sp|P06224|RPOD_BACSU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|225185201|emb|CAB14450.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. subtilis str. 168]
 gi|296149520|gb|EFG90416.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305413417|gb|ADM38536.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|320018277|gb|ADV93263.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
          Length = 371

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGRVNLLSAKEE---IAYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 279 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 339 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 371



 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 6/157 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++      + E
Sbjct: 14  DQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELIS-----ENE 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +ED      + +     L           +DPVRMYL+E+G + LLS + EIA A++IE
Sbjct: 69  ETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAQKIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 164


>gi|313888947|ref|ZP_07822607.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845120|gb|EFR32521.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 362

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E   I   +        +AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 93  VRMYLKEIGKISLLTAEEEVEIAKRME---EGDELAKKELAEANLRLVVSIAKRYVGRGM 149

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 150 SFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 209

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++   + R+P PEEIA ++ + VE VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 210 INKLVRVQRQLVQDLGRDPLPEEIAAEMNLDVERVREIQKIAQEPVSLETPIGEEEDSHL 269

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D   +SP D+A    L+E    VL +LT RE++VL +RFG+      TLEEVGK+
Sbjct: 270 GDFIPDDEILSPQDAATFTLLKEQLNTVLETLTDREKKVLTLRFGLDDGRARTLEEVGKE 329

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 330 FDVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 362



 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 41/160 (25%), Positives = 68/160 (42%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +  ++   +++K  ++ G +T EE+       E+ S+ +++   +    GI         
Sbjct: 9   ESIEEIKDQLLKDGKKDGKLTYEEIGDAFEKYEIDSDDIDELYKVFEKEGI--------- 59

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                 D  D         V  +        + DDPVRMYL+E+G I LL+ E E+ IAK
Sbjct: 60  ---NLVDKKDSKDDDDEVDVTKEDLSVPKGVTVDDPVRMYLKEIGKISLLTAEEEVEIAK 116

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R+E G  +    L E+ L     I  R  +  G + L  I
Sbjct: 117 RMEEGDELAKKELAEANLRLVVSIAKRY-VGRGMSFLDLI 155


>gi|315656627|ref|ZP_07909514.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|315492582|gb|EFU82186.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 564

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 134/260 (51%), Positives = 188/260 (72%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  + R +  +V+    +  +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL
Sbjct: 309 MTPKQIRELHYVVQ----DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGL 364

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M  
Sbjct: 365 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 424

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P 
Sbjct: 425 DLGREPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPA 484

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEA
Sbjct: 485 DAVSFMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEA 544

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HP+RS+ LR +L+
Sbjct: 545 KTMSKLRHPARSQSLRDYLN 564



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR-AMMMASL 157
           +         +K +   +T DPV+ YL+++G + LL+ E E+ ++KRIEAG  A  +   
Sbjct: 245 SEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKT 304

Query: 158 CESPLTFQALIIWRDELNDGTT 179
            +  +T + +      + DG  
Sbjct: 305 KQETMTPKQIRELHYVVQDGQM 326


>gi|291550178|emb|CBL26440.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 373

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGKVPLLSAEREIELAQRME---EGDEEAKKELAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK++ MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 221 INKLIRVSRQLLQELGREPLPEEIAKEMDMPVERVREILKISQEPVSLETPIGEEEDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 281 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGRE 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 341 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 373



 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 45/158 (28%), Positives = 73/158 (46%), Gaps = 3/158 (1%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
           D  K ++ L +++   + ++E+N F    E++++QME     L    I+V+    D  DE
Sbjct: 10  DRLKDLVALGKKKKSILDVQEINDFFNDMELNADQMEKVFDYLEANNIDVLRISGDTPDE 69

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +    + S   +  +           S +DPVRMYL+E+G + LLS E EI +A+R+
Sbjct: 70  VDVDLDDIIISEEDDVDMENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAQRM 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 130 EEGDEEAKKELAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|87307035|ref|ZP_01089181.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
 gi|87290408|gb|EAQ82296.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
          Length = 519

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 161/406 (39%), Positives = 233/406 (57%), Gaps = 40/406 (9%)

Query: 278 PKVMCALDEI-AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           P  +  LD +    YR+ R     + +  +  ++ V+    + + VKLV  L L   RI+
Sbjct: 152 PHNLKTLDTLLKRNYRDYRIATSKSRSESQRAEAWVRLGRRRRRSVKLVEELGLRTQRIE 211

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD-PHWVSYAKDFPEGEW 395
             +  L D SKRI   +  +               ++ +G E +   W++          
Sbjct: 212 SKIGTLEDFSKRIDELKVRIDEH------------KKAKGHESERADWIA---------- 249

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
                           E ++I V T  + +  R  V+ ++    E   AK+E+ E NLRL
Sbjct: 250 ----------------EYRNILVATQETPTSLRRRVNQLKVIYSEYQQAKRELSEGNLRL 293

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AKKY NRGL FLDLIQEGN GLM+A +KF++  G+KF TYA WW++QAITR++ADQ
Sbjct: 294 VVSIAKKYRNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQ 353

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S TIRIPVHM + + +V   AR++  +  REPT EE A++    VE  R+VL +++ PIS
Sbjct: 354 SRTIRIPVHMVETMSRVRNVARQLLQEKGREPTLEETARRAGTTVEEARRVLAMSRYPIS 413

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+ P+G+ + S  GD + D  A SP   A Q  LR   +RVL +L+ RE  ++++R+G+G
Sbjct: 414 LDRPVGNSEDSQFGDLLPDGEAESPAIGAAQEMLRTRISRVLKTLSYREREIIKLRYGLG 473

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               +TLEEVG  F VTRERIRQIEAKA+RKL+ PSRS++L  FLD
Sbjct: 474 DGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPSRSQELVGFLD 519



 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 39/125 (31%), Positives = 57/125 (45%), Gaps = 3/125 (2%)

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           +  + V+DGD  +      DS +  S   +S  FL    D  +  +DDPVRMYL +MG I
Sbjct: 24  DASVEVLDGDSDDTPLVDVDSDNDNSVDDSSDEFLG---DDGETWSDDPVRMYLTQMGEI 80

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+R+ EI +A++IE  RA     L E     Q  I     + DG       + +    
Sbjct: 81  PLLTRQEEIFLARKIELTRAKFRGMLLECDYVIQDAIKVLRRVQDGELPFDRTVQVSVTD 140

Query: 192 GPESK 196
             E +
Sbjct: 141 RLEKE 145


>gi|318080032|ref|ZP_07987364.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 340

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 122/296 (41%), Positives = 182/296 (61%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ ++   +   V                         +       AK
Sbjct: 45  RQYLREIGRIPLLTAADEVDLARRVEAGLFAEAKLAGPGPLDTRLALDLDRLVVLGRAAK 104

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW++
Sbjct: 105 RRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIR 164

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  R +  +   EP+  E+A  L +  E V +
Sbjct: 165 QAMSRALADQARTIRVPVHVVELINRVVRVQRGLLQERGHEPSHAEVAALLGLTKERVGE 224

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL TP+G ED   LGD IED +A SP +SA    LR     VL++L  RE 
Sbjct: 225 VLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVLSTLGERER 284

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+  + + +LR +LD
Sbjct: 285 QVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHAFADQLRGYLD 340



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++          D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 30  ERTPAPPGGHAPDLFRQYLREIGRIPLLTAADEVDLARRVEAGL 73


>gi|291484966|dbj|BAI86041.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto
           BEST195]
          Length = 371

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGRVNLLSAKEE---IAYAKKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 279 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 339 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 371



 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 72/157 (45%), Gaps = 6/157 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++      + E
Sbjct: 14  DQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELIS-----ENE 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +ED      + +     L           +DPVRMYL+E+G + LLS + EIA AK+IE
Sbjct: 69  ETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAKKIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 164


>gi|257068601|ref|YP_003154856.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
 gi|256559419|gb|ACU85266.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
          Length = 433

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 135/250 (54%), Positives = 178/250 (71%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 184 RELTMIADDGRAAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYA 243

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE
Sbjct: 244 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 303

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E
Sbjct: 304 LAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQE 363

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPS
Sbjct: 364 QLHSVLDTLSEREAGVVSMRFGLEDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 423

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 424 RSQVLRDYLD 433



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 29/49 (59%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +      ++     +T DPV+ YL+++G + LL+   E+ +A+RIEAG 
Sbjct: 112 AEDDAPAQQVVTAGATADPVKDYLKQIGKVALLNAAQEVELAERIEAGL 160


>gi|271968332|ref|YP_003342528.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270511507|gb|ACZ89785.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 561

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 140/327 (42%), Positives = 195/327 (59%), Gaps = 25/327 (7%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR---- 435
           +   V    D  +      VA    +   +++ +K I     ++  +   +   +     
Sbjct: 235 NEDEVLILSDDDDDAPVPQVAAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF 294

Query: 436 ---------------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
                                    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLI
Sbjct: 295 AEEQLGTDGDKLPVDVRAELEWIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLI 354

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R
Sbjct: 355 QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLAR 414

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R+M   + REPTPEE+A++L M  E V +V K  +EPISL TP+G+E  S  GD IED
Sbjct: 415 VQRQMLQDLGREPTPEELARELDMTPEKVVEVQKYGREPISLHTPLGEEGDSEFGDLIED 474

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A+ P D+     L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRE
Sbjct: 475 SEAIVPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRE 534

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 535 RIRQIESKTMSKLRHPSRSQVLRDYLD 561



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 21/59 (35%), Positives = 34/59 (57%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + D     S+        + +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 235 NEDEVLILSDDDDDAPVPQVAAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGL 293



 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 11/63 (17%), Positives = 29/63 (46%)

Query: 15 HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
             S  S   + ++   +++++  R +G++  E++   +   ++   Q+   +  LS  G
Sbjct: 19 PASSTRSKPSELNEPVIQQLMERGRSQGFLESEDVRKAVEEADIPMAQVAGILRSLSKEG 78

Query: 75 INV 77
          I V
Sbjct: 79 ITV 81


>gi|269302545|gb|ACZ32645.1| RNA polymerase sigma factor RpoD [Chlamydophila pneumoniae LPCoLN]
          Length = 570

 Score =  223 bits (569), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 196/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 288 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 347

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 348 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 407

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED  
Sbjct: 408 KKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESSFGDFLEDTA 467

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 468 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERI 527

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 528 RQIEAKALRKMRHPIRSKQLRAFLD 552



 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 44/181 (24%), Positives = 87/181 (48%), Gaps = 10/181 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           ++++  + +    + S    ++++ LA+++G++T EE+N  LP    + EQ++  +  L+
Sbjct: 2   NTQNSQATEVSSEEESQKKLEELVALAKEQGFITYEEINEILPMSFDTPEQIDQVLIFLT 61

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            M I V++  D          ++        +  L+      + + DDPVRMYL+EMG++
Sbjct: 62  GMDIQVLNQID----------VERQKEKKKEAKELEGLARRTEGTPDDPVRMYLKEMGTV 111

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+RE E+ I+KRIE  +  +   +     + +  I     L  G     +II  +   
Sbjct: 112 PLLTREEEVEISKRIEKAQVQIERIILRFRYSAKEAISIAHYLISGKERFDKIISEKEVE 171

Query: 192 G 192
            
Sbjct: 172 D 172


>gi|118618666|ref|YP_906998.1| RNA polymerase sigma factor [Mycobacterium ulcerans Agy99]
 gi|118570776|gb|ABL05527.1| RNA polymerase sigma factor SigA [Mycobacterium ulcerans Agy99]
          Length = 501

 Score =  223 bits (569), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 134/286 (46%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC---EASIAKKEMVEANLRL 455
              EV+   +I   + +  +   ++    +   +  R       +   AK  ++EANLRL
Sbjct: 216 AEEEVELAKRIEAGLYATQLMAELTDRGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 275

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 276 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 335

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 336 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 395

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 396 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 455

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 456 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 501



 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/72 (36%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 159 EEEIAEPSEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 218

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 219 EVELAKRIEAGL 230


>gi|312139434|ref|YP_004006770.1| sigma-70 factor siga [Rhodococcus equi 103S]
 gi|325672677|ref|ZP_08152373.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|311888773|emb|CBH48085.1| sigma-70 factor SigA [Rhodococcus equi 103S]
 gi|325556554|gb|EGD26220.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 459

 Score =  223 bits (569), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 159 VRAYLKQIGKVALLNAEEEVELAKRIEAGLFATHKMNEMAEKGEKPSPTDRRNLNWITRD 218

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 219 GNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 278

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 279 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 338

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 339 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 398

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 399 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 458

Query: 681 D 681
           D
Sbjct: 459 D 459



 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 36/64 (56%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRI
Sbjct: 125 EKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRI 184

Query: 147 EAGR 150
           EAG 
Sbjct: 185 EAGL 188


>gi|520418|gb|AAA50747.1| major sigma factor [Chlamydophila psittaci]
          Length = 571

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 175/498 (35%), Positives = 271/498 (54%), Gaps = 19/498 (3%)

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR----SKVDSPPENAEND 254
           F  G +     + +   Q++ + + +E EG  +       D       ++ + P     +
Sbjct: 61  FLTGMDIQVLNQADVERQKERKKEAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREE 120

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI------AEVYRELRSLQDNAVNGQKDE 308
           E  + +  + +   +  +  + R     A+          E + ++ S ++        +
Sbjct: 121 EVEISKRIEKAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVEDKAHFLK 180

Query: 309 KSSVKCKVLKEK---LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                  +LKE+   L  L+  L  N    +   +   D+ K  +  +  L      + +
Sbjct: 181 LLPKLISLLKEEDAYLESLLFRLKQNNLSKEETAKLNDDLEKCRIRTQAYLRCFHCRHNV 240

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPE--GEWKNFVACEVDSILKIRNEIKSISVETGIS 423
             + F E           +    +  +   E   F A ++D+    +  +    V  G +
Sbjct: 241 T-EDFGEVVFKAYDSFLQLEQQINDLKVRAERNKFAAAKLDA---AKRRLYKREVAAGRT 296

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+GLMK
Sbjct: 297 LEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMK 356

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++  + 
Sbjct: 357 AVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKLMMET 416

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED    SP ++
Sbjct: 417 GKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESSFGDFLEDTGVESPAEA 476

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIRQIEAKA
Sbjct: 477 TGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKA 536

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RK++HP RSK+LR+FLD
Sbjct: 537 LRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E ++
Sbjct: 20  QKKLEELVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+      + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  I     L +G     +II  +    
Sbjct: 130 KAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVED 174


>gi|52786447|ref|YP_092276.1| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|163119552|ref|YP_079858.2| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|319644974|ref|ZP_07999207.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
 gi|52348949|gb|AAU41583.1| SigA [Bacillus licheniformis ATCC 14580]
 gi|145903060|gb|AAU24220.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus
           licheniformis ATCC 14580]
 gi|317392783|gb|EFV73577.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
          Length = 373

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 198/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E       +         +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLSAKEEIEYAKKIE---EGDEESKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 44/174 (25%), Positives = 78/174 (44%), Gaps = 9/174 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++    F+   D   ++ +  ++RG +T EE+   +   ++ S+QM++    L
Sbjct: 2   ADKQAHETETEFTFEQVRD---QLTEAGKKRGVLTYEEIAERMSSFDIESDQMDEYYEFL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
              G+ ++      + E +ED      + +     L           +DPVRMYL+E+G 
Sbjct: 59  GEQGVELIS-----ENEETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 113

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + EI  AK+IE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 VNLLSAKEEIEYAKKIEEGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|15618665|ref|NP_224951.1| RNA polymerase sigma factor [Chlamydophila pneumoniae CWL029]
 gi|15836289|ref|NP_300813.1| RNA polymerase sigma factor [Chlamydophila pneumoniae J138]
 gi|33242115|ref|NP_877056.1| RNA polymerase sigma factor [Chlamydophila pneumoniae TW-183]
 gi|6831651|sp|Q9Z7F0|RPOD_CHLPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|4377063|gb|AAD18894.1| RNA Polymerase Sigma-66 [Chlamydophila pneumoniae CWL029]
 gi|8979129|dbj|BAA98964.1| RNA polymerase sigma-66 [Chlamydophila pneumoniae J138]
 gi|33236625|gb|AAP98713.1| sigma factor 70 [Chlamydophila pneumoniae TW-183]
          Length = 572

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 196/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGSESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 87/181 (48%), Gaps = 10/181 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           ++++  + +    + S    ++++ LA+++G++T EE+N  LP    + EQ++  +  L+
Sbjct: 4   NTQNSQATEVSSEEESQKKLEELVALAKEQGFITYEEINEILPMSFDTPEQIDQVLIFLT 63

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            M I V++  D+E                  +  L+      + + DDPVRMYL+EMG++
Sbjct: 64  GMDIQVLNQIDVE----------RQKEKKKEAKELEGLARRTEGTPDDPVRMYLKEMGTV 113

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+RE E+ I+KRIE  +  +   +     + +  I     L  G     +II  +   
Sbjct: 114 PLLTREEEVEISKRIEKAQVQIERIILRFRYSAKEAISIAHYLISGKERFDKIISEKEVE 173

Query: 192 G 192
            
Sbjct: 174 D 174


>gi|318058872|ref|ZP_07977595.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|333027299|ref|ZP_08455363.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
 gi|332747151|gb|EGJ77592.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
          Length = 338

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 122/296 (41%), Positives = 182/296 (61%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ ++   +   V                         +       AK
Sbjct: 43  RQYLREIGRIPLLTAADEVDLARRVEAGLFAEAKLAGPGPLDTRLALDLDRLVVLGRAAK 102

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW++
Sbjct: 103 RRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIR 162

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  R +  +   EP+  E+A  L +  E V +
Sbjct: 163 QAMSRALADQARTIRVPVHVVELINRVVRVQRGLLQERGHEPSHAEVAALLGLTKERVGE 222

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL TP+G ED   LGD IED +A SP +SA    LR     VL++L  RE 
Sbjct: 223 VLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVLSTLGERER 282

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+  + + +LR +LD
Sbjct: 283 QVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHAFADQLRGYLD 338



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++          D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 28  ERTPAPPGGHAPDLFRQYLREIGRIPLLTAADEVDLARRVEAGL 71


>gi|153816193|ref|ZP_01968861.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
 gi|145846528|gb|EDK23446.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
          Length = 383

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 114 VRMYLKEIGKVPLLSAEREIELAKRME---EGDEDAKKELAEANLRLVVSIAKRYVGRGM 170

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 171 LFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 230

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK+L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 231 INKLIRVSRQLLQELGREPLPEEIAKELDMPVERVREILKISQEPVSLETPIGEEEDSHL 290

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 291 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 350

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 351 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 383



 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 72/157 (45%), Gaps = 4/157 (2%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   +++ L +++   + ++E+N F    E+S+EQME     L    I+V+      D +
Sbjct: 23  EKMNELVALGKKKKSILDVQEINDFFADMELSAEQMEKVFEYLEGHNIDVL--RITADTD 80

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D  ++ +      +           S +DPVRMYL+E+G + LLS E EI +AKR+E
Sbjct: 81  DDVDIDNMIAEEEEVDMENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAKRME 140

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 141 EGDEDAKKELAEANLRLVVSIAKRY-VGRGMLFLDLI 176


>gi|297570260|ref|YP_003691604.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296926175|gb|ADH86985.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 555

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 164/409 (40%), Positives = 231/409 (56%), Gaps = 6/409 (1%)

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           + P  +  LDEIA+  +    +  + V G  +       +  K  L ++  +L L +   
Sbjct: 148 IAPPALAYLDEIAKKIQHGNRMLSDIVRGLDELDKETHEEKQKNFLWRIEEALRLARETT 207

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            L  +QL          E             R                +           
Sbjct: 208 ALRRDQLNAAGSNEGAQERRQQSRIDR---NRKAQAALFADDRFSAKHLQAMVRLLRELE 264

Query: 396 KNFVACE---VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
              +  +    D    ++    +   + G+   E   +++ +  GE  +  AK  +V++N
Sbjct: 265 SKLIGPKPGGQDQDAALQEWHFTCLEQYGLDRQELSALLAQISLGEEISREAKNRLVQSN 324

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+SVAKKY  RGLQ LDL+QEGNIGLMKA EKF++  GYKFSTYA WW++QA+TR+I
Sbjct: 325 LRLVVSVAKKYAGRGLQLLDLVQEGNIGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAI 384

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ  TIRIPVHM D I+++++ A+    +  REPTPEE+A+ L + +  V+ +LKI KE
Sbjct: 385 ADQGRTIRIPVHMIDTINRMLKGAKEYQRQHGREPTPEEMAEHLGVDIAKVKSILKIAKE 444

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+SL+TP+G  + S L DFIED ++ SP ++ I  +L++   RVL +LTPREE VLR+RF
Sbjct: 445 PLSLDTPVGSGEDSFLSDFIEDADSTSPDEATIYDSLQDNLARVLKTLTPREEMVLRLRF 504

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           GI   TD TLEEVG+ F VTRERIRQIEAKA++KLKHP+R   L  F D
Sbjct: 505 GIDTATDLTLEEVGENFSVTRERIRQIEAKALKKLKHPTRKSILSPFYD 553



 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/205 (21%), Positives = 79/205 (38%), Gaps = 7/205 (3%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIEL 133
            V + DD         +    +                + +TD  DPV++YL+EMG++ L
Sbjct: 63  TVSEDDDTSAGADLPGNYRADNDDDGDDEVGDPYFWPGESATDQVDPVKVYLQEMGAVAL 122

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           LS E E+A+AK IE G   +  +L  +P     L     ++  G  +L +I+     +  
Sbjct: 123 LSSEEEVAVAKEIERGERTIQDALVIAPPALAYLDEIAKKIQHGNRMLSDIVRGLDELDK 182

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           E+     H  +  ++  R + +    R+        + +A         +  S  +    
Sbjct: 183 ET-----HEEKQKNFLWRIEEALRLARETTALRRDQLNAAGSNEGAQERRQQSRIDRNRK 237

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRP 278
            +  L  D+  SA  L AM   LR 
Sbjct: 238 AQAALFADDRFSAKHLQAMVRLLRE 262


>gi|302545597|ref|ZP_07297939.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463215|gb|EFL26308.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 443

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 192/321 (59%), Gaps = 24/321 (7%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR--------- 435
               D    E          S    R  ++ I     +S +E   +   V          
Sbjct: 123 DAEADSGPAERPARAETTGPSSDLFRQYLREIGRIPLLSAAEEVELARRVEAGLFAEEKL 182

Query: 436 ---------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
                          +      +AK+ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+G
Sbjct: 183 ASAPDLDSQLALDLDRLVVLGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLG 242

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++A EKFD+  GYKFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM 
Sbjct: 243 LIRAVEKFDYARGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRML 302

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EPTPEE+A  L +  E V +VL++ +EP+SL  P+G+ED   LGD IED +A SP
Sbjct: 303 QERGYEPTPEEVAIHLDLTPERVSEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASP 362

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++SA    LRE    VL++L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 363 VESAAFLLLREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIE 422

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           +K + KL+  + + +LR +LD
Sbjct: 423 SKTLNKLRDHAFADQLRGYLD 443



 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 2/108 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +    E   +      + ++S    +  +      + D  R YLRE+G I LLS   E
Sbjct: 106 DPETAATEADAEPDTEPDAEADSGPAERPARAETTGPSSDLFRQYLREIGRIPLLSAAEE 165

Query: 140 IAIAKRIEAGRAMMMASLCESP-LTFQALIIWRDELNDGTTLLREIID 186
           + +A+R+EAG       L  +P L  Q  +     +  G    R +I+
Sbjct: 166 VELARRVEAGLF-AEEKLASAPDLDSQLALDLDRLVVLGRMAKRRLIE 212


>gi|291454591|ref|ZP_06593981.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
 gi|581664|emb|CAA53564.1| sigma factor (RNA polymerase subunit) [Streptomyces griseus]
 gi|291357540|gb|EFE84442.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
          Length = 510

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 258 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 317

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 318 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 377

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 378 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 437

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 438 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 497

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 498 HPSRSQVLRDYLD 510



 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +    EG+         + +       ++ +A  +T DPV+ YL+++G + LL+ E E+ 
Sbjct: 175 EEGAPEGTGGESQGFVLSDDDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQEVE 234

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +AKRIEAG       L  +      L    + + +    
Sbjct: 235 LAKRIEAGLF-AEDKLANADKIAPKLKRELEIIAEDGRR 272


>gi|50842515|ref|YP_055742.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|289425323|ref|ZP_06427100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289427207|ref|ZP_06428923.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|295130592|ref|YP_003581255.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|50840117|gb|AAT82784.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           KPA171202]
 gi|289154301|gb|EFD02989.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289159676|gb|EFD07864.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|291377120|gb|ADE00975.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|332675432|gb|AEE72248.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           266]
          Length = 506

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 209 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 268

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 269 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 328

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 329 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 388

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 389 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 448

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 449 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 506



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 160 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 219

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 220 ALLNAVEEVDLAKRIEAGL 238


>gi|15644200|ref|NP_229250.1| RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
 gi|6831649|sp|P77994|RPOD_THEMA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|4982015|gb|AAD36519.1|AE001796_11 RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
          Length = 399

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 138/272 (50%), Positives = 189/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     ++ ++ R +    +        AK++++ +NLRLV+S+AK+Y  RGL
Sbjct: 123 IKMYLKEIGKIPLLTPAQERELARRAQ---MGDKKAKEKLITSNLRLVVSIAKRYMGRGL 179

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 180 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 239

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R    K   EP+ EE+AK +  P E ++++L+  KE ISLE+PIG+++ S +
Sbjct: 240 INKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSI 299

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+ D +  SP   A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ 
Sbjct: 300 EDFVADDSIASPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQY 359

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK L+S L
Sbjct: 360 FNVTRERIRQIEVKALRKLRHPSRSKYLKSLL 391



 Score = 95.3 bits (235), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 38/146 (26%), Positives = 63/146 (43%), Gaps = 6/146 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVVDGDDLED 85
           +   KK+I L +++GY+T E+++   PPD     +  +E     L   GIN+V      +
Sbjct: 32  ERRIKKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIV----ENE 87

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E  E S           +  +  +     +  D ++MYL+E+G I LL+   E  +A+R
Sbjct: 88  PEEEEISASSDEQELEELLEKESPEIHDSSNVRDSIKMYLKEIGKIPLLTPAQERELARR 147

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR 171
            + G       L  S L     I  R
Sbjct: 148 AQMGDKKAKEKLITSNLRLVVSIAKR 173


>gi|294501280|ref|YP_003564980.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|295706627|ref|YP_003599702.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
 gi|294351217|gb|ADE71546.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|294804286|gb|ADF41352.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
          Length = 377

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E  ++   +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVDLLSAEEEINLAKRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVQRQLLQDLGREPSPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A SP + A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQDATSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 48/173 (27%), Positives = 79/173 (45%), Gaps = 5/173 (2%)

Query: 13  SEHEDSDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           +E       L  D + +  K ++ ++ ++RG +T EE+   +   E+ S+QM++    L 
Sbjct: 2   AEKSAQSKQLDSDLTIEQVKDQLTEIGKKRGVLTYEEIAERMANFEIESDQMDEYYEYLG 61

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
             G+ V+   +  D++      D+   +      L           +DPVRMYL+E+G +
Sbjct: 62  EQGVEVMSESEANDDDADP---DIQELSKEEEFDLNDLSVPPGVKINDPVRMYLKEIGRV 118

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +LLS E EI +AKRIE G       L E+ L     I  R  +  G   L  I
Sbjct: 119 DLLSAEEEINLAKRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 170


>gi|308174309|ref|YP_003921014.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|307607173|emb|CBI43544.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|328554255|gb|AEB24747.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens TA208]
 gi|328912652|gb|AEB64248.1| RNA polymerase sigma factor rpoD [Bacillus amyloliquefaciens LL3]
          Length = 373

 Score =  223 bits (568), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLSAKEE---ITYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 45/174 (25%), Positives = 78/174 (44%), Gaps = 9/174 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L  D   D   ++ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQTHETETELTLDQVKD---QLTETGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
              G+ ++      + E +ED      + +     L           +DPVRMYL+E+G 
Sbjct: 59  GEQGVELIS-----ENEETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 113

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + EI  A++IE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 VNLLSAKEEITYAQKIEEGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|312622967|ref|YP_004024580.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203434|gb|ADQ46761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 417

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 148 VRMYLKEIGKIPLLTPEEEIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 204

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 205 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 264

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  +  REPTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 265 INKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHL 324

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVG++
Sbjct: 325 GDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGRE 384

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 385 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 417



 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 53/183 (28%), Positives = 82/183 (44%), Gaps = 20/183 (10%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
           +  K     SD +    +   +     +  +++I L + +G++T  E+   L   E+ + 
Sbjct: 48  STKKSTESKSDGKKISEEKKTLI---REKVRELISLGQSKGFLTYSEIQEILDKVELDAS 104

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q+E+    L +MGI+VVD    E+E   +D  +L                    + DDPV
Sbjct: 105 QVENIYDTLESMGIDVVDDRVSEEELLKDDIENL----------------PEGIAIDDPV 148

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L
Sbjct: 149 RMYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFL 207

Query: 182 REI 184
             I
Sbjct: 208 DLI 210


>gi|271963879|ref|YP_003338075.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270507054|gb|ACZ85332.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 392

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 133/260 (51%), Positives = 197/260 (75%), Gaps = 8/260 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  EF+ +V        + + AK+ ++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL
Sbjct: 141 LAFPEFKELV-------WQGTRAKQRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGL 193

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  
Sbjct: 194 IRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLHQ 253

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REP PEEIA ++ +P++ V ++ +I +EP+SL++PI  E+ S LGDFIED +AV P+
Sbjct: 254 DLGREPAPEEIALEMDLPIDRVIEIQRIAQEPVSLQSPI-GEEDSDLGDFIEDADAVVPM 312

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++A    L++    +LA+L+ RE+R++++RFG+      TLEEVG++F VTRERIRQIE+
Sbjct: 313 EAAAFIMLQDQLDDILATLSDREQRIIQLRFGLADGHPRTLEEVGREFGVTRERIRQIES 372

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HP+R++ LR +LD
Sbjct: 373 KTLAKLRHPTRAQMLRDYLD 392



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 77/375 (20%), Positives = 134/375 (35%), Gaps = 64/375 (17%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D    ++   R+RG VT++++ A L   E+ S+ +E  V ML+  G+ V++    E+ 
Sbjct: 22  SVDQVADLVAKGRERGSVTVDDVAAALDKSELPSDALERVVRMLAEHGVEVLEPQGEEET 81

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             S++      +                  T D VR+YLRE+G + LL+ E E+ +AK I
Sbjct: 82  TRSDEEDVGKRAP-----------------TSDLVRIYLREIGRVPLLTAEEEVELAKSI 124

Query: 147 EAGR-------------------------AMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           EAG                                L E+ L     I  R  +  G   L
Sbjct: 125 EAGLFAEDKLTSVVSRLAFPEFKELVWQGTRAKQRLIEANLRLVVSIAKRY-VGRGMLFL 183

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
             I         E   G     E   Y K    S        Q     I   A+  +   
Sbjct: 184 DLI--------QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPV 235

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             V++  +      +   +   + A    A+E  L    +  + EI  + +E  SLQ  +
Sbjct: 236 HMVETINKLVRVQRQLHQDLGREPAPEEIALEMDLP---IDRVIEIQRIAQEPVSLQ--S 290

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE-------- 353
             G++D       +     +     +  + Q ++D ++  L D  +RI+           
Sbjct: 291 PIGEEDSDLGDFIEDADAVVPMEAAAFIMLQDQLDDILATLSDREQRIIQLRFGLADGHP 350

Query: 354 GELLRLAQSYGIKRD 368
             L  + + +G+ R+
Sbjct: 351 RTLEEVGREFGVTRE 365


>gi|332670669|ref|YP_004453677.1| RpoD subfamily RNA polymerase sigma-70 subunit [Cellulomonas fimi
           ATCC 484]
 gi|332339707|gb|AEE46290.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas fimi
           ATCC 484]
          Length = 538

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 180/253 (71%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 286 KLRRELEWIAGDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 345

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 346 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 405

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 406 PEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 465

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   +VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 466 LQEQLHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 525

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 526 HPSRSQVLRDYLD 538



 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/122 (19%), Positives = 50/122 (40%), Gaps = 28/122 (22%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
            ++   E +ED    + ++ I+  D  +  + E + ++ + +      +        + +
Sbjct: 152 DEDGGDEDIEDV--DIEDVEIDEADAIEDVEVEATAETPEESEDGDEETTEAAPAAKAEE 209

Query: 115 --------------------------RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                                      +T DPV+ YL+++G + LL+ E E+ +AKRIEA
Sbjct: 210 ESEDSGGFVYSDADDDDAPAQQVVTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEA 269

Query: 149 GR 150
           G 
Sbjct: 270 GL 271


>gi|251796255|ref|YP_003010986.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
 gi|247543881|gb|ACT00900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
          Length = 376

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 166/374 (44%), Positives = 235/374 (62%), Gaps = 21/374 (5%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           E+   +  +  +++++ +     +  +ID   EQL D+   +++   +  R   + G   
Sbjct: 24  EQGKKRASLTYKEIMEKLSPFDQDPEQIDEFFEQLDDLGIEVLNE-RDEDRDPLNRGEDS 82

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +        RE D          P G   N           +R  +K I     +S  + 
Sbjct: 83  E--------RESDDFNFDDDLALPPGIKIN---------DPVRMYLKEIGRVPLLSADDE 125

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   +         AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 126 IELARRIE---NGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEK 182

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP
Sbjct: 183 FDHQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP 242

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEEIA ++ +  + VR+++KI +EP+SLETPIG+ED SHLGDFIED+ A++P D+A   
Sbjct: 243 TPEEIAAEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAAAYE 302

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAKA+RKL
Sbjct: 303 LLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 362

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSK+L+ FL+
Sbjct: 363 RHPSRSKRLKDFLE 376



 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 46/169 (27%), Positives = 78/169 (46%), Gaps = 4/169 (2%)

Query: 17  DSDDSLVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           D    L  +   D  K ++I+  ++R  +T +E+   L P +   EQ+++    L ++GI
Sbjct: 4   DQHTELDAEQKLDLVKEQLIEQGKKRASLTYKEIMEKLSPFDQDPEQIDEFFEQLDDLGI 63

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V++  D + +    +  + +   S+   F            +DPVRMYL+E+G + LLS
Sbjct: 64  EVLNERDEDRDPL--NRGEDSERESDDFNFDDDLALPPGIKINDPVRMYLKEIGRVPLLS 121

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            + EI +A+RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 122 ADDEIELARRIENGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 169


>gi|218133123|ref|ZP_03461927.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991996|gb|EEC58000.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
          Length = 448

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 179 VRMYLKEIGKVPLLSAEEEIELAKRME---NGDVEAKNRLAEANLRLVVSIAKRYVGRGM 235

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 236 LFLDLIQEGNLGLIKAVDKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 295

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK++ +PVE VR++ KI++EP+SLETPIG+E+ SHL
Sbjct: 296 INKLLRVSRQLLQELGREPTPEEIAKEMDIPVERVREIQKISQEPVSLETPIGEEEDSHL 355

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P + A    L+E    VL +LT RE++VLR+RFG+      TLEEVG++
Sbjct: 356 GDFIQDDNVPVPAEEAASTILKEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGRE 415

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR FLD
Sbjct: 416 FNVTRERIRQIEAKALRKLRHPSRSRKLRDFLD 448



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 39/141 (27%), Positives = 61/141 (43%), Gaps = 6/141 (4%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
           +  +E+       E  ++++E     L    ++V   DD+E+EE       +     +  
Sbjct: 107 LDYQEIIDSFTDAEFDADKVEKVFDFLEANNVDVKISDDVEEEEDI-----ILDPEDDID 161

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +           S +DPVRMYL+E+G + LLS E EI +AKR+E G       L E+ L 
Sbjct: 162 IEKIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEEEIELAKRMENGDVEAKNRLAEANLR 221

Query: 164 FQALIIWRDELNDGTTLLREI 184
               I  R  +  G   L  I
Sbjct: 222 LVVSIAKRY-VGRGMLFLDLI 241


>gi|319935434|ref|ZP_08009871.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809650|gb|EFW06063.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 422

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 154/274 (56%), Positives = 199/274 (72%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +S  E   +   +         AKK++  ANLRLV+S+AK+Y  RG+
Sbjct: 151 VKMYLKEIGRVELLSHDEEIDLAKRI---LEGDEEAKKKLAAANLRLVVSIAKRYVGRGM 207

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 208 LFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 267

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++  ++ REP  EEIA+K+  M  E VR++ KI+ EP+SLETPIG+ED SH
Sbjct: 268 INKLTRVQRQLIQELGREPLAEEIAEKMDGMTPEKVREIQKISLEPVSLETPIGEEDDSH 327

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED+ A+SP D A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 328 LGDFIEDEGAMSPDDYAANELLKDELNEVLLELTDREEKVLRLRFGLDDGRTRTLEEVGK 387

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHPSRSK+L+ FLD
Sbjct: 388 EFNVTRERIRQIEAKALRKLKHPSRSKRLKDFLD 421



 Score = 73.7 bits (179), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 51/231 (22%), Positives = 83/231 (35%), Gaps = 53/231 (22%)

Query: 29  DSWKKMIKLARQR--GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           +  K +IK       G ++ ++L+AFL   ++  E  E+ +  +++ GI + DG D  + 
Sbjct: 15  EDLKNLIKETADALGGTLSQDDLDAFLTKYDLDDESAEELLQFITDSGIVIEDGLDALEL 74

Query: 87  EGSE-------DSLDLASSASNSSVF---------------------------------- 105
           +  E       D  DL       ++                                   
Sbjct: 75  DDEELLKGVGTDLDDLEGLEDLGALEGLDDALGEDVPDLDFVGDFDMMTGDTANMYTHND 134

Query: 106 -LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
              + +  ++   +DPV+MYL+E+G +ELLS + EI +AKRI  G       L  + L  
Sbjct: 135 DDDENQLGSNVKINDPVKMYLKEIGRVELLSHDEEIDLAKRILEGDEEAKKKLAAANLRL 194

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
              I  R  +  G   L  I         E   G     E   Y K    S
Sbjct: 195 VVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDYTKGFKFS 236


>gi|304389369|ref|ZP_07371334.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|304327487|gb|EFL94720.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
          Length = 564

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 134/260 (51%), Positives = 188/260 (72%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  + R +  +V+    +  +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL
Sbjct: 309 MTPKQIRELHYVVQ----DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGL 364

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M  
Sbjct: 365 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 424

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P 
Sbjct: 425 DLGREPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPA 484

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEA
Sbjct: 485 DAVSFMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEA 544

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HP+RS+ LR +L+
Sbjct: 545 KTMSKLRHPARSQSLRDYLN 564



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR-AMMMASL 157
           +         +K +   +T DPV+ YL+++G + LL+ E E+ ++KRIEAG  A  +   
Sbjct: 245 SEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKT 304

Query: 158 CESPLTFQALIIWRDELNDGTT 179
            +  +T + +      + DG  
Sbjct: 305 KQETMTPKQIRELHYVVQDGQM 326


>gi|323490072|ref|ZP_08095293.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
 gi|323396368|gb|EGA89193.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
          Length = 384

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 200/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +   E   +  ++ +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 115 VRMYLKEIGRVDLLKAEEEVRLAKLIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 171

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 172 LFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 231

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + R+P+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 232 INKLIRVQRQLLQDLGRDPSPEEIGEEMDLLPEKVREILKIAQEPVSLETPIGEEDDSHL 291

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED +A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 292 GDFIEDSDAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 351

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 352 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 384



 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 51/215 (23%), Positives = 85/215 (39%), Gaps = 15/215 (6%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    +R  + ++ +            +++ K++I+  ++ G +  E++   L   E+ S
Sbjct: 1   MAEKSERQTEVEASNVPLTTEGPEATVEEAKKQLIEAGKKTGELNYEQIADKLAIFEMES 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           + +E+ +  L   GI      +LE +   E+ LD     +     L           +DP
Sbjct: 61  DAVEEFIDQLEGHGI------ELERKSDDEEHLDRLMKPTEDKFDLNDLSVPPGVKINDP 114

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G ++LL  E E+ +AK IE G       L E+ L     I  R  +  G   
Sbjct: 115 VRMYLKEIGRVDLLKAEEEVRLAKLIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLF 173

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           L  I         E   G     E   Y K    S
Sbjct: 174 LDLI--------QEGNMGLIKAVEKFDYSKGFKFS 200


>gi|46445811|ref|YP_007176.1| RNA polymerase sigma factor [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399452|emb|CAF22901.1| probable transcription initiation factor sigma 70 [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 554

 Score =  223 bits (568), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 176/495 (35%), Positives = 262/495 (52%), Gaps = 41/495 (8%)

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            +           Y K   S     R++  E    IE A    +    +       A   
Sbjct: 88  KRSEGSPDDPVRMYLKEMGSVPLLSREEEVEISKRIEKAQVQIERIILRFRYATSEAIAI 147

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE--------LRSLQDNAVNGQK 306
              L   ++    +++  E   + + M  L  I ++ +E        L  + D  +    
Sbjct: 148 ANYLLTGKERFDKSITEKEVVNKQEFMNLLPRICQLLKEEDLILERLLEQINDPNIKKND 207

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
             K     +  + ++   +  L L  + ID  VE +     R +  E E+  L      +
Sbjct: 208 RLKLIEDIEKCRIRMQAYLRRLHLRHNIIDDFVEVILRAYDRFLFLEKEIQELTPRA--E 265

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           R+ F                                   +   + ++    +  G S+ +
Sbjct: 266 RNKFAGA-------------------------------KLAAAQRKLNKRELAAGRSLDD 294

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F+  V M+++   ++  AK+EMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+GLMKA E
Sbjct: 295 FKKDVKMLQRWMDKSQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVE 354

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++  +  RE
Sbjct: 355 KFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKLMMETGRE 414

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+PEE+AK+L +  E VR++ KI + PISL+  +GD   S  GDF+ED  A SP ++   
Sbjct: 415 PSPEELAKELGITAERVREIYKIAQHPISLQAEVGDGGESQFGDFLEDTGADSPAEATGY 474

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + L++    VL++L+ RE +VL  RFG+      TLEEVG +F VTRERIRQIEAKA+RK
Sbjct: 475 SILKDKMGEVLSTLSDRERKVLIQRFGLLDGKPKTLEEVGVEFNVTRERIRQIEAKALRK 534

Query: 667 LKHPSRSKKLRSFLD 681
           ++HP RSK+L++FLD
Sbjct: 535 MRHPIRSKQLKAFLD 549



 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 44/168 (26%), Positives = 79/168 (47%), Gaps = 10/168 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
                +++ +++ +G++T EE+N  LP    S++Q++  +  LS M I V++  +     
Sbjct: 15  QQKIDELVAISKDQGFITYEEINEILPMSFDSADQIDQILIFLSGMDIQVLNQSE----- 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                +D        +  L+     ++ S DDPVRMYL+EMGS+ LLSRE E+ I+KRIE
Sbjct: 70  -----VDRQKERKKEAKELESMPKRSEGSPDDPVRMYLKEMGSVPLLSREEEVEISKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
             +  +   +          I   + L  G     + I  +  +  + 
Sbjct: 125 KAQVQIERIILRFRYATSEAIAIANYLLTGKERFDKSITEKEVVNKQE 172


>gi|89897819|ref|YP_514929.1| RNA polymerase sigma factor [Chlamydophila felis Fe/C-56]
 gi|89331191|dbj|BAE80784.1| DNA-directed RNA polymerase sigma 70 [Chlamydophila felis Fe/C-56]
          Length = 570

 Score =  223 bits (568), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 146/277 (52%), Positives = 199/277 (71%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +   +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYT
Sbjct: 276 KLDAAKRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYT 335

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVH
Sbjct: 336 NRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH 395

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+  
Sbjct: 396 MIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGG 455

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RFG+      TLEE
Sbjct: 456 ESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEE 515

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 516 VGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 552



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E ++
Sbjct: 18  QKKLEELVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLAGMDIQVLNQADVERQK 77

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+      + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 78  ERKK----------EAKELEGLARRTEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  I     L +G     +II  +    
Sbjct: 128 KAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVED 172


>gi|313764456|gb|EFS35820.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA1]
 gi|313772162|gb|EFS38128.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL074PA1]
 gi|313792142|gb|EFS40243.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA1]
 gi|313801905|gb|EFS43139.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA2]
 gi|313807517|gb|EFS46004.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA2]
 gi|313815995|gb|EFS53709.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA1]
 gi|313818559|gb|EFS56273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA2]
 gi|313820326|gb|EFS58040.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA1]
 gi|313822867|gb|EFS60581.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA2]
 gi|313825201|gb|EFS62915.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA1]
 gi|313827777|gb|EFS65491.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA2]
 gi|313830354|gb|EFS68068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL007PA1]
 gi|313833727|gb|EFS71441.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL056PA1]
 gi|314915449|gb|EFS79280.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA4]
 gi|314918269|gb|EFS82100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA1]
 gi|314920081|gb|EFS83912.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA3]
 gi|314925214|gb|EFS89045.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA3]
 gi|314931603|gb|EFS95434.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL067PA1]
 gi|314955756|gb|EFT00156.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA1]
 gi|314958170|gb|EFT02273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA1]
 gi|314962801|gb|EFT06901.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA1]
 gi|314967832|gb|EFT11931.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA1]
 gi|314973358|gb|EFT17454.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA1]
 gi|314976037|gb|EFT20132.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL045PA1]
 gi|314978425|gb|EFT22519.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA2]
 gi|314983942|gb|EFT28034.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA1]
 gi|314988126|gb|EFT32217.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA2]
 gi|314989931|gb|EFT34022.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA3]
 gi|315080641|gb|EFT52617.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL078PA1]
 gi|315084314|gb|EFT56290.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA2]
 gi|315085657|gb|EFT57633.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA3]
 gi|315088921|gb|EFT60897.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA1]
 gi|315095903|gb|EFT67879.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL038PA1]
 gi|315098534|gb|EFT70510.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA2]
 gi|315101108|gb|EFT73084.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA1]
 gi|315105654|gb|EFT77630.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA1]
 gi|315108328|gb|EFT80304.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA2]
 gi|327326185|gb|EGE67975.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA2]
 gi|327330255|gb|EGE72004.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL097PA1]
 gi|327331940|gb|EGE73677.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA3]
 gi|327443141|gb|EGE89795.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA2]
 gi|327445925|gb|EGE92579.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA2]
 gi|327448095|gb|EGE94749.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA1]
 gi|327450784|gb|EGE97438.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA3]
 gi|327453139|gb|EGE99793.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL092PA1]
 gi|327453872|gb|EGF00527.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL083PA2]
 gi|328753472|gb|EGF67088.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL020PA1]
 gi|328754202|gb|EGF67818.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA1]
 gi|328754546|gb|EGF68162.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA2]
 gi|328760854|gb|EGF74420.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL099PA1]
          Length = 511

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 214 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 273

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 334 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 393

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 394 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 453

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 454 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 511



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 165 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 224

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 225 ALLNAVEEVDLAKRIEAGL 243


>gi|294055048|ref|YP_003548706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614381|gb|ADE54536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 639

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 183/507 (36%), Positives = 275/507 (54%), Gaps = 11/507 (2%)

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E I+    I    +      ++  +Y+ R++ ++EKE    Q    D      + +  + 
Sbjct: 117 EEIENVISILQNLEIEVLDDSQVEAYKARQEETEEKEVRTSQNDILDDPVRMYLKQMGQV 176

Query: 243 KVDSPPENAENDER-NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY------RELR 295
            + +  E     +R    E     A   +A+  + +  V+  L    E +      +++ 
Sbjct: 177 PLLTREEEVAISKRIEKAELRAQDALFSTALTLEFQNDVVQKLLNREERFDRVVLDKKIE 236

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           S +    +  K  + + K           +   +   +  +    +   + K      G 
Sbjct: 237 SREAYFNSLPKLLEDAHKLGDRIYSAWDSMEEAAAAGNETNRKRARTR-MKKYEAELSGV 295

Query: 356 LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           L +      I  + FL+      ++        D    +       +   +  I   ++ 
Sbjct: 296 LKKYCLKLKIF-EDFLKDLTPTYMELK--ELYDDLETADKVTARRRKQVDVKAIERRLEE 352

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I +E  I   E   I+  VR G  EA  AK EMVEANLRLVIS+AKKYTNRGL FLDLIQ
Sbjct: 353 IKLEFKIESKELLDIIREVRIGTREAHKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQ 412

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GLMKA EKF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + ++KV++ 
Sbjct: 413 EGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETLNKVMQV 472

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            +++  ++  EPT EE+A ++ +P+E V+ ++K+ ++PISL++P+GD D ++ GDFIEDK
Sbjct: 473 QKQLLQELGHEPTAEEVADEMNLPIERVQSIMKMAQQPISLQSPVGDSDDTNFGDFIEDK 532

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A +P D    + LRE  T VL SLT RE RVL +RFG+      TLEEVG+QF VTRER
Sbjct: 533 GAENPYDMTAYSLLREKITDVLDSLTERERRVLSLRFGLADGYSRTLEEVGRQFKVTRER 592

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           IRQIEAKA+RK++HP+R ++L  F +G
Sbjct: 593 IRQIEAKALRKMRHPTRIRQLHGFFEG 619



 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 63/342 (18%), Positives = 144/342 (42%), Gaps = 27/342 (7%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +  ++  + +I++++++G++T +++N  LP    + E++E+ +++L N+ I V+D   +E
Sbjct: 81  EKLNEKIRGLIRMSKEQGFLTYKDINKGLPESVNNPEEIENVISILQNLEIEVLDDSQVE 140

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                      A  A       ++ + S +   DDPVRMYL++MG + LL+RE E+AI+K
Sbjct: 141 -----------AYKARQEETEEKEVRTSQNDILDDPVRMYLKQMGQVPLLTREEEVAISK 189

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE        +L  + LT +       +L +       ++  +     E+         
Sbjct: 190 RIEKAELRAQDALFSTALTLEFQNDVVQKLLNREERFDRVVLDKKIESREAYF------- 242

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
            +S  K  + + +         +   E+AA  ++ +R +  +  +  E +   + +    
Sbjct: 243 -NSLPKLLEDAHKLGDRIYSAWDSMEEAAAAGNETNRKRARTRMKKYEAELSGVLKKYCL 301

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                      L P  M    E+ E+Y +L    + A       +  V  K ++ +L ++
Sbjct: 302 KLKIFEDFLKDLTPTYM----ELKELYDDL----ETADKVTARRRKQVDVKAIERRLEEI 353

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
                +    +  ++ ++   ++     + E++       I 
Sbjct: 354 KLEFKIESKELLDIIREVRIGTREAHKAKTEMVEANLRLVIS 395


>gi|148380889|ref|YP_001255430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           3502]
 gi|153931224|ref|YP_001385198.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|153937635|ref|YP_001388667.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|153940633|ref|YP_001392215.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|168179368|ref|ZP_02614032.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|168181623|ref|ZP_02616287.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|170757237|ref|YP_001782571.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|170761654|ref|YP_001788251.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|187778482|ref|ZP_02994955.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226950364|ref|YP_002805455.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|237796391|ref|YP_002863943.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|148290373|emb|CAL84500.1| RNA polymerase sigma factor (sigma-43) [Clostridium botulinum A
           str. ATCC 3502]
 gi|152927268|gb|ABS32768.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|152933549|gb|ABS39048.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|152936529|gb|ABS42027.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|169122449|gb|ACA46285.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|169408643|gb|ACA57054.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|182669799|gb|EDT81775.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|182675034|gb|EDT86995.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|187772107|gb|EDU35909.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226843729|gb|ACO86395.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|229260977|gb|ACQ52010.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|295320212|gb|ADG00590.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           230613]
 gi|322807253|emb|CBZ04827.1| RNA polymerase sigma factor RpoD [Clostridium botulinum H04402 065]
          Length = 361

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +        +AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 92  VRMYLKEIGKVALLTSEEEIELAQRIE---AGDMVAKKKLAEANLRLVVSIAKRYVGRGM 148

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 149 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 208

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEE+AK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 209 INKLIRVSRQLLQELGREPQPEEVAKIMEMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 268

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 269 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 328

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 329 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 361



 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 46/154 (29%), Positives = 76/154 (49%), Gaps = 17/154 (11%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            +++I   ++ G ++ +E+   L   ++S EQ+E    +L +MG+ V    D+ D +  E
Sbjct: 18  VRRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESMGVEV--TGDMNDIDVKE 75

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +DL+                   + DDPVRMYL+E+G + LL+ E EI +A+RIEAG 
Sbjct: 76  EDIDLSVPE--------------GIAIDDPVRMYLKEIGKVALLTSEEEIELAQRIEAGD 121

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +    L E+ L     I  R  +  G   L  I
Sbjct: 122 MVAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 154


>gi|62185569|ref|YP_220354.1| RNA polymerase sigma factor [Chlamydophila abortus S26/3]
 gi|62148636|emb|CAH64409.1| major sigma factor [Chlamydophila abortus S26/3]
          Length = 571

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 175/498 (35%), Positives = 272/498 (54%), Gaps = 19/498 (3%)

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR----SKVDSPPENAEND 254
           F  G +     + +   Q++ + + +E EG  +       D       ++ + P     +
Sbjct: 61  FLTGMDIQVLNQADVERQKERKKEAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREE 120

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI------AEVYRELRSLQDNAVNGQKDE 308
           E  + +  + +   +  +  + R     A+          E + ++ S ++        +
Sbjct: 121 EVEISKRIEKAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVEDKAHFLK 180

Query: 309 KSSVKCKVLKEK---LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                  +LKE+   L  L+ +L  N    +   +   D+ K  +  +  L      + +
Sbjct: 181 LLPKLISLLKEEDAYLESLLLALKQNNLSKEETAKLNEDLEKCRIRTQAYLRCFHCRHNV 240

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPE--GEWKNFVACEVDSILKIRNEIKSISVETGIS 423
             + F E           +    +  +   E   F A ++D+    +  +    V  G +
Sbjct: 241 T-EDFGEVVFKAYDSFLQLEQQINDLKVRAERNKFAAAKLDA---AKRRLYKREVAAGRT 296

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+GLMK
Sbjct: 297 LEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMK 356

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++  + 
Sbjct: 357 AVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKLMMET 416

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED    SP ++
Sbjct: 417 GKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESSFGDFLEDTGVESPAEA 476

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIRQIEAKA
Sbjct: 477 TGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKA 536

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RK++HP RSK+LR+FLD
Sbjct: 537 LRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E ++
Sbjct: 20  QKKLEELVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+      + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  I     L +G     +II  +    
Sbjct: 130 KAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVED 174


>gi|297202863|ref|ZP_06920260.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297148238|gb|EDY59236.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 512

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 260 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 319

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 320 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 379

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 380 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 439

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 440 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 499

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 500 HPSRSQVLRDYLD 512



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 194 SDDDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 252

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            +      L    + + +    
Sbjct: 253 NADKLAPKLKRELEIIAEDGRR 274


>gi|291543225|emb|CBL16334.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus sp. 18P13]
          Length = 360

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 149/270 (55%), Positives = 201/270 (74%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S  E   +   + K     S AKK + EANLRLV+S+AKKY  RG+QFL
Sbjct: 94  YLKEIGRVPLLSAEEEIELAQRMSK---GDSYAKKRLSEANLRLVVSIAKKYVGRGMQFL 150

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I K
Sbjct: 151 DLIQEGNLGLIKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETITK 210

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +   ++ ++   EPT +EIA++L MPVE VR++++I ++P+SLETPIG+E+ SHLGDF
Sbjct: 211 VKKIISQLLHETGHEPTADEIAERLEMPVEKVREIMRIAQDPVSLETPIGEEEDSHLGDF 270

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D +A +P ++A    L+E    VL++LT RE +VL++RFG+      TLEEVG++F V
Sbjct: 271 IPDDDAPAPAEAASLILLKEQLNEVLSTLTEREAKVLKLRFGLEDGRSRTLEEVGREFEV 330

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRERIRQIEAKA+RKL+HPSRSKK++ FLD
Sbjct: 331 TRERIRQIEAKALRKLRHPSRSKKVKDFLD 360



 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 41/158 (25%), Positives = 72/158 (45%), Gaps = 8/158 (5%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
            ++S   +I+ A+  G ++  ELN      ++ +EQ++       N  I +V       E
Sbjct: 4   KNESIDALIERAKASGKLSTRELNDAFERFDLDAEQIDSFYETCINNNIEIV-------E 56

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +   D+       S+ S  L+    +   + DDPV++YL+E+G + LLS E EI +A+R+
Sbjct: 57  DFMPDTDLKLGLDSDLSDDLEMALSTEGIAIDDPVKIYLKEIGRVPLLSAEEEIELAQRM 116

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             G +     L E+ L     I  +  +  G   L  I
Sbjct: 117 SKGDSYAKKRLSEANLRLVVSIAKKY-VGRGMQFLDLI 153


>gi|295839080|ref|ZP_06826013.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295827312|gb|EDY44634.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 360

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 122/296 (41%), Positives = 180/296 (60%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ ++   +   V                         +       AK
Sbjct: 65  RQYLREIGRIPLLNAADEVELARRVEAGLFAEEKLAGPGPLDTRLALDLDRLVVLGRAAK 124

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  G+KFSTYA WW++
Sbjct: 125 RRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIR 184

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  R +  +   EP   E+A  L +  E V +
Sbjct: 185 QAMSRALADQARTIRVPVHVVELINRVVRARRTLLQERGHEPCDAEVAAVLGLTPERVGE 244

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL TP+G ED   LGD IED +A SP +SA    LR     VL++L  RE 
Sbjct: 245 VLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVLSTLGERER 304

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+    + +LR +LD
Sbjct: 305 QVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHVFADQLRGYLD 360



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +          D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 50  DRAPAPPGGHAPDLFRQYLREIGRIPLLNAADEVELARRVEAGL 93


>gi|239940961|ref|ZP_04692898.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 15998]
 gi|239987439|ref|ZP_04708103.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 11379]
          Length = 363

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 124/296 (41%), Positives = 187/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +       AK
Sbjct: 68  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEERLTGTPDLDSRLAGDLDRLVVMGRTAK 127

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 128 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 187

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+IA +L +  E V +
Sbjct: 188 QAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIAVELDLTPERVTE 247

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED    GD IED +A SP++SA    LR+    VL++L  RE 
Sbjct: 248 VLRLAQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAAFLLLRQHLEAVLSTLGERER 307

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR +LD
Sbjct: 308 KVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDHAFADQLRGYLD 363



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/70 (25%), Positives = 30/70 (42%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +      G      +  +         + +  +   T D  R YLRE+G I LL+   E+
Sbjct: 27  ETAAGPPGHAPEAVMVEATHLPEPPDPRNRADSGGPTSDLFRQYLREIGRIPLLTAAEEV 86

Query: 141 AIAKRIEAGR 150
            +A+R+EAG 
Sbjct: 87  ELARRVEAGL 96


>gi|296120487|ref|YP_003628265.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
 gi|296012827|gb|ADG66066.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
          Length = 550

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 165/467 (35%), Positives = 260/467 (55%), Gaps = 43/467 (9%)

Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
           E  R+  +E   + + A K++ D  SKV+S     +   +    +  +    L  M    
Sbjct: 119 EVTRNQFREELLECDYALKMAFDTLSKVNSGELPFDRTIKVSVTESKEKNQILGRM---- 174

Query: 277 RPKVMCALDEIAEV-YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            P  +  ++ + +    +     D   +  + +++  +    + K+VKL+  LSL   R+
Sbjct: 175 -PHNLKTIENLRKQAIGDFEKSIDANASSDERKEAEKQHLKRRRKMVKLIEELSLRTQRL 233

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
              +++L  IS+R+   + ++  L                                    
Sbjct: 234 QPTMKRLEQISRRMCDLQRQIDSLKH---------------------------------- 259

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              +    D    I  E+  + + T  +    R  V  VR+   +   A +++   NLRL
Sbjct: 260 ---LKSARDERANIHKELHDLMMMTLETPEGLRQRVERVRERFAKYEQAMRDLSGGNLRL 316

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  GYKFSTYA WW++QAITR+IADQ
Sbjct: 317 VVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWWIRQAITRAIADQ 376

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + + K+ + A+++  ++ REPT EE A+   + +E  R+V+KI++ PIS
Sbjct: 377 ARTIRIPVHMIETMSKLRKVAKKLLQEMGREPTLEETAEAAGVSLEETRRVMKISRHPIS 436

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+ P+G+ + S+ GDFIED N  SP+ +A Q  L++    VL +LT RE  ++++R+G+G
Sbjct: 437 LDRPVGESEDSYFGDFIEDDNTESPVMAATQEMLKDKIDNVLKTLTYREREIIKLRYGLG 496

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
               +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RSK+L+ FLDG
Sbjct: 497 DGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSKQLKGFLDG 543



 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/299 (18%), Positives = 122/299 (40%), Gaps = 24/299 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D    ++I   +++G++T  ++N +LP + ++ E++++ +  +   G+ +V  D +    
Sbjct: 5   DQGLHELIVRGKKQGFLTYSQINDYLPDEAMNPEKLDELLGSIWEEGLKIVTDDQVGMIV 64

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +      +      V  +K K       DDPVRMYL +MG I LL+RE EI++AK IE
Sbjct: 65  EEKKKPRTRAKNGKEVVVEEKSKK-----IDDPVRMYLTQMGEIPLLTREKEISLAKTIE 119

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             R      L E     +       ++N G       I +                E + 
Sbjct: 120 VTRNQFREELLECDYALKMAFDTLSKVNSGELPFDRTIKVSVT----------ESKEKNQ 169

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
              R   + +   +  ++  GD E +   +     + ++  ++ +   + +   E+    
Sbjct: 170 ILGRMPHNLKTIENLRKQAIGDFEKSIDANASSDERKEAEKQHLKRRRKMVKLIEE---- 225

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            LS    +L+P     +  + ++ R +  LQ    + +  + +  +   + ++L  L+ 
Sbjct: 226 -LSLRTQRLQP----TMKRLEQISRRMCDLQRQIDSLKHLKSARDERANIHKELHDLMM 279


>gi|229916320|ref|YP_002884966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
 gi|229467749|gb|ACQ69521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
          Length = 364

 Score =  223 bits (567), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 95  VRMYLKEIGRVDLLSAKDETELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 151

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 152 LFLDLIQEGNMGLIKAVEKFDYMKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 211

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIAK++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 212 INKLIRVQRQLLQDLGREPSPEEIAKEMELTPEKVREILKIAQEPVSLETPIGEEDDSHL 271

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 272 GDFIEDQDAMAPQDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 331

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FLD
Sbjct: 332 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLD 364



 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 58/261 (22%), Positives = 104/261 (39%), Gaps = 17/261 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           ++ +++ KL +++G V+++ +   L   EV S+ +++ +  L    I V +     +E  
Sbjct: 11  NAIEELEKLGKKKGVVSMQAIQDRLSHFEVDSDFIDNFIEDLEAKDIRVTEDAADAEETP 70

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++          +  V L           +DPVRMYL+E+G ++LLS + E  +AKRIE 
Sbjct: 71  AKK--------EDEEVDLNDLSVPPGIKINDPVRMYLKEIGRVDLLSAKDETELAKRIEQ 122

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G       L E+ L     I  R  +  G   L  I         E   G     E   Y
Sbjct: 123 GDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDY 173

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            K    S        Q     I   A+  +     V++  +      + L +   + +  
Sbjct: 174 MKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPE 233

Query: 269 LSAMEDQLRPKVMCALDEIAE 289
             A E +L P+ +  + +IA+
Sbjct: 234 EIAKEMELTPEKVREILKIAQ 254


>gi|282854019|ref|ZP_06263356.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|282583472|gb|EFB88852.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|314922986|gb|EFS86817.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL001PA1]
 gi|314966763|gb|EFT10862.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA2]
 gi|314981097|gb|EFT25191.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA3]
 gi|315091922|gb|EFT63898.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA4]
 gi|315093321|gb|EFT65297.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL060PA1]
 gi|327327588|gb|EGE69364.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL103PA1]
          Length = 510

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 213 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 272

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 273 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 332

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 333 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMTAEKV 392

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 393 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 452

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 453 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 510



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 164 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 223

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 224 ALLNAVEEVDLAKRIEAGL 242


>gi|313812944|gb|EFS50658.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA1]
          Length = 511

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 214 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 273

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 334 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 393

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 394 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 453

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 454 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 511



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 165 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 224

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 225 ALLNAVEEVDLAKRIEAGL 243


>gi|311069121|ref|YP_003974044.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
 gi|310869638|gb|ADP33113.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
          Length = 373

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLSAKEE---ITYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 45/174 (25%), Positives = 78/174 (44%), Gaps = 9/174 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L  D   D   ++ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQTHETETELTIDQVKD---QLTEAGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
              G+ ++      + E +ED      + +     L           +DPVRMYL+E+G 
Sbjct: 59  GEQGVELIS-----ENEETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 113

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + EI  A++IE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 VNLLSAKEEITYAQKIEEGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|302537370|ref|ZP_07289712.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
 gi|302446265|gb|EFL18081.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
          Length = 526

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 274 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 333

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 334 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 393

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 394 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 453

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 454 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 513

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 514 HPSRSQVLRDYLD 526



 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           S+       ++     +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L  
Sbjct: 209 SDDEDDAPAQQVVVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLAN 267

Query: 160 SPLTFQALIIWRDELNDGTTL 180
           S      L    + + +    
Sbjct: 268 SDKLAPKLKRELEIIAEDGRR 288


>gi|254386999|ref|ZP_05002279.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194345824|gb|EDX26790.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 520

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 268 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 327

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 328 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 387

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 388 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 447

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 448 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 507

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 508 HPSRSQVLRDYLD 520



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/117 (25%), Positives = 50/117 (42%), Gaps = 16/117 (13%)

Query: 79  DGDDLEDEEGSEDSLDLASSA---------------SNSSVFLQKRKDSADRSTDDPVRM 123
           D D+  DEE +ED+   A +                S+       ++ +   +T DPV+ 
Sbjct: 167 DADEAGDEESAEDAPGAAKAEGDEEEEGGESKGFVISDDEDDAPAQQVAVAGATADPVKD 226

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL+++G + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 227 YLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 282


>gi|157693020|ref|YP_001487482.1| RNA polymerase sigma factor RpoD [Bacillus pumilus SAFR-032]
 gi|157681778|gb|ABV62922.1| DNA-directed RNA polymerase sigma subunit SigA [Bacillus pumilus
           SAFR-032]
          Length = 373

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLSAKEE---ITYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 46/174 (26%), Positives = 79/174 (45%), Gaps = 9/174 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L F+   D   K+ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQAHETETELTFEQVRD---KLTETGKKRGVLTYEEIAERMSSFEIESDQMDEYYEYL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
              G+ ++      + E +ED      + +     L           +DPVRMYL+E+G 
Sbjct: 59  GEQGVELIS-----ENEETEDPNVQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 113

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + EI  A++IE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 VNLLSAKEEITYAQKIEEGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|126434760|ref|YP_001070451.1| RNA polymerase sigma factor [Mycobacterium sp. JLS]
 gi|126234560|gb|ABN97960.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 480

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 134/290 (46%), Positives = 195/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L    ++  +      + + + R     ++    +   AK  ++EA
Sbjct: 195 AEEEVELAKRIEAGLFATQKLAELAEKGEKLPVQQRRD----MQWICRDGDRAKNHLLEA 250

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 251 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRA 310

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +
Sbjct: 311 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAR 370

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+R
Sbjct: 371 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLR 430

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 431 FGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 480



 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 138 DEEIAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 197

Query: 139 EIAIAKRIEAGRAMMMASLCE 159
           E+ +AKRIEAG       L E
Sbjct: 198 EVELAKRIEAGLF-ATQKLAE 217


>gi|153306|gb|AAA26763.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450078|prf||1920369B RNA polymerase:SUBUNIT=sigma
          Length = 525

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 273 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 332

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 333 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 392

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 393 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 452

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 453 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 512

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 513 HPSRSQVLRDYLD 525



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/102 (26%), Positives = 43/102 (42%), Gaps = 1/102 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D    E EE  E   +     S+       ++     +T DPV+ YL+++G + LL+ E 
Sbjct: 187 DAPKAEAEEEEEGGENKGFVISDDEDDAPAQQVVVAGATADPVKDYLKQIGKVPLLNAEQ 246

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 247 EVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 287


>gi|154686781|ref|YP_001421942.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens FZB42]
 gi|154352632|gb|ABS74711.1| RpoD [Bacillus amyloliquefaciens FZB42]
          Length = 373

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVNLLSAKEE---ITYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 341 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 373



 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 44/174 (25%), Positives = 78/174 (44%), Gaps = 9/174 (5%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D +  +++  L  D   +   ++ +  ++RG +T EE+   +   E+ S+QM++    L
Sbjct: 2   ADKQTHETETELTLDQVKE---QLTETGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
              G+ ++      + E +ED      + +     L           +DPVRMYL+E+G 
Sbjct: 59  GEQGVELIS-----ENEETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGR 113

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + EI  A++IE G       L E+ L     I  R  +  G   L  I
Sbjct: 114 VNLLSAKEEITYAQKIEEGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|108799152|ref|YP_639349.1| RNA polymerase sigma factor [Mycobacterium sp. MCS]
 gi|119868267|ref|YP_938219.1| RNA polymerase sigma factor [Mycobacterium sp. KMS]
 gi|108769571|gb|ABG08293.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694356|gb|ABL91429.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
          Length = 480

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 134/290 (46%), Positives = 195/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L    ++  +      + + + R     ++    +   AK  ++EA
Sbjct: 195 AEEEVELAKRIEAGLFATQKLAELAEKGEKLPVQQRRD----MQWICRDGDRAKNHLLEA 250

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 251 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRA 310

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +
Sbjct: 311 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAR 370

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+R
Sbjct: 371 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLR 430

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 431 FGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 480



 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 138 DEEIAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 197

Query: 139 EIAIAKRIEAGRAMMMASLCE 159
           E+ +AKRIEAG       L E
Sbjct: 198 EVELAKRIEAGLF-ATQKLAE 217


>gi|329943340|ref|ZP_08292114.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
 gi|332287916|ref|YP_004422817.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313848489|emb|CBY17493.1| major sigma factor [Chlamydophila psittaci RD1]
 gi|325507028|gb|ADZ18666.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328814887|gb|EGF84877.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
          Length = 571

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 175/498 (35%), Positives = 272/498 (54%), Gaps = 19/498 (3%)

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR----SKVDSPPENAEND 254
           F  G +     + +   Q++ + + +E EG  +       D       ++ + P     +
Sbjct: 61  FLTGMDIQVLNQADVERQKERKKEAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREE 120

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI------AEVYRELRSLQDNAVNGQKDE 308
           E  + +  + +   +  +  + R     A+          E + ++ S ++        +
Sbjct: 121 EVEISKRIEKAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVEDKAHFLK 180

Query: 309 KSSVKCKVLKEK---LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                  +LKE+   L  L+ +L  N    +   +   D+ K  +  +  L      + +
Sbjct: 181 LLPKLISLLKEEDAYLESLLLALKQNNLSKEETAKLNDDLEKCRIRTQAYLRCFHCRHNV 240

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPE--GEWKNFVACEVDSILKIRNEIKSISVETGIS 423
             + F E           +    +  +   E   F A ++D+    +  +    V  G +
Sbjct: 241 T-EDFGEVVFKAYDSFLQLEQQINDLKVRAERNKFAAAKLDA---AKRRLYKREVAAGRT 296

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+GLMK
Sbjct: 297 LEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMK 356

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++  + 
Sbjct: 357 AVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKLMMET 416

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EPTPEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+ED    SP ++
Sbjct: 417 GKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESSFGDFLEDTGVESPAEA 476

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERIRQIEAKA
Sbjct: 477 TGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKA 536

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RK++HP RSK+LR+FLD
Sbjct: 537 LRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E ++
Sbjct: 20  QKKLEELVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+      + + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  I     L +G     +II  +    
Sbjct: 130 KAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVED 174


>gi|325962990|ref|YP_004240896.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469077|gb|ADX72762.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 437

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 177/253 (69%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 185 KYKRELEFIIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 244

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 245 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 304

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 305 PEELALELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 364

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 365 LQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 424

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 425 HPSRSQVLRDYLD 437



 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-------RSTDDPVRMYLREMG 129
           +++G D  +E+   D +  A+ +    V+     D A         +T DPV+ YL+++G
Sbjct: 89  ILEGPDAVEEDAEADPVKGAAGSGKGFVYSDADDDDAPVQQVMSAGATADPVKDYLKQIG 148

Query: 130 SIELLSREGEIAIAKRIEAGR 150
            + LL+ E E+ +A RIEAG 
Sbjct: 149 KVALLNAEQEVDLALRIEAGL 169


>gi|290956933|ref|YP_003488115.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
 gi|260646459|emb|CBG69556.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
          Length = 516

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 264 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 323

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 324 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 383

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 384 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 443

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 444 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 503

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 504 HPSRSQVLRDYLD 516



 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 48/101 (47%), Gaps = 3/101 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G   ++ EG+E++  + S         Q+   +A  +T DPV+ YL+++G + LL+ E E
Sbjct: 181 GKPGDEPEGTENAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLKQIGKVPLLNAEQE 238

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +AKRIEAG       L  +      L    + + +    
Sbjct: 239 VELAKRIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 278


>gi|254382896|ref|ZP_04998252.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
 gi|194341797|gb|EDX22763.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
          Length = 362

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 128/296 (43%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         K      +AK
Sbjct: 67  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAGHTDLDLQLTLDLDKLVVMGRMAK 126

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 127 RRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 186

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E V +
Sbjct: 187 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTVEEVAVHLELTPERVLE 246

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 247 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFFLLREHLEAVLSTLGERER 306

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 307 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 362



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                S    + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 52  TADSGSGSGPSADLFRQYLREIGRIPLLTAAEEVELARRVEAGL 95


>gi|306822519|ref|ZP_07455897.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
 gi|304554064|gb|EFM41973.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
          Length = 472

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 201/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T  S  +F+     ++    +   AK  ++EANLRLV+
Sbjct: 189 AEQEVDLSERIEAGLYAQHLLDTEASQMDFKRR-RELKWAANDGKKAKDHLLEANLRLVV 247

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 248 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 307

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 308 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 367

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 368 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 427

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 428 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 471



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 161 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 203


>gi|225351336|ref|ZP_03742359.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157680|gb|EEG70963.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 472

 Score =  223 bits (567), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 189 AEQEVDLSERIEAGLYAQHLLDTESDQMDFKR-KRELKWAANDGRRAKDHLLEANLRLVV 247

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 248 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 307

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 308 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 367

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 368 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLSPREAGVIKMRYGLEDG 427

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 428 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 471



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 34/57 (59%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D     + +     KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 147 DDDDDENLTPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 203


>gi|254430902|ref|ZP_05044605.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
 gi|197625355|gb|EDY37914.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
          Length = 503

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 256 KFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 315

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 316 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEI 375

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 376 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 434

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 435 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 494

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 495 NGVLKEYI 502



 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           A     +      +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 170 AGDEKAAKALASIKVGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 220


>gi|315103424|gb|EFT75400.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA2]
          Length = 510

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 213 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 272

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 273 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 332

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 333 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMTAEKV 392

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 393 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 452

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 453 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 510



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 164 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 223

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 224 ALLNAVEEVDLAKRIEAGL 242


>gi|72162538|ref|YP_290195.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71916270|gb|AAZ56172.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thermobifida
           fusca YX]
          Length = 616

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/261 (51%), Positives = 182/261 (69%), Gaps = 4/261 (1%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ++  E   +         +   AKK ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+G
Sbjct: 360 ELTPEEREEL----EWIAEDGKRAKKHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLG 415

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M 
Sbjct: 416 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQML 475

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
             + REPTPEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  A+ P
Sbjct: 476 QDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIQP 535

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            ++     L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE
Sbjct: 536 GEAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIE 595

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           +K + KL+HPSRS+ LR +LD
Sbjct: 596 SKTMSKLRHPSRSQVLRDYLD 616



 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 10/108 (9%)

Query: 53  LPPDEVSSEQMEDT---VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           L   ++  +  E+T   + ++ +    VV+ ++    + S D  + A +  + S  L   
Sbjct: 241 LEATDLLEDNFEETGADLELVDDTDDEVVELEETTPAKRSRDLPEKADADDDDSFVLYDD 300

Query: 110 KDSAD-------RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            D A         +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 301 DDDAPAAQVVAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGL 348


>gi|111115542|ref|YP_710160.1| RNA polymerase sigma factor RpoD [Borrelia afzelii PKo]
 gi|110890816|gb|ABH01984.1| RNA polymerase sigma-70 factor [Borrelia afzelii PKo]
          Length = 631

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 176/653 (26%), Positives = 312/653 (47%), Gaps = 38/653 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +I     R  ++  EL+  LP D +  E ++   ++L + GI +V+     D  G+E
Sbjct: 12  IESIITHVGDRKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVGTE 71

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  D       +S       D   +S                    E ++ I  +++   
Sbjct: 72  DGNDEEEEVEIASDRSFMVLDDGFQSD-------------------EEDVDIDVKLDDCD 112

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                         +  I  +D+L  G       +  ++      K       +      
Sbjct: 113 --------------EEGISIKDDLGSGYIKSN--VLKDSHSEDPIKLYLKEIGKEFLLTG 156

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            ++    K+ D  +    +I     +  ++   + +   +    E     ++D    +  
Sbjct: 157 NQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDRDKESNP 216

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSL 328
              ++ +         +  V   L S  DN     +      +  + KE+L   +L+  +
Sbjct: 217 DYYNKKKRIASFYKIPLKPVQDRLISYVDNKHRVYELGGDIFEKNLKKERLALKELLRDI 276

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
            L Q  + +  +   D + +I   + +   +     I++   L    GR+L         
Sbjct: 277 PLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEI 335

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +      ++ +  ++      + E++ I +     + +   +   + KG+     AK ++
Sbjct: 336 EKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEIAKGKQMMQHAKDQL 395

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAI
Sbjct: 396 IKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAI 455

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  
Sbjct: 456 TRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDEELSDRLGWELKKVKTVKS 515

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +++EP+SLETPIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V+
Sbjct: 516 VSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVV 575

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 576 KMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|304403970|ref|ZP_07385632.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
 gi|304346948|gb|EFM12780.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
          Length = 377

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + K       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 108 VRMYLKEIGRVPLLSADDEVELAKRIEK---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD   GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA ++ +  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 225 INKLIRVSRQLLQELGREPAPEEIAAEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 285 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377



 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 47/174 (27%), Positives = 80/174 (45%), Gaps = 5/174 (2%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + D     +   D   ++I+  ++R  +T +E+   L P +   EQ+++    L
Sbjct: 2   ANDQHTELDTEQKLELIKD---QLIEHGKKRSSLTYKEIMEKLAPFDQDPEQIDEFFEQL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            ++GI VV+ +D E     +D        ++   F            +DPVRMYL+E+G 
Sbjct: 59  DDLGIEVVNEND-ESPISRDDHDRDRDQENDEFNFDDDLALPPGIKINDPVRMYLKEIGR 117

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + LLS + E+ +AKRIE G       L E+ L     I  R  +  G   L  I
Sbjct: 118 VPLLSADDEVELAKRIEKGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 170


>gi|25028360|ref|NP_738414.1| RNA polymerase sigma factor [Corynebacterium efficiens YS-314]
 gi|23493645|dbj|BAC18614.1| sigma factor SigA [Corynebacterium efficiens YS-314]
          Length = 506

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 128/250 (51%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 257 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 316

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 317 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 376

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 377 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 436

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 437 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 496

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 497 RSQVLRDYLD 506



 Score = 56.4 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 14/104 (13%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           EE  AF+P DE+  +  ++   +              E+EE  ED          S+   
Sbjct: 140 EEDPAFIPGDELEQD--DEVAPL------------GEEEEEEEEDDGSSVWDEDESATLR 185

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 186 QARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 229


>gi|315078017|gb|EFT50068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA2]
          Length = 511

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 214 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 273

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 334 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 393

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 394 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 453

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 454 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 511



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 165 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 224

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 225 ALLNAVEEVDLAKRIEAGL 243


>gi|87307232|ref|ZP_01089377.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87289972|gb|EAQ81861.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 507

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 157/496 (31%), Positives = 257/496 (51%), Gaps = 15/496 (3%)

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
            F +         R  +   +E++D+ E   D        +    ++   P  +  +E +
Sbjct: 4   AFDNDDFEQDPAARFPADAAEEQEDMFEDPSDDSQIDDPIRMYLMQMGEIPMLSRQEEVD 63

Query: 258 LDEDEDDSAHTLS---AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK- 313
                +             D +  + +  L+++ +    L    + +V   K++K+ ++ 
Sbjct: 64  AARQIEFWRTRFRHAFISNDFILEQSVQLLEQVRDGKLRLDRTVEVSVTNAKEKKNIMRR 123

Query: 314 ----CKVLKEKLVKLVGSLSLNQSRIDLLVEQL---YDISKRIMHNEGELLRLAQSYGIK 366
                  L++ L   V    +  S+   L E+     ++ +R       +  L       
Sbjct: 124 IGPNLVTLRKLLTGNVTDFKVVISKTASLAERCAASKNMIRRRAKAVRLIEELNLRTNKI 183

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
             +  +    RE+    +       +   K  V+    ++ ++R E++ +   T  S + 
Sbjct: 184 SALLPKL---REISER-MDTLLGQIDEATKAGVSRTGQTVNELRTELRYLMKVTLESPTM 239

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R  +  + + + E   AK+ +   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +
Sbjct: 240 LRRRLLRISEFQEEYDAAKRLLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVD 299

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITR+IADQS TIR+PVHM D + KV    R +  ++ R+
Sbjct: 300 KFEYQRGYKFSTYATWWIRQAITRAIADQSRTIRVPVHMIDTMGKVRAVTRDLLQELGRD 359

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE+A++  + ++  R +LK+ + P+SL+ P+GD D S  G+F+ED     PL    Q
Sbjct: 360 PTAEEVAERAGLSIDDARVILKMNRNPLSLDQPVGDHDDSFFGEFLEDHRDEDPLYETHQ 419

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++    VL +L  RE  ++R+R+G+     +TLEEVGK F VTRER+RQIE+KA+RK
Sbjct: 420 QALKDRLCEVLEALNHREREIIRLRYGLTDGYSYTLEEVGKIFSVTRERVRQIESKAVRK 479

Query: 667 LKHPSRSKKLRSFLDG 682
           L+ P RS+ L SFL+G
Sbjct: 480 LQQPYRSRGLASFLEG 495



 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 31/119 (26%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D DD E +  +    D A    +          S D   DDP+RMYL +MG I +LSR+
Sbjct: 5   FDNDDFEQDPAARFPADAAEEQED-----MFEDPSDDSQIDDPIRMYLMQMGEIPMLSRQ 59

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            E+  A++IE  R     +   +    +  +   +++ DG   L   +++      E K
Sbjct: 60  EEVDAARQIEFWRTRFRHAFISNDFILEQSVQLLEQVRDGKLRLDRTVEVSVTNAKEKK 118


>gi|329940007|ref|ZP_08289289.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329300833|gb|EGG44729.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 512

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 260 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 319

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 320 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 379

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 380 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 439

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 440 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 499

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 500 HPSRSQVLRDYLD 512



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 3/98 (3%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ++ EG+E +  + S         Q+   +A  +T DPV+ YL+++G + LL+ E E+ +
Sbjct: 180 ADEPEGTESAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLKQIGKVPLLNAEQEVEL 237

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           AKRIEAG       L  +      L    + + +    
Sbjct: 238 AKRIEAGLF-AEDKLASADKLAPKLKRELEIIAEDGRR 274


>gi|325677627|ref|ZP_08157279.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
 gi|324110595|gb|EGC04759.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
          Length = 366

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 147/271 (54%), Positives = 204/271 (75%), Gaps = 1/271 (0%)

Query: 412 EIKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +K I     ++  E   +  M+    + +AS A+K + EANLRLV+S+AK+Y  RG+ F
Sbjct: 96  YLKEIGRVPLLTSEEEIQLAEMMSGDNDRDASKARKRLAEANLRLVVSIAKRYVGRGMSF 155

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I 
Sbjct: 156 LDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIT 215

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           KV + + ++ +K   +P+PEEIA+ L M VE VR++++I ++P+SLETPIG+E+ SHLGD
Sbjct: 216 KVKKASSQLLHKNGHDPSPEEIAEDLDMSVEKVREIMRIAQDPVSLETPIGEEEDSHLGD 275

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FI D +A +P ++A    L+E   +VL++LT REE+VLR+RFG+      TLEEVG++F 
Sbjct: 276 FIPDDDAPAPAEAASLVLLKEQIDQVLSTLTEREEKVLRLRFGLEDGRSRTLEEVGQEFK 335

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+HP+RS K+R +LD
Sbjct: 336 VTRERIRQIEAKALRKLRHPNRSNKVRDYLD 366



 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 40/189 (21%), Positives = 74/189 (39%), Gaps = 18/189 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +++  +Q G +T +E+   L       +QM+      S + I ++D   ++D     
Sbjct: 8   LENLLEHGKQTGKLTTKEITDALEKLNFDVDQMDGVYEKCSELNIEIIDDVVVDDTLDFN 67

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI---- 146
           +  D           +     +   + DDPV++YL+E+G + LL+ E EI +A+ +    
Sbjct: 68  NPEDDLEQED-----VDISLSTDGIAIDDPVKIYLKEIGRVPLLTSEEEIQLAEMMSGDN 122

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           +   +     L E+ L     I  R  +  G + L  I         E   G     E  
Sbjct: 123 DRDASKARKRLAEANLRLVVSIAKRY-VGRGMSFLDLI--------QEGNMGLIKAVEKF 173

Query: 207 SYQKREDSS 215
            Y+K    S
Sbjct: 174 DYKKGFKFS 182


>gi|187250727|ref|YP_001875209.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
 gi|186970887|gb|ACC97872.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
          Length = 571

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 153/436 (35%), Positives = 255/436 (58%), Gaps = 8/436 (1%)

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +  E   + L      +   L+ M  +L+           E+   ++ L++ +++ +   
Sbjct: 140 DQEEMTTKELMPRGKRTTRELNNMRKKLKEAAKFIGKREGEITELMKKLREPSISDKMLN 199

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ---SYGI 365
           K +   +  ++++V  +  L+LNQ++I  L  ++  +++RI  +  +L R  +    Y  
Sbjct: 200 KYTEALEKKQKEVVDSIIKLNLNQNKIKRLTNRIKSLAQRIAESRNDLNRFDEYFGQYAE 259

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            + +F +  +G+ +    +     F   E    +   +++I  IR+  + +     +S  
Sbjct: 260 VKKLFTQASKGK-ISKAELKKKTRFTYEE----LETAINNIDMIRSRHEKLINTLPMSEK 314

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EF      +   E      K ++++ANLRLV+S+AKK+ N  L+  DLIQEG +GLMKA 
Sbjct: 315 EFLAFNDRIVFFEDMILQDKLKLIKANLRLVVSIAKKHVNSNLELSDLIQEGGLGLMKAV 374

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKF++  G+KFSTYA WW++Q+I R+IADQ+ TIRIPVHM++ + K+ +   +   +  R
Sbjct: 375 EKFEYKRGFKFSTYATWWIRQSINRAIADQANTIRIPVHMKELVSKLTKVTNKFRQEHGR 434

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP+ E+ +K L + +E V+ VLKI ++PISL TP+G+++ S+L DFIEDK   +P  +A 
Sbjct: 435 EPSLEDYSKSLRLSMEKVKGVLKIMQDPISLSTPVGEDEDSNLEDFIEDKAGANPTVTAS 494

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               ++  + VL +L+ RE +++R+RFGI      TLEEVGK F VTRER+RQIEAKAIR
Sbjct: 495 DFLRKQEVSEVLNTLSEREAKIIRLRFGIDSGYPRTLEEVGKMFNVTRERVRQIEAKAIR 554

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSR+K L+ + D
Sbjct: 555 KLRHPSRTKMLKDYSD 570



 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 59/338 (17%), Positives = 138/338 (40%), Gaps = 17/338 (5%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + + ++ ++K ++++ ++ G++T++E+N  L    +S+E ++  +  L ++GI VVD   
Sbjct: 1   MVNVANKAFKDLVEVGKENGFLTLDEINRSLTSSSMSAEDIDGLMGTLEDLGIQVVDRKK 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            +    +E         +N                 + +RMYL EMG + LLSR+ EI +
Sbjct: 61  YKSVAMAEKEAYTEEFMANPD-------------ISNSIRMYLSEMGKVPLLSRDEEITL 107

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           A+ +      +   + ESP+T + +  W + ++      +E++        E        
Sbjct: 108 ARNVREREKELRKLVLESPITMREICNWEELVDQEEMTTKELMPRGKRTTRELNNMRKKL 167

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E   +  + +    +    ++E     +   K ++    K     ++      N ++ +
Sbjct: 168 KEAAKFIGKREGEITELMKKLREPSISDKMLNKYTEALEKKQKEVVDSIIKLNLNQNKIK 227

Query: 263 --DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL-KE 319
              +   +L+    + R   +   DE    Y E++ L   A  G+  +    K      E
Sbjct: 228 RLTNRIKSLAQRIAESRND-LNRFDEYFGQYAEVKKLFTQASKGKISKAELKKKTRFTYE 286

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           +L   + ++ + +SR + L+  L    K  +     ++
Sbjct: 287 ELETAINNIDMIRSRHEKLINTLPMSEKEFLAFNDRIV 324


>gi|239982743|ref|ZP_04705267.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 491

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 239 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 298

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 299 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 358

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 359 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 418

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 419 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 478

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 479 HPSRSQVLRDYLD 491



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +    EG+         + +       ++ +A  +T DPV+ YL+++G + LL+ E E+ 
Sbjct: 156 EEGAPEGTGGESQGFVLSDDDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQEVE 215

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +AKRIEAG       L  +      L    + + +    
Sbjct: 216 LAKRIEAGLF-AEDKLANADKIAPKLKRELEIIAEDGRR 253


>gi|266625476|ref|ZP_06118411.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288862622|gb|EFC94920.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 381

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 131/272 (48%), Positives = 190/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    + + ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 113 VRMYLKEIGTVPLLSADEE---LRLAKRKADGDEDAKERLIEANLRLVVSIAKRYTGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 170 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A  L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 230 INKMSKMQRKLTLELGYEPSVTELADALDMSEDKVMEIMQIAREPASLETPIGEEDDSNL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 290 GDFVADNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 349

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 350 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/199 (26%), Positives = 80/199 (40%), Gaps = 22/199 (11%)

Query: 25  DFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG---INVVDG 80
           D   +   K+++L + +   + + E+N F   D ++ EQM+   + L N G   I V+D 
Sbjct: 4   DNFLEKLGKLVELGKTKHNALDVTEINNFFMGDSLTPEQMDQIYSYLENRGVDVIPVIDD 63

Query: 81  DDLEDEEGSEDSLDLASS---------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
             L D+    D   L            A    + L          T+DPVRMYL+E+G++
Sbjct: 64  SILADDVLLSDDALLLDDDLDDSFIKGADEEDIDLDAIDLLEGIGTEDPVRMYLKEIGTV 123

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LLS + E+ +AKR   G       L E+ L     I  R     G + L  +       
Sbjct: 124 PLLSADEELRLAKRKADGDEDAKERLIEANLRLVVSIAKRY-TGRGMSFLDLV------- 175

Query: 192 GPESKGGFFHGTEGHSYQK 210
             E   G   G E   Y K
Sbjct: 176 -QEGNLGLIKGVEKFDYTK 193


>gi|297588502|ref|ZP_06947145.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
 gi|297573875|gb|EFH92596.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
          Length = 389

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +S  E    V + ++ E  +  AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 120 VKMYLKEIGKIPLLSAEEE---VKLAQEMENGSKRAKKKLAEANLRLVVSIAKRYVGRGM 176

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 177 SFLDLIQEGNLGLMKAVDKFDYTRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 236

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VR  R++   + R+PT EEIAK++ + VE VR+V KI +EP+SLETPIG+E+ SHL
Sbjct: 237 INRLVRIERQLLQDLGRDPTNEEIAKEMGIEVEKVREVRKIAQEPVSLETPIGEEEDSHL 296

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A++P ++A    LRE    +L +L  RE +VL +RFG+   T  TLEEVGK 
Sbjct: 297 GDFIEDDTAIAPDEAANFTMLREELEGILNTLNERERKVLALRFGLVDGTPRTLEEVGKD 356

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KL+ FL+
Sbjct: 357 FDVTRERIRQIEAKALRKLKHPSRSQKLKDFLE 389



 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 41/173 (23%), Positives = 73/173 (42%), Gaps = 15/173 (8%)

Query: 26  FSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
              D+  ++I++  +  G VTI++         +  + +ED   +L    I + + +D  
Sbjct: 11  IKKDALNQLIEIGNENDGIVTIKDFKNIDDISCLDEDDIEDIRNLLIENNIEIFESNDEI 70

Query: 85  DEEGSEDSLDLASSASNSSVFLQKR-------------KDSADRSTDDPVRMYLREMGSI 131
           +++ S    D      + S+  +                D    + DDPV+MYL+E+G I
Sbjct: 71  EKKSSSKDDDNDDIEDDESIDDEDDDDIKDDKKIIEDVSDIKGINVDDPVKMYLKEIGKI 130

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LLS E E+ +A+ +E G       L E+ L     I  R  +  G + L  I
Sbjct: 131 PLLSAEEEVKLAQEMENGSKRAKKKLAEANLRLVVSIAKRY-VGRGMSFLDLI 182


>gi|5030433|gb|AAC44889.2| sigma 70-type sigma factor SigA [Thermotoga maritima]
          Length = 407

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 138/272 (50%), Positives = 189/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     ++ ++ R +    +        AK++++ +NLRLV+S+AK+Y  RGL
Sbjct: 131 IKMYLKEIGKIPLLTPAQERELARRAQ---MGDKKAKEKLITSNLRLVVSIAKRYMGRGL 187

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 188 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 247

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R    K   EP+ EE+AK +  P E ++++L+  KE ISLE+PIG+++ S +
Sbjct: 248 INKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSI 307

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+ D +  SP   A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ 
Sbjct: 308 EDFVADDSIASPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQY 367

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK L+S L
Sbjct: 368 FNVTRERIRQIEVKALRKLRHPSRSKYLKSLL 399



 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 38/146 (26%), Positives = 63/146 (43%), Gaps = 6/146 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVVDGDDLED 85
           +   KK+I L +++GY+T E+++   PPD     +  +E     L   GIN+V      +
Sbjct: 40  ERRIKKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIV----ENE 95

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E  E S           +  +  +     +  D ++MYL+E+G I LL+   E  +A+R
Sbjct: 96  PEEEEISASSDEQELEELLEKESPEIHDSSNVRDSIKMYLKEIGKIPLLTPAQERELARR 155

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR 171
            + G       L  S L     I  R
Sbjct: 156 AQMGDKKAKEKLITSNLRLVVSIAKR 181


>gi|148270473|ref|YP_001244933.1| RpoD family RNA polymerase sigma factor [Thermotoga petrophila
           RKU-1]
 gi|170289132|ref|YP_001739370.1| RpoD family RNA polymerase sigma factor [Thermotoga sp. RQ2]
 gi|147736017|gb|ABQ47357.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga
           petrophila RKU-1]
 gi|170176635|gb|ACB09687.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga sp. RQ2]
          Length = 407

 Score =  222 bits (566), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 138/272 (50%), Positives = 189/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     ++ ++ R +    +        AK++++ +NLRLV+S+AK+Y  RGL
Sbjct: 131 IKMYLKEIGKIPLLTPAQERELARRAQ---MGDKKAKEKLITSNLRLVVSIAKRYMGRGL 187

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 188 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 247

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R    K   EP+ EE+AK +  P E ++++L+  KE ISLE+PIG+++ S +
Sbjct: 248 INKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSI 307

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+ D +  SP   A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ 
Sbjct: 308 EDFVADDSIASPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQY 367

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK L+S L
Sbjct: 368 FNVTRERIRQIEVKALRKLRHPSRSKYLKSLL 399



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 38/148 (25%), Positives = 65/148 (43%), Gaps = 6/148 (4%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDL 83
             +   KK+I L +++GY+T E+++   PPD  +  +  +E     L   GIN+V     
Sbjct: 38  QVEKRIKKLISLGKKKGYITYEDIDKAFPPDFEDFDTNLIERIHEELEKHGINIV----E 93

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            + E  E S+          +  +  +     +  D ++MYL+E+G I LL+   E  +A
Sbjct: 94  SESEEEEMSVPGDEQELEELLERESPEIHDSSNVRDSIKMYLKEIGKIPLLTPAQERELA 153

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWR 171
           +R + G       L  S L     I  R
Sbjct: 154 RRAQMGDKKAKEKLITSNLRLVVSIAKR 181


>gi|258653895|ref|YP_003203051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258557120|gb|ACV80062.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 448

 Score =  222 bits (565), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 132/289 (45%), Positives = 195/289 (67%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L     ++          ++ R  +  +++   +   AK  ++EAN
Sbjct: 163 AEEEVDLAKRIEAGLYSSERMRQFEEAGERLPNQMRRDLRWIKR---DGERAKNHLLEAN 219

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++
Sbjct: 220 LRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 279

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  + V ++ +  +E
Sbjct: 280 ADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPDKVLEIQQYARE 339

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RF
Sbjct: 340 PISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQAVLQTLSEREAGVVRLRF 399

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 400 GLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 448



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/71 (35%), Positives = 37/71 (52%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G D   ++  E           S    Q RKD+   ++ D VR YL+++G + LL+ E E
Sbjct: 107 GKDATPDKPGESEEFTWDDEEESEALKQARKDAELTASADSVRAYLKQIGKVALLNAEEE 166

Query: 140 IAIAKRIEAGR 150
           + +AKRIEAG 
Sbjct: 167 VDLAKRIEAGL 177


>gi|320010942|gb|ADW05792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 358

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 126/296 (42%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     +S ++   +   V                         +      +AK
Sbjct: 63  RQYLREIGRIPLLSAADEVELARRVEAGLFAEERLAGTPDPDSGLAVDLDRLVVMGRMAK 122

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 123 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 182

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EP PEE+A +L +  E V +
Sbjct: 183 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPAPEEVAAQLDLTPERVSE 242

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED    GD IED +A SP+++A    LRE    VL++L  RE 
Sbjct: 243 VLRLAQEPVSLHAPVGEEDDVAFGDLIEDGDAASPVETAAFLLLREHLEVVLSTLGERER 302

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 303 KVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLDKLRGHAFADQLRGYLD 358



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E        L        +   + +  +   T D  R YLRE+G I LLS   E+ +A+R
Sbjct: 27  ETAGTPEPVLEEPVEPRELPGPRSRPDSGGPTSDLFRQYLREIGRIPLLSAADEVELARR 86

Query: 146 IEAGRAMMMASLCESP 161
           +EAG       L  +P
Sbjct: 87  VEAGLF-AEERLAGTP 101


>gi|262202178|ref|YP_003273386.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
 gi|262085525|gb|ACY21493.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
          Length = 489

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 189 VRAYLKQIGKVALLNAEEEVELAKRIEAGLFATERLRRIMESGEKITTAQKRDLNWISRD 248

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 249 GNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 308

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 309 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 368

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 369 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 428

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 429 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 488

Query: 681 D 681
           D
Sbjct: 489 D 489



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
               E     + + D       S    Q RKD+   ++ D VR YL+++G + LL+ E E
Sbjct: 148 AAAKETATPEKTAGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEE 207

Query: 140 IAIAKRIEAGR--AMMMASLCES 160
           + +AKRIEAG      +  + ES
Sbjct: 208 VELAKRIEAGLFATERLRRIMES 230


>gi|331696864|ref|YP_004333103.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951553|gb|AEA25250.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 461

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 136/301 (45%), Positives = 190/301 (63%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV----------------------------RKGECE 440
           +R  +K I     ++  E   +   +                            R    +
Sbjct: 161 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERLRRAIESGEKVSPQLRRDLRWIVRD 220

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 221 GERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 280

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 281 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 340

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VLA+L
Sbjct: 341 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLATL 400

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 401 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 460

Query: 681 D 681
           D
Sbjct: 461 D 461



 Score = 57.2 bits (136), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/64 (37%), Positives = 34/64 (53%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG  
Sbjct: 132 SGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLY 191

Query: 152 MMMA 155
               
Sbjct: 192 AAER 195


>gi|134098380|ref|YP_001104041.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006918|ref|ZP_06564891.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133911003|emb|CAM01116.1| RNA polymerase major sigma factor [Saccharopolyspora erythraea NRRL
           2338]
          Length = 467

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 136/289 (47%), Positives = 193/289 (66%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L     ++           + R     +R    +   AK  ++EAN
Sbjct: 182 AEEEVELAKRIEAGLYAAERLRQAEEAEERLAMQMR---RDLRWIVRDGERAKNHLLEAN 238

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++
Sbjct: 239 LRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 298

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +E
Sbjct: 299 ADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYARE 358

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  IGDE  S LGDFIED  AV  +D+     L++    VLA+L+ RE  V+R+RF
Sbjct: 359 PISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRF 418

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 419 GLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 467



 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 37/136 (27%), Positives = 61/136 (44%), Gaps = 9/136 (6%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ 107
           E++  +  D  S +     VA L+ + + + +   + ++E  +   D       S    Q
Sbjct: 99  EIDEPIETDLTSPD-----VADLAEVEVEIPEEPTVPEDEDGKADSDFVWDEEESEALRQ 153

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM----MASLCESPLT 163
            RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG         A   E  L 
Sbjct: 154 ARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERLRQAEEAEERLA 213

Query: 164 FQALIIWRDELNDGTT 179
            Q     R  + DG  
Sbjct: 214 MQMRRDLRWIVRDGER 229


>gi|289423762|ref|ZP_06425557.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
 gi|289155801|gb|EFD04471.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
          Length = 385

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 147/273 (53%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +   E      ++         +K+++VEANLRLV+S+AK+Y  RG+
Sbjct: 116 VRMYLKEIGKIPLLKPHEEVEFARLM---SEGDERSKQKLVEANLRLVVSIAKRYVGRGM 172

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 173 LFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 232

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+P PEEIAK + M  + VR+++KI ++P+SLETPIG+E+ SHL
Sbjct: 233 INKLIRVSRQLLQELGRDPKPEEIAKVMNMSEDKVREIMKIAQDPVSLETPIGEEEDSHL 292

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++A +P ++A  + L+E    VL +L  RE++VL++RFG+      TLEEVGK+
Sbjct: 293 GDFIPDEDAPAPAEAAAYSLLKEQIEEVLNTLNDREQKVLKLRFGLEDGRARTLEEVGKE 352

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR +LD
Sbjct: 353 FDVTRERIRQIEAKALRKLRHPSRSKKLRDYLD 385



 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 35/150 (23%), Positives = 58/150 (38%), Gaps = 10/150 (6%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
           VT+ ++       ++  +  E+    L N+GI V++  + + +    +  DL   + +  
Sbjct: 30  VTLYDIMEAFQDKDLDKDVAENLYETLGNLGIEVINDKEFKADINLNEPDDLDIKSIDEE 89

Query: 104 VFLQKRKD---------SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
                                S DDPVRMYL+E+G I LL    E+  A+ +  G     
Sbjct: 90  SSEDTETAETETAEIAVPKGISIDDPVRMYLKEIGKIPLLKPHEEVEFARLMSEGDERSK 149

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREI 184
             L E+ L     I  R  +  G   L  I
Sbjct: 150 QKLVEANLRLVVSIAKRY-VGRGMLFLDLI 178


>gi|331003577|ref|ZP_08327074.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412418|gb|EGG91809.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 409

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 129/272 (47%), Positives = 190/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E   +       +     AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 140 VRMYLKEIGTVPLLTANEELELAKR---KQDGDEYAKQRLIEANLRLVVSIAKRYTGRGM 196

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  G+K STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 197 SFLDLVQEGNLGLIKGVEKFDYTKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 256

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A +L M  E V ++++I +EP SLETPIG+ED S+L
Sbjct: 257 INKMSKMQRKLTLELGYEPSVTELANELGMTEEKVMEIMQIAREPASLETPIGEEDDSNL 316

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N ++P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 317 GDFVADANVLTPEGNVESVMLREHIDTLLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 376

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 377 FKVTRERIRQIEAKALRKLRNPVRSKRIRDFL 408



 Score = 91.4 bits (225), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 69/347 (19%), Positives = 129/347 (37%), Gaps = 37/347 (10%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD------------DLEDEEGSED 91
           ++I E+N F    E+++E +E   + L N GI + +              ++ DE+    
Sbjct: 51  LSIGEINDFFADTELNTESIEQIYSYLENKGIEINEDSVDDMNIDIDNIDNITDEDSLLL 110

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             D     S   + L          T+DPVRMYL+E+G++ LL+   E+ +AKR + G  
Sbjct: 111 DDDEFDKDSEEDIDLSAIDLLEGVGTEDPVRMYLKEIGTVPLLTANEELELAKRKQDGDE 170

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
                L E+ L     I  R     G + L  +         E   G   G E   Y K 
Sbjct: 171 YAKQRLIEANLRLVVSIAKRY-TGRGMSFLDLV--------QEGNLGLIKGVEKFDYTKG 221

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
              S        Q     +   A+  +     V++  + ++   +   E   + + T  A
Sbjct: 222 FKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVTELA 281

Query: 272 MEDQLRPKVMCALDEIAEVYRELRS----------LQDNAVNGQKDEKSSVKCKVLKEKL 321
            E  +  + +  + +IA     L +              A       + +V+  +L+E +
Sbjct: 282 NELGMTEEKVMEIMQIAREPASLETPIGEEDDSNLGDFVADANVLTPEGNVESVMLREHI 341

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
             L+G L   + ++ +L   L D       +   L  + + + + R+
Sbjct: 342 DTLLGDLKERERQVIVLRFGLED------GHPRTLEEVGKEFKVTRE 382


>gi|315645989|ref|ZP_07899110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315278750|gb|EFU42064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 376

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   + + + +       AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 107 VRMYLKEIGRVPLLSADDEIELANRIEQ---GDEEAKRRLAEANLRLVVSIAKRYVGRGM 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 164 LFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 223

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP+PEEIA ++ + VE VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 224 INKLIRVSRQLLQELGREPSPEEIAAEMELSVEKVREIMKIAQEPVSLETPIGEEDDSHL 283

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 284 GDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 343

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 344 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 376



 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 81/349 (23%), Positives = 138/349 (39%), Gaps = 25/349 (7%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           ++ +H + +     D   D   ++I+  ++R  ++ +++   L P +  +EQME+    L
Sbjct: 2   ANDQHTELETEFTLDQVKD---QLIEQGKKRSVLSYKDIMEKLSPFDQDTEQMEEFYEQL 58

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +++GI+VV+ +D  DE     S D  S  +    F            +DPVRMYL+E+G 
Sbjct: 59  ADLGIDVVNEND--DEGTHRQSEDSESRENEDFGFDDDLSLPPGIKINDPVRMYLKEIGR 116

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LLS + EI +A RIE G       L E+ L     I  R  +  G   L  I      
Sbjct: 117 VPLLSADDEIELANRIEQGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI------ 169

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
              E   G     E   Y+K    S        Q     I   A+  +     V++  + 
Sbjct: 170 --QEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 227

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                + L E   + +    A E +L    +  + EI ++ +E  SL+            
Sbjct: 228 IRVSRQLLQELGREPSPEEIAAEMEL---SVEKVREIMKIAQEPVSLETPIGEEDDSH-- 282

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 L + +         + +  +LL EQL D+   +   E  +LRL
Sbjct: 283 ------LGDFIEDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRL 325


>gi|73748391|ref|YP_307630.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|147669171|ref|YP_001213989.1| RpoD family RNA polymerase sigma factor [Dehalococcoides sp. BAV1]
 gi|289432439|ref|YP_003462312.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
 gi|73660107|emb|CAI82714.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|146270119|gb|ABQ17111.1| RNA polymerase, sigma 70 subunit, RpoD family [Dehalococcoides sp.
           BAV1]
 gi|288946159|gb|ADC73856.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
          Length = 520

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 210/273 (76%), Gaps = 3/273 (1%)

Query: 412 EIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           EI   + +T       RH  S+   +   E +A  A++ +++ANLRLV+SVAKK+  RG+
Sbjct: 248 EISDHTYDTTFINHLERHEASLKYYLDNLEIDAKRAERHLIQANLRLVVSVAKKHIGRGM 307

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGNIGL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 308 PLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 367

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++  +R++S K+ REPTP+EIA ++ +P E VR++ K+++ P+SLE+PIG+E+ SHL
Sbjct: 368 INKLLSISRQLSQKLGREPTPDEIALEMDLPPEKVREIAKVSQLPVSLESPIGEEEDSHL 427

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+NA++P D+A +  L+E    VL SLTPRE RVL++RFG+      TLEEVGK+
Sbjct: 428 GDFIEDQNALAPPDAASRQLLKEQIDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKE 487

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 488 FNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 520



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/96 (29%), Positives = 42/96 (43%), Gaps = 6/96 (6%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR- 150
             D   S  N  + +   +       DDPVRMYL E+G + LLS E E  +AK++E G+ 
Sbjct: 72  DTDEEISPLNIDLDIPLEQIDTQGIVDDPVRMYLHEIGRVPLLSAEDEKTLAKKMEEGKR 131

Query: 151 -AMMMASLCE----SPLTFQALIIWRDELNDGTTLL 181
              +     E     P   ++ +    EL   T +L
Sbjct: 132 IREIRQECLEKRGRYPSAAESFLCMLRELAQATEVL 167


>gi|302522320|ref|ZP_07274662.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302431215|gb|EFL03031.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 514

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 262 KLQRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 321

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 322 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 381

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 382 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 441

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 442 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 501

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 502 HPSRSQVLRDYLD 514



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 48/114 (42%), Gaps = 10/114 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD---------RSTDDPVRMYLR 126
            ++D +  E+  G  D     ++   S  F+    D  D          +T DPV+ YL+
Sbjct: 164 ELLDEESTEETPGKGDEAAEPAAGGESQGFVLSDDDEDDAPAQQVAAAGATADPVKDYLK 223

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++G + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 224 QIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLQRELEIIAEDGRR 276


>gi|219558712|ref|ZP_03537788.1| RNA polymerase sigma factor [Mycobacterium tuberculosis T17]
          Length = 530

 Score =  222 bits (565), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRH---IVSMVRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +        +     +   AK  ++EANLRL
Sbjct: 245 AEEEVELAKRIEAGLYATQLMTELSERGEKLPGIHHRDMMWICRDGDRAKNHLLEANLRL 304

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 305 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 364

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 365 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 424

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 425 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 484

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 485 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 530



 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 188 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 247

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 248 EVELAKRIEAGL 259


>gi|188587782|ref|YP_001920276.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251778486|ref|ZP_04821406.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188498063|gb|ACD51199.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243082801|gb|EES48691.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 374

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +       +        +AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGKVPLLSSEQEIDYAKRIE---EGDPVAKKKLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEEI+K + +PV+ VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 222 INKLIRVQRQLLQELGRDPFPEEISKVMELPVDKVREIQKIAQEPVSLETPIGEEEDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 282 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 342 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 374



 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 51/184 (27%), Positives = 76/184 (41%), Gaps = 17/184 (9%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M  G K + +   +++               K +I   ++ G +T +E+   +   ++S 
Sbjct: 1   MAEGGKESMEQKVKNKAEKGKEDKSAKMAMVKGLIDKGKKNGSLTYKEIMDEIDHIDLSP 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+E    +L  MGI V+ G     E   E  L +                    + DDP
Sbjct: 61  EQIEKIYEVLEMMGIEVIGGATDAPEVEEEIDLTV----------------LEGIAIDDP 104

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYL+E+G + LLS E EI  AKRIE G  +    L E+ L     I  R  +  G   
Sbjct: 105 VRMYLKEIGKVPLLSSEQEIDYAKRIEEGDPVAKKKLAEANLRLVVSIAKRY-VGRGMLF 163

Query: 181 LREI 184
           L  I
Sbjct: 164 LDLI 167


>gi|216263390|ref|ZP_03435385.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
 gi|215980234|gb|EEC21055.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
          Length = 631

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 175/653 (26%), Positives = 311/653 (47%), Gaps = 38/653 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +I     R  ++  EL+  LP D +  E ++   ++L + GI +V+     D  G+E
Sbjct: 12  IESIITHVGDRKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVGTE 71

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  D       +        D   +S                    E ++ I  +++   
Sbjct: 72  DGNDEEEEVEIAPDRSFMVLDDGFQSD-------------------EEDVDIDVKLDDCD 112

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                         +  I  +D+L  G       +  ++      K       +      
Sbjct: 113 --------------EEGISIKDDLGSGYIKSN--VLKDSHSEDPIKLYLKEIGKEFLLTG 156

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            ++    K+ D  +    +I     +  ++   + +   +    E     ++D    +  
Sbjct: 157 NQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDRDKESNP 216

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSL 328
              ++ +         +  V   L S  DN     +      +  + KE+L   +L+  +
Sbjct: 217 DYYNKKKRIASFYKIPLKPVQDRLISYVDNKHRVYELGGDIFEKNLKKERLALKELLRDI 276

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
            L Q  + +  +   D + +I   + +   +     I++   L    GR+L         
Sbjct: 277 PLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEI 335

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +      ++ +  ++      + E++ I +     + +   +   + KG+     AK ++
Sbjct: 336 EKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEIAKGKQMMQHAKDQL 395

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAI
Sbjct: 396 IKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAI 455

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  
Sbjct: 456 TRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDEELSDRLGWELKKVKTVKS 515

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +++EP+SLETPIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V+
Sbjct: 516 VSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVV 575

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 576 KMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|283779933|ref|YP_003370688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438386|gb|ADB16828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 545

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 145/379 (38%), Positives = 214/379 (56%), Gaps = 36/379 (9%)

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             +   +  +    + K V+LV  ++L  +R+  L ++L DI  R+     ++       
Sbjct: 188 MHERRDAWKRLVRRRNKCVRLVEEMNLRNNRLQPLFDKLSDILGRMKTLRSQI------- 240

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
                        RE + H VS  +                +  ++R E+  +   T  +
Sbjct: 241 -------------REANIHGVSGGR----------------TAQQLRKELVHLMRITLET 271

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
            +  +  +    +       AK+ +   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+
Sbjct: 272 PATLKRRIVRTNEYRENYDAAKRVLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMR 331

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KF++  GYKFSTYA WW++QAITR+IADQS TIR+PVHM D + KV    R++  ++
Sbjct: 332 AVDKFEYARGYKFSTYATWWIRQAITRAIADQSRTIRVPVHMIDTMSKVRAVTRQLVQEL 391

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTPEE+A+   + ++  R VLK+ ++P+SL+ P+GD D S+ G+F+ D     PL  
Sbjct: 392 GREPTPEEVARVAGLTLDDARCVLKMARQPLSLDQPVGDHDDSYFGEFLADHREEDPLYD 451

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q  L+      +  L  RE  +LR+R+G+     +TLEEVGK F VTRER+RQIE KA
Sbjct: 452 THQQALKHQIEEAMQGLNYREREILRLRYGLTDGYAYTLEEVGKIFSVTRERVRQIETKA 511

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           +RKL+ P R++ L SFLDG
Sbjct: 512 VRKLQQPYRNRSLTSFLDG 530



 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 35/129 (27%), Positives = 54/129 (41%), Gaps = 6/129 (4%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
             +       +D     D E  E  +D+  ++ +           +  +TDDPVRMYL +
Sbjct: 32  DRIGTHDEFELDAFAEVDVEIDEIEVDVEVASEHGDEL------ESVDATDDPVRMYLMQ 85

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG I LL+R  EI  A+ IEA R     S+  +    Q  +   + + DG   L   I++
Sbjct: 86  MGQIPLLNRTQEIDSARTIEATRLKFRHSMLATDYVLQGAVELLERVRDGQLRLDRTIEV 145

Query: 188 EACIGPESK 196
                 E K
Sbjct: 146 SVTNTSEKK 154


>gi|326204489|ref|ZP_08194346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985282|gb|EGD46121.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 359

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 160/374 (42%), Positives = 230/374 (61%), Gaps = 31/374 (8%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           ++   K  +  ++++     + L    I+ + E L  +   ++ +    +          
Sbjct: 17  DRGKQKGMLTYKEIIDAFEEIELEPEHIEKIYETLETMGVDVVGDMEAEMEEI------- 69

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                +    ELD                            +R  +K I     +S  E 
Sbjct: 70  -----QLTDEELDISIPEGISIDDP----------------VRMYLKEIGKVPLLSADEE 108

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   +         AK+ + EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GL+KA EK
Sbjct: 109 IDLAHRME---NGDIEAKRRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEK 165

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP
Sbjct: 166 FDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP 225

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P+EIAK++ M V+ VR+++KI++EP+SLETPIG+E+ SHLGDFI D +A +P ++A   
Sbjct: 226 QPDEIAKEIGMSVDKVREIMKISQEPVSLETPIGEEEDSHLGDFIPDDDAPAPAEAAAFT 285

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 286 LLKEQLIDVLDTLTAREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKL 345

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +LD
Sbjct: 346 RHPSRSKKLKDYLD 359



 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 47/160 (29%), Positives = 69/160 (43%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +      K++I   +Q+G +T +E+       E+  E +E     L  MG++VV   + E
Sbjct: 6   ESRKALLKELIDRGKQKGMLTYKEIIDAFEEIELEPEHIEKIYETLETMGVDVVGDMEAE 65

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            EE      +L  S                 S DDPVRMYL+E+G + LLS + EI +A 
Sbjct: 66  MEEIQLTDEELDIS------------IPEGISIDDPVRMYLKEIGKVPLLSADEEIDLAH 113

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R+E G       L E+ L     I  R  +  G   L  I
Sbjct: 114 RMENGDIEAKRRLAEANLRLVVSIAKRY-VGRGMQFLDLI 152


>gi|40143|emb|CAA27538.1| unnamed protein product [Bacillus subtilis]
 gi|143454|gb|AAA22709.1| RNA polymerase sigma-43 factor [Bacillus subtilis]
 gi|1303833|dbj|BAA12489.1| RpoD [Bacillus subtilis]
          Length = 371

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 157/273 (57%), Positives = 201/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    ++  +K E     +K+ + EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGRVNLLSAKEE---IAYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLI EGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIHEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEIA+ + +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 219 INKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 279 GDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 339 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 371



 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 6/157 (3%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++ +  ++RG +T EE+   +   E+ S+QM++    L   G+ ++      + E
Sbjct: 14  DQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELI-----SENE 68

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +ED      + +     L           +DPVRMYL+E+G + LLS + EIA A++IE
Sbjct: 69  ETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAQKIE 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EGDEESKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 164


>gi|289178873|gb|ADC86119.1| HrdB [Bifidobacterium animalis subsp. lactis BB-12]
          Length = 522

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EFR     ++    +   AK  ++EANLRLV+
Sbjct: 239 AEQEVDLSERIEAGLYAQHLLDTEGDTMEFRR-KRELKWAAADGKKAKDHLLEANLRLVV 297

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 298 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 357

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 358 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 417

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 418 TPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFRQVLETLSPREAGVIKMRYGLEDG 477

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 478 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 521



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ +   +   +     KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 194 DNDEDDEALLANPGVNPKRRVVTTGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 253


>gi|326332703|ref|ZP_08198965.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
 gi|325949484|gb|EGD41562.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
          Length = 530

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 140/289 (48%), Positives = 191/289 (66%), Gaps = 7/289 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L    ++      T   + E   I         +   AK  ++EAN
Sbjct: 249 AEMEVELAKRIEAGLFAEEKLGKGGKITPKMLDELEWIAE-------DGKRAKNHLLEAN 301

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++
Sbjct: 302 LRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 361

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +E
Sbjct: 362 ADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGRE 421

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ RE  V+ MRF
Sbjct: 422 PISLHTPLGEDGDSEFGDLIEDSEAIVPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRF 481

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 482 GLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 530



 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 37/73 (50%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V  D    E+  E        +++      ++      +T DPV+ YL+++G + LL+ E
Sbjct: 191 VAADPTIKEDEKEAEKQSFVVSTSDDTDEPEQTVMVAGATADPVKDYLKQIGKVPLLNAE 250

Query: 138 GEIAIAKRIEAGR 150
            E+ +AKRIEAG 
Sbjct: 251 MEVELAKRIEAGL 263


>gi|318066953|emb|CBY89091.1| RNA polymerase sigma70 factor [Halomonas koreensis]
          Length = 365

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 122/397 (30%), Positives = 181/397 (45%), Gaps = 54/397 (13%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M++L   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREVMSALAYLPGAVDSILEAYDAT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       ++ +E             E 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEAETPEEP----EAGAGEGDED 123

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                 +D S     PE A      +    + +    +A+E Q R               
Sbjct: 124 DDSDEDEDDSGGGPDPEEARARFEQIRAQNEAAR---AAIESQGR--------------- 165

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                            +S + +    +L +L   + L     + LV Q+    +++   
Sbjct: 166 -----------------ASREAQEELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQ 208

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   + R  F++   G E    W+          + + +      I + + 
Sbjct: 209 EKAVMQLCVKKAKVPRKTFIKAFPGNESRQDWLDDFMAENAR-YADRLDPLKGDIQRAQR 267

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        + ++E + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 268 KIAFEEEMVQLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 327

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 328 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 364


>gi|298346920|ref|YP_003719607.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
 gi|298236981|gb|ADI68113.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
          Length = 563

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 134/260 (51%), Positives = 188/260 (72%), Gaps = 4/260 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  + R +  +V+    +  +AK  ++EANLRLV+++AKKYT RG+ FLDLIQEGN+GL
Sbjct: 308 MTPKQIRELHYVVQ----DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGL 363

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M  
Sbjct: 364 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 423

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + REPTP+E+A++L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P 
Sbjct: 424 DLGREPTPDELAQELEMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPA 483

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+     L+E   RVL +L+ RE  V+ MRFG+      TL+E+G+++ VTRERIRQIEA
Sbjct: 484 DAVSFMMLQEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEA 543

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           K + KL+HP+RS+ LR +L+
Sbjct: 544 KTMSKLRHPARSQSLRDYLN 563



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +         +K +   +T DPV+ YL+++G + LL+ E E+ ++KRIEAG 
Sbjct: 244 SEKDDADEPAQKVTVAGATSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGL 295


>gi|308371101|ref|ZP_07423832.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308379284|ref|ZP_07485758.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308405944|ref|ZP_07494511.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|308329814|gb|EFP18665.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308357496|gb|EFP46347.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308365045|gb|EFP53896.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|323718698|gb|EGB27860.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CDC1551A]
          Length = 530

 Score =  222 bits (564), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 192/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 245 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 304

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 305 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 364

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 365 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 424

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 425 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 484

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 485 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 530



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 188 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 247

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 248 EVELAKRIEAGL 259


>gi|1072017|gb|AAA81640.1| sigma factor [Mycobacterium bovis]
 gi|1072019|gb|AAA81641.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 192/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 362

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 363 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 422

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 423 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 482

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 483 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 246 EVELAKRIEAGL 257


>gi|171742642|ref|ZP_02918449.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
 gi|171278256|gb|EDT45917.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
          Length = 461

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 201/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T  S  +F+     ++    +   AK  ++EANLRLV+
Sbjct: 178 AEQEVDLSERIEAGLYAQHLLDTEASQMDFKRR-RELKWAANDGKKAKDHLLEANLRLVV 236

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 237 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 296

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 297 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 356

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 357 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 416

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 417 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 460



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 150 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 192


>gi|307325028|ref|ZP_07604232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889174|gb|EFN20156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 502

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 250 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 309

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 310 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 369

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 370 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 429

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 430 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 489

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 490 HPSRSQVLRDYLD 502



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 1/101 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G    +   +E        + +       ++ +A  +T DPV+ YL+++G + LL+ E E
Sbjct: 165 GKPGPEGAEAEPENAGFVLSDDDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQE 224

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +AKRIEAG       L  S      L    + + +    
Sbjct: 225 VELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 264


>gi|326443878|ref|ZP_08218612.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 537

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 285 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 344

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 345 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 404

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 405 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 464

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 465 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 524

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 525 HPSRSQVLRDYLD 537



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE+ +E        +         ++ +   +T DPV+ YL+++G + LL+ E E+ +AK
Sbjct: 205 DEDEAEGESKGFVLSDEDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAK 264

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           RIEAG       L  +      L    + + +    
Sbjct: 265 RIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 299


>gi|281412780|ref|YP_003346859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
 gi|281373883|gb|ADA67445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 407

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 138/272 (50%), Positives = 189/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     ++ ++ R +    +        AK++++ +NLRLV+S+AK+Y  RGL
Sbjct: 131 IKMYLKEIGKIPLLTPAQERELARRAQ---MGDKKAKEKLITSNLRLVVSIAKRYMGRGL 187

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 188 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 247

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R    K   EP+ EE+AK +  P E ++++L+  KE ISLE+PIG+++ S +
Sbjct: 248 INKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSI 307

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+ D +  SP   A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ 
Sbjct: 308 EDFVADDSIASPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQY 367

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK L+S L
Sbjct: 368 FNVTRERIRQIEVKALRKLRHPSRSKYLKSLL 399



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 38/146 (26%), Positives = 64/146 (43%), Gaps = 6/146 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPD--EVSSEQMEDTVAMLSNMGINVVDGDDLED 85
           +   KK+I L +++GY+T E+++   PPD  +  +  +E     L   GIN+V      +
Sbjct: 40  EKRIKKLISLGKKKGYITYEDIDKAFPPDFEDFDTNLIERIHEELEKHGINIV----ENE 95

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E  E S           +  +  +     +  D ++MYL+E+G I LL+   E  +A+R
Sbjct: 96  PEEEEISASSDEQELEELLERESPEIHDSSNVRDSIKMYLKEIGKIPLLTPAQERELARR 155

Query: 146 IEAGRAMMMASLCESPLTFQALIIWR 171
            + G       L  S L     I  R
Sbjct: 156 AQMGDKKAKEKLITSNLRLVVSIAKR 181


>gi|325971191|ref|YP_004247382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
 gi|324026429|gb|ADY13188.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
          Length = 685

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 158/433 (36%), Positives = 232/433 (53%), Gaps = 15/433 (3%)

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   +E        L   + +        L ++    +     ++  ++  +D       
Sbjct: 261 EGQEEEYNAKDYKELVTNQKRFTQFYREQLKDVQASLKNYIVKKEQMISSGEDVLHDETL 320

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
              +  L+K +  + L    I        D   RI   + +  +L     I         
Sbjct: 321 IKTRIALLKKLAKVDLQPEEITSFTHDFVDAENRIRSYKEKKQQLENKLHIS-------- 372

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK-------SISVETGISISEF 427
             +EL       A      + +  +    D+I  +  E++        I  +   +    
Sbjct: 373 SAKELRQLGRDLATQSRSAKIEEELHLSSDTIKDLIRELQLTDKDLRQIEYQFEETCENI 432

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
               + ++ G+     AK  ++ ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EK
Sbjct: 433 LQHSTKIKYGQKMMKDAKDRLIRANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEK 492

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+KVVR +R +   + REP
Sbjct: 493 FEYRKGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVVRESRMLMQSLGREP 552

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A+KL      V+ V  + +EPISLETP+G+E+ S L DFIEDK   +P      +
Sbjct: 553 TDEEVAEKLGWTESKVKAVKNVAREPISLETPVGEEEDSLLSDFIEDKEVENPATQTAYS 612

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VLA+L  RE+ VL+MRFG+      TLEEVG  F +TRERIRQIEAKA+R+L
Sbjct: 613 LLQEQLKDVLATLPAREQEVLKMRFGLEDGYSLTLEEVGLYFELTRERIRQIEAKALRRL 672

Query: 668 KHPSRSKKLRSFL 680
           +HP RS+KL+ F+
Sbjct: 673 RHPKRSRKLKDFI 685



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 47/260 (18%), Positives = 99/260 (38%), Gaps = 8/260 (3%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           D +D S DDP+R+YLRE+G   LL+ + E+ ++K++E G  ++   + ES +        
Sbjct: 193 DKSDSSGDDPIRLYLREIGKENLLTADQEVELSKKMEDGALIIKEVIQESGVMITRFYDI 252

Query: 171 RDELN---DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
              LN   +G        D +  +  + +   F+  +    Q    +   K+   +   E
Sbjct: 253 IKTLNTKIEGQEEEYNAKDYKELVTNQKRFTQFYREQLKDVQASLKNYIVKKEQMISSGE 312

Query: 228 GDIESAAKVSK-----DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
             +     +          +KVD  PE   +   +  + E+         +       + 
Sbjct: 313 DVLHDETLIKTRIALLKKLAKVDLQPEEITSFTHDFVDAENRIRSYKEKKQQLENKLHIS 372

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           +  E+ ++ R+L +   +A   ++   SS   K L  +L      L   + + +   E +
Sbjct: 373 SAKELRQLGRDLATQSRSAKIEEELHLSSDTIKDLIRELQLTDKDLRQIEYQFEETCENI 432

Query: 343 YDISKRIMHNEGELLRLAQS 362
              S +I + +  +      
Sbjct: 433 LQHSTKIKYGQKMMKDAKDR 452



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 5/99 (5%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S    K M+  + + G+VT E++   L P   + E +++ +  LS + I V + D++ 
Sbjct: 5   NISQAIVKDMVARSAETGHVTKEDIRKALAPQNATDEAVDEIMQTLSELEIVVTESDEVP 64

Query: 85  DEE-----GSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
                    SED +D         V L +     D S D
Sbjct: 65  SAALFSDGPSEDEIDTDMDEEPDDVDLLEDDLEDDLSVD 103


>gi|289570879|ref|ZP_06451106.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
 gi|289544633|gb|EFD48281.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
          Length = 528

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRH---IVSMVRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +        +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPGIHHRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 362

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 363 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 422

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 423 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 482

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 483 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 246 EVELAKRIEAGL 257


>gi|282862331|ref|ZP_06271393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282562670|gb|EFB68210.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 515

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 263 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 322

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 323 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 382

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 383 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 442

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 443 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 502

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 503 HPSRSQVLRDYLD 515



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 197 SDDDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 255

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            S      L    + + +    
Sbjct: 256 NSDKLAPKLKRELEIIAEDGRR 277


>gi|88856913|ref|ZP_01131565.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88813881|gb|EAR23751.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 454

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 194/284 (68%), Gaps = 1/284 (0%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRH-IVSMVRKGECEASIAKKEMVEANLRLVI 457
            A EV+  ++I   + +      +  SE R  +   ++    +   AK  ++ ANLRLV+
Sbjct: 171 AAQEVELAMRIEAGLFAEDKLAEMKPSEVRSTLGRELQWVAKDGQRAKSHLLGANLRLVV 230

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 231 SLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQAR 290

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+ R  R+M   + REPTPEE++++L M  E V +V K  +EPISL 
Sbjct: 291 TIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKVVEVQKYGREPISLH 350

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED  AV P D+     L++    +L SL+ RE  V+RMRFG+G  
Sbjct: 351 TPLGEDGDSEFGDLIEDTEAVVPADAVGFTMLQKQLESLLDSLSEREAGVIRMRFGLGDG 410

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G  F VTRERIRQIE+K + KL+HPSRS+ LR +L+
Sbjct: 411 MPKTLDQIGDTFGVTRERIRQIESKTMAKLRHPSRSQSLRDYLE 454



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 10/87 (11%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD----------RSTDDPVRM 123
            I   DG+D   ++  E+       A  +   +    D  D           +T DPV+ 
Sbjct: 99  EIVEADGEDESKDDDQEEKSTSKDEALPTGALVLSLVDDEDDVPVYSAAITGATADPVKD 158

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGR 150
           YL+++G + LL+   E+ +A RIEAG 
Sbjct: 159 YLKQIGKVALLNAAQEVELAMRIEAGL 185


>gi|297626466|ref|YP_003688229.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922231|emb|CBL56801.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 509

 Score =  221 bits (563), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 136/248 (54%), Positives = 177/248 (71%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                 +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G
Sbjct: 262 YEWITEDGHRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKG 321

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW+KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A
Sbjct: 322 YKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELA 381

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     L+E  
Sbjct: 382 KELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVNFTLLQEQL 441

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS
Sbjct: 442 HDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRS 501

Query: 674 KKLRSFLD 681
           + LR +LD
Sbjct: 502 QVLRDYLD 509



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 8/81 (9%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMG 129
           VD    E ++   +  +   +A +    L    +  +         +T DPV+ YL+++G
Sbjct: 161 VDDSKFEKDKKEAEKDEAKINADSQGFSLSDNDEDDEPEQQVMVAGATADPVKDYLKQIG 220

Query: 130 SIELLSREGEIAIAKRIEAGR 150
            + LL+   E+ +AKRIEAG 
Sbjct: 221 KVALLNAAQEVDLAKRIEAGL 241


>gi|283781338|ref|YP_003372093.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283439791|gb|ADB18233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 524

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 155/405 (38%), Positives = 229/405 (56%), Gaps = 38/405 (9%)

Query: 278 PKVMCALDEI-AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           P  +  LD +      +  +    +    K + +  +    + + V+LV  L L   RI+
Sbjct: 157 PHNLRTLDVLLKRNRHDYLTALSKSQPKAKRKLAWTRLSRRRRRSVRLVEELGLRTQRIE 216

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            ++  L D + RI+    ++       G   D              W+S           
Sbjct: 217 QMIRTLEDFNNRIVFLRRQIENHKAQKGNPAD-----------RKQWLS----------- 254

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
                          E++SI V T  + +  +  V M+++   +   AK+E+ E NLRLV
Sbjct: 255 ---------------ELRSILVATQETPASMQKRVDMLKRVYTDYQQAKRELSEGNLRLV 299

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AKKY NRGL FLDLIQEGN GLM+A +KF++  G+KF TYA WW++QAITR++ADQS
Sbjct: 300 VSIAKKYRNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQS 359

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + + +V   +R++  ++ REPT EE A+K    V+  R+VL +++ PISL
Sbjct: 360 RTIRIPVHMVETMSRVRNVSRQLLQELGREPTLEETARKAKTTVDEARRVLAMSRYPISL 419

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           + P+G+ + SH GD + D  A SP   A Q  LR    +VL +L+ RE  ++++R+G+G 
Sbjct: 420 DRPVGNSEDSHFGDLLPDGTAESPATGASQEMLRTRINKVLKTLSYREREIIKLRYGLGD 479

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              +TLEEVG  F VTRERIRQIEAKA+RKL+ PSRS++L  FLD
Sbjct: 480 GYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPSRSQELVGFLD 524



 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 35/152 (23%), Positives = 59/152 (38%), Gaps = 4/152 (2%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSV 104
            + L      D V + + ++     +   +  ++  DD  D E  +++ D          
Sbjct: 2   YDALLEEFDDDAVRAPEDDE---GFAAQAVAELELEDDGVDLEVVDNAADAEVPTKLDDE 58

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
            L    +  +  +DDPVRMYL +MG I LL+R  EI +AK+IE  R      L E     
Sbjct: 59  ELLGLGEDGESWSDDPVRMYLTQMGEIPLLTRAQEIYLAKKIEVTRRRFRTKLLECDYVI 118

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           Q        +++G       + +      E  
Sbjct: 119 QQAFKVLKRVHEGELPFDRTVQVSVTDHLEKD 150


>gi|169824520|ref|YP_001692131.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302380672|ref|ZP_07269137.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|303233690|ref|ZP_07320344.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
 gi|167831325|dbj|BAG08241.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302311615|gb|EFK93631.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|302495124|gb|EFL54876.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
          Length = 388

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +S  E    V + ++ E  +  AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 119 VKMYLKEIGKIPLLSADEE---VQLAQEMENGSKRAKKKLAEANLRLVVSIAKRYVGRGM 175

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 176 SFLDLIQEGNLGLMKAVDKFDYTRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 235

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++VR  R++   + R+PT EEIAK++ + VE VR+V KI +EP+SLETPIG+E+ SHL
Sbjct: 236 INRLVRIERQLLQDLGRDPTNEEIAKEMGIEVEKVREVRKIAQEPVSLETPIGEEEDSHL 295

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A++P ++A    LRE    +L +L  RE +VL +RFG+   T  TLEEVGK 
Sbjct: 296 GDFIEDDTAIAPDEAANFTMLREELEGILNTLNERERKVLALRFGLVDGTPRTLEEVGKD 355

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KL+ FL+
Sbjct: 356 FDVTRERIRQIEAKALRKLKHPSRSQKLKDFLE 388



 Score = 84.1 bits (206), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 41/172 (23%), Positives = 73/172 (42%), Gaps = 14/172 (8%)

Query: 26  FSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
              D+  ++I++  +  G VTI++         +  E +ED   +L    I + + +D  
Sbjct: 11  IKKDALNQLIEIGNENDGIVTIKDFKKIDDLTSLDEEDIEDIRNLLIENNIEIFESNDDI 70

Query: 85  DEEGSEDSLDLASSASNSSV------------FLQKRKDSADRSTDDPVRMYLREMGSIE 132
           +++ S+D          S               ++   D    + DDPV+MYL+E+G I 
Sbjct: 71  EKKSSKDDDTDDLDVDESLEDDDDEDEKNDKKVIEDVSDIKGINVDDPVKMYLKEIGKIP 130

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LLS + E+ +A+ +E G       L E+ L     I  R  +  G + L  I
Sbjct: 131 LLSADEEVQLAQEMENGSKRAKKKLAEANLRLVVSIAKRY-VGRGMSFLDLI 181


>gi|15609840|ref|NP_217219.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Rv]
 gi|15842241|ref|NP_337278.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CDC1551]
 gi|31793875|ref|NP_856368.1| RNA polymerase sigma factor [Mycobacterium bovis AF2122/97]
 gi|121638578|ref|YP_978802.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148662544|ref|YP_001284067.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148823893|ref|YP_001288647.1| RNA polymerase sigma factor [Mycobacterium tuberculosis F11]
 gi|167970074|ref|ZP_02552351.1| RNA polymerase sigma factor RpoD [Mycobacterium tuberculosis H37Ra]
 gi|218754439|ref|ZP_03533235.1| RNA polymerase sigma factor [Mycobacterium tuberculosis GM 1503]
 gi|224991070|ref|YP_002645759.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253798215|ref|YP_003031216.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|254551759|ref|ZP_05142206.1| RNA polymerase sigma factor [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260187720|ref|ZP_05765194.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CPHL_A]
 gi|289448358|ref|ZP_06438102.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289553511|ref|ZP_06442721.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289762874|ref|ZP_06522252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|294994205|ref|ZP_06799896.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 210]
 gi|297635311|ref|ZP_06953091.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN 4207]
 gi|297732307|ref|ZP_06961425.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN R506]
 gi|306780885|ref|ZP_07419222.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|306790106|ref|ZP_07428428.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|306798608|ref|ZP_07436910.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|306804467|ref|ZP_07441135.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|306807495|ref|ZP_07444163.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|306968762|ref|ZP_07481423.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|307080806|ref|ZP_07489976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|313659640|ref|ZP_07816520.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN V2475]
 gi|61234251|sp|P0A602|RPOD_MYCTU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|61234258|sp|P0A603|RPOD_MYCBO RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1072023|gb|AAA81643.1| sigma factor [Mycobacterium bovis]
 gi|1072025|gb|AAA81644.1| sigma factor [Mycobacterium tuberculosis str. Erdman]
 gi|1171102|gb|AAA86043.1| sigma factor MysA [Mycobacterium tuberculosis H37Rv]
 gi|2181994|emb|CAB09463.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium
           tuberculosis H37Rv]
 gi|13882532|gb|AAK47092.1| RNA polymerase principal sigma factor SigA [Mycobacterium
           tuberculosis CDC1551]
 gi|31619469|emb|CAD94907.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium bovis
           AF2122/97]
 gi|121494226|emb|CAL72704.1| RNA polymerase sigma factor sigA [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148506696|gb|ABQ74505.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148722420|gb|ABR07045.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis F11]
 gi|224774185|dbj|BAH26991.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253319718|gb|ACT24321.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|289421316|gb|EFD18517.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289438143|gb|EFD20636.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289710380|gb|EFD74396.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|308326286|gb|EFP15137.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|308333457|gb|EFP22308.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|308341125|gb|EFP29976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|308346090|gb|EFP34941.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|308348951|gb|EFP37802.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|308353649|gb|EFP42500.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|308361450|gb|EFP50301.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|326904319|gb|EGE51252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis W-148]
 gi|328457987|gb|AEB03410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           4207]
          Length = 528

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 192/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 362

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 363 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 422

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 423 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 482

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 483 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 246 EVELAKRIEAGL 257


>gi|325107209|ref|YP_004268277.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967477|gb|ADY58255.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 590

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 145/406 (35%), Positives = 236/406 (58%), Gaps = 38/406 (9%)

Query: 278 PKVMCALDEIAEVYRE-LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           P  +  L+ + +  +       D  ++ Q+ +++       + K+V LV  +SL   R+ 
Sbjct: 213 PHNLKTLEYLQQKNQHDFARSIDQELSAQERKEARHSLDTRRRKMVTLVEEMSLRTQRLQ 272

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
            L ++L  IS+R+   +  +  +++                                   
Sbjct: 273 PLFKRLQQISQRMQELQSRMKVVSRRQ--------------------------------- 299

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
                  D   +++ E+  + + T  +    +  V  + +   +   A +E+   NLRLV
Sbjct: 300 ----NSADEKAQLQRELHDLMLMTYETPETLKGRVREIEERYHDYETAMRELSGGNLRLV 355

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AKKY NRG+ FLDLIQEGN GLM+A +K+++  GYKFSTYA WW++QAITR+IADQ+
Sbjct: 356 VSIAKKYRNRGMNFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWWIRQAITRAIADQA 415

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + + K+ +  + +  ++ REPT EE+A+   + +E  R+V+KI+++PISL
Sbjct: 416 RTIRIPVHMIETMSKLRKVGKDLVQELGREPTIEEMAEAAEVSLEEARRVMKISRQPISL 475

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           + PIG+ + S+ GDFIED +  SP+ +A Q  L++    VL +LT RE  ++++R+G+G 
Sbjct: 476 DRPIGEGEDSYFGDFIEDHSTDSPVSTATQEMLKDKIDHVLKTLTYREREIIKLRYGLGD 535

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RS +L+ F++ 
Sbjct: 536 GYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSHQLKGFIES 581



 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 87/177 (49%), Gaps = 6/177 (3%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE- 84
             DD+ +++IK  +++G++T  ++N +LP ++V+ E+++  +  L  +G+ +V    +  
Sbjct: 30  QLDDNLQQLIKQGQKQGFLTFSQVNEYLPDEDVNPEKLDTLLLSLEELGMEIVSEKHVSK 89

Query: 85  -----DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                D E ++      S +   +  L +  D   R  DDPVR+YL +MG I LL+R+ E
Sbjct: 90  KKVQLDAEAAQRKKKKPSKSEKRNGELAEDDDEGSRRIDDPVRIYLTQMGEIPLLTRDEE 149

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           I +AK+IE  R      L  +    ++ I    +++ G       I +      E +
Sbjct: 150 ITLAKKIEVTRKRFRRQLLSNDCAMRSAIETLAKVHRGELPFDRTIKVSLTESVEKE 206


>gi|224534471|ref|ZP_03675047.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
 gi|224514148|gb|EEF84466.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
          Length = 631

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 174/653 (26%), Positives = 312/653 (47%), Gaps = 38/653 (5%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +I     R  ++  EL+  LP D +  E ++   ++L + GI++V+     D  G+E
Sbjct: 12  IESIITNLGDRKSLSFSELSNLLPDDILEPEILDCICSVLEDKGISLVNKISELDLVGTE 71

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  +        S       D   +S                    E ++ I  +++   
Sbjct: 72  DGNEEEEEMEIDSDRSFIVLDDGFQSD-------------------EEDVDIDVKLDDCD 112

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                         +  I  +D+L  G       +  ++      K       +      
Sbjct: 113 --------------EEGISVKDDLGSGYIKSN--VLKDSHSEDPIKLYLKEIGKEFLLTG 156

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            ++    K+ D  +    +I     +  ++   + +   +    E     ++D    +  
Sbjct: 157 NQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDRDKESNP 216

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSL 328
              ++ +         +  +   L S  DN     +      +  + KE+L   +L+  +
Sbjct: 217 DYYNKKKRIASFYKIPLKPIQDRLISYVDNKHKVYELGGDIFEKNLKKERLALKELLRDI 276

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
            L Q  + +  +   D + +I   + +   +     I++   L    GR+L         
Sbjct: 277 PLYQDELRIFSDDYIDSANKIRDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKRIEI 335

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +      ++ +  ++      + E++ I +     + +   +   + KG+     AK ++
Sbjct: 336 EKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEIAKGKQMMQHAKDQL 395

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAI
Sbjct: 396 IKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAI 455

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  
Sbjct: 456 TRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKS 515

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +++EP+SLETPIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V+
Sbjct: 516 VSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVV 575

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 576 KMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|50954703|ref|YP_061991.1| RNA polymerase sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50951185|gb|AAT88886.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 440

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 134/254 (52%), Positives = 182/254 (71%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   +R    +   AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EK
Sbjct: 187 RELERELRWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEK 246

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REP
Sbjct: 247 FDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREP 306

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE++K+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+    
Sbjct: 307 TPEELSKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDIEAVVPADAVGFT 366

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    +L SL+ RE  V+RMRFG+G     TL+++G  F VTRERIRQIE+K + KL
Sbjct: 367 MLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMAKL 426

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +L+
Sbjct: 427 RHPSRSQSLRDYLE 440



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A +    +     +   +T DPV+ YL+++G + LL+   E+ +A RIEAG       L 
Sbjct: 122 AVDEDDDIPVYSTTITGATADPVKDYLKQIGKVPLLNAAEEVELAMRIEAGLF-AEDRLA 180

Query: 159 ESP 161
            +P
Sbjct: 181 NTP 183


>gi|146295919|ref|YP_001179690.1| RpoD family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409495|gb|ABP66499.1| RNA polymerase, sigma 70 subunit, RpoD [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 411

 Score =  221 bits (562), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 156/273 (57%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   + +       AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 142 VRMYLKEIGKIPLLTPEEEIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRGM 198

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 199 LFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 258

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  +  REPTPEEIAK++ MPVE VR++LKI +EP+SLETPIG+E+ SHL
Sbjct: 259 INKLVRVSRQLLQEKGREPTPEEIAKEMNMPVEKVREILKIAQEPVSLETPIGEEEDSHL 318

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P ++A  + L+E    VL SL  RE++VL++RFG+      TLEEVGK+
Sbjct: 319 GDFIPDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTLEEVGKE 378

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ FL+
Sbjct: 379 FNVTRERIRQIEAKALRKLRHPSRSKKLKDFLE 411



 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 55/182 (30%), Positives = 85/182 (46%), Gaps = 22/182 (12%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  K+N D  ++ E+       +   +  +++I L + +G++T  E+   L   E+ + Q
Sbjct: 45  LSSKKNIDDKNKTEEKK-----NLIREKVRELISLGQSKGFLTYSEIQEILDKVELDANQ 99

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E+    L NMGI+VVD    E+E   +D  +L                    + DDPVR
Sbjct: 100 IENIYDTLENMGIDVVDDRVSEEELLKDDLENL----------------PEGIAIDDPVR 143

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL+E+G I LL+ E EI +AKRIE G       L E+ L     I  R  +  G   L 
Sbjct: 144 MYLKEIGKIPLLTPEEEIELAKRIEQGDEEAKKRLAEANLRLVVSIAKRY-VGRGMLFLD 202

Query: 183 EI 184
            I
Sbjct: 203 LI 204


>gi|210615118|ref|ZP_03290449.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
 gi|210150426|gb|EEA81435.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
          Length = 370

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 155/273 (56%), Positives = 205/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLSAEEEIELAKRM---AEGDEDAKKRLAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIA++L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPLPEEIAEELDMPVERVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 278 GDFIQDDNVPVPAEAAAATLLKEQLGEVLDTLTDREQKVLRLRFGMNDGRARTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 79/189 (41%), Gaps = 12/189 (6%)

Query: 28  DDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  K ++ L +++   + I+E+N      E+ +EQME     L +  I+V+      D 
Sbjct: 9   EEKLKNLVALGKKKKSILEIQEINEVFSDMELEAEQMEKIFEYLESQNIDVLRISP--DT 66

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + ++D   L +      +           S +DPVRMYL+E+G + LLS E EI +AKR+
Sbjct: 67  DDADDVEILLTDEDEVDMEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELAKRM 126

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G       L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 127 AEGDEDAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLIKAVEKF 177

Query: 207 SYQKREDSS 215
            YQK    S
Sbjct: 178 DYQKGFKFS 186


>gi|189485247|ref|YP_001956188.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
 gi|170287206|dbj|BAG13727.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
          Length = 573

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 150/405 (37%), Positives = 243/405 (60%), Gaps = 5/405 (1%)

Query: 280 VMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           V+  ++ I +        L+  +++ +  E+   K K  + ++V L+  L+LNQ +I  L
Sbjct: 171 VVKKINRIEKNINTYEKKLKLKSISCKDKEQYKEKVKEFRSEIVSLIVELNLNQDKIRRL 230

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           + ++  I++++   +  L R  + Y           +    +   +S A+          
Sbjct: 231 INKIKTIAQKLNEIKEGLRRFERKYKNSFSKVQVLFKS--CNLGKISSAEFKKSTGLSMK 288

Query: 399 -VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            VA ++ ++  +  +  ++     I+  E       +R+ E      K +++EAN RLV+
Sbjct: 289 DVAEDIANVKTLLVKQTNLKDGFVITPEEMIETDRRIRELEYVIHRDKMKLIEANFRLVV 348

Query: 458 SVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           S+AKK+     L+  DLIQEGN+GL KA EKF+W  G+KFSTYA WW++Q+I R+IADQ+
Sbjct: 349 SIAKKHVGISNLELSDLIQEGNLGLSKAVEKFEWKRGFKFSTYATWWIRQSINRAIADQA 408

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM++ I K+ ++ +     + REPT +E +K L +  + +R++LK+ +EP+SL
Sbjct: 409 RTIRIPVHMKELISKLTKSKKECQQNMGREPTIQEYSKILKLSCDRIRRILKMMQEPVSL 468

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
             P+G+E+ S L DFIED+N+ +P+    Q  L+    +VLA+L PRE  ++R+R+GIG+
Sbjct: 469 AMPVGEEEDSRLEDFIEDQNSPNPVVKTQQYRLQLELEKVLATLAPREAEIIRLRYGIGI 528

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               TLEEVGK+F +TRER+RQIEAKAIRKLK+P R+K LR +LD
Sbjct: 529 GYPSTLEEVGKKFGITRERVRQIEAKAIRKLKYPRRNKSLREYLD 573



 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 92/567 (16%), Positives = 199/567 (35%), Gaps = 47/567 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
             D +K +I   +++GY+T E ++  LP   + +E+++     L N+GI V+D  +   +
Sbjct: 3   KKDLFKGLIDTGKEQGYLTYEAISKNLPQRSMIAEEIDGFFVTLDNLGIKVLDNREYRSD 62

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  +   ++          +++   + +    +PVRMYL EM  + LL R  E+ + K I
Sbjct: 63  KVKKSRGEV----------VERSMKTVNEEDINPVRMYLSEMAKVPLLERNMELKLVKSI 112

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI-----------------IDLEA 189
                 + + + ESPL  + +  W   ++      +E+                 I +  
Sbjct: 113 RENEDRLKSIVLESPLIIKEIRNWETLISQQEMTTKELMPRGRKSKAQLIGMGLKIKIVV 172

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                 +       +    +      +E+ ++ V+E   +I S       ++ K+     
Sbjct: 173 KKINRIEKNINTYEKKLKLKSISCKDKEQYKEKVKEFRSEIVSLIVELNLNQDKIRRLIN 232

Query: 250 NAENDERNLDEDEDDSAH-------TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
             +   + L+E ++           + S ++   +   +  +           S++D A 
Sbjct: 233 KIKTIAQKLNEIKEGLRRFERKYKNSFSKVQVLFKSCNLGKISSAEFKKSTGLSMKDVAE 292

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL-YDISKRIMHNEGELLRLAQ 361
           +    +   VK   LK+  V     +     RI  L   +  D  K I  N   ++ +A+
Sbjct: 293 DIANVKTLLVKQTNLKDGFVITPEEMIETDRRIRELEYVIHRDKMKLIEANFRLVVSIAK 352

Query: 362 SY-GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            + GI      +  Q  E +       + F       F       I +  N   +    T
Sbjct: 353 KHVGISNLELSDLIQ--EGNLGLSKAVEKFEWKRGFKFSTYATWWIRQSINRAIADQART 410

Query: 421 GISISEFRHIVSMVRKGECEASIAKKE--MVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
                  + ++S + K + E          ++   +++     +        L ++QE  
Sbjct: 411 IRIPVHMKELISKLTKSKKECQQNMGREPTIQEYSKILKLSCDRIRR----ILKMMQE-P 465

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           + L     + +      F            T+    Q    ++   +  +  +++R   R
Sbjct: 466 VSLAMPVGEEEDSRLEDFIEDQNSPNPVVKTQQYRLQLELEKVLATLAPREAEIIR--LR 523

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRK 565
               I    T EE+ KK  +  E VR+
Sbjct: 524 YGIGIGYPSTLEEVGKKFGITRERVRQ 550


>gi|317500513|ref|ZP_07958736.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089388|ref|ZP_08338287.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316898102|gb|EFV20150.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404756|gb|EGG84294.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 370

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 101 VRMYLKEIGKVPLLSAEREIELAKRME---EGDEDAKKELAEANLRLVVSIAKRYVGRGM 157

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 158 LFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 217

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK+L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 218 INKLIRVSRQLLQELGREPLPEEIAKELDMPVERVREILKISQEPVSLETPIGEEEDSHL 277

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 278 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 337

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 338 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 370



 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 72/157 (45%), Gaps = 4/157 (2%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +   +++ L +++   + ++E+N F    E+S+EQME     L    I+V+      D +
Sbjct: 10  EKMNELVALGKKKKSILDVQEINDFFADMELSAEQMEKVFEYLEGHNIDVL--RITADTD 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D  ++ +      +           S +DPVRMYL+E+G + LLS E EI +AKR+E
Sbjct: 68  DDVDIDNMIAEEEEVDMENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAKRME 127

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 128 EGDEDAKKELAEANLRLVVSIAKRY-VGRGMLFLDLI 163


>gi|325263837|ref|ZP_08130570.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030875|gb|EGB92157.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 369

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 159/273 (58%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGKVPLLSAEREIELAQRME---DGDEDAKKELAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 LFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPTPEEIAK+L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 217 INKLIRVSRQLLQELGREPTPEEIAKELDMPVERVREILKISQEPVSLETPIGEEEDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 277 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 336

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 337 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 369



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 45/158 (28%), Positives = 73/158 (46%), Gaps = 5/158 (3%)

Query: 28  DDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           D+  K+++ L +++   + ++E+N F    E+ +EQME     L +  I+V+     ED 
Sbjct: 9   DERLKELVVLGKKKKSILELQEINDFFNDMELDAEQMEKVFDHLESNNIDVLRISGDED- 67

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D   + +      +           S +DPVRMYL+E+G + LLS E EI +A+R+
Sbjct: 68  --DVDVEVIITDEEEVDMENIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEREIELAQRM 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 126 EDGDEDAKKELAEANLRLVVSIAKRY-VGRGMLFLDLI 162


>gi|328907303|gb|EGG27069.1| RNA polymerase sigma factor RpoD [Propionibacterium sp. P08]
          Length = 506

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 209 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIPEKDREDYEWIAEDGKV 268

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 269 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 328

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 329 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMTAEKV 388

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 389 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 448

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 449 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 506



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           +D  D + +E ++D   +   A   S+      D  +       +T DPV+ YL+++G +
Sbjct: 160 IDERDYDPDEAAKDEQQINKEAEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 219

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 220 ALLNAVEEVDLAKRIEAGL 238


>gi|119961685|ref|YP_947521.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
 gi|119948544|gb|ABM07455.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
          Length = 437

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 133/253 (52%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 185 KLKRELEFVIHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 244

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 245 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 304

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 305 PEELALELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 364

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 365 LQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 424

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 425 HPSRSQVLRDYLD 437



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 5/97 (5%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
             ++      E+       +G + V+      ++ +  S      +         ++  +
Sbjct: 78  EDEDFDPAAAEEV-----EVGEDDVEDGATATKDKAAPSGSGFVYSDADDDDAPVQQVMS 132

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +T DPV+ YL+++G + LL+ E E+ +A RIEAG 
Sbjct: 133 AGATADPVKDYLKQIGKVALLNAEQEVDLALRIEAGL 169


>gi|293400669|ref|ZP_06644814.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305695|gb|EFE46939.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 396

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 151/274 (55%), Positives = 197/274 (71%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +   E   I   ++        AKK+++ ANLRLV+S+AKKY  RG+
Sbjct: 124 VKMYLKEIGRVELLDPKEEPEIARRIQ---AGDEEAKKKLISANLRLVVSIAKKYVGRGM 180

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 181 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 240

Query: 529 IHKVVRTARRMSNKIKREPTPEEIA-KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++   + R+P+ EEIA K   +  E VR++ KI  EP+SLETPIG+ED SH
Sbjct: 241 INKLTRIQRQLVQDLGRDPSAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEEDDSH 300

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A+SP + A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 301 LGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGK 360

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 361 EFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394



 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 94/257 (36%), Gaps = 24/257 (9%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS-------- 98
           +++   +   ++S    ++ +   S+ GI V D +D  D    +  +             
Sbjct: 36  KDIMDAVEHLDMSDADFDELLQWFSDNGIAVKDDEDDVDLLDDDALVGDDDDIDFLDDED 95

Query: 99  ------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                 A+      Q   +S+    +DPV+MYL+E+G +ELL  + E  IA+RI+AG   
Sbjct: 96  EEEDSLAAEIESLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEE 155

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
               L  + L     I  +  +  G   L  I         E   G     E   Y K  
Sbjct: 156 AKKKLISANLRLVVSIAKKY-VGRGMLFLDLI--------QEGNMGLVKAVEKFDYTKGF 206

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE-NDERNLDEDEDDSAHTLSA 271
             S        Q     I   A+  +     V++  +      +   D   D SA  ++A
Sbjct: 207 KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAA 266

Query: 272 MEDQLRPKVMCALDEIA 288
             + + P+ +  + +IA
Sbjct: 267 KMENISPEKVREIQKIA 283


>gi|308177806|ref|YP_003917212.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
 gi|307745269|emb|CBT76241.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
          Length = 403

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 141/283 (49%), Positives = 190/283 (67%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EVD  L+I   + +         S  + +     +   +  IAK  ++EANLRLV+S
Sbjct: 121 AEQEVDLALRIEAGLFATDKLEKDDGSMDQRLRWDYEQIIHDGKIAKNHLLEANLRLVVS 180

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ T
Sbjct: 181 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQART 240

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL T
Sbjct: 241 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHT 300

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  AV P D+     L+E    VL +L+ RE  V+ MRFG+    
Sbjct: 301 PLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQ 360

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 361 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 403



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-------RSTDDPVRMYLREM 128
            V   D  +D E S DS D  S   +    L    D A         +T DPV+ YL+++
Sbjct: 54  TVASTDADDDAEPSTDSKDSKSEDDSKGFTLSSGDDDAPQQQVMVAGATADPVKDYLKQI 113

Query: 129 GSIELLSREGEIAIAKRIEAGR 150
           G + LL+ E E+ +A RIEAG 
Sbjct: 114 GKVALLNAEQEVDLALRIEAGL 135


>gi|182418305|ref|ZP_02949600.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237666788|ref|ZP_04526773.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182377687|gb|EDT75231.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237657987|gb|EEP55542.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 369

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 169/410 (41%), Positives = 246/410 (60%), Gaps = 41/410 (10%)

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           ME + + K     D+  +   ++ ++++    G+K+   + K      ++++ +  + L 
Sbjct: 1   MEQKAKGKAAKTKDDKNDKNVKMSAVKELLDKGKKNGSLTYK------EIMEAMDHIDLG 54

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             +I+ + E L  ++  I+                           E            P
Sbjct: 55  PEQIEKIYEALEMMNIEIIGEA-----------------------NETADAEEEIDLSVP 91

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           EG   +           +R  +K I     +S  +       + +G      AKK++ EA
Sbjct: 92  EGIAID---------DPVRMYLKEIGKVPLLSSEQEIEYAQQIEEGN---QRAKKKLAEA 139

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 140 NLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRA 199

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IADQ+ TIRIPVHM + I+K++R  R++  ++ R+P PEEI+K + +PV+ VR++ KI +
Sbjct: 200 IADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPFPEEISKVMDLPVDKVREIQKIAQ 259

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EP+SLETPIG+E+ SHLGDFI D  A +P ++A    L+E    VL +LTPREE+VLR+R
Sbjct: 260 EPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLR 319

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 320 FGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 369



 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 38/155 (24%), Positives = 65/155 (41%), Gaps = 17/155 (10%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K+++   ++ G +T +E+   +   ++  EQ+E     L  M I ++           
Sbjct: 25  AVKELLDKGKKNGSLTYKEIMEAMDHIDLGPEQIEKIYEALEMMNIEII----------- 73

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                  ++ +  +            + DDPVRMYL+E+G + LLS E EI  A++IE G
Sbjct: 74  -----GEANETADAEEEIDLSVPEGIAIDDPVRMYLKEIGKVPLLSSEQEIEYAQQIEEG 128

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                  L E+ L     I  R  +  G   L  I
Sbjct: 129 NQRAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 162


>gi|23295779|gb|AAN12882.1| principal sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis]
          Length = 508

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EFR     ++    +   AK  ++EANLRLV+
Sbjct: 225 AEQEVDLSERIEAGLYAQHLLDTEGDTMEFRR-KRELKWAAADGKKAKDHLLEANLRLVV 283

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 284 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 343

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 344 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 403

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 404 TPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFRQVLETLSPREAGVIKMRYGLEDG 463

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 464 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 507



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ +   +   +     KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 180 DNDEDDEALLANPGVNPKRRVVTTGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 239


>gi|269793869|ref|YP_003313324.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
 gi|269096054|gb|ACZ20490.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
          Length = 342

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 133/250 (53%), Positives = 175/250 (70%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  +VEANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKFD+ 
Sbjct: 93  RELEVITADGVRAKSHLVEANLRLVVSIAKKYTGRGLLFLDLIQEGNTGLIRAVEKFDYA 152

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQ+ TIRIPVHM + I+KV R  R+M   + REPTPEE
Sbjct: 153 KGFKFSTYATWWIRQAITRGMADQARTIRIPVHMVEVINKVSRAQRQMLQDLGREPTPEE 212

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L M  E V +V K  +EPISL TP+G+E  S  GD IED  AV P D+   + L++
Sbjct: 213 LALELDMTPEKVLEVQKHGREPISLHTPLGEEGGSEFGDLIEDTEAVVPADAVNFSFLQQ 272

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L +L+ RE  V+ MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPS
Sbjct: 273 QIHGILDTLSEREAGVITMRYGLTDGLPKTLDQIGHVYGVTRERIRQIESKTMSKLRHPS 332

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 333 RSQVLRDYLD 342



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 30/66 (45%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +    D +   S            A  +T DPV+ YL+ +G + LL+ E EI IA RIE
Sbjct: 13  PTASQTDDSFVLSTDEEDAPAPTVLAAGATADPVKDYLKIIGRVPLLNAEQEIEIAMRIE 72

Query: 148 AGRAMM 153
           AG    
Sbjct: 73  AGMLAA 78


>gi|223936990|ref|ZP_03628898.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894271|gb|EEF60724.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 614

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 166/511 (32%), Positives = 248/511 (48%), Gaps = 43/511 (8%)

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
            +E  D    L  + D       +         E      +     E E+  +  + G  
Sbjct: 142 AEEQEDEKGRLDILDDPVRMYLRQMGKVPLLTREQEVAICKRIEEAENEQRRIIYSFGFA 201

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
                   +                    +  D     L  +  ++R       ++ AE 
Sbjct: 202 AKEHIALAEKLISEPPKERFDRVIVDKKIDSRDRHLKALRQLVKKVREMDQEVDEKYAEW 261

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
                S +D             + K L +KL          Q  I+ ++    +I  +I 
Sbjct: 262 REAKVSAKDKVF---------AEFKKLDKKLQDTFPKFYYKQKVIEEMILVAQNIHDKIQ 312

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            +    + L ++                         +   + EW               
Sbjct: 313 ASLRTTVDLEKARK-------------------SDQQQAILKSEW--------------- 338

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +I ++     +  +E+      + +   +A  AK EM EANLRLVIS+ KKYTNRGL F
Sbjct: 339 QKINALEEFARMPNNEYLKNFEALNQYAAKAHQAKTEMAEANLRLVISIGKKYTNRGLAF 398

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LD+IQEGN+GLMK  EKF++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I 
Sbjct: 399 LDIIQEGNMGLMKGVEKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIEIIG 458

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K++R  +++  +  RE TPEEIA ++ + VE V+ +LK+ ++PIS++  +GD D +  GD
Sbjct: 459 KLMRAQKQLLQEFGREATPEEIADEMQISVERVKSILKMAQQPISMQASVGDSDDATFGD 518

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIEDK+A +P D    + L++    VLA+LT RE R++ +RFG+      TLEEVGKQ+ 
Sbjct: 519 FIEDKSAENPSDMTSYSLLKDKLNDVLATLTERERRIVELRFGLVDGYARTLEEVGKQYK 578

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIEAKA+RKL+HP+R + L+ FL+
Sbjct: 579 VTRERIRQIEAKALRKLRHPTRVRHLKGFLE 609



 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 49/259 (18%), Positives = 100/259 (38%), Gaps = 20/259 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  K+++ LA+++G++T +++N  LP   V+ + ++     L+N+ I +VD  +++  + 
Sbjct: 80  EKVKELVLLAKEQGHLTYDDINDALPDTVVTPDDLDQVYTKLNNLEIEIVDAAEVDRVKQ 139

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E                           DDPVRMYLR+MG + LL+RE E+AI KRIE 
Sbjct: 140 PEAEEQEDE-------------KGRLDILDDPVRMYLRQMGKVPLLTREQEVAICKRIEE 186

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDG--TTLLREIIDLEACIGPESKGGFFHGTEGH 206
                   +       +  I   ++L           +I     +  +      H     
Sbjct: 187 AENEQRRIIYSFGFAAKEHIALAEKLISEPPKERFDRVI-----VDKKIDSRDRHLKALR 241

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              K+     ++  +   E      SA      +  K+D   ++         +  ++  
Sbjct: 242 QLVKKVREMDQEVDEKYAEWREAKVSAKDKVFAEFKKLDKKLQDTFPKFYYKQKVIEEMI 301

Query: 267 HTLSAMEDQLRPKVMCALD 285
                + D+++  +   +D
Sbjct: 302 LVAQNIHDKIQASLRTTVD 320


>gi|313897367|ref|ZP_07830910.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
 gi|312957737|gb|EFR39362.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
          Length = 398

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 151/274 (55%), Positives = 197/274 (71%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +   E   I   ++        AKK+++ ANLRLV+S+AKKY  RG+
Sbjct: 126 VKMYLKEIGRVELLDPKEEPEIARRIQ---AGDEEAKKKLISANLRLVVSIAKKYVGRGM 182

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 183 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 242

Query: 529 IHKVVRTARRMSNKIKREPTPEEIA-KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++   + R+P+ EEIA K   +  E VR++ KI  EP+SLETPIG+ED SH
Sbjct: 243 INKLTRIQRQLVQDLGRDPSAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEEDDSH 302

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A+SP + A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 303 LGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGK 362

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 363 EFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 396



 Score = 70.6 bits (171), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 54/278 (19%), Positives = 100/278 (35%), Gaps = 26/278 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +D  ++ +   +Q   +  +++   +    ++    +D     S+  I V + DD  D  
Sbjct: 17  EDIKQEFLDEYKQNDVLYQKDVMDAVEHLAMTDTDFDDLFQWFSDNDIEVKNEDDDVDLM 76

Query: 88  GSEDSLDLASS----------------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
             +  +                     A++     Q   +S+    +DPV+MYL+E+G +
Sbjct: 77  DDDALVATEDDDDIDFLDDDTDEEDTLAADIENLEQSFANSSHTKINDPVKMYLKEIGRV 136

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL  + E  IA+RI+AG       L  + L     I  +  +  G   L  I       
Sbjct: 137 ELLDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKY-VGRGMLFLDLI------- 188

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   G     E   Y K    S        Q     I   A+  +     V++  +  
Sbjct: 189 -QEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 247

Query: 252 E-NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
               +   D   D SA  ++A  + + P+ +  + +IA
Sbjct: 248 RIQRQLVQDLGRDPSAEEIAAKMENISPEKVREIQKIA 285


>gi|297622151|ref|YP_003710288.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
 gi|297377452|gb|ADI39282.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
          Length = 555

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 146/262 (55%), Positives = 198/262 (75%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G S+ E++  V M+++   ++  AK+EMVE+NLRLVIS+AKKYTNRGL FLDLIQEGN+
Sbjct: 289 AGRSLEEYKKDVRMLQRWMDKSQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNM 348

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A+++
Sbjct: 349 GLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGAKKL 408

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  REPTPEE+A +L +  E +R++ KI + PISL+  +GD   S  GDF+ED  A S
Sbjct: 409 MMETGREPTPEELANELGLSAERIREIYKIAQHPISLQAEVGDGGESQFGDFLEDTGADS 468

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++   + L++    VL +LT RE +VL  RFG+      TLEEVG +F VTRERIRQI
Sbjct: 469 PAEATGYSILKDKMNEVLLTLTDRERKVLIQRFGLNDGKPKTLEEVGVEFNVTRERIRQI 528

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RK++HP+RSK+L++FLD
Sbjct: 529 EAKALRKMRHPTRSKQLKAFLD 550



 Score =  106 bits (264), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 79/172 (45%), Gaps = 10/172 (5%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           ++  +    +         +++ +A+ +G++T EE+N  LP    +++Q++  +  LS M
Sbjct: 2   KNNSTPKEAISQQHQQKIDELVAIAKDQGFITYEEINDVLPMTIDTADQIDQILIFLSGM 61

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            + +++             ++        +  L+      + + DDPVRMYL+EMGS+ L
Sbjct: 62  DVQILNQ----------SEVERQKEKKKEAKELEGLPRRVEGTPDDPVRMYLKEMGSVPL 111

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           L+RE E+ I+KRIE  +  +   +     + +  I     L +      + I
Sbjct: 112 LTREEEVEISKRIEKAQHQIERIIMRFRNSSRETIAICSALINNKERFDKCI 163


>gi|29832222|ref|NP_826856.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29609340|dbj|BAC73391.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 389

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 131/296 (44%), Positives = 190/296 (64%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         K      +AK
Sbjct: 94  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLSSTPDLDSQLGLDLDKLVVMGRMAK 153

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 154 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 213

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +P E V +
Sbjct: 214 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLDLPGERVSE 273

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 274 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDATSPVESAAFLLLREHLDAVLSTLGERER 333

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 334 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 389



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 2/101 (1%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  +    +    +      + R +     + D  R YLRE+G I LL+   E+ +A+R+
Sbjct: 59  ESVDVVETVELVEAPEPPAPRARSNDTGGPSSDLFRQYLREIGRIPLLTAAEEVELARRV 118

Query: 147 EAGRAMMMASLCESPLTFQAL-IIWRDELNDGTTLLREIID 186
           EAG       L  +P     L +     +  G    R +I+
Sbjct: 119 EAGLF-AEEKLSSTPDLDSQLGLDLDKLVVMGRMAKRRLIE 158


>gi|229815176|ref|ZP_04445512.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
 gi|229809186|gb|EEP44952.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
          Length = 448

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 143/285 (50%), Positives = 206/285 (72%), Gaps = 5/285 (1%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           +A ++++ L   +++ K  + E  ++ +E R ++      E     AK+ ++ ANLRLV+
Sbjct: 167 LAMKIEAGLDAADKLEKQEAGEIELTRAEMRRLMR----VEQVGLDAKQALISANLRLVV 222

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 223 SIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYATWWIRQAITRAIADQAR 282

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ M  + VR++ KI++EP+SLE
Sbjct: 283 TIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMDMSADRVREIQKISQEPVSLE 342

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+E+ S LGDFIED  AV P D+A  + L+E  T+VL  L  RE +V+ +RFG+   
Sbjct: 343 TPIGEEEDSQLGDFIEDAQAVVPADAASFSMLQEQLTQVLDGLAERERKVIELRFGLEDG 402

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+ 
Sbjct: 403 HPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLEN 447



 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 37/166 (22%), Positives = 65/166 (39%), Gaps = 40/166 (24%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D + +K++ L  + G VT +E+   L   +V+  Q+      L + G+ +V   + +D E
Sbjct: 13  DATIEKLLDLGSKAGSVTEDEIQIVLKNVDVTDAQLSSIYQFLRDRGVEIVSATEDDDSE 72

Query: 88  ----------------------GSEDSLDLASSASNSSVFLQKRKDSADRS--------- 116
                                   +  L +A  A       + +K +             
Sbjct: 73  LIVDDDDRDVSHDDDDLDGDESDEDHDLKMARQADAEMASTKSKKKARTVRTTRSRSRAR 132

Query: 117 ---------TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                    T DPVRMYL+E+G ++LL+   E+ +A +IEAG    
Sbjct: 133 GIDASTVMLTGDPVRMYLKEIGKVDLLTAAEEVDLAMKIEAGLDAA 178


>gi|329766845|ref|ZP_08258374.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
 gi|328838571|gb|EGF88177.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
          Length = 361

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 155/274 (56%), Positives = 203/274 (74%), Gaps = 1/274 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +R  +K I     +S  +   +  ++    E E   AKK++ EANLRLV+S+AK+Y  RG
Sbjct: 88  VRMYLKEIGKVPLLSKEKELELSKIIETGTEAEKEQAKKDLAEANLRLVVSIAKRYVGRG 147

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 148 MLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 207

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I++++R  R++   + REP PEEIAKK+ M  E VR++LKI +EP+SLETPIG+ED SH
Sbjct: 208 TINRLIRIQRQLLQDLGREPKPEEIAKKMNMTPEKVREILKIAQEPVSLETPIGEEDDSH 267

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK+A SP++ A    L+E    +L +LT REE VL++RFG+     HTLEEVG 
Sbjct: 268 LGDFIEDKDAQSPVEHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKTHTLEEVGS 327

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKAIRKLKHPS+  KL+ F++
Sbjct: 328 AFGVTRERIRQIEAKAIRKLKHPSKLNKLKGFME 361



 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 52/179 (29%), Positives = 78/179 (43%), Gaps = 27/179 (15%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           +G +T EE+   L   ++SSE M+D    L++  I +++ + +E+EE   D  DL+  A 
Sbjct: 22  QGELTQEEIVDALSKLDISSEAMDDFYEELNSEDIILINANHVEEEEEELDLEDLSVPA- 80

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG----RAMMMAS 156
                           T+DPVRMYL+E+G + LLS+E E+ ++K IE G    +      
Sbjct: 81  -------------GIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIETGTEAEKEQAKKD 127

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           L E+ L     I  R  +  G   L  I         E   G     E   Y K    S
Sbjct: 128 LAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDYSKGFKFS 177


>gi|300858628|ref|YP_003783611.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686082|gb|ADK29004.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206337|gb|ADL10679.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis C231]
 gi|302330894|gb|ADL21088.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276579|gb|ADO26478.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis I19]
          Length = 517

 Score =  221 bits (562), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 129/250 (51%), Positives = 180/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 268 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 327

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E
Sbjct: 328 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQE 387

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 388 LAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQD 447

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 448 QLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 507

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 508 RSQVLRDYLD 517



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 188 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 240


>gi|239991260|ref|ZP_04711924.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 515

 Score =  220 bits (561), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 263 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 322

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 323 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 382

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 383 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 442

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 443 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 502

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 503 HPSRSQVLRDYLD 515



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 197 SDDDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 255

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            +      L    + + +    
Sbjct: 256 NADKLAPKLKRELEIIAEDGRR 277


>gi|149175263|ref|ZP_01853885.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148845872|gb|EDL60213.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 561

 Score =  220 bits (561), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 164/517 (31%), Positives = 275/517 (53%), Gaps = 35/517 (6%)

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           LL  I ++E  I P+         +     +  D    +  D V+     +     +++D
Sbjct: 43  LLLTIEEIELDIIPDQIITILQPEKPKGRSRTSDDLSRRIDDPVRMYLTQMGEIPLLTRD 102

Query: 240 DRSKVDSPPENAENDER-----------NLDEDEDDSAHTLSAMEDQLRPKVMCALDE-- 286
           +  ++    E      R              E  D    +    +  ++  V   L++  
Sbjct: 103 EEIRLAKKIEITRRRFRRELLSSDYAMRQAIEILDKVHKSELPFDRTIKVSVTEGLEKNQ 162

Query: 287 -IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            +  +   L++L+  +     D +  V  ++ K + ++   SL   + ++  L+E+L   
Sbjct: 163 ILGRMPHNLKTLEFLSNKNASDFQQFVNPELTKSQRMEAYASLQKRRRKMATLIEELSLR 222

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
           ++R+      L +++Q                      ++  +D         +    D 
Sbjct: 223 TQRLQIGMKRLEQISQR---------------------MTELEDQIRDMSDMRIKNSKDD 261

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
              +  E++ +   T  +    R  +  V++   +   A +E+   NLRLV+S+AKKY N
Sbjct: 262 RANLERELQDLVAMTMETPETLRERIKAVKQRYLDYETAMRELSGGNLRLVVSIAKKYRN 321

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL FLDLIQEGN GLM+A +K+++  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM
Sbjct: 322 RGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM 381

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + + K+ + ++++  +  REPT EE A+   + +E  R+VLKI++ PISL+ P+G+ + 
Sbjct: 382 IETMSKLRKVSKQLLQENGREPTLEETAEVAGISLEETRRVLKISRHPISLDRPVGESED 441

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S+ GDFIED ++ SP+++A Q  L++    VL +LT RE  ++++RFG+G    +TLEEV
Sbjct: 442 SYFGDFIEDSDSDSPVNTASQEMLKDKIDHVLKTLTYREREIIKLRFGLGDGYTYTLEEV 501

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+ F VTRER+RQIEAKA+RKL+HP RSK+L+ F++G
Sbjct: 502 GRIFKVTRERVRQIEAKAVRKLQHPVRSKQLQGFIEG 538



 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 39/169 (23%), Positives = 79/169 (46%), Gaps = 12/169 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D    ++I+  +++GY+T ++++A+LP + ++ E++++ +  +  + ++++    +   +
Sbjct: 5   DARLNELIENGKKQGYLTYDQVSAYLPDEALNPEKLDNLLLTIEEIELDIIPDQIITILQ 64

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +                 +  D   R  DDPVRMYL +MG I LL+R+ EI +AK+IE
Sbjct: 65  PEKPKGR------------SRTSDDLSRRIDDPVRMYLTQMGEIPLLTRDEEIRLAKKIE 112

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
             R      L  S    +  I   D+++         I +    G E  
Sbjct: 113 ITRRRFRRELLSSDYAMRQAIEILDKVHKSELPFDRTIKVSVTEGLEKN 161


>gi|307324812|ref|ZP_07604018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889694|gb|EFN20674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 414

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 130/296 (43%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     +S  E   +   V                         +      +AK
Sbjct: 119 RQYLREIGRIPLLSAVEEVELARRVEAGLFAEEKLGNTPDLDSQLAVDLDRLVVLGRVAK 178

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 179 RRLIEANLRLVVSVAKRYIGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 238

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTPEE+A  L +  E V +
Sbjct: 239 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPEEVAAHLDLLPERVSE 298

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 299 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 358

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 359 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 414



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +            +      + D  R YLRE+G I LLS   E+ +A+R+EAG 
Sbjct: 92  VDTVVEPVEPIEPPARADTSGPSADLFRQYLREIGRIPLLSAVEEVELARRVEAGL 147


>gi|307718768|ref|YP_003874300.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532493|gb|ADN02027.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 580

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 164/418 (39%), Positives = 245/418 (58%), Gaps = 15/418 (3%)

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A + +L+      L +IA   ++    +   +    +     +    ++ L+     + L
Sbjct: 170 AEKKRLQQAYRDFLKKIAVSLKQYHEEKRRLLQRGVNILEHEEFLKTRDNLLLKAAEIPL 229

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
            Q  I  L ++  D +++I     E   + +  G+K          REL       A   
Sbjct: 230 QQEEIQQLQQKFLDTARKIEEYRREQESIERRLGVK--------DVRELRLLGRGLASAD 281

Query: 391 PEGEWKNFVACEVDSILKIRN-------EIKSISVETGISISEFRHIVSMVRKGECEASI 443
                +  +    + I +          ++K+  +E   +I +   +   + +G      
Sbjct: 282 ERKRIEERLNMSAEDIKETIRQFQLTEKKLKAFEIEFEATIPQILEMSKEIARGHHLMKT 341

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK ++++ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF++  GYKFSTYA WW
Sbjct: 342 AKDKLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWW 401

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSI+DQ+ TIR+PVHM ++I+KV R AR++   + REPT EEIA +L  P+  V
Sbjct: 402 IRQAITRSISDQARTIRVPVHMIEQINKVQREARQLMQVLGREPTDEEIADRLGWPLSRV 461

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V  + +EPISLE+PIG+E+ S +GDFIEDK A++P      A L++    VLA+L PR
Sbjct: 462 KSVKNVAREPISLESPIGEEEDSSVGDFIEDKTAINPSHQTAYALLQQQIKDVLATLPPR 521

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R+L+HP RS++L+ +L+
Sbjct: 522 EQEVLKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPKRSRRLKDYLE 579



 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 58/346 (16%), Positives = 130/346 (37%), Gaps = 14/346 (4%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLEDEEG 88
           S +K+I+  +++G +T ++L+ FLP +   SE+ +++ +A+L    I VV+ DD E  E 
Sbjct: 16  SVQKLIEYGKRKGILTYDDLSDFLPEEISDSEEKIQEVLAVLEEAHIQVVEEDDSEGGES 75

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
              +                       STDDP+R+YLRE+G   LL+ E E++++K++E 
Sbjct: 76  KAKNRRRVVITERE------------GSTDDPIRLYLREIGRENLLTAEEEVSLSKQMEE 123

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G  ++   L  S +          ++          +  E      ++            
Sbjct: 124 GETIIKEVLKHSGVLLSLFYQVAQKIFSKKNPEDLGLTKEELTEYLAEKKRLQQAYRDFL 183

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSK-DDRSKVDSPPENAENDERNLDEDEDDSAH 267
           +K   S ++   +  +  +  +           R  +          +  + + +     
Sbjct: 184 KKIAVSLKQYHEEKRRLLQRGVNILEHEEFLKTRDNLLLKAAEIPLQQEEIQQLQQKFLD 243

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T   +E+  R +         +  RELR L     +  + ++   +  +  E + + +  
Sbjct: 244 TARKIEEYRREQESIERRLGVKDVRELRLLGRGLASADERKRIEERLNMSAEDIKETIRQ 303

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             L + ++     +      +I+    E+ R        +D  ++ 
Sbjct: 304 FQLTEKKLKAFEIEFEATIPQILEMSKEIARGHHLMKTAKDKLIQA 349


>gi|225021265|ref|ZP_03710457.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945998|gb|EEG27207.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 617

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 127/250 (50%), Positives = 179/250 (71%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 368 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 427

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E
Sbjct: 428 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPYE 487

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  + V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 488 LSKEMDITEDKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQD 547

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 548 QLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 607

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 608 RSQVLRDYLD 617



 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQK-RKDSADRSTDDPVRMYLREMGSIELLSRE 137
           D DD       ED    +    + S  L++ RKD+   ++ D VR YL+++G + LL+ E
Sbjct: 268 DDDDAMPPVDEEDEDSSSVWDEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAE 327

Query: 138 GEIAIAKRIEAGR 150
            E+++AKRIEAG 
Sbjct: 328 QEVSLAKRIEAGL 340


>gi|227499774|ref|ZP_03929874.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227218160|gb|EEI83426.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 606

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 157/351 (44%), Positives = 228/351 (64%), Gaps = 13/351 (3%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           LN ++ D +V  +Y     I+       ++  +  +  D F+      E         K 
Sbjct: 269 LNITKSDEIVNLVYISFNDILSKAANKEQIKTNDRMILDDFINTSSRAE---------KI 319

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
           +           E+D  +++R+    I  E  ++  +F  +    ++    +  AK+++ 
Sbjct: 320 YDGVGLSKKELSEIDESIELRDLAFKIINEDILNDDDFMEL----KRAVINSKRAKQKLA 375

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW++QAIT
Sbjct: 376 ETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQAIT 435

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA+++ + V+ V+++ KI
Sbjct: 436 RAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVDKVQEIRKI 495

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           ++EP+SLETPIG+ED SHLGDFIED  AV P ++A    LRE    VL+ L  RE+RVL+
Sbjct: 496 SQEPVSLETPIGEEDDSHLGDFIEDDTAVDPGEAANYTMLREQLNDVLSCLGAREKRVLQ 555

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 556 LRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 606


>gi|154502790|ref|ZP_02039850.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
 gi|153796673|gb|EDN79093.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
          Length = 371

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 158/273 (57%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S      +   +         AKKE+ EANLRLV+S+AK+Y  RG+
Sbjct: 102 VRMYLKEIGKVPLLSADREIELAQRME---EGDEDAKKELAEANLRLVVSIAKRYVGRGM 158

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 159 LFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 218

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK+L MPVE VR++LKI++EP+SLETPIG+E+ SHL
Sbjct: 219 INKLIRVSRQLLQELGREPLPEEIAKELDMPVERVREILKISQEPVSLETPIGEEEDSHL 278

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A Q  L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 279 GDFIQDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLEEVGKE 338

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 339 FDVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 371



 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 74/157 (47%), Gaps = 3/157 (1%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +  ++++   +++   + I+E+N F    E+ +EQME     L    I+V+     +D +
Sbjct: 10  ERLRELVAQGKKKKSILEIQEINDFFADMELEAEQMEKVFEYLEANNIDVLRISSDDDLD 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D + +A  A +  +           S +DPVRMYL+E+G + LLS + EI +A+R+E
Sbjct: 70  VDMDVI-MAEEADDVDMENIDLSVPDGVSIEDPVRMYLKEIGKVPLLSADREIELAQRME 128

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       L E+ L     I  R  +  G   L  I
Sbjct: 129 EGDEDAKKELAEANLRLVVSIAKRY-VGRGMLFLDLI 164


>gi|297559739|ref|YP_003678713.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844187|gb|ADH66207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 364

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 128/252 (50%), Positives = 180/252 (71%), Gaps = 1/252 (0%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                +     E   AK+ ++EANLRLV+S+AK+Y  RGL  LDL+QEGN+GL++A EKF
Sbjct: 111 RTAEELACLVEEGRRAKRSLIEANLRLVVSIAKRYMGRGLLLLDLVQEGNLGLIRAVEKF 170

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+KVVR   ++  ++ REP+
Sbjct: 171 DYGKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVVRVQHQLHQQLGREPS 230

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEI+       + V ++ +I +EP+SL++PI  E+ S  GDFIED +AV+P+++A    
Sbjct: 231 VEEISSAAGFVGQRVVEIQRIAREPVSLQSPI-GEEESDFGDFIEDSDAVAPVEAAAFTV 289

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    +L  L+ RE R++R+RFG+     HTLEEVG++F VTRERIRQIEAK + KL+
Sbjct: 290 LQEQLGAILGGLSDRERRIIRLRFGMADGHPHTLEEVGREFGVTRERIRQIEAKTLAKLR 349

Query: 669 HPSRSKKLRSFL 680
           HPSR+  LR F+
Sbjct: 350 HPSRAGSLRDFI 361



 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/198 (23%), Positives = 67/198 (33%), Gaps = 51/198 (25%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           G V+  E+ + L   +   + ++  VA L+ +G+ V   +D   E+              
Sbjct: 9   GPVSRGEVASALERLDAPPDYLDQAVAHLARIGVEVAGPEDTGSEDPGP----------- 57

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR----------- 150
                    D   RS  D VR+YLRE+G + LLS E E+ +AK +E G            
Sbjct: 58  -------VADGGRRSGSDLVRLYLREIGRVPLLSAEQEVELAKAVEVGLYAQHCAPVEGV 110

Query: 151 -------------AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
                             SL E+ L     I  R  +  G  LL  +         E   
Sbjct: 111 RTAEELACLVEEGRRAKRSLIEANLRLVVSIAKRY-MGRGLLLLDLV--------QEGNL 161

Query: 198 GFFHGTEGHSYQKREDSS 215
           G     E   Y K    S
Sbjct: 162 GLIRAVEKFDYGKGFKFS 179


>gi|318066993|emb|CBY89111.1| RNA polymerase sigma70 factor [Salinicola halophilus]
          Length = 368

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 121/397 (30%), Positives = 185/397 (46%), Gaps = 51/397 (12%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG++ELL+REGEI IAKRIE G   +M+SL   P    +++ + D+ 
Sbjct: 19  GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGLREVMSSLAYLPGAVDSVLAFYDQT 78

Query: 175 NDGTT--LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
            D      L ++             GF    EG       +  +E E  +V + + D E 
Sbjct: 79  QDEEAPGRLSDLF-----------SGFIDPDEGIPGVAEVELPEEVEP-EVGDKDEDDEE 126

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
             +   D  S+    PE A      + E  + +   ++                      
Sbjct: 127 GDEEEDDSSSEGGPDPEEARVRFEQIREQNESAKAAIA---------------------- 164

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                        +    S + +  + +L  L   + L+    + LV Q+    +++   
Sbjct: 165 -------------EHGFGSKEVEAEQARLAVLFSPIKLSPKHFERLVGQVRISVEQVREQ 211

Query: 353 EGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++   +   + R  F+    G E    W           + + +A     + + + 
Sbjct: 212 EKSIMQVFVKQGKVPRKTFISEFLGSETTESWFDDFVAKHTK-YADRLAPFRGDVQRAQR 270

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I        +++ + + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 271 KIDFEQEMVQLNVGQLKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 330

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 331 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 367


>gi|297243591|ref|ZP_06927522.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
 gi|296888342|gb|EFH27083.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
          Length = 489

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 140/284 (49%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T I   EF+     ++    +   AK  ++EANLRLV+
Sbjct: 206 AEQEVDLSERIEAGLYAQHLLDTQIDQMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 264

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 265 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 324

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 325 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 384

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L PRE  V++MR+G+   
Sbjct: 385 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLAPREAGVIKMRYGLEDG 444

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 445 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 488



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 178 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 220


>gi|160947542|ref|ZP_02094709.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
 gi|158446676|gb|EDP23671.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
          Length = 382

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +S  E R +   +         AKK++ E NLRLV+S+AK+Y  RG+
Sbjct: 113 VKMYLKEIGKIPLLSADEERILAENME---AGDIEAKKKLAETNLRLVVSIAKRYVGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 170 QFLDLIQEGNMGLMKAVEKFDFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++  ++ REPT EEI++ + + V+ V ++ KI +EP+SLETPIG+ED SHL
Sbjct: 230 INKLVRIERQLVQELGREPTNEEISEHMGIEVDKVNEIRKIAQEPVSLETPIGEEDDSHL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A++P ++A  + L+E   +VL++L+ RE++VL +RFG+   T  TLEEVGK+
Sbjct: 290 GDFIEDETAIAPDEAANFSMLKEQLNQVLSTLSDREKKVLELRFGLNDGTPRTLEEVGKE 349

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKLKHPSRS+KL+ FL+
Sbjct: 350 FEVTRERIRQIEAKALRKLKHPSRSQKLKDFLE 382



 Score = 73.7 bits (179), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 40/131 (30%), Positives = 65/131 (49%), Gaps = 5/131 (3%)

Query: 58  VSSEQMEDTVAMLSNMGIN-VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
           +  + +E+  + L+   +  + +G++LED E  ED +DL     ++     K +D +D  
Sbjct: 46  IDIDDIEEIKSKLAENQVEFIDEGENLEDIEIVEDLIDLEDEKEDAEDEEIKLEDFSDLK 105

Query: 117 ---TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
               DDPV+MYL+E+G I LLS + E  +A+ +EAG       L E+ L     I  R  
Sbjct: 106 GFNIDDPVKMYLKEIGKIPLLSADEERILAENMEAGDIEAKKKLAETNLRLVVSIAKRY- 164

Query: 174 LNDGTTLLREI 184
           +  G   L  I
Sbjct: 165 VGRGMQFLDLI 175


>gi|291526136|emb|CBK91723.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale DSM
           17629]
 gi|291527130|emb|CBK92716.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale M104/1]
          Length = 418

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 149/248 (60%), Positives = 200/248 (80%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++   + + AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G
Sbjct: 171 LQRDVDKGADAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKG 230

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA
Sbjct: 231 YKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIA 290

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K++ MPVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E  
Sbjct: 291 KEMNMPVERVREILKISQEPVSLETPIGEEEDSHLGDFIKDDNVPVPADAAAFTLLKEQL 350

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LT RE++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 351 EEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 410

Query: 674 KKLRSFLD 681
           +KL+ +L+
Sbjct: 411 RKLKDYLE 418



 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 31/147 (21%), Positives = 62/147 (42%), Gaps = 8/147 (5%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + KK+ +   ++ ++       +F     + +    +++  +  +E+  F     +  E+
Sbjct: 1   MAKKKEQKDMAQEQEQ----RLNFQQKLIEILELGKKKKNMLEYQEIADFFKDLNLDPEK 56

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            E  +  L   GI+V+        +   D   +        V           S +DPVR
Sbjct: 57  FEMVIDYLEQNGIDVL----KISNDDDVDDDIILDDEDEVEVEKIDLSVPEGVSVEDPVR 112

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAG 149
           MYL+E+G + LLS + EI +A+ +E G
Sbjct: 113 MYLKEIGKVPLLSADEEIELAQNMEDG 139


>gi|298253932|ref|ZP_06977519.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
 gi|297532075|gb|EFH71050.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
          Length = 489

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 140/284 (49%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T I   EF+     ++    +   AK  ++EANLRLV+
Sbjct: 206 AEQEVDLSERIEAGLYAQHLLDTQIDQMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 264

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 265 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 324

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 325 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 384

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L PRE  V++MR+G+   
Sbjct: 385 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLAPREAGVIKMRYGLEDG 444

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 445 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 488



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 178 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 220


>gi|157364824|ref|YP_001471591.1| RpoD family RNA polymerase sigma factor [Thermotoga lettingae TMO]
 gi|157315428|gb|ABV34527.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga lettingae
           TMO]
          Length = 400

 Score =  220 bits (561), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 138/272 (50%), Positives = 192/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     ++ S+ R +    +        AK++++E+NLRLV+S+AK+Y  RGL
Sbjct: 125 IKMYLREIGKIPLLTPSQERELARRAQ---IGNKRAKEKLIESNLRLVVSIAKRYIGRGL 181

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 182 PFLDLIQEGNIGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 241

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R    K   +P+ EE+AK +  PV+ V ++L+ +KE +SLE P+G+++ S +
Sbjct: 242 INKLNRITREYYQKHGEQPSLEELAKLMDKPVDKVEEILQASKETVSLEAPVGEDEDSTV 301

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D+N  SP   A++  +RE   +VL +L PRE  VL+MR+G+      TLEEVG+ 
Sbjct: 302 GDFVADENITSPKKEAMRMLMREELEKVLKTLNPREAMVLKMRYGLLDGKAKTLEEVGQY 361

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK L+S +
Sbjct: 362 FNVTRERIRQIEVKALRKLRHPSRSKYLKSLI 393



 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 39/161 (24%), Positives = 72/161 (44%), Gaps = 8/161 (4%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAML 70
            E      +L  +  +   + +IK  +++G++T ++++   PPD     +  +E     L
Sbjct: 21  KEKSARRKALTGEEIEKRVRNLIKTGKKKGFITYDDIDKAFPPDYDGFDTSLIEHIYEEL 80

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
               IN+      +D E  E+ +D    +   S+  +  +   + +  DP++MYLRE+G 
Sbjct: 81  EKNKINI------QDTEPIEEIIDEDVESEIPSLLEEGPEIYDNVALKDPIKMYLREIGK 134

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           I LL+   E  +A+R + G       L ES L     I  R
Sbjct: 135 IPLLTPSQERELARRAQIGNKRAKEKLIESNLRLVVSIAKR 175


>gi|218515956|ref|ZP_03512796.1| RNA polymerase sigma factor RpoD [Rhizobium etli 8C-3]
          Length = 321

 Score =  220 bits (561), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 149/335 (44%), Positives = 194/335 (57%), Gaps = 31/335 (9%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S    D              + S  +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGELAPSGGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTY------SGPEAKAAPQFQSPEKIEADRKAAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
             S      D   +   P           +EDED+S  +L+AME +LRP+VM  LD IAE
Sbjct: 235 ARSGDDDITDVGGEGLPP--------EEEEEDEDESNLSLAAMEAELRPQVMETLDTIAE 286

Query: 290 VYRELRSLQDN------AVNGQKDEKSSVKCKVLK 318
            Y++LR LQD       + +G        + K LK
Sbjct: 287 TYKKLRKLQDQQVEQRLSASGTLSSAQERRYKELK 321


>gi|309801431|ref|ZP_07695558.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
 gi|308221946|gb|EFO78231.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
          Length = 461

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 201/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T  S  +F+     ++    +   AK  ++EANLRLV+
Sbjct: 178 AEQEVDLSERIEAGLYAQHLLDTEASQMDFKRR-RELKWAANDGKKAKDHLLEANLRLVV 236

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 237 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 296

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 297 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 356

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 357 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 416

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 417 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 460



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 150 KRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 192


>gi|324997280|ref|ZP_08118392.1| RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 469

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 136/301 (45%), Positives = 190/301 (63%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV----------------------------RKGECE 440
           +R  +K I     ++  E   +   +                            R    +
Sbjct: 169 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYGAERIRKLFESNDKLSPQMRRDLRWIVRD 228

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 229 GERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 288

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 289 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 348

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VLA+L
Sbjct: 349 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLATL 408

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 409 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 468

Query: 681 D 681
           D
Sbjct: 469 D 469



 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/73 (38%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 139 KSADFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGL 198

Query: 151 --AMMMASLCESP 161
             A  +  L ES 
Sbjct: 199 YGAERIRKLFESN 211


>gi|329934715|ref|ZP_08284756.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
 gi|329305537|gb|EGG49393.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
          Length = 363

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 126/296 (42%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGEC------------------------EASIAK 445
           R  ++ I     ++ +E   +   V  G                             +AK
Sbjct: 68  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLGSTPDLDSRLALDLDTLVVRGRMAK 127

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 128 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 187

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EP+ EE+A +L +  E V +
Sbjct: 188 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPSAEEVAAQLDLSPERVGE 247

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+E+   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 248 VLRLAQEPVSLHAPVGEEEDVALGDLIEDGDATSPVESAAFLLLREHLDAVLSTLGERER 307

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +L+
Sbjct: 308 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAYADQLRGYLE 363



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 38/100 (38%), Gaps = 2/100 (2%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G       A +             S    + D  R YLRE+G I LL+   E+ +A+R+E
Sbjct: 34  GEAVEPAEAVATEEPPPVRAASGASGSSPSSDLFRQYLREIGRIPLLTAAEEVELARRVE 93

Query: 148 AGRAMMMASLCESPLTFQAL-IIWRDELNDGTTLLREIID 186
           AG       L  +P     L +     +  G    R +I+
Sbjct: 94  AGLF-AEEKLGSTPDLDSRLALDLDTLVVRGRMAKRRLIE 132


>gi|50726933|gb|AAT81163.1| principal sigma factor [Streptomyces ansochromogenes]
          Length = 440

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 188 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 247

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 248 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 307

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 308 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 367

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 368 LQEQPDSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 427

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 428 HPSRSQVLRDYLD 440



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 48/106 (45%), Gaps = 2/106 (1%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           + V++   + DE    ++     S  +      ++  +A  +T DPV+ YL+++G + LL
Sbjct: 99  VGVLEDTKVADEPEGTETAGFVLSDEDEDDAPAQQVAAA-GATADPVKDYLKQIGKVPLL 157

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 158 NAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 202


>gi|270307915|ref|YP_003329973.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
 gi|270153807|gb|ACZ61645.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
          Length = 520

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 145/242 (59%), Positives = 199/242 (82%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +A  A++ +++ANLRLV+SVAKK+  RG+  LDLIQEGNIGL++A EKFD+  G+KFSTY
Sbjct: 279 DAKRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTY 338

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I+K++  +R++S K+ REPTP+EIA ++ +P
Sbjct: 339 ATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIALEMDLP 398

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            E VR++ K+++ P+SLE+PIG+E+ SHLGDFIED+NA++P D+A +  L+E    VL S
Sbjct: 399 PEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVLGS 458

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LTPRE RVL++RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +
Sbjct: 459 LTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDY 518

Query: 680 LD 681
           L+
Sbjct: 519 LE 520



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/142 (21%), Positives = 57/142 (40%), Gaps = 7/142 (4%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE-DSLDLASSASNSSVF 105
            +++     +  S + +E  +  +++  I     ++    E       D      N  + 
Sbjct: 26  ADIHDEQDAEAESDKLVEPDLKDIADTDIPAELTEEELAAEADMMPDTDEEIGPLNIDLE 85

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMMMASLCE---- 159
           +   +       DDPVRMYL E+G + LLS E E  +AK++E G+    +     E    
Sbjct: 86  IPLEQVDTQGIVDDPVRMYLHEIGRVPLLSAEDEKTLAKKMEEGKRIREIRQECLEKRGR 145

Query: 160 SPLTFQALIIWRDELNDGTTLL 181
            P   ++ +    EL   T +L
Sbjct: 146 YPSAAESFLCMLRELAQATEVL 167


>gi|308234847|ref|ZP_07665584.1| RNA polymerase sigma factor [Gardnerella vaginalis ATCC 14018]
 gi|311114490|ref|YP_003985711.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
 gi|310945984|gb|ADP38688.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
          Length = 434

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 140/284 (49%), Positives = 201/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T I   EF+     ++    +   AK  ++EANLRLV+
Sbjct: 151 AEQEVDLSERIEAGLYAQHLLDTQIDQMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 209

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 210 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 269

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 270 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 329

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 330 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLSPREAGVIKMRYGLEDG 389

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 390 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 433



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 123 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 165


>gi|315226631|ref|ZP_07868419.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
 gi|315120763|gb|EFT83895.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
          Length = 690

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 130/250 (52%), Positives = 187/250 (74%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW 
Sbjct: 439 RELKWAANDGRKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWK 498

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E
Sbjct: 499 KGFKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDE 558

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L MPVE V++V K  +EPISL TP+G++  S  GD IED +A++P ++   + L+E
Sbjct: 559 LARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQE 618

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL +L+PRE  V++MR+G+      TL+++G  + VTRERIRQIE+K + KL+HPS
Sbjct: 619 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHPS 678

Query: 672 RSKKLRSFLD 681
           RS+ L+ FLD
Sbjct: 679 RSQTLQDFLD 688



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 30/43 (69%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+     +T DPV+ YL+++G + LL+ + E+ +++RIEAG 
Sbjct: 377 KRRILTTGATSDPVKDYLKQIGRVNLLNAQQEVDLSERIEAGL 419


>gi|182438860|ref|YP_001826579.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326779516|ref|ZP_08238781.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178467376|dbj|BAG21896.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326659849|gb|EGE44695.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 363

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 124/296 (41%), Positives = 185/296 (62%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +       AK
Sbjct: 68  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEERLAGTPDLDSRLAGDLDRLVVMGRTAK 127

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 128 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 187

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+IA  L +  E V  
Sbjct: 188 QAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIAVDLDLTPERVTD 247

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +EP+SL  P+G+ED    GD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 248 ILRLAQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 307

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+  + + +LR +LD
Sbjct: 308 KVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDHAFADQLRGYLD 363



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +      G      +  +         + +  +  +T D  R YLRE+G I LL+   E+
Sbjct: 27  ETTAGPPGHAPEAVMVEATHLPDPPEPRNRADSGGATSDLFRQYLREIGRIPLLTAAEEV 86

Query: 141 AIAKRIEAGRAMMMASLCESP 161
            +A+R+EAG       L  +P
Sbjct: 87  ELARRVEAGLF-AEERLAGTP 106


>gi|218249968|ref|YP_002375211.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
 gi|218165156|gb|ACK75217.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
          Length = 631

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 177/641 (27%), Positives = 308/641 (48%), Gaps = 34/641 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D   SED  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVVSEDGNDEEEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +S D+ + + ++       L    E  I+ + + G   +  ++ + 
Sbjct: 82  IESDRNFMILDDGFQSDDEDIDIDVK-------LDDCDEEDISVKDDLGSGYIKGNVLKD 134

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
             +   +             L+EI       G +          G S  +    ++    
Sbjct: 135 SHSEDPI----------KLYLKEIGKEFLLTGNQEVELAKQMDSGESIIENILKNEGLVI 184

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           ++       I S  +  +  + + D   E++ +               L  ++D+L   V
Sbjct: 185 ENYYNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIASFYKIPLKPIQDRLISYV 244

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                           + D   +           K  +  L +L+  + L Q  + +  +
Sbjct: 245 -----------DNKHRVYDLGGDIF-----EKNLKKERLALKELLRDIPLYQEELRIFSD 288

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
              D + +I   + +   +     I++   L    GR+L         +      ++ + 
Sbjct: 289 DYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDAIK 347

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S+A
Sbjct: 348 EQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVSIA 407

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ TIR
Sbjct: 408 KKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQARTIR 467

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLETPI
Sbjct: 468 VPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI 527

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+      
Sbjct: 528 GEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSL 587

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 588 TLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|153309|gb|AAA26764.1| principal sigma-like factor [Streptomyces aureofaciens]
          Length = 528

 Score =  220 bits (560), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 132/250 (52%), Positives = 177/250 (70%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 279 RELEILVEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYT 338

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQS TIRIPVHM + I+K+ R  R+M   + REPTPEE
Sbjct: 339 KGFKFSTYATWWIRQAITRAMADQSRTIRIPVHMVEIINKLARVQRQMLQDLGREPTPEE 398

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + K+L M  E V +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E
Sbjct: 399 LGKELDMTPEKVIEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTFLQE 458

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L +L+ RE  V+ MR+G+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 459 QLQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPS 518

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 519 RSQVLRGYLD 528



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       +      +T DPV+ YL+ +G + LL+ E E+ +AKRIEAG 
Sbjct: 210 SDDDEDDAPAQTVMVAGATADPVKDYLKLIGKVPLLNAEQEVELAKRIEAGL 261


>gi|221632805|ref|YP_002522027.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
 gi|221156346|gb|ACM05473.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
          Length = 369

 Score =  220 bits (560), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 135/297 (45%), Positives = 193/297 (64%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK------------------------GECEASIA 444
           +R  ++ I     ++  E   +   + +                         + +   A
Sbjct: 73  VRLYLQEIGETALLTPQEEVWLAQRIERGKIAKVRLERGDYKSEDERLALVADKEDGERA 132

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +++ANLRLV+SVAKKY  RGL FLDLIQEGNIGLMKA EKFD+  GYKFSTYA WW+
Sbjct: 133 RAHLIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATEKFDYKRGYKFSTYATWWI 192

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+I+DQS TIR+PVH+ + I+++ + + R+   ++REPT  E+A+ L MP E +R
Sbjct: 193 RQAITRAISDQSRTIRLPVHVGETINRIKKISHRLQQILEREPTQLEVARALDMPEEKIR 252

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++L+  + P+SLE PIG +  + LGDFIED+   +PL+ A Q  LR+     L+ LT RE
Sbjct: 253 QILEAARLPVSLEAPIGQDGDAFLGDFIEDETQPAPLEIASQQLLRQQLEEALSRLTERE 312

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            R++ +R+G+      TLEEVG++F +TRERIRQIEAKA+RKL+HPS S+ LR +LD
Sbjct: 313 RRIIILRYGLEDGQFRTLEEVGREFGITRERIRQIEAKALRKLRHPSCSRFLRGYLD 369



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 37/78 (47%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           +R D    ST D VR+YL+E+G   LL+ + E+ +A+RIE G+   +        +    
Sbjct: 60  ERFDDDGLSTSDTVRLYLQEIGETALLTPQEEVWLAQRIERGKIAKVRLERGDYKSEDER 119

Query: 168 IIWRDELNDGTTLLREII 185
           +    +  DG      +I
Sbjct: 120 LALVADKEDGERARAHLI 137


>gi|318059566|ref|ZP_07978289.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075441|ref|ZP_07982773.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 446

 Score =  220 bits (560), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 194 KLQRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 253

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 254 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 313

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 314 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 373

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 374 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 433

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 434 HPSRSQVLRDYLD 446



 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 48/114 (42%), Gaps = 10/114 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD---------RSTDDPVRMYLR 126
            ++D +  E+  G  D     ++   S  F+    D  D          +T DPV+ YL+
Sbjct: 96  ELLDEESTEETPGKGDEAAEPAAGGESQGFVLSDDDEDDAPAQQVAAAGATADPVKDYLK 155

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++G + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 156 QIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLQRELEIIAEDGRR 208


>gi|257784627|ref|YP_003179844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
 gi|257473134|gb|ACV51253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
          Length = 455

 Score =  220 bits (559), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 137/254 (53%), Positives = 190/254 (74%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     + + E     AK++++ ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EK
Sbjct: 201 RAEQRRLMRIESVGLDAKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEK 260

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++     R+P
Sbjct: 261 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDFGRDP 320

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEEI  ++ M  + VR++ KI++EP+SLETPIG+E+ S LGDFIED  AV+P D+A  +
Sbjct: 321 TPEEIGSEMGMSPDRVREIQKISQEPVSLETPIGEEEDSQLGDFIEDSTAVAPPDAASDS 380

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE   +VL SL  RE +V++ RFG+      TLEEVGK+F VTRERIRQIE+K + KL
Sbjct: 381 MLREQLEQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGKEFGVTRERIRQIESKTLAKL 440

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS +L+ +++
Sbjct: 441 RHPSRSGRLKDYME 454



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/79 (27%), Positives = 41/79 (51%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V +  ++++   S     ++    +S    ++   +    T DPVRMYL+E+G ++LL+ 
Sbjct: 110 VNEAREVKEALRSVSKAKVSKPKRSSRARARRSDTTTVMLTGDPVRMYLKEIGKVDLLTA 169

Query: 137 EGEIAIAKRIEAGRAMMMA 155
             E+ +A +IEAG A    
Sbjct: 170 SEEVHLAMKIEAGTAASQK 188


>gi|148658692|ref|YP_001278897.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148570802|gb|ABQ92947.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 401

 Score =  220 bits (559), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 132/249 (53%), Positives = 180/249 (72%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +   E   A++ +++ANLRLV+S+AKKY  RG+  LDLIQEGNIGLM+A EKFD+  
Sbjct: 153 QLHRWVQEGQAARERLIQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRK 212

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR IADQS TIR+PVH+ + I++V+R + R+     R+PTP+EI
Sbjct: 213 GYKFSTYATWWIRQAITRVIADQSRTIRLPVHVGETINRVMRASNRIQQTTGRDPTPDEI 272

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L +PVE VR+VL+  ++ ISLETPIG E  + L DFIED   V+P+DSA    LRE 
Sbjct: 273 ALELGIPVEKVRRVLEAARQTISLETPIGTEGDTVLADFIEDGKGVTPMDSASHHILREQ 332

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               L  L  RE R++++R+G+      TLEEVG++F +TRERIRQIEA+ +RKL+HP  
Sbjct: 333 IDSALEKLPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLRKLRHPHY 392

Query: 673 SKKLRSFLD 681
            + LR +L+
Sbjct: 393 GRGLRGYLE 401



 Score = 61.8 bits (148), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 23/111 (20%), Positives = 45/111 (40%), Gaps = 2/111 (1%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-RKDSADRSTDDPVRMYLREMGSIELL 134
           ++++    E  + + D+              +    D      DDPVR+YLRE+G + LL
Sbjct: 60  HILERTAGEPFDQTIDAFHADRDHEEDEALDRDFDADVESMGVDDPVRVYLREIGRVNLL 119

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           + + EI +A+++E G       L +        +     + +G      +I
Sbjct: 120 TAQEEIMLAQQVERGE-QASERLQKGDYAPSERLQLHRWVQEGQAARERLI 169


>gi|169630092|ref|YP_001703741.1| RNA polymerase sigma factor [Mycobacterium abscessus ATCC 19977]
 gi|169242059|emb|CAM63087.1| Probable RNA polymerase sigma factor RpoD (Sigma-A) [Mycobacterium
           abscessus]
          Length = 467

 Score =  220 bits (559), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 134/286 (46%), Positives = 192/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T ++    +   +    +     +   AK  ++EANLRL
Sbjct: 182 AEEEVELAKRIEAGLYATQIVTELTEKGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 241

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 242 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 301

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 302 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 361

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 362 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLT 421

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 422 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 467



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/69 (39%), Positives = 38/69 (55%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ 
Sbjct: 128 DDEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVE 187

Query: 142 IAKRIEAGR 150
           +AKRIEAG 
Sbjct: 188 LAKRIEAGL 196


>gi|240169695|ref|ZP_04748354.1| RNA polymerase sigma factor [Mycobacterium kansasii ATCC 12478]
          Length = 518

 Score =  220 bits (559), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 188/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM----------------------------VRKGECE 440
           +R  +K I     ++  E   +                               +     +
Sbjct: 218 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAERGEKLPAAQRRDMMWICRD 277

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 278 GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 337

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 338 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 397

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 398 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTL 457

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 458 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 517

Query: 681 D 681
           D
Sbjct: 518 D 518



 Score = 65.2 bits (157), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 34/110 (30%), Positives = 57/110 (51%), Gaps = 5/110 (4%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE-EGSEDSLDLASSASNSSVFLQKRKD 111
           L P    ++++E     ++  G  V D +++ +  E  + S D       S    Q RKD
Sbjct: 151 LDPTVEDTDEVES--PAVAAPGSAVDDEEEIAEPTEKDKASGDFVWDEDESEALRQARKD 208

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMMMASLCE 159
           +   ++ D VR YL+++G + LL+ E E+ +AKRIEAG     +MA + E
Sbjct: 209 AELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAE 258


>gi|315185629|gb|EFU19397.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta thermophila DSM
           6578]
          Length = 568

 Score =  220 bits (559), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 165/418 (39%), Positives = 245/418 (58%), Gaps = 15/418 (3%)

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A + +L+      L +IA   ++    +   +    +     +    ++ L+     + L
Sbjct: 158 AEKKRLQQAYRDFLKKIAVSLKQYHEEKRRLLQRGVNILEHEEFLKTRDNLLLKAAEIPL 217

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
            Q  I  L ++  D +++I     E   + +  G+K          REL       A   
Sbjct: 218 QQEEIQQLQQKFLDTARKIEEYRREQESIERRLGVK--------DVRELRLLGRGLASAD 269

Query: 391 PEGEWKNFVACEVDSILKIRN-------EIKSISVETGISISEFRHIVSMVRKGECEASI 443
                +  +    + I +          ++K+  +E   +I +   +   + +G      
Sbjct: 270 ERKRIEERLNMSAEDIKETIRQFQLTEKKLKAFEIEFEATIPQILEMSKEIARGHHLMKT 329

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK ++++ANLRLV+S+AKKYTNRGL F DL+QEGNIGL+KA EKF++  GYKFSTYA WW
Sbjct: 330 AKDKLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWW 389

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITRSI+DQ+ TIR+PVHM ++I+KV R AR++   + REPT EEIA +L  P+  V
Sbjct: 390 IRQAITRSISDQARTIRVPVHMIEQINKVQREARQLMQVLGREPTDEEIADRLGWPLSRV 449

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + V  + +EPISLE+PIG+E+ S +GDFIEDK AV+P      A L++    VLA+L PR
Sbjct: 450 KSVKNVAREPISLESPIGEEEDSSVGDFIEDKTAVNPSHQTAYALLQQQIKDVLATLPPR 509

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+ VL+MRFG+      TLEEVG  F VTRERIRQIEAKA+R+L+HP RS++L+ +L+
Sbjct: 510 EQEVLKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPKRSRRLKDYLE 567



 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 58/346 (16%), Positives = 130/346 (37%), Gaps = 14/346 (4%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLEDEEG 88
           S +K+I+  +++G +T ++L+ FLP +   SE+ +++ +A+L    I VV+ DD E  E 
Sbjct: 4   SVQKLIEYGKRKGILTYDDLSDFLPEEISDSEEKIQEVLAVLEEAHIQVVEEDDSEGGES 63

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
              +                       STDDP+R+YLRE+G   LL+ E E++++K++E 
Sbjct: 64  KAKNRRRVVITERE------------GSTDDPIRLYLREIGRENLLTAEEEVSLSKQMEE 111

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G  ++   L  S +          ++          +  E      ++            
Sbjct: 112 GENIIKEVLKHSGVLLSLFYQVAQKIFSKKNPEDLGLTKEELTEYLAEKKRLQQAYRDFL 171

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSK-DDRSKVDSPPENAENDERNLDEDEDDSAH 267
           +K   S ++   +  +  +  +           R  +          +  + + +     
Sbjct: 172 KKIAVSLKQYHEEKRRLLQRGVNILEHEEFLKTRDNLLLKAAEIPLQQEEIQQLQQKFLD 231

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           T   +E+  R +         +  RELR L     +  + ++   +  +  E + + +  
Sbjct: 232 TARKIEEYRREQESIERRLGVKDVRELRLLGRGLASADERKRIEERLNMSAEDIKETIRQ 291

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             L + ++     +      +I+    E+ R        +D  ++ 
Sbjct: 292 FQLTEKKLKAFEIEFEATIPQILEMSKEIARGHHLMKTAKDKLIQA 337


>gi|328955627|ref|YP_004372960.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
 gi|328455951|gb|AEB07145.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
          Length = 442

 Score =  220 bits (559), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 145/287 (50%), Positives = 201/287 (70%), Gaps = 3/287 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRL 455
            A EVD  +KI   +++          E    R  +  + + E     AK+ ++ ANLRL
Sbjct: 156 AADEVDLAMKIEAGLEAAEKLESSDRGEIALTRADMRRLSRIEQVGLEAKQALISANLRL 215

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ
Sbjct: 216 VVSIAKRYVGRGMHFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYATWWIRQAITRAIADQ 275

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+VR  R++  ++ R+PTPEEI  ++ M  + VR++ KI++EP+S
Sbjct: 276 ARTIRIPVHMVETINKLVRVQRQLLQELGRDPTPEEIGAEMEMSADRVREIQKISQEPVS 335

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ S LGDFIED  AV P D+A  + LRE   +VL SL  RE +V+ +RFG+ 
Sbjct: 336 LETPIGEEEDSQLGDFIEDAQAVVPPDAASFSMLREQLVQVLDSLADRERKVIELRFGLN 395

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
                TLEEVG+ F VTRERIRQIE+K + KL+HPSRS KL+ +++ 
Sbjct: 396 DGHPRTLEEVGRDFGVTRERIRQIESKTLAKLRHPSRSSKLKDYIES 442



 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/156 (23%), Positives = 62/156 (39%), Gaps = 35/156 (22%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED- 91
           +++    + G V+ +++       E+S  Q+      L   GI+V+  DD +     E+ 
Sbjct: 18  QLLDKGTKSGSVSEDDIQIAFKEIEISDAQLASIYQSLRERGIDVIAHDDEDVTVPLEEA 77

Query: 92  -----------------SLDLASSASNSSVFLQKRKDSADRS-----------------T 117
                             + +A  A       + +K S  RS                 T
Sbjct: 78  PGDDLVSDLDDDNIEDHDIKVAKIADAEMAAAKPKKKSRVRSSRSRARLRGLDASTVMLT 137

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
            DPVRMYL+E+G ++LL+   E+ +A +IEAG    
Sbjct: 138 GDPVRMYLKEIGKVDLLTAADEVDLAMKIEAGLEAA 173


>gi|32476381|ref|NP_869375.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|32446926|emb|CAD78832.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|327539012|gb|EGF25646.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica WH47]
          Length = 519

 Score =  220 bits (559), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 165/500 (33%), Positives = 256/500 (51%), Gaps = 28/500 (5%)

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +          +   E +   ++  ++ +  +        V                 
Sbjct: 28  PVDDSEDDNAVSVADAPEGEVQLDSPDELIALDESETWSDDPVRMYLTQMGEIPLLTRRQ 87

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           E + A  +     + R K++     + E Y+ L+ +    +   +  + SV  ++ KE++
Sbjct: 88  EIELAKRIEETRRRFRTKLLENHYVLVEAYKTLKKVYRGQLPFDRTVQVSVTDRLEKEQI 147

Query: 322 V----KLVGSLS--LNQSRIDLLVEQLYDISKRIMHNEGELLR--------LAQSYGIK- 366
           +      + +L   LN++R D  V        R        L         L +  G++ 
Sbjct: 148 IGRLPHNLKTLQTLLNRNRHDWKVAMSKSAPARRRAEAWRALARRRRRAVRLVEELGLRT 207

Query: 367 -----RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
                R   LE+   R  +   +   +   +           + +L  R +I +   ET 
Sbjct: 208 QRIETRIGLLEKFSRRLDEIDELVRQQKRTKHG-----REVREQLLHERRQILTACQETP 262

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
            S    R+ V M+     +   AK+E+ E NLRLV+S+AKKY NRGL FLDLIQEGN GL
Sbjct: 263 TS---LRNRVKMLGSVYSDYQQAKRELSEGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGL 319

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M+A +KF++  G+KF TYA WW++QAITR++ADQS TIRIPVHM + + +V   AR++  
Sbjct: 320 MRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQSRTIRIPVHMVETMSRVRNVARQLLQ 379

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REP+ EE A++  + +E  R+VL +++ PISL+ P+G+ + S  GD + D  A SP 
Sbjct: 380 ELGREPSIEETARRADVTIEEARRVLTMSRFPISLDRPVGNSEDSQFGDLLPDGTAESPQ 439

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             A Q  LR+  T VL SL+ RE  ++++R+G+G    +TLEEVG  F VTRERIRQIEA
Sbjct: 440 IGATQEMLRQRITGVLKSLSYREREIIKLRYGLGDGYSYTLEEVGHIFKVTRERIRQIEA 499

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+ PSRS+ L  FLD
Sbjct: 500 KAVRKLQQPSRSQDLVGFLD 519



 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 32/116 (27%), Positives = 46/116 (39%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           DD ED+     +          S       D ++  +DDPVRMYL +MG I LL+R  EI
Sbjct: 30  DDSEDDNAVSVADAPEGEVQLDSPDELIALDESETWSDDPVRMYLTQMGEIPLLTRRQEI 89

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            +AKRIE  R      L E+            ++  G       + +      E +
Sbjct: 90  ELAKRIEETRRRFRTKLLENHYVLVEAYKTLKKVYRGQLPFDRTVQVSVTDRLEKE 145


>gi|333024008|ref|ZP_08452072.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
 gi|332743860|gb|EGJ74301.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
          Length = 493

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 241 KLQRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 300

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 301 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 360

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 361 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 420

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 421 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 480

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 481 HPSRSQVLRDYLD 493



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 48/114 (42%), Gaps = 10/114 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD---------RSTDDPVRMYLR 126
            ++D +  E+  G  D     ++   S  F+    D  D          +T DPV+ YL+
Sbjct: 143 ELLDEESTEETPGKGDEAAEPAAGGESQGFVLSDDDEDDAPAQQVAAAGATADPVKDYLK 202

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++G + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 203 QIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLQRELEIIAEDGRR 255


>gi|269215371|ref|ZP_06159225.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
 gi|269131227|gb|EEZ62301.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
          Length = 383

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 140/254 (55%), Positives = 194/254 (76%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     + + E     AK++++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EK
Sbjct: 129 RRDKRRLTRVEAVGLDAKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEK 188

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P
Sbjct: 189 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQDLNRDP 248

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEEI +K+ +  E VR++ KI++EP+SLETPIG+E+ S LGDFIED +AV P D+A  +
Sbjct: 249 TPEEIGEKMGLSAERVREIQKISQEPVSLETPIGEEEDSQLGDFIEDDSAVVPPDAASFS 308

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E  ++VL  L  RE +V+ +RFG+     HTLEEVG++F VTRERIRQIE+K + KL
Sbjct: 309 MLQEQLSKVLDGLAERERKVISLRFGLEDGHPHTLEEVGREFGVTRERIRQIESKTLAKL 368

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS KL+ +L+
Sbjct: 369 RHPSRSSKLKDYLE 382



 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 32/103 (31%), Positives = 52/103 (50%), Gaps = 2/103 (1%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGI--NVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           LN     D++++E  +D  A LS+  +   + + +         +   L+SS ++     
Sbjct: 8   LNEESLGDDLAAEDGKDVDANLSDEELLEGIPENELKAASTSEINLPKLSSSRASKVRRR 67

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                SA   T DPVRMYL+E+G + LL+   EI +A +IEAG
Sbjct: 68  SSDGSSAVMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAG 110


>gi|305681425|ref|ZP_07404232.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
 gi|305659630|gb|EFM49130.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
          Length = 608

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 127/250 (50%), Positives = 179/250 (71%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 359 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 418

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP E
Sbjct: 419 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPYE 478

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  + V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 479 LSKEMDITEDKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQD 538

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 539 QLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 598

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 599 RSQVLRDYLD 608



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQK-RKDSADRSTDDPVRMYLREMGSIELLSRE 137
           D DD       ED    +    + S  L++ RKD+   ++ D VR YL+++G + LL+ E
Sbjct: 259 DDDDAMPPVDEEDEDSSSVWDEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAE 318

Query: 138 GEIAIAKRIEAGR 150
            E+++AKRIEAG 
Sbjct: 319 QEVSLAKRIEAGL 331


>gi|160915039|ref|ZP_02077252.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
 gi|158432838|gb|EDP11127.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
          Length = 398

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 152/274 (55%), Positives = 197/274 (71%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +   E   I   ++        AKK+++ ANLRLV+S+AKKY  RG+
Sbjct: 126 VKMYLKEIGRVELLDPKEEPEIARRIQ---AGDEEAKKKLISANLRLVVSIAKKYVGRGM 182

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 183 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 242

Query: 529 IHKVVRTARRMSNKIKREPTPEEIA-KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++   + R+PT EEIA K   +  E VR++ KI  EP+SLETPIG+ED SH
Sbjct: 243 INKLTRIQRQLVQDLGRDPTAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEEDDSH 302

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A+SP + A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 303 LGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGK 362

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 363 EFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 396



 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 34/156 (21%), Positives = 64/156 (41%), Gaps = 16/156 (10%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS----- 98
           ++  ++   +   ++S   +++     +  GI+V   +  +     +D+L          
Sbjct: 34  LSQSDVMDAIEHLDMSDSDLDELFDWFAENGIDVKSDEADDVNLLDDDALASEDDDLDFI 93

Query: 99  ----------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                     AS+     Q   +S+    +DPV+MYL+E+G +ELL  + E  IA+RI+A
Sbjct: 94  DDDDDGDDTLASDIEHLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQA 153

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L  + L     I  +  +  G   L  I
Sbjct: 154 GDEEAKKKLISANLRLVVSIAKKY-VGRGMLFLDLI 188


>gi|328915181|gb|AEB56014.1| transcription initiation factor sigma 70 [Chlamydophila psittaci
           6BC]
          Length = 561

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 146/277 (52%), Positives = 199/277 (71%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +   +  +    V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYT
Sbjct: 268 KLDAAKRRLYKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYT 327

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL FLDLIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVH
Sbjct: 328 NRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH 387

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+KV+R A+++  +  +EPTPEE+A++L +  + VR++ KI + PISL+  +G+  
Sbjct: 388 MIETINKVLRGAKKLMMETGKEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGG 447

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S  GDF+ED    SP ++   + L++    VL +LT RE  VL  RFG+      TLEE
Sbjct: 448 ESSFGDFLEDTGVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEE 507

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG  F VTRERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 508 VGSAFNVTRERIRQIEAKALRKMRHPIRSKQLRAFLD 544



 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 44/168 (26%), Positives = 84/168 (50%), Gaps = 10/168 (5%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + +    ++++ LA+ +G++T EE+N  LP    + EQ++  +  L+ M I V++  D+E
Sbjct: 7   EEAQKKLEELVSLAKDQGFITYEEINEILPMSFDTPEQIDQVLIFLTGMDIQVLNQADVE 66

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            ++  +            +  L+      + + DDPVRMYL+EMG++ LL+RE E+ I+K
Sbjct: 67  RQKERKK----------EAKELEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREEEVEISK 116

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           RIE  +  +   +     + +  I     L +G     +II  +    
Sbjct: 117 RIEKAQVQIERIILRFRYSSKEAISIAQYLINGKERFDKIISEKEVED 164


>gi|302542036|ref|ZP_07294378.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302459654|gb|EFL22747.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 502

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 250 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 309

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 310 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 369

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 370 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 429

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 430 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 489

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 490 HPSRSQVLRDYLD 502



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 1/101 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G    +    E        +         ++ +A  +T DPV+ YL+++G + LL+ E E
Sbjct: 165 GKPAPEGAEPEPENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQE 224

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +AKRIEAG       L  S      L    + + +    
Sbjct: 225 VELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 264


>gi|238924709|ref|YP_002938225.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
 gi|238876384|gb|ACR76091.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
          Length = 434

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 149/248 (60%), Positives = 200/248 (80%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++   + + AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G
Sbjct: 187 LQRDVDKGADAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKG 246

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA
Sbjct: 247 YKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIA 306

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K++ MPVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E  
Sbjct: 307 KEMNMPVERVREILKISQEPVSLETPIGEEEDSHLGDFIKDDNVPVPADAAAFTLLKEQL 366

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LT RE++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS
Sbjct: 367 EEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 426

Query: 674 KKLRSFLD 681
           +KL+ +L+
Sbjct: 427 RKLKDYLE 434



 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 31/147 (21%), Positives = 62/147 (42%), Gaps = 8/147 (5%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + KK+ +   ++ ++       +F     + +    +++  +  +E+  F     +  E+
Sbjct: 17  MAKKKEQKDMAQEQEQ----RLNFQQKLIEILELGKKKKNMLEYQEIADFFKDLNLDPEK 72

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            E  +  L   GI+V+        +   D   +        V           S +DPVR
Sbjct: 73  FEMVIDYLEQNGIDVL----KISNDDDVDDDIILDDEDEVEVEKIDLSVPEGVSVEDPVR 128

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAG 149
           MYL+E+G + LLS + EI +A+ +E G
Sbjct: 129 MYLKEIGKVPLLSADEEIELAQNMEDG 155


>gi|15605346|ref|NP_220132.1| RNA polymerase sigma factor [Chlamydia trachomatis D/UW-3/CX]
 gi|76789354|ref|YP_328440.1| RNA polymerase sigma factor [Chlamydia trachomatis A/HAR-13]
 gi|166154830|ref|YP_001654948.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|166155705|ref|YP_001653960.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|255311437|ref|ZP_05354007.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276]
 gi|255317738|ref|ZP_05358984.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276s]
 gi|255348997|ref|ZP_05381004.1| RNA polymerase sigma factor [Chlamydia trachomatis 70]
 gi|255503536|ref|ZP_05381926.1| RNA polymerase sigma factor [Chlamydia trachomatis 70s]
 gi|255507214|ref|ZP_05382853.1| RNA polymerase sigma factor [Chlamydia trachomatis D(s)2923]
 gi|301336109|ref|ZP_07224353.1| RNA polymerase sigma factor [Chlamydia trachomatis L2tet1]
 gi|1710679|sp|P18333|RPOD_CHLTR RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|144609|gb|AAA23165.1| RNA polymerase sigma-subunit [Chlamydia trachomatis]
 gi|3329060|gb|AAC68218.1| RNA Polymerase Sigma-66 [Chlamydia trachomatis D/UW-3/CX]
 gi|76167884|gb|AAX50892.1| RpoD [Chlamydia trachomatis A/HAR-13]
 gi|165930818|emb|CAP04316.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931693|emb|CAP07270.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|289525658|emb|CBJ15139.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296435222|gb|ADH17400.1| RNA polymerase sigma factor [Chlamydia trachomatis E/150]
 gi|296436151|gb|ADH18325.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9768]
 gi|296438011|gb|ADH20172.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11074]
 gi|296438941|gb|ADH21094.1| RNA polymerase sigma factor [Chlamydia trachomatis E/11023]
 gi|297140513|gb|ADH97271.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9301]
 gi|297748745|gb|ADI51291.1| RpoD [Chlamydia trachomatis D-EC]
 gi|297749625|gb|ADI52303.1| RpoD [Chlamydia trachomatis D-LC]
          Length = 571

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 194/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 84/165 (50%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E ++
Sbjct: 20  QRKLEELVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+     ++ + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRSEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  +     L +G     +I+  +    
Sbjct: 130 KAQVQIERIILRFRYSTKEAVSIAQYLINGKERFDKIVSEKEVED 174


>gi|158320313|ref|YP_001512820.1| RpoD family RNA polymerase sigma factor [Alkaliphilus oremlandii
           OhILAs]
 gi|158140512|gb|ABW18824.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           oremlandii OhILAs]
          Length = 372

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 162/374 (43%), Positives = 242/374 (64%), Gaps = 18/374 (4%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK   +  +   +++  +  + L++ +ID + +    +   I+ ++ ++    +   +  
Sbjct: 17  EKGKKRGMITYSEVMDALEDVDLDKEQIDEIYDHFSSMGIDIVGDKRDM---VEDLDMMD 73

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +  LE     E          +  E +        +D    +R  +K I     +S  E 
Sbjct: 74  ESVLEPEVEAE----------EIIEDDASLLKGVNIDD--PVRMYLKEIGKVPLLSAEEE 121

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   +   +     AKK +VEANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EK
Sbjct: 122 IELAKRM---DAGDEEAKKRLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 178

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R+P
Sbjct: 179 FDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGRDP 238

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            PEEIA ++ +  E VR++LKI +EP+SLETPIG+E+ SHLGDFI D++A +P ++A  +
Sbjct: 239 KPEEIAAEMDLSEEKVREILKIAQEPVSLETPIGEEEDSHLGDFIPDEDAPAPAEAAAFS 298

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+E    VL +LTPRE++VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 299 LLKEQLVEVLDTLTPREQKVLRLRFGLDDGRARTLEEVGKKFDVTRERIRQIEAKALRKL 358

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRSKKL+ +L+
Sbjct: 359 RHPSRSKKLKDYLE 372



 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 47/161 (29%), Positives = 77/161 (47%), Gaps = 2/161 (1%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDL 83
           +   ++ K +I+  ++RG +T  E+   L   ++  EQ+++     S+MGI++V D  D+
Sbjct: 6   NSKKETVKNLIEKGKKRGMITYSEVMDALEDVDLDKEQIDEIYDHFSSMGIDIVGDKRDM 65

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            ++    D   L        +           + DDPVRMYL+E+G + LLS E EI +A
Sbjct: 66  VEDLDMMDESVLEPEVEAEEIIEDDASLLKGVNIDDPVRMYLKEIGKVPLLSAEEEIELA 125

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           KR++AG       L E+ L     I  R  +  G   L  I
Sbjct: 126 KRMDAGDEEAKKRLVEANLRLVVSIAKRY-VGRGMLFLDLI 165


>gi|150015739|ref|YP_001307993.1| RNA polymerase sigma factor RpoD [Clostridium beijerinckii NCIMB
           8052]
 gi|149902204|gb|ABR33037.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 376

 Score =  220 bits (559), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 206/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +    ++  ++ E     AKK++ EANLRLV+S+AK+Y  RG+
Sbjct: 107 VRMYLKEIGKVPLLSSEQE---ITYAKEIEEGNQKAKKKLAEANLRLVVSIAKRYVGRGM 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 164 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 223

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEEI+K + +PV+ VR++ KI +EP+SLETPIG+E+ SHL
Sbjct: 224 INKLIRVQRQLLQELGRDPFPEEISKVMELPVDKVREIQKIAQEPVSLETPIGEEEDSHL 283

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 284 GDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRARTLEEVGKE 343

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 344 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 376



 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 42/156 (26%), Positives = 69/156 (44%), Gaps = 18/156 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            + K++I   ++ G +T +E+   +   ++S EQ+E    +L   G+ ++          
Sbjct: 32  AAVKELIDKGKKNGSLTYKEIMEAMDHIDLSPEQIEKIYEVLEMTGVEII---------- 81

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                ++A + +   + L         + DDPVRMYL+E+G + LLS E EI  AK IE 
Sbjct: 82  ----GEIADTETEEEIDLSV---PEGIAIDDPVRMYLKEIGKVPLLSSEQEITYAKEIEE 134

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       L E+ L     I  R  +  G   L  I
Sbjct: 135 GNQKAKKKLAEANLRLVVSIAKRY-VGRGMLFLDLI 169


>gi|320008126|gb|ADW02976.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 515

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 263 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 322

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 323 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 382

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 383 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 442

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 443 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 502

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 503 HPSRSQVLRDYLD 515



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 197 SDDDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 255

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            S      L    + + +    
Sbjct: 256 NSDKLAPKLKRELEIIAEDGRR 277


>gi|309812669|ref|ZP_07706413.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
 gi|308433364|gb|EFP57252.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
          Length = 550

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 298 KLKRELWWIASDGKNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 357

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 358 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 417

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 418 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 477

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 478 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 537

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 538 HPSRSQVLRDYLD 550



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/98 (27%), Positives = 48/98 (48%), Gaps = 2/98 (2%)

Query: 54  PPDEVSSE-QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS 112
           P + V+ + +++D V      G   VD       E  ++         +      ++  +
Sbjct: 187 PDEVVAEDVEIDDVVVTDVEAGAEEVDEAKKPAGEAEDEKGGFVLRPGDEDDAPAQQVVT 246

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 247 A-GATADPVKDYLKQIGKVALLNAEQEVELAKRIEAGL 283


>gi|296437079|gb|ADH19249.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11222]
          Length = 571

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 194/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 84/165 (50%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E ++
Sbjct: 20  QRKLEELVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+     ++ + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRSEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  +     L +G     +I+  +    
Sbjct: 130 KAQVQIERIILRFRYSTKEAVSIAQYLINGKERFDKIVSEKEVED 174


>gi|223889384|ref|ZP_03623970.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
 gi|223885070|gb|EEF56174.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
          Length = 631

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 175/643 (27%), Positives = 305/643 (47%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D   SED  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDGGIRLVNKISELDLVVSEDGNDEEEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +S                    E +I I  +++             
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDIDVKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L  G       +  ++      K       +       ++    K+ 
Sbjct: 113 ----EEDISVKDDLGSGYIKGN--VLKDSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQM 166

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D  +    +I     +  ++   + +   +    E     ++D    +     ++ +   
Sbjct: 167 DSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIA 226

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
                 +  +   L S  DN            +  + KE+L   +L+  + L Q  + + 
Sbjct: 227 SFYKIPLKPIQDRLISYVDNKHRVYDLGGDIFEKNLKKERLALKELLRDIPLYQEELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|239621277|ref|ZP_04664308.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|239515738|gb|EEQ55605.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
          Length = 488

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EF+     ++    +   AK  ++EANLRLV+
Sbjct: 205 AEQEVDLSERIEAGLYAQHLLDTESEGMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 263

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 264 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 323

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 324 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 383

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 384 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 443

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 444 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 487



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             +   E+G+    D      N       KR+  A  +T DPV+ YL+++G + LL+ E 
Sbjct: 148 APEQPKEKGAYVVSDTDDEEENIIPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQ 207

Query: 139 EIAIAKRIEAGR 150
           E+ +++RIEAG 
Sbjct: 208 EVDLSERIEAGL 219


>gi|237803044|ref|YP_002888238.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|231274278|emb|CAX11073.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
          Length = 571

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 193/265 (72%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP +    + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEVTGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 84/165 (50%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E ++
Sbjct: 20  QRKLEELVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+     ++ + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRSEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  +     L +G     +I+  +    
Sbjct: 130 KAQVQIERIILRFRYSTKEAVSIAQYLINGKERFDKIVSEKEVED 174


>gi|294815528|ref|ZP_06774171.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294328127|gb|EFG09770.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 529

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 277 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 336

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 337 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 396

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 397 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 456

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 457 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 516

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 517 HPSRSQVLRDYLD 529



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE+ +E        +         ++ +   +T DPV+ YL+++G + LL+ E E+ +AK
Sbjct: 197 DEDEAEGESKGFVLSDEDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAK 256

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           RIEAG       L  +      L    + + +    
Sbjct: 257 RIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 291


>gi|225551881|ref|ZP_03772824.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
 gi|225371676|gb|EEH01103.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
          Length = 631

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 180/643 (27%), Positives = 307/643 (47%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D   SED  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIGLVNKISELDLVVSEDGNDEEEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +                     E +I I  +++             
Sbjct: 82  IESDRNFMILDDGFQGD-------------------EEDIDIDVKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L  G      ++       P        G E      +E    ++  
Sbjct: 113 ----EEDISVKDDLGSGYIK-SNVLKDSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQMD 167

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                 E  +++   V ++  + V++     E +E    E + D   +      + R   
Sbjct: 168 SGESIIENILKNEGLVIENYCNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIAS 227

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
              +  +  +   L S  DN            +  + KE+L   +L+  + L Q  + + 
Sbjct: 228 FYKI-PLKPIQDRLISYVDNKHRVYDLGGDIFEKNLKKERLALKELLRDIPLYQEELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|182435494|ref|YP_001823213.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776131|ref|ZP_08235396.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|11132962|sp|P77951|HRDB_STRGR RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|1617256|gb|AAB16905.1| principal sigma factor [Streptomyces griseus]
 gi|178464010|dbj|BAG18530.1| RNA polymerase principal sigma factor hrdB [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656464|gb|EGE41310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 514

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 262 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 321

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 322 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 381

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 382 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 441

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 442 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 501

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 502 HPSRSQVLRDYLD 514



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 48/113 (42%), Gaps = 9/113 (7%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASS--------ASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
            ++DGD+  +E  +    +            + +       ++ +   +T DPV+ YL++
Sbjct: 165 EILDGDEAAEEVKAGKGEEEEGEGENKGFVLSDDDEDDAPAQQVAVAGATADPVKDYLKQ 224

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +G + LL+ E E+ +AKRIEAG       L  +      L    + + +    
Sbjct: 225 IGKVPLLNAEQEVELAKRIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 276


>gi|320527310|ref|ZP_08028495.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
 gi|320132334|gb|EFW24879.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
          Length = 468

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 145/274 (52%), Positives = 196/274 (71%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +   +   I   +         A+  ++ +NLRLV+S+AKKY  RG+
Sbjct: 197 VKMYLKEIGRVPLLKPEDEPEIAKRIE---EGDEEARNILISSNLRLVVSIAKKYVGRGM 253

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 254 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 313

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++  ++ R+P+ EEI++++  +  E VR++ KI  EP+SLETPIG+ED SH
Sbjct: 314 INKLTRVQRQLVQELGRDPSAEEISQRMEGISPEKVREIQKIALEPVSLETPIGEEDDSH 373

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A+SP   A    L++    VL+ LT REE+VLR+RFG+      TLEEVG+
Sbjct: 374 LGDFIEDKEALSPDQYASNQLLKDEINSVLSGLTEREEKVLRLRFGLYDGRTRTLEEVGR 433

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHPSRSK+L+ F D
Sbjct: 434 EFSVTRERIRQIEAKALRKLKHPSRSKRLKDFFD 467



 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/186 (22%), Positives = 72/186 (38%), Gaps = 29/186 (15%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D   + +K++   A++ G +  +++ A L   ++S + M++     +   I +V+ DD+
Sbjct: 78  LDELKEDYKEI---AKKSGSIAQKDIMASLEHLDMSDDDMDELWDWFNTENIQIVEDDDI 134

Query: 84  EDEEGSEDSLDLASSASNSSV-------------------------FLQKRKDSADRSTD 118
           E+   +ED           +                           L       +   +
Sbjct: 135 EELTATEDDDLDLLDDDVDNEEDENVDDKDHDLDEDDEEKPLSNLLDLTSFSSGGNVQLN 194

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPV+MYL+E+G + LL  E E  IAKRIE G       L  S L     I  +  +  G 
Sbjct: 195 DPVKMYLKEIGRVPLLKPEDEPEIAKRIEEGDEEARNILISSNLRLVVSIAKKY-VGRGM 253

Query: 179 TLLREI 184
             L  I
Sbjct: 254 LFLDLI 259


>gi|254232809|ref|ZP_04926136.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
 gi|124601868|gb|EAY60878.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
          Length = 528

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 134/286 (46%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+ L++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLRLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 362

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 363 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 422

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 423 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 482

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 483 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 528



 Score = 61.8 bits (148), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 246 EVELAKRIEAGL 257


>gi|288923254|ref|ZP_06417393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288345398|gb|EFC79788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 400

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 127/296 (42%), Positives = 196/296 (66%), Gaps = 24/296 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV------------------------RKGECEASIA 444
           +R  +K+I     ++ +E   +   +                        +  E +  IA
Sbjct: 104 VRMYLKTIGRVRLLTAAEEVDLAKRIEAGLFASEKLAATRKISPQLRQDLQAVEQDGQIA 163

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++VEANLRLV+S+AK+Y  RG+  LDLIQEGN+GL++A EKFD+  GYKFSTYA WW+
Sbjct: 164 KRKLVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 223

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+TR++ADQ  TIRIPVHM + ++KV R  R++  ++ REP+PEEI  ++ +    V 
Sbjct: 224 RQAVTRALADQGRTIRIPVHMAETVNKVTRIQRQLLQELGREPSPEEIGTQIDLTAHKVE 283

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++LKI + P++LETPIG E  S LGDFIED +A++P ++A    L++    VL +L  RE
Sbjct: 284 EILKIAQTPVALETPIGAEQDSQLGDFIEDDDAIAPFEAASSVLLQKHIESVLHTLPARE 343

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++V+++RFG+      TLE++G++F + +ERIRQIE++ + KL HP+RS++LR +L
Sbjct: 344 KKVIQLRFGLTDGQPRTLEQIGREFGIPQERIRQIESRTLAKLSHPARSQRLRDYL 399



 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 65/375 (17%), Positives = 122/375 (32%), Gaps = 61/375 (16%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +   + I   ++ G+VT E++   L   E+  E  +  + +L++ GI V+D  D      
Sbjct: 25  EKLAEFITRGKENGFVTPEDVATALLDAELPPENSDAVLRLLADDGIEVLDEID------ 78

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                                + ++   T DPVRMYL+ +G + LL+   E+ +AKRIEA
Sbjct: 79  -------DDVPDPPGRRRGPEEHASAMPTSDPVRMYLKTIGRVRLLTAAEEVDLAKRIEA 131

Query: 149 GR---------------------------AMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           G                             +    L E+ L     I  R  +  G  LL
Sbjct: 132 GLFASEKLAATRKISPQLRQDLQAVEQDGQIAKRKLVEANLRLVVSIAKRY-VGRGMLLL 190

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
             I         E   G     E   Y K    S        Q     +    +  +   
Sbjct: 191 DLI--------QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAVTRALADQGRTIRIPV 242

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
              ++  +      + L E   + +      +  L    +  + +IA+    L +     
Sbjct: 243 HMAETVNKVTRIQRQLLQELGREPSPEEIGTQIDLTAHKVEEILKIAQTPVALETPIGAE 302

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE-------- 353
            + Q  +       +   +    V    L Q  I+ ++  L    K+++           
Sbjct: 303 QDSQLGDFIEDDDAIAPFEAASSV----LLQKHIESVLHTLPAREKKVIQLRFGLTDGQP 358

Query: 354 GELLRLAQSYGIKRD 368
             L ++ + +GI ++
Sbjct: 359 RTLEQIGREFGIPQE 373


>gi|283780465|ref|YP_003371220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438918|gb|ADB17360.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 544

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 146/389 (37%), Positives = 222/389 (57%), Gaps = 37/389 (9%)

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           +    L   + + ++ ++S       + K ++LV  LSL   R+  L++++  ++ R+  
Sbjct: 188 KAFGKLIRPSTSREERQQSRRTFLRGRGKCLQLVEELSLRTRRVQPLMKEMEQLASRMER 247

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
               L  + Q  G                                            +R 
Sbjct: 248 VRARLKAIKQEDG-------------------------------------RRFERRSLRR 270

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+  + +ET  S    R     +++   E   AK+++   NLRLV+S+AKKY NRGL FL
Sbjct: 271 ELHHLMMETLESPRSLRARCVAMQRQYIEYEAAKRQLSSGNLRLVVSIAKKYRNRGLSFL 330

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN GLM+A +K+++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM D + K
Sbjct: 331 DLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIDVLSK 390

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    +++  ++ REPT EE+   + +P+E V++VL I + P+SL+ P+GD + S  G+F
Sbjct: 391 LRNVQKKLLQELGREPTTEEVTALVDLPLEEVKRVLDIGRHPVSLDRPVGDSEDSSFGEF 450

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IED  + +P+  A    LRE    +L +LT RE  ++R+R+G+     +TLEEVG+ F V
Sbjct: 451 IEDTASDNPVLCATNGILRERIDGLLKTLTWREREIIRLRYGLCDGYTYTLEEVGRIFKV 510

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQIEAKA+RKL+HP RSK+L  FL
Sbjct: 511 TRERVRQIEAKAVRKLQHPVRSKQLEGFL 539



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 38/156 (24%), Positives = 75/156 (48%), Gaps = 7/156 (4%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             K+++     +GY+T E++N +LP  +V+ E++++ +  L + GI +VD   +E  +  
Sbjct: 7   ELKELVAKGNTQGYLTYEDVNNYLPDQDVNPEKLDNLLVALEHAGIELVDQPPVEPGKPR 66

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                        S  +  + + + +   DP+R+YL +M  I LLSR+ EI++AK+IE  
Sbjct: 67  L-------FVPRESDAVPLKPEESKKLNSDPIRLYLSQMAEIPLLSRQEEISLAKKIEVT 119

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           R     ++       +A +    ++  G       I
Sbjct: 120 RKRFRRTILSCDYAMRATVQTLTQVYAGELPFDRTI 155


>gi|297156708|gb|ADI06420.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 515

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 263 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 322

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 323 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 382

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 383 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 442

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 443 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 502

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 503 HPSRSQVLRDYLD 515



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           +         ++ +A  +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 197 SDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 255

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            S      L    + + +    
Sbjct: 256 NSDKLAPKLKRELEIIAEDGRR 277


>gi|15595057|ref|NP_212846.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi B31]
 gi|216264471|ref|ZP_03436463.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221217929|ref|ZP_03589396.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225548954|ref|ZP_03769931.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|225549892|ref|ZP_03770853.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|226320452|ref|ZP_03796018.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|226321409|ref|ZP_03796936.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|3915854|sp|P52323|RPOD_BORBU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2688647|gb|AAC67061.1| RNA polymerase sigma-70 factor (rpoD) [Borrelia burgdorferi B31]
 gi|215980944|gb|EEC21751.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221192235|gb|EEE18455.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225369351|gb|EEG98803.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|225370557|gb|EEG99993.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|226233205|gb|EEH31957.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|226234094|gb|EEH32809.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|312148540|gb|ADQ31199.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           JD1]
          Length = 631

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 182/643 (28%), Positives = 308/643 (47%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D   SED  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVVSEDGNDEEEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +S                    E +I I  +++             
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDIDVKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L  G      + D      P        G E      +E    ++  
Sbjct: 113 ----EEDISVKDDLGSGYIKGNVLKD-SHSEDPIKLYLKEIGKEFLLTGNQEVELAKQMD 167

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                 E  +++   V ++  + V++     E +E    E + D   +      + R   
Sbjct: 168 SGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIAS 227

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
              +  +  +   L S  DN            +  + KE+L   +L+  + L Q  + + 
Sbjct: 228 FYKI-PLKPIQDRLISYVDNKHRVYDLGGDIFEKNLKKERLALKELLRDIPLYQEELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|332980900|ref|YP_004462341.1| RNA polymerase sigma-70 subunit RpoD [Mahella australiensis 50-1
           BON]
 gi|332698578|gb|AEE95519.1| RNA polymerase, sigma 70 subunit, RpoD [Mahella australiensis 50-1
           BON]
          Length = 356

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 158/334 (47%), Positives = 224/334 (67%), Gaps = 8/334 (2%)

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELD-----PHWVSYAKDFPEGEWKNFVACEVDSIL 407
             E++ + +   I  D   + +   E          + +  +  E + +  +   V+   
Sbjct: 26  YKEIMDMLEDVDIDPDQIDKLYDTLETLGIDVIEEPIEHEDNVVEEDLEAGLPEGVNIDD 85

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +R  +K I     +S  E   +   + +       AKK + EANLRLV+S+AK+Y  RG
Sbjct: 86  PVRMYLKEIGKIPLLSSDEEIELAKRIEQ---GDEEAKKRLAEANLRLVVSIAKRYVGRG 142

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 143 MLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 202

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+VR +R++  ++ REP PEE+A+++ + V+ VR ++KI +EP+SLETPIG+E+ SH
Sbjct: 203 TINKLVRVSRQLMQELGREPAPEEVAEEMGISVDKVRDIMKIAQEPVSLETPIGEEEDSH 262

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFI D +A +P ++A    L+E    VL +LTPREE+VLR+RFG+      TLEEVGK
Sbjct: 263 LGDFIPDDDAPAPAEAAAFTLLKEQLMDVLDTLTPREEKVLRLRFGLDDGRARTLEEVGK 322

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKL+HPSRSKKL+ +L+
Sbjct: 323 EFDVTRERIRQIEAKALRKLRHPSRSKKLKDYLE 356



 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 43/154 (27%), Positives = 71/154 (46%), Gaps = 15/154 (9%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K++I+  + +G +T +E+   L   ++  +Q++     L  +GI+V++     ++   E
Sbjct: 11  LKQLIETGKSKGVLTYKEIMDMLEDVDIDPDQIDKLYDTLETLGIDVIEEPIEHEDNVVE 70

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + L+                     + DDPVRMYL+E+G I LLS + EI +AKRIE G 
Sbjct: 71  EDLE--------------AGLPEGVNIDDPVRMYLKEIGKIPLLSSDEEIELAKRIEQGD 116

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  R  +  G   L  I
Sbjct: 117 EEAKKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 149


>gi|300784507|ref|YP_003764798.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
 gi|299794021|gb|ADJ44396.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
          Length = 467

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 197/289 (68%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L     +++   E    +++ R  +  + +   +   AK  ++EAN
Sbjct: 182 AEEEVELAKRIEAGLYAAERVRTAEEEGEKLVTQMRRDLKWIVR---DGERAKNHLLEAN 238

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++
Sbjct: 239 LRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 298

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +E
Sbjct: 299 ADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDISPEKVLEIQQYARE 358

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RF
Sbjct: 359 PISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRF 418

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 419 GLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 467



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 24/65 (36%), Positives = 35/65 (53%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 137 DNPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGL 196

Query: 151 AMMMA 155
                
Sbjct: 197 YAAER 201


>gi|195941530|ref|ZP_03086912.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 80a]
          Length = 631

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 176/643 (27%), Positives = 301/643 (46%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D   SED  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVVSEDGNDEEEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM--MMASLC 158
             S       D   +S                    E +I I  +++        +    
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDIDVKLDDCDEEDISVKDDL 122

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
            S      ++      +     L+EI       G +          G S  +    ++  
Sbjct: 123 GSGYIKSNVLKDSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQMDSGESIIENILKNEGL 182

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
             ++       I S  +  +  + + D   E++ +               L  ++D+L  
Sbjct: 183 VIENYYNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIASFYKIPLKPIQDRLIS 242

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            V                + D   +           K  +  L +L+  + L Q  + + 
Sbjct: 243 YV-----------DNKHRVYDLGGDIF-----EKNLKKERLALKELLRDIPLYQEELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQKIILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|237804965|ref|YP_002889119.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273265|emb|CAX10180.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
          Length = 571

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 194/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDGGESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 84/165 (50%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               ++++ LA+ +G++T EE+N  LPP   + EQ++  +  L+ M + V++  D+E ++
Sbjct: 20  QRKLEELVTLAKDQGFITYEEINEILPPSFDTPEQIDQVLIFLAGMDVQVLNQADVERQK 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +            +  L+     ++ + DDPVRMYL+EMG++ LL+RE E+ I+KRIE
Sbjct: 80  ERKK----------EAKELEGLAKRSEGTPDDPVRMYLKEMGTVPLLTREEEVEISKRIE 129

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
             +  +   +     + +  +     L +G     +I+  +    
Sbjct: 130 KAQVQIERIILRFRYSTKEAMSIAQYLINGKERFDKIVSEKEVED 174


>gi|254382161|ref|ZP_04997522.1| sigma factor [Streptomyces sp. Mg1]
 gi|194341067|gb|EDX22033.1| sigma factor [Streptomyces sp. Mg1]
          Length = 416

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 132/250 (52%), Positives = 177/250 (70%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 167 RELEILVEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYT 226

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQS TIRIPVHM + I+K+ R  R+M   + REPTPEE
Sbjct: 227 KGFKFSTYATWWIRQAITRAMADQSRTIRIPVHMVEIINKLARVQRQMLQDLGREPTPEE 286

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + K+L M  E V +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E
Sbjct: 287 LGKELDMTPEKVIEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTFLQE 346

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L +L+ RE  V+ MR+G+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 347 QLQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPS 406

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 407 RSQVLRDYLD 416



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           + +       +      +T DPV+ YL+ +G + LL+ E E+ +AKRIEAG 
Sbjct: 98  SDDDEDDAPAQTVMVAGATADPVKDYLKLIGKVPLLNAEQEVELAKRIEAGL 149


>gi|294629207|ref|ZP_06707767.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292832540|gb|EFF90889.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 386

 Score =  219 bits (558), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 127/296 (42%), Positives = 189/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 91  RQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLSSTPDLDSRLAGDLDRLVVSGRMAK 150

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 151 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 210

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP E+A +L +  + V +
Sbjct: 211 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPAEVAAQLDLTPDRVGE 270

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL++L  RE 
Sbjct: 271 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLSTLGERER 330

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 331 KVVQLRYGLMDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 386



 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/110 (24%), Positives = 46/110 (41%), Gaps = 3/110 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASS-ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           D  +  D+  + ++LD      +         +  +   + D  R YLRE+G I LL+  
Sbjct: 47  DAPEAPDDPDAPEALDAPDPLDAVEPPRAAPARTESGGPSADLFRQYLREIGRIPLLTAA 106

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE-LNDGTTLLREIID 186
            E+ +A+R+EAG       L  +P     L    D  +  G    R +I+
Sbjct: 107 EEVELARRVEAGLF-AEEKLSSTPDLDSRLAGDLDRLVVSGRMAKRRLIE 155


>gi|312149387|gb|ADQ29458.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           N40]
          Length = 631

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 174/643 (27%), Positives = 312/643 (48%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+       + SE  L ++ + +
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVN-------KISELDLVVSENGN 74

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           +    ++   D      DD  +            S E +I I  +++             
Sbjct: 75  DEEEEVEIESDRNFMILDDGFQ------------SDEEDIDIDVKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L  G       +  ++      K       +       ++    K+ 
Sbjct: 113 ----EEDISVKDDLGSGYIKGN--VLKDSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQM 166

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D  +    +I     +  ++   + +   +    E     ++D    +     ++ +   
Sbjct: 167 DSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIA 226

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
                 +  +   L S  DN            +  + KE+L   +L+  + L Q  + + 
Sbjct: 227 SFYKIPLKPIQDRLISYVDNKHRVYDLGGDIFEKNLKKERLALKELLRDIPLYQEELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRMILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|260578861|ref|ZP_05846767.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
 gi|258603008|gb|EEW16279.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
          Length = 552

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/290 (46%), Positives = 197/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L     ++ I      +S    R +    R+ + +   AK  ++EA
Sbjct: 267 AEQEVSLAKRIEAGLYAAYRLQEIKESGEKLSPMHRRDL----REIDRDGRRAKNHLLEA 322

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 323 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKGYKFSTYATWWIRQAITRA 382

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ + V+ V ++ +  +
Sbjct: 383 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAREMDITVDKVLEIQQYAR 442

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+++R
Sbjct: 443 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLR 502

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 503 FGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 552



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG      
Sbjct: 229 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYR 286


>gi|295695448|ref|YP_003588686.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
 gi|295411050|gb|ADG05542.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
          Length = 379

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   + +       AK  +++ANLRLV+S+AK+Y  RG+
Sbjct: 110 VRMYLKEIGRVPLLSAEEEIELAKRIEQ---GDEEAKAALIKANLRLVVSIAKRYVGRGM 166

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 167 LFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 226

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ R+PTPEEIA+++ M  + VR+++KI +EP+SLETPIG+ED SHL
Sbjct: 227 INKLIRVSRQLLQELGRDPTPEEIAEEMDMSPDKVREIMKIAQEPVSLETPIGEEDDSHL 286

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +A++P D+A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 287 GDFIPDDDALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKV 346

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 347 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 379



 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 51/172 (29%), Positives = 83/172 (48%), Gaps = 2/172 (1%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
              +D+ +    +  +   +++++  R+RG +T  E+   L P E   +QM++    LS 
Sbjct: 3   EPGDDNKERQPEESLEQVKQQLVETGRKRGALTYHEIMDRLAPFEQDPDQMDEFFDYLSE 62

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            GI V++ ++ ED    ED+   A    +    L+          +DPVRMYL+E+G + 
Sbjct: 63  QGIEVLNENE-EDLVLEEDNEHPAEEEDHEEYDLEDLSVPPGVKINDPVRMYLKEIGRVP 121

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LLS E EI +AKRIE G     A+L ++ L     I  R  +  G   L  I
Sbjct: 122 LLSAEEEIELAKRIEQGDEEAKAALIKANLRLVVSIAKRY-VGRGMLFLDLI 172


>gi|283783165|ref|YP_003373919.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
 gi|283441732|gb|ADB14198.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
          Length = 489

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 140/284 (49%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T I   EF+     ++    +   AK  ++EANLRLV+
Sbjct: 206 AEQEVDLSERIEAGLYAQHLLDTQIDQMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 264

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 265 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 324

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 325 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 384

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L PRE  V++MR+G+   
Sbjct: 385 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLAPREAGVIKMRYGLEDG 444

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 445 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 488



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 178 KRRVIATGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 220


>gi|238916620|ref|YP_002930137.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
 gi|238871980|gb|ACR71690.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
          Length = 434

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 153/273 (56%), Positives = 203/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E       +         AKK + EANLRLV+S+AK+Y  RG+
Sbjct: 165 VRMYLKEIGKVPLLSADEEIEYAKRME---EGDEEAKKRLAEANLRLVVSIAKRYVGRGM 221

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EK+D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 222 QFLDLIQEGNLGLIKAVEKYDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 281

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R++  ++ REP+PEEIA+ + +PVE VR++ KI++EP+SLETPIG+E+ SHL
Sbjct: 282 INKLVRVQRQLLQELGREPSPEEIAENMDIPVERVREIQKISQEPVSLETPIGEEEDSHL 341

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI+D N   P ++A    L+E    VL +LT RE++VLR+RFG+      TLEEVGK+
Sbjct: 342 GDFIQDDNVPVPAEAAASTLLKEQLVEVLGTLTEREQKVLRLRFGMDDGRARTLEEVGKE 401

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRS+KLR +LD
Sbjct: 402 FNVTRERIRQIEAKALRKLRHPSRSRKLRDYLD 434



 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 41/181 (22%), Positives = 77/181 (42%), Gaps = 8/181 (4%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSD-DSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQM 63
           K     ++E+ D+DD+   +    +  + ++ +A+++   +  +E+  +    +  +++M
Sbjct: 53  KEEVKEETENSDADDAEAQEAKFWEKIEGILAIAKKKKNVLDYQEIMTYFQDTDFEADRM 112

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           E    +L    ++V       ++   ED   +        +             DDPVRM
Sbjct: 113 EKVFEILELKKVDV-----RMNDVPDEDEDIILDDEDEIDIEKIDLSVPDGIGLDDPVRM 167

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G + LLS + EI  AKR+E G       L E+ L     I  R  +  G   L  
Sbjct: 168 YLKEIGKVPLLSADEEIEYAKRMEEGDEEAKKRLAEANLRLVVSIAKRY-VGRGMQFLDL 226

Query: 184 I 184
           I
Sbjct: 227 I 227


>gi|270283843|ref|ZP_05965086.2| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
 gi|270277549|gb|EFA23403.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
          Length = 485

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 131/250 (52%), Positives = 187/250 (74%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW 
Sbjct: 235 RELKWAANDGKKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWK 294

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ R  R+M   + REPTP+E
Sbjct: 295 KGFKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDE 354

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L MPVE V++V K  +EPISL TP+G++     GD IED +A++P D+   + L+E
Sbjct: 355 LARELDMPVEKVQEVQKYGREPISLHTPLGEDGDPEFGDLIEDTDAIAPSDAVAFSLLQE 414

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL +L+PRE  V++MR+G+      TL+++G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 415 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 474

Query: 672 RSKKLRSFLD 681
           RS+ LR FLD
Sbjct: 475 RSQTLRDFLD 484



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/43 (41%), Positives = 30/43 (69%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 174 KRRVVTTGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 216


>gi|224532358|ref|ZP_03672988.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
 gi|224512665|gb|EEF83036.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
          Length = 631

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 175/643 (27%), Positives = 306/643 (47%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D   SED  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVVSEDGNDEEEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +S                    E +I I  +++             
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDIDVKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L+ G       +  ++      K       +       ++    K+ 
Sbjct: 113 ----EEDISVKDDLSSGYIKGN--VLKDSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQM 166

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D  +    +I     +  ++   + +   +    E     ++D    +     ++ +   
Sbjct: 167 DSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREKDKDKESSPDYYNKKKRIA 226

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
                 +  +   L S  DN            +  + KE+L   +L+  + L Q  + + 
Sbjct: 227 SFYKIPLKPIQDRLISYVDNKHRVYDLGGDIFEKNLKKERLALKELLRDIPLYQEELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKKIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +       +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|304437692|ref|ZP_07397644.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369325|gb|EFM22998.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 381

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 146/274 (53%), Positives = 198/274 (72%), Gaps = 3/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V + R+ E     A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVPLLTAEEE---VDLARRMEAGDETARHRLEEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 168 MFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K +R +R++  ++ R+PTPEEIA ++ + V  VR+++KI++EP+SLETPIG+E+ +HL
Sbjct: 228 INKYIRVSRQLLQELGRDPTPEEIAHRMGLSVARVREIMKISQEPVSLETPIGEEEDTHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DFIED+ A  P D+A    L+E  + VL +L PRE  VLR+RFG+      TLEEVG+ 
Sbjct: 288 SDFIEDEAAPDPADAASMLLLKEQISEVLTTLAPREAEVLRLRFGLVDGRSRTLEEVGQN 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKL+HP R +KL+   D 
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPVRLRKLQGNFDA 381



 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 44/153 (28%), Positives = 69/153 (45%), Gaps = 3/153 (1%)

Query: 34  MIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++K  R  G  +T  EL   L  D V+ + M+       + GI ++D  D+  E+ + D 
Sbjct: 22  LLKKGRANGGTLTCSELMDALAQDSVTPDAMDALYQRCMDEGIEIIDDADVGAEDDAADF 81

Query: 93  LDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            D       +   +          + DDPVRMYL+E+G + LL+ E E+ +A+R+EAG  
Sbjct: 82  ADDLEDKDETDADVDIDLSVPEGVALDDPVRMYLKEIGRVPLLTAEEEVDLARRMEAGDE 141

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                L E+ L     I  R  +  G   L  I
Sbjct: 142 TARHRLEEANLRLVVSIAKRY-VGRGMMFLDLI 173


>gi|148654464|ref|YP_001274669.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566574|gb|ABQ88719.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 541

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 140/242 (57%), Positives = 186/242 (76%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   A++++ +ANLRLV+SVAKKY  RGLQ LDLIQEGN+GL++A EKFD+  G+KFSTY
Sbjct: 300 QGKTAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVEKFDYRKGFKFSTY 359

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR+IADQ+ TIRIPVHM + I++++R +RRM  ++ REPT EE+++ L +P
Sbjct: 360 ATWWIRQAITRAIADQARTIRIPVHMVETINRLMRESRRMLQELGREPTDEELSRALGIP 419

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ VR + K + EP+SLETP+G E+ S LGDFIED   ++P D+A    LRE   +VL  
Sbjct: 420 VDKVRSIRKTSLEPVSLETPVGQEEDSQLGDFIEDSKVLAPSDAASHQMLREQVEQVLNQ 479

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT RE RVL++RFG+      TLEEVGK+F VTRERIRQIE KA+RKL+HP   KKLR +
Sbjct: 480 LTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQIEVKALRKLRHPRLGKKLRDY 539

Query: 680 LD 681
           L+
Sbjct: 540 LE 541



 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/122 (27%), Positives = 54/122 (44%), Gaps = 9/122 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            S   ++ + +QRG+VT  E+   L   +  S+++ +    L   GI   D       E 
Sbjct: 37  TSLSDLLAIGKQRGFVTEGEIAQLLANSDADSDRLAEIQQALQAAGIATRD-------EM 89

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                ++         F     +    S +D VRMYLRE+G + LL+   EI +A++IE 
Sbjct: 90  ITGGAEIDIPFEEEGDFDD--LNVEGISVNDTVRMYLREIGRVPLLNARQEILLAQKIEI 147

Query: 149 GR 150
           G 
Sbjct: 148 GE 149


>gi|144616|gb|AAA23168.1| sigma-A protein (sigA) [Chlamydia muridarum]
          Length = 571

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 145/265 (54%), Positives = 195/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AK+EMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKQEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDSGESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++   +VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEATGYSMLKDKMKKVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 44/174 (25%), Positives = 87/174 (50%), Gaps = 10/174 (5%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            D+   +      ++++ LA+ +G++T EE+N  LPP   S EQ++  +  L+ M + V+
Sbjct: 11  ADAAQEEEIQRKLEELVTLAKDQGFITYEEINEILPPSFDSPEQIDQVLIFLAGMDVQVL 70

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  D+E ++  +            +  L+     ++ + DDPVRMYL+EMG++ LL+RE 
Sbjct: 71  NQADVERQKERKK----------EAKELEGLAKRSEGTPDDPVRMYLKEMGTVPLLTREE 120

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           E+ I+KRIE  +  +   +     + +  +     L +G     +I+  +    
Sbjct: 121 EVEISKRIEKAQVQIERIILRFRYSTKEAVSIAQYLINGKERFDKIVSXKEVED 174


>gi|1582791|prf||2119302A sigma factor
          Length = 445

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 193 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 252

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 253 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 312

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 313 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 372

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 373 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 432

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 433 HPSRSQVLRDYLD 445



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 48/113 (42%), Gaps = 9/113 (7%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASS--------ASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
            ++DGD+  +E  +    +            + +       ++ +   +T DPV+ YL++
Sbjct: 96  EILDGDEAAEEVKAGKGEEEEGEGENKGFVLSDDDEDDAPAQQVAVAGATADPVKDYLKQ 155

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +G + LL+ E E+ +AKRIEAG       L  +      L    + + +    
Sbjct: 156 IGKVPLLNAEQEVELAKRIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 207


>gi|302525743|ref|ZP_07278085.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434638|gb|EFL06454.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 476

 Score =  219 bits (557), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 197/289 (68%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L     +++   E    +++ R  +  + +   +   AK  ++EAN
Sbjct: 191 AEEEVELAKRIEAGLYAAERVRTAEEEGEKLVTQMRRDLKWIVR---DGERAKNHLLEAN 247

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++
Sbjct: 248 LRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 307

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +E
Sbjct: 308 ADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDISPEKVLEIQQYARE 367

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RF
Sbjct: 368 PISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRF 427

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 428 GLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 476



 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 25/67 (37%), Positives = 36/67 (53%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S D+ D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEA
Sbjct: 144 SSDNPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEA 203

Query: 149 GRAMMMA 155
           G      
Sbjct: 204 GLYAAER 210


>gi|156740279|ref|YP_001430408.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231607|gb|ABU56390.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 541

 Score =  219 bits (557), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 166/495 (33%), Positives = 262/495 (52%), Gaps = 42/495 (8%)

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
           +  + + D + E +  ++SA   ++D+     +  +    +E +LD+   +       + 
Sbjct: 62  AGSDADSDRLAEIQQALQSAGIATRDEMIAGGAEIDVHFEEEGDLDDLSVEGISINDTVR 121

Query: 274 DQLRP------------KVMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKVLKEK 320
             LR              ++    EI E     R+ L  +    Q D   +   + L++ 
Sbjct: 122 MYLREIGRVPLLTARQETLLAQKIEIGEYLESYRTQLAADWRPEQIDSVGAQMYQRLQKT 181

Query: 321 LVKLVGSLSLNQSRIDL---------LVEQLYDISKRIMHNEGELL-----RLAQSYGIK 366
              +  ++ L  + ++           + ++  I +R+   + ++       L + + + 
Sbjct: 182 WPVVEDAIRLLYAIVEQPLPDPLTPGCLREVSAIQERMTFEQRQMFDKRRNELIKQHRMT 241

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            + F +                        + +   V   L +     S+     +    
Sbjct: 242 AEQFDQTFA---------------QATIIFSLLPAAVQQRLALSANWPSVEEVQHMCADV 286

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              +         +   A++++ +ANLRLV+SVAKKY  RGLQ LDLIQEGN+GL++A E
Sbjct: 287 RDQLWRDWNLAIEQGKTAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVE 346

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I++++R +RRM  ++ RE
Sbjct: 347 KFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLMRESRRMLQELGRE 406

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE+++ L +PV+ VR + K + EP+SLETP+G E+ S LGDFIED   ++P D+A  
Sbjct: 407 PTDEELSRALGIPVDKVRSIRKTSLEPVSLETPVGQEEDSQLGDFIEDSKVLAPSDAASH 466

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LRE   +VL  LT RE RVL++RFG+      TLEEVGK+F VTRERIRQIE KA+RK
Sbjct: 467 QMLREQVEQVLNQLTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQIEVKALRK 526

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP   KKLR +L+
Sbjct: 527 LRHPRLGKKLRDYLE 541



 Score = 79.9 bits (195), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 9/122 (7%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            S   ++ + +QRG+VT  E+   L   +  S+++ +    L + GI   D       E 
Sbjct: 37  TSLSDLLAIGKQRGFVTEGEIAQLLAGSDADSDRLAEIQQALQSAGIATRDEMIAGGAEI 96

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                            L         S +D VRMYLRE+G + LL+   E  +A++IE 
Sbjct: 97  --------DVHFEEEGDLDDL-SVEGISINDTVRMYLREIGRVPLLTARQETLLAQKIEI 147

Query: 149 GR 150
           G 
Sbjct: 148 GE 149


>gi|229817449|ref|ZP_04447731.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
 gi|229785238|gb|EEP21352.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
          Length = 482

 Score =  219 bits (557), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 137/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 199 AEQEVDLSERIEAGLYAQHLLDTEGDTMDFKR-KRELKWAANDGKKAKDHLLEANLRLVV 257

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 258 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 317

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 318 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 377

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L++   +VL +L+PRE  V++MR+G+   
Sbjct: 378 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQDQFKQVLETLSPRESGVIKMRYGLEDG 437

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 438 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 481



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 18/43 (41%), Positives = 30/43 (69%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 171 KRRVVTAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 213


>gi|257791063|ref|YP_003181669.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|317488219|ref|ZP_07946788.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325830757|ref|ZP_08164141.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
 gi|257474960|gb|ACV55280.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|316912661|gb|EFV34201.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325487164|gb|EGC89607.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
          Length = 409

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 142/277 (51%), Positives = 199/277 (71%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I      ++ +       I   R     + + E     AK++++EANLRLV+S+AK+Y 
Sbjct: 132 KIEAGVAAMEELEKAEDEGIELERREKRRLGRIEQVGIDAKQQLIEANLRLVVSIAKRYV 191

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVH
Sbjct: 192 GRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 251

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+VR  R++  ++ REP+PEEI K++ +P E VR++ KI++EP+SLETPIG+E+
Sbjct: 252 MVETINKLVRIQRQLLQELGREPSPEEIGKEMGLPAERVREIQKISQEPVSLETPIGEEE 311

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDFIED  AV P D+A  + L+E  ++VL  L  RE +V+ +RFG+      TLEE
Sbjct: 312 DSQLGDFIEDDAAVVPPDAASFSMLQEQLSKVLDGLAERERKVISLRFGLEDGHPRTLEE 371

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 372 VGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 408



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           SV  +    S    T DPVRMYL+E+G + LL+   EI +A +IEAG A M         
Sbjct: 90  SVRKRNADASVTMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVAAMEELEKAEDE 149

Query: 163 TFQALIIWRDELNDGTT 179
             +  +  R++   G  
Sbjct: 150 GIE--LERREKRRLGRI 164


>gi|224531865|ref|ZP_03672497.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
 gi|224511330|gb|EEF81736.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
          Length = 631

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 177/643 (27%), Positives = 302/643 (46%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D  G+E+  D      
Sbjct: 22  RKSLSFSELSNLLPDDILEPEVLDCICSILEDRGIRLVNKISELDLVGTEEGNDEDEEVE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM--MMASLC 158
             S       D   +S                    E +I I  +++        +    
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDIDGKLDDCDEEDISVKDDL 122

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
            S      ++      +     L+EI       G +          G    +    ++  
Sbjct: 123 GSGYIKSNVLKDSHSEDPIKLYLKEIGKEFLLTGNQEVELAKQMDSGEGIIENILKNEGL 182

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
             ++       I S  +  +  + + D   EN  +               L  ++D+L  
Sbjct: 183 VIENYYNLVNTIYSRMEREEFFKREKDRDKENNPDYYNKKKRIASFYKIPLKPIQDRLIS 242

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            V    D    VY                +      K  +  L +L+  + L Q  + + 
Sbjct: 243 YV----DNKHRVYE------------LGGDILEKNLKRERSALKELLRDIPLYQDELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKRIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +     + +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|154249128|ref|YP_001409953.1| RpoD family RNA polymerase sigma factor [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153064|gb|ABS60296.1| RNA polymerase, sigma 70 subunit, RpoD family [Fervidobacterium
           nodosum Rt17-B1]
          Length = 372

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 130/269 (48%), Positives = 188/269 (69%), Gaps = 3/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     ++ SE + +    +        AK+E++ +NLRLV+S+AK+Y  +GL
Sbjct: 98  IKMYLRDIGKIRLLTPSEEKRLAQRAQ---MGDQRAKEELIISNLRLVVSMAKRYLGKGL 154

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEG++GL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + 
Sbjct: 155 SFLDLIQEGSLGLIKAVEKFDWSKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVET 214

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R    +   EP+ E IA+++  PV+ + ++L+   E +SLETP+ +ED S +
Sbjct: 215 INKIQKIKREYVQEHGEEPSIEYIAEQVGKPVDKIEEILQAAPETLSLETPVNEEDDSSM 274

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D++  SP   AI+  +RE   ++L +L  RE++VL+MR+G+      TLEEVG+ 
Sbjct: 275 GDFIADESIGSPKKEAIRTLMREEIDKLLETLNDREKKVLKMRYGLYNGKPMTLEEVGQF 334

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           F VTRERIRQIE KA+RKL+HPSRS+ LR
Sbjct: 335 FGVTRERIRQIEVKALRKLRHPSRSRYLR 363



 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/163 (22%), Positives = 67/163 (41%), Gaps = 15/163 (9%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPP---DEVSSEQMEDTVAMLSNMGINVVDGD 81
           +      +K+++L +++GY+T ++++   PP   D + S  ++     L    I + D  
Sbjct: 10  EELQKKLEKLVELGKRKGYITYDDIDRTFPPGDADSLDSNFLDMVYETLEKNKIEIRDTT 69

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           DL + E               +   +  +        D ++MYLR++G I LL+   E  
Sbjct: 70  DLMNIE-----------EEVKAYLSESPEIFNSTEPKDLIKMYLRDIGKIRLLTPSEEKR 118

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +A+R + G       L  S L     +  R  L  G + L  I
Sbjct: 119 LAQRAQMGDQRAKEELIISNLRLVVSMAKRY-LGKGLSFLDLI 160


>gi|224542125|ref|ZP_03682664.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524962|gb|EEF94067.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
          Length = 418

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 159/310 (51%), Positives = 211/310 (68%), Gaps = 7/310 (2%)

Query: 376 GRELDPHWVSYAKDFPEGEW---KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           G +LD  +    K + + +     N +   V     ++  +K I     ++  +   +  
Sbjct: 111 GNDLDMDFGDTNKMYNQSDDDDDMNQLGSNVKINDPVKMYLKEIGRVDLLTHEQEIELAK 170

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +         AKKE+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  
Sbjct: 171 RI---LEGDEQAKKELAAANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTK 227

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R++  ++ REPT EEI
Sbjct: 228 GFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQELGREPTAEEI 287

Query: 553 AKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A+K+  M    VR++ KI+ EP+SLETPIG+ED SHLGDFIED+ A+SP D A    L++
Sbjct: 288 AEKMDGMTPAKVREIQKISLEPVSLETPIGEEDDSHLGDFIEDEGAMSPDDYASNELLKD 347

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL  LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHPS
Sbjct: 348 ELNEVLLELTDREEKVLRLRFGLDDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPS 407

Query: 672 RSKKLRSFLD 681
           RSK+L+ FLD
Sbjct: 408 RSKRLKDFLD 417



 Score = 78.0 bits (190), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 45/212 (21%), Positives = 80/212 (37%), Gaps = 44/212 (20%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           ++ + +   +  +  +   K +I  A+ +G  +T ++L+AF    ++  E  E+ +  ++
Sbjct: 2   AKKDKAVQGITLEELE---KMLISAAKAKGNRLTQDDLDAFQSRYDLDDEAYENLIDAIN 58

Query: 72  NMGINVVDG------DDLEDEEGSEDSLDLASSAS------------------------- 100
              I + DG      DD +   G  D LD                               
Sbjct: 59  ENHIEIEDGLDALEIDDDDFMAGGADDLDDLEGLEVDTDDDTGDDDIANLDFGNDLDMDF 118

Query: 101 --------NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                    S       +  ++   +DPV+MYL+E+G ++LL+ E EI +AKRI  G   
Sbjct: 119 GDTNKMYNQSDDDDDMNQLGSNVKINDPVKMYLKEIGRVDLLTHEQEIELAKRILEGDEQ 178

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L  + L     I  R  +  G   L  I
Sbjct: 179 AKKELAAANLRLVVSIAKRY-VGRGMLFLDLI 209


>gi|294631847|ref|ZP_06710407.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292835180|gb|EFF93529.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 515

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 263 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 322

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 323 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 382

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 383 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 442

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 443 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 502

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 503 HPSRSQVLRDYLD 515



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/111 (24%), Positives = 52/111 (46%), Gaps = 5/111 (4%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            + +++ + LED + +E+     S+    +         ++ +A  +T DPV+ YL+++G
Sbjct: 168 DVELLEDEVLEDPKAAEEPEGTESAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIG 227

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 228 KVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 277


>gi|33863540|ref|NP_895100.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9313]
 gi|33640989|emb|CAE21447.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9313]
          Length = 461

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 214 KFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 273

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 274 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 333

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 334 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDTENPEQDVAKNLLRED 392

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 393 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIRQIEAKALRKLRHPNR 452

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 453 NGVLKEYI 460



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 31/64 (48%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E E     +   + + + +      +       T+D +R+YL+E+G I LL  + EI +
Sbjct: 115 AETESSQAAAKATSEADAKARALANIKIGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIEL 174

Query: 143 AKRI 146
           A++I
Sbjct: 175 ARKI 178


>gi|212715646|ref|ZP_03323774.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
 gi|212661013|gb|EEB21588.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
          Length = 448

 Score =  218 bits (556), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 165 AEQEVDLSERIEAGLYAQHLLDTESDQMDFKR-KRELKWAANDGRRAKDHLLEANLRLVV 223

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 224 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 283

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 284 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 343

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 344 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFRQVLETLSPREAGVIKMRYGLEDG 403

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 404 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 447



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 34/57 (59%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D     + +     KR+  A  +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 123 DDDDDENLTPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 179


>gi|309775524|ref|ZP_07670524.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916618|gb|EFP62358.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 397

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 151/274 (55%), Positives = 197/274 (71%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +   E   I   ++        AKK+++ ANLRLV+S+AKKY  RG+
Sbjct: 125 VKMYLKEIGRVELLDPKEEPEIAQRIQ---DGDEEAKKKLISANLRLVVSIAKKYVGRGM 181

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 182 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 241

Query: 529 IHKVVRTARRMSNKIKREPTPEEIA-KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++   + R+P+ EEIA K   +  E VR++ KI  EP+SLETPIG+ED SH
Sbjct: 242 INKLTRIQRQLVQDLGRDPSAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEEDDSH 301

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A+SP + A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 302 LGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGK 361

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHP+RSK+L+ F+D
Sbjct: 362 EFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 395



 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 35/172 (20%), Positives = 67/172 (38%), Gaps = 16/172 (9%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           DD  ++ ++  +Q   +  +++   +    ++    +D     ++  I V + DD  D  
Sbjct: 17  DDIKQEFLEEYKQNDALYQKDVMDAVEHLAMTDTDFDDLFQWFADNDIEVKNEDDDVDLL 76

Query: 88  GSEDSLDLASS---------------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
             +                       A++     Q   +S+    +DPV+MYL+E+G +E
Sbjct: 77  DDDALATADDDDIDFLDDDTDEEDTLAADIENLEQSFANSSHTKINDPVKMYLKEIGRVE 136

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LL  + E  IA+RI+ G       L  + L     I  +  +  G   L  I
Sbjct: 137 LLDPKEEPEIAQRIQDGDEEAKKKLISANLRLVVSIAKKY-VGRGMLFLDLI 187


>gi|29828986|ref|NP_823620.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29606091|dbj|BAC70155.1| RNA polymerase major sigma factor, sigma-70 family [Streptomyces
           avermitilis MA-4680]
          Length = 512

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 260 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 319

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 320 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 379

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 380 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 439

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 440 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 499

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 500 HPSRSQVLRDYLD 512



 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 25/114 (21%), Positives = 45/114 (39%), Gaps = 1/114 (0%)

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           V +L +  +          EE           +         ++ +A  +T DPV+ YL+
Sbjct: 162 VELLDDEAVEETAAPGKAGEEPEGTENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLK 221

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++G + LL+ E E+ +AKRIEAG       L  +      L    + + +    
Sbjct: 222 QIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 274


>gi|1072021|gb|AAA81642.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 362

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 363 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 422

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 423 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 482

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL HPSRS+ LR +LD
Sbjct: 483 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLHHPSRSQVLRDYLD 528



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 246 EVELAKRIEAGL 257


>gi|213691851|ref|YP_002322437.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|213523312|gb|ACJ52059.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|320457946|dbj|BAJ68567.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 464

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EF+     ++    +   AK  ++EANLRLV+
Sbjct: 181 AEQEVDLSERIEAGLYAQHLLDTESEGMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 239

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 240 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 299

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 300 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 359

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 360 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 419

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 420 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 463



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             +   E+G+    D      N       KR+  A  +T DPV+ YL+++G + LL+ E 
Sbjct: 124 APEQPKEKGAYVVSDTDDEEENIIPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQ 183

Query: 139 EIAIAKRIEAGR 150
           E+ +++RIEAG 
Sbjct: 184 EVDLSERIEAGL 195


>gi|256545301|ref|ZP_05472665.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
 gi|256398982|gb|EEU12595.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
          Length = 614

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 146/280 (52%), Positives = 207/280 (73%), Gaps = 4/280 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +++   K +N  K I  + G    + + +   +     +A+ AK+++ E NLRLV+S+A
Sbjct: 339 KDLERFTKTKNLCKKIFEDQGFDADDVKRLNRAI----FDANRAKQKLAETNLRLVVSIA 394

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW++QAITR+IADQ+ TIR
Sbjct: 395 KKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIR 454

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+VR  R++   + R+P+ EEIA+++ + VE V+++ KI +EP+SLETPI
Sbjct: 455 IPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKVQEIRKIAQEPVSLETPI 514

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+E+ SHLGDFIED  A++P D+A  + LR+    VL+ L  RE+RVL++RFG+   T  
Sbjct: 515 GEEEDSHLGDFIEDDTAINPDDAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPR 574

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 575 TLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 614


>gi|169351085|ref|ZP_02868023.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
 gi|169292147|gb|EDS74280.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
          Length = 415

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 160/317 (50%), Positives = 207/317 (65%), Gaps = 4/317 (1%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
               F         D   +    D      KN +   V     ++  +K I     +S  
Sbjct: 101 PDLDFDGDFDMMTSDTLHMYQVADADAEMDKNQLGSNVKINDPVKMYLKEIGRVELLSHD 160

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +    + + +K       AKKE+  ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 161 DE---IKLAKKILEGDEAAKKELAAANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAV 217

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +  ++ R
Sbjct: 218 EKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRLLIQELGR 277

Query: 546 EPTPEEIAKK-LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           EPT EEIA++   M  E VR++ KI+ EP+SLETPIG+ED SHLGDFIED+  +SP D A
Sbjct: 278 EPTAEEIAERIDGMTPEKVREIQKISLEPVSLETPIGEEDDSHLGDFIEDEGVMSPDDYA 337

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L++    VL  LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+
Sbjct: 338 ANELLKDELNEVLLELTDREEKVLRLRFGLDDGRTRTLEEVGKEFSVTRERIRQIEAKAL 397

Query: 665 RKLKHPSRSKKLRSFLD 681
           RKLKHPSRSK+L+ FLD
Sbjct: 398 RKLKHPSRSKRLKDFLD 414



 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 46/212 (21%), Positives = 81/212 (38%), Gaps = 47/212 (22%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG--DDLEDEEGS---------- 89
           G +T ++++ +L   ++S +  ED +  + N  I + D   DD++ E+            
Sbjct: 27  GILTQDQIDTYLSTYDLSDDLAEDLLEFIGNNDIIISDDGLDDIDVEDDMLLTGAADDLD 86

Query: 90  -------------------EDSLDLASSA-------SNSSVFLQKRKDSADRSTDDPVRM 123
                              +   D+ +S        +++   + K +  ++   +DPV+M
Sbjct: 87  IDLDLGDDLLGDDTPDLDFDGDFDMMTSDTLHMYQVADADAEMDKNQLGSNVKINDPVKM 146

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G +ELLS + EI +AK+I  G       L  + L     I  R  +  G   L  
Sbjct: 147 YLKEIGRVELLSHDDEIKLAKKILEGDEAAKKELAAANLRLVVSIAKRY-VGRGMLFLDL 205

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           I         E   G     E   Y K    S
Sbjct: 206 I--------QEGNMGLIKAVEKFDYTKGFKFS 229


>gi|223985702|ref|ZP_03635749.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
 gi|223962313|gb|EEF66778.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
          Length = 408

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 150/274 (54%), Positives = 199/274 (72%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     ++  +   I   ++        AK+ ++ +NLRLV+S+AKKY  RG+
Sbjct: 136 VKMYLKEIGRVPLLNPEDEPEIARRIQ---AGDEEAKRILISSNLRLVVSIAKKYVGRGM 192

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 193 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 252

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           I+K+ R  R++   + REPT EEIA+K+  +  + VR++ KI  EP+SLETPIG+ED SH
Sbjct: 253 INKLTRVQRQLVQDLGREPTAEEIAEKMENITPDKVREIQKIALEPVSLETPIGEEDDSH 312

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK+A+SP   A    L++    VL  LT REE+VLR+RFG+      TLEEVGK
Sbjct: 313 LGDFIEDKDAMSPDQYANNQLLKDEINNVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGK 372

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQIEAKA+RKLKHP+RSK+LR F+D
Sbjct: 373 EFNVTRERIRQIEAKALRKLKHPTRSKRLRDFVD 406



 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/162 (22%), Positives = 63/162 (38%), Gaps = 25/162 (15%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED--------------------- 85
           +++   L   +++   M+D     +  GI++ + DD+E+                     
Sbjct: 38  KDVMDALEHLDLTDNDMDDLYEWFAAEGIDISEDDDIEELENIEIPEAGAMTQDIGDDLE 97

Query: 86  ---EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
              E+  ED  +            +    S     +DPV+MYL+E+G + LL+ E E  I
Sbjct: 98  FLAEDAGEDFDEEVEDVEVPIDLSETYSSSPYVRINDPVKMYLKEIGRVPLLNPEDEPEI 157

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           A+RI+AG       L  S L     I  +  +  G   L  I
Sbjct: 158 ARRIQAGDEEAKRILISSNLRLVVSIAKKY-VGRGMLFLDLI 198


>gi|284031355|ref|YP_003381286.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810648|gb|ADB32487.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 442

 Score =  218 bits (555), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 135/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  +   +   +                              +   
Sbjct: 145 VKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEQLSDESAKLKDKVRDEYDWISEDGRR 204

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 205 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 264

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V
Sbjct: 265 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 324

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P ++     L+E    VL +L+ R
Sbjct: 325 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPAEAVSFTLLQEQLHAVLDTLSER 384

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 385 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 442



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASS-----ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           VD  D + +       +L        +        +++     +T DPV+ YL+++G + 
Sbjct: 97  VDEADFQPDAVKPLEKELTEDQGFIVSEADETDEPEQQVMVAGATADPVKDYLKQIGKVP 156

Query: 133 LLSREGEIAIAKRIEAGR 150
           LL+ E E+ +AKRIEAG 
Sbjct: 157 LLNAEQEVELAKRIEAGL 174


>gi|68536164|ref|YP_250869.1| RNA polymerase sigma factor [Corynebacterium jeikeium K411]
 gi|68263763|emb|CAI37251.1| RNA polymerase sigma factor A [Corynebacterium jeikeium K411]
          Length = 544

 Score =  218 bits (555), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 135/290 (46%), Positives = 197/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L     ++ I      +S    R +    R+ + +   AK  ++EA
Sbjct: 259 AEQEVSLAKRIEAGLYAAYRLQEIKESGEKLSPMHRRDL----REIDRDGRRAKNHLLEA 314

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 315 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKGYKFSTYATWWIRQAITRA 374

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ + V+ V ++ +  +
Sbjct: 375 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAREMDITVDKVLEIQQYAR 434

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+++R
Sbjct: 435 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLR 494

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 495 FGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 544



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG      
Sbjct: 221 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYR 278


>gi|302386858|ref|YP_003822680.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197486|gb|ADL05057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 380

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 130/272 (47%), Positives = 191/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    + + ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 112 VRMYLKEIGTVPLLNAEEE---LRLAKRKADGDDDAKERLIEANLRLVVSIAKRYTGRGM 168

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 169 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 228

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A+ L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 229 INKMSKMQRKLTLELGYEPSVSELAEALDMSEDKVMEIMQIAREPASLETPIGEEDDSNL 288

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 289 GDFVADNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 348

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 349 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 380



 Score = 91.8 bits (226), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 50/198 (25%), Positives = 78/198 (39%), Gaps = 21/198 (10%)

Query: 25  DFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           D   D   K+++LA+ +   + + E+N F   +E+++EQM+     L N G++V+   D 
Sbjct: 4   DNFLDKLGKLVELAKTKHNALDVTEINNFFMGEELTTEQMDQIYTYLENRGVDVIPVIDD 63

Query: 84  EDEEGSEDSLDLA-----------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
                     D                    + L          T+DPVRMYL+E+G++ 
Sbjct: 64  SVLTDDVLLSDDLLLDDDLDDSFIKDVDEEDIDLDAIDLLEGIGTEDPVRMYLKEIGTVP 123

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+ E E+ +AKR   G       L E+ L     I  R     G + L  +        
Sbjct: 124 LLNAEEELRLAKRKADGDDDAKERLIEANLRLVVSIAKRY-TGRGMSFLDLV-------- 174

Query: 193 PESKGGFFHGTEGHSYQK 210
            E   G   G E   Y K
Sbjct: 175 QEGNLGLIKGVEKFDYTK 192


>gi|254821650|ref|ZP_05226651.1| RNA polymerase sigma factor [Mycobacterium intracellulare ATCC
           13950]
          Length = 488

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM----------------------------VRKGECE 440
           +R  +K I     ++  E   +                               ++    +
Sbjct: 188 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTEMTERGDKLPAAQRRDMQWICRD 247

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 248 GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 307

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 308 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 367

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 368 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 427

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 428 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 487

Query: 681 D 681
           D
Sbjct: 488 D 488



 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 37/68 (54%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +
Sbjct: 150 AEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVEL 209

Query: 143 AKRIEAGR 150
           AKRIEAG 
Sbjct: 210 AKRIEAGL 217


>gi|241889518|ref|ZP_04776817.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
 gi|241863825|gb|EER68208.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
          Length = 361

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 155/274 (56%), Positives = 202/274 (73%), Gaps = 1/274 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +R  +K I     +S  +   +  ++    E E   AKK++ EANLRLV+S+AK+Y  RG
Sbjct: 88  VRMYLKEIGKVPLLSKEKELELSKIIETGTEEEKEQAKKDLAEANLRLVVSIAKRYVGRG 147

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 148 MLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 207

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I++++R  R++   + REP PEEIAKK+ M  E VR++LKI +EP+SLETPIG+ED SH
Sbjct: 208 TINRLIRIQRQLLQDLGREPKPEEIAKKMNMTPEKVREILKIAQEPVSLETPIGEEDDSH 267

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A SP++ A    L+E    +L +LT REE VL++RFG+     HTLEEVG 
Sbjct: 268 LGDFIEDKEAQSPVEHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKTHTLEEVGS 327

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKAIRKLKHPS+  KL+ F++
Sbjct: 328 AFGVTRERIRQIEAKAIRKLKHPSKLNKLKGFME 361



 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 53/179 (29%), Positives = 77/179 (43%), Gaps = 27/179 (15%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           +G +T EE+   L   ++SSE M+D    L+N  I +++ +  E+EE   D  DL+  A 
Sbjct: 22  QGELTQEEIVDALSKLDISSEAMDDFYEELNNEDIILINANHEEEEEEELDLEDLSVPA- 80

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG----RAMMMAS 156
                           T+DPVRMYL+E+G + LLS+E E+ ++K IE G    +      
Sbjct: 81  -------------GIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIETGTEEEKEQAKKD 127

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           L E+ L     I  R  +  G   L  I         E   G     E   Y K    S
Sbjct: 128 LAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFDYSKGFKFS 177


>gi|94266972|ref|ZP_01290621.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93452327|gb|EAT02958.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 353

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 148/268 (55%), Positives = 193/268 (72%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +      G+       I + + +G+  +  AK  +V+ANLRLV+SVAKKY  RGLQ LDL
Sbjct: 85  QQCLQNHGLDQEGLAEIQAGIARGQEVSQEAKNRLVQANLRLVVSVAKKYAGRGLQLLDL 144

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ  TIRIPVHM D I++++
Sbjct: 145 IQEGNIGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQGRTIRIPVHMIDTINRML 204

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           + A+    +  REPTP+E+A+ L + V  V+ VLKI KEP+SL+TP+G+ + S L DFIE
Sbjct: 205 KGAKEFQRQHGREPTPDEMAQHLGVEVAKVKSVLKIAKEPLSLDTPVGNSNDSFLADFIE 264

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  A SP ++ I  NL+    RVL +L+PREE VLR+RFG+    D TLEEVG+ F VTR
Sbjct: 265 DTEAASPDEATIYENLQSNLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTR 324

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIEAKA++KLKHP+R  +L SF D
Sbjct: 325 ERIRQIEAKALKKLKHPARRNQLSSFYD 352


>gi|313140538|ref|ZP_07802731.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
 gi|313133048|gb|EFR50665.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
          Length = 500

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 217 AEQEVDLSERIEAGLYAQHLLDTESDGMDFKR-KRELKWAANDGKKAKDHLLEANLRLVV 275

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 276 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 335

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 336 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 395

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 396 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 455

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 456 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 499



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 39/71 (54%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +   E+G+    D     + +     KR+  A  +T DPV+ YL+++G + LL+ E E
Sbjct: 161 EPEQPKEKGAFVVRDDDDDENLTPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQE 220

Query: 140 IAIAKRIEAGR 150
           + +++RIEAG 
Sbjct: 221 VDLSERIEAGL 231


>gi|227549126|ref|ZP_03979175.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078794|gb|EEI16757.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 520

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 134/293 (45%), Positives = 196/293 (66%), Gaps = 3/293 (1%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR---HIVSMVRKGECEASIAKKEM 448
           + E +  +A  +++ L  ++ +  +         E +    +   +R    +   AK  +
Sbjct: 228 DAELEVSLAKRIEAGLYAQHRLDEMERAAAEGDKEAKLTPAVKRDLRAVARDGRKAKNHL 287

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAI
Sbjct: 288 LEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIRQAI 347

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V ++ +
Sbjct: 348 TRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKVLEIQQ 407

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+
Sbjct: 408 YAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVV 467

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 468 RLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 520



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/70 (32%), Positives = 38/70 (54%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +  E ++ +            S+   Q RKD+   ++ D VR YL+++G + LL  E E+
Sbjct: 174 EAAEVDDEAAVDSSSVWDIEESAALRQARKDAQLTASADSVRAYLKQIGKVALLDAELEV 233

Query: 141 AIAKRIEAGR 150
           ++AKRIEAG 
Sbjct: 234 SLAKRIEAGL 243


>gi|323142246|ref|ZP_08077080.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
 gi|322413309|gb|EFY04194.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
          Length = 546

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 180/496 (36%), Positives = 265/496 (53%), Gaps = 20/496 (4%)

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           LE      +         G+     E SS E E   V E     +      K+       
Sbjct: 70  LELVDDDNASDEDILPLVGNDEDNDEPSSSELENMSVPEGISIDDPVRMYLKEIGRVPLL 129

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL-RSLQDNAVNGQ 305
             E+     + +D+           M  +L      A D  + +  +L  SL++      
Sbjct: 130 IGEDEVKLAKRMDKGRQAERIQRGRMI-ELEEPAFTAEDSGSALIEKLRHSLKEEWQITN 188

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                 V   + K + V    ++   +  I    +      +R+M  +  L+   + + +
Sbjct: 189 MRSVFRVAQMIKKRQSVGQPYTVEDYEDLIFEFTKDERLHLQRLMAEQRCLIPGCEQFVV 248

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R+                S   D    + K  +    + +   R +  ++         
Sbjct: 249 TRET---------------SDIDDHKLYQIKAILNELRERMSDGREKDSAVVEAYCNLDE 293

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F  ++  V     +   AK+ + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA 
Sbjct: 294 DFEKLLKAV---AHQGDEAKQCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAV 350

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ R
Sbjct: 351 DKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGR 410

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP PEEIAK++   V+ VR+++KI +EP+SLETPIG+E+ SHLGDFIED +A +P D+A 
Sbjct: 411 EPLPEEIAKEMDTSVDRVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDHDAPAPADAAS 470

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              LRE    VL +LT RE+RVL +RFG+      TLEEVG+ F VTRERIRQIEAKA+R
Sbjct: 471 FTLLREQLEEVLETLTIREKRVLELRFGLEDGRSRTLEEVGQHFGVTRERIRQIEAKALR 530

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+HPSRSKKL+ FL+
Sbjct: 531 KLRHPSRSKKLKDFLE 546



 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 34/142 (23%), Positives = 69/142 (48%), Gaps = 2/142 (1%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLAR-QRGYVTIEELNAFL-PPDEVSSEQMEDTVAML 70
           ++      +     + +   ++I+  +  +G +T  ++       ++++ E +E    ++
Sbjct: 6   NKEGGDTMAAATKITQEQIDELIRKGKANKGVLTYGDVMNLTNTLEDITPEDVEHIYEVI 65

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +  G+ +VD D+  DE+      +   +   SS  L+        S DDPVRMYL+E+G 
Sbjct: 66  TRKGLELVDDDNASDEDILPLVGNDEDNDEPSSSELENMSVPEGISIDDPVRMYLKEIGR 125

Query: 131 IELLSREGEIAIAKRIEAGRAM 152
           + LL  E E+ +AKR++ GR  
Sbjct: 126 VPLLIGEDEVKLAKRMDKGRQA 147


>gi|210633964|ref|ZP_03297935.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
 gi|210159008|gb|EEA89979.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
          Length = 445

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 141/285 (49%), Positives = 204/285 (71%), Gaps = 5/285 (1%)

Query: 399 VACEVDSILKIRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           +A ++++ L   ++++        ++ +E R ++      E     AK+ ++ ANLRLV+
Sbjct: 164 LAMKIEAGLDAADKLEKQEAGEIELTRAEMRRLMR----VEQVGLDAKQALISANLRLVV 219

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 220 SIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYATWWIRQAITRAIADQAR 279

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VR  R++   + R+PTPEEI  ++ M  + VR++ KI++EP+SLE
Sbjct: 280 TIRIPVHMVETINKLVRVQRQLLQDLGRDPTPEEIGAEMDMSADRVREIQKISQEPVSLE 339

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+E+ S LGDFIED  AV P D+A  + L+E  T+VL  L  RE +V+ +RFG+   
Sbjct: 340 TPIGEEEDSQLGDFIEDAQAVVPADAASFSMLQEQLTQVLDGLAERERKVIELRFGLVDG 399

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+ 
Sbjct: 400 HPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLEN 444



 Score = 76.4 bits (186), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/163 (22%), Positives = 66/163 (40%), Gaps = 37/163 (22%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE--- 84
           D + +K++ L  + G VT +E+   L   +V+  Q+      L + G+ +V  ++ +   
Sbjct: 13  DTTIEKLLNLGSKAGSVTEDEIQIVLKDVDVTDAQLTSIYQFLRDRGVEIVSANEDDESE 72

Query: 85  ----------------DEEGSEDSLDLASSASNSSVFLQKRKDSADRS------------ 116
                           DE   +  L +A  A       + +K +                
Sbjct: 73  LVVDDDDRDAMDDLDGDESDEDHDLKMAKQADAEMASTKSKKKARTVRTTRSRSRTRGID 132

Query: 117 ------TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                 T DPVRMYL+E+G ++LL+   E+ +A +IEAG    
Sbjct: 133 ASTVMLTGDPVRMYLKEIGKVDLLTAAEEVDLAMKIEAGLDAA 175


>gi|296270363|ref|YP_003652995.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296093150|gb|ADG89102.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 555

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 180/253 (71%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            + + +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 303 DVKAELEWIAEDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 362

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 363 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 422

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A++L M  E V +V K  +EPISL TP+G+E  S  GD IED  AV P D+     
Sbjct: 423 PEELARELDMTPEKVIEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTL 482

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 483 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 542

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 543 HPSRSQVLRDYLD 555



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 79  DGDDLEDEEGSEDSLDLASSA----SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           + D+L+ +E   D LD         S+        + +A  +T DPV+ YL+++G + LL
Sbjct: 212 EDDELDGDEPKADELDQGDDDVLILSDDDDDAPSAQVAAAGATADPVKDYLKQIGKVPLL 271

Query: 135 SREGEIAIAKRIEAGR 150
           + E E+ +AKRIEAG 
Sbjct: 272 NAEQEVELAKRIEAGL 287


>gi|145224520|ref|YP_001135198.1| RNA polymerase sigma factor [Mycobacterium gilvum PYR-GCK]
 gi|315444851|ref|YP_004077730.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
 gi|145217006|gb|ABP46410.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
 gi|315263154|gb|ADT99895.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
          Length = 488

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 188/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 188 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYCTQLMAEFAEKGEKLTTAQRRDYMWICRD 247

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 248 GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 307

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 308 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 367

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 368 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 427

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 428 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 487

Query: 681 D 681
           D
Sbjct: 488 D 488



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 38/72 (52%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D    E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 146 DDSLPEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 205

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 206 EVELAKRIEAGL 217


>gi|311064624|ref|YP_003971349.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
 gi|310866943|gb|ADP36312.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
          Length = 506

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 223 AEQEVDLSERIEAGLYAQHLLDTESDGMDFKR-KRELKWAANDGKKAKDHLLEANLRLVV 281

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 282 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 341

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 342 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 401

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 402 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 461

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 462 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 505



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 39/71 (54%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +   E+G+    D     + +     KR+  A  +T DPV+ YL+++G + LL+ E E
Sbjct: 167 EPEQPKEKGAFVVRDDDDDENLTPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQE 226

Query: 140 IAIAKRIEAGR 150
           + +++RIEAG 
Sbjct: 227 VDLSERIEAGL 237


>gi|224283384|ref|ZP_03646706.1| RNA polymerase sigma factor [Bifidobacterium bifidum NCIMB 41171]
          Length = 506

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 223 AEQEVDLSERIEAGLYAQHLLDTESDGMDFKR-KRELKWAANDGKKAKDHLLEANLRLVV 281

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 282 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 341

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 342 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 401

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 402 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 461

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 462 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 505



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 39/71 (54%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +   E+G+    D     + +     KR+  A  +T DPV+ YL+++G + LL+ E E
Sbjct: 167 EPEQPKEKGAFVVRDDDDDENLTPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQE 226

Query: 140 IAIAKRIEAGR 150
           + +++RIEAG 
Sbjct: 227 VDLSERIEAGL 237


>gi|260890619|ref|ZP_05901882.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260859664|gb|EEX74164.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 392

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 161/395 (40%), Positives = 234/395 (59%), Gaps = 17/395 (4%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
              Q+   +     K + + KV+  + +  V S+  +  +ID L+++L D   +I+    
Sbjct: 3   DKKQNLKNSLANFIKQAREQKVVSYEEINSVLSIGFSTEKIDQLIKKLTDDGVQIVDTAR 62

Query: 355 ELLRLAQS-------YGIKRDVFLER---HQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           E   L +          ++   F +        E+D   V              +A  +D
Sbjct: 63  EKEDLLKVPDSIEAIEKMEISDFEDSHDEFVESEIDDSEVDKLLQTD----LLKMAESMD 118

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
               I+  ++ I     +S  E       V         AK++++E+NLRLV+S+AKK+T
Sbjct: 119 VDEPIKMYLREIGQIPLLSYEEEIDYAQRV---LNGEEEAKQKLIESNLRLVVSIAKKHT 175

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW++QAITR+IADQ  TIRIPVH
Sbjct: 176 NRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPVH 235

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ + +R +  +  +EPT EE+A+KL +PVE V+ +L++ ++PISLETP+G E+
Sbjct: 236 MIETINKIKKESRIILQETGKEPTAEELAEKLELPVEKVKSILEMNQDPISLETPVGSEE 295

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDF+ED    +P D+  +  L+E    VL +L  REE VLR R+G+   +  TLEE
Sbjct: 296 DSELGDFVEDDKFANPYDATTRVLLKEQLDEVLKTLNEREEMVLRYRYGLDDGSQKTLEE 355

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           VGK F VTRERIRQIE KA+RKL+HPSR KKL  +
Sbjct: 356 VGKIFNVTRERIRQIEVKALRKLRHPSRRKKLEDY 390



 Score = 83.7 bits (205), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 54/210 (25%), Positives = 83/210 (39%), Gaps = 32/210 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD------ 81
            +S    IK AR++  V+ EE+N+ L     S+E+++  +  L++ G+ +VD        
Sbjct: 9   KNSLANFIKQAREQKVVSYEEINSVL-SIGFSTEKIDQLIKKLTDDGVQIVDTAREKEDL 67

Query: 82  ----------------DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
                           D ED        ++  S  +  +     K +     D+P++MYL
Sbjct: 68  LKVPDSIEAIEKMEISDFEDSHDEFVESEIDDSEVDKLLQTDLLKMAESMDVDEPIKMYL 127

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RE+G I LLS E EI  A+R+  G       L ES L     I  +   N G  +L  I 
Sbjct: 128 REIGQIPLLSYEEEIDYAQRVLNGEEEAKQKLIESNLRLVVSIAKK-HTNRGLKMLDLI- 185

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSS 215
                   E   G     E   Y+K    S
Sbjct: 186 -------QEGNMGLMKAVEKFEYEKGFKFS 208


>gi|41408918|ref|NP_961754.1| RNA polymerase sigma factor [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397277|gb|AAS05137.1| SigA [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 509

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 161/490 (32%), Positives = 247/490 (50%), Gaps = 36/490 (7%)

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G  ++      +       +  S++  +       + D        +D  ++ D   E  
Sbjct: 56  GAAAEPAKKTRSSAKGADAKAPSARGTKAAKGGPADPDALDTDGAVEDLDTEPDLEGEPG 115

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
           E+ + + D + DD    ++A +  + P       E  E      +    A    +  + S
Sbjct: 116 EDLDIDTDLNLDDLEEDVAADDADIEPGDAEE-GEDEEAAAPKAAGATVADEDDEIAEPS 174

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
            K K   + +     S +L Q+R D    +L   +  +     ++ ++A           
Sbjct: 175 EKDKASGDFVWDEDESEALRQARRD---AELTASADSVRAYLKQIGKVALLNA------- 224

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                       V  AK    G +   +  E                   +  ++ R   
Sbjct: 225 ---------EEEVELAKRIEAGLYATQLMSE------------MAERGEKLPAAQRRD-- 261

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 262 --MMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 319

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +     REPTPEE
Sbjct: 320 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDPGREPTPEE 379

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 380 LAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 439

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 440 QLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 499

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 500 RSQVLRDYLD 509



 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q R+D+   ++ D VR YL+++G + LL+ E 
Sbjct: 167 DDEIAEPSEKDKASGDFVWDEDESEALRQARRDAELTASADSVRAYLKQIGKVALLNAEE 226

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M+ + E
Sbjct: 227 EVELAKRIEAGLYATQLMSEMAE 249


>gi|298242664|ref|ZP_06966471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297555718|gb|EFH89582.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 394

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 111/272 (40%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            IR  +  I     ++  +   I   V         A+K +VEANLRLV+S+AK+Y N+G
Sbjct: 125 AIRQYLAEIGRFPLLTSEQELTIAWRV---ANGDMEAQKRLVEANLRLVVSIAKRYNNQG 181

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQEGN+GL++A +KFD   G++FSTYA WW++QAI+R++A+ + TI +PVH+ +
Sbjct: 182 ISLLDLIQEGNLGLIRAVQKFDPQRGFRFSTYATWWIRQAISRAVAEHTRTIHVPVHVVE 241

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R  R++   + R+P PEEIA+ + +  E V ++  I + PISL+ P+ +++  H
Sbjct: 242 LIYKMKRITRQLYQDLGRDPFPEEIAQAINLTKERVVELQSIAEAPISLDAPLIEDEQYH 301

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +ED +A +P +      LR+  +R L +L+ RE +V+ +R+G+     HTLEE+  
Sbjct: 302 LADMLEDTHAAAPAEVVTHQVLRDHISRALETLSQRERQVIELRYGLYDGYCHTLEELSA 361

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            F +TRERIRQIE KA+R L+HP +   L  +
Sbjct: 362 YFKLTRERIRQIEVKALRTLRHPIQIHMLHDY 393



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G     ++            + +  +DR  D+ +R YL E+G   LL+ E E+ IA R+ 
Sbjct: 93  GKAAQNEMQDDVFFEEEEEAETEGESDREVDNAIRQYLAEIGRFPLLTSEQELTIAWRVA 152

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            G       L E+ L    ++      N+    L ++I
Sbjct: 153 NGDMEAQKRLVEANLRL--VVSIAKRYNNQGISLLDLI 188


>gi|57234646|ref|YP_181295.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
 gi|57225094|gb|AAW40151.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
          Length = 520

 Score =  218 bits (554), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 183/520 (35%), Positives = 278/520 (53%), Gaps = 36/520 (6%)

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                  E       +D   E   +D+ E +       K+++ D   +      AE  E 
Sbjct: 2   PAEKDKKEFSPDDTYDDKDIEDGLEDIHEEQDAEAENDKMAEPDLKDIADTDIPAELTEE 61

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV-------YRELRSLQDNAVNGQKDEK 309
            L  + D    T   +   L   +   L++I             L  +    +   +DEK
Sbjct: 62  ELAAEADMMPDTDEEI-GPLNIDLEIPLEQIDTQGIVDDPVRMYLHEIGRVPLLSAEDEK 120

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK--- 366
           +  K     +++ ++       + R     E    + + +      L +L Q  G+    
Sbjct: 121 TLAKKMEEGKRIREIRQECLEKRGRYPSAAESFLCMLRELSQATEVLFQLGQELGMDTSA 180

Query: 367 ------RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK--IRNEIKSISV 418
                  D  L      E+D        D             ++  +   +  ++   ++
Sbjct: 181 SLKNVIHDPKLRTAIDHEIDQQLTKNISDNTGKSMAEIEQSFINLAINSSLLPKVILDAI 240

Query: 419 ETGISISE--------------FRHIVSM---VRKGECEASIAKKEMVEANLRLVISVAK 461
              ++I E               RH  S+   +   E +A  A++ +++ANLRLV+SVAK
Sbjct: 241 PEKMTIPEIATYTNDPAFISHLERHEASLKYYLDNLEIDAKRAERHLIQANLRLVVSVAK 300

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           K+  RG+  LDLIQEGNIGL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRI
Sbjct: 301 KHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWWIRQAITRAIADQARTIRI 360

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM + I+K++  +R++S K+ REPTP+EIA ++ +P E VR++ K+++ P+SLE+PIG
Sbjct: 361 PVHMVETINKLLSISRQLSQKLGREPTPDEIAVEMDLPPEKVREIAKVSQLPVSLESPIG 420

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E+ SHLGDFIED+NA++P D+A +  L+E    VL SLTPRE RVL++RFG+      T
Sbjct: 421 EEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVLGSLTPRERRVLQLRFGLEDGRSRT 480

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +L+
Sbjct: 481 LEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLE 520



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/146 (23%), Positives = 53/146 (36%), Gaps = 16/146 (10%)

Query: 45  TIEE--LNAFLPP--DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           T ++  +   L    +E  +E   D +A      I   D      EE      D+     
Sbjct: 15  TYDDKDIEDGLEDIHEEQDAEAENDKMAEPDLKDIADTDIPAELTEEELAAEADMMPDTD 74

Query: 101 NSSVFLQKRKDSADRSTD------DPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AM 152
                L    +      D      DPVRMYL E+G + LLS E E  +AK++E G+    
Sbjct: 75  EEIGPLNIDLEIPLEQIDTQGIVDDPVRMYLHEIGRVPLLSAEDEKTLAKKMEEGKRIRE 134

Query: 153 MMASLCE----SPLTFQALIIWRDEL 174
           +     E     P   ++ +    EL
Sbjct: 135 IRQECLEKRGRYPSAAESFLCMLREL 160


>gi|302670285|ref|YP_003830245.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
 gi|302394758|gb|ADL33663.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
          Length = 521

 Score =  218 bits (554), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 153/283 (54%), Positives = 211/283 (74%), Gaps = 4/283 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  +++      E+        +S +  + + +++     E   AKK + EANLRLV+S
Sbjct: 243 LAQAMEAGADAEKELADDKDVNKLSDARKKELNAII----YEGEEAKKRLAEANLRLVVS 298

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ T
Sbjct: 299 IAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQART 358

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K++R +R++  ++ REP PEE+AK++ MPVE VR++LKI++EP+SLET
Sbjct: 359 IRIPVHMVETINKLIRVSRQLLQELGREPLPEEVAKEMNMPVERVREILKISQEPVSLET 418

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ SHLGDFI+D N   P D+A    L+E    VL +LT RE++VLR+RFG+    
Sbjct: 419 PIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLVEVLGTLTEREQKVLRLRFGLDDGR 478

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+KL+ +LD
Sbjct: 479 ARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDYLD 521



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 39/154 (25%), Positives = 77/154 (50%), Gaps = 6/154 (3%)

Query: 2   TIGKKRNRDSDSEHEDSDDS----LVFDFSDDSWKKMIKLARQR-GYVTIEELNAFLPPD 56
           T G+K   D ++  ++S+D        +      K+++ LA+++   +   E++ F    
Sbjct: 97  TKGRKSKADKEAPSQNSEDGEIDEATRELFSQKVKEILALAKKKKNVLEYAEISDFFAEL 156

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR- 115
            ++ EQ ++ + +L N GI+V+   + + ++  +D   L                  D  
Sbjct: 157 NLNEEQFDNVLEVLENSGIDVLRVSEDDVDDIPDDDDMLLVDDDEEVDMENIDLSVPDGI 216

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S +DPVRMYL+E+G + LL+ + EI +A+ +EAG
Sbjct: 217 SIEDPVRMYLKEIGKVPLLTADQEIDLAQAMEAG 250


>gi|219847152|ref|YP_002461585.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219541411|gb|ACL23149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 398

 Score =  218 bits (554), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 134/370 (36%), Positives = 207/370 (55%), Gaps = 34/370 (9%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           I  LV  L +  ++I      L       G+      E   G E     ++ +    + +
Sbjct: 38  IQRLVPNLEESVEQIDSIYAAL----AEAGVPVHDGDEPVSGDES----LTPSVTDLDLD 89

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV-------------------- 434
            +   A   DS+   R  ++ I     ++  + + +  M+                    
Sbjct: 90  DELSDALLSDSV---RLYLREIGQVPLLTAEQEKQLAQMIERGQAAERKLATLPPDSPEA 146

Query: 435 ---RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              R+ + +   A+++M  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD  
Sbjct: 147 AKLRRIKEQGDEARQKMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHT 206

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW+KQA++R++ADQS  +R+PVH+ + ++++    R+++  + REPT  E
Sbjct: 207 KGYKFSTYATWWIKQALSRALADQSRLVRLPVHLGETLNRIQSARRQLTQSLGREPTDTE 266

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L M  E +R++ +  ++P+SL TP+G+E  S L DFI D +A+   D+A    LR+
Sbjct: 267 LANHLGMSEEKLRELRRTAQDPVSLATPVGEEADSTLADFIPDPHALDADDAAASGMLRQ 326

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                L  L+ RE RVL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP 
Sbjct: 327 QIAAALDQLSERERRVLELRYGLADGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPR 386

Query: 672 RSKKLRSFLD 681
             K L+ +LD
Sbjct: 387 LGKLLKDYLD 396



 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 43/148 (29%), Positives = 68/148 (45%), Gaps = 10/148 (6%)

Query: 14  EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
           + +   D      S    + +I   RQ+G+VT E++   +P  E S EQ++   A L+  
Sbjct: 3   QSQPETDRTSSAISPADVQALIAQGRQQGFVTFEDIQRLVPNLEESVEQIDSIYAALAEA 62

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
           G+ V DGD         + +    S + S   L    + +D    D VR+YLRE+G + L
Sbjct: 63  GVPVHDGD---------EPVSGDESLTPSVTDLDLDDELSDALLSDSVRLYLREIGQVPL 113

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESP 161
           L+ E E  +A+ IE G+      L   P
Sbjct: 114 LTAEQEKQLAQMIERGQ-AAERKLATLP 140


>gi|297571337|ref|YP_003697111.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
 gi|296931684|gb|ADH92492.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 510

 Score =  218 bits (554), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 140/285 (49%), Positives = 191/285 (67%), Gaps = 5/285 (1%)

Query: 399 VACEVDSILKIRNEI--KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
              EV+   +I   +  + I   T I     R  + ++ +   +   AK  ++EANLRLV
Sbjct: 229 AEEEVELAKRIEAGLFAQHILETTTIDDPRKRRELEIISRDGHK---AKNHLLEANLRLV 285

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+
Sbjct: 286 VSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDYAKGYKFSTYATWWIRQAITRAMADQA 345

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R  R+M   + REPT EE+A +L M  E V +V K  +EPISL
Sbjct: 346 RTIRIPVHMVEVINKLARVQRQMLQDLGREPTVEELAHELDMTEEKVIEVQKYGREPISL 405

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
            TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ RE  V+ MRFG+  
Sbjct: 406 HTPLGEDGDSEFGDLIEDSEAVVPADAVGFTLLQEQLHQVLDTLSEREAGVVSMRFGLTD 465

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 466 GQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 510



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 79  DGDDLEDEEGSEDSLDLASS---ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           D  D E E   E +   + +     +       ++     +T DPV+ YL+++G + LL+
Sbjct: 169 DEADEEHEAVKETTAKRSGAFIVRDSDDTDEPVQRVHVAGATADPVKDYLKQIGKVALLN 228

Query: 136 REGEIAIAKRIEAGR 150
            E E+ +AKRIEAG 
Sbjct: 229 AEEEVELAKRIEAGL 243


>gi|326384438|ref|ZP_08206118.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196783|gb|EGD53977.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 466

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 166 VRAYLKQIGKVALLNAEEEVELAKRIEAGLFATERLRRVMESGEKLSVAQRRDLSWISRD 225

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 226 GNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 285

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 286 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 345

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 346 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLDTL 405

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 406 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 465

Query: 681 D 681
           D
Sbjct: 466 D 466



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E   D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRI
Sbjct: 132 KEDEAKPDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRI 191

Query: 147 EAGR 150
           EAG 
Sbjct: 192 EAGL 195


>gi|21224164|ref|NP_629943.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289768642|ref|ZP_06528020.1| transcription initiation factor sigma [Streptomyces lividans TK24]
 gi|12644145|sp|P18183|HRDB_STRCO RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|3036885|emb|CAA18518.1| major vegetative sigma factor [Streptomyces coelicolor A3(2)]
 gi|289698841|gb|EFD66270.1| transcription initiation factor sigma [Streptomyces lividans TK24]
          Length = 511

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 259 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 318

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 319 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 378

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 379 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 438

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 439 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 498

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 499 HPSRSQVLRDYLD 511



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +      EE           +         ++ +A  +T DPV+ YL+++G + LL+ E 
Sbjct: 173 EEPKAATEEPEGTENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQ 232

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 233 EVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 273


>gi|222100016|ref|YP_002534584.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
 gi|221572406|gb|ACM23218.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
          Length = 392

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 138/272 (50%), Positives = 190/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     ++ ++ R +    +        AK++++ +NLRLV+S+AK+Y  RGL
Sbjct: 116 IKMYLKEIGKIPLLTPAQERELARRAQ---MGDKKAKEKLITSNLRLVVSIAKRYMGRGL 172

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 173 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 232

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  R    K   EP+ EE+AK +  P E ++++L+  KE ISLE+PIG+++ S +
Sbjct: 233 INKLNRLRREYYQKYGEEPSVEELAKMMGKPPEKIKEILEAAKETISLESPIGEDEDSSI 292

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF+ D++  SP   A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ 
Sbjct: 293 EDFVADESVPSPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQY 352

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK L+S L
Sbjct: 353 FNVTRERIRQIEVKALRKLRHPSRSKYLKSLL 384



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/173 (23%), Positives = 73/173 (42%), Gaps = 9/173 (5%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPP--DEV 58
           M   K+     +   E+  +       +   KK+I   +++GY+T E+++   PP  +E 
Sbjct: 1   MAEKKEAIMKDEQITENEQEKKFPPQIEKRIKKLINQGKKKGYITYEDIDKAFPPNYEEF 60

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
            +  +E     L   GIN+V       E  SE+  + ++      +  +  +     +  
Sbjct: 61  DTNLIEKIYEELEKHGINIV-------ESDSEEETETSTEELEELLEKESPEIHDASNVR 113

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           D ++MYL+E+G I LL+   E  +A+R + G       L  S L     I  R
Sbjct: 114 DSIKMYLKEIGKIPLLTPAQERELARRAQMGDKKAKEKLITSNLRLVVSIAKR 166


>gi|18477828|emb|CAC83737.1| RNA polymerase sigma 70 [Rhodococcus fascians]
          Length = 474

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 174 VRAYLKQIGKVALLNAEEEVELAKRIEAGLFAVEKMRESAEKGEKLPVAQRRDMTWICRD 233

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 234 GNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 293

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 294 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 353

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 354 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 413

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 414 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 473

Query: 681 D 681
           D
Sbjct: 474 D 474



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 38/75 (50%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +    E     + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 132 EDATSEPTAEDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 191

Query: 139 EIAIAKRIEAGRAMM 153
           E+ +AKRIEAG   +
Sbjct: 192 EVELAKRIEAGLFAV 206


>gi|213964575|ref|ZP_03392775.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
 gi|213952768|gb|EEB64150.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
          Length = 520

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 130/250 (52%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R+   +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 271 RDLREISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 330

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE
Sbjct: 331 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEE 390

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 391 LAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQD 450

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 451 QLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 510

Query: 672 RSKKLRSFLD 681
           RS+ LR +L+
Sbjct: 511 RSQVLRDYLE 520



 Score = 54.8 bits (130), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/53 (43%), Positives = 36/53 (67%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +   S+   Q RKD+A  ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 197 NEDESARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGL 249


>gi|291436829|ref|ZP_06576219.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
 gi|291339724|gb|EFE66680.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
          Length = 509

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 257 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 316

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 317 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 376

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 377 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 436

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 437 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 496

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 497 HPSRSQVLRDYLD 509



 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 5/111 (4%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            + +VD + LED + +E+     S+    +         ++ +A  +T DPV+ YL+++G
Sbjct: 162 DVELVDDEVLEDTKVAEEPEGAESAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIG 221

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 222 KVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 271


>gi|282861771|ref|ZP_06270835.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282563587|gb|EFB69125.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 355

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 118/253 (46%), Positives = 180/253 (71%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   + +   +  +A++ ++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKF
Sbjct: 103 RLAQDLGRLVVQGRMAERRLIEANLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKF 162

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EP+
Sbjct: 163 DYTRGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGHEPS 222

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A +L +  E V  +L++ +EP+SL  P+G+ED    GD IED +A SP++SA    
Sbjct: 223 AEEVAAQLDLTPERVETILRLAQEPVSLHAPVGEEDDVAFGDLIEDGDAPSPVESAAFLL 282

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE    VL++L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + +L+
Sbjct: 283 LREHLEAVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLARLR 342

Query: 669 HPSRSKKLRSFLD 681
             + + +LR +LD
Sbjct: 343 DHAFADQLRGYLD 355



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
              + V     +      + D  R YLRE+G I LL    E+ +A+R+EAG       L 
Sbjct: 37  EEPADVPEPTGRPETGGPSSDLFRQYLREIGRIPLLGAADEVELARRVEAGLF-AEERLA 95

Query: 159 ESPL 162
            +P 
Sbjct: 96  ATPG 99


>gi|257438255|ref|ZP_05614010.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199332|gb|EEU97616.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 359

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 143/273 (52%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     +++ +   +    +      + A++++ EANLRLV+SVAK+Y  RGL
Sbjct: 89  VKAYLKEIGRVPLLTMEQELELARAAQ---AGDADARRKLSEANLRLVVSVAKRYAGRGL 145

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKAAEKF+   G++FSTYA WW++Q+ITR+IADQ   IRIPVH+ + 
Sbjct: 146 PFLDLIQEGNLGLMKAAEKFEPDRGFRFSTYATWWIRQSITRAIADQGRVIRIPVHLVES 205

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I++V +TA  +  K  REPT EEIA +L M  + VR++L++ ++PISLETP+G+E+ +HL
Sbjct: 206 INRVKKTAGELLRKNGREPTAEEIAVRLDMEPDRVRELLQLAQDPISLETPVGEEEDAHL 265

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DFI+D+ A  P+D A +  LR     VL SLTPREERVL +RFG+      TLEE+GK+
Sbjct: 266 EDFIQDEEAGVPVDEAGRELLRRELANVLKSLTPREERVLTLRFGLEDGQARTLEELGKE 325

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSR+K+LR +L+
Sbjct: 326 FNVTRERIRQIEAKALRKLRHPSRAKRLRDYLE 358



 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 35/148 (23%), Positives = 63/148 (42%), Gaps = 12/148 (8%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
              +++  K +   AR R  +T E+++  +   E     ++   A L   GI V      
Sbjct: 4   LSQTEELVKILAGRAR-RHTLTPEQISRAMDEQEYDVSGLDALYAALEARGIRV------ 56

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  D+          L+    +   + DDPV+ YL+E+G + LL+ E E+ +A
Sbjct: 57  -----TEEEADMPMLDETQIGELEHELSAEGVALDDPVKAYLKEIGRVPLLTMEQELELA 111

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWR 171
           +  +AG A     L E+ L     +  R
Sbjct: 112 RAAQAGDADARRKLSEANLRLVVSVAKR 139


>gi|254391058|ref|ZP_05006266.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
 gi|197704753|gb|EDY50565.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
          Length = 514

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 262 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 321

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 322 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 381

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 382 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 441

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 442 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 501

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 502 HPSRSQVLRDYLD 514



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE+ +E        +         ++ +   +T DPV+ YL+++G + LL+ E E+ +AK
Sbjct: 182 DEDEAEGESKGFVLSDEDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAK 241

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           RIEAG       L  +      L    + + +    
Sbjct: 242 RIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 276


>gi|256375630|ref|YP_003099290.1| RNA polymerase sigma factor SigB [Actinosynnema mirum DSM 43827]
 gi|255919933|gb|ACU35444.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 330

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 112/246 (45%), Positives = 171/246 (69%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R    +   AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G
Sbjct: 83  LRALVRDGLRAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKG 142

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR +ADQ  TIR+PVH+ ++++K+ R  R +  ++ RE T EE+A
Sbjct: 143 FKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQVNKLARIKRDLHQQLGREATNEELA 202

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +  +    V  +L   ++P+SL+ P+G E+ + LGDFIED +A     + I   L++  
Sbjct: 203 AESGLSPTKVSDLLDHARDPVSLDMPVGAEEDAPLGDFIEDSDATDAESAVISGLLQDDL 262

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RVLA+L  RE+ V+R+R+G+      TL+++GKQF ++RER+RQIE + + KL+   R+
Sbjct: 263 RRVLATLEQREQAVIRLRYGLEDGQPRTLDQIGKQFGLSRERVRQIEREVMSKLRQGERA 322

Query: 674 KKLRSF 679
            KLR++
Sbjct: 323 AKLRAY 328



 Score = 44.8 bits (104), Expect = 0.044,   Method: Composition-based stats.
 Identities = 18/49 (36%), Positives = 25/49 (51%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++S         A     D VR+YL  +G   LL+   E+ +AKRIEAG
Sbjct: 14  DTSAPSVDLDLDAQGPAADLVRVYLNGIGKTALLTAAQEVELAKRIEAG 62


>gi|15835519|ref|NP_297278.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270285702|ref|ZP_06195096.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270289710|ref|ZP_06196012.1| RNA polymerase sigma factor [Chlamydia muridarum Weiss]
 gi|301337097|ref|ZP_07225299.1| RNA polymerase sigma factor [Chlamydia muridarum MopnTet14]
 gi|7388084|sp|P56835|RPOD_CHLMU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|7190932|gb|AAF39698.1| RNA polymerase sigma factor RpoD [Chlamydia muridarum Nigg]
          Length = 571

 Score =  217 bits (553), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 146/265 (55%), Positives = 194/265 (73%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLDLIQE
Sbjct: 290 EVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQE 349

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV+R A
Sbjct: 350 GNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKVLRGA 409

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  +  +EPTPEE+ ++L    + VR++ KI + PISL+  +GD   S  GDF+ED  
Sbjct: 410 KKLMMETGKEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEVGDSGESSFGDFLEDTA 469

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VTRERI
Sbjct: 470 VESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERI 529

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 530 RQIEAKALRKMRHPIRSKQLRAFLD 554



 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 90/181 (49%), Gaps = 10/181 (5%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           D+    + D+   +      ++++ LA+ +G++T EE+N  LPP   S EQ++  +  L+
Sbjct: 4   DTLDSQAADAAQEEEIQRKLEELVTLAKDQGFITYEEINEILPPSFDSPEQIDQVLIFLA 63

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
            M + V++  D+E ++  +            +  L+     ++ + DDPVRMYL+EMG++
Sbjct: 64  GMDVQVLNQADVERQKERKK----------EAKELEGLAKRSEGTPDDPVRMYLKEMGTV 113

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+RE E+ I+KRIE  +  +   +     + +  +     L +G     +I+  +   
Sbjct: 114 PLLTREEEVEISKRIEKAQVQIERIILRFRYSTKEAVSIAQYLINGKERFDKIVSEKEVE 173

Query: 192 G 192
            
Sbjct: 174 D 174


>gi|317495391|ref|ZP_07953760.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
 gi|316914450|gb|EFV35927.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
          Length = 361

 Score =  217 bits (553), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 153/274 (55%), Positives = 202/274 (73%), Gaps = 1/274 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEA-SIAKKEMVEANLRLVISVAKKYTNRG 467
           +R  +K I     +S  +   +  ++  G       AKK++ EANLRLV+S+AK+Y  RG
Sbjct: 88  VRMYLKEIGKVPLLSKEKELELSKIIESGTESEKEQAKKDLAEANLRLVVSIAKRYVGRG 147

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 148 MLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 207

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I++++R  R++   + REP PEEIAKK+ M  + VR++LKI +EP+SLETPIG+ED SH
Sbjct: 208 TINRLIRVQRQLLQDLGREPKPEEIAKKMNMTPDKVREILKIAQEPVSLETPIGEEDDSH 267

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK+A SP++ A    L+E    +L +LT REE VL++RFG+     HTLEEVG 
Sbjct: 268 LGDFIEDKDAQSPVEHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKTHTLEEVGS 327

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKAIRKLKHPS+  KL+ F++
Sbjct: 328 AFGVTRERIRQIEAKAIRKLKHPSKLNKLKGFME 361



 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 80/188 (42%), Gaps = 28/188 (14%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K++++  +++G +T EE+   L   ++SSE M+D    L+N  I +++ +          
Sbjct: 14  KELLEKGKKQGELTQEEIIEALSKLDISSETMDDFYEELNNEDIILINEN---------- 63

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-- 149
                       + L+     A   T+DPVRMYL+E+G + LLS+E E+ ++K IE+G  
Sbjct: 64  -----HEEEEEELDLEDLSVPAGIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIESGTE 118

Query: 150 --RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             +      L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 119 SEKEQAKKDLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 169

Query: 208 YQKREDSS 215
           Y K    S
Sbjct: 170 YSKGFKFS 177


>gi|313113550|ref|ZP_07799138.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310624065|gb|EFQ07432.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 377

 Score =  217 bits (553), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 143/273 (52%), Positives = 198/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     ++  +   +    +        A++++ EANLRLV+SVAK+Y  RGL
Sbjct: 107 VKAYLKEIGRVPLLTAEQETELARAAQ---AGDEDARRKLSEANLRLVVSVAKRYAGRGL 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKAAEKF+   G+KFSTYA WW++Q+ITR+IADQ  TIRIPVH+ + 
Sbjct: 164 PFLDLIQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQSITRAIADQGRTIRIPVHLVES 223

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I++V +    +  K  REPT EEIA +L M  + VR++L++ ++PISLETP+G+E+ +HL
Sbjct: 224 INRVKKMTGDLLRKNGREPTAEEIAVQLDMEPDRVRELLQLAQDPISLETPVGEEEDAHL 283

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DFI+D++A  P+D A +  LR     VL SLTPREERV+ +RFG+     HTLEE+GK+
Sbjct: 284 EDFIQDEDAGVPVDEAGRQLLRRELFSVLKSLTPREERVIALRFGLEDGRAHTLEELGKE 343

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRER+RQIEAKA+RKL+HPSR+K+LR +LD
Sbjct: 344 FNVTRERVRQIEAKALRKLRHPSRAKRLRDYLD 376



 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 68/160 (42%), Gaps = 12/160 (7%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           + E + +        +++  + +   AR    +T E+++  +   +    Q+++    L 
Sbjct: 10  EQERKGAGTMQKLSQTEELARTLAARARHH-ALTPEQISRAMDEQDYDVAQLDELYTALE 68

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           + G+++           +E+  DL +        L+    +   + DDPV+ YL+E+G +
Sbjct: 69  DRGVHL-----------TEEEADLPALDETQIGRLEHELSAEGVALDDPVKAYLKEIGRV 117

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            LL+ E E  +A+  +AG       L E+ L     +  R
Sbjct: 118 PLLTAEQETELARAAQAGDEDARRKLSEANLRLVVSVAKR 157


>gi|87311289|ref|ZP_01093411.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87286029|gb|EAQ77941.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 567

 Score =  217 bits (553), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 163/515 (31%), Positives = 262/515 (50%), Gaps = 12/515 (2%)

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L +++      G E            +   R  S+QE       E   D     ++SK 
Sbjct: 49  KLDKLLTELEQKGIELVTSAPEDDFDDAPTSRAPSAQEFREAIDDEEGTDTFVPEEISKA 108

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +   +        +      + E   A  +     Q R  V+     +      L  +  
Sbjct: 109 NDDPIRMYLSQMASIPLLTRDQEIALAKKIEITRKQFRRSVLACDFAMRTTVEILTKVHR 168

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGS--------LSLNQSRIDLLVEQLYDISKRIMH 351
             +   +  K S+  ++ KE++   +          L  NQ    +L+ +      R+  
Sbjct: 169 GELPFDRTIKVSLTEQLTKEQIQARMPHNLRTLNHLLDQNQRDFKVLLRKSTSREDRLAA 228

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV----ACEVDSIL 407
               + R  +   +  ++ L   +   +      +A    +   +  +    +   D   
Sbjct: 229 KRRFIRRRQKCLQLVEEMSLRTRRVLPVMKQLEDFASRMEQIRNRMDLIGDQSSFKDERA 288

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +R E++ + + T  S    R      R+   E    K+E+   NLRLV+S+AKKY NRG
Sbjct: 289 NLRQELRDLMILTLESPRGLRQRCERYRRQFDEYEKVKRELSSGNLRLVVSIAKKYRNRG 348

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L FLDLIQEGN GLM+A +K+++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM D
Sbjct: 349 LSFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMID 408

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            + K+    +R+  +++REPT +EIA++  + +E VR+V+ I ++P+SL+ PIG+ + S 
Sbjct: 409 VLSKLRNVQKRLLQELRREPTMDEIARRAEIDLEEVRRVMDIGRQPVSLDRPIGESEDSS 468

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            G+FIED +  +P+ SA    LR+    +L +LT RE  ++++R+G+G    +TLEEVG+
Sbjct: 469 FGEFIEDSHEETPIRSASNQILRDRIQGLLKTLTYREREIIKLRYGLGDGYTYTLEEVGR 528

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            F VTRER+RQIEAKA+RKL+HP RS++L  FL G
Sbjct: 529 IFKVTRERVRQIEAKAVRKLQHPVRSQQLEGFLAG 563



 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 79/453 (17%), Positives = 174/453 (38%), Gaps = 43/453 (9%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
              ++   +  D     +++  + +GY+T +E+N +LP +  S E+++  +  L   GI 
Sbjct: 4   KGKEAFHVELCDQDLIALMERGKTQGYLTYDEVNNYLPDEASSPEKLDKLLTELEQKGIE 63

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----RKDSADRSTDDPVRMYLREMGSI 131
           +V     +D + +  S   ++     ++  ++       +   ++ DDP+RMYL +M SI
Sbjct: 64  LVTSAPEDDFDDAPTSRAPSAQEFREAIDDEEGTDTFVPEEISKANDDPIRMYLSQMASI 123

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+R+ EIA+AK+IE  R     S+       +  +    +++ G       I      
Sbjct: 124 PLLTRDQEIALAKKIEITRKQFRRSVLACDFAMRTTVEILTKVHRGELPFDRTI------ 177

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
               K            Q R   +       + + + D +   + S     ++ +     
Sbjct: 178 ----KVSLTEQLTKEQIQARMPHNLRTLNHLLDQNQRDFKVLLRKSTSREDRLAAKRRFI 233

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN--AVNGQKDEK 309
              ++ L   E+ S  T   +       VM  L++ A    ++R+  D     +  KDE+
Sbjct: 234 RRRQKCLQLVEEMSLRTRRVL------PVMKQLEDFASRMEQIRNRMDLIGDQSSFKDER 287

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH----NEGELLRLAQSYGI 365
           ++++ + L++ ++  + S    + R +    Q  +  K        N   ++ +A+ Y  
Sbjct: 288 ANLR-QELRDLMILTLESPRGLRQRCERYRRQFDEYEKVKRELSSGNLRLVVSIAKKYRN 346

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF------------VACEVDSILKIRNEI 413
           +   FL+  Q  E +   +     +       F                 D    IR  +
Sbjct: 347 RGLSFLDLIQ--EGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPV 404

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             I V + +   + + ++  +R+      IA++
Sbjct: 405 HMIDVLSKLRNVQ-KRLLQELRREPTMDEIARR 436


>gi|288574317|ref|ZP_06392674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570058|gb|EFC91615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  217 bits (552), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 143/273 (52%), Positives = 198/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     +  SE   +   V        +AK+++++ANLRLV+S+AKKY  RG+
Sbjct: 112 VRMYLREIGKVDLLDASEEVELAKRVE---DGDQVAKQKIIDANLRLVVSIAKKYIGRGM 168

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 169 LFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 228

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  ++ REPT EEI++ + +    V ++ +I + P+SLETPIG+E+ S L
Sbjct: 229 INKMVRVSRQLVQRMGREPTDEEISEAMEIESTKVEEIRRIAQLPVSLETPIGEEEDSQL 288

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++  SP D+A    L E    +L +L+ RE  VLR RFG+     +TLEEVG++
Sbjct: 289 GDFIEDRDMPSPEDAASCNLLHEQIEDMLDALSDREREVLRYRFGLEDGRSYTLEEVGRR 348

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR FL+
Sbjct: 349 FGVTRERIRQIEAKALRKLRHPSRSKKLRDFLE 381



 Score =  105 bits (262), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 43/161 (26%), Positives = 77/161 (47%), Gaps = 5/161 (3%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                +  +++I   R+ GYVT +++  F+P +  S++ +E+    L  +GI V++  D 
Sbjct: 19  LKMYMERIRQLIMQGRKNGYVTQKDIEKFIPIEFWSTDVLENVFDNLMELGIEVIEDGD- 77

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                 +     ASS+    V++ +     D    DPVRMYLRE+G ++LL    E+ +A
Sbjct: 78  ---PRLKSDKSEASSSDEEHVYVDELGKLDDIPLTDPVRMYLREIGKVDLLDASEEVELA 134

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           KR+E G  +    + ++ L     I  +  +  G   L  I
Sbjct: 135 KRVEDGDQVAKQKIIDANLRLVVSIAKKY-IGRGMLFLDLI 174


>gi|183601374|ref|ZP_02962744.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683429|ref|YP_002469812.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191127|ref|YP_002968521.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           Bl-04]
 gi|241196533|ref|YP_002970088.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           DSM 10140]
 gi|183218980|gb|EDT89621.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219621079|gb|ACL29236.1| principal sigma factor RpoD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249519|gb|ACS46459.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240251087|gb|ACS48026.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|295794116|gb|ADG33651.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 488

 Score =  217 bits (552), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EFR     ++    +   AK  ++EANLRLV+
Sbjct: 205 AEQEVDLSERIEAGLYAQHLLDTEGDTMEFRR-KRELKWAAADGKKAKDHLLEANLRLVV 263

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 264 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 323

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 324 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 383

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P ++   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 384 TPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFRQVLETLSPREAGVIKMRYGLEDG 443

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 444 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 487



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ +   +   +     KR+     +T DPV+ YL+++G + LL+ E E+ +++RIEAG 
Sbjct: 160 DNDEDDEALLANPGVNPKRRVVTTGATADPVKDYLKQIGRVSLLNAEQEVDLSERIEAGL 219


>gi|48745|emb|CAA37175.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 442

 Score =  217 bits (552), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 190 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 249

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 250 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 309

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 310 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 369

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 370 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 429

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 430 HPSRSQVLRDYLD 442



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +      EE           +         ++ +A  +T DPV+ YL+++G + LL+ E 
Sbjct: 104 EEPKAATEEPEGTENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQ 163

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 164 EVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 204


>gi|269127406|ref|YP_003300776.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312364|gb|ACY98738.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 385

 Score =  217 bits (552), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 133/268 (49%), Positives = 194/268 (72%), Gaps = 5/268 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++    IS  E   +         E + AK+ ++EANLRLV+S+AK+Y  RG+ FLDL
Sbjct: 123 EKLARAAFISPRERLDL----ELIAREGARAKQRLIEANLRLVVSIAKRYVGRGMLFLDL 178

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+V
Sbjct: 179 IQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 238

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++   + REPTP EI  ++ +P E V ++ +I +EP+SL++PI  E+ S LGDFIE
Sbjct: 239 RVQRQLHQDLGREPTPAEIGAEMGLPAERVVEIQRIAQEPVSLQSPI-GEEDSDLGDFIE 297

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +AV PL++A    L++    +L +L+ RE+R++++RFG+      TLEEVG++F VTR
Sbjct: 298 DADAVVPLEAAAFILLQDQLEDILCTLSEREQRIIQLRFGLTDGHPRTLEEVGREFGVTR 357

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIE+K + KL+HPSR++ LR +L+
Sbjct: 358 ERIRQIESKTLAKLRHPSRAQMLREYLE 385



 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/153 (27%), Positives = 66/153 (43%), Gaps = 22/153 (14%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           S D    ++   R+ G VT++++ A +   E+ ++ +E  V  L+  G+ V++      E
Sbjct: 12  SVDQVADLVVRGREHGGVTVDDVAAAIDRSELPADSLERVVLALAEQGVEVLESPGETGE 71

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               D  DL                     T D VR+YLRE+G + LL+ E E+ +AK I
Sbjct: 72  LSRADEDDLGK----------------RVPTSDLVRIYLREIGRVPLLTAEEEVELAKTI 115

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           EAG         E  L   A I  R+ L+    
Sbjct: 116 EAGLF------AEEKLARAAFISPRERLDLELI 142


>gi|332799075|ref|YP_004460574.1| RpoD subfamily RNA polymerase sigma-70 [Tepidanaerobacter sp. Re1]
 gi|332696810|gb|AEE91267.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tepidanaerobacter
           sp. Re1]
          Length = 374

 Score =  217 bits (552), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   +         AK+ + EANLRLV+S+AKKY  RG+
Sbjct: 105 VRMYLKEIGKVPLLSAEEEIMLSKRIE---EGDKEAKRRLAEANLRLVVSIAKKYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNLGLMKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEEIA+++ +PVE VR+++KI +EP+SL TPIG+E+ S L
Sbjct: 222 INKLIRIQRQLLQELGRDPLPEEIAEEMELPVEKVREIMKIAQEPVSLATPIGEEEDSFL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A++P D+A    L+E    VL +LTPREE+VLR+RFG+      TLEEVG+ 
Sbjct: 282 GDFIPDDEALAPADAAAYLLLKEQLEDVLETLTPREEKVLRLRFGLDDGRPRTLEEVGQV 341

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 342 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 374



 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 80/183 (43%), Gaps = 17/183 (9%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPP-DEVSSE 61
           + KK   +  S+ +   D +         + +I+  ++ G ++  E+   L   +++ +E
Sbjct: 1   MAKKEQIEKKSDKKPVQDKMKI------VRDLIEKGKKNGVLSYGEIMDALEDIEDLDTE 54

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           Q++        MGI V+D  +   EE + + +       ++             + DDPV
Sbjct: 55  QIDKIYESFEEMGIEVLDDGEEIPEEETLEEVPTEEIDLSA---------PEGVAIDDPV 105

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMYL+E+G + LLS E EI ++KRIE G       L E+ L     I  +  +  G   L
Sbjct: 106 RMYLKEIGKVPLLSAEEEIMLSKRIEEGDKEAKRRLAEANLRLVVSIAKKY-VGRGMLFL 164

Query: 182 REI 184
             I
Sbjct: 165 DLI 167


>gi|160941160|ref|ZP_02088497.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435721|gb|EDP13488.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
          Length = 381

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 130/272 (47%), Positives = 190/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +    ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 113 VRMYLKEIGTVPLLTADEELDLA---QRKADGDEFAKERLIEANLRLVVSIAKRYTGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 170 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A+ L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 230 INKMSKMQRKLTLELGYEPSVTELAEALDMTEDKVMEIMQIAREPASLETPIGEEDDSNL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 290 GDFVADNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 349

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 350 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/199 (24%), Positives = 76/199 (38%), Gaps = 22/199 (11%)

Query: 25  DFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           D      +K+++ A+ +   +   E+N F   D +S EQM+   + L    I+VV   D 
Sbjct: 4   DDFLKKLEKLVEHAKTKHNTLDAGEINDFFTGDNLSPEQMDQIYSYLEGRNIDVVPVLDE 63

Query: 84  E------------DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
                        D +   D       A    + L          T+DPVRMYL+E+G++
Sbjct: 64  AMLTEDTVLLDDIDLDLDLDDDSFIKDAEEEEIDLDAVDLLEGIGTEDPVRMYLKEIGTV 123

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+ + E+ +A+R   G       L E+ L     I  R     G + L  +       
Sbjct: 124 PLLTADEELDLAQRKADGDEFAKERLIEANLRLVVSIAKRY-TGRGMSFLDLV------- 175

Query: 192 GPESKGGFFHGTEGHSYQK 210
             E   G   G E   Y K
Sbjct: 176 -QEGNLGLIKGVEKFDYTK 193


>gi|289706929|ref|ZP_06503266.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
 gi|289556364|gb|EFD49718.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
          Length = 509

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 140/283 (49%), Positives = 192/283 (67%), Gaps = 1/283 (0%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EVD  ++I   + +  V    +  ++R     ++    +   AK  ++EANLRLV+S
Sbjct: 228 AEQEVDLAMRIEAGLYAEHVVQHEASDDYRER-RDIQLIIADGRKAKNHLLEANLRLVVS 286

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ T
Sbjct: 287 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQART 346

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL T
Sbjct: 347 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHT 406

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  AV P D+     L+E    VL +L+ RE  V+ MRFG+    
Sbjct: 407 PLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQ 466

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 467 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 509



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +S      ++     +T DPV+ YL+++G + LL+ E E+ +A RIEAG 
Sbjct: 192 DDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAMRIEAGL 242


>gi|310287737|ref|YP_003938995.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
 gi|309251673|gb|ADO53421.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
          Length = 506

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 138/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     +F+     ++    +   AK  ++EANLRLV+
Sbjct: 223 AEQEVDLSERIEAGLYAQHLLDTESDGMDFKR-KRELKWAANDGKKAKDHLLEANLRLVV 281

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 282 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 341

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 342 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 401

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 402 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 461

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 462 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 505



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 39/71 (54%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +   E+G+    D     + +     KR+  A  +T DPV+ YL+++G + LL+ E E
Sbjct: 167 EPEQPKEKGAFVVRDDDDDENLTPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQE 226

Query: 140 IAIAKRIEAGR 150
           + +++RIEAG 
Sbjct: 227 VDLSERIEAGL 237


>gi|227495524|ref|ZP_03925840.1| sigma factor [Actinomyces coleocanis DSM 15436]
 gi|226831071|gb|EEH63454.1| sigma factor [Actinomyces coleocanis DSM 15436]
          Length = 505

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 134/253 (52%), Positives = 183/253 (72%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   ++    +  ++K  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 253 KLRRELQILVHDGQLSKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 312

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 313 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 372

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  A+ P D+     
Sbjct: 373 PEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPTDAVSFTL 432

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   +VL +L+ RE  V+ MRFG+G     TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 433 LQEQLHKVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 492

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 493 HPSRSQVLRDYLD 505



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 34/71 (47%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G    +E  +         +         +K +   +T DPV+ YL+++G + LL+   E
Sbjct: 167 GKPDAEETQAVVKTGGFVVSEFDDTDEPVQKVTVAGATTDPVKDYLKQIGKVSLLTAADE 226

Query: 140 IAIAKRIEAGR 150
           + +A+RIEAG 
Sbjct: 227 VDLARRIEAGL 237


>gi|329769784|ref|ZP_08261185.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
 gi|328838146|gb|EGF87764.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
          Length = 362

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 154/274 (56%), Positives = 202/274 (73%), Gaps = 1/274 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +R  +K I     +S  +   +  ++    E E   AKK++ EANLRLV+S+AK+Y  RG
Sbjct: 89  VRMYLKEIGKVPLLSKEKELELSKIIENGTEEEKEQAKKDLAEANLRLVVSIAKRYVGRG 148

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 149 MLFLDLIQEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 208

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I++++R  R++   + REP PEEIAKK+ M  + VR++LKI +EP+SLETPIG+ED SH
Sbjct: 209 TINRLIRVQRQLLQDLGREPKPEEIAKKMNMTPDKVREILKIAQEPVSLETPIGEEDDSH 268

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIEDK A SP++ A    L+E    +L +LT REE VL++RFG+     HTLEEVG 
Sbjct: 269 LGDFIEDKEAQSPVEHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKTHTLEEVGS 328

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKAIRKLKHPS+  KL+ F++
Sbjct: 329 AFGVTRERIRQIEAKAIRKLKHPSKLNKLKGFME 362



 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 54/188 (28%), Positives = 84/188 (44%), Gaps = 27/188 (14%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K+ I+  +++G +T EE+   L   +VSSE ++D    L+   I +++ + +E+EE   D
Sbjct: 14  KEFIEKGKKQGELTQEEILDALSKLDVSSEAVDDFYEELNREDIILINANQVEEEEEELD 73

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG-- 149
             DL+  A                 T+DPVRMYL+E+G + LLS+E E+ ++K IE G  
Sbjct: 74  LEDLSVPA--------------GIRTNDPVRMYLKEIGKVPLLSKEKELELSKIIENGTE 119

Query: 150 --RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             +      L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 120 EEKEQAKKDLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 170

Query: 208 YQKREDSS 215
           Y+K    S
Sbjct: 171 YEKGFKFS 178


>gi|317506483|ref|ZP_07964284.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
 gi|316255244|gb|EFV14513.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
          Length = 452

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 130/250 (52%), Positives = 180/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     + + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 203 RDMNWVVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 262

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE
Sbjct: 263 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEE 322

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + +++ +P E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 323 LGREMDIPPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 382

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+RMRFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 383 QLQAVLETLSEREAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 442

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 443 RSQVLRDYLD 452



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 38/67 (56%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ++EE    + D       S    Q RK++   ++ D VR YL+++G + LL+ E E+ +A
Sbjct: 115 DEEEPERTAGDFVWDEDESEALRQARKNAELTASADSVRAYLKQIGKVALLNAEQEVELA 174

Query: 144 KRIEAGR 150
           KRIEAG 
Sbjct: 175 KRIEAGL 181


>gi|87302644|ref|ZP_01085461.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87282988|gb|EAQ74945.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 469

 Score =  217 bits (552), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 222 KFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 281

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 282 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 341

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 342 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 400

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 401 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 460

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 461 NGVLKEYI 468



 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 31/59 (52%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            + D      +A+N+      +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 128 EAADGAKDKKTAANAKALASIKVGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 186


>gi|169829158|ref|YP_001699316.1| RNA polymerase sigma factor rpoD [Lysinibacillus sphaericus C3-41]
 gi|168993646|gb|ACA41186.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Lysinibacillus sphaericus C3-41]
          Length = 375

 Score =  217 bits (551), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEQEIKLAERIEQ---GDEEARKRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDSEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 44/158 (27%), Positives = 75/158 (47%), Gaps = 8/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM-GINVVDGDDLEDE 86
           DD+ K + + A+  G ++++E++  L P E+ +E++      L     I ++  ++ E+E
Sbjct: 18  DDAKKFLQEKAKTEGEISMKEISEKLTPYELENEEIFHFAEDLEKHKDIQIIGKEEFEEE 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                   +   A+  +  L           +DPVRMYL+E+G ++LLS E EI +A+RI
Sbjct: 78  SL------MKEEANEETFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEQEIKLAERI 131

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 132 EQGDEEARKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|295836123|ref|ZP_06823056.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295825874|gb|EDY42152.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 493

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 241 KLQRELEIIAEDGGRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 300

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 301 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 360

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 361 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 420

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 421 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 480

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 481 HPSRSQVLRDYLD 493



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 10/114 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD---------RSTDDPVRMYLR 126
            ++D +  E+  G  +     ++   S  F+    D  D          +T DPV+ YL+
Sbjct: 143 ELLDEESTEETPGKGEEAAEPAAGGESQGFVLSDDDEDDAPAQQVAAAGATADPVKDYLK 202

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++G + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 203 QIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLQRELEIIAEDGGR 255


>gi|291295726|ref|YP_003507124.1| RNA polymerase sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
 gi|290470685|gb|ADD28104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
          Length = 507

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 162/490 (33%), Positives = 252/490 (51%), Gaps = 25/490 (5%)

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            K        G     +     E E D + E         +    +      P  +    
Sbjct: 40  KKTAASKPKSGSPKSAKGTVVAEPEEDILDEELVADMDELEPPDLEEDLEVGPDLDEIAP 99

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
                     +A +   + ++L    +  ++ +   + EL +L  +    + +E   +  
Sbjct: 100 PPRKGGGLAPAALSDEDLTEELLEADLEDIEMLEPDF-ELGTLPIDEAEEEIEEDLPLPR 158

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
               + + + +  +          +E+  D+++R+        RLA+  G+  ++     
Sbjct: 159 ISTSDPVRQYLHEIGQVPLLT---LEEEIDLARRVEEGVAAAQRLAEETGLDAELIRHVL 215

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           + +                     +  + ++I  +   ++++         E +  + + 
Sbjct: 216 RSQ-------VQGSSRVASIPGTDLRIDPETIAAVDARLRAL-------PREVKRYLHIA 261

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R    +  I ++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   +
Sbjct: 262 R----DGEICRQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEFKRRF 317

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR+M  ++ REP+ EEIA 
Sbjct: 318 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQMQQELGREPSYEEIAD 377

Query: 555 KL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            +      + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E 
Sbjct: 378 AMGPGWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDSAAQSMLSEE 437

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPS 671
             + L  L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H S
Sbjct: 438 LEKALGKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 497

Query: 672 RSKKLRSFLD 681
           R++KLR FLD
Sbjct: 498 RTRKLRDFLD 507



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/125 (24%), Positives = 54/125 (43%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            ++   +++ D  + E    D          +   +++       ST DPVR YL E+G 
Sbjct: 115 EDLTEELLEADLEDIEMLEPDFELGTLPIDEAEEEIEEDLPLPRISTSDPVRQYLHEIGQ 174

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           + LL+ E EI +A+R+E G A       E+ L  + +         G++ +  I   +  
Sbjct: 175 VPLLTLEEEIDLARRVEEGVAAAQRLAEETGLDAELIRHVLRSQVQGSSRVASIPGTDLR 234

Query: 191 IGPES 195
           I PE+
Sbjct: 235 IDPET 239


>gi|296171852|ref|ZP_06852951.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
 gi|295893936|gb|EFG73705.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
          Length = 503

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 188/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM----------------------------VRKGECE 440
           +R  +K I     ++  E   +                               +     +
Sbjct: 203 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAERGDKLPAAQRRDMMWICRD 262

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 263 GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 322

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 323 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 382

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 383 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 442

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 443 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 502

Query: 681 D 681
           D
Sbjct: 503 D 503



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRI
Sbjct: 169 EKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRI 228

Query: 147 EAGR--AMMMASLCE 159
           EAG     +MA + E
Sbjct: 229 EAGLYATQLMAEMAE 243


>gi|119953489|ref|YP_945698.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
 gi|119862260|gb|AAX18028.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
          Length = 630

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 174/652 (26%), Positives = 311/652 (47%), Gaps = 45/652 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            K ++     +  +T E+L+ FL  D +  + ++    +L N GI++V+      E+   
Sbjct: 20  IKAILSHLGDKKAITFEDLSTFLSGDMLDPDNIDYIYGVLENEGISLVN------EKMES 73

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  D+        +  Q         +DD                      I  +++   
Sbjct: 74  DICDIDEFDEADKLDSQCMMLDDSIQSDD---------------------EIDDKLDEFD 112

Query: 151 AMMMASLCESPLTFQA-LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             ++     S    ++ L+   +  +     L+EI       G +          G S  
Sbjct: 113 DEVLDKEDFSSGYIKSGLLKDSNSEDPIRLYLKEIGKEFLLTGNQEVELAKQMDSGESII 172

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           +    ++    ++       I S     +  + + +   +N         +  +      
Sbjct: 173 ENILKNEGLVIENYYNLVNAIYSRVDKEEFFKKEKEREKDNNF-------DYYNKKKRIT 225

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
           S  +  L+P      D + +      SL +   +  ++  +S +       + +++ S+ 
Sbjct: 226 SFYKASLKPF----QDRLIKYIERKHSLYELGEDIFEESITSERL-----HIKEMLKSVP 276

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           L Q  + +  +   D + +I   + +   +     I +   L    GR+L         +
Sbjct: 277 LYQEELRIFSDDYIDSASKIKDLKRQQKSILDRLKIDKVRNLRIL-GRDLAIPERRERIE 335

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
                 ++ +  ++      + E++ I +     + +   +   + KG+     AK +++
Sbjct: 336 KSLNIREDLIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEILKGKQMMQHAKDQLI 395

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAIT
Sbjct: 396 KANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAIT 455

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           RSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +
Sbjct: 456 RSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDEELSSRLGWDLKKVKTVKNV 515

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           ++EP+SLETPIG+E+ S L DFIEDK   +P        L++    VL +L  RE+ V++
Sbjct: 516 SREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSFVVLQDQIRAVLGTLPEREQEVVK 575

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 576 MRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 627


>gi|227488750|ref|ZP_03919066.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227091172|gb|EEI26484.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
          Length = 599

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 128/248 (51%), Positives = 180/248 (72%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G
Sbjct: 352 LRTVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 411

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+A
Sbjct: 412 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELA 471

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++  
Sbjct: 472 KEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQL 531

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS
Sbjct: 532 QDVLKTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 591

Query: 674 KKLRSFLD 681
           + LR +L+
Sbjct: 592 QVLRDYLE 599



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 271 DEEESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 323


>gi|239626154|ref|ZP_04669185.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239520384|gb|EEQ60250.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 381

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 130/272 (47%), Positives = 192/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 113 VRMYLKEIGTVPLLTADEE---LNLAQRKADGDDYAKERLIEANLRLVVSIAKRYTGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 170 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A+ L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 230 INKMSKMQRKLTLELGYEPSVTELAEALDMTEDKVMEIMQIAREPASLETPIGEEDDSNL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 290 GDFVADNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 349

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 350 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 50/199 (25%), Positives = 77/199 (38%), Gaps = 22/199 (11%)

Query: 25  DFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           D      +K+++ A+ +   +   E+N F   D +S EQM+   + L N  I+VV   D 
Sbjct: 4   DDFLKKLEKLVEHAKSKHNTLDAGEINDFFTGDNLSPEQMDQIYSYLENRNIDVVPVLDE 63

Query: 84  E------------DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
                        D +   D       A    + L          T+DPVRMYL+E+G++
Sbjct: 64  AMLTEDTVLLDDIDLDLDLDDDSFIKDAEEEEIDLDAVDLLEGIGTEDPVRMYLKEIGTV 123

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
            LL+ + E+ +A+R   G       L E+ L     I  R     G + L  +       
Sbjct: 124 PLLTADEELNLAQRKADGDDYAKERLIEANLRLVVSIAKRY-TGRGMSFLDLV------- 175

Query: 192 GPESKGGFFHGTEGHSYQK 210
             E   G   G E   Y K
Sbjct: 176 -QEGNLGLIKGVEKFDYTK 193


>gi|227547666|ref|ZP_03977715.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
 gi|227211921|gb|EEI79817.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
          Length = 464

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EF+     ++    +   AK  ++EANLRLV+
Sbjct: 181 AEQEVDLSERIEAGLYAQHLLDTESEGMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 239

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 240 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 299

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 300 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 359

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 360 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 419

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 420 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 463



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             +   E+G+    D      N       KR+  A  +T DPV+ YL+++G + LL+ E 
Sbjct: 124 APEQPKEKGAYVVSDTDDEEENIIPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQ 183

Query: 139 EIAIAKRIEAGR 150
           E+ +++RIEAG 
Sbjct: 184 EVDLSERIEAGL 195


>gi|23465986|ref|NP_696589.1| RNA polymerase sigma factor [Bifidobacterium longum NCC2705]
 gi|46191322|ref|ZP_00206768.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bifidobacterium longum DJO10A]
 gi|189439160|ref|YP_001954241.1| RNA polymerase sigma factor [Bifidobacterium longum DJO10A]
 gi|312132592|ref|YP_003999931.1| rpod [Bifidobacterium longum subsp. longum BBMN68]
 gi|317482450|ref|ZP_07941467.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689398|ref|YP_004209132.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691364|ref|YP_004220934.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|23326702|gb|AAN25225.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           longum NCC2705]
 gi|189427595|gb|ACD97743.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium longum
           DJO10A]
 gi|311773536|gb|ADQ03024.1| RpoD [Bifidobacterium longum subsp. longum BBMN68]
 gi|316916110|gb|EFV37515.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456220|dbj|BAJ66842.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|320460734|dbj|BAJ71354.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 474

 Score =  217 bits (551), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EF+     ++    +   AK  ++EANLRLV+
Sbjct: 191 AEQEVDLSERIEAGLYAQHLLDTESEGMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 249

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 250 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 309

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 310 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 369

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 370 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 429

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 430 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 473



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             +   E+G+    D      N       KR+  A  +T DPV+ YL+++G + LL+ E 
Sbjct: 134 APEQPKEKGAYVVSDTDDEEENIIPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQ 193

Query: 139 EIAIAKRIEAGR 150
           E+ +++RIEAG 
Sbjct: 194 EVDLSERIEAGL 205


>gi|302525710|ref|ZP_07278052.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434605|gb|EFL06421.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 317

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 110/266 (41%), Positives = 180/266 (67%), Gaps = 4/266 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     ++    + + ++VR    +  +AK  ++EANLRLV+S+AK+YT RG+  LDL
Sbjct: 54  HMLDTAEDLTPQRRKELRALVR----DGHVAKNHLLEANLRLVVSLAKRYTGRGMPLLDL 109

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQ  TIR+PVH+ ++++K+ 
Sbjct: 110 IQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQVNKLA 169

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  ++ R+ T EE++ +  +PV  +  +L  +++P+SL+ P+G E+ + LGDFIE
Sbjct: 170 RIRRDLHQQLGRDATHEELSAESGIPVHKISDLLDQSRDPVSLDMPVGTEEDAPLGDFIE 229

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  A     + I   L++   RVLA+L  RE+ V+R+R+G+      TL+++GK F ++R
Sbjct: 230 DSEATDAESAVISGLLQDDLRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSR 289

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ER+RQIE + + KL+   R+ +LR++
Sbjct: 290 ERVRQIEREVMAKLRQGERADRLRAY 315



 Score = 43.3 bits (100), Expect = 0.12,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 24/48 (50%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S   L      A     D VR+YL  +G   LL+   E+ +AKRIEAG
Sbjct: 2   SVGALTDADLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAG 49


>gi|219684458|ref|ZP_03539402.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
 gi|219672447|gb|EED29500.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
          Length = 631

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 175/643 (27%), Positives = 309/643 (48%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D  G+ED  D    + 
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDFICSILEDRGIILVNKISELDLVGTEDGNDEEEESE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +S                    E +I I  +++             
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDINGKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L  G      + D  +      K       +       ++    K+ 
Sbjct: 113 ----EEDISVKDDLGSGYIKSNALKDSHS--EDPIKLYLKEIGKEFLLTGNQEVELAKQM 166

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D  +    +I     +  ++   + +   +    E     ++D    +     ++ +   
Sbjct: 167 DSGESIIENILKNEGLVIENYYNLINTIYSRMEREEFFKREKDKDKESNPDYYNKKKRIA 226

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
                 +  +   L S  DN     +      +  +  E+L   +L+ ++ L Q  + + 
Sbjct: 227 SFYKIPLKPIQDRLISYVDNKHRVYELGGDIFEKNLKSERLALKELLRNVPLYQDELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKRIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +     + +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLVQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|330444010|ref|YP_004376996.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
 gi|328807120|gb|AEB41293.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
          Length = 562

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 145/269 (53%), Positives = 197/269 (73%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +    V  G ++ EF+  V M+++   ++  AKKEMVE+NLRLVIS+AKKYTNRGL FLD
Sbjct: 276 LHKREVAAGRTLEEFKKDVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLD 335

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGN+GLMKA EKF++  GYKFSTYA WW++QA+TR+IADQ+ TIRIPVHM + I+KV
Sbjct: 336 LIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMIETINKV 395

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R A+++  +  +EP+PEE+A++L +  + VR++ KI + PISL+  +G+   S  GDF+
Sbjct: 396 LRGAKKLMMETGKEPSPEELAEELGLTPDRVREIYKIAQHPISLQAEVGEGGESAFGDFL 455

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED    SP ++   + L++    VL +LT RE  VL  RFG+      TLEEVG  F VT
Sbjct: 456 EDTAVESPAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVT 515

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEAKA+RK++HP RSK+LR+FLD
Sbjct: 516 RERIRQIEAKALRKMRHPIRSKQLRAFLD 544



 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 45/173 (26%), Positives = 86/173 (49%), Gaps = 10/173 (5%)

Query: 20  DSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
           D+   + +    ++++ LA+++G++T EE+N  LP    S EQ++  +  L+ M I +++
Sbjct: 2   DASSEEEAQKKLEELVSLAKEQGFITYEEINEILPMSFDSPEQIDQVLIFLAGMDIQILN 61

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D+E ++  +  +            L+      + + DDPVRMYL+EMG++ LL+RE E
Sbjct: 62  QIDVERQKERKKEVKE----------LEGLAKRTEGTPDDPVRMYLKEMGTVPLLTREEE 111

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           + I+KRIE  +  +   +     + +  I     L  G     +II  +    
Sbjct: 112 VEISKRIEKAQVQIERIILRFRYSTKEAISIAHYLITGKERFDKIISEKEVED 164


>gi|302534283|ref|ZP_07286625.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443178|gb|EFL14994.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 361

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 132/325 (40%), Positives = 196/325 (60%), Gaps = 24/325 (7%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR----- 435
           P  +   +  P    ++  A    S    R  ++ I     ++ +E   +   V      
Sbjct: 37  PEVLELIEPVPPQRGRDNGAGTGPSADLFRQYLREIGRIPLLTAAEEVELARRVEAGLFA 96

Query: 436 -------------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                              K      +AK+ ++E+NLRLV+SVAK+Y  RGL  LDL+QE
Sbjct: 97  EEKLAGATDLDSQLAVDLDKLVVMGRMAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQE 156

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GL++A EKFD+  GYKFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  
Sbjct: 157 GNLGLIRAVEKFDYARGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQ 216

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           RRM  +   EPT EE+A  L +  E V +VL++ +EP+SL  P+G+ED   LGD IED +
Sbjct: 217 RRMLQERGYEPTAEEVAAHLELTPERVLEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGD 276

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP++SA    LRE    VL++L  RE +V+++R+G+      TLEE+G+ F VTRERI
Sbjct: 277 AASPMESAAFFLLREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERI 336

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIE+K + KL+  + + +LR +LD
Sbjct: 337 RQIESKTLNKLRDHAFADQLRGYLD 361



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 43/108 (39%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + +    E+  ++  ++            +   +    + D  R YLRE+G I LL+   
Sbjct: 23  EAEADTVEDAGDEEPEVLELIEPVPPQRGRDNGAGTGPSADLFRQYLREIGRIPLLTAAE 82

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E+ +A+R+EAG          + L  Q  +     +  G    R +I+
Sbjct: 83  EVELARRVEAGLFAEEKLAGATDLDSQLAVDLDKLVVMGRMAKRRLIE 130


>gi|290967746|ref|ZP_06559301.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
 gi|290782262|gb|EFD94835.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
          Length = 423

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 155/369 (42%), Positives = 232/369 (62%), Gaps = 11/369 (2%)

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL-ERHQGRELDP 381
            ++  L L Q +  L   ++ ++ +       ++ ++ +++  K    + E   G E D 
Sbjct: 55  HILQLLRLGQKQGSLTYTEIMNVMEEDELTTEQIDKMYETFADKGIDIIGEESNGNEHDE 114

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK---- 436
              +  +  P+    +    E  +I   +R  +K I     +S  E   +   + K    
Sbjct: 115 ISDTENEHVPDLRTVDLSVPEGINIDDPVRMYLKEIGRVPLLSADEEITLAKAIEKGNDE 174

Query: 437 -----GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
                 +     AKK++ +ANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+ 
Sbjct: 175 NATVADKKNGIDAKKKLTDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVDKFDYS 234

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  +  R+P PEE
Sbjct: 235 KGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRISRQLIQEKGRDPLPEE 294

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+K+ +PVE VR+++KI +EP+SLETPIG+E+ SHLGDFIED+ AV+P D+A    L+E
Sbjct: 295 IAEKMEIPVERVREIMKIAQEPVSLETPIGEEEDSHLGDFIEDQEAVAPDDAASFILLKE 354

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               V + LT RE +VL +RFG+      TLEEVG+ F VTRERIRQIE KA+ KL++  
Sbjct: 355 QIEEVFSCLTDRERKVLYLRFGLKDGRPRTLEEVGQYFNVTRERIRQIEGKALGKLRNWG 414

Query: 672 RSKKLRSFL 680
           + +K++ FL
Sbjct: 415 KREKIKDFL 423



 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 39/164 (23%), Positives = 71/164 (43%), Gaps = 16/164 (9%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++++L +++G +T  E+   +  DE+++EQ++      ++ GI+++     E      D 
Sbjct: 58  QLLRLGQKQGSLTYTEIMNVMEEDELTTEQIDKMYETFADKGIDIIGE---ESNGNEHDE 114

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           +    +     +           + DDPVRMYL+E+G + LLS + EI +AK IE G   
Sbjct: 115 ISDTENEHVPDLRTVDLSVPEGINIDDPVRMYLKEIGRVPLLSADEEITLAKAIEKGNDE 174

Query: 153 ------------MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                           L ++ L     I  R  +  G   L  I
Sbjct: 175 NATVADKKNGIDAKKKLTDANLRLVVSIAKRY-VGRGMLFLDLI 217


>gi|289523410|ref|ZP_06440264.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503102|gb|EFD24266.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 412

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I   + ++  E   +   V +GE EA     +++EANLRLV+S+AKKY  RGL
Sbjct: 143 VRMYLREIGKISLLTPEEEVELAKRVEEGEEEAKK---KLIEANLRLVVSIAKKYIGRGL 199

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 200 SFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 259

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REPT EEIA+ L +P E V  + +I +EP+SLETPIG+E+ S L
Sbjct: 260 INKLIRVSRQLVQQLGREPTIEEIAQSLGLPPEKVEDIQRIAQEPVSLETPIGEEEDSQL 319

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+EDK + +P D+     LRE    +L  LT RE  VLR+RFG+     HTLEEVGK+
Sbjct: 320 GDFLEDKESPNPEDATAGQLLREQLEEMLGELTEREREVLRLRFGLEDGHAHTLEEVGKR 379

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+LR +L+
Sbjct: 380 FNVTRERIRQIEAKALRKLRHPSRSKRLRDYLE 412



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/176 (27%), Positives = 90/176 (51%), Gaps = 11/176 (6%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS-SEQMEDTVA 68
           D +S+  +  +S       ++ +++++  RQ+G++T ++L  +LP + +S ++ M++  +
Sbjct: 40  DQESQELEDMESHEMAELIENIRELLQEGRQKGFITYDDLEKYLPQEALSEADIMDNVYS 99

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L  +GI+V + D L++         +        V L++  D    S  DPVRMYLRE+
Sbjct: 100 NLLELGIDVKEEDKLQE---------IRQGELLPQVSLEELSDIESVSISDPVRMYLREI 150

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G I LL+ E E+ +AKR+E G       L E+ L     I  +  +  G + L  I
Sbjct: 151 GKISLLTPEEEVELAKRVEEGEEEAKKKLIEANLRLVVSIAKKY-IGRGLSFLDLI 205


>gi|239917829|ref|YP_002957387.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
 gi|281413678|ref|ZP_06245420.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family protein [Micrococcus
           luteus NCTC 2665]
 gi|239839036|gb|ACS30833.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
          Length = 497

 Score =  217 bits (551), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 140/283 (49%), Positives = 192/283 (67%), Gaps = 1/283 (0%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              EVD  ++I   + +  V    +  ++R     ++    +   AK  ++EANLRLV+S
Sbjct: 216 AEQEVDLAMRIEAGLYAEHVVQHEASDDYRER-RDIQLIIADGRKAKNHLLEANLRLVVS 274

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ T
Sbjct: 275 LAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQART 334

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R+M   + REPTPEE+AK+L M  E V +V K  +EPISL T
Sbjct: 335 IRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHT 394

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++  S  GD IED  AV P D+     L+E    VL +L+ RE  V+ MRFG+    
Sbjct: 395 PLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQ 454

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 455 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 497



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +S      ++     +T DPV+ YL+++G + LL+ E E+ +A RIEAG 
Sbjct: 180 DDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAMRIEAGL 230


>gi|51598964|ref|YP_073152.1| RNA polymerase sigma factor RpoD [Borrelia garinii PBi]
 gi|51573535|gb|AAU07560.1| RNA polymerase sigma-70 factor [Borrelia garinii PBi]
          Length = 631

 Score =  216 bits (550), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 175/643 (27%), Positives = 308/643 (47%), Gaps = 38/643 (5%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D  G+ED  D    + 
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDFICSILEDRGIILVNKISELDLVGTEDGNDEEEESE 81

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             S       D   +S                    E +I I  +++             
Sbjct: 82  IESDRNFMILDDGFQSD-------------------EEDIDIDGKLDDCD---------- 112

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
               +  I  +D+L  G      + D  +      K       +       ++    K+ 
Sbjct: 113 ----EEDISVKDDLGSGYIKSNALKDSHS--EDPIKLYLKEIGKEFLLTGNQEVELAKQM 166

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D  +    +I     +  ++   + +   +    E     ++D    +     ++ +   
Sbjct: 167 DSGESIIENILKNEGLVIENYYNLINTIYSRMEREEFFKREKDKDKESNPDYYNKKKRIA 226

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV--KLVGSLSLNQSRIDLL 338
                 +  +   L S  DN     +      +  +  E+L   +L+  + L Q  + + 
Sbjct: 227 SFYKIPLKPIQDRLISYVDNKHRVYELGGDIFEKNLKSERLALKELLRDVPLYQDELRIF 286

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +   D + +I   + +   +     I++   L    GR+L         +      ++ 
Sbjct: 287 SDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVL-GRDLTIAEKRIEIEKSLKLKEDA 345

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  ++      + E++ I +     + +   +   + KG+     AK ++++ANLRLV+S
Sbjct: 346 IKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEIAKGKQMMQHAKDQLIKANLRLVVS 405

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA WW++QAITRSI+DQ+ T
Sbjct: 406 IAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWWIRQAITRSISDQART 465

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++ V+ V  +++EP+SLET
Sbjct: 466 IRVPVHMIEQINRLNRETRYLVQVLGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLET 525

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG+E+ S L DFIEDK   +P +      L++    +L +L  RE+ V++MRFG+    
Sbjct: 526 PIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGY 585

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 586 SLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 628


>gi|269121540|ref|YP_003309717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
 gi|268615418|gb|ACZ09786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
          Length = 387

 Score =  216 bits (550), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 141/281 (50%), Positives = 201/281 (71%), Gaps = 3/281 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  +D    I+  ++ I     ++  E    +++ +K       AK++++E+NLRLV+S
Sbjct: 108 LAEIMDVDEPIKMYLREIGQIPLLTYEEE---IALAQKVLENDEEAKQKLIESNLRLVVS 164

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKK+TNRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW++QAITR+IADQ  T
Sbjct: 165 IAKKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRT 224

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ + +R +  +  +E T EE+AKKL +PV+ V+ +L++ ++PISLET
Sbjct: 225 IRIPVHMIETINKIKKESRIILQETGKEATAEELAKKLEIPVDKVKSILEMNQDPISLET 284

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G E+ S LGDF+ED   ++P D+  +  L+E    VL +L+ REE VLR R+G+   +
Sbjct: 285 PVGSEEDSELGDFVEDDKFLNPYDATTRVLLKEQLDGVLKTLSEREEMVLRYRYGLDDGS 344

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  +
Sbjct: 345 PKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRKKLEDY 385



 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 50/205 (24%), Positives = 85/205 (41%), Gaps = 27/205 (13%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-------- 79
            D   +++K A++ G ++ EE+N  +P D    E+++  +  + + GI++VD        
Sbjct: 9   KDKLLELVKQAKEDGVISYEEINGVIPED-FPVEKIDQLIRGIEDKGISIVDTLVEKKDY 67

Query: 80  ---------GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                        E EE   +  ++  +  N  +     K +     D+P++MYLRE+G 
Sbjct: 68  MESNSTKKSAKIPEIEEEEFNEEEIDETEVNELLHTDLIKLAEIMDVDEPIKMYLREIGQ 127

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           I LL+ E EIA+A+++          L ES L     I  +   N G  +L  I      
Sbjct: 128 IPLLTYEEEIALAQKVLENDEEAKQKLIESNLRLVVSIAKK-HTNRGLKMLDLI------ 180

Query: 191 IGPESKGGFFHGTEGHSYQKREDSS 215
              E   G     E   Y+K    S
Sbjct: 181 --QEGNMGLMKAVEKFEYEKGFKFS 203


>gi|308233952|ref|ZP_07664689.1| RNA polymerase, sigma 70 subunit, RpoD [Atopobium vaginae DSM
           15829]
 gi|328943964|ref|ZP_08241429.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
 gi|327491933|gb|EGF23707.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
          Length = 441

 Score =  216 bits (550), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 186/253 (73%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     + + E     AK+ +  ANLRL +S+AK+Y  RG+ FLDLIQEGN+GL++A EK
Sbjct: 187 RAEQRRLMRIEQVGLDAKQALTSANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEK 246

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  + +   + REP
Sbjct: 247 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQKELLQDLGREP 306

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEEI +++ M  + VR++ KI++EP+SLETPIG+E+ S LGDFIED  AV+P D+A  +
Sbjct: 307 TPEEIGEQMKMSADRVREIQKISQEPVSLETPIGEEEDSSLGDFIEDSTAVAPPDAASDS 366

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE   +VL  L  RE +V++ RFG+      TLEEVG++F VTRERIRQIE+K + KL
Sbjct: 367 MLREQLNQVLDGLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKL 426

Query: 668 KHPSRSKKLRSFL 680
           +HPSRS +L+ ++
Sbjct: 427 RHPSRSGRLKDYI 439



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 36/181 (19%), Positives = 67/181 (37%), Gaps = 30/181 (16%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
            E + D  + +       K+   A   G  ++ +E+   L   +  ++++ D    L   
Sbjct: 4   QESNQDVQLSEELQSIVDKLSSQANTAGNKLSEDEIQIALSDFDTDADELSDVYQALRAQ 63

Query: 74  GI----NVVDGDDLEDEEGSEDSLDLA-------------------------SSASNSSV 104
            I    +VV+ DD +  +      D                           S+  +S  
Sbjct: 64  HITITADVVNLDDDDLLDDDLKDDDEEDPDLAAARAETRAATEILRAATKKRSNKRSSRA 123

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
             ++   SA   T DPVRMYL+E+G ++LL+   E+ +A +I+AG               
Sbjct: 124 RTRRIDSSAVMLTGDPVRMYLKEIGKVDLLNASEEVHLAMKIQAGTDASKKLEAAENGEI 183

Query: 165 Q 165
           +
Sbjct: 184 E 184


>gi|133468|sp|P27785|RPOD_STRAU RecName: Full=RNA polymerase sigma factor rpoD
          Length = 317

 Score =  216 bits (550), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 125/296 (42%), Positives = 186/296 (62%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 22  RQYLREIGRIPLLTAAEEVDLARRVEAGLFAEEKLGGAADLDSQLAVDLDRLVVMGRMAK 81

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 82  RRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 141

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E V +
Sbjct: 142 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTAEEVAVHLELTPERVLE 201

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA      E    VL++L  RE 
Sbjct: 202 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFFLRCEHLEAVLSTLGERER 261

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 262 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 317



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 25/44 (56%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +  +      + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 7   RGAESGGAGPSADLFRQYLREIGRIPLLTAAEEVDLARRVEAGL 50


>gi|299535819|ref|ZP_07049140.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
 gi|298729019|gb|EFI69573.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
          Length = 375

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 152/273 (55%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEQEIALAERIEQ---GDEEARKRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDSEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 45/158 (28%), Positives = 76/158 (48%), Gaps = 8/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM-GINVVDGDDLEDE 86
           DD+ K + + A+  G ++++E++  L P E+ +E++      L     I ++  ++ E+E
Sbjct: 18  DDAKKFLQEKAKTEGEISMKEISEKLTPYELENEEIFHFAEDLEKHKDIQIIGKEEFEEE 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                   +   A+  +  L           +DPVRMYL+E+G ++LLS E EIA+A+RI
Sbjct: 78  SL------MKEEANEETFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEQEIALAERI 131

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 132 EQGDEEARKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|111023771|ref|YP_706743.1| RNA polymerase sigma factor SigB [Rhodococcus jostii RHA1]
 gi|110823301|gb|ABG98585.1| sigma factor, sigma 70 type, group 2 (proven non-essential)
           [Rhodococcus jostii RHA1]
          Length = 323

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 113/266 (42%), Positives = 184/266 (69%), Gaps = 4/266 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +S ++ R + ++VR    E   A+  ++EANLRLV+S+AK+YT RG+  LDL
Sbjct: 60  HILETGKRLSPAKKRDLATVVR----EGQSARAHLLEANLRLVVSLAKRYTGRGMPLLDL 115

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ 
Sbjct: 116 IQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLA 175

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIE
Sbjct: 176 RIKRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIE 235

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK F ++R
Sbjct: 236 DSEATSAENAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSR 295

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ER+RQIE + + KL+   R+++LRS+
Sbjct: 296 ERVRQIEREVMGKLRQGDRAERLRSY 321



 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + S ++ + +        A     D VR+YL  +G   LL+   E+ ++KRIEAG    
Sbjct: 1   MTSPSTTTRIRPSAADLDAQSPAADLVRVYLNGIGRTALLTAADEVELSKRIEAGLYAA 59


>gi|154484558|ref|ZP_02027006.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
 gi|149734406|gb|EDM50323.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
          Length = 429

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 129/274 (47%), Positives = 190/274 (69%), Gaps = 3/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +    ++      +AK++++EANLRLV+S+AK+YT RG+
Sbjct: 159 VRMYLKEIGTVPLLTADEELELA---KRKTEGDIVAKEKLIEANLRLVVSIAKRYTGRGM 215

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++AD + TIR+PVHM + 
Sbjct: 216 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADHARTIRVPVHMVET 275

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+++ +  R+++ ++  EP+ +E+A  L M  E V ++++I +EP SLETPIG+ED S+L
Sbjct: 276 INRMSKMQRKLTLELGYEPSTKELATALDMTEEKVLEIMQIAREPASLETPIGEEDDSNL 335

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE  V+ +RFG+      TLEEVGK 
Sbjct: 336 GDFVADNNTVTPEANIESVMLREHIDVLLQDLKDREREVIILRFGLRDGHPRTLEEVGKI 395

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKL++P RSKK++ FL+ 
Sbjct: 396 FNVTRERIRQIEAKALRKLRNPVRSKKIKDFLNN 429



 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 78/385 (20%), Positives = 135/385 (35%), Gaps = 65/385 (16%)

Query: 29  DSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV--------- 78
               ++I+LA ++   +TI E+  F   D+++ +Q  D V  L+   IN+          
Sbjct: 22  QKVAELIELAHKKEDRLTINEVQDFFKDDDLTEKQKTDVVTELTGKKINITMEVDVNEPK 81

Query: 79  ---------DGDDLEDEEGSEDSLDLASSASNSS-------------------------- 103
                    D  D +  E  E ++DL +  ++                            
Sbjct: 82  APKADSAKSDDADNDFPEDGEATVDLVAEPTDEDIAMVAADEGDLLEPTDENFENDEEET 141

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           V            T+DPVRMYL+E+G++ LL+ + E+ +AKR   G  +    L E+ L 
Sbjct: 142 VEFDAVDLLEGVGTEDPVRMYLKEIGTVPLLTADEELELAKRKTEGDIVAKEKLIEANLR 201

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
               I  R     G + L  +         E   G   G E   Y K    S        
Sbjct: 202 LVVSIAKRY-TGRGMSFLDLV--------QEGNLGLIKGVEKFDYTKGYKLSTYATWWIR 252

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAE-NDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
           Q     +   A+  +     V++    ++   +  L+   + S   L+   D    KV+ 
Sbjct: 253 QSVTRALADHARTIRVPVHMVETINRMSKMQRKLTLELGYEPSTKELATALDMTEEKVL- 311

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
              EI ++ RE  SL+                          + S+ L +  ID+L++ L
Sbjct: 312 ---EIMQIAREPASLETPIGEEDDSNLGDFVADNNTVTPEANIESVMLRE-HIDVLLQDL 367

Query: 343 YDISKRIMHNEGELLRLAQSYGIKR 367
            D  + ++     +LR     G  R
Sbjct: 368 KDREREVI-----ILRFGLRDGHPR 387


>gi|327539483|gb|EGF26098.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 562

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 160/525 (30%), Positives = 259/525 (49%), Gaps = 35/525 (6%)

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           E  +G +            +       S+   ++       +IES A   +D  S+ D  
Sbjct: 31  ETLMGKKLSRRSLQDDAFDAEDSVNRRSRTMGQEFSDSISEEIESGAAGDEDVVSRRDEF 90

Query: 248 PENAENDERNL------------DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           P +   D   +             + E  +A  + A  ++ R  +M     +    + L+
Sbjct: 91  PTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQIEATRERYRHCMMATDFMLQAALKLLQ 150

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD----------I 345
            ++D  +   +  + SV     K+ ++K +     N   +D L+ Q              
Sbjct: 151 QVRDKQLRLDRTIEVSVTNAAEKKAIMKRIVP---NTRTLDYLLRQNRGDYMVAINSSLP 207

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP--HWVSYAKDFPEGEWKNFVACEV 403
            +R       L  + +     R V     +  +L P    +  + +  +           
Sbjct: 208 MRRRRAAWRNL--VIRRNKAVRLVEEMNLRTNKLQPIFEKLRRSCERMQEIKAILADAHR 265

Query: 404 DSI------LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++       ++R+E++S+   T  +       V        +   AK+ +   NLRLV+
Sbjct: 266 STMPGMPSGDELRSELRSLMRLTYETPRTLSRRVDRCDTYRDDYDAAKRVLSAGNLRLVV 325

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKY NRGL FLDLIQEGN GLM+A +KF+   GYKFSTYA WW++QAITR+IADQS 
Sbjct: 326 SIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWWIRQAITRAIADQSR 385

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM D ++K+ +  R +  +  REPT EE++K+  + ++  R +LK++++P+SL+
Sbjct: 386 TIRVPVHMIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDTRVILKMSRQPLSLD 445

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+GD D S  G+F++D     PL    +  L+      + +L  RE  +LR+R+G+   
Sbjct: 446 QPVGDHDDSVFGEFLQDHRDDDPLVETNREALKHQIDLAMETLNYREREILRLRYGLADG 505

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             +TLEEVG+ F VTRER+RQIE+KA+RKL+ P R+K L SFLDG
Sbjct: 506 YTYTLEEVGRIFQVTRERVRQIESKAVRKLQQPYRAKSLVSFLDG 550



 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 33/112 (29%), Positives = 53/112 (47%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E     S ++ S A+     + +R +     T+DPVRMYL +MG I LL+R+ E+A A++
Sbjct: 64  EFSDSISEEIESGAAGDEDVVSRRDEFPTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQ 123

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           IEA R      +  +    QA +    ++ D    L   I++      E K 
Sbjct: 124 IEATRERYRHCMMATDFMLQAALKLLQQVRDKQLRLDRTIEVSVTNAAEKKA 175


>gi|118469122|ref|YP_887090.1| RNA polymerase sigma factor [Mycobacterium smegmatis str. MC2 155]
 gi|555680|gb|AAA85642.1| sigma factor MysA [Mycobacterium smegmatis]
 gi|118170409|gb|ABK71305.1| sigma factor MysA [Mycobacterium smegmatis str. MC2 155]
          Length = 466

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 134/290 (46%), Positives = 195/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L    ++  +      + + + R     ++    +   AK  ++EA
Sbjct: 181 AEEEVELAKRIEAGLYATQKLAELAEKGEKLPVQQRRD----MQWICRDGDRAKNHLLEA 236

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 237 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRA 296

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +
Sbjct: 297 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAR 356

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+R
Sbjct: 357 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLR 416

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 417 FGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 466



 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/81 (37%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D D  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 124 DDDIDEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 183

Query: 139 EIAIAKRIEAGRAMMMASLCE 159
           E+ +AKRIEAG       L E
Sbjct: 184 EVELAKRIEAGLY-ATQKLAE 203


>gi|297191610|ref|ZP_06909008.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297151002|gb|EFH30922.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 516

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 264 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 323

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 324 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 383

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 384 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 443

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 444 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 503

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 504 HPSRSQVLRDYLD 516



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/111 (27%), Positives = 46/111 (41%), Gaps = 10/111 (9%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD---------RSTDDPVRMYLREMG 129
           +G++L DE       D       S  F+    D  D          +T DPV+ YL+++G
Sbjct: 169 EGEELLDEVQPAGKGDEEEPEGESKGFVLSDDDEDDAPAQQVAVAGATADPVKDYLKQIG 228

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 229 KVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 278


>gi|226366207|ref|YP_002783990.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|226244697|dbj|BAH55045.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|254553060|dbj|BAH85842.1| RNA polymerase sigma B factor [Rhodococcus opacus]
          Length = 323

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 113/266 (42%), Positives = 184/266 (69%), Gaps = 4/266 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +S ++ R + ++VR    E   A+  ++EANLRLV+S+AK+YT RG+  LDL
Sbjct: 60  HILETGKRLSPAKKRDLATVVR----EGQSARAHLLEANLRLVVSLAKRYTGRGMPLLDL 115

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ 
Sbjct: 116 IQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLA 175

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIE
Sbjct: 176 RIKRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIE 235

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK F ++R
Sbjct: 236 DSEATSAENAVIAGLLHSDVRTVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSR 295

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ER+RQIE + + KL+   R+++LRS+
Sbjct: 296 ERVRQIEREVMGKLRQGDRAERLRSY 321



 Score = 41.0 bits (94), Expect = 0.69,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 28/59 (47%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + S ++ + +        A     D VR+YL  +G   LL+   E+ ++KRIEAG    
Sbjct: 1   MTSPSTTTRIRPSAADLDAQSPAADLVRVYLNGIGRTALLTAADEVELSKRIEAGLYAA 59


>gi|54025745|ref|YP_119987.1| RNA polymerase sigma factor SigB [Nocardia farcinica IFM 10152]
 gi|54017253|dbj|BAD58623.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 322

 Score =  216 bits (550), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 114/264 (43%), Positives = 182/264 (68%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     +S ++ + +  +VR    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 61  LETSKRLSAAKKKDLAMIVR----DGQAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 116

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 117 EGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 176

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T EE+A +  +PVE +  +L  +++P+SL+ P+G+++ + LGDFIED 
Sbjct: 177 KRELHQQLGREATDEELAAESGIPVEKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDS 236

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A S   + I   L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER
Sbjct: 237 EATSAESAVIAGLLHHDVRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRER 296

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R+ +LR++
Sbjct: 297 VRQIEREVMAKLRKGERADRLRAY 320



 Score = 42.5 bits (98), Expect = 0.25,   Method: Composition-based stats.
 Identities = 19/54 (35%), Positives = 27/54 (50%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +S + + V        A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 2   TSPATTRVRASDSDLDAQSPAADLVRVYLNGIGRTALLTAADEVELAKRIEAGL 55


>gi|319949012|ref|ZP_08023109.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
 gi|319437300|gb|EFV92323.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
          Length = 460

 Score =  216 bits (550), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 135/301 (44%), Positives = 190/301 (63%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV----------------------------RKGECE 440
           +R  +K I     ++  E   +   +                            +  E +
Sbjct: 160 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATWYMAQVTERGEKLTTAQRRDFKWIERD 219

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 220 GVRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 279

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 280 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 339

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 340 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLRSVLDTL 399

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 400 SEREAGVVRLRFGLTDGLPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 459

Query: 681 D 681
           D
Sbjct: 460 D 460



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/100 (29%), Positives = 45/100 (45%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
             L  +  +SE  +  V +         +    E     + S D       S    Q RK
Sbjct: 90  DALEVEPDTSELEDVEVDVEDVEDEQADEETKEEPSAKDKASGDFVWDEDESEALRQARK 149

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 150 DAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGL 189


>gi|315652381|ref|ZP_07905370.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
 gi|315485355|gb|EFU75748.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
          Length = 410

 Score =  216 bits (550), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 129/272 (47%), Positives = 191/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++ +E   +    ++ +     AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 141 VRMYLKEIGTVPLLTANEELELA---KRKQDGDEYAKQRLIEANLRLVVSIAKRYTGRGM 197

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  G+K STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 198 SFLDLVQEGNLGLIKGVEKFDYTKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 257

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A  L M  E V ++++I +EP SLETPIG+ED S+L
Sbjct: 258 INKMSKMQRKLTLELGYEPSVTELANALDMTEEKVMEIMQIAREPASLETPIGEEDDSNL 317

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N ++P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 318 GDFVADSNVLTPEGNVESVMLREHIDTLLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 377

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 378 FKVTRERIRQIEAKALRKLRNPVRSKRIRDFL 409



 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/218 (22%), Positives = 79/218 (36%), Gaps = 23/218 (10%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMED 65
            N+ S S    +   +         + ++         + I E+N F    E++S+ +E 
Sbjct: 13  ENKASKSMESANKKKMSPQEFLQKLEDLVNKGIASDMKLNIGEINDFFAGIELNSDSIEQ 72

Query: 66  TVAMLSNMGINVVDGD-------------DLEDEEGSEDSLDLASSASNSSVFLQKRKDS 112
             + L N GI + +                 +++    D  D     S   + L      
Sbjct: 73  IYSYLENKGIEINENSSDDLNIDIDNIDNITDEDSLLLDDEDEFDKDSEEDIDLSAIDLL 132

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
               T+DPVRMYL+E+G++ LL+   E+ +AKR + G       L E+ L     I  R 
Sbjct: 133 EGVGTEDPVRMYLKEIGTVPLLTANEELELAKRKQDGDEYAKQRLIEANLRLVVSIAKRY 192

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
               G + L  +         E   G   G E   Y K
Sbjct: 193 -TGRGMSFLDLV--------QEGNLGLIKGVEKFDYTK 221


>gi|293376344|ref|ZP_06622581.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325843397|ref|ZP_08167955.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645033|gb|EFF63106.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489319|gb|EGC91693.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 456

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 147/250 (58%), Positives = 197/250 (78%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              R+   E   AKK +VEANLRLV+S+AK++  RG+ FLDLIQEGN+GL+KA EKFD+ 
Sbjct: 206 EEARRVIQEGEYAKKRLVEANLRLVVSIAKRHVGRGMLFLDLIQEGNMGLIKAVEKFDYR 265

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP PEE
Sbjct: 266 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQELGREPLPEE 325

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           I++K+ +  E VR++LKI++EP+SLE+P+G+ED SHLGDFI D +A+SP + A    L++
Sbjct: 326 ISEKMGIAPEKVREILKISQEPVSLESPVGEEDDSHLGDFIPDADALSPSEFASNEMLKK 385

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +LT REERVLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPS
Sbjct: 386 ELDDVLETLTDREERVLRLRFGLEDGRTRTLEEVGKEFGVTRERIRQIEAKALRKLRHPS 445

Query: 672 RSKKLRSFLD 681
           RS++L+ F++
Sbjct: 446 RSRRLKDFME 455



 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 33/141 (23%), Positives = 65/141 (46%), Gaps = 23/141 (16%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++IKL ++RGY+T +E+N      ++  E +   + +  + GI++V  + + +     ++
Sbjct: 17  QLIKLGKKRGYLTYDEINNSFEQVQLDPEMISSFLDLYDSEGISIVKSEKIVETPEVGET 76

Query: 93  LDLA-----------------------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            +                             +      + + ++    +DPVRMYL+E+G
Sbjct: 77  EEEDTVLLLPDFDADEDEDNIPANFSTEDEVDLEEKFDEFEFTSQFKINDPVRMYLKEIG 136

Query: 130 SIELLSREGEIAIAKRIEAGR 150
            +ELLS + EI  AK+IE G 
Sbjct: 137 RVELLSSQEEINFAKKIERGD 157


>gi|227542254|ref|ZP_03972303.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227182083|gb|EEI63055.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 603

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 128/248 (51%), Positives = 180/248 (72%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G
Sbjct: 356 LRTVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 415

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+A
Sbjct: 416 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELA 475

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++  
Sbjct: 476 KEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQL 535

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS
Sbjct: 536 QDVLKTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 595

Query: 674 KKLRSFLD 681
           + LR +L+
Sbjct: 596 QVLRDYLE 603



 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 275 DEEESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 327


>gi|302335781|ref|YP_003800988.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
 gi|301319621|gb|ADK68108.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
          Length = 453

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 134/254 (52%), Positives = 190/254 (74%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     + + E     AK+ ++ ANLRL +S+AK+Y  RG+ FLDLIQEGN+GL++A EK
Sbjct: 199 RAEQRRLMRIEQVGLEAKQALISANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEK 258

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P
Sbjct: 259 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVQRQLLQDLGRDP 318

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEEI  ++ +  + VR++ KI++EP+SLETPIG+E+ S LGDFIED +AV+P ++A  +
Sbjct: 319 TPEEIGAEMGISADRVREIQKISQEPVSLETPIGEEEDSSLGDFIEDSSAVAPPEAASDS 378

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE   +VL SL  RE +V++ RFG+      TLEEVG++F VTRERIRQIE+K + KL
Sbjct: 379 MLREQLEQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKL 438

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS +L+ +++
Sbjct: 439 RHPSRSGRLKDYME 452



 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/150 (19%), Positives = 56/150 (37%), Gaps = 41/150 (27%)

Query: 44  VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
           +T +++   +   +V  +++ D    +   G+++V   + +     +D   L +  ++  
Sbjct: 34  ITEDDIQVAIAEMDVDDDELSDIYEAVRARGVSIVASGESQPVSAVDDEDGLDALEADGK 93

Query: 104 VFLQ-----------------------------------------KRKDSADRSTDDPVR 122
             L                                          K   SA   T DPVR
Sbjct: 94  AALDDEDDEDDEISKARKEARVANEVLRSVPKPKGRKRSSRARAHKLDSSAVMLTGDPVR 153

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           MYL+E+G ++LL+   E+ +A +IEAG   
Sbjct: 154 MYLKEIGKVDLLTASEEVHLAMKIEAGTEA 183


>gi|256784755|ref|ZP_05523186.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 492

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 240 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 299

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 300 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 359

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 360 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 419

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 420 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 479

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 480 HPSRSQVLRDYLD 492



 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +      EE           +         ++ +A  +T DPV+ YL+++G + LL+ E 
Sbjct: 154 EEPKAATEEPEGTENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQ 213

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 214 EVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 254


>gi|296454312|ref|YP_003661455.1| RpoD family RNA polymerase sigma-70 factor [Bifidobacterium longum
           subsp. longum JDM301]
 gi|296183743|gb|ADH00625.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. longum JDM301]
          Length = 474

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EF+     ++    +   AK  ++EANLRLV+
Sbjct: 191 AEQEVDLSERIEAGLYAQHLLDTESEGMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 249

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 250 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 309

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 310 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 369

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 370 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 429

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 430 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 473



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             +   E+G+    D      N       KR+  A  +T DPV+ YL+++G + LL+ E 
Sbjct: 134 APEQPKEKGAYVVSDTDDEEENIIPSGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQ 193

Query: 139 EIAIAKRIEAGR 150
           E+ +++RIEAG 
Sbjct: 194 EVDLSERIEAGL 205


>gi|32474487|ref|NP_867481.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32445025|emb|CAD75027.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 568

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 160/525 (30%), Positives = 259/525 (49%), Gaps = 35/525 (6%)

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           E  +G +            +       S+   ++       +IES A   +D  S+ D  
Sbjct: 37  ETLMGKKLSRRSLQDDAFDAEDSVNRRSRTMGQEFSDSISEEIESGAAGDEDVVSRRDEF 96

Query: 248 PENAENDERNL------------DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           P +   D   +             + E  +A  + A  ++ R  +M     +    + L+
Sbjct: 97  PTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQIEATRERYRHCMMATDFMLQAALKLLQ 156

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD----------I 345
            ++D  +   +  + SV     K+ ++K +     N   +D L+ Q              
Sbjct: 157 QVRDKQLRLDRTIEVSVTNAAEKKAIMKRIVP---NTRTLDYLLRQNRGDYMVAINSSLP 213

Query: 346 SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP--HWVSYAKDFPEGEWKNFVACEV 403
            +R       L  + +     R V     +  +L P    +  + +  +           
Sbjct: 214 MRRRRAAWRNL--VIRRNKAVRLVEEMNLRTNKLQPIFEKLRRSCERMQEIKAILADAHR 271

Query: 404 DSI------LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++       ++R+E++S+   T  +       V        +   AK+ +   NLRLV+
Sbjct: 272 STMPGMPSGDELRSELRSLMRLTYETPRTLSRRVDRCDTYRDDYDAAKRVLSAGNLRLVV 331

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKY NRGL FLDLIQEGN GLM+A +KF+   GYKFSTYA WW++QAITR+IADQS 
Sbjct: 332 SIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWWIRQAITRAIADQSR 391

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM D ++K+ +  R +  +  REPT EE++K+  + ++  R +LK++++P+SL+
Sbjct: 392 TIRVPVHMIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDTRVILKMSRQPLSLD 451

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+GD D S  G+F++D     PL    +  L+      + +L  RE  +LR+R+G+   
Sbjct: 452 QPVGDHDDSVFGEFLQDHRDDDPLVETNREALKHQIDLAMETLNYREREILRLRYGLADG 511

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             +TLEEVG+ F VTRER+RQIE+KA+RKL+ P R+K L SFLDG
Sbjct: 512 YTYTLEEVGRIFQVTRERVRQIESKAVRKLQQPYRAKSLVSFLDG 556



 Score = 81.0 bits (198), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 33/112 (29%), Positives = 53/112 (47%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E     S ++ S A+     + +R +     T+DPVRMYL +MG I LL+R+ E+A A++
Sbjct: 70  EFSDSISEEIESGAAGDEDVVSRRDEFPTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQ 129

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           IEA R      +  +    QA +    ++ D    L   I++      E K 
Sbjct: 130 IEATRERYRHCMMATDFMLQAALKLLQQVRDKQLRLDRTIEVSVTNAAEKKA 181


>gi|320161271|ref|YP_004174495.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319995124|dbj|BAJ63895.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 409

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 131/303 (43%), Positives = 195/303 (64%), Gaps = 23/303 (7%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMV-----------------------RKG 437
             +D+   I   +K +S    ++  E   +   +                       R+ 
Sbjct: 105 ANIDTDDTIGLYLKEVSRVPLLTAEEEVELAQRIERGRMAREELARGNVSPKRRQELRRL 164

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             +   A++ ++ AN RLVISVAKKY  RG+ FLDLIQEGNIGL++A +KFD+  G+KFS
Sbjct: 165 IEDGWAAREHLITANSRLVISVAKKYMGRGVPFLDLIQEGNIGLIRATKKFDYRRGHKFS 224

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QA+TR+IADQ  TIR+PVHM D+I+K++R   +++ ++ REP+ EE+A+ L 
Sbjct: 225 TYATWWIRQAVTRAIADQGRTIRVPVHMGDQINKLLRVQHQLTQRLGREPSVEELAEALD 284

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +P   V  ++++ + P+SLETP  DE+ S LGDFIED+ A  P D+A    LR+    VL
Sbjct: 285 VPPRKVENMIQVARRPLSLETPTDDEEDSVLGDFIEDEEAPPPDDTATYNLLRQHLEEVL 344

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L PRE R+L++R+G+     +TLEEVG++  VTRER+RQIEA+A+ +L+HPS  +KLR
Sbjct: 345 NTLPPREVRILQLRYGLLDGQAYTLEEVGRKMGVTRERVRQIEAQALSRLRHPSIRRKLR 404

Query: 678 SFL 680
            +L
Sbjct: 405 DYL 407



 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 44/154 (28%), Positives = 73/154 (47%), Gaps = 2/154 (1%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D       ++I L RQ+ YVTI+++  F P  E   EQ+E+  A L + GI  ++ + +E
Sbjct: 16  DEEYPVIARLIDLGRQKSYVTIDDILHFFPEAEQDVEQLEEAFAALMSAGIPYLEDEIVE 75

Query: 85  DEEGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +    E       +             D A+  TDD + +YL+E+  + LL+ E E+ +A
Sbjct: 76  EPAEEELEAHEEGAVEEEGEEKSLALDDLANIDTDDTIGLYLKEVSRVPLLTAEEEVELA 135

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +RIE GR M    L    ++ +     R  + DG
Sbjct: 136 QRIERGR-MAREELARGNVSPKRRQELRRLIEDG 168


>gi|328882302|emb|CCA55541.1| RNA polymerase principal sigma factor HrdA [Streptomyces venezuelae
           ATCC 10712]
          Length = 336

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 126/296 (42%), Positives = 188/296 (63%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++  E   +   V                         +      IAK
Sbjct: 41  RQYLREIGRIPLLTAEEEVDLARRVEAGLFAEEKLANTPDLDSRLASDLDRLVVLGRIAK 100

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++++EANLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 101 RKLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 160

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++V+R  RRM  +   EPT EE+A +L +  E V +
Sbjct: 161 QAMSRALADQARTIRVPVHVVELINRVIRVQRRMLQERGYEPTAEEVAAQLDLAPERVGE 220

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+E+   LGD IED +A SP++SA    LR     VL++L  RE 
Sbjct: 221 VLRLAQEPVSLHAPVGEEEDVALGDLIEDGDAASPVESAAFLLLRRHLEDVLSTLGERER 280

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 281 KVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLGKLRDHAYADQLRGYLD 336



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E                ++     +  + D  R YLRE+G I LL+ E E+ +A+R+EAG
Sbjct: 9   EPPAAAPDEQPEIPPQRRRPDLGGNGPSSDLFRQYLREIGRIPLLTAEEEVDLARRVEAG 68

Query: 150 RAMMMASLCESPLTFQALIIWRDE-LNDGTTLLREIID 186
                  L  +P     L    D  +  G    R++I+
Sbjct: 69  LF-AEEKLANTPDLDSRLASDLDRLVVLGRIAKRKLIE 105


>gi|118465794|ref|YP_882772.1| RNA polymerase sigma factor [Mycobacterium avium 104]
 gi|254776035|ref|ZP_05217551.1| RNA polymerase sigma factor [Mycobacterium avium subsp. avium ATCC
           25291]
 gi|118167081|gb|ABK67978.1| sigma factor MysA [Mycobacterium avium 104]
          Length = 496

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 159/494 (32%), Positives = 249/494 (50%), Gaps = 36/494 (7%)

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           ++  G  ++      +       +  S +  +       + D        +D  ++ D  
Sbjct: 39  KSEAGAAAEPAKKTRSSAKGADAKAPSGRGTKAAKGGPADPDALDTDGAVEDLDTEPDLE 98

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            E  E+ + + D + DD    ++A +  + P      ++      +         + +  
Sbjct: 99  GEPGEDLDIDTDLNLDDLEEDVAADDADIEPGDAEEGEDEEAAAPKAAGATAADEDDEIA 158

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           E S  K K   + +     S +L Q+R D    +L   +  +     ++ ++A       
Sbjct: 159 EPSE-KDKASGDFVWDEDESEALRQARKD---AELTASADSVRAYLKQIGKVALLNA--- 211

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                           V  AK    G +   +  E                   +  ++ 
Sbjct: 212 -------------EEEVELAKRIEAGLYATQLMSE------------MAERGEKLPAAQR 246

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 247 RD----MMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 302

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 303 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 362

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+    
Sbjct: 363 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFT 422

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 423 LLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 482

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 483 RHPSRSQVLRDYLD 496



 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 154 DDEIAEPSEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 213

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M+ + E
Sbjct: 214 EVELAKRIEAGLYATQLMSEMAE 236


>gi|291457726|ref|ZP_06597116.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
 gi|291380779|gb|EFE88297.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
          Length = 472

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 139/284 (48%), Positives = 200/284 (70%), Gaps = 2/284 (0%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T     EF+     ++    +   AK  ++EANLRLV+
Sbjct: 189 AEQEVDLSERIEAGLYAQHLLDTESEGMEFKR-KRELKWAAADGKKAKDHLLEANLRLVV 247

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+ FLDLIQEGN+GL++A EKFDW  G+KFSTYA WW++QAITR++ADQ+ 
Sbjct: 248 SLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQAR 307

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R  R+M   + REPTP+E+A++L MPVE V++V K  +EPISL 
Sbjct: 308 TIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLH 367

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TP+G++  S  GD IED +A++P D+   + L+E   +VL +L+PRE  V++MR+G+   
Sbjct: 368 TPLGEDGDSEFGDLIEDTDAIAPSDAVAFSLLQEQFKQVLETLSPREAGVIKMRYGLEDG 427

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL+++G+ + VTRERIRQIE+K + KL+HPSRS+ LR FLD
Sbjct: 428 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQTLRDFLD 471



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNS-SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             +   E+G+    D      N       KR+  A  +T DPV+ YL+++G + LL+ E 
Sbjct: 132 APEQPKEKGAYVVSDTDDEEENIIPAGNPKRRVIAAGATADPVKDYLKQIGRVSLLNAEQ 191

Query: 139 EIAIAKRIEAGR 150
           E+ +++RIEAG 
Sbjct: 192 EVDLSERIEAGL 203


>gi|238927759|ref|ZP_04659519.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
 gi|238884475|gb|EEQ48113.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
          Length = 382

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 145/274 (52%), Positives = 197/274 (71%), Gaps = 3/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V + R+ E     A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 112 VRMYLKEIGRVPLLTAEEE---VELARRMEAGDEAARHRLEEANLRLVVSIAKRYAGRGM 168

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 169 MFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 228

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K +R +R++  ++ R+PTPEEIA ++ + V  VR+++KI++EP+SLETPIG+E+ + L
Sbjct: 229 INKYIRISRQLLQELGRDPTPEEIAHRMGLSVARVREIMKISQEPVSLETPIGEEEDTRL 288

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DFIED+ A  P D+A    L+E  + VL +L PRE  VLR+RFG+      TLEEVG+ 
Sbjct: 289 SDFIEDEAAPDPADAASMLLLKEQISEVLTTLAPREAEVLRLRFGLVDGRSRTLEEVGQN 348

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIEAKA+RKL+HP R +KL+   D 
Sbjct: 349 FGVTRERIRQIEAKALRKLRHPVRLRKLQGNFDS 382



 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 68/157 (43%), Gaps = 4/157 (2%)

Query: 31  WKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
             +++K  +  G  +T  EL   L  + V+ + M++         I +VD  D+  +E  
Sbjct: 19  ITQLMKRGKGNGGTLTCSELMEALVQEGVTPDAMDELYQHCMEENIEIVDDADVGADEEL 78

Query: 90  EDSLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            D  D+       +        S     + DDPVRMYL+E+G + LL+ E E+ +A+R+E
Sbjct: 79  SDFTDIEDKDETDADVDVDTVLSVPEGVALDDPVRMYLKEIGRVPLLTAEEEVELARRME 138

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AG       L E+ L     I  R     G   L  I
Sbjct: 139 AGDEAARHRLEEANLRLVVSIAKRYA-GRGMMFLDLI 174


>gi|240142885|ref|YP_002967398.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
 gi|240012832|gb|ACS44057.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
          Length = 531

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 137/353 (38%), Positives = 203/353 (57%), Gaps = 2/353 (0%)

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
            L   RID LV  L      +M     L R+ +  G      +    G   D    + A 
Sbjct: 178 KLATDRIDDLVASLEAPGAALMAAARVLGRILEKRGGLAADLVPVLDG--TDAVADAVAS 235

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                           + L     +  +++  G S+  FR +   VR    +   A+  +
Sbjct: 236 GEGPFALSPAEGEAEGAALAAARAVDEVAIPFGGSVRRFRLVQREVRAAHGDLRKARDTL 295

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V +NLRLV SVAKKYTNR L  LDL+QEGNIGLM+A EKFD+  G+KFSTYA+WW+KQ+I
Sbjct: 296 VTSNLRLVFSVAKKYTNRPLPILDLVQEGNIGLMRAIEKFDYRRGWKFSTYAIWWIKQSI 355

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +RSIAD   TIR+PVH+ +K  K+ RTA R+  ++ R P+P E+A+ L + V  V +++ 
Sbjct: 356 SRSIADHGRTIRLPVHLHEKAAKIDRTAARLRAELGRPPSPPELAQALDIDVRQVERLMN 415

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +++E +SL+ P+G++     GD +ED+ A  P+  A  A L++  +  +  L  RE+ ++
Sbjct: 416 MSRETVSLDLPVGEDGDVRFGDLVEDEKAPDPVGLADLAKLKDAVSDAVGDLPEREQTII 475

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGIG     TLEE+G+ F ++RER+RQ+E+KAI++L+ P     LR FLD
Sbjct: 476 RMRFGIGYADQMTLEEIGQHFRISRERVRQVESKAIQRLRSPEIGAYLRKFLD 528



 Score = 44.4 bits (103), Expect = 0.063,   Method: Composition-based stats.
 Identities = 21/74 (28%), Positives = 32/74 (43%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
                    +  D +  Y RE+G   +L+RE E+A+AKR+EA R  + AS        + 
Sbjct: 46  ASEPTRGPEAVPDALSFYAREIGRHRVLTREEEVALAKRVEAARLSLFASFVALGSMARF 105

Query: 167 LIIWRDELNDGTTL 180
              WR  +  G   
Sbjct: 106 AAEWRSAVVSGAMR 119


>gi|239928504|ref|ZP_04685457.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 490

 Score =  216 bits (549), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 179/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 238 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 297

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 298 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 357

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 358 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 417

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 418 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 477

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 478 HPSRSQVLRDYLD 490



 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 5/111 (4%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASS----ASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            + +VD + LED + +E+     S+    +         ++ +A  +T DPV+ YL+++G
Sbjct: 143 DVELVDDEVLEDTKVAEEPEGAESAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIG 202

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 203 KVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 252


>gi|126652263|ref|ZP_01724442.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
 gi|126590995|gb|EAZ85107.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
          Length = 375

 Score =  215 bits (548), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   + +       A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 106 VRMYLKEIGRVDLLSAEQEIALAERIEQ---GDEEARKRLAEANLRLVVSIAKRYVGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 163 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 223 INKLIRVQRQLLQDLGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED  A SP D A    L+E    V+ +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 283 GDFIEDSEAQSPSDHAAYELLKEQLEDVIDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 343 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 375



 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 45/158 (28%), Positives = 76/158 (48%), Gaps = 8/158 (5%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM-GINVVDGDDLEDE 86
           DD+ K + + A+  G ++++E++  L P E+ +E++      L     I ++  ++ E+E
Sbjct: 18  DDAKKFLQEKAKTEGEISMKEISEKLTPYELENEEIFHFAEDLEKHKDIQIIGKEEFEEE 77

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                   +   A+  +  L           +DPVRMYL+E+G ++LLS E EIA+A+RI
Sbjct: 78  SL------MKEEANEETFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEQEIALAERI 131

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E G       L E+ L     I  R  +  G   L  I
Sbjct: 132 EQGDEEARKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 168


>gi|255325126|ref|ZP_05366232.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311739588|ref|ZP_07713423.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|255297691|gb|EET77002.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311305404|gb|EFQ81472.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 490

 Score =  215 bits (548), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 136/288 (47%), Positives = 192/288 (66%), Gaps = 7/288 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E   +    +D + K R E    +  + +   + R I         +   AK  ++EANL
Sbjct: 210 EAGLYAQHRMDEMEKARAEGDKAAKLSPMEKRDLRSIAR-------DGRKAKNHLLEANL 262

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++A
Sbjct: 263 RLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMA 322

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E+AK++ +  E V ++ +  +EP
Sbjct: 323 DQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKVLEIQQYAREP 382

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG
Sbjct: 383 ISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFG 442

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 443 LTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 490



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 161 DEEESAALRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 213


>gi|145295815|ref|YP_001138636.1| RNA polymerase sigma factor [Corynebacterium glutamicum R]
 gi|140845735|dbj|BAF54734.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 494

 Score =  215 bits (548), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 128/250 (51%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 245 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 304

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 305 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 364

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 365 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 424

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 425 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 484

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 485 RSQVLRDYLD 494



 Score = 54.1 bits (128), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 165 DEDESATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 217


>gi|257126628|ref|YP_003164742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
 gi|257050567|gb|ACV39751.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
          Length = 392

 Score =  215 bits (548), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 161/395 (40%), Positives = 235/395 (59%), Gaps = 17/395 (4%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
              Q+   +     K + + KV+  + +  V S+  +  +I+ L+++L D   +I+  + 
Sbjct: 3   DKKQNLKNSLANFIKQAREQKVVSYEEINSVLSIGFSTEKIEQLIKKLTDDGVQIVDTKK 62

Query: 355 E-------LLRLAQSYGIKRDVFLE---RHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           E          LA    ++   F +        E+D   V              +A  +D
Sbjct: 63  EKEDLLKVPETLADIEKMEISDFEDTHDEFVESEIDDSEVDKLLQTD----LLKMAESMD 118

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
               I+  ++ I     +S  E       V         AK++++E+NLRLV+S+AKK+T
Sbjct: 119 VDEPIKMYLREIGQIPLLSYEEEIDYAQRV---LDGEEEAKQKLIESNLRLVVSIAKKHT 175

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW++QAITR+IADQ  TIRIPVH
Sbjct: 176 NRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPVH 235

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K+ + +R +  +  +EPT EE+A+KL +PVE V+ +L++ ++PISLETP+G E+
Sbjct: 236 MIETINKIKKESRIILQETGKEPTAEELAEKLELPVEKVKSILEMNQDPISLETPVGSEE 295

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S LGDF+ED    +P D+  +  L+E    VL +L  REE VLR R+G+   +  TLEE
Sbjct: 296 DSELGDFVEDDKFANPYDATTRILLKEQLDEVLKTLNEREEMVLRYRYGLDDGSQKTLEE 355

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           VGK F VTRERIRQIE KA+RKL+HPSR KKL  +
Sbjct: 356 VGKIFNVTRERIRQIEVKALRKLRHPSRRKKLEDY 390



 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 53/210 (25%), Positives = 80/210 (38%), Gaps = 32/210 (15%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            +S    IK AR++  V+ EE+N+ L     S+E++E  +  L++ G+ +VD    +++ 
Sbjct: 9   KNSLANFIKQAREQKVVSYEEINSVL-SIGFSTEKIEQLIKKLTDDGVQIVDTKKEKEDL 67

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDD----------------------PVRMYL 125
                          S F     +  +   DD                      P++MYL
Sbjct: 68  LKVPETLADIEKMEISDFEDTHDEFVESEIDDSEVDKLLQTDLLKMAESMDVDEPIKMYL 127

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           RE+G I LLS E EI  A+R+  G       L ES L     I  +   N G  +L  I 
Sbjct: 128 REIGQIPLLSYEEEIDYAQRVLDGEEEAKQKLIESNLRLVVSIAKK-HTNRGLKMLDLI- 185

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSS 215
                   E   G     E   Y+K    S
Sbjct: 186 -------QEGNMGLMKAVEKFEYEKGFKFS 208


>gi|226366217|ref|YP_002784000.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226244707|dbj|BAH55055.1| RNA polymerase sigma factor SigA [Rhodococcus opacus B4]
 gi|254553058|dbj|BAH85841.1| RNA polymerase sigma A factor [Rhodococcus opacus]
          Length = 457

 Score =  215 bits (548), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 193/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  +   +S S  +   +    +     + + AK  ++EANLRL
Sbjct: 172 AEEEVELAKRIEAGLYATQIMQELSDSGEKLPAAQRRDMSWICRDGNRAKNHLLEANLRL 231

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 232 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 291

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 292 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 351

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 352 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLT 411

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 412 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 457



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEA
Sbjct: 125 DKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEA 184

Query: 149 GR--AMMMASLCES 160
           G     +M  L +S
Sbjct: 185 GLYATQIMQELSDS 198


>gi|158316157|ref|YP_001508665.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158111562|gb|ABW13759.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 400

 Score =  215 bits (547), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 134/296 (45%), Positives = 196/296 (66%), Gaps = 24/296 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK------------------------GECEASIA 444
           +R  +K+I     ++  E   +   +                           E +  IA
Sbjct: 104 VRMYLKAIGRVRLLTAEEEVDLAKRIEAGLFASEKLAAIRRTSPRLRRDLEAIEQDGQIA 163

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++VEANLRLV+S+AK+Y  RG+  LDLIQEGN+GL++A EKFD+  GYKFSTYA WW+
Sbjct: 164 KRKLVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 223

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+TR+IADQ  TIRIPVHM + I+KV R  R++   + REP+PEEIA ++ +    V 
Sbjct: 224 RQAVTRAIADQGRTIRIPVHMVETINKVTRIQRQLLQDLGREPSPEEIATQVDLAPHRVE 283

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++LK+ + P++LETPIG+E  S LGDFIED +A+ P ++A    L+E    VL +L+ RE
Sbjct: 284 EILKVGQTPVALETPIGEEQDSQLGDFIEDNDAIVPFEAASFVLLQEQIDSVLHTLSERE 343

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++V+++RFG+      TLE+VG++F VTRERIRQIE++ + KL HP+RS++LR +L
Sbjct: 344 KKVIQLRFGLTDGQPRTLEQVGREFGVTRERIRQIESRTLAKLSHPARSQRLRDYL 399



 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 74/391 (18%), Positives = 138/391 (35%), Gaps = 67/391 (17%)

Query: 19  DDSLVFDFS------DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +D+   D S      ++  + +I   ++ G+VT +++ A L   E+  E  +  + +L+ 
Sbjct: 9   EDAPPTDLSAPDEAAEEKIRSLIARGKENGFVTPDDIAAALLAAELPPESSDVVLRLLAE 68

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            GI V+D       E   D+ D+ S              S      DPVRMYL+ +G + 
Sbjct: 69  DGIEVLD-------EVGGDASDMPSRRREGEELALTTPPS------DPVRMYLKAIGRVR 115

Query: 133 LLSREGEIAIAKRIEAGR---------------------------AMMMASLCESPLTFQ 165
           LL+ E E+ +AKRIEAG                             +    L E+ L   
Sbjct: 116 LLTAEEEVDLAKRIEAGLFASEKLAAIRRTSPRLRRDLEAIEQDGQIAKRKLVEANLRLV 175

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
             I  R  +  G  LL  I         E   G     E   Y K    S        Q 
Sbjct: 176 VSIAKRY-VGRGMLLLDLI--------QEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 226

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
               I    +  +     V++  +      + L +   + +    A +  L P  +  + 
Sbjct: 227 VTRAIADQGRTIRIPVHMVETINKVTRIQRQLLQDLGREPSPEEIATQVDLAPHRVEEIL 286

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           ++ +    L    +  +  ++D +     +     +     S  L Q +ID ++  L + 
Sbjct: 287 KVGQTPVAL----ETPIGEEQDSQLGDFIEDNDAIVPFEAASFVLLQEQIDSVLHTLSER 342

Query: 346 SKRIMHNE--------GELLRLAQSYGIKRD 368
            K+++             L ++ + +G+ R+
Sbjct: 343 EKKVIQLRFGLTDGQPRTLEQVGREFGVTRE 373


>gi|302557983|ref|ZP_07310325.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302475601|gb|EFL38694.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 509

 Score =  215 bits (547), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 135/253 (53%), Positives = 178/253 (70%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 257 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 316

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW+ QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 317 DYTKGYKFSTYATWWICQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 376

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+     
Sbjct: 377 PEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTL 436

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+
Sbjct: 437 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLR 496

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 497 HPSRSQVLRDYLD 509



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 3/102 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D    E+ EG+E++  + S         Q+   +A  +T DPV+ YL+++G + LL+ E 
Sbjct: 173 DTKATEEPEGAENAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLKQIGKVPLLNAEQ 230

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 231 EVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 271


>gi|168704760|ref|ZP_02737037.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 556

 Score =  215 bits (547), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 153/409 (37%), Positives = 238/409 (58%), Gaps = 38/409 (9%)

Query: 275 QLRPKVMCALDEIAE-VYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
           Q  P  +  L+ + E    + + L D    G + E    + ++ + K V LV  LS+   
Sbjct: 179 QRMPHNLRTLEPLMEGNVEDFQRLSDERTPGDERETIRERLRLRRRKTVTLVEELSIRTQ 238

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           ++  L+++L  IS+R+   E E+  L                G                 
Sbjct: 239 KVQPLMKKLEQISQRMDELEAEIETL---------------SGNRT-------------- 269

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
                     +    +  E++ + + T    +  R  V ++++   E   AK+++   NL
Sbjct: 270 --------AKEERANLEKELQDLMLITLEEPASLRRRVGIMKQRFAEYEQAKRDLSGGNL 321

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKY NRGL FLDLIQEGN GLM+A +K++   G+KFSTYA WW++QAITR+IA
Sbjct: 322 RLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEHRRGFKFSTYATWWIRQAITRAIA 381

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + + K+   ++++  ++ REPT +E A    +  E  ++VLKI+++P
Sbjct: 382 DQARTIRIPVHMIETMSKLRNVSKQLLQELGREPTVQETADAAKISYEECKRVLKISRQP 441

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISL+ P+G+ + S+ GDFIED +  SP+++A    L++    VL +LT RE  ++++R+G
Sbjct: 442 ISLDRPVGESEDSYFGDFIEDNSVESPVNAATNEMLKDKIEGVLKTLTYREREIIKLRYG 501

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +G    +TLEEVG+ F VTRER+RQIEAKA+RKL+HP RS++L  FLDG
Sbjct: 502 LGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSRQLEGFLDG 550



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 47/211 (22%), Positives = 88/211 (41%), Gaps = 5/211 (2%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLP---PDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           +D+  K +++  +Q G +T +E+N  LP        S+++E  + +L   GI+V+D DD 
Sbjct: 5   NDEVLKALVERGKQVGSLTYDEVNTALPEGRDGVPESDRLEHVLEILDANGISVIDEDDG 64

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E    +  + D A +   +  +     D   R  DDPVRMYL +MG IELL+R+ E+++A
Sbjct: 65  EAVADAPVAADAAVADPEAPSYEDSDGD--GRHIDDPVRMYLTQMGQIELLNRKQEVSLA 122

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
            +IE  R      + E     + ++     ++ G       I +      E         
Sbjct: 123 MKIELTRRRFRRKVLECDYAMRQVVETLKRVHSGDLPFDRTIKVSQTENLEKDKILQRMP 182

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAA 234
                 +       ++   + +     +   
Sbjct: 183 HNLRTLEPLMEGNVEDFQRLSDERTPGDERE 213


>gi|257063660|ref|YP_003143332.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256791313|gb|ACV21983.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 394

 Score =  215 bits (547), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 135/239 (56%), Positives = 190/239 (79%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            AK +++EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA W
Sbjct: 155 DAKDQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 214

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ R+P+PEEI +K+ +  E 
Sbjct: 215 WIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGRDPSPEEIGEKMGLSAER 274

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR++ K+++EP+SLETPIG+E+ S LGDFIED +A+ P+D+A  A ++E  ++VL +L  
Sbjct: 275 VREIQKLSQEPVSLETPIGEEEDSQLGDFIEDDSAIVPVDAASFAMMQEQLSKVLDTLGE 334

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE  V+  RFG+     HTLEEVG++F VTRERIRQIE+K + KL+HPSRS KL+ +L+
Sbjct: 335 RERNVVIKRFGLEDGQPHTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSSKLKDYLE 393



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/96 (27%), Positives = 46/96 (47%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
             D  S+E  +DT     ++   + + +       +     + ++ S+ S   +    S 
Sbjct: 26  EDDIASAEDKDDTAIEDEDLLEGIPEEELKAPSAAAATLPKIKNNRSSRSRVRRSADTSV 85

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              T DPVRMYL+E+G + LL+   E+ +A +IEAG
Sbjct: 86  TMLTGDPVRMYLKEIGKVPLLTPSEEVDLAMKIEAG 121


>gi|311895920|dbj|BAJ28328.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 389

 Score =  215 bits (547), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 130/303 (42%), Positives = 186/303 (61%), Gaps = 30/303 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR------------------------------KGE 438
           +R  ++ I     ++  E   +   +                               +  
Sbjct: 87  LRQYLREIGRVRLLTAVEEVELARAIEAGLFAEEALDRVPPAAERRPADERLLGDLDRLV 146

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
               IAK+ ++EANLRLV+SVAK+Y  RGL  LDLIQEGN+GL++A EKFD+  GYKFST
Sbjct: 147 VLGRIAKRRLIEANLRLVVSVAKRYVGRGLTLLDLIQEGNVGLIRAVEKFDYARGYKFST 206

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++V+R  R +  +   EPT  E+   L +
Sbjct: 207 YATWWIRQAMSRALADQARTIRVPVHVVELINRVLRVQRGLLQERGVEPTAAEVGAVLQL 266

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR+VLK+ +EP+SL TP+G+ED   LGD IED +A SP +SA    LRE    VLA
Sbjct: 267 PPERVREVLKLAQEPVSLHTPVGEEDDVALGDLIEDADAASPPESAAFLLLREHLEAVLA 326

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE +V+++R+G+      TLEE+G  F VTRERIRQIEAK + KL+  + + +LR 
Sbjct: 327 TLGERERQVVQLRYGLDDGRPRTLEEIGHLFGVTRERIRQIEAKTLGKLRDHAFADQLRG 386

Query: 679 FLD 681
           +LD
Sbjct: 387 YLD 389



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           +    +   D       D +R YLRE+G + LL+   E+ +A+ IEAG      +L   P
Sbjct: 68  ADEPPEPALDEGTGPAADLLRQYLREIGRVRLLTAVEEVELARAIEAGLF-AEEALDRVP 126

Query: 162 LTFQALIIWRDELNDGTTLLREIIDL 187
                     +       LL ++  L
Sbjct: 127 PA-------AERRPADERLLGDLDRL 145


>gi|226306291|ref|YP_002766251.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229491301|ref|ZP_04385127.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|226185408|dbj|BAH33512.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229321840|gb|EEN87635.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 323

 Score =  215 bits (547), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 112/258 (43%), Positives = 183/258 (70%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++++ R + ++VR    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 68  LTVAKKRDLATIVR----EGQSARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGL 123

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 124 IRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 183

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIED  A S  
Sbjct: 184 QLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDSEATSAE 243

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ I   L      VL +L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE 
Sbjct: 244 NAVIAGLLHSDVRSVLGTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIER 303

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL+   R++KLRS+
Sbjct: 304 EVMGKLRVGDRAEKLRSY 321



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/92 (22%), Positives = 37/92 (40%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           + S ++ + +        A     D VR+YL  +G   LL+   E+ +AKRIEAG     
Sbjct: 1   MTSPSTTTRIRPSAADLDAQSPAADLVRVYLNGIGRTALLTAADEVELAKRIEAGLYASH 60

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIID 186
                  LT          + +G +    +++
Sbjct: 61  VLATGKRLTVAKKRDLATIVREGQSARSHLLE 92


>gi|256375646|ref|YP_003099306.1| RNA polymerase sigma factor [Actinosynnema mirum DSM 43827]
 gi|255919949|gb|ACU35460.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 435

 Score =  215 bits (546), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 137/289 (47%), Positives = 195/289 (67%), Gaps = 3/289 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L     ++    E+     + R     +R    +   AK  ++EAN
Sbjct: 150 AEEEVELAKRIEAGLYAAERLRRAEDESEKLTPQMR---RDLRWIVRDGERAKNHLLEAN 206

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++
Sbjct: 207 LRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 266

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +E
Sbjct: 267 ADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYARE 326

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISL+  IGDE  S LGDFIED  AV  +D+     L++    VLA+L+ RE  V+R+RF
Sbjct: 327 PISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRF 386

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 387 GLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 435



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 33/69 (47%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                  D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRI
Sbjct: 101 NAKPGEGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRI 160

Query: 147 EAGRAMMMA 155
           EAG      
Sbjct: 161 EAGLYAAER 169


>gi|257066626|ref|YP_003152882.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256798506|gb|ACV29161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 602

 Score =  215 bits (546), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 157/352 (44%), Positives = 227/352 (64%), Gaps = 15/352 (4%)

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           LN +  D +V  +Y     I+        +  +  +  + F+   Q           AK 
Sbjct: 265 LNITESDEIVNLIYLSFNDILSKAANKEHIKTNDSMILEDFIITSQ----------RAKK 314

Query: 390 FPEGEWKNFVA-CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             E    +     E++  + +R+    +  +  +S  +   +    R+    +  AKK++
Sbjct: 315 ISENIALDKDELMEIEETIALRDLAYKVINDEDLSDEDILDL----RRAVLNSKRAKKKL 370

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            E NLRLV+S+AKKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW++QAI
Sbjct: 371 AETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQAI 430

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQ+ TIRIPVHM + I+K+VR  R++   + R+P+ EEIA+++ + VE V+++ K
Sbjct: 431 TRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGLEVEKVQEIRK 490

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I++EP+SLETPIG+ED SHLGDFIED +A+ P ++A    LRE    VL+ L  RE+RVL
Sbjct: 491 ISQEPVSLETPIGEEDDSHLGDFIEDDSAIDPGEAANYTMLREQLNDVLSCLGAREKRVL 550

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++RFG+   T  TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 551 QLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 602


>gi|225388546|ref|ZP_03758270.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
 gi|225045391|gb|EEG55637.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
          Length = 381

 Score =  215 bits (546), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 130/272 (47%), Positives = 191/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    + + ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 113 VRMYLKEIGTVPLLTADEE---LQLAQRKAEGDEAAKERLIEANLRLVVSIAKRYTGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 170 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+A+ L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 230 INKMSKMQRKLTLELGYEPSVTELAEALDMTEDKVMEIMQIAREPASLETPIGEEDDSNL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 290 GDFVADNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 349

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 350 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 381



 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 71/160 (44%), Gaps = 13/160 (8%)

Query: 25  DFSDDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV---DG 80
           D      +K+++LA+ +   +   E+N F   D +S EQM+   + L N  I+VV   D 
Sbjct: 4   DDFLKKLEKLVELAKGKHNTLDAGEINDFFAGDSLSPEQMDHIYSYLENRNIDVVPELDE 63

Query: 81  DDLEDEEGSEDSLDLA---------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
             L +E    D LDL                 + L          T+DPVRMYL+E+G++
Sbjct: 64  KMLSEESALLDDLDLDLDLDDDSFMKDTEEEEIDLDAVDLLEGIGTEDPVRMYLKEIGTV 123

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            LL+ + E+ +A+R   G       L E+ L     I  R
Sbjct: 124 PLLTADEELQLAQRKAEGDEAAKERLIEANLRLVVSIAKR 163


>gi|296139587|ref|YP_003646830.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027721|gb|ADG78491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 483

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 131/252 (51%), Positives = 181/252 (71%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I   +     + + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD
Sbjct: 232 IRRDMNWIARDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFD 291

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP
Sbjct: 292 YTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTP 351

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L
Sbjct: 352 EELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLL 411

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+H
Sbjct: 412 QDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRH 471

Query: 670 PSRSKKLRSFLD 681
           PSRS+ LR +LD
Sbjct: 472 PSRSQVLRDYLD 483



 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/72 (38%), Positives = 40/72 (55%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +D E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 141 DAEDDEPSEQDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 200

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 201 EVELAKRIEAGL 212


>gi|300087894|ref|YP_003758416.1| RNA polymerase sigma 70 subunit RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299527627|gb|ADJ26095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 502

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 180/515 (34%), Positives = 285/515 (55%), Gaps = 40/515 (7%)

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           PE         +    +       E++ D  +  E    + ++++ D+    DS PE AE
Sbjct: 2   PEKLNRSPGDEDETKTKPVTIEQNEEDEDRPEPDEPQDVNPSELNDDEDEDSDSIPEEAE 61

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
           +   +L+   +   H +     ++    +  +  +     ++ + +  A    ++ + + 
Sbjct: 62  HIMPDLEVPLEQLEHGIVDDPVRMYLHEIGRVPLLNAETEKMLAKKMEAGKRIREIRQTC 121

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK--RIMHNEGELLRLAQSYGIKRDVF 370
           + +  +            N + +++++  L ++ K    +    + L L  S   K  VF
Sbjct: 122 RERDER------------NPNSVEVIICMLQELVKAAETVAVLQKQLGLEVSTNFKEAVF 169

Query: 371 -------LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
                  +E+   +EL                +  +   ++S L  +  +  IS ET +S
Sbjct: 170 APKLRASIEQEIDQELTKSIAEEQGQPVSQIEQALIDLSLNSELLPQKVLDGISPETDLS 229

Query: 424 ISEFRHIVSMVRKGECEASI-----------------AKKEMVEANLRLVISVAKKYTNR 466
             E   +V+                            A++ +++ANLRLV+SVAKK+  R
Sbjct: 230 --EINELVARPEFVARLEHYEHQFKSYLDTIEIESGKAERHLIQANLRLVVSVAKKHIGR 287

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+  LDLIQEGNIGL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM 
Sbjct: 288 GMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 347

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K++  +R MS K+ REPTP+EIA ++ +P E VR++ K+++ P+SLE+PIG+E+ S
Sbjct: 348 ETINKLLSISRSMSQKLGREPTPDEIAAEMELPPEKVREIAKVSQLPVSLESPIGEEEDS 407

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED+NA+ P D+A +  L+E    VL SLTPRE RVL++RFG+      TLEEVG
Sbjct: 408 HLGDFIEDQNALPPPDAASRQLLKEQIDNVLDSLTPRERRVLQLRFGLEDGRSRTLEEVG 467

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           K+F VTRERIRQIEAKA+RKL+HP+RS+KL+ +L+
Sbjct: 468 KEFNVTRERIRQIEAKALRKLRHPTRSRKLKDYLE 502



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-----TDDPVRMYLREMGSIEL 133
           +  D+   E ++D  + + S    +  +    +           DDPVRMYL E+G + L
Sbjct: 36  EPQDVNPSELNDDEDEDSDSIPEEAEHIMPDLEVPLEQLEHGIVDDPVRMYLHEIGRVPL 95

Query: 134 LSREGEIAIAKRIEAGRAM 152
           L+ E E  +AK++EAG+ +
Sbjct: 96  LNAETEKMLAKKMEAGKRI 114


>gi|62390750|ref|YP_226152.1| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|41326088|emb|CAF20251.1| RNA POLYMERASE SIGMA 70 FACTOR [Corynebacterium glutamicum ATCC
           13032]
          Length = 494

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 128/250 (51%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 245 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 304

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 305 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 364

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 365 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 424

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 425 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 484

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 485 RSQVLRDYLD 494



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 165 DEDESATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 217


>gi|237785650|ref|YP_002906355.1| RNA polymerase sigma factor [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237758562|gb|ACR17812.1| RNA polymerase sigma factor A [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 621

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 137/290 (47%), Positives = 200/290 (68%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L   ++++ + +  T +S ++ R +    R    +   AK  ++EA
Sbjct: 336 AEQEVSLAQRIEAGLYANHKLEELKASNTKLSPAQSRDL----RSIAHDGRKAKNHLLEA 391

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITRS
Sbjct: 392 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRS 451

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ +  + V ++ +  +
Sbjct: 452 MADQARTIRIPVHMVEVINKLGRIQRELLQDLSREPTPEELAREMDITEDKVLEIQQYAR 511

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +LT RE  V+R+R
Sbjct: 512 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLKTLTEREAGVVRLR 571

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 572 FGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 621



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 21/53 (39%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++A+RIEAG 
Sbjct: 298 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAQRIEAGL 350


>gi|111023781|ref|YP_706753.1| RNA polymerase sigma factor [Rhodococcus jostii RHA1]
 gi|110823311|gb|ABG98595.1| sigma factor, sigma 70 type, probable group 1 (principle sigma
           factor) [Rhodococcus jostii RHA1]
          Length = 457

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 193/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  +   +S S  +   +    +     + + AK  ++EANLRL
Sbjct: 172 AEEEVELAKRIEAGLYATQIMQELSDSGEKLPAAQRRDMSWICRDGNRAKNHLLEANLRL 231

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 232 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 291

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 292 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 351

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 352 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLT 411

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 412 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 457



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEA
Sbjct: 125 DKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEA 184

Query: 149 GR--AMMMASLCES 160
           G     +M  L +S
Sbjct: 185 GLYATQIMQELSDS 198


>gi|300784474|ref|YP_003764765.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
 gi|299793988|gb|ADJ44363.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
          Length = 343

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 110/266 (41%), Positives = 178/266 (66%), Gaps = 4/266 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     ++      + ++VR    +  +AK  ++EANLRLV+S+AK+YT RG+  LDL
Sbjct: 80  HMLDTGENLTTKRRTELAALVR----DGHVAKNHLLEANLRLVVSLAKRYTGRGMPLLDL 135

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQ  TIR+PVH+ ++++K+ 
Sbjct: 136 IQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQVNKLA 195

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  ++ R+ T EE+A +  +P   +  +L  +++P+SL+ P+G E+ + LGDFIE
Sbjct: 196 RIKRDLHQQLGRDATHEELAAESGIPAHKISDLLDHSRDPVSLDMPVGTEEDAPLGDFIE 255

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  A     + I   L++   RVLA+L  RE+ V+R+R+G+      TL+++GK F ++R
Sbjct: 256 DSEATDAESAVISGLLQDDLRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSR 315

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ER+RQIE + + KL+   R+ +LR++
Sbjct: 316 ERVRQIEREVMSKLRQGERADRLRAY 341



 Score = 44.4 bits (103), Expect = 0.062,   Method: Composition-based stats.
 Identities = 25/86 (29%), Positives = 31/86 (36%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                   S S   L      A     D VR+YL  +G   LLS   E+ +AKRIEAG  
Sbjct: 18  PAQTTEEPSMSLGALTDADLDAQSPAADLVRVYLNGIGKTALLSAADEVELAKRIEAGVF 77

Query: 152 MMMASLCESPLTFQALIIWRDELNDG 177
                     LT +        + DG
Sbjct: 78  AQHMLDTGENLTTKRRTELAALVRDG 103


>gi|296393381|ref|YP_003658265.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180528|gb|ADG97434.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 441

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 136/290 (46%), Positives = 197/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L  +  ++        +  +  R +  +VR    + + AK  ++EA
Sbjct: 156 AEQEVELAKRIEAGLYAQERLRIAAEEGDRLPTTSRRDLNWVVR----DGNRAKNHLLEA 211

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 212 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIRQAITRA 271

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+ +++ +P E V ++ +  +
Sbjct: 272 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELGREMDIPPEKVLEIQQYAR 331

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+RMR
Sbjct: 332 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQAVLETLSEREAGVVRMR 391

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 392 FGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 441



 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/116 (25%), Positives = 51/116 (43%), Gaps = 21/116 (18%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL--------------------D 94
            DE+S + +E   + + ++ I + D    E+    ++                      D
Sbjct: 56  EDELSMDDLEPVESDI-DIDIALEDDPIAEEGFNGDEPEGSDAAPAEEADEEEPERASGD 114

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                  S    Q RK++   ++ D VR YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 115 FVWDEDESEALRQARKNAELTASADSVRAYLKQIGKVALLNAEQEVELAKRIEAGL 170


>gi|300781032|ref|ZP_07090886.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
 gi|300532739|gb|EFK53800.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
          Length = 536

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 130/250 (52%), Positives = 180/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 287 RDLRAVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 346

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E
Sbjct: 347 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQE 406

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 407 LAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 466

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 467 QLQDVLHTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 526

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 527 RSQVLRDYLD 536



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 33/53 (62%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL  E E+++AKRIEAG 
Sbjct: 207 DIEESAALRQARKDAQLTASADSVRAYLKQIGKVALLDAEQEVSLAKRIEAGL 259


>gi|134098366|ref|YP_001104027.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006932|ref|ZP_06564905.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|133910989|emb|CAM01102.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 324

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 113/246 (45%), Positives = 175/246 (71%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++    +  +AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G
Sbjct: 77  LKAVVRDGVLAKNHLMEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKG 136

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  K+ RE T EE+A
Sbjct: 137 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKIARIKRDLHQKLGREATDEELA 196

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +  + VE V  +L  +++P+SL+ P+G E+ + LGDFIED  +    ++ I   L++  
Sbjct: 197 NEAGLTVEKVADLLDHSRDPVSLDMPVGAEEDAPLGDFIEDAESADAENAVISGFLQDDL 256

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RVL++L  RE+ V+RMR+G+      TL+++GK F ++RER+RQIE + + KL+   R+
Sbjct: 257 RRVLSTLEEREQAVIRMRYGLDDGQPRTLDQIGKAFGLSRERVRQIEREVMSKLRQGDRA 316

Query: 674 KKLRSF 679
            KLR++
Sbjct: 317 DKLRAY 322



 Score = 46.0 bits (107), Expect = 0.024,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 25/48 (52%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           S     +        + D VR+YL  +G   LL+ + E+ +AKRIEAG
Sbjct: 9   SDAAAIEADLDTQGPSADLVRVYLNGIGRTALLTAQEEVDLAKRIEAG 56


>gi|88807657|ref|ZP_01123169.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
 gi|88788871|gb|EAR20026.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
          Length = 447

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 200 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 259

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 260 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 319

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 320 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 378

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 379 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 438

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 439 NGVLKEYI 446



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 34/68 (50%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D      + G+    + A + + + V    +       T+D +R+YL+E+G I LL  + 
Sbjct: 97  DTPQSAADAGTSTKEEKAKADAKAKVLASIKVGPKGVYTEDSIRVYLQEIGRIRLLRPDE 156

Query: 139 EIAIAKRI 146
           EI +A++I
Sbjct: 157 EIELARKI 164


>gi|269219424|ref|ZP_06163278.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211120|gb|EEZ77460.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 592

 Score =  215 bits (546), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 137/285 (48%), Positives = 191/285 (67%), Gaps = 2/285 (0%)

Query: 399 VACEVDSILKIRNEI--KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
              EV+   +I   +  + I     +  ++ R  +  ++    +   AK  ++EANLRLV
Sbjct: 308 AEEEVELARRIEAGLYAQHILESGSLDKAKDRMYMRELKLISRDGQQAKNHLLEANLRLV 367

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+
Sbjct: 368 VSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDFTKGFKFSTYATWWIRQAITRAMADQA 427

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIRIPVHM + I+K+ R  R+M   + REPT  E+AK+L M  E V +V K  +EPISL
Sbjct: 428 RTIRIPVHMVEVINKLARVQRQMLQDLGREPTTIELAKELDMTEEKVIEVQKYGREPISL 487

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
            TP+G++  S  GD IED  AV P D+     L+E   +VL +L+ RE  V+ MRFG+  
Sbjct: 488 HTPLGEDGDSEFGDLIEDSEAVVPADAVGFTLLQEQLRQVLDTLSEREAGVVAMRFGLTD 547

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 548 GQTKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 592



 Score = 53.7 bits (127), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +        +     +T DPV+ YL+++G + LL+ E E+ +A+RIEAG 
Sbjct: 272 DSDESDEPAVRVHVAGATADPVKDYLKQIGKVPLLNAEEEVELARRIEAGL 322


>gi|187918567|ref|YP_001884130.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
 gi|119861415|gb|AAX17210.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
          Length = 630

 Score =  214 bits (545), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 182/660 (27%), Positives = 317/660 (48%), Gaps = 53/660 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE-- 84
           +  + K ++     +  +T E+L+ FL  D +  E ++    +L N GI++++       
Sbjct: 16  NSKAIKAILSYLGDKKVITFEDLSTFLSGDMLEPENIDYMYGVLENEGISLINEKMESAI 75

Query: 85  ---DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
              DE      LD      + SV      D      +D               + + E  
Sbjct: 76  CSIDEFDEASKLDSQCMILDDSVQSDDELDDKLDEFEDE--------------TLDKEDF 121

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
            +  I++G   +  S  E P+                  L+EI           K     
Sbjct: 122 SSGYIKSGL--LKDSNSEDPI---------------RLYLKEI----------GKEFLLT 154

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
           G +     K+ DS +    + ++     IE+   +     S+VD      +  ER  D +
Sbjct: 155 GNQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNAIYSRVDKEEFFKKEKEREKDNN 214

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
            D        +    +  +    D + +   +   L +   +  ++  ++ +       +
Sbjct: 215 FDYYNKK-KRITSFYKASLKSFQDRLVKYIEKKHRLYELGEDIFEESINNERL-----HI 268

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
            +++ S+ L Q  + +  +   D + +I   + +   +     I +   L    GR+L  
Sbjct: 269 KEMLKSVPLYQEELRIFSDDYIDSASKIKDLKRQQKSILDRLKIDKVRNLRIL-GRDLAI 327

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
                  +      ++ +  ++      + E++ I +     + +   +   + KG+   
Sbjct: 328 PERRERIEQSLNIREDLIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEILKGKQMM 387

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++  G+KFSTYA 
Sbjct: 388 QHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYAT 447

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE++ +L   ++
Sbjct: 448 WWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDEELSARLGWDLK 507

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P        L++    VL +L 
Sbjct: 508 KVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSFVVLQDQIRSVLGTLP 567

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P +++KL+ +L+
Sbjct: 568 EREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPKKTQKLKDYLE 627


>gi|283795510|ref|ZP_06344663.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291077175|gb|EFE14539.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
          Length = 377

 Score =  214 bits (545), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 130/272 (47%), Positives = 190/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    + + ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 109 VRMYLKEIGTVPLLSAEEE---LRLAKRKAEGDVSAKERLIEANLRLVVSIAKRYTGRGM 165

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 166 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 225

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E++  L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 226 INKMSKMQRKLTLELGYEPSVAELSAALDMSEDKVMEIMQIAREPASLETPIGEEDDSNL 285

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 286 GDFVADGNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 345

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 346 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 377



 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 45/154 (29%), Positives = 69/154 (44%), Gaps = 7/154 (4%)

Query: 25  DFSDDSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           D   +  +K++ LA+ ++  + I E+N F   D +S+EQME   + L    I+V+     
Sbjct: 6   DNFLEKLRKLVDLAKTKQNALDIAEINDFFAADNLSTEQMEQIYSYLEQNNIDVIPEVID 65

Query: 84  EDEEGSEDSLDLA------SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           E     E  L          +     + L          T+DPVRMYL+E+G++ LLS E
Sbjct: 66  ETSLNDELLLLDDVDDDFMKNGEEEDIDLDAIDLLEGIGTEDPVRMYLKEIGTVPLLSAE 125

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            E+ +AKR   G       L E+ L     I  R
Sbjct: 126 EELRLAKRKAEGDVSAKERLIEANLRLVVSIAKR 159


>gi|256390959|ref|YP_003112523.1| RNA polymerase sigma factor [Catenulispora acidiphila DSM 44928]
 gi|256357185|gb|ACU70682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 559

 Score =  214 bits (545), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 138/257 (53%), Positives = 183/257 (71%), Gaps = 3/257 (1%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EFR  + ++     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A
Sbjct: 306 PEFRRELDII---AEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRA 362

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + 
Sbjct: 363 VEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLG 422

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+AK+L M  E V +V K  +EPISL TP+G++  S  GD IED  AV P D+ 
Sbjct: 423 REPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAV 482

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQIE+K +
Sbjct: 483 SFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTM 542

Query: 665 RKLKHPSRSKKLRSFLD 681
            KL+HPSRS+ LR +LD
Sbjct: 543 SKLRHPSRSQVLRDYLD 559



 Score = 57.5 bits (137), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGS 130
           VV   D E EE SE             V      D+         +T DPV+ YL+++G 
Sbjct: 213 VVAVADEEGEEASEGDGATPGDKEEGFVLSDDEDDAPAQQVASAGATADPVKDYLKQIGK 272

Query: 131 IELLSREGEIAIAKRIEAGR 150
           + LL+ E E+ +AKRIEAG 
Sbjct: 273 VPLLNAEQEVELAKRIEAGL 292


>gi|153304|gb|AAA26762.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450077|prf||1920369A RNA polymerase:SUBUNIT=sigma
          Length = 393

 Score =  214 bits (545), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 125/296 (42%), Positives = 186/296 (62%), Gaps = 24/296 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAK 445
           R  ++ I     ++ +E   +   V                         +      +AK
Sbjct: 98  RQYLREIGRIPLLTAAEEVDLARRVEAGLFAEEKLGGAADLDSQLAVDLDRLVVMGRMAK 157

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++E+NLRLV+SVAK+Y  RGL  LDL+QEGN+GL++A EKFD+  GYKFSTYA WW++
Sbjct: 158 RRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 217

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPT EE+A  L +  E V +
Sbjct: 218 QAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTAEEVAVHLELTPERVLE 277

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA      E    VL++L  RE 
Sbjct: 278 VLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFFLRCEHLEAVLSTLGERER 337

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+++R+G+      TLEE+G+ F VTRERIRQIE+K + KL+  + + +LR +LD
Sbjct: 338 KVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDHAFADQLRGYLD 393



 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 41/100 (41%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
           A  P    + E +++ V   ++        +  EDE   E    L           +  +
Sbjct: 27  AAAPEARRTDEPVDEAVDEAADPAARAAGDETAEDEGPDEGPEVLELIEHVPPPRTRGAE 86

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                 + D  R YLRE+G I LL+   E+ +A+R+EAG 
Sbjct: 87  SGGAGPSADLFRQYLREIGRIPLLTAAEEVDLARRVEAGL 126


>gi|303233350|ref|ZP_07320019.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
 gi|302480479|gb|EFL43570.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
          Length = 441

 Score =  214 bits (545), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 140/283 (49%), Positives = 203/283 (71%), Gaps = 5/283 (1%)

Query: 399 VACEVDSILKIRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           +A ++++  K   +++        +S SE R ++      E     AK+ +  ANLRL +
Sbjct: 161 LAMKIEAGNKATEQLEKAEKGEIELSRSEMRRLMR----EEQVGLDAKQALTSANLRLTV 216

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 217 SIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAIADQAR 276

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM + I+K+VR  R++  ++ R+P+PEEI K++ M  + +R++ KI++EP+SLE
Sbjct: 277 TIRIPVHMVETINKLVRIQRQLLQELGRDPSPEEIGKEMNMSPDKIREIQKISQEPVSLE 336

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+E+ S LGDFIED  AV+P D+A  + LRE   +VL SL  RE +V++ RFG+   
Sbjct: 337 TPIGEEEDSSLGDFIEDSTAVAPPDAASDSMLREQLNQVLDSLADRERKVIKFRFGLEDG 396

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEEVG++F VTRERIRQIE+K + KL+HPSRS +L+ ++
Sbjct: 397 HPRTLEEVGREFGVTRERIRQIESKTLAKLRHPSRSARLKDYV 439



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/67 (34%), Positives = 36/67 (53%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E    +    SS  +S    ++   S    T DPVRMYL+E+G ++LL+ + E+ +A +
Sbjct: 105 NEELRAAAKRKSSKRSSRSRARRIDSSTVMLTGDPVRMYLKEIGKVDLLTADDEVHLAMK 164

Query: 146 IEAGRAM 152
           IEAG   
Sbjct: 165 IEAGNKA 171


>gi|120403451|ref|YP_953280.1| RNA polymerase sigma factor [Mycobacterium vanbaalenii PYR-1]
 gi|119956269|gb|ABM13274.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 478

 Score =  214 bits (545), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 134/286 (46%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC---EASIAKKEMVEANLRL 455
              EV+   +I   + +  +   ++    +   +  R       +   AK  ++EANLRL
Sbjct: 193 AEEEVELAKRIEAGLYATQLMAELADKGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 252

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 253 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 312

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 313 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 372

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 373 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLT 432

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 433 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 478



 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 38/72 (52%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D    E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 136 DDGVAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 195

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 196 EVELAKRIEAGL 207


>gi|297566693|ref|YP_003685665.1| RpoD subfamily RNA polymerase sigma-70 subunit [Meiothermus
           silvanus DSM 9946]
 gi|296851142|gb|ADH64157.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus
           silvanus DSM 9946]
          Length = 483

 Score =  214 bits (545), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 153/326 (46%), Positives = 209/326 (64%), Gaps = 19/326 (5%)

Query: 364 GIKRDVFLERHQGRELDP-HWVSYAKDFPEGEWKNFVACEV----DSILKIRNEIKSISV 418
           G+    FL +  G E D    V  A+             EV    ++I  + + ++++  
Sbjct: 169 GVASAQFLAQETGLETDLIRQVLRAQVQGGARIHQVPGMEVKLDPETITAVDSRLRAL-- 226

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
                  E +  + + R    +  +A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN
Sbjct: 227 -----PREVKRHLHIAR----DGELARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGN 277

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            GL++A EKF++   YKFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR+
Sbjct: 278 QGLIRAVEKFEYKRRYKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQ 337

Query: 539 MSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           M  ++ REPT EEI++ +      + V +  KI +EP+SLETPIGDE  S  GDFI D++
Sbjct: 338 MQQELGREPTYEEISEAMGPGWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEH 397

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             SP+DSA Q+ L E   + L  L+ RE  VL++R G+    +HTLEEVG  F VTRERI
Sbjct: 398 MASPVDSAAQSMLSEELEKALGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERI 457

Query: 657 RQIEAKAIRKLK-HPSRSKKLRSFLD 681
           RQIE KA+RKLK H SR++KLR FLD
Sbjct: 458 RQIENKALRKLKYHESRTRKLRDFLD 483



 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 28/114 (24%), Positives = 47/114 (41%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +  + +       L         F +    +   ST DPVR YL E+G + LL+ E EI 
Sbjct: 102 EFLEPDLDLLEPTLELETEEEDSFDEDLPLTTRVSTSDPVRQYLHEIGQVPLLTLEEEID 161

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           +A+R+E G A       E+ L    +         G   + ++  +E  + PE+
Sbjct: 162 LARRVEDGVASAQFLAQETGLETDLIRQVLRAQVQGGARIHQVPGMEVKLDPET 215


>gi|226306303|ref|YP_002766263.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
 gi|226185420|dbj|BAH33524.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
          Length = 452

 Score =  214 bits (545), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 133/286 (46%), Positives = 193/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + ++ +   ++    +   +    +     + + AK  ++EANLRL
Sbjct: 167 AEEEVELAKRIEAGLYAVQIMQDLADKGEKLPAAQRRDMSWICRDGNRAKNHLLEANLRL 226

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 227 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 286

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 287 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 346

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 347 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLT 406

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 407 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 452



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 39/76 (51%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +    E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 110 EETAAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 169

Query: 139 EIAIAKRIEAGRAMMM 154
           E+ +AKRIEAG   + 
Sbjct: 170 EVELAKRIEAGLYAVQ 185


>gi|163849112|ref|YP_001637156.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222527085|ref|YP_002571556.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670401|gb|ABY36767.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222450964|gb|ACM55230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 398

 Score =  214 bits (544), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 120/296 (40%), Positives = 186/296 (62%), Gaps = 23/296 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-----------------------RKGECEASIAK 445
           +R  ++ I     ++  + + +  ++                       ++ + +   A+
Sbjct: 101 VRLYLREIGQVPLLTAEQEKRLAQLIEQGQEAERKLATLPPDSPEAARLKQLKAKGEEAR 160

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++M  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD+  GYKFSTYA WW+K
Sbjct: 161 QQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWWIK 220

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQS  +R+PVH+ + ++++    R+++  + REPT  E+A  L M  E +R+
Sbjct: 221 QALSRALADQSRLVRLPVHLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEKLRE 280

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + +  ++P+SL TP+G+E  S L DFI D +A+   D+A    LR+  T  L  L+ RE 
Sbjct: 281 LRRTAQDPVSLATPVGEEADSTLADFIPDPHALDADDAAASGMLRQQITAALDQLSERER 340

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RVL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 341 RVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 396



 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 74/151 (49%), Gaps = 12/151 (7%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           + S+ E    +   + +D   + +I   RQ+G+VT E++   +P  + S E ++   A L
Sbjct: 2   TQSQPETDRAAPAINPAD--LQALIAQGRQQGFVTFEDIQRLVPNPDESIELIDSIYAAL 59

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +  G+ V +GD+   ++           +S +++ L    + +D    D VR+YLRE+G 
Sbjct: 60  AEAGVPVQEGDETALDD---------EPSSPATMDLDLDDELSDALLSDSVRLYLREIGQ 110

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           + LL+ E E  +A+ IE G+      L   P
Sbjct: 111 VPLLTAEQEKRLAQLIEQGQ-EAERKLATLP 140


>gi|323484891|ref|ZP_08090246.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323693741|ref|ZP_08107938.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323401772|gb|EGA94115.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323502192|gb|EGB18057.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 374

 Score =  214 bits (544), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 130/272 (47%), Positives = 191/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E    + + ++       AK+ ++EANLRLV+S+AK+YT RG+
Sbjct: 106 VRMYLKEIGTVPLLSADEE---LRLAKRKAEGDDNAKERLIEANLRLVVSIAKRYTGRGM 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GL+K  EKFD+  GYK STYA WW++Q++TR++ADQ+ TIR+PVHM + 
Sbjct: 163 SFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVET 222

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R+++ ++  EP+  E+++ L M  + V ++++I +EP SLETPIG+ED S+L
Sbjct: 223 INKMSKMQRKLTLELGYEPSVAELSEALEMSEDKVMEIMQIAREPASLETPIGEEDDSNL 282

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D N V+P  +     LRE    +L  L  RE +V+ +RFG+      TLEEVGK+
Sbjct: 283 GDFVADSNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLEEVGKE 342

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 343 FNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 374



 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 44/149 (29%), Positives = 71/149 (47%), Gaps = 6/149 (4%)

Query: 29  DSWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-----DGDD 82
           +  K+++ LA+ ++  + I E+N F   D +S+EQME   + L N  I+++     +   
Sbjct: 8   EKLKRLVDLAKTKQNALDITEINNFFAGDNLSTEQMEQIYSYLENSNIDIIPEVIDETIL 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ED+    D  D         + L          T+DPVRMYL+E+G++ LLS + E+ +
Sbjct: 68  AEDDALLLDDADDDFLKEEEEIDLDAIDLLEGIGTEDPVRMYLKEIGTVPLLSADEELRL 127

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWR 171
           AKR   G       L E+ L     I  R
Sbjct: 128 AKRKAEGDDNAKERLIEANLRLVVSIAKR 156


>gi|23308878|ref|NP_601117.2| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|21324681|dbj|BAB99304.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigA)
           [Corynebacterium glutamicum ATCC 13032]
          Length = 498

 Score =  214 bits (544), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 128/250 (51%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 249 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 308

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 309 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 368

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 369 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 428

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 429 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 488

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 489 RSQVLRDYLD 498



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 169 DEDESATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 221


>gi|284049111|ref|YP_003399450.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283953332|gb|ADB48135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 589

 Score =  214 bits (544), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 182/528 (34%), Positives = 278/528 (52%), Gaps = 10/528 (1%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T    +   + L      +    +++  +  E           +S    ++     + 
Sbjct: 65  PKTAAEYLAEFEALAKKNHGVLTYKEIQDRLQNEDTVSVDEMDAIYSKLAEKNIEVVDDG 124

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            + +E E   E   KV + + + + S PE    D+      ++     L A +D+++   
Sbjct: 125 AEDEEPETIDEDELKVDESELANL-SVPEGVIVDDPVRMYLKEIGRVPLLAGDDEIKLAK 183

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKD---EKSSVKCKVL--KEKLVKLVGSLSLNQSRI 335
                  A+   +    +       K     K   +   L  +E +     S+SL   + 
Sbjct: 184 RADKGNQAKAILKGEKPEGEFPPVNKRLSIGKLLEEANELLTQEGIWVDKRSVSLAYRKA 243

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
             L    + +             + +   + R   L+ ++ +       +      E   
Sbjct: 244 QTLTGPDHVLDAEAYQEMVSDFTMDEKKRLNR--LLQENKYKIAHGQKHAQEASEKEEGS 301

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISE-FRHIVSMVRKGECEASIAKKEMVEANLR 454
                 E+ ++++ +   + +  ET   I E  +    ++ + E     AKK + EANLR
Sbjct: 302 SLGTLQELFAVVEDKAAHQKVDEETQKQIEEGKKRFNRLLHRMEFCGDNAKKCLSEANLR 361

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IAD
Sbjct: 362 LVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIAD 421

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K+VR +R++  ++ REPTPEEIAK++ + VE VR++ KI +EP+
Sbjct: 422 QARTIRIPVHMVETINKLVRVSRQLLQELGREPTPEEIAKEMDVSVERVREIQKIAQEPV 481

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFG 633
           SLETPIG+E+ SHLGDFIED+ A SP D+A    L+E   +VL   L+ RE RVL +RFG
Sbjct: 482 SLETPIGEEEDSHLGDFIEDQEAPSPADAASYTLLQEQLGKVLQEHLSARERRVLELRFG 541

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +      TLEEVG+ F VTRERIRQIEAKA+RKL+ P RSK L+ FL+
Sbjct: 542 LMDGRTRTLEEVGQYFGVTRERIRQIEAKALRKLRSPKRSKPLKEFLE 589



 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 55/294 (18%), Positives = 98/294 (33%), Gaps = 10/294 (3%)

Query: 31  WKKMIKLARQR-GYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
             +   LA++  G +T +E+   L   D VS ++M+   + L+   I VVD    ++E  
Sbjct: 72  LAEFEALAKKNHGVLTYKEIQDRLQNEDTVSVDEMDAIYSKLAEKNIEVVDDGAEDEEPE 131

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D  +L    S     L           DDPVRMYL+E+G + LL+ + EI +AKR + 
Sbjct: 132 TIDEDELKVDESE----LANLSVPEGVIVDDPVRMYLKEIGRVPLLAGDDEIKLAKRADK 187

Query: 149 GRAMMMASLCESPLT----FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           G         E P          +     L +   LL +                     
Sbjct: 188 GNQAKAILKGEKPEGEFPPVNKRLSIGKLLEEANELLTQEGIWVDKRSVSLAYRKAQTLT 247

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G  +    ++ QE   D   + +  +    + +K   +      + A   E         
Sbjct: 248 GPDHVLDAEAYQEMVSDFTMDEKKRLNRLLQENKYKIAHGQKHAQEASEKEEGSSLGTLQ 307

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
               +   +   +        +I E  +    L         + K  +    L+
Sbjct: 308 ELFAVVEDKAAHQKVDEETQKQIEEGKKRFNRLLHRMEFCGDNAKKCLSEANLR 361


>gi|262038195|ref|ZP_06011589.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747776|gb|EEY35221.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 393

 Score =  214 bits (544), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 156/396 (39%), Positives = 232/396 (58%), Gaps = 18/396 (4%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
              +D         K + + K++  + +  + S+  +  +ID L+++L D    I+    
Sbjct: 3   EKKEDLKKRLANLMKQAKEEKIVSYEEINSILSVGFSTQKIDQLIKKLQDDGVNIVDTLK 62

Query: 355 ELLRLAQSYGIKRDVFLE-----------RHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
           +   L +   I  +   +                E+D   V              +A  +
Sbjct: 63  DKQELLKVNKILSEDLEKVEVVDFDDSEDEFVENEIDDSEVDKLLQTD----LLKMAESM 118

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D    I+  ++ I     +S  E       V         AK++++E+NLRLV+S+AKK+
Sbjct: 119 DVDEPIKMYLREIGQIPLLSYEEEIDYAQRV---LKGDEEAKQKLIESNLRLVVSIAKKH 175

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGL+ LDLIQEGN+GLMKA EKF++  G+KFSTYA WW++QAITR+IADQ  TIRIPV
Sbjct: 176 TNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPV 235

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ + +R +  +  +EPT EE++KKL +PV+ V+ +L++ ++PISLETP+G E
Sbjct: 236 HMIETINKIKKESRIILQETGKEPTAEELSKKLEIPVDKVKNILEMNQDPISLETPVGSE 295

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDF+ED   ++P D+  +  L+E    +L +L  REE VLR R+G+   +  TLE
Sbjct: 296 EDSELGDFVEDDKFLNPYDATTRVLLKEQLDEILKTLNEREEMVLRYRYGLDDGSQKTLE 355

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EVGK F VTRERIRQIE KA+RKL+HPSR KKL  +
Sbjct: 356 EVGKIFNVTRERIRQIEVKALRKLRHPSRRKKLEDY 391



 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 49/214 (22%), Positives = 79/214 (36%), Gaps = 33/214 (15%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +        ++K A++   V+ EE+N+ L     S+++++  +  L + G+N+VD    +
Sbjct: 6   EDLKKRLANLMKQAKEEKIVSYEEINSIL-SVGFSTQKIDQLIKKLQDDGVNIVDTLKDK 64

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDS-----------------------ADRSTDDPV 121
            E    + +          V     +D                             D+P+
Sbjct: 65  QELLKVNKILSEDLEKVEVVDFDDSEDEFVENEIDDSEVDKLLQTDLLKMAESMDVDEPI 124

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           +MYLRE+G I LLS E EI  A+R+  G       L ES L     I  +   N G  +L
Sbjct: 125 KMYLREIGQIPLLSYEEEIDYAQRVLKGDEEAKQKLIESNLRLVVSIAKK-HTNRGLKML 183

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
             I         E   G     E   Y+K    S
Sbjct: 184 DLI--------QEGNMGLMKAVEKFEYEKGFKFS 209


>gi|12958492|gb|AAK09321.1|AF320817_2 sigma factor SigA [[Brevibacterium] flavum]
          Length = 498

 Score =  214 bits (544), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 128/250 (51%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 249 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 308

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 309 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 368

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 369 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 428

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 429 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 488

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 489 RSQVLRDYLD 498



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 169 DEDESATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 221


>gi|54025729|ref|YP_119971.1| RNA polymerase sigma factor [Nocardia farcinica IFM 10152]
 gi|54017237|dbj|BAD58607.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 454

 Score =  214 bits (544), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 134/301 (44%), Positives = 189/301 (62%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR----------------------------KGECE 440
           +R  +K I     ++  E   +   +                                 +
Sbjct: 154 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAEKMREFAESGEKLPVAMRRDYNWIVRD 213

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA
Sbjct: 214 GNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 273

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  
Sbjct: 274 TWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITP 333

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L
Sbjct: 334 EKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETL 393

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +L
Sbjct: 394 SEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 453

Query: 681 D 681
           D
Sbjct: 454 D 454



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E E+ +AKRIEAG
Sbjct: 123 KASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAG 182

Query: 150 RAMM 153
               
Sbjct: 183 LYAA 186


>gi|213162104|ref|ZP_03347814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 225

 Score =  214 bits (544), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 160/222 (72%), Positives = 187/222 (84%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TI
Sbjct: 3   AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 62

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETP
Sbjct: 63  RIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETP 122

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTD
Sbjct: 123 IGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTD 182

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 183 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 224


>gi|269926188|ref|YP_003322811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789848|gb|ACZ41989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 463

 Score =  214 bits (544), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 127/305 (41%), Positives = 196/305 (64%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           RE         K     +    +   +   ++  N+   +   + + ++    +++   K
Sbjct: 158 RESFAKDEEVKKLLEAEQDMYLLPPLITEYIERSNKCPDVKTVSQVLLANKSIVINHWNK 217

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
              E   AK +++EAN RLV+S+AKKY  RGL  LDLIQEGNIGLM+AA+KFD+  GYKF
Sbjct: 218 VRKEGEGAKCKLIEANTRLVVSIAKKYLGRGLSLLDLIQEGNIGLMRAADKFDYTRGYKF 277

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QA+TR+IADQS TIR+PVH+ + + K+ +T++++  ++  EPT E+++ +L
Sbjct: 278 STYATWWIRQAVTRAIADQSRTIRLPVHVCETVSKIHKTSQKLQQELGHEPTIEQLSSEL 337

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP++ V ++ + +K P+SLE PIG++  S LGDF+ED + ++P+  A    LRE    V
Sbjct: 338 GMPMKKVVQIQQASKFPVSLEAPIGEDGDSMLGDFLEDVHVLNPVQKAANDILREQINSV 397

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L P+E +VL +RFG+      TLEEVG +F +TRER+RQIE  A+R+L+     K+L
Sbjct: 398 LQNLPPKERKVLELRFGLVDGKCRTLEEVGNEFAITRERVRQIECTALRRLRENHLIKQL 457

Query: 677 RSFLD 681
           R FL+
Sbjct: 458 RDFLE 462



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 52/329 (15%), Positives = 118/329 (35%), Gaps = 30/329 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD---PVRMY 124
           + + +  +   +  +LE E+ + +  D A++  +         +  +   DD   PV+MY
Sbjct: 16  SFIEDAHLQSEESFELESEDIAIEFSDDATNDVDQEGSDLSDLEHIEGYADDLDEPVQMY 75

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTLL 181
           LRE+G + LL+ E E+ +A++IE  R      +     + +T  A +      + G    
Sbjct: 76  LREIGKVPLLTAEQEVILARKIELSRRLDEYWLQQHTNADVTLVA-LKIYKSASLGYVQA 134

Query: 182 REII--DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           +E +  D+   +    +    H  E  +  +      E E+D         E   + +K 
Sbjct: 135 KEWLPTDVSLPLSELYQAAITHARESFAKDEEVKKLLEAEQDMYLLPPLITEYIERSNKC 194

Query: 240 DRSKVDSPPENA-------------ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
              K  S    A             +  E    +  + +   + ++  +   + +  LD 
Sbjct: 195 PDVKTVSQVLLANKSIVINHWNKVRKEGEGAKCKLIEANTRLVVSIAKKYLGRGLSLLDL 254

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           I E    L    D     +  + S+       + +   +     ++ L    +   V ++
Sbjct: 255 IQEGNIGLMRAADKFDYTRGYKFSTYATWWIRQAVTRAIADQSRTIRL-PVHVCETVSKI 313

Query: 343 YDISKRIMHNEG---ELLRLAQSYGIKRD 368
           +  S+++    G    + +L+   G+   
Sbjct: 314 HKTSQKLQQELGHEPTIEQLSSELGMPMK 342


>gi|315651467|ref|ZP_07904490.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
 gi|315486287|gb|EFU76646.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
          Length = 389

 Score =  213 bits (543), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 138/274 (50%), Positives = 200/274 (72%), Gaps = 1/274 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-RKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+  +K I     +S+ E  ++   +    E     A+K+M E+NLRLV+S+AK+Y  RG
Sbjct: 116 IKMYLKEIGKIPLLSVDEEMNLAKKICDPDEAVRKEARKQMAESNLRLVVSIAKRYMGRG 175

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +QFLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 176 MQFLDLIQEGNLGLLRAVEKFDYQKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVE 235

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+++++  R++  +  REP P+E+AK + +PV  VR+++    EP+S+ETPIGDED SH
Sbjct: 236 TINRLIKIQRKLVQEFGREPRPDEVAKVMGIPVSKVREIMSFALEPVSMETPIGDEDDSH 295

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDF++D NA  P++ A+   L +    V+ SLT RE++V+ +RFG+      TLEEVGK
Sbjct: 296 LGDFLQDSNAKIPVNFAMDVLLHDQLMEVIKSLTEREQKVILLRFGLEDGKPRTLEEVGK 355

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F +TRERIRQIEAK++RKL++PS+ ++L+ FL+
Sbjct: 356 VFGITRERIRQIEAKSLRKLRNPSKVRRLKDFLE 389



 Score = 63.7 bits (153), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 39/164 (23%), Positives = 67/164 (40%), Gaps = 22/164 (13%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE-----GSEDSLDLA 96
           G +T  ++      +++  E + + +  L    I V + DD E ++       E+ + L 
Sbjct: 20  GKLTALKIKKIFSENDIPKEYLSEFIDFLEKRDIIVEEEDDNEPQDFDSGSDPEEYILLK 79

Query: 97  SSASNSSVFLQKRKDSADR------------STDDPVRMYLREMGSIELLSREGEIAIAK 144
            +  +        KD  D             + +D ++MYL+E+G I LLS + E+ +AK
Sbjct: 80  DAEFDDEFNEDDIKDLKDINLNILEDLDDYIAIEDSIKMYLKEIGKIPLLSVDEEMNLAK 139

Query: 145 RI----EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +I    EA R      + ES L     I  R  +  G   L  I
Sbjct: 140 KICDPDEAVRKEARKQMAESNLRLVVSIAKRY-MGRGMQFLDLI 182


>gi|237740231|ref|ZP_04570712.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
 gi|229422248|gb|EEO37295.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
          Length = 269

 Score =  213 bits (543), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 138/269 (51%), Positives = 190/269 (70%), Gaps = 3/269 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             ++ I     ++  E                 A ++++E+NLRLV+S+AKK+TNRGL+ 
Sbjct: 1   MYLREIGQVPLLTHDEEIEYAKRA---YEGDEEASQKLIESNLRLVVSIAKKHTNRGLKL 57

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + I+
Sbjct: 58  LDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETIN 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ + +R    +  ++ +PE +A++L M VE ++ + ++ +EPISLETP+G E+ S LGD
Sbjct: 118 KIKKESRIYLQETGKDASPEILAERLGMEVEKIKAIQEMNQEPISLETPVGSEEDSELGD 177

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           F+ED+   SP ++  +A LRE    VL +L+PREE+VLR R+G+  ++  TLEEVGK F 
Sbjct: 178 FVEDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFN 237

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 238 VTRERIRQIEVKALRKLRHPSRKKKLEDF 266



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/62 (38%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLRE+G + LL+ + EI  AKR   G       L ES L     I  +   N G  LL 
Sbjct: 1   MYLREIGQVPLLTHDEEIEYAKRAYEGDEEASQKLIESNLRLVVSIAKK-HTNRGLKLLD 59

Query: 183 EI 184
            I
Sbjct: 60  LI 61


>gi|168335371|ref|ZP_02693465.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Epulopiscium
           sp. 'N.t. morphotype B']
          Length = 364

 Score =  213 bits (543), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 142/273 (52%), Positives = 204/273 (74%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  +   +   +         A+K + EANLRLV+S+AK+Y  RG+
Sbjct: 95  VRMYLKEIGKVPLLSADDEIKLAKRME---SGDEEARKRLAEANLRLVVSIAKRYVGRGM 151

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 152 LFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 211

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++  ++ R+P PEEIA+++ + V  VR+++KI++EP++LETPIG+E+ ++L
Sbjct: 212 INKLMRIQRQLLQELGRDPQPEEIAREMELSVNKVREIMKISQEPVALETPIGEEEDTNL 271

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D++A +P ++A    L+E    VL +LT RE++VL++RFG+      TLEEVG++
Sbjct: 272 GDFLADEDAPAPAEAAAFTLLKEQLIEVLDTLTDREQKVLKLRFGLDDGRARTLEEVGRE 331

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR +L+
Sbjct: 332 FNVTRERIRQIEAKALRKLRHPSRSKKLRDYLE 364



 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/157 (26%), Positives = 71/157 (45%), Gaps = 17/157 (10%)

Query: 30  SWKKMIKLAR-QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-DGDDLEDEE 87
              +++ LA+ + G +  +++       E+   ++E     L    I+++ +  ++E+E 
Sbjct: 16  RLDQLLVLAKDKNGVLEQKDITDAFLDLELEPTKIEQVYEFLEAQSIDIIGEISNIENEN 75

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +ED +D                     S DDPVRMYL+E+G + LLS + EI +AKR+E
Sbjct: 76  LNEDIIDFT--------------LPEGVSIDDPVRMYLKEIGKVPLLSADDEIKLAKRME 121

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G       L E+ L     I  R  +  G   L  I
Sbjct: 122 SGDEEARKRLAEANLRLVVSIAKRY-VGRGMLFLDLI 157


>gi|38233991|ref|NP_939758.1| RNA polymerase sigma factor [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200253|emb|CAE49937.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 502

 Score =  213 bits (543), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 129/250 (51%), Positives = 180/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 253 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 312

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E
Sbjct: 313 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQE 372

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 373 LAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQD 432

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 433 QLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 492

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 493 RSQVLRDYLD 502



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/80 (35%), Positives = 44/80 (55%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
             M  + +  DD  D++  ED          S+   Q RKD+   ++ D VR YL+++G 
Sbjct: 146 DEMHTDELGEDDSSDDDSDEDEGSSVWDEDESAALRQARKDAELSASADSVRAYLKQIGK 205

Query: 131 IELLSREGEIAIAKRIEAGR 150
           + LL+ E E+++AKRIEAG 
Sbjct: 206 VALLNAEQEVSLAKRIEAGL 225


>gi|271962349|ref|YP_003336545.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270505524|gb|ACZ83802.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 324

 Score =  213 bits (543), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 131/295 (44%), Positives = 184/295 (62%), Gaps = 23/295 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-----------------------KGECEASIAK 445
           +R+ ++ I+    ++  +   +   V                            +   AK
Sbjct: 29  VRDYLRQIARIPLLTAGQEVELARRVEAGLFARERLGAEGLPAALRAELECVADDGRRAK 88

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
              VEANLRLV+S+AK++  RG+  LDLIQEGN+GL++A EKFD  LG+KFSTYA WW+K
Sbjct: 89  DRFVEANLRLVVSIAKRHAGRGVPLLDLIQEGNLGLIRAVEKFDHRLGFKFSTYATWWIK 148

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QAITR++ADQ+ T+R+PVHM + I+KV R  R++   + REPTPEEIA +L +  E V +
Sbjct: 149 QAITRAMADQARTVRVPVHMVEMINKVARVERQLLCDLGREPTPEEIAAELDLTPEKVTE 208

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +    +EPISL TP+GDE  S LGD IED  AV+P  +     L+E    +LA+LT RE 
Sbjct: 209 IKGHGREPISLHTPLGDEGDSELGDLIEDAEAVTPEAAVAFTLLQEQVRALLATLTGREA 268

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            V+ MRFG       TL+E+G+ + +TRERIRQIE+K + +L+HPSRS+ LR +L
Sbjct: 269 GVISMRFGFADGRPWTLDEIGRVYGLTRERIRQIESKTMSRLRHPSRSQPLRDYL 323



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           L S+ + +   +     +   +T DPVR YLR++  I LL+   E+ +A+R+EAG     
Sbjct: 3   LGSTLTQTGDEVLTLLKAEMGATADPVRDYLRQIARIPLLTAGQEVELARRVEAGLFARE 62

Query: 155 ASLCE-SPLTFQALIIWRDELNDGTTLLRE 183
               E  P   +A +     + D     ++
Sbjct: 63  RLGAEGLPAALRAELEC---VADDGRRAKD 89


>gi|160945279|ref|ZP_02092505.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443010|gb|EDP20015.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|295105509|emb|CBL03053.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 360

 Score =  213 bits (543), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 145/270 (53%), Positives = 199/270 (73%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++  +    +++ +      + A++ + EANLRLV+SVAK+Y  RGL FL
Sbjct: 93  YLKEIGRVPLLTAGQE---MALAKAARAGDADARRALSEANLRLVVSVAKRYAGRGLPFL 149

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GLMKAAEKF+   G+KFSTYA WW++Q+ITR+IADQ  TIRIPVH+ + I++
Sbjct: 150 DLIQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQSITRAIADQGRTIRIPVHLVESINR 209

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +TA  + +K  REPT EEIA  L M  + VR++L++++EPISLETP+G+E+ +HL DF
Sbjct: 210 VKKTAGDLLHKNGREPTVEEIAAALDMEPDKVRELLQLSQEPISLETPVGEEEDAHLEDF 269

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I+D++A  P+D A +  LR     VL SLTPREERV+ +RFG+      TLEE+GK+F V
Sbjct: 270 IQDEDAGVPVDEAGRQLLRRELLHVLKSLTPREERVITLRFGLEDGRARTLEELGKEFNV 329

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRER+RQIEAKA+RKL+HPSR+K LR +LD
Sbjct: 330 TRERVRQIEAKALRKLRHPSRAKLLRDYLD 359



 Score = 67.6 bits (163), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 33/148 (22%), Positives = 64/148 (43%), Gaps = 11/148 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
              +++  + +   A  R  +T E+++  +   +    Q+++  A L   G+++      
Sbjct: 4   LSQTEELARSLAAKA-HRHTLTTEQISRAMEEADFDIAQLDELYAALEQRGVHL------ 56

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                 E+  +L          L+    S   + DDPV+ YL+E+G + LL+   E+A+A
Sbjct: 57  ----AEEEPAELPVLDDAQIGRLENELSSEGVALDDPVKTYLKEIGRVPLLTAGQEMALA 112

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWR 171
           K   AG A    +L E+ L     +  R
Sbjct: 113 KAARAGDADARRALSEANLRLVVSVAKR 140


>gi|307298746|ref|ZP_07578549.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
 gi|306915911|gb|EFN46295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
          Length = 416

 Score =  213 bits (542), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 136/272 (50%), Positives = 187/272 (68%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I   + ++ S  R +    +KGE     AK+E++ ANLRLV+S+AK+Y  RGL
Sbjct: 139 IKMYLKEIGKISLLTPSRERELARRAQKGE---PKAKEELITANLRLVVSIAKRYIGRGL 195

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + 
Sbjct: 196 TFLDLIQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVET 255

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +  R         PT EE+        E + ++L  +KE +SLE+PI  ++ S +
Sbjct: 256 INKLNKVIREHLQDHGEYPTIEELGNLTGKTPEKIEEILAASKETVSLESPISGDEESTM 315

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D +   P ++A++  LRE   ++L +L+PRE  VL+MR+G+      TLEEVG+ 
Sbjct: 316 GDFIHDDSMEQPEEAAMKMLLREQIDQILDTLSPREAMVLKMRYGLLDGKTKTLEEVGQF 375

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK+L++ L
Sbjct: 376 FNVTRERIRQIEVKALRKLRHPSRSKQLKALL 407



 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 45/186 (24%), Positives = 82/186 (44%), Gaps = 7/186 (3%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDE--V 58
           +      +     E  D+   +  +  D   KK+++  +++G+VT E++++  PPD    
Sbjct: 21  LAEKIADDEADSDETGDNSALMTKEEIDKRIKKLLRQGKKKGFVTYEDIDSAFPPDYEGF 80

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
            S  +E          IN+V+ + +E     +D ++  SS    S+     +   + S  
Sbjct: 81  DSSLVESIYEEFEKNKINIVEKEPVE----DDDDIESESSEELVSILETTPEMYDNISLK 136

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DP++MYL+E+G I LL+   E  +A+R + G       L  + L     I  R  +  G 
Sbjct: 137 DPIKMYLKEIGKISLLTPSRERELARRAQKGEPKAKEELITANLRLVVSIAKRY-IGRGL 195

Query: 179 TLLREI 184
           T L  I
Sbjct: 196 TFLDLI 201


>gi|13195265|gb|AAK15630.1|AF326348_2 RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 467

 Score =  213 bits (542), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 133/278 (47%), Positives = 189/278 (67%), Gaps = 4/278 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             + ++   I        +S ++ R +    R    +   AK  ++EANLRLV+S+AK+Y
Sbjct: 194 HRLDEMERLIAEGDAAAKLSPAQKRDL----RWIARDGRKAKNHLLEANLRLVVSLAKRY 249

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPV
Sbjct: 250 TGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 309

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+K+ R  R +   + REPTP+E+AK++ +  E V ++ +  +EPISL+  IGDE
Sbjct: 310 HMVEVINKLGRIQRELLQDLGREPTPQELAKEMDITEEKVLEIQQYAREPISLDQTIGDE 369

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+      TL+
Sbjct: 370 GDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLD 429

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 430 EIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 467



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG------RA 151
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++A+RIEAG        
Sbjct: 138 DEDESATLRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAERIEAGLYAQHRLD 197

Query: 152 MMMASLCESPLTFQ 165
            M   + E     +
Sbjct: 198 EMERLIAEGDAAAK 211


>gi|294782673|ref|ZP_06747999.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
 gi|294481314|gb|EFG29089.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
          Length = 500

 Score =  213 bits (542), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 144/305 (47%), Positives = 203/305 (66%), Gaps = 4/305 (1%)

Query: 376 GRELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E +P ++    +     E    +         I+  ++ I     ++  E        
Sbjct: 196 GDEFNPDYIEDINEEELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYA--- 252

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +K       A ++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GY
Sbjct: 253 KKAYEGDEEASQKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGY 312

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A+
Sbjct: 313 KFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAE 372

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L M VE ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE   
Sbjct: 373 RLGMEVEKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELD 432

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR K
Sbjct: 433 GVLKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 492

Query: 675 KLRSF 679
           KL  F
Sbjct: 493 KLEDF 497



 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/103 (29%), Positives = 43/103 (41%), Gaps = 4/103 (3%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D  DE   +   D+     ++   L           D+P++MYLRE+G + LL+ + EI 
Sbjct: 194 DFGDEFNPDYIEDINEEELSNEKLLN---LGNSAKVDEPIKMYLREIGQVPLLTHDEEIE 250

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            AK+   G       L ES L     I  +   N G  LL  I
Sbjct: 251 YAKKAYEGDEEASQKLIESNLRLVVSIAKK-HTNRGLKLLDLI 292



 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           +  I   ++ G  T EE+N  L  D   +E +E  +    + GI +++    + +  ++ 
Sbjct: 19  RDFITRVKEAGETTYEEINEELAAD-FPTEDIEGLINTFLDEGIKILNKTKKKTKTKTKT 77

Query: 92  SLDLASSASNSS 103
                +   + S
Sbjct: 78  EAKDETKTKSKS 89


>gi|159901184|ref|YP_001547431.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159894223|gb|ABX07303.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 375

 Score =  213 bits (542), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 132/256 (51%), Positives = 189/256 (73%), Gaps = 1/256 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
                + +++   E+  A++ +++ANLRLV+S+AKKY  RG+ FLDLIQEGNIGLM+A E
Sbjct: 120 LLEEKARLQQQVLESEAARQHLIQANLRLVVSIAKKYVGRGMSFLDLIQEGNIGLMRATE 179

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD+  G+KFSTYA WW++QAITRSI+D S TIR+PVH+ + I++V RTA ++   ++RE
Sbjct: 180 KFDYHKGFKFSTYATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALERE 239

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P+ EEI + L +P + VR+VL++ ++P+SLETP+G+E  S LGDFIED  +  PLD A +
Sbjct: 240 PSAEEIGEALGLPADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATE 299

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LRE    VL  L  RE R++ +R+G+      TLEEVG++F +TRERIRQIEAK +RK
Sbjct: 300 HLLREQLDEVLCKLDERERRIIELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRK 359

Query: 667 LKHPSR-SKKLRSFLD 681
           L+HP+   +KLR++L+
Sbjct: 360 LRHPAFGGRKLRAYLE 375



 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/148 (22%), Positives = 62/148 (41%), Gaps = 9/148 (6%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           ARQ  Y+T +++   LPP + ++   ++         I +++             +D   
Sbjct: 4   ARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPILEEPPTAAVHLRSRDVDDDD 63

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
                   L++       S DDPVRMYLRE+G + LL+   E  +AK++E G   M+  L
Sbjct: 64  --------LERSLIREGVSLDDPVRMYLREIGQVHLLTAHEETMLAKQLERGERAMIR-L 114

Query: 158 CESPLTFQALIIWRDELNDGTTLLREII 185
                  +     + ++ +     + +I
Sbjct: 115 ARHEYLLEEKARLQQQVLESEAARQHLI 142


>gi|296269171|ref|YP_003651803.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091958|gb|ADG87910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 367

 Score =  213 bits (542), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 142/289 (49%), Positives = 207/289 (71%), Gaps = 9/289 (3%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ L   +++       GI   E   +V        E   AK+ ++EAN
Sbjct: 88  AEEEVELAKAIEAGLFAEDKLCEK-KAAGIECPELEDLV-------WEGIRAKQRLIEAN 139

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+I
Sbjct: 140 LRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAI 199

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + I+K+VR  R++   + REPTPEEIAK++ +PVE V ++ +I +E
Sbjct: 200 ADQARTIRIPVHMVETINKLVRVQRQLHQDLGREPTPEEIAKEMDLPVERVVEIQRIAQE 259

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+SL++PI  E+ S LGDFIED +AV PL++A    L++    +L++L+ RE+R++++RF
Sbjct: 260 PVSLQSPI-GEEDSDLGDFIEDADAVVPLEAAAFILLQDHLDDILSTLSEREQRIIQLRF 318

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG++F VTRERIRQIE+K + KL+HP+R++ LR +LD
Sbjct: 319 GLADGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPTRAQVLRDYLD 367



 Score = 65.2 bits (157), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/121 (29%), Positives = 57/121 (47%), Gaps = 19/121 (15%)

Query: 39  RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS 98
           R RG V I+++       E S + ++  V ML++  + V+  +D +     E+  D    
Sbjct: 9   RTRGGVAIDDVAVAADRTEPSDDALDRVVQMLADEDLEVLAAEDEDPIRFDEEDFD---- 64

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                         +   T+D VR+YLRE+G + LL+ E E+ +AK IEAG       LC
Sbjct: 65  --------------SGAPTNDLVRIYLREIGKVPLLTAEEEVELAKAIEAGLF-AEDKLC 109

Query: 159 E 159
           E
Sbjct: 110 E 110


>gi|227499199|ref|ZP_03929334.1| RNA polymerase [Acidaminococcus sp. D21]
 gi|226904646|gb|EEH90564.1| RNA polymerase [Acidaminococcus sp. D21]
          Length = 582

 Score =  213 bits (542), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 147/258 (56%), Positives = 196/258 (75%), Gaps = 1/258 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + +    ++ +       AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA
Sbjct: 325 EDRKRFNRVLHRAAMCGEKAKKALSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKA 384

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR +R++  ++ 
Sbjct: 385 VEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRVSRQLLQELG 444

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEEIA+++ +PVE VR++ KI +EP+SLETPIG+E+ SHLGDFIED+ A SP ++A
Sbjct: 445 REPTPEEIAQEMDVPVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDQEAPSPAEAA 504

Query: 605 IQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               L+E   +VL   L+PRE RVL +RFG+      TLEEVG+ F VTRERIRQIEAKA
Sbjct: 505 SYTLLQEQLGKVLQEHLSPRERRVLELRFGLLDGRTRTLEEVGQYFGVTRERIRQIEAKA 564

Query: 664 IRKLKHPSRSKKLRSFLD 681
           +RKL+ P RSK L+ FL+
Sbjct: 565 LRKLRSPKRSKPLKEFLE 582



 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 106/287 (36%), Gaps = 21/287 (7%)

Query: 39  RQRGYVTIEELNAFLPP-DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           +  G +T +E+   +   D +S ++M++  + L+   I VVD    E+E  + D  +L  
Sbjct: 75  KNSGVLTYKEIQDRMQNTDSISVDEMDEIYSKLAEKNIEVVDDHAEEEEPENMDDEELTI 134

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
             S     L           DDPVRMYL+E+G + LLS   EI +AKR + G    +   
Sbjct: 135 EESE----LSNLSVPEGVIVDDPVRMYLKEIGRVPLLSGNDEIKLAKRTDKGNQAAVILD 190

Query: 158 CESP----------LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            +SP          L+   L+   ++         EI      +    +       +  S
Sbjct: 191 GQSPEVEREPVNKRLSAAKLLDTIEQYLKEE----EIWCDSRTVSIVYRFILAETQDNPS 246

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             +    +        +          K     RS      +   +D+  L E  D  A 
Sbjct: 247 LDEAAIEAYSPAFTVDERKRLQRLLLEKGYHLTRSPKTGSGDEEVDDKSYLPELYDLFAA 306

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
               +E +    +   L+E  + +  +  L   A+ G+K +K+  + 
Sbjct: 307 VSEKVETKPDESLSIRLEEDRKRFNRV--LHRAAMCGEKAKKALSEA 351


>gi|225377779|ref|ZP_03755000.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
 gi|225210363|gb|EEG92717.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
          Length = 426

 Score =  213 bits (542), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 165/426 (38%), Positives = 249/426 (58%), Gaps = 16/426 (3%)

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
           M  +   +V     E A +    +      +          K  +  +++      + L 
Sbjct: 1   MAKKTENEVKETKKEAAVMDEAAKEKFQQKLKDLLALAKKKKNMLEYQEISDFFADMQLE 60

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH--------- 382
             + D +++ L   +  ++    +         +  +  +E  +     P          
Sbjct: 61  AEQFDKILDFLEANNIDVLRITDDDSDDEILLDVDDEDEIEVEKIDLSVPDGVSIEDPVR 120

Query: 383 -WVSYAKDFP--EGEWKNFVACEVDSILKIRNEIKSI----SVETGISISEFRHIVSMVR 435
            ++      P    E +  +A  +++    + +I  +       T   ++E +  +  ++
Sbjct: 121 MYLKEIGKVPLLSAEEEIELAKNMEAGAVAKEKIAILKSREEKATEEELAEIKEEIKNLQ 180

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K       AKK + EANLRLV+S+AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYK
Sbjct: 181 KDLDAGDEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYK 240

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R +R++  ++ REP+PEEIA +
Sbjct: 241 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAE 300

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MPVE VR++LKI++EP+SLETPIG+E+ SHLGDFI+D N   P D+A    L+E    
Sbjct: 301 MNMPVERVREILKISQEPVSLETPIGEEEDSHLGDFIQDDNVPVPADAAAFTLLKEQLEE 360

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT RE++VL +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPSRS+K
Sbjct: 361 VLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRK 420

Query: 676 LRSFLD 681
           L+ +L+
Sbjct: 421 LKDYLE 426



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 36/150 (24%), Positives = 66/150 (44%), Gaps = 4/150 (2%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVS 59
           M    +       +     D    +      K ++ LA+++   +  +E++ F    ++ 
Sbjct: 1   MAKKTENEVKETKKEAAVMDEAAKEKFQQKLKDLLALAKKKKNMLEYQEISDFFADMQLE 60

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +EQ +  +  L    I+V+    + D++  ++ L          V           S +D
Sbjct: 61  AEQFDKILDFLEANNIDVL---RITDDDSDDEILLDVDDEDEIEVEKIDLSVPDGVSIED 117

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           PVRMYL+E+G + LLS E EI +AK +EAG
Sbjct: 118 PVRMYLKEIGKVPLLSAEEEIELAKNMEAG 147


>gi|124022438|ref|YP_001016745.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9303]
 gi|123962724|gb|ABM77480.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
          Length = 444

 Score =  213 bits (542), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 189/267 (70%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +    +   +FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 185 KEWAALVEMPNIKFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDL 237

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 238 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 297

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 298 KTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 357

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P     +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 358 -SDTENPEQDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFEVTR 416

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 417 ERIRQIEAKALRKLRHPNRNGVLKEYI 443



 Score = 42.5 bits (98), Expect = 0.24,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 31/64 (48%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E E     +   + + + +      +       T+D +R+YL+E+G I LL  + EI +
Sbjct: 98  AETESSQAAAKASSEADAKARALANIKIGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIEL 157

Query: 143 AKRI 146
           A++I
Sbjct: 158 ARKI 161


>gi|87123878|ref|ZP_01079728.1| Sigma-70 factor [Synechococcus sp. RS9917]
 gi|86168447|gb|EAQ69704.1| Sigma-70 factor [Synechococcus sp. RS9917]
          Length = 456

 Score =  213 bits (542), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 190/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +    + + +FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 197 KEWAALVEMPVIKFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDL 249

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 250 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 309

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 310 KTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 369

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P     +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 370 -ADIENPEQDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTR 428

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 429 ERIRQIEAKALRKLRHPNRNGVLKEYI 455



 Score = 41.0 bits (94), Expect = 0.77,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 139 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 173


>gi|292670109|ref|ZP_06603535.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648297|gb|EFF66269.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 382

 Score =  213 bits (542), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 144/273 (52%), Positives = 194/273 (71%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   +         A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 112 VRMYLKEIGRVPLLTADEEIELARRME---AGDESARHRLEEANLRLVVSIAKRYVGRGM 168

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 169 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 228

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K +R +R++   + R+PT EE+AK++ +    VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 229 INKYIRISRQLLQDLGRDPTAEEVAKEMGLSTLRVREIMKIAQEPVSLETPIGEEEDSHL 288

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A+ P D+A    L+E  T VL +L PRE  VLR+RFG+      TLEEVG+ 
Sbjct: 289 GDFIEDEAALDPADAASVMLLKEQITEVLQTLAPREAEVLRLRFGLEDGRSRTLEEVGQS 348

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HP R +KL+   D
Sbjct: 349 FGVTRERIRQIEAKALRKLRHPVRLRKLQGNFD 381



 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/155 (25%), Positives = 71/155 (45%), Gaps = 4/155 (2%)

Query: 33  KMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++++ ++  G  +T  EL   L    ++ + M+     L +  + +VD  +  +  G E 
Sbjct: 21  ELLERSKANGDTLTCSELVEALEQQMMTPDAMDMLYQRLIDGNVEIVDDTEAGEMIGEEP 80

Query: 92  SLDLASSASNSSVFLQKRKDS--ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +        + +    + + S     + DDPVRMYL+E+G + LL+ + EI +A+R+EAG
Sbjct: 81  ADLEEDLDKDDAELDLETELSVPEGVAVDDPVRMYLKEIGRVPLLTADEEIELARRMEAG 140

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                  L E+ L     I  R  +  G   L  I
Sbjct: 141 DESARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI 174


>gi|259507416|ref|ZP_05750316.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
 gi|259164981|gb|EEW49535.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
          Length = 381

 Score =  213 bits (541), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 128/250 (51%), Positives = 181/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 132 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 191

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 192 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 251

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 252 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 311

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 312 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 371

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 372 RSQVLRDYLD 381



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/60 (38%), Positives = 35/60 (58%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D          S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 45  DDGSSVWDEDESATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 104


>gi|303229406|ref|ZP_07316196.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
 gi|303230872|ref|ZP_07317619.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514632|gb|EFL56627.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302515942|gb|EFL57894.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 388

 Score =  213 bits (541), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 143/281 (50%), Positives = 196/281 (69%), Gaps = 9/281 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR---------KGECEASIAKKEMVEANLRLVISV 459
           +R  +K I     +S  E   +   +          K    +  AKK++V+ANLRLV+S+
Sbjct: 108 VRMYLKEIGRVPLLSADEEIVLAKQIEAGAEEDATYKEIQLSKKAKKKLVDANLRLVVSI 167

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAITR+IADQ+ TI
Sbjct: 168 AKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIADQARTI 227

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++R +R++     REPTPEEIA+ + +  E VR++ KI +EP+SLETP
Sbjct: 228 RIPVHMVETINKLIRISRQLLQDKGREPTPEEIAEGMGITAERVREIQKIAQEPVSLETP 287

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+E+ SHLGDFIED++AV+P D+A    L+E    V   LT RE++VL +RFG+     
Sbjct: 288 IGEEEDSHLGDFIEDQDAVAPDDAASYILLQEQIEDVFTCLTDREQQVLILRFGLKDGKP 347

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 348 RTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 388



 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 44/175 (25%), Positives = 81/175 (46%), Gaps = 17/175 (9%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
            +++   ++++  R+ G +T  E++  L    E+++EQ++D     + + I VV   + +
Sbjct: 9   QTEEIVAQLLEKGRKSGVLTQSEISDALHEQSELTAEQLDDIYVTFNKLNIEVVPDVEDD 68

Query: 85  DEEGSEDSLDLASS---ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D++ + +  D   +   A++           A  + DDPVRMYL+E+G + LLS + EI 
Sbjct: 69  DKDDAIEPDDDVDNDRDAASEKNISIDLSVDASVNIDDPVRMYLKEIGRVPLLSADEEIV 128

Query: 142 IAKRIEAGRAM------------MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +AK+IEAG                   L ++ L     I  R  +  G   L  I
Sbjct: 129 LAKQIEAGAEEDATYKEIQLSKKAKKKLVDANLRLVVSIAKRY-VGRGMLFLDLI 182


>gi|312139424|ref|YP_004006760.1| sigma-70 factor sigb [Rhodococcus equi 103S]
 gi|325672687|ref|ZP_08152383.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
 gi|311888763|emb|CBH48075.1| sigma-70 factor SigB [Rhodococcus equi 103S]
 gi|325556564|gb|EGD26230.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
          Length = 322

 Score =  213 bits (541), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 110/264 (41%), Positives = 186/264 (70%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ +  ++ ++ R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 61  LATKKRLTAAKKRDLATIVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 116

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 117 EGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 176

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T EE++++  +P   +  +L  +++P+SL+ P+G+++ + LGDFIED 
Sbjct: 177 KRELHQQLGREATDEELSQESGIPEHKIADLLDHSRDPVSLDMPVGNDEEAPLGDFIEDS 236

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK F ++RER
Sbjct: 237 EATSAENAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRER 296

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R+ +LR++
Sbjct: 297 VRQIEREVMGKLRQGERADRLRAY 320



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 20/68 (29%), Positives = 31/68 (45%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VR+YL  +G   LL+   E+ +A+RIEAG         +  LT          + DG 
Sbjct: 24  DLVRVYLNGIGRTALLTAADEVDLARRIEAGLYAAHVLATKKRLTAAKKRDLATIVRDGE 83

Query: 179 TLLREIID 186
              R +++
Sbjct: 84  AARRHLLE 91


>gi|51244645|ref|YP_064529.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50875682|emb|CAG35522.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 534

 Score =  213 bits (541), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 151/328 (46%), Positives = 211/328 (64%), Gaps = 15/328 (4%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNF-------VACEVDSILKIRNEIKSISVET 420
               E  + R L   +V+      E   K F       +A E D   +     + +    
Sbjct: 205 KQIAELFEDRVLSSEYVNMVAQAAEDLSKRFRKIFVELIAGEGDLPEEEMRSPEELERLV 264

Query: 421 GI--------SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            +        S+     ++  V +G   +  AK+ +V ANLRLVISV+K++ NRGLQF D
Sbjct: 265 DLQFIRESGSSLQSLNELLKEVEEGRFISKEAKEALVRANLRLVISVSKRFVNRGLQFSD 324

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA EKFD+  G+KFSTYA WW++Q+ITR IADQ  TIR+PVHM + I+++
Sbjct: 325 LIQEGNIGLMKAVEKFDYRRGFKFSTYATWWIRQSITRGIADQGRTIRLPVHMIETINRM 384

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R ++    +  REP+ EE+A +L   V+ V+  LKI K+ ISL+TP+GD+  ++LGDFI
Sbjct: 385 LRVSKDFYLEEHREPSVEEVAGQLGTEVDKVKSALKIAKDAISLDTPVGDDGETYLGDFI 444

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            DKN + P   A+ A+L+E  ++VL+SL+PREE+VL+MR+GI    ++TLEEVG+ F VT
Sbjct: 445 VDKNCLGPDGFAMVASLKECLSQVLSSLSPREEKVLKMRYGILEKREYTLEEVGRCFNVT 504

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RERIRQIEA+AI KLKHPSR   L+ F+
Sbjct: 505 RERIRQIEAQAISKLKHPSRCGDLKVFM 532



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 108/301 (35%), Gaps = 24/301 (7%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              D L     A    +   +RK     +  D + +Y+REMGS++LL  + E  +A+ IE
Sbjct: 47  AGSDLLKEGVRAPKRRISSSQRKQGDSTAAADSMNIYMREMGSLKLLKYDDERKLAQTIE 106

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII----DLEACIGPESKGGFFH-- 201
            G+  +  ++ +S L    L+  ++ + +    +   +    D +  +  E+   F    
Sbjct: 107 KGKKQVQFAVLQSTLAMPILLQMKETIVENPGKISLFVGGIPDAQFDVIAEACDVFLANW 166

Query: 202 ----GTEGHSYQKREDSSQEKERDDVQET-----------EGDIESAAKVSKDDRSKVDS 246
               G +G   +  +         D +E              ++     +S +  + V  
Sbjct: 167 QTCVGLDGQRKKYLKKYLSPSLSADAREKLLFNILQCGKQIAELFEDRVLSSEYVNMVAQ 226

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
             E+     R +   E  +       E+   P+ +  L ++  +     SLQ      ++
Sbjct: 227 AAEDLSKRFRKIFV-ELIAGEGDLPEEEMRSPEELERLVDLQFIRESGSSLQSLNELLKE 285

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
            E+     K  KE LV+    L L  S     V +    S  I      L++  + +  +
Sbjct: 286 VEEGRFISKEAKEALVRAN--LRLVISVSKRFVNRGLQFSDLIQEGNIGLMKAVEKFDYR 343

Query: 367 R 367
           R
Sbjct: 344 R 344


>gi|320530862|ref|ZP_08031899.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136896|gb|EFW28841.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 381

 Score =  213 bits (541), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 145/273 (53%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V + R+ E   + A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVPLLTAEEE---VELARRMEAGDASARHRLEEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + 
Sbjct: 168 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R +  ++ R+ T EEIAK++ + V  VR+++KI +EP+SLETP+G+E+ SHL
Sbjct: 228 INKLVRVSRSLLQELGRDATAEEIAKEMGLSVVRVREIMKIAQEPVSLETPVGEEEDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A+ P D+A    L+E  + VL +L PRE  VLR+RFG+      TLEEVG+ 
Sbjct: 288 GDFIEDEAALDPADAASMMLLKEQISEVLKTLAPREAEVLRLRFGLEDGRSRTLEEVGQS 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HP R +KL+   +
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPVRLRKLQGNFE 380



 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 75/352 (21%), Positives = 130/352 (36%), Gaps = 28/352 (7%)

Query: 30  SWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED--E 86
              +++K  ++ G  +T  EL   L   ++S ++M+D        G+ +VD  D+E    
Sbjct: 17  RIDELLKRGKENGGTLTFSELIEELEKSDMSPDEMDDLYGRFQEFGVEIVDDTDMEAMAA 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E +E      +                  + DDPVRMYL+E+G + LL+ E E+ +A+R+
Sbjct: 77  EDAESLAADDADMEQEEAVEIDLSVPEGVALDDPVRMYLKEIGRVPLLTAEEEVELARRM 136

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG A     L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 137 EAGDASARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLLKAVEKF 187

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     +   A+  +     V++  +        L E   D+ 
Sbjct: 188 DYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKLVRVSRSLLQELGRDAT 247

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRS----------LQDNAVNGQKDEKSSVKCKV 316
               A E  L    +  + +IA+    L +                    D   +    +
Sbjct: 248 AEEIAKEMGLSVVRVREIMKIAQEPVSLETPVGEEEDSHLGDFIEDEAALDPADAASMML 307

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           LKE++ +++ +L+  ++ +  L   L D           L  + QS+G+ R+
Sbjct: 308 LKEQISEVLKTLAPREAEVLRLRFGLED------GRSRTLEEVGQSFGVTRE 353


>gi|229491308|ref|ZP_04385134.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|229321847|gb|EEN87642.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 430

 Score =  213 bits (541), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 133/286 (46%), Positives = 193/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + ++ +   ++    +   +    +     + + AK  ++EANLRL
Sbjct: 145 AEEEVELAKRIEAGLYAVQIMQDLADKGEKLPAAQRRDMSWICRDGNRAKNHLLEANLRL 204

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 205 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 264

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 265 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 324

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 325 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLT 384

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 385 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 430



 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 39/76 (51%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +    E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 88  EETAAEPSEKDKASGDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 147

Query: 139 EIAIAKRIEAGRAMMM 154
           E+ +AKRIEAG   + 
Sbjct: 148 EVELAKRIEAGLYAVQ 163


>gi|23013686|ref|ZP_00053554.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 322

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 115/321 (35%), Positives = 178/321 (55%), Gaps = 8/321 (2%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M        +     +++ D  + D    + KKM+   ++RGYVT +ELNA +PP+EVSS
Sbjct: 1   MATKSTNTAEVSENQDEAMDGPLLDTLGVAVKKMVAKGKERGYVTYDELNAAMPPEEVSS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           EQ+EDT+AMLS +GINVV+ ++ ED        +   +   S       +D     TDDP
Sbjct: 61  EQIEDTMAMLSELGINVVESEEGEDNAPEAAEEEATETEGYSGAGNVDEEDL--GRTDDP 118

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMYLREMGS+ELLSREGEIAIAKRIEAGR MM+  +CESPLT +A++ W D L +G  L
Sbjct: 119 VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTLRAVVDWHDALVEGKML 178

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           LR+IIDL+A  G +         E    +    +++E   +   E + + E+  + ++ +
Sbjct: 179 LRDIIDLDATYGAD-----PEPDELAEVEAEGVAAEEPAPEAAVEAKPEGEAKPEGAEGE 233

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           + +        E +     E+ ++++ +L+AME +L P V+   + IA  + +L  +QD 
Sbjct: 234 KEEGAEGEGEVEGEAEGEAEEGEENSISLAAMEIELLPIVLETFEVIAATHHKLEKVQDQ 293

Query: 301 AVNG-QKDEKSSVKCKVLKEK 320
            +    K E  +   +   +K
Sbjct: 294 RLAALHKGEAVTPAMEKTYDK 314


>gi|196234461|ref|ZP_03133287.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
 gi|196221517|gb|EDY16061.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
          Length = 479

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 131/266 (49%), Positives = 190/266 (71%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++++  E  ++ SE    +  +++ + +A  A+ EMVE NLRLV+S+A++Y NRG  FLD
Sbjct: 211 MRNLQAEMWLNPSELNVELQEMKRWQRKALEARTEMVECNLRLVVSIAREYQNRGQPFLD 270

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLM+A E+F++  GYKF+T A WW++QAI+RSIA+Q+ TIRIP HM D + K+
Sbjct: 271 LIQEGNIGLMRAVERFEYRRGYKFATCATWWIRQAISRSIANQARTIRIPTHMIDLLAKL 330

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R  R+M+ +  R+PT E++A +L +P+  VR +LK+ +EPIS+ TP+G+E  S LGDFI
Sbjct: 331 IRVQRQMTQESGRDPTAEDLAGELHLPLRRVRALLKMAEEPISIHTPVGEEGGSRLGDFI 390

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED +   P   A  A LRE    VL +LT RE  +L  RFG+    + TLEE+G+ F VT
Sbjct: 391 EDHSVEDPSKQAAVAMLREKINAVLHTLTEREREILEQRFGLIDGRERTLEEIGRHFKVT 450

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRS 678
           RER+RQIEAKA+RK++HP R ++L+ 
Sbjct: 451 RERVRQIEAKALRKMRHPERRRQLQG 476



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 1/98 (1%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            S    D  S         + R+ S     +D +R+YLR+     LLSRE E  I +R+E
Sbjct: 20  ESSAEPDRISRRQPEQGEDEIRRPSTSGGMEDHLRLYLRQT-PHRLLSREQEADICRRVE 78

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           A    +   L     T  A +     L      L  ++
Sbjct: 79  AAEEQIRQHLYRFGSTAHAHLQLVRRLLAREERLDHVV 116


>gi|194477302|ref|YP_002049481.1| RNA polymerase sigma factor [Paulinella chromatophora]
 gi|171192309|gb|ACB43271.1| RNA polymerase sigma factor [Paulinella chromatophora]
          Length = 460

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 139/300 (46%), Positives = 200/300 (66%), Gaps = 8/300 (2%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +  A+   +  +   +A + +       + K  +    +S+ +FR  + + R+    
Sbjct: 168 DEEIELARKISDLLYLEELAGQFEGRKGYYPDNKEWAALVEMSLIKFRRRLMLGRR---- 223

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA
Sbjct: 224 ---AKAKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 280

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +
Sbjct: 281 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTI 340

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L
Sbjct: 341 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATL 399

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 400 SPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 459



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 31/67 (46%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
              + + +      D+    + +      +       T+D +R+YL+E+G I LL  + E
Sbjct: 111 STPISETKSESKITDVDDKDAKAKALASIKIGPKGVYTEDSIRVYLQEIGRIRLLRPDEE 170

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 171 IELARKI 177


>gi|325849230|ref|ZP_08170681.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325480230|gb|EGC83297.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 612

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 145/280 (51%), Positives = 206/280 (73%), Gaps = 4/280 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +++   K +   K I  + G    + + +   +     +A+ AK+++ E NLRLV+S+A
Sbjct: 337 KDLERFEKTKELCKKIFEDQGFDADDVKRLNRAI----FDANRAKQKLAETNLRLVVSIA 392

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW++QAITR+IADQ+ TIR
Sbjct: 393 KKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIR 452

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+VR  R++   + R+P+ EEIA+++ + VE V+++ KI +EP+SLETPI
Sbjct: 453 IPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKVQEIRKIAQEPVSLETPI 512

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+E+ SHLGDFIED  A++P D+A  + LR+    VL+ L  RE+RVL++RFG+   T  
Sbjct: 513 GEEEDSHLGDFIEDDTAINPDDAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPR 572

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 573 TLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 612



 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/156 (22%), Positives = 65/156 (41%), Gaps = 25/156 (16%)

Query: 26  FSDDSWKKMIKLAR-----QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
             DD  K++I   +     Q G VT +++  F    E+  E  +  +  + + GI +V+ 
Sbjct: 9   LEDDLLKEIIDEFKSISESQDGIVTYKQVYTFETFKEMEDESKKYVIGQIISNGIEIVEE 68

Query: 81  D--------------------DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           +                    +   +E  ED +   S        + + +       DDP
Sbjct: 69  ERTVLDEEDDDEIIDDIDDEDEDFSDEKLEDHMKKVSKKQKVERKIVQEETITGIKLDDP 128

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           V+MYL+E+G ++LL    EI +AK++E G   + + 
Sbjct: 129 VKMYLKEIGKVKLLDAHEEIFLAKKMELGDIALRSK 164


>gi|15894582|ref|NP_347931.1| RNA polymerase sigma factor RpoD [Clostridium acetobutylicum ATCC
           824]
 gi|464686|sp|P33656|RPOD_CLOAB RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15024230|gb|AAK79271.1|AE007642_3 RNA polymerase sigma factor RPOD [Clostridium acetobutylicum ATCC
           824]
 gi|312373|emb|CAA80625.1| major vegetative sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|325508714|gb|ADZ20350.1| major vegetative sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 378

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 154/273 (56%), Positives = 207/273 (75%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +   ++        A+K++ EANLRLV+S+AK+Y  RG+
Sbjct: 109 VRMYLKEIGKVPLLSPEEEIDLAQRIK---NGDRSARKKLAEANLRLVVSIAKRYVGRGM 165

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 166 LFLDLIQEGNLGLIKAVEKFDFKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 225

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R +R++  ++ REP PEEIAK + MPV+ VR+++KI +EP+SLETPIG+E+ SHL
Sbjct: 226 INKLIRVSRQLLQELGREPQPEEIAKIMDMPVDKVREIMKIAQEPVSLETPIGEEEDSHL 285

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D  A +P D+A    L+E   ++L +LTPREE+VLR+RFG+      TLEEVGK+
Sbjct: 286 GDFIPDDEAPAPADAAAFRMLKEQLLKILNTLTPREEKVLRLRFGLDDGRARTLEEVGKE 345

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKL+ +LD
Sbjct: 346 FNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 378



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 52/181 (28%), Positives = 84/181 (46%), Gaps = 20/181 (11%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
           G+K+N    S+ E + +    +      K +I   ++ G +T +E+   L   ++  EQ+
Sbjct: 11  GEKKNSKKVSKEESAKEK---NEKMKIVKNLIDKGKKSGSLTYKEIMDELQEVDLGPEQI 67

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           E    +L ++G++VV   D+ + E  E+ LDL                    + DDPVRM
Sbjct: 68  EKIYEVLESVGVDVV--GDMHEIEVEEEDLDLT--------------IPEGIAIDDPVRM 111

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G + LLS E EI +A+RI+ G       L E+ L     I  R  +  G   L  
Sbjct: 112 YLKEIGKVPLLSPEEEIDLAQRIKNGDRSARKKLAEANLRLVVSIAKRY-VGRGMLFLDL 170

Query: 184 I 184
           I
Sbjct: 171 I 171


>gi|313897024|ref|ZP_07830571.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974471|gb|EFR39939.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 381

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 145/273 (53%), Positives = 199/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    V + R+ E   + A+  + EANLRLV+S+AK+Y  RG+
Sbjct: 111 VRMYLKEIGRVPLLTAEEE---VELARRMEAGDASARHRLEEANLRLVVSIAKRYVGRGM 167

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + 
Sbjct: 168 LFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVET 227

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R +  ++ R+ T EEIAK++ + V  VR+++KI +EP+SLETP+G+E+ SHL
Sbjct: 228 INKLVRVSRSLLQELGRDATAEEIAKEMGLSVVRVREIMKIAQEPVSLETPVGEEEDSHL 287

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A+ P D+A    L+E  + VL +L PRE  VLR+RFG+      TLEEVG+ 
Sbjct: 288 GDFIEDEAALDPADAASMMLLKEQISEVLKTLAPREAEVLRLRFGLEDGRSRTLEEVGQS 347

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HP R +KL+   +
Sbjct: 348 FGVTRERIRQIEAKALRKLRHPVRLRKLQGNFE 380



 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 75/352 (21%), Positives = 130/352 (36%), Gaps = 28/352 (7%)

Query: 30  SWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED--E 86
              +++K  ++ G  +T  EL   L   ++S ++M+D        G+ +VD  D+E    
Sbjct: 17  RIDELLKRGKENGGTLTFSELIEELEKSDMSPDEMDDLYGRFREFGVEIVDDTDMEAMAA 76

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E +E      +                  + DDPVRMYL+E+G + LL+ E E+ +A+R+
Sbjct: 77  EDAESLAADDADMEQEEAVEIDLSVPEGVALDDPVRMYLKEIGRVPLLTAEEEVELARRM 136

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG A     L E+ L     I  R  +  G   L  I         E   G     E  
Sbjct: 137 EAGDASARHRLEEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNLGLLKAVEKF 187

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y K    S        Q     +   A+  +     V++  +        L E   D+ 
Sbjct: 188 DYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKLVRVSRSLLQELGRDAT 247

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRS----------LQDNAVNGQKDEKSSVKCKV 316
               A E  L    +  + +IA+    L +                    D   +    +
Sbjct: 248 AEEIAKEMGLSVVRVREIMKIAQEPVSLETPVGEEEDSHLGDFIEDEAALDPADAASMML 307

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           LKE++ +++ +L+  ++ +  L   L D           L  + QS+G+ R+
Sbjct: 308 LKEQISEVLKTLAPREAEVLRLRFGLED------GRSRTLEEVGQSFGVTRE 353


>gi|159896548|ref|YP_001542795.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889587|gb|ABX02667.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 400

 Score =  212 bits (540), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 153/364 (42%), Positives = 228/364 (62%), Gaps = 8/364 (2%)

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
           ++ +++ S      +++ + + L   + R+     +   +  S   + D   E     + 
Sbjct: 43  EIQQIIDSQRDEDKQLEEIRDTLQKANIRVEETGDDDDEITVSENPEADFSNEGISVNDT 102

Query: 380 DPHWVSYAKDFP--EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
              ++      P  +GE +  +A  ++   K + E+  I  +  +S  E   +   + + 
Sbjct: 103 VRLYLREIGLVPLLKGEQEVELARAMEDGDKAQQEL--IENDHTLSDVERLALRRRIDR- 159

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A++ +  ANLRLV+SVAKKY  RGL  LDLIQEGN+GL++A EKF++  G+KFS
Sbjct: 160 ---GEQAREHLTTANLRLVVSVAKKYIGRGLSLLDLIQEGNVGLIRAVEKFNYTKGFKFS 216

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR+IADQ+ TIRIPVHM + I++++RTARR++ +  REP+ EE+A+ L 
Sbjct: 217 TYATWWIRQAITRAIADQARTIRIPVHMVETINRMMRTARRLTQENGREPSDEELAQALD 276

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + VE VR + K + EP+SLETP+G E+ S LGDF+ D+   +P D+A    LRE   +VL
Sbjct: 277 LTVEKVRSIRKTSMEPVSLETPVGQEEDSQLGDFLPDEKLEAPSDAASHQMLREQVAQVL 336

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             LT RE+RVL++RFG+   T  TLEEVGK+F VTRERIRQIE KA+RKL+HP   KKLR
Sbjct: 337 DQLTEREKRVLKLRFGLEDGTQRTLEEVGKEFGVTRERIRQIEVKALRKLRHPRFGKKLR 396

Query: 678 SFLD 681
            +L+
Sbjct: 397 DYLE 400



 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 42/171 (24%), Positives = 73/171 (42%), Gaps = 20/171 (11%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           DS+   +++DD        D    ++   ++RGYVT  E+   +       +Q+E+    
Sbjct: 9   DSELAGDETDDFPALRTLSD----LLATGKKRGYVTPGEIQQIIDSQRDEDKQLEEIRDT 64

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           L    I V        EE  +D  ++  S +  + F      +   S +D VR+YLRE+G
Sbjct: 65  LQKANIRV--------EETGDDDDEITVSENPEADF-----SNEGISVNDTVRLYLREIG 111

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ--ALIIWRDELNDGT 178
            + LL  E E+ +A+ +E G       L E+  T      +  R  ++ G 
Sbjct: 112 LVPLLKGEQEVELARAMEDGDK-AQQELIENDHTLSDVERLALRRRIDRGE 161


>gi|313837136|gb|EFS74850.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA2]
 gi|314927842|gb|EFS91673.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL044PA1]
 gi|314971907|gb|EFT16005.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA3]
          Length = 370

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 137/298 (45%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 73  VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIPEKDREDYEWIAEDGKV 132

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 133 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 192

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 193 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELANELDMTAEKV 252

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G++  S  GD IED  A+ P D+     L+E    VL +L+ R
Sbjct: 253 IEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAIVPADAVNFTLLQEQLHDVLDTLSER 312

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  V+ MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 313 EAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 370



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           +D  D + +E ++D   +   A   S+      D  +       +T DPV+ YL+++G +
Sbjct: 24  IDERDYDPDEAAKDEQQINKEAEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 83

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 84  ALLNAVEEVDLAKRIEAGL 102


>gi|33866957|ref|NP_898516.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639558|emb|CAE08942.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 467

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 119/351 (33%), Positives = 193/351 (54%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +      R++     LL+  +          E ++  EL     +    +P  
Sbjct: 122 RVDLLTNEEEVTLARLVQRREALLQQQRDLATSDAAIGELYRLEELQRREANQHSHWPTK 181

Query: 394 -EWKNFVACEVDSILKIRNEIKS-ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW         S+ +++  I++        +  E R + + +R        AK  M++A
Sbjct: 182 QEWARAAHL---SLAELQQRIEAGYGAWAREANLEARELKTALR----NGRRAKDHMIQA 234

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q +TR+
Sbjct: 235 NLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGMTRA 294

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+PVH+ +K++++ R  + ++    R  +  ++A+ L +  + VR+ L    
Sbjct: 295 IATQSRTIRLPVHVTEKLNRIKRAQQEIATNEGRIASIADLARALKLSEDTVRQTLARVP 354

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +SL+T +G +  + LGD IED  A +P  +     L      +L  LT RE  VLR R
Sbjct: 355 RSVSLDTRVGRDQDTQLGDLIEDGKA-TPEQTLTHDELHNDLEHLLDELTSREAAVLRRR 413

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 414 FGLEDDTPQTLAQIGEALKLSRERVRQIETRALLKLRQPQRRSKVRDYIQG 464



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 95/258 (36%), Gaps = 27/258 (10%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           + +D   RST D +R+YL+++G ++LL+ E E+ +A+ ++                 +AL
Sbjct: 100 ETRDRRSRSTTDLLRLYLQDIGRVDLLTNEEEVTLARLVQRR---------------EAL 144

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           +  + +L      + E+  LE     E+       T+    +    S  E ++       
Sbjct: 145 LQQQRDLATSDAAIGELYRLEELQRREANQHSHWPTKQEWARAAHLSLAELQQRIEAGYG 204

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
                A   +++ ++ +        N  R  D     +   + A+  + + + M  LD +
Sbjct: 205 AWAREANLEARELKTAL-------RNGRRAKDHMIQANLRLVVAVAKKYQQRGMELLDLV 257

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            E    L    +     +    S+       + +   +     ++ L     + L  ++ 
Sbjct: 258 QEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGMTRAIATQSRTIRLPVHVTEKL-NRIK 316

Query: 344 DISKRIMHNEGELLRLAQ 361
              + I  NEG +  +A 
Sbjct: 317 RAQQEIATNEGRIASIAD 334


>gi|212697198|ref|ZP_03305326.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675973|gb|EEB35580.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 617

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 145/280 (51%), Positives = 206/280 (73%), Gaps = 4/280 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +++   K +   K I  + G    + + +   +     +A+ AK+++ E NLRLV+S+A
Sbjct: 342 KDLERFEKTKELCKKIFEDQGFDADDVKRLNRAI----FDANRAKQKLAETNLRLVVSIA 397

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  RG+ FLDLIQEGN+GLMKA +K+D+  G+KFSTYA WW++QAITR+IADQ+ TIR
Sbjct: 398 KKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIR 457

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPVHM + I+K+VR  R++   + R+P+ EEIA+++ + VE V+++ KI +EP+SLETPI
Sbjct: 458 IPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKVQEIRKIAQEPVSLETPI 517

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+E+ SHLGDFIED  A++P D+A  + LR+    VL+ L  RE+RVL++RFG+   T  
Sbjct: 518 GEEEDSHLGDFIEDDTAINPDDAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPR 577

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEEVGK+F VTRERIRQIEAKA+RKLK P++S+ L+ FL
Sbjct: 578 TLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSELLKDFL 617



 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/156 (22%), Positives = 64/156 (41%), Gaps = 25/156 (16%)

Query: 26  FSDDSWKKMIKLAR-----QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
             DD  K++I   +     Q G VT +++  F    E+  E  +  +  + + GI +V+ 
Sbjct: 14  LEDDLLKEIIDEFKSISESQDGIVTYKQVYTFETFKEMEDESKKYVIGQIISNGIEIVEE 73

Query: 81  DDLE--------------------DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           +                        +E  ED +   S        + + +       DDP
Sbjct: 74  ERTVLDEEDDDEIIDDIDDEDEDFSDEKLEDHMKKVSKKQKVERKIVQEETITGIKLDDP 133

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           V+MYL+E+G ++LL    EI +AK++E G   + + 
Sbjct: 134 VKMYLKEIGKVKLLDAHEEIFLAKKMELGDIALRSK 169


>gi|145594022|ref|YP_001158319.1| RNA polymerase sigma factor [Salinispora tropica CNB-440]
 gi|145303359|gb|ABP53941.1| RNA polymerase sigma factor RpoD [Salinispora tropica CNB-440]
          Length = 542

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 131/254 (51%), Positives = 183/254 (72%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 289 RDMQRDMMWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 348

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 349 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 408

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 409 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 468

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 469 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 528

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 529 RHPSRSQVLRDYLD 542



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 64  EDTVAMLSNMGINVVDGDDL------EDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           E+  A + +    VVD           D   S    D       S    Q R+D+   ++
Sbjct: 182 EELAAEIED---VVVDEPAELTRAAEADAASSASDNDFEWDDEESEALKQARRDAELTAS 238

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            D VR YL+++G + LL+ E E+ +AKRIEAG 
Sbjct: 239 ADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGL 271


>gi|331001843|ref|ZP_08325365.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412817|gb|EGG92200.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 389

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 137/274 (50%), Positives = 198/274 (72%), Gaps = 1/274 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRG 467
           I+  +K I     +++ +   +   +   +      A K M E+NLRLV+S+AK+Y  RG
Sbjct: 116 IKMYLKEIGKIPLLNVDDEMDLAKKISDPDESIRKEAAKRMAESNLRLVVSIAKRYMGRG 175

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 176 MQLLDLIQEGNLGLLRAVEKFDYKKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVE 235

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+++++T R++   + REP+PEE+AK++ + V  VR+++    EP+S+ETPIGDED SH
Sbjct: 236 TINRLIKTQRKLVQILGREPSPEEVAKEMNISVPKVREIMSFALEPVSMETPIGDEDDSH 295

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDF++D NA  P++ A+   L +    V+  LT RE++V+ +RFG+      TLEEVGK
Sbjct: 296 LGDFLQDYNAKVPVNFAMDVLLHDQLMDVIKLLTEREQKVILLRFGLEDGKPRTLEEVGK 355

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F +TRERIRQIEAK++RKL++PS+SK+LR FL+
Sbjct: 356 VFGITRERIRQIEAKSLRKLRNPSKSKRLRDFLE 389



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/157 (24%), Positives = 65/157 (41%), Gaps = 22/157 (14%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG-----DDLEDEEGSEDSLDLASSASNSS 103
           +  F   +++  E + + +  L N  I + +       D + +   ED + L     +  
Sbjct: 27  IQKFFSENDIPKEYLPEFIEFLENKDILIDEDFEKEPTDFDTDTDPEDYILLKDGDFDDE 86

Query: 104 VFLQKRKDSAD------------RSTDDPVRMYLREMGSIELLSREGEIAIAKRI----E 147
              +  KD  D             S +DP++MYL+E+G I LL+ + E+ +AK+I    E
Sbjct: 87  FNEEDIKDLRDIDLNVLDDLNDYVSIEDPIKMYLKEIGKIPLLNVDDEMDLAKKISDPDE 146

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + R      + ES L     I  R  +  G  LL  I
Sbjct: 147 SIRKEAAKRMAESNLRLVVSIAKRY-MGRGMQLLDLI 182


>gi|227872476|ref|ZP_03990816.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
 gi|227841677|gb|EEJ51967.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
          Length = 385

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 204/313 (65%), Gaps = 16/313 (5%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           D F++  +G E+D   V   +     +              +R  +K I     ++  E 
Sbjct: 88  DDFVKEEEGEEIDLDAVDLLEGIGTEDP-------------VRMYLKEIGTVPLLTAEEE 134

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
               ++  K +     AK+ ++EANLRLV+S+AK+YT RG+ FLDL+QEGN+GL+K  EK
Sbjct: 135 ---YALAMKKQEGDEYAKQRLIEANLRLVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEK 191

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G+K STYA WW++Q++TR++ADQ+ TIR+PVHM + I+K+ +  R+++ ++  EP
Sbjct: 192 FDPEKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMSKMQRKLTLELGYEP 251

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E+A+ L M  E V+++++I +EP SLETPIG+ED S+LGDF+ D N +SP  +    
Sbjct: 252 SVKELAEHLDMTEEKVQEIMQIAREPASLETPIGEEDDSNLGDFVADTNVLSPEGNVESV 311

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LRE    +L  L  RE +V+ +RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL
Sbjct: 312 MLREHIDTLLGDLKERERQVIVLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKL 371

Query: 668 KHPSRSKKLRSFL 680
           ++P RSK++R FL
Sbjct: 372 RNPVRSKRIRDFL 384



 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 16/166 (9%)

Query: 22  LVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI---NV 77
           +  +  +     +++ A+  +  + + E+   +    ++ EQME  + +L N GI    +
Sbjct: 1   MEREELEKILASLLQKAKSNKNSIDLGEVQEAVKEFSLNEEQMEQVLLLLENKGIEINPI 60

Query: 78  VDGDDLEDEEGS------------EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           +D D L+  E              ED  D         + L          T+DPVRMYL
Sbjct: 61  LDEDALKTIEKDGDKAEPDALLPLEDDDDFVKEEEGEEIDLDAVDLLEGIGTEDPVRMYL 120

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           +E+G++ LL+ E E A+A + + G       L E+ L     I  R
Sbjct: 121 KEIGTVPLLTAEEEYALAMKKQEGDEYAKQRLIEANLRLVVSIAKR 166


>gi|1657704|gb|AAC44535.1| sigma factor MytB [Mycobacterium tuberculosis]
          Length = 345

 Score =  212 bits (539), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 179/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 96  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 151

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 152 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 211

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 212 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 271

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 272 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKL 331

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 332 RHGERADRLRSY 343



 Score = 44.1 bits (102), Expect = 0.076,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++  + +A + + ++         A     D VR+YL  +G   LL+  GE+ +AKRIEA
Sbjct: 17  ADREVAMADAPTRATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNPAGEVELAKRIEA 76

Query: 149 GR 150
           G 
Sbjct: 77  GL 78


>gi|227504950|ref|ZP_03934999.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
 gi|227198459|gb|EEI78507.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
          Length = 465

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 136/288 (47%), Positives = 191/288 (66%), Gaps = 7/288 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E   +    +D + K R E    +  + +   + R I         +   AK  ++EANL
Sbjct: 185 EAGLYAQYRMDEMEKARAEGDKAAKLSPMEKRDLRSIAR-------DGRKAKNHLLEANL 237

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++A
Sbjct: 238 RLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMA 297

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQ+ TIRIPVHM + I+K+ R  R +   + REPTP E+AK++ +  E V ++ +  +EP
Sbjct: 298 DQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPIELAKEMDITEEKVLEIQQYAREP 357

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG
Sbjct: 358 ISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFG 417

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 418 LTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 465



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/44 (47%), Positives = 32/44 (72%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 145 QARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 188


>gi|157833814|pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
           Escherichia Coli Rna Polymerase
          Length = 339

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 114/382 (29%), Positives = 166/382 (43%), Gaps = 48/382 (12%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEI IAKRIE G   +  S+ E P     L+   + +      L ++I           
Sbjct: 5   EGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLI----------- 53

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            GF                  +   +  + + D +                PE A     
Sbjct: 54  TGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKF- 112

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
                             +LR + +   D I                     +S    + 
Sbjct: 113 -----------------AELRAQYVVTRDTIKAK-----------------GRSHATAQE 138

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
              KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  F+    
Sbjct: 139 EILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFT 198

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G E    W + A    +  W   +    + + +   +++ I  ETG++I + + I   + 
Sbjct: 199 GNETSDTWFNAAIAMNKP-WSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMS 257

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYK
Sbjct: 258 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 317

Query: 496 FSTYAMWWVKQAITRSIADQSC 517
           FSTYA WW++QAITRSIADQ+ 
Sbjct: 318 FSTYATWWIRQAITRSIADQAR 339


>gi|256377300|ref|YP_003100960.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255921603|gb|ACU37114.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 349

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 126/297 (42%), Positives = 185/297 (62%), Gaps = 25/297 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMV-------------------------RKGECEASIA 444
           R  +K+I     ++  +   +   V                         R+   +   A
Sbjct: 53  RAYLKAIGRVRLLTADQEVELARRVEAGLYAEHLLDLPPAARGSRRPIELRRVVRDGQRA 112

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++EANLRLV+S+AK+YT +G+  LD+IQEGN+GL++A EKFD+  G+KFSTYA WW+
Sbjct: 113 KDHLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFSTYATWWI 172

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR++ADQS TIR+PVHM + + K+ R  R + ++  RE T EE+A +L +  E V 
Sbjct: 173 RQAITRALADQSRTIRLPVHMVEVVTKLARVERDLLHRNGREATAEEVAVELDVTPEKVV 232

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++ +  + P+SL+  IG E  + +GD I D+NAV+PL++   A L      VL +LTPRE
Sbjct: 233 ELRQHARTPVSLDQTIGAEADTSIGDLIADENAVAPLEAVSSALLSADLRAVLDTLTPRE 292

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+RMR+G      HTLEEVG+ + VTRERIRQIE++ + KL+HP+RS+ L  +LD
Sbjct: 293 AGVVRMRYGFPDGVLHTLEEVGRVYGVTRERIRQIESRTMAKLQHPARSRGLEGYLD 349



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 30/54 (55%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +  +  +    R+D+   +  D  R YL+ +G + LL+ + E+ +A+R+EAG 
Sbjct: 28  ETDEDIKLAATLRRDAEAANAADSTRAYLKAIGRVRLLTADQEVELARRVEAGL 81


>gi|116075287|ref|ZP_01472547.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
 gi|116067484|gb|EAU73238.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
          Length = 479

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 190/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +    + + +FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 220 KEWAALVEMPLIKFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDL 272

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 273 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 332

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 333 KTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 392

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P     +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 393 -ADIENPEQDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTR 451

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 452 ERIRQIEAKALRKLRHPNRNGVLKEYI 478



 Score = 40.6 bits (93), Expect = 0.90,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 162 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 196


>gi|18477825|emb|CAC83730.1| sigma factor [Rhodococcus fascians]
          Length = 323

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 118/284 (41%), Positives = 189/284 (66%), Gaps = 7/284 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + +     +S  + R++  +VR    + S A+  ++EANLRL
Sbjct: 42  AEEEVDLAKRIEAGLYAKQVLENTKRLSAVKKRNLAIIVR----DGSAARSHLLEANLRL 97

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQ
Sbjct: 98  VVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQ 157

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S TIR+PVH+ ++++K+ R  R +  ++ RE T EE++ +  + VE +  +L  +++P+S
Sbjct: 158 SRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELSSESGIAVEKIADLLDHSRDPVS 217

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+ P+G ++ + LGDFIED  A S  ++ I   L      VL +L  RE++V+R+R+G+ 
Sbjct: 218 LDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHSDVRVVLGTLDEREQQVIRLRYGLD 277

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
                TL+++GK F ++RER+RQIE + + KL+   R++KLRS+
Sbjct: 278 DGQPRTLDQIGKLFGLSRERVRQIEREVMVKLRQGDRAEKLRSY 321



 Score = 44.8 bits (104), Expect = 0.046,   Method: Composition-based stats.
 Identities = 17/32 (53%), Positives = 22/32 (68%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D VR+YL  +G   LL+ E E+ +AKRIEAG 
Sbjct: 25  DLVRVYLNGIGRTALLTAEEEVDLAKRIEAGL 56


>gi|239616750|ref|YP_002940072.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
 gi|239505581|gb|ACR79068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
          Length = 405

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 136/272 (50%), Positives = 187/272 (68%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     ++ S+ R +    +K       A++E++ ANLRLV+S+AK+Y  RGL
Sbjct: 128 IKMYLKEIGKIPLLTPSKERELARRAQK---GDKKAREELITANLRLVVSIAKRYIGRGL 184

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGNIGL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + 
Sbjct: 185 SFLDLIQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVET 244

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV +  R    +    PT EE+ K      E + ++L  +KE +SLE+PI  ++ S +
Sbjct: 245 INKVNKVIREHLQEHGEYPTVEELGKLTGKTPEKIEEILAASKETVSLESPISGDEESTM 304

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D++   P ++AI+  LRE    VL +L+PRE  VL+MR+G+      TLEEVG+ 
Sbjct: 305 GDFVHDESIEKPEEAAIKMLLREQIDEVLDTLSPREAMVLKMRYGLLDGKTKTLEEVGQF 364

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE KA+RKL+HPSRSK+L++ L
Sbjct: 365 FNVTRERIRQIEVKALRKLRHPSRSKQLKALL 396



 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/144 (24%), Positives = 63/144 (43%), Gaps = 6/144 (4%)

Query: 43  YVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSAS 100
           Y+T E+++   PPD     S  +E     L    + +++ +  ED+E   +S     +  
Sbjct: 51  YITYEDIDNAFPPDYEGFDSSLVEVIYEELEKNKVRILEKEPTEDQE---ESGQENPAED 107

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
             ++     +   + S  DP++MYL+E+G I LL+   E  +A+R + G       L  +
Sbjct: 108 IETLLESAPEMYDNISLKDPIKMYLKEIGKIPLLTPSKERELARRAQKGDKKAREELITA 167

Query: 161 PLTFQALIIWRDELNDGTTLLREI 184
            L     I  R  +  G + L  I
Sbjct: 168 NLRLVVSIAKRY-IGRGLSFLDLI 190


>gi|325106737|ref|YP_004267805.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967005|gb|ADY57783.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 575

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 145/437 (33%), Positives = 234/437 (53%), Gaps = 45/437 (10%)

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           ++ N  E   +     S  E+  + +++  ++      R L  L       +  E+ S +
Sbjct: 155 EKVNTGELPFERTLRTSETENAQKEQILGRMEPNLRTLRHLMDLNRIDFEIRLSEEVSKE 214

Query: 314 CKVL--------KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            +          + K+  L   LSL   R+  +++++  +++R      ++ RL +    
Sbjct: 215 DRQAAKQRMVIRRRKMASLAEELSLRTQRLQPIIKRMDQLAERFSQLIRDIKRLKR---- 270

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
                                            +      +  +++E+  +  +T     
Sbjct: 271 ---------------------------------IPSAAADVQLMQDELNELVQDTLELPE 297

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EF      +++     + AK+++   NLRLV+S+AKKY NRGL FLDLIQEGN GLM+  
Sbjct: 298 EFIARTREIKRRFGFWTEAKQKLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGV 357

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK+++  GYKFSTYA WW++QAITR++AD + TIRIPVHM   I  +   A ++  +  R
Sbjct: 358 EKYEYRRGYKFSTYATWWIRQAITRAVADHARTIRIPVHMFQSISTLKAKAEQIRQETGR 417

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPT EE+A  + M VE   +++K  K P+SL+TP+G+ + S  GDF++D +  +P D+A+
Sbjct: 418 EPTMEELAAAIDMSVEETERIMKTWKHPVSLDTPVGESEDSSFGDFLQDDSENTPADTAM 477

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q  LR+    VL SLT RE  ++++R+G+G    +TLEE G+ F VTRERIRQIE+KA+R
Sbjct: 478 QQMLRDKINHVLKSLTYREREIIKLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALR 537

Query: 666 KLKHPSRSKKLRSFLDG 682
           KL+H +RS  L+ F+D 
Sbjct: 538 KLQHQTRSNHLKGFVDA 554



 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 62/335 (18%), Positives = 124/335 (37%), Gaps = 38/335 (11%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD-----DL 83
           +S + ++K A + G ++ + ++ FLP +      ++  V  L  + I++ D        +
Sbjct: 7   ESIQPLMKSALKAGRLSYQSMDEFLPDEGGDPTLIDQIVLALDQLEIDMYDDPSGRIQKI 66

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            ++ G  +       AS               S+ DP+RMYL +MG+I LL+R  EI +A
Sbjct: 67  PEKIGLPNQPIEEEDASEDDAVPAVVGPETPVSSRDPIRMYLSQMGNIPLLTRADEIYLA 126

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+IE  R     +  ES  T   ++   +++N G                         +
Sbjct: 127 KQIEVTRKRFRRTAMESDFTLAIVVDMFEKVNTGEL---------------PFERTLRTS 171

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E  + QK +   + +          D+       +          + A+           
Sbjct: 172 ETENAQKEQILGRMEPNLRTLRHLMDLNRIDFEIRLSEEVSKEDRQAAKQRMVIRRRKMA 231

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
             A  LS    +L+P ++  +D++AE + +L                    K LK ++  
Sbjct: 232 SLAEELSLRTQRLQP-IIKRMDQLAERFSQLIR----------------DIKRLK-RIPS 273

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
               + L Q  ++ LV+   ++ +  +    E+ R
Sbjct: 274 AAADVQLMQDELNELVQDTLELPEEFIARTREIKR 308


>gi|172040581|ref|YP_001800295.1| RNA polymerase sigma factor [Corynebacterium urealyticum DSM 7109]
 gi|171851885|emb|CAQ04861.1| RNA polymerase sigma factor A [Corynebacterium urealyticum DSM
           7109]
          Length = 545

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 136/290 (46%), Positives = 197/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L     +K I      +S    R +    R+ + +   AK  ++EA
Sbjct: 260 AEQEVSLAKRIEAGLYANYRLKQIKESGERLSPMNRRDL----REIDRDGRKAKNHLLEA 315

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 316 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIRQAITRA 375

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+A+++ + V+ V ++ +  +
Sbjct: 376 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAREMDITVDKVLEIQQYAR 435

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+++R
Sbjct: 436 EPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLR 495

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 496 FGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 545



 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 9/98 (9%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +   D       S+   Q R+D+A  ++ D VR YL+++G + LL+ E E+++AKRIE
Sbjct: 212 SKDGRDDSVWDEDESAALRQARRDAALTASADSVRAYLKQIGKVALLNAEQEVSLAKRIE 271

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTL-LREI 184
           AG          +    + +    + L+      LREI
Sbjct: 272 AG--------LYANYRLKQIKESGERLSPMNRRDLREI 301


>gi|159899067|ref|YP_001545314.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159892106|gb|ABX05186.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 386

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 130/298 (43%), Positives = 188/298 (63%), Gaps = 25/298 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-------------------------RKGECEASI 443
           +R  ++ I     ++ +E   +   +                         ++       
Sbjct: 89  VRMYLQEIGQVPLLTAAEEVDLAKKMEVAHAANDTLLQDDGMLEHSDRISLKRHIDTGRA 148

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW
Sbjct: 149 ARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWW 208

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVHM + I +V RT+ ++   ++REPTPEEIA+ + +    V
Sbjct: 209 IRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHKLQQTMQREPTPEEIAEAMGITASKV 268

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L+ +  P+SLE P+G E    +GDFIED    +P+D+A    LRE    VL  L  R
Sbjct: 269 RRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRVSTPVDAAAMTMLREQIEEVLQKLPER 328

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 329 ERKIIQLRYGLKDGRYRTLEEVGLEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 386



 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/116 (31%), Positives = 59/116 (50%), Gaps = 4/116 (3%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           K +   A+ +  +  E++ + LP  E + E +E     +   GI VVD D+  +    + 
Sbjct: 4   KLLELAAKNQNRIKREDILSVLPEPETNIEALESLYEQIEEAGIEVVDADEAPNVADLDL 63

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            LDL S             D +D + DDPVRMYL+E+G + LL+   E+ +AK++E
Sbjct: 64  DLDLDSDHDLDGAL----PDLSDIALDDPVRMYLQEIGQVPLLTAAEEVDLAKKME 115


>gi|227486750|ref|ZP_03917066.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227235220|gb|EEI85235.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 601

 Score =  212 bits (538), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 160/380 (42%), Positives = 226/380 (59%), Gaps = 14/380 (3%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A N   D+  S K   +   L      + LN    D +V  +Y     ++        + 
Sbjct: 236 AQNSIDDDDLSRKDANILCDLFDSFDHM-LNIIENDEVVSMVYSSFNDLLKKAANKDAIK 294

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
            +  +  D  L+  +  E                  +  A  +  I+  RN    +    
Sbjct: 295 TNDQMIIDNLLKTSEFAE---------SIRNRKILSDDEASYLSYIIDQRNMSLKMLNRE 345

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
             +  E + +    +    ++  AK+++ E NLRLV+S+AKKY  RG+ FLDLIQEGN+G
Sbjct: 346 EFNEDELKKL----KVDVLKSQRAKEKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMG 401

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +K+D+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++ 
Sbjct: 402 LMKAVDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLV 461

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
             + R+P+ EEIA  + + VE V ++ KI +EP+SLETPIG+ED SHLGDFIED  A+ P
Sbjct: 462 QDLGRDPSNEEIADIMGIEVEKVSEIRKIAQEPVSLETPIGEEDDSHLGDFIEDDTAIDP 521

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            ++A    LRE    VL+ L  RE+RVL++RFG+   T  TLEEVGK+F VTRERIRQIE
Sbjct: 522 GEAANYTMLREQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIE 581

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           AKA+RKLK P++S+ L+ FL
Sbjct: 582 AKALRKLKSPNKSELLKDFL 601



 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/147 (24%), Positives = 74/147 (50%), Gaps = 15/147 (10%)

Query: 17  DSDDSLVFDFSDDSWKKMIKLAR-----QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           +SDD+ + +  DD   ++I+        Q G +T  ++  F    ++  E  +  +A ++
Sbjct: 3   NSDDNKLLE--DDVLNEIIEEFESLSESQDGMITYSQIFDFDDFKDMDKESQKLILARIA 60

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST--------DDPVRM 123
           + GI +V+  + E ++  E   D+        +  ++ +   D++         DDPV+M
Sbjct: 61  SSGIEIVERSETELDQEEEIEDDIEEEEQEEEIDEKELEKEIDKTVDNLVGIKLDDPVKM 120

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGR 150
           YL+E+G ++LL+   EI +A+R+E G 
Sbjct: 121 YLKEIGKVDLLTATEEIILARRMETGE 147


>gi|294102609|ref|YP_003554467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
 gi|293617589|gb|ADE57743.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
          Length = 377

 Score =  212 bits (538), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 142/273 (52%), Positives = 197/273 (72%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     +  ++   +   V         AK+++++ANLRLV+S+AKKY  RG+
Sbjct: 108 VRMYLREIGKVPLLEPAQEVELAKRVE---AGEEEAKQQIIDANLRLVVSIAKKYIGRGM 164

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIR+PVHM + 
Sbjct: 165 LFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRVPVHMVET 224

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR +R++  K+ REPT EEIA ++ +    V ++ +I + P+SLETPIG+E+ S L
Sbjct: 225 INKMVRVSRQLVQKLGREPTDEEIAAEMEIEPSKVEEIRRIAQLPVSLETPIGEEEDSQL 284

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED++  SP ++A    L E    +L +L+ RE  VL+ RFG+     +TLEEVGK+
Sbjct: 285 GDFIEDRDLPSPEEAAASHLLHEQIDEMLEALSEREREVLQYRFGLEDGRSYTLEEVGKR 344

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIEAKA+RKL+HPSRSKKLR FLD
Sbjct: 345 FGVTRERIRQIEAKALRKLRHPSRSKKLRDFLD 377



 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 79/176 (44%), Gaps = 7/176 (3%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
              + + +               + +I+  + +G+VT +++  F+P +  S++ +ED V+
Sbjct: 2   ESKNKQTKRDATREELATYMGKVRDLIQEGQTKGFVTQKDIEKFIPVEFWSADVLEDVVS 61

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L  MGI V +      EEG E +  +A   + +     +     D    DPVRMYLRE+
Sbjct: 62  NLMEMGIEVTE------EEGKERAQHIAEEEALAQPADGEIGKLDDIPLTDPVRMYLREI 115

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G + LL    E+ +AKR+EAG       + ++ L     I  +  +  G   L  I
Sbjct: 116 GKVPLLEPAQEVELAKRVEAGEEEAKQQIIDANLRLVVSIAKKY-IGRGMLFLDLI 170


>gi|148238947|ref|YP_001224334.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 7803]
 gi|147847486|emb|CAK23037.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. WH 7803]
          Length = 450

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 203 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 262

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 263 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 322

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 323 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 381

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 382 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 441

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 442 NGVLKEYI 449



 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 25/43 (58%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           V    +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 125 VLASIKVGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 167


>gi|225388598|ref|ZP_03758322.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
 gi|225045346|gb|EEG55592.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
          Length = 405

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 141/304 (46%), Positives = 195/304 (64%), Gaps = 3/304 (0%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           RE    +    +D    E    V   V +   IR  +K I     ++  E      + ++
Sbjct: 104 REKPSEYAEAEEDLFSEEAPQKVLEGVSTGDPIREYLKEIGAIALLTPEEE---AGLAKR 160

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K +VEANLRLV+S+AK+YT RG+ FLDL+QEGNIGLMKA EKFD+  GY+ 
Sbjct: 161 CAEGDEEAGKRLVEANLRLVVSIAKRYTGRGMSFLDLVQEGNIGLMKAVEKFDYEKGYRL 220

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WWVKQAITR++ADQ+ TIR+PVHM + ++K+ RT R +S ++ R+P+  E+A+ +
Sbjct: 221 STYATWWVKQAITRALADQARTIRLPVHMVEAVNKIRRTQRDLSVQLGRDPSNRELAEAV 280

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M  + V ++++ + + +SLETP+GDED S LGDF+ D    S  D A    LRE    +
Sbjct: 281 GMTEKRVEELIQTSGDTVSLETPVGDEDGSSLGDFVADNAGDSTEDQAENVLLREEIDSM 340

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  RE +V+++RFG+      TLEEVG+QF VTRERIRQIE  A+RKL++P RSKK+
Sbjct: 341 LQGLNERERQVIKLRFGLENGRPLTLEEVGRQFNVTRERIRQIETAALRKLRNPVRSKKV 400

Query: 677 RSFL 680
           R FL
Sbjct: 401 RDFL 404



 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 45/208 (21%), Positives = 71/208 (34%), Gaps = 44/208 (21%)

Query: 38  ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-- 95
           A+Q  ++ +  +   L   +V+ E++E+  + L   GI V   +   + E   D  D   
Sbjct: 18  AKQENFLELTAVLDCLRDVQVTPEELEEVYSRLERKGIRVGTPEGDAELEPELDLEDDFD 77

Query: 96  ---------------------------------ASSASNSSVFLQKRKDSADRSTDDPVR 122
                                            A +  +       +K     ST DP+R
Sbjct: 78  TGLDAGVLGKDKLLTGDEETEDGLVLREKPSEYAEAEEDLFSEEAPQKVLEGVSTGDPIR 137

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
            YL+E+G+I LL+ E E  +AKR   G       L E+ L     I  R     G + L 
Sbjct: 138 EYLKEIGAIALLTPEEEAGLAKRCAEGDEEAGKRLVEANLRLVVSIAKRY-TGRGMSFLD 196

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQK 210
            +         E   G     E   Y+K
Sbjct: 197 LV--------QEGNIGLMKAVEKFDYEK 216


>gi|148823899|ref|YP_001288653.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis F11]
 gi|253798208|ref|YP_003031209.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308232219|ref|ZP_07415326.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308369834|ref|ZP_07419229.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308371106|ref|ZP_07423839.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308372374|ref|ZP_07428435.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308373485|ref|ZP_07432499.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308374669|ref|ZP_07436917.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308375503|ref|ZP_07444157.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308377104|ref|ZP_07441142.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308378072|ref|ZP_07481430.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308379289|ref|ZP_07485765.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308380449|ref|ZP_07489983.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
 gi|148722426|gb|ABR07051.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis F11]
 gi|253319711|gb|ACT24314.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308214646|gb|EFO74045.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308326293|gb|EFP15144.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308329821|gb|EFP18672.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308333464|gb|EFP22315.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308337459|gb|EFP26310.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308341132|gb|EFP29983.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308346083|gb|EFP34934.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308348958|gb|EFP37809.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308353656|gb|EFP42507.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308357503|gb|EFP46354.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308361457|gb|EFP50308.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
          Length = 345

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 179/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 96  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 151

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 152 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 211

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 212 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 271

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 272 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKL 331

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 332 RHGERADRLRSY 343



 Score = 44.1 bits (102), Expect = 0.072,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++  + +A + + ++         A     D VR+YL  +G   LL+  GE+ +AKRIEA
Sbjct: 17  ADREVAMADAPTRATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEA 76

Query: 149 GR 150
           G 
Sbjct: 77  GL 78


>gi|291458966|ref|ZP_06598356.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418220|gb|EFE91939.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 388

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 140/346 (40%), Positives = 215/346 (62%), Gaps = 8/346 (2%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDV--FLERHQGRELDPHWVSYAKDFPEGEWKN 397
           EQ+ ++ + I + + E+  +     IK       +     EL P            E   
Sbjct: 45  EQMDNVVRLIENRKIEINPVVDEAAIKDLEAGKAKASPDDELLPLDDESFLKEESEEIDL 104

Query: 398 FVACEVDSI---LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
                ++ I     +R  +K I   + +S  E     ++  + +     AK+ ++EANLR
Sbjct: 105 DAVDLLEGIGTEDPVRMYLKEIGTVSLLSAEEE---YALAIRKQQGDEAAKQRLIEANLR 161

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+S+AK+YT RG+ FLDL+QEGN+GL+K  EKFD   G+K STYA WW++Q++TR++AD
Sbjct: 162 LVVSIAKRYTGRGMSFLDLVQEGNLGLIKGVEKFDPEKGFKLSTYATWWIRQSVTRALAD 221

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIR+PVHM + I+K+ +  R+++ ++  EP+ +E+A+ L M  + V+++++I +EP 
Sbjct: 222 QARTIRVPVHMVETINKMSKMQRKLTLELGYEPSVKELAEHLDMSEDKVQEIMQIAREPA 281

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETPIG+ED S+LGDF+ D N ++P  +     LRE    +L  L  RE +V+ +RFG+
Sbjct: 282 SLETPIGEEDDSNLGDFVADANVLTPESNVEAVMLREHIDSLLGDLKERERQVIVLRFGL 341

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                 TLEEVGK+F VTRERIRQIEAKA+RKL++P RSK++R FL
Sbjct: 342 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSKRIRDFL 387



 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 45/184 (24%), Positives = 70/184 (38%), Gaps = 23/184 (12%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI---NVVDGDDLEDEEGSEDSLDLAS 97
           +  + + E+        +S EQM++ V ++ N  I    VVD   ++D E  +       
Sbjct: 25  KNAIDMSEILESFRQSGLSEEQMDNVVRLIENRKIEINPVVDEAAIKDLEAGKAKASPDD 84

Query: 98  S-----------ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                         +  + L          T+DPVRMYL+E+G++ LLS E E A+A R 
Sbjct: 85  ELLPLDDESFLKEESEEIDLDAVDLLEGIGTEDPVRMYLKEIGTVSLLSAEEEYALAIRK 144

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           + G       L E+ L     I  R     G + L  +         E   G   G E  
Sbjct: 145 QQGDEAAKQRLIEANLRLVVSIAKRY-TGRGMSFLDLV--------QEGNLGLIKGVEKF 195

Query: 207 SYQK 210
             +K
Sbjct: 196 DPEK 199


>gi|291522892|emb|CBK81185.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 366

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 140/272 (51%), Positives = 193/272 (70%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   +             AK  ++EANLRLV+S+AKKY  RG+
Sbjct: 96  VRMYLKEIGSVKLLSPEEEVELSKRAE---AGDQKAKDRIIEANLRLVVSIAKKYVGRGI 152

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++Q+ITR IAD+  TIR+PVHM + 
Sbjct: 153 PFLDLIQEGNMGLIKAVEKFDYAKGFKFSTYATWWIRQSITRGIADKGKTIRVPVHMVET 212

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K +R +R +  ++ REPT EEIA++L    + V + L+I+++P+S+++PIG+E+ S L
Sbjct: 213 INKTLRMSRNLLQELGREPTSEEIAERLGTTKQKVEEALEISRDPVSMDSPIGEEEDSSL 272

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+N +SP DSA    L++     L +LT RE +V+ +RFG+      TLEEVGK+
Sbjct: 273 GDFIEDENMLSPSDSADYQMLKKELVNALDTLTDRERKVIELRFGLIDGQARTLEEVGKE 332

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIEAKA+RKL+HPSRS+KL+ FL
Sbjct: 333 FKVTRERIRQIEAKALRKLRHPSRSRKLKDFL 364



 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 64/339 (18%), Positives = 135/339 (39%), Gaps = 50/339 (14%)

Query: 31  WKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
              +++ A+++   +   ++N      E   E+ME+    L    I++++  + +D    
Sbjct: 10  LNSLLEKAKKKKNELDYGDINDAFKGFEFDEEKMEEVYEFLEAKNIDIINIPEAQD---- 65

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D  +           L         S +DPVRMYL+E+GS++LLS E E+ ++KR EAG
Sbjct: 66  -DDDEFLDHQEEEVELLDDVDALEGVSLEDPVRMYLKEIGSVKLLSPEEEVELSKRAEAG 124

Query: 150 RAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGP------- 193
                  + E+ L     I  +         D + +G   L + ++              
Sbjct: 125 DQKAKDRIIEANLRLVVSIAKKYVGRGIPFLDLIQEGNMGLIKAVEKFDYAKGFKFSTYA 184

Query: 194 --------------------------ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
                                     E+       +     +   + + E+  + +  T+
Sbjct: 185 TWWIRQSITRGIADKGKTIRVPVHMVETINKTLRMSRNLLQELGREPTSEEIAERLGTTK 244

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
             +E A ++S+D  S      E  ++   +  EDE+  + + SA    L+ +++ ALD +
Sbjct: 245 QKVEEALEISRDPVSMDSPIGEEEDSSLGDFIEDENMLSPSDSADYQMLKKELVNALDTL 304

Query: 288 AEVYRELRSLQDNAVNGQKD--EKSSVKCKVLKEKLVKL 324
            +  R++  L+   ++GQ    E+   + KV +E++ ++
Sbjct: 305 TDRERKVIELRFGLIDGQARTLEEVGKEFKVTRERIRQI 343


>gi|302537866|ref|ZP_07290208.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302446761|gb|EFL18577.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 481

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 132/250 (52%), Positives = 177/250 (70%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 232 RELEILVEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYT 291

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR++ADQS TIRIPVHM + I+K+ R  R+M   + REPTPEE
Sbjct: 292 KGFKFSTYATWWIRQAITRAMADQSRTIRIPVHMVEIINKLARVQRQMLQDLGREPTPEE 351

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + K+L M  E V +V K  +EPISL TP+G+E  S  GD IED  AV P D+     L+E
Sbjct: 352 LGKELDMTPEKVIEVQKYGREPISLHTPLGEEGDSEFGDLIEDSEAVVPADAVSFTFLQE 411

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L +L+ RE  V+ MR+G+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 412 QLQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPS 471

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 472 RSQVLRDYLD 481



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
            ++  E+    +      V D  D  +EE  +        + +       +      +T 
Sbjct: 125 DADDAEN--PAVEGEDWAVEDLADETEEEAPKAGGQGFVLSDDDEDDAPAQTVMVAGATA 182

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           DPV+ YL+ +G + LL+ E E+ +AKRIEAG 
Sbjct: 183 DPVKDYLKLIGKVPLLNAEQEVELAKRIEAGL 214


>gi|118472772|ref|YP_887083.1| RNA polymerase sigma factor SigB [Mycobacterium smegmatis str. MC2
           155]
 gi|118174059|gb|ABK74955.1| sigma factor SigB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 113/248 (45%), Positives = 178/248 (71%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 70  RDLQAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYT 129

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE
Sbjct: 130 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEE 189

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I   L  
Sbjct: 190 LAEESGIPVEKINDLLEHSRDPVSLDMPVGTDEEAPLGDFIEDSEAMSAENAVISELLHT 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL++  
Sbjct: 250 DIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLRNGE 309

Query: 672 RSKKLRSF 679
           R+ +LRS+
Sbjct: 310 RADRLRSY 317



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +N++         A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 2   ANATTSRVDTDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGL 52


>gi|300933014|ref|ZP_07148270.1| RNA polymerase sigma factor [Corynebacterium resistens DSM 45100]
          Length = 571

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 135/290 (46%), Positives = 197/290 (67%), Gaps = 5/290 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            E +  +A  +++ L     ++ I      +S    R +    R+ E +   AK  ++EA
Sbjct: 286 AEQEVSLAKRIEAGLYAAYRLQEIKESGEKLSPMHRRDL----REIERDGRRAKNHLLEA 341

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+
Sbjct: 342 NLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKGYKFSTYATWWIRQAITRA 401

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REP+PEE+A+++ + V+ V ++ +  +
Sbjct: 402 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPSPEELAREMDITVDKVLEIQQYAR 461

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+++R
Sbjct: 462 EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQDVLHTLSDREAGVVKLR 521

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 522 FGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 571



 Score = 54.5 bits (129), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG      
Sbjct: 248 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYR 305


>gi|296117756|ref|ZP_06836340.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969487|gb|EFG82728.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
          Length = 471

 Score =  211 bits (537), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 130/250 (52%), Positives = 180/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 222 RDLRWIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 281

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTP+E
Sbjct: 282 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPQE 341

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 342 LAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQD 401

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+HPS
Sbjct: 402 QLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 461

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 462 RSQVLRDYLD 471



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/53 (39%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++A+RIEAG 
Sbjct: 142 DEDESATLRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAERIEAGL 194


>gi|207093142|ref|ZP_03240929.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 319

 Score =  211 bits (536), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 127/260 (48%), Positives = 192/260 (73%), Gaps = 1/260 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  ++ + I+  +++G+  +  AK +M ++NLRLV+S+AK++T+RGL FLDLIQEGNIGL
Sbjct: 58  LDPNKLKEILEQIKRGKLISDRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGL 117

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF+   G+KFSTYA WW+KQAI+R+IADQ+ TIRIP+HM D I+++ +  R+   
Sbjct: 118 MKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQ 177

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  +EP  E +A+++ + ++ V+ V+K+TKEPISLETP+G++D    GDF+EDKN VS +
Sbjct: 178 ENGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSI 237

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIE 660
           D  ++ +L+     VL  L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE
Sbjct: 238 DHIMREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIE 297

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           + AI+KL+ P   + LR++L
Sbjct: 298 SSAIKKLRSPQYGRILRNYL 317


>gi|217077377|ref|YP_002335095.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
 gi|217037232|gb|ACJ75754.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
          Length = 371

 Score =  211 bits (536), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 136/269 (50%), Positives = 184/269 (68%), Gaps = 3/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     +S S  R +    +        AK+++VE+NLRLV+S+AK+Y  +GL
Sbjct: 97  IKMYLKDIGKIPLLSQSMERELARRAQ---LGDERAKQKLVESNLRLVVSIAKRYVGKGL 153

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + 
Sbjct: 154 SFLDLIQEGNVGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVET 213

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV +  R    +   E   EE+AK +  PVE V ++L+  KE  SLE P+G++D S +
Sbjct: 214 INKVQKIMREYYQEHGTEIPIEELAKLIGKPVEKVEEILQAAKETTSLEAPVGEDDDSTV 273

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D+   SP   A++  +RE   +VL +L  RE+ VL+MR+G+      TLEEVG+ 
Sbjct: 274 GDFIADETIASPKKEAMRMLIREEVDKVLETLNDREKLVLKMRYGLIDGKAKTLEEVGQY 333

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           F VTRERIRQIE KA+RKL+HPSRS+ L+
Sbjct: 334 FNVTRERIRQIEVKALRKLRHPSRSRYLK 362



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/165 (24%), Positives = 70/165 (42%), Gaps = 14/165 (8%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPP---DEVSSEQMEDTVAMLSNMGINVVD 79
             D  D   +K+I + +++G+VT E+++   PP   DE     +E     L    + + +
Sbjct: 6   TVDSLDSKIEKLIAIGKEKGFVTYEDIDKMFPPEKADEFDGNVLEKVYEELEKNNVAITE 65

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                     E + D     +      +  K   + +T D ++MYL+++G I LLS+  E
Sbjct: 66  ----------ETTNDGIEDVTLEDFLEESPKFYDNMATKDLIKMYLKDIGKIPLLSQSME 115

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             +A+R + G       L ES L     I  R  +  G + L  I
Sbjct: 116 RELARRAQLGDERAKQKLVESNLRLVVSIAKRY-VGKGLSFLDLI 159


>gi|308232215|ref|ZP_07415319.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308373480|ref|ZP_07667590.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
 gi|308214639|gb|EFO74038.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308337452|gb|EFP26303.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
          Length = 413

 Score =  211 bits (536), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 192/286 (67%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 128 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 187

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 188 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 247

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 248 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 307

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+ 
Sbjct: 308 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLT 367

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 368 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 413



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 71  DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 130

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 131 EVELAKRIEAGL 142


>gi|108799144|ref|YP_639341.1| RNA polymerase sigma factor SigB [Mycobacterium sp. MCS]
 gi|119868259|ref|YP_938211.1| RNA polymerase sigma factor SigB [Mycobacterium sp. KMS]
 gi|126434752|ref|YP_001070443.1| RNA polymerase sigma factor SigB [Mycobacterium sp. JLS]
 gi|108769563|gb|ABG08285.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694348|gb|ABL91421.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
 gi|126234552|gb|ABN97952.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 319

 Score =  210 bits (535), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 115/252 (45%), Positives = 181/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +P E +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 186 TDEELAEESGIPAEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 246 LLHTDIRHVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 305

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 306 RNGERADRLRSY 317



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +N++         A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 2   ANATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGL 52


>gi|309791233|ref|ZP_07685765.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308226795|gb|EFO80491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 391

 Score =  210 bits (535), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 132/289 (45%), Positives = 189/289 (65%), Gaps = 7/289 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++    R  I      +G    E     ++          +++ +++AN
Sbjct: 110 AEKEVELAKSMEAGDIARQRIDREEYTSGRERMELERAYAL-------GCESRQHLIQAN 162

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW++QAITR+I
Sbjct: 163 LRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWWIRQAITRAI 222

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQS TIR+PVHM + I +V RT+ ++   ++REPTPEEIA+ + +    VR+ L+ +  
Sbjct: 223 ADQSRTIRLPVHMGEAISQVKRTSHKLQQSMQREPTPEEIAEAMGISAGKVRRTLEASMH 282

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+SLE P+G E    +GDFIED    +P ++A  A LRE    VL  L  RE +++++R+
Sbjct: 283 PLSLEMPVGQEGEGRMGDFIEDDRISTPSEAAAAAMLREQIEEVLQKLPERERKIIQLRY 342

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 343 GLKDGRYRTLEEVGVEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 391



 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 38/154 (24%), Positives = 71/154 (46%), Gaps = 11/154 (7%)

Query: 32  KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED 91
           ++++++AR RGY+T  ++    P  E+   +++   A +   G+ VV+            
Sbjct: 17  ERLLEIARARGYLTYNDILEAFPQPELHVAEVDQLYATMQAEGLKVVES----------- 65

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           + +L +        L +  D  D + DDPVRMYL+E+G + LL+ E E+ +AK +EAG  
Sbjct: 66  AAELEAPHPADEDTLTELPDLTDIAFDDPVRMYLQEIGQVPLLTAEKEVELAKSMEAGDI 125

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
                  E   + +  +        G    + +I
Sbjct: 126 ARQRIDREEYTSGRERMELERAYALGCESRQHLI 159


>gi|237736224|ref|ZP_04566705.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
 gi|229421777|gb|EEO36824.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
          Length = 351

 Score =  210 bits (535), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 141/271 (52%), Positives = 189/271 (69%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     +S  E                 A ++++EANLRLV+S+AKK+TNRGL
Sbjct: 82  IKMYLREIGQIPLLSHDEELEYAKRA---LEGDEWASQQLIEANLRLVVSIAKKHTNRGL 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 139 KLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 198

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ S L
Sbjct: 199 INKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSEL 258

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED   ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEVGK 
Sbjct: 259 GDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKI 318

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 319 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 349



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 29/90 (32%), Positives = 39/90 (43%), Gaps = 1/90 (1%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           L     +  +       S D   D+P++MYLRE+G I LLS + E+  AKR   G     
Sbjct: 56  LEDIGDDEYISDDLFTLSGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWAS 115

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREI 184
             L E+ L     I  +   N G  LL  I
Sbjct: 116 QQLIEANLRLVVSIAKK-HTNRGLKLLDLI 144


>gi|21449377|gb|AAM54109.1|AF453501_35 RNA polymerase sigma factor [Actinosynnema pretiosum subsp.
           auranticum]
          Length = 348

 Score =  210 bits (535), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 125/297 (42%), Positives = 185/297 (62%), Gaps = 25/297 (8%)

Query: 410 RNEIKSISVETGISISEFRHIVSMV-------------------------RKGECEASIA 444
           R  +K+I     ++  +   +   V                         R+   +   A
Sbjct: 52  RAYLKAIGRVRLLTADQEVELARRVEAGLYAEHLLDLPPAARGSRRPVELRRVVRDGQRA 111

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++EANLRLV+S+AK+YT +G+  LD+IQEGN+GL++A EKFD+  G+KFSTYA WW+
Sbjct: 112 KDHLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFSTYATWWI 171

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR++ADQS TIR+PVHM + + K+ R  R + ++  RE T EE+A +L +  E V 
Sbjct: 172 RQAITRALADQSRTIRLPVHMVEVVTKLARIERDLLHRNGREATAEEVAVELDVTPEKVV 231

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++ +  + P+SL+  IG E  + +GD I D+NAV+PL++   A L      VL +LTPRE
Sbjct: 232 ELRQHARTPVSLDQTIGAEADTSIGDLIADENAVAPLEAVSSALLSADLRAVLETLTPRE 291

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+RMR+G      HTL+EVG+ + VTRERIRQIE++ + KL+HP+RS+ L  +LD
Sbjct: 292 AGVVRMRYGFPDGVLHTLDEVGRVYGVTRERIRQIESRTMAKLQHPARSRGLEGYLD 348



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 30/54 (55%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +  +  +    R+D+   +  D  R YL+ +G + LL+ + E+ +A+R+EAG 
Sbjct: 27  ETDEDIKLAATLRRDAEAANAADSTRAYLKAIGRVRLLTADQEVELARRVEAGL 80


>gi|331696792|ref|YP_004333031.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951481|gb|AEA25178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 348

 Score =  210 bits (535), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 110/251 (43%), Positives = 174/251 (69%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                +R    + + A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKF
Sbjct: 96  DYARDLRAVARDGARARNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKF 155

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR +ADQ+ TIR+PVH+ ++++K+ R  R M  ++ RE T
Sbjct: 156 DYAKGFKFSTYATWWIRQAITRGMADQARTIRLPVHLVEQVNKLARIKRDMHQRLGREAT 215

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A++  +P E +  +L   ++P+SL+ P+G E+ + LGDFIED  A    ++ I   
Sbjct: 216 HAELAEESGLPEEKIADLLDHARDPVSLDMPVGSEEEAPLGDFIEDAEAADAENTVISHL 275

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +   RVLA+L  RE+ V+RMR+G+      TL+++G++F ++RER+RQIE + + KL+
Sbjct: 276 LHDDLRRVLATLDEREQNVIRMRYGLDDGQPCTLDQIGRRFGLSRERVRQIEREVMAKLR 335

Query: 669 HPSRSKKLRSF 679
              R+ +LR++
Sbjct: 336 VGERADRLRAY 346



 Score = 44.1 bits (102), Expect = 0.072,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +  +  +++ V L   +  A     D VR+YL  +G   LL+   E+ +AKRIEAG
Sbjct: 21  EREALQADTPVELSADELDAQSPAADLVRVYLNGIGKTALLTAAQEVDLAKRIEAG 76


>gi|145224529|ref|YP_001135207.1| RNA polymerase sigma factor SigB [Mycobacterium gilvum PYR-GCK]
 gi|145217015|gb|ABP46419.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
          Length = 329

 Score =  210 bits (534), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 182/252 (72%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 80  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 136 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 196 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 255

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 256 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 315

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 316 RNGDRADRLRSY 327



 Score = 42.5 bits (98), Expect = 0.24,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 30/57 (52%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D  ++ +N++     +   A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 6   DQEAAMANATTSRFDQDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGL 62


>gi|309791990|ref|ZP_07686468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225984|gb|EFO79734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 396

 Score =  210 bits (534), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 123/289 (42%), Positives = 188/289 (65%), Gaps = 8/289 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  ++   K + +IK +   T     E R       +   + + A+++M  AN
Sbjct: 114 AEQEKRLAQTIERGQKAQVKIKDL-DPTSAEAVELR-------RQIEKGNDARQQMAAAN 165

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD   G+KFSTYA WW+KQA++R++
Sbjct: 166 LRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHDKGFKFSTYATWWIKQALSRAL 225

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQS  +R+PVH+ + ++++    R+++ ++ REP   E+A +L+M  E +R++ +  ++
Sbjct: 226 ADQSRLVRLPVHLGETLNRIQAARRQLTQRLGREPYDSELADELSMSQEKLRELRRTAQD 285

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+SL TP+G+E  S L DFI D +A+   D+A    LR+     L  LT RE +VL +R+
Sbjct: 286 PVSLATPVGEEADSTLADFIPDPHALDADDAAASGMLRQQIATALDQLTERERKVLELRY 345

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 346 GLTDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 394



 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 42/148 (28%), Positives = 69/148 (46%), Gaps = 11/148 (7%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            + +I L RQRG+VT EE+ A +P  E + + ++   A L+   I V D  D    E   
Sbjct: 19  VQGLIALGRQRGFVTFEEIQALVPNPEEAIDAIDSLYATLAEASIPVRDSADDATLE--- 75

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                    + S+V +   +  +D    D VR+YLRE+G + LL+ E E  +A+ IE G+
Sbjct: 76  -------EETISTVVIDLDEGLSDALLGDSVRLYLREIGQVPLLTAEQEKRLAQTIERGQ 128

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGT 178
                 + +   T    +  R ++  G 
Sbjct: 129 K-AQVKIKDLDPTSAEAVELRRQIEKGN 155


>gi|19704653|ref|NP_604215.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714957|gb|AAL95514.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 331

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 143/303 (47%), Positives = 202/303 (66%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +P ++    +     E    +         I+  ++ I     ++  E        +K
Sbjct: 29  EFNPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYA---KK 85

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 86  AYEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 145

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 146 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 205

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 206 GMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 265

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 266 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 325

Query: 677 RSF 679
             F
Sbjct: 326 EDF 328



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/103 (30%), Positives = 45/103 (43%), Gaps = 4/103 (3%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           + +DE   E   D++    ++   L           D+P++MYLRE+G + LL+ E EI 
Sbjct: 25  EFDDEFNPEYIEDVSEDELSNEKLLN---LGNSAKVDEPIKMYLREIGQVPLLTHEEEID 81

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            AK+   G       L ES L     I  +   N G  LL  I
Sbjct: 82  YAKKAYEGDEEASKKLIESNLRLVVSIAKK-HTNRGLKLLDLI 123


>gi|118618673|ref|YP_907005.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
 gi|118570783|gb|ABL05534.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
          Length = 323

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 180/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    + + A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 74  RELAAVVR----DGAEARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 129

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +   + RE 
Sbjct: 130 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREIHQNLGREA 189

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 190 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVIAE 249

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 250 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCKL 309

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 310 RHGERADRLRSY 321



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 18/32 (56%), Positives = 23/32 (71%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D VR+YL  +G   LL+ EGE+ +AKRIEAG 
Sbjct: 25  DLVRVYLNGIGKTALLNAEGEVELAKRIEAGL 56


>gi|326384463|ref|ZP_08206143.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326196808|gb|EGD54002.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 332

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 111/264 (42%), Positives = 180/264 (68%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ +  ++ ++ R    +VR    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 71  LATKKRLTPAKKRDYAILVR----EGEQARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 126

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  GYKFSTYA WW++QAI+R +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 127 EGNLGLIRAVEKFDYAKGYKFSTYATWWIRQAISRGMADQSRTIRLPVHLVEQVNKLARI 186

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T EE+A +  +P E +  ++  +++P+SL+ P+G+++ + LGDFIED 
Sbjct: 187 RRELHQQLGREATDEELALESGIPAEKIADLMDHSRDPVSLDMPVGNDEEAPLGDFIEDA 246

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A S     I   L      VL++L  RE +V+ MR+G+      TL+++G+ F ++RER
Sbjct: 247 EATSAETVVIANLLHSDIRSVLSTLDEREMQVITMRYGLDDGQPRTLDQIGRAFGLSRER 306

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R++KLR++
Sbjct: 307 VRQIEREVMGKLRQGDRAEKLRAY 330



 Score = 40.6 bits (93), Expect = 0.79,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 30/55 (54%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            + ++ +   L ++   A   + D VR+YL  +G   LL+ E E+ ++K IEAG 
Sbjct: 11  EARSTRTRPALTEQDLDAQSPSADLVRVYLNGIGRTALLNAEQEVDLSKAIEAGL 65


>gi|257056422|ref|YP_003134254.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
 gi|256586294|gb|ACU97427.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
          Length = 439

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 139/335 (41%), Positives = 199/335 (59%), Gaps = 31/335 (9%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD---SILKIRNEIKSISVETGISISEFRHIVSMV 434
           E D +   +  D  E E       + +   S   +R  +K I     ++  E   +   +
Sbjct: 105 ESDANDPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRI 164

Query: 435 ----------------------------RKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
                                       +    +   AK  ++EANLRLV+S+AK+YT R
Sbjct: 165 EAGLYAAERLRIAEEEGEKLSTQMRRDLKWIVRDGERAKSHLLEANLRLVVSLAKRYTGR 224

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM 
Sbjct: 225 GMAFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMV 284

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S
Sbjct: 285 EVINKLGRIQRELLQDLGREPTPEELAKEMDISPEKVLEIQQYAREPISLDQTIGDEGDS 344

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G
Sbjct: 345 QLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIG 404

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           + + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 405 QVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 439



 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/80 (35%), Positives = 40/80 (50%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V +  D  DEE   +  D       S    Q RKD+   ++ D VR YL+++G + LL+
Sbjct: 94  TVTEDTDESDEESDANDPDFVWDEEESEALRQARKDAELTASADSVRAYLKQIGKVALLN 153

Query: 136 REGEIAIAKRIEAGRAMMMA 155
            E E+ +AKRIEAG      
Sbjct: 154 AEEEVELAKRIEAGLYAAER 173


>gi|238063497|ref|ZP_04608206.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
 gi|237885308|gb|EEP74136.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
          Length = 534

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 132/254 (51%), Positives = 184/254 (72%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +V  +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 281 REMVRDLGWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 340

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 341 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 400

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 401 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 460

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 461 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 520

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 521 RHPSRSQVLRDYLD 534



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/101 (24%), Positives = 43/101 (42%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
             ++  E++   +  +       +      D   S    D       S    Q R+D+  
Sbjct: 168 EGDIDPEELAAEIEDVVVEEPVELAQAAAADAASSATDNDFEWDDEESEALKQARRDAEL 227

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
            ++ D VR YL+++G + LL+ E E+ +AKRIEAG      
Sbjct: 228 TASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAER 268


>gi|293375429|ref|ZP_06621710.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325844412|ref|ZP_08168139.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645982|gb|EFF64011.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489086|gb|EGC91470.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 464

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 145/250 (58%), Positives = 193/250 (77%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
               +   EA  AKK +VE+NLRLV+S+A+++  RG+ FLDLIQEGN+GL+KA EKFD+ 
Sbjct: 214 EEADRVLHEAEYAKKRLVESNLRLVVSIARRHIGRGMLFLDLIQEGNMGLIKAVEKFDYR 273

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+VR  R++  ++ REP PEE
Sbjct: 274 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLVRIQRQLVQELGREPLPEE 333

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+K+ +  E  R++LKI++EPISLE+P+GDE  S LGDFI D +A+SP D      L++
Sbjct: 334 IAEKMEITPEKAREILKISQEPISLESPVGDEADSSLGDFIPDADALSPSDFTSNEMLKK 393

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +LT REERVLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKL+HPS
Sbjct: 394 ELAEVLETLTDREERVLRLRFGLEDGHTRTLEEVGKEFGVTRERIRQIEAKALRKLRHPS 453

Query: 672 RSKKLRSFLD 681
           RS++L+ F++
Sbjct: 454 RSRRLKDFME 463



 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/223 (16%), Positives = 78/223 (34%), Gaps = 46/223 (20%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           K+IKL ++RGY+T +E+N      ++  E +   + +  +  I++V    + +    +  
Sbjct: 17  KLIKLGKKRGYLTYDEINNSFAEVQLDPEMISSFLDLYESEQIDIVKAKKVVETPKVKKE 76

Query: 93  LDLASS-------------------------------ASNSSVFLQKRKDSADRSTDDPV 121
           +                                               + ++     DPV
Sbjct: 77  VKETPKVQNTEEEQTTTEEADFEENEEEENIPADFKIEEEDEEPFDAFEITSQLKLSDPV 136

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
            MYL+E+G +ELLS + EI  AK+IE G               + ++ +R        L 
Sbjct: 137 HMYLKEIGRVELLSSQEEIKFAKKIERGD------------ILEEILKYR---RQNEALP 181

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           +E+ID    +  ++              +  +   ++   + +
Sbjct: 182 QELIDRIDLLIQDAGEAHDGNELLVGITELTEEEADRVLHEAE 224


>gi|320449783|ref|YP_004201879.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
 gi|320149952|gb|ADW21330.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
          Length = 494

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 143/261 (54%), Positives = 187/261 (71%), Gaps = 7/261 (2%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E +  + + R    E   A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++
Sbjct: 238 PKELKRYLHLAR----EGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIR 293

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR +  ++
Sbjct: 294 AVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARSLQQEL 353

Query: 544 KREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            REPT EEIA+ +      + V + LKI +EP+SLETPIGDE  S  GDFI D+N  SP+
Sbjct: 354 GREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPV 413

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE 
Sbjct: 414 DAAAQSLLAEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIEN 473

Query: 662 KAIRKLK-HPSRSKKLRSFLD 681
           KA+RKLK H SR++KLR FLD
Sbjct: 474 KALRKLKYHESRTRKLRDFLD 494



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 34/129 (26%), Positives = 52/129 (40%), Gaps = 10/129 (7%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS--------ADRSTDDPVRMYL 125
            I + +  D   +E   ++ DL       S      +             ST DPVR YL
Sbjct: 97  EIFLDEPLDPMADESYLEADDLLLPEEGPSPDYLGEELFEEEEELALPKVSTSDPVRQYL 156

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN-DGTTLLREI 184
            E+G + LL+ E EI +A+++E G    +  L E+    Q LI         GT  + +I
Sbjct: 157 HEIGQVPLLTLEEEIELARKVEEG-MEAIKKLSEATGLDQDLIREVVRAKILGTARISQI 215

Query: 185 IDLEACIGP 193
             L   + P
Sbjct: 216 PGLRDKLDP 224


>gi|315444860|ref|YP_004077739.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263163|gb|ADT99904.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 319

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 182/252 (72%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 246 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 305

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 306 RNGDRADRLRSY 317



 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +N++     +   A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 2   ANATTSRFDQDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGL 52


>gi|313680173|ref|YP_004057912.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Oceanithermus
           profundus DSM 14977]
 gi|313152888|gb|ADR36739.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oceanithermus
           profundus DSM 14977]
          Length = 484

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 153/345 (44%), Positives = 218/345 (63%), Gaps = 20/345 (5%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           E+  D+++R+   E  + RLA+  G++ D+  +  + +      V +    P        
Sbjct: 157 EEEIDLARRVEEGEAAVERLAEFTGLEADLIKKVIRAQ------VRHGGRVPHIPGYEAE 210

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             + D+I  +   ++++           +  + + R    +  IA++ ++EANLRLV+S+
Sbjct: 211 RVDEDTIQAVDARLRALPKPQ-------KRYLHIAR----DGEIARQHLIEANLRLVVSI 259

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW++QAI R+IADQ+ TI
Sbjct: 260 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTYATWWIRQAINRAIADQARTI 319

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLE 577
           RIPVHM + I+K+ RTAR++  ++ RE T  EIA  +      + V +  KI +EP+SLE
Sbjct: 320 RIPVHMVETINKLTRTARQLQQELGREATYAEIADAMGPGWDAKKVEETFKIAQEPVSLE 379

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGDE  S  GDFI D++  SP+DSA Q+ L E   + L+ L+ RE  VL++R G+   
Sbjct: 380 TPIGDEKDSFYGDFIPDEHLASPVDSAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDG 439

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
            +HTLEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 440 REHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 484



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 1/94 (1%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V++    E+E  +E +++        +   +    +   ST DPVR YL E+G + LL+
Sbjct: 96  EVLEPILDEEEVVAEAAVEAPIEEEVIAKPEEPVTIATRVSTSDPVRQYLHEIGQVPLLT 155

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
            E EI +A+R+E G    +  L E       LI 
Sbjct: 156 LEEEIDLARRVEEGE-AAVERLAEFTGLEADLIK 188


>gi|255994475|ref|ZP_05427610.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
 gi|255993188|gb|EEU03277.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
          Length = 447

 Score =  210 bits (534), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 149/289 (51%), Positives = 204/289 (70%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A +V   L  +NEI+          + ++  + ++ + + + + A  ++ EAN
Sbjct: 159 REEEKILATQVKHALAKQNEIRERLERLKEGSATYKKEMKLLDEYKQDYNKAMHQLCEAN 218

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK + +RG+ FLDLIQEGN+GLMKA +KFD    +KFSTYA WW++QAITR+I
Sbjct: 219 LRLVVSIAKNHKDRGMHFLDLIQEGNLGLMKAVDKFDVDRNFKFSTYATWWIRQAITRAI 278

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ+ TIRIPVHM + IHK+ R +R +  ++ REP PEEIAK++ +  E VR +L+I++E
Sbjct: 279 ADQARTIRIPVHMVETIHKLTRISRTLLQELGREPKPEEIAKEMDITTEKVRDILRISQE 338

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+SLE PIG+E+ SHLGDFI D    SPLD A  + LR+    VL +L  RE  VL++RF
Sbjct: 339 PVSLEKPIGEEEDSHLGDFIPDTEVPSPLDVAFSSMLRDELLEVLNTLGERERNVLKLRF 398

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEEVGKQF VTRERIRQIE+KAIRKLKHP+ SKKLR ++D
Sbjct: 399 GLVDGKQRTLEEVGKQFDVTRERIRQIESKAIRKLKHPNMSKKLRDYID 447



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/133 (23%), Positives = 51/133 (38%), Gaps = 16/133 (12%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
             +P DE   E M     +L   GI +        E  + +     +      V   +R 
Sbjct: 84  DEIPFDENDVECM---YELLKENGIGI-------KEFEAAEENIAKNGERADKVVDIRRI 133

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI------EAGRAMMMASLCESPLTF 164
                  DDPV+MYL+E+G + LL+RE E  +A ++      +      +  L E   T+
Sbjct: 134 VRTSIGIDDPVKMYLKEIGQVPLLTREEEKILATQVKHALAKQNEIRERLERLKEGSATY 193

Query: 165 QALIIWRDELNDG 177
           +  +   DE    
Sbjct: 194 KKEMKLLDEYKQD 206


>gi|229825188|ref|ZP_04451257.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
 gi|229790560|gb|EEP26674.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
          Length = 372

 Score =  210 bits (533), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 146/273 (53%), Positives = 202/273 (73%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     + + E    + + +        A+K++ EANLRLV+S+AK+Y  RG+
Sbjct: 103 VRMYLKEIGKVPLLDMDEE---IKLAKSMAEGDDEARKKLTEANLRLVVSIAKRYLGRGM 159

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW+KQ+ITR+IADQ+ TIRIPVHM + 
Sbjct: 160 QFLDLIQEGNMGLIKAVEKFDYTKGYKFSTYATWWIKQSITRAIADQARTIRIPVHMVET 219

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R+++  + REP PEEI K+L M  E VR ++KI +EP+S ETPIG+E+ SH+
Sbjct: 220 INKLIRAQRQLTQTLGREPQPEEIGKELNMEPEKVRSIMKIAQEPVSFETPIGEEEDSHI 279

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFI D + ++P+++A  A L+E    VL SLT RE RV+++RFG+      TLEEVGK+
Sbjct: 280 GDFIPDDSNMAPVEAATHAILKEQLEEVLDSLTEREARVIKLRFGLEDGRTRTLEEVGKE 339

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           F VTRERIRQIE+KA+RKL+ PSRS+KL+ +L+
Sbjct: 340 FNVTRERIRQIESKALRKLRQPSRSRKLKDYLE 372



 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 45/160 (28%), Positives = 72/160 (45%), Gaps = 4/160 (2%)

Query: 28  DDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV--VDGDDLE 84
               K+++K A+++ G +  E++ A     E+S +++E     L   GI+V  +D  D  
Sbjct: 7   KSKLKELVKDAKEKKGVLEAEDVKAVFAGREISEDELEKCYRYLERQGIDVLIIDELDDV 66

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           DE+    S +         +   +       ST+DPVRMYL+E+G + LL  + EI +AK
Sbjct: 67  DEDKILISTEDNDEIEREKIEETEITVPEGISTEDPVRMYLKEIGKVPLLDMDEEIKLAK 126

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +  G       L E+ L     I  R  L  G   L  I
Sbjct: 127 SMAEGDDEARKKLTEANLRLVVSIAKRY-LGRGMQFLDLI 165


>gi|227833276|ref|YP_002834983.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184260|ref|ZP_06043681.1| RNA polymerase sigma factor [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454292|gb|ACP33045.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
          Length = 485

 Score =  210 bits (533), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 133/264 (50%), Positives = 183/264 (69%), Gaps = 4/264 (1%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +S  E R     +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEG
Sbjct: 226 KAAKLSPMEKRD----MRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEG 281

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R
Sbjct: 282 NLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQR 341

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +   + REPTP E+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  A
Sbjct: 342 ELLQDLGREPTPLELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEA 401

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V  +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIR
Sbjct: 402 VIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIR 461

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIE+K + KL+HPSRS+ LR +LD
Sbjct: 462 QIESKTMSKLRHPSRSQVLRDYLD 485



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 156 DEDESAALRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 208


>gi|320160330|ref|YP_004173554.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319994183|dbj|BAJ62954.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 543

 Score =  210 bits (533), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 168/532 (31%), Positives = 257/532 (48%), Gaps = 47/532 (8%)

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
           A + P         TE           + +E   +++   +   A  + +D +      P
Sbjct: 19  ASVKPPRVSNVEEPTENEMDVTIPLPEEAEEEVLLEKDLIEDTEADSLVEDWQELALEEP 78

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQ---LRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
            +  ++     E  +D          Q   L       L    E +R L +L+ +     
Sbjct: 79  GDLLDESLATLEFSEDPVRLYLKEIGQINLLDADSEFRLAARIEAWRHLEALEKHLAPKD 138

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                S   +V+  +L+       L +   +L   +L D+   ++  E +LLR       
Sbjct: 139 GTGYYSSLYQVIARELLTEWS--RLEEDAHNLQQGELPDL--SLILAEAQLLRSHWQASE 194

Query: 366 KRDVFLERHQGREL---DPHWVSYAKDFPEGEWKNFV-----ACEVDSILKIRNEIKSIS 417
               +L  +    L   DP W    +         +V     A  + + L+  + +  + 
Sbjct: 195 P--SYLRTYLDNGLWGKDPLWEGLVRHAFSVFINLYVLPPQLAQPLMNYLREVHALPRVE 252

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
                   E   +   V      A  A + ++ ANLRLV+S+AK+Y  RG+ FLDLIQEG
Sbjct: 253 FFVEHMPDEDI-LAEEVEGVRRRAEDANQTLIRANLRLVVSIAKRYLGRGVSFLDLIQEG 311

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GL++A  KFD   GYKFSTYA WW++Q+I+R IA+Q+ TIRIPVH+ + I +++R  R
Sbjct: 312 NLGLLRAVNKFDPTRGYKFSTYATWWIRQSISRYIAEQARTIRIPVHLFESITRLLRVQR 371

Query: 538 RMSNKIKREPTPEEIA-----------------------------KKLAMPVEGVRKVLK 568
            +  ++ REPT EE+A                             ++       V++VL+
Sbjct: 372 TLIQQLGREPTAEELALEAGFLSDEDAQAIRKARAEGKSIDPELMRRWNFATSKVQRVLQ 431

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             +EP+SLE P+GDED+S LGDFIED  A+ P+D+A +  LRE     L+ L+ RE +VL
Sbjct: 432 SAEEPVSLERPVGDEDSSQLGDFIEDDEALEPMDAAAREMLREQVQNALSILSERERQVL 491

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +RFG+    DHTLEEV + F VTRERIRQIEAKA+RKL+HP+RS+ LR +L
Sbjct: 492 ELRFGLIDGKDHTLEEVSRYFNVTRERIRQIEAKALRKLRHPTRSRHLREYL 543



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 33/68 (48%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D +ED E      D    A      L     +    ++DPVR+YL+E+G I LL  + E 
Sbjct: 56  DLIEDTEADSLVEDWQELALEEPGDLLDESLATLEFSEDPVRLYLKEIGQINLLDADSEF 115

Query: 141 AIAKRIEA 148
            +A RIEA
Sbjct: 116 RLAARIEA 123


>gi|1519642|gb|AAB07554.1| SigD [Chloroflexus aurantiacus J-10-fl]
          Length = 398

 Score =  210 bits (533), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 120/296 (40%), Positives = 183/296 (61%), Gaps = 23/296 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-----------------------RKGECEASIAK 445
           +R  ++ I     ++  + + +  ++                       ++ + +   A+
Sbjct: 101 VRLYLREIGQVPLLTAEQEKRLAQLIEQGQEAERKLATLPPDSPEAARLKQLKAKGEEAR 160

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            EM  ANLRLV+S+AK+Y +RGL  LDLIQEG++GL++A EKFD+  GYKFSTYA WW+K
Sbjct: 161 HEMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWWIK 220

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA++R++ADQS  +R+PVH+ + ++++    R+++  + REPT  E+A  L M  E +  
Sbjct: 221 QALSRALADQSRLVRLPVHLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEKLAT 280

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           V +  ++P+SL TP+G+E  S L DFI D +A+   D+A    +R+  T  L  L+ RE 
Sbjct: 281 VRRTAQDPVSLATPVGEEANSTLADFIPDPHALDADDAAASGIVRQQITAALDQLSERER 340

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RVL +R+G+      TLEEVGK F VTRER+RQIE KA+RKL+HP   K L+ +LD
Sbjct: 341 RVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHPRLGKLLKDYLD 396



 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 74/151 (49%), Gaps = 12/151 (7%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           + S+ E    +   + +D   + +I   RQ+G+VT E++   +P  + S E ++   A L
Sbjct: 2   TQSQPETDRAAPAINPAD--LQALIAQGRQQGFVTFEDIQRLVPNPDESIELIDSIYAAL 59

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +  G+ V +GD+   ++           +S +++ L    + +D    D VR+YLRE+G 
Sbjct: 60  AEAGVPVQEGDETALDD---------EPSSPATMDLDLDDELSDALLSDSVRLYLREIGQ 110

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           + LL+ E E  +A+ IE G+      L   P
Sbjct: 111 VPLLTAEQEKRLAQLIEQGQ-EAERKLATLP 140


>gi|156744261|ref|YP_001434390.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156235589|gb|ABU60372.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 399

 Score =  210 bits (533), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 127/262 (48%), Positives = 179/262 (68%), Gaps = 2/262 (0%)

Query: 422 ISISEFRHIVSMVRKGECEAS--IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           +   E+      +   +  A    A++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNI
Sbjct: 138 LECEEYSSWQERMMYEQQVAQGNEARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNI 197

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLM+A EKFD+  G+KFSTYA WW++QAITR+IADQS TIR+PVHM + I +V R + ++
Sbjct: 198 GLMRAVEKFDYTKGHKFSTYATWWIRQAITRAIADQSRTIRLPVHMGEAISQVKRASHKL 257

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              ++REPTPEEIA  + +    VR+ L+ +  P+SLE P+G E    +GDFIED    +
Sbjct: 258 QQMMQREPTPEEIADAMGISSTKVRRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRIST 317

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P ++A  + LRE    VL  L  RE +++++R+G+      TLEEVG +F +TRERIRQI
Sbjct: 318 PAEAAAASMLREQLEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQI 377

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EA A+RKL+HP   KKLR +LD
Sbjct: 378 EAVALRKLRHPHLGKKLRGYLD 399



 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 45/157 (28%), Positives = 76/157 (48%), Gaps = 10/157 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            + + ++ + R RG++T  E+   LP  E     ++   A L   GI VV+      + G
Sbjct: 21  QTLEYLLDIGRTRGFLTYNEILEALPQPEYHVADVDQLYASLQAEGIRVVETPLDMSDHG 80

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +    +L          L +  D  D + DDPVRMYL+E+G + LLS E E+ +AK +EA
Sbjct: 81  AVGDDEL----------LAEMPDLTDVALDDPVRMYLQEIGQVPLLSAEQEVMLAKAMEA 130

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G     A  CE   ++Q  +++  ++  G    + +I
Sbjct: 131 GHRARRALECEEYSSWQERMMYEQQVAQGNEARQHLI 167


>gi|258653916|ref|YP_003203072.1| RNA polymerase sigma factor SigB [Nakamurella multipartita DSM
           44233]
 gi|258557141|gb|ACV80083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 334

 Score =  210 bits (533), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 105/264 (39%), Positives = 173/264 (65%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +  +  +S    + +    R    +   A+  ++ ANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 73  LESDVEMSPQRRKDL----RMVVRDGGRARNHLLVANLRLVVSLAKRYTGRGMPLLDLIQ 128

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAI+R +ADQ  TIR+PVH+ ++++K+ R 
Sbjct: 129 EGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAISRGMADQGRTIRLPVHLVEQVNKLSRL 188

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ R+ T  E+A +  +P E +  +L   ++P+SL+ P+G ++ + LGDFIED 
Sbjct: 189 KRELHQQLGRDATLAELAHESGIPEEKIADLLDHARDPVSLDMPVGSDEEAPLGDFIEDS 248

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            + S   + +   + +   RVL +L  RE+ V+R+R+G+      TL+E+G+ F ++RER
Sbjct: 249 ESTSAEAAVVAGFMHDDINRVLRTLDDREQTVVRLRYGLDDGRPRTLDEIGRHFGISRER 308

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE  ++ KL+   RS+ LRS+
Sbjct: 309 VRQIERDSMAKLRVGDRSEVLRSY 332



 Score = 46.4 bits (108), Expect = 0.014,   Method: Composition-based stats.
 Identities = 18/42 (42%), Positives = 24/42 (57%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                A   + D VR+YL  +G   LL+ E E+ +AKRIEAG
Sbjct: 25  DEDLDAQGPSADLVRVYLNGIGKTALLTAEQEVELAKRIEAG 66


>gi|19910022|dbj|BAB87262.1| RNA polymerase sigma factor [Guillardia theta]
          Length = 490

 Score =  210 bits (533), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 132/275 (48%), Positives = 184/275 (66%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +R +++     +  + +     V   R     A  AK+ MV ANLRLV+S+AK+Y NR
Sbjct: 168 ISLREKLQREPTSSEWTAACKVSDVKKFRSILHNARRAKERMVAANLRLVVSIAKRYVNR 227

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLIQEG++GL++AAEKFD   G+KFSTYA WWVKQA+TR+IAD S TIR+PVH+ 
Sbjct: 228 GMSLQDLIQEGSLGLIRAAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVHLY 287

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           D I  + +T R ++ +I R PT EEIA+K+ M VE +R VL+  +  +SLE P+ ++D  
Sbjct: 288 DTISAIRKTTRTLNIEIGRSPTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLKNDDDA 347

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S L DFIE  +  SP +   ++ LR+    V+ SL+PRE  V+RMR+G+      TLEE+
Sbjct: 348 SQLSDFIE-ADQESPEEHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEI 406

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+ F VTRER+RQIEAKAIRKL+ P RS  LR ++
Sbjct: 407 GQIFSVTRERVRQIEAKAIRKLRQPYRSSILRDYV 441



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 22/50 (44%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            +        + +        DD VR YL+ +G + LL  E EI +A+ I
Sbjct: 108 DTGEEDGSITKPQTVKGLHKADDSVRWYLQLIGRVRLLRPEEEIQLAREI 157


>gi|271966792|ref|YP_003340988.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270509967|gb|ACZ88245.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 331

 Score =  210 bits (533), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 128/297 (43%), Positives = 185/297 (62%), Gaps = 25/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ ++ I     +S  +   +   +                              +   
Sbjct: 34  VKDYLRRIGKVALLSAEQEVELARRIEAGLFAAECLGTQAQAPSTVVRAELEWLAEDGLR 93

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK++T RG+ F DLIQEGN+GL++AAEKFD+  G+KFSTYA WW
Sbjct: 94  AKNHLLEANLRLVVSIAKRHTGRGMAFADLIQEGNLGLIRAAEKFDYTKGFKFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQA+TR++ADQ  TIRIPVHM + I+KV R  R+M   + REP+P+E+A +L M VE +
Sbjct: 154 IKQAVTRALADQGRTIRIPVHMVEVINKVARVQRQMMVTLGREPSPQELAVELDMTVEKI 213

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +V K  +EPISL TP+G E  +  GD IED  A+ P ++     L+     VL +L+ R
Sbjct: 214 TEVQKYGREPISLHTPLGAEGDAEFGDVIEDSEAILPEEAVTFILLQRQLHAVLEALSER 273

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R+RFG+      TL+E+GK F VTRERIRQIE+K + KL+HP+R++ LR +L
Sbjct: 274 EAGVMRLRFGLADGQPKTLDEIGKVFGVTRERIRQIESKTMSKLRHPARARALRDYL 330



 Score = 44.8 bits (104), Expect = 0.049,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +D + + S              +A       V+ YLR +G + LLS E E+ +A+RIEAG
Sbjct: 6   DDDVLILSDHDEDDRSSGAAAAAASSDA---VKDYLRRIGKVALLSAEQEVELARRIEAG 62

Query: 150 R--AMMMASLCESPLTF 164
              A  + +  ++P T 
Sbjct: 63  LFAAECLGTQAQAPSTV 79


>gi|262202171|ref|YP_003273379.1| sigma-70 family RNA polymerase sigma factor [Gordonia bronchialis
           DSM 43247]
 gi|262085518|gb|ACY21486.1| RNA polymerase sigma factor, sigma-70 family [Gordonia bronchialis
           DSM 43247]
          Length = 337

 Score =  210 bits (533), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 113/264 (42%), Positives = 183/264 (69%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++ +  +S ++ R +  +VR    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 76  LATKKRLSAAKKRDLAIVVR----EGEAARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 131

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 132 EGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 191

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T EE+A +  +P E +  +L  +++P+SL+ P+G ++ + LGDFIED 
Sbjct: 192 KRELHQQLGREATDEELANESGIPAEKIADLLDHSRDPVSLDMPVGSDEEAPLGDFIEDA 251

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            A S   + I   +      VLA+L  RE++V+RMR+G+      TL+++G+ F ++RER
Sbjct: 252 EATSAESAVIAGLMHTDVRAVLATLDEREQQVIRMRYGLDDGQPRTLDQIGRMFGLSRER 311

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL+   R+++LR++
Sbjct: 312 VRQIEREVMGKLRQGDRAERLRAY 335



 Score = 44.1 bits (102), Expect = 0.074,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 30/55 (54%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           A  A+ +   + ++   A     D VR+YL  +G   LL+ E E+ +AK+IEAG 
Sbjct: 16  ADDATRTRPAMTEQDLDAQSPAADLVRVYLNGIGRTALLNAEQEVELAKQIEAGL 70


>gi|239626174|ref|ZP_04669205.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47_FAA]
 gi|239520404|gb|EEQ60270.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47FAA]
          Length = 409

 Score =  210 bits (533), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 137/274 (50%), Positives = 193/274 (70%), Gaps = 3/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  +K I   + ++  E   +    R+     + A +++VEANLRLV+S+AK+YT RG+
Sbjct: 139 IREYLKEIGSISLLTPEEETDLA---RRKSEGDAEAGRQLVEANLRLVVSIAKRYTGRGM 195

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GLMKA EKFD+  GY+ STYA WWVKQ+ITRS+ADQS TIR+PVHM + 
Sbjct: 196 GFLDLVQEGNLGLMKAVEKFDYSKGYRLSTYATWWVKQSITRSLADQSRTIRLPVHMVEA 255

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R  R +S ++ REP+ EEIA+++ MP + V ++++ + + +SLETP+GDE+ S+L
Sbjct: 256 VNKIRRAQRSLSVRLGREPSTEEIAEEVGMPEKRVTELIQASGDTVSLETPVGDEEGSNL 315

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D    S  D A    LRE    +L  L PRE  V+ +RFG+      TLEEVG++
Sbjct: 316 GDFVADDANASTEDKAESFLLREEIDAMLQGLNPREREVIILRFGLETGHPLTLEEVGRR 375

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F VTRERIRQIE  A+RKL++PS+S+K+R FL G
Sbjct: 376 FNVTRERIRQIETAALRKLRNPSKSRKIRDFLPG 409



 Score = 64.9 bits (156), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/181 (20%), Positives = 64/181 (35%), Gaps = 39/181 (21%)

Query: 30  SWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
             +++  LA  R   + + E+       +V+ E+MED    L   G+ +   ++ E+   
Sbjct: 9   KLEQLAALAASRENRLEMTEVLDAFKELQVTPEEMEDVYRKLERKGVQIQVPEEGEETLP 68

Query: 89  SEDSLDLASSASNSSVFLQK--------------------------------------RK 110
             D +     A      +++                                       +
Sbjct: 69  DSDLILEDDLALEDGGMVKEDFRWKFRDSDSDDLDEGGLGGLGGSEESGEEELDEYRSER 128

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
                ST DP+R YL+E+GSI LL+ E E  +A+R   G A     L E+ L     I  
Sbjct: 129 ILDGVSTADPIREYLKEIGSISLLTPEEETDLARRKSEGDAEAGRQLVEANLRLVVSIAK 188

Query: 171 R 171
           R
Sbjct: 189 R 189


>gi|78185245|ref|YP_377680.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9902]
 gi|78169539|gb|ABB26636.1| Sigma-70 factor [Synechococcus sp. CC9902]
          Length = 451

 Score =  210 bits (533), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 139/300 (46%), Positives = 200/300 (66%), Gaps = 8/300 (2%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +  A+   +  +   +A + +S      + K  +    + +  FR  + + R+    
Sbjct: 159 DEEIELARKIADLLYLEELAAQFESDNGREPDKKEWAALVEMPLIRFRRRLMLGRR---- 214

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA
Sbjct: 215 ---AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 271

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +
Sbjct: 272 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTI 331

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L
Sbjct: 332 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATL 390

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 391 SPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 450



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 134 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 168


>gi|312898762|ref|ZP_07758151.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
 gi|310620193|gb|EFQ03764.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
          Length = 437

 Score =  210 bits (533), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 146/281 (51%), Positives = 200/281 (71%), Gaps = 9/281 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEAS---------IAKKEMVEANLRLVISV 459
           +R  +K I     +S  E   +   +  G  E +         IAKK++ +ANLRLV+S+
Sbjct: 157 VRMYLKEIGRVPLLSAEEEITLAKRIEAGSAEGATPEEVSAGNIAKKKLTDANLRLVVSI 216

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RG+ FLDLIQEGN+GL+KA EKFD+  GYKFSTYA WW++QAITR+IADQ+ TI
Sbjct: 217 AKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTI 276

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++R +R++     REP PEEIA+K+ +PVE VR+++KI +EP+SLETP
Sbjct: 277 RIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEKMGVPVERVREIMKIAQEPVSLETP 336

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+E+ SHLGDFIED+ A++P D+A    L+E    V + LT RE +VL +RFG+     
Sbjct: 337 IGEEEDSHLGDFIEDQEAIAPDDAASFILLKEQIEDVFSCLTDRERKVLYLRFGLKDGRP 396

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TLEEVG+ F VTRERIRQIE KA+ KL++  + +K++ FL
Sbjct: 397 RTLEEVGQHFNVTRERIRQIEGKALSKLRNWGKREKIKDFL 437



 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 42/168 (25%), Positives = 76/168 (45%), Gaps = 15/168 (8%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +   ++ +  +Q+G ++  E+   +   ++++++M+      ++ G++V+   +  +E  
Sbjct: 67  EKINELTEKGKQQGSLSYSEIMNAMGDCDMTADEMDRMYEHFTDNGVDVLGESEQLNE-- 124

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +E   D A   S +             + DDPVRMYL+E+G + LLS E EI +AKRIEA
Sbjct: 125 NESLNDDADDDSENETVNVNLSVPEGVNIDDPVRMYLKEIGRVPLLSAEEEITLAKRIEA 184

Query: 149 GRAM------------MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G A                 L ++ L     I  R  +  G   L  I
Sbjct: 185 GSAEGATPEEVSAGNIAKKKLTDANLRLVVSIAKRY-VGRGMLFLDLI 231


>gi|28572422|ref|NP_789202.1| RNA polymerase sigma factor [Tropheryma whipplei TW08/27]
 gi|28410553|emb|CAD66939.1| RNA polymerase principal sigma factor hrdb [Tropheryma whipplei
           TW08/27]
          Length = 387

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 134/252 (53%), Positives = 183/252 (72%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +R    +   AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKF
Sbjct: 135 KLKRELRWVVRDGQRAKDHLLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKF 194

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R++   + REPT
Sbjct: 195 DYVKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLSRVQRQLLQDLGREPT 254

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P+E+ ++L MP E V +V K  +EPISL TP+GDE  S  GD IED +AV+P D+   + 
Sbjct: 255 PDELGRELDMPPERVVEVQKYGREPISLHTPLGDEGDSEFGDLIEDVDAVAPDDAVGFSM 314

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++    +L SL+ RE  V+RMRFG+  +   TL+ VG+ F VTRERIRQIEAK + KL+
Sbjct: 315 LQQQLRLLLDSLSEREAGVIRMRFGLDYDMPKTLDYVGEYFDVTRERIRQIEAKTMAKLR 374

Query: 669 HPSRSKKLRSFL 680
           HPSRS+ LR +L
Sbjct: 375 HPSRSQCLRDYL 386



 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D     +GSE   +    A                +T DPV+ YL+++G + LL+ + E
Sbjct: 50  SDTDVASQGSEGDFEAIVLADTKDDESTPASPVISGATADPVKDYLKQIGKVSLLTADEE 109

Query: 140 IAIAKRIEAGRAMMMASLCES 160
           +++AKRIEAG       L ES
Sbjct: 110 VSLAKRIEAGLF-AEEKLSES 129


>gi|315502644|ref|YP_004081531.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|315409263|gb|ADU07380.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 551

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +          E    R +   +     +   AK  ++EANLRL
Sbjct: 266 AEQEVELAKRIEAGLYAAERLRAADEGEEKLVRDLQRDLMWISRDGERAKNHLLEANLRL 325

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 326 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 385

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 386 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 445

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+   + L++   +VL +L+ RE  V+R+RFG+ 
Sbjct: 446 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQTLSEREAGVVRLRFGLT 505

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 506 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 551



 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 27/102 (26%), Positives = 44/102 (43%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  E+  E++   +  +       +      D   S    D       S    Q R+D+ 
Sbjct: 184 PDGEIDPEELAAEIEDVVVEEPAELTQAAEADAASSATDNDFEWDDEESEALKQARRDAE 243

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
             ++ D VR YL+++G + LL+ E E+ +AKRIEAG      
Sbjct: 244 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAER 285


>gi|317969651|ref|ZP_07971041.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0205]
          Length = 470

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 190/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +    + + +FR  + + R+       AK++MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 211 KEWATLVEMPLVKFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDL 263

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 264 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 323

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +  R+PT EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 324 KTTKTLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 383

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P     +  LRE    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 384 -ADIENPEQDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTR 442

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 443 ERIRQIEAKALRKLRHPNRNGVLKEYI 469



 Score = 42.5 bits (98), Expect = 0.22,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +A  +      +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 136 EKDAAKTAKALASIKIGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 187


>gi|309389374|gb|ADO77254.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 310

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 134/276 (48%), Positives = 193/276 (69%), Gaps = 5/276 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K +     +   E   +   + +       A++++ EANLRLV+S+AKKY  +G+
Sbjct: 38  VRVYLKEMGKVDLLDKEEEVELAKRIEQ---GDQRAREQLTEANLRLVVSIAKKYIGQGM 94

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN GLMKA EKFD+  GYKFSTYA WW++Q+ITR++ADQ+ TIRIPVHM + 
Sbjct: 95  SFLDLIQEGNKGLMKAVEKFDYTKGYKFSTYATWWIRQSITRALADQARTIRIPVHMVET 154

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTS 586
           ++K+ R  +R+   ++REPT EEI +++ M  E V +   L + ++P SL+TPIG+E  S
Sbjct: 155 MNKLRRIEKRLKKDLEREPTLEEIGEEMNMEPEKVLEIQKLAMNQQPTSLDTPIGEEKDS 214

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HL DFIED++A +P   A    L++    VL +LT RE+R++++RFG+      TL+EVG
Sbjct: 215 HLKDFIEDQDAPAPEMLASSELLKDQLETVLDTLTDREKRIIKLRFGLEDGRQRTLKEVG 274

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            QF VTRERIRQI+AKA+RKL+HP+RSK+LR +L+ 
Sbjct: 275 SQFGVTRERIRQIQAKALRKLRHPTRSKELRGYLNN 310



 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 53/269 (19%), Positives = 101/269 (37%), Gaps = 19/269 (7%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
                     DD VR+YL+EMG ++LL +E E+ +AKRIE G       L E+ L     
Sbjct: 25  DLSIPDGAGIDDSVRVYLKEMGKVDLLDKEEEVELAKRIEQGDQRAREQLTEANLRLVVS 84

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           I  +  +  G + L  I         E   G     E   Y K    S        Q   
Sbjct: 85  IAKKY-IGQGMSFLDLI--------QEGNKGLMKAVEKFDYTKGYKFSTYATWWIRQSIT 135

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
             +   A+  +     V++  +    ++R   + E +   TL  + +++  +    L+  
Sbjct: 136 RALADQARTIRIPVHMVETMNKLRRIEKRLKKDLEREP--TLEEIGEEMNMEPEKVLEIQ 193

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
                +  +  D  +  +KD       +       +++ S  L + +++ +++ L D  K
Sbjct: 194 KLAMNQQPTSLDTPIGEEKDSHLKDFIEDQDAPAPEMLASSELLKDQLETVLDTLTDREK 253

Query: 348 RIMHN--------EGELLRLAQSYGIKRD 368
           RI+          +  L  +   +G+ R+
Sbjct: 254 RIIKLRFGLEDGRQRTLKEVGSQFGVTRE 282


>gi|289553505|ref|ZP_06442715.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
 gi|289438137|gb|EFD20630.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
          Length = 338

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 179/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 89  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 144

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 145 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 204

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 205 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 264

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 265 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKL 324

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 325 RHGERADRLRSY 336



 Score = 44.1 bits (102), Expect = 0.093,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++  + +A + + ++         A     D VR+YL  +G   LL+  GE+ +AKRIEA
Sbjct: 10  ADREVAMADAPTRATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEA 69

Query: 149 GR 150
           G 
Sbjct: 70  GL 71


>gi|302866088|ref|YP_003834725.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
 gi|302568947|gb|ADL45149.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
          Length = 551

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +          E    R +   +     +   AK  ++EANLRL
Sbjct: 266 AEQEVELAKRIEAGLYAAERLRAADEGEEKLVRDLQRDLMWISRDGERAKNHLLEANLRL 325

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 326 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 385

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 386 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 445

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+   + L++   +VL +L+ RE  V+R+RFG+ 
Sbjct: 446 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQTLSEREAGVVRLRFGLT 505

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 506 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 551



 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 27/102 (26%), Positives = 44/102 (43%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  E+  E++   +  +       +      D   S    D       S    Q R+D+ 
Sbjct: 184 PDGEIDPEELAAEIEDVVVEEPAELTQAAEADAASSATDNDFEWDDEESEALKQARRDAE 243

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
             ++ D VR YL+++G + LL+ E E+ +AKRIEAG      
Sbjct: 244 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAER 285


>gi|159037077|ref|YP_001536330.1| RNA polymerase sigma factor [Salinispora arenicola CNS-205]
 gi|157915912|gb|ABV97339.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 532

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 135/286 (47%), Positives = 191/286 (66%), Gaps = 3/286 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +          E    R +   +     +   AK  ++EANLRL
Sbjct: 247 AEQEVELAKRIEAGLYAAERLRATEEGEEKLNRDMQRDLMWISRDGERAKNHLLEANLRL 306

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ
Sbjct: 307 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQ 366

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +EPIS
Sbjct: 367 ARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPIS 426

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+  IGDE  S LGDFIED  AV  +D+   + L++   +VL +L+ RE  V+R+RFG+ 
Sbjct: 427 LDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQTLSEREAGVVRLRFGLT 486

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 487 DGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 532



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/99 (27%), Positives = 43/99 (43%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
           EV  E++   +  +       +      D   S    D       S    Q R+D+   +
Sbjct: 168 EVDPEELAAEIEDVVVDEPAELTQAAEADAANSATDNDFEWDDEESEALKQARRDAELTA 227

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           + D VR YL+++G + LL+ E E+ +AKRIEAG      
Sbjct: 228 SADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAER 266


>gi|320355021|ref|YP_004196360.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320123523|gb|ADW19069.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 533

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 159/426 (37%), Positives = 236/426 (55%), Gaps = 32/426 (7%)

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           +    D+    L+AM D    +V  A +   +       L+  A N  ++ +   +   +
Sbjct: 135 IRGLSDNDEKELTAMRDAFLDQVEKANELDGKRRELFLELKKTAGNEARERQLVDEILKV 194

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            E +  L     +    I  + + + +++++                             
Sbjct: 195 GEAISALFRDYRMCSKGILSVADAVKELAQKFNKVRV----------------------- 231

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK---SISVETGISISEFRHIVSMV 434
                 V+  ++       + +  E   I     E +    ++   GIS   F  +   +
Sbjct: 232 ------VARQQELLLAARHHQLDDEQGQIRPAEVEQRVTLELAETIGISWPAFIEVQQEI 285

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             G   A  AK+ +V ANLRLVISV+KK+ NRG+Q  DLIQEGNIGLMKA EK+D+  GY
Sbjct: 286 EIGRETARQAKETLVRANLRLVISVSKKFMNRGMQLPDLIQEGNIGLMKAVEKYDYKRGY 345

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QA+TR IADQ  TIR+PVHM + I++++R ++       REPTPEE+AK
Sbjct: 346 KFSTYATWWIRQAVTRGIADQGRTIRLPVHMIETINRMLRFSKDFQRIESREPTPEEMAK 405

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L   VE V+  LK  K+ ISL+ P+ DE+ + L DFIED     P + +I  +L+    
Sbjct: 406 QLGTDVEKVQVALKTAKDAISLDAPVNDEEDTLLSDFIEDHAHPDPQEHSITESLKRCLC 465

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +V+ SLTPREE+VLRMR+GI +  DHTLEEVG+ F VTRERIRQIEA+A++KL+HP+RS+
Sbjct: 466 KVMGSLTPREEKVLRMRYGIEIGCDHTLEEVGQCFAVTRERIRQIEAQALKKLRHPARSQ 525

Query: 675 KLRSFL 680
            L++F+
Sbjct: 526 DLQAFI 531



 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 77/492 (15%), Positives = 161/492 (32%), Gaps = 21/492 (4%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREMGSIELLSREGEI 140
           ++ED+    + ++  SS    +   ++  D     S+ DP+ +YLREMG+  LL  E E+
Sbjct: 31  EVEDDWAVRNGIERRSSFDRRAGEDRRSGDRRGMGSSIDPMNIYLREMGNQRLLKHEEEM 90

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            +A+ +E G   + +++    L   AL    + L  G   +  +I   +    +      
Sbjct: 91  ELARMVEEGETRIQSAVLRLTLGITALNDLAENLLRGNVRINSVIRGLSDNDEKELTAMR 150

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                   +  E   + +E     +     E+  +   D+  KV         D R   +
Sbjct: 151 DAFLDQVEKANELDGKRRELFLELKKTAGNEARERQLVDEILKVGEAISALFRDYRMCSK 210

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                A  +  +  +     + A  +   +      L D     +  E        L E 
Sbjct: 211 GILSVADAVKELAQKFNKVRVVARQQELLLAARHHQLDDEQGQIRPAEVEQRVTLELAET 270

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +     +    Q  I++  E      + ++     L+       + R + L     +E +
Sbjct: 271 IGISWPAFIEVQQEIEIGRETARQAKETLVRANLRLVISVSKKFMNRGMQLPDLI-QEGN 329

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNE-IKSISVETGISISEFRHIVSMVRKGEC 439
              +   + +       F       I +     I        + +     I  M+R  + 
Sbjct: 330 IGLMKAVEKYDYKRGYKFSTYATWWIRQAVTRGIADQGRTIRLPVHMIETINRMLRFSKD 389

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG------NIGLMKAAEKFDWCLG 493
                  + +E+       +AK+    G      +Q         I L       +  L 
Sbjct: 390 ------FQRIESREPTPEEMAKQL---GTDVEK-VQVALKTAKDAISLDAPVNDEEDTLL 439

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F         Q  + + + + C  ++   +  +  KV+R   R   +I  + T EE+ 
Sbjct: 440 SDFIEDHAHPDPQEHSITESLKRCLCKVMGSLTPREEKVLR--MRYGIEIGCDHTLEEVG 497

Query: 554 KKLAMPVEGVRK 565
           +  A+  E +R+
Sbjct: 498 QCFAVTRERIRQ 509


>gi|15609847|ref|NP_217226.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Rv]
 gi|15842248|ref|NP_337285.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CDC1551]
 gi|31793882|ref|NP_856375.1| RNA polymerase sigma factor SigB [Mycobacterium bovis AF2122/97]
 gi|121638585|ref|YP_978809.1| RNA polymerase sigma factor SigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148662551|ref|YP_001284074.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215412516|ref|ZP_03421250.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           94_M4241A]
 gi|215446963|ref|ZP_03433715.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|224991077|ref|YP_002645766.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|254365367|ref|ZP_04981412.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289444252|ref|ZP_06433996.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289448365|ref|ZP_06438109.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289570886|ref|ZP_06451113.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289575408|ref|ZP_06455635.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289751363|ref|ZP_06510741.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289754812|ref|ZP_06514190.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289758838|ref|ZP_06518216.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|289762881|ref|ZP_06522259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|298526180|ref|ZP_07013589.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|307085405|ref|ZP_07494518.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|313659647|ref|ZP_07816527.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           V2475]
 gi|1171103|gb|AAA86044.1| sigma factor MysB [Mycobacterium tuberculosis H37Rv]
 gi|2182001|emb|CAB09470.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium tuberculosis H37Rv]
 gi|13882539|gb|AAK47099.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis CDC1551]
 gi|31619476|emb|CAD94914.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium bovis AF2122/97]
 gi|121494233|emb|CAL72711.1| RNA polymerase sigma factor sigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|134150880|gb|EBA42925.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148506703|gb|ABQ74512.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|224774192|dbj|BAH26998.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|289417171|gb|EFD14411.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289421323|gb|EFD18524.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289539839|gb|EFD44417.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289544640|gb|EFD48288.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289691950|gb|EFD59379.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289695399|gb|EFD62828.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289710387|gb|EFD74403.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|289714402|gb|EFD78414.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|298495974|gb|EFI31268.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|308365051|gb|EFP53902.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|326904326|gb|EGE51259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis W-148]
          Length = 323

 Score =  209 bits (532), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 179/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 74  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 129

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 130 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 189

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 190 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 249

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 250 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKL 309

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 310 RHGERADRLRSY 321



 Score = 42.1 bits (97), Expect = 0.34,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +A + + ++         A     D VR+YL  +G   LL+  GE+ +AKRIEAG 
Sbjct: 1   MADAPTRATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGL 56


>gi|150020921|ref|YP_001306275.1| RpoD family RNA polymerase sigma factor [Thermosipho melanesiensis
           BI429]
 gi|149793442|gb|ABR30890.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosipho
           melanesiensis BI429]
          Length = 370

 Score =  209 bits (531), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 134/269 (49%), Positives = 186/269 (69%), Gaps = 3/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I     +S S  R +    ++       AK+++VE+NLRLV+S+AK+Y  +GL
Sbjct: 96  IKMYLKDIGKIPLLSQSMERELARRAQQ---GDERAKQKLVESNLRLVVSIAKRYVGKGL 152

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIR+PVHM + 
Sbjct: 153 SFLDLIQEGNVGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVET 212

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+KV +  R    +   E   EE+AK +  PVE V ++L+  KE  SLE P+G+++ S +
Sbjct: 213 INKVQKIMRDYYQQHGTEIPIEELAKIIGKPVEKVEEILQAAKETTSLEAPVGEDEDSTV 272

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D++  SP   A++  +RE   +VL +L  RE+ VL+MR+G+      TLEEVG+ 
Sbjct: 273 GDFVADESIASPKKEAMRMLIREEVEKVLETLNDREKLVLKMRYGLIDGKSKTLEEVGQY 332

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           F VTRERIRQIE KA+RKL+HPSRS+ L+
Sbjct: 333 FNVTRERIRQIEVKALRKLRHPSRSRYLK 361



 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 39/160 (24%), Positives = 71/160 (44%), Gaps = 14/160 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPP---DEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +   +K+IK+ +++G+VT ++++  LPP   D+     +E     L    I + + +  E
Sbjct: 10  EKQIEKLIKVGKEKGFVTYDDIDKMLPPEKIDDFDGNILEKVYEELEKNNILITENNPQE 69

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
             E            S      +  +   + +T D ++MYL+++G I LLS+  E  +A+
Sbjct: 70  QIE----------DVSLEDFLEESPRFYDNMATKDLIKMYLKDIGKIPLLSQSMERELAR 119

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R + G       L ES L     I  R  +  G + L  I
Sbjct: 120 RAQQGDERAKQKLVESNLRLVVSIAKRY-VGKGLSFLDLI 158


>gi|227503480|ref|ZP_03933529.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
 gi|227075983|gb|EEI13946.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
          Length = 493

 Score =  209 bits (531), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 156/441 (35%), Positives = 235/441 (53%), Gaps = 30/441 (6%)

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV-YRELRSLQDN 300
              DSP  +AE       ED +D   ++               ++I E  +     L ++
Sbjct: 82  EPQDSPANSAEKAPSEEAEDAEDQLDSVEQDAPADDVDFDPTHEDIEEDEFDAPTDLDED 141

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            +  +  E+           +     S++L Q+R D    QL   +  +     ++ ++A
Sbjct: 142 DIQEELGEEEDEDEVEDTSSVWDEEESVALRQARKD---AQLTASADSVRAYLKQIGKVA 198

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
                                +           E   +    +D + K R E    +  +
Sbjct: 199 L-------------------LNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEGDKAAKLS 239

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +   + R I         +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+G
Sbjct: 240 PMEKRDLRSIAR-------DGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 292

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R + 
Sbjct: 293 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELL 352

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
             + REPTP+E+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  
Sbjct: 353 QDLGREPTPQELAKEMDITEEKVMEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIA 412

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE
Sbjct: 413 VDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIE 472

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           +K + KL+HPSRS+ LR +LD
Sbjct: 473 SKTMSKLRHPSRSQVLRDYLD 493



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 33/53 (62%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S    Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 164 DEEESVALRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 216


>gi|239934546|emb|CAR94587.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 296

 Score =  209 bits (531), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 145/316 (45%), Positives = 194/316 (61%), Gaps = 26/316 (8%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELLSREGEIAIAKRIEAGR  M++ LCESPLTFQA+IIWRD LND   LLREIIDLE 
Sbjct: 1   TVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQAIIIWRDALNDSQILLREIIDLET 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                       G E       E   +EK       +    +     +    + V     
Sbjct: 61  TYA---------GPEAKQAPVIERVEEEKPAAGNDRSRSRRDDDDITNVGGDTPV----- 106

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVN 303
                  + D+++D++  +L+AME +LRP+VM  LD IA+ YR+LR LQD       A +
Sbjct: 107 ------EDDDDEDDEANLSLAAMEAELRPQVMETLDVIADTYRKLRKLQDQQVENRLAAS 160

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           G        + K LK++L+K V SLSLNQ+RI+ LV QLYDI+KR++ NEG LLRLA+SY
Sbjct: 161 GSLSPSQERRYKELKDQLIKAVKSLSLNQNRIEALVAQLYDINKRLVQNEGRLLRLAESY 220

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           G++R+ FL+ +QG ELDP+W+    +     WK F   E D+I  +R EI++++ ET IS
Sbjct: 221 GVRREDFLKEYQGNELDPNWLKAVSNLTTRGWKEFTKNEKDTIKNLRTEIQNMAQETAIS 280

Query: 424 ISEFRHIVSMVRKGEC 439
           ISEFR IV+ V+KGE 
Sbjct: 281 ISEFRRIVNQVQKGER 296


>gi|148654372|ref|YP_001274577.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566482|gb|ABQ88627.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 402

 Score =  209 bits (531), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 127/249 (51%), Positives = 178/249 (71%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M  +   + + A++ +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  
Sbjct: 154 MYEQQVAQGNEARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTK 213

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR+IADQS TIR+PVHM + I +V RT+ ++   ++REPTPEEI
Sbjct: 214 GHKFSTYATWWIRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHKLQQTMQREPTPEEI 273

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + +    VR+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE 
Sbjct: 274 ADAMGISSTKVRRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASMLREQ 333

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL  L  RE +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP  
Sbjct: 334 LEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKLRHPHL 393

Query: 673 SKKLRSFLD 681
            KKLR +LD
Sbjct: 394 GKKLRGYLD 402



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 45/157 (28%), Positives = 75/157 (47%), Gaps = 10/157 (6%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
            + + ++++ R RG++T  E+   LP  E     ++   A L   GI VV+      + G
Sbjct: 24  QTLEYLLEIGRTRGFLTYNEILEALPQPEHHIADVDQLYASLQAEGIRVVETPLDIHDNG 83

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S    +L          L    D  D + DDPVRMYL+E+G + LLS E E+ +AK +EA
Sbjct: 84  STGDDEL----------LADMPDLTDVALDDPVRMYLQEIGQVPLLSAEQEVMLAKAMEA 133

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G     A   E   ++Q  +++  ++  G    + +I
Sbjct: 134 GHRARRALEREEYSSWQERVMYEQQVAQGNEARQHLI 170


>gi|298247391|ref|ZP_06971196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297550050|gb|EFH83916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 385

 Score =  209 bits (531), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 115/302 (38%), Positives = 181/302 (59%), Gaps = 18/302 (5%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK------------------GEC 439
            +    +    +   ++ +     ++  +   +   + +                     
Sbjct: 84  LIEAAGEPGDTLETYLREMGRVPLLTSEQEVQLAQQIERGKLEQERARLLKVPPEHAIMD 143

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            A  A+  + EANLRLV+S+A+KY  RG+   DLIQEGN GLM A EKFD+  G+KFSTY
Sbjct: 144 SAQNARDRLTEANLRLVVSIARKYMGRGMALADLIQEGNAGLMLAVEKFDYTRGFKFSTY 203

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R+IA+Q+ TIR+PVH  + ++++ RT+ ++  ++ REP+ EEIA+++ + 
Sbjct: 204 ATWWIRQAINRAIANQARTIRLPVHFHEAVNRLHRTSSQLFQELGREPSAEEIAERMHIS 263

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V+ V  +L+  K+PISLE+P+GD+  S LGDF+ED+   SP D   +  LRE    VL  
Sbjct: 264 VDTVYDILEAGKQPISLESPVGDDGDSSLGDFVEDQVTASPADITTRNILREQIAHVLDE 323

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  RE  +++  FG     +HTL E+G+   ++RER+RQIEAKA+RKL+    S++L+ F
Sbjct: 324 LNERERHIIQYHFGFLDGKEHTLAEIGENLHLSRERVRQIEAKALRKLRQSYSSRQLKDF 383

Query: 680 LD 681
           L+
Sbjct: 384 LN 385



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR-AMMMASLCESP---LTFQALIIWRDEL 174
           D +  YLREMG + LL+ E E+ +A++IE G+     A L + P       +    RD L
Sbjct: 93  DTLETYLREMGRVPLLTSEQEVQLAQQIERGKLEQERARLLKVPPEHAIMDSAQNARDRL 152

Query: 175 NDGTTLL 181
            +    L
Sbjct: 153 TEANLRL 159


>gi|310777992|ref|YP_003966325.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747315|gb|ADO81977.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 408

 Score =  209 bits (531), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 141/287 (49%), Positives = 194/287 (67%), Gaps = 3/287 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E    ++  VD    I+  ++ I     ++  +    +   +        A +++VEAN
Sbjct: 123 PEKLMTISSGVDVDEPIKMYLREIGQVPLLTHKQE---IEHAKNSAEGDEWATQQLVEAN 179

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+I
Sbjct: 180 LRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAI 239

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQ  TIRIPVHM + I+K+ + +R    +  ++ TPE +A++L M  E ++ +L++ ++
Sbjct: 240 ADQGRTIRIPVHMIETINKIKKESRIYLQETGKDATPEVLAERLGMESEKIKAILEMNQD 299

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PISLETP+G E+ S LGDF+ED   +SP +   +  L+E    VL SL+ REE+VLR R+
Sbjct: 300 PISLETPVGSEEDSELGDFVEDNKMLSPYEQTNRNLLKEQLDDVLQSLSEREEKVLRFRY 359

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G+      TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 360 GLDDGCPRTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 406



 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 74/199 (37%), Gaps = 42/199 (21%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++  + +I+ + +   +T EE+N  L  D+   +++E  +  + + GI ++  ++LE 
Sbjct: 5   IRNEKARALIRKSIEEKVITFEEVNEAL-QDDFPVDKIEFLINGMIDQGIKIIRREELEK 63

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRST---------------------------- 117
            +  +     +  A+   V ++  +                                   
Sbjct: 64  VKSEDKDGKTSVKAATPKVAVKVDEKLDSEQVETNKKVKKVEGDFNPAEIEEVTEEELSP 123

Query: 118 ------------DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
                       D+P++MYLRE+G + LL+ + EI  AK    G       L E+ L   
Sbjct: 124 EKLMTISSGVDVDEPIKMYLREIGQVPLLTHKQEIEHAKNSAEGDEWATQQLVEANLRLV 183

Query: 166 ALIIWRDELNDGTTLLREI 184
             I  +   N G  LL  I
Sbjct: 184 VSIAKK-HTNRGLKLLDLI 201


>gi|257467207|ref|ZP_05631518.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315918337|ref|ZP_07914577.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313692212|gb|EFS29047.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 352

 Score =  209 bits (531), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 142/271 (52%), Positives = 192/271 (70%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     ++  E   +    +K       A K ++EANLRLV+S+AKK+TNRGL
Sbjct: 82  IKMYLREIGQIPLLTHKEELELA---KKALEGDEFANKRLIEANLRLVVSIAKKHTNRGL 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 139 KLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 198

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ S L
Sbjct: 199 INKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGSEEDSEL 258

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEVGK 
Sbjct: 259 GDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEVGKI 318

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 319 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 349



 Score = 54.8 bits (130), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 1/94 (1%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ +L           +  + S     D+P++MYLRE+G I LL+ + E+ +AK+   G 
Sbjct: 52  DASELEEIPEEELTNEELAELSNGMKVDEPIKMYLREIGQIPLLTHKEELELAKKALEGD 111

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  +   N G  LL  I
Sbjct: 112 EFANKRLIEANLRLVVSIAKK-HTNRGLKLLDLI 144


>gi|253581343|ref|ZP_04858569.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836707|gb|EES65241.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 414

 Score =  209 bits (531), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 140/271 (51%), Positives = 188/271 (69%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     +S  E                 A K+++EANLRLV+S+AKK+TNRGL
Sbjct: 145 IKMYLREIGQIPLLSHDEELEYAKRA---LEGDEWASKQLIEANLRLVVSIAKKHTNRGL 201

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 202 KLLDLIQEGNIGLMKAVEKFEYSKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 261

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE + ++L M V+ V+ + ++ ++PISLETP+G E+ S L
Sbjct: 262 INKIKKEARIYLQETGKDATPEVLGERLGMEVDKVKAIQEMNQDPISLETPVGSEEDSEL 321

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED   ++P +   ++ LRE    VL +L+ REERVLR R+G+   +  TLEEVGK 
Sbjct: 322 GDFVEDHKMLNPYELTNRSLLREQLNGVLNTLSSREERVLRYRYGLDDGSPKTLEEVGKI 381

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 382 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 412



 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 47/205 (22%), Positives = 75/205 (36%), Gaps = 48/205 (23%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++    +++ A +  ++T EE+N  L  D    E++E  +  +   GI +V  +DLE 
Sbjct: 5   IKNEKVLSLVRKAMENKFITYEEINEELKSD-FPVEKIEQLITGMMEQGIEIVRQEDLEK 63

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKD---------------------------------- 111
           E+    SL    +     +   + K+                                  
Sbjct: 64  EKKLAASLKKDKNKDEEPISKTQDKEEFPDEDEIDDLLDERTEDLDDFEHFNPEELEEIS 123

Query: 112 ------------SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
                       S D   D+P++MYLRE+G I LLS + E+  AKR   G       L E
Sbjct: 124 EDELVSDDLFNLSGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASKQLIE 183

Query: 160 SPLTFQALIIWRDELNDGTTLLREI 184
           + L     I  +   N G  LL  I
Sbjct: 184 ANLRLVVSIAKK-HTNRGLKLLDLI 207


>gi|269798255|ref|YP_003312155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282850493|ref|ZP_06259872.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294792116|ref|ZP_06757264.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
 gi|294793987|ref|ZP_06759124.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|269094884|gb|ACZ24875.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282579986|gb|EFB85390.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294455557|gb|EFG23929.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|294457346|gb|EFG25708.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
          Length = 386

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 162/385 (42%), Positives = 229/385 (59%), Gaps = 11/385 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRI-DLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           K  + S   +++++ L K   S  L QS I D L EQ    ++++      L +L     
Sbjct: 3   KKVQKSQIEEIVEQLLEKGRKSGVLTQSEISDALHEQTEITAEQLDDIYTTLGKLNVEIV 62

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
              D         E D           +      V   V+    +R  +K I     +S 
Sbjct: 63  ADIDADDTDSHTIETDEDE-DEVSSEKKISIDLSVDSGVNIDDPVRMYLKEIGRVPLLSA 121

Query: 425 SEFRHIVSMVR---------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
            E   +   +          K    +  AKK++V+ANLRLV+S+AK+Y  RG+ FLDLIQ
Sbjct: 122 DEEIVLAKQIEAGAQEDATYKDIQLSKKAKKKLVDANLRLVVSIAKRYVGRGMLFLDLIQ 181

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL+KA +KFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R 
Sbjct: 182 EGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRI 241

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           +R++     REP PEEIA+ + + VE VR++ KI +EP+SLETPIG+E+ SHLGDFIED+
Sbjct: 242 SRQLLQDKGREPLPEEIAEGMGITVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDQ 301

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +A++P D+A    L+E    V   LT RE++VL +RFG+      TLEEVG+ F VTRER
Sbjct: 302 DAIAPDDAASYILLQEQIEDVFTCLTDREQQVLILRFGLKDGKPRTLEEVGQHFNVTRER 361

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIE KA+ KL++  +  K++ FL
Sbjct: 362 IRQIEGKALTKLRNRGKRDKIKDFL 386



 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 43/171 (25%), Positives = 77/171 (45%), Gaps = 15/171 (8%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  +++++  R+ G +T  E++  L    E+++EQ++D    L  + + +V   D +D 
Sbjct: 11  EEIVEQLLEKGRKSGVLTQSEISDALHEQTEITAEQLDDIYTTLGKLNVEIVADIDADDT 70

Query: 87  EGSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +      D      +S   +       +  + DDPVRMYL+E+G + LLS + EI +AK+
Sbjct: 71  DSHTIETDEDEDEVSSEKKISIDLSVDSGVNIDDPVRMYLKEIGRVPLLSADEEIVLAKQ 130

Query: 146 IEAGRAM------------MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           IEAG                   L ++ L     I  R  +  G   L  I
Sbjct: 131 IEAGAQEDATYKDIQLSKKAKKKLVDANLRLVVSIAKRY-VGRGMLFLDLI 180


>gi|306836272|ref|ZP_07469254.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
 gi|304567864|gb|EFM43447.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
          Length = 492

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 157/451 (34%), Positives = 237/451 (52%), Gaps = 36/451 (7%)

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
            SAA+      +  +  P  AE+ E  +D  E D+       +           D   + 
Sbjct: 78  ASAAEPQDSPANSAEKAPSEAEDAEDQIDAVEQDAPADDVDFDPTHEDIEEDEFDAPTD- 136

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
                 L ++ +  +  E+           +     S++L Q+R D    QL   +  + 
Sbjct: 137 ------LDEDDIQEELGEEEDEDEVEDTSSVWDEEESVALRQARKD---AQLTASADSVR 187

Query: 351 HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
               ++ ++A                     +           E   +    +D + K R
Sbjct: 188 AYLKQIGKVAL-------------------LNAEQEVSLAKRIEAGLYAQHRMDEMEKAR 228

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            E    +  + +   + R I         +   AK  ++EANLRLV+S+AK+YT RG+ F
Sbjct: 229 AEGDKAAKLSPMEKRDLRSIAR-------DGRKAKNHLLEANLRLVVSLAKRYTGRGMAF 281

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+
Sbjct: 282 LDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVIN 341

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R  R +   + REPTP+E+AK++ +  E V ++ +  +EPISL+  IGDE  S LGD
Sbjct: 342 KLGRIQRELLQDLGREPTPQELAKEMDITEEKVMEIQQYAREPISLDQTIGDEGDSQLGD 401

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIED  AV  +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + 
Sbjct: 402 FIEDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 461

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 462 VTRERIRQIESKTMSKLRHPSRSQVLRDYLD 492



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 33/53 (62%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S    Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 163 DEEESVALRQARKDAQLTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 215


>gi|324999213|ref|ZP_08120325.1| RNA polymerase sigma factor SigB [Pseudonocardia sp. P1]
          Length = 380

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 112/251 (44%), Positives = 175/251 (69%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                +R    + ++AK  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKF
Sbjct: 128 QYRRDLRAVVRDGALAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKF 187

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR +ADQ+ TIR+PVH+ ++++K+ R  R M  +  REP+
Sbjct: 188 DYTKGFKFSTYATWWIRQAITRGMADQARTIRLPVHLVEQVNKLARIKRDMHQRQGREPS 247

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A++  +P   +  +L   ++P+SL+ P+G E+ + LGDFIED  A    ++ I + 
Sbjct: 248 EAELAQESGIPEHKISDLLDHARDPVSLDMPVGSEEEAPLGDFIEDAEATDAENTVISSL 307

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +   RVLA+L  RE++V+RMRFG+      TL+++G+ F ++RER+RQIE + + KL+
Sbjct: 308 LSDDLRRVLATLEDREQKVIRMRFGLDDGQPRTLDQIGRAFTLSRERVRQIEREVMAKLR 367

Query: 669 HPSRSKKLRSF 679
              R+ KLR++
Sbjct: 368 VGERADKLRAY 378



 Score = 44.4 bits (103), Expect = 0.064,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +     L ++   +S  L +  D+   +  D VR+YL  +G   LL+   E+ +AKRIE
Sbjct: 46  ATAQDTALETTVPGASAALAEDLDAQSPAA-DLVRVYLNGIGRTALLTAAEEVDLAKRIE 104

Query: 148 AG 149
           AG
Sbjct: 105 AG 106


>gi|116072877|ref|ZP_01470142.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
 gi|116064403|gb|EAU70164.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
          Length = 451

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 204 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 263

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 264 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 323

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 324 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 382

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 383 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 442

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 443 NGVLKEYI 450



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 134 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 168


>gi|1149588|emb|CAA89984.1| SigA sigma factor [Corynebacterium glutamicum]
          Length = 497

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 127/250 (50%), Positives = 180/250 (72%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R    +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+ 
Sbjct: 248 RDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYS 307

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +  ++ REPTP+E
Sbjct: 308 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQELGREPTPQE 367

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+     L++
Sbjct: 368 LSKEMDISEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQD 427

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+ RE  V+++RFG+      TL+E+G+ + VTRERIRQIE+K + K +HPS
Sbjct: 428 QLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKRRHPS 487

Query: 672 RSKKLRSFLD 681
           RS+ LR +LD
Sbjct: 488 RSQVLRDYLD 497



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               S+   Q RKD+   ++ D VR YL+++G + LL+ E E+++AKRIEAG 
Sbjct: 168 DEDESATLRQARKDAELTASADSVRAYLKQIGKVALLNAEQEVSLAKRIEAGL 220


>gi|203288141|ref|YP_002223156.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
 gi|201085361|gb|ACH94935.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
          Length = 630

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 144/432 (33%), Positives = 242/432 (56%), Gaps = 2/432 (0%)

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           + E   +   E E D+       + ++       L    +   +    + + +    ++ 
Sbjct: 198 DKEEFFKKDREREKDNNFDYYNKKKRITSFYKSLLKPFQDRLVKYVE-RKHRLYELGEDI 256

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                   + ++ +L+ S+ L Q  + L  +   D + +I   + +   +     I +  
Sbjct: 257 FEESITNERLQIKELLKSIPLYQEELRLFSDDYIDSASKIKDLKRQQKSILDRLKIDKVR 316

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
            L    GR+L         +      ++ +  ++      + E++ I +     + +   
Sbjct: 317 NLRIL-GRDLAIPEKRERIEKSLNIREDLIKEQITEAQLAQKELERIEMYYEYPMDKIIS 375

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF+
Sbjct: 376 MSEEILKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFE 435

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT 
Sbjct: 436 YKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQILGKDPTD 495

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P        L
Sbjct: 496 EELSIRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSFVIL 555

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++    VL +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+
Sbjct: 556 QDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIESKALRRLKN 615

Query: 670 PSRSKKLRSFLD 681
           P +++KL+ +L+
Sbjct: 616 PKKTQKLKDYLE 627



 Score = 67.6 bits (163), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 59/357 (16%), Positives = 136/357 (38%), Gaps = 43/357 (12%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---GDDLEDEEGSEDSLDLAS 97
           +  +T E+L+ FL  D +  + ++    +L N GI +++   G D+ D +  +++  L S
Sbjct: 30  KKEITFEDLSTFLSGDMLEPDNIDCIYGILENEGIGLINEKIGSDICDVDELDEASKLDS 89

Query: 98  ---------------------------SASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                                         + +    K     D +++DP+R+YL+E+G 
Sbjct: 90  QCMMLDDAIQVDDELDDKLDDFDDEVLDKEDYNSGYIKSGLLKDSNSEDPIRLYLKEIGK 149

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI----IWRDELNDGTT----LLR 182
             LL+   E+ +AK++++G +++   L    L  +            ++          R
Sbjct: 150 EFLLTGNQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNAIYSRVDKEEFFKKDRER 209

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E  +       + +   F+ +    +Q R     E++    +  E   E +    +    
Sbjct: 210 EKDNNFDYYNKKKRITSFYKSLLKPFQDRLVKYVERKHRLYELGEDIFEESITNERLQIK 269

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA-EVYRELRSLQDNA 301
           ++       + + R   +D  DSA  +  ++ Q +      LD +  +  R LR L  + 
Sbjct: 270 ELLKSIPLYQEELRLFSDDYIDSASKIKDLKRQQK----SILDRLKIDKVRNLRILGRDL 325

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
              +K E+      + ++ + + +    L Q  ++ +         +I+    E+L+
Sbjct: 326 AIPEKRERIEKSLNIREDLIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEILK 382


>gi|203284607|ref|YP_002222347.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
 gi|201084050|gb|ACH93641.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
          Length = 630

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 144/432 (33%), Positives = 242/432 (56%), Gaps = 2/432 (0%)

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           + E   +   E E D+       + ++       L    +   +    + + +    ++ 
Sbjct: 198 DKEEFFKKDREREKDNNFDYYNKKKRITSFYKSLLKPFQDRLVKYVE-RKHRLYELGEDI 256

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                   + ++ +L+ S+ L Q  + L  +   D + +I   + +   +     I +  
Sbjct: 257 FEESITNERLQIKELLKSIPLYQEELRLFSDDYIDSASKIKDLKRQQKSILDRLKIDKVR 316

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
            L    GR+L         +      ++ +  ++      + E++ I +     + +   
Sbjct: 317 NLRIL-GRDLAIPEKRERIEKSLNIREDLIKEQITEAQLAQKELERIEMYYEYPMDKIIS 375

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF+
Sbjct: 376 MSEEILKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFE 435

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT 
Sbjct: 436 YKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTD 495

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P        L
Sbjct: 496 EELSIRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTSFVVL 555

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++    VL +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+
Sbjct: 556 QDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKN 615

Query: 670 PSRSKKLRSFLD 681
           P +++KL+ +L+
Sbjct: 616 PKKTQKLKDYLE 627



 Score = 67.6 bits (163), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 59/357 (16%), Positives = 136/357 (38%), Gaps = 43/357 (12%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD---GDDLEDEEGSEDSLDLAS 97
           +  +T E+L+ FL  D +  + ++    +L N GI +++   G D+ D +  +++  L S
Sbjct: 30  KKEITFEDLSTFLSGDMLEPDNIDCIYGILENEGIGLINEKIGSDICDVDELDEASKLDS 89

Query: 98  ---------------------------SASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                                         + +    K     D +++DP+R+YL+E+G 
Sbjct: 90  QCMMLDDAIQVDDELDDKLDDFDDEVLDKEDYNSGYIKSGLLKDSNSEDPIRLYLKEIGK 149

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI----IWRDELNDGTT----LLR 182
             LL+   E+ +AK++++G +++   L    L  +            ++          R
Sbjct: 150 EFLLTGNQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNAIYSRVDKEEFFKKDRER 209

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E  +       + +   F+ +    +Q R     E++    +  E   E +    +    
Sbjct: 210 EKDNNFDYYNKKKRITSFYKSLLKPFQDRLVKYVERKHRLYELGEDIFEESITNERLQIK 269

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA-EVYRELRSLQDNA 301
           ++       + + R   +D  DSA  +  ++ Q +      LD +  +  R LR L  + 
Sbjct: 270 ELLKSIPLYQEELRLFSDDYIDSASKIKDLKRQQK----SILDRLKIDKVRNLRILGRDL 325

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
              +K E+      + ++ + + +    L Q  ++ +         +I+    E+L+
Sbjct: 326 AIPEKRERIEKSLNIREDLIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEILK 382


>gi|167970067|ref|ZP_02552344.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215404675|ref|ZP_03416856.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           02_1987]
 gi|215428138|ref|ZP_03426057.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T92]
 gi|215431649|ref|ZP_03429568.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           EAS054]
 gi|218754446|ref|ZP_03533242.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis GM
           1503]
 gi|219558719|ref|ZP_03537795.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T17]
 gi|254551766|ref|ZP_05142213.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260187727|ref|ZP_05765201.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|260201835|ref|ZP_05769326.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T46]
 gi|260206019|ref|ZP_05773510.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis K85]
 gi|289746512|ref|ZP_06505890.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|294994199|ref|ZP_06799890.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis 210]
 gi|297635318|ref|ZP_06953098.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           4207]
 gi|297732314|ref|ZP_06961432.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           R506]
 gi|289687040|gb|EFD54528.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|323718704|gb|EGB27866.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CDC1551A]
 gi|328457981|gb|AEB03404.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           4207]
          Length = 333

 Score =  208 bits (530), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 179/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 84  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 139

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 140 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREA 199

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 200 TDEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 259

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 260 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKL 319

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 320 RHGERADRLRSY 331



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++  + +A + + ++         A     D VR+YL  +G   LL+  GE+ +AKRIEA
Sbjct: 5   ADREVAMADAPTRATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEA 64

Query: 149 GR 150
           G 
Sbjct: 65  GL 66


>gi|169630111|ref|YP_001703760.1| RNA polymerase sigma factor SigB [Mycobacterium abscessus ATCC
           19977]
 gi|169242078|emb|CAM63106.1| RNA polymerase sigma factor [Mycobacterium abscessus]
          Length = 323

 Score =  208 bits (529), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 112/241 (46%), Positives = 177/241 (73%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E + A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 81  REGNAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFST 140

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE + EE+A++  +
Sbjct: 141 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQRLGREASDEELAEESGI 200

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE +  +L  +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I   L      VLA
Sbjct: 201 PVEKIGDLLDHSRDPVSLDMPVGTDEEAPLGDFIEDTEAMSAENAVIAELLHSDVRSVLA 260

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE + + KL+H  R+++LRS
Sbjct: 261 TLDEREQQVIRLRYGLDDGQARTLDQIGKLFGLSRERVRQIEREVMAKLRHGDRAERLRS 320

Query: 679 F 679
           +
Sbjct: 321 Y 321



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +A++ +  +   +     A     D VR+YL  +G   LL+ E E+ +AKRIEAG 
Sbjct: 1   MANATTRPARTTESEDLDAQSPAADLVRVYLNGIGKTALLTAEDEVELAKRIEAGL 56


>gi|312200424|ref|YP_004020485.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311231760|gb|ADP84615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 403

 Score =  208 bits (529), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 120/262 (45%), Positives = 191/262 (72%), Gaps = 4/262 (1%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             +S  +   ++++ R    +  +A +++VEANLRLV+S+AK+Y  RG+ FLD++QEGN+
Sbjct: 146 EEMSPGQRLDLIAVER----DGQVAARQLVEANLRLVVSIAKRYAGRGMLFLDVVQEGNL 201

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKFD+  GYKFSTYA WWV+QAITR++ADQS T+R+PVH+ + ++++VR  R +
Sbjct: 202 GLIRAVEKFDYTKGYKFSTYATWWVRQAITRALADQSRTVRLPVHLVELLNQLVRLRREL 261

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ RE T EE+A  L +    V ++ +I++EP+SL++P+GD+  + LGD IED  A+ 
Sbjct: 262 LMELGREATREELATALGVTANRVDELQRISREPVSLDSPVGDDADTELGDLIEDTAAIE 321

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+++A+ +      + VL +L  RE RV+++RFG+     HTLEE+G++F +TRERIRQI
Sbjct: 322 PVEAAMVSVRAAQLSAVLRALPDRERRVIQLRFGLADGQVHTLEEIGREFGLTRERIRQI 381

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E + + KL+HP+RS+ LRS+L+
Sbjct: 382 EQRTLAKLRHPARSEALRSYLE 403



 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 32/62 (51%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +   D A      +      + +A  +  DPVRMYL  +G   LL+ EGE+ +AKRIEA
Sbjct: 74  EDGDGDAADEPKTPARRRAATRTTATTTVFDPVRMYLASIGKTPLLTAEGEVDLAKRIEA 133

Query: 149 GR 150
           G 
Sbjct: 134 GL 135


>gi|28493466|ref|NP_787627.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
 gi|28476507|gb|AAO44596.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
          Length = 387

 Score =  208 bits (529), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 134/252 (53%), Positives = 183/252 (72%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +R    +   AK  ++ ANLRLV+S+AK+YT RG+QFLDLIQEGN+GL++A EKF
Sbjct: 135 KLKRELRWVVRDGQRAKDHLLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKF 194

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R++   + REPT
Sbjct: 195 DYVKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLSRVQRQLLQDLGREPT 254

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P+E+ ++L MP E V +V K  +EPISL TP+GDE  S  GD IED +AV+P D+   + 
Sbjct: 255 PDELGRELDMPPERVVEVQKYGREPISLHTPLGDEGDSEFGDLIEDVDAVAPDDAVGFSM 314

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++    +L SL+ RE  V+RMRFG+  +   TL+ VG+ F VTRERIRQIEAK + KL+
Sbjct: 315 LQQQLRLLLDSLSEREAGVIRMRFGLDDDMPKTLDYVGEYFDVTRERIRQIEAKTMAKLR 374

Query: 669 HPSRSKKLRSFL 680
           HPSRS+ LR +L
Sbjct: 375 HPSRSQCLRDYL 386



 Score = 57.5 bits (137), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D     +GSE   +    A                +T DPV+ YL+++G + LL+ + E
Sbjct: 50  SDTDVASKGSEGDFEAIVLADTKDDESTPASPVISGATADPVKDYLKQIGKVSLLTADEE 109

Query: 140 IAIAKRIEAGRAMMMASLCES 160
           +++AKRIEAG       L ES
Sbjct: 110 VSLAKRIEAGLF-AEEKLSES 129


>gi|113954073|ref|YP_731235.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
 gi|113881424|gb|ABI46382.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
          Length = 440

 Score =  208 bits (529), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 140/300 (46%), Positives = 199/300 (66%), Gaps = 8/300 (2%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              +  A+   +      +A + +S      E K  +    + +  FR  + + R+    
Sbjct: 148 DEEIELARKIADLLHLEELAAQFESDNGKLPETKEWAALVEMPVIRFRRRLMLGRR---- 203

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA
Sbjct: 204 ---AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 260

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +
Sbjct: 261 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTI 320

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L
Sbjct: 321 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATL 379

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 380 SPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 439



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 25/43 (58%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           V    +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 115 VLASIKVGPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 157


>gi|120403441|ref|YP_953270.1| RNA polymerase sigma factor SigB [Mycobacterium vanbaalenii PYR-1]
 gi|119956259|gb|ABM13264.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 329

 Score =  208 bits (529), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 116/252 (46%), Positives = 181/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 80  RDLAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 136 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I  
Sbjct: 196 TDEELAAESGIPVEKITDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSAENAVISE 255

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL
Sbjct: 256 LLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKL 315

Query: 668 KHPSRSKKLRSF 679
           ++  R+ +LRS+
Sbjct: 316 RNGERADRLRSY 327



 Score = 41.4 bits (95), Expect = 0.60,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 12/87 (13%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           D  ++ +N++     +   A     D VR+YL  +G   LL+   E+ +AKRIEAG    
Sbjct: 6   DQEAAMANATTSRIDQDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYA- 64

Query: 154 MASLCESPLTFQALIIWRDELNDGTTL 180
                      Q L+  R  L +    
Sbjct: 65  -----------QHLLDTRKRLGENRKR 80


>gi|189348175|ref|YP_001941371.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
 gi|189338313|dbj|BAG47381.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 612

 Score =  208 bits (529), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 112/355 (31%), Positives = 188/355 (52%), Gaps = 2/355 (0%)

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD-PHWVS 385
            L L+   ++ +   L   ++R       + R+ +  GI        H   + D   W++
Sbjct: 258 PLRLSARAVERIGAPLRGRARRHREQLARMTRVLRHAGIPSQTTWRYHDAHDDDHARWLA 317

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A      E +  +     ++ + R+ + S +  + +       + + +   E     AK
Sbjct: 318 -AGIAAHPECEPALKRSAPALFEARDALASEARASVLPPRTVALLDARLDAIERATRAAK 376

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW++
Sbjct: 377 TALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIR 436

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q+IT ++AD   TIR+P H  D I+K+ R AR    +     TP E+A ++  PV+ VR 
Sbjct: 437 QSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGATATPAELAAQMGEPVDKVRD 496

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++ I KEP+S + PI  +      D + D +  SP D+A  A  R      +  L PRE 
Sbjct: 497 LMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREA 556

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++R+R+G+      +L ++G++  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 557 LIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASGTLAVLRPFV 611



 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 54/171 (31%), Positives = 77/171 (45%), Gaps = 2/171 (1%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+               +   +  +I L   RG+VT  +L   LP D+     ++   A+
Sbjct: 3   DARQPAPAGGHDDTLASASTRFAGLIALGLSRGFVTRGDLIDALPDDDAHDAGIDAATAV 62

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLA--SSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           L+ +GI V D    E     +     A  S A+          D     T DPVR+YLRE
Sbjct: 63  LAELGIAVSDDAHAETGWSLDRYFRPAPLSRAAAERNGAFAAFDLLVPRTTDPVRLYLRE 122

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           MG++ LL+ + EIA A+RIE GRA  +A LC  P    AL   R E+ +G 
Sbjct: 123 MGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGR 173


>gi|163848612|ref|YP_001636656.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526547|ref|YP_002571018.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163669901|gb|ABY36267.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450426|gb|ACM54692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 381

 Score =  208 bits (529), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 127/248 (51%), Positives = 176/248 (70%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +   +   A+  +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G
Sbjct: 134 LERAVQQGQDARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKG 193

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQS TIR+PVHM + I +V RT+ R+   ++REPTPEEIA
Sbjct: 194 HKFSTYATWWIRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHRLQQTMQREPTPEEIA 253

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +    VR+ L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE  
Sbjct: 254 DAMGISAGKVRRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASLLREQL 313

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL  L  RE +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   
Sbjct: 314 EEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHPHLG 373

Query: 674 KKLRSFLD 681
           KKLR +LD
Sbjct: 374 KKLRGYLD 381



 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 42/155 (27%), Positives = 68/155 (43%), Gaps = 7/155 (4%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            ++++  AR RGY+T  ++ A  P  E    +++   AML   GI V++  D  D     
Sbjct: 2   IEQLLAAARVRGYITHADILATFPNPEHDIAEIDQLYAMLQAEGIKVIESSDELDGPT-- 59

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                       +  +    D  D + DDPVRMYL+E+G + LL+ E E+ +AK +EAG 
Sbjct: 60  -----DFEPDPDADLIADLPDLGDIAFDDPVRMYLQEIGQVPLLTAEQEVELAKAMEAGA 114

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           A       E   + +        +  G      +I
Sbjct: 115 AARQRLDREEYTSARERFELERAVQQGQDARHHLI 149


>gi|238018971|ref|ZP_04599397.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
 gi|237864455|gb|EEP65745.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
          Length = 387

 Score =  208 bits (529), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 141/281 (50%), Positives = 195/281 (69%), Gaps = 9/281 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK---------EMVEANLRLVISV 459
           +R  +K I     +S  E   +   +  G  E +  K          ++V+ANLRLV+S+
Sbjct: 107 VRMYLKEIGRVPLLSADEEIVLAKQIEAGAAEDATYKDVQLAKKAKKKLVDANLRLVVSI 166

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAITR+IADQ+ TI
Sbjct: 167 AKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIADQARTI 226

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++R +R++     REP PEEIA+ + + VE VR++ KI +EP+SLETP
Sbjct: 227 RIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERVREIQKIAQEPVSLETP 286

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+E+ SHLGDFIED++A++P D+A    L+E    V   LT RE++VL +RFG+     
Sbjct: 287 IGEEEDSHLGDFIEDQDAIAPDDAASYILLQEQIEDVFTCLTDREQQVLILRFGLKDGKP 346

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 347 RTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 387



 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 40/128 (31%), Positives = 68/128 (53%), Gaps = 3/128 (2%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  +++++  R+ G +T  E++  L    ++++EQ++D       + I VV   D ED 
Sbjct: 11  EEIVEQLLEKGRKTGVLTQSEISDALHEQTDLTAEQLDDIYTTFGKLNIEVVADIDGEDA 70

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSREGEIAIAK 144
           + +    +       SS        S D   + DDPVRMYL+E+G + LLS + EI +AK
Sbjct: 71  DANPIEPEEEDEEDTSSEKNISIDLSVDSGVNIDDPVRMYLKEIGRVPLLSADEEIVLAK 130

Query: 145 RIEAGRAM 152
           +IEAG A 
Sbjct: 131 QIEAGAAE 138


>gi|183982017|ref|YP_001850308.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
 gi|183175343|gb|ACC40453.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
          Length = 333

 Score =  208 bits (529), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 118/252 (46%), Positives = 180/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    + + A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 84  RELAAVVR----DGAEARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 139

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 140 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 199

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A +  +PVE +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 200 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 259

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 260 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCKL 319

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 320 RHGERADRLRSY 331



 Score = 44.1 bits (102), Expect = 0.088,   Method: Composition-based stats.
 Identities = 21/62 (33%), Positives = 31/62 (50%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           ++   ++A   +   V        A     D VR+YL  +G   LL+ EGE+ +AKRIEA
Sbjct: 5   ADREGEMAQPIARGIVGRVDSDLDAQSPAADLVRVYLNGIGKTALLNAEGEVELAKRIEA 64

Query: 149 GR 150
           G 
Sbjct: 65  GL 66


>gi|296171822|ref|ZP_06852936.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295893958|gb|EFG73726.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 329

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 115/241 (47%), Positives = 173/241 (71%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 87  RDGQAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFST 146

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A +  +
Sbjct: 147 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEELAAESGI 206

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I   L      VLA
Sbjct: 207 PVEKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLA 266

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL+H  R+ +LRS
Sbjct: 267 TLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRHGERADRLRS 326

Query: 679 F 679
           +
Sbjct: 327 Y 327



 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 29/59 (49%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +   + +N+S         A     D VR+YL  +G   LL+  GE+ +AKRIEAG 
Sbjct: 4   QAEREVAMANASTSRFDGDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGL 62


>gi|161522996|ref|YP_001585925.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|160346549|gb|ABX19633.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
          Length = 625

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 112/355 (31%), Positives = 188/355 (52%), Gaps = 2/355 (0%)

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD-PHWVS 385
            L L+   ++ +   L   ++R       + R+ +  GI        H   + D   W++
Sbjct: 271 PLRLSARAVERIGAPLRGRARRHREQLARMTRVLRHAGIPSQTTWRYHDAHDDDHARWLA 330

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            A      E +  +     ++ + R+ + S +  + +       + + +   E     AK
Sbjct: 331 -AGIAAHPECEPALKRSAPALFEARDALASEARASVLPPRTVALLDARLDAIERATRAAK 389

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA +++D   G++FSTYA WW++
Sbjct: 390 TALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIR 449

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q+IT ++AD   TIR+P H  D I+K+ R AR    +     TP E+A ++  PV+ VR 
Sbjct: 450 QSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGATATPAELAAQMGEPVDKVRD 509

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++ I KEP+S + PI  +      D + D +  SP D+A  A  R      +  L PRE 
Sbjct: 510 LMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREA 569

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++R+R+G+      +L ++G++  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 570 LIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASGTLAVLRPFV 624



 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 54/171 (31%), Positives = 77/171 (45%), Gaps = 2/171 (1%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D+               +   +  +I L   RG+VT  +L   LP D+     ++   A+
Sbjct: 16  DARQPAPAGGHDDTLASASTRFAGLIALGLSRGFVTRGDLIDALPDDDAHDAGIDAATAV 75

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLA--SSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           L+ +GI V D    E     +     A  S A+          D     T DPVR+YLRE
Sbjct: 76  LAELGIAVSDDAHAETGWSLDRYFRPAPLSRAAAERNGAFAAFDLLVPRTTDPVRLYLRE 135

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           MG++ LL+ + EIA A+RIE GRA  +A LC  P    AL   R E+ +G 
Sbjct: 136 MGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGR 186


>gi|291522137|emb|CBK80430.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 365

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 138/273 (50%), Positives = 191/273 (69%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E   +   ++     +  A K+M EANLRLV+S+AK+Y  RG+
Sbjct: 95  VRMYLKEIGNIPLLTPEEEVELAKEMK---EGSKQAAKKMAEANLRLVVSIAKRYVGRGM 151

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GL+KA EK+D+  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + 
Sbjct: 152 QFLDLIQEGNVGLIKAIEKYDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVET 211

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +  R ++ ++ REP+ EEIA+ + M V  VR++LK+ +E +SLETP+G E+ SHL
Sbjct: 212 MNKLTKVQRSLTQELGREPSVEEIAENVHMDVNRVREILKLVQETVSLETPVGSEEESHL 271

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DFIED +   P D A    L++    VL  L  RE++VLRMRFG+    +HTLEEVG++
Sbjct: 272 ADFIEDDHTPLPSDEAAFGQLKDDIRSVLDKLNEREQKVLRMRFGLDDGKEHTLEEVGQE 331

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             VTRERIRQIEAKA+RKL+   +S  L  +L+
Sbjct: 332 LHVTRERIRQIEAKALRKLRQSGKSAGLEGYLN 364



 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 71/157 (45%), Gaps = 10/157 (6%)

Query: 29  DSWKKMIKLARQRGY-VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D  K+++  A++R   +T + ++ F     ++ EQME     L + GI V   +D  D  
Sbjct: 10  DKLKELVPFAKEREQELTSDMISDFFGHMPLTEEQMEKIYDYLESNGIFVDRSNDEPDRR 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +++ +       S              TDDPVRMYL+E+G+I LL+ E E+ +AK ++
Sbjct: 70  MLDEAEEEIDPNDISV--------PEGIRTDDPVRMYLKEIGNIPLLTPEEEVELAKEMK 121

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       + E+ L     I  R  +  G   L  I
Sbjct: 122 EGSKQAAKKMAEANLRLVVSIAKRY-VGRGMQFLDLI 157


>gi|34763652|ref|ZP_00144580.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|237742311|ref|ZP_04572792.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
 gi|27886661|gb|EAA23826.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|229429959|gb|EEO40171.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
          Length = 340

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 143/303 (47%), Positives = 202/303 (66%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +P ++    +     E    +         I+  ++ I     ++  E        +K
Sbjct: 38  EFNPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYA---KK 94

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 95  AYEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 154

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 155 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 214

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 215 GMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 274

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 275 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 334

Query: 677 RSF 679
             F
Sbjct: 335 EDF 337



 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/130 (24%), Positives = 49/130 (37%), Gaps = 4/130 (3%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
            D +  E  +                 + +DE   E   D++    ++   L        
Sbjct: 7   DDLLEDETEDKLDDTDEENDETEEHFTEFDDEFNPEYIEDVSEDELSNEKLLN---LGNS 63

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
              D+P++MYLRE+G + LL+ + EI  AK+   G       L ES L     I  +   
Sbjct: 64  AKVDEPIKMYLREIGQVPLLTHDEEIEYAKKAYEGDEEASKKLIESNLRLVVSIAKK-HT 122

Query: 175 NDGTTLLREI 184
           N G  LL  I
Sbjct: 123 NRGLKLLDLI 132


>gi|219847900|ref|YP_002462333.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542159|gb|ACL23897.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 381

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 129/297 (43%), Positives = 185/297 (62%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR------------------------KGECEASIA 444
           +R  ++ I     ++  +   +   +                         +   +   A
Sbjct: 85  VRMYLQEIGQVPLLTAEQEVELAKAMEAGAIARQRLDREEYASARERFELERAVQQGQDA 144

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G+KFSTYA WW+
Sbjct: 145 RHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYATWWI 204

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQS TIR+PVHM + I +V RT+ R+   ++REPTPEEIA  + +    VR
Sbjct: 205 RQAITRAIADQSRTIRLPVHMGEAISQVKRTSHRLQQTMQREPTPEEIADAMGISAGKVR 264

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L+ +  P+SLE P+G E    +GDFIED    +P ++A  + LRE    VL  L  RE
Sbjct: 265 RTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAAAASLLREQLEEVLMKLPERE 324

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   KKLR +LD
Sbjct: 325 RKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHPHLGKKLRGYLD 381



 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 41/155 (26%), Positives = 65/155 (41%), Gaps = 7/155 (4%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
            ++++  AR RGY+T  ++ A  P  E    +++   AML   GI VV+  D  D     
Sbjct: 2   IEQLLAAARVRGYITHADILATFPNPEHDIAEIDQLYAMLQAEGIRVVESSDELDGPT-- 59

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                               D  + + DDPVRMYL+E+G + LL+ E E+ +AK +EAG 
Sbjct: 60  -----DFEPETDHDLTVDLPDLGEIAFDDPVRMYLQEIGQVPLLTAEQEVELAKAMEAGA 114

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
                   E   + +        +  G      +I
Sbjct: 115 IARQRLDREEYASARERFELERAVQQGQDARHHLI 149


>gi|329121328|ref|ZP_08249954.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|327469737|gb|EGF15203.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 396

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 152/363 (41%), Positives = 215/363 (59%), Gaps = 11/363 (3%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
               +      SLN  ++D L + L+D +  ++ ++              D  L   +  
Sbjct: 30  YNYFIDFAKEKSLNVKQLDQLSQLLHDHNIELVLDDENPEDEDIILDEDIDENL--IEDS 87

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           + D  W    KD+ + E  ++   + +    +R  ++       +S  E   +   + KG
Sbjct: 88  DDDKDWEKQEKDWTKVENNDYAVTQGNVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKG 147

Query: 438 EC---------EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +           A  AKKEM  ANLRLV+S+AKKY  RG+ FLDLIQEGNIGL+KA +KF
Sbjct: 148 KMLDATEEDKLRAEDAKKEMANANLRLVVSIAKKYPGRGMPFLDLIQEGNIGLLKAVDKF 207

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+K+ R  R+   +  RE +
Sbjct: 208 DYKKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVETINKMNRIGRKFLQEFGREAS 267

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+AK++ + VE +R+  K  ++PISLETPIG+++ SHLGDFIED+   SP + A    
Sbjct: 268 NEELAKEMGISVEKIREAKKAAQDPISLETPIGEKEDSHLGDFIEDQKTSSPEEEAAATM 327

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE   ++L  LT RE+ VL +RFG+   T  TLEEVGK F VTRERIRQIE KA++KL+
Sbjct: 328 RREQIYKLLNELTEREKGVLALRFGMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKLR 387

Query: 669 HPS 671
             +
Sbjct: 388 KLA 390



 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 34/135 (25%), Positives = 59/135 (43%), Gaps = 14/135 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN-VVDGDDLEDEEGS 89
            K++     + G ++      F     ++ +Q++    +L +  I  V+D ++ EDE+  
Sbjct: 15  IKELKAKETEEGVLSYNYFIDFAKEKSLNVKQLDQLSQLLHDHNIELVLDDENPEDEDII 74

Query: 90  EDSLDLASSASNSSVFLQKRKDSAD-------------RSTDDPVRMYLREMGSIELLSR 136
            D     +   +S       K   D              +  DPVR+YLRE G+  LLS 
Sbjct: 75  LDEDIDENLIEDSDDDKDWEKQEKDWTKVENNDYAVTQGNVSDPVRLYLRECGATPLLSA 134

Query: 137 EGEIAIAKRIEAGRA 151
           E E+ +AK+IE G+ 
Sbjct: 135 EEEMTLAKQIEKGKM 149


>gi|288920765|ref|ZP_06415065.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288347841|gb|EFC82118.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 425

 Score =  208 bits (528), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 127/268 (47%), Positives = 187/268 (69%), Gaps = 4/268 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +  + G++    R +  +V     +   AK+++V ANLRLV+SVAKKY+ RG+  LDL
Sbjct: 162 HKLETDEGLAEDLRRDLGLLV----TDGQAAKQQLVSANLRLVVSVAKKYSGRGMTLLDL 217

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEGN+GL++A EKFD+  GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ 
Sbjct: 218 VQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKIT 277

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++ + + REPT EE+A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIE
Sbjct: 278 RLQRQLVSTLGREPTDEELAFELDMPIEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIE 337

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +A SP D+A    +++    VL +L PRE  V+R+RFG+     HTL EVG +  +TR
Sbjct: 338 DSDATSPADAASYGAMQDEIDNVLGALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTR 397

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ERIRQIE   +R+L+ P+ + +LR FLD
Sbjct: 398 ERIRQIERDTLRELRKPAVAGRLREFLD 425



 Score = 77.2 bits (188), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/126 (25%), Positives = 56/126 (44%), Gaps = 13/126 (10%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +    +  ++I   R+ G ++  EL   L   ++  E +   +A L   GI++V      
Sbjct: 46  ELDVSAVAELIARGRETGELSRAELREALEAADIGVELLPALIARLGAAGIDLV------ 99

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                    +  S  + +      R  +    T D VRMYLRE+G + LL+   E+ ++K
Sbjct: 100 -------EEEEESERAPAGATTPGRTVADHAGTADLVRMYLREIGKVPLLNAAQEVELSK 152

Query: 145 RIEAGR 150
           R+EAG 
Sbjct: 153 RVEAGL 158


>gi|118463509|ref|YP_882780.1| RNA polymerase sigma factor SigB [Mycobacterium avium 104]
 gi|254776043|ref|ZP_05217559.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|118164796|gb|ABK65693.1| sigma factor SigB [Mycobacterium avium 104]
          Length = 319

 Score =  208 bits (528), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 112/241 (46%), Positives = 173/241 (71%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 77  RDGQAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A +  +
Sbjct: 137 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEELAAESGI 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I   L      VLA
Sbjct: 197 PIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLA 256

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL++  R+ +LRS
Sbjct: 257 TLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRNGERADRLRS 316

Query: 679 F 679
           +
Sbjct: 317 Y 317



 Score = 40.6 bits (93), Expect = 0.86,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 27/51 (52%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +N+S         A     D VR+YL  +G   LL+  GE+ +AKRIEAG 
Sbjct: 2   ANASTSRFDGDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGL 52


>gi|22298160|ref|NP_681407.1| RNA polymerase sigma factor RpoD [Thermosynechococcus elongatus
           BP-1]
 gi|22294339|dbj|BAC08169.1| principal RNA polymerase sigma factor [Thermosynechococcus
           elongatus BP-1]
          Length = 418

 Score =  208 bits (528), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 134/267 (50%), Positives = 185/267 (69%), Gaps = 1/267 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + +         E    V   R        AK++MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 152 EELERNPEPWAKELGMTVPAFRHRLFVGRKAKEKMVQSNLRLVVSIAKKYMNRGLSFQDL 211

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 212 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 271

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 272 KTTKLLSQEMGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 331

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   +  LRE    VL +L+PRE  VL++R+G+      TLEE+G+ F VTR
Sbjct: 332 -SDGETPEDQVSKHLLREDLETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTR 390

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 391 ERIRQIEAKALRKLRHPNRNSVLKEYI 417



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/99 (30%), Positives = 54/99 (54%), Gaps = 2/99 (2%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +ED VA+LS+ G++ V+ ++ E E+  E S DL    +      ++ +      T+D +R
Sbjct: 47  LEDEVALLSDYGLDAVEIEEEESEDFEEVSDDLDGKPTKGRASRRRTQVKKKHYTEDSIR 106

Query: 123 MYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           +YL+E+G I LL  + EI +A++I        +   LC+
Sbjct: 107 LYLQEIGRIRLLRADEEIELARKIADLLEMERVRDRLCQ 145


>gi|254821657|ref|ZP_05226658.1| RNA polymerase sigma factor SigB [Mycobacterium intracellulare ATCC
           13950]
          Length = 319

 Score =  208 bits (528), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 113/241 (46%), Positives = 173/241 (71%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 77  RDGKAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFST 136

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A +  +
Sbjct: 137 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEELAAESGI 196

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PV+ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I   L      VLA
Sbjct: 197 PVDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLA 256

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL++  R+ +LRS
Sbjct: 257 TLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRNGERADRLRS 316

Query: 679 F 679
           +
Sbjct: 317 Y 317



 Score = 40.6 bits (93), Expect = 0.85,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 27/51 (52%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +N+S         A     D VR+YL  +G   LL+  GE+ +AKRIEAG 
Sbjct: 2   ANASTSRFDGDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGL 52


>gi|160941150|ref|ZP_02088487.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435711|gb|EDP13478.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
          Length = 406

 Score =  208 bits (528), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 137/272 (50%), Positives = 189/272 (69%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  +K I     ++  E   +    R+       A +++VEANLRLV+S+AK+YT RG+
Sbjct: 137 IREYLKEIGSIALLTPEEESDLA---RRKSEGDVEAGRKLVEANLRLVVSIAKRYTGRGM 193

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GLMKA EKFD+  GY+ STYA WWVKQ+ITRS+ADQS TIR+PVHM + 
Sbjct: 194 SFLDLVQEGNLGLMKAVEKFDYAKGYRLSTYATWWVKQSITRSLADQSRTIRLPVHMVEA 253

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R  R +S K+ REP+ EE+A+++ M  + V ++++ + + +SLETP+GDE+ S+L
Sbjct: 254 VNKIRRAQRSLSVKLGREPSMEEVAEEVNMSGKRVAELIQASGDTVSLETPVGDEEGSNL 313

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ D    S  D A    LRE    +L  L PRE  V+ +RFG+      TLEEVGK+
Sbjct: 314 GDFVADDANASTEDKAESFLLREEIDSMLQGLNPREREVIILRFGLETGHPLTLEEVGKR 373

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F VTRERIRQIE  A+RKL++PS+SKK+R FL
Sbjct: 374 FNVTRERIRQIETAALRKLRNPSKSKKIRDFL 405



 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 66/180 (36%), Gaps = 37/180 (20%)

Query: 29  DSWKKMI-KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV---------- 77
              ++++ + A Q G + + ++       +++ E+MED    L   G+++          
Sbjct: 8   KRLEQLVGEAAAQEGRLEMTQVLDHFRDVQMTPEEMEDVYLKLERKGVHIQAPEEPEEEL 67

Query: 78  -------VDGDDLEDEEGSEDSLDLASSASNSSVFLQ-------------------KRKD 111
                   D  +L+    +++         +    L                    + + 
Sbjct: 68  PEGDFLLDDDAELDQPSLAKEEFRWGRDRLDPDEMLDGGSMVSGGDEEEEEYDGYGQERL 127

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
               ST DP+R YL+E+GSI LL+ E E  +A+R   G       L E+ L     I  R
Sbjct: 128 LEGVSTADPIREYLKEIGSIALLTPEEESDLARRKSEGDVEAGRKLVEANLRLVVSIAKR 187


>gi|289642419|ref|ZP_06474565.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507764|gb|EFD28717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 425

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 126/253 (49%), Positives = 182/253 (71%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   ++    +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKF
Sbjct: 173 ELRRDLQTLVRDGHAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKF 232

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT
Sbjct: 233 DYAKGYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPT 292

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    
Sbjct: 293 DEELALELDMPIEQVVELRRYAQDTVSLETAVGDDGDSVLGDFIEDADATSPADAASYGA 352

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++    VL SLTPRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+
Sbjct: 353 MQDEIEGVLNSLTPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELR 412

Query: 669 HPSRSKKLRSFLD 681
            P+ + +LR FLD
Sbjct: 413 KPAVAGRLREFLD 425



 Score = 67.2 bits (162), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 32/132 (24%), Positives = 51/132 (38%), Gaps = 18/132 (13%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           DD+   D +     +++   R+ G ++  EL   L   ++  E +   VA L        
Sbjct: 45  DDTDELDVTQ--VAELVARGRESGELSRAELREALETADLGLELLPVLVARL-------- 94

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                         +               R  S    T D VRMYLRE+G + LL+   
Sbjct: 95  --------TTLGVEVLEEEEEEAPGGAAATRATSEHAGTADLVRMYLREIGKVPLLNAAQ 146

Query: 139 EIAIAKRIEAGR 150
           E+ ++KR+EAG 
Sbjct: 147 EVELSKRVEAGL 158


>gi|37520903|ref|NP_924280.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35211898|dbj|BAC89275.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 350

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 128/343 (37%), Positives = 195/343 (56%), Gaps = 42/343 (12%)

Query: 379 LDPHWVSYAKDFPEGEWKNF-------VACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            D  W        E E +         V    D ++++   ++ I     +  +E   + 
Sbjct: 7   SDDLWSDEVLVEAEAETEVLAPEEFTVVRGSTDDLVRL--YLQEIGRVALLKPAEEIELA 64

Query: 432 SMVRKG--------------------------------ECEASIAKKEMVEANLRLVISV 459
             +                                     E   AK  +V+ANLRLV+SV
Sbjct: 65  RRIATWLSLEEKRSKFQAVAAESWLESANLTPQQWSTIVREGERAKAHLVKANLRLVVSV 124

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY  RGL  LDLIQEG +GL++AAEKFD+  G+KFSTYA WW++Q ITR+IA Q+ TI
Sbjct: 125 AKKYQGRGLHLLDLIQEGTLGLIRAAEKFDYTRGFKFSTYATWWIRQGITRAIAMQARTI 184

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVH+ +K++++ +  R++S ++ R P+ +EIA+ + M  + +R V K  + P+SLETP
Sbjct: 185 RLPVHIVEKVNRIKKATRQLSQQLGRSPSEDEIAQAVEMDADQLRFVRKAIQLPVSLETP 244

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G E+ + LGD I+ K    P    ++  + +    +L +LTPRE  VLR+R+G+     
Sbjct: 245 VGREEDTALGDLIQAK-GNEPEHGVVRDLMNQDLESLLQTLTPRERDVLRLRYGLIDGRS 303

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            TL+EVG+QF +TRERIRQIEA+A+RKL+HP R +++R +L+G
Sbjct: 304 RTLDEVGQQFGLTRERIRQIEARALRKLRHPQRLQRVREYLEG 346



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
               L  + + + V   +       STDD VR+YL+E+G + LL    EI +A+RI
Sbjct: 12  SDEVLVEAEAETEVLAPEEFTVVRGSTDDLVRLYLQEIGRVALLKPAEEIELARRI 67


>gi|240169688|ref|ZP_04748347.1| RNA polymerase sigma factor SigB [Mycobacterium kansasii ATCC
           12478]
          Length = 319

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 117/252 (46%), Positives = 180/252 (71%), Gaps = 4/252 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + ++VR    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 70  RELAAVVR----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 125

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 126 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREA 185

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +PV+ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I  
Sbjct: 186 TDEELAEESGIPVDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAE 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      VLA+L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL
Sbjct: 246 LLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCKL 305

Query: 668 KHPSRSKKLRSF 679
           +H  R+ +LRS+
Sbjct: 306 RHGERADRLRSY 317



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 24/49 (48%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           ++         A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 4   ATTSRADSDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGL 52


>gi|218282286|ref|ZP_03488585.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
 gi|218216721|gb|EEC90259.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
          Length = 409

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 146/290 (50%), Positives = 205/290 (70%), Gaps = 9/290 (3%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           + + +  +A ++    + + +IK+      +S  E + +  ++     +   AK+ ++ +
Sbjct: 127 DPKEEPIIARQIQEGEQAKEDIKN----PDLSEEEKKKLAKII----ADGEEAKQTLISS 178

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+S+AKKY  RG+ FLDLIQEGN GL+KA EKFD+  G+KFSTYA WW++Q+ITR+
Sbjct: 179 NLRLVVSIAKKYVGRGMLFLDLIQEGNCGLIKAVEKFDYTKGFKFSTYATWWIRQSITRA 238

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKIT 570
           IADQ+ TIRIPVHM + I+K+ R  R++   + R+P PEEIA+K+  +  E VR++ KI 
Sbjct: 239 IADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPMPEEIAEKMENISAEKVREIQKIA 298

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +P+SLETPIG+ED SHLGDFIEDK+ +SP D      L++    VL  LT REE+VLR+
Sbjct: 299 LDPVSLETPIGEEDDSHLGDFIEDKDTLSPDDYTNNQLLKDEINAVLQGLTEREEKVLRL 358

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLK+P+R K+LR F+
Sbjct: 359 RFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKNPNRCKRLRDFV 408



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A   S   +   +++    +DPV+MYL+E+G I LL  + E  IA++I+ G       + 
Sbjct: 91  AEEISQLEKTFANASHAKINDPVKMYLKEIGQIPLLDPKEEPIIARQIQEGE-QAKEDIK 149

Query: 159 ESPLTFQALIIWRDELNDGTTLLREII 185
              L+ +        + DG    + +I
Sbjct: 150 NPDLSEEEKKKLAKIIADGEEAKQTLI 176


>gi|72383665|ref|YP_293020.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL2A]
 gi|72003515|gb|AAZ59317.1| sigma-70 factor [Prochlorococcus marinus str. NATL2A]
          Length = 420

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 133/250 (53%), Positives = 183/250 (73%), Gaps = 1/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++  R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD 
Sbjct: 169 LARFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDH 228

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT E
Sbjct: 229 EKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEE 288

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LR
Sbjct: 289 EIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKTLLR 347

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 348 EDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHP 407

Query: 671 SRSKKLRSFL 680
           +R+  L+ ++
Sbjct: 408 NRNGVLKEYI 417



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 53  LPPDEVSSEQMEDTVAM--LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
           LP +  +  +++  +    L      V + D   D++    S+  ++  + +      + 
Sbjct: 40  LPQESSNDLKIDLDLEADKLIAEANKVPEADIDLDDDDDNASVLSSAQEAAAKALASIKI 99

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                 T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 100 GPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 135


>gi|111225055|ref|YP_715849.1| alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
 gi|111152587|emb|CAJ64329.1| Alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
          Length = 373

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 124/242 (51%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTY
Sbjct: 132 DGHAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTY 191

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP
Sbjct: 192 ATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMP 251

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL  
Sbjct: 252 IEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGG 311

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR F
Sbjct: 312 LNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLREF 371

Query: 680 LD 681
           LD
Sbjct: 372 LD 373



 Score = 71.0 bits (172), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 32/121 (26%), Positives = 52/121 (42%), Gaps = 17/121 (14%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           +  ++I   R+ G ++  EL   L   ++  E +   +A LS  G+              
Sbjct: 3   AVAEVIARGREAGEISRSELRDALESADIGLELLPALIAKLSAAGV-------------- 48

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                L    +   V    R  +    T D VRMYLRE+G + LL+   E+ ++KR+EAG
Sbjct: 49  ---ELLEEEETTDDVTAATRSTAEHAGTADLVRMYLREIGKVPLLNAAQEVELSKRVEAG 105

Query: 150 R 150
            
Sbjct: 106 L 106


>gi|312195044|ref|YP_004015105.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226380|gb|ADP79235.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 424

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 124/253 (49%), Positives = 182/253 (71%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   ++    +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKF
Sbjct: 172 ELHRDLKLLVRDGEAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKF 231

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT
Sbjct: 232 DYAKGYKFSTYATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPT 291

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A +L MP+E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    
Sbjct: 292 DEELALELDMPLEQVVELRRYAQDTVSLETTVGDDGDSVLGDFIEDSDATSPADAASYGA 351

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++    VL +L+PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+
Sbjct: 352 MQDEIDHVLGNLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELR 411

Query: 669 HPSRSKKLRSFLD 681
            P+ + +LR FLD
Sbjct: 412 KPAVAGRLREFLD 424



 Score = 79.9 bits (195), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/133 (28%), Positives = 61/133 (45%), Gaps = 16/133 (12%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           ++D    D S  +  ++I   R  G V+  EL   L   +V  E +   VA L   G+ V
Sbjct: 41  AEDIDELDVS--AVAELIARGRDSGEVSRSELREALESADVGVELLPALVARLVAAGVEV 98

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+ +D               +  +++     R  +    T D VRMYLRE+G + LL+  
Sbjct: 99  VEEEDG--------------AERSAAPSETGRVTAEHAGTADLVRMYLREIGRVPLLNAA 144

Query: 138 GEIAIAKRIEAGR 150
            E+ ++KR+EAG 
Sbjct: 145 QEVELSKRVEAGL 157


>gi|124025264|ref|YP_001014380.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL1A]
 gi|123960332|gb|ABM75115.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. NATL1A]
          Length = 420

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 133/250 (53%), Positives = 183/250 (73%), Gaps = 1/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++  R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD 
Sbjct: 169 LTRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDH 228

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT E
Sbjct: 229 EKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEE 288

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LR
Sbjct: 289 EIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKTLLR 347

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 348 EDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHP 407

Query: 671 SRSKKLRSFL 680
           +R+  L+ ++
Sbjct: 408 NRNGVLKEYI 417



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 53  LPPDEVSSEQMEDTVAM--LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
           LP +  +  +++  +    L      V + D   D++    S+  ++  + +      + 
Sbjct: 40  LPQESSNDLKIDLDLEADKLIAEANKVPEADIDLDDDDDNASVLSSAQEAAAKALASIKI 99

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                 T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 100 GPKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 135


>gi|269925486|ref|YP_003322109.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789146|gb|ACZ41287.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 338

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 125/296 (42%), Positives = 193/296 (65%), Gaps = 23/296 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGEC-----------------------EASIAK 445
           +R  ++ I +   ++  +   +   + +G+                        E   A+
Sbjct: 43  VRMYLREIGLVPLLTAEQEVELAKKMERGKKAQSVLDSGKYEPEQRDKLLAEVDEGERAR 102

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + ++EANLRLV+SVAKK+ NRGL  LDLI+EGNIGLM+A +KFD+  G+KFSTYA WW++
Sbjct: 103 RHLIEANLRLVVSVAKKHMNRGLSLLDLIEEGNIGLMRATDKFDYRKGFKFSTYATWWIR 162

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA+TR+IADQ+ TIR+PVH+ + ++ + + +R++S ++ REPT EE+A+ + M  E VR 
Sbjct: 163 QAVTRAIADQARTIRLPVHITETMNHLYKASRKLSQELGREPTCEELAEYMGMNPEKVRL 222

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++ ++ P+SLE P+G +  S LG FI D    +P+D AI   L+   ++VL SLT +E 
Sbjct: 223 IMRASRHPLSLEGPVGTDGDSSLGQFIPDSTTETPVDLAIGEVLKRELSKVLNSLTEKER 282

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +V+ +R+G+  ++ HTLEEVG +  VTRER+RQIEAKA+ KL+ P +   LR FLD
Sbjct: 283 KVMVLRYGLEGSSPHTLEEVGHRLGVTRERVRQIEAKALEKLRKPGKLNHLRDFLD 338



 Score = 61.8 bits (148), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 5/91 (5%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM--MMA 155
                     K+++      DD VRMYLRE+G + LL+ E E+ +AK++E G+    ++ 
Sbjct: 20  EDLPEEAEYDKQEEDLSEDLDDSVRMYLREIGLVPLLTAEQEVELAKKMERGKKAQSVLD 79

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIID 186
           S    P     L+    E+++G    R +I+
Sbjct: 80  SGKYEPEQRDKLLA---EVDEGERARRHLIE 107


>gi|257056437|ref|YP_003134269.1| RNA polymerase sigma factor SigB [Saccharomonospora viridis DSM
           43017]
 gi|256586309|gb|ACU97442.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 342

 Score =  207 bits (527), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 119/282 (42%), Positives = 187/282 (66%), Gaps = 3/282 (1%)

Query: 399 VACEVDSILKIRNEI-KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
              EVD   +I   +     ++T   +SE R   + + +   +   AK  +++ANLRLV+
Sbjct: 61  AEEEVDLAKRIEAGVFAQHVLDTSDDLSEERK--AELSEVVRDGEEAKNHLLQANLRLVV 118

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQ  
Sbjct: 119 SLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRGMADQGR 178

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVH+ ++++K+ R  R +  ++ RE T EE+A +  +  + V  +L   ++P+SL+
Sbjct: 179 TIRLPVHLVEQVNKLARIKRDLHQRLGREATHEELAAESGIAEKKVADLLDHARDPVSLD 238

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+G ++ + LGDFIED  A +  +S I   L++   RVLA+L  REE V+R+R+G+   
Sbjct: 239 MPVGADEDAPLGDFIEDSEAANAENSVISTLLQDDLRRVLATLDDREEHVIRLRYGLDDG 298

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              TL+++GK F ++RER+RQIE + + KL+H  R+ KLR++
Sbjct: 299 QPRTLDQIGKHFSLSRERVRQIEREVMAKLRHGERADKLRAY 340



 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 27/92 (29%), Positives = 38/92 (41%), Gaps = 18/92 (19%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           +S + +E     +    I V   DD+      E  LD    A+                 
Sbjct: 1   MSVQTLEREARGIRERDIPVPTDDDVMPAPAEEADLDAQGPAA----------------- 43

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D VR+YL  +G   LL+ E E+ +AKRIEAG
Sbjct: 44  -DLVRVYLNGIGKTALLTAEEEVDLAKRIEAG 74


>gi|94984583|ref|YP_603947.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94554864|gb|ABF44778.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 532

 Score =  207 bits (527), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 144/291 (49%), Positives = 199/291 (68%), Gaps = 9/291 (3%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E +  +A  ++   + R  ++       +     R ++  +     + + A++ ++EANL
Sbjct: 248 EEEIALARRIEEGEEARKMLEEAGD--ELDDRARRRLMRQM----EDGAAARQGLIEANL 301

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW++QAI R+IA
Sbjct: 302 RLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIRQAINRAIA 361

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITK 571
           DQ+ TIRIPVHM + I+K+ RTAR++  ++ REPT EEIA+ +        V +V K+++
Sbjct: 362 DQARTIRIPVHMVETINKLTRTARQLQQELSREPTYEEIAEAMGPGWDAAKVEEVQKVSQ 421

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EP+SLETPIGDE  S  GDFI D+N  SP+D+A +  L E   + L+ LT RE  VL+ R
Sbjct: 422 EPVSLETPIGDEKDSFYGDFIPDENLDSPVDNAAKTLLSEELEKALSKLTEREALVLKFR 481

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
            G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 482 KGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLKYHESRTRKLRDFLD 532



 Score = 65.6 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/101 (32%), Positives = 54/101 (53%), Gaps = 2/101 (1%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR--KDSA 113
           D  S+E  ED    L+   I V D D+ + ++  E+  + A + + ++   ++R   D  
Sbjct: 165 DPESAEAFEDMQLYLAGQNIEVQDLDEEDQDDDLEEGEEGAVTGAAANDDEEERYFDDMP 224

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
              ++DPVR YL E+G + LL+ E EIA+A+RIE G     
Sbjct: 225 RAVSNDPVRQYLHEIGRVPLLTLEEEIALARRIEEGEEARK 265


>gi|330466485|ref|YP_004404228.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
 gi|328809456|gb|AEB43628.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
          Length = 535

 Score =  207 bits (527), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 131/254 (51%), Positives = 183/254 (72%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EK
Sbjct: 282 RDMQRDLLWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 341

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REP
Sbjct: 342 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREP 401

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   +
Sbjct: 402 TPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFS 461

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   +VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL
Sbjct: 462 LLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKL 521

Query: 668 KHPSRSKKLRSFLD 681
           +HPSRS+ LR +LD
Sbjct: 522 RHPSRSQVLRDYLD 535



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/101 (25%), Positives = 43/101 (42%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
             +V  E++   +  +       +      D   S    D       S    Q R+D+  
Sbjct: 169 EGDVDPEELAAEIEDVVVEEPAELAQAAEADAASSASDNDFEWDDEESEALKQARRDAEL 228

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
            ++ D VR YL+++G + LL+ E E+ +AKRIEAG      
Sbjct: 229 TASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAER 269


>gi|318041167|ref|ZP_07973123.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0101]
          Length = 464

 Score =  207 bits (527), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 217 KFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 276

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 277 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEI 336

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 337 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 395

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 396 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 455

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 456 NGVLKEYI 463



 Score = 41.7 bits (96), Expect = 0.38,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 31/73 (42%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            ++V     L            A   + +      +       T+D +R+YL+E+G I L
Sbjct: 109 NLDVAADQLLAAAANKAADAKPAEKDAKAKALASIKVGPKGVYTEDSIRVYLQEIGRIRL 168

Query: 134 LSREGEIAIAKRI 146
           L  + EI +A++I
Sbjct: 169 LRPDEEIELARKI 181


>gi|159903037|ref|YP_001550381.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9211]
 gi|159888213|gb|ABX08427.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9211]
          Length = 425

 Score =  207 bits (527), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 132/248 (53%), Positives = 182/248 (73%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 178 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 237

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEI
Sbjct: 238 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEI 297

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  ++ +P     +  LRE 
Sbjct: 298 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDSENPELDVAKTLLRED 356

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 357 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 416

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 417 NGVLKEYI 424



 Score = 44.8 bits (104), Expect = 0.045,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
           +  +A  +N  I      + E         D     ++       +       T+D +R+
Sbjct: 64  DQLLAEANNNEI----NPETEITLNMNSLDDSNDQEASDKTLASIKIGPKGVYTEDSIRV 119

Query: 124 YLREMGSIELLSREGEIAIAKRI 146
           YL+E+G I LL  + EI +A++I
Sbjct: 120 YLQEIGRIRLLRPDEEIELARKI 142


>gi|113953359|ref|YP_732042.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
 gi|113880710|gb|ABI45668.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
          Length = 376

 Score =  207 bits (526), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 113/350 (32%), Positives = 198/350 (56%), Gaps = 8/350 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +   +  R++     L R  + +              EL     ++   +P  
Sbjct: 31  RVDLLTAEDEVVLSRLVQQYERLKREERQFAEDHPAIERLLCLEELQLREANHLSHWPTR 90

Query: 394 -EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            EW       +  + K     +       +  ++ R +   +R+       A+  M++AN
Sbjct: 91  QEWARAAEMPLQELNKGLT--QGYETWANLISTDSRELQLRLRR----GRKARDRMIQAN 144

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV++VAKKY +RG++ LDL+QEG +GL +A EKFD   G++FSTY+ WW++Q ITR+I
Sbjct: 145 LRLVVAVAKKYQHRGMELLDLVQEGTLGLERAVEKFDSTRGFRFSTYSYWWIRQGITRAI 204

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L++  + VR+ L     
Sbjct: 205 ATQSRTIRLPVHITEKLNRIKRVQQEIASNEGRTASMTDLARELSVSEDTVRQTLARVPR 264

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SLET +G +  + LG+ +ED++A +P  +  + +L +    +L  LTPRE  V+R RF
Sbjct: 265 SVSLETKVGRDQDTQLGELLEDEHA-TPEQTLTRDSLHDDLEHLLNELTPREATVIRCRF 323

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +T  TL ++G+   ++RER+RQIE +A+ KL+ P R  K+R ++  
Sbjct: 324 GLEDDTPRTLAQIGEDMNLSRERVRQIETRALLKLRQPQRRNKVRDYIQS 373



 Score = 37.5 bits (85), Expect = 7.5,   Method: Composition-based stats.
 Identities = 9/34 (26%), Positives = 24/34 (70%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           +D +R+YL+++G ++LL+ E E+ +++ ++    
Sbjct: 19  NDLLRLYLQDIGRVDLLTAEDEVVLSRLVQQYER 52


>gi|260435157|ref|ZP_05789127.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260413031|gb|EEX06327.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 458

 Score =  207 bits (526), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 211 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 270

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 271 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 330

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 331 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 389

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 390 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 449

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 450 NGVLKEYI 457



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 141 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 175


>gi|239931595|ref|ZP_04688548.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291439967|ref|ZP_06579357.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
 gi|291342862|gb|EFE69818.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
          Length = 335

 Score =  207 bits (526), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 124/324 (38%), Positives = 191/324 (58%), Gaps = 24/324 (7%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG--- 437
           P  +  A+D         ++ ++ +  ++++ ++ IS    ++  +   +   +  G   
Sbjct: 9   PEDLLLAEDGETDAPAPRLSSDLGTADQVKDYLRLISRVRLLTAEQEVELAKRIEAGLYA 68

Query: 438 ---------------------ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                                  +   AK  + EANLRLV+SVAK+YT RGLQF+DLIQE
Sbjct: 69  ERLLAEEPVLEPRYRRELGLLAEDGRRAKNHLTEANLRLVVSVAKRYTGRGLQFMDLIQE 128

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN GL++A EKFD+  G+KFSTYA WW+KQ ITR++ADQS TIRIPVH  + I++V R  
Sbjct: 129 GNAGLIRAVEKFDYTKGFKFSTYATWWIKQGITRAMADQSRTIRIPVHAVEVINRVARVR 188

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R +      EPTPE++A++ ++ VE + ++    +EP+SL+ P+ +E     GD I D +
Sbjct: 189 RELIRATGTEPTPEDVAERASISVEKLAELDAYAREPVSLDLPLSEEGGGEFGDLIVDSD 248

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           + SP +     +L+     VLA L+PRE  ++ +R+G+      TLEE+G+ + VTRERI
Sbjct: 249 SPSPWEVVAFGHLQRAVRSVLADLSPREAGIISLRYGLFGERPRTLEEIGQVYGVTRERI 308

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQIE+K + KL+HP+RS  LR +L
Sbjct: 309 RQIESKTMSKLRHPARSHALRDYL 332



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A +        + S+D  T D V+ YLR +  + LL+ E E+ +AKRIEAG       L 
Sbjct: 15  AEDGETDAPAPRLSSDLGTADQVKDYLRLISRVRLLTAEQEVELAKRIEAGLY-AERLLA 73

Query: 159 ESPLT 163
           E P+ 
Sbjct: 74  EEPVL 78


>gi|296393377|ref|YP_003658261.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180524|gb|ADG97430.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 377

 Score =  207 bits (526), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 108/258 (41%), Positives = 178/258 (68%), Gaps = 4/258 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++    R + ++ R    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL
Sbjct: 122 LTPQRRRELKTVAR----DGQAARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQEGNLGL 177

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  
Sbjct: 178 IRAMEKFDYAKGFKFSTYATWWIRQAITRGVADQSRTIRLPVHLVEQVNKLSRIKRELHQ 237

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ RE T EE++++  +P   +  +L  +++P+SL+ P+G ++ + LGDFIED    S  
Sbjct: 238 QLGREATSEELSRETGIPEHRIADLLDHSRDPVSLDMPVGADEEAPLGDFIEDSEGASAE 297

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ I   L      VLA+L   E++V+R+R+G+      TL+++GK F ++RER+RQIE 
Sbjct: 298 NAVIAGFLHRDVRTVLATLNEVEQQVIRLRYGLDDGQPRTLDQIGKVFSLSRERVRQIER 357

Query: 662 KAIRKLKHPSRSKKLRSF 679
           + + KL++  R+++LRS+
Sbjct: 358 EVMVKLRNGDRAERLRSY 375



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 74  GINVVD---GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           GI  VD    D+  + E +    +  +  +  S    +          D VR+YL  +G 
Sbjct: 31  GIKPVDSAPEDNAAELEAAVSDEEPETQDAAPSGRYAEGDLDTQSPAADLVRVYLNGIGR 90

Query: 131 IELLSREGEIAIAKRIEAGR 150
             LL+   E+ +AK IEAG 
Sbjct: 91  TALLTAADEVELAKSIEAGL 110


>gi|323342093|ref|ZP_08082326.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464518|gb|EFY09711.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 459

 Score =  207 bits (526), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 147/245 (60%), Positives = 188/245 (76%), Gaps = 1/245 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             +   A++ ++ ANLRLV+S+AKKY  RG+ FLDLIQEGN+GL+KA EKFD+  G+KFS
Sbjct: 213 YYDGLEARRILISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFS 272

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL- 556
           TYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ R  R +   + REPT EEIA ++ 
Sbjct: 273 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRSLVQTLGREPTAEEIAAEME 332

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  E VR++ KI  +P+SLETPIG+ED SHLGDFIEDK+A+SP + A    L+E    V
Sbjct: 333 NITPEKVREIQKIALDPVSLETPIGEEDDSHLGDFIEDKDALSPDEYANNQLLKEEIKMV 392

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIEAKA+RKLKHP+RSK+L
Sbjct: 393 LEGLTEREEKVLRLRFGLEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRL 452

Query: 677 RSFLD 681
           R F+D
Sbjct: 453 RDFVD 457



 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/148 (17%), Positives = 61/148 (41%), Gaps = 19/148 (12%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV------ 77
               ++  +  +K   ++  +  +++   +    ++ +  E+     +  GI +      
Sbjct: 6   LKTLEEVKESFLKQYEKKRVLLNDDVEKAIDHLNLNDDDSEELFEWFTEKGIILSDDEDD 65

Query: 78  -------------VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
                        VD D + DE   ++  D + +  + S +  +   +     +DPV+MY
Sbjct: 66  IDEEVMLEAGEPDVDDDFISDEAEEDEIFDDSLNKVDLSSYENELTSANMVRINDPVKMY 125

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAM 152
           L+E+G + LL  + E  IA+R++ G   
Sbjct: 126 LKEIGRVNLLDAKDEPEIARRLQEGEQA 153


>gi|33864481|ref|NP_896041.1| putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641261|emb|CAE22391.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
          Length = 376

 Score =  207 bits (526), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 123/351 (35%), Positives = 196/351 (55%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R++LL  +      R++     LL+  +     ++   E  +  EL     +++  +P  
Sbjct: 31  RVELLTNEEEVTLARLVQRREALLKQERKLASNQEAIKELQRLEELQQREANHSCHWPTK 90

Query: 394 -EWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  KI    K+    TG+   E +  +   R+       AK +M++A
Sbjct: 91  QEWAMAAGLTLAELQEKIETGYKTWGALTGLDPLELKRSLRAGRR-------AKDQMIQA 143

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 144 NLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRA 203

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+P+H+ +K++++ R  + +++   R  +  ++AK L +  E VR  L    
Sbjct: 204 IATQSRTIRLPMHITEKLNRIKRVQQEIASSQGRLASIADLAKALGLSEETVRLTLMRVP 263

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             ISLET IG E  + LGD +ED NA +P +   +  L      +L  L+ RE  V+R R
Sbjct: 264 RSISLETRIGQEQDTQLGDLLEDSNA-TPEEKLTRNQLHNDLEILLDELSNREATVIRRR 322

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G+   ++RER+RQIE  A+ KL+ P R  K+R ++  
Sbjct: 323 FGLEDDTPQTLTQIGEAMHLSRERVRQIETHALLKLRQPQRRCKVRDYIQN 373



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 87/252 (34%), Gaps = 27/252 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           + DPVR+YL+++G +ELL+ E E+ +A+ ++                 +AL+    +L  
Sbjct: 18  STDPVRLYLQDIGRVELLTNEEEVTLARLVQRR---------------EALLKQERKLAS 62

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               ++E+  LE     E+       T+         +  E +       +         
Sbjct: 63  NQEAIKELQRLEELQQREANHSCHWPTKQEWAMAAGLTLAELQEKIETGYKTWGALTGLD 122

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             + +  +           R  D+    +   + A+  + + + +  LD + E    L  
Sbjct: 123 PLELKRSL-------RAGRRAKDQMIQANLRLVVAVAKKYQQRGIELLDLVQEGTLGLER 175

Query: 297 LQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
             +     +    S+       + +   +     ++ L    I   + ++  + + I  +
Sbjct: 176 AVEKFDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRL-PMHITEKLNRIKRVQQEIASS 234

Query: 353 EGELLRLAQSYG 364
           +G L  +A    
Sbjct: 235 QGRLASIADLAK 246


>gi|162605994|ref|XP_001713512.1| RNA-polymerase sigma factor [Guillardia theta]
 gi|13794432|gb|AAK39807.1|AF165818_15 RNA-polymerase sigma factor [Guillardia theta]
          Length = 460

 Score =  207 bits (526), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 131/275 (47%), Positives = 185/275 (67%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +R++++     +  + +     V   R     A  AK+ MV ANLRLV+S+AK+Y NR
Sbjct: 151 ISLRDKLRREPTNSEWTAACKVSDVRKFRSILHNARRAKERMVAANLRLVVSIAKRYVNR 210

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLIQEG++GL++AAEKFD   G+KFSTYA WWVKQA+TR+IAD S TIR+PVH+ 
Sbjct: 211 GMSLQDLIQEGSLGLIRAAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVHLY 270

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D I  + +T R ++ +I R PT EEIAK++ M VE +R VL+  +  +SLE P+ ++D +
Sbjct: 271 DTISAIRKTTRNLNIEIGRSPTEEEIAKRMDMSVEKLRNVLQSAQPTLSLERPLKNDDDT 330

Query: 587 H-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L DFIE  +  SP +   ++ LR+    V+ SL+PRE  V+RMR+G+      TLEE+
Sbjct: 331 SQLSDFIE-ADQESPEEHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEI 389

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+ F VTRER+RQIEAKAIRKL+ P RS  LR ++
Sbjct: 390 GQIFSVTRERVRQIEAKAIRKLRQPYRSSILRDYV 424



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
            +      +         +  DD VR YL+ +G + LL  + EI +A+ I
Sbjct: 91  ENTEEDDFYQNNGLSKNIQKADDSVRWYLQLIGRVRLLRPDEEIQLAREI 140


>gi|41408924|ref|NP_961760.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397283|gb|AAS05143.1| SigB [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 332

 Score =  207 bits (526), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 112/241 (46%), Positives = 173/241 (71%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 90  RDGQAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFST 149

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A +  +
Sbjct: 150 YATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEELAAESGI 209

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P++ +  +L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I   L      VLA
Sbjct: 210 PIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLA 269

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE +V+R+RFG+      TL+++GK F ++RER+RQIE   + KL++  R+ +LRS
Sbjct: 270 TLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRNGERADRLRS 329

Query: 679 F 679
           +
Sbjct: 330 Y 330



 Score = 41.0 bits (94), Expect = 0.69,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 29/59 (49%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             +   + +N+S         A     D VR+YL  +G   LL+  GE+ +AKRIEAG 
Sbjct: 7   QAEREVAMANASTSRFDGDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGL 65


>gi|25991936|gb|AAN76995.1|AF481769_1 primary sigma 70 transcriptional factor [Frankia sp. ACN14a]
          Length = 385

 Score =  206 bits (525), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 124/242 (51%), Positives = 177/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTY
Sbjct: 144 DGHAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTY 203

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP
Sbjct: 204 ATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMP 263

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL  
Sbjct: 264 IEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGG 323

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR F
Sbjct: 324 LNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLREF 383

Query: 680 LD 681
           LD
Sbjct: 384 LD 385



 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 36/132 (27%), Positives = 56/132 (42%), Gaps = 19/132 (14%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           DD    D S  +  ++I   R+ G ++  EL   L   ++  E +   +A LS  G+   
Sbjct: 6   DDGDELDVS--AVAEVIARGREAGEISRSELRDALESADIGLELLPALIAKLSAAGV--- 60

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                           L    +   V    R  +    T D VRMYLRE+G + LL+   
Sbjct: 61  --------------ELLEEEETTDDVTAATRSTAEHAGTADLVRMYLREIGKVPLLNAAQ 106

Query: 139 EIAIAKRIEAGR 150
           E+ ++KR+EAG 
Sbjct: 107 EVELSKRVEAGL 118


>gi|313892356|ref|ZP_07825948.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|313119215|gb|EFR42415.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
          Length = 393

 Score =  206 bits (525), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 152/363 (41%), Positives = 215/363 (59%), Gaps = 11/363 (3%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
               +      SLN  ++D L + L+D +  ++ ++              D  L   +  
Sbjct: 27  YNYFIDFAKEKSLNVKQLDQLSQLLHDHNIELVLDDENPEDEDIILDEDIDENL--IEDS 84

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           + D  W    KD+ + E  ++   + +    +R  ++       +S  E   +   + KG
Sbjct: 85  DDDKDWEKQEKDWTKVENNDYAVTQGNVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKG 144

Query: 438 EC---------EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +           A  AKKEM  ANLRLV+S+AKKY  RG+ FLDLIQEGNIGL+KA +KF
Sbjct: 145 KMLDATEEDKLRAEDAKKEMANANLRLVVSIAKKYPGRGMPFLDLIQEGNIGLLKAVDKF 204

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITRSIADQ+ TIR+PVHM + I+K+ R  R+   +  RE +
Sbjct: 205 DYKKGYKFSTYATWWIRQAITRSIADQARTIRVPVHMVETINKMNRIGRKFLQEFGREAS 264

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+AK++ + VE +R+  K  ++PISLETPIG+++ SHLGDFIED+   SP + A    
Sbjct: 265 NEELAKEMGISVEKIREAKKAAQDPISLETPIGEKEDSHLGDFIEDQKTSSPEEEAAATM 324

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE   ++L  LT RE+ VL +RFG+   T  TLEEVGK F VTRERIRQIE KA++KL+
Sbjct: 325 RREQIYKLLNELTEREKGVLALRFGMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKLR 384

Query: 669 HPS 671
             +
Sbjct: 385 KLA 387



 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/135 (25%), Positives = 59/135 (43%), Gaps = 14/135 (10%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN-VVDGDDLEDEEGS 89
            K++     + G ++      F     ++ +Q++    +L +  I  V+D ++ EDE+  
Sbjct: 12  IKELKAKETEEGVLSYNYFIDFAKEKSLNVKQLDQLSQLLHDHNIELVLDDENPEDEDII 71

Query: 90  EDSLDLASSASNSSVFLQKRKDSAD-------------RSTDDPVRMYLREMGSIELLSR 136
            D     +   +S       K   D              +  DPVR+YLRE G+  LLS 
Sbjct: 72  LDEDIDENLIEDSDDDKDWEKQEKDWTKVENNDYAVTQGNVSDPVRLYLRECGATPLLSA 131

Query: 137 EGEIAIAKRIEAGRA 151
           E E+ +AK+IE G+ 
Sbjct: 132 EEEMTLAKQIEKGKM 146


>gi|254424926|ref|ZP_05038644.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196192415|gb|EDX87379.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 404

 Score =  206 bits (525), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 133/246 (54%), Positives = 184/246 (74%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+   +   AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GY
Sbjct: 159 RRRLYQGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 218

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA 
Sbjct: 219 KFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQELGRKPTEEEIAT 278

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE   
Sbjct: 279 RMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDEVSKSLLREDLE 337

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL++L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+ 
Sbjct: 338 SVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS 397

Query: 675 KLRSFL 680
            L+ ++
Sbjct: 398 VLKEYI 403



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 32/67 (47%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +    EEG+         A+      +  +      T+D +R+YL+E+G I LL  E E
Sbjct: 55  DETGVAEEGTATKAKATRGAAKGKARRRTAQTKKKHYTEDSIRLYLQEIGRIRLLRAEEE 114

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 115 IELARKI 121


>gi|108805110|ref|YP_645047.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766353|gb|ABG05235.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 366

 Score =  206 bits (525), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 134/296 (45%), Positives = 199/296 (67%), Gaps = 3/296 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A         + +A  V +   IR  +  I     ++ ++   +   + +       +
Sbjct: 73  ERAAGREGDNPASQLAHAVATGDSIRMYLAEIGRVPLLTHADEIRLAKAISR---GCKRS 129

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K ++VEANLRLV+S+AKKY NRG+ FLDLIQEGNIGL++AAEKFD+  G+KFSTYA WW+
Sbjct: 130 KDKLVEANLRLVVSIAKKYRNRGVSFLDLIQEGNIGLIRAAEKFDYRKGFKFSTYATWWI 189

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IAD+  TIRIPVHM +K++K  RT RRM+  + REPT EE+A++L +PVE V 
Sbjct: 190 RQAITRAIADKGRTIRIPVHMVEKVNKYHRTQRRMTQALGREPTDEEVAEELGVPVEEVL 249

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++ +I++  ISLETP+GD+++S LGDF+ED +AV+P D+  ++ L+      L  L  RE
Sbjct: 250 RLQEISQRSISLETPVGDDESSSLGDFLEDASAVTPTDAVSESLLKLHLREALDELPERE 309

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +++ MRFG+  +   TLEEVG++F +TRER+RQI+ K +  L+   R++ LR +L
Sbjct: 310 RQIIEMRFGMKDDRPRTLEEVGREFDITRERVRQIQMKTLNLLREQRRTQNLREYL 365



 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 36/152 (23%), Positives = 66/152 (43%), Gaps = 7/152 (4%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           +++   R +G+++ E++   +   ++S ++ E+  A L    I +VD +     E + + 
Sbjct: 15  ELLSKGRSQGFLSAEDVADLVREGDLSPDEAEELYATLEEEDITLVDEELEGAAEVTPER 74

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                  + +S            +T D +RMYL E+G + LL+   EI +AK I  G   
Sbjct: 75  AAGREGDNPASQLAHAV------ATGDSIRMYLAEIGRVPLLTHADEIRLAKAISRGCKR 128

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               L E+ L     I  +   N G + L  I
Sbjct: 129 SKDKLVEANLRLVVSIAKKYR-NRGVSFLDLI 159


>gi|295101750|emb|CBK99295.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 359

 Score =  206 bits (525), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 139/241 (57%), Positives = 184/241 (76%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A++ + EANLRLV+SVAK+Y  RGL FLDLIQEGN+GLMKAAEKF+   G+KFSTYA
Sbjct: 118 DEDARRRLSEANLRLVVSVAKRYAGRGLPFLDLIQEGNLGLMKAAEKFEPDRGFKFSTYA 177

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q+ITR+IADQ  TIRIPVH+ + I++V +TA  +  +  REPT EEIA +L M  
Sbjct: 178 TWWIRQSITRAIADQGRTIRIPVHLVESINRVKKTAGELLRRTGREPTAEEIAAQLDMEP 237

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             VR+++++ ++PISLETP+G+E+ +HL DFI+D  A  P D A +  LR     VL SL
Sbjct: 238 ARVRELIQLAQDPISLETPVGEEEDAHLEDFIQDDEAGVPADEAGRQLLRRELMNVLKSL 297

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TPREERV+ +RFG+      TLEE+G++F VTRER+RQIEAKA+RKL+HPSR+K+LR +L
Sbjct: 298 TPREERVIALRFGLEDGRARTLEELGREFNVTRERVRQIEAKALRKLRHPSRAKRLRDYL 357

Query: 681 D 681
           D
Sbjct: 358 D 358



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 62/350 (17%), Positives = 126/350 (36%), Gaps = 27/350 (7%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
              +++  K +   AR R  +T E+++  +   +     +++  A L   G+ V      
Sbjct: 4   MSQTEEMAKMLAGRAR-RHILTPEQVSRAMEEQDFDPAGLDELYAALETRGVQV------ 56

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +E+  +L          L+    +   + DDPV+ YL+E+G + LLS E E A+A
Sbjct: 57  -----AEEETELPLLDEEQIGKLEHELSAEGVALDDPVKTYLKEIGRVPLLSAEEEAALA 111

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID-----LEACIGPESKGG 198
           +  +AG       L E+ L     +  R     G   L  I +     ++A    E   G
Sbjct: 112 RAAQAGDEDARRRLSEANLRLVVSVAKRYA-GRGLPFLDLIQEGNLGLMKAAEKFEPDRG 170

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           F   T    + ++  +    ++         +  +    K    ++          E   
Sbjct: 171 FKFSTYATWWIRQSITRAIADQGRTIRIPVHLVESINRVKKTAGELLRRTGREPTAEEIA 230

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
            + + + A     ++    P  +       E       +QD+      DE      ++L+
Sbjct: 231 AQLDMEPARVRELIQLAQDPISLETPVGEEEDAHLEDFIQDDEAGVPADEAGR---QLLR 287

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
            +L+ ++ SL+  + R+  L   L D           L  L + + + R+
Sbjct: 288 RELMNVLKSLTPREERVIALRFGLED------GRARTLEELGREFNVTRE 331


>gi|37522141|ref|NP_925518.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35213141|dbj|BAC90513.1| principal RNA polymerase sigma factor [Gloeobacter violaceus PCC
           7421]
          Length = 400

 Score =  206 bits (524), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 139/277 (50%), Positives = 196/277 (70%), Gaps = 8/277 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D + +   E++  +   GI+  +FR  ++  R+       AK +MV++NLRLV+S+AKKY
Sbjct: 131 DQVTESEQELRRWAEAAGIAYEQFRDRIAYGRR-------AKDKMVQSNLRLVVSIAKKY 183

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 184 MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 243

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 244 HLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 303

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 304 EDSRLGDFIE-ADGETPEDKVAKNLLREDLEAVLNTLSPRERDVLRLRYGLDDGRMKTLE 362

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 363 EIGQLFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 399



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 35/64 (54%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E+++        A+ A+ +    ++ +      T+D +R+YL+E+G I LL  + EI +
Sbjct: 25  AEEDDPYAAQAAEAADAAAARPARRRSRAQRAHYTEDSIRVYLQEIGRIRLLRADEEIEL 84

Query: 143 AKRI 146
           A++I
Sbjct: 85  ARQI 88


>gi|296139548|ref|YP_003646791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027682|gb|ADG78452.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 330

 Score =  206 bits (524), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 106/248 (42%), Positives = 172/248 (69%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 81  RDLAFIVRDGQAARQHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYA 140

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE T  E
Sbjct: 141 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIRRELHQQLGREATDAE 200

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +  +P E +  ++  +++P+SL+ P+G ++ + LGDFIED  A S   + I   +  
Sbjct: 201 LAAESGIPAEKIADLMDHSRDPVSLDMPVGSDEEAPLGDFIEDAEAASAESAVISTLMHS 260

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VLA+L  RE++V+R+R+G+      TL+++GK F ++RER+RQIE + + KL++  
Sbjct: 261 DVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGE 320

Query: 672 RSKKLRSF 679
           R+ +LR++
Sbjct: 321 RADRLRAY 328



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 21/55 (38%), Positives = 28/55 (50%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           A +A      L +    A     D VR+YL  +G   LL+ E E+ +AKRIEAG 
Sbjct: 9   APAAERVRPELTEADLDAQSPAADLVRVYLNGIGRTALLTAEDEVELAKRIEAGL 63


>gi|226356403|ref|YP_002786143.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226318393|gb|ACO46389.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 547

 Score =  206 bits (524), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 143/291 (49%), Positives = 199/291 (68%), Gaps = 10/291 (3%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E +  +A  ++   + R   K +  +  +     R ++  +     + + A++ ++EANL
Sbjct: 264 EEEIALARRIEEGEEAR---KLLEEDVELDDRGRRRLMRQM----EDGANARQGLIEANL 316

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW++QAI R+IA
Sbjct: 317 RLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIRQAINRAIA 376

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITK 571
           DQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T EEIA+ +        V +V K+++
Sbjct: 377 DQARTIRIPVHMVETINKLTRTARQLQQELSREATHEEIAEAMGPGWDAAKVEEVQKVSQ 436

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EP+SLETPIGDE  S  GDFI D+N  SP+++A +  L E   + L+ LT RE  VL+ R
Sbjct: 437 EPVSLETPIGDEKDSFYGDFIPDENLDSPVENAAKTLLSEELEKALSKLTEREAMVLKFR 496

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
            G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 497 KGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLKYHESRTRKLRDFLD 547



 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 43/135 (31%), Positives = 65/135 (48%), Gaps = 10/135 (7%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPP-------DEVSSEQMEDTVAMLSNMGINVVDGDD 82
           S + M+K  R  G ++ EE+ A L         D  S +  ED    L+   I V D D+
Sbjct: 147 SIQDMLKAGRAAGVLSSEEVAAALGLALEANGLDPESPDAFEDMQLYLAGQNIEVQDLDE 206

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRK---DSADRSTDDPVRMYLREMGSIELLSREGE 139
            EDE+  +D+       + ++    + K   D     ++DPVR YL E+G + LL+ E E
Sbjct: 207 DEDEDTDDDAEVEEVPGARAATDDDEEKYFDDMPRAVSNDPVRQYLHEIGRVSLLTLEEE 266

Query: 140 IAIAKRIEAGRAMMM 154
           IA+A+RIE G     
Sbjct: 267 IALARRIEEGEEARK 281


>gi|124024644|ref|YP_001018951.1| type II alternative RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
 gi|123964930|gb|ABM79686.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9303]
          Length = 376

 Score =  206 bits (524), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 124/351 (35%), Positives = 197/351 (56%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R++LL  +      R++     LL+  +     ++   E  +  EL     +++  +P  
Sbjct: 31  RVELLTHEEEVTLARLVQRREALLKQERQLASSQEAIKELQRLEELQQREANHSCHWPTK 90

Query: 394 -EWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  KI    K+    TG+   E +  +   R+       AK +M++A
Sbjct: 91  QEWAMAAGLTLAELQDKIETGYKTWGALTGLDPLELKRSLRAGRR-------AKDQMIQA 143

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 144 NLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPARGFRFSTYAYWWIRQGITRA 203

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+P+H+ +K++++ R  + +++   R  +  ++AK L +  E VR  L    
Sbjct: 204 IATQSRTIRLPMHITEKLNRIKRVQQEIASNQGRLASIADLAKALGLSEETVRLTLMRVP 263

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             ISLET IG E  S LGD +ED NA +P +   +  L      +L  L+ RE  V+R R
Sbjct: 264 RSISLETRIGQEQDSQLGDLLEDSNA-TPEEKLTRDQLHNDLEILLDELSNREATVIRRR 322

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G+   ++RER+RQIE+ A+ KL+ P R  K+R ++  
Sbjct: 323 FGLEDDTPQTLTQIGEAMHLSRERVRQIESHALLKLRQPQRRCKVRDYIQN 373



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 87/252 (34%), Gaps = 27/252 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           + DPVR+YL+++G +ELL+ E E+ +A+ ++                 +AL+    +L  
Sbjct: 18  STDPVRLYLQDIGRVELLTHEEEVTLARLVQRR---------------EALLKQERQLAS 62

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               ++E+  LE     E+       T+         +  E +       +         
Sbjct: 63  SQEAIKELQRLEELQQREANHSCHWPTKQEWAMAAGLTLAELQDKIETGYKTWGALTGLD 122

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             + +  +           R  D+    +   + A+  + + + +  LD + E    L  
Sbjct: 123 PLELKRSL-------RAGRRAKDQMIQANLRLVVAVAKKYQQRGIELLDLVQEGTLGLER 175

Query: 297 LQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
             +     +    S+       + +   +     ++ L    I   + ++  + + I  N
Sbjct: 176 AVEKFDPARGFRFSTYAYWWIRQGITRAIATQSRTIRL-PMHITEKLNRIKRVQQEIASN 234

Query: 353 EGELLRLAQSYG 364
           +G L  +A    
Sbjct: 235 QGRLASIADLAK 246


>gi|56752254|ref|YP_172955.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 6301]
 gi|81300658|ref|YP_400866.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 7942]
 gi|56687213|dbj|BAD80435.1| group2 RNA polymerase sigma factor RpoD5 [Synechococcus elongatus
           PCC 6301]
 gi|81169539|gb|ABB57879.1| group2 RNA polymerase sigma factor SigC [Synechococcus elongatus
           PCC 7942]
          Length = 398

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 118/288 (40%), Positives = 180/288 (62%), Gaps = 9/288 (3%)

Query: 395 WKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           W   V C +  + + ++  +   +    + + E + +         E   AK  M++ANL
Sbjct: 116 WAKIVDCSLTELRQALQLGLHRWAEVCQLDLEELKQVCK-------EGQRAKDHMIKANL 168

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA
Sbjct: 169 RLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIA 228

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            QS TIR+PVH+ +K++++ +  R+++    R    EEIA++L M  + VR+VL    + 
Sbjct: 229 TQSRTIRLPVHVTEKLNRIKKAQRKIAQTKGRTANLEEIAQELEMTPDQVREVLLRVPKS 288

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLET +G E  + LGD +E  +  +P +   Q +L     R+L  L  RE  V+RMRFG
Sbjct: 289 ISLETRVGKEKDTELGDLLETTD-FTPEERLTQESLSNDLQRLLLELNHRERDVIRMRFG 347

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +     ++L E+G+   ++RER+RQIEAKA++KL+HP R  ++R +L+
Sbjct: 348 LRDGQIYSLAEIGQVLDLSRERVRQIEAKALQKLRHPRRRNQIRDYLE 395



 Score = 40.6 bits (93), Expect = 0.81,   Method: Composition-based stats.
 Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 9/101 (8%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E E  S D  +L+ + S+ +V        + R + D +R+YL+++G + LL R+ E++ A
Sbjct: 11  EYEAVSSDVANLSETPSSEAVETA----VSSRQSTDLIRLYLQDIGRVRLLGRDEEVSEA 66

Query: 144 KRIEAGRAMMMASLCESPLTFQA--LIIWRDELNDGTTLLR 182
           + +   +  M      + +  +   ++    +L +G   L 
Sbjct: 67  RWV---QRYMQLLAVRNCVAVEEGGVLKDYVDLQEGRDRLT 104


>gi|254750874|ref|ZP_05202913.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Vollum]
          Length = 359

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 144/259 (55%), Positives = 187/259 (72%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 104 VRMYLKEIGRVDLLSAEEEIRLATRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 161 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 220

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 221 INKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHL 280

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDFIED+ A SP D A    L+E    VL +LT REE VLR+RFG+      TLEEVGK 
Sbjct: 281 GDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 340

Query: 649 FCVTRERIRQIEAKAIRKL 667
           F VTRERIRQIEAKA+RKL
Sbjct: 341 FGVTRERIRQIEAKALRKL 359



 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 77/176 (43%), Gaps = 11/176 (6%)

Query: 9   RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
            D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2   ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
            L   GI++V        +  E   +   + +     L           +DPVRMYL+E+
Sbjct: 59  YLGEQGIDLV-------GDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEI 111

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G ++LLS E EI +A RIE G       L E+ L     I  R  +  G   L  I
Sbjct: 112 GRVDLLSAEEEIRLATRIEEGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI 166


>gi|170076898|ref|YP_001733536.1| group 2 sigma factor [Synechococcus sp. PCC 7002]
 gi|169884567|gb|ACA98280.1| Group 2 sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 115/273 (42%), Positives = 181/273 (66%), Gaps = 8/273 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR   +  + + G+S+ E   I+          + AK+ M++ANLRLV+SVAKKY NRGL
Sbjct: 131 IRQGKQRWAEQVGLSVKELDSILK-------AGAKAKEHMIQANLRLVVSVAKKYQNRGL 183

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEG +GL +A +KFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K
Sbjct: 184 ELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK 243

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +  R++S      P+ +++A+ L M  E VR+VL+     +SLE  +G +  + L
Sbjct: 244 LNKIKKAQRQISQTQGCTPSLDDVAQALEMTPEQVREVLQKVPRSVSLEIRVGKDRDTEL 303

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD +E ++A SP ++ ++ +L+     +L  LT RE  V+++R+G+G    ++L E+G+ 
Sbjct: 304 GDLLETQDA-SPEENLVRESLQRDLHNLLTELTDREREVIQLRYGLGDGKTYSLAEIGRM 362

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             ++RER+RQIEAKA++KL+ P R   +R +LD
Sbjct: 363 LELSRERVRQIEAKALQKLRQPKRRNIMRDYLD 395



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 35/71 (49%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                 +GS DSL   +S    +VF        +  T D VR+YL+++G + LL R+ E+
Sbjct: 4   AKQSKSQGSFDSLTETASNDELAVFDPDETTLRNGQTTDLVRLYLQDIGRVPLLERDEEL 63

Query: 141 AIAKRIEAGRA 151
             A++++    
Sbjct: 64  TEARKVQNYIQ 74


>gi|162447798|ref|YP_001620930.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
 gi|161985905|gb|ABX81554.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
          Length = 419

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 138/249 (55%), Positives = 189/249 (75%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  +     +   AK+++VEAN RLV+S+AKKYT RGL FLDLIQEGN+GLM+A +KFD+
Sbjct: 166 VQSLEDTIRKGHYAKEKLVEANYRLVVSIAKKYTQRGLLFLDLIQEGNMGLMRAVDKFDY 225

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K++R  R++  ++ R+ T E
Sbjct: 226 EKGFKFSTYATWWIRQAITRAVADQARTIRIPVHMVETINKMIRIQRQLVQELGRDATIE 285

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+K+ +  E V+ + +I KEPISLE P+G+E+ S LGDFI D NA++P D  +Q  ++
Sbjct: 286 EIAEKMDITPEKVQNIQRIAKEPISLEAPVGEEEDSSLGDFISDPNALNPHDYMMQEMVK 345

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +T   VL +LT REE+VLR+R+G+     HTLEEVG++F VTRERIRQIEAKA+RKL+ P
Sbjct: 346 KTLDEVLETLTDREEKVLRLRYGLLDGKTHTLEEVGREFGVTRERIRQIEAKALRKLRSP 405

Query: 671 SRSKKLRSF 679
            R  KL+ F
Sbjct: 406 QRQNKLKEF 414



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/115 (22%), Positives = 41/115 (35%), Gaps = 17/115 (14%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           +  +  I V    ++EDE        L          L      +    DDPVRMYL+E+
Sbjct: 66  LFDDEDIEV--ELEVEDEPDEFSLSSLEVEEVEEEELLNIDAIPSSIKVDDPVRMYLKEI 123

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           G I LL+ + E   A  +  GR                 +   + + +G   L +
Sbjct: 124 GQIPLLNIDDERKYAIMVYQGRVA---------------LEQLEAVRNGEVDLSD 163


>gi|88809466|ref|ZP_01124974.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786685|gb|EAR17844.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 376

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 121/351 (34%), Positives = 201/351 (57%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +      R +     LL   +    +           EL     ++   +P  
Sbjct: 31  RVDLLTSEEEVTLSRQVQQRERLLVQERDLSTRIAAIRVLLDLEELQQREANHISHWPTR 90

Query: 394 -EWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  + ++ NE  ++ + E+G+   E +  +   R+       A+  M++A
Sbjct: 91  QEWARAAELPLSELNRLLNEGYTLWAKESGLDTKELQQRLREGRR-------ARDRMIQA 143

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 144 NLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRA 203

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+PVH+ +K++++ R  + ++++  R  +  ++AK+L +  E VR+ L    
Sbjct: 204 IATQSRTIRLPVHITEKLNRIKRVQQEIASEKGRLASVSDLAKELGVSEETVRQTLARVP 263

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +SLET +G +  + LGD +ED +A +P  +  + +L +    +L  L+PRE  V+R R
Sbjct: 264 RSVSLETRVGKDQDTQLGDLLEDGHA-TPEQTLTRDSLHDDLEHLLEELSPREAEVIRSR 322

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL E+G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 323 FGLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQPQRRSKVRDYIQG 373



 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 98/262 (37%), Gaps = 22/262 (8%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +D +R+YL+++G ++LL+ E E+ ++++++                   L++   +L+  
Sbjct: 19  NDLLRLYLQDIGRVDLLTSEEEVTLSRQVQQRER---------------LLVQERDLSTR 63

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
              +R ++DLE     E+       T     +  E    E  R   +      + +   +
Sbjct: 64  IAAIRVLLDLEELQQREANHISHWPTRQEWARAAELPLSELNRLLNEGYTLWAKESGLDT 123

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           K+ + ++           R  D     +   + A+  + + + M  LD + E    L   
Sbjct: 124 KELQQRL-------REGRRARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERA 176

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            +     +    S+     +++ + + + + S        + E+L  I +       E  
Sbjct: 177 VEKFDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNRIKRVQQEIASEKG 236

Query: 358 RLAQSYGIKRDVFLERHQGREL 379
           RLA    + +++ +     R+ 
Sbjct: 237 RLASVSDLAKELGVSEETVRQT 258


>gi|149178485|ref|ZP_01857074.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148842698|gb|EDL57072.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 588

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 162/523 (30%), Positives = 259/523 (49%), Gaps = 11/523 (2%)

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           +I    +      L  I D  A I  E           HS   +       +        
Sbjct: 39  LIEYIVVGLEERGLDLIDDPNADIDDEEVASVDSSANTHSDVAQGADEDSDDASSSIVEP 98

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
               S+    +   S++ + P  + + E  L +  + +         +    +  A+D +
Sbjct: 99  ETSLSSRDPIRMYLSQMGNIPLLSRSREIFLAKKIEITRKRFRRTVLESDFALKIAIDTL 158

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKC--------KVLKEKLVKLVGSLSLNQSRIDLLV 339
            +V+      +        ++ +  +           LK  L K      L QS     V
Sbjct: 159 EKVFAGELPFERTLRTSDTEDATKDQIMGRMPYNIATLKALLQKNNEDFELIQSGELGKV 218

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           EQ  ++ KR++    ++  L +   + R   L+    R                ++K   
Sbjct: 219 EQ-REVQKRMVVRRQKMATLCEELCL-RTQRLQPVLKRIHQIAGRMREVQEQLEDYKQLR 276

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
               D  L +  E+  +++    +  +F+     +++   + + AK+++   NLRLV+S+
Sbjct: 277 HKATDHRL-LERELSELTIMVVETSEDFQTRSREIKRRFDDWTEAKQQLSGGNLRLVVSI 335

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY NRGL FLDLIQEGN GLM+  EK+++  GYKFSTYA WW++QAITR++AD + TI
Sbjct: 336 AKKYRNRGLSFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATWWIRQAITRAVADHARTI 395

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM   I  +   + ++  +  REPT EE+A  + + VE   +++K  K PISL+TP
Sbjct: 396 RIPVHMFQSISTLKARSEQIRQETGREPTMEELADSVGLGVEETERIMKTWKHPISLDTP 455

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G+ + S  GDF+ED +  SP D+A++  L++    VL SLT RE  ++R+R+G+G    
Sbjct: 456 VGESEDSSFGDFLEDGHESSPADAAMREMLKDKIEHVLKSLTYREREIIRLRYGLGDGYS 515

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +TLEE G+ F VTRERIRQIE+KA+RKL+H +RS  LR F+D 
Sbjct: 516 YTLEETGRIFKVTRERIRQIESKALRKLQHQTRSAHLRGFVDA 558



 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 39/163 (23%), Positives = 78/163 (47%), Gaps = 10/163 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D +   + + A ++G++T ++++ FLP +      +E  V  L   G++++D  + + ++
Sbjct: 5   DANLNLLFQEAEKQGFLTFQQVHTFLPDEGGDPSLIEYIVVGLEERGLDLIDDPNADIDD 64

Query: 88  GSEDSLDLASSASNSSVFLQKR----------KDSADRSTDDPVRMYLREMGSIELLSRE 137
               S+D +++  +                  +     S+ DP+RMYL +MG+I LLSR 
Sbjct: 65  EEVASVDSSANTHSDVAQGADEDSDDASSSIVEPETSLSSRDPIRMYLSQMGNIPLLSRS 124

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            EI +AK+IE  R     ++ ES    +  I   +++  G   
Sbjct: 125 REIFLAKKIEITRKRFRRTVLESDFALKIAIDTLEKVFAGELP 167


>gi|262068176|ref|ZP_06027788.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
 gi|291378119|gb|EFE85637.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
          Length = 502

 Score =  206 bits (523), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 143/303 (47%), Positives = 202/303 (66%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +P ++    +     E    +         I+  ++ I     ++  E        +K
Sbjct: 200 EFNPDYIEDISEEELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYA---KK 256

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A ++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 257 AYEGDEEASQKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 316

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 317 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 376

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M VE ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 377 GMEVEKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDGV 436

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 437 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 496

Query: 677 RSF 679
             F
Sbjct: 497 EDF 499



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 30/101 (29%), Positives = 44/101 (43%), Gaps = 4/101 (3%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           EDE   +   D++    ++   L           D+P++MYLRE+G + LL+ + EI  A
Sbjct: 198 EDEFNPDYIEDISEEELSNEKLLN---LGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYA 254

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           K+   G       L ES L     I  +   N G  LL  I
Sbjct: 255 KKAYEGDEEASQKLIESNLRLVVSIAKK-HTNRGLKLLDLI 294



 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 32 KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79
          ++ +K  ++ G +T EE+N  L  D   +E++E+ +    + GI +++
Sbjct: 11 REFVKKVKEVGKITYEEINEELAAD-FPAEKIEELINTFLDEGIKILN 57


>gi|298244288|ref|ZP_06968094.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551769|gb|EFH85634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 334

 Score =  205 bits (522), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 113/270 (41%), Positives = 178/270 (65%), Gaps = 3/270 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I +   ++  +   +   V +       A++ ++EANLRLV+S+AK+Y+N+GL
Sbjct: 64  VKQYLKEIGMYPLLTAEQELQLAERVAR---GDQYARQRLIEANLRLVVSIAKRYSNQGL 120

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGNIGLM+A +KFD+  G++FSTYA WW++QAI+R+IA+ S +I IPVH+ + 
Sbjct: 121 PLLDLIQEGNIGLMRATQKFDYKRGFRFSTYATWWIRQAISRAIAEHSRSIHIPVHVVEL 180

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ R  RR+  +   EP PE++A +L +P E V ++L ++++PISL+ P+ D++  HL
Sbjct: 181 IYKIKRITRRLYQEQGVEPLPEQVAAELGLPRERVVELLNVSEQPISLDAPMADDEEYHL 240

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +ED +    +D   Q   RE   + +  L PRE  ++ MR+G+      +L+EV   
Sbjct: 241 SDMLEDTSMAPTIDVVSQQLQREHIEQAMTVLNPRERTIIEMRYGLKDGHSLSLDEVSVL 300

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           F +TRERIRQIE KA+RKL++P R + LR 
Sbjct: 301 FHLTRERIRQIEVKALRKLRYPERYEGLRD 330



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 2/102 (1%)

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--RSTDDPVRMYLREMG 129
           +  + V        ++  +D +++ S         ++     D   + DD V+ YL+E+G
Sbjct: 13  DTEVTVTLSKRKHTKDLMDDGVEIESEKDFIYACEEEVDGEEDQRGAVDDSVKQYLKEIG 72

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
              LL+ E E+ +A+R+  G       L E+ L     I  R
Sbjct: 73  MYPLLTAEQELQLAERVARGDQYARQRLIEANLRLVVSIAKR 114


>gi|148241988|ref|YP_001227145.1| RNA polymerase sigma factor RpoD [Synechococcus sp. RCC307]
 gi|147850298|emb|CAK27792.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. RCC307]
          Length = 401

 Score =  205 bits (522), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 132/248 (53%), Positives = 180/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 154 KFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 213

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 214 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 273

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 274 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPDQDVAKNLLRED 332

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+ KL+HP+R
Sbjct: 333 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALLKLRHPNR 392

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 393 NGVLKEYI 400



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 84  PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 118


>gi|257470878|ref|ZP_05634968.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|317065080|ref|ZP_07929565.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690756|gb|EFS27591.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 418

 Score =  205 bits (522), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 140/271 (51%), Positives = 188/271 (69%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     +S  E                 A K+++EANLRLV+S+AKK+TNRGL
Sbjct: 149 IKMYLREIGQIPLLSHDEELEYAKRA---LEGDDWASKQLIEANLRLVVSIAKKHTNRGL 205

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 206 KLLDLIQEGNIGLMKAVEKFEYSKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 265

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE + ++L M V+ V+ + ++ ++PISLETP+G E+ S L
Sbjct: 266 INKIKKEARIYLQETGKDATPEVLGERLGMEVDKVKAIQEMNQDPISLETPVGSEEDSEL 325

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED   ++P +   ++ LRE    VL +L+ REERVLR R+G+   +  TLEEVGK 
Sbjct: 326 GDFVEDHKMLNPYELTNRSLLREQLNGVLNTLSSREERVLRYRYGLDDGSPKTLEEVGKI 385

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 386 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 416



 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/209 (22%), Positives = 75/209 (35%), Gaps = 52/209 (24%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++    +++ A +  ++T EE+N  L  D    E++E  +  +   GI +V  +DLE 
Sbjct: 5   IKNEKVLSLVRKAMENKFITYEEINEELKSD-FPVEKIEQLITGMMEQGIEIVRQEDLEK 63

Query: 86  EEGSE----------------------DSLDLASSASNSSVFLQKRKD------------ 111
           E+                         D  +         +  ++ +D            
Sbjct: 64  EKKLAASLKKDKDKDKDKDEEPISKTQDKEEFPDEDEIDDLLEERTEDLDDFEHFNPEEL 123

Query: 112 ----------------SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                           S D   D+P++MYLRE+G I LLS + E+  AKR   G      
Sbjct: 124 EEINEDELVSDDLFNLSGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDDWASK 183

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
            L E+ L     I  +   N G  LL  I
Sbjct: 184 QLIEANLRLVVSIAKK-HTNRGLKLLDLI 211


>gi|1769598|gb|AAB39998.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score =  205 bits (522), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 114/273 (41%), Positives = 178/273 (65%), Gaps = 8/273 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR   +  + + G+S+ E   I+          + AK+ M++ANLRLV+SVAKKY NRGL
Sbjct: 131 IRQGKQRWAEQVGLSVKELDSILK-------AGAKAKEHMIQANLRLVVSVAKKYQNRGL 183

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEG +GL +A +KFD   GY+FSTYA WW++Q ITR    QS TIR+PVH+ +K
Sbjct: 184 ELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWWIRQGITRGDRTQSRTIRLPVHVTEK 243

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +  R++S      P+ +++A+ L M  E VR+VL+     +SLE  +G +  + L
Sbjct: 244 LNKIKKAQRQISQTQGCTPSLDDVAQALEMTPEQVREVLQKVPRSVSLEIRVGKDRDTEL 303

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD +E ++A SP ++ ++ +L+     +L  LT RE  V+++R+G+G    ++L E+G+ 
Sbjct: 304 GDLLETQDA-SPEENLVRESLQRDLHNLLTELTDREREVIQLRYGLGDGKTYSLAEIGRM 362

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             V+RER+RQIEAKA++KL+ P R   +R +LD
Sbjct: 363 LDVSRERVRQIEAKALQKLRQPKRRNIMRDYLD 395



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 35/71 (49%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                 +GS DSL   +S    +VF        +  T D VR+YL+++G + LL R+ E+
Sbjct: 4   AKQSKSQGSFDSLTETASNDELAVFDPDETTLRNGQTTDLVRLYLQDIGRVPLLERDEEL 63

Query: 141 AIAKRIEAGRA 151
             A++++    
Sbjct: 64  TEARKVQNYIQ 74


>gi|317506478|ref|ZP_07964279.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
 gi|316255239|gb|EFV14508.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
          Length = 348

 Score =  205 bits (522), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 111/264 (42%), Positives = 183/264 (69%), Gaps = 4/264 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I+   G++    R + ++VR    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQ
Sbjct: 87  INTSEGLTPQRRRELKAVVR----DGRAARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQ 142

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R 
Sbjct: 143 EGNLGLIRAMEKFDYSKGFKFSTYATWWIRQAITRGVADQSRTIRLPVHLVEQVNKLSRI 202

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R +  ++ RE T EE++++  +P   +  +L  +++P+SL+ P+G ++ + LGDFIED 
Sbjct: 203 KRELHQQLGREATSEELSRETGIPEHRIADLLDHSRDPVSLDMPVGADEEAPLGDFIEDS 262

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              S  ++ I   L      VLA+L+  E++V+R+R+G+      TL+++GK F ++RER
Sbjct: 263 EGASAENAVIAGFLHRDVRSVLATLSDSEQQVIRLRYGLDDGQPRTLDQIGKIFSLSRER 322

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSF 679
           +RQIE + + KL++  R+++LRS+
Sbjct: 323 VRQIEREVMVKLRNGDRAERLRSY 346



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP----VRMYLREMGSIE 132
           VV+  +  + E   D+     + +   + +   +   D  T  P    VR+YL  +G   
Sbjct: 4   VVNAPEEAEVELEADASAEEIAEAPGRLHVASERLQEDLDTQSPAADLVRVYLNGIGRTA 63

Query: 133 LLSREGEIAIAKRIEAGR 150
           LL+ E E+ +AK IEAG 
Sbjct: 64  LLTAEDEVTLAKSIEAGL 81


>gi|596248|gb|AAC44104.1| primary sigma factor [Borrelia burgdorferi]
          Length = 543

 Score =  205 bits (522), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 138/371 (37%), Positives = 224/371 (60%), Gaps = 1/371 (0%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+  + L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 171 EKNLKKERLALKELLRDIPLYQEELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 230

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +       +   +
Sbjct: 231 LRVL-GRDLTIAEKKIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPTDKIISM 289

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 290 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 349

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 350 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDE 409

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 410 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 469

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P
Sbjct: 470 DQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNP 529

Query: 671 SRSKKLRSFLD 681
            +++KL+ +L+
Sbjct: 530 KKTQKLKDYLE 540



 Score = 56.4 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/295 (15%), Positives = 108/295 (36%), Gaps = 5/295 (1%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           M+ + G    + D   D +  +   +  S   +      K     D  ++DP+++YL+E+
Sbjct: 1   MILDDGFQSDEEDIDIDVKLDDCDEEDISVKDDLGSGYIKGNVLKDSHSEDPIKLYLKEI 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII----WRDELNDGTTLLRE- 183
           G   LL+   E+ +AK++++G +++   L    L  +            +       RE 
Sbjct: 61  GKEFLLTGNQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNTIYSRMEREEFFKREK 120

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
             D E+     +K            +  +D       +  +  +   +   K  K +R  
Sbjct: 121 DKDKESSPDYYNKKKRIASFYKIPLKPIQDRLISYVDNKHRVYDLGGDIFEKNLKKERLA 180

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +     +    +  L    DD   + + ++D  R + +       E  R+LR L  +   
Sbjct: 181 LKELLRDIPLYQEELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRVLGRDLTI 240

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
            +K  +     K+ ++ + + +    L Q  ++ +       + +I+    E+ +
Sbjct: 241 AEKKIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPTDKIISMSEEIAK 295


>gi|158313089|ref|YP_001505597.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108494|gb|ABW10691.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 423

 Score =  205 bits (521), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 124/242 (51%), Positives = 178/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTY
Sbjct: 182 DGQAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTY 241

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP
Sbjct: 242 ATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMP 301

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL +
Sbjct: 302 IEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIDNVLGA 361

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR F
Sbjct: 362 LNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLREF 421

Query: 680 LD 681
           LD
Sbjct: 422 LD 423



 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 58/126 (46%), Gaps = 15/126 (11%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           +    +  ++I   R+ G ++  EL   L   ++  E +   ++ L   GI++V+ ++  
Sbjct: 46  ELDVSAIAELIARGRETGELSRSELREALEAADIGVELLPALISRLGAAGIDLVEEEEER 105

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
              G+  +    +  +                T D VRMYLRE+G + LL+   E+ ++K
Sbjct: 106 VTPGAPAAGRTVADHA---------------GTADLVRMYLREIGKVPLLNAAQEVELSK 150

Query: 145 RIEAGR 150
           R+EAG 
Sbjct: 151 RVEAGL 156


>gi|33866315|ref|NP_897874.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8102]
 gi|33639290|emb|CAE08298.1| Putative principal RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
          Length = 471

 Score =  205 bits (521), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 224 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 283

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 284 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 343

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 344 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 402

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 403 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 462

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 463 NGVLKEYI 470



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 154 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 188


>gi|168012500|ref|XP_001758940.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
 gi|12697780|dbj|BAB21618.1| PpSIG2 [Physcomitrella patens]
 gi|14669832|dbj|BAB62008.1| PpSIG2 [Physcomitrella patens]
 gi|162690077|gb|EDQ76446.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
          Length = 579

 Score =  205 bits (521), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 127/289 (43%), Positives = 188/289 (65%), Gaps = 6/289 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGI--SISEFRHIVSMVRKGEC----EASIAKKEMVEAN 452
           ++ ++  +LK+ N   ++  E G   +I E+   V M +        +   AK +MV +N
Sbjct: 285 LSHQIQDLLKLENIKSNLEREIGRNATIGEWSRAVGMEQNAFEARLKKGRFAKDKMVNSN 344

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK Y  RG+   DLIQEG++GL++ AEKFD   G+KFSTYA WW++QA+TRSI
Sbjct: 345 LRLVVSIAKNYQGRGMTLQDLIQEGSMGLVRGAEKFDPTKGFKFSTYAHWWIRQAVTRSI 404

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           ADQS TIR+P+H+ + I ++ +  R +  +  RE   EE+A+ + + VE ++ V+K  K 
Sbjct: 405 ADQSRTIRLPIHLYEVISRINKAKRMLVQEHGREARNEEVAELVGLTVEKLKSVVKSAKA 464

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P S+E PIG +  + LG+ + D +  SP D+ ++  +R+    VL +L PRE  VLR+RF
Sbjct: 465 PGSMERPIGKDGDTTLGELVADTDVDSPEDAIVKQLMRQDIEGVLRTLNPREREVLRLRF 524

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+      TLEE+G+ F VTRERIRQIEAKA+RKL+ PSR+  LR +LD
Sbjct: 525 GLDDGRSKTLEEIGQIFKVTRERIRQIEAKAMRKLRQPSRNSILREYLD 573



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 31/57 (54%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  +A+  +++    + +K        DPVR YLR++G  +LL+   E+ ++ +I+ 
Sbjct: 235 AEKVATDLASAPPLPKPKKPQLAADPSDPVRAYLRDIGRTKLLTAREEVDLSHQIQD 291


>gi|303279757|ref|XP_003059171.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459007|gb|EEH56303.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 587

 Score =  205 bits (521), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 118/249 (47%), Positives = 172/249 (69%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +++       AK +M++ANLRLV+S+AK+Y N+ + F DLIQEG +GL++ AEKFD+ 
Sbjct: 321 RELKERLDAGKRAKNQMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKFDFK 380

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QA+TRSI+DQS TIR+PVH+ + I ++ +  R++  K  R+PT EE
Sbjct: 381 RGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVHLFEIISRMSKVERQLVMKYGRDPTTEE 440

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+ + M VE + ++ K +  PISL   + D+D+  + + + D +A  P D+  +  L+E
Sbjct: 441 IAEVMDMTVEKINQIQKASLVPISLSQSVNDDDSRTVEETLVDDHAEHPDDATGKVLLKE 500

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L+PRE  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKL+ PS
Sbjct: 501 DLENVLNTLSPRERDVLRLRYGMDDGRVKTLEEIGNVFSVTRERIRQIEAKALRKLRQPS 560

Query: 672 RSKKLRSFL 680
           R+  LR +L
Sbjct: 561 RNGILREYL 569



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             D + +  S    + A N      KR  S  R   D ++ YL+++GS+ LL+ E E+ +
Sbjct: 218 AADGKSATISSSATTRAGNVVRKTTKRDPSTSRRQTDSMKTYLKDIGSVSLLTGEQEVEL 277

Query: 143 AKRIEA 148
           A RI+ 
Sbjct: 278 AMRIQD 283


>gi|9837536|gb|AAG00589.1|AF288784_1 SigC [Synechococcus elongatus PCC 7942]
          Length = 398

 Score =  205 bits (521), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 118/288 (40%), Positives = 179/288 (62%), Gaps = 9/288 (3%)

Query: 395 WKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           W   V C +  + + ++  +   +    + + E + +         E   AK  M++ANL
Sbjct: 116 WAKIVDCSLTELRQALQLGLHRWAEVCQLDLEELKQVCK-------EGQRAKDHMIKANL 168

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA
Sbjct: 169 RLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIA 228

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            QS TIR+PVH+ +K+ ++ +  R+++    R    EEIA++L M  + VR+VL    + 
Sbjct: 229 TQSRTIRLPVHVTEKLTRIKKAQRKIAQTKGRTANLEEIAQELEMTPDQVREVLLRVPKS 288

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISLET +G E  + LGD +E  +  +P +   Q +L     R+L  L  RE  V+RMRFG
Sbjct: 289 ISLETRVGKEKDTELGDLLETTD-FTPEERLTQESLSNDLQRLLLELNHRERDVIRMRFG 347

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +     ++L E+G+   ++RER+RQIEAKA++KL+HP R  ++R +L+
Sbjct: 348 LRDGQIYSLAEIGQVLDLSRERVRQIEAKALQKLRHPRRRNQIRDYLE 395



 Score = 40.6 bits (93), Expect = 0.79,   Method: Composition-based stats.
 Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 9/101 (8%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E E  S D  +L+ + S+ +V        + R + D +R+YL+++G + LL R+ E++ A
Sbjct: 11  EYEAVSSDVANLSETPSSEAVETA----VSSRQSTDLIRLYLQDIGRVRLLGRDEEVSEA 66

Query: 144 KRIEAGRAMMMASLCESPLTFQA--LIIWRDELNDGTTLLR 182
           + +   +  M      + +  +   ++    +L +G   L 
Sbjct: 67  RWV---QRYMQLLAVRNCVAVEEGGVLKDYVDLQEGRDRLT 104


>gi|258645217|ref|ZP_05732686.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
 gi|260402567|gb|EEW96114.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
          Length = 388

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 143/276 (51%), Positives = 190/276 (68%), Gaps = 6/276 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVR------KGECEASIAKKEMVEANLRLVI 457
           D +     EI +I + TG    E   +V          + +  A  AKK + +ANLRLV+
Sbjct: 109 DPVKMYLKEIGAIKLLTGSQEIELAKLVEKGSFDDATGRDKMAADEAKKALSDANLRLVV 168

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKY  RGLQFLDLIQEGN+GL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ 
Sbjct: 169 SIAKKYLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQAR 228

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+PVHM + I+K+ R +R++  +  RE T EE+AK + + V  +R+V KI ++PISLE
Sbjct: 229 TIRVPVHMVETINKLNRISRQLLQEKGREATNEELAKAMGVSVAKIREVKKIAQDPISLE 288

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+++ SHLGDFIED  A++P D+A    LRE    +L  LT RE +VL +RFG+   
Sbjct: 289 TPIGEKEDSHLGDFIEDHEAIAPDDAAGSILLREQIDELLRELTDRERQVLELRFGLKDG 348

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLEEVGK F VTRERIRQIE KA+ KLK  ++S
Sbjct: 349 RPRTLEEVGKYFDVTRERIRQIEGKALTKLKKSAKS 384



 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/164 (20%), Positives = 65/164 (39%), Gaps = 13/164 (7%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDS 92
           ++    R+ G ++ +++  F     +  + +     +L    I++   +D  DE+     
Sbjct: 23  ELRDKVRKDGTISNKDIMLFFTEKNLGQDDLSAVYELLHESNIDINFDEDASDEDLEILE 82

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR-- 150
            +      +          S   + DDPV+MYL+E+G+I+LL+   EI +AK +E G   
Sbjct: 83  DEETDDEKDIVEISDVMNTSDSINIDDPVKMYLKEIGAIKLLTGSQEIELAKLVEKGSFD 142

Query: 151 ----------AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                          +L ++ L     I  +  L  G   L  I
Sbjct: 143 DATGRDKMAADEAKKALSDANLRLVVSIAKKY-LGRGLQFLDLI 185


>gi|320334918|ref|YP_004171629.1| RpoD subfamily RNA polymerase sigma-70 factor [Deinococcus
           maricopensis DSM 21211]
 gi|319756207|gb|ADV67964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           maricopensis DSM 21211]
          Length = 525

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 142/300 (47%), Positives = 195/300 (65%), Gaps = 27/300 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK------------------------GECEASIA 444
           +R  +  I     +++ E   +   + +                           + + A
Sbjct: 226 VRQYLHEIGRVPLLTLEEEISLARRIEEGEEARKVLDEQPELEDRQRRRLQRQVEDGAAA 285

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW+
Sbjct: 286 RQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWI 345

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEG 562
           +QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ REPT EEIA+ +        
Sbjct: 346 RQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREPTYEEIAEAMGPGWDAAK 405

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+++A +  L E   + L+ LT 
Sbjct: 406 VEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVENAAKTLLSEELEKALSKLTE 465

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 466 REAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLKYHESRTRKLRDFLD 525



 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 40/139 (28%), Positives = 67/139 (48%), Gaps = 11/139 (7%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPP-------DEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + + +IK+ R  G ++ E++ A L         D  SS+  ED    L  + I+     D
Sbjct: 131 AIQDLIKIGRTAGVLSSEDVAAALSTALEANGLDPESSDAFEDLQIYLQGLSID---IQD 187

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++D+E +E   +  +  +  +       D     ++DPVR YL E+G + LL+ E EI++
Sbjct: 188 VDDDEDTEAEAEAETDEAAENEEEGYFDDMPRAVSNDPVRQYLHEIGRVPLLTLEEEISL 247

Query: 143 AKRIEAGRAMMMASLCESP 161
           A+RIE G       L E P
Sbjct: 248 ARRIEEGE-EARKVLDEQP 265


>gi|166368188|ref|YP_001660461.1| RNA polymerase sigma factor RpoD [Microcystis aeruginosa NIES-843]
 gi|166090561|dbj|BAG05269.1| principal RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 416

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 147/337 (43%), Positives = 209/337 (62%), Gaps = 12/337 (3%)

Query: 355 ELLRLAQSYGIKRD--VFLERHQGRE-----LDPHWVSYAKDFPEGEWKNFVACEVD-SI 406
            LLR  +   + R     L+  + RE      D  W      F   E       E +  +
Sbjct: 80  RLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIEKIIAEKSEKEPKL 139

Query: 407 LKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             I+  +    +   +        +  +S  ++       AK++MV++NLRLV+S+AKKY
Sbjct: 140 SDIKAYLGKTELMAPLVEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKY 199

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 200 MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 259

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S +++R+PT EEIA K+ M +E +R + K  + PISLETPIG E
Sbjct: 260 HLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKE 319

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 320 EDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 378

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 379 EIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415



 Score = 40.6 bits (93), Expect = 0.98,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           T+D +R+YL+E+G I LL  E EI +A++I
Sbjct: 65  TEDSIRIYLQEIGRIRLLRAEEEIELARKI 94


>gi|169883526|gb|ACA97858.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 416

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 147/337 (43%), Positives = 209/337 (62%), Gaps = 12/337 (3%)

Query: 355 ELLRLAQSYGIKRD--VFLERHQGRE-----LDPHWVSYAKDFPEGEWKNFVACEVD-SI 406
            LLR  +   + R     L+  + RE      D  W      F   E       E +  +
Sbjct: 80  RLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIEKIIVEKSEKEPKL 139

Query: 407 LKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             I+  +    +   +        +  +S  ++       AK++MV++NLRLV+S+AKKY
Sbjct: 140 SDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKY 199

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 200 MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 259

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S +++R+PT EEIA K+ M +E +R + K  + PISLETPIG E
Sbjct: 260 HLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKE 319

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 320 EDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 378

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 379 EIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415



 Score = 40.6 bits (93), Expect = 0.93,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           T+D +R+YL+E+G I LL  E EI +A++I
Sbjct: 65  TEDSIRIYLQEIGRIRLLRAEEEIELARKI 94


>gi|1710685|sp|P52322|RPOD_MICAE RecName: Full=RNA polymerase sigma factor rpoD1
 gi|786173|dbj|BAA08853.1| sigma factor [Microcystis aeruginosa]
 gi|1783286|dbj|BAA12850.1| principal sigma factor [Microcystis aeruginosa]
          Length = 416

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 147/337 (43%), Positives = 209/337 (62%), Gaps = 12/337 (3%)

Query: 355 ELLRLAQSYGIKRD--VFLERHQGRE-----LDPHWVSYAKDFPEGEWKNFVACEVD-SI 406
            LLR  +   + R     L+  + RE      D  W      F   E       E +  +
Sbjct: 80  RLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIEKIIVEKSEKEPKL 139

Query: 407 LKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             I+  +    +   +        +  +S  ++       AK++MV++NLRLV+S+AKKY
Sbjct: 140 SDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKY 199

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 200 MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 259

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S +++R+PT EEIA K+ M +E +R + K  + PISLETPIG E
Sbjct: 260 HLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKE 319

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 320 EDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 378

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 379 EIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415



 Score = 40.6 bits (93), Expect = 0.93,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           T+D +R+YL+E+G I LL  E EI +A++I
Sbjct: 65  TEDSIRIYLQEIGRIRLLRAEEEIELARKI 94


>gi|298241844|ref|ZP_06965651.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297554898|gb|EFH88762.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 366

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 105/269 (39%), Positives = 171/269 (63%), Gaps = 3/269 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ ++ I     ++ +E   +           +IA++++VE+NLRLVIS+A++YT+ G+ 
Sbjct: 99  QSYLRDIRGYGLLTHAEEIDLAQRA---AAGDTIARRKLVESNLRLVISIARRYTSTGVP 155

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            +DLIQEGN+GLM+AAEKFD   G  F TYA WW++QA++R+  +QS  I +P H+  ++
Sbjct: 156 LIDLIQEGNLGLMRAAEKFDHQRGCHFGTYATWWIRQAVSRAAGEQSRMIHLPEHVSTRL 215

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            KV R + ++S +   +P PE+IA+     V+ V+ +L + ++P+SL+TP+ DE    LG
Sbjct: 216 RKVRRISAQLSQENGLDPMPEQIAEACHFEVDEVKNLLGVIEQPVSLDTPVDDETRYSLG 275

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +ED    +P ++A +  L E   R LA LTPRE  V+ +R+GIG     TL EVGK+ 
Sbjct: 276 DTLEDDTTPAPAETASRHLLGEELHRALAVLTPRERSVVMLRYGIGDGRSRTLLEVGKEL 335

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            ++RER+RQ+E  A+ KL+  + ++ L  
Sbjct: 336 GISRERVRQLEVVALMKLRSVTNAQALHD 364



 Score = 44.1 bits (102), Expect = 0.081,   Method: Composition-based stats.
 Identities = 20/74 (27%), Positives = 32/74 (43%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           S S++         +    ++D  + YLR++    LL+   EI +A+R  AG  +    L
Sbjct: 75  STSSAHTHRGGVTSTKANGSEDAFQSYLRDIRGYGLLTHAEEIDLAQRAAAGDTIARRKL 134

Query: 158 CESPLTFQALIIWR 171
            ES L     I  R
Sbjct: 135 VESNLRLVISIARR 148


>gi|159026614|emb|CAO86546.1| rpoD1 [Microcystis aeruginosa PCC 7806]
          Length = 416

 Score =  205 bits (520), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 147/337 (43%), Positives = 209/337 (62%), Gaps = 12/337 (3%)

Query: 355 ELLRLAQSYGIKRD--VFLERHQGRE-----LDPHWVSYAKDFPEGEWKNFVACEVD-SI 406
            LLR  +   + R     L+  + RE      D  W      F   E       E +  +
Sbjct: 80  RLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIEKIIVEKSEKEPKL 139

Query: 407 LKIRNEIKSISVETGISISEF---RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             I+  +    +   +        +  +S  ++       AK++MV++NLRLV+S+AKKY
Sbjct: 140 SDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKY 199

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 200 MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 259

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S +++R+PT EEIA K+ M +E +R + K  + PISLETPIG E
Sbjct: 260 HLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKE 319

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 320 EDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 378

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 379 EIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 415



 Score = 40.6 bits (93), Expect = 0.94,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           T+D +R+YL+E+G I LL  E EI +A++I
Sbjct: 65  TEDSIRIYLQEIGRIRLLRAEEEIELARKI 94


>gi|300868700|ref|ZP_07113311.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
 gi|300333261|emb|CBN58503.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
          Length = 462

 Score =  204 bits (519), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 121/273 (44%), Positives = 181/273 (66%), Gaps = 1/273 (0%)

Query: 411 NEIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +E+K I  E     +E   + +  + +   E   AK  M++ANLRLV+SVAKKY NRGL+
Sbjct: 188 SELKRIMAEGKRRWAELAGVTLEALDQMITEGIQAKDHMIQANLRLVVSVAKKYQNRGLE 247

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLIQEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K+
Sbjct: 248 LLDLIQEGTLGLERAVEKFDPTRGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKL 307

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ +  R++S +  R  + E+IA +L M    VR+VL      +SLET +G+E  + LG
Sbjct: 308 NKIKKAQRKISQEKGRTASIEDIAAELGMTAPQVREVLLRVPRSVSLETKVGNEKDTELG 367

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D ++D ++VSP +  ++  L     ++LA LT RE  V+ MRFG+G    ++L E+G+  
Sbjct: 368 DLLDDADSVSPEELLMREALHRDLQQLLADLTSRERDVILMRFGLGDGHPYSLAEIGRAL 427

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            ++RER+RQIEAKA++KL+ P R  ++R +L+ 
Sbjct: 428 DLSRERVRQIEAKALQKLRQPKRRNRVRDYLES 460



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 48/344 (13%), Positives = 111/344 (32%), Gaps = 41/344 (11%)

Query: 80  GDDLEDEEGSEDSLDLASSASNS-SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
             D+ + +  +   DL             K  ++A R T D VR+YL+E+G + LL R+ 
Sbjct: 64  QPDVVEGDAEQAVEDLQEDEIEVLDGDTAKFNNTASRRTTDLVRLYLQEIGRVRLLGRDE 123

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E++ A++++                 + L +          L+R  ++L       +   
Sbjct: 124 EVSEAQKVQRY--------------IRLLELRNTAAEQEEGLIRRYVELIEARDRLAAQL 169

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
               +          +   + +  + E +      A V+ +   ++ +    A++     
Sbjct: 170 GHRPSLERWAALAGVAEVSELKRIMAEGKRRWAELAGVTLEALDQMITEGIQAKDHMIQA 229

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC---- 314
                 +   + ++  + + + +  LD I E    L    +     +    S+       
Sbjct: 230 ------NLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYAYWWIR 283

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE---LLRLAQSYGI------ 365
           + +   +     ++ L    I   + ++    ++I   +G    +  +A   G+      
Sbjct: 284 QGITRAIATQSRTIRL-PVHITEKLNKIKKAQRKISQEKGRTASIEDIAAELGMTAPQVR 342

Query: 366 ------KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
                  R V LE   G E D        D      +  +  E 
Sbjct: 343 EVLLRVPRSVSLETKVGNEKDTELGDLLDDADSVSPEELLMREA 386


>gi|555686|gb|AAA85644.1| sigma factor MysB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score =  204 bits (519), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 110/244 (45%), Positives = 174/244 (71%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   A++ ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 70  RDLQAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYT 129

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE
Sbjct: 130 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEE 189

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +PVE +  +L+ +++P+SL+ P+G ++ + LGDFIED  A+S  ++ I   L  
Sbjct: 190 LAEESGIPVEKINDLLEHSRDPVSLDMPVGTDEEAPLGDFIEDSEAMSAENAVISELLHT 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VLA+L  RE++V+R+RFG+      TL+++GK F ++RER+RQIE + + KL++  
Sbjct: 250 DIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLRNGE 309

Query: 672 RSKK 675
           R+ +
Sbjct: 310 RADQ 313



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +N++         A     D VR+YL  +G   LL+   E+ +AKRIEAG 
Sbjct: 2   ANATTSRVDTDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGL 52


>gi|78212231|ref|YP_381010.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9605]
 gi|78196690|gb|ABB34455.1| Sigma-70 factor [Synechococcus sp. CC9605]
          Length = 435

 Score =  204 bits (519), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 133/248 (53%), Positives = 181/248 (72%), Gaps = 1/248 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   
Sbjct: 188 RFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 247

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEI
Sbjct: 248 GYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEI 307

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P     +  LRE 
Sbjct: 308 AESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLRED 366

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VLA+L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R
Sbjct: 367 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNR 426

Query: 673 SKKLRSFL 680
           +  L+ ++
Sbjct: 427 NGVLKEYI 434



 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 118 PKGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 152


>gi|21466008|pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466014|pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
          Length = 332

 Score =  204 bits (518), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 140/261 (53%), Positives = 188/261 (72%), Gaps = 7/261 (2%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E +  + + R    E   A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++
Sbjct: 76  PKELKRYLHIAR----EGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIR 131

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++
Sbjct: 132 AVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQEL 191

Query: 544 KREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            REP+ EEIA+ +      + V + LKI +EP+SLETPIGDE  S  GDFI D+N  SP+
Sbjct: 192 GREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPV 251

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++A Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE 
Sbjct: 252 EAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIEN 311

Query: 662 KAIRKLK-HPSRSKKLRSFLD 681
           KA+RKLK H SR++KLR FL+
Sbjct: 312 KALRKLKYHESRTRKLRDFLE 332



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN- 175
           T DPVR YL E+G + LL+ E EI +A+++E G    +  L E+    Q LI        
Sbjct: 1   TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG-MEAIKKLSEATGLDQELIREVVRAKI 59

Query: 176 DGTTLLREI 184
            GT  + E+
Sbjct: 60  LGTARVEEV 68


>gi|55980501|ref|YP_143798.1| RNA polymerase pricipal sigma factor RpoD [Thermus thermophilus
           HB8]
 gi|209447478|pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447484|pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|55771914|dbj|BAD70355.1| RNA polymerase pricipal sigma factor (RpoD) [Thermus thermophilus
           HB8]
          Length = 423

 Score =  204 bits (518), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 145/281 (51%), Positives = 197/281 (70%), Gaps = 14/281 (4%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++ +I  ++KS+         E +  + + R    E   A++ ++EANLRLV+S+AKKY
Sbjct: 154 KTVEEIDQKLKSL-------PKEHKRYLHIAR----EGEAARQHLIEANLRLVVSIAKKY 202

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T RGL FLDLIQEGN GL++A EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPV
Sbjct: 203 TGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPV 262

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIG 581
           HM + I+K+ RTAR++  ++ REPT EEIA+ +      + V + LKI +EP+SLETPIG
Sbjct: 263 HMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG 322

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE  S  GDFI D++  SP+D+A Q+ L E   + L+ L+ RE  VL++R G+    +HT
Sbjct: 323 DEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHT 382

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           LEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 383 LEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 423



 Score = 37.1 bits (84), Expect = 8.9,   Method: Composition-based stats.
 Identities = 28/116 (24%), Positives = 46/116 (39%), Gaps = 2/116 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +D +     +                ++       ST DPVR YL E+G + LL+ E 
Sbjct: 39  DLEDPDLTLEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEE 98

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN-DGTTLLREIIDLEACIGP 193
           E+ +A+++E G    +  L E       LI         G+  +R I  L+  + P
Sbjct: 99  EVELARKVEEG-MEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDP 153


>gi|46198472|ref|YP_004139.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
 gi|21730342|pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730348|pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|49259060|pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259066|pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|78101162|pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101168|pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101224|pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101230|pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101236|pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101242|pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101248|pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101254|pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101260|pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101266|pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101762|pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101768|pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|83754377|pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754383|pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|210061069|pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061075|pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|4239959|dbj|BAA74758.1| principal sigma factor [Thermus thermophilus]
 gi|46196094|gb|AAS80512.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
          Length = 423

 Score =  204 bits (518), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 145/281 (51%), Positives = 197/281 (70%), Gaps = 14/281 (4%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++ +I  ++KS+         E +  + + R    E   A++ ++EANLRLV+S+AKKY
Sbjct: 154 KTVEEIDQKLKSL-------PKEHKRYLHIAR----EGEAARQHLIEANLRLVVSIAKKY 202

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T RGL FLDLIQEGN GL++A EKF++   +KFSTYA WW++QAI R+IADQ+ TIRIPV
Sbjct: 203 TGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPV 262

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIG 581
           HM + I+K+ RTAR++  ++ REPT EEIA+ +      + V + LKI +EP+SLETPIG
Sbjct: 263 HMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG 322

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DE  S  GDFI D++  SP+D+A Q+ L E   + L+ L+ RE  VL++R G+    +HT
Sbjct: 323 DEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHT 382

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           LEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 383 LEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 423



 Score = 37.1 bits (84), Expect = 8.9,   Method: Composition-based stats.
 Identities = 28/116 (24%), Positives = 46/116 (39%), Gaps = 2/116 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +D +     +                ++       ST DPVR YL E+G + LL+ E 
Sbjct: 39  DLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEE 98

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN-DGTTLLREIIDLEACIGP 193
           E+ +A+++E G    +  L E       LI         G+  +R I  L+  + P
Sbjct: 99  EVELARKVEEG-MEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDP 153


>gi|254423226|ref|ZP_05036944.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190715|gb|EDX85679.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 431

 Score =  204 bits (518), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 117/288 (40%), Positives = 185/288 (64%), Gaps = 9/288 (3%)

Query: 395 WKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           W      ++  +     + K + +   G+S+ E   I       + E + AK+ M++ANL
Sbjct: 149 WAKASGVDMPDLKPTLAQGKRLWAEIAGMSVEEIVEI-------QNEGTRAKEHMIKANL 201

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA
Sbjct: 202 RLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIA 261

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            QS TIR+PVH+ +K++K+ +  R++S    R    E+IAK+L M V  +R+VL      
Sbjct: 262 TQSRTIRLPVHITEKLNKIKKAQRKISQTQGRTAKAEDIAKELDMTVAQIREVLLKVPRS 321

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL+T +G +  + LGD +E ++ +SP D  ++ +L+    ++L  LT RE+ V+ +RFG
Sbjct: 322 VSLDTKVGKDRDTELGDLLETED-ISPEDRLMRESLKRELHQLLTDLTTREQEVITLRFG 380

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +     ++L E+G+   ++RER+RQIE+KA++KL+ P R  ++R +L+
Sbjct: 381 LDDGVPYSLAEIGRTLELSRERVRQIESKALQKLRQPKRRNRVRDYLE 428



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 32/72 (44%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D  + E       D +S      +      +     + D VR+YL+E+G + LL R+ E
Sbjct: 36  DDPSDTELTLTKEDDESSDVYIEGLDSDTHANPRATRSTDLVRLYLQEIGRVSLLERDEE 95

Query: 140 IAIAKRIEAGRA 151
           +A A+R++    
Sbjct: 96  VAEAQRVQQHME 107


>gi|160331013|ref|XP_001712214.1| rpoD [Hemiselmis andersenii]
 gi|159765661|gb|ABW97889.1| rpoD [Hemiselmis andersenii]
          Length = 485

 Score =  204 bits (518), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 132/275 (48%), Positives = 184/275 (66%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +R +++     +  + +     V   R     A  AK+ MV ANLRLV+S+AK+Y NR
Sbjct: 168 ISLREKLQREPTSSEWTAACKVSDVKKFRAILHNARRAKERMVAANLRLVVSIAKRYVNR 227

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLIQEG++GL++AAEKFD   G+KFSTYA WWVKQA+TR+IAD S TIR+PVH+ 
Sbjct: 228 GMSLQDLIQEGSLGLIRAAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVHLY 287

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           D I  + +T R ++ +I R PT EEIA+K+ M VE +R VL+  +  +SLE P+ ++D  
Sbjct: 288 DTISAIRKTTRTLNIEIGRSPTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLKNDDDA 347

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S L DFIE  +  SP +   ++ LR+    V+ SL+PRE  V+RMR+G+      TLEE+
Sbjct: 348 SQLSDFIE-ADQESPEEHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEI 406

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+ F VTRER+RQIEAKAIRKL+ P RS  LR ++
Sbjct: 407 GQIFSVTRERVRQIEAKAIRKLRQPYRSSILRDYV 441



 Score = 44.1 bits (102), Expect = 0.072,   Method: Composition-based stats.
 Identities = 24/109 (22%), Positives = 48/109 (44%), Gaps = 6/109 (5%)

Query: 39  RQRGYVT-IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLAS 97
           ++  ++T   E N  L  + + +   + T   L+   +  +       EE S + ++   
Sbjct: 54  KKFSFITMYSEKNFHLSINSIQAIPFKKTFQELTEGEMEEIIRSFGHQEEISSEIINDED 113

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              + S  ++  + +     DD VR YL+ +G + LL  E EI +A+ I
Sbjct: 114 ERDSKSQTVRGLQKA-----DDSVRWYLQLIGRVRLLRPEEEIQLAREI 157


>gi|289578595|ref|YP_003477222.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528308|gb|ADD02660.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 273

 Score =  204 bits (518), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 124/273 (45%), Positives = 188/273 (68%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   ++ IS    ++  E   ++  +         AKK  +E+NLRLV+S+AK Y  +G+
Sbjct: 4   IGMYLREISHIPLLTPEEENELLKRIE---EGDEEAKKRFIESNLRLVVSIAKGYVGKGI 60

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGN+GL+KA E+FD+  GYKFSTYA WW+KQ ITR+IADQ+ TIRIPVHM + 
Sbjct: 61  SFPDLIQEGNLGLLKAVERFDYRKGYKFSTYATWWIKQTITRAIADQARTIRIPVHMVES 120

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+++  ++   K+ REP+ EEIA+++ +  +  + +L+I +  +SLE P+G+++   L
Sbjct: 121 VNKLLKIQKQFLQKLGREPSIEEIAEEMNISEKKAKVLLEIVQGIVSLEEPVGEDENGKL 180

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD I DK AV P++      L+E    VL++L PREE+VLR+RFG+      TLEEVGK+
Sbjct: 181 GDIIADKEAVDPVEELESMLLKEQVDEVLSTLAPREEKVLRLRFGLDDGKIRTLEEVGKE 240

Query: 649 F-CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              ++RER+RQIE KA+++L+HP+RS++L+ FL
Sbjct: 241 LGGISRERVRQIETKALKRLRHPNRSRRLKEFL 273



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 24/51 (47%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           D + MYLRE+  I LL+ E E  + KRIE G         ES L     I 
Sbjct: 2   DYIGMYLREISHIPLLTPEEENELLKRIEEGDEEAKKRFIESNLRLVVSIA 52


>gi|257453204|ref|ZP_05618503.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|317059738|ref|ZP_07924223.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|313685414|gb|EFS22249.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
          Length = 436

 Score =  203 bits (517), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 142/271 (52%), Positives = 192/271 (70%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     ++  E   +    +K       A K ++EANLRLV+S+AKK+TNRGL
Sbjct: 166 IKMYLREIGQIPLLTHKEELELA---KKALEGDEFANKRLIEANLRLVVSIAKKHTNRGL 222

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 223 KLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 282

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ S L
Sbjct: 283 INKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGSEEDSEL 342

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEVGK 
Sbjct: 343 GDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEVGKI 402

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 403 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 433



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 1/94 (1%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D+ +L           +  + S     D+P++MYLRE+G I LL+ + E+ +AK+   G 
Sbjct: 136 DASELEEIPEEELTNEELAELSNGMKVDEPIKMYLREIGQIPLLTHKEELELAKKALEGD 195

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 L E+ L     I  +   N G  LL  I
Sbjct: 196 EFANKRLIEANLRLVVSIAKK-HTNRGLKLLDLI 228



 Score = 38.3 bits (87), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 26 FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
            ++    +I+ A +   +T EE+N  L  D    EQ++  ++ +   GI +
Sbjct: 5  IKNEKVLSLIRKAMKEKVITYEEINDELKED-FPLEQIDKLISGMIEQGIEI 55


>gi|86742187|ref|YP_482587.1| sigma 38 [Frankia sp. CcI3]
 gi|86569049|gb|ABD12858.1| sigma 38 [Frankia sp. CcI3]
          Length = 422

 Score =  203 bits (517), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 124/242 (51%), Positives = 178/242 (73%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTY
Sbjct: 181 DGHAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTY 240

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP
Sbjct: 241 ATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMP 300

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL  
Sbjct: 301 IEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGG 360

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L+PRE  V+R+RFG+     HTL EVG +  +TRERIRQIE   +R+L+ P+ + +LR F
Sbjct: 361 LSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKPAVAGRLREF 420

Query: 680 LD 681
           LD
Sbjct: 421 LD 422



 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 36/132 (27%), Positives = 61/132 (46%), Gaps = 19/132 (14%)

Query: 19  DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
           DD+   D S  +  ++I   R+ G ++  EL   L   ++  E +   +A L+ +GI ++
Sbjct: 43  DDTDELDVS--AVAEVIARGREAGEISRSELRDVLESADIGIELLPALIARLNAVGIELL 100

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D ++  D                       R  +    T D VRMYLRE+G + LL+   
Sbjct: 101 DEEEASD-----------------DATAASRSTAEHAGTADLVRMYLREIGKVPLLNAAQ 143

Query: 139 EIAIAKRIEAGR 150
           E+ ++KR+EAG 
Sbjct: 144 EVELSKRVEAGL 155


>gi|219849486|ref|YP_002463919.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543745|gb|ACL25483.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 345

 Score =  203 bits (517), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 125/307 (40%), Positives = 185/307 (60%), Gaps = 24/307 (7%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC------------------- 439
           V     S+  +++ ++ I     ++  E   +   + +G                     
Sbjct: 39  VEQFEPSLDAVQHYLQEIGRVALLTAVEEVELAERIERGNAAEQRLATATDLTPRERCEL 98

Query: 440 -----EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                E   A++ +++ANLRLV+S+AKKY  RGL  LDLIQEGNIGLM+A EKFD   G 
Sbjct: 99  LKAVQEGEEARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHHKGN 158

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++QA+TR++A+Q  TIR+PVHM + + +V R A R++  ++R+PTPEEIA 
Sbjct: 159 RFSTYATWWIRQAVTRALAEQGRTIRLPVHMSESVAQVKRIADRLAQSLERQPTPEEIAM 218

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L  PVE ++++L+  + P+SLETP+GDE    LGDFI D+   +P + A Q  L     
Sbjct: 219 ALGQPVERIQRILEAARCPVSLETPVGDEGEHTLGDFITDEELPAPGEIAAQKLLHRDLC 278

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L  L+ RE R++ +R+G+      TLEEVG+   +TRER RQIEA+A+R+L+ P   +
Sbjct: 279 AALNQLSDRERRIIDLRYGLLDGRRRTLEEVGRVLGMTRERARQIEAEALRRLRSPEIGQ 338

Query: 675 KLRSFLD 681
            LR +LD
Sbjct: 339 HLRDYLD 345



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/103 (21%), Positives = 39/103 (37%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ED        +      +        +      + D V+ YL+E+G + LL+   E+ +
Sbjct: 11  QEDVSFPAHEREDRFGHEDELFNPDLGEVEQFEPSLDAVQHYLQEIGRVALLTAVEEVEL 70

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           A+RIE G A        + LT +        + +G    R +I
Sbjct: 71  AERIERGNAAEQRLATATDLTPRERCELLKAVQEGEEARRHLI 113


>gi|297163178|gb|ADI12890.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 336

 Score =  203 bits (517), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 122/243 (50%), Positives = 170/243 (69%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK  +VEANLRLV+SVAK+YT RGL FLDLIQEGN GL++AAEKFD+  G+KFST
Sbjct: 93  EDGHRAKTHLVEANLRLVVSVAKRYTGRGLAFLDLIQEGNTGLIRAAEKFDYAKGFKFST 152

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW+KQA++R++ADQS TIR+PVH  + I+++ R  R +      EPTPE++A+K  +
Sbjct: 153 YATWWIKQAVSRALADQSRTIRVPVHTVELINRIARVRRELILDTGAEPTPEQVAEKAEV 212

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PV  + ++   TKEP+SL   + DE  S  GD I D +  SP D    + L++    +LA
Sbjct: 213 PVGRLAELDGYTKEPVSLHVALSDEGDSEFGDLIVDSDTPSPWDMVTFSLLQQALRTLLA 272

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            +TPRE  ++ +R+G+      TLEE+G+ + VTRERIRQIE++ + KL+HPSRS+ LR 
Sbjct: 273 EMTPREAGIISLRYGLFGGRARTLEEIGQVYGVTRERIRQIESRTMSKLRHPSRSQALRD 332

Query: 679 FLD 681
           +LD
Sbjct: 333 YLD 335



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +E E G E+  DL ++  +    L          + DPV+ YL+ +  + LL+ E E+ +
Sbjct: 5   VETESGLENPADLPAAEDDEPTALLDTP----VGSTDPVKDYLKLIARVRLLTAEQEVDL 60

Query: 143 AKRIEAGRAMMMASLCESPLT 163
           AKRIEAG       L E P  
Sbjct: 61  AKRIEAGLY-AERLLRERPGL 80


>gi|226226576|ref|YP_002760682.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089767|dbj|BAH38212.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 286

 Score =  203 bits (517), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 161/272 (59%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    IS  E   +   +R+       A  ++V +NLR V+SVAKKY N+G+
Sbjct: 17  LDQYLRDISAYPLISREEEAELARRIRQ---GDQEALDKLVRSNLRFVVSVAKKYQNQGV 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL++AA KFD   G KF +YA+WW++QAI +++A+QS  +R+P++    
Sbjct: 74  SLSDLINEGNLGLIRAARKFDETKGIKFISYAVWWIRQAILQALAEQSRIVRVPLNRAGT 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           +H++ + A  +  ++ RE T  EIA  + +  E V K + I++  +SL+ P+   + + L
Sbjct: 134 LHRIGKRANALLQELGREATHAEIAHGMDITEEEVAKTMSISQVHLSLDAPLTPGEDNRL 193

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D++ D    +P D      L E     L  L  RE ++LR+ FGI      TLEE+G Q
Sbjct: 194 LDYLPDTVHPTPEDQTFDKALTEAIEESLGGLKEREAKILRLYFGIDGADPMTLEEIGSQ 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             +TRER+RQI+ KA+ +L+H SRSK L SFL
Sbjct: 254 LGITRERVRQIKEKALSRLRHVSRSKSLESFL 285



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLR++ +  L+SRE E  +A+RI  G    +  L  S L F  ++    +  +    L +
Sbjct: 20  YLRDISAYPLISREEEAELARRIRQGDQEALDKLVRSNLRF--VVSVAKKYQNQGVSLSD 77

Query: 184 IID 186
           +I+
Sbjct: 78  LIN 80


>gi|218295160|ref|ZP_03495996.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
 gi|218244363|gb|EED10888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
          Length = 439

 Score =  203 bits (517), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 150/345 (43%), Positives = 223/345 (64%), Gaps = 21/345 (6%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           E+  D+++++      + +L+++ G+ +++  E  + + L    +       E       
Sbjct: 113 EEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEK------ 166

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             +  ++ ++  ++KS+         E +  + + R    E   A++ ++EANLRLV+S+
Sbjct: 167 -LDPKTVEEVDGKLKSL-------PKELKRYLHIAR----EGEAARQHLIEANLRLVVSI 214

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYT RGL FLDLIQEGN GL++A EKF++   +KFSTYA WW++QAI R+IADQ+ TI
Sbjct: 215 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTI 274

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLE 577
           RIPVHM + I+K+ RTAR++  ++ REP+ EEIA+ +      + V + LKI +EP+SLE
Sbjct: 275 RIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE 334

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGDE  S  GDFI D+N  SP+++A Q+ L E   + L+ L+ RE  VL++R G+   
Sbjct: 335 TPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDG 394

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
            +HTLEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 395 REHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD 439



 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/117 (29%), Positives = 55/117 (47%), Gaps = 3/117 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS-ADRSTDDPVRMYLREMGSIELLSRE 137
           + +DL D    E  L+         +  ++ + S    ST DPVR YL E+G + LL+ E
Sbjct: 54  ELEDLADPLDLEGPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLE 113

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN-DGTTLLREIIDLEACIGP 193
            EI +A+++E G    +  L E+    Q LI         GT  +++I  L+  + P
Sbjct: 114 EEIDLARKVEEG-MEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKLDP 169


>gi|284928680|ref|YP_003421202.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
 gi|284809139|gb|ADB94844.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
          Length = 420

 Score =  203 bits (517), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 141/307 (45%), Positives = 197/307 (64%), Gaps = 7/307 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVD------SILKIRNEIKSISVETGISISEFRHIVSM 433
           D  W      +   E         +       +  +  E K+IS    I   E +  +  
Sbjct: 114 DEQWAKRIFQWENIEQIIRTQSSKEKEPKWSEVTSLLQEKKTISNLEKIWELEQKSYLPK 173

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            ++       AK +MV +NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   G
Sbjct: 174 FKRRLYLGRKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKG 233

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA
Sbjct: 234 YKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIA 293

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE  
Sbjct: 294 TRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDL 352

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+
Sbjct: 353 ENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRN 412

Query: 674 KKLRSFL 680
             L+ ++
Sbjct: 413 SVLKEYI 419



 Score = 42.1 bits (97), Expect = 0.30,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIELLS 135
           +D D  E    S +S+       N  +   +R+D++ +   T+D +R+YL+E+G I LL 
Sbjct: 21  IDEDINETSSDSINSITTEPDGKNRKISASRRRDTSKKKPYTEDSIRVYLQEIGRIRLLR 80

Query: 136 REGEIAIAKRI 146
            E EI +A++I
Sbjct: 81  AEEEIELARKI 91


>gi|224533326|ref|ZP_03673920.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
 gi|224513491|gb|EEF83848.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
          Length = 255

 Score =  203 bits (516), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 124/250 (49%), Positives = 183/250 (73%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++ 
Sbjct: 3   EEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYK 62

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT EE
Sbjct: 63  RGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDEE 122

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L++
Sbjct: 123 LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQD 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+LK+P 
Sbjct: 183 QIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRLKNPK 242

Query: 672 RSKKLRSFLD 681
           +++KL+ +L+
Sbjct: 243 KTQKLKDYLE 252


>gi|317061552|ref|ZP_07926037.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
 gi|313687228|gb|EFS24063.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 363

 Score =  203 bits (516), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 142/271 (52%), Positives = 192/271 (70%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     ++  E   +    +K       A K ++EANLRLV+S+AKK+TNRGL
Sbjct: 93  IKMYLREIGQIPLLTHKEELELA---KKALEGDEFANKRLIEANLRLVVSIAKKHTNRGL 149

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 150 KLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 209

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ S L
Sbjct: 210 INKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGSEEDSEL 269

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEVGK 
Sbjct: 270 GDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEVGKI 329

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 330 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 360



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/104 (30%), Positives = 48/104 (46%), Gaps = 1/104 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +DL D+E   D+ DL           +  + S     D+P++MYLRE+G I LL+ + E+
Sbjct: 53  EDLLDKEEDFDASDLEELPEEELSNEELAELSNGMKVDEPIKMYLREIGQIPLLTHKEEL 112

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +AK+   G       L E+ L     I  +   N G  LL  I
Sbjct: 113 ELAKKALEGDEFANKRLIEANLRLVVSIAKK-HTNRGLKLLDLI 155


>gi|327398426|ref|YP_004339295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
 gi|327181055|gb|AEA33236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
          Length = 491

 Score =  203 bits (516), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 161/391 (41%), Positives = 237/391 (60%), Gaps = 23/391 (5%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
           + K +  K  L + +  +      I+ L +++ +  +++ +    L     SY    D  
Sbjct: 104 AKKIEEHKNNLTRKLIEMPFTCEAIEELRQKIIEGEEKVKNISNALD---LSYKYDDDES 160

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK-------------------IRN 411
            E H  +E     +    +  +   K     E+  + +                    ++
Sbjct: 161 DEDHTSKETLLKILESIIEKYQQLSKAQYQEEISQLKEDIFNHFTEIALSDKYIQKMTQS 220

Query: 412 EIKSISVETGISISE-FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            I  +     +   E    I++ + K   E    K+ M++ANLRLV+S+AKK+ NRGL F
Sbjct: 221 FIDRVKSNKNLPNRERLIDILNEIEKERKEVEEVKQRMIKANLRLVVSIAKKHLNRGLSF 280

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGNIGLMK+ +KFD+  G+KFSTYA WW++Q+I+R+IADQ+ TIRIPVHM + I+
Sbjct: 281 LDLIQEGNIGLMKSVDKFDYKKGFKFSTYATWWIRQSISRAIADQARTIRIPVHMIETIN 340

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+VR ++ +  +  +EPT +E+A+ L M  E ++ ++KI KEPISLETPIGD++ +HL D
Sbjct: 341 KIVRASKLLIQENGKEPTAQELAEYLGMDEEKIKSIIKIAKEPISLETPIGDDNDTHLED 400

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIED  + SPLD  I++NL+E    VL++LT RE +VL MR+GIG   DHTLEEVGK   
Sbjct: 401 FIEDTKSESPLDYVIKSNLKEKVEEVLSTLTDRERKVLMMRYGIGDGFDHTLEEVGKVLG 460

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VTRER+RQIEAKA+RKL+HP RS+ L SF++
Sbjct: 461 VTRERVRQIEAKALRKLRHPKRSRVLASFVE 491



 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 92/183 (50%), Gaps = 21/183 (11%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + +DD+ ++++   +++GYVT +E+N  LP + +S ++++D +    ++ I++VD D + 
Sbjct: 4   NLNDDAIRRILSEGKKKGYVTYDEINDILP-EGISVDEIDDIIRQCDDLDIDIVDTDKVS 62

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
            E+  E+          S+                 +RMYLREMG+I LLSRE EI IAK
Sbjct: 63  SEKNIEEFELEEDEEVGSA-----------------IRMYLREMGNIPLLSREEEIEIAK 105

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI---IDLEACIGPESKGGFFH 201
           +IE  +  +   L E P T +A+   R ++ +G   ++ I   +DL      +       
Sbjct: 106 KIEEHKNNLTRKLIEMPFTCEAIEELRQKIIEGEEKVKNISNALDLSYKYDDDESDEDHT 165

Query: 202 GTE 204
             E
Sbjct: 166 SKE 168


>gi|254302832|ref|ZP_04970190.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148323024|gb|EDK88274.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 418

 Score =  203 bits (515), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 143/303 (47%), Positives = 200/303 (66%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +P ++    +     E    +         I+  ++ I     ++  E          
Sbjct: 116 EFNPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRA-- 173

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 174 -YEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 232

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 233 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 292

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M VE ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 293 GMEVEKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 352

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 353 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 412

Query: 677 RSF 679
             F
Sbjct: 413 EDF 415



 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/208 (21%), Positives = 72/208 (34%), Gaps = 51/208 (24%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
             ++  + +IK A + G +T EE+N  L  D   +E +E  +  +   GI +VD + L++
Sbjct: 5   IKNEKARALIKKAVEEGIITYEEINEELGDD-FPAENIEQLINEMLEQGIKIVDEEQLDE 63

Query: 86  EEGSE-------------------------------------------------DSLDLA 96
               E                                                 +   + 
Sbjct: 64  LGEDELREKDLGDDYVDSEEHDDLLEDDTDDKLDDTDDENDDTEESFTEFDDEFNPEYIE 123

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
             + +     +          D+P++MYLRE+G + LL+ + EI  AKR   G       
Sbjct: 124 DVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYEGDEEASKK 183

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREI 184
           L ES L     I  +   N G  LL  I
Sbjct: 184 LIESNLRLVVSIAKK-HTNRGLKLLDLI 210


>gi|158334991|ref|YP_001516163.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158305232|gb|ABW26849.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 371

 Score =  203 bits (515), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 132/250 (52%), Positives = 183/250 (73%), Gaps = 1/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++  R        AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD 
Sbjct: 122 LNRFRHRLHAGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDH 181

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT E
Sbjct: 182 EKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEE 241

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   ++ LR
Sbjct: 242 EIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKSLLR 300

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L+PRE  VL++R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 301 EDLETVLDTLSPRERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 360

Query: 671 SRSKKLRSFL 680
           +R+  L+ ++
Sbjct: 361 NRNSVLKEYI 370



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E   A  +++   V D      E+         + A  +    Q +K      T+D +R
Sbjct: 8   LEAIQAPANDLDNLVEDAASSTSEDNQAGEGGKTTKARTARRRGQSKKKHY---TEDSIR 64

Query: 123 MYLREMGSIELLSREGEIAIAKRI 146
           +YL+E+G I LL  + EI +A++I
Sbjct: 65  LYLQEIGRIRLLRADEEIELARKI 88


>gi|313893234|ref|ZP_07826811.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313442587|gb|EFR61002.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 386

 Score =  203 bits (515), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 141/281 (50%), Positives = 195/281 (69%), Gaps = 9/281 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK---------EMVEANLRLVISV 459
           +R  +K I     +S  E   +   +  G  E +  K          ++V+ANLRLV+S+
Sbjct: 106 VRMYLKEIGRVPLLSADEEIVLAKQIEAGAAEDATYKDIQLAKKAKKKLVDANLRLVVSI 165

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAITR+IADQ+ TI
Sbjct: 166 AKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIADQARTI 225

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++R +R++     REP PEEIA+ + + VE VR++ KI +EP+SLETP
Sbjct: 226 RIPVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERVREIQKIAQEPVSLETP 285

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+E+ SHLGDFIED++A++P D+A    L+E    V   LT RE++VL +RFG+     
Sbjct: 286 IGEEEDSHLGDFIEDQDAIAPDDAASYILLQEQIEDVFTCLTDREQQVLILRFGLKDGKP 345

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TLEEVG+ F VTRERIRQIE KA+ KL++  +  K++ FL
Sbjct: 346 RTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRDKIKDFL 386



 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 40/127 (31%), Positives = 68/127 (53%), Gaps = 2/127 (1%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLED- 85
           ++  +++++  R+ G +T  E++  L    E+++EQ++D    L  + I VV   D ED 
Sbjct: 11  EEIVEQLLEKGRKTGVLTQSEISDALHEQAEITAEQLDDIYTTLGKLNIEVVADIDAEDV 70

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +E      + A    +           +  + DDPVRMYL+E+G + LLS + EI +AK+
Sbjct: 71  DENPIVPEEDAEEVVSEKSISIDLSVDSGVNIDDPVRMYLKEIGRVPLLSADEEIVLAKQ 130

Query: 146 IEAGRAM 152
           IEAG A 
Sbjct: 131 IEAGAAE 137


>gi|116333403|ref|YP_794930.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
 gi|116098750|gb|ABJ63899.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
          Length = 368

 Score =  203 bits (515), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 144/276 (52%), Positives = 186/276 (67%), Gaps = 4/276 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
           E D   V   K   + E K+        I   +R  +K I     ++  E    V++  +
Sbjct: 73  EPDARAVKAQKAVSKKELKDASTTTGVKINDPVRMYLKEIGRVNLLTADEE---VALALR 129

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E     AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EKFD+  G+KF
Sbjct: 130 IENGEEAAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKF 189

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REPTPEEI  ++
Sbjct: 190 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEM 249

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            MP E VR++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A    L+E    V
Sbjct: 250 DMPTEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLESV 309

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           L +LT REE VLR+RFG+      TLEEVGK F VT
Sbjct: 310 LDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVT 345



 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/203 (26%), Positives = 93/203 (45%), Gaps = 18/203 (8%)

Query: 16  EDSDDSLVFDF--SDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSN 72
           + + D  +FD    + + + +IK  ++ G++T ++L   +  P  + ++QM+  +  +S+
Sbjct: 3   KKTTDQPMFDQKAYNKTVRALIKDTKKAGHITYDDLTDKVATPYTLDAKQMDKLLETISD 62

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            GI+VVD       +G  D+  + +  + S   L+    +     +DPVRMYL+E+G + 
Sbjct: 63  AGISVVDA------KGEPDARAVKAQKAVSKKELKDASTTTGVKINDPVRMYLKEIGRVN 116

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+ + E+A+A RIE G       L E+ L     I  R  +  G   L  I        
Sbjct: 117 LLTADEEVALALRIENGEEAAKQELAEANLRLVVSIAKRY-VGRGMQFLDLI-------- 167

Query: 193 PESKGGFFHGTEGHSYQKREDSS 215
            E   G     E   Y+K    S
Sbjct: 168 QEGNMGLMKAVEKFDYRKGFKFS 190


>gi|157412913|ref|YP_001483779.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9215]
 gi|157387488|gb|ABV50193.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9215]
          Length = 393

 Score =  203 bits (515), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  ++ M     R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 132 SVREWAELIDMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 191

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 192 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 251

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 252 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 310

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 311 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 370

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 371 IEAKALRKLRHPNRNGVLKEYI 392



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + S          +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 60  SDSEEEDKGLGNIKLGPKGIYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 110


>gi|291301996|ref|YP_003513274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571216|gb|ADD44181.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 559

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 131/283 (46%), Positives = 192/283 (67%), Gaps = 3/283 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  +++ L     ++ +        ++ R  +  V +   +   AK  ++ ANLRLV+S
Sbjct: 280 LAKRIEAGLYAVERLRQLKEAGEEIPTQVRRDLEWVTR---DGDRAKNHLLAANLRLVVS 336

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR++ADQ+ T
Sbjct: 337 LAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQART 396

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IRIPVHM + I+K+ R  R +   + REP PEE+AK++ +  E V ++ +  +EPISL+ 
Sbjct: 397 IRIPVHMVEVINKLGRIQRELLQDLGREPAPEELAKEMDISPEKVLEIQQYAREPISLDQ 456

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            IGDE  S LGDFIED  AV  +D+   + L+    +VL +L+ RE  V+R+RFG+    
Sbjct: 457 TIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQGQLQQVLQTLSEREAGVVRLRFGLTDGQ 516

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 517 PRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 559



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 36/69 (52%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  E S        +S    Q RKD+   ++ D VR YL+++G + LL+   E+ +AKRI
Sbjct: 225 EDGEGSDGFDWDDEDSEALKQARKDAEMTASADSVRAYLKQIGKVPLLNAAQEVELAKRI 284

Query: 147 EAGRAMMMA 155
           EAG   +  
Sbjct: 285 EAGLYAVER 293


>gi|91203809|emb|CAJ71462.1| strongly similar to transcription initiation factor sigma RpoD
           [Candidatus Kuenenia stuttgartiensis]
          Length = 551

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 156/429 (36%), Positives = 240/429 (55%), Gaps = 29/429 (6%)

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           ++ N  E   D    + AM +  +  ++      A+  R +           K +++  K
Sbjct: 147 EDVNNGELSFDRTLKVDAMVENYKDDILEEFPRSAKYLRSIIQKNKEDYQRLKRKQTPEK 206

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
            K      +KL+ ++   + +    +E++   +KRI      L  +A             
Sbjct: 207 EK------IKLLRTIRNRRRKGIRRLEEINIRTKRIQPMMKRLQEIA------------- 247

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
                     +   +   +   KN  +   +   ++  +  ++      +    +  +  
Sbjct: 248 ----------LEMEQLEQQIGEKNGRSKANNHYKELEEQYLALENTVLETGERLKRRLLS 297

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +     E   AK+++  ANLRLV+S+AKKY NRGL FLDLIQEGN GLM+A +K+++  G
Sbjct: 298 IESIYKEHESAKRKLSGANLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRG 357

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + + K+   ++++     REPT EEIA
Sbjct: 358 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETMSKIRNISKKLLQDKGREPTIEEIA 417

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +++ + V   R+VLKI++  ISL+ P+G+ + S  GDFIED+ A SP+ +A Q  L++  
Sbjct: 418 REVKISVPEARRVLKISRHQISLDRPVGESEDSSFGDFIEDEKAESPVAAATQEMLKDKI 477

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL +LT RE  ++++R+GIG    +TLEEVGK F VTRER+RQIEAKA+RKL+HP RS
Sbjct: 478 ESVLETLTYREREIIKLRYGIGDGYTYTLEEVGKIFKVTRERVRQIEAKAVRKLQHPIRS 537

Query: 674 KKLRSFLDG 682
           +KL  FLDG
Sbjct: 538 RKLEGFLDG 546



 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/354 (18%), Positives = 149/354 (42%), Gaps = 17/354 (4%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPD-EVSSEQMEDTVAMLSNMGINVVDGDD 82
            +  +   K + +  +++GY+T EELN  LP D E+   +++D + ML  +GI+++D  D
Sbjct: 1   MENLNQKIKLLTQKGKEKGYLTYEELNDMLPDDAEIPPGKIDDILMMLDELGIDLIDEAD 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +   EG E      +   + S F      +     DDPVRMYL +MG I LL+R+ EI +
Sbjct: 61  I---EGREVVDSEEAEHYSESEFGFGEVSTVTEKIDDPVRMYLTQMGEIPLLTRDEEIML 117

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AK+IE  R   +  +  S L+ Q  +   +++N+G       + ++A +           
Sbjct: 118 AKKIEITRRGFLKKVLHSDLSLQTCLKIVEDVNNGELSFDRTLKVDAMVENYKDDILEEF 177

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                Y +      +++   ++  +          + ++ K+     N         E+ 
Sbjct: 178 PRSAKYLRSIIQKNKEDYQRLKRKQTP--------EKEKIKLLRTIRNRRRKGIRRLEEI 229

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           +     +  M  +L+   +    E+ ++ +++      +      ++   +   L+  ++
Sbjct: 230 NIRTKRIQPMMKRLQEIAL----EMEQLEQQIGEKNGRSKANNHYKELEEQYLALENTVL 285

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIM-HNEGELLRLAQSYGIKRDVFLERHQ 375
           +    L      I+ + ++     +++   N   ++ +A+ Y  +   FL+  Q
Sbjct: 286 ETGERLKRRLLSIESIYKEHESAKRKLSGANLRLVVSIAKKYRNRGLSFLDLIQ 339


>gi|325283594|ref|YP_004256135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
 gi|324315403|gb|ADY26518.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
          Length = 487

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 141/301 (46%), Positives = 194/301 (64%), Gaps = 28/301 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-------------------------RKGECEASI 443
           +R  +  I     +++ E   +   +                         ++   + + 
Sbjct: 187 VRQYLHEIGRVPLLTLEEEIALARRIEDGEFARVELEEKGEELDDRGRRALQRRMEDGAA 246

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW
Sbjct: 247 ARQGLIEANLRLVVSIAKKYTGRGLNFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWW 306

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE-- 561
           ++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE  PEEIA+ +    +  
Sbjct: 307 IRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREALPEEIAEAMGPGWDAN 366

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V +V K+++EP+SLETPIGDE  S  GDFI D N  SP+D+A +  L E   + L  LT
Sbjct: 367 KVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDDNLDSPVDNAAKTLLSEELEKALGKLT 426

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFL 680
            RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KLR FL
Sbjct: 427 EREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLKYHESRTRKLRDFL 486

Query: 681 D 681
           +
Sbjct: 487 E 487



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/151 (22%), Positives = 64/151 (42%), Gaps = 11/151 (7%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVT-------IEELNAFLPPDEVS 59
               +D     +D S    ++  + ++++K A+  G VT       +         D  S
Sbjct: 70  DEGAADKPARKADGSDRAYYAHPAIQELLKGAKATGLVTSEEAAAALATALEAHGMDPDS 129

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           S++ +D    L++  I        +++   +++              +   D     ++D
Sbjct: 130 SDEFDDLQLYLASKNIE----LQDDEDPEEDEADTDKDDDEEGEEEERYYDDMPRAVSND 185

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           PVR YL E+G + LL+ E EIA+A+RIE G 
Sbjct: 186 PVRQYLHEIGRVPLLTLEEEIALARRIEDGE 216


>gi|164688461|ref|ZP_02212489.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
 gi|164602874|gb|EDQ96339.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
          Length = 306

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 132/268 (49%), Positives = 185/268 (69%), Gaps = 3/268 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S  E   I   +        +AKK +VE+NLRLV+S+A+KY  + +  L
Sbjct: 37  YLKEIGKIPLLSRQEELDIAKRI---CEGDEVAKKILVESNLRLVVSIARKYARKEMAML 93

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG +GL++AAEKFD+  G+KFSTYA WW+KQ ITR+IADQS TIR+PVHM +KI+K
Sbjct: 94  DLIQEGTLGLIRAAEKFDYTKGFKFSTYATWWIKQGITRAIADQSRTIRVPVHMVEKINK 153

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V   + +++ ++ REP PEEIAK++ +PVE V +V++I++ P S+E+ IG ED + L   
Sbjct: 154 VSTISSQLAKELGREPKPEEIAKRMHVPVEKVVQVIRISQRPQSIESTIGQEDDTELEQV 213

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I DK A SP +   ++ L++    VL +L+ RE+ V+++RFG+G     TLEEVG+ F V
Sbjct: 214 IPDKEAHSPEEIVTRSLLKDQIEYVLDTLSEREKGVIKLRFGLGDGEKKTLEEVGRAFNV 273

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TRER RQIE KA+RKL HPSRS KL  +
Sbjct: 274 TRERARQIEKKALRKLAHPSRSNKLLDY 301



 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/98 (30%), Positives = 42/98 (42%), Gaps = 9/98 (9%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DD +++YL+E+G I LLSR+ E+ IAKRI  G  +    L ES L     I    +    
Sbjct: 31  DDSMKIYLKEIGKIPLLSRQEELDIAKRICEGDEVAKKILVESNLRLVVSIAR--KYARK 88

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
              + ++I        E   G     E   Y K    S
Sbjct: 89  EMAMLDLI-------QEGTLGLIRAAEKFDYTKGFKFS 119


>gi|116074180|ref|ZP_01471442.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116069485|gb|EAU75237.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 364

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 117/350 (33%), Positives = 194/350 (55%), Gaps = 8/350 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP-E 392
           R+DLL  +   +  R +     LL   ++   +        +  +L     ++   +P +
Sbjct: 19  RVDLLTNEEEVLLARQVQQREVLLAEERALAGEHPTIQRLLELEQLQQREANHVCHWPTK 78

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            EW        + +  +  E     + +  S  E + +   +R    E   A+  M++AN
Sbjct: 79  KEWAEAAGLTQEQLTTVLRE--GYGIWSDHSALESKELQKRLR----EGRRARDRMIQAN 132

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV++VAKKY  RGL+ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+I
Sbjct: 133 LRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRAI 192

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A QS TIR+PVH+ +K++++ +  + ++    R  +  ++++ L +  E VR  L     
Sbjct: 193 ATQSRTIRLPVHVTEKLNRIKKVQQEIATNEGRIASISDLSRALGISEETVRLTLMRVPR 252

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SLET +G +  + LGD +ED +A +P  +  + +L      +L  LT RE  V+R RF
Sbjct: 253 SVSLETRVGKDQDTQLGDLLEDCHA-TPEQTLTKNSLHSDLEELLGELTAREAEVIRRRF 311

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +T  TL E+G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 312 GLEDDTPLTLAEIGETMGLSRERVRQIETRALLKLRQPQRRSKVRDYILG 361



 Score = 41.4 bits (95), Expect = 0.60,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM--ASLCESPLTFQALII 169
             S +D +R+YL+++G ++LL+ E E+ +A++++    ++    +L     T Q L+ 
Sbjct: 3   TGSGNDLLRLYLQDIGRVDLLTNEEEVLLARQVQQREVLLAEERALAGEHPTIQRLLE 60


>gi|15827487|ref|NP_301750.1| RNA polymerase sigma factor SigB [Mycobacterium leprae TN]
 gi|221229964|ref|YP_002503380.1| RNA polymerase sigma factor SigB [Mycobacterium leprae Br4923]
 gi|699187|gb|AAA62952.1| u1764a [Mycobacterium leprae]
 gi|13093037|emb|CAC31395.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933071|emb|CAR71109.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 319

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 112/233 (48%), Positives = 169/233 (72%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++Q
Sbjct: 85  HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQ 144

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A +  +P+E +  +
Sbjct: 145 AITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQNLGREATDEELAAESGIPIEKINDL 204

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L+ +++P+SL+ P+G E+ + LGDFIED  A+S  ++ I   L      VLA+L  RE +
Sbjct: 205 LEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLHTDIRSVLATLDEREHQ 264

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           V+R+RFG+      TL+++GK F ++RER+RQIE   + KL++  R+ +LRS+
Sbjct: 265 VIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMCKLRNGERADRLRSY 317



 Score = 40.6 bits (93), Expect = 0.81,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 12/81 (14%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           + ++         A     D VR+YL  +G   LL+   E+ +AKRIEAG          
Sbjct: 2   AEATTNRVDSDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYA------- 54

Query: 160 SPLTFQALIIWRDELNDGTTL 180
                + L+  R    +G   
Sbjct: 55  -----EHLLQTRKRFGEGRKR 70


>gi|33239946|ref|NP_874888.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33237472|gb|AAP99540.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 438

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 130/236 (55%), Positives = 179/236 (75%), Gaps = 1/236 (0%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW+
Sbjct: 203 KEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWI 262

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITR+IADQS TIR+PVH+ + I ++ +T + +S +  R+P+ EEIA+ + M +E +R
Sbjct: 263 RQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIEKLR 322

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            + K  + PISLETPIG E+ S LGDFIE  ++ +P     +  LRE    VLA+L+PRE
Sbjct: 323 FIAKSAQLPISLETPIGKEEDSRLGDFIE-SDSENPELDVAKTLLREDLEGVLATLSPRE 381

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 382 RDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLRHPNRNGVLKEYI 437



 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 1/93 (1%)

Query: 55  PDEVSSEQMEDTV-AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
              +S E +E     +L+   +   +   L+ +       DL  + +        +    
Sbjct: 63  EPILSDENLEIAADQLLNATEMKNEESASLDIQNNDSLIGDLTDAEAREKALASIKLGPK 122

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 123 GVYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 155


>gi|309792450|ref|ZP_07686915.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225522|gb|EFO79285.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 311

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 169/277 (61%), Gaps = 4/277 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I   R   + ++ E   + SE       + +     + A+ +++ +NLRLV+S+A++Y 
Sbjct: 39  QIEAGREAARRLADEHPFTPSER----WRLEQQVHAGANARAQLINSNLRLVVSIARRYQ 94

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL  LDLIQEG++GLM+A +KFD   G KFSTYA +W++Q++ R+IAD   T+R+PVH
Sbjct: 95  GHGLSLLDLIQEGSLGLMRAVDKFDPSRGLKFSTYATYWIRQSVGRAIADHGRTVRLPVH 154

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++ ++ R  +R++ ++ R+PTPEE+A +L +  + V +  +    P SL+    D+ 
Sbjct: 155 LGERLSRLARARQRLTQRLDRDPTPEEVADELGITTDQVTRAEQAALTPASLDETHSDDG 214

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           T  L + I D    +PLD      LR+     ++ LT RE  +L +R+G+   T  TLE+
Sbjct: 215 TGALAEVISDPLEPTPLDHVAHGLLRDDLCEAMSHLTQRERSILNLRYGLEGETALTLEQ 274

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +G++  +TRER+RQ+E++A+RKL+ P   ++L  + +
Sbjct: 275 IGQRLSLTRERVRQLESEALRKLRDPHLGRRLHGYFE 311



 Score = 41.4 bits (95), Expect = 0.52,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +YL E+G   LL+ + E  +A +IEAGR        E P T         +++ G
Sbjct: 17  LYLNEIGDEPLLTFDQEQHLAAQIEAGREAARRLADEHPFTPSERWRLEQQVHAG 71


>gi|255325135|ref|ZP_05366241.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
 gi|255297700|gb|EET77011.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
          Length = 365

 Score =  202 bits (514), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 105/265 (39%), Positives = 177/265 (66%), Gaps = 4/265 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++    ++ +E R +  + R    E   A+  ++EANLRLV+S+AK+YT RG+  LDLI
Sbjct: 103 KLNNAEKLTRAEKRDLKILAR----EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLI 158

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R
Sbjct: 159 QEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSR 218

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R M   + RE T EE++++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED
Sbjct: 219 IKREMYQSLGREATNEELSEESGIDENKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIED 278

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A     + + +        V+ +L  RE+ V+R+R+G+      TL+++G++F ++RE
Sbjct: 279 AEATDAETAVVASMRHSDIRGVIDTLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRE 338

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE + + KL+  +R+ +LR +
Sbjct: 339 RVRQIEREVMAKLRDGNRADRLREY 363



 Score = 44.4 bits (103), Expect = 0.065,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +          +R  + D  + D VR+YL  +G   LLS E E+ +A+ IE G 
Sbjct: 44  TTDEEQEVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQAIEVGL 98


>gi|168009564|ref|XP_001757475.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691169|gb|EDQ77532.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 591

 Score =  202 bits (514), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 115/242 (47%), Positives = 164/242 (67%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   +K +MV +NLRLV+S+ K Y  RG+   DLIQEG++GL++ AEKFD   G+KFSTY
Sbjct: 346 EGRYSKDKMVNSNLRLVVSIVKNYQGRGMTLPDLIQEGSMGLIRGAEKFDPDKGFKFSTY 405

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QA+TR+IADQS  IR+P+H+ + I ++ +  + +  +  R+P  EE+A+ + M 
Sbjct: 406 AHWWIRQAVTRAIADQSRIIRLPIHLYEVISRINKAKKMLIQEHGRQPRDEEVAELVGMS 465

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE ++ ++K  K P S++  IG E    +G+ I DK+  SP D  I+  L++    VL +
Sbjct: 466 VEKLKFIVKSAKTPSSMDRLIGKEKDQSIGEMIADKDVESPEDDLIRQVLKQDVDGVLCT 525

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L PRE  VLR+RFG+      TLEE+G  F VTRERIRQIEAKA+RKL+ PSR+  LR +
Sbjct: 526 LNPREREVLRLRFGLDDGQSRTLEEIGTLFKVTRERIRQIEAKAMRKLRQPSRNGVLREY 585

Query: 680 LD 681
           LD
Sbjct: 586 LD 587



 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 41/68 (60%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E +  LA++ +++    + +K    +   DPVR YLR++G  +LL+   E+A++++I+A 
Sbjct: 245 EKAEKLATALASAPPAPRPKKPQISQEPTDPVRAYLRDIGKTKLLTASEEVALSRKIQAR 304

Query: 150 RAMMMASL 157
             +++  +
Sbjct: 305 DLLVLEKV 312


>gi|291459241|ref|ZP_06598631.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418495|gb|EFE92214.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 398

 Score =  202 bits (513), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 131/279 (46%), Positives = 190/279 (68%), Gaps = 3/279 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +++   +R  +K I     +S  E + +    R+ +    +A++ +VEANLRLV+S+AK+
Sbjct: 121 IETDDPVRFYLKEIGTIPLLSPEEEKELA---RRSKEGDPLARQRLVEANLRLVVSIAKR 177

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           YT RG+  LDLIQEGN+GLMK  EKF+   G+K STYA WW++Q ITR++ADQS TIR+P
Sbjct: 178 YTGRGMSILDLIQEGNLGLMKGVEKFEPDKGFKLSTYATWWIRQGITRALADQSRTIRVP 237

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+KV RT RR++ ++  EP+P+E+A  L M  E ++++L ++K+P SLETP+GD
Sbjct: 238 VHMVESINKVTRTQRRLTLELGYEPSPKELAASLNMTEEKLKEILDVSKQPTSLETPVGD 297

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ S+L DF+ D+  +SP  +A    LRE   ++L +L  RE  VL  RFG+     HTL
Sbjct: 298 EEDSNLSDFVADEKMISPEQNAANVMLREEIDKLLENLKDRERDVLIHRFGLHGEESHTL 357

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVG+ F VTRER+RQIEAKA++K+  P     L  FL+
Sbjct: 358 EEVGQMFGVTRERVRQIEAKALKKISLPKYKNALAGFLE 396



 Score = 82.2 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/219 (20%), Positives = 84/219 (38%), Gaps = 26/219 (11%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQ-RGYVTIEELNAFLPPDEVSSEQ 62
            KK +++++ + +     L+     +   ++I+  ++ +  +   EL       ++  EQ
Sbjct: 3   KKKTDKEAEEKRQLGKTELL-----EIVSELIQEGKENKDSIDETELADAFRGYDIPEEQ 57

Query: 63  MEDTVAMLSNMGINV-----------VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            E     +   G+ +           ++  + + E  +  S +         + L+    
Sbjct: 58  FEHIRKYIEESGVEINPVLSDSMLSQIESGEEDGEMEALSSEEEFPDEEEERLDLESLSL 117

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                TDDPVR YL+E+G+I LLS E E  +A+R + G  +    L E+ L     I  R
Sbjct: 118 LTGIETDDPVRFYLKEIGTIPLLSPEEEKELARRSKEGDPLARQRLVEANLRLVVSIAKR 177

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                G ++L  I         E   G   G E     K
Sbjct: 178 Y-TGRGMSILDLI--------QEGNLGLMKGVEKFEPDK 207


>gi|291566491|dbj|BAI88763.1| group 2 RNA polymerase sigma factor SigC [Arthrospira platensis
           NIES-39]
          Length = 385

 Score =  202 bits (513), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 115/272 (42%), Positives = 182/272 (66%), Gaps = 2/272 (0%)

Query: 412 EIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           E+K I  E     +E  ++ V  +++ + E   AK  M++ANLRLV+SVAKKY NRGL+ 
Sbjct: 113 ELKQIMAEGKRCWAELANLSVEELKQVQREGIQAKDHMIKANLRLVVSVAKKYQNRGLEL 172

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q ITR+IA QS TIR+PVH+ +K++
Sbjct: 173 LDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQGITRAIATQSRTIRLPVHITEKLN 232

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ +  R++S +  R  T ++IA +L M  + +R+VL      +SLET +G +  + LGD
Sbjct: 233 KIKKAQRKISQEKSRTATIDDIATELKMTPDQIREVLLRVPRSVSLETKVGTDKDTELGD 292

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E + + +P +  ++ +L      +LA L+ +E  V++MR+G+G    ++L E+G+   
Sbjct: 293 LLETEES-TPEELLMRESLYRELQHILADLSGKERAVIQMRYGLGDGHPYSLAEIGRALD 351

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ++RER+RQIEAKA++KL+ P R  ++R +LD 
Sbjct: 352 LSRERVRQIEAKALQKLRQPKRRNRVRDYLDS 383



 Score = 44.1 bits (102), Expect = 0.079,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA--MMMASLCESPL 162
            +   +    R T D VR+YL+E+G + LL R+ E++ A++++       +  +  E+  
Sbjct: 15  DVDLSEAHTSRRTTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYVQLVELRDTEAETNG 74

Query: 163 TF 164
             
Sbjct: 75  GV 76


>gi|282899714|ref|ZP_06307678.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195593|gb|EFA70526.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 390

 Score =  202 bits (513), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 139/263 (52%), Positives = 185/263 (70%), Gaps = 8/263 (3%)

Query: 425 SEFRHIVSMV-------RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            EFR     V       R        AK +MV++NLRLV+S+AKKY NRGL F DLIQEG
Sbjct: 128 PEFREWAEAVKLPLPTFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEG 187

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           ++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T +
Sbjct: 188 SLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTK 247

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  + 
Sbjct: 248 LLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDG 306

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            +P D   ++ LRE   RVL SL PRE  VLR+R+G+      TLEE+G+ F VTRERIR
Sbjct: 307 ETPEDQVSKSLLREDLERVLDSLGPRERDVLRLRYGLDNGRMKTLEEIGQIFNVTRERIR 366

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QIEAKA+RKL+HP+R+  L+ ++
Sbjct: 367 QIEAKALRKLRHPNRNSVLKEYI 389



 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V DGD  +  E   D  D  S  +  S    + K      T+D +R+YL+E+G I LL  
Sbjct: 40  VDDGDIDDFLEPQTDEDDAKSGKAAKSRRRTQTKKKPF--TEDSIRLYLQEIGRIRLLRA 97

Query: 137 EGEIAIAKRI 146
           + EI +A++I
Sbjct: 98  DEEIELARKI 107


>gi|206889536|ref|YP_002248786.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741474|gb|ACI20531.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 479

 Score =  202 bits (513), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 150/377 (39%), Positives = 227/377 (60%), Gaps = 9/377 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL-----VEQLYDISKRIMHNEGELLRLA 360
           ++ + + K +  K  + + V  LSL Q  ++ +      E L +  K        ++RL 
Sbjct: 96  EEVELAKKLQEGKSIIKETVMGLSLYQKILEEINKEEDSETLTEEDKAEEALSRTIIRLE 155

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               +  D+     + +E         +   +           +   +I  EIK I  E+
Sbjct: 156 N---LINDIEKIEQKIKEYGSLKELRKQINEKKRVGENTKQLENLYKEIHAEIKKIENES 212

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G+ I E ++I   + K +C     K E++  NLRLV+++AK Y  RGL  LDLI+EGNIG
Sbjct: 213 GLKIDELKNIWQKIYKAKCLVEDTKNELITRNLRLVVNIAKNYVGRGLPLLDLIEEGNIG 272

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA +KF +  G+KFSTYA WW++QAITR++ DQ+ TIR+PVHM +  ++V + +R ++
Sbjct: 273 LMKAVDKFKYEKGFKFSTYATWWIRQAITRALIDQTKTIRVPVHMMEFYNRVTKASRELT 332

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ REP  EEIA+KL +PV  V +V +  ++PI L+TPI  ++ + L DFI DK + SP
Sbjct: 333 QQLGREPNNEEIAEKLGVPVRKVEEVFRAIQDPIGLQTPI-GDEDTELEDFIGDKTSPSP 391

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +  A +  L E   R+L +LTP+EE+V++MRFGIG + DHTLEEVG+   +TRER+RQIE
Sbjct: 392 VSEAERTELSEHIQRILKTLTPKEEKVIKMRFGIGEDRDHTLEEVGRYLSITRERVRQIE 451

Query: 661 AKAIRKLKHPSRSKKLR 677
            KA+RKLKHPSR + L+
Sbjct: 452 TKALRKLKHPSRMRLLK 468



 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 57/274 (20%), Positives = 121/274 (44%), Gaps = 32/274 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            D +++++ L ++RG +T +E+N  LP +  S E++ED + +LS+MG+ VVD        
Sbjct: 4   RDIFEEIVNLGKKRGKLTYDEINEALPSEYYSPEEIEDLIDVLSDMGVRVVD-------- 55

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                              ++ +   +   +D V+ Y   MG I +L++E E+ +AK+++
Sbjct: 56  ----------EDEEEVFLEEEEEIEEEEHVEDLVQAYFNSMGDIPILTKEEEVELAKKLQ 105

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLL----------REIIDLEACIGPESKG 197
            G++++  ++    L +Q ++   ++  D  TL           R II LE  I    K 
Sbjct: 106 EGKSIIKETVMGLSL-YQKILEEINKEEDSETLTEEDKAEEALSRTIIRLENLINDIEK- 163

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                        +E   Q  E+  V E    +E+  K    +  K+++      ++ +N
Sbjct: 164 --IEQKIKEYGSLKELRKQINEKKRVGENTKQLENLYKEIHAEIKKIENESGLKIDELKN 221

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
           + +    +   +   +++L  + +  +  IA+ Y
Sbjct: 222 IWQKIYKAKCLVEDTKNELITRNLRLVVNIAKNY 255


>gi|67921267|ref|ZP_00514786.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67857384|gb|EAM52624.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 414

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 144/338 (42%), Positives = 207/338 (61%), Gaps = 6/338 (1%)

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD-- 404
           +  +    ++  L Q   I R+   E       D  W      +   E +       +  
Sbjct: 78  EEEIELARKIADLLQLERI-REALWEELDQEPNDDQWGHRIFQWENIEQRLCSQKNKEPK 136

Query: 405 --SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
              I+   N+ + IS        + +  +   ++       AK +MV +NLRLV+S+AKK
Sbjct: 137 WSDIVAELNKAEIISDLEKTWKQQSKAYLPKFKRRLYLGRRAKDKMVHSNLRLVVSIAKK 196

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+P
Sbjct: 197 YMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLP 256

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VH+ + I ++ +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG 
Sbjct: 257 VHLYETISRIKKTTKLLSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGK 316

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TL
Sbjct: 317 EEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTL 375

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 376 EEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 413



 Score = 42.5 bits (98), Expect = 0.27,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLRE 127
            L+   I V    D + E  S D ++  +  +      ++R  S  +  T+D +R+YL+E
Sbjct: 9   TLTESQIEVSFFIDEDLETPSNDIVEPETKKTRKISASRRRDPSKKKPYTEDSIRVYLQE 68

Query: 128 MGSIELLSREGEIAIAKRI 146
           +G I LL  E EI +A++I
Sbjct: 69  IGRIRLLRAEEEIELARKI 87


>gi|94263318|ref|ZP_01287133.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456273|gb|EAT06403.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 442

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 120/255 (47%), Positives = 183/255 (71%), Gaps = 1/255 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R     +        +AK  M++ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+A  
Sbjct: 189 LRQNYCRIELYARSIEVAKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVF 248

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD+  G KFSTYA WW++QAITR+I D++ TIR+PVH  +   +  +    +  ++ RE
Sbjct: 249 RFDYTKGNKFSTYASWWIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGRE 308

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTP EI++K  +P+E +  + + ++EPISLETP+  +D S LGDF+E++ ++SP ++   
Sbjct: 309 PTPVEISEKTGLPMEKILAIFEASREPISLETPV-GDDDSTLGDFLENQESISPYEAVKG 367

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L E  T +L++L+PREE+++R+RFGIG + ++TLEE+GK+F V+RERIRQIE KA+ +
Sbjct: 368 NQLAERVTTILSTLSPREEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNR 427

Query: 667 LKHPSRSKKLRSFLD 681
           L+H SR +KL++FLD
Sbjct: 428 LRHSSRREKLKNFLD 442



 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 61/156 (39%), Gaps = 13/156 (8%)

Query: 33  KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD--------DLE 84
           ++++  +  G +T+  LN  +P D+   + ++     L    I VV  D        + +
Sbjct: 8   RLLEAGKDDGCITLSFLNDLIPDDK-DPDAIDGIFDFLQENNIEVVTRDSGGDKKNLEGK 66

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           +  G+    D +         +++     + +T      YLREMG  +LL+ E E   +K
Sbjct: 67  EPAGNHSEDDESGGKEPVKTAVREDLAEPEETTT----TYLREMGLFDLLTPEEEEKYSK 122

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            I  G   ++ ++ +       +    + ++     
Sbjct: 123 TIREGFNAILNTIRQDRSGLPEMRQLAERIDLWEKR 158


>gi|298248273|ref|ZP_06972078.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
 gi|297550932|gb|EFH84798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
          Length = 1341

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 117/321 (36%), Positives = 188/321 (58%), Gaps = 24/321 (7%)

Query: 380  DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK--- 436
            +  W S   D  +  +++     VDS   +R   + I+    ++  + + +   ++    
Sbjct: 1023 NEEWSSEVDDDFDQIYESLYEVVVDS---LRQYFREITQFPLLNAEQEKKLAHQIKFGQQ 1079

Query: 437  -----------------GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
                                +  IA+++++E NLRLVISVAKKY   G Q  DLIQEGN+
Sbjct: 1080 AKEELEKRGEASSYIHVRIQQGKIAREKLIEHNLRLVISVAKKYARVGRQLEDLIQEGNL 1139

Query: 480  GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            GL++A EKFD   GY+FSTYA WW++QAITRS+A+QS TIR+PV++ +K+H++ R  R +
Sbjct: 1140 GLIRACEKFDTDKGYRFSTYATWWIRQAITRSLAEQSRTIRLPVYLVEKLHQLHRGQRDL 1199

Query: 540  SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              ++ REPT EE+AK   + ++ V++ L + ++ +SL+ PIG E  + LG+ IE   +  
Sbjct: 1200 ELQLGREPTLEELAKHQNLDIDKVQEYLVLRQQILSLDAPIGAEQETTLGEMIEQPRSDP 1259

Query: 600  PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              +    A+ +E  ++++ +LT R+ RV+ +RFG+     H LEE+G    VTRER+RQI
Sbjct: 1260 QENINNYAD-KEAVSQLMQNLTERQRRVISLRFGLEDGKIHKLEEIGSMLNVTRERVRQI 1318

Query: 660  EAKAIRKLKHPSRSKKLRSFL 680
            E KA+R+LK  +   +L   L
Sbjct: 1319 EEKALRQLKIDAYRLQLNDLL 1339



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 14/106 (13%)

Query: 47   EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
             EL   LP  +   +Q E   ++L +  I ++D  + E              +S      
Sbjct: 989  SELLNVLPELQNEEKQSEAI-SILQDASITIIDYQNEE-------------WSSEVDDDF 1034

Query: 107  QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
             +  +S      D +R Y RE+    LL+ E E  +A +I+ G+  
Sbjct: 1035 DQIYESLYEVVVDSLRQYFREITQFPLLNAEQEKKLAHQIKFGQQA 1080


>gi|1519636|gb|AAB07551.1| SigA [Chloroflexus aurantiacus J-10-fl]
          Length = 343

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 122/245 (49%), Positives = 172/245 (70%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +   +   A+  +++ANLRLV+S+AKKYT+ GL  +DL+QEGNIGLM+A EKFD+  G
Sbjct: 96  LERAVQQGQDARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKG 155

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR+IADQS TIR+PVHM + I +V RT+ R+   ++R+ TPEEIA
Sbjct: 156 HKFSTYATWWIRQAITRAIADQSRTIRLPVHMGEAISQVKRTSHRLQQTMQRDATPEEIA 215

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +    VR+ L+ +  P+SLE P+G E    +GDFIED    +P ++   + LRE  
Sbjct: 216 DAMGISAGKVRRTLEASMHPLSLEMPVGQEGEGRMGDFIEDDRISTPAEAPAASLLREQL 275

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VL  L  RE +++++R+G+      TLEEVG +F +TRERIRQIEA A+RKL+HP   
Sbjct: 276 EEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHPHLG 335

Query: 674 KKLRS 678
           KKLR+
Sbjct: 336 KKLRA 340



 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           ML   GI V++  D  D   ++            +  +    D  D + DDPVRMYL+E+
Sbjct: 1   MLQAEGIKVIESSDELDGRPTD------FEPDPDADLIADLPDLGDIAFDDPVRMYLQEI 54

Query: 129 GSIELLSREGEIAI 142
           G + LL+ E E+ +
Sbjct: 55  GQVPLLTAEQEVEL 68


>gi|330961076|gb|EGH61336.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 326

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 78/365 (21%), Positives = 142/365 (38%), Gaps = 48/365 (13%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L +++            G+    +G
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDG 173

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            +         + +    +  + + E+A     ++  +    P  A+     + +  + +
Sbjct: 174 IAPPAEVPPPVDPKAAKAEGDDEEEETAEATDDEEEVESGPDPVIAQQRFGAVSDQMEIT 233

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              L                                   +K  +           L +L 
Sbjct: 234 RKAL-----------------------------------KKFGRDDKHAIAEMVALAELF 258

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W 
Sbjct: 259 MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWT 318

Query: 385 SYAKD 389
                
Sbjct: 319 DALAK 323


>gi|21466021|pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|11527292|gb|AAG36964.1|AF291720_1 sigma factor SigA [Thermus aquaticus]
          Length = 438

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 149/345 (43%), Positives = 223/345 (64%), Gaps = 21/345 (6%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           E+  D+++++      + +L+++ G+ +++  E  + + L    +       E       
Sbjct: 112 EEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEK------ 165

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             +  ++ ++  ++KS+         E +  + + R    E   A++ ++EANLRLV+S+
Sbjct: 166 -PDPKTVEEVDGKLKSL-------PKELKRYLHIAR----EGEAARQHLIEANLRLVVSI 213

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYT RGL FLDLIQEGN GL++A EKF++   +KFSTYA WW++QAI R+IADQ+ TI
Sbjct: 214 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTI 273

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLE 577
           RIPVHM + I+K+ RTAR++  ++ REP+ EEIA+ +      + V + LKI +EP+SLE
Sbjct: 274 RIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE 333

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGDE  S  GDFI D+N  SP+++A Q+ L E   + L+ L+ RE  VL++R G+   
Sbjct: 334 TPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDG 393

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
            +HTLEEVG  F VTRERIRQIE KA+RKLK H SR++KLR FL+
Sbjct: 394 REHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLE 438



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/117 (29%), Positives = 54/117 (46%), Gaps = 3/117 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS-ADRSTDDPVRMYLREMGSIELLSRE 137
           + +DL D    E  L+         +  ++ + S    ST DPVR YL E+G + LL+ E
Sbjct: 53  ELEDLADPLDLEGPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLE 112

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN-DGTTLLREIIDLEACIGP 193
            EI +A+++E G    +  L E+    Q LI         GT  +++I  L+    P
Sbjct: 113 EEIDLARKVEEG-MEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDP 168


>gi|284122199|ref|ZP_06386842.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283829365|gb|EFC33758.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 414

 Score =  201 bits (512), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 118/281 (41%), Positives = 177/281 (62%), Gaps = 1/281 (0%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              +    + +  +RN +    ++T +     + +   + +   +   AK+ +V+ NLRL
Sbjct: 131 APALNEAEERLAGLRNALPGRGLKTRMLGKRLQRLQHELAEHRVQLERAKEGLVQHNLRL 190

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +AK++T RG+ FLDLIQEGNIGLM+AAE+F +  G+KFSTYA WWV+Q I R++ADQ
Sbjct: 191 VVDIAKRFTGRGMGFLDLIQEGNIGLMRAAERFQYRKGFKFSTYATWWVRQGILRAVADQ 250

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S TIR+PVH  +   ++++ + R++ K+ REP+ EEIA  LA+  E V+   +   EPIS
Sbjct: 251 SRTIRVPVHTTEAWQRMIKISHRLAQKLGREPSNEEIALALAVKPERVQHTTQAFLEPIS 310

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            + P   +  + LGD + D +A  P +   +  +R    R+L  LTPREE+V+R+RFGIG
Sbjct: 311 FDQP-NADGETFLGDCLPDDHASPPDEHLQEEQMRSQLHRLLRVLTPREEQVIRLRFGIG 369

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
                TLEEVGK   VTRERIRQIE  A++KL+ P+   +L
Sbjct: 370 NGQSRTLEEVGKLLNVTRERIRQIEVLAMKKLREPTVKAQL 410


>gi|295098975|emb|CBK88064.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium cylindroides
           T2-87]
          Length = 368

 Score =  201 bits (512), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 145/262 (55%), Positives = 193/262 (73%), Gaps = 5/262 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I E + + S+V     +   AK+ ++ +NLRLV+S+AKKY  RG+ FLDLIQEGN GL
Sbjct: 111 LDIEERKKLASVV----ADGEEAKQVLISSNLRLVVSIAKKYVGRGMLFLDLIQEGNCGL 166

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA EKFD+  G+KFSTYA WW++Q+ITR+IADQ+ TIRIPVHM + I+K+ R  R++  
Sbjct: 167 IKAVEKFDYTKGFKFSTYATWWIRQSITRAIADQARTIRIPVHMVETINKLTRIQRQLVQ 226

Query: 542 KIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            + R+P PEEIA+K+  +  + VR++ KI  +P+SLETPIG+ED SHLGDFIEDK  +SP
Sbjct: 227 DLGRDPLPEEIAEKMENITADKVREIQKIALDPVSLETPIGEEDDSHLGDFIEDKETLSP 286

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D      L++    VL  LT REE+VLR+RFG+      TLEEVGK+F VTRERIRQIE
Sbjct: 287 DDYTNNQLLKDEINNVLQGLTEREEKVLRLRFGLMDGRTRTLEEVGKEFNVTRERIRQIE 346

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA+RKLKHP+RSK+L+ F+  
Sbjct: 347 AKALRKLKHPNRSKRLKDFVKS 368



 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 1/107 (0%)

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
           +M   V+D  D + +   +D++D  S     S   Q   +++    +DPV+MYL+E+G I
Sbjct: 22  DMEEEVIDDVDEDLDSRIDDAVDENSIEDEISQLEQTFANASHTKINDPVKMYLKEIGQI 81

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
            LL  + E  IAKRI+ G       L E  L  +        + DG 
Sbjct: 82  PLLDPKEEPIIAKRIQDGE-AAKKKLEEPDLDIEERKKLASVVADGE 127


>gi|298491609|ref|YP_003721786.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298233527|gb|ADI64663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 390

 Score =  201 bits (512), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 138/280 (49%), Positives = 193/280 (68%), Gaps = 6/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVA 460
            + ++R+ +    +E      E+   V +     R        AK +MV++NLRLV+S+A
Sbjct: 112 ELERVRDRLYE-QLEREPQFKEWAEAVQLPLPTFRYRLHVGRRAKDKMVQSNLRLVVSIA 170

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR
Sbjct: 171 KKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIR 230

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPI
Sbjct: 231 LPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI 290

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G E+ S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      
Sbjct: 291 GKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMK 349

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 350 TLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 389



 Score = 44.4 bits (103), Expect = 0.068,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 35/67 (52%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D   D+     S +  + +  ++   ++ +      T+D +R+YL+E+G I LL  + E
Sbjct: 41  DDGEIDDFLEPQSDEDDAKSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEE 100

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 101 IELARKI 107


>gi|209525810|ref|ZP_03274346.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209493783|gb|EDZ94102.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 407

 Score =  201 bits (511), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 114/272 (41%), Positives = 182/272 (66%), Gaps = 2/272 (0%)

Query: 412 EIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           ++K I  E     +E  ++ V  +++ + E   AK  M++ANLRLV+SVAKKY NRGL+ 
Sbjct: 135 QLKQIMAEGKRCWAELANLSVEELKQVQREGLQAKDHMIKANLRLVVSVAKKYQNRGLEL 194

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q ITR+IA QS TIR+PVH+ +K++
Sbjct: 195 LDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQGITRAIATQSRTIRLPVHITEKLN 254

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ +  R++S +  R  T ++IA +L M  + +R+VL      +SLET +G +  + LGD
Sbjct: 255 KIKKAQRKISQEKSRTATIDDIATELKMTPDQIREVLLRVPRSVSLETKVGTDKDTELGD 314

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E + + +P +  ++ +L      +LA L+ +E  V++MR+G+G    ++L E+G+   
Sbjct: 315 LLETEES-TPEELLMRESLYRELQNLLADLSGKERAVIQMRYGLGDGHPYSLAEIGRALD 373

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ++RER+RQIEAKA++KL+ P R  ++R +LD 
Sbjct: 374 LSRERVRQIEAKALQKLRQPKRRNRVRDYLDS 405



 Score = 41.7 bits (96), Expect = 0.43,   Method: Composition-based stats.
 Identities = 14/75 (18%), Positives = 34/75 (45%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +       +  +  L            +   +  + R T D VR+YL+E+G + LL ++ 
Sbjct: 11  ESTQTFPTKDKDMELPTDELIRLDFSDVDLSEAQSSRRTTDLVRLYLQEIGRVRLLGKDE 70

Query: 139 EIAIAKRIEAGRAMM 153
           E++ A++++    ++
Sbjct: 71  EVSEAQKVQRYVQLV 85


>gi|78778882|ref|YP_396994.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9312]
 gi|78712381|gb|ABB49558.1| Sigma-70 factor [Prochlorococcus marinus str. MIT 9312]
          Length = 393

 Score =  201 bits (511), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  ++ M     R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 132 SVREWAELIDMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 191

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 192 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 251

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 252 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 310

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 311 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 370

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 371 IEAKALRKLRHPNRNGVLKEYI 392



 Score = 44.4 bits (103), Expect = 0.065,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 32/67 (47%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                +E   E++ + + S          +       T+D +R+YL+E+G I LL  + E
Sbjct: 44  ESSYSNESSLENNNEFSDSEDADKGLGNIKLGPKGIYTEDSIRVYLQEIGRIRLLRPDEE 103

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 104 IELARKI 110


>gi|282896628|ref|ZP_06304643.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281198498|gb|EFA73384.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 390

 Score =  201 bits (511), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 139/263 (52%), Positives = 185/263 (70%), Gaps = 8/263 (3%)

Query: 425 SEFRHIVSMV-------RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            EFR     V       R        AK +MV++NLRLV+S+AKKY NRGL F DLIQEG
Sbjct: 128 PEFREWAEAVKLPLPTFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEG 187

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           ++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T +
Sbjct: 188 SLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTK 247

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  + 
Sbjct: 248 LLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDG 306

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            +P D   ++ LRE   RVL SL PRE  VLR+R+G+      TLEE+G+ F VTRERIR
Sbjct: 307 ETPEDQVSKSLLREDLERVLDSLGPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 366

Query: 658 QIEAKAIRKLKHPSRSKKLRSFL 680
           QIEAKA+RKL+HP+R+  L+ ++
Sbjct: 367 QIEAKALRKLRHPNRNSVLKEYI 389



 Score = 45.6 bits (106), Expect = 0.027,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V DGD  +  E   D  D  S  +  S    + K      T+D +R+YL+E+G I LL  
Sbjct: 40  VDDGDIDDFLEPQTDEDDAKSGKAAKSRRRTQTKKKPF--TEDSIRLYLQEIGRIRLLRA 97

Query: 137 EGEIAIAKRI 146
           + EI +A++I
Sbjct: 98  DEEIELARKI 107


>gi|126659035|ref|ZP_01730176.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
 gi|126619692|gb|EAZ90420.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
          Length = 416

 Score =  201 bits (511), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 198/320 (61%), Gaps = 7/320 (2%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD------SILKIRNEIKSISVET 420
           R+   E       D  W      +   E         +       +  +  + + IS   
Sbjct: 97  REALWEELDQEPTDEQWGKRIFQWENIEQMLRAQSSKEKEPKWSEVTDMLQKAEIISDLE 156

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
                E +  +   ++       AK +MV +NLRLV+S+AKKY NRGL F DLIQEG++G
Sbjct: 157 KTWKLESKAYLPKFKRRLYLGRKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 216

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S
Sbjct: 217 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLS 276

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P
Sbjct: 277 QEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETP 335

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 336 EDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 395

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           AKA+RKL+HP+R+  L+ ++
Sbjct: 396 AKALRKLRHPNRNSILKEYI 415



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIELLSREGEI 140
            ED + S + +  A       +   +R+D   +   T+D +R+YL+E+G I LL  E EI
Sbjct: 22  DEDPDTSTNDIAEADGKKTRKITASRRRDPGKKKPYTEDSIRVYLQEIGRIRLLRAEEEI 81

Query: 141 AIAKRI 146
            +A++I
Sbjct: 82  ELARKI 87


>gi|169838629|ref|ZP_02871817.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 323

 Score =  201 bits (510), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 133/276 (48%), Positives = 191/276 (69%), Gaps = 6/276 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     +S  E   +   V         AK +M EAN+RLV+S+AK+Y+ RGL
Sbjct: 51  VRLYLREIGKIPLLSAEEEMELAHRV---VQGDKKAKDKMAEANMRLVVSIAKRYSGRGL 107

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN GL++A EKFD   G+KFSTYA WW++QAITR+IADQ+  IRIPVHM + 
Sbjct: 108 DFLDLIQEGNTGLLRAVEKFDPDKGFKFSTYATWWIRQAITRAIADQARVIRIPVHMVET 167

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DT 585
           I+K++RT RRM+ ++ REPT EE++K+L M  + +  V+KI ++  SL+  +G +   + 
Sbjct: 168 INKLLRTQRRMTQELNREPTIEELSKELDMEPDKIEYVMKIKQDIHSLDAGVGRDGDEED 227

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDFIED++  +P +SA    L+E    +L+SL+ RE+++++MRFG+     HTLEEV
Sbjct: 228 SVLGDFIEDEDTATPEESASSQLLKEQVQGILSSLSDREQKIIKMRFGLENGKSHTLEEV 287

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G++F VTRERIRQIEAKA+ KL+    +KKL  +L+
Sbjct: 288 GQEFAVTRERIRQIEAKALAKLRKHKDAKKLHEYLN 323



 Score = 61.8 bits (148), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           ++VD     D +             +      +  D     +DD VR+YLRE+G I LLS
Sbjct: 9   DIVDATLQVDFDEPNIDDLADEEEPDEQTLNGQYLDDV---SDDSVRLYLREIGKIPLLS 65

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            E E+ +A R+  G       + E+ +     I  R
Sbjct: 66  AEEEMELAHRVVQGDKKAKDKMAEANMRLVVSIAKR 101


>gi|297569039|ref|YP_003690383.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296924954|gb|ADH85764.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 445

 Score =  201 bits (510), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 121/255 (47%), Positives = 183/255 (71%), Gaps = 1/255 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R     +        +AK  M++ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+A  
Sbjct: 192 LRQCYCRIELYARSIEVAKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVF 251

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD+  G KFSTYA WW++QAITR+I D++ TIR+PVH  +   +  +    +  ++ RE
Sbjct: 252 RFDYTKGNKFSTYASWWIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGRE 311

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PTP EI++K  +P+E +  + + ++EPISLETP+  +D S LGDF+E++ +VSP ++   
Sbjct: 312 PTPAEISEKTGLPMEKILAIFEASREPISLETPV-GDDDSTLGDFLENQESVSPYEAVKG 370

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L E  T +L++L+PREE+++R+RFGIG + ++TLEE+GK+F V+RERIRQIE KA+ +
Sbjct: 371 NQLAERVTTILSTLSPREEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNR 430

Query: 667 LKHPSRSKKLRSFLD 681
           L+H SR +KL++FLD
Sbjct: 431 LRHSSRREKLKNFLD 445



 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/166 (18%), Positives = 66/166 (39%), Gaps = 16/166 (9%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV------- 78
            S +   K+++  +  G +T+  LN  +P D+   + ++     L    I V+       
Sbjct: 1   MSANIKNKLLEAGKDDGCITLSFLNDLIPDDK-DPDAIDGIFDFLQEHNIEVITHDKHGG 59

Query: 79  ----DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
               DG  L+D++  + S         + +  ++     + +T      YLREMG  +LL
Sbjct: 60  KKNLDGKRLDDKDQDDSSDMEDEEPLAAKMAGREDLAEPEETTT----TYLREMGQFDLL 115

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + E E   +K I  G   +++++ +       +    + ++     
Sbjct: 116 TPEEEEKYSKTIREGFNAIISAIRKDRSGLAEMKELAERIDMWEKR 161


>gi|220907205|ref|YP_002482516.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863816|gb|ACL44155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 455

 Score =  201 bits (510), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 139/493 (28%), Positives = 234/493 (47%), Gaps = 48/493 (9%)

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            +G  S   ++   +       E        +D    E D         +    V++   
Sbjct: 9   MVGTMSAIPYYDAMDDDERSGAESRHSGPRSEDDSVLEEDSLETLAEPGELDLLVEANGL 68

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A  D   L++  ++       +  + +         + E+ R     +D  V+  +  +
Sbjct: 69  EANGDGSLLEDWPEEDVEEAVQLAGRGQRTTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQ 128

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
             ++   L++++      +      ID     ++D     + +   L R A+  G+    
Sbjct: 129 RYMRLVELRDQVQADHQPIQQYVHLID-----IHDRLAAQLGHRPPLERWAREAGVV--- 180

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
                         +       +  W   +   V  + +I+ E                 
Sbjct: 181 -----------AGQLKTLLAEGKQAWATAIGMMVGELDQIQKE----------------- 212

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
                         AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD
Sbjct: 213 -----------GVRAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFD 261

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +    P+ 
Sbjct: 262 PTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGHTPSI 321

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           E+IA +L M V  VR++L      +SLET +G +  + LGD +E  + +SP +  ++ +L
Sbjct: 322 EDIATELEMTVPQVRELLVRVPRSVSLETKVGKDKDTELGDLLETDD-LSPEEMMMRESL 380

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                ++LA LT RE  V+ MRFG+G    ++L ++G+   ++RER+RQIEAKA++KL+ 
Sbjct: 381 HRELEKLLADLTSRERDVISMRFGLGDGHAYSLADIGRALDLSRERVRQIEAKALQKLRQ 440

Query: 670 PSRSKKLRSFLDG 682
           P R  ++R +LD 
Sbjct: 441 PKRRNRVRDYLDS 453



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 2/100 (2%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  E  S   ED++  L+  G   +D     +   +     L        V    +    
Sbjct: 37  PRSEDDSVLEEDSLETLAEPG--ELDLLVEANGLEANGDGSLLEDWPEEDVEEAVQLAGR 94

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
            + T D VR+YL+E+G + LL R+ E++ A++++    ++
Sbjct: 95  GQRTTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMRLV 134


>gi|1588486|prf||2208419B RNA polymerase sigma factor
          Length = 391

 Score =  201 bits (510), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 135/267 (50%), Positives = 189/267 (70%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +   G+ + +FR  +            AK +MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 132 KEWAEAAGMPLKDFRRRL-------FHGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDL 184

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 185 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 244

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S ++ R+PT EEIA+++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 245 KTTKILSQELGRKPTEEEIAERMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 304

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   ++ LRE    VL +L+ RE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 305 -ADGETPEDQVSKSLLREDLENVLDTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 363

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 364 ERIRQIEAKALRKLRHPNRNSILKEYI 390



 Score = 41.0 bits (94), Expect = 0.77,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           T+D +R+YL+E+G I LL  E EI +A++I        M   L E
Sbjct: 79  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERMREQLTE 123


>gi|78214100|ref|YP_382879.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78198559|gb|ABB36324.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 377

 Score =  201 bits (510), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 118/351 (33%), Positives = 192/351 (54%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +      R++     LL   Q          E H+  EL     +    +P  
Sbjct: 32  RVDLLTNEEEVTLARLVQRREALLSQQQKLAESDAAIGELHRLEELQRREANQHSHWPTK 91

Query: 394 -EWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  +I    ++ + +  +   + +  +            AK  M++A
Sbjct: 92  QEWARAADLPLPELQQRIDRGYQAWAEQAQLEAKDLKLALR-------NGRRAKDHMIQA 144

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 145 NLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRA 204

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + VR+ L    
Sbjct: 205 IATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTVRQTLARVP 264

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +SL+T +G E  + LGD IED +A +P  +     L      +L  LT RE  VLR R
Sbjct: 265 RSVSLDTRVGREQDTQLGDLIEDGHA-TPEQTLTHDELHNDLEHLLDELTSREAAVLRRR 323

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P R  K+R ++  
Sbjct: 324 FGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQRRSKIRDYIQS 374



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 94/259 (36%), Gaps = 28/259 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T D +R+YL+++G ++LL+ E E+ +A+ ++                 +AL+  + +L +
Sbjct: 19  TTDLLRLYLQDIGRVDLLTNEEEVTLARLVQRR---------------EALLSQQQKLAE 63

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               + E+  LE     E+       T+    +  +    E ++   +  +   E A   
Sbjct: 64  SDAAIGELHRLEELQRREANQHSHWPTKQEWARAADLPLPELQQRIDRGYQAWAEQAQLE 123

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +KD +  +        N  R  D     +   + A+  + + + M  LD + E    L  
Sbjct: 124 AKDLKLAL-------RNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLER 176

Query: 297 LQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLL--VEQLYDISKRIM 350
             +     +    S+       + +   +     ++ L     + L  ++++        
Sbjct: 177 AVEKFDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASNE 236

Query: 351 HNEGELLRLAQSYGIKRDV 369
                +  LA+  GI  D 
Sbjct: 237 GRIASIADLARELGISEDT 255


>gi|254525463|ref|ZP_05137515.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
 gi|221536887|gb|EEE39340.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
          Length = 393

 Score =  200 bits (509), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  ++ M     R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 132 SVREWAELIDMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 191

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 192 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 251

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 252 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 310

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 311 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 370

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 371 IEAKALRKLRHPNRNGVLKEYI 392



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +E  V   SN     +      +E   E++ + + S          +       T+D +R
Sbjct: 27  LETVVEGDSNKNFQNLQTSSELNESSIENNNEFSDSEEEDKGLGNIKLGPKGIYTEDSIR 86

Query: 123 MYLREMGSIELLSREGEIAIAKRI 146
           +YL+E+G I LL  + EI +A++I
Sbjct: 87  VYLQEIGRIRLLRPDEEIELARKI 110


>gi|126695861|ref|YP_001090747.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9301]
 gi|126542904|gb|ABO17146.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9301]
          Length = 394

 Score =  200 bits (509), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  ++ M     R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 133 SVREWAELIDMPLPKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 192

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 193 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 252

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 253 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 311

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 312 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 371

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 372 IEAKALRKLRHPNRNGVLKEYI 393



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 32/67 (47%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +L +     ++ + + S          +       T+D +R+YL+E+G I LL  + E
Sbjct: 45  SAELNESSIENNNNEFSDSEEEDKGLGNIKLGPKGIYTEDSIRVYLQEIGRIRLLRPDEE 104

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 105 IELARKI 111


>gi|327313374|ref|YP_004328811.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
 gi|326944913|gb|AEA20798.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
          Length = 327

 Score =  200 bits (509), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 108/317 (34%), Positives = 179/317 (56%), Gaps = 6/317 (1%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV--DSILKIRNEIKSISVETGIS 423
            + +F   +    L+    +          +  +   +       +   ++ I  E  IS
Sbjct: 13  NKVIFSRFYLFNSLNLCKFAVTLHNATHMRQLKITKSITNRESASLDKYLQEIGHEEMIS 72

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E   +   +RK       A + + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+K
Sbjct: 73  IEEEVELAQRIRK---GDRKALERLTKANLRFVVSVAKQYQNQGLSLPDLINEGNLGLIK 129

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+ +   +   + 
Sbjct: 130 AAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKINKILNQFEQEN 189

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +R P+  EIA+   +P E +   +K++   +S++ P  D+D S L D I + N  S    
Sbjct: 190 ERRPSIGEIAQSTDIPEEKIADAIKVSSRHVSVDAPFYDDDQSSLLDVIPNDNVPSTDRG 249

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            ++ +LRE   RVL  L  RE++V+   FGI    + TLEE+G ++ +TRER+RQI+ KA
Sbjct: 250 LVEESLREEIGRVLQVLEDREKKVVEAYFGINQ-REMTLEEIGSKYNLTRERVRQIKEKA 308

Query: 664 IRKLKHPSRSKKLRSFL 680
           IR+L+  + SK L+++L
Sbjct: 309 IRRLRQQTNSKVLKAYL 325



 Score = 41.4 bits (95), Expect = 0.52,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  E++S E E+ +A+RI  G    +  L ++ L F  ++    +  +    L +
Sbjct: 61  YLQEIGHEEMISIEEEVELAQRIRKGDRKALERLTKANLRF--VVSVAKQYQNQGLSLPD 118

Query: 184 IID 186
           +I+
Sbjct: 119 LIN 121


>gi|318040801|ref|ZP_07972757.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CB0101]
          Length = 381

 Score =  200 bits (509), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 176/274 (64%), Gaps = 8/274 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +IR + ++ +  + +S++E +  +            A+  M++ANLRLV++VAKKY  R
Sbjct: 106 EQIRQKQQAWAEHSNLSVAELKQAL-------HHGRRARDRMIQANLRLVVAVAKKYQQR 158

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G++ LDL+QEG +GL +A EK+D   G++FSTYA WW++Q ITR+IA QS TIR+PVH+ 
Sbjct: 159 GMELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVT 218

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +K++++ +  R+++ +  R  +  ++A++L +  E VR  L      +SL+T +G E  +
Sbjct: 219 EKLNRIKKAQRQIATEHGRLASVSDLARELGLSEEVVRLTLMRVPRSVSLDTRVGREQDT 278

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LGD +ED +A +P     + +L +    +L  LT RE  V+R+R+G+  +T  TL ++G
Sbjct: 279 QLGDLLEDSHA-TPEQELTRESLHDDLESLLEELTAREAAVIRLRYGLEDDTPQTLSQIG 337

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   ++RER+RQIE++A+ KL+ P R  +++ ++
Sbjct: 338 EDLHLSRERVRQIESRALLKLRQPQRRCRVQDYM 371



 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCESPLTFQALIIWRD 172
           R + D VR+YL+++G ++LLS E E+ +A++++           L  +    Q LI   D
Sbjct: 16  RGSTDLVRLYLQDIGRVDLLSHEEELTLARQVQRRERLLRERRRLAATHPALQELIDLED 75

Query: 173 E 173
           +
Sbjct: 76  D 76


>gi|225011103|ref|ZP_03701566.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
 gi|225004737|gb|EEG42696.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
          Length = 287

 Score =  200 bits (509), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+  E   +   ++      ++A + +  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIDLINAQEEVELAQRIK---AGDAVALERLTTANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++QAI +++A+Q+  +R+P++    
Sbjct: 75  TLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQARIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+PEEIAK+L M V  V++ LK +   +S++ P+ D + S L
Sbjct: 135 INKINKAFSYLEQAHQRPPSPEEIAKELEMTVSDVKQSLKNSGRHVSMDAPLIDGENSSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D ++  ++  P  + IQ++L    TR L +L+PRE  V+++ +GIG     TL E+G  
Sbjct: 195 YDVLDYGDSPRPDQALIQSSLHTEITRALDTLSPREADVIKLFYGIGEQPPMTLAEIGLT 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI  KAIRKL+H S++K L+++L
Sbjct: 255 FDLTRERVRQIREKAIRKLRHSSKNKLLKTYL 286



 Score = 41.7 bits (96), Expect = 0.42,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I+L++ + E+ +A+RI+AG A+ +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKIDLINAQEEVELAQRIKAGDAVALERLTTANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|170078618|ref|YP_001735256.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
 gi|558881|gb|AAB41506.1| SigA [Synechococcus sp. PCC 7002]
 gi|169886287|gb|ACB00001.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
          Length = 375

 Score =  200 bits (509), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 135/267 (50%), Positives = 189/267 (70%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +   G+ + +FR  +            AK +MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 116 KEWAEAAGMPLKDFRRRL-------FHGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDL 168

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 169 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 228

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S ++ R+PT EEIA+++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 229 KTTKILSQELGRKPTEEEIAERMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 288

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   ++ LRE    VL +L+ RE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 289 -ADGETPEDQVSKSLLREDLENVLDTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 347

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 348 ERIRQIEAKALRKLRHPNRNSILKEYI 374



 Score = 40.6 bits (93), Expect = 0.85,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           T+D +R+YL+E+G I LL  E EI +A++I        M   L E
Sbjct: 63  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERMREQLTE 107


>gi|28210583|ref|NP_781527.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
 gi|28203021|gb|AAO35464.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 282

 Score =  200 bits (509), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 131/274 (47%), Positives = 197/274 (71%), Gaps = 5/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K I     ++  E   +   + K       AK E++++NLRLV+S+AKKY  RGL
Sbjct: 13  INMYLKEIGQSDLLTAEEEIDLAKRIEK---GDERAKSELIKSNLRLVVSIAKKYIGRGL 69

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDL+QEGN+GLMKA +K+D+  GY+FSTYA WW+KQA+TRSIADQS TIRIPVHM + 
Sbjct: 70  SFLDLVQEGNLGLMKAVDKYDYKKGYRFSTYATWWIKQAVTRSIADQSRTIRIPVHMNEV 129

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K++RT +++  ++ REPT EEIA+   + +E ++++  ++++P+SLETP+G+ + + L
Sbjct: 130 ISKMIRTKKKLEQELDREPTEEEIAETAEISIEKIKRIYNVSQDPVSLETPVGENEDTIL 189

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGK 647
            +FI D   + P D   +  L +T + VL++L+PREER++R+R+G+ G     TLEE+G+
Sbjct: 190 QNFISDDRYL-PEDKVTEQMLGDTLSNVLSTLSPREERIVRLRYGLVGDGESRTLEEIGR 248

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F +TRERIRQIEA+AIRKL+HP+R KKL+ + +
Sbjct: 249 EFNLTRERIRQIEARAIRKLRHPTRIKKLQGYFE 282



 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 9/87 (10%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            + S  +  DD + MYL+E+G  +LL+ E EI +AKRIE G     + L +S L     I
Sbjct: 1   MEASNAKVVDDYINMYLKEIGQSDLLTAEEEIDLAKRIEKGDERAKSELIKSNLRLVVSI 60

Query: 169 IWR---------DELNDGTTLLREIID 186
             +         D + +G   L + +D
Sbjct: 61  AKKYIGRGLSFLDLVQEGNLGLMKAVD 87


>gi|19553123|ref|NP_601125.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|62390759|ref|YP_226161.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|1149591|emb|CAA89988.1| SigB sigma factor [Corynebacterium glutamicum]
 gi|21324689|dbj|BAB99312.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigB)
           [Corynebacterium glutamicum ATCC 13032]
 gi|41326097|emb|CAF20260.1| RNA POLYMERASE SIGMA FACTOR [Corynebacterium glutamicum ATCC 13032]
          Length = 331

 Score =  200 bits (509), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 104/252 (41%), Positives = 171/252 (67%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   ++    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 78  RAMKRDLKVLAKDGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 137

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +   + RE 
Sbjct: 138 FDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKRELYQHLGREA 197

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +
Sbjct: 198 TNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDAESAVVAS 257

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL +L PRE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL
Sbjct: 258 MRHSDIRAVLNTLEPREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMSKL 317

Query: 668 KHPSRSKKLRSF 679
           +   R+ +LR +
Sbjct: 318 RDGERASRLREY 329



 Score = 44.4 bits (103), Expect = 0.068,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 29/63 (46%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  S    ++         +R  + D  + D VR+YL  +G   LL+ E E+ +A+ IE
Sbjct: 1   MTAPSTQDLATTEREVDPGSRRGQTNDNPSQDLVRVYLNGIGKTALLTAEDEVELAQTIE 60

Query: 148 AGR 150
            G 
Sbjct: 61  VGL 63


>gi|254416308|ref|ZP_05030062.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196176990|gb|EDX72000.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 416

 Score =  200 bits (508), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 119/260 (45%), Positives = 174/260 (66%), Gaps = 2/260 (0%)

Query: 424 ISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +E   + V  + + + E   AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL 
Sbjct: 156 WAELAELTVKELEQVQAEGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLE 215

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +A EKFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +
Sbjct: 216 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQE 275

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R  T E+IAK+L M    VR+VL      +SLE  +G E  + LGD +E +   SP D
Sbjct: 276 QGRTATIEDIAKELEMDAPQVREVLMRVPRSVSLEIKVGKEKDTELGDLLETEET-SPED 334

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++  L+    ++LA LT RE  V+ MRFG+G    ++L E+G+   ++RER+RQIEAK
Sbjct: 335 VLMREALQRDLQQLLADLTSRERDVICMRFGLGDGHPYSLAEIGRALELSRERVRQIEAK 394

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A++KL+ P R  ++R +L+ 
Sbjct: 395 ALQKLRQPKRRNRVRDYLEA 414



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 8/103 (7%)

Query: 82  DLEDEEGSEDS--LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           DL+D  G  D+   +         +       SA+R T D VR+YL+E+G + LL R+ E
Sbjct: 21  DLQDNHGDIDNSVDEFVDPDIEEDIDTTSFAKSANRRTTDLVRLYLQEIGRVRLLRRDEE 80

Query: 140 IAIAKRIEAGRA----MMMASLCESPLT--FQALIIWRDELND 176
           ++ A++++            +  E P+   F  LI   D L  
Sbjct: 81  VSEAQKVQRYMRLLDLRAKFATPEEPVIEHFVHLIETHDRLAS 123


>gi|296121158|ref|YP_003628936.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013498|gb|ADG66737.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 577

 Score =  200 bits (508), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 134/404 (33%), Positives = 223/404 (55%), Gaps = 35/404 (8%)

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
           P  +  ++ + +  ++  +L   A+   ++     +  + + KL  L   LS+   R+  
Sbjct: 167 PHNLPTIERMLDENKQDFTLLRAAIGTPEEAVIRERMAIRRSKLATLCEELSVRTQRLQP 226

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           ++ ++  IS R+   + ++        +                              + 
Sbjct: 227 VMRRMEQISLRMTELQKQISARQIR-KMP--------------------MTAADVAAAEA 265

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   +  + ++               ++F+  +  V +     + +K+++   NLRLV+
Sbjct: 266 ELEGLIQDVQEL--------------PADFQKRIRRVLEKFGGWTRSKQQLSGGNLRLVV 311

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AKKY NRGL FLDLIQEGN GLM+  EK+++  GYKFSTYA WW++QAITR++AD + 
Sbjct: 312 SIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEFRRGYKFSTYATWWIRQAITRAVADHAR 371

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIRIPVHM   I  +   + ++  +  REPT EE+A  + M VE   +++K  K P+SL+
Sbjct: 372 TIRIPVHMFQSISTLKNKSEQIRQETGREPTIEELALAVDMSVEDTERIMKTWKHPMSLD 431

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIG+ + S  GDF+ED +  +P D+A++  LR+    VL SLT RE  ++R+R+G+G  
Sbjct: 432 TPIGESEDSSFGDFLEDSHESTPADNALREMLRDKIDIVLRSLTYREREIIRLRYGLGDG 491

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             +TLEE G+ F VTRERIRQIE+KA++KL+H +R+  L+ F++
Sbjct: 492 YSYTLEETGRIFKVTRERIRQIESKALKKLQHHTRAHHLQGFVE 535



 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 44/210 (20%), Positives = 86/210 (40%), Gaps = 13/210 (6%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D S  + ++++     RG++T  E++ ++P +      +++ +  L   G++ V+ +  
Sbjct: 1   MDQSQLALRELLNQGASRGFLTYAEIDRYIPDEGGDPALVDELIMALEAAGLDAVEPEGG 60

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            D   S   L++    SNSS             + DP+RMYL +MG I LL+RE EI +A
Sbjct: 61  IDPLQSLPPLEMLEPESNSS-------------SRDPIRMYLSQMGHIPLLTREREIYLA 107

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           K+IE  R      + ES    + ++    ++  G       +        +         
Sbjct: 108 KQIEMTRRWFRRRMLESDFAIRIVVDTVHKVRLGELPFERTLRTSDTESVQKDQILARMP 167

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESA 233
                 +R     +++   ++   G  E A
Sbjct: 168 HNLPTIERMLDENKQDFTLLRAAIGTPEEA 197


>gi|320353903|ref|YP_004195242.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320122405|gb|ADW17951.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 439

 Score =  200 bits (508), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 124/267 (46%), Positives = 181/267 (67%), Gaps = 1/267 (0%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           SI+        E   + + +         AK  M+ ANLRLV+S+AK+Y ++GL   DLI
Sbjct: 174 SIANRNYPDKRELFELSTKIEAYNRSIEFAKDSMIRANLRLVVSIAKRYMHQGLTLADLI 233

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GLM+A  +FD+  G KFSTYA WW++QAITR+I D++ TIR+PVH  +   +  +
Sbjct: 234 QEGNLGLMRAVFRFDYKKGNKFSTYASWWIRQAITRAILDKTRTIRLPVHFLELRSQFFK 293

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
               +  ++ REPTP EI+K   +P++ +  +L+ ++EPISLETP+  +D S LGDF+E+
Sbjct: 294 AFYSLLKELGREPTPVEISKMTDLPMDKILAILEASREPISLETPV-GDDDSTLGDFLEN 352

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           + + SP D+     L    T VL++LT REE+++R+RFGIG   ++TLEE+GK+F V+RE
Sbjct: 353 QESESPYDAVQNRELAHRVTEVLSTLTDREEKIIRLRFGIGEKAEYTLEEIGKRFNVSRE 412

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE KA+ +L+H SR +KLR FLD
Sbjct: 413 RIRQIEKKALNRLRHSSRREKLRFFLD 439



 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 26/147 (17%), Positives = 55/147 (37%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           +++  +  G +T + LN  LP        +E+    L    I +V  ++    +      
Sbjct: 9   LLEAGKDEGCITFQHLNELLPEQVKDPGAIEELFDFLGENNIEIVTQEESGKRKTLSGEE 68

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                +           DS +  +++    YLREMG  +LL+ E E   +K I  G   +
Sbjct: 69  WTGKKSGEEDNASDTLPDSEEHESEETTTTYLREMGQFDLLTPEEEAKYSKTIREGFDAI 128

Query: 154 MASLCESPLTFQALIIWRDELNDGTTL 180
           + ++ +       + +  D ++     
Sbjct: 129 IEAIRQDASGVAEIKMLVDRIDLWQRR 155


>gi|325857152|ref|ZP_08172442.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
 gi|325483215|gb|EGC86193.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
          Length = 327

 Score =  200 bits (508), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 108/317 (34%), Positives = 179/317 (56%), Gaps = 6/317 (1%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV--DSILKIRNEIKSISVETGIS 423
            + +F   +    L+    +          +  +   +       +   ++ I  E  IS
Sbjct: 13  NKVIFSRFYLFNSLNLCKFAVTLHNATHMRQLKITKSITNRESASLDKYLQEIGHEEMIS 72

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E   +   +RK       A + + +ANLR V+SVAK+Y N+GL   DLI EGN+GL+K
Sbjct: 73  IEEEVELAQRIRK---GDRKALERLTKANLRFVVSVAKQYQNQGLSLPDLINEGNLGLIK 129

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    ++K+ +   +   + 
Sbjct: 130 AAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSVNKINKILNQFEQEN 189

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +R P+  EIA+   +P E +   +K++   +S++ P  D+D S L D I + N  S    
Sbjct: 190 ERRPSIGEIAQSTDIPEEKIADAIKVSSRHVSVDAPFYDDDQSSLLDVIPNDNVPSTDRG 249

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            ++ +LRE   RVL  L  RE++V+   FGI    + TLEE+G ++ +TRER+RQI+ KA
Sbjct: 250 LVEESLREEIGRVLQVLEDREKKVVEAYFGINQ-REMTLEEIGSKYNLTRERVRQIKEKA 308

Query: 664 IRKLKHPSRSKKLRSFL 680
           IR+L+  + SK L+++L
Sbjct: 309 IRRLRQQTNSKVLKAYL 325



 Score = 41.4 bits (95), Expect = 0.55,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  E++S E E+ +A+RI  G    +  L ++ L F  ++    +  +    L +
Sbjct: 61  YLQEIGHEEMISIEEEVELAQRIRKGDRKALERLTKANLRF--VVSVAKQYQNQGLSLPD 118

Query: 184 IID 186
           +I+
Sbjct: 119 LIN 121


>gi|317968274|ref|ZP_07969664.1| putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 382

 Score =  200 bits (508), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 100/267 (37%), Positives = 173/267 (64%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           ++ +  + +SI+E +  +   R+       A+  M++ANLRLV++VAKKY  RG++ LDL
Sbjct: 113 EAWATLSELSIAELKQALHQGRR-------ARDRMIQANLRLVVAVAKKYQQRGMELLDL 165

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG +GL +A EK+D   G++FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++++ 
Sbjct: 166 VQEGTLGLERAVEKYDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEKLNRIK 225

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  R+++++  R  +  ++AK+L +  E +R  L      +SL+T +G +  + LGD +E
Sbjct: 226 KAQRQIASEHGRLASVADLAKELGLSEEVIRLTLMRVPRSVSLDTRVGRDQDTELGDLLE 285

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +A +P  +  +  L +    +L  L+ RE  V+R+RFG+  +T  TL ++G+   ++R
Sbjct: 286 DGHA-TPEQALTKTQLHDDLEALLEELSGREAEVIRLRFGLENDTPQTLSQIGEDLHLSR 344

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQIE +A+ KL+ P R  ++  +L
Sbjct: 345 ERVRQIETRALLKLRQPQRRCRVHDYL 371



 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/32 (40%), Positives = 24/32 (75%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           R + D VR+YL+++G ++LLS E E+ +A+ +
Sbjct: 16  RGSSDLVRLYLQDIGRVDLLSHEEELTLARLV 47


>gi|123965795|ref|YP_001010876.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9515]
 gi|123200161|gb|ABM71769.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9515]
          Length = 397

 Score =  200 bits (508), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  ++ M     R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 136 SVREWAELIDMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 195

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 196 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 255

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 256 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 314

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 315 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 374

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 375 IEAKALRKLRHPNRNGVLKEYI 396



 Score = 46.0 bits (107), Expect = 0.020,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 36/64 (56%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L+D+E  E++ + + S   +      +       T+D +R+YL+E+G I LL  + EI +
Sbjct: 51  LKDKEIIENNEEFSGSDEEAKALGNIKLGPKGIYTEDSIRVYLQEIGRIRLLRPDEEIEL 110

Query: 143 AKRI 146
           A++I
Sbjct: 111 ARKI 114


>gi|78185801|ref|YP_378235.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78170095|gb|ABB27192.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 377

 Score =  200 bits (508), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 118/351 (33%), Positives = 198/351 (56%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +      R++     LL+  +          E H+  EL     ++   +P  
Sbjct: 32  RVDLLTSEEEVTLARLVQRRETLLKQQRELSDTNQAIGELHRLEELQRREANHHSHWPTK 91

Query: 394 -EWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW    A  +  +  +I    ++ + +  I   E +  +            AK  M++A
Sbjct: 92  QEWARAAALTLQELQNRIDAGYEAWAEKAAIDAKELKLSLR-------NGRRAKDHMIQA 144

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q +TR+
Sbjct: 145 NLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGMTRA 204

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + VR+ L+   
Sbjct: 205 IATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTVRQTLERVP 264

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +SL++ +G +  + LGD IED  A +P ++     L      +L  LTPRE  VLR R
Sbjct: 265 RSVSLDSRVGKDQDTQLGDLIEDGKA-TPEETLTHDELHNDLEGLLDELTPREASVLRRR 323

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P +  K+R ++ G
Sbjct: 324 FGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQKRSKIRDYIQG 374



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 44/268 (16%), Positives = 96/268 (35%), Gaps = 28/268 (10%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           + +      T D +R+YL+++G ++LL+ E E+ +A+ ++                 + L
Sbjct: 10  ETRSRRSSGTADLLRLYLQDIGRVDLLTSEEEVTLARLVQRR---------------ETL 54

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           +  + EL+D    + E+  LE     E+       T+    +    + QE +       E
Sbjct: 55  LKQQRELSDTNQAIGELHRLEELQRREANHHSHWPTKQEWARAAALTLQELQNRIDAGYE 114

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
              E AA  +K+ +  +        N  R  D     +   + A+  + + + M  LD +
Sbjct: 115 AWAEKAAIDAKELKLSL-------RNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLV 167

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLL--VEQ 341
            E    L    +     +    S+       + +   +     ++ L     + L  +++
Sbjct: 168 QEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGMTRAIATQSRTIRLPVHVTEKLNRIKR 227

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDV 369
           +             +  LA+  GI  D 
Sbjct: 228 VQQEIASNEGRIASIADLARELGISEDT 255


>gi|237785656|ref|YP_002906361.1| RNA polymerase sigma factor SigB [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237758568|gb|ACR17818.1| RNA polymerase sigma factor B [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 326

 Score =  200 bits (508), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 108/248 (43%), Positives = 171/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 78  RDLKAVAKDGRAARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYT 137

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE
Sbjct: 138 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEE 197

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +    +  +LK +++P+SL+ P+G ++ + LGDFIED  A    ++ + +    
Sbjct: 198 LAEESGIDESKIDLLLKQSRDPVSLDMPVGTDEEAPLGDFIEDSEATDAEEAVVASLRHS 257

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VLA+L  RE+ V+R+RFG+      TL+++G++F ++RER+RQIE + + KL+   
Sbjct: 258 DIRTVLATLEKREQDVIRLRFGLDDGVPRTLDQIGREFGLSRERVRQIEREVMAKLRKGE 317

Query: 672 RSKKLRSF 679
           R+ KLRS+
Sbjct: 318 RADKLRSY 325



 Score = 41.0 bits (94), Expect = 0.68,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 32/54 (59%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           S+ +  +    +R ++ +  + D VR+YL  +G   LL+ E E+ +++RIEAG 
Sbjct: 7   STTTEVNGDPGRRANNNENPSADLVRVYLNGIGRTALLNAEDEVELSQRIEAGL 60


>gi|330466466|ref|YP_004404209.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
 gi|328809437|gb|AEB43609.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
          Length = 335

 Score =  200 bits (508), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 128/330 (38%), Positives = 199/330 (60%), Gaps = 1/330 (0%)

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
           M      + +    GI     L+    R +    V    +          A EV+   +I
Sbjct: 5   MMEHRTSVGIEAEPGIDTLTDLDATDERGVSTDLVRAYLNGIGRTKLLTAAQEVELAKRI 64

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
              + +    T  +      + + +     E   AK  ++EANLRLV+S+AK+YT RG+ 
Sbjct: 65  EAGLFAEEKLTTCTPVS-AQLQADLTLIAQEGQAAKNHLLEANLRLVVSIAKRYTGRGMA 123

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM +++
Sbjct: 124 FLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEQV 183

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +++VR  R +S  + REP+  EIA+ L +P   V +++   +EP+SL+  +G++  S LG
Sbjct: 184 NRMVRARRELSVSLGREPSVAEIARALDVPEFQVIELISYDREPVSLDQTVGEDGESALG 243

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DF+   +  S +D A +  LR   + VLA+L+ RE+ V+R+RFG+      TL+EVG++F
Sbjct: 244 DFVAAVDPSSMVDDADRGELRNEVSIVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREF 303

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            ++RERIRQIE   + KL+ P R+++L ++
Sbjct: 304 GLSRERIRQIEKVTLLKLRAPERAQRLEAY 333



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 23/54 (42%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +                  + D VR YL  +G  +LL+   E+ +AKRIEAG 
Sbjct: 15  EAEPGIDTLTDLDATDERGVSTDLVRAYLNGIGRTKLLTAAQEVELAKRIEAGL 68


>gi|123968088|ref|YP_001008946.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           AS9601]
 gi|123198198|gb|ABM69839.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. AS9601]
          Length = 394

 Score =  200 bits (508), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  ++ M     R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 133 SVREWAELIDMPLAKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 192

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 193 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 252

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 253 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 311

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 312 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 371

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 372 IEAKALRKLRHPNRNGVLKEYI 393



 Score = 42.5 bits (98), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           + S          +       T+D +R+YL+E+G I LL  + EI +A++I
Sbjct: 61  SDSEEEDKGLGNIKLGPKGIYTEDSIRVYLQEIGRIRLLRPDEEIELARKI 111


>gi|298490007|ref|YP_003720184.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231925|gb|ADI63061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 417

 Score =  200 bits (508), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 110/260 (42%), Positives = 174/260 (66%), Gaps = 2/260 (0%)

Query: 424 ISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +E   + V  +   + +   AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL 
Sbjct: 157 WAEIAKLKVEELENVQSQGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE 216

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +A EKFD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R++S +
Sbjct: 217 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKISQE 276

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R PT E++A +L M    VR+VL      +SLET +G +  + LG+ +E  ++++P +
Sbjct: 277 KGRTPTLEDLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDSITPEE 335

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++ +L++    +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+K
Sbjct: 336 MLMRESLQKDLHHLLADLTSRERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESK 395

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A++KL+ P R   +R +L+ 
Sbjct: 396 ALQKLRQPKRRNLIRDYLES 415



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 1/103 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             DL  ++G     DL      ++V       + +R + D VR+YL+E+G + LL R+ E
Sbjct: 22  EPDLGIDDGDFSLDDLQDLDIAAAVDSHNLAANTNRRSTDLVRLYLQEIGRVRLLGRDEE 81

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           ++ A++++     +   L  +      +I+    L +    L 
Sbjct: 82  VSEAQKVQRYLR-LRIVLANAAKQGDTVIVPYQRLIEVQERLS 123


>gi|307152414|ref|YP_003887798.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982642|gb|ADN14523.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 377

 Score =  200 bits (507), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 192/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  + + G+ +  F+  + + R+       AK +MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 118 KEWAQQVGMELPAFQRRLYLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDL 170

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 171 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 230

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 231 KTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 290

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 291 -ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 349

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 350 ERIRQIEAKALRKLRHPNRNSILKEYI 376



 Score = 41.4 bits (95), Expect = 0.50,   Method: Composition-based stats.
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 6/51 (11%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI------EAGRAMMMASLCESP 161
           T+D +R+YL+E+G I LL  E EI +A++I      E  R  +  +L   P
Sbjct: 65  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERLREKLRRNLGRYP 115


>gi|145295824|ref|YP_001138645.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum R]
 gi|12958494|gb|AAK09322.1|AF320818_1 sigma factor SigB [[Brevibacterium] flavum]
 gi|140845744|dbj|BAF54743.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 331

 Score =  200 bits (507), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 105/252 (41%), Positives = 171/252 (67%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   ++    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 78  RAMKRDLKVLAKDGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 137

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 138 FDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREA 197

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +
Sbjct: 198 TNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDAESAVVAS 257

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL +L PRE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL
Sbjct: 258 MRHSDIRAVLNTLEPREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMSKL 317

Query: 668 KHPSRSKKLRSF 679
           +   R+ +LR +
Sbjct: 318 RDGERASRLREY 329



 Score = 44.1 bits (102), Expect = 0.074,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 29/63 (46%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  S    ++         +R  + D  + D VR+YL  +G   LL+ E E+ +A+ IE
Sbjct: 1   MTAPSTQDLATTEREVDPGSRRGQTNDNPSQDLVRVYLNGIGKTALLTAEDEVELAQTIE 60

Query: 148 AGR 150
            G 
Sbjct: 61  VGL 63


>gi|86608944|ref|YP_477706.1| sigma-70 family RNA polymerase sigma factor [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557486|gb|ABD02443.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 320

 Score =  200 bits (507), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 111/271 (40%), Positives = 177/271 (65%), Gaps = 3/271 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ ++    ++  +   +  ++ +G      AK+E+V ANLRLV+S+AKKY NRG+ FLD
Sbjct: 47  LREMARYPLLNAEQEVKLGRLIAEGGAAGERAKRELVRANLRLVVSIAKKYLNRGVPFLD 106

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG IGL++AAEKF++  GYKFSTYA WW++Q ITR++A+Q   +RIPVHM +K+++V
Sbjct: 107 LIQEGTIGLIRAAEKFEYERGYKFSTYAYWWIRQGITRAVANQGRLVRIPVHMVEKLNQV 166

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK---ITKEPISLETPIGDEDTSHLG 589
            R  R ++  + R PT  EIA+ L +  + +  +L      ++ +SL TP+G E+   L 
Sbjct: 167 KRIRRELTETLNRRPTQAEIAEALEISPDKLDALLTLLEAGRQTLSLHTPVGKEEDRELM 226

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             IED N+++P        L      +L  L+PRE+ +L++R+G+     HTL E+G+ F
Sbjct: 227 QLIEDANSLTPESQMDLHLLSAQLEEMLEQLSPREQEILKLRYGLKDGHLHTLSEIGQLF 286

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++RER+RQI+A+A+RKL+HP R + L  ++
Sbjct: 287 GLSRERVRQIQARAMRKLRHPRRQEILADWM 317



 Score = 44.1 bits (102), Expect = 0.088,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 76/229 (33%), Gaps = 13/229 (5%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDE 173
           ++D V ++LREM    LL+ E E+ + + I  G          L  + L     I  +  
Sbjct: 39  SEDSVGVFLREMARYPLLNAEQEVKLGRLIAEGGAAGERAKRELVRANLRLVVSIAKKY- 97

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           LN G   L  I         E   G     E   Y++    S        Q     + + 
Sbjct: 98  LNRGVPFLDLI--------QEGTIGLIRAAEKFEYERGYKFSTYAYWWIRQGITRAVANQ 149

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            ++ +     V+   +         +           A   ++ P  + AL  + E  R+
Sbjct: 150 GRLVRIPVHMVEKLNQVKRIRRELTETLNRRPTQAEIAEALEISPDKLDALLTLLEAGRQ 209

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
             SL       +  E   +  +       +    L L  ++++ ++EQL
Sbjct: 210 TLSLHTPVGKEEDRELMQL-IEDANSLTPESQMDLHLLSAQLEEMLEQL 257


>gi|257464031|ref|ZP_05628416.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 436

 Score =  200 bits (507), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 142/271 (52%), Positives = 192/271 (70%), Gaps = 3/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I     ++  E   +    +K       A K ++EANLRLV+S+AKK+TNRGL
Sbjct: 166 IKMYLREIGQIPLLTHKEELELA---KKALEGDEFANKRLIEANLRLVVSIAKKHTNRGL 222

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + LDLIQEGNIGLMKA EKF++  GYKFSTYA WW++QAITR+IADQ  TIRIPVHM + 
Sbjct: 223 KLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 282

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ + AR    +  ++ TPE +A++L M VE V+ + ++ ++PISLETP+G E+ S L
Sbjct: 283 INKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGSEEDSEL 342

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF+ED+  ++P +   ++ LRE    VL SL+ REE+VLR R+G+   +  TLEEVGK 
Sbjct: 343 GDFVEDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEVGKI 402

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           F VTRERIRQIE KA+RKL+HPSR KKL  F
Sbjct: 403 FKVTRERIRQIEVKALRKLRHPSRRKKLEDF 433



 Score = 57.5 bits (137), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/104 (30%), Positives = 48/104 (46%), Gaps = 1/104 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +DL D+E   D+ DL           +  + S     D+P++MYLRE+G I LL+ + E+
Sbjct: 126 EDLLDKEEDFDASDLEELPEEELSNEELAELSNGMKVDEPIKMYLREIGQIPLLTHKEEL 185

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +AK+   G       L E+ L     I  +   N G  LL  I
Sbjct: 186 ELAKKALEGDEFANKRLIEANLRLVVSIAKK-HTNRGLKLLDLI 228


>gi|330955107|gb|EGH55367.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae Cit 7]
          Length = 216

 Score =  200 bits (507), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 149/215 (69%), Positives = 180/215 (83%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM 
Sbjct: 1   GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ S
Sbjct: 61  ETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDS 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           HLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRMRFGI MNTDHTLEEVG
Sbjct: 121 HLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVG 180

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           KQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 181 KQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 215


>gi|296327931|ref|ZP_06870466.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296154887|gb|EFG95669.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 418

 Score =  200 bits (507), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 143/303 (47%), Positives = 202/303 (66%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +P ++    +     E    +         I+  ++ I     ++  E        +K
Sbjct: 116 EFNPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYA---KK 172

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 173 AYEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 232

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 233 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 292

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 293 GMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 352

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 353 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 412

Query: 677 RSF 679
             F
Sbjct: 413 EDF 415



 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 49/208 (23%), Positives = 74/208 (35%), Gaps = 51/208 (24%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---DD 82
             ++  + +IK A + G +T EE+N  L  D   +E +E  +  +   GI +VD    D+
Sbjct: 5   IKNEKARALIKKAVEEGIITYEEINEELGDD-FPAENIEQLINEMLEQGIKIVDEEQLDE 63

Query: 83  LEDEEGSEDSLDLA------------------------------------SSASNSSVFL 106
           L ++E  E  L+                                          N     
Sbjct: 64  LGEDELREKELEDDYTDNEEHDDLLEDDSEDKIDENEDENDETEEHFTEFDDEFNPEYIE 123

Query: 107 QKRKDS----------ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
              +D                D+P++MYLRE+G + LL+ E EI  AK+   G       
Sbjct: 124 DVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYAKKAYEGDEEASKK 183

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREI 184
           L ES L     I  +   N G  LL  I
Sbjct: 184 LIESNLRLVVSIAKK-HTNRGLKLLDLI 210


>gi|51246355|ref|YP_066239.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50877392|emb|CAG37232.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 447

 Score =  200 bits (507), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 118/258 (45%), Positives = 179/258 (69%), Gaps = 1/258 (0%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E   + + +        +AK  M+ ANLRLV+S+AK+Y ++GL   DLIQEGN+GLM+
Sbjct: 191 IRELFELQAKLEAYSRSIEVAKDTMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMR 250

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  +FD+  G KFSTYA WW++QAITR+I D++ TIR+PVH  +   +  +    +  ++
Sbjct: 251 AVFRFDYTKGNKFSTYASWWIRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYALFKEL 310

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            REPTP EI+K   +P++ +  +L+ ++EPISLETP+  +D S LGDF+E++ + SP ++
Sbjct: 311 GREPTPLEISKTTNLPMDKILSILEASREPISLETPV-GDDDSTLGDFLENQESQSPYEA 369

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L    T +L++L+ REE+++R+RFGIG   ++TLEE+GK+F V+RERIRQIE KA
Sbjct: 370 VQNRELSGRVTEILSTLSDREEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEKKA 429

Query: 664 IRKLKHPSRSKKLRSFLD 681
           + +L+H SR  KL+ F+D
Sbjct: 430 LNRLRHSSRRDKLKFFVD 447



 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/166 (18%), Positives = 62/166 (37%), Gaps = 10/166 (6%)

Query: 22  LVFDFSDDSWK-KMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV-- 78
           +         K K+++  ++ G ++ + LN  +P D      +E     L   GI +V  
Sbjct: 1   MELSLVQTELKEKLLETGKKEGCISFDALNKLIPDDVKDPTAIEKIFNFLGAHGIEIVTI 60

Query: 79  ----DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
               +   L  E   +  +DL     + +      +      T      YLREMG  +LL
Sbjct: 61  EKSGEKRTLSGEIWEKSEVDLELEIEDGAALSGDEESHESEETTT---TYLREMGRFDLL 117

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + E E   +K I  G   ++ ++       Q +++  + ++     
Sbjct: 118 TPEEEAKYSKTIRQGFEAIIFAIRGDRSGVQEMVVLCERIDLWEKR 163


>gi|148240795|ref|YP_001226182.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849334|emb|CAK24885.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 376

 Score =  200 bits (507), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 119/350 (34%), Positives = 196/350 (56%), Gaps = 8/350 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +      R +     LL   +    +           EL     ++   +P  
Sbjct: 31  RVDLLTSEEEVTLSRQVQQRERLLVQERDLSTRIAAIRVLLDLEELQQREANHISHWPTR 90

Query: 394 -EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            EW       +  + ++ NE  ++      S  E + +    ++   E   A+  M++AN
Sbjct: 91  QEWARAAEMPLVELNRVLNEGYTL--WAEESGLEAKEL----QRRLREGRRARDRMIQAN 144

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+I
Sbjct: 145 LRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRAI 204

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A QS TIR+PVH+ +K++++ R  + ++++  R  +  ++AK+L +  + VR+ L     
Sbjct: 205 ATQSRTIRLPVHITEKLNRIKRVQQEIASEQGRLASVSDLAKELGVSEDTVRQTLARVPR 264

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SLET +G +  + LGD +ED +A +P  +  +  L +    +L  L PRE  V+R RF
Sbjct: 265 SVSLETRVGKDQDTQLGDLLEDGHA-TPEQTLTRDALHDDLEHLLDELNPREAEVIRSRF 323

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +T  TL E+G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 324 GLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQPQRRSKVRDYIQG 373



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 94/251 (37%), Gaps = 22/251 (8%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           +D +R+YL+++G ++LL+ E E+ ++++++                   L++   +L+  
Sbjct: 19  NDLLRLYLQDIGRVDLLTSEEEVTLSRQVQQRER---------------LLVQERDLSTR 63

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
              +R ++DLE     E+       T     +  E    E  R   +      E +   +
Sbjct: 64  IAAIRVLLDLEELQQREANHISHWPTRQEWARAAEMPLVELNRVLNEGYTLWAEESGLEA 123

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           K+ + ++       +   +        +   + A+  + + + M  LD + E    L   
Sbjct: 124 KELQRRLREGRRARDRMIQA-------NLRLVVAVAKKYQQRGMELLDLVQEGTLGLERA 176

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            +     +    S+     +++ + + + + S        + E+L  I +       E  
Sbjct: 177 VEKFDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNRIKRVQQEIASEQG 236

Query: 358 RLAQSYGIKRD 368
           RLA    + ++
Sbjct: 237 RLASVSDLAKE 247


>gi|38233998|ref|NP_939765.1| RNA polymerase sigma factor SigB [Corynebacterium diphtheriae NCTC
           13129]
 gi|38605711|sp|P33118|RPSB_CORDI RecName: Full=RNA polymerase sigma factor sigB
 gi|38200260|emb|CAE49944.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 329

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 107/252 (42%), Positives = 174/252 (69%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 76  RAMKRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE 
Sbjct: 136 FDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +
Sbjct: 196 TNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDAESAVVAS 255

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL +L  RE+ V+R+R+G+      TL+++G+QF ++RER+RQIE + + KL
Sbjct: 256 LRHSDIRTVLDTLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMSKL 315

Query: 668 KHPSRSKKLRSF 679
           +  +R++KLR++
Sbjct: 316 RDGARAEKLRAY 327



 Score = 41.7 bits (96), Expect = 0.36,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 29/56 (51%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              +++ +     +R  + D  + D VR+YL  +G   LL+ E E+ +A+ IE G 
Sbjct: 6   DVEASTETVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLNAEDEVELAQTIEVGL 61


>gi|218661052|ref|ZP_03516982.1| RNA polymerase sigma factor RpoD [Rhizobium etli IE4771]
          Length = 276

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 132/290 (45%), Positives = 172/290 (59%), Gaps = 25/290 (8%)

Query: 1   MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
           M    K N D++ E + + D  + D SDD+ KKMIK A++RGYVT++ELNA LP +EV+S
Sbjct: 1   MATKVKENEDAEVERDGASDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTS 60

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL-----------ASSASNSSVFLQKR 109
           EQ+EDT++MLS+MGINV++ ++ E+   S    D              + S  +     +
Sbjct: 61  EQIEDTMSMLSDMGINVIEDEEAEEAGASGGGDDDDAGGDEDSEGGELAPSGGTALATAK 120

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALII
Sbjct: 121 KKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALII 180

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
           WRDELN+GTTLLREIIDLE                   +Q  E    +++  + +E    
Sbjct: 181 WRDELNEGTTLLREIIDLETTYS------GPEAKAAPQFQSPEKIEADRKAAEEKEKTRR 234

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             S      D   +   P           +EDED+S  +L+AME +LRP+
Sbjct: 235 ARSGDDDITDVGGEGLPP--------EEEEEDEDESNLSLAAMEAELRPQ 276


>gi|1173127|sp|P43344|RPOD_SERMA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
          Length = 215

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 152/214 (71%), Positives = 179/214 (83%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           LQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 1   LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 61  TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 121 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREXKVLRMRFGIDMNTDHTLEEVGK 180

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 181 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 214


>gi|260436706|ref|ZP_05790676.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260414580|gb|EEX07876.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 377

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 118/351 (33%), Positives = 193/351 (54%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R+DLL  +      R++     LL   +          E H+  EL     +    +P  
Sbjct: 32  RVDLLTNEEEVTLARLVQRREALLLQQRELAESDAAIGELHRLEELQRREANQHSHWPTK 91

Query: 394 -EWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  +I    ++ + +  +   + +  +            AK  M++A
Sbjct: 92  QEWARAAGLPLPDLQQRIELGYQAWAEQAQLEAKDVKLALR-------NGRRAKDHMIQA 144

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+
Sbjct: 145 NLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRA 204

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + VR+ L    
Sbjct: 205 IATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTVRQTLARVP 264

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +SL+T +G E  + LGD IED +A +P  +     L      +L  LT RE  VLR R
Sbjct: 265 RSVSLDTRVGREQDTQLGDLIEDGHA-TPEQTLTHDELHNDLEDLLDELTSREAAVLRRR 323

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 324 FGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQRRSKVRDYIQG 374



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 93/259 (35%), Gaps = 28/259 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T D +R+YL+++G ++LL+ E E+ +A+ ++                 +AL++ + EL +
Sbjct: 19  TTDLLRLYLQDIGRVDLLTNEEEVTLARLVQRR---------------EALLLQQRELAE 63

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               + E+  LE     E+       T+    +       + ++      +   E A   
Sbjct: 64  SDAAIGELHRLEELQRREANQHSHWPTKQEWARAAGLPLPDLQQRIELGYQAWAEQAQLE 123

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +KD +  +        N  R  D     +   + A+  + + + M  LD + E    L  
Sbjct: 124 AKDVKLAL-------RNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLER 176

Query: 297 LQDNAVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLL--VEQLYDISKRIM 350
             +     +    S+       + +   +     ++ L     + L  ++++        
Sbjct: 177 AVEKFDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASNE 236

Query: 351 HNEGELLRLAQSYGIKRDV 369
                +  LA+  GI  D 
Sbjct: 237 GRIASIADLARELGISEDT 255


>gi|319948428|ref|ZP_08022566.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
 gi|319437910|gb|EFV92892.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
          Length = 322

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 109/246 (44%), Positives = 174/246 (70%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+  G
Sbjct: 75  LKTIVAEGEAARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKG 134

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE T EE+A
Sbjct: 135 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATLEELA 194

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++  +P   + ++L  +++P+SL+ P+G ++ + LGDFIED  A S  ++ +   +    
Sbjct: 195 EESGIPAHKIEELLDHSRDPVSLDMPVGADEEAPLGDFIEDAEATSAENTVVSNVMHSDV 254

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VLA+L  RE++V+ +RFG+      TL+++GK+F ++RER+RQIE + + KL+   R+
Sbjct: 255 RAVLATLEEREQQVITLRFGLDDGQPRTLDQIGKRFGLSRERVRQIEREVMAKLREGRRA 314

Query: 674 KKLRSF 679
            KLRS+
Sbjct: 315 DKLRSY 320



 Score = 42.1 bits (97), Expect = 0.28,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +        + D VR+YL  +G   LL+ E E+ ++KRIEAG 
Sbjct: 12  TEADPEGQSPSADLVRVYLNGIGKTALLNAEDEVELSKRIEAGL 55


>gi|186686393|ref|YP_001869589.1| RNA polymerase sigma factor RpoD [Nostoc punctiforme PCC 73102]
 gi|8118663|gb|AAF73062.1|AF265349_1 primary vegetative sigma factor [Nostoc punctiforme]
 gi|186468845|gb|ACC84646.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 389

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 134/246 (54%), Positives = 181/246 (73%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R        AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GY
Sbjct: 144 RYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 203

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA 
Sbjct: 204 KFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIAT 263

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE   
Sbjct: 264 RMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLE 322

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +VL SL+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+ 
Sbjct: 323 KVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS 382

Query: 675 KLRSFL 680
            L+ ++
Sbjct: 383 VLKEYI 388



 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           +DE     S +  + +  ++   ++ +      T+D +R+YL+E+G I LL  + EI +A
Sbjct: 44  DDEFLEPQSDEDDAKSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELA 103

Query: 144 KRIEA--GRAMMMASLCE 159
           ++I        +   L E
Sbjct: 104 RKIADLLELERVRERLSE 121


>gi|270487764|ref|ZP_06204838.1| sigma-70, region 4 [Yersinia pestis KIM D27]
 gi|270336268|gb|EFA47045.1| sigma-70, region 4 [Yersinia pestis KIM D27]
          Length = 215

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 151/214 (70%), Positives = 179/214 (83%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +QFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM +
Sbjct: 1   MQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SH
Sbjct: 61  TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGK
Sbjct: 121 LGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGK 180

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 181 QFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 214


>gi|156742920|ref|YP_001433049.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234248|gb|ABU59031.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 348

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 125/329 (37%), Positives = 195/329 (59%), Gaps = 25/329 (7%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E D   V+  ++      +  +  +  ++  I++ ++ I     ++ +E   +   + +
Sbjct: 21  NEDDTAPVTDIEEMTAETLEETLEPDS-TLDSIQHYLQEIGRVPLLTAAEEIELAERMER 79

Query: 437 ------------------------GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
                                       A  A++ +++ANLRLV+S+AKKY  RGL  LD
Sbjct: 80  GAAAERRLASGEDLSPQLRQALLADVAAAQEARRHLIQANLRLVVSIAKKYVGRGLSLLD 139

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLM+A EKFD+  G +FSTYA WW++QA+TR+IA+Q  TIR+PVHM + + +V
Sbjct: 140 LIQEGNIGLMRAVEKFDYHKGNRFSTYATWWIRQAVTRAIAEQGRTIRLPVHMSESVGQV 199

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            RTA R++  ++R+PTPEEIA  L  P E + +VL+ ++ P+SLETP+G++    LGDF+
Sbjct: 200 KRTADRLAQALERQPTPEEIATALGQPTERIERVLEASRRPVSLETPVGEDGEHTLGDFL 259

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           +D    +P+++A Q  LR      L  L  RE R++ +R+G+      TLEEVG+   +T
Sbjct: 260 QDSELPTPVEAASQQLLRRDLAAALDRLNERERRIIDLRYGLVDGQRRTLEEVGRVLGMT 319

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER RQIEA+A+R+L+ P     LR +L+
Sbjct: 320 RERARQIEAEALRRLRAPDVGLHLRDYLE 348



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D  D   E  +ED     +     +    +     D ST D ++ YL+E+G + LL+   
Sbjct: 11  DELDERQEIVNEDDTAPVTDIEEMTAETLEETLEPD-STLDSIQHYLQEIGRVPLLTAAE 69

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           EI +A+R+E G A          L+ Q       ++       R +I
Sbjct: 70  EIELAERMERGAAAERRLASGEDLSPQLRQALLADVAAAQEARRHLI 116


>gi|172035791|ref|YP_001802292.1| RNA polymerase sigma factor RpoD [Cyanothece sp. ATCC 51142]
 gi|171697245|gb|ACB50226.1| group 1 sigma-70 RNA polymerase sigma factor A [Cyanothece sp. ATCC
           51142]
          Length = 416

 Score =  199 bits (506), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 197/320 (61%), Gaps = 7/320 (2%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD------SILKIRNEIKSISVET 420
           R+   E       D  W      +   E         D       +  +  +   IS   
Sbjct: 97  REALWEELDQEPTDEQWGKRIFQWENIEQMLRAQSAKDKDPKWSEVTTMLQQADIISDLE 156

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
                E +  +   ++       AK +MV +NLRLV+S+AKKY NRGL F DLIQEG++G
Sbjct: 157 KTWKLESKAYLPKFKRRLYLGRKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 216

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S
Sbjct: 217 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLS 276

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P
Sbjct: 277 QEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETP 335

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 336 EDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 395

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           AKA+RKL+HP+R+  L+ ++
Sbjct: 396 AKALRKLRHPNRNSILKEYI 415



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 2/66 (3%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIELLSREGEI 140
            ED E S + +    +     +   +R+D + +   T+D +R+YL+E+G I LL  E EI
Sbjct: 22  DEDIESSGNDIAETETKKTRKISASRRRDPSKKKPYTEDSIRVYLQEIGRIRLLRAEEEI 81

Query: 141 AIAKRI 146
            +A++I
Sbjct: 82  ELARKI 87


>gi|218439766|ref|YP_002378095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172494|gb|ACK71227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 418

 Score =  199 bits (505), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 119/290 (41%), Positives = 175/290 (60%), Gaps = 9/290 (3%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVE-TGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           +W +     V  + +I NE K       G+ + E   I             AK  M++AN
Sbjct: 135 KWADAAEVSVFEVKQILNEGKRHWANLAGLKVQELEQIQK-------AGIEAKNHMIKAN 187

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+SVAK+Y NRGL+ LDLIQEG +GL +A EKFD   GY+FSTYA WW++Q ITR+I
Sbjct: 188 LRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAI 247

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A QS  IR+PVH+ +K++K+ +  R+M+    R PT EE+A ++ M    +R+VL     
Sbjct: 248 ATQSRIIRLPVHITEKLNKIKKAQRKMAQIKGRTPTMEELAVEVDMTAPQIREVLMRVPR 307

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SLE  +G E  + L D +E   A SP +S +   LR+    +LA LT RE  V++MR+
Sbjct: 308 SVSLEIKVGKEKDTELVDLLETTEA-SPEESLVNETLRQDLQNLLADLTTREREVIQMRY 366

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G      ++L ++G+   ++RER+RQIEAKAI+KL+ P R  ++R + + 
Sbjct: 367 GFKDGKCYSLADIGRALQLSRERVRQIEAKAIQKLRQPKRRNQIRDYFEA 416



 Score = 45.2 bits (105), Expect = 0.036,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 31/66 (46%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   E   +    A  +   +     +  RST D VR+YL+++G + LL ++ E+  A+ 
Sbjct: 29  EMAIEIEENPLLEADFTETEITPSSPTQTRSTTDLVRLYLQDIGRVPLLKKDEEVQNAQE 88

Query: 146 IEAGRA 151
           ++    
Sbjct: 89  LQRYMQ 94


>gi|87123422|ref|ZP_01079273.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86169142|gb|EAQ70398.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 376

 Score =  199 bits (505), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 123/350 (35%), Positives = 193/350 (55%), Gaps = 8/350 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           R++LL  +   +  R +    +LLR  +       V     +  EL     ++   +P  
Sbjct: 31  RVNLLSNEEEVLLARQVQRREQLLRQERELAEAHPVLRRLLELEELQQREANHHCHWPTR 90

Query: 394 -EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            EW       V  +  I NE       + +   E   + + +R    +   A+  M+ AN
Sbjct: 91  QEWARAAGMSVAELQTILNE--GYGTWSRLIELEPCTLKAQLR----DGRRARDRMIAAN 144

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV++VAKKY  RGL+ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q ITR+I
Sbjct: 145 LRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGITRAI 204

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A QS TIR+PVH+ +K++++ R  + ++++  R  T  ++A+KL +  E VR  L     
Sbjct: 205 ATQSRTIRLPVHVTEKLNRIKRVQQEIASQEGRIATLTDLAQKLGLSEETVRLTLMRVPR 264

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SLE  +G E  + LGD +ED  A +P     +  L      +L  LT RE  V+R+RF
Sbjct: 265 SVSLELRVGKEQDTQLGDLLEDGKA-TPEQELTRDALHHDLEHLLDELTDREAAVIRLRF 323

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G+  +T  TL ++G+   ++RER+RQIE +A+ KL+ P R  K+R ++ G
Sbjct: 324 GLDNDTPCTLAQIGETMALSRERVRQIETRALLKLRQPQRRCKVRDYIQG 373



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 30/55 (54%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +S        S   + +D +R+YL+++G + LLS E E+ +A++++    ++   
Sbjct: 3   TSERSTGVSRSRAGAGNDLLRLYLQDIGRVNLLSNEEEVLLARQVQRREQLLRQE 57


>gi|186681474|ref|YP_001864670.1| RNA polymerase sigma factor SigC [Nostoc punctiforme PCC 73102]
 gi|186463926|gb|ACC79727.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 416

 Score =  199 bits (505), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 121/338 (35%), Positives = 197/338 (58%), Gaps = 10/338 (2%)

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +++       + LA +  +  +V +   +  E+     S     P  E     A  V S 
Sbjct: 85  QKVQRYLRMRIVLANAAKLGDEVIIPYLRLVEVQERLTSELGHRPSLERWAATADIVLSD 144

Query: 407 LK--IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           L+  + N  +  +    +++ E   + S           AK+ M++ANLRLV+SVAKKY 
Sbjct: 145 LRPTLANGKRRWAEIAKLTVEELEQVQSQ-------GLQAKEHMIKANLRLVVSVAKKYQ 197

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL+ LDL+QEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH
Sbjct: 198 NRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVH 257

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +K++K+ +  R+++ +  R PT E++A +L M    VR+VL      +SLET +G + 
Sbjct: 258 ITEKLNKIKKAQRKIAQEKGRTPTLEDLATELEMTPTQVREVLLRVPRSVSLETKVGKDK 317

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            + LG+ +E  + V+P +  ++ +L+     +L+ LT RE  V+ MRFG+     ++L E
Sbjct: 318 DTELGELLE-TDCVTPEEMLMRESLQRDLHHLLSDLTSRERDVILMRFGLADGHPYSLAE 376

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +G+   ++RER+RQIE+KA++KL+ P R   +R +L+ 
Sbjct: 377 IGRALDLSRERVRQIESKALQKLRQPKRRNLIRDYLES 414



 Score = 51.4 bits (121), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 1/102 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D     + SE S+D       +SV       S +R + D VR+YL+E+G + LL R+ E+
Sbjct: 22  DSDLTVDESELSVDDLQELEIASVDNANFAASTNRRSTDLVRLYLQEIGRVRLLGRDEEV 81

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           + A++++     M   L  +      +II    L +    L 
Sbjct: 82  SEAQKVQRYLR-MRIVLANAAKLGDEVIIPYLRLVEVQERLT 122


>gi|158335266|ref|YP_001516438.1| RNA polymerase sigma factor SigC [Acaryochloris marina MBIC11017]
 gi|158305507|gb|ABW27124.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  199 bits (505), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 115/267 (43%), Positives = 177/267 (66%), Gaps = 8/267 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
            + +  +S +E   IV            AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQ
Sbjct: 163 WAEKAELSNAELDQIVKQ-------GIKAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQ 215

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ + 
Sbjct: 216 EGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKA 275

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R++S    R  + E+IA+++ M  E +R++L      +SLE  +G +  + LGD +E  
Sbjct: 276 QRKLSQSKGRTASIEDIAQEMDMTPEQIRELLVRVPRSVSLEIKVGKDKDTELGDLLETD 335

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           + +SP +  ++ +L++   ++LA LTPRE  V+ MRFG+     H+L ++GK   ++RER
Sbjct: 336 D-ISPEELIMRESLQQELKQLLADLTPRERDVITMRFGLNDGKTHSLAQIGKSLDLSRER 394

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +RQIE+KA++KL+ P R  ++R FL+ 
Sbjct: 395 VRQIESKALQKLRQPKRRNRIRDFLEA 421



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 48/300 (16%), Positives = 108/300 (36%), Gaps = 22/300 (7%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +  E E      LD  +S   +++ +     +  R T D VR+YL+E+G + LL R+ E
Sbjct: 29  NEPEEVEFDPNADLDDDASEDLAALKMTPISAANRRGTTDLVRLYLQEIGRVSLLERDEE 88

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           +A A++++    ++         T +  +     +      L ++ D    +        
Sbjct: 89  VAEAQKVQRYMHLL--------ETREEFLESH-PVIAEYARLTDVRDRLTAM-------L 132

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
            H    + + K  D      +  + E +      A++S  +  ++      A+       
Sbjct: 133 GHRPSFNRWAKEADIPVADLKPRLAEGKTAWAEKAELSNAELDQIVKQGIKAKEHMIQA- 191

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
                +   + ++  + + + +  LD I E    L    +     +    S+     +++
Sbjct: 192 -----NLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQ 246

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            + + + + S        + E+L  I K          R A    I +++ +   Q REL
Sbjct: 247 GITRAIATQSRTIRLPVHITEKLNKIKKAQRKLSQSKGRTASIEDIAQEMDMTPEQIREL 306


>gi|168009782|ref|XP_001757584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691278|gb|EDQ77641.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 583

 Score =  199 bits (505), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 119/280 (42%), Positives = 176/280 (62%), Gaps = 5/280 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVA 460
            + KIR E++   +    ++SE+   VS+    +     E   AK ++V +NLRLV+S+ 
Sbjct: 301 KLEKIRAELQR-DIGREPTLSEWSQAVSLDQTSLELRVKEGRSAKDKLVNSNLRLVVSIV 359

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K Y  RG+   DLIQEG++GL++ AEKFD  +GYKFSTYA WW++QA+TR+IADQS  IR
Sbjct: 360 KNYQGRGMTLPDLIQEGSLGLIRGAEKFDPEMGYKFSTYATWWIRQAVTRAIADQSRIIR 419

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVH+ + I ++ +    +S ++ R+P  EE+A  + M VE +  ++K  + P S++ PI
Sbjct: 420 LPVHIYEVISRINKAKMTISQELGRQPRDEEVAAMVGMSVEKLLFIVKSARPPTSMDRPI 479

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +    LG+ + DK   SP D  +   L++    VL SL P E  VLR+RFG+      
Sbjct: 480 GKDGEQSLGEMVADKGVGSPEDDIMTQVLKQDIEDVLRSLNPMEREVLRLRFGLSGAQSM 539

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL+++G  F VTRERIRQIEAKA+RKL+HPS    L+  +
Sbjct: 540 TLKDLGIIFKVTRERIRQIEAKALRKLRHPSWKTLLQDHV 579



 Score = 40.6 bits (93), Expect = 0.92,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 35/59 (59%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           E +   AS+ +++    + +K    R+  DP+R YLR++   +LLS   E+A++++I+ 
Sbjct: 240 EKAEKTASALASAPPVPKPKKLQIMRTPSDPIRSYLRDIKRTKLLSASEEVALSRKIQD 298


>gi|33861053|ref|NP_892614.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|33639785|emb|CAE18955.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus subsp. pastoris str. CCMP1986]
          Length = 396

 Score =  199 bits (505), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 5/262 (1%)

Query: 423 SISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           S+ E+  +    +S  R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 135 SVREWAELTDMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 194

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + 
Sbjct: 195 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 254

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +S +  R+P+ EEIA+ + M +E +R + K  + PISLETPIG E+ S LGDFIE  +  
Sbjct: 255 LSQEFGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADIE 313

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P     +  LRE    VLA+L+PRE  VLR+R+GI      TLEE+G+ F VTRERIRQ
Sbjct: 314 NPEQDVSKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQ 373

Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
           IEAKA+RKL+HP+R+  L+ ++
Sbjct: 374 IEAKALRKLRHPNRNGVLKEYI 395



 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 32/67 (47%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
              L DE   E+  +   S   +      +       T+D +R+YL+E+G I LL  + E
Sbjct: 47  QKPLNDEGSIENKDEFNGSDEEAKAIGNVKLGPKGIYTEDSIRVYLQEIGRIRLLRPDEE 106

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 107 IELARKI 113


>gi|22298042|ref|NP_681289.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
 gi|22294220|dbj|BAC08051.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 375

 Score =  199 bits (505), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 107/292 (36%), Positives = 183/292 (62%), Gaps = 9/292 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKS-ISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
              +W   +   V  +       +   +    I++SE +HI             AK +++
Sbjct: 89  SRAQWAAGLKMSVAELQTCVQAGRQAWAKAANITLSELQHIERQ-------GQRAKNQLL 141

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +ANLRLV+++AKKY + G++FLDLIQEG++GL +A EKFD   G++FSTYA WW++Q+IT
Sbjct: 142 QANLRLVVNIAKKYQHHGVEFLDLIQEGSLGLERAVEKFDPTKGFRFSTYAYWWIRQSIT 201

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R++A QS TIR+P+HM +K++K+ R  RR++ +    P+  +IA++L + V  VR+VL  
Sbjct: 202 RAVASQSRTIRLPIHMVEKLNKIKRAQRRLAAQRGAMPSLADIAQELNLEVSQVRQVLMA 261

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
             + ++LE  +G +  + L + IE   A +P +  ++ +LR T  ++L+ L+PRE +V+ 
Sbjct: 262 VPKSVALEQRVGSDQETELQELIESP-APTPDEVIMRESLRTTLKQLLSDLSPRERQVME 320

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +R+G+G      L EV     ++RERIRQIE +A++KL+ P R ++++ +L+
Sbjct: 321 LRYGLGEQPALELAEVAVLLGLSRERIRQIEHRALQKLRQPQRRREIQDYLE 372



 Score = 45.2 bits (105), Expect = 0.037,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           V +  +  S    T D VR YL+E+G + LL+   E+ +A++++  +
Sbjct: 7   VAIPIQPLSERPLTTDLVRQYLQEIGRVPLLTPSEELRLAEQVQQYQ 53


>gi|119489756|ref|ZP_01622514.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454330|gb|EAW35480.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 391

 Score =  199 bits (505), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 138/280 (49%), Positives = 192/280 (68%), Gaps = 6/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMV----RKGECEASIAKKEMVEANLRLVISVA 460
            + +IR ++   +        E+   V M     R+       AK +MV++NLRLV+S+A
Sbjct: 113 ELERIREKLVEHN-HCEPEDREWASAVDMALPEFRRRLYLGRRAKDKMVQSNLRLVVSIA 171

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR
Sbjct: 172 KKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIR 231

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPI
Sbjct: 232 LPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI 291

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      
Sbjct: 292 GKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMK 350

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 351 TLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 390



 Score = 44.4 bits (103), Expect = 0.063,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 45/89 (50%), Gaps = 4/89 (4%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIELL 134
           +++ DD ++E+  E   +    + +  V   +R+  A +   T+D +R+YL+E+G I LL
Sbjct: 37  LIEDDDSQEEDYVESQSEEEDESKSEGVAKSRRRTQAKKKHYTEDSIRLYLQEIGRIRLL 96

Query: 135 SREGEIAIAKRIEA--GRAMMMASLCESP 161
             + EI +A+RI        +   L E  
Sbjct: 97  RADEEIELARRIADLLELERIREKLVEHN 125


>gi|302344687|ref|YP_003809216.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301641300|gb|ADK86622.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 363

 Score =  199 bits (505), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 119/277 (42%), Positives = 176/277 (63%), Gaps = 1/277 (0%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D + + ++++       G    +   +V  + +   E   A  EMVEANLRL +S+AKKY
Sbjct: 86  DVMAEAKDQVSRCCRRLGEKKVDVEQLVRDINRARREVEAAVSEMVEANLRLAVSIAKKY 145

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           T RGL F DLIQEGNIGLMKA  ++D+  GY+FST+A WW++Q I+R+I DQ+ TIRIP+
Sbjct: 146 TFRGLSFADLIQEGNIGLMKAVNRYDYRTGYRFSTFASWWIRQTISRAIYDQARTIRIPI 205

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ +   K  R    +  ++ REPTP+E+A+K+ +  + V++++ +T +  SLETP+  E
Sbjct: 206 HLLELRSKYFRVYYGLLKELGREPTPKEVAEKVGITEDKVKEIINLTLDSTSLETPV-GE 264

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   LGDFIE+K+A  P     +  +       L SL  RE R+L MRFG+G   +HTLE
Sbjct: 265 DGDELGDFIENKDAEDPFSMVGETEMHGHLEAALDSLDGRERRILEMRFGLGDEDEHTLE 324

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EVG+ F ++RER+RQIE KA+++L+HP     L   +
Sbjct: 325 EVGQVFGLSRERVRQIEKKALQRLRHPQWRTILEDHV 361


>gi|237744142|ref|ZP_04574623.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
 gi|229431371|gb|EEO41583.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
          Length = 417

 Score =  199 bits (505), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 141/301 (46%), Positives = 199/301 (66%), Gaps = 4/301 (1%)

Query: 380 DPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +P ++    +     E    +         I+  ++ I     ++  E            
Sbjct: 117 NPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRA---Y 173

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFST
Sbjct: 174 EGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFST 233

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L M
Sbjct: 234 YATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERLGM 293

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    VL 
Sbjct: 294 EVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAVLK 353

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  
Sbjct: 354 TLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKLED 413

Query: 679 F 679
           F
Sbjct: 414 F 414



 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 49/206 (23%), Positives = 75/206 (36%), Gaps = 49/206 (23%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL-- 83
             ++  + +IK A + G +T EE+N  L  D   +E +E  +  +   GI +VD + L  
Sbjct: 6   IKNEKARALIKKAVEEGIITYEEINEELGDD-FPAENIEQLINEMLEQGIKIVDEEQLDE 64

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSA---------------------------- 113
             EDE   ++S +  +        L+   D                              
Sbjct: 65  LGEDELKGKNSEEDYTDNEEHDDLLEDETDEKLDTDEENEETETFTEFDDEFNPEYIEDV 124

Query: 114 ---------------DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                              D+P++MYLRE+G + LL+ + EI  AKR   G       L 
Sbjct: 125 SEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYEGDEEASKKLI 184

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI 184
           ES L     I  +   N G  LL  I
Sbjct: 185 ESNLRLVVSIAKK-HTNRGLKLLDLI 209


>gi|332709863|ref|ZP_08429819.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
 gi|332351234|gb|EGJ30818.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
          Length = 417

 Score =  199 bits (505), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 117/262 (44%), Positives = 175/262 (66%), Gaps = 2/262 (0%)

Query: 422 ISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           +  +E   +    + + + E   AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +G
Sbjct: 155 LRWAELAELTSKELEQVQAEGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLG 214

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L +A EKFD   GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S
Sbjct: 215 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKIS 274

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +  R  T ++IA +L M    VR+VL      +SLE  +G E  + LGD +E +   SP
Sbjct: 275 QERGRTATIDDIAVELEMTAAQVREVLLRVPRSVSLEIKVGKERDTELGDLLETEET-SP 333

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +  ++  L+    ++LA LT RE  V+RMRFG+G N  ++L E+G+   ++RER+RQIE
Sbjct: 334 EEVLMREALQRDLQQLLADLTNRERDVIRMRFGLGDNQPYSLAEIGRALDLSRERVRQIE 393

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA++KL+ P R  ++R +L+ 
Sbjct: 394 AKALQKLRQPKRRNRVRDYLEA 415



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 34/68 (50%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E S+D                 ++ R T D VR+YL+E+G + LL R+ E++ A+++
Sbjct: 28  DDGEGSVDDLVDVEIEGADAASLTKNSTRRTTDLVRLYLQEIGRVRLLRRDEEVSEAQKV 87

Query: 147 EAGRAMMM 154
           +    ++ 
Sbjct: 88  QRYMKLLR 95


>gi|284991968|ref|YP_003410522.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284065213|gb|ADB76151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 327

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 114/251 (45%), Positives = 175/251 (69%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +    +    +   AK+ ++EANLRLV+SVAK+YT  G+ FLDLIQEGN+GL++A EKFD
Sbjct: 76  LQRDYKALAADGKAAKRHLLEANLRLVVSVAKRYTGHGMTFLDLIQEGNVGLIRAVEKFD 135

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITR++AD   TIR+PVH+ ++++KVVRT RR+  +++REPT 
Sbjct: 136 YTKGFKFSTYATWWIRQAITRAMADSGRTIRLPVHLAEQVNKVVRTRRRIHQELEREPTA 195

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+  +L M  E + ++L+ +++ +SL+  +G ++ S LGDFIED +A    D+     +
Sbjct: 196 EELGLELDMTPERITELLEYSRDLVSLDQTVGADEESRLGDFIEDADAAVAEDAVAFQMM 255

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     VL++L  RE  V+ +RFG+      TLE++GKQF ++RER+RQIE + + KL+ 
Sbjct: 256 KGDVRNVLSTLEERERDVVVLRFGLDGGQPRTLEQIGKQFGLSRERVRQIERETMAKLRD 315

Query: 670 PSRSKKLRSFL 680
           P R+  LR +L
Sbjct: 316 PQRADALRDYL 326



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 33/58 (56%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           L  +++ +      ++  D++   + D VR+YL  +G   LL+ E E+ ++KRIEAG 
Sbjct: 4   LQSSTTDTLEVRSSRREPDTSGLVSTDLVRVYLNTIGKTALLTAEQEVELSKRIEAGL 61


>gi|254421657|ref|ZP_05035375.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
 gi|196189146|gb|EDX84110.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
          Length = 467

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 106/249 (42%), Positives = 172/249 (69%), Gaps = 1/249 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +R+   +A  AK+ M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +AAEKFD   
Sbjct: 218 QLRQKLRQARAAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKFDPDK 277

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR+IA+ + TIR+P+H+ +K++K+ +  R +  +++R PT  E+
Sbjct: 278 GYKFSTYAYWWIRQGITRTIANDARTIRLPIHIVEKLNKLKKAQRELRKELQRTPTEVEV 337

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  L M  E +R + ++ ++ +SL   +G  + + L + +ED N++SP     ++ +R+ 
Sbjct: 338 AAALEMTPEQLRTLQQVQRKSLSLNHRVGKGEDTELMELLEDGNSLSPESQISESMMRQE 397

Query: 613 TTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            + VL   LT RE+ ++ +R+G+     HTLEEVG  F ++RER+RQI+ KA+RKL+ P 
Sbjct: 398 ISDVLTEVLTEREKEIIALRYGLTTGETHTLEEVGGIFQLSRERVRQIQTKAMRKLRRPQ 457

Query: 672 RSKKLRSFL 680
            + +L+++L
Sbjct: 458 VAARLKNWL 466


>gi|168703618|ref|ZP_02735895.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 521

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 143/509 (28%), Positives = 231/509 (45%), Gaps = 23/509 (4%)

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E++        G    + + + +  E +D        E       +  S  D      
Sbjct: 15  DDETREDLDEKAHGRDEDEDDLADESDEDEDTALEPARGEDEGAAEDEYASGPDDALGLY 74

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA-------LDEIAEVYRELRSLQ---DNA 301
                ++     +    L+   +  R +   A       LD   E + ++ + Q   D  
Sbjct: 75  LRQMGSIPLLNREKELALAKRLEHHRNRFRAAALLCPRLLDRAREKFEQIAAGQTPIDPN 134

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLS-LNQSRIDLLVEQLYDISK--RIMHNEGELLR 358
           ++        +    +  +L   + +L  L Q   ++      D  +  R        LR
Sbjct: 135 IDAYSSADLRLTRAQIHARLATDLPTLGVLLQQDAEVFAAGARDEYRGSRSDWQRDRFLR 194

Query: 359 LAQSYGI-----KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           LA+   +      R   LER    EL+      A +       +  A       ++  ++
Sbjct: 195 LAKCRRLVHELSPRTEILERWTD-ELN----DLADELKHLAIAHAAAASPADRARLGRQL 249

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +       ++  E   +V ++RK        +KE+ EANLRLV+S+AK Y NRGL F DL
Sbjct: 250 RDAECRACMTADELAALVRVLRKRRLAYQAVRKELAEANLRLVVSIAKNYRNRGLPFSDL 309

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN GLM+A +K++W L +KF TYA WWV+Q ITR++ D + T+R+P H    + ++ 
Sbjct: 310 IQEGNRGLMRAVDKYEWRLEFKFGTYATWWVRQGITRALHDNARTVRVPCHQISLLSRME 369

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +    ++    REPT EE+A+ L +  E  R +  + + P+SL   +G +    L DF+ 
Sbjct: 370 KLRGELTVATGREPTSEELAEALGVKPEEARSLRIVGRHPVSLNDSVGGDGERALEDFLS 429

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +   P +      L+E    VL SL PRE  V+ +RFG+   T  TL+EV KQ+ +TR
Sbjct: 430 DTHISPPGEHVDANLLKERIGEVLKSLAPREREVIELRFGLKDGTPKTLDEVAKQYGITR 489

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ERIRQIEA+ + KL+ P+RS +L  F D 
Sbjct: 490 ERIRQIEARGLLKLRQPTRSCRLEEFADA 518



 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 61/180 (33%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                      +D      DD + +YLR+MGSI LL+RE E+A+AKR+E  R    A+  
Sbjct: 49  EPARGEDEGAAEDEYASGPDDALGLYLRQMGSIPLLNREKELALAKRLEHHRNRFRAAAL 108

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
             P          +++  G T +   ID  +           H              Q+ 
Sbjct: 109 LCPRLLDRAREKFEQIAAGQTPIDPNIDAYSSADLRLTRAQIHARLATDLPTLGVLLQQD 168

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                     +   +    + DR    +      ++     E  +     L+ + D+L+ 
Sbjct: 169 AEVFAAGARDEYRGSRSDWQRDRFLRLAKCRRLVHELSPRTEILERWTDELNDLADELKH 228


>gi|254430889|ref|ZP_05044592.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197625342|gb|EDY37901.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 327

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 173/286 (60%), Gaps = 10/286 (3%)

Query: 399 VACEVDSILKIRN--EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           +  E + +L+ R   E+ + +   G+  ++ R  +   R+       AK+ M++ANLRLV
Sbjct: 46  LVQEREELLRQRGDGELTAWAGRCGVPPADLRQALHRGRR-------AKERMLQANLRLV 98

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++VAKKY  RGL  LDLIQEG +GL +A E++D   G++FSTYA WW++Q ITR++A QS
Sbjct: 99  VAVAKKYQRRGLDLLDLIQEGTLGLERAVERYDPRRGFRFSTYAYWWIRQGITRALASQS 158

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+PVH+ + ++++      ++ +  R+PT  E+A+ + +    +R  L     P+SL
Sbjct: 159 RTIRLPVHVTETLNRIRTCQGELTREHGRQPTLAELARAVGLDEARLRSTLAHIPRPVSL 218

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           E  +G    + L D +ED +A +P  +  +  L      +L  L+ RE  V+R RFG+  
Sbjct: 219 EGRVGANADTPLVDLLEDDHA-TPEQTLTRQQLHADLEALLDELSAREATVIRQRFGLDD 277

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +T  TL E+G+Q  ++RER+RQIE++A+ KL+ P    ++R +LD 
Sbjct: 278 DTPRTLAEIGEQLQLSRERVRQIESRALLKLRQPQNRCRVRDYLDS 323



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 28/42 (66%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
            ++ DP+R+YLRE+G ++LL +E EI +A+ ++    ++   
Sbjct: 16  GASSDPIRLYLREIGRVDLLRQEEEILLARLVQEREELLRQR 57


>gi|119512308|ref|ZP_01631394.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119463021|gb|EAW43972.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 391

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 138/280 (49%), Positives = 193/280 (68%), Gaps = 6/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVS----MVRKGECEASIAKKEMVEANLRLVISVA 460
            + ++R+ ++   +E      E+   V       R        AK +MV++NLRLV+S+A
Sbjct: 113 ELERVRDRLQE-QLEREPEYREWAEAVQIPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIA 171

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR
Sbjct: 172 KKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIR 231

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPI
Sbjct: 232 LPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI 291

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G E+ S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      
Sbjct: 292 GKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMK 350

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 351 TLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 390



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 37/67 (55%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            DD EDE     S +  + +  ++   ++ +      T+D +R+YL+E+G I LL  + E
Sbjct: 42  NDDGEDEFLEPQSDEDDTKSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEE 101

Query: 140 IAIAKRI 146
           I +A++I
Sbjct: 102 IELARKI 108


>gi|332518972|ref|ZP_08395439.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
 gi|332044820|gb|EGI81013.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
          Length = 287

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       +A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQVALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M +  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQAHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLNSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLGNQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQVALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|145594010|ref|YP_001158307.1| RNA polymerase sigma factor SigB [Salinispora tropica CNB-440]
 gi|145303347|gb|ABP53929.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 332

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 116/242 (47%), Positives = 175/242 (72%), Gaps = 1/242 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFST
Sbjct: 89  AEGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFST 148

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM ++++++VRT R +S  + REPT  E+A+ L +
Sbjct: 149 YATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRTRRELSVSLGREPTVAEVARTLDI 208

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-ANLRETTTRVL 617
           P   V +++   +EP+SL+  +G++  S LGDF+   ++ +  D  +    LR+    VL
Sbjct: 209 PEIQVIELISYDREPVSLDQTVGEDGESPLGDFVAAVDSTAGTDDTVSGGELRQEMCGVL 268

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL+ P R+++L 
Sbjct: 269 ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLHKLRAPERAQRLE 328

Query: 678 SF 679
           ++
Sbjct: 329 AY 330



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 29/69 (42%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
              S +              + D VR YL+ +G  +LL+   E+ +++RIEAG       
Sbjct: 11  RPTSGADTLTDLDATDERGVSTDLVRAYLQGIGRTKLLTAAQEVELSRRIEAGLFAATKL 70

Query: 157 LCESPLTFQ 165
              +P++  
Sbjct: 71  ATCTPVSVA 79


>gi|220906934|ref|YP_002482245.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863545|gb|ACL43884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 378

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 132/250 (52%), Positives = 181/250 (72%), Gaps = 1/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +   R        AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD 
Sbjct: 129 LQSFRHRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDH 188

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT E
Sbjct: 189 EKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEE 248

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LR
Sbjct: 249 EIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLR 307

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    VL +L+PRE  VL++R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP
Sbjct: 308 EDLETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHP 367

Query: 671 SRSKKLRSFL 680
           +R+  L+ ++
Sbjct: 368 NRNSVLKEYI 377



 Score = 42.5 bits (98), Expect = 0.22,   Method: Composition-based stats.
 Identities = 20/69 (28%), Positives = 36/69 (52%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ DD E+    E + D    A       ++ +      T+D +R+YL+E+G I LL  +
Sbjct: 27  LETDDSEELLDEEAAEDGDGKAGKGRSTRRRSQAKKKHYTEDSIRLYLQEIGRIRLLRAD 86

Query: 138 GEIAIAKRI 146
            EI +A++I
Sbjct: 87  EEIELARKI 95


>gi|163787530|ref|ZP_02181977.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159877418|gb|EDP71475.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  198 bits (504), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M +  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQSHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRDLLHESLRTEIERALETLTPREADVIRLYFGLGNQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQIALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|256027745|ref|ZP_05441579.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260494274|ref|ZP_05814405.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289765702|ref|ZP_06525080.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260198420|gb|EEW95936.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289717257|gb|EFD81269.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
          Length = 416

 Score =  198 bits (503), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 141/301 (46%), Positives = 199/301 (66%), Gaps = 4/301 (1%)

Query: 380 DPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +P ++    +     E    +         I+  ++ I     ++  E            
Sbjct: 116 NPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRA---Y 172

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKFST
Sbjct: 173 EGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFST 232

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L M
Sbjct: 233 YATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERLGM 292

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    VL 
Sbjct: 293 EVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAVLK 352

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  
Sbjct: 353 TLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKLED 412

Query: 679 F 679
           F
Sbjct: 413 F 413



 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 49/206 (23%), Positives = 75/206 (36%), Gaps = 49/206 (23%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL-- 83
             ++  + +IK A + G +T EE+N  L  D   +E +E  +  +   GI +VD + L  
Sbjct: 5   IKNEKARALIKKAVEEGIITYEEINEELGDD-FPAENIEQLINEMLEQGIKIVDEEQLDE 63

Query: 84  --EDEEGSEDSLDLASSASNSSVFLQKRKDSA---------------------------- 113
             EDE   ++S +  +        L+   D                              
Sbjct: 64  LGEDELKGKNSEEDYTDNEEHDDLLEDETDEKLDTDEENEETETFTEFDDEFNPEYIEDV 123

Query: 114 ---------------DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                              D+P++MYLRE+G + LL+ + EI  AKR   G       L 
Sbjct: 124 SEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYEGDEEASKKLI 183

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI 184
           ES L     I  +   N G  LL  I
Sbjct: 184 ESNLRLVVSIAKK-HTNRGLKLLDLI 208


>gi|284046806|ref|YP_003397146.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951027|gb|ADB53771.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 380

 Score =  198 bits (503), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 132/275 (48%), Positives = 187/275 (68%), Gaps = 3/275 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            S+  +R  ++SI     ++  +  H+   + +       AK++M+EANLRLV+S+AK Y
Sbjct: 107 PSLDSLRLYLRSIGRVNLLTAEQEVHLAQRIER---GDMRAKQQMIEANLRLVVSIAKGY 163

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             RGL FLDLIQEG++GL++A EKFD   G+KFSTYA WW++QA+TR+IAD+  TIRIPV
Sbjct: 164 LGRGLTFLDLIQEGSLGLIRAVEKFDHRRGFKFSTYATWWIRQAVTRAIADKGRTIRIPV 223

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM +K++KVV   R++   + REPTPEEIA +L   V  VR +L++ ++P+SLE PIG+E
Sbjct: 224 HMVEKLNKVVHVERQLVQSLGREPTPEEIAAELECTVREVRDILRMAQQPVSLEKPIGEE 283

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDF+ED+ A SP + A +   R+   R L +L  RE  V+ MRFG+G     TLE
Sbjct: 284 EESELGDFVEDQTAESPFELASENLRRDNVRRALQALPQREREVIEMRFGLGGGRPRTLE 343

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           EVG+ F VTRERIRQIE   ++KL+    +++LR 
Sbjct: 344 EVGRAFNVTRERIRQIENHTLKKLEALPEAQRLRD 378



 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 46/168 (27%), Positives = 82/168 (48%), Gaps = 4/168 (2%)

Query: 18  SDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
           +D++ + +   + ++++I   ++RGY+T EE+   L   EV+ EQ+++  A L   GI+V
Sbjct: 10  ADEAPIAEM--EEFRQLIAEGQERGYLTFEEIATTLEEVEVTKEQVQELHAHLEEHGIDV 67

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK-DSADRSTDDPVRMYLREMGSIELLSR 136
           V+ D       +  +         SS   ++ + D     + D +R+YLR +G + LL+ 
Sbjct: 68  VEADGKPAVSAAGAAEGERPDTRRSSGSAKRPEIDLTVEPSLDSLRLYLRSIGRVNLLTA 127

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+ +A+RIE G       + E+ L     I     L  G T L  I
Sbjct: 128 EQEVHLAQRIERGDMRAKQQMIEANLRLVVSIAKGY-LGRGLTFLDLI 174


>gi|254495200|ref|ZP_05108124.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
 gi|85819552|gb|EAQ40709.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
          Length = 287

 Score =  198 bits (503), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 175/272 (64%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +  +++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQLIK---AGDQRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+PEEIAKKL M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKMYAFLEQENERPPSPEEIAKKLDMTVNDVKESMKNSGRHVSMDAPLIEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+++ FG+G +   TLEE+G+ 
Sbjct: 195 YDVLNSGESPNPDRVLLHESLRIEINRALETLTPREADVVKLYFGLGEHQPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L ++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILMTYL 286



 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+ I+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQLIKAGDQRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|213964561|ref|ZP_03392761.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
 gi|213952754|gb|EEB64136.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
          Length = 329

 Score =  198 bits (503), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 106/248 (42%), Positives = 173/248 (69%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             V+    E   A+  ++EANLRLV+S+AK+YTNRG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 80  RDVKILAKEGKAARAHLLEANLRLVVSLAKRYTNRGMPLLDLIQEGNLGLIRAMEKFDYT 139

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R +  ++ RE T EE
Sbjct: 140 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKISRIKRELYQQLGREATNEE 199

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +P   +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    ++ + +    
Sbjct: 200 LAEESGIPEAKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIEDSEATDAEEAVVASLRHH 259

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL++L  RE+ V+++R+G+      TL+++G+ F ++RER+RQIE + + KL+   
Sbjct: 260 DVRKVLSTLEIREQEVIKLRYGLDDGLPRTLDQIGRHFGLSRERVRQIEREVMSKLREGD 319

Query: 672 RSKKLRSF 679
           R+ KLR +
Sbjct: 320 RADKLREY 327



 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 27/53 (50%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
                 +    +R  +    + D VR+YL  +G   LLS E E+ ++KRIEAG
Sbjct: 9   DELEGQARDKGRRTGNNSNPSADLVRVYLNGIGKTALLSAEEEVELSKRIEAG 61


>gi|300867798|ref|ZP_07112441.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
 gi|300334215|emb|CBN57613.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
          Length = 391

 Score =  198 bits (503), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 137/266 (51%), Positives = 190/266 (71%), Gaps = 8/266 (3%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             +   G+ +  FRH + + R+       AK +MV++NLRLV+S+AKKY NRGL F DLI
Sbjct: 133 EWANAVGMPLPAFRHRLHLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLI 185

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +
Sbjct: 186 QEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKK 245

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE 
Sbjct: 246 TTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE- 304

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRE
Sbjct: 305 SDGETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRE 364

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 365 RIRQIEAKALRKLRHPNRNSILKEYI 390



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/112 (26%), Positives = 54/112 (48%), Gaps = 5/112 (4%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVV---DGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           + P+  + E + +   +L    I +    +GDD ED   ++   D A S S  +   ++ 
Sbjct: 12  IQPEIETIELLANARGVLPESEIELFIDDEGDDREDFLDAQPEEDDAKSGSKVAKARRRA 71

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           +      T+D +R+YL+E+G I LL  + EI +A++I        +   LCE
Sbjct: 72  QAKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREQLCE 123


>gi|86610159|ref|YP_478921.1| RNA polymerase sigma factor SigC [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558701|gb|ABD03658.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 366

 Score =  198 bits (503), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 114/251 (45%), Positives = 173/251 (68%), Gaps = 1/251 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +++ +     AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD  
Sbjct: 115 EKLQQIQRIGKRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPK 174

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R PT E+
Sbjct: 175 KGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKLSQEKGRTPTIED 234

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L M    VR++L      +SLET +G +  + LGD +E  + +SP ++ ++  L  
Sbjct: 235 IASELEMTPPQVRELLVRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEETMMREALHR 293

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++L+ LT RE  V+RMRFG+G    ++L E+G+   ++RER+RQIEAKA++KL+ P 
Sbjct: 294 DLQQLLSDLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPK 353

Query: 672 RSKKLRSFLDG 682
           R  ++R +L+ 
Sbjct: 354 RRNRVRDYLEA 364



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 36/65 (55%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G  D L+ A  A       +  ++   R + D VR+YL+E+G + LL R+ E+A+A+++
Sbjct: 14  DGPADLLEAAEEAEVDLADGEFLEEEPTRRSTDLVRLYLQEIGRVPLLGRDEEVALAQKV 73

Query: 147 EAGRA 151
           +    
Sbjct: 74  QDYMK 78


>gi|113478384|ref|YP_724445.1| RNA polymerase sigma factor RpoD [Trichodesmium erythraeum IMS101]
 gi|110169432|gb|ABG53972.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 386

 Score =  198 bits (502), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 135/282 (47%), Positives = 188/282 (66%), Gaps = 5/282 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + ++   +    +S        E       +         AK++MV++NLRLV+S
Sbjct: 109 LERIREELIYHLDREPQVSEWANAVDMELPKFKRRL----ILGRRAKEKMVQSNLRLVVS 164

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS T
Sbjct: 165 IAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRT 224

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVH+ + I ++ +T + +S ++ R+PT EEIA  + M +E +R + K  + PISLET
Sbjct: 225 IRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATSMEMTIEKLRFIAKSAQLPISLET 284

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG E+ S LGDFIE  +  +P D   +  LRE    VL SL+PRE  VLR+R+G+    
Sbjct: 285 PIGKEEDSRLGDFIE-SDGETPEDEVSKNLLREDLESVLNSLSPRERDVLRLRYGLDDGR 343

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 344 MKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 385



 Score = 44.4 bits (103), Expect = 0.069,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
             + I + D ++  D +  ED L     A + +    K+K      T+D +R+YL+E+G 
Sbjct: 32  DELEILIGDREEYIDAQSDEDDLKSGKVAKSRTRTAGKKK----HYTEDSIRLYLQEIGR 87

Query: 131 IELLSREGEIAIAKRI 146
           I LL  + EI +A++I
Sbjct: 88  IRLLRADEEIELARKI 103


>gi|75907387|ref|YP_321683.1| RNA polymerase sigma factor SigC [Anabaena variabilis ATCC 29413]
 gi|75701112|gb|ABA20788.1| RNA polymerase, sigma subunit, RpsC/SigC [Anabaena variabilis ATCC
           29413]
          Length = 416

 Score =  198 bits (502), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 109/255 (42%), Positives = 171/255 (67%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  V  + K + +   +K+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EK
Sbjct: 161 KMTVEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 220

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R P
Sbjct: 221 FDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTP 280

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +  ++ 
Sbjct: 281 TLEDLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDGVTPEEMLMRE 339

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+     +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL
Sbjct: 340 SLQRDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKL 399

Query: 668 KHPSRSKKLRSFLDG 682
           + P R   +R +L+ 
Sbjct: 400 RQPKRRNLIRDYLES 414



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 37/71 (52%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D     + S+ S+D       ++        SA+R + D VR+YL+E+G + LL R+ E+
Sbjct: 22  DPDIAIDDSDLSVDEIQELEIAAADPATFGASANRRSTDLVRLYLQEIGRVRLLGRDEEV 81

Query: 141 AIAKRIEAGRA 151
           + A++++    
Sbjct: 82  SEAQKVQRYLK 92


>gi|17229184|ref|NP_485732.1| RNA polymerase sigma factor SigC [Nostoc sp. PCC 7120]
 gi|20141790|sp|Q03066|RPSC_ANASP RecName: Full=RNA polymerase sigma-C factor
 gi|17135512|dbj|BAB78058.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score =  198 bits (502), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 109/255 (42%), Positives = 171/255 (67%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  V  + K + +   +K+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EK
Sbjct: 161 KMTVEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 220

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R P
Sbjct: 221 FDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTP 280

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +  ++ 
Sbjct: 281 TLEDLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDGVTPEEMLMRE 339

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+     +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL
Sbjct: 340 SLQRDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKL 399

Query: 668 KHPSRSKKLRSFLDG 682
           + P R   +R +L+ 
Sbjct: 400 RQPKRRNLIRDYLES 414



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 37/71 (52%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D     + S+ S+D       ++        SA+R + D VR+YL+E+G + LL R+ E+
Sbjct: 22  DPDIAIDDSDLSVDEIQELEIAAADPATFGASANRRSTDLVRLYLQEIGRVRLLGRDEEV 81

Query: 141 AIAKRIEAGRA 151
           + A++++    
Sbjct: 82  SEAQKVQRYLK 92


>gi|256845590|ref|ZP_05551048.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294785121|ref|ZP_06750409.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
 gi|256719149|gb|EEU32704.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294486835|gb|EFG34197.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
          Length = 418

 Score =  198 bits (502), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 143/303 (47%), Positives = 202/303 (66%), Gaps = 4/303 (1%)

Query: 378 ELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           E +P ++    +     E    +         I+  ++ I     ++  E        +K
Sbjct: 116 EFNPEYIEDVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYA---KK 172

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF++  GYKF
Sbjct: 173 AYEGDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKF 232

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  ++ +PE +A++L
Sbjct: 233 STYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKESRIYLQETGKDASPEILAERL 292

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            M V+ ++ + ++ +EPISLETP+G E+ S LGDF+ED+   SP ++  +A LRE    V
Sbjct: 293 GMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYEATNRAILREELDAV 352

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L +L+PREE+VLR R+G+  ++  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL
Sbjct: 353 LKTLSPREEKVLRYRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKKKL 412

Query: 677 RSF 679
             F
Sbjct: 413 EDF 415



 Score = 75.6 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/208 (22%), Positives = 76/208 (36%), Gaps = 51/208 (24%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG---DD 82
             ++  + +IK A + G +T EE+N  L  D   +E +E  +  +   GI +VD    D+
Sbjct: 5   IKNEKVRALIKKAVEEGIITYEEINEELGDD-FPAENIEQLINEMLEQGIKIVDEEQLDE 63

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSA----------------------------- 113
           L ++E  E +L+     +     L + +                                
Sbjct: 64  LGEDELREKNLEEEYVDNEEHDDLLEDETEDKLDDTDEENDETEEHFTEFDDEFNPEYIE 123

Query: 114 -----------------DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
                                D+P++MYLRE+G + LL+ + EI  AK+   G       
Sbjct: 124 DVSEDELSNEKLLNLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKKAYEGDEEASKK 183

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREI 184
           L ES L     I  +   N G  LL  I
Sbjct: 184 LIESNLRLVVSIAKK-HTNRGLKLLDLI 210


>gi|159037062|ref|YP_001536315.1| RNA polymerase sigma factor SigB [Salinispora arenicola CNS-205]
 gi|157915897|gb|ABV97324.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 328

 Score =  198 bits (502), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 120/241 (49%), Positives = 179/241 (74%), Gaps = 1/241 (0%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTY
Sbjct: 86  EGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTY 145

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAITR++ADQS TIRIPVHM ++++++VRT R +S  + REPT  E+A+ L +P
Sbjct: 146 ATWWIRQAITRAMADQSRTIRIPVHMVEQVNRMVRTRRDLSVSLGREPTVTEVARALDVP 205

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLA 618
              + +++   +EP+SL+  +G++  S LGDF+   NA  +P ++A +  LR+    VLA
Sbjct: 206 EVQIIELISYDREPVSLDQAVGEDGESPLGDFVAVVNATAAPDNTAERGELRQEVRGVLA 265

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   +RKL+ P R+++L +
Sbjct: 266 TLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLRKLRAPERAQRLAA 325

Query: 679 F 679
           +
Sbjct: 326 Y 326



 Score = 43.3 bits (100), Expect = 0.12,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
            + S +              + D VR YL  +G  +LL+   E+ +++RIEAG     A 
Sbjct: 7   RATSGTDSLTDLDATDERGVSTDLVRAYLYGIGKTKLLTAAQEVELSRRIEAGLF-AEAK 65

Query: 157 LCESPLTFQALIIWRDELNDGTTLLRE 183
           L         L    + +       ++
Sbjct: 66  LAACTPVSATLRADLELVAVEGRAAKD 92


>gi|225021249|ref|ZP_03710441.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945982|gb|EEG27191.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 391

 Score =  198 bits (502), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 107/248 (43%), Positives = 171/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 142 RDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYA 201

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE
Sbjct: 202 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEE 261

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +    
Sbjct: 262 LAEESGIDESKIELLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEAADAESAVVASLRHS 321

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               V+ +L  RE+ V+RMR+G+      TL+++G+QF ++RER+RQIE + +RKL+   
Sbjct: 322 DIRDVIGTLEDREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMRKLRDGQ 381

Query: 672 RSKKLRSF 679
           R++KLR +
Sbjct: 382 RAEKLREY 389



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           +  ED   ++ +   ++VD D   D+    D  D  S+   +     +R  + D  + D 
Sbjct: 36  DNEEDLDVVMGDEPTDLVDDDPGADD--ILDPTDEESAFDLAVDRGSRRGQNNDNPSADL 93

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           VR+YL  +G   LL+ E E+ +A+ IE G 
Sbjct: 94  VRVYLNGIGKTALLTAEDEVHLAQTIEVGL 123


>gi|218438948|ref|YP_002377277.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171676|gb|ACK70409.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 376

 Score =  198 bits (502), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 192/267 (71%), Gaps = 8/267 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  + + G+ +  F+  + + R+       AK +MV++NLRLV+S+AKKY NRGL F DL
Sbjct: 117 KEWAEQVGMELPAFQRRLYLGRR-------AKDKMVQSNLRLVVSIAKKYMNRGLSFQDL 169

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ 
Sbjct: 170 IQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIK 229

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E+ S LGDFIE
Sbjct: 230 KTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE 289

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+G+ F VTR
Sbjct: 290 -ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 348

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 349 ERIRQIEAKALRKLRHPNRNSILKEYI 375



 Score = 44.8 bits (104), Expect = 0.049,   Method: Composition-based stats.
 Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 8/94 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS--TDDPVRMYLREMGSIEL 133
            ++D  D   EE  E+++   +S     V   +R+D+  +   T+D +R+YL+E+G I L
Sbjct: 21  FIIDDIDETAEEELEEAVADDNSKKTRKVTATRRRDAGKKKPYTEDSIRIYLQEIGRIRL 80

Query: 134 LSREGEIAIAKRI------EAGRAMMMASLCESP 161
           L  E EI +A++I      E  R  +  SL   P
Sbjct: 81  LRAEEEIELARKIADLLELERLREKLRRSLGRYP 114


>gi|142114|gb|AAA22047.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score =  197 bits (501), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 109/255 (42%), Positives = 171/255 (67%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  V  + K + +   +K+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EK
Sbjct: 161 KMTVEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 220

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R P
Sbjct: 221 FDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTP 280

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +  ++ 
Sbjct: 281 TLEDLAIELDMTPTQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDGVTPEEMLMRE 339

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L+     +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL
Sbjct: 340 SLQRDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKL 399

Query: 668 KHPSRSKKLRSFLDG 682
           + P R   +R +L+ 
Sbjct: 400 RQPKRRNLIRDYLES 414



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 37/71 (52%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D     + S+ S+D       ++        SA+R + D VR+YL+E+G + LL R+ E+
Sbjct: 22  DPDIAIDDSDLSVDEIQELEIAAADPATFGRSANRRSTDLVRLYLQEIGRVRLLGRDEEV 81

Query: 141 AIAKRIEAGRA 151
           + A++++    
Sbjct: 82  SEAQKVQRYLK 92


>gi|163754266|ref|ZP_02161389.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
 gi|161326480|gb|EDP97806.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
          Length = 287

 Score =  197 bits (501), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKTFAYLEQSHERIPSAEEIAKELDMTVNDVKESMKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +L+    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLNSGESPNPDKELLHESLKTEIERALETLTPREADVIRLYFGLGNQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQIALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|86607034|ref|YP_475797.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
 gi|86555576|gb|ABD00534.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
          Length = 404

 Score =  197 bits (501), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 131/256 (51%), Positives = 184/256 (71%), Gaps = 1/256 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E +  +   R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++A
Sbjct: 149 EEVKMSLPEFRRRLHRGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRA 208

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           AEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +  +++S ++ 
Sbjct: 209 AEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKVTKQLSQELG 268

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R PT EEIA ++ + +E +R + K  + PISLETPIG E+ S LGDFIE +   +P +  
Sbjct: 269 RRPTEEEIATRMEITIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESE-GETPEERV 327

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  LRE    VL +LTPRE  VL++R+G+      TLEE+G+ F VTRERIRQIEAKA+
Sbjct: 328 AKVLLREDLESVLETLTPRERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKAL 387

Query: 665 RKLKHPSRSKKLRSFL 680
           RKL+HP+R+  L+ ++
Sbjct: 388 RKLRHPNRNSVLKEYI 403



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           TDD +R+YL+E+G I LL  + EI +A++I
Sbjct: 87  TDDSIRVYLQEIGRIRLLRADEEIELARKI 116


>gi|300933022|ref|ZP_07148278.1| RNA polymerase sigma factor SigB [Corynebacterium resistens DSM
           45100]
          Length = 337

 Score =  197 bits (501), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 106/252 (42%), Positives = 170/252 (67%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 84  RARKRDLKILAREGKAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 143

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 144 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREA 203

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +LK +++P+SL+ P+G ++ + LGDFIED +A     + + +
Sbjct: 204 TNEELAEESGIEESKIELLLKQSRDPVSLDMPVGSDEEAPLGDFIEDSDATDAEAAVVAS 263

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL +L  RE+ V+++R+G+      TL+++G++F ++RER+RQIE + + KL
Sbjct: 264 LRHSDVRAVLGTLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKL 323

Query: 668 KHPSRSKKLRSF 679
           +   R+ KLR +
Sbjct: 324 REGHRADKLREY 335



 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D        +    +R+ + +  + D VR+YL  +G   LL+ E E+ +++RIE G 
Sbjct: 14  DSDDRDGGQTEDKGRRRGNNENPSADLVRVYLNGIGKTALLTAEDEVELSQRIEVGL 70


>gi|86141299|ref|ZP_01059845.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85831858|gb|EAQ50313.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 287

 Score =  197 bits (500), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 172/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+PEEIAK+L M V  V++ LK     +S++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQANERPPSPEEIAKELDMTVNEVKESLKNAGRHVSMDAPLIEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +L     R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELLSESLSTEIERALETLTPREADVVRLYFGLGHQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|319953761|ref|YP_004165028.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319422421|gb|ADV49530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  197 bits (500), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 109/272 (40%), Positives = 176/272 (64%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++K       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIKK---GDQAALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R+P+PEEIAK+L M VE V++ LK +   +S++ P+ D + S+L
Sbjct: 135 INKINKTFAFLEQAHERQPSPEEIAKELDMTVEDVKQSLKNSGRHVSMDAPLIDGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLAGQHSMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKKGDQAALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|148657222|ref|YP_001277427.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569332|gb|ABQ91477.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 349

 Score =  197 bits (500), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 119/301 (39%), Positives = 183/301 (60%), Gaps = 24/301 (7%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGE------------------------CE 440
           ++  I++ ++ I     ++ +E   +   + +G                           
Sbjct: 49  TLDSIQHYLQEIGRVPLLTAAEEVELAERMERGAAAARRLASAEDLSPQLRQALLDDVAA 108

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A++ +++ANLRLV+S+AKKY  RGL  LDLIQEGNIGLM+A EKFD   G +FSTYA
Sbjct: 109 GQEARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHRKGNRFSTYA 168

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QA+TR+IA+Q  TIR+PVHM + + +V R A R++  ++R+PTPEEIA  L  P 
Sbjct: 169 TWWIRQAVTRAIAEQGRTIRLPVHMSESVGQVKRAADRLAQVLERQPTPEEIATALGQPT 228

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E + +VL+ ++ P+SLE P+G++    LGDF++D +  +P+++A    LR      L  L
Sbjct: 229 ERIERVLEASRRPVSLEMPVGEDGEHTLGDFLQDSDLPTPVEAASHQLLRRDLAAALDRL 288

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE R++ +R+G+      TLEEVG+   +TRER RQIEA+A+R+L+ P     LR +L
Sbjct: 289 NERERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALRRLRAPDVGLHLRDYL 348

Query: 681 D 681
           +
Sbjct: 349 E 349



 Score = 42.1 bits (97), Expect = 0.28,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 43/106 (40%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +  E +E + +      +           +     ST D ++ YL+E+G + LL+   E
Sbjct: 12  DELDERQEIAGEGEMAPIADIEELAAENLEETLESDSTLDSIQHYLQEIGRVPLLTAAEE 71

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           + +A+R+E G A          L+ Q      D++  G    R +I
Sbjct: 72  VELAERMERGAAAARRLASAEDLSPQLRQALLDDVAAGQEARRHLI 117


>gi|295132793|ref|YP_003583469.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294980808|gb|ADF51273.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 287

 Score =  197 bits (500), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++      + A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDNRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M +  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQSHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDKDLLHESLRTEIERALETLTPREADVIRLYFGLGDQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDNRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|86606677|ref|YP_475440.1| RNA polymerase sigma factor SigC [Synechococcus sp. JA-3-3Ab]
 gi|86555219|gb|ABD00177.1| RNA polymerase sigma-70 factor family [Synechococcus sp. JA-3-3Ab]
          Length = 364

 Score =  197 bits (500), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 116/251 (46%), Positives = 174/251 (69%), Gaps = 1/251 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +++ +     AK+ M++ANLRLV+SVAKKY NRGL+ LDLIQEG +GL +A EKFD  
Sbjct: 113 EKLQQIQRIGKRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPK 172

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R PT E+
Sbjct: 173 KGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKLSQEKGRTPTIED 232

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L M V  VR++L      +SLET +G +  + LGD +E  + +SP ++ ++  L  
Sbjct: 233 IASELEMTVPQVRELLVRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEETMMREALHR 291

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++LA LT RE  V+RMRFG+G    ++L E+G+   ++RER+RQIEAKA++KL+ P 
Sbjct: 292 DLQQLLADLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPK 351

Query: 672 RSKKLRSFLDG 682
           R  ++R +L+ 
Sbjct: 352 RRNRVRDYLEA 362



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/72 (30%), Positives = 37/72 (51%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +L D     D LD A  A       +  ++   R + D VR+YL+E+G + LL R+ E
Sbjct: 5   EPELNDILLDGDLLDPAEEAEVDLAESEFAEEEPARRSTDLVRLYLQEIGRVPLLGRDEE 64

Query: 140 IAIAKRIEAGRA 151
           +A+A+R++    
Sbjct: 65  VALAQRVQDYMK 76


>gi|25028367|ref|NP_738421.1| RNA polymerase sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259507424|ref|ZP_05750324.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
 gi|23493652|dbj|BAC18621.1| sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259164989|gb|EEW49543.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
          Length = 333

 Score =  196 bits (499), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 106/252 (42%), Positives = 171/252 (67%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 80  RAMKRDLKVLAKEGKKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 139

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 140 FDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREA 199

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +
Sbjct: 200 TNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDAETAVVAS 259

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL++L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL
Sbjct: 260 MRHSDIRSVLSTLEQREQDVIRLRYGLEDGVPRTLDQIGRRFGLSRERVRQIEREVMSKL 319

Query: 668 KHPSRSKKLRSF 679
           +   R+ KLR +
Sbjct: 320 RDGERAAKLREY 331



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 25/52 (48%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                    +R  + D  + D VR+YL  +G   LL+ E E+ +A+ IE G 
Sbjct: 14  DDREVDLGSRRGQTNDNPSQDLVRVYLNGIGKTALLTAEDEVELAQTIEVGL 65


>gi|269925873|ref|YP_003322496.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789533|gb|ACZ41674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 326

 Score =  196 bits (499), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 115/245 (46%), Positives = 171/245 (69%), Gaps = 2/245 (0%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           + +    +A++ M+E NLRLV+S+A++Y  RGL   DLI+EGN+GLM+AA+KFD+  GY+
Sbjct: 83  RDKERGEMARRRMIECNLRLVVSIARRYAGRGLPLSDLIEEGNLGLMRAADKFDYRRGYR 142

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QA+TR++A QS  +R+PVH+ + +H + + + R+S ++ REPT EEIA +
Sbjct: 143 FSTYATWWIRQAVTRALASQSRVVRLPVHVTELMHNITKVSHRLSQELGREPTSEEIAAE 202

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +  E VR+V+K ++ P+SLE P G++    + + IED N  SP D   +  LRE    
Sbjct: 203 LNITPERVREVVKASQYPMSLEQPYGEDGDGTVEEIIEDPNIESPADQVSRDILREQILA 262

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  LT RE +VL +R+G+  N  +TLEEVGK   VTRERIRQIE +A+ KL+    ++ 
Sbjct: 263 LLDDLTDRERQVLDLRYGLTGNHSYTLEEVGKVLGVTRERIRQIEKEALSKLR--PHAES 320

Query: 676 LRSFL 680
           LRSF+
Sbjct: 321 LRSFM 325



 Score = 46.0 bits (107), Expect = 0.023,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 2/94 (2%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            D   +                  ++D V +YLR++G+I LL+   EIA+AK IE GR  
Sbjct: 6   TDEPFAEDYVQENDSYISAEESSGSEDSVSVYLRDIGAIPLLTPMEEIALAKAIEKGRQA 65

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
                    L+ +       +   G    R +I+
Sbjct: 66  TRK--LHQDLSPEEREAALRDKERGEMARRRMIE 97


>gi|305664513|ref|YP_003860800.1| putative sigma factor A [Maribacter sp. HTCC2170]
 gi|88708530|gb|EAR00766.1| putative sigma factor A [Maribacter sp. HTCC2170]
          Length = 287

 Score =  196 bits (499), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M VE V++ LK +   +S++ P+   + S+L
Sbjct: 135 INKINKTFAFLEQAHERMPSAEEIAKELDMTVEDVKQSLKNSGRHVSMDAPLIAGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLAGQHSMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQIALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|119512139|ref|ZP_01631231.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
 gi|119463229|gb|EAW44174.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
          Length = 442

 Score =  196 bits (499), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 110/260 (42%), Positives = 174/260 (66%), Gaps = 2/260 (0%)

Query: 424 ISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +E   + V  + + + +   AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL 
Sbjct: 182 WAEIAQLTVEELEQVQSQGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE 241

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +A EKFD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +
Sbjct: 242 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQE 301

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R PT E++A +L M    VR+VL      +SLET +G +  + LG+ +E  + V+P +
Sbjct: 302 KGRTPTLEDLAIELEMTPTQVREVLLKVPRSVSLETKVGKDKDTELGELLE-TDCVTPEE 360

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++ +L++    +LA LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+K
Sbjct: 361 MLMRESLQKDLHSLLADLTSRERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESK 420

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
           A++KL+ P R   +R +L+ 
Sbjct: 421 ALQKLRQPKRRNLIRDYLES 440



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 37/72 (51%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           ++    +  E S D       ++V       + +R + D VR+YL+E+G + LL R+ E+
Sbjct: 48  EEELIIDDGELSADEIQELEVAAVDPANFAGNTNRRSTDLVRLYLQEIGRVRLLGRDEEV 107

Query: 141 AIAKRIEAGRAM 152
           + A++++    M
Sbjct: 108 SEAQKVQRYLRM 119


>gi|86609652|ref|YP_478414.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558194|gb|ABD03151.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 403

 Score =  196 bits (499), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 131/256 (51%), Positives = 183/256 (71%), Gaps = 1/256 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E +  +   R+       AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++A
Sbjct: 148 EEVKMSLPEFRRRLHRGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRA 207

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           AEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +  + +S ++ 
Sbjct: 208 AEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKVTKLLSQELG 267

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R+PT EEIA ++ + +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D  
Sbjct: 268 RKPTEEEIATRMEITIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDRV 326

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  LRE    VL +LT RE  VL++R+G+      TLEE+G+ F VTRERIRQIEAKA+
Sbjct: 327 AKVLLREDLESVLETLTARERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKAL 386

Query: 665 RKLKHPSRSKKLRSFL 680
           RKL+HP+R+  L+ ++
Sbjct: 387 RKLRHPNRNSVLKEYI 402



 Score = 40.2 bits (92), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           TDD +R+YL+E+G I LL  + EI +A++I
Sbjct: 86  TDDSIRVYLQEIGRIRLLRADEEIELARKI 115


>gi|221633247|ref|YP_002522472.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
 gi|221156052|gb|ACM05179.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
          Length = 340

 Score =  196 bits (499), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 117/274 (42%), Positives = 180/274 (65%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I+    ++  E   +   ++      + A +  V +NLRLV+S+AK+Y  RGL
Sbjct: 70  LRLYLRDIAEAPLLTPEEEVELAKRIK---EGDTEALQRFVRSNLRLVVSIAKRYVGRGL 126

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGNIGLM+A EKFDW  GY+FSTYA WW++QAITR+IADQ  TIR+PVHM D 
Sbjct: 127 SLLDLIQEGNIGLMRAVEKFDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPVHMTDS 186

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I +  RT  +++ ++ R+PTPEEIA+ +++  E + ++++  +  +SL+ P+ +ED + L
Sbjct: 187 ITRYHRTTTQLAQELGRQPTPEEIAEAMSVQPEKIAQIVRAAQRAVSLDQPLSEEDETSL 246

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD I D+ A SP + A ++ +R     +L  LTPRE  VL++R+G+      TL EVG  
Sbjct: 247 GDLIADELAQSPEELAEESLMRRDIAEILEMLTPRERLVLQLRYGLSDGEPRTLAEVGDL 306

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             ++RER+RQIE +A+RKL+  +R ++L  +  G
Sbjct: 307 LGISRERVRQIENEALRKLRRIAR-ERLAEYYAG 339



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 46/109 (42%), Gaps = 4/109 (3%)

Query: 79  DGDDLEDEEGSEDSLDLASSASN---SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           +  +   EE + + ++          S   L+    S      DP+R+YLR++    LL+
Sbjct: 25  EASEAFAEERAIEPVEAEIVEPEALLSDAELEDLFRSDPSLASDPLRLYLRDIAEAPLLT 84

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+ +AKRI+ G    +     S L     I  R  +  G +LL  I
Sbjct: 85  PEEEVELAKRIKEGDTEALQRFVRSNLRLVVSIAKRY-VGRGLSLLDLI 132


>gi|254416030|ref|ZP_05029786.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177205|gb|EDX72213.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 380

 Score =  196 bits (499), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 137/279 (49%), Positives = 192/279 (68%), Gaps = 4/279 (1%)

Query: 405 SILKIRNEIK---SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            + +IR+ +        + G    E    +   R+       AK++MV++NLRLV+S+AK
Sbjct: 102 ELERIRDRLYDQLEREPKEGEWAKEVEMELPAFRQRLFLGRRAKEKMVQSNLRLVVSIAK 161

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+
Sbjct: 162 KYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRL 221

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG
Sbjct: 222 PVHLYETISRIKKTTKILSQELGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPIG 281

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      T
Sbjct: 282 KEEDSRLGDFIE-ADGETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKT 340

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           LEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 341 LEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 379



 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 32/68 (47%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D  D   E    +  +  S         ++ +      T+D +R+YL+E+G I LL  + 
Sbjct: 30  DMADGNSEAVQPEPGEEDSKPGKVRSTRRRTQAKKKHYTEDSIRLYLQEIGRIRLLRADE 89

Query: 139 EIAIAKRI 146
           EI +A++I
Sbjct: 90  EIELARKI 97


>gi|297625160|ref|YP_003706594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
 gi|297166340|gb|ADI16051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
          Length = 446

 Score =  196 bits (499), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 155/368 (42%), Positives = 216/368 (58%), Gaps = 30/368 (8%)

Query: 344 DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN--FVAC 401
           D+ K +     E+  LA+   +  D F E     +LD       +D  E E +       
Sbjct: 79  DLMKVLEARGVEIADLAEDEVLDEDEFDEVDALGDLDEPEDELVRDREEIEARAEAMAGS 138

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMV-------------------------RK 436
            + +   +R  +  I   + +++ E   +   +                         ++
Sbjct: 139 RLSTNDPVRQYLHEIGRVSLLTLEEEISLARRIEEGEAAQKRLDEEGDSLPEREQRALKR 198

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
              +  +A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKF
Sbjct: 199 IVEDGEMARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYRRRYKF 258

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ REP+ EE+A+ +
Sbjct: 259 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREPSYEEVAEAM 318

Query: 557 --AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
                 E V +V K+++EP+SLETPIGDE  S  GDFI D N  SP+D A +  L E   
Sbjct: 319 GPGWSAEKVEEVFKVSQEPVSLETPIGDEKDSFYGDFIPDDNVESPVDQASKTLLSEELE 378

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRS 673
           + L  LT RE  VL+ R G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H SR+
Sbjct: 379 KALDKLTERESMVLKFRKGLVDGREHTLEEVGAHFGVTRERIRQIENKALRKLKYHESRT 438

Query: 674 KKLRSFLD 681
           +KLR FLD
Sbjct: 439 RKLRDFLD 446



 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/144 (26%), Positives = 68/144 (47%), Gaps = 19/144 (13%)

Query: 30  SWKKMIKLARQRGYVTIEEL-------NAFLPPDEVSSEQMEDTVAMLSNMGINVVD--G 80
           + +++++ A + G V  EE+       N  L   +      +D + +L   G+ + D   
Sbjct: 38  AIQRLLEAATRDGSVNTEEMTTALTAANEALAEGDTEI-SFDDLMKVLEARGVEIADLAE 96

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR---------STDDPVRMYLREMGSI 131
           D++ DE+  ++   L          ++ R++   R         ST+DPVR YL E+G +
Sbjct: 97  DEVLDEDEFDEVDALGDLDEPEDELVRDREEIEARAEAMAGSRLSTNDPVRQYLHEIGRV 156

Query: 132 ELLSREGEIAIAKRIEAGRAMMMA 155
            LL+ E EI++A+RIE G A    
Sbjct: 157 SLLTLEEEISLARRIEEGEAAQKR 180


>gi|218245044|ref|YP_002370415.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257058068|ref|YP_003135956.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218165522|gb|ACK64259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256588234|gb|ACU99120.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 379

 Score =  196 bits (498), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 135/279 (48%), Positives = 190/279 (68%), Gaps = 4/279 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIV---SMVRKGECEASIAKKEMVEANLRLVISVAK 461
            + +IR ++          +   + I       ++       AK +MV +NLRLV+S+AK
Sbjct: 101 ELERIREKMTEHMGRFPTDLEWSQAINMEWHAFQRRLYLGRKAKDKMVHSNLRLVVSIAK 160

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+
Sbjct: 161 KYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRL 220

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVH+ + I ++ +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG
Sbjct: 221 PVHLYETISRIKKTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIG 280

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      T
Sbjct: 281 KEEDSRLGDFIE-ADGENPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKT 339

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           LEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 340 LEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 378



 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNS-------SVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +D D+ E+ E   D       A+         S   ++  +     T+D +R+YL+E+G 
Sbjct: 21  IDPDEGEEIELMTDEALDEVMANPEGKKTRKLSASRRRDPNKKKPYTEDSIRIYLQEIGR 80

Query: 131 IELLSREGEIAIAKRI 146
           I LL  E EI +A++I
Sbjct: 81  IRLLRAEEEIELARKI 96


>gi|163847594|ref|YP_001635638.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222525449|ref|YP_002569920.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163668883|gb|ABY35249.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449328|gb|ACM53594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 345

 Score =  196 bits (498), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 121/307 (39%), Positives = 187/307 (60%), Gaps = 24/307 (7%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC------------------- 439
           +     ++  +++ ++ I   + ++ +E   +   + +G                     
Sbjct: 39  IEQVEPTLDAVQHYLQEIGRVSLLTAAEEIELAERIERGNEAEAQLATATDLTPRERYEL 98

Query: 440 -----EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                +   A++ +++ANLRLV+S+AKKY  RGL  LDLIQEGNIGLM+A EKFD+  G 
Sbjct: 99  LQAVQQGEEARRHLIQANLRLVVSIAKKYVGRGLALLDLIQEGNIGLMRAVEKFDYHKGN 158

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++QA+TR+IA+Q  TIR+PVHM + + +V R A R++  ++R+PT EEIA 
Sbjct: 159 RFSTYATWWIRQAVTRAIAEQGRTIRLPVHMSESVGQVKRIAERLAQSLERQPTAEEIAM 218

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L  PVE ++++L+  + P+SLETP+GDE    LGDF+ D+   +P + A Q  LR    
Sbjct: 219 ALGQPVERIQRILEAARRPVSLETPVGDEGEHTLGDFLTDEELPTPGEMAAQKLLRRDLC 278

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L  L  RE R++ +R+G+      TLEEVG+   +TRER RQIEA+A+R+L+ P   +
Sbjct: 279 AALDRLNDRERRIIDLRYGLVDGRRRTLEEVGRVLGMTRERARQIEAEALRRLRSPEVGQ 338

Query: 675 KLRSFLD 681
            LR +L+
Sbjct: 339 HLRDYLE 345



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 37/104 (35%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           + E+        D         +            T D V+ YL+E+G + LL+   EI 
Sbjct: 10  EKEEVSLHTHERDERFGHEEEILSPDLSDIEQVEPTLDAVQHYLQEIGRVSLLTAAEEIE 69

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +A+RIE G          + LT +        +  G    R +I
Sbjct: 70  LAERIERGNEAEAQLATATDLTPRERYELLQAVQQGEEARRHLI 113


>gi|37522577|ref|NP_925954.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35213578|dbj|BAC90949.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 305

 Score =  196 bits (498), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 114/269 (42%), Positives = 180/269 (66%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ +S    ++  +   +  ++  G  EA  AK+ +V ANLRLV+S+AKKY NRG+ FLD
Sbjct: 36  LREMSRYPLLTSEQEVELAQVIATGGSEAEAAKRRLVRANLRLVVSIAKKYLNRGVPFLD 95

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG IGLM+AAEKFD+  G+KFSTYA WW++Q ITR+IA QS T+R+PVHM +K+++V
Sbjct: 96  LIQEGAIGLMRAAEKFDFERGFKFSTYAYWWIRQGITRAIASQSRTVRLPVHMVEKLNQV 155

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R  R+++ ++ R+PT  E+A+ L + ++ + ++L   +  +SL   +G E+ + L   I
Sbjct: 156 KRVRRQLTQELARKPTKPEMAEALELDIDKLDEILDAGRRTLSLHVKVGKEEDTELLQLI 215

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED + +SP +      L E    +L  LTPRE  ++ +RFG+     +TL ++G+ + ++
Sbjct: 216 EDSDTISPSEVLDHNLLVEQIESLLHLLTPRERDIIELRFGLADGNSYTLADIGEMYNLS 275

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQI+AKA+RKL+HP R   LR + +
Sbjct: 276 RERVRQIQAKAMRKLRHPRRQVLLRDWAE 304



 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCE 159
           S   Q+R  ++  S +D V  +LREM    LL+ E E+ +A+ I  G          L  
Sbjct: 14  SDPQQRRGRTSQASLEDSVGQFLREMSRYPLLTSEQEVELAQVIATGGSEAEAAKRRLVR 73

Query: 160 SPLTFQALIIWRDELNDGTTLLREI 184
           + L     I  +  LN G   L  I
Sbjct: 74  ANLRLVVSIAKKY-LNRGVPFLDLI 97


>gi|88801442|ref|ZP_01116970.1| putative sigma factor A [Polaribacter irgensii 23-P]
 gi|88782100|gb|EAR13277.1| putative sigma factor A [Polaribacter irgensii 23-P]
          Length = 287

 Score =  196 bits (498), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +  +++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQLIK---AGDQRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+ EEIAKKL M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKMYAFLEQENERPPSAEEIAKKLDMTVNDVKESMKNSGRHVSMDAPLIEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+++ FG+G +   TLEE+G+ 
Sbjct: 195 YDVLNSGESPNPDRKLLHESLRIEIDRALETLTPREADVVKLYFGLGEHQPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L ++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILMTYL 286



 Score = 45.2 bits (105), Expect = 0.035,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+ I+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQLIKAGDQRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|219849586|ref|YP_002464019.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543845|gb|ACL25583.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 314

 Score =  196 bits (498), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 98/279 (35%), Positives = 171/279 (61%), Gaps = 4/279 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             +I + R   + ++ E  +  +E + + + V         A+ +++ +NLRLV+S+A++
Sbjct: 37  AQTIAQGRRAAERLTNEPSLHSTEKKRLAAQV----AAGEQARAQLINSNLRLVVSIARR 92

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL  LDLIQEG+IGLM+A +KFD   G KFSTYA +W++Q+I R+IAD S T+R+P
Sbjct: 93  YQGHGLTLLDLIQEGSIGLMRAVDKFDAGRGLKFSTYATYWIRQSIGRAIADHSRTVRLP 152

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VH+ +++ ++ R  + ++ ++ REPT EE+A    + VE V +  +    P SL+    +
Sbjct: 153 VHLGERLSRLARLRQELAQQLDREPTLEELANAAGLSVEQVERAEQAGLAPTSLDEAHTE 212

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +    L + + D    +P D   +  L+      L+ L+PRE  +LR+R+G+     HTL
Sbjct: 213 DGGGALSEILTDPLQPTPFDEVSEGMLQADVQAALSQLSPRERNILRLRYGLDGEPMHTL 272

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++G++  +TRER+RQ+E +A+RKL+ PS   +L+ +++
Sbjct: 273 EQIGQRLRLTRERVRQLEYEALRKLRDPSLYPQLQGYVN 311



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/73 (26%), Positives = 31/73 (42%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
            RS  D + +YL E+G+  LL+ E E  +A+ I  GR        E  L          +
Sbjct: 8   GRSASDTIVLYLNEIGAEPLLTFEQEQQLAQTIAQGRRAAERLTNEPSLHSTEKKRLAAQ 67

Query: 174 LNDGTTLLREIID 186
           +  G     ++I+
Sbjct: 68  VAAGEQARAQLIN 80


>gi|110638185|ref|YP_678394.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
 gi|110280866|gb|ABG59052.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
          Length = 287

 Score =  196 bits (498), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 101/274 (36%), Positives = 172/274 (62%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   +R       +A +++ +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTPDEEVDLAKRIR---EGDQLALEKLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  K +REP+P+E+A+ L +    V   LKI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSELEQKYEREPSPDELAEVLEVSTAEVVDTLKISGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+ +  +P  S +  +LR    R L++LT RE  V+ + FG+      TLEE+G
Sbjct: 193 SLLDVLENSSESAPDSSLMNDSLRREVQRALSTLTQREADVISLYFGLNGEHSMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+H SRSK L+ +L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRHTSRSKALKPYL 286



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +AKRI  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPDEEVDLAKRIREGDQLALEKLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|300777898|ref|ZP_07087756.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
 gi|57471279|gb|AAW50925.1| RpoD [Chryseobacterium indologenes]
 gi|300503408|gb|EFK34548.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
          Length = 288

 Score =  196 bits (498), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   +R        A +++++ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGKVELITADEEVELAQRIR---AGDRAALEKLIKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GLMKAA+++D   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+PEE+A+ L M  E +++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + SP    +  +L+    R L +LTPRE  ++R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPSPDKDLMLESLQIEIERALNTLTPREADLVRLYFGLNGKHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAI++LKH +RSK L+S+L
Sbjct: 255 FDLTRERVRQIKEKAIKRLKHNTRSKILKSYL 286



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G +EL++ + E+ +A+RI AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVELITADEEVELAQRIRAGDRAALEKLIKANLRF--VVSVSKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|224024118|ref|ZP_03642484.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
 gi|224017340|gb|EEF75352.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
          Length = 317

 Score =  196 bits (498), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 175/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 49  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 105

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 106 SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 165

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 166 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 225

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGI    + TLEE+G +
Sbjct: 226 LDVLVNDDSPMADRSLVNESLSREIDRALSTLTEREKDIIQMFFGIN-TQEMTLEEIGDK 284

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 285 FGLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 316



 Score = 44.4 bits (103), Expect = 0.067,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 52  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 109

Query: 184 IID 186
           +I+
Sbjct: 110 LIN 112


>gi|156742838|ref|YP_001432967.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234166|gb|ABU58949.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 351

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 116/249 (46%), Positives = 170/249 (68%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ +   +A  A++ +++ANLRLV+SVAKKY    L F+DL+QEGNIGLM+A EKFD   
Sbjct: 103 LLERRVVQAEEARRRLIQANLRLVVSVAKKYIGGPLSFMDLVQEGNIGLMRAVEKFDASK 162

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +FSTYA WW++QAITR+IA+QS  IR+PVH+ D I +V R ARR+   ++REPT +EI
Sbjct: 163 GNRFSTYATWWIRQAITRAIAEQSRLIRLPVHLSDVIAQVRRVARRLEQSLEREPTIKEI 222

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + MP   V+ +L+ + +PISLE PI ++    +G+ + D  A +P++ A Q  L+  
Sbjct: 223 AEAVGMPERKVKMLLQASAQPISLEQPITNDGEGQIGELLADDGADAPMEIATQHMLQRD 282

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + L  L  RE  VLR+R+G+      TLEE+G  F +TRER RQIEA A+R L+ P  
Sbjct: 283 LEQALMDLPDRERAVLRLRYGLTDGRRRTLEEIGSAFGITRERTRQIEADALRLLRRPGV 342

Query: 673 SKKLRSFLD 681
           S +L+++L+
Sbjct: 343 SARLQAYLE 351



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E   D        ++ +  + +R  S+  + DD  +MYLRE+G + LLS   E+A+A  I
Sbjct: 22  EQEADPESDVFWQTDFADVVAQRA-SSGETLDDSTQMYLREIGQVSLLSAAEEVALANDI 80

Query: 147 EAGRA-MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            AGR      ++       + L++ R  +       R I
Sbjct: 81  SAGREAQERLNVQHFDSVDERLLLERRVVQAEEARRRLI 119


>gi|300858635|ref|YP_003783618.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686089|gb|ADK29011.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206344|gb|ADL10686.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis C231]
 gi|302330901|gb|ADL21095.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276586|gb|ADO26485.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis I19]
          Length = 329

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 107/252 (42%), Positives = 172/252 (68%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   ++    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 76  RAMKRDLKVLVKDGRKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 135

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 136 FDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREA 195

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +
Sbjct: 196 TNEELAEESGIDESKIEILLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDAESAVVAS 255

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL +L  RE+ V+RMR+G+      TL+++G+QF ++RER+RQIE + + KL
Sbjct: 256 LRHSDIRSVLDTLERREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMTKL 315

Query: 668 KHPSRSKKLRSF 679
           +  +R+ KLR++
Sbjct: 316 RDGARADKLRAY 327



 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM-MASLCESPLTFQ 165
            +R  + D  + D VR+YL  +G   LLS E E+ +A+ IE G     +    E PLT  
Sbjct: 18  SRRGQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQTIEVGLYAAHLLEDSEEPLTRA 77

Query: 166 ALIIWRDELNDGTT 179
                +  + DG  
Sbjct: 78  MKRDLKVLVKDGRK 91


>gi|260063687|ref|YP_003196767.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88783132|gb|EAR14305.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQAALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M VE V++ LK +   +S++ P+ D + S+L
Sbjct: 135 INKINKTFAFLEQAHERVPSAEEIAKELDMTVEDVKQSLKNSGRHVSMDAPLIDGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDKELLHESLRTEIERALETLTPREADVIRLYFGLAGQHSMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQAALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|328954372|ref|YP_004371706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454696|gb|AEB10525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 436

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 125/257 (48%), Positives = 185/257 (71%), Gaps = 1/257 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + +   +R+ E E   A+ EM++ANLRLV+S+AKKY +RGL F DLIQEGN+GLMKA
Sbjct: 181 EEIKQLAKKIREKENEVVRARDEMIKANLRLVVSIAKKYLHRGLSFSDLIQEGNLGLMKA 240

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++D+  GY+ ST+A WW++Q ITR+I D++ TIRIPVH+++  ++  R    +  ++ 
Sbjct: 241 VTRYDYTTGYRLSTFASWWIRQTITRAIYDKTRTIRIPVHLQEIRNRCYRAFYDLLKELG 300

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP  +EIA++  +P + +  V  ++ EPISLETP+  ++   LGDFI +  A+SP DS 
Sbjct: 301 REPLLKEIAERSGVPEDKILVVTNLSDEPISLETPV-GDEGDRLGDFIRNDQAISPFDSI 359

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I + L E T  +L++LTPREE++++MRFGIG   +HTLEE+G++F V+RERIRQIE KA+
Sbjct: 360 ISSELSEKTDAILSTLTPREEKIMKMRFGIGAEVEHTLEEIGREFKVSRERIRQIEKKAL 419

Query: 665 RKLKHPSRSKKLRSFLD 681
           ++LKHP+R   L  FL+
Sbjct: 420 KRLKHPTRKATLEDFLE 436



 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 27/134 (20%), Positives = 56/134 (41%), Gaps = 6/134 (4%)

Query: 26  FSDDSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
              D   K+I L +++G Y+T + LN  +P D +   ++++    L    I VVD  +  
Sbjct: 1   MDRDYIDKIIHLGKEKGGYLTYDNLNELIPSDIIDPTEIKEVFDSLQEEEIEVVDSIEDV 60

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                E + +   +    +   ++  +         V  Y REM    +L+ E E  + +
Sbjct: 61  SYPSMELTEETGEAEIEEAFDTEEVPEQEGI-----VAAYFREMLRYSVLTPEEEKELGR 115

Query: 145 RIEAGRAMMMASLC 158
            I+ G+  ++  + 
Sbjct: 116 IIKNGQETILRLVS 129


>gi|332707223|ref|ZP_08427276.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
 gi|332353957|gb|EGJ33444.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
          Length = 373

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 133/246 (54%), Positives = 181/246 (73%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R        AK++MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GY
Sbjct: 128 RYRLHVGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 187

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA 
Sbjct: 188 KFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIAD 247

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE   
Sbjct: 248 RMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKNLLREDLE 306

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL +L+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+ 
Sbjct: 307 SVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS 366

Query: 675 KLRSFL 680
            L+ ++
Sbjct: 367 ILKEYI 372



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           +++ D   D+       +  S         ++ +      T+D +R+YL+E+G I LL  
Sbjct: 21  LIEDDVNRDDLVDAQPDEENSKPGKGRSNRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRA 80

Query: 137 EGEIAIAKRIEA--GRAMMMASLCE 159
           + EI +A++I        +   L E
Sbjct: 81  DEEIELARKIADLLELERVRERLSE 105


>gi|269126637|ref|YP_003300007.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311595|gb|ACY97969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 444

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 113/251 (45%), Positives = 171/251 (68%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  M+EANLRLV+SVAKKY++RGL  LD++QEGN+GL++A EKF
Sbjct: 192 ELREELEWVAADGREAKSHMLEANLRLVVSVAKKYSDRGLSLLDVVQEGNLGLIRAVEKF 251

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYAMWW++QAI R  AD + TIR+PVH+ + + K+ R  R M  ++ REPT
Sbjct: 252 DYTKGFKFSTYAMWWIRQAIQRGFADSARTIRLPVHVLEMLSKLSRVERDMHQRLGREPT 311

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEE+A +L      VR++L+ +++PISL++ IG++  + +GD IED ++    +   +  
Sbjct: 312 PEELAAELDKSPAQVRELLRTSRQPISLDSTIGEDGETRIGDLIEDIDSPEASEMVDRQL 371

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +   R L+ L+PREE ++ MRFG+   T  TL+E+GK   +TRERIRQ+E +++ KL+
Sbjct: 372 MADQLRRSLSILSPREEMIMSMRFGLYDGTPRTLDEIGKHLGLTRERIRQLEKESLSKLR 431

Query: 669 HPSRSKKLRSF 679
           HPS +  L  F
Sbjct: 432 HPSNATPLLDF 442



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 58/170 (34%), Gaps = 40/170 (23%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +   + S    + +++  R +G++++ E+        +S  Q    +  +S  G+++   
Sbjct: 8   APFQEASSTPLEALLERGRAQGHLSLGEVREAFRAAGISPAQGRSILREISEAGVSLAAE 67

Query: 81  DDL----------------------------------------EDEEGSEDSLDLASSAS 100
           D+                                         E  E   +   L   A 
Sbjct: 68  DEAPASNGRKSTRAAGKKPGATAGAKAASTGNRTAAPEQADVPEAAEEPLEDEALQIDAL 127

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +        D    S  D V  YL+ +G  +LL+ E E+ +AKRIEAG 
Sbjct: 128 QADTADALDLDDMSSSMGDSVHTYLKSIGRRQLLTAEQEVELAKRIEAGL 177


>gi|328950970|ref|YP_004368305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451294|gb|AEB12195.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
          Length = 477

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 139/257 (54%), Positives = 186/257 (72%), Gaps = 7/257 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + + R    +  +A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++A EK
Sbjct: 225 KRYLHLAR----DGELARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEK 280

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++   YKFSTYA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  +  REP
Sbjct: 281 FEYKRRYKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQEKGREP 340

Query: 548 TPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + EEIA+ +      + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+D+A 
Sbjct: 341 SYEEIAEAMGPGWDAKRVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDAAA 400

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           Q+ L E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA+R
Sbjct: 401 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALR 460

Query: 666 KLK-HPSRSKKLRSFLD 681
           KLK H SR++KLR FLD
Sbjct: 461 KLKYHESRTRKLRDFLD 477



 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 44/175 (25%), Positives = 77/175 (44%), Gaps = 20/175 (11%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELN----AFLP--P 55
           +  K+R R +      ++D L       + + +++  ++ G ++ EE+       LP   
Sbjct: 23  STTKRRRRSAKKTEGTAEDVLESR----AVRTLLQKGKKSGSLSQEEVRQVMEEALPNLD 78

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
           D+   E  E+ + +L   GI+V+  D+  +E   E   DL+      +  +         
Sbjct: 79  DDAFEESYEEVIDLLEGEGIDVLSEDEELEEPILEGEDDLSEDEPAIATRV--------- 129

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           S  DPVR YL E+G + LL+ E EI +A+R+E G    +  L E       LI  
Sbjct: 130 SISDPVRQYLHEIGQVPLLTLEEEIDLARRVEEGE-AAIEKLSEFTGLDAHLIKQ 183


>gi|305681000|ref|ZP_07403807.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
 gi|305659205|gb|EFM48705.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
          Length = 365

 Score =  196 bits (497), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 107/248 (43%), Positives = 171/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 116 RDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYA 175

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE
Sbjct: 176 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEE 235

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +    
Sbjct: 236 LAEESGIDESKIELLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEAADAESAVVASLRHS 295

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               V+ +L  RE+ V+RMR+G+      TL+++G+QF ++RER+RQIE + +RKL+   
Sbjct: 296 DIRDVIGTLEDREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMRKLRDGQ 355

Query: 672 RSKKLRSF 679
           R++KLR +
Sbjct: 356 RAEKLREY 363



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           +  ED   ++ +   ++VD D   D+    D  D  S+   +     +R  + D  + D 
Sbjct: 10  DNEEDLDVVMGDEPTDLVDDDPGADD--ILDPTDEESAFDLAVDRGSRRGQNNDNPSADL 67

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           VR+YL  +G   LL+ E E+ +A+ IE G 
Sbjct: 68  VRVYLNGIGKTALLTAEDEVHLAQTIEVGL 97


>gi|319441590|ref|ZP_07990746.1| RNA polymerase sigma factor SigB [Corynebacterium variabile DSM
           44702]
          Length = 397

 Score =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 105/252 (41%), Positives = 170/252 (67%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EK
Sbjct: 144 RARKRDLKILAREGRAARTHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEK 203

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE 
Sbjct: 204 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREA 263

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  +LK +++P+SL+ P+G ++ + LGDFIED ++     + + +
Sbjct: 264 TNEELAEESGIDESKIETLLKQSRDPVSLDMPVGSDEEAPLGDFIEDSDSTDAEAAVVAS 323

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   VL +L  RE+ V+++R+G+      TL+++G+ F ++RER+RQIE + + KL
Sbjct: 324 LRHSDVRAVLDTLEEREQDVIKLRYGLDDGMPRTLDQIGRSFGLSRERVRQIEREVMAKL 383

Query: 668 KHPSRSKKLRSF 679
           +   R++KLR +
Sbjct: 384 REGERAEKLREY 395



 Score = 41.0 bits (94), Expect = 0.65,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +A +      +R+ + +  + D VR+YL  +G   LL+   E+ +++RIEAG 
Sbjct: 78  AAEDRPKDKGRRRGNNENPSADLVRVYLNGIGKTALLTAADEVELSQRIEAGL 130


>gi|15807631|ref|NP_294640.1| RNA polymerase sigma-A factor [Deinococcus radiodurans R1]
          Length = 360

 Score =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 144/291 (49%), Positives = 198/291 (68%), Gaps = 10/291 (3%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E +  +A  ++   + R   K +  +  +     R ++  +     + + A++ ++EANL
Sbjct: 77  EEEIALARRIEEGEEAR---KQLEEDESLDDRSRRRLMRQME----DGAAARQGLIEANL 129

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKYT RGL FLDLIQEGN GL++A EKF++   YKFSTYA WW++QAI R+IA
Sbjct: 130 RLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIRQAINRAIA 189

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITK 571
           DQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T EEIA+ +        V +V K+++
Sbjct: 190 DQARTIRIPVHMVETINKLTRTARQLQQELSREATHEEIAEAMGPGWDAAKVEEVQKVSQ 249

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EP+SLETPIGDE  S  GDFI D+N  SP+D+A +  L E   + L  LT RE  VL+ R
Sbjct: 250 EPVSLETPIGDEKDSFYGDFIPDENLDSPVDNAAKTLLSEELEKALGKLTEREAMVLKFR 309

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
            G+    +HTLEEVG++F VTRERIRQIE KA+RKLK H SR++KLR FLD
Sbjct: 310 KGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLKYHESRTRKLRDFLD 360



 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 34/66 (51%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED++   + A       +   D     ++DPVR YL E+G + LL+ E EIA+A+RIE G
Sbjct: 30  EDAVPGTAQAQQDDDEEKYFDDMPRAVSNDPVRQYLHEIGRVSLLTLEEEIALARRIEEG 89

Query: 150 RAMMMA 155
                 
Sbjct: 90  EEARKQ 95


>gi|217140|dbj|BAA01749.1| principal sigma factor [Synechococcus elongatus PCC 7942]
          Length = 384

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 148 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 207

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 208 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 267

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL++L+PR
Sbjct: 268 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPR 326

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 327 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 383



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLS 135
           VV+           D++D   S         K K    ++ T+D +R+YL+E+G I LL 
Sbjct: 31  VVEPATTIAPTADVDAIDDEDSVGEDEDAAAKAKAKVRKTYTEDSIRLYLQEIGRIRLLR 90

Query: 136 REGEIAIAKRIEA--GRAMMMASLCE 159
            + EI +A++I        +   L E
Sbjct: 91  ADEEIELARQIADLLALERIRDELLE 116


>gi|124006216|ref|ZP_01691051.1| RpoD [Microscilla marina ATCC 23134]
 gi|123988140|gb|EAY27798.1| RpoD [Microscilla marina ATCC 23134]
          Length = 287

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 101/274 (36%), Positives = 173/274 (63%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   +R       +A +++ +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTPDEEVELAKRIR---EGDQVALEKLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  K +REP+P+E+A+ L +    V   LKI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSELEQKYEREPSPDELAEVLDVTTSEVVDTLKISGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+++ V P    +  +LR+   R L++LT RE  V+ + FG+      TLEE+G
Sbjct: 193 SLLDVLENESEVKPDSELMNDSLRKEVQRALSTLTQREADVITLYFGLNGEHAMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+H SRSK L+ +L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRHTSRSKALKPYL 286



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +AKRI  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPDEEVELAKRIREGDQVALEKLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|120434745|ref|YP_860432.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
 gi|117576895|emb|CAL65364.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
          Length = 287

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDDRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M +  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQSHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDKELLHESLRTEIERALETLTPREADVIRLYFGLGDQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDDRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|332292552|ref|YP_004431161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|332170638|gb|AEE19893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 287

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDHRALEKLTKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+PEEIAK+L M +  V++ LK +   IS++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQANERPPSPEEIAKELDMSINDVKESLKNSGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +L+    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLNSGESPNPDRELLHESLKTEIERALETLTPREADVVRLYFGLGDQQPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDHRALEKLTKANLRF--VVSVSKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|227503471|ref|ZP_03933520.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|306836281|ref|ZP_07469263.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
 gi|227075974|gb|EEI13937.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|304567873|gb|EFM43456.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
          Length = 337

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 105/265 (39%), Positives = 177/265 (66%), Gaps = 4/265 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++    ++ +E R +  + R    E   A+  ++EANLRLV+S+AK+YT RG+  LDLI
Sbjct: 75  KLNNAEKLTRAEKRDLKILAR----EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLI 130

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R
Sbjct: 131 QEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSR 190

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R M   + RE T EE++++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED
Sbjct: 191 IKREMYQSLGREATNEELSEESGIDENKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIED 250

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A     + + +        V+ +L  RE+ V+R+R+G+      TL+++G++F ++RE
Sbjct: 251 AEATDAETAVVASMRHSDIRGVIDTLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRE 310

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE + + KL+  +R+ +LR +
Sbjct: 311 RVRQIEREVMAKLRDGNRADRLREY 335



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 27/55 (49%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +          +R  + D  + D VR+YL  +G  +LLS E E+ +A+ IE G 
Sbjct: 16  TTDEEQEVDRGSRRNQTNDNPSADLVRVYLNGIGKTDLLSAEDEVELAQTIEVGL 70


>gi|318066939|emb|CBY89084.1| RNA polymerase sigma70 factor [Halomonas elongata]
          Length = 367

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 111/394 (28%), Positives = 158/394 (40%), Gaps = 46/394 (11%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             T DPVRMY+REMG+++LL+REGEI IAKRIE G   +M+SL   P    +++   D  
Sbjct: 19  GRTTDPVRMYMREMGTVKLLTREGEIQIAKRIEEGTREVMSSLAYLPGAVASILDAYDAT 78

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            D     R        I P+   G     E    +                         
Sbjct: 79  QDEEAPGRLSDLFSGFIDPD--EGIPGVAEAEVPEPEPXXXXXXXXXXXXXXXXXXXXXX 136

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                                                            L  +A+ +  L
Sbjct: 137 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXFLPLKMVAKQFERL 196

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                                         VG + ++       VEQ+    K ++    
Sbjct: 197 ------------------------------VGQVRIS-------VEQVCAQEKAVIQL-- 217

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIK 414
                 +   + R  F++   G E    W+         ++ + +A     I + + +I 
Sbjct: 218 ----CVKKVKVPRKTFIKSFPGNESRQTWLDKFMAE-NAKYADRLAPLKGDIQRAQRKIA 272

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
                  + +++ + +   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLI
Sbjct: 273 FEEEMVALVVTDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 332

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           QEGNIGLMKA +KF++  GYKFSTYA WW++QAI
Sbjct: 333 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 366


>gi|227833285|ref|YP_002834992.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184270|ref|ZP_06043691.1| RNA polymerase sigma factor SigB [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454301|gb|ACP33054.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
          Length = 331

 Score =  195 bits (496), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 107/265 (40%), Positives = 177/265 (66%), Gaps = 4/265 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++    ++ +E R +  + R    E   A+  ++EANLRLV+S+AK+YT RG+  LDLI
Sbjct: 69  KLANAEKLTRAEKRDLKILAR----EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLI 124

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R
Sbjct: 125 QEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSR 184

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R M   + RE T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED
Sbjct: 185 IKREMYQSLGREATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIED 244

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A     + + +        V+ SL  RE+ V+R+R+G+      TL+++G++F ++RE
Sbjct: 245 AEATDAETAVVASMRHSDIRSVIGSLEEREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRE 304

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE + + KL+  +R+ +LR +
Sbjct: 305 RVRQIEREVMAKLREGNRADRLREY 329



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 28/63 (44%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +  +  +            +R  + D  + D VR+YL  +G   LLS E E+ +A+ IE
Sbjct: 2   ATSSAASVQDEDGQEVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQTIE 61

Query: 148 AGR 150
            G 
Sbjct: 62  VGL 64


>gi|284046131|ref|YP_003396471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950352|gb|ADB53096.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 367

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 121/270 (44%), Positives = 181/270 (67%), Gaps = 3/270 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     ++  E   +   + +       AK++MVE+NLRLV+S+AK Y N+GL
Sbjct: 99  LQLFLKDIGKVRLLTAQEEVDLAKRIER---GDLDAKQKMVESNLRLVVSIAKNYRNQGL 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEG +GL++AAEKFD+  G+KFSTYA WW++QAI R++AD++ TIRIPVH+ +K
Sbjct: 156 PFLDLIQEGTLGLVRAAEKFDYRKGFKFSTYATWWIRQAIARALADKARTIRIPVHVVEK 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R  R++  ++ REPT EEIA    +  E V  + +  + P+SLE P+GDE+ S  
Sbjct: 216 LNKIGRAERKLVTELGREPTAEEIADVTGIDPEEVDSIKRSAQAPVSLEKPVGDEEESEF 275

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G FI D+ A SP + A +   +E     L +L+ RE RVL +R+G+G     TL+EVG+ 
Sbjct: 276 GQFIADERAESPYERAAEILTKEALREALENLSYRERRVLELRYGLGGEHPRTLDEVGRT 335

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           F VTRERIRQIE ++++KL+  + ++KLR 
Sbjct: 336 FNVTRERIRQIENQSLKKLQSLAEAQKLRD 365



 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 29/145 (20%), Positives = 57/145 (39%), Gaps = 3/145 (2%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  K ++    Q G +T  E+   +   ++    +ED    L    I +V+     D   
Sbjct: 10  EEIKGLVNRGTQLGVLTYAEIARAVSELDLDESDVEDLHGFLERAEIELVEE---IDPAT 66

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  +    +         +   D     T D ++++L+++G + LL+ + E+ +AKRIE 
Sbjct: 67  TASNQVERAPDRRRGRRARTALDLKPDMTTDSLQLFLKDIGKVRLLTAQEEVDLAKRIER 126

Query: 149 GRAMMMASLCESPLTFQALIIWRDE 173
           G       + ES L     I     
Sbjct: 127 GDLDAKQKMVESNLRLVVSIAKNYR 151


>gi|116071891|ref|ZP_01469159.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116065514|gb|EAU71272.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 355

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 116/351 (33%), Positives = 196/351 (55%), Gaps = 10/351 (2%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP-E 392
           R+DLL  +      R++     LL+  +          E H+  EL     ++   +P +
Sbjct: 10  RVDLLTSEEEVTLARLVQRRETLLKQQRELSDTNPAIGELHRLEELQRREANHHSHWPTK 69

Query: 393 GEWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            EW       +  +  +I     + + +  I   E +  +            AK  M++A
Sbjct: 70  QEWARAAGLSLQELQSRIDAGYVAWAEQAAIEAKELKLSLR-------NGRRAKDHMIQA 122

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV++VAKKY  RG++ LDL+QEG +GL +A EKFD   G++FSTYA WW++Q +TR+
Sbjct: 123 NLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQGMTRA 182

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IA QS TIR+PVH+ +K++++ R  + +++   R  +  ++A++L +  + VR+ L+   
Sbjct: 183 IATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIASIADLARELGISEDTVRQTLERVP 242

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +SL++ +G +  + LGD IED  A +P ++     L      +L  LT RE  VLR R
Sbjct: 243 RSVSLDSRVGKDQDTQLGDLIEDGKA-TPEETLTHDELHNDLEGLLDELTTREAAVLRRR 301

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           FG+  +T  TL ++G++  ++RER+RQIE +A+ KL+ P +  K+R ++ G
Sbjct: 302 FGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQPQKRSKIRDYIQG 352



 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 42/255 (16%), Positives = 91/255 (35%), Gaps = 28/255 (10%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +R+YL+++G ++LL+ E E+ +A+ ++                 + L+  + EL+D    
Sbjct: 1   MRLYLQDIGRVDLLTSEEEVTLARLVQRR---------------ETLLKQQRELSDTNPA 45

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E+  LE     E+       T+    +    S QE +           E AA  +K+ 
Sbjct: 46  IGELHRLEELQRREANHHSHWPTKQEWARAAGLSLQELQSRIDAGYVAWAEQAAIEAKEL 105

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           +  +        N  R  D     +   + A+  + + + M  LD + E    L    + 
Sbjct: 106 KLSL-------RNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEK 158

Query: 301 AVNGQKDEKSSVKC----KVLKEKLVKLVGSLSLNQSRIDLL--VEQLYDISKRIMHNEG 354
               +    S+       + +   +     ++ L     + L  ++++            
Sbjct: 159 FDPTRGFRFSTYAYWWIRQGMTRAIATQSRTIRLPVHVTEKLNRIKRVQQEIASNEGRIA 218

Query: 355 ELLRLAQSYGIKRDV 369
            +  LA+  GI  D 
Sbjct: 219 SIADLARELGISEDT 233


>gi|225011624|ref|ZP_03702062.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
 gi|225004127|gb|EEG42099.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
          Length = 287

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIK---AGDQIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M +  V++ LK +   +S++ P+ + + S+L
Sbjct: 135 INKINKTYAFLEQAHERAPSAEEIAKELDMTINDVKESLKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLNSGESPNPDRVLLHESLRTEIERALETLTPREADVVRLYFGLGDQHAMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ E E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITAEEEVELAQRIKAGDQIALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|170076992|ref|YP_001733630.1| group II sigma-70 type sigma factor [Synechococcus sp. PCC 7002]
 gi|1769590|gb|AAB95227.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169884661|gb|ACA98374.1| Group II sigma-70 type sigma factor (RpoD family) [Synechococcus
           sp. PCC 7002]
          Length = 365

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 183/289 (63%), Gaps = 1/289 (0%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                F+    +  L+++ ++         +       V  +     +  +AK++M+ +N
Sbjct: 76  AHSVKFLNDAEERRLELQEQLGRSPTNEEWASVLGLETVKQLNSALYKGRVAKRKMIRSN 135

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+I
Sbjct: 136 LRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTI 195

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A+ + TIR+P+H+ +K++K+ +  R +   ++R PT  E+A++L +  + + ++L++ ++
Sbjct: 196 ANDARTIRLPIHIVEKLNKLKKAQRTLKQTLQRNPTEAELAQELDITADQLHQLLQLRRQ 255

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMR 631
            +SL   +G  + + L D +ED     P +   +A +R+    VL   LT RE+ V+ +R
Sbjct: 256 SLSLNHRVGKGEDTELVDLLEDDGLQLPEERMSEAMMRQELWDVLGDVLTDREKEVIALR 315

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +G+     HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+S+L
Sbjct: 316 YGLSSEQPHTLEEVGGMFNLSRERVRQIQSKAMRKLRRPQVARRLKSWL 364



 Score = 37.9 bits (86), Expect = 5.7,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D       E S  +  +  + +     R        +D V  + +EM    LL  + E
Sbjct: 15  AQDSHQATELESSNSMVEAEFSETELTNLR--GVRSRNEDTVGAFFKEMARYPLLKPDEE 72

Query: 140 IAIAKRI------EAGRAMMMASLCESP 161
           I +A  +      E  R  +   L  SP
Sbjct: 73  IQLAHSVKFLNDAEERRLELQEQLGRSP 100


>gi|307152083|ref|YP_003887467.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982311|gb|ADN14192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 418

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 111/285 (38%), Positives = 176/285 (61%), Gaps = 2/285 (0%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVI 457
           +    D+      E+K    E     +E  ++ V  + + +     AK++M++ANLRLV+
Sbjct: 133 LERLADAAEITVFELKKTLYEGKRHWAELANLEVQELERVQKAGIYAKEQMIKANLRLVV 192

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y NRGL+ LDLIQEG +GL +A +KFD   GY+FSTYA WW++Q ITR+IA QS 
Sbjct: 193 SVAKRYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWWIRQGITRAIATQSR 252

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            IR+PVH+ +K++K+ +  R+++      P+ EE++++L M    +R+VL      +SLE
Sbjct: 253 IIRLPVHITEKLNKIKKAQRKIAQLKGATPSIEELSQELEMSPPQIREVLMRVPRSVSLE 312

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +G E  + L D +E   A SP D+     LR+    +LA LT RE  V+++R+G    
Sbjct: 313 IKVGKEKDTELIDLLETTEA-SPEDNIANEALRQDLHNLLADLTTREREVIQLRYGFKDG 371

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             ++L ++G+   ++RER+RQIEAKAI+KL+ P R  ++R + + 
Sbjct: 372 KSYSLADIGRTLQLSRERVRQIEAKAIQKLRQPKRRNQIRDYFEA 416



 Score = 45.2 bits (105), Expect = 0.032,   Method: Composition-based stats.
 Identities = 38/270 (14%), Positives = 94/270 (34%), Gaps = 25/270 (9%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           E   D   ++  S         +  R+T D VR+YL+++G + LL ++ E+  A+ ++  
Sbjct: 33  EIDNDALLASDISETETVTASKTHTRATTDLVRLYLQDIGRVPLLKKDEEVQNAQDLQRY 92

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
                          Q L +    + +G  +++  + L       +       +      
Sbjct: 93  --------------IQLLELRSVAIANGDLVIKNFVSLIEKRDQLTSQLGHRPSLERLAD 138

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
             E +  E ++   +      E A    ++      +     E   +        +   +
Sbjct: 139 AAEITVFELKKTLYEGKRHWAELANLEVQELERVQKAGIYAKEQMIKA-------NLRLV 191

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            ++  + + + +  LD I E    L    D     +    S+     +++ + + + +  
Sbjct: 192 VSVAKRYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWWIRQGITRAIAT-- 249

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             QSRI  L   + +   +I   + ++ +L
Sbjct: 250 --QSRIIRLPVHITEKLNKIKKAQRKIAQL 277


>gi|298245985|ref|ZP_06969791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553466|gb|EFH87331.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 417

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 114/280 (40%), Positives = 181/280 (64%), Gaps = 7/280 (2%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A E D+++    EI  + + T       R I  + ++ E     A K+ + ANLRLV+S+
Sbjct: 144 AGESDAVMTYLREIGRVPMITH-----EREI-ELAQRIESGDRDAMKQFILANLRLVVSI 197

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RGL  LDLIQEGNIGL++A +++DW  G++FST+A WW++QAI+R++AD+  TI
Sbjct: 198 AKRYVGRGLTLLDLIQEGNIGLIRAVQRYDWRRGHRFSTHATWWIRQAISRAVADKGRTI 257

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PV++   ++++ R  +R+  ++ REP+ +E+A+   +    + ++      P+SLE P
Sbjct: 258 RLPVYVNTALNRIRRERQRLLQELGREPSEQELAEATGLDPVRMIELQAAPGAPVSLELP 317

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNT 638
           +G++D   LGD + D  + SP D A    L++   RVL S LTPRE+ VL++RFG+G   
Sbjct: 318 VGEDDDQELGDVLPDTESASPEDLATTQTLKDEVQRVLESVLTPREQLVLQLRFGLGNGQ 377

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            H LE+VG++  +TRER+RQIEA A+ KL+ P   ++LR 
Sbjct: 378 AHPLEQVGRELGITRERVRQIEAGALAKLRQPPVLERLRG 417



 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 70/179 (39%), Gaps = 15/179 (8%)

Query: 6   KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
           + +   ++E +D    L  D SD +  ++         +T E+L+     +E   E+++D
Sbjct: 49  REDTHDETELDDDQLELDHDLSDTASLELEDEP----TLT-EDLHDTERDEEDHHEEVDD 103

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
           ++  L  M                            S    +   + AD    D V  YL
Sbjct: 104 SLLTLPPM---------TPAASQPAVRRGATPRRRRSEDQEENAANGADAGESDAVMTYL 154

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RE+G + +++ E EI +A+RIE+G    M     + L     I  R  +  G TLL  I
Sbjct: 155 REIGRVPMITHEREIELAQRIESGDRDAMKQFILANLRLVVSIAKRY-VGRGLTLLDLI 212


>gi|167754493|ref|ZP_02426620.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
 gi|167659118|gb|EDS03248.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
          Length = 286

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 173/272 (63%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   ++K       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKEELITVEEEVELAQRIKK---GDQEALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   R   + +R P+PEE+A +L +P E V   L++    +S++ P  D + + L
Sbjct: 135 LNKINKAFARFEQEHERTPSPEELANELELPKEKVTDTLRVAGRHVSVDAPFADGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++ +     I  +L     R L +LT RE  +++  FGIG +   TLEE+G++
Sbjct: 195 LDVLVNPDSPNADRGLINESLSTEVDRALETLTERERDIIKYFFGIGCSE-MTLEEIGEK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H SRSK L+S+L
Sbjct: 254 FDLTRERVRQIKEKAIRRLRHSSRSKLLKSYL 285



 Score = 44.8 bits (104), Expect = 0.044,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  EL++ E E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKEELITVEEEVELAQRIKKGDQEALEKLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|255535549|ref|YP_003095920.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
 gi|255341745|gb|ACU07858.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
          Length = 294

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 98/272 (36%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   +R       +A +++++ANLR V+SV+K+Y N+GL
Sbjct: 24  LDKYLQEIGKVDLITADEEVDLAQKIR---AGDRVALEKLIKANLRFVVSVSKQYQNQGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GLMKAA+++D   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 81  SLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 140

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+PEE+A+ L M  + +++ +K +   +S++ P+ + + S+L
Sbjct: 141 INKINKAYAHLEQENERPPSPEELAEVLDMSEDDIKESMKNSGRHLSMDAPLVEGEDSNL 200

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + SP    +  +L+    R L +LTPRE  ++R+ FG+      TLEE+G+ 
Sbjct: 201 YDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGET 260

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAI++LKH +RSK L+S+L
Sbjct: 261 FDLTRERVRQIKEKAIKRLKHNTRSKILKSYL 292



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A++I AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 27  YLQEIGKVDLITADEEVDLAQKIRAGDRVALEKLIKANLRF--VVSVSKQYQNQGLSLPD 84

Query: 184 IID 186
           +I+
Sbjct: 85  LIN 87


>gi|87300555|ref|ZP_01083397.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
 gi|87284426|gb|EAQ76378.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
          Length = 398

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 99/283 (34%), Positives = 165/283 (58%), Gaps = 16/283 (5%)

Query: 415 SISVETGISISEFRHIVSM---------------VRKGECEASIAKKEMVEANLRLVISV 459
             +    + ++E R ++                 +++       A+  M++ANLRLV++V
Sbjct: 114 QWAEACDLPVAELRRLLQEGHRTWAACLDLSLSDLQQRLLRGRRARDRMIQANLRLVVAV 173

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY  RG++ LDL+QEG +GL +A EK+D   G++FSTYA WW++Q +TR+IA QS TI
Sbjct: 174 AKKYQKRGVELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAYWWIRQGVTRAIATQSRTI 233

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVH+ +K++++ +  R+ ++   R  +  E+A+ L    E VR  L      ISLE  
Sbjct: 234 RLPVHVTEKLNRIKKAQRQFASDHGRTASLAELAEALQWSEEAVRLTLLRVPRSISLEAK 293

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G +  + LGD +E   + +P  S  +  L      +L  L+ RE  V+R+RFG+  +T 
Sbjct: 294 VGRDQDTPLGDLLE-ATSDTPEQSLTRQQLHSDLDALLDELSEREAEVIRLRFGLADDTP 352

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            TL ++G+   ++RER+RQIE +A+ KL+ P+R  ++  +L G
Sbjct: 353 RTLAQIGEGMQLSRERVRQIETRALHKLRQPARRCRVHDYLAG 395



 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 19/74 (25%), Positives = 42/74 (56%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E E   +      S  ++S   ++ R     R + D VR+YL+++G +++L++E E+ +A
Sbjct: 7   EPEVEVDLDAGPDSVTASSGRAVRGRSPLPSRVSADLVRLYLQDIGRVDMLNQEEELLLA 66

Query: 144 KRIEAGRAMMMASL 157
           ++++A  A++   L
Sbjct: 67  RQVQAREALLSQRL 80


>gi|305666839|ref|YP_003863126.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
 gi|88709063|gb|EAR01297.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
          Length = 287

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 171/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+  E   +   +R       +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIELINAQEEVELAQRIR---AGDQVALEKLTTANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  KLPDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M V  V++ LK T   +S++ P+   + S+L
Sbjct: 135 INKIKKTFSYLEQAHERPPSAEEIAKELEMTVTEVKQSLKNTGRHVSMDAPLRQGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    +  P    +Q +L     R L +L+PRE  V+++ +GIG     TL E+G+ 
Sbjct: 195 YDVLRSGESPRPDKILLQQSLNTEINRALETLSPREADVVKLYYGIGDQQSMTLAEIGQT 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI  KAIRKL+H SRSK L+++L
Sbjct: 255 FDLTRERVRQIREKAIRKLRHNSRSKLLKTYL 286



 Score = 42.1 bits (97), Expect = 0.31,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  IEL++ + E+ +A+RI AG  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKIELINAQEEVELAQRIRAGDQVALEKLTTANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|271965471|ref|YP_003339667.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270508646|gb|ACZ86924.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 452

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 115/292 (39%), Positives = 179/292 (61%), Gaps = 24/292 (8%)

Query: 412 EIKSISVETGISISEFRHIVSMVR------------------------KGECEASIAKKE 447
            +KSI   T ++ ++   +   +                             +   AK  
Sbjct: 159 YLKSIGRRTLLTAAQEVELAKRIEAGLYAESKLEAEPGLSAAARDDLEWVAEDGRRAKDH 218

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+SVAKKYT+RG+  LD++QEGN+GL++A EKFD+  GYKFSTYAMWW++QA
Sbjct: 219 MLEANLRLVVSVAKKYTDRGMALLDVVQEGNLGLIRAVEKFDYTKGYKFSTYAMWWIRQA 278

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R  AD + TIR+PVH+ + + K+ R  R M  ++ REPTPEE+A +L    + + ++L
Sbjct: 279 IQRGFADSARTIRLPVHVLEMLSKLSRVERDMHQRLGREPTPEELAVELDKTPDQIEELL 338

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           + +++PISL   IG++  + +GD IED ++    +   +  L E    VL +L+PRE ++
Sbjct: 339 RTSRQPISLNATIGEDGETTIGDLIEDVDSPEASEVVDRQLLGEQLRGVLGNLSPREAKI 398

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           + +RFG+     HTL+E+GK   +TRERIRQ+E +++ KL+HPS ++ L  +
Sbjct: 399 MALRFGLVDGKPHTLDEIGKHLGLTRERIRQLEKESLSKLRHPSNTRPLLDW 450



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 30/205 (14%), Positives = 64/205 (31%), Gaps = 51/205 (24%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD------ 82
            + ++++   R +G++++ EL        +S  +    +  L+  G+++   ++      
Sbjct: 14  TTLEQLLDRGRVQGHLSLAELRHAFAEAGISPTEGRSILRELTEAGVSLAAENEPALAAG 73

Query: 83  ----------------------------------LEDEEGSEDSLDLASSASNSS----- 103
                                             +  E  ++D  D    A +       
Sbjct: 74  AKKPAAKSTARKTTTRKTKAASDKTAAPENNKSTVRAEPAAKDRKDAGPEAGDEEWTAPE 133

Query: 104 -----VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                       D       D V  YL+ +G   LL+   E+ +AKRIEAG     + L 
Sbjct: 134 EAELEAEPTLDLDDQSSVMGDSVHTYLKSIGRRTLLTAAQEVELAKRIEAGLY-AESKLE 192

Query: 159 ESPLTFQALIIWRDELNDGTTLLRE 183
             P    A     + + +     ++
Sbjct: 193 AEPGLSAAARDDLEWVAEDGRRAKD 217


>gi|86132636|ref|ZP_01051229.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
 gi|85816878|gb|EAQ38063.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
          Length = 287

 Score =  195 bits (495), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 176/272 (64%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIK---AGDHRALEQLTKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+PEEIAK+L M ++ V++ LK +   IS++ P+ + + S+L
Sbjct: 135 INKINKTFAFLEQANERPPSPEEIAKELDMTIKDVKESLKNSGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P  + +  +L+    R L +LTPRE  V+R+ FG+G     +LEE+G+ 
Sbjct: 195 YDVLNSGESPNPDRALLHESLKTEIERALETLTPREADVVRLYFGLGDQRPMSLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ E E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITAEEEVELAQRIKAGDHRALEQLTKANLRF--VVSVSKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|116749951|ref|YP_846638.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116699015|gb|ABK18203.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 433

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 127/279 (45%), Positives = 183/279 (65%), Gaps = 1/279 (0%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            D ILK+               + +R ++   R        AK+EMV+ANLRLV+S+AK+
Sbjct: 156 RDKILKVIVRTFERGTMDYPGNARYREMLVRSRAIMLAIDSAKQEMVKANLRLVLSIAKR 215

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  RG+ F DLIQEGN+GL+KA  +FD   G +FSTYA WWV+Q+I R I D++ TIR+P
Sbjct: 216 YRGRGMSFDDLIQEGNLGLLKAVGRFDHTKGNRFSTYATWWVRQSIIRGIYDKTRTIRLP 275

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VH  +  +   +    +  ++ REP+P+EIA++  +P++ V+ VL +  +PISLETPI  
Sbjct: 276 VHFIELKNLFFKVFYELLKELGREPSPQEIAERAKLPLDKVQMVLTLAAQPISLETPI-G 334

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ED   LGDFIED+ A SP++      L E T  +L+SL PREE++LR+RFGI      TL
Sbjct: 335 EDEQRLGDFIEDERAASPMEECSDRELAEITRSLLSSLQPREEKILRLRFGIDGQPAETL 394

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++GK F V++ERIRQIE KA+RKL++P+R   L++F++
Sbjct: 395 EKIGKTFKVSKERIRQIEKKALRKLRNPNRQSCLKTFME 433



 Score = 45.2 bits (105), Expect = 0.041,   Method: Composition-based stats.
 Identities = 24/103 (23%), Positives = 45/103 (43%), Gaps = 3/103 (2%)

Query: 61  EQMEDTV--AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           + ++D V    L    + + +  D+E  E  +     A         L +   +A    +
Sbjct: 26  DLIDDQVLDERLKRANLGLEEDRDMEGPEAEDILEAAAEREEEDEDLLPEGVTAAGEDFE 85

Query: 119 -DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
            D V  YL+E+ S  LL++E E  +A+ I  G+  ++  +CE 
Sbjct: 86  EDHVTCYLKEVSSYPLLTQERETELAQVIREGQEELVRMVCEC 128


>gi|56750888|ref|YP_171589.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 6301]
 gi|56685847|dbj|BAD79069.1| principal RNA polymerase sigma factor RpoD1 [Synechococcus
           elongatus PCC 6301]
          Length = 399

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 223 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 282

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL++L+PR
Sbjct: 283 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPR 341

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 342 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 398



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSA-SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           VV+           D++D   S   +     + +       T+D +R+YL+E+G I LL 
Sbjct: 46  VVEPATTIAPTADVDAIDDEDSVGEDEDAAAKAKAKVPKTYTEDSIRLYLQEIGRIRLLR 105

Query: 136 REGEIAIAKRIEA--GRAMMMASLCE 159
            + EI +A++I        +   L E
Sbjct: 106 ADEEIELARQIADLLALERIRDELLE 131


>gi|311739612|ref|ZP_07713447.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305428|gb|EFQ81496.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 337

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 105/265 (39%), Positives = 177/265 (66%), Gaps = 4/265 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++    ++ +E R +  + R    E   A+  ++EANLRLV+S+AK+YT RG+  LDLI
Sbjct: 75  KLNNAEKLTRAEKRDLKILAR----EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLI 130

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R
Sbjct: 131 QEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSR 190

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R M   + RE T EE++++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED
Sbjct: 191 IKREMYQSLGREATNEELSEESGIDENKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIED 250

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A     + + +        V+ +L  RE+ V+R+R+G+      TL+++G++F ++RE
Sbjct: 251 AEATDAETAVVASMRHSDIRGVIDTLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRE 310

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE + + KL+  +R+ +LR +
Sbjct: 311 RVRQIEREVMAKLRDGNRADRLREY 335



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +          +R  + D  + D VR+YL  +G   LLS E E+ +A+ IE G 
Sbjct: 16  TTDEEQEVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQAIEVGL 70


>gi|172040574|ref|YP_001800288.1| RNA polymerase sigma factor SigB [Corynebacterium urealyticum DSM
           7109]
 gi|171851878|emb|CAQ04854.1| RNA polymerase sigma factor B [Corynebacterium urealyticum DSM
           7109]
          Length = 340

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 108/248 (43%), Positives = 170/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             V+    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 91  RDVKILAREGKAARTHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYK 150

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE
Sbjct: 151 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATYEE 210

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +P + +  ++K +++P+SL+ P+G ++ + LGDFIED  A     + + +    
Sbjct: 211 LAEESGIPEDRIEMLMKQSRDPVSLDMPVGTDEEAPLGDFIEDSEAEDAEAAVVASLRHS 270

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VLA+L  RE+ V+ +R+G+      TL+++G+QF ++RER+RQIE + + KL+   
Sbjct: 271 DIRSVLATLEQREQDVITLRYGLDDGLPRTLDQIGRQFGLSRERVRQIEREVMAKLREGQ 330

Query: 672 RSKKLRSF 679
           R+ KLR +
Sbjct: 331 RADKLREY 338



 Score = 43.7 bits (101), Expect = 0.095,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 36/76 (47%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
               S    SS    +   ++R+ + +  + D VR+YL  +G   LL+ E E+ +++RIE
Sbjct: 11  APATSTKDDSSQQEQNTDRRRRRGNNENPSADLVRVYLNGIGKTALLTAEDEVELSQRIE 70

Query: 148 AGRAMMMASLCESPLT 163
           AG           PLT
Sbjct: 71  AGLYAEQLLKSGEPLT 86


>gi|126663248|ref|ZP_01734246.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
 gi|126624906|gb|EAZ95596.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
          Length = 287

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 172/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIAK+L M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKMYALLEQSNERPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    I  +L+    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELIHESLQTEIERALETLTPREADVVRLYFGLGDQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|163846411|ref|YP_001634455.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222524178|ref|YP_002568649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163667700|gb|ABY34066.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222448057|gb|ACM52323.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 313

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 98/272 (36%), Positives = 171/272 (62%), Gaps = 4/272 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R   + +  E  + ++E + +++ V         A+ +++ +NLRLV+S+A++Y   GL 
Sbjct: 44  RRAAERLHNEPLLPLAEKQRLIAQV----NAGEQARAQLINSNLRLVVSIARRYQGHGLS 99

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLIQEG++GLM+A +KFD   G KFSTYA +W++Q+I R+IAD S T+R+PVH+ +++
Sbjct: 100 LLDLIQEGSVGLMRAVDKFDASRGLKFSTYATYWIRQSIGRAIADHSRTVRLPVHLGERL 159

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            ++ R  + +S ++ REPT EE+A+   + VE V +  +    P SL+ P  ++    L 
Sbjct: 160 SRLSRLRQELSQQLDREPTLEELAQAAGLSVEQVERAEQAGLAPTSLDEPHTEDGGGALA 219

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + + D    +P D   ++ L+      L  L+PRE  +LR+R+G+     HTLE++G++ 
Sbjct: 220 EILTDPLQPTPFDEVSESMLQADVQHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRL 279

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +TRER+RQ+E +A+RKL+ PS   +L+ +++
Sbjct: 280 RLTRERVRQLEHEALRKLRDPSLHPQLQGYVN 311



 Score = 43.7 bits (101), Expect = 0.096,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 33/73 (45%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
            RS  DP+ +YL E+G+  LL+ E E  +A+ +  GR        E  L          +
Sbjct: 8   GRSASDPIVLYLNEIGAEPLLTFEQEQHLAQTMSQGRRAAERLHNEPLLPLAEKQRLIAQ 67

Query: 174 LNDGTTLLREIID 186
           +N G     ++I+
Sbjct: 68  VNAGEQARAQLIN 80


>gi|313206169|ref|YP_004045346.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|312445485|gb|ADQ81840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|315023147|gb|EFT36160.1| RNA polymerase sigma factor RpoD [Riemerella anatipestifer RA-YM]
 gi|325336386|gb|ADZ12660.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Riemerella anatipestifer RA-GD]
          Length = 288

 Score =  195 bits (494), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   +R       +A +++++ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQKIR---AGDKVALEKLIKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GLMKAA+++D   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+PEE+A+ L M  E +++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + SP    +  +L+    R L +LTPRE  ++R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAI++LKH SRSK L+S+L
Sbjct: 255 FDLTRERVRQIKEKAIKRLKHNSRSKILKSYL 286



 Score = 45.6 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A++I AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRF--VVSVSKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|146299193|ref|YP_001193784.1| RpoD family RNA polymerase sigma factor [Flavobacterium johnsoniae
           UW101]
 gi|57471283|gb|AAW50927.1| RpoD [Flavobacterium johnsoniae]
 gi|146153611|gb|ABQ04465.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacterium
           johnsoniae UW101]
          Length = 287

 Score =  194 bits (493), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 172/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIAK+L M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKMYALLEQSNERPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    I  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELIHESLRTEIERSLETLTPREADVVRLYFGLGDQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|206895369|ref|YP_002247042.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206737986|gb|ACI17064.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 360

 Score =  194 bits (493), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 123/289 (42%), Positives = 181/289 (62%), Gaps = 5/289 (1%)

Query: 395 WKNFVACEVDSILKIRN-EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           ++  +  E + + ++    +  +     ++  + R +   + K     + A++E+++ NL
Sbjct: 73  YEQGLPEEEEQVRELMQVYLHDVGQYDLLTAEQERILAQRIEK---NDAAAREELIKRNL 129

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLVIS+AKKYTN+GL F++LIQEGNIGL+KA EKFDW  GYKFSTYA WW+KQAITR++A
Sbjct: 130 RLVISIAKKYTNKGLSFMELIQEGNIGLIKAVEKFDWRKGYKFSTYATWWIKQAITRALA 189

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKE 572
           DQS  IR PVHM +  H+  +    + N++ REPT +E+A+ L    + V         E
Sbjct: 190 DQSRLIRRPVHMVEAYHQFQKKLNELYNQLGREPTVQELAEALGFSEDKVLALKQMSNPE 249

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P SL+  IGD+D S + DF+ D    +      +   R     VL++L  RE  ++ MR+
Sbjct: 250 PQSLDATIGDQDDSRVQDFVPDTGEGAADKYFWEEERRRVLEEVLSTLNKREREIIEMRY 309

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           G+    +HTLEEVG  F +TRER+RQIE KA+RKL+HP+R +KLR +LD
Sbjct: 310 GLVDGVEHTLEEVGASFNITRERVRQIETKALRKLRHPTRIRKLREYLD 358



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 23/121 (19%), Positives = 48/121 (39%), Gaps = 18/121 (14%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L   L P+++  ++++     L   GI+++  +     E                V  ++
Sbjct: 34  LINSLNPEDLDVDEID---MFLEEKGISIIPEEPRIYGEN---------------VSYEQ 75

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
                +    + +++YL ++G  +LL+ E E  +A+RIE   A     L +  L     I
Sbjct: 76  GLPEEEEQVRELMQVYLHDVGQYDLLTAEQERILAQRIEKNDAAAREELIKRNLRLVISI 135

Query: 169 I 169
            
Sbjct: 136 A 136


>gi|17232755|ref|NP_489303.1| RNA polymerase sigma factor RpoD [Nostoc sp. PCC 7120]
 gi|75907632|ref|YP_321928.1| RNA polymerase sigma factor RpoD [Anabaena variabilis ATCC 29413]
 gi|133465|sp|P26683|RPOD_ANASP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|142108|gb|AAA22043.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134402|dbj|BAB76962.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|75701357|gb|ABA21033.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 390

 Score =  194 bits (493), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 134/246 (54%), Positives = 181/246 (73%), Gaps = 1/246 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R        AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GY
Sbjct: 145 RYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 204

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA 
Sbjct: 205 KFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIAT 264

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ M +E +R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE   
Sbjct: 265 RMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLE 323

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +VL SL+PRE  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+ 
Sbjct: 324 KVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS 383

Query: 675 KLRSFL 680
            L+ ++
Sbjct: 384 VLKEYI 389



 Score = 45.2 bits (105), Expect = 0.037,   Method: Composition-based stats.
 Identities = 20/106 (18%), Positives = 48/106 (45%), Gaps = 2/106 (1%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
           + ++  ++E    ++      ++  D   DE     + +  + +  ++   ++ +     
Sbjct: 17  EIMNQPEIELDDLLIEEDEDLLLADDGDIDEFLEPQTDEDDAKSGKAAKSRRRTQSKKKH 76

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
            T+D +R+YL+E+G I LL  + EI +A++I        +   L E
Sbjct: 77  YTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRERLSE 122


>gi|296269678|ref|YP_003652310.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296092465|gb|ADG88417.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 478

 Score =  194 bits (493), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 110/246 (44%), Positives = 173/246 (70%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +     +   AK  M+EANLRLV+SVAKKYT+RG+  LD++QEGN+GL++A EKFD+  G
Sbjct: 231 LEWVIEDGKRAKDHMLEANLRLVVSVAKKYTDRGMSLLDVVQEGNLGLIRAVEKFDYTKG 290

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYAMWW++QAI R  AD + TIR+PVH+ + + K+ R  R M  ++ REPTPEE+A
Sbjct: 291 YKFSTYAMWWIRQAIQRGFADSARTIRLPVHVLEMLSKLSRVERDMHQRLGREPTPEELA 350

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L    + + ++L+ +++PISL++ IG++  + +GD IED +++   +   +  L E  
Sbjct: 351 VELDKTPDQIEELLRTSRQPISLDSTIGEDGETCIGDLIEDVDSLEASEIVDRQLLAEQL 410

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L +L+PRE +++ +RFG+     HTL+E+GK+  +TRERIRQ+E +++ KL+HPS +
Sbjct: 411 KGMLDNLSPREAKIMSLRFGLVDGKPHTLDEIGKRLGLTRERIRQLEKESLSKLRHPSNA 470

Query: 674 KKLRSF 679
           + L  +
Sbjct: 471 RPLMDW 476



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D DDL  E+   D  D   + ++ +       D       D V  YL+ +G   LL+   
Sbjct: 138 DLDDLAPEDL--DIRDAEITDADLADGGTADLDDTSSVLGDSVHTYLKSIGRRTLLTAAQ 195

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 196 EVELAKRIEAGL 207


>gi|228472793|ref|ZP_04057551.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
 gi|228275844|gb|EEK14610.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
          Length = 287

 Score =  194 bits (493), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     IS  E   +   ++       IA + + +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLISADEEVELAQRIK---AGDKIALERLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNMGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIAK+L M V  V++ +K +   IS++ P+ + + S+L
Sbjct: 135 INKINKMYAYLEQTHERVPSAEEIAKELDMSVNDVKESMKNSGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +L+    R L +LTPRE  V+R+ FG+G N   TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDKELMHESLKTEIERALETLTPREADVIRLYFGLGENYPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FELTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.4 bits (108), Expect = 0.017,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L+S + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLISADEEVELAQRIKAGDKIALERLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|326335966|ref|ZP_08202143.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325691930|gb|EGD33892.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 287

 Score =  194 bits (493), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     IS  E   +   ++       +A + + +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLISADEEVELAQRIK---AGDKVALERLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNMGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIA++L M V  V++ +K +   IS++ P+ + + S+L
Sbjct: 135 INKINKMYAYLEQTHERIPSAEEIARELDMSVSDVKESMKNSGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +L+    R L +LTPRE  V+R+ FG+G N   TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDKELMHESLKTEIERALETLTPREADVIRLYFGLGENYPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FELTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.0 bits (107), Expect = 0.024,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L+S + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLISADEEVELAQRIKAGDKVALERLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|325280261|ref|YP_004252803.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312070|gb|ADY32623.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 286

 Score =  194 bits (492), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 173/272 (63%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKEDLITVEEEVELAQRIRK---GDQKALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   R   + +R P+PEE+A  L +P E V   L+++   IS++ P  + + + L
Sbjct: 135 LNKINKAFSRFEQENERRPSPEELADSLDLPAEKVADTLRVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     + I  +L     R L++LT RE  ++++ FGI    + TLEE+G++
Sbjct: 195 LDVLVNDDSPIADRTLINESLSTEVERALSTLTERERDIIKLFFGIN-TQEMTLEEIGEK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H SRSK L+++L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRHSSRSKLLKTYL 285



 Score = 44.1 bits (102), Expect = 0.075,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGKEDLITVEEEVELAQRIRKGDQKALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|81299460|ref|YP_399668.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 7942]
 gi|93141306|sp|P38023|RPOD1_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD1
 gi|81168341|gb|ABB56681.1| Sigma-70 factor [Synechococcus elongatus PCC 7942]
          Length = 399

 Score =  194 bits (492), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 180/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 223 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 282

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL++L+PR
Sbjct: 283 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPR 341

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 342 ERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 398



 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLS 135
           VV+           D++D   S         K K    ++ T+D +R+YL+E+G I LL 
Sbjct: 46  VVEPATTIAPTADVDAIDDEDSVGEDEDAAAKAKAKVRKTYTEDSIRLYLQEIGRIRLLR 105

Query: 136 REGEIAIAKRIEA--GRAMMMASLCE 159
            + EI +A++I        +   L E
Sbjct: 106 ADEEIELARQIADLLALERIRDELLE 131


>gi|298244164|ref|ZP_06967970.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551645|gb|EFH85510.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 316

 Score =  194 bits (492), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 122/273 (44%), Positives = 180/273 (65%), Gaps = 3/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ IS    +S      +      GE     A+  ++EANLRLV+S+AKKY  +GL
Sbjct: 47  LRLYLREISRIPLLSAVSESRLAERAENGE---KEARNHLIEANLRLVVSIAKKYVGQGL 103

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGL++A  KFD+  G++FSTYA WW+KQAITR+I + +  +R+PV++ ++
Sbjct: 104 SLEDLIGEGNIGLIRAVTKFDYRKGFRFSTYATWWIKQAITRAILEGTRVVRLPVYIMEE 163

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + +V RT R++  ++ REPTPE I ++L M  E V ++L   ++  SL+ P+ +E+ + L
Sbjct: 164 VMRVKRTTRQLYQELGREPTPEIIGERLGMTAERVSELLIWAEKVFSLDAPLSEEEENTL 223

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD IED     P++   Q  LRE   +VL  LT RE +V+ +RFG+  + DHTLEEVGK+
Sbjct: 224 GDIIEDVRERGPMEITDQQLLREEIRKVLGQLTVRERQVIELRFGLIDDHDHTLEEVGKK 283

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             VTRER+RQIE +AIRKL+HP  S+ L+ +LD
Sbjct: 284 LKVTRERVRQIEERAIRKLRHPQASRILKDYLD 316



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/91 (21%), Positives = 36/91 (39%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +     +     D+       +++     +  + +  +  D +R+YLRE+  I LLS   
Sbjct: 5   EESKHLERNVMFDADHDREKTADTERETVQETELSSLAQSDSLRLYLREISRIPLLSAVS 64

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           E  +A+R E G       L E+ L     I 
Sbjct: 65  ESRLAERAENGEKEARNHLIEANLRLVVSIA 95


>gi|313159603|gb|EFR58965.1| putative RNA polymerase sigma factor RpoD [Alistipes sp. HGB5]
          Length = 286

 Score =  194 bits (492), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 173/272 (63%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   ++K       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKEELITVEEEVELAQRIKK---GDQEALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   R   + +R P+PEE+A +L +P E V   L++    +S++ P  D + + L
Sbjct: 135 LNKINKAFARFEQEHERTPSPEELATELELPKEKVTDTLRVAGRHVSVDAPFADGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++ +     I  +L     R L +LT RE  +++  FGIG +   TLEE+G++
Sbjct: 195 LDVLVNPDSPNADRGLINESLSTEVDRALETLTDRERDIIKYFFGIGTSE-MTLEEIGEK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H SRSK L+S+L
Sbjct: 254 FDLTRERVRQIKEKAIRRLRHSSRSKLLKSYL 285



 Score = 44.8 bits (104), Expect = 0.043,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  EL++ E E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKEELITVEEEVELAQRIKKGDQEALEKLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|166363676|ref|YP_001655949.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166086049|dbj|BAG00757.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 414

 Score =  194 bits (492), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 106/269 (39%), Positives = 171/269 (63%), Gaps = 8/269 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +  +   G+ + E   I+++        + AK++M++ANLRLV+SVAKKY NRGL+ LDL
Sbjct: 152 QRWAHLAGLEVGELEEIIAL-------GTRAKEQMIKANLRLVVSVAKKYQNRGLELLDL 204

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG +GL +A +KFD   GY+FSTYA WW++Q +TR+IA +S  IR+PVH+ +K++++ 
Sbjct: 205 IQEGTLGLERAVKKFDPTKGYRFSTYAYWWIRQGMTRAIATKSQIIRLPVHITEKLNRIK 264

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  R++S    R  T EEIA++LA+  E VR++L      +SLE  +G E  + L D +E
Sbjct: 265 KAQRKISQMRGRTATVEEIAQELALTPEAVRELLMTVPRSVSLEIKVGKEKDTELLDLLE 324

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            + AVS  +  +  +L+     +LA LT RE  V+ +R+G      H+L ++G+   ++R
Sbjct: 325 IE-AVSSENHFVYESLQRDIRELLADLTAREREVIELRYGFLDGKSHSLADIGRTLELSR 383

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ER+RQIE KA++KL+      ++R + + 
Sbjct: 384 ERVRQIELKALQKLRQSQLHNQIRDYFEA 412



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 35/69 (50%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E   +   D   S     +     K  ++ +T D VR+YL+++G + LL R+ E+  A++
Sbjct: 25  ENSLDLDEDFLGSDLEDDLVSSPEKSYSNGTTTDLVRLYLQDIGRVPLLKRDEEVEQAQQ 84

Query: 146 IEAGRAMMM 154
           ++   +++ 
Sbjct: 85  VQRHLSLLK 93


>gi|297184127|gb|ADI20246.1| hypothetical protein [uncultured Sphingobacterium sp. EB080_L08E11]
          Length = 287

 Score =  194 bits (492), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVELITAEEEVELAQRIK---AGDQIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+  EI+K L M    V++ ++ +   +S++ P+ + + S+L
Sbjct: 135 INKINKAYAYLEQEHERPPSAAEISKHLEMSESDVKESMRNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +   ++  P +  +  +LR    R LA+LTPRE  V+R+ FG+G     TLEE+G++
Sbjct: 195 YDVLNSSDSPHPDEDLMMDSLRTEIERSLATLTPREGDVIRLYFGLGGQHPMTLEEIGEK 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR++KH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRMKHTSRSKILKTYL 286



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G +EL++ E E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVELITAEEEVELAQRIKAGDQIALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|291515538|emb|CBK64748.1| RNA polymerase sigma factor, sigma-70 family [Alistipes shahii WAL
           8301]
          Length = 286

 Score =  194 bits (492), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 173/272 (63%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   ++K       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKEELITVEEEVELAQRIKK---GDQEALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   R   + +R P+PEE+A +L +P E V   L++    +S++ P  D + + L
Sbjct: 135 LNKINKAFARFEQEHERTPSPEELATELELPKEKVTDTLRVAGRHVSVDAPFADGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++ +     I  +L     R L +LT RE  +++  FGIG +   TLEE+G++
Sbjct: 195 LDVLVNPDSPNADRGLINESLSTEVDRALETLTERERDIIKYFFGIGTSE-MTLEEIGEK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H SRSK L+S+L
Sbjct: 254 FDLTRERVRQIKEKAIRRLRHSSRSKLLKSYL 285



 Score = 44.8 bits (104), Expect = 0.046,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  EL++ E E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKEELITVEEEVELAQRIKKGDQEALEKLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|108803721|ref|YP_643658.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764964|gb|ABG03846.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 365

 Score =  193 bits (491), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 123/274 (44%), Positives = 179/274 (65%), Gaps = 3/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +  I     +S ++  ++   + +       AK  +  ANLRLV+S+AKKY  RG
Sbjct: 95  AVQMYLDEIGKTPLLSKAQEVYLAKRIER---GDRRAKAHLTRANLRLVVSIAKKYAGRG 151

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQEGNIGLM+A EKFD+  GYKFSTYA WW++QA+TR+IAD+  TIR+PVHM +
Sbjct: 152 VSLLDLIQEGNIGLMRAVEKFDYRKGYKFSTYATWWIRQAVTRAIADKGRTIRVPVHMVE 211

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           KI+K  R  R +++++ R+PT EE+A+++ + VE V ++ ++++  ISLETP+G++ +S 
Sbjct: 212 KINKYYRVQRTLASELNRDPTDEEVAREMGVEVEEVERIRQVSRRSISLETPVGEDHSSE 271

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFI D+ + SP D A  + L+      L  L  RE  VL  RFG+      TLEEVG+
Sbjct: 272 LGDFIADEESESPHDLAKSSLLKARMREALNGLPERERMVLEYRFGLTGGQPKTLEEVGE 331

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +F VTRERIRQI+  A+ K+K    +  LR  LD
Sbjct: 332 RFDVTRERIRQIQLTALAKIKSSPHAASLRDLLD 365



 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/141 (24%), Positives = 59/141 (41%), Gaps = 7/141 (4%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  +++ +  ++ G +   E+   L   ++S+E+++    +L   G+ +VD        G
Sbjct: 11  EEVRELFEAGQEAGVLESGEVLDLLQEVDLSTEEIQQVYGLLREQGVEIVDS-------G 63

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                          V      D   R T D V+MYL E+G   LLS+  E+ +AKRIE 
Sbjct: 64  FLSESPEEEEEDVQVVEEVLEGDLKSRYTGDAVQMYLDEIGKTPLLSKAQEVYLAKRIER 123

Query: 149 GRAMMMASLCESPLTFQALII 169
           G     A L  + L     I 
Sbjct: 124 GDRRAKAHLTRANLRLVVSIA 144


>gi|332666643|ref|YP_004449431.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332335457|gb|AEE52558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 289

 Score =  193 bits (491), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 96/277 (34%), Positives = 171/277 (61%), Gaps = 4/277 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   +++       A +++ +ANLR V+SVAK+Y N+
Sbjct: 16  QSLEKYLQEIGKVDLLTPEEEVELAKRIKQ---GDQAALEKLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLSDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +    +  + +REP+PEE+A+ L +P E V   L +    +S++ P  + + +
Sbjct: 133 GSLNKINKAFSELEQEFEREPSPEELAEMLEIPTEEVETTLGVAARHVSMDAPFVEGEDN 192

Query: 587 HLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            L D +E+    S         +LR    R L++LT R+  V+++ FGIG+    +LE++
Sbjct: 193 SLLDVLENNTTPSTDAGLDYNESLRREIERSLSTLTDRQCDVIKLYFGIGVEHPMSLEDI 252

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           G++F +TRER+RQI+ KAI KL+  +RSK L+++L G
Sbjct: 253 GEKFGLTRERVRQIKDKAINKLRSANRSKLLKNYLGG 289



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ E E+ +AKRI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPEEEVELAKRIKQGDQAALEKLTKANLRF--VVSVAKQYQNQGLSLSD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|300727119|ref|ZP_07060538.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775663|gb|EFI72254.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 295

 Score =  193 bits (491), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 166/273 (60%), Gaps = 4/273 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ I  E  IS+ E   +   ++K       A + + +ANLR V+SVAK+Y N+G
Sbjct: 25  ALDRYLQEIGHEDLISVDEEVELAQRIKK---GDKRALERLTKANLRFVVSVAKQYQNQG 81

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGN+GL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++   
Sbjct: 82  LSLPDLINEGNLGLIKAAKKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVG 141

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            ++K+ R       + +R P+ +EIA  + +P + +   L +    +S++ P  + + + 
Sbjct: 142 SVNKINRLVNSFEQENERRPSVDEIADNIDLPEDKIADALNVNTHHVSVDAPFQEGEDNS 201

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + + +  S     +  +LRE   RVL +L  RE  V+   FGIG     TLEE+G 
Sbjct: 202 LLDVLPNTDIPSADSELVHESLREEIARVLETLNQRERNVVEAFFGIGQAE-MTLEEIGD 260

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++ +TRER+RQI+ KAIR+L+H +++K L+S+L
Sbjct: 261 KYGLTRERVRQIKEKAIRRLRHNTKNKYLKSYL 293



 Score = 41.7 bits (96), Expect = 0.38,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S + E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 29  YLQEIGHEDLISVDEEVELAQRIKKGDKRALERLTKANLRF--VVSVAKQYQNQGLSLPD 86

Query: 184 IID 186
           +I+
Sbjct: 87  LIN 89


>gi|227488742|ref|ZP_03919058.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227542262|ref|ZP_03972311.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227091164|gb|EEI26476.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227182091|gb|EEI63063.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 327

 Score =  193 bits (491), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 105/252 (41%), Positives = 174/252 (69%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +   +++   E   A+  M+EANLRLV+S+AK+Y+ RG+  LDLIQEGN+GL++A EK
Sbjct: 74  RAMKRDLKELAREGDKARNHMLEANLRLVVSLAKRYSGRGMPLLDLIQEGNLGLIRAMEK 133

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  +  RE 
Sbjct: 134 FDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQFGREV 193

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +    +  + + +++P+SL+ P+G ++ + LGDFIED  A    ++ + +
Sbjct: 194 TNEELAEESGIDENKIEMLFRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDAEEAVVVS 253

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                   V+ +L  RE+ V+RMR+G+      TL+++G+++ ++RER+RQIE + + KL
Sbjct: 254 LRHSDIRAVIDTLEGREQDVIRMRYGLDDGVPRTLDQIGRRYGLSRERVRQIEREVMAKL 313

Query: 668 KHPSRSKKLRSF 679
           +  SR++KLR++
Sbjct: 314 REGSRAEKLRAY 325



 Score = 42.5 bits (98), Expect = 0.27,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 25/54 (46%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
               N      +R  + D    D VR+YL  +G   LLS E E+ +AK +E G 
Sbjct: 6   KQEDNKVDPRNRRHQTNDNPAADLVRVYLNGIGKTPLLSAEEEVELAKTVEVGL 59


>gi|227549119|ref|ZP_03979168.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078816|gb|EEI16779.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 331

 Score =  193 bits (491), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 103/248 (41%), Positives = 169/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 82  RDLKILAKQGRRARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYA 141

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + REPT EE
Sbjct: 142 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIRREMYQSLGREPTNEE 201

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++ +  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    D+ + +   +
Sbjct: 202 LSDESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEATDAEDAVVSSLRHD 261

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  L  RE+ V+R+R+G+      TL+++G+QF ++RER+RQIE + + KL+   
Sbjct: 262 DIQDIIGGLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMAKLRVGE 321

Query: 672 RSKKLRSF 679
           R+ +LR +
Sbjct: 322 RADRLRDY 329



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           A+          +R  + D  + D VR+YL  +G   LL    E+ +A+RIE G 
Sbjct: 9   AADQEEPVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLDAAEEVELAQRIEVGL 63


>gi|238063483|ref|ZP_04608192.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237885294|gb|EEP74122.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 334

 Score =  193 bits (490), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 114/242 (47%), Positives = 174/242 (71%), Gaps = 1/242 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  G+KFST
Sbjct: 91  AEGRTAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM ++++++VR  R ++  + REPT  E+A+ + +
Sbjct: 151 YATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRARRELAVTLGREPTVAEVARAMDV 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL 617
           P   V +++   +EP+SL+  +G++  S LGDF+   + A  P  +A+   LR     VL
Sbjct: 211 PEFQVIELISYDREPVSLDQAVGEDGESALGDFVAAVDPAAEPGATAVDGELRNEVRIVL 270

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL+ P R+++L 
Sbjct: 271 ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRAPERAQRLE 330

Query: 678 SF 679
           ++
Sbjct: 331 AY 332



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/100 (21%), Positives = 38/100 (38%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E          + + +              + D VR YL  +G  +LL+ E E+ +AKRI
Sbjct: 3   ENQIGPAATIDAEAAADTLTDLDATDERGVSTDLVRAYLNGIGRTKLLTAEQEVELAKRI 62

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EAG          +P++          + +G T    +++
Sbjct: 63  EAGLFAEEKLATCTPVSTVLRADLEIIVAEGRTAKDHLLE 102


>gi|325294741|ref|YP_004281255.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065189|gb|ADY73196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 322

 Score =  193 bits (490), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 101/284 (35%), Positives = 171/284 (60%), Gaps = 3/284 (1%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V     +   +KSIS    +S  E        +        A K++VE+NLR V+
Sbjct: 42  LIESFVPDKDSLDAFLKSISKIPLLSREEEIEYAKRAK---AGDKEALKKLVESNLRFVV 98

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKY   GL   DLI EG +GL++AA +FD   G KF +YA+WW++Q+I +++A Q+ 
Sbjct: 99  SVAKKYLGCGLPLHDLIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTG 158

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            ++IPV     ++K+ R+   +  K+ REPT EE+A+ + M  + + ++L + + P+SL+
Sbjct: 159 AVKIPVKQAVLVNKITRSYGELLKKLGREPTTEELAEYVGMEPKEIERLLTVCQVPLSLD 218

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGDE+ +   DF++ +      +  +Q  L+++   +L  LTP+E++++ MRFG+  N
Sbjct: 219 TPIGDEEDTTFKDFLKGEGTAEVEEKVVQEELKQSIQEMLEQLTPQEKKIIIMRFGLDGN 278

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL E+G++  ++RER+RQ+E +A +K+K  +  KKL  FL+
Sbjct: 279 EPKTLREIGEKLGISRERVRQLETRAKKKMKEYALRKKLNVFLN 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/121 (23%), Positives = 45/121 (37%), Gaps = 3/121 (2%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D         L S     +  +      +     D +  +L+ +  I LLSRE EI  AK
Sbjct: 17  DNPIDAIDESLPSEVDLFNQQIDPSLIESFVPDKDSLDAFLKSISKIPLLSREEEIEYAK 76

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           R +AG    +  L ES L F  ++    +       L ++I  E  +G       F   +
Sbjct: 77  RAKAGDKEALKKLVESNLRF--VVSVAKKYLGCGLPLHDLI-AEGILGLIEAARRFDPDK 133

Query: 205 G 205
           G
Sbjct: 134 G 134


>gi|309790481|ref|ZP_07685041.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227468|gb|EFO81136.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 346

 Score =  193 bits (490), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 125/329 (37%), Positives = 191/329 (58%), Gaps = 25/329 (7%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E D   ++   +      +     E  +   +++ ++ I   + ++ +E   +   + +
Sbjct: 19  HESDLERLADVDELANDAPEQPKHAE-PTPDAVQHYLQEIGRVSLLTANEEVELSERIER 77

Query: 437 GEC------------------------EASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           G+                           + A++ +++ANLRLV+S+AKKY  RGL  LD
Sbjct: 78  GDEAEERLATEDQLSGTQRRNLEHEVERGNDARRHLIQANLRLVVSIAKKYVGRGLSLLD 137

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLM+A EKFD   G +FSTYA WW++QA+TRSIA+Q  TIR+PVHM + + +V
Sbjct: 138 LIQEGNIGLMRAVEKFDHRKGNRFSTYATWWIRQAVTRSIAEQGRTIRLPVHMSESVSQV 197

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            RT+ R+S  ++R+P+ EEIA  L  P E + +VL+  + P+SLETP+GDE    LGDF+
Sbjct: 198 KRTSERLSQSLERQPSAEEIAIALGQPTERIERVLEAARRPVSLETPVGDEGEHTLGDFL 257

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +  +P D A    LR+     L  L  RE R++ +R+G+      TLEEVG+   +T
Sbjct: 258 PDDDLPTPGDFASAQLLRQDLCAALDHLNERERRIIDLRYGLLDGRRRTLEEVGRTLGMT 317

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER RQIEA+A+R+L+ P   + LR +L+
Sbjct: 318 RERARQIEAEALRRLRSPDVGQHLRDYLE 346



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 1/100 (1%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE  E  L+  +     +    ++   A   T D V+ YL+E+G + LL+   E+ +++R
Sbjct: 16  EEEHESDLERLADVDELANDAPEQPKHA-EPTPDAVQHYLQEIGRVSLLTANEEVELSER 74

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           IE G         E  L+         E+  G    R +I
Sbjct: 75  IERGDEAEERLATEDQLSGTQRRNLEHEVERGNDARRHLI 114


>gi|227504896|ref|ZP_03934945.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
 gi|227198489|gb|EEI78537.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
          Length = 337

 Score =  193 bits (490), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 109/265 (41%), Positives = 178/265 (67%), Gaps = 4/265 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++    I+ +E R +  +VR    E   A+  ++EANLRLV+S+AK+YT RG+  LDLI
Sbjct: 75  KLANAEKITRAEKRDLKILVR----EGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLI 130

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R
Sbjct: 131 QEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSR 190

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R M   + RE T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED
Sbjct: 191 IKREMYQSLGREATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGTDEEAPLGDFIED 250

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A     + + A        V+ +L  RE+ V+R+R+G+      TL+++G++F ++RE
Sbjct: 251 AEATDAETAVVAAMRHSDIRGVIETLEEREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRE 310

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE + + KL+  +R+ +LR +
Sbjct: 311 RVRQIEREVMAKLRDGNRADRLREY 335



 Score = 44.4 bits (103), Expect = 0.068,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 30/62 (48%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D    + +         +R  + D  + D VR+YL  +G   LLS E E+ +A+RIE 
Sbjct: 9   AADLGKDSLAEEQEVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQRIEV 68

Query: 149 GR 150
           G 
Sbjct: 69  GL 70


>gi|284052417|ref|ZP_06382627.1| RNA polymerase sigma factor RpoD [Arthrospira platensis str.
           Paraca]
 gi|291570496|dbj|BAI92768.1| principal RNA polymerase sigma factor SigA [Arthrospira platensis
           NIES-39]
          Length = 387

 Score =  193 bits (490), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 151 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 210

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 211 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 270

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 271 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLESVLDTLSPR 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 330 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 386



 Score = 43.7 bits (101), Expect = 0.095,   Method: Composition-based stats.
 Identities = 22/109 (20%), Positives = 43/109 (39%), Gaps = 12/109 (11%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS 112
           L   +   + +E+              G  L +E     S    +    ++   ++ +  
Sbjct: 21  LSDPKSDPDLVENLFEH----------GKSLPEELEESQSDTELAKTGGAAKSRRRAQTK 70

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
               T+D +R+YL+E+G I LL  + EI +A++I        +   L E
Sbjct: 71  KKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREKLIE 119


>gi|68536171|ref|YP_250876.1| RNA polymerase sigma factor SigB [Corynebacterium jeikeium K411]
 gi|260578869|ref|ZP_05846775.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
 gi|68263770|emb|CAI37258.1| RNA polymerase sigma factor B [Corynebacterium jeikeium K411]
 gi|258603016|gb|EEW16287.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
          Length = 343

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 104/248 (41%), Positives = 170/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 94  RDLKVLAREGKAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYT 153

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M  ++ RE T EE
Sbjct: 154 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNEE 213

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++++  +    +  +LK +++P+SL+ P+G ++ + LGDFIED +A     + + +    
Sbjct: 214 LSEESGIEESKIEMLLKQSRDPVSLDMPVGSDEEAPLGDFIEDSDATDAETAVVASLRHS 273

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL +L  RE+ V+++R+G+      TL+++G++F ++RER+RQIE + + KL+   
Sbjct: 274 DVRAVLGTLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREGD 333

Query: 672 RSKKLRSF 679
           R+ KLR +
Sbjct: 334 RADKLREY 341



 Score = 44.1 bits (102), Expect = 0.090,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 35/70 (50%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           DD  +   +      ++  S+      +R+ + +  + D VR+YL  +G   LL+ E E+
Sbjct: 7   DDEYNGINNGQGNGDSTDDSDKKEDKGRRRGNNENPSADLVRVYLNGIGKTALLTAEDEV 66

Query: 141 AIAKRIEAGR 150
            ++KRIE G 
Sbjct: 67  ELSKRIEVGL 76


>gi|117928920|ref|YP_873471.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649383|gb|ABK53485.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
          Length = 413

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 120/265 (45%), Positives = 181/265 (68%), Gaps = 3/265 (1%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++  T     E R  +  +R    + + AK  M+EANLRLV+SVAK+Y+NRG+ FLD+I
Sbjct: 150 KLNDPTLQLTEEERRDLEAIR---DDGARAKAHMLEANLRLVVSVAKRYSNRGMAFLDVI 206

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN+GL++A EKFD+  GYKFSTYAMWW++QAITR++ADQ+ TIR+PVH+ ++++K+ R
Sbjct: 207 QEGNLGLIRAVEKFDYTKGYKFSTYAMWWIRQAITRALADQARTIRLPVHVVEQLNKLTR 266

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R +  +  REPT EE+A +L    E + ++L+  ++P+SL+ P+GD++ + LGD IED
Sbjct: 267 LQRELHQQFGREPTAEELAAELDRTPEQIEEMLRNARQPVSLDNPVGDDEDTLLGDLIED 326

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +  D+     + +T  R LA L PRE RV+ +RFG+     HTL+E+G+   +TRE
Sbjct: 327 MEAPAASDALEYQAMIDTVHRALAGLDPREARVIALRFGLVGGRPHTLDEIGRDVGLTRE 386

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSF 679
           R+RQIE +A+ KL+ P+    L  +
Sbjct: 387 RVRQIEREALAKLRDPNSPDSLLDW 411



 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLAS-----SASNSSVFLQKRKDSADRSTDDPVRMYL 125
             + ++VV+ D   +    E+ LD  S        +  +            + DPVR YL
Sbjct: 61  EELVVDVVEDDAPAEIPTEEELLDAVSRPAGFDDESDDLVEDDLDLDDAGLSHDPVRNYL 120

Query: 126 REMGSIELLSREGEIAIAKRIEAG 149
            E+G   LL    E+ +AKRIEAG
Sbjct: 121 NEIGRTPLLDAAQEVELAKRIEAG 144


>gi|226355184|ref|YP_002784924.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226317174|gb|ACO45170.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 399

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 140/333 (42%), Positives = 191/333 (57%), Gaps = 27/333 (8%)

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM-- 433
           G E D             E +  ++ +      +R  +  I     +S  E   +     
Sbjct: 67  GLEADLDSAPVDATKDAEELEIHISADAYQGDSLRQYLHEIGQIELLSAVEEMDLARRYE 126

Query: 434 ----------------------VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
                                 +++   +   AKK + EANLRLV+S+AKKY NRGL  L
Sbjct: 127 EGEAARNELESNPDLDDRHRRHLQRLVEDGEAAKKSLTEANLRLVVSIAKKYANRGLNLL 186

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN GL++A EKF++  GYKFSTYA WW++QA+TR+IAD+S TIR+PVHM + I+K
Sbjct: 187 DLIQEGNQGLIRAVEKFEYRRGYKFSTYATWWIRQALTRAIADKSRTIRVPVHMVETINK 246

Query: 532 VVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           + R +R++  ++ REP  EE+A+ +      E V    K+  EPISLETPIGDE  S  G
Sbjct: 247 LSRISRQLEMELSREPLAEEMAEAMGPGWDAEKVTDTQKVGHEPISLETPIGDEGDSFYG 306

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DF+ D+   SP+ +A Q  L E   R L+SL  RE  VL++R G     +HTLEEVG+  
Sbjct: 307 DFLPDERFGSPVQNASQTLLSEALERALSSLGEREALVLKLRNGFVDGREHTLEEVGQLL 366

Query: 650 CVTRERIRQIEAKAIRKLKH-PSRSKKLRSFLD 681
            VTRER+RQIE+KA+RKLK+  S +  LR FLD
Sbjct: 367 SVTRERVRQIESKALRKLKYGESLNAGLRDFLD 399



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 38/75 (50%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VD + L+D  G E  LD A   +       +   SAD    D +R YL E+G IELLS  
Sbjct: 57  VDPEVLDDGLGLEADLDSAPVDATKDAEELEIHISADAYQGDSLRQYLHEIGQIELLSAV 116

Query: 138 GEIAIAKRIEAGRAM 152
            E+ +A+R E G A 
Sbjct: 117 EEMDLARRYEEGEAA 131


>gi|326800649|ref|YP_004318468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326551413|gb|ADZ79798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 286

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 99/274 (36%), Positives = 166/274 (60%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I+  E   +   +R        A + + + NLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLHEIGKVDLITAEEEVILAQKIR---EGDQAALERLTKTNLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 73  GLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   R+  + +REP+PEE+A  L   V+ +   L  +   +S++ P    + +
Sbjct: 133 GSLSKISKAFSRLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+ +  +   + I  +L E   R LA+LT RE  ++ + FG+G N   +LEE+G
Sbjct: 193 TLLDVLENHD-PNTDSNLIDESLSEEIKRSLATLTEREREIIVLFFGLGSNHPLSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 252 ETFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G ++L++ E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLHEIGKVDLITAEEEVILAQKIREGDQAALERLTKTNLRF--VVSVAKQYQNQGLTLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|159896899|ref|YP_001543146.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889938|gb|ABX03018.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 391

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 117/323 (36%), Positives = 187/323 (57%), Gaps = 18/323 (5%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            + D           +  +   V   V   L+   E++ ++ E  I++++          
Sbjct: 69  NDEDVELAIVNLRRKKTLYSEAVEDSVQMYLREIGEVELLTAEEEITLAKQIETGRKAEH 128

Query: 437 GECEASIA------------------KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
                  A                  ++++ +ANLRLV+SVAKKY    + F+DLIQEGN
Sbjct: 129 QLQTEQYATWDERTALERRVDFGNEGRRKLTQANLRLVVSVAKKYIGNHMSFMDLIQEGN 188

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGLM+A EKFD+  G +FSTYA WW++QA+TR+IA+QS TIR+PVH+ + I ++ R A +
Sbjct: 189 IGLMRAVEKFDYRKGNRFSTYATWWIRQAVTRAIAEQSRTIRLPVHLSESIAQMRRVAYQ 248

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +   ++RE TP+E+A  L + +  V+++L  + +P+SLE PIG E    +G+F+ D    
Sbjct: 249 LEQALQREATPDELADALGVSLRKVKRMLNASVQPVSLEQPIGKEGQGRVGEFLADDTDE 308

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +PL+ A +  L++     L+ L  RE ++L +R+G+      TLEEVG +F +TRER RQ
Sbjct: 309 APLEQATRMMLQDELADALSQLPDRERQILLLRYGLADGKRRTLEEVGAEFGITRERTRQ 368

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           IEA+A+R L+ P+  + LR++LD
Sbjct: 369 IEAEAMRHLRQPNVGQHLRAYLD 391



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/83 (31%), Positives = 41/83 (49%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                 + V L+++K     + +D V+MYLRE+G +ELL+ E EI +AK+IE GR     
Sbjct: 70  DEDVELAIVNLRRKKTLYSEAVEDSVQMYLREIGEVELLTAEEEITLAKQIETGRKAEHQ 129

Query: 156 SLCESPLTFQALIIWRDELNDGT 178
              E   T+         ++ G 
Sbjct: 130 LQTEQYATWDERTALERRVDFGN 152


>gi|255076341|ref|XP_002501845.1| predicted protein [Micromonas sp. RCC299]
 gi|226517109|gb|ACO63103.1| predicted protein [Micromonas sp. RCC299]
          Length = 595

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 117/243 (48%), Positives = 163/243 (67%), Gaps = 3/243 (1%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK  M++ANLRLV+S+AK+Y N+ + F DLIQEG +GL++ AEKFD+  GYKFSTYA
Sbjct: 342 GKRAKNAMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKFDFKRGYKFSTYA 401

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QA+TRSI+DQS TIR+PVH+ + I ++ +  R+M  K+ R+PT EE+A  + M V
Sbjct: 402 HWWIRQAVTRSISDQSRTIRLPVHLFEIISRMSKVERQMVLKLGRDPTHEELADAMEMTV 461

Query: 561 EGVRKVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           E ++++ K +  PISL   + +   ED   + D + D     P     +  L+E    VL
Sbjct: 462 EKIKQIKKASLVPISLSQTVNNSNGEDKRTVEDTLIDDYTEHPEGETGKVLLKEDLENVL 521

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L PRE  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKL+ PSR+  LR
Sbjct: 522 NTLNPRERDVLRLRYGLDDGRVKTLEEIGNVFSVTRERIRQIEAKALRKLRQPSRNGILR 581

Query: 678 SFL 680
            +L
Sbjct: 582 EYL 584



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 36/63 (57%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E GS    + AS+A +       RK++  +   D ++ YL+++G++ LL+   E+ +AKR
Sbjct: 237 EPGSAQEANEASAAESRRNRRIARKNADTKKQTDSMKTYLKDIGTVSLLTGAEEVELAKR 296

Query: 146 IEA 148
           I+ 
Sbjct: 297 IQD 299


>gi|333030005|ref|ZP_08458066.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
 gi|332740602|gb|EGJ71084.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
          Length = 286

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 178/272 (65%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   ++K      +A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIKK---GDRVALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+P+E+A +L MPV+ V   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFAKFEQEYERRPSPQELADELEMPVDKVTDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L E   R L++L  RE+++++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLSEEIDRALSTLEDREKQIIKMFFGIGC-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQNNRSKLLKSYL 285



 Score = 42.9 bits (99), Expect = 0.16,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI+ G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIKKGDRVALEKLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|72161811|ref|YP_289468.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915543|gb|AAZ55445.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 438

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 113/267 (42%), Positives = 175/267 (65%), Gaps = 4/267 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++       +S +E   +         +   AK  M+EANLRLV+SVAKKY++RG+  LD
Sbjct: 174 LEESPGPQEMSETEREEL----EWIAEDGRRAKAHMLEANLRLVVSVAKKYSDRGMPLLD 229

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           ++QEGN+GL++A EKFD+  GYKFSTYAMWW++QAI R  AD + TIR+PVH+ + + K+
Sbjct: 230 VVQEGNLGLIRAVEKFDYAKGYKFSTYAMWWIRQAIQRGFADSARTIRLPVHVLELLSKL 289

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            R  R M   + REPTP+E+A++L      + ++L+IT++PISL++ IG++  + +GD I
Sbjct: 290 SRLERDMHQTLGREPTPDELAQELGKTPAQIEELLRITRQPISLDSTIGEDGETRIGDLI 349

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED +A    +   +  + +   R L  L PRE  ++ +RFG+      TL+E+GK   +T
Sbjct: 350 EDVDASEASEVVDRQLMADQLRRALDDLEPREATIMSLRFGLFDGRPRTLDEIGKHLGLT 409

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSF 679
           RERIRQ+E +++ KL+HPSR+++L  F
Sbjct: 410 RERIRQLEKQSLSKLRHPSRARQLLDF 436



 Score = 66.4 bits (160), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/191 (21%), Positives = 78/191 (40%), Gaps = 26/191 (13%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           S +    S  +   + +  +  ++I   R RG+V++ EL        ++  +    +  L
Sbjct: 2   SRTAQAASPVTAEIEAASATLDELIARGRARGHVSLSELRTAFSEAGITPAEGRSLLREL 61

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDL------------------------ASSASNSSVFL 106
           S+ G+ + + +D   + G +D+L+                         A + + ++   
Sbjct: 62  SDTGVRIANNEDTPVDPGDDDTLEAVLETTSKGSGRRRSAKKRSRKKQPAQAGAETTDAP 121

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS--LCESPLTF 164
           +   D    +  D V  YL+ +G  ELL+ E E+ +AKRIEAG         L ESP   
Sbjct: 122 EADLDDHSPALGDSVHTYLKAIGRRELLTAEQEVELAKRIEAGLYAEYKLGWLEESPGPQ 181

Query: 165 QALIIWRDELN 175
           +     R+EL 
Sbjct: 182 EMSETEREELE 192


>gi|269925789|ref|YP_003322412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789449|gb|ACZ41590.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 363

 Score =  193 bits (489), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 113/270 (41%), Positives = 178/270 (65%), Gaps = 3/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++  E   +   + K     + A +  V ANLRLV+S+AK+Y  RGL  L
Sbjct: 95  YLREIGSVPLLTPKEEVELAKRIEK---GDTEALQRFVLANLRLVVSIAKRYVGRGLPLL 151

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLM+A +KFDW  G++FSTYA WW++QAITR+I D+S  IR+P H+ +++++
Sbjct: 152 DLIQEGNIGLMRAVQKFDWRKGHRFSTYATWWIRQAITRAIGDKSREIRLPAHINEELNR 211

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + R  +++S  + REPTPEEIA+K     E VR++L   ++P+SL+TP+G+E  S LG+F
Sbjct: 212 INRIRQQLSQTVNREPTPEEIAEKAGTSPERVRELLGYLQQPVSLDTPVGEEADSTLGEF 271

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D  A    ++  +    E    +   LTPRE+RVL++R+G+G    ++LE+VG++  V
Sbjct: 272 VPDVRANPEEEATDEVLKTEMDRVLDEVLTPREKRVLQLRYGLGDGHTYSLEKVGRELGV 331

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TRER+RQ+E +A+ KL+     +KL  +++
Sbjct: 332 TRERVRQLEKQALEKLRRGPAIRKLAEYME 361



 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 12/157 (7%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           +++ K++I L + +G+VT  ++   +P  E + +        L   GI V+  +  E E 
Sbjct: 10  EEAIKRLITLGKSKGHVTERDVFELVPEAEDNIDCFNQVSDALIREGIEVLPEETTEAEA 69

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G E+ LD       +  +L            D V++YLRE+GS+ LL+ + E+ +AKRIE
Sbjct: 70  GPEEDLDQTLEELENDGYL-----------TDAVKIYLREIGSVPLLTPKEEVELAKRIE 118

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G    +     + L     I  R  +  G  LL  I
Sbjct: 119 KGDTEALQRFVLANLRLVVSIAKRY-VGRGLPLLDLI 154


>gi|78779769|ref|YP_397881.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713268|gb|ABB50445.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 313

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 109/270 (40%), Positives = 176/270 (65%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ + + T  G    + +   +  ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMILTEDGQLNEKIKEFTTQQKRIIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLAAIRKVSRELAHKLGAMPSRIEIAEAMDIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNTEEPLDKVEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 19/118 (16%), Positives = 38/118 (32%), Gaps = 7/118 (5%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIA-----KRIEAGRAMMMASLCESPLTF 164
            +   R  +DP+  YL+ +G + LL+   EI +        I      +   + E     
Sbjct: 9   AEPPKRRGNDPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKIKEFTTQQ 68

Query: 165 QALIIWRDELNDGTTL--LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           + +I       +      LR ++ +      +         EG    +R     +  R
Sbjct: 69  KRIIKIGRRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTR 126


>gi|116073370|ref|ZP_01470632.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068675|gb|EAU74427.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 313

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 110/270 (40%), Positives = 173/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ +   T  G    +     S  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQQLMALTQDGTIPIDSDQFSSKDRRIIRVGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + MP+E +  +L+      SL+ P+  E+
Sbjct: 159 LSERLTTIRKVSLDLAHKLGAMPSRLEIAEAMDMPLEELDSLLRQALTTSSLDAPVNGEE 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D ++  PL    Q+   E   R L+ L+ +E+ VL +RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADNSSDEPLAKVEQSIHHEQLGRWLSHLSDQEQHVLNLRFGLNGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RERIRQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERIRQVELKALRKLRNLTRR 308



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +       DS  R + DP+  YL  +G I LL+   EI +  +++ 
Sbjct: 2   ASLAAGLADSQRRRSSDPISWYLATIGRIPLLTPAEEIELGNQVQQ 47


>gi|325954752|ref|YP_004238412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
 gi|323437370|gb|ADX67834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
          Length = 288

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       +A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIK---AGDRVALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +  + +R P+ EEI++ L M    V++ LK +   +S++ P+ + + S+L
Sbjct: 135 INKINKAYALLEQEHERAPSAEEISEVLDMSEGDVKESLKNSGRHVSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + SP ++ +  +LR    R L +LTPRE  ++R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLNIGESPSPDNTLMIESLRVEIERALQTLTPREADLIRLYFGLNGAHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L++++
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYI 286



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ E E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITAEEEVELAQRIKAGDRVALEKLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|282900041|ref|ZP_06308000.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195073|gb|EFA70011.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 432

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 107/255 (41%), Positives = 173/255 (67%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  V  + + + +   AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EK
Sbjct: 177 KLTVEELDQIQSQGIQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 236

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ +  R+++ +  R P
Sbjct: 237 FDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTP 296

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T E++A +L M    VR+VL      +SLET +G +  + LG+ +E  + ++P ++ ++ 
Sbjct: 297 TLEDLALELDMTPNQVREVLLRVPRSVSLETKVGKDKDTELGELLE-TDTITPEETLMRE 355

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L++    +L+ LT RE  V+ MRFG+     ++L E+G+   ++RER+RQIE+KA++KL
Sbjct: 356 SLQKDIHHLLSDLTTREREVILMRFGLADGHSYSLAEIGRALELSRERVRQIESKALQKL 415

Query: 668 KHPSRSKKLRSFLDG 682
           + P R   +R +L+ 
Sbjct: 416 RQPKRRNLVRDYLES 430



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 59/148 (39%), Gaps = 1/148 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNS-SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           DG DL +E   +D  D+        +    +     +R + D VR+YL+E+G + LL R+
Sbjct: 35  DGGDLSEELSLDDLQDIEQEEDIEIAAVDPQNLVGNNRRSTDLVRVYLQEIGKVRLLGRD 94

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  A++++    + +     +      ++ +   +     L+ E+    +     S  
Sbjct: 95  EEVGEAQKVQRHLKIRLLLANAAKQGDALVVPYLQLIEVQERLVSELGHRPSLERWASTA 154

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQE 225
           G        +  + +    E  +  V+E
Sbjct: 155 GIKLVDLKPTLSEGKRRWAEIAKLTVEE 182


>gi|225436223|ref|XP_002273602.1| PREDICTED: similar to SIGB (SIGMA FACTOR B); DNA binding /
           DNA-directed RNA polymerase/ transcription factor [Vitis
           vinifera]
          Length = 578

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 100/247 (40%), Positives = 155/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+        K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 330 LRRRTNYGIRCKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKG 389

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  R P  EE+A
Sbjct: 390 FKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVA 449

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D +A +  +  I+  +RE  
Sbjct: 450 EATGLSMKRLNAVLLTPKAPRSLDQKIGINQNLKPSEVIADPDAETAEELLIKQFMREDL 509

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL PRE++V+R R+G+      TL+E+G+   V+RERIRQIE+ A RKLK+  R+
Sbjct: 510 EKVLNSLNPREKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQIESCAFRKLKNKRRT 569

Query: 674 KKLRSFL 680
           K L+ +L
Sbjct: 570 KHLQQYL 576


>gi|325297456|ref|YP_004257373.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
 gi|324317009|gb|ADY34900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
          Length = 286

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 175/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRAALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+Q+  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQARIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELDIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLSREIDRALSTLTDREKEIIQMFFGIG-TQEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 285



 Score = 44.1 bits (102), Expect = 0.086,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRAALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|327405377|ref|YP_004346215.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320885|gb|AEA45377.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 288

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 98/275 (35%), Positives = 177/275 (64%), Gaps = 4/275 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I  E  I+  E   +   +++       A +++  ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQDIGKEELITAEEEVELARKIKQ---GDQRALEKLTRANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA+KFD   G+KF +YA+WW++Q+I +++A+Q+  +R+P++  
Sbjct: 73  GLTLPDLINEGNLGLIKAAQKFDETRGFKFISYAVWWIRQSILQALAEQARIVRLPLNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDT 585
             ++K+ +   R+  + +R P+ EE+A+ L +P + +++ L ++   +S++ P+   ED 
Sbjct: 133 GSLNKINKAFSRLEQEFERPPSAEELAEALEVPEDKIKESLNVSGRHVSMDAPLSSSEDG 192

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + + ++     + +  +L++   R L++LT +E  ++R+ FGIGMN   TLEE+
Sbjct: 193 GTLMDVMANADSPKADHALMAESLQKEIERSLSTLTDKEREIIRLFFGIGMNHGLTLEEI 252

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +F +TRER+RQI+ KAIR+L+H SR+K L+++L
Sbjct: 253 GAKFNLTRERVRQIKEKAIRRLRHTSRNKLLKAYL 287



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++G  EL++ E E+ +A++I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDIGKEELITAEEEVELARKIKQGDQRALEKLTRANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|213963182|ref|ZP_03391440.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
 gi|213954266|gb|EEB65590.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
          Length = 287

 Score =  192 bits (488), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 172/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK---AGDVAALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIA++L M V  V++ +K     IS++ P+ + + S+L
Sbjct: 135 INKINKMYAYLEQANERVPSAEEIARELDMSVNDVKESMKNAGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I    + +P  S I  +LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVIRSNESPNPDKSLILDSLRTEIERALETLTPREADVIRLYFGLGDQHAMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRVDLITADEEVELAQRIKAGDVAALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|325103187|ref|YP_004272841.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
 gi|324972035|gb|ADY51019.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
          Length = 286

 Score =  192 bits (488), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 98/274 (35%), Positives = 166/274 (60%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I+  E   +   +R        A + + + NLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLHEIGKVDLITAEEEVILAQKIR---EGDQAALERLTKTNLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 73  GLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   ++  + +REP+PEE+A  L   V+ +   L  +   +S++ P    + +
Sbjct: 133 GSLSKISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+ N  +     I  +L E   R L++LT RE  ++ + FG+G N   +LEE+G
Sbjct: 193 TLLDVLENDN-PNTDSMLIDESLSEEIKRSLSTLTEREREIIVLFFGLGSNHPLSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 252 EKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G ++L++ E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLHEIGKVDLITAEEEVILAQKIREGDQAALERLTKTNLRF--VVSVAKQYQNQGLTLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|218248849|ref|YP_002374220.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257061911|ref|YP_003139799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218169327|gb|ACK68064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256592077|gb|ACV02964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 417

 Score =  192 bits (488), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 114/272 (41%), Positives = 178/272 (65%), Gaps = 2/272 (0%)

Query: 412 EIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           E+K+I  +     ++   I +  +   E     AK++M++ANLRLV+SVAKKY +RGL+ 
Sbjct: 145 ELKTILGQGKERWAQLADIELDQLETIEKVGIRAKEQMIKANLRLVVSVAKKYQHRGLEL 204

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEG +GL +A EKFD   GY+FSTYA WW++Q ITR+I+ QS  IR+PVH+ +K++
Sbjct: 205 LDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAISTQSRIIRLPVHITEKLN 264

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ R  R++S +  R+ T EE++K+L M  E +R+VL      +SLE  +G E  + L D
Sbjct: 265 KIKRAQRKLSQEKGRKATIEEMSKELDMSAEQIREVLLRIPRSVSLEVKVGKEKDTELVD 324

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E     SP +S I  +LR+    +L  LT RE+ V+++R+G    T ++L ++G+   
Sbjct: 325 LLE-TECQSPEESLISESLRKDLQVLLEDLTEREQDVIKLRYGFEDGTCYSLADIGRVLE 383

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ++RER+RQIEAKA++KL+ P R  ++R + + 
Sbjct: 384 LSRERVRQIEAKALQKLRQPRRRNQIRDYFES 415



 Score = 42.1 bits (97), Expect = 0.27,   Method: Composition-based stats.
 Identities = 39/294 (13%), Positives = 108/294 (36%), Gaps = 23/294 (7%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E + +  + +       +   + + +  + + D VR+YL+++G + LL++E E+  A+++
Sbjct: 29  EKAYELREGSLELELHGIDFTEAEKNHHQGSTDLVRLYLQDIGRVPLLNQEEEVIKAQQV 88

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDE-LNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           ++                  L+  R +    G   ++++I++ A I         +    
Sbjct: 89  QSY---------------VELLDLRQKAAQAGDRAIQQLIEM-AEIHDRLFISLGYRPSW 132

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
             + K    S  + +  + + +      A +  D    ++     A+            +
Sbjct: 133 DRWAKAAQISVGELKTILGQGKERWAQLADIELDQLETIEKVGIRAKEQMIKA------N 186

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              + ++  + + + +  LD I E    L    +     +    S+     +++ + + +
Sbjct: 187 LRLVVSVAKKYQHRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAI 246

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            + S        + E+L  I +       E  R A    + +++ +   Q RE+
Sbjct: 247 STQSRIIRLPVHITEKLNKIKRAQRKLSQEKGRKATIEEMSKELDMSAEQIREV 300


>gi|56750024|ref|YP_170725.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
 gi|56684983|dbj|BAD78205.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
          Length = 316

 Score =  192 bits (488), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 107/237 (45%), Positives = 165/237 (69%), Gaps = 1/237 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+ M++ANLRLV+SVAKKY  +GL+FLDLIQEG +GL +A EKFD   GYKFSTYA
Sbjct: 78  GQRAKERMIKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYA 137

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q++TR+IA QS TIR+PVH+ +++ ++ +  R +++++ R P+ +EIA+ + +P+
Sbjct: 138 FWWIRQSMTRAIACQSRTIRLPVHLTERLSQIRKVTRELAHELGRLPSRQEIAEAVQLPL 197

Query: 561 EGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +  +L+ +++  SL+ P+  ED  S LG+ I D N   P+D    A  RE     L  
Sbjct: 198 NDLETILRQSRQCTSLDAPVSGEDGKSFLGELIADPNGNEPMDIMENAMQREQLDAWLEH 257

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LTP+E +VL +RFG+G    HTL E+G+   V+RER+RQ+E KA+RKL++ ++  ++
Sbjct: 258 LTPQERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKLRNLTKRSRI 314


>gi|1519638|gb|AAB07552.1| SigB [Chloroflexus aurantiacus J-10-fl]
          Length = 346

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 113/296 (38%), Positives = 175/296 (59%), Gaps = 23/296 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-----------------------RKGECEASIAK 445
           ++  ++ I     ++  E   +                            + +  A   +
Sbjct: 51  VQLYLQEIGQVPLLTAEEEVELARQYSRGKEARQRLRNEDSPTTANGCGWRWKWLAVKRR 110

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
              ++ANLRLV+SVAKKY    + F+DL+QEGNIGLM+A EKFD+  G +FSTYA WW++
Sbjct: 111 GGRIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWIR 170

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           QA+TR+IA+QS  IR+PVH+ + I  + R   R+  +++REPT EE+A  L M V  V++
Sbjct: 171 QAVTRAIAEQSRLIRLPVHLSESIVHLRRAIYRLEQELEREPTAEELAHALNMSVRKVKR 230

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++ + +PISLE P+ +E    + + + D+   SP++ A Q  L    T  L  L  RE 
Sbjct: 231 LIRASTQPISLEQPLNNEQEGRVSETLADETVASPMEIAEQKMLHAELTAALNELPERER 290

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++L++R+G+      TLEEVG  F +TRER RQIEA+A+R+L+HPS  ++L S+LD
Sbjct: 291 KILQLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHPSVGQRLHSYLD 346



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 79  DGDDLEDE-EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +  +L+ E +G  D        +          +      +D V++YL+E+G + LL+ E
Sbjct: 8   EATELDAEWDGDVDPEPEDLEVAELEPLDDLESEGDFEPVEDSVQLYLQEIGQVPLLTAE 67

Query: 138 GEIAIAKRIEAGRAMMMA 155
            E+ +A++   G+     
Sbjct: 68  EEVELARQYSRGKEARQR 85


>gi|298209056|ref|YP_003717235.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
 gi|83848983|gb|EAP86852.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
          Length = 287

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   +R      + A +++ +ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIR---AGDNRALEKLTKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R PTPEEIA++L M +  V++ LK +   +S++ P+ D + S+L
Sbjct: 135 INKINKMYAYLEQSNQRPPTPEEIAQELEMTISEVKESLKNSGRHLSMDAPLVDGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D ++   + +P    +  +L+    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLKFGESPNPEKDLLVESLQTEIDRALETLTPREADVIRLYFGLGQQQPLTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KA R+LKH SRSK L+++L
Sbjct: 255 FELTRERVRQIKEKATRRLKHTSRSKILKTYL 286



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ E E+ +A+RI AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITAEEEVELAQRIRAGDNRALEKLTKANLRF--VVSVSKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|313674339|ref|YP_004052335.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Marivirga
           tractuosa DSM 4126]
 gi|312941037|gb|ADR20227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marivirga
           tractuosa DSM 4126]
          Length = 287

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 172/274 (62%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   +++      +A +++ +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTPDEEVDLAVRIKQ---GDQLALEKLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  K +REP+P+E+A+ L +    V   +KI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSTLEQKFEREPSPDELAEVLEVTSNEVVDTMKISGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+    SP D  +  +LR    R L++LT RE  V+ + FG+      TLEE+G
Sbjct: 193 SLLDVLENDGEESPDDELMNDSLRREVQRALSTLTQREADVITLYFGLNGEHSMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+H SRSK L+ +L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRHTSRSKALKPYL 286



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +A RI+ G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPDEEVDLAVRIKQGDQLALEKLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|325285575|ref|YP_004261365.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324321029|gb|ADY28494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 175/272 (64%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       +A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQVALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R+P+ EEIAK+L M +E V++ LK +   +S++ P+ D + S+L
Sbjct: 135 INKINKTFAFLEQAHERKPSAEEIAKELDMTIEDVKQSLKNSGRHVSMDAPLIDGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELLIESLRTEIERALETLTPREADVIRLYFGLAEQHSMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.4 bits (108), Expect = 0.019,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQVALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|262340892|ref|YP_003283747.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
 gi|262272229|gb|ACY40137.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
          Length = 287

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 164/274 (59%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  E        R      + A  ++V ANLR V+SVAK+Y N+
Sbjct: 16  ESLDKYLHEIGKIPLLTPEEEVEYARRAR---EGDASAIDKLVNANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+K   +FD   G+K  +Y +WW++QAI ++IA+QS +IR P +  
Sbjct: 73  GLSLCDLINEGNLGLIKGILRFDETRGFKCISYVVWWIRQAILQAIAEQSRSIRQPTNKL 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+++T  ++  +++R P+  EIA+ L M  + V + +K +   +S++ P+ + + S
Sbjct: 133 ALLNKILKTLAQLEQELQRTPSAREIAEYLDMNEKDVEESIKNSGRHVSMDAPLIEGEDS 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +L D +    +  P +   + +LR+   R+L +L+ RE RV+ + FG+  +   TLEEVG
Sbjct: 193 NLYDLVRSDESPRPDEHLEKESLRKDIKRILETLSERERRVIILHFGLNGSPPMTLEEVG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   +TRER+RQIE+ A+++LKH SRSK L+ +L
Sbjct: 253 QSCDLTRERVRQIESIALKRLKHSSRSKILKPYL 286



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G I LL+ E E+  A+R   G A  +  L  + L F  ++    +  +    L +
Sbjct: 21  YLHEIGKIPLLTPEEEVEYARRAREGDASAIDKLVNANLRF--VVSVAKQYQNQGLSLCD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera]
          Length = 575

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 100/247 (40%), Positives = 155/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+        K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 327 LRRRTNYGIRCKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKG 386

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  R P  EE+A
Sbjct: 387 FKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVA 446

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D +A +  +  I+  +RE  
Sbjct: 447 EATGLSMKRLNAVLLTPKAPRSLDQKIGINQNLKPSEVIADPDAETAEELLIKQFMREDL 506

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL PRE++V+R R+G+      TL+E+G+   V+RERIRQIE+ A RKLK+  R+
Sbjct: 507 EKVLNSLNPREKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQIESCAFRKLKNKRRT 566

Query: 674 KKLRSFL 680
           K L+ +L
Sbjct: 567 KHLQQYL 573


>gi|53714034|ref|YP_100026.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|60682231|ref|YP_212375.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|253564677|ref|ZP_04842133.1| RpoD [Bacteroides sp. 3_2_5]
 gi|255010339|ref|ZP_05282465.1| putative sigma factor A [Bacteroides fragilis 3_1_12]
 gi|265766346|ref|ZP_06094387.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|313148138|ref|ZP_07810331.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
 gi|52216899|dbj|BAD49492.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|57471281|gb|AAW50926.1| RpoD [Bacteroides fragilis]
 gi|60493665|emb|CAH08454.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|251946142|gb|EES86519.1| RpoD [Bacteroides sp. 3_2_5]
 gi|263254014|gb|EEZ25479.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|301163709|emb|CBW23263.1| putative sigma factor A [Bacteroides fragilis 638R]
 gi|313136905|gb|EFR54265.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
          Length = 286

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELAGELDIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQ-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|227536516|ref|ZP_03966565.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300773589|ref|ZP_07083458.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|227243593|gb|EEI93608.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300759760|gb|EFK56587.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 286

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 168/274 (61%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I+  E   +   +R       +A +++ + NLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLHEIGKVDLITAEEEVILAQRIR---EGDQVALEKLTKTNLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 73  GLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   ++  + +REP+PEE+A  L   V+ V   L  +   +S++ P    + +
Sbjct: 133 GSLSKISKAFSKLEQEYEREPSPEELADILETTVDKVSDTLSNSGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+ +      S I  +L E   R LA+LT RE  ++ + FG+G N   +LEE+G
Sbjct: 193 TLLDVLENHD-PDTDSSLIDESLSEEIKRSLATLTEREREIIVLFFGLGSNHQLSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 252 EKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285



 Score = 46.8 bits (109), Expect = 0.011,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G ++L++ E E+ +A+RI  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLHEIGKVDLITAEEEVILAQRIREGDQVALEKLTKTNLRF--VVSVAKQYQNQGLTLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|209523577|ref|ZP_03272131.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495982|gb|EDZ96283.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 387

 Score =  192 bits (487), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 179/237 (75%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 151 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 210

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +
Sbjct: 211 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 270

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 271 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLESVLDTLSPR 329

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 330 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 386



 Score = 44.8 bits (104), Expect = 0.052,   Method: Composition-based stats.
 Identities = 23/109 (21%), Positives = 45/109 (41%), Gaps = 12/109 (11%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS 112
           L   +   + +E+              G+ L+ E     S    + A ++    ++ +  
Sbjct: 21  LSDPKSDPDLVENLFEH----------GESLQQELEESQSETELAKAGSAGKSRRRAQTK 70

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
               T+D +R+YL+E+G I LL  + EI +A++I        +   L E
Sbjct: 71  KKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREKLIE 119


>gi|309790033|ref|ZP_07684607.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227888|gb|EFO81542.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 358

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 114/326 (34%), Positives = 186/326 (57%), Gaps = 25/326 (7%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVR---- 435
             W       P+ E +     E ++I   I+  +  I     +S  E R +   +R    
Sbjct: 33  DAWEPVDVLEPDLEAEEEPDLEPEAIEDSIQIYLHEIGQVALLSAEEERDLAMQIRAGKE 92

Query: 436 --------------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
                                       A++ +++ANLRLV+SVAKKY N  + F+DL+Q
Sbjct: 93  AQMQLDTERFANGAARAQLELTVARGHEARRRLIQANLRLVVSVAKKYINSPMAFMDLVQ 152

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGNIGLM+A EKFD   G +FSTYA WW++QA++RSIA+QS  IR+PVH+ + + ++ R 
Sbjct: 153 EGNIGLMRAVEKFDHTKGNRFSTYATWWIRQAVSRSIAEQSRVIRLPVHLSESLVQMRRA 212

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
             ++  + +REPT +EIA  + + +  V+++L+ + +P+SLE P+ +E    +G+ + D+
Sbjct: 213 IYKLEQQFEREPTAQEIAHSMGLSLRKVKRLLQASAQPVSLEQPLNNEQEGRVGEVLADE 272

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           N  +P+D A Q    +     L  L  RE ++L++R+G+      TLEEVG  F +TRER
Sbjct: 273 NVETPMDLATQKMFHQELYAALNDLPDRERKILQLRYGLFDGQRRTLEEVGMAFGITRER 332

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RQIEA+A+R+L+ P   ++L+++L+
Sbjct: 333 TRQIEAEAMRRLRQPQVGQRLQAYLE 358



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 29/55 (52%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
              +  ++  D    + +D +++YL E+G + LLS E E  +A +I AG+   M 
Sbjct: 42  EPDLEAEEEPDLEPEAIEDSIQIYLHEIGQVALLSAEEERDLAMQIRAGKEAQMQ 96


>gi|282897491|ref|ZP_06305492.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281197586|gb|EFA72481.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 429

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 109/269 (40%), Positives = 174/269 (64%), Gaps = 8/269 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +       +++ E   I S           AK+ M++ANLRLV+SVAKKY NRGL+ LDL
Sbjct: 167 RRWGEIAQLTVEELDEIQSQ-------GIQAKEHMIKANLRLVVSVAKKYQNRGLELLDL 219

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG +GL +A EKFD   GY+FSTYA WW++Q ITR+IA  S TIR+PVH+ +K++K+ 
Sbjct: 220 VQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEKLNKIK 279

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  R+++ +  R PT E++A +L M    VR+VL      +SLET +G +  + LG+ +E
Sbjct: 280 KAQRKIAQEKGRTPTLEDLALELDMTPNQVREVLLRVPRSVSLETKVGKDKDTELGELLE 339

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             + ++P ++ ++ +L++    +L+ LT RE  V+ MRFG+     ++L E+G+   ++R
Sbjct: 340 -TDTITPEETLMRESLQKDIHHLLSDLTTREREVILMRFGLADGHSYSLAEIGRALELSR 398

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ER+RQIE+KA++KL+ P R   +R +L+ 
Sbjct: 399 ERVRQIESKALQKLRQPKRRNLVRDYLES 427



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 72/185 (38%), Gaps = 2/185 (1%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNS-SVFLQKRKDSA 113
             E + +Q + T+  L    ++  DG DL +E   +D  D+        +    +   + 
Sbjct: 9   EVEYNPQQSDLTLPELDLSDVS-TDGGDLSEELSLDDLQDIEQEEDVEIAAVEPQNLVAN 67

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              + D VR+YL+E+G + LL R+ E+  A++++    + +     +      ++++   
Sbjct: 68  YGRSTDLVRVYLQEIGKVRLLGRDEEVGEAQKVQRHLKIRLLLANAAKQGDALIVLYLQL 127

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +     L+ E+    +     S  G        +  + +    E  +  V+E +      
Sbjct: 128 IEVQERLVSELGHRPSLERWASTAGIKLMDLKPTLSEGKRRWGEIAQLTVEELDEIQSQG 187

Query: 234 AKVSK 238
            +  +
Sbjct: 188 IQAKE 192


>gi|261749591|ref|YP_003257277.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
 gi|261497684|gb|ACX84134.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
          Length = 287

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 97/274 (35%), Positives = 165/274 (60%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  E        R      S A +++V ANLR V+SVAK+Y N+
Sbjct: 16  ESLDKYLHEIGKIPLLTPEEEVEYARRAR---EGDSSAIEKLVNANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+K   +FD   G+K  +Y +WW++QAI ++IA+QS +IR P +  
Sbjct: 73  GLSLCDLINEGNLGLIKGILRFDETRGFKCISYVVWWIRQAILQAIAEQSRSIRQPTNKL 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+++T  ++  +++R P+  EIA+ L M  + V + +K +   +S++ P+ + + S
Sbjct: 133 ALLNKILKTLAQLEQELQRTPSAREIAEHLDMNEKDVEESIKNSGRHVSMDAPLIEGEDS 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +L D +    +  P +   + +LR+   R+L +L+ RE RV+ + FG+  +   TLEEVG
Sbjct: 193 NLYDLVRSDESPRPDEHLERESLRKDIKRILETLSERERRVIILHFGLNGSPPMTLEEVG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   +TRER+RQIE+ A+++LKH SRSK L+ +L
Sbjct: 253 QSCDLTRERVRQIESIALKRLKHSSRSKILKPYL 286



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G I LL+ E E+  A+R   G +  +  L  + L F  ++    +  +    L +
Sbjct: 21  YLHEIGKIPLLTPEEEVEYARRAREGDSSAIEKLVNANLRF--VVSVAKQYQNQGLSLCD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|260062909|ref|YP_003195989.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88784477|gb|EAR15647.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 175/272 (64%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+ +E   +   +++      +A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIDLITANEEVELAQRIKQ---GDQLALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  KLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +    +R P+ EEIAK+L M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKIKKTFSYLEQAHERPPSAEEIAKELDMTVSEVKQSIKNSGRHVSMDAPLREGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    +  P  S +  +L     R L +L+PRE  V+++ +GIG     TL E+G+ 
Sbjct: 195 YDVLRSGESPKPDKSLMLQSLNTEINRALETLSPREADVVKLYYGIGDQQSMTLAEIGQT 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI  KAIRKL+H SRSK L+++L
Sbjct: 255 FDLTRERVRQIREKAIRKLRHHSRSKLLKAYL 286



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I+L++   E+ +A+RI+ G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQDISKIDLITANEEVELAQRIKQGDQLALEKLTKANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|148907004|gb|ABR16646.1| unknown [Picea sitchensis]
          Length = 592

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 100/281 (35%), Positives = 175/281 (62%), Gaps = 5/281 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVISVA 460
            + +IR + K  + +   +++++  ++      ++        +  +++  NLRLVISVA
Sbjct: 312 KLDRIRAKYKEKTGKEP-TLAQWAEVIGVDQKTLKMRLEVGRDSFDKIINCNLRLVISVA 370

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K Y NRGL   DLIQ G++GLM++AEKFD+  G+KFSTYA WW++Q+IT+++ +QS TIR
Sbjct: 371 KNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGFKFSTYAYWWIRQSITKALTEQSRTIR 430

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +PVH+ + + ++    R +  + KR+PT EE+A+   + +  +R V + ++ P SL+  +
Sbjct: 431 LPVHIVESMTRIRTAWRLLYQEHKRDPTKEEVAEVAGISMTRLRHVTRCSRVPTSLDRCV 490

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +      + + D N+ S      +   ++   RVL +LT RE++V+R+R+G+      
Sbjct: 491 GKDMDEKFSEIVADTNSESTETIVSKELFKKDLDRVLDTLTAREKQVVRLRYGLDDGRMK 550

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +L EVG+ F ++RER+RQIE KA+RKL+   R++ L+ +LD
Sbjct: 551 SLHEVGENFSLSRERVRQIEMKAMRKLRQNHRTQHLKHYLD 591


>gi|94311053|ref|YP_584263.1| RNA polymerase sigma factor RpoS [Cupriavidus metallidurans CH34]
 gi|93354905|gb|ABF08994.1| RNA polymerase sigma 38 (sigma S) factor [Cupriavidus metallidurans
           CH34]
          Length = 386

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ + G+     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 114 VQHYLNRISIKPLLSAPEELHFSTLAKGGDFS---ARQVMIERNLRLVVSIAKGYLNRGV 170

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 171 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 230

Query: 529 IHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 231 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 290

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 291 SLLDFLSDEHNAAPDQEVAHRELENLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 350

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 351 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 381



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 41/278 (14%), Positives = 83/278 (29%), Gaps = 28/278 (10%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------- 171
           D V+ YL  +    LLS   E+  +   + G       + E  L     I          
Sbjct: 112 DTVQHYLNRISIKPLLSAPEELHFSTLAKGGDFSARQVMIERNLRLVVSIAKGYLNRGVP 171

Query: 172 --DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
             D + +G   L   I+            +       S ++   +     R  V      
Sbjct: 172 LLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIREL 231

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
            +        ++   D    + E+    L +  D+    L+  E       +    ++  
Sbjct: 232 NQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNE---HTTSLDTPFDLDP 288

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKVL------------KEKLVKLVGSLSLNQSRIDL 337
               L  L D        E +  + + L            +  + +  G   +  + ++ 
Sbjct: 289 GSSLLDFLSDEHNAAPDQEVAHRELENLMKLWLARLSEKHRYVVERRFGLNHIEPATLEE 348

Query: 338 LVEQLYDISKRIMHNEGE----LLRLAQSYGIKRDVFL 371
           L E++    +R+   + E    L R   S G+++D  L
Sbjct: 349 LAEEMGLTRERVRQIQQEALVKLKRHFASQGVRKDAVL 386


>gi|296117743|ref|ZP_06836327.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969474|gb|EFG82715.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 334

 Score =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 103/248 (41%), Positives = 169/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    E   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 85  RDMKILVKEGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYA 144

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE
Sbjct: 145 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEE 204

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A     + + +    
Sbjct: 205 LAEESGIEENKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEATDAETAVVASMRHS 264

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               V+ +L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+  +
Sbjct: 265 DIRDVIGTLEQREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMAKLRDGN 324

Query: 672 RSKKLRSF 679
           R+ +LR +
Sbjct: 325 RADRLREY 332



 Score = 43.7 bits (101), Expect = 0.099,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 32/63 (50%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +++S D + +         +R  + D  + D VR+YL  +G   LLS E E+ +A+ IE
Sbjct: 5   SAQNSHDASDNNEKEVDRGSRRGQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQAIE 64

Query: 148 AGR 150
            G 
Sbjct: 65  IGL 67


>gi|312888769|ref|ZP_07748333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311298769|gb|EFQ75874.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 286

 Score =  191 bits (486), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 97/274 (35%), Positives = 166/274 (60%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I+  E   +   +R        A + + + NLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLHEIGKVDLITAEEEVILAQKIR---EGDQAALERLTKTNLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 73  GLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   ++  + +REP+PEE+A  L   V+ +   L  +   +S++ P    + +
Sbjct: 133 GSLSKISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D + D +  +     I  +L E   R L++LT RE  ++ + FG+G N+  +LEE+G
Sbjct: 193 TLLDVL-DNHEPNTDFHLINESLAEEIKRSLSTLTEREREIVVLFFGLGSNSPFSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 252 EKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 48/273 (17%), Positives = 104/273 (38%), Gaps = 27/273 (9%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G ++L++ E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLHEIGKVDLITAEEEVILAQKIREGDQAALERLTKTNLRF--VVSVAKQYQNQGLTLGD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQK--------------REDSSQEKERDDVQETEGD 229
           +I+ E  +G       F  T+G  +                 E S   +   +   +   
Sbjct: 79  LIN-EGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLSK 137

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDED-----DSAHTLSAMEDQLRPKVMCAL 284
           I  A    + +  +  SP E A+  E  +D+  D         ++ A   Q     +  +
Sbjct: 138 ISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEENTLLDV 197

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            +  E   +   + ++     K   S++  +  +E +V   G  S +   ++ + E+   
Sbjct: 198 LDNHEPNTDFHLINESLAEEIKRSLSTLTERE-REIVVLFFGLGSNSPFSLEEIGEKFNL 256

Query: 345 ISKRIMHN-EGELLRLAQSYGIKRDVFLERHQG 376
             +R+    +  L RL  +    R   L+ + G
Sbjct: 257 TRERVRQIKDKALQRLRHT---SRSKILKSYLG 286


>gi|206889845|ref|YP_002248858.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741783|gb|ACI20840.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 427

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 135/371 (36%), Positives = 216/371 (58%), Gaps = 11/371 (2%)

Query: 318 KEKLVKLVGSLSLNQSRIDLLV-------EQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
           K +L+K +  +   Q +I  L        E+  ++       E ++ ++ + +    +  
Sbjct: 57  KMELIKELLHIPFVQKKIYELSNVFSKNPEKAKEMLD--DEEEIDIEQIKERFIKVSENI 114

Query: 371 LERHQGRELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
            +  + ++    ++    D P   E  N    E+D   +   + +++   TG++  EF  
Sbjct: 115 KKIMRRKKTTKEFLKKIFDIPLRDELTNMFVEELDKFRREIIKGENLQPITGMTNEEFLD 174

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
               ++K   E + AK +M+E+NL+LV+S+AKKYT RGL   DLIQEGNIGLMKA EKF+
Sbjct: 175 HFMTIKKIFNEFTEAKNKMIESNLKLVVSIAKKYTGRGLNLEDLIQEGNIGLMKAVEKFE 234

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTY+ WW++Q+I R+IA+ S TIRIPVH+ D I K+ +  R +    + EP  
Sbjct: 235 YKKGFKFSTYSTWWIRQSINRAIAEHSKTIRIPVHVIDNICKINKIYRELYQNSENEPDI 294

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEI+  L +P + +   L I+KEP+S++     +D S L +FIED N+ +P + A+  +L
Sbjct: 295 EEISLNLNIPSDKIADFLAISKEPVSID-MSLRDDDSLLKEFIEDMNSPNPYEEALHDDL 353

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    +V + L+ RE+ +L  R+GI      +L+EVGK+F V+RERIRQIE +A+RKLK 
Sbjct: 354 KHLIEKVFSLLSKREKEILMRRYGINEEKPKSLDEVGKEFSVSRERIRQIELRAMRKLKR 413

Query: 670 PSRSKKLRSFL 680
             R K LR F+
Sbjct: 414 LCRLKWLREFI 424



 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 30/222 (13%), Positives = 72/222 (32%), Gaps = 17/222 (7%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
             S   +  +  + +  +    T D + +Y + + S  +LS++ E  +AK I   +  ++
Sbjct: 2   DKSKNFSEELAEKDQIVNKTSPTYDSLNLYFKCISSFPVLSKQEEKNLAKTITDKKMELI 61

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEGHSYQKRED 213
             L   P   + +    +  +      +E++D E  I  E  K  F   +E      R  
Sbjct: 62  KELLHIPFVQKKIYELSNVFSKNPEKAKEMLDDEEEIDIEQIKERFIKVSENIKKIMRRK 121

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
            + ++    + +                  +     N   +E +    E      L  + 
Sbjct: 122 KTTKEFLKKIFDI----------------PLRDELTNMFVEELDKFRREIIKGENLQPIT 165

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                + +     I +++ E    ++  +        S+  K
Sbjct: 166 GMTNEEFLDHFMTIKKIFNEFTEAKNKMIESNLKLVVSIAKK 207


>gi|81300366|ref|YP_400574.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
 gi|81169247|gb|ABB57587.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
          Length = 310

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 107/237 (45%), Positives = 165/237 (69%), Gaps = 1/237 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK+ M++ANLRLV+SVAKKY  +GL+FLDLIQEG +GL +A EKFD   GYKFSTYA
Sbjct: 72  GQRAKERMIKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYA 131

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q++TR+IA QS TIR+PVH+ +++ ++ +  R +++++ R P+ +EIA+ + +P+
Sbjct: 132 FWWIRQSMTRAIACQSRTIRLPVHLTERLSQIRKVTRELAHELGRLPSRQEIAEAVQLPL 191

Query: 561 EGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +  +L+ +++  SL+ P+  ED  S LG+ I D N   P+D    A  RE     L  
Sbjct: 192 NDLETILRQSRQCTSLDAPVSGEDGKSFLGELIADPNGNEPMDIMENAMQREQLDAWLEH 251

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LTP+E +VL +RFG+G    HTL E+G+   V+RER+RQ+E KA+RKL++ ++  ++
Sbjct: 252 LTPQERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKLRNLTKRSRI 308


>gi|297561520|ref|YP_003680494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845968|gb|ADH67988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 468

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 109/241 (45%), Positives = 166/241 (68%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK  M+EANLRLV+SVAKKY++RG+  LD++QEGN+GL++A EKFD+  G+KFST
Sbjct: 226 EDGRKAKSHMLEANLRLVVSVAKKYSDRGMSLLDVVQEGNLGLIRAVEKFDYTKGFKFST 285

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YAMWW++QAI R  AD + TIR+PVH+ + + KV R  R M   + REPTPEE+  +L  
Sbjct: 286 YAMWWIRQAIQRGFADSARTIRLPVHVLELLSKVSRLERDMHQALGREPTPEELGLELDK 345

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               + ++L++T++PISL++ IG++  + +GD IED +A    +   +  + +     L+
Sbjct: 346 TPAQIEELLRVTRQPISLDSTIGEDGETRIGDLIEDVDASEASEVVDRQLMADQLRNALS 405

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L PRE  ++ +RFG+      TL+E+GK   +TRERIRQ+E +++ KL+HPSR+++L  
Sbjct: 406 DLEPREATIMSLRFGLMDGRPRTLDEIGKHLGLTRERIRQLEKQSLSKLRHPSRAQQLLD 465

Query: 679 F 679
           F
Sbjct: 466 F 466



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/169 (17%), Positives = 59/169 (34%), Gaps = 45/169 (26%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV----VDGDD 82
           +D     ++   R +G++++ EL A      VS+      +  L+  G+ +     D   
Sbjct: 27  ADAVLTDLLDRGRAQGHLSLSELRAAFTAAAVSTGDGRSILRELTENGVRLANGGDDSAP 86

Query: 83  LEDEEGSEDSLDLA-----------------------------------------SSASN 101
           + D +  +D L+                                           +  + 
Sbjct: 87  VADPDAEDDVLEDTLIATVPDTDEAPRAEGKTAPRKGPSPRRKTRSTRRVKKAEPAQTTT 146

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +   +   D    +  D V  YL+ +G  +LL+ E E+ +AKR+EAG 
Sbjct: 147 DAETGEADLDDQSPAMGDSVHTYLKAIGRRQLLTAEQEVDLAKRVEAGL 195


>gi|26452898|dbj|BAC43527.1| putative plastid RNA polymerase sigma-subunit SIG1 [Arabidopsis
           thaliana]
          Length = 572

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 155/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+     ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 322 LRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKG 381

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA
Sbjct: 382 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIA 441

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  AV+P D  I+  +R+  
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTPEDILIKEFMRQDL 501

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL  RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  R+
Sbjct: 502 DKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRN 561

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 562 NHLQQYL 568


>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 572

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 100/247 (40%), Positives = 154/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK     ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 322 LRKRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKG 381

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA
Sbjct: 382 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIA 441

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  AV+  D  I+  +R+  
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDL 501

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL  RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  RS
Sbjct: 502 DKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRS 561

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 562 NHLQQYL 568


>gi|189461487|ref|ZP_03010272.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198275894|ref|ZP_03208425.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
 gi|189431821|gb|EDV00806.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198271523|gb|EDY95793.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
          Length = 286

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 175/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      IA +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRIALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGI    + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLSREIDRALSTLTEREKDIIQMFFGIN-TQEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 285



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRIALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|302867958|ref|YP_003836595.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|302570817|gb|ADL47019.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 314

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 113/248 (45%), Positives = 166/248 (66%), Gaps = 3/248 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
            +R+   +   A+  M+EANLRLV+SVAK+Y   G L  LDLIQEG IGLM+A EKFD  
Sbjct: 65  RLRRLVADGRRARHHMIEANLRLVVSVAKRYALAGRLPLLDLIQEGTIGLMRAVEKFDHR 124

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KFSTYA WW+KQAI R++ DQS TIR+P H+ + +++V RT R ++ ++ REPTP E
Sbjct: 125 RGLKFSTYATWWIKQAIGRALTDQSRTIRLPAHLVEVLNRVNRTRRTLAGELDREPTPAE 184

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +A ++ +P E V  +L+  +EP+SL TP+ G   T+ LGD + D+ A  P    + +  R
Sbjct: 185 VAARVEVPAEKVELLLRHDREPVSLHTPVAGAAGTTELGDLLPDE-APGPAGVVVSSWRR 243

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL +L+ RE  V+  R+G+  +   TL+E+G +  +TRER+RQIE++A+RKL+HP
Sbjct: 244 RYLDEVLGTLSEREAAVICQRYGLDDDRPSTLDEIGTRIGLTRERVRQIESQALRKLRHP 303

Query: 671 SRSKKLRS 678
           +R++ L  
Sbjct: 304 TRARVLAD 311



 Score = 44.8 bits (104), Expect = 0.042,   Method: Composition-based stats.
 Identities = 17/38 (44%), Positives = 21/38 (55%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +A   T D V  YLR +G   LL+ E E  +  RIEAG
Sbjct: 7   AAAGHTTDAVAAYLRTIGRTPLLTAEQETRLGARIEAG 44


>gi|319955596|ref|YP_004166863.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424256|gb|ADV51365.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 172/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+ +E   +   +R       +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIDLITANEEVDLAQRIR---EGDQLALEKLTTANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++QAI +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIAK+L M V  V++ LK T   +S++ P+ + + S+L
Sbjct: 135 INKIKKAFSYLEQAHERPPSAEEIAKELEMTVSEVQQSLKNTGRHVSMDAPLKEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + I    + +P    +Q +L     R L +L+ RE  V+++ +GIG     TLEE+G+ 
Sbjct: 195 YNVIGSGESPNPDKQLLQQSLNIEINRALETLSQREADVVKLYYGIGDQHSMTLEEIGQT 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI  KAIRKLKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIREKAIRKLKHNSRSKILKTYL 286



 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I+L++   E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKIDLITANEEVDLAQRIREGDQLALEKLTTANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|78185087|ref|YP_377522.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|116072338|ref|ZP_01469605.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|78169381|gb|ABB26478.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
 gi|116064860|gb|EAU70619.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 313

 Score =  191 bits (485), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 112/270 (41%), Positives = 176/270 (65%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T     +F+   + +  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQAMMAFTEDGSKDFKVEDLTTKQRRMLRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P   EIA+ + +PVE +  +L+      SL+ P+  E+
Sbjct: 159 LSERLTTIRKVSLDLAHKLGAMPNRLEIAEAMDIPVEELDSLLRQALTTSSLDAPVNGEE 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +A  PLD   Q    E   R L+ L+ +E+ VLR+RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSSADEPLDIVEQRIHHEQLGRWLSHLSEQEQNVLRLRFGLEGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRMMEVSRERVRQVELKALRKLRNLTRR 308



 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             K  ++  R + DPV  YL  +G I LL+   EI +  +++A
Sbjct: 5   ASKPLETQRRRSSDPVSWYLSTIGRIPLLTAAEEIELGNQVQA 47


>gi|12958587|gb|AAK09363.1|AF321124_1 RpoS [Vibrio harveyi]
          Length = 327

 Score =  191 bits (485), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 106/293 (36%), Positives = 173/293 (59%), Gaps = 3/293 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +    +  +   +        S+   +  +  I     ++  E    V   R+       
Sbjct: 27  LEKPSNGTKTAAREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEA 83

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 84  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 143

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V
Sbjct: 144 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDV 203

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 204 SKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPK 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 264 QKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 316



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/100 (28%), Positives = 40/100 (40%), Gaps = 1/100 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D   SE   +     SN +    + +  A   + D  ++YL E+G   LL+ E E+  A+
Sbjct: 16  DNAQSEGISNGLEKPSNGTKTAAREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYAR 75

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  RALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 114


>gi|291302005|ref|YP_003513283.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571225|gb|ADD44190.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 323

 Score =  191 bits (485), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 104/252 (41%), Positives = 162/252 (64%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +R+   E   AK  +++ANLRLV+S+AK+Y  RG+  LDLIQEGN+GL++A EKF
Sbjct: 71  QLERDLRQIVAEGRRAKSMLLKANLRLVVSIAKRYVGRGVALLDLIQEGNLGLIRAVEKF 130

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G+KFSTYA WW++QAITR++ADQ+ TIR+P H  ++I+++ +  R ++ +  REP 
Sbjct: 131 DYTKGFKFSTYATWWIRQAITRAMADQARTIRVPAHTAEQINRIAKIRRELTAEQGREPR 190

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA+++ +    V ++L   ++PISL+ P+ D+  + L D +      +   +   A 
Sbjct: 191 HEEIAERMGLEPYRVLELLSYDRDPISLDQPVSDDRQTPLSDLVARPVDPAAEPNPANAQ 250

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+   R L  L  RE  VLR RFGI      TLEEVG++  ++RER+RQ+E  ++ KL+
Sbjct: 251 LRQELERALTDLPARERAVLRARFGIDDGRQRTLEEVGEELGLSRERVRQLEKLSLNKLR 310

Query: 669 HPSRSKKLRSFL 680
            P  ++ L  +L
Sbjct: 311 EPGMARALAEYL 322



 Score = 37.1 bits (84), Expect = 9.7,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            D VR YL  +G   L++   E+ +AK IE G 
Sbjct: 22  TDSVRAYLNGIGKHRLINAAEEVDLAKAIETGL 54


>gi|325287834|ref|YP_004263624.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324323288|gb|ADY30753.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+ +E   +   +R        A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIDLITANEEVELAQKIR---AGDEAALEKLTNANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  KLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIAK+L + V  V++ +K +   +S++ P  + + S+L
Sbjct: 135 INKIKKAFSYLEQTHERPPSAEEIAKELELSVSEVKQSMKNSGRHVSMDAPFKEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I+   + +P +  +  +L     R L +L+PRE  V+++ +GIG     TLEE+G+ 
Sbjct: 195 YDVIKYGESPNPDEKLMHQSLNTEINRALETLSPREADVVKLYYGIGDKHSMTLEEIGQI 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI  KAIRKLKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIREKAIRKLKHNSRSKILKTYL 286



 Score = 42.1 bits (97), Expect = 0.28,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I+L++   E+ +A++I AG    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKIDLITANEEVELAQKIRAGDEAALEKLTNANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|268315720|ref|YP_003289439.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
 gi|262333254|gb|ACY47051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
          Length = 279

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 98/269 (36%), Positives = 171/269 (63%), Gaps = 3/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +   +++       A  ++  ANLR V+SVAKKY  +GL
Sbjct: 10  LDQYLQEIGKIPLLTPEEEVELARRIKQ---GDEEALHKLTRANLRFVVSVAKKYQGQGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN GL+KAA++FD   G+KF +YA+WW++QAI +++A+QS  +R+P++    
Sbjct: 67  SLADLINEGNYGLIKAAQRFDETRGFKFISYAVWWIRQAILQALAEQSRVVRLPLNRIGT 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K+ + + R++ + +R P+ EE+A++L + VE +R+ L+ T   +S++ P  D+D + L
Sbjct: 127 ISKIRKVSARLAQEHERAPSAEELAEELNIDVEKIREALQHTGRALSMDAPFTDDDDNSL 186

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + ++   SP +  ++ +L+    R L++L PRE  ++R+ FGIG     TLEE+G++
Sbjct: 187 LDVLPNEEDTSPDEGLMEESLKIDIERALSTLHPREAEIIRLYFGIGREHPLTLEEIGQR 246

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           F +TRER+RQI+ KA+RKL+   R ++L+
Sbjct: 247 FGLTRERVRQIKEKALRKLRQKHRREELQ 275



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G I LL+ E E+ +A+RI+ G    +  L  + L F  ++    +       L +
Sbjct: 13  YLQEIGKIPLLTPEEEVELARRIKQGDEEALHKLTRANLRF--VVSVAKKYQGQGLSLAD 70

Query: 184 IID 186
           +I+
Sbjct: 71  LIN 73


>gi|317502748|ref|ZP_07960858.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315666141|gb|EFV05698.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 287

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 168/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +++       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEDLISVEEEVELAQKIKR---GDRRALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R   ++  + +  PT EEIA K+ +P E V   +K     +S++ P  + + + L
Sbjct: 135 VNKIKRVLNKLEQENEHFPTIEEIAAKVDIPEEKVADAIKSNGRHVSVDAPFAEGEENSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + NA    +  +Q +LR+  +  L SL  RE  ++   FGI      TLEE+G +
Sbjct: 195 LDVLPNSNAQMADNVLVQESLRDEISSALKSLNERERNIIEAFFGINQAE-MTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L++ S++K L+++L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRNNSKNKSLKAYL 285



 Score = 41.4 bits (95), Expect = 0.60,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S E E+ +A++I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGHEDLISVEEEVELAQKIKRGDRRALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|148240072|ref|YP_001225459.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147848611|emb|CAK24162.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 313

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 107/240 (44%), Positives = 160/240 (66%), Gaps = 1/240 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+       AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GY
Sbjct: 69  RRLIRVGQRAKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGY 128

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+
Sbjct: 129 KFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRLEIAE 188

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + MPVE +  +L+      SL+ P+  E+  S LGD I D +   PLD   Q    E  
Sbjct: 189 AMDMPVEELDSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLEEPLDRVEQRMHHEQL 248

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R ++ L+ +E+ VL +RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 249 GRWMSHLSDQEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLRNLTRR 308



 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                 ++  R + DP+  YL  +G I LL+   EI +  +++ 
Sbjct: 4   AAAGVSETQRRRSSDPISWYLATIGRIPLLTPAEEIELGNQVQQ 47


>gi|284036901|ref|YP_003386831.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
 gi|283816194|gb|ADB38032.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
          Length = 287

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 102/274 (37%), Positives = 171/274 (62%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E    V++ +K      ++ + + +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTPDEE---VTLAQKIREGDQLSLERLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  K +REP+PEE+A  L +    V   LKI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSDLEQKFEREPSPEELAAVLEISAAEVVDTLKISGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+     P    I  +LR+   R L++LT RE  V+ + FG+      TLEE+G
Sbjct: 193 SLLDVLENDGEDKPDSGLINDSLRKEVQRALSTLTQREADVITLYFGLNGEHAMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+H SRSK L+++L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRHTSRSKALKTYL 286



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +A++I  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPDEEVTLAQKIREGDQLSLERLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|119773417|ref|YP_926157.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
 gi|119765917|gb|ABL98487.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
          Length = 969

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 134/364 (36%), Positives = 207/364 (56%), Gaps = 16/364 (4%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV---FLERHQG 376
           +     S+ L +  +++L++ LY+   ++   + EL+ L      + R       E+  G
Sbjct: 611 VQDTFRSIVLTEDALNILIKALYESIDKVSDIKTELVNLYTREIKLPRKTAESVAEQKMG 670

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
           REL                ++ +     +I +++ ++++I+ +TGI +   + I S ++K
Sbjct: 671 REL-----ISQLKTEYPLCEDKLERHAGAINRLQAQMQNINQKTGIDLYSLQDIGSKIKK 725

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            + + S A+ EM+  NLRLV+SVA KY  RGL+  DL+QEGNIGLMKA EKFD   G+KF
Sbjct: 726 LQRDISAARDEMITFNLRLVLSVANKYLGRGLELADLVQEGNIGLMKAVEKFDHRKGFKF 785

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++QAITR+IADQ+  IRIPVH+ + ++K++  ++ +++K  R P   E++  L
Sbjct: 786 STYATWWIRQAITRAIADQARIIRIPVHVNESLNKLISASKVLTHKFGRGPKISELSLIL 845

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           +MP   V  + +I       E                D  A+SP +  I  +       +
Sbjct: 846 SMPETKVENLKQILVMEPVAEADHNTNG-------YVDWAAMSPEEEIIDDDRDTNIKDL 898

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  LT +E++VL +RFGI   T+ TLEEVG+QF VTRERIRQIEAK+++KL H SRS  L
Sbjct: 899 LKGLTDKEKKVLELRFGINAATELTLEEVGQQFDVTRERIRQIEAKSLKKLAHTSRSSHL 958

Query: 677 RSFL 680
             F 
Sbjct: 959 AIFF 962


>gi|332878128|ref|ZP_08445857.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332683866|gb|EGJ56734.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 287

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 173/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK---EGDVAALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIA++L M V  V++ +K +   IS++ P+ + + S+L
Sbjct: 135 INKINKMYAYLEQANERVPSAEEIARELDMSVNDVKESMKNSGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I    + +P    I A+LR    R L +LTPRE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVIRSNESPNPDKELILASLRTEIERALETLTPREADVIRLYFGLGDQHAMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRVDLITADEEVELAQRIKEGDVAALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|150005266|ref|YP_001300010.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212694793|ref|ZP_03302921.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|237710938|ref|ZP_04541419.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|237727237|ref|ZP_04557718.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D4]
 gi|254883735|ref|ZP_05256445.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|265750524|ref|ZP_06086587.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294777100|ref|ZP_06742557.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|319643459|ref|ZP_07998082.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
 gi|149933690|gb|ABR40388.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212662647|gb|EEB23221.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|229434093|gb|EEO44170.1| RNA polymerase sigma factor rpoD [Bacteroides dorei 5_1_36/D4]
 gi|229454782|gb|EEO60503.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|254836528|gb|EET16837.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|263237420|gb|EEZ22870.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294448969|gb|EFG17512.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|317384864|gb|EFV65820.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
          Length = 286

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 175/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGI    + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTEREKDIIQMFFGIN-TQEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  SRSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQNSRSKLLKSYL 285



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|153840560|ref|ZP_01993227.1| RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149745777|gb|EDM56907.1| RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 415

 Score =  191 bits (484), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 104/264 (39%), Positives = 164/264 (62%), Gaps = 3/264 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  I     ++  E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  
Sbjct: 1   MYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLAL 57

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ T R+P+H+  +++
Sbjct: 58  LDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTTRLPIHVVKELN 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
             +RTAR +S K+  EPT EEIA +L +PVE V K+L++ +   S++TPIG +    L D
Sbjct: 118 IYLRTARELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNERISSVDTPIGGDGEKALLD 177

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D N   P  S    +++ +    L  L P+++ VL  RFG+      TLEEVG++  
Sbjct: 178 IIPDANNSDPEVSTQDDDIKSSLIHWLEELNPKQKEVLARRFGLLGYEPSTLEEVGREIG 237

Query: 651 VTRERIRQIEAKAIRKLKHPSRSK 674
           +TRER+RQI+ + +R+L+     K
Sbjct: 238 LTRERVRQIQVEGLRRLREMKEKK 261



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL E+G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL 
Sbjct: 1   MYLGEIGFSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLD 59

Query: 183 EI 184
            I
Sbjct: 60  LI 61


>gi|150026087|ref|YP_001296913.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772628|emb|CAL44111.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
          Length = 287

 Score =  191 bits (484), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 171/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK---AGDQRALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIAK+L M V  V++ +K +   +S++ P+ + + S+L
Sbjct: 135 INKINKMYALLEQSNERPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    I  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVLRSGESPNPDRELIIESLRTEIERSLETLTPREADVVRLYFGLADQHPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITADEEVELAQRIKAGDQRALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|1553017|gb|AAC45100.1| primary sigma factor [Borrelia burgdorferi 297]
          Length = 450

 Score =  191 bits (484), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 133/357 (37%), Positives = 212/357 (59%), Gaps = 1/357 (0%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+  + L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKKERLALKELLRDIPLYQEELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +       +   +
Sbjct: 155 LRVL-GRDLTIAEKKIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPTDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|302392313|ref|YP_003828133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302204390|gb|ADL13068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 275

 Score =  191 bits (484), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 111/275 (40%), Positives = 174/275 (63%), Gaps = 2/275 (0%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N I     +    +      +S+ RK +   S AK +++  NLRLV+S+A K+  +GL
Sbjct: 1   MINSINQYYQDISHDLLTKEEEISLARKAQAGDSEAKDKLIRHNLRLVVSIANKHQGKGL 60

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+QEGNIGL+ A EKFD   GY+FSTYA WW+KQ +TR+IA+Q  TIRIPVH+  K
Sbjct: 61  DLQDLVQEGNIGLITAVEKFDPDKGYRFSTYASWWIKQRVTRAIANQGKTIRIPVHVWQK 120

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS 586
            +K+ +    +  ++ REPT EEIA++  + +E +++V+++  +    SL   +GD+  +
Sbjct: 121 TNKIFKVKDDLQTELGREPTAEEIAEETDISLEKIKEVMRVITDQNLASLNQFVGDDRDT 180

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LG  +   +A  P++   Q  L+E    +L  L+ RE  V+R+RFG+  +   TL+EVG
Sbjct: 181 ELGQLVPSGSADDPVEGTSQQLLKEDLEELLTELSDREAEVIRLRFGLRDSRPRTLKEVG 240

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++  VTRERIRQI+ KA+ +LKHP+R K+L+ +L+
Sbjct: 241 EELGVTRERIRQIQLKALNRLKHPTRIKQLKGYLE 275


>gi|302866072|ref|YP_003834709.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315502628|ref|YP_004081515.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302568931|gb|ADL45133.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315409247|gb|ADU07364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 328

 Score =  191 bits (484), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 117/252 (46%), Positives = 174/252 (69%), Gaps = 1/252 (0%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            + + +     E   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 75  ELHADLALIAAEGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKF 134

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM ++++++VR  R +S  + REPT
Sbjct: 135 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEQVNRMVRVRRELSVTLGREPT 194

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQA 607
             E+A  L +P   V +++   +EP+SL+  +G++  S LGDF+   +    P D+A   
Sbjct: 195 VSEVATALEIPEFQVIELISYDREPVSLDQAVGEDGESALGDFVAAVDPRTEPGDAATNG 254

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR     VLA+L+ RE+ V+R+RFG+      TL+EVG++F ++RERIRQIE   + KL
Sbjct: 255 ELRNEVRIVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKL 314

Query: 668 KHPSRSKKLRSF 679
           + P R+ +L ++
Sbjct: 315 RDPERANRLEAY 326



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 23/57 (40%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
            +                     + D VR YL  +G  +LL+   E+ ++KRIEAG 
Sbjct: 4   QMIEHQDMDVTLTDLDATDERGVSTDLVRAYLNGIGRTKLLTAAQEVELSKRIEAGL 60


>gi|149278388|ref|ZP_01884525.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255532892|ref|YP_003093264.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|149230758|gb|EDM36140.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255345876|gb|ACU05202.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  191 bits (484), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 97/274 (35%), Positives = 165/274 (60%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I+  E   +   +R        A + + + NLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLHEIGKVDLITAEEEVILARKIR---EGDQAALERLTKTNLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 73  GLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   ++  + +REP+PEE+A  L   V+ +   L  +   +S++ P    + +
Sbjct: 133 GSLSKISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+    +   S I  +L E   R L++LT RE  ++ + FG+  N   +LEE+G
Sbjct: 193 TLLDVLENHE-PNTDSSLINESLSEEIKRSLSTLTEREREIIVLFFGLSTNHPLSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KA+++L+H SRSK L+S+L
Sbjct: 252 EKFNLTRERVRQIKDKALQRLRHTSRSKILKSYL 285



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 48/273 (17%), Positives = 104/273 (38%), Gaps = 27/273 (9%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G ++L++ E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLHEIGKVDLITAEEEVILARKIREGDQAALERLTKTNLRF--VVSVAKQYQNQGLTLGD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQK--------------REDSSQEKERDDVQETEGD 229
           +I+ E  +G       F  T+G  +                 E S   +   +   +   
Sbjct: 79  LIN-EGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSLSK 137

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDED-----DSAHTLSAMEDQLRPKVMCAL 284
           I  A    + +  +  SP E A+  E  +D+  D         ++ A   Q     +  +
Sbjct: 138 ISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEENTLLDV 197

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            E  E   +   + ++     K   S++  +  +E +V   G  + +   ++ + E+   
Sbjct: 198 LENHEPNTDSSLINESLSEEIKRSLSTLTERE-REIIVLFFGLSTNHPLSLEEIGEKFNL 256

Query: 345 ISKRIMHN-EGELLRLAQSYGIKRDVFLERHQG 376
             +R+    +  L RL  +    R   L+ + G
Sbjct: 257 TRERVRQIKDKALQRLRHT---SRSKILKSYLG 286


>gi|164687939|ref|ZP_02211967.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
 gi|164602352|gb|EDQ95817.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
          Length = 294

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 129/274 (47%), Positives = 178/274 (64%), Gaps = 5/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +K I     +S  E    V + +K   E   AK++ + AN RLV+S+AKKY    
Sbjct: 23  AMKMYLKEIEEYKMLSAVEE---VELAKKVNEEIPEAKEDFINANYRLVVSIAKKYRKEN 79

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA WW+KQ+ITR I D   TIRIPVH+  
Sbjct: 80  VDILDLIQAGNIGLIKAVEKYDYTKGYKFSTYATWWIKQSITRYIDDCENTIRIPVHLHQ 139

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+ V R  + +SN ++REP+ EE+A    M V+ V ++LK  K  +SL+TPI +++ S 
Sbjct: 140 RINFVKRKKQELSNVLQREPSLEELADICDMDVDKVIEILKRDKNVVSLDTPIKEDEDSS 199

Query: 588 LGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L +FI      S   +    Q NL+E    +L  L+ +E++VLRMRFG+  +   TLEE+
Sbjct: 200 LVEFIPSDANFSDVVMHEVEQHNLKEKINELLTGLSEQEQKVLRMRFGLDDDDPKTLEEI 259

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GK F VTRERIRQIEAKAIRKL+HPSR  +L++F
Sbjct: 260 GKVFGVTRERIRQIEAKAIRKLRHPSRLNQLKNF 293


>gi|15223259|ref|NP_172330.1| SIG2 (RNA POLYMERASE SIGMA SUBUNIT 2); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana]
 gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana]
 gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana]
 gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana]
 gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
 gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana]
 gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana]
 gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana]
          Length = 572

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 98/247 (39%), Positives = 154/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+     ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 322 LRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKG 381

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA
Sbjct: 382 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIA 441

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  AV+  D  I+  +R+  
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDL 501

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL  RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  R+
Sbjct: 502 DKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRN 561

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 562 NHLQQYL 568


>gi|148243538|ref|YP_001228695.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851848|emb|CAK29342.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 370

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 103/282 (36%), Positives = 174/282 (61%), Gaps = 16/282 (5%)

Query: 415 SISVETGISISEFRHIVSM---------------VRKGECEASIAKKEMVEANLRLVISV 459
             +   G+S  E R  V                 +++       AK+ M++ANLRLV++V
Sbjct: 87  QWAQACGLSAGELRAQVQAGNKAWAELLDMSPGDLQRQLLHGRRAKERMIQANLRLVVAV 146

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY +RG++ LDL+QEG +GL +  EK+D   G++FSTYA WW++Q ITR+IA QS TI
Sbjct: 147 AKKYQHRGMELLDLVQEGTLGLERGVEKYDPTRGFRFSTYAYWWIRQGITRAIATQSRTI 206

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVH+ +K++++ +  R +++++ R  T ++++++L +  E VR+ L      +SL+T 
Sbjct: 207 RLPVHITEKLNRIKKAQRDIASRLGRTATLKDLSQELQLSEEVVRQTLMRVPRSVSLDTR 266

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G +  + LGD +ED    +P     +  L +    +L  L+ RE RV+R+RFG+  +T 
Sbjct: 267 VGRDMDTELGDLLED-GMPTPEQRLTREKLHDDLLVLLNELSGREARVIRLRFGLDDDTP 325

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            TL E+GK   ++RER+RQIE++A+ KL+ P R  ++R +++
Sbjct: 326 QTLAEIGKTLDLSRERVRQIESRALHKLRLPERRGRVRDYME 367



 Score = 41.7 bits (96), Expect = 0.44,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 32/49 (65%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           ++  S  RST D VR+YL+++G ++LLS E E+ +A+ ++    +++  
Sbjct: 4   RQASSKRRSTADLVRLYLQDIGRVDLLSHEEELTLARLVQKREQLVVER 52


>gi|16332132|ref|NP_442860.1| RNA polymerase sigma factor RpoD [Synechocystis sp. PCC 6803]
 gi|47717353|sp|P74565|RPOD_SYNY3 RecName: Full=RNA polymerase sigma factor rpoD
 gi|1653761|dbj|BAA18672.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 425

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 133/237 (56%), Positives = 181/237 (76%), Gaps = 1/237 (0%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK +MV++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IADQS TIR+PVH+ + I ++ +T + +S +++R+PT EEIA+K+ M +E +
Sbjct: 249 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKL 308

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R + K  + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PR
Sbjct: 309 RFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPR 367

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  VLR+R+G+      TLEE+G+ F VTRERIRQIEAKA+RKL+HP+R+  L+ ++
Sbjct: 368 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 424



 Score = 41.0 bits (94), Expect = 0.62,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E  E  +            ++K        T+D +R+YL+E+G I LL  E EI +A++I
Sbjct: 39  EDLEQEVAATEGKEKKVRKIRKDAVKKKPYTEDSIRIYLQEIGRIRLLRAEEEIELARQI 98


>gi|150007022|ref|YP_001301765.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154495210|ref|ZP_02034215.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218256952|ref|ZP_03474423.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|255015941|ref|ZP_05288067.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_7]
 gi|256841904|ref|ZP_05547409.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262384222|ref|ZP_06077357.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298377447|ref|ZP_06987400.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|301308863|ref|ZP_07214815.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
 gi|149935446|gb|ABR42143.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154085357|gb|EDN84402.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218225859|gb|EEC98509.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|256736220|gb|EEU49549.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262293925|gb|EEY81858.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298265861|gb|EFI07521.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|300833387|gb|EFK64005.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
          Length = 286

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 175/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +++       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQAIKR---GDRRALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELDIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + +A     S +  +L +   R LA+LT RE  +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDAPIADRSLMNESLAKEIDRALATLTERECEIIKMFFGIGC-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQGTRSKLLKSYL 285



 Score = 42.1 bits (97), Expect = 0.28,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+ I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQAIKRGDRRALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|124023660|ref|YP_001017967.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123963946|gb|ABM78702.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 313

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 108/270 (40%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T  G    + +   +  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQTMMSLTQDGSVAPDDKEFTTHQRRMIRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + +PV+ +  +L+      SL+ P+  E+
Sbjct: 159 LSERLTTIRKVSLDLAHKLGAMPSRSEIAEAMDIPVDELDSLLRQALTTSSLDAPVNGEE 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q    E   R L+ L+ +E+ VL++RFG+  +  HTL 
Sbjct: 219 GRSFLGDLIADSSLGEPLDKVEQRIHHEQLGRWLSHLSEQEQHVLKLRFGLETHDRHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLMEVSRERVRQVELKALRKLRNLTRR 308



 Score = 40.6 bits (93), Expect = 0.87,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 22/44 (50%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
              K  ++  R + DPV  YL  +G I LL+   EI +  +++ 
Sbjct: 4   AAPKSAETQRRRSSDPVSWYLTTIGRIPLLTPAEEIELGNQVQT 47


>gi|91216377|ref|ZP_01253344.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
 gi|91185515|gb|EAS71891.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
          Length = 287

 Score =  190 bits (483), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++       +A +++ +ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQKIK---AGDDLALEKLTKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I  ++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILSALAEQSRVVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +T   +  + +R P+P+EIAK+L M V  V++ LK +   +S++ P+ + + S+L
Sbjct: 135 INKINKTFAILEQRHQRPPSPDEIAKELEMTVNDVKESLKNSGRHLSMDAPLIEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D ++   + +P +  +  +L+    R L +LT RE  V+R+ FG+G     TLEE+G+ 
Sbjct: 195 YDVLKFGESPNPENDLLHESLQTEIERALETLTTREADVIRLYFGLGNQQPMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ K +R+LKH SRS  L+++L
Sbjct: 255 FGLTRERVRQIKEKGVRRLKHTSRSTILKTYL 286



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ E E+ +A++I+AG  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLITAEEEVELAQKIKAGDDLALEKLTKANLRF--VVSVSKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|295087657|emb|CBK69180.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
          Length = 286

 Score =  190 bits (483), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELAVELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQ-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|256819198|ref|YP_003140477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
 gi|256580781|gb|ACU91916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
          Length = 287

 Score =  190 bits (483), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 171/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK---AGDVAALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIA++L M V  V++ +K     IS++ P+ + + S+L
Sbjct: 135 INKINKMYAYLEQANERVPSAEEIARELDMSVNDVKESMKNAGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I    + +P  S I  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVIRSNESPNPDKSLILDSLRTEIERALETLTPREADVVRLYFGLSDQHAMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRVDLITADEEVELAQRIKAGDVAALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|1553019|gb|AAC45101.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  190 bits (483), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 138/418 (33%), Positives = 228/418 (54%), Gaps = 2/418 (0%)

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             E   +   + + +S       + ++       L  I +        +        D  
Sbjct: 35  EREEFFKREKDKDKESNPNYYNKKKRIASFYKVPLKPIQDRLISYVDSKHRVYELGGDI- 93

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                K  +  L +L+ ++ L Q  + +  +   D + +I   + +   +     I++  
Sbjct: 94  FEKNLKSERLALKELLRNVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIR 153

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
            L    GR+L         +      ++ +  ++      + E++ I +     + +   
Sbjct: 154 DLRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIIS 212

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +   + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF+
Sbjct: 213 MSEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFE 272

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT 
Sbjct: 273 YKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTD 332

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L
Sbjct: 333 EELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVL 392

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 393 QDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|225440035|ref|XP_002276710.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score =  190 bits (483), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 94/303 (31%), Positives = 169/303 (55%), Gaps = 12/303 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGI--------SISEFRHIV----SMVRKGE 438
           PE         E + I++I+  ++   V+  +        ++ E+   V     +++   
Sbjct: 256 PETRKLLTAKEESELIVQIQELMRLEEVKKRLQSHLKREPTVVEWAEAVGLSCQVLQSQL 315

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              + ++++++ ANLR+V+ +AK+Y  RGL   DL+QEG++GLM + EKF    G +F++
Sbjct: 316 HSGNRSRQKLIYANLRMVVHIAKQYQGRGLNLQDLLQEGSMGLMNSVEKFKPNAGCRFAS 375

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA+ ++I   S TIR+P +M   + KV    R    +   +PT EEIA+++ +
Sbjct: 376 YAYWWIRQAVRKAIFQHSRTIRLPENMYSLLGKVKEAKRLFIQEGHHDPTKEEIAERVGI 435

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +E ++++L  T+ P+S++ P+  +  +   +   D     P  S  +  +R+    +L 
Sbjct: 436 TIEKLQRLLLHTRMPLSMQQPVWADQDTTFQEVTADTGIEIPDVSVAKQLMRQHVRNLLH 495

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTP+E R++R+RFGIG     TL E+G  F  ++ER+RQ+E +A+ KLK    S  L S
Sbjct: 496 VLTPKERRIIRLRFGIGDGIPRTLSEIGLVFGFSKERVRQLEQRALHKLKQCLSSHGLES 555

Query: 679 FLD 681
           + D
Sbjct: 556 YTD 558


>gi|311747140|ref|ZP_07720925.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
 gi|126578848|gb|EAZ83012.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
          Length = 287

 Score =  190 bits (483), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 171/274 (62%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   +R       +A +++ +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTADEEVVLAKRIR---EGDQLALEKLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  + +REP+PEE+A+ L +    V   +KI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSELEQRFEREPSPEELAEVLEVTANEVVDTMKISGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+     P D  +  +LR+   R L++LT RE  V+ + FG+      TLEE+G
Sbjct: 193 SLLDVLENDGDEKPDDGLMNDSLRKEVQRALSTLTQREADVITLYFGLNGEHAMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+H SRSK L+ +L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRHTSRSKTLKPYL 286



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +AKRI  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTADEEVVLAKRIREGDQLALEKLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|29346721|ref|NP_810224.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|153808302|ref|ZP_01960970.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|160882661|ref|ZP_02063664.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|160891864|ref|ZP_02072867.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167762326|ref|ZP_02434453.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|218130148|ref|ZP_03458952.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|237712837|ref|ZP_04543318.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|237718434|ref|ZP_04548915.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|255693898|ref|ZP_05417573.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|260173882|ref|ZP_05760294.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides sp. D2]
 gi|262408807|ref|ZP_06085352.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270296469|ref|ZP_06202669.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|293371428|ref|ZP_06617859.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|294648199|ref|ZP_06725739.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294810777|ref|ZP_06769425.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298484065|ref|ZP_07002233.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|299149080|ref|ZP_07042142.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|315922146|ref|ZP_07918386.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|317476641|ref|ZP_07935886.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|317480344|ref|ZP_07939445.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|329955895|ref|ZP_08296698.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
 gi|29338618|gb|AAO76418.1| RNA polymerase sigma factor rpoD (Sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|149129205|gb|EDM20421.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|156111976|gb|EDO13721.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|156858342|gb|EDO51773.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167699969|gb|EDS16548.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|217987652|gb|EEC53980.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|229447165|gb|EEO52956.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|229452367|gb|EEO58158.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|260620263|gb|EEX43134.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|262353018|gb|EEZ02113.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270273873|gb|EFA19735.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|292633625|gb|EFF52183.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|292636474|gb|EFF54952.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294442110|gb|EFG10929.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298269746|gb|EFI11339.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|298513841|gb|EFI37728.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|313696021|gb|EFS32856.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|316903519|gb|EFV25372.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|316907237|gb|EFV28946.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|328525275|gb|EGF52325.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
          Length = 286

 Score =  190 bits (482), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQ-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|145347899|ref|XP_001418397.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578626|gb|ABO96690.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 344

 Score =  190 bits (482), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 117/251 (46%), Positives = 165/251 (65%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  + +   +   AK EM++ANLRLV+S+AKKY N  + F DLIQEG +GL++ AEKFD+
Sbjct: 78  VQALHQRLRDGKSAKNEMIQANLRLVVSIAKKYANSNMSFQDLIQEGCVGLIRGAEKFDF 137

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QA+TRSI+DQS TIR+PVH+ + I ++ +  ++ +    R PT E
Sbjct: 138 QRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVHLFEIISRISKMEQKFALHNGRNPTTE 197

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA ++ M  E + ++ K  + P+SL +T  GD     + D + D  A  P   + ++ L
Sbjct: 198 EIAAEMDMSAEKITQIKKAAQAPVSLAQTMGGDNKGRTVEDTLVDVTAEGPEKVSGKSLL 257

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E    VL +L PRE  VLR+R+G+      TLEE+G  F VTRERIRQIEAKA+RKLK 
Sbjct: 258 KEDLENVLNTLNPRERDVLRLRYGLDDGRVKTLEEIGTVFSVTRERIRQIEAKALRKLKQ 317

Query: 670 PSRSKKLRSFL 680
           PSR+  L+ + 
Sbjct: 318 PSRNSILQEYF 328



 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCE 159
            D +R YL+++GS+ LL+   E+ +AKRI+       +  +L E
Sbjct: 14  TDSMRSYLKDIGSVTLLNAGQEVELAKRIQDLMHLESIRENLVE 57


>gi|94985446|ref|YP_604810.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94555727|gb|ABF45641.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 403

 Score =  190 bits (482), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 127/300 (42%), Positives = 182/300 (60%), Gaps = 27/300 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM------------------------VRKGECEASIA 444
           +R  +  I     ++++E   +                           +++   + + A
Sbjct: 104 LRQYLHEIGRVPLLTVAEEMDLARRYEEGEAARQALDSNPDLDDRTRRQLQRQVEDGAAA 163

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+ ++EANLRLV+S+AK+YTNRGL  LDLIQEGN GL++A EKF++  GYKFSTYA WW+
Sbjct: 164 KQALIEANLRLVVSIAKRYTNRGLGLLDLIQEGNQGLIRAVEKFEYRRGYKFSTYATWWI 223

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEG 562
           +Q++TR+IAD+S TIR+PVHM + I+++ R  R++  ++ REP P EIA+ +        
Sbjct: 224 RQSLTRAIADKSRTIRVPVHMVETINRLSRMTRQLEMELSREPLPAEIAEAMGPGWDAAK 283

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V +  K+  EP+SLE PIG+E  S  GDF+ D    SP+ +A QA L E   R   +L  
Sbjct: 284 VEETQKVGWEPMSLEMPIGEEGDSTYGDFLPDDRFASPIQNASQALLSEALERAFGTLNE 343

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           RE  VLR+R G     +HTLEEVG+   VTRER+RQIE KA+RKLK     ++ LR FL+
Sbjct: 344 REALVLRLRHGFVDGHEHTLEEVGQLLSVTRERVRQIENKALRKLKYQEGLTRGLRDFLE 403



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 35/76 (46%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           G +  DEE   +    A +A+         + S   S  D +R YL E+G + LL+   E
Sbjct: 63  GAEALDEELQLEDEAPAVAANAGDEEAFALEASPALSQGDSLRQYLHEIGRVPLLTVAEE 122

Query: 140 IAIAKRIEAGRAMMMA 155
           + +A+R E G A   A
Sbjct: 123 MDLARRYEEGEAARQA 138


>gi|253573078|ref|ZP_04850470.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
 gi|251837335|gb|EES65434.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
          Length = 286

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTEREKEIIQMFFGIGQ-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285



 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|260683114|ref|YP_003214399.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260686712|ref|YP_003217845.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
 gi|260209277|emb|CBA62619.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260212728|emb|CBE03837.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
          Length = 301

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 119/274 (43%), Positives = 174/274 (63%), Gaps = 5/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +K I     +S  E   +   +      +S+AK++ + +N RLV+S+AK+Y    
Sbjct: 30  AMKMYLKEIEEYKMLSAGEEVELAKEI---INSSSVAKEKFINSNYRLVVSIAKRYKRDS 86

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA WW+KQ+ITR I D   TIRIP+H+  
Sbjct: 87  IDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQ 146

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+ V +  + + N + REPT +EIA    + V+ V ++L+  K  +SL+TP+ +++ S 
Sbjct: 147 RINFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPLKEDEDSS 206

Query: 588 LGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L +FI          +    Q NL+E    +L  L  +E++VLRMRFGI  +   TLE++
Sbjct: 207 LVEFIPSDADFKDVVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDPKTLEQI 266

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GK F VTRERIRQIEAKAIRKL+HPS+ K+L+ F
Sbjct: 267 GKVFGVTRERIRQIEAKAIRKLRHPSKLKQLKHF 300



 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 9/98 (9%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
              +  + ++MYL+E+   ++LS   E+ +AK I    ++       S       I  R 
Sbjct: 23  GSSNVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSVAKEKFINSNYRLVVSIAKRY 82

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           +        R+ ID+   I      G     E + Y+K
Sbjct: 83  K--------RDSIDMLDLI-QAGNIGLIKAVEKYDYKK 111


>gi|2353173|gb|AAB69385.1| sigma factor 2 [Arabidopsis thaliana]
          Length = 574

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 98/247 (39%), Positives = 154/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+     ++ K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 324 LRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKG 383

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  + P  EEIA
Sbjct: 384 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIA 443

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  AV+  D  I+  +R+  
Sbjct: 444 EATGLSMKRLMAVLLSPKPPRSLDRKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDL 503

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL  RE++V+R RFG+      TL+E+G+   V+RER+RQIE+ A RKLK+  R+
Sbjct: 504 DKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRN 563

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 564 NHLQQYL 570


>gi|189467039|ref|ZP_03015824.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224535443|ref|ZP_03675982.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319901765|ref|YP_004161493.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
 gi|189435303|gb|EDV04288.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224522909|gb|EEF92014.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319416796|gb|ADV43907.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
          Length = 286

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      IA +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRIALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTDREKEIIQMFFGIGQ-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRIALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|1553013|gb|AAC45098.1| primary sigma factor [Borrelia afzelii]
 gi|1553015|gb|AAC45099.1| primary sigma factor [Borrelia afzelii]
 gi|1553021|gb|AAC45102.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 133/357 (37%), Positives = 213/357 (59%), Gaps = 1/357 (0%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+  + L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKKERLALKELLRDIPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|329960773|ref|ZP_08299079.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
 gi|328532374|gb|EGF59175.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
          Length = 286

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      IA +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRIALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     S +  +L     R L++LT RE+ +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRSLVNESLAREIDRALSTLTEREKEIIQMFFGIGQ-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +RSK L+S+L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQSNRSKLLKSYL 285



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRIALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|153835750|ref|ZP_01988417.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156975773|ref|YP_001446680.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
 gi|148867581|gb|EDL66895.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156527367|gb|ABU72453.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
          Length = 328

 Score =  190 bits (482), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 106/295 (35%), Positives = 174/295 (58%), Gaps = 3/295 (1%)

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           + +    +  +   +        S+   +  +  I     ++  E    V   R+     
Sbjct: 26  NELEKTSNRTKTAAREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGD 82

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA 
Sbjct: 83  EAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 142

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE
Sbjct: 143 WWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVE 202

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L 
Sbjct: 203 DVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELN 262

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 263 PKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 317



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+  + ++      + +     SN +    + +  A   + D  ++YL E+G   LL+ E
Sbjct: 10  VEEFEYDNASTEGIANNELEKTSNRTKTAAREEFDASSKSLDATQLYLGEIGFSPLLTAE 69

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 115


>gi|330504211|ref|YP_004381080.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
 gi|328918497|gb|AEB59328.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
          Length = 335

 Score =  190 bits (482), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 164/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+ EEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSAEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   TLEE
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSDLTDKQREVVVRRFGLRGHESCTLEE 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 297 VGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 330



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 1/100 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           + +G +    +  + + S+   ++ K        D  ++YL E+G   LL+ E E+  A+
Sbjct: 28  EVQGDDLEAPVTRTKAKSATPSKQHKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFAR 87

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             + G       + ES L     I  R  +N G +LL  I
Sbjct: 88  LAQKGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 126


>gi|1553025|gb|AAC45104.1| primary sigma factor [Borrelia garinii]
 gi|1553031|gb|AAC45107.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  190 bits (482), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 140/417 (33%), Positives = 233/417 (55%), Gaps = 11/417 (2%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQDNAVNGQKDEKS--------- 310
           + ++        + +  P        IA  Y+  L+ +QD  ++   ++           
Sbjct: 35  EREEFFKREKDKDKESNPDYYNKKKRIASFYKVPLKPIQDRLISYVDNKHRVYELGGDIF 94

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+ ++ L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKSERLALKELLRNVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|254514875|ref|ZP_05126936.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
 gi|219677118|gb|EED33483.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
          Length = 367

 Score =  190 bits (482), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 90/272 (33%), Positives = 163/272 (59%), Gaps = 3/272 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E +H   +V+K       A+K M+E+NLRLV+++A++Y 
Sbjct: 91  TLDPTQLYLNEIGFVPLLSADEEKHYARLVQK---GDEAARKRMIESNLRLVVNIARRYL 147

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +RG+  LDLI+EGN+GLM+A EKFD   G++FSTYA WW++Q I R I +Q+ TIR+P+H
Sbjct: 148 HRGMSLLDLIEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIH 207

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +   ++  +R AR ++ ++  +PT +EIA +       V +++ + +   S++ P+G   
Sbjct: 208 VVKDLNGCLRAARELTQQLDHDPTTQEIASRTHKTATEVSRLMGLNERVSSMDAPLGPNS 267

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S + + I D++   P +     ++ ++    L  L+ ++  V+  RFG+      TLEE
Sbjct: 268 DSSVAETIADEHGCDPSEQIQDDDVHDSVAHWLDELSEKQREVVVRRFGLLGYDSCTLEE 327

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VG++  +TRER+RQI+ +A+++L+     + L
Sbjct: 328 VGQEIGLTRERVRQIQVEALKRLRRILERQGL 359



 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
               +  S F       A + T DP ++YL E+G + LLS + E   A+ ++ G      
Sbjct: 70  DEPVTAQSPFNDTDDHDARQITLDPTQLYLNEIGFVPLLSADEEKHYARLVQKGDEAARK 129

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
            + ES L     I  R  L+ G +LL  I
Sbjct: 130 RMIESNLRLVVNIARRY-LHRGMSLLDLI 157


>gi|1553011|gb|AAC45097.1| primary sigma factor [Borrelia afzelii]
          Length = 450

 Score =  190 bits (481), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 140/417 (33%), Positives = 232/417 (55%), Gaps = 11/417 (2%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQDNAVNGQKDEKS--------- 310
           + ++        + +  P        IA  Y+  L+ +QD  ++   ++           
Sbjct: 35  EREEFFKREKDKDKESNPDYYNKKKRIASFYKIPLKPIQDRLISYVDNKHRVYELGGDIF 94

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+  + L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKSERLALKELLRDVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|88809137|ref|ZP_01124646.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88787079|gb|EAR18237.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 313

 Score =  190 bits (481), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 107/240 (44%), Positives = 160/240 (66%), Gaps = 1/240 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+       AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GY
Sbjct: 69  RRLIRVGQRAKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGY 128

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+
Sbjct: 129 KFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTSIRKVSLDLAHKLGAMPSRLEIAE 188

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + MPVE +  +L+      SL+ P+  E+  S LGD I D +   PLD   Q    E  
Sbjct: 189 AMDMPVEELDSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSLEEPLDRVEQRIHHEQL 248

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R ++ L+ +E+ VL +RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 249 GRWMSHLSDQEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLRNLTRR 308



 Score = 38.3 bits (87), Expect = 3.9,   Method: Composition-based stats.
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
                 ++  R + DP+  YL  +G I LL+   EI +  +++ 
Sbjct: 4   AAAGVSETQRRRSSDPISWYLATIGRIPLLTPAEEIELGNQVQK 47


>gi|254975054|ref|ZP_05271526.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-66c26]
 gi|255092443|ref|ZP_05321921.1| RNA polymerase sigma factor rpoD [Clostridium difficile CIP 107932]
 gi|255100524|ref|ZP_05329501.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-63q42]
 gi|255308764|ref|ZP_05352935.1| RNA polymerase sigma factor rpoD [Clostridium difficile ATCC 43255]
 gi|255314181|ref|ZP_05355764.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-76w55]
 gi|255516860|ref|ZP_05384536.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-97b34]
 gi|255649961|ref|ZP_05396863.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-37x79]
 gi|306520043|ref|ZP_07406390.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-32g58]
          Length = 294

 Score =  190 bits (481), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 119/274 (43%), Positives = 174/274 (63%), Gaps = 5/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +K I     +S  E   +   +      +S+AK++ + +N RLV+S+AK+Y    
Sbjct: 23  AMKMYLKEIEEYKMLSAGEEVELAKEI---INSSSVAKEKFINSNYRLVVSIAKRYKRDS 79

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA WW+KQ+ITR I D   TIRIP+H+  
Sbjct: 80  IDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQ 139

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+ V +  + + N + REPT +EIA    + V+ V ++L+  K  +SL+TP+ +++ S 
Sbjct: 140 RINFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPLKEDEDSS 199

Query: 588 LGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L +FI          +    Q NL+E    +L  L  +E++VLRMRFGI  +   TLE++
Sbjct: 200 LVEFIPSDADFKDVVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDPKTLEQI 259

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GK F VTRERIRQIEAKAIRKL+HPS+ K+L+ F
Sbjct: 260 GKVFGVTRERIRQIEAKAIRKLRHPSKLKQLKHF 293



 Score = 37.1 bits (84), Expect = 9.3,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 9/98 (9%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
              +  + ++MYL+E+   ++LS   E+ +AK I    ++       S       I  R 
Sbjct: 16  GSSNVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSVAKEKFINSNYRLVVSIAKRY 75

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           +        R+ ID+   I      G     E + Y+K
Sbjct: 76  K--------RDSIDMLDLI-QAGNIGLIKAVEKYDYKK 104


>gi|315224630|ref|ZP_07866455.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
 gi|314945415|gb|EFS97439.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
          Length = 287

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 171/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK---AGDVAALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+ EEIA++L M V  V++ +K     IS++ P+ + + S+L
Sbjct: 135 INKINKMYAYLEQANERVPSAEEIARELDMSVNDVKESMKNAGRHISMDAPLVEGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I    + +P  + I  +LR    R L +LTPRE  V+R+ FG+      TLEE+G+ 
Sbjct: 195 YDVIRSNESPNPDKALILDSLRTEIERALETLTPREADVVRLYFGLSDQHAMTLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+LKH SRSK L+++L
Sbjct: 255 FDLTRERVRQIKEKAIRRLKHTSRSKILKTYL 286



 Score = 46.4 bits (108), Expect = 0.019,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ + E+ +A+RI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRVDLITADEEVELAQRIKAGDVAALEKLTKANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|86608149|ref|YP_476911.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556691|gb|ABD01648.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 361

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 117/317 (36%), Positives = 183/317 (57%), Gaps = 12/317 (3%)

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI------KSISVETGISISEFRH 429
           G  L+   V +  +      +   A E++   KI+ ++      +    + G   S+   
Sbjct: 44  GSRLNEDPVDHYLNTIGRVPRIDHAEEIELSRKIQQKLLIDQARQEWRQQRGEDPSDEAL 103

Query: 430 IVSM------VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             ++      +R    +   A+++++ ANLRLV+SVAKKY NRG+ FLDLIQEGNIGL++
Sbjct: 104 AEALQISVSTLRSRIRQGEQAQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNIGLIR 163

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKF+   G++FSTYA WW++Q ITR IA+Q+ TIR+PVHM DK+  + RT R +    
Sbjct: 164 ATEKFNAERGFRFSTYAHWWIRQGITRCIANQARTIRLPVHMVDKVRLLKRTNRELMKLQ 223

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            R PT  E+A+ L + V+ +R + +    P+SL+ P+G E  S LGD ++D+    P   
Sbjct: 224 GRRPTEAELAEALGIKVKKLRMIQQAAALPLSLDVPVGQEGESRLGDLLQDERQEQPFQG 283

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  ++++     + +L P E +VL +R+G+      TL EVG  F +TRERIRQIE  A
Sbjct: 284 ILVQSMQQDVRSAMQTLKPIERQVLELRYGLDGQQARTLREVGDHFNLTRERIRQIERDA 343

Query: 664 IRKLKHPSRSKKLRSFL 680
           +RKL+    S+ L  ++
Sbjct: 344 LRKLRVGYSSRALAQYI 360


>gi|1553027|gb|AAC45105.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 140/417 (33%), Positives = 233/417 (55%), Gaps = 11/417 (2%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQDNAVNGQKDEKS--------- 310
           + ++        + +  P        IA  Y+  L+ +QD  ++   ++           
Sbjct: 35  EREEFFKREKDKDKESNPDYYNKKKRIASFYKIPLKPIQDRLISYVDNKHRVYELGGDIF 94

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+ ++ L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKSERLALKELLRNVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|149370109|ref|ZP_01889960.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149356600|gb|EDM45156.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 287

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 168/272 (61%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +     I+  E   +   ++        A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEVGKIDLITAEEEVELAQKIK---AGDQRALEKLTNANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA +FD   G+KF +YA+WW++QAI +++A+QS  +R+P++    
Sbjct: 75  TLPDLINEGNVGLIKAASRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+PEEIAK+L M +  V++ +K +   IS++ P+ + +  +L
Sbjct: 135 INKINKAFTHLEQAHQRPPSPEEIAKELDMTINDVKESIKNSGRSISMDAPLTEGEDYNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P  + +  +LR    R L +LTPRE  V+++ FG+      TLEE+G  
Sbjct: 195 YDVLNTGESPNPDQALLLESLRTEIERALETLTPRESDVIKLYFGLSDQRPMTLEEIGST 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KA+R+LKH SRS  L+++L
Sbjct: 255 FDLTRERVRQIKEKAVRRLKHTSRSTILKTYL 286



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G I+L++ E E+ +A++I+AG    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEVGKIDLITAEEEVELAQKIKAGDQRALEKLTNANLRF--VVSVAKQYQNQGLTLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLIKAASRFDETRGFK 101


>gi|1553033|gb|AAC45108.1| primary sigma factor [Borrelia japonica]
          Length = 450

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 133/357 (37%), Positives = 212/357 (59%), Gaps = 1/357 (0%)

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+  + L Q  + +  +   D + +I     +   +     I++   
Sbjct: 95  EKNLKRERLALKELLQDIPLYQDELRIFSDDYIDSANKIKDLSRQQRIILNRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKGIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLIQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|1553023|gb|AAC45103.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 140/417 (33%), Positives = 233/417 (55%), Gaps = 11/417 (2%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQDNAVNGQKDEK---------S 310
           + ++        + +  P        IA  Y+  L+ +QD  ++   ++           
Sbjct: 35  EREEFFKREKDKDKESNPDYYNKKKRIASFYKVPLKPIQDRLISYVDNKHRVYELGGDIL 94

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+ ++ L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKSERLALKELLRNVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|226945910|ref|YP_002800983.1| RNA polymerase sigma factor RpoS [Azotobacter vinelandii DJ]
 gi|16226165|gb|AAL16091.1|AF421351_3 stationary phase sigma factor [Azotobacter vinelandii]
 gi|226720837|gb|ACO80008.1| RNA polymerase sigma factor [Azotobacter vinelandii DJ]
          Length = 334

 Score =  190 bits (481), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 98/295 (33%), Positives = 169/295 (57%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +  AK       ++       ++   +  +  I     ++ +E  H   + ++       
Sbjct: 38  LPVAKSRQANLKQHKYIDYTRALDATQLYLNEIGFSPLLTPAEEVHFARLAQR---GDPA 94

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 95  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA  L  PV  V
Sbjct: 155 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEEIANLLEKPVAEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P D     +L ++  + L  LT +
Sbjct: 215 KRMLGLNERVTSVDVSLGPDSDKTLLDVLTDDRPSDPCDLLQDDDLSQSIDQWLFDLTEK 274

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 275 QREVVVRRFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 329



 Score = 44.8 bits (104), Expect = 0.051,   Method: Composition-based stats.
 Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 2/104 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D+  E+  +D  DL   A +    L++ K        D  ++YL E+G   LL+   E+
Sbjct: 24  ADIVLEDVLDDEPDLPV-AKSRQANLKQHKYIDYTRALDATQLYLNEIGFSPLLTPAEEV 82

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             A+  + G       + ES L     I  R  +N G +LL  I
Sbjct: 83  HFARLAQRGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 125


>gi|126699102|ref|YP_001087999.1| RNA polymerase sigma factor rpoD [Clostridium difficile 630]
 gi|115250539|emb|CAJ68363.1| RNA polymerase sigma factor SigA2 (sigma-43) [Clostridium
           difficile]
          Length = 296

 Score =  190 bits (481), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 119/274 (43%), Positives = 174/274 (63%), Gaps = 5/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +K I     +S  E   +   +      +S+AK++ + +N RLV+S+AK+Y    
Sbjct: 25  AMKMYLKEIEEYKMLSAGEEVELAKEI---INSSSVAKEKFINSNYRLVVSIAKRYKRDS 81

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA WW+KQ+ITR I D   TIRIP+H+  
Sbjct: 82  IDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQ 141

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+ V +  + + N + REPT +EIA    + V+ V ++L+  K  +SL+TP+ +++ S 
Sbjct: 142 RINFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPLKEDEDSS 201

Query: 588 LGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L +FI          +    Q NL+E    +L  L  +E++VLRMRFGI  +   TLE++
Sbjct: 202 LVEFIPSDADFKDVVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDPKTLEQI 261

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           GK F VTRERIRQIEAKAIRKL+HPS+ K+L+ F
Sbjct: 262 GKVFGVTRERIRQIEAKAIRKLRHPSKLKQLKHF 295



 Score = 37.1 bits (84), Expect = 9.6,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 9/98 (9%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
              +  + ++MYL+E+   ++LS   E+ +AK I    ++       S       I  R 
Sbjct: 18  GSSNVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSVAKEKFINSNYRLVVSIAKRY 77

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           +        R+ ID+   I      G     E + Y+K
Sbjct: 78  K--------RDSIDMLDLI-QAGNIGLIKAVEKYDYKK 106


>gi|113475621|ref|YP_721682.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166669|gb|ABG51209.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 410

 Score =  190 bits (481), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 127/419 (30%), Positives = 220/419 (52%), Gaps = 22/419 (5%)

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           +     + ++++    +   ++E+    +++ S Q N     +D   S   ++ +  L++
Sbjct: 12  EDTLQSNNLQNECSEHLGQTINELTIEDKKVDSSQINTNYSGRDSVRSYLQEIGRVDLLQ 71

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHW 383
               +S  Q     +   L ++  +    E E+ R  +   I RD    R   +     W
Sbjct: 72  RDQEVSTAQKVQRYV--HLLELRNKAAEQEQEIQRYVEMIKI-RDRLAARLGHKPSFERW 128

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +        G        E+ ++ K+R      +  TG+++ E   I       + E   
Sbjct: 129 LK------AGNLSMAELKEIIAVGKLR-----WAKLTGLNVKELEQI-------QTEGIE 170

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ +M+  NLRLV+S+AKKY NRG++ LDLIQEG +GL +A EKFD   GY+FSTYA WW
Sbjct: 171 ARHQMISTNLRLVVSIAKKYQNRGVELLDLIQEGTLGLERAVEKFDPQRGYRFSTYAYWW 230

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ITR+IA QS TIR+P+H+ +K++K+ +  +++  +       EEIA++L +    V
Sbjct: 231 IRQGITRAIATQSRTIRLPIHVSEKLNKIKKVQQKIFQEKGYTAKVEEIARELKITAAQV 290

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+VL      +SLET +G +  + LG+ +E K+A SP +  I+ +L +    +L  LT R
Sbjct: 291 REVLVKIPHSVSLETKVGRDRDTELGELLETKDA-SPEEMLIRESLVQALKELLLDLTQR 349

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E  V+ MR+G+      +L E+     ++RER+RQIE KA+ KL+ P    +++ +L+ 
Sbjct: 350 ERYVITMRYGLEDGRACSLSEIASALKLSRERVRQIEVKALHKLRQPKFRNQIQDYLES 408



 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 22/96 (22%), Positives = 41/96 (42%), Gaps = 5/96 (5%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E SE      +  +     +   + + + S  D VR YL+E+G ++LL R+ E++ A++
Sbjct: 22  NECSEHLGQTINELTIEDKKVDSSQINTNYSGRDSVRSYLQEIGRVDLLQRDQEVSTAQK 81

Query: 146 IEAGRA--MMMASLCESPLTFQ---ALIIWRDELND 176
           ++       +     E     Q    +I  RD L  
Sbjct: 82  VQRYVHLLELRNKAAEQEQEIQRYVEMIKIRDRLAA 117


>gi|219847826|ref|YP_002462259.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542085|gb|ACL23823.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 361

 Score =  190 bits (481), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 112/297 (37%), Positives = 177/297 (59%), Gaps = 24/297 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK------------------------GECEASIA 444
           ++  ++ I     ++  E   +    R+                         +     A
Sbjct: 65  VQLYLQEIGQVPLLTAEEEVELARQYRRGKEARQRLQNEDYANDRERMRLEIEQARGEEA 124

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ +++ANLRLV+SVAKKY    + F+DL+QEGNIGLM+A EKFD+  G +FSTYA WW+
Sbjct: 125 RRRLIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWI 184

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+TR+IA+QS  IR+PVH+ + I  + R   R+  +++REPTPEE+A  L M +  V+
Sbjct: 185 RQAVTRAIAEQSRLIRLPVHLSESIVHLRRAIYRLEQELEREPTPEELAHALNMSLRKVK 244

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++L+ + +PISLE P+  +    + + + D+ A SP++ A Q  L+      L  L  RE
Sbjct: 245 RLLRASTQPISLEQPLNADQEGRVSETLADETAASPMEIAEQNMLQAELNAALNELPERE 304

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            ++L++R+G+      TLEEVG  F +TRER RQIEA+A+R+L+HPS   +L  +L+
Sbjct: 305 RKILQLRYGLLDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHPSVGNRLFGYLE 361



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 39/99 (39%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +G  +      +   S   L    D      +D V++YL+E+G + LL+ E E+ +A++ 
Sbjct: 31  DGDVELEAEDEALIESLEDLSDEIDVDIEPVEDSVQLYLQEIGQVPLLTAEEEVELARQY 90

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
             G+        E     +  +    E   G    R +I
Sbjct: 91  RRGKEARQRLQNEDYANDRERMRLEIEQARGEEARRRLI 129


>gi|296451502|ref|ZP_06893237.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296880149|ref|ZP_06904116.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
 gi|296259567|gb|EFH06427.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296428874|gb|EFH14754.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
          Length = 301

 Score =  190 bits (481), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 118/274 (43%), Positives = 174/274 (63%), Gaps = 5/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +K I     +S  E   +   +      +S+AK++ + +N RLV+S+AK+Y    
Sbjct: 30  AMKMYLKEIEEYKMLSAGEEVELAKEI---INSSSVAKEKFINSNYRLVVSIAKRYKRDS 86

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA WW+KQ+ITR I D   TIRIP+H+  
Sbjct: 87  IDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQ 146

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+ V +  + + N + REPT +EIA    + V+ V ++L+  K  +SL+TP+ +++ S 
Sbjct: 147 RINFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPLKEDEDSS 206

Query: 588 LGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L +FI          +    Q NL+E    +L  L  +E++VLRMRFGI  +   TLE++
Sbjct: 207 LVEFIPSDADFKDVVMHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDPKTLEQI 266

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G+ F VTRERIRQIEAKAIRKL+HPS+ K+L+ F
Sbjct: 267 GRVFGVTRERIRQIEAKAIRKLRHPSKLKQLKHF 300



 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 9/98 (9%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
              +  + ++MYL+E+   ++LS   E+ +AK I    ++       S       I  R 
Sbjct: 23  GSSNVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSVAKEKFINSNYRLVVSIAKRY 82

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           +        R+ ID+   I      G     E + Y+K
Sbjct: 83  K--------RDSIDMLDLI-QAGNIGLIKAVEKYDYKK 111


>gi|318042101|ref|ZP_07974057.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 309

 Score =  190 bits (481), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 108/268 (40%), Positives = 171/268 (63%), Gaps = 3/268 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ N+++++   T              +K       +K+ M++ANLRLV+SVAKKY  +
Sbjct: 39  IELGNQVQAMMRLTEEEP--ENGYTDQQKKTIRVGRRSKERMMKANLRLVVSVAKKYQGK 96

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ 
Sbjct: 97  GLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLS 156

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           +++  + + +  +++K+   P+ +EIA+ + MP++ +  +L+      SL+ P+  E+  
Sbjct: 157 ERLTAIRKVSLDLAHKLGAMPSRKEIAEAMDMPIDELDSLLRQALTTSSLDAPVNGEEGR 216

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGD I D + V PLD   +    E   R L+ LT +E +VL +RFG+     HTL E+
Sbjct: 217 SFLGDLIADNSHVEPLDQVERGMHHEQLGRWLSHLTEQERQVLELRFGLEGEERHTLAEI 276

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           G+   V+RER+RQ+E KA+RKL+H +R 
Sbjct: 277 GRMLDVSRERVRQVELKALRKLRHLTRR 304


>gi|281425773|ref|ZP_06256686.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|281400034|gb|EFB30865.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
          Length = 287

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 169/272 (62%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +++       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEDLISVEEEVELAQKIKR---GDRRALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R   ++  + ++ PT EEIA K+ +P + V   +K     +S++ P+ + + + L
Sbjct: 135 VNKIKRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIKSNGRHVSVDAPLAEGEENSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + NA       +Q +LR+     L SL  RE  ++   FGI  +   TLEE+G +
Sbjct: 195 LDILPNNNAQMADSVLVQESLRDEVANALQSLNERERNIVEAFFGINQSE-MTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H +++K L+++L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRHNTKNKNLKAYL 285



 Score = 41.0 bits (94), Expect = 0.64,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S E E+ +A++I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGHEDLISVEEEVELAQKIKRGDRRALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|146281946|ref|YP_001172099.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri A1501]
 gi|145570151|gb|ABP79257.1| sigma factor RpoS [Pseudomonas stutzeri A1501]
          Length = 332

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 165/274 (60%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 57  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 113

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 114 NRGLSLLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 173

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 174 VVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVTSVDVSLGPDT 233

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +  +  +L  +  + L+ L+ ++  V+  RFG+  +   TLEE
Sbjct: 234 DKTLLDTLTDDRPTDPCELLLDDDLSASIDQWLSDLSEKQREVVIRRFGLRGHEASTLEE 293

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+R+L+       L S
Sbjct: 294 VGQEIGLTRERVRQIQVEALRRLREILERNGLSS 327



 Score = 44.8 bits (104), Expect = 0.051,   Method: Composition-based stats.
 Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 6/119 (5%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-----DPVRMYL 125
             +  +V D   L +     D  D  + A+++            +  D     D  ++YL
Sbjct: 6   QALEFDVDDAVLLMETPIHFDQKDKVTKAASAGRPKAASSTRQHKFIDYNRALDATQLYL 65

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+G   LL+ E E+  A+  + G       + ES L     I  R  +N G +LL  +
Sbjct: 66  NEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLV 123


>gi|198282770|ref|YP_002219091.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666687|ref|YP_002424966.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198247291|gb|ACH82884.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518900|gb|ACK79486.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 317

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 101/275 (36%), Positives = 159/275 (57%), Gaps = 3/275 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E       R  ++ I     ++  +    V++ R  +     A+  M+E+NLRLV+ VA+
Sbjct: 39  EAPDWDATRCYLREIGHRPLLTAEQE---VTLGRMVQTGDQAARCTMIESNLRLVVKVAR 95

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+
Sbjct: 96  HYLNRGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQNIERALMNQTRTIRL 155

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  ++  V+R  R ++  ++R+PTPEE+A+ L   V+ VR  L++     SL+ P G
Sbjct: 156 PIHVMKELSAVLRATRCLAQTLQRDPTPEEVAEALDRSVDAVRDCLEMDGRVTSLDMPYG 215

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L D + D NA          NL     + +A++T +   VL  RFG+      T
Sbjct: 216 KGSDRSLADLVADTNAPGVEQRLENQNLSRQVHQWIATMTEKHRLVLLWRFGLDGTDGAT 275

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LEEVG +  +TRER+RQI+ +A+  L+H   ++ L
Sbjct: 276 LEEVGSRLGITRERVRQIQVEALLVLRHRIEAEGL 310



 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 1/103 (0%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D +++ G  D+  ++    ++   +   +D  +    D  R YLRE+G   LL+ E E+ 
Sbjct: 7   DEDEDGGFPDAPPISEQDEDAPEKIDGAEDFGEAPDWDATRCYLREIGHRPLLTAEQEVT 66

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + ++ G      ++ ES L    + + R  LN G  LL  I
Sbjct: 67  LGRMVQTGDQAARCTMIESNLRL-VVKVARHYLNRGLPLLDLI 108


>gi|1553029|gb|AAC45106.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 140/417 (33%), Positives = 232/417 (55%), Gaps = 11/417 (2%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQDNAVNGQKDEKS--------- 310
           + ++        + +  P        IA  Y+  L+ +QD  +    ++           
Sbjct: 35  EREEFFKREKDKDKESNPDYYNKKKRIASFYKVPLKPIQDRLIRYVDNKHRVYELGGDIF 94

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
               K  +  L +L+ ++ L Q  + +  +   D + +I   + +   +     I++   
Sbjct: 95  EKNLKSERLALKELLRNVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRD 154

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L    GR+L         +      ++ +  ++      + E++ I +     + +   +
Sbjct: 155 LRVL-GRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISM 213

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG+     AK ++++ANLRLV+S+AKKY NRGL F DL+QEGNIGL+KA EKF++
Sbjct: 214 SEEIAKGKQMMQHAKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEY 273

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSI+DQ+ TIR+PVHM ++I+++ R  R +   + ++PT E
Sbjct: 274 KRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLNRETRYLVQVLGKDPTDE 333

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++ +L   ++ V+ V  +++EP+SLETPIG+E+ S L DFIEDK   +P +      L+
Sbjct: 334 ELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTSFVVLQ 393

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +    +L +L  RE+ V++MRFG+      TLEEVG  F VTRERIRQIE+KA+R+L
Sbjct: 394 DQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIRQIESKALRRL 450


>gi|296387874|ref|ZP_06877349.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAb1]
          Length = 334

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 98/274 (35%), Positives = 165/274 (60%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 59  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 115

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 116 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 175

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 176 VVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDS 235

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L E+  + L  LT ++  V+  RFG+  +   TLEE
Sbjct: 236 DKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEE 295

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 296 VGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 329



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 26/115 (22%), Positives = 50/115 (43%), Gaps = 2/115 (1%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREMG 129
            +  + +++   + DE  +++     ++   ++ F  K+    D     D  ++YL E+G
Sbjct: 12  HDDEVLLLEPGIMLDESSADEQPSPRTTPKATTSFSSKQHKHIDYTRALDATQLYLNEIG 71

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+  + G       + ES L     I  R  +N G +LL  I
Sbjct: 72  FSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 125


>gi|282877766|ref|ZP_06286579.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
 gi|281300082|gb|EFA92438.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
          Length = 298

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 97/273 (35%), Positives = 168/273 (61%), Gaps = 4/273 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ I  E  ISI E   +   ++K       A +++ +ANLR V+SVAK+Y N+G
Sbjct: 28  ALDKYLQEIGHEDLISIEEEIELAQRIKK---GDRKALEKLTKANLRFVVSVAKQYQNQG 84

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++   
Sbjct: 85  LSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVG 144

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            ++K+ R   +   + +R P  +EIA ++ +P + + + +K+  + IS++ PI +   S 
Sbjct: 145 SVNKINRILNKFEQEHERRPNVDEIADQIDLPEDKIVEAMKVNGKHISVDAPIMEGADSS 204

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + +  +    +  +  +LRE     L  L  RE  ++   +GI    + TLEE+G 
Sbjct: 205 LLDVLPNTESPMADNELVMESLREEVASALNVLNERERNIIECFYGINQ-REMTLEEIGD 263

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +F +TRER+RQI+ KA+R+L+  ++SK+L+++L
Sbjct: 264 KFGLTRERVRQIKEKALRRLRQNTKSKQLKAYL 296



 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 98/251 (39%), Gaps = 18/251 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S E EI +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 32  YLQEIGHEDLISIEEEIELAQRIKKGDRKALEKLTKANLRF--VVSVAKQYQNQGLSLPD 89

Query: 184 IID------LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           +I+      ++A    +   GF   +    + ++       E+  +     +   +    
Sbjct: 90  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 149

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
               +K +   E   N +   D+ +      + AM+   +   + A          L  L
Sbjct: 150 NRILNKFEQEHERRPNVDEIADQIDLPEDKIVEAMKVNGKHISVDAPIMEGADSSLLDVL 209

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            +       +E   +  + L+E++   +  L+  +  I   +E  Y I++R M     L 
Sbjct: 210 PNTESPMADNE---LVMESLREEVASALNVLNERERNI---IECFYGINQREMT----LE 259

Query: 358 RLAQSYGIKRD 368
            +   +G+ R+
Sbjct: 260 EIGDKFGLTRE 270


>gi|299140647|ref|ZP_07033785.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298577613|gb|EFI49481.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 287

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 169/272 (62%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +++       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEDLISVEEEVELAQKIKR---GDRRALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R   ++  + ++ PT EEIA K+ +P + V   +K     +S++ P+ + + + L
Sbjct: 135 VNKIKRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIKSNGRHVSVDAPLAEGEENSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + NA       +Q +LR+     L SL  RE  ++   FGI  +   TLEE+G +
Sbjct: 195 LDILPNNNAQMADSMLVQESLRDEVANALQSLNERERNIIEAFFGINQSE-MTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H +++K L+++L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRHNTKNKNLKAYL 285



 Score = 41.0 bits (94), Expect = 0.76,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S E E+ +A++I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGHEDLISVEEEVELAQKIKRGDRRALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|255655509|ref|ZP_05400918.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-23m63]
          Length = 294

 Score =  189 bits (480), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 118/274 (43%), Positives = 174/274 (63%), Gaps = 5/274 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +K I     +S  E   +   +      +S+AK++ + +N RLV+S+AK+Y    
Sbjct: 23  AMKMYLKEIEEYKMLSAGEEVELAKEI---INSSSVAKEKFINSNYRLVVSIAKRYKRDS 79

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQ GNIGL+KA EK+D+  GYKFSTYA WW+KQ+ITR I D   TIRIP+H+  
Sbjct: 80  IDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQ 139

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+ V +  + + N + REPT +EIA    + V+ V ++L+  K  +SL+TP+ +++ S 
Sbjct: 140 RINFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPLKEDEDSS 199

Query: 588 LGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L +FI          +    Q NL+E    +L  L  +E++VLRMRFGI  +   TLE++
Sbjct: 200 LVEFIPSDADFKDVVMHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDPKTLEQI 259

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G+ F VTRERIRQIEAKAIRKL+HPS+ K+L+ F
Sbjct: 260 GRVFGVTRERIRQIEAKAIRKLRHPSKLKQLKHF 293



 Score = 37.1 bits (84), Expect = 9.9,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 9/98 (9%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
              +  + ++MYL+E+   ++LS   E+ +AK I    ++       S       I  R 
Sbjct: 16  GSSNVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSVAKEKFINSNYRLVVSIAKRY 75

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           +        R+ ID+   I      G     E + Y+K
Sbjct: 76  K--------RDSIDMLDLI-QAGNIGLIKAVEKYDYKK 104


>gi|113954655|ref|YP_729975.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882006|gb|ABI46964.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 313

 Score =  189 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 112/270 (41%), Positives = 172/270 (63%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++     T  G    +     S  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKFMELTQDGSVSPDSEEFSSKDRRMIRVGQRAKQRMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EI++ L MPVE +  +L+      SL+ P+  ED
Sbjct: 159 LSERLTTIRKVSLDLAHKLGAMPSRLEISEALDMPVEELDSLLRQALTTSSLDAPVNGED 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +A  PLD   Q    E   R L+ L+ +E+ VL +RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSSAEEPLDKVEQRIHHEQLGRWLSHLSEQEQHVLTLRFGLNGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           ++G+   V+RER+RQ+E K++RKL++ +R 
Sbjct: 279 QIGRLLDVSRERVRQVELKSLRKLRNLTRR 308



 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/45 (24%), Positives = 22/45 (48%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            +  ++  R + DP+  YL  +G I LL+   EI +  +++    
Sbjct: 6   ARTSETQRRRSSDPISWYLATIGRIPLLTAAEEIELGNQVQKFME 50


>gi|260902364|ref|ZP_05910759.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
 gi|308110564|gb|EFO48104.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
          Length = 329

 Score =  189 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 113/296 (38%), Positives = 176/296 (59%), Gaps = 7/296 (2%)

Query: 385 SYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             AK     E K  V  E D    S+   +  +  I     ++  E    V   R+    
Sbjct: 26  ELAKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRG 82

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 83  DEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 142

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV
Sbjct: 143 TWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPV 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L
Sbjct: 203 EDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEEL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 263 NPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 318



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + +     E + D+    SS++       + +  A   + D  ++YL E+G   LL+
Sbjct: 9   KVEEFEYDNASETTSDNELAKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLT 68

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 69  AEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 116


>gi|33866155|ref|NP_897714.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639130|emb|CAE08136.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 313

 Score =  189 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 109/270 (40%), Positives = 174/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T  G    E   +    R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQAMMTLTEDGSKTFEDHELTGKQRRMLRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + +P++ +  +L+      SL+ P+  E+
Sbjct: 159 LSERLTTIRKVSLDLAHKLGAMPSRVEIAEAMDIPLDELDSLLRQALTTSSLDAPVNGEE 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q    E   R L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSSLDEPLDIVEQRIHHEQLGRWLSHLSEQEQHVLKLRFGLEGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLMDVSRERVRQVELKALRKLRNLTRR 308



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 24/43 (55%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            QK  DS  R + DPV  YL  +G I LL+   EI +  +++A
Sbjct: 5   AQKPTDSQRRRSSDPVSWYLATIGRIPLLTPAEEIELGNQVQA 47


>gi|145284374|gb|ABP51953.1| RpoS [Vibrio alginolyticus]
          Length = 328

 Score =  189 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 171/286 (59%), Gaps = 3/286 (1%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            +   +        S+   +  +  I     ++  E    V   R+       A+K M+E
Sbjct: 35  SKATAREKFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIE 91

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R
Sbjct: 92  SNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER 151

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           ++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V K+L++ 
Sbjct: 152 ALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLN 211

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+++ VL  
Sbjct: 212 ERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPKQKEVLAR 271

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 272 RFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQGL 317



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 42/107 (39%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+    ++        +L  S+   S    + K  A   + D  ++YL E+G   LL+ E
Sbjct: 10  VEEFAFDNASVKTIDNELERSSPTESKATAREKFDASSKSLDATQLYLGEIGFSPLLTAE 69

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 115


>gi|15598818|ref|NP_252312.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|116051619|ref|YP_789542.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218890153|ref|YP_002439017.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa LESB58]
 gi|254242320|ref|ZP_04935642.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|1173167|sp|P45684|RPOS_PSEAE RecName: Full=RNA polymerase sigma factor rpoS
 gi|9949780|gb|AAG07010.1|AE004782_8 sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|440378|dbj|BAA05131.1| RNA polymerase principal sigma factor [Pseudomonas aeruginosa]
 gi|52632371|gb|AAU85546.1| RNA polymerase sigma factor [Pseudomonas sp. M18]
 gi|115586840|gb|ABJ12855.1| sigma factor RpoS [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126195698|gb|EAZ59761.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|218770376|emb|CAW26141.1| sigma factor RpoS [Pseudomonas aeruginosa LESB58]
          Length = 334

 Score =  189 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 98/274 (35%), Positives = 165/274 (60%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 59  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 115

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 116 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 175

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 176 VVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDS 235

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L E+  + L  LT ++  V+  RFG+  +   TLEE
Sbjct: 236 DKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEE 295

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 296 VGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 329



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 1/102 (0%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L++    E     A+  + +S   ++ K        D  ++YL E+G   LL+ E E+  
Sbjct: 25  LDESSADEQPSPRATPKATTSFSSKQHKHIDYTRALDATQLYLNEIGFSPLLTPEEEVHF 84

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           A+  + G       + ES L     I  R  +N G +LL  I
Sbjct: 85  ARLAQKGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 125


>gi|121998209|ref|YP_001002996.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
           SL1]
 gi|121589614|gb|ABM62194.1| RNA polymerase, sigma 38 subunit, RpoS [Halorhodospira halophila
           SL1]
          Length = 336

 Score =  189 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 162/272 (59%), Gaps = 3/272 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I   + ++  E    V++ R+ +   + A+  M+E+NLRLV+ +A++Y 
Sbjct: 61  ALDATQLYLNEIGHASLLTAEEE---VALARRVQQGDAAARARMIESNLRLVVKIARRYM 117

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL FLDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R I +Q+ TIR+P+H
Sbjct: 118 NRGLAFLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIH 177

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +I++ +RT RR++  +  EPT +EIA  +    E VR++  + +   S++ PIG + 
Sbjct: 178 VIKEINQYLRTQRRLTQTLDHEPTVDEIADAMGRSPEDVRRMRGLNEGTTSVDVPIGKDS 237

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D I D+    P +     ++       L  LT ++  VL  RFG+  +  +TLE+
Sbjct: 238 DRVLLDAIPDETQGMPENVLEDDDVVRHLQDWLGFLTDKQRAVLERRFGLNGHERYTLEQ 297

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VG Q  VTRER+RQI+  A+R+L+        
Sbjct: 298 VGTQVGVTRERVRQIQIDALRRLRELMERDGY 329



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/103 (29%), Positives = 46/103 (44%), Gaps = 1/103 (0%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D   E      +D  S    +    + R  +  R+  D  ++YL E+G   LL+ E E+A
Sbjct: 26  DDPGELIQPYGIDEGSEPEPARRPRRSRSSTECRTALDATQLYLNEIGHASLLTAEEEVA 85

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +A+R++ G A   A + ES L     I  R  +N G   L  I
Sbjct: 86  LARRVQQGDAAARARMIESNLRLVVKIARRY-MNRGLAFLDLI 127


>gi|327480191|gb|AEA83501.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri DSM 4166]
          Length = 332

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 164/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 57  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 113

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 114 NRGLSLLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 173

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 174 VVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVTSVDVSLGPDT 233

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +  +  +L  +    L+ L+ ++  V+  RFG+  +   TLEE
Sbjct: 234 DKTLLDTLTDDRPTDPCELLLDDDLSNSIDLWLSDLSEKQREVVIRRFGLRGHEASTLEE 293

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+R+L+       L S
Sbjct: 294 VGQEIGLTRERVRQIQVEALRRLREILERNGLSS 327



 Score = 44.8 bits (104), Expect = 0.047,   Method: Composition-based stats.
 Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 6/119 (5%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-----DPVRMYL 125
             +  +V D   L +     D  D  + A+++            +  D     D  ++YL
Sbjct: 6   QALEFDVDDAVLLMETPIHFDQKDKVTKAASAGRPKAASSTRQHKFIDYNRALDATQLYL 65

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+G   LL+ E E+  A+  + G       + ES L     I  R  +N G +LL  +
Sbjct: 66  NEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLV 123


>gi|294660419|ref|NP_853171.2| RNA polymerase sigma factor RpoD [Mycoplasma gallisepticum str.
           R(low)]
 gi|284812078|gb|AAP56739.2| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(low)]
 gi|284930653|gb|ADC30592.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(high)]
          Length = 643

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 160/515 (31%), Positives = 261/515 (50%), Gaps = 44/515 (8%)

Query: 176 DGTTLLREIIDLEACIGPESKGGF--FHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           D    L   ID       + +  F  F      S  K  D S++ E DD +    D  S 
Sbjct: 157 DENLDLNNEIDFADFDNKDDEIDFSDFKHENYSSAFKETDFSEQDELDDKEFNLSDFFSD 216

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           +K+  D        P  A+  +R        S      +  ++        +   E  R 
Sbjct: 217 SKLDIDQ-------PITAQKRQRGRKPKHAPSNEKNDLVYHEVLEASSKTKNNDQESIRA 269

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            ++L           K+     +  E+++ +  +    ++    ++E+L D   ++  N 
Sbjct: 270 TKTL---------LAKAKATKSLSNEEIIDVFKNYEFTEAEDLEILEELKDNKIKLEDNV 320

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            E + L          F +     E+D +             K+ V   V +       +
Sbjct: 321 EEKISL----------FRKNQDLSEIDKNLDDLISKGAST--KDKVEDNVKAF------L 362

Query: 414 KSISVETGISISEFRHIVSMV-RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            ++     ++  E   I  ++          A  ++V +NLRLV S+AKKY NRGL F+D
Sbjct: 363 GTLGSSKILNFGEEIQIAKLLGSTDPETREYAINQLVTSNLRLVTSIAKKYLNRGLDFVD 422

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG+IGLMKA  KF++ LG KFSTYA WW++QAITR+IADQ+ T+RIPVHM + I+K+
Sbjct: 423 LIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQAITRAIADQARTVRIPVHMVETINKL 482

Query: 533 VRTARRMSNKIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++T R ++ ++ R+PT EE+ + +         + V  + K+ +EP+SL+ PIG ++ S 
Sbjct: 483 IKTERMLTQQLGRDPTLEELTEAMGGQVNGFTPKKVADIKKLNQEPVSLDKPIGHDEESQ 542

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIG-MNTDHTLEEV 645
             DF++D++ + P +   +  + E    + + +LT +EE+++RMR+G+   +   TLEEV
Sbjct: 543 FVDFVKDRDILKPDEYTEKLIVTEHINELFINTLTKKEEQIIRMRYGLHPWHQQMTLEEV 602

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++F VTRERIRQIE+KA+RKLKHPS++ +LRSFL
Sbjct: 603 GQKFNVTRERIRQIESKALRKLKHPSKNARLRSFL 637



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 62/159 (38%), Gaps = 7/159 (4%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K ++  A+    ++ EE+       E +  +  + +  L +  I +   D++E++   
Sbjct: 269 ATKTLLAKAKATKSLSNEEIIDVFKNYEFTEAEDLEILEELKDNKIKL--EDNVEEKISL 326

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE-- 147
                  S    +   L  +  S     +D V+ +L  +GS ++L+   EI IAK +   
Sbjct: 327 FRKNQDLSEIDKNLDDLISKGASTKDKVEDNVKAFLGTLGSSKILNFGEEIQIAKLLGST 386

Query: 148 --AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               R   +  L  S L     I  +  LN G   +  I
Sbjct: 387 DPETREYAINQLVTSNLRLVTSIAKKY-LNRGLDFVDLI 424


>gi|256420372|ref|YP_003121025.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256035280|gb|ACU58824.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 291

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 97/275 (35%), Positives = 171/275 (62%), Gaps = 4/275 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     I+  E  ++   +++       A +++ +ANLR V+SVAK+Y N+
Sbjct: 18  QSLEKYLQEIGKVDLITPEEEVNLAIRIKQ---GDQRALEKLTKANLRFVVSVAKQYQNQ 74

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 75  GLSLSDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKV 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
              +K+ +   ++  + +REP+P+E+A  L +  E V   L +    +S++ P  D + +
Sbjct: 135 GLSNKISKAYSQLEQEFEREPSPDELATILEINTEEVEATLGVAARHVSMDAPFIDGEDN 194

Query: 587 HLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            L D + + NAV+  +     + LR    R L++LT R++ V+ + FGI +    +LE++
Sbjct: 195 SLLDVLANPNAVNADEELDHHDSLRREIERSLSTLTDRQKDVIILYFGIAVEHPMSLEDI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++F +TRER+RQI+ KAI KL+  SRSK LR++L
Sbjct: 255 GEKFGLTRERVRQIKDKAITKLRTTSRSKLLRNYL 289



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++L++ E E+ +A RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 23  YLQEIGKVDLITPEEEVNLAIRIKQGDQRALEKLTKANLRF--VVSVAKQYQNQGLSLSD 80

Query: 184 IID 186
           +I+
Sbjct: 81  LIN 83


>gi|300704422|ref|YP_003746025.1| RNA polymerase sigma factor rpos [Ralstonia solanacearum CFBP2957]
 gi|299072086|emb|CBJ43418.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CFBP2957]
          Length = 376

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTRAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 161 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 220

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  +
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPFDLDPGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 281 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 340

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 341 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 371



 Score = 41.4 bits (95), Expect = 0.49,   Method: Composition-based stats.
 Identities = 29/150 (19%), Positives = 48/150 (32%), Gaps = 22/150 (14%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-------------DP 120
            I VVD    E        +      ++S+    + ++  + + +             D 
Sbjct: 44  DIEVVDTLTDEMPASEPADIVDTPDTNDSADEPDEEEEEEEAAPEEDFRTVLQAELAADT 103

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           V+ YL  +    LL+   E+  + R +AG       + E  L     I     LN G  L
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTRAKAGEFAARQVMIERNLRLVVSIAKGY-LNRGVPL 162

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           L  I         E   G  H  E    ++
Sbjct: 163 LDLI--------EEGNLGLMHAIEKFDPER 184


>gi|146308041|ref|YP_001188506.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina ymp]
 gi|145576242|gb|ABP85774.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas mendocina ymp]
          Length = 335

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 96/291 (32%), Positives = 166/291 (57%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     ++  E  H   + +K        +K 
Sbjct: 43  AKHATPSKQHKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKR 99

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 100 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 159

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA  L  PV  V+++L
Sbjct: 160 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEEIANLLEKPVGEVKRML 219

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 220 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSDLTDKQREV 279

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 280 VVRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 330



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 31/131 (23%), Positives = 51/131 (38%), Gaps = 13/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  +V  E +      L   GI + +    E E        +A + +  +   ++ K   
Sbjct: 9   PEFDVDDELL------LMEPGIVLGEVQSDEVETP------VARAKAKHATPSKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LL+ E E+  A+  + G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|89890814|ref|ZP_01202323.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
 gi|89516959|gb|EAS19617.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
          Length = 287

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 171/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+  E   +  +++K       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIDLITAEEEVELAQLIKK---GDQRALEKLTTANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  KLPDLINEGNAGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P+PEE+AK+L M V  V++ LK     +S++ P+ + +TS+L
Sbjct: 135 INKINKAFSHLEQLHERPPSPEELAKELDMTVSDVKQSLKNAGRHVSMDAPLKEGETSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    + +P    +  +L    TR L +L+ +E  V+ + FGIG     +LEE+G+ 
Sbjct: 195 YDVVRSGESPNPDRELMHESLTLEITRALETLSQKEADVISLYFGIGNQQPMSLEEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ K I++L+  SRSK L+S+L
Sbjct: 255 FDLTRERVRQIKEKGIKRLRQNSRSKILKSYL 286



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I+L++ E E+ +A+ I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKIDLITAEEEVELAQLIKKGDQRALEKLTTANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|288926163|ref|ZP_06420090.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608876|ref|ZP_07883849.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337055|gb|EFC75414.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249403|gb|EFU29419.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 286

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 171/272 (62%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  +++ E   +   +RK       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEELVTVEEEVELAQRIRK---GDRHALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNMGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R   +   + +R P+ +EIA  + +P + +   LK+    +S++ P  D D + L
Sbjct: 135 VNKINRMLNKFEQENERRPSIDEIADSVDLPEDKIEDALKVNTRHVSVDAPFVDGDDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + +A     + +  +LRE  +R L +L  RE  ++   FGI  N + TLEE+G +
Sbjct: 195 IDILPNSDAPMADKALVMESLREEISRALRTLNERERNIIECFFGIN-NPEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+H ++++ L+++L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRHNTKNRVLKAYL 285


>gi|157413850|ref|YP_001484716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388425|gb|ABV51130.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 313

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 109/270 (40%), Positives = 176/270 (65%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ + + T  G    + +   +  ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMILTEDGQLNEKIKEFTTQQKRTIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDANERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 40.6 bits (93), Expect = 0.89,   Method: Composition-based stats.
 Identities = 11/43 (25%), Positives = 24/43 (55%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           L  + +   R ++DP+  YL+ +G + LL+   EI +  +++ 
Sbjct: 5   LPTKAEQPKRRSNDPISWYLQNIGRVPLLTPAEEIELGNQVQK 47


>gi|260434805|ref|ZP_05788775.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260412679|gb|EEX05975.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 312

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 110/270 (40%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T     EF    + +  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 38  IELGNQVQAMMSLTEDGSREFEDGELTTAQRRLLRIGRRAKERMMKANLRLVVSVAKKYQ 97

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 98  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 157

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + +P++ +  +L+      SL+ P+  E+
Sbjct: 158 LSERLTTIRKVSLDLAHKLGAMPSRVEIAEAMDIPLDELDSLLRQALTTSSLDAPVNGEE 217

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PL+   Q    E   R L+ L+ +E+ VLRMRFG+  N  HTL 
Sbjct: 218 GRSFLGDLIADSSLDEPLEIVEQRIHHEQLGRWLSHLSEQEQHVLRMRFGLEGNERHTLA 277

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 278 EIGRLMEVSRERVRQVELKALRKLRNLTRR 307



 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             K  ++  R + DPV  YL  +G I LL+   EI +  +++A
Sbjct: 4   ASKPLETQRRRSSDPVSWYLATIGRIPLLTPAEEIELGNQVQA 46


>gi|2792523|gb|AAC38577.1| alternative RNA sigma factor RpoS [Ralstonia solanacearum]
          Length = 376

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTRAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 161 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 220

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 281 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 340

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 341 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 371



 Score = 42.1 bits (97), Expect = 0.27,   Method: Composition-based stats.
 Identities = 34/163 (20%), Positives = 51/163 (31%), Gaps = 24/163 (14%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ 107
           E+   L  +  +SE  +            +VD  D  D     D  +    A+    F  
Sbjct: 46  EVVDALTDEMPASEPAD------------IVDTPDTNDSADEPDEEEEDEEAAPEEDFRT 93

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
             +        D V+ YL  +    LL+   E+  + R +AG       + E  L     
Sbjct: 94  VLQAELAA---DTVQHYLNRISIKPLLTPAEELHFSTRAKAGEFAARQVMIERNLRLVVS 150

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           I     LN G  LL  I         E   G  H  E    ++
Sbjct: 151 IAKGY-LNRGVPLLDLI--------EEGNLGLMHAIEKFDPER 184


>gi|87125501|ref|ZP_01081346.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86166801|gb|EAQ68063.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 312

 Score =  189 bits (479), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 106/240 (44%), Positives = 161/240 (67%), Gaps = 1/240 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+       AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GY
Sbjct: 69  RRMIRVGKRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGY 128

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+
Sbjct: 129 KFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRVEIAE 188

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + MP++ +  +L+      SL+ P+  E+  S LGD I D +   PLD   Q+   E  
Sbjct: 189 AMDMPLDELDALLRQALTTSSLDAPVNGEEGRSFLGDLIADTSHDEPLDKVEQSIHHEQL 248

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L+ L+ +E+ VL +RFG+  N  HTL E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 249 GRWLSHLSEQEQYVLGLRFGLNGNERHTLAEIGRLMEVSRERVRQVELKALRKLRNLTRR 308



 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 12/46 (26%), Positives = 22/46 (47%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +       +S  R + DP+  YL  +G I LL+   EI +  +++ 
Sbjct: 2   ASLAAGLAESQRRRSSDPISWYLATIGRIPLLTPAEEIELGNQVQE 47


>gi|78212423|ref|YP_381202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196882|gb|ABB34647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 312

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 110/270 (40%), Positives = 174/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T     E     + +  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 38  IELGNQVQAMMAFTEDGSREIEDGELTTAQRRLLRIGRRAKERMMKANLRLVVSVAKKYQ 97

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 98  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 157

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + +P++ +  +L+      SL+ P+  E+
Sbjct: 158 LSERLTTIRKVSLDLAHKLGAMPSRVEIAEAMDIPLDELDSLLRQALTTSSLDAPVNGEE 217

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q    E   R L+ L+ +E+ VLRMRFG+  N  HTL 
Sbjct: 218 GRSFLGDLIADSSLDEPLDIVEQRIHHEQLGRWLSHLSEQEQHVLRMRFGLEGNERHTLA 277

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 278 EIGRLMEVSRERVRQVELKALRKLRNLTRR 307



 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             K  ++  R + DPV  YL  +G I LL+   EI +  +++A
Sbjct: 4   ASKPLETQRRRSSDPVSWYLATIGRIPLLTPAEEIELGNQVQA 46


>gi|16331222|ref|NP_441950.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1001398|dbj|BAA10020.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 345

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 104/250 (41%), Positives = 170/250 (68%), Gaps = 3/250 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V+ + +   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD 
Sbjct: 96  VTKLHRYLGQGERAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDP 155

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +T R +S ++ R  TP 
Sbjct: 156 TKGYKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKTQRELSQQLGRSATPA 215

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+AK L +    +R+ L ++++PISL+  +GD   + L + +ED+  VSP     Q ++R
Sbjct: 216 EVAKALEIDPSQIREYLSLSRQPISLDVRVGDNQDTELSELLEDE-GVSPDAYITQESMR 274

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    +LA LTP+++ VL MRFG+    + +L ++G+   ++RER+RQ+E +A+ +LK  
Sbjct: 275 QDLQNLLAELTPQQQAVLTMRFGLNDGQELSLAKIGQHLNISRERVRQLENQALAQLKR- 333

Query: 671 SRSKKLRSFL 680
            R   +  ++
Sbjct: 334 -RRANMAEYI 342



 Score = 42.1 bits (97), Expect = 0.27,   Method: Composition-based stats.
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               S    T D VR YL E+G + LL+ E EI + K+++ 
Sbjct: 24  SSPTSPPTFTADMVRSYLHEIGRVPLLTHEQEIILGKQVQQ 64


>gi|319790059|ref|YP_004151692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114561|gb|ADU97051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 318

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/284 (36%), Positives = 171/284 (60%), Gaps = 3/284 (1%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V     +   +KSIS    +S  E   +    +        A K++VE+NLR V+
Sbjct: 38  LIESFVPDKDSLDAFLKSISKIPLLSREEEIELAKRAK---AGDKEALKKLVESNLRFVV 94

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKY   GL   DLI EG +GL++AA +FD   G KF +YA+WW++Q+I +++A Q+ 
Sbjct: 95  SVAKKYLGCGLPLHDLIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTG 154

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            ++IPV     ++K+ R+   +  K+ REPT EE+A  + M  + V ++L I + P+SL+
Sbjct: 155 AVKIPVKQAVLVNKITRSYGELLKKLGREPTIEELADYVGMEPKEVERLLSICQVPLSLD 214

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           TPIGDE+ +   DF++ +      +  +Q  L+++   +L  LTP+E++++ MRFG+  N
Sbjct: 215 TPIGDEEDTTFKDFLKGEGTAEVEEKVVQEELKQSIQEMLEQLTPQEKKIIIMRFGLDGN 274

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              TL E+G++  ++RER+RQ+E +A +K+K  +  KKL  FL+
Sbjct: 275 EPKTLREIGEKLGISRERVRQLETRAKKKMKEYALRKKLNVFLN 318



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/128 (24%), Positives = 52/128 (40%), Gaps = 5/128 (3%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ ++    EG E+      S  N  +        +     D +  +L+ +  I LLSRE
Sbjct: 8   LEDEENLGLEGIEEGESAELSLFNQEI--DPSLIESFVPDKDSLDAFLKSISKIPLLSRE 65

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI +AKR +AG    +  L ES L F  ++    +       L ++I  E  +G     
Sbjct: 66  EEIELAKRAKAGDKEALKKLVESNLRF--VVSVAKKYLGCGLPLHDLI-AEGILGLIEAA 122

Query: 198 GFFHGTEG 205
             F   +G
Sbjct: 123 RRFDPDKG 130


>gi|37523331|ref|NP_926708.1| RNA polymerase sigma factor SigC [Gloeobacter violaceus PCC 7421]
 gi|35214335|dbj|BAC91703.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 362

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 115/248 (46%), Positives = 172/248 (69%), Gaps = 1/248 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +++     S AKK+M+EANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD   G
Sbjct: 113 LKRQVLAGSRAKKKMIEANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKG 172

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y+FSTYA WW++Q ITR+IA QS TIR+PVH+ +K++++ +T R++S  + R PT  EIA
Sbjct: 173 YRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNRIKKTQRKLSQNLGRTPTISEIA 232

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L M    VR+++      +SLET +G +  + LG  + +   VSP +SA+Q +LR   
Sbjct: 233 EELEMEPAHVRELMSRVPRSVSLETRVGKDKDTELG-ELLEAEEVSPEESAVQESLRRDV 291

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L  LT RE  V+ MR+G+     ++L E+G+   ++RER+RQIE+KA++KL+ P R 
Sbjct: 292 KELLDDLTLRERDVITMRYGLLDGRTYSLSEIGRALDLSRERVRQIESKALQKLRQPRRR 351

Query: 674 KKLRSFLD 681
            K+R +L+
Sbjct: 352 AKVRDYLE 359



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 75  INVVDGD----DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +++VD D      E E G +  LD  +  +   V +   + +   S+ D VR+YL+E+G 
Sbjct: 1   MHIVDIDRMATPDELEGGPDPVLDPQTLEAFVQVDITDERPARPGSSTDLVRVYLQEIGR 60

Query: 131 IELLSREGEIAIAKRIEA 148
           + LL R+ E+ +A++++ 
Sbjct: 61  VPLLGRDEEVELAQQVQK 78


>gi|284931435|gb|ADC31373.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. F]
          Length = 646

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 155/515 (30%), Positives = 260/515 (50%), Gaps = 44/515 (8%)

Query: 176 DGTTLLREIIDLEACIGPESKGGF--FHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           D    L   ID       + +  F  F      S  K  D S++ E DD +    D  S 
Sbjct: 160 DENLDLNNEIDFADFDSKDEEIDFSDFKHENYSSAFKETDFSEQDELDDKEFNLSDFFSD 219

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           +K+  D            +      +E  D   H +     + +     ++  I  +  +
Sbjct: 220 SKLDIDQPITAQKRQRGRKPKHAPSNEKNDLVYHEVLEASSKTKNNDQESIRAIKTLLAK 279

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            ++ +  +                 E+++ +  +    ++    ++++L D   ++  N 
Sbjct: 280 AKATKSLSN----------------EEIIDVFKNYEFTEAEDLEILQELKDNKIKLEDNV 323

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            E + L          F +     E+D +             K+ V   V +       +
Sbjct: 324 EEKISL----------FRKNQDLSEIDKNLDDLISKGAST--KDKVEDNVKAF------L 365

Query: 414 KSISVETGISISEFRHIVSMV-RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            ++     ++  E   I  ++          A  ++V +NLRLV S+AKKY NRGL F+D
Sbjct: 366 GTLGSSKILNFGEEIQIAKLLGSTDPETREYAINQLVTSNLRLVTSIAKKYLNRGLDFVD 425

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG+IGLMKA  KF++ LG KFSTYA WW++QAITR+IADQ+ T+RIPVHM + I+K+
Sbjct: 426 LIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQAITRAIADQARTVRIPVHMVETINKL 485

Query: 533 VRTARRMSNKIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++T R ++ ++ R+PT EE+ + +         + V  + K+ +EP+SL+ PIG ++ S 
Sbjct: 486 IKTERMLTQQLGRDPTLEELTEAMGGQVNGFTPKKVADIKKLNQEPVSLDKPIGHDEESQ 545

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIG-MNTDHTLEEV 645
             DF++D++ + P +   +  + E    + + +LT +EE+++RMR+G+   +   TLEEV
Sbjct: 546 FVDFVKDRDILKPDEYTEKLIVTEHINELFVNTLTKKEEQIIRMRYGLHPWHQQMTLEEV 605

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++F VTRERIRQIE+KA+RKLKHPS++ +LRSFL
Sbjct: 606 GQKFNVTRERIRQIESKALRKLKHPSKNARLRSFL 640



 Score = 44.8 bits (104), Expect = 0.050,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 62/159 (38%), Gaps = 7/159 (4%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K ++  A+    ++ EE+       E +  +  + +  L +  I +   D++E++   
Sbjct: 272 AIKTLLAKAKATKSLSNEEIIDVFKNYEFTEAEDLEILQELKDNKIKL--EDNVEEKISL 329

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE-- 147
                  S    +   L  +  S     +D V+ +L  +GS ++L+   EI IAK +   
Sbjct: 330 FRKNQDLSEIDKNLDDLISKGASTKDKVEDNVKAFLGTLGSSKILNFGEEIQIAKLLGST 389

Query: 148 --AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               R   +  L  S L     I  +  LN G   +  I
Sbjct: 390 DPETREYAINQLVTSNLRLVTSIAKKY-LNRGLDFVDLI 427


>gi|255034849|ref|YP_003085470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947605|gb|ACT92305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 287

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 171/274 (62%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E    V++ +K      +A + + +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTPDEE---VTLAQKIRDGDQLALERLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  + +REP+PEE+A+ L +    V   +KI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSELEQRFEREPSPEELAEVLEISSSEVVDTMKISGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+     P    +  +LR+   R L +LT RE  V+ + FG+      TLEE+G
Sbjct: 193 SLLDVLENDLEDKPDSGLVNESLRKEVQRALCTLTQREADVIALYFGLNGEHAMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+H SRSK L+++L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRHVSRSKALKTYL 286



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +A++I  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPDEEVTLAQKIRDGDQLALERLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|256371066|ref|YP_003108890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256007650|gb|ACU53217.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 337

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 116/310 (37%), Positives = 175/310 (56%), Gaps = 25/310 (8%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE----------------- 438
           K     E + ++++   +  I     ++  +   +   + +                   
Sbjct: 30  KERQEREDEDLVRL--YLGDIGSHELLTKDDEAELGRRMDRARDAQRQLDAGVKEPARRA 87

Query: 439 ------CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
                  +   AK+  ++ANLRLV+S+AK+Y   GL  LDLIQEGN+GL+ A EKFDW  
Sbjct: 88  ELEELVRQGEEAKRAFIQANLRLVVSIAKRYQASGLPLLDLIQEGNMGLIHAVEKFDWRK 147

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QAITR IA+   TIR+PVH  D + +V R   ++  ++ R PT  E+
Sbjct: 148 GFKFSTYATWWIRQAITRGIANTGRTIRLPVHAGDSLSRVQRAQVQLEVRLGRAPTVREL 207

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A ++ +P + + + L+   EP+SL  P+ D+  + LGD +ED  + +P D A +  L   
Sbjct: 208 AAEVDLPYDKLVEALRFRAEPVSLSEPLRDDGDAELGDVVEDSQSATPFDVAAEHLLPSE 267

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +R+LA L  RE  +LR+R+G+      TLEEVG+ F +TRERIRQIEA+A+ KL+HPS 
Sbjct: 268 VSRLLAPLDGREREILRLRYGLDRGEPRTLEEVGEYFHLTRERIRQIEARAMSKLRHPSA 327

Query: 673 SKKLRSFLDG 682
               R  L G
Sbjct: 328 DIGARDLLTG 337



 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 32/59 (54%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           +S  +S       K+  +R  +D VR+YL ++GS ELL+++ E  + +R++  R     
Sbjct: 17  ASQESSGGGELVTKERQEREDEDLVRLYLGDIGSHELLTKDDEAELGRRMDRARDAQRQ 75


>gi|282880271|ref|ZP_06288987.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
 gi|281305866|gb|EFA97910.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
          Length = 292

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 95/273 (34%), Positives = 163/273 (59%), Gaps = 4/273 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ I  E  +S  E   +   ++K       A  ++ +ANLR V+SVAK+Y N+G
Sbjct: 22  ALDKYLQEIGREDLLSTEEEIELAQRIKK---GDRKALDKLTKANLRFVVSVAKQYQNQG 78

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++   
Sbjct: 79  LSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVG 138

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            ++K+ +   +   + +R P   EIA+++ +P + V   +K   + +S++ P  D D + 
Sbjct: 139 SVNKINQLQNKFEQEFERRPNSSEIAERIDIPEDKVIDAMKANGKHVSVDAPFSDGDDNS 198

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D +     +  +  +LR+     L +L  RE  V+   +GI      TLEE+G 
Sbjct: 199 LIDVLPDSDIPMADNELVMESLRKEIADALHTLNERERNVIECFYGINQPE-MTLEEIGD 257

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++ +TRER+RQI  KA+RKL+  +++K+L+S+L
Sbjct: 258 RYGLTRERVRQIREKALRKLRKNTKNKQLKSYL 290



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 100/251 (39%), Gaps = 18/251 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +LLS E EI +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 26  YLQEIGREDLLSTEEEIELAQRIKKGDRKALDKLTKANLRF--VVSVAKQYQNQGLSLPD 83

Query: 184 IID------LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           +I+      ++A    +   GF   +    + ++       E+  +     +   +    
Sbjct: 84  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 143

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
              ++K +   E   N     +  +      + AM+   +   + A     +    +  L
Sbjct: 144 NQLQNKFEQEFERRPNSSEIAERIDIPEDKVIDAMKANGKHVSVDAPFSDGDDNSLIDVL 203

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            D+ +    +E   +  + L++++   + +L+  +     ++E  Y I++  M     L 
Sbjct: 204 PDSDIPMADNE---LVMESLRKEIADALHTLNERER---NVIECFYGINQPEMT----LE 253

Query: 358 RLAQSYGIKRD 368
            +   YG+ R+
Sbjct: 254 EIGDRYGLTRE 264


>gi|313109026|ref|ZP_07794999.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
 gi|310881501|gb|EFQ40095.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
          Length = 344

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 98/274 (35%), Positives = 165/274 (60%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 69  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 125

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 126 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 185

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 186 VVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDS 245

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L E+  + L  LT ++  V+  RFG+  +   TLEE
Sbjct: 246 DKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEE 305

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 306 VGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 339



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 31/141 (21%), Positives = 53/141 (37%), Gaps = 10/141 (7%)

Query: 45  TIEELNA-FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
           T    N   L  +    +  ++ +  L   GI + +    E           A+  + +S
Sbjct: 4   THARDNDMALKKEGPEFDHDDEVL--LLEPGIMLDESSADEQPSPR------ATPKATTS 55

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
              ++ K        D  ++YL E+G   LL+ E E+  A+  + G       + ES L 
Sbjct: 56  FSSKQHKHIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLR 115

Query: 164 FQALIIWRDELNDGTTLLREI 184
               I  R  +N G +LL  I
Sbjct: 116 LVVKIARRY-VNRGLSLLDLI 135


>gi|152985831|ref|YP_001346901.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
 gi|150960989|gb|ABR83014.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
          Length = 344

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 98/274 (35%), Positives = 166/274 (60%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 69  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 125

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 126 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 185

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 186 VVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDS 245

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L E+  + L+ LT ++  V+  RFG+  +   TLEE
Sbjct: 246 DKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLSELTDKQREVVIRRFGLRGHESSTLEE 305

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 306 VGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 339



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 27/115 (23%), Positives = 51/115 (44%), Gaps = 2/115 (1%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREMG 129
            +  + +++   + DE  +++   L ++   ++ F  K+    D     D  ++YL E+G
Sbjct: 22  HDDEVLLLEPGIMLDELSADEQPSLRATPKATTSFSSKQHKHIDYTRALDATQLYLNEIG 81

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+  + G       + ES L     I  R  +N G +LL  I
Sbjct: 82  FSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 135


>gi|123966683|ref|YP_001011764.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201049|gb|ABM72657.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 313

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 109/270 (40%), Positives = 173/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ +   T  G    + +      ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMTLTEDGQLNEKTKEFTPQQKRTIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLATIRKVSRELAHKLGAMPSRIEIAEAMEIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L  L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLTHLSEQEQHVLKLRFGLDGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 10/46 (21%), Positives = 22/46 (47%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  +    +   R  +DP+  YL  +G + LL+   EI +  +++ 
Sbjct: 2   ASSVSTSTEPQKRRGNDPISWYLSNIGRVPLLTPAEEIELGNQVQK 47


>gi|291566702|dbj|BAI88974.1| group 2 RNA polymerase sigma factor SigB [Arthrospira platensis
           NIES-39]
          Length = 334

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 111/267 (41%), Positives = 170/267 (63%), Gaps = 10/267 (3%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +  S + G+S SE   I++  R+       AK++M+EANLRLV+S+AKKY  R ++FLDL
Sbjct: 76  EEWSAKAGLSESEMTDIINRGRR-------AKQKMIEANLRLVVSIAKKYQKRNMEFLDL 128

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA  S TIR+P+H+ +K++K+ 
Sbjct: 129 IQEGTLGLERGVEKFDPMRGYKFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEKLNKIK 188

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  +  R  TP EIAK L +    +R  L  ++ P+SL+  +GD   + L D +E
Sbjct: 189 RVQRELFQQYGRNATPTEIAKALDLEPSQIRDYLLASRHPVSLDLRVGDNQDTELQDLLE 248

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D++A S      Q  LR+    ++A LTP++  VL +R+G+    + +L +VG Q  ++R
Sbjct: 249 DESA-SADSYVTQQLLRQDLKDMMADLTPQQREVLTLRYGLNDGKEMSLSKVGVQMNISR 307

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQ+E +A+  L+   R  ++R +L
Sbjct: 308 ERVRQLENQALNHLRR--RKAQVREYL 332



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + + ++      ++    ++ D VR YL E+G + LL+RE EI   K+++ 
Sbjct: 4   ATAKTTQTELTSRNPRSGASMDAVRTYLHEIGRVPLLTREEEIIYGKKVQQ 54


>gi|299067258|emb|CBJ38455.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CMR15]
          Length = 376

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTLAKAGEFP---ARQVMIERNLRLVVSIAKGYLNRGV 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 161 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 220

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  +
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPFDLDPGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 281 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 340

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 341 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 371



 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 32/153 (20%), Positives = 50/153 (32%), Gaps = 26/153 (16%)

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-------------- 118
             I VVD   L DE  + +  D+A ++  +    ++ +D                     
Sbjct: 43  EDIEVVD--PLVDEVPAAERADVADTSDANDSADEEDEDEESEEAAPEEDFRTVLQAELA 100

Query: 119 -DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D V+ YL  +    LL+   E+  +   +AG       + E  L     I     LN G
Sbjct: 101 ADTVQHYLNRISIKPLLTPAEELHFSTLAKAGEFPARQVMIERNLRLVVSIAKGY-LNRG 159

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             LL  I         E   G  H  E    ++
Sbjct: 160 VPLLDLI--------EEGNLGLMHAIEKFDPER 184


>gi|300691814|ref|YP_003752809.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
 gi|299078874|emb|CBJ51535.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
          Length = 377

 Score =  188 bits (478), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 105 VQHYLNRISIKPLLTPAEELHFSTLAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 162 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 221

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  +
Sbjct: 222 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPFDLDPGT 281

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 282 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 341

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 342 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 372



 Score = 40.6 bits (93), Expect = 0.93,   Method: Composition-based stats.
 Identities = 29/151 (19%), Positives = 47/151 (31%), Gaps = 23/151 (15%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--------------D 119
            I VVD    E        +   + A++S+    +  +  + +                D
Sbjct: 44  DIEVVDTLIDEMPAAEPTDVADTADANDSADEPDEEDEDDEDAAPEEDFRTVLQAELAAD 103

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
            V+ YL  +    LL+   E+  +   +AG       + E  L     I     LN G  
Sbjct: 104 TVQHYLNRISIKPLLTPAEELHFSTLAKAGEFAARQVMIERNLRLVVSIAKGY-LNRGVP 162

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           LL  I         E   G  H  E    ++
Sbjct: 163 LLDLI--------EEGNLGLMHAIEKFDPER 185


>gi|254481825|ref|ZP_05095068.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
 gi|214037954|gb|EEB78618.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
          Length = 353

 Score =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 96/298 (32%), Positives = 168/298 (56%), Gaps = 3/298 (1%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +D      A+                S+   +  +  I     ++  E ++   +  K  
Sbjct: 52  VDTQVTEEAQFDRAKARTATARKVGKSLDVTQLYLNEIGYSPLLTADEEKYYARLAIK-- 109

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                 +K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 110 -GDESGRKRMIESNLRLVVKISRRYINRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFST 168

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPT EEIA  L  
Sbjct: 169 YATWWIRQTIERGIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPTAEEIADMLDR 228

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P   V+++L + +   S++TP+G +    + D I D +   P      ++++++    L 
Sbjct: 229 PAADVKRMLGLNERVTSMDTPVGPDSDKAVVDTIADTHESDPSQLLQDSDIKDSIGSWLD 288

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            L+ ++  V+  RFG+      TLEEVG++  +TRER+RQI+ +A+++L+    ++ L
Sbjct: 289 ELSEKQREVVARRFGLRGYESSTLEEVGREIGLTRERVRQIQVEALKRLRGIMETQGL 346



 Score = 46.0 bits (107), Expect = 0.020,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 35/98 (35%), Gaps = 1/98 (1%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E S     +   A       +         + D  ++YL E+G   LL+ + E   A+  
Sbjct: 48  EASGVDTQVTEEAQFDRAKARTATARKVGKSLDVTQLYLNEIGYSPLLTADEEKYYARLA 107

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             G       + ES L     I  R  +N G TLL  I
Sbjct: 108 IKGDESGRKRMIESNLRLVVKISRRY-INRGLTLLDLI 144


>gi|83747939|ref|ZP_00944970.1| RpoS [Ralstonia solanacearum UW551]
 gi|83725357|gb|EAP72504.1| RpoS [Ralstonia solanacearum UW551]
          Length = 381

 Score =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 109 VQHYLNRISIKPLLTPAEELHFSTRAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 165

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 166 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 225

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 226 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDSGT 285

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 286 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 345

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 346 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 376



 Score = 41.0 bits (94), Expect = 0.64,   Method: Composition-based stats.
 Identities = 50/341 (14%), Positives = 102/341 (29%), Gaps = 46/341 (13%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--------------- 118
            I VVD    E        +   S A++S+    + ++  +   +               
Sbjct: 44  DIEVVDTLTDEMPASEPADIVDTSDANDSADEPDEEEEDEEEEDEEAAPEEDFRTVLQAE 103

Query: 119 ---DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR---- 171
              D V+ YL  +    LL+   E+  + R +AG       + E  L     I       
Sbjct: 104 LAADTVQHYLNRISIKPLLTPAEELHFSTRAKAGEFAARQVMIERNLRLVVSIAKGYLNR 163

Query: 172 -----DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
                D + +G   L   I+            +       S ++   +     R  V   
Sbjct: 164 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVI 223

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
               +        ++S +D    + E+    L +  ++    LS  E       +    +
Sbjct: 224 RELNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLNE---HTTSLDTPFD 280

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVL------------KEKLVKLVGSLSLNQSR 334
           +      L  L D        E +  +   L            +  + +  G   +  + 
Sbjct: 281 LDSGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPAT 340

Query: 335 IDLLVEQLYDISKRIMHNEGE----LLRLAQSYGIKRDVFL 371
           ++ L  ++    +R+   + E    L R   S G+++D  L
Sbjct: 341 LEELAAEMGLTRERVRQIQQEALVKLKRHFASQGVRKDAVL 381


>gi|298208827|ref|YP_003717006.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
 gi|83848754|gb|EAP86623.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
          Length = 288

 Score =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 102/273 (37%), Positives = 174/273 (63%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N ++ +S    I+  E   +   +R       IA +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LNNYLQDVSKLDLITAEEEVELAQRIR---EGDQIALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+ S  +R+P++    
Sbjct: 75  RLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEHSRVVRLPLNKIGV 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSH 587
           I+K+ +T   +    +R P+  EIAK+L MPV  V+  +K +   +S++ P  + E+ S+
Sbjct: 135 INKINKTFSYLEQAYERPPSAAEIAKELDMPVSKVKTAMKNSGRSLSMDAPFQEGENDSN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++   + SP ++ +Q +L     R L +LT RE  V+R+ +G+G     TL+E+G+
Sbjct: 195 LYDVLKSGESPSPDNNLMQDSLSVEIERALDTLTEREADVIRLNYGLGGQQPLTLQEIGE 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  K IR+L+H S+SK L+ +L
Sbjct: 255 TFDLSRERVRQIREKGIRRLRHESKSKILKKYL 287



 Score = 45.6 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  ++L++ E E+ +A+RI  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQDVSKLDLITAEEEVELAQRIREGDQIALEKLTKANLRF--VVSVAKQYQNQGLRLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|86143196|ref|ZP_01061598.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85830101|gb|EAQ48561.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 288

 Score =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 100/273 (36%), Positives = 173/273 (63%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +S    I+  E   +   +R       +A + + +ANLR V+SVAK+Y N+GL
Sbjct: 18  LNTYLQDVSKLDMITADEEVELAQRIR---EGDQVALERLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++I++ S T+R+P++    
Sbjct: 75  KLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAISEHSRTVRLPLNKIGT 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSH 587
           I K+ +    +   ++R P+ EEIAK+L M V  V+  +K +   +S++ P  + E+ S+
Sbjct: 135 ISKINKAFSYLEQSLERPPSAEEIAKELDMTVAKVKLAMKNSGRNLSMDAPFKEGENDSN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++   + +P    +Q +L     R L +L+PRE  V+++ +G+G    HTL+E+G+
Sbjct: 195 LYDVLKSGESPNPDADLMQESLGTEIERALETLSPRESDVIKLNYGLGGEQPHTLQEIGE 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  K IR+L+H SRSK L+++L
Sbjct: 255 MFDLSRERVRQIREKGIRRLRHTSRSKVLKTYL 287



 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  +++++ + E+ +A+RI  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQDVSKLDMITADEEVELAQRIREGDQVALERLTKANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|187764347|gb|ACD36026.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 322

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 96/265 (36%), Positives = 163/265 (61%), Gaps = 3/265 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 53  ALDATQLYLNEIGFSPLLTPEEEVHFARLAQK---GDPAGRKRMIESNLRLVVKIARRYV 109

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 110 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 169

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 170 VVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDS 229

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L E+  + L  LT ++  V+  RFG+  +   TLEE
Sbjct: 230 DKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEE 289

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           VG++  +TRER+RQI+ +A+++L+ 
Sbjct: 290 VGQEIGLTRERVRQIQVEALKRLRE 314



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 50/131 (38%), Gaps = 13/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +    E           A+  + +S   ++ K   
Sbjct: 2   PEFDIDDEVL------LLEPGIMLDESSADEQPSPR------ATPKATTSFSSKQHKHID 49

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LL+ E E+  A+  + G       + ES L     I  R  
Sbjct: 50  YTRALDATQLYLNEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRY- 108

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 109 VNRGLSLLDLI 119


>gi|330040254|ref|XP_003239821.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
 gi|327206746|gb|AEA38923.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
          Length = 414

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 117/250 (46%), Positives = 171/250 (68%), Gaps = 2/250 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V   +     +  AK+ M+ ANLRLV+S+AK+Y+NRG+   DL+QEG++GL++A EKFD 
Sbjct: 146 VQKFKTVLYNSRKAKERMIAANLRLVVSIAKRYSNRGMSLQDLVQEGSLGLIRATEKFDS 205

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW+KQ+++R+IAD S TIR+PVH+ D +  + +T R ++ ++ R PT E
Sbjct: 206 EKGFKFSTYATWWIKQSVSRAIADHSRTIRLPVHLYDTLSAIKKTTRILTIELGRSPTEE 265

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA K+ + V+ +R VL+  +  +SLE PI ++ DT+ L DFIE  +  SP +   ++ L
Sbjct: 266 EIACKMDVTVDKLRSVLQSAQPTLSLEKPIKNDGDTAQLSDFIE-ADQESPDEHVEKSML 324

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+    V+ SL+ RE  V+RMR+G+      TLEE+G+ F VTRER+RQIEAKAIRKL+ 
Sbjct: 325 RDDLRDVINSLSLRERDVIRMRYGLDDGKIRTLEEIGQIFSVTRERVRQIEAKAIRKLRQ 384

Query: 670 PSRSKKLRSF 679
           P RS   +  
Sbjct: 385 PYRSSIFKDH 394



 Score = 44.1 bits (102), Expect = 0.078,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 33/82 (40%)

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           + +  +      V   +  +  +      +  +      V   + +      +DD VR Y
Sbjct: 30  NLINNVEKNFYEVKKNEVKKIIKSFNTQREFKNKIEEPEVAKFQSETKPVHKSDDSVRWY 89

Query: 125 LREMGSIELLSREGEIAIAKRI 146
           L+ +G ++LL  E EI +A+ I
Sbjct: 90  LQLIGKVKLLKPEEEIQLAREI 111


>gi|254230502|ref|ZP_04923875.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262393289|ref|YP_003285143.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|151936974|gb|EDN55859.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262336883|gb|ACY50678.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
          Length = 328

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 107/298 (35%), Positives = 174/298 (58%), Gaps = 3/298 (1%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +D      +    +   +        S+   +  +  I     ++  E    V   R+  
Sbjct: 23  IDNELEKSSSTESKTAAREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRAL 79

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 80  RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 139

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +
Sbjct: 140 YATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDI 199

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L 
Sbjct: 200 PVEDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLE 259

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 260 ELNPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQGL 317



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+    ++        +L  S+S  S    + +  A   + D  ++YL E+G   LL+ E
Sbjct: 10  VEEFAFDNASVKTIDNELEKSSSTESKTAAREEFDASSKSLDATQLYLGEIGFSPLLTAE 69

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 115


>gi|332829288|gb|EGK01942.1| hypothetical protein HMPREF9455_00064 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 286

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 177/272 (65%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   ++K       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQAIKK---GDRAALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R+P+ EE+A++L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERKPSAEELAEQLDIPVDKIADSLKVSGRHISMDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + +A     + I  +L++   R L++LT RE  +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDAPIADRTLINESLQQEIERALSTLTERESEIIKMFFGIGY-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAI++L+  SRSK L+S+L
Sbjct: 254 FQLTRERVRQIKEKAIKRLRQNSRSKLLKSYL 285



 Score = 41.7 bits (96), Expect = 0.45,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+ I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQAIKKGDRAALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|332880149|ref|ZP_08447831.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332681908|gb|EGJ54823.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 286

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     + +  +L     R L++L+ RE+ +++M FGI  + + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRTLVNESLSREIDRALSTLSEREKEIIQMFFGIN-HQEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  ++SK L+S+L
Sbjct: 254 FNLTRERVRQIKEKAIRRLRQNTKSKLLKSYL 285



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|160902123|ref|YP_001567704.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359767|gb|ABX31381.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 418

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 124/275 (45%), Positives = 178/275 (64%), Gaps = 8/275 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K IS    +S S  R +    +K       A+ E+++ANLRLVIS+AK+YT RGL FL
Sbjct: 148 YLKEISKVELLSPSRERQLARRAQK---GDQKARDELIKANLRLVISIAKRYTGRGLTFL 204

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGL+KA +KFDW  G+KFSTYA WW++QAITR+IADQ+ TIRIPVH+ + I++
Sbjct: 205 DLIQEGNIGLIKAVDKFDWRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHLVETINR 264

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG----DEDTSH 587
           + +  R    +    P+ +E+A+ L  P + + ++L   K+ +SL +PI     D++ S 
Sbjct: 265 MNKVIREYLQENGDYPSAQELAEILDKPEDKINEILMSAKDVLSLNSPISSGNGDDEESE 324

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            GDFI      +P + A +  ++E    VL +L  +E  VL+MR+G       TLEEVG+
Sbjct: 325 TGDFIS-TEETTPEEEAQKMIMKERLEEVLDTLNSKEALVLKMRYGFLDGKQKTLEEVGQ 383

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            F VTRERIRQIE KA+RKL+HP+R  +L+  ++ 
Sbjct: 384 FFNVTRERIRQIETKALRKLRHPNRVAQLKDIVES 418



 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 41/195 (21%), Positives = 80/195 (41%), Gaps = 13/195 (6%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLV--------FDFSDDSWKKMIKLARQRGY-VTIEELNAF 52
            +    N D +   +D D   V            D     +I  A+ +G  ++  +++  
Sbjct: 14  IMKSIENIDFEDAEKDGDTVKVKVKKSHEEAKSVDTFISLLINKAKNKGNKLSYSDIDHA 73

Query: 53  LP---PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           +P    +E+ S+ +E     L   GI +++ +  E+E+ + +  +  +          + 
Sbjct: 74  IPTDLSEEIDSDYIEKIYEALEAEGIEILEEEVEEEEKDALNETEYENEEVEELFSDTEL 133

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           K   + S  DP+++YL+E+  +ELLS   E  +A+R + G       L ++ L     I 
Sbjct: 134 KMYDNISLGDPIKIYLKEISKVELLSPSRERQLARRAQKGDQKARDELIKANLRLVISIA 193

Query: 170 WRDELNDGTTLLREI 184
            R     G T L  I
Sbjct: 194 KRY-TGRGLTFLDLI 207


>gi|226357433|ref|YP_002787172.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226319423|gb|ACO47418.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 363

 Score =  188 bits (477), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 125/300 (41%), Positives = 182/300 (60%), Gaps = 27/300 (9%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV------------------------RKGECEASIA 444
           +R  +  I     ++++E   +   +                        ++   +   A
Sbjct: 63  VRQYLHEIGRVPLLTVTEEIDLARRMEAGQEARTQLETEHELGERERRRLQRTVEDGEHA 122

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++++EANLRLV+S+AKKY NRG+  LDLIQEGN GL++ AEKF++  G+KFSTYA WW+
Sbjct: 123 KQQLIEANLRLVVSIAKKYANRGMGLLDLIQEGNQGLIRGAEKFEYRRGFKFSTYATWWI 182

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEG 562
           +QA+ R+IADQ+  IRIPVHM + I+K+ RT R++  ++ REP+  E A+ +        
Sbjct: 183 RQAVNRAIADQARNIRIPVHMVETINKLNRTTRQLQMELSREPSHAETAEAMGPGWDEVK 242

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V + L++T++ ISL TP+GDE  S + DF+ D    SPL       + E   R LA+L P
Sbjct: 243 VEETLRLTRDTISLATPVGDEGDSSIADFLPDDRRESPLSRVSSVLMSEALDRTLATLEP 302

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681
           RE  V+R+R G+    +HTLEEVGK F VTRERIRQIE KA+RK+K   S+   LR +L+
Sbjct: 303 REALVIRLRNGLEDGREHTLEEVGKHFGVTRERIRQIENKALRKIKYEQSKRGSLRDYLE 362



 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 46/101 (45%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++  D  +EE + +     +  S S     +  D     ++DPVR YL E+G + LL+  
Sbjct: 20  LESLDEPEEELTGEEPAAEAEDSPSEETWSELVDHPVIVSNDPVRQYLHEIGRVPLLTVT 79

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
            EI +A+R+EAG+        E  L  +     +  + DG 
Sbjct: 80  EEIDLARRMEAGQEARTQLETEHELGERERRRLQRTVEDGE 120


>gi|257092978|ref|YP_003166619.1| RNA polymerase sigma factor RpoS [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257045502|gb|ACV34690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 319

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 99/267 (37%), Positives = 161/267 (60%), Gaps = 3/267 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ + +I  +  +S +E  +     R GE     A+++M+E NLRLV+++AK Y NRG+ 
Sbjct: 50  QHYLNAIGAKPLLSPAEEVNWARRARAGEFP---ARQKMIEHNLRLVVNIAKHYLNRGIP 106

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL+ A EK+D   G++FSTYA WW++Q+I R+I +QS TIR+PVH+   I
Sbjct: 107 LLDLIEEGNLGLIHAIEKYDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHVVKDI 166

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           + V+R  R + +   RE  P+ IA  +  PVE VR+V+ + +   SL+ P+  + +  +G
Sbjct: 167 NLVLRAIRHLESASGREICPDRIAHLIDRPVEDVRRVMALNERIASLDAPLQVDPSQTVG 226

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++ + P +      L E     L  L  +  +VL  R+G+G +   TLEE+    
Sbjct: 227 DLIADESLLDPDELLQSNELGELLRNWLGQLAGKHRQVLERRYGLGGSEPSTLEEIAFDL 286

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +TRER+RQI+ +A+  L+   R + +
Sbjct: 287 NLTRERVRQIQIEALDHLRRIIRRRGV 313



 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 20/99 (20%), Positives = 36/99 (36%), Gaps = 9/99 (9%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                 +D  + YL  +G+  LLS   E+  A+R  AG       + E  L    ++   
Sbjct: 40  PEVELLNDVTQHYLNAIGAKPLLSPAEEVNWARRARAGEFPARQKMIEHNLRL--VVNIA 97

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
               +    L ++I+       E   G  H  E +  ++
Sbjct: 98  KHYLNRGIPLLDLIE-------EGNLGLIHAIEKYDPER 129


>gi|209527735|ref|ZP_03276230.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209491813|gb|EDZ92173.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 332

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 110/267 (41%), Positives = 169/267 (63%), Gaps = 10/267 (3%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
              S + G+S SE   I++  R+       AK++M+EANLRLV+S+AKKY  R ++FLDL
Sbjct: 74  AEWSAKAGLSESEMTEIMNRGRR-------AKQKMIEANLRLVVSIAKKYQKRNMEFLDL 126

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA  S TIR+P+H+ +K++K+ 
Sbjct: 127 IQEGTLGLERGVEKFDPMRGYKFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEKLNKIK 186

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  +  R  TP EIAK L +    +R  L  ++ P+SL+  +GD   + L D +E
Sbjct: 187 RVQRELFQQYGRNATPTEIAKALDLEPSQIRDYLLASRHPVSLDLRVGDNQDTELQDLLE 246

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D++A S  +   Q  LR+    ++A LTP++  VL +R+G+    + +L +VG    ++R
Sbjct: 247 DESA-SADNYVTQQLLRQDLKDLMADLTPQQREVLTLRYGLNDGKEMSLSKVGVHMNISR 305

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQ+E +A+  L+   R  ++R +L
Sbjct: 306 ERVRQLENQALNHLRR--RKAQVREYL 330



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + + ++      ++    ++ D VR YL E+G + LL+RE EI   K+++ 
Sbjct: 2   ATAKTTQTELTSRNPRSGASMDAVRTYLHEIGRVPLLTREEEIIYGKKVQQ 52


>gi|330836598|ref|YP_004411239.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
 gi|329748501|gb|AEC01857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
          Length = 293

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 104/269 (38%), Positives = 169/269 (62%), Gaps = 5/269 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    ++  E   +  +  +G      A+  +VE+NLR V+++AKKY N+GL   
Sbjct: 27  YLKEINRIPMLTHEEEYKVAKLAAEGN---QKARNRLVESNLRFVVNIAKKYQNQGLPLG 83

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLM A EKFD   GY F +YA+WW++QAI ++I+++S T+R+P++  +++ +
Sbjct: 84  DLINEGNIGLMNAIEKFDVDKGYHFISYAVWWIRQAILKAISEKSRTVRLPLNRANELMQ 143

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGD 590
           + +  + + N+   EPT EEI +   +    V  ++ I+KE +SL+ P+  +   S +GD
Sbjct: 144 IQKAQKSLMNESGAEPTMEEIGRLTQLDPSHVADLIAISKEMVSLDAPVFTDSGNSSVGD 203

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FI+D  A SP D  I + L+E   +VLA+L+ +E  +L  RFG+      +L+E+G+ + 
Sbjct: 204 FIQD-GADSPDDVIIDSALKEDINKVLATLSEKEMEILEFRFGLNGQHPMSLKEIGELYN 262

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +T+ERIRQIE KAI +L+ PSR K L  +
Sbjct: 263 LTKERIRQIEKKAIERLQQPSRIKMLVGY 291



 Score = 44.1 bits (102), Expect = 0.081,   Method: Composition-based stats.
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +YL+E+  I +L+ E E  +AK    G       L ES L F  ++    +  +    L 
Sbjct: 26  IYLKEINRIPMLTHEEEYKVAKLAAEGNQKARNRLVESNLRF--VVNIAKKYQNQGLPLG 83

Query: 183 EIIDLEACIGPESKGGFFHGTEG 205
           ++I+ E  IG  +    F   +G
Sbjct: 84  DLIN-EGNIGLMNAIEKFDVDKG 105


>gi|17545926|ref|NP_519328.1| RNA polymerase sigma factor RpoS [Ralstonia solanacearum GMI1000]
 gi|17428221|emb|CAD14909.1| rna polymerase sigma s (sigma-38) factor transcription regulator
           protein [Ralstonia solanacearum GMI1000]
          Length = 377

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 105 VQHYLNRISIKPLLTPAEELHFSTLAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 162 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 221

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 222 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 281

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 282 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELA 341

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 342 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 372



 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 31/153 (20%), Positives = 50/153 (32%), Gaps = 27/153 (17%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP------------- 120
            + VVD   L DE  + +  D+A ++  +    +  ++  D     P             
Sbjct: 44  DVEVVD--PLIDEAPAAEPADIADTSDANDSADESDEEDEDGEEAAPEEDFRTVLQAELA 101

Query: 121 ---VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
              V+ YL  +    LL+   E+  +   +AG       + E  L     I     LN G
Sbjct: 102 ADTVQHYLNRISIKPLLTPAEELHFSTLAKAGEFAARQVMIERNLRLVVSIAKGY-LNRG 160

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             LL  I         E   G  H  E    ++
Sbjct: 161 VPLLDLI--------EEGNLGLMHAIEKFDPER 185


>gi|163848723|ref|YP_001636767.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526666|ref|YP_002571137.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670012|gb|ABY36378.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450545|gb|ACM54811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 360

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 115/280 (41%), Positives = 177/280 (63%), Gaps = 2/280 (0%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA--SIAKKEMVEANLRLVISVAK 461
           + +   R   +       +   +F +    +R     A    A++ +++ANLRLV+SVAK
Sbjct: 81  EEVELARQYSRGKEARQRLRNEDFANDRERMRLEMEMARGEEARRRLIQANLRLVVSVAK 140

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY    + F+DL+QEGNIGLM+A EKFD+  G +FSTYA WW++QA+TR+IA+QS  IR+
Sbjct: 141 KYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWIRQAVTRAIAEQSRLIRL 200

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVH+ + I  + R   R+  +++REPT EE+A  L M V  V+++++ + +PISLE P+ 
Sbjct: 201 PVHLSESIVHLRRAIYRLEQELEREPTAEELAHALNMSVRKVKRLIRASTQPISLEQPLN 260

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +E    + + + D+   SP++ A Q  L    T  L  L  RE ++L++R+G+      T
Sbjct: 261 NEQEGRVSETLADETVASPMEIAEQKMLHAELTAALNELPERERKILQLRYGLIDGQRRT 320

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVG  F +TRER RQIEA+A+R+L+HPS  ++L S+LD
Sbjct: 321 LEEVGATFGITRERTRQIEAEALRRLRHPSVGQRLHSYLD 360



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 79  DGDDLEDE-EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +  +L+ E +G  D        +          +      +D V++YL+E+G + LL+ E
Sbjct: 21  EATELDAEWDGDVDPEPEDLEVAELEPLDDLESEGDFEPVEDSVQLYLQEIGQVPLLTAE 80

Query: 138 GEIAIAKRIEAGRAMMMA 155
            E+ +A++   G+     
Sbjct: 81  EEVELARQYSRGKEARQR 98


>gi|162455526|ref|YP_001617893.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161166108|emb|CAN97413.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 715

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 137/489 (28%), Positives = 231/489 (47%), Gaps = 18/489 (3%)

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD--SPPE 249
            P ++GG             +D ++E           D E  A     D   +D    PE
Sbjct: 235 DPLAQGGTATPEIAALGLLEDDQTEETVVRPRPAEILDEERTADFIDLDLGPLDRLPQPE 294

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A N +R L + ED    ++ A     R     AL  +     EL + +       +   
Sbjct: 295 RARNQDRELKDVEDGGGDSMLA-----RYFRDMALHPVMGPDEELDTARAVERTEVEHWV 349

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK--- 366
           + +      E ++  +          ++   Q+ ++ K +   + +  +L          
Sbjct: 350 ALLSYLPAAEYILTALEEDVAKAGEDEVKAPQIAEMQKLVRLAKKQKGKLLAEQEKPWTQ 409

Query: 367 -RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
             +      +  + D  W++ A           +  E D    + +  ++      + +S
Sbjct: 410 LSEELAAAVRLPDSDRLWMARAFGIARD-----LVREPDFEDDVSDPEETRPTRPRLPMS 464

Query: 426 -EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
             +R  +  V +       AK   V+ANLRLV+S+A++Y    L  +DLIQEGNIGLMKA
Sbjct: 465 GSYRRYLDRVERSFQAQHDAKNRFVKANLRLVVSIARRYNRGRLPLIDLIQEGNIGLMKA 524

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E+FD   GY+FSTYA WW++ AI+R++AD+   +RIPVHM D  ++V R  + +  +  
Sbjct: 525 VERFDHSRGYRFSTYASWWIRHAISRALADKGRAVRIPVHMLDTYNRVARATQAIIARTG 584

Query: 545 REPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EPT EE+ K+  +P E + KV     + P SL+ P+GDED     DF++++NA+SP D 
Sbjct: 585 HEPTIEELEKETGVPREKLDKVKDFYAETPFSLDRPVGDEDGRKFIDFLQEENALSPFDH 644

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                  +   R+L +LTP E R++R RFG+    + TL+E+G ++ ++RERIRQ++ +A
Sbjct: 645 LANRKWSDEVRRLLTTLTPIESRIIRWRFGLDDEDELTLKEIGDKYNLSRERIRQLQEQA 704

Query: 664 IRKLKHPSR 672
           + K++   R
Sbjct: 705 LGKIRKQMR 713


>gi|123969020|ref|YP_001009878.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199130|gb|ABM70771.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 313

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 108/270 (40%), Positives = 174/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ + + T       +     +  ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMILTEDGQLNEKVNEFTTQQKRTIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDANERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 40.6 bits (93), Expect = 0.86,   Method: Composition-based stats.
 Identities = 10/40 (25%), Positives = 23/40 (57%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + +   R ++DP+  YL+ +G + LL+   EI +  +++ 
Sbjct: 8   QSEPPKRRSNDPISWYLQNIGRVPLLTPAEEIELGNQVQK 47


>gi|257438148|ref|ZP_05613903.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199479|gb|EEU97763.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 461

 Score =  188 bits (476), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 129/245 (52%), Positives = 179/245 (73%), Gaps = 2/245 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E R     + K   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+
Sbjct: 205 PLTEERR--QELLKIRRDGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 262

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KAAEKFD   G++FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +
Sbjct: 263 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQ 322

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EPTPEE+AK + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  
Sbjct: 323 NGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGK 382

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A +A + +   + L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAK
Sbjct: 383 AADRAMVAQQINQALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAK 442

Query: 663 AIRKL 667
           AIRKL
Sbjct: 443 AIRKL 447



 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 21/140 (15%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD-------- 81
           + K+++      G +T  E         +    +E    +L   GI ++D +        
Sbjct: 4   TLKELLTKG--EGTLTAGEAKTLASQCRMD---VETLYTLLEERGIKILDDEADGDTSLD 58

Query: 82  ------DLEDEEGSEDSLDLASSASNSSVFL--QKRKDSADRSTDDPVRMYLREMGSIEL 133
                 ++E  E + D L L     +          K + D   DDPV+ YL+++G I L
Sbjct: 59  VEGIMAEVESAEANSDELGLGDENEDDPAEENPADLKAAMDELLDDPVKNYLKQIGQIPL 118

Query: 134 LSREGEIAIAKRIEAGRAMM 153
           LS E E+ ++KRI AG    
Sbjct: 119 LSAEQEVDLSKRIHAGAEAA 138


>gi|241662747|ref|YP_002981107.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12D]
 gi|240864774|gb|ACS62435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ralstonia
           pickettii 12D]
          Length = 378

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 106 VQHYLNRISIKPLLTPAEELHFSTLAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 163 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 222

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 283 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNYIEPATLEELA 342

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 343 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 373



 Score = 41.0 bits (94), Expect = 0.76,   Method: Composition-based stats.
 Identities = 35/155 (22%), Positives = 52/155 (33%), Gaps = 15/155 (9%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK----RKDSADR 115
           +E++E   A++ ++   V D  DL D   S D  D        +         RK     
Sbjct: 43  AEEIEVVDALVDDL--PVSDSADLNDTSDSADEPDEEEEEGEEAEEAAPEEDFRKVLQAE 100

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
              D V+ YL  +    LL+   E+  +   +AG       + E  L     I     LN
Sbjct: 101 LAADTVQHYLNRISIKPLLTPAEELHFSTLAKAGEFAARQVMIERNLRLVVSIAKGY-LN 159

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            G  LL  I         E   G  H  E    ++
Sbjct: 160 RGVPLLDLI--------EEGNLGLMHAIEKFDPER 186


>gi|33861845|ref|NP_893406.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33640213|emb|CAE19748.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 313

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 110/270 (40%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ + V T  G    + +      ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMVLTEDGQLNEKTKEFTPQDKRTIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLATIRKISRELAHKLGAMPSRIEIAEAMEIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/46 (21%), Positives = 21/46 (45%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +       +   R  +DP+  YL  +G + LL+   EI +  +++ 
Sbjct: 2   AASATTSTEPQKRRGNDPISWYLSNIGRVPLLTPAEEIELGNQVQK 47


>gi|91227834|ref|ZP_01262007.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269965239|ref|ZP_06179373.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
 gi|91188344|gb|EAS74640.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269830225|gb|EEZ84452.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
          Length = 328

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 107/298 (35%), Positives = 174/298 (58%), Gaps = 3/298 (1%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +D      +    +   +        S+   +  +  I     ++  E    V   R+  
Sbjct: 23  IDNELERSSSTESKATAREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRAL 79

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 80  RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 139

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +
Sbjct: 140 YATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDI 199

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L 
Sbjct: 200 PVEDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLE 259

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 260 ELNPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQGL 317



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+    ++        +L  S+S  S    + +  A   + D  ++YL E+G   LL+ E
Sbjct: 10  VEEFAFDNASVKTIDNELERSSSTESKATAREEFDASSKSLDATQLYLGEIGFSPLLTAE 69

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 115


>gi|260424772|ref|ZP_05733235.2| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
 gi|260403136|gb|EEW96683.1| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
          Length = 394

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 130/261 (49%), Positives = 174/261 (66%), Gaps = 9/261 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR---------KGECEASIAKKEMVEANLRLVISV 459
           +R  ++       ++  +   +   +          + +  A+ AKKEM  ANLRLV+S+
Sbjct: 117 VRLYLRECGTTPLLTSEQEMKLAQTIEIGKMPEATDEQKRMAAEAKKEMANANLRLVVSI 176

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY  RG+ FLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++QAITRSIADQ+ TI
Sbjct: 177 AKKYPGRGMPFLDLIQEGNMGLLKAVDKFDYTKGYKFSTYATWWIRQAITRSIADQARTI 236

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVHM + I+K+ R  R    +  RE T EE+AK++   VE +R+  K  ++PISLETP
Sbjct: 237 RVPVHMVETINKMNRVGRHFLQEHGREATNEELAKEMETSVEKIREAKKAAQDPISLETP 296

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+++ SHLGDFIED+   SP D A     RE   ++L +LT RE+ V+ +R+GI   T 
Sbjct: 297 IGEKEDSHLGDFIEDQKTASPEDEAAATMRREQIHQLLETLTEREKGVIALRYGIDDGTQ 356

Query: 640 HTLEEVGKQFCVTRERIRQIE 660
            TLEEVGK F VTRERIRQIE
Sbjct: 357 RTLEEVGKYFGVTRERIRQIE 377



 Score = 66.4 bits (160), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/193 (19%), Positives = 68/193 (35%), Gaps = 33/193 (17%)

Query: 31  WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE---- 86
            K++       G +  +++  F     ++S+Q++     L   G+ ++  +D +DE    
Sbjct: 15  LKELQDKVNADGNIKYDDILLFTKEKSLTSKQLDSVFKALHEGGVEIIYEEDGKDEFRDG 74

Query: 87  --------EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                   E  ED    A               +      DPVR+YLRE G+  LL+ E 
Sbjct: 75  ESEEEFEDELLEDGDAEADVDEKEWEKGDGDISADPAGITDPVRLYLRECGTTPLLTSEQ 134

Query: 139 EIAIAKRIEAGRA------------MMMASLCESPLTFQALIIWR---------DELNDG 177
           E+ +A+ IE G+                  +  + L     I  +         D + +G
Sbjct: 135 EMKLAQTIEIGKMPEATDEQKRMAAEAKKEMANANLRLVVSIAKKYPGRGMPFLDLIQEG 194

Query: 178 TTLLREIIDLEAC 190
              L + +D    
Sbjct: 195 NMGLLKAVDKFDY 207


>gi|186680839|ref|YP_001864035.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186463291|gb|ACC79092.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 378

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 113/284 (39%), Positives = 187/284 (65%), Gaps = 4/284 (1%)

Query: 401 CEVDSILKIRNEI--KSISVETGISI-SEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
             ++ I +++  +  K     T + I SE       +     +  +AK++M+ +NLRLV+
Sbjct: 94  RFLEEIRELQAALNLKLGQEPTKLEIASELEMTEKQLESRLYQGRVAKRKMIRSNLRLVV 153

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTYA WW++QAITR+IA+ + 
Sbjct: 154 SIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWWIRQAITRAIANDAR 213

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ +K++K+ +  R +  K+ R PT  E+A+ L + V+ +R++ ++ ++ +SL 
Sbjct: 214 TIRLPIHIVEKLNKLKKAQRELKQKLCRNPTEGEMAEALDISVQQLRQLQQLRRQALSLN 273

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGM 636
             +G E+ + L D +ED++ +SP     +  +R+    VL   LTPRE+ V+ +R+G+  
Sbjct: 274 HRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTT 333

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ +L
Sbjct: 334 SEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKGWL 377



 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 4/97 (4%)

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST--DDPVR 122
           + +   +++    +D  D   +E     ++   S       +   + S    T  DD V 
Sbjct: 10  EILENAADIEEPSLDSLDAVADEEPPIVVENLESDERDGDDMAAARPSGYNKTEHDDAVG 69

Query: 123 MYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASL 157
            + +EM    LL  + E+ +A+R+        + A+L
Sbjct: 70  AFFKEMARYPLLKADEEVELARRVRFLEEIRELQAAL 106


>gi|269837876|ref|YP_003320104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269787139|gb|ACZ39282.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 341

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 115/258 (44%), Positives = 171/258 (66%), Gaps = 3/258 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  ++ I+    ++  E   +   +         A +  V +NLRLV+S+AK+Y  RGL
Sbjct: 72  IRLYLRDIAQAPLLTAEEEVELAKRIE---EGDVEALQRFVRSNLRLVVSIAKRYVGRGL 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEGN+GL++A +K+DW  GY+FSTYA WW++QAITR+IADQ  TIR+PVHM D 
Sbjct: 129 SLLDLIQEGNLGLIRAVQKYDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPVHMIDS 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I +  RT  +++ ++ R P  EE+A+ +++P E V + ++  +  ISLE PIG+++   L
Sbjct: 189 ITRYRRTVMQLTQELGRPPRAEEVAEAMSVPPEKVEQFIRAAQRTISLEKPIGEDEEGTL 248

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I D+ A SP + A++  L+     VL  LTPRE  VL++RFG+G  + HTL EVG+Q
Sbjct: 249 ADLIADEVARSPEEEAVETLLQRDVAEVLEELTPRERLVLQLRFGLGNGSPHTLSEVGQQ 308

Query: 649 FCVTRERIRQIEAKAIRK 666
             ++RER+RQIE++A+RK
Sbjct: 309 LDISRERVRQIESEALRK 326



 Score = 60.6 bits (145), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 1/92 (1%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           +++   A+       +          DP+R+YLR++    LL+ E E+ +AKRIE G   
Sbjct: 44  VEVEEDAAALDEDWDELLQHDPTLATDPIRLYLRDIAQAPLLTAEEEVELAKRIEEGDVE 103

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +     S L     I  R  +  G +LL  I
Sbjct: 104 ALQRFVRSNLRLVVSIAKRY-VGRGLSLLDLI 134


>gi|187928144|ref|YP_001898631.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12J]
 gi|187725034|gb|ACD26199.1| RNA polymerase, sigma 70 subunit, RpoD family [Ralstonia pickettii
           12J]
          Length = 378

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 106 VQHYLNRISIKPLLTPAEELHFSTLAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 163 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 222

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 283 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNYIEPATLEELA 342

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 343 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 373



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 35/155 (22%), Positives = 52/155 (33%), Gaps = 15/155 (9%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK----RKDSADR 115
           +E++E   A++ ++   V D  DL D   S D  D        +         RK     
Sbjct: 43  AEEIEVVDALVDDL--PVADSADLNDTSDSADESDEEEEEGEEAEEAAPEEDFRKVLQAE 100

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
              D V+ YL  +    LL+   E+  +   +AG       + E  L     I     LN
Sbjct: 101 LAADTVQHYLNRISIKPLLTPAEELHFSTLAKAGEFAARQVMIERNLRLVVSIAKGY-LN 159

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            G  LL  I         E   G  H  E    ++
Sbjct: 160 RGVPLLDLI--------EEGNLGLMHAIEKFDPER 186


>gi|309782329|ref|ZP_07677056.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
 gi|308918947|gb|EFP64617.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
          Length = 378

 Score =  188 bits (476), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 164/271 (60%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  ++ + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 106 VQHYLNRISIKPLLTPAEELHFSTLAKAGEF---AARQVMIERNLRLVVSIAKGYLNRGV 162

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 163 PLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 222

Query: 529 IHKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    E V+ VL + +   SL+TP   +  +
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGT 282

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  SP        L +     LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 283 SLLDFLSDEHGASPDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNYIEPATLEELA 342

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 343 AEMGLTRERVRQIQQEALVKLKRHFASQGVR 373



 Score = 40.6 bits (93), Expect = 0.93,   Method: Composition-based stats.
 Identities = 35/155 (22%), Positives = 52/155 (33%), Gaps = 15/155 (9%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK----RKDSADR 115
           +E++E   A++ ++   V D  DL D   S D  D        +         RK     
Sbjct: 43  AEEIEVVDALVDDL--PVADSADLNDTSDSADEPDEEEEEGEEAEEAPPEEDFRKVLQAE 100

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
              D V+ YL  +    LL+   E+  +   +AG       + E  L     I     LN
Sbjct: 101 LAADTVQHYLNRISIKPLLTPAEELHFSTLAKAGEFAARQVMIERNLRLVVSIAKGY-LN 159

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            G  LL  I         E   G  H  E    ++
Sbjct: 160 RGVPLLDLI--------EEGNLGLMHAIEKFDPER 186


>gi|91200070|emb|CAJ73113.1| similar to transcription initiation factor sigma 70 [Candidatus
           Kuenenia stuttgartiensis]
          Length = 491

 Score =  187 bits (475), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 124/271 (45%), Positives = 177/271 (65%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I  I     +   E + I+  +     E  +A+K   E NLRLV+S+AKKY  RG+ F 
Sbjct: 218 DINEIEALFAMPAKELKKIIFSINSIYNEYVMARKRFSEGNLRLVVSIAKKYRKRGMAFH 277

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN GLM+A +K+D+ +G+KFSTYA WW+KQAI R+  ++  TIRIPVHM D I+K
Sbjct: 278 DLIQEGNTGLMRAVDKYDYRMGFKFSTYATWWIKQAIIRATEEKVRTIRIPVHMMDVINK 337

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
               A+        +   E IA+    P+  + ++L+IT +PISLETPIG +  +   DF
Sbjct: 338 STYVAKAGQGSSAEKIQLEAIARDTNTPLPEIYRLLQITSQPISLETPIGSDGETMFEDF 397

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I+DK   +P+  A ++ L+E   +VL +L+ RE  ++++RFGI     H+LEE+GK+F +
Sbjct: 398 IQDKKIDAPIFLAQRSLLKEQIQKVLDTLSYREREIIKLRFGISDGYTHSLEEIGKRFNI 457

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TRERIRQIEA A+RKL+HP RS+KL  FL+G
Sbjct: 458 TRERIRQIEAIALRKLQHPVRSRKLEGFLEG 488



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 33/76 (43%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +  ++       D VR+YL EM  I LL+   EI +AK+I     ++   +       + 
Sbjct: 27  EWNQEEEKSRDYDSVRLYLNEMAKIPLLTPAEEIYLAKKIRVMSRLLHRKVLGFDYALEM 86

Query: 167 LIIWRDELNDGTTLLR 182
            I   + +   + L++
Sbjct: 87  YIRLLEGVESESELVQ 102


>gi|126696812|ref|YP_001091698.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126543855|gb|ABO18097.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 313

 Score =  187 bits (475), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 108/270 (40%), Positives = 174/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ + + T       +     +  ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMILTEDGQLNEKTNEFTTQQKRTIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDANERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 41.4 bits (95), Expect = 0.58,   Method: Composition-based stats.
 Identities = 11/43 (25%), Positives = 24/43 (55%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           L  + +   R ++DP+  YL+ +G + LL+   EI +  +++ 
Sbjct: 5   LPTQAEPPKRRSNDPISWYLQNIGRVPLLTPAEEIELGNQVQK 47


>gi|325971114|ref|YP_004247305.1| RNA polymerase, sigma 70 family subunit [Spirochaeta sp. Buddy]
 gi|324026352|gb|ADY13111.1| putative RNA polymerase, sigma 70 family subunit [Spirochaeta sp.
           Buddy]
          Length = 293

 Score =  187 bits (475), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 99/279 (35%), Positives = 177/279 (63%), Gaps = 6/279 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D    +   +K I+    ++  E   +    +K       A+K M+E+NLR V++VAKKY
Sbjct: 18  DDANILSMYLKEINQIPLLTPQEELVLAKRAQK---GDEFARKRMIESNLRFVVNVAKKY 74

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N+G+  +DLI EGNIGLM A EKFD   GY F +YA+WW++Q+I ++I ++S  +R+P+
Sbjct: 75  QNQGMPLVDLINEGNIGLMTALEKFDPDKGYHFISYAVWWIRQSIMKAINEKSRAVRLPL 134

Query: 524 HMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +  +++ ++ +  R +   +   +P+ EEI        + V  +L I+++ ISL+ P+  
Sbjct: 135 NRTNELLQMHKAQRSLMKDLSTDDPSMEEIGTLTGFDPKHVSNLLSISRDLISLDAPVFT 194

Query: 583 EDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           + + S++GDFIED++  +P  S + A+L+E    +LA+L+ +E  ++ +RFG+   T  +
Sbjct: 195 DGSASNIGDFIEDESQ-NPEQSLLDASLKEDVRSLLATLSDKERDIIELRFGLEGKTPMS 253

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L+E+G+ + +T+ERIRQIE KA+ +L++PS+SK + S++
Sbjct: 254 LKEIGELYNLTKERIRQIEKKALERLRNPSKSKMVESYI 292



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL+E+  I LL+ + E+ +AKR + G       + ES L F  ++    +  +    L 
Sbjct: 25  MYLKEINQIPLLTPQEELVLAKRAQKGDEFARKRMIESNLRF--VVNVAKKYQNQGMPLV 82

Query: 183 EIIDLEACIGPESKGGFFHGTEG 205
           ++I+ E  IG  +    F   +G
Sbjct: 83  DLIN-EGNIGLMTALEKFDPDKG 104


>gi|85813983|emb|CAD20831.2| sigma factor [Spinacia oleracea]
          Length = 575

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 93/249 (37%), Positives = 154/249 (61%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R+     +  K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD  
Sbjct: 325 RTLRRRLNHGTFCKDKMIKSNVRLVISIAKNYQGSGMNLQDLVQEGCRGLVRGAEKFDAS 384

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW+KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  ++P  EE
Sbjct: 385 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLLSENGKQPNNEE 444

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+   + ++ +  VL   K P SL+  IG        + I D  A +  D   +  +R+
Sbjct: 445 VAEATGLSMKRLTAVLMTPKAPRSLDQKIGFNMNLKPSEVIADPEAETAEDLLTKQFMRQ 504

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL +L+ RE++V+R RFG+      TL+E+G+   V+RERIRQIE+ A RKL++  
Sbjct: 505 DLEKVLDTLSSREKQVIRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLQNKK 564

Query: 672 RSKKLRSFL 680
           ++  L+ ++
Sbjct: 565 KTINLQQYM 573


>gi|89092114|ref|ZP_01165069.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
 gi|89083849|gb|EAR63066.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
          Length = 339

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 103/275 (37%), Positives = 162/275 (58%), Gaps = 3/275 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
              ++   +  +  I     +S  E  +   +          A+K M+E+NLRLV+ +A+
Sbjct: 60  NAKNLDATQLYLNEIGFSPLLSAEEEVYFSRLA---LKGDEAARKRMIESNLRLVVKIAR 116

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+
Sbjct: 117 RYINRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 176

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  +++  +R AR ++ K+  EP+PEEIA+ +  PVE V ++L + +   S++TP+G
Sbjct: 177 PIHVVKELNVYLRAARELAQKLDHEPSPEEIAELVDKPVENVERMLGLNERVSSVDTPMG 236

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            +    L D I D  +  P      +N+     R L +L  +   VL  RFG+      T
Sbjct: 237 KDSDKSLLDTIPDTVSSDPATLLQNSNISGNLDRWLDALPEKHAEVLSRRFGLRGYEMST 296

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LEEVGK+  +TRER+RQI+ +A+RKL+       L
Sbjct: 297 LEEVGKEIGLTRERVRQIQVEALRKLRDIVEKNGL 331



 Score = 45.2 bits (105), Expect = 0.035,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           KD  +    D  ++YL E+G   LLS E E+  ++    G       + ES L     I 
Sbjct: 56  KDLLNAKNLDATQLYLNEIGFSPLLSAEEEVYFSRLALKGDEAARKRMIESNLRLVVKIA 115

Query: 170 WRDELNDGTTLLREI 184
            R  +N G TLL  I
Sbjct: 116 RRY-INRGLTLLDLI 129


>gi|148271746|ref|YP_001221307.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147829676|emb|CAN00592.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 347

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 112/270 (41%), Positives = 169/270 (62%), Gaps = 11/270 (4%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +   T ++ +E R   ++ +    +   AK+ +V ANLRLV+S+AK+YT RGL FLDLIQ
Sbjct: 86  LDTRTDLTPAERREYQTLAQ----DGMRAKQHLVNANLRLVVSIAKRYTGRGLPFLDLIQ 141

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW+KQ+ITR +AD S TIRIPVH  + I+++   
Sbjct: 142 EGNMGLVRAVEKFDYQAGFKFSTYASWWIKQSITRGMADTSRTIRIPVHTVEHINRINAV 201

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFI 592
            R ++ ++ R+P+ EEIA++   PV  VR +L   +EP+SL+  +   G +  + + D I
Sbjct: 202 QRELAVELGRDPSMEEIARESDTPVTKVRYLLDRAQEPMSLQVLVGGSGGDGDTEMADLI 261

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED +   P+D   Q  +     R++  L  R+  V+RMRFG+      +L  V +Q  VT
Sbjct: 262 EDADVTQPIDVVTQQLMAAHVMRLIDGLAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVT 321

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RER+RQIE K + KL+ P     L +++ G
Sbjct: 322 RERVRQIEKKVLAKLRIPE----LETYIRG 347



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/70 (24%), Positives = 32/70 (45%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D   +   +    +      +   L +       ++ D V+ YLR++G + LL+ E E
Sbjct: 10  AADTTSDTELDQVESVRPVDPYADSDLPEPSLVTPGASTDAVKDYLRQIGRVPLLTAEQE 69

Query: 140 IAIAKRIEAG 149
           + +A+RIE G
Sbjct: 70  VTVARRIEVG 79


>gi|330995823|ref|ZP_08319720.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
 gi|329574553|gb|EGG56118.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
          Length = 286

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +RK      +A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK---GDRVALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+PEE+A +L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERRPSPEELADELEIPVDKISDTLKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++     + +  +L     R L++L+ RE+ +++M FGI  + + TLEE+G +
Sbjct: 195 LDVLVNDDSPMADRTLVNESLAREIDRALSTLSEREKEIIQMFFGIN-HQEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  ++SK L+S+L
Sbjct: 254 FNLTRERVRQIKEKAIRRLRQNTKSKLLKSYL 285



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI  G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRKGDRVALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|325269188|ref|ZP_08135807.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|324988417|gb|EGC20381.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
          Length = 287

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 168/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  ISI E   +   +RK       A + + +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEEMISIEEEVELAQRIRK---GDRKALERLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   R   + +R P+ +EIA+   +P + +   +K     +S++ P  D++ S L
Sbjct: 135 VNKINKILNRFEQENERRPSIDEIAQSTDLPEDKIADAMKANSRHVSVDAPFYDDEQSSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I + NA S     ++ +LRE   RVL  L  RE+ V+   FGI    + TLEE+G +
Sbjct: 195 LDVIPNDNAPSTDRGLVEESLREEIGRVLQILEDREKMVVEAYFGINQ-REMTLEEIGSK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI+ KAIR+L+  + SK L+++L
Sbjct: 254 YNLTRERVRQIKEKAIRRLRQQTNSKVLKAYL 285



 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  E++S E E+ +A+RI  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGHEEMISIEEEVELAQRIRKGDRKALERLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|332885662|gb|EGK05908.1| hypothetical protein HMPREF9456_02172 [Dysgonomonas mossii DSM
           22836]
          Length = 286

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   ++K       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQAIKK---GDRAALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R+P+ EE+A++L +PV+ +   LK++   IS++ P  + + + L
Sbjct: 135 LNKISKAFSKFEQENERKPSAEELAEQLDIPVDKIADSLKVSGRHISMDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + +A       I  +L++   R L++LT RE  +++M FGIG   + TLEE+G +
Sbjct: 195 LDVLVNDDAPIADRKLINESLQQEIERALSTLTERESEIIKMFFGIGY-QEMTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAI++L+  SRSK L+S+L
Sbjct: 254 FQLTRERVRQIKEKAIKRLRQNSRSKLLKSYL 285



 Score = 41.4 bits (95), Expect = 0.50,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+ I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQAIKKGDRAALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|295102137|emb|CBK99682.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 461

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 129/245 (52%), Positives = 179/245 (73%), Gaps = 2/245 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            ++E R     + K   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+
Sbjct: 205 PLTEERR--QELLKTRRDGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 262

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KAAEKFD   G++FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +
Sbjct: 263 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQ 322

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EPTPEE+AK + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  
Sbjct: 323 NGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGK 382

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A +A + +   + L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAK
Sbjct: 383 AADRAMVAQQINQALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAK 442

Query: 663 AIRKL 667
           AIRKL
Sbjct: 443 AIRKL 447



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 53/345 (15%), Positives = 117/345 (33%), Gaps = 44/345 (12%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K+++      G ++ +E         +    +E    +L   GI +++ +   D    
Sbjct: 4   TLKELLTKG--EGTLSAQEAKTLAAQCRMD---VETLYTLLEERGIKIIEDEADADVNLD 58

Query: 90  EDSLDLASSASNSSVFL----------------QKRKDSADRSTDDPVRMYLREMGSIEL 133
            DS+      + ++                      K + D   DDPV+ YL+++G I L
Sbjct: 59  VDSIIAEVENAENNSDELSLGGDDEEEAAEENPADLKAAMDELLDDPVKNYLKQIGQIPL 118

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           LS E E+ ++KRI AG                 L   R + +        I    A    
Sbjct: 119 LSAEQEVDLSKRIHAGAEAA-----------HILQADRQKYSAPEY----IKKNSARFSF 163

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           E        TE    +  E  S++ E    +E   +      ++++ R ++     +  N
Sbjct: 164 EEDENSRSYTEDIDEEGSEKPSEDAEEKAAEEEAMEAVENGPLTEERRQELLKTRRDGLN 223

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
             R+L E       +++          +  LD I E    L    +     +    S+  
Sbjct: 224 ARRSLSEANLRLVVSIAKKHV---GHNLAFLDLIQEGNIGLIKAAEKFDCDRGFRFSTYA 280

Query: 314 C----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                + +   +     ++ +    ++ +  ++   + ++++  G
Sbjct: 281 TWWIRQAITRAIADQARTIRIPVHMVETI-NRMRQATNQLVYQNG 324


>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa]
 gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa]
          Length = 564

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 101/247 (40%), Positives = 155/247 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK    A + K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++  EKFD   G
Sbjct: 316 LRKRLNYAILCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGVEKFDASKG 375

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QA+ RS++DQS TIR+P HM D  ++V    ++  ++  R P  +E+A
Sbjct: 376 FKFSTYAHWWIRQAVRRSLSDQSRTIRLPFHMVDATYRVKEARKQFYSENGRHPDDKEVA 435

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  +G      L +   D  A +  D  ++  +++  
Sbjct: 436 EATGLSMKRLSAVLLTPKAPRSLDQKMGFNMDLKLSEVTADPEAETAEDLLMKEFMKKDL 495

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RVL SL+PRE +V+R RFG+      TL+E+G+   V+RERIRQIE  A RKLK+ +R+
Sbjct: 496 ERVLESLSPRENQVIRWRFGMEDGRMKTLQEIGELMGVSRERIRQIELSAFRKLKNKNRT 555

Query: 674 KKLRSFL 680
           K+LR +L
Sbjct: 556 KQLRQYL 562


>gi|77359643|ref|YP_339218.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874554|emb|CAI85775.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 324

 Score =  187 bits (475), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 108/277 (38%), Positives = 168/277 (60%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     +S  E    V   RK       ++K M+E+NLRLV+ +
Sbjct: 41  EEVTKNLDATQLYLGEIGFSPLLSAEEE---VFFSRKSLKGCEASRKRMIESNLRLVVKI 97

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 98  ARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 157

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR ++ K+  EPT EEIA  L  PVE V K+L++ ++  S++ P
Sbjct: 158 RLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAACLDKPVEDVTKMLRLNEKIASVDMP 217

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG E+ + L D I D N V P       ++ +     L  L P++  VL  RFG+     
Sbjct: 218 IGGENDTALLDIIADDNNVGPEGEVQNNDMNKHIVDWLGELNPKQREVLARRFGLLGYEP 277

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLE+VG++  +TRER+RQI+ +A+R+LK   + + L
Sbjct: 278 STLEDVGREIGLTRERVRQIQVEALRRLKDILQQEGL 314



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/109 (22%), Positives = 45/109 (41%), Gaps = 2/109 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VD + L D +  E ++D  S+    +V              D  ++YL E+G   LLS E
Sbjct: 7   VDKNTLVDNKLDETAVDDDSTPLLEAVDDDVFVKEEVTKNLDATQLYLGEIGFSPLLSAE 66

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E+  +++   G       + ES L    ++      N+    L ++I+
Sbjct: 67  EEVFFSRKSLKGCEASRKRMIESNLRL--VVKIARRYNNRGLALLDLIE 113


>gi|254432880|ref|ZP_05046583.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
 gi|197627333|gb|EDY39892.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
          Length = 331

 Score =  187 bits (474), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 106/281 (37%), Positives = 167/281 (59%), Gaps = 19/281 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKK------------------EMVEANL 453
            + SI  E  ++ +E   + + V+        AK                    M++ANL
Sbjct: 46  YLASIGREPLLTPAEEIELGNQVQAMMQLLEAAKPSYSDHEKKLLRIGKRSKQRMMKANL 105

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA
Sbjct: 106 RLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIA 165

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            QS TIR+PVH+ +++  + + +  +++K+   P+  EIA+ + MP++ +  +L+     
Sbjct: 166 CQSRTIRLPVHLSERLSAIRKVSLDLAHKLGAMPSRHEIAEAMDMPLDELDGLLRQALTT 225

Query: 574 ISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            SL+ P+  ++  S LGD I D +   PLD   +    E     +  L+ +E  VL++RF
Sbjct: 226 SSLDAPVNGDEGRSFLGDLIADSSEEEPLDRVERGLNHEQLDHWMNHLSEQERHVLQLRF 285

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           G+     HTL E+G+Q  V+RER+RQ+E KA+RKL++ +R 
Sbjct: 286 GLEGRDRHTLAEIGRQLDVSRERVRQVELKALRKLRNLTRR 326


>gi|323493642|ref|ZP_08098763.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
 gi|323312165|gb|EGA65308.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
          Length = 326

 Score =  187 bits (474), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 108/292 (36%), Positives = 172/292 (58%), Gaps = 3/292 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
              K  P  + K        S+   +  +  I     ++  E    V   R+       A
Sbjct: 27  ESTKPTPTEDVKEEFDASTKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEAA 83

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW+
Sbjct: 84  RKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWI 143

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V 
Sbjct: 144 RQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDVS 203

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P++
Sbjct: 204 KMLRLNERISSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDDDIKNSLIHWLDELNPKQ 263

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 264 KEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQGL 315



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/104 (26%), Positives = 41/104 (39%), Gaps = 1/104 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +  E  E + D+     S   +     K +  A   + D  ++YL E+G   LL+ E E+
Sbjct: 11  EQFEVGEETMDTFQATESTKPTPTEDVKEEFDASTKSLDATQLYLGEIGFSPLLTAEEEV 70

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 71  LYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 113


>gi|254422659|ref|ZP_05036377.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190148|gb|EDX85112.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 298

 Score =  187 bits (474), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 111/268 (41%), Positives = 172/268 (64%), Gaps = 10/268 (3%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             +   GIS +E   IV+           AK  MVEANLRLV+SVAKKY  R +  LDLI
Sbjct: 41  EWAAAGGISEAELAAIVT-------AGEQAKHRMVEANLRLVVSVAKKYIKRNVDLLDLI 93

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +
Sbjct: 94  QEGTIGMQRGVEKFDPSKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKK 153

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R+ + +  R PT  EIA+     ++ VR+ L  +++P+SL+  +GD   + LGD +ED
Sbjct: 154 AQRQFTQQHGRTPTASEIAQATGFTIKQVREYLDRSRQPLSLDLKVGDNQDTQLGDLLED 213

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +  +P D A  ++L+    R++A LTP++++V+ +RFG+    + TL ++G    ++RE
Sbjct: 214 -DGQTPDDYATASSLKSDLKRIMADLTPQQQQVIALRFGLEDGKNMTLAKIGAMLDISRE 272

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           R+RQIE +A+ KL+   R   +R +L G
Sbjct: 273 RVRQIEREALTKLRK--RQSDMREYLAG 298


>gi|163802977|ref|ZP_02196864.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
 gi|159173267|gb|EDP58095.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
          Length = 328

 Score =  187 bits (474), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 106/295 (35%), Positives = 174/295 (58%), Gaps = 3/295 (1%)

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           + +    +  +   +        S+   +  +  I     ++  E    V   R+     
Sbjct: 26  NELVKTSNKSKTATREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGD 82

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA 
Sbjct: 83  EAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 142

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE
Sbjct: 143 WWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVE 202

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L 
Sbjct: 203 DVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLILWLEELN 262

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 263 PKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 317



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 29/107 (27%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V+  D +D      + +     SN S    + +  A   + D  ++YL E+G   LL+ E
Sbjct: 10  VEEFDYDDASMEGIASNELVKTSNKSKTATREEFDASSKSLDATQLYLGEIGFSPLLTAE 69

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 115


>gi|172036788|ref|YP_001803289.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
 gi|171698242|gb|ACB51223.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
          Length = 420

 Score =  187 bits (474), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 115/293 (39%), Positives = 173/293 (59%), Gaps = 9/293 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKS-ISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
              +W       V  + +I  + K   +    I I E   I             +K EM+
Sbjct: 134 SWEKWAKASEVSVFELKEILAQGKQQWATLANIDIQELEEIQK-------SGIRSKDEMI 186

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +ANLRLV+SVAKKY +RGL+ LDLIQEG +GL KA EKFD   GY+FSTYA WW++Q IT
Sbjct: 187 KANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAYWWIRQGIT 246

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IA QS  IR+PVH+ +K++K+ +  R++S    R  T EEI K+L M    VR+V   
Sbjct: 247 RAIATQSRIIRLPVHVTEKLNKIKQVQRQISQAKGRNATLEEIGKELNMTPTQVREVFMK 306

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
               +SLE  +G E  + L D +E ++ +SP ++    +LR     +L  LT RE+ V++
Sbjct: 307 IPRSVSLEIKVGKEKDTELVDLLESED-ISPEENLAIESLRRDIGILLEDLTEREQEVIK 365

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +R+G      ++L ++G+   ++RER+RQIEAKA++KL+ P R  ++R + + 
Sbjct: 366 LRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQKLRQPRRRNQIRDYFES 418



 Score = 45.2 bits (105), Expect = 0.040,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 36/72 (50%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D E  E + +  D        S+   +   S +R T D VR+YL+++G + LL +E E
Sbjct: 25  DSDTESNEITSELGDDLLELELQSIDFTETDPSTNRVTTDLVRLYLQDIGRVPLLKKEEE 84

Query: 140 IAIAKRIEAGRA 151
           ++ +K+++    
Sbjct: 85  VSKSKQVQRYVE 96


>gi|313886597|ref|ZP_07820310.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332300881|ref|YP_004442802.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
 gi|312923953|gb|EFR34749.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332177944|gb|AEE13634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 286

 Score =  187 bits (474), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 166/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I   + IS  E   +   + +G      A  ++VEANLR V+SVAK+Y N+GL
Sbjct: 18  LDRYLQEIGRTSLISPEEEVELAREIHRGN---RRALNKLVEANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIG++KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGL 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             K+ +   +      R P+P+EIA +L +P + +R+ LK+  +  SL+ P  + + +++
Sbjct: 135 QQKMNKAIVKFEQLNGRRPSPQEIAAELELPEDKIREALKVQGKHQSLDAPFVEGEDNNM 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + +++  S   S I  +L     R+L  L  RE  VLR  FGIG     TLEE+G++
Sbjct: 195 LDVLVNEDTPSTDSSLINESLSAEIDRILDQLGDREAEVLRCFFGIGCPE-MTLEEIGER 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++RER+RQI+ KAIR+LK   R + L+++L
Sbjct: 254 TKLSRERVRQIKEKAIRRLKQSDRCEYLKAYL 285



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G   L+S E E+ +A+ I  G    +  L E+ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRTSLISPEEEVELAREIHRGNRRALNKLVEANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  IG       F  T G  
Sbjct: 79  LIN-EGNIGMIKAAEKFDETRGFK 101


>gi|86607249|ref|YP_476012.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
 gi|86555791|gb|ABD00749.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
          Length = 361

 Score =  187 bits (474), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 117/314 (37%), Positives = 182/314 (57%), Gaps = 12/314 (3%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI------KSISVETGISISEFRHIVS 432
           L+   V +  +      +   A E++   KI+ ++      +    + G   S+     +
Sbjct: 47  LNEDAVDHYLNTIGRVPRIDHAEEIELSRKIQQKLLIDQARREWRQQWGQDPSDEELAAA 106

Query: 433 M------VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           +      +R    +   A+++++ ANLRLV+SVAKKY NRG+ FLDLIQEGN+GL++A E
Sbjct: 107 LQIPVSTLRSRIRQGEQAQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNMGLIRATE 166

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF+   G++FSTYA WW++Q ITR IA+Q+ TIR+PVHM DK+  + RT R +     R 
Sbjct: 167 KFNAERGFRFSTYAHWWIRQGITRCIANQARTIRLPVHMVDKVRLLKRTNRELMKARGRR 226

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E+A+ L + V+ +R + +    P+SL+ P+G E  S LGD + D+    P +  + 
Sbjct: 227 PTEAELAEALGIKVKKLRMIQQAAALPLSLDVPVGQEGESRLGDLLPDERQEQPFEEILV 286

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR+     + +L P E +VL +R+G+      TL EVG  F +TRERIRQIE  A+RK
Sbjct: 287 QSLRQDVRSAMQALKPIERQVLELRYGLDGQRARTLREVGDHFNLTRERIRQIERDALRK 346

Query: 667 LKHPSRSKKLRSFL 680
           L+    S+ L  ++
Sbjct: 347 LRLGHPSRALAQYI 360


>gi|218710550|ref|YP_002418171.1| RNA polymerase sigma factor RpoS [Vibrio splendidus LGP32]
 gi|218323569|emb|CAV19793.1| RNA polymerase sigma factor rpoS (Sigma-38 factor) [Vibrio
           splendidus LGP32]
          Length = 335

 Score =  187 bits (474), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 110/313 (35%), Positives = 178/313 (56%), Gaps = 3/313 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + ++ F       E +    +      + E K        S+   +  +  I     ++
Sbjct: 15  AVTKEEFDLSQATTEQEALGKAKRTVTKKTEAKEETEVTSKSLDATQLYLGEIGFSPLLT 74

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++
Sbjct: 75  AEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIR 131

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+
Sbjct: 132 AVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKL 191

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EPT EEIA KL  PV  V K+L++ +   S++TPIG +    L D I D N   P  S
Sbjct: 192 DHEPTAEEIASKLDKPVGDVSKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVS 251

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              ++++ +    L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + 
Sbjct: 252 TQDSDIKNSLIFWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEG 311

Query: 664 IRKLKHPSRSKKL 676
           +R+L+     + L
Sbjct: 312 LRRLREILIKQGL 324



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/108 (23%), Positives = 40/108 (37%), Gaps = 1/108 (0%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V   +    +  +E      +  + +     K +      + D  ++YL E+G   LL+ 
Sbjct: 16  VTKEEFDLSQATTEQEALGKAKRTVTKKTEAKEETEVTSKSLDATQLYLGEIGFSPLLTA 75

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 122


>gi|254527154|ref|ZP_05139206.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538578|gb|EEE41031.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 313

 Score =  187 bits (474), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 109/270 (40%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ + + T  G    +     +  ++       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQKMMILTEDGQLNEKINEFTTQQKRTIKIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +R +++K+   P+  EIA+ + + VE +  VL+      SL+ P+  +D
Sbjct: 159 LSERLASIRKVSRDLAHKLGAMPSRIEIAEAMEIDVEELDSVLRQALSTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D N   PLD   Q   +E   + L+ L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSNNEEPLDQVEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDANERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKALRKLRNLTRK 308



 Score = 40.6 bits (93), Expect = 0.84,   Method: Composition-based stats.
 Identities = 11/43 (25%), Positives = 24/43 (55%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           L  + +   R ++DP+  YL+ +G + LL+   EI +  +++ 
Sbjct: 5   LPTKAEQPKRRSNDPISWYLQNIGRVPLLTPAEEIELGNQVQK 47


>gi|34540402|ref|NP_904881.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
 gi|34396715|gb|AAQ65780.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
          Length = 287

 Score =  187 bits (474), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 171/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +++       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLISVEEEVELAQAIKR---GDRKALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGT 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+++  ++   + +R P+  E+AK+L +  + +   +K++   IS++ P  + + + L
Sbjct: 135 LNKIIKAQQKFEQENERRPSSAELAKELDIAEDKIADTMKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + +++  +   S I  +L     R L++LT RE  ++++ FGI    + TLEE+G +
Sbjct: 195 LDVLVNEDTPNTDKSLINESLAVEIERALSTLTEREAEIVKLFFGIAGCQEMTLEEIGDK 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  ++ K L+ +L
Sbjct: 255 FGLTRERVRQIKEKAIRRLRQSNKCKNLKGYL 286



 Score = 41.4 bits (95), Expect = 0.58,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S E E+ +A+ I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLISVEEEVELAQAIKRGDRKALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|300781025|ref|ZP_07090879.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
 gi|300532732|gb|EFK53793.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
          Length = 330

 Score =  187 bits (474), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 102/248 (41%), Positives = 169/248 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    +   A+  ++EANLRLV+S+AK+YT RG+  LDLIQEGN+GL++A EKFD+ 
Sbjct: 81  RDLKILAKQGRKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYS 140

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITR +ADQS TIR+PVH+ ++++K+ R  R M   + REP+ EE
Sbjct: 141 KGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIRREMYQSLGREPSNEE 200

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A    D+ +     +
Sbjct: 201 LAEESGIDESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEAADAEDAVVSVLRHD 260

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  L  RE+ V+R+R+G+      TL+++G++F ++RER+RQIE + + KL+   
Sbjct: 261 DIHDIINGLEQREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMSKLRVGE 320

Query: 672 RSKKLRSF 679
           R+ +LR +
Sbjct: 321 RADRLRDY 328



 Score = 44.1 bits (102), Expect = 0.085,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
                     +R  + D  + D VR+YL  +G   LL+ E E+ +A++IE G 
Sbjct: 10  DEKEEVDRGSRRNQTNDNPSADLVRVYLNGIGKTALLNAEEEVELAQQIEVGL 62


>gi|85057387|ref|YP_456303.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789492|gb|ABC65224.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 465

 Score =  187 bits (474), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 208/324 (64%), Gaps = 13/324 (4%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL-----KIRNEI-KSIS 417
            I ++   + H   ++D     Y K+  +    +    +  SIL     + + ++ K  +
Sbjct: 140 KISKEEISKIHSDIKMDDSVRMYLKEIGQIPLLSLAEEQKKSILVFLGKQAKQKLAKHKT 199

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            E  +S  + +     +++    A  AK  +VE+N RLV+S+AK+Y  RG+ FLDLIQEG
Sbjct: 200 KEIELSEDQLQEAHDQIKQ----ARRAKDILVESNYRLVVSIAKRYIGRGILFLDLIQEG 255

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLM+A +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVH+ + I+K+    R
Sbjct: 256 NMGLMRAVDKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHIVETINKMALCTR 315

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDK 595
           +++ K+K++PT EE+A K+ +  E +R +  I K+PISLE P    +ED + LGDFI D 
Sbjct: 316 KLTQKLKKKPTVEELADKMNISAEKIRSIQYIEKKPISLEAPARENEEDETSLGDFISDP 375

Query: 596 NAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           N +SP +  ++   ++    VL  +LT REE+VL+MR+G+     HTLEEVG  F VTRE
Sbjct: 376 NILSPHEYMMKEVTQKLLDEVLENTLTEREEKVLKMRYGLLDGKTHTLEEVGTLFGVTRE 435

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRS 678
           RIRQIE+KA+R+L+ P++  KL+S
Sbjct: 436 RIRQIESKALRRLRTPAKQSKLKS 459



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/129 (21%), Positives = 47/129 (36%), Gaps = 10/129 (7%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
            +    +  +D+   + +  I+       ED    E   +L           +  K  +D
Sbjct: 99  DENKDEDNTQDSEEDIQDFDIS------EEDLISDEKITELEEDEDEKISKEEISKIHSD 152

Query: 115 RSTDDPVRMYLREMGSIELLSREGE----IAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
              DD VRMYL+E+G I LLS   E    I +    +A + +      E  L+   L   
Sbjct: 153 IKMDDSVRMYLKEIGQIPLLSLAEEQKKSILVFLGKQAKQKLAKHKTKEIELSEDQLQEA 212

Query: 171 RDELNDGTT 179
            D++     
Sbjct: 213 HDQIKQARR 221


>gi|260878982|ref|ZP_05891337.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|260895455|ref|ZP_05903951.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|157674653|gb|ABV60415.1| RpoS [Vibrio parahaemolyticus]
 gi|308088215|gb|EFO37910.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|308090442|gb|EFO40137.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|328474140|gb|EGF44945.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 10329]
          Length = 329

 Score =  187 bits (474), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 112/296 (37%), Positives = 175/296 (59%), Gaps = 7/296 (2%)

Query: 385 SYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              K     E K  V  E D    S+   +  +  I     ++  E    V   R+    
Sbjct: 26  ELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRG 82

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 83  DEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 142

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV
Sbjct: 143 TWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPV 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L
Sbjct: 203 EDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEEL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 263 NPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 318



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + +     E + D+    SS++       + +  A   + D  ++YL E+G   LL+
Sbjct: 9   KVEEFEYDNASETTIDNELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLT 68

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 69  AEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 116


>gi|158969744|gb|ABW86844.1| RpoS [Vibrio alginolyticus]
          Length = 330

 Score =  186 bits (473), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 105/298 (35%), Positives = 175/298 (58%), Gaps = 1/298 (0%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +D      +    +   +        S+   +  +  I     + ++    ++   R+  
Sbjct: 23  IDNELERSSSTESKATAREEFDASSKSLDATQLYLGEIGFSPLLILTAEEEVL-YARRAL 81

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FST
Sbjct: 82  RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFST 141

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +
Sbjct: 142 YATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDI 201

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L 
Sbjct: 202 PVEDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLE 261

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 262 ELNPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQGL 319



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 43/109 (39%), Gaps = 3/109 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL--S 135
           V+    ++        +L  S+S  S    + +  A   + D  ++YL E+G   LL  +
Sbjct: 10  VEEFAFDNASVKTIDNELERSSSTESKATAREEFDASSKSLDATQLYLGEIGFSPLLILT 69

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  AEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 117


>gi|72382695|ref|YP_292050.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|124026414|ref|YP_001015529.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|72002545|gb|AAZ58347.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|123961482|gb|ABM76265.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 313

 Score =  186 bits (473), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 107/270 (39%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T  G    + +   S  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQTLMSLTEDGQIKEQSKEFTSHQRRLIRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + + +E +  +L+      SL+ P+  ++
Sbjct: 159 LSERLATIRKVSLDLAHKLGAMPSRIEIAEAMEIELEELDSILRQALTTSSLDAPVNGDE 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q   +E   R L+ L+ +E+ V+R+RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADGSGEEPLDKVEQKIHQEQLGRWLSHLSEQEQHVIRLRFGLEGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLLQVSRERVRQVELKALRKLRNLTRK 308



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             K  +S  R + DP+  YL  +G + LL+   EI +  +++ 
Sbjct: 5   APKPAESQKRRSSDPISWYLSSIGRVPLLTPAEEIELGNQVQT 47


>gi|33862619|ref|NP_894179.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33634535|emb|CAE20521.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 313

 Score =  186 bits (473), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 108/270 (40%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++++   T  G    + +   +  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQTMMSLTQDGSVAPDDKEFTTHQRRMIRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  EIA+ + +PV+ +  +L+      SL+ P+  E+
Sbjct: 159 LSERLTTIRKVSLDLAHKLGAIPSRSEIAEAMDIPVDELDSLLRQALTTSSLDAPVNGEE 218

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q    E   R L+ L+ +E+ VL++RFG+  +  HTL 
Sbjct: 219 RRSFLGDLIADSSLGEPLDKVEQRIHHEQLGRWLSHLSEQEQHVLKLRFGLETHDRHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 279 EIGRLMEVSRERVRQVELKALRKLRNLTRR 308



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 22/44 (50%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
              K  ++  R + DPV  YL  +G I LL+   EI +  +++ 
Sbjct: 4   AAPKSAETQRRRSSDPVSWYLTTIGRIPLLTPAEEIELGNQVQT 47


>gi|113477482|ref|YP_723543.1| RNA polymerase sigma factor SigD [Trichodesmium erythraeum IMS101]
 gi|110168530|gb|ABG53070.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 319

 Score =  186 bits (473), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 106/264 (40%), Positives = 174/264 (65%), Gaps = 4/264 (1%)

Query: 418 VETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             T +  +E + +    +++   E   AK++MVEANLRLV+SVAKKY  R +  LDLIQE
Sbjct: 57  EPTLLEWAEAKELSKSELQRIIREGERAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQE 116

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  
Sbjct: 117 GTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKVQ 176

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R+++ ++ R  T  EIA++L +  + +R+ L+  + P+SL+  +GD   + LGD +ED  
Sbjct: 177 RQLTQQLGRSATTGEIAEELGLTPKQIRECLERARLPLSLDLRVGDNQDTELGDLLEDTG 236

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A SP D A+Q+++R     ++  LTP++++VL +RFG+      TL ++G    ++RER+
Sbjct: 237 A-SPEDYALQSSMRTDLESIMVDLTPQQKQVLALRFGLEDGQTMTLSKIGAHLNISRERV 295

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQIE +A+ KL+   R + +  +L
Sbjct: 296 RQIEREALSKLRK--RKQDMNDYL 317



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCESPLTFQALIIWRDE 173
           S  D V  YLRE+G + LLS E EI   K+++          +L E+      L+ W + 
Sbjct: 7   SDIDSVCTYLREIGRVPLLSHEEEILYGKQVQRLTALQEFNQTLAEALGREPTLLEWAEA 66

Query: 174 LNDGTTLLREII 185
                + L+ II
Sbjct: 67  KELSKSELQRII 78


>gi|257064907|ref|YP_003144579.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256792560|gb|ACV23230.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 314

 Score =  186 bits (473), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 114/240 (47%), Positives = 169/240 (70%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     + + +     AK ++V ANLRLV+S+AKKY  RGL  LDL+QEGN+GL++A EK
Sbjct: 64  RRECRKLLRVQRAGQEAKDKLVAANLRLVVSIAKKYRGRGLPLLDLVQEGNLGLIRAVEK 123

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+K STYA WW++QA+TR+IAD++ TIR+PVH+   ++KVVR    ++++++R+P
Sbjct: 124 FDYTKGFKLSTYATWWIRQAVTRAIADKARTIRLPVHVVGLMNKVVRVQHELADELERDP 183

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +P EIA +L +  + V ++LK+  EP+SLETP+GD+ TS +GDFIED+N+    D+A +A
Sbjct: 184 SPAEIADRLGISEQCVVELLKLGSEPLSLETPVGDDKTSEIGDFIEDRNSEDAFDAAAEA 243

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR+     L+ L  RE +++ +RFGI      TL ++G Q  VTRERIRQIE+K +  L
Sbjct: 244 MLRDDVASALSRLPERERKIIELRFGIVDGEPRTLAQIGDQLGVTRERIRQIESKTLGDL 303



 Score = 45.2 bits (105), Expect = 0.042,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           D +RMYLR++G ++LL+   E+ +AK+ + G     A+L +  
Sbjct: 15  DSIRMYLRDIGKVDLLTPAEEVELAKKYQTGL-AAEAALAQMN 56


>gi|113477826|ref|YP_723887.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110168874|gb|ABG53414.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 384

 Score =  186 bits (473), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 105/251 (41%), Positives = 166/251 (66%), Gaps = 1/251 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S +     +   AK+ M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +AAEKFD  
Sbjct: 132 SQLDHRLHQCRTAKRRMISSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKFDPD 191

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q ITR+IA+Q  TIR+PVH+ ++I+K+ R  R +   + R P   E
Sbjct: 192 KGYKFSTYAYWWIRQGITRTIANQGRTIRLPVHVVEQINKLRRVYRDLRRSLNRIPNDTE 251

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA++L + +  +R + +I ++ +SL   +G ++ + L DF+ED    +P        +R+
Sbjct: 252 IAQELEISLPQLRNLQQIRRKTLSLNHRLGTDENTELLDFLEDNENSTPEAQMNDMMMRQ 311

Query: 612 TTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL   L+ RE+ V+ +R+G+     HTL+EV +   ++RER+RQI+AKA+RKL+ P
Sbjct: 312 DILEVLNHVLSNREQDVISLRYGLITGEPHTLDEVSRMINLSRERVRQIQAKAMRKLRRP 371

Query: 671 SRSKKLRSFLD 681
             +++L+ +L+
Sbjct: 372 QVAERLKGWLN 382


>gi|318040855|ref|ZP_07972811.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 321

 Score =  186 bits (472), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 106/283 (37%), Positives = 162/283 (57%), Gaps = 16/283 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRK---------------GECEASIAKK 446
             DSI    + I  + + T     E  H V ++++                      A+ 
Sbjct: 30  SADSIGWYLSNIGRVPLLTAAEEIELAHHVQLMKQLQELPSDQLTPRQKHQIRMGCRARD 89

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q
Sbjct: 90  RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 149

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P   E+A  + M  E +  +
Sbjct: 150 GMTRAIDNSARTIRLPIHVSEKLSKMRRITRELSHRFGRQPNRLELAHAMGMQPEELEDL 209

Query: 567 LKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  +    SL+     +D  S LG+ I D N+   +DS  +   +E     L+ L  RE 
Sbjct: 210 ISQSAPCASLDAHARGDDDRSTLGELIADPNSNESMDSMDRNLQKEHLGTWLSQLNERER 269

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R++ +RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 270 RIIELRFGLEGQEPLTLAEIGRQINVSRERVRQLEAKAILKLR 312



 Score = 37.5 bits (85), Expect = 7.9,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++   +  +SN S           R + D +  YL  +G + LL+   EI +A  + 
Sbjct: 1   MDANNSTASGPSSNRSTPRYGASRQGGRLSADSIGWYLSNIGRVPLLTAAEEIELAHHV- 59

Query: 148 AGRAMMMASLCESP 161
                +M  L E P
Sbjct: 60  ----QLMKQLQELP 69


>gi|313112817|ref|ZP_07798464.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624887|gb|EFQ08195.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 458

 Score =  186 bits (472), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 132/247 (53%), Positives = 180/247 (72%), Gaps = 4/247 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+KAAEKFD   G++
Sbjct: 213 KTRRDGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGFR 272

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +   EPTPEE+AK 
Sbjct: 273 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGHEPTPEELAKA 332

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  +A +A + +    
Sbjct: 333 MDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGKAADRAMVAQQINL 392

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAKAIRKL     S+K
Sbjct: 393 ALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRKL----HSRK 448

Query: 676 LRSFLDG 682
             S L+G
Sbjct: 449 CLSLLNG 455



 Score = 58.3 bits (139), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 52/342 (15%), Positives = 120/342 (35%), Gaps = 41/342 (11%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K+++      G ++ +E  A      +     E    +L   GI V++ D     +  
Sbjct: 4   TLKELLTKG--EGTISAKEAKALAAQCRMDE---ETLYTLLEERGIKVLEEDAEPTLDVD 58

Query: 90  EDSLDLASSASNSSVFL-------------QKRKDSADRSTDDPVRMYLREMGSIELLSR 136
               ++ ++ +N+                    K + D   DDPV+ YL+++G I LLS 
Sbjct: 59  SIMAEVENAENNNDDMGISEDEEEQSEENPADLKAAMDELLDDPVKNYLKQIGQIPLLSA 118

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E E+ +++RI AG                 ++    +   G   +++     A    E  
Sbjct: 119 EQEVELSRRIHAGAEAA------------HILQADRQKYGGPEYIKK---NSARFSFEED 163

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                 TE    +  E  S++ E    +E   +      +S + R+++     +  N  R
Sbjct: 164 ENSRSYTEDLDEEGNEKPSEDAEEKAAEEEAMEAVENGPLSDEKRAELLKTRRDGLNARR 223

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-- 314
           +L E       +++          +  LD I E    L    +     +    S+     
Sbjct: 224 SLSEANLRLVVSIAKKHV---GHNLAFLDLIQEGNIGLIKAAEKFDCDRGFRFSTYATWW 280

Query: 315 --KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             + +   +     ++ +    ++ +  ++   + ++++  G
Sbjct: 281 IRQAITRAIADQARTIRIPVHMVETI-NRMRQATNQLVYQNG 321


>gi|269123266|ref|YP_003305843.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
 gi|268314592|gb|ACZ00966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
          Length = 379

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 149/372 (40%), Positives = 230/372 (61%), Gaps = 12/372 (3%)

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           K + + K++  + +  +   + +Q +I+    +L +++  I++      ++A     K++
Sbjct: 17  KIAKEEKIISREEINKLMKNNFSQDKIEATFFKLQELNVEIVN------KIADKNKSKKE 70

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
             +ER++  EL+ +      +    E    V+   D    I+  ++ I     +   E  
Sbjct: 71  --IERNKKEELEINIDEKEVEALLNEDLTTVSESSDVDEPIKMYLREIGQIPLLKSEEEF 128

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +         AK++++E+NLRLV+S+AKK+TNRGL+ LDLIQEGNIGLMKA EKF
Sbjct: 129 ELARRI---GEGDERAKQQLMESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKF 185

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +   G+KFSTYA WW++QAITR+IADQ  TIRIPVHM + I+K+ + +R    +  +EPT
Sbjct: 186 ESDKGFKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKASRIHLQETGKEPT 245

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            + +A+ + MPVE V+ +L++ ++PISLETP+G ED S LGDF+ED   ++P ++ +++ 
Sbjct: 246 DDYLAEIVEMPVEKVKNILEMNQDPISLETPVGSEDDSELGDFVEDDKFLNPHEATVRSV 305

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+E    VL   L  REE+VLR+R+G+      TLEEVGK F VTRERIRQIE KAI KL
Sbjct: 306 LKEKLNDVLRKELNEREEQVLRLRYGLDDGAPKTLEEVGKIFDVTRERIRQIEVKAINKL 365

Query: 668 KHPSRSKKLRSF 679
           K+  + K L  F
Sbjct: 366 KNIKKKKGLEDF 377



 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 74/165 (44%), Gaps = 10/165 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG------- 80
            +S   +IK+A++   ++ EE+N  +  +  S +++E T   L  + + +V+        
Sbjct: 9   KESLSNLIKIAKEEKIISREEINKLM-KNNFSQDKIEATFFKLQELNVEIVNKIADKNKS 67

Query: 81  -DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             ++E  +  E  +++      + +       S     D+P++MYLRE+G I LL  E E
Sbjct: 68  KKEIERNKKEELEINIDEKEVEALLNEDLTTVSESSDVDEPIKMYLREIGQIPLLKSEEE 127

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             +A+RI  G       L ES L     I  +   N G  LL  I
Sbjct: 128 FELARRIGEGDERAKQQLMESNLRLVVSIAKK-HTNRGLKLLDLI 171


>gi|88705821|ref|ZP_01103530.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
 gi|88699892|gb|EAQ97002.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
          Length = 331

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 90/272 (33%), Positives = 163/272 (59%), Gaps = 3/272 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E +H   + +K       A+K M+E+NLRLV+ +A++Y 
Sbjct: 55  TLDPTQLYLNEIGFVPLLTADEEKHYARLTQK---GDEAARKRMIESNLRLVVKIARRYL 111

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +RG+  LDLI+EGN+GLM+A EKFD   G++FSTYA WW++Q I R I +Q+ TIR+P+H
Sbjct: 112 HRGMSLLDLIEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIH 171

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +   ++  +R AR ++ ++  EPT +EIA +     + V +++ + +   S++ P+G + 
Sbjct: 172 VVKDLNGCLRAARELTQQLDHEPTTQEIASRTHKSAKEVSRLMGLNERVSSVDAPLGPDS 231

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S + + I D +   P +     ++ ++    L  LT ++  V+  RFG+  +   TLEE
Sbjct: 232 DSSVVETIADDHLCDPSEQLQNDDVHDSVADWLNELTDKQREVVMRRFGLLGHESSTLEE 291

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VG++  +TRER+RQI+ +A+++L+     + L
Sbjct: 292 VGQEIGLTRERVRQIQVEALKRLRRILERQGL 323



 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
                + +    + T DP ++YL E+G + LL+ + E   A+  + G       + ES L
Sbjct: 41  EASADEVEAPTQQITLDPTQLYLNEIGFVPLLTADEEKHYARLTQKGDEAARKRMIESNL 100

Query: 163 TFQALIIWRDELNDGTTLLREI 184
                I  R  L+ G +LL  I
Sbjct: 101 RLVVKIARRY-LHRGMSLLDLI 121


>gi|113868347|ref|YP_726836.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha H16]
 gi|113527123|emb|CAJ93468.1| DNA-directed RNA polymerase sigma subunit (sigma38) [Ralstonia
           eutropha H16]
          Length = 392

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 99/271 (36%), Positives = 161/271 (59%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ +        A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 120 VQHYLNRISIKPLLSAPEELHFSTLAK---DGDFAARQVMIERNLRLVVSIAKGYLNRGV 176

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 177 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 236

Query: 529 IHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 237 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 296

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 297 SLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 356

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 357 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 387



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 49/329 (14%), Positives = 100/329 (30%), Gaps = 28/329 (8%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
            +L++    +V  DD ++ E  E+      + S +      R         D V+ YL  
Sbjct: 67  DLLADDSERIVRDDDEDESEDEEEESAENGTDSAAPEHDDFRTVLHTELAADTVQHYLNR 126

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR---------DELNDGT 178
           +    LLS   E+  +   + G       + E  L     I            D + +G 
Sbjct: 127 ISIKPLLSAPEELHFSTLAKDGDFAARQVMIERNLRLVVSIAKGYLNRGVPLLDLIEEGN 186

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
             L   I+            +       S ++   +     R  V       +       
Sbjct: 187 LGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRH 246

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            ++   D    + E+    L +  D+    L+  E       +    ++      L  L 
Sbjct: 247 LEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNE---HTTSLDTPFDLDPGSSLLDFLS 303

Query: 299 DNAVNGQKDEKSSVKCKVL------------KEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           D        E +  + + L            +  + +  G   +  + ++ L E++    
Sbjct: 304 DEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELAEEMGLTR 363

Query: 347 KRIMHNEGE----LLRLAQSYGIKRDVFL 371
           +R+   + E    L R   S G+++D  L
Sbjct: 364 ERVRQIQQEALVKLKRHFASQGVRKDAVL 392


>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
 gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
          Length = 569

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 99/249 (39%), Positives = 156/249 (62%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +RK     +I K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD  
Sbjct: 319 RTLRKRINHGTICKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 378

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW+KQA+ +S++DQS TIR+P HM +  ++V    +++ ++  R P  EE
Sbjct: 379 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPDDEE 438

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+   + ++ +  VL   K P SL+  IG        + I D  A +  +  ++  +++
Sbjct: 439 VAEAAGLSMKRLSAVLLTPKAPRSLDQKIGMNMDLKPSEVIADPEAETAEELLMKQFMKQ 498

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL +L PRE +V+R RFG+      TL+E+G+   V+RERIRQIE+ A RKLK+  
Sbjct: 499 DLEKVLNTLNPRETQVVRWRFGLEDGRMKTLQEIGEIMGVSRERIRQIESSAFRKLKNKK 558

Query: 672 RSKKLRSFL 680
           R+K+L+ +L
Sbjct: 559 RTKQLKQYL 567


>gi|308804840|ref|XP_003079732.1| SigA (ISS) [Ostreococcus tauri]
 gi|116058189|emb|CAL53378.1| SigA (ISS) [Ostreococcus tauri]
          Length = 525

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 126/285 (44%), Positives = 183/285 (64%), Gaps = 7/285 (2%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLV 456
             ++SI +  N I+       +S S++       VS +R+   +   AK EM++ANLRLV
Sbjct: 232 MHLESIRE--NLIEETGPGVELSESQWAAAAGLNVSALRQRLHDGKAAKNEMIQANLRLV 289

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AKKY N  + F DLIQEG +GL++ AEKFD+  GYKFSTYA WW++QA+TRSI+DQS
Sbjct: 290 VSIAKKYANTNMSFQDLIQEGCVGLIRGAEKFDFQRGYKFSTYAHWWIRQAVTRSISDQS 349

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+PVH+ + I ++ +  ++ +    R PT EEIA ++ M VE + ++ K  + P+SL
Sbjct: 350 RTIRLPVHLFEIISRISKMEQKFALYNGRPPTLEEIASEMEMSVEKITQIKKAAQAPVSL 409

Query: 577 -ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            +T  G+     + D + D NA  P   + ++ L+E    VL +L PRE  VLR+R+G+ 
Sbjct: 410 AQTMGGENKGRTIEDTLIDANAEGPEKVSGKSLLKEDLENVLNTLNPRERDVLRLRYGLD 469

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                TLEE+G  F VTRERIRQIEAKA+RKLK PSR++ L+ + 
Sbjct: 470 DGRVKTLEEIGTVFSVTRERIRQIEAKALRKLKQPSRNQVLQEYF 514



 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCE 159
           R + D +R YL+++GS+ LL+   E+ +AKRI+       +  +L E
Sbjct: 197 RPSTDSMRSYLKDIGSVTLLNAGQEVELAKRIQDLMHLESIRENLIE 243


>gi|228471226|ref|ZP_04056039.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
 gi|228307041|gb|EEK16123.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
          Length = 286

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 166/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I   + IS  E   +   + +G      A  ++VEANLR V+SVAK+Y N+GL
Sbjct: 18  LDRYLQEIGRTSLISPEEEVELAREIHRGN---RRALNKLVEANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIG++KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGL 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             K+ +   +      R P+P+EIA +L +P + +R+ LK+  +  SL+ P  + + +++
Sbjct: 135 QQKMNKAIVKFEQLNGRRPSPQEIADELELPEDKIREALKVQGKHQSLDAPFVEGEDNNM 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + +++  S   S I  +L     R+L  L  RE  VLR  FGIG     TLEE+G++
Sbjct: 195 LDVLVNEDTPSTDSSLINESLSAEIDRILEQLGDREAEVLRCFFGIGCPE-MTLEEIGER 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++RER+RQI+ KAIR+LK   R + L+++L
Sbjct: 254 TKLSRERVRQIKEKAIRRLKQSDRCEYLKAYL 285



 Score = 46.0 bits (107), Expect = 0.023,   Method: Composition-based stats.
 Identities = 41/270 (15%), Positives = 98/270 (36%), Gaps = 21/270 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G   L+S E E+ +A+ I  G    +  L E+ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRTSLISPEEEVELAREIHRGNRRALNKLVEANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID------LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           +I+      ++A    +   GF   +    + ++       E+  +     +     +  
Sbjct: 79  LINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGLQQKM 138

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                K +       + +   DE E        A++ Q + + + A     E    L  L
Sbjct: 139 NKAIVKFEQLNGRRPSPQEIADELELPEDKIREALKVQGKHQSLDAPFVEGEDNNMLDVL 198

Query: 298 ----QDNAVNGQKDEKSSVKCKVLKEKL-------VKLVGSLSLNQSRIDLLVEQLYDIS 346
                 +  +   +E  S +   + E+L       ++    +   +  ++ + E+     
Sbjct: 199 VNEDTPSTDSSLINESLSAEIDRILEQLGDREAEVLRCFFGIGCPEMTLEEIGERTKLSR 258

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQG 376
           +R+   + + +R  +     R  +L+ + G
Sbjct: 259 ERVRQIKEKAIRRLKQS--DRCEYLKAYLG 286


>gi|282895663|ref|ZP_06303788.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199357|gb|EFA74222.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 396

 Score =  186 bits (472), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 113/281 (40%), Positives = 180/281 (64%), Gaps = 1/281 (0%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            EV  +     E    S   G   ++F      +     +  +AK++M+ +NLRLV+S+A
Sbjct: 115 EEVKDLQAALEEQFGHSATKGEIANKFDLNEKQLENRLYQGRVAKRKMIRSNLRLVVSIA 174

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTYA WW++QAITR+IA+ + TIR
Sbjct: 175 KRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWWIRQAITRAIANDARTIR 234

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R +  K  R PT  E+A+ L M V+ +R++ ++ ++ +SL   +
Sbjct: 235 LPIHIVEKLNKLKKAQRELKQKFARNPTEAEMAEFLEMTVQQLRQLQQLRRQALSLNHRV 294

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTD 639
           G E+ + L D +ED++  SP     +  +R+    VL   LT RE+ V+ +R+G+  +  
Sbjct: 295 GKEEDTELMDLLEDEDNQSPEAKMNENMMRQEIWEVLGDVLTSREKDVISLRYGLTTSEP 354

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ +L
Sbjct: 355 CTLEEVGNIFNLSRERVRQIQSKAMRKLRRPHIAKRLKGWL 395



 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 41/105 (39%), Gaps = 15/105 (14%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST------------ 117
           L+++G   +  + +E EE S D L+      +S +   +  +                  
Sbjct: 22  LADLGTMEILDNAVEHEEPSLDGLEAVVLEDSSILENLESDERDGDEMAAVRPSGYNKTE 81

Query: 118 -DDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCE 159
            DD V  + +EM    LL  + E+ +A R+        + A+L E
Sbjct: 82  HDDAVGAFFKEMARYPLLKPDEEVELAHRVRFLEEVKDLQAALEE 126


>gi|251771333|gb|EES51914.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           ferrodiazotrophum]
          Length = 307

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 96/269 (35%), Positives = 158/269 (58%), Gaps = 4/269 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                 I  +   ++++     +S SE   +   +       + A++ M+ +NLRLV+ +
Sbjct: 21  EGVSGDIGSLALYLRTLRDYPLLSASEEVDLARRI---ATGDAEARERMILSNLRLVVMI 77

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK+Y  RGL F DLI+EGN+GLMKA +++D   G++FSTYA WW++Q+I R++ +    I
Sbjct: 78  AKRYAGRGLPFPDLIEEGNLGLMKAVDRYDPEKGFRFSTYASWWIRQSIERAVINLGHMI 137

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVHMR+K+++ +    +M +   REP P E A+K  + VE    +  +    ISL+ P
Sbjct: 138 RLPVHMREKVNRYLAAVEQMVS-TGREPDPSEAARKAGLTVEEFESLYPLIAATISLDAP 196

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G++D + L D + D  A SPL+   +          L+ L PRE  +L +RFG+     
Sbjct: 197 VGEQDENTLKDVLGDPEADSPLEVVSRREEGRELEAALSVLRPRERDILFLRFGLSGEDP 256

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+G++  +TRER+RQIEA A+ K++
Sbjct: 257 KTLDEIGRRLGITRERVRQIEAVALSKMR 285



 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 21/103 (20%), Positives = 40/103 (38%), Gaps = 11/103 (10%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDD--PVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           + + + +           ++  + D   + +YLR +    LLS   E+ +A+RI  G A 
Sbjct: 2   IETFSDDPGEIEPPVDVPSEGVSGDIGSLALYLRTLRDYPLLSASEEVDLARRIATGDAE 61

Query: 153 MMASLCESPLTFQALIIWR---------DELNDGTTLLREIID 186
               +  S L    +I  R         D + +G   L + +D
Sbjct: 62  ARERMILSNLRLVVMIAKRYAGRGLPFPDLIEEGNLGLMKAVD 104


>gi|330959229|gb|EGH59489.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 336

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 95/291 (32%), Positives = 164/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 44  AKHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 100

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 101 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 160

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 161 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLERPVGEVKRML 220

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 221 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREV 280

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 331



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 11/131 (8%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +          +  S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLTEASNDKQPAAAVSG----RVKAKHSTSLKQHKYID 57

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 58  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 116

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 117 VNRGLSLLDLI 127


>gi|229588834|ref|YP_002870953.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens SBW25]
 gi|229360700|emb|CAY47558.1| RNA polymerase sigma factor [Pseudomonas fluorescens SBW25]
          Length = 334

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 166/295 (56%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     ++  E  H   + +K       
Sbjct: 38  VRAKSKNSTALKQHKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQK---GDPA 94

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 95  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 155 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVAEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 215 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 274

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 275 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 329



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 52/136 (38%), Gaps = 13/136 (9%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+   P  ++  E +      L   GI        E       ++    + S +S  L++
Sbjct: 3   LSKEAPEFDIDDEVL------LMETGIA------TESMSNEGPAVPSVRAKSKNSTALKQ 50

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LL+ E E+  A+  + G       + ES L     I
Sbjct: 51  HKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 110

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 111 ARRY-VNRGLSLLDLI 125


>gi|148242803|ref|YP_001227960.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851113|emb|CAK28607.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 309

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 111/268 (41%), Positives = 172/268 (64%), Gaps = 3/268 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ N+++++   T +   E     +  +K       +K+ M++ANLRLV+SVAKKY  +
Sbjct: 39  IELGNQVQTM--MTLVEQGEEATYTAREKKLIRVGRRSKERMMKANLRLVVSVAKKYQGK 96

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL+ LDLIQEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ 
Sbjct: 97  GLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLS 156

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           +++  V +    +++K+   P+  EIA +L M +E +  +L+      SL+ PI  E+  
Sbjct: 157 ERLATVRKATMDLAHKLGAMPSRREIATELGMGLEELDGLLRQALTTSSLDAPISGEEGR 216

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LG+ I D     PLD+  +    E   R L+ LT +E++VL MRFG+G    HTL E+
Sbjct: 217 SFLGELIADPRNEEPLDAVERRMHHEQLGRWLSYLTAQEKQVLEMRFGLGGEQRHTLAEI 276

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           G+   V+RER+RQ+E KA+RKL++ +R 
Sbjct: 277 GRLMEVSRERVRQVELKALRKLRNLTRR 304



 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/116 (14%), Positives = 42/116 (36%), Gaps = 3/116 (2%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
              +++ +  +DPV  YL  +G + LL+   EI +  +++    ++      +    +  
Sbjct: 7   TAAENSRKRGNDPVSWYLSSIGRVPLLTPAEEIELGNQVQTMMTLVEQGEEATYTAREKK 66

Query: 168 IIWRDELNDGTTL---LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           +I     +    +   LR ++ +      +         EG    +R     +  R
Sbjct: 67  LIRVGRRSKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTR 122


>gi|4105839|gb|AAD02575.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 589

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 114/304 (37%), Positives = 173/304 (56%), Gaps = 14/304 (4%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIK---SISVETGISISEFRHIVSMVRKGECEA 441
              +   E  +   +    + + +    +      ++ET +S+SE R           + 
Sbjct: 276 EEKEICQEIAFFTHLEAVREDLRRRIGRLPREHEWAMETNMSVSELR-------GKLIKG 328

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AK  MV ANLRLVI  AK++ NRG+ F DL+QEG+IGL++  EK+D   G++FSTYA 
Sbjct: 329 RRAKNRMVAANLRLVICFAKRFRNRGVAFQDLVQEGSIGLIRGVEKYDANRGFRFSTYAS 388

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q I +++ + S   R+PVH+ + I ++ R +  + N + REPT  EIA K+ MP E
Sbjct: 389 WWIRQGIHKALLECSKMFRLPVHVNEMIKEIRRCSYELMNILGREPTKLEIAMKVGMPEE 448

Query: 562 GVRKVLKITKEPISLETPIGDEDTS----HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V  +L+  +  +SLE P+   D+S     LGD +    + SP DSA   +LR    R L
Sbjct: 449 KVIFLLQRAQTALSLEMPLRGSDSSLESRTLGDVVSSTASPSPEDSAFGTSLRYDLERAL 508

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + L  RE  V+RMRFG+      +L EVG  FCVTRER+RQIE +A+RKL+ P  +  L+
Sbjct: 509 SQLDFREREVIRMRFGLDDGRTKSLGEVGSLFCVTRERVRQIETRALRKLRDPRCNIFLK 568

Query: 678 SFLD 681
            +++
Sbjct: 569 EYME 572


>gi|260361829|ref|ZP_05774845.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
 gi|308114475|gb|EFO52015.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
          Length = 329

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 112/296 (37%), Positives = 174/296 (58%), Gaps = 7/296 (2%)

Query: 385 SYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              K     E K  V  E D    S+   +  +  I     ++  E    V   R+    
Sbjct: 26  ELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRG 82

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+K M E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 83  DEAARKRMFESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 142

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV
Sbjct: 143 TWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPV 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L
Sbjct: 203 EDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEEL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 263 NPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 318



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + +     E + D+    SS++       + +  A   + D  ++YL E+G   LL+
Sbjct: 9   KVEEFEYDNASETTIDNELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLT 68

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 69  AEEEVLYARRALRGDEAARKRMFESNLRLVVKISRRYS-NRGLALLDLI 116


>gi|153839213|ref|ZP_01991880.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149747278|gb|EDM58264.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 104/266 (39%), Positives = 165/266 (62%), Gaps = 3/266 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  I     ++  E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  
Sbjct: 1   MYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLAL 57

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ T R+P+H+  +++
Sbjct: 58  LDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTTRLPIHVVKELN 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
             +RTAR +S K+  EPT EEIA +L +PVE V K+L++ +   S++TPIG +    L D
Sbjct: 118 IYLRTARELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNERISSVDTPIGGDGEKALLD 177

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D N   P  S    +++ +    L  L P+++ VL  RFG+      TLEEVG++  
Sbjct: 178 IIPDANNSDPEVSTQDDDIKSSLIHWLEELNPKQKEVLARRFGLLGYEPSTLEEVGREIG 237

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKL 676
           +TRER+RQI+ + +R+L+     + L
Sbjct: 238 LTRERVRQIQVEGLRRLREILIKQGL 263



 Score = 44.8 bits (104), Expect = 0.045,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL E+G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL 
Sbjct: 1   MYLGEIGFSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLD 59

Query: 183 EI 184
            I
Sbjct: 60  LI 61


>gi|160937287|ref|ZP_02084649.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
 gi|158439851|gb|EDP17600.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
          Length = 298

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 121/301 (40%), Positives = 176/301 (58%), Gaps = 11/301 (3%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +   K   + +  N    E DS+      +K   V   ++  E   +  +++     +  
Sbjct: 7   LKQEKTLEKAKVDNVYEIETDSVQW---YLKQAGVGPLLTKEEEIELAYLIQ---EGSDE 60

Query: 444 AKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           A+++M+ +NLRLVI+ AKKY      L  LDLIQEGN+GL+KA EK++  LG++FSTYA 
Sbjct: 61  ARQKMISSNLRLVINQAKKYVTYTQSLTLLDLIQEGNLGLIKAVEKYNPELGFRFSTYAS 120

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW+KQAITR+I+     IR+PVH  + I KV R    +  +     TPE++         
Sbjct: 121 WWIKQAITRAISVLDKAIRLPVHFCEDIQKVKRATHEIMQQNDI-VTPEKLKDITGFSEG 179

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + K+L      ISLETP+G  + + LGDF+ED    S  + A++  ++   +R +  L 
Sbjct: 180 KIEKILMNMNHTISLETPVG--EEATLGDFVEDTLTPSIEEQAMENAMQREISRQMECLR 237

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           PRE+ +L +RFG+     HTLEEVGKQ  VTRERIRQIE KA+RKL+HP+RS+ LR F+ 
Sbjct: 238 PREQTILALRFGLNGQNPHTLEEVGKQMGVTRERIRQIEMKALRKLRHPNRSRYLREFIL 297

Query: 682 G 682
           G
Sbjct: 298 G 298



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 27/63 (42%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
                + + D+      D V+ YL++ G   LL++E EI +A  I+ G       +  S 
Sbjct: 10  EKTLEKAKVDNVYEIETDSVQWYLKQAGVGPLLTKEEEIELAYLIQEGSDEARQKMISSN 69

Query: 162 LTF 164
           L  
Sbjct: 70  LRL 72


>gi|330946209|gb|EGH47399.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 230

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 128/229 (55%), Positives = 168/229 (73%), Gaps = 1/229 (0%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           R  FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E
Sbjct: 1   RADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAE 59

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +
Sbjct: 60  IKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 119

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 120 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 179

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           PTPEE+ +++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED 
Sbjct: 180 PTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDS 228


>gi|104783164|ref|YP_609662.1| RNA polymerase sigma factor RpoS [Pseudomonas entomophila L48]
 gi|95112151|emb|CAK16878.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudomonas entomophila L48]
          Length = 335

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 97/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   + +K       
Sbjct: 39  VRTKSKQGASLKQHKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIASLLEKPVAEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L  LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 55/136 (40%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  + +      L   GI V++ D + DE           + S     L++
Sbjct: 3   LSKEVPEFDIDDDLL------LMETGI-VLETDVVSDEPAVPS----VRTKSKQGASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|6175878|gb|AAF05319.1|AF178851_2 sigma factor 38 [Pseudomonas putida]
          Length = 335

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 95/274 (34%), Positives = 160/274 (58%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI +P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIPLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++   R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYSRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  + +      L   GI V++ D + DE      +    + + S   L++
Sbjct: 3   LSKEVPEFDIDDDVL------LMETGI-VLETDVVSDEPA----VSSVRTRAKSGSSLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|170723213|ref|YP_001750901.1| RNA polymerase sigma factor RpoS [Pseudomonas putida W619]
 gi|169761216|gb|ACA74532.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           W619]
          Length = 335

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 162/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 55/136 (40%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           LN   P  ++  + +      L   GI V++ D + DE           + + S   L++
Sbjct: 3   LNKEAPEFDIDDDVL------LMETGI-VLETDVVSDEPAVPS----VRTRAKSGSTLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|5305130|emb|CAB46191.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 335

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 162/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 55/136 (40%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           LN   P  ++  + +      L   GI V++ D + DE           + + S   L++
Sbjct: 3   LNKEAPEFDIDDDVL------LMETGI-VLETDVVSDEPAVPS----VRTRAKSGSSLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|73541783|ref|YP_296303.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha JMP134]
 gi|72119196|gb|AAZ61459.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 391

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 99/271 (36%), Positives = 161/271 (59%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ +        A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 119 VQHYLNRISIKPLLSAPEELHFSTLAK---DGDFSARQVMIERNLRLVVSIAKGYLNRGV 175

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 176 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 235

Query: 529 IHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 236 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 295

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 296 SLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 355

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 356 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 386



 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 43/298 (14%), Positives = 86/298 (28%), Gaps = 28/298 (9%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A  +      R         D V+ YL  +    LLS   E+  +   + G       + 
Sbjct: 97  AEAAPEHDDFRTVLHTELAADTVQHYLNRISIKPLLSAPEELHFSTLAKDGDFSARQVMI 156

Query: 159 ESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
           E  L     I            D + +G   L   I+            +       S +
Sbjct: 157 ERNLRLVVSIAKGYLNRGVPLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIE 216

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           +   +     R  V       +        ++   D    + E+    L +  D+    L
Sbjct: 217 RAIMNQARTVRLPVHVIRELNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVL 276

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL------------ 317
           +  E       +    ++      L  L D        E +  + + L            
Sbjct: 277 ALNE---HTTSLDTPFDLDPGSSLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKH 333

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE----LLRLAQSYGIKRDVFL 371
           +  + +  G   +  + ++ L E++    +R+   + E    L R   S G+++D  L
Sbjct: 334 RYVVERRFGLNHIEPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQGVRKDAVL 391


>gi|325277035|ref|ZP_08142696.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
 gi|324097832|gb|EGB96017.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
          Length = 335

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 162/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  + +      L   GI V++ D + DE      +    + + S   L++
Sbjct: 3   LSKEVPEFDIDDDVL------LMETGI-VLETDVVSDEPA----VSSVRTRAKSGSSLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|28200488|gb|AAO31615.1| RNA polymerase subunit sigma factor S [Vibrio vulnificus]
          Length = 343

 Score =  186 bits (471), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 111/313 (35%), Positives = 182/313 (58%), Gaps = 10/313 (3%)

Query: 371 LERHQGRELDPHW---VSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGIS 423
           ++     ++D  +   +   +     E K  +  E D    S+   +  +  I     ++
Sbjct: 10  VKDFDVNQMDDDFNDDIEINEKEDLTEEKVKLREEFDASNKSLDATQLYLGEIGFSPLLT 69

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++
Sbjct: 70  AEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIR 126

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+
Sbjct: 127 AVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKL 186

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EPT EEIA +L +PV+ V K+L++ +   S++TPIG +    L D I D N   P  S
Sbjct: 187 DHEPTAEEIAAQLDIPVDDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVS 246

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               ++R +    L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + 
Sbjct: 247 TQDEDMRVSLIHWLEELNPKQKEVLARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEG 306

Query: 664 IRKLKHPSRSKKL 676
           +R+L+     + L
Sbjct: 307 LRRLREVLIKQGL 319



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 49/107 (45%), Gaps = 2/107 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D + ++D+   +  ++     +   V L++  D++++S  D  ++YL E+G   LL+ E
Sbjct: 13  FDVNQMDDDFNDDIEINEKEDLTEEKVKLREEFDASNKSL-DATQLYLGEIGFSPLLTAE 71

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 72  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 117


>gi|323345452|ref|ZP_08085675.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093566|gb|EFZ36144.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 295

 Score =  186 bits (471), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 171/272 (62%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +RK       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 27  LDKYLQEIGHEELISVEEEVELAQRIRK---GDRKALEKLTKANLRFVVSVAKQYQNQGL 83

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 84  SLPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGS 143

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ R   +   + +R P+ EEIA ++ +P E +   +KI  + IS++ P  + + + L
Sbjct: 144 VNKINRALNKFEQENERHPSIEEIADRIDLPEEKIIDAMKINGKHISVDAPFAEGEDNSL 203

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + +  + +  +  +  +LR+  +RVL  L  RE  ++   FGI    D TLEE+G +
Sbjct: 204 LDIMPNTESPTADERLVSESLRDEISRVLLLLNERERMIIEAFFGINQ-QDMTLEEIGDK 262

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L++ ++S  L+SFL
Sbjct: 263 FGLTRERVRQIKEKAIRRLRNNTKSSLLKSFL 294



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 98/251 (39%), Gaps = 18/251 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  EL+S E E+ +A+RI  G    +  L ++ L F  ++    +  +    L +
Sbjct: 30  YLQEIGHEELISVEEEVELAQRIRKGDRKALEKLTKANLRF--VVSVAKQYQNQGLSLPD 87

Query: 184 IID------LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           +I+      ++A    +   GF   +    + ++       E+  +     +   +    
Sbjct: 88  LINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVNKI 147

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
               +K +   E   + E   D  +      + AM+   +   + A     E    L  +
Sbjct: 148 NRALNKFEQENERHPSIEEIADRIDLPEEKIIDAMKINGKHISVDAPFAEGEDNSLLDIM 207

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            +       +   S   + L++++ +++    L   R  +++E  + I+++ M     L 
Sbjct: 208 PNTESPTADERLVS---ESLRDEISRVLL---LLNERERMIIEAFFGINQQDMT----LE 257

Query: 358 RLAQSYGIKRD 368
            +   +G+ R+
Sbjct: 258 EIGDKFGLTRE 268


>gi|40353309|gb|AAR84418.1| essential primary sigma 70 factor [Frankia sp. D11]
 gi|40353317|gb|AAR84422.1| essential primary sigma 70 factor [Frankia sp. HR2714]
 gi|40353319|gb|AAR84423.1| essential primary sigma 70 factor [Frankia sp. Flec]
          Length = 255

 Score =  186 bits (471), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 129/258 (50%), Positives = 189/258 (73%), Gaps = 6/258 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 1   AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 57

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 58  VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 117

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 118 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 177

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 178 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 237

Query: 636 MNTDHTLEEVGKQFCVTR 653
                TLEEVG++F VTR
Sbjct: 238 DGHPRTLEEVGREFGVTR 255


>gi|330807812|ref|YP_004352274.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327375920|gb|AEA67270.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 335

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 39  VRAKSKHSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.2 bits (105), Expect = 0.037,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 58/136 (42%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L   GI +   D + ++EG+        + S  S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETGIAM---DSMSNDEGATPPS--VRAKSKHSASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|295103972|emb|CBL01516.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 457

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 130/245 (53%), Positives = 178/245 (72%), Gaps = 2/245 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +SE R     + K   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+
Sbjct: 201 PLSEERR--QELLKTRRDGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 258

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KAAEKFD   G++FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +
Sbjct: 259 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQ 318

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EPTPEE+AK + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  
Sbjct: 319 NGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGK 378

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A +A + +     L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAK
Sbjct: 379 AADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAK 438

Query: 663 AIRKL 667
           AIRKL
Sbjct: 439 AIRKL 443



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/137 (20%), Positives = 59/137 (43%), Gaps = 18/137 (13%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K+++      G ++ +E  A      +    ++    +L   GI V++ ++    +  
Sbjct: 4   TLKELLTKG--EGTLSAQEAKALAAQCRMD---VDTLYTLLEERGIKVLEEENEPSLDVD 58

Query: 90  EDSLDLASSASNSSVFL-------------QKRKDSADRSTDDPVRMYLREMGSIELLSR 136
               ++ ++ +N+                    K + D   DDPV+ YL+++G I LLS 
Sbjct: 59  SIIAEVENAENNNDDMGLADENEEDAEENPADLKAAMDELLDDPVKNYLKQIGQIPLLSA 118

Query: 137 EGEIAIAKRIEAGRAMM 153
           E E+ +++RI AG    
Sbjct: 119 EQEVELSRRIHAGAEAA 135


>gi|26988355|ref|NP_743780.1| RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148549360|ref|YP_001269462.1| RNA polymerase sigma factor RpoS [Pseudomonas putida F1]
 gi|167032190|ref|YP_001667421.1| RNA polymerase sigma factor RpoS [Pseudomonas putida GB-1]
 gi|24983106|gb|AAN67244.1|AE016351_6 RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148513418|gb|ABQ80278.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           F1]
 gi|166858678|gb|ABY97085.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           GB-1]
 gi|313500209|gb|ADR61575.1| RpoS [Pseudomonas putida BIRD-1]
          Length = 335

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 162/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  + +      L   GI V++ D + DE      +    + + S   L++
Sbjct: 3   LSKEVPEFDIDDDVL------LMETGI-VLETDVVSDEPA----VSSVRTRAKSGSSLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|170782897|ref|YP_001711231.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
 gi|169157467|emb|CAQ02657.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
          Length = 347

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 112/266 (42%), Positives = 167/266 (62%), Gaps = 7/266 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +   T ++ +E R   ++ +    +   AK+ +V ANLRLV+S+AK+YT RGL FLDLIQ
Sbjct: 86  LDTRTDLTPAERREYQTLAQ----DGMRAKQHLVNANLRLVVSIAKRYTGRGLPFLDLIQ 141

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL++A EKFD+  G+KFSTYA WW+KQ+ITR +AD S TIRIPVH  + I+++   
Sbjct: 142 EGNMGLVRAVEKFDYQAGFKFSTYASWWIKQSITRGMADTSRTIRIPVHTVEHINRINAV 201

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTSHLGDFI 592
            R + +++ R+P+ EEIA++   PV  VR +L   +EP+SL+  +   G +  + + D I
Sbjct: 202 QRELGDELGRDPSMEEIARESDTPVTKVRYLLDRAQEPMSLQVLVGGSGGDGDTEMADLI 261

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED +   P+D   Q  +    TR++  L  R+  V+RMRFG+      +L  V +Q  VT
Sbjct: 262 EDADVTQPIDVVTQQLMAAHVTRLIDGLAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVT 321

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRS 678
           RER+RQIE K + KL+ P     +R 
Sbjct: 322 RERVRQIEKKVLAKLRIPELEMYIRG 347



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSAD----RSTDDPVRMYLREMGSIELLSREGEIA 141
           E  S+  LD   SA     +              ++ D V+ YLR++G + LL+ E E++
Sbjct: 12  ETASDTELDHIESARPVDPYADSDLPEPSLVTPGASTDAVKDYLRQIGRVPLLTAELEVS 71

Query: 142 IAKRIEAG 149
           +A+RIE G
Sbjct: 72  VARRIEVG 79


>gi|40353315|gb|AAR84421.1| essential primary sigma 70 factor [Frankia sp. HRX401a]
          Length = 255

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 128/258 (49%), Positives = 188/258 (72%), Gaps = 6/258 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 1   AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 57

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FL LIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 58  VVSIAKRYVGRGMLFLHLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 117

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 118 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 177

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 178 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLT 237

Query: 636 MNTDHTLEEVGKQFCVTR 653
                TLEEVG++F VTR
Sbjct: 238 DGHPRTLEEVGREFGVTR 255


>gi|119509984|ref|ZP_01629125.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119512944|ref|ZP_01632006.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119462397|gb|EAW43372.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119465308|gb|EAW46204.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
          Length = 389

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 106/250 (42%), Positives = 173/250 (69%), Gaps = 1/250 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD  
Sbjct: 139 KQLESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPD 198

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K+ R P   E
Sbjct: 199 KGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKLCRNPNEAE 258

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ L + V+ +R++ ++ ++ +SL   +G E+ + L D +ED++ +SP     +  +R+
Sbjct: 259 MAEALEISVQQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQ 318

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL   LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P
Sbjct: 319 EIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRP 378

Query: 671 SRSKKLRSFL 680
             +K+L+ +L
Sbjct: 379 HIAKRLKGWL 388



 Score = 40.6 bits (93), Expect = 0.85,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 40/103 (38%), Gaps = 12/103 (11%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
           E + E  + T+ +L      VV+ +    E    D  D    A+       K +      
Sbjct: 25  ETTVEHEDQTLELLE----PVVESEPPIIENLESDERDGDDMAAARPSGYNKTEH----- 75

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASL 157
            DD V  + +EM    LL  + E+ +A+R+        + A+L
Sbjct: 76  -DDAVGAFFKEMARYPLLKPDEEVELARRVRFLEEVREVQAAL 117


>gi|87301096|ref|ZP_01083937.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87284064|gb|EAQ76017.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 308

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 104/237 (43%), Positives = 159/237 (67%), Gaps = 1/237 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             ++       AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   
Sbjct: 62  RQKQLLRLGRRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTR 121

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  V R +  +++K+   P+  EI
Sbjct: 122 GYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLSAVRRVSLELAHKLGAMPSRSEI 181

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRE 611
           A+ +A+P++ +  +L+ +    SL+ P+  E+  S LGD I D +   PLD   +    E
Sbjct: 182 AEAMAIPIQELDGLLRQSLTTSSLDAPVNGEEGRSFLGDLIADSSHDEPLDQVERGMHHE 241

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R L+ L+ +E +VL +RFG+  +  HTL E+G+   V+RER+RQ+E KA+RKL+
Sbjct: 242 QLERWLSYLSEQERQVLDLRFGLDGHERHTLAEIGRLLDVSRERVRQVELKALRKLR 298



 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 20/110 (18%), Positives = 39/110 (35%), Gaps = 5/110 (4%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ--ALIIWRD 172
           R   DP+  YL  +G + LL+   EI +  ++      ++ S  E P + +   L+    
Sbjct: 13  RRGSDPISWYLGTIGRVPLLTPAEEIELGNQV-QAMMQLIDSGVEDPPSLRQKQLLRLGR 71

Query: 173 ELNDGTTL--LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
              +      LR ++ +      +         EG    +R     +  R
Sbjct: 72  RAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTR 121


>gi|16331621|ref|NP_442349.1| RNA polymerase sigma factor SigC [Synechocystis sp. PCC 6803]
 gi|2500787|sp|Q59996|RPSC_SYNY3 RecName: Full=Probable RNA polymerase sigma-C factor
 gi|1001684|dbj|BAA10419.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 404

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 115/269 (42%), Positives = 172/269 (63%), Gaps = 8/269 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  +   G+++ E  +I       E +   AK  M++ANLRLV+SVAKKY NRGL+ LDL
Sbjct: 142 KRWAELAGLTVEELENI-------EKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDL 194

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG +GL +A EKFD   GY+FSTY+ WW++Q ITR+IA QS  IR+PVH+ +K++K+ 
Sbjct: 195 IQEGTLGLERAVEKFDPTKGYRFSTYSYWWIRQGITRAIATQSRMIRLPVHITEKLNKIK 254

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++S +    P  +E+A++L M  E VR+VL      +SLE  +G +  + L D +E
Sbjct: 255 RAQRKISQEKGHTPKIDEVAEELGMTPEQVREVLTQVPRSVSLELKVGQDKDTELMDLLE 314

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  SP D  ++  L+     +L  LTPRE+ V+ +RFG      H+L E+G+   ++R
Sbjct: 315 -TDTQSPEDELMREALQNDMQEILLDLTPREQEVIALRFGFQDGVAHSLSEIGRILNLSR 373

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ER+RQIEAKA++KL+HP R  ++R + + 
Sbjct: 374 ERVRQIEAKALQKLRHPRRRDRIRDYYEN 402



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            L+     ++S            + + D VR+YL+++G I LL R+ E+ IA+++++   
Sbjct: 22  PLEEEDLTADSQDLEYTAVAHRQQFSTDLVRLYLQDIGRIPLLKRDEEVHIAQQVQSYLR 81

Query: 152 --MMMASLCESPLTFQ 165
              +     ES     
Sbjct: 82  LVEIQNRAAESDAAID 97


>gi|188994502|ref|YP_001928754.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
 gi|188594182|dbj|BAG33157.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
          Length = 287

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 170/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +++       A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLISVEEEVELAQAIKR---GDRKALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGT 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+++  ++   + +R P+  E+AK+L +  + +   +K++   IS++ P  + + + L
Sbjct: 135 LNKIIKAQQKFEQENERRPSSAELAKELDIAEDKIADTMKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + +++  +   S I  +L     R L++LT RE  ++++ FGI    + TLEE+G +
Sbjct: 195 LDVLVNEDTPNTDKSLINESLAVEIERALSTLTEREAEIVKLFFGIAGCQEMTLEEIGDK 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  +  K L+ +L
Sbjct: 255 FGLTRERVRQIKEKAIRRLRQSNECKNLKGYL 286



 Score = 41.0 bits (94), Expect = 0.66,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L+S E E+ +A+ I+ G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLISVEEEVELAQAIKRGDRKALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|254509205|ref|ZP_05121302.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
 gi|219547863|gb|EED24891.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
          Length = 331

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 105/277 (37%), Positives = 168/277 (60%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 47  DASAKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKI 103

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 104 SRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 163

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V K+L++ +   S++TP
Sbjct: 164 RLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDVSKMLRLNERISSVDTP 223

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D N   P  S    +++ +    L  L P+++ VL  RFG+     
Sbjct: 224 IGGDGEKALLDIIPDVNNSDPEVSTQDDDIKSSLVHWLDELNPKQKEVLARRFGLLGYEP 283

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 284 STLEEVGREINLTRERVRQIQVEGLRRLREILIKQGL 320



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 1/96 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +    ++ ++ +     K +  A   + D  ++YL E+G   LL+ E E+  A+R   
Sbjct: 24  ESEQESPSTKSTPAEEVKGKEEFDASAKSLDATQLYLGEIGFSPLLTAEEEVLYARRALR 83

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       + ES L     I  R   N G  LL  I
Sbjct: 84  GDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 118


>gi|160942567|ref|ZP_02089814.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446151|gb|EDP23154.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
          Length = 457

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 130/245 (53%), Positives = 178/245 (72%), Gaps = 2/245 (0%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +SE R     + K   +   A++ + EANLRLV+S+AKK+    L FLDLIQEGNIGL+
Sbjct: 201 PLSEERR--QELLKTRRDGLNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 258

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KAAEKFD   G++FSTYA WW++QAITR+IADQ+ TIRIPVHM + I+++ +   ++  +
Sbjct: 259 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQ 318

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              EPTPEE+AK + M VE VR++ ++ +EP SLE+P+G+E+ S LGDF+ D+NA +P  
Sbjct: 319 NGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPVGEEEDSSLGDFVADENAEAPGK 378

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +A +A + +     L SLTPREE+V+R+RFG+      TLEEVG+ F VTRER+RQIEAK
Sbjct: 379 AADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAK 438

Query: 663 AIRKL 667
           AIRKL
Sbjct: 439 AIRKL 443



 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/137 (19%), Positives = 59/137 (43%), Gaps = 18/137 (13%)

Query: 30  SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
           + K+++      G ++ +E  A      +    ++    +L   GI +++ ++    +  
Sbjct: 4   TLKELLTKG--EGTLSAQEAKALAAQCRMD---VDTLYTLLEERGIKILEEENEPSLDVD 58

Query: 90  EDSLDLASSASNSSVFL-------------QKRKDSADRSTDDPVRMYLREMGSIELLSR 136
               ++ ++ +N+                    K + D   DDPV+ YL+++G I LLS 
Sbjct: 59  SIIAEVENAENNNDDMGLADENEEDAEENPADLKAAMDELLDDPVKNYLKQIGQIPLLSA 118

Query: 137 EGEIAIAKRIEAGRAMM 153
           E E+ +++RI AG    
Sbjct: 119 EQEVELSRRIHAGAEAA 135


>gi|77457359|ref|YP_346864.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf0-1]
 gi|77381362|gb|ABA72875.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas fluorescens
           Pf0-1]
          Length = 335

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 39  VRAKSKHSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L   GI   D D + ++EG+        + S  S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETGI---DSDSMSNDEGAAPPS--VRAKSKHSASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|261210105|ref|ZP_05924403.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
 gi|260840870|gb|EEX67412.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
          Length = 336

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 109/299 (36%), Positives = 176/299 (58%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           EL       A +    + +        S+   +  +  I     ++  E    V   R+ 
Sbjct: 28  ELSSDEELVAVEGASDDAREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLYARRA 84

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 85  LRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 144

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L 
Sbjct: 145 TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELD 204

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV+ V K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L
Sbjct: 205 RPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 265 DELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 323



 Score = 54.5 bits (129), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/115 (26%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
             +  + V++ DD       E S D    A   +    + +  A   + D  +MYL E+G
Sbjct: 15  FEDEALEVLEADD-------ELSSDEELVAVEGASDDAREEFDASAKSLDATQMYLSEIG 67

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 68  FSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|186702713|gb|ACC91623.1| RNA polymerase sigma factor [Pseudomonas sp. CT07]
          Length = 336

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 95/291 (32%), Positives = 164/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 44  SKHSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 100

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 101 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 160

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 161 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRML 220

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 221 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDKQREV 280

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 VVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 331



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 36/136 (26%), Positives = 56/136 (41%), Gaps = 11/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L   GI+  D     DE  +  S+   S     S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMEAGID-SDSSMSNDEGAAPPSVRSKSKH---SASLKQ 52

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 53  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 112

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 113 ARRY-VNRGLSLLDLI 127


>gi|209524631|ref|ZP_03273179.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495089|gb|EDZ95396.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 331

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 177/278 (63%), Gaps = 6/278 (2%)

Query: 406 ILKIRNEIKSI--SVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + + RNE+        T    +E  ++ V+ ++    +  +AK++MVEANLRLV+SVAKK
Sbjct: 55  LQEKRNELAKQLGYEPTEAQWAELVNLSVAQLQHILHQGQLAKRKMVEANLRLVVSVAKK 114

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P
Sbjct: 115 YIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLP 174

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+ +K++K+ +  R+++ ++ R  T  E+A +L +  + +R+ L+ ++ P+SL+  +GD
Sbjct: 175 IHITEKLNKIKKAQRQLAQQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLDLRVGD 234

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              + L D +ED +  SP   A+ ++LR     ++  LT ++ +VL +RFG+      TL
Sbjct: 235 NQDTELVDLLEDTS-NSPEQFALNSSLRSDLESLMTDLTDQQRQVLALRFGLDDGQTLTL 293

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++G +  ++RER+RQIE +A+ KL+   R + +  +L
Sbjct: 294 AKIGDRLNISRERVRQIEREALTKLRK--RKQDVNDYL 329



 Score = 44.8 bits (104), Expect = 0.051,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
               +A  S  D VR YLRE+G + LL+ E EI   K+++  
Sbjct: 11  DAMKTAKTSDTDSVRAYLREIGRVPLLTHEQEIVYGKQVQQA 52


>gi|312129690|ref|YP_003997030.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Leadbetterella
           byssophila DSM 17132]
 gi|311906236|gb|ADQ16677.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leadbetterella
           byssophila DSM 17132]
          Length = 287

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 97/274 (35%), Positives = 168/274 (61%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   +R       ++ + + +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGKVDLLTPDEEVILAQKIR---DGDQLSLERLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +T   +  + +REP+PEE+A+ L +    V   +KI+   +S++ P    + +
Sbjct: 133 GSLNKISKTFSELEQRFEREPSPEELAEVLEISANEVVDTMKISGRHVSVDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +E+   + P    +  +LR    R L++LT RE  V+   FG+      TLEE+G
Sbjct: 193 SLLDVLENDTEIRPDQELMNDSLRREVLRALSTLTQREAEVIMFYFGLNGEQAMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++F +TRER+RQI+ KAIR+L+  SRSK L+++L
Sbjct: 253 EKFNLTRERVRQIKEKAIRRLRQTSRSKALKAYL 286



 Score = 44.4 bits (103), Expect = 0.068,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ + E+ +A++I  G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGKVDLLTPDEEVILAQKIRDGDQLSLERLTKANLRF--VVSVAKQYQNQGLSLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|33150232|gb|AAP97086.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
 gi|103488976|gb|ABF71881.1| RpoS [Pseudomonas chlororaphis]
          Length = 334

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 38  VRAKSKHSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 94

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 95  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 155 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 215 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 274

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 275 QREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 329



 Score = 44.4 bits (103), Expect = 0.063,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 54/136 (39%), Gaps = 13/136 (9%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L    I      D    EGS   +    + S  S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETDI----ATDSMSNEGSA--VPSVRAKSKHSASLKQ 50

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 51  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 110

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 111 ARRY-VNRGLSLLDLI 125


>gi|84390122|ref|ZP_00991384.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
 gi|84376776|gb|EAP93651.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
          Length = 326

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 111/313 (35%), Positives = 179/313 (57%), Gaps = 3/313 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + ++ F       E +    +      + E K  V     S+   +  +  I     ++
Sbjct: 6   AVTKEEFDLNQATTEPEALGKAKRTVKKKTEAKEEVEVTSKSLDATQLYLGEIGFSPLLT 65

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++
Sbjct: 66  AEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIR 122

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+
Sbjct: 123 AVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKL 182

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EPT EEIA KL  PV  V K+L++ +   S++TPIG +    L D I D N   P  S
Sbjct: 183 DHEPTAEEIASKLDKPVGDVSKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVS 242

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              ++++ +    L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + 
Sbjct: 243 TQDSDIKNSLIFWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEG 302

Query: 664 IRKLKHPSRSKKL 676
           +R+L+     + L
Sbjct: 303 LRRLREILIKQGL 315



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 25/108 (23%), Positives = 40/108 (37%), Gaps = 1/108 (0%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V   +   ++  +E      +  +       K +      + D  ++YL E+G   LL+ 
Sbjct: 7   VTKEEFDLNQATTEPEALGKAKRTVKKKTEAKEEVEVTSKSLDATQLYLGEIGFSPLLTA 66

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 67  EEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 113


>gi|212550562|ref|YP_002308879.1| RNA polymerase primary sigma factor [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|212548800|dbj|BAG83468.1| putative RNA polymerase primary sigma factor [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 286

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 100/268 (37%), Positives = 167/268 (62%), Gaps = 4/268 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ IS E  +SI +   +    R        A  ++V ANLR V+SVAK+Y N+GL   D
Sbjct: 22  LQEISHEELLSIEKEIELARRSR---LGDRSALDKLVRANLRFVVSVAKQYQNQGLSLPD 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 79  LINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGSLNKI 138

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   +   K +R+P+ EE+A++L +P + V + L+I+   IS++ P  D + + L D +
Sbjct: 139 SKALSKFEQKHERKPSSEELAQELELPEDKVSETLRISNRHISIDAPFADGEENSLLDVL 198

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            + +  +     I  +L +     L  L  RE+ +++M FGIG   +  LEE+G  F +T
Sbjct: 199 TNDDTPAAYHGLIHESLSQEINNALLILNDREKEIIKMSFGIGQ-QEMNLEEIGDAFNLT 257

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQI+ KAI+KLK  +R+  L+++L
Sbjct: 258 RERVRQIKEKAIKKLKQNNRNNGLKNYL 285


>gi|262164038|ref|ZP_06031777.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
 gi|262027566|gb|EEY46232.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
          Length = 336

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 109/299 (36%), Positives = 175/299 (58%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           EL         +    E +        S+   +  +  I     ++  E    V   R+ 
Sbjct: 28  ELSSDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLYARRA 84

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 85  LRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 144

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L 
Sbjct: 145 TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELD 204

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV+ V K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L
Sbjct: 205 KPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 265 DELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREVLVKQGL 323



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 30/115 (26%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
             +  + V++ DD       E S D     +  +    + +  A   + D  +MYL E+G
Sbjct: 15  FEDEALEVLEADD-------ELSSDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIG 67

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 68  FSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|40353313|gb|AAR84420.1| essential primary sigma 70 factor [Frankia sp. ACN1ag]
          Length = 255

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 129/258 (50%), Positives = 189/258 (73%), Gaps = 6/258 (2%)

Query: 399 VACEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              EVD   +I   +   + ++V T  +  + R  +  + +   +  IAK+++VEANLRL
Sbjct: 1   AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRL 57

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y  RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ
Sbjct: 58  VVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 117

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K++R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+S
Sbjct: 118 ARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVS 177

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           LETPIG+E+ SHLGDFIED +AV P+D+A    L+E    VL +L+ RE++V+++RFG+ 
Sbjct: 178 LETPIGEEEDSHLGDFIEDCDAVVPVDAASFILLQEXLDSVLHTLSDREKKVIQLRFGLT 237

Query: 636 MNTDHTLEEVGKQFCVTR 653
                TLEEVG++F VTR
Sbjct: 238 DGHPRTLEEVGREFGVTR 255


>gi|327404710|ref|YP_004345548.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320218|gb|AEA44710.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 289

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 102/274 (37%), Positives = 168/274 (61%), Gaps = 5/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     I+  E   +   ++        A + + +ANLR V+SV+K+Y N+GL
Sbjct: 18  LDKYLQEIGRVELITAEEEVELAKRIK---AGDKRALERLTKANLRFVVSVSKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAE+FD   G+KF +YA+WW++Q+I +++A+Q+  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAERFDETRGFKFISYAVWWIRQSILQALAEQARIVRLPLNKIGT 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--S 586
           I+K+ R    +    +R P+ +E+A+ L   VE VR+ L  T   +S++ P+ D D   S
Sbjct: 135 INKINRAYSELEQVYERPPSADELAEFLECSVEDVRQSLANTARHLSMDAPLVDGDESSS 194

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + +    SP +   + +LR+   R L+SL+ RE  V+R+ +G+      TLEE+G
Sbjct: 195 SMYDVLPNDALPSPENELNKESLRKEIERSLSSLSGREGDVVRLYYGLNGKHALTLEEIG 254

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             F +TRER+RQI+ KAIR+LKH SRS+ L+S+L
Sbjct: 255 DLFDLTRERVRQIKEKAIRRLKHTSRSRMLKSYL 288



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G +EL++ E E+ +AKRI+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRVELITAEEEVELAKRIKAGDKRALERLTKANLRF--VVSVSKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|323495851|ref|ZP_08100919.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
 gi|323319067|gb|EGA72010.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
          Length = 331

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 106/277 (38%), Positives = 168/277 (60%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 47  DASAKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKI 103

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 104 SRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 163

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV+ V K+L++ +   S++TP
Sbjct: 164 RLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATKLDKPVDDVSKMLRLNERISSVDTP 223

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D N   P  S    +++ +    L  L P+++ VL  RFG+     
Sbjct: 224 IGGDGEKALLDIIPDVNNSDPEVSTQDDDIKNSLIHWLDELNPKQKEVLARRFGLLGYEP 283

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 284 STLEEVGREINLTRERVRQIQVEGLRRLREILIKQGL 320



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           +    +K    A   + D  ++YL E+G   LL+ E E+  A+R   G       + ES 
Sbjct: 37  AEEVKEKEDFDASAKSLDATQLYLGEIGFSPLLTAEEEVLYARRALRGDEAARKRMIESN 96

Query: 162 LTFQALIIWRDELNDGTTLLREI 184
           L     I  R   N G  LL  I
Sbjct: 97  LRLVVKISRRYS-NRGLALLDLI 118


>gi|146739110|gb|ABQ42602.1| chloroplast RNA-polymerase sigma factor precursor [Heterosigma
           akashiwo]
          Length = 404

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 102/309 (33%), Positives = 168/309 (54%), Gaps = 16/309 (5%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM-------VRKGECEA 441
           D    + +  +  ++   ++I   + ++    G   +E   +  +       +RK    A
Sbjct: 86  DMLTAQEEILLTRQIKRGMEIEKALVTLEKTLGRKPTEEEWVNFVGLKSIDDIRKNLKRA 145

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S +K  ++ ANLRLV+S AK Y  RG+ F DL+QEG  GL KA EKFD   G++FSTYA 
Sbjct: 146 SKSKSAIINANLRLVVSTAKAYQYRGVSFQDLVQEGTCGLHKATEKFDPRKGFRFSTYAT 205

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW+KQ I R++ DQS  +R+PVH+ D +  + R       +  REPT  E+A+   +  +
Sbjct: 206 WWIKQGIMRAVTDQSRVVRLPVHVHDALFHIRRAKANFWTEHLREPTLAELAEATGLTPQ 265

Query: 562 GVRKVLKITKEPISLE--------TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +     +  +  S++        T   ++    + D  +D        + ++ +LR+  
Sbjct: 266 KIVFYDTVKDKVSSIDKTVGIGTKTNSMEKSQIAISDMCKDSRNKPEETAQVE-SLRQDI 324

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +R++ +L+PRE+ V+RMR+G+      TLEE+G  F VTRER+RQIEA+A+ KL+ P R+
Sbjct: 325 SRLINTLSPREQDVVRMRYGLDDGEIRTLEEIGSIFSVTRERVRQIEARALHKLRQPYRN 384

Query: 674 KKLRSFLDG 682
            +L+  LD 
Sbjct: 385 HRLKGQLDS 393


>gi|257487049|ref|ZP_05641090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|320323089|gb|EFW79178.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329639|gb|EFW85628.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330878042|gb|EGH12191.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330985141|gb|EGH83244.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331009312|gb|EGH89368.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 335

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 164/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +     +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPPAASGRTKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|126667564|ref|ZP_01738534.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
 gi|126627990|gb|EAZ98617.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
          Length = 333

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 102/275 (37%), Positives = 167/275 (60%), Gaps = 3/275 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +   +  +  I     ++  E  +   + RKGE      +K M+E+NLRLV+ +A+
Sbjct: 55  SSKQLDATQLYLNEIGFSPLLTPEEEVYFARLARKGEESG---RKRMIESNLRLVVKIAR 111

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R I +Q+ TIR+
Sbjct: 112 RYVNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRL 171

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  +++  +R AR ++ ++  EPT EEIA+K+  PV+ V+++L + +   S++TPIG
Sbjct: 172 PIHVVKELNLYLRAARELTQQLDHEPTAEEIARKVDKPVKDVKRMLGLNERVASMDTPIG 231

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L D + D+ A  P D     N+     + +  L+ +++ VL  RFG+      T
Sbjct: 232 AGGEKSLLDTVADEGASDPADVLQDNNISVCLQQWIDQLSEKQQEVLARRFGLRGYPVST 291

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LEEVG++  +TRER+RQI+ +A+R+L+     + L
Sbjct: 292 LEEVGQEIGLTRERVRQIQVEALRRLREILEKEGL 326



 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 29/112 (25%), Positives = 42/112 (37%), Gaps = 11/112 (9%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD----------DPVRMYLREMGSIE 132
            + E+  +  L    +AS   V  +     A R             D  ++YL E+G   
Sbjct: 14  EQSEDAEKKKLKSGDTASPRKVATKTSAKPASRPASSRYYSSSKQLDATQLYLNEIGFSP 73

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LL+ E E+  A+    G       + ES L     I  R  +N G TLL  I
Sbjct: 74  LLTPEEEVYFARLARKGEESGRKRMIESNLRLVVKIARRY-VNRGLTLLDLI 124


>gi|157688389|gb|ABV64841.1| RpoS [Pseudomonas sp. 122]
          Length = 334

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 166/295 (56%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     ++  E  H   + +K       
Sbjct: 38  VRTKSKNSSALKQHKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQK---GDPA 94

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 95  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 155 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 215 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 274

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 275 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 329



 Score = 45.2 bits (105), Expect = 0.032,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 52/136 (38%), Gaps = 13/136 (9%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+   P  ++  E +      L   GI       +E       +     + S +S  L++
Sbjct: 3   LSKEAPEFDIDDEVL------LMESGIA------MESMSNEGPATPSVRTKSKNSSALKQ 50

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LL+ E E+  A+  + G       + ES L     I
Sbjct: 51  HKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 110

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 111 ARRY-VNRGLSLLDLI 125


>gi|302187929|ref|ZP_07264602.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           642]
          Length = 335

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 95/291 (32%), Positives = 164/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 43  AKHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 99

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 100 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 159

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 160 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRML 219

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 220 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREV 279

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 280 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 44.8 bits (104), Expect = 0.054,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +             + +  S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAVSG-----RTKAKHSTSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|258623525|ref|ZP_05718526.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|262172378|ref|ZP_06040056.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
 gi|258584187|gb|EEW08935.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|261893454|gb|EEY39440.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
          Length = 336

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 109/299 (36%), Positives = 175/299 (58%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           EL         +    E +        S+   +  +  I     ++  E    V   R+ 
Sbjct: 28  ELSSDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLYARRA 84

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 85  LRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 144

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L 
Sbjct: 145 TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELD 204

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV+ V K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L
Sbjct: 205 KPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 265 DELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 323



 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 30/115 (26%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
             +  + V++ DD       E S D     +  +    + +  A   + D  +MYL E+G
Sbjct: 15  FEDEALEVLEADD-------ELSSDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIG 67

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 68  FSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|39939114|ref|NP_950880.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|39722223|dbj|BAD04713.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 460

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 129/268 (48%), Positives = 186/268 (69%), Gaps = 7/268 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K  + E  +S  + +     + +    A  AK  +VE+N RLV+S+AK+Y  RG+ FLDL
Sbjct: 191 KHKTKEIELSEEQLQEAHDQIEQ----ARRAKDILVESNYRLVVSIAKRYIGRGILFLDL 246

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GLM+A +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVH+ + I+K+ 
Sbjct: 247 IQEGNMGLMRAVDKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHIVETINKMA 306

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDF 591
              R+++ K+K++PT EE+A K+ +  E +R +  I K+PISLE P    +ED + LGDF
Sbjct: 307 LCTRKLTQKLKKKPTVEELADKMNISAEKIRSIQYIEKKPISLEAPARENEEDETSLGDF 366

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           I D N +SP +  ++   ++    VL  +LT REE+VL+MR+G+     HTLEEVG  F 
Sbjct: 367 ISDPNILSPHEYMMKEVTQKLLDEVLENTLTDREEKVLKMRYGLLDGKTHTLEEVGTLFG 426

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VTRERIRQIE+KA+R+L+ P++  KL+S
Sbjct: 427 VTRERIRQIESKALRRLRTPAKQSKLKS 454



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 31/147 (21%), Positives = 53/147 (36%), Gaps = 17/147 (11%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N   P    +++   D  + L+N  +   D +  ED     +        S   +   ++
Sbjct: 70  NDTQPQTNTTNDDFTDLDSELTNANLENTDDNKDEDNTQDSEEDIQDFDISEEDLISDEK 129

Query: 110 -------------KDSADRSTDDPVRMYLREMGSIELLSREGE----IAIAKRIEAGRAM 152
                        K  +D   DD VRMYL+E+G I LLS   E    I +    +A + +
Sbjct: 130 LIELEEDEDEKISKIHSDIKMDDSVRMYLKEIGQIPLLSLAEEQKKSILVFLGKQAKQKL 189

Query: 153 MMASLCESPLTFQALIIWRDELNDGTT 179
                 E  L+ + L    D++     
Sbjct: 190 AKHKTKEIELSEEQLQEAHDQIEQARR 216


>gi|193216316|ref|YP_001997515.1| RpoD family RNA polymerase, sigma 70 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193089793|gb|ACF15068.1| RNA polymerase, sigma 70 subunit, RpoD family [Chloroherpeton
           thalassium ATCC 35110]
          Length = 299

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 101/283 (35%), Positives = 171/283 (60%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
             +   ++ I     ++  E   +   ++K            EA  A +++++ANLR V+
Sbjct: 16  QSLDRYLQEIGKFDLLTAQEEIELTRQIKKGDGQPIDSKEYREARRALEKLIKANLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLSLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P+ EE+A  L M    +   LKI    IS++
Sbjct: 136 IVRLPLNRVGTLNKIGKAFSQLEQEYERDPSTEELAHLLDMNSSEITDTLKIAGRHISVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++ +   P    +Q +LR    R L++L+PRE  V+R  FGIGM 
Sbjct: 196 APFAQGDDNRLLDVLQNDSQ-RPDHGLLQESLRLEVERSLSALSPREADVIRSYFGIGME 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+H   S  L+ ++
Sbjct: 255 NPLTLEEIGERFKLTRERVRQIKEKAIRRLRHSPYSNVLKEYI 297


>gi|34499137|ref|NP_903352.1| RNA polymerase sigma factor RpoS [Chromobacterium violaceum ATCC
           12472]
 gi|34104988|gb|AAQ61344.1| RNA sigma factor RpoS [Chromobacterium violaceum ATCC 12472]
          Length = 316

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 102/270 (37%), Positives = 160/270 (59%), Gaps = 4/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     ++  E    +++ R+       A+++M+E NLRLV+++AK Y NRGL  L
Sbjct: 49  YLNDIGNNALLTPQEE---LALARRVVAGEFEARQKMIEHNLRLVVNIAKHYINRGLALL 105

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGNIGLM A EKFD   G++FSTYA WW++Q+I R+I +QS TIR+PVH+  +++ 
Sbjct: 106 DLIEEGNIGLMHALEKFDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHVIKELNV 165

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            +R +R + ++I REP+ EEIA  +  PVE VRKVL + +   SL+ P+  +    +G+ 
Sbjct: 166 YLRASRHLESQIGREPSVEEIAHLVGKPVEDVRKVLNLNERMASLDAPLDIDPMLSIGES 225

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D+    P      + L       L+ L  ++  V+  R+G+      TLEE+     +
Sbjct: 226 IPDEQHEEPELQLHNSQLEMFVHDWLSQLNEKQRLVIERRYGLNGYEICTLEELAASLNL 285

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL-RSFL 680
           TRER+RQI+ + + +L+   R K + R FL
Sbjct: 286 TRERVRQIQIEGLEQLRRILRRKGISRDFL 315



 Score = 42.1 bits (97), Expect = 0.30,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL ++G+  LL+ + E+A+A+R+ AG       + E  L     I     +N G 
Sbjct: 44  DVTQIYLNDIGNNALLTPQEELALARRVVAGEFEARQKMIEHNLRLVVNIAKHY-INRGL 102

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            LL  I         E   G  H  E    ++
Sbjct: 103 ALLDLI--------EEGNIGLMHALEKFDPER 126


>gi|269929031|ref|YP_003321352.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269788388|gb|ACZ40530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 359

 Score =  185 bits (469), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 160/272 (58%), Gaps = 3/272 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + I   R     +     +   E    +  +      A  A+++++  NLRLV+S
Sbjct: 82  LLTHREEIEYSRAVRAGLEARKRLEAGEDSEELHQI---IERAKAAREKLIRHNLRLVVS 138

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY   GL  +DLIQEGNIGLM A E++D  LGY+FSTYA +W++QAI R++A+QS T
Sbjct: 139 IAKKYRTSGLPLIDLIQEGNIGLMTAVERYDPELGYRFSTYATFWIRQAIGRAVANQSRT 198

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM D I KV RT  ++     R  T +E+A+ L + VE + +         SL+ 
Sbjct: 199 IRVPVHMHDLISKVRRTEAQLEQLHGRPATDQELAQALDLDVERIEQARSAIPRTSSLDK 258

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIG++  S +GD + D  +   +D A+ + +R+   R L SL+ RE  VL +RFG+G   
Sbjct: 259 PIGEDGESTIGDLLPDPASDEVVDQAVTSAIRDQIRRSLESLSERERGVLTLRFGLGGQQ 318

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL E+ + + ++RER+RQIE +A+ KL++ 
Sbjct: 319 PQTLAEIAEYYGISRERVRQIEKEALAKLRNS 350


>gi|48727551|gb|AAT46075.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
          Length = 334

 Score =  185 bits (469), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 38  VRAKSKHSASLKQHKHIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 94

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 95  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 154

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 155 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 214

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 215 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 274

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 275 QREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 329



 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 54/136 (39%), Gaps = 13/136 (9%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L    I      D    EGS   +    + S  S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETDI----ATDSMSNEGSA--VPSVRAKSKHSASLKQ 50

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 51  HKHIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 110

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 111 ARRY-VNRGLSLLDLI 125


>gi|25900789|emb|CAD57977.1| RNA polymerase sigma factor [Pseudomonas oleovorans]
          Length = 335

 Score =  185 bits (469), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 159/274 (58%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I  Q+ TIR+P H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMSQTRTIRLPFH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + + +L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLERLREILEKNGLSS 330



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  + +      L   GI V++ D + DE      +    + + S   L++
Sbjct: 3   LSKEVPEFDIDDDLL------LMETGI-VLETDVVSDEPA----VSSVRTRAKSGSSLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|22298374|ref|NP_681621.1| RNA polymerase sigma factor [Thermosynechococcus elongatus BP-1]
 gi|22294553|dbj|BAC08383.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 309

 Score =  185 bits (469), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 108/267 (40%), Positives = 176/267 (65%), Gaps = 10/267 (3%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +  +    ++ +E  +I+            AK++M+EANLRLV+SVAKKY  R L+ LDL
Sbjct: 51  EEWAAACNLTPTELCNILKR-------GERAKQKMIEANLRLVVSVAKKYQKRNLELLDL 103

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+ 
Sbjct: 104 VQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIK 163

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           RT R ++ K+ R  TP E+AK L +  E +R+ L + ++P+SL+  +GD   + LG+ +E
Sbjct: 164 RTQRELAQKLGRSATPAEVAKALELEPEQIREYLTLARQPVSLDLRVGDNQDTELGELLE 223

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +++SP       +LR+     LA LTP++ +VL +R+G+G   + +L +VG+Q  ++R
Sbjct: 224 D-DSLSPEQFTTVESLRDDVNLWLAELTPQQRQVLTLRYGLGDGQELSLAKVGEQLNLSR 282

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQ+E +A+  L+   R +++  +L
Sbjct: 283 ERVRQLERQALDHLRR--RRQQMYEYL 307



 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 12/28 (42%), Positives = 20/28 (71%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEA 148
           VR YL+E+G + LL+ E EI + K+++ 
Sbjct: 2   VRTYLQEIGRVPLLTHEQEIILGKQVQQ 29


>gi|17231741|ref|NP_488289.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|8489803|gb|AAF75759.1|AF262218_1 group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|17133384|dbj|BAB75948.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
          Length = 390

 Score =  185 bits (469), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 183/285 (64%), Gaps = 2/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    D    ++ +I     +  ++  +       +     +  +AK++M+ +NLRLV
Sbjct: 106 RFLEEVRDLQADLQLQIGQHPTKAQVA-GQLEITEKQLENRLYQGRVAKRKMIRSNLRLV 164

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 165 VSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWWIRQAITRAIANDA 224

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +  K  R P+  E+A+ L + V  +R++ ++ ++ +SL
Sbjct: 225 RTIRLPIHIVEKLNKLKKAQRELKQKFSRNPSEAEMAEALEISVPQLRQLQQLRRQALSL 284

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIG 635
              +G E+ + L D +ED++ +SP     +  +R+    VL   LTPRE+ V+ +R+G+ 
Sbjct: 285 NHRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLT 344

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ +L
Sbjct: 345 TSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKGWL 389



 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST--DDPVR 122
           + +  +     + +D  +L  EE    + +L S   +S   +   + S    T  DD V 
Sbjct: 22  EIIESVVEHEEHSLDTLELIIEEEPPITENLDSEERDSGDEMAAARPSGYNKTEHDDAVG 81

Query: 123 MYLREMGSIELLSREGEIAIAKRI 146
            + +EM    LL  + E+ +A+R+
Sbjct: 82  AFFKEMARYPLLKPDEEVELARRV 105


>gi|260591639|ref|ZP_05857097.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260536439|gb|EEX19056.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 287

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 167/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  ISI E   +   +RK       A + + +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEEMISIEEEVELAQQIRK---GDRKALERLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    
Sbjct: 75  SLSDLINEGNFGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+ +EIA+   +P E + +  KI    IS++ P  D+D S L
Sbjct: 135 VNKINKVLNKFEQENERRPSIDEIAQDTDIPEEKIIEAFKINTHHISVDAPFHDDDESSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I +    S   S ++ +LR    RVL  L  RE++V+   FGI    + TLEE+G +
Sbjct: 195 LDVIPNDAIPSTDKSLVEESLRAEIGRVLDILEDREKKVIEAYFGINQ-REMTLEEIGSK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI+ KAIR+L+  + SK L+++L
Sbjct: 254 YGLTRERVRQIKEKAIRRLRQQTNSKILKAYL 285



 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  E++S E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGHEEMISIEEEVELAQQIRKGDRKALERLTKANLRF--VVSVAKQYQNQGLSLSD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|313891780|ref|ZP_07825385.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|329121139|ref|ZP_08249770.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|313119774|gb|EFR42961.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|327471301|gb|EGF16755.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 374

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 133/261 (50%), Positives = 180/261 (68%), Gaps = 9/261 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVISV 459
           ++  +K I     ++  E   +   V K          +  A  AKK + +ANLRLV+S+
Sbjct: 99  VKMYLKEIGTVDLLTAEEEVTLAKAVEKGLLLGATEEEKINADKAKKALSDANLRLVVSI 158

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY  RGLQFLDLIQEGN+GL+KA +KFD+  GYKFSTYA WW++Q+ITR+IADQ+ TI
Sbjct: 159 AKKYLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGYKFSTYATWWIRQSITRAIADQARTI 218

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVHM + I+K+ R +R++  +  REPT  EIAK + + V  VR+V KI ++PISLETP
Sbjct: 219 RVPVHMVETINKLNRISRQLLQEKGREPTEYEIAKAMDVSVGKVREVKKIAQDPISLETP 278

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+++ SHLGDFIED++A++P D+     L+E    +L +LT RE +VL +RFG+     
Sbjct: 279 IGEKEDSHLGDFIEDQDAIAPDDATDSILLKEQIEELLTNLTDRERQVLELRFGLKDGRP 338

Query: 640 HTLEEVGKQFCVTRERIRQIE 660
            TLEEVG  F VTRERIRQIE
Sbjct: 339 RTLEEVGNNFDVTRERIRQIE 359



 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/169 (20%), Positives = 69/169 (40%), Gaps = 21/169 (12%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           ++  +++ + + + G ++ + +N F+  + +  E ++   A L   GI+V          
Sbjct: 14  EEWIEELNEKSDKDGMISGDIVNDFVNENHIDIEGLDLLNAALHEHGIDVY--------M 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
                 D   +         K      +  DDPV+MYL+E+G+++LL+ E E+ +AK +E
Sbjct: 66  NVPGDEDSEENNKPLKKIQPKPSKRVSQGIDDPVKMYLKEIGTVDLLTAEEEVTLAKAVE 125

Query: 148 AGR------------AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G                  +L ++ L     I  +  L  G   L  I
Sbjct: 126 KGLLLGATEEEKINADKAKKALSDANLRLVVSIAKKY-LGRGLQFLDLI 173


>gi|157169065|ref|YP_258338.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
 gi|1000294|gb|AAB02846.1| RpoS [Pseudomonas fluorescens Pf-5]
 gi|157061761|gb|AAY90494.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
          Length = 335

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 39  VRTKSKSSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVAEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L    I   D D + + EG+        + S SS  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMESSI---DMDSMSNNEGATPPS--VRTKSKSSASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|298488362|ref|ZP_07006394.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298157184|gb|EFH98272.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 335

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 163/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L  +  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSHSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +     +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPPAASGRAKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|85712119|ref|ZP_01043172.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
 gi|85694109|gb|EAQ32054.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
          Length = 333

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 103/265 (38%), Positives = 166/265 (62%), Gaps = 3/265 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     ++  E    +   R+       A+K M+E+NLRLV+ +A++Y NRGL  L
Sbjct: 63  YLSEIGFSPLLTAEEE---IFYSRRALKGDIAARKRMIESNLRLVVKIARRYCNRGLALL 119

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++ 
Sbjct: 120 DLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNV 179

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            +R AR +++K+  EPT E+IA  L  PVE + K+L++ +   S++TPIG ++   L D 
Sbjct: 180 YLRAARELAHKLDHEPTAEDIAASLNKPVEDITKMLRLNERVTSVDTPIGGDNDKALLDI 239

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+    P       +L+E  T  L +L P+++ VL  RFG+      TLE+VG +  +
Sbjct: 240 LTDEADDGPEGVLQDGDLKERITEWLDALNPKQKEVLARRFGLLGYEPSTLEDVGHEIGL 299

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQI+ +A+RKL+   R + L
Sbjct: 300 TRERVRQIQVEALRKLRDFLRQQGL 324



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 3/111 (2%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            ++V++  +++    S+D  D  +S    ++          +   D  ++YL E+G   L
Sbjct: 15  EVDVLEEGEVDPSTLSDDVRD--NSEEEQALEEALVSSGQYQRKMDATQIYLSEIGFSPL 72

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L+ E EI  ++R   G       + ES L     I  R   N G  LL  +
Sbjct: 73  LTAEEEIFYSRRALKGDIAARKRMIESNLRLVVKIARRY-CNRGLALLDLV 122


>gi|289626003|ref|ZP_06458957.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289651481|ref|ZP_06482824.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330868573|gb|EGH03282.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 335

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 164/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.6 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +     +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPPAASGRAKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|282900303|ref|ZP_06308254.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
 gi|281194808|gb|EFA69754.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
          Length = 399

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 108/250 (43%), Positives = 172/250 (68%), Gaps = 1/250 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD  
Sbjct: 149 KQLESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPD 208

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K  R PT  E
Sbjct: 209 KGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKFARNPTEVE 268

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ L M V+ +R++ ++ ++ +SL   +G E+ + L D +ED++  SP     +  +R+
Sbjct: 269 MAEFLEMTVQQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNQSPEAKMNENMMRQ 328

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL   LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P
Sbjct: 329 EIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRP 388

Query: 671 SRSKKLRSFL 680
             +K+L+ +L
Sbjct: 389 HIAKRLKGWL 398



 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 9/102 (8%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            EQ E ++  L N+   V +   + +   S++       A+  S + +          DD
Sbjct: 35  VEQEEPSLDNLDNLEAVVFEDSSILESLESDERDGDEMGAARPSGYNKTEH-------DD 87

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCE 159
            V  + +EM    LL  + E+ +A+R+        + A+L E
Sbjct: 88  AVGAFFKEMARYPLLKPDEEVELARRVRFLEEVKDLQAALEE 129


>gi|66044622|ref|YP_234463.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           B728a]
 gi|289675304|ref|ZP_06496194.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           FF5]
 gi|6644290|gb|AAF20993.1|AF208000_1 RpoS [Pseudomonas syringae pv. syringae]
 gi|24415296|gb|AAN59882.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|24415299|gb|AAN59884.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|63255329|gb|AAY36425.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Pseudomonas syringae pv. syringae B728a]
 gi|330896091|gb|EGH28312.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 335

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 164/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 44.4 bits (103), Expect = 0.064,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 50/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +          +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAVSGRTKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|291565943|dbj|BAI88215.1| group 2 RNA polymerase sigma factor SigD [Arthrospira platensis
           NIES-39]
          Length = 331

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 176/278 (63%), Gaps = 6/278 (2%)

Query: 406 ILKIRNEIKS--ISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + + RNE+        T    +E  ++ V+ ++    +  +AK++MVEANLRLV+SVAKK
Sbjct: 55  LQEKRNELAKQLAYEPTEAQWAELVNLSVAQLQHILHQGQLAKRKMVEANLRLVVSVAKK 114

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P
Sbjct: 115 YIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLP 174

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+ +K++K+ +  R+++ ++ R  T  E+A +L +  + +R+ L+ ++ P+SL+  +GD
Sbjct: 175 IHITEKLNKIKKAQRQLAQQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLDLRVGD 234

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              + L D +ED    SP   A+ ++LR     ++  LT ++ +VL +RFG+      TL
Sbjct: 235 NQDTELVDLLEDT-TNSPEQFALNSSLRSDLESLMTDLTDQQRQVLALRFGLDDGQTLTL 293

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++G +  ++RER+RQIE +A+ KL+   R + +  +L
Sbjct: 294 AKIGDRLNISRERVRQIEREALTKLRK--RKQDVNDYL 329



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI------AKRIEAGRAMMMASLCESP 161
               +A  S  D VR YLRE+G + LL+ E EI        A  ++  R  +   L   P
Sbjct: 11  DAMKTAKTSDTDSVRAYLREIGRVPLLTHEQEIVYGKQVQQATLLQEKRNELAKQLAYEP 70


>gi|153827661|ref|ZP_01980328.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
 gi|149737861|gb|EDM52766.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
          Length = 305

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 80/337 (23%), Positives = 133/337 (39%), Gaps = 39/337 (11%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K+++   +++GY+T  E+N  LP + V SEQ+ED + M+++MGI VV+     D+ 
Sbjct: 6   QSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQ-KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              D   +    +  +        +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  ALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES-KGGFFHGTEG 205
           E G   + +++ E P T   ++   D +      L ++I     + P   +      T  
Sbjct: 126 EDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLI--SGFVDPNDMETEAPTATHI 183

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
            S     D + E +     E E + E     S D   +V   PE A      L       
Sbjct: 184 GSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELR------ 237

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                           Q+  +   +  + S +     + ++ + 
Sbjct: 238 -----------------------------GKFQNLQLAVNEFGRDSHQASEASDLVLDIF 268

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
               L   + D LVE L     R+   E  +++    
Sbjct: 269 REFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVE 305


>gi|171909626|ref|ZP_02925096.1| RNA polymerase sigma factor [Verrucomicrobium spinosum DSM 4136]
          Length = 298

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 106/263 (40%), Positives = 162/263 (61%), Gaps = 3/263 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++  +   +   ++K       A+  M+ ANLRLV+ +A+ Y N GL  L
Sbjct: 13  YLREIGKTDLLTPQQEVELAERIKK---GDPEARSHMIRANLRLVVKIAQDYANYGLPLL 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLMKA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVHM DKI K
Sbjct: 70  DLISEGNIGLMKAVERFDPNKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHMVDKISK 129

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + R A  MS ++ REPT +E+++++ +    + ++   +  P SL+ PI ++D++  G+ 
Sbjct: 130 MRRVAMAMSEELGREPTDDELSEEIGIDRGKLSQLKVASMRPASLDAPISEDDSTEFGEI 189

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+NA +P D     N+      +L  L  RE +++  RFG+      TLEEVG++F V
Sbjct: 190 VGDENAQTPFDLLSHKNMHSQLDGLLTVLDERERKIIDARFGLNGQKARTLEEVGQEFGV 249

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           TRERIRQ++  A+RKL+   + K
Sbjct: 250 TRERIRQLQNIALRKLRRALQKK 272



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 3/85 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +++YLRE+G  +LL+ + E+ +A+RI+ G     + +  + L    ++    +  +    
Sbjct: 10  IKIYLREIGKTDLLTPQQEVELAERIKKGDPEARSHMIRANLRL--VVKIAQDYANYGLP 67

Query: 181 LREIIDLEACIGPESKGGFFHGTEG 205
           L ++I  E  IG       F   +G
Sbjct: 68  LLDLIS-EGNIGLMKAVERFDPNKG 91


>gi|71736784|ref|YP_275947.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557337|gb|AAZ36548.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 335

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 163/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+      TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGYESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +     +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPPAASGRTKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|258623793|ref|ZP_05718750.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
 gi|258583916|gb|EEW08708.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
          Length = 336

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 108/299 (36%), Positives = 175/299 (58%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E+         +    E +        S+   +  +  I     ++  E    V   R+ 
Sbjct: 28  EISSDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLYARRA 84

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 85  LRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 144

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L 
Sbjct: 145 TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELD 204

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV+ V K+L++ +   S++TPIG +    L D + D N   P  S    ++RE+    L
Sbjct: 205 KPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSNNADPEFSTQDDDIRESLLNWL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 265 DELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 323



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/113 (29%), Positives = 42/113 (37%), Gaps = 7/113 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD------DPVRMYLREMGSI 131
           V+  D EDE       D   S+    V  +   D      D      D  +MYL E+G  
Sbjct: 10  VEEFDFEDEALEVLEADDEISSDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIGFS 69

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  PLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|75907421|ref|YP_321717.1| sigma 28 (flagella/sporulation) [Anabaena variabilis ATCC 29413]
 gi|75701146|gb|ABA20822.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 378

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 106/250 (42%), Positives = 172/250 (68%), Gaps = 1/250 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     +  +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +A EKFD  
Sbjct: 128 KQLENRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPD 187

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K  R P+  E
Sbjct: 188 KGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELKQKFSRNPSEAE 247

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ L + V  +R++ ++ ++ +SL   +G E+ + L D +ED++ +SP     +  +R+
Sbjct: 248 MAEALEISVPQLRQLQQLRRQALSLNHRVGKEEDTELMDLLEDEDNLSPEAKMNENMMRQ 307

Query: 612 TTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL   LTPRE+ V+ +R+G+  +   TLEEVG  F ++RER+RQI++KA+RKL+ P
Sbjct: 308 EIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRP 367

Query: 671 SRSKKLRSFL 680
             +K+L+ +L
Sbjct: 368 HIAKRLKGWL 377



 Score = 43.3 bits (100), Expect = 0.12,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST--DDPVR 122
           + +  +     + +D  +L  EE    + +L S   +S   +   + S    T  DD V 
Sbjct: 10  EIIESVVEHEEHSLDALELIIEEEPPITDNLDSEERDSGDEMAAARPSGYNKTEHDDAVG 69

Query: 123 MYLREMGSIELLSREGEIAIAKRI 146
            + +EM    LL  + E+ +A+R+
Sbjct: 70  AFFKEMARYPLLKPDEEVELARRV 93


>gi|330894625|gb|EGH27286.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. mori
           str. 301020]
          Length = 335

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 164/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYARALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.2 bits (105), Expect = 0.032,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 51/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +     +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPPAASGRAKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YARALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|332532870|ref|ZP_08408743.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332037716|gb|EGI74167.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 324

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 106/280 (37%), Positives = 167/280 (59%), Gaps = 3/280 (1%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
                   ++   +  +  I     +S  E    V   RK       ++K M+E+NLRLV
Sbjct: 38  FAKEEVTKNLDATQLYLGEIGFSPLLSAEEE---VFFSRKSLRGCEASRKRMIESNLRLV 94

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+
Sbjct: 95  VKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQT 154

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR ++ K+  EPT +EIA  L  PVE V K+L++ +   S+
Sbjct: 155 RTIRLPIHVVKELNVYLRTARELTQKLDHEPTADEIAACLDRPVEDVTKMLRLNERIASV 214

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           + PIG E+ S L D I D+ +  P       ++ +     L  L P++  VL  RFG+  
Sbjct: 215 DMPIGGENDSVLLDIIPDEKSAGPEGEVQNNDINKHIVDWLGELNPKQREVLARRFGLLG 274

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLE+VG++  +TRER+RQI+ +A+R+LK   + + L
Sbjct: 275 YEPSTLEDVGREIGLTRERVRQIQVEALRRLKDILQQEGL 314



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 44/109 (40%), Gaps = 2/109 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +D     DE+  +  +D +++  +     +           D  ++YL E+G   LLS E
Sbjct: 7   LDKHTTTDEKFDDIDVDESTALLDKVDDDEIFAKEEVTKNLDATQLYLGEIGFSPLLSAE 66

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E+  +++   G       + ES L    ++      N+    L ++I+
Sbjct: 67  EEVFFSRKSLRGCEASRKRMIESNLRL--VVKIARRYNNRGLALLDLIE 113


>gi|313203522|ref|YP_004042179.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Paludibacter
           propionicigenes WB4]
 gi|312442838|gb|ADQ79194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paludibacter
           propionicigenes WB4]
          Length = 287

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 102/273 (37%), Positives = 174/273 (63%), Gaps = 5/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I++ E   +   +R       IA +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIR---AGDRIALEKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R+P+PEE+A  L +PV+ +   +K++   IS++ P  + + + L
Sbjct: 135 LNKINKAFSKFEQENERKPSPEELADVLDIPVDKIADTMKVSGRHISVDAPFVEGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            D + + ++ +     I  +L +   RVLA +L+ RE  +++  FGIG+    TLEE+G 
Sbjct: 195 LDVMINDDSPNADRVLINESLSKEIERVLAFTLSDRERDIVKKFFGIGVAE-MTLEEIGD 253

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +F +TRER+RQI+ KAIRKL+  ++SK L+ FL
Sbjct: 254 EFGLTRERVRQIKEKAIRKLRPNAKSKLLKGFL 286



 Score = 44.4 bits (103), Expect = 0.058,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  +L++ E E+ +A+RI AG  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREDLITVEEEVELAQRIRAGDRIALEKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|127512145|ref|YP_001093342.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637440|gb|ABO23083.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella loihica
           PV-4]
          Length = 324

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 106/301 (35%), Positives = 178/301 (59%), Gaps = 4/301 (1%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVR 435
            E D    +  +   + E +  V  ++  ++   +  +  I     +S  E    V   R
Sbjct: 19  NESDLSVTNSKEVLKDAELEQQVQDDLQKNLDATQLYLSEIGFSPLLSAEEE---VYFSR 75

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K       ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++
Sbjct: 76  KALKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFR 135

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA++
Sbjct: 136 FSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEQ 195

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +P   V K+LK+ +   S++TP+G ++   L D + D + V P       ++ ++  R
Sbjct: 196 LDLPSSDVSKMLKLNERITSVDTPLGGDNDKALLDVLADDDCVGPDYKVQDDDMSKSVVR 255

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++L+    ++ 
Sbjct: 256 WLDELNSKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLRDLLSAQG 315

Query: 676 L 676
           L
Sbjct: 316 L 316



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 42/109 (38%), Gaps = 2/109 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V    ++  +   D     S        L+++     +   D  ++YL E+G   LLS E
Sbjct: 9   VAEPLVDLSKNESDLSVTNSKEVLKDAELEQQVQDDLQKNLDATQLYLSEIGFSPLLSAE 68

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E+  +++   G       + ES L    ++      N+    L ++I+
Sbjct: 69  EEVYFSRKALKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 115


>gi|194290015|ref|YP_002005922.1| RNA polymerase sigma factor rpos [Cupriavidus taiwanensis LMG
           19424]
 gi|193223850|emb|CAQ69859.1| RNA polymerase sigma factor rpoS [Cupriavidus taiwanensis LMG
           19424]
          Length = 395

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 99/271 (36%), Positives = 161/271 (59%), Gaps = 5/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  +S  E  H  ++ +        A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 123 VQHYLNRISIKPLLSAPEELHFSTLAK---DGDFAARQVMIERNLRLVVSIAKGYLNRGV 179

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 180 PLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 239

Query: 529 IHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +++V+R  R +       R+ + E+IA  L    + V+ VL + +   SL+TP   +  S
Sbjct: 240 LNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPFDLDPGS 299

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L DF+ D++  +P        L       LA L+ +   V+  RFG+      TLEE+ 
Sbjct: 300 SLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNHIEPATLEELA 359

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++  +TRER+RQI+ +A+ KLK    S+ +R
Sbjct: 360 EEMGLTRERVRQIQQEALVKLKRHFASQGVR 390



 Score = 39.1 bits (89), Expect = 3.0,   Method: Composition-based stats.
 Identities = 43/299 (14%), Positives = 88/299 (29%), Gaps = 28/299 (9%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           + S ++     R         D V+ YL  +    LLS   E+  +   + G       +
Sbjct: 100 TESAAAEHDDFRTVLHTELAADTVQHYLNRISIKPLLSAPEELHFSTLAKDGDFAARQVM 159

Query: 158 CESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
            E  L     I            D + +G   L   I+            +       S 
Sbjct: 160 IERNLRLVVSIAKGYLNRGVPLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSI 219

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
           ++   +     R  V       +        ++   D    + E+    L +  D+    
Sbjct: 220 ERAIMNQARTVRLPVHVIRELNQVLRAKRHLEKGGTDGRDASLEDIAHLLGKTPDEVQDV 279

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL----------- 317
           L+  E       +    ++      L  L D        E +  + + L           
Sbjct: 280 LALNE---HTTSLDTPFDLDPGSSLLDFLSDEHNAAPDQEVAHRELEGLMKLWLARLSEK 336

Query: 318 -KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE----LLRLAQSYGIKRDVFL 371
            +  + +  G   +  + ++ L E++    +R+   + E    L R   S G+++D  L
Sbjct: 337 HRYVVERRFGLNHIEPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQGVRKDAVL 395


>gi|119487601|ref|ZP_01621211.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
 gi|119455770|gb|EAW36906.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
          Length = 404

 Score =  185 bits (468), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 116/273 (42%), Positives = 181/273 (66%), Gaps = 2/273 (0%)

Query: 411 NEIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +++K I        +E   + V  + + + E   AK  M++ANLRLV+SVAKKY NRGL+
Sbjct: 131 SDLKPIIAAGKRRWAELAELTVEELDQVQTEGIKAKDHMIKANLRLVVSVAKKYQNRGLE 190

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q ITR+IA QS TIR+PVH+ +K+
Sbjct: 191 LLDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQGITRAIATQSRTIRLPVHITEKL 250

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ +  R++S +  R  T ++IA +L M    VR+VL      +SLET +G +  + LG
Sbjct: 251 NKIKKAQRKISQEKGRIATIDDIAAELEMTPAQVREVLLKVPRSVSLETKVGSDKDTELG 310

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + +E + A SP D  ++ +L     ++LA L+ RE  V++MR+G+G    ++L E+G++ 
Sbjct: 311 ELLETEEA-SPEDQLMRESLHRDLQQLLADLSDRERDVIQMRYGLGNGHTYSLAEIGREL 369

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            ++RER+RQIEAKA++KL+ P R  ++R +L+ 
Sbjct: 370 ELSRERVRQIEAKALQKLRQPKRRNRVRDYLES 402



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 47/282 (16%), Positives = 103/282 (36%), Gaps = 26/282 (9%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D + E+ S+   DL   +       QK K++ +R T D VR+YL+E+G + LL R+ E+A
Sbjct: 11  DRDLEDLSKQPSDLDLESMEEIDPAQKTKNNNNRRTTDLVRVYLQEIGRVRLLGRDEEVA 70

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
            A++++  + ++        L  +A    +  L     LL+    L A +G       + 
Sbjct: 71  EAQKVQRYQRLIQ-------LRDKAAAEEKGILETFAMLLQTRSRLVAQLGHSPSLERWA 123

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
              G      +      +R   +  E  +E   +V  +     D   +            
Sbjct: 124 AVSGVEVSDLKPIIAAGKRRWAELAELTVEELDQVQTEGIKAKDHMIKA----------- 172

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC----KVL 317
              +   + ++  + + + +  LD I E    L    +     +    S+       + +
Sbjct: 173 ---NLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQGI 229

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              +     ++ L    I   + ++    ++I   +G +  +
Sbjct: 230 TRAIATQSRTIRL-PVHITEKLNKIKKAQRKISQEKGRIATI 270


>gi|260775503|ref|ZP_05884400.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608684|gb|EEX34849.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 327

 Score =  184 bits (467), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 107/293 (36%), Positives = 173/293 (59%), Gaps = 3/293 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++ A      + K        S+   +  +  I     ++  E    V   R+       
Sbjct: 27  LTTANRTQAEDAKEEFDASTKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEA 83

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 84  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 143

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 144 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDV 203

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 204 SKMLRLNERISSVDTPIGGDGEKALLDIIPDVNNSDPEVSTQDDDIKSSLIHWLDELNPK 263

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 264 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQGL 316



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 41/105 (39%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +   +        +  ++A+ +     K +  A   + D  ++YL E+G   LL+ E E
Sbjct: 11  EEFELEPTMESIQANGLTTANRTQAEDAKEEFDASTKSLDATQLYLGEIGFSPLLTAEEE 70

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 71  VLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 114


>gi|229496411|ref|ZP_04390127.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
 gi|229316639|gb|EEN82556.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
          Length = 287

 Score =  184 bits (467), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 169/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I + E   +   +R+G      A+ ++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREELIDVDEEVRLAQEIRRGN---RRAQDKLTRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGA 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             K+ +   +   + +R P+  E+A  L    E V   LK   + +S++ P  D + + L
Sbjct: 135 QAKIKKAIEQFEQENERRPSIAELAIILDQSEEKVAVTLKSFSKHVSIDAPFVDGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + +++A S   S ++ +L     RVL++L+ RE  ++++ FGIG N + TLEE+G +
Sbjct: 195 LDVLVNEDAPSTDRSLMRDSLNTEIDRVLSTLSEREAEIIKLFFGIGPNPEMTLEEIGDK 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIRKL+  ++  +L+SFL
Sbjct: 255 FGLTRERVRQIKEKAIRKLRAGNKCDQLKSFL 286



 Score = 41.0 bits (94), Expect = 0.71,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  EL+  + E+ +A+ I  G       L  + L F  ++    +  +    L +
Sbjct: 21  YLQEIGREELIDVDEEVRLAQEIRRGNRRAQDKLTRANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +ID
Sbjct: 79  LID 81


>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]
          Length = 575

 Score =  184 bits (467), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 96/247 (38%), Positives = 153/247 (61%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK     +  K  M+++N+RLVIS+AK Y   G+ F DL+QEG  GL++ AEKFD   G
Sbjct: 322 LRKRITHGTQCKDRMIKSNIRLVISIAKNYQGAGMDFQDLVQEGCRGLVRGAEKFDATKG 381

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++DQS  IR+P HM +  ++V    +++ ++  ++P  EE+A
Sbjct: 382 FKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKQPKNEEVA 441

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  IG        + I D  A +  D  ++  +R+  
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIGINLNLKPSEVIADPEAETSEDILMKQFMRQDL 501

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL+ RE++V+R RFG+      TL+E+G+   V+RER+RQI+  A RKLK+  R+
Sbjct: 502 DKVLDSLSTREKQVIRWRFGMEDGRMKTLQEIGETMGVSRERVRQIDTSAFRKLKNKKRN 561

Query: 674 KKLRSFL 680
             L+ +L
Sbjct: 562 SHLQQYL 568


>gi|56267933|gb|AAV85439.1| RpoS [Listonella anguillarum]
 gi|56267935|gb|AAV85440.1| RpoS [Listonella anguillarum]
 gi|167987243|gb|ACA13292.1| RpoS [Listonella anguillarum]
 gi|222101826|gb|ACM44037.1| RNA polymerase sigma factor [Listonella anguillarum]
          Length = 333

 Score =  184 bits (467), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 108/277 (38%), Positives = 168/277 (60%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 49  DASTKSLDATQMYLSEIGFSPLLTAQEE---VLYARRSLRGDEAARKRMIESNLRLVVKI 105

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 106 SRRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 165

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PVE V K+L++ +   S++TP
Sbjct: 166 RLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAFQLDKPVEDVSKMLRLNERISSVDTP 225

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D N   P  S    ++RE+    L  L P+++ VL  RFG+     
Sbjct: 226 IGGDGDKALLDIIPDTNNSDPEISTQDDDIRESLLNWLDELNPKQKEVLARRFGLLGYEP 285

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 286 STLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 322



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/112 (27%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIE 132
           +   +  ++ D    ++ L    S S+  V ++  K+  D ST   D  +MYL E+G   
Sbjct: 10  VEEFEDQEIMDSIEVDEELTTTKSQSDDDVQIEDAKEGFDASTKSLDATQMYLSEIGFSP 69

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LL+ + E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  LLTAQEEVLYARRSLRGDEAARKRMIESNLRLVVKISRRYG-NRGLALLDLI 120


>gi|2618586|dbj|BAA23365.1| sigma factor [Vibrio cholerae]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 110/303 (36%), Positives = 176/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    S  +          V  E D    S+   +  +  I     ++  E    V  
Sbjct: 24  ETDAELTSDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY  WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYTTWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D      E  +E + D    A   +    + +  A   + D  +MYL E+G   LL+ E 
Sbjct: 17  DEALEVLETDAELTSDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEE 76

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|37680992|ref|NP_935601.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
 gi|37199742|dbj|BAC95572.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
          Length = 330

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 111/313 (35%), Positives = 182/313 (58%), Gaps = 10/313 (3%)

Query: 371 LERHQGRELDPHW---VSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGIS 423
           ++     ++D  +   +   +     E K  +  E D    S+   +  +  I     ++
Sbjct: 10  VKDFDVNQMDDDFNDDIEINEKEDLTEEKVTLREEFDASNKSLDATQLYLGEIGFSPLLT 69

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++
Sbjct: 70  AEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIR 126

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+
Sbjct: 127 AVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKL 186

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EPT EEIA +L +PV+ V K+L++ +   S++TPIG +    L D I D N   P  S
Sbjct: 187 DHEPTAEEIAAQLDIPVDDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVS 246

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               ++R +    L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + 
Sbjct: 247 TQDEDMRVSLIHWLEELNPKQKEVLARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEG 306

Query: 664 IRKLKHPSRSKKL 676
           +R+L+     + L
Sbjct: 307 LRRLREVLIKQGL 319



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 49/107 (45%), Gaps = 2/107 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D + ++D+   +  ++     +   V L++  D++++S  D  ++YL E+G   LL+ E
Sbjct: 13  FDVNQMDDDFNDDIEINEKEDLTEEKVTLREEFDASNKSL-DATQLYLGEIGFSPLLTAE 71

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 72  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 117


>gi|1405331|dbj|BAA11832.1| chloroplast RNA polymerase sigma subunit [Cyanidium caldarium]
          Length = 591

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 106/250 (42%), Positives = 160/250 (64%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  +R+   +   AK+ MV ANLRLV+S+AK+Y+NRG+   DLIQEG+IGL++  EKFD 
Sbjct: 339 VEKLREHIRDGRKAKERMVTANLRLVVSIAKRYSNRGVALQDLIQEGSIGLIRGVEKFDA 398

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW++Q+ITR+I+D S +IR+PVH+ D I  + +  + +  ++ R P+ E
Sbjct: 399 ERGFRFSTYATWWIRQSITRAISDSSRSIRLPVHVHDTISLIRKQTKALQVELGRPPSEE 458

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI + + +     R V++ ++  +SLETP+   D  H              ++  +  LR
Sbjct: 459 EICESVGIDRAKYRLVMECSRNIVSLETPLRSGDDVHFLGESLIAPEERAEENCSRDTLR 518

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E+  +VL  L+ RE  V+RMRFG+      TLEEVG +F VTRERIRQIE+KA++KL+ P
Sbjct: 519 ESIEKVLHCLSTREREVIRMRFGLTDGRPRTLEEVGSRFNVTRERIRQIESKALKKLRTP 578

Query: 671 SRSKKLRSFL 680
           + +  L  +L
Sbjct: 579 AENNFLDEYL 588



 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 7/92 (7%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V    + E+ E   +S +L        V       S   + DD +R YLRE+G  +LL 
Sbjct: 234 EVYSNSETEEAESQIESDELLDFIVEE-VDPADVDLSTVEAKDDTIRSYLREIGRYQLLH 292

Query: 136 REGEIAIAKRI------EAGRAMMMASLCESP 161
              EI ++K++      E  +        +SP
Sbjct: 293 PGEEIELSKQVCILMDLEQFQRSFREEHGKSP 324


>gi|254415890|ref|ZP_05029647.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177317|gb|EDX72324.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 352

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 101/247 (40%), Positives = 168/247 (68%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K   + + AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 107 LKKIINQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRG 166

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q+  IR+P+H+ +K++K+ +  R +S ++ R  TP EI 
Sbjct: 167 YKFSTYAYWWIRQAITRAIAQQARAIRLPIHITEKLNKIKKVQRELSQRLGRNATPTEIG 226

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L +    +R+ L I ++P+SL+  +GD   + L D +ED +  +P+    Q +LR+  
Sbjct: 227 QELELEPAQIREYLSIARQPVSLDVRVGDNQDTELSDLLED-SGPTPVHYTTQESLRQDL 285

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  VL +RFG+    + +L +VG++  ++RER+RQ+E +A+ +L+   R 
Sbjct: 286 DNLLAELTPQQREVLALRFGLEDGNELSLAKVGQRLNLSRERVRQLEHQALAQLRR--RH 343

Query: 674 KKLRSFL 680
             +R ++
Sbjct: 344 ATVREYI 350



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG--RAMMMASLCESPLTF 164
            K K +    + D VR YL E+G + LL+ E EI   K+++          +L E+    
Sbjct: 31  TKPKTTKPTFSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMPLLEAKDALAETLERE 90

Query: 165 QALIIWRDELNDGTTLLREIID 186
             +  W D ++   + L++II+
Sbjct: 91  PTMQEWADHVDLEESALKKIIN 112


>gi|114320976|ref|YP_742659.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227370|gb|ABI57169.1| RNA polymerase, sigma 38 subunit, RpoS [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 342

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 99/270 (36%), Positives = 164/270 (60%), Gaps = 3/270 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+   +  +  I     +S  E  +     ++     + A+  M+E+NLRLV+ +A++Y 
Sbjct: 67  SLDATQIYLNEIGYSPLLSAEEEVYFSRRAQR---GDAAARARMIESNLRLVVKIARRYM 123

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL FLDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 124 NRGLAFLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 183

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +I++ +R AR+++ ++  EP+ EEIA  +   VE VR++  + +   S++ PIG + 
Sbjct: 184 VIKEINQYLRAARKLTQELDHEPSVEEIADHMGRDVEDVRRMRGLNEGTTSVDVPIGRDA 243

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D I D+N V P+ +    ++       L  LT ++  V+  RFG+  +   TLE+
Sbjct: 244 DRVLLDAIPDENNVDPVSALQDGDVFGNLEAWLGELTEKQRAVVERRFGLNGHDRATLEQ 303

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           VG +  VTRER+RQI+  A+R+L+     +
Sbjct: 304 VGNEIGVTRERVRQIQIDALRRLREVMERE 333



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/120 (26%), Positives = 45/120 (37%), Gaps = 8/120 (6%)

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-------DPVRMY 124
           +M I   D  D   E  S D     +    +    +       R T        D  ++Y
Sbjct: 15  DMDIVDSDDRDNRSEPVSLDGDTPQALTGETEPVNRPEPRLPRRRTQSAYQASLDATQIY 74

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L E+G   LLS E E+  ++R + G A   A + ES L     I  R  +N G   L  I
Sbjct: 75  LNEIGYSPLLSAEEEVYFSRRAQRGDAAARARMIESNLRLVVKIARRY-MNRGLAFLDLI 133


>gi|116668483|gb|ABK15514.1| sigma factor [Pseudomonas alkylphenolia]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 95/274 (34%), Positives = 162/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   +    +      +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIASLLEKPVGEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDKQREVVIRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L   GI V++ D + DE      +    + +     L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETGI-VLETDVVSDEPA----VSSVRTRAKQGSTLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|186681941|ref|YP_001865137.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186464393|gb|ACC80194.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 339

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 103/250 (41%), Positives = 169/250 (67%), Gaps = 3/250 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
             ++     +   AK++M++ANLRLV++VAKKY +R L+F+DLIQEG +GL +  +KFD 
Sbjct: 91  AEVLELQLSQGHQAKQKMIQANLRLVVAVAKKYQHRNLEFMDLIQEGTLGLERGVDKFDP 150

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            LGYKFSTYA WW++Q ITR+IA Q  TIR+P+H+ +K++K+ R  R +S ++ R PT  
Sbjct: 151 ALGYKFSTYAYWWIRQGITRAIAQQGRTIRLPIHVFEKLNKIKRVQRELSQQLGRVPTTA 210

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L++    VR+ L + ++P SLE  +G++  + L D +ED +  SP D A++ +L 
Sbjct: 211 EIANALSLTPSQVRECLYLARQPFSLEARVGEQQDTELQDILED-DGPSPEDYAVEESLH 269

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    +LA L+P++  +L +RFG+    + +L ++G +  ++RER+RQIE KA+  L+  
Sbjct: 270 QDLQDLLAKLSPQQREILTLRFGLTDGYELSLAQIGDRMGISRERVRQIEQKALSLLRR- 328

Query: 671 SRSKKLRSFL 680
            + +++RS+L
Sbjct: 329 -QKEQVRSYL 337



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 17/39 (43%), Positives = 28/39 (71%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             D   R+TDD VR YL+E+G ++LL+RE E+  A++++
Sbjct: 20  AADKKPRATDDIVRSYLQEIGRVDLLTREQEVIFAQQVQ 58


>gi|330950646|gb|EGH50906.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae Cit 7]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 95/274 (34%), Positives = 162/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   +    +      +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIANLLERPVGEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 44.4 bits (103), Expect = 0.065,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 50/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +          +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAVSGRTKVKQ-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|254255220|ref|ZP_04948536.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124900957|gb|EAY71707.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 241

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 96/239 (40%), Positives = 147/239 (61%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A+  + +ANLRLV+S+AK+Y +RGL F DLIQEGNIGL+KA E++D+  G++FSTYA 
Sbjct: 2   QPARIALFDANLRLVVSIAKRYRDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYAT 61

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++Q++T ++AD   TIR+P H  D ++K+ R AR    +     TP ++A  +  PV+
Sbjct: 62  WWIRQSVTHALADLGRTIRVPTHTVDALNKLARLAREHRQRAGSAATPAQLAAHIGEPVD 121

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR +L I KEP+S + P+  +      D   D    SP D+A    LR T    +  L 
Sbjct: 122 KVRDLLAIVKEPVSADLPVSPDGDLTFIDVAPDTATPSPEDAADATQLRRTIAAAIERLP 181

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RE  VL++R+G+  +   +L ++G+Q  ++ ER+RQIEA A+ +L+       LR F+
Sbjct: 182 QREAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRASDALAVLRPFI 240


>gi|153214922|ref|ZP_01949705.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|153826929|ref|ZP_01979596.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|153829928|ref|ZP_01982595.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|229530348|ref|ZP_04419736.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|254226840|ref|ZP_04920411.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|254291219|ref|ZP_04962015.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|262190768|ref|ZP_06048995.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
 gi|124114995|gb|EAY33815.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|125620637|gb|EAZ49000.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|148874616|gb|EDL72751.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|149739232|gb|EDM53500.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|150422913|gb|EDN14864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|229332121|gb|EEN97609.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|262033353|gb|EEY51864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 111/303 (36%), Positives = 177/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    S  +          V  E D    S+   +  +  I     ++  E    V  
Sbjct: 24  ETDAELASDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 53.3 bits (126), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D      E  +E + D    A   +    + +  A   + D  +MYL E+G   LL+ E 
Sbjct: 17  DEALEVLETDAELASDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEE 76

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|148909485|gb|ABR17840.1| unknown [Picea sitchensis]
          Length = 495

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 97/248 (39%), Positives = 160/248 (64%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++        +  +++  NLRLVISVAK Y NRGL   DLIQ G++GLM++AEKFD+  G
Sbjct: 247 LKMRLEVGRDSFDKIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRG 306

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++Q+IT+++ +QS TIR+PVH+ + + ++    R +  + KR+PT EE+A
Sbjct: 307 FKFSTYAYWWIRQSITKALTEQSRTIRLPVHIVESMTRIRTAWRLLYQEHKRDPTKEEVA 366

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + +  +R V + ++ P SL+  +G +      + + D N+ S      +   ++  
Sbjct: 367 EVAGISMTRLRHVTRCSRVPTSLDRCVGKDMDEKFSEIVADTNSESTETIVSKELFKKDL 426

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RVL +LT RE++V+R+R+G+      +L EVG+ F ++RER+RQIE KA+RKL+   R+
Sbjct: 427 DRVLDTLTAREKQVVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAMRKLRQNHRT 486

Query: 674 KKLRSFLD 681
           + L+ +LD
Sbjct: 487 QHLKHYLD 494


>gi|147674644|ref|YP_001216035.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262169845|ref|ZP_06037535.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
 gi|146316527|gb|ABQ21066.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|227012360|gb|ACP08570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262021579|gb|EEY40290.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 111/303 (36%), Positives = 177/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    S  +          V  E D    S+   +  +  I     ++  E    V  
Sbjct: 24  ETDAELTSDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D      E  +E + D    A   +    + +  A   + D  +MYL E+G   LL+ E 
Sbjct: 17  DEALEVLETDAELTSDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEE 76

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|153802558|ref|ZP_01957144.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
 gi|124121921|gb|EAY40664.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 105/277 (37%), Positives = 170/277 (61%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 50  DASAKSLDATQMYLSEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKI 106

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 107 SRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 166

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V K+L++ +   S++TP
Sbjct: 167 RLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISSVDTP 226

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D + D +   P  S    ++RE+    L  L P+++ VL  RFG+     
Sbjct: 227 IGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPKQKEVLARRFGLLGYEP 286

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 287 STLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 323



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/113 (27%), Positives = 44/113 (38%), Gaps = 7/113 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD------DPVRMYLREMGSI 131
           V+  D EDE     + D   ++    V ++   +      D      D  +MYL E+G  
Sbjct: 10  VEEFDFEDEALEVLATDAELASDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFS 69

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  PLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|229512804|ref|ZP_04402271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|229350053|gb|EEO15006.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|327483355|gb|AEA77762.1| RNA polymerase sigma factor RpoS [Vibrio cholerae LMA3894-4]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 111/303 (36%), Positives = 177/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    S  +          V  E D    S+   +  +  I     ++  E    V  
Sbjct: 24  ETDTELASDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/113 (27%), Positives = 43/113 (38%), Gaps = 7/113 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD------DPVRMYLREMGSI 131
           V+  D EDE       D   ++    V ++   +      D      D  +MYL E+G  
Sbjct: 10  VEEFDFEDEALEVLETDTELASDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFS 69

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  PLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|15640556|ref|NP_230185.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590676|ref|ZP_01678009.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121728563|ref|ZP_01681585.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|153819103|ref|ZP_01971770.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|153823615|ref|ZP_01976282.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227080717|ref|YP_002809268.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229507145|ref|ZP_04396651.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229508992|ref|ZP_04398480.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229519660|ref|ZP_04409103.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229606176|ref|YP_002876824.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254850774|ref|ZP_05240124.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255744238|ref|ZP_05418191.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262149032|ref|ZP_06028176.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
 gi|6094129|sp|O51804|RPOS_VIBCH RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38 factor
 gi|2897902|gb|AAC38175.1| sigma S [Vibrio cholerae]
 gi|9654961|gb|AAF93702.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121547462|gb|EAX57570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121629175|gb|EAX61616.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|126510335|gb|EAZ72929.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|126518864|gb|EAZ76087.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227008605|gb|ACP04817.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229344349|gb|EEO09324.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229353917|gb|EEO18851.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229355890|gb|EEO20810.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229368831|gb|ACQ59254.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254846479|gb|EET24893.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255738178|gb|EET93570.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262031177|gb|EEY49797.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
          Length = 335

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 111/303 (36%), Positives = 177/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    S  +          V  E D    S+   +  +  I     ++  E    V  
Sbjct: 24  ETDAELTSDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D      E  +E + D    A   +    + +  A   + D  +MYL E+G   LL+ E 
Sbjct: 17  DEALEVLETDAELTSDEELVAVEGASEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEE 76

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|315127432|ref|YP_004069435.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
 gi|315015946|gb|ADT69284.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
          Length = 323

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 110/285 (38%), Positives = 170/285 (59%), Gaps = 3/285 (1%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           E E          ++   +  +  I     +S  E    V   RK       ++K M+E+
Sbjct: 32  EDEDVFVKEEVTKNLDATQLYLGEIGFSPLLSAEEE---VFFARKSLKGCEASRKRMIES 88

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+
Sbjct: 89  NLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 148

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+ L  PVE V K+L++ +
Sbjct: 149 IMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAESLDRPVEDVTKMLRLNE 208

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           +  S++ PIG E+ S L D I D+  V P       ++       L  L P++  VL  R
Sbjct: 209 KIASVDMPIGSENDSALLDVIADEKNVGPEGEVQNNDMNTHIIDWLGELNPKQREVLARR 268

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           FG+      TLE+VG++  +TRER+RQI+ +A+R+LK   + + L
Sbjct: 269 FGLLGYEPSTLEDVGREIGLTRERVRQIQVEALRRLKDILQQEGL 313



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 45/106 (42%), Gaps = 6/106 (5%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           DD  D+   ED   L     +  VF+++       +T    ++YL E+G   LLS E E+
Sbjct: 13  DDKFDDSKVEDPTQLLDDVEDEDVFVKEEVTKNLDAT----QLYLGEIGFSPLLSAEEEV 68

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
             A++   G       + ES L    ++      N+    L ++I+
Sbjct: 69  FFARKSLKGCEASRKRMIESNLRL--VVKIARRYNNRGLALLDLIE 112


>gi|168000881|ref|XP_001753144.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162695843|gb|EDQ82185.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 581

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 101/250 (40%), Positives = 153/250 (61%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +      E   AK ++V +NLRLV+S+ K Y  RG+   DLIQ G++GL++ AEKFD  +
Sbjct: 330 LFELRIKEGQCAKDKLVNSNLRLVVSIVKNYQGRGMTLPDLIQRGSLGLIRGAEKFDPEM 389

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++QA+TRSI DQS  IR+PVH+ + I ++ ++   ++    R+   EE+
Sbjct: 390 GFKFSTYATWWIRQAVTRSITDQSRIIRLPVHIYEVISRINKSRMMIAEDQGRQARDEEV 449

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + + VE +  +LK  + P S++  IG +    L + + DK   S  D      L++ 
Sbjct: 450 ATAVGISVEKLDFILKSARLPASMDQLIGRDKDLPLWEMVADKGFNSADDFLTNEVLKQD 509

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              VL +L+P E  VLR+RFG+      TL+++G  F VTRERIRQIE +A+RKL+HP+R
Sbjct: 510 IDGVLQTLSPTEREVLRLRFGLDDAQSMTLKDIGIFFKVTRERIRQIEVRALRKLRHPTR 569

Query: 673 SKKLRSFLDG 682
              L+  +  
Sbjct: 570 RNILQGHVKN 579


>gi|27364956|ref|NP_760484.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|320155343|ref|YP_004187722.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
 gi|27361102|gb|AAO10011.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|319930655|gb|ADV85519.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
          Length = 330

 Score =  184 bits (467), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 111/313 (35%), Positives = 182/313 (58%), Gaps = 10/313 (3%)

Query: 371 LERHQGRELDPHW---VSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGIS 423
           ++     ++D  +   +   +     E K  +  E D    S+   +  +  I     ++
Sbjct: 10  VKDFDVNQMDDDFNDDIEINEKEDLTEEKVKLREEFDASNKSLDATQLYLGEIGFSPLLT 69

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++
Sbjct: 70  AEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIR 126

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+
Sbjct: 127 AVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKL 186

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EPT EEIA +L +PV+ V K+L++ +   S++TPIG +    L D I D N   P  S
Sbjct: 187 DHEPTAEEIAAQLDIPVDDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVS 246

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               ++R +    L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + 
Sbjct: 247 TQDEDMRVSLIHWLEELNPKQKEVLARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEG 306

Query: 664 IRKLKHPSRSKKL 676
           +R+L+     + L
Sbjct: 307 LRRLREVLIKQGL 319



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 49/107 (45%), Gaps = 2/107 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D + ++D+   +  ++     +   V L++  D++++S  D  ++YL E+G   LL+ E
Sbjct: 13  FDVNQMDDDFNDDIEINEKEDLTEEKVKLREEFDASNKSL-DATQLYLGEIGFSPLLTAE 71

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 72  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 117


>gi|332994558|gb|AEF04613.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas sp. SN2]
          Length = 330

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 103/265 (38%), Positives = 163/265 (61%), Gaps = 3/265 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++K M+ +NLRLV+ +A++Y
Sbjct: 51  KNLDATQLYLGEIGFSPLLSAEEE---VFFARKALRGCEASRKRMIVSNLRLVVKIARRY 107

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 108 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 167

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R AR +S K+  EPT EEIA  L  PVE V K+L++ +   S++TPIG E
Sbjct: 168 HVVKELNVYLRAARELSQKLDHEPTAEEIALALDKPVEDVTKMLRLNERITSVDTPIGGE 227

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D+    P ++   ++++      L  L P++  VL  RFG+      TLE
Sbjct: 228 NDKALLDILADEKEFGPEENLQDSDIKSNIVGWLEELNPKQREVLARRFGLMGYEPSTLE 287

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           +VG +  +TRER+RQI+ +A+R+L+
Sbjct: 288 DVGAEIGLTRERVRQIQVEALRRLR 312



 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 47/297 (15%), Positives = 90/297 (30%), Gaps = 18/297 (6%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D  ++ D      +  + S  ++++               D  ++YL E+G   LLS E 
Sbjct: 14  DDLNVIDIPADLKTDKIISDDTDTNSEELVLSQDDQPKNLDATQLYLGEIGFSPLLSAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI-------IDLEACI 191
           E+  A++   G       +  S L     I  R   N G  LL  I       I      
Sbjct: 74  EVFFARKALRGCEASRKRMIVSNLRLVVKIARRYN-NRGLALLDLIEEGNLGLIRAVEKF 132

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            PE    F         Q  E +   + R          E    +            E  
Sbjct: 133 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPT 192

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLR--------PKVMCALDEIA--EVYRELRSLQDNA 301
             +     +   +    +  + +++               LD +A  + +    +LQD+ 
Sbjct: 193 AEEIALALDKPVEDVTKMLRLNERITSVDTPIGGENDKALLDILADEKEFGPEENLQDSD 252

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           +               +E L +  G +    S ++ +  ++    +R+   + E LR
Sbjct: 253 IKSNIVGWLEELNPKQREVLARRFGLMGYEPSTLEDVGAEIGLTRERVRQIQVEALR 309


>gi|330872696|gb|EGH06845.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 335

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 94/291 (32%), Positives = 164/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 43  AKQSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 99

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 100 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 159

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 160 VERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRML 219

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 220 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREV 279

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 280 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +        + +  S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAASG-----RTKAKQSTSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|163786482|ref|ZP_02180930.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159878342|gb|EDP72398.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 167/272 (61%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+  E   +  +++K      +A  ++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKIPLITAEEEVELAQLIKK---GDQVALDKLTTANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN GL+KAA++FD   G+KF +YA+WW++QAI +++A+QS  +R+P++    
Sbjct: 75  KLPDLINEGNAGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLPLNKIGT 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+ +    +    +R P  EEIA++L +    V++ +K +   +S++ P+ D +T  L
Sbjct: 135 INKINKAFSHLEQLHQRPPNAEEIARELDISAREVKQSMKNSGRHLSMDAPLKDGETFSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +    +  P  + ++ +L     R L +LT +E  V+R+ FGIG     TLEE+G  
Sbjct: 195 YDVVSATESPRPDKNLMKESLNLEVERALETLTQKESDVIRLNFGIGDQPPMTLEEIGGI 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI  K IR+L+H S+SK L+++L
Sbjct: 255 YDLTRERVRQIREKGIRRLRHASKSKILKTYL 286



 Score = 44.1 bits (102), Expect = 0.083,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I L++ E E+ +A+ I+ G  + +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKIPLITAEEEVELAQLIKKGDQVALDKLTTANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|331006084|ref|ZP_08329420.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
 gi|330420121|gb|EGG94451.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
          Length = 342

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 102/273 (37%), Positives = 162/273 (59%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       A+K M+E+NLRLV+ ++++Y
Sbjct: 63  KTLDATQIYLNEIGFSPLLSAEEE---VFFARKSLKGEEAARKRMIESNLRLVVKISRRY 119

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 120 VNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 179

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R AR +S K+  EP+ EEIA  L  PV  V K+L + +   S++  IG +
Sbjct: 180 HVVKELNVYLRAARELSQKLDHEPSAEEIANLLDKPVADVEKMLGLNERVNSIDVNIGPQ 239

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D I D++   P+     +++  +    L  LT ++  VL  RFG+      TLE
Sbjct: 240 GDKTLSDTIPDQHVSDPVSLLQDSDMSASIDGWLTELTEKQREVLCRRFGLRGYETSTLE 299

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           EVG++  +TRER+RQI+ +A+++LK     + L
Sbjct: 300 EVGREIGLTRERVRQIQVEALKRLKDIMELQGL 332



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/107 (28%), Positives = 41/107 (38%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VD    +  E S       S  + SS           + T D  ++YL E+G   LLS E
Sbjct: 25  VDTTINDSTEKSAKKSSDDSDDNASSAKTTSTTKIEAQKTLDATQIYLNEIGFSPLLSAE 84

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A++   G       + ES L     I  R  +N G  LL  I
Sbjct: 85  EEVFFARKSLKGEEAARKRMIESNLRLVVKISRRY-VNRGLALLDLI 130


>gi|302345330|ref|YP_003813683.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302149662|gb|ADK95924.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 284

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 166/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  ISI E   +   +R        A + + +ANLR V+SVAK+Y N+GL
Sbjct: 15  LDKYLQEIGHEEMISIEEEVELAQKIR---NGDRKALERLTKANLRFVVSVAKQYQNQGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    
Sbjct: 72  SLPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSS 131

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+ +EIA+   +P + +   +K+    +S++ P  D++ S L
Sbjct: 132 VNKINKILTQFEQENERRPSIDEIAQNTDIPEDKIVDAMKVNSRHVSVDAPFYDDEQSSL 191

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I + N  S     ++ +LRE   R L  L  RE+ V+   FGI    + TLEE+G +
Sbjct: 192 LDVIPNDNTPSTDKELVEESLREEIGRALQILEDREKVVIEAYFGINQ-REMTLEEIGSK 250

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI+ KAIR+L+  S SK L+++L
Sbjct: 251 YNLTRERVRQIKEKAIRRLRQLSNSKVLKAYL 282



 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  E++S E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 18  YLQEIGHEEMISIEEEVELAQKIRNGDRKALERLTKANLRF--VVSVAKQYQNQGLSLPD 75

Query: 184 IID 186
           +I+
Sbjct: 76  LIN 78


>gi|33241312|ref|NP_876254.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|33238842|gb|AAQ00907.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 339

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 100/256 (39%), Positives = 159/256 (62%), Gaps = 1/256 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +    G+      +I +  R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL
Sbjct: 75  HHVQKMKGLLDIPKENINTRQRHQIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDL 134

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ 
Sbjct: 135 VQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMR 194

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFI 592
           R +R +S+ + R+P   E+A +L M  + +  ++  +    SL++    E+  S LG+ I
Sbjct: 195 RISRELSHNLGRQPNRVELANELGMEPKDLEDLMAQSAPCASLDSHARGEEDRSTLGELI 254

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D N   P++   +   +E  +  L+ L  RE++++R+RFG+      TL E+G+Q  V+
Sbjct: 255 PDPNYDEPMECMDRNMQKEHLSGWLSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVS 314

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ+EAKAI KL+
Sbjct: 315 RERVRQLEAKAILKLR 330



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 73  MGIN---VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI    V        E+ S          +  +     R   A R   D +  YL  +G
Sbjct: 1   MGIPLESVKGDSSSPSEKISLPKTSKEERQNKITTSSAGRGRPAGRVGTDSIGFYLSSIG 60

Query: 130 SIELLSREGEIAIAKRIEA 148
            + LL+   EI +A  ++ 
Sbjct: 61  RVPLLTPAEEIELAHHVQK 79


>gi|37519772|ref|NP_923149.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35210763|dbj|BAC88144.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 356

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 103/254 (40%), Positives = 165/254 (64%), Gaps = 1/254 (0%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     +   E   +   + +G  +   AK+++V+ANLRLV+S+AKKY NRG+ FL
Sbjct: 85  YLQEIGRIPLLKPEEEVMLARAIAQGGPKGEWAKRKLVQANLRLVVSIAKKYLNRGVPFL 144

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG++GL++AAEKF+   GYKFSTYA WW++QAITR++A Q+ T+R+PVH+ +KI++
Sbjct: 145 DLIQEGSMGLIRAAEKFEHERGYKFSTYAYWWIRQAITRAVASQARTVRLPVHLVEKINR 204

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +  R ++ ++ R P+  E+A+ L +  E +  +L+  +  +SL   +G E+ + L   
Sbjct: 205 VKKVRRTLAQELGRTPSQGELAEALELAEEDLEHILRAARRTVSLNITVGKEEDTELIHL 264

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           IED     P     + ++R   + +L   LTPRE  +L++RFG+      TL++VG+ F 
Sbjct: 265 IEDSQTDQPDVHIDRESMRVEVSDLLDRHLTPRERDILQLRFGLRDGQQRTLDQVGRMFD 324

Query: 651 VTRERIRQIEAKAI 664
           ++RERIRQI+AKA 
Sbjct: 325 LSRERIRQIQAKAF 338



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELN 175
           D V +YL+E+G I LL  E E+ +A+ I  G          L ++ L     I  +  LN
Sbjct: 80  DSVGLYLQEIGRIPLLKPEEEVMLARAIAQGGPKGEWAKRKLVQANLRLVVSIAKKY-LN 138

Query: 176 DGTTLLREI 184
            G   L  I
Sbjct: 139 RGVPFLDLI 147


>gi|330968927|gb|EGH68993.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 335

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 164/290 (56%), Gaps = 3/290 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L 
Sbjct: 161 ERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLG 220

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V+
Sbjct: 221 LNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVV 280

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 281 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 30/123 (24%), Positives = 50/123 (40%), Gaps = 7/123 (5%)

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            ++D V +L   GI + +  + +          +       S  L++ K        D  
Sbjct: 11  DIDDEV-LLMEAGIVLKEASNEKQPAAVSGRTKVKH-----STSLKQHKYIDYTRALDAT 64

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  +N G +LL
Sbjct: 65  QLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLL 123

Query: 182 REI 184
             I
Sbjct: 124 DLI 126


>gi|325280730|ref|YP_004253272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312539|gb|ADY33092.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 289

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 110/288 (38%), Positives = 173/288 (60%), Gaps = 9/288 (3%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K     E  SI K   EI  I V   +S  E   +   +R        A++++V +NLR 
Sbjct: 8   KQITGRESYSIEKYLQEIGKIHV---LSPEEEADLAKKIR---SGDRAAREKLVLSNLRF 61

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+SVAK+Y N GL   DLI EGN+GL+KAAE FD   G+KF +YA+WW++Q+I ++IA+ 
Sbjct: 62  VVSVAKQYQNHGLTLGDLINEGNVGLIKAAECFDETKGFKFISYAVWWIRQSILQAIAEN 121

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +  IR+P++    I+KV R    +  + +REPT EEIA+K+ M  E V++ +KI  +P+S
Sbjct: 122 ARLIRLPLNKISTINKVNRCYTLLEQEFQREPTEEEIAEKMDMTPEEVKENMKIATKPVS 181

Query: 576 LETPIGDEDTS-HLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           ++ P+  ++ S  L D     D +  +P  S  Q +L+    R  A+L+ RE  +L M +
Sbjct: 182 MDAPLTTDEESISLYDVYIAPDPSIQAPESSLNQDSLKTDIERSFAALSVREATILSMYY 241

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+   +  +LEE+G +  +T ER+RQ++ KAIRKLK    +K+L+++L
Sbjct: 242 GLNGYSSMSLEEIGTKLGLTSERVRQVKTKAIRKLKEVKNNKRLKTYL 289



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G I +LS E E  +AK+I +G       L  S L F  ++    +  +    L +
Sbjct: 21  YLQEIGKIHVLSPEEEADLAKKIRSGDRAAREKLVLSNLRF--VVSVAKQYQNHGLTLGD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T+G  
Sbjct: 79  LIN-EGNVGLIKAAECFDETKGFK 101


>gi|28868771|ref|NP_791390.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|301383956|ref|ZP_07232374.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           Max13]
 gi|302064158|ref|ZP_07255699.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           K40]
 gi|302134085|ref|ZP_07260075.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|3132688|gb|AAC16326.1| sigma factor [Pseudomonas syringae pv. tomato]
 gi|28852010|gb|AAO55085.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|331016398|gb|EGH96454.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 335

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 95/291 (32%), Positives = 164/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 43  AKQSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 99

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 100 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 159

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 160 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRML 219

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 220 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREV 279

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 280 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +        + +  S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAASG-----RTKAKQSTSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|54310169|ref|YP_131189.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
 gi|46914610|emb|CAG21387.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
          Length = 342

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 100/265 (37%), Positives = 166/265 (62%), Gaps = 3/265 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E    V   R+      IA+K M+E+NLRLV+ ++++Y
Sbjct: 62  KALDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEIARKRMIESNLRLVVKISRRY 118

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 119 SNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 178

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT E+IA KL  PV+ V ++L++ +   S++ PIG +
Sbjct: 179 HVVKELNVYLRTARELAQKLDHEPTAEDIALKLEKPVDDVNRMLRLNERVSSVDNPIGGD 238

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D I D+   SP  S    +++ +    L  L P++  VL  RFG+      TLE
Sbjct: 239 SEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 298

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           +VG++  +TRER+RQI+ + +R+L+
Sbjct: 299 DVGREIGLTRERVRQIQVEGLRRLR 323



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 42/107 (39%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +D D   +      +    + +  SS  +   K    +   D  ++YL E+G   LL+ E
Sbjct: 24  LDQDIDIEAIADAAAASTKAESEESSNDVDVSKYGTTQKALDATQLYLGEIGFSPLLTAE 83

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G  +    + ES L     I  R   N G  LL  +
Sbjct: 84  EEVLYARRALRGDEIARKRMIESNLRLVVKISRRYS-NRGLALLDLV 129


>gi|86146341|ref|ZP_01064665.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
 gi|85835820|gb|EAQ53954.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
          Length = 326

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 108/285 (37%), Positives = 171/285 (60%), Gaps = 3/285 (1%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           + E K        S+   +  +  I     ++  E    V   R+       A+K M+E+
Sbjct: 34  KTEAKEETEVTSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIES 90

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+
Sbjct: 91  NLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 150

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           + +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA KL  PV  V K+L++ +
Sbjct: 151 LMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIASKLDKPVGDVSKMLRLNE 210

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              S++TPIG +    L D I D N   P  S   ++++ +    L  L P+++ VL  R
Sbjct: 211 RVSSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDSDIKNSLIFWLDELNPKQKEVLARR 270

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           FG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 271 FGLLGYEPSTLEEVGREISLTRERVRQIQVEGLRRLREILIKQGL 315



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 25/108 (23%), Positives = 41/108 (37%), Gaps = 1/108 (0%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V   +   ++  +E      +  + +     K +      + D  ++YL E+G   LL+ 
Sbjct: 7   VTKEEFDLNQATTEQEALGKAKRTVTKKTEAKEETEVTSKSLDATQLYLGEIGFSPLLTA 66

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 67  EEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 113


>gi|148978207|ref|ZP_01814737.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
 gi|145962629|gb|EDK27905.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
          Length = 326

 Score =  184 bits (466), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 110/313 (35%), Positives = 177/313 (56%), Gaps = 3/313 (0%)

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + ++ F       E +           + E K        S+   +  +  I     ++
Sbjct: 6   AVTKEEFDLDQVTTESEILEQGKRTATKKAEVKEETEVTSKSLDATQLYLGEIGFSPLLT 65

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++
Sbjct: 66  AEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIR 122

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+
Sbjct: 123 AVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKL 182

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EPT EEIA KL  PV  V K+L++ +   S++TPIG +    L D I D N   P  S
Sbjct: 183 DHEPTAEEIASKLDKPVGDVSKMLRLNERVSSVDTPIGGDGEKALLDIIPDINNSDPEVS 242

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              ++++ +    L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + 
Sbjct: 243 TQDSDIKNSLIFWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEG 302

Query: 664 IRKLKHPSRSKKL 676
           +R+L+     + L
Sbjct: 303 LRRLREILIKQGL 315



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/108 (24%), Positives = 41/108 (37%), Gaps = 1/108 (0%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           V   +   D+  +E  +      + +     K +      + D  ++YL E+G   LL+ 
Sbjct: 7   VTKEEFDLDQVTTESEILEQGKRTATKKAEVKEETEVTSKSLDATQLYLGEIGFSPLLTA 66

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 67  EEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 113


>gi|288803307|ref|ZP_06408740.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288334127|gb|EFC72569.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 287

 Score =  184 bits (466), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 166/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  ISI E   +   +R        A + + +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEEMISIEEEVELAQKIR---NGDRKALERLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  IR+P++    
Sbjct: 75  SLPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+ +EIA+   +P + +   +K+    +S++ P  D++ S L
Sbjct: 135 VNKINKILTQFEQENERRPSIDEIAQNTDIPEDKIVDAMKVNSRHVSVDAPFYDDEQSSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I + N  S     ++ +LRE   R L  L  RE+ V+   FGI    + TLEE+G +
Sbjct: 195 LDVIPNDNTPSTDKELVEESLREEIGRALQILEDREKVVIEAYFGINQ-REMTLEEIGSK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI+ KAIR+L+  S SK L+++L
Sbjct: 254 YNLTRERVRQIKEKAIRRLRQLSNSKVLKAYL 285



 Score = 37.9 bits (86), Expect = 5.1,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G  E++S E E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGHEEMISIEEEVELAQKIRNGDRKALERLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|148469868|gb|ABQ65863.1| stationary sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  184 bits (466), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 165/295 (55%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 39  VRAKSRHSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPEHGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.2 bits (105), Expect = 0.037,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 58/136 (42%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L   GI +   D + ++EG+        + S  S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETGIAM---DSMSNDEGATPPS--VRAKSRHSASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|91792562|ref|YP_562213.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
 gi|91714564|gb|ABE54490.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
          Length = 327

 Score =  184 bits (466), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 103/277 (37%), Positives = 165/277 (59%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +
Sbjct: 46  EDLQKNLDATQLYLGEIGFSPLLSAEEE---VFFSRKALKGCEKSRNRMIESNLRLVVKI 102

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 103 ARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 162

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR+++ K+  EPT EEIA KL +    V ++LK+ ++  S++TP
Sbjct: 163 RLPIHVVKELNVYLRTARQLAQKLDHEPTAEEIAAKLDVSTSDVSRMLKLNEKITSVDTP 222

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G ++   L D I D ++V P       +L  +    L  L  ++  VL  RFG+     
Sbjct: 223 LGGDNEKALLDVIADDDSVGPDYQVQDEDLSNSIVGWLNELNTKQREVLARRFGLLGYEP 282

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLE VG +  +TRER+RQI+ +A+++LK    S+ L
Sbjct: 283 STLENVGAEIGLTRERVRQIQVEALKRLKDLLSSQGL 319



 Score = 41.0 bits (94), Expect = 0.77,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 51/135 (37%), Gaps = 11/135 (8%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            +VD      +EG++ S           +  Q ++D   +   D  ++YL E+G   LLS
Sbjct: 12  KLVDLSTKTKKEGAQKSDKAVDLVQQLEIEQQVQEDL--QKNLDATQLYLGEIGFSPLLS 69

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            E E+  +++   G       + ES L    ++      N+    L ++I+       E 
Sbjct: 70  AEEEVFFSRKALKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE-------EG 120

Query: 196 KGGFFHGTEGHSYQK 210
             G     E    ++
Sbjct: 121 NLGLIRAVEKFDPER 135


>gi|148657263|ref|YP_001277468.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569373|gb|ABQ91518.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 345

 Score =  183 bits (465), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 121/328 (36%), Positives = 188/328 (57%), Gaps = 28/328 (8%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR-- 435
           E+D  W++   D  E      ++         +  ++ I   + +S  E   + + +R  
Sbjct: 22  EIDSFWLTDISDLDEKR----LSRSETIDDSTQMYLREIGQVSLLSAEEEITLANDIRAG 77

Query: 436 ----------------------KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
                                 +   +A  A++ +++ANLRLV+S+AKKY    L F+DL
Sbjct: 78  REAQERLKSHRFESLAERLLLERRVMQAEEARRRLIQANLRLVVSIAKKYIGGPLSFMDL 137

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEGNIGLM+A EKFD   G +FSTYA WW++QAITR+IA+QS  IR+PVH+ D I ++ 
Sbjct: 138 VQEGNIGLMRAVEKFDAGKGNRFSTYATWWIRQAITRAIAEQSRLIRLPVHLSDVIAQLR 197

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R ARR+   ++REPT EEIA  + MP   V+ +L+ + +PISLE PI  +    + + + 
Sbjct: 198 RVARRLEQSLEREPTVEEIAAAIDMPEHKVKLLLQASAQPISLEQPITSDGEGQISELLA 257

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +A +P++ A +  L+    + L  L  RE  VL++R+G+      TLEEVG  F +TR
Sbjct: 258 DDDADAPMEIATRRMLQHDLAQALMELPDRERAVLQLRYGLTDGRRRTLEEVGSAFGITR 317

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ER RQIEA A+R+L+ P    +L+++L+
Sbjct: 318 ERTRQIEADALRQLRRPGIGARLQAYLE 345



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 3/107 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +D    E    + ++ S        L +++ S   + DD  +MYLRE+G + LLS E E
Sbjct: 8   ANDQHRVEDDPGAEEIDSFWLTDISDLDEKRLSRSETIDDSTQMYLREIGQVSLLSAEEE 67

Query: 140 IAIAKRIEAGRAMMMASLCE--SPLTFQALIIWRDELNDGTTLLREI 184
           I +A  I AGR      L         + L++ R  +       R I
Sbjct: 68  ITLANDIRAGR-EAQERLKSHRFESLAERLLLERRVMQAEEARRRLI 113


>gi|260767191|ref|ZP_05876133.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|260617799|gb|EEX42976.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|315181178|gb|ADT88092.1| RNA polymerase sigma factor RpoS [Vibrio furnissii NCTC 11218]
          Length = 329

 Score =  183 bits (465), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 106/277 (38%), Positives = 169/277 (61%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 45  DASTKSLDATQMYLSEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKI 101

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 102 SRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 161

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V K+L++ +   S++TP
Sbjct: 162 RLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAVELDKPVDDVSKMLRLNERISSVDTP 221

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D N   P  S    ++R++    L  L P+++ VL  RFG+     
Sbjct: 222 IGGDGDKALLDIIPDINNSDPEVSTQDDDIRDSLVAWLDELNPKQKEVLARRFGLLGYEP 281

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 282 STLEEVGREINLTRERVRQIQVEGLRRLREILMKQGL 318



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/109 (23%), Positives = 42/109 (38%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + +   +   +  +    ++  N      + +  A   + D  +MYL E+G   LL+
Sbjct: 9   KVEEFEFDSEAVNNAATDQELTTNDNDQSEEVREEFDASTKSLDATQMYLSEIGFSPLLT 68

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 69  AEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 116


>gi|145596092|ref|YP_001160389.1| RpoD family RNA polymerase sigma factor [Salinispora tropica
           CNB-440]
 gi|145305429|gb|ABP56011.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora tropica
           CNB-440]
          Length = 332

 Score =  183 bits (465), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 97/247 (39%), Positives = 170/247 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + +++   E + AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+ 
Sbjct: 84  AELQRLVAEGARAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYE 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+
Sbjct: 144 RGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQ 203

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA  L + VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP D  +    R+
Sbjct: 204 IATALGVTVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEDIVLTGLERQ 263

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L+ L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +
Sbjct: 264 RIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELA 323

Query: 672 RSKKLRS 678
           R++ L++
Sbjct: 324 RAEGLQA 330


>gi|300865041|ref|ZP_07109868.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
 gi|300336978|emb|CBN55018.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
          Length = 334

 Score =  183 bits (465), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 104/287 (36%), Positives = 179/287 (62%), Gaps = 8/287 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           +    +  + +   ++R E   +     + +SE     + +++   +   AK++M+EANL
Sbjct: 54  QMMQLLEAKEELAKELRREPTEVEWALQVQLSE-----AELKRLMHQGRRAKQKMIEANL 108

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA
Sbjct: 109 RLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFSTYAYWWIRQAITRAIA 168

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
             + TIR+P+H+ +K++K+ +  R ++ ++ R PTP EI   L +    +R+ L + + P
Sbjct: 169 QHARTIRLPIHITEKLNKIKKVQRELAQQLGRSPTPAEIGSALELHPSQIREYLLMARHP 228

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL+  +GD   + L + +ED++A SP D      LR+    ++A LTP++  VL +RFG
Sbjct: 229 VSLDLRVGDNQDTELQELLEDESA-SPDDYITGELLRQDLNNLMAELTPQQRDVLSLRFG 287

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +    + +L +VG++  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 288 LEDGHEMSLAKVGERLKLSRERVRQLEHQALAHLRR--RQAQVREYL 332



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/34 (44%), Positives = 22/34 (64%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            S+ D VR YL E+G + LL+RE EI   K+++ 
Sbjct: 21  DSSTDTVRTYLHEIGRVALLTREQEIIYGKQVQQ 54


>gi|119944449|ref|YP_942129.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
 gi|119863053|gb|ABM02530.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
          Length = 322

 Score =  183 bits (465), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 105/273 (38%), Positives = 170/273 (62%), Gaps = 3/273 (1%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K  VA EV S+   +  +  I     ++  E    V   R+      +++K M+E+NLRL
Sbjct: 37  KIAVANEVKSMDATQLYLGEIGFSPLLTAEEE---VYYARRLLRGDQVSRKRMIESNLRL 93

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ ++++Y NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 94  VVKISRRYNNRGLSLLDLVEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQ 153

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  K++  +RTAR +++ +  EPT EEIA+ L +  + V K+LK+ +   S
Sbjct: 154 TRTIRLPIHIVKKLNVYLRTARELTHTLTHEPTAEEIAEVLGVSAKEVSKILKLNERISS 213

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++ PIG+     L D I D+   SP +   +A+++    + L  L P++  VL  RFG+ 
Sbjct: 214 VDIPIGNNSDKELLDIIPDRKEASPENELQEADMKLRIVKWLEDLNPKQREVLARRFGLL 273

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TLE VGK+  +TRER+RQI+ +A++ L+
Sbjct: 274 GYEAATLENVGKEIGLTRERVRQIQVEALKYLR 306



 Score = 46.4 bits (108), Expect = 0.017,   Method: Composition-based stats.
 Identities = 23/133 (17%), Positives = 50/133 (37%), Gaps = 9/133 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++       +  E++     +  +      K   + +  + D  ++YL E+G   LL+ E
Sbjct: 7   LESKKSLPFDLDENADTDTDTIDDEDFSAAKIAVANEVKSMDATQLYLGEIGFSPLLTAE 66

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            E+  A+R+  G  +    + ES L    ++      N+    L ++++       E   
Sbjct: 67  EEVYYARRLLRGDQVSRKRMIESNLRL--VVKISRRYNNRGLSLLDLVE-------EGNL 117

Query: 198 GFFHGTEGHSYQK 210
           G     E    +K
Sbjct: 118 GLIRAVEKFDPEK 130


>gi|312883942|ref|ZP_07743659.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309368400|gb|EFP95935.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 325

 Score =  183 bits (465), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 108/293 (36%), Positives = 171/293 (58%), Gaps = 3/293 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
               K     E K        S+   +  +  I     ++  E    V   R+       
Sbjct: 25  ADDIKSTQAEEAKEEFDASTKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEA 81

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 82  ARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 141

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V
Sbjct: 142 IRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIALQLDKPVDDV 201

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+
Sbjct: 202 SKMLRLNERISSVDTPIGGDGEKALLDIIPDVNNSDPEVSTQDDDIKSSLIDWLDELNPK 261

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 262 QKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 314



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/107 (28%), Positives = 48/107 (44%), Gaps = 3/107 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIELLSRE 137
              +E+ E S++++D   +    S   ++ K+  D ST   D  ++YL E+G   LL+ E
Sbjct: 7   ATKVEEFEVSDETMDGFQADDIKSTQAEEAKEEFDASTKSLDATQLYLGEIGFSPLLTAE 66

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 67  EEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 112


>gi|88812406|ref|ZP_01127656.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88790413|gb|EAR21530.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 356

 Score =  183 bits (465), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 98/269 (36%), Positives = 159/269 (59%), Gaps = 3/269 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              D++   +  +  I     ++  E  +     +        A+K M+E+NLRLV+ +A
Sbjct: 77  EHQDTLDPTQIYLNEIGYSPLLTAKEEVYYARRAQG---GDESARKRMIESNLRLVVKIA 133

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           ++Y NRGL FLDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR
Sbjct: 134 RRYMNRGLAFLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIR 193

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+  +I++ +R AR++  ++  EPT EEIA  +   +E VR ++ + +   S++ PI
Sbjct: 194 LPIHVIKEINQYLRVARQLVQRLDHEPTLEEIAIAMDRSIEDVRHMMGLNEGVTSVDIPI 253

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +    L D I D+    P  +    ++       L  LT ++  V+  RFG+  +   
Sbjct: 254 GRDADRVLLDAIPDEVNPDPFAALQDEDVVSHLDAWLNELTEKQRAVVERRFGLHGHEKA 313

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TLEEVG +  VTRER+RQI+  A++KL+ 
Sbjct: 314 TLEEVGDEIGVTRERVRQIQIDALKKLRE 342



 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 29/127 (22%), Positives = 50/127 (39%), Gaps = 11/127 (8%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS----------T 117
           AM     + +     +E+ + +ED   L    ++S+    + +                T
Sbjct: 22  AMAKKQAVEIDTDVAVENLDLTEDEFVLDEREASSAPAGNQDEQDVGERCAQRKMEHQDT 81

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            DP ++YL E+G   LL+ + E+  A+R + G       + ES L     I  R  +N G
Sbjct: 82  LDPTQIYLNEIGYSPLLTAKEEVYYARRAQGGDESARKRMIESNLRLVVKIARRY-MNRG 140

Query: 178 TTLLREI 184
              L  I
Sbjct: 141 LAFLDLI 147


>gi|308048570|ref|YP_003912136.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
 gi|307630760|gb|ADN75062.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
          Length = 328

 Score =  183 bits (465), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 102/273 (37%), Positives = 170/273 (62%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E  +     ++   + + ++  M+E+NLRLV+ +A++Y
Sbjct: 51  KNLDATQLYLSEIGFSPLLTAEEEVYYARRAQR---DCAKSRNRMIESNLRLVVKIARRY 107

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 108 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 167

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR +++ +  EPT EEIA KL  PVE V ++LK+ ++  S++TPIG +
Sbjct: 168 HVVKELNVYLRTARELAHTLDHEPTAEEIAMKLDKPVEDVSRMLKLNEKISSVDTPIGGD 227

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D I D + V P   A   ++  +  R L  L  ++  VL  RFG+      TLE
Sbjct: 228 SDKALLDVIADDDRVCPEVQAQDDDINGSVVRWLGELNSKQREVLARRFGLLGYEPSTLE 287

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG++  +TRER+RQI+ +A+R+L+    ++ L
Sbjct: 288 DVGREIGLTRERVRQIQVEALRRLRELIGAQGL 320



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           G+ + ++  ++   SS  + +      +   D  ++YL E+G   LL+ E E+  A+R +
Sbjct: 23  GTPEEVEANNTEERSSSNIDQLVQDDLQKNLDATQLYLSEIGFSPLLTAEEEVYYARRAQ 82

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              A     + ES L    ++      N+    L ++I+
Sbjct: 83  RDCAKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 119


>gi|157374437|ref|YP_001473037.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
           HAW-EB3]
 gi|157316811|gb|ABV35909.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
           HAW-EB3]
          Length = 323

 Score =  183 bits (465), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 173/300 (57%), Gaps = 3/300 (1%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E D       K       +        ++   +  +  I     +S  E    V   RK
Sbjct: 19  NESDSVTKKGNKAQENELEQQVQDDLQKNLDATQLYLSEIGFSPLLSAEEE---VYFSRK 75

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++F
Sbjct: 76  ALKGCGKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRF 135

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA+KL
Sbjct: 136 STYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEKL 195

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P   V ++LK+ +   S++TP+G ++   L D + D ++V P       ++ ++  + 
Sbjct: 196 DLPSADVSRMLKLNERITSVDTPLGGDNDKALLDVLADDDSVGPDYKVQDEDMSKSVVKW 255

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK    S+ L
Sbjct: 256 LDELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGSQGL 315



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 46/131 (35%), Gaps = 9/131 (6%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            + L D   +E               L+++     +   D  ++YL E+G   LLS E E
Sbjct: 10  AEPLVDLSKNESDSVTKKGNKAQENELEQQVQDDLQKNLDATQLYLSEIGFSPLLSAEEE 69

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           +  +++   G       + ES L    ++      N+    L ++I+       E   G 
Sbjct: 70  VYFSRKALKGCGKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE-------EGNLGL 120

Query: 200 FHGTEGHSYQK 210
               E    ++
Sbjct: 121 IRAVEKFDPER 131


>gi|153207564|ref|ZP_01946247.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161829847|ref|YP_001597499.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918356|ref|ZP_02218442.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212211994|ref|YP_002302930.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212218001|ref|YP_002304788.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120576532|gb|EAX33156.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161761714|gb|ABX77356.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918006|gb|EDR36610.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212010404|gb|ACJ17785.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212012263|gb|ACJ19643.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 352

 Score =  183 bits (465), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 103/282 (36%), Positives = 168/282 (59%), Gaps = 3/282 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            +    + K     E  S    +  ++ +  +  ++  E   I   V K       A+K+
Sbjct: 60  AELANAKAKTKKRRETRSSDPTQIYLRELGFQPLLNAKEELKIARRVHK---GDPKARKQ 116

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+ +A+ Y NRGL FLDLI+EGN+GLM A EKFD   G++FSTYA WW++Q 
Sbjct: 117 MIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLMTAVEKFDPERGFRFSTYATWWIRQT 176

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +QS T+R+P+H+  +++  +RTA++++ ++  E TPE++A  +  PV+ +R+++
Sbjct: 177 IERAIMNQSRTVRLPIHVIKELNVYLRTAKKLTQEVDHEATPEDVAHLIDKPVQEIRRIM 236

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +     S++ PI ++    L D + D N + P       +L++   R LA L  R   V
Sbjct: 237 DLAPSATSIDVPISEDGQKSLVDTLADDNNIDPARLIQNVDLQDHIERWLAQLDERHREV 296

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +RFG+  N   TLE VGK   +TRER+RQI+  A+++L+H
Sbjct: 297 VILRFGLHENEKGTLEAVGKAVGLTRERVRQIQIDALQQLRH 338



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
            +  +    K K   +  + DP ++YLRE+G   LL+ + E+ IA+R+  G       + 
Sbjct: 59  DAELANAKAKTKKRRETRSSDPTQIYLRELGFQPLLNAKEELKIARRVHKGDPKARKQMI 118

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI 184
           E+ L     I  R  +N G   L  I
Sbjct: 119 EANLRLVVKIA-RHYVNRGLPFLDLI 143


>gi|237800176|ref|ZP_04588637.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331023033|gb|EGI03090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 335

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 163/274 (59%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  +   + +K        +K M+E+NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVYFARLSQK---GDPAGRKRMIESNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EPTPEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPTPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 32/131 (24%), Positives = 52/131 (39%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  D +    +     +  S+S     L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASDEKQPPAASGRTKVKQSSS-----LKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  + G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVYFARLSQKGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|26554290|ref|NP_758224.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
 gi|26454299|dbj|BAC44628.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
          Length = 427

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 132/377 (35%), Positives = 213/377 (56%), Gaps = 32/377 (8%)

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH-----QGRELDPHWVSY 386
           +  I  L  +    +K +     E+L     + +  D +LE       +G E+D +  + 
Sbjct: 48  KKFIKELSSKKRKKNKVV---AEEILIYFDRFDLTNDDYLEIFDWLKQEGIEIDRNPFTS 104

Query: 387 AKDFPEGEWKNFVACEVDSILK----------------IRNEIKSISVETGISISEFRHI 430
                  E K+ VA ++D I+                 I++ +  +     ++  E + I
Sbjct: 105 NNSDDIKELKSNVASKIDYIVHDVTTPMSSTRDKVDDGIKSFLNVLGSSKMLTSQEEQEI 164

Query: 431 VSMV-RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
             M+  + +     A  +++ +NLRLV S+AKKY NRGL   DL+QEG++GLMKA  KFD
Sbjct: 165 GKMLDSEDKTIREYAINQLMTSNLRLVTSIAKKYLNRGLDLEDLLQEGSLGLMKAITKFD 224

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           + LG KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ +  R++  +  R+PTP
Sbjct: 225 YKLGNKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLSKAERQLMQEYGRDPTP 284

Query: 550 EEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           EE+A  +         + +  + K+  +P+SL+ P+G ++ S   DF++D + ++P    
Sbjct: 285 EELADAMDGTAAGFTAKKILNIKKLNIDPVSLDKPVGKDEESKFVDFVKDDDNLNPEQFT 344

Query: 605 IQANLRETTTRVLAS-LTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAK 662
            +  + E    +L   L  +EE ++RMR+G+       TLEEVG+++ +TRER+RQIEAK
Sbjct: 345 EKELMGEHIDDILKKFLQEKEEDIIRMRYGLPPYSHPMTLEEVGEKYGITRERVRQIEAK 404

Query: 663 AIRKLKHPSRSKKLRSF 679
           A+RK+KHPS+S  L+ F
Sbjct: 405 ALRKIKHPSKSGILKGF 421



 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 21/143 (14%), Positives = 55/143 (38%), Gaps = 2/143 (1%)

Query: 15  HEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
            ++ +   +        K++    R++  V  EE+  +    +++++   +    L   G
Sbjct: 35  QKNINRDDLVTAKKKFIKELSSKKRKKNKVVAEEILIYFDRFDLTNDDYLEIFDWLKQEG 94

Query: 75  INVVDGD--DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           I +          ++  E   ++AS        +     S     DD ++ +L  +GS +
Sbjct: 95  IEIDRNPFTSNNSDDIKELKSNVASKIDYIVHDVTTPMSSTRDKVDDGIKSFLNVLGSSK 154

Query: 133 LLSREGEIAIAKRIEAGRAMMMA 155
           +L+ + E  I K +++    +  
Sbjct: 155 MLTSQEEQEIGKMLDSEDKTIRE 177


>gi|254413477|ref|ZP_05027247.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196179584|gb|EDX74578.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 331

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 173/284 (60%), Gaps = 7/284 (2%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
           N +    +S+ +      ++      S      + S +R        AK++MVEANLRLV
Sbjct: 52  NALEQTKESLFEQLGYEPTLCEWAKASSLSEAELQSCIR----AGQTAKRKMVEANLRLV 107

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +SVAKKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++ 
Sbjct: 108 VSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKG 167

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R++S  + R  T  E+A +L +  + VR+ L+  ++P+SL
Sbjct: 168 RTIRLPIHITEKLNKIKKAQRQLSQTLGRAATISELATELDLTPKQVREYLEKARQPLSL 227

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +  +GD   + LG+ +ED +  SP D A  + ++    +++A LT ++  VL +RFG+  
Sbjct: 228 DLRVGDNQDTELGELLED-SGPSPEDFATYSAMQVDLEKLMADLTEQQREVLMLRFGLVD 286

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               TL ++G Q  ++RER+RQIE +A+ KL+   R   +R ++
Sbjct: 287 GQPMTLAKIGDQLKISRERVRQIEREALSKLRK--RQADMREYI 328



 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCE 159
           ++ D VR YL+E+G + LL+ E EI   K+++          SL E
Sbjct: 18  TSTDLVRTYLQEIGRVPLLTHEQEILYGKQVQRLNALEQTKESLFE 63


>gi|149190125|ref|ZP_01868401.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
 gi|148836014|gb|EDL52975.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
          Length = 325

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 107/284 (37%), Positives = 170/284 (59%), Gaps = 3/284 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E K+       S+   +  +  I     ++  E    V   R+       A+K M+E+N
Sbjct: 34  SEDKDMYDASAKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALKGDEAARKRMIESN 90

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++
Sbjct: 91  LRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAL 150

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA+KL  PV  V K+L++ + 
Sbjct: 151 MNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAQKLDKPVSDVSKMLRLNER 210

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TPIG +    L D I D     P  S    +++ +    L  L P+++ VL  RF
Sbjct: 211 ISSVDTPIGGDGEKALLDIIPDSTHSDPEVSTQDDDIKSSLIHWLDELNPKQKEVLARRF 270

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 271 GLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRDILIKQGL 314



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 1/100 (1%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D E     +   +  ++ S+   K    A   + D  ++YL E+G   LL+ E E+  A+
Sbjct: 14  DVETESTEIVENALTNDESISEDKDMYDASAKSLDATQLYLGEIGFSPLLTAEEEVLYAR 73

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  RALKGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 112


>gi|154706690|ref|YP_001423754.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355976|gb|ABS77438.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 352

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 103/282 (36%), Positives = 168/282 (59%), Gaps = 3/282 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            +    + K     E  S    +  ++ +  +  ++  E   I   V K       A+K+
Sbjct: 60  AELANAKAKTKKRRETRSSDPTQIYLRELGFQPLLNAKEELKIARRVHK---GDPKARKQ 116

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+ +A+ Y NRGL FLDLI+EGN+GLM A EKFD   G++FSTYA WW++Q 
Sbjct: 117 MIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLMSAVEKFDPERGFRFSTYATWWIRQT 176

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +QS T+R+P+H+  +++  +RTA++++ ++  E TPE++A  +  PV+ +R+++
Sbjct: 177 IERAIMNQSRTVRLPIHVIKELNVYLRTAKKLTQEVDHEATPEDVAHLIDKPVQEIRRIM 236

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +     S++ PI ++    L D + D N + P       +L++   R LA L  R   V
Sbjct: 237 DLAPSATSIDVPISEDGQKSLVDTLADDNNIDPARLIQNVDLQDHIERWLAQLDERHREV 296

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +RFG+  N   TLE VGK   +TRER+RQI+  A+++L+H
Sbjct: 297 VILRFGLHENEKGTLEAVGKAVGLTRERVRQIQIDALQQLRH 338



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
            +  +    K K   +  + DP ++YLRE+G   LL+ + E+ IA+R+  G       + 
Sbjct: 59  DAELANAKAKTKKRRETRSSDPTQIYLRELGFQPLLNAKEELKIARRVHKGDPKARKQMI 118

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI 184
           E+ L     I  R  +N G   L  I
Sbjct: 119 EANLRLVVKIA-RHYVNRGLPFLDLI 143


>gi|284051429|ref|ZP_06381639.1| RNA polymerase sigma factor SigD [Arthrospira platensis str.
           Paraca]
          Length = 319

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 176/278 (63%), Gaps = 6/278 (2%)

Query: 406 ILKIRNEIKSI--SVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + + RNE+        T    +E  ++ V+ ++    +  +AK++MVEANLRLV+SVAKK
Sbjct: 43  LQEKRNELAKQLGYEPTEAQWAELVNLSVAQLQHILHQGQLAKRKMVEANLRLVVSVAKK 102

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P
Sbjct: 103 YIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLP 162

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+ +K++K+ +  R+++ ++ R  T  E+A +L +  + +R+ L+ ++ P+SL+  +GD
Sbjct: 163 IHITEKLNKIKKAQRQLAQQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLDLRVGD 222

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              + L D +ED    SP   A+ ++LR     ++  LT ++ +VL +RFG+      TL
Sbjct: 223 NQDTELVDLLEDT-TNSPEQFALNSSLRSDLESLMTDLTDQQRQVLALRFGLDDGQTLTL 281

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++G +  ++RER+RQIE +A+ KL+   R + +  +L
Sbjct: 282 AKIGDRLNISRERVRQIEREALTKLRK--RKQDVNDYL 317



 Score = 44.1 bits (102), Expect = 0.086,   Method: Composition-based stats.
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            +A  S  D VR YLRE+G + LL+ E EI   K+++  
Sbjct: 2   KTAKTSDTDSVRAYLREIGRVPLLTHEQEILYGKQVQQA 40


>gi|193089925|gb|ACF15191.1| RpoS [Pseudomonas sp. DF41]
          Length = 335

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 95/291 (32%), Positives = 163/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 43  SKHSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 99

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G +FSTYA WW++Q 
Sbjct: 100 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGSRFSTYATWWIRQT 159

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 160 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRML 219

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 220 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDKQWEV 279

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 280 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 45.2 bits (105), Expect = 0.039,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 55/136 (40%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L   GI +       DE  +  S+   S     S  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMETGIAM--DSMSNDEGATPPSVRGKSKH---SASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|312959424|ref|ZP_07773941.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
 gi|311286141|gb|EFQ64705.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
          Length = 335

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 166/295 (56%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     ++  E  H   + +K       
Sbjct: 39  VRTKSKNSTALKQHKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQK---GDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+   P  ++  E +      L   GI   D + + ++EG+        + S +S  L++
Sbjct: 3   LSKEAPEFDIDDEVL------LMETGI---DKESMLNDEGAAKPS--VRTKSKNSTALKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LL+ E E+  A+  + G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|29654959|ref|NP_820651.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|81788312|sp|Q9KI19|RPOS_COXBU RecName: Full=RNA polymerase sigma factor rpoS
 gi|7340285|gb|AAF61172.1|AF244357_1 stress response sigma factor RpoS [Coxiella burnetii]
 gi|29542228|gb|AAO91165.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
          Length = 352

 Score =  183 bits (464), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 102/282 (36%), Positives = 168/282 (59%), Gaps = 3/282 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            +    + K     E  S    +  ++ +  +  ++  E   I   V K       A+K+
Sbjct: 60  AELANAKAKTKKRRETRSSDPTQIYLRELGFQPLLNAKEELKIARRVHK---GDPKARKQ 116

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+ +A+ Y NRGL FLDLI+EGN+GL+ A EKFD   G++FSTYA WW++Q 
Sbjct: 117 MIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLLTAVEKFDPERGFRFSTYATWWIRQT 176

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +QS T+R+P+H+  +++  +RTA++++ ++  E TPE++A  +  PV+ +R+++
Sbjct: 177 IERAIMNQSRTVRLPIHVIKELNVYLRTAKKLTQEVDHEATPEDVAHLIDKPVQEIRRIM 236

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +     S++ PI ++    L D + D N + P       +L++   R LA L  R   V
Sbjct: 237 DLAPSATSIDVPISEDGQKSLVDTLADDNNIDPARLIQNVDLQDHIERWLAQLDERHREV 296

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +RFG+  N   TLE VGK   +TRER+RQI+  A+++L+H
Sbjct: 297 VILRFGLHENEKGTLEAVGKAVGLTRERVRQIQIDALQQLRH 338



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
            +  +    K K   +  + DP ++YLRE+G   LL+ + E+ IA+R+  G       + 
Sbjct: 59  DAELANAKAKTKKRRETRSSDPTQIYLRELGFQPLLNAKEELKIARRVHKGDPKARKQMI 118

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI 184
           E+ L     I  R  +N G   L  I
Sbjct: 119 EANLRLVVKIA-RHYVNRGLPFLDLI 143


>gi|302338230|ref|YP_003803436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635415|gb|ADK80842.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 291

 Score =  183 bits (464), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 100/270 (37%), Positives = 176/270 (65%), Gaps = 4/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    +S  +      +          AK+ ++++NLR V++VAKKY N+GL   
Sbjct: 23  YLKEINKVPLLSREDEDRYARLA---ADGDEHAKEMLIKSNLRFVVNVAKKYQNQGLPLA 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLM A E++D   GY F +YA+WW++QAI ++I++++  IR+P++  +++ +
Sbjct: 80  DLINEGNIGLMNAIERYDVDKGYHFISYAVWWIRQAILKAISEKARMIRLPLNRANELVQ 139

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGD 590
           + +  + +  + K EP  EEIA+ + M  E V  ++ I+++ +SLE+PI  + + S LGD
Sbjct: 140 IEKAKKGLQLEGKEEPEFEEIARVVGMDAEHVASLVNISRDLVSLESPIYTDRSQSELGD 199

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           FIED +  SP ++ ++ +L+E   +VL +L+ +E  ++R RFG+      +L+++G ++ 
Sbjct: 200 FIEDVDYKSPDETLMEQSLKEDIAKVLDTLSEKEADIIRHRFGLDGRAPLSLKDIGDRYN 259

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +T+ERIRQIE KAI++L+HPSR + L S++
Sbjct: 260 LTKERIRQIEKKAIKRLQHPSRRQYLESYI 289



 Score = 44.8 bits (104), Expect = 0.052,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +YL+E+  + LLSRE E   A+    G       L +S L F  ++    +  +    
Sbjct: 20  ISIYLKEINKVPLLSREDEDRYARLAADGDEHAKEMLIKSNLRF--VVNVAKKYQNQGLP 77

Query: 181 LREIID 186
           L ++I+
Sbjct: 78  LADLIN 83


>gi|261250229|ref|ZP_05942805.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
 gi|260939345|gb|EEX95331.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
          Length = 323

 Score =  183 bits (464), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 171/289 (59%), Gaps = 3/289 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
           K     E K        S+   +  +  I     ++  E    V   R+       A+K 
Sbjct: 27  KPKQAEEAKEEFDASTKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEAARKR 83

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 84  MIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 143

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L  PV+ V K+L
Sbjct: 144 IERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIATQLDKPVDDVSKML 203

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+++ V
Sbjct: 204 RLNERISSVDTPIGGDGEKALLDIIPDINNSDPEVSTQDDDIKSSLIHWLDELNPKQKEV 263

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 264 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQGL 312



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
              +E+ E  ++++    +         K +  A   + D  ++YL E+G   LL+ E E
Sbjct: 7   ATKVEEFEIDQETVQSQKTTKPKQAEEAKEEFDASTKSLDATQLYLGEIGFSPLLTAEEE 66

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 67  VLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 110


>gi|126660028|ref|ZP_01731150.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
 gi|126618706|gb|EAZ89453.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
          Length = 418

 Score =  183 bits (464), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 117/293 (39%), Positives = 174/293 (59%), Gaps = 9/293 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKS-ISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
              +W       V  + +I  + K   + E  I + E   I             AK EM+
Sbjct: 132 SWEKWAKASEVSVFELKEILAQGKQQWATEANIDVKELDEIQK-------SGIRAKDEMI 184

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +ANLRLV+SVAKKY +RGL+ LDLIQEG +GL KA EKFD   GY+FSTYA WW++Q IT
Sbjct: 185 KANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAYWWIRQGIT 244

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+IA QS  IR+PVH+ +K++K+ +  R++S    R  T EEI K+L M    VR VL  
Sbjct: 245 RAIATQSRIIRLPVHITEKLNKIKQVQRKISQAKGRSATLEEIGKELNMSSTQVRDVLMK 304

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
               +SLE  +G E  + L D +E ++ +SP ++    +LR     +L  LT RE+ V++
Sbjct: 305 IPRSVSLEIKVGKEKDTELVDLLESED-ISPEENLAIESLRRDIGILLEDLTEREQEVIK 363

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +R+G      ++L ++G+   ++RER+RQIEAKA++KL+ P R  ++R + + 
Sbjct: 364 LRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQKLRQPRRRNQIRDYFES 416



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 48/317 (15%), Positives = 106/317 (33%), Gaps = 19/317 (5%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           V   + ED E + +  D        ++   +   S  R T D VR+YL+++G + LL +E
Sbjct: 21  VTESNKEDNEITSELGDDLFELELQNIDFTETDTSTHRVTTDLVRLYLQDIGRVPLLKKE 80

Query: 138 GEIAIAKRIEAGRA--MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            E++ +K+++       +     E+        +    ++D          L A +G   
Sbjct: 81  EEVSKSKQVQRYVELLDIRNQAAEANEPLMKQFVDIHRIHD---------QLMAYLGHRP 131

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
               +      S  + ++   + ++    E   D++   ++ K      D   +      
Sbjct: 132 SWEKWAKASEVSVFELKEILAQGKQQWATEANIDVKELDEIQKSGIRAKDEMIKANLRLV 191

Query: 256 RNLDEDEDDSAHTLSAMEDQLR---PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
            ++ +        L  +  +      K +   D I        +         +   +  
Sbjct: 192 VSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAYWWIRQGITRAIATQS 251

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLL---VEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
           +   L   + + +  +   Q +I         L +I K +  +  ++  +     I R V
Sbjct: 252 RIIRLPVHITEKLNKIKQVQRKISQAKGRSATLEEIGKELNMSSTQVRDVLM--KIPRSV 309

Query: 370 FLERHQGRELDPHWVSY 386
            LE   G+E D   V  
Sbjct: 310 SLEIKVGKEKDTELVDL 326


>gi|238060708|ref|ZP_04605417.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
 gi|237882519|gb|EEP71347.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
          Length = 331

 Score =  183 bits (464), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 97/245 (39%), Positives = 166/245 (67%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +   E   AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+  G
Sbjct: 86  LERVAAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERG 145

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+IA
Sbjct: 146 FKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNAARQLTRELGSDPEPEQIA 205

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L + VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP D  +    R+  
Sbjct: 206 AALGVTVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEDIVLTGLERQRI 265

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L  L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +R+
Sbjct: 266 EGLLNHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARA 325

Query: 674 KKLRS 678
           + L++
Sbjct: 326 EGLQA 330


>gi|292492664|ref|YP_003528103.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
 gi|291581259|gb|ADE15716.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
          Length = 325

 Score =  183 bits (464), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 86/268 (32%), Positives = 154/268 (57%), Gaps = 3/268 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +   R  +  I     ++  E  +   + ++        +K M+E+NLRLV+ +A+
Sbjct: 47  NEQELDATRLYLSEIGFAPLLTAEEEVYHARLAQR---GDPAGRKRMIESNLRLVVKIAR 103

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL+ A EKFD  +G++FSTYA WW++Q I R++ +Q+ T+R+
Sbjct: 104 RYMNRGLALLDLIEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRL 163

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVH+  +I    R A +++ +++ +PT EE+A++L   VE ++++  +     S++T   
Sbjct: 164 PVHVVKEIKSYQRVASKLAQELEHDPTFEELAQQLDKSVEEIKRMWSLKDNIASMDTGYR 223

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            +    L D + D+    P       +++      L+ L  ++  V+  RFG+      T
Sbjct: 224 SDQEKTLLDTLPDEGTPDPTTLLQNDDMQSRLELWLSQLNNKQREVVIRRFGLQGYESQT 283

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LE+VG+   VTRER+RQI+ +A+++L+ 
Sbjct: 284 LEQVGQAIGVTRERVRQIQLEALKRLRR 311



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 28/117 (23%), Positives = 40/117 (34%), Gaps = 9/117 (7%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           L+ A           +     +    D  R+YL E+G   LL+ E E+  A+  + G   
Sbjct: 26  LEPAPQQLPIDPEEVQENPPYNEQELDATRLYLSEIGFAPLLTAEEEVYHARLAQRGDPA 85

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
               + ES L     I  R  +N G  LL  I         E   G  H  E    +
Sbjct: 86  GRKRMIESNLRLVVKIARRY-MNRGLALLDLI--------EEGNLGLIHAVEKFDPE 133


>gi|325673633|ref|ZP_08153324.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|325555654|gb|EGD25325.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 448

 Score =  183 bits (464), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 165/263 (62%), Gaps = 6/263 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T  + +E R +    R+   +   A+  M+EANLRLV+S A+ Y  RGL  LDL+QE
Sbjct: 190 SRTTRPAPAERRDL----RQIVQDGRSARTRMIEANLRLVVSTAQNYEGRGLDMLDLVQE 245

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN GL++A EKFD+ LG KFSTYA WW++QAITR IAD+S TIR+PVH+ + + ++    
Sbjct: 246 GNTGLIRAVEKFDYRLGNKFSTYATWWIRQAITRGIADKSRTIRLPVHVVEDLSRMTTVR 305

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                ++ R  T  E+A++  + +E VR++    +  +S+E     +D + L   IED  
Sbjct: 306 VEGEIELGRALTDAEVAQRADLTLEKVRELDDCDRTVLSIEALTDSDDGAGLD--IEDDC 363

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A  P ++  +A++RE    VL +LT RE  V+++R G+      TLEE+GK + VTRERI
Sbjct: 364 AHDPYEALHRADVRERIDIVLETLTEREAGVMKLRHGLVDGVPRTLEEIGKVYKVTRERI 423

Query: 657 RQIEAKAIRKLKHPSRSKKLRSF 679
           RQIEAK ++ L+ PSR+ +LR F
Sbjct: 424 RQIEAKTLQLLREPSRADELRPF 446



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           ++  VA  +++GI V +               +    S+ +        +AD      ++
Sbjct: 97  LDALVASFTDLGIEVREARHEVMPTRPPRPAVMLRERSSPARTSGNESAAADG-----LQ 151

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGR 150
            YL+ +  ++LL+ + E+ +++ IEAG 
Sbjct: 152 WYLKRIRRVDLLTADEEVELSRSIEAGL 179


>gi|170691127|ref|ZP_02882293.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
 gi|170144376|gb|EDT12538.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
          Length = 202

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 132/201 (65%), Positives = 166/201 (82%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R++  
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 60

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EP P  +A+K+ MP + +RK++KI KEPIS+ETPIGD+D SHLGDFIED N V+P 
Sbjct: 61  ETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPA 120

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D+A+ A++R+    VL SLTPRE +VLRMRFGI M+TDHTLEEVGKQF VTRERIRQIEA
Sbjct: 121 DAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEA 180

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           KA+RKL+HPSRS KL+SFL+G
Sbjct: 181 KALRKLRHPSRSDKLKSFLEG 201


>gi|46205316|ref|ZP_00048697.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 326

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 121/291 (41%), Positives = 156/291 (53%), Gaps = 44/291 (15%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
            +S S +              TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A
Sbjct: 44  EASGSRAVAVATPTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREAMIA 103

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-GPESKGGFFHGTEGHSYQKREDS 214
            LCESPLTFQA+IIWRDEL DG  LLR+IIDLEA   GP+++GG     EG   +  E+ 
Sbjct: 104 GLCESPLTFQAIIIWRDELVDGKVLLRDIIDLEATYAGPDARGGPQVAEEGEESEDGEEG 163

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
               E  D                                    DED+ ++  +L+AME 
Sbjct: 164 PVPPEGGD------------------------------------DEDDMENNVSLAAMEA 187

Query: 275 QLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
           +++P+V+   D IA  YR+LR LQ+      A  G      + K   LK+ +V  V SLS
Sbjct: 188 EIKPRVLETFDNIASNYRKLRKLQNEEAEFKASGGTVTPAQTKKQAELKDIVVTDVKSLS 247

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           LN  RI+  VEQ+YDI +R++ +EG L+  A    +    F   +Q R  D
Sbjct: 248 LNAKRIEAPVEQVYDIHERLISHEGRLI-CAAELRVSPHEF-RPYQVRVTD 296


>gi|330469769|ref|YP_004407512.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328812740|gb|AEB46912.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 333

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 102/280 (36%), Positives = 180/280 (64%), Gaps = 7/280 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           ++  +++ L   + +    V  G++  E   +V+       E   AK   + ANLRLV+S
Sbjct: 60  LSKAIEAGLYAEHLLGEDRVPEGVTRDELTRLVA-------EGERAKDLFIRANLRLVVS 112

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y   G+  LDLIQEGN GL++A EKFD+  GYKFSTYA WW++QAI+R+IA Q  T
Sbjct: 113 IARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGYKFSTYATWWIRQAISRAIAQQERT 172

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+PVH+ + ++++   AR+++ ++  +P PE+IA  L + VE V ++++ +++ +SL+T
Sbjct: 173 VRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIAAALGVTVERVNELVRWSQDTVSLDT 232

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+GD+  ++LGD + D +A SP +  +    R+    +L  L  R   ++R R+G+    
Sbjct: 233 PVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLNHLDDRSAGIMRARYGLEDGR 292

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +H+L EV  +F ++RERIRQ+E +A+ +L+  +R++ L++
Sbjct: 293 EHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQA 332


>gi|282899735|ref|ZP_06307698.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195350|gb|EFA70284.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 332

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 178/287 (62%), Gaps = 7/287 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           +    +    D++ +  N   S+      +  + + +  ++     +  IAK++MVEANL
Sbjct: 51  QKSTALYETKDNLAQELNRQPSLEEWAKAAQLDPQELNRLL----GQGEIAKRKMVEANL 106

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FSTYA WW++QAITR+IA
Sbjct: 107 RLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPSKGYRFSTYAYWWIRQAITRAIA 166

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +++ TIR+P+H+ +K++K+ +  R +S  + R P+  E+A++L +  + VR  L+  + P
Sbjct: 167 EKARTIRLPIHITEKLNKIKKAQRYLSQTLGRSPSIAELAQELEITPKQVRDCLEKARLP 226

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL+  +GD   + LG+ +ED  A SP D  IQ++L     R++  LTP++  V+++RFG
Sbjct: 227 LSLDLRLGDNYDTELGEMLEDPGA-SPEDYVIQSSLSSELDRMMTHLTPQQREVIKLRFG 285

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +      TL  +G+   ++RER+RQIE +A+ +L+    S  +  +L
Sbjct: 286 LVDGQSMTLARIGEVLNISRERVRQIEREALTRLRRCKTS--MSEYL 330



 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            D VR YLRE+G + LL+ E EI   K+++ 
Sbjct: 22  TDIVRTYLREIGKVPLLTHEQEIYYGKQVQK 52


>gi|94500747|ref|ZP_01307276.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
 gi|94427069|gb|EAT12050.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
          Length = 331

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 161/273 (58%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E  H   + RK        +K M+E+NLRLV+ +A++Y
Sbjct: 50  KNLDATQLYLNEIGFSPLLTPQEEVHFARLARK---GDEKGRKRMIESNLRLVVKIARRY 106

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 107 VNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 166

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R AR ++ K+  EPT EEIA  L  PV+ V+++L + +   S++TP+G  
Sbjct: 167 HVVKELNVYLRAARELTQKLDHEPTAEEIADLLEKPVDDVKRMLGLNERVTSVDTPLGYN 226

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               + D I D+    P       ++  +    L  LT ++  V+  RFG+      TLE
Sbjct: 227 SDKAILDTIADEAVSDPCQVLQDDDISSSLDGWLDELTEKQREVIARRFGLRGYEISTLE 286

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           EVG +  +TRER+RQI+ +A+++L+     + L
Sbjct: 287 EVGFEIGLTRERVRQIQVEALKRLREIMEKQGL 319



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 28/110 (25%), Positives = 46/110 (41%), Gaps = 7/110 (6%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRK------DSADRSTDDPVRMYLREMGSIELL 134
            D  ++    D ++LA +   +S   +K +      D   +   D  ++YL E+G   LL
Sbjct: 9   QDQFEDNNDSDVIELAEAEVKTSAKSKKTEISDVGQDHDVQKNLDATQLYLNEIGFSPLL 68

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + E+  A+    G       + ES L     I  R  +N G TLL  I
Sbjct: 69  TPQEEVHFARLARKGDEKGRKRMIESNLRLVVKIARRY-VNRGLTLLDLI 117


>gi|56459854|ref|YP_155135.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
 gi|56178864|gb|AAV81586.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
          Length = 322

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 105/299 (35%), Positives = 171/299 (57%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E        A +  E    +        +   +  +  I     ++  E    V   R+ 
Sbjct: 18  ESIVDSTDSAAEELEEALSSSSTQYQKKMDATQLYLGEIGFSPLLTAEEE---VFYSRRA 74

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A++ M+E+NLRLV+ +A++Y+NRGL  LDL++EGN+GL++A EKFD   G++FS
Sbjct: 75  LKGDKAARRRMIESNLRLVVKIARRYSNRGLPLLDLVEEGNLGLIRAVEKFDPERGFRFS 134

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EPT E+IAK L 
Sbjct: 135 TYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELAHKLDHEPTAEDIAKSLN 194

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV  + K+L++ +   S++TPIG ++   L D + D     P       NL+   T  L
Sbjct: 195 KPVGDITKMLRLNERIGSVDTPIGGDNDKALLDILTDDADTGPEGVLQDENLKGNITEWL 254

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            SL  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ +A+RKL+   + + L
Sbjct: 255 QSLNQKQREVLARRFGLMGYEPSTLEDVGREIGLTRERVRQIQVEALRKLRDSLKQQGL 313



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/108 (17%), Positives = 42/108 (38%), Gaps = 2/108 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  +  +    E  +D   SA+           +  +   D  ++YL E+G   LL+ E 
Sbjct: 7   EAVENVEANEDESIVDSTDSAAEELEEALSSSSTQYQKKMDATQLYLGEIGFSPLLTAEE 66

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E+  ++R   G       + ES L    ++      ++    L ++++
Sbjct: 67  EVFYSRRALKGDKAARRRMIESNLRL--VVKIARRYSNRGLPLLDLVE 112


>gi|229520830|ref|ZP_04410252.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
 gi|229342063|gb|EEO07059.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
          Length = 335

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 111/303 (36%), Positives = 176/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    S  +             E D    S+   +  +  I     ++  E    V  
Sbjct: 24  ETDAELASDEELVAVEGASEDAREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  VRTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYVRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D      E  +E + D    A   +    + +  A   + D  +MYL E+G   LL+ E 
Sbjct: 17  DEALEVLETDAELASDEELVAVEGASEDAREEFDASAKSLDATQMYLSEIGFSPLLTAEE 76

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|33240812|ref|NP_875754.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238341|gb|AAQ00407.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 313

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 108/270 (40%), Positives = 175/270 (64%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVET--GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ +   T  G+   + +   S  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQVMMNLTEDGMVNEKTKKFTSHERRSIRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P   EIA+++ + VE +  +L+      SL+ P+  +D
Sbjct: 159 LSERLATIRKVSLDLAHKLGAMPNRLEIAEEMDIEVEELDSILRQALTTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q+  +E   R L  L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSSVEEPLDKVEQSIHQEQLGRWLTHLSEQEQHVLKLRFGLEGNDRHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E K++RKL++ +R 
Sbjct: 279 EIGRLLEVSRERVRQVELKSLRKLRNLTRK 308



 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 22/42 (52%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             K  +S  R + DP+  YL  +G + LL+   EI +  +++
Sbjct: 5   APKPAESQKRRSTDPISWYLATIGRVPLLTPAEEIELGNQVQ 46


>gi|312601028|gb|ADQ90283.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 168]
          Length = 676

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 367 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 424

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 425 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 484

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 485 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLG 544

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 545 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 604

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 605 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 664

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 665 TPHRRLSLRDF 675


>gi|158338579|ref|YP_001519756.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158308820|gb|ABW30437.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 91/256 (35%), Positives = 152/256 (59%), Gaps = 5/256 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++  E    +++ R+ +     AK++M+EANLRLV+S+AKK+ NRGL  L
Sbjct: 11  YLKEIGRFPLLTHEEE---ITLARQVQAGNPRAKRKMIEANLRLVVSIAKKHQNRGLPLL 67

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL  A +KF+   G +FSTYA WW+ Q +TRS+ ++   +R+PV      ++
Sbjct: 68  DLIQEGNLGLSIAVDKFEPEQGNRFSTYAYWWILQGVTRSLQNKGRVVRLPVKHWQVGNQ 127

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + RT  ++S ++ REPT  EIA  + M +  ++K L   +E +SL+  +G E  + LGD 
Sbjct: 128 IKRTRHQLSQELGREPTVVEIADAMEMDLTRLKKYLHSLQETVSLDKFVGSEQDTTLGDL 187

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE  ++       +  +     +  LA L  R+  V+  R+G+      ++E++G++  +
Sbjct: 188 IEGNDSTQSYLDLLLQDE--ELSGYLALLDDRQRFVISERYGLEDGKPKSMEKIGQKLGI 245

Query: 652 TRERIRQIEAKAIRKL 667
           +RER+RQI  KA++ L
Sbjct: 246 SRERVRQIIKKAMQTL 261



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D +  YL+E+G   LL+ E EI +A++++AG       + E+ L     I  + + N G 
Sbjct: 6   DSLHYYLKEIGRFPLLTHEEEITLARQVQAGNPRAKRKMIEANLRLVVSIAKKHQ-NRGL 64

Query: 179 TLLREI 184
            LL  I
Sbjct: 65  PLLDLI 70


>gi|186685842|ref|YP_001869038.1| RNA polymerase sigma factor SigD [Nostoc punctiforme PCC 73102]
 gi|186468294|gb|ACC84095.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 104/258 (40%), Positives = 170/258 (65%), Gaps = 8/258 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  +  T +   E    ++       +  IAK++MVEANLRLV+SVAKKY  R +  LD
Sbjct: 73  LEEWAKATKLEPVELNEAIA-------DGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLD 125

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG+IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR+P+H+ +K++K+
Sbjct: 126 LIQEGSIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKI 185

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +  R++S K+ R PT  E+A++L +  + VR+ L+  + P+SL+  +GD   + LG+ +
Sbjct: 186 KKAQRQLSQKLGRAPTAGELAQELELTPKQVREYLEKARLPLSLDLRLGDNYDTELGEML 245

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED  A SP +  +Q++L     R++  LTP++  V+ +RFG+      TL ++G+   ++
Sbjct: 246 EDPGA-SPEEFVMQSSLSYDLDRLMGDLTPQQREVITLRFGLTDGQALTLAKIGEILNIS 304

Query: 653 RERIRQIEAKAIRKLKHP 670
           RER+RQIE +A+ KL+  
Sbjct: 305 RERVRQIEREALTKLRKS 322



 Score = 44.1 bits (102), Expect = 0.081,   Method: Composition-based stats.
 Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCESPLTFQALIIWRDELN 175
            D VR YLRE+G + LL+ E EI   K+++          SL         L  W     
Sbjct: 22  TDLVRTYLREIGRVPLLTHEEEIFYGKQVQRSCTLHESRESLATQLGRQPTLEEWAKATK 81

Query: 176 DGTTLLREII 185
                L E I
Sbjct: 82  LEPVELNEAI 91


>gi|330964173|gb|EGH64433.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 335

 Score =  183 bits (463), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 94/291 (32%), Positives = 164/291 (56%), Gaps = 3/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E  H   +    +      +K 
Sbjct: 43  AKQSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKR 99

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 100 MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 159

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PE+IA  L  PV  V+++L
Sbjct: 160 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEDIANLLEKPVGEVKRML 219

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 220 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREV 279

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 280 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 330



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +        + +  S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAASG-----RTKAKQSTSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|304312494|ref|YP_003812092.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
 gi|301798227|emb|CBL46449.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
          Length = 342

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 166/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E    V   R+     + A+K M+E+NLRLV+ +A++Y
Sbjct: 65  KTLDATQIYLNEIGFSPLLTPEEE---VYYARRALRGNADARKRMIESNLRLVVKIARRY 121

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 122 VNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 181

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R AR ++ K+  EPTPEEI+  L  P+E V+++L + +   S+++P+G +
Sbjct: 182 HVVKELNVYLRAARELTQKLDHEPTPEEISALLDKPLEDVKRMLGLNERISSVDSPVGFD 241

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D I D     P +    A+L+ +    L  L  ++  V+  RFG+      TLE
Sbjct: 242 SDKSLLDTIADTKNTDPAELLQDADLKNSIDYWLDQLPGKQREVIARRFGLRGFEMSTLE 301

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           EVG++  +TRER+RQI+ +A+++L+     + L
Sbjct: 302 EVGREIGLTRERVRQIQVEALKRLRDLLEKQGL 334



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 1/92 (1%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
            +   ++  S     +R++     T D  ++YL E+G   LL+ E E+  A+R   G A 
Sbjct: 42  EEGDFASDESDAETFRRQEGGITKTLDATQIYLNEIGFSPLLTPEEEVYYARRALRGNAD 101

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               + ES L     I  R  +N G +LL  I
Sbjct: 102 ARKRMIESNLRLVVKIARRY-VNRGLSLLDLI 132


>gi|257061333|ref|YP_003139221.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8802]
 gi|256591499|gb|ACV02386.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 328

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 108/268 (40%), Positives = 175/268 (65%), Gaps = 7/268 (2%)

Query: 417 SVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  T  S  E+   V++    ++K   + + AK++M+EANLRLV+++AKKY  R ++FLD
Sbjct: 61  AQGTEPSDKEWAKAVNLKEPELQKTIEQGNRAKRKMIEANLRLVVAIAKKYQKRNMEFLD 120

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+
Sbjct: 121 LIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKI 180

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +T R +S K+ R  TP EIA  L +    +R+ L + ++PISL+  +GD   + L + +
Sbjct: 181 KKTQRELSQKLGRSATPAEIAAVLEIEPSQIRECLSMARQPISLDVRVGDNQDTELSELL 240

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED  A SP     Q  LR+    ++  LTP++  VL +RFG+    + +L ++GK+  ++
Sbjct: 241 EDHEA-SPDQYITQELLRQDLKNLMEELTPQQRSVLILRFGLEDGKELSLAKIGKKLNIS 299

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQ+E +A+ +L+   R   ++ +L
Sbjct: 300 RERVRQLEHQALAQLRR--RRANVKEYL 325



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCESPLTFQALIIWRDEL 174
           + D VR YL E+G + LL+ E EI   K+++       M   L ++  T  +   W   +
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQRMMSLFEMKDQLTQAQGTEPSDKEWAKAV 75

Query: 175 NDGTTLLREIID 186
           N     L++ I+
Sbjct: 76  NLKEPELQKTIE 87


>gi|218439771|ref|YP_002378100.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7424]
 gi|218172499|gb|ACK71232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 328

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 102/287 (35%), Positives = 180/287 (62%), Gaps = 7/287 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           +    +  + D +     +  +++            +   +++       AK++M+EANL
Sbjct: 46  QKMMTLLEKKDQLAIELGKEPNLTEWANQVQMSEEELNRAIQQ----GKRAKRKMIEANL 101

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA
Sbjct: 102 RLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIA 161

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            Q+ TIR+P+H+ +K++K+ +T R +S ++ R  TP EIAK L +    +R+ L ++++P
Sbjct: 162 QQARTIRLPIHITEKLNKIKKTQRELSQQLGRSATPAEIAKALDLEPAQIREFLSMSRQP 221

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISL+  +GD   + L + +ED+  +SP +   Q  +R+    +LA LTP++  VL +RFG
Sbjct: 222 ISLDVRVGDNQDTELSELLEDE-GISPDNYITQELMRQDLHDLLAELTPQQREVLSLRFG 280

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +    + +L ++G++  ++RER+RQ+E +A+ +L+   R   ++ ++
Sbjct: 281 LQDGKELSLAKIGQRMNISRERVRQLEHQALSQLRR--RRSNVKEYI 325



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D VR YL E+G + LL+ E EI   K+++ 
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQK 47


>gi|218247332|ref|YP_002372703.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8801]
 gi|218167810|gb|ACK66547.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 328

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 108/268 (40%), Positives = 175/268 (65%), Gaps = 7/268 (2%)

Query: 417 SVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  T  S  E+   V++    ++K   + + AK++M+EANLRLV+++AKKY  R ++FLD
Sbjct: 61  AQGTEPSDKEWAKAVNLKEPELKKTIEQGNRAKRKMIEANLRLVVAIAKKYQKRNMEFLD 120

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+
Sbjct: 121 LIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKI 180

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +T R +S K+ R  TP EIA  L +    +R+ L + ++PISL+  +GD   + L + +
Sbjct: 181 KKTQRELSQKLGRSATPAEIAAVLEIEPSQIRECLSMARQPISLDVRVGDNQDTELSELL 240

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED  A SP     Q  LR+    ++  LTP++  VL +RFG+    + +L ++GK+  ++
Sbjct: 241 EDHEA-SPDQYITQELLRQDLKNLMEELTPQQRSVLILRFGLEDGKELSLAKIGKKLNIS 299

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQ+E +A+ +L+   R   ++ +L
Sbjct: 300 RERVRQLEHQALAQLRR--RRANVKEYL 325



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCESPLTFQALIIWRDEL 174
           + D VR YL E+G + LL+ E EI   K+++       M   L ++  T  +   W   +
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQRMMSLFEMKDQLTQAQGTEPSDKEWAKAV 75

Query: 175 NDGTTLLREIID 186
           N     L++ I+
Sbjct: 76  NLKEPELKKTIE 87


>gi|33867026|ref|NP_898585.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639627|emb|CAE09011.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 328

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 99/263 (37%), Positives = 161/263 (61%), Gaps = 4/263 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ + ++ +     +       + S  R        A+  M+ ANLRLV+SVAKKY N+
Sbjct: 60  IELAHHVQEMKQLQELP---EEELTSRHRHKIRMGKRARDRMMAANLRLVVSVAKKYQNQ 116

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ 
Sbjct: 117 GLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHIS 176

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           +K+ K+ R +R +S++  R+P   E+A  + +    +  ++  +    SL+     E+  
Sbjct: 177 EKLSKMRRISRELSHRFGRQPNRLELASAMGIEPRELEDLISQSAPCASLDAHARGEEDR 236

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LG+ I D N   P++   ++  +E     L+ L  RE+++LR+RFG+G     TL E+
Sbjct: 237 STLGELIPDPNGEEPMEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEI 296

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 297 GRQINVSRERVRQLEAKAILKLR 319



 Score = 37.5 bits (85), Expect = 8.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 17/36 (47%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             R   D +  YL  +G I LL+   EI +A  ++ 
Sbjct: 33  GGRLATDSIGFYLSSIGRIPLLTAAEEIELAHHVQE 68


>gi|19910026|dbj|BAB87264.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 427

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 111/247 (44%), Positives = 164/247 (66%), Gaps = 7/247 (2%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           +   A+  +V++NLR V+S+AKKY N+  +   DLIQEG+IGLMKAAE+FD   G+KF T
Sbjct: 174 KGRRARARLVQSNLRWVVSIAKKYANKHTMPLQDLIQEGSIGLMKAAERFDLDKGFKFLT 233

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI RS+ DQ  TIR+PVH+ D ++ + +T +++++++ R PTPEE+A +L +
Sbjct: 234 YATWWIRQAIFRSLQDQGRTIRLPVHVHDSLYLIKKTRQQLASRLGRIPTPEELADELNI 293

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSH-----LGDFIEDKNAVSPLDSAIQANLRETT 613
           PV  +  + +    PISLE+PI  E +S      LGDFIE +  + P +   +  LRE  
Sbjct: 294 PVSRLAFITQAASLPISLESPISSETSSTKARNNLGDFIESE-CLQPDEQLERTMLREDL 352

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             VLA+L  RE  ++RMR+G+   +  TL+E+G+   +TRERIRQIE  A+RKLK P R 
Sbjct: 353 ENVLATLKARERDIIRMRYGLVDGSPKTLDEIGEIVGLTRERIRQIEQSAMRKLKAPYRK 412

Query: 674 KKLRSFL 680
             L  ++
Sbjct: 413 AILCDYI 419


>gi|239995277|ref|ZP_04715801.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii ATCC
           27126]
          Length = 330

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 103/265 (38%), Positives = 164/265 (61%), Gaps = 3/265 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E    V   R+       ++K M+ +NLRLV+ +A++Y
Sbjct: 51  KNLDATQLYLGEIGFSPLLTAEEE---VYFARRSLKGCEASRKRMIVSNLRLVVKIARRY 107

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 108 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 167

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R +R +S K+  EPT EEIA  L  PVE V K+L++ +   S++TPIG E
Sbjct: 168 HVVKELNVYLRASRELSQKLDHEPTAEEIALALDKPVEDVTKMLRLNERITSVDTPIGGE 227

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D I D+   SP +S   ++++      L  L P++  VL  RFG+      TLE
Sbjct: 228 NDKALLDIIADEKEFSPEESLQDSDIKSNIVTWLEELNPKQREVLARRFGLMGYEPSTLE 287

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           +VG +  +TRER+RQI+ +A+R+L+
Sbjct: 288 DVGAEIGLTRERVRQIQVEALRRLR 312



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 51/303 (16%), Positives = 95/303 (31%), Gaps = 23/303 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP-----VRMYLREMGSIE 132
           ++    +D E  +   D+ +  + ++    +  D+     D P      ++YL E+G   
Sbjct: 8   LESTPQDDVEVIDMPADMKADETLTNDADLENDDAIFSQDDQPKNLDATQLYLGEIGFSP 67

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI-------I 185
           LL+ E E+  A+R   G       +  S L     I  R   N G  LL  I       I
Sbjct: 68  LLTAEEEVYFARRSLKGCEASRKRMIVSNLRLVVKIARRYN-NRGLALLDLIEEGNLGLI 126

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
                  PE    F         Q  E +   + R          E    +         
Sbjct: 127 RAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRASRELSQK 186

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLR--------PKVMCALDEIA--EVYRELR 295
              E    +     +   +    +  + +++               LD IA  + +    
Sbjct: 187 LDHEPTAEEIALALDKPVEDVTKMLRLNERITSVDTPIGGENDKALLDIIADEKEFSPEE 246

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           SLQD+ +               +E L +  G +    S ++ +  ++    +R+   + E
Sbjct: 247 SLQDSDIKSNIVTWLEELNPKQREVLARRFGLMGYEPSTLEDVGAEIGLTRERVRQIQVE 306

Query: 356 LLR 358
            LR
Sbjct: 307 ALR 309


>gi|159027100|emb|CAO89285.1| rpoD [Microcystis aeruginosa PCC 7806]
          Length = 328

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 177/274 (64%), Gaps = 8/274 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            ++  E + +     +++SE     + + +       AK++M+EANLRLV+++AKKY  R
Sbjct: 60  KQLGREPQHLEWADSVNLSE-----NELDRALKTGDRAKRKMIEANLRLVVAIAKKYQKR 114

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ 
Sbjct: 115 NMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT 174

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +K++K+ RT R ++ K+ R  TP EIA +L +    +R+ L + ++PISL+  +GD   +
Sbjct: 175 EKLNKIKRTQRELAQKLGRSATPAEIALELDLEPAQIREYLSMARQPISLDVRVGDNQDT 234

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L + +ED + VSP     Q  LR+    +LA LTP++  V+ +RFG+    + +L ++G
Sbjct: 235 ELSELLED-SGVSPDTFITQELLRQDLANLLAELTPQQREVITLRFGLTDGKELSLAKIG 293

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++  ++RER+RQ+E +A+  L+   R   ++ ++
Sbjct: 294 QRMNISRERVRQLEHQALAHLRR--RRANVKEYI 325



 Score = 42.1 bits (97), Expect = 0.34,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCESPLTFQALIIWRDELND 176
           D VR YL E+G + LL+ E EI   K+++          +L +        + W D +N 
Sbjct: 18  DMVRTYLHEIGRVPLLTHEQEIIYGKQVQRMMSLLEAKEALSKQLGREPQHLEWADSVNL 77

Query: 177 GTTLLR 182
               L 
Sbjct: 78  SENELD 83


>gi|56750962|ref|YP_171663.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81299380|ref|YP_399588.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
 gi|123769297|sp|Q31QR8|RPOD4_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD4
 gi|56685921|dbj|BAD79143.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81168261|gb|ABB56601.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
          Length = 311

 Score =  182 bits (462), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 109/276 (39%), Positives = 171/276 (61%), Gaps = 19/276 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGEC------------------EASIAKKEMVEANL 453
            + SI     ++  E   +   V+                          AK +M++ANL
Sbjct: 24  YLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQAVLQAGQRAKTKMLKANL 83

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY N+GL+ LDLIQEG++GL +A EKFD  LGYKFSTYA WW++Q++TR+I 
Sbjct: 84  RLVVSVAKKYQNQGLELLDLIQEGSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAID 143

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           + + TIR+P+H+ +KI ++ +  R +++++KR P+  EIA+ L +P++ V  +L  +   
Sbjct: 144 NHARTIRLPIHVSEKISRIKKMTRELTHQLKRLPSRAEIAEALKLPLQDVEMLLSQSTPC 203

Query: 574 ISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            SL+     +D  S LGD I D  ++ P+D+  +    E  +  LA LT RE++VL++RF
Sbjct: 204 TSLDAQARGDDGRSFLGDLIPDPKSLEPMDAMDRHIQHEQISTWLAHLTEREQQVLQLRF 263

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           G+     HTL E+G++  V+RERIRQ+EA+A++KL+
Sbjct: 264 GLHDGEQHTLAEIGRRLNVSRERIRQVEARALQKLR 299



 Score = 41.0 bits (94), Expect = 0.71,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 2/108 (1%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           +R T D V  YL  +G I LL+ E E+ ++++++   A++     ES    QA++     
Sbjct: 14  ERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQAVLQAGQR 73

Query: 174 LNDGTTL--LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                    LR ++ +      +         EG    +R     +  
Sbjct: 74  AKTKMLKANLRLVVSVAKKYQNQGLELLDLIQEGSLGLERAVEKFDPA 121


>gi|145300341|ref|YP_001143182.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853113|gb|ABO91434.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 327

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 103/281 (36%), Positives = 170/281 (60%), Gaps = 4/281 (1%)

Query: 397 NFVACEVDSILKI-RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
             +A EV+ ++   +  +  I     ++  E    V   R+       A+K M+E+NLRL
Sbjct: 41  ELMAPEVNKVMDATQLYLGEIGFSPLLTAEEE---VYYARRALRGDKAARKRMIESNLRL 97

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 98  VVKIACRYNNRGLVLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 157

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+++  EPT E+IA  L   V+ V ++LK+ ++  S
Sbjct: 158 TRTIRLPIHVVKELNVYLRTARELSHRLDHEPTAEDIAFALDRSVDDVNRMLKLNEKITS 217

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TPIG +    L D + D+  + P   +   ++R +    L  L P++  VL  RFG+ 
Sbjct: 218 VDTPIGGDRDKALLDVLSDERGMGPELESQDDDMRASIVHWLEELNPKQREVLARRFGLL 277

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
                TLE+VG +  +TRER+RQI+ + +R+L+     + L
Sbjct: 278 GYEPATLEDVGSEIGLTRERVRQIQVEGLRRLREILLGQGL 318



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            +          D  ++YL E+G   LL+ E E+  A+R   G       + ES L    
Sbjct: 40  DELMAPEVNKVMDATQLYLGEIGFSPLLTAEEEVYYARRALRGDKAARKRMIESNLRLVV 99

Query: 167 LIIWRDELNDGTTLLREI 184
            I  R   N G  LL  I
Sbjct: 100 KIACRYN-NRGLVLLDLI 116


>gi|89075068|ref|ZP_01161509.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
 gi|89049155|gb|EAR54720.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
          Length = 337

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 98/269 (36%), Positives = 167/269 (62%), Gaps = 3/269 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     ++  E    V   R+      +A+K M+E+NLRLV+ +
Sbjct: 54  EATQKALDATQLYLGEIGYSPLLTAEEE---VLYARRALRGDEVARKRMIESNLRLVVKI 110

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 111 SRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 170

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR ++ K+  EPT E+IA++L  PV+ V ++L++ +   S++ P
Sbjct: 171 RLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAQQLEKPVDDVNRMLRLNERVSSVDNP 230

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D+   SP  S    +++ +    L  L P++  VL  RFG+     
Sbjct: 231 IGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNPKQREVLARRFGLLGYEA 290

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 291 STLEDVGREIGLTRERVRQIQVEGLRRLR 319



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 5/114 (4%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
             + I+V          G       AS  ++ +   +  K  A +   D  ++YL E+G 
Sbjct: 17  EELDIDV----PATTSAGDSSETTAASPVTDDTDDAELAKYEATQKALDATQLYLGEIGY 72

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E+  A+R   G  +    + ES L     I  R   N G  LL  +
Sbjct: 73  SPLLTAEEEVLYARRALRGDEVARKRMIESNLRLVVKISRRYS-NRGLALLDLV 125


>gi|149911458|ref|ZP_01900075.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
 gi|149805489|gb|EDM65496.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
          Length = 319

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 102/280 (36%), Positives = 171/280 (61%), Gaps = 3/280 (1%)

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             + E ++ +  +  S+   +  +  I     ++  E    V   R+     + ++K M+
Sbjct: 28  MGKFEDEHLIPNDAKSLDATQLYLGEIGFSPLLTAEEE---VFYARRALRGDASSRKRMI 84

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I 
Sbjct: 85  ESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIE 144

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+I +Q+ TIR+P+H+  +++  +R AR +++++  EPT E+IA KL  PV  V K+L++
Sbjct: 145 RAIMNQTRTIRLPIHVVKELNVYLRAARELAHELDHEPTAEDIADKLDKPVADVSKMLRL 204

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +   S++TPIG +    L D I D+    P       +++ +  R L  L P++  VL 
Sbjct: 205 NERISSVDTPIGGDSEKALLDIISDEKGDGPESRTQNDDIKFSIIRWLEELNPKQREVLA 264

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RFG+      TLE+VG++  +TRER+RQI+ +A+R+L+ 
Sbjct: 265 RRFGLLGYDASTLEDVGREIGLTRERVRQIQVEALRRLRE 304



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 25/111 (22%), Positives = 44/111 (39%), Gaps = 3/111 (2%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            + D + L+  E      D  +       F  +     D  + D  ++YL E+G   LL+
Sbjct: 3   KITDANKLKIAENKVSDNDKKARPGMGK-FEDEHLIPNDAKSLDATQLYLGEIGFSPLLT 61

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E E+  A+R   G A     + ES L    ++      N+    L ++I+
Sbjct: 62  AEEEVFYARRALRGDASSRKRMIESNLRL--VVKIARRYNNRGLALLDLIE 110


>gi|1514627|emb|CAA62840.1| starvation sigma factor [Pseudomonas putida]
          Length = 335

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 94/265 (35%), Positives = 161/265 (60%), Gaps = 3/265 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   +V+K        +K M+++NLRLV+ +A++Y 
Sbjct: 60  ALDATQLYLNEIGFSPLLSPEEEVHFAPLVQK---GDPAGRKRMMQSNLRLVVKIARRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 177 VVKELNVYLRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGPDS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L  LT ++  V+  RFG+  +   TLE+
Sbjct: 237 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLED 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           VG +  +TRER+RQI+ + +++L+ 
Sbjct: 297 VGLEIGLTRERVRQIQVEGLKRLRE 321



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 33/136 (24%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  + +      L   GI V++ D + DE      +    + + S   L++
Sbjct: 3   LSKEVPEFDIDDDVL------LMETGI-VLETDVVSDEPA----VSSVRTRAKSGSSLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A  ++ G       + +S L     I
Sbjct: 52  HKYIDYSRALDATQLYLNEIGFSPLLSPEEEVHFAPLVQKGDPAGRKRMMQSNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
 gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
          Length = 546

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 88/303 (29%), Positives = 159/303 (52%), Gaps = 7/303 (2%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
                               V  +++S       I   +   GIS  + +  +       
Sbjct: 248 TAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPDLKSEIHR----- 302

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+T
Sbjct: 303 --GRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 360

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q+I +SI   S TIR+P ++   + KV    +    +    P+ E++A  + +
Sbjct: 361 YAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEQLAGHVGV 420

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E + K+L  T+ P+S++ PI  +  +   +   D    +P  S  +  +R     +L 
Sbjct: 421 STEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQMMRNHVRNLLN 480

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+P+E R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L +
Sbjct: 481 VLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQHMNSHGLHA 540

Query: 679 FLD 681
           + D
Sbjct: 541 YAD 543


>gi|2289784|dbj|BAA21674.1| rpoS sigma factor [Pseudomonas tolaasii]
          Length = 336

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 166/295 (56%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     ++  E  H   + +K       
Sbjct: 40  VRTKSKNSTALKQHKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQK---GDPA 96

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 97  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 156

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 157 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEV 216

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +G +    L D + D     P +     +L ++  + L+ LT +
Sbjct: 217 KRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTDK 276

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 277 QREVVIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 331



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 58/136 (42%), Gaps = 11/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+   P  ++  E       +L  M I + + + + ++EGS        + S +S  L++
Sbjct: 3   LSKEAPEFDIDDE-------VLLEMEI-LTEKESMSNDEGSATPS--VRTKSKNSTALKQ 52

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LL+ E E+  A+  + G       + ES L     I
Sbjct: 53  HKYIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLSQKGDPAGRKRMIESNLRLVVKI 112

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 113 ARRY-VNRGLSLLDLI 127


>gi|13357909|ref|NP_078183.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|170762330|ref|YP_001752432.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|11357048|pir||E82901 RNA polymerase sigma factor UU349 [imported] - Ureaplasma
           urealyticum
 gi|6899329|gb|AAF30758.1|AE002132_2 RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|168827907|gb|ACA33169.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
          Length = 448

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 117/287 (40%), Positives = 171/287 (59%), Gaps = 15/287 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+  +  +     +   E      M +        I K ++  +N+RLV S+AKKY NRG
Sbjct: 157 IKAYLGVLGESKMLRSDEETEYAKMVISDDPSLVKIGKNQLYTSNMRLVTSIAKKYLNRG 216

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG+ GL+KA +KFD   G+KFSTYA WW++Q+ITR+IADQ+  IRIPVHM +
Sbjct: 217 LDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIRQSITRAIADQARQIRIPVHMVE 276

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLA------------MPVEGVRKVLKITKEPIS 575
            I+K+ +  R +  ++ R+PT EEIA+ +             +  + V ++ K+  +P+S
Sbjct: 277 TINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQAKNQKEQLITAQKVVEIKKLNVDPVS 336

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGI 634
           L+  IG ++ S   DFI D   +SP     +  L +    +    L   E+RV++MR+G+
Sbjct: 337 LDKQIGHDEESQFSDFISDDEIISPEKYTEKKALNDQINEMFEKVLNDNEQRVIKMRYGL 396

Query: 635 GMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                 +TLEEVG+   VTRER RQIE+KAIRKLKHPS++ KLRSF+
Sbjct: 397 LPFERPYTLEEVGEYLGVTRERARQIESKAIRKLKHPSKTAKLRSFI 443


>gi|172035560|ref|YP_001802061.1| RNA polymerase sigma factor [Cyanothece sp. ATCC 51142]
 gi|171697014|gb|ACB49995.1| group 2 sigma-70 RNA polymerase sigma factor B [Cyanothece sp. ATCC
           51142]
          Length = 328

 Score =  182 bits (462), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 106/278 (38%), Positives = 177/278 (63%), Gaps = 7/278 (2%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + + +   +  S+         E + +   + +       AK++M+EANLRLV+++AKK
Sbjct: 55  KEELAQSLGKEPSLQEWAKEVNLEEKALTKALEQ----GERAKRKMIEANLRLVVAIAKK 110

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA Q+ TIR+P
Sbjct: 111 YQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLP 170

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+ +K++K+ +T R +S  + R  TP EIA++L +    +R+ L I ++PISL+  +GD
Sbjct: 171 IHITEKLNKIKKTQRELSQTLGRSATPAEIAQELEIEPSQIREFLSIARQPISLDVRVGD 230

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              + L + +ED+  VSP     Q  LR+  + ++A LTP++  VL +RFG+    + +L
Sbjct: 231 NQDTELSELLEDQ-GVSPDIYITQELLRQDLSNLMAELTPQQRTVLTLRFGLEDGKELSL 289

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++GK+  ++RER+RQ+E +A+ +L+   R   ++ +L
Sbjct: 290 AKIGKRLNISRERVRQLEHQALAQLRR--RRGNVKEYL 325



 Score = 41.0 bits (94), Expect = 0.71,   Method: Composition-based stats.
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCESPLTFQALIIWRDEL 174
           + D VR YL E+G + LL+ E EI   K+++           L +S     +L  W  E+
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIIYGKQVQKMMSLLETKEELAQSLGKEPSLQEWAKEV 75

Query: 175 NDGTTLLR 182
           N     L 
Sbjct: 76  NLEEKALT 83


>gi|213969149|ref|ZP_03397288.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
 gi|213926147|gb|EEB59703.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
          Length = 334

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 96/291 (32%), Positives = 164/291 (56%), Gaps = 4/291 (1%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                   ++       ++   +  +  I     +S  E    V   R  +      +K 
Sbjct: 43  AKQSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEE----VHFARLSQSGDPAGRKR 98

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 99  MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 158

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L
Sbjct: 159 IERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRML 218

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L ++  + L+ LT ++  V
Sbjct: 219 GLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREV 278

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 279 VIRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 329



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 52/131 (39%), Gaps = 13/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +    +        + +  S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAASG-----RTKAKQSTSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPE-EVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 114

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 115 VNRGLSLLDLI 125


>gi|144575263|gb|AAZ53437.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           7448]
          Length = 676

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 367 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 424

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 425 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 484

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 485 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLG 544

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 545 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 604

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 605 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 664

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 665 TPHRRLSLRDF 675


>gi|53987186|gb|AAV27387.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 676

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 367 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 424

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 425 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 484

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 485 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLG 544

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 545 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 604

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 605 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 664

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 665 TPHRRLSLRDF 675


>gi|298492420|ref|YP_003722597.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298234338|gb|ADI65474.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 389

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 182/285 (63%), Gaps = 2/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    D    +  E+      + ++   F      +     +  +AK++M+ +NLRLV
Sbjct: 105 RFLEEVKDLQAALEEELGQQPSRSEVAAK-FEMTEKQLESRLYQGRVAKRKMIRSNLRLV 163

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG +GL +A EKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 164 VSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWWIRQAITRAIANDA 223

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +  K+ R P+  E+A  L + ++ +R++ ++ ++ +SL
Sbjct: 224 RTIRLPIHIVEKLNKLKKAQRELKQKLARNPSEAEMATALEISIQQLRQLQQLRRQALSL 283

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIG 635
              +G E+ + L D +ED++  SP     +  +R+    VL   LTPRE+ V+ +R+G+ 
Sbjct: 284 NHRVGKEEDTELMDLLEDEDNQSPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLT 343

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +   TLEEVG  F ++RER+RQI++KA+RKL+ P  +K+L+ +L
Sbjct: 344 TSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLRRPHIAKRLKGWL 388


>gi|291298947|ref|YP_003510225.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290568167|gb|ADD41132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 330

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 103/273 (37%), Positives = 176/273 (64%), Gaps = 7/273 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  V++ L  +  I       G++ +E   +V        +   AK++ ++ANLRLV+S
Sbjct: 42  LAKAVEAGLYAQRLIGDDQQPEGVTEAELGRLV-------LDGQKAKEQFIKANLRLVVS 94

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y   G+  LDLIQEGN GL++A EKFD+  G+KFSTYA WW++QAI+R+IA Q  T
Sbjct: 95  IARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYQRGFKFSTYATWWIRQAISRAIAQQERT 154

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+PVH+ + ++++  TAR+++ ++  +P PE+IA  L + VE V ++++ +++ +SL+T
Sbjct: 155 VRLPVHLVEDVNRMRNTARQLTRELGADPEPEQIANALGVTVERVNELIRWSQDTVSLDT 214

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           PIGD+  ++LGD + D +  +P D  I    RE    +L  L  R   +++ R+G+    
Sbjct: 215 PIGDDGDTNLGDLVADSDEPTPEDVVIAGMERERIDMMLGHLDERSAGIVKARYGLEDGR 274

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +H+L EV  +F ++RERIRQ+E +A+ +LK  +
Sbjct: 275 EHSLTEVAHRFALSRERIRQLEIQALARLKELA 307


>gi|262401766|ref|ZP_06078332.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
 gi|262352183|gb|EEZ01313.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
          Length = 336

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 109/303 (35%), Positives = 178/303 (58%), Gaps = 7/303 (2%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSM 433
           E D    +  +        + V  E D    S+   +  +  I     ++  E    V  
Sbjct: 24  EADDELTNDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIGFSPLLTAEEE---VLY 80

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G
Sbjct: 81  ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERG 140

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA
Sbjct: 141 FRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIA 200

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L  PV+ V K+L++ +   S++TPIG +    L D + D +   P  S    ++RE+ 
Sbjct: 201 LELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +  L P+++ VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     
Sbjct: 261 LGWMDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK 320

Query: 674 KKL 676
           + L
Sbjct: 321 QGL 323



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/115 (25%), Positives = 45/115 (39%), Gaps = 8/115 (6%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
             +  + V++ DD       E + D     +  +    + +  A   + D  +MYL E+G
Sbjct: 15  FEDEALEVLEADD-------ELTNDEELVTAEGASDEVREEFDASAKSLDATQMYLSEIG 67

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 68  FSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|320159820|ref|YP_004173044.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319993673|dbj|BAJ62444.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 396

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 123/295 (41%), Positives = 184/295 (62%), Gaps = 26/295 (8%)

Query: 412 EIKSISVETGISISEFRHIVSMVRK-------------------------GECEASIAKK 446
            +K +S    +S  E   +   + +                            +   A++
Sbjct: 102 YLKEMSRVPLLSSEEEVELAKRIERGRAAKKELTRNSARLSPQRRGELEAQIQDGESARE 161

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +++AN RLV+S+AK+Y  RG+ FLDLIQEGN+GLMKA EK+++  G++FSTYA WW++Q
Sbjct: 162 HLIKANTRLVVSIAKRYIGRGVPFLDLIQEGNLGLMKAVEKYEYQRGFRFSTYATWWIRQ 221

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITRSIADQ  TIR+PVHM D+I ++ RT   M  K+ R PT EE+A  + +    V  +
Sbjct: 222 TITRSIADQGRTIRVPVHMVDRIRRLYRTTHEMEQKLGRTPTNEELADAIGIKASKVDWM 281

Query: 567 LKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++++  P+SLE+PI ++ + S LG FIED+   SP+ +     LRE    VL +L  RE 
Sbjct: 282 MRVSWLPLSLESPINEDEEDSELGQFIEDQVTPSPMQTTYSNLLREKIQEVLDTLPAREA 341

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+LR+RFG+     +TLEEVG++F +TRERIRQIE KA+R+L+HP R+++L+ +L
Sbjct: 342 RILRLRFGLENGRTYTLEEVGQKFGLTRERIRQIENKALRRLRHPRRARQLKDYL 396



 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 5/127 (3%)

Query: 29  DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEG 88
           +  K +++ A  +GY+T E+L    P      E+ E  +  L   G+++ D ++ E    
Sbjct: 12  EILKMLLEKADVQGYLTTEDLMEAYPNVGEDHERFEAILLALRRHGVDIYDTEENEYPFP 71

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            ED                +  D    S+DD V +YL+EM  + LLS E E+ +AKRIE 
Sbjct: 72  DEDIDGAFIEEDP-----VQTFDLNRISSDDTVGLYLKEMSRVPLLSSEEEVELAKRIER 126

Query: 149 GRAMMMA 155
           GRA    
Sbjct: 127 GRAAKKE 133


>gi|239934542|emb|CAR94585.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 297

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 114/306 (37%), Positives = 166/306 (54%), Gaps = 16/306 (5%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           R   IAIAKRIEAGR  M+A LCESP+TFQA+I+WR+ELN+   LLR+IIDL+A +G   
Sbjct: 2   RARXIAIAKRIEAGRDTMIAGLCESPVTFQAIIVWREELNEERVLLRDIIDLDATLG--- 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   +G      E ++     +         E+ AK              +  +  
Sbjct: 59  --------KGPGQPGNEANNANAGGNAASNEAVKAEAPAKQENAAEGDAPKTDASEADVS 110

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKS 310
            + D+D+ DS  +L+AME  LRP+V+   D+IA  Y++L  L++        N     + 
Sbjct: 111 DDDDDDDADSNMSLAAMEALLRPQVLEIFDKIAANYKKLHKLEEARIEGKVGNDPLSTQQ 170

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
             +   L+++ V LV SL LN +RI+ LV+ +Y I+KR++  EG LLRLA  +G+ R  F
Sbjct: 171 EKRYVKLRDETVTLVQSLHLNNNRIEALVDLMYSINKRLIGFEGRLLRLADYHGVDRAEF 230

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L++++  ELD +W           W+ F   E   I +IR+EI  IS ETG+ I EFR I
Sbjct: 231 LDQYRSHELDANWSRRVGRLKSKGWQEFTKKERVQIKEIRDEIAQISQETGLEIGEFRRI 290

Query: 431 VSMVRK 436
           V  V+K
Sbjct: 291 VHTVQK 296


>gi|186683480|ref|YP_001866676.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186465932|gb|ACC81733.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 104/287 (36%), Positives = 178/287 (62%), Gaps = 8/287 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           +    +A +    ++++ +         I+I E + ++  +     +   AK++M++ANL
Sbjct: 52  KMMALLATKEKLAIQLKRQPTQKEWIENINIGE-KSLLQQL----HQGQKAKQKMIQANL 106

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKY    L FLDLIQEG++GL +  EKFD   GYKFSTY  WW++QAITR+IA
Sbjct: 107 RLVVSIAKKYQRHNLDFLDLIQEGSLGLERGVEKFDPTKGYKFSTYGYWWIRQAITRAIA 166

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q  TIR+P+H+ +K++K+ R  R ++ K+ R PT  +IA++L++  + +R  L + ++P
Sbjct: 167 EQGRTIRLPIHITEKLNKIKRIQRELTQKLGRTPTAVDIAEELSLDPKQIRDYLLLARQP 226

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLE  +G +    L D +ED N +SP   A    L++    +L+ L P++ ++L  RFG
Sbjct: 227 VSLELRVGSDKDIELQDMLED-NGLSPELYADHKFLQQNIQNLLSKLNPQQRQILTFRFG 285

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +    + +L E+G++  ++RER+RQIE +A+  L+      K+ S+L
Sbjct: 286 LTDGNELSLAEIGQRMGISRERVRQIEQQALGSLRR--HKDKIHSYL 330



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 18/44 (40%), Positives = 24/44 (54%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +  K      T D VR YLRE+G I LL+ E EI  AK+++ 
Sbjct: 9   LEESNKKEKLLYTADTVRAYLREIGRIPLLTHEQEINFAKQVQK 52


>gi|196232822|ref|ZP_03131672.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196223021|gb|EDY17541.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 296

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 106/263 (40%), Positives = 165/263 (62%), Gaps = 3/263 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++  +   + + ++K       A+  M+ +NLRLV+ +A  Y N GL  L
Sbjct: 16  YLREIGQIPLLTPEQEIELAAKIKK---GDKAARSLMIRSNLRLVVKIAHDYANLGLPLL 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLMKA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ DKI K
Sbjct: 73  DLISEGNIGLMKAVERFDPAKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDKISK 132

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + R A +MS ++ REPT +E+A+++ +    + ++  ++  P SL+ PI D+D++  G+ 
Sbjct: 133 MRRVALQMSEELGREPTDDELAEEVGLSSGKISQLKTVSIRPASLDAPISDDDSTEFGEI 192

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D  A++P +     NLR+    +L  L  RE++++  RFG+      TLEEVGK+F V
Sbjct: 193 VGDLEALTPFERLRDKNLRDEVGDLLEVLDEREKKIIFSRFGLDGGKAKTLEEVGKKFGV 252

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           TRERIRQ++  A+ KL+   + K
Sbjct: 253 TRERIRQLQNIALMKLRRALQKK 275



 Score = 54.5 bits (129), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
           +   +D  +++YLRE+G I LL+ E EI +A +I+ G     + +  S L     I   D
Sbjct: 5   SGEDSDSGIKIYLREIGQIPLLTPEQEIELAAKIKKGDKAARSLMIRSNLRLVVKIAH-D 63

Query: 173 ELNDGTTLLREI 184
             N G  LL  I
Sbjct: 64  YANLGLPLLDLI 75


>gi|298250072|ref|ZP_06973876.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297548076|gb|EFH81943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 319

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 107/280 (38%), Positives = 173/280 (61%), Gaps = 5/280 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             D +  +   I+        +I + R +    R  + EA  AK++++EANLRLV+ +A+
Sbjct: 43  SKDEVTDLAQRIEKAQA----NIRKQRGLSRSARLDDNEAQEAKRQLIEANLRLVMHIAR 98

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY   G+  +DLIQEGN+GLM A +KFD+  GY+FSTYA WW++Q ITR++++Q+  IR+
Sbjct: 99  KYRGFGVDLMDLIQEGNLGLMHAVDKFDYKKGYRFSTYATWWIRQYITRALSEQAHMIRV 158

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P++  ++I ++ R  R+M      EPT EE+A ++ + V  V  +L   +E ISL+ P  
Sbjct: 159 PLYKIEEIKRLGRVKRKMQQGETGEPTLEELAVQMEISVPEVIALLSTNQETISLDMPRK 218

Query: 582 -DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +D   L + +ED    SP    +   L+E    +L  LTPRE++VL++RFG+  N +H
Sbjct: 219 GGDDEISLSEVLEDDPIYSPERVVLTQTLQEQVQDILNCLTPREKKVLQLRFGLNGNGEH 278

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +L E GK+  ++ E +RQ+E +A++KL HP R ++L+ FL
Sbjct: 279 SLTETGKKMGLSHEAVRQMEFRALKKLGHPCRDRRLQDFL 318


>gi|159039487|ref|YP_001538740.1| RpoD family RNA polymerase sigma factor [Salinispora arenicola
           CNS-205]
 gi|157918322|gb|ABV99749.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 329

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 96/247 (38%), Positives = 169/247 (68%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + +++   E   AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+ 
Sbjct: 82  AELQRLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYE 141

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+
Sbjct: 142 RGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQ 201

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA  L + VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP +  +    R+
Sbjct: 202 IATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQ 261

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L+ L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +
Sbjct: 262 RIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELA 321

Query: 672 RSKKLRS 678
           R++ L++
Sbjct: 322 RAEGLQA 328


>gi|159904372|ref|YP_001551716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889548|gb|ABX09762.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 338

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 97/256 (37%), Positives = 155/256 (60%), Gaps = 1/256 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +   E   + +  R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL
Sbjct: 74  HHVQKMKELLDIEKEKLSARQRHQIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDL 133

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ 
Sbjct: 134 VQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMR 193

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFI 592
           R +R +S++  R+P   E+A  + +  + +  ++  +    SL++    E+  S LG+ I
Sbjct: 194 RISRELSHRFGRQPNRVELANAMGIEPQDLEDLVAQSAPCASLDSHARGEEDRSTLGELI 253

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D N   P+    +   +E     L+ L  RE++++R+RFG+      TL E+G+Q  V+
Sbjct: 254 PDPNYDEPMAGMDRKMQKEHLGGWLSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVS 313

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ+EAKAI KL+
Sbjct: 314 RERVRQLEAKAILKLR 329



 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 73  MGINVVDGDD--LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           MGI +   +D      + +  S        ++      R  +  R   D +  YL  +G 
Sbjct: 1   MGIPLESTNDGSSSSVDLAISSNSKNQQEKSAGNSQASRNRTGGRLATDSIGFYLSSIGR 60

Query: 131 IELLSREGEIAIAKRIEA 148
           + LL+   EI +A  ++ 
Sbjct: 61  VPLLTPAEEIELAHHVQK 78


>gi|298490639|ref|YP_003720816.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298232557|gb|ADI63693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 327

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 166/247 (67%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VKQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K+ R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED+   SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVRVGDNQDTELQEMLEDE-GPSPEYYTTQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  VL +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 NNLLAELTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQALAHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 ANVKEYV 325



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 26/42 (61%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + ++   + T D VR YLRE+G + LL+RE EI   K+++ 
Sbjct: 6   TQTENLNTKFTADMVRTYLREIGRVPLLTREQEIVYGKQVQQ 47


>gi|16330303|ref|NP_441031.1| RNA polymerase sigma factor SigD [Synechocystis sp. PCC 6803]
 gi|1652792|dbj|BAA17711.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 318

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 111/280 (39%), Positives = 174/280 (62%), Gaps = 7/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVA 460
           S+ +I+  +        +S SE+       +  + K   E   AK++MVEANLRLV+SVA
Sbjct: 40  SLNEIKKSLAEGKDGEPVSPSEWAKAADLSIRELEKAIKEGERAKRKMVEANLRLVVSVA 99

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR
Sbjct: 100 KKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIR 159

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R++S +  R  +  E+A+ L +  + VR+ L+ ++ P+SL+  +
Sbjct: 160 LPIHITEKLNKIKKAQRQLSQEKGRAASIAELAEHLELTPKQVREYLERSRHPLSLDLRV 219

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD   + LGD +ED +   P D A  A+L+     ++A LTP++  VL +RFG+      
Sbjct: 220 GDNQDTELGDLLED-DGPLPEDFATYASLQLDLDSLMAELTPQQREVLILRFGLNDGQPL 278

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL  +G    ++RER+RQIE +A+ KL+   R   ++ +L
Sbjct: 279 TLASIGSMLSISRERVRQIEREALNKLRK--RKSMIQEYL 316



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           R++ D VR YLRE+G + LL+ E EI  AK+I+       +  SL E
Sbjct: 4   RTSPDSVRAYLREIGRVPLLTHEEEIVYAKQIQQVVSLNEIKKSLAE 50


>gi|119513754|ref|ZP_01632741.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
 gi|119461595|gb|EAW42645.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
          Length = 327

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 104/268 (38%), Positives = 169/268 (63%), Gaps = 10/268 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   + +  +   E   IV+           AK++M+EANLRLV+++AKKY  R ++FLD
Sbjct: 68  LPEWAAQVNLPEKEVTQIVAQ-------GKRAKQKMIEANLRLVVAIAKKYQKRNMEFLD 120

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+
Sbjct: 121 LIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKI 180

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +  R ++ K  R PTP EIA +L +    +R+ L + ++P+SL+  +GD   + L + +
Sbjct: 181 KKVQRELAQKFGRSPTPTEIAHELELEPMQIREYLNMARQPVSLDVKVGDNQDTELQEML 240

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED+   SP     Q  LR+    +LA LTP++ +VL +RFG+    + +L +VG++  ++
Sbjct: 241 EDE-GPSPEYYTTQEFLRQDLNNLLAELTPQQRQVLALRFGLEDGNEMSLAKVGERLNLS 299

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RER+RQ+E +A+  L+   R   ++ ++
Sbjct: 300 RERVRQLEHQALAHLRR--RRANVKEYV 325



 Score = 45.2 bits (105), Expect = 0.033,   Method: Composition-based stats.
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLC 158
           ++   K ++   + T D VR YLRE+G + LL+R+ EI   K+++          +L 
Sbjct: 2   AIVNTKTENLNTKFTADMVRTYLREIGRVPLLTRDEEIIFGKQVQQMMTLLDAKQALA 59


>gi|302391919|ref|YP_003827739.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
 gi|302203996|gb|ADL12674.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
          Length = 273

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 112/272 (41%), Positives = 180/272 (66%), Gaps = 3/272 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I     E G  +   +    + +  +     A+KE++E NLRLV+S+AKKY  +G++F D
Sbjct: 3   INQYYQEMGHDLLSKKEEAKLAKGAQNGDQEARKELIEHNLRLVVSIAKKYRGKGMEFED 62

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQEGN+GLMKA +KFD   GY+FSTYA WW++Q+ITR++  ++ TIR+PVH+ +K  KV
Sbjct: 63  MIQEGNLGLMKAIDKFDPDKGYRFSTYATWWIRQSITRAL-PEAKTIRVPVHVWEKTTKV 121

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGD 590
            +   ++ N++ REPT EEI+++  +  E V+++++I+ +    SL   +GD++ + LG+
Sbjct: 122 FKAKEKLYNQLNREPTFEEISEETGIDSEKVKEIIRISSDQNLASLNNLVGDDENTELGE 181

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D +   P+    +  L+E    VL  LT RE  ++R+RFG+  N   TL+EV  +F 
Sbjct: 182 LIADDDVEEPMTDLNRQFLQEDLEEVLEELTDREAEIIRLRFGLKDNWPKTLQEVADRFK 241

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ++RERIRQI+ KA+R+L+HPSRSK L++++ G
Sbjct: 242 LSRERIRQIQEKALRRLRHPSRSKALKAYIAG 273


>gi|16330349|ref|NP_441077.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1652838|dbj|BAA17757.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 369

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 109/251 (43%), Positives = 168/251 (66%), Gaps = 1/251 (0%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V        +   AK+ M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD 
Sbjct: 119 VRQFEIWLYQLRAAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDP 178

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  ++KR P   
Sbjct: 179 DKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHVVEKLNKIKKAQRSLKQELKRNPNEG 238

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  L +    +R++L++ ++ +SL   +G  + + L D +ED+    P D   ++ LR
Sbjct: 239 ELAAALDITPAQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQQLQLPEDLMNESMLR 298

Query: 611 ETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                VLA  LT RE  V+ +R+GI  +  +TLEEVG  F ++RER+RQI++KA+RKL+ 
Sbjct: 299 REIVEVLAEVLTEREMEVICLRYGIASHQSYTLEEVGNMFNLSRERVRQIQSKAMRKLRR 358

Query: 670 PSRSKKLRSFL 680
           P  +++L+ +L
Sbjct: 359 PQVARRLKGWL 369



 Score = 37.5 bits (85), Expect = 8.3,   Method: Composition-based stats.
 Identities = 18/91 (19%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-TDDPVRMYLREMGSIELLSR 136
           VD     D      ++      +        ++ S +++ ++D V  + +EM    LLS 
Sbjct: 15  VDQWQALDGLADGQAIANDDPPAIEVTLGDGQQGSFNKAVSEDTVGAFFKEMARYPLLSA 74

Query: 137 EGEIAIAKRI------EAGRAMMMASLCESP 161
             E+ +A++I      E  R  +   L  +P
Sbjct: 75  AEEVELARQIRLLVSAEDVRQQLTQQLERTP 105


>gi|120553862|ref|YP_958213.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei
           VT8]
 gi|120323711|gb|ABM18026.1| RNA polymerase, sigma 38 subunit, RpoS [Marinobacter aquaeolei VT8]
          Length = 332

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 102/275 (37%), Positives = 167/275 (60%), Gaps = 3/275 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +   +  +  I     ++  E  +   + RKGE      +K M+E+NLRLV+ +A+
Sbjct: 54  NQKQLDATQLYLNEIGFSPLLTPEEEVYFARLARKGEESG---RKRMIESNLRLVVKIAR 110

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+
Sbjct: 111 RYVNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 170

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  +++  +R AR ++ K+  EPT EEIA+ +  PV+ V+++L + +   S++TPIG
Sbjct: 171 PIHVVKELNLYLRAARELTQKLDHEPTAEEIARMVDKPVDDVKRMLGLNERVASMDTPIG 230

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L D + D+ A  P D     N+     + +  L+ +++ VL  RFG+      T
Sbjct: 231 AGSDKSLMDTVADEGASDPADLLQDNNMCSCLEKWIDQLSDKQQEVLSRRFGLRGYPIST 290

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LEEVG++  +TRER+RQI+ +A+R+L+     + L
Sbjct: 291 LEEVGQEIGLTRERVRQIQVEALRRLREILEKEGL 325



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/127 (25%), Positives = 54/127 (42%), Gaps = 4/127 (3%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           +S EQ +  +  ++++       D L  E+  E +     +A     F  + K  +++  
Sbjct: 1   MSVEQEDIIIDRVADLE---DADDQLLAEDKPEKASAEDETAEVEDGFPAQGKYYSNQKQ 57

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D  ++YL E+G   LL+ E E+  A+    G       + ES L     I  R  +N G
Sbjct: 58  LDATQLYLNEIGFSPLLTPEEEVYFARLARKGEESGRKRMIESNLRLVVKIARRY-VNRG 116

Query: 178 TTLLREI 184
            TLL  I
Sbjct: 117 LTLLDLI 123


>gi|144227447|gb|AAZ44150.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           J]
          Length = 676

 Score =  182 bits (461), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 367 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 424

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 425 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 484

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 485 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLD 544

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 545 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 604

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 605 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 664

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 665 TPHRRLSLRDF 675


>gi|50955189|ref|YP_062477.1| ECF subfamily RNA polymerase sigma-70 factor [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50951671|gb|AAT89372.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 308

 Score =  181 bits (460), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 106/264 (40%), Positives = 158/264 (59%), Gaps = 4/264 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++   G+S  E R +  +      +   A +  +EANLRLV+S+AK+Y  RGL  +DL
Sbjct: 49  ERLATRPGLSPREKRELHVL----SDDGKRAFERFIEANLRLVVSIAKRYAGRGLAVMDL 104

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  G KFSTYA WW++Q+I R IAD +  IRIPVH  +KI K+ 
Sbjct: 105 IQEGNLGLVRAVEKFDYRTGNKFSTYATWWIRQSILRGIADTARVIRIPVHTVEKIDKLD 164

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R +  ++ R PT EEIA   ++    V K+     E +SL  P+G+ + + LGD IE
Sbjct: 165 RIRRDLGGELGRTPTLEEIADAASLTPAEVHKLQMSDSETVSLAVPVGENEGAELGDLIE 224

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D +A  P +              L  L  R+ +V+RMRFG+      TL+EVG  + +TR
Sbjct: 225 DGDAPGPSERVEVEFRHRDLEERLRELPLRDAKVVRMRFGLDGRKPMTLDEVGAVYGITR 284

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLR 677
           ER+RQ+E +++++L+ P   + LR
Sbjct: 285 ERVRQLETRSLKRLRSPELLEYLR 308



 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 18/33 (54%), Positives = 24/33 (72%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           T+DPVR YL  +G   LL+ E E+++AKRIE G
Sbjct: 12  TNDPVRDYLNSIGRTWLLTAEDEVSLAKRIEVG 44


>gi|160872453|ref|ZP_02062585.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
 gi|159121252|gb|EDP46590.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
          Length = 330

 Score =  181 bits (460), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 157/271 (57%), Gaps = 3/271 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           +++   +  +  I     +S  E  +   ++ K       A+K M+E+NLRLV+ +A+ Y
Sbjct: 54  ETLGATQLYLNEIGFSPLLSAEEEVYYARLIAK---GDQDARKRMIESNLRLVVKIARHY 110

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGLQFLDLI+EGN+GLM A EKFD   G++FSTYA WWV+QAI R+I +Q+ T+R+P+
Sbjct: 111 NNRGLQFLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWVRQAIERAIMNQARTVRLPI 170

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  ++ AR ++ K+  +PT +EIAK L  P E V ++L + +   S++ P   E
Sbjct: 171 HVVKELNVYLQAARELTQKLDHKPTSDEIAKWLDRPFEEVERMLGLNEHITSVDAPASSE 230

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L + + D     P       NLR+     L  L+  +  V+  R+G+      TLE
Sbjct: 231 ADKPLLETLSDNRENDPEHILEGENLRKRLEGWLKQLSTNQREVIARRYGLLGCDRMTLE 290

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           EVG+   +TRER+RQI+ + ++ L+     +
Sbjct: 291 EVGEVIGLTRERVRQIQVEGLKTLRKIMEKQ 321



 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 32/89 (35%), Gaps = 9/89 (10%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           ++YL E+G   LLS E E+  A+ I  G       + ES L     I      N G   L
Sbjct: 60  QLYLNEIGFSPLLSAEEEVYYARLIAKGDQDARKRMIESNLRLVVKIARHYN-NRGLQFL 118

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQK 210
             I         E   G  H  E    ++
Sbjct: 119 DLI--------EEGNLGLMHAVEKFDPER 139


>gi|171920947|ref|ZP_02932089.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|185178923|ref|ZP_02964687.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188024158|ref|ZP_02996885.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188518597|ref|ZP_03004049.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|188524519|ref|ZP_03004514.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195868018|ref|ZP_03080013.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198273631|ref|ZP_03206166.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209554143|ref|YP_002284749.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225550349|ref|ZP_03771298.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
 gi|225551084|ref|ZP_03772030.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|171903184|gb|EDT49473.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|184209186|gb|EDU06229.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188018789|gb|EDU56829.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188997798|gb|EDU66895.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|195659715|gb|EDX53095.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195660310|gb|EDX53572.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198249659|gb|EDY74440.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209541644|gb|ACI59873.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225378899|gb|EEH01264.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|225379503|gb|EEH01865.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
          Length = 448

 Score =  181 bits (460), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 117/287 (40%), Positives = 171/287 (59%), Gaps = 15/287 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+  +  +     +   E      M +        I K ++  +N+RLV S+AKKY NRG
Sbjct: 157 IKAYLGVLGESKMLRSDEETEYAKMVISNDPALIKIGKNQLYTSNMRLVTSIAKKYLNRG 216

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG+ GL+KA +KFD   G+KFSTYA WW++Q+ITR+IADQ+  IRIPVHM +
Sbjct: 217 LDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIRQSITRAIADQARQIRIPVHMVE 276

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLA------------MPVEGVRKVLKITKEPIS 575
            I+K+ +  R +  ++ R+PT EEIA+ +             +  + V ++ K+  +P+S
Sbjct: 277 TINKLTKAERSLIQELGRDPTAEEIAQAMNKASQAKNQKEQLITAQKVVEIKKLNVDPVS 336

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGI 634
           L+  IG ++ S   DFI D   +SP     +  L +    +    L   E+RV++MR+G+
Sbjct: 337 LDKQIGHDEESQFSDFISDDEIISPEKYTEKKALNDQINEMFEKVLNDNEQRVIKMRYGL 396

Query: 635 GMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                 +TLEEVG+   VTRER RQIE+KAIRKLKHPS++ KLRSF+
Sbjct: 397 LPFERPYTLEEVGEHLGVTRERARQIESKAIRKLKHPSKTAKLRSFI 443


>gi|289208462|ref|YP_003460528.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
 gi|288944093|gb|ADC71792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
          Length = 359

 Score =  181 bits (460), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 97/274 (35%), Positives = 158/274 (57%), Gaps = 3/274 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I+  ++ I     ++  E R    + R         ++ M+E NLRLV+ +A++Y 
Sbjct: 82  ELDAIQIYLRDIEYRPLLTPEEERKYARLAR---DGDESGRRRMIECNLRLVVKIARRYL 138

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q I R++ +Q  TIRIPVH
Sbjct: 139 NRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERALMNQGRTIRIPVH 198

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  ++    R AR ++ ++ R+PT EE+A++L  PV  ++K+  +++   S++ P G + 
Sbjct: 199 VSKELRMHARIARNLTQELGRDPTEEELAQRLGKPVADIQKLRAMSEPSTSMDLPPGPDG 258

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D NA  P       +++      L  L  ++  VL  RFG+      TLE+
Sbjct: 259 ERSLTDILADVNAQEPSSLLEDQDIQHLVDEWLGELDYKQREVLVRRFGLHGFERSTLEQ 318

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           VG +  VTRER+RQI+  A+++L+    S+ ++ 
Sbjct: 319 VGAEIGVTRERVRQIQMDALKRLRRLLESRGMKG 352



 Score = 44.1 bits (102), Expect = 0.083,   Method: Composition-based stats.
 Identities = 27/111 (24%), Positives = 42/111 (37%), Gaps = 8/111 (7%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP-------VRMYLREMGSIEL 133
           D L  EE  E+  D+ +      +  ++      R+  D        +++YLR++    L
Sbjct: 39  DPLATEESPEEVDDVPAPEDEKELSPEQDVPVRPRTLRDARPAELDAIQIYLRDIEYRPL 98

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L+ E E   A+    G       + E  L     I  R  LN G  LL  I
Sbjct: 99  LTPEEERKYARLARDGDESGRRRMIECNLRLVVKIARRY-LNRGLPLLDLI 148


>gi|197294657|ref|YP_001799198.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853984|emb|CAM11947.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 476

 Score =  181 bits (460), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 122/260 (46%), Positives = 182/260 (70%), Gaps = 7/260 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + + S +     +A+ AK  +VE+N RLV+S+AK+Y  RG+ FLDLIQEGN+GL
Sbjct: 217 LSDQEVKQLESQI----IQANQAKDVLVESNYRLVVSIAKRYIGRGVLFLDLIQEGNMGL 272

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M+A +KFD+  G + STYA +WV Q +TR+IADQ+ TIRIPVH+ + I+K+    R+++ 
Sbjct: 273 MRAVDKFDYQKGLRLSTYATYWVIQGVTRAIADQARTIRIPVHIVETINKMSLCTRKLTQ 332

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVS 599
           ++K++PT EE+A+K+ +P + +R +  I K+PISLE P     ED + LGDFI D N +S
Sbjct: 333 ELKKKPTIEELAEKMNIPADKLRSIQYIEKKPISLEVPPAENKEDETSLGDFISDPNVLS 392

Query: 600 PLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           P +  ++   ++    VL  +LT REE+VL+MR+G      +TLEE+G  F VTRERIRQ
Sbjct: 393 PHEYMMKEVTQKLLDEVLENTLTEREEKVLKMRYGFLDGKVYTLEEIGNLFGVTRERIRQ 452

Query: 659 IEAKAIRKLKHPSRSKKLRS 678
           IE+KA+R+L+ P++  KL+S
Sbjct: 453 IESKALRRLRTPAKQSKLKS 472



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 17/45 (37%), Positives = 23/45 (51%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
                 +        K ++D   DD VRMYL+E+G I LLS+E E
Sbjct: 146 EIDPEDDKFSKENITKINSDIKIDDSVRMYLKEIGRIPLLSKEEE 190


>gi|219883041|ref|YP_002478205.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
 gi|219862047|gb|ACL42388.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
          Length = 951

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 108/268 (40%), Positives = 153/268 (57%), Gaps = 2/268 (0%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               G +  E R  +  +         A  ++V  NLRLV+S+AK++T RG+ FLDLIQE
Sbjct: 501 EHLLGTARPEGRRAILELESVASAGRDAVLKLVSCNLRLVVSIAKRHTGRGMDFLDLIQE 560

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN GL +A +KFD+  G+KFSTYA WW++QAITR IADQS TIR+PVH  +++  V    
Sbjct: 561 GNAGLYRAVQKFDYTKGFKFSTYATWWIRQAITRGIADQSRTIRLPVHFHEQVVSVFIAE 620

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIED 594
           R       R+ T EEIA+     V+ +  V +    P SL+  + +       LG+ + D
Sbjct: 621 RNFLQSEGRDGTAEEIAEACGKTVDEINAVRRHRTPPASLDWEVPNGKGGVELLGETLYD 680

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +  +  D+A+ A L+      L  L+ RE  VL  RFG+      TL+++G  + VTRE
Sbjct: 681 PDEPTAYDAAVLAQLQSAVHGALDRLSEREAGVLAYRFGLATGEQLTLDQIGTIYGVTRE 740

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           RIRQIEAKA   L+ P+ + +LR F DG
Sbjct: 741 RIRQIEAKAFAALREPAAAAQLRDFFDG 768



 Score = 37.1 bits (84), Expect = 9.2,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 3/94 (3%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
           E   E +E  +A  +     V +  ++      E          + S + +        S
Sbjct: 408 ETDVEAVEAFLAY-TEHETKVPEVPEVPQAPAVEPPAAPFVLERDDSDWSEAPVLE--GS 464

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
             D VR+YL +  S +LL+ E    +   IEAG 
Sbjct: 465 IGDDVRLYLEQASSFDLLTHEEVTDLGMAIEAGL 498


>gi|317969130|ref|ZP_07970520.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0205]
          Length = 309

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 105/240 (43%), Positives = 162/240 (67%), Gaps = 1/240 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +K       +K+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKFD   GY
Sbjct: 65  KKIMRVGKRSKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGY 124

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P+ +EIA+
Sbjct: 125 KFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTAIRKVSLELAHKLGAMPSRKEIAE 184

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++ MP++ +  +L+      SL+ P+  E+  S LGD I D++   PLD   +   +E  
Sbjct: 185 EMDMPLDELDSLLRQALTTSSLDAPVNGEEGRSFLGDLIADQSNSEPLDQVERGIHQEQL 244

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  LT +E +VL +RFG+     HTL E+G+   V+RER+RQ+E KA+RKL+H +R 
Sbjct: 245 GRWLTHLTDQERQVLELRFGLEGEERHTLAEIGRMLEVSRERVRQVELKALRKLRHLTRR 304


>gi|291464752|gb|ADE05834.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 300

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 90/342 (26%), Positives = 140/342 (40%), Gaps = 44/342 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+   
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L +II     I P             +         E +  D  E E + E     
Sbjct: 61  EQLRLSDII--SGFIDPNETE-----DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGD 113

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           + DD       PE A      L    + +  ++                           
Sbjct: 114 NSDDEGDSGPDPEVAREKFGELRAQYEVTRLSI--------------------------- 146

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                   QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +
Sbjct: 147 --------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERII 198

Query: 357 LRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           L+L  +   + +  F+      E D  W  Y K   +  W   +    + +L+   +++ 
Sbjct: 199 LKLCVEQAKMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQ 257

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           I  ETG+SI++ + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 258 IEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVI 299


>gi|1519640|gb|AAB07553.1| SigC [Chloroflexus aurantiacus J-10-fl]
          Length = 312

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 95/272 (34%), Positives = 164/272 (60%), Gaps = 5/272 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R   + +  E  + ++E + +++ V      A   + +++ +NLRLV+S+A++Y    L 
Sbjct: 44  RRAAERLHNEPLLPLAEKQRLIAQV-----NAGTGRAQLINSNLRLVVSIARRYQGHALS 98

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLIQEG++GLM A +KFD   G KFSTYA +W++Q+I R+IAD S T+R+PVH+ +++
Sbjct: 99  LLDLIQEGSVGLMGAVDKFDASRGLKFSTYATYWIRQSIGRAIADHSRTVRLPVHLGERL 158

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            ++ R  + +S ++ REPT EE+A          R   +    P SL+ P  ++    L 
Sbjct: 159 SRLSRLRQELSQQLDREPTLEELAAGCRPERRAGRTAEQAGLAPTSLDEPHTEDGGGALA 218

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + + D    +P D   ++ L+      L  L+PRE  +LR+R+G+     HTLE++G++ 
Sbjct: 219 EILTDPLQPTPFDEVSESMLQADVQHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRL 278

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +TRER+RQ+E +A+RKL+ PS   +L+ +++
Sbjct: 279 RLTRERVRQLEHEALRKLRDPSLHPQLQGYVN 310



 Score = 44.8 bits (104), Expect = 0.054,   Method: Composition-based stats.
 Identities = 21/71 (29%), Positives = 32/71 (45%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
            RS  DP+ +YL E+G+  LL+ E E  +A+ +  GR        E  L          +
Sbjct: 8   GRSASDPIVLYLNEIGAEPLLTFEQEQHLAQTMSQGRRAAERLHNEPLLPLAEKQRLIAQ 67

Query: 174 LNDGTTLLREI 184
           +N GT   + I
Sbjct: 68  VNAGTGRAQLI 78


>gi|218440063|ref|YP_002378392.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172791|gb|ACK71524.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 372

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 107/275 (38%), Positives = 184/275 (66%), Gaps = 5/275 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + ++     +     + +   R + + + +       AK++M+ +NLRLV+S+AK+Y NR
Sbjct: 101 IDLQRPPTKLEWAQAMGLQNERQLENRLYR----GRSAKRKMIRSNLRLVVSIAKRYLNR 156

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ 
Sbjct: 157 GVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIV 216

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +K++K+ +  R +  ++ R PT +E+A+ L +  E +R++L++ ++ +SL   +G  + +
Sbjct: 217 EKLNKLKKAQRVLKQQLHRNPTEKELAQALEVDAENLRQLLQLRRQSLSLNHRVGKGEDT 276

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            L D +ED++   P +   +A +R+  + VL   LT RE+ V+ +R+G+  +  +TLEEV
Sbjct: 277 ELVDLLEDEDLQLPEEKMNEAMMRQDISAVLTDVLTEREKDVIALRYGLSTSQPYTLEEV 336

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 337 GGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 371



 Score = 37.9 bits (86), Expect = 6.3,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 26/60 (43%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ED+  +   ++L  +  N           +  ++DD V  + +EM    LL  E EI +A
Sbjct: 24  EDKAQAVAQVELELANLNDETGNPYPAGYSKTNSDDTVGAFFKEMARYPLLKPEEEIELA 83


>gi|126175320|ref|YP_001051469.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125998525|gb|ABN62600.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS155]
          Length = 326

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 166/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK     + ++  M+E+NLRLV+ +A++Y
Sbjct: 49  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKALKGCAKSRNRMIESNLRLVVKIARRY 105

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 106 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 165

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT EEIA+KL +    V ++LK+ ++  S++TP+  +
Sbjct: 166 HVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQVSSADVSRMLKLNEKITSVDTPLWGD 225

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D + V P       ++  +  + L  L  ++  VL  RFG+      TLE
Sbjct: 226 NDKALLDILADDDNVGPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG +  +TRER+RQI+ +A+++L+    S+ L
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQGL 318



 Score = 40.6 bits (93), Expect = 0.86,   Method: Composition-based stats.
 Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 2/95 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             +  +S     + ++++     +   D  ++YL E+G   LLS E E+  +++   G A
Sbjct: 25  EKEEVASDLVQELGIEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEEVYFSRKALKGCA 84

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
                + ES L    ++      N+    L ++I+
Sbjct: 85  KSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 117


>gi|307152078|ref|YP_003887462.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982306|gb|ADN14187.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 328

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 103/287 (35%), Positives = 180/287 (62%), Gaps = 7/287 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           +    +  + D +        S++            +   +++       AK++M+EANL
Sbjct: 46  QKMMTLLEKKDELAIQLEREPSLTEWANHVQMSEEELNRAIQQ----GKRAKRKMIEANL 101

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA
Sbjct: 102 RLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIA 161

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            Q+ TIR+P+H+ +K++K+ +T R +S ++ R  TP EIAK L +  + +R+ L ++++P
Sbjct: 162 QQARTIRLPIHITEKLNKIKKTQRELSQQLGRSATPSEIAKALDLEPDQIREFLSMSRQP 221

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           ISL+  +GD   + L + +ED+  +SP +   Q  +R+    +LA LTP++  VL +RFG
Sbjct: 222 ISLDVRVGDNQDTELSELLEDE-GISPDNYITQELMRQDLQDLLAELTPQQREVLSLRFG 280

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +    + +L ++G++  ++RER+RQ+E +A+ +L+   R   ++ ++
Sbjct: 281 LQDGKELSLAKIGQRMNISRERVRQLEHQALSQLRR--RRSNVKEYI 325



 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D VR YL E+G + LL+ E EI   K+++ 
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQK 47


>gi|119493081|ref|ZP_01624006.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
 gi|119452826|gb|EAW34001.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
          Length = 331

 Score =  181 bits (460), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 105/267 (39%), Positives = 177/267 (66%), Gaps = 8/267 (2%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++  TG+S +E  H          +  IAK++M+ +NLRLV+S+AK+Y NRG+ FLDLI
Sbjct: 71  ELATATGLSEAELNH-------QFQQGIIAKQKMISSNLRLVVSIAKRYLNRGVPFLDLI 123

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG +GL +A EKFD   GYKFSTYA WW++Q ITR+IA+Q  T+R+PVH+ ++++K+  
Sbjct: 124 QEGALGLNRATEKFDPDKGYKFSTYAYWWIRQGITRTIANQGRTVRLPVHVVEQLNKLQG 183

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             + +   ++R+PT +E+A+ L++  + +R + ++ ++ +SL   +G E+ S L D +ED
Sbjct: 184 IHQDLRRSLRRKPTEDELAEALSISPQQLRLLEQVRRKSLSLNHRVGSEENSELMDLLED 243

Query: 595 KNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             ++SP     +  +R+    VL S L  RE+ +L +R+G+     +TL+EV     ++R
Sbjct: 244 YESLSPESQINELMMRQELLEVLRSVLNEREQDILSLRYGLTTGVPYTLDEVSGMCSLSR 303

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQI+AKA+RKL+ P  +++L+ ++
Sbjct: 304 ERVRQIQAKAMRKLRRPQVAERLKGWI 330


>gi|260911780|ref|ZP_05918352.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634106|gb|EEX52224.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 287

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 98/272 (36%), Positives = 167/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   +RK       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEELISVEEEVELAQRIRK---GDRKALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+PV+    
Sbjct: 75  SLQDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPVNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+  EIA+K  +P + +   +K+T   IS++ P  D + + L
Sbjct: 135 VNKINKILNKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGRHISVDAPFVDGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + +  +  +  ++ +LR      L  L  RE  V+   FGI      TLEE+G +
Sbjct: 195 LDLLTNSDMPTVDNELVKESLRAEIAEALQFLNERERNVIEAFFGINQME-MTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI+ KAIR+L++ +++K L+++L
Sbjct: 254 YGLTRERVRQIKEKAIRRLRNNTKNKMLKTYL 285



 Score = 43.7 bits (101), Expect = 0.099,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
            S      D +  YL+E+G  EL+S E E+ +A+RI  G    +  L ++ L F  ++  
Sbjct: 8   KSITNRESDSLDKYLQEIGHEELISVEEEVELAQRIRKGDRKALEKLTKANLRF--VVSV 65

Query: 171 RDELNDGTTLLREIID 186
             +  +    L+++I+
Sbjct: 66  AKQYQNQGLSLQDLIN 81


>gi|113474981|ref|YP_721042.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166029|gb|ABG50569.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 496

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 116/294 (39%), Positives = 177/294 (60%), Gaps = 8/294 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-MVRKGE-----CEASIAKK 446
            E +  +A ++D +L +    + +  +   S +E        + K E      +   AK 
Sbjct: 204 PEEEIHLAHQIDGLLALEKIYEKLEEKLNRSPNEIEWATEAKMSKWELCDRLEQGRRAKN 263

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +MV ANLRLV SVAK+Y NRGL F DLIQEG IGL++A EKFD   GYKFSTY +WW++Q
Sbjct: 264 QMVTANLRLVTSVAKRYQNRGLDFQDLIQEGVIGLLRATEKFDHTKGYKFSTYGIWWIRQ 323

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AITR+I D S  +R+PV++ + I ++ +  +++S +     T EE+A ++ M  E ++ +
Sbjct: 324 AITRAICDYSRIVRLPVYLYETISQIKKIVKQISIECSP-LTAEEVATRMEMTTEKLQFI 382

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           ++  +E +SL+ PI   +     + I+  N  +P     +  L+E    VL +LT RE  
Sbjct: 383 IECAQETLSLDYPINKGENIIYKEMIK-FNGETPTKYVFENCLQEDVESVLKTLTERERN 441

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           VL+MRFG+    + TL+E+G  F +TRERIRQIEAKA+RKL+ P R+  LR ++
Sbjct: 442 VLQMRFGLDDGQEKTLKEIGDTFNLTRERIRQIEAKALRKLEDPKRNHILREYI 495


>gi|225159269|ref|ZP_03725570.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224802166|gb|EEG20437.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 373

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 107/267 (40%), Positives = 168/267 (62%), Gaps = 4/267 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ I     +++ E   +   +R+       A+  M+ ANLRLV+ +A  Y + GL
Sbjct: 61  LQLYLQEIGKTPLLTLDEEVTLARRIRR---GDKAARDHMISANLRLVVKIAMDYKDFGL 117

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI EGNIGL+KA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ DK
Sbjct: 118 PLLDLISEGNIGLVKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDK 177

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSH 587
           I ++ RTA  ++ ++ REP+ EEIA +L +P   V  +  ++  P SL+ P+G++ D+S 
Sbjct: 178 IARMRRTAMALTEQLGREPSDEEIAMELQIPTSKVAHLKSVSVRPASLDAPVGEDGDSST 237

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            G+ + D+NAVSP +S  + +       ++ SL PRE  ++R RFG+    + TLEEVG+
Sbjct: 238 FGELVGDENAVSPFESLKERSRNADLKEMVDSLEPREAEIIRYRFGLDGRDELTLEEVGQ 297

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +F VTRER+RQ++  A+ K++      
Sbjct: 298 KFKVTRERVRQLQNLALSKMRKAMSRH 324



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
             A  +            +    ++  +++YL+E+G   LL+ + E+ +A+RI  G    
Sbjct: 36  QDAPPSFLEKPAEAPADTAPLERSN--LQLYLQEIGKTPLLTLDEEVTLARRIRRGDKAA 93

Query: 154 MASLCESPLTFQALIIWRDE 173
              +  + L     I    +
Sbjct: 94  RDHMISANLRLVVKIAMDYK 113


>gi|90580346|ref|ZP_01236153.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
 gi|90438648|gb|EAS63832.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
          Length = 337

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 98/269 (36%), Positives = 167/269 (62%), Gaps = 3/269 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     ++  E    V   R+      +A+K M+E+NLRLV+ +
Sbjct: 54  EATQKALDATQLYLGEIGYSPLLTAEEE---VLYARRALRGDEVARKRMIESNLRLVVKI 110

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 111 SRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 170

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR ++ K+  EPT E+IA++L  PV+ V ++L++ +   S++ P
Sbjct: 171 RLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAQQLEKPVDDVNRMLRLNERVSSVDNP 230

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D+   SP  S    +++ +    L  L P++  VL  RFG+     
Sbjct: 231 IGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNPKQREVLARRFGLLGYEA 290

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 291 STLEDVGREIGLTRERVRQIQVEGLRRLR 319



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/114 (23%), Positives = 43/114 (37%), Gaps = 5/114 (4%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
             + I+V                  AS  ++ +   +  K  A +   D  ++YL E+G 
Sbjct: 17  EELDIDV----PATTSADDSSETTAASPVTDDTDDAELAKYEATQKALDATQLYLGEIGY 72

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E+  A+R   G  +    + ES L     I  R   N G  LL  +
Sbjct: 73  SPLLTAEEEVLYARRALRGDEVARKRMIESNLRLVVKISRRYS-NRGLALLDLV 125


>gi|108804071|ref|YP_644008.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765314|gb|ABG04196.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 294

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 111/280 (39%), Positives = 163/280 (58%), Gaps = 4/280 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
              E ++   +   +  I     ++  E   +    +K       A+++++E NLRLV+S
Sbjct: 14  AGREPETPELLAKYLAHIGQGELLTHQEEIELSRRAKK---GDRKARQKLIEKNLRLVVS 70

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKY   GL F DLIQEGNIGLMKA EKFD   G++FSTYA WW++QA+ R++AD+  T
Sbjct: 71  VAKKYRGYGLPFEDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRT 130

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVHM +KI KV RT   +S +++REPT EEIA++L   VE VR  +    +  SL+ 
Sbjct: 131 IRVPVHMTEKIRKVSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQ 190

Query: 579 PIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           P+  E++ S LGDFIED+      D+ ++          +  L  R   VL  R+G+   
Sbjct: 191 PVSSEESASELGDFIEDERTSDTPDTVLKELESSQLKEAIERLPERARYVLVRRYGLDDR 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
              TL E+G +  ++RER+RQ++ +A R LK     + LR
Sbjct: 251 EPATLAELGDELKISRERVRQLQREAERILKSGEHGRVLR 290



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 46/260 (17%), Positives = 88/260 (33%), Gaps = 25/260 (9%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR---------DEL 174
           YL  +G  ELL+ + EI +++R + G       L E  L     +  +         D +
Sbjct: 27  YLAHIGQGELLTHQEEIELSRRAKKGDRKARQKLIEKNLRLVVSVAKKYRGYGLPFEDLI 86

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD-DVQETEGDIESA 233
            +G   L + ++      PE    F         Q  + +  +K R   V     +    
Sbjct: 87  QEGNIGLMKAVEK---FDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEKIRK 143

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
              + ++ S         E   R L+ D +D   T+SAM D        + +E A    +
Sbjct: 144 VSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPVSSEESASELGD 203

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN-----------QSRIDLLVEQL 342
                +   +        ++   LKE + +L                   + +  L ++L
Sbjct: 204 FIE-DERTSDTPDTVLKELESSQLKEAIERLPERARYVLVRRYGLDDREPATLAELGDEL 262

Query: 343 YDISKRIMHNEGELLRLAQS 362
               +R+   + E  R+ +S
Sbjct: 263 KISRERVRQLQREAERILKS 282


>gi|78185860|ref|YP_378294.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78170154|gb|ABB27251.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 328

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 99/270 (36%), Positives = 165/270 (61%), Gaps = 4/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ + ++ +     +   E   + S  +        A+  M+ ANLRLV+SVAKKY N+
Sbjct: 60  IELAHHVQDMKQLKELPQEE---LTSRQKHKIRMGKRARDRMMAANLRLVVSVAKKYQNQ 116

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ 
Sbjct: 117 GLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHIS 176

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           +K+ K+ R +R +S++  R+P   E+A  + +    +  ++  +    SL+     E+  
Sbjct: 177 EKLSKMRRISRELSHRFGRQPNRLELASAMGIEPRELEDLITQSAPCASLDAHARGEEDR 236

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LG+ I D N   P++   ++  +E     L+ L  RE+++LR+RFG+G     TL E+
Sbjct: 237 STLGELIPDPNGEEPMEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEI 296

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           G+Q  V+RER+RQ+EAKAI KL+  +  ++
Sbjct: 297 GRQINVSRERVRQLEAKAILKLRTMTNHQQ 326



 Score = 37.5 bits (85), Expect = 7.2,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 5/49 (10%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           + R   D +  YL  +G + LL+   EI +A  ++      M  L E P
Sbjct: 33  SGRLATDSIGFYLSSIGRVPLLTAAEEIELAHHVQD-----MKQLKELP 76


>gi|302035824|ref|YP_003796146.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
 gi|300603888|emb|CBK40220.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
          Length = 419

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 115/251 (45%), Positives = 166/251 (66%), Gaps = 1/251 (0%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +S ++        AK E+V  NLRLV++VAK YT RGL  LDL+QEGNIGLMKA
Sbjct: 165 KELDAALSQLKASRITLETAKDELVRCNLRLVVNVAKHYTGRGLTLLDLVQEGNIGLMKA 224

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           AE++    G+KFSTYA WW++Q ITRS+ADQS TIRIPVH  +  ++++R +RR+  ++ 
Sbjct: 225 AERYQHRKGFKFSTYATWWIRQGITRSLADQSRTIRIPVHQTEASNRILRASRRLVQQLG 284

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R+P  EE+A  + M  + + + ++  +EP++LE  +  +  + LG+ + D+ AV P    
Sbjct: 285 RQPRLEEVASTMRMRPDRLHETIQAFQEPVALEHRV-GDGGTELGELLPDQQAVPPDAHV 343

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  L     R+L +LTPRE+ V+R+RFGIG +   TLE+VG+   VTRERIRQIEAKA+
Sbjct: 344 NRTELTREMDRILGTLTPREQTVIRLRFGIGEDQARTLEQVGQHLSVTRERIRQIEAKAL 403

Query: 665 RKLKHPSRSKK 675
           +KLK P   + 
Sbjct: 404 KKLKTPMVKEM 414



 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 33/85 (38%), Gaps = 3/85 (3%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV---RMYLREMGSIE 132
            V    D  +     DS+     A   +       +   RS   P     +Y R  G   
Sbjct: 18  EVDPDADDPEASTLLDSIVQGDQAETDADSEDAAPEKPARSASSPFLLESLYFRSFGERP 77

Query: 133 LLSREGEIAIAKRIEAGRAMMMASL 157
           LL R+ EIA+AK+++ G   +  +L
Sbjct: 78  LLERDEEIALAKQLDLGTRQIRLTL 102


>gi|288927719|ref|ZP_06421566.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330553|gb|EFC69137.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 287

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 96/272 (35%), Positives = 167/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  IS+ E   +   ++K       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGHEELISVEEEVELAQRIKK---GDRKALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLQDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +   +   + +R P+  EIA+K  +P + +   +K+T   IS++ P  D + + L
Sbjct: 135 VNKINKILSKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGRHISVDAPFVDGEDNSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + +  +  +  ++ +LR      L  L  RE  V+   FGI      TLEE+G +
Sbjct: 195 LDLLANTDTPTVDNELVKESLRAEIADALQYLNERERNVIEAFFGINQME-MTLEEIGDK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +TRER+RQI+ KAIR+L++ +++K L+++L
Sbjct: 254 YGLTRERVRQIKEKAIRRLRNNTKNKMLKTYL 285



 Score = 44.1 bits (102), Expect = 0.092,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
            S      D +  YL+E+G  EL+S E E+ +A+RI+ G    +  L ++ L F  ++  
Sbjct: 8   KSITNRESDSLDKYLQEIGHEELISVEEEVELAQRIKKGDRKALEKLTKANLRF--VVSV 65

Query: 171 RDELNDGTTLLREIID 186
             +  +    L+++I+
Sbjct: 66  AKQYQNQGLSLQDLIN 81


>gi|171920395|ref|ZP_02931720.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|183508771|ref|ZP_02958238.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701631|ref|ZP_02971335.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
 gi|171902833|gb|EDT49122.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|182675710|gb|EDT87615.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186700864|gb|EDU19146.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
          Length = 448

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 117/287 (40%), Positives = 171/287 (59%), Gaps = 15/287 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+  +  +     +   E      M +        I K ++  +N+RLV S+AKKY NRG
Sbjct: 157 IKAYLGVLGESKMLRSDEETEYAKMVISDDPSLVKIGKNQLYTSNMRLVTSIAKKYLNRG 216

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG+ GL+KA +KFD   G+KFSTYA WW++Q+ITR+IADQ+  IRIPVHM +
Sbjct: 217 LDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIRQSITRAIADQARQIRIPVHMVE 276

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLA------------MPVEGVRKVLKITKEPIS 575
            I+K+ +  R +  ++ R+PT EEIA+ +             +  + V ++ K+  +P+S
Sbjct: 277 TINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQAKNQKEQLITAQKVVEIKKLNVDPVS 336

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGI 634
           L+  IG ++ S   DFI D   +SP     +  L +    +    L   E+RV++MR+G+
Sbjct: 337 LDKQIGHDEESQFSDFISDDEIISPEKYTEKKALNDQINEMFEKVLNDNEQRVIKMRYGL 396

Query: 635 GMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                 +TLEEVG+   VTRER RQIE+KAIRKLKHPS++ KLRSF+
Sbjct: 397 LPFERPYTLEEVGEYLGVTRERARQIESKAIRKLKHPSKTAKLRSFI 443


>gi|78214165|ref|YP_382944.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78198624|gb|ABB36389.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 328

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 98/256 (38%), Positives = 155/256 (60%), Gaps = 1/256 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +       + S  R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL
Sbjct: 64  HHVQAMKQLQELPEEELTSRHRHKIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDL 123

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ 
Sbjct: 124 VQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMR 183

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFI 592
           R +R +S++  R+P   E+A  + +    +  ++  +    SL+     E+  S LG+ I
Sbjct: 184 RISRELSHRFGRQPNRLELASAMGIEPRELEDLISQSAPCASLDAHARGEEDRSTLGELI 243

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D N   P++   ++  +E     L+ L  RE+++L++RFG+G     TL E+G+Q  V+
Sbjct: 244 PDPNGEEPMEGMDRSIQKEHLGGWLSQLNEREQKILKLRFGLGGEEPLTLAEIGRQINVS 303

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ+EAKAI KL+
Sbjct: 304 RERVRQLEAKAILKLR 319



 Score = 37.5 bits (85), Expect = 8.7,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E  +          +  S   +       R   D +  YL  +G I LL+   EI +A  
Sbjct: 6   ESSATTKQSSRKEPALPSTGRRPSTRQGGRLATDSIGFYLSSIGRIPLLTAAEEIELAHH 65

Query: 146 IEAGRAMMMASLCESP 161
           +       M  L E P
Sbjct: 66  V-----QAMKQLQELP 76


>gi|282858973|ref|ZP_06268111.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588253|gb|EFB93420.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 286

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 93/274 (33%), Positives = 161/274 (58%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   ++ I  E  ++  E   +   +RK       A + +  ANLR V+SVAK+Y  +
Sbjct: 16  MSLDKYLQEIGNEELLTPEEEVELAQRIRK---GDKKALERLTRANLRFVVSVAKQYQTQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA Q   IR+P +  
Sbjct: 73  GIDLPDLINEGNMGLIKAAKRFDETRGFKFISYAVWWIRQSILQAIAAQGRLIRLPANQI 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ R   +   + +R P  +E+A+++ +  E +   L ++   +S+++P  D++  
Sbjct: 133 GVVNKITRILNKFEQENERIPNIDELAREVDLSEEHIEDALSLSFRQVSMDSPFKDDEGV 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   N  S   S +  +L+E  +R L  L+ RE++VL   +GIG     +LEE+G
Sbjct: 193 SLLDVMPSTNVPSTDKSLVDESLKEEISRALKILSEREQKVLCAYYGIGQLE-MSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +F ++RER+RQI+ KAIR L+    +K LR +L
Sbjct: 252 DKFGLSRERVRQIKEKAIRNLRKAGNNKTLRVYL 285



 Score = 46.0 bits (107), Expect = 0.019,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 28/52 (53%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           YL+E+G+ ELL+ E E+ +A+RI  G    +  L  + L F   +  + +  
Sbjct: 21  YLQEIGNEELLTPEEEVELAQRIRKGDKKALERLTRANLRFVVSVAKQYQTQ 72


>gi|163749990|ref|ZP_02157234.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
 gi|161330264|gb|EDQ01245.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
          Length = 323

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 104/300 (34%), Positives = 170/300 (56%), Gaps = 3/300 (1%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E D       K       +        ++   +  +  I     +S  E    V   RK
Sbjct: 19  NESDVETKKGNKLQEAELEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEE---VYFSRK 75

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++F
Sbjct: 76  SLKGCGKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRF 135

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA KL
Sbjct: 136 STYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAAKL 195

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P   V ++LK+ +   S++TP+G ++   L D +   + V P       ++ ++  + 
Sbjct: 196 DLPCSDVSRMLKLNERITSVDTPLGGDNDKALLDVLAADDNVGPDYKVQNEDMSKSVVKW 255

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK    ++ L
Sbjct: 256 LDELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGAQGL 315



 Score = 44.4 bits (103), Expect = 0.062,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 48/131 (36%), Gaps = 9/131 (6%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            + L D   +E  ++           L+++     +   D  ++YL E+G   LLS E E
Sbjct: 10  AEPLVDLSKNESDVETKKGNKLQEAELEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEE 69

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           +  +++   G       + ES L    ++      N+    L ++I+       E   G 
Sbjct: 70  VYFSRKSLKGCGKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE-------EGNLGL 120

Query: 200 FHGTEGHSYQK 210
               E    ++
Sbjct: 121 IRAVEKFDPER 131


>gi|294673737|ref|YP_003574353.1| RNA polymerase sigma factor RpoD [Prevotella ruminicola 23]
 gi|294473567|gb|ADE82956.1| putative RNA polymerase sigma factor RpoD [Prevotella ruminicola
           23]
          Length = 286

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 168/273 (61%), Gaps = 4/273 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ IS ET IS  E   +   ++K     + A + + +ANLR V+SVAK+Y N+G
Sbjct: 17  ALEKYLQEISKETMISAEEEVELAQRIKK---GDTKALERLTKANLRFVVSVAKQYQNQG 73

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGN+GL+KAAE+FD   G+KF +YA+WW++Q+I ++I++QS  +R+P++   
Sbjct: 74  LSLPDLINEGNLGLLKAAERFDETRGFKFISYAVWWIRQSILQAISEQSRIVRLPLNQVG 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            ++K+ R   R     +R P+ +EIA+K+ +P E + + + I    IS++ P  + + + 
Sbjct: 134 SVNKINREINRFEQLNERRPSVDEIAEKVDLPQEKIDEAMAINGHQISVDAPFVEGEDNS 193

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + + +A    +  ++ +L+      L++L  RE  V+   +GI      TLEE+G 
Sbjct: 194 LLDVMANSDAPLADNQLVEESLKSEIQNALSALNERERNVVEASYGINQPE-LTLEEIGT 252

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +F +TRER+RQI+ KAIRKL++   +K L+++L
Sbjct: 253 KFGLTRERVRQIKEKAIRKLRNSKANKFLKTYL 285



 Score = 39.4 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+    ++S E E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEISKETMISAEEEVELAQRIKKGDTKALERLTKANLRF--VVSVAKQYQNQGLSLPD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|108805426|ref|YP_645363.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766669|gb|ABG05551.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 282

 Score =  181 bits (459), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 95/270 (35%), Positives = 154/270 (57%), Gaps = 4/270 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R        A++ ++E+NLRLV+++AK+Y  RG+
Sbjct: 9   LTQYLGRIREGRLLTAGEEVELSRRAR---AGDGAARRRLIESNLRLVVAIAKRYRGRGV 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGN GL++A EKFD  +G +FSTYA WW++QA+TR++ADQ   +R+P H+ D 
Sbjct: 66  PFEDLIQEGNAGLIRAVEKFDPEMGNRFSTYATWWIRQAVTRAVADQGRAVRLPAHVVDS 125

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSH 587
           ++++ R    +S ++ REPT EE+A +L    E  R++ ++++   S+   +  +ED + 
Sbjct: 126 VYRLRRAESALSVELGREPTDEEVAGRLGTSPEEARRLREVSQPISSISARLGDEEDGAE 185

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD + D+ A            R      + SL  RE RVLR+R G+      TL EV +
Sbjct: 186 LGDLLPDEAASEEYARVEAGPWRGVLREAVGSLPEREARVLRLRHGLDGERARTLREVSE 245

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
              +++ER RQ+E KA+R L+    +  LR
Sbjct: 246 ILGISQERARQVELKALRTLRSGRYAGSLR 275


>gi|218247827|ref|YP_002373198.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8801]
 gi|257060853|ref|YP_003138741.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8802]
 gi|218168305|gb|ACK67042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256591019|gb|ACV01906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 318

 Score =  181 bits (459), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 109/283 (38%), Positives = 174/283 (61%), Gaps = 7/283 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +    +S+ +   +  +I+     +    + +    R        AK++MVEANLRLV+
Sbjct: 41  ALETLKESLTEELGQEPTIAQWAKAAKMTQKEL----RSAIEAGEAAKRKMVEANLRLVV 96

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S 
Sbjct: 97  SVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSR 156

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ +K++K+ +  R++S +  R  T  E+A++L +    VR+ L+  ++P+SL+
Sbjct: 157 TIRLPIHITEKLNKIKKAQRQLSQEKGRAATIAELAEELELTPRQVREYLERARQPLSLD 216

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD   + LGD +ED    SP D A  ++L+    R++  LTP+++ VL +RFG+   
Sbjct: 217 LRVGDNQDTELGDLLEDTGQ-SPEDYATHSSLQLDLDRLMEELTPQQKEVLALRFGLSDG 275

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TL ++G    ++RER+RQIE +A+ KL+   R   +R +L
Sbjct: 276 KPLTLAKIGSILNISRERVRQIEREALAKLRK--RKANIREYL 316



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/34 (52%), Positives = 25/34 (73%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +S+ DPVR YLRE+G + LL+ E EI  AKR++
Sbjct: 4   SKSSPDPVRAYLREIGRVPLLTHEEEILYAKRVQ 37


>gi|77163721|ref|YP_342246.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254436220|ref|ZP_05049727.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
 gi|76882035|gb|ABA56716.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207089331|gb|EDZ66603.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
          Length = 321

 Score =  181 bits (459), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 87/258 (33%), Positives = 155/258 (60%), Gaps = 3/258 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     ++  E  +   + +KG       +K M+E+NLRLV+ ++++Y NRGL  L
Sbjct: 53  YLSEIGCAPLLTAEEEVYHARLAKKGNPAG---RKRMIESNLRLVVKISRRYMNRGLALL 109

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL+ A EKFD  +G++FSTYA WW++Q I R++ +Q+ T+R+PVH+  +I  
Sbjct: 110 DLIEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHVVKEIKS 169

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R A +++ +++ +P+ EE+A++L  PVE +++V  +     S++T   +     L D 
Sbjct: 170 YQRVANKLAQELEHDPSFEELAQQLNKPVEEIKRVWSLKDNTASMDTGYRNNQEKTLLDA 229

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D++A  P       +++      L+ L  ++  V+  RFG+      TLE+VG+   V
Sbjct: 230 LPDEDAPDPTVLLQNDDMQSRLKLWLSQLNDKQREVVIRRFGLQGYEPQTLEQVGQAIGV 289

Query: 652 TRERIRQIEAKAIRKLKH 669
           TRER+RQI+ + +++L+ 
Sbjct: 290 TRERVRQIQLETLKRLRR 307



 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 25/91 (27%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D   +YL E+G   LL+ E E+  A+  + G       + ES L     I  R  +N G 
Sbjct: 48  DATHLYLSEIGCAPLLTAEEEVYHARLAKKGNPAGRKRMIESNLRLVVKISRRY-MNRGL 106

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
            LL  I         E   G  H  E    +
Sbjct: 107 ALLDLI--------EEGNLGLIHAVEKFDPE 129


>gi|189218244|ref|YP_001938886.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189185102|gb|ACD82287.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 287

 Score =  181 bits (459), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 109/268 (40%), Positives = 170/268 (63%), Gaps = 4/268 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  ++ IS    ++  +   +   +++       A+++M++ANLRLV+ +A  Y N G
Sbjct: 7   ALKLYLREISQIPLLTKEKEVELAKRIQQ---GDQEARRQMIQANLRLVVKIAHDYANSG 63

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGNIGLMKA ++FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ D
Sbjct: 64  LPLPDLISEGNIGLMKAVDRFDPSKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVD 123

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTS 586
           KI K+ R A ++S  + R+PT EE+A++L M    V ++  I   P SL+  +  +ED +
Sbjct: 124 KIAKMRRVAMQLSEILGRDPTDEELAEELGMSTTKVAELRTIAIRPASLDATVGEEEDGT 183

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            LG+ ++D++A SP  S +  NL+ T   +L  L  RE ++L +RFG+  N   TLEE+G
Sbjct: 184 ALGELVKDESAASPDQSVLDQNLKNTIMELLPKLDERERKILSLRFGLEGNEQMTLEEIG 243

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           K+F VTRERIRQ++  A+RK++     +
Sbjct: 244 KEFHVTRERIRQLQNIALRKIRKELEKQ 271



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            D  +++YLRE+  I LL++E E+ +AKRI+ G       + ++ L    ++    +  +
Sbjct: 4   NDSALKLYLREISQIPLLTKEKEVELAKRIQQGDQEARRQMIQANLRL--VVKIAHDYAN 61

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEG 205
               L ++I  E  IG       F  ++G
Sbjct: 62  SGLPLPDLIS-EGNIGLMKAVDRFDPSKG 89


>gi|90407885|ref|ZP_01216060.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
 gi|90310976|gb|EAS39086.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
          Length = 313

 Score =  181 bits (459), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 101/267 (37%), Positives = 163/267 (61%), Gaps = 3/267 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++  E    V   R+      +A+K M+E+NLRLV+ ++++YTNRGL 
Sbjct: 42  QLYLGEIGFSPLLTAQEE---VYYARRSLRGDDVARKRMIESNLRLVVKISRRYTNRGLS 98

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  K+
Sbjct: 99  LLDLVEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKKL 158

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +RTAR +S+ +  EPT E+IA  L +P + V K+LK+ +   S++ PIG+     L 
Sbjct: 159 NVYLRTARELSHSLTHEPTAEDIALALDIPAKDVSKILKLNERISSVDIPIGNNSDKELL 218

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+  + P +     +++      L  L P++  VL  RFG+      TLE VGK+ 
Sbjct: 219 DIIPDRKEIIPENELENEDMKLRIVEWLEDLNPKQREVLARRFGLLGYEAATLENVGKEI 278

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +TRER+RQI+ +A++ L+     + L
Sbjct: 279 GLTRERVRQIQVEALKCLREVLSQQGL 305



 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 28/114 (24%), Positives = 47/114 (41%), Gaps = 9/114 (7%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +++S  +  + K + S+D    D  ++YL E+G   LL+ + E+  A+R   G  +    
Sbjct: 17  ATSSKLAPKVTKTRSSSDTKVMDATQLYLGEIGFSPLLTAQEEVYYARRSLRGDDVARKR 76

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           + ES L     I  R   N G +LL  +         E   G     E    +K
Sbjct: 77  MIESNLRLVVKISRRY-TNRGLSLLDLV--------EEGNLGLIRAVEKFDPEK 121


>gi|126661338|ref|ZP_01732404.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126617371|gb|EAZ88174.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 328

 Score =  181 bits (459), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 109/286 (38%), Positives = 181/286 (63%), Gaps = 8/286 (2%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             N +  + +   ++  E         ++I E       ++K   +   AK++M+EANLR
Sbjct: 48  MMNLLEKKEELAQRVGKEPSIQEWAKEVNIEE-----KALQKALEQGERAKRKMIEANLR 102

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA 
Sbjct: 103 LVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQ 162

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIR+P+H+ +K++K+ +T R +S  + R  TP EIA++L +    +R+ L I ++PI
Sbjct: 163 QARTIRLPIHITEKLNKIKKTQRELSQSLGRSATPAEIAQELEIEPSQIREFLSIARQPI 222

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL+  +GD   + L + +ED+  VSP     Q  LR+  + ++A LTP++  VL +RFG+
Sbjct: 223 SLDVRVGDNQDTELSELLEDQ-GVSPDIYITQELLRQDLSNLMAELTPQQRTVLTLRFGL 281

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               + +L ++GK+  ++RER+RQ+E +A+ +L+   R   ++ +L
Sbjct: 282 EDGKELSLAKIGKRLNISRERVRQLEHQALAQLRR--RRGNVKEYL 325



 Score = 40.6 bits (93), Expect = 0.98,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCESPLTFQALIIWRDEL 174
           + D VR YL E+G + LL+ E EI   K+++           L +      ++  W  E+
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIIYGKQVQTMMNLLEKKEELAQRVGKEPSIQEWAKEV 75

Query: 175 NDGTTLLR 182
           N     L+
Sbjct: 76  NIEEKALQ 83


>gi|312891071|ref|ZP_07750594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311296379|gb|EFQ73525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  181 bits (458), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 90/274 (32%), Positives = 162/274 (59%), Gaps = 4/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I+  E   +   +R        A + + + NLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLTEIGKVDLITADEEVILAQKIR---EGDQAALERLTKTNLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I  ++A+QS  +R+P++  
Sbjct: 73  GLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILSAVAEQSRIVRLPLNQI 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ +   ++  + +REP+  E+A  L    + +   L  +   +S++ P    + +
Sbjct: 133 GSLNKIRQAFSKLEQQYEREPSQAELADILETTEDKICDSLSNSGRHVSMDAPFVQGEEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +++ N  +  D  ++ +L +   R L +L  RE  V+ + FG+G N   +LEE+G
Sbjct: 193 TLLDVLQN-NEPTTDDYLMEESLSQEIMRSLVTLAEREREVIVLFFGLGNNYPLSLEEIG 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +++ +TRER+RQI+ KA+++L+H SRS  L+S+L
Sbjct: 252 EKYNLTRERVRQIKDKALQRLRHTSRSNLLQSYL 285



 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G ++L++ + E+ +A++I  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLTEIGKVDLITADEEVILAQKIREGDQAALERLTKTNLRF--VVSVAKQYQNQGLTLGD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|119774181|ref|YP_926921.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
 gi|119766681|gb|ABL99251.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
          Length = 327

 Score =  181 bits (458), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 102/307 (33%), Positives = 174/307 (56%), Gaps = 7/307 (2%)

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK----IRNEIKSISVETGISISEFRH 429
             G+E D       ++    +         D + +     +  +  I     ++  E   
Sbjct: 16  FSGKEADTDTNMDGEEVSLVQDLELEQQVQDDLQRNLDATQLYLSEIGFSPLLTAEEE-- 73

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            V   RK       ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD
Sbjct: 74  -VYYSRKALRGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFD 132

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT 
Sbjct: 133 PERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTA 192

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEIA KL +P   V ++LK+ ++  S++ P+G ++   L D + D ++V P       ++
Sbjct: 193 EEIAAKLNLPSVEVSRMLKLNEKITSVDVPLGGDNDKALLDVLPDDDSVGPDYKVQDEDI 252

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +    L  L  ++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+++L+ 
Sbjct: 253 SNSVVNWLNELNTKQREVLARRFGLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRD 312

Query: 670 PSRSKKL 676
              ++ L
Sbjct: 313 ILSAQGL 319



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 22/125 (17%), Positives = 49/125 (39%), Gaps = 9/125 (7%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E  ++ ++D    +    + L+++     +   D  ++YL E+G   LL+ E E+  +++
Sbjct: 20  EADTDTNMDGEEVSLVQDLELEQQVQDDLQRNLDATQLYLSEIGFSPLLTAEEEVYYSRK 79

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
              G       + ES L    ++      N+    L ++I+       E   G     E 
Sbjct: 80  ALRGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE-------EGNLGLIRAVEK 130

Query: 206 HSYQK 210
              ++
Sbjct: 131 FDPER 135


>gi|332140079|ref|YP_004425817.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|332143123|ref|YP_004428861.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550101|gb|AEA96819.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327553145|gb|AEA99863.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 330

 Score =  181 bits (458), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 103/265 (38%), Positives = 164/265 (61%), Gaps = 3/265 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E    V   R+       ++K M+ +NLRLV+ +A++Y
Sbjct: 51  KNLDATQLYLGEIGFSPLLTAEEE---VYFARRSLKGCEASRKRMIVSNLRLVVKIARRY 107

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 108 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 167

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R +R +S K+  EPT EEIA  L  PVE V K+L++ +   S++TPIG E
Sbjct: 168 HVVKELNVYLRASRELSQKLDHEPTAEEIAAALDKPVEDVTKMLRLNERITSVDTPIGGE 227

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D I D+   SP +S   ++++      L  L P++  VL  RFG+      TLE
Sbjct: 228 NDKALLDIIADEKEFSPEESLQDSDIKSNIITWLEELNPKQREVLARRFGLMGYEPSTLE 287

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           +VG +  +TRER+RQI+ +A+R+L+
Sbjct: 288 DVGAEIGLTRERVRQIQVEALRRLR 312



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 51/303 (16%), Positives = 95/303 (31%), Gaps = 23/303 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP-----VRMYLREMGSIE 132
           ++    +D E  +   D+ +  + ++    +  D+     D P      ++YL E+G   
Sbjct: 8   LESKSQDDLEVIDMPADMKADEALTNDAELENDDAIFSQDDQPKNLDATQLYLGEIGFSP 67

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI-------I 185
           LL+ E E+  A+R   G       +  S L     I  R   N G  LL  I       I
Sbjct: 68  LLTAEEEVYFARRSLKGCEASRKRMIVSNLRLVVKIARRYN-NRGLALLDLIEEGNLGLI 126

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
                  PE    F         Q  E +   + R          E    +         
Sbjct: 127 RAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRASRELSQK 186

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLR--------PKVMCALDEIA--EVYRELR 295
              E    +     +   +    +  + +++               LD IA  + +    
Sbjct: 187 LDHEPTAEEIAAALDKPVEDVTKMLRLNERITSVDTPIGGENDKALLDIIADEKEFSPEE 246

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           SLQD+ +               +E L +  G +    S ++ +  ++    +R+   + E
Sbjct: 247 SLQDSDIKSNIITWLEELNPKQREVLARRFGLMGYEPSTLEDVGAEIGLTRERVRQIQVE 306

Query: 356 LLR 358
            LR
Sbjct: 307 ALR 309


>gi|159903877|ref|YP_001551221.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889053|gb|ABX09267.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 313

 Score =  181 bits (458), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 105/270 (38%), Positives = 171/270 (63%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +++ N+++ +   T     + +     S  R+       AK+ M++ANLRLV+SVAKKY 
Sbjct: 39  IELGNQVQVMMNLTEDGSIDVKSEEFTSHQRRLIRIGRRAKERMMKANLRLVVSVAKKYQ 98

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +GL+ LDL+QEG++GL +A EKFD   GYKFSTYA WW++Q++TR+IA QS TIR+PVH
Sbjct: 99  GKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVH 158

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           + +++  + + +  +++K+   P+  E+A+ + +  E +  +L+      SL+ P+  +D
Sbjct: 159 LSERLATIRKISSDLAHKLGAMPSRAELAEAMEIDAEELDSILRQALTTSSLDAPVNGDD 218

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
             S LGD I D +   PLD   Q   +E   R L  L+ +E+ VL++RFG+  N  HTL 
Sbjct: 219 GRSFLGDLIADSSLEEPLDKVEQRIHQEQLGRWLTHLSEQEQHVLKLRFGLEGNERHTLA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E+G+   V+RER+RQ+E K++RKL++ +R 
Sbjct: 279 EIGRLLQVSRERVRQVELKSLRKLRNLTRK 308



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 22/42 (52%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             K  +S  R + DP+  YL  +G + LL+   EI +  +++
Sbjct: 5   APKAAESQKRRSSDPISWYLSTIGRVPLLTPAEEIELGNQVQ 46


>gi|119511025|ref|ZP_01630145.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119464276|gb|EAW45193.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 332

 Score =  181 bits (458), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 103/277 (37%), Positives = 175/277 (63%), Gaps = 5/277 (1%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           ++   +    DS++       S+      +  E   +   +     +   AK++MVEANL
Sbjct: 51  QFSRILHEVRDSLINQIGREPSLEEWALAANLEVAELNDAI----ADGETAKRKMVEANL 106

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FSTYA WW++QAITR+IA
Sbjct: 107 RLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIA 166

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +++ TIR+P+H+ +K++K+ +  R++S ++ R P+  E+A++L +  + VR+ L+  + P
Sbjct: 167 EKARTIRLPIHITEKLNKIKKAQRQLSQQLGRAPSAAELAQELDLTPKQVREYLERARLP 226

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL+  +GD   + LG+ +ED  A SP +  +Q++L     R++  LTP+++ V+++RFG
Sbjct: 227 LSLDLRLGDNYDTELGEMLEDPGA-SPEEFVMQSSLSYDLERLMEELTPQQKEVIKLRFG 285

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +      TL ++G    ++RER+RQIE +A+ KL+  
Sbjct: 286 LLDGQALTLAKIGDILNISRERVRQIEREALTKLRKS 322



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 14/30 (46%), Positives = 20/30 (66%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            D VR YLRE+G + LL+ E EI   K+++
Sbjct: 22  TDLVRTYLREIGRVPLLTHEEEIQYGKQVQ 51


>gi|256370771|ref|YP_003108596.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
 gi|256009563|gb|ACU52923.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
          Length = 334

 Score =  181 bits (458), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 91/271 (33%), Positives = 155/271 (57%), Gaps = 2/271 (0%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEA-SIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             ++ I     +S  +   +  + RK      S A ++++++NLR V+SVAK+Y N+GL 
Sbjct: 63  KYLEEIGKIPLLSQKKELELAKLARKELNAGCSTALEQLIKSNLRFVVSVAKQYQNQGLS 122

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI EGN+GL+K   +FD   G+K  +Y +WW++QAI ++IADQ+  IR P +     
Sbjct: 123 LSDLINEGNLGLIKGISRFDEKKGFKCISYCVWWIRQAILQAIADQARCIRCPTNKLAFY 182

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +KVV+T  ++  K+K +PT  +I   L    + V + LK + +P SL+ PI + + ++L 
Sbjct: 183 NKVVKTYSKLEQKLKMQPTVNDIVVYLNSSEKEVEEALKNSIQPTSLDAPILEGEDTNLY 242

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D ++ + +  P     + +  +   R+L +L+ +E +V+ + +G G     TLE+V    
Sbjct: 243 DVLKSETSPEPDFKLEKESFFKDIKRLLETLSEKESQVISLHYGFGC-KPMTLEKVAFLL 301

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +TRER RQIE   I++L+   R K LR +L
Sbjct: 302 KLTRERCRQIEINGIKRLRISYRKKLLRPYL 332



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 124 YLREMGSIELLSREGEIAIA----KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           YL E+G I LLS++ E+ +A    K + AG +  +  L +S L F  ++    +  +   
Sbjct: 64  YLEEIGKIPLLSQKKELELAKLARKELNAGCSTALEQLIKSNLRF--VVSVAKQYQNQGL 121

Query: 180 LLREIID 186
            L ++I+
Sbjct: 122 SLSDLIN 128


>gi|113954631|ref|YP_732094.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
 gi|113881982|gb|ABI46940.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
          Length = 340

 Score =  181 bits (458), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 98/260 (37%), Positives = 160/260 (61%), Gaps = 2/260 (0%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +++  + I E        R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QE
Sbjct: 80  AMKELLDIQEEERTPKQ-RHRIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQE 138

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ +  
Sbjct: 139 GAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRKIT 198

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDK 595
           R +S++  R+P   E+A  + +    + +++  +    SL+     E+  S LG+ I D 
Sbjct: 199 RELSHRFGRQPNRLELAHAMGIEPRDLEELIAQSAPCASLDAHARGEEDRSTLGELIPDP 258

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           N   P++   ++  +E     L+ L  RE+++LR+RFG+G     TL E+G+Q  V+RER
Sbjct: 259 NGDEPMEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEIGRQINVSRER 318

Query: 656 IRQIEAKAIRKLKHPSRSKK 675
           +RQ+E+KAI KL+  +  ++
Sbjct: 319 VRQLESKAILKLRTMTNHQQ 338



 Score = 37.5 bits (85), Expect = 8.3,   Method: Composition-based stats.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S+ R   D +  YL  +G + LL+   EI +A  ++A
Sbjct: 44  SSGRLATDSIGHYLSSIGRVPLLTAAEEIELAHHVQA 80


>gi|220907092|ref|YP_002482403.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7425]
 gi|219863703|gb|ACL44042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 318

 Score =  180 bits (457), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 107/249 (42%), Positives = 168/249 (67%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++       +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD  
Sbjct: 71  AELQGVVNRGELAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R++S ++ R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L +  + VR+ L+ +++P+SL+  +GD   + LG+ +ED  A SP D   QA+LR 
Sbjct: 191 LAQELELTPKQVREYLERSRQPLSLDVRVGDNQDTELGELLEDT-AASPEDFTSQASLRA 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              R++A LTP++ +VL +RFG+      TL +VG    ++RER+RQIE +A+ KL+   
Sbjct: 250 DLDRLMADLTPQQRQVLSLRFGLEDGQPLTLAKVGDMLNISRERVRQIEREALSKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   +  +L
Sbjct: 308 RKADIYEYL 316



 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 14/34 (41%), Positives = 22/34 (64%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            ++ D VR YLRE+G + LL+ E EI   K+++ 
Sbjct: 5   ETSKDLVRAYLREIGRVPLLTHEQEILYGKQVQQ 38


>gi|304383342|ref|ZP_07365808.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335510|gb|EFM01774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 287

 Score =  180 bits (457), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 98/272 (36%), Positives = 167/272 (61%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  +++ E   +   +R+       A +++ +ANLR V+SVAK+Y N+GL
Sbjct: 18  LEKYLQEIGHEELLTVEEEVELAQRIRR---GDRQALEKLTKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++++ +   R   + +R P+ EEIA K+ +  E V  VLK+    +S++ P  + D + L
Sbjct: 135 VNRINKMLNRFEQENERRPSMEEIADKVNLSQEKVADVLKVNSRQVSVDAPFTEGDETSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + + ++       ++ +LRE   R L  L  RE  ++   FGI      TLEE+G +
Sbjct: 195 LDVLCNNDSPMADRELVRESLREEINRTLQVLNERERNIVEAFFGINQGE-KTLEEIGNK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQI+ KAIR+L+  ++S+ L+++L
Sbjct: 254 FGLTRERVRQIKEKAIRRLRQNTKSRLLKAYL 285


>gi|72080402|ref|YP_287460.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 7448]
          Length = 489

 Score =  180 bits (457), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 180 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 237

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 238 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 297

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 298 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLG 357

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 358 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 417

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 418 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 477

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 478 TPHRRLSLRDF 488


>gi|149378178|ref|ZP_01895895.1| nonessential primary sigma factor [Marinobacter algicola DG893]
 gi|149357540|gb|EDM46045.1| nonessential primary sigma factor [Marinobacter algicola DG893]
          Length = 333

 Score =  180 bits (457), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 101/275 (36%), Positives = 166/275 (60%), Gaps = 3/275 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +   +  +  I     ++  E  +   + RKGE      +K M+E+NLRLV+ +A+
Sbjct: 55  SQKQLDATQLYLNEIGFSPLLTPEEEVYFARLARKGEESG---RKRMIESNLRLVVKIAR 111

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+
Sbjct: 112 RYVNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 171

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  +++  +R AR ++ K+  EP+ EEIA+ +  PV  V+++L + +   S++TPIG
Sbjct: 172 PIHVVKELNLYLRAARELTQKLDHEPSAEEIARMVDKPVADVKRMLGLNERVASMDTPIG 231

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L D + D+ A  P D     N+     + +  L+ +++ VL  RFG+      T
Sbjct: 232 TGGEKSLLDTVADEGASDPADLLQDNNMCSCVEKWIDQLSDKQQEVLSRRFGLRGYPIST 291

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LEEVG++  +TRER+RQI+ +A+R+L+     + L
Sbjct: 292 LEEVGQEIGLTRERVRQIQVEALRRLREILEKEGL 326



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/114 (27%), Positives = 50/114 (43%), Gaps = 6/114 (5%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-----DPVRMYLREMGS 130
            V D +D +D+  +ED ++   +A   +V  ++   +  R        D  ++YL E+G 
Sbjct: 12  RVSDVEDADDQLLAEDKVEAKETAEVEAVETEEDIPAQGRYFTSQKQLDATQLYLNEIGF 71

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E+  A+    G       + ES L     I  R  +N G TLL  I
Sbjct: 72  SPLLTPEEEVYFARLARKGEESGRKRMIESNLRLVVKIARRY-VNRGLTLLDLI 124


>gi|254786794|ref|YP_003074223.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
 gi|237685659|gb|ACR12923.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
          Length = 337

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 165/272 (60%), Gaps = 3/272 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E    V   R+       A+K M+E+NLRLV+ ++++Y 
Sbjct: 60  NLDATQLYLNEIGFSPLLSADEE---VYFARRALKGDEAARKRMIESNLRLVVKISRRYV 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 117 NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR +S K+  EP+ EEIA+ L  PVE V ++L + +   S++ PIG   
Sbjct: 177 VVKELNVYLRAARELSQKLDHEPSAEEIAELLEKPVEDVERMLALNERVTSMDAPIGPAS 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              + D + D+    P++    ++L  +    L  L+ ++  V+  RFG+  +   TLEE
Sbjct: 237 EKTVVDTVPDQQVSDPVELLEDSDLSTSLNSWLDELSEKQREVVARRFGLRGHETSTLEE 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VG++  +TRER+RQI+ +A+R+L+     + L
Sbjct: 297 VGREIGLTRERVRQIQVEALRRLRDILEKQGL 328



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 38/226 (16%), Positives = 72/226 (31%), Gaps = 8/226 (3%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           ++++  ++  S     ++      D +  +     + S S +        + + +   D 
Sbjct: 4   QELDTVLSYASLEQDTLIPHGVDFDYDEYDSDSSSSKSRSRNGRSSSAESEDSYQRNLDA 63

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            ++YL E+G   LLS + E+  A+R   G       + ES L     I  R  +N G  L
Sbjct: 64  TQLYLNEIGFSPLLSADEEVYFARRALKGDEAARKRMIESNLRLVVKISRRY-VNRGLAL 122

Query: 181 LREI-------IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           L  I       I       PE    F         Q  E +   + R          E  
Sbjct: 123 LDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELN 182

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +            E +  +   L E   +    + A+ +++   
Sbjct: 183 VYLRAARELSQKLDHEPSAEEIAELLEKPVEDVERMLALNERVTSM 228


>gi|117617733|ref|YP_855373.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559140|gb|ABK36088.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 327

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 102/281 (36%), Positives = 171/281 (60%), Gaps = 4/281 (1%)

Query: 397 NFVACEVDSILKI-RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
             +A E++ ++   +  +  I     ++  E    V   R+       A+K M+E+NLRL
Sbjct: 41  ELMAPELNKVMDATQLYLGEIGFSPLLTAEEE---VYYARRALRGDKAARKRMIESNLRL 97

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 98  VVKIARRYNNRGLVLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 157

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+++  EPT E+IA  L   V+ V ++LK+ ++  S
Sbjct: 158 TRTIRLPIHVVKELNVYLRTARELSHRLDHEPTAEDIAFALDRSVDDVNRMLKLNEKITS 217

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TPIG +    L D + D+  + P   +   ++R +    L  L P++  VL  RFG+ 
Sbjct: 218 VDTPIGGDRDKALLDVLSDERGMGPELESQDDDMRASIVHWLEELNPKQREVLARRFGLL 277

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
                TLE+VG +  +TRER+RQI+ + +R+L+     + L
Sbjct: 278 GYEPATLEDVGAEIGLTRERVRQIQVEGLRRLREILLGQGL 318



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
            +          D  ++YL E+G   LL+ E E+  A+R   G       + ES L    
Sbjct: 40  DELMAPELNKVMDATQLYLGEIGFSPLLTAEEEVYYARRALRGDKAARKRMIESNLRLVV 99

Query: 167 LIIWRDELNDGTTLLREI 184
            I  R   N G  LL  I
Sbjct: 100 KIARRYN-NRGLVLLDLI 116


>gi|18404292|ref|NP_565856.1| SIGF (RNA POLYMERASE SIGMA-SUBUNIT F); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana]
 gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana]
 gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis
           thaliana]
 gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana]
          Length = 547

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 96/358 (26%), Positives = 184/358 (51%), Gaps = 14/358 (3%)

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV-FLERHQGRELDPHWVSYAKDFPEGEW 395
           +V     + +R  +            G + +     ++++    +   +      PE + 
Sbjct: 187 IVRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQ 246

Query: 396 KNFVACEVDSILKIRNEIKSISVETGI--------SISEFRHIV----SMVRKGECEASI 443
                 E + I  I++ +K   V+T +        +I E+   +     +++        
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+TYA WW
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 366

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q+I +SI   S TIR+P ++   + KV    +    +    P+ EE+A  + +  E +
Sbjct: 367 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKL 426

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K+L  T+ P+S++ PI  +  +   +   D    +P  S  +  +R     +L  L+P+
Sbjct: 427 DKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPK 486

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L ++ D
Sbjct: 487 ERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYAD 544


>gi|120598086|ref|YP_962660.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146293843|ref|YP_001184267.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
           CN-32]
 gi|120558179|gb|ABM24106.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sp.
           W3-18-1]
 gi|145565533|gb|ABP76468.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           putrefaciens CN-32]
          Length = 326

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 101/273 (36%), Positives = 168/273 (61%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 49  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKALKGCEKSRNRMIESNLRLVVKIARRY 105

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 106 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 165

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT EEIA+KL +P   V ++LK+ ++  S++TP+G +
Sbjct: 166 HVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQVPSADVSRMLKLNEKITSVDTPLGGD 225

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D ++V P       ++  +  + L  L  ++  VL  RFG+      TLE
Sbjct: 226 NDKALIDILADDDSVGPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG +  +TRER+RQI+ +A+++L+    S+ L
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQGL 318



 Score = 41.4 bits (95), Expect = 0.49,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 44/104 (42%), Gaps = 3/104 (2%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +E  E   +  D+A+         Q+ +D   +   D  ++YL E+G   LLS E E+  
Sbjct: 17  VETAEFDLEKEDIATDLVQELGLEQQVQDDL-QKNLDATQLYLGEIGFSPLLSAEEEVYF 75

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +++   G       + ES L    ++      N+    L ++I+
Sbjct: 76  SRKALKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 117


>gi|170727680|ref|YP_001761706.1| RpoD family RNA polymerase sigma factor [Shewanella woodyi ATCC
           51908]
 gi|169813027|gb|ACA87611.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella woodyi
           ATCC 51908]
          Length = 322

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 173/300 (57%), Gaps = 4/300 (1%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E D    + AK                ++   +  +  I     +S  E    V   RK
Sbjct: 19  NESDIE-STTAKTEGAELENQVQDDLQKNLDATQLYLSEIGFSPLLSAEEE---VYFSRK 74

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  ++  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++F
Sbjct: 75  ALKGCDKSRNRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRF 134

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EPT EEIA+KL
Sbjct: 135 STYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAHKLDHEPTAEEIAEKL 194

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +P   V ++LK+ +   S++TP+G ++   L D + D + V P       ++ ++  + 
Sbjct: 195 DLPSADVSRMLKLNERITSVDTPLGGDNDKALLDVLADDDNVGPDYKVQDEDMSKSVVKW 254

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  L  ++  VL  RFG+      TLE VGK+  +TRER+RQI+ +A+++LK    ++ L
Sbjct: 255 LDELNTKQREVLARRFGLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLSAQGL 314



 Score = 44.4 bits (103), Expect = 0.058,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 46/107 (42%), Gaps = 3/107 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            + L D   +E  ++  ++ +  +    + +D   +   D  ++YL E+G   LLS E E
Sbjct: 10  AEPLVDLAKNESDIESTTAKTEGAELENQVQDDL-QKNLDATQLYLSEIGFSPLLSAEEE 68

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +  +++   G       + ES L    ++      N+    L ++I+
Sbjct: 69  VYFSRKALKGCDKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 113


>gi|119468990|ref|ZP_01612015.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
 gi|119447642|gb|EAW28909.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
          Length = 324

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 105/280 (37%), Positives = 166/280 (59%), Gaps = 3/280 (1%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
                   ++   +  +  I     +S  E    V   RK       ++K M+E+NLRLV
Sbjct: 38  FAKEEVTKNLDATQLYLGEIGFSPLLSAEEE---VFFARKSLKGCEASRKRMIESNLRLV 94

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+
Sbjct: 95  VKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQT 154

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+ L  PVE V K+L++ ++  S+
Sbjct: 155 RTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAECLDKPVEDVTKMLRLNEKIASV 214

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           + PIG E+ S L D + D+    P        + +     L  L  ++  VL  RFG+  
Sbjct: 215 DMPIGGENDSVLLDILPDEKGNGPEGEVQDTEINKHIVDWLGELNLKQREVLARRFGLLG 274

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLE+VG++  +TRER+RQI+ +A+R+LK   + + L
Sbjct: 275 YEPSTLEDVGREIGLTRERVRQIQVEALRRLKDILQQEGL 314



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 6/109 (5%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +  DD  DE   E++  L     +  +F ++       +T    ++YL E+G   LLS E
Sbjct: 11  ISNDDKFDENTVEEATPLLEKVDDEDIFAKEEVTKNLDAT----QLYLGEIGFSPLLSAE 66

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E+  A++   G       + ES L    ++      N+    L ++I+
Sbjct: 67  EEVFFARKSLKGCEASRKRMIESNLRL--VVKIARRYNNRGLALLDLIE 113


>gi|90412104|ref|ZP_01220111.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
 gi|90327082|gb|EAS43461.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
          Length = 334

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 99/265 (37%), Positives = 166/265 (62%), Gaps = 3/265 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E    V   R+      IA+K M+E+NLRLV+ ++++Y
Sbjct: 54  KALDATQLYLGEIGFSPLLTAEEE---VLYARRALRGDEIARKRMIESNLRLVVKISRRY 110

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 111 SNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 170

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT E+IA +L  PV+ V ++L++ +   S++ PIG +
Sbjct: 171 HVVKELNVYLRTARELAQKLDHEPTAEDIALQLEKPVDDVNRMLRLNERVSSVDNPIGGD 230

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D I D+   SP  S    +++ +    L  L P++  VL  RFG+      TLE
Sbjct: 231 SEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 290

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           +VG++  +TRER+RQI+ + +R+L+
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLR 315



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           N+ +  ++E    +  +   A    +SS  +   K    +   D  ++YL E+G   LL+
Sbjct: 14  NLDEDINIEAIADAAAASTKAEPEESSSDDVDVSKYGTTQKALDATQLYLGEIGFSPLLT 73

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G  +    + ES L     I  R   N G  LL  +
Sbjct: 74  AEEEVLYARRALRGDEIARKRMIESNLRLVVKISRRYS-NRGLALLDLV 121


>gi|161936260|ref|YP_115577.2| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 489

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 180 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 237

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 238 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 297

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 298 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLG 357

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 358 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 417

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 418 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 477

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 478 TPHRRLSLRDF 488


>gi|332308186|ref|YP_004436037.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332175515|gb|AEE24769.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 327

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 103/299 (34%), Positives = 171/299 (57%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +        +    +  +       ++   +  +  I     +S  E    V   R+ 
Sbjct: 22  EKELVKAEKESEDTFKDIVSSKDAPSKNLDATQLYLGEIGFSPLLSAEEE---VYFSRRA 78

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 +++ M+ +NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKFD   G++FS
Sbjct: 79  LKGDEASRQRMIVSNLRLVVKIARRYNNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFS 138

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RT+R ++ K+  EPT EEIA+ + 
Sbjct: 139 TYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTSRELAQKLDHEPTAEEIAEAVQ 198

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV  V K+L++ +   S++TPIG ++ + L D I D N   P +     N++ +    L
Sbjct: 199 RPVADVTKMLRLNERITSVDTPIGSDNDNVLLDIIADDNGHDPEEDLQDKNVKLSIVGWL 258

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L P++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+LK     K L
Sbjct: 259 EDLNPKQREVLARRFGLLGYEPSTLEDVGVEIGLTRERVRQIQVEALRRLKDMLGHKGL 317



 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 39/104 (37%), Gaps = 2/104 (1%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            + EE  E  L  A   S  +         A     D  ++YL E+G   LLS E E+  
Sbjct: 15  DDIEEAVEKELVKAEKESEDTFKDIVSSKDAPSKNLDATQLYLGEIGFSPLLSAEEEVYF 74

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ++R   G       +  S L    ++      N+    L ++++
Sbjct: 75  SRRALKGDEASRQRMIVSNLRL--VVKIARRYNNRGLALLDLVE 116


>gi|88798286|ref|ZP_01113872.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
 gi|88779062|gb|EAR10251.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
          Length = 344

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 170/272 (62%), Gaps = 3/272 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+   +  +  I     +S  E  +   + RKGE      +K M+E+NLRLV+ +A++Y 
Sbjct: 68  SLDATQLYLNEIGFSPLLSPEEEVYFARLARKGEPAG---RKRMIESNLRLVVKIARRYL 124

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 125 NRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 184

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EPTPE+IA+ L  PVE V+K+L + +   S++TPIG   
Sbjct: 185 VVKELNVYLRAARELAQKLDHEPTPEDIAQLLEKPVEDVKKMLALNERVTSIDTPIGPSS 244

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L + I D  A  P D+    +L+ +  R L  L+ ++  V+  RFG+      TLE+
Sbjct: 245 EKSLLETISDDRASDPSDTLQDDDLKASIDRWLDELSEKQREVVARRFGLRGYETSTLED 304

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VG++  +TRER+RQI+ +++R+L+     + L
Sbjct: 305 VGREIGLTRERVRQIQVESLRRLRDIMEKQGL 336



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 40/193 (20%), Positives = 60/193 (31%), Gaps = 8/193 (4%)

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ED+   A  + +         +   + + D  ++YL E+G   LLS E E+  A+    G
Sbjct: 41  EDTQAEAEESDDGEFQEALNANGNLQRSLDATQLYLNEIGFSPLLSPEEEVYFARLARKG 100

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREI-------IDLEACIGPESKGGFFHG 202
                  + ES L     I  R  LN G TLL  I       I       PE    F   
Sbjct: 101 EPAGRKRMIESNLRLVVKIARRY-LNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTY 159

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                 Q  E +   + R          E    +            E    D   L E  
Sbjct: 160 ATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELAQKLDHEPTPEDIAQLLEKP 219

Query: 263 DDSAHTLSAMEDQ 275
            +    + A+ ++
Sbjct: 220 VEDVKKMLALNER 232


>gi|114562238|ref|YP_749751.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
 gi|114333531|gb|ABI70913.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 323

 Score =  180 bits (457), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 164/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     ++  E    V   RK       ++  M+E+NLRLV+ ++++Y
Sbjct: 46  KNLDATQLYLGEIGFSPLLTAEEE---VFFSRKSLKGCEKSRNRMIESNLRLVVKISRRY 102

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 103 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 162

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR+++ K+  EPT EEIA+KL +    V ++LK+ +   S+++P+  +
Sbjct: 163 HIVKELNVYLRTARQLAQKLDHEPTAEEIAEKLDVSTGDVSRMLKLNERITSVDSPLSGD 222

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D I D ++V P       +L  +    L  L  ++  VL  RFG+      TLE
Sbjct: 223 NEKALLDVIADDDSVGPDYRVQNEDLSNSIVGWLNELNTKQREVLARRFGLLGYEPSTLE 282

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VG +  +TRER+RQI+ +A+++LK    S+ L
Sbjct: 283 NVGAEIGLTRERVRQIQVEALKRLKDLLGSQGL 315



 Score = 40.6 bits (93), Expect = 0.83,   Method: Composition-based stats.
 Identities = 25/109 (22%), Positives = 40/109 (36%), Gaps = 7/109 (6%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            +VD      E  ++    +        V    +K+       D  ++YL E+G   LL+
Sbjct: 12  CLVDLAKQPPEVATDKRDLVQQLDIEEKVQDDLQKNL------DATQLYLGEIGFSPLLT 65

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  +++   G       + ES L     I  R   N G  LL  I
Sbjct: 66  AEEEVFFSRKSLKGCEKSRNRMIESNLRLVVKISRRYN-NRGLALLDLI 113


>gi|312134852|ref|YP_004002190.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774903|gb|ADQ04390.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 273

 Score =  180 bits (456), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 97/256 (37%), Positives = 161/256 (62%), Gaps = 3/256 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +++ S    ++  E   +   + +       AK+++  AN RLV ++AK+Y   GL + D
Sbjct: 9   LQAASEYELLTPEEEIELAKRIEQ---GDEKAKEKLFRANKRLVANIAKRYRGFGLDYED 65

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEG IGLM A  K+D+  GY+F+TYA WW++QAIT++I +    IR+P+H+ +++ K+
Sbjct: 66  LMQEGFIGLMNAVNKYDYRQGYRFATYATWWIRQAITKAIYNTGRNIRVPIHLHEQMFKI 125

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +  R++  +  REPT  EIAK++    + V+K+L +  E +SL+TPIG++  + +GDF+
Sbjct: 126 RKVYRKLLQENNREPTIREIAKEMNWSTKKVQKMLDLFNEIVSLDTPIGEDGLATIGDFM 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D  A S  ++  +  L E  T+    L+ +E+RV+ +R+G+      TLEEVG    +T
Sbjct: 186 IDDKAFSYFENVEKQLLVEQLTKYFDKLSEKEKRVIVLRYGLADGKGRTLEEVGNALNLT 245

Query: 653 RERIRQIEAKAIRKLK 668
           RERIRQIE KA+RK++
Sbjct: 246 RERIRQIEIKALRKIR 261



 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 19/42 (45%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           ELL+ E EI +AKRIE G       L  +     A I  R  
Sbjct: 16  ELLTPEEEIELAKRIEQGDEKAKEKLFRANKRLVANIAKRYR 57


>gi|330446961|ref|ZP_08310612.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491152|dbj|GAA05109.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 333

 Score =  180 bits (456), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 98/269 (36%), Positives = 167/269 (62%), Gaps = 3/269 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     ++  E    V   R+      +A+K M+E+NLRLV+ +
Sbjct: 50  EATQKALDATQLYLGEIGYSPLLTAEEE---VLYARRALRGDEVARKRMIESNLRLVVKI 106

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 107 SRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 166

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR ++ K+  EPT E+IA++L  PV+ V ++L++ +   S++ P
Sbjct: 167 RLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAQQLEKPVDDVNRMLRLNERVSSVDNP 226

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D+   SP  S    +++ +    L  L P++  VL  RFG+     
Sbjct: 227 IGGDSEKALLDIIPDEKGGSPESSTQDDDIKNSIVHWLQELNPKQREVLARRFGLLGYEA 286

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 287 STLEDVGREIGLTRERVRQIQVEGLRRLR 315



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  ++     S D      + S +       K  A +   D  ++YL E+G   LL+ E 
Sbjct: 17  EDVEMNVPMPSADDSSDTEAISVNDDDADIAKYEATQKALDATQLYLGEIGYSPLLTAEE 76

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G  +    + ES L     I  R   N G  LL  +
Sbjct: 77  EVLYARRALRGDEVARKRMIESNLRLVVKISRRYS-NRGLALLDLV 121


>gi|158340427|ref|YP_001521783.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310668|gb|ABW32282.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 273

 Score =  180 bits (456), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 96/260 (36%), Positives = 159/260 (61%), Gaps = 5/260 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +S  E    + + R+ +     AK+ M+E NLRLV+S+AKK+ NRGL F+
Sbjct: 10  YLKEIGRYPLLSHEEE---IQLARQAKAGNLRAKQRMIECNLRLVVSIAKKHQNRGLPFM 66

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG+IGL +A EKF+   GY+FSTYA WW++Q ITRSI + S  IR+PV      ++
Sbjct: 67  DLIQEGSIGLSRAVEKFEPEQGYRFSTYAYWWIRQGITRSIQNNSRVIRLPVWHWQTGNQ 126

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +T R++S +  REPT  E+A+ + + ++ +++ +   ++ +SL+  +G E  + LG+ 
Sbjct: 127 IKQTQRQLSQEFGREPTLAELAEAMEIDLDKLKQNMHHLQDVLSLDMQVGKEQDTTLGEL 186

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE + +       +  +  E  +  L+ L  R+  V+  R+G+      T++++G+Q  V
Sbjct: 187 IEAEQSTPTHLELLNQS--EEVSSYLSLLDERQRYVIVQRYGLEDGEAKTMQDIGQQLGV 244

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           +RERIRQI  KA++KL+  S
Sbjct: 245 SRERIRQIINKAMKKLQKNS 264



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
            D    YL+E+G   LLS E EI +A++ +AG       + E  L     I  + +
Sbjct: 4   TDSTGAYLKEIGRYPLLSHEEEIQLARQAKAGNLRAKQRMIECNLRLVVSIAKKHQ 59


>gi|260436326|ref|ZP_05790296.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260414200|gb|EEX07496.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 308

 Score =  180 bits (456), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 98/256 (38%), Positives = 155/256 (60%), Gaps = 1/256 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +       + S  R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL
Sbjct: 44  HHVQAMKQLQELPEEELTSRHRHKIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDL 103

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ 
Sbjct: 104 VQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMR 163

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFI 592
           R +R +S++  R+P   E+A  + +    +  ++  +    SL+     E+  S LG+ I
Sbjct: 164 RISRELSHRFGRQPNRLELASAMGIEPRELEDLISQSAPCASLDAHARGEEDRSTLGELI 223

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D N   P++   ++  +E     L+ L  RE+++L++RFG+G     TL E+G+Q  V+
Sbjct: 224 PDPNGEEPMEGMDRSIQKEHLGGWLSQLNEREQKILKLRFGLGGEEPLTLAEIGRQINVS 283

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ+EAKAI KL+
Sbjct: 284 RERVRQLEAKAILKLR 299


>gi|153001641|ref|YP_001367322.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS185]
 gi|160876377|ref|YP_001555693.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS195]
 gi|217972427|ref|YP_002357178.1| RNA polymerase sigma 70 subunit RpoD subfamily [Shewanella baltica
           OS223]
 gi|151366259|gb|ABS09259.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS185]
 gi|160861899|gb|ABX50433.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS195]
 gi|217497562|gb|ACK45755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS223]
 gi|315268567|gb|ADT95420.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS678]
          Length = 326

 Score =  180 bits (456), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 100/273 (36%), Positives = 167/273 (61%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK     + ++  M+E+NLRLV+ +A++Y
Sbjct: 49  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKALKGCAKSRNRMIESNLRLVVKIARRY 105

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 106 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 165

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT EEIA+KL +    V ++LK+ ++  S++TP+G +
Sbjct: 166 HVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQVSSADVSRMLKLNEKITSVDTPLGGD 225

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D + V P       ++  +  + L  L  ++  VL  RFG+      TLE
Sbjct: 226 NDKALLDILADDDNVGPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG +  +TRER+RQI+ +A+++L+    S+ L
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQGL 318



 Score = 40.6 bits (93), Expect = 0.87,   Method: Composition-based stats.
 Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 2/95 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             +  +S     + ++++     +   D  ++YL E+G   LLS E E+  +++   G A
Sbjct: 25  EKEEVASDLVQELGIEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEEVYFSRKALKGCA 84

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
                + ES L    ++      N+    L ++I+
Sbjct: 85  KSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 117


>gi|37524720|ref|NP_928064.1| RNA polymerase sigma factor RpoS [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784145|emb|CAE13014.1| RNA polymerase sigma factor (sigma-38) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 332

 Score =  180 bits (456), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 175/271 (64%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+      +A++ M+E+NLRLV+ ++++Y+N
Sbjct: 57  LDATQLYLGEIGFSPLLTAEEE---VFFARRALRGDVLARQRMIESNLRLVVKISRRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+PEEIA++L  PV+ V ++L++ +  IS++TPI  +  
Sbjct: 174 VKELNVYLRTARELAHKLDHEPSPEEIAEQLDKPVDDVSRMLRLNERIISVDTPISGDSD 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P  +  + +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDVLSDENETGPEGTTQEDDMKKSIVKWLFELNSKQREVLARRFGLLGYEAETLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           GK+  +TRER+RQI+ + +R+LK   +++ L
Sbjct: 294 GKEIGLTRERVRQIQVEGLRRLKDIMQTQGL 324



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 28/114 (24%), Positives = 42/114 (36%), Gaps = 6/114 (5%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA-----DRSTDDPVRMYLREMGS 130
            + D  DL++     D  D     ++         D        +   D  ++YL E+G 
Sbjct: 10  ELYDDADLDESGIEADDFDEKLLKNDGDDLTDFENDLDVLQGMSQRVLDATQLYLGEIGF 69

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E+  A+R   G  +    + ES L     I  R   N G  LL  I
Sbjct: 70  SPLLTAEEEVFFARRALRGDVLARQRMIESNLRLVVKISRRYS-NRGLALLDLI 122


>gi|159026170|emb|CAO88820.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 318

 Score =  180 bits (456), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 105/249 (42%), Positives = 167/249 (67%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R+       AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD  
Sbjct: 71  EQLRRELGAGDFAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++    R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQDKGRAATIAE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L +  + VR  L+ +++P+SL+  +GD   + LG+ +ED   +SP D    ++L+ 
Sbjct: 191 LAEELDLTPKQVRDYLERSRQPLSLDLKVGDNQDTELGELLEDT-GLSPEDYTAHSSLQV 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +++A LTP+++ V+ +RFG+      TL ++G +  ++RER+RQIE +AI KL+   
Sbjct: 250 DLEKLMADLTPQQKEVICLRFGLDNGQPLTLAKIGVRLNISRERVRQIEREAIAKLRK-- 307

Query: 672 RSKKLRSFL 680
           R  K+R +L
Sbjct: 308 RKAKIREYL 316



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 17/30 (56%), Positives = 22/30 (73%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            DPVR YLRE+G + LLS E EI  AK+++
Sbjct: 8   TDPVRAYLREIGRVPLLSHEEEILYAKQVQ 37


>gi|158340842|ref|YP_001522010.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311083|gb|ABW32696.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 299

 Score =  180 bits (456), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 104/284 (36%), Positives = 160/284 (56%), Gaps = 12/284 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + +   +    +++   GIS +E   I             AK  M+  NLRLV++
Sbjct: 24  LLTHAEEVSLGQQIQSALNPPQGISQAELDQIQKR-------GKRAKHRMICGNLRLVVT 76

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKKY  RG+  +DLIQEG++GL +A EKFD   GY+FSTYA WW++Q+ITR+IA QS T
Sbjct: 77  IAKKYQKRGMDLIDLIQEGSLGLERAVEKFDPAKGYRFSTYAYWWIRQSITRAIAMQSHT 136

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISL 576
           IRIPVHM +K++++ R  R +S  + R PT +E+  +L + +E ++K L+  +   P SL
Sbjct: 137 IRIPVHMTEKLNRIKRVRRELSQTLGRTPTHQEMVAELGITLEQLQKTLQAAQISNPESL 196

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
              +G +    LGD +ED    SP +   Q  LR      LA L   E  VL +R+G+  
Sbjct: 197 NIRVGKDQEMELGDLLEDLQMPSPNEVVEQDFLRNALWSALAQLNDNERTVLILRYGLED 256

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             + +L  V +Q  ++RE +R++E  A  KL    +S  L+ F+
Sbjct: 257 GRERSLYRVSQQMGISREWVRKLEQTAKSKL---LQSGNLQDFM 297


>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa]
 gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa]
          Length = 567

 Score =  180 bits (456), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 97/247 (39%), Positives = 156/247 (63%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK      + K +M+++N+RLVIS+AK Y   G+   DL+QEG  GL++ AEKFD   G
Sbjct: 319 LRKRLNYGILCKDKMIKSNVRLVISIAKNYQGTGMNLQDLVQEGCRGLVRGAEKFDASKG 378

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW+KQA+ +S++D+S TIR+P HM D  ++V    +++ ++  R P  +E+A
Sbjct: 379 FKFSTYAHWWIKQAVRKSLSDRSRTIRLPFHMVDATYRVKEARKQLYSENGRHPDDKEVA 438

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   + ++ +  VL   K P SL+  +G      L +   D  A +  D  ++  +++  
Sbjct: 439 EAAGLSMKRLSAVLLTPKAPRSLDQKMGFNMDLKLSEVTADPEAETAEDLLMKEFMKKDL 498

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +VL SL+PRE +V+R RFG+      TL+E+G+   V+RER+RQIE  A RKLK+ +R+
Sbjct: 499 AKVLGSLSPRENQVVRWRFGMEDGRMKTLQEIGELMGVSRERVRQIELSAFRKLKNKNRT 558

Query: 674 KKLRSFL 680
           K+LR ++
Sbjct: 559 KQLRQYM 565


>gi|149278736|ref|ZP_01884871.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149230355|gb|EDM35739.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 286

 Score =  180 bits (456), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 87/272 (31%), Positives = 149/272 (54%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +  I     +S+ E   +   ++K       A  ++V+ NLR V+SVAKKY N+GL
Sbjct: 18  IDKYLTDIGRIGLLSVEEELGLARRIKK---GDEAALDKLVKTNLRFVVSVAKKYQNKGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q  DLI EGN+GL+KAA++FD   G+KF ++A+WW++Q+I +++ADQ   IR+P +    
Sbjct: 75  QLADLISEGNLGLIKAAQRFDDTKGFKFISFAVWWIRQSIMQALADQKRMIRLPGNQVLG 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K+ + A  +   ++R PT EE+A         V   L       SL+    +E    L
Sbjct: 135 IIKINKAADELEQVLERAPTYEELAMATEFSEAKVADYLDSAPLSYSLDMTTHEESDFSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + ++N     +  ++ ++ E   R L+ L  RE+ ++   FG+  +T  TL+++   
Sbjct: 195 MDTLVNENTPDTDELMMKESMSEDVRRSLSILPEREKWIIIFFFGLDNHTALTLDDMTDV 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +++ERIRQ++ +A++ LK   R   L  ++
Sbjct: 255 FQLSKERIRQLKDRALKTLKTSCRKSFLAEYI 286



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL ++G I LLS E E+ +A+RI+ G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLTDIGRIGLLSVEEELGLARRIKKGDEAALDKLVKTNLRF--VVSVAKKYQNKGLQLAD 78

Query: 184 II 185
           +I
Sbjct: 79  LI 80


>gi|166367266|ref|YP_001659539.1| RNA polymerase sigma factor SigD [Microcystis aeruginosa NIES-843]
 gi|166089639|dbj|BAG04347.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 318

 Score =  180 bits (455), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 104/249 (41%), Positives = 166/249 (66%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R+       AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD  
Sbjct: 71  EQLRRELGAGDFAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++    R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQDKGRAATIAE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L +  + VR  L+ +++P+SL+  +GD   + LG+ +ED   +SP D    ++L+ 
Sbjct: 191 LAEELDLTPKQVRDYLERSRQPLSLDLKVGDNQDTELGELLEDT-GLSPEDYTAYSSLQV 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +++A LTP+++ V+ +RFG+      TL ++G +  ++RER+RQIE +AI KL+   
Sbjct: 250 DLEKLMADLTPQQKEVICLRFGLDNGQPLTLAKIGVRLNISRERVRQIEREAIAKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   +R +L
Sbjct: 308 RKGNIREYL 316



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/30 (53%), Positives = 22/30 (73%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            DPVR YLRE+G + LL+ E EI  AK+++
Sbjct: 8   TDPVRAYLREIGRVPLLTHEEEILYAKQVQ 37


>gi|83644704|ref|YP_433139.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
 gi|83632747|gb|ABC28714.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
          Length = 332

 Score =  180 bits (455), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 105/326 (32%), Positives = 180/326 (55%), Gaps = 6/326 (1%)

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI---R 410
            E    A+      D+ L   +  E +           +G    F   E  S   +   +
Sbjct: 3   AERESYAEDLAYDVDIDLAEIEAEEFEDDESDVVVSIDQGRTGRFSLGEGQSYRNLDATQ 62

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  I     ++  E  H   M R+        +K M+E+NLRLV+ +A++Y NRGL  
Sbjct: 63  IYLNEIGFSPLLTPEEEVHFARMARR---GDEKGRKRMIESNLRLVVKIARRYVNRGLSL 119

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++
Sbjct: 120 LDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELN 179

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
             +R +R ++ K+  EP+ EEIA  L  PV+ V+++L + +   S+++PIG      L D
Sbjct: 180 VYLRASRELTQKLDHEPSAEEIADLLEKPVKDVKRMLGLNERITSVDSPIGGNAEKSLLD 239

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            + D+ +  P +    ++L+    R L  L+ +++ V+  RFG+      TLEEVG++  
Sbjct: 240 TVADEASNDPAELLQDSDLKGCLDRWLDQLSDKQQEVIARRFGLRGYPMSTLEEVGQEIG 299

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKL 676
           +TRER+RQI+ +A+++++     + L
Sbjct: 300 LTRERVRQIQVEALKRMRELLEKEGL 325



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +D  ++E EE  +D  D+  S            +       D  ++YL E+G   LL+ E
Sbjct: 18  IDLAEIEAEEFEDDESDVVVSIDQGRTGRFSLGEGQSYRNLDATQIYLNEIGFSPLLTPE 77

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+    G       + ES L     I  R  +N G +LL  I
Sbjct: 78  EEVHFARMARRGDEKGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 123


>gi|37523928|ref|NP_927305.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35214934|dbj|BAC92300.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 344

 Score =  180 bits (455), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 119/315 (37%), Positives = 187/315 (59%), Gaps = 12/315 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI------KSISVETGISISEFRHIVSM 433
               V    +      +     E+    +I+ ++      + +++  G    E      M
Sbjct: 30  SDDLVDLYLNEIGRIPRVTPEEEIHLARRIQAKLAIDGAREELAMRLGRPSPEEDVAAFM 89

Query: 434 VRKGEC------EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            R  +       +   A+++++ ANLRLV+S+AKKY  R + FLDLIQEGNIGLM+A EK
Sbjct: 90  GRDPKALIEATRQGLWAQRKLINANLRLVVSIAKKYIGRNVPFLDLIQEGNIGLMRATEK 149

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY+FSTYA WW++Q+ITR+IA+Q+ TIR+P+HM +K+ KV R  R  + ++ R P
Sbjct: 150 FDPEKGYRFSTYATWWIRQSITRAIANQARTIRLPIHMVEKVRKVRREMRMATLELGRRP 209

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E+A +LA+ V+ +R + +++++P+SL+ P+G E    LG+ IED  A  P D  +Q 
Sbjct: 210 SEDELASRLAIKVKKLRTIQEVSRQPVSLDMPVGSEGDISLGEMIEDGTAERPFDELVQK 269

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L       +  L P E  VL +RFG+      TL EVG++F +TRERIRQIE++A+RKL
Sbjct: 270 ALASELYAAMNVLKPVEREVLALRFGLKGEEGLTLREVGERFDLTRERIRQIESEALRKL 329

Query: 668 KHPSRSKKLRSFLDG 682
           +   R + L+ ++ G
Sbjct: 330 RRSKRKQILQQYVGG 344



 Score = 41.4 bits (95), Expect = 0.54,   Method: Composition-based stats.
 Identities = 16/37 (43%), Positives = 25/37 (67%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S  + +DD V +YL E+G I  ++ E EI +A+RI+A
Sbjct: 25  SEAQGSDDLVDLYLNEIGRIPRVTPEEEIHLARRIQA 61


>gi|166364164|ref|YP_001656437.1| RNA polymerase sigma factor [Microcystis aeruginosa NIES-843]
 gi|166086537|dbj|BAG01245.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 328

 Score =  180 bits (455), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 166/247 (67%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +       AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   G
Sbjct: 82  LDRALKTGDRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+ RT R ++ K+ R  TP EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKRTQRELAQKLGRSATPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +L +    +R+ L + ++PISL+  +GD   + L + +ED + VSP     Q  LR+  
Sbjct: 202 LELELEPAQIREYLSMARQPISLDVRVGDNQDTELSELLED-SGVSPDTFITQELLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  V+ +RFG+    + +L ++G++  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 ANLLAELTPQQREVITLRFGLTDGKELSLAKIGQRMNISRERVRQLEHQALAHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 ANVKEYI 325



 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCESPLTFQALIIWRDELND 176
           D VR YL E+G + LL+ E EI   K+++          +L +        + W D +N 
Sbjct: 18  DMVRTYLHEIGRVPLLTHEQEIIYGKQVQRMMSLLETKEALSKQLGREPDRLEWADSVNL 77

Query: 177 GTTLLR 182
               L 
Sbjct: 78  SENELD 83


>gi|261856530|ref|YP_003263813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
 gi|261836999|gb|ACX96766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
          Length = 343

 Score =  180 bits (455), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 103/276 (37%), Positives = 163/276 (59%), Gaps = 3/276 (1%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F A + +S+  +R  ++ +  E  ++  E    V   R+ +     A+++M+  NLRLVI
Sbjct: 60  FSASDSESVDPVRLYLRDVETERLLTAEEE---VIYSRRAQSGDESARQKMIVCNLRLVI 116

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            +A++Y NRGL  LDLI+EGNIGLM+A EKFD   G++FSTYA WW++Q I R + +QS 
Sbjct: 117 KIARRYMNRGLDLLDLIEEGNIGLMRAVEKFDPERGFRFSTYATWWIRQTIERGLMNQSR 176

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           T+R+PVH+  ++H   R AR+++     E T E+IA  L  PV  V K++   +   S +
Sbjct: 177 TVRLPVHVVKEVHTFNRAARKIAQNQNAEVTAEQIADHLDRPVNEVLKIMAFNERQSSFD 236

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +P+  +    L D I D+ +  P +    A +     +++A L  ++  VL  R+G+   
Sbjct: 237 SPLKGDGEFSLLDLIPDQESNQPDELLQDAGVHGFLDQLIAQLESKQREVLVRRYGLRGY 296

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             HTLEEVG    VTRER+RQI+ +A+R+LK  ++ 
Sbjct: 297 ETHTLEEVGNHLGVTRERVRQIQLEAVRRLKSLAKK 332



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/107 (28%), Positives = 47/107 (43%), Gaps = 2/107 (1%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VD ++L   +  E   D+ S   N          S   S  DPVR+YLR++ +  LL+ E
Sbjct: 29  VDEEELLAVDDVELDDDIDSPEKNEEELTTTFSASDSESV-DPVRLYLRDVETERLLTAE 87

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  ++R ++G       +    L    + I R  +N G  LL  I
Sbjct: 88  EEVIYSRRAQSGDESARQKMIVCNLRL-VIKIARRYMNRGLDLLDLI 133


>gi|157961021|ref|YP_001501055.1| RpoD family RNA polymerase sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846021|gb|ABV86520.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella pealeana
           ATCC 700345]
          Length = 322

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 103/273 (37%), Positives = 166/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 45  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKSLKGCEKSRNRMIESNLRLVVKIARRY 101

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 102 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 161

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR +++K+  EPT EEIA KL +P   V ++LK+ +   S++TP+G E
Sbjct: 162 HVVKELNVYLRTARELAHKLDHEPTAEEIADKLDLPSADVSRMLKLNERITSVDTPLGGE 221

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D + D + V P       ++ ++  + L  L  ++  VL  RFG+      TLE
Sbjct: 222 SDKALLDVLADDDNVGPDYKVQDEDMSKSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 281

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VGK+  +TRER+RQI+ +A+++LK    ++ L
Sbjct: 282 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQGL 314



 Score = 44.1 bits (102), Expect = 0.092,   Method: Composition-based stats.
 Identities = 20/106 (18%), Positives = 43/106 (40%), Gaps = 2/106 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +    +  +DS +  +        L+++     +   D  ++YL E+G   LLS E E+
Sbjct: 10  AEQPKNDSVKDSSNTLTKQDVKEAELEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEEV 69

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
             +++   G       + ES L    ++      N+    L ++I+
Sbjct: 70  YFSRKSLKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 113


>gi|67924587|ref|ZP_00518002.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853561|gb|EAM48905.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 328

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 108/297 (36%), Positives = 185/297 (62%), Gaps = 4/297 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +++ ++   G+    +   ++   ++ +++         S  E       + +   +   
Sbjct: 33  LTHEQEIIYGKQVQKMMNFLEKKEELADKLGKEPTVKEWS-KELEIEQKALNQALEQGER 91

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+++AKKY  R ++FLDLIQEG++GL +  EKFD   GYKFSTYA WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S  + R  TP EIA++L +    +
Sbjct: 152 IRQAITRAIAQQSRTIRLPIHITEKLNKIKKTQRELSQTLGRSATPSEIAQELEIEPSQI 211

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L I ++PISL+  +GD   + L + +ED+  VSP     Q  LR+    ++A LTP+
Sbjct: 212 REFLSIARQPISLDVRVGDNQDTELSELLEDQ-GVSPDLYITQELLRQDLRNLMAELTPQ 270

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  VL +RFG+    + +L ++GK+  ++RER+RQ+E +A+ +L+   R   ++ +L
Sbjct: 271 QRTVLTLRFGLEDGKELSLAKIGKRMNISRERVRQLEHQALAQLRR--RRANVKEYL 325



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D VR YL E+G + LL+ E EI   K+++ 
Sbjct: 16  SADMVRTYLHEIGRVPLLTHEQEIIYGKQVQK 47


>gi|332667453|ref|YP_004450241.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332336267|gb|AEE53368.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 288

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 156/275 (56%), Gaps = 4/275 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L +   +  I     ++  +   +   +R+       A  ++  ANLR V+SVAK+Y N+
Sbjct: 16  LALDKYLNDIGKIPMLTADDEAELARRIRQ---GDDDAMAKLTRANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GLMKAA++FD   G+KF +YA+WW++Q+I ++I + S  +R+P++  
Sbjct: 73  GLSLSDLINEGNVGLMKAAKRFDETKGFKFISYAVWWIRQSILQAIVEYSRIVRLPLNKV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-T 585
              +KV         + +REP+ EE+ + L M    V  +LK     +S++ P+  E+  
Sbjct: 133 GSYNKVNEAYLAFIQQFEREPSNEELGELLEMNPREVGNMLKGNGRHVSVDAPLSGEEGD 192

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S + D I D++ + P    ++ +L++   + L+ L  RE  VL   +G+      TLEE+
Sbjct: 193 STMLDVITDEDDMGPDFRLMEQSLKDEVKQGLSILNIREVEVLSAYYGLEGQKPLTLEEI 252

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+ + +TRER+RQI+ +AIR+L+       LRS+L
Sbjct: 253 GEMYGLTRERVRQIKERAIRRLRKSYNRNNLRSYL 287



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL ++G I +L+ + E  +A+RI  G    MA L  + L F  ++    +  +    L +
Sbjct: 21  YLNDIGKIPMLTADDEAELARRIRQGDDDAMAKLTRANLRF--VVSVAKQYQNQGLSLSD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T+G  
Sbjct: 79  LIN-EGNVGLMKAAKRFDETKGFK 101


>gi|253700182|ref|YP_003021371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775032|gb|ACT17613.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 333

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 170/274 (62%), Gaps = 5/274 (1%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K  V    D  +K+   ++ I     ++  E + + + +   +     A+  M+ +NLRL
Sbjct: 45  KAAVVEHFDDAIKL--YLREIQKTKLLTADEEKELAARI---DLGDKAARDRMIVSNLRL 99

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +Q
Sbjct: 100 VVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQ 159

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S TIR+PVH+ D I+K++R  R +  K+ REPT +E+A  L + +  VR+++ + K+  S
Sbjct: 160 SRTIRLPVHVSDDINKMLRVTRELVQKMNREPTIKEVADTLEVNITYVRRLMVLLKKTYS 219

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +E P+G+ +   L D IED + +SP       N  E  ++   +L+  E+++L +RFG+ 
Sbjct: 220 IERPMGENNDYFLIDTIEDTSTISPAVLLEDLNKYELVSKWFETLSDAEKKILTLRFGLD 279

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                TL+ +G+ F VTRERIRQIEAK++ KL+ 
Sbjct: 280 DKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRK 313



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/104 (25%), Positives = 45/104 (43%), Gaps = 1/104 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D  +D +  E     A +   + V  ++ K +     DD +++YLRE+   +LL+ + E 
Sbjct: 16  DAEQDPDSLELEEVEAEADEPAEVEEEEIKAAVVEHFDDAIKLYLREIQKTKLLTADEEK 75

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +A RI+ G       +  S L     I  R  +N G   L  I
Sbjct: 76  ELAARIDLGDKAARDRMIVSNLRLVVKIAKRY-INRGLPFLDLI 118


>gi|160902085|ref|YP_001567666.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359729|gb|ABX31343.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 424

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 118/273 (43%), Positives = 174/273 (63%), Gaps = 8/273 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K IS    ++ S  R +    +        A++E+++ANLRLVIS+AK+Y   GL FL
Sbjct: 153 YLKEISKSKLLTPSRERKLARRAQ---MGDKRAREELIKANLRLVISIAKRYVGHGLGFL 209

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA  KFDW  GYKFSTY+ WW++QAITR+IADQ  T+RIPVH+ + I++
Sbjct: 210 DLIQEGNIGLMKAVAKFDWKKGYKFSTYSYWWIRQAITRAIADQGRTVRIPVHLVETINR 269

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE----DTSH 587
           + R   +   +    P  EE++  +  PV+ +++VL   K   SL  PI ++      S 
Sbjct: 270 MNRVVNKYIQENGEVPDLEELSVLMDKPVDKMKEVLISAKNIFSLNAPISNDVDAEGESE 329

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + DFI D ++ +P +   +  +R+    ++ +L+P+E  +L+MR+G       TLEEVG+
Sbjct: 330 VLDFI-DSDSPTPDEEGRKMIIRQKMEMIIDTLSPKEAMILKMRYGFVDGKQKTLEEVGE 388

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F VTRERIRQIE+K+IRKLKHP+R K + + +
Sbjct: 389 FFNVTRERIRQIESKSIRKLKHPARKKMIENII 421



 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/153 (22%), Positives = 59/153 (38%), Gaps = 13/153 (8%)

Query: 44  VTIEELNAFLPP---DEVSSEQMEDTVAMLSNMGINVVDGD---------DLEDEEGSED 91
           VT EE++  +P    ++ + E +      L    I+VVDG          + E E   E 
Sbjct: 61  VTFEEIDESIPSQMREDFTLEFLITFYNELKKSNISVVDGSSGNFCEEDEEKELEVNEEF 120

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                           + +   + S  DP+++YL+E+   +LL+   E  +A+R + G  
Sbjct: 121 KDSEEYEEIFEDFSDVEVEMCDNISLQDPIKIYLKEISKSKLLTPSRERKLARRAQMGDK 180

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                L ++ L     I  R  +  G   L  I
Sbjct: 181 RAREELIKANLRLVISIAKRY-VGHGLGFLDLI 212


>gi|71893415|ref|YP_278861.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae J]
          Length = 489

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 179/311 (57%), Gaps = 11/311 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P+     K + +  + N +    D I      I        ++  E R +   ++  
Sbjct: 180 ENSPNQYHKPKVYSDEVYLNKLTDTSDMIKWYMRWIGKYGKL--LTAEEERELAKKMKIK 237

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  +++ NLRLV++ AK+Y NRGL F+DLI EGN+G++KA  K+D+  G+KFS
Sbjct: 238 GRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFS 297

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITR++ADQ+  IRIPVHM + I+K+ +  R +  +    PT EEI+++L 
Sbjct: 298 TYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQQEKGLNPTAEEISERLD 357

Query: 558 --MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                + +R + KI  +PISL+  IG E+ S   DFI+D+N +SP+D AI+    +    
Sbjct: 358 GEFSPDKIRYIKKINIDPISLDKAIGKEEDSSFSDFIKDENMISPVDYAIREEKAKVLLE 417

Query: 616 VLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +L   E   ++ R+G+G N +      H+ EE+     VT+ER+RQIEAK ++KL+
Sbjct: 418 MIDSTLDYDERDFIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLR 477

Query: 669 HPSRSKKLRSF 679
            P R   LR F
Sbjct: 478 TPHRRLSLRDF 488


>gi|116514228|ref|YP_813134.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
 gi|116093543|gb|ABJ58696.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
          Length = 378

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 116/282 (41%), Positives = 172/282 (60%), Gaps = 10/282 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT- 464
              +R  +K I     +S  E   +   ++        AK E+  ANLRLV+S+AK+Y  
Sbjct: 101 YDSVRMYLKEIGKVPLLSRDEEVEVAKRIK---NGDESAKDELAAANLRLVVSIAKRYAK 157

Query: 465 -NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA WW++QAITR++ADQ   IRIPV
Sbjct: 158 HNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPV 217

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG 581
           H+ + I+K+ R  R +   + R   PEE+A ++  P++ V++++ + K     SL+  +G
Sbjct: 218 HVVESINKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQKVQEIITVAKNQETDSLDKSVG 277

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH 640
           +E  S LGD +ED  A++P +      L++  + ++   LT RE +VL++RFG+     H
Sbjct: 278 EEGDSQLGDLLEDNKAINPEEYTAFEMLKDQLSGMMGEFLTDREAKVLKLRFGLENYEPH 337

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+   VTRER+RQIE KA++KLK    S  L+ +   
Sbjct: 338 TLEEVGRSLGVTRERVRQIEDKAVKKLKQ--HSDLLQDYFSA 377



 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/189 (21%), Positives = 72/189 (38%), Gaps = 13/189 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +I   ++   +  ++L    L P  ++  +    V   ++ GI++VD       
Sbjct: 15  EKAVKMVITGLKKTKQIREKDLKARLLLPYGLNDAETAKLVEEFADNGISIVDDQGEPSA 74

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +   +                 S +    D VRMYL+E+G + LLSR+ E+ +AKRI
Sbjct: 75  LALKAEEEAEKKEQKELAA-----SSDNDQVYDSVRMYLKEIGKVPLLSRDEEVEVAKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           + G       L  + L     I  R   ++G   + ++I        E   G     +  
Sbjct: 130 KNGDESAKDELAAANLRLVVSIAKRYAKHNGKMGILDLI-------QEGNIGLMKAVDKF 182

Query: 207 SYQKREDSS 215
            Y K    S
Sbjct: 183 DYSKGFKFS 191


>gi|313123887|ref|YP_004034146.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280450|gb|ADQ61169.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 378

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 119/282 (42%), Positives = 177/282 (62%), Gaps = 10/282 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT- 464
              +R  +K I     +S  E   +   +        +AK E+  ANLRLV+S+AK+Y  
Sbjct: 101 YDSVRMYLKEIGKVPLLSRDEEVEVAKRIE---NGDELAKDELAAANLRLVVSIAKRYAK 157

Query: 465 -NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA WW++QAITR++ADQ   IRIPV
Sbjct: 158 HNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPV 217

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG 581
           H+ + I+K+ R  R +   + R+  PEE+A ++  P++ V++++ + K     SL+ P+G
Sbjct: 218 HVVESINKMNRIQRILQQDLDRDAKPEELAAEMNEPLQKVQEIITVAKNQETDSLDKPVG 277

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH 640
           +E  S LGD +ED  A++P +      L++  + ++   LT RE +VL++RFG+  +  H
Sbjct: 278 EEGDSQLGDLLEDNKAINPEEYTASEMLKDQLSSMMGEFLTDREAKVLKLRFGLENDEPH 337

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+   VTRER+RQIEAKA++KLKH   S  L+ +   
Sbjct: 338 TLEEVGRSLGVTRERVRQIEAKAVKKLKH--HSDLLQDYFSA 377



 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 74/189 (39%), Gaps = 13/189 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +I   ++   +  ++L    L P  ++  +    V   ++ GI++VD       
Sbjct: 15  EKAVKMVITGLKKTKQIREKDLKARLLLPYGLNDAETAKLVEEFADNGISIVDDQGEPSA 74

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +   +         V       S +    D VRMYL+E+G + LLSR+ E+ +AKRI
Sbjct: 75  LALKAEEEAEKKEQKELVA-----SSDNDRVYDSVRMYLKEIGKVPLLSRDEEVEVAKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G  +    L  + L     I  R   ++G   + ++I        E   G     +  
Sbjct: 130 ENGDELAKDELAAANLRLVVSIAKRYAKHNGKMGILDLI-------QEGNIGLMKAVDKF 182

Query: 207 SYQKREDSS 215
            Y K    S
Sbjct: 183 DYSKGFKFS 191


>gi|257058077|ref|YP_003135965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|256588243|gb|ACU99129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 375

 Score =  180 bits (455), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 109/298 (36%), Positives = 185/298 (62%), Gaps = 1/298 (0%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +   ++        F+        ++  E++    +   + +                  
Sbjct: 77  LEAQEEIELAYSVQFLVEAEQKRQQLLEELQHPPTKAQWAQAMGFDSQRQFENRLYRGRT 136

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 137 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A++L M    +
Sbjct: 197 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQKLQRNPNEKELAQELEMTPPQL 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +  LR   + VL+  LT 
Sbjct: 257 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEEQMNEGMLRNEISAVLSDVLTE 316

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 317 REKDVISLRYGLSTSQPHTLEEVGGMFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 374



 Score = 41.4 bits (95), Expect = 0.60,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  DLE  E   +++++  S  +  +  Q         +DD V  + +EM    LL  +
Sbjct: 21  FETGDLEQVEADFEAVEVEFSELSDDLGHQYPPGYRKTVSDDTVGAFFKEMSRYPLLEAQ 80

Query: 138 GEIAIAKRIE 147
            EI +A  ++
Sbjct: 81  EEIELAYSVQ 90


>gi|300812193|ref|ZP_07092635.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496829|gb|EFK31909.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 378

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 119/282 (42%), Positives = 176/282 (62%), Gaps = 10/282 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT- 464
              +R  +K I     +S  E   +   +         AK E+  ANLRLV+S+AK+Y  
Sbjct: 101 YDSVRMYLKEIGKVPLLSRDEEVEVAKRIE---NGDESAKDELAAANLRLVVSIAKRYAK 157

Query: 465 -NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA WW++QAITR++ADQ   IRIPV
Sbjct: 158 HNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPV 217

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG 581
           H+ + I+K+ R  R +   + R+  PEE+A ++  P++ V++++ + K     SL+ P+G
Sbjct: 218 HVVESINKMNRIQRTLQQDLDRDAKPEELAAEMNEPLQKVQEIITVAKNQETDSLDKPVG 277

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH 640
           +E  S LGD +ED  A++P +      L++  + ++   LT RE +VL++RFG+  +  H
Sbjct: 278 EEGDSQLGDLLEDNKAINPEEYTASEMLKDQLSIMMGEFLTDREAKVLKLRFGLENDEPH 337

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+   VTRER+RQIEAKA++KLKH   S  L+ +   
Sbjct: 338 TLEEVGRSLGVTRERVRQIEAKAVKKLKH--HSDLLQDYFSA 377



 Score = 81.4 bits (199), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 73/189 (38%), Gaps = 13/189 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +I   ++   +  ++L    L P  ++  +    V   ++ GI++VD       
Sbjct: 15  EKAVKMVITGLKKTKQIREKDLKARLLLPYGLNDAETAKLVEEFADNGISIVDDQGEPSA 74

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +   +         V       S +    D VRMYL+E+G + LLSR+ E+ +AKRI
Sbjct: 75  LALKAEEEAEKKEQKELVA-----SSDNDRVYDSVRMYLKEIGKVPLLSRDEEVEVAKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L  + L     I  R   ++G   + ++I        E   G     +  
Sbjct: 130 ENGDESAKDELAAANLRLVVSIAKRYAKHNGKMGILDLI-------QEGNIGLMKAVDKF 182

Query: 207 SYQKREDSS 215
            Y K    S
Sbjct: 183 DYSKGFKFS 191


>gi|282900289|ref|ZP_06308240.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281194794|gb|EFA69740.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 327

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 164/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++        AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  +G
Sbjct: 82  LKHKISTGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K+ R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L I ++PISL+  +GD   + L + +ED + +SP     Q  LR   
Sbjct: 202 KELELEPAQIREYLNIARQPISLDVRVGDNQDTELQEMLED-HGLSPEHYTTQEFLRHDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  V+ +RFG+    + +L +VG +  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 NNLLAELTPQQREVVILRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQALTHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 SNVKEYV 325



 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S   ++  +   + T D VR YLRE+G + LL+RE EI   K+++ 
Sbjct: 2   STVKKESDNGKTKLTADMVRTYLREIGRVPLLNREQEIIYGKQVQQ 47


>gi|238898782|ref|YP_002924464.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466542|gb|ACQ68316.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 335

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 94/271 (34%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 64  LDATQLYLGEIGYSPLLTAAEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYIN 120

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 121 RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV 180

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 181 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 240

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P ++    +++++  + L  L+ ++  VL  RFG+      TLEEV
Sbjct: 241 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLFELSTKQREVLARRFGLLGYEPATLEEV 300

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G +  +TRER+RQI+ + + +LK   +++ L
Sbjct: 301 GCEIGLTRERVRQIQVEGLLRLKEMLQTQGL 331



 Score = 45.2 bits (105), Expect = 0.040,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
            +   D  ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  
Sbjct: 60  TQRVLDATQLYLGEIGYSPLLTAAEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY- 118

Query: 174 LNDGTTLLREI 184
           +N G  LL  I
Sbjct: 119 INRGLPLLDLI 129


>gi|218245053|ref|YP_002370424.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|218165531|gb|ACK64268.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 375

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 109/298 (36%), Positives = 185/298 (62%), Gaps = 1/298 (0%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +   ++        F+        ++  E++    +   + +                  
Sbjct: 77  LEAQEEIELAYSVQFLVEAEQKRQQLLEELQHPPTKAQWAQAMGFDSQRQFENRLYRGRT 136

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW
Sbjct: 137 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 196

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P  +E+A++L M    +
Sbjct: 197 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRILKQKLQRNPNEKELAQELEMTPPQL 256

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTP 622
           R++L++ ++ +SL   +G  + + L D +ED++   P +   +  LR   + VL+  LT 
Sbjct: 257 RQLLQLRRQSLSLNHRVGKGEDTELVDLLEDQDLQLPEEQMNEGMLRNEISAVLSDVLTE 316

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE+ V+ +R+G+  +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 317 REKDVISLRYGLSTSQPHTLEEVGGMFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 374



 Score = 41.7 bits (96), Expect = 0.42,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            +  DLE  E   +++++  S  +  +  Q         +DD V  + +EM    LL  +
Sbjct: 21  FETGDLEQVEADLEAVEVEFSELSDDLGHQYPPGYRKTVSDDTVGAFFKEMSRYPLLEAQ 80

Query: 138 GEIAIAKRIE 147
            EI +A  ++
Sbjct: 81  EEIELAYSVQ 90


>gi|325686024|gb|EGD28082.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 378

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 119/282 (42%), Positives = 175/282 (62%), Gaps = 10/282 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT- 464
              +R  +K I     +S  E   +   +         AK E+  ANLRLV+S+AK+Y  
Sbjct: 101 YDSVRMYLKEIGKVPLLSRDEEVEVAKRIE---NGDESAKDELAAANLRLVVSIAKRYAK 157

Query: 465 -NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA WW++QAITR++ADQ   IRIPV
Sbjct: 158 HNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPV 217

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG 581
           H+ + I+K+ R  R +   + R+  PEE+A ++  P++ V++++ + K     SL+ P+G
Sbjct: 218 HVVESINKMNRIQRILQQDLDRDAKPEELAAEMNEPLQKVQEIITVAKNQETDSLDKPVG 277

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH 640
           +E  S LGD +ED  A +P +      L++  + ++   LT RE +VL++RFG+  +  H
Sbjct: 278 EEGDSQLGDLLEDNKATNPEEYTAFEMLKDQLSSMMGEFLTNREAKVLKLRFGLENDEPH 337

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+   VTRER+RQIEAKA++KLKH   S  L+ +   
Sbjct: 338 TLEEVGRSLGVTRERVRQIEAKAVKKLKH--HSDLLQDYFSA 377



 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 73/189 (38%), Gaps = 13/189 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +I   ++   +  ++L    L P  ++  +    V   ++ GI++VD       
Sbjct: 15  EKAVKMVITGLKKTKQIREKDLKARLLLPYGLNDAETAKLVEEFADNGISIVDDQGEPSA 74

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +   +         V       S +    D VRMYL+E+G + LLSR+ E+ +AKRI
Sbjct: 75  LALKAEEEAEKKEQKELVA-----SSDNDRVYDSVRMYLKEIGKVPLLSRDEEVEVAKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G       L  + L     I  R   ++G   + ++I        E   G     +  
Sbjct: 130 ENGDESAKDELAAANLRLVVSIAKRYAKHNGKMGILDLI-------QEGNIGLMKAVDKF 182

Query: 207 SYQKREDSS 215
            Y K    S
Sbjct: 183 DYSKGFKFS 191


>gi|220906009|ref|YP_002481320.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219862620|gb|ACL42959.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 372

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 97/250 (38%), Positives = 164/250 (65%), Gaps = 1/250 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++       +AK +M+ +NLRLV+S+AK+Y NRG+ FLDL+QEG +GL +A EKFD  
Sbjct: 122 QQLQIRIYRGQVAKSKMIRSNLRLVVSIAKRYLNRGVPFLDLVQEGALGLNRATEKFDPE 181

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++Q ITR+IA+ S TIR+P+H+ +K++K+ +  R +  +++R PT +E
Sbjct: 182 KGFKFSTYAYWWIRQGITRAIANDSRTIRLPIHIVEKLNKLKKLQRHLKKELQRNPTEQE 241

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L + +E ++ + +  ++ +SL   +G E+ + L D +E  +  SP     +  +R+
Sbjct: 242 LADALEITLEQLQMLQRARQQALSLNRRVGREEDTELLDLLEADSTQSPEKQMGEVMMRQ 301

Query: 612 TTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             +++L   LT +E  V+ +R+G+     +TLEEV   F ++RER+RQI+ KAI KL+  
Sbjct: 302 EISQLLDLVLTKQERDVIILRYGLVSGEPNTLEEVSGLFNLSRERVRQIQNKAIGKLRRS 361

Query: 671 SRSKKLRSFL 680
           + +  LR++L
Sbjct: 362 AIAHHLRNWL 371



 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 8/79 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST--------DDPVRMYLRE 127
            V   + LE      D      +    +V  +   D+    +        DD V  +L++
Sbjct: 9   TVDSPEPLEMHPPLLDPFLDLEAEDPEAVMAELHIDNLAARSSGYRKTGLDDAVGAFLKD 68

Query: 128 MGSIELLSREGEIAIAKRI 146
           M    LL    EI +A+R+
Sbjct: 69  MARYPLLQPSEEIELARRV 87


>gi|282895449|ref|ZP_06303586.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199482|gb|EFA74345.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 327

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 164/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++        AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  +G
Sbjct: 82  LKHKISTGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++ K+ R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L I ++PISL+  +GD   + L + +ED + +SP     Q  LR   
Sbjct: 202 KELELEPAQIREYLNIARQPISLDVRVGDNQDTELQEMLED-DGLSPEHYTTQEFLRHDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  V+ +RFG+    + +L +VG +  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 NNLLAELTPQQREVVTLRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQALTHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 SNVKEYV 325



 Score = 44.4 bits (103), Expect = 0.063,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S   ++  +   + T D VR YLRE+G + LL+RE EI   K+++ 
Sbjct: 2   STVKKESDNGKTKLTADMVRTYLREIGRVPLLNREQEIIYGKQVQQ 47


>gi|257892237|ref|ZP_05671890.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
 gi|257828616|gb|EEV55223.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
          Length = 332

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 129/236 (54%), Positives = 170/236 (72%), Gaps = 3/236 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 100 VRMYLKEIGRVSLLTAEEE---VALALKIEEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 216

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 217 INKLIRIQRQLLQDLGREPTPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 276

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           GDFIED+ A SP + A    L+E    VL +LT REE VLR+RFG+      TLEE
Sbjct: 277 GDFIEDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEE 332



 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 46/191 (24%), Positives = 78/191 (40%), Gaps = 15/191 (7%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
             + +    IK  + +  V  ++L+  L  P  +++++M+  +  + + GI+VVD +   
Sbjct: 9   TYEAAVAAFIKENKPKRQVVYDDLSNQLATPFTLNADEMDKLIQKIEDAGISVVDENGDP 68

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
                + +   A  A    +             +DPVRMYL+E+G + LL+ E E+A+A 
Sbjct: 69  SIHSLKSAEKKAEQAKTEDL-----SAPTGVKINDPVRMYLKEIGRVSLLTAEEEVALAL 123

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           +IE G       L E+ L     I  R  +  G   L  I         E   G     E
Sbjct: 124 KIEEGDQEAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVE 174

Query: 205 GHSYQKREDSS 215
              Y+K    S
Sbjct: 175 KFDYRKGFKFS 185


>gi|297614550|gb|ADI48581.1| putative DNA-directed RNA polymerase sigma 38 subunit [uncultured
           bacterium fss6]
          Length = 322

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 101/277 (36%), Positives = 168/277 (60%), Gaps = 4/277 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
                +   +  +  I     +S  E  H   + RK     + A+  M+E+NLRLV+ +A
Sbjct: 40  NYQKKMDATQLYLSEIGYSPLLSAEEEVHFSRLARK---GDAKARARMIESNLRLVVKIA 96

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           ++YTNRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR
Sbjct: 97  RRYTNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIR 156

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+  +++  +R AR +++ +  EPT E+IA+KL + V  V ++L++ +   S++TP+
Sbjct: 157 LPIHVVKELNSYLRAARELAHTLDHEPTAEDIAEKLDVSVADVSRMLRLNERVTSVDTPM 216

Query: 581 GDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           G  D    L D + D N   P     + ++R+     L +L  ++  VL  RFG+     
Sbjct: 217 GGSDNDKTLVDMLTDDNDYGPEGDMQEEDVRDHIMTWLENLNEKQREVLARRFGLLGYEP 276

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLE+VG++  +TRER+RQI+ +A+R+L+   R + L
Sbjct: 277 ATLEDVGREIGLTRERVRQIQVEALRRLRDMLRQQGL 313



 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  D  DE+        A   S+ +           +   D  ++YL E+G   LLS E 
Sbjct: 6   EDIDEVDEQELLSMEQSAPDDSDEAFEEILANRVNYQKKMDATQLYLSEIGYSPLLSAEE 65

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  ++    G A   A + ES L     I  R   N G  LL  +
Sbjct: 66  EVHFSRLARKGDAKARARMIESNLRLVVKIARRY-TNRGLALLDLV 110


>gi|302869477|ref|YP_003838114.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315504060|ref|YP_004082947.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302572336|gb|ADL48538.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315410679|gb|ADU08796.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 333

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 96/245 (39%), Positives = 166/245 (67%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +   E   AK   + ANLRLV+S+A++Y   G+  LDLIQEGN GL++A EKFD+  G
Sbjct: 88  LERLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERG 147

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++QAI+R+IA Q  T+R+PVH+ + ++++   AR+++ ++  +P PE+IA
Sbjct: 148 FKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIA 207

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L + VE V ++++ +++ +SL+TP+GD+  ++LGD + D +A SP +  +    R+  
Sbjct: 208 TALGVTVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRI 267

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +L  L  R   ++R R+G+    +H+L EV  +F ++RERIRQ+E +A+ +L+  +R+
Sbjct: 268 EGLLNHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARA 327

Query: 674 KKLRS 678
           + L++
Sbjct: 328 EGLQA 332


>gi|41855|emb|CAA78689.1| KatF [Escherichia coli]
          Length = 377

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 46/117 (39%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V+D   L ++E S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVLDEKALVEQEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|90020900|ref|YP_526727.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
 gi|89950500|gb|ABD80515.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
          Length = 333

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 101/277 (36%), Positives = 168/277 (60%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     +S  E    V   RK       ++K M+E+NLRLV+ +
Sbjct: 51  DAYQKNLDATQLYLNEIGFSPLLSAEEE---VFFARKALKGCEASRKRMIESNLRLVVKI 107

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 108 ARRYVNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 167

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +R AR +S K+  EP+PEEIA  L  P+E V ++L + +   S++ P
Sbjct: 168 RLPIHVVKELNVYLRAARELSQKLDHEPSPEEIATLLEKPLEDVERMLALNERVTSMDVP 227

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG      + D + D++   P++   +++L ++    L  L+ ++  V+  RFG+  +  
Sbjct: 228 IGPSSEKTVVDTVADQDVSDPVELLQESDLSQSLDGWLDELSEKQREVVARRFGLRGHET 287

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVGK+  +TRER+RQI+ +A+R+L+     + L
Sbjct: 288 STLEEVGKEIGLTRERVRQIQVEALRRLRDILEKQGL 324



 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 28/120 (23%), Positives = 45/120 (37%), Gaps = 9/120 (7%)

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVF--------LQKRKDSADRSTDDPVRMY 124
             I +   ++ E    +  + D+ S+    S               + A +   D  ++Y
Sbjct: 4   QEIEISRFEEEESIIATGITFDVESAKEPESPTRKRATATRASAESEDAYQKNLDATQLY 63

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L E+G   LLS E E+  A++   G       + ES L     I  R  +N G  LL  I
Sbjct: 64  LNEIGFSPLLSAEEEVFFARKALKGCEASRKRMIESNLRLVVKIARRY-VNRGLALLDLI 122


>gi|253988173|ref|YP_003039529.1| RNA polymerase sigma factor RpoS [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779623|emb|CAQ82784.1| rna polymerase sigma factor (sigma-38) [Photorhabdus asymbiotica]
          Length = 332

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 175/271 (64%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+      +A++ M+E+NLRLV+ ++++Y+N
Sbjct: 57  LDATQLYLGEIGFSPLLTAEEE---VFFARRALRGDVLARRRMIESNLRLVVKISRRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+PEEIA++L  PV+ V ++L++ +  IS++TPI  +  
Sbjct: 174 VKELNVYLRTARELAHKLDHEPSPEEIAEQLDKPVDDVSRMLRLNERIISVDTPISSDSD 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P  +  + +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDVLSDENETGPEGTTQEDDMKKSIVKWLFELNSKQREVLARRFGLLGYEAETLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           GK+  +TRER+RQI+ + +R+LK   +++ L
Sbjct: 294 GKEIGLTRERVRQIQVEGLRRLKDIMQTQGL 324



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 46/117 (39%), Gaps = 9/117 (7%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A L   GI   D D+   + G +D  DL +                ++   D  ++YL E
Sbjct: 15  ADLDESGIEADDFDEKLLKNGEDDLTDLEND--------LDVLQGMNQRVLDATQLYLGE 66

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G  +    + ES L     I  R   N G  LL  I
Sbjct: 67  IGFSPLLTAEEEVFFARRALRGDVLARRRMIESNLRLVVKISRRYS-NRGLALLDLI 122


>gi|158335492|ref|YP_001516664.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158305733|gb|ABW27350.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 327

 Score =  179 bits (454), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 107/249 (42%), Positives = 162/249 (65%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S +     +   AK++M+EANLRLV+SVAKKY  R L+ LDLIQEG +GL +  EKFD  
Sbjct: 80  SQLELSLHQGQQAKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGTLGLERGVEKFDPT 139

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+ +  R +S K+ R  TP E
Sbjct: 140 RGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKAQRELSQKLGRSATPAE 199

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+ L +    +R  L I ++PISL+  +GD   + L D +ED +  SP        LR+
Sbjct: 200 IAEALELEPSQIRDYLTIARQPISLDLRVGDNQDTELRDLLED-DGQSPEQFTTTEALRD 258

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++L  LTP++  VL +RFG+    + +L +VG+Q  ++RER+RQ+E +A+  L+   
Sbjct: 259 DVNQLLKELTPQQRDVLMLRFGLNNGKELSLAKVGQQLSLSRERVRQLERQALDYLRR-- 316

Query: 672 RSKKLRSFL 680
           R  ++R ++
Sbjct: 317 RKGEVREYI 325



 Score = 41.4 bits (95), Expect = 0.58,   Method: Composition-based stats.
 Identities = 15/34 (44%), Positives = 21/34 (61%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             T D VR YL E+G + LL+ E EI   K+++A
Sbjct: 14  SPTTDMVRTYLHEIGRVPLLTHEEEIVFGKQVQA 47


>gi|90416198|ref|ZP_01224130.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90331923|gb|EAS47137.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 306

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 108/265 (40%), Positives = 167/265 (63%), Gaps = 4/265 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++ +E    V   RK       A+K M+E+NLRLV+ +A++Y NRGL+ L
Sbjct: 34  YLKEIGYAPLLTAAEE---VFYARKLLKGDESARKRMIESNLRLVVKIARRYVNRGLELL 90

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGNIGLM+A EKFD  LGY+FSTYA WW++Q I R + +Q+ TIR+PVH+  +++ 
Sbjct: 91  DLIEEGNIGLMRAVEKFDPELGYRFSTYATWWIRQTIERGLMNQTRTIRLPVHIVKELNV 150

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            VR +R+++ ++   PTPEEIA+++  PVE V K+  +++   S++ P+  E+   L + 
Sbjct: 151 YVRASRKLAQRLDHTPTPEEIAEEVDKPVEDVLKIFSLSERISSIDIPV-AENEKSLIET 209

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I  + A SP       NL E   + LA L  ++  VL  RFG+  + + TLE+VG++  +
Sbjct: 210 ISAEGASSPERQVEGENLSEVLNKWLAQLPEKQREVLVRRFGLLHHQEETLEQVGREIGL 269

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQI+  A+R+L+   R   L
Sbjct: 270 TRERVRQIQVDALRRLRDVLRKHGL 294



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 32/93 (34%), Gaps = 1/93 (1%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
              L           Q           D   +YL+E+G   LL+   E+  A+++  G  
Sbjct: 2   ESALKVDIEKVQNDDQGSSSEVSHQVIDATSLYLKEIGYAPLLTAAEEVFYARKLLKGDE 61

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                + ES L     I  R  +N G  LL  I
Sbjct: 62  SARKRMIESNLRLVVKIARRY-VNRGLELLDLI 93


>gi|209695924|ref|YP_002263854.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
 gi|208009877|emb|CAQ80190.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
          Length = 321

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 100/302 (33%), Positives = 170/302 (56%), Gaps = 6/302 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNF---VACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           E D   V   +   + E K+    V+     +   +  +  I     ++  E  +   + 
Sbjct: 12  EFDLDVVDETELTTKTEKKSERLEVSSSQKVMDATQLYLSEIGFSPLLTAEEEVYFSRLA 71

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                    A+  M+E+NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G+
Sbjct: 72  ---LKGDVAARSRMIESNLRLVVKIARRYNHRGLALLDLVEEGNLGLIRAVEKFDPERGF 128

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPEEIA+
Sbjct: 129 RFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPEEIAE 188

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           KL  PV  V ++L++ +   S+++ +  +    L D I D     P       ++ E+  
Sbjct: 189 KLDKPVSDVSRMLRLNERVASVDSMVAGDSDKALLDIIPDTKHADPESETQTNDINESLV 248

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L  L P+++ V+  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+     +
Sbjct: 249 GWLGQLNPKQKEVVARRFGLLGYEASTLEQVGREIGLTRERVRQIQVEGLRRLREIMTQQ 308

Query: 675 KL 676
            L
Sbjct: 309 GL 310



 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 43/101 (42%), Gaps = 2/101 (1%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE   D +D     + +    ++ + S+ +   D  ++YL E+G   LL+ E E+  ++ 
Sbjct: 11  EEFDLDVVDETELTTKTEKKSERLEVSSSQKVMDATQLYLSEIGFSPLLTAEEEVYFSRL 70

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              G     + + ES L    ++      N     L ++++
Sbjct: 71  ALKGDVAARSRMIESNLRL--VVKIARRYNHRGLALLDLVE 109


>gi|254424042|ref|ZP_05037760.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196191531|gb|EDX86495.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 319

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 169/286 (59%), Gaps = 13/286 (4%)

Query: 397 NFVACEVDSILKIRNE---IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
             +    D + +  +    +   +  T +S    +  V            AK +M+ +NL
Sbjct: 40  MKLEAIRDDLTETMDREPTLAEWAEATNLSPEALKKTVE-------IGQQAKDKMMRSNL 92

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKY    L  +DLIQEG++GL +  EKFD   GY+FSTYA WW++QAITR+IA
Sbjct: 93  RLVVSIAKKYRGSKLDMMDLIQEGSLGLCRGVEKFDPLKGYRFSTYAYWWIRQAITRAIA 152

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           D   TIR+P+H+ +K+ K+ +  R +S ++ R  T  E+A+K+++P E VR++ + ++ P
Sbjct: 153 DTGRTIRLPIHINEKLSKIRKAQREVSLELGRPATVSEVAEKVSLPAEKVRELQRQSRLP 212

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL   IG E  + LG  +E  ++ SP + A Q  L+    ++LA LT R++ V+ MRFG
Sbjct: 213 LSLNMRIGSEQNTELGALLE-SDSQSPEEYATQNLLKRDIGQLLARLTERQKDVISMRFG 271

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +      TL ++G    ++RER+RQIE KA+R L+H  R   L+ +
Sbjct: 272 LDDGKKKTLAQIGHDLDISRERVRQIERKALRTLRHTGRG--LKEY 315


>gi|294055548|ref|YP_003549206.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614881|gb|ADE55036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 342

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 105/263 (39%), Positives = 163/263 (61%), Gaps = 3/263 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     ++  E   +   ++KG      A+  M+ ANLRLV+ +A  Y N GL
Sbjct: 47  LRAYMQEIGKTALLTPQEEVELAKRIQKGN---KAARDHMISANLRLVVKIAHDYNNFGL 103

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLI EGNIGL+KA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ DK
Sbjct: 104 PLMDLISEGNIGLVKAVERFDPSKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDK 163

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I  + +    +++++ REPT EEIA  + MPV  V  +  ++  P SL+ P+G++  +  
Sbjct: 164 IAYMRKITAELADELDREPTDEEIAYTMGMPVNKVAHLKSVSVRPSSLDAPVGEDGDTSF 223

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ + D+N  +PL++  + +L      ++A L  RE  ++R+RFG+      TLEEVG+Q
Sbjct: 224 GELVGDENQATPLENLQEKSLSNDMHSMIALLDQREAEIIRLRFGLDGEHPLTLEEVGEQ 283

Query: 649 FCVTRERIRQIEAKAIRKLKHPS 671
           F +TRER+RQI+  AI K++   
Sbjct: 284 FKITRERVRQIQNIAIHKMRRLM 306



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +R Y++E+G   LL+ + E+ +AKRI+ G       +  + L    ++    + N+    
Sbjct: 47  LRAYMQEIGKTALLTPQEEVELAKRIQKGNKAARDHMISANLRL--VVKIAHDYNNFGLP 104

Query: 181 LREIIDLEACIGPESKGGFFHGTEG 205
           L ++I  E  IG       F  ++G
Sbjct: 105 LMDLIS-EGNIGLVKAVERFDPSKG 128


>gi|109900163|ref|YP_663418.1| RNA polymerase, sigma 28 subunit [Pseudoalteromonas atlantica T6c]
 gi|109702444|gb|ABG42364.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudoalteromonas atlantica
           T6c]
          Length = 327

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 104/299 (34%), Positives = 171/299 (57%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +        +    +  +       ++   +  +  I     +S  E    V   R+ 
Sbjct: 22  EKELVKAEKDSEDKFKDIVSSKEAPSKNLDATQLYLGEIGFSPLLSAEEE---VYFSRRA 78

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 +++ M+ +NLRLV+ +A++Y NRGL  LDL++EGN+GL++A EKFD   G++FS
Sbjct: 79  LKGDEASRQRMIVSNLRLVVKIARRYNNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFS 138

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RT+R ++ K+  EPT EEIA+ + 
Sbjct: 139 TYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTSRELAQKLDHEPTAEEIAEAVQ 198

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV  V K+L++ +   S++TPIG E+ + L D I D N   P +     N++ +    L
Sbjct: 199 KPVADVTKMLRLNERITSVDTPIGSENDNVLLDIIADDNGHDPEEDLQDKNVKLSIVGWL 258

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             L P++  VL  RFG+      TLE+VG +  +TRER+RQI+ +A+R+LK     K L
Sbjct: 259 EDLNPKQREVLARRFGLLGYEPSTLEDVGVEIGLTRERVRQIQVEALRRLKDMLGHKGL 317



 Score = 46.0 bits (107), Expect = 0.023,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 38/104 (36%), Gaps = 2/104 (1%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            + EE  E  L  A   S            A     D  ++YL E+G   LLS E E+  
Sbjct: 15  DDIEEAVEKELVKAEKDSEDKFKDIVSSKEAPSKNLDATQLYLGEIGFSPLLSAEEEVYF 74

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           ++R   G       +  S L    ++      N+    L ++++
Sbjct: 75  SRRALKGDEASRQRMIVSNLRL--VVKIARRYNNRGLALLDLVE 116


>gi|113474616|ref|YP_720677.1| RNA polymerase sigma factor [Trichodesmium erythraeum IMS101]
 gi|110165664|gb|ABG50204.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 336

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 103/249 (41%), Positives = 165/249 (66%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  
Sbjct: 89  KVLKQAIKQGQRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPT 148

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+ R  R +   + R PTP E
Sbjct: 149 RGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKRVQRELIQSLGRSPTPSE 208

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+ L +    +R+ L + + PISL+  +GD   + L + +ED+ + SP D      LR+
Sbjct: 209 IAQALELEPSQIREYLLMARHPISLDLRVGDNQDTELQELLEDETS-SPDDYITGELLRQ 267

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +LA L+ ++ RVL +RFG+    + +L +VG +  ++RER+RQ+E +A+  L+   
Sbjct: 268 DINTLLAELSEQQRRVLVLRFGLEDGKEMSLAKVGDKLQLSRERVRQLEHQALAFLRR-- 325

Query: 672 RSKKLRSFL 680
           R  K+R ++
Sbjct: 326 RQAKVREYV 334



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               S+ D VR YL E+G + LL+RE EI   K+++ 
Sbjct: 20  PTTYSSMDTVRTYLHEIGRVPLLTREEEIVYGKQVQQ 56


>gi|149197281|ref|ZP_01874333.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139827|gb|EDM28228.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 404

 Score =  179 bits (453), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 101/242 (41%), Positives = 153/242 (63%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK       +   MVE NLRLVIS+A+KY+N    FLDLIQEGNIGL+ A EK+D   GY
Sbjct: 159 RKSYYRMENSVNAMVEGNLRLVISIARKYSNSQEGFLDLIQEGNIGLVSAVEKYDASFGY 218

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FSTYA WW++QA++R+  +   T+++P ++  K++K+ RT R +  K  RE T +E+++
Sbjct: 219 TFSTYATWWIRQAVSRARTELVRTMKLPANIMVKVNKIYRTERELFQKFGREATIDEVSE 278

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            + +    +R + ++ ++PISL+T + +E T  LGD + + + V P     Q  L E+  
Sbjct: 279 AVELSPAKIRSLKRMCQQPISLQTTVSEEHTGELGDIVSNDDDVLPDAEVEQKQLHESLV 338

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +L  L  RE+ +LRMRFG+     HTLE +  +F ++RERIRQIE  A++KL+ P+  K
Sbjct: 339 AMLDILNEREQEILRMRFGLADGEYHTLENIANEFGISRERIRQIETSALKKLRRPTAVK 398

Query: 675 KL 676
            L
Sbjct: 399 CL 400


>gi|17231292|ref|NP_487840.1| RNA polymerase sigma factor [Nostoc sp. PCC 7120]
 gi|8489801|gb|AAF75758.1|AF262217_2 group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
 gi|17132934|dbj|BAB75499.1| group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
          Length = 327

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 100/247 (40%), Positives = 165/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VKQTVTQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++  + R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQTLGRSPSPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED +  SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVKVGDNQDTELQEMLED-DGPSPEYYTTQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  V+ +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 NTLLAELTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQALAHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 ANVKEYV 325



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCESPLTFQAL 167
           +D+  + T D VR YLRE+G + LL+RE EI   K+++          +L +      +L
Sbjct: 9   EDTNTKFTADMVRTYLREIGRVPLLTREQEIVYGKQVQQMMSLIDAKEALAKKLDREPSL 68

Query: 168 IIWRDELNDGTTLLREII 185
             W D +    T +++ +
Sbjct: 69  PEWADHVQKSETEVKQTV 86


>gi|58257340|gb|AAK30051.2| RpoS sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 92/295 (31%), Positives = 162/295 (54%), Gaps = 3/295 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V           ++       ++   +  +  I     +S  E  H   +    +     
Sbjct: 39  VRTKSKSSASLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPA 95

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 96  GRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 155

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +  AR ++ K+  EP+PEEIA  L  PV  V
Sbjct: 156 IRQTIERAIMNQTRTIRLPIHVVKELNVYLGAARELTQKLDHEPSPEEIANMLEKPVTEV 215

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L + +   S++  +  +    + D + D       +   + +L +   + L+ LT +
Sbjct: 216 KRMLGLNERVSSVDVSLDPDSDKTVLDTLTDDRPTDRCEVLQEDDLSQGIDQWLSELTEK 275

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 276 QREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQIEGLKRLREILEKNGLSS 330



 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 12/136 (8%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+  +P  ++  E +      L    I   D D + + EG+        + S SS  L++
Sbjct: 3   LSKEVPEFDIDDEVL------LMESSI---DMDSMSNNEGATPPS--VRTKSKSSASLKQ 51

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I
Sbjct: 52  HKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 111

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 112 ARRY-VNRGLSLLDLI 126


>gi|149370424|ref|ZP_01890113.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149355975|gb|EDM44532.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 288

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 100/273 (36%), Positives = 167/273 (61%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ +S    I+  E   +   +R        A  ++  ANLR VISVAK+Y N+GL
Sbjct: 18  LNSYLQDVSKIDMITAEEEVELAQRIR---EGDKRALDKLTRANLRFVISVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNKIGD 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSH 587
           I+KV + +  +    +R PT +EIA +L + V  V+  +K +   IS++ P  + E+ ++
Sbjct: 135 INKVKKASIHLQQVYERVPTAQEIANELDITVSSVKSSMKNSNRSISMDAPFQEGENDNN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D I    + +P +  +Q +L+    R L +L+ RE  V+++ FG+  N   TL+E+G 
Sbjct: 195 LYDVISSGESPNPDNGLMQESLKTEIDRALDTLSQREADVVKLNFGLSGNPVMTLQEIGD 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  KAIR+L+H S+S  L  +L
Sbjct: 255 TFDLSRERVRQIREKAIRRLRHESKSHILMKYL 287



 Score = 43.7 bits (101), Expect = 0.095,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I++++ E E+ +A+RI  G    +  L  + L F  +I    +  +    L +
Sbjct: 21  YLQDVSKIDMITAEEEVELAQRIREGDKRALDKLTRANLRF--VISVAKQYQNQGLSLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|115358293|ref|YP_775431.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
 gi|115283581|gb|ABI89097.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 516

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/255 (41%), Positives = 163/255 (63%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +  G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 263 RALGAALSDGQQKVRDGTRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEK 322

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 323 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRA 382

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +P   +R VL +  EP+SL+TP+  +  + L D IED+ + SP +     
Sbjct: 383 TPAELAAESGLPEGKLRAVLALPAEPLSLDTPL-PDAETGLVDLIEDQASASPFERLADT 441

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  T +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 442 RMRECVTSLLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 501

Query: 668 KHPSRSKKLRSFLDG 682
           +  + ++   SFLD 
Sbjct: 502 RTAAEAEGAESFLDA 516



 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 41/151 (27%), Positives = 74/151 (49%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TLRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PASPAPFAGAAPVDVDRDALDEGRALLGDLARGTSASTDPLALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ +L   P    AL+   
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALLARH 157


>gi|6463986|dbj|BAA86958.1| group 2 sigma factor RpoD4 [Synechococcus sp. PCC 7942]
          Length = 311

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 108/276 (39%), Positives = 170/276 (61%), Gaps = 19/276 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGEC------------------EASIAKKEMVEANL 453
            + SI     ++  E   +   V+                          AK +M++ANL
Sbjct: 24  YLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQAVLQAGQRAKTKMLKANL 83

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKK  N+GL+ LDLIQEG++GL +A EKFD  LGYKFSTYA WW++Q++TR+I 
Sbjct: 84  RLVVSVAKKCQNQGLELLDLIQEGSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAID 143

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           + + TIR+P+H+ +KI ++ +  R +++++KR P+  EIA+ L +P++ V  +L  +   
Sbjct: 144 NHARTIRLPIHVSEKISRIKKMTRELTHQLKRLPSRAEIAEALKLPLQDVEMLLSQSTPC 203

Query: 574 ISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            SL+     +D  S LGD I D  ++ P+D+  +    E  +  LA LT RE++VL++RF
Sbjct: 204 TSLDAQARGDDGRSFLGDLIPDPKSLEPMDAMDRHIQHEQISTWLAHLTEREQQVLQLRF 263

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           G+     HTL E+G++  V+RERIRQ+EA+A++KL+
Sbjct: 264 GLHDGEQHTLAEIGRRLNVSRERIRQVEARALQKLR 299



 Score = 40.6 bits (93), Expect = 0.83,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 5/50 (10%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           +R T D V  YL  +G I LL+ E E+ +++++      +M +L E+P  
Sbjct: 14  ERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKV-----QLMMALLENPDA 58


>gi|87301519|ref|ZP_01084359.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283736|gb|EAQ75690.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 322

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/283 (36%), Positives = 162/283 (57%), Gaps = 16/283 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMV---------------RKGECEASIAKK 446
             DSI    + I  + + T     E  H V  +               R        A+ 
Sbjct: 31  SADSIGWYLSNIGRVPLLTAAEEIELAHHVQAMKLLLELPDASLTPRQRHQIRMGGRARD 90

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q
Sbjct: 91  RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 150

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P   E++  + M ++ +  +
Sbjct: 151 GMTRAIDNSARTIRLPIHVSEKLSKMRRITRELSHRFGRQPNRLELSHAMGMDIKDLEDL 210

Query: 567 LKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  +    SL+     E+  S LG+ I D  +  P+D   ++  +E     L+ L  RE+
Sbjct: 211 ISQSAPCASLDAHARGEEDRSTLGELIADPASTEPMDHMDRSIQKEHLGTWLSQLNEREQ 270

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +LR+RFG+      TL E+G++  V+RER+RQ+EAKAI KL+
Sbjct: 271 EILRLRFGLEGKEPLTLAEIGRKINVSRERVRQLEAKAIMKLR 313



 Score = 42.1 bits (97), Expect = 0.30,   Method: Composition-based stats.
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
           LAS  +  +  + + K    R + D +  YL  +G + LL+   EI +A  +       M
Sbjct: 9   LASKKAKPAARVAQPKTGGGRLSADSIGWYLSNIGRVPLLTAAEEIELAHHV-----QAM 63

Query: 155 ASLCESPLT 163
             L E P  
Sbjct: 64  KLLLELPDA 72


>gi|304410159|ref|ZP_07391778.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|307302130|ref|ZP_07581888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
 gi|304351568|gb|EFM15967.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|306914168|gb|EFN44589.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
          Length = 326

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 166/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK     + ++  M+E+NLRLV+ +A++Y
Sbjct: 49  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKALKGCAKSRNRMIESNLRLVVKIARRY 105

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 106 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 165

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT EEIA+KL +    V ++LK+ ++  S++ P+G +
Sbjct: 166 HVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQVSSADVSRMLKLNEKITSVDMPLGGD 225

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D + V P       ++  +  + L  L  ++  VL  RFG+      TLE
Sbjct: 226 NDKALLDILADDDNVGPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG +  +TRER+RQI+ +A+++L+    S+ L
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQGL 318



 Score = 40.6 bits (93), Expect = 0.95,   Method: Composition-based stats.
 Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 2/95 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             +  +S     + ++++     +   D  ++YL E+G   LLS E E+  +++   G A
Sbjct: 25  EKEEVASDLVQELGIEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEEVYFSRKALKGCA 84

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
                + ES L    ++      N+    L ++I+
Sbjct: 85  KSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 117


>gi|148240837|ref|YP_001226224.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849376|emb|CAK24927.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 339

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/283 (37%), Positives = 162/283 (57%), Gaps = 16/283 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMV---------------RKGECEASIAKK 446
             DSI    + I  + + T     E  H V  +               R        A+ 
Sbjct: 48  STDSIGYYLSSIGRVPLLTAAEEIELAHHVQAMKELLDVPEGERTPRQRHRIRMGKRARD 107

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q
Sbjct: 108 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P   E+A  + +    + ++
Sbjct: 168 GMTRAIDNSARTIRLPIHISEKLSKMRRITRELSHRFGRQPNRLELANAMGIEPRDLEEL 227

Query: 567 LKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  +    SL+     E+  S LG+ I D N   P++   ++  +E     L+ L  RE+
Sbjct: 228 ISQSAPCASLDAHARGEEDRSTLGELIPDPNGDEPMEGMDRSIQKEHLGGWLSQLNDREQ 287

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 288 KILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330



 Score = 41.7 bits (96), Expect = 0.46,   Method: Composition-based stats.
 Identities = 21/92 (22%), Positives = 33/92 (35%), Gaps = 8/92 (8%)

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +    +       E  L   S  S+ S       +      R + D +  YL  +G
Sbjct: 1   MGIPLESKAEASKASAVEPVLPATSPRSSGSRTRSASSRASRQTGRLSTDSIGYYLSSIG 60

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            + LL+   EI +A  +       M  L + P
Sbjct: 61  RVPLLTAAEEIELAHHV-----QAMKELLDVP 87


>gi|294141938|ref|YP_003557916.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
 gi|293328407|dbj|BAJ03138.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
          Length = 328

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 101/273 (36%), Positives = 167/273 (61%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 51  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKSLKGCGKSRNRMIESNLRLVVKIARRY 107

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 108 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 167

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR +++K+  EPT EEIA KL +P   V ++LK+ +   S++TP+G +
Sbjct: 168 HVVKELNVYLRTARELAHKLDHEPTAEEIAAKLDLPSSDVSRMLKLNERITSVDTPLGGD 227

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D +   ++V P       ++ ++  + L  L  ++  VL  RFG+      TLE
Sbjct: 228 NDKALLDVLAADDSVGPDYKVQDEDMSKSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 287

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VGK+  +TRER+RQI+ +A+++LK    ++ L
Sbjct: 288 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQGL 320



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 46/131 (35%), Gaps = 9/131 (6%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            + L D   +E               L+++     +   D  ++YL E+G   LLS E E
Sbjct: 15  AEPLVDLSKNESKTQTKKGKKLQEAELEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEE 74

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           +  +++   G       + ES L    ++      N+    L ++I+       E   G 
Sbjct: 75  VYFSRKSLKGCGKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE-------EGNLGL 125

Query: 200 FHGTEGHSYQK 210
               E    ++
Sbjct: 126 IRAVEKFDPER 136


>gi|300112902|ref|YP_003759477.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299538839|gb|ADJ27156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 310

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 87/258 (33%), Positives = 154/258 (59%), Gaps = 3/258 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     ++  E  +   + +KG       +K M+E+NLRLV+ ++++Y NRGL  L
Sbjct: 42  YLSEIGFAPLLTAEEEVYYARLAKKGNSAG---RKRMIESNLRLVVKISRRYMNRGLALL 98

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL+ A EKFD  +G++FSTYA WW++Q I R++ +Q+ T+R+PVH+  +I  
Sbjct: 99  DLIEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHVVKEIKS 158

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R A +++ +++ +P+ EE+A++L  PVE +++V  +     S++T   +     L D 
Sbjct: 159 YQRVANKLAQELEHDPSFEELAQQLDKPVEEIKRVWSLKDNTASMDTGYRNNQEKTLLDA 218

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+ A  P       +++      L+ L  ++  V+  RFG+      TLE+VG+   V
Sbjct: 219 LPDEGAPDPTVLLQNDDMQARLELWLSQLNDKQREVVIRRFGLQGYEPQTLEQVGQAIGV 278

Query: 652 TRERIRQIEAKAIRKLKH 669
           TRER+RQI+ + +++L+ 
Sbjct: 279 TRERVRQIQLETLKRLRR 296



 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 27/109 (24%), Positives = 41/109 (37%), Gaps = 9/109 (8%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++S    +   S +    D   +YL E+G   LL+ E E+  A+  + G +     + ES
Sbjct: 19  STSPENTRESQSLNDHEFDATHLYLSEIGFAPLLTAEEEVYYARLAKKGNSAGRKRMIES 78

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
            L     I  R  +N G  LL  I         E   G  H  E    +
Sbjct: 79  NLRLVVKISRRY-MNRGLALLDLI--------EEGNLGLIHAVEKFDPE 118


>gi|167834949|ref|ZP_02461832.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 301

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 96/241 (39%), Positives = 159/241 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+K+ +RGL   DL+QEGN+GL++A EKF++  G+KFSTYA 
Sbjct: 59  SAATARMAEANLRLVLSIARKHASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYAT 118

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D++ +V + A R+  +     +  E++    +PVE
Sbjct: 119 WWIRQAISRAIADRARTIRVPVHVGDEVRRVRKVADRIERRSGARASLAELSAATGLPVE 178

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R +L + +EP SL  P+G++D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 179 RLRAMLMLPREPRSLNAPLGNDDQAEFGDLVEDASTPSLFDALAHGQMCDVVTSLLKTMS 238

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  Q  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 239 AQEADILRRRFGIGGDEPWSYEQIAAQTGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 298

Query: 682 G 682
            
Sbjct: 299 A 299


>gi|172063054|ref|YP_001810705.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171995571|gb|ACB66489.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 520

 Score =  179 bits (453), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/255 (41%), Positives = 163/255 (63%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +  G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 267 RALGAALSDGQQKIRDGTRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEK 326

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 327 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRA 386

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +P   +R VL +  EP+SL+TP+  +  + L D IED+ + SP +     
Sbjct: 387 TPAELAAETGLPEGKLRAVLALPAEPLSLDTPL-PDAETGLVDLIEDQASASPFERLADT 445

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  T +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 446 RMRECVTSLLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 505

Query: 668 KHPSRSKKLRSFLDG 682
           +  + ++   SFLD 
Sbjct: 506 RTAAEAEGAESFLDA 520



 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 41/151 (27%), Positives = 74/151 (49%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TLRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PAAPAPFAGAAPVDVDRDALDEGRALLGDLARGTSASTDPLALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ +L   P    AL+   
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALLARH 157


>gi|166078602|gb|ABY81278.1| alternative sigma factor S [Listonella anguillarum]
          Length = 332

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 107/277 (38%), Positives = 167/277 (60%), Gaps = 4/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 49  DASTKSLDATQMYLSEIGFSPLLTAQEE---VLYARRSLRGDEAARKRMIESNLRLVVKI 105

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TI
Sbjct: 106 SRRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTI 165

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S K+  EPT EEIA +L  P E V K+L++ +   S++TP
Sbjct: 166 RLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAFQLDKP-EDVSKMLRLNERISSVDTP 224

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG +    L D I D N   P  S    ++RE+    L  L P+++ VL  RFG+     
Sbjct: 225 IGGDGDKALLDIIPDTNNSDPEISTQDDDIRESLLNWLDELNPKQKEVLARRFGLLGYEP 284

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 285 STLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 321



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/112 (27%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIE 132
           +   +  ++ D    ++ L    S S+  V ++  K+  D ST   D  +MYL E+G   
Sbjct: 10  VEEFEDQEIMDSIEVDEELTTTKSQSDDDVQIEDAKEGFDASTKSLDATQMYLSEIGFSP 69

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LL+ + E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  LLTAQEEVLYARRSLRGDEAARKRMIESNLRLVVKISRRYG-NRGLALLDLI 120


>gi|158340411|ref|YP_001521767.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310652|gb|ABW32266.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 86/263 (32%), Positives = 156/263 (59%), Gaps = 5/263 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ ++ I     +S  E  ++   V+        AK+ M+E NLRLV+S+AKK+ NRGL 
Sbjct: 9   QSYLQEIGRYPLLSPEEEINLARQVK---AGNLRAKQRMIECNLRLVVSIAKKHQNRGLP 65

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLIQEGNIGL +A EKFD   G +FSTYA WW+ Q ITR++ +++  IR+P+H+    
Sbjct: 66  LLDLIQEGNIGLSRAVEKFDLNQGCRFSTYAYWWIWQGITRALHNKTKMIRLPIHLNQLH 125

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+ RT  +++ +  R+P+ +E+A  + +    +++ L++++E ISL+  + +     LG
Sbjct: 126 SKIKRTYFQLNQEYGRQPSLDEVAYAMDIDPTHIQEQLQLSQEVISLDKFVSENQGDTLG 185

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + +   ++       +    ++  ++++  L+ R++ ++  RFG+      TL E+ K  
Sbjct: 186 ELVAKDHSSQKYFENL--MNKDELSKLMGHLSERQQFIIGQRFGLEDGQPKTLVEIAKLL 243

Query: 650 CVTRERIRQIEAKAIRKLKHPSR 672
            ++RE IR+IE KA ++LK  ++
Sbjct: 244 DMSREGIRRIEKKAFQQLKKYAQ 266



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           +T D  + YL+E+G   LLS E EI +A++++AG       + E  L     I  + + N
Sbjct: 3   TTPDSTQSYLQEIGRYPLLSPEEEINLARQVKAGNLRAKQRMIECNLRLVVSIAKKHQ-N 61

Query: 176 DGTTLLREI 184
            G  LL  I
Sbjct: 62  RGLPLLDLI 70


>gi|95930284|ref|ZP_01313022.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95133747|gb|EAT15408.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 296

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 103/267 (38%), Positives = 169/267 (63%), Gaps = 3/267 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+  +  I     ++  E R   ++  K E     A+ +M+E+NLRLV+ +AK+Y NRG
Sbjct: 28  AIKYYLHDIQKSKLLTAEEER---ALATKVEAGDEQARAKMIESNLRLVVKIAKRYMNRG 84

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D
Sbjct: 85  LPFLDLIEEGNMGLIKAVERFQVAKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 144

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            ++++++  + +  K+  EP+  +IA+ +  PVE VR++ ++ K+  S+E P+GD D   
Sbjct: 145 NVNRMLKATKEVLKKLNHEPSEAQIAEAMGAPVEEVRRLQQLVKKTYSIEHPLGDNDNYS 204

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +ED + ++P +     +  +   + L+SL   E  +L +RFG+      TL+ +GK
Sbjct: 205 LMDTLEDSSVINPAELLENQDQYDFVNKWLSSLKENERDILMLRFGLNDCEPETLDTIGK 264

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
           ++ VTRERIRQIEAK++ KL+   R +
Sbjct: 265 RYGVTRERIRQIEAKSLDKLRRMMREE 291



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           + S DD ++ YL ++   +LL+ E E A+A ++EAG     A + ES L     I  R  
Sbjct: 22  ETSGDDAIKYYLHDIQKSKLLTAEEERALATKVEAGDEQARAKMIESNLRLVVKIAKRY- 80

Query: 174 LNDGTTLLREI 184
           +N G   L  I
Sbjct: 81  MNRGLPFLDLI 91


>gi|298373668|ref|ZP_06983657.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
 gi|298274720|gb|EFI16272.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
          Length = 287

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 100/273 (36%), Positives = 168/273 (61%), Gaps = 5/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I  E  I+I +   +   +RK       A  ++V ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQEIGREELITIEQEVELAQRIRK---GDHAALDKLVRANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  SLPDLIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNQVGA 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ +  +R   + +R P+ EEIA  L + ++ +   +K++   IS++ P  D + + L
Sbjct: 135 LNKINKAFQRFEQEHERLPSVEEIATDLEISLDKITDTMKVSGRHISVDAPFVDGEDNTL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASL-TPREERVLRMRFGIGMNTDHTLEEVGK 647
            D + + ++ +     +  +L     R L +L   RE  +++M FGIG     TLEE+G 
Sbjct: 195 LDVLMNDSSPATDQKLMSESLLTEIERALDALLQERERDIVKMFFGIGCAE-MTLEEIGD 253

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           QF +TRER+RQI+ KAIR+L+  S++K L+ +L
Sbjct: 254 QFGLTRERVRQIKEKAIRRLRGNSKNKLLKVYL 286



 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K   S      D +  YL+E+G  EL++ E E+ +A+RI  G    +  L  + L F  +
Sbjct: 5   KIAPSITNRESDSLDKYLQEIGREELITIEQEVELAQRIRKGDHAALDKLVRANLRF--V 62

Query: 168 IIWRDELNDGTTLLREIID 186
           +    +  +    L ++ID
Sbjct: 63  VSVAKQYQNQGLSLPDLID 81


>gi|220934609|ref|YP_002513508.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219995919|gb|ACL72521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 344

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 95/270 (35%), Positives = 161/270 (59%), Gaps = 3/270 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +   R  +  I     ++  E  H   + +K        +++M+E NLRLV+ +A++Y 
Sbjct: 68  ELDATRLYLSEIEFSPLLTPEEEVHYARLAQK---GDEAGRRKMIECNLRLVVKIARRYM 124

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H
Sbjct: 125 NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIH 184

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +RTAR+++ ++  EPT EE+A+ L  PV  V+++L +++   S++ PIG + 
Sbjct: 185 VIKELNVYLRTARKLAQELDHEPTAEEVARHLDRPVGDVKRILALSERVTSVDLPIGKDG 244

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D I D+    P       ++ +     L  L  ++  V+  RFG+      TLE+
Sbjct: 245 ERALLDVIPDEQTPEPSILIQDEDVVQFVDEWLQELDEKQREVIVRRFGLHGYERSTLEQ 304

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           VG +  VTRER+RQI+  A+++L+    S+
Sbjct: 305 VGAELGVTRERVRQIQMDALKRLRKILESR 334



 Score = 43.3 bits (100), Expect = 0.12,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 47/131 (35%), Gaps = 6/131 (4%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  E+  E  ED +     +G    D D+        + +D      + +  +    D  
Sbjct: 10  PAGELEDEIREDKLEAPDELG----DEDEALVLADETEDVDEEEEDEDPATKVYAAGDVP 65

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  R+YL E+    LL+ E E+  A+  + G       + E  L     I  R  
Sbjct: 66  KGEL-DATRLYLSEIEFSPLLTPEEEVHYARLAQKGDEAGRRKMIECNLRLVVKIARRY- 123

Query: 174 LNDGTTLLREI 184
           +N G  LL  I
Sbjct: 124 MNRGLALLDLI 134


>gi|167469361|ref|ZP_02334065.1| RNA polymerase sigma factor RpoS [Yersinia pestis FV-1]
          Length = 277

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 99/265 (37%), Positives = 171/265 (64%), Gaps = 3/265 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E    V   R+       +++ M+E+NLRLV+ +A++Y+NRGL  L
Sbjct: 8   YLGEIGYSPLLSAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYSNRGLALL 64

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++ 
Sbjct: 65  DLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNV 124

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
            +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L D 
Sbjct: 125 YLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDI 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++  +
Sbjct: 185 LSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGL 244

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQI+ + +R+L+   +++ L
Sbjct: 245 TRERVRQIQVEGLRRLREILQTQGL 269



 Score = 41.4 bits (95), Expect = 0.53,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +YL E+G   LLS E E+  A+R   G       + ES L     I  R   N G  LL 
Sbjct: 7   LYLGEIGYSPLLSAEEEVYFARRALRGDVSSRRRMIESNLRLVVKIARRYS-NRGLALLD 65

Query: 183 EI 184
            I
Sbjct: 66  LI 67


>gi|300868245|ref|ZP_07112876.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
 gi|300333769|emb|CBN58060.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
          Length = 319

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 108/266 (40%), Positives = 168/266 (63%), Gaps = 10/266 (3%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             +   G+S +E        ++       AK+ MVEANLRLV+SVAKKY  R +  LDLI
Sbjct: 62  EWAEAAGLSETEL-------QRTIHAGERAKRMMVEANLRLVVSVAKKYIKRNVDLLDLI 114

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +
Sbjct: 115 QEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKK 174

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R ++ K+ R  T  E+A +L +  + +R+ L+  + P+SL+  +GD   + LGD +ED
Sbjct: 175 AQRYLAQKLGRAATANELAAELELTPKQIREYLERARLPLSLDLRVGDNQDTELGDLLED 234

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A SP D A+QA+LR     ++A LT ++  VL +RFG+      TL ++G +  ++RE
Sbjct: 235 TGA-SPEDFALQASLRADLEMLMADLTQQQREVLALRFGLEDGQTLTLSKIGDRLNISRE 293

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+RQIE +A+ KL+   R + +  +L
Sbjct: 294 RVRQIEREALTKLRK--RKQDMDDYL 317



 Score = 44.4 bits (103), Expect = 0.064,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLC 158
                S  D VR YLRE+G + LL+ E EI   K+++          +L 
Sbjct: 2   KPPKSSDTDSVRAYLREIGRVPLLTHEQEILYGKQVQRTTALHEAKNALA 51


>gi|124024683|ref|YP_001018990.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123964969|gb|ABM79725.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 344

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 99/253 (39%), Positives = 158/253 (62%), Gaps = 2/253 (0%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +++  + + E  H     R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QE
Sbjct: 84  AMKELLELPEQDHTPRQ-RHKIRMGKRARDRMMSANLRLVVSVAKKYQNQGLELLDLVQE 142

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +
Sbjct: 143 GAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRIS 202

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDK 595
           R +S++  R+P   E+A  + +  + +  ++  +    SL+     E+  S LG+ I D 
Sbjct: 203 RELSHRFGRQPNRLELAHAMGIQPQDLEDLIAQSAPCASLDAHARGEEDRSTLGELIPDP 262

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           N   P++   ++  +E     L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER
Sbjct: 263 NGAEPMEGLDRSIQKEHLGGWLSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRER 322

Query: 656 IRQIEAKAIRKLK 668
           +RQ+EAKAI KL+
Sbjct: 323 VRQLEAKAILKLR 335



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             ++     S+   + A+ A  +    + +     R   D +  YL  +G + LL+   E
Sbjct: 16  SSEVVLPSTSKQPSEKANRAGRNGQTSRNQNRQGGRLGTDAIGFYLSSIGRVPLLTAAEE 75

Query: 140 IAIAKRIEAGRAMMMASLCESP 161
           I +A  +       M  L E P
Sbjct: 76  IELAHHV-----QAMKELLELP 92


>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 548

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 90/369 (24%), Positives = 182/369 (49%), Gaps = 13/369 (3%)

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           E++  +  +  L +   +  V +  +I      +    ++   + G      L       
Sbjct: 184 EEVKTVRSTRRLERQSKNRRVTKTKEIFHEPYSSRRAGVQKKINEGFDPKDPLRLF---- 239

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN--EIKSISVETGISISEFRHIVSM--- 433
               W    K     + ++ +  +V  ++ + N  E   +      ++ E+   V +   
Sbjct: 240 ---LWGPETKQLLTAKEESELIGQVQDLMSLENVKEKFKLQFGRDPTLVEWADAVGLSYS 296

Query: 434 -VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            ++      + ++++++ ANLR+V+ +AK+Y  RGL   DL+QEG++GLMK+ EKF   +
Sbjct: 297 VMQSQLHSGNRSREKLINANLRMVVHIAKQYQGRGLSLQDLLQEGSMGLMKSIEKFKPQV 356

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F+TYA WW++Q + ++I   S TIR+P ++   + KV    R    +    PT EE+
Sbjct: 357 GCRFATYAYWWIRQTVRKAIFQHSRTIRLPENVYHTLGKVSEAKRSYIMEGNHNPTKEEL 416

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK++ +    + ++L + + P+S++  +  +  +   +   D     P     +  +R+ 
Sbjct: 417 AKRIGITTVRLERLLYMARMPLSMQQTVWADQETTFQEITADIEVEIPELCVAKQLMRKH 476

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +L  L PRE +++R+R+GI      +L E+G  F +++ER+RQ+E++A+ KLK    
Sbjct: 477 VLSLLNILNPRERKIIRLRYGIEDGKKKSLSEIGSVFGLSKERVRQLESRALYKLKQCLA 536

Query: 673 SKKLRSFLD 681
           S  L ++ D
Sbjct: 537 SHGLEAYAD 545


>gi|332708935|ref|ZP_08428906.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352477|gb|EGJ32046.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 333

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/249 (41%), Positives = 170/249 (68%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++K   + + AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD  
Sbjct: 86  AELKKAIDQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPT 145

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA Q+  IR+P+H+ +K++K+ +  R +S  + R  TP E
Sbjct: 146 RGYKFSTYAYWWIRQAITRAIAQQARAIRLPIHITEKLNKIKKVQRELSQTLGRNATPTE 205

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IAK+L +    +R+ L I ++PISL+  +GD   + L + +ED + ++P++   Q +LR+
Sbjct: 206 IAKELDLEPAQIREYLSIARQPISLDVRVGDNQDTELSELLED-DGLTPVNYTTQESLRQ 264

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +LA LTP++  VL +RFG+    + +L +VGK+  ++RER+RQ+E +A+ +L+   
Sbjct: 265 DLNLLLAELTPQQREVLALRFGLEDGKELSLAKVGKRLNLSRERVRQLEHQALAQLRR-- 322

Query: 672 RSKKLRSFL 680
           R    R ++
Sbjct: 323 RHANFREYI 331



 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA-----GRAMMMASLCESPLTFQALIIWR 171
           + D VR YL E+G + LL+ E EI   K+++      G    +A   E   T +    W 
Sbjct: 22  SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMALLGEKATLAQELEREPTTEE---WA 78

Query: 172 DELNDGTTLLREIID 186
             +N     L++ ID
Sbjct: 79  SYVNKSEAELKKAID 93


>gi|119489578|ref|ZP_01622338.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454490|gb|EAW35638.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 319

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/267 (39%), Positives = 170/267 (63%), Gaps = 10/267 (3%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
              +   G+S+ E +  +        +   AK++MVEANLRLV+SVAKKY  R +  LDL
Sbjct: 61  AEWAENAGVSLKELKQALE-------DGQTAKRKMVEANLRLVVSVAKKYIKRNVDLLDL 113

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ 
Sbjct: 114 IQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIK 173

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  R ++  + R  T  E+A +L +  + +R+ L+  + P+SL+  +GD   + LGD +E
Sbjct: 174 KAQRSLAQDLGRAATIAELADELDLNPKQIREYLERARLPLSLDLRVGDNQDTELGDLLE 233

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D  A SP D A+Q+++R     ++A LT ++ +VL +RFG+      TL ++G +  ++R
Sbjct: 234 DDGA-SPEDYALQSSMRSDLEVLMADLTDQQRQVLALRFGLENGQTMTLAKIGDRLNISR 292

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ER+RQIE +A+ KL+   R + +  +L
Sbjct: 293 ERVRQIEREALTKLRK--RKQDMGDYL 317



 Score = 41.7 bits (96), Expect = 0.40,   Method: Composition-based stats.
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            D VR YLRE+G + LL+ E EI   K+++ 
Sbjct: 9   TDSVRTYLREIGRVPLLTHEQEILYGKQVQQ 39


>gi|186684216|ref|YP_001867412.1| RNA polymerase sigma factor [Nostoc punctiforme PCC 73102]
 gi|186466668|gb|ACC82469.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 327

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 165/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VQQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++  + R PTP EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQTLGRSPTPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED +  SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVKVGDNQDTELQEMLED-SGPSPEYYTNQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  VL +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 NNLLAELTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQALAHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 ANVQEYV 325



 Score = 46.0 bits (107), Expect = 0.024,   Method: Composition-based stats.
 Identities = 17/42 (40%), Positives = 26/42 (61%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + ++   R T D VR YLRE+G + LL+RE EI   K+++ 
Sbjct: 6   TQTENLNTRFTADMVRTYLREIGRVPLLTREQEIVYGKQVQQ 47


>gi|269101863|ref|ZP_06154560.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161761|gb|EEZ40257.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 333

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 103/302 (34%), Positives = 177/302 (58%), Gaps = 4/302 (1%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI-RNEIKSISVETGISISE 426
           D  +E   G  ++    + A D    E  +    +   +L   +  +  I     ++  E
Sbjct: 16  DDEIELDTGDAVNAKNTATADDDSAEELSSGSNNQAQKVLDATQLYLGEIGFSPLLTAEE 75

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               V   R+      +A+K M+E+NLRLV+ ++++Y+NRGL  LDL++EGN+GL++A E
Sbjct: 76  E---VLYARRALRGDDVARKRMIESNLRLVVKISRRYSNRGLALLDLVEEGNLGLIRAVE 132

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  E
Sbjct: 133 KFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELAQKLDHE 192

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT E+IA +L  PV+ V ++L++ +   S++ PI  +    L D I D+   +P  S   
Sbjct: 193 PTAEDIAIQLEKPVDDVNRMLRLNERVSSVDNPISGDADKALLDIIPDEKGGTPEVSTQT 252

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +++ +    L  L P++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+
Sbjct: 253 DDIKSSIVDWLDELNPKQREVLARRFGLLGYEASTLEDVGREIGLTRERVRQIQVEGLRR 312

Query: 667 LK 668
           L+
Sbjct: 313 LR 314



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 47/107 (43%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +   D   + ++ + A++  +S+  L    ++  +   D  ++YL E+G   LL+ E
Sbjct: 15  FDDEIELDTGDAVNAKNTATADDDSAEELSSGSNNQAQKVLDATQLYLGEIGFSPLLTAE 74

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G  +    + ES L     I  R   N G  LL  +
Sbjct: 75  EEVLYARRALRGDDVARKRMIESNLRLVVKISRRYS-NRGLALLDLV 120


>gi|170765845|ref|ZP_02900656.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
 gi|170124991|gb|EDS93922.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
          Length = 434

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 109/349 (31%), Positives = 196/349 (56%), Gaps = 14/349 (4%)

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF------ 390
            L   +    + I  N   ++++A+ YG +    L+  +  E +   +   + F      
Sbjct: 83  ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIE--EGNLGLIRAVEKFDPERGF 140

Query: 391 ---PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                  W      E   + + R  +  I     ++  E    V   R+       +++ 
Sbjct: 141 RFSTYATWWIRQTIERAIMNQTRTYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRR 197

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 198 MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 257

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 258 IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 317

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 318 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 377

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 378 LARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 426



 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/114 (39%), Positives = 71/114 (62%), Gaps = 3/114 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ T 
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTY 165



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|220907004|ref|YP_002482315.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7425]
 gi|219863615|gb|ACL43954.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 327

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/242 (42%), Positives = 162/242 (66%), Gaps = 3/242 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK++M+EANLRLV+SVAKKY  R L+ LDLIQEG +GL +  EKFD   GYKFST
Sbjct: 87  RRGQRAKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGTLGLERGVEKFDPTRGYKFST 146

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA Q+ T+R+P+H+ +K++K+ +  R +S ++ R  TP EIA++L +
Sbjct: 147 YAYWWIRQAITRAIAQQARTVRLPIHITEKLNKIKKAQRVLSQRLGRSATPAEIAQELEL 206

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               +R+ L + ++P+SL+  +GD   + L D +ED ++ SP        LR+    +LA
Sbjct: 207 EPSQIREYLTLARQPVSLDLRVGDNQDTELRDLLED-DSPSPEQYTTGEALRDDVNHLLA 265

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTP++  VL +RFG+    + +L +VG+Q  ++RER+RQ+E +A+  L+   R  ++R 
Sbjct: 266 ELTPQQREVLTLRFGLEDGKELSLAKVGEQLSLSRERVRQLERQALDHLRR--RKLQVRE 323

Query: 679 FL 680
           +L
Sbjct: 324 YL 325



 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 15/46 (32%), Positives = 24/46 (52%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S    K +      + D VR YL E+G + LL+ E EI + K+++ 
Sbjct: 2   STLKTKTQTRDSMVSTDMVRTYLHEIGRVPLLTHEQEIVLGKQVQQ 47


>gi|75908126|ref|YP_322422.1| RNA polymerase sigma factor [Anabaena variabilis ATCC 29413]
 gi|75701851|gb|ABA21527.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 327

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 100/247 (40%), Positives = 165/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V++   +   AK++M+EANLRLV+++AKKY  R ++FLDLIQEG +GL +  EKFD   G
Sbjct: 82  VKQTVTQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRG 141

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q  TIR+P+H+ +K++K+ +  R ++  + R P+P EIA
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQTLGRSPSPAEIA 201

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L +    +R+ L + ++P+SL+  +GD   + L + +ED+   SP     Q  LR+  
Sbjct: 202 KELELEPAQIREYLNMARQPVSLDVKVGDNQDTELQEMLEDE-GPSPEYYTTQEFLRQDL 260

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +LA LTP++  V+ +RFG+    + +L +VG++  ++RER+RQ+E +A+  L+   R 
Sbjct: 261 NTLLAELTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQALAHLRR--RR 318

Query: 674 KKLRSFL 680
             ++ ++
Sbjct: 319 ANVKEYV 325



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCESPLTFQAL 167
           +D+  + T D VR YLRE+G + LL+RE EI   K+++          +L +      +L
Sbjct: 9   EDTNTKFTADMVRTYLREIGRVPLLTREQEIVYGKQVQQMMSLIDAKEALAKKLDREPSL 68

Query: 168 IIWRDELNDGTTLLREII 185
             W D +    T +++ +
Sbjct: 69  PEWADHVQKSETEVKQTV 86


>gi|391964|gb|AAA03294.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 362

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 94/271 (34%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGKIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RT R +S+K+  EP+  EIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTVRELSHKLDYEPSAVEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  V+  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVIARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVQGLRRLREILQTQGL 334



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +  L            D  ++YL +
Sbjct: 27  AEFDENGVEVFDEKPLVEEEPSDNYLAEEELLSQGATQL----------VLDATQLYLGK 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|126659670|ref|ZP_01730799.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126619015|gb|EAZ89755.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 369

 Score =  178 bits (452), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 181/285 (63%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    ++  ++R E++    +     +                  AK++M+ +NLRLV
Sbjct: 84  QFLVQAEETRQQLREELQRPPTKAEWGQAMGFETQKQFEHRLHRGRTAKRKMIRSNLRLV 143

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 144 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 203

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +R++L++ ++ +SL
Sbjct: 204 RTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVSPSQLRQLLQLRRQSLSL 263

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED+    P +   +  LR   + VL+  LT RE+ V+ +R+G+ 
Sbjct: 264 NHRVGKGEDTELVDLLEDQELQLPEELMNEGMLRYEVSAVLSDVLTQREKDVISLRYGLC 323

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 324 TAQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 368



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 6/90 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++  +LE  E    S+++  S+ +  +  Q  +      +DD V  + +EM    LL+ +
Sbjct: 15  IEAGELEQTENELQSVEVEISSLSDELGNQYPEGYRKTVSDDTVGAFFKEMSRYPLLNAQ 74

Query: 138 GEIAIAKRI------EAGRAMMMASLCESP 161
            E+ +A  +      E  R  +   L   P
Sbjct: 75  EEVELANHVQFLVQAEETRQQLREELQRPP 104


>gi|104774138|ref|YP_619118.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423219|emb|CAI98047.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125917|gb|ADY85247.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 378

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 116/282 (41%), Positives = 172/282 (60%), Gaps = 10/282 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT- 464
              +R  +K I     +S  E   +   ++        AK E+  ANLRLV+S+AK+Y  
Sbjct: 101 YDSVRMYLKEIGKVPLLSRDEEVEVAKRIK---NGDESAKDELAAANLRLVVSIAKRYAK 157

Query: 465 -NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N  +  LDLIQEGNIGLMKA +KFD+  G+KFSTYA WW++QAITR++ADQ   IRIPV
Sbjct: 158 HNGKMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPV 217

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG 581
           H+ + I+K+ R  R +   + R   PEE+A ++  P++ V++++ + K     SL+  +G
Sbjct: 218 HVVESINKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQKVQEIITVAKNQETDSLDKSVG 277

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH 640
           +E  S LGD +ED  A++P +      L++  + ++   LT RE +VL++RFG+     H
Sbjct: 278 EEGDSQLGDLLEDNKAINPEEYTAFEMLKDQLSGMMGEFLTDREAKVLKLRFGLENYEPH 337

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           TLEEVG+   VTRER+RQIE KA++KLK    S  L+ +   
Sbjct: 338 TLEEVGRSLGVTRERVRQIEDKAVKKLKQ--HSDLLQDYFSA 377



 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/189 (21%), Positives = 72/189 (38%), Gaps = 13/189 (6%)

Query: 28  DDSWKKMIKLARQRGYVTIEEL-NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           + + K +I   ++   +  ++L    L P  ++  +    V   ++ GI++VD       
Sbjct: 15  EKAVKMVITGLKKTKRIREKDLKARLLLPYGLNDAETAKLVEEFADNGISIVDDQGEPSA 74

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
              +   +                 S +    D VRMYL+E+G + LLSR+ E+ +AKRI
Sbjct: 75  LALKAEEEAEKKEQKELAA-----SSDNDQVYDSVRMYLKEIGKVPLLSRDEEVEVAKRI 129

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           + G       L  + L     I  R   ++G   + ++I        E   G     +  
Sbjct: 130 KNGDESAKDELAAANLRLVVSIAKRYAKHNGKMGILDLI-------QEGNIGLMKAVDKF 182

Query: 207 SYQKREDSS 215
            Y K    S
Sbjct: 183 DYSKGFKFS 191


>gi|72383143|ref|YP_292498.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002993|gb|AAZ58795.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 340

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 95/256 (37%), Positives = 155/256 (60%), Gaps = 1/256 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +         +  +        A+  M+ ANLRLV+SVAKKY N+GL+ LDL
Sbjct: 76  HHVQQMKDLLNLPLEERSTRQKHKIKMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDL 135

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ 
Sbjct: 136 VQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMR 195

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFI 592
           R +R +S++  R+P   E+A  + +  + +  ++  +    SL+     E+  S LG+ I
Sbjct: 196 RISRELSHRFGRQPNRLELANAMGIEPQDLEDLVSQSAPCASLDAHARGEEDRSTLGELI 255

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D N+  P++   ++  +E     L+ L  RE++++R+RFG+      TL E+G+Q  V+
Sbjct: 256 PDPNSDEPMEGMDRSIQKEHLGGWLSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVS 315

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ+EAKAI KL+
Sbjct: 316 RERVRQLEAKAILKLR 331



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 26/153 (16%), Positives = 54/153 (35%), Gaps = 6/153 (3%)

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST----DDPVRMYLREM 128
           MGI +    ++ D    + +    S   ++S    ++  S+ R +     D +  YL  +
Sbjct: 1   MGIPLESAKEISDVSSGKSNSASTSQKLSASTVSSQKSRSSRRQSNRLATDAIGFYLTSI 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL--LREIID 186
           G + LL+   EI +A  ++  + ++   L E     +  I       D      LR ++ 
Sbjct: 61  GRVPLLTPAEEIELAHHVQQMKDLLNLPLEERSTRQKHKIKMGKRARDRMMAANLRLVVS 120

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           +      +         EG    +R     +  
Sbjct: 121 VAKKYQNQGLELLDLVQEGAIGLERAVDKFDPA 153


>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila]
          Length = 547

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 93/303 (30%), Positives = 169/303 (55%), Gaps = 12/303 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGI--------SISEFRHIVSM----VRKGE 438
           PE +       E + I  I++ IK   V+T +        +I E+   + +    ++   
Sbjct: 242 PETKQLLTAKEEAELIAHIQHLIKLEKVKTKLESQNGCEPTIGEWAEAMGLSSPVLKSEI 301

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+T
Sbjct: 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q+I +SI   S TIR+P ++   + KV    +         P+ E++A  + +
Sbjct: 362 YAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCIQDGNYRPSKEQLASHVGV 421

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E + K+L  T+ P+S++ PI  +  +   +   D    +P  S  +  +R     +L 
Sbjct: 422 STEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEVTPDSGIETPSMSVGKQLMRNHVRNLLN 481

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+P+E+R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L +
Sbjct: 482 VLSPKEKRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMSSHGLNA 541

Query: 679 FLD 681
           + D
Sbjct: 542 YAD 544


>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa]
 gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa]
          Length = 535

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 83/250 (33%), Positives = 150/250 (60%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++      + ++++++ ANLR+V+ +AK+Y NRGL   DL+QEG +GLMK+ EKF   
Sbjct: 283 HVLKLQLHSGNRSREKLINANLRMVVHIAKRYQNRGLGLQDLLQEGTVGLMKSIEKFKPQ 342

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F+TYA WW++Q IT++I   S TIR+P ++   + KV+   R    +   +PT EE
Sbjct: 343 AGCRFATYAYWWIRQTITKAIFQHSRTIRLPENVYGLLGKVMEAKRSYIQEGNHQPTAEE 402

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+++ + ++ + K+L  T+ P+S++  +  +  +   +   D     P  S  +  +R+
Sbjct: 403 IARRVGIAIDKLEKLLCFTRTPLSMQQTVWSDQNTTFQEITADTEIEIPDMSVAKQLMRK 462

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L+ +E R++R+RFGI      +L E+G  F +++ER+RQ+E++A+ KLK   
Sbjct: 463 HIRGLLNILSLKERRIIRLRFGIEDGKQKSLSEIGNVFGLSKERVRQLESRALYKLKQCV 522

Query: 672 RSKKLRSFLD 681
            S  L ++ D
Sbjct: 523 GSHGLDAYAD 532


>gi|134293382|ref|YP_001117118.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
 gi|134136539|gb|ABO57653.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 518

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/255 (40%), Positives = 165/255 (64%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +R G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 265 RALGAALRDGQQKLGDGTRAMLEANLRLVLSIARKYVNRGVDLPDLVQDGCLGLMRAIEK 324

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 325 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQSQRVQRHALRFRQRHGRRA 384

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A    +  + +R +L +  EP+SL+TP+  +  + L D IED+ + SP +     
Sbjct: 385 TPAELAADTGLAEDKLRALLALPAEPLSLDTPL-PDAETGLVDLIEDQTSASPFERLANT 443

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  + +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 444 RMRECVSSLLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 503

Query: 668 KHPSRSKKLRSFLDG 682
           +  ++++  +SFLD 
Sbjct: 504 RTAAQAEGAQSFLDA 518



 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 42/151 (27%), Positives = 75/151 (49%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++  A ++GY+T  +L   LPPD  S++ +E   A L+++GI+V+D 
Sbjct: 7   TLRADTPLDPIIQLLARAGEQGYLTHADLVDALPPDSDSADALEVVRAALADIGIDVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+     + S  L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PAAPAPFVGTTPVDVDRDTLDESRALLGDLARGASASTDPMALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ +L   P    AL+   
Sbjct: 127 VLAREIETGRHQILHALAGYPPAVDALLARH 157


>gi|56750866|ref|YP_171567.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 6301]
 gi|56685825|dbj|BAD79047.1| group2 RNA polymerase sigma factor RpoD3 [Synechococcus elongatus
           PCC 6301]
          Length = 326

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 100/280 (35%), Positives = 173/280 (61%), Gaps = 7/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVA 460
            + ++R  ++S   +   S  E+       +  +R+ +     AK++M+EANLRLV+SVA
Sbjct: 48  KLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVA 107

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR
Sbjct: 108 KKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIR 167

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R++S ++ R  T  E+A  L +    VR  L+  + P+SL+  +
Sbjct: 168 LPIHITEKLNKIKKMQRQLSQQLGRTATLPELAAALDLTPAQVRDYLEKARHPLSLDLRV 227

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD   + LGD +E  +  +P +  +QA++R    R+L  LT ++ +V+ +R+G+      
Sbjct: 228 GDNQDTELGDLLE-TDCTTPEEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVM 286

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL  +G +  ++RER+RQ+E +A+  L+      +++ +L
Sbjct: 287 TLASIGDRLQISRERVRQLEREALHTLRQA--RSQVQEYL 324



 Score = 44.8 bits (104), Expect = 0.052,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 23/36 (63%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  T D VR YLRE+G + LL+ E E+ + KR++ 
Sbjct: 10  TETPTSDLVRTYLREIGRVPLLTHEEEVVLGKRVQQ 45


>gi|124026883|ref|YP_001015998.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961951|gb|ABM76734.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 340

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 95/256 (37%), Positives = 155/256 (60%), Gaps = 1/256 (0%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +         +  +        A+  M+ ANLRLV+SVAKKY N+GL+ LDL
Sbjct: 76  HHVQQMKDLLNLPLEERSTRQKHKIKMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDL 135

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ 
Sbjct: 136 VQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMR 195

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFI 592
           R +R +S++  R+P   E+A  + +  + +  ++  +    SL+     E+  S LG+ I
Sbjct: 196 RISRELSHRFGRQPNRLELANAMGIEPQDLEDLVSQSAPCASLDAHARGEEDRSTLGELI 255

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D N+  P++   ++  +E     L+ L  RE++++R+RFG+      TL E+G+Q  V+
Sbjct: 256 PDPNSDEPMEGMDRSIQKEHLGGWLSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVS 315

Query: 653 RERIRQIEAKAIRKLK 668
           RER+RQ+EAKAI KL+
Sbjct: 316 RERVRQLEAKAILKLR 331



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 27/153 (17%), Positives = 56/153 (36%), Gaps = 6/153 (3%)

Query: 73  MGINVVDGDDLED----EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           MGI +    ++ D    +  S  +    S+++ SS   +  +  ++R   D +  YL  +
Sbjct: 1   MGIPLESAKEISDVSLGKSNSASTSQKLSASTVSSQKSRSSRRQSNRLATDAIGFYLTSI 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL--LREIID 186
           G + LL+   EI +A  ++  + ++   L E     +  I       D      LR ++ 
Sbjct: 61  GRVPLLTPAEEIELAHHVQQMKDLLNLPLEERSTRQKHKIKMGKRARDRMMAANLRLVVS 120

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
           +      +         EG    +R     +  
Sbjct: 121 VAKKYQNQGLELLDLVQEGAIGLERAVDKFDPA 153


>gi|123967121|ref|YP_001012202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201487|gb|ABM73095.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 339

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 100/248 (40%), Positives = 153/248 (61%), Gaps = 2/248 (0%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I E     S  R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL
Sbjct: 84  LKIPEI-ERSSRNRHLIKVGKRARDRMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGL 142

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S 
Sbjct: 143 ERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRVSRELSQ 202

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSP 600
           K  R+PT  E+A  + +  + +  ++  +    SL+     E+  S LG+ I D N   P
Sbjct: 203 KSGRQPTRLEMATAMGIDQKDLEDLISQSAPCASLDAHARGEEDRSTLGELIPDPNGEEP 262

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           ++   +   +E     L  L  RE++++++RFG+      TL E+G+Q  V+RER+RQ+E
Sbjct: 263 MEGMDRTIQKEHLGTWLTQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLE 322

Query: 661 AKAIRKLK 668
           AKAI KL+
Sbjct: 323 AKAILKLR 330



 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 22/122 (18%), Positives = 44/122 (36%), Gaps = 2/122 (1%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
           + SS+  ++ +  + R   D +  YL  +G + LL+   EI +A  ++  + M+     E
Sbjct: 31  TKSSLSAKQSQKKSARLASDSIGYYLSSIGRVPLLTAAEEIELAHHVQNMKKMLKIPEIE 90

Query: 160 SPLTFQALIIWRDELNDGTTL--LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
                + LI       D      LR ++ +      +         EG    +R     +
Sbjct: 91  RSSRNRHLIKVGKRARDRMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFD 150

Query: 218 KE 219
             
Sbjct: 151 PA 152


>gi|108804647|ref|YP_644584.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765890|gb|ABG04772.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 304

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 110/271 (40%), Positives = 159/271 (58%), Gaps = 4/271 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++      +    +K       A+++++E NLRLV+SVAKKY   GL
Sbjct: 35  LAGYLDRIGRWRLLTRDGEIELSRRAKK---GDRKARQKLIEKNLRLVVSVAKKYRGYGL 91

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F DLIQEGNIGLMKA EKFD   G++FSTYA WW++QA+ R++AD+  TIR+PVHM +K
Sbjct: 92  PFEDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK 151

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SH 587
           I KV RT   +S +++REPT EEIA++L   VE VR  +    +  SL+ P+  E++ S 
Sbjct: 152 IRKVSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPVSSEESASE 211

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED+      D+ ++          +  L  R   VL  R+G+      TL E+G 
Sbjct: 212 LGDFIEDERTSDTPDTVLKELESSQLKEAIERLPERARYVLVRRYGLDDREPATLAELGD 271

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  ++RER+RQ++ +A R LK   R    RS
Sbjct: 272 ELKISRERVRQLQREAERLLKAGIRRTSPRS 302



 Score = 45.2 bits (105), Expect = 0.035,   Method: Composition-based stats.
 Identities = 52/297 (17%), Positives = 101/297 (34%), Gaps = 26/297 (8%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
            ++ ++  S      +      +  T + +  YL  +G   LL+R+GEI +++R + G  
Sbjct: 6   EVERSAVRSREGAPAEACCSDPEPETPELLAGYLDRIGRWRLLTRDGEIELSRRAKKGDR 65

Query: 152 MMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIGPESKGGFFHG 202
                L E  L     +  +         D + +G   L + ++      PE    F   
Sbjct: 66  KARQKLIEKNLRLVVSVAKKYRGYGLPFEDLIQEGNIGLMKAVEK---FDPERGFRFSTY 122

Query: 203 TEGHSYQKREDSSQEKERD-DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                 Q  + +  +K R   V     +       + ++ S         E   R L+ D
Sbjct: 123 ATWWIRQAVQRAVADKGRTIRVPVHMTEKIRKVSRTFNELSLELEREPTDEEIARRLEWD 182

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
            +D   T+SAM D        + +E A    +     +   +        ++   LKE +
Sbjct: 183 VEDVRLTISAMPDATSLDQPVSSEESASELGDFIE-DERTSDTPDTVLKELESSQLKEAI 241

Query: 322 VKLVGSLSLN-----------QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +L                   + +  L ++L    +R+   + E  RL    GI+R
Sbjct: 242 ERLPERARYVLVRRYGLDDREPATLAELGDELKISRERVRQLQREAERL-LKAGIRR 297


>gi|22297808|ref|NP_681055.1| RNA polymerase sigma factor SigD [Thermosynechococcus elongatus
           BP-1]
 gi|22293985|dbj|BAC07817.1| group2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 315

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 105/242 (43%), Positives = 163/242 (67%), Gaps = 3/242 (1%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD   GY+FST
Sbjct: 75  ENGERAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFST 134

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R++S ++ R  T  E+A +L +
Sbjct: 135 YAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQRLGRAATINELAAELEL 194

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               VR+ L+  ++P+SL+  +GD   + LG+ +ED +++SP + A Q+ LR    R++A
Sbjct: 195 TPAQVREYLERARQPLSLDVRVGDNQDTELGELLED-SSISPEEFATQSLLRSDLERLMA 253

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            LTP++  VL +RFG+      TL +VG+   ++RER+RQIE +A+ KL+   R   +  
Sbjct: 254 ELTPQQRHVLSLRFGLENGQPLTLAKVGELLNISRERVRQIEREALSKLRK--RRGDIHE 311

Query: 679 FL 680
           +L
Sbjct: 312 YL 313



 Score = 41.7 bits (96), Expect = 0.43,   Method: Composition-based stats.
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCESPLTFQALIIWRD 172
            ++ D VR YLRE+G + LL+ E E+   K+++       +   L            W  
Sbjct: 2   DTSKDLVRTYLREIGRVPLLTHEQEVIYGKQVQQLAAMNEIREKLAAELNREPTRAEWAA 61

Query: 173 ELNDGTTLLREIID 186
             N     L  II+
Sbjct: 62  AANISEGELETIIE 75


>gi|78188365|ref|YP_378703.1| RNA polymerase sigma factor rpoD (sigma-A) [Chlorobium
           chlorochromatii CaD3]
 gi|78170564|gb|ABB27660.1| RNA polymerase sigma factor rpoD (Sigma-A) [Chlorobium
           chlorochromatii CaD3]
          Length = 299

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 96/285 (33%), Positives = 167/285 (58%), Gaps = 10/285 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTAEDEVRLTKAIKEGFDMPVDTPEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P   E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEYERDPNTRELASLLEMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHM-PDYGLTRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++ G
Sbjct: 255 NPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKVLKEYIGG 299


>gi|212634213|ref|YP_002310738.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
 gi|212555697|gb|ACJ28151.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
          Length = 322

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 102/273 (37%), Positives = 166/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 45  KNLDATQLYLGEIGFSPLLSAEEE---VFFSRKSLKGCEKSRNRMIESNLRLVVKIARRY 101

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 102 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 161

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR +++K+  EPT EEIA+KL +    V ++LK+ +   S++TP+G E
Sbjct: 162 HVVKELNVYLRTARELAHKLDHEPTAEEIAEKLDLSSSDVSRMLKLNERITSVDTPLGGE 221

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D + D + V P       ++ ++  + L  L  ++  VL  RFG+      TLE
Sbjct: 222 SDKALLDVLADDDNVGPDYKVQDEDMSKSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 281

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VGK+  +TRER+RQI+ +A+++LK    ++ L
Sbjct: 282 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQGL 314



 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 3/107 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            ++  +    E   DL+  A   +   Q+ +D   +   D  ++YL E+G   LLS E E
Sbjct: 10  AEEPTNVSVKESKSDLSKKAVKEAELEQQVQDDL-QKNLDATQLYLGEIGFSPLLSAEEE 68

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +  +++   G       + ES L    ++      N+    L ++I+
Sbjct: 69  VFFSRKSLKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 113


>gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS [Herminiimonas arsenicoxydans]
 gi|133738387|emb|CAL61432.1| RNA polymerase sigma factor rpoS (Sigma-38) [Herminiimonas
           arsenicoxydans]
          Length = 344

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 90/263 (34%), Positives = 158/263 (60%), Gaps = 5/263 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ +  I     +++ E  H  ++ ++G      A+++M+E NLRLV+S+AK Y NRG+ 
Sbjct: 73  QHYLNQIGARPLLTVPEEVHFATLAKQGNF---AARQKMIEHNLRLVVSIAKHYINRGVV 129

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++
Sbjct: 130 LLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVVREL 189

Query: 530 HKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++ +R    +  +    ++ T E+IA  +   VE V+ +L +++   SL+ P+  +  S 
Sbjct: 190 NQTLRAKFHLEAQHHDGKDATAEDIAHLVERSVEDVQDILALSEHASSLDAPLDGDPQSS 249

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++  +A  P   A    +       L  L+ ++  V+  RFG+  +   TLEE+  
Sbjct: 250 LMDLLQGDHANDPDVLAEHQEMIVLVRDWLDKLSDKQRLVITRRFGLDNDDPATLEELAT 309

Query: 648 QFCVTRERIRQIEAKAIRKLKHP 670
           +  VTRER+RQI+ +A+ KLK  
Sbjct: 310 EMHVTRERVRQIQQEALVKLKRS 332



 Score = 46.4 bits (108), Expect = 0.019,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 37/97 (38%), Gaps = 1/97 (1%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
           GS+D       A   +   + +K  +   + D  + YL ++G+  LL+   E+  A   +
Sbjct: 39  GSDDVESHEPEALEVAGIDELKKVLSSELSTDATQHYLNQIGARPLLTVPEEVHFATLAK 98

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            G       + E  L     I     +N G  LL  I
Sbjct: 99  QGNFAARQKMIEHNLRLVVSIAKHY-INRGVVLLDLI 134


>gi|332711345|ref|ZP_08431277.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332349894|gb|EGJ29502.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 319

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 101/249 (40%), Positives = 162/249 (65%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S ++        AK++MVEANLRLV++VAKKY  R L+ LDLIQEG IGL +  EKFD  
Sbjct: 71  SQLKSSIAVGESAKRKMVEANLRLVVAVAKKYIKRNLELLDLIQEGTIGLQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +  R++S K+ R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQKLGRTATISE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L +  + +R+  +  ++P+SLE  +GD   + L + +ED     P D   Q+ ++ 
Sbjct: 191 LAIELNLTPDQLREYFEQARQPLSLELRVGDNKDTELVELLEDT-GPGPEDFVNQSLMQL 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + +  LTP++ +VLR+R+G+      TL ++G+   ++RER+RQIE +AI KL+   
Sbjct: 250 DLEKFMDDLTPQQRQVLRLRYGLAEVEPMTLAKIGQHLNISRERVRQIEREAIAKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   +R ++
Sbjct: 308 RQGDMREYI 316



 Score = 44.8 bits (104), Expect = 0.051,   Method: Composition-based stats.
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           + D VR YL+E+G + LL+ E EI+  K+++       +  SL +
Sbjct: 7   STDLVRTYLKEIGRVPLLTHEQEISYGKKVKQLTTLKEVKESLVQ 51


>gi|289746505|ref|ZP_06505883.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687033|gb|EFD54521.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
          Length = 216

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/202 (50%), Positives = 143/202 (70%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G  ++ EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +
Sbjct: 15  GADRSVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQREL 74

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              + REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV 
Sbjct: 75  LQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVV 134

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D+     L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQI
Sbjct: 135 AVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQI 194

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           E+K + KL+HPSRS+ LR +LD
Sbjct: 195 ESKTMSKLRHPSRSQVLRDYLD 216


>gi|12483895|gb|AAG53883.1|AF275947_2 sigma factor RpoS [Escherichia coli]
          Length = 366

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|172035517|ref|YP_001802018.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
 gi|171696971|gb|ACB49952.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
          Length = 374

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 107/285 (37%), Positives = 183/285 (64%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    ++  +++  ++    +   + +                  AK++M+ +NLRLV
Sbjct: 89  QFLVQAEETRQQLQEALQHSPSKAEWAKAMGFETQKQFEHRLHRGRTAKRKMIRSNLRLV 148

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 149 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 208

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +R++L++ ++ +SL
Sbjct: 209 RTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVSPSQLRQLLQLRRQSLSL 268

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED++   P +   +  LR   + VL+  LT RE+ V+ +R+G+ 
Sbjct: 269 NHRVGKGEDTELVDLLEDQDLQLPEELMNEGMLRYEVSAVLSDVLTQREKDVISLRYGLC 328

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 329 TSQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 373



 Score = 45.6 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 6/90 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++  + E  E    S+++  S+ +  +  Q  +      +DD V  + +EM    LL+ E
Sbjct: 20  IETVEFEQTEHELQSVEVEISSLSDELGNQYPEGYRKTVSDDTVGAFFKEMSRYPLLNAE 79

Query: 138 GEIAIAKRI------EAGRAMMMASLCESP 161
            E+ +A  +      E  R  +  +L  SP
Sbjct: 80  EEVELAHHVQFLVQAEETRQQLQEALQHSP 109


>gi|307151291|ref|YP_003886675.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306981519|gb|ADN13400.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 318

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/249 (41%), Positives = 165/249 (66%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R+       AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD  
Sbjct: 71  EELRRTMAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R+++ K  R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLAQKQGRAATISE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L +    VR+ L+  ++P+SL+  +GD   + LG+ +ED    SP D A  ++L+ 
Sbjct: 191 LAQELELTPRQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GTSPEDYATHSSLQL 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++++ LTP++  VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+   
Sbjct: 250 DLEKLMSDLTPQQREVLALRFGLVDGQPLTLAKIGVRLNISRERVRQIEREALSKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   ++ +L
Sbjct: 308 RKANIKEYL 316



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/30 (56%), Positives = 23/30 (76%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            DPVR YLRE+G + LL+ E EI +AKR++
Sbjct: 8   TDPVRAYLREIGRVPLLTHEEEIVLAKRVQ 37


>gi|195938492|ref|ZP_03083874.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 279

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 98/270 (36%), Positives = 172/270 (63%), Gaps = 3/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L+ +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y NR
Sbjct: 5   LRTQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGNR 61

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 62  GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 121

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +   
Sbjct: 122 KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEK 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG
Sbjct: 182 ALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVG 241

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 242 REIGLTRERVRQIQVEGLRRLREILQTQGL 271



 Score = 42.1 bits (97), Expect = 0.34,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           ++YL E+G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL
Sbjct: 8   QLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALL 66

Query: 182 REI 184
             I
Sbjct: 67  DLI 69


>gi|192358973|ref|YP_001982681.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
 gi|190685138|gb|ACE82816.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
          Length = 335

 Score =  178 bits (451), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 102/277 (36%), Positives = 159/277 (57%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                ++   +  +  I     +  +E    V   RK       A+K M+E+NLRLV+ +
Sbjct: 54  DKFAKNLDATQIYLNEIGFSPLLLSAEE---VFFARKALKGDEAARKRMIESNLRLVVKI 110

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 111 SRRYVNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 170

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +R AR +S K+  EPTPEEIA  L  PV  V  +L + +   S++ P
Sbjct: 171 RLPIHVVKELNVYLRAARELSQKLDHEPTPEEIANLLEKPVADVEHMLSLNERVTSIDAP 230

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG      + D I D +   P      ++L  +    L  LT ++  VL  RFG+     
Sbjct: 231 IGASSDRTVADTIADTHVSDPAALLQDSDLTASLDHWLEELTEKQREVLARRFGLRGYEV 290

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEEVG +  +TRER+RQI+ +A+++L+     + L
Sbjct: 291 STLEEVGHEIGLTRERVRQIQVEALKRLRDIMEKQGL 327



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 25/117 (21%), Positives = 42/117 (35%), Gaps = 1/117 (0%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
               N  + ++   + ++ E      D   S   +    ++  D       D  ++YL E
Sbjct: 10  TTYDNDDVFLMQDLEADEAESLLAEEDAELSKPVAITPTERFLDDKFAKNLDATQIYLNE 69

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL    E+  A++   G       + ES L     I  R  +N G  LL  I
Sbjct: 70  IGFSPLLLSAEEVFFARKALKGDEAARKRMIESNLRLVVKISRRY-VNRGLALLDLI 125


>gi|298490014|ref|YP_003720191.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231932|gb|ADI63068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 332

 Score =  178 bits (450), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/232 (44%), Positives = 161/232 (69%), Gaps = 1/232 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E  IAK+ MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  AEGEIAKRRMVEANLRLVVSVAKKYIKRNIDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S K+ R PT  E+A +L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQKLGRAPTAIELADELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               VR+ L+  + P+SL+  +GD   + LG+ +ED  A +P D  IQ++L     R++ 
Sbjct: 212 TPRQVRECLEKARLPLSLDLRLGDNYDTELGEMLEDTGA-TPEDFVIQSSLSSDIERLMK 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            LTP+++ V+++RFG+      TL ++G+   ++RER+RQIE +A+ KL+  
Sbjct: 271 ELTPQQKEVIKLRFGLIDGQALTLSKIGEILNISRERVRQIEREALTKLRKS 322



 Score = 44.1 bits (102), Expect = 0.083,   Method: Composition-based stats.
 Identities = 14/32 (43%), Positives = 20/32 (62%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
            D VR YLRE+G + LL+ E EI   K+++  
Sbjct: 22  TDLVRTYLREIGRVPLLTHEEEIHYGKQVQRC 53


>gi|238896221|ref|YP_002920957.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae NTUH-K2044]
 gi|238548539|dbj|BAH64890.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 366

 Score =  178 bits (450), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 91  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYSN 147

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 148 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 207

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 208 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 267

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 268 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 327

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 328 GREIGLTRERVRQIQVEGLRRLREILQGQGL 358



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/117 (28%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     GI V D   L +EE S+  L      S  +           +   D  ++YL E
Sbjct: 51  AEFDENGIEVFDEKALVEEEPSDSDLAEEELLSQGA----------TQRVLDATQLYLGE 100

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 101 IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 156


>gi|86130344|ref|ZP_01048944.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332293359|ref|YP_004431968.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|85819019|gb|EAQ40178.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332171445|gb|AEE20700.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 288

 Score =  178 bits (450), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 101/273 (36%), Positives = 165/273 (60%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + N ++ +S    I+  E   +   ++KG+  A  A   +  ANLR VISVAK+Y N+GL
Sbjct: 18  LNNYLQDVSKIDLITAEEEVELAQRIQKGDERALDA---LTRANLRFVISVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++IA+ + T+R+P++   +
Sbjct: 75  SLSDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEHARTVRLPLNKIGE 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSH 587
           I K+ +    +    +R+PT  EIAK L +  E V+  LK     +S++ P    E+ ++
Sbjct: 135 ISKINKAMVYLQQVHERKPTSGEIAKYLDISEEKVKISLKNVSRSLSMDAPFAEGENDNN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +    +  P    +Q +L     R L +LT +E  V+R+ +G+G     TL+E+G 
Sbjct: 195 LYDVLSSSESPRPDRELMQESLSIEINRALDTLTEKEAEVVRLNYGLGNQPAMTLQEIGD 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  KAI++L+H S+SK L  +L
Sbjct: 255 IFDLSRERVRQIREKAIKRLRHTSKSKILMKYL 287



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I+L++ E E+ +A+RI+ G    + +L  + L F  +I    +  +    L +
Sbjct: 21  YLQDVSKIDLITAEEEVELAQRIQKGDERALDALTRANLRF--VISVAKQYQNQGLSLSD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|57864855|gb|AAW57030.1| putative group 2 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 368

 Score =  178 bits (450), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 107/285 (37%), Positives = 183/285 (64%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    ++  +++  ++    +   + +                  AK++M+ +NLRLV
Sbjct: 83  QFLVQAEETRQQLQEALQHSPSKAEWAKAMGFETQKQFEHRLHRGRTAKRKMIRSNLRLV 142

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 143 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 202

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +R++L++ ++ +SL
Sbjct: 203 RTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVSPSQLRQLLQLRRQSLSL 262

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED++   P +   +  LR   + VL+  LT RE+ V+ +R+G+ 
Sbjct: 263 NHRVGKGEDTELVDLLEDQDLQLPEELMNEGMLRYEVSAVLSDVLTQREKDVISLRYGLC 322

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 323 TSQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 367



 Score = 45.2 bits (105), Expect = 0.032,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 39/90 (43%), Gaps = 6/90 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++  + E  E    S+++  S+ +  +  Q  +      +DD V  + +EM    LL+ E
Sbjct: 14  IETVEFEQTEHELQSVEVEISSLSDELGNQYPEGYRKTVSDDTVGAFFKEMSRYPLLNAE 73

Query: 138 GEIAIAKRI------EAGRAMMMASLCESP 161
            E+ +A  +      E  R  +  +L  SP
Sbjct: 74  EEVELAHHVQFLVQAEETRQQLQEALQHSP 103


>gi|189500956|ref|YP_001960426.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
 gi|189496397|gb|ACE04945.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
          Length = 299

 Score =  178 bits (450), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 94/283 (33%), Positives = 166/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVR---------KGECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   ++              A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYELLTAEDEVKLTKAIKAGYDMPVDTTEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++ +   P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQN-DGHKPDHGLTRDSLNLEVERSLSVLAPREADVIRSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAI++L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIKRLRQSAYSKVLKEYI 297


>gi|10197699|gb|AAG14981.1|AF242209_6 alternative sigma factor [Escherichia coli]
          Length = 360

 Score =  178 bits (450), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|317968319|ref|ZP_07969709.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 260

 Score =  178 bits (450), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 96/241 (39%), Positives = 152/241 (63%), Gaps = 1/241 (0%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            + +  +      + A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KF
Sbjct: 11  ELTARQKHQIRMGTRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S++  R+P 
Sbjct: 71  DPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHVSEKLSKMRRITRELSHRFGRQPN 130

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQA 607
             E+A  + M  E + +++  +    SL+     +D  S LG+ I D N+   +DS  + 
Sbjct: 131 RLELAHAMGMQPEELEELITQSAPCASLDAHARGDDDRSTLGELIADPNSNESMDSMDRN 190

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +E     L+ L  RE +++ +RFG+      TL E+G+Q  V+RER+RQ+E+KAI KL
Sbjct: 191 LQKEHLGTWLSQLNERERKIIELRFGLAGQEPLTLAEIGRQINVSRERVRQLESKAILKL 250

Query: 668 K 668
           +
Sbjct: 251 R 251


>gi|330828425|ref|YP_004391377.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803561|gb|AEB48760.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 327

 Score =  178 bits (450), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 105/293 (35%), Positives = 176/293 (60%), Gaps = 4/293 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKI-RNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
             A +  E      +A E++ ++   +  +  I     ++  E    V   R+       
Sbjct: 29  EVAAEADETISDELLAPELNKVMDATQLYLGEIGFSPLLTAEEE---VYYARRALRGDKA 85

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 86  ARKRMIESNLRLVVKIARRYNNRGLVLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 145

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+++  EPT E+IA  L   V+ V
Sbjct: 146 IRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELSHRLDHEPTAEDIAFALDRSVDDV 205

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++LK+ ++  S++TPIG +    L D + D+  + P   + + ++R +    L  L P+
Sbjct: 206 NRMLKLNEKITSVDTPIGGDRDKALLDVLSDERGMGPELESQEDDMRSSIVHWLEELNPK 265

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+    S+ L
Sbjct: 266 QREVLARRFGLLGYEPATLEDVGAEIGLTRERVRQIQVEGLRRLREILLSQGL 318



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 37/106 (34%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + +   + E  E       +A        +          D  ++YL E+G   LL+ E 
Sbjct: 12  ELEFDAEPESHEVEELQEVAAEADETISDELLAPELNKVMDATQLYLGEIGFSPLLTAEE 71

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 72  EVYYARRALRGDKAARKRMIESNLRLVVKIARRYN-NRGLVLLDLI 116


>gi|116074244|ref|ZP_01471506.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069549|gb|EAU75301.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  178 bits (450), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 104/283 (36%), Positives = 161/283 (56%), Gaps = 16/283 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMV---------------RKGECEASIAKK 446
             DSI    + I  I + T     E  H V  +               R        A+ 
Sbjct: 50  STDSIGYYLSSIGRIPLLTPAEEIELAHHVQAMKQLLETPEDERTPRERHKIRMGKRARD 109

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q
Sbjct: 110 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 169

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+A  + +    +  +
Sbjct: 170 GMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLELAHAMGIEPRDLEDL 229

Query: 567 LKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  +    SL+     E+  S LG+ I D N    ++   ++  +E     L+ L  RE+
Sbjct: 230 ISQSAPCASLDAHARGEEDRSTLGELIPDPNGEDSMEGMDRSIQKEHLGGWLSQLNEREQ 289

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++L++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 290 KILKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 332



 Score = 40.2 bits (92), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
               R + D +  YL  +G I LL+   EI +A  +       M  L E+P
Sbjct: 44  KQGGRLSTDSIGYYLSSIGRIPLLTPAEEIELAHHV-----QAMKQLLETP 89


>gi|304413872|ref|ZP_07395289.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304283592|gb|EFL91987.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 332

 Score =  178 bits (450), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+  C    +++ M+E+NLRLV+ +A++Y N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+ EEIA++L  PV+ V ++L++ +   S+++P+G +  
Sbjct: 174 VKELNVYLRTARELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D +   P D+    +++ +  + L  L  ++  VL  RFG+      TLE V
Sbjct: 234 KALLDILSDDSENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRFGLLGYEAATLENV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           GK+  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GKEIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +        E S        +          +  +   D  ++YL E+G   LL+ E
Sbjct: 17  FDEESSVLGMFDEKSSMEDEILEDELEEDDLLLQNVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALCGDQQSRRRMIESNLRLVVKIARRYG-NRGLALLDLI 122


>gi|332708973|ref|ZP_08428943.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352162|gb|EGJ31732.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 373

 Score =  177 bits (449), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 105/250 (42%), Positives = 172/250 (68%), Gaps = 1/250 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +        +AK++M+ +NLRLV+S+AK+Y NRG+ FLDLIQEG +GL +AAEKFD  
Sbjct: 123 RQLEGNLYRGRVAKRKMIRSNLRLVVSIAKRYINRGVPFLDLIQEGALGLNRAAEKFDPD 182

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ +K++K+ +  R +  K++R P   E
Sbjct: 183 KGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRELKQKLQRNPNELE 242

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ L + +  +R++L++ +  +SL   +G  + + L D +ED +   P D   ++ +R+
Sbjct: 243 LAQALEISLSHLRQLLELRRRSLSLNHRVGKGEDTELMDLLEDNDLRLPEDKMNESMMRQ 302

Query: 612 TTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               VL+  LT RE+ V+ +R+G+  +  +TLEEVG  F ++RER+RQI++KA+RKL+ P
Sbjct: 303 EIWEVLSDVLTEREKDVISLRYGLASSEPYTLEEVGGMFNLSRERVRQIQSKAMRKLRRP 362

Query: 671 SRSKKLRSFL 680
             +++LR +L
Sbjct: 363 QVARRLRDWL 372



 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 27/65 (41%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D  + E ++          +  + +    +     +DD V  + +EM    LL  + E+ 
Sbjct: 24  DHIEPEETDLQRVAVEFTEDDELVVSTSHNFRKSGSDDTVGAFFKEMARYPLLKPDEEVD 83

Query: 142 IAKRI 146
           +A+R+
Sbjct: 84  LARRV 88


>gi|41853|emb|CAA34435.1| katF [Escherichia coli K-12]
          Length = 362

 Score =  177 bits (449), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+  EIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAVEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L ++E S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKPLVEQEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|92114749|ref|YP_574677.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797839|gb|ABE59978.1| RNA polymerase, sigma 38 subunit, RpoS [Chromohalobacter salexigens
           DSM 3043]
          Length = 325

 Score =  177 bits (449), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 102/301 (33%), Positives = 174/301 (57%), Gaps = 5/301 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEV--DSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E+D   ++  K+    E            S+   +  +  I     ++  E  H   + +
Sbjct: 21  EVDADEIANDKEEEAFEKALHRDDNTYHQSLDATQIYLNEIGFSPLLTPEEEVHYGRLAQ 80

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K        ++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++
Sbjct: 81  K---GDPAGRQRMIESNLRLVVKIARRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFR 137

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +R AR ++ ++  E T EEIA+ 
Sbjct: 138 FSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRAARELTQRLDHEATAEEIAEF 197

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L  PV  V+K+L + +   S++ P+G E    L D + D+N   P    +  ++++    
Sbjct: 198 LDKPVGTVKKMLGLNERVSSVDYPMGGESDKPLIDTLADENEAGPESLLVGNDVKQHVDD 257

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            LA LT ++  V+  RFG+  +   TLEEVG++  +TRER+RQI+ +A++KL+     + 
Sbjct: 258 WLAELTDKQMEVVVRRFGLRGHEAATLEEVGEEIGLTRERVRQIQVEALKKLRRVLEKQG 317

Query: 676 L 676
           L
Sbjct: 318 L 318



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 29/113 (25%), Positives = 44/113 (38%), Gaps = 1/113 (0%)

Query: 72  NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI 131
              I  VD DD++ E   +           +      R D+    + D  ++YL E+G  
Sbjct: 5   ERDIQGVDLDDVDSEMEVDADEIANDKEEEAFEKALHRDDNTYHQSLDATQIYLNEIGFS 64

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E+   +  + G       + ES L     I  R  LN G +LL  I
Sbjct: 65  PLLTPEEEVHYGRLAQKGDPAGRQRMIESNLRLVVKIARRY-LNRGLSLLDLI 116


>gi|21219415|ref|NP_625194.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|256789543|ref|ZP_05527974.1| RNA polymerase principal sigma factor HrdC [Streptomyces lividans
           TK24]
 gi|289773432|ref|ZP_06532810.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
 gi|123520|sp|P18184|HRDC_STRCO RecName: Full=RNA polymerase principal sigma factor hrdC
 gi|48741|emb|CAA37173.1| unnamed protein product [Streptomyces coelicolor A3(2)]
 gi|6562877|emb|CAB62686.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|289703631|gb|EFD71060.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
          Length = 339

 Score =  177 bits (449), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 95/287 (33%), Positives = 169/287 (58%), Gaps = 3/287 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ ++ R E+++            R  +    +   +   AK  MV AN
Sbjct: 54  AEDEVRLATRIEAGVRAREELETADTGEPAPTPRRRRTLE---ETVHDGQEAKDHMVRAN 110

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK++ +RGL  LD+IQEGN+GL++A EKFD   G+KFSTYA WW++QAI R +
Sbjct: 111 LRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYATWWIRQAIERGL 170

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A  + T+R+PVH+ +++ K+ +  R++   + REPT EE+A +  + V+ V  + ++ ++
Sbjct: 171 ATHARTVRLPVHVVEQLQKLAKVERKLRAGLDREPTTEEVAAESGIDVDKVVWLRRVGRD 230

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SL+TP+ +   + +GD I D   +   + A    L       + +L PRE  +L +R+
Sbjct: 231 AVSLDTPVDETGDTVVGDLIPDTEVLRAPEVAEFQALAAELREAVGTLAPRESLILSLRY 290

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G+      TL++V +   +TRER+RQ+E +++  L+ P   ++L  +
Sbjct: 291 GLHDGRPRTLQQVAQHVGLTRERVRQLEKESLAHLRAPENRERLLDW 337



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           D +  YL ++G+  LL+ E E+ +A RIEAG   
Sbjct: 37  DLLGQYLTQIGATPLLTAEDEVRLATRIEAGVRA 70


>gi|119357820|ref|YP_912464.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
 gi|119355169|gb|ABL66040.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
          Length = 299

 Score =  177 bits (449), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 95/283 (33%), Positives = 166/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTAEDEVKLTKAIKEGYDTPVDTVEYRRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P   E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKILKEYI 297


>gi|226327187|ref|ZP_03802705.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
 gi|225204405|gb|EEG86759.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
          Length = 201

 Score =  177 bits (449), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 137/200 (68%), Positives = 165/200 (82%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 60

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++ REP+PEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     PL
Sbjct: 61  EMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL 120

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           DSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEA
Sbjct: 121 DSATSESLRSATHEVLAGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 180

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           KA+RKL+HPSRS+ LRSFLD
Sbjct: 181 KALRKLRHPSRSEVLRSFLD 200


>gi|110596913|ref|ZP_01385203.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
 gi|110341600|gb|EAT60060.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
          Length = 299

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 95/283 (33%), Positives = 165/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   ++              A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTAEDEVKLTKAIKDGFDMPVDTTEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P   E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELATLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHL-PDYGLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|170700559|ref|ZP_02891561.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170134549|gb|EDT02875.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 519

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 105/255 (41%), Positives = 163/255 (63%), Gaps = 1/255 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + + +  G+ +     + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EK
Sbjct: 266 RALGAALSDGQQKVRDGTRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEK 325

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QA+ R++AD+S TIR+PVH+ D+  +V R A R   +  R  
Sbjct: 326 FEYRRGFKFSTYATWWIRQAVARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRA 385

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +P   +R VL +  EP+SL+TP+  +  + L D IED+ + SP +     
Sbjct: 386 TPAELAAESGLPEGKLRAVLALPAEPLSLDTPL-PDAETGLVDLIEDQASASPFERLADT 444

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RE  T +L S+TP E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L
Sbjct: 445 RMRECVTSLLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATL 504

Query: 668 KHPSRSKKLRSFLDG 682
           +  + ++   SFLD 
Sbjct: 505 RTAAEAEGAESFLDA 519



 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 43/179 (24%), Positives = 80/179 (44%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +L  D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TLRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R + ++ LL RE EI
Sbjct: 67  PAAPAPFAGAAPVDVDRDALDEGRALLGDLARGTSASTDPLALYMRRIHAVPLLKREDEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
            +A+ IE GR  ++ +L   P    AL+              E  D++      +   +
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALLARHGATGVSGAAADEGDDIDGEGDTPAPARY 185


>gi|145219258|ref|YP_001129967.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris
           vibrioformis DSM 265]
 gi|145205422|gb|ABP36465.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeovibrioides
           DSM 265]
          Length = 299

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 94/283 (33%), Positives = 167/283 (59%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTADDEVRLTKAIKEGFDMPLDTTEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V++  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHL-PDHGLNRDSLTLEVERSLSVLAPREADVIKSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|158337052|ref|YP_001518227.1| RNA polymerase sigma factor SigD [Acaryochloris marina MBIC11017]
 gi|158307293|gb|ABW28910.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 108/249 (43%), Positives = 169/249 (67%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++K   E   AK++MVEANLRLV+SVAKKY  R +  LDLIQEG IG+ +  EKFD  
Sbjct: 71  AELQKALHEGEAAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++  TIR+P+H+ +K++K+ +T R++S K+ R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEKLNKIKKTQRQLSQKLGRAATISE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L +  + VR+ L+  ++P+SL+  +GD   + LG+ IED +  SP +  +QA+LR 
Sbjct: 191 LATSLDLTTKQVREYLERARQPLSLDVRVGDNQDTELGELIEDPS-ESPENFTLQASLRG 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              R++A LT ++++VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+   
Sbjct: 250 DLERLMADLTDQQQQVLHLRFGLDDGQPLTLAKIGDRLSISRERVRQIEREALSKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   +  +L
Sbjct: 308 RKADISEYL 316



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLRE+G + LL+ E E+   K+++ 
Sbjct: 9   DSVRSYLREIGRVPLLTHEEEVTFGKQVQH 38


>gi|77165179|ref|YP_343704.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254434741|ref|ZP_05048249.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|76883493|gb|ABA58174.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207091074|gb|EDZ68345.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 303

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 90/263 (34%), Positives = 155/263 (58%), Gaps = 4/263 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++       +S  E RH   + ++       A+  ++E+NLR+VI +A ++ NRGL  +
Sbjct: 42  YMREAGKVPLLSAEEERHYARLAQQ---GDREARNHIIESNLRIVIRMATRHINRGLPLM 98

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL+ A EKF+  LG++FSTYA WW++QAI R++ +Q+ TIR+P+H+  KI  
Sbjct: 99  DLIEEGNLGLIDAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRVPIHVFKKIRC 158

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             + AR    +   EP   EIAK L  P+E +++ L +    ISL+ P+ ++    L D 
Sbjct: 159 YQKEARYFRQRYNIEPHLGEIAKLLHEPLERIQRYLSLQAPEISLDDPLSEDTDDCLVDL 218

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+   +P       + + +    L+ L  R++ +++ R+G+      TLEE+G++  +
Sbjct: 219 LPDER-NNPAILWEIFDKKASIHNQLSQLPERQQEIIKCRYGLDGYEVTTLEEIGQKLGI 277

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           TRER+RQI+  AI++L+    S+
Sbjct: 278 TRERVRQIQQTAIKRLRKIIESE 300



 Score = 51.0 bits (120), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 9/87 (10%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +Y+RE G + LLS E E   A+  + G       + ES L    +I       +    L 
Sbjct: 41  LYMREAGKVPLLSAEEERHYARLAQQGDREARNHIIESNLRI--VIRMATRHINRGLPLM 98

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQ 209
           ++I+       E   G     E  + +
Sbjct: 99  DLIE-------EGNLGLIDAVEKFNPE 118


>gi|307153454|ref|YP_003888838.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306983682|gb|ADN15563.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 372

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 189/290 (65%), Gaps = 9/290 (3%)

Query: 397 NFVACEVDSILKIRNEIK----SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            F+    +   +++ +++     +     + +   R + + + +       AK++M+ +N
Sbjct: 87  KFLMESEEKRQELQVQLERPPSKLEWAQAMGLKNERQLENRLYR----GRAAKRKMIRSN 142

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+I
Sbjct: 143 LRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTI 202

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A+ + TIR+P+H+ +K++K+ +  R +  ++ R PT +E+A+ L +  E +R++L++ ++
Sbjct: 203 ANDARTIRLPIHIVEKLNKLKKAQRVLKQQLHRNPTEQELAQALEIDCEHLRQLLQLRRQ 262

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMR 631
            +SL   +G  + + L D +ED+    P +   +A +R+    VL   LT RE+ V+ +R
Sbjct: 263 SLSLNHRVGKGEDTELVDLLEDEELQLPEEKMNEAMMRQDIAAVLTDVLTEREKDVIALR 322

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +G+  +  +TLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L+
Sbjct: 323 YGLITSQPYTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWLN 372


>gi|52841515|ref|YP_095314.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52628626|gb|AAU27367.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 359

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 175/274 (63%), Gaps = 3/274 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             ++   +  +  I     ++  E  H  ++          A+K+M+E+NLRLV+ +A++
Sbjct: 83  AKALDATQLYLGEIGFSPLLTAEEEIHYATLA---LKGDMEARKKMIESNLRLVVKIARR 139

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y NRGL  LDLI+EGN+GLMK+ EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P
Sbjct: 140 YLNRGLPLLDLIEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLP 199

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+  +++  +R AR+++ K+  EP+PEEIA+ +  P+E V+K+L +  +  S++TPIG 
Sbjct: 200 IHVVKELNVYLRAARQLTQKLDHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGF 259

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++T  L D I D+N+++P +     NLR+    +L  LT  +++V+  RFG+      TL
Sbjct: 260 DETKSLLDTIADENSLNPAELLTNENLRQHIESLLDKLTENQQQVIARRFGLRGFEKATL 319

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E+VGK+  +TRER+RQI+ +A++ L+       L
Sbjct: 320 EDVGKEIDLTRERVRQIQVEALKTLRTLLERVGL 353



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D   D E  E+ LD     ++   F   ++        D  ++YL E+G   LL+ E 
Sbjct: 47  EEDVEPDIEKMEEELDELPEFTDDETFPSFQRGKNIAKALDATQLYLGEIGFSPLLTAEE 106

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI  A     G       + ES L     I  R  LN G  LL  I
Sbjct: 107 EIHYATLALKGDMEARKKMIESNLRLVVKIARRY-LNRGLPLLDLI 151


>gi|254496518|ref|ZP_05109389.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
 gi|254354257|gb|EET12921.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
          Length = 342

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 104/259 (40%), Positives = 170/259 (65%), Gaps = 3/259 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     +S  E  H  ++          A+K+M+E+NLRLV+ ++++Y NRGL 
Sbjct: 73  QLYLSEIGFSPLLSAEEEVHYATLA---LKGDVAARKKMIESNLRLVVKISRRYLNRGLP 129

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GLMK+ EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  ++
Sbjct: 130 LLDLIEEGNLGLMKSVEKFDPNRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKEL 189

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +R AR+++ K+  EP+PEEIA+ +  P+E V+K+L +  +  S++TPIG ++   L 
Sbjct: 190 NVYLRAARQLTQKLDHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDENKSLL 249

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+N+V+P +     NLR     +L  LT  +++V+  RFG+      TLE+VGK+ 
Sbjct: 250 DTIADENSVNPAELLTNENLRLHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEI 309

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +TRER+RQI+ +A++ L+
Sbjct: 310 DLTRERVRQIQVEALKTLR 328



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/109 (24%), Positives = 40/109 (36%), Gaps = 2/109 (1%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-RKDSADRSTDDPVRMYLREMGSIELLS 135
           +++ DDL+         ++     +  V      +        D  ++YL E+G   LLS
Sbjct: 27  LMEEDDLDSLAEKASDEEVELPDFSDDVAFPSFSRGKNALKMMDATQLYLSEIGFSPLLS 86

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A     G       + ES L     I  R  LN G  LL  I
Sbjct: 87  AEEEVHYATLALKGDVAARKKMIESNLRLVVKISRRY-LNRGLPLLDLI 134


>gi|124266448|ref|YP_001020452.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
 gi|124259223|gb|ABM94217.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
          Length = 343

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 97/287 (33%), Positives = 154/287 (53%), Gaps = 11/287 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P  E     A E +    ++  ++ I      +  E   + +  R        A+++M+E
Sbjct: 47  PVQEHLPIAAGEGEVGNTLQTYLREIRRAPLFTPDEEFAMATRAR---AGDFAARQQMIE 103

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
            NLRLV+S+AK Y +RGL   DLI+EGN+GLM A  KF+   G++FSTYA WW++Q+I R
Sbjct: 104 RNLRLVVSIAKSYLSRGLPMTDLIEEGNLGLMHAIGKFEPERGFRFSTYASWWIRQSIER 163

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-----IKREPTPEEIAKKLAMPVEGVRK 565
           +I  Q+  +R+PVH+  ++++V++  R +  +       R    +EIA  L  PV  V +
Sbjct: 164 AIMHQARLVRLPVHVVRELNQVLKARRALEGEAAASADGRTVRVDEIAAALGRPVTEVSE 223

Query: 566 VLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +L+  ++P SL+ P+          LGD + D+ A  PL   +   L       L  L+ 
Sbjct: 224 LLRFAEQPTSLDAPLERQAGNGAETLGDMVADEQATDPLGHTLNHELDVLLEHGLGELSE 283

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE  VL  R+G+      TLE + ++  +TRERIRQI+ +A+ KLK 
Sbjct: 284 REREVLAGRYGLHDREPETLEVLAERLGLTRERIRQIQQEALLKLKR 330



 Score = 43.7 bits (101), Expect = 0.094,   Method: Composition-based stats.
 Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 3/110 (2%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           +      V       + +    + ++ YLRE+    L + + E A+A R  AG       
Sbjct: 41  ADDLPEPVQEHLPIAAGEGEVGNTLQTYLREIRRAPLFTPDEEFAMATRARAGDFAARQQ 100

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           + E  L     I     L+ G   + ++I+ E  +G     G F    G 
Sbjct: 101 MIERNLRLVVSIAKSY-LSRG-LPMTDLIE-EGNLGLMHAIGKFEPERGF 147


>gi|282896368|ref|ZP_06304389.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
 gi|281198656|gb|EFA73536.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
          Length = 332

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 102/276 (36%), Positives = 173/276 (62%), Gaps = 5/276 (1%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           +    +    D++ +  N   S+      +  + + +  ++     +  IAK++MVEANL
Sbjct: 51  QKSTALYETKDNLAQELNRQPSLEEWAKAAQLDPQELNRLL----AQGEIAKRKMVEANL 106

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RL++SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FSTYA WW++QAITR+IA
Sbjct: 107 RLLVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPSKGYRFSTYAYWWIRQAITRAIA 166

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +++ TIR+P+H+ +K++K+ +  R +S  + R P+  E+A++L +  + VR  L+  + P
Sbjct: 167 EKARTIRLPIHITEKLNKIKKAQRDLSQTLGRSPSIAELAQELEITPKQVRDCLEKARLP 226

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL+  +GD   + LG+ +ED  A SP D  IQ++L     R++  LT ++  V+++RFG
Sbjct: 227 LSLDLRLGDNYDTELGEMLEDPGA-SPEDYVIQSSLSSELERMMTHLTTQQREVIKLRFG 285

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      TL  +G+   ++RER+RQIE +A+ +L+ 
Sbjct: 286 LVDGQSMTLARIGEVLNISRERVRQIEREALTRLRR 321



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            D VR YLRE+G + LL+ E EI   K+++ 
Sbjct: 22  TDIVRTYLREIGKVPLLTHEQEIYYGKQVQK 52


>gi|259909441|ref|YP_002649797.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224965063|emb|CAX56595.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
          Length = 277

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 2   LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V ++L++ +   S++TP+G +  
Sbjct: 119 VKELNVYLRTARELSHKLDHEPSAEEIAQKLDKPVDDVSRMLRLNERITSVDTPLGGDSE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 179 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 238

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 239 GREIGLTRERVRQIQVEGLRRLREILQGQGL 269



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
             D  ++YL E+G   LL+ E E+  A+R   G       + ES L     I  R   N 
Sbjct: 1   MLDATQLYLGEIGYSPLLTAEEEVFFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NR 59

Query: 177 GTTLLREI 184
           G  LL  I
Sbjct: 60  GLALLDLI 67


>gi|167623164|ref|YP_001673458.1| RpoD family RNA polymerase sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353186|gb|ABZ75799.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           halifaxensis HAW-EB4]
          Length = 321

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 101/273 (36%), Positives = 166/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 44  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKSLKGCEKSRNRMIESNLRLVVKIARRY 100

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 101 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 160

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR +++K+  EPT EEIA++L +    V ++LK+ +   S++TP+G E
Sbjct: 161 HVVKELNVYLRTARELAHKLDHEPTAEEIAEQLDLSSSDVSRMLKLNERITSVDTPLGGE 220

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D + D + V P       ++ ++  + L  L  ++  VL  RFG+      TLE
Sbjct: 221 SDKALLDVLADDDNVGPDYKVQDEDISKSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 280

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VGK+  +TRER+RQI+ +A+++LK    ++ L
Sbjct: 281 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQGL 313



 Score = 42.1 bits (97), Expect = 0.31,   Method: Composition-based stats.
 Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 2/98 (2%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S++S +  +        L+++     +   D  ++YL E+G   LLS E E+  +++   
Sbjct: 17  SDESTNKLTKQDVKEAELEQQVQDDLQKNLDATQLYLGEIGFSPLLSAEEEVYFSRKSLK 76

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           G       + ES L    ++      N+    L ++I+
Sbjct: 77  GCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 112


>gi|153814577|ref|ZP_01967245.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|317501262|ref|ZP_07959466.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089991|ref|ZP_08338881.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848071|gb|EDK24989.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|316897329|gb|EFV19396.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330402905|gb|EGG82471.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 273

 Score =  177 bits (449), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 112/273 (41%), Positives = 168/273 (61%), Gaps = 4/273 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             E+     +R  +  I     +  +E + +   +         A+  + E NLRLV+S+
Sbjct: 3   KEEIQESEPLRIYLNEIGEIPLLDETEEKELGRRI---SDGDESARARLEEGNLRLVVSI 59

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK YT RGL  +DLIQEGNIGLM AAEK+D+    +FSTYA WW+K+AITR+I  QS  I
Sbjct: 60  AKHYTGRGLPLMDLIQEGNIGLMHAAEKYDYTKDNRFSTYASWWIKEAITRAIDQQSREI 119

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-MPVEGVRKVLKITKEPISLET 578
           R+PVH+ + I +V + A+ +  +  RE  P EIAKKL     E V+ +L   + P+SLET
Sbjct: 120 RVPVHVAENIKRVQKAAKELQQEFGREAEPGEIAKKLGDRTEEEVKNILSYIRNPVSLET 179

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+G++    LGDF+ED++  +P D+      +E    +L +L  RE+ V+ +RFG+G + 
Sbjct: 180 PVGEDGEDSLGDFVEDRSETTPEDAMDVLVRKEEVQELLETLNDREKEVISLRFGLGKDR 239

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +TLEE+G+   +TRER+RQIE+KA+ KL+  +
Sbjct: 240 TYTLEEIGESLGITRERVRQIESKAMEKLRKKA 272



 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 58/167 (34%), Gaps = 10/167 (5%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR- 171
            +    +P+R+YL E+G I LL    E  + +RI  G     A L E  L     I    
Sbjct: 4   EEIQESEPLRIYLNEIGEIPLLDETEEKELGRRISDGDESARARLEEGNLRLVVSIAKHY 63

Query: 172 --------DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
                   D + +G   L    +            +       +  +  D    + R  V
Sbjct: 64  TGRGLPLMDLIQEGNIGLMHAAEKYDYTKDNRFSTYASWWIKEAITRAIDQQSREIRVPV 123

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                +I+   K +K+ + +     E  E  ++  D  E++  + LS
Sbjct: 124 H-VAENIKRVQKAAKELQQEFGREAEPGEIAKKLGDRTEEEVKNILS 169


>gi|78780175|ref|YP_398287.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|123969439|ref|YP_001010297.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|126697226|ref|YP_001092112.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|78713674|gb|ABB50851.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
 gi|123199549|gb|ABM71190.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
 gi|126544269|gb|ABO18511.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 339

 Score =  177 bits (448), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 105/281 (37%), Positives = 165/281 (58%), Gaps = 16/281 (5%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRK---------------GECEASIAKKEM 448
           DSI    + I  + + T     E  H V  ++K                      A+  M
Sbjct: 50  DSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETDRTQRNLYQIKIGKRARDRM 109

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +
Sbjct: 110 MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 169

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++ 
Sbjct: 170 TRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLIS 229

Query: 569 ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +    SL+     E+  S LG+ I D N   P++   +   +E     L+ L  RE+++
Sbjct: 230 QSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQKI 289

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 290 MKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330



 Score = 44.1 bits (102), Expect = 0.091,   Method: Composition-based stats.
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 8/94 (8%)

Query: 73  MGINVVDGDDLEDEEGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +       D    E  L      S  S SS+  ++ +  + R   D +  YL  +G
Sbjct: 1   MGIPLESAKSSSDNNFDEPRLPNTAGKSRKSKSSLTAKQSQKKSGRLASDSIGYYLSSIG 60

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            + LL+   EI +A  ++      M  L + P T
Sbjct: 61  RVPLLTPAEEIELAHHVQN-----MKKLLQIPET 89


>gi|237809473|ref|YP_002893913.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
 gi|237501734|gb|ACQ94327.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
          Length = 324

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 98/267 (36%), Positives = 160/267 (59%), Gaps = 4/267 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++  E    V   R+       A+  M+E+NLRLV+ +A++Y NRGL 
Sbjct: 53  QLYLGEIGFSPLLTAEE----VYFARRALRGDDAARNRMIESNLRLVVKIARRYNNRGLA 108

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDL++EGN+GL++A EKFD   G++FSTYA WW++Q + R+I +Q+ TIR+P+H+  ++
Sbjct: 109 LLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTVERAIMNQTRTIRLPIHVVKEL 168

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +RTAR ++ ++  EPT E+IA  L  PVE V ++LK+ +   S++TPI  +    L 
Sbjct: 169 NVYLRTARELAQRLDHEPTAEDIASLLDKPVEEVSRMLKLNERICSVDTPIAGDGDKSLI 228

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D + D     P D     +++ +    L  L P++  VL  RFG+      TLEEVG++ 
Sbjct: 229 DILTDDRINCPEDQTQDDDMQHSIVIWLEQLNPKQREVLARRFGLLGYEPATLEEVGEEI 288

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +TRER+RQI+ + +R++K     + L
Sbjct: 289 GLTRERVRQIQVEGLRRMKEMLTQQGL 315



 Score = 42.5 bits (98), Expect = 0.23,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 3/108 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D D LE ++  E           +    + +         D  ++YL E+G   LL+ E 
Sbjct: 10  DQDLLELQDPVEMDDIAEIDVDVTEPADELQLSPTLNRIMDATQLYLGEIGFSPLLTAE- 68

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           E+  A+R   G       + ES L    ++      N+    L ++++
Sbjct: 69  EVYFARRALRGDDAARNRMIESNLRL--VVKIARRYNNRGLALLDLVE 114


>gi|189424151|ref|YP_001951328.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420410|gb|ACD94808.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 320

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 105/264 (39%), Positives = 165/264 (62%), Gaps = 3/264 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++    + +   V +       A+ +M+EANLRLV+ +AK+Y NRGL FL
Sbjct: 60  YLRDIQRTPLLNAEAEKELARRVEQ---GDKAARNQMIEANLRLVVKIAKRYLNRGLPFL 116

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GLMKA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D I +
Sbjct: 117 DLIEEGNLGLMKAVERFSLEKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDISR 176

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +++ +R++S ++ REP+ +E+A  + +    +RK++ + +   S++ PIG+ +   L D 
Sbjct: 177 MLKVSRQLSQELHREPSVQELADAMQIKPLHIRKLMILLRRTCSMDVPIGEGNDFFLVDT 236

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IED NAVSP D     +  E        L+  E  +L +RFG+      TL+ +G+ F V
Sbjct: 237 IEDTNAVSPADLLENIDRYELIAEHFDQLSENERTILGLRFGLDDRDPQTLDTIGQSFGV 296

Query: 652 TRERIRQIEAKAIRKLKHPSRSKK 675
           TRERIRQIEAK++ KLK  ++S K
Sbjct: 297 TRERIRQIEAKSLEKLKALAKSSK 320



 Score = 59.9 bits (143), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/109 (27%), Positives = 45/109 (41%), Gaps = 3/109 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST--DDPVRMYLREMGSIELLS 135
           +D   L+DE+        A  A   +        +       DDPV++YLR++    LL+
Sbjct: 12  LDAPGLDDEQEPPVDFVAAIEAEEDTTLEVDDLPALVEQIPLDDPVKIYLRDIQRTPLLN 71

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E  +A+R+E G       + E+ L     I  R  LN G   L  I
Sbjct: 72  AEAEKELARRVEQGDKAARNQMIEANLRLVVKIAKRY-LNRGLPFLDLI 119


>gi|311694174|gb|ADP97047.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 331

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 101/275 (36%), Positives = 166/275 (60%), Gaps = 3/275 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
               +   +  +  I     ++  E  +   + RKGE      +K M+E+NLRLV+ +A+
Sbjct: 53  SQKQLDATQLYLNEIGFSPLLTPEEEVYFARLARKGEESG---RKRMIESNLRLVVKIAR 109

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+
Sbjct: 110 RYVNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 169

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  +++  +R AR ++ K+  EP+ EEIA+ +  PV  V+++L + +   S++TPIG
Sbjct: 170 PIHVVKELNLYLRAARELTQKLDHEPSAEEIARMVDKPVADVKRMLGLNERVASMDTPIG 229

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L D + D+ A  P D     N+     + +  L+ +++ VL  RFG+      T
Sbjct: 230 AGGEKSLLDTVADEGASDPADLLQDNNMCSCLEKWIDQLSDKQQEVLSRRFGLRGYPVST 289

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           LEEVG++  +TRER+RQI+ +A+R+L+     + L
Sbjct: 290 LEEVGQEIGLTRERVRQIQVEALRRLREILEKEGL 324



 Score = 56.4 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/127 (24%), Positives = 50/127 (39%), Gaps = 5/127 (3%)

Query: 58  VSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRST 117
           +S+EQ +  +  +S+M     D +D    E   +       A        + +    +  
Sbjct: 1   MSAEQEDIIIDRVSDMD----DAEDQLLAEEKVEKEPTEEVAEVEEDIPTQGRYFTSQKQ 56

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D  ++YL E+G   LL+ E E+  A+    G       + ES L     I  R  +N G
Sbjct: 57  LDATQLYLNEIGFSPLLTPEEEVYFARLARKGEESGRKRMIESNLRLVVKIARRY-VNRG 115

Query: 178 TTLLREI 184
            TLL  I
Sbjct: 116 LTLLDLI 122


>gi|269926941|ref|YP_003323564.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269790601|gb|ACZ42742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 596

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 121/236 (51%), Positives = 166/236 (70%), Gaps = 1/236 (0%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I   + K   E  IA+K ++EANLRLV+S+AKKYT RG+  LDLIQEGNIGL+KA EKF
Sbjct: 240 DIQDKITKWIAEGDIARKRLIEANLRLVVSIAKKYTGRGITLLDLIQEGNIGLIKAVEKF 299

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
               GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K+ +  RR++ ++ REPT
Sbjct: 300 RHQKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMGEAINKIAQARRRLTQELGREPT 359

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            +EIA  L +PVE +R+V KI++EPISLE P+G+E+ + LGDFI+D  A +P+D+A Q+ 
Sbjct: 360 EQEIANYLGIPVEKIREVQKISQEPISLENPVGEEEDTSLGDFIQDHKAPAPMDAASQSL 419

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           LR+   +VL  L+ RE  VL MRFG+         EV     V+  ++ Q E++ +
Sbjct: 420 LRDQIDQVLKHLSERERGVLLMRFGLDC-EPRPYREVAHILAVSPNQVMQAESRVL 474



 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 34/76 (44%), Positives = 46/76 (60%)

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           I   LRE    V+  +   E  ++R RFG+ +    TLEEVG+ F VTRERIRQIE+KA+
Sbjct: 520 IDQKLREALASVMLHVPAPERDMMRFRFGLDIGQPRTLEEVGRAFGVTRERIRQIESKAL 579

Query: 665 RKLKHPSRSKKLRSFL 680
           RKL+     ++L   L
Sbjct: 580 RKLRRDVFRRQLEDLL 595



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E   D +DL    S      +  +D    + DDP+R+YLRE+G   LLS+E EI +A++ 
Sbjct: 43  ENDADYVDLEIEESLQDP--EDLEDLEGTNLDDPIRLYLREIGKENLLSQEQEIELARKN 100

Query: 147 EAG 149
           E G
Sbjct: 101 ERG 103


>gi|254526617|ref|ZP_05138669.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538041|gb|EEE40494.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 339

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 105/281 (37%), Positives = 165/281 (58%), Gaps = 16/281 (5%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRK---------------GECEASIAKKEM 448
           DSI    + I  + + T     E  H V  ++K                      A+  M
Sbjct: 50  DSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETERTQRNLYQIKIGKRARDRM 109

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +
Sbjct: 110 MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 169

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++ 
Sbjct: 170 TRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLIS 229

Query: 569 ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +    SL+     E+  S LG+ I D N   P++   +   +E     L+ L  RE+++
Sbjct: 230 QSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQKI 289

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 290 MKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 8/94 (8%)

Query: 73  MGINVVDGDDLEDEEGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +       D    E  L      S  S SS+  ++ +  + R   D +  YL  +G
Sbjct: 1   MGIPLESAKSSSDNNFDEPRLPNTAGKSRKSKSSLTAKQSQKKSGRFASDSIGYYLSSIG 60

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            + LL+   EI +A  ++      M  L + P T
Sbjct: 61  RVPLLTPAEEIELAHHVQN-----MKKLLQIPET 89


>gi|328474970|gb|EGF45764.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 346

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 122/235 (51%), Positives = 166/235 (70%), Gaps = 3/235 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 221

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R +   + R+P+PEEI +++ +P E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 222 INKLIRVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHL 281

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           GDFIED++A SP D A    L+E    VL +LT REE VLR+RFG+      T  
Sbjct: 282 GDFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTFR 336



 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 47/170 (27%), Positives = 79/170 (46%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + S +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTKNTKPVAELSVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167


>gi|221636011|ref|YP_002523887.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
 gi|221157983|gb|ACM07101.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
          Length = 334

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 99/253 (39%), Positives = 151/253 (59%), Gaps = 7/253 (2%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           +E G    E R +V            A+++++  NLRLV+S+AK+Y +  L  +DLIQEG
Sbjct: 80  IEAGEDTPELRELVRK-------GQEAREKLIRHNLRLVVSIAKRYRSSELPLIDLIQEG 132

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           NIGLM A E++D  LGY+FSTYA +W++QAI R++A+ S TIR+PVHM D I K+ R   
Sbjct: 133 NIGLMTAVERYDPELGYRFSTYATFWIRQAIGRAVANLSRTIRVPVHMHDLIAKIRRAEA 192

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  +  R  T EE+A+ L + V  + +         SL+ PIG++  S +GD + D  +
Sbjct: 193 QIEQQKGRPATNEELAELLGIDVARIEQARTQIPRTSSLDKPIGEDGESSIGDLLPDPRS 252

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              ++ A+   +RE   R L  LT RE  VL MRFG+      TL E+     ++RER+R
Sbjct: 253 DDVVEEALTNAIREQIRRSLEQLTERERTVLVMRFGLDGEQPRTLAEIADALKISRERVR 312

Query: 658 QIEAKAIRKLKHP 670
           Q+E +A++KL++ 
Sbjct: 313 QVEKEALQKLRNS 325


>gi|67922139|ref|ZP_00515654.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856039|gb|EAM51283.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 318

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 110/280 (39%), Positives = 178/280 (63%), Gaps = 8/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE----ASIAKKEMVEANLRLVISVA 460
           ++ K+R EI         + S++     + RK  C        AK++MVEANLRLV+SVA
Sbjct: 41  NLEKLREEIIQ-ETGKEPTNSQWAKAAKLSRKEFCSVVEAGEAAKRKMVEANLRLVVSVA 99

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR
Sbjct: 100 KKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIR 159

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R +S +  R  T  E+A++L +  + VR  L+ +++P+SL+  +
Sbjct: 160 LPIHITEKLNKIKKAQRELSQQKGRAATISELAEELDLTPKQVRDYLERSRQPLSLDLRV 219

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD   + LGD +ED+   SP D A  ++L+    +++  LT ++++V+ +RFG+      
Sbjct: 220 GDNQDTELGDLLEDEGQ-SPEDFATHSSLQFDLEKLMEDLTIQQKQVIALRFGLMDGQPL 278

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL ++G +  ++RER+RQIE +A+ KL+   R   ++ +L
Sbjct: 279 TLAKIGSRLNISRERVRQIEREALSKLRK--RKANIQEYL 316



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/34 (52%), Positives = 24/34 (70%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +S  DPVR YL+E+G + LLS E EI  AKR++
Sbjct: 4   TKSNPDPVRAYLKEIGRVPLLSHEEEILYAKRVQ 37


>gi|307546200|ref|YP_003898679.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
 gi|307218224|emb|CBV43494.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
          Length = 330

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 97/299 (32%), Positives = 171/299 (57%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E++      + +  E            S+   +  +  I     ++  E  H   + R+ 
Sbjct: 28  EIEAGAADDSDEAFEKALSREDRHHHHSLDATQIYLNEIGFSPLLTPEEEVHYGRLARQ- 86

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                  +  M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 87  --GDPQGRSRMIESNLRLVVKIARRYLNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFS 144

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+P+H+  +++  +R AR ++ K+  E T EEIA  L 
Sbjct: 145 TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRAARELTQKLDHEATAEEIADHLD 204

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV  V++++ + +   S++ P+G E    L + + D N + P  + +  ++++     L
Sbjct: 205 KPVASVKRMMGLNERVSSVDYPVGSESDKPLIETLTDDNDLGPESTLVDGDVKQHVDDWL 264

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           A LT ++  V+  RFG+  +   TLE+VG++  +TRER+RQI+ +A++KL+     + L
Sbjct: 265 AELTDKQREVVVRRFGLRGHEASTLEQVGEEIGLTRERVRQIQVEALKKLRRMLDKQGL 323



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/105 (26%), Positives = 41/105 (39%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             D +  E  E     A  +  +      R+D     + D  ++YL E+G   LL+ E E
Sbjct: 18  EADDDAVETVEIEAGAADDSDEAFEKALSREDRHHHHSLDATQIYLNEIGFSPLLTPEEE 77

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +   +    G     + + ES L     I  R  LN G TLL  I
Sbjct: 78  VHYGRLARQGDPQGRSRMIESNLRLVVKIARRY-LNRGLTLLDLI 121


>gi|302543058|ref|ZP_07295400.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460676|gb|EFL23769.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           himastatinicus ATCC 53653]
          Length = 333

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 107/241 (44%), Positives = 151/241 (62%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +     E + AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+ 
Sbjct: 85  EELEAIAAEGARAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYT 144

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   E
Sbjct: 145 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEHME 204

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA++L    E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E
Sbjct: 205 IAEELGSTPERVSDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSE 264

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  L  R   +++ R+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +
Sbjct: 265 ELEDLIGRLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMA 324

Query: 672 R 672
           R
Sbjct: 325 R 325



 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 15/91 (16%), Positives = 33/91 (36%), Gaps = 2/91 (2%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMM 153
            ++   +      R    + +  D V MYL E+    LL    E+ +++ +EAG     +
Sbjct: 10  QATTGGADGANSVRATGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQAVEAGVYAQQI 69

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +    E      A     + +       +++
Sbjct: 70  LDGEAEDTGAAGASREELEAIAAEGARAKDV 100


>gi|167949414|ref|ZP_02536488.1| RNA polymerase, sigma 70 subunit, RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 309

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 80/318 (25%), Positives = 132/318 (41%), Gaps = 61/318 (19%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDL 83
           +      K++I   +++G++T  E+N  LP   V  EQ+ED V M+++MGI V +   DL
Sbjct: 4   EQQRSQLKQLIAKGKEQGFLTYAEVNDHLPEGIVEPEQIEDIVRMINDMGITVHETAPDL 63

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           ED+  S++++     A+  +       DS    T DPVRMY+REMG++ELL+REGE+ IA
Sbjct: 64  EDKTLSDEAVTSDDDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIA 123

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   + A+L   P+T + L     ++ +G   + ++I+           GF    
Sbjct: 124 KRIEDGLKQVSAALATFPVTIEMLHSMLTKVGEGEKRMADVIN-----------GFIDPN 172

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E            +   D                ++D   VD+ P+  E           
Sbjct: 173 ETDEIPIPRPPRAKDSGD----------------EEDEEPVDTGPDPEE----------- 205

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
                           V     E+ + Y  L S        +K  +++ K +   E   +
Sbjct: 206 ----------------VAAKTKELGKRYNALCS------ALKKHGRNNPKTQKALEACAE 243

Query: 324 LVGSLSLNQSRIDLLVEQ 341
                 L  +  + LV Q
Sbjct: 244 SFLEFKLVPNAFNHLVRQ 261


>gi|162450883|ref|YP_001613250.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161161465|emb|CAN92770.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 463

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 101/234 (43%), Positives = 153/234 (65%), Gaps = 1/234 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V ANLRLV + A++  +RG+  LDLIQEGN+GL++AAEKFD+  GY+FSTYAMWW+KQA+
Sbjct: 231 VRANLRLVAAAARQLRHRGVPLLDLIQEGNLGLIRAAEKFDYRRGYRFSTYAMWWIKQAL 290

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +R++  Q   IR+PVH+ +   + ++  R +  +  RE  PEE+A++  + +E ++ + +
Sbjct: 291 SRALLYQGQVIRVPVHIAETRRRALQARRELEQEHAREAAPEEVAERSGLSMEKLQALRE 350

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           +   P+ L+ P+GD+D +  GDF   + A  P +  +   L    + +L SLTPRE  VL
Sbjct: 351 MALPPVYLDAPVGDDDGARQGDFFASEGAA-PDELLVHRRLHAQVSALLESLTPRERDVL 409

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           R+RFG+     HTL E+G  F V+RER+RQIE  A+ KL+  SR + L + L G
Sbjct: 410 RLRFGLDGGQPHTLAEIGGMFSVSRERVRQIEESALSKLRTLSRRQALETPLGG 463



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/120 (22%), Positives = 56/120 (46%), Gaps = 3/120 (2%)

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSS---VFLQKRKDSADRSTDDPVRMYL 125
           +L      +++G     E  +E+ +   +    SS       +R     R ++D   +YL
Sbjct: 10  LLGEAETTIMEGRGAVAETRAEEPIGADTRPPPSSRRGAPTSQRAAPPARPSEDVAAVYL 69

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +E+ +   LSRE E+ + +RIE+    M+ +   SP+  +AL    D++  G   + +++
Sbjct: 70  QEISASAPLSRELEVELGRRIESAERAMVEAWVASPVALRALAALADDVRAGRVDMSDLL 129


>gi|223937956|ref|ZP_03629855.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223893357|gb|EEF59819.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 353

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 100/258 (38%), Positives = 162/258 (62%), Gaps = 3/258 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ +     ++  E   +   ++K       A+++M++ANLRLV+ +A++Y + G+  L
Sbjct: 87  YLREVGQTKLLTPQEEVDLAKRIKK---GDKKAREQMIKANLRLVVKIAREYEDYGMPLL 143

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GLMKA E+FD   G K STY+ WW+KQ+I R++A+QS TIR+PVH+ DK+  
Sbjct: 144 DLINEGNMGLMKAVERFDPAKGAKLSTYSAWWIKQSIKRALANQSKTIRLPVHVVDKLFH 203

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + + + ++   + REPT EE+  +L    + V ++      P SLE P+GD++TS + D 
Sbjct: 204 MRQASVKLQEVLGREPTDEELGDELGFSAQKVAQLRTAAIRPASLEAPLGDDETSRIADV 263

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+ A +P +   +         ++A+L PRE  +LR RFG+  + + TLEEVG++F V
Sbjct: 264 VRDETADTPYEQLEEKTNTSMLRELVATLDPREAEILRYRFGLDGDPERTLEEVGQKFGV 323

Query: 652 TRERIRQIEAKAIRKLKH 669
           TRERIRQI+  A+ KL+ 
Sbjct: 324 TRERIRQIQNVALNKLRK 341



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/138 (19%), Positives = 56/138 (40%), Gaps = 13/138 (9%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            VV+ D+   E+ S+    +    +     ++++    + + +    +YLRE+G  +LL+
Sbjct: 43  KVVEIDEPTLEQLSKTETSVPREVAPVEQPVERQPYDGNTAFN----LYLREVGQTKLLT 98

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            + E+ +AKRI+ G       + ++ L    ++    E  D    L ++I+       E 
Sbjct: 99  PQEEVDLAKRIKKGDKKAREQMIKANLRL--VVKIAREYEDYGMPLLDLIN-------EG 149

Query: 196 KGGFFHGTEGHSYQKRED 213
             G     E     K   
Sbjct: 150 NMGLMKAVERFDPAKGAK 167


>gi|148358826|ref|YP_001250033.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|296106871|ref|YP_003618571.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
 gi|148280599|gb|ABQ54687.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|295648772|gb|ADG24619.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
          Length = 341

 Score =  177 bits (448), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 108/299 (36%), Positives = 178/299 (59%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E D        D               ++   +  +  I     ++  E  H  ++    
Sbjct: 40  EEDLDEFPEFTDDEVFPSFQRGKNIAKALDATQLYLGEIGFSPLLTAEEEIHYATLA--- 96

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+K+M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GLMK+ EKFD   G++FS
Sbjct: 97  LKGDMEARKKMIESNLRLVVKIARRYLNRGLPLLDLIEEGNLGLMKSVEKFDPKRGFRFS 156

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP+PEEIA+ + 
Sbjct: 157 TYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEPSPEEIAEMVD 216

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            P+E V+K+L +  +  S++TPIG ++T  L D I D+N+++P +     NLR+    +L
Sbjct: 217 KPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDTIADENSLNPAELLTNENLRQHIESLL 276

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L+       L
Sbjct: 277 DKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTLRTLLERVGL 335



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 31/106 (29%), Positives = 42/106 (39%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D   D E  E+ LD     ++  VF   ++        D  ++YL E+G   LL+ E 
Sbjct: 29  EEDVEPDIEKMEEDLDEFPEFTDDEVFPSFQRGKNIAKALDATQLYLGEIGFSPLLTAEE 88

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI  A     G       + ES L     I  R  LN G  LL  I
Sbjct: 89  EIHYATLALKGDMEARKKMIESNLRLVVKIARRY-LNRGLPLLDLI 133


>gi|172038507|ref|YP_001805008.1| RNA polymerase sigma factor SigD [Cyanothece sp. ATCC 51142]
 gi|171699961|gb|ACB52942.1| group 2 sigma-70 RNA polymerase sigma factor D [Cyanothece sp. ATCC
           51142]
          Length = 318

 Score =  177 bits (448), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 109/266 (40%), Positives = 170/266 (63%), Gaps = 10/266 (3%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             +    +S  EFR IV            AK++MVEANLRLV+SVAKKY  R L  LDLI
Sbjct: 61  QWAKAAKLSKREFRSIVE-------SGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLI 113

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +
Sbjct: 114 QEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKK 173

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R +S +  R  T  E+A++L +  + VR+ L+  ++P+SL+  +GD   + LGD +ED
Sbjct: 174 AQRELSQQKGRAATVTELAEELDLTPKQVREYLERARQPLSLDLRVGDNQDTELGDLLED 233

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +  SP D A  ++L+    R++  LT +++ V+ +RFG+      TL ++G +  ++RE
Sbjct: 234 -DGQSPEDFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNISRE 292

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+RQIE +A+ KL+   R   ++ +L
Sbjct: 293 RVRQIEREALSKLRK--RKANIQEYL 316



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/34 (50%), Positives = 24/34 (70%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +S  DPVR YL+E+G + LL+ E EI  AKR++
Sbjct: 4   TKSNPDPVRAYLKEIGRVPLLTHEEEILYAKRVQ 37


>gi|88858314|ref|ZP_01132956.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
 gi|88819931|gb|EAR29744.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
          Length = 339

 Score =  177 bits (448), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 171/290 (58%), Gaps = 3/290 (1%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D   +   +D    E        V ++   +  +  I     +S  E    V   RK   
Sbjct: 39  DLDDIESVEDEDADEEIIAKDAIVKNLDATQIYLGEIGFSPLLSAEEE---VYFSRKSLK 95

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
               ++K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTY
Sbjct: 96  GCEASRKRMIESNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTY 155

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EPT EEIA+KL  P
Sbjct: 156 ATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRTARELTQKLDHEPTAEEIAEKLDRP 215

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           VE V K+L++ ++  S++TPIG +    L D + D+    P       ++RE     L  
Sbjct: 216 VEDVTKMLRLNEKITSVDTPIGGDSEKALLDILADEKGGGPESCIQDEDIRENIVHWLEE 275

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  ++  VL  RFG+      TLE+VGK+  +TRER+RQI+ +A+R+LK 
Sbjct: 276 LNAKQREVLARRFGLLGYEPSTLEDVGKEIGLTRERVRQIQVEALRRLKE 325



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 23/111 (20%), Positives = 44/111 (39%), Gaps = 2/111 (1%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V++ +  +D     + LD   S  +     +     A     D  ++YL E+G   LLS
Sbjct: 23  KVMEDEIQDDLLDEVEDLDDIESVEDEDADEEIIAKDAIVKNLDATQIYLGEIGFSPLLS 82

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E E+  +++   G       + ES L    ++      N+    L ++I+
Sbjct: 83  AEEEVYFSRKSLKGCEASRKRMIESNLRL--VVKIARRYNNRGLALLDLIE 131


>gi|24374942|ref|NP_718985.1| RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
 gi|24349657|gb|AAN56429.1|AE015779_6 RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
          Length = 326

 Score =  177 bits (448), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 165/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 49  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKALKGCEKSRNRMIESNLRLVVKIARRY 105

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 106 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 165

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT EEIA+KL +    V ++LK+ ++  S++ P+G +
Sbjct: 166 HVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQVSSVDVSRMLKLNEKITSVDVPLGGD 225

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D + V P       ++  +  + L  L  ++  VL  RFG+      TLE
Sbjct: 226 NDKALLDVLADDDNVGPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG +  +TRER+RQI+ +A+++L+    ++ L
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGAQGL 318



 Score = 41.7 bits (96), Expect = 0.43,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 44/104 (42%), Gaps = 3/104 (2%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++  E   D  D+A+         Q+ +D   +   D  ++YL E+G   LLS E E+  
Sbjct: 17  VDTAEFDLDKEDIAADLVQELGLEQQVQDDL-QKNLDATQLYLGEIGFSPLLSAEEEVYF 75

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +++   G       + ES L    ++      N+    L ++I+
Sbjct: 76  SRKALKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 117


>gi|157414303|ref|YP_001485169.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388878|gb|ABV51583.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 339

 Score =  176 bits (447), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 105/281 (37%), Positives = 165/281 (58%), Gaps = 16/281 (5%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRK---------------GECEASIAKKEM 448
           DSI    + I  + + T     E  H V  ++K                      A+  M
Sbjct: 50  DSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETERTQRNLYQIKIGKRARDRM 109

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +
Sbjct: 110 MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 169

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++ 
Sbjct: 170 TRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLIS 229

Query: 569 ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +    SL+     E+  S LG+ I D N   P++   +   +E     L+ L  RE+++
Sbjct: 230 QSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQKI 289

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 290 MKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330



 Score = 43.7 bits (101), Expect = 0.095,   Method: Composition-based stats.
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 8/94 (8%)

Query: 73  MGINVVDGDDLEDEEGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +       D    E  L      S  S SS+  ++ +  + R   D +  YL  +G
Sbjct: 1   MGIPLESAKSSSDNNFDEPRLPNTAGKSRKSKSSLTAKQSQKKSGRLASDSIGYYLSSIG 60

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            + LL+   EI +A  ++      M  L + P T
Sbjct: 61  RVPLLTPAEEIELAHHVQN-----MKKLLQIPET 89


>gi|239927194|ref|ZP_04684147.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291435537|ref|ZP_06574927.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291338432|gb|EFE65388.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
          Length = 339

 Score =  176 bits (447), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 154/249 (61%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     +     +   AK  M+ ANLRLV+S+AK++ +RGL  LD+IQEGN+GL++A EK
Sbjct: 86  RERWRELEAAVHDGQAAKDRMIRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEK 145

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G+KFSTYA WW++QAI R +A  + T+R+PVH+ +++ K+ +  RR+   + REP
Sbjct: 146 FDHTKGFKFSTYATWWIRQAIERGVATHARTVRLPVHVVEQLQKLGKVERRLHLSLDREP 205

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EE+A++  +  + V  + ++ ++ +SL+TP+ D   + +GD I D   +   + A   
Sbjct: 206 TVEEVARESGLAEKKVVWLRRVGRQVVSLDTPVDDTGDTVVGDLIPDTEVLQAPEVAEFQ 265

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L E     + +L PRE  +L +R+G+      TL+EV     +TRER+RQ+E +++ +L
Sbjct: 266 ALAEELRGAVDTLAPREALILSLRYGLHDGQTRTLQEVADHVGLTRERVRQLEKQSLAQL 325

Query: 668 KHPSRSKKL 676
           +   + ++L
Sbjct: 326 REREQGERL 334



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 21/41 (51%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
                  D +  YLR++G+  LL  E E+ +A+RI AG   
Sbjct: 30  PEPDQEPDLLGQYLRQIGATPLLDAEDEVRLAQRIAAGLRA 70


>gi|254421571|ref|ZP_05035289.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196189060|gb|EDX84024.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 390

 Score =  176 bits (447), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 107/247 (43%), Positives = 164/247 (66%), Gaps = 3/247 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +         +K++M+EANLRLV++VAKKY  R L+FLDLIQEG +GL +  EKFD   G
Sbjct: 144 LDHHMRRGQRSKRKMIEANLRLVVAVAKKYQKRNLEFLDLIQEGTLGLERGVEKFDPMKG 203

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++QAITR+IA Q+ TIR+P+H+ +K++K+ R  R +S K+ R P   EI 
Sbjct: 204 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKRVQRELSQKLGRSPNAAEIG 263

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L +  + VR+ L I ++PISL+  IGD   + L D +ED  A SP D  +Q +LR   
Sbjct: 264 QELELEPKQVREYLSIARQPISLDVRIGDNQDTELQDLLEDDGA-SPEDYTVQQSLRSDI 322

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R+L+ LT +++ V+ +RFG+      +L +VG++  ++RER+RQ+E +A++ L+   R 
Sbjct: 323 FRMLSELTSQQQEVINLRFGLADGNPLSLAKVGQRMGISRERVRQLEQQALKHLRR--RK 380

Query: 674 KKLRSFL 680
             +  +L
Sbjct: 381 ASINGYL 387



 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           T D VR YL E+G + LLS E EI + K+++ 
Sbjct: 72  TTDAVRSYLHEIGRVPLLSHEDEIVLGKQVQK 103


>gi|149917806|ref|ZP_01906301.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
 gi|149821326|gb|EDM80728.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
          Length = 431

 Score =  176 bits (447), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 100/252 (39%), Positives = 161/252 (63%), Gaps = 1/252 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           +   V+ VR+   +   AK + V+ANLRLV+S+A+++ +  +   DLIQEGNIGLMKA +
Sbjct: 180 YAEYVANVRRSSRKLRSAKNKFVKANLRLVVSIARRFNHGRMPLQDLIQEGNIGLMKAVD 239

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD+  G++FSTY  WW++ AI+R+IAD+   +R+PVHM D  HKV +  R +  K+ RE
Sbjct: 240 RFDYRKGFRFSTYGSWWIRHAISRAIADKGRQVRLPVHMIDAYHKVNKARRELEAKLGRE 299

Query: 547 PTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           PT EE+A+   + +  + R    +   PISL+ P+ D D   +GDF+ED+NA  P +   
Sbjct: 300 PTREELAQHTGIALAKIERMGTMLVDNPISLDKPVSDADGRKMGDFLEDENAEDPGEGLE 359

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L E   R+++ L P E  ++R RFG+  + + TL+E+G Q+ ++RERIRQ++ +A+ 
Sbjct: 360 ADALNEQVKRLVSKLRPIEADIIRKRFGLIDDEELTLKEIGGQYSLSRERIRQLQEQALG 419

Query: 666 KLKHPSRSKKLR 677
           K++   +  +L 
Sbjct: 420 KIRRELKRLELM 431


>gi|218441429|ref|YP_002379758.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7424]
 gi|218174157|gb|ACK72890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 318

 Score =  176 bits (447), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 103/249 (41%), Positives = 163/249 (65%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +       AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD  
Sbjct: 71  EELHRAIAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R++S    R  T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQAKGRAATISE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L +    VR  L+  ++P+SL+  +GD   + LG+ +ED    SP D A  ++L+ 
Sbjct: 191 LAEELELTPRQVRDYLERARQPLSLDLKVGDNQDTELGELLEDT-GTSPEDYATHSSLQV 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++++ LTP+++ VL +RFG+      TL ++G +  ++RER+RQIE +A+ KL+   
Sbjct: 250 DLEKLMSDLTPQQKEVLALRFGLVDGQPLTLAKIGVRLNISRERVRQIEREALSKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   ++ +L
Sbjct: 308 RKGNIKEYL 316



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/30 (56%), Positives = 23/30 (76%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            DPVR YLRE+G + LL+ E EI +AKR++
Sbjct: 8   TDPVRAYLREIGRVPLLTHEEEIVLAKRVQ 37


>gi|15606622|ref|NP_214002.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
 gi|2983844|gb|AAC07398.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
          Length = 310

 Score =  176 bits (447), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 96/303 (31%), Positives = 167/303 (55%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K IS    ++  E + +    ++       A K++VE+NLR V+SVAK+Y   GL
Sbjct: 10  INQYLKKISKIPLLTPEEEKELARRAKQ---GDKEALKKLVESNLRFVVSVAKQYIGYGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F +LI  GN+GL++AA++FD   G KF +YA+WW++QAI ++++ Q+  +RIP+     
Sbjct: 67  PFSELIAAGNLGLLEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQSHI 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKK-------------------------------LA 557
           I+K+      +S K++REP+PEEIA++                                 
Sbjct: 127 INKISHIYGELSKKLEREPSPEEIAEELSKQMIAKELEKELGREPTEEEIEERFKKEGYK 186

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E V K L++ + P+SL+ P+G+ + +   DF+         +  IQ  +++    +L
Sbjct: 187 ITPEEVEKYLQVCRVPLSLDAPVGENEDTFFIDFLSKHGTAEVEEKVIQEVIQKEIDDLL 246

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + LT +E +V+ +RFG+  N   TL E+G+   ++RER+RQ+E +A+RKL+  +  + L+
Sbjct: 247 SKLTDKERKVIELRFGLKGNEPKTLREIGEILGLSRERVRQLETRALRKLRSLAMKRHLK 306

Query: 678 SFL 680
            FL
Sbjct: 307 DFL 309



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 15/46 (32%), Positives = 24/46 (52%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           YL+++  I LL+ E E  +A+R + G    +  L ES L F   + 
Sbjct: 13  YLKKISKIPLLTPEEEKELARRAKQGDKEALKKLVESNLRFVVSVA 58


>gi|194334634|ref|YP_002016494.1| RNA polymerase sigma-32 subunit RpoH [Prosthecochloris aestuarii
           DSM 271]
 gi|194312452|gb|ACF46847.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris aestuarii
           DSM 271]
          Length = 299

 Score =  176 bits (447), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 95/283 (33%), Positives = 165/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYELLTAEDEVKLTMAIKEGYDMPVDTPEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEFERDPNTKELATVLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D ++  +   P     + +L     R L+ L PRE  V+R  FGIGM 
Sbjct: 196 APFAQGDDNRLLDVLQ-HDGQKPDHGLTRDSLTLEVERSLSVLAPREADVIRSYFGIGME 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|113969467|ref|YP_733260.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|114046700|ref|YP_737250.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117919573|ref|YP_868765.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
 gi|113884151|gb|ABI38203.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888142|gb|ABI42193.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117611905|gb|ABK47359.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
          Length = 326

 Score =  176 bits (447), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 165/273 (60%), Gaps = 3/273 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            ++   +  +  I     +S  E    V   RK       ++  M+E+NLRLV+ +A++Y
Sbjct: 49  KNLDATQLYLGEIGFSPLLSAEEE---VYFSRKALKGCEKSRNRMIESNLRLVVKIARRY 105

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+
Sbjct: 106 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 165

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +RTAR ++ K+  EPT EEIA+KL +    V ++LK+ ++  S++ P+G +
Sbjct: 166 HVVKELNVYLRTARELAQKLDHEPTAEEIAEKLQVSSVDVSRMLKLNEKITSVDIPLGGD 225

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L D + D + V P       ++  +  + L  L  ++  VL  RFG+      TLE
Sbjct: 226 NDKALLDVLADDDNVGPDYKVQDEDISNSVVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +VG +  +TRER+RQI+ +A+++L+    ++ L
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGAQGL 318



 Score = 41.4 bits (95), Expect = 0.48,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 44/104 (42%), Gaps = 3/104 (2%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           ++  E   D  D+A+         Q+ +D   +   D  ++YL E+G   LLS E E+  
Sbjct: 17  VDTAEFDLDKEDIAADLVQELGLEQQVQDDL-QKNLDATQLYLGEIGFSPLLSAEEEVYF 75

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +++   G       + ES L    ++      N+    L ++I+
Sbjct: 76  SRKALKGCEKSRNRMIESNLRL--VVKIARRYNNRGLALLDLIE 117


>gi|206208346|gb|ACI06117.1| RNA polymerase sigma subunit [Parvibaculum sp. P31]
          Length = 269

 Score =  176 bits (447), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 174/306 (56%), Gaps = 42/306 (13%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           AGR  M+A LCESPLTFQA+IIWRDELN+G  LLR+IIDL+A                  
Sbjct: 1   AGRETMIAGLCESPLTFQAIIIWRDELNEGKILLRDIIDLDATYA--------------- 45

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                                    A KV     +     P   E +E  +D+++ +S  
Sbjct: 46  ----------------------GPDAKKVDHSQAALAGEAPPREEPEEEEVDDEDAESNM 83

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN-----GQKDEKSSVKCKVLKEKLV 322
           +L+AME +L+P+V+   D+IA  Y++LR LQD  V       +   +   + + L E ++
Sbjct: 84  SLAAMEAELKPQVLETFDKIAADYKKLRKLQDQKVEFQLKGEELSSQQEKRYQKLTEDVI 143

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
             V SLSLN +RI+ LVEQLY I+KR+M  EG LLR A+S+GI RD FL+++ G ELDP+
Sbjct: 144 DEVKSLSLNNNRIESLVEQLYSINKRLMGLEGRLLRTAESHGIPRDEFLKQYFGNELDPN 203

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
           W+          W +F   + D I ++R EI++++ ETG+ I E+R IV+MV+KGE EA 
Sbjct: 204 WIRRVSRLKGKGWTSFTKDDRDQIKELREEIQTLASETGLDIQEYRRIVAMVQKGEREAR 263

Query: 443 IAKKEM 448
           IAKKEM
Sbjct: 264 IAKKEM 269


>gi|225849654|ref|YP_002729888.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
 gi|225646208|gb|ACO04394.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
          Length = 281

 Score =  176 bits (447), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 91/270 (33%), Positives = 154/270 (57%), Gaps = 4/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+ ++    ++  E + +    +K       A K++VE NLR V++VAK +   G+   
Sbjct: 14  YIQKMAEHPLLTPEEEKELAKRAKK---GDKEALKKLVEGNLRFVVNVAKNFMGWGVPLT 70

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  GN+GL++AA++FD     KF +YA+WW++QAI ++I  Q+  +RIPV     I K
Sbjct: 71  DLIAAGNLGLIEAAKRFDPERDVKFISYAVWWIRQAIMQTIFQQTGAVRIPVKESLFISK 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGD 590
           V  T  ++  ++KREPT EEIA+K+    + V+  L++ + P SL+ P+G+E +   L D
Sbjct: 131 VKETYEKLKEELKREPTIEEIAEKVGASPKKVKNALQVVRMPYSLDKPLGEEGEDLTLLD 190

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +  K         ++ +L +    +L  L  RE  ++  RFG+      TL EVG+   
Sbjct: 191 VLSKKGTEDVEKEIVEESLHKELNTLLNVLDERERAIIEHRFGLNGEEPKTLTEVGEILG 250

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++RER+RQ+E +A++KL+  +  + L+ FL
Sbjct: 251 ISRERVRQLEQRALKKLRALAMKRHLKDFL 280



 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           +Y+++M    LL+ E E  +AKR + G    +  L E  L F
Sbjct: 13  LYIQKMAEHPLLTPEEEKELAKRAKKGDKEALKKLVEGNLRF 54


>gi|33864510|ref|NP_896070.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641290|emb|CAE22420.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 344

 Score =  176 bits (447), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 96/237 (40%), Positives = 151/237 (63%), Gaps = 1/237 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +
Sbjct: 99  RQRHKIRMGKRARDRMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAM 158

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+
Sbjct: 159 GYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLEL 218

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRE 611
           A  + +  + +  ++  +    SL+     E+  S LG+ I D +   P++   ++  +E
Sbjct: 219 AHAMGIQPQDLEDLIAQSAPCASLDAHARGEEDRSTLGELIPDPDGAEPMEGLDRSIQKE 278

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 279 HLGGWLSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRERVRQLEAKAILKLR 335



 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           + A+ A  +    + +     R   D +  YL  +G + LL+   EI +A  +       
Sbjct: 30  ETANRAGRNGQASRNQNRQGGRLGTDAIGFYLSSIGRVPLLTAAEEIELAHHV-----QA 84

Query: 154 MASLCESP 161
           M  L E P
Sbjct: 85  MKELLELP 92


>gi|189345950|ref|YP_001942479.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
 gi|189340097|gb|ACD89500.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
          Length = 299

 Score =  176 bits (447), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 95/283 (33%), Positives = 166/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTADDEVKLTMAIKEGYDMPVDTVEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P   E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKVLKEYI 297


>gi|6273430|emb|CAB60192.1| putative sigma-like transcription factor [Arabidopsis thaliana]
          Length = 487

 Score =  176 bits (446), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 93/303 (30%), Positives = 169/303 (55%), Gaps = 12/303 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGI--------SISEFRHIV----SMVRKGE 438
           PE +       E + I  I++ +K   V+T +        +I E+   +     +++   
Sbjct: 182 PETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDI 241

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                ++++++ ANLRLV+ +AK+Y NRGL F DL+QEG++GLMK+ EKF    G +F+T
Sbjct: 242 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 301

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q+I +SI   S TIR+P ++   + KV    +    +    P+ EE+A  + +
Sbjct: 302 YAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGV 361

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E + K+L  T+ P+S++ PI  +  +   +   D    +P  S  +  +R     +L 
Sbjct: 362 STEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLN 421

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+P+E R++++RFGI      +L E+G+ + +++ER+RQ+E++A+ +LK    S  L +
Sbjct: 422 VLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHA 481

Query: 679 FLD 681
           + D
Sbjct: 482 YAD 484


>gi|255020521|ref|ZP_05292585.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
 gi|254970041|gb|EET27539.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
          Length = 316

 Score =  176 bits (446), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 99/299 (33%), Positives = 160/299 (53%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +P  V   +   +                 R  ++ I     ++  E  +   +V++ 
Sbjct: 14  EANPVEVEEVEGALDEAESVAPGEADLDWDATRIYLQEIGHNPLLTAEEEIYYGRLVQQ- 72

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+  M+E NLRLV+ VA++Y +RG+  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 73  --GDVRARTRMIECNLRLVVRVARRYLHRGMPLLDLIEEGNLGLIRAVEKFDPERGFRFS 130

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R++ +Q+ TIR+PVH+  ++  V+R AR +  +++REP+ +E+A  L 
Sbjct: 131 TYATWWIRQNIERALMNQTRTIRLPVHVMKELAVVLRAARCLEQELRREPSVDEVAAALD 190

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV+ VR  L++     SL+     +    L + + D  A  P       NL       L
Sbjct: 191 RPVDQVRGCLEMDGRVTSLDNSGQRDQGRDLNEVLSDAEAQGPEAMVAAQNLAVRLQSWL 250

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           A L+ +   VL  RFG+      TLEEVG +  +TRER+RQI+ +A+  L+    ++ L
Sbjct: 251 AGLSEKHRLVLSWRFGLDGGDGATLEEVGTRLGITRERVRQIQVEALLILRRRIEAEGL 309



 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 4/106 (3%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D  +++D E +   ++    A + +  +   +   D    D  R+YL+E+G   LL+ E 
Sbjct: 6   DTQEIDDGEANPVEVEEVEGALDEAESVAPGEADLDW---DATRIYLQEIGHNPLLTAEE 62

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI   + ++ G       + E  L     +  R  L+ G  LL  I
Sbjct: 63  EIYYGRLVQQGDVRARTRMIECNLRLVVRVARRY-LHRGMPLLDLI 107


>gi|302336705|ref|YP_003801911.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301633890|gb|ADK79317.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 322

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 95/251 (37%), Positives = 158/251 (62%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +   R  E     ++  M+ +NLRLV+S+AKKY +RGL FLDLI EGNIGL++A E+FD
Sbjct: 72  YLFRKRTIEAVLRKSRDRMITSNLRLVVSIAKKYQHRGLSFLDLIDEGNIGLIEAVERFD 131

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +    KFSTY  WW++Q++ +++AD+  TIRIP+H+ + I K+    + ++ ++ R+P+ 
Sbjct: 132 YTKRCKFSTYGTWWIQQSVIKALADKGRTIRIPIHVLNIIRKLFSVTKHLTQELGRDPSS 191

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA  + +PVE V  +L+ + E  SL+  + DE+ + L D +   + + P +S     L
Sbjct: 192 AEIAAYMDLPVERVESILQYSGETASLDVTVDDENITSLSDLVFSDDYIEPFESVFHVTL 251

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++    +L  L+ RE+ ++++RFG+   T  TLEE+G    +TRER+RQI+ KAI KL+ 
Sbjct: 252 KDLLDTILGQLSEREQTIIKLRFGLADRTPLTLEEIGSILGITRERVRQIQNKAIEKLRS 311

Query: 670 PSRSKKLRSFL 680
            +  ++L   +
Sbjct: 312 IAAIQELEEIV 322



 Score = 38.3 bits (87), Expect = 4.2,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 24/42 (57%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
               D +  DP+ +YL+++ +  LL++E E+ I + I+  + 
Sbjct: 12  DSDVDFNDSDPLSLYLKQISAYPLLTKEEELMIGREIQERKQ 53


>gi|119897381|ref|YP_932594.1| RNA polymerase sigma factor RpoS [Azoarcus sp. BH72]
 gi|119669794|emb|CAL93707.1| putative RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 311

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 94/265 (35%), Positives = 158/265 (59%), Gaps = 3/265 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E   +   VR        A++ M+E NLRLV+++AK Y NRG+  L
Sbjct: 44  YLNEIGANPLLSAEEEAALARRVR---AGDFDARQTMIERNLRLVVNIAKHYLNRGIPLL 100

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL++EGN+GLM A EKFD   G++FSTYA WW++Q I R+I +QS TIR+PVH+  ++++
Sbjct: 101 DLVEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKELNQ 160

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V+R  R +      + + +EIA++L  P+E VR +L +++   SL+ P+  + T  +G+ 
Sbjct: 161 VLRAQRVVEAASNGDFSLDEIARRLDKPIEEVRAILALSEHTASLDAPLDIDPTLSIGES 220

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D++A +P      A +       +  L  ++  V+R R+GIG     TLEE+  +  +
Sbjct: 221 LADEHAETPESQIHNAEIEGLIRAWIDMLNDKQRLVIRHRYGIGECELMTLEELAARLEL 280

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQI+ +A+ +L+   + + +
Sbjct: 281 TRERVRQIQLEALGQLRRILKRRGI 305



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 23/120 (19%), Positives = 44/120 (36%), Gaps = 9/120 (7%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           +S +                   +    D  ++YL E+G+  LLS E E A+A+R+ AG 
Sbjct: 11  ESHEPDLPLEVEVFAEPHAPVFENDFLSDVTQIYLNEIGANPLLSAEEEAALARRVRAGD 70

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                ++ E  L    ++       +    L ++++       E   G  H  E    ++
Sbjct: 71  FDARQTMIERNLRL--VVNIAKHYLNRGIPLLDLVE-------EGNLGLMHALEKFDPER 121


>gi|88809396|ref|ZP_01124904.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786615|gb|EAR17774.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 339

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/253 (38%), Positives = 156/253 (61%), Gaps = 2/253 (0%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +++  + + E        R        A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QE
Sbjct: 79  AMKELLDVPEDERTPRQ-RHRIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQE 137

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R  
Sbjct: 138 GAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRIT 197

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDK 595
           R +S++  R+P   E++  + +    + +++  +    SL+     E+  S LG+ I D 
Sbjct: 198 RELSHRFGRQPNRLELSNAMGIAPRDLEELIAQSAPCASLDAHARGEEDRSTLGELIPDP 257

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           N   P++   ++  +E     L+ L  RE+++LR+RFG+      TL E+G+Q  V+RER
Sbjct: 258 NGDEPMEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGLDGAEPLTLAEIGRQINVSRER 317

Query: 656 IRQIEAKAIRKLK 668
           +RQ+EAKAI KL+
Sbjct: 318 VRQLEAKAILKLR 330



 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 19/92 (20%), Positives = 33/92 (35%), Gaps = 8/92 (8%)

Query: 73  MGINV---VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +   V+       E    +    ++   S     +      R + D +  YL  +G
Sbjct: 1   MGIPLESEVEASKPSSTEPVLPATSQRNTGLRSRQTANRSSRQVGRLSTDSIGYYLSTIG 60

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            + LL+   EI +A  +       M  L + P
Sbjct: 61  RVPLLTAAEEIELAHHV-----QAMKELLDVP 87


>gi|332999494|gb|EGK19079.1| RNA polymerase sigma factor RpoS [Shigella flexneri VA-6]
          Length = 359

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 96/269 (35%), Positives = 170/269 (63%), Gaps = 3/269 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G++  +TRER+RQI+ + +R+L+   +++
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQ 320



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|297159879|gb|ADI09591.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           bingchenggensis BCW-1]
          Length = 333

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 107/234 (45%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E + AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 92  AEGARAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA +L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEHSEIAAELGS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 TTERVSDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++ R+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 RLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 325



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 2/91 (2%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMM 153
            +++S +      R    + +  D V MYL E+    LL    E+ +++ IEAG     +
Sbjct: 10  QATSSGADGANSVRATGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQAIEAGVYAQQI 69

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +    E      A     + +       +++
Sbjct: 70  LDGEIEDAPAAGASRGELEAIAAEGARAKDV 100


>gi|33862253|ref|NP_893814.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634471|emb|CAE20156.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 339

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 105/281 (37%), Positives = 161/281 (57%), Gaps = 16/281 (5%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE---------------ASIAKKEM 448
           DSI    + I  + + T     E  H V  ++K                      A+  M
Sbjct: 50  DSIGYYLSSIGRVPLLTAAEEIELAHHVQNMKKMLEIPEIERSSKHLRLIKIGKRARDRM 109

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+SVAKKY N+GL  LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +
Sbjct: 110 MSANLRLVVSVAKKYQNQGLDLLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 169

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+I + + TIR+P+H+ +K+ K+ R +R +S K  R+PT  E+A  + +  + +  ++ 
Sbjct: 170 TRAIDNSARTIRLPIHISEKLSKMRRVSRELSQKSGRQPTRLEMATAMGIEQKDLEDLIS 229

Query: 569 ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +    SL+     E+  S LG+ I D N   P++   +   +E     L  L  RE+++
Sbjct: 230 QSAPCASLDAHARGEEDRSTLGELIPDPNGEEPMEGMDRTIQKEHLGTWLTQLNEREQKI 289

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 290 MKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330



 Score = 41.0 bits (94), Expect = 0.70,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 31/68 (45%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           EE    +    +  +  S+  ++ +  + R   D +  YL  +G + LL+   EI +A  
Sbjct: 17  EEPRLPNTAGKTRKTKPSLTAKQNQKKSARLASDSIGYYLSSIGRVPLLTAAEEIELAHH 76

Query: 146 IEAGRAMM 153
           ++  + M+
Sbjct: 77  VQNMKKML 84


>gi|300724640|ref|YP_003713965.1| sigma S (sigma 38) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|6643920|gb|AAF20816.1|AF198628_2 RpoS [Xenorhabdus nematophila]
 gi|297631182|emb|CBJ91877.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus nematophila ATCC
           19061]
          Length = 331

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       A++ M+E+NLRLV+ ++++Y+N
Sbjct: 56  LDATQLYLGEIGFSPLLTAEEE---VLFARRALRGDIAARQRMIESNLRLVVKISRRYSN 112

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 113 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 172

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EPT EEIA++L  PVE + +++++ +   S++TPI  +  
Sbjct: 173 VKELNVYLRTARELAHKLDHEPTVEEIAERLDKPVEDISRMMRLNERITSVDTPISGDSD 232

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P  +    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 233 KALLDILSDENDSGPETTIQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAETLEDV 292

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+    ++ L
Sbjct: 293 GREIGLTRERVRQIQVEGLRRLRDILHTQGL 323



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/113 (25%), Positives = 42/113 (37%), Gaps = 5/113 (4%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS----ADRSTDDPVRMYLREMGSI 131
            + D  DL++     D  D A   +   V             ++   D  ++YL E+G  
Sbjct: 10  ELYDDADLDENSMEADDFDEALLKNGDDVTNLDEDLDLLQGVNQRMLDATQLYLGEIGFS 69

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  PLLTAEEEVLFARRALRGDIAARQRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|260599105|ref|YP_003211676.1| RNA polymerase sigma factor RpoS [Cronobacter turicensis z3032]
 gi|260218282|emb|CBA33240.1| RNA polymerase sigma factor rpoS [Cronobacter turicensis z3032]
          Length = 351

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 76  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYSN 132

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 133 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 192

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 193 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 252

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 253 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 312

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 313 GREIGLTRERVRQIQVEGLRRLREILQGQGL 343



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     + +   D  ++YL E+G   LL+ E 
Sbjct: 37  EFDENGVEAFDEKALVEEEPSDNDLAEEELLSQGSTQRVLDATQLYLGEIGYSPLLTAEE 96

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 97  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 141


>gi|270157097|ref|ZP_06185754.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|289164492|ref|YP_003454630.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
 gi|269989122|gb|EEZ95376.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|288857665|emb|CBJ11508.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
          Length = 341

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 112/309 (36%), Positives = 186/309 (60%), Gaps = 7/309 (2%)

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           D F+E+    E D     ++ D     ++   A  +  +   +  +  I     +S  E 
Sbjct: 34  DSFIEK--SEEEDFELPDFSDDHAFPSFRGKSA--IKMMDATQLYLSEIGFSPLLSAEEE 89

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            H  ++          A+K+M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GLMK+ EK
Sbjct: 90  VHYATLA---LKGDVAARKKMIESNLRLVVKISRRYLNRGLPLLDLIEEGNLGLMKSVEK 146

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP
Sbjct: 147 FDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEP 206

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +PEEIA+ +  P+E V+K+L +  +  S++TPIG ++   L D I D+N+V+P +     
Sbjct: 207 SPEEIAEMVDKPLEDVQKLLGLNDKVTSVDTPIGFDENKSLLDTIPDENSVNPAELLTNE 266

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           NLR     +L  LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L
Sbjct: 267 NLRLHIESLLDKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTL 326

Query: 668 KHPSRSKKL 676
           +       L
Sbjct: 327 RSLLEKMGL 335



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 27/105 (25%), Positives = 37/105 (35%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            DDL+      +  D      +        +  +     D  ++YL E+G   LLS E E
Sbjct: 30  EDDLDSFIEKSEEEDFELPDFSDDHAFPSFRGKSAIKMMDATQLYLSEIGFSPLLSAEEE 89

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  A     G       + ES L     I  R  LN G  LL  I
Sbjct: 90  VHYATLALKGDVAARKKMIESNLRLVVKISRRY-LNRGLPLLDLI 133


>gi|78186275|ref|YP_374318.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
 gi|78166177|gb|ABB23275.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
          Length = 299

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 93/283 (32%), Positives = 166/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTADDEVRLTKAIKEGFDMPVDTTEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V++  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHL-PDHGLNRDSLTLEVERSLSVLAPREADVIKSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  +  K L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRTSAYCKVLKEYI 297


>gi|315185771|gb|EFU19537.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 338

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 101/275 (36%), Positives = 164/275 (59%), Gaps = 3/275 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I +I+  ++ +S    +   +  H     R+ +      K  M+ ANLRLV+S+AKKY 
Sbjct: 66  EIQRIKLRLRELSS---LPEEQRAHHFEEERRLDQRLRELKNRMITANLRLVVSIAKKYQ 122

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +RGL  LDLI EGNIGL++A E+FD+  G +FSTY  WW++QAI +S+AD+S  IRIP+H
Sbjct: 123 HRGLSLLDLIDEGNIGLIEAVERFDYTKGCRFSTYGTWWIRQAIVKSLADKSRVIRIPIH 182

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I  V   ++ ++ ++ R+PT EE+++   +P   V +++++++E  SL+  + +E+
Sbjct: 183 MLNTIKNVFMLSKELAQELGRDPTEEELSRYTGLPDRRVAEIMQVSQETASLDITVDEEN 242

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            + LGD + D     P +      LR+     L+ L+ RE  V+ +RFG+      TLEE
Sbjct: 243 MTTLGDLVSDDEDQGPFEKVFHRYLRDVLLEALSDLSERERNVISLRFGLNGEGPLTLEE 302

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            GK   +TRER+RQI+ KA+ KL+     +  R +
Sbjct: 303 TGKLLGITRERVRQIQEKALAKLREMGFIRDFRHY 337


>gi|290511076|ref|ZP_06550445.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
 gi|289776069|gb|EFD84068.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
          Length = 347

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 72  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYSN 128

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 129 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 188

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 189 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 248

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 249 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 308

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 309 GREIGLTRERVRQIQVEGLRRLREILQGQGL 339



 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/117 (28%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     GI V D   L +EE S+  L      S  +           +   D  ++YL E
Sbjct: 32  AEFDENGIEVFDEKALVEEEPSDSDLAEEELLSQGA----------TQRVLDATQLYLGE 81

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 82  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 137


>gi|148243603|ref|YP_001228760.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851913|emb|CAK29407.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 323

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 98/276 (35%), Positives = 159/276 (57%), Gaps = 19/276 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMV------------------RKGECEASIAKKEMVEANL 453
            + +I     ++ +E   +   V                  R+       A+  M+ ANL
Sbjct: 39  YLSNIGRVPLLTAAEEIELAHQVQQMKQLSEIPAEERTPKQRQQVRMGCRARDRMMAANL 98

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I 
Sbjct: 99  RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 158

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           + + TIR+P+H+ +K+ K+ R  R ++++  R+P   E+A  + M  + + ++L  +   
Sbjct: 159 NSARTIRLPIHISEKLSKMRRITRELTHRFGRQPNRLELAHAMGMEPDELEELLSQSAPC 218

Query: 574 ISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            SL+     E+  S LG+ I D +    ++S  +   +E     +  L  RE+++L++RF
Sbjct: 219 ASLDAHARGEEDRSTLGELIPDPSCNDSMESMDRRIQKEHLGTWITQLNEREQKILKLRF 278

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           G+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 279 GLEGAEPQTLAEIGRQINVSRERVRQLEAKAILKLR 314



 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 5/50 (10%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           + R + D +  YL  +G + LL+   EI +A +++      M  L E P 
Sbjct: 28  SGRLSTDSIGWYLSNIGRVPLLTAAEEIELAHQVQQ-----MKQLSEIPA 72


>gi|167745452|ref|ZP_02417579.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|317472996|ref|ZP_07932299.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|167655173|gb|EDR99302.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|316899541|gb|EFV21552.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 347

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 119/299 (39%), Positives = 188/299 (62%), Gaps = 4/299 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           + ++     G      A        ++  +  I     +S  +   +   +      +  
Sbjct: 51  IEFSDFTAAGHADTAEAENAVMEDSVKAYLHRIGRIPLLSKDQEERLAKEIE---AGSQS 107

Query: 444 AKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           AK +M+ +NLRLV+SVAK+Y    G+  LDLIQEGNIGLMKA +KFD+  GYKFSTYAMW
Sbjct: 108 AKDKMINSNLRLVVSVAKRYAAGSGMALLDLIQEGNIGLMKAVDKFDYRRGYKFSTYAMW 167

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q++TR+IADQ+ TIRIPVHM++K+ KV   AR+   +  REP  +E+A+ + +  + 
Sbjct: 168 WIRQSVTRAIADQARTIRIPVHMKEKMGKVSGAARKFLEENGREPNADELAELMEISRDQ 227

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + +++++  + +SL++P+G+E+ + L +F+ D++      +A Q  L E    +L+ LT 
Sbjct: 228 MDEIMRLYSDTVSLDSPVGEEEDAMLMNFVADESMPEQYQTAEQGILSEQINEILSELTE 287

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RE+ +LR+RFG   N   TLEEVG+++ VTRERIRQIE KA+RKLK    +K LR++++
Sbjct: 288 REQTILRLRFGFVENRIWTLEEVGREYHVTRERIRQIEGKALRKLKMKKETKSLRAYIE 346



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 54/333 (16%), Positives = 109/333 (32%), Gaps = 42/333 (12%)

Query: 28  DDSWKKMIKL-ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
           ++  +++IK   +    + ++E++       +S ++ +  +  L +  I           
Sbjct: 4   EERIQELIKAAGQNHNVIQLDEVDQVF-DKSLSEQEFDYVIGRLKDQNI----------- 51

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
                       +  ++       ++ +   +D V+ YL  +G I LLS++ E  +AK I
Sbjct: 52  ----------EFSDFTAAGHADTAEAENAVMEDSVKAYLHRIGRIPLLSKDQEERLAKEI 101

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG       +  S L     +  R     G  LL  I         E   G     +  
Sbjct: 102 EAGSQSAKDKMINSNLRLVVSVAKRYAAGSGMALLDLI--------QEGNIGLMKAVDKF 153

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
            Y++    S        Q       + A  ++  R  V    +  +         E++  
Sbjct: 154 DYRRGYKFSTYAMWWIRQSV---TRAIADQARTIRIPVHMKEKMGKVSGAARKFLEENGR 210

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
              +    +L       +DEI  +Y +  SL               +  +L   +     
Sbjct: 211 EPNADELAELMEISRDQMDEIMRLYSDTVSL--------DSPVGEEEDAMLMNFVADESM 262

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 +   +L EQ+ +I   +   E  +LRL
Sbjct: 263 PEQYQTAEQGILSEQINEILSELTEREQTILRL 295


>gi|81299483|ref|YP_399691.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 7942]
 gi|123557285|sp|Q31QG5|RPOD3_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD3
 gi|81168364|gb|ABB56704.1| group2 RNA polymerase sigma factor SigD [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 100/280 (35%), Positives = 173/280 (61%), Gaps = 7/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVA 460
            + ++R  ++S   +   S  E+       +  +R+ +     AK++M+EANLRLV+SVA
Sbjct: 42  KLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVA 101

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR
Sbjct: 102 KKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIR 161

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R++S ++ R  T  E+A  L +    VR  L+  + P+SL+  +
Sbjct: 162 LPIHITEKLNKIKKMQRQLSQQLGRTATLPELAAALDLTPAQVRDYLEKARHPLSLDLRV 221

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD   + LGD +E  +  +P +  +QA++R    R+L  LT ++ +V+ +R+G+      
Sbjct: 222 GDNQDTELGDLLE-TDCTTPEEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVM 280

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL  +G +  ++RER+RQ+E +A+  L+      +++ +L
Sbjct: 281 TLASIGDRLQISRERVRQLEREALHTLRQA--RSQVQEYL 318



 Score = 44.4 bits (103), Expect = 0.071,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 23/36 (63%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  T D VR YLRE+G + LL+ E E+ + KR++ 
Sbjct: 4   TETPTSDLVRTYLREIGRVPLLTHEEEVVLGKRVQQ 39


>gi|284929771|ref|YP_003422293.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
 gi|284810215|gb|ADB95912.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
          Length = 318

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 102/249 (40%), Positives = 162/249 (65%), Gaps = 3/249 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +         AK++MVEANLRLV+SVAKKY  R L  LDLIQEG IG+ +  EKFD  
Sbjct: 71  RELHSAIASGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPT 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ +  R +S    R+ T  E
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRELSQARGRDATIAE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A++L +  + VR+ L+  ++P+SL+  +GD   + LGD +ED +  SP D A  ++L+ 
Sbjct: 191 LAEELDLTPKQVREYLERARQPLSLDLRVGDNQDTELGDLLED-DGPSPEDFATHSSLQF 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  LT +++ V+ +RFG+      TL ++G +  ++RER+RQIE +A+ KL+   
Sbjct: 250 DLEILMEDLTTQQKEVIALRFGLTDGQPLTLAKIGCRLNISRERVRQIEREALSKLRK-- 307

Query: 672 RSKKLRSFL 680
           R   ++ +L
Sbjct: 308 RKANIQEYL 316



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/34 (52%), Positives = 24/34 (70%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +S  DPVR YLRE+G + LL+ E EI  AKR++
Sbjct: 4   TKSNLDPVRSYLREIGRVPLLTHEEEILYAKRVQ 37


>gi|75908113|ref|YP_322409.1| RNA polymerase sigma factor SigD [Anabaena variabilis ATCC 29413]
 gi|75701838|gb|ABA21514.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 332

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 100/232 (43%), Positives = 160/232 (68%), Gaps = 1/232 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  +AK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  ADGEVAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S ++ R PT  E+A +L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQRLGRAPTAGELANELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR+ L+  + P+SL+  +GD   + LG+ +ED  A SP D  +Q++L      ++ 
Sbjct: 212 TPKQVREYLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEDFVMQSSLSNDLEVLME 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            LTP+++ V+ +RFG+      TL  +G+   ++RER+RQIE +A+ KL+  
Sbjct: 271 QLTPQQKEVITLRFGLIDGQALTLARIGEILNISRERVRQIEREALTKLRKS 322



 Score = 44.1 bits (102), Expect = 0.083,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLC 158
            D VR YLRE+G + LLS E EI   K+++       +   L 
Sbjct: 22  TDLVRTYLREIGRVPLLSHEEEIRYGKQVQRSTTLQEVREELA 64


>gi|23306706|gb|AAN15274.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306708|gb|AAN15270.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306710|gb|AAN15272.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 277

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 2   LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 119 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 179 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 238

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 239 GREIGLTRERVRQIQVEGLRRLREILQTQGL 269



 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
             D  ++YL E+G   LL+ E E+  A+R   G       + ES L     I  R   N 
Sbjct: 1   MLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NR 59

Query: 177 GTTLLREI 184
           G  LL  I
Sbjct: 60  GLALLDLI 67


>gi|304373196|ref|YP_003856405.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
 gi|304309387|gb|ADM21867.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
          Length = 524

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 110/298 (36%), Positives = 175/298 (58%), Gaps = 11/298 (3%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  +KN ++   D I      I        ++  E  ++   ++ G      A+  ++  
Sbjct: 229 DAAYKNKLSDTNDIIKWYMRWIGKYGKL--LTPEEENNLAKQIKNGGRAGKRARHTLINR 286

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVI+ AK+Y NRGL F+DLI EGN G++KA +K+D+  GYKFSTYA WW++QAITR+
Sbjct: 287 NLRLVINNAKRYKNRGLTFIDLISEGNQGILKAVDKYDYTKGYKFSTYATWWIRQAITRA 346

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVEGVRKVLKI 569
           +ADQ+  IRIPVHM + I+K+ +  R +  +    PT E+IA+ +      E VR   KI
Sbjct: 347 VADQARIIRIPVHMVETINKINKIERELQQEYGVTPTDEQIAEVMGGDFTAEKVRYTKKI 406

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVL 628
             +PISL+  IG E+ S   DFI+D++ +SP+D + +    +   +++  +L   E+  +
Sbjct: 407 NIDPISLDKAIGKEEDSSFSDFIKDESVISPIDYSEREEKTKILKQMIENNLDNDEKVFI 466

Query: 629 RMRFGIGMN------TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             R+G G +        H+ +E+ K+  VT+ERIRQIE+K ++KL+HP +  K R  +
Sbjct: 467 MKRYGFGTDPNGEQYRIHSFDELAKERGVTKERIRQIESKILKKLRHPQKKWKQRDLI 524


>gi|290476558|ref|YP_003469463.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
 gi|289175896|emb|CBJ82699.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
          Length = 331

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 95/277 (34%), Positives = 170/277 (61%), Gaps = 3/277 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                 +   +  +  I     ++  E    V   R+       A++ M+E+NLRLV+ +
Sbjct: 50  EVNQRVLDATQLYLGEIGFSPLLTAEEE---VLFARRALRGDIAARQRMIESNLRLVVKI 106

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 107 SRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 166

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +++K+  EP+ EEIA+KL  P++ V +++++ +   S++TP
Sbjct: 167 RLPIHIVKELNVYLRTARELAHKLDHEPSVEEIAEKLDRPIDDVSRMMRLNERITSVDTP 226

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           I  +    L D + D+N   P  +    +++++  + L  L  ++  VL  RFG+     
Sbjct: 227 ISGDSDKALLDILSDENDSGPETTIQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEA 286

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLE+VG++  +TRER+RQI+ + +R+L+    ++ L
Sbjct: 287 ETLEDVGREIGLTRERVRQIQVEGLRRLRDILHTQGL 323



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 28/113 (24%), Positives = 41/113 (36%), Gaps = 5/113 (4%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK----DSADRSTDDPVRMYLREMGSI 131
            + D  DL++     D  D A       +             ++   D  ++YL E+G  
Sbjct: 10  ELYDEADLDEHGMEADDFDEALLKDGDGLTNADENLDLLQEVNQRVLDATQLYLGEIGFS 69

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 70  PLLTAEEEVLFARRALRGDIAARQRMIESNLRLVVKISRRYS-NRGLALLDLI 121


>gi|167843756|ref|ZP_02469264.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|254197157|ref|ZP_04903580.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|169653899|gb|EDS86592.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
          Length = 482

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTTASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|182415180|ref|YP_001820246.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177842394|gb|ACB76646.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 353

 Score =  176 bits (446), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 113/264 (42%), Positives = 169/264 (64%), Gaps = 4/264 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ I     ++I E   +   +RK       A+  M++ANLRLV+ +A  Y + GL
Sbjct: 51  LQLYLQEIGKTALLTIDEEISLAKRIRK---GDKAARDHMIKANLRLVVKIAMDYKDFGL 107

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI EGNIGL+KA E+FD   G K STYA WW+KQ+I R++A+QS TIR+PVH+ DK
Sbjct: 108 PLLDLISEGNIGLIKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDK 167

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSH 587
           I K+ RTA  ++ ++ REPT EE+A +L +P   V  +  ++  P SL+ P+G+E D++ 
Sbjct: 168 ISKMRRTAMALTEELGREPTDEELAIELQIPTSKVAHLKSVSVRPASLDAPVGEEGDSAT 227

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            G+ + D NAVSP +   + NL      ++ASL  RE  ++R+RFG+    + TLEEVG+
Sbjct: 228 FGEIVGDDNAVSPFEGLREKNLNSDLHAMVASLDEREAEIIRLRFGLDGKDELTLEEVGR 287

Query: 648 QFCVTRERIRQIEAKAIRKLKHPS 671
           +F VTRERIRQ+E  A+ K++   
Sbjct: 288 RFHVTRERIRQLEYLALSKMRKAM 311



 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 20/95 (21%), Positives = 40/95 (42%), Gaps = 1/95 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP-VRMYLREMGSIELLSREG 138
               E E  +  +++L  +  +      +  D      D   +++YL+E+G   LL+ + 
Sbjct: 9   STPDETETYTAPTVELPDAPPSFLEKPDRVADVPVAHGDRSNLQLYLQEIGKTALLTIDE 68

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           EI++AKRI  G       + ++ L     I    +
Sbjct: 69  EISLAKRIRKGDKAARDHMIKANLRLVVKIAMDYK 103


>gi|2624188|emb|CAA05499.1| rpoS gene [Kluyvera cryocrescens]
          Length = 345

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 70  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 126

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 127 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 186

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 187 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 246

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 247 KALLDILADENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 306

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 307 GREIGLTRERVRQIQVEGLRRLREILQGQGL 337



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E  L+    + +     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 31  EFDENGAETFDEKVLNEEEPSDSELAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 90

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 91  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 135


>gi|42526449|ref|NP_971547.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|41816642|gb|AAS11428.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|325473389|gb|EGC76584.1| RNA polymerase sigma factor [Treponema denticola F0402]
          Length = 286

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 101/277 (36%), Positives = 164/277 (59%), Gaps = 4/277 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  +   +K I+    ++  E      +  K       AK  +V +NLR V++VAKKY 
Sbjct: 12  EMNSLATYLKEINQIPLLTAEEEIKYAKLAEK---GDEDAKNMLVNSNLRFVVNVAKKYQ 68

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N+GL  +DLI EGNIGLM AAE+FD   GYKF +YA+WW+KQ+I ++I ++S  IR+P++
Sbjct: 69  NQGLPLMDLISEGNIGLMNAAERFDVSKGYKFISYAVWWIKQSILKAICEKSRMIRLPLN 128

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
             +++ ++ +  + +           EIA  L M    V  ++   +EPIS++ P+ DE 
Sbjct: 129 RANELVQIEKAKKEIDFSGNETKELNEIAGILNMDNSMVHTIMNAAREPISIDAPVFDEP 188

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +S + DF++D+    P D A+  +LR+    +L +L  RE  ++R RFG+G     +L+
Sbjct: 189 GSSSVNDFLQDETHQMPEDYAMDMSLRDEVNELLKNLDDREAEIIRYRFGLGGYAPLSLK 248

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           EVG  F +T+ERIRQIE KA+++LK P+  +KL  ++
Sbjct: 249 EVGLIFNLTKERIRQIEKKALQQLKKPAEKQKLAVYV 285



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+  I LL+ E EI  AK  E G       L  S L F  ++    +  +    L +
Sbjct: 19  YLKEINQIPLLTAEEEIKYAKLAEKGDEDAKNMLVNSNLRF--VVNVAKKYQNQGLPLMD 76

Query: 184 II 185
           +I
Sbjct: 77  LI 78


>gi|226226116|ref|YP_002760222.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089307|dbj|BAH37752.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 295

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 93/281 (33%), Positives = 158/281 (56%), Gaps = 3/281 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A        +   +  +S    +  +E   +   +R        A +E+V+ NLR VIS
Sbjct: 16  IAPSEPERDILDQYLYEVSTYPLLKAAEEIELAKKIR---AGDQDALQELVKRNLRFVIS 72

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKY NRGL  +DLI EGN+GL+ AA KFD   G KF +YA+WW++QAI  S+A Q  T
Sbjct: 73  VAKKYQNRGLPLIDLIGEGNVGLLTAARKFDPDQGVKFISYAVWWIRQAILSSLARQGRT 132

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+P++    + ++++ +  +  K++REP+PEE+A+   + V+ V+ +  +    + L+ 
Sbjct: 133 VRVPLNRTADLSRIIKASEILRQKLRREPSPEELAQVTGLSVDVVQSLAALNTGDVRLDA 192

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+  +    L +           + A+   L +   + L++L PR+ +VLR+ FG+    
Sbjct: 193 PMDPDGDRSLIERFVADEMPDTEEEAMNRFLTDEIEQALSTLPPRDAKVLRLYFGLEGGR 252

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +HTLEE+G    VTRER+RQ+  +A+++L+     + L SF
Sbjct: 253 EHTLEEIGSMLGVTRERVRQLRDRALKRLREGDVGRALSSF 293



 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+ +  LL    EI +AK+I AG    +  L +  L F  +I    +  +    L +
Sbjct: 29  YLYEVSTYPLLKAAEEIELAKKIRAGDQDALQELVKRNLRF--VISVAKKYQNRGLPLID 86

Query: 184 IIDLEACIGPESKGGFFHGTEG 205
           +I  E  +G  +    F   +G
Sbjct: 87  LI-GEGNVGLLTAARKFDPDQG 107


>gi|326794473|ref|YP_004312293.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
 gi|326545237|gb|ADZ90457.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
          Length = 329

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 98/270 (36%), Positives = 163/270 (60%), Gaps = 4/270 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                S+   +  +  I     ++  E  +   +          A+K M+E+NLRLV+ +
Sbjct: 45  EDNSKSLDVTQLYLSEIGFSPLLTAEEEVYFARLA---LKGDEAARKRMIESNLRLVVKI 101

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 102 SRRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 161

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +R AR ++ ++  EP+PEEIA KL  PVE V+K+L + +   S+++P
Sbjct: 162 RLPIHVVKELNVYLRAARELTQQLDHEPSPEEIADKLDRPVEDVQKMLSLNERISSIDSP 221

Query: 580 I-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           + G E    L + I D    +P D   + ++  +    L +L  ++  V+  RFG+    
Sbjct: 222 LGGSEGDKSLVEVIPDTQHSNPEDERQEGDVLNSIDGWLDALNEKQREVIARRFGLRGYE 281

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TLE+VG +  +TRER+RQI+ +A+RKL+
Sbjct: 282 PSTLEDVGAEIGLTRERVRQIQVEALRKLR 311



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            ++ +   D  +   +    S    +  +  +  + D  ++YL E+G   LL+ E E+  
Sbjct: 16  ADNVDLELDLEEGQDTTEFDSAVSARYSNEDNSKSLDVTQLYLSEIGFSPLLTAEEEVYF 75

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           A+    G       + ES L     I  R  LN G +LL  I
Sbjct: 76  ARLALKGDEAARKRMIESNLRLVVKISRRY-LNRGLSLLDLI 116


>gi|291278687|ref|YP_003495522.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290753389|dbj|BAI79766.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 298

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 102/275 (37%), Positives = 163/275 (59%), Gaps = 4/275 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D +  I   +  I     +S  E   +   + +       AK  M+  NL+LV+S+AKKY
Sbjct: 22  DDLESITIYLNEIIKYPTLSKEEEIELSKRIEQ---GDEEAKNLMINCNLKLVVSIAKKY 78

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGLQ +DLI EGNIGL+KA EKFD+  G+KFSTYA WW++QAI R++ +Q+  +RIPV
Sbjct: 79  NNRGLQLIDLINEGNIGLIKAVEKFDYRKGFKFSTYATWWIRQAIERALVNQTKMVRIPV 138

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           HM + I+KV +   ++  K+KREPT  E++ +  M +  ++K +   ++ IS++  I ++
Sbjct: 139 HMNENINKVKKATEKLRRKLKREPTLFELSTECNMSLLTIQKTIDAMQQNISIDGTINED 198

Query: 584 DTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D S L D + D  +   P    +Q   RE     +  L   E+ ++  RFG+      TL
Sbjct: 199 DNSTLHDILPDPESKADPFKKIVQEKNRELIMNWIECLNENEKELIIKRFGLDGKEPETL 258

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           +++GK+  VTRER+RQIE + + KL++  ++K ++
Sbjct: 259 DKIGKRLGVTRERVRQIEKRILTKLRNHLKTKNIK 293



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 27/118 (22%), Positives = 45/118 (38%), Gaps = 11/118 (9%)

Query: 100 SNSSVFLQKRKDSADRSTDD--PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
                     + + D  TDD   + +YL E+     LS+E EI ++KRIE G       +
Sbjct: 4   ELDKELENIEEITNDVPTDDLESITIYLNEIIKYPTLSKEEEIELSKRIEQGDEEAKNLM 63

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
               L  + ++    + N+    L ++I+       E   G     E   Y+K    S
Sbjct: 64  INCNL--KLVVSIAKKYNNRGLQLIDLIN-------EGNIGLIKAVEKFDYRKGFKFS 112


>gi|91217671|ref|ZP_01254628.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
 gi|91184175|gb|EAS70561.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
          Length = 288

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 100/273 (36%), Positives = 167/273 (61%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    I+  E   +   +R        A +++  ANLR V+SVAK+Y N+GL
Sbjct: 18  LDKYLQDISKVDLITAEEEVELAQRIR---EGDQAALEKLTNANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    
Sbjct: 75  KLPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNKIGV 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTSH 587
           I+K+ +T   +    +R P+  EIAK+L M    V+  LK +   +S++ P  + E+ S+
Sbjct: 135 INKINKTFSHLEQVNERPPSAIEIAKELDMSEAQVKVALKNSGRHLSMDAPFKEGENDSN 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +    + +P D  ++ +L     R L +L+ RE  V+R+ +GIG     TL+E+G 
Sbjct: 195 LYDVLSSAESPTPDDQLMRDSLSIEINRALETLSQREADVIRLNYGIGNQPAMTLQEIGD 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            F ++RER+RQI  K IR+LKH S++K L+ +L
Sbjct: 255 TFDLSRERVRQIREKGIRRLKHQSKNKMLKKYL 287



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  ++L++ E E+ +A+RI  G    +  L  + L F  ++    +  +    L +
Sbjct: 21  YLQDISKVDLITAEEEVELAQRIREGDQAALEKLTNANLRF--VVSVAKQYQNQGLKLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|48743|emb|CAA37174.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 332

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 109/241 (45%), Positives = 154/241 (63%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+ 
Sbjct: 84  EELQALIDESERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYR 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P E
Sbjct: 144 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAE 203

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L    E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E
Sbjct: 204 IAAELGSTPERVHDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSE 263

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  L PR   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +
Sbjct: 264 ELDDLIGRLDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLA 323

Query: 672 R 672
           R
Sbjct: 324 R 324



 Score = 38.3 bits (87), Expect = 4.6,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++   S      R +  + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SAAGETSGSATSVRANGGELADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAG 64


>gi|254430144|ref|ZP_05043847.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
 gi|197624597|gb|EDY37156.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
          Length = 318

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 94/243 (38%), Positives = 153/243 (62%), Gaps = 1/243 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              +    ++    A  A+  M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +
Sbjct: 67  LEELTPKQKRQIRMAQRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVD 126

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ +K+ K+ R  R +S+++ R+
Sbjct: 127 KFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISEKLSKMRRITRELSHRLGRQ 186

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAI 605
           P   E++  + M  E + +++  +    SL+     ++  S LG+ I D  +    DS  
Sbjct: 187 PNRLELSHAMDMRPEELEELMAQSAPCASLDAHARGDEDRSTLGELIADPASNEHFDSMD 246

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   +E     L+ L  RE++++++RFG+  +   TL E+G+   V+RER+RQ+EAKAI 
Sbjct: 247 RHIQKEHLGAWLSQLNEREQKIIKLRFGLEGSEPLTLAEIGRLINVSRERVRQLEAKAIM 306

Query: 666 KLK 668
           KL+
Sbjct: 307 KLR 309



 Score = 37.9 bits (86), Expect = 6.1,   Method: Composition-based stats.
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             R + D +  YL  +G + LL+   EI +A  ++AG+ 
Sbjct: 23  TGRLSADSIGWYLSNIGRVPLLTPAEEIELAHHVQAGKR 61


>gi|222056415|ref|YP_002538777.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221565704|gb|ACM21676.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 358

 Score =  176 bits (445), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 103/269 (38%), Positives = 171/269 (63%), Gaps = 3/269 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+  ++ I     ++  E + + + + +       A+ +M+E+NLRLV+ +AK+Y NRG
Sbjct: 84  AIKLYLREIQKTKLLTADEEKELAARIDR---GDKAARDKMIESNLRLVVKIAKRYINRG 140

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D
Sbjct: 141 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 200

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K++R  R +  KI REP+ +E+A  + +    +R+++ + K+  S+E P+G+ +   
Sbjct: 201 DINKMLRITRELLQKINREPSIKEVATAMEVNSAYIRRLMVLLKKTYSIERPMGENNDYF 260

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D IED + VSP +     N  E  ++   +L+  E+++L +RFG+      TL+ +G+
Sbjct: 261 LIDTIEDTSTVSPAELLEDVNRYEMVSKWFDTLSDNEKKILTLRFGLDDKDPQTLDTIGR 320

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            F VTRERIRQIEAK++ KL+    + +L
Sbjct: 321 SFGVTRERIRQIEAKSLEKLRKIMEATEL 349



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 30/128 (23%), Positives = 49/128 (38%), Gaps = 11/128 (8%)

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR----------S 116
           VAM ++  I V  G++   E       ++   A       +  +                
Sbjct: 21  VAMDNDETIGVFPGEEPHKELDLFMEPEVEPDAVELEQVEEVEEHEEVEEEEIKVAVVEH 80

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            DD +++YLRE+   +LL+ + E  +A RI+ G       + ES L     I  R  +N 
Sbjct: 81  FDDAIKLYLREIQKTKLLTADEEKELAARIDRGDKAARDKMIESNLRLVVKIAKRY-INR 139

Query: 177 GTTLLREI 184
           G   L  I
Sbjct: 140 GLPFLDLI 147


>gi|119492598|ref|ZP_01623816.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119453067|gb|EAW34237.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 333

 Score =  176 bits (445), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 105/297 (35%), Positives = 178/297 (59%), Gaps = 4/297 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++  ++   G+    +  +++   K+  +++    +T  + +E       + +       
Sbjct: 39  LTQEEEIHYGKQVQQMMKQLEEKDKLTKKLEHEPSKTEWA-NEVELTEDELDRILDCGRR 97

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD   GYKFSTYA WW
Sbjct: 98  AKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFSTYAYWW 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+QAITR+IA    TIR+P+H+ +K++K+ R  R +  K  R PTP EIA+ L +    +
Sbjct: 158 VRQAITRAIAQNGRTIRLPIHITEKLNKIKRVQRDLVQKYGRNPTPTEIAEALELEPSQI 217

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+ L  ++ PISL+  +GD   + L + +ED+ A S  +      LR+    ++  LTP+
Sbjct: 218 REYLLASRHPISLDLRVGDNQDTELQELLEDETA-SADNYVTHELLRQDLKSLIDELTPQ 276

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  V+ +R+G+    + +L +VG +  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 277 QREVILLRYGLEDGKELSLSKVGARMSISRERVRQLENQALNHLRR--RKSQVREYL 331



 Score = 41.7 bits (96), Expect = 0.36,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 10/86 (11%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
             ++++    + D VR YL E+G + LL++E EI   K+++     MM  L E     + 
Sbjct: 12  STKRNTRPGVSVDTVRTYLHEIGRVPLLTQEEEIHYGKQVQ----QMMKQLEEKDKLTKK 67

Query: 167 L------IIWRDELNDGTTLLREIID 186
           L        W +E+      L  I+D
Sbjct: 68  LEHEPSKTEWANEVELTEDELDRILD 93


>gi|149188695|ref|ZP_01866986.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
 gi|148837356|gb|EDL54302.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
          Length = 296

 Score =  176 bits (445), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 100/267 (37%), Positives = 157/267 (58%), Gaps = 5/267 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
             K ++    +S  + RHI    R      ++A++ ++ +NLRLVI  AK+Y+NRGL F 
Sbjct: 27  YFKEVAGHDLLSAEDERHIARKAR---AGDTLARQHLINSNLRLVIRTAKRYSNRGLDFY 83

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL++A +KFD  LGY+FSTYA+WW++QAI R+I +Q  TIR+PVH+  +I +
Sbjct: 84  DLINEGNIGLIQAVDKFDPELGYRFSTYAVWWIQQAIDRAIMNQGRTIRVPVHVTKQIRE 143

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLG 589
             + A  +  +   EPT  EIA++     E V K+LK++++ +SL+    +E     HL 
Sbjct: 144 CSKAAHELRKEGNHEPTSSEIAERTGRAPEEVSKLLKLSEQSLSLDNGWDEEGDKKDHLQ 203

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              +D     P    +  NL +    ++ SL  ++  +L  RFG+  +   TLE+VG+  
Sbjct: 204 TIDDDDVFELPEQDIVTQNLNKALIDLVDSLPDKQRVILHHRFGLLDDDPKTLEQVGEIV 263

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VTRER+RQI+  A+  L+   + + L
Sbjct: 264 GVTRERVRQIQKSAMETLRDKLKRQNL 290


>gi|288940519|ref|YP_003442759.1| RNA polymerase sigma-70 subunit RpoD subfamily [Allochromatium
           vinosum DSM 180]
 gi|288895891|gb|ADC61727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Allochromatium
           vinosum DSM 180]
          Length = 338

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 87/276 (31%), Positives = 157/276 (56%), Gaps = 3/276 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +          R  +  I     ++  E      + +      + A++ M+  NLRLV+ 
Sbjct: 57  IEASEADFDATRIYLNEIGESRLLTAEEEIRFARLAQ---AGDNAARQRMIVCNLRLVVK 113

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ T
Sbjct: 114 IARRYLNRGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 173

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+P+H+  +I+  ++ +R+++  +  +PT E+IA+ L  P+  V+++L + +   S++T
Sbjct: 174 VRLPIHVVKEINIYLKASRQLAQSLDHDPTSEDIAQLLDRPINEVKRMLGLNERITSVDT 233

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P   +    L D ++D  +  P +     ++       L  L  ++  V+  RFG+  + 
Sbjct: 234 PYSKDADKPLVDMLQDDGSSDPTERIQDDDIHVNIEHWLGLLNDKQREVVERRFGLHGHE 293

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + TLE V ++  VTRER+RQI+  A+R+L+    S+
Sbjct: 294 NSTLESVARELGVTRERVRQIQMDALRRLRDILESE 329



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 27/86 (31%), Positives = 36/86 (41%), Gaps = 1/86 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
             +SS    +R   A  +  D  R+YL E+G   LL+ E EI  A+  +AG       + 
Sbjct: 45  DGDSSSVTGERPIEASEADFDATRIYLNEIGESRLLTAEEEIRFARLAQAGDNAARQRMI 104

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI 184
              L     I  R  LN G  LL  I
Sbjct: 105 VCNLRLVVKIARRY-LNRGLPLLDLI 129


>gi|197119058|ref|YP_002139485.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
 gi|197088418|gb|ACH39689.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
          Length = 333

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 170/274 (62%), Gaps = 5/274 (1%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K  V    D  +K+   ++ I     ++  E + + + +   +     A+  M+ +NLRL
Sbjct: 45  KAAVVEHFDDAIKL--YLREIQKTKLLTADEEKELAARI---DLGDKAARDRMIVSNLRL 99

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +Q
Sbjct: 100 VVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQ 159

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S TIR+PVH+ D I+K++R  R +  K+ REP+ +E+A  L + V  VR+++ + K+  S
Sbjct: 160 SRTIRLPVHVSDDINKMLRVTRELVQKMNREPSIKEVADTLEVNVTYVRRLMVLLKKTYS 219

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +E P+G+ +   L D IED + +SP       N  E  ++   +L+  E+++L +RFG+ 
Sbjct: 220 IERPMGENNDYFLIDTIEDTSTISPAVLLEDLNKYELVSKWFETLSDAEKKILTLRFGLD 279

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                TL+ +G+ F VTRERIRQIEAK++ KL+ 
Sbjct: 280 DKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRK 313



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/104 (25%), Positives = 45/104 (43%), Gaps = 1/104 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           D  +D +  E     A +   + V  ++ K +     DD +++YLRE+   +LL+ + E 
Sbjct: 16  DAEQDPDALELEEVEAEADEPAEVEEEEIKAAVVEHFDDAIKLYLREIQKTKLLTADEEK 75

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            +A RI+ G       +  S L     I  R  +N G   L  I
Sbjct: 76  ELAARIDLGDKAARDRMIVSNLRLVVKIAKRY-INRGLPFLDLI 118


>gi|5771430|gb|AAD51396.1|AF117715_5 stationary phase specific sigma factor homolog [Legionella
           pneumophila]
          Length = 341

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 175/274 (63%), Gaps = 3/274 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             ++   +  +  I     ++  E  H  ++          A+K+M+E+NLRLV+ +A++
Sbjct: 65  AKALDATQLYLGEIGFSPLLTAEEEIHYATLA---LKGDMEARKKMIESNLRLVVKIARR 121

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y NRGL  LDLI+EGN+GLMK+ EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P
Sbjct: 122 YLNRGLPLLDLIEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLP 181

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+  +++  +R AR+++ K+  EP+PEEIA+ +  P+E V+K+L +  +  S++TPIG 
Sbjct: 182 IHVVKELNVYLRAARQLTQKLDHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGF 241

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++T  L D I D+N+++P +     NLR+    +L  LT  +++V+  RFG+      TL
Sbjct: 242 DETKSLLDTIADENSLNPAELLTNENLRQHIESLLDKLTENQQQVIARRFGLRGFEKATL 301

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           E+VGK+  +TRER+RQI+ +A++ L+       L
Sbjct: 302 EDVGKEIDLTRERVRQIQVEALKTLRTLLERVGL 335



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D   D E  E+ LD     ++   F   ++        D  ++YL E+G   LL+ E 
Sbjct: 29  EEDVEPDIEKMEEELDELPEFTDDETFPSFQRGKNIAKALDATQLYLGEIGFSPLLTAEE 88

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI  A     G       + ES L     I  R  LN G  LL  I
Sbjct: 89  EIHYATLALKGDMEARKKMIESNLRLVVKIARRY-LNRGLPLLDLI 133


>gi|53717743|ref|YP_106729.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52208157|emb|CAH34087.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
          Length = 482

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVNASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|76812098|ref|YP_331741.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254261622|ref|ZP_04952676.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|76581551|gb|ABA51026.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254220311|gb|EET09695.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
          Length = 482

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTTASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|197286082|ref|YP_002151954.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227356592|ref|ZP_03840979.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
 gi|194683569|emb|CAR44440.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227163348|gb|EEI48275.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
          Length = 329

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 110/305 (36%), Positives = 179/305 (58%), Gaps = 11/305 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSIL--------KIRNEIKSISVETGISISEFRHIV 431
           +      A    E E ++    E++ I           +  +  I     +S  E    V
Sbjct: 19  NMEEFDEAAATKEAENESDAQDEIELIEGVNQRALDATQLYLGEIGYSPLLSAEEE---V 75

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              R+       +++ M+E+NLRLV+ ++++YTNRGL  LDLI+EGN+GL++A EKFD  
Sbjct: 76  FFARRALRGDIPSRQRMIESNLRLVVKISRRYTNRGLALLDLIEEGNLGLIRAVEKFDPE 135

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EE
Sbjct: 136 KGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSVEE 195

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+ L  PV+ V K+L++ +   S++TPIG +    L D I D+N   P  +    NL+E
Sbjct: 196 IAQTLDKPVDDVSKMLRLNERISSVDTPIGGDSDKALLDIISDENEEGPEATIQNNNLKE 255

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + L  L P++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+LK   
Sbjct: 256 NIVKWLFELNPKQREVLARRFGLLGYEAETLEDVGREIGLTRERVRQIQVEGLRRLKDIL 315

Query: 672 RSKKL 676
           + + L
Sbjct: 316 QGQGL 320



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 42/106 (39%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D  D   EE  E +    +   + +    +  +  ++   D  ++YL E+G   LLS E 
Sbjct: 14  DDIDENMEEFDEAAATKEAENESDAQDEIELIEGVNQRALDATQLYLGEIGYSPLLSAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVFFARRALRGDIPSRQRMIESNLRLVVKISRRY-TNRGLALLDLI 118


>gi|254253854|ref|ZP_04947171.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898499|gb|EAY70342.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 547

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 104/234 (44%), Positives = 158/234 (67%), Gaps = 1/234 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA WW++QA
Sbjct: 314 MLEANLRLVLSIARKYMNRGVDLPDLVQDGCVGLMRAIEKFEYRRGFKFSTYATWWIRQA 373

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +  + +R +L
Sbjct: 374 VARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLDEDKLRAIL 433

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +  EP+SL+TP+ D DT  L D IED+ + SP +    A +RE  T +L S+TP E  V
Sbjct: 434 ALPAEPVSLDTPLPDTDTG-LVDTIEDQASASPFERLADARMRECVTSLLRSVTPTEADV 492

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  ++FLD
Sbjct: 493 LRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTVAEAEGAQTFLD 546



 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 43/151 (28%), Positives = 76/151 (50%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +   D   D   +++ LA ++GY+T  +L   LPP+  S++ +E   A L+++GI V+D 
Sbjct: 42  AARADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSADALEVVRAALADIGIAVLDE 101

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    L         ++ DP+ +Y+R M ++ LL+RE EI
Sbjct: 102 PPAPVPFTGAAPVDVDRDALDEGRALLGELARGASASTDPLALYMRRMHAVPLLTREDEI 161

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           A+A+ IE GR  ++ +L   P    AL+   
Sbjct: 162 ALAREIETGRHQVLHALAGCPAAVDALLARH 192


>gi|268591356|ref|ZP_06125577.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
 gi|291313333|gb|EFE53786.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
          Length = 328

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 108/308 (35%), Positives = 185/308 (60%), Gaps = 8/308 (2%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF--------R 428
            +LD   ++   D  + + ++ V    D +  ++N  + +   T I +SE          
Sbjct: 13  NDLDESNLNDTFDESQFKEEDLVTELDDEMDLLQNTNQRVLDATQIYLSEIGFSPLLTAE 72

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V   R+       +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 73  EEVFYARRALRGDIASRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKF 132

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+
Sbjct: 133 DPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPS 192

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA++L  PVE V ++L++ +   S++TPI  +    L + + D N   P ++    +
Sbjct: 193 PEEIAEQLDKPVEDVSRMLRLNERITSVDTPIAGDSEKSLLEVLSDDNDSGPENTIQDND 252

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + L  L P++  VL  RFG+      TLEEVG++  +TRER+RQI+ + +++LK
Sbjct: 253 LKENIVKWLYELNPKQREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLKRLK 312

Query: 669 HPSRSKKL 676
                ++L
Sbjct: 313 DILHGEEL 320



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 39/106 (36%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D D+    +  ++S                   + ++   D  ++YL E+G   LL+ E 
Sbjct: 14  DLDESNLNDTFDESQFKEEDLVTELDDEMDLLQNTNQRVLDATQIYLSEIGFSPLLTAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVFYARRALRGDIASRQRMIESNLRLVVKISRRYN-NRGLALLDLI 118


>gi|167916992|ref|ZP_02504083.1| RNA polymerase sigma factor [Burkholderia pseudomallei BCC215]
          Length = 482

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDFGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|77919031|ref|YP_356846.1| DNA-directed RNA polymerase, sigma 70/sigma 32 subunit [Pelobacter
           carbinolicus DSM 2380]
 gi|77545114|gb|ABA88676.1| RNA polymerase, sigma 38 subunit, RpoS [Pelobacter carbinolicus DSM
           2380]
          Length = 347

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 101/273 (36%), Positives = 164/273 (60%), Gaps = 3/273 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E  S   I+  +K I     ++  + R +   + +       A+  M+E+NLRLV+ +AK
Sbjct: 62  EGPSDDAIKLYLKEIQKTKLLTAEDERMLARRISQ---GDMAARDRMIESNLRLVVKIAK 118

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +QS TIR+
Sbjct: 119 RYMNRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRL 178

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVH+ D I+K ++ +R + ++  REP  EEIA+ + +    +R+++ + K+  S+E P+G
Sbjct: 179 PVHVSDDINKFIKISRELVHQYNREPKVEEIAEYMGVEPAYIRRLMVLVKKTYSIEHPMG 238

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +     L D IED  A +P       +          +L+  E  +L +RFG+      T
Sbjct: 239 ENRDYSLIDTIEDPKADNPSTFVDDIDKYAHVCNWFETLSENEREILMLRFGLDDQEPQT 298

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L+ +G++F VTRERIRQIEAK+++KL++    +
Sbjct: 299 LDTIGRRFGVTRERIRQIEAKSLQKLRNLMEEQ 331



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D++D       S V   ++    +  +DD +++YL+E+   +LL+ E E  +A+RI  G 
Sbjct: 39  DNVDEVEEREESEVEESEKSKKDEGPSDDAIKLYLKEIQKTKLLTAEDERMLARRISQGD 98

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                 + ES L     I  R  +N G   L  I
Sbjct: 99  MAARDRMIESNLRLVVKIAKRY-MNRGLPFLDLI 131


>gi|223936758|ref|ZP_03628668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894609|gb|EEF61060.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 352

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 106/262 (40%), Positives = 166/262 (63%), Gaps = 3/262 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+  ++ I     ++  +   + + ++K       A++ M++ANLRLV+ +A+ Y   G
Sbjct: 84  AIKLYLREIGQVQLLTPQQEIELAARIKK---GDKKARELMIKANLRLVVKIARDYEGIG 140

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  LDLI EGNIGLMKA E+FD   G K STY  WW+KQ+I R++A+QS TIR+PVH+ D
Sbjct: 141 LPLLDLISEGNIGLMKAVERFDPAKGGKLSTYGSWWIKQSIKRALANQSKTIRLPVHLVD 200

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           KI K+ RTA ++   + REP+ EE+A +L +    V ++      P SL+ PIGDED+++
Sbjct: 201 KISKMRRTALKLQEILGREPSDEELADELNISAMRVSQMRTAAIRPASLDAPIGDEDSNN 260

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             + ++D+NA +P +   +  + +    ++ +L PRE  +LR RFG+      TLEEVG+
Sbjct: 261 FAEVVQDENADTPYEQLEEKTVTKMLQELVKTLDPREATILRARFGLDGGNQKTLEEVGQ 320

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +F VTRER+RQI+  A++KL+ 
Sbjct: 321 KFGVTRERVRQIQNIALKKLRK 342



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/98 (20%), Positives = 39/98 (39%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           + +       E      +  A  A    +     ++      D  +++YLRE+G ++LL+
Sbjct: 40  HEISAKSKPVELEESSPVIDAVPAVVEDLAPIHERERTSYDGDTAIKLYLREIGQVQLLT 99

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
            + EI +A RI+ G       + ++ L     I    E
Sbjct: 100 PQQEIELAARIKKGDKKARELMIKANLRLVVKIARDYE 137


>gi|4929285|gb|AAD33933.1|AF144608_2 RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus]
          Length = 321

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 107/279 (38%), Positives = 166/279 (59%), Gaps = 7/279 (2%)

Query: 385 SYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              K     E K  V  E D    S+   +  +  I     ++  E    V   R+    
Sbjct: 26  ELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRG 82

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 83  DEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 142

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV
Sbjct: 143 TWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPV 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L
Sbjct: 203 EDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEEL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            P+++ VL  RFG+      TLEEVG++  +TRER+R++
Sbjct: 263 NPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRRL 301



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + +     E + D+    SS++       + +  A   + D  ++YL E+G   LL+
Sbjct: 9   KVEEFEYDNASETTIDNELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLT 68

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 69  AEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 116


>gi|67925121|ref|ZP_00518496.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853040|gb|EAM48424.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 374

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 108/285 (37%), Positives = 186/285 (65%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    ++  +++ E++    +   + +              +  IAK++M+ +NLRLV
Sbjct: 89  QFLLEVEETKQRLKEELQRTPSKAECAEALGFETAKQFEHRLHKGRIAKRKMIRSNLRLV 148

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 149 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 208

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +  K++R P  +E+A +L +    +R++L++ ++ +SL
Sbjct: 209 RTIRLPIHVVEKLNKLKKAQRVLKQKLQRNPNEKELADELEVTPPQLRQLLQLRRQSLSL 268

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED++   P +   +  L+   + VL+  LT RE+ V+ +R+G+ 
Sbjct: 269 NHRVGKGEDTELVDLLEDQDLQLPEELMNEGMLQYEVSAVLSDVLTQREKDVISLRYGLC 328

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  HTLEEVG  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 329 TSQPHTLEEVGGIFNLSRERVRQIQSKAMRKLRRPQVARRLKGWL 373



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ + LE  +    S+++  S+ +  +  Q  +      +DD V  + +EM    LL+ E
Sbjct: 20  MEAEGLEQTDKELQSVEVELSSLSDELGNQYPEGYRKTVSDDTVGAFFKEMSRYPLLNAE 79

Query: 138 GEIAIAK------RIEAGRAMMMASLCESP 161
            E+ +A+       +E  +  +   L  +P
Sbjct: 80  EEVELAQQVQFLLEVEETKQRLKEELQRTP 109


>gi|197335185|ref|YP_002156867.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
 gi|197316675|gb|ACH66122.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
          Length = 321

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 97/301 (32%), Positives = 168/301 (55%), Gaps = 5/301 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDS--ILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E D   ++ A+     E    +        +   +  +  I     ++  E  +   +  
Sbjct: 13  EFDLDTINDAELTSIEEESERLEVSSSQKVMDATQLYLGEIGFSPLLTAEEEVYFSRLA- 71

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   A+  M+E+NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G++
Sbjct: 72  --LKGDEAARARMIESNLRLVVKIARRYNHRGLALLDLVEEGNLGLIRAVEKFDPERGFR 129

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPEEIA+K
Sbjct: 130 FSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPEEIAEK 189

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L  PV  V ++L++ +   S+++ +  E    L D + D     P     + ++  +   
Sbjct: 190 LDKPVSDVSRMLRLNERVASVDSMVAGESDKALLDILPDTKNSDPESETQKDDINTSLVG 249

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L P+++ V+  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+    ++ 
Sbjct: 250 WLGQLNPKQKEVVARRFGLLGYEAATLEQVGVEIGLTRERVRQIQVEGLRRLREIMTNQG 309

Query: 676 L 676
           L
Sbjct: 310 L 310



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 3/103 (2%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E EE   D+++ A   S      ++ + S+ +   D  ++YL E+G   LL+ E E+  +
Sbjct: 10  EVEEFDLDTINDAELTSIEEES-ERLEVSSSQKVMDATQLYLGEIGFSPLLTAEEEVYFS 68

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +    G     A + ES L    ++      N     L ++++
Sbjct: 69  RLALKGDEAARARMIESNLRL--VVKIARRYNHRGLALLDLVE 109


>gi|312796084|ref|YP_004029006.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
 gi|312167859|emb|CBW74862.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
          Length = 358

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/270 (35%), Positives = 157/270 (58%), Gaps = 12/270 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 79  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEF---DARQMMIERNLRLVVSIAKGYLNRGV 135

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 136 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 195

Query: 529 IHKVVRTARRMS---------NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           +++V+R  R +              R+ + ++IA  +    E V  +L + +   SL+ P
Sbjct: 196 LNQVLRAKRHLERNASAPASGADEHRDASVDDIAYLIGKTPEEVADILALNEHTASLDAP 255

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +  S L D + D+ + SP   A    L   T   L+ L  +   V+  RFG+     
Sbjct: 256 LELDPASSLLDLLSDEQSQSPDAEAQHRELETLTRVWLSRLPDKHRHVIERRFGLNNIEP 315

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TLEE+  +  +TRER+RQI+ +A+ +LK 
Sbjct: 316 ATLEELADEMGLTRERVRQIQQEALARLKR 345



 Score = 39.8 bits (91), Expect = 1.8,   Method: Composition-based stats.
 Identities = 52/322 (16%), Positives = 99/322 (30%), Gaps = 41/322 (12%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D+E   +      +A         R       T D ++ YL  +    LL+ E E   ++
Sbjct: 43  DDEPVSEQGAAEEAAVAEPDPDDFRALLKAELTADTIQHYLNRISVKPLLTVEEEQRYSR 102

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
             +AG       + E  L     I     LN G  LL  I   E  +G       F  T 
Sbjct: 103 LAKAGEFDARQMMIERNLRLVVSIAKGY-LNRGVPLLDLI--EEGNLGLMHAIEKFDPTR 159

Query: 205 GHSYQ-----------KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           G  +            +R   +Q +          ++    +  +       +P   A+ 
Sbjct: 160 GFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLERNASAPASGADE 219

Query: 254 DERNLDED--------EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
                 +D         ++ A  L+  E       + A  E+      L  L D      
Sbjct: 220 HRDASVDDIAYLIGKTPEEVADILALNE---HTASLDAPLELDPASSLLDLLSDEQSQSP 276

Query: 306 KDEKSSVKCKVL------------KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
             E    + + L            +  + +  G  ++  + ++ L +++    +R+   +
Sbjct: 277 DAEAQHRELETLTRVWLSRLPDKHRHVIERRFGLNNIEPATLEELADEMGLTRERVRQIQ 336

Query: 354 GELLRLAQSY----GIKRDVFL 371
            E L   + Y    G+ +D  L
Sbjct: 337 QEALARLKRYFASNGVPKDAVL 358


>gi|224824776|ref|ZP_03697883.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
 gi|224603269|gb|EEG09445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
          Length = 316

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 100/292 (34%), Positives = 163/292 (55%), Gaps = 3/292 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
               +    E +   +   D     +  +  I     +S  E + +  +V         A
Sbjct: 22  DTVAETDSEEVQEAASAYDDIADVTQIYLNDIGNNALLSPQEEQSLARLV---VQGDFEA 78

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++M+E NLRLV+++AK+Y NRGL  LDLI+EGNIGLM A EKFD   G++FSTYA WW+
Sbjct: 79  RQKMIEHNLRLVVNIAKRYINRGLALLDLIEEGNIGLMHALEKFDPERGFRFSTYATWWI 138

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q+I R+I +QS TIR+PVH+  +++  +R +R + ++I REP+ EEIA+ +  PVE VR
Sbjct: 139 RQSIERAIMNQSRTIRLPVHVIKELNVYLRASRHLESQIGREPSVEEIAQLVDKPVEDVR 198

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +V+ + +   SL+ P+  +    +G+ I D     P        L       +A L  ++
Sbjct: 199 RVMNLNERMASLDAPLDIDPMLSIGESIPDDQHDEPEIQLHNTQLENFVHEWMAQLNDKQ 258

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             V+  R+G+  +   TLEE+     +TRER+RQI+ + + +L+   R K +
Sbjct: 259 RMVIERRYGLNGHEICTLEELASTLSLTRERVRQIQIEGLEQLRRILRRKGI 310



 Score = 41.4 bits (95), Expect = 0.50,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 1/93 (1%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
                 + + +     +   SA     D  ++YL ++G+  LLS + E ++A+ +  G  
Sbjct: 17  EEASDDTVAETDSEEVQEAASAYDDIADVTQIYLNDIGNNALLSPQEEQSLARLVVQGDF 76

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
                + E  L     I  R  +N G  LL  I
Sbjct: 77  EARQKMIEHNLRLVVNIAKRY-INRGLALLDLI 108


>gi|126453822|ref|YP_001064420.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|167736534|ref|ZP_02409308.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|217424965|ref|ZP_03456461.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242317344|ref|ZP_04816360.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254188239|ref|ZP_04894751.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|254295684|ref|ZP_04963141.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|126227464|gb|ABN91004.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|157805995|gb|EDO83165.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157935919|gb|EDO91589.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|217391985|gb|EEC32011.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242140583|gb|EES26985.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
          Length = 482

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTTASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|124386302|ref|YP_001028216.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126449023|ref|YP_001081831.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126450673|ref|YP_001081854.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|124294322|gb|ABN03591.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126241893|gb|ABO04986.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126243543|gb|ABO06636.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
          Length = 482

 Score =  175 bits (444), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IA+++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIAERARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 49/142 (34%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R       +              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYANVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|237810316|ref|YP_002894767.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
 gi|237504080|gb|ACQ96398.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
          Length = 482

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|254182275|ref|ZP_04888872.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184212813|gb|EDU09856.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 482

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|313672395|ref|YP_004050506.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939151|gb|ADR18343.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 337

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 89/266 (33%), Positives = 156/266 (58%), Gaps = 3/266 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K +S    +S  E   +   +         AK+ M+  NLRLV+S+AKKY N+G+   
Sbjct: 70  YLKELSKCPVLSKEEECELARRIE---EGDEKAKETMINCNLRLVVSIAKKYANKGVPLE 126

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL++A EKFD+  G+KFSTYA WW++QAI R+I   +  +R+PVH+ + I K
Sbjct: 127 DLISEGNIGLIRAVEKFDYRKGFKFSTYATWWIRQAIERAIIANTKIVRVPVHVLEYIKK 186

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +++    +   + R PT  E++    + +  + K ++  +  +S++ PI +++  ++ + 
Sbjct: 187 ILKAKSELQETLGRNPTYTELSTYTGITLSNIYKAVEAMRHDVSIDAPISEDEQENMHNL 246

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D     P D A + N+++  ++ +  L   E+ ++ +R+G+      TL+EVGK+  +
Sbjct: 247 IPDNIHTDPFDHAFELNIQKLVSKWMGYLNETEKLIITLRYGLDGKRSRTLDEVGKELNL 306

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLR 677
           TRERIRQIE + + KL+    +K++ 
Sbjct: 307 TRERIRQIEKRVLNKLRSFFHNKRIE 332



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/160 (20%), Positives = 65/160 (40%), Gaps = 16/160 (10%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
           D  +SE ++D    L+N  + V+D +++ +++     +      ++S   +   K S+  
Sbjct: 9   DNKTSEIIDD---NLTNFYLVVIDEENVSEDDFLSGGVLEEEEEADSLEGVDDSKGSSAE 65

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
           +       YL+E+    +LS+E E  +A+RIE G      ++    L    ++    +  
Sbjct: 66  TLV----FYLKELSKCPVLSKEEECELARRIEEGDEKAKETMINCNLRL--VVSIAKKYA 119

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           +    L ++I        E   G     E   Y+K    S
Sbjct: 120 NKGVPLEDLI-------SEGNIGLIRAVEKFDYRKGFKFS 152


>gi|189501483|ref|YP_001957200.1| RNA polymerase sigma factor [Candidatus Amoebophilus asiaticus 5a2]
 gi|189496924|gb|ACE05471.1| RNA polymerase sigma factor, sigma-70 family [Candidatus
           Amoebophilus asiaticus 5a2]
          Length = 287

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 169/274 (61%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ I     ++  E   +   ++       IA +++ +ANLR V+SVAK+Y N+
Sbjct: 16  QSLDKYLQEIGRVDLLTPEEEVELAKRIK---SGDKIALEQLTKANLRFVVSVAKQYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+K+A++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++  
Sbjct: 73  GLSLSDLINEGNLGLIKSAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ RT  ++  K KREPT EE+A++L +    +   +KI+   +S++ P    +  
Sbjct: 133 GTLNKLSRTFSQLEQKYKREPTAEELAEELEVTPGEISDTMKISGRHVSMDAPFVQGEEH 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +ED +   P D+ I  +L +   R L+ LT RE  V+   FG+      TLEE+G
Sbjct: 193 SLLDVLEDDDEDKPDDTLIDESLCKDIERALSLLTEREAGVISYYFGLKGTNPMTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +F +TRER+RQI+ KAI+KL+H + SK L+++L
Sbjct: 253 TRFNLTRERVRQIKEKAIKKLRHVASSKTLKNYL 286



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G ++LL+ E E+ +AKRI++G  + +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQEIGRVDLLTPEEEVELAKRIKSGDKIALEQLTKANLRF--VVSVAKQYQNQGLSLSD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|134284106|ref|ZP_01770800.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167900733|ref|ZP_02487938.1| RNA polymerase sigma factor [Burkholderia pseudomallei NCTC 13177]
 gi|167908960|ref|ZP_02496051.1| RNA polymerase sigma factor [Burkholderia pseudomallei 112]
 gi|226194652|ref|ZP_03790247.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|134244558|gb|EBA44662.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|225933353|gb|EEH29345.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
          Length = 482

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|54294183|ref|YP_126598.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|54297202|ref|YP_123571.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53750987|emb|CAH12398.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53754015|emb|CAH15486.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|307609996|emb|CBW99528.1| RNA polymerase sigma factor RpoS [Legionella pneumophila 130b]
          Length = 341

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 107/299 (35%), Positives = 179/299 (59%), Gaps = 3/299 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +   +    D               ++   +  +  I     ++  E  H  ++    
Sbjct: 40  EEELDELPEFTDDEAFPSFQRGKNIAKALDATQLYLGEIGFSPLLTAEEEIHYATLA--- 96

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A+K+M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GLMK+ EKFD   G++FS
Sbjct: 97  LKGDMEARKKMIESNLRLVVKIARRYLNRGLPLLDLIEEGNLGLMKSVEKFDPKRGFRFS 156

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR+++ K+  EP+PEEIA+ + 
Sbjct: 157 TYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARQLTQKLDHEPSPEEIAEMVD 216

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            P+E V+K+L +  +  S++TPIG ++T  L D I D+N+++P +     NLR+    +L
Sbjct: 217 KPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDTIADENSLNPAELLTNENLRQHIESLL 276

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             LT  +++V+  RFG+      TLE+VGK+  +TRER+RQI+ +A++ L+       L
Sbjct: 277 DKLTENQQQVIARRFGLRGFEKATLEDVGKEIDLTRERVRQIQVEALKTLRTLLERVGL 335



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D   D E  E+ LD     ++   F   ++        D  ++YL E+G   LL+ E 
Sbjct: 29  EEDIEPDIEKMEEELDELPEFTDDEAFPSFQRGKNIAKALDATQLYLGEIGFSPLLTAEE 88

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           EI  A     G       + ES L     I  R  LN G  LL  I
Sbjct: 89  EIHYATLALKGDMEARKKMIESNLRLVVKIARRY-LNRGLPLLDLI 133


>gi|218194307|gb|EEC76734.1| hypothetical protein OsI_14770 [Oryza sativa Indica Group]
          Length = 563

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 94/249 (37%), Positives = 150/249 (60%), Gaps = 1/249 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +RK        K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD  
Sbjct: 310 RTLRKRLDHGIYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDAS 369

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTY+ WW+KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EE
Sbjct: 370 KGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEE 429

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA    MP++ V   + + K  +SL++ IG  D ++  +   D  A +  +   + +++ 
Sbjct: 430 IAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKR 488

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + L +LT RE +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   
Sbjct: 489 DVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKK 548

Query: 672 RSKKLRSFL 680
           R   L+ +L
Sbjct: 549 RVNALKDYL 557


>gi|126441635|ref|YP_001057174.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126221128|gb|ABN84634.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 482

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IA+++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIAERARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTTASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|111018672|ref|YP_701644.1| sigma factor, sigma 70 type, group 2 [Rhodococcus jostii RHA1]
 gi|110818202|gb|ABG93486.1| sigma factor, sigma 70 type, probable group 2 [Rhodococcus jostii
           RHA1]
          Length = 520

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 110/263 (41%), Positives = 168/263 (63%), Gaps = 6/263 (2%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
             +S    R +  + R    +   AK+  +EANLRLV+S+A++Y  RGL  LDL+QEGN+
Sbjct: 263 EKLSDQRHRDLHRVCR----DGQHAKRRFLEANLRLVVSIARRYQGRGLDLLDLVQEGNL 318

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKFD+  G+KFSTYA WW++QAITR++ADQS  IRIPVHM ++I ++ +   R+
Sbjct: 319 GLIRAVEKFDYKTGFKFSTYATWWIRQAITRALADQSRVIRIPVHMVEQIDQLGKERARL 378

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           + +  REPTP E+A  L   +E +  + K  +  +SL+  +  ++  H G   ED  AV 
Sbjct: 379 TKETGREPTPSELATALDTTIEHIGDLEKYDQRVLSLD--VLTDNAEHDGLDFEDDLAVV 436

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             + A +    ET   VL+ L+ R+ +V+R+R+G+  +  +TL+E+GK + VTRERIRQI
Sbjct: 437 AEEVAERRRFYETLESVLSPLSERDAQVIRLRYGLTGSDPYTLDEIGKIYGVTRERIRQI 496

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           E+K ++ +K  S +  LR F D 
Sbjct: 497 ESKLLKAMKEESVADILRPFYDS 519



 Score = 38.3 bits (87), Expect = 4.7,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           +  S     L     +     +   D  +  T D +R Y + +    LL    E  +A+R
Sbjct: 185 DNASNSKTALPPELDDGDPGAEAATDVDEYETVDSIRAYSKSIKKRSLLVSGDESELAER 244

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDE 173
           IEAG       L E+    + L   R  
Sbjct: 245 IEAGLYAAY-LLKEAEDAGEKLSDQRHR 271


>gi|21221637|ref|NP_627416.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|256787171|ref|ZP_05525602.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
 gi|289771070|ref|ZP_06530448.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
 gi|19856654|sp|P18249|HRDD_STRCO RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|7799522|emb|CAB90986.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701269|gb|EFD68698.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
          Length = 332

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 109/241 (45%), Positives = 154/241 (63%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++    E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+ 
Sbjct: 84  EELQALIDESERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYR 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P E
Sbjct: 144 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAE 203

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L    E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E
Sbjct: 204 IAAELGSTPERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSE 263

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  L PR   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +
Sbjct: 264 ELDDLIGRLDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLA 323

Query: 672 R 672
           R
Sbjct: 324 R 324



 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++   S      R +  + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SAAGETSGSATSVRANGGELADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAG 64


>gi|91070600|gb|ABE11500.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-8F9]
          Length = 340

 Score =  175 bits (443), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 104/281 (37%), Positives = 165/281 (58%), Gaps = 16/281 (5%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRK---------------GECEASIAKKEM 448
           DSI    + I  + + T     E  H V  ++K                      ++  M
Sbjct: 51  DSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETDRTQRNLYQIKIGKKSRDRM 110

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           + ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +
Sbjct: 111 MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 170

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++ 
Sbjct: 171 TRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLIS 230

Query: 569 ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +    SL+     E+  S LG+ I D N   P++   +   +E     L+ L  RE+++
Sbjct: 231 QSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQKI 290

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 291 MKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 8/94 (8%)

Query: 73  MGINVVDGDDLEDEEGSEDSL---DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +       D    E  L      S  S SS+  ++ +  + R   D +  YL  +G
Sbjct: 2   MGIPLESAKSSSDNNFDEPRLPNTAGKSRKSKSSLTAKQGQKKSGRLASDSIGYYLSSIG 61

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            + LL+   EI +A  ++      M  L + P T
Sbjct: 62  RVPLLTPAEEIELAHHVQN-----MKKLLQIPET 90


>gi|251733367|emb|CAR82433.1| RNA polymerase sigma factor [Agrobacterium vitis]
          Length = 202

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 123/192 (64%), Positives = 150/192 (78%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+  V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  ACAGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++QG ELDP+W+    +     WK+F   E ++I +IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYQGAELDPNWMKSVGNLAARGWKDFAREENNTIREIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|53724654|ref|YP_101962.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|121599433|ref|YP_994127.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|167001162|ref|ZP_02266961.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
 gi|238561900|ref|ZP_00441190.2| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|254176911|ref|ZP_04883568.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254203640|ref|ZP_04910000.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208616|ref|ZP_04914964.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254360328|ref|ZP_04976598.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|52428077|gb|AAU48670.1| RNA polymerase sigma factor RpoD, putative [Burkholderia mallei
           ATCC 23344]
 gi|121228243|gb|ABM50761.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|147745152|gb|EDK52232.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147750492|gb|EDK57561.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148029568|gb|EDK87473.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|160697952|gb|EDP87922.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|238523583|gb|EEP87020.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|243062992|gb|EES45178.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
          Length = 482

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IA+++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 300 WWIRQAISRAIAERARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 360 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 479



 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTAASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|315185379|gb|EFU19152.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 292

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 94/270 (34%), Positives = 171/270 (63%), Gaps = 4/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    +S  E  H   +  +       AK+++V ANLR V++VAKKY N+GL   
Sbjct: 24  YLKEINRIPLLSREEEDHYARLAAQ---GDQDAKEKLVTANLRFVVNVAKKYQNQGLPLA 80

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+ A E+FD   GY F +YA+WW++QAI ++I+++S  IR+P++  +++ +
Sbjct: 81  DLISEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRANELVQ 140

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGD 590
           + +  + +  +       +++A+ L    + V  +L ++KE +SL+TP+ ++ D++ LGD
Sbjct: 141 IEKARKLVQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDTPVYEDRDSAMLGD 200

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +++D+ +  P D  ++  L+E    VLA+LT +E  +++ RFG+      +L+E+G  + 
Sbjct: 201 YLKDEASRPPEDVVLEKTLQEEIQEVLATLTEKEAEIIQYRFGLNGRHPMSLKEIGDMYN 260

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +T+ERIRQIE KA++K++   ++K L ++L
Sbjct: 261 LTKERIRQIEKKALKKIQQSEKAKVLETYL 290



 Score = 44.1 bits (102), Expect = 0.073,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 84/252 (33%), Gaps = 15/252 (5%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +YL+E+  I LLSRE E   A+    G       L  + L F  ++    +  +    L 
Sbjct: 23  LYLKEINRIPLLSREEEDHYARLAAQGDQDAKEKLVTANLRF--VVNVAKKYQNQGLPLA 80

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++I        E   G  +  E     K             Q     I   +++ +   +
Sbjct: 81  DLI-------SEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLN 133

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           + +   +  +  +    E  + +     A         +  L  +++ Y  L +      
Sbjct: 134 RANELVQIEKARKLVQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDT------ 187

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              +D  S++    LK++  +    + L ++  + + E L  ++++          L   
Sbjct: 188 PVYEDRDSAMLGDYLKDEASRPPEDVVLEKTLQEEIQEVLATLTEKEAEIIQYRFGLNGR 247

Query: 363 YGIKRDVFLERH 374
           + +      + +
Sbjct: 248 HPMSLKEIGDMY 259


>gi|310766652|gb|ADP11602.1| RNA polymerase sigma factor RpoS [Erwinia sp. Ejp617]
          Length = 330

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAQKLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L       N           A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEVFDEKALVGNEPGDNDLAEEDLLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVFFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|160902263|ref|YP_001567844.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359907|gb|ABX31521.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 414

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 133/269 (49%), Positives = 187/269 (69%), Gaps = 5/269 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++ S  R +    +KG+ +A     E+V+ANLRLVIS+AK+YT RGL FL
Sbjct: 139 YLREIGGIKLLTPSRERQLAIRAKKGDKKAKD---ELVKANLRLVISIAKRYTGRGLTFL 195

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGL++A EKFDW  G+KFSTYA WWV+QAITR+IADQ+ TIRIPVH+ + I++
Sbjct: 196 DLIQEGNIGLIRAVEKFDWKRGFKFSTYATWWVRQAITRAIADQARTIRIPVHLVESINR 255

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
           +    R+   +    P+ E++A+ L  P+E + ++L  TKE IS++ PI   D++ +++G
Sbjct: 256 MNIVIRKHLQETGEYPSTEKLAELLDKPLEKMDEILLATKEIISVDAPISGSDDEEAYIG 315

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DF+ED  A  P + A++  L+E   +VL SL P+E  VL+MR+G+      TLEEVG  F
Sbjct: 316 DFLEDSEADQPEEIAVRMILKEEIEKVLESLRPKEATVLKMRYGLLDGKMKTLEEVGNFF 375

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            VTRERIRQIE KA+RKL+HPSRS +L+ 
Sbjct: 376 NVTRERIRQIEVKALRKLRHPSRSLQLKE 404



 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 76/179 (42%), Gaps = 8/179 (4%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRG-YVTIEELNAFLP---PDEVSSEQMED 65
           D D      D     +  +   +K+I++A+++   +T  +++  +P    D +    ++ 
Sbjct: 24  DQDKIRVKRDKECYIEELERGLEKLIEIAKEKNNTITYRDIDECIPHNLSDVIDGSFLDK 83

Query: 66  TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
               L + GI +++    +  +  E+  +            ++ +   + + ++P+++YL
Sbjct: 84  IHEKLESEGIEIIESSQEDQIQEEEEFFN---DGLEELFQERESQIFDNSAVNEPIKIYL 140

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           RE+G I+LL+   E  +A R + G       L ++ L     I  R     G T L  I
Sbjct: 141 REIGGIKLLTPSRERQLAIRAKKGDKKAKDELVKANLRLVISIAKRY-TGRGLTFLDLI 198


>gi|59712674|ref|YP_205450.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
 gi|59480775|gb|AAW86562.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
          Length = 321

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 97/301 (32%), Positives = 168/301 (55%), Gaps = 5/301 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDS--ILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E D   ++ A+     E    +        +   +  +  I     ++  E  +   +  
Sbjct: 13  EFDLDTINDAELTSIEEESERLEVSSSQKVMDATQLYLGEIGFSPLLTAEEEVYFSRLA- 71

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   A+  M+E+NLRLV+ +A++Y +RGL  LDL++EGN+GL++A EKFD   G++
Sbjct: 72  --LKGDEAARARMIESNLRLVVKIARRYNHRGLALLDLVEEGNLGLIRAVEKFDPERGFR 129

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR +S K+  EPTPEEIA+K
Sbjct: 130 FSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELSQKLDHEPTPEEIAEK 189

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L  PV  V ++L++ +   S+++ +  E    L D + D     P     + ++  +   
Sbjct: 190 LDKPVSDVSRMLRLNERVASVDSMVAGESDKALLDILPDTKNSDPESETQKDDINTSLVG 249

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L P+++ V+  RFG+      TLE+VG +  +TRER+RQI+ + +R+L+    ++ 
Sbjct: 250 WLGQLNPKQKEVVARRFGLLGYEAATLEQVGIEIGLTRERVRQIQVEGLRRLREIMTNQG 309

Query: 676 L 676
           L
Sbjct: 310 L 310



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 3/103 (2%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           E EE   D+++ A   S      ++ + S+ +   D  ++YL E+G   LL+ E E+  +
Sbjct: 10  EVEEFDLDTINDAELTSIEEES-ERLEVSSSQKVMDATQLYLGEIGFSPLLTAEEEVYFS 68

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +    G     A + ES L    ++      N     L ++++
Sbjct: 69  RLALKGDEAARARMIESNLRL--VVKIARRYNHRGLALLDLVE 109


>gi|188534815|ref|YP_001908612.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
 gi|188029857|emb|CAO97741.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
          Length = 330

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L       N           A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEVFDEKALVGNEPGDNDLAEEDLLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVFFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|330723944|gb|AEC46314.1| RNA polymerase sigma factor [Mycoplasma hyorhinis MCLD]
          Length = 524

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 110/298 (36%), Positives = 176/298 (59%), Gaps = 11/298 (3%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +  +KN ++   D I      I        ++  E  ++   ++ G      A+  ++  
Sbjct: 229 DAAYKNKLSDTNDIIKWYMRWIGKYGKL--LTPEEENNLAKQIKNGGRAGKRARHTLINR 286

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLVI+ AK+Y NRGL F+DLI EGN G++KA +K+D+  GYKFSTYA WW++QAITR+
Sbjct: 287 NLRLVINNAKRYKNRGLTFIDLISEGNQGILKAVDKYDYTKGYKFSTYATWWIRQAITRA 346

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVEGVRKVLKI 569
           +ADQ+  IRIPVHM + I+K+ +  R +  +    PT E+IA+ +      E VR   KI
Sbjct: 347 VADQARIIRIPVHMVETINKINKIERELQQEYGVTPTDEQIAEVMGGDFTAEKVRYTKKI 406

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVL 628
             +PISL+  IG E+ S   DFI+D++ +SP+D + +    +   +++  +L   E+  +
Sbjct: 407 NIDPISLDKAIGKEEYSSFSDFIKDESVISPIDYSEREEKTKILKQMIENNLDNDEKVFI 466

Query: 629 RMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             R+G G + +      H+ +E+ K+  VT+ERIRQIE+K ++KL+HP +  K R  +
Sbjct: 467 MKRYGFGTDPNGEQYRIHSFDELAKERGVTKERIRQIESKILKKLRHPQKKWKQRDLI 524


>gi|284009102|emb|CBA76093.1| RNA polymerase sigma factor RpoS [Arsenophonus nasoniae]
          Length = 329

 Score =  175 bits (443), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 99/271 (36%), Positives = 168/271 (61%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+     + + + M+E+NLRLV+ ++++Y+N
Sbjct: 54  LDATQLYLGEIGYSPLLTAEEE---VFYARRALRGDAASLQRMIESNLRLVVKISRRYSN 110

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 111 RGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 170

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR ++ K+  EP+ EEIA++L  PV+ V ++L++ +   S++TPIG +  
Sbjct: 171 VKELNVYLRIARELAQKLDHEPSAEEIAERLDKPVDDVSRMLRLNERISSVDTPIGGDSD 230

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D N   P  +    N++E+  + L  L  ++  VL  RFG+      TLEEV
Sbjct: 231 KALLDVLSDDNDSGPEGTIQANNMKESIVKWLFELNAKQREVLARRFGLLGYESETLEEV 290

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+LK    ++ L
Sbjct: 291 GREIGLTRERVRQIQVEGLRRLKDILHNQGL 321



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 27/105 (25%), Positives = 42/105 (40%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            +   D E  ++SL      +           + ++   D  ++YL E+G   LL+ E E
Sbjct: 16  DETSMDAEAFDESLLKEEDLNLEQDDDLDLFQNINQRVLDATQLYLGEIGYSPLLTAEEE 75

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  A+R   G A  +  + ES L     I  R   N G  LL  I
Sbjct: 76  VFYARRALRGDAASLQRMIESNLRLVVKISRRYS-NRGLALLDLI 119


>gi|262197687|ref|YP_003268896.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081034|gb|ACY17003.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 465

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 96/296 (32%), Positives = 176/296 (59%), Gaps = 3/296 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           + A    + +     A   D     R + +  +V      ++FR+ V  VR  E  A  A
Sbjct: 170 ARAIHPVDNDKIFLDAVLEDLYAMARRKSQVRNVSFSTRRADFRNYVDQVRAAEHAARNA 229

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E V+ANLRLV+S+A+++ +  +   DLIQEGN+GL+KA E++D+  G++FSTYA WW+
Sbjct: 230 RNEFVKANLRLVVSIARRFNHGRMSLADLIQEGNLGLIKAVERYDYRRGFRFSTYASWWI 289

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + AI R++AD+   +R+PVHM D  H++++   +++N + R+PT EE+++   + VE + 
Sbjct: 290 RHAIGRALADKGREVRLPVHMLDAHHRLLKAQHQLTNTLGRQPTSEELSEAANLSVEKIE 349

Query: 565 KVL-KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLT 621
           K+   +  + +SL+ P+ DED   + + ++D +        + A   + +   + L +L 
Sbjct: 350 KMRTHLLDQALSLDRPMNDEDGRSVAEVLQDPHGEEHSALNVLAQRTMSDEVRKTLQTLR 409

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           P E  +LR RFG+  + + TL+++G+Q+ ++RERIRQ++ +A+ K++   R K + 
Sbjct: 410 PIEADILRRRFGLDNDEELTLKQIGEQYNLSRERIRQLQEQALTKMRVALRRKAMM 465


>gi|89109528|ref|AP_003308.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|218547743|ref|YP_002381534.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|85675562|dbj|BAE76818.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|218355284|emb|CAQ87891.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|320645931|gb|EFX14912.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str.
           493-89]
          Length = 291

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 16  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 72

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 73  RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 132

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 133 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 192

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 193 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 252

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 253 GREIGLTRERVRQIQVEGLRRLREILQTQGL 283



 Score = 44.1 bits (102), Expect = 0.079,   Method: Composition-based stats.
 Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
              +     A +   D  ++YL E+G   LL+ E E+  A+R   G       + ES L 
Sbjct: 2   AEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLR 61

Query: 164 FQALIIWRDELNDGTTLLREI 184
               I  R   N G  LL  I
Sbjct: 62  LVVKIARRYG-NRGLALLDLI 81


>gi|17231302|ref|NP_487850.1| RNA polymerase sigma factor SigD [Nostoc sp. PCC 7120]
 gi|8489797|gb|AAF75755.1|AF262216_2 group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
 gi|17132944|dbj|BAB75509.1| group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
          Length = 332

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 101/232 (43%), Positives = 160/232 (68%), Gaps = 1/232 (0%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +  IAK++MVEANLRLV+SVAKKY  R +  LDLIQEG+IG+ +  EKFD   GY+FST
Sbjct: 92  ADGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IA+++ TIR+P+H+ +K++K+ +  R++S ++ R PT  E+A +L +
Sbjct: 152 YAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQRLGRAPTAGELANELEL 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + VR+ L+  + P+SL+  +GD   + LG+ +ED  A SP D  +Q++L      ++ 
Sbjct: 212 TPKQVREYLEKARLPLSLDLRLGDNYDTELGEMLEDPGA-SPEDFVMQSSLSNDLEVLME 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            LTP+++ V+ +RFG+      TL  +G+   ++RER+RQIE +A+ KL+  
Sbjct: 271 QLTPQQKEVITLRFGLIDGQALTLARIGEILNISRERVRQIEREALTKLRKS 322



 Score = 44.8 bits (104), Expect = 0.049,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLC 158
            D VR YLRE+G + LLS E EI   K+++       M   L 
Sbjct: 22  TDLVRTYLREIGRVPLLSHEEEIRYGKQVQRSTTLQEMREELA 64


>gi|170078438|ref|YP_001735076.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169886107|gb|ACA99820.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 318

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 107/282 (37%), Positives = 174/282 (61%), Gaps = 10/282 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E+         +K  +    +S  E +       K       AK++MVEANLRLV+S
Sbjct: 45  LKAELAEKQDQEPSLKEWAQAANLSQRELK-------KQLLLGKQAKQKMVEANLRLVVS 97

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S T
Sbjct: 98  VAKKYIKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRT 157

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+ +K++K+ +  R+++    R  +  E+A +L +  + VR  L+ +++P+SL+ 
Sbjct: 158 IRLPIHITEKLNKIKKAQRQLAQANGRSASIPELADELGLTTKQVRDYLEKSRQPLSLDL 217

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +GD + + L + +ED + ++P D A  A L+    R+L  LT +++ VL +RFG+   T
Sbjct: 218 RVGDNNDTELIELLED-DGLTPDDYATHAALKRDLARMLNDLTAQQQEVLTLRFGLRDGT 276

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            HTL ++G+   ++RER+RQIE +A+ KL+   R  ++  +L
Sbjct: 277 PHTLAKIGEHLSISRERVRQIEREALAKLRK--RKAEMGEYL 316



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           + DPVR YL+E+G + LL+ E E+  ++R++       + A L E
Sbjct: 7   SADPVRTYLKEIGRVPLLTHEEEVLYSRRVQKMVNLEKLKAELAE 51


>gi|269960386|ref|ZP_06174759.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
 gi|269834813|gb|EEZ88899.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
          Length = 255

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 99/230 (43%), Positives = 155/230 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 15  RMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 74

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PVE V K+
Sbjct: 75  TIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPVEDVSKM 134

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L P+++ 
Sbjct: 135 LRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEELNPKQKE 194

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 195 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQGL 244


>gi|71278347|ref|YP_267823.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
 gi|71144087|gb|AAZ24560.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
          Length = 296

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 157/272 (57%), Gaps = 3/272 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     ++  E  +   +          ++K M+E+NLRLV+ +A++Y 
Sbjct: 20  NLDATQIYLSEIGFSPLLTAEEEVYFSRLA---LKGDEPSRKRMIESNLRLVVKIARRYN 76

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 77  NRGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 136

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R +R +  K+  EPT E+IA+ L  PV  V K+L++ +   S++TP   E 
Sbjct: 137 VVKELNIYLRASRELIQKLDHEPTAEDIAQHLDRPVADVNKMLRLNERIASVDTPFAGES 196

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D I D+ +  P       ++       L  L  ++  VL  RFG+      TLE 
Sbjct: 197 DKALLDVIADEKSTGPESDLQSEDMSNNIIHWLNELNTKQREVLARRFGLLGYEASTLEN 256

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           VG++  +TRER+RQI+ +A+++L+     + L
Sbjct: 257 VGREIGLTRERVRQIQVEALKRLRDILSQQNL 288



 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
                  S  D  ++YL E+G   LL+ E E+  ++    G       + ES L    ++
Sbjct: 12  ESKEDAPSNLDATQIYLSEIGFSPLLTAEEEVYFSRLALKGDEPSRKRMIESNLRL--VV 69

Query: 169 IWRDELNDGTTLLREIID 186
                 N+    L ++I+
Sbjct: 70  KIARRYNNRGLPLLDLIE 87


>gi|303235908|ref|ZP_07322511.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
 gi|302483781|gb|EFL46773.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
          Length = 293

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 90/273 (32%), Positives = 161/273 (58%), Gaps = 4/273 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++  S E  + + E   +   +R        A + + +ANLR V+SVAK+Y N+G
Sbjct: 23  ALEKYLQDTSREAMVGLDEEIELAKRIR---EGDEKALERLTKANLRFVVSVAKQYQNQG 79

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGN GL+KAA+K+D   G+KF +YA+WW++Q+I ++I++QS  +R+P++   
Sbjct: 80  LALPDLINEGNFGLIKAAQKYDETRGFKFISYAVWWIRQSIMQAISEQSRMVRVPINQMG 139

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +++ +   +   + +R P+  E+ + + +  E + + L +    +S++ P    +   
Sbjct: 140 SANRIRKFINQFEQEHERYPSLSELTEHIDLLEEKIVEALAMATTQVSMDAPFTSNEEGS 199

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + +KNA S  D  +  +L       LASL+ RE+ +++  FGI      +LEE+G+
Sbjct: 200 LLDVLPNKNAPSADDLLVAESLSTEVANALASLSEREQIIIKCFFGINQPE-MSLEEIGE 258

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +  +TRER+RQI+ KAI +L+  S+S++L+SFL
Sbjct: 259 RTGLTRERVRQIKEKAIIRLRKNSQSERLKSFL 291


>gi|326518320|dbj|BAJ88189.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326533296|dbj|BAJ93620.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 552

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 155/247 (62%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK        K  MV +N+RLVIS+A+++   GL+  DLIQEG  GL++ AEKFD   G
Sbjct: 301 LRKRLDHGIHCKNRMVTSNVRLVISIAREFEGPGLELYDLIQEGMQGLIRGAEKFDASKG 360

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQA+ +S+++Q+   R+P HM +  ++V    +R+  K+KR P+ EEIA
Sbjct: 361 FRFSTYSHWWIKQAMRKSVSEQTQIFRLPAHMVEASYRVKECTKRLRRKLKRRPSNEEIA 420

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + MPV+ V   + + K  +SL++ IG  D ++  +   D +A +  +   + ++++  
Sbjct: 421 VDIGMPVKRVEAAVSLPKYSVSLDSKIGSTDMTY-QEVTADPSAETAEEMLNRMSMKKDV 479

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            + L +L+PRE +V+++RFGI      TL+E+G    V+RERIRQIE+ A RKL+   + 
Sbjct: 480 HQALDTLSPRERQVVKLRFGINDGRIRTLQEIGNIMGVSRERIRQIESGAFRKLRGKKKV 539

Query: 674 KKLRSFL 680
           K L  +L
Sbjct: 540 KCLMDYL 546


>gi|194337394|ref|YP_002019188.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309871|gb|ACF44571.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 299

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 94/283 (33%), Positives = 166/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTAEDEVKLTKAIKEGFDMPVDTTEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P   E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEFERDPNTRELATLLEMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P     + +L     R L+ L PRE  V++  FGIGM+
Sbjct: 196 APFAQGDDNRLLDVLQNDGHL-PDYGLNRDSLTLEVERSLSVLAPREADVIKSYFGIGMD 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  + SK L+ ++
Sbjct: 255 NPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKILKEYI 297


>gi|116071837|ref|ZP_01469105.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065460|gb|EAU71218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 284

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 99/270 (36%), Positives = 165/270 (61%), Gaps = 4/270 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ + ++ +     +   E   + S  +        A+  M+ ANLRLV+SVAKKY N+
Sbjct: 16  IELAHHVQDMKQLKELPQEE---LTSRQKHKIRMGKRARDRMMAANLRLVVSVAKKYQNQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q +TR+I + + TIR+P+H+ 
Sbjct: 73  GLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHIS 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
           +K+ K+ R +R +S++  R+P   E+A  + +    +  ++  +    SL+     E+  
Sbjct: 133 EKLSKMRRISRELSHRFGRQPNRLELASAMGIEPRELEDLITQSAPCASLDAHARGEEDR 192

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LG+ I D N   P++   ++  +E     L+ L  RE+++LR+RFG+G     TL E+
Sbjct: 193 STLGELIPDPNGEEPMEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEI 252

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           G+Q  V+RER+RQ+EAKAI KL+  +  ++
Sbjct: 253 GRQINVSRERVRQLEAKAILKLRTMTNHQQ 282


>gi|302552062|ref|ZP_07304404.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302469680|gb|EFL32773.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 332

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 119/303 (39%), Positives = 170/303 (56%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +  H G   D   V    D          A EV+    I   + +  V  G   ++    
Sbjct: 23  VRAHGGEIADRDLVGMYLDEIARTPLLDAAREVELSQVIEAGVFAKQVLDGFEETKAEAT 82

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              +     +A  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+
Sbjct: 83  REELESLVADAERAKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDY 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P 
Sbjct: 143 RKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPT 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA +L    E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     
Sbjct: 203 EIAAELGSTPERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    ++  L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  
Sbjct: 263 EELDDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKL 322

Query: 671 SRS 673
           +RS
Sbjct: 323 ARS 325


>gi|330982601|gb|EGH80704.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 459

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 89/251 (35%), Positives = 149/251 (59%), Gaps = 3/251 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++   +  +  I     +S  E  H   +    +      +K M+E+NLRLV+ +A++Y 
Sbjct: 13  ALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRMIESNLRLVVKIARRYV 69

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H
Sbjct: 70  NRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 129

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G + 
Sbjct: 130 VVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPDS 189

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   TLE+
Sbjct: 190 DKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHESSTLED 249

Query: 645 VGKQFCVTRER 655
           VG +  +TRER
Sbjct: 250 VGLEIGLTRER 260



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 9/92 (9%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  +N G 
Sbjct: 15  DATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY-VNRGL 73

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           +LL  I         E   G     E    ++
Sbjct: 74  SLLDLI--------EEGNLGLIRAVEKFDPER 97


>gi|312171353|emb|CBX79612.1| RNA polymerase sigma factor rpoS [Erwinia amylovora ATCC BAA-2158]
          Length = 330

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L       N           A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEVFDEKALVGNEPGDNELAEEDLLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVFFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|292487251|ref|YP_003530123.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
 gi|292900377|ref|YP_003539746.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|3183703|emb|CAA10959.1| RpoS [Erwinia amylovora]
 gi|291200225|emb|CBJ47353.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|291552670|emb|CBA19715.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
          Length = 330

 Score =  175 bits (442), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA+KL  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L       N           A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEVFDEKALVGNEPGDNELAEEDLLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVFFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|307718169|ref|YP_003873701.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
 gi|306531894|gb|ADN01428.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
          Length = 303

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 93/270 (34%), Positives = 171/270 (63%), Gaps = 4/270 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    ++  E  H   +  +       AK+++V ANLR V++VAKKY N+GL   
Sbjct: 35  YLKEINRIPLLTREEEDHYARLAAQ---GDQHAKEKLVTANLRFVVNVAKKYQNQGLPLA 91

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+ A E+FD   GY F +YA+WW++QAI ++I+++S  IR+P++  +++ +
Sbjct: 92  DLISEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRANELVQ 151

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGD 590
           + +  + +  +       +++A+ L    + V  +L ++KE +SL+TP+ ++ D++ LGD
Sbjct: 152 IEKARKLVQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDTPVYEDRDSAMLGD 211

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +++D+ +  P D  ++  L+E    VLA+LT +E  +++ RFG+      +L+E+G  + 
Sbjct: 212 YLKDEASRPPEDVVLEKTLQEEIQEVLATLTEKEAEIIQYRFGLNGRHPMSLKEIGDLYN 271

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +T+ERIRQIE KA++K++   ++K L ++L
Sbjct: 272 LTKERIRQIEKKALKKIQQSEKAKILETYL 301



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 98/284 (34%), Gaps = 15/284 (5%)

Query: 91  DSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D   +A+  +  +V  +K++   D    + + +YL+E+  I LL+RE E   A+    G 
Sbjct: 2   DFASIAAEEAMETVKRKKKRRVQDSGDANVLSLYLKEINRIPLLTREEEDHYARLAAQGD 61

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
                 L  + L F  ++    +  +    L ++I        E   G  +  E     K
Sbjct: 62  QHAKEKLVTANLRF--VVNVAKKYQNQGLPLADLI-------SEGNIGLLNAIERFDPDK 112

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                        Q     I   +++ +   ++ +   +  +  +    E  + +     
Sbjct: 113 GYHFISYAVWWIRQAILKAISEKSRMIRLPLNRANELVQIEKARKLVQTESGEHNEIKKV 172

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
           A         +  L  +++ Y  L +         +D  S++    LK++  +    + L
Sbjct: 173 AETLDYDEDHVANLLNLSKEYVSLDT------PVYEDRDSAMLGDYLKDEASRPPEDVVL 226

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            ++  + + E L  ++++          L   + +      + +
Sbjct: 227 EKTLQEEIQEVLATLTEKEAEIIQYRFGLNGRHPMSLKEIGDLY 270


>gi|183600216|ref|ZP_02961709.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
 gi|188022512|gb|EDU60552.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
          Length = 328

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 110/308 (35%), Positives = 185/308 (60%), Gaps = 8/308 (2%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF--------R 428
            +LD   +  A D  + + ++ V    D +  ++N  + +   T I +SE          
Sbjct: 13  NDLDDSMMDDAFDESQFKEEDLVTELDDEMDLLQNTNQRVLDATQIYLSEIGFSPLLTAE 72

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V   R+       +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 73  EEVFYARRALRGDVASRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKF 132

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+
Sbjct: 133 DPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPS 192

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA++L  PVE V ++L++ +   S++TPI  +    L + + D+N   P  +    N
Sbjct: 193 AEEIAEQLDKPVEDVSRMLRLNERITSVDTPIAGDSEKSLLEVLSDENESGPEHTIQDNN 252

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + L  L P++  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 253 LKENIVKWLFELNPKQREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLRRLK 312

Query: 669 HPSRSKKL 676
              + ++L
Sbjct: 313 DILQGEEL 320



 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D DD   ++  ++S                   + ++   D  ++YL E+G   LL+ E 
Sbjct: 14  DLDDSMMDDAFDESQFKEEDLVTELDDEMDLLQNTNQRVLDATQIYLSEIGFSPLLTAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVFYARRALRGDVASRQRMIESNLRLVVKISRRYN-NRGLALLDLI 118


>gi|291550766|emb|CBL27028.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 280

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 114/258 (44%), Positives = 169/258 (65%), Gaps = 4/258 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E R +     K       A++++ E NLRLV+S+AK YT RG+  +
Sbjct: 20  YLNEIGQIPLLSEEEERDLGC---KSASGDEDARRKLEEGNLRLVVSLAKHYTGRGITLM 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLM AAEK+D+    +FSTYA WW+K+A+ R+I  QS  IR+PVH+ + + K
Sbjct: 77  DLIQEGNIGLMHAAEKYDYTKENRFSTYASWWIKEAMQRAIDQQSREIRVPVHVAENMKK 136

Query: 532 VVRTARRMSNKIKREPTPEEIAKKL-AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           V + ++ +  K  RE TPEEIA+++     E V+++L   + P+SLETP+G++  ++LGD
Sbjct: 137 VQKISKDLQQKFGREATPEEIAEEMKDKSPEFVKEILSYLQNPVSLETPVGEDGENNLGD 196

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +EDK+A +P D+  Q   +E    +L SL  RE +V+R+RFG+     HTLEE+G +  
Sbjct: 197 MVEDKDATTPEDAMNQLVQKEEVQELLESLNDRERQVIRLRFGLEDGKTHTLEEIGDELN 256

Query: 651 VTRERIRQIEAKAIRKLK 668
           VTRER+RQIEA+A+ KL+
Sbjct: 257 VTRERVRQIEARAMEKLR 274



 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 32/174 (18%), Positives = 58/174 (33%), Gaps = 10/174 (5%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
            +           +P+++YL E+G I LLS E E  +  +  +G       L E  L   
Sbjct: 2   EKDLNLPEGTEVTEPLKIYLNEIGQIPLLSEEEERDLGCKSASGDEDARRKLEEGNLRLV 61

Query: 166 ALIIWR---------DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
             +            D + +G   L    + +     E++   +         +R    Q
Sbjct: 62  VSLAKHYTGRGITLMDLIQEGNIGLMHAAE-KYDYTKENRFSTYASWWIKEAMQRAIDQQ 120

Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            +E         +++   K+SKD + K        E  E   D+  +     LS
Sbjct: 121 SREIRVPVHVAENMKKVQKISKDLQQKFGREATPEEIAEEMKDKSPEFVKEILS 174


>gi|126659335|ref|ZP_01730471.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
 gi|126619417|gb|EAZ90150.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
          Length = 318

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 109/279 (39%), Positives = 177/279 (63%), Gaps = 6/279 (2%)

Query: 405 SILKIRNEIKSI--SVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAK 461
           ++ K+R++I        T I  ++   I    ++        AK++MVEANLRLV+SVAK
Sbjct: 41  NLEKLRDDIIEETGQEPTEIQWAKTAKISRKELQSIIEIGEAAKRKMVEANLRLVVSVAK 100

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY  R L  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA++S TIR+
Sbjct: 101 KYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRL 160

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+ +K++K+ +  R +S +  R  T  E+A++L +  + VR+ L+  ++P+SL+  +G
Sbjct: 161 PIHITEKLNKIKKAQRELSQQKGRAATVVELAEELDLTPKQVREYLERARQPLSLDLRVG 220

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D   + LGD +ED +  SP D A  ++L+    R++  LT +++ V+ +RFG+      T
Sbjct: 221 DNQDTELGDLLED-DGQSPEDFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLT 279

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L ++G +  ++RER+RQIE +A+ KL+   R   ++ +L
Sbjct: 280 LAKIGSRLNISRERVRQIEREALSKLRK--RKANIQEYL 316



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/34 (50%), Positives = 24/34 (70%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            +S  DPVR YL+E+G + LL+ E EI  AKR++
Sbjct: 4   TKSNPDPVRAYLKEIGRVPLLTHEEEILYAKRVQ 37


>gi|87123382|ref|ZP_01079233.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86169102|gb|EAQ70358.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 293

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 163/284 (57%), Gaps = 16/284 (5%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMV---------------RKGECEASIAK 445
              DSI    + I  + + T     E  H V  +               R        A+
Sbjct: 1   MSTDSIGYYLSSIGRVPLLTAAEEIELAHHVQAMKQLLELPEAERTPRQRHQIRMGKRAR 60

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++
Sbjct: 61  DRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIR 120

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q +TR+I + + TIR+P+H+ +K+ K+ R +R +S++  R+P   E+A  + +  + +  
Sbjct: 121 QGMTRAIDNSARTIRLPIHISEKLSKMRRISRELSHRFGRQPNRLELAHAMGIEPKDLED 180

Query: 566 VLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++  +    SL+     E+  S LG+ I D N   P++   ++  +E     LA L  RE
Sbjct: 181 LISQSAPCASLDAHARGEEDRSTLGELIPDPNGAEPMEGMDRSIQKEHLGGWLAQLNDRE 240

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++LR+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 241 QKILRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 284



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
           + D +  YL  +G + LL+   EI +A  +       M  L E P  
Sbjct: 2   STDSIGYYLSSIGRVPLLTAAEEIELAHHV-----QAMKQLLELPEA 43


>gi|2961260|emb|CAA73683.1| rpoS [Enterobacter cloacae]
          Length = 346

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 71  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 127

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 128 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 187

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 188 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 247

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 248 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 307

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 308 GREIGLTRERVRQIQVEGLRRLREILQGQGL 338



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 32  EFDENGAEAFDEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 91

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 92  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 136


>gi|78222633|ref|YP_384380.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78193888|gb|ABB31655.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter metallireducens
           GS-15]
          Length = 326

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 106/262 (40%), Positives = 170/262 (64%), Gaps = 3/262 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+  ++ I   T ++  E + + S + K       A+ +M+E+NLRLV+ +AK+Y NRG
Sbjct: 57  AIKLYLREIQRTTLLTADEEKVLASRIAK---GDKAARDKMIESNLRLVVKIAKRYINRG 113

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D
Sbjct: 114 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 173

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K+++  R + N+  REPT +E+A ++ +    +R+++ + K+  S+E P+G+     
Sbjct: 174 DINKMLKITRELVNRFNREPTVKEVATEMNVNSAYIRRLMVLLKKTYSIERPMGENSDYF 233

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D IED ++VSP       N  E  ++  ASL+  E+++L +RFG+      TL+ +G+
Sbjct: 234 LIDTIEDTSSVSPAVLLEDLNKYEIVSKWFASLSENEQKILTLRFGLEDKEPQTLDTIGR 293

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
            F VTRERIRQIEAK++ KL+ 
Sbjct: 294 SFGVTRERIRQIEAKSLEKLRK 315



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 29/117 (24%), Positives = 46/117 (39%), Gaps = 11/117 (9%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSS----------VFLQKRKDSADRSTDDPVRMYLRE 127
           ++ + +E EE +E   D       +S             ++ K       DD +++YLRE
Sbjct: 5   LEKEAVEPEEHAERQPDDFLEPEPTSFEYEEAEEEEEQEEEIKVVEVEHFDDAIKLYLRE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +    LL+ + E  +A RI  G       + ES L     I  R  +N G   L  I
Sbjct: 65  IQRTTLLTADEEKVLASRIAKGDKAARDKMIESNLRLVVKIAKRY-INRGLPFLDLI 120


>gi|226328647|ref|ZP_03804165.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
 gi|225203380|gb|EEG85734.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
          Length = 327

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 107/292 (36%), Positives = 177/292 (60%), Gaps = 3/292 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             ++   + E +        ++   +  +  I     ++  E    V   R+       +
Sbjct: 31  EESESDAQDEIELIEGVNQRALDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDIPS 87

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ M+E+NLRLV+ ++++YTNRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW+
Sbjct: 88  RQRMIESNLRLVVKISRRYTNRGLALLDLIEEGNLGLIRAVEKFDPEKGFRFSTYATWWI 147

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA+ L  PVE V 
Sbjct: 148 RQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSVEEIAESLDKPVEDVS 207

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K+L++ +   S++TPIG +    L D I D+N   P  +    NL+E   + L  L P++
Sbjct: 208 KMLRLNERITSVDTPIGGDSDKALLDIISDENEEGPEATIQNNNLKENIIKWLFELNPKQ 267

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+LK   +S+ L
Sbjct: 268 REVLARRFGLLGYEAETLEDVGREIGLTRERVRQIQVEGLRRLKDILQSQGL 319



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/118 (26%), Positives = 47/118 (39%), Gaps = 4/118 (3%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR---STDDPVRMYLR 126
           +S   + V +    E EE  E+  ++A+    S    Q   +  +       D  ++YL 
Sbjct: 1   MSQSTLRVDELYTDEIEENMEEFDEVAAKEEESESDAQDEIELIEGVNQRALDATQLYLG 60

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 61  EIGYSPLLTAEEEVFFARRALRGDIPSRQRMIESNLRLVVKISRRY-TNRGLALLDLI 117


>gi|223998999|ref|XP_002289172.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220974380|gb|EED92709.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 318

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 104/252 (41%), Positives = 160/252 (63%), Gaps = 4/252 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V+ ++K    +  AK  + E+NLRLVIS+AK+Y  RGL   DL QEG +GL +A EKFD 
Sbjct: 64  VTQIKKQIRRSLRAKAALTESNLRLVISIAKRYQGRGLNMQDLCQEGTLGLTRACEKFDP 123

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA WW+KQ I R+IADQ+ TIR+PVH+ D++  V +  R + N++ R+ T E
Sbjct: 124 ERGFRFSTYATWWIKQGIMRAIADQARTIRLPVHIHDQLSIVRKAERDLQNELGRDATKE 183

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQA 607
           E+A K+ M  + +  + + +   IS+E  +G    E +  + D + D +      +  + 
Sbjct: 184 EVAAKVGMKPDKIEFLKRASVGSISMEQELGTSGSERSFTIQDTLGDPDQKPVDMAQYR- 242

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L++   R++ +L  RE+ V+RMRFG+      TLEE+GK+F VTRERIRQIEA+A+ KL
Sbjct: 243 MLQDDVGRLICTLNAREQAVIRMRFGLDDGKAKTLEEIGKKFSVTRERIRQIEARALHKL 302

Query: 668 KHPSRSKKLRSF 679
           + P R+  ++ +
Sbjct: 303 RQPYRNHTVKCY 314


>gi|297611772|ref|NP_001067832.2| Os11g0448400 [Oryza sativa Japonica Group]
 gi|62701714|gb|AAX92787.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|108864350|gb|ABA93405.2| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|255680064|dbj|BAF28195.2| Os11g0448400 [Oryza sativa Japonica Group]
          Length = 564

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 94/249 (37%), Positives = 150/249 (60%), Gaps = 1/249 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +RK        K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD  
Sbjct: 311 RTLRKRLDHGIYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDAS 370

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTY+ WW+KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EE
Sbjct: 371 KGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEE 430

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA    MP++ V   + + K  +SL++ IG  D ++  +   D  A +  +   + +++ 
Sbjct: 431 IAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKR 489

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + L +LT RE +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   
Sbjct: 490 DVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKK 549

Query: 672 RSKKLRSFL 680
           R   L+ +L
Sbjct: 550 RVNALKDYL 558


>gi|284104060|ref|ZP_06386126.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283830219|gb|EFC34468.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 271

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 93/269 (34%), Positives = 160/269 (59%), Gaps = 3/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +K I     ++ +E   +   +++       A  ++  ANLR V+SVAKK+  +GL
Sbjct: 2   LDQYLKEIGQIDLVTPAEEAELARRIKQ---GDEEALLKLTRANLRFVVSVAKKFQGQGL 58

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN GL+KAA++FD   G+KF +YA+WW++Q+I +++A+Q   +R+P++    
Sbjct: 59  HLTDLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQGRVVRLPLNQIGT 118

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K+ +++ R++ + +R+P  EE+A  L + +E VR  ++ T   +S++ P  +ED + L
Sbjct: 119 ISKIRKSSARLAQEHERDPNLEELATDLQIDIEKVRSAMQRTARHLSMDAPFNEEDENSL 178

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +       P +     +L+      L+SL PRE  + R+ FG+G     TLEE+G +
Sbjct: 179 LDVLPSNEIAPPDEPLRGESLKIDIEVALSSLCPREAEITRLYFGVGREHPLTLEEIGLR 238

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           F +TRER+RQI+ KA+RKL+   R + L+
Sbjct: 239 FDLTRERVRQIKEKALRKLRQKHRREDLK 267



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+G I+L++   E  +A+RI+ G    +  L  + L F  ++    +       L +
Sbjct: 5   YLKEIGQIDLVTPAEEAELARRIKQGDEEALLKLTRANLRF--VVSVAKKFQGQGLHLTD 62

Query: 184 IID 186
           +I+
Sbjct: 63  LIN 65


>gi|167717486|ref|ZP_02400722.1| RNA polymerase sigma factor [Burkholderia pseudomallei DM98]
          Length = 294

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 96/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 52  SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 111

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 112 WWIRQAISRAVADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 171

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 172 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 231

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 232 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 291


>gi|86134980|ref|ZP_01053562.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
 gi|85821843|gb|EAQ42990.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
          Length = 287

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 93/272 (34%), Positives = 169/272 (62%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +    + I     I+  E   +   ++        A  ++V+ANLR V+SVAK+Y N+GL
Sbjct: 18  LEKYFQEIGKIDLITADEEVELALKIK---AGDQRALDKLVKANLRFVVSVAKQYQNQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +S+A+QS  +R+P++    
Sbjct: 75  KLSDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSIMQSLAEQSRIVRLPLNKIGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K+ +   ++  + +R PT  EIA +L   V  V + +K +   +S++ P  + + S+L
Sbjct: 135 ISKINKVYSKLEQRNERIPTYVEIANELDTTVRNVAQSMKNSGRHVSMDAPFREGEDSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + ++   +  P  + ++ +L     R L +L+ +E +V++M FG+G +T  +L E+G+ 
Sbjct: 195 YNVLKSDESPRPDKNLMKQSLDIEIDRALETLSHKEAKVIKMFFGLGNHTASSLSEIGET 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F +TRER+RQ++ +AIR+L++ SR++ LR +L
Sbjct: 255 FDLTRERVRQVKQRAIRRLQNKSRTEVLRYYL 286



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y +E+G I+L++ + E+ +A +I+AG    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YFQEIGKIDLITADEEVELALKIKAGDQRALDKLVKANLRF--VVSVAKQYQNQGLKLSD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|212711364|ref|ZP_03319492.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
 gi|212686093|gb|EEB45621.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
          Length = 328

 Score =  174 bits (441), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 108/308 (35%), Positives = 185/308 (60%), Gaps = 8/308 (2%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF--------R 428
            +LD + +  A D  + + ++  +   +    +++  + +   T I +SE          
Sbjct: 13  NDLDENAMDEAFDESQFKEEDLASELDEETDLLQSASQRVLDATQIYLSEIGFSPLLTAE 72

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V   R+       +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 73  EEVFYARRALRGDVASRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKF 132

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+
Sbjct: 133 DPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPS 192

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA++L  PVE V ++L++ +   S++TPI  +    L + + D N   P ++    N
Sbjct: 193 PEEIAERLDKPVEDVSRMLRLNERITSVDTPIAGDSEKSLLEVLSDDNESGPENTIQDNN 252

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + L  L P++  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 253 LKENIVKWLYELNPKQREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLRRLK 312

Query: 669 HPSRSKKL 676
              + + L
Sbjct: 313 DILQGEDL 320



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 42/106 (39%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D D+   +E  ++S       ++          SA +   D  ++YL E+G   LL+ E 
Sbjct: 14  DLDENAMDEAFDESQFKEEDLASELDEETDLLQSASQRVLDATQIYLSEIGFSPLLTAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVFYARRALRGDVASRQRMIESNLRLVVKISRRYN-NRGLALLDLI 118


>gi|221134005|ref|ZP_03560310.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  174 bits (441), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 98/272 (36%), Positives = 161/272 (59%), Gaps = 4/272 (1%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
                  S+   +  +  I     +S  E    V   RK       A++ M+ +NLRLV+
Sbjct: 39  LAGEIKKSLDNTQLYLNEIGFSPLLSAEEE---VLHGRKALKGDKDARERMIVSNLRLVV 95

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            +A++Y +RGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ 
Sbjct: 96  KIARRYKDRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTR 155

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           T+R+P+H+  +++  +RTAR ++ ++  EPT EEIA KL +  E V K+L++ +   S++
Sbjct: 156 TVRLPIHVVKELNIYLRTARNLAQELDHEPTAEEIADKLDVSTEDVNKMLRLNERIKSVD 215

Query: 578 TPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           + +  E D + L D + D N   P +   + +++      L  L P++  VL  RFG+  
Sbjct: 216 SYLSHESDGNSLLDILPDSNHSGPEEKNQEDDIKNNIVMWLQELNPKQREVLSRRFGLMG 275

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TLE VG +  +TRER+RQI+ +A+R+LK
Sbjct: 276 FEPDTLENVGAEIGLTRERVRQIQVEALRRLK 307



 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 42/277 (15%), Positives = 89/277 (32%), Gaps = 21/277 (7%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
           ++  F         + + D  ++YL E+G   LLS E E+   ++   G       +  S
Sbjct: 30  DTDAFNDLSLAGEIKKSLDNTQLYLNEIGFSPLLSAEEEVLHGRKALKGDKDARERMIVS 89

Query: 161 PLTFQALIIWRDELNDGTTLLREI-------IDLEACIGPESKGGFFHGTEGHSYQKRED 213
            L     I  R + + G  LL  +       I       PE    F         Q  E 
Sbjct: 90  NLRLVVKIARRYK-DRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER 148

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
           +   + R          E    +        +   E    +  +  +   +  + +  + 
Sbjct: 149 AIMNQTRTVRLPIHVVKELNIYLRTARNLAQELDHEPTAEEIADKLDVSTEDVNKMLRLN 208

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK------------VLKEKL 321
           ++++  V   L   ++    L  L D+  +G +++      K              +E L
Sbjct: 209 ERIK-SVDSYLSHESDGNSLLDILPDSNHSGPEEKNQEDDIKNNIVMWLQELNPKQREVL 267

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
            +  G +      ++ +  ++    +R+   + E LR
Sbjct: 268 SRRFGLMGFEPDTLENVGAEIGLTRERVRQIQVEALR 304


>gi|308189916|ref|YP_003922847.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
 gi|307624658|gb|ADN68963.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
          Length = 489

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 190/320 (59%), Gaps = 15/320 (4%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           LE ++  E++ +     KD             V   ++   +   +     ++I E + +
Sbjct: 174 LESYENEEINLNDNKVIKDKDLTNKLTETNDIVKWYMRWIGKYGKL-----LTIEEEKKL 228

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA  K++ 
Sbjct: 229 AQEMEKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIVKAVSKYNV 288

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  ++  EPT E
Sbjct: 289 SKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQELGYEPTDE 348

Query: 551 EIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            IA++       E VR + KI  +PISL+  IG E+ S   DF++D++ V+P+D A Q  
Sbjct: 349 MIAERYGNGYDAEKVRYIRKINIDPISLDKQIGKENDSSFSDFVKDESVVNPVDYASQEE 408

Query: 609 LRETTTRVLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEA 661
           L ET   +L  SL   E  ++  RFG+G++ +      H+LE++ ++  V++ERIRQIE 
Sbjct: 409 LVETLNSILEKSLDDDERILICKRFGVGVDENGNKYPIHSLEKLAEERNVSKERIRQIEN 468

Query: 662 KAIRKLKHPSRS-KKLRSFL 680
           K +RKLK  +R  + L+ F+
Sbjct: 469 KILRKLKSSTRKGRHLKDFI 488



 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREG 138
            ++ ED    E   +   + +++ V   K   +    T+D V+ Y+R +G   +LL+ E 
Sbjct: 165 NNEDEDSLELESYENEEINLNDNKVIKDKDLTNKLTETNDIVKWYMRWIGKYGKLLTIEE 224

Query: 139 EIAIAKRIEAGRAMMMAS 156
           E  +A+ +E G      +
Sbjct: 225 EKKLAQEMEKGGFRGKRA 242


>gi|307718699|ref|YP_003874231.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
 gi|306532424|gb|ADN01958.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
          Length = 338

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 100/275 (36%), Positives = 161/275 (58%), Gaps = 3/275 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I +I+  ++ +S    +   +  H     R+ +      K  M+ ANLRLV+S+AKKY 
Sbjct: 66  EIQRIKLRLRELSS---LPEEQRAHHFEEERRLDQRLRELKNRMITANLRLVVSIAKKYQ 122

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +RGL  LDLI EGNIGL++A E+FD+  G +FSTY  WW++QAI +S+AD+S  IRIP+H
Sbjct: 123 HRGLSLLDLIDEGNIGLIEAVERFDYTKGCRFSTYGTWWIRQAIVKSLADKSRVIRIPIH 182

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I  V   ++ ++ ++ R+PT EE+++   +P   V +++++++E  SL+  + +E+
Sbjct: 183 MLNTIKNVFMLSKELAQELGRDPTEEELSRYTGLPDRRVAEIMQVSQETASLDITVDEEN 242

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            + LGD + D     P +      L +     L  L+ RE  V+ +RFG+      TLEE
Sbjct: 243 MTTLGDLVSDDEDQGPFEKVFHRYLHDVLLEALGDLSERERNVISLRFGLNGEGPLTLEE 302

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            GK   +TRER+RQI+ KA+ KL+     K    +
Sbjct: 303 TGKLLGITRERVRQIQEKALAKLREMGFIKDFHHY 337


>gi|167822153|ref|ZP_02453624.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 9]
          Length = 299

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 57  SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 116

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 117 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 176

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 177 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 236

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 237 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 296


>gi|251733363|emb|CAR82431.1| RNA polymerase sigma factor [Agrobacterium rhizogenes]
 gi|251733369|emb|CAR82434.1| RNA polymerase sigma factor [Rhizobium tropici]
 gi|251733371|emb|CAR82435.1| RNA polymerase sigma factor [Rhizobium tropici]
          Length = 202

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 123/195 (63%), Positives = 149/195 (76%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q  + +G        + K LK++LVK V SLSLNQ+RID LVEQLYDI+KR++ NEG LL
Sbjct: 8   QRLSASGTLSSAQERRYKELKDELVKSVKSLSLNQNRIDALVEQLYDINKRLVQNEGRLL 67

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E  +I  IR EI++++
Sbjct: 68  RLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFAKSENTTIRDIRQEIQNLA 127

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 128 TETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 187

Query: 478 NIGLMKAAEKFDWCL 492
           NIGLMKA +KF++  
Sbjct: 188 NIGLMKAVDKFEYRR 202


>gi|261345855|ref|ZP_05973499.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
 gi|282566345|gb|EFB71880.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
          Length = 328

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 108/308 (35%), Positives = 188/308 (61%), Gaps = 8/308 (2%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF--------R 428
            +LD + +  A D  + + ++ V+ + +    +++  + +   T I +SE          
Sbjct: 13  NDLDENAMDDAFDESQFKEEDLVSEQDEETDLLQSTSQRVLDATQIYLSEIGFSPLLTAE 72

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V   R+       +++ M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 73  EEVFYARRALRGDIASRQRMIESNLRLVVKISRRYNNRGLALLDLIEEGNLGLIRAVEKF 132

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR ++ K+  EP+
Sbjct: 133 DPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNIYLRTARELAQKLDHEPS 192

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           PEEIA++L  PVE V ++L++ +   S++TPI  +    L + + D N   P ++    +
Sbjct: 193 PEEIAEQLDKPVEDVSRMLRLNERITSVDTPIAGDSEKSLLEVLSDDNDSGPENTIQDND 252

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + L  L P++  VL  RFG+      TLEEVG++  +TRER+RQI+ + +R+LK
Sbjct: 253 LKENIVKWLYELNPKQREVLARRFGLLGYEAETLEEVGREIGLTRERVRQIQVEGLRRLK 312

Query: 669 HPSRSKKL 676
              + ++L
Sbjct: 313 DILQGEEL 320



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D D+   ++  ++S        +          S  +   D  ++YL E+G   LL+ E 
Sbjct: 14  DLDENAMDDAFDESQFKEEDLVSEQDEETDLLQSTSQRVLDATQIYLSEIGFSPLLTAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVFYARRALRGDIASRQRMIESNLRLVVKISRRYN-NRGLALLDLI 118


>gi|301049496|ref|ZP_07196454.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
 gi|300298727|gb|EFJ55112.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
          Length = 342

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAKEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ + E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAKEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|24114036|ref|NP_708546.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2a str. 301]
 gi|24053158|gb|AAN44253.1| similar to sigmaD(70) factor of RNA polymerase [Shigella flexneri
           2a str. 301]
 gi|281602111|gb|ADA75095.1| RNA polymerase sigma factor [Shigella flexneri 2002017]
          Length = 342

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|251733359|emb|CAR82429.1| RNA polymerase sigma factor [Rhizobium leguminosarum]
          Length = 202

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 122/195 (62%), Positives = 149/195 (76%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q  + +G        + K LK++L+K V SLSLNQ+RID LVEQLYDI+KR++ NEG LL
Sbjct: 8   QRLSASGTLSTAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDINKRLVSNEGRLL 67

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E  +I  IR EI++++
Sbjct: 68  RLAESYGVKRDSFLEQYQGAELDPNWMKSIGNLAARGWKEFARGENTTIRDIRQEIQNLA 127

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETGISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 128 TETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 187

Query: 478 NIGLMKAAEKFDWCL 492
           NIGLMKA +KF++  
Sbjct: 188 NIGLMKAVDKFEYRR 202


>gi|319955411|ref|YP_004166678.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424071|gb|ADV51180.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 286

 Score =  174 bits (440), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 93/272 (34%), Positives = 165/272 (60%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +    + IS    I+ +E   +   +R       +A   +V ANLR V+SVAK+Y   GL
Sbjct: 18  LEKYFQEISKLDMITANEEVELAIKIR---EGDQVALNTLVNANLRFVVSVAKQYQGSGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I ++I++ S  +R+P++   +
Sbjct: 75  RLSDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAISELSRMVRLPLNKIGE 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K+ +    +   ++R P   EIA++L M    V+  +K T + +S++ P  + ++S+L
Sbjct: 135 IGKINKVFSYLEQSLQRPPNAIEIARELDMSTSQVKLAMKNTGKHLSMDAPFAEGESSNL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + ++ K A SP  + +Q +L      +L++L  RE  ++R+ +GIG     +L E+G+ 
Sbjct: 195 YNVVQSKEANSPDTNLMQESLSSDIGDLLSTLPSRESDIIRLYYGIGEKAPMSLTEIGEI 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           F ++RER+RQI  KAIR L+  S+ + L+++L
Sbjct: 255 FDISRERVRQIREKAIRVLRRKSQKEVLKAYL 286



 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y +E+  +++++   E+ +A +I  G  + + +L  + L F  ++    +       L +
Sbjct: 21  YFQEISKLDMITANEEVELAIKIREGDQVALNTLVNANLRF--VVSVAKQYQGSGLRLSD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  +G       F  T G  
Sbjct: 79  LIN-EGNVGLVKAAKRFDETRGFK 101


>gi|330721381|gb|EGG99448.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC2047]
          Length = 321

 Score =  174 bits (440), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 96/277 (34%), Positives = 163/277 (58%), Gaps = 3/277 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
              S+   +  +  I     +S  E  +   +           +K M+E+NLRLV+ +++
Sbjct: 42  SKKSLDATQLYLNEIGFSPLLSAEEEVYYARLA---LKGDEAGRKRMIESNLRLVVKISR 98

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+
Sbjct: 99  RYVNRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRL 158

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P+H+  +++  +R AR ++ K+  EP+ EEIA+ L  PVE V+++LK+ +   S++ P+G
Sbjct: 159 PIHVVKELNVYLRAARELTQKLDHEPSAEEIAEMLDRPVENVKRMLKLNERVTSIDAPMG 218

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            +    + + I  +N   P +     NL    T  L  L+ ++  V+  RFG+      T
Sbjct: 219 GDSERSMAENITGENVDDPSELLQNDNLHGNLTHWLGELSEKQREVIARRFGLLGYEMST 278

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           LE+VG +  +TRER+RQI+ +A+++L+     + L S
Sbjct: 279 LEQVGSEIGLTRERVRQIQVEALKRLRAVMEKEGLSS 315



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 27/106 (25%), Positives = 44/106 (41%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D   ++ ++   D   +           Q ++D + + + D  ++YL E+G   LLS E 
Sbjct: 7   DKAMVDTQDALLDEETVEEKQDQLVSEGQIKEDLSSKKSLDATQLYLNEIGFSPLLSAEE 66

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+    G       + ES L     I  R  +N G TLL  I
Sbjct: 67  EVYYARLALKGDEAGRKRMIESNLRLVVKISRRY-VNRGLTLLDLI 111


>gi|41861|emb|CAA78692.1| KatF [Escherichia coli]
          Length = 342

 Score =  174 bits (440), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 46/117 (39%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V+D   L ++E S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVLDEKALVEQEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|320173409|gb|EFW48608.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae CDC 74-1112]
          Length = 342

 Score =  174 bits (440), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|300718097|ref|YP_003742900.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
 gi|299063933|emb|CAX61053.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
          Length = 330

 Score =  174 bits (440), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 172/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+ EEIA++L  PVE V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELTHKLDHEPSAEEIAEQLDKPVEDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQAQGL 322



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     A N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEVFDEKALVGNEPADNEIAEDELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVFFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|18073320|emb|CAC81021.1| mutant RpoS sigma factor [Escherichia coli]
          Length = 302

 Score =  174 bits (440), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 27  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 83

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 84  RGLALLDLIEEGNQGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 143

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 144 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 203

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 204 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 263

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 264 GREIGLTRERVRQIQVEGLRRLREILQTQGL 294



 Score = 45.2 bits (105), Expect = 0.034,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 1/87 (1%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           ++ N     +     A +   D  ++YL E+G   LL+ E E+  A+R   G       +
Sbjct: 7   NSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRM 66

Query: 158 CESPLTFQALIIWRDELNDGTTLLREI 184
            ES L     I  R   N G  LL  I
Sbjct: 67  IESNLRLVVKIARRYG-NRGLALLDLI 92


>gi|51595126|ref|YP_069317.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           32953]
 gi|153948385|ref|YP_001402250.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|170025640|ref|YP_001722145.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           YPIII]
 gi|186894139|ref|YP_001871251.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588408|emb|CAH20016.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Yersinia pseudotuberculosis IP
           32953]
 gi|152959880|gb|ABS47341.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|169752174|gb|ACA69692.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis YPIII]
 gi|186697165|gb|ACC87794.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis PB1/+]
          Length = 332

 Score =  174 bits (440), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVDDEPTESELADDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|167813607|ref|ZP_02445287.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
          Length = 302

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 97/240 (40%), Positives = 157/240 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF+   G+KFSTYA 
Sbjct: 60  SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYAT 119

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +P E
Sbjct: 120 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKAADRIERRSGVSASLAELSEATGLPAE 179

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+     + +  T +L +++
Sbjct: 180 RLRAVLTLPREPRSLNAPLGDDDQAEFGDIVEDTSTPSLFDALAHGQMCDVVTSLLKTMS 239

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  +  V+RE++R+IE +A++ L+  + +     FLD
Sbjct: 240 AQEADILRRRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLRVTAEACNAHDFLD 299


>gi|167561013|ref|ZP_02353929.1| RNA polymerase sigma factor [Burkholderia oklahomensis EO147]
          Length = 476

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 98/240 (40%), Positives = 161/240 (67%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A  +M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A +KF++  G+KFSTYA 
Sbjct: 234 SAATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFKFSTYAT 293

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +  E
Sbjct: 294 WWIRQAISRAVADRARTIRLPVHVGDQARRVRKIADRIKQRSGMRASLAELSEATELSTE 353

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL++ +EP SL TP+GD+D +  GD +ED +  S  D+   A +R+    +L +++
Sbjct: 354 RLRAVLELPREPRSLNTPLGDDDQAEFGDLVEDASTPSLFDALAGAQMRDVVASLLKTMS 413

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +     FLD
Sbjct: 414 AQEADILRRRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKRALQTLRVTAEACNAHDFLD 473



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/133 (19%), Positives = 53/133 (39%), Gaps = 8/133 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD----- 81
            +    ++++LA         ++      D  SS+ +E  +  L+++  +  D       
Sbjct: 3   YEQGIDRLLELAGAHDDAAYADVRDEF--DGASSDALEHDLGDLNHLDHHATDESGGPAS 60

Query: 82  -DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D +    +    D      + S             + DP+ +++R M ++ LL+   EI
Sbjct: 61  FDDKPARSAHVDADWHDDVDSPSSERSGDAAVDTTISTDPLALFVRRMHAVPLLNHAQEI 120

Query: 141 AIAKRIEAGRAMM 153
           A+A  IEAGR  +
Sbjct: 121 ALASEIEAGRQQV 133


>gi|167568274|ref|ZP_02361148.1| RNA polymerase sigma factor [Burkholderia oklahomensis C6786]
          Length = 483

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 98/240 (40%), Positives = 161/240 (67%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A  +M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A +KF++  G+KFSTYA 
Sbjct: 241 SAATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFKFSTYAT 300

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R++AD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +  E
Sbjct: 301 WWIRQAISRAVADRARTIRLPVHVGDQARRVRKIADRIKQRSGMRASLAELSEATELSTE 360

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL++ +EP SL TP+GD+D +  GD +ED +  S  D+   A +R+    +L +++
Sbjct: 361 RLRAVLELPREPRSLNTPLGDDDQAEFGDLVEDASTPSLFDALAGAQMRDVVASLLKTMS 420

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +     FLD
Sbjct: 421 AQEADILRRRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKRALQTLRVTAEACNAHDFLD 480



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/133 (19%), Positives = 53/133 (39%), Gaps = 8/133 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD----- 81
            +    ++++LA         ++      D  SS+ +E  +  L+++  +  D       
Sbjct: 10  YEQGIDRLLELAGAHDDAAYADVRDEF--DGASSDALEHDLGDLNHLDHHATDESGGPAS 67

Query: 82  -DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            D +    +    D      + S             + DP+ +++R M ++ LL+   EI
Sbjct: 68  FDDKPARSAHVDADWHDDVDSPSSERSGDAAVDTTISTDPLALFVRRMHAVPLLNHAQEI 127

Query: 141 AIAKRIEAGRAMM 153
           A+A  IEAGR  +
Sbjct: 128 ALASEIEAGRQQV 140


>gi|88802114|ref|ZP_01117642.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
 gi|88782772|gb|EAR13949.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
          Length = 287

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 102/285 (35%), Positives = 178/285 (62%), Gaps = 6/285 (2%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K     + +S+ K   EI  I     I+  E   +   ++ G+ +A  A   +V ANLR 
Sbjct: 8   KQVTNRDAESLDKYFQEISKIG---LITADEEVELALKIKVGDSKALDA---LVSANLRF 61

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+SVAK+Y  +GL+  DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+Q
Sbjct: 62  VVSVAKQYQGQGLKLSDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSIMQALAEQ 121

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S  +R+P++    I+K+ +   R+    +R PT +EIAK+L M    V + LK +   +S
Sbjct: 122 SRIVRLPLNKIGSINKIKKIYARLEQNEQRMPTHKEIAKQLDMTEAEVEQSLKNSGRHVS 181

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++ P  + + S+L + ++  ++  P    +  +L+    R L +LT +E +V++M +GIG
Sbjct: 182 MDAPFKEGEDSNLYNVLQSGDSPRPDSQLMAQSLKIEIERALGTLTYKEAKVIKMYYGIG 241

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                +LEE+G++F +TRER+RQ++ KAIR+L+  S+++ LR++L
Sbjct: 242 NEAMASLEEIGEKFDLTRERVRQVKQKAIRRLQSGSKTQMLRTYL 286



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y +E+  I L++ + E+ +A +I+ G +  + +L  + L F  ++    +       L +
Sbjct: 21  YFQEISKIGLITADEEVELALKIKVGDSKALDALVSANLRF--VVSVAKQYQGQGLKLSD 78

Query: 184 IID 186
           +I+
Sbjct: 79  LIN 81


>gi|311742672|ref|ZP_07716481.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
 gi|311314300|gb|EFQ84208.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
          Length = 320

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 90/242 (37%), Positives = 147/242 (60%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     +     E   A +E ++ANLRLV+S+A+KY    +  LDL+QEGN GL++A EK
Sbjct: 71  RATAEELEWIAAEGERALQEFIQANLRLVVSIARKYGRSAMPMLDLVQEGNTGLIRAVEK 130

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WWV+QAITR IA Q+  +R+PVH+ +++++V    R +   +  +P
Sbjct: 131 FDYVKGFKFSTYATWWVRQAITRGIAQQARVVRLPVHVVEELNQVTAARRNLERTLGYDP 190

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P EI+ +L M V+ V  +L   ++ +SL+TP+ ++  + LGD I  + A  P  S +  
Sbjct: 191 EPAEISAELGMDVDRVIDLLSWGRDHVSLDTPVDEDGDTSLGDLIARETAPGPDSSMMSD 250

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    +++  L  RE  ++R R+G+       L ++GK+  ++ ER+RQ+E +A+ KL
Sbjct: 251 ATRGMIAQLIDHLGEREADIVRARYGLLDGRQQKLADIGKRHGISAERVRQLEREALAKL 310

Query: 668 KH 669
           + 
Sbjct: 311 RR 312



 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 16/39 (41%), Positives = 20/39 (51%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           S D    D V MYL E+    LL    E+ ++K IEAG 
Sbjct: 12  SRDGEGRDSVGMYLAEIARTPLLDAGREVELSKTIEAGL 50


>gi|22124745|ref|NP_668168.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM 10]
 gi|45440189|ref|NP_991728.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108808779|ref|YP_652695.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|108810903|ref|YP_646670.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|145600262|ref|YP_001164338.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|153997601|ref|ZP_02022701.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162420853|ref|YP_001605522.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165925871|ref|ZP_02221703.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165936700|ref|ZP_02225267.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166010016|ref|ZP_02230914.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166212931|ref|ZP_02238966.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|167398742|ref|ZP_02304266.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167421704|ref|ZP_02313457.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167423190|ref|ZP_02314943.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|218930373|ref|YP_002348248.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|229838982|ref|ZP_04459141.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229896462|ref|ZP_04511630.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|229899549|ref|ZP_04514690.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229901116|ref|ZP_04516239.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|270489294|ref|ZP_06206368.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294505063|ref|YP_003569125.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957564|gb|AAM84419.1|AE013686_2 RNA polymerase, sigma S (sigma38) factor [Yersinia pestis KIM 10]
 gi|45435045|gb|AAS60605.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108774551|gb|ABG17070.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|108780692|gb|ABG14750.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|115348984|emb|CAL21944.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|145211958|gb|ABP41365.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|149289238|gb|EDM39318.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162353668|gb|ABX87616.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165915349|gb|EDR33959.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165922483|gb|EDR39660.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165990923|gb|EDR43224.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166205718|gb|EDR50198.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|166960623|gb|EDR56644.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167051246|gb|EDR62654.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167057360|gb|EDR67106.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|224483372|gb|ACN50513.1| RpoS [Yersinia pestis]
 gi|229681841|gb|EEO77934.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|229687041|gb|EEO79116.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695348|gb|EEO85395.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229700536|gb|EEO88567.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|262363123|gb|ACY59844.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367053|gb|ACY63610.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337798|gb|EFA48575.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294355522|gb|ADE65863.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320016550|gb|ADW00122.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 332

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVDDEPTESELADDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVSSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|154506043|ref|ZP_02042781.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
 gi|153793542|gb|EDN75962.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
          Length = 297

 Score =  173 bits (439), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 112/237 (47%), Positives = 165/237 (69%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+     + A+++M EANLRLV++VAK Y  +G+QF+DLIQEGNIGLM+A EKFD+  G 
Sbjct: 57  RQIAEGDTEARRKMEEANLRLVVAVAKHYAGKGMQFMDLIQEGNIGLMRAVEKFDYTKGS 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA+WW+K+AI R++  QS  IR+PV +   ++K+ +T R+M   + RE   EEIAK
Sbjct: 117 KFSTYAVWWIKEAILRALDSQSREIRVPVRVAQNMNKISKTERKMEQTLGREVAAEEIAK 176

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L M  E V ++    K P+SLETP+GDE+ S+L DFIED    +P ++      +E   
Sbjct: 177 ELHMTTEEVERMQSYIKNPVSLETPVGDEENSNLEDFIEDTQEPTPEEAVAALVQKEEVQ 236

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +L++LT +E+++LR+R+G+     HTLEE G+   VTRERIRQ+E++A+ KL+  +
Sbjct: 237 EMLSTLTEKEQKILRLRYGLEDGNVHTLEETGQILGVTRERIRQLESRALEKLRKSA 293


>gi|62734062|gb|AAX96171.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|125589330|gb|EAZ29680.1| hypothetical protein OsJ_13741 [Oryza sativa Japonica Group]
          Length = 563

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 94/249 (37%), Positives = 150/249 (60%), Gaps = 1/249 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +RK        K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD  
Sbjct: 311 RTLRKRLDHGIYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDAS 370

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTY+ WW+KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EE
Sbjct: 371 KGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEE 430

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA    MP++ V   + + K  +SL++ IG  D ++  +   D  A +  +   + +++ 
Sbjct: 431 IAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKR 489

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + L +LT RE +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   
Sbjct: 490 DVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKK 549

Query: 672 RSKKLRSFL 680
           R   L+ +L
Sbjct: 550 RVNALKDYL 558


>gi|297170837|gb|ADI21856.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured verrucomicrobium HF0130_25O04]
          Length = 303

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 109/262 (41%), Positives = 173/262 (66%), Gaps = 3/262 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ IS    +++ E   + S ++        A++ M+ ANLRLV+ +AK+Y+N GL  L
Sbjct: 12  YLRQISTVPLLTVEEEIELASRIK---NGDEKARETMITANLRLVVKIAKEYSNIGLSLL 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLMKA E+FD   G K STY  WW+KQAI R++A+QS TIR+PVHM D++ +
Sbjct: 69  DLINEGNIGLMKAVERFDPSKGGKLSTYGAWWIKQAIKRALANQSKTIRLPVHMVDRVTQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + RT+ +++ K+ REPT EE+A ++ +PV  +  +  ++++P SL++P+G+ D S LG+ 
Sbjct: 129 IRRTSVQLAEKLGREPTDEELAAEMNLPVARITLLKSVSRKPASLDSPLGENDGSTLGEM 188

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+ + +P +     +L      VLA L PRE  ++R+RFG+      TLEEVG++  V
Sbjct: 189 VADEKSANPYEHLQSKSLVGDVNSVLAQLEPREADIIRLRFGLEGLEPLTLEEVGEKIGV 248

Query: 652 TRERIRQIEAKAIRKLKHPSRS 673
           TRER+RQ++ +A+R+L+    S
Sbjct: 249 TRERVRQLQEQALRQLRKNMAS 270



 Score = 45.2 bits (105), Expect = 0.033,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +YLR++ ++ LL+ E EI +A RI+ G      ++  + L     I  ++  N G +LL 
Sbjct: 11  IYLRQISTVPLLTVEEEIELASRIKNGDEKARETMITANLRLVVKIA-KEYSNIGLSLLD 69

Query: 183 EI 184
            I
Sbjct: 70  LI 71


>gi|251733361|emb|CAR82430.1| RNA polymerase sigma factor [Agrobacterium tumefaciens]
          Length = 202

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 123/192 (64%), Positives = 148/192 (77%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+  V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  ACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++ G ELDP+W+    +     WK F   E ++I +IR EI+++S ET
Sbjct: 71  ESYGVKRDSFLEQYHGAELDPNWMKSIANLAARGWKEFAREESNTIREIRQEIQNLSTET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|281357254|ref|ZP_06243743.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281316285|gb|EFB00310.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 428

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 109/274 (39%), Positives = 165/274 (60%), Gaps = 5/274 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R   K +     ++  E    +  + +   E    +++M+EANLRLVIS+A+KY NRGL 
Sbjct: 152 RQRRKLLEDRFLMTYEELTGEIRKLLEIHEELQNLRQKMIEANLRLVISIAQKYRNRGLP 211

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           F DLIQEGN+GL++A EKFD+ LG KFSTYA WW+K  I+RSIA+QS  IRIP HM   I
Sbjct: 212 FNDLIQEGNLGLLRALEKFDFRLGNKFSTYASWWIKHNISRSIAEQSRVIRIPAHMVHAI 271

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHL 588
           + +    +R      REP  +E+A  L MPV  +  + K++ + ISL+ P+   ED + L
Sbjct: 272 NSMTWAEQRFIQSHGREPEIDELAAVLEMPVARISAIRKMSCQTISLQAPVSSSEDGAML 331

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I D +  +P+    +  L +    +L +L  R+++++ +RFG+       L ++ ++
Sbjct: 332 EDLIADDSTANPVRDFARKILYDKLYEMLRTLPERDQQIIILRFGLFGQPCLPLVDISRR 391

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           F +TRERIRQ+EAK I  L+ P++ K    +LDG
Sbjct: 392 FNLTRERIRQLEAKIIENLRSPAKLK----YLDG 421


>gi|319777141|ref|YP_004136792.1| putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
 gi|238810060|dbj|BAH69850.1| hypothetical protein [Mycoplasma fermentans PG18]
 gi|318038216|gb|ADV34415.1| Putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
          Length = 489

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 190/320 (59%), Gaps = 15/320 (4%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           LE ++  E++ +     KD             V   ++   +   +     ++I E + +
Sbjct: 174 LESYENEEINLNDNKVIKDKDLTNKLTETNDIVKWYMRWIGKYGKL-----LTIEEEKKL 228

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA  K++ 
Sbjct: 229 AQEMEKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIVKAVSKYNV 288

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  ++  EPT E
Sbjct: 289 SKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQELGYEPTDE 348

Query: 551 EIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            IA++       E VR + KI  +PISL+  IG E+ S   DF++D++ V+P+D A Q  
Sbjct: 349 MIAERYGNGYDAEKVRYIRKINIDPISLDKQIGKENDSSFSDFVKDESVVNPVDYASQEE 408

Query: 609 LRETTTRVLA-SLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEA 661
           L ET   +L  SL   E  ++  RFG+G++ +      H+LE++ ++  V++ERIRQIE 
Sbjct: 409 LVETLNSILEKSLDDDERILICKRFGVGVDENGNKYPIHSLEKLAEERNVSKERIRQIEN 468

Query: 662 KAIRKLKHPSRS-KKLRSFL 680
           K +RKLK  +R  + L+ F+
Sbjct: 469 KILRKLKSSTRKGRHLKDFI 488



 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREG 138
            ++ ED    E   +   + +++ V   K   +    T+D V+ Y+R +G   +LL+ E 
Sbjct: 165 NNEDEDSLELESYENEEINLNDNKVIKDKDLTNKLTETNDIVKWYMRWIGKYGKLLTIEE 224

Query: 139 EIAIAKRIEAGRAMMMAS 156
           E  +A+ +E G      +
Sbjct: 225 EKKLAQEMEKGGFRGKRA 242


>gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor RpoS [Janthinobacterium sp. Marseille]
 gi|151280837|gb|ABR89247.1| RNA polymerase nonessential primary-like sigma factor
           [Janthinobacterium sp. Marseille]
          Length = 345

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 89/263 (33%), Positives = 156/263 (59%), Gaps = 5/263 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ +  I     +++ E  H  ++ ++G      A+++M+E NLRLV+S+AK Y NRG+ 
Sbjct: 74  QHYLNQIGTRPLLTVPEEVHFATLAKQGNF---AARQKMIEHNLRLVVSIAKHYINRGVI 130

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++
Sbjct: 131 LLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVVREL 190

Query: 530 HKVVRTARRMSNKI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++ +R    +  +    ++ T E+IA  +   VE V+ +L +++   SL+ P+  +  S 
Sbjct: 191 NQTLRAKFHLEAQHHDGKDATAEDIAHLVDRSVEDVQDILALSEHATSLDAPLDGDPQSS 250

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++  +A  P   A    +       L  L  ++  V+  RFG+  +   TLE +  
Sbjct: 251 LMDLLQGDHANDPDALAEHNEMTVLVHDWLEKLPDKQRLVITRRFGLDNDDPATLEALAA 310

Query: 648 QFCVTRERIRQIEAKAIRKLKHP 670
           +  VTRER+RQI+ +A+ KLK  
Sbjct: 311 EMHVTRERVRQIQQEALVKLKRS 333



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 47/126 (37%), Gaps = 1/126 (0%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
             E  +   + LS    +  +  D+ D++G    L    +    +   + +K  A   + 
Sbjct: 11  DDENSDALSSELSLQADDDAEKSDITDDDGDAVELAERVAPVEVAGIDELKKVLATELST 70

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  + YL ++G+  LL+   E+  A   + G       + E  L     I     +N G 
Sbjct: 71  DATQHYLNQIGTRPLLTVPEEVHFATLAKQGNFAARQKMIEHNLRLVVSIAKHY-INRGV 129

Query: 179 TLLREI 184
            LL  I
Sbjct: 130 ILLDLI 135


>gi|91212108|ref|YP_542094.1| RNA polymerase sigma factor RpoS [Escherichia coli UTI89]
 gi|117624976|ref|YP_853964.1| RNA polymerase sigma factor RpoS [Escherichia coli APEC O1]
 gi|227888284|ref|ZP_04006089.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|237706630|ref|ZP_04537111.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|254037782|ref|ZP_04871840.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|300815849|ref|ZP_07096073.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300820522|ref|ZP_07100673.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300906754|ref|ZP_07124436.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300919222|ref|ZP_07135745.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300922264|ref|ZP_07138390.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300930600|ref|ZP_07145992.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300941124|ref|ZP_07155636.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300946980|ref|ZP_07161206.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300954984|ref|ZP_07167395.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300976231|ref|ZP_07173328.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300976795|ref|ZP_07173612.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|301027157|ref|ZP_07190526.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|301306156|ref|ZP_07212232.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|301326219|ref|ZP_07219602.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301645276|ref|ZP_07245227.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|309795208|ref|ZP_07689627.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|331643427|ref|ZP_08344558.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331648464|ref|ZP_08349552.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331654219|ref|ZP_08355219.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331674247|ref|ZP_08375007.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331678721|ref|ZP_08379395.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332280596|ref|ZP_08393009.1| sigma factor RpoS [Shigella sp. D9]
 gi|11036547|gb|AAG27177.1|AF270497_2 RpoS [Escherichia coli]
 gi|91073682|gb|ABE08563.1| sigma factor RpoS [Escherichia coli UTI89]
 gi|115514100|gb|ABJ02175.1| sigma factor RpoS [Escherichia coli APEC O1]
 gi|120538764|emb|CAM07120.1| sigma factor S [Escherichia coli]
 gi|226839406|gb|EEH71427.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|226899670|gb|EEH85929.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|227834553|gb|EEJ45019.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|300308576|gb|EFJ63096.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300318076|gb|EFJ67860.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300395189|gb|EFJ78727.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|300401448|gb|EFJ84986.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300409981|gb|EFJ93519.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|300413667|gb|EFJ96977.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300421394|gb|EFK04705.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300453367|gb|EFK16987.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300454167|gb|EFK17660.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300461542|gb|EFK25035.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300526786|gb|EFK47855.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300531778|gb|EFK52840.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300838588|gb|EFK66348.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|300847064|gb|EFK74824.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301076441|gb|EFK91247.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|308121179|gb|EFO58441.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|315254525|gb|EFU34493.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 85-1]
 gi|315289257|gb|EFU48652.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 110-3]
 gi|315293697|gb|EFU53049.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 153-1]
 gi|315298766|gb|EFU58020.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 16-3]
 gi|323377395|gb|ADX49663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           KO11]
 gi|324005707|gb|EGB74926.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 57-2]
 gi|324015519|gb|EGB84738.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 60-1]
 gi|324017012|gb|EGB86231.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 117-3]
 gi|331036898|gb|EGI09122.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331042211|gb|EGI14353.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331047601|gb|EGI19678.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331068341|gb|EGI39736.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331073551|gb|EGI44872.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332102948|gb|EGJ06294.1| sigma factor RpoS [Shigella sp. D9]
          Length = 342

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 124 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 183

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 184 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 243

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 244 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 303

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 304 GREIGLTRERVRQIQVEGLRRLREILQTQGL 334



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|118581147|ref|YP_902397.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118503857|gb|ABL00340.1| RNA polymerase, sigma 70 subunit, RpoD family [Pelobacter
           propionicus DSM 2379]
          Length = 323

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 110/279 (39%), Positives = 172/279 (61%), Gaps = 5/279 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           D  E E    V    D  +KI   ++ I     ++  + + +   + K       A+ +M
Sbjct: 43  DHAEAELPPAVLETFDDAIKI--YLRDIQRTPLLTAEQEKEVARQIEK---GDMAARNKM 97

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F+     +FSTYA WW++QAI
Sbjct: 98  IESNLRLVVKIAKRYINRGLPFLDLIEEGNLGLIKAVERFNLAKECRFSTYATWWIRQAI 157

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R++ +QS TIR+PVH+ D I+++ +  RR+S  ++REP   EIA+++ + +  VR+++ 
Sbjct: 158 DRALVNQSRTIRLPVHVSDDINRMAKVTRRLSQTLQREPHAHEIAEEMNVKLAYVRRLMT 217

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S+ETPIGD     L D IED + V+P D     +  E  +     L+  E+++L
Sbjct: 218 LLRRTCSMETPIGDGSDYFLIDTIEDTSMVAPSDLLENIDRYEQISEHFKELSESEQKIL 277

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +RFG+      TL+ +G+ F VTRERIRQIEAK++ KL
Sbjct: 278 ALRFGLDDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKL 316



 Score = 56.4 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 42/105 (40%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +L   +  E S        +      +   +   + DD +++YLR++    LL+ E E
Sbjct: 20  ASELVANDTEEPSTFSEEEEGSDDHAEAELPPAVLETFDDAIKIYLRDIQRTPLLTAEQE 79

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             +A++IE G       + ES L     I  R  +N G   L  I
Sbjct: 80  KEVARQIEKGDMAARNKMIESNLRLVVKIAKRY-INRGLPFLDLI 123


>gi|29143180|ref|NP_806522.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|695759|emb|CAA57298.1| sigma S [Salmonella enterica subsp. enterica serovar Typhi]
 gi|3820469|emb|CAA76807.1| RNA polymerase sigma subunit [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|29138813|gb|AAO70382.1| RNA polymerase sigma subunit RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 384

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 95/260 (36%), Positives = 164/260 (63%), Gaps = 3/260 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIR 665
           G++  +TRER+RQI+ + +R
Sbjct: 292 GREIGLTRERVRQIQVEGLR 311



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|1350861|sp|P47765|RPOS_YEREN RecName: Full=RNA polymerase sigma factor rpoS
 gi|687583|gb|AAC43391.1| RpoS [Yersinia enterocolitica]
          Length = 331

 Score =  173 bits (439), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 98/267 (36%), Positives = 172/267 (64%), Gaps = 3/267 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+NRGL 
Sbjct: 60  QLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSNRGLA 116

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  ++
Sbjct: 117 LLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKEL 176

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L 
Sbjct: 177 NVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALL 236

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++ 
Sbjct: 237 DILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREI 296

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +TRER+RQI+ + +R+L+   +++ L
Sbjct: 297 GLTRERVRQIQVEGLRRLREILQAQGL 323



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 41/105 (39%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            ++  + E  ++   +    + S +   +       S  D  ++YL E+G   LL+ E E
Sbjct: 18  DENSTETEIFDEKALVEDEPTESELAEDELLAQGVTSGADATQLYLGEIGYSPLLTAEEE 77

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 78  VYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 121


>gi|239930706|ref|ZP_04687659.1| RNA polymerase principal sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291439071|ref|ZP_06578461.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341966|gb|EFE68922.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 332

 Score =  173 bits (439), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 117/302 (38%), Positives = 170/302 (56%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +  H G   D   V    D          A EV+    I   + +  +  G   S+    
Sbjct: 23  VRAHSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAGVFARQILDGYEESKVGAT 82

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              ++    +A  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+
Sbjct: 83  TEELQALVDDAERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDY 142

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P 
Sbjct: 143 RKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPA 202

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A +L    E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     
Sbjct: 203 EVAAELGSTPERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRS 262

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E    ++  L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  
Sbjct: 263 EELDDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKL 322

Query: 671 SR 672
           +R
Sbjct: 323 AR 324



 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++          R  S + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SAAGETVDSASSVRAHSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAG 64


>gi|56475838|ref|YP_157427.1| RNA polymerase sigma factor RpoS [Aromatoleum aromaticum EbN1]
 gi|56311881|emb|CAI06526.1| RNA sigma factor RpoS [Aromatoleum aromaticum EbN1]
          Length = 311

 Score =  173 bits (439), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 89/242 (36%), Positives = 148/242 (61%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+       A++ M+E NLRLV+++AK Y NRG+  LDL++EGN+GLM A EKFD   G+
Sbjct: 64  RRVRTGDFPARQIMIERNLRLVVNIAKHYLNRGIPLLDLVEEGNLGLMHALEKFDPERGF 123

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q I R+I +QS TIR+PVH+  ++++V+R  R +      E T E++A 
Sbjct: 124 RFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKELNQVLRAQRTLEASGNGEFTLEQVAH 183

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L   V+ VR +L +++   SL+ P+  + T  +G+ + D  A  P      A + +   
Sbjct: 184 RLDKSVDEVRAILALSEHTASLDAPLEIDPTLSIGESLADDQAEPPDTHIQDAEVEKLIQ 243

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             +  L  ++  V+R R+G+      TLEE+  + C+TRER+RQI+ +A+ +L+   + +
Sbjct: 244 EWIGMLNEKQRLVIRHRYGLDECEVMTLEELASRLCLTRERVRQIQLEALGQLRRTVKRR 303

Query: 675 KL 676
            +
Sbjct: 304 GI 305


>gi|32351878|dbj|BAC78528.1| plastid sigma factor 2A [Oryza sativa Japonica Group]
          Length = 564

 Score =  173 bits (439), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 94/249 (37%), Positives = 150/249 (60%), Gaps = 1/249 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +RK        K  MV +N+RLVIS+A+++   G++  DLIQEG  GL++ AEKFD  
Sbjct: 311 RTLRKRLDHGIYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEKFDAS 370

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTY+ WW+KQA+ +S+++QS   R+P HM +  ++V    +R+  K+KR PT EE
Sbjct: 371 KGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASYRVKECIKRLRRKLKRRPTNEE 430

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA    MP++ V   + + K  +SL++ IG  D ++  +   D  A +  +   + +++ 
Sbjct: 431 IAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTDMTY-QEVTADPTAETAEEMLNRLSMKR 489

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + L +LT RE +V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   
Sbjct: 490 DVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIRQIESAAFRKLRSKK 549

Query: 672 RSKKLRSFL 680
           R   L+ +L
Sbjct: 550 RVNALKDYL 558


>gi|238791265|ref|ZP_04634904.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
 gi|238729398|gb|EEQ20913.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
          Length = 332

 Score =  173 bits (438), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPTESELADDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|302519838|ref|ZP_07272180.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302428733|gb|EFL00549.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 341

 Score =  173 bits (438), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 148/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             +  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 100 EASERAKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 159

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 160 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGS 219

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 220 TPERVSDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAVSPEQSVMTLLRSEELDELIG 279

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 280 RLDERTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKLAH 333



 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 26/54 (48%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           AS +  +      R  S + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 20  ASGSGETRGSRGARSMSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAG 73


>gi|254449272|ref|ZP_05062719.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
 gi|198261127|gb|EDY85425.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
          Length = 308

 Score =  173 bits (438), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 103/298 (34%), Positives = 170/298 (57%), Gaps = 5/298 (1%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDS--ILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            D    +      E + ++F A E+ S  +   R  +K I     ++  +  H   +V+ 
Sbjct: 5   TDEVEATREAGTAEEKEEHFTAAELSSSQLDATRLYLKEIEFSPLLTAEQEIHYGRLVQ- 63

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A+++M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++F
Sbjct: 64  --EGDEAARRKMIESNLRLVVKISRRYMNRGLPLLDLIEEGNLGLIRAVEKFDPEKGFRF 121

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW++Q I R + +Q+ TIR+P+H+  +++  +R AR M  +  REPTPEE+AK L
Sbjct: 122 STYATWWIRQTIERGLMNQTRTIRLPIHVIKELNVYLRAARAMQQEFAREPTPEEVAKHL 181

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             PV+ V ++  + +   S++ PIG E  S L D I D +   P        +       
Sbjct: 182 DKPVDDVCRMYGLNERVASVDVPIGKEGDSLLLDLIADDSVPDPTALLQSEEVAAYVDHW 241

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  L  +++ V+  RFG+      TLE +G +  VTRER+RQI+ ++++KL+    ++
Sbjct: 242 LEELDAKQKAVVERRFGLHGQDYATLEVIGHELGVTRERVRQIQMESLKKLRKILEAE 299



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 37/99 (37%), Gaps = 1/99 (1%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E +++      + +               S  D  R+YL+E+    LL+ E EI   + 
Sbjct: 2   AENTDEVEATREAGTAEEKEEHFTAAELSSSQLDATRLYLKEIEFSPLLTAEQEIHYGRL 61

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           ++ G       + ES L     I  R  +N G  LL  I
Sbjct: 62  VQEGDEAARRKMIESNLRLVVKISRRY-MNRGLPLLDLI 99


>gi|973980|gb|AAB05357.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 609

 Score =  173 bits (438), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 103/288 (35%), Positives = 157/288 (54%), Gaps = 38/288 (13%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + +    A  A++ +V ANLRLV+SVAK++TNRGL   DLIQEG+IGL+K AE+FD+
Sbjct: 320 AEELTRNLLRAQRARESLVAANLRLVVSVAKQFTNRGLSMQDLIQEGSIGLIKGAERFDY 379

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYAMWW++QA+ R+IAD S  IRIP  + D   ++ R    +S+ + R+PT  
Sbjct: 380 RTGFRFSTYAMWWIRQAMQRAIADTSRPIRIPSTITDLSVQIYRARLELSSTLGRDPTDA 439

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDE------------------------- 583
           E+A  L + V+ ++ V   T +   +SL+ P+  +                         
Sbjct: 440 ELADFLDISVQRLQDVKLYTNQSATVSLDAPVSRQVTNTCIKSKGTGDTDVFSSKADGKL 499

Query: 584 -----------DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
                          LGD ++   +VSP      + +R+     L+ L P E  V+RMRF
Sbjct: 500 SKNGYGSRHKLGDFTLGDTVQTDESVSPEHMMADSLMRDDIECALSLLNPYEREVIRMRF 559

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+      +++EV   +CV   RIR+IEA+A+RKL+HPS    LR ++
Sbjct: 560 GLDDGRMKSVDEVCAYYCVQTSRIRRIEARALRKLRHPSVWHMLRDYI 607


>gi|206602787|gb|EDZ39268.1| RNA polymerase, RpoD-like sigma subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 499

 Score =  173 bits (438), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 102/270 (37%), Positives = 158/270 (58%), Gaps = 7/270 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E D +  + + +K +     ++  E + +   VR        A++ M+++NLRLV+S+AK
Sbjct: 42  EDDHLSALGSYLKKLQKSHLLTFEEEQDLAKRVR---AGDESARQAMIQSNLRLVVSIAK 98

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y  RGL   DLI+EGN+GLMKA  KFD   G++FSTYA WW++QAI R I +Q   IR+
Sbjct: 99  RYIGRGLLLEDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIRL 158

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM +K++  +    R      ++P  E +A+K  + V  ++++  + K  +SL+TPIG
Sbjct: 159 PVHMMEKVNAYLNAIERQVAD-GQQPDIENLARKNGLKVRDLQEIQALLKNTVSLDTPIG 217

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI---GMNT 638
           D + S L D + D  + SP+ +       +     LA L  +E RV+ +RFG+   G   
Sbjct: 218 DREDSTLKDILVDPTSFSPISTIESREEGDRLRESLALLKDKERRVIHLRFGLPGEGPEE 277

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TLE +G+   VTRER+RQIEA A+ KL+
Sbjct: 278 GMTLEAIGQMLGVTRERVRQIEASAMAKLR 307



 Score = 43.7 bits (101), Expect = 0.099,   Method: Composition-based stats.
 Identities = 34/132 (25%), Positives = 56/132 (42%), Gaps = 5/132 (3%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I   D      +E +EDS    S A  +S  L++     D  +   +  YL+++    LL
Sbjct: 5   IPENDSPWFSPDEQTEDSGKSLSRAGEASESLERGDLEDDHLSA--LGSYLKKLQKSHLL 62

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E E  +AKR+ AG      ++ +S L     I  R  +  G  LL ++I+ E  +G  
Sbjct: 63  TFEEEQDLAKRVRAGDESARQAMIQSNLRLVVSIAKRY-IGRG-LLLEDLIE-EGNLGLM 119

Query: 195 SKGGFFHGTEGH 206
                F   +G 
Sbjct: 120 KAVSKFDPDKGF 131


>gi|17158751|ref|NP_478262.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|464687|sp|Q03065|RPSB_ANASP RecName: Full=RNA polymerase sigma-B factor
 gi|424021|pir||B47017 probable transcription initiation factor sigma SigB - Anabaena sp
 gi|142112|gb|AAA22046.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134700|dbj|BAB77258.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
          Length = 332

 Score =  173 bits (438), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 104/245 (42%), Positives = 161/245 (65%), Gaps = 3/245 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +   +  IAK++M++ANLRLV+S+AKKY  R L+FLDLIQEG +GL +  EKFD  LGYK
Sbjct: 89  QQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYK 148

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q ITR+IA QS TIR+P+HM DK++K+    R +S K+       EIA+ 
Sbjct: 149 FSTYAYWWIRQGITRAIAQQSRTIRLPIHMADKLNKIKCVQRELSQKLGYIAGVTEIAQA 208

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +    +R+ L++ ++P+SL+  IG E  + L D ++D + +SP   A +  L +    
Sbjct: 209 LNLEPSQIREYLQLVRQPVSLDMRIGFEQDTQLQDLLKD-DGMSPERYAERELLYQDIHN 267

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +LA LTP+++ VL +RFG+    + TL ++ ++  ++RER+RQ+E +A+  L+       
Sbjct: 268 LLAKLTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERVRQVEKQALTLLRRYGIDS- 326

Query: 676 LRSFL 680
            RS+L
Sbjct: 327 -RSYL 330



 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S S V   K K++    T D V +YL ++G + LLS E EI  A++++ 
Sbjct: 4   STSQVTKLKSKNNEFSYTADAVSIYLHKIGRVPLLSHEQEIFFAQQVQQ 52


>gi|82701632|ref|YP_411198.1| RNA polymerase sigma factor RpoS [Nitrosospira multiformis ATCC
           25196]
 gi|82409697|gb|ABB73806.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosospira multiformis
           ATCC 25196]
          Length = 317

 Score =  173 bits (438), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 86/265 (32%), Positives = 151/265 (56%), Gaps = 3/265 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
               I     ++  E   +   VR+       A+++M+E NLRLV+++AK YTN G+  L
Sbjct: 50  YFNEIGHNALLTPKEEAELTRRVRQ---NDFAARQKMIECNLRLVVNIAKHYTNHGVALL 106

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+G+M A +KFD   G++FSTYA WW++Q I R I +QS TIR+PVH+   ++ 
Sbjct: 107 DLIEEGNMGMMHALDKFDPERGFRFSTYATWWIRQNIERCIMNQSRTIRLPVHVIKDLNI 166

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +++ AR +     ++P  E++A  L   V+ V+++L + +  +SL+ P+  +    +GD 
Sbjct: 167 ILQAARHLEAHTGKDPKAEDVAHLLGRTVKEVQRMLSLNQSMMSLDAPLDVDPLLSIGDA 226

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D  +  P     Q+ ++      L  L  ++  ++  R+G+      TLE++     +
Sbjct: 227 IADDQSPGPDLMWEQSEIKGRVQDWLNRLNDKQRYIIEQRYGLNGYETQTLEQLAASLDL 286

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQI+ +A++ L+   R + +
Sbjct: 287 TRERVRQIQLEALQTLRMILRCEGV 311



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 2/106 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  D E+    EDSL+    A+++         S D    D  ++Y  E+G   LL+ + 
Sbjct: 6   EYTDEEELFEKEDSLEQDDEAADTPSSAIT-DTSNDFLLTDVTQIYFNEIGHNALLTPKE 64

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E  + +R+          + E  L     I      N G  LL  I
Sbjct: 65  EAELTRRVRQNDFAARQKMIECNLRLVVNIAKHY-TNHGVALLDLI 109


>gi|292491540|ref|YP_003526979.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580135|gb|ADE14592.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 311

 Score =  173 bits (438), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 99/268 (36%), Positives = 156/268 (58%), Gaps = 6/268 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++       +S  E +H   + ++       A+  M+E+NLR+VI +A ++ NRGL  +
Sbjct: 42  YMRDAGKAPLLSAEEEKHYARLAQQ---GDRKARDRMIESNLRMVIKMATRHVNRGLPLM 98

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL+ A EKFD  LG++FSTYA WW++QAI R++ +Q  T+RIPVH+   I +
Sbjct: 99  DLIEEGNLGLIHAVEKFDPELGFRFSTYASWWIEQAIERALMNQVRTVRIPVHVLKTIRR 158

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R A+R+      EP  EEIAK L  P+E +++ L       SL  P+ +++   L D 
Sbjct: 159 YQREAKRLGQTHNTEPRLEEIAKALNEPLEKIQRYLSFQIPETSLNDPLSEDNEDCLADL 218

Query: 592 IEDK-NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           + D+ N  + L      N+  T    L+ LT R++ VL+ R+G+      TLEEVG+   
Sbjct: 219 LPDERNNPAILWEIFDKNI--TINHQLSQLTDRQQEVLKRRYGLDGYEATTLEEVGQTIG 276

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +TRER+RQI+  AI++L+    S+  + 
Sbjct: 277 ITRERVRQIQQTAIKRLRAIVESESSKE 304



 Score = 44.8 bits (104), Expect = 0.051,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 9/87 (10%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +Y+R+ G   LLS E E   A+  + G       + ES L    +I       +    L 
Sbjct: 41  LYMRDAGKAPLLSAEEEKHYARLAQQGDRKARDRMIESNLRM--VIKMATRHVNRGLPLM 98

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQ 209
           ++I+       E   G  H  E    +
Sbjct: 99  DLIE-------EGNLGLIHAVEKFDPE 118


>gi|281420133|ref|ZP_06251132.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405933|gb|EFB36613.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 290

 Score =  173 bits (438), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 157/275 (57%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     +SI E   +   +RKG      AK +++EANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPMVSIDEEIELAQAIRKGGRAGERAKNKLIEANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAE+FD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAERFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++KV +   +   + +R P+ EE+A +  +  + + + +  +   +S++ P  D+D +
Sbjct: 136 GSLNKVNQEINKFEQENQRRPSVEELAARTGVDEDKISQSMAASGHHVSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +   +VL   L  RE +++   +GIG  T+  LEE+
Sbjct: 196 SMADVMASGDDARTDKQVDHESMAQDLRQVLKVCLKDRELKIICACYGIG-ETEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  K+I KL+   +   L  +L
Sbjct: 255 GDKMGLTRERVRQIREKSITKLRESGKIGILMKYL 289



 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   ++S + EI +A+ I  G          L E+ L F  ++    +       
Sbjct: 21  YLVEIGRAPMVSIDEEIELAQAIRKGGRAGERAKNKLIEANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLIKAAERFDETRGFK 104


>gi|251733349|emb|CAR82424.1| RNA polymerase sigma factor [Sinorhizobium americanum]
 gi|251733415|emb|CAR82457.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733417|emb|CAR82458.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733419|emb|CAR82459.1| RNA polymerase sigma factor [Sinorhizobium terangae]
          Length = 202

 Score =  173 bits (438), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 123/192 (64%), Positives = 147/192 (76%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYSGAELDPNWMKSISNLAGKGWKEFAKAENQTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|262197834|ref|YP_003269043.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081181|gb|ACY17150.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 436

 Score =  173 bits (438), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 93/250 (37%), Positives = 145/250 (58%), Gaps = 3/250 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   +  V+      +  + E V ANLRLV+++A++Y   G+   DLIQEGN+GLM A  
Sbjct: 185 FGEYLRAVKSSFARGARLRNEFVHANLRLVVTMARRYDRGGMPLADLIQEGNLGLMHAVS 244

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD+  G +FSTYA WW++ AI R++AD+S  +RIPVHM +   ++ +   ++  ++ RE
Sbjct: 245 RFDYRRGLRFSTYACWWIRHAIGRALADKSRAVRIPVHMLEAQQQLAKVQAKLIGELGRE 304

Query: 547 PTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHLGDFIEDK--NAVSPLDS 603
           PTP E+AK   +P+  + +    +  +P+SL+ P+ D+D    GD + D      SP+D 
Sbjct: 305 PTPSELAKAAQVPLAKLNQMHRYLMGQPMSLDRPLYDDDDRAFGDMLADPLSEDSSPVDD 364

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L      +L  LTP E  VLR RFG+  + + T  E+G Q+ ++RERIRQI+  A
Sbjct: 365 LTTQTLTSRVETLLDHLTPIEADVLRQRFGLMDDEERTFREIGDQYDLSRERIRQIQNAA 424

Query: 664 IRKLKHPSRS 673
           + KL+     
Sbjct: 425 LGKLRRALER 434


>gi|251733379|emb|CAR82439.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733381|emb|CAR82440.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733383|emb|CAR82441.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733385|emb|CAR82442.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733421|emb|CAR82460.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
 gi|251733423|emb|CAR82461.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
          Length = 202

 Score =  173 bits (438), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 123/192 (64%), Positives = 147/192 (76%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|170077819|ref|YP_001734457.1| sigma-70 factor [Synechococcus sp. PCC 7002]
 gi|169885488|gb|ACA99201.1| sigma-70 factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score =  173 bits (438), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 101/286 (35%), Positives = 182/286 (63%), Gaps = 9/286 (3%)

Query: 401 CEVDSILKIRNEIKSISV--ETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLR 454
            +V  ++ ++ + +++    +   +  E+     +    +++       AK++M+EANLR
Sbjct: 43  KQVQRLMALQEKRQTLEESLDREATREEWAEAAQLTPKQLQRDLQIGERAKRKMIEANLR 102

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+++AKKY  R L+FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA 
Sbjct: 103 LVVAIAKKYQKRNLEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQ 162

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q  TIR+P+H+ +K++K+ +T R+++  + R  T  EIA+ L +    +R+  ++++ PI
Sbjct: 163 QGRTIRLPIHITEKLNKIKKTQRQLAQDLGRAATIAEIAEALELEPAQIREYFRVSRHPI 222

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL+  +GD   + L D +ED +  SP ++     L++    ++A LTP+++ V+ +RFG+
Sbjct: 223 SLDVRVGDNQDTELMDLLED-SGESPDNNVTYELLKQDLRDLIADLTPQQQEVIILRFGL 281

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               + +L ++GK+  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 282 NDGKELSLAKIGKRMNLSRERVRQLERQALNHLRR--RRSQIREYL 325



 Score = 41.7 bits (96), Expect = 0.36,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCES 160
           ++  +  +S+ D VR YLRE+G + LL+ E EI   K+++          +L ES
Sbjct: 7   QQAPNNGKSSADMVRTYLREIGRVPLLTHEEEIVYGKQVQRLMALQEKRQTLEES 61


>gi|123441128|ref|YP_001005116.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332160357|ref|YP_004296934.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122088089|emb|CAL10877.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318604409|emb|CBY25907.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664587|gb|ADZ41231.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859888|emb|CBX70219.1| RNA polymerase sigma factor rpoS [Yersinia enterocolitica W22703]
          Length = 332

 Score =  173 bits (438), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQAQGL 324



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|269114989|ref|YP_003302752.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis]
 gi|268322614|emb|CAX37349.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis ATCC 23114]
          Length = 538

 Score =  173 bits (438), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 108/275 (39%), Positives = 171/275 (62%), Gaps = 14/275 (5%)

Query: 422 ISISEFRHIVSMVRK-----GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           ++ +E + +   +++        +   A+  +V+ NLRLVI+ AK+Y NRGL F+DLI E
Sbjct: 258 LTTNEEQALAKKMQEAKEANNYYKYKKARDMLVKRNLRLVINNAKRYKNRGLNFIDLISE 317

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN G+MKA  K+D+  G+KFSTYA WW++QAITR++ADQ+ T+R+PVHM + I+K+++  
Sbjct: 318 GNAGIMKAVSKYDYTKGFKFSTYATWWIRQAITRAVADQARTVRVPVHMVETINKILKIE 377

Query: 537 RRMSNKIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           R +  +    PT EEIAKK       E VR + KI  +PISL+  IG E+ S   DF++D
Sbjct: 378 RELQQENGYPPTDEEIAKKYGGDFTAEKVRYIRKINIDPISLDKNIGKEENSSFSDFVKD 437

Query: 595 KNAVSPLDSAIQANLRETTTRVLAS-LTPR-EERVLRMRFGIGM-----NTDHTLEEVGK 647
           ++ +SP   A    L      ++   L+ + +  ++R RFGI          HTL+E+ K
Sbjct: 438 ESVISPTSYASHEELSVIINEMIEEGLSDQADRDLIRKRFGINDLKGNKYKPHTLDELSK 497

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +  +++E++RQ+E K +RKLKHP + +KL+ F + 
Sbjct: 498 ELGISKEKVRQLETKVLRKLKHPQKRRKLKEFFNS 532


>gi|107103136|ref|ZP_01367054.1| hypothetical protein PaerPA_01004205 [Pseudomonas aeruginosa PACS2]
          Length = 236

 Score =  173 bits (438), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 93/231 (40%), Positives = 151/231 (65%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +R AR +++K+  EP+PEEIA  L  PV  V+++L
Sbjct: 61  IERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + +   S++  +G +    L D + D     P +     +L E+  + L  LT ++  V
Sbjct: 121 GLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +  RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 181 VIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 231


>gi|302560146|ref|ZP_07312488.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302477764|gb|EFL40857.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 332

 Score =  173 bits (438), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 106/241 (43%), Positives = 152/241 (63%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++     +  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+ 
Sbjct: 84  EELQALYDASERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYR 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P E
Sbjct: 144 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAE 203

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L    E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E
Sbjct: 204 VAAELGSTPERVVDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSE 263

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++  L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +
Sbjct: 264 ELDDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLA 323

Query: 672 R 672
           R
Sbjct: 324 R 324



 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++   +      R    + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SATGETADSARSVRAHGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAG 64


>gi|238761664|ref|ZP_04622639.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
 gi|238700178|gb|EEP92920.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
          Length = 332

 Score =  173 bits (438), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQAQGL 324



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVSSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|162448460|ref|YP_001610827.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159042|emb|CAN90347.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 446

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 110/247 (44%), Positives = 168/247 (68%), Gaps = 1/247 (0%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +G    + AK E+V+ANLRL +++A+++   G+  LDL+QEGN+GL++AA+KF++  G++
Sbjct: 201 RGRRAVAQAKSELVQANLRLAVAIAREHQRFGVPLLDLVQEGNLGLIRAADKFEYRRGHR 260

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F TYA WW+KQAI R+I +Q   +R+PVH+     +VVR  R +  +  REP+ EEIA++
Sbjct: 261 FGTYAAWWIKQAIKRTILNQGKPVRMPVHLTAIRSQVVRARRDLVQERGREPSVEEIAER 320

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             + VE VR + ++  EP+SL+ P+G+E  +  GD + + +  +P D   +  L E T  
Sbjct: 321 SGLTVEKVRVISELALEPLSLDAPVGEEGDTRYGDLLAN-DEPTPADMLARRRLIEQTRE 379

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L SL PRE  +LR RFG+  N D TLEE+G+ F +TRERIRQIEAK + KL+  SR ++
Sbjct: 380 LLDSLQPRERELLRRRFGLDGNEDETLEEIGQSFSLTRERIRQIEAKLLEKLRTRSRQRE 439

Query: 676 LRSFLDG 682
           L S+L+G
Sbjct: 440 LGSYLEG 446



 Score = 44.8 bits (104), Expect = 0.050,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 39/82 (47%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +Y R +   + L+REGE+AI +RIEAG      +   SP+  + L    +++  G   LR
Sbjct: 50  LYFRALAGSQPLTREGEVAIGRRIEAGALACFEAWVRSPVALRELASTAEDVQVGALSLR 109

Query: 183 EIIDLEACIGPESKGGFFHGTE 204
           +++       PE+        E
Sbjct: 110 DLLCEADAGDPEADASAKRLAE 131


>gi|238786006|ref|ZP_04629967.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
 gi|238713067|gb|EEQ05118.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
          Length = 332

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 38/107 (35%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +        +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKASVEDEPTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|295838256|ref|ZP_06825189.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|197698235|gb|EDY45168.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 341

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 148/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             +  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 100 EASERAKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 159

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 160 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGS 219

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 220 TPERVSDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAVSPEQSVMTLLRSEELDELIG 279

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 280 RLDERTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKLAH 333



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 37/89 (41%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           AS +  +      R  S + +  D V MYL E+    LL    E+ +++ IEAG      
Sbjct: 20  ASGSGETRGSRGARSMSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVFARQI 79

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
              E+    +A     + L + +   +++
Sbjct: 80  LDGETDSKNEASREELEALWEASERAKDV 108


>gi|83746507|ref|ZP_00943558.1| RNA polymerase sigma factor rpoD [Ralstonia solanacearum UW551]
 gi|83726838|gb|EAP73965.1| RNA polymerase sigma factor rpoD [Ralstonia solanacearum UW551]
          Length = 504

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 110/229 (48%), Gaps = 3/229 (1%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
           +  +        +      K +IKL + RGY+T  E+N  LP D V +E M+  VA L++
Sbjct: 243 AATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLND 302

Query: 73  MGINVVDGDDLEDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +GI V +     +      +  S+     A   +       DS    T DPVRMY+REMG
Sbjct: 303 IGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMG 362

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIEAG   M+ ++   P+T   ++   + + +    + E ID   
Sbjct: 363 TVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGLI 422

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            +  E++       E    ++ ++   E+E +D     G   SA ++ +
Sbjct: 423 DLNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAASARQLEE 471


>gi|238797130|ref|ZP_04640632.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
 gi|238718977|gb|EEQ10791.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
          Length = 332

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|162458864|ref|NP_001104924.1| sigma-like factor2B [Zea mays]
 gi|4336608|gb|AAD17855.1| sigma factor SIG2B [Zea mays]
          Length = 527

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 92/247 (37%), Positives = 152/247 (61%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+        K  MV++N+RLVIS+AK++   G++F DLIQ+G  GL++ AEKFD   G
Sbjct: 276 LRRRLNHGVYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEKFDASKG 335

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR P+ EEIA
Sbjct: 336 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRLPSNEEIA 395

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               M +  V   + + K  +S  + +G  D ++  + + D +A +  ++  +  +++  
Sbjct: 396 VDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTY-QEIMPDTSAETAEETLHRWLMKKDV 454

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L SL+PR+++V+R RFGI      TL ++G+   V+RERIRQIE  A RKL+  +R 
Sbjct: 455 NTALDSLSPRKKQVMRYRFGIEGGRARTLHDIGQLMGVSRERIRQIELGAFRKLRSKNRL 514

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 515 QSLQHYL 521


>gi|315137348|dbj|BAJ44507.1| RNA polymerase sigma factor RpoS [Escherichia coli DH1]
          Length = 330

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLTRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L + E S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVELEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|108803849|ref|YP_643786.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765092|gb|ABG03974.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 289

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 106/278 (38%), Positives = 159/278 (57%), Gaps = 4/278 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             E ++   I      I     ++  E   +    +K       A+++++E NLRLV+SV
Sbjct: 10  ERENETPELIPGYFARIDKGELLTHQEEIELSRRAKK---GDRKARQKLIEKNLRLVVSV 66

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY   GL F DLIQEGNIGLMKA EKFD   G++FSTYA WW++QA+ R++AD+  TI
Sbjct: 67  AKKYRGYGLPFEDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTI 126

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVHM +KI K+ RT   +S +++REPT EE+A+ L    E VR+V     +  SL  P
Sbjct: 127 RVPVHMTEKIRKMARTYNELSAQLEREPTDEEVAEALGWTPEEVREVKGAMPDATSLNQP 186

Query: 580 I-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  DED+S +G+F+ED+ A     +  +        + +  L  R   VL  R+G+    
Sbjct: 187 LSSDEDSSEIGEFVEDERASDTAGAVARDIENAALRKAIERLPERNRHVLVRRYGLDDRE 246

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TL E+ ++  V+RER+RQ++ +A R ++       L
Sbjct: 247 PATLAELSEELGVSRERVRQLQREAERMIQESEFGAVL 284


>gi|83815083|ref|YP_446059.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
 gi|83756477|gb|ABC44590.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
          Length = 313

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 168/283 (59%), Gaps = 6/283 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V+ E   + +   EI  I +              + R+ E     A  ++  ANLR V+S
Sbjct: 37  VSREQRMLDQYLQEIGKIDLLEPEEEV------ELARRIEDGDEEALHKLCRANLRFVVS 90

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKY  +GL   DLI EGN GL+KAA++FD   G+KF +YA+WW++QAI +++A+QS  
Sbjct: 91  VAKKYQGQGLSLADLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRV 150

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+P++    I K+ + + R+   + R+P  EE+A++L + V+ VR+ +K T   +S++ 
Sbjct: 151 VRLPLNRIGTISKIRKASARLQQDLDRKPNIEELAEELEIDVQKVREAMKHTSRHLSMDA 210

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P  +ED + L D + D++  SP +  +  +++    R L++L  RE  + R+ FGIG   
Sbjct: 211 PFNEEDDNSLLDVLPDEDNDSPDEEMLSESVKIDIERALSALHDREAEITRLYFGIGREH 270

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEE+GK+F +TRER+RQI+ KA+RKL+     + L+   D
Sbjct: 271 PLTLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQDLQPHTD 313


>gi|23306702|gb|AAN15269.1| RNA polymerase sigma factor S variant [Escherichia coli]
          Length = 330

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L + E S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEYEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|148264661|ref|YP_001231367.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146398161|gb|ABQ26794.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter uraniireducens
           Rf4]
          Length = 336

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 105/262 (40%), Positives = 170/262 (64%), Gaps = 3/262 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+  ++ I     ++  E + + + + KGE     A+ +M+E+NLRLV+ +AK+Y NRG
Sbjct: 62  AIKLYLREIQKTKLLTADEEKELAARIDKGE---KAARDKMIESNLRLVVKIAKRYINRG 118

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D
Sbjct: 119 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 178

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I+K++R  R +  K+ REP+ +E+A  + +    +R+++ + K+  S+E P+G+ +   
Sbjct: 179 DINKMLRITRELVQKVNREPSIKEVATAMDVNSAYIRRLMVLLKKTYSIERPMGENNDYF 238

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D IED + VSP +     N  E  ++   +L+  E+R+L +RFG+      TL+ +G+
Sbjct: 239 LIDTIEDTSTVSPAELLEDVNRYEMVSKWFETLSDSEKRILTLRFGLDDKDPQTLDTIGR 298

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
            F VTRERIRQIEAK++ KL+ 
Sbjct: 299 SFGVTRERIRQIEAKSLEKLRK 320



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 55/126 (43%), Gaps = 3/126 (2%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           + + +ED      +  +++    +LE +     S++    A    V  ++ K +     D
Sbjct: 3   NDDLIEDFAGDEQHKDLDIFIEPELEPDAVELGSVEEVEEAEE--VEEEEIKVAVVEHFD 60

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D +++YLRE+   +LL+ + E  +A RI+ G       + ES L     I  R  +N G 
Sbjct: 61  DAIKLYLREIQKTKLLTADEEKELAARIDKGEKAARDKMIESNLRLVVKIAKRY-INRGL 119

Query: 179 TLLREI 184
             L  I
Sbjct: 120 PFLDLI 125


>gi|238754524|ref|ZP_04615879.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
 gi|238707353|gb|EEP99715.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
          Length = 332

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L     + +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPSESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|251733405|emb|CAR82452.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733407|emb|CAR82453.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733425|emb|CAR82462.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733427|emb|CAR82463.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733429|emb|CAR82464.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733431|emb|CAR82465.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733433|emb|CAR82466.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733435|emb|CAR82467.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733437|emb|CAR82468.1| RNA polymerase sigma factor [Ensifer adhaerens]
          Length = 202

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 122/192 (63%), Positives = 147/192 (76%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLNQ+R+D LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELIKAVKSLSLNQNRVDSLVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYSGAELDPNWMKSISNLAGKGWKEFAKSENQTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|146312853|ref|YP_001177927.1| RNA polymerase sigma factor RpoS [Enterobacter sp. 638]
 gi|145319729|gb|ABP61876.1| RNA polymerase, sigma 38 subunit, RpoS [Enterobacter sp. 638]
          Length = 330

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 40/106 (37%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E  L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGTESFDEKVLVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|332297439|ref|YP_004439361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332180542|gb|AEE16230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 287

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 104/271 (38%), Positives = 170/271 (62%), Gaps = 5/271 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    +S  E   +      G+  A      +V ANLR V++VAKKY N GL  +
Sbjct: 19  YLKEINKIPLLSREEETDLAVKAAAGDKAAKD---RIVNANLRFVVNVAKKYQNHGLDLV 75

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLM A E+FD   GY F +YA+WW++Q+I ++I ++S  IR+P++  +++ +
Sbjct: 76  DLISEGNIGLMTAIERFDVSKGYHFISYAVWWIRQSILKAICEKSRMIRLPLNRANELVQ 135

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHLG 589
           +    + ++     E    E+A  L M V  VR++L I+++ ISL+  I   D+D++ +G
Sbjct: 136 IEHARKLVAQDKTEEEEITEVADMLNMDVSHVREMLNISRDMISLDASIRSSDQDSASIG 195

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           +F+ED     P D+ + A++++    VL +LT +E  VLR RFG+  N   +L+EVG +F
Sbjct: 196 EFLEDSRYEDPADTVLNASMQDDIDGVLGTLTDKEADVLRYRFGLNGNKSMSLKEVGDKF 255

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +T+ERIRQIE KAI++L+HP+R+ +L +++
Sbjct: 256 NLTKERIRQIEKKAIKRLQHPARTVRLEAYV 286


>gi|294629875|ref|ZP_06708435.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292833208|gb|EFF91557.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 332

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 109/256 (42%), Positives = 156/256 (60%), Gaps = 7/256 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T  +  E + +V            AK   + +NLRLV++VA++Y   GL  LDLIQE
Sbjct: 76  ESKTEATPEELQALVD-------AGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQE 128

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN GL++A EKFD+  G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  
Sbjct: 129 GNAGLVRAVEKFDYRKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQ 188

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R  + +  R+P P EIA +L    E V  VL   ++P+SL   + DE  +  GD +ED +
Sbjct: 189 REFNRENGRDPEPAEIAAELGSTPERVADVLDWARDPVSLNMSVDDEGETQFGDLLEDTS 248

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           AVSP  S +     E    ++  L  R   +++MR+GI    + TL EVGK+  +TRERI
Sbjct: 249 AVSPEQSVMTLLRSEELDDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERI 308

Query: 657 RQIEAKAIRKLKHPSR 672
           RQIE  A+ +LK  +R
Sbjct: 309 RQIEKHALLELKKLAR 324



 Score = 37.5 bits (85), Expect = 7.4,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++   +      R    + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SATGETADAASSVRAHGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQVIEAG 64


>gi|4100838|gb|AAD01001.1| RpoS [Escherichia coli]
 gi|4100840|gb|AAD01002.1| RpoS [Escherichia coli]
 gi|4100842|gb|AAD01003.1| RpoS [Escherichia coli]
          Length = 328

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|269925235|ref|YP_003321858.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269788895|gb|ACZ41036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 344

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/247 (39%), Positives = 158/247 (63%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K   E   A+ +++E NLRLV+S+A++Y   G+   DLI+EGN+GLM+AAEKFDW  G
Sbjct: 97  LKKAVEEGKAARHKLIEHNLRLVVSIARRYVGHGMPLADLIEEGNLGLMRAAEKFDWRRG 156

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++QA+TR +A+   TIR+PVH+ + + K+ R  +R+S ++ REPT +E+A
Sbjct: 157 FRFSTYATWWIRQAVTRGLAEGGRTIRLPVHVGEALTKIGRETQRLSLELGREPTNQELA 216

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +   +  E + +    ++ P+SLE P+G++  ++LG+ +ED  A +P   A    L E  
Sbjct: 217 EATGLSPERIDEYKNASRLPLSLEAPLGEDGETNLGEVLEDTEAANPEHIADHTMLGEDI 276

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L  R+  ++ MR+G+      TLE  G++  VTRER RQIE +A+ +L+     
Sbjct: 277 KRALERLNERQRAIIIMRYGLYGGQPMTLEAAGRKLGVTRERARQIEQEALNRLRQSDAK 336

Query: 674 KKLRSFL 680
           + L S +
Sbjct: 337 QFLASHV 343



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 3/109 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D  D  DE   +  L+   +  + +  L++  D       D + +YLRE+G  +LL+ E
Sbjct: 8   FDILDNLDEIILDSELEDLEADLSPASLLEEEMDREL--IGDSLGIYLREIGRAQLLTAE 65

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E+A+A+ IE G+      L    ++ + L   +  + +G     ++I+
Sbjct: 66  EEVALAQAIERGQ-EAEQRLQSDDISPEELDDLKKAVEEGKAARHKLIE 113


>gi|124514327|gb|EAY55841.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           rubarum]
          Length = 499

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 102/270 (37%), Positives = 158/270 (58%), Gaps = 7/270 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E D +  + + +K +     ++  E + +   VR        A++ M+++NLRLV+S+AK
Sbjct: 42  EDDHLSALGSYLKKLQKSHLLTFEEEQDLAKRVR---AGDESARQAMIQSNLRLVVSIAK 98

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y  RGL   DLI+EGN+GLMKA  KFD   G++FSTYA WW++QAI R I +Q   IR+
Sbjct: 99  RYIGRGLLLEDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIRL 158

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           PVHM +K++  +    R      ++P  E +A+K  + V  ++++  + K  +SL+TPIG
Sbjct: 159 PVHMMEKVNAYLNAIERQVAD-GQQPDIETLARKNGLKVRDLQEIQALLKNTVSLDTPIG 217

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI---GMNT 638
           D + S L D + D  + SP+ +       +     LA L  +E RV+ +RFG+   G   
Sbjct: 218 DREDSTLKDILVDPTSFSPISTIESREEGDRLRESLALLKDKERRVIHLRFGLPGEGPEE 277

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TLE +G+   VTRER+RQIEA A+ KL+
Sbjct: 278 GMTLEAIGQMLGVTRERVRQIEASAMAKLR 307



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 33/132 (25%), Positives = 56/132 (42%), Gaps = 5/132 (3%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I   D      +E +EDS    S A  ++  L++     D  +   +  YL+++    LL
Sbjct: 5   IPENDSPWFSPDEQTEDSGKSVSRADEANEPLERGDLEDDHLSA--LGSYLKKLQKSHLL 62

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E E  +AKR+ AG      ++ +S L     I  R  +  G  LL ++I+ E  +G  
Sbjct: 63  TFEEEQDLAKRVRAGDESARQAMIQSNLRLVVSIAKRY-IGRG-LLLEDLIE-EGNLGLM 119

Query: 195 SKGGFFHGTEGH 206
                F   +G 
Sbjct: 120 KAVSKFDPDKGF 131


>gi|307324239|ref|ZP_07603447.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889970|gb|EFN20948.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 334

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 105/228 (46%), Positives = 147/228 (64%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA WW+
Sbjct: 99  KDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYATWWI 158

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA +L   +E V 
Sbjct: 159 RQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEHAEIAVELGSTMERVS 218

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++  L  R 
Sbjct: 219 DVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIGRLDDRT 278

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +++ R+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 279 ASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 326



 Score = 39.1 bits (89), Expect = 2.9,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++A  +      R    + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SAAAGGTDGANSVRASGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQSIEAG 64


>gi|19910024|dbj|BAB87263.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 431

 Score =  173 bits (437), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 116/301 (38%), Positives = 178/301 (59%), Gaps = 15/301 (4%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGI--SISEFRHIVSM-----VRKGECEASIA 444
           + E +  +A  +++  K+    + +  +TG+  +  E+    ++     +R      ++A
Sbjct: 128 KAEDEIELAKRIETFRKLEKVKEHMKWKTGVEPTDEEWARAAALSDAEELRHMVRVGTLA 187

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +  +V ANLR V++VAKKY      +   DLIQEGNIGL++A EKFD  +GY+F+TYA W
Sbjct: 188 RDRLVRANLRWVVAVAKKYHKQRGTMSMQDLIQEGNIGLIRAVEKFDPRMGYRFTTYATW 247

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAITRSI + S  IR+P H  +KI+++ R    +S  + R+PT  EIA+ + +    
Sbjct: 248 WIRQAITRSIQNSSREIRLPAHRHEKINRIKRATVALSRSLGRQPTEAEIAEHVGLDPSR 307

Query: 563 VRKVLK--ITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +RK ++       +SL+ PI + D  ++ +GDFI  +N   P D A +  +RE+  R LA
Sbjct: 308 MRKFVESAAAVATVSLDVPINESDNQSATIGDFIRSEN-EGPADRAERELMRESVARTLA 366

Query: 619 S-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L+ RE  VLRMRFG+      TL +VG+   VTRER+RQIE KA+RKL+ P  S  LR
Sbjct: 367 KALSEREYMVLRMRFGLDDGEPKTLNQVGETLGVTRERVRQIEMKALRKLRRPGFSSALR 426

Query: 678 S 678
            
Sbjct: 427 D 427



 Score = 44.4 bits (103), Expect = 0.071,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 28/57 (49%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           L    +      +  + +    ++D  R YL+E+G I LL  E EI +AKRIE  R 
Sbjct: 88  LVEEVAAPVAPPRAPRVARKGLSEDSGRRYLQEIGEISLLKAEDEIELAKRIETFRK 144


>gi|73671310|gb|AAZ80066.1| RpoS variant [Escherichia coli LW1655F+]
          Length = 330

 Score =  172 bits (436), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L + E S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEYEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|117165089|emb|CAJ88642.1| putative RNA polymerase principal sigma factor HrdC [Streptomyces
           ambofaciens ATCC 23877]
          Length = 338

 Score =  172 bits (436), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 92/287 (32%), Positives = 165/287 (57%), Gaps = 3/287 (1%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +A  +++ ++   E+++            R  +    +   +   AK  MV AN
Sbjct: 53  AEDEVTLARRIEAGVRAMEELEAADTGEPAPTPARRRALE---ETVRDGRAAKDHMVRAN 109

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+S+AK++ +RGL  LD+IQEGN+GL++A EKFD   G+KFSTYA WW++QAI R +
Sbjct: 110 LRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYATWWIRQAIERGL 169

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
           A  + T+R+PVH+ +++ K+ +  R++  ++ REPT +E+A +  +  + V  + ++ ++
Sbjct: 170 ATHARTVRLPVHVVEQLQKLAKVERKLRGRLDREPTADEVAAESGIDGDKVVWLRRVGRD 229

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SL+TP+ +   + +GD I D   +   + A    L       + +L PRE  +L +R+
Sbjct: 230 AVSLDTPVDEAGETVVGDLIPDTEVLQAPEVAEFQALAAELREAVGTLAPREAMILSLRY 289

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G+      TL +V +   +TRER+RQ+E  ++  L+ P    +L  +
Sbjct: 290 GLHDGRPRTLHQVAQHVGLTRERVRQLEKASLDHLRAPETRDRLLDW 336



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
               A+  +  L+ R    D    D +  YL ++G+  LL+ E E+ +A+RIEAG   M
Sbjct: 13  EDRRAATRTARLRSRIPEPDEEP-DLLGQYLAQIGATALLTAEDEVTLARRIEAGVRAM 70


>gi|216659|dbj|BAA02747.1| RNA polymerase sigma subunit, sigma-38 [Escherichia coli]
 gi|23306698|gb|AAN15268.1| RNA polymerase sigma factor S variant [Escherichia coli]
 gi|260448208|gb|ACX38630.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           DH1]
          Length = 330

 Score =  172 bits (436), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L + E S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVELEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|251733357|emb|CAR82428.1| RNA polymerase sigma factor [Rhizobium giardinii]
          Length = 202

 Score =  172 bits (436), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 119/192 (61%), Positives = 144/192 (75%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+  V SLSLNQ+R+D LVEQLYDI+KR++ NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELITAVKSLSLNQNRVDSLVEQLYDINKRLVQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++ G ELDP+W+    +     WK F   E   I  IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYSGAELDPNWMKSIANLAAKGWKEFAKNENTMIRNIRAEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISISEFR IV MV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|238758207|ref|ZP_04619386.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
 gi|238703537|gb|EEP96075.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
          Length = 332

 Score =  172 bits (436), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 173/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 40/107 (37%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L    S  +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDESTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|16130648|ref|NP_417221.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|170082316|ref|YP_001731636.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238901878|ref|YP_002927674.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
 gi|1710676|sp|P13445|RPOS_ECOLI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|882634|gb|AAA69251.1| RNA polymerase sigma subunit RpoS (sigma-38) [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1789098|gb|AAC75783.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|23306700|gb|AAN15267.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|23306712|gb|AAN15273.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|169890151|gb|ACB03858.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238863502|gb|ACR65500.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
          Length = 330

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 51.0 bits (120), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L ++E S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEQEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|27735253|sp|P35540|RPOS_SHIFL RecName: Full=RNA polymerase sigma factor rpoS
 gi|332753598|gb|EGJ83977.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-671]
 gi|333000355|gb|EGK19938.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-218]
 gi|333015759|gb|EGK35097.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-304]
          Length = 330

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|322420057|ref|YP_004199280.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320126444|gb|ADW14004.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 330

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 106/274 (38%), Positives = 170/274 (62%), Gaps = 5/274 (1%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K  V    D  +K+   ++ I     ++  E + + + +   +     A+  M+ +NLRL
Sbjct: 46  KAAVVEHFDDAIKL--YLREIQKTKLLTADEEKELAARI---DLGDKAARDRMIVSNLRL 100

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +AK+Y NRGL FLDLI+EGN+GL+KA E+F      +FSTYA WW++Q+I R++ +Q
Sbjct: 101 VVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQ 160

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S TIR+PVH+ D I+K++R  R +  K+ REPT +E+A  L + V  VR+++ + K+  S
Sbjct: 161 SRTIRLPVHVSDDINKMLRVTRELVQKMNREPTIKEVADTLEVNVTYVRRLMVLLKKTYS 220

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +E P+G+ +   L D IED + +SP       N  E  ++   +L+  E+++L +RFG+ 
Sbjct: 221 IERPMGENNDYFLIDTIEDTSTISPAVLLEDLNKYELVSKWFETLSDAEKKILTLRFGLE 280

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                TL+ +G+ F VTRERIRQIEAK++ KL+ 
Sbjct: 281 DKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRK 314



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 27/117 (23%), Positives = 47/117 (40%), Gaps = 2/117 (1%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
            +L       +D +   D +  E          ++ V  ++ K +     DD +++YLRE
Sbjct: 5   ELLEEKEPLFLDAEQDPDPDPLELEEAEEVD-EHAEVEEEEIKAAVVEHFDDAIKLYLRE 63

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +   +LL+ + E  +A RI+ G       +  S L     I  R  +N G   L  I
Sbjct: 64  IQKTKLLTADEEKELAARIDLGDKAARDRMIVSNLRLVVKIAKRY-INRGLPFLDLI 119


>gi|83272624|gb|ABC00797.1| RpoS [Escherichia coli]
          Length = 330

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I + + TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNPTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|308187918|ref|YP_003932049.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
 gi|308058428|gb|ADO10600.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
          Length = 330

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 172/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDIPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQAQGL 322



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/106 (25%), Positives = 42/106 (39%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L    ++ +     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEIFDEKALVENEASDSDVAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVFFARRALRGDIPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|238750591|ref|ZP_04612091.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
 gi|238711239|gb|EEQ03457.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
          Length = 332

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 172/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQGQGL 324



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 39/107 (36%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|193212077|ref|YP_001998030.1| RNA polymerase sigma 32 subunit RpoH [Chlorobaculum parvum NCIB
           8327]
 gi|193085554|gb|ACF10830.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobaculum parvum NCIB
           8327]
          Length = 299

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 93/283 (32%), Positives = 166/283 (58%), Gaps = 10/283 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVI 457
           L +   ++ I     ++  +   +   +++             A  A  ++++ NLR V+
Sbjct: 16  LSLDRYLQEIGKYDLLTAEDEVKLTMAIKEGYDMPVDTVEYKRAKRALDKLIKGNLRFVV 75

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS 
Sbjct: 76  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+P++    ++K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++
Sbjct: 136 IVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVD 195

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P    D + L D +++   + P  +  + +L     R L+ L PRE  V+R  FGIGM 
Sbjct: 196 APFAQGDDNRLLDVLQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFGIGME 254

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TLEE+G++F +TRER+RQI+ KAIR+L+  +  + L+ ++
Sbjct: 255 NPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYKEVLKEYI 297


>gi|83720670|ref|YP_440648.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|167617444|ref|ZP_02386075.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
 gi|83654495|gb|ABC38558.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 483

 Score =  172 bits (436), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 100/241 (41%), Positives = 159/241 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF++  G+KFSTYA 
Sbjct: 241 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYAT 300

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +  E
Sbjct: 301 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKVADRIERRSGARASLAELSEATGLSAE 360

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+  Q  + +  T +L +++
Sbjct: 361 RLRAVLMLPREPRSLNAPLGDDDQAEFGDIVEDASTPSLFDALAQGQMCDVVTSLLKTMS 420

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +   R FLD
Sbjct: 421 AQEADILRRRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQTLRITADACNARDFLD 480

Query: 682 G 682
            
Sbjct: 481 A 481



 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/144 (22%), Positives = 54/144 (37%), Gaps = 12/144 (8%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPP----------DEVSSEQMEDTVAMLSNMGIN 76
            +    ++++LA  R      EL                D    E ++   +   + G  
Sbjct: 10  YEQGIDRLLELACARDDTEYAELADEFASAPSDTHAHAHDLGEPEFLDRHASD-ESAGTG 68

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
                         D  D     + SS       D    ST DP+ +++R M ++ LL+ 
Sbjct: 69  SFGDKPTRAAHADADWHDGDVVDAQSSEPSDATPDDTAVST-DPLALFVRRMHAVPLLTH 127

Query: 137 EGEIAIAKRIEAGRAMMMASLCES 160
             EIA+A  IEAGR  ++ +L E+
Sbjct: 128 AQEIALATEIEAGREQVLQALAET 151


>gi|291320189|ref|YP_003515450.1| DNA directed RNA polymerase sigma factor [Mycoplasma agalactiae]
 gi|290752521|emb|CBH40493.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae]
          Length = 509

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 121/321 (37%), Positives = 186/321 (57%), Gaps = 15/321 (4%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           LE     E+D   +S      + + KN +    D +      I        +   E   +
Sbjct: 194 LEDFSAEEID---LSANLSVKKEDLKNKLTETNDIVKWYMRWIGKYGKL--LQPEEEFEL 248

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            + + KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K++ 
Sbjct: 249 ATEMDKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIIKAVQKYNV 308

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR++ADQS T+R+PVHM + I+K+ +  R +  +   +PT E
Sbjct: 309 NKGFKFSTYATWWIRQAITRAVADQSRTVRVPVHMVETINKITKIERELQQENGVDPTDE 368

Query: 551 EIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++       E VR + KI   PISL+  IG E+ S   DF++D++ V+P+D A    
Sbjct: 369 EIAQRYGNDFTAEKVRHIRKINIGPISLDKQIGKENDSSFSDFVKDESVVNPVDYASHEE 428

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEA 661
           L ET   +L  +L   E  ++  R+G+G + +       +LEE+  +  V++ERIRQIE 
Sbjct: 429 LVETLNAILKDTLDADEYELICKRYGVGFDNNGEKYKVFSLEELALERNVSKERIRQIEN 488

Query: 662 KAIRKLK-HPSRSKKLRSFLD 681
           K +RKLK  P RS+ L+ F++
Sbjct: 489 KILRKLKSSPERSRYLKVFME 509



 Score = 38.3 bits (87), Expect = 4.4,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREGE 139
           D LE E+ S + +DL+++ S     L+ +       T+D V+ Y+R +G   +LL  E E
Sbjct: 190 DTLELEDFSAEEIDLSANLSVKKEDLKNKLTE----TNDIVKWYMRWIGKYGKLLQPEEE 245

Query: 140 IAIAKRIEAGRAMMMAS 156
             +A  ++ G      +
Sbjct: 246 FELATEMDKGGFRGKRA 262


>gi|163783667|ref|ZP_02178655.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881072|gb|EDP74588.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 309

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/303 (32%), Positives = 162/303 (53%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K IS    +S  E + +    +        + K++VE+NLR V+SVAK+Y   GL
Sbjct: 9   INQYLKRISKIPLLSPEEEKELARKAK---EGDEESLKKLVESNLRFVVSVAKQYIGYGL 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            F +LI  GN+GL++AA++FD   G KF +YA+WW++QAI ++++ Q+  +RIP+     
Sbjct: 66  PFSELIAAGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQSHL 125

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKK-------------------------------LA 557
           I K+      ++ +++REPTPEE+A++                                 
Sbjct: 126 ISKIGTIYAELAKELEREPTPEEVAEQLSKEMIAKELTKELGREPTDEEVQKKFKKEGYK 185

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E V K L++ + P+SL+ P+G+ + +   DF+         +S IQ  L +    +L
Sbjct: 186 ISPEEVEKYLQVCRIPLSLDAPVGENEDTFFVDFLSKHGTAEVEESVIQEVLEKEIYDLL 245

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L  +E RV+ +RFG+  N   TL E+G    V+RER+RQ+E +A+RKL+  +  + L+
Sbjct: 246 DKLPEKERRVVELRFGLKGNEPKTLREIGDILGVSRERVRQLETRALRKLRSLAMKRHLK 305

Query: 678 SFL 680
            FL
Sbjct: 306 DFL 308



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/46 (32%), Positives = 23/46 (50%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           YL+ +  I LLS E E  +A++ + G    +  L ES L F   + 
Sbjct: 12  YLKRISKIPLLSPEEEKELARKAKEGDEESLKKLVESNLRFVVSVA 57


>gi|152971625|ref|YP_001336734.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580660|ref|YP_002236889.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|262041489|ref|ZP_06014687.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288933843|ref|YP_003437902.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|330008320|ref|ZP_08306195.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
 gi|150956474|gb|ABR78504.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569718|gb|ACI11494.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|259041148|gb|EEW42221.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288888572|gb|ADC56890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|328535178|gb|EGF61679.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
          Length = 330

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/117 (28%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     GI V D   L +EE S+  L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGIEVFDEKALVEEEPSDSDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|291286384|ref|YP_003503200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290883544|gb|ADD67244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 322

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 105/313 (33%), Positives = 176/313 (56%), Gaps = 4/313 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + ++  LE       +   +    D  E E +       + +   +  +  IS    ++ 
Sbjct: 7   VDKEELLEEEPTDLSEVEEIETKLDTCETEPEPKYEYSSEDLEVFKIYLNEISKYPVLTR 66

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +   +   + K     + +K+ M++ NLRLV+S+AKKY NRG+  +DL++EGNIGL+KA
Sbjct: 67  EQEGELSQGIEK---GCNDSKETMIKCNLRLVVSIAKKYINRGMNLVDLVEEGNIGLLKA 123

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  G+KFSTYA WW++QAI R+I +Q   +RIPVHM + I KV++T   +  K+ 
Sbjct: 124 VEKFDYTKGFKFSTYATWWIRQAIERAIINQCRMVRIPVHMSENISKVMKTQNELQQKLG 183

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDS 603
           REPT  E++    MP+  ++KV    K+  SL+ P+G +++S L +FI D    + P   
Sbjct: 184 REPTIHELSTACKMPLSTLKKVFDAIKQDTSLDMPVGGDESSTLHEFIADDEKYLDPYLK 243

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               + +E   + L  L+  E+ ++  R+G+  N   TLE +G    +TRER+RQIE + 
Sbjct: 244 IENTSKKEIIFKWLTFLSDNEKTIIIRRYGLTGNDPETLESIGNDLGITRERVRQIEKRV 303

Query: 664 IRKLKHPSRSKKL 676
           + K+++   +KK+
Sbjct: 304 LSKMRNLLATKKI 316



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/110 (21%), Positives = 47/110 (42%), Gaps = 2/110 (1%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV-RMYLREMGSIELL 134
            +VD ++L +EE ++ S          +   +        S D  V ++YL E+    +L
Sbjct: 5   EIVDKEELLEEEPTDLSEVEEIETKLDTCETEPEPKYEYSSEDLEVFKIYLNEISKYPVL 64

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +RE E  +++ IE G      ++ +  L     I  +  +N G  L+  +
Sbjct: 65  TREQEGELSQGIEKGCNDSKETMIKCNLRLVVSIAKKY-INRGMNLVDLV 113


>gi|251733353|emb|CAR82426.1| RNA polymerase sigma factor [Bradyrhizobium japonicum]
          Length = 205

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 106/199 (53%), Positives = 136/199 (68%)

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
              L+  +           K + LK++++  V SL LNQ+RID LVEQLYDI+KR++ +E
Sbjct: 7   QNQLESTSHGPSLSPHQERKYRKLKDEIIVEVKSLRLNQARIDSLVEQLYDINKRLVSHE 66

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
           G L+RLA S+G+ R+ FL  + G ELDP W++         WKNFV  E D I  +R+E+
Sbjct: 67  GRLMRLADSHGVAREDFLRNYTGSELDPRWLNRVSKLSAKGWKNFVHIEKDRIKDLRHEV 126

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             ++  TG+ I EFR IV  V+KGE EA  AKKEMVEANLRLVIS+AKKYTNRGLQFLDL
Sbjct: 127 HQLAALTGLEIVEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDL 186

Query: 474 IQEGNIGLMKAAEKFDWCL 492
           IQEGNIGLMKA +KF++  
Sbjct: 187 IQEGNIGLMKAVDKFEYRR 205


>gi|317049278|ref|YP_004116926.1| RpoD subfamily RNA polymerase sigma-70 factor [Pantoea sp. At-9b]
 gi|316950895|gb|ADU70370.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pantoea sp.
           At-9b]
          Length = 330

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 172/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDIPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 42/109 (38%), Gaps = 6/109 (5%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDS-----ADRSTDDPVRMYLREMGSIELLS 135
           +D E EE   +  D  +   N        ++      A +   D  ++YL E+G   LL+
Sbjct: 13  EDAEFEENGAEVFDEKALVENEPGDNDVAEEELLSQGATQRVLDATQLYLGEIGYSPLLT 72

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 73  AEEEVFFARRALRGDIPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|251733355|emb|CAR82427.1| RNA polymerase sigma factor [Rhizobium galegae]
          Length = 202

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 123/195 (63%), Positives = 148/195 (75%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q  A  G        + K LK++L+  V SLSLNQ+R+D LVEQLYDISKR+M NEG LL
Sbjct: 8   QRLAATGTLSSAQERRYKELKDELITAVKSLSLNQNRVDSLVEQLYDISKRLMQNEGRLL 67

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
           RLA+SYG+KRD FLE++QG ELDP+W+    +     WK F   E  +I  IR EI++++
Sbjct: 68  RLAESYGVKRDSFLEQYQGAELDPNWMKSIANLAARGWKEFARAENTTIRDIRQEIQNLA 127

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ETGISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEG
Sbjct: 128 TETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 187

Query: 478 NIGLMKAAEKFDWCL 492
           NIGLMKA +KF++  
Sbjct: 188 NIGLMKAVDKFEYRR 202


>gi|326324968|dbj|BAJ84180.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Oranienburg]
          Length = 330

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  L+LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 36/93 (38%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           E+  A+R   G       + ES L     I  R
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARR 108


>gi|215404668|ref|ZP_03416849.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|298526173|ref|ZP_07013582.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
 gi|298495967|gb|EFI31261.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
          Length = 197

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 102/197 (51%), Positives = 140/197 (71%)

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + 
Sbjct: 1   MEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLG 60

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REPTPEE+AK++ +  E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+ 
Sbjct: 61  REPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAV 120

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K +
Sbjct: 121 SFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTM 180

Query: 665 RKLKHPSRSKKLRSFLD 681
            KL+HPSRS+ LR +LD
Sbjct: 181 SKLRHPSRSQVLRDYLD 197


>gi|257457314|ref|ZP_05622485.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257445236|gb|EEV20308.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 286

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 102/273 (37%), Positives = 170/273 (62%), Gaps = 8/273 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I+    +S+ +    V   +        AKK ++E+NLR V++VAKKY N+ +  +
Sbjct: 17  YLREINKIPLLSVEDE---VKYAKAAAAGDEKAKKILIESNLRFVVNVAKKYQNKNIPIM 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLM AA++FD   GYKF +YA+WW++QAI ++I ++S  IR+P++  +++ +
Sbjct: 74  DLISEGNIGLMNAADRFDPDKGYKFISYAVWWIRQAILKAICEKSRMIRLPLNRANELVQ 133

Query: 532 VVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SH 587
           + +   +++ K   EP  +E   IA+ L +  E VR ++   ++P+SL+ P  ++++ + 
Sbjct: 134 IEKAR-KLTGKTGTEPEDKELTAIAQDLRIEPEMVRTIMNAARDPVSLDAPQFNDNSAAS 192

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            GDFIED   + P   A+  +LRE    +LASL+ RE  +LR RFG+      +L+EVG 
Sbjct: 193 TGDFIEDTRYMQPESYALDIDLRENVDALLASLSEREAEILRYRFGLNGYEQLSLKEVGT 252

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +F +T+ERIRQIE KA+ +L+      +L SF+
Sbjct: 253 RFNLTKERIRQIEKKALERLQSVGHQHELESFV 285



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLRE+  I LLS E E+  AK   AG       L ES L F  ++    +  +    + +
Sbjct: 17  YLREINKIPLLSVEDEVKYAKAAAAGDEKAKKILIESNLRF--VVNVAKKYQNKNIPIMD 74

Query: 184 IIDLEACIGPESKGGFFHGTEG 205
           +I  E  IG  +    F   +G
Sbjct: 75  LIS-EGNIGLMNAADRFDPDKG 95


>gi|218200736|gb|EEC83163.1| hypothetical protein OsI_28384 [Oryza sativa Indica Group]
          Length = 537

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 89/321 (27%), Positives = 156/321 (48%), Gaps = 7/321 (2%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI--SI 424
           RD         + + H  S  +  P      F+      ++KI    + + V+ G   ++
Sbjct: 215 RDRETTEFLTAKEERHLFSKIQAKPYFYPVIFIFRTAQILMKIEEAHRKLEVQCGREPTL 274

Query: 425 SEFRHIV----SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           +E+   V      ++         +++M  +N RLVI VA+KY   GL   DL+Q+G  G
Sbjct: 275 AEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSG 334

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMK  EKF+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV +      
Sbjct: 335 LMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECI 394

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   +PT   +A++  + +E + K+   T++P S++  +  ++     +  ED N   P
Sbjct: 395 ME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPP 453

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             S  +  +R+     L  L+PRE+ ++  RFGI      TL  +G  F +++ERIRQ++
Sbjct: 454 DLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQ 513

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
            +A+ KLK  +  +    + D
Sbjct: 514 NRALEKLKRSASLQGFDVYFD 534


>gi|219130701|ref|XP_002185497.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403028|gb|EEC42984.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 329

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 100/260 (38%), Positives = 163/260 (62%), Gaps = 14/260 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K    +  AK  + E+N+RLV+S+AK+Y +RGL F DL QEG +GL +A EKFD   G
Sbjct: 67  LKKQIRRSLRAKAALTESNIRLVVSIAKRYQHRGLSFQDLAQEGILGLTRACEKFDPERG 126

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW+KQ+I R+IADQ  TIR+PVH+ D+I+ + +  R +  ++ R+   EEI 
Sbjct: 127 FRFSTYASWWIKQSIMRAIADQGRTIRLPVHIHDQINALRKVERELKAELGRDARLEEIT 186

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG-------------DEDTSHLGDFIEDKNAVSP 600
           +K  +  E +  + +++++ +S+E  +               +    LGD + D  A  P
Sbjct: 187 EKSTLTAEKIEFLNRVSQQDVSMEQELRTSKSKGSSAGLGGPDGGLTLGDVMGDPEA-QP 245

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            + A    L++  +R++ +L  RE+ V+RMRFG+      TLEE+G++F VTRERIRQIE
Sbjct: 246 AEEASYQMLKDDISRLICTLNSREQAVIRMRFGLDDGKAKTLEEIGRRFSVTRERIRQIE 305

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           ++A+ KL+ P R+  ++ ++
Sbjct: 306 SRALHKLRQPYRNHAVKCYV 325


>gi|329296050|ref|ZP_08253386.1| RNA polymerase sigma factor RpoS [Plautia stali symbiont]
          Length = 330

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 172/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDIPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/109 (27%), Positives = 41/109 (37%), Gaps = 6/109 (5%)

Query: 81  DDLEDEEGSEDSLDLA-----SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           DD E EE   +  D         + N     +     A +   D  ++YL E+G   LL+
Sbjct: 13  DDAEFEENGAEVFDEKVLVENEPSDNEVAEEELLSQGATQRVLDATQLYLGEIGYSPLLT 72

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 73  AEEEVFFARRALRGDIPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|149377551|ref|ZP_01895291.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
 gi|149358164|gb|EDM46646.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
          Length = 332

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 136/236 (57%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+    A+ +++ ++ +NLRL + +A++Y NRG+   D+IQ+ N+GL+KA E+FD   
Sbjct: 85  RCRRAYHLATSSRQRLIRSNLRLAVHIARRYANRGIPMSDVIQDANVGLIKAVERFDPTK 144

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW+ + + R +   +  +  P ++ D+I  + RT+  +   + R P+  E+
Sbjct: 145 GFRFSTYAYWWISEEVKRCMKRGTRLVHTPENVVDEIRLLQRTSLALYQTLGRTPSQTEL 204

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+++ +    + ++  +    +S++ P+  E    LG+ +   +  +P     Q + + T
Sbjct: 205 AREIEVSPSRIGELRALASMEVSVDLPVSTEGNITLGESLSADDQSAPDHDMAQRDRKRT 264

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +LA L+ RE+ VL  R+G+ +    TL+ +     ++RER+RQIE  A++KL+
Sbjct: 265 LATLLAELSSREKDVLARRYGLDLPEPETLQVISDDLGISRERVRQIEKSALKKLQ 320


>gi|81300555|ref|YP_400763.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
 gi|123556657|sp|Q31ME3|RPOD2_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD2
 gi|81169436|gb|ABB57776.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 102/249 (40%), Positives = 171/249 (68%), Gaps = 3/249 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +   +   AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD 
Sbjct: 72  LEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDP 131

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S ++ R  T  
Sbjct: 132 SKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATAS 191

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ L +P+E VR+ +++ ++P+SL+  +GD   + L + +ED+ + SP D   Q +LR
Sbjct: 192 ELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQS-SPSDYVEQESLR 250

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++A LTP+++ V+ +R+G+      +L +VG++  ++RER+R++E +A+  L+  
Sbjct: 251 RDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRR- 309

Query: 671 SRSKKLRSF 679
            RS+ L  +
Sbjct: 310 -RSRLLAEY 317


>gi|254388870|ref|ZP_05004102.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294813166|ref|ZP_06771809.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441537|ref|ZP_08216271.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|197702589|gb|EDY48401.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294325765|gb|EFG07408.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
          Length = 333

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 106/234 (45%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + +NLRLV++VA++Y   GL  LDL+QEGN GL++A EKFD+  G+KFST
Sbjct: 92  AEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLVQEGNAGLVRAVEKFDYSKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP   EIA++L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREKGREPEAAEIAQELGS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D   +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 TPERVTDVLDWARDPVSLNMAVDDAGETQFGDLLEDTSAVSPEQSVLTLLRSEGLDDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   ++RMR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 272 KLDQRTASIIRMRYGIMDGRERTLTEVGKEHGLTRERIRQIEKHALLELKRMAR 325



 Score = 37.9 bits (86), Expect = 6.0,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + +   +      R  S + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SETKGTTGRAGSVRAVSGETADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAG 64


>gi|167579340|ref|ZP_02372214.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
          Length = 482

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 100/241 (41%), Positives = 159/241 (65%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A   M EANLRLV+S+A+KY +RGL   DL+QEGN+GL++A EKF++  G+KFSTYA 
Sbjct: 240 SAATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYAT 299

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI+R+IAD++ TIR+PVH+ D+  +V + A R+  +     +  E+++   +  E
Sbjct: 300 WWIRQAISRAIADRARTIRVPVHVGDEARRVRKVADRIERRSGARASLAELSEATGLSAE 359

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL + +EP SL  P+GD+D +  GD +ED +  S  D+  Q  + +  T +L +++
Sbjct: 360 RLRAVLMLPREPRSLNAPLGDDDQAEFGDIVEDASTPSLFDALAQGQMCDVVTSLLKTMS 419

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +E  +LR RFGIG +   + E++  Q  V+RE+IR+IE +A++ L+  + +   R FLD
Sbjct: 420 AQEADILRRRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQTLRITADACNARDFLD 479

Query: 682 G 682
            
Sbjct: 480 A 480



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/144 (21%), Positives = 55/144 (38%), Gaps = 13/144 (9%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPP----------DEVSSEQMEDTVAMLSNMGIN 76
            +    ++++LA  R      EL                D    E ++   +   + G  
Sbjct: 10  YEQGIDRLLELACARDDTEYAELADEFASAPSDTHTHAHDLGEPEFLDRHASD-ESAGTG 68

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
                         D  D    A +S        D+A   + DP+ +++R M ++ LL+ 
Sbjct: 69  SFGDKPTRAAHADADWHDDVVDAQSSEPSDATPDDTAV--STDPLALFVRRMHAVPLLTH 126

Query: 137 EGEIAIAKRIEAGRAMMMASLCES 160
             EIA+A  IEAGR  ++ +L E+
Sbjct: 127 AQEIALAAEIEAGREQVLQALAET 150


>gi|297200336|ref|ZP_06917733.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|197709451|gb|EDY53485.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 332

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 107/235 (45%), Positives = 152/235 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  EESERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L  
Sbjct: 151 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEIAAELGS 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 211 NAERVVDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 271 RLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|218515736|ref|ZP_03512576.1| RNA polymerase sigma factor RpoD [Rhizobium etli 8C-3]
          Length = 191

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 138/190 (72%), Positives = 158/190 (83%), Gaps = 1/190 (0%)

Query: 494 YKFSTYAMWWV-KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           YK   YA WW+           +       VHM + I+K+VRT+R+M ++I REPTPEE+
Sbjct: 2   YKVLDYATWWMPSGDHPLDRRTRPARSAFRVHMIETINKIVRTSRQMLHEIGREPTPEEL 61

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+KLAMP+E VRKVLKI KEPISLETP+GDE+ SHLGDFIEDKNA+ P+D+AIQANLRET
Sbjct: 62  AEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRET 121

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIEAKA+RKLKHPSR
Sbjct: 122 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 181

Query: 673 SKKLRSFLDG 682
           S+KLRSFLD 
Sbjct: 182 SRKLRSFLDS 191


>gi|284431341|gb|ADB84485.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vitians]
          Length = 294

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 83/337 (24%), Positives = 141/337 (41%), Gaps = 48/337 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGR 377
           L  +   I  +E ++L LA +   + R  F+   +G 
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRFWEGN 294


>gi|283786707|ref|YP_003366572.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
 gi|282950161|emb|CBG89797.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
          Length = 330

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|333001093|gb|EGK20663.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-272]
 gi|333015402|gb|EGK34741.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-227]
          Length = 330

 Score =  172 bits (435), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RT R +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTVRELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|320662323|gb|EFX29720.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str. USDA
           5905]
          Length = 330

 Score =  171 bits (434), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/117 (28%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  S           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGS----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|251733409|emb|CAR82454.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733411|emb|CAR82455.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733413|emb|CAR82456.1| RNA polymerase sigma factor [Sinorhizobium saheli]
          Length = 202

 Score =  171 bits (434), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 122/192 (63%), Positives = 147/192 (76%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+M NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLMQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KR+ FLE++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|242238323|ref|YP_002986504.1| RNA polymerase sigma factor RpoS [Dickeya dadantii Ech703]
 gi|242130380|gb|ACS84682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech703]
          Length = 330

 Score =  171 bits (434), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAERLDRPVDDVNRMLRLNERITSVDTPLGGDSD 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQNNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 51.8 bits (122), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 12/119 (10%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G++V D   L +EE S+  L      S  +               D  ++YL E
Sbjct: 15  ADFEENGVDVFDEKALAEEETSDSELLEDDLLSQGTAQ----------RVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +G   LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVSSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|194246700|ref|YP_002004339.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
 gi|193807057|emb|CAP18493.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
          Length = 419

 Score =  171 bits (434), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 121/265 (45%), Positives = 179/265 (67%), Gaps = 5/265 (1%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            E  +S  E   +  +++     ++ AK  +VEAN RLV+S+AK+Y  RGL+FLDLIQEG
Sbjct: 154 KEIELSEKEISELNDILK----ISNKAKHRLVEANYRLVVSIAKRYIRRGLEFLDLIQEG 209

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N GLM+A EKF+   G K STYA +W+ Q I R++ADQ+  IR+PVH+ D+I+ +     
Sbjct: 210 NRGLMRAIEKFNIDKGCKLSTYATFWIVQKILRAVADQARIIRLPVHIVDRINIISMAKS 269

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++  K+ REPT EE+++ + +  + +R +  I K+PISLE  +G++D S LG+FI D ++
Sbjct: 270 KLRLKLHREPTIEELSEFINISEKKLRIIEIIKKKPISLEARVGEKDDSSLGEFISDPDS 329

Query: 598 VSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           +SP D  +Q  ++ T   +L  +LT REE++LRMR+G+     HTLEEVG  F VTRERI
Sbjct: 330 LSPHDYMLQEIMKNTLNEILEDTLTDREEKILRMRYGLSNGKVHTLEEVGNVFGVTRERI 389

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLD 681
           RQIEAKA R+L+ P+R  KL++  +
Sbjct: 390 RQIEAKAFRRLRTPARQNKLKTLYN 414



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 4/94 (4%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           S ++++D    L      +++ +DL  E+   D+L L         FL   K+  D    
Sbjct: 55  SEDKIKDLSDSLDE---IILEEEDLVYED-ETDTLVLDEFEEKKEEFLNIDKNPIDLKFY 110

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           DPV++YL+E+G I LL+ E E    + +  GR  
Sbjct: 111 DPVKIYLKEIGQIPLLTLEEEQEQFRLVYDGREA 144


>gi|6010728|gb|AAF01230.1|AF184099_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  171 bits (434), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEDEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|320538977|ref|ZP_08038652.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
 gi|320030910|gb|EFW12914.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
          Length = 332

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 95/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+      ++++ M+E+NLRLV+ +A +Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVLSRRRMIESNLRLVVKIALRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+++  EP+ EEIA++L  PV  V  +L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHRLDHEPSAEEIAEQLDKPVGDVSHMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P  +    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILADEKDNGPEGTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYESATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQTQGL 324



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/107 (28%), Positives = 43/107 (40%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L    S+ N     +    S  +   D  ++YL E+G   LL+ E
Sbjct: 17  FDQNGTEAESFDEKALLEEESSENDLAEEELLSQSVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G  +    + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVLSRRRMIESNLRLVVKIALRYS-NRGLALLDLI 122


>gi|170731361|ref|YP_001763308.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
 gi|169814603|gb|ACA89186.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 857

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 101/243 (41%), Positives = 149/243 (61%), Gaps = 2/243 (0%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + S          +A++ M  ANL+LV  +AKKY   G    DL QEGNIGL+KA E+FD
Sbjct: 501 LASQYANAMKAYQLARERMAVANLKLVFHLAKKYRYSGEPLDDLAQEGNIGLLKAVERFD 560

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           W  G+KFSTYA WW++Q I R +AD+  T+R+PVH+ +K  ++ R  + + ++  R P  
Sbjct: 561 WRRGFKFSTYATWWIRQQIGRHLADKCRTVRVPVHVHEKAQRLSRETQALESETGRAPEL 620

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA +L M V+ V ++ ++  EP+ +       D     +   D  +  P+D   ++ L
Sbjct: 621 HEIAARLNMAVQKVAELQRLAPEPLPIHELPI--DELIAVEVRSDFVSPDPMDIVSKSEL 678

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ET  ++L++L P+EE+ LR+RFGIG+    TLEE+G Q+ VTRER+RQIE  A+R LKH
Sbjct: 679 LETIDKLLSTLKPKEEQTLRLRFGIGVEEALTLEEIGCQYGVTRERVRQIEVAALRNLKH 738

Query: 670 PSR 672
           P R
Sbjct: 739 PRR 741



 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 53/395 (13%), Positives = 123/395 (31%), Gaps = 52/395 (13%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED-----SLDLASSASNSSVFLQKRKDSA 113
           + +       +++++G  V +  +      +E+       + +              DS 
Sbjct: 266 NPDVEAQLSMIINDLGAEVDERFEYASVSATENFEVYVKPEESPDEEEIVANALTSIDSL 325

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
             +  +P+ +Y +E     L+S + E+A+++ +E+     + +L   P      +     
Sbjct: 326 ASNRTEPLYIYQKEFQRKRLISADEEVALSRAMESELERALDALAAWPRGIDLTLAAGHV 385

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +  G   L                  +        Q   + + E E D    T       
Sbjct: 386 VRTGQQPL-----------------AWLSLGPADTQSELEPTSEGENDAGAATSDPTGET 428

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
           A+   D + ++    + A +    LD          SA +      +   L  +    R 
Sbjct: 429 AEHDSDLQFEICPRGDQASDFMDALDRL--AGLPVGSAQQGAGWQAIRETLSALRLNRRF 486

Query: 294 LRSLQDNAVNGQ-----KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           L  L D A  G      +   +    ++ +E++      L  +             ++K+
Sbjct: 487 LLELADLADGGDSGLASQYANAMKAYQLARERMAVANLKLVFH-------------LAKK 533

Query: 349 IMHNEGELLRLAQS------YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++   L  LAQ         ++R  +    +       W+         +    V   
Sbjct: 534 YRYSGEPLDDLAQEGNIGLLKAVERFDWRRGFKFSTYATWWIRQQIGRHLADKCRTVRVP 593

Query: 403 V---DSILKIRNEIKSISVETGISISEFRHIVSMV 434
           V   +   ++  E +++  ETG +  E   I + +
Sbjct: 594 VHVHEKAQRLSRETQALESETGRAP-ELHEIAARL 627


>gi|87118598|ref|ZP_01074497.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
 gi|86166232|gb|EAQ67498.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
          Length = 330

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 104/302 (34%), Positives = 171/302 (56%), Gaps = 5/302 (1%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEV-DSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             L+   V   ++F       +   +V  ++   +  +  I     +S  E    V   R
Sbjct: 22  NSLNLDEVDSNEEFESAVNARYANEDVGKNLDVTQMYLSEIGFSPLLSAEEE---VYYAR 78

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K       ++K M+E+NLRLV+ ++++Y NRGL  LDLI+EGN+GL++A EKFD   G++
Sbjct: 79  KSLKGDESSRKRMIESNLRLVVKISRRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFR 138

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ E+IA  
Sbjct: 139 FSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEDIADM 198

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           L  PVE V+K+L + +   S+++P+G  D    L + I D+    P D    +++     
Sbjct: 199 LDRPVEDVQKMLSLNERISSIDSPVGGMDTDKSLVEIIADEQHAGPEDERQFSDVVHNID 258

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L  L  ++  V+  RFG+      TLE+VG +  +TRER+RQI+ +A+RKLK     +
Sbjct: 259 HWLNDLNEKQREVIARRFGLRGYEPSTLEDVGAEIGLTRERVRQIQVEALRKLKLMMEKQ 318

Query: 675 KL 676
            L
Sbjct: 319 GL 320



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/103 (29%), Positives = 43/103 (41%), Gaps = 1/103 (0%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           D  D E S +  ++ S+    S    +  +       D  +MYL E+G   LLS E E+ 
Sbjct: 16  DDNDIENSLNLDEVDSNEEFESAVNARYANEDVGKNLDVTQMYLSEIGFSPLLSAEEEVY 75

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            A++   G       + ES L     I  R  LN G +LL  I
Sbjct: 76  YARKSLKGDESSRKRMIESNLRLVVKISRRY-LNRGLSLLDLI 117


>gi|15832849|ref|NP_311622.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           Sakai]
 gi|74313307|ref|YP_311726.1| RNA polymerase sigma factor RpoS [Shigella sonnei Ss046]
 gi|110642882|ref|YP_670612.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110806628|ref|YP_690148.1| RNA polymerase sigma factor RpoS [Shigella flexneri 5 str. 8401]
 gi|157157336|ref|YP_001464064.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|157162189|ref|YP_001459507.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|168749933|ref|ZP_02774955.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755487|ref|ZP_02780494.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|168778725|ref|ZP_02803732.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|168787997|ref|ZP_02813004.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|170019013|ref|YP_001723967.1| RNA polymerase sigma factor RpoS [Escherichia coli ATCC 8739]
 gi|170684160|ref|YP_001744890.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|191166775|ref|ZP_03028601.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|191171134|ref|ZP_03032684.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|193065048|ref|ZP_03046123.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|193069671|ref|ZP_03050623.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194431745|ref|ZP_03064036.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194438995|ref|ZP_03071079.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208812039|ref|ZP_03253368.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209395891|ref|YP_002272204.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920184|ref|YP_002294268.1| RNA polymerase sigma factor RpoS [Escherichia coli SE11]
 gi|217326648|ref|ZP_03442731.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218559734|ref|YP_002392647.1| RNA polymerase sigma factor RpoS [Escherichia coli S88]
 gi|218696339|ref|YP_002404006.1| RNA polymerase sigma factor RpoS [Escherichia coli 55989]
 gi|218706235|ref|YP_002413754.1| RNA polymerase sigma factor RpoS [Escherichia coli UMN026]
 gi|253772403|ref|YP_003035234.1| RNA polymerase sigma factor RpoS [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162672|ref|YP_003045780.1| RNA polymerase sigma factor RpoS [Escherichia coli B str. REL606]
 gi|256019474|ref|ZP_05433339.1| RNA polymerase sigma factor RpoS [Shigella sp. D9]
 gi|256024751|ref|ZP_05438616.1| RNA polymerase sigma factor RpoS [Escherichia sp. 4_1_40B]
 gi|260845388|ref|YP_003223166.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|260869420|ref|YP_003235822.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|261226035|ref|ZP_05940316.1| RNA polymerase sigma factor [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256708|ref|ZP_05949241.1| RNA polymerase, sigma S factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284068|ref|YP_003500886.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293406233|ref|ZP_06650159.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|293412096|ref|ZP_06654819.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|293415987|ref|ZP_06658627.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|293449062|ref|ZP_06663483.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|298381970|ref|ZP_06991567.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|300899982|ref|ZP_07118185.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|301027336|ref|ZP_07190677.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|306812377|ref|ZP_07446575.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|307139429|ref|ZP_07498785.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|307312831|ref|ZP_07592461.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|312973048|ref|ZP_07787221.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|331658855|ref|ZP_08359797.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331664297|ref|ZP_08365203.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331669480|ref|ZP_08370326.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331684360|ref|ZP_08384952.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|10197692|gb|AAG14975.1|AF242208_8 alternative sigma factor [Escherichia coli]
 gi|10197707|gb|AAG14988.1|AF242210_7 alternative sigma factor [Escherichia coli]
 gi|10197712|gb|AAG14992.1|AF242211_4 alternative sigma factor [Escherichia coli]
 gi|15529697|gb|AAL01412.1|AF410776_1 RpoS [Escherichia coli]
 gi|15529700|gb|AAL01414.1|AF410777_1 RpoS [Escherichia coli]
 gi|4887559|emb|CAB43502.1| alternative sigma factor, sigma 38 [Escherichia coli]
 gi|13363066|dbj|BAB37018.1| sigma factor RpoS [Escherichia coli O157:H7 str. Sakai]
 gi|37924617|gb|AAP59881.1| sigma S [Shigella boydii]
 gi|73856784|gb|AAZ89491.1| RNA polymerase, sigma S (sigma38) factor [Shigella sonnei Ss046]
 gi|83272618|gb|ABC00794.1| RpoS [Escherichia coli]
 gi|83272620|gb|ABC00795.1| RpoS [Escherichia coli]
 gi|83272622|gb|ABC00796.1| RpoS [Escherichia coli]
 gi|83272626|gb|ABC00798.1| RpoS [Escherichia coli]
 gi|110344474|gb|ABG70711.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110616176|gb|ABF04843.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|134036992|gb|ABO47833.1| sigma 38 factor [Escherichia coli]
 gi|134037004|gb|ABO47841.1| sigma 38 factor [Escherichia coli]
 gi|134037007|gb|ABO47843.1| sigma 38 factor [Escherichia coli]
 gi|134037010|gb|ABO47845.1| sigma 38 factor [Escherichia coli]
 gi|134037013|gb|ABO47847.1| sigma 38 factor [Escherichia coli]
 gi|157067869|gb|ABV07124.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|157079366|gb|ABV19074.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|169753941|gb|ACA76640.1| RNA polymerase, sigma 70 subunit, RpoD family [Escherichia coli
           ATCC 8739]
 gi|170521878|gb|ACB20056.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|188015788|gb|EDU53910.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003307|gb|EDU72293.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357252|gb|EDU75671.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|189372241|gb|EDU90657.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|190903146|gb|EDV62869.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|190908434|gb|EDV68023.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|192927345|gb|EDV81964.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|192957034|gb|EDV87485.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194420101|gb|EDX36179.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194422116|gb|EDX38119.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208733316|gb|EDZ82003.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209157291|gb|ACI34724.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209747660|gb|ACI72137.1| sigma factor RpoS [Escherichia coli]
 gi|209747662|gb|ACI72138.1| sigma factor RpoS [Escherichia coli]
 gi|209747664|gb|ACI72139.1| sigma factor RpoS [Escherichia coli]
 gi|209913443|dbj|BAG78517.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE11]
 gi|217319015|gb|EEC27440.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353071|emb|CAU98896.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli 55989]
 gi|218366503|emb|CAR04255.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli S88]
 gi|218433332|emb|CAR14232.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli UMN026]
 gi|222034438|emb|CAP77180.1| RNA polymerase sigma factor rpoS [Escherichia coli LF82]
 gi|242378296|emb|CAQ33073.1| RNA polymerase, sigma S (sigma 38) factor, subunit of RNA
           polymerase sigma 38 [Escherichia coli BL21(DE3)]
 gi|253323447|gb|ACT28049.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974573|gb|ACT40244.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253978740|gb|ACT44410.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|257760535|dbj|BAI32032.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|257765776|dbj|BAI37271.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|281179747|dbj|BAI56077.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE15]
 gi|290763941|gb|ADD57902.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291322152|gb|EFE61581.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|291426239|gb|EFE99271.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|291432176|gb|EFF05158.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|291468867|gb|EFF11358.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|298277110|gb|EFI18626.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|299879329|gb|EFI87540.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|300356491|gb|EFJ72361.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|305854415|gb|EFM54853.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|306907266|gb|EFN37772.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|307554720|gb|ADN47495.1| sigma factor RpoS [Escherichia coli ABU 83972]
 gi|307625683|gb|ADN69987.1| RNA polymerase sigma factor RpoS [Escherichia coli UM146]
 gi|309703100|emb|CBJ02432.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli ETEC
           H10407]
 gi|310332990|gb|EFQ00204.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|312947273|gb|ADR28100.1| RNA polymerase sigma factor RpoS [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062022|gb|ADT76349.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli W]
 gi|315615130|gb|EFU95767.1| RNA polymerase sigma factor RpoS [Escherichia coli 3431]
 gi|320186525|gb|EFW61253.1| RNA polymerase sigma factor RpoS [Shigella flexneri CDC 796-83]
 gi|320189070|gb|EFW63729.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194880|gb|EFW69509.1| RNA polymerase sigma factor RpoS [Escherichia coli WV_060327]
 gi|320202392|gb|EFW76962.1| RNA polymerase sigma factor RpoS [Escherichia coli EC4100B]
 gi|320651231|gb|EFX19666.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str. H
           2687]
 gi|320656781|gb|EFX24669.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320667375|gb|EFX34333.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323159951|gb|EFZ45921.1| RNA polymerase sigma factor RpoS [Escherichia coli E128010]
 gi|323167243|gb|EFZ52960.1| RNA polymerase sigma factor RpoS [Shigella sonnei 53G]
 gi|323172966|gb|EFZ58597.1| RNA polymerase sigma factor RpoS [Escherichia coli LT-68]
 gi|323180167|gb|EFZ65719.1| RNA polymerase sigma factor RpoS [Escherichia coli 1180]
 gi|323183273|gb|EFZ68670.1| RNA polymerase sigma factor RpoS [Escherichia coli 1357]
 gi|323188842|gb|EFZ74127.1| RNA polymerase sigma factor RpoS [Escherichia coli RN587/1]
 gi|323935702|gb|EGB32016.1| RNA polymerase sigma protein RpoS [Escherichia coli E1520]
 gi|323941428|gb|EGB37611.1| RNA polymerase sigma proteinRpoS [Escherichia coli E482]
 gi|323946373|gb|EGB42401.1| RNA polymerase sigma protein RpoS [Escherichia coli H120]
 gi|323951037|gb|EGB46913.1| RNA polymerase sigma proteinRpoS [Escherichia coli H252]
 gi|323957044|gb|EGB52769.1| RNA polymerase sigma proteinRpoS [Escherichia coli H263]
 gi|323960599|gb|EGB56225.1| RNA polymerase sigma proteinRpoS [Escherichia coli H489]
 gi|323966893|gb|EGB62322.1| RNA polymerase sigma proteinRpoS [Escherichia coli M863]
 gi|323971530|gb|EGB66763.1| RNA polymerase sigma proteinRpoS [Escherichia coli TA007]
 gi|323978651|gb|EGB73733.1| RNA polymerase sigma proteinRpoS [Escherichia coli TW10509]
 gi|324111374|gb|EGC05356.1| RNA polymerase sigma proteinRpoS [Escherichia fergusonii B253]
 gi|324119995|gb|EGC13873.1| RNA polymerase sigma proteinRpoS [Escherichia coli E1167]
 gi|325496210|gb|EGC94069.1| sigma factor RpoS [Escherichia fergusonii ECD227]
 gi|326339191|gb|EGD63006.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1044]
 gi|326342926|gb|EGD66694.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1125]
 gi|330908777|gb|EGH37291.1| RNA polymerase sigma factor RpoS [Escherichia coli AA86]
 gi|331053437|gb|EGI25466.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331058228|gb|EGI30209.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331063148|gb|EGI35061.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331077975|gb|EGI49181.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|332344623|gb|AEE57957.1| RNA polymerase sigma factor RpoS [Escherichia coli UMNK88]
          Length = 330

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|94502401|ref|ZP_01308854.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
 gi|94451042|gb|EAT14014.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
          Length = 341

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 142/238 (59%), Gaps = 1/238 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A   +V+ANLR VIS+AK+Y N+GL   DLI EGN GL+K   +FD   G+K  +Y +W
Sbjct: 103 YALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVW 162

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I ++I+D++  +R P +     +KV +T  ++  K+K  P+ + I+  L +  + 
Sbjct: 163 WIRQSILQAISDKARCVRYPTNKLAFYNKVNKTYSKLEQKLKMPPSIKYISDYLNVSEKD 222

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V + L  + +  SL+ P+G+ D S+L D I+   +     S  + +L++    +L +L+ 
Sbjct: 223 VEEALINSIKHTSLDAPLGEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKILLETLSE 282

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +++ + +G+G      LE++     +TRER RQIE  AI++LK  SR + L S+L
Sbjct: 283 RESQIITLHYGLGCF-SMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKEILLSYL 339


>gi|197302434|ref|ZP_03167489.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
 gi|197298332|gb|EDY32877.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
          Length = 283

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 108/263 (41%), Positives = 170/263 (64%), Gaps = 4/263 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +   E + +    R+       A++ + E NLRLV+S+AK YT RG+  +
Sbjct: 24  YLNEIGQIPLLDAEEEKELG---RRSVDGDEEARRRLEEGNLRLVVSIAKHYTGRGIPLM 80

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLM+A EK+D+    +FSTYA WW+K+AI R+I  QS  IR+PVH+ + + K
Sbjct: 81  DLIQEGNIGLMRAVEKYDFTKENRFSTYASWWIKEAIQRAIDQQSREIRVPVHVAEAMKK 140

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           V R ++ +   + RE TPEEIA+KL     E V+ +L   + P+SLETP+G++  ++LGD
Sbjct: 141 VQRISKELQQSLGREATPEEIAEKLGDKSTEDVKNILSYLQNPVSLETPVGEDGENNLGD 200

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +EDK + +P ++      +E  + +L +L  RE++V+R+R+G+     HTLEE+G++  
Sbjct: 201 MVEDKASPTPEEAMNLLVQKEEVSELLNALNDREKQVIRLRYGLEDGKTHTLEEIGEELK 260

Query: 651 VTRERIRQIEAKAIRKLKHPSRS 673
           VTRER+RQIE++A+ KL++ +  
Sbjct: 261 VTRERVRQIESRAMEKLRNKAER 283



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 59/178 (33%), Gaps = 10/178 (5%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
                ++          +P+++YL E+G I LL  E E  + +R   G       L E  
Sbjct: 2   EKSMEKELNIPEGTEVTEPLKIYLNEIGQIPLLDAEEEKELGRRSVDGDEEARRRLEEGN 61

Query: 162 LTFQALIIWR---------DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           L     I            D + +G   L   ++            +       + Q+  
Sbjct: 62  LRLVVSIAKHYTGRGIPLMDLIQEGNIGLMRAVEKYDFTKENRFSTYASWWIKEAIQRAI 121

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
           D    + R  V      ++   ++SK+ +  +       E  E+  D+  +D  + LS
Sbjct: 122 DQQSREIRVPVH-VAEAMKKVQRISKELQQSLGREATPEEIAEKLGDKSTEDVKNILS 178


>gi|300114080|ref|YP_003760655.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299540017|gb|ADJ28334.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 303

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 90/263 (34%), Positives = 148/263 (56%), Gaps = 4/263 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++       ++  E R+   +          A+  ++E+NLR+VI VA ++ NRGL  +
Sbjct: 42  YMREAGKVPLLNAEEERYYARLA---LQGDREARNRIIESNLRIVIKVASRHVNRGLPLM 98

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL+ A EKF+  LG++FSTYA WW++QAI R++ +Q+ TIR+PVH+  KI  
Sbjct: 99  DLIEEGNLGLINAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRLPVHVFKKIRS 158

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             +       +   EP   EIAK L  P+E V++ L +     SL+ P+ ++    L D 
Sbjct: 159 YQKEVILFRQRYNIEPRSGEIAKLLHEPLERVQRYLSLQALETSLDDPLNEDTEDCLADL 218

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D+     L   I  + + +    L+ L  R++ +L+ R+G+      TLEE+G    +
Sbjct: 219 LPDERNNPALLWEIF-DKKASIYNQLSQLPERQQEILKRRYGLDGYEVTTLEEIGHNLGI 277

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           TRER+RQI+  AI++L+    S+
Sbjct: 278 TRERVRQIQQAAIKRLRKIIESE 300



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +Y+RE G + LL+ E E   A+    G       + ES L    +I       +    L 
Sbjct: 41  LYMREAGKVPLLNAEEERYYARLALQGDREARNRIIESNLRI--VIKVASRHVNRGLPLM 98

Query: 183 EIID 186
           ++I+
Sbjct: 99  DLIE 102


>gi|269126860|ref|YP_003300230.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311818|gb|ACY98192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 360

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 96/273 (35%), Positives = 163/273 (59%), Gaps = 7/273 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  ++  L   + ++   V  G++  E   +V+           AK+  VEANLRLV+S
Sbjct: 40  LAKAIEGGLYAEHLLEEDRVPPGVTRQELEELVA-------AGVRAKQRFVEANLRLVVS 92

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+KY    L  +DLIQEGN+GLM+A EKFD+  G+KFSTYA WW++Q+I R ++  + T
Sbjct: 93  IARKYPTDALPLIDLIQEGNLGLMRAVEKFDYRRGFKFSTYATWWIRQSIGRGLSHTART 152

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+PVH+ +++ ++ R  R++  ++ REPT EE+A+ L   V+ V ++L+  ++P SL+ 
Sbjct: 153 IRLPVHVEEELSRLRRAERQLGRELGREPTREELAEALGAAVDHVDELLRWRRDPASLDA 212

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            + D   + +GD +ED   VSP    +  +      R+L  L  RE  +LR RFGI    
Sbjct: 213 AVDDAGETPMGDLLEDPEGVSPEAEVLALDDIAGLARLLDRLPERESAILRARFGIEDGQ 272

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +  ++G ++ ++  R+RQI  +++R+L+  +
Sbjct: 273 PLSYAQIGARYGLSHNRVRQITDRSLRRLRQLA 305



 Score = 37.9 bits (86), Expect = 6.0,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 22/47 (46%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
              + + DS +    D V  YL  +G   LL  + E+ +AK IE G 
Sbjct: 2   AATRTKGDSVETQDKDLVGAYLDRIGRTHLLDAQEEVDLAKAIEGGL 48


>gi|296104425|ref|YP_003614571.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058884|gb|ADF63622.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295097322|emb|CBK86412.1| RNA polymerase sigma factor RpoS [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 330

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEAFDEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|332298226|ref|YP_004440148.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181329|gb|AEE17017.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 332

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 98/265 (36%), Positives = 167/265 (63%), Gaps = 1/265 (0%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I + ++ I+ +     +  +E       + + E +  + K +M++ANLRLV+S+AK+Y 
Sbjct: 58  AIQEHKSRIRQL-KSGLLEPAENSPAYEEIDRLERDLLVLKNKMIQANLRLVVSIAKRYQ 116

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +RGL  LDLI EGNIGL++A ++F+     +FSTY +WW++QAI +S+AD+   IR+PVH
Sbjct: 117 HRGLGLLDLIDEGNIGLIEAVDRFEPARNCRFSTYGIWWIRQAIIKSLADKGRVIRVPVH 176

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           M + I+K    A+ ++ +  REPT  E+A+ L +  E V   +++++E  SLET + D++
Sbjct: 177 MLNTINKCFFMAKLLTQEYGREPTTAELARFLCVTNEKVEDYIRLSQEMSSLETNVDDDN 236

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           ++ LGD + D+N  +P++    A L +T   VL  L+ RE  ++R+R+G+      TL E
Sbjct: 237 STRLGDLLTDENGEAPIERVFAAALTDTVNLVLNQLSEREMSIIRLRYGLDGKAPRTLTE 296

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
            G    +TRER+RQI+ K ++KL+ 
Sbjct: 297 TGNVLGITRERVRQIQEKTLKKLRE 321


>gi|254409611|ref|ZP_05023392.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196183608|gb|EDX78591.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 374

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 105/275 (38%), Positives = 181/275 (65%), Gaps = 6/275 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            ++  +  +  +   + ++E +    + R       I+K++M+ +NLRLV+S+AK+Y NR
Sbjct: 104 QELGRKPTNAELAQALDLTERQFENRLYR-----GQISKRKMIRSNLRLVVSIAKRYLNR 158

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+ FLDLIQEG +GL +AAEKFD   GYKFSTYA WW++QAITR+IA+ + TIR+P+H+ 
Sbjct: 159 GVPFLDLIQEGALGLNRAAEKFDPAKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIV 218

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +K++K+ +  R +  K++R P   E+A+ L +    +R++L++ +  +SL   +G  + +
Sbjct: 219 EKLNKLKKVQRELKQKLQRTPDETELAEALDISRTNLRQLLQLRRRSLSLNHRVGKGEDT 278

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            L D +ED +   P     ++ +R+  + VL+  LT RE+ V+ +R+G+     +TLEEV
Sbjct: 279 ELVDLLEDNDLHLPEQQMSESMMRQEISDVLSDVLTEREKDVISLRYGLATPESYTLEEV 338

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G  F ++RER+RQI++KA+RKL+ P  +++L+ +L
Sbjct: 339 GSMFNLSRERVRQIQSKAMRKLRRPQVARRLQGWL 373



 Score = 41.0 bits (94), Expect = 0.65,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 30/61 (49%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  ++ +++  S + +     ++      S+DD V  + +EM    LL  E EI +A ++
Sbjct: 30  DNDQNQVEVEFSETETRAGKSRQSGYHKTSSDDTVGAFFKEMARYPLLKPEEEIELATQV 89

Query: 147 E 147
           +
Sbjct: 90  Q 90


>gi|311278284|ref|YP_003940515.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
 gi|308747479|gb|ADO47231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
          Length = 330

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 31/118 (26%), Positives = 47/118 (39%), Gaps = 5/118 (4%)

Query: 71  SNMGINVVDGDDLEDEEG----SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           + + ++ V+ D   DE G     E +L     + N     +     A +   D  ++YL 
Sbjct: 4   NTLKVHEVNEDAEFDENGMEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLG 63

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 64  EIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|253689710|ref|YP_003018900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251756288|gb|ACT14364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 330

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 46/117 (39%), Gaps = 12/117 (10%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
               G++V D   L +E+ +++           S   +       +   D  ++YL E+G
Sbjct: 17  FDENGLDVFDDKALAEEDTNDND----------SAEDELLSQGVPQRVLDATQLYLGEIG 66

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 67  YSPLLTAEEEVYFARRALRGDVPSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|171322339|ref|ZP_02911166.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171092333|gb|EDT37699.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 234

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 102/235 (43%), Positives = 154/235 (65%), Gaps = 1/235 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA WW++QA
Sbjct: 1   MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+  +  +P   +R VL
Sbjct: 61  VARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELIAETGLPEGKLRAVL 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            +  EP+SL+TP+  +  + L D IED+ + SP +      +RE  T +L S+TP E  V
Sbjct: 121 ALPAEPLSLDTPL-PDAETGLVDLIEDQASASPFEHLADTRMRECVTSLLRSVTPAEADV 179

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           LR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++   SFLD 
Sbjct: 180 LRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTVAEAEGAESFLDA 234


>gi|242041441|ref|XP_002468115.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
 gi|241921969|gb|EER95113.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
          Length = 528

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 94/247 (38%), Positives = 149/247 (60%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+        K  MV++N+RLVIS+AK++   G++F DLIQEG  GL++ AEKFD   G
Sbjct: 277 LRRRLNHGVYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQEGMQGLIRGAEKFDASKG 336

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR P+ EEIA
Sbjct: 337 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLRRELKRLPSNEEIA 396

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               M +  V   + + K  +S  + +G  D ++  + + D +A +  +   +  +++  
Sbjct: 397 VDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTY-QEIMPDTSAETAEEVLHRWLMKKDV 455

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L SL+PRE+ V+R RFGI      TL ++G+   V+RERIRQIE  A RKL+   R 
Sbjct: 456 NTALESLSPREKLVMRYRFGIEGGRPRTLHDIGQIMGVSRERIRQIELGAFRKLRSKKRV 515

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 516 QSLQHYL 522


>gi|317493947|ref|ZP_07952364.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918274|gb|EFV39616.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 328

 Score =  171 bits (434), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 172/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 53  LDATQLYLGEIGYSPLLTAEEE---VFFARRALRGDDASRRRMIESNLRLVVKIARRYSN 109

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 110 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 169

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV  V ++L++ +   S++TP+G +  
Sbjct: 170 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDRPVTDVSRMLRLNERITSVDTPLGGDSE 229

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 230 KALLDILTDENESGPEDTTQSDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 289

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 290 GREIGLTRERVRQIQVEGLRRLREILQAQGL 320



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D  E+ E + D   L    +      +    +  +   D  ++YL E+G   LL+ E 
Sbjct: 14  EVDFDENGEEAFDEKVLVEEPTEVDSSDELMAQAVSQRVLDATQLYLGEIGYSPLLTAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVFFARRALRGDDASRRRMIESNLRLVVKIARRYS-NRGLALLDLI 118


>gi|320180825|gb|EFW55748.1| RNA polymerase sigma factor RpoS [Shigella boydii ATCC 9905]
          Length = 330

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|256425191|ref|YP_003125844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040099|gb|ACU63643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 285

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 87/274 (31%), Positives = 158/274 (57%), Gaps = 5/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   ++ IS    ++  E   +   ++        A + +   NLR V+SVAK+Y ++
Sbjct: 16  QAVEKYLQEISKIPLLTPEEETVLAQRIK---MGDQKALERLTTGNLRFVVSVAKQYQHQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+Q   +R+P +  
Sbjct: 73  GLSLSDLINEGNLGLIKAAQRFDETKGFKFISYAVWWIRQSILQALAEQGRLVRLPQNKI 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
              +K  +       + +REP+ EE+A+ L M    +  + +     +SL+ P+ + +  
Sbjct: 133 GTYNKANKAYMAFEQENEREPSTEELAEILEMSESEINNIFQSNTRHMSLDAPVHEAEDV 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            +GD +E  +     D  ++ +LRE   RVL SL+PRE  ++   FG+      T+E++G
Sbjct: 193 AMGDLLEGGDITD--DDVMRDSLREEIRRVLKSLSPREAEIVNAYFGLDGENGATIEQIG 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +++ +T+ERIRQI+ +AI++L+    S  L+S+L
Sbjct: 251 QKYDLTKERIRQIKERAIKRLQKARYSGALKSYL 284



 Score = 44.8 bits (104), Expect = 0.047,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           V  YL+E+  I LL+ E E  +A+RI+ G    +  L    L F  ++    +       
Sbjct: 18  VEKYLQEISKIPLLTPEEETVLAQRIKMGDQKALERLTTGNLRF--VVSVAKQYQHQGLS 75

Query: 181 LREIID 186
           L ++I+
Sbjct: 76  LSDLIN 81


>gi|6010726|gb|AAF01229.1|AF184098_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A +KFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVQKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|1519644|gb|AAB07555.1| SigA [Chlorobaculum tepidum]
          Length = 299

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 92/243 (37%), Positives = 156/243 (64%), Gaps = 1/243 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              A  A  ++++ NLR V+SVAK+Y N+GL   DLI EGN+GL+KAA++FD   G+KF 
Sbjct: 56  YKRAKRALDKLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFI 115

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P  +E+A  L 
Sbjct: 116 SYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDPNTKELADLLD 175

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M  + V   LKI    +S++ P    D + L D +++   + P  +  + +L     R L
Sbjct: 176 MDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHM-PDYTLNRDSLSLEVERSL 234

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           + L PRE  V+R  FGIGM+   TLEE+G++F +TRER+RQI+ KAIR+L+  + +K L+
Sbjct: 235 SVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYNKVLK 294

Query: 678 SFL 680
            ++
Sbjct: 295 EYI 297


>gi|291618595|ref|YP_003521337.1| RpoS [Pantoea ananatis LMG 20103]
 gi|291153625|gb|ADD78209.1| RpoS [Pantoea ananatis LMG 20103]
 gi|327394975|dbj|BAK12397.1| RNA polymerase sigma factor RpoS [Pantoea ananatis AJ13355]
          Length = 330

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VLFARRALRGDIPSRRRMIESNLRLVVKIARRYSN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQGQGL 322



 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + ++   E   E +L    S  N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFEENGAEIFDEKALVENESGDNDVAEEELLAQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVLFARRALRGDIPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 120


>gi|16761696|ref|NP_457313.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16766230|ref|NP_461845.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56414872|ref|YP_151947.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|62181426|ref|YP_217843.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157148284|ref|YP_001455603.1| RNA polymerase sigma factor RpoS [Citrobacter koseri ATCC BAA-895]
 gi|167550225|ref|ZP_02343982.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168230998|ref|ZP_02656056.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|168235962|ref|ZP_02661020.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|168242664|ref|ZP_02667596.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168261948|ref|ZP_02683921.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168463936|ref|ZP_02697853.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|168820376|ref|ZP_02832376.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|194442500|ref|YP_002042165.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451079|ref|YP_002046882.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194470798|ref|ZP_03076782.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194738113|ref|YP_002115873.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197263839|ref|ZP_03163913.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197363800|ref|YP_002143437.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198243199|ref|YP_002216890.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200388856|ref|ZP_03215468.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204928102|ref|ZP_03219302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|207858184|ref|YP_002244835.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213052392|ref|ZP_03345270.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213648321|ref|ZP_03378374.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|224584701|ref|YP_002638499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|237729723|ref|ZP_04560204.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|238909692|ref|ZP_04653529.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|283835495|ref|ZP_06355236.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|61236740|sp|P0A2E5|RPOS_SALTY RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236751|sp|P0A2E6|RPOS_SALTI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236761|sp|P0A2E7|RPOS_SALDU RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|1073666|pir||S49471 transcription initiation factor sigma kaltF - Salmonella
           choleraesuis
 gi|6010738|gb|AAF01235.1|AF184104_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|558645|emb|CAA57640.1| katF (rpoS) [Salmonella enterica]
 gi|602087|emb|CAA54798.1| KatF [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16421473|gb|AAL21804.1| sigma S (sigma 38) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503997|emb|CAD06030.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhi]
 gi|56129129|gb|AAV78635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|62129059|gb|AAX66762.1| sigma S (sigma 38) factor of RNA polymerase, major sigmafactor
           during stationary phase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157085489|gb|ABV15167.1| hypothetical protein CKO_04101 [Citrobacter koseri ATCC BAA-895]
 gi|194401163|gb|ACF61385.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194409383|gb|ACF69602.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194457162|gb|EDX46001.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194713615|gb|ACF92836.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195633598|gb|EDX52012.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197095277|emb|CAR60830.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|197242094|gb|EDY24714.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197290706|gb|EDY30060.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|197937715|gb|ACH75048.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|199605954|gb|EDZ04499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204322424|gb|EDZ07621.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205324779|gb|EDZ12618.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205334505|gb|EDZ21269.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205338030|gb|EDZ24794.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205342988|gb|EDZ29752.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|205349304|gb|EDZ35935.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|206709987|emb|CAR34342.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|224469228|gb|ACN47058.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|226908329|gb|EEH94247.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|261248060|emb|CBG25894.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. D23580]
 gi|267995054|gb|ACY89939.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|291068697|gb|EFE06806.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|301159483|emb|CBW19002.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. SL1344]
 gi|312913942|dbj|BAJ37916.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320087327|emb|CBY97092.1| RNA polymerase sigma factor rpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|321225598|gb|EFX50652.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614255|gb|EFY11186.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621681|gb|EFY18534.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624542|gb|EFY21375.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322628873|gb|EFY25656.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633400|gb|EFY30142.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636024|gb|EFY32732.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322639617|gb|EFY36303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646916|gb|EFY43419.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322652217|gb|EFY48576.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654704|gb|EFY51023.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322658925|gb|EFY55178.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322664508|gb|EFY60702.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668243|gb|EFY64400.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322673777|gb|EFY69878.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677838|gb|EFY73901.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681332|gb|EFY77364.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322683734|gb|EFY79744.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322715910|gb|EFZ07481.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323131276|gb|ADX18706.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323193878|gb|EFZ79081.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200347|gb|EFZ85429.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202369|gb|EFZ87413.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205603|gb|EFZ90568.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323210115|gb|EFZ95018.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323216417|gb|EGA01144.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323220766|gb|EGA05207.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323226390|gb|EGA10598.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230730|gb|EGA14848.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234919|gb|EGA19005.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238958|gb|EGA23008.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241658|gb|EGA25689.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248195|gb|EGA32131.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323251221|gb|EGA35094.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323257395|gb|EGA41091.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323263241|gb|EGA46779.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323264257|gb|EGA47763.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271083|gb|EGA54511.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624653|gb|EGE30998.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989795|gb|AEF08778.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 330

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|148377531|ref|YP_001256407.1| RNA polymerase sigma factor [Mycoplasma agalactiae PG2]
 gi|148291577|emb|CAL58963.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae PG2]
          Length = 509

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 121/321 (37%), Positives = 188/321 (58%), Gaps = 15/321 (4%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           LE     E+D   +S      + + KN +    D +      I        +   E   +
Sbjct: 194 LEDFSAEEID---LSANLSVKKEDLKNKLTETNDIVKWYMRWIGKYGKL--LQPEEEFEL 248

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            + + KG  +   A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K++ 
Sbjct: 249 ATEMDKGGFKGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIIKAVQKYNV 308

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR++ADQS T+R+PVHM + I+K+ +  R +  +   +PT E
Sbjct: 309 NKGFKFSTYATWWIRQAITRAVADQSRTVRVPVHMVETINKITKIERELQQENGVDPTDE 368

Query: 551 EIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++       E VR + KI  +PISL+  IG E+ S   DF++D++ V+P+D A    
Sbjct: 369 EIAQRYGNDFTAEKVRHIRKINIDPISLDKQIGKENDSSFSDFVKDESVVNPVDYASHEE 428

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEA 661
           L ET   +L  +L   E  ++  R+G+G + +       +LEE+  +  V++ERIRQIE 
Sbjct: 429 LVETLNAILKDTLDADEYELICKRYGVGFDNNGEKYKVFSLEELALERNVSKERIRQIEN 488

Query: 662 KAIRKLK-HPSRSKKLRSFLD 681
           K +RKLK  P RS+ L+ F++
Sbjct: 489 KILRKLKSSPERSRYLKVFME 509



 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREGE 139
           D LE E+ S + +DL+++ S     L+ +       T+D V+ Y+R +G   +LL  E E
Sbjct: 190 DTLELEDFSAEEIDLSANLSVKKEDLKNKLTE----TNDIVKWYMRWIGKYGKLLQPEEE 245

Query: 140 IAIAKRIEAG 149
             +A  ++ G
Sbjct: 246 FELATEMDKG 255


>gi|320640384|gb|EFX09923.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           G5101]
          Length = 330

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+++  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHQLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|251733373|emb|CAR82436.1| RNA polymerase sigma factor [Sinorhizobium arboris LMG 14919]
 gi|251733375|emb|CAR82437.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733377|emb|CAR82438.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733393|emb|CAR82446.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733395|emb|CAR82447.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733397|emb|CAR82448.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733399|emb|CAR82449.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733401|emb|CAR82450.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733403|emb|CAR82451.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
          Length = 202

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 121/192 (63%), Positives = 146/192 (76%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+  NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLTQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KR+ FLE++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVKREAFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|1769596|gb|AAB39997.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 317

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 104/280 (37%), Positives = 171/280 (61%), Gaps = 9/280 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVISVA 460
           ++ K++ E+     +   S+ E+          ++K       AK++MVEANLRLV+SVA
Sbjct: 41  NLEKLKAELAEKQDQEP-SLKEWAQAANLSQRQLKKQLLLGKQAKQKMVEANLRLVVSVA 99

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+QS TIR
Sbjct: 100 KKYIKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEQSRTIR 159

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R+++    R  +  E+A +L +  + VR  L+ +++P+SL+  +
Sbjct: 160 LPIHITEKLNKIKKAQRQLAQANGRSASIPELADELGLTTKQVRDYLEKSRQPLSLDLRV 219

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD + + L +  +D            A L+    R+L  LT +++ VL +RFG+   T H
Sbjct: 220 GDNNDTELIELEDDGELPDDYA--THAALKRDLARMLNDLTAQQQEVLTLRFGLRDGTPH 277

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL ++G+   ++RER+RQIE  ++ KL+   + +KL  +L
Sbjct: 278 TLAKIGEHLNISRERVRQIEHGSLAKLRK--QKRKLGEYL 315



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASLCE 159
           + DPVR YL+E+G + LL+ E E+  ++R++       + A L E
Sbjct: 7   SADPVRTYLKEIGRVPLLTHEEEVLYSRRVQKMVNLEKLKAELAE 51


>gi|15803258|ref|NP_289290.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 EDL933]
 gi|12517195|gb|AAG57848.1|AE005502_2 RNA polymerase, sigma S (sigma38) factor; synthesis of many growth
           phase related proteins [Escherichia coli O157:H7 str.
           EDL933]
          Length = 330

 Score =  171 bits (433), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + DD   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDDNRVEVFDEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|82545186|ref|YP_409133.1| RNA polymerase sigma factor RpoS [Shigella boydii Sb227]
 gi|81246597|gb|ABB67305.1| RNA polymerase sigma S factor [Shigella boydii Sb227]
 gi|332092174|gb|EGI97252.1| RNA polymerase sigma factor RpoS [Shigella boydii 3594-74]
          Length = 331

 Score =  171 bits (433), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 2/271 (0%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEEE--VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 112

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 113 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 172

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 173 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 232

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 233 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 292

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 293 GREIGLTRERVRQIQVEGLRRLREILQTQGL 323



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 32/118 (27%), Positives = 45/118 (38%), Gaps = 12/118 (10%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSR-EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+  E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 121


>gi|1519382|gb|AAC46141.1| RNA polymerase subunit sigma 38 [Pectobacterium carotovorum]
          Length = 330

 Score =  171 bits (433), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 168/271 (61%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L + +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLALNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 46/117 (39%), Gaps = 12/117 (10%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
               G++V D   L +E+ +++           S   +       +   D  ++YL E+G
Sbjct: 17  FEENGLDVFDDKALAEEDTNDND----------SAEDELLSQGVPQRVLDATQLYLGEIG 66

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 67  YSPLLTAEEEVYFARRALRGDVPSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|441116|gb|AAA61628.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|1090521|prf||2019251A RNA polymerase sigma factor
          Length = 330

 Score =  171 bits (433), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRDLRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRDLRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|271963319|ref|YP_003337515.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270506494|gb|ACZ84772.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 312

 Score =  171 bits (433), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 92/238 (38%), Positives = 153/238 (64%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +       AK E ++ANLRLV++VA+KY+ RG+  +DL+QEGN+GL++A EKFD+ 
Sbjct: 70  EELERLAVSGQRAKDEFIQANLRLVVAVARKYSGRGMPLIDLVQEGNLGLVRAVEKFDYR 129

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q++ R+I +Q+  +R+P H  +++ +++R  R M  +  +EPT  +
Sbjct: 130 RGYKFSTYATWWIRQSVGRAIHEQARPVRLPTHAGEQMTRLMRVRRDMLAEFDQEPTDAD 189

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L +P+E VR++ +   +P+SL+  +GDED + LGD I D+    P   A+    RE
Sbjct: 190 LAAVLELPIERVRELRRWASDPVSLQLGVGDEDETELGDMIADETWADPEQQAMDILERE 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              + L  L  +   +LR R+G+    +HTL EVG+++ + R+R R+IE  A+ +L+ 
Sbjct: 250 RLEQWLTGLEGQTREMLRWRYGLMDGREHTLTEVGERYGIGRDRARRIERDALARLRK 307



 Score = 42.9 bits (99), Expect = 0.16,   Method: Composition-based stats.
 Identities = 16/32 (50%), Positives = 22/32 (68%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D +  YL E+G + LL+ E E+ +AKRIEAG 
Sbjct: 18  DLLGTYLAEIGRVPLLTAEEEVELAKRIEAGL 49


>gi|50122451|ref|YP_051618.1| RNA polymerase sigma factor RpoS [Pectobacterium atrosepticum
           SCRI1043]
 gi|227114060|ref|ZP_03827716.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
 gi|227327750|ref|ZP_03831774.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
 gi|49612977|emb|CAG76428.1| RNA polymerase sigma factor [Pectobacterium atrosepticum SCRI1043]
          Length = 330

 Score =  171 bits (433), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 46/117 (39%), Gaps = 12/117 (10%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
               G++V D   L +E+ +++           S   +       +   D  ++YL E+G
Sbjct: 17  FEENGLDVFDDKALAEEDTNDND----------SAEDELLSQGVPQRVLDATQLYLGEIG 66

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 67  YSPLLTAEEEVYFARRALRGDVPSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|218701232|ref|YP_002408861.1| RNA polymerase sigma factor RpoS [Escherichia coli IAI39]
 gi|218371218|emb|CAR19049.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli IAI39]
 gi|327251469|gb|EGE63155.1| RNA polymerase sigma factor RpoS [Escherichia coli STEC_7v]
          Length = 330

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFSFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|205353865|ref|YP_002227666.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273646|emb|CAR38635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|326628975|gb|EGE35318.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 330

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|20330084|emb|CAD30008.1| RNA polymerase sigma factor [Burkholderia cepacia]
          Length = 362

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357



 Score = 41.4 bits (95), Expect = 0.48,   Method: Composition-based stats.
 Identities = 24/103 (23%), Positives = 34/103 (33%), Gaps = 1/103 (0%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +  D E      +    A  S      R       T D ++ YL  +    LL+ E E  
Sbjct: 45  EARDAEADGGDDEREGRAEASPDVDDFRTLLQAELTADTIQHYLNRISVKPLLTVEEEQR 104

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 105 YSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 146


>gi|56752354|ref|YP_173055.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
 gi|56687313|dbj|BAD80535.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
          Length = 320

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 102/249 (40%), Positives = 171/249 (68%), Gaps = 3/249 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +   +   AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD 
Sbjct: 72  LEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGFEKFDP 131

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S ++ R  T  
Sbjct: 132 SKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATAS 191

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ L +P+E VR+ +++ ++P+SL+  +GD   + L + +ED+ + SP D   Q +LR
Sbjct: 192 ELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQS-SPSDYVEQESLR 250

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++A LTP+++ V+ +R+G+      +L +VG++  ++RER+R++E +A+  L+  
Sbjct: 251 RDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRR- 309

Query: 671 SRSKKLRSF 679
            RS+ L  +
Sbjct: 310 -RSRLLAEY 317


>gi|254444043|ref|ZP_05057519.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198258351|gb|EDY82659.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 377

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 174/287 (60%), Gaps = 4/287 (1%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +F     +     E+     IR  ++ I     ++ ++    V++ R+ +     A+  M
Sbjct: 61  NFRAPAPQKKEKAELPDRNSIRTYLQEIGRIDLLTPAQE---VTLARRIQAGEKEARDLM 117

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +++NLRLV+ +A  Y + GL  LDLI EGNIGL+KA E+FD   G K STYA WW+KQ+I
Sbjct: 118 IKSNLRLVVKIAHDYKDFGLPVLDLISEGNIGLVKAVERFDPDKGGKLSTYAAWWIKQSI 177

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R++A+QS TIR+PVH+ DKI ++ + A  ++ ++ REPT +E+A+ L MPV  V  +  
Sbjct: 178 KRALANQSKTIRLPVHLVDKISRMRKMALMLTEELGREPTDQELAEMLEMPVNKVSHLKS 237

Query: 569 ITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++  P SL  P+G++  S   G+ + D NA +P ++  + +LR     ++  L  RE  +
Sbjct: 238 VSVRPTSLNAPVGEDGNSTEFGEIVGDDNAPTPYENLHEKSLRGDLHEMIDGLEDREAEI 297

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +R+RFG+  ++  TLEEVG+ F +TRER+RQ++  A+ K++    SK
Sbjct: 298 IRLRFGLNGDSPLTLEEVGQVFDITRERVRQLQNIALSKMRKIMASK 344



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 36/70 (51%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
               ++K+ A+    + +R YL+E+G I+LL+   E+ +A+RI+AG       + +S L 
Sbjct: 64  APAPQKKEKAELPDRNSIRTYLQEIGRIDLLTPAQEVTLARRIQAGEKEARDLMIKSNLR 123

Query: 164 FQALIIWRDE 173
               I    +
Sbjct: 124 LVVKIAHDYK 133


>gi|2385506|dbj|BAA22190.1| RpoD2 protein [Synechococcus elongatus PCC 7942]
          Length = 320

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 102/249 (40%), Positives = 171/249 (68%), Gaps = 3/249 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +   +   AK++M+EANLRLV+S+AKKY  R ++FLDLIQEG +GL +  EKFD 
Sbjct: 72  LEDLDREIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDP 131

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GYKFSTYA WW++QAITR+IA QS TIR+P+H+ +K++K+ +T R +S ++ R  T  
Sbjct: 132 SKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATAS 191

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ L +P+E VR+ +++ ++P+SL+  +GD   + L + +ED+ + SP D   Q +LR
Sbjct: 192 ELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQS-SPSDYVEQESLR 250

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++A LTP+++ V+ +R+G+      +L +VG++  ++RER+R++E +A+  L+  
Sbjct: 251 RDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRR- 309

Query: 671 SRSKKLRSF 679
            RS+ L  +
Sbjct: 310 -RSRLLAEY 317


>gi|291464746|gb|ADE05831.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 300

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 90/342 (26%), Positives = 142/342 (41%), Gaps = 44/342 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+   
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L +II            GF    E                          E  A  
Sbjct: 61  EQLRLSDII-----------SGFIDPNE-------------------------TEDMAPT 84

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +    S++       E++E   DEDED  +                   E+   Y     
Sbjct: 85  ATHIGSELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV--- 141

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                ++ QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +
Sbjct: 142 ---TRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMVERVRVQERII 198

Query: 357 LRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           ++L  +   + +  F+      E +  W  Y K   +      V  + + I +   +++ 
Sbjct: 199 MKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQ 257

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           I  ETG+SI++ + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 258 IEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVI 299


>gi|322831414|ref|YP_004211441.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
 gi|321166615|gb|ADW72314.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
          Length = 328

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 99/293 (33%), Positives = 173/293 (59%), Gaps = 3/293 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V    D    E           +   +  +  I     ++  E    V   R+       
Sbjct: 31  VEETADNDAEEELLSQTVSQRVLDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVP 87

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++ M+E+NLRLV+ +A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW
Sbjct: 88  SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 147

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +++K+  EP+ EEIA++L  PV  V
Sbjct: 148 IRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELAHKLDHEPSAEEIAEQLDKPVHDV 207

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  +
Sbjct: 208 SRMLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAK 267

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 268 QREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 320



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D D  E+   + D   +    +++    +    +  +   D  ++YL E+G   LL+ E 
Sbjct: 14  DVDFDENSAEAFDEKAIVEETADNDAEEELLSQTVSQRVLDATQLYLGEIGYSPLLTAEE 73

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 74  EVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 118


>gi|291464750|gb|ADE05833.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 300

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 90/342 (26%), Positives = 142/342 (41%), Gaps = 44/342 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+   
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L +II            GF    E                          E  A  
Sbjct: 61  EQLRLSDII-----------SGFIDPNE-------------------------TEDMAPT 84

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +    S++       E++E   DEDED  +                   E+   Y     
Sbjct: 85  ATHIGSELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV--- 141

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                ++ QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +
Sbjct: 142 ---TRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERII 198

Query: 357 LRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           ++L  +   + +  F+      E +  W  Y K   +      V  + + I +   +++ 
Sbjct: 199 MKLCVEQAKMPKKTFVGAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQ 257

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           I  ETG+SI++ + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 258 IEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVI 299


>gi|332087476|gb|EGI92604.1| RNA polymerase sigma factor RpoS [Shigella boydii 5216-82]
          Length = 330

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  V   RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNSKQREVPARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|294634769|ref|ZP_06713298.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
 gi|291091828|gb|EFE24389.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
          Length = 328

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       ++K M+E+NLRLV+ ++++Y+N
Sbjct: 54  LDATQLYLGEIGYAPLLTAEEE---VFFARRALRGDEASRKRMIESNLRLVVKISRRYSN 110

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 111 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 170

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV  V ++L++ +   S++TP+G +  
Sbjct: 171 VKELNVYLRTARELSHKLDHEPSAEEIAEQLEKPVHDVSRMLRLNERITSVDTPLGGDSE 230

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D     +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 231 KALLDILTDENESGPEDCTQNDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 290

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 291 GREIGLTRERVRQIQVEGLRRLREILQGQGL 321



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/108 (28%), Positives = 46/108 (42%), Gaps = 3/108 (2%)

Query: 79  DGDDLED--EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           D  +LED  E+G ++   +  S  N  V  +    +  +   D  ++YL E+G   LL+ 
Sbjct: 13  DEIELEDGVEDGFDEKALVDESMENDLVDDELLSQAISQRVLDATQLYLGEIGYAPLLTA 72

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 73  EEEVFFARRALRGDEASRKRMIESNLRLVVKISRRYS-NRGLALLDLI 119


>gi|239981636|ref|ZP_04704160.1| RNA polymerase principal sigma factor hrdD [Streptomyces albus
           J1074]
 gi|291453499|ref|ZP_06592889.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|17366575|sp|Q59914|HRDD_STRGR RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|510454|emb|CAA56305.1| sigma factor [Streptomyces griseus]
 gi|291356448|gb|EFE83350.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 332

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 107/234 (45%), Positives = 150/234 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  AEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L+ 
Sbjct: 151 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNRENGRDPEPAEIAAELSS 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 211 TPERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 271 QLDDRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAH 324



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +AS  +      + + + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 10  QPAASGETGAAGSVRATGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAG 63


>gi|261880495|ref|ZP_06006922.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270332834|gb|EFA43620.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  171 bits (432), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 154/275 (56%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   +RKG  E   AK +++ +NLR V+SVAK+Y ++
Sbjct: 16  EALDRYLVEIGRAPLISIDEEIELSQKIRKGGREGQRAKDKLITSNLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KA EKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLINEGNIGLIKATEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +       + +R P+ +EIA+ + +    +R  +      +S++ P  +++++
Sbjct: 136 GTLSKINKEINNFEQRHERRPSTQEIAEAIDVEAGKIRMSMMADGHHVSIDAPFQEDESN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +       A   ++ +    VL S L  RE  ++R  FGIG +    LEE+
Sbjct: 196 SMADIMASGDDTRTDKRADHESMAQELNTVLESVLKEREITIIRECFGIGCHE-LGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  K+I KL+     K L  +L
Sbjct: 255 GDRLGLTRERVRQIREKSIAKLRESGNIKILMKYL 289


>gi|251733365|emb|CAR82432.1| RNA polymerase sigma factor [Agrobacterium rubi]
          Length = 202

 Score =  171 bits (432), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 121/192 (63%), Positives = 148/192 (77%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+  V SLSLNQ+R+D LVEQLYDISKR+M NEG+LLRLA
Sbjct: 11  ACTGTLSTGQERRYKELKDQLITAVKSLSLNQNRVDSLVEQLYDISKRLMQNEGKLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG+KRD FLE++ G ELDP+W+    +     WK F   E ++I  IR EI++++ ET
Sbjct: 71  ESYGVKRDSFLEQYHGAELDPNWMKSIANLAAKGWKEFAREENNTIRDIRLEIQNLAQET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|47459124|ref|YP_015986.1| RNA polymerase sigma factor [Mycoplasma mobile 163K]
 gi|47458453|gb|AAT27775.1| DNA-directed RNA polymerase sigma factor [Mycoplasma mobile 163K]
          Length = 488

 Score =  171 bits (432), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 111/269 (41%), Positives = 169/269 (62%), Gaps = 11/269 (4%)

Query: 422 ISISEFRHIVSMVR--KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           +   E       +   +   +   A   ++  NLRLVI+ AKKY NRGL F+DLI EGN 
Sbjct: 215 LDKEEEIKYSKQIEEDRNGRKGKKAFNALIHHNLRLVINNAKKYKNRGLSFIDLISEGNA 274

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+KAA K+D+  G+KFSTYA WWV+QAITR++ADQ+  +R+PVHM + I+K+++  R +
Sbjct: 275 GLIKAATKYDYRRGFKFSTYATWWVRQAITRAVADQARIVRVPVHMVETINKIIKIEREL 334

Query: 540 SNKIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
             ++   PT ++IA+K       E V+ + KI  +PISL+  IG +D S   DF++D++ 
Sbjct: 335 HQELGVPPTDKQIAEKYGNNFTAEKVQYIRKINIDPISLDKSIGKDDDSSFSDFVKDESV 394

Query: 598 VSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTD------HTLEEVGKQFC 650
           VSPL+ A Q  L    T +L   L   E  +++ RFGIG++ D      H+LEE+  +  
Sbjct: 395 VSPLEFASQNELSGILTDILEKHLDEAERDLIKKRFGIGVDKDGNRISSHSLEELAAELQ 454

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +++E++R +E+K +RKLKHP + KKL+ F
Sbjct: 455 ISKEKVRSLESKILRKLKHPQKRKKLKEF 483


>gi|261822742|ref|YP_003260848.1| RNA polymerase sigma factor RpoS [Pectobacterium wasabiae WPP163]
 gi|5912456|emb|CAB56153.1| RpoS protein [Pectobacterium carotovorum]
 gi|261606755|gb|ACX89241.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           wasabiae WPP163]
          Length = 330

 Score =  170 bits (431), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDIPSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 46/117 (39%), Gaps = 12/117 (10%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
               G++V D   L +E+ ++          + S   +       +   D  ++YL E+G
Sbjct: 17  FDENGLDVFDDKALAEEDTND----------SDSAEDELLSQGVPQRVLDATQLYLGEIG 66

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
              LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 67  YSPLLTAEEEVYFARRALRGDIPSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|288926192|ref|ZP_06420119.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608841|ref|ZP_07883815.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337084|gb|EFC75443.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249448|gb|EFU29463.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  170 bits (431), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 158/275 (57%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  IS E  +SI E   +   +RKG  E   AK+++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLAEISHEPMVSIDEETELAQAIRKGGREGERAKEKLVRANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLGLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   +   +  R P+ +E+A+   +  + + + L      +S++ P  ++D +
Sbjct: 136 GAVSKINQVTSKFVQEHNRRPSIQELAQITGIDEQKIEQSLNADSHHMSIDAPFAEDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++      VL + L  RE R+++  FGIG +    LEE+
Sbjct: 196 SMADVLASGDDSRTDKQVDFESMASELNNVLKNVLKEREIRIVKECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++  +TRER+RQI  K+I K++    ++ L  +L
Sbjct: 255 GEEMGLTRERVRQIREKSILKIRESGNARILMKYL 289


>gi|161502017|ref|YP_001569129.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863364|gb|ABX19987.1| hypothetical protein SARI_00033 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 330

 Score =  170 bits (431), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFSFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|251733387|emb|CAR82443.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733389|emb|CAR82444.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733391|emb|CAR82445.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
          Length = 202

 Score =  170 bits (431), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 120/192 (62%), Positives = 146/192 (76%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLNQ+RID LVEQLYDISKR+  NEG LLRLA
Sbjct: 11  AATGTLSPAQERRYKELKDELIKAVKSLSLNQNRIDALVEQLYDISKRLTQNEGRLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG++R+ FLE++ G ELDP+W+    +     WK F   E  +I  IR EI++++ ET
Sbjct: 71  ESYGVRREAFLEQYSGAELDPNWMKSISNLAGKGWKEFARAENQTIRDIRQEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           GISI+EFR IVSMV+KGE EA IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 GISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|313678638|ref|YP_004056378.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
 gi|312950821|gb|ADR25416.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
          Length = 509

 Score =  170 bits (431), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 120/321 (37%), Positives = 187/321 (58%), Gaps = 15/321 (4%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           LE     E+D   +S      + + KN +    D +      I        +   E   +
Sbjct: 194 LEDFSAEEID---LSANLSVKKEDLKNKLTETNDIVKWYMRWIGKYGKL--LQPEEEFEL 248

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            + + KG      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G++KA +K++ 
Sbjct: 249 ATEMDKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIIKAVQKYNV 308

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+KFSTYA WW++QAITR++ADQS T+R+PVHM + I+K+ +  R +  +   +PT E
Sbjct: 309 NKGFKFSTYATWWIRQAITRAVADQSRTVRVPVHMVETINKITKIERELQQENGVDPTDE 368

Query: 551 EIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++       E VR + KI  +PISL+  IG E+ S   DF++D++ V+P++ A    
Sbjct: 369 EIAQRYGNDFTAEKVRHIRKINIDPISLDKQIGKENDSSFSDFVKDESVVNPVEYASHEE 428

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEA 661
           L ET   +L  +L   E  ++  R+G+G + +       +LEE+  +  V++ERIRQIE 
Sbjct: 429 LVETLNTILKDTLDADEYELICKRYGVGFDNNGEKYKVFSLEELALERNVSKERIRQIEN 488

Query: 662 KAIRKLK-HPSRSKKLRSFLD 681
           K +RKLK  P RS+ L+ F++
Sbjct: 489 KILRKLKSSPERSRYLKVFME 509



 Score = 37.9 bits (86), Expect = 6.0,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREGE 139
           D LE E+ S + +DL+++ S     L+ +       T+D V+ Y+R +G   +LL  E E
Sbjct: 190 DTLELEDFSAEEIDLSANLSVKKEDLKNKLTE----TNDIVKWYMRWIGKYGKLLQPEEE 245

Query: 140 IAIAKRIEAGRAMMMAS 156
             +A  ++ G      +
Sbjct: 246 FELATEMDKGGFRGKRA 262


>gi|288819153|ref|YP_003433501.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|288788553|dbj|BAI70300.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|308752737|gb|ADO46220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 310

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 88/303 (29%), Positives = 159/303 (52%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K ++    ++  E + +    +        A +++VE+NLR VI++AK+Y   GL
Sbjct: 10  INQYLKKVAKIPLLTPEEEKEVARRAK---EGDQEAFRKLVESNLRFVINIAKQYLGYGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI  GN GL++AA++FD   G KF +YA+WW++QAI ++++ Q+  +RIP+     
Sbjct: 67  PLSELIAAGNHGLIEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQAHV 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLA------------------------------- 557
           I+++     R+  +++REPTPEE+A + +                               
Sbjct: 127 INRIGSIYSRLFRELEREPTPEEVAIEYSKEILSRELERELGRKPTKDEVEQRFKKEGFK 186

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  E V K L++ + P+SL+ P+G+ + +   DF+         +  I   L +    +L
Sbjct: 187 ISPEEVEKCLQVCRIPLSLDAPVGENEDTFFVDFLSQHGTADVEERIINEVLEKEIGDML 246

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L  +E RV+ +RFG+      TL E+G    ++RER+RQ+E +A+RKL++ +  + L+
Sbjct: 247 DRLPEKERRVIELRFGLRGEEPRTLREIGDILNISRERVRQLETRALRKLRNMAMKRHLK 306

Query: 678 SFL 680
            FL
Sbjct: 307 DFL 309



 Score = 44.8 bits (104), Expect = 0.052,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I LL+ E E  +A+R + G       L ES L F  +I    +       L E
Sbjct: 13  YLKKVAKIPLLTPEEEKEVARRAKEGDQEAFRKLVESNLRF--VINIAKQYLGYGLPLSE 70

Query: 184 II 185
           +I
Sbjct: 71  LI 72


>gi|119503379|ref|ZP_01625463.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119461025|gb|EAW42116.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 430

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 84/242 (34%), Positives = 140/242 (57%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R  +  +R+     + A+ ++V  NLRLV S+A +Y  RG+ +LDL+QEG +GL++AAE
Sbjct: 171 ERETMKALRRELRIYTEARDKLVMHNLRLVYSIAGRYKGRGVSYLDLVQEGTLGLIRAAE 230

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  G++FSTY   W+ QA+ R + D    IR+P H+++++ ++ +       +   E
Sbjct: 231 KFEFEKGFRFSTYCFNWITQAVRRYVGDVGTLIRLPTHVQEQMGRLYKEKAIEQLRTGVE 290

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P  E +A KL M +E  R++L++    +SL+ P  D+D   L D +  +      DSA Q
Sbjct: 291 PDEETLAAKLGMDIEKTRQLLQMRNLGVSLDAPRFDDDEGTLLDTLSGEPYGGTEDSAEQ 350

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A+L +     + +L P E+RV+  R+G+      +  EV     V+RE +RQ+E  A+RK
Sbjct: 351 ASLHKFLGGAVDALEPSEQRVVVARWGLHDGPPLSRAEVADSLGVSREWVRQLERSALRK 410

Query: 667 LK 668
           LK
Sbjct: 411 LK 412


>gi|11133042|sp|Q60012|HRDD_STRVF RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|1407711|gb|AAB03580.1| sigma factor [Streptomyces viridifaciens]
          Length = 332

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 104/232 (44%), Positives = 148/232 (63%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFSTYA
Sbjct: 93  GERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYA 152

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P E+A +L    
Sbjct: 153 TWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEVAAELGSTP 212

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V  VL   ++P+SL   + D   +  GD +ED +AVSP  S +     E    ++  L
Sbjct: 213 ERVIDVLDWARDPVSLNMAVDDAGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIGRL 272

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 273 DQRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324



 Score = 37.9 bits (86), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +++   +      R    + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  SATGETADSASSVRAHGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAG 64


>gi|284431339|gb|ADB84484.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. vitians]
 gi|284431343|gb|ADB84486.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. vitians]
 gi|284431345|gb|ADB84487.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. vitians]
          Length = 294

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 82/337 (24%), Positives = 139/337 (41%), Gaps = 48/337 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDDAADDDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGR 377
           L  +   I  +E ++L LA +   + R  F+   +G 
Sbjct: 258 LRGVVNGIKDHERKVLHLATAVARMPRKDFIRSWEGN 294


>gi|269140216|ref|YP_003296917.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|228204742|gb|ACP74149.1| RNA polymerase sigma factor [Edwardsiella tarda]
 gi|267985877|gb|ACY85706.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|304560047|gb|ADM42711.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda FL6-60]
          Length = 328

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 98/271 (36%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       ++K M+E+NLRLV+ ++++Y+N
Sbjct: 54  LDATQLYLGEIGYAPLLTAEEE---VFFARRALRGDEASRKRMIESNLRLVVKISRRYSN 110

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 111 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 170

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV  V ++L++ +   S++TP+G +  
Sbjct: 171 VKELNVYLRTARELSHKLDHEPSAEEIAERLEKPVHDVSRMLRLNERITSVDTPLGGDSE 230

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D     +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 231 KALLDILTDENESGPEDCTQNDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 290

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 291 GREIGLTRERVRQIQVEGLRRLREILQMQGL 321



 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/108 (28%), Positives = 45/108 (41%), Gaps = 3/108 (2%)

Query: 79  DGDDLED--EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           D  +LED  E+G ++   +  S  N     +    S  +   D  ++YL E+G   LL+ 
Sbjct: 13  DEVELEDGVEDGFDEKALVEESMENDITDDELLSQSVSQRVLDATQLYLGEIGYAPLLTA 72

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 73  EEEVFFARRALRGDEASRKRMIESNLRLVVKISRRYS-NRGLALLDLI 119


>gi|158339615|ref|YP_001521004.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158309856|gb|ABW31472.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 86/260 (33%), Positives = 154/260 (59%), Gaps = 5/260 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K I+    +S  E    + + R+ +  +  AK+ M+E NLR V+S+AKKY NRGL  LDL
Sbjct: 13  KEIARYPLLSHEEE---IQLARQAQAGSLRAKQRMIECNLRFVVSIAKKYQNRGLPLLDL 69

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG+IGL  A +KFD   G +FSTYA WW++Q IT ++  +S  I +P +  D + K+ 
Sbjct: 70  IQEGSIGLSTAVDKFDLAQGCRFSTYAYWWIRQGITAAVRAKSRPIYLPHYHWDTVGKIK 129

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  R ++ ++ REP+  E+++   +  + + + L++ ++  SL+  +G +    L D + 
Sbjct: 130 KHFRVLTQQLGREPSLSELSEATNIKPKTISRTLQLFQQISSLDQLVGPQQKDTLLDMLA 189

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            ++  +    ++Q  L +  ++V+ASL  RE  VL  R+G+  +   +++E+G+Q  ++ 
Sbjct: 190 GEDQPTHYLESLQ--LDDELSQVMASLDERERFVLSQRYGLEDDHPKSMKEIGQQIGLSH 247

Query: 654 ERIRQIEAKAIRKLKHPSRS 673
           E IR I  K ++KL+  ++S
Sbjct: 248 EGIRLILKKIMQKLERYAQS 267



 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------- 171
           D +  + +E+    LLS E EI +A++ +AG       + E  L F   I  +       
Sbjct: 6   DSLHFFFKEIARYPLLSHEEEIQLARQAQAGSLRAKQRMIECNLRFVVSIAKKYQNRGLP 65

Query: 172 --DELNDGTTLLREIIDLEAC 190
             D + +G+  L   +D    
Sbjct: 66  LLDLIQEGSIGLSTAVDKFDL 86


>gi|161833810|ref|YP_001598006.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
 gi|152206300|gb|ABS30610.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
          Length = 351

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 142/238 (59%), Gaps = 1/238 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A   +V+ANLR VIS+AK+Y N+GL   DLI EGN GL+K   +FD   G+K  +Y +W
Sbjct: 113 YALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVW 172

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I ++I+D++  +R P +     +KV +T  ++  K+K  P+ + I+  L +  + 
Sbjct: 173 WIRQSILQAISDKARCVRYPTNKLAFYNKVNKTYSKLEQKLKMPPSIKYISDYLNVSEKD 232

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V + L  + +  SL+ P+G+ D S+L D I+   +     S  + +L++    +L +L+ 
Sbjct: 233 VEEALINSIKHTSLDAPLGEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKILLETLSE 292

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +++ + +G+G      LE++     +TRER RQIE  AI++LK  SR + L S+L
Sbjct: 293 RESQIITLHYGLGCF-SMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKEILLSYL 349


>gi|195953303|ref|YP_002121593.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
 gi|195932915|gb|ACG57615.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
          Length = 311

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 154/304 (50%), Gaps = 35/304 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K +S    ++  E +      +        A K +VEANLR V+SVAK+Y   G+
Sbjct: 10  INQYMKRVSSVKLLTPQEEKEFAKRAK---AGDKEALKALVEANLRFVVSVAKQYMGYGI 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI  GN+GL++AA +FD     KF +YA+WWV+QAI ++++ Q+  +RIPV     
Sbjct: 67  PLSELIAAGNLGLLEAATRFDPDKNVKFISYAVWWVRQAIMQALSQQTGAVRIPVKHSHL 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLA------------------------------- 557
           I  V      +  +++REPT +EIA  +                                
Sbjct: 127 ISAVGLAYNELLKELEREPTYKEIADYINKKNIIREFKKETGFAPTEEELEQSMTQEHKY 186

Query: 558 -MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  E V+K L+I K P+SL+TP+GD   +   D +   +     +  I+  L +    +
Sbjct: 187 TVTEEDVKKCLQICKTPLSLDTPVGDNPDTLFVDLLSISDTDEIEEGVIKDVLEKELHDI 246

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++ L  +E +VL +R+G+  N   TL E+G    ++RER+RQ+E +AI+KL+  +  + L
Sbjct: 247 ISKLPEKERKVLELRYGLNGNEPLTLREIGDALGISRERVRQLETRAIKKLRSFALKRHL 306

Query: 677 RSFL 680
           + FL
Sbjct: 307 KDFL 310



 Score = 44.4 bits (103), Expect = 0.071,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y++ + S++LL+ + E   AKR +AG    + +L E+ L F  ++    +       L E
Sbjct: 13  YMKRVSSVKLLTPQEEKEFAKRAKAGDKEALKALVEANLRF--VVSVAKQYMGYGIPLSE 70

Query: 184 II 185
           +I
Sbjct: 71  LI 72


>gi|46201746|ref|ZP_00054445.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 756

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 106/247 (42%), Positives = 147/247 (59%), Gaps = 7/247 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +  G   A  A++    ANL+LV+  AKK+   GL + D IQEGN+GL+KA E+FD  
Sbjct: 515 RRMEAGLETARRARERFALANLKLVVWGAKKF--GGLTWPDRIQEGNLGLLKAVERFDHR 572

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KFSTYA WW+KQA+TR++AD+  TIRIPVH ++ + K+ R    +     RE  PEE
Sbjct: 573 RGAKFSTYATWWIKQAVTRAVADKGRTIRIPVHAQEAMRKLRRAQNEVFALTGREALPEE 632

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + +   +P+  VR+ L + +EP SL+        + +           P +    A ++ 
Sbjct: 633 VGELTEIPLARVRRFLAVAEEPASLDVEEVGLHAAEMA-----SREPDPEERLAVAEIKA 687

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                L  L PRE  V+R+RFGIG   ++TLEE+G+QF VTRERIRQIEAKA+RKL HP 
Sbjct: 688 MVRGQLELLPPREATVIRLRFGIGCEREYTLEEIGQQFGVTRERIRQIEAKALRKLSHPG 747

Query: 672 RSKKLRS 678
           R K L+ 
Sbjct: 748 RIKALQG 754



 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/126 (23%), Positives = 56/126 (44%), Gaps = 10/126 (7%)

Query: 65  DTVAMLSNMGINVVDGD---DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +   ML +MG+ V D     D   E G+ D  D       +      R  +++R+  DP+
Sbjct: 299 NLRVMLGDMGVVVDDDPFSPDRPSETGASDDEDDRFQDEVAEGLAFLRNLNSNRA--DPL 356

Query: 122 RMYLREMGSIEL--LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
             Y   +G +    L+R+ E ++A  IE G    +A++  SP     L+   + +  G T
Sbjct: 357 THY---IGGLPRDRLTRDDEASLAMEIERGTKAALAAVAMSPAAVSELLTAVEAVIRGET 413

Query: 180 LLREII 185
             ++++
Sbjct: 414 PPQDVL 419


>gi|288919497|ref|ZP_06413828.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
 gi|288349100|gb|EFC83346.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
          Length = 936

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 93/252 (36%), Positives = 135/252 (53%), Gaps = 4/252 (1%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E             E + A   +V  N RLV S+A KY  +GL+  DL Q G IGL++
Sbjct: 454 HEELGRDFRRQLGPTDERARAHDALVLHNQRLVHSIALKYEGQGLELEDLSQHGMIGLLR 513

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KFD   GYKFSTY+ WW++QAITR++AD+   IR+P H  +K++KV R   ++   +
Sbjct: 514 AVQKFDATKGYKFSTYSTWWIRQAITRALADEGRLIRLPAHFVEKVNKVRRVLGQLGMSV 573

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTSHLGDF--IEDKNAVSP 600
                   +A    +  + V + L    +  + L+TP+GD   + LG+   +       P
Sbjct: 574 DGADVVT-VAAAAGLSEQEVERCLLALHQRVVGLDTPVGDGGDTVLGELVGLPAPPDTDP 632

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                +  LR    R LA L+PR   V+R+RFG       TLE++G+ F VTRERIRQIE
Sbjct: 633 DTVLDRKWLRMAVARSLAELSPRNAEVVRLRFGFDDGEPRTLEQIGQVFGVTRERIRQIE 692

Query: 661 AKAIRKLKHPSR 672
            KA+ +L+ P R
Sbjct: 693 KKALEQLREPLR 704


>gi|39996625|ref|NP_952576.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|39983506|gb|AAR34899.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|298505638|gb|ADI84361.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           sulfurreducens KN400]
          Length = 328

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 111/305 (36%), Positives = 179/305 (58%), Gaps = 6/305 (1%)

Query: 366 KRDVFLERHQGR-ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
             + F+E      EL+        + P    KN      D  +K+   ++ I     ++ 
Sbjct: 18  PGEDFIEPEPTTFELEAAEEEEEPEEPAEVGKNIEQEHFDDAIKL--YLREIQRTRLLTA 75

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + +   + K       A+ +M+E+NLRLV+ +AK+Y NRGL FLDLI+EGN+GL+KA
Sbjct: 76  DEEKELAGRIAK---GDKAARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKA 132

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E+F      +FSTYA WW++Q+I R++ +QS TIR+PVH+ D I+K+++  R +  ++ 
Sbjct: 133 VERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDINKMLKITRELVQRLN 192

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           REP+ +E+A ++ +    VR+++ + K+  S+E P+G+     L D IED + VSP    
Sbjct: 193 REPSVKEVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSDYFLIDTIEDTSTVSPAVLL 252

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              N  E  ++  ASL+  E+ +L +RFG+      TL+ +G+ F VTRERIRQIEAK++
Sbjct: 253 EDLNKYEIVSKWFASLSENEQTILTLRFGLEDKEPQTLDTIGRSFGVTRERIRQIEAKSL 312

Query: 665 RKLKH 669
            KL+ 
Sbjct: 313 EKLRK 317



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/123 (23%), Positives = 48/123 (39%), Gaps = 6/123 (4%)

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDS-----LDLASSASNSSVFLQKRKDSADRSTDDPV 121
           ++ ++ +    +D  D   E+  E       L+ A          +  K+      DD +
Sbjct: 1   MSDMNELDEKELDAPDEPGEDFIEPEPTTFELEAAEEEEEPEEPAEVGKNIEQEHFDDAI 60

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           ++YLRE+    LL+ + E  +A RI  G       + ES L     I  R  +N G   L
Sbjct: 61  KLYLREIQRTRLLTADEEKELAGRIAKGDKAARDKMIESNLRLVVKIAKRY-INRGLPFL 119

Query: 182 REI 184
             I
Sbjct: 120 DLI 122


>gi|23428544|gb|AAL11451.1| RNA polymerase sigma-38 subunit [Serratia plymuthica]
          Length = 331

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 56  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 112

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 113 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 172

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 173 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 232

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 233 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 292

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 293 GREIGLTRERVRQIQVEGLRRLREILQLQGL 323



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 1/105 (0%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            ++  + E  ++   +   AS S +  +       +   D  ++YL E+G   LL+ E E
Sbjct: 18  DENATEAESFDEKALVEEEASESDLAEELLSQGVTQRVLDATQLYLGEIGYSPLLTAEEE 77

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 78  VYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 121


>gi|289805538|ref|ZP_06536167.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 321

 Score =  170 bits (431), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 96/269 (35%), Positives = 170/269 (63%), Gaps = 3/269 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G++  +TRER+RQI+ + +R+L+   +++
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQ 320



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|208821597|ref|ZP_03261917.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218690868|ref|YP_002399080.1| RNA polymerase sigma factor RpoS [Escherichia coli ED1a]
 gi|260856852|ref|YP_003230743.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|208741720|gb|EDZ89402.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218428432|emb|CAR09358.2| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli ED1a]
 gi|257755501|dbj|BAI27003.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|284922677|emb|CBG35765.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli 042]
          Length = 330

 Score =  170 bits (431), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|293977922|ref|YP_003543352.1| sigma-70 family RNA polymerase sigma factor [Candidatus Sulcia
           muelleri DMIN]
 gi|292667853|gb|ADE35488.1| RNA polymerase sigma factor, sigma-70 family [Candidatus Sulcia
           muelleri DMIN]
          Length = 342

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 142/238 (59%), Gaps = 1/238 (0%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A   +V+ANLR VIS+AK+Y N+GL   DLI EGN GL+K   +FD   G+K  +Y +W
Sbjct: 104 YALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVW 163

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++Q+I ++I+D++  +R P +     +KV +T  ++  K+K  P+ + I+  L +  + 
Sbjct: 164 WIRQSILQAISDKARCVRYPTNKLAFYNKVNKTYSKLEQKLKMPPSIKYISDYLNVSEKD 223

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           V + L  + +  SL+ P+G+ D S+L D I+   +     S  + +L++    +L +L+ 
Sbjct: 224 VEEALINSIKHTSLDAPLGEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKILLETLSE 283

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RE +++ + +G+G      LE++     +TRER RQIE  AI++LK  SR + L S+L
Sbjct: 284 RESQIITLHYGLGCF-SMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKEILLSYL 340


>gi|262364691|gb|ACY61248.1| RNA polymerase sigma factor RpoD [Yersinia pestis D182038]
          Length = 248

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 62/183 (33%), Positives = 98/183 (53%), Gaps = 1/183 (0%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDE 86
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++   D +D 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDADDL 65

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
             +E++ D    A+ ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRI
Sbjct: 66  MLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 125

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P     L+   D +  G + L ++I        E        T   
Sbjct: 126 EDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATTLVL 185

Query: 207 SYQ 209
           +Y 
Sbjct: 186 NYP 188


>gi|153875311|ref|ZP_02003170.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
 gi|152068225|gb|EDN66830.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
          Length = 314

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 99/267 (37%), Positives = 155/267 (58%), Gaps = 3/267 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            +++   R  +  I     ++  E        ++G      A+  M+E NLRLV+ +A+ 
Sbjct: 36  RENLDATRLYLNEIGKSKLLTAEEEIKYARRAQQGN---EAARNRMIEGNLRLVVKIARN 92

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y NRGL  LDLI+EGN+GLM+A  KFD   G++FSTYA WW++Q I R+I +Q+ TIR+P
Sbjct: 93  YMNRGLALLDLIEEGNLGLMRAVNKFDPEKGFRFSTYATWWIRQTIERAIMNQNRTIRLP 152

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           +H+  +I++ +RT   +S  +  EPT EEIAK L    + V K+L++ +  IS+++P  +
Sbjct: 153 IHVLKEINQCLRTNHVLSQTLDHEPTSEEIAKTLKKSKQEVEKLLEVNERAISMDSPWMN 212

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                L D I D+    P      A++ +     L+ LT ++  V+  RFGIG   + TL
Sbjct: 213 YSEKSLIDNIPDELNPDPRLILEDADIIKCLHLWLSQLTDKQRLVVERRFGIGNGDEATL 272

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           EE+G +  +TRER+RQI+  A  +LK 
Sbjct: 273 EEIGAELELTRERVRQIQITATERLKE 299



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           +  +S   ++ + +   R   D  R+YL E+G  +LL+ E EI  A+R + G       +
Sbjct: 19  TDDHSKSEVEPQTNFNRRENLDATRLYLNEIGKSKLLTAEEEIKYARRAQQGNEAARNRM 78

Query: 158 CESPLTFQALIIWRDELNDGTTLLREI 184
            E  L     I  R+ +N G  LL  I
Sbjct: 79  IEGNLRLVVKIA-RNYMNRGLALLDLI 104


>gi|159897807|ref|YP_001544054.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159890846|gb|ABX03926.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
          Length = 303

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 101/284 (35%), Positives = 156/284 (54%), Gaps = 24/284 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVS--------------MVRKGECEA----------SIA 444
           ++  +  I+    ++  E + +                 + +    A            A
Sbjct: 15  LQRYLNEIAETPLLAAEEEQKLTQIVHVARQAQPTPACRIERCPSCALFEQCVTKLKEPA 74

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +++V ANLRLV+S+AK+Y   GL F DLIQEGNIGLM A E+FD   G +FSTYA WW+
Sbjct: 75  HEQLVRANLRLVVSIAKRYRGFGLPFQDLIQEGNIGLMNAIERFDATKGVRFSTYATWWI 134

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QAITRS+A+Q   IR+PVH  + + KV R   ++   + REP+  EI+  L +P E + 
Sbjct: 135 RQAITRSLANQGRLIRLPVHRWELLIKVRRIETKLLQALGREPSANEISTALGVPEEKIC 194

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +L I + PISL TP  +E    LGD + D++    L+  + +   + T  +L  L+ +E
Sbjct: 195 DLLSIAQVPISLATPKNEETDMLLGDSLPDEDWEDELECLLTSIDAQYTRAMLNQLSEQE 254

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + VL +R+G+      +L EVG     TR+RI+QIEA A++ L+
Sbjct: 255 QEVLTLRYGLKDGKSRSLSEVGAVVGRTRQRIQQIEAGALQVLR 298


>gi|29830237|ref|NP_824871.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607348|dbj|BAC71406.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 331

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 107/235 (45%), Positives = 152/235 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            ++  AK   +++NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 90  ADSERAKDVFIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 149

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P EIA +L  
Sbjct: 150 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEIAAELDS 209

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 210 NPARVTDVLDWARDPVSLNMHVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 269

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 270 RLDQRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 324



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 34/89 (38%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
            S+A  +      R    + +  D V MYL E+    LL    E+ +++ IEAG      
Sbjct: 10  KSAAGGTDAASSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAGVFARQI 69

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
              E     +A     + L   +   +++
Sbjct: 70  LDGEEEPRAEATREELESLVADSERAKDV 98


>gi|332765694|gb|EGJ95907.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2930-71]
          Length = 330

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EG++GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGDLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLRETLQTQGL 322



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|182416213|ref|YP_001821279.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843427|gb|ACB77679.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 347

 Score =  170 bits (430), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 148/272 (54%), Gaps = 4/272 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A E D    ++  ++ I     ++  E   +   VR+     + A+  M+ ANLRLV+ +
Sbjct: 26  AAESDGRSSLQIYLQDIGQTPLLTAREEFALAERVRR---GDAGARDHMIRANLRLVVRI 82

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AK Y   GL   DLI EGN+GL+ A ++FD  +G K STYA WW++QAI R+ A  +  I
Sbjct: 83  AKDYAQYGLPLADLISEGNVGLIHAVDRFDPRIGGKLSTYAAWWIRQAIRRAFAHHARAI 142

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+PVHM D+I ++ R    +S +  RE T +E+A +L  PVE +         P SL+  
Sbjct: 143 RLPVHMLDRIARLRRAQASLSEQFGREATTDELAAELQAPVEKIALWKSAGDAPFSLDAA 202

Query: 580 IGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +G    S  L + I D+ A +       A        ++A+L  RE  +LR+RFG+  + 
Sbjct: 203 VGTGSESRRLSETIRDERAPTAFTQLRDATTARDLRAIIATLDVREATILRLRFGLDGDE 262

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL  V  +F +TRER+RQ+E +A++ +++ 
Sbjct: 263 PQTLHAVSLRFGITRERVRQLERRALQNVRNA 294



 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDD---PVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +D  S   ++   L +R  + D +  D    +++YL+++G   LL+   E A+A+R+  G
Sbjct: 4   IDNESIGPSTGEVLSRRSSARDAAESDGRSSLQIYLQDIGQTPLLTAREEFALAERVRRG 63

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
            A     +  + L    ++    +       L ++I
Sbjct: 64  DAGARDHMIRANLRL--VVRIAKDYAQYGLPLADLI 97


>gi|329902595|ref|ZP_08273157.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548742|gb|EGF33384.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 334

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 85/269 (31%), Positives = 154/269 (57%), Gaps = 5/269 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     +++++  H  ++ +        A++ M+E NLRLV+S+AK Y NRG+ 
Sbjct: 63  QLYLNQIGARALLTVAQEVHYATLAK---AGDFPARQVMIEHNLRLVVSIAKHYINRGVV 119

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++
Sbjct: 120 LLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIREL 179

Query: 530 HKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++V+R    +   +   ++ + ++IA       E V+ +L ++  P SL+ P+  +  S 
Sbjct: 180 NQVLRAKYHLEALHHDGKDASIDDIAHLTGRSAEDVQDILALSDHPASLDAPLDADPGSS 239

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +       P   A Q          LA L+ ++  ++  RFG+  +   TLE +  
Sbjct: 240 LMDLLPGDPGDGPEARAEQHETALLVRDWLARLSDKQRLIITRRFGLEDDDPATLEALAA 299

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  VTRER+RQ++ +A+ KLK    ++ +
Sbjct: 300 EIGVTRERVRQVQQEALIKLKRALATRGV 328



 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 5/110 (4%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD----SADRSTDDPVRMYLREMGSIELL 134
           DG   ED   +    D  + ++ ++V +    D     A   + D  ++YL ++G+  LL
Sbjct: 16  DGASNEDGLDARGDGDADNDSAGATVLVDSIDDIRKVLASELSTDTTQLYLNQIGARALL 75

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +   E+  A   +AG       + E  L     I     +N G  LL  I
Sbjct: 76  TVAQEVHYATLAKAGDFPARQVMIEHNLRLVVSIAKHY-INRGVVLLDLI 124


>gi|270057069|gb|ACZ59656.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 296

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 86/339 (25%), Positives = 139/339 (41%), Gaps = 44/339 (12%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+      
Sbjct: 1   PVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQL 60

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L +II     I P             +         E +  D  E E + E     S D
Sbjct: 61  RLSDII--SGFIDPNE-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSD 113

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           D       PE A     +L    + +  ++                              
Sbjct: 114 DEGDGGPDPEVAREKFGDLRAQYEVTRLSI------------------------------ 143

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L
Sbjct: 144 -----QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKL 198

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+      E +  W  Y K   +      +  + + +L+   +++ I  
Sbjct: 199 CVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSTRLLEMD-EEVLRSIGKLQQIEE 257

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           ETG+SI++ + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 258 ETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVI 296


>gi|291464748|gb|ADE05832.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 300

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 90/342 (26%), Positives = 141/342 (41%), Gaps = 44/342 (12%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+R GEI IAKRIE G   + +S+ E P     L+   D+   
Sbjct: 1   TTDPVRMYMREMGTVELLTRGGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L +II            GF    E                          E  A  
Sbjct: 61  EQLRLSDII-----------SGFIDPNE-------------------------TEDMAPT 84

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           +    S++       E++E   DEDED  +                   E+   Y     
Sbjct: 85  ATHIGSELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV--- 141

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                ++ QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +
Sbjct: 142 ---TRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERII 198

Query: 357 LRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
           ++L  +   + +  F+      E +  W  Y K   +      V  + D I +   +++ 
Sbjct: 199 MKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQ 257

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           I  ETG+SI++ + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 258 IEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVI 299


>gi|162458688|ref|NP_001104923.1| sigma factor SIG2A [Zea mays]
 gi|4336606|gb|AAD17854.1| sigma factor SIG2A [Zea mays]
          Length = 539

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 153/247 (61%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK        K  MV +N+RLVIS+A+++   G+ F DLIQEG  GL++ AEKFD   G
Sbjct: 288 LRKRLNYGIYCKNRMVTSNVRLVISIAREFEGPGMDFYDLIQEGMQGLIRGAEKFDSSKG 347

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQA+ +S+++QS   R+P HM +  ++V    +R+  K++R PT EEIA
Sbjct: 348 FRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASYRVKECTKRLRRKLRRRPTNEEIA 407

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               +P++ V   + + K  +SL++ IG  D ++  +   D +A +  +   + ++++  
Sbjct: 408 VDTGIPIKRVEAAVNLPKYSVSLDSKIGSTDMTY-QEVTADPSAETAEEMLNRMSMKKDV 466

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L +LT RE++V+ +RFG+      TL+E+G    V+RERIRQIE+ A RKL+   + 
Sbjct: 467 HMALDTLTTREKQVVVLRFGLEDGRIRTLQEIGNIMGVSRERIRQIESGAFRKLRSKKKV 526

Query: 674 KKLRSFL 680
           K L+ +L
Sbjct: 527 KALKDYL 533


>gi|291287615|ref|YP_003504431.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
 gi|290884775|gb|ADD68475.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
          Length = 301

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 83/273 (30%), Positives = 157/273 (57%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ + SIS    ++ ++   I   ++        A   ++  NL+ V+S+A +Y N GL
Sbjct: 33  LKHYLNSISAYKPMTKAQEFAIGERIQ---AGDEDALNTLILCNLKFVVSIANRYRNTGL 89

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+I +GN+GL++AA++FD     KF +YA+WW++Q+I +++A+QS T+++P+     
Sbjct: 90  PIADIINQGNLGLVEAAKRFDHTKDVKFISYAVWWIRQSIIQALAEQSGTVKLPIKQAGI 149

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+     +++ K+ REPT  E+A++L M    +  VL++++  +SLE PI D +    
Sbjct: 150 LYKINGATEKLNKKLNREPTASELAEQLEMDEADIENVLRVSRNYLSLEAPIKDGEDRSF 209

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +E        +  I   L+     ++  L  RE +++  RFG+      TLEE+G+ 
Sbjct: 210 IDLLE-SGTKDIEEDIISKTLKTALDDIVDELDERESQIIEWRFGLNEEAPKTLEEIGEL 268

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             ++RER+RQ+E +A+ KL+  +   KL+ FL+
Sbjct: 269 MDISRERVRQLETRALSKLRKKAMKNKLQDFLN 301


>gi|282881579|ref|ZP_06290248.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
 gi|281304565|gb|EFA96656.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
          Length = 290

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 91/275 (33%), Positives = 150/275 (54%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     R   +  R P+  E++    +  E + + +      +S++ P  D + +
Sbjct: 136 GSLNKINHEINRFEQEHHRRPSITELSDATNIDEEKIGQSMMADGHHVSIDAPFQDGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL   L  RE  +++  FGIG +    LEE+
Sbjct: 196 TMLDVMPSGDDSRTDRQVDHESMAQELNTVLNKVLKDREITIIKECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGNAKILMKYL 289



 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIID 186
           L ++ID
Sbjct: 79  LTDLID 84


>gi|328883104|emb|CCA56343.1| RNA polymerase principal sigma factor HrdD [Streptomyces venezuelae
           ATCC 10712]
          Length = 333

 Score =  170 bits (430), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 107/235 (45%), Positives = 149/235 (63%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 AK   +++NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFS
Sbjct: 91  YAAGERAKDLFIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFS 150

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  REP P EIA +L 
Sbjct: 151 TYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGREPEPAEIAAELD 210

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
              E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++
Sbjct: 211 TKPERVVDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLI 270

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  R   ++RMR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  + 
Sbjct: 271 DKLDHRTASIIRMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKMAH 325



 Score = 38.3 bits (87), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 2/92 (2%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMM 153
            S+ S ++     R    + +  D V MYL E+    LL    E+ +++ IEAG     +
Sbjct: 11  TSATSGAARASSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVYARQI 70

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREII 185
           +    ES     +          G       I
Sbjct: 71  LDGEVESEAAGASREELEALYAAGERAKDLFI 102


>gi|251788478|ref|YP_003003199.1| RNA polymerase sigma factor RpoS [Dickeya zeae Ech1591]
 gi|247537099|gb|ACT05720.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya zeae
           Ech1591]
          Length = 330

 Score =  170 bits (430), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDLSSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/119 (22%), Positives = 45/119 (37%), Gaps = 12/119 (10%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G++V D   L +EE  +  L      S  +               D  ++YL E
Sbjct: 15  AEFDENGVDVFDDKALAEEETGDSDLLDEELLSQGTAQ----------RVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +G   LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDLSSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|255531277|ref|YP_003091649.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344261|gb|ACU03587.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  170 bits (429), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 87/272 (31%), Positives = 152/272 (55%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +  I+    +S+ E   +   +RK       A   +V+ANLR V+SVAKKY N+G+
Sbjct: 18  IEKYLYDIARIDLLSVEEEIVLAQKIRK---GDQSALDRLVKANLRFVVSVAKKYQNQGI 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA++FD   G+KF ++A+WW++Q+I  +IA+Q   +R+P +    
Sbjct: 75  RLSDLIAEGNLGLIKAAQRFDETKGFKFISFAVWWIRQSIMIAIAEQKRIVRLPANQIGG 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I K+ +    +  +++R P+ EE+ + + +P E V   L       SL+T I +E    L
Sbjct: 135 IMKINKAMADLEQQLERVPSLEEVCEFIELPEEKVVDYLHHAPMTTSLDTVIAEESGFTL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + IED N      + +Q ++     R++  L  RE+ +L M +G+G      L+E+G +
Sbjct: 195 AETIEDTNVEKTDTTVLQHSVTVDVKRLMRGLPEREKEILSMFYGLGGYPAIGLDEIGGK 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             + +ER+RQI+ KA++ L+       +  ++
Sbjct: 255 MNLGKERVRQIKDKALKTLRSEQPKAYMMEYI 286



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K + S      D +  YL ++  I+LLS E EI +A++I  G    +  L ++ L F  +
Sbjct: 5   KIEQSITNRDSDSIEKYLYDIARIDLLSVEEEIVLAQKIRKGDQSALDRLVKANLRF--V 62

Query: 168 IIWRDELNDGTTLLREII 185
           +    +  +    L ++I
Sbjct: 63  VSVAKKYQNQGIRLSDLI 80


>gi|258648419|ref|ZP_05735888.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851166|gb|EEX71035.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 286

 Score =  170 bits (429), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 95/273 (34%), Positives = 156/273 (57%), Gaps = 4/273 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   +  I  E  IS  E   +   + K     + A +++ +ANLR V+SVAK+Y N+G
Sbjct: 17  ALDKYLVEIGREGLISTDEEVELAQRIHK---GDAEALEKLTKANLRFVVSVAKQYQNQG 73

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGN+GL++AA+KFD   G+KF +YA+WW++Q+I ++I++QS  +R+P++   
Sbjct: 74  LALNDLIDEGNLGLIRAAQKFDETRGFKFISYAVWWIRQSILQAISEQSRIVRMPLNQVG 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              K+ +       + +R P+ +E+A  L   V  V++ +    + +S++ P  D+D++ 
Sbjct: 134 FQSKLTKAIVNFEQEFERRPSVQELADILDTDVAKVQEAMGTNGKKVSVDAPFQDDDSNS 193

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D + D+NA    D   + +L       L +LT RE  VL+M FGIG N   T EEV  
Sbjct: 194 LIDIMTDENAPGTDDQMEKESLSSDLDAALGTLTERERLVLKMLFGIGRNE-MTAEEVAN 252

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              +TRER+RQI+ +A+R+L+       L  +L
Sbjct: 253 SLSLTRERVRQIKERALRRLREADNIHILTKYL 285



 Score = 44.1 bits (102), Expect = 0.088,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G   L+S + E+ +A+RI  G A  +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLVEIGREGLISTDEEVELAQRIHKGDAEALEKLTKANLRF--VVSVAKQYQNQGLALND 78

Query: 184 IID 186
           +ID
Sbjct: 79  LID 81


>gi|188090554|gb|ACD49511.1| RNA polymerase sigma factor [Xanthomonas oryzae]
          Length = 290

 Score =  170 bits (429), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +     +  +     + P+  E                           V 
Sbjct: 170 DEDALDEDDDEDGDDAAAEEEVGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMQNLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|271501815|ref|YP_003334841.1| RpoD subfamily RNA polymerase sigma-70 subunit [Dickeya dadantii
           Ech586]
 gi|270345370|gb|ACZ78135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech586]
          Length = 330

 Score =  170 bits (429), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 12/119 (10%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G++V D   L +EE S+  L      S  +               D  ++YL E
Sbjct: 15  AEFDENGVDVFDDKALAEEETSDSDLLDEELLSQGTAQ----------RVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +G   LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVSSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|330817175|ref|YP_004360880.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
 gi|327369568|gb|AEA60924.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
          Length = 366

 Score =  170 bits (429), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 88  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 145 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 204

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 205 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 264

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 265 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNNIEPA 324

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 325 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 361


>gi|157369077|ref|YP_001477066.1| RNA polymerase sigma factor RpoS [Serratia proteamaculans 568]
 gi|157320841|gb|ABV39938.1| RNA polymerase, sigma 70 subunit, RpoD family [Serratia
           proteamaculans 568]
          Length = 332

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQMQGL 324



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L    ++ +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENATEAESFDEKALVEEEASESDLAEEELLSQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|146164092|gb|ABQ08723.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164097|gb|ABQ08724.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164102|gb|ABQ08725.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164105|gb|ABQ08726.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|146164119|gb|ABQ08727.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 293

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 85/335 (25%), Positives = 135/335 (40%), Gaps = 44/335 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P             +         E +  D  E E + +     S DD
Sbjct: 61  LSDII--SGFIDPNE-----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDD 113

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            +     PE A      L    + +  ++                               
Sbjct: 114 EADTGPDPEVAREKFGELRAQYEVTRLSI------------------------------- 142

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               Q + ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L 
Sbjct: 143 ----QNNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLC 198

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E D  W  Y K   +      V  + D +L+   +++ I VE
Sbjct: 199 VEQAKMPKKTFVAAFTNNECDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVE 257

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           TG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 TGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 292


>gi|225848935|ref|YP_002729099.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225644026|gb|ACN99076.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 285

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 82/275 (29%), Positives = 149/275 (54%), Gaps = 9/275 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+SI     ++  + + I+  ++        A ++++ +NLR VI++AK+Y   G+   
Sbjct: 13  YIRSIYKIPLLTPEQEKEILEKIK---LGDKEAFQKLILSNLRFVINIAKRYAGYGIPLQ 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  GNIGL++AA++FD   G KF +YA+WW+KQ+I  +++ +   IR P  ++    K
Sbjct: 70  DLISAGNIGLIEAAKRFDPSKGVKFISYAIWWIKQSIINTLSQEGDIIRKPTKIQSLFQK 129

Query: 532 VVRTARRMSNKIKREPTPEEIAK---KLAMPVEG--VRKVLKITKEPISLETPI-GDEDT 585
           +      + + + REP+ +EI     +  + VE   +   L   +  ISL+ PI   ++ 
Sbjct: 130 ISNAYFYLKDSLNREPSVDEIHSFLLREGLEVEKDTIENYLFFNQHFISLDEPILSQDED 189

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            HL D I +          I  ++ +    +L +L+PRE+++L  RFG+      TL+EV
Sbjct: 190 IHLSDTISNSGTEDIERKLIDEDILKFIDELLDTLSPREKQILIHRFGLYGEEPKTLKEV 249

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G    ++RER+RQIE + ++KL+  +  +K+   +
Sbjct: 250 GNIVGISRERVRQIEIRLLKKLRKLATKRKIEDLI 284



 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           V  Y+R +  I LL+ E E  I ++I+ G       L  S L F  +I            
Sbjct: 10  VEYYIRSIYKIPLLTPEQEKEILEKIKLGDKEAFQKLILSNLRF--VINIAKRYAGYGIP 67

Query: 181 LREII 185
           L+++I
Sbjct: 68  LQDLI 72


>gi|256376033|ref|YP_003099693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255920336|gb|ACU35847.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 320

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 100/245 (40%), Positives = 161/245 (65%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   +   AK  M+ ANLRLV+SVAKK++ RGL  LD++QEGN+GL++A EKFD+ 
Sbjct: 71  RALNQVVADGRDAKDHMIRANLRLVVSVAKKHSFRGLPLLDVVQEGNLGLIRAVEKFDYS 130

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA+WW++QAI R +A+Q+ T+R+PVH+ +++ K+ +  R++  ++ REPT EE
Sbjct: 131 KGYKFSTYAIWWIRQAIERGLAEQTRTVRLPVHVVEELSKIKKAERKLRAELDREPTVEE 190

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A    +    V ++    +  ISLETP+GDE ++ + D IED +A S  D+  QA    
Sbjct: 191 LAGATGLRAPRVAELRDAGRATISLETPVGDEGSASVADLIEDADAASAYDAVEQAAFSS 250

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               ++ +L  R+  ++  R+G+     HTL+EV ++  +TRERIRQ+E +++R L+ P 
Sbjct: 251 ELRALVETLPARQALIVSRRYGLTDGRVHTLQEVAEELGLTRERIRQLEKESLRFLRDPQ 310

Query: 672 RSKKL 676
            ++ L
Sbjct: 311 HNRGL 315



 Score = 40.6 bits (93), Expect = 0.99,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           +  +    +R+ S   +  D    YLR++GS  LL+   E+ +++RIEAG
Sbjct: 4   TKPNADQSRRRASEQAADADLFGQYLRQVGSTPLLTAAEEVVLSRRIEAG 53


>gi|53719139|ref|YP_108125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei K96243]
 gi|53723558|ref|YP_103014.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 23344]
 gi|67639892|ref|ZP_00438721.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|76810144|ref|YP_333760.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121600326|ref|YP_993163.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124385284|ref|YP_001026062.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126440772|ref|YP_001059233.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126450398|ref|YP_001080670.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|126452489|ref|YP_001066500.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|134277449|ref|ZP_01764164.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|167002252|ref|ZP_02268042.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|167719257|ref|ZP_02402493.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei DM98]
 gi|167738254|ref|ZP_02411028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 14]
 gi|167815444|ref|ZP_02447124.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 91]
 gi|167823855|ref|ZP_02455326.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 9]
 gi|167845396|ref|ZP_02470904.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei B7210]
 gi|167893937|ref|ZP_02481339.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 7894]
 gi|167902387|ref|ZP_02489592.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei NCTC
           13177]
 gi|167910629|ref|ZP_02497720.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 112]
 gi|167918658|ref|ZP_02505749.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei BCC215]
 gi|217421435|ref|ZP_03452939.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|226197238|ref|ZP_03792815.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237812557|ref|YP_002897008.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|242315690|ref|ZP_04814706.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|254178572|ref|ZP_04885227.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|254179542|ref|ZP_04886141.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|254189067|ref|ZP_04895578.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|254197294|ref|ZP_04903716.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|254199960|ref|ZP_04906326.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|254206293|ref|ZP_04912645.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|254261861|ref|ZP_04952915.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
 gi|254297419|ref|ZP_04964872.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|254358292|ref|ZP_04974565.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|28394113|gb|AAO34104.1| rpoS [Burkholderia pseudomallei]
 gi|52209553|emb|CAH35506.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52426981|gb|AAU47574.1| RNA polymerase sigma factor [Burkholderia mallei ATCC 23344]
 gi|76579597|gb|ABA49072.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121229136|gb|ABM51654.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124293304|gb|ABN02573.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126220265|gb|ABN83771.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126226131|gb|ABN89671.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|126243268|gb|ABO06361.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|134251099|gb|EBA51178.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|147749556|gb|EDK56630.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|147753736|gb|EDK60801.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|148027419|gb|EDK85440.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|157807858|gb|EDO85028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|157936746|gb|EDO92416.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|160699611|gb|EDP89581.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|169654035|gb|EDS86728.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|184210082|gb|EDU07125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|217395177|gb|EEC35195.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|225930617|gb|EEH26627.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237506433|gb|ACQ98751.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|238520504|gb|EEP83963.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|242138929|gb|EES25331.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|243062069|gb|EES44255.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|254220550|gb|EET09934.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
          Length = 359

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 104/316 (32%), Positives = 172/316 (54%), Gaps = 13/316 (4%)

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK--IRNEIKSISVETGISISEFRH 429
             ++ R+ DP      +   + +  +F A     +    I++ +  ISV+  +++ E + 
Sbjct: 42  RDYESRDADPDESGEGRGDAQPDLDDFRALLQAELTADTIQHYLNRISVKPLLTVEEEQR 101

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
              + + GE E   A++ M+E NLRLV+S+AK Y NRG+  LDLI+EGN+GLM A EKFD
Sbjct: 102 YSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGVPLLDLIEEGNLGLMHAIEKFD 158

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK----- 544
              G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +          
Sbjct: 159 PTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEKNSMSTGEA 218

Query: 545 ---REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              RE + ++IA       E V  +L + +   SL+ P+  +  S L D + D  + SP 
Sbjct: 219 AERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPLDLDPASSLLDLLPDDQSQSPD 278

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  L   T   L+ L+ +   V+  RFG+      TLEE+  +  +TRER+RQI+ 
Sbjct: 279 AEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPATLEELADEMGLTRERVRQIQQ 338

Query: 662 KAIRKLKHPSRSKKLR 677
           +A+ +LK    S  +R
Sbjct: 339 EALVRLKRFFASNGVR 354



 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 26/112 (23%), Positives = 39/112 (34%), Gaps = 7/112 (6%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS------TDDPVRMYLREMGSIE 132
           + +D  D E   +S D     S       +      R+      T D ++ YL  +    
Sbjct: 33  EDEDAADNERDYESRDADPDESGEGRGDAQPDLDDFRALLQAELTADTIQHYLNRISVKP 92

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  LLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 143


>gi|282865528|ref|ZP_06274579.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282559572|gb|EFB65123.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 333

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 106/234 (45%), Positives = 148/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 92  AEGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 NTERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   ++RMR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 272 KLDNRTASIIRMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAH 325



 Score = 37.9 bits (86), Expect = 6.4,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMM 153
           ++ +  +      R    + +  D V MYL E+    LL    E+ +++ IEAG     +
Sbjct: 11  SAESGGTDRASSVRAGGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTIEAGVYAQQI 70

Query: 154 MASLCESPLTFQALIIWRDELNDGTT 179
           +    ES             + +G  
Sbjct: 71  LDGEVESEAGGAKREELEALVAEGER 96


>gi|213859421|ref|ZP_03385125.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 319

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 96/264 (36%), Positives = 167/264 (63%), Gaps = 3/264 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
           G++  +TRER+RQI+ + +R+L+ 
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLRE 315



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|6010736|gb|AAF01234.1|AF184103_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +T ER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTCERVRQIQVEGLRRLREILQTQGL 322



 Score = 51.0 bits (120), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|58698251|ref|ZP_00373170.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535223|gb|EAL59303.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 379

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 98/352 (27%), Positives = 178/352 (50%), Gaps = 25/352 (7%)

Query: 24  FDFSDDSWKKMIKLA-RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
            +      K ++  + ++ G++T +++N  L  +  SS+ ++D +++L + GINV++  +
Sbjct: 8   AEDKKKIIKDLVTKSIKKGGFITFDDINDKLSDENFSSDFIDDAISLLQDSGINVLESSE 67

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            E     ED    +  +            +     DDPVR+YL++M S++LLSR  EI I
Sbjct: 68  DE-----EDIPSNSDDSKLDDDDTSPNVTATLVQNDDPVRIYLQDMSSVKLLSRADEIEI 122

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AK+IE+ +  M+ ++ E+ +T + + +WRD+L++G  LLREIIDL+A    +        
Sbjct: 123 AKKIESEKHNMLRAIIETSVTLKVIKVWRDDLSNGALLLREIIDLDAIYNSDFN------ 176

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  K E    E+  +DV+++E   E A   S D++   DS   + E D  N D   
Sbjct: 177 ----VVPKEESEESEESAEDVEDSEDVSEDAEYCSDDEK---DSKKSDDEKDGNNEDISS 229

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            +   ++  ME  L PKV+ ALDEI  +  E   L+ N+ N       S + + L  ++ 
Sbjct: 230 VNLNVSILEMESDLLPKVIVALDEIITLTNEALILRKNSKNF------SNELENLYNQIW 283

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F + +
Sbjct: 284 SIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVY 335


>gi|270264030|ref|ZP_06192298.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
 gi|270042223|gb|EFA15319.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
          Length = 332

 Score =  170 bits (429), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 294 GREIGLTRERVRQIQVEGLRRLREILQLQGL 324



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L    ++ +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENATEAESFDEKALVEEEASESDLAEEELLSQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|125543279|gb|EAY89418.1| hypothetical protein OsI_10924 [Oryza sativa Indica Group]
          Length = 540

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 149/247 (60%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK        K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G
Sbjct: 289 LRKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKG 348

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA
Sbjct: 349 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIA 408

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               MP+  V   + + K  +SL + +G  D ++  +   D +  +  +   +  ++E  
Sbjct: 409 SDTGMPLRRVEAAMSLPKYTVSLTSKVGCTDMTY-QEITPDTSTETAEEMLHRWLMKEDV 467

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L+PRE +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + 
Sbjct: 468 DRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKV 527

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 528 QSLQHYL 534


>gi|167993163|ref|ZP_02574258.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205328726|gb|EDZ15490.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
          Length = 330

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRPLREILQTQGL 322



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|318056947|ref|ZP_07975670.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|318078687|ref|ZP_07986019.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actF]
          Length = 307

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 148/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             +  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 66  EASERAKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 125

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 126 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELGS 185

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 186 TPERVSDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAVSPEQSVMTLLRSEELDELIG 245

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 246 RLDERTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKLAH 299


>gi|313673100|ref|YP_004051211.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939856|gb|ADR19048.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 327

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 89/273 (32%), Positives = 162/273 (59%), Gaps = 4/273 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ I  I     ++  E   +   +++       A  +++ +N++ V+S+A +Y N G+
Sbjct: 59  IKDFINKIDKFKPLTREEEYELGKRIQQ---GDQEALNKLILSNIKFVVSMANRYKNTGV 115

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI +GN+GL++AA++FD   G KF +YA+WW++QA+ + +A+QS T+++P+     
Sbjct: 116 SLSDLINQGNLGLVEAAKRFDPDKGVKFISYAVWWIRQAMIQLLAEQSGTVKLPIKQASL 175

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+      +S K  REPT EEI++ L +P E +  +L ++K  +S E+PI D +    
Sbjct: 176 LYKINEAIETLSKKYHREPTSEEISEYLNIPKENIENILMVSKNYLSFESPIKDGEDRTF 235

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +E    +   D  I   L++T   ++  L  RE ++L+MR+G+      TLEEVG  
Sbjct: 236 LDLME-SRTIKVEDEVINHTLKDTLQSLIQELDEREAKILKMRYGLDGENPMTLEEVGNI 294

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             ++RER+RQIE++A+ KL+  +  K+L+ +L+
Sbjct: 295 LNISRERVRQIESRALSKLRKKAVKKRLQDYLN 327



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 52/112 (46%), Gaps = 2/112 (1%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           ++ ++  +  +EE  +++LD      + S   +  + +    TDD ++ ++ ++   + L
Sbjct: 13  VDELNESEDVNEEALDENLDAILEDLDISESPENLEIAISSLTDDSIKDFINKIDKFKPL 72

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +RE E  + KRI+ G    +  L  S    + ++   +   +    L ++I+
Sbjct: 73  TREEEYELGKRIQQGDQEALNKLILSN--IKFVVSMANRYKNTGVSLSDLIN 122


>gi|238921111|ref|YP_002934626.1| RNA polymerase sigma factor RpoS [Edwardsiella ictaluri 93-146]
 gi|238870680|gb|ACR70391.1| RNA polymerase sigma factor RpoS, putative [Edwardsiella ictaluri
           93-146]
          Length = 328

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       ++K M+E+NLRLV+ ++++Y+N
Sbjct: 54  LDATQLYLSEIGYAPLLTAEEE---VFFARRALRGDEASRKRMIESNLRLVVKISRRYSN 110

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 111 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 170

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+ EEIA++L  PV  V ++L++ +   S++TP+G +  
Sbjct: 171 VKELNVYLRTARELAHKLDHEPSAEEIAERLEKPVHDVSRMLRLNERITSVDTPLGGDSE 230

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+N   P D     +++++    L  L  ++  VL  RFG+      TLE+V
Sbjct: 231 KALLDILTDENESGPEDCTQNDDMKQSIVNWLFELNAKQREVLARRFGLLGYEAATLEDV 290

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 291 GREIGLTRERVRQIQVEGLRRLREILQMQGL 321



 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 31/108 (28%), Positives = 45/108 (41%), Gaps = 3/108 (2%)

Query: 79  DGDDLED--EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           D  +LED  E+G ++   +  S  N     +    S  +   D  ++YL E+G   LL+ 
Sbjct: 13  DEVELEDGVEDGFDEKDLVEESMENDITDDELLSQSVSQRVLDATQLYLSEIGYAPLLTA 72

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 73  EEEVFFARRALRGDEASRKRMIESNLRLVVKISRRYS-NRGLALLDLI 119


>gi|290959686|ref|YP_003490868.1| sigma factor HrdD [Streptomyces scabiei 87.22]
 gi|260649212|emb|CBG72326.1| sigma factor HrdD [Streptomyces scabiei 87.22]
          Length = 332

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 104/234 (44%), Positives = 151/234 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            ++  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  ADSERAKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L  
Sbjct: 151 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEIAAELGS 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 211 NADRVTDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +R
Sbjct: 271 RLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324



 Score = 39.1 bits (89), Expect = 2.7,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 34/89 (38%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           +S++  +      R    + +  D V MYL E+    LL    E+ +++ IEAG      
Sbjct: 11  SSASGRTDAARSVRASGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQVIEAGVFAQQI 70

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
              E      A     + L   +   ++I
Sbjct: 71  LDGEEEAQADATREELEALVADSERAKDI 99


>gi|254794681|ref|YP_003079518.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14359]
 gi|254594081|gb|ACT73442.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O157:H7
           str. TW14359]
          Length = 330

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  +    L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWPFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|307132339|ref|YP_003884355.1| RNA polymerase sigma-S (sigma 38) factor [Dickeya dadantii 3937]
 gi|306529868|gb|ADM99798.1| RNA polymerase, sigma S (sigma 38) factor [Dickeya dadantii 3937]
          Length = 330

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 169/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRLREILQVQGL 322



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/119 (23%), Positives = 45/119 (37%), Gaps = 12/119 (10%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     GI+V D   L +EE S+         S  +               D  ++YL E
Sbjct: 15  AEFDENGIDVFDDKALAEEETSDSDQLDEELLSQGTAQ----------RVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +G   LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVSSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|82778108|ref|YP_404457.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae Sd197]
 gi|81242256|gb|ABB62966.1| RNA polymerase, sigma S factor [Shigella dysenteriae Sd197]
          Length = 330

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 171/271 (63%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 292 GREIDLTRERVRQIQVEGLRRLREILQTQGL 322



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|311897949|dbj|BAJ30357.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 323

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 120/298 (40%), Positives = 171/298 (57%), Gaps = 13/298 (4%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKI------RNEIKSISVETGISISEFRHIV 431
           E D   V    D          A EV+  L+I      ++ +       G+S  E R I 
Sbjct: 23  EADRDLVGMYLDEIARTPLLDAAEEVELSLRIEAGVFAQHLLDEGEGLDGVSTEELRAIA 82

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
                   +A  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+ 
Sbjct: 83  E-------DAERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYS 135

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ +  R  + ++ REP P E
Sbjct: 136 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRKVQREKAKELGREPDPAE 195

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L    + V+ VL   ++P+SL   + DE  +  GD +ED  AVSP D+ +    RE
Sbjct: 196 IAAELDTTEQRVKDVLDWARDPVSLNMAVDDEGETQFGDLVEDTGAVSPEDAVMVMLRRE 255

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               ++  L  R   ++R R+G+    + TL EVGKQ  +TRERIRQIE  A+ +LK 
Sbjct: 256 ELDGLIGRLDDRTASIIRSRYGMEDGRERTLTEVGKQHGLTRERIRQIEKHALAELKK 313



 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           + +   +  + +   +  D V MYL E+    LL    E+ ++ RIEAG
Sbjct: 9   DRADRTRTARPTNLEADRDLVGMYLDEIARTPLLDAAEEVELSLRIEAG 57


>gi|83721572|ref|YP_442747.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|167581696|ref|ZP_02374570.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis TXDOH]
 gi|167619812|ref|ZP_02388443.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis Bt4]
 gi|257138958|ref|ZP_05587220.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|83655397|gb|ABC39460.1| RpoS [Burkholderia thailandensis E264]
          Length = 363

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 160/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 85  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 141

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 142 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 201

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 202 LNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 261

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 262 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 321

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 322 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 358



 Score = 40.6 bits (93), Expect = 0.85,   Method: Composition-based stats.
 Identities = 26/116 (22%), Positives = 39/116 (33%), Gaps = 11/116 (9%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD----------RSTDDPVRMYLREM 128
           + +D  D E   +  +  S  S      +    S D            T D ++ YL  +
Sbjct: 33  EDEDAADSERDYEPREADSDDSPGEGRGETADASPDLDDFRALLQAELTADTIQHYLNRI 92

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
               LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  SVKPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 147


>gi|288927698|ref|ZP_06421545.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330532|gb|EFC69116.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 290

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/275 (34%), Positives = 152/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   +RKG  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     +   + +R P+  E++    +  E + + L      +S++ P  D + +
Sbjct: 136 GSLNKINHEINKFEQENQRHPSVSELSDATNIDEEKIGQSLMADGHHVSIDAPFQDGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +       A   ++      VLA  L  RE  ++R  FGIG +    LEE+
Sbjct: 196 CMLDVMASGDDSRTDKQADHESMALELNSVLAKVLKDREITIIRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGNAKILMKYL 289



 Score = 39.1 bits (89), Expect = 2.7,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I  G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLIKAAQKFDETRGFK 104


>gi|182438069|ref|YP_001825788.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326778714|ref|ZP_08237979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178466585|dbj|BAG21105.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326659047|gb|EGE43893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 333

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 108/258 (41%), Positives = 154/258 (59%), Gaps = 6/258 (2%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +   TG +  E    +        E   AK   + +NLRLV++VA++Y   GL  LDLI
Sbjct: 74  EVESTTGDAKREELEAL------VAEGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLI 127

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN GL++A EKFD+  G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R
Sbjct: 128 QEGNAGLVRAVEKFDYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRR 187

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R  + +  R+P   EIA +L    E V  VL   ++P+SL   + D+  +  GD +ED
Sbjct: 188 VQREFNREHGRDPEHAEIAAELDSNAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLED 247

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +AVSP  S +     E    ++  L  R   +++MR+GI    + TL EVGKQ  +TRE
Sbjct: 248 TSAVSPEQSVMTLLRSEELEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRE 307

Query: 655 RIRQIEAKAIRKLKHPSR 672
           RIRQIE  A+ +LK  + 
Sbjct: 308 RIRQIEKHALLELKRMAH 325



 Score = 37.5 bits (85), Expect = 7.9,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           ++++  +      R    + +  D V MYL E+    LL    E+ +++ IEAG
Sbjct: 11  STASGETGRAGSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTIEAG 64


>gi|288800917|ref|ZP_06406374.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288332378|gb|EFC70859.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 287

 Score =  169 bits (428), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/272 (34%), Positives = 163/272 (59%), Gaps = 4/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+ E  ++  E    +++ RK +     A +++  ANLR V+SVAK+Y ++GL
Sbjct: 18  LDKYLQEITQEKLLTTEEE---ITLARKIKEGDKDALQKLTRANLRFVVSVAKQYQHQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I +++ADQS  +R+P++    
Sbjct: 75  SLPDLINEGNIGLIKAAEKFDDTRGFKFISYAVWWIRQSIMQALADQSRLVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+ + + +   + +R+P+  EIA+++ +P E V   +K     +S++ P+ D + + L
Sbjct: 135 VNKINKISHKFEQEFERKPSIAEIAEEINLPQERVSDAIKGNNRHVSMDAPLTDGNDNGL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D ++           +  +LRE     L  L  RE  V+   +GI      TL+E+G +
Sbjct: 195 ADLLQGNEGPDIDTHLLLESLREELKLALNILDERERFVIEAFYGINQPE-MTLQEIGAK 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             +TRER RQI  KAIRKL+  +++K L+S+L
Sbjct: 254 KGLTRERARQIREKAIRKLRKNTQNKLLKSYL 285



 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+   +LL+ E EI +A++I+ G    +  L  + L F  ++    +       L +
Sbjct: 21  YLQEITQEKLLTTEEEITLARKIKEGDKDALQKLTRANLRF--VVSVAKQYQHQGLSLPD 78

Query: 184 IIDLEACIGPESKGGFFHGTEGHS 207
           +I+ E  IG       F  T G  
Sbjct: 79  LIN-EGNIGLIKAAEKFDDTRGFK 101


>gi|256372040|ref|YP_003109864.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008624|gb|ACU54191.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 294

 Score =  169 bits (427), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 85/269 (31%), Positives = 143/269 (53%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +    V   I + E +    +          A++  VE N+ LV+S+A++Y   G+   D
Sbjct: 25  LPDEEVALSIVLQEAQEAEDVPPDVAAVVQAARERFVEGNMGLVVSIARRYVQPGISLDD 84

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEG IGL++A + +D   G++FSTYA WW++QAI +++      + +P  +  ++ +V
Sbjct: 85  LVQEGTIGLLRAIDLYDGRRGFRFSTYATWWIRQAIAQALTRTRRDVVLPRGIAAELARV 144

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
               R +   + R+P+  E+A    +    VR++    +  +SL+  +G+E    L D +
Sbjct: 145 EVQRRELEQALGRQPSMAELAAASGIDELRVRELQGYARSVLSLDQAVGEERDVTLADIV 204

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D++A    ++   A+LR      LA L PRE  VL  RFG+  N  H+LE+    F + 
Sbjct: 205 PDRDAEPIEETIEHADLRTVIAGALAHLEPREREVLAFRFGLEGNEPHSLEDAAAYFGIA 264

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RERIRQIEA+AI +L+    +  LR  L+
Sbjct: 265 RERIRQIEARAIARLRRGDLAPVLRRVLE 293


>gi|115452175|ref|NP_001049688.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|29893614|gb|AAP06868.1| unknown protein [Oryza sativa Japonica Group]
 gi|32351880|dbj|BAC78529.1| plastid sigma factor 2B [Oryza sativa Japonica Group]
 gi|108707414|gb|ABF95209.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|113548159|dbj|BAF11602.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|215704451|dbj|BAG93885.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|215765869|dbj|BAG87566.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 540

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 149/247 (60%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK        K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G
Sbjct: 289 LRKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKG 348

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA
Sbjct: 349 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIA 408

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               MP+  V   + + K  +SL + +G  D ++  +   D +  +  +   +  ++E  
Sbjct: 409 SDTGMPLRRVEAAMSLPKYTVSLTSKVGCTDMTY-QEITPDTSTETAEEMLHRWLMKEDV 467

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L+PRE +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + 
Sbjct: 468 DRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKV 527

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 528 QSLQHYL 534


>gi|260911629|ref|ZP_05918210.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634235|gb|EEX52344.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 290

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 95/275 (34%), Positives = 152/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   +RKG  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     +   + +R P+  E++    +  E + + L      +S++ P  D + +
Sbjct: 136 GSLNKINHEINKFEQENQRHPSVSELSDATNLDEEKIGQSLMADGHHVSIDAPFQDGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +       A   ++      VLA  L  RE  ++R  FGIG +    LEE+
Sbjct: 196 CMLDVMASGDDSRTDKQADHESMALELNSVLAKVLKDREITIIRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGNAKILMKYL 289



 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I  G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLIKAAQKFDETRGFK 104


>gi|188090464|gb|ACD49466.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris]
 gi|188090522|gb|ACD49495.1| RNA polymerase sigma factor [Xanthomonas campestris pv. incanae]
 gi|188090532|gb|ACD49500.1| RNA polymerase sigma factor [Xanthomonas campestris pv. raphani]
          Length = 290

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 136/334 (40%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGTFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTELLLSDYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDADEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKAYVKYGAEHKNVA------KAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|302518878|ref|ZP_07271220.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302427773|gb|EFK99588.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 201

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 95/201 (47%), Positives = 139/201 (69%)

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++A EKFD+  G+KFSTYA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  R + 
Sbjct: 1   LIRAVEKFDYTRGFKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRGLL 60

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   EP+  E+A  L +  E V +VL++ +EP+SL TP+G ED   LGD IED +A SP
Sbjct: 61  QERGHEPSHAEVAALLGLTKERVGEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSP 120

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +SA    LR     VL++L  RE +V+++R+G+      TLEE+G  F VTRERIRQIE
Sbjct: 121 PESAALLLLRRHLEDVLSTLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIE 180

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
           AK + KL+  + + +LR +LD
Sbjct: 181 AKTLAKLRSHAFADQLRGYLD 201


>gi|188090476|gb|ACD49472.1| RNA polymerase sigma factor [Xanthomonas vesicatoria ATCC 35937]
 gi|188090480|gb|ACD49474.1| RNA polymerase sigma factor [Xanthomonas vesicatoria]
          Length = 290

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDIAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|107029001|ref|YP_626096.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia AU 1054]
 gi|105898165|gb|ABF81123.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
          Length = 362

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DPDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357


>gi|6463980|dbj|BAA86957.1| group 2 sigma factor RpoD3 [Synechococcus sp. PCC 7942]
          Length = 320

 Score =  169 bits (427), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 98/280 (35%), Positives = 169/280 (60%), Gaps = 7/280 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVA 460
            + ++R  ++S   +   S  E+       +  +R+ +     AK++M+EANLRLV+SVA
Sbjct: 42  KLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVA 101

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKY  R +  LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+++ TIR
Sbjct: 102 KKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIR 161

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R++S ++    T  E+A  L +    VR  L+  + P+SL+  +
Sbjct: 162 LPIHITEKLNKIKKMQRQLSQQLS-TATLPELAAALDLTPAQVRDYLEKARHPLSLDLRV 220

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD   + LGD +E        +  +QA++R    R+L  LT ++ +V+ +R+G+      
Sbjct: 221 GDNQDTELGDLLETDMQRRRKEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVM 280

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TL  +G +  ++RER+RQ+E +A+  L+      +++ +L
Sbjct: 281 TLASIGDRLQISRERVRQLEREALHTLRQA--RSQVQEYL 318



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 23/36 (63%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  T D VR YLRE+G + LL+ E E+ + KR++ 
Sbjct: 4   TETPTSDLVRTYLREIGRVPLLTHEEEVVLGKRVQQ 39


>gi|167587040|ref|ZP_02379428.1| RNA polymerase sigma factor RpoS [Burkholderia ubonensis Bu]
          Length = 360

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 198

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 199 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 258

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 259 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 318

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 319 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 355



 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 26/113 (23%), Positives = 39/113 (34%), Gaps = 8/113 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS-------TDDPVRMYLREMGSI 131
           D DD+ D E   ++ D            +   +  D         T D ++ YL  +   
Sbjct: 33  DEDDVADNEREFEARDADGGDDEREGSAEASPELDDFRAMLQAELTADTIQHYLNRISVK 92

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  PLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 144


>gi|87303408|ref|ZP_01086196.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87282056|gb|EAQ74018.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 330

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 101/283 (35%), Positives = 169/283 (59%), Gaps = 7/283 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVI 457
           E+  + +   E++  +     S +E+        +++++       AK+ MV ANLRLV+
Sbjct: 49  ELMRLEETEQELEMRAGGQKPSAAEWASAAGLSPALLKRKLSSGRRAKERMVAANLRLVV 108

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 109 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 168

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V+ +L   ++P+SLE
Sbjct: 169 TIRLPIHITETLNKLKKGQRELSQELGRTPTLSELAVCVELPEEEVKDLLCRARQPVSLE 228

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           T +GD + + L D ++    + P +S     LR     +L  L   +  VL MR+GI  +
Sbjct: 229 TKVGDGEDTELLDLLQGDGTL-PAESVDSECLRGDMRALLEQLPELQRSVLSMRYGIDGD 287

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              +L  + +   ++R++ R +E +A+  ++  SRS +L  +L
Sbjct: 288 EPMSLTSIARTLGMSRDKTRNLERRALEGIR--SRSCRLEGYL 328



 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 13/32 (40%), Positives = 22/32 (68%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           T D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 18  TGDLVRSYLRDIGRVPLLTHEQEITLGRQVQE 49


>gi|302535003|ref|ZP_07287345.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443898|gb|EFL15714.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 325

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 108/258 (41%), Positives = 155/258 (60%), Gaps = 6/258 (2%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            I  +  +   E    ++       E   AK+  + +NLRLV++VA++Y   GL  LDLI
Sbjct: 66  EIERDGELPAREELEALA------AEGERAKEVFIRSNLRLVVAVARRYPRSGLPLLDLI 119

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGN GL++A EKFD+  G+KFSTYA WW++QAITRSIADQS TIR+PVH+ +++ ++ R
Sbjct: 120 QEGNAGLVRAVEKFDYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRR 179

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R  + +  R+P   EIA  L    + V  VL   ++P+SL   + DE  +  GD +ED
Sbjct: 180 IQREFNRENGRDPEHAEIAAALDSTEKRVGDVLDWARDPVSLNMSVDDEGDTQFGDLLED 239

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +A+SP  S +     E    +L  L  R   +++MR+GI    + TL EVGKQ  +TRE
Sbjct: 240 TSAISPEQSVLSLLRSEELEDLLGKLDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRE 299

Query: 655 RIRQIEAKAIRKLKHPSR 672
           RIRQIE  A+ +LK  +R
Sbjct: 300 RIRQIEKHALLELKRMAR 317


>gi|149916650|ref|ZP_01905152.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
 gi|149822367|gb|EDM81756.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
          Length = 398

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 108/352 (30%), Positives = 184/352 (52%), Gaps = 9/352 (2%)

Query: 335 IDLLVEQ--LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP- 391
           I  LVE+  + D  + +   E + LR+       R+    R    +              
Sbjct: 47  IADLVEEALVRDEVEDLPKAELDDLRVRSRAYRDRETKGNREIFDQSRETLARRMAGIDR 106

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISV-ETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           +G++   V+ ++ +I   R ++  +S+         F   V   R        AK E V+
Sbjct: 107 DGKYGELVSVDLQAIEANRRDVVRLSITYPPRGSRPFARYVQRARSAHQALCWAKNEFVQ 166

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+++A++Y  R +   DLIQEGNIGLMKA ++FD   GY+FSTYA WW++ +I R
Sbjct: 167 ANLRLVVTIARRYDQRLMPLSDLIQEGNIGLMKAVDRFDGKRGYRFSTYATWWIRHSINR 226

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           ++A++  T+R+P H+   I ++ R  R +  +    P+ +E+AK+  +    VRK+ K++
Sbjct: 227 ALANKGRTVRLPAHVSADIQRIQRATRELETRTGESPSVDELAKETGLSKTRVRKLSKLS 286

Query: 571 -KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
              P+SL+ P  D+D+  L D +ED +A    D     ++ E     +++L P E  +LR
Sbjct: 287 LHNPVSLDAPSSDDDSRGLLDRLEDSSAPRLADMVELEDMSEHLREAMSALEPIEADILR 346

Query: 630 MRFGIG----MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            R+G+G         TL E+G+   ++RERIRQ++ +A+ KL+     + L+
Sbjct: 347 RRYGLGVAGEEFEAMTLRELGEMHQLSRERIRQLQQRALNKLRREFARRGLQ 398


>gi|188090582|gb|ACD49525.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola]
 gi|188090670|gb|ACD49569.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola]
          Length = 290

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 138/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +     +  +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDAAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|188090516|gb|ACD49492.1| RNA polymerase sigma factor [Xanthomonas vasicola]
 gi|188090552|gb|ACD49510.1| RNA polymerase sigma factor [Xanthomonas vasicola]
          Length = 290

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|329941264|ref|ZP_08290543.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
 gi|329299795|gb|EGG43694.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
          Length = 332

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 107/235 (45%), Positives = 150/235 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 91  EAGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFST 150

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P P EIA +L  
Sbjct: 151 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEPAEIAAELGS 210

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + DE  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 211 NAERVTDVLDWARDPVSLNMSVDDEGETQFGDLLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  R   +++MR+GI    + TL EVGK+  +TRERIRQIE  A+ +LK  +RS
Sbjct: 271 RLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325



 Score = 39.1 bits (89), Expect = 3.0,   Method: Composition-based stats.
 Identities = 17/89 (19%), Positives = 34/89 (38%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
           +++   +      R  + + +  D V MYL E+    LL    E+ +++ IEAG      
Sbjct: 11  SATGETADAAGSVRTHAGEIADRDLVGMYLDEIARTPLLDAAKEVELSQVIEAGVFARQI 70

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
              E      A     + L +     +++
Sbjct: 71  LEGEEESRADASREELEALVEAGERAKDV 99


>gi|320536473|ref|ZP_08036507.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320146682|gb|EFW38264.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 282

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 95/246 (38%), Positives = 159/246 (64%), Gaps = 1/246 (0%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +       AK ++++ANLR V++VAKKY N+GL  +DLI EGNIGLM AA++FD   GYK
Sbjct: 36  RAAEGDKAAKDKLIQANLRFVVNVAKKYQNQGLPLMDLISEGNIGLMNAADRFDVTKGYK 95

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F +YA+WW++Q+I ++I ++S  IR+P++   ++ ++ +T + + +    E   +E+A  
Sbjct: 96  FISYAVWWIRQSILKAICEKSRMIRLPLNRVGELIQIEKTRKEIRSTASEEEELKEVADI 155

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           LA+  + V+ ++ I +EP+SL+ P+ D+     +GDFIED     P    +  +L+E+  
Sbjct: 156 LALDHDTVKMIVNIGREPVSLDAPLFDDAANGKMGDFIEDAQYEQPEAYMLDVSLKESID 215

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +V+ +L  RE  +LR RFG+      +L++VGK F +T+ERIRQIE K++ +LK  S   
Sbjct: 216 KVINTLPKREAEILRYRFGLNGYKQLSLKDVGKIFNLTKERIRQIEKKSLEQLKATSYKY 275

Query: 675 KLRSFL 680
           KL +++
Sbjct: 276 KLDAYV 281


>gi|288799880|ref|ZP_06405339.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288333128|gb|EFC71607.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 290

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 91/275 (33%), Positives = 151/275 (54%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI +   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDDEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     +   + +R P+  E++    +  E + + L      +S++ P  D + +
Sbjct: 136 GSLNKINHEINKFEQENQRHPSVSELSDATNIDEEKIGQSLMADGHHVSIDAPFQDGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL   L  RE  ++R  FGIG +    LEE+
Sbjct: 196 CMLDVMPSSDDSRTDRQVDHESMAQELEAVLNKVLKDREITIIRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGNAKILMKYL 289



 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDDEIELAQKIKKGGPEGERAKDKLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIID 186
           L ++ID
Sbjct: 79  LTDLID 84


>gi|6175927|gb|AAF05340.1|AF182105_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  168 bits (426), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 96/262 (36%), Positives = 165/262 (62%), Gaps = 3/262 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
           G++  +TRER+RQI+ + +R+L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRL 313



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|188090470|gb|ACD49469.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. juglandis]
 gi|188090536|gb|ACD49502.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. celebensis]
 gi|188090548|gb|ACD49508.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090572|gb|ACD49520.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|188090602|gb|ACD49535.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090648|gb|ACD49558.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|188090652|gb|ACD49560.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|188090676|gb|ACD49572.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090678|gb|ACD49573.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090680|gb|ACD49574.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090682|gb|ACD49575.1| RNA polymerase sigma factor [Xanthomonas dyei pv. dysoxyli]
 gi|188090684|gb|ACD49576.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|290796520|gb|ADD64830.1| RNA polymerase sigma factor [Xanthomonas dyei pv. laureliae]
 gi|290796522|gb|ADD64831.1| RNA polymerase sigma factor [Xanthomonas dyei pv. laureliae]
 gi|290796524|gb|ADD64832.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796526|gb|ADD64833.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796528|gb|ADD64834.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796530|gb|ADD64835.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796532|gb|ADD64836.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796536|gb|ADD64838.1| RNA polymerase sigma factor [Xanthomonas dyei]
 gi|290796540|gb|ADD64840.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 290

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|87301677|ref|ZP_01084517.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283894|gb|EAQ75848.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 349

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 101/285 (35%), Positives = 168/285 (58%), Gaps = 7/285 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVI 457
           E+  + +   E++  +     S +E+        +++++       AK+ MV ANLRLV+
Sbjct: 65  ELMRLEEAEQELEMRAGGQKPSAAEWASAAGLSPALLKRKLSSGRRAKERMVAANLRLVV 124

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 125 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 184

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V+ +L   ++P+SLE
Sbjct: 185 TIRLPIHITETLNKLKKGQRELSQELGRTPTLSELAVCVELPEEEVKDLLCRARQPVSLE 244

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           T +GD + + L D ++    + P +S     LR     +L  L   +  VL MR+GI + 
Sbjct: 245 TKVGDGEDTELLDLLQGDGTL-PAESVDSECLRGDMRALLEQLPELQRSVLSMRYGIDVE 303

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              +L  +G+   ++R+RIR +E   +  L+    S +++ + D 
Sbjct: 304 EPMSLTGIGRILGMSRDRIRNLERDGLASLRRL--SDQVKDYSDA 346



 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 36  DLVRSYLRDIGRVPLLTHEQEITLGRQVQE 65


>gi|134295851|ref|YP_001119586.1| RNA polymerase sigma factor RpoS [Burkholderia vietnamiensis G4]
 gi|134139008|gb|ABO54751.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 361

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 98/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEF---DARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 22/114 (19%), Positives = 36/114 (31%), Gaps = 1/114 (0%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
               +   +      E  ++   +    A  +      R       T D ++ YL  +  
Sbjct: 33  DEEDVAETETGLDTREAEADGDDEREGRAEAAPDVDDFRALLQAELTADTIQHYLNRISV 92

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  KPLLTVEEEQRYSRLAKAGEFDARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|307822780|ref|ZP_07653011.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307736384|gb|EFO07230.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 448

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 93/279 (33%), Positives = 159/279 (56%), Gaps = 1/279 (0%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +  I+      +       +S ++ +  V+ +   E     +++ + EAN  LV+ +A 
Sbjct: 171 NLPDIIDAMRASQFDEQFLFLSGTDMQQYVTDMIFAEQLWLSSRQALAEANSGLVLFLAN 230

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y    L F DL+QEG  GL++A +KFD+ LG++FSTYA +W+KQAI+R+++     +R+
Sbjct: 231 QYKCGFLDFDDLVQEGQTGLLRAIDKFDYHLGFQFSTYAAYWIKQAISRALSRNERVVRV 290

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P      IHKV+R    + +K  REP+ +E+ +   +P + +  +L I++  +SLE    
Sbjct: 291 PCEQVANIHKVLRAKNELLSKTGREPSIKELTEYSKIPDDQINVILSISQTAVSLENLDD 350

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           DED+    DF+E +   +P     Q++L+    + +  L PRE +V+   FGI    + T
Sbjct: 351 DEDSLAPIDFLEQQVFANPFKKIEQSDLKAWLGKAIKILDPRELKVICCHFGINTGNEMT 410

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L+E+G +  +TRER+RQI+ KA+ K+K  S  K+L SFL
Sbjct: 411 LQEIGAELNLTRERVRQIQVKALNKMK-LSYGKQLMSFL 448


>gi|188090598|gb|ACD49533.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
 gi|188090644|gb|ACD49556.1| RNA polymerase sigma factor [Xanthomonas codiaei]
 gi|188090646|gb|ACD49557.1| RNA polymerase sigma factor [Xanthomonas codiaei]
          Length = 291

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +  L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDVAAIFTTFKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090580|gb|ACD49524.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. manihotis]
 gi|188090650|gb|ACD49559.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 291

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +  L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDVAAIFTTFKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|225450015|ref|XP_002272444.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 426

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 146/247 (59%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + K  C    +++ + ++  RLV+S+A +Y  +GL   DLIQEG+IGL++ AE+FD   G
Sbjct: 179 LDKMLCNGRESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRG 238

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YK STY  WW++QAI R+IA++S  IR+P  + + + K+      +S +++R PT +EIA
Sbjct: 239 YKLSTYVYWWIRQAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIA 298

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + + + V  VR V + ++ PIS++  +  +    L + I   +  +P     +  +++  
Sbjct: 299 EFIDVNVSTVRLVSERSRTPISVDQAVTSQGCMTLQEIIPGPDETTPQKMVKRQLMKQEV 358

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L +L  RE  +LR+ FGI   T  + EE+G+   ++RER+RQI + A+ KL+  S  
Sbjct: 359 ERALNTLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQTSVV 418

Query: 674 KKLRSFL 680
             L+ ++
Sbjct: 419 DYLKLYM 425


>gi|188090502|gb|ACD49485.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
 gi|188090508|gb|ACD49488.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vignicola]
 gi|188090594|gb|ACD49531.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
 gi|188090622|gb|ACD49545.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           aurantifolii]
 gi|188090672|gb|ACD49570.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. phaseoli]
          Length = 291

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 139/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090466|gb|ACD49467.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
 gi|188090468|gb|ACD49468.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
 gi|188090500|gb|ACD49484.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           malvacearum]
 gi|188090504|gb|ACD49486.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. glycines]
 gi|188090514|gb|ACD49491.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. cajani]
 gi|188090574|gb|ACD49521.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. glycines]
 gi|188090578|gb|ACD49523.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           malvacearum]
 gi|188090616|gb|ACD49542.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
 gi|188090660|gb|ACD49564.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri]
          Length = 291

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 139/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090528|gb|ACD49498.1| RNA polymerase sigma factor [Xanthomonas vesicatoria]
          Length = 290

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDIAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKEFIRSW 290


>gi|6175918|gb|AAF05334.1|AF182102_2 RNA polymerase sigma subunit [Escherichia coli]
 gi|6175933|gb|AAF05344.1|AF182107_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 96/262 (36%), Positives = 166/262 (63%), Gaps = 3/262 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
           G++  +TRER+RQI+ + +R+L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRL 313



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|148238489|ref|YP_001223876.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847028|emb|CAK22579.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 355

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 94/274 (34%), Positives = 156/274 (56%), Gaps = 5/274 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVI 457
           E+  +     E++       +  +E      +    +++       AK+ MV ANLRLV+
Sbjct: 74  ELMDLEATEAELQEKRGGEAVPAAELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVV 133

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 134 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 193

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S  + R P+  E+A  + +P + V++++   ++P+SLE
Sbjct: 194 TIRLPIHITEMLNKLKKGQRELSQDLGRTPSVTELAAFVELPEDEVKELMCRARQPVSLE 253

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L D +     +          L+     +L  L   +ERVLRMR+G+   
Sbjct: 254 MKVGDGDDTELLDLLAGDGELPSE-QVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGE 312

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 313 DPMSLTGIGRVIGISRDRVRNLERDGLAGLRRLS 346



 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 13/46 (28%), Positives = 24/46 (52%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S   +        +  D VR YLR++G + LLS + EI + ++++ 
Sbjct: 29  SGPTKAMASRPSGTDVDLVRSYLRDIGRVPLLSHQQEITLGRQVQE 74


>gi|116689841|ref|YP_835464.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia HI2424]
 gi|170733180|ref|YP_001765127.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia MC0-3]
 gi|116647930|gb|ABK08571.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|169816422|gb|ACA91005.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           MC0-3]
          Length = 362

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357


>gi|170703618|ref|ZP_02894360.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
 gi|170131475|gb|EDT00061.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
          Length = 361

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 25/114 (21%), Positives = 39/114 (34%), Gaps = 9/114 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMGS 130
           D DD+ + E   ++ D  +          +     D          T D ++ YL  +  
Sbjct: 33  DEDDVAENERDIEASDAEADGDGEREGRPEAAPDVDDFRALLQAELTADTIQHYLNRISV 92

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|188090604|gb|ACD49536.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris]
          Length = 290

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTELLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|167562539|ref|ZP_02355455.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis EO147]
 gi|167569723|ref|ZP_02362597.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis C6786]
          Length = 362

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 98/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE     A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEF---DARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357



 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 21/103 (20%), Positives = 36/103 (34%), Gaps = 1/103 (0%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +  + +  +   +   +A  +      R       T D ++ YL  +    LL+ E E  
Sbjct: 45  ESREADSDDSGEERGGTADAAPDLDDFRALLQAELTADTIQHYLNRISVKPLLTVEEEQR 104

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 105 YSRLAKAGEFDARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 146


>gi|261879347|ref|ZP_06005774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334050|gb|EFA44836.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 91/275 (33%), Positives = 154/275 (56%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     I++ E   +   +RKG  E   AK+++V+ANLR V+SVAK+Y ++
Sbjct: 16  EALDRYLVEIGRVPMITVDEEIELAQAIRKGGKEGERAKEKLVKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLGLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+     +   +  R P+ +E+A+   +    + + +K     +S++ P  ++D +
Sbjct: 136 GALSKINAEISKFEQENHRPPSVQELARLTNIEEAKIEQTMKADNHHMSIDAPFQEDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL   L  RE  ++R  FGIG +    LEE+
Sbjct: 196 SMADVLSSGDDSRADRQVDYESMSKELDTVLCNVLKERERTIVRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    ++ L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIVKLRESGHAQLLIKYL 289



 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 84/254 (33%), Gaps = 25/254 (9%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAM---MMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G + +++ + EI +A+ I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGRVPMITVDEEIELAQAIRKGGKEGERAKEKLVKANLRF--VVSVAKQYQHQGLG 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQK-----------REDSSQEKERDDVQETEGD 229
           L ++ID E  IG       F  T G  +             +  + Q +         G 
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGA 137

Query: 230 IESAAKVSKDDRSKVDSPPE--------NAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +            +   PP         N E  +       D+   ++ A   +     M
Sbjct: 138 LSKINAEISKFEQENHRPPSVQELARLTNIEEAKIEQTMKADNHHMSIDAPFQEDDDNSM 197

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +    +  R  R +   +++ + D       K  +  +V+    +  ++  ++ + +Q
Sbjct: 198 ADVLSSGDDSRADRQVDYESMSKELDTVLCNVLKERERTIVRECFGIGCHEKGLEEIGDQ 257

Query: 342 LYDISKRIMHNEGE 355
           L    +R+     +
Sbjct: 258 LGLTRERVRQIREK 271


>gi|158340954|ref|YP_001522121.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311195|gb|ABW32807.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 91/265 (34%), Positives = 150/265 (56%), Gaps = 5/265 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K +     +S  E   +   V+        AK+ M+E NLRLV+S+AKK+ + GL
Sbjct: 8   VQAYLKEMGRYPLLSHEEEIRLARQVK---AGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLIQEG+IGL  A +KFD   G KFSTYA WW+ +AI R++  QS TI IP+H  ++
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRALKSQSRTIYIPIHQWER 124

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            H++ +  R+++ +  R PT +E++    +    +R  L+  +   SL+ P+G E    L
Sbjct: 125 AHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAVSSLDQPVGPEQKDAL 184

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I+ ++A   +   ++    +  TR +A LT RE  ++  R+G+      ++  +GKQ
Sbjct: 185 IDLIQTEDAALSIMDGLEIE--DALTRCMAYLTERERFIVDQRYGLTDGQPKSMGVIGKQ 242

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             V+RER+RQI   A++K+    RS
Sbjct: 243 IGVSRERVRQILNIAMKKMTRQVRS 267



 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------ 171
           +D V+ YL+EMG   LLS E EI +A++++AG       + E  L     I  +      
Sbjct: 5   NDSVQAYLKEMGRYPLLSHEEEIRLARQVKAGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 172 ---DELNDGTTLLREIIDLEAC 190
              D + +G+  L   +D    
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDL 86


>gi|28899327|ref|NP_798932.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
 gi|28807551|dbj|BAC60816.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
          Length = 319

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 104/275 (37%), Positives = 158/275 (57%), Gaps = 7/275 (2%)

Query: 385 SYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              K     E K  V  E D    S+   +  +  I     ++  E    V   R+    
Sbjct: 26  ELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLTAEEE---VLYARRALRG 82

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA
Sbjct: 83  DEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYA 142

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEIA +L +PV
Sbjct: 143 TWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEIAAQLDIPV 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V K+L++ +   S++TPIG +    L D I D N   P  S    +++ +    L  L
Sbjct: 203 EDVSKMLRLNERISSVDTPIGGDGEKALLDIIPDANNSDPEVSTQDDDIKSSLIHWLEEL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            P+++ VL  RFG+      TLEEVG +     ER
Sbjct: 263 NPKQKEVLARRFGLLGYEPSTLEEVGLRLKKWDER 297



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 1/109 (0%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V + +     E + D+    SS++       + +  A   + D  ++YL E+G   LL+
Sbjct: 9   KVEEFEYDNASETTIDNELEKSSSTTEGKTAVREEFDASSKSLDATQLYLGEIGFSPLLT 68

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 69  AEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLI 116


>gi|6175921|gb|AAF05336.1|AF182103_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  168 bits (424), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 96/262 (36%), Positives = 165/262 (62%), Gaps = 3/262 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     +   E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLPAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
           G++  +TRER+RQI+ + +R+L
Sbjct: 292 GREIGLTRERVRQIQVEGLRRL 313



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL  E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLPAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|188090674|gb|ACD49571.1| RNA polymerase sigma factor [Xanthomonas bromi]
          Length = 290

 Score =  168 bits (424), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 136/334 (40%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|146164121|gb|ABQ08728.1| RNA polymerase sigma-70 factor [Aeromonas sharmana]
          Length = 292

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 132/335 (39%), Gaps = 45/335 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+   G   
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLDQYDKHEAGQIR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     +            +         S  ++E    ++ E + E     S D 
Sbjct: 61  LGDIISGFVSLD--------EADDMPPTATHIGSELDEEELADEDDEDEDEDEDGDSDDS 112

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  PE A      L    D +  ++ A                             
Sbjct: 113 DDDGGPDPELAREKFGELRAQSDVTRDSIKAY---------------------------- 144

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-L 359
                   +   + ++  +KL  +     L   + D LV  + D+ +R+   E  +++  
Sbjct: 145 -------GREDERTQLEIQKLADVFRQFRLVPKQFDRLVNNMRDMMERVRVQERIIMKGC 197

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+     +E D  W   A       W   +    + + +   +++ +  E
Sbjct: 198 VERAKMPKKNFVALFTNKESDLSWF-LAARAAGKSWSVALEDVAEDVERAVTKLQQVEDE 256

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           TG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 TGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|114776318|ref|ZP_01451363.1| RpoS [Mariprofundus ferrooxydans PV-1]
 gi|114553148|gb|EAU55546.1| RpoS [Mariprofundus ferrooxydans PV-1]
          Length = 282

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 90/259 (34%), Positives = 157/259 (60%), Gaps = 4/259 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ IS    ++ +E    +++ ++       A   MV+ANLRLV+ ++++Y NRG+   
Sbjct: 14  YMREISRYELLTAAEE---IALAKRIGAGDKEAHHYMVQANLRLVVKISRRYMNRGVALA 70

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GL++A EKFD   G +FSTYA WW++QA+ R+I +QS TIR+PVH+  +++ 
Sbjct: 71  DLIEEGNLGLIRAVEKFDVTHGCRFSTYATWWIRQAVERAIMNQSRTIRVPVHVGKELYA 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   R+ ++++R+PT  EIA+ + + V+ +++++       S +  + D+    L D 
Sbjct: 131 LTKHTNRLRSELERDPTDVEIAEAMGVSVQRIQELMGAAVRTDSADDMLHDDSDFTLYDV 190

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM-NTDHTLEEVGKQFC 650
             D+ A SP D        E     ++ L  +E  V+R+R+G+       TLE +G+Q  
Sbjct: 191 TADEAAESPGDQMQTVLRNEILQVWMSKLEKKEREVVRLRYGLDDAGDPWTLEMIGEQLG 250

Query: 651 VTRERIRQIEAKAIRKLKH 669
           VTRERIRQI+ +A++KL+ 
Sbjct: 251 VTRERIRQIQVQALQKLRR 269



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           +P+ +Y+RE+   ELL+   EIA+AKRI AG       + ++ L    ++       +  
Sbjct: 9   EPMAIYMREISRYELLTAAEEIALAKRIGAGDKEAHHYMVQANLRL--VVKISRRYMNRG 66

Query: 179 TLLREIID 186
             L ++I+
Sbjct: 67  VALADLIE 74


>gi|167836384|ref|ZP_02463267.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis
           MSMB43]
          Length = 366

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 97/269 (36%), Positives = 157/269 (58%), Gaps = 11/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKI--------KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +            +RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSLSTGAAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TLEE+  +  +TRER+RQI+ +A+ +LK 
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKR 349



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 2/107 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQK-RKDSADRSTDDPVRMYLREMGSIELLSRE 137
           + D    +  S+DS +  S A+++S  L   R       T D ++ YL  +    LL+ E
Sbjct: 41  ERDYEPRDADSDDSGEGRSDAADASPDLDDFRALLQAELTADTIQHYLNRISVKPLLTVE 100

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 101 EEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 146


>gi|78066590|ref|YP_369359.1| RNA polymerase sigma factor RpoS [Burkholderia sp. 383]
 gi|77967335|gb|ABB08715.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 362

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357



 Score = 41.0 bits (94), Expect = 0.77,   Method: Composition-based stats.
 Identities = 26/115 (22%), Positives = 39/115 (33%), Gaps = 10/115 (8%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA---------DRSTDDPVRMYLREMG 129
           D DD+ D E   ++ D  S   +     +                  T D ++ YL  + 
Sbjct: 33  DEDDVADNERDLEARDSDSEGGDDEREGRAEAAPDVDDFRTMLQAELTADTIQHYLNRIS 92

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  VKPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 146


>gi|320010254|gb|ADW05104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 333

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 104/234 (44%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E+  AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 92  AESERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHTEIAAELDT 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D+  +  GD +ED +A+SP  S +     E    ++ 
Sbjct: 212 NAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAISPEQSVMTLLRSEELEDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 272 KLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAH 325



 Score = 37.9 bits (86), Expect = 6.6,   Method: Composition-based stats.
 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMMMASLCESPL 162
           D V MYL E+    LL    E+ +++ IEAG     ++  + ES  
Sbjct: 34  DLVGMYLDEIARTPLLDAAKEVELSQTIEAGVFAQQILDGVVESDA 79


>gi|221198089|ref|ZP_03571135.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
 gi|221204352|ref|ZP_03577369.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221175209|gb|EEE07639.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221182021|gb|EEE14422.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
          Length = 338

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 60  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 116

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 117 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 176

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 177 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 236

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 237 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 296

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 297 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 333



 Score = 40.6 bits (93), Expect = 0.99,   Method: Composition-based stats.
 Identities = 26/114 (22%), Positives = 39/114 (34%), Gaps = 9/114 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMGS 130
           + DD+ D E   ++ D  S   +            D          T D ++ YL  +  
Sbjct: 10  EDDDVADNERDFEARDADSEGGDEREDRPDAAPDVDDFRALLQAELTADTIQHYLNRISV 69

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 70  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 122


>gi|75812337|ref|YP_319956.1| sigma-28 [Anabaena variabilis ATCC 29413]
 gi|75705093|gb|ABA24767.1| Sigma-28 [Anabaena variabilis ATCC 29413]
          Length = 316

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 97/238 (40%), Positives = 153/238 (64%), Gaps = 1/238 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + V +       AK++M+ ANLRLV+S+AKKY  R L+FLDL+QEG IGL +  EKFD  
Sbjct: 69  AQVNQILELGQRAKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPN 128

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYK STYA WWV QAITR+IA++S T+R+P+H+ +K++++ +  R     + R P+  E
Sbjct: 129 RGYKLSTYAYWWVTQAITRAIAEKSRTVRLPIHVNEKLNQIKKVQREFFQTLGRRPSVAE 188

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+KL +    +R+ LK+    ISL+  +GD   + L + +  +  VSP ++     LR+
Sbjct: 189 IAQKLELEPSQIREYLKVASGTISLDLKVGDNQETELSELLASE-GVSPNENTTHEMLRQ 247

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +LASL P +  VL +RFG+  N + +L ++ ++  ++RER+RQI+ KA+  L+ 
Sbjct: 248 DLSDLLASLKPMQREVLILRFGLLDNQEQSLAQISEKLNLSRERVRQIQQKAMTALRR 305



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 21/32 (65%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + D +R+YL+E+G   LL+ + EI   ++++ 
Sbjct: 5   SSDLIRIYLQEIGQFPLLTSDQEITYGRQVQQ 36


>gi|297580668|ref|ZP_06942594.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
 gi|297535084|gb|EFH73919.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
          Length = 236

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 91/216 (42%), Positives = 144/216 (66%)

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           ++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR
Sbjct: 9   RRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIR 68

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V K+L++ +   S++TPI
Sbjct: 69  LPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISSVDTPI 128

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +    L D + D +   P  S    ++RE+    L  L P+++ VL  RFG+      
Sbjct: 129 GGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPKQKEVLARRFGLLGYEPS 188

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 189 TLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 224


>gi|152995337|ref|YP_001340172.1| RpoD family RNA polymerase sigma factor [Marinomonas sp. MWYL1]
 gi|150836261|gb|ABR70237.1| RNA polymerase, sigma 70 subunit, RpoD family [Marinomonas sp.
           MWYL1]
          Length = 338

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 92/270 (34%), Positives = 158/270 (58%), Gaps = 4/270 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A    ++   +  +  I     ++  E  +   +          A+  M+E+NLRLV+ +
Sbjct: 54  ADSSRNLDVTQLYLSEIGFSPLLTAEEEVYFSRL---SLKGDQKARTRMIESNLRLVVKI 110

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 111 SRRYLNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 170

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +R AR ++ K+  EP+ EEIA+ L  PVE V+K+L + ++  S++  
Sbjct: 171 RLPIHVVKELNVYLRAARELTQKLDHEPSAEEIAEMLDCPVEDVQKMLGLNEKVSSIDAT 230

Query: 580 IGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            G + +   L + + D     P       ++  +    L  L+ ++  V+  RFG+  + 
Sbjct: 231 FGGDNNDKSLVEILADTLHQGPEADRQDGDVLNSIELWLDELSEKQCEVITRRFGLRGHE 290

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TLE VG +  +TRER+RQI+ +A+RKL+
Sbjct: 291 ASTLEHVGAEIGLTRERVRQIQVEALRKLR 320



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 2/112 (1%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLA-SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
            I   D D L+DE   +  +D         S    +  D+      D  ++YL E+G   
Sbjct: 15  NIGDFDLDTLDDELIGDVLVDEELVDEEFESAVSARYADADSSRNLDVTQLYLSEIGFSP 74

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LL+ E E+  ++    G       + ES L     I  R  LN G +LL  I
Sbjct: 75  LLTAEEEVYFSRLSLKGDQKARTRMIESNLRLVVKISRRY-LNRGLSLLDLI 125


>gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
 gi|300075048|gb|ADJ64447.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
          Length = 337

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 92/269 (34%), Positives = 164/269 (60%), Gaps = 5/269 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ +  I  +  ++ +E  H  +  + GE    +A+++M+E NLRLV+S+AK Y NRG+ 
Sbjct: 66  QHYLNKIGAKPLLTAAEELHFATQAKAGEF---VARQKMIEHNLRLVVSIAKHYINRGVA 122

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GLM+A +KF+   G++FSTYA WW++Q+I R+I +Q+ T+R+PVHM  ++
Sbjct: 123 LLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMVREL 182

Query: 530 HKVVRTARRMS--NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           ++++R    +    +  R+ + E+IA  +  PVE V+ VL +++   SL+TP+ ++  + 
Sbjct: 183 NQILRAKYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDVLALSEHAASLDTPLDNDPQAS 242

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +       P   A    +       L SL+ ++  V+  RFG+  +   TLE++  
Sbjct: 243 LMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPSTLEQLAS 302

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  +TRER+RQ++ +A+ KLK    S+ +
Sbjct: 303 EMGITRERVRQVQQEALIKLKRLLTSRGV 331



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/134 (21%), Positives = 53/134 (39%), Gaps = 13/134 (9%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
             LP  +   E+++D+V  +             E E    D+ +    A+ +    + +K
Sbjct: 7   DHLPDQDPREEELDDSVDEID------------EPEVIDGDAGEEVQEAAPAEGVDELKK 54

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
             A   + D  + YL ++G+  LL+   E+  A + +AG  +    + E  L     I  
Sbjct: 55  VLAAELSTDTTQHYLNKIGAKPLLTAAEELHFATQAKAGEFVARQKMIEHNLRLVVSIAK 114

Query: 171 RDELNDGTTLLREI 184
              +N G  LL  I
Sbjct: 115 HY-INRGVALLDLI 127


>gi|296268951|ref|YP_003651583.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091738|gb|ADG87690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 311

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 96/238 (40%), Positives = 151/238 (63%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +       AK E ++ANLRLV++VA+KY  RG+  +DL+QEGN+GL++A EKFD+ 
Sbjct: 68  EELERIAISGRRAKDEFIKANLRLVVAVARKYAGRGMPLIDLVQEGNVGLVRAVEKFDYR 127

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++QA+ RSI +Q   +R+P H  +++ +++R  R +  + + EP+ EE
Sbjct: 128 RGYKFSTYATWWIRQAVGRSIHEQGRPVRLPTHAGEQMTRLMRVRRDILAEQEMEPSDEE 187

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L MP+E VR++ +   +P+SL+  +G+ED + LGD I D     P   AI    +E
Sbjct: 188 LADVLDMPIERVRELRRWASDPVSLQLGVGEEDETELGDMIADDAWADPEQQAIDTLDKE 247

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              R L  L  R   +LR R+G+    +HTL EVG+++ + R+R R++E  A+R L+ 
Sbjct: 248 RLERWLTDLDGRLSEMLRWRYGLVDGKEHTLTEVGERYGIGRDRARRMERDALRHLRK 305



 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 16/32 (50%), Positives = 22/32 (68%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D +  YL E+G + LL+ E E+ +AKRIEAG 
Sbjct: 16  DLLGTYLAEIGRVPLLTAEEEVELAKRIEAGL 47


>gi|323388685|gb|ADX60147.1| SIGMA70-like transcription factor [Zea mays]
          Length = 428

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 93/247 (37%), Positives = 152/247 (61%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+        K  MV++N+RLVIS+AK++   G++F DLIQ+G  GL++ AEKFD   G
Sbjct: 177 LRRRLNHGVYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEKFDASKG 236

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR P+ EEIA
Sbjct: 237 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRLPSNEEIA 296

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               M +  V   + + K  +S  + +G  D ++  + + D +A +  ++  +  +++  
Sbjct: 297 VDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTY-QEIMPDTSAETAEETLHRWLMKKDV 355

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              L SL+PRE++V+R RFGI      TL ++G+   V+RERIRQIE  A RKL+  +R 
Sbjct: 356 NTALDSLSPREKQVMRYRFGIEGGRARTLHDIGQLMGVSRERIRQIELGAFRKLRSKNRL 415

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 416 QSLQHYL 422


>gi|188090562|gb|ACD49515.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. alfalfae]
          Length = 291

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 138/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEDAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090478|gb|ACD49473.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090482|gb|ACD49475.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090492|gb|ACD49480.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. begoniae]
 gi|188090506|gb|ACD49487.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vasculorum]
 gi|188090510|gb|ACD49489.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vasculorum]
 gi|188090530|gb|ACD49499.1| RNA polymerase sigma factor [Xanthomonas axonopodis]
 gi|188090540|gb|ACD49504.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090550|gb|ACD49509.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. ricini]
 gi|188090566|gb|ACD49517.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090570|gb|ACD49519.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. alfalfae]
 gi|188090590|gb|ACD49529.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. vasculorum]
 gi|188090614|gb|ACD49541.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. ricini]
 gi|188090620|gb|ACD49544.1| RNA polymerase sigma factor [Xanthomonas perforans]
 gi|188090654|gb|ACD49561.1| RNA polymerase sigma factor [Xanthomonas alfalfae subsp.
           citrumelonis]
 gi|188090656|gb|ACD49562.1| RNA polymerase sigma factor [Xanthomonas alfalfae subsp.
           citrumelonis]
 gi|188090658|gb|ACD49563.1| RNA polymerase sigma factor [Xanthomonas alfalfae subsp.
           citrumelonis]
 gi|188090666|gb|ACD49567.1| RNA polymerase sigma factor [Xanthomonas albilineans]
 gi|188090688|gb|ACD49578.1| RNA polymerase sigma factor [Xanthomonas perforans]
          Length = 291

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 138/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090474|gb|ACD49471.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. pruni]
          Length = 290

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATAVARMPRKDFIRSW 290


>gi|115351809|ref|YP_773648.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria AMMD]
 gi|115281797|gb|ABI87314.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 361

 Score =  168 bits (424), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 25/114 (21%), Positives = 39/114 (34%), Gaps = 9/114 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMGS 130
           D DD+ + E   ++ D  +          +     D          T D ++ YL  +  
Sbjct: 33  DEDDVAENERDLEASDAEADGDGEREGRAEAAPDVDDFRALLQAELTADTIQHYLNRISV 92

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|161524626|ref|YP_001579638.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|189350618|ref|YP_001946246.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221212761|ref|ZP_03585737.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
 gi|160342055|gb|ABX15141.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia multivorans
           ATCC 17616]
 gi|189334640|dbj|BAG43710.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221166974|gb|EED99444.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
          Length = 361

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 26/114 (22%), Positives = 39/114 (34%), Gaps = 9/114 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMGS 130
           + DD+ D E   ++ D  S   +            D          T D ++ YL  +  
Sbjct: 33  EDDDVADNERDFEARDADSEGGDEREDRPDAAPDVDDFRALLQAELTADTIQHYLNRISV 92

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|188090642|gb|ACD49555.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           malvacearum]
          Length = 291

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 138/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                 D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSGDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|1769588|gb|AAB95226.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 98/286 (34%), Positives = 180/286 (62%), Gaps = 9/286 (3%)

Query: 401 CEVDSILKIRNEIKSISV--ETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLR 454
            +V  ++ ++ + +++    +   +  E+     +    +++       AK++M+EANLR
Sbjct: 43  KQVQRLMALQEKRQTLEESLDRERTREEWAEAAQLTPKQLQRDLQIGERAKRKMIEANLR 102

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+++A+    R L+FLDLIQEG++GL +  EKFD   GYKFSTYA WW++QAITR+IA 
Sbjct: 103 LVVAIARNIKKRNLEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQ 162

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q  TIR+P+H+ +K++K+ +T R+++  + R  T  EIA+ L +    +R+  ++++ PI
Sbjct: 163 QGRTIRLPIHITEKLNKIKKTQRQLAQDLGRAATIAEIAEALELEPAQIREYFRVSRHPI 222

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL+  +GD   + L D +ED +  SP ++     L++    ++A LTP+++ V+ +RFG+
Sbjct: 223 SLDVRVGDNQDTELMDLLED-SGESPDNNVTYELLKQDLRDLIADLTPQQQEVIILRFGL 281

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               + +L ++GK+  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 282 NDGKELSLAKIGKRMNLSRERVRQLERQALNHLRR--RRSQIREYL 325



 Score = 41.7 bits (96), Expect = 0.39,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE--AGRAMMMASLCES 160
           ++  +  +S+ D VR YLRE+G + LL+ E EI   K+++          +L ES
Sbjct: 7   QQAPNNGKSSADMVRTYLREIGRVPLLTHEEEIVYGKQVQRLMALQEKRQTLEES 61


>gi|325521809|gb|EGD00541.1| RNA polymerase sigma factor RpoS [Burkholderia sp. TJI49]
          Length = 339

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 61  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 117

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 118 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 177

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 178 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 237

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 238 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 297

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 298 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 334



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 10/115 (8%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA---------DRSTDDPVRMYLREMG 129
           D DD+ D E   ++ D  +   +     +                  T D ++ YL  + 
Sbjct: 10  DEDDVADNERDFEARDADTEGGDDEREGRAEAAPDVDDFRALLQAELTADTIQHYLNRIS 69

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 70  VKPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 123


>gi|188090520|gb|ACD49494.1| RNA polymerase sigma factor [Xanthomonas pisi]
          Length = 290

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKEFIRSW 290


>gi|188090488|gb|ACD49478.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
 gi|188090490|gb|ACD49479.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
          Length = 284

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 138/334 (41%), Gaps = 55/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  Q L+   ++  +G   L EI+            GF    E         S +     
Sbjct: 121 LAVQTLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPVVVASDE----- 164

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                +   +   +V   +     + P+ AE                           V 
Sbjct: 165 -DSAADASDDDDEEVEAAEEEAGPTGPDPAE---------------------------VA 196

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +D +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 197 RRMDALATEYAKFKK------AHAKNGAEHKLVTKLRTDIAEVFVTLKLPLPLTDVLVRK 250

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 251 LRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 284


>gi|294155544|ref|YP_003559928.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
 gi|291599870|gb|ADE19366.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
          Length = 490

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 110/272 (40%), Positives = 173/272 (63%), Gaps = 11/272 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E R +  ++ KG      A+ +++  NLRLVI+ AKKY NRGL F+DLI EGN G+
Sbjct: 219 LKPDEERRLAKLMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRGLTFIDLISEGNAGI 278

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +K++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  
Sbjct: 279 LKAVQKYNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQ 338

Query: 542 KIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++  EPT  +IA +       E VR + KI  +PISL+  IG E+ S   DF++D + ++
Sbjct: 339 ELGHEPTDAQIANRFGNEYTEEKVRYIRKINIDPISLDKQIGKENDSSFSDFVKDDSVMT 398

Query: 600 PLDSAIQANLRETTTRVLASLTPR-EERVLRMRFGIGMNTD------HTLEEVGKQF-CV 651
           P+D A Q  L E    ++     R E  ++  RFG+G++++      H+L+E+ K+   V
Sbjct: 399 PVDFASQEQLSELLLELINKSLERDERELICKRFGVGVDSEGNKYRVHSLDELAKERGGV 458

Query: 652 TRERIRQIEAKAIRKLKHPSRS-KKLRSFLDG 682
           ++ER+RQIE K +RKLK+ S++ + LR F+  
Sbjct: 459 SKERVRQIENKILRKLKNSSKNGRHLRDFIKN 490



 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 93  LDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREGEIAIAKRIEAGRA 151
            D      ++ +   K   +    T+D V+ Y+R +G   ELL  + E  +AK +E G  
Sbjct: 177 ADEEVLLEDTQIASGKSLTNKLTETNDIVKWYMRWIGKYGELLKPDEERRLAKLMEKGGF 236

Query: 152 MMMAS 156
               +
Sbjct: 237 RGKRA 241


>gi|188090544|gb|ACD49506.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
 gi|188090546|gb|ACD49507.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
          Length = 291

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + E + +
Sbjct: 121 LSTELLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDDAAEDDDE 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              + +   E A     D                                        V 
Sbjct: 181 ADGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090662|gb|ACD49565.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           aurantifolii]
 gi|188090664|gb|ACD49566.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv.
           aurantifolii]
          Length = 287

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 135/334 (40%), Gaps = 52/334 (15%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              E   + +      ++       P E                              V 
Sbjct: 170 SDDEAVDEDDDDDAAEEEAGPTGPDPVE------------------------------VA 199

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 200 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 253

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 254 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 287


>gi|218438398|ref|YP_002376727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171126|gb|ACK69859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 98/285 (34%), Positives = 164/285 (57%), Gaps = 18/285 (6%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC----------------EASIA 444
              +++  ++  ++ I     +S  +   + + V+                    +   A
Sbjct: 1   MTKETVDNVKAYLQEIGRTPLLSSQQEVELATQVQNMMALLDKENLTPEEIKIIQQGKRA 60

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++M+ ANLRLV+S+AKKY  RGL FLDLIQEG+IGL++  EKFD   GYKFSTYA WW+
Sbjct: 61  KRKMISANLRLVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWWI 120

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+TR+IADQS TIR+P H+ + ++K+ R  R+++ ++ R PT EEIA +L + +  +R
Sbjct: 121 RQAMTRAIADQSRTIRLPSHLTESLNKLKRITRQLTGELGRRPTEEEIATELEISMNELR 180

Query: 565 KVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            + +      S    +  +D  + L + + D +A        Q  L     ++L +L PR
Sbjct: 181 TIRQADHRTRSYSLNMKMDDEQTELAELLADDSANPNEF-VAQIELSSMVEQLLETLPPR 239

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ ++ +R+G+      +LEEVG    ++RER+RQ++ +A+R LK
Sbjct: 240 QQEIIALRYGLKNGKQMSLEEVGHHCNLSRERVRQLQNRAMRTLK 284



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 4/54 (7%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
            + T D V+ YL+E+G   LLS + E+ +A +++     MMA L +  LT + +
Sbjct: 2   TKETVDNVKAYLQEIGRTPLLSSQQEVELATQVQ----NMMALLDKENLTPEEI 51


>gi|300726043|ref|ZP_07059501.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776650|gb|EFI73202.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 93/275 (33%), Positives = 154/275 (56%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  IS    ISI E   +   +++G  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  ESLDKYLGEISRAPMISIEEEIDLAQQIKRGGREGERAKSKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++QAI ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAEKFDETRGFKFISYAVWWIRQAILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + KV +   +   K +R PT +E++++  +  E + + +  + + +S++ P  + + +
Sbjct: 136 GSLSKVNQEINKFEQKYQRVPTIQELSQRTDIDEEKIAQSMMASGKHVSIDAPFQEGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               ++     +VL + L  RE  ++R  FGIG      LEE+
Sbjct: 196 SMVDIMASGEDSRTDKEVDHESMSYDLNQVLETVLNEREITIIRDCFGIGCPE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G    +TRER+RQI  K+I KL+   +   L  +L
Sbjct: 255 GDLLGLTRERVRQIREKSITKLRESGKIGVLMKYL 289


>gi|302036606|ref|YP_003796928.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
 gi|300604670|emb|CBK41002.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
          Length = 332

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 93/275 (33%), Positives = 163/275 (59%), Gaps = 3/275 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
            + +  I++ ++ +   T ++  E + +   V         A++EM+EANLRLVIS+ K+
Sbjct: 56  AEGLDTIKSYLREVRKSTLLNFKEEQALGKRV---MAGDEAARQEMIEANLRLVISIGKR 112

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y NRG  F D+++EGN+GL+KA EKF++  G++FSTYA WW++Q I R+I +Q   +R+P
Sbjct: 113 YMNRGFPFADIVEEGNLGLIKAVEKFNYKRGFRFSTYASWWIRQFIERAIINQGKLVRLP 172

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VH+ +++++ +    ++ +++ REP  +E+A KL   V  V  + ++ +   SL++PI D
Sbjct: 173 VHVVERLNRYLGKVEQLVHELGREPRADEVAAKLKTSVAEVDDLKQLVRTTCSLDSPISD 232

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              + L D IED   ++P ++      R      +  L  +E  V+  RFG+      TL
Sbjct: 233 RQDTFLRDVIEDPLCLTPAETTEGVMRRAELMAWVKELPEKERTVILARFGLDGAESRTL 292

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           EE+G++  +TRER+RQIE  A+ +L+     K ++
Sbjct: 293 EEIGQEMGLTRERVRQIETAALARLRGIIERKTMK 327



 Score = 44.4 bits (103), Expect = 0.066,   Method: Composition-based stats.
 Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 2/100 (2%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  ED+   + + +  S    +  +S      D ++ YLRE+    LL+ + E A+ KR+
Sbjct: 28  DEDEDAESGSHAEAEESGADNRPAESGRAEGLDTIKSYLREVRKSTLLNFKEEQALGKRV 87

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            AG       + E+ L    +I       +      +I++
Sbjct: 88  MAGDEAARQEMIEANLRL--VISIGKRYMNRGFPFADIVE 125


>gi|282877365|ref|ZP_06286188.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
 gi|281300417|gb|EFA92763.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
          Length = 290

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 149/275 (54%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     R   +  R P+  E++    +  + + + +      +S++ P  D + +
Sbjct: 136 GSLNKINHEINRFEQENHRRPSISELSDATNIDEDKISQSMMADGHHVSIDAPFQDGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               ++ +    VL   L  RE  +++  FGIG +    LEE+
Sbjct: 196 TMLDVMPSGEDSRTDRHVDHESMAQELDAVLNKVLKEREIIIIKECFGIGRHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGNAKILMKYL 289



 Score = 38.3 bits (87), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIID 186
           L ++ID
Sbjct: 79  LTDLID 84


>gi|188090472|gb|ACD49470.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. axonopodis]
 gi|188090630|gb|ACD49549.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. axonopodis]
          Length = 291

 Score =  167 bits (423), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 139/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L++  +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLVDYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|162458769|ref|NP_001105507.1| sigma-like factor6 [Zea mays]
 gi|4336610|gb|AAD17856.1| sigma factor SIG6 [Zea mays]
          Length = 541

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 80/270 (29%), Positives = 137/270 (50%), Gaps = 9/270 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  +   G+S  E        +         +++M  +N RLVI VA+KY   GL   D
Sbjct: 277 VEEWAQAVGMSCREL-------QSCVRTGRRCREKMARSNFRLVIHVARKYEGCGLDIQD 329

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+Q+G  GLMK  EKF+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV
Sbjct: 330 LVQDGCCGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKV 389

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +           +PT E +A++  + +E + K+   T++  S++  +  +D     +  
Sbjct: 390 GKARMECIMD-GEQPTNEVVARRAGITIEKLAKLRAKTRKVRSMQDRVWSDDGVTYQEIT 448

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           ED N   P  S  +  +R+     L   L+PRE+ ++  RFGI      TL  +G  + +
Sbjct: 449 EDPNIEGPEVSVDRLMMRQQVRSFLTGILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGL 508

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++ERIRQ++ KA+ KL++   ++    + D
Sbjct: 509 SKERIRQVQNKALDKLRNSISAQGFHVYFD 538


>gi|254386169|ref|ZP_05001481.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194345026|gb|EDX25992.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 325

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 150/234 (64%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK+  + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 84  AEGERAKEVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 143

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 144 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHTEIAAELDT 203

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + V  VL   ++P+SL   + D+  +  GD +ED +A+SP  S +     E    +L 
Sbjct: 204 TAKRVGDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAISPEQSVLSLLRSEELEDLLG 263

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 264 KLDQRTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMAR 317


>gi|15240693|ref|NP_196877.1| SIG4 (SIGMA FACTOR 4); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|3983260|gb|AAC97954.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972296|dbj|BAA78110.1| RNA polymerase sigma subunit SigD [Arabidopsis thaliana]
 gi|9758039|dbj|BAB08700.1| sigma-like factor [Arabidopsis thaliana]
 gi|332004550|gb|AED91933.1| sigma factor 4 [Arabidopsis thaliana]
          Length = 419

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 85/241 (35%), Positives = 141/241 (58%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    A++++     RLV+S+A  Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 174 CRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLST 233

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y  WW+KQAI R+IA +S  +++P  M +   KV   +  ++ K++R+P+ EEIA+ L +
Sbjct: 234 YVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNL 293

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V  VR  ++ ++ P+SL+          L + +   +   P +   + +++    ++L 
Sbjct: 294 NVSAVRLAVERSRSPVSLDRVASQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLG 353

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SLT RE RVL + FG+   T  + EE+GK   ++RER+RQI   A++KL++      L+ 
Sbjct: 354 SLTARESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRNVHNVNDLKI 413

Query: 679 F 679
           +
Sbjct: 414 Y 414


>gi|323453176|gb|EGB09048.1| hypothetical protein AURANDRAFT_53467 [Aureococcus anophagefferens]
          Length = 468

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 97/257 (37%), Positives = 152/257 (59%), Gaps = 12/257 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            K   +   AK  M+ ANLRLV+S++K+Y +RGL F D+IQEG  GL +A EKFD   G+
Sbjct: 204 EKARKKCLKAKAAMINANLRLVVSISKRYQHRGLHFQDVIQEGTFGLTRAVEKFDPEKGF 263

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA WW+KQA+ R+IADQS TIR+PVH+ D++  + +  R +  ++ RE T EE+A 
Sbjct: 264 KFSTYATWWIKQAVMRAIADQSRTIRLPVHVHDQLQSMKKVTRDLGAELGRECTDEELAG 323

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIG------------DEDTSHLGDFIEDKNAVSPLD 602
           KL +    +  +    ++ +S++  +               + + L D + D  A+    
Sbjct: 324 KLDLATTKMDWLRSCERQTMSMDATVRVSGKGSSAGTGGAGNEAKLSDNLADAAALPDER 383

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  ++   +    +  +L+ RE  V+R+RFG+      TLEE+G  F +TRER+RQIEA+
Sbjct: 384 AETKSLQSDIHGLLRTALSDRECDVVRLRFGLDDGKARTLEEIGTVFSITRERVRQIEAR 443

Query: 663 AIRKLKHPSRSKKLRSF 679
           A+ KL+ P R+  L ++
Sbjct: 444 ALHKLRQPYRNHMLEAY 460


>gi|206560255|ref|YP_002231019.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia J2315]
 gi|198036296|emb|CAR52192.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 362

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357



 Score = 40.6 bits (93), Expect = 0.87,   Method: Composition-based stats.
 Identities = 24/115 (20%), Positives = 40/115 (34%), Gaps = 10/115 (8%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA---------DRSTDDPVRMYLREMG 129
           D DD+ + E   ++ D  +   +     ++                 T D ++ YL  + 
Sbjct: 33  DEDDVAENERDLEARDAEAEGGDDEREGRQEAAPDVDDFRTLLQAELTADTIQHYLNRIS 92

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  VKPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 146


>gi|307155201|ref|YP_003890585.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306985429|gb|ADN17310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 295

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 98/284 (34%), Positives = 163/284 (57%), Gaps = 16/284 (5%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC----------------EASIA 444
              +++  ++  ++ I     ++  +   + + V+K                   +   A
Sbjct: 1   MTKETVDNVKAYLQEIGRTPLLNAQQEIELATQVQKMMALIDKENPTPEEKRIIQQGKRA 60

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K++M+ ANLRLV+S+AKKY  RGL FLDLIQEG+IGL++  EKFD   GYKFSTYA WW+
Sbjct: 61  KRKMINANLRLVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWWI 120

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+TR+IADQS TIR+P H+ + ++K+ R  R+++ ++ R PT +E+A  L + +  + 
Sbjct: 121 RQAMTRAIADQSRTIRLPSHLTESLNKLKRVTRQLTGELGRRPTEQELANALELSLHELH 180

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            + +      S    +  ED     + +   N+ +P D   Q  LR     +L SL PR+
Sbjct: 181 AIRQADHRTRSYSLNMKMEDEQTELEELLADNSETPNDFVAQIELRSMVDELLESLPPRQ 240

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + ++ +R+G+      +LEEVG    ++RER+RQ++ +A+R LK
Sbjct: 241 QEIIALRYGLKNGRQMSLEEVGNYCNLSRERVRQLQNRAMRTLK 284



 Score = 39.1 bits (89), Expect = 2.7,   Method: Composition-based stats.
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            + T D V+ YL+E+G   LL+ + EI +A +++ 
Sbjct: 2   TKETVDNVKAYLQEIGRTPLLNAQQEIELATQVQK 36


>gi|87302558|ref|ZP_01085375.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
 gi|87282902|gb|EAQ74859.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
          Length = 307

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 87/257 (33%), Positives = 142/257 (55%), Gaps = 7/257 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E      + R+       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL++A 
Sbjct: 48  EACDYNDVERRTIRTGERAKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLVRAV 107

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK+D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+      
Sbjct: 108 EKYDPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLLQANGL 167

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
             +P+E+A  + +P+  V  +L        +SL+  +    D + L D +          
Sbjct: 168 TASPQELAATMHLPLAEVEDLLSCELRSITVSLQGVVKSKSDPTELVDVLASDEMPPMER 227

Query: 603 SAIQANLRETTTRVLA--SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQI 659
           + + +    +  R+L   +LTPRE  V+ +RFG+ G +   TL EV +Q   +RE  RQ+
Sbjct: 228 AEL-SERSASVWRLLDVSNLTPRERTVVMLRFGLDGGHEWRTLAEVARQLGCSREYCRQV 286

Query: 660 EAKAIRKLKHPSRSKKL 676
             +A+RKL+       L
Sbjct: 287 VQRALRKLRKAGVQSGL 303


>gi|293363636|ref|ZP_06610388.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
 gi|292552792|gb|EFF41550.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
          Length = 492

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 107/270 (39%), Positives = 170/270 (62%), Gaps = 11/270 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   + + +   + KG      A+ +++  NLRLVI+ AKKY NRGL F+DLI EGN G+
Sbjct: 221 LKPDQEKQLAKQMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRGLTFIDLISEGNAGI 280

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +K++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  
Sbjct: 281 LKAVQKYNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQ 340

Query: 542 KIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++  EPT  +IA +       E VR + KI  +PISL+  IG E+ S   DF++D N ++
Sbjct: 341 ELGHEPTDSQIANRFGNDYTEEKVRYIRKINVDPISLDKQIGKENDSSFSDFVKDDNILN 400

Query: 600 PLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMN------TDHTLEEVGKQF-CV 651
           P+D A Q  L E    ++   L   E  ++  R+G+G++        H+L+E+ ++   V
Sbjct: 401 PVDYASQEQLSELLIDLIDKSLEKDERELICKRYGVGVDSNGEKYRVHSLDELARERGGV 460

Query: 652 TRERIRQIEAKAIRKLKHPSRS-KKLRSFL 680
           ++ERIRQIE K +RKLK+ S++ + L+ F+
Sbjct: 461 SKERIRQIENKILRKLKNSSKNGRHLKDFI 490


>gi|188090542|gb|ACD49505.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. hederae]
 gi|188090558|gb|ACD49513.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. pelargonii]
 gi|188090560|gb|ACD49514.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. pelargonii]
 gi|290796546|gb|ADD64843.1| RNA polymerase sigma factor [Xanthomonas hortorum]
          Length = 291

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDDAADDDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090696|gb|ACD49582.1| RNA polymerase sigma factor [Xanthomonas sacchari]
          Length = 286

 Score =  167 bits (422), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 137/334 (41%), Gaps = 53/334 (15%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E         S  +    
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPPVAVSDDDS--- 166

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              + + D +    V   +     + P+ AE                           V 
Sbjct: 167 -ATDADADEDDDEDVDTAEEDAGPTGPDPAE---------------------------VA 198

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 199 RRMEVLATEYAKFKK------AHAKNGAEHKLVTKLRNDIAEVFVTLKLPLPLTDVLVRK 252

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 253 LRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 286


>gi|126660003|ref|ZP_01731125.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126618681|gb|EAZ89428.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 297

 Score =  167 bits (422), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 98/286 (34%), Positives = 166/286 (58%), Gaps = 17/286 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE----------------ASIAKK 446
              +  +R+ ++SI     +S +E   +   ++                        A+ 
Sbjct: 4   KKKVDTVRHYLQSIGKTPLLSGAEEIKLAEEIQAMLPLLEKEELNKEEKKIVVIGQRARD 63

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M++ANLRLV+S+AKKY N GL  LDLIQEG++GL++  EKFD   GYKFSTYA WW++Q
Sbjct: 64  KMIQANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWWIRQ 123

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA+QS TIR+P+H+ + ++K  ++ R ++ K+ R+PT +EIA+ + + V+ +R +
Sbjct: 124 GITRAIAEQSRTIRLPIHINENLNKYRKSIRELTLKLGRKPTQQEIAENMDITVDKLRFL 183

Query: 567 LKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            +   +  S    I  ++  + LG  + D+  VSP D   Q        R+L +L+PR++
Sbjct: 184 QQAAFKTKSRSLNIVIDENNTELGQLLPDEEGVSPSDFVKQQEKISQINRMLENLSPRQK 243

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+ +RFG+      + + +G+Q  ++ ER RQI ++A+R L+  S
Sbjct: 244 EVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALRILRKQS 289



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +   D VR YL+ +G   LLS   EI +A+ I+A
Sbjct: 2   PTKKKVDTVRHYLQSIGKTPLLSGAEEIKLAEEIQA 37


>gi|307128696|ref|YP_003880726.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
 gi|306483158|gb|ADM90028.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
          Length = 288

 Score =  167 bits (422), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 84/274 (30%), Positives = 148/274 (54%), Gaps = 3/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  E        RK       A   +++ANLR V+SVAK+Y N+
Sbjct: 16  ESLDKYLYEIGKIPLLNNEEEIQFAKFARKTYNI--KAINFLIKANLRFVVSVAKQYQNQ 73

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GL+K   +FD   G+K  +Y++WW++Q+I ++IAD+S  +R P +  
Sbjct: 74  GLNLSDLINEGNLGLIKGIFRFDERKGFKCISYSVWWIRQSILQAIADKSRCVRCPTNKL 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
              +KV +    +    +  P+ ++I + L    + + + LK + +  SL+ PI + + S
Sbjct: 134 AFYNKVNKKYSELEQIYQIPPSIKQIGEYLNSNEKEIEEALKNSVKHTSLDAPIIEGENS 193

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +L D I+   +  P     + +L++   R+L +L+ +E +++ + +G+  +T   LEE+ 
Sbjct: 194 NLYDIIKYDESPHPDLDLEKESLKKDIKRLLDTLSEKEAQIITLHYGLESSTI-NLEEIS 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               +TRER RQIE   +R+LK  SR   LR +L
Sbjct: 253 FLLNLTRERCRQIEIYGLRRLKQSSRKNILRFYL 286



 Score = 37.9 bits (86), Expect = 6.3,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA-MMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           YL E+G I LL+ E EI  AK          +  L ++ L F  ++    +  +    L 
Sbjct: 21  YLYEIGKIPLLNNEEEIQFAKFARKTYNIKAINFLIKANLRF--VVSVAKQYQNQGLNLS 78

Query: 183 EIID 186
           ++I+
Sbjct: 79  DLIN 82


>gi|188090640|gb|ACD49554.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. populi]
          Length = 289

 Score =  167 bits (422), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 50/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D E     + ++ +    P                                V 
Sbjct: 170 DEDAVDEDAEDGDDDAAEEEAGPTGPDPVE----------------------------VA 201

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 202 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 255

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 256 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 289


>gi|188090632|gb|ACD49550.1| RNA polymerase sigma factor [Xanthomonas melonis]
 gi|188090634|gb|ACD49551.1| RNA polymerase sigma factor [Xanthomonas melonis]
 gi|188090636|gb|ACD49552.1| RNA polymerase sigma factor [Xanthomonas melonis]
 gi|188090638|gb|ACD49553.1| RNA polymerase sigma factor [Xanthomonas melonis]
          Length = 291

 Score =  167 bits (422), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 136/334 (40%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEIAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + + + D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPIAAADDDAVDGDED 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D  + +   E A     D                                        V 
Sbjct: 181 DDGDEDASEEEAGPTGPDPAE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +  L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDVAAIFTTFKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|240047243|ref|YP_002960631.1| RNA polymerase sigma factor [Mycoplasma conjunctivae HRC/581]
 gi|239984815|emb|CAT04802.1| RNA polymerase sigma factor [Mycoplasma conjunctivae]
          Length = 533

 Score =  167 bits (422), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 112/303 (36%), Positives = 169/303 (55%), Gaps = 11/303 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D H     K F +  ++N +    D I      I        ++  E + +   +     
Sbjct: 226 DIHESRKPKIFSDDTYRNKLTDTNDIIKWYMRWIGKYGKL--LTYEEEQELARKMEIPGR 283

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
               A+  +++ NLRLVI+ AK+Y NRGL F+DLI EGN+G+MKA  K+D   G+KFSTY
Sbjct: 284 VGRKARDTLIKRNLRLVINNAKRYKNRGLNFIDLISEGNLGIMKAISKYDRTKGFKFSTY 343

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-- 557
           A WW++Q+ITR++ADQ+  IRIPVHM + I+K+ +  R +  K    P+ EEIA  +   
Sbjct: 344 ATWWIRQSITRAVADQARLIRIPVHMVETINKINKIERELQQKNGVTPSAEEIADVMGAD 403

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
              E VR + KI  +PISL+  IG E+ S   DFI+D++ +SP D A Q    +    ++
Sbjct: 404 FTPEKVRYIRKINIDPISLDKAIGKEEDSSFSDFIKDESVISPSDYAEQEEKSKVLIEMI 463

Query: 618 A-SLTPREERVLRMRFGIGMN------TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             +L   E+  +  R+GIG +        H+ +E+     VT+ERIRQIE+K ++KL+ P
Sbjct: 464 KNNLEEEEQEFIMRRYGIGNDKNGRQYRAHSYDELAADRGVTKERIRQIESKILKKLRAP 523

Query: 671 SRS 673
            R 
Sbjct: 524 QRR 526



 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 42/99 (42%), Gaps = 9/99 (9%)

Query: 58  VSSEQMEDT------VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN--SSVFLQKR 109
           + SE +++       +  + +     VD      +   ED +D      +    +F    
Sbjct: 181 LDSEDLDNIDIDSSDLEDIDDEDFTEVDDSLKIQDIDDEDYMDHHDIHESRKPKIFSDDT 240

Query: 110 KDSADRSTDDPVRMYLREMGSI-ELLSREGEIAIAKRIE 147
             +    T+D ++ Y+R +G   +LL+ E E  +A+++E
Sbjct: 241 YRNKLTDTNDIIKWYMRWIGKYGKLLTYEEEQELARKME 279


>gi|290796542|gb|ADD64841.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 289

 Score =  166 bits (421), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 137/333 (41%), Gaps = 49/333 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
           L  +   I  +E ++L LA +   + R  F+  
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRS 289


>gi|188090498|gb|ACD49483.1| RNA polymerase sigma factor [Xanthomonas cassavae]
 gi|188090624|gb|ACD49546.1| RNA polymerase sigma factor [Xanthomonas cassavae]
 gi|188090626|gb|ACD49547.1| RNA polymerase sigma factor [Xanthomonas cassavae]
          Length = 290

 Score =  166 bits (421), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 137/334 (41%), Gaps = 49/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+            GF    E         ++      
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAV 169

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D    + D +        +     + P+  E                           V 
Sbjct: 170 DEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VA 202

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 203 TRMENLANEYAKFKKI------HAKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 256

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 257 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|194696078|gb|ACF82123.1| unknown [Zea mays]
 gi|323388703|gb|ADX60156.1| SIGMA70-like transcription factor [Zea mays]
          Length = 541

 Score =  166 bits (421), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 85/323 (26%), Positives = 152/323 (47%), Gaps = 16/323 (4%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE------IKSISVE 419
             + F    + RE      +  +     + +N +  E      ++ +      ++  +  
Sbjct: 225 PDEPFRLFLRDRETTEFLTAKEEKQMFSQIQNLMKLEGAQ-RNLQAQCGREPTVEEWAQA 283

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
            G+S  E        +         +++M  +N RLVI VA+KY   GL   DL+Q+G  
Sbjct: 284 VGMSCREL-------QSCVRTGRRCREKMARSNFRLVIHVARKYEGCGLDIQDLVQDGCC 336

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMK  EKF+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV +     
Sbjct: 337 GLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMEC 396

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
                 +PT E +A++  + +E + K+   T++  S++  +  +D     +  ED N   
Sbjct: 397 IMD-GEQPTNEVVARRAGITIEKLAKLRAKTRKVRSMQDRVWSDDGVTYQEITEDPNIEG 455

Query: 600 PLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           P  S  +  +R+     L   L+PRE+ ++  RFGI      TL  +G  + +++ERIRQ
Sbjct: 456 PEVSVDRLMMRQQVRSFLTGILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQ 515

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           ++ KA+ KL++   ++    + D
Sbjct: 516 VQNKALDKLRNSISAQGFHVYFD 538


>gi|307824679|ref|ZP_07654903.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
 gi|307734333|gb|EFO05186.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
          Length = 342

 Score =  166 bits (421), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 90/269 (33%), Positives = 159/269 (59%), Gaps = 3/269 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            +  S+   R  +  +S    ++  + +   S           A+K M+E+NLRLV+ ++
Sbjct: 63  RQDKSMDATRVYLNELSRSQLLTADQEKIYGSRA---LLGDEAARKIMIESNLRLVVKIS 119

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           ++Y NRGL  LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR
Sbjct: 120 RRYLNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIR 179

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+  +++  ++  R +S  ++ EP  E+IA+ L +PV  V K+LK+ +   S++ P 
Sbjct: 180 LPIHIVKEMNTYLKAQRHLSQLLEHEPNAEDIAEHLDIPVNKVEKMLKLNERVTSIDMPG 239

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +    L + I D  ++SP +   +  ++    + +  L+ ++  V+  R+G+      
Sbjct: 240 GKDFDKPLVESISDGESLSPAEKIQEDGIKHNIAKWVFQLSEKQREVICRRYGLCGYEGS 299

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TLE+V ++  VTRER+RQI+   ++++K 
Sbjct: 300 TLEQVAQELGVTRERVRQIQMDGLKRMKE 328



 Score = 37.5 bits (85), Expect = 7.3,   Method: Composition-based stats.
 Identities = 27/112 (24%), Positives = 38/112 (33%), Gaps = 9/112 (8%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A    +      +S    + D  R+YL E+   +LL+ + E     R   G       + 
Sbjct: 49  AQADDIDEIITIESRQDKSMDATRVYLNELSRSQLLTADQEKIYGSRALLGDEAARKIMI 108

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
           ES L     I  R  LN G  LL  I         E   G  H  E    ++
Sbjct: 109 ESNLRLVVKISRRY-LNRGLPLLDLI--------EEGNLGLMHAVEKFDPER 151


>gi|91070519|gb|ABE11426.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-3E5]
          Length = 231

 Score =  166 bits (421), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 96/222 (43%), Positives = 149/222 (67%), Gaps = 1/222 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+SVAKKY N+GL+ LDL+QEG IGL +A +KFD  +GYKFSTYA WW++Q 
Sbjct: 1   MMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQG 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +TR+I + + TIR+P+H+ +K+ K+ R +R +S+K  R+PT  E+A ++ +  + +  ++
Sbjct: 61  MTRAIDNSARTIRLPIHISEKLSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKDLEDLI 120

Query: 568 KITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
             +    SL+     E+  S LG+ I D N   P++   +   +E     L+ L  RE++
Sbjct: 121 SQSAPCASLDAHARGEEDRSTLGELIPDPNCEEPMEGMDRTIQKEHLGTWLSQLNEREQK 180

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++R+RFG+      TL E+G+Q  V+RER+RQ+EAKAI KL+
Sbjct: 181 IMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 222


>gi|225849737|ref|YP_002729971.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
 gi|225645950|gb|ACO04136.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
          Length = 285

 Score =  166 bits (421), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 82/275 (29%), Positives = 151/275 (54%), Gaps = 9/275 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            + SIS    +S  E + I    +        A ++++++NLR V++VAK YT  G+ F 
Sbjct: 13  YLNSISKIPLLSPEEEKEIAKKAK---EGDKEALEKLIKSNLRFVVNVAKNYTGYGIPFQ 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  GNIGL++AA++FD   G +F +YA+WW+KQ+I ++I  Q   I+IP   ++   K
Sbjct: 70  ELISAGNIGLIEAAKRFDPERGVRFISYAIWWIKQSILQTIQSQKDIIKIPQKTQNLSMK 129

Query: 532 VVRTARRMSNKIKREPTPEEIAKK------LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           +      +  ++ REP   EI +       + +  E +   L I +  +SL+TP+  ++ 
Sbjct: 130 IDTAYLELKERLNREPKYSEIKEYLKEHENIDIDEETIENYLLIKRHSVSLDTPVDMDEG 189

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           +   D I   +     ++ ++ ++ +    +L+ L+ RE  ++  RFG+      TL E+
Sbjct: 190 TFFIDLISKHSTKDIEENIVRESIEKEIEYILSHLSERERFIIVNRFGLNGEEPKTLREI 249

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           GK+  ++RER+RQIE +A++K++  +  K L+  L
Sbjct: 250 GKELGISRERVRQIEIRALKKIRALATKKHLKDLL 284



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 21/41 (51%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           YL  +  I LLS E E  IAK+ + G    +  L +S L F
Sbjct: 13  YLNSISKIPLLSPEEEKEIAKKAKEGDKEALEKLIKSNLRF 53


>gi|188090512|gb|ACD49490.1| RNA polymerase sigma factor [Xanthomonas oryzae]
          Length = 289

 Score =  166 bits (421), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 137/333 (41%), Gaps = 49/333 (14%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNS 102
            E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  
Sbjct: 1   AEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEE 60

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL
Sbjct: 61  AAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPL 120

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           + + L+   +   +G   L EI+            GF    E         ++      D
Sbjct: 121 STEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVD 169

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
               + D +     +  +     + P+  E                           V  
Sbjct: 170 EDALDEDDDEDGDDAAAEEEVGPTGPDPVE---------------------------VAT 202

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
            +  +A  Y + + +        K+          +E +  +  +L L     D LV QL
Sbjct: 203 RMQNLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQL 256

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
             +   I  +E ++L LA +   + R  F+   
Sbjct: 257 RGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 289


>gi|171321354|ref|ZP_02910311.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
 gi|171093372|gb|EDT38562.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
          Length = 361

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 25/114 (21%), Positives = 39/114 (34%), Gaps = 9/114 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMGS 130
           D DD+ + E   ++ D  +          +     D          T D ++ YL  +  
Sbjct: 33  DEDDVAENERDIEASDAEADGDGEREGRTEAAPDVDDFRALLQAELTADTIQHYLNRISV 92

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|213029652|ref|ZP_03344099.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 322

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 95/260 (36%), Positives = 164/260 (63%), Gaps = 3/260 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKAIR 665
           G++  +TRER+RQI+ + +R
Sbjct: 292 GREIGLTRERVRQIQVEGLR 311



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|7416823|dbj|BAA94072.1| rpoS [Rubrivivax gelatinosus]
          Length = 322

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 96/272 (35%), Positives = 155/272 (56%), Gaps = 7/272 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ ++ I     +S  E        R        A++ M+E NLRLV+S+AK Y  RG+
Sbjct: 48  LQSYLRDIRRAPLMSAEEEHATAVRAR---AGDFAARQAMIERNLRLVVSIAKHYVGRGM 104

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLI+EGN+GLM A  KF+   G++FSTYA WW++Q+I R+I  Q+  IR+PVH+  +
Sbjct: 105 PMIDLIEEGNLGLMHATGKFEPERGFRFSTYASWWIRQSIERAIMHQARLIRLPVHVVRE 164

Query: 529 IHKVVRTARRMS----NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +++V++  R +      + +R  + +E+A  L  PVE V ++LK+ ++P SL+ P+  E 
Sbjct: 165 LNQVLKARRALESARRGEAERPVSVDEVAAALQRPVEEVAELLKLAEQPTSLDMPLERES 224

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              + D + D++A+ PL   +           LA L  RE  VL  RFG+      TLEE
Sbjct: 225 GESMLDTVADEDAIDPLGLTLSREAVHLLDNGLAELNEREREVLAGRFGLRDREPETLEE 284

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  +  +TRERIRQI+ +A+ KLK     + +
Sbjct: 285 LAARLGLTRERIRQIQQEALLKLKRRMVRRGV 316



 Score = 41.7 bits (96), Expect = 0.40,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 42/128 (32%), Gaps = 3/128 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D  D   E         +     ++    +     +    + ++ YLR++    L+S E 
Sbjct: 6   DAHDGPAEGSDTFEPGASPEVPEAAEAPAQVPADGEGEHGNTLQSYLRDIRRAPLMSAEE 65

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           E A A R  AG      ++ E  L     I     +  G  ++  I   E  +G     G
Sbjct: 66  EHATAVRARAGDFAARQAMIERNLRLVVSIAKHY-VGRGMPMIDLI--EEGNLGLMHATG 122

Query: 199 FFHGTEGH 206
            F    G 
Sbjct: 123 KFEPERGF 130


>gi|188090484|gb|ACD49476.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
          Length = 284

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 138/334 (41%), Gaps = 55/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  Q L+   ++  +G   L EI+            GF    E         S +     
Sbjct: 121 LAVQTLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPVVVASDE----- 164

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                +   +   +V   +     + P+ AE                           V 
Sbjct: 165 -DSAADASDDDDEEVEAAEEEAGPTGPDPAE---------------------------VA 196

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +D +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 197 RRMDALATEYAKFKK------AHAKNGAEHKLVTKLRTDIAEVFVTLKLPLPLTDVLVRK 250

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 251 LRDTMAQVKDHERRVLHLATHVARMPRKEFIRSW 284


>gi|88809912|ref|ZP_01125417.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786102|gb|EAR17264.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 355

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 94/274 (34%), Positives = 158/274 (57%), Gaps = 5/274 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVI 457
           E+  +  +  E++       +  +E      +    +++       AK+ MV ANLRLV+
Sbjct: 74  ELMELESVEAELQEKRGGEAVLAAELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVV 133

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 134 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 193

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P + V++++   ++P+SLE
Sbjct: 194 TIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEDEVKELMCRARQPVSLE 253

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L D +     +          L+     +L  L   +ERVLRMR+G+   
Sbjct: 254 MKVGDGDDTELLDLLAGDGELPSE-QVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGE 312

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 313 EPMSLTGIGRVIGISRDRVRNLERDGLAGLRRLS 346



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 23/43 (53%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +        +  D VR YLR++G + LLS + EI + ++++ 
Sbjct: 32  AKTTASRPSGTDVDLVRSYLRDIGRVPLLSHQQEITLGRQVQE 74


>gi|188090700|gb|ACD49584.1| RNA polymerase sigma factor [Xanthomonas sacchari]
          Length = 286

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 137/334 (41%), Gaps = 53/334 (15%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E         S  +    
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPPVAVSDDDS--- 166

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              + + D +    V   +     + P+ AE                           V 
Sbjct: 167 -ATDADADEDDDEDVDTAEEDAGPTGPDPAE---------------------------VA 198

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 199 RRMEVLATEYAKFKK------AHAKNGAEHKLVTKLRNDIAEVFVTLKLPLPLTDVLVRK 252

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 253 LRDTMAQVKDHERRVLHLATHVARVPRKDFIRSW 286


>gi|188090524|gb|ACD49496.1| RNA polymerase sigma factor [Xanthomonas hortorum pv. taraxaci]
 gi|188090686|gb|ACD49577.1| RNA polymerase sigma factor [Xanthomonas gardneri ATCC 19865]
 gi|188090690|gb|ACD49579.1| RNA polymerase sigma factor [Xanthomonas cynarae]
 gi|188090692|gb|ACD49580.1| RNA polymerase sigma factor [Xanthomonas cynarae]
          Length = 291

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDDAADDDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATAVARMPRKDFIRSW 291


>gi|148656381|ref|YP_001276586.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
 gi|148568491|gb|ABQ90636.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
          Length = 398

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 89/249 (35%), Positives = 141/249 (56%), Gaps = 2/249 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +    +  A   ++  NLRLV  +A +Y    R L F DL+QEG IGL+KA E+FD  
Sbjct: 148 AERRIKASEEAIDTLMRCNLRLVAKIATRYMPYARHLTFDDLLQEGRIGLLKAIERFDQN 207

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              + STYA++W++Q+I R++ADQ   +R+PVH+ +++H++ +T  +      REP   E
Sbjct: 208 CRGRLSTYAVYWIRQSIQRALADQDRMVRLPVHIVEQLHRLRKTCEQFRCIHGREPGDAE 267

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L + +  VR + ++ +   S++ P+G +  + LG+ I D     P     Q  L  
Sbjct: 268 LANALGVSLAKVRSLWRVAQHHTSIDRPVGADTNTFLGELIADDREEGPDFICEQQLLHA 327

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL  L+ RE  +L  R+G+     HTLEE+G+ F +TRERIRQIE KA+++L    
Sbjct: 328 VLREVLGHLSSRERDILERRYGLIDGQTHTLEEIGQIFGLTRERIRQIERKALKRLNRGE 387

Query: 672 RSKKLRSFL 680
             + L+ FL
Sbjct: 388 YRRILQPFL 396


>gi|188090608|gb|ACD49538.1| RNA polymerase sigma factor [Xanthomonas theicola]
 gi|188090610|gb|ACD49539.1| RNA polymerase sigma factor [Xanthomonas theicola]
 gi|188090612|gb|ACD49540.1| RNA polymerase sigma factor [Xanthomonas theicola]
          Length = 286

 Score =  166 bits (421), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 135/334 (40%), Gaps = 53/334 (15%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  ++L+   ++  +G   L EI+            GF    E                D
Sbjct: 121 LAVESLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAP----PPVVAASD 165

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D        ++   V   +     + P+ AE                           V 
Sbjct: 166 DDAADADADDADDDVDTAEEDAGPTGPDPAE---------------------------VA 198

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +D +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 199 RRMDLLASEYAKFKK------AHAKNGAEHKLVTKLRTDIAEVFVTLKLPLPLTDVLVRK 252

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L     ++  +E  +L LA     + R  F+   
Sbjct: 253 LRATMAQVKDHERRVLHLATHVARMPRKDFIRSW 286


>gi|158341079|ref|YP_001522246.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311320|gb|ABW32932.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 89/265 (33%), Positives = 149/265 (56%), Gaps = 5/265 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K +     +S  E   +   V+        AK+ M+E NLRLV+S+AKK+ + GL
Sbjct: 8   VQAYLKEMGRYPLLSHEEEIRLARQVK---AGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLIQEG+IGL  A +KFD   G KFSTYA WW+ +AI R++  QS TI IP+H  ++
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRALKSQSRTIYIPIHQWER 124

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            H++ +  R+++ +  R PT +E++    +    +R  L+  +   SL+ P+G E    L
Sbjct: 125 AHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAISSLDQPVGPEQKDAL 184

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I+ ++A   +   ++    +  TR +A LT RE  ++  R+G+      ++  +GK 
Sbjct: 185 IDLIQTEDAALSIMDGLEIE--DALTRCMAYLTERERFIVDQRYGLTDGQPKSMGAIGKP 242

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             ++RER+RQI   A++K+    RS
Sbjct: 243 IGISRERVRQILNIAMKKMTRQVRS 267



 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------ 171
           +D V+ YL+EMG   LLS E EI +A++++AG       + E  L     I  +      
Sbjct: 5   NDSVQAYLKEMGRYPLLSHEEEIRLARQVKAGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 172 ---DELNDGTTLLREIIDLEAC 190
              D + +G+  L   +D    
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDL 86


>gi|302851352|ref|XP_002957200.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
 gi|300257450|gb|EFJ41698.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
          Length = 733

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 148/251 (58%), Gaps = 3/251 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V            AK+ ++++N RLV++V K+Y  +G+   DL+ EG  GL++  E +D 
Sbjct: 461 VMAYNMRYDAGLKAKELLLKSNYRLVMTVCKRYIGKGMHLQDLVSEGVKGLLRGVEMYDA 520

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++F TYA WW++QA++RS+A+    +R+PVHM +++ K+      ++ ++ REP+ E
Sbjct: 521 SRGFRFGTYAHWWIRQAVSRSMAETGRAVRLPVHMIEQLTKLKNATAALAMELNREPSVE 580

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ + +P   V  +L   +   S+E+ IG +D   + D ++D+   +        ++R
Sbjct: 581 EMAEAVGLPPSRVELLLDAARAASSMESAIGGDDGLTIKDAVQDERMAADEAFGSD-SMR 639

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL--K 668
                +L  L+ RE  VLR+RFG+    + TLE++G +  VTRERIRQ+EAKA+RKL  K
Sbjct: 640 ADVESMLEGLSDREACVLRLRFGLEDGVEWTLEDIGSRLGVTRERIRQLEAKALRKLQVK 699

Query: 669 HPSRSKKLRSF 679
               + KL+ +
Sbjct: 700 TIDVTGKLKDY 710


>gi|193222342|emb|CAL62001.1| Putative RNA polymerase sigma-70 factor [Herminiimonas
           arsenicoxydans]
          Length = 808

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 101/243 (41%), Positives = 160/243 (65%), Gaps = 5/243 (2%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A+ +M  ANL+LV S A KY+  G++FLDLIQEGNIGL++A EKFD+  G+KFSTYA+
Sbjct: 434 EEARSQMAIANLKLVHSTATKYSWSGMEFLDLIQEGNIGLLRAIEKFDYRRGFKFSTYAI 493

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR+IADQ+  IR+PVH+ + I++V R   ++ + + +    +EI+  L+MP+ 
Sbjct: 494 WWIRQAITRAIADQTRLIRVPVHLVESINQVERHKNQVEHILGKSLKAQEISDALSMPLR 553

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVL 617
            V + L      ++++  I  E  +     + ++N    + +P   AI+ +L +   R+L
Sbjct: 554 KVEQCLAANVSILNIDDLIERETENQDEALVLEENLIDPSATPEQLAIKTSLSKVLNRIL 613

Query: 618 ASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + L  +E  +LR+RFG+  N   HTLEEVG+   +TRER+RQIEAKA+ ++++P+R K +
Sbjct: 614 SDLPEKEAHILRLRFGLYKNVEPHTLEEVGQLLGITRERVRQIEAKALTRIRYPNRRKDI 673

Query: 677 RSF 679
             F
Sbjct: 674 AIF 676



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 82/232 (35%), Gaps = 7/232 (3%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED---TVA 68
           +SE  +S   ++ D   +S + +I+   + G V + ++       E   +        + 
Sbjct: 159 ESESTNSFRKILDDDKLNSIRTLIEQGLRNGGVRLSQVVELAVDFESDGKGNNLYLCLIR 218

Query: 69  MLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM 128
           + S++GI V D +     E +        +  N ++     + S      DP R Y +  
Sbjct: 219 IFSDIGIVVDDDESWWSSETTHSDQPYEGAIVNEALEYLSIQLSGRG---DPGRYYYKAY 275

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
            + +LLSR  E  + K IE G     + +    +    L+     +  G   +R +I  +
Sbjct: 276 SN-QLLSRFDEQELGKVIEKGLDDAGSCIGNCRILLGELLKAAQLVKQGNMPVRSLIKFD 334

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
                +        +     +     SQ    ++  +    I +    SK +
Sbjct: 335 QGSDDDEIDEDASESLLEEDEGALPRSQGTFIEEFNKRIAVIRNLVDGSKGE 386


>gi|158339957|ref|YP_001521127.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310198|gb|ABW31813.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 85/269 (31%), Positives = 149/269 (55%), Gaps = 5/269 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +   +   ++ +     +S  E   +    +     +  AK+ M+E NLRLV+S+AKK+ 
Sbjct: 4   NYDSLHYYLQEMGRYPLLSHEEEIELARQAK---AGSLRAKQRMIECNLRLVVSIAKKHQ 60

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRGL  LDLIQEG+IGL  A +KF+   G +FSTYA WW++Q IT ++  +S  I +P +
Sbjct: 61  NRGLPLLDLIQEGSIGLSTAVDKFEIAQGCRFSTYAYWWIRQGITAALRAKSRPIYLPQY 120

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
             + I+K+ +  R ++ K+ REP+  E+++   +  + +   L++ ++  SL+ P+G E 
Sbjct: 121 QWEMINKIKKHYRELNQKLGREPSLSELSESTEIKPKTINLTLQLFQKISSLDQPVGPEQ 180

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D +   N  +    ++Q +  E    V+A L  RE  VL  R+G+  +   ++ E
Sbjct: 181 KDSLLDLLPGDNQPTLYMESLQRD--EQLFHVMAHLDERERLVLSQRYGLEDDQPKSMRE 238

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +G+Q  ++ E IR I  K ++KL+  + S
Sbjct: 239 IGEQIGLSHEGIRLILKKIMKKLERYAES 267



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------- 171
           D +  YL+EMG   LLS E EI +A++ +AG       + E  L     I  +       
Sbjct: 6   DSLHYYLQEMGRYPLLSHEEEIELARQAKAGSLRAKQRMIECNLRLVVSIAKKHQNRGLP 65

Query: 172 --DELNDGTTLLREIIDLEAC 190
             D + +G+  L   +D    
Sbjct: 66  LLDLIQEGSIGLSTAVDKFEI 86


>gi|302555769|ref|ZP_07308111.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302473387|gb|EFL36480.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 339

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 85/243 (34%), Positives = 152/243 (62%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +   +   AK  MV ANLRLV+S+A+++ +RGL  LD+IQEGN+GL++A EKFD   G
Sbjct: 92  LEETARDGQRAKDHMVRANLRLVVSMARRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKG 151

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +KFSTYA WW++Q+I R +A  + T+R+P+ + +++ K+ +  RR+   + REP+  E+A
Sbjct: 152 FKFSTYATWWIRQSIERGLAAHARTVRLPMQVVEQLQKIAKVERRLQLDLGREPSVAEVA 211

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++  +  + +  + ++ ++ +SL+TP+ D   + +GD I D   +   + A    L E  
Sbjct: 212 RESGLAEDRIDWLRRVGRQAVSLDTPVDDTGETVVGDLIPDTEVLQAPEVAEYTALAEEL 271

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              + +L PRE  +L +R+G+      T +EV ++  +TRER+RQ+E  ++ +L+ P   
Sbjct: 272 REAVGTLGPREAMILSLRYGLHDGHTRTRDEVARRVGLTRERVRQLEKASLARLREPENR 331

Query: 674 KKL 676
           ++L
Sbjct: 332 ERL 334



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 13/35 (37%), Positives = 23/35 (65%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           D +  YL ++G+  LL+ E E+ +A+R+EAG   +
Sbjct: 37  DLLGQYLAQIGATPLLTAEDEVRLARRMEAGVRAL 71


>gi|1017750|gb|AAA79182.1| RpoS [Serratia entomophila]
          Length = 332

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 170/271 (62%), Gaps = 3/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV  V ++L++ +   S++TP+G +  
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVHDVSRMLRLNERMPSVDTPLGGDSE 233

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 234 KALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 293

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 294 GREIVLTRERVRQIQVEGLRRLREILQMQGL 324



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 41/107 (38%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L    ++ N     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENGTEAESFDEKALVEEEASENDLAEEELLSQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|172060780|ref|YP_001808432.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria MC40-6]
 gi|171993297|gb|ACB64216.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MC40-6]
          Length = 361

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 25/114 (21%), Positives = 39/114 (34%), Gaps = 9/114 (7%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD--------RSTDDPVRMYLREMGS 130
           D DD+ + E   ++ D  +          +     D          T D ++ YL  +  
Sbjct: 33  DEDDVAENERDLEASDAEADGDGEREGRAEAAPDVDDFRALLQAELTADTIQHYLNRISV 92

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|238027063|ref|YP_002911294.1| RNA polymerase sigma factor RpoS [Burkholderia glumae BGR1]
 gi|76057940|emb|CAJ30487.1| stationary phase sigma factor [Burkholderia plantarii]
 gi|121663602|emb|CAM12359.1| stationary phase sigma factor [Burkholderia glumae]
 gi|237876257|gb|ACR28590.1| Stationary phase sigma factor [Burkholderia glumae BGR1]
          Length = 364

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 104/321 (32%), Positives = 165/321 (51%), Gaps = 18/321 (5%)

Query: 372 ERHQGRELDPHWVS-----YAKDFPEGEWKNFVACEVDSILK--IRNEIKSISVETGISI 424
             ++ RE D                  E  +F A     +    I++ +  ISV+  +++
Sbjct: 42  REYEARESDAEESDGEREGRGGSESAPEPDDFRAVLQAELTADTIQHYLNRISVKPLLTV 101

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+  LDLI+EGN+GLM A
Sbjct: 102 EEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGVPLLDLIEEGNLGLMHA 158

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +     
Sbjct: 159 IEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEKNSM 218

Query: 545 REPTPEE--------IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                 E        IA       E V  +L + +   SL+ P+  +  S L D + D  
Sbjct: 219 STGEAAERREAGIDDIAYLTGKTAEEVTDILALNEHTASLDAPLDLDPASSLLDLLPDDQ 278

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           + SP        L   T   L+ L+ +   V+  RFG+      TLEE+  +  +TRER+
Sbjct: 279 SQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPATLEELADEMGLTRERV 338

Query: 657 RQIEAKAIRKLKHPSRSKKLR 677
           RQI+ +A+ +LK    S  +R
Sbjct: 339 RQIQQEALVRLKRFFASNGVR 359



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 26/117 (22%), Positives = 42/117 (35%), Gaps = 12/117 (10%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-----------DPVRMYLRE 127
           D DD  + E   ++ +  +  S+     +   +SA    D           D ++ YL  
Sbjct: 33  DDDDTAESEREYEARESDAEESDGEREGRGGSESAPEPDDFRAVLQAELTADTIQHYLNR 92

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +    LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 93  ISVKPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 148


>gi|2398853|dbj|BAA22215.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 571

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 147/284 (51%), Gaps = 5/284 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +      + +   ++ S+S     +    +    ++ +        + E+V++   LV+ 
Sbjct: 291 MERIRTQLEEESGKVASLSCWAAAAGMNEK----LLMRNLHYGWYCRDELVKSTRSLVLF 346

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W++++++  ++  +  
Sbjct: 347 LARNYRGMGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARG 406

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPT-PEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           + IP  +   I+ + +  + +      +    EEIAK     V+ +R   +  K   S++
Sbjct: 407 VHIPSSIIRTINHIQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRAANQCLKVVGSID 466

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD  T+   +F  D    SP ++ ++ + R     +L  L PRE++V+ +R+G+   
Sbjct: 467 KKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDY 526

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              +LEE+GK F V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 527 RPKSLEEIGKLFKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570


>gi|188090518|gb|ACD49493.1| RNA polymerase sigma factor [Xanthomonas hortorum]
          Length = 291

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDDAADDDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKEFIRSW 291


>gi|14581457|gb|AAK29754.1| stationary phase sigma factor RpoS [Azotobacter vinelandii]
          Length = 238

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/241 (36%), Positives = 145/241 (60%), Gaps = 3/241 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     ++ +E  H   + ++        +K M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 1   LNEIGFSPLLTPAEEVHFARLAQR---GDPAGRKRMIESNLRLVVKIARRYVNRGLSLLD 57

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 58  LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVY 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +R AR ++ K+  EP+ EEIA  L  PV  V+++L + +   S++  +G +    L D +
Sbjct: 118 LRAARELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDVL 177

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D     P D     +L ++  + L  LT ++  V+  RFG+  +   TLEEVG++  +T
Sbjct: 178 TDDRPFDPCDLLQDDDLSQSIDQWLFDLTEKQREVVVRRFGLRGHESCTLEEVGQEIGLT 237

Query: 653 R 653
           R
Sbjct: 238 R 238



 Score = 37.9 bits (86), Expect = 5.4,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L E+G   LL+   E+  A+  + G       + ES L     I  R  +N G +LL  I
Sbjct: 1   LNEIGFSPLLTPAEEVHFARLAQRGDPAGRKRMIESNLRLVVKIARRY-VNRGLSLLDLI 59


>gi|115475493|ref|NP_001061343.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|30698490|dbj|BAC76602.1| Sig6 [Oryza sativa Japonica Group]
 gi|40253642|dbj|BAD05586.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|40253689|dbj|BAD05631.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|113623312|dbj|BAF23257.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|215712228|dbj|BAG94355.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 572

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 83/320 (25%), Positives = 152/320 (47%), Gaps = 11/320 (3%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
             + F    + RE      +  +     + +  +      I +   ++  +      +++
Sbjct: 257 PDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMK-----IEEAHRKL-EVQCGREPTLA 310

Query: 426 EFRHIV----SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           E+   V      ++         +++M  +N RLVI VA+KY   GL   DL+Q+G  GL
Sbjct: 311 EWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGL 370

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK  EKF+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV +       
Sbjct: 371 MKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIM 430

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   +PT   +A++  + +E + K+   T++P S++  +  ++     +  ED N   P 
Sbjct: 431 E-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPD 489

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            S  +  +R+     L  L+PRE+ ++  RFGI      TL  +G  F +++ERIRQ++ 
Sbjct: 490 LSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQN 549

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
           +A+ KLK  +  +    + D
Sbjct: 550 RALEKLKRSASLQGFDVYFD 569


>gi|261879259|ref|ZP_06005686.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334090|gb|EFA44876.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 291

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 88/276 (31%), Positives = 155/276 (56%), Gaps = 3/276 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I+ E  +S  E   +   + KG  E   A+  +V  NLR V+SVAK+Y ++
Sbjct: 16  EALDRYLSEIAREPMLSPDEEAMLAQAIHKGGPEGDRARDRLVSGNLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+  +DLI EGN+GL+KAAEKFD   G+KF +YA+WW++Q+I  ++A +S  +R+P++  
Sbjct: 76  GISLIDLINEGNMGLVKAAEKFDETRGFKFISYAVWWIRQSIMEALAVKSRIVRMPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
               KV+RT      +  R P+  E+A+ L +    +   +       S++ P+G+++  
Sbjct: 136 GIYGKVIRTTESFLQEHGRVPSNHELAEILQVEEAQITAAMSAGARATSIDAPLGNDEDG 195

Query: 587 HLGDFIE-DKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEE 644
            + D +  D + +    S  + ++ +    +L   L+ RE+R+++  FGIG+    +LEE
Sbjct: 196 SMADMLASDDSGMKSDSSLDKESMNQFINDLLREVLSAREQRIIKESFGIGVME-KSLEE 254

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +     +TRERIRQ+  KA+RK++    +  LR +L
Sbjct: 255 IADSMGMTRERIRQVREKALRKIRFSKYASTLRQYL 290


>gi|254252249|ref|ZP_04945567.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
 gi|124894858|gb|EAY68738.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
          Length = 361

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 159/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 199

Query: 529 IHKVVRTARRMSNKIK--------REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +             RE + ++IA       E V  +L + +   SL+ P+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDAPL 259

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   L+ L+ +   V+  RFG+      
Sbjct: 260 DLDPASSLLDLLPDDQSQSPDAEVQHRELETLTRAWLSRLSDKHRHVIERRFGLNHIEPA 319

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 320 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 356



 Score = 41.7 bits (96), Expect = 0.40,   Method: Composition-based stats.
 Identities = 26/115 (22%), Positives = 41/115 (35%), Gaps = 2/115 (1%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-RKDSADRSTDDPVRMYLREMG 129
            +    V +  DLE  +   D  D      +++  +   R       T D ++ YL  + 
Sbjct: 32  DDEDDVVENERDLEARDAESDGDDEREDRPDAAPDVDDFRALLQAELTADTIQHYLNRIS 91

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 92  VKPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 145


>gi|153311|gb|AAA26765.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450079|prf||1920369C RNA polymerase:SUBUNIT=sigma
          Length = 325

 Score =  166 bits (420), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 149/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            E   AK+  + +NLRLV++V ++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 84  AEGERAKEVFIRSNLRLVVAVVRRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 143

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 144 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNRENGRDPEHAEIAAELDS 203

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + V  VL   ++P+SL   + DE  +  GD +ED +A+SP  S +     E    +L 
Sbjct: 204 TEKRVGDVLDWARDPVSLNMSVDDEGDTQFGDLLEDTSAISPEQSVLSLLRSEELEDLLG 263

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  +R
Sbjct: 264 KLDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAR 317


>gi|188090486|gb|ACD49477.1| RNA polymerase sigma factor [Xanthomonas hyacinthi]
          Length = 284

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 138/334 (41%), Gaps = 55/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  Q L+   ++  +G   L EI+            GF    E         S +     
Sbjct: 121 LAVQTLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPVVVASDE----- 164

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                +   +   +V   +     + P+ AE                           V 
Sbjct: 165 -DSAADASDDDDEEVEAAEEEAGPTGPDPAE---------------------------VA 196

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +D +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 197 RRMDALATEYAKFKK------AHAKNGAEHKLVTKLRTDIAEVFVTLKLPLPLTDVLVRK 250

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 251 LRDTMAQVKDHERRVLHLATHVARMPRKEFIRCW 284


>gi|281357500|ref|ZP_06243988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
 gi|281316103|gb|EFB00129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
          Length = 432

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 95/259 (36%), Positives = 140/259 (54%), Gaps = 1/259 (0%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +  I+    ++  E   +   +          A+  +++ANLRLV+ +A  +   GL  
Sbjct: 163 YMGEIARIPLVNKKEEAELADAIHGDNEDRHEDARSTLIKANLRLVVKIAHDFKGLGLPL 222

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLI EGNIGLM+A EKFD   G KFS+YA WW+KQ++ R++A+QS TIRIPV    KI+
Sbjct: 223 LDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRALANQSRTIRIPVQSAGKIN 282

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+     +++ ++ REP+  EIA+ L      V  +        SL  PI   +     D
Sbjct: 283 KIKSVRMKLAEELGREPSDAEIAEHLDFSERTVAGLRLADLRTFSLHDPIQQGEEGEFQD 342

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D++A++P               +L  L  RE R+L MRFG+  N   TLEEV ++  
Sbjct: 343 IIPDRHAMTPDQILGDVESVFRLMDLLEKLEERERRILEMRFGLRGNRPLTLEEVSQEIG 402

Query: 651 VTRERIRQIEAKAIRKLKH 669
            TRER+RQI+ +A+ KLK 
Sbjct: 403 RTRERVRQIQNQALAKLKQ 421


>gi|323345487|ref|ZP_08085710.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093601|gb|EFZ36179.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 160/275 (58%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     +SI E   +  ++RKG  E   AK++++ ANLR V+SVAK+Y ++
Sbjct: 16  ESLDKYLLEIGRLPMVSIDEETELAQLIRKGGKEGERAKEKLINANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+     +   + +R P+ +E+A    +    + + ++     +S++ P  D+D +
Sbjct: 136 GALSKINSEVAKFEQEHQRRPSTQELASLTNIDENKISQTMRADNHHMSIDAPFSDDDEN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +         + ++       +A+ L PRE  +L+  FGIG  T+  LEE+
Sbjct: 196 SMADVLASGDDSRADRIVDRESMNSDLDDAMANALKPREVAILKESFGIGC-TEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++F +TRER+RQI  K+I+KL+    ++ L  +L
Sbjct: 255 GEEFGLTRERVRQIREKSIQKLRESGYARILVKYL 289


>gi|291445451|ref|ZP_06584841.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348398|gb|EFE75302.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 333

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 104/234 (44%), Positives = 148/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 92  ADGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 151

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 152 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELDS 211

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 212 NAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 272 KLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAH 325



 Score = 38.3 bits (87), Expect = 4.6,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMM 153
           ++++  +      R    + +  D V MYL E+    LL    E+ +++ IEAG     +
Sbjct: 11  STASGETDRASSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTIEAGVYAQQI 70

Query: 154 MASLCESPLTFQALIIWRDELNDGTT 179
           +    ES             + DG  
Sbjct: 71  LDGEVESDAGDAKREELEALVADGER 96


>gi|159029420|emb|CAO90796.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 377

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 181/285 (63%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    +   K++  +     +T  +I+        +         AK++M+ +NLRLV
Sbjct: 92  KFLMEAEEVRQKLQENLHRPPTKTEWAIALELDNERQLENRLYRGRTAKRKMIRSNLRLV 151

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 152 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 211

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +   ++R P   E+A+ L +  E +R++L++ ++ +SL
Sbjct: 212 RTIRLPIHIVEKLNKLKKAQRILKQDLQRNPNERELAEALEITPEQLRQLLQLRRQSLSL 271

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED +   P D   +  +R+    VL+  LT RE+ V+ +R+G+ 
Sbjct: 272 NHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLA 331

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 332 TSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 376



 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ D ++  E +++ +  +   +  +            S +D V  + +EM    LLS E
Sbjct: 23  LELDSVDFGERTDEDMTESLPETLKNTRGSSGTGYDKGSNEDTVGAFFKEMARYPLLSAE 82

Query: 138 GEIAIAKRIE--AGRAMMMASLCE 159
            EI +A  ++       +   L E
Sbjct: 83  EEIELAYLVKFLMEAEEVRQKLQE 106


>gi|317503800|ref|ZP_07961812.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315665097|gb|EFV04752.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 290

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   ++KG  +   AK+++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ R   +   + +R+P+  E++    +  E + + L      +S++ P  + + +
Sbjct: 136 GSLNKINREINKFEQEYQRKPSLSELSHATKIEEEKIDQSLMADSHHVSIDAPFQEGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++      VL   L  RE  ++R  FGIG +    LEE+
Sbjct: 196 SMVDVMAGGDDSRTDKQVDHESMALELESVLRKVLKEREITIIRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGYAKILMKYL 289



 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|5804831|emb|CAB53534.1| RpoS protein [Escherichia coli O157:H7]
 gi|332087634|gb|EGI92761.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 155-74]
          Length = 298

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 95/248 (38%), Positives = 164/248 (66%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V   R+       +++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKF
Sbjct: 43  EEVYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKF 102

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+
Sbjct: 103 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPS 162

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA++L  PV+ V ++L++ +   S++TP+G +    L D + D+    P D+    +
Sbjct: 163 AEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDD 222

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++  + L  L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 223 MKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 282

Query: 669 HPSRSKKL 676
              +++ L
Sbjct: 283 EILQTQGL 290


>gi|158341157|ref|YP_001522480.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158311398|gb|ABW33009.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 274

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/260 (33%), Positives = 151/260 (58%), Gaps = 5/260 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    +S  E    + + R+       AK+ ++E NLRLV+S+AKK+ NRGL   
Sbjct: 11  YLKEIARYPILSHEEE---ILLARQVNAGNLRAKQRLIECNLRLVVSIAKKHQNRGLPLQ 67

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG+IGL  A +KFD   G +FSTYA WW++Q +T ++  +S  I +P +  + I K
Sbjct: 68  DLIQEGSIGLSNAVDKFDLAQGCRFSTYAYWWIRQGVTAALRAKSRPIYLPQYQWEMISK 127

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  R ++ ++ REP+  E+AK   +  + + + L + ++  SL+ P+G +    L D 
Sbjct: 128 IKKHFRELNQQLGREPSLSELAKATNLKPKTISRTLHLFQKVSSLDQPVGHQQKDTLLDL 187

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +  ++  +    ++Q  L E  ++V+A L  RE+ VL  RFG+  +   ++ E+G+Q  +
Sbjct: 188 MAGEDQPTLYLESLQ--LDEQLSQVMAHLDKREQFVLSQRFGLEDDQPKSMREIGEQIGL 245

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           +RE IR I  K ++KL+  +
Sbjct: 246 SREGIRLILNKIMKKLQKNT 265



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D +  YL+E+    +LS E EI +A+++ AG       L E  L    ++    +  +  
Sbjct: 6   DSLHFYLKEIARYPILSHEEEILLARQVNAGNLRAKQRLIECNLRL--VVSIAKKHQNRG 63

Query: 179 TLLREII 185
             L+++I
Sbjct: 64  LPLQDLI 70


>gi|323345236|ref|ZP_08085459.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093350|gb|EFZ35928.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  166 bits (419), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 152/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI +   +   ++KG  E   AK+ +V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIEDEIELAQKIKKGGPEGERAKERLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     +   + +R P+  E++    +  E + + +      +S++ P  D + +
Sbjct: 136 GSLNKINHEINKFEQENQRRPSISELSDATNIDEEKIGQSMMADGHHVSIDAPFQDGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +      +    ++      VL+  L  RE  +++  FGIG +    LEE+
Sbjct: 196 TMLDVMPGGDDSRTDRNVDHESMAMELNSVLSRVLKDREITIIKECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGNAKILMKYL 289



 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S E EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIEDEIELAQKIKKGGPEGERAKERLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIID 186
           L ++ID
Sbjct: 79  LTDLID 84


>gi|294507979|ref|YP_003572037.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
 gi|294344307|emb|CBH25085.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
          Length = 279

 Score =  166 bits (419), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 168/283 (59%), Gaps = 6/283 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V+ E   + +   EI  I +              + R+ E     A  ++  ANLR V+S
Sbjct: 3   VSREQRMLDQYLQEIGKIDLLEPEEEV------ELARRIEDGDEEALHKLCRANLRFVVS 56

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKY  +GL   DLI EGN GL+KAA++FD   G+KF +YA+WW++QAI +++A+QS  
Sbjct: 57  VAKKYQGQGLSLADLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRV 116

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+P++    I K+ + + R+   + R+P  EE+A++L + V+ VR+ +K T   +S++ 
Sbjct: 117 VRLPLNRIGTISKIRKASARLQQDLDRKPNIEELAEELEIDVQKVREAMKHTSRHLSMDA 176

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P  +ED + L D + D++  SP +  +  +++    R L++L  RE  + R+ FGIG   
Sbjct: 177 PFNEEDDNSLLDVLPDEDNDSPDEEMLSESVKIDIERALSALHDREAEITRLYFGIGREH 236

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             TLEE+GK+F +TRER+RQI+ KA+RKL+     + L+   D
Sbjct: 237 PLTLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQDLQPHTD 279


>gi|188090694|gb|ACD49581.1| RNA polymerase sigma factor [Xanthomonas cynarae]
          Length = 291

 Score =  166 bits (419), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDDAADDDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATAVARMPRKEFIRSW 291


>gi|158340730|ref|YP_001521898.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158310971|gb|ABW32584.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 269

 Score =  166 bits (419), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 152/262 (58%), Gaps = 5/262 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K ++    +S  E   +    +     +  AK+ M+E NLRLV+S+AKK+ NRGL  L
Sbjct: 12  YLKEMARYPLLSHEEEIELARQAK---AGSLRAKQRMIECNLRLVVSIAKKHQNRGLPLL 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEG+IGL  A +KFD   G +FSTYA WW++Q IT ++ ++S  I +P +  DK +K
Sbjct: 69  DLIQEGSIGLSTAVDKFDLAQGCRFSTYAYWWIRQGITAALREKSRPIYLPHNHWDKANK 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +  R ++  + R+P+  E+++   +  + + + L++ ++  SL+ P+G E    L D 
Sbjct: 129 IKKHYRELNQTLGRKPSLSELSEATDIKPKTINRTLQLFQKVSSLDQPVGPEQKDSLLDL 188

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +   +  +    ++Q  L E  ++V+A+L  RE  VL  R+G+  N   +++ +G+Q  +
Sbjct: 189 LAGDDQPTQYMESLQ--LDEELSQVMANLDERERFVLSQRYGLEDNQPKSMKAIGQQIGL 246

Query: 652 TRERIRQIEAKAIRKLKHPSRS 673
           + E IR I  K ++KL+  + S
Sbjct: 247 SHEAIRLILNKIMKKLERYAVS 268



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------- 171
           D +  YL+EM    LLS E EI +A++ +AG       + E  L     I  +       
Sbjct: 7   DSLHFYLKEMARYPLLSHEEEIELARQAKAGSLRAKQRMIECNLRLVVSIAKKHQNRGLP 66

Query: 172 --DELNDGTTLLREIIDLEAC 190
             D + +G+  L   +D    
Sbjct: 67  LLDLIQEGSIGLSTAVDKFDL 87


>gi|169883528|gb|ACA97859.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 377

 Score =  166 bits (419), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 181/285 (63%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    +   K++  +     +T  +I+        +         AK++M+ +NLRLV
Sbjct: 92  KFLMEAEEVRQKLQENLHRPPTKTEWAIALELDNERQLENRLYRGRTAKRKMIRSNLRLV 151

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 152 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 211

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +   ++R P   E+A+ L +  E +R++L++ ++ +SL
Sbjct: 212 RTIRLPIHIVEKLNKLKKAQRILKQDLQRNPNERELAEALEITPEQLRQLLQLRRQSLSL 271

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED +   P D   +  +R+    VL+  LT RE+ V+ +R+G+ 
Sbjct: 272 NHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLA 331

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 332 TSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 376



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ D ++  E +++ +  +   +  +            S +D V  + +EM    LLS E
Sbjct: 23  LELDSVDFNERTDEDMTESLPETLKNTRGSSGTGYDKGSNEDTVGAFFKEMARYPLLSAE 82

Query: 138 GEIAIAKRIE--AGRAMMMASLCE 159
            EI +A  ++       +   L E
Sbjct: 83  EEIELAYSVKFLMEAEEVRQKLQE 106


>gi|188090496|gb|ACD49482.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
          Length = 291

 Score =  166 bits (419), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 138/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + +++ D
Sbjct: 121 LSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + E   E A     D                                        V 
Sbjct: 181 EDGDDEAAEEEAGPTGPDSVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKEFIRSW 291


>gi|188090556|gb|ACD49512.1| RNA polymerase sigma factor [Xanthomonas vasicola]
 gi|188090668|gb|ACD49568.1| RNA polymerase sigma factor [Xanthomonas vasicola]
          Length = 289

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 137/333 (41%), Gaps = 49/333 (14%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNS 102
            E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  
Sbjct: 1   AEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEE 60

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL
Sbjct: 61  AAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPL 120

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           + + L+   +   +G   L EI+            GF    E         ++      D
Sbjct: 121 STEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVD 169

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
               + D +        +     + P+  E                           V  
Sbjct: 170 EDAVDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VAT 202

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
            ++ +A  Y + + +        K+          +E +  +  +L L     D LV QL
Sbjct: 203 RMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQL 256

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
             +   I  +E ++L LA +   + R  F+   
Sbjct: 257 RGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 289


>gi|304383076|ref|ZP_07365551.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335762|gb|EFM02017.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 290

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 149/275 (54%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   ++KG  E   AK ++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+     +   + +R P+  E++    +  E + + L      +S++ P  + + +
Sbjct: 136 GSLNKINHEINKFEQENQRHPSVSELSDVTHIDEEKIGQSLMADGHHVSIDAPFQEGEEN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               ++ +    VL   L  RE  ++R  FGIG +    LEE+
Sbjct: 196 CMLDVMAGGEDSRTDRLVDHESMAQELNTVLCKVLKDREITIIRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  K+I KL+     K L  +L
Sbjct: 255 GDRLGLTRERVRQIREKSIAKLRDSGNVKVLMKYL 289



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLIKAAQKFDETRGFK 104


>gi|158339245|ref|YP_001520422.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158309486|gb|ABW31103.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 90/265 (33%), Positives = 150/265 (56%), Gaps = 5/265 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K +     +S  E   +   V+        AK+ M+E NLRLV+S+AKK+ + GL
Sbjct: 8   VQAYLKEMGRYPLLSHEEEIRLARQVK---AGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLIQEG+IGL  A +KFD   G KFSTYA WW+ +AI R++  QS TI IP+H  ++
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRALKSQSRTIYIPIHQWER 124

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            H++ +  R+++ +  R PT +E++    +    +R  L+  +   SL+ P+G E    L
Sbjct: 125 AHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAVSSLDQPVGPEQKDAL 184

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I+ ++A   +   ++    +  TR +A LT RE  ++  R+G+      ++  +GKQ
Sbjct: 185 IDLIQTEDAPLSIMDGLEIE--DALTRCMAYLTERERFIVDQRYGLTDGQPKSMGAIGKQ 242

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             ++RER+RQI   A++K+    RS
Sbjct: 243 IDISRERVRQILNIAMKKMTRQVRS 267



 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR------ 171
           +D V+ YL+EMG   LLS E EI +A++++AG       + E  L     I  +      
Sbjct: 5   NDSVQAYLKEMGRYPLLSHEEEIRLARQVKAGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 172 ---DELNDGTTLLREIIDLEAC 190
              D + +G+  L   +D    
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDL 86


>gi|326332710|ref|ZP_08198972.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
 gi|325949491|gb|EGD41569.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
          Length = 315

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 94/238 (39%), Positives = 150/238 (63%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + +     E   A +E + ANLRLV+S+A+KY    +  LDLIQEGN GL++A EKFD+ 
Sbjct: 70  AELEWLAEEGHRATREFINANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYT 129

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WWV+QAITR IA Q+  +R+PVH+ +++++V    R +  ++ R+P PEE
Sbjct: 130 KGYKFSTYATWWVRQAITRGIAQQARVVRLPVHVVEELNQVGGARRTLERQLGRDPEPEE 189

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L M ++ V  +L   ++ +SL+TPI ++  + LGD +  ++A SP    I    RE
Sbjct: 190 IAAELGMDIDRVLDLLSWGRDHVSLDTPIDEDGDTSLGDLMAQESAPSPDMDVIDVESRE 249

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               ++  L  R   ++R R+G+     H L ++G +  ++ ER+RQ+E +A++KL+ 
Sbjct: 250 RLNSLVGQLDERSADIVRSRYGLTDGRQHKLADIGVKHGISAERVRQLEREALQKLRR 307


>gi|302802267|ref|XP_002982889.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
 gi|302818650|ref|XP_002990998.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300141329|gb|EFJ08042.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300149479|gb|EFJ16134.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
          Length = 292

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 88/249 (35%), Positives = 137/249 (55%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +R+    A   +  MV +NL LVI VA+K+  +G    DLIQEG  GL+   EKFD  
Sbjct: 35  QELRRKLKHAKRCRTNMVSSNLGLVIKVARKFGLKGTTIEDLIQEGINGLLHGVEKFDTS 94

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY +WW++ ++ R+   +S   ++P+H+ D   +V++T  R+  +    PT EE
Sbjct: 95  RGFRLSTYVLWWIELSVRRASVKRSIMCQVPMHLFDTHTRVLKTRARIFEERGTFPTNEE 154

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L    + V     + + P SL+  +   D   L + + D    S L  A +A L+E
Sbjct: 155 VATILGTTAQKVHLAANLMRHPKSLDDNVPGCDNVTLLEILPDPEVESSLLVAEKALLKE 214

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +VL  L PRE+ VL +R+GIG   D TLEE+   F ++RER+RQIE +A+ K+    
Sbjct: 215 QLDKVLNLLKPREKEVLTLRYGIGDGRDRTLEELSHHFNLSRERVRQIEKRALAKIHELG 274

Query: 672 RSKKLRSFL 680
             + L SF+
Sbjct: 275 GKELLASFV 283


>gi|119717204|ref|YP_924169.1| sigma-70 region 3 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119537865|gb|ABL82482.1| sigma-70 region 3 domain protein [Nocardioides sp. JS614]
          Length = 319

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 90/229 (39%), Positives = 144/229 (62%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A    + ANLRLV+S+A+KY    +  LDLIQEGN GL++A EKFD+  GYKFSTYA
Sbjct: 83  GRKAVDTFITANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYTKGYKFSTYA 142

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WWV+QAITR IA Q+  +R+PVH+ +++++V    R +  K+ REP P EIA++L M V
Sbjct: 143 TWWVRQAITRGIAQQARVVRLPVHVVEELNQVGGARRTLERKLGREPEPREIAEELGMEV 202

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + V  ++   +E +SL++P+ ++  + LGD +  + A  P  + I    R+    ++  L
Sbjct: 203 DRVLDLMAWGREHVSLDSPVDEDGDTSLGDLMAQETAPGPDLNFIDVESRDRLNSLVGKL 262

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             R   ++R R+G+     H L ++G +  ++ ER+RQ+E +A++KL+ 
Sbjct: 263 DDRAADIIRSRYGLVDGRQHKLADIGAKHGISAERVRQLEREALQKLRR 311


>gi|120553093|ref|YP_957444.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
 gi|120322942|gb|ABM17257.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 330

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 72/292 (24%), Positives = 148/292 (50%), Gaps = 8/292 (2%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E D   ++             +A   D+   +R+ + S+      S        +  R+
Sbjct: 37  SETDERRLARKLIRSLRVIHTELALPEDTPQTLRDVVGSLGDACAFS--------ARCRR 88

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               A   +  ++++NLRL + +A++Y + G+   DLIQ+ N+GL+KA E++D   G++F
Sbjct: 89  AYHLALACRHRLIQSNLRLAVHIARRYGHHGIAMSDLIQDANVGLIKAVERYDPGKGFRF 148

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA WW+ + + R +      +  P ++ ++I ++ + + R+   + REPT  E+A+++
Sbjct: 149 STYAYWWISEEVRRCLQRGVRVVHTPENVVEEIRQLQKVSMRLHQSLGREPTQSELAREM 208

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                 + ++  +    +S + P+ ++ +  L D ++      P       +      R+
Sbjct: 209 EATPSRIGELRALAAREVSTDVPLVEDGSVTLADSLDAGADTRPDQPFRARDRMIRLERM 268

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L+ RE  +L  R+G+G+    TL+ + +Q  ++RER+RQIE  A+RKL+
Sbjct: 269 MGALSDRERDILTRRYGLGLIEPETLQTISEQLGLSRERVRQIEKGALRKLQ 320


>gi|125602683|gb|EAZ42008.1| hypothetical protein OsJ_26557 [Oryza sativa Japonica Group]
          Length = 497

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 89/321 (27%), Positives = 156/321 (48%), Gaps = 7/321 (2%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI--SI 424
           RD         + + H  S  +  P      F+      ++KI    + + V+ G   ++
Sbjct: 175 RDRETTEFLTAKEERHLFSKIQAKPYFYPVIFIFRTAQILMKIEEAHRKLEVQCGREPTL 234

Query: 425 SEFRHIV----SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           +E+   V      ++         +++M  +N RLVI VA+KY   GL   DL+Q+G  G
Sbjct: 235 AEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSG 294

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMK  EKF+   G +F TYA WW++Q+I +SI   S  IR+P  +   + KV +      
Sbjct: 295 LMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECI 354

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            +   +PT   +A++  + +E + K+   T++P S++  +  ++     +  ED N   P
Sbjct: 355 ME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPP 413

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             S  +  +R+     L  L+PRE+ ++  RFGI      TL  +G  F +++ERIRQ++
Sbjct: 414 DLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQ 473

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
            +A+ KLK  +  +    + D
Sbjct: 474 NRALEKLKRSASLQGFDVYFD 494


>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa]
 gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa]
          Length = 559

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 159/318 (50%), Gaps = 6/318 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF--VACEVDSILKIRNEIKSISVETGI 422
           + +  F++R          ++  +       K    +     ++ +   ++ S+S     
Sbjct: 244 LPKPTFVKRTSSSSSRRSLIARNEAKMTRGVKVASDLERIRTTLEEETGQVVSLSCWAEA 303

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           +  + + +   ++         + E+++    LV+ +A+ Y   G+   DLIQ GN+GL+
Sbjct: 304 TGLDKKVLQQQLQF----GWYCRDELIKNTHSLVLYIARNYRGMGIAMEDLIQAGNLGLL 359

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           + AE+FD   GY+FSTY  +W+++++ + +   +  I+IP  +   I+K+ +  + +SN 
Sbjct: 360 QGAERFDPTRGYRFSTYVQYWIRKSMLKIVERHARGIQIPYALSRSINKIQKARKALSNS 419

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R P   E+AK   + +  +    K  +   SL+  IG+   +   +FI D +  +P +
Sbjct: 420 HGRYPDDWEVAKFTGLSLAKIESAQKCLRVVASLDQKIGEGHYAKYSEFIPDMSIQNPEE 479

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           + ++ ++RE    +L  L  RE++V+ +R+G   N   +L E+G+ F V++ER+R+IE K
Sbjct: 480 AVMRQHMREEIYDLLRGLDSREKQVMVLRYGFKDNQPKSLAEIGRLFRVSKERVRKIEKK 539

Query: 663 AIRKLKHPSRSKKLRSFL 680
            + KL+     + L  ++
Sbjct: 540 IMIKLRDEGIRRNLSRYM 557


>gi|209883307|ref|YP_002287164.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209871503|gb|ACI91299.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 387

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 124/385 (32%), Positives = 191/385 (49%), Gaps = 12/385 (3%)

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           D   N     +     +V  E + +   +LS +  R +   E L     R+       L 
Sbjct: 11  DQLPNPFLVTELEDNSEVRSESVERAFRTLSADSERAEG--ELLRSDIDRV--YLRRKLT 66

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +A+   +++ +     +  E D    +  +     + K     E   + +     K I  
Sbjct: 67  IAECATVEQQLRALGVRIVEDDEDEDNQTEPSNSQKKKYLNEMEERELGRTIRLAKDIQY 126

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEG 477
                      +    R+    A  AK   VE+NL  V  +A +  N + L   DL QEG
Sbjct: 127 AA------LEDLNQYERQLVHRAEKAKARFVESNLLYVRKLANRKRNLKHLTADDLFQEG 180

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+KA E FD  LG++F TYA WW++Q ++R++ D   TIR+PVH  +   K+ R   
Sbjct: 181 LMGLLKATELFDPELGFRFKTYATWWIQQYMSRALDDGDRTIRLPVHRHEYFRKIKRKTA 240

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +++ ++ REPT  E+A +L +  E + K+L        +E      + + +  +  D++ 
Sbjct: 241 KLTFELGREPTLNELATELGLERERLAKLLWRLHVTECVEADAPIGEDTTVLSYKADES- 299

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S LD      LR    RVLA+L PREER++RMRFG+  + + TLE +G  F VTRERIR
Sbjct: 300 PSILDLVALQQLRTMVARVLATLVPREERIIRMRFGLDGSGEQTLEAIGNVFGVTRERIR 359

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
           QIEAKA+RKLKHPSRS+ LR+FL+ 
Sbjct: 360 QIEAKALRKLKHPSRSRALRTFLES 384


>gi|14970557|emb|CAC44359.1| RpoS protein [Erwinia chrysanthemi]
          Length = 332

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 97/273 (35%), Positives = 169/273 (61%), Gaps = 5/273 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVSSRRRMIESNLRLVVKIARRYNN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    ++++   + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKDNGPEDTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQIEAKA--IRKLKHPSRSKKL 676
           G++  +TRER+RQI+ +   +R+L+   + + L
Sbjct: 292 GREIGLTRERVRQIQVQVEGLRRLREILQVQGL 324



 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/119 (23%), Positives = 45/119 (37%), Gaps = 12/119 (10%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     GI+V D   L +EE S+         S  +               D  ++YL E
Sbjct: 15  AEFDENGIDVFDDKALAEEETSDSDQLDEELLSQGTAQ----------RVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           +G   LL+ E E+  A+R   G       + ES L    ++      N+    L ++I+
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVSSRRRMIESNLRL--VVKIARRYNNRGLALLDLIE 121


>gi|284431201|gb|ADB84362.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 292

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 134/335 (40%), Gaps = 45/335 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P          +         S   ++    ++ E + E       +D
Sbjct: 61  LSDII--SGFIDPN------EADDVAPTATHIGSELSEDDLADEDEEDEDEDGDGDDAED 112

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  PE A      L    + +  ++                               
Sbjct: 113 EGDGGPDPEVAREKFGELRAQYEVTRLSI------------------------------- 141

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L 
Sbjct: 142 ----QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLC 197

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E +  W  Y K   +      +  + D +L+   +++ I  E
Sbjct: 198 VEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMDED-VLRAIGKLQQIEEE 256

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           TG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 TGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|188090600|gb|ACD49534.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 291

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 136/334 (40%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDLEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+       +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYQAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDEAADNDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDATEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y   + +        K+  +       +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYATFKKIY------AKNGAAHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090564|gb|ACD49516.1| RNA polymerase sigma factor [Xanthomonas cucurbitae]
          Length = 291

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 138/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                ED + E + D
Sbjct: 121 LSTELLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAASEDDAAEDDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|126697159|ref|YP_001092045.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126544202|gb|ABO18444.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 344

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 103/287 (35%), Positives = 168/287 (58%), Gaps = 7/287 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSM----VRKGECEASIAKK 446
            E +  +  +V   +++      IS  TG   SI E    +++    ++K       AK+
Sbjct: 52  HEQEITLGRQVQEYMQVERAELEISELTGDKPSIDELSTKLNLSTSVIKKRLRAGQRAKE 111

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q
Sbjct: 112 RMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQ 171

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V+ +
Sbjct: 172 GITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSELAKYVELPEDDVKDL 231

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +    +P+SLET +GD + + L D +     + P +      +R     +L  L   + R
Sbjct: 232 MCKAGQPVSLETKVGDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDLHSLLHQLPDLQCR 290

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           VLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S +
Sbjct: 291 VLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSHN 337



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           SS + S   L         +  D VR YLR++G + LLS E EI + ++++    +  A 
Sbjct: 13  SSETISENKLTSIASLKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAE 72

Query: 157 L 157
           L
Sbjct: 73  L 73


>gi|108707415|gb|ABF95210.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|215695353|dbj|BAG90544.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 343

 Score =  165 bits (418), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 149/247 (60%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK        K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G
Sbjct: 92  LRKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKG 151

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA
Sbjct: 152 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIA 211

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               MP+  V   + + K  +SL + +G  D ++  +   D +  +  +   +  ++E  
Sbjct: 212 SDTGMPLRRVEAAMSLPKYTVSLTSKVGCTDMTY-QEITPDTSTETAEEMLHRWLMKEDV 270

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L+PRE +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + 
Sbjct: 271 DRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKV 330

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 331 QSLQHYL 337


>gi|288926119|ref|ZP_06420047.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608396|ref|ZP_07883384.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337159|gb|EFC75517.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249856|gb|EFU29857.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  165 bits (417), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 154/275 (56%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++I E   +   +++G  +A  AK+++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPMVTIEEEIELAQAIKRGGRDAERAKEKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++KV     R   +  R P+ +E++ +  +  E +++ +      +S++ P  + + +
Sbjct: 136 GSLNKVNHEINRFEQEHHRRPSVQELSDRTHIDEEKIQQSMMADGHHVSIDAPFQEGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++      VL   L  RE+ ++R  FGIG   +  LEE+
Sbjct: 196 SMVDVMAGSDDSRTDRQVDHDSMAMELNSVLDRVLKEREQIIIRECFGIGC-QEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+     K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSITKLRESGNVKILMKYL 289


>gi|322504100|emb|CBX46975.1| RNA polymerase subunit D, sigma factor [Pseudomonas sp. C2(2009)]
          Length = 290

 Score =  165 bits (417), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 141/336 (41%), Gaps = 49/336 (14%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIE G   +M+++   P T   ++     +     
Sbjct: 2   PVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGG 61

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L E++            G+    +G    +       KE                 + +
Sbjct: 62  RLAEVL-----------SGYIDPDDGSVPDEAAAPVPVKE---------------GAAAE 95

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +    +    + E +E +   D +++A   +A+ +Q + KV+ AL               
Sbjct: 96  ESDDEEEDESDDEEEEGDGGPDPEEAARRFTAVAEQ-QDKVLKALK-------------- 140

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 K  + S +       L +L   + L   + D LV ++ D   R+   E  +++L
Sbjct: 141 ------KHGRGSKQAIEELAALAELFMPIKLVPKQYDALVTRVRDALDRLRTQERAIMQL 194

Query: 360 AQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                 + R  FL    G E+D  W +      + ++   +      I + + ++  +  
Sbjct: 195 CVRDARMPRADFLRLFPGNEIDMDWAADLAK-GKAKYAEALGNLQADIQRCQQKLADLEA 253

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           E  ++++E + I   +  GE +A  AKKEMVEANLR
Sbjct: 254 ECSLTLAEIKDINRRMSIGEAKARRAKKEMVEANLR 289


>gi|40353311|gb|AAR84419.1| essential primary sigma 70 factor [Frankia sp. ACN14a]
          Length = 214

 Score =  165 bits (417), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 112/213 (52%), Positives = 164/213 (76%), Gaps = 3/213 (1%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S+ T  +  + R  +  + +   +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDLIQE
Sbjct: 5   SIATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQE 61

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  
Sbjct: 62  GNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQ 121

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R++   + REP+PEEIAK++ +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIED +
Sbjct: 122 RQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIEDCD 181

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           AV P+D+A    L+E    VL +L+ RE++V++
Sbjct: 182 AVVPVDAASFILLQEQLDSVLHTLSDREKKVIQ 214


>gi|40353301|gb|AAR84414.1| essential primary sigma 70 factor [Frankia sp. ORS020607]
 gi|40353303|gb|AAR84415.1| essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|40353305|gb|AAR84416.1| essential primary sigma 70 factor [Frankia sp. CeD]
          Length = 217

 Score =  165 bits (417), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 112/216 (51%), Positives = 166/216 (76%), Gaps = 3/216 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++V T  +  + R  +  + +   +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDL
Sbjct: 5   EKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDL 61

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++
Sbjct: 62  IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 121

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++   + REP+PEEIAK++ +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIE
Sbjct: 122 RIQRQLLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIE 181

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           D +AV P+D+A    L+E    VL +L+ RE++V++
Sbjct: 182 DCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQ 217


>gi|312964996|ref|ZP_07779236.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
 gi|312290552|gb|EFR18432.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
          Length = 237

 Score =  165 bits (417), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 93/229 (40%), Positives = 158/229 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 181 LARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 229


>gi|188090494|gb|ACD49481.1| RNA polymerase sigma factor [Xanthomonas albilineans]
 gi|188090628|gb|ACD49548.1| RNA polymerase sigma factor [Xanthomonas albilineans]
          Length = 286

 Score =  165 bits (417), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 136/334 (40%), Gaps = 53/334 (15%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E                 
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPVVVAEDDSA--- 166

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              +  GD +  A V   +     + P+ AE                           V 
Sbjct: 167 -AADAAGDEDEDADVDASEEDAGPTGPDPAE---------------------------VA 198

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ ++  Y + +          K+         L+  + ++  +L L     D LV +
Sbjct: 199 RRMEVLSAEYAKFKKAY------AKNGAEHKLVAKLRNDIAEVFVTLKLPLPLTDALVRK 252

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 253 LRDAMAQVKEHERRVLHLATHVARMPRKDFIRSW 286


>gi|221212711|ref|ZP_03585688.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
 gi|221167810|gb|EEE00280.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
          Length = 522

 Score =  165 bits (417), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 104/234 (44%), Positives = 155/234 (66%), Gaps = 1/234 (0%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +V+ +  G+ +   A + M+EANLRLV+S+A+KY NRG+   DL+Q+G IGLM+A EK
Sbjct: 269 RALVAALNDGQQKVRDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEK 328

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F++  G+KFSTYA WW++QAI R++AD++ TIR+PVH+ D+  +V R A R   +  R+P
Sbjct: 329 FEYRRGFKFSTYATWWIRQAIARAVADRARTIRVPVHVGDQHQRVRRQALRFRQRTGRQP 388

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           TP E+A +  +  + +R +L +  EP+SL+TP+ D DT  L D IED+ + SP +     
Sbjct: 389 TPAELAAETGLAEDKLRAILALPAEPVSLDTPLPDADTG-LVDLIEDETSASPFEQLAGT 447

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +RE    +L S+TP E  VLR RFG+G     T + + K   ++RER+RQIE 
Sbjct: 448 RMRECVRSLLRSVTPTEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEK 501



 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 42/147 (28%), Positives = 75/147 (51%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D    
Sbjct: 10  ADTPLDPIIQLLALASEQGYLTHADLVDALPPESDSPDALDVVRAALADIGITVLDEPAA 69

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  ++D+   A      L         ++ DP+ +Y+R M ++ LL+RE EIA+A
Sbjct: 70  PPPFAAAPAVDVDRDALEEGRALLGDLARGASASTDPLALYMRRMHAVPLLTREDEIALA 129

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIW 170
           + +E GR  M+ +L   P    AL+  
Sbjct: 130 RELETGRHQMLHALAGCPPAVDALLAR 156


>gi|172037252|ref|YP_001803753.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
 gi|171698706|gb|ACB51687.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 297

 Score =  165 bits (417), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 99/286 (34%), Positives = 169/286 (59%), Gaps = 17/286 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVR----------------KGECEASIAKK 446
              +  +R+ ++SI     +S  E   +   ++                K   +   A+ 
Sbjct: 4   KKKVDTVRHYLQSIGKTPLLSGPEEIKLAEEIQAMLPLLEKEALSKEEEKIVAKGQRARD 63

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +M++ANLRLV+S+AKKY N GL  LDLIQEG++GL++  EKFD   GYKFSTYA WW++Q
Sbjct: 64  KMIQANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWWIRQ 123

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA+QS TIR+P+H+ + ++K  ++ R ++ K+ R+PT +EIA+ + + V+ +R +
Sbjct: 124 GITRAIAEQSRTIRLPIHINENLNKYRKSIRELTLKLGRKPTQQEIAENMDISVDKLRFL 183

Query: 567 LKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            +   +  S    I  ++  + LG  + D+++VSP D   Q        R+L +L+PR++
Sbjct: 184 QQAAFKTKSRSLNIVIDENHTELGQLLPDEDSVSPSDFVKQQEKISQINRMLENLSPRQK 243

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+ +RFG+      + + +G+Q  ++ ER RQI ++A+R L+  S
Sbjct: 244 EVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALRILRKQS 289



 Score = 38.7 bits (88), Expect = 3.0,   Method: Composition-based stats.
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +   D VR YL+ +G   LLS   EI +A+ I+A
Sbjct: 2   PTKKKVDTVRHYLQSIGKTPLLSGPEEIKLAEEIQA 37


>gi|6010724|gb|AAF01228.1|AF184097_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 326

 Score =  165 bits (417), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 95/271 (35%), Positives = 167/271 (61%), Gaps = 7/271 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI    H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI----HI 167

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 168 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 227

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 228 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 287

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 288 GREIGLTRERVRQIQVEGLRRLREILQTQGL 318



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|281423630|ref|ZP_06254543.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|299141293|ref|ZP_07034430.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|281402182|gb|EFB33013.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|298577253|gb|EFI49122.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 290

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 152/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ISI E   +   ++KG  +   AK+++V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             ++K+ R   +   + +R+P+  E++    +  E + + L      +S++ P  + + +
Sbjct: 136 GSLNKINREINKFEQEFQRKPSLAELSSATKIEEEKIDQSLMADSHHVSIDAPFQEGEDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               ++      VL   L  RE  ++R  FGIG +    LEE+
Sbjct: 196 SMVDVMAGGEDSRTDKQVDHESMALELESVLRKVLKDREITIIRECFGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G Q  +TRER+RQI  K+I KL+    +K L  +L
Sbjct: 255 GDQLGLTRERVRQIREKSIAKLRDSGYAKILMKYL 289



 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L+S + EI +A++I+ G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|168768834|ref|ZP_02793841.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
 gi|189362139|gb|EDU80558.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
          Length = 329

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 170/271 (62%), Gaps = 4/271 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L     ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFE-NAKQREVLARRFGLLGYEAATLEDV 290

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 291 GREIGLTRERVRQIQVEGLRRLREILQTQGL 321



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|300727091|ref|ZP_07060510.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775635|gb|EFI72226.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 94/275 (34%), Positives = 159/275 (57%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  IS E  +SI E   +   +RKG      AK+++V+ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLAEISREPMVSIDEETELAQQIRKGGRAGDRAKEKLVKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   +   +  R P+ +E+A    +  + ++K L      +S++ P  D+D +
Sbjct: 136 GAVSKINQVTAKFVQEHNRRPSADELATLTGIDADKIQKSLNADSHQMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           +++     VL S L  RE ++++  FGIG   +  LEE+
Sbjct: 196 SMSDMLSSGDDSRTDRQVDYESMQNDMEGVLKSVLKDRELKIVKDCFGIG-GPEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++  +TRER+RQI  K+I K++    +K L  +L
Sbjct: 255 GEEMGLTRERVRQIREKSIMKIRQSGNAKLLMKYL 289


>gi|309702135|emb|CBJ01450.1| putative RNA polymerase sigma factor [Escherichia coli ETEC H10407]
          Length = 697

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 110/274 (40%), Positives = 162/274 (59%), Gaps = 7/274 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +++ I       I +  H VS+          A K  + ANLRLV+++AKK+  RGL  
Sbjct: 414 RDLQQIVERAQTLIPDECHNVSL---YVSSYRDAWKGFIHANLRLVVAIAKKHCGRGLDI 470

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGN+GL+KA EKFD+  G+KFSTYA WW++Q I+R+IADQ+  IR+PVH  +   
Sbjct: 471 EDLIQEGNLGLIKAVEKFDFRRGFKFSTYASWWIRQKISRAIADQAQLIRLPVHFYEHFR 530

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI---SLETPIGDEDTSH 587
           +   +  ++ ++    PT   + +   +P   + ++ K  ++ +          D + + 
Sbjct: 531 RWRSSRDQLLHRQGITPTLRRLQEMTDLPERQLLQMAKYEEQTVLIGDFHEDAQDREAAL 590

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            GD +  +   +         LRE  + VL +L PRE ++++MRFGIGM  D TLEEVGK
Sbjct: 591 SGDALLTRRDFTSAPVQSLE-LREHISSVLNTLLPRETQIIKMRFGIGMTQDFTLEEVGK 649

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           QF VTRERIRQIEAKA+RKL+H SR+ KL  F++
Sbjct: 650 QFDVTRERIRQIEAKALRKLRHHSRASKLGGFVE 683


>gi|302338308|ref|YP_003803514.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635493|gb|ADK80920.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 281

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 89/246 (36%), Positives = 148/246 (60%), Gaps = 4/246 (1%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           RK +     A+  ++EANLRLV+ +AK Y   G   LDLIQEGN+GL++AAEK+D     
Sbjct: 37  RKIQSGDEAARHRLIEANLRLVVKIAKSYVTPGFGLLDLIQEGNMGLIRAAEKYDHRKQV 96

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q+I R+IA +   IR+P    + + K+ RT  ++S +++ EP+ EEIA 
Sbjct: 97  RFSTYAAWWIRQSIVRAIAKKQKAIRLPHRKNNLLKKIQRTYYQLSQELEHEPSAEEIAV 156

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           ++ +    V ++L++    +SL+     +D S L D +ED +   P    I  +++E T 
Sbjct: 157 EIGIEPSIVDQMLQVGNPVVSLD-CEIGDDASTLLDMLED-STYEPERVCINKSMQEDTM 214

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L  L  RE ++L  RF       +TL+++G +  ++ E +RQIE +AIRKL+    ++
Sbjct: 215 HFLDHLKERERQILLYRFAFFGGKKYTLKKIGMEMGISPETVRQIEMRAIRKLRD--HAE 272

Query: 675 KLRSFL 680
           +++ +L
Sbjct: 273 EMKDYL 278


>gi|300725901|ref|ZP_07059364.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776838|gb|EFI73385.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 94/275 (34%), Positives = 154/275 (56%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  IS E  I+I +   +   +RKG      AK ++V+ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLAEISHEPMINIDQEIELAQAIRKGGRAGERAKDKLVKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+  T  +     +R P+ +EI++   +  E + + +K      S++ P  D + +
Sbjct: 136 GALSKINATISKFEQDNQRRPSIQEISRLTGIEEEKIEQSIKADNHHTSIDAPFQDGEEN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               ++ +    VL + L  RE ++L   +GIG +    LEE+
Sbjct: 196 SMVDIMASGEDTRTDRQVDHDSMAQELHSVLKNVLKDREIKILCECYGIGCHE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  K+I KL+    SK L  +L
Sbjct: 255 GDRMGLTRERVRQIREKSILKLREAGCSKVLMKYL 289


>gi|322504098|emb|CBX46974.1| RNA polymerase subunit D, sigma factor [Pseudomonas sp. C2(2009)]
          Length = 289

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 141/336 (41%), Gaps = 49/336 (14%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
           PVRMY+REMG++ELL+REGEI IAKRIE G   +M+++   P T   ++     +     
Sbjct: 1   PVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGG 60

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L E++            G+    +G    +       KE                 + +
Sbjct: 61  RLAEVL-----------SGYIDPDDGSVPDEAAAPVPVKE---------------GAAAE 94

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +    +    + E +E +   D +++A   +A+ +Q + KV+ AL               
Sbjct: 95  ESDDEEEDESDDEEEEGDGGPDPEEAARRFTAVAEQ-QDKVLKALK-------------- 139

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 K  + S +       L +L   + L   + D LV ++ D   R+   E  +++L
Sbjct: 140 ------KHGRGSKQAIEELAALAELFMPIKLVPKQYDALVTRVRDALDRLRTQERAIMQL 193

Query: 360 AQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                 + R  FL    G E+D  W +      + ++   +      I + + ++  +  
Sbjct: 194 CVRDARMPRADFLRLFPGNEIDMDWAADLAK-GKAKYAEALGNLQADIQRCQQKLADLEA 252

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           E  ++++E + I   +  GE +A  AKKEMVEANLR
Sbjct: 253 ECSLTLAEIKDINRRMSIGEAKARRAKKEMVEANLR 288


>gi|188090702|gb|ACD49585.1| RNA polymerase sigma factor [Stenotrophomonas maltophilia]
          Length = 284

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 79/334 (23%), Positives = 137/334 (41%), Gaps = 55/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED----EEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED + M++ MGI+V +     +     +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L + P
Sbjct: 61  EAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGQFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           ++ ++L+   +   +G   L E+I     +G              +     D+  E + D
Sbjct: 121 VSVESLLNDYEAHKEGKKRLAEVI-----VGFNDLVDEEPAPPAVAADDSADADAEGDED 175

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +G  E AA    D                                        V 
Sbjct: 176 EDDDVDGGDEEAAPTGPDPEE-------------------------------------VA 198

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +++ +   +                     L+E++  +  +L L     D+L +Q
Sbjct: 199 ARMQALSDAFNAFKKAATKGDK--------KNLPRLREEMSAVFVTLKLPLPLTDVLTKQ 250

Query: 342 LYDISKRIMHNEGELLRLAQ-SYGIKRDVFLERH 374
           L D    I  +E  +L LA  +  + R  F+   
Sbjct: 251 LRDTMASIKAHERRVLNLATVTARMPRKDFIRSW 284


>gi|78062752|ref|YP_372660.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
 gi|77970637|gb|ABB12016.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 511

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 104/241 (43%), Positives = 159/241 (65%), Gaps = 1/241 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A + M+EANLRLV+S+A+KY NRG+   DL+Q+G++GLM+A EKF++  G+KFSTYA 
Sbjct: 272 RDATRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGSLGLMRAIEKFEYRRGFKFSTYAT 331

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAITR++AD++ TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +  +
Sbjct: 332 WWIRQAITRAVADRARTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLDED 391

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL +  EP+SL+ P+ D DT  L + IED+ + SP +      +RE    +L S+T
Sbjct: 392 KLRAVLALPAEPVSLDAPLPDADTG-LVELIEDQASASPFEQLADTRMRECVRSLLRSVT 450

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           P E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  +SFLD
Sbjct: 451 PAEADVLRRRFGLGGTEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENAQSFLD 510

Query: 682 G 682
            
Sbjct: 511 A 511



 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 41/151 (27%), Positives = 75/151 (49%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +   D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TPRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
                       +D+   A +    +         ++ DP+ +Y+R M ++ LL+REGEI
Sbjct: 67  PAAPAPFAGSAPVDVDRDALDEGRAMLGDLARGTGASTDPLALYMRRMQAVPLLTREGEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ +L   P    AL+   
Sbjct: 127 VLAREIETGRHQILHALAGYPAAVDALLARH 157


>gi|239942002|ref|ZP_04693939.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 15998]
 gi|239988467|ref|ZP_04709131.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 11379]
          Length = 308

 Score =  165 bits (416), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 104/234 (44%), Positives = 148/234 (63%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK   + +NLRLV++VA++Y   GL  LDLIQEGN GL++A EKFD+  G+KFST
Sbjct: 67  ADGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFST 126

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQS TIR+PVH+ +++ ++ R  R  + +  R+P   EIA +L  
Sbjct: 127 YATWWIRQAITRSIADQSRTIRLPVHLVEELGRIRRVQREFNREHGRDPEHAEIAAELDS 186

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  VL   ++P+SL   + D+  +  GD +ED +AVSP  S +     E    ++ 
Sbjct: 187 NAERVGNVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIG 246

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            L  R   +++MR+GI    + TL EVGKQ  +TRERIRQIE  A+ +LK  + 
Sbjct: 247 KLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAH 300


>gi|254432638|ref|ZP_05046341.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627091|gb|EDY39650.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 335

 Score =  165 bits (416), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 102/288 (35%), Positives = 170/288 (59%), Gaps = 12/288 (4%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVI 457
           E+ ++ ++  E+   +  T  S +E         ++++K       AK+ MV ANLRLV+
Sbjct: 49  ELMALEEMEQELTMRAGGTAPSAAELAKAAGLSPAVLKKRLQAGRRAKERMVAANLRLVV 108

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 109 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 168

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V+ +L   ++P+SLE
Sbjct: 169 TIRLPIHITETLNKLKKGQRELSQELGRTPTVTELAGYVELPEEEVKDLLCRARQPVSLE 228

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           T +GD + + L D +     + P +      L+     +L  L   + RVL+MR+G+   
Sbjct: 229 TKVGDGEDTELLDLLAGDGEL-PEERVDGECLKGDLRALLEQLPELQGRVLKMRYGLDPE 287

Query: 638 -----TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
                   +L  + K   ++R++ R +E KA+  ++  S+S++L  +L
Sbjct: 288 GQGLTEPMSLSSIAKNLGMSRDKTRNLERKALEGIR--SQSRRLEGYL 333



 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASL 157
           D VR YLR++G + LL+ E EI + ++++       M   L
Sbjct: 20  DLVRSYLRDIGRVPLLTHEQEITLGRQVQELMALEEMEQEL 60


>gi|281420881|ref|ZP_06251880.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405173|gb|EFB35853.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 287

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 90/274 (32%), Positives = 168/274 (61%), Gaps = 7/274 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+ E  +S  E   +   +RK       A + + +ANLR V+SVAK+Y N+G+
Sbjct: 18  LEKYLQDIAHEELLSTDEEVELAQRIRK---GDRRALERLTKANLRFVVSVAKQYQNQGI 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN+GL+KAA+KFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++    
Sbjct: 75  SLPDLINEGNVGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRLVRLPLNQVGS 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
           ++K+ R   +   + +R+P+ +EIA ++ +P + +   +K   T   +S++ P  D++  
Sbjct: 135 VNKINREMSKFEQEFERKPSVDEIADRIDLPEDKIEDAMKATSTSRHLSVDAPFSDDEDG 194

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + + +  +        +LR    R+L +L  ++++++   +GIG   + TLEE+G
Sbjct: 195 SMLDLMANSDDPT-DKELQTESLRAEIERLLKTLPDKDQKIIAAFYGIG-TPELTLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++ +TRER+RQI+ K IR+L++ +  K L+S+L
Sbjct: 253 TKYHLTRERVRQIKEKTIRRLRNKTTDKLLKSYL 286



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 78/209 (37%), Gaps = 6/209 (2%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++   ELLS + E+ +A+RI  G    +  L ++ L F  ++    +  +    L +
Sbjct: 21  YLQDIAHEELLSTDEEVELAQRIRKGDRRALERLTKANLRF--VVSVAKQYQNQGISLPD 78

Query: 184 IID--LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           +I+      I    K     G +  SY          +    Q     +      S +  
Sbjct: 79  LINEGNVGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRLVRLPLNQVGSVNKI 138

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY--RELRSLQD 299
           ++  S  E     + ++DE  D        +ED ++         +   +   E  S+ D
Sbjct: 139 NREMSKFEQEFERKPSVDEIADRIDLPEDKIEDAMKATSTSRHLSVDAPFSDDEDGSMLD 198

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
              N        ++ + L+ ++ +L+ +L
Sbjct: 199 LMANSDDPTDKELQTESLRAEIERLLKTL 227


>gi|254282580|ref|ZP_04957548.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
 gi|219678783|gb|EED35132.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
          Length = 429

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 79/257 (30%), Positives = 140/257 (54%), Gaps = 1/257 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R  +  +R    + + A+  +V  NLRLV S+A +Y  RG+ +LDL+QEG +GL++AAE
Sbjct: 171 ERDSLKALRSALNDYTKARDALVMHNLRLVYSIAARYKGRGVNYLDLVQEGTLGLIRAAE 230

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF++  GY+FSTY   W+ Q++ R + D    IR P H+++++ ++ R     + +   E
Sbjct: 231 KFEFEKGYRFSTYCFNWITQSVRRYVGDVGSLIRFPTHVQEQMGRLYREKALETARTGIE 290

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P  E +AK L M ++  R++L++    +SL+ P  D+D   + D +         D+A Q
Sbjct: 291 PDEETLAKNLGMDLDKTRELLQLRNLGVSLDAPRFDDDEGTMVDSMTGDTFGDTEDTAEQ 350

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +L    T  + +L P E  V+  R+G+      +  E+  +  V+RE +RQ+E   ++K
Sbjct: 351 DSLNRFLTNAIDTLEPAERDVVTARWGLHSGPPLSRAEIADKLGVSREWVRQLERSGLKK 410

Query: 667 LKHPSR-SKKLRSFLDG 682
           L+  S  ++    F+  
Sbjct: 411 LRGQSEINEAYSDFISA 427


>gi|312885799|ref|ZP_07745431.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311301606|gb|EFQ78643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 80/265 (30%), Positives = 140/265 (52%), Gaps = 4/265 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  +     +S  E   +   +R        A   + + NLR V+SVAKKY ++
Sbjct: 16  QSLETYLNELGRTDLLSAEEEVVLAQKIR---LGDQAALDRLTKTNLRFVVSVAKKYQHQ 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GLMKAA+KFD   G+KF +YA+WW++Q I  +IA+ S  IR+P++  
Sbjct: 73  GLPLSDLISEGNVGLMKAAKKFDETKGFKFISYAVWWIRQCILSAIAEHSRMIRLPMNQV 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ +    +  +++R+PT  E+A+ L    + V   L       S + P   ED +
Sbjct: 133 GDITKMNKALALLEQQMERQPTTNELAEYLETSEDKVSDALYFATRTASYDAPFRTEDEN 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           +L D +      +  +  + +N +E   ++L++LT R++ V+R  FG+   T     ++ 
Sbjct: 193 NLLDVLPGNEQATDHELMVLSNQQE-VRQLLSTLTSRDQEVIRWTFGLDGKTALPPIDIA 251

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
               ++ ER+RQI  +A++ L+  +
Sbjct: 252 PLLGISAERVRQIRNQALQTLREQA 276



 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL E+G  +LLS E E+ +A++I  G    +  L ++ L F  ++    +       L +
Sbjct: 21  YLNELGRTDLLSAEEEVVLAQKIRLGDQAALDRLTKTNLRF--VVSVAKKYQHQGLPLSD 78

Query: 184 II 185
           +I
Sbjct: 79  LI 80


>gi|311696748|gb|ADP99621.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 332

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 138/237 (58%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S  R+    A+  +++++++NLRL + +A++Y   G+   DLIQ+ N+GL+KA E+FD  
Sbjct: 84  SRCRRAFHLATACRRKLIQSNLRLAVHIARRYGQHGIPMSDLIQDANVGLIKAVERFDPT 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTYA WW+ + + R +   +  +  P ++ D+I ++ + + RM   + R P+  E
Sbjct: 144 KGFRFSTYAYWWISEEVKRCLQRGTRLVHTPENVVDEIRQLHKVSLRMHQSLGRTPSQSE 203

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+++      + ++  +    IS + P+ ++ +  LGD ++  + ++P       + + 
Sbjct: 204 LAREMEASPSRIGELRALATREISTDVPLVEDGSVTLGDSLDAGDQMAPDHPMSDRDRQR 263

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T   +L+ L  RE+ +L  R+G+G+    TL+ +     ++RER+RQIE  A++KL+
Sbjct: 264 TLKSMLSELNDREKDILSRRYGLGLPEPETLQVISDDLGISRERVRQIEKTALKKLQ 320


>gi|17233195|ref|NP_490285.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17135717|dbj|BAB78263.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 316

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 99/238 (41%), Positives = 153/238 (64%), Gaps = 1/238 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + V +       AK++M+ ANLRLV+S+AKKY  R L+FLDL+QEG IGL +  EKFD  
Sbjct: 69  AQVNQILELGQRAKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPN 128

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYK STYA WWV QAITR+IA++S T+R+P+H+ +K++++ +  R     + R  T  E
Sbjct: 129 RGYKLSTYAYWWVTQAITRAIAEKSRTVRLPIHVNEKLNQIKKVQREFFQTLGRRATVAE 188

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+KL +    +R+ LK+    ISL+  IGD   + L + +  +  VSP ++     LR+
Sbjct: 189 IAQKLELEPSQIREYLKVASGTISLDLKIGDNKETELSELLASE-GVSPDENITHEMLRQ 247

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +LASL P +  VL +RFG+  N + +L ++G++  ++RER+RQI+ KA+  L+ 
Sbjct: 248 DLSDLLASLKPMQREVLILRFGLLDNQEQSLAQIGEKLNLSRERVRQIQQKAMTALRR 305



 Score = 41.7 bits (96), Expect = 0.37,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 6/55 (10%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI------EAGRAMMMASLCESPLTFQ 165
           + D VR+YL+E+G   LL+ + EI  A+ +      +  +  +   L   P T +
Sbjct: 5   SSDLVRIYLQEIGQFPLLTSDQEITYARLVQQMIALQEQQHELTQKLEREPTTLE 59


>gi|325269444|ref|ZP_08136061.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325855020|ref|ZP_08171736.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|327313288|ref|YP_004328725.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
 gi|324988365|gb|EGC20331.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325483998|gb|EGC86938.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|326946004|gb|AEA21889.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
          Length = 290

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ +       K  R P+  E+A+   +    +R+        +S++ P  D+D +
Sbjct: 136 GAISKINQVTNEFVQKHNRRPSIHELAELTGIDEARIRQSQSADNHHMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL  +L  RE +++   FGIG   +  LEE+
Sbjct: 196 SMSDMLSSGDDSRTDRGVDFESMSDDLRAVLQNTLKDREIKIVTECFGIGC-QEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 255 GTEMGLTRERVRQIREKAIEKIRESGNARVLMKYL 289



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   +++ + EI +A+ I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|89901551|ref|YP_524022.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
 gi|89346288|gb|ABD70491.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
          Length = 350

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 82/292 (28%), Positives = 145/292 (49%), Gaps = 10/292 (3%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
            +A     G     +    +S   +   ++ +   T  +  E   +    R        A
Sbjct: 49  EHASPALPGAGLEALDAAGESGDALTVYLRQVRRTTLFTPQEEFELAGRAR---AGDFAA 105

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ M+E NLRLV+S+AK Y  RG+  LDLI+EGN+GLM A +KF+   G++FSTYA WW+
Sbjct: 106 RQSMIEHNLRLVVSIAKAYMGRGVPLLDLIEEGNLGLMHAIDKFEPERGFRFSTYATWWI 165

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP------EEIAKKLAM 558
           +Q++ R++  Q   +R+PV++  ++ +V+R  R + +      +       E++A  L  
Sbjct: 166 RQSVDRALMCQGRVVRLPVNVVRELQQVLRARRALESDAAFVVSRPDGIRVEDVAALLGR 225

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
               V  +L + + P SL+  +     +   GD + D+    P        +       +
Sbjct: 226 DPVHVADLLGLAEAPRSLDAALDRSGETQTFGDSLVDEITADPSGVTQVHEVERLLEEWV 285

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +L+ RE+ VL  RFG+      TL+ +  +  +TRER+RQ++ +A+ KLK 
Sbjct: 286 GTLSEREKEVLEGRFGLHDREPETLDVLSARLDLTRERVRQVQNEALAKLKR 337



 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 60/324 (18%), Positives = 103/324 (31%), Gaps = 35/324 (10%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           VDG +   +   +  L   +S +     L+     A   + D + +YLR++    L + +
Sbjct: 32  VDGGEYAADSVVKHGLSEHASPALPGAGLEALD--AAGESGDALTVYLRQVRRTTLFTPQ 89

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLE 188
            E  +A R  AG      S+ E  L     I            D + +G   L   ID  
Sbjct: 90  EEFELAGRARAGDFAARQSMIEHNLRLVVSIAKAYMGRGVPLLDLIEEGNLGLMHAIDKF 149

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKER-----DDVQETEGDIESAAKVSKDDRSK 243
               PE    F         Q  + +   + R      +V      +  A +  + D + 
Sbjct: 150 E---PERGFRFSTYATWWIRQSVDRALMCQGRVVRLPVNVVRELQQVLRARRALESDAAF 206

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           V S P+    ++       D           +    +  ALD   E      SL D    
Sbjct: 207 VVSRPDGIRVEDVAALLGRDPVHVADLLGLAEAPRSLDAALDRSGETQTFGDSLVDEITA 266

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGS---------LSLN---QSRIDLLVEQLYDISKRIMH 351
                    + + L E+ V  +             L+      +D+L  +L    +R+  
Sbjct: 267 DPSGVTQVHEVERLLEEWVGTLSEREKEVLEGRFGLHDREPETLDVLSARLDLTRERVRQ 326

Query: 352 NEGELLRLAQSY----GIKRDVFL 371
            + E L   + Y    GI RD  +
Sbjct: 327 VQNEALAKLKRYLAHRGITRDALI 350


>gi|87310114|ref|ZP_01092246.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87287104|gb|EAQ79006.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 516

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 103/250 (41%), Positives = 150/250 (60%), Gaps = 4/250 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + +       A++ +  ANLRLV+S+AK +  RGL +LDLIQEGN+GLM+A EKFD  L
Sbjct: 260 RIMQAHEGLCRAQRAITSANLRLVVSIAKSFRGRGLSYLDLIQEGNLGLMRAVEKFDPSL 319

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKF+TYA WW++QA+ + +ADQ  TIR+P  M+D+I K+      +S + + EP  E  
Sbjct: 320 GYKFATYATWWIRQAVMKGLADQGRTIRLPARMQDRIQKINVAKAILSQEHRSEPPIELT 379

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK+  +    V    ++ +  +SL+  + + D    GD +   +A     SA +  L   
Sbjct: 380 AKQAELTEREVVAADRLGRTIMSLD--VSNNDDDSFGDTLASGDAEQ--SSADEQRLPLA 435

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             ++L  LT RE+ ++R RFG+      TLEEV + F VTRERIRQIE+ AIRKL+ P  
Sbjct: 436 INQLLQELTSREQEIVRRRFGMFDGRVQTLEEVSQAFSVTRERIRQIESAAIRKLRQPHL 495

Query: 673 SKKLRSFLDG 682
            +KL  FL+ 
Sbjct: 496 IRKLDDFLEA 505



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/124 (16%), Positives = 36/124 (29%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
                  +    K    +D   DD +R YL EM    LLS   E    +R+   R     
Sbjct: 40  EEVGDEDAAPPSKDTTPSDAWDDDALRRYLNEMSRSPLLSANEERLATERVITARKRFQR 99

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            L    +  + +     E  DG+  L    ++        +       +  +  +     
Sbjct: 100 RLFGCGVAVKQVEKLIVETLDGSRRLDRTFEITVTSAARKQAEMLKLQQALANLRNAKQR 159

Query: 216 QEKE 219
              +
Sbjct: 160 NADD 163


>gi|166368031|ref|YP_001660304.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166090404|dbj|BAG05112.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 377

 Score =  164 bits (415), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 180/285 (63%), Gaps = 1/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    +   K++  +     +T  + +        +         AK++M+ +NLRLV
Sbjct: 92  KFLMEAEEVRQKLQENLHRPPTKTEWASALQLDNERQLENRLYRGRTAKRKMIRSNLRLV 151

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 152 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 211

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +  R +   ++R P   E+A+ L M  E +R++L++ ++ +SL
Sbjct: 212 RTIRLPIHIVEKLNKLKKAQRILKQDLQRNPNERELAEALEMTPEQLRQLLQLRRQSLSL 271

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED +   P D   +  +R+    VL+  LT RE+ V+ +R+G+ 
Sbjct: 272 NHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLA 331

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 332 TSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 376



 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 2/84 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ D ++  E +++ L      +  +            S +D V  + +EM    LLS E
Sbjct: 23  LELDSVDFAERTDEELTEHLPETLKNTRGSSGTGYDKGSNEDTVGAFFKEMARYPLLSAE 82

Query: 138 GEIAIAKRIE--AGRAMMMASLCE 159
            EI +A  ++       +   L E
Sbjct: 83  EEIELAYSVKFLMEAEEVRQKLQE 106


>gi|303235620|ref|ZP_07322227.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
 gi|302484067|gb|EFL47055.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
          Length = 290

 Score =  164 bits (415), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ + +     K  R P+  E+A    +    +R+        +S++ P  D+D +
Sbjct: 136 GAISKINQVSNEFIQKHNRRPSIHELADLTGIDEARIRQSQSADNHHMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +      +    ++ +    VL  +L  RE R++   FGIG      LEE+
Sbjct: 196 SMSDMLASGDDSRTDKAVDFESMSDDLNAVLQNTLKDRERRIVIECFGIGCPE-KGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  KAI K++    +K L  +L
Sbjct: 255 GTEMALTRERVRQIREKAIEKIRLSGNAKVLMKYL 289



 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 24/103 (23%), Positives = 40/103 (38%), Gaps = 6/103 (5%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTF 164
           K   S    T + +  YL E+G   +++ + EI +A+ I  G          L ++ L F
Sbjct: 5   KISKSITNRTSEALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF 64

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             ++    +       L ++ID E  IG       F  T G  
Sbjct: 65  --VVSVAKQYQHQGLSLTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|149916815|ref|ZP_01905317.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149822532|gb|EDM81921.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 421

 Score =  164 bits (415), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 99/301 (32%), Positives = 167/301 (55%), Gaps = 9/301 (2%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE-FRHIVSMVRKGECEASI 443
           + A    +G + + VA ++++I   R E  ++ V      S  F   V  VR        
Sbjct: 120 AMAALDLDGNYSDCVAADLEAIDAHRREGVALEVSYPPKGSRPFARYVQKVRSSGHALRW 179

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +K + V+ANLRLV+++A+++ +  +   DL+QEGN+GLMKA ++FD   GY+FSTYA WW
Sbjct: 180 SKNKFVKANLRLVVTIARRFDHGLMPLQDLVQEGNLGLMKAVDRFDPTRGYRFSTYATWW 239

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R++A++  T+R+P H+   + ++ R  R +  K    PTPE++A+   +    V
Sbjct: 240 IRHAINRALANKGRTVRLPAHVSADLQRLRRVTRELEAKTGETPTPEQLAQAAGLSKTRV 299

Query: 564 RKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           RK+ K+T +P +SL+ P  D+D   L D +ED +     D      L E     L +L P
Sbjct: 300 RKLSKLTLDPTVSLDAPSHDDDARGLLDRLEDASVPVAADILEHQALNEHLRDALYNLQP 359

Query: 623 REERVLRMRFGIG-------MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            E  +L+ R+GI             TL ++G++  ++RERIRQ++ +A+ KL+     ++
Sbjct: 360 IELDILKRRYGIATSEAESVDFEPMTLRQLGERHSLSRERIRQLQERALTKLRREFARRE 419

Query: 676 L 676
           L
Sbjct: 420 L 420



 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES-PLTF 164
               K    R ++ P+  YL  +  +++L+ E E+ +A  I   R     +L    P   
Sbjct: 6   ESSSKRRPVRKSESPLGAYLSTVSKVDVLTPEQELNLATEISDRRLTHWRALLSYTPFAA 65

Query: 165 QALIIWRDELNDGTT 179
               +  D+L +G  
Sbjct: 66  AIADVVEDKLREGEV 80


>gi|260590675|ref|ZP_05856133.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260537416|gb|EEX20033.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 290

 Score =  164 bits (414), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ +       K  R P+  E+A+   +    +R+        +S++ P  D+D +
Sbjct: 136 GAISKINQVTNEFVQKHNRRPSIHELAELTGIEESRIRQSQSADNHHMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL  +L  RE +++   FGIG   +  LEE+
Sbjct: 196 SMSDMLSSGDDSRTDKGVDFESMSDDLRAVLQNTLKDREIKIVTECFGIGC-QEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 255 GTEMGLTRERVRQIREKAIEKIRESGNARVLMKYL 289



 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   +++ + EI +A+ I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|288801981|ref|ZP_06407422.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302347072|ref|YP_003815370.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|288335416|gb|EFC73850.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302150546|gb|ADK96807.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 290

 Score =  164 bits (414), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ +       +  R P+  E+A+   +    +R+        +S++ P  D+D +
Sbjct: 136 GAISKINQVTNEFVQQHNRRPSIHELAELTGIDEARIRQSQSADNHHMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL  +L  RE +++   FGIG   +  LEE+
Sbjct: 196 SMSDMLSSGDDSRTDRGVDFESMSDDLRAVLQNTLKDREIKIVTECFGIGC-QEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 255 GTEMGLTRERVRQIREKAIEKIRESGNARVLMKYL 289



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   +++ + EI +A+ I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|188090698|gb|ACD49583.1| RNA polymerase sigma factor [Xanthomonas sacchari]
          Length = 285

 Score =  164 bits (414), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 137/333 (41%), Gaps = 53/333 (15%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNS 102
            E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+  
Sbjct: 1   AEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEE 60

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G   + A+L   PL
Sbjct: 61  AAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPL 120

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
             + L+   ++  +G   L EI+            GF    E         S  +     
Sbjct: 121 AVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPPVAVSDDDS---- 165

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
             + + D +    V   +     + P+ AE                           V  
Sbjct: 166 ATDADADEDDDEDVDTAEEDAGPTGPDPAE---------------------------VAR 198

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
            ++ +A  Y + +          K+         L+  + ++  +L L     D+LV +L
Sbjct: 199 RMEVLATEYAKFKK------AHAKNGAEHKLVTKLRNDIAEVFVTLKLPLPLTDVLVRKL 252

Query: 343 YDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
            D   ++  +E  +L LA     + R  F+   
Sbjct: 253 RDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 285


>gi|40353307|gb|AAR84417.1| essential primary sigma 70 factor [Frankia sp. ARgP5ag]
          Length = 217

 Score =  164 bits (414), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 111/216 (51%), Positives = 165/216 (76%), Gaps = 3/216 (1%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++V T  +  + R  +  + +   +  IAK+++VEANLRLV+S+AK+Y  RG+ FLDL
Sbjct: 5   EKLAVATKKTSPQMRRDLEAIER---DGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDL 61

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGN+GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++
Sbjct: 62  IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 121

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           R  R++   + REP+PE IAK++ +  + VR++LK+++EP+SLETPIG+E+ SHLGDFIE
Sbjct: 122 RIQRQLLQDLGREPSPEVIAKEMDLTPDKVREILKVSQEPVSLETPIGEEEDSHLGDFIE 181

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           D +AV P+D+A    L+E    VL +L+ RE++V++
Sbjct: 182 DCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVIQ 217


>gi|159470255|ref|XP_001693275.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
 gi|42742499|gb|AAM88387.2|AF525691_1 RNA polymerase sigma factor [Chlamydomonas reinhardtii]
 gi|47076042|emb|CAF25319.1| sigma-like transcription factor [Chlamydomonas reinhardtii]
 gi|158277533|gb|EDP03301.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
          Length = 752

 Score =  164 bits (414), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 89/254 (35%), Positives = 150/254 (59%), Gaps = 8/254 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  ++        AK+ ++++N +LV++V K +  +G    DL+ EG  GL+K  EK+D 
Sbjct: 477 VESLKLRYDAGLKAKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDA 536

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++F TYA WW++QA++RS+A+    +R+P+HM +++ ++   + ++  ++ REPT  
Sbjct: 537 TKGFRFGTYAHWWIRQAVSRSLAETGRAVRLPMHMIEQLTRLKNLSAKLQTQLAREPTLP 596

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ---A 607
           E+AK   +PV  V+ +++  +   SL+TPI     + LG  ++D        +  +    
Sbjct: 597 ELAKAAGLPVTRVQMLMETARSAASLDTPI---GGNELGPTVKDSVEDEREAADEEFGSD 653

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR     +L  L  RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL
Sbjct: 654 SLRNDMEAMLLELPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKL 713

Query: 668 KHPS--RSKKLRSF 679
           +  +   S KL  +
Sbjct: 714 RVKTIDVSGKLMEY 727


>gi|126215762|gb|ABN81001.1| putative RNA polymerase sigma-B factor [Rhodococcus opacus]
          Length = 194

 Score =  164 bits (414), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 87/194 (44%), Positives = 138/194 (71%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLIQEGN+GL++A EKFD+  G+KFSTYA WW++QAITR +ADQS TIR+PVH+ +
Sbjct: 1   MPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +++K+ R  R +  ++ RE T +E+A++  +P   +  +L  +++P+SL+ P+G+++ + 
Sbjct: 61  QVNKLARIKRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEEAP 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGDFIED  A S  ++ I   L      VLA+L  RE++V+R+R+G+      TL+++GK
Sbjct: 121 LGDFIEDSEATSAENAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGK 180

Query: 648 QFCVTRERIRQIEA 661
            F ++RER+RQIE 
Sbjct: 181 LFGLSRERVRQIER 194


>gi|188090526|gb|ACD49497.1| RNA polymerase sigma factor [Xanthomonas fragariae]
 gi|188090568|gb|ACD49518.1| RNA polymerase sigma factor [Xanthomonas fragariae]
          Length = 291

 Score =  164 bits (414), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 137/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L    G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNAGNSGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + E + D
Sbjct: 121 LSTEMLLAHYEAHKEGKKRLAEIVVGFNDLIEEADAAATALAAAGPVAAADDEAVEDDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D  + +   E A     D                                        V 
Sbjct: 181 DDGDDDAAEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKI------HAKNGTEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|188090596|gb|ACD49532.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 291

 Score =  163 bits (413), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 136/334 (40%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  +P D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHVPDDLVDLEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+       +G   L EI+     +  E+                ED + + +  
Sbjct: 121 LSTEMLLADYQAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDEAADNDDA 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +  + +   E A     D                                        V 
Sbjct: 181 EDGDDDATEEEAGPTGPDPVE-------------------------------------VA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y   + +        K+  +       +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYATFKKIY------AKNGAAHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|255532556|ref|YP_003092928.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255345540|gb|ACU04866.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 289

 Score =  163 bits (413), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 84/257 (32%), Positives = 140/257 (54%), Gaps = 3/257 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +  I   +     E   +VS +R        A   +++ NLR V+SVAKKY ++GL+ 
Sbjct: 20  SYLSEIGRISLTDPEEEFRLVSAIR---NGDQEALHRLIKGNLRFVVSVAKKYQDKGLKL 76

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIGL+KAA +FD   G+KF T+A+WWV+QAI ++IA+Q   IR+P +    I 
Sbjct: 77  GDLINEGNIGLIKAAHRFDATRGFKFITFAVWWVRQAILQAIAEQRRLIRLPGNQLLGIS 136

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++ +   ++  +++R PT EE+A      V+ V           SL+  I +E  S L +
Sbjct: 137 RLNQAVLKLEQQLERMPTVEELAVYTGFTVDKVMDYTANAAFTYSLDDVIKEESGSTLME 196

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D+         + A+L     R L  L+ RE++++ + +G+       +E++ K   
Sbjct: 197 VIADEATHQTDHFTLAASLSTDLNRALDILSKREQKIIILFYGLNGYPQTAIEDMQKILK 256

Query: 651 VTRERIRQIEAKAIRKL 667
           +++ERIRQ++ KA + L
Sbjct: 257 LSKERIRQLKDKAHKTL 273



 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 36/96 (37%), Gaps = 3/96 (3%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S  +   D V  YL E+G I L   E E  +   I  G    +  L +  L F  ++   
Sbjct: 9   SIAKRDSDVVESYLSEIGRISLTDPEEEFRLVSAIRNGDQEALHRLIKGNLRF--VVSVA 66

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            +  D    L ++I+ E  IG       F  T G  
Sbjct: 67  KKYQDKGLKLGDLIN-EGNIGLIKAAHRFDATRGFK 101


>gi|318041996|ref|ZP_07973952.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 318

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 139/242 (57%), Gaps = 7/242 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 66  KRTMRVGERAKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 125

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ ++     R+  +   +P+ +++++
Sbjct: 126 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARLLQRHGSQPSAQQLSE 185

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + +PV+ V  +L        +SL+  +    D + L D +  ++          A    
Sbjct: 186 AMDLPVQEVEDLLGCELRSVTVSLQGVVKSKSDPTELVDVLPSEDLPPMER-CELAERNA 244

Query: 612 TTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++L    LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 245 AVWKLLDQSNLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 304

Query: 669 HP 670
             
Sbjct: 305 KA 306


>gi|125585746|gb|EAZ26410.1| hypothetical protein OsJ_10293 [Oryza sativa Japonica Group]
          Length = 497

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 95/247 (38%), Positives = 149/247 (60%), Gaps = 1/247 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +RK        K  MV++N+RLVIS+A+++   G++F DLIQEG  GL++ AEKFD   G
Sbjct: 246 LRKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKG 305

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTY+ WW+KQAI +S+ +Q+  IR+P HM +   +V    RR+  ++KR PT EEIA
Sbjct: 306 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECRRRLRRQLKRLPTNEEIA 365

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               MP+  V   + + K  +SL + +G  D ++  +   D +  +  +   +  ++E  
Sbjct: 366 SDTGMPLRRVEAAMSLPKYTVSLTSKVGCTDMTY-QEITPDTSTETAEEMLHRWLMKEDV 424

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L  L+PRE +V+R RFG+      TL ++G+   V+RERIRQIE  A RKL+   + 
Sbjct: 425 DRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQIELVAFRKLRGRKKV 484

Query: 674 KKLRSFL 680
           + L+ +L
Sbjct: 485 QSLQHYL 491


>gi|297518365|ref|ZP_06936751.1| RNA polymerase sigma factor RpoS [Escherichia coli OP50]
          Length = 327

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 168/271 (61%), Gaps = 6/271 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S     EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELS---DHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 228

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 229 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 288

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 289 GREIGLTRERVRQIQVEGLRRLREILQTQGL 319



 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|188090538|gb|ACD49503.1| RNA polymerase sigma factor [Xanthomonas albilineans]
          Length = 285

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 134/334 (40%), Gaps = 54/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED + M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E                 
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLVEEEPAPVVVAEDDGAA-- 167

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
              + + D ++    S++D       P                               V 
Sbjct: 168 -DADADEDEDADVDASEEDAGPTGPDPVE-----------------------------VA 197

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ ++  Y + +          K+         L+  + ++  +L L     D LV +
Sbjct: 198 RRMEVLSTEYVKFKKAY------AKNGAEHKLVAKLRNDIAEVFVTLKLPLPLTDALVRK 251

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 252 LRDAMAQVKEHERRVLHLATHVARMPRKDFIRWW 285


>gi|299472559|emb|CBN79861.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 694

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 113/301 (37%), Positives = 173/301 (57%), Gaps = 13/301 (4%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM------VRKGECEASIAK 445
           +   +  +  ++   +   N    + +  G   SE    V++      + K    AS AK
Sbjct: 65  KPHEEIVLGRQIQKGVSYENTRDHLQLMRGYEPSEEEWAVALGMDREELVKELSRASKAK 124

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             M+ ANLRLV+SVAK+Y  + L F DLIQEG  GL+KAAEKFD   G+KFSTYA WW+K
Sbjct: 125 MAMLAANLRLVVSVAKRYRFQKLSFQDLIQEGTFGLVKAAEKFDPERGFKFSTYATWWIK 184

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q+I R IADQS  IR+PVH+ D +++V +    M++K  + PT +E+A+ L +    ++ 
Sbjct: 185 QSIMRGIADQSRIIRLPVHVHDFLNRVRKATLEMTDKNGKLPTDDELAEHLEVSAVRIQY 244

Query: 566 VLKITKEPISLET--PIGDEDTSHLGDFIEDKNAVS-----PLDSAIQANLRETTTRVLA 618
                +  +S+E    I  + ++  G  +E    VS     P   A    +++  T +L 
Sbjct: 245 YRDAAQATLSMEAPRNIASKTSTSPGKKVEMGQGVSGPEKTPDKQAQSDVMKQKVTELLM 304

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L+ RE+ V++ RFG+G     TLEEVG+ F +TRER+RQIEA+A+ KL+ P R+ ++R 
Sbjct: 305 TLSIREQEVVKARFGLGGALPRTLEEVGRDFRLTRERVRQIEARALHKLRQPYRNYRVRD 364

Query: 679 F 679
           F
Sbjct: 365 F 365


>gi|251733351|emb|CAR82425.1| RNA polymerase sigma factor [Mesorhizobium loti]
          Length = 202

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 114/192 (59%), Positives = 145/192 (75%)

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           A  G        + K LK++L+K V SLSLN +RI+ LVEQLYDI+KR++ NEG+LLRLA
Sbjct: 11  AAAGTLSPSQDRRLKELKDQLIKAVKSLSLNTARIEALVEQLYDINKRLVQNEGKLLRLA 70

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +SYG++R+ FL+ +QG ELDP+W     +     WK F   E D+I  +R EI++++ ET
Sbjct: 71  ESYGVRREEFLKEYQGSELDPNWTRAIGNLTSRGWKEFTKNEKDAIKDLRAEIQNLATET 130

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            ISI EFR IV+ V+KGE EA+IAKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIG
Sbjct: 131 AISILEFRKIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 190

Query: 481 LMKAAEKFDWCL 492
           LMKA +KF++  
Sbjct: 191 LMKAVDKFEYRR 202


>gi|188090534|gb|ACD49501.1| RNA polymerase sigma factor [Xanthomonas translucens pv. cerealis]
          Length = 285

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 138/334 (41%), Gaps = 54/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E         S  +    
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPAVVASDDDSAA- 168

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                  D +   +V   +     + P+ AE                           V 
Sbjct: 169 ----DASDDDDDEEVEAAEEEAGPTGPDPAE---------------------------VA 197

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 198 RRMELLATEYAKFKK------AHAKNGAEHKVVAKLRTDIAEVFVTLKLPLPLTDVLVRK 251

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 252 LRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 285


>gi|15232364|ref|NP_190960.1| SIGC (RNA POLYMERASE SIGMA-SUBUNIT C); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|2353175|gb|AAB69386.1| sigma factor 3 [Arabidopsis thaliana]
 gi|2463554|dbj|BAA22530.1| SigC [Arabidopsis thaliana]
 gi|5478585|dbj|BAA82450.1| sigma factor SigC [Arabidopsis thaliana]
 gi|7630012|emb|CAB88354.1| sigma factor SigC [Arabidopsis thaliana]
 gi|133778870|gb|ABO38775.1| At3g53920 [Arabidopsis thaliana]
 gi|332645638|gb|AEE79159.1| RNApolymerase sigma-subunit C [Arabidopsis thaliana]
          Length = 571

 Score =  163 bits (413), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 72/284 (25%), Positives = 146/284 (51%), Gaps = 5/284 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +      + +   ++ S+S     +    +    ++ +        + E+V++   LV+ 
Sbjct: 291 MERIRTQLEEESGKVASLSCWAAAAGMNEK----LLMRNLHYGWYCRDELVKSTRSLVLF 346

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W++++++  ++  +  
Sbjct: 347 LARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARG 406

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPT-PEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           + IP  +   I+ + +  + +      +    EEIAK     V+ +R   +  K   S++
Sbjct: 407 VHIPSSIIRTINHIQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRAANQCLKVVGSID 466

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD  T+   +F  D    SP ++ ++ + R     +L  L PRE++V+ +R+G+   
Sbjct: 467 KKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDY 526

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              +LEE+GK   V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 527 RPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570


>gi|284042443|ref|YP_003392783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283946664|gb|ADB49408.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 285

 Score =  163 bits (413), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 91/270 (33%), Positives = 151/270 (55%), Gaps = 4/270 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++       ++ +E   +   + +       AK+ MV +NLRLV+S+A+ Y  +GL
Sbjct: 18  LQLLMREARNWPLLTPAEEIELARRIER---GDLSAKERMVNSNLRLVMSIARHYQGQGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+QEG +GL++A EKFDW  G++FSTYA  W++Q+I R + +   TIR+PVH+  +
Sbjct: 75  GMGDLVQEGTLGLIRAVEKFDWRKGFRFSTYATLWIRQSIQRGLENTGRTIRLPVHVGQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             KV R  R ++ K  R+ T EEIA+   +PVE V +  +  +EP SL+ P+G++  + L
Sbjct: 135 ARKVARIRRELTAKHGRDATDEEIAEAARLPVEQVIEAGRADREPTSLDAPVGEDGDTAL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G  I+  +   P +        ET  R +  L   E+ V+ +RFG       TL ++G++
Sbjct: 195 GALIK-TDTPEPDEEVADTLRHETVQRAIDDLPDNEKTVIHLRFGTAGEPPQTLTQIGRR 253

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             V+  R R+IE +A+R+L   +    LR 
Sbjct: 254 LGVSSSRAREIEEQALRRLSRETSLSALRE 283



 Score = 47.1 bits (110), Expect = 0.008,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 29/62 (46%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
             + +T DP+++ +RE  +  LL+   EI +A+RIE G       +  S L     I   
Sbjct: 9   DTNDTTFDPLQLLMREARNWPLLTPAEEIELARRIERGDLSAKERMVNSNLRLVMSIARH 68

Query: 172 DE 173
            +
Sbjct: 69  YQ 70


>gi|193216688|ref|YP_001999930.1| RNA polymerase sigma factor [Mycoplasma arthritidis 158L3-1]
 gi|193002011|gb|ACF07226.1| RNA polymerase sigma-70 factor [Mycoplasma arthritidis 158L3-1]
          Length = 513

 Score =  163 bits (412), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 140/508 (27%), Positives = 238/508 (46%), Gaps = 36/508 (7%)

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           +L      +     F   E +   ++++    +E  DV   +   +       D     +
Sbjct: 19  ELAKATKKDKNKKAFSQDEIYELLEKKNLELSEEATDVLFEKLLEQGVLSSDIDFGDDDE 78

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
               +      N  + +        A++D+L  + +  L+   E   E     D      
Sbjct: 79  INETDFFESLANDKKSKKTKKTKTDALDDELHEEDIEDLEPTLEDLEE-----DEDFKED 133

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            D++  ++  + + +   +      +  + D   E+L D        E E          
Sbjct: 134 LDDEKDLEEDIDENEEFGIESEADDSSPQYDNYTEKLSDDFDEDEDIEAE---------- 183

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
                L+ +   E+            +    N +    D +      I        ++  
Sbjct: 184 ---NLLKEYDTYEIKLE--DQHISREDNMLSNKLTETNDIVKWYMRWIGKYGKL--LTPK 236

Query: 426 EFRHIV-----SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           + R +      ++          A+  +V+ NLRLVI+ AK+Y NRGL F+DLI EGN G
Sbjct: 237 KERELAIKMEEALANNNYYRYKRARDMLVKRNLRLVINNAKRYKNRGLSFIDLISEGNSG 296

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           +MKA  K+D+  G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+++  R + 
Sbjct: 297 IMKAVSKYDYKKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKILKIERELQ 356

Query: 541 NKIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
            +    PT EEIAKK       E VR + KI  +PISL+  IG E+ S   DF++D++ +
Sbjct: 357 QEFGYPPTDEEIAKKFGGDFTAEKVRYIRKINIDPISLDKNIGKEENSSFSDFVKDESVI 416

Query: 599 SPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMN------TDHTLEEVGKQFCV 651
           SP D A Q  L      ++ +SL P ++ ++R R+G+G +        HTL+E+ K+  +
Sbjct: 417 SPNDFASQQELAVILNEMINSSLDPEDQALIRKRYGVGQDPSGVPYRPHTLDELAKELNI 476

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           ++E++R++EAK +RKLKHP + KKL+ F
Sbjct: 477 SKEKVRKLEAKILRKLKHPQKRKKLKEF 504


>gi|40353299|gb|AAR84413.1| alternative primary sigma 70 factor [Frankia sp. ORS020607]
          Length = 220

 Score =  163 bits (412), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 101/195 (51%), Positives = 147/195 (75%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   AK+++V ANLRLV+SVAKKY+ RG+  LDL+QEGN+GL++A EKFD+  GYKFSTY
Sbjct: 19  DGHAAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTY 78

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A WW++QAI R++ADQ+ TIRIPVH+ ++I+K+ R  R++ + + REPT EE+A +L MP
Sbjct: 79  ATWWIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMP 138

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E V ++ +  ++ +SLET +GD+  S LGDFIED +A SP D+A    +++    VL  
Sbjct: 139 IEQVVELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGG 198

Query: 620 LTPREERVLRMRFGI 634
           L+PRE  V+R+RFG+
Sbjct: 199 LSPREREVMRLRFGL 213


>gi|222832319|gb|EEE70796.1| predicted protein [Populus trichocarpa]
          Length = 294

 Score =  163 bits (412), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 76/323 (23%), Positives = 131/323 (40%), Gaps = 60/323 (18%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
                   K +IKL + RGY+T  E+N  LP   V +E +E  ++ML++MG+ V +    
Sbjct: 27  MSTRRQRLKALIKLGKTRGYLTHSEINDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPD 86

Query: 84  EDE---EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +      +  S      A   +       DS    T DPVRMY+REMG++ELL+REGEI
Sbjct: 87  AETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEI 146

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   MM ++  SP T   ++   +E+ +G  ++  I+D           GF 
Sbjct: 147 EIAKRIEGGLMDMMEAISASPATIAEILAMSEEIREGKVVISTIVD-----------GFV 195

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
           +  E   Y   ED  +E + D                                       
Sbjct: 196 NANEDDDYVAEEDFDEEDDDDGK------------------------------------- 218

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                +  L+   ++L+ + +   D + E + ++  + D    G      +     +++ 
Sbjct: 219 ---GGSKALTKKLEELKNEALRRFDAMRENFDKMHKVYDKEGYG------TPTYIKVQKA 269

Query: 321 LVKLVGSLSLNQSRIDLLVEQLY 343
           L + + ++      I+ L + + 
Sbjct: 270 LTEELMTIRFTAQTIEKLCDLVR 292


>gi|317969234|ref|ZP_07970624.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 311

 Score =  163 bits (412), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 136/241 (56%), Gaps = 7/241 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 57  KRTMRVGERAKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ ++     R+  +    P  +++A 
Sbjct: 117 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARLMQRNGMAPNSQQLAT 176

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            L +P++ +  +L        +SL+  +    D + L D +  ++          A    
Sbjct: 177 ALGLPLDEIEDLLGCELRSVTVSLQGIVKSKSDPTELVDVLPSEDLPPMER-CELAERNA 235

Query: 612 TTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++L    LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 236 AVWKLLDQSNLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 295

Query: 669 H 669
            
Sbjct: 296 K 296


>gi|284031338|ref|YP_003381269.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810631|gb|ADB32470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 316

 Score =  163 bits (412), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 91/228 (39%), Positives = 143/228 (62%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A++  V ANLRLV+S+A++Y    +  LDL+QEGN GL++A EKFD+  G+KFSTYA
Sbjct: 80  GQRAQQRFVTANLRLVVSIARRYGRSQMPLLDLVQEGNTGLIRAVEKFDYRKGFKFSTYA 139

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WWV+QAITR IA Q+  +R+PVH+ ++++++    R +  K+ REP  +EIA +L +  
Sbjct: 140 TWWVRQAITRGIAQQARVVRLPVHVVEQLNQIGSARRTLERKLGREPEIDEIAAELDLDE 199

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V ++++I ++ ISL+ PI DE  + LGD I  + A  P      A+ R     ++  L
Sbjct: 200 ERVTELIRIGRDHISLDNPIDDEGETSLGDLIAAETAPGPDQLVADASDRSGLFSLVDQL 259

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PR   V+R R+G+       L ++G    ++ ER+RQIE +A+ +L+
Sbjct: 260 DPRSADVIRRRYGLHDGRQAKLADIGAVHGISAERVRQIEREALGRLR 307



 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 21/42 (50%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           R         D V +YL E+    LL+ E E+ +A+ +EAG 
Sbjct: 5   RSTDEGIDGKDSVGLYLEEIARTPLLTAEEEVELAETVEAGL 46


>gi|302746282|gb|ADL62731.1| RpoD [Morganella morganii subsp. morganii]
          Length = 277

 Score =  163 bits (412), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 122/323 (37%), Gaps = 47/323 (14%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L ++I     + P +        E        +   E   +++ + + D +   +   D 
Sbjct: 61  LSDLIT--GFVDPNA--------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDS 110

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  PE A      L    + +                                Q  
Sbjct: 111 DDDNSIDPELARQKFEALRVQHEKAR-------------------------------QQI 139

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            ++G+    ++ + + L E    +     L   + D LV  + ++  R+   E  +++L 
Sbjct: 140 KIHGRDHPNTNAEIQQLSE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLC 195

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+    G E    W + A    +  W   +    + + +    ++ I  E
Sbjct: 196 VEQSKMPKKNFITLFTGNETSDSWFTAAVAMNKP-WSEKLQDVAEEVERSLQRLRQIEEE 254

Query: 420 TGISISEFRHIVSMVRKGECEAS 442
           TG++I E + I+  +  G  +A 
Sbjct: 255 TGLTIEEVKDIIRRMSIGVAKAR 277


>gi|253761922|ref|XP_002489335.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
 gi|241946983|gb|EES20128.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
          Length = 238

 Score =  163 bits (412), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 91/233 (39%), Positives = 150/233 (64%), Gaps = 1/233 (0%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV +N+RLVIS+A+++   G+   DLIQEG  GL++ AEKFD   G++FSTY+ WW+KQA
Sbjct: 1   MVTSNVRLVISIAREFEGPGMDLYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWIKQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + +S+++QS   R+P HM +  ++V    +R+  K++R PT EEIA    MP++ V   +
Sbjct: 61  MRKSVSEQSQIFRLPAHMVEASYRVKECTKRLRRKLRRRPTNEEIALDTGMPIKRVEAAV 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            + K  +SL++ IG  D ++  +   D +A +  +   + ++++   + L +LT RE++V
Sbjct: 121 NLPKYSVSLDSKIGSTDMTY-QEVTADPSAETAEEMLNRMSMKKDVHKALDTLTTREKQV 179

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +RFG+  +   TL+E+G    V+RERIRQIE+ A RKL+   R K L+ +L
Sbjct: 180 VVLRFGLEDDRIRTLQEIGNIMGVSRERIRQIESGAFRKLRSKKRVKALKDYL 232


>gi|237738339|ref|ZP_04568820.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
 gi|229420219|gb|EEO35266.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
          Length = 273

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 99/268 (36%), Positives = 153/268 (57%), Gaps = 5/268 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     +   E   ++   +        AK +++  NLRLV+++AK Y NRGL  +
Sbjct: 11  YLEDIRKYKVLEKDEETELLKKAK---AGDIEAKNKLILCNLRLVVNIAKNYVNRGLSLI 67

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN GL+ A EKFD   G++FSTYA+WW+KQ+IT++I  +   IRIP +  D + K
Sbjct: 68  DLISEGNFGLIYAIEKFDMKKGFRFSTYAVWWIKQSITKAIICKGRGIRIPSYKYDLLSK 127

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V R       +    PT EEI++ L +  E + +++   ++P+SL   IG  D   L D 
Sbjct: 128 VNRYVLNRVREEGIYPTVEEISEDLNVNKEKIEEIMVAFQDPMSLSASIG--DDIQLEDI 185

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I + +  S  D  I+   RE   +++  L  RE+++L++RFG+     HTLEE+G+ F +
Sbjct: 186 IANNSETSIEDDIIEEMGREQVRQIVKVLDEREKQILKLRFGLDGEEIHTLEEIGQTFNI 245

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           TRER+RQIE K ++KLK      K + F
Sbjct: 246 TRERVRQIEKKTLKKLKMQCEKNKDKFF 273


>gi|188996015|ref|YP_001930266.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
 gi|188931082|gb|ACD65712.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
          Length = 285

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 146/275 (53%), Gaps = 9/275 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KSI     +S  E   ++  V+        A ++++ +NLR VI++AK+Y   G+ F 
Sbjct: 13  YLKSIYKIPLLSKEEEESLLKKVK---EGDKEALQKLIISNLRFVINIAKRYAGYGIPFS 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  GNIGL++AA+KFD   G +F +YA+WW++Q+I  +I  +S  I+ P  M     K
Sbjct: 70  DLISAGNIGLIEAAKKFDTSRGVRFISYAVWWIRQSIINTIQHESEIIKKPNRMYAYASK 129

Query: 532 VVRTARRMSNKIKREPTPEEIA---KKLAMPVEG--VRKVLKITKEPISLETPIG-DEDT 585
           +      + + + REP+ +EI    K   + VE   V          +SL+TPI   ++ 
Sbjct: 130 INNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLDTPIEGTDND 189

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D I   N +       + +L+     +L +L+PRE  +L  RFG+      TL EV
Sbjct: 190 LVLEDTISVYNTLDIEKDINEEDLKRAIEALLDTLSPRERTILIHRFGLNGEEPKTLNEV 249

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+   ++RER+RQIE + ++KL+  ++ KKL   +
Sbjct: 250 GEMVGLSRERVRQIENRILKKLRKIAKIKKLEDLI 284



 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           V  YL+ +  I LLS+E E ++ K+++ G    +  L  S L F  +I            
Sbjct: 10  VDFYLKSIYKIPLLSKEEEESLLKKVKEGDKEALQKLIISNLRF--VINIAKRYAGYGIP 67

Query: 181 LREII 185
             ++I
Sbjct: 68  FSDLI 72


>gi|269104472|ref|ZP_06157168.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161112|gb|EEZ39609.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 294

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 99/270 (36%), Positives = 162/270 (60%), Gaps = 5/270 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  +K I+++  ++  E    +   RK     + +KK M+E+NLRLV+S+AKKY   G+
Sbjct: 18  IQLYLKDIALKPLLTKDEE---ILYSRKALVGDAKSKKVMIESNLRLVVSIAKKYRGSGM 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q  D+I EGNIGL+ A EKFD   G++FSTYA WW+KQ I R+I +Q+ TIR+PVH+  +
Sbjct: 75  QLSDMIDEGNIGLITAVEKFDPERGFRFSTYATWWIKQTIERAIHNQARTIRLPVHVSKE 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH- 587
           I+ ++RT +++      EPT EE+A +L   VE +  +L      +S +  I  ED++  
Sbjct: 135 INTILRTHKQLMKTNNSEPTHEEVADELDKSVEDISALLSYDAPVMSFDQTISSEDSNSQ 194

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            +  FI D +   P     + ++++ T  +L  L PR+  +L  RFG+      TL++V 
Sbjct: 195 TMASFISDDSDNGPDAQIDKNDIQKLTLTMLEGLNPRDREILCRRFGLMGYEAQTLQQVA 254

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++  +TRERIRQ++  ++ KLK+  + +K 
Sbjct: 255 EEVGLTRERIRQLQVSSLNKLKNVLQREKY 284



 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 3/102 (2%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
            ++ + D      +D +++YL+++    LL+++ EI  +++   G A     + ES L  
Sbjct: 2   DIKNKVDDTTSFDNDVIQLYLKDIALKPLLTKDEEILYSRKALVGDAKSKKVMIESNLRL 61

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             ++    +       L ++ID E  IG  +    F    G 
Sbjct: 62  --VVSIAKKYRGSGMQLSDMID-EGNIGLITAVEKFDPERGF 100


>gi|17158744|ref|NP_478255.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17134693|dbj|BAB77251.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 323

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 96/267 (35%), Positives = 165/267 (61%), Gaps = 9/267 (3%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K ++    +S  E + I           + AK++M+ ANLRLV+++AKKY  R L+ +DL
Sbjct: 64  KELAKYVQLSEIEVKDIFQQ-------GTQAKQKMMVANLRLVVAIAKKYQRRNLELMDL 116

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG++GL +  EKFD   GYKFSTYA WW+ QA+TR+I+ QS TIR+P+H+ +K++K  
Sbjct: 117 IQEGSLGLERGVEKFDPTRGYKFSTYAYWWISQAMTRAISQQSRTIRLPIHITEKLNKFK 176

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  R +S K+KR P+ +EIA+K+ +    +R++L I+++P SL+  +GD + + L + + 
Sbjct: 177 KVQRELSQKLKRSPSADEIAEKMKLNPAQIRELLMISRQPASLDKQVGDNEDTELQELLT 236

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           +    SP     Q  +R+     L  LTP++++VL + +G+  N + TL +V +   ++ 
Sbjct: 237 EVPETSPEIQVTQNLMRQDIYLSLRELTPQQQQVLILHYGLEDNYELTLTQVAQHLNISE 296

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            R+R +E +A+  L+    +  LR ++
Sbjct: 297 RRVRYLEKQALSYLRRCQTN--LREYI 321


>gi|91978897|gb|ABE66424.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 289

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 82/332 (24%), Positives = 132/332 (39%), Gaps = 44/332 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSD 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P             +         E +  D  E E + +     S DD + 
Sbjct: 61  II--SGFIDPNE-----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDDEAD 113

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
               PE A      L    + +  ++                                  
Sbjct: 114 TGPDPEVAREKFGELRAQYEVTRLSI---------------------------------- 139

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            Q + ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L  + 
Sbjct: 140 -QNNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQ 198

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E D  W  Y K   +      V  + D +L+   +++ I VETG+
Sbjct: 199 AKMPKKTFVAAFTNNECDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVETGL 257

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 SIAQIKDINRRMSIGEAKARRAKKEMVEANLR 289


>gi|146164086|gb|ABQ08722.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
          Length = 293

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/336 (25%), Positives = 142/336 (42%), Gaps = 46/336 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P                         E DDV  T   I S        
Sbjct: 61  LSDII--SGFIDPN------------------------EADDVAPTATHIGSELSEDDLA 94

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD- 299
               D   +  E+ + + D+ +      ++                  E + ELR+  + 
Sbjct: 95  DEDEDEDEDEDEDGDSSDDDGDGGPDPEVA-----------------REKFGELRAQYEV 137

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             ++ Q + ++  + +    +L  +     L   + D LV  + ++ +R+   E  +L+L
Sbjct: 138 TRLSIQNNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKL 197

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  
Sbjct: 198 CVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKSWSPRLVEMDED-VLRAIGKLQQIEE 256

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ETG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 ETGLSITQIKDINRRMSIGEAKARRAKKEMVEANLR 292


>gi|213423374|ref|ZP_03356362.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 271

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 111/316 (35%), Gaps = 48/316 (15%)

Query: 72  NMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
           +MGI V++   D +D   +E++      A  ++  +    +S    T DPVRMY+REMG+
Sbjct: 1   DMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGT 60

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P     L+   D +      L ++I     
Sbjct: 61  VELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI----- 115

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  GF                  +   +  + + D +                PE 
Sbjct: 116 ------TGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPEL 169

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A                       +LR + +   D I                     +S
Sbjct: 170 AREKF------------------AELRAQYVVTRDTIKAK-----------------GRS 194

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
               +    KL ++     L   + D LV  +  +  R+   E  +++L  +   + +  
Sbjct: 195 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 254

Query: 370 FLERHQGRELDPHWVS 385
           F+    G E    W +
Sbjct: 255 FITLFTGNETSETWFN 270


>gi|188090592|gb|ACD49530.1| RNA polymerase sigma factor [Xanthomonas fragariae]
 gi|188090606|gb|ACD49537.1| RNA polymerase sigma factor [Xanthomonas fragariae]
          Length = 291

 Score =  163 bits (411), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 138/334 (41%), Gaps = 48/334 (14%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L    G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNAGNSGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L+ + L+   +   +G   L EI+     +  E+                +D + E + D
Sbjct: 121 LSTEMLLAHYEAHKEGKKRLAEIVVGFNDLIEEADAAATALAAAGPVAAADDEAVEDDDD 180

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           D  + +   E A     D                                       +V 
Sbjct: 181 DDGDDDAAEEEAGPTGPDP-------------------------------------MEVA 203

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + + +        K+          +E +  +  +L L     D LV Q
Sbjct: 204 TRMENLANEYAKFKKI------HAKNGTEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQ 257

Query: 342 LYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
           L  +   I  +E ++L LA +   + R  F+   
Sbjct: 258 LRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 291


>gi|149200267|ref|ZP_01877288.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
 gi|149136631|gb|EDM25063.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  162 bits (410), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 97/269 (36%), Positives = 153/269 (56%), Gaps = 3/269 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            IRN + +IS  + ++  E   + + ++     +  A+++++ +NLRLV+ +A  +   G
Sbjct: 7   AIRNYMHNISDYSLVTKEEEVDLAADIK---LGSDKAREKLIVSNLRLVVKIAHDFKGLG 63

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGNIGLM+A EKFD   G KFS+YA WW+KQ++ R +A+QS TIRIPV    
Sbjct: 64  LPLSDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRGLANQSRTIRIPVQSAG 123

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           KI+K+      +  K+ REPT +EIA  L      V  +  +    ISL+  + D +   
Sbjct: 124 KINKIRNARIELKEKLMREPTDQEIATYLEFSKRTVSGLSTVGGSTISLQAKLQDGEDGE 183

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + DK + +  D   +A    +  + +  LT RE+ VL +RFG+      TLEEV +
Sbjct: 184 IQDIVADKASQTASDIIGEAESINSMMKFIVYLTDREKLVLELRFGLLSGRPKTLEEVSQ 243

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TRER+RQI+ +A++KL+   + + L
Sbjct: 244 AIGRTRERVRQIQNQALKKLRERMQRESL 272



 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 33/99 (33%), Gaps = 9/99 (9%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D +R Y+  +    L+++E E+ +A  I+ G       L  S L    ++    +    
Sbjct: 5   SDAIRNYMHNISDYSLVTKEEEVDLAADIKLGSDKAREKLIVSNLRL--VVKIAHDFKGL 62

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
              L ++I        E   G     E     K    S 
Sbjct: 63  GLPLSDLI-------SEGNIGLMRAVEKFDPAKGAKFSS 94


>gi|309786170|ref|ZP_07680798.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
 gi|308925915|gb|EFP71394.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
          Length = 237

 Score =  162 bits (410), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 93/229 (40%), Positives = 158/229 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 181 LARRFGLLGYEAATLEDVGREIDLTRERVRQIQVEGLRRLREILQTQGL 229


>gi|1769413|dbj|BAA13122.1| RpoD2 sigma factor [Microcystis aeruginosa]
          Length = 376

 Score =  162 bits (410), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 108/285 (37%), Positives = 181/285 (63%), Gaps = 2/285 (0%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+    +   K++  +     +T  +I+        +         AK++M+ +NLRLV
Sbjct: 92  KFLMEAEEVRQKLQENLHRPPTKTEWAIALELDNERQLENRLYRGRTAKRKMIRSNLRLV 151

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK+Y NRG+ FLDLIQEG IGL +AAEKFD   GYKFSTYA WW++QAITR+IA+ +
Sbjct: 152 VSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWWIRQAITRTIANDA 211

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+ +K++K+ +    +   ++R P   E+A++L +  E +R++L++ ++ +SL
Sbjct: 212 RTIRLPIHIVEKLNKLKKAQI-LKQDLQRNPNERELAERLEITPEQLRQLLQLRRQSLSL 270

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIG 635
              +G  + + L D +ED +   P D   +  +R+    VL+  LT RE+ V+ +R+G+ 
Sbjct: 271 NHRVGKGEDTELVDLLEDDDLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLA 330

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +  +TLEEVG  F ++RER+RQI+ KA+RKL+ P  +++L+ +L
Sbjct: 331 TSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLRRPQVARRLKGWL 375



 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           ++ D ++  E +++ L  +   +  +            S +D V  + +EM    LLS E
Sbjct: 23  LELDSVDFGERTDEDLTESLPETLKNTRGSSGTGYDKGSNEDTVGAFFKEMARYPLLSAE 82

Query: 138 GEIAIAKRIE--AGRAMMMASLCE 159
            EI +A  ++       +   L E
Sbjct: 83  EEIELAYSVKFLMEAEEVRQKLQE 106


>gi|146164076|gb|ABQ08721.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
          Length = 293

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 85/336 (25%), Positives = 142/336 (42%), Gaps = 46/336 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P                         E DDV  T   I S        
Sbjct: 61  LSDII--SGFIDPN------------------------EADDVAPTATHIGSELSEDDLA 94

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD- 299
               D   +  E+ + + D+ +      ++                  E + ELR+  + 
Sbjct: 95  DEDEDEDEDEDEDGDSSDDDGDGGPDPEVA-----------------REKFGELRAQYEV 137

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             ++ Q + ++  + +    +L  +     L   + D LV  + ++ +R+   E  +L+L
Sbjct: 138 TRLSIQNNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKL 197

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+      E +  W  Y K   +      V  + + +L+   +++ I  
Sbjct: 198 CVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKSWSPRLVEMD-EDVLRAIGKLQQIEE 256

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ETG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 ETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 292


>gi|78780107|ref|YP_398219.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713606|gb|ABB50783.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 344

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 103/285 (36%), Positives = 166/285 (58%), Gaps = 7/285 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETG--ISISEFRHIVSM----VRKGECEASIAKK 446
            E +  +  +V   +++      I   TG   SI E    +++    ++K       AK+
Sbjct: 52  HEQEITLGRQVQEYMQVERAELEIIELTGDKPSIEELSSKLNLSIPIIKKRLRAGQRAKE 111

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q
Sbjct: 112 RMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQ 171

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P E V+ +
Sbjct: 172 GITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSELAKYVELPEEDVKDL 231

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +    +P+SLET +GD + + L D +     + P +      +R     +L  L   + R
Sbjct: 232 MCKAGQPVSLETKVGDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDLHSLLHQLPDLQCR 290

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           VLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 291 VLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLS 335



 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           SS + S   L         +  D VR YLR++G + LLS E EI + ++++    +  A 
Sbjct: 13  SSETLSENKLATISSLKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAE 72

Query: 157 L 157
           L
Sbjct: 73  L 73


>gi|299472557|emb|CBN79859.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 835

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 96/285 (33%), Positives = 160/285 (56%), Gaps = 12/285 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVR----KGECEASIAKKEMVEANLRLVISVA 460
            + ++R+ +++ +     S  E+   + + +    +    A  AK+ M+ ANLRLV+S+A
Sbjct: 258 QLERVRDRLET-THGAAPSCEEWASTLHLTKDELLRELAVADEAKEHMISANLRLVVSMA 316

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           + Y  RGL F DLIQEG +GL+KA EKF+  +G++F TYA WW+K++I   IA+QS  IR
Sbjct: 317 RGYRGRGLAFPDLIQEGTMGLVKACEKFNPEMGFQFYTYARWWIKKSILTGIANQSRVIR 376

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P  +   +  + +    ++    + PT EE+  KL   VE ++   +      S+   I
Sbjct: 377 LPTQVHAFLSSIRKYTYELTVD-GKVPTDEELGDKLGATVEKIQHYRQAALRTDSISLDI 435

Query: 581 GDED------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
              +         LG  I +K+   P D+     ++   T +LA+L  RE++V+R R+G+
Sbjct: 436 RASNKVSDGAADDLGTQIGEKSTPDPEDATQAFYMKGKVTALLATLKDREQKVVRARYGL 495

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              T  TLEE+G+   +TRER+RQIE+KA+ KL+ P R+ ++R  
Sbjct: 496 DGATSKTLEEIGRDLGLTRERVRQIESKALSKLRQPYRNYRVREH 540


>gi|310779070|ref|YP_003967403.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309748393|gb|ADO83055.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 275

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 97/269 (36%), Positives = 156/269 (57%), Gaps = 6/269 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++  E   ++   +        AK +++ +NLRLV+++AK Y ++G+ F+
Sbjct: 11  YLEDIRSYNILTKEEELDLLIRAK---SGCEDAKHKLILSNLRLVVNIAKSYVHKGMGFI 67

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN GLM A EKFD   G++FSTYA+WW+KQ+I+++I  +   IRIP +  D ++K
Sbjct: 68  DLISEGNFGLMHAIEKFDVEKGFRFSTYAVWWIKQSISKAIISKGREIRIPSYKHDLLNK 127

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +       K    P  E+IA  L +  + V+KV+   ++ +SL   IG  D   L D 
Sbjct: 128 VNKFIMEFVMKNSVYPNIEDIALGLEITPKKVQKVMLEFQDLLSLNASIG--DDIFLEDT 185

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I   +  S  D  +    R     +L  L PRE+ +L++R+G+     HTLEE+GK F +
Sbjct: 186 ISQPDEESLEDEVLGEIGRNEINDILEVLKPREKEILKLRYGLDGYEIHTLEEIGKSFSI 245

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TRER+RQIE K ++KL++   S++L+ +L
Sbjct: 246 TRERVRQIEKKTLQKLRNKF-SEELKPYL 273


>gi|188090584|gb|ACD49526.1| RNA polymerase sigma factor [Xanthomonas translucens pv. secalis]
 gi|188090586|gb|ACD49527.1| RNA polymerase sigma factor [Xanthomonas translucens]
 gi|188090588|gb|ACD49528.1| RNA polymerase sigma factor [Xanthomonas translucens pv. undulosa]
          Length = 285

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 138/334 (41%), Gaps = 54/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E         S  +    
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPAVVASDDDSAA- 168

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                  D +   +V   +     + P+ AE                           V 
Sbjct: 169 ----DASDDDDDEEVEAAEEEAGPTGPDPAE---------------------------VA 197

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          K+         L+  + ++  +L L     D+LV +
Sbjct: 198 RRMELLATEYAKFKK------AHAKNGAEHKLVTKLRTDIAEVFVTLKLPLPLTDVLVRK 251

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 252 LRDTMAQVKDHERRVLHLATHVARMPRKEFIRSW 285


>gi|297736323|emb|CBI24961.3| unnamed protein product [Vitis vinifera]
          Length = 319

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 146/247 (59%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + K  C    +++ + ++  RLV+S+A +Y  +GL   DLIQEG+IGL++ AE+FD   G
Sbjct: 72  LDKMLCNGRESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRG 131

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YK STY  WW++QAI R+IA++S  IR+P  + + + K+      +S +++R PT +EIA
Sbjct: 132 YKLSTYVYWWIRQAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIA 191

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + + + V  VR V + ++ PIS++  +  +    L + I   +  +P     +  +++  
Sbjct: 192 EFIDVNVSTVRLVSERSRTPISVDQAVTSQGCMTLQEIIPGPDETTPQKMVKRQLMKQEV 251

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R L +L  RE  +LR+ FGI   T  + EE+G+   ++RER+RQI + A+ KL+  S  
Sbjct: 252 ERALNTLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQTSVV 311

Query: 674 KKLRSFL 680
             L+ ++
Sbjct: 312 DYLKLYM 318


>gi|188090576|gb|ACD49522.1| RNA polymerase sigma factor [Xanthomonas translucens pv. graminis]
          Length = 285

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 138/334 (41%), Gaps = 54/334 (16%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASN 101
             E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+ 
Sbjct: 1   YAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAE 60

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
            +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   P
Sbjct: 61  EAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGAFP 120

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
           L  + L+   ++  +G   L EI+            GF    E         S  +    
Sbjct: 121 LAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEPAPAVVASDDDSAA- 168

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
                  D +   +V   +     + P+ AE                           V 
Sbjct: 169 ----DASDDDDDEEVEAAEEEAGPTGPDPAE---------------------------VA 197

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             ++ +A  Y + +          ++         L+  + ++  +L L     D+LV +
Sbjct: 198 RRMELLATEYAKFKK------AHARNGAEHKLVTKLRTDIAEVFVTLKLPLPLTDVLVRK 251

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
           L D   ++  +E  +L LA     + R  F+   
Sbjct: 252 LRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 285


>gi|289805026|ref|ZP_06535655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 196

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 92/193 (47%), Positives = 128/193 (66%), Gaps = 2/193 (1%)

Query: 353 EGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           E  +++L  +   + +  F+    G E    W + A    +  W   +    + + +   
Sbjct: 4   ERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKP-WSEKLHDVAEEVQRCLQ 62

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFL
Sbjct: 63  KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 122

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K
Sbjct: 123 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 182

Query: 532 VVRTARRMSNKIK 544
           + R +R+M  ++ 
Sbjct: 183 LNRISRQMLQEMG 195


>gi|188090618|gb|ACD49543.1| RNA polymerase sigma factor [Xanthomonas populi]
          Length = 290

 Score =  162 bits (410), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 81/333 (24%), Positives = 136/333 (40%), Gaps = 48/333 (14%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNS 102
            E+N  LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  
Sbjct: 1   AEVNDHLPDDLVDLEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEE 60

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +       D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL
Sbjct: 61  AAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPL 120

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           + + L+       +G   L EI+     +  E+                ED + + +  +
Sbjct: 121 STEMLLADYQAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSEDEAADNDDAE 180

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
             + +   E A     D                                        V  
Sbjct: 181 DGDDDATEEEAGPTGPDPVE-------------------------------------VAT 203

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
            ++ +A  Y   + +        K+  +       +E +  +  +L L     D LV QL
Sbjct: 204 RMENLANEYATFKKIY------AKNGAAHKLVVKAREDMAAIFTTLKLPLPLTDALVTQL 257

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
             +   I  +E ++L LA +   + R  F+   
Sbjct: 258 RGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 290


>gi|289549268|ref|YP_003474256.1| RNA polymerase, sigma 70 family subunit [Thermocrinis albus DSM
           14484]
 gi|289182885|gb|ADC90129.1| putative RNA polymerase, sigma 70 family subunit [Thermocrinis
           albus DSM 14484]
          Length = 310

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 88/303 (29%), Positives = 159/303 (52%), Gaps = 34/303 (11%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +K +S    ++  E + +    +      + A +++VE+NLR VIS+AK+Y   GL
Sbjct: 10  LAQYLKKVSKIPLLTPEEEKELARRAK---EGDTEALRKLVESNLRFVISIAKQYQGYGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI  GN GL++AA++FD   G KF +YA+WW++QAI ++++ QS  +RIP+     
Sbjct: 67  PLSELIAAGNYGLVEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQSGAVRIPLKQSHV 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKL-------------------------------A 557
           I+++     ++  + ++EPT EE+A +                                 
Sbjct: 127 INRIASIYSKLYKEQEKEPTAEEVAYEYTKEILQKEMERELGRPPTEEEIERRIKKEGLK 186

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +  + V K L+I K P+SL+ PIG+++ +   D +    +    +  +   L +    +L
Sbjct: 187 ISPQEVEKCLQICKAPLSLDAPIGEDEDTFFVDLLSKHGSADVEEKVLTEFLEKEIEEML 246

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             L  +E RV+ +RFG+      TL E+G+   ++RER+RQ+E +A+RKL++ +  K L+
Sbjct: 247 DKLPEKERRVIELRFGLRGEEPRTLREIGEILNISRERVRQLETRALRKLRNMAMKKHLK 306

Query: 678 SFL 680
            FL
Sbjct: 307 DFL 309



 Score = 45.2 bits (105), Expect = 0.033,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++  I LL+ E E  +A+R + G    +  L ES L F  +I    +       L E
Sbjct: 13  YLKKVSKIPLLTPEEEKELARRAKEGDTEALRKLVESNLRF--VISIAKQYQGYGLPLSE 70

Query: 184 II 185
           +I
Sbjct: 71  LI 72


>gi|282859310|ref|ZP_06268422.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282587890|gb|EFB93083.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 290

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ +       K  R P+  E+A+   +    +R+        +S++ P  D+D +
Sbjct: 136 GAISKINQVTNEFIQKHNRRPSIHELAEMTGIDEARIRQSQSADNHHMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +   +           ++ +    VL  +L  RE +++   FGIG   +  LEE+
Sbjct: 196 SMSDMLSSGDDSRTDKGVDFESMSDDLRAVLQNTLKEREIKIVTECFGIGC-QEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 255 GTEMALTRERVRQIREKAIEKIRESGNARVLMKYL 289



 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRA---MMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   +++ + EI +A+ I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|157414236|ref|YP_001485102.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388811|gb|ABV51516.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 344

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 94/238 (39%), Positives = 149/238 (62%), Gaps = 1/238 (0%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   G
Sbjct: 99  IKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARG 158

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+A
Sbjct: 159 YKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSELA 218

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K + +P + V+ ++    +P+SLET +GD + + L D +     + P +      +R   
Sbjct: 219 KYVELPEDDVKDLMCKAGQPVSLETKVGDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDL 277

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             +L  L   + RVLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 278 HSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLS 335



 Score = 42.5 bits (98), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           D VR YLR++G + LLS E EI + ++++    +  A L
Sbjct: 35  DLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMEVERAEL 73


>gi|161521004|ref|YP_001584431.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|189352818|ref|YP_001948445.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
 gi|160345054|gb|ABX18139.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
 gi|189336840|dbj|BAG45909.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 525

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 101/220 (45%), Positives = 147/220 (66%), Gaps = 1/220 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A + M+EANLRLV+S+A+KY NRG+   DL+Q+G IGLM+A EKF++  G+KFSTYA 
Sbjct: 286 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYAT 345

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI R++AD++ TIR+PVH+ D+  +V R A R   +  R+PTP E+A +  +  +
Sbjct: 346 WWIRQAIARAVADRARTIRVPVHVGDQHQRVRRQALRFRQRTGRQPTPAELAAETGLAED 405

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R +L +  EP+SL+TP+ D DT  L D IED+ + SP +      +RE    +L S+T
Sbjct: 406 KLRAILALPAEPVSLDTPLPDADTG-LVDLIEDETSASPFEQLAGTRMRECVRSLLRSVT 464

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           P E  VLR RFG+G     T + + K   ++RER+RQIE 
Sbjct: 465 PTEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEK 504



 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 41/147 (27%), Positives = 74/147 (50%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D    
Sbjct: 10  ADTPLDPIIQLLALASEQGYLTHADLVDALPPESDSPDALDVVRAALADIGITVLDEPAA 69

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  ++D+          L         ++ DP+ +Y+R M ++ LL+RE EIA+A
Sbjct: 70  PPPFAAAPAVDVDRDTLEEGRALLGDLARGASASTDPLALYMRRMHAVPLLTREDEIALA 129

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIW 170
           + +E GR  M+ +L   P    AL+  
Sbjct: 130 RELETGRHQMLHALAGCPPAVDALLAR 156


>gi|71908137|ref|YP_285724.1| RNA polymerase sigma factor RpoS [Dechloromonas aromatica RCB]
 gi|71847758|gb|AAZ47254.1| RNA polymerase, sigma 38 subunit, RpoS [Dechloromonas aromatica
           RCB]
          Length = 309

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 90/260 (34%), Positives = 145/260 (55%), Gaps = 3/260 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I  +  ++ +E      +VR        A++ M+E NLRLV+++AK Y NRG+ 
Sbjct: 40  QLYLSEIGAKPLLTPAEELATSRLVR---EGDFSARQRMIEHNLRLVVNIAKHYLNRGIP 96

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL+ A EKFD   G++FSTYA WW++Q I R I +QS TIR+PVH+  +I
Sbjct: 97  LLDLIEEGNLGLIHALEKFDPERGFRFSTYATWWIRQNIERGIMNQSRTIRLPVHIVKEI 156

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           + V+R  R + +  KR+ T E IA  +  PV  VR++L + +   SL+ P+  +    + 
Sbjct: 157 NVVLRAMRHLESADKRDSTVERIALLIDRPVADVRRILSLNEHIASLDAPLEIDPNHTMA 216

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + I D     P      + +       L  LT R+  V+  R+G+      TL+ +    
Sbjct: 217 EVIADDGESDPESLLQSSEVGSLVDDWLEQLTERQRSVIERRYGLSGADLATLDVIACDL 276

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +TRER+RQI+ + + +L+ 
Sbjct: 277 GLTRERVRQIQMEGLDRLRK 296



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 9/105 (8%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
             +R        +D  ++YL E+G+  LL+   E+A ++ +  G       + E  L   
Sbjct: 24  EPERVLPEIELLEDVTQLYLSEIGAKPLLTPAEELATSRLVREGDFSARQRMIEHNLRL- 82

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
            ++       +    L ++I+       E   G  H  E    ++
Sbjct: 83  -VVNIAKHYLNRGIPLLDLIE-------EGNLGLIHALEKFDPER 119


>gi|33862185|ref|NP_893746.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634403|emb|CAE20088.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 333

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 101/287 (35%), Positives = 165/287 (57%), Gaps = 7/287 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVET--GISISEFRHIVSM----VRKGECEASIAKK 446
            E +  +  +V   +++      I   T    S  E    +++    ++K       AK+
Sbjct: 41  HEQEITLGRQVQEYMQVERAEIEIMELTDNKPSPEELAEKLNLSTSQIKKRLRAGQRAKE 100

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q
Sbjct: 101 RMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQ 160

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V+ +
Sbjct: 161 GITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTISELAKYVELPEDDVKDL 220

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +    +P+SLET +GD + + L D +     + P +      +R     +L  L   + R
Sbjct: 221 MCKAGQPVSLETKVGDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDLHSLLHQLPDLQCR 279

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           VLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S S
Sbjct: 280 VLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSES 326



 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 14/39 (35%), Positives = 24/39 (61%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           D VR YLR++G + LLS E EI + ++++    +  A +
Sbjct: 24  DLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAEI 62


>gi|281420436|ref|ZP_06251435.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405493|gb|EFB36173.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 291

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 97/276 (35%), Positives = 158/276 (57%), Gaps = 3/276 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  +SI E   +   +RKG  E   AK+++V+ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMVSIDEEIELAQKIRKGGREGERAKEKLVKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+     +   + +R+P+  E+A+   M    + + +K     +S++ P G +D  
Sbjct: 136 GALSKISAEISKFEQENQRKPSVAELAQITKMEESKIDQTIKADNHHMSIDAPFGSDDDD 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEE 644
           + + D +   +           ++     RVL S L  RE ++L   +GIG +    LEE
Sbjct: 196 NAMVDVMASGDDSRTDKGVDFESMASELDRVLNSVLKDRERKILCYCYGIGCHE-KGLEE 254

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +G +F +TRER+RQI  K+I KL+   + K L  +L
Sbjct: 255 IGSEFNLTRERVRQIREKSIIKLRDSGKIKILMKYL 290



 Score = 37.9 bits (86), Expect = 6.5,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAM---MMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   ++S + EI +A++I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGREPMVSIDEEIELAQKIRKGGREGERAKEKLVKANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|221196694|ref|ZP_03569741.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
 gi|221203363|ref|ZP_03576382.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221177297|gb|EEE09725.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221183248|gb|EEE15648.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
          Length = 524

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 102/220 (46%), Positives = 148/220 (67%), Gaps = 1/220 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A + M+EANLRLV+S+A+KY NRG+   DL+Q+G IGLM+A EKF++  G+KFSTYA 
Sbjct: 285 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYAT 344

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI R++AD++ TIR+PVH+ D+  +V R A R   +  R+PTP E+A +  +  +
Sbjct: 345 WWIRQAIARAVADRARTIRVPVHVGDQHQRVRRQALRFRQRTGRQPTPAELAAETGLAED 404

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R +L +  EP+SL+TP+ D DT  L D IED+ + SP +    A +RE    +L S+T
Sbjct: 405 KLRAILALPAEPVSLDTPLPDADTG-LVDLIEDETSASPFEQLAGARMRECVRSLLRSVT 463

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           P E  VLR RFG+G     T + + K   ++RER+RQIE 
Sbjct: 464 PAEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEK 503



 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 42/147 (28%), Positives = 75/147 (51%)

Query: 24  FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D    
Sbjct: 10  ADTPLDPIIQLLALASEQGYLTHADLVDALPPESDSPDALDVVRAALADIGITVLDEPAA 69

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                +  ++D+   A      L         ++ DP+ +Y+R M ++ LL+RE EIA+A
Sbjct: 70  PPPFAAAPAVDVDRDALEEGRALLGDLARGASASTDPLALYMRRMHAVPLLTREDEIALA 129

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIW 170
           + +E GR  M+ +L   P    AL+  
Sbjct: 130 RELETGRHQMLHALAGCPPAVDALLAR 156


>gi|146164074|gb|ABQ08719.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp. ranae]
          Length = 293

 Score =  162 bits (409), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 84/336 (25%), Positives = 141/336 (41%), Gaps = 46/336 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P                         E DDV  T   I S        
Sbjct: 61  LSDII--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLA 94

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD- 299
               D   +   + + + D+ +      ++                  E + ELR+  + 
Sbjct: 95  DEDEDEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEV 137

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             ++ Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L
Sbjct: 138 TRLSIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKL 197

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  
Sbjct: 198 CVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEE 256

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ETG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 ETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 292


>gi|294673146|ref|YP_003573762.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294474130|gb|ADE83519.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  161 bits (408), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 85/271 (31%), Positives = 149/271 (54%), Gaps = 2/271 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  IS    I+  +   +   +RKG    + AK+++V ANLR V+SVAK+Y ++
Sbjct: 16  ESLNKYLTDISRIPMITPEQEVELAQTIRKGGRTGAKAKEKLVNANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+  +DLI EGN+GL+ AA+KFD   G+KF +YA+WW++Q+I ++IAD S  +R P    
Sbjct: 76  GIPLIDLISEGNVGLITAADKFDETRGFKFISYAIWWIRQSILQAIADYSGMVRRPQSQI 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
              +K+         K +R P+ EE+++ +++ +E + K ++      S++ PI D+DT+
Sbjct: 136 AISNKIKNATNAFMLKNQRNPSAEELSEIISLEIEKIEKAIQSEAHVASIDAPISDDDTT 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D I      +        ++      VL A L+ RE  ++   FGIG      L+++
Sbjct: 196 TMADSIASTAEYASDRKVDYESMCSDVMLVLGAVLSERERAIVVQSFGIGCPE-RGLDDI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G    ++RER+RQI  + + K++  + S  L
Sbjct: 255 GSSMGLSRERVRQIRERGLDKIRKSNMSYIL 285



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA-GRAMMMASLCESPLTFQA 166
           K   S    T++ +  YL ++  I +++ E E+ +A+ I   GR    A         + 
Sbjct: 5   KISKSITTRTEESLNKYLTDISRIPMITPEQEVELAQTIRKGGRTGAKAKEKLVNANLRF 64

Query: 167 LIIWRDELNDGTTLLREII 185
           ++    +       L ++I
Sbjct: 65  VVSVAKQYQHQGIPLIDLI 83


>gi|158334481|ref|YP_001515653.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158304722|gb|ABW26339.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  161 bits (408), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 100/250 (40%), Positives = 163/250 (65%), Gaps = 3/250 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS ++K       A ++MVE+NLRLV+S+AKKY    L+FLDLIQEG IGL +  EKFD 
Sbjct: 70  VSQLQKELKLGQTANRKMVESNLRLVVSIAKKYNKAKLEFLDLIQEGTIGLQRGVEKFDP 129

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++QA+TR+IA+Q  TIR+P+H+ +K++K+ +  R++S K+ R+PT  
Sbjct: 130 TKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEKLNKLRKVKRQLSLKLHRDPTVA 189

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A ++ +  + V   L   +  ISL+  +GD+  + L + +ED +A SP D A  + L+
Sbjct: 190 ELATEMELSPKKVEAFLSYARHSISLDVQVGDQQNTELWELLEDPHA-SPEDYATASYLQ 248

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               ++L  L P++  V+ +R+G+      TL +VG++  V+RE +R++E +A + L+  
Sbjct: 249 SDLAKLLNVLNPQQREVITLRYGLIDQNPLTLAKVGERLNVSREWVRRVEREAFQLLR-- 306

Query: 671 SRSKKLRSFL 680
           S+   L+ +L
Sbjct: 307 SQKVVLQEYL 316


>gi|195939453|ref|ZP_03084835.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 305

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 94/254 (37%), Positives = 160/254 (62%), Gaps = 3/254 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIRQI 659
           G++  +TRER+RQI
Sbjct: 292 GREIGLTRERVRQI 305



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|298500963|ref|ZP_07010764.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
 gi|297540211|gb|EFH76271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
          Length = 233

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 90/220 (40%), Positives = 146/220 (66%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + ++++Y+NR L  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+
Sbjct: 2   VKISRRYSNRRLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 61

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR +S ++  EPTPEEIA +L  PV+ V K+L++ +   S+
Sbjct: 62  RTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISSV 121

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +TPIG +    L D + D +   P  S    ++RE+    L  L P+++ VL  RFG+  
Sbjct: 122 DTPIGGDGDKALLDILPDSHNADPEFSTQDDDIRESLLNWLDELNPKQKEVLARRFGLLG 181

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLEEVG++  +TRER+RQI+ + +R+L+     + L
Sbjct: 182 YEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQGL 221


>gi|78184480|ref|YP_376915.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78168774|gb|ABB25871.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 309

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 96/290 (33%), Positives = 154/290 (53%), Gaps = 12/290 (4%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
            E +  +  +V +++ I  E   I+  TG S           R        AK +M+ AN
Sbjct: 21  PEQELMLGRKVQAMVAI-TEPCLIAGGTGPSC----EYNDNQRFVIRRGERAKNQMITAN 75

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q + R++
Sbjct: 76  LRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQGLNRAL 135

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--T 570
           + QS TIRIPV++ +K+ K+     R+  +     T E++A+ + +P+  V  +L     
Sbjct: 136 STQSRTIRIPVNVNEKLTKLRAAKARIMQRNGLTATGEQLAEFMNVPLTEVEDLLACELR 195

Query: 571 KEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTPREERV 627
              +SL+  +    D S L D +          + I A    +   +L  A+LTP+E +V
Sbjct: 196 SVTVSLQGIVKSKSDPSELVDILPSDEIPPMERAEI-AERSASVWALLSKANLTPKEHKV 254

Query: 628 LRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+       L
Sbjct: 255 VTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKTGIQSGL 304


>gi|296127362|ref|YP_003634614.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296019178|gb|ADG72415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 309

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 101/291 (34%), Positives = 170/291 (58%), Gaps = 22/291 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASI----------------------AKKEMV 449
            +K I     +S  E   +   +     + ++                       + ++V
Sbjct: 17  YLKQIGEIRRLSKEEELDLWQRLEVCRDKKALLLEKEDEESKKELESLEKEIDSIQHKLV 76

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           ++NLRLVIS+AK+Y N G+ F+D+I EGNIGL++A ++F++  G+KFSTY +WW+KQ+I 
Sbjct: 77  KSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYKKGFKFSTYGVWWIKQSIV 136

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           + I+ +   IR P+H+   I K ++T++ ++ K+ REPT +EIAK++ +  + +  ++  
Sbjct: 137 KEISSKRHIIRFPMHIARLIKKSIQTSKVLTQKLGREPTTDEIAKEMKIDRKTLSYIMIF 196

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T++  S+++   + D + +   IEDKN  SP   A   +LR+T T  L  L  +E  V+ 
Sbjct: 197 TQDTASVDSFFKNSDNNDMTSIIEDKNFPSPHQKAFMDSLRDTLTEALKCLDEKERTVII 256

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            RFG+      TLE+ GK+  +TRER+RQI+ KAI+KL   + SK+L+SFL
Sbjct: 257 SRFGLYGKEAKTLEDTGKELNITRERVRQIQIKAIKKLAGLNLSKELKSFL 307


>gi|218440090|ref|YP_002378419.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172818|gb|ACK71551.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 94/284 (33%), Positives = 168/284 (59%), Gaps = 18/284 (6%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVR----------------KGECEASIAKKEM 448
            +  +R+ ++ I     ++  E   + + V+                K   +  IAK++M
Sbjct: 5   KLDPVRSYLQEIGRIPLLNSEEEVQLATKVQNMLPLLEKENLTAAEKKIVEQGQIAKRKM 64

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ANLRLV+S+AK+Y  RGL  LDLIQEG++GL++A EKFD   GYKFSTYA WWV+QAI
Sbjct: 65  IQANLRLVVSIAKRYQRRGLSLLDLIQEGSLGLIRAVEKFDPSKGYKFSTYAYWWVRQAI 124

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR++A++S TIR+P+HM + ++++ ++ R ++ ++ R+P  +E+A+++ +PVE +R++  
Sbjct: 125 TRALAEKSRTIRLPIHMTENLNQLKKSVRELTGELGRKPNEQEVAQRMEIPVEKLREIRH 184

Query: 569 ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
                 +    I  +D  + LG+ + D+ ++       Q  L      +L  L PR+  +
Sbjct: 185 AVYRTDAKSLNITLDDNQTELGEVLPDETSLPIEF-VSQWELVTKINDLLEDLPPRQREI 243

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           + +RFG+      + +E+G+Q  ++ ER RQ+  +A+R LK  +
Sbjct: 244 ITLRFGLQTGKRMSYKEIGRQCGISHERARQLLNRAMRTLKQKA 287



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 14/30 (46%), Positives = 22/30 (73%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           DPVR YL+E+G I LL+ E E+ +A +++ 
Sbjct: 7   DPVRSYLQEIGRIPLLNSEEEVQLATKVQN 36


>gi|226309754|ref|YP_002769648.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226092702|dbj|BAH41144.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 314

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 95/265 (35%), Positives = 144/265 (54%), Gaps = 8/265 (3%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + +   +  ++R        A++ +V A LR V+S A ++  RG+ FLDLIQEG IGL  
Sbjct: 49  LDKEEELACLIRYQRDGDLEARETIVRAYLRYVVSTALRHLKRGMPFLDLIQEGTIGLFT 108

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KFD   G +   Y+ WW+ QAITR+I D++  IRIPVHM ++I +  +    + + +
Sbjct: 109 AIDKFDVGRGVRLYHYSHWWISQAITRAINDKATLIRIPVHMHEQIRQYQKQVLHLVHAL 168

Query: 544 KREPTPEEIAKKLAMPVEGVRK-VLKITKEPISLETPI-------GDEDTSHLGDFIEDK 595
            R P  +EIA  L +P+E V    L +  +  S++  +         ED S     I D 
Sbjct: 169 NRTPDRQEIAVLLDIPLEKVEAIELALMMKMESIDAELDSEKWQTWHEDESLSYAEIMDD 228

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
              S  D   + +LR      L  L+PR + ++ MR+G+  +  +TLEEVGK F +TRER
Sbjct: 229 GLSSLDDWIEKVDLRSQMRAALDRLSPRAQEIISMRYGLYDDQVYTLEEVGKMFGLTRER 288

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIEA  I +L+    S  L+ +L
Sbjct: 289 IRQIEATTIDRLRTQKASHVLKDYL 313


>gi|146164080|gb|ABQ08720.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp.
           dhakensis]
 gi|284431199|gb|ADB84361.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 293

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 83/336 (24%), Positives = 141/336 (41%), Gaps = 46/336 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P                         E DDV  T   I S        
Sbjct: 61  LSDII--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLA 94

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD- 299
               D   +   + + + D+ +      ++                  E + ELR+  + 
Sbjct: 95  DEDEDEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEV 137

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
             ++ Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L
Sbjct: 138 TRLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKL 197

Query: 360 A-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
             +   + +  F+      E +  W  Y K   +      V  + + +L+   +++ I  
Sbjct: 198 CVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEE 256

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ETG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 ETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 292


>gi|123967051|ref|YP_001012132.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201417|gb|ABM73025.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 333

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 101/287 (35%), Positives = 166/287 (57%), Gaps = 7/287 (2%)

Query: 393 GEWKNFVACEVDSILKI-RNEIKSISVETGISISEFRHI-----VSMVRKGECEASIAKK 446
            E +  +  +V   +++ R E++ I +       E          S ++K       AK+
Sbjct: 41  HEQEITLGRQVQEYMQVERAELEIIELTDNKPSVEELAAKLNLSSSQIKKRLRAGQRAKE 100

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q
Sbjct: 101 RMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQ 160

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V+ +
Sbjct: 161 GITRAIAEKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTISELAKYVELPEDDVKDL 220

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           +    +P+SLET +GD + + L D +     + P +      +R     +L  L   + R
Sbjct: 221 MCKAGQPVSLETKVGDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDLHSLLHQLPDLQCR 279

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           VLRMR+G+  +   +L  +G+   ++R+R+R +E   +R L+  S +
Sbjct: 280 VLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSEN 326



 Score = 41.7 bits (96), Expect = 0.45,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           D VR YLR++G + LLS E EI + ++++    +  A L
Sbjct: 24  DLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAEL 62


>gi|168029696|ref|XP_001767361.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
 gi|56603661|dbj|BAD80742.1| plastid sigma factor PpSIG5 [Physcomitrella patens]
 gi|162681425|gb|EDQ67852.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
          Length = 632

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 116/538 (21%), Positives = 216/538 (40%), Gaps = 39/538 (7%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           +  A +     +     L     DLEA     SK       +G       +     E D 
Sbjct: 115 SLSARLEHAYRIPSLEILKS---DLEARFDSVSKEEELESDDGSIADGSVEEQSTPEADS 171

Query: 223 VQETEGDIESAAKVSKDDRSKVD----SPPENAENDERNLDEDEDDSAHTL----SAMED 274
           V+++  +  S   V+ D   +      S        +R+      +    L    +++  
Sbjct: 172 VRKSVRNGRSKVGVNTDSNVEGGVKSSSVKSPKAVKKRSSRRQNVEGNRILKITKNSVTR 231

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           Q R   +     + E   ++   Q  A +     + S++ ++        +    L  S 
Sbjct: 232 QPRKVAVRTPSHLTETGHQVAEDQQVAADRGGKRRLSLRSRIA-------MKQNKLEASV 284

Query: 335 IDLLVEQLYDISKRIMHN---EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
           ++     +   +           E   L   Y    D+           P W    +   
Sbjct: 285 VEKPGPTVDSWNMDPEDQLLWSQEAEELINKYTTSMDL---------AAPLWDKLDRGLL 335

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM------VRKGECEASIAK 445
               +N +A  +  + K+    K +  + G   ++     +       +R+       A+
Sbjct: 336 TAVEENRLAVFMKPMKKLEKLQKVLMKQLGRDPTDEEWAAAAGVDLLIMRRRLALGRAAR 395

Query: 446 KEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            ++++ NLRLV+S A KY   +  L   DL QEG IGLM+A +KFD   GY+FSTY ++W
Sbjct: 396 TKLIQRNLRLVLSQAYKYHKDSMSLSIQDLCQEGVIGLMQAVDKFDPGKGYRFSTYGIYW 455

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ +I R+       +R P ++      + R    + +++ R+PT +EI K L +  +  
Sbjct: 456 IRNSILRAQTKSGHMLRSPHNVSTHRVNIQRAKVELFSELGRQPTNDEIRKHLGITADRF 515

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R +L+      SL           + + + +++A+  L     + ++     VL SL P+
Sbjct: 516 RDILRTNMRTSSLHEHDRITGREKVENLVSEEDALDTLAGGT-SMVQYGLDDVLDSLRPK 574

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E  VLR RFG+      +L EVG    ++RE +R+ E + I KL+HP+R + LR++L+
Sbjct: 575 ENLVLRQRFGLDGKGQRSLSEVGLILNLSREMVRRYELRGILKLQHPTRVEYLRNYLN 632


>gi|282854020|ref|ZP_06263357.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|282583473|gb|EFB88853.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|314922987|gb|EFS86818.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL001PA1]
 gi|314966764|gb|EFT10863.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA2]
 gi|314981098|gb|EFT25192.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA3]
 gi|315091924|gb|EFT63900.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA4]
 gi|315093320|gb|EFT65296.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL060PA1]
 gi|315103425|gb|EFT75401.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA2]
 gi|327327589|gb|EGE69365.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL103PA1]
          Length = 312

 Score =  161 bits (408), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 155/272 (56%), Gaps = 6/272 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +++ +  R  ++  +  T  + +E  H      +   +   A    V ANLRLV+
Sbjct: 39  ALARRIEAGVFARAVLEGHAETTSDATTEELH------QIAADGDEALAHFVRANLRLVV 92

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WWV+QAI+R IA Q  
Sbjct: 93  SVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWWVRQAISRGIAQQGR 152

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V ++++  ++ +SL+
Sbjct: 153 IVRLPVHVAEQVNQVSAARRNLERQLGREPETFEIADELEITEERVIELIRFGRDHVSLD 212

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+ D+  + LGD I  + +  P D  + A  R     +L  L  R   V+R R+G+   
Sbjct: 213 APVEDDGDTSLGDLIARETSPGPDDIVLDAEDRSRLEGLLDDLDERSADVVRRRYGLVDG 272

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 273 RQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|290796538|gb|ADD64839.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 286

 Score =  161 bits (407), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 135/330 (40%), Gaps = 49/330 (14%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNSSVF 105
           N  LP D V  EQMED ++M++ MGI+V     D + L   +G+  + ++  +A+  +  
Sbjct: 1   NDHLPDDLVDPEQMEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAA 60

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
                D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ +
Sbjct: 61  ALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTE 120

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
            L+   +   +G   L EI+            GF    E         ++      D   
Sbjct: 121 MLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDA 169

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D +        +     + P+  E                           V   ++
Sbjct: 170 VDEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VATRME 202

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            +A  Y + + +        K+          +E +  +  +L L     D LV QL  +
Sbjct: 203 NLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGV 256

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
              I  +E ++L LA +   + R  F+   
Sbjct: 257 VNGIKDHERKVLHLATTVARMPRKDFIRSW 286


>gi|113954561|ref|YP_729335.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881912|gb|ABI46870.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 335

 Score =  161 bits (407), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 95/274 (34%), Positives = 159/274 (58%), Gaps = 5/274 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVI 457
           E+  +  +  E+K       ++  E         + +++       AK+ MV ANLRLV+
Sbjct: 54  ELMDLEALEAELKDQRGGEEVAREEVAKAAGVSAAQLKRKLQAGRRAKERMVAANLRLVV 113

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 114 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 173

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P E V+ ++   ++P+SLE
Sbjct: 174 TIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEEEVKDLMCRARQPVSLE 233

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L + +     + P D      L+     +L+ L   + +VLRMR+G+   
Sbjct: 234 MKVGDGDDTELLELLAGDGEL-PSDQVEGECLKGDLRDLLSQLPELQGKVLRMRYGMDGE 292

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 293 EPMSLTGIGRIIGISRDRVRNLERDGLAGLRRLS 326



 Score = 41.4 bits (95), Expect = 0.60,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 30/54 (55%)

Query: 95  LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +A +A+ +S         A  +  D VR YLR++G + LLS + EI + ++++ 
Sbjct: 1   MAPAAAVASRPASASTGRASGAEVDLVRSYLRDIGRVPLLSHQQEITLGRQVQE 54


>gi|284027885|gb|ADB66757.1| RNA polymerase sigma-70 factor [Aeromonas sp. CECT 5178]
          Length = 295

 Score =  161 bits (407), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 84/335 (25%), Positives = 135/335 (40%), Gaps = 42/335 (12%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II            GF +  E              E        G       ++ +D
Sbjct: 61  LSDII-----------SGFVNPDEA------------DEMGPTATHIGSELGEDDLADED 97

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            S  +   E+ E D  + D D             +LR +       I             
Sbjct: 98  SSDEEEEDEDEEGDGNDDDGDGGPDPEVAREKFAELRAQYEITRQSIRS----------- 146

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-L 359
                 + ++  + +    +L  +     L   + D LV  + ++ +R+   E  +L+  
Sbjct: 147 ------NGRAHEETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMC 200

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E +  W  Y K   +       A E D +L+   +++ I  E
Sbjct: 201 VEQAKMPKKTFVSAFTNNECETAWFEYQKQAGKAWSAPLAAME-DEVLRSIGKLQQIEEE 259

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           TG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 260 TGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 294


>gi|149177995|ref|ZP_01856592.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
 gi|148843188|gb|EDL57554.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
          Length = 279

 Score =  161 bits (407), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 91/259 (35%), Positives = 153/259 (59%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +K I+    +S  E R + + +         A+  MV ANLRLV+++A+ Y+ +GL
Sbjct: 17  LETYLKEINETALLSAEEERELSNRIE---HGDKEARDRMVRANLRLVVNIARAYSGKGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +G +FSTYA +W+KQ+I R++ + + TIRIP +M + 
Sbjct: 74  PLQDLIEEGNLGLLRAVEGFDPEMGTRFSTYASYWIKQSIKRALVNSAKTIRIPAYMVEL 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  R   ++ + + R PT EE+A++L +P + ++ V K  +   S       +    L
Sbjct: 134 LTKWRRATAQLQDTLDRTPTTEEVARELDLPPKKLKIVKKAIQLYNSSPQSEQHDAGWSL 193

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ I D     P D  ++ +  +   R+L  +  RE  +LRMRFG+  +   TL+E+G+ 
Sbjct: 194 GEMIPDDRLKGPDDELVENDNLKHVFRLLKEIPEREANILRMRFGLDGDEPKTLKEIGQA 253

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE++A++KL
Sbjct: 254 LGLTRERVRQIESEALKKL 272



 Score = 45.2 bits (105), Expect = 0.037,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 2/87 (2%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
           +  +  +P+  YL+E+    LLS E E  ++ RIE G       +  + L    ++    
Sbjct: 9   SSSAVQNPLETYLKEINETALLSAEEERELSNRIEHGDKEARDRMVRANLRL--VVNIAR 66

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGF 199
             +     L+++I+        +  GF
Sbjct: 67  AYSGKGLPLQDLIEEGNLGLLRAVEGF 93


>gi|23978335|dbj|BAC21137.1| principal sigma factor [Phormidium sp. IAM M-99]
          Length = 203

 Score =  161 bits (407), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 110/204 (53%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++N RLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VLA+L+PRE+ VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLEGVLATLSPREKDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+ +G+      TLEE+G+ F VT
Sbjct: 180 RLHYGLDDGRMKTLEEIGQIFNVT 203


>gi|225848787|ref|YP_002728951.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643846|gb|ACN98896.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 282

 Score =  161 bits (407), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 96/284 (33%), Positives = 164/284 (57%), Gaps = 5/284 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A +   +  ++  ++ +     ++  E R +    +K       A K++VE NLR V++
Sbjct: 1   MANQDQELTTLQLYMQQMGKYPMLTPEEERELAIRAKK---GDKEALKKLVEGNLRFVVN 57

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK +   G+   DLI  GN+GL++AA++FD     KF +YA+WW++QAI ++I  Q+  
Sbjct: 58  IAKNFMGWGVPLTDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGA 117

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +RIP+     I KV     ++   + REPT EEIAK+L   V+ V+  L I ++PISL+ 
Sbjct: 118 VRIPIKESLFISKVKNAYEKLKESLGREPTEEEIAKELKTSVKKVKNALAIVRQPISLDM 177

Query: 579 PIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           P+G+  E+   L D +  K         +++ L+E   R+L  L  RE  ++++R+G+  
Sbjct: 178 PLGEGGEEDFTLLDILSKKGTEDVEKDLVESTLKEEFERLLNVLDEREREIIKLRYGLEG 237

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
               TLEEVG+   ++RER+RQ+E +A++KLK  +  K L++FL
Sbjct: 238 LEPKTLEEVGEMLGISRERVRQLEQRALKKLKAVALKKHLQNFL 281



 Score = 44.1 bits (102), Expect = 0.092,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           +++Y+++MG   +L+ E E  +A R + G    +  L E  L F
Sbjct: 11  LQLYMQQMGKYPMLTPEEERELAIRAKKGDKEALKKLVEGNLRF 54


>gi|296314331|ref|ZP_06864272.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
 gi|296838970|gb|EFH22908.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
          Length = 281

 Score =  161 bits (407), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 139/317 (43%), Gaps = 39/317 (12%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           + + +N +   E++D    L  +      +++I + ++RGY+T  E+N  LP D   ++Q
Sbjct: 1   MSRNQNHE---EYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 57

Query: 63  MEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
           +++ V+M+S +GI V +   D ED   S+++      A   +       DS    T DPV
Sbjct: 58  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEAEAALSSADSEFGRTTDPV 117

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG ++LL+RE EI IAK+IE     M+ ++   P +   ++   +++      +
Sbjct: 118 RMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRV 177

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E++                                   + + +    + +   +   + 
Sbjct: 178 DEVV-----------------------------------EAIIDPNEVLLNELGLGHLET 202

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +  + P  +  ++  + +E E+D+    +A   +L+ KV+    +I + Y+++    +  
Sbjct: 203 TVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIGRLEKH 262

Query: 302 VNGQKDEKSSVKCKVLK 318
            +  KD  +       K
Sbjct: 263 HSRHKDYLAYRDAIANK 279


>gi|123969371|ref|YP_001010229.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199481|gb|ABM71122.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 344

 Score =  161 bits (406), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 100/271 (36%), Positives = 161/271 (59%), Gaps = 6/271 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVISVA 460
            + +I  EI  +      SI E    +++    ++K       AK+ MV ANLRLV+SVA
Sbjct: 67  EVERIELEIIEL-TGEKPSIDELSAKLNLTTSTIKKRLRAGQRAKERMVAANLRLVVSVA 125

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S  IR
Sbjct: 126 KKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIR 185

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V+ ++    +P+SLET +
Sbjct: 186 LPIHITEMLNKLKKGQRELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQPVSLETKV 245

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           GD + + L D +     + P +      +R     +L  L   + RVLRMR+G+  +   
Sbjct: 246 GDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPM 304

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 305 SLTGIGRVLGISRDRVRNLERDGLRGLRRLS 335



 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
           D VR YLR++G + LLS E EI + ++++    
Sbjct: 35  DLVRSYLRDIGRVPLLSHEQEITLGRQVQEYME 67


>gi|186687052|ref|YP_001870195.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186469355|gb|ACC85154.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 316

 Score =  161 bits (406), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 104/274 (37%), Positives = 167/274 (60%), Gaps = 8/274 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           L++  +   + + T +  +E     + ++    +   AK++MV ANLRLV+SVAKKY N 
Sbjct: 49  LQLNRQPTDLELATSLGQNE-----AELQSVIQQGQKAKQKMVTANLRLVVSVAKKYQNY 103

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            L FLDL+QEG +GL +  EKFD   GYK STY  WW+ Q+ITR++AD+S TIR+P+H+ 
Sbjct: 104 SLDFLDLLQEGALGLQRGIEKFDPNKGYKLSTYVYWWITQSITRAVADKSRTIRLPIHIN 163

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           +K++K+ R  +++S  + R P   EIA+ L +    +R+ L+I+K  +SLE  +GDE  S
Sbjct: 164 EKLNKIRRVQQQLSQSLGRPPVVAEIAESLNLSPNQIREYLQISKPLVSLEKRVGDEGES 223

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +S  +     +L++   ++LA L PR+  VL +RFG+  N   TL +V 
Sbjct: 224 ELADILP-MDGISLDEQITLESLQQDLAKLLALLKPRQREVLTLRFGLSDNQQLTLSQVA 282

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           K+  ++RE IR+ E  A+  L+  S   K++ +L
Sbjct: 283 KRLNLSRETIRKTEHLALSILR--SHQNKIKDYL 314



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             T D VR YL+E+G   LL+ + EI  A+ ++ 
Sbjct: 3   SPTTDSVRSYLKEIGRYPLLTPDQEITNARLVQQ 36


>gi|88854620|ref|ZP_01129287.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88816428|gb|EAR26283.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 1108

 Score =  161 bits (406), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 95/252 (37%), Positives = 142/252 (56%), Gaps = 1/252 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++        A      +N RLV S+A++Y N GL + DLIQEG +GL++A +KFD+ 
Sbjct: 671 RELQWVAKNGEKAFARFAASNYRLVFSIARRYVNNGLDYADLIQEGALGLLRAIQKFDYM 730

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WWV+QAITR++AD   TIRIPVHM ++ +K+ + AR    +  R+PT  E
Sbjct: 731 KGFKFSTYATWWVRQAITRALADLGSTIRIPVHMVEQQNKLRQAARSFELQNDRKPTISE 790

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A    +  +   + L      +S++  +   +       +    +V+P+D  I A  R 
Sbjct: 791 LAAGAEVTEQDASRALGYEYSFLSIDKELDPGEGFGSLHNLLVDESVAPVDLLIHAEFRG 850

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               VL++L  RE   ++MRFGIG     TL+ +G  F VTRERIRQIE K +  L+  +
Sbjct: 851 AMNNVLSALPKRESTTIQMRFGIGGQDPATLDHIGDIFGVTRERIRQIEKKTMESLRSSA 910

Query: 672 RSK-KLRSFLDG 682
             + +L  FLD 
Sbjct: 911 EVQGRLGDFLDA 922


>gi|23978369|dbj|BAC21149.1| principal sigma factor [Pseudanabaena sp. PCC 7403]
          Length = 203

 Score =  161 bits (406), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 111/204 (54%), Positives = 151/204 (74%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-SDGETPDDQVAKSLLREDLESVLGTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|206563110|ref|YP_002233873.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
 gi|198039150|emb|CAR55114.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 508

 Score =  161 bits (406), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 104/241 (43%), Positives = 158/241 (65%), Gaps = 1/241 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA 
Sbjct: 269 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYAT 328

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +  +
Sbjct: 329 WWIRQAIARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLAED 388

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL +  EP+SL+TP+ D DT  L + IED+ + SP +      +R+    +L S+T
Sbjct: 389 KLRAVLALPAEPVSLDTPLPDADTG-LVELIEDQASASPFEQLADTRMRDCVRSLLRSVT 447

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           P E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  +SFLD
Sbjct: 448 PTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENAQSFLD 507

Query: 682 G 682
            
Sbjct: 508 A 508



 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 39/151 (25%), Positives = 76/151 (50%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +   D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TPRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             +         +++   A +    +         ++ DP+ +Y+R M ++ LL+REGEI
Sbjct: 67  PAVPAPFAGAAPVEVDRDALDEGRAMLGDLARGTSASTDPLALYMRRMHAVPLLTREGEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ ++   P    AL+   
Sbjct: 127 VLAREIETGRHQVLHAIAGYPPAVDALLERH 157


>gi|33866043|ref|NP_897602.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639018|emb|CAE08024.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 308

 Score =  161 bits (406), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 89/258 (34%), Positives = 141/258 (54%), Gaps = 14/258 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + ++            AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A
Sbjct: 54  DEEKAVIRR-------GERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRA 106

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EK+D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +  
Sbjct: 107 VEKYDPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNG 166

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPL 601
             PT E++A  + +P+  V  +L        +SL+  +    D S L D +         
Sbjct: 167 LTPTAEQLADFMEIPIAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPSDELPPME 226

Query: 602 DSAIQANLRETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQ 658
            + I A    +   +L  A+LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ
Sbjct: 227 RAEI-AERSASVWTLLGKANLTPKERTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQ 285

Query: 659 IEAKAIRKLKHPSRSKKL 676
           +  +A+RKL+       L
Sbjct: 286 VVQRALRKLRKTGIQSGL 303


>gi|313792143|gb|EFS40244.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA1]
 gi|313801904|gb|EFS43138.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA2]
 gi|313838730|gb|EFS76444.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL086PA1]
 gi|314962802|gb|EFT06902.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA1]
 gi|315078018|gb|EFT50069.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA2]
 gi|327453138|gb|EGE99792.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL092PA1]
          Length = 312

 Score =  161 bits (406), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 141/238 (59%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   +   A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+ 
Sbjct: 67  KELHQIAADGDEALARFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYA 126

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WWV+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   E
Sbjct: 127 KGFKFSTYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFE 186

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L +  E V ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRS 246

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +L  L  R   V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 247 RLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|296134902|ref|YP_003642144.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
 gi|295795024|gb|ADG29814.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
          Length = 351

 Score =  161 bits (406), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 82/265 (30%), Positives = 143/265 (53%), Gaps = 5/265 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  +++ +  I  +   +  +     +  +        A++ MVE NLRLV+S+AK Y  
Sbjct: 76  VSALQSYLNHIRAKPLFTPEQEFETATRAK---AGDFEARQAMVEHNLRLVVSIAKAYVG 132

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DLI+EGN+GL+ A EKF+   G++FSTYA WW++Q+I R++  Q  TIR+PVH+
Sbjct: 133 RGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWWIRQSIERALMQQVRTIRLPVHV 192

Query: 526 RDKIHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
             ++++V+R  + +      + + + E++A  L    E V  +L + ++P SL+     +
Sbjct: 193 IRELNQVLRARKHLEQAADYRGQTSDEDVAALLGRSTEEVADLLALAEQPTSLDALRETQ 252

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
                 D   D+NA+S  +      +       +  L  RE  V+  RFG+      TLE
Sbjct: 253 SGESYADQFADQNALSMEEQTQTREVEALVDSWVGELAEREREVIEARFGLHGRELETLE 312

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
            + ++  +TRER+RQI+ +++ KLK
Sbjct: 313 SLAQRLGLTRERVRQIQQESLLKLK 337



 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 28/87 (32%), Gaps = 9/87 (10%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL  + +  L + E E   A R +AG      ++ E  L     I     +  G  L   
Sbjct: 82  YLNHIRAKPLFTPEQEFETATRAKAGDFEARQAMVEHNLRLVVSIAKAY-VGRGAALGDL 140

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQK 210
           I         E   G  H  E    ++
Sbjct: 141 I--------EEGNLGLIHAIEKFEPER 159


>gi|86608620|ref|YP_477382.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557162|gb|ABD02119.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 319

 Score =  160 bits (405), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 99/249 (39%), Positives = 147/249 (59%), Gaps = 10/249 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S   GI ++E + I+            AKK MVE NLRLV+S+AK+Y NRGL FLD
Sbjct: 52  VEGWSQRLGIPLAELQQILRQ-------GEAAKKRMVECNLRLVVSIAKRYRNRGLPFLD 104

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG IGL +A EKFD   GYKFSTYA WW++Q++ R I ++   IR+P HM +K+ +V
Sbjct: 105 LIQEGTIGLTRAVEKFDPTRGYKFSTYATWWIRQSVNRGIQNKGRMIRLPAHMYEKVSQV 164

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDF 591
            R  R +S +    P  EE+   L +  +  R+++      + SL   +GDED + L  F
Sbjct: 165 KRRYRELSAERGSRPQAEEVFDSLDIG-DNYRELITRHMAEMRSLNVGVGDEDGTELQHF 223

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D++   P++   Q   RE    ++  L+ RE +V+  R+G+  +   TL E+G+   +
Sbjct: 224 IPDED-NDPVEHLTQLARREEVRALVGQLSERERQVIVARYGLDGSRGLTLREIGEHIGL 282

Query: 652 TRERIRQIE 660
           +RER+RQIE
Sbjct: 283 SRERVRQIE 291


>gi|78211648|ref|YP_380427.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196107|gb|ABB33872.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 335

 Score =  160 bits (405), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 93/255 (36%), Positives = 155/255 (60%), Gaps = 8/255 (3%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++  +G+S  + +  +            AK+ MV ANLRLV+SVAKKYT R ++ LDLI
Sbjct: 78  QLAKASGLSSIQLKRKLQ-------HGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLI 130

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +
Sbjct: 131 QEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKK 190

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             R +S ++ R PT  E+A+ + +P + V+ ++   ++P+SLE  +GD D + L + +  
Sbjct: 191 GQRELSQELGRTPTVTELAEFVELPEDDVKDLMCRARQPVSLEMKVGDGDDTELLELLSG 250

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
              + P D   +  L+     +L  L   +E+VLRMR+G+      +L  +G+   ++R+
Sbjct: 251 DGDL-PSDQVEEDCLKGDLRSLLGQLPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRD 309

Query: 655 RIRQIEAKAIRKLKH 669
           R+R +E   +  L+ 
Sbjct: 310 RVRNLERDGLAGLRR 324



 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 26  DLVRSYLRDIGRVPLLTHEQEITLGRQVQE 55


>gi|307565781|ref|ZP_07628247.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
 gi|307345508|gb|EFN90879.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
          Length = 290

 Score =  160 bits (405), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 152/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  E  I++ E   +   + KG  +   AK+++++ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGREPMITVDEEIELAQEIHKGGLKGERAKEKLIKANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQV 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K+ +       K  R P+  E+A+   +    +R+        +S++ P  D+D +
Sbjct: 136 GAISKINQVTNEFIQKHNRRPSIHELAEITGIDEARIRQSQSADNHHMSIDAPFSDDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               ++ +    VL  +L  RE +++   FGIG   +  LEE+
Sbjct: 196 SMSDMLSSGEDSRTDKGVDFESMSDDLRAVLQNTLKEREIKIVTECFGIGC-QEKGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  KAI K++    ++ L  +L
Sbjct: 255 GTEMALTRERVRQIREKAIEKIRESGNARVLMKYL 289



 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   +++ + EI +A+ I  G          L ++ L F  ++    +       
Sbjct: 21  YLVEIGREPMITVDEEIELAQEIHKGGLKGERAKEKLIKANLRF--VVSVAKQYQHQGLS 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|116071698|ref|ZP_01468966.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065321|gb|EAU71079.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 332

 Score =  160 bits (405), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 93/237 (39%), Positives = 151/237 (63%), Gaps = 1/237 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +++   +   AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   
Sbjct: 86  QLKRKLQQGHRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTR 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+
Sbjct: 146 GYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTEL 205

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + +P + V+ ++   ++P+SLE  +GD D + L + +   N + P D   +  L+  
Sbjct: 206 AQFVDLPEDEVKDLMCRARQPVSLEMKVGDGDDTELLELLSGDNEL-PSDQVEEDCLKGD 264

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +L  L   +E+VLRMRFG+      +L  +G+   ++R+R+R +E   +  L+ 
Sbjct: 265 LRSLLGQLPHLQEQVLRMRFGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRR 321



 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 23  DLVRSYLRDIGRVPLLTHEQEITLGRQVQQ 52


>gi|33864638|ref|NP_896197.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33632161|emb|CAE06617.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 332

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 92/239 (38%), Positives = 151/239 (63%), Gaps = 1/239 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +++       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   
Sbjct: 86  QLKRKLQHGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTR 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+
Sbjct: 146 GYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTITEL 205

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + +P + V+ ++   ++P+SLE  +GD D + L + +   +A  P D   +  ++  
Sbjct: 206 AQYVELPEDDVKDLMCRARQPVSLEMKVGDGDDTELLELLA-GDADLPSDQVEEDCMKGD 264

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +L  L   +E+VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 265 LRSLLGQLPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRRIS 323



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 23  DLVRSYLRDIGRVPLLTHEQEITLGRQVQD 52


>gi|78183723|ref|YP_376157.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78168017|gb|ABB25114.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 332

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 93/237 (39%), Positives = 151/237 (63%), Gaps = 1/237 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +++   +   AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   
Sbjct: 86  QLKRKLQQGHRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTR 145

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+
Sbjct: 146 GYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTEL 205

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + +P + V+ ++   ++P+SLE  +GD D + L + +   N + P D   +  L+  
Sbjct: 206 AQFVDLPEDEVKDLMCRARQPVSLEMKVGDGDDTELLELLSGDNEL-PSDQVEEDCLKGD 264

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +L  L   +E+VLRMRFG+      +L  +G+   ++R+R+R +E   +  L+ 
Sbjct: 265 LRSLLGQLPHLQEQVLRMRFGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRR 321



 Score = 41.0 bits (94), Expect = 0.75,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 23  DLVRSYLRDIGRVPLLTHEQEITLGRQVQQ 52


>gi|307150096|ref|YP_003885480.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306980324|gb|ADN12205.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 298

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 89/253 (35%), Positives = 162/253 (64%), Gaps = 4/253 (1%)

Query: 422 ISISEFRH--IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           +S+ E +   + +  +K   +   AK++M++ANLRLV+S+AK+Y  RGL  LDLIQEG++
Sbjct: 38  LSLLELKKDNLAAAEQKIIEQGQRAKQQMIQANLRLVVSIAKRYQRRGLSLLDLIQEGSL 97

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++A EKFD   GYKFSTYA WWV+QAITR++A++S TIR+P+HM + ++ + ++ R +
Sbjct: 98  GLIRAVEKFDPSKGYKFSTYAYWWVRQAITRALAEKSRTIRLPIHMTENLNHLKKSVREL 157

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAV 598
           + ++ R+PT +E+A+++ +P+E ++++        +    I  +D  + LG+ + D+ ++
Sbjct: 158 TGELGRKPTEQEVAQRMEIPLEKLQEIRHAVYRTDAKSLNITLDDNQTELGEVLPDETSL 217

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                + +  L      +L  L PR+  ++ +RFG+      + +E+G+Q  ++ ER RQ
Sbjct: 218 PIDFVSERE-LMTKVDDLLEDLPPRQREIITLRFGLLTGKRMSYKEIGRQCGISHERARQ 276

Query: 659 IEAKAIRKLKHPS 671
           +  +A+R LK  +
Sbjct: 277 LLNRAMRTLKQKA 289



 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 15/30 (50%), Positives = 22/30 (73%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           DPVR YL+E+G I LL+ E EI +A +++ 
Sbjct: 7   DPVRSYLQEIGRIPLLNSEEEIQLATKVQK 36


>gi|198283622|ref|YP_002219943.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667581|ref|YP_002426250.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248143|gb|ACH83736.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519794|gb|ACK80380.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 316

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 85/274 (31%), Positives = 146/274 (53%), Gaps = 4/274 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A   D    I+  ++ I     ++  E    VS+    +     A+  +VE NLRLV+ +
Sbjct: 44  AGASDHFDAIKLYLQEIGHNPLLTAEEE---VSLGLSAQQGDITARNRLVECNLRLVVRI 100

Query: 460 AKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           A++Y  +  L  LDLI+EGN+GL++AAE FD   G++FSTYA WW++Q I R I  QS  
Sbjct: 101 ARRYQRQHTLPLLDLIEEGNLGLIRAAELFDPTRGFRFSTYATWWIRQNIDRGIMQQSRV 160

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           +R+P H+   +  V+R++R+++  ++ +P  E++A+ +   V  V   L+  +  +SL+ 
Sbjct: 161 VRLPTHIIKNLSAVLRSSRQIAQTMQGDPRVEDVAQVMGKSVAYVEDCLQQDRRVVSLDA 220

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P   E +  L   + D +      S  + +L+    R L  L  R   +L  RFGI    
Sbjct: 221 PSRWEGSPSLAQTLVDADQADLGASLEEQDLQRQIHRALLGLDVRHRTILIRRFGIDGQD 280

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +L  +GK+  V+ ER+RQ++ +A+  L+  + 
Sbjct: 281 GASLSAIGKELGVSHERVRQLQEEALDLLRQHTE 314



 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/130 (20%), Positives = 46/130 (35%), Gaps = 4/130 (3%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--DPVRMYLREMGSIELLSR 136
           D  D  +E       +                     ++D  D +++YL+E+G   LL+ 
Sbjct: 9   DVPDALEEIAEVGQDEACLWPETPEFDAIADPAWEAGASDHFDAIKLYLQEIGHNPLLTA 68

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E E+++    + G       L E  L     I  R +    T  L ++I+ E  +G    
Sbjct: 69  EEEVSLGLSAQQGDITARNRLVECNLRLVVRIARRYQRQH-TLPLLDLIE-EGNLGLIRA 126

Query: 197 GGFFHGTEGH 206
              F  T G 
Sbjct: 127 AELFDPTRGF 136


>gi|294674467|ref|YP_003575083.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294473044|gb|ADE82433.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 153/275 (55%), Gaps = 2/275 (0%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I  +  ++I E   +   +R+G  E   AK+ +V ANLR V+SVAK+Y ++
Sbjct: 16  EALDKYLVEIGRQPLVTIDEEIELAQAIRRGGPEGEKAKERLVTANLRFVVSVAKQYQHQ 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGNIGL+KAAEKFD   G+KF +YA+WW++Q+I ++IA+QS  +R+P++  
Sbjct: 76  GLTLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQS 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             + K+ +   +   + +R P+  E+A+   +    + +  K     +S++ P G++D +
Sbjct: 136 GALSKINQEINKFEQQHQRRPSVTELAELTQIEESKIEQTAKADSHHMSIDAPFGEDDDN 195

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            + D +               +L      VL + L  RE ++++  FGIG   +  LEE+
Sbjct: 196 SMADMLSSGEDTRTDKLVDYESLTSDLDNVLRNVLKDRELKIVKECFGIGC-QERGLEEI 254

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G +  +TRER+RQI  K+I KL     ++ L  +L
Sbjct: 255 GAEMGLTRERVRQIREKSITKLHDSGYARILMKYL 289



 Score = 37.5 bits (85), Expect = 7.9,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL E+G   L++ + EI +A+ I  G          L  + L F  ++    +       
Sbjct: 21  YLVEIGRQPLVTIDEEIELAQAIRRGGPEGEKAKERLVTANLRF--VVSVAKQYQHQGLT 78

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 79  LTDLID-EGNIGLVKAAEKFDETRGFK 104


>gi|50842514|ref|YP_055741.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289425060|ref|ZP_06426837.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289427240|ref|ZP_06428956.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|295130591|ref|YP_003581254.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|50840116|gb|AAT82783.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289154038|gb|EFD02726.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289159709|gb|EFD07897.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|291376720|gb|ADE00575.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|313764457|gb|EFS35821.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA1]
 gi|313772161|gb|EFS38127.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL074PA1]
 gi|313807516|gb|EFS46003.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA2]
 gi|313810025|gb|EFS47746.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA1]
 gi|313815996|gb|EFS53710.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA1]
 gi|313818558|gb|EFS56272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA2]
 gi|313820325|gb|EFS58039.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA1]
 gi|313822868|gb|EFS60582.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA2]
 gi|313825200|gb|EFS62914.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA1]
 gi|313827776|gb|EFS65490.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA2]
 gi|313830353|gb|EFS68067.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL007PA1]
 gi|313833726|gb|EFS71440.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL056PA1]
 gi|314915450|gb|EFS79281.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA4]
 gi|314918267|gb|EFS82098.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA1]
 gi|314920080|gb|EFS83911.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA3]
 gi|314925213|gb|EFS89044.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA3]
 gi|314931602|gb|EFS95433.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL067PA1]
 gi|314955755|gb|EFT00155.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA1]
 gi|314958169|gb|EFT02272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA1]
 gi|314960004|gb|EFT04106.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA2]
 gi|314967831|gb|EFT11930.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA1]
 gi|314973357|gb|EFT17453.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA1]
 gi|314976035|gb|EFT20130.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL045PA1]
 gi|314978426|gb|EFT22520.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA2]
 gi|314983943|gb|EFT28035.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA1]
 gi|314988127|gb|EFT32218.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA2]
 gi|314989932|gb|EFT34023.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA3]
 gi|315080642|gb|EFT52618.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL078PA1]
 gi|315084315|gb|EFT56291.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA2]
 gi|315085658|gb|EFT57634.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA3]
 gi|315088920|gb|EFT60896.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA1]
 gi|315095902|gb|EFT67878.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL038PA1]
 gi|315098533|gb|EFT70509.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA2]
 gi|315101109|gb|EFT73085.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA1]
 gi|315105655|gb|EFT77631.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA1]
 gi|315108329|gb|EFT80305.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA2]
 gi|327326184|gb|EGE67974.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA2]
 gi|327331941|gb|EGE73678.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA3]
 gi|327443142|gb|EGE89796.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA2]
 gi|327445926|gb|EGE92580.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA2]
 gi|327448094|gb|EGE94748.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA1]
 gi|327450785|gb|EGE97439.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA3]
 gi|327453871|gb|EGF00526.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA2]
 gi|328753473|gb|EGF67089.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL020PA1]
 gi|328754203|gb|EGF67819.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA1]
 gi|328754545|gb|EGF68161.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA2]
 gi|328760855|gb|EGF74421.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL099PA1]
 gi|332675431|gb|AEE72247.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           266]
          Length = 312

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 141/238 (59%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   +   A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+ 
Sbjct: 67  KELHQIAADGDEALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYA 126

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WWV+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   E
Sbjct: 127 KGFKFSTYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFE 186

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L +  E V ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRS 246

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +L  L  R   V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 247 RLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|302746276|gb|ADL62728.1| RpoD [Morganella morganii subsp. morganii]
          Length = 274

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 118/315 (37%), Gaps = 47/315 (14%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L ++I     + P +        E        +   E   +++ + + D +   +   D 
Sbjct: 61  LSDLIT--GFVDPNA--------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDS 110

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  PE A      L    + +                                Q  
Sbjct: 111 DDDNSIDPELARQKFEALRVQHEKAR-------------------------------QQI 139

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            ++G+    ++ + + L E    +     L   + D LV  + ++  R+   E  +++L 
Sbjct: 140 KIHGRDHPNTNAEIQQLSE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLC 195

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+    G E    W + A    +  W   +    + + +    ++ I  E
Sbjct: 196 VEQSKMPKKNFITLFTGNETSDSWFTAAVAMNKP-WSEKLQDVAEEVERSLQRLRQIEEE 254

Query: 420 TGISISEFRHIVSMV 434
           TG++I + + I   +
Sbjct: 255 TGLTIEQVKDINRRM 269


>gi|188997117|ref|YP_001931368.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932184|gb|ACD66814.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 281

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 98/282 (34%), Positives = 162/282 (57%), Gaps = 5/282 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E D +  ++  ++ +     +S  E + +    ++       A K++VE NLR V+S+A
Sbjct: 2   AEQDELTTLQLYMQQMGKHPMLSPEEEKELAIRAKQ---GDKEALKKLVEGNLRFVVSIA 58

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           K +   G+   DLI  GN+GL++AA++FD     KF +YA+WW++QAI ++I  Q+  +R
Sbjct: 59  KNFMGWGVPLTDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGAVR 118

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IPV     I KV  T  ++  ++ REPT EEIAK+L   V+ V+  L I + PISL+ P+
Sbjct: 119 IPVKESLFIAKVKETYEKLKEELGREPTEEEIAKRLNTSVKKVKNALSIVRLPISLDMPL 178

Query: 581 GD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           G+  E+   L D +  K         I+  + +    +L  L  RE+ +++MR+G+    
Sbjct: 179 GEGGEEDFTLLDVLSKKGTEDIEKELIEETIHKELESMLDVLDEREKEIIKMRYGLDGEE 238

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             TLEEVG++  ++RER+RQ+E +A++KLK  +  K L+ FL
Sbjct: 239 PKTLEEVGEKLGISRERVRQLEQRALKKLKAVALKKHLKDFL 280



 Score = 43.7 bits (101), Expect = 0.096,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           +++Y+++MG   +LS E E  +A R + G    +  L E  L F   I 
Sbjct: 10  LQLYMQQMGKHPMLSPEEEKELAIRAKQGDKEALKKLVEGNLRFVVSIA 58


>gi|332526107|ref|ZP_08402245.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
 gi|332109950|gb|EGJ10578.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
          Length = 320

 Score =  160 bits (405), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 97/279 (34%), Positives = 155/279 (55%), Gaps = 7/279 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E +    +++ ++ I     +S  E        R        A++ M+E NLRLV+S+AK
Sbjct: 39  EAEHGNTLQSYLRDIRRAPLMSAEEEHATAVRAR---AGDFAARQTMIERNLRLVVSIAK 95

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y  RG+  +DLI+EGN+GLM A  KF+   G++FSTYA WW++Q+I R+I  Q+  IR+
Sbjct: 96  HYVGRGMPMIDLIEEGNLGLMHATGKFEPERGFRFSTYASWWIRQSIERAIMHQARLIRL 155

Query: 522 PVHMRDKIHKVVRTARRMSNKIKRE----PTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           PVH+  ++++V++  R + +    E     + +E+A  L  PV+ V ++LK+ ++P SL+
Sbjct: 156 PVHVVRELNQVLKARRALESSRHGEAERPVSVDEVAAALGRPVDEVAELLKLAEQPTSLD 215

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+  E    + D + D +AV PL   +           LA L  RE  VL  RFG+   
Sbjct: 216 MPLEREGGESMLDTVADDDAVDPLGLTLSREAVHLLDHGLAELNEREREVLAGRFGLHDR 275

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              TLEE+  +  +TRERIRQI+ +A+ KLK     + +
Sbjct: 276 EPETLEELAVRLGLTRERIRQIQQEALLKLKRRMMRRGV 314



 Score = 39.1 bits (89), Expect = 2.7,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 44/131 (33%), Gaps = 3/131 (2%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V   D  +      D+ +  ++     +         +    + ++ YLR++    L+S
Sbjct: 1   MVTRRDAHDGPAEGSDTFEPGAAPEAPELAASPPPADGEAEHGNTLQSYLRDIRRAPLMS 60

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            E E A A R  AG      ++ E  L     I     +  G  ++  I   E  +G   
Sbjct: 61  AEEEHATAVRARAGDFAARQTMIERNLRLVVSIAKHY-VGRGMPMIDLI--EEGNLGLMH 117

Query: 196 KGGFFHGTEGH 206
             G F    G 
Sbjct: 118 ATGKFEPERGF 128


>gi|297626467|ref|YP_003688230.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922232|emb|CBL56802.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 309

 Score =  160 bits (405), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 93/285 (32%), Positives = 154/285 (54%), Gaps = 25/285 (8%)

Query: 412 EIKSISVETGISISEFRHIVSMVR-------------------------KGECEASIAKK 446
            ++SI+    ++ +E   +  ++                              E   A +
Sbjct: 22  YLESIAKTPLLTAAEEVELARLIEVGQYAQAVLRGEVKTKTKATEEELLGIAEEGERAMQ 81

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
             V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WWV+Q
Sbjct: 82  HFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWWVRQ 141

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           AI+R IA Q   +R+PVH+ ++++++    R +  ++ REP   EIA +L +    V  +
Sbjct: 142 AISRGIAQQGRIVRLPVHVAEQVNQISAVRRNLERQLGREPEVSEIANELGLEENKVIDL 201

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           ++ ++E +SL+ P+ D+  + LGD I  + A  P +  +    R     +LA+L  R   
Sbjct: 202 IRYSREHVSLDAPVEDDGDTSLGDLIARETAPGPDELVLDLEDRSRLEALLANLDDRSAD 261

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           V+R R+G+       L ++GK + +T ER+RQIE  A+ +L+  +
Sbjct: 262 VMRRRYGLLDGHQAKLSDIGKVWGITAERVRQIERAALNQLRTSA 306



 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 11/32 (34%), Positives = 18/32 (56%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150
           D V +YL  +    LL+   E+ +A+ IE G+
Sbjct: 17  DSVGLYLESIAKTPLLTAAEEVELARLIEVGQ 48


>gi|254526733|ref|ZP_05138785.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538157|gb|EEE40610.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 333

 Score =  160 bits (405), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 100/278 (35%), Positives = 165/278 (59%), Gaps = 6/278 (2%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           E+      E++ I    ++     + T +++S      S+++K       AK+ MV ANL
Sbjct: 53  EYMEVERAELELIELAGDKPSIDELSTKLNLST-----SIIKKRLRAGQRAKERMVAANL 107

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA
Sbjct: 108 RLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQGITRAIA 167

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           ++S  IR+P+H+ + ++K+ +  R +S ++ R PT  E+AK + +P + V+ ++    +P
Sbjct: 168 EKSRAIRLPIHITEMLNKLKKGQRELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQP 227

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SLET +GD + + L D +     + P +      +R     +L  L   + RVLRMR+G
Sbjct: 228 VSLETKVGDGEDTVLLDLLAGGEDL-PDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYG 286

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +  +   +L  +G+   ++R+R+R +E   +R L+  S
Sbjct: 287 MDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLS 324



 Score = 41.7 bits (96), Expect = 0.37,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
           D VR YLR++G + LLS E EI + ++++    +  A L
Sbjct: 24  DLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMEVERAEL 62


>gi|313812945|gb|EFS50659.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA1]
          Length = 312

 Score =  160 bits (404), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 141/238 (59%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   +   A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+ 
Sbjct: 67  KELHQIAADGDEALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYA 126

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WWV+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   E
Sbjct: 127 KGFKFSTYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGREPETFE 186

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L +  E V ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRS 246

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +L  L  R   V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 247 RLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|327330254|gb|EGE72003.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL097PA1]
          Length = 312

 Score =  160 bits (404), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 141/238 (59%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   +   A    V ANLRLV+SVA+KY    +  LDL+QEGN GL++A EKFD+ 
Sbjct: 67  KELHQIAADGDEALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYA 126

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WWV+QAI+R IA Q   +R+PVH+ +++++V    R +  ++ REP   E
Sbjct: 127 KGFKFSTYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRSLERQLGREPETFE 186

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA +L +  E V ++++  ++ +SL+ P+ D+  + LGD I  + +  P D  + A  R 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPVEDDGDTSLGDLIARETSPGPDDIVLDAEDRS 246

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +L  L  R   V+R R+G+       L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 247 RLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALASMRQ 304


>gi|300871837|ref|YP_003786710.1| RNA polymerase sigma factor RpoD [Brachyspira pilosicoli 95/1000]
 gi|300689538|gb|ADK32209.1| RNA polymerase sigma factor, RpoD [Brachyspira pilosicoli 95/1000]
          Length = 314

 Score =  160 bits (404), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 103/305 (33%), Positives = 182/305 (59%), Gaps = 12/305 (3%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRN--EIKSISVETGISI----------SEFRHIVSMVR 435
           K     E+K  V+  +  I +IR   + + + +   + +           +       + 
Sbjct: 8   KKDINEEYKGPVSVYLKQIGEIRRLTKEEELELWQRLEVCRENKNKLIDEDEEKYSKEIE 67

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           + + E    + ++V++NLRLVIS+AK+Y N G+ F+D+I EGNIGL++A ++F++  G+K
Sbjct: 68  EIDKEIDSIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYRKGFK 127

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTY +WW+KQ+I + I+ +   IR P+H+   I K ++ ++ ++ ++ REP+ +EIAK+
Sbjct: 128 FSTYGVWWIKQSIVKEISSKRHIIRFPMHIARLIKKSIQISKNLTQQLGREPSIDEIAKE 187

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +  + +  ++  T+E  S+++   + D + +  FIEDKN  SP   A   +LR+T T 
Sbjct: 188 MKIDRKTLSSIIVFTQETASVDSFFKNSDNNDMTSFIEDKNFPSPHQDAFMESLRDTLTE 247

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L +L  +E  V+  RFG+      TLE+ GK+  +TRER+RQI+ KA++KL   + SK+
Sbjct: 248 ALKALDEKERTVIIERFGLYGKEPKTLEDTGKELNITRERVRQIQIKALKKLSGLNLSKE 307

Query: 676 LRSFL 680
           L+SFL
Sbjct: 308 LKSFL 312


>gi|107026582|ref|YP_624093.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116692228|ref|YP_837761.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|105895956|gb|ABF79120.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116650228|gb|ABK10868.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
          Length = 514

 Score =  160 bits (404), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 104/241 (43%), Positives = 158/241 (65%), Gaps = 1/241 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA 
Sbjct: 275 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYAT 334

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +  +
Sbjct: 335 WWIRQAIARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLAED 394

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL +  EP+SL+TP+ D DT  L + IED+ + SP +      +R+    +L S+T
Sbjct: 395 KLRAVLALPAEPVSLDTPLPDADTG-LVELIEDQASASPFEQLADTRMRDCVRSLLRSVT 453

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           P E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  +SFLD
Sbjct: 454 PTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENAQSFLD 513

Query: 682 G 682
            
Sbjct: 514 A 514



 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 77/151 (50%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +   D   D   +++ LA ++GY+T  +L   LPP+  SS+ ++   A L+++GI V+D 
Sbjct: 7   TPRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSSDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             +         +++   A +    +         ++ DP+ +Y+R M ++ LL+REGEI
Sbjct: 67  PAVPAPFAGAAPVEVDRDALDEGRAMLGDLARGTSASTDPLALYMRRMHAVPLLTREGEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ ++   P    AL+   
Sbjct: 127 VLAREIETGRHQVLHAIAGYPPAVDALLERH 157


>gi|294338839|emb|CAZ87173.1| RNA polymerase sigma factor rpoS [Thiomonas sp. 3As]
          Length = 351

 Score =  160 bits (404), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 82/265 (30%), Positives = 142/265 (53%), Gaps = 5/265 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  ++  +  I  +   +  +     +  +        A++ MVE NLRLV+S+AK Y  
Sbjct: 76  VSALQAYLNHIRAKPLFTPEQEFETATRAK---AGDFEARQAMVEHNLRLVVSIAKAYVG 132

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DLI+EGN+GL+ A EKF+   G++FSTYA WW++Q+I R++  Q  TIR+PVH+
Sbjct: 133 RGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWWIRQSIERALMQQVRTIRLPVHV 192

Query: 526 RDKIHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
             ++++V+R  + +      + + + E++A  L    E V  +L + ++P SL+     +
Sbjct: 193 IRELNQVLRARKHLEQAADYRGQTSDEDVAALLGRSTEEVTDLLALAEQPTSLDALRETQ 252

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
                 D   D+NA+S  +      +       +  L  RE  V+  RFG+      TLE
Sbjct: 253 SGESYADQFADQNALSMEEQTQTREVEALVDSWVGELAEREREVIEARFGLHGRELETLE 312

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
            + ++  +TRER+RQI+ +++ KLK
Sbjct: 313 SLAQRLGLTRERVRQIQQESLLKLK 337



 Score = 37.5 bits (85), Expect = 6.9,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 30/90 (33%), Gaps = 9/90 (10%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++ YL  + +  L + E E   A R +AG      ++ E  L     I     +  G  L
Sbjct: 79  LQAYLNHIRAKPLFTPEQEFETATRAKAGDFEARQAMVEHNLRLVVSIAKAY-VGRGAAL 137

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQK 210
              I         E   G  H  E    ++
Sbjct: 138 GDLI--------EEGNLGLIHAIEKFEPER 159


>gi|23978337|dbj|BAC21138.1| principal sigma factor [Pseudanabaena sp. PCC 7367]
          Length = 203

 Score =  160 bits (404), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 110/204 (53%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-SDGETPDDQVAKNLLREDLENVLGTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           ++R+G+      TLEE+G+ F VT
Sbjct: 180 KLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|87123242|ref|ZP_01079093.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86168962|gb|EAQ70218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 309

 Score =  160 bits (403), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 95/274 (34%), Positives = 158/274 (57%), Gaps = 5/274 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVI 457
           E+  +  +  E++       +  +E      +    +++       AK+ MV ANLRLV+
Sbjct: 28  ELMELEALEAELRDQRGGEAVPAAELATAAGLSALQLKRKLQAGRRAKERMVAANLRLVV 87

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 88  SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 147

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V+ ++   ++P+SLE
Sbjct: 148 TIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAGFVELPEEEVKDLMCRARQPVSLE 207

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L + +     + P +      L+     +L  L   + RVLRMR+G+   
Sbjct: 208 MKVGDGDDTELLELLAGDGEL-PEEQVEVECLKGDLRDLLEQLPDLQRRVLRMRYGMDGE 266

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 267 EPMSLTGIGRVIGISRDRVRNLERDGLAGLRRLS 300


>gi|194476921|ref|YP_002049100.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
 gi|171191928|gb|ACB42890.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
          Length = 321

 Score =  160 bits (403), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 100/295 (33%), Positives = 174/295 (58%), Gaps = 9/295 (3%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM------VRKGECEASIAKK 446
            E +  +  +V  ++ I+   + + ++ GI  ++     S+      V++       AK+
Sbjct: 30  HEQEITLGRQVQELICIQETEQKLELKNGIKPTQEELANSLDLSINQVKRKIIHGKRAKE 89

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +MV +NLRLV+S+AKKYT R ++ LDL+QEG IGL++  EKFD   GYKFSTYA WW++Q
Sbjct: 90  QMVSSNLRLVVSIAKKYTKRSMELLDLVQEGTIGLIRGVEKFDPTRGYKFSTYAYWWIRQ 149

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+I++QS TIR+P+H+ ++++K+ +  R +S  + R PT  E+AK + +  + V+++
Sbjct: 150 GITRAISEQSRTIRLPIHITEELNKLKKAQRDLSQSLGRTPTVIELAKMIKLTEKEVKEL 209

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L   K+P+SLE  IGD D + L + +  +  +       +  LR     ++  L   + R
Sbjct: 210 LCHAKQPVSLEMKIGDGDDTVLLELLPSEIELPEEYVN-RKCLRRDLLALVEQLPEIQVR 268

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +L+MR+G       TL  +G+   ++R+R+R +E   I +L+  S+S  +  +LD
Sbjct: 269 ILKMRYGFDSTEPLTLTGIGRVLGMSRDRVRNLERDGINRLQKLSKS--IEGYLD 321



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 23/41 (56%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           +  +    S  D VR YL+E+  I LL+ E EI + ++++ 
Sbjct: 2   QTPNDQTSSDADLVRSYLKEISRIPLLTHEQEITLGRQVQE 42


>gi|89901840|ref|YP_524311.1| sigma 28 [Rhodoferax ferrireducens T118]
 gi|89346577|gb|ABD70780.1| sigma 28 [Rhodoferax ferrireducens T118]
          Length = 726

 Score =  160 bits (403), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 112/259 (43%), Positives = 153/259 (59%), Gaps = 6/259 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +       +       A+ +MV ANL+LV+ +AKKY   G    DL+QEGNIGL+KA 
Sbjct: 353 EVQESAIEFSQAMQAYRQARDQMVIANLKLVLFIAKKYLYSGQPLDDLLQEGNIGLIKAV 412

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +++DW  G+K STYA WW++Q + R +AD+S TIR+PVH+  K  ++   A  +     R
Sbjct: 413 DRYDWRRGFKLSTYATWWIRQQVGRYVADKSKTIRLPVHVYVKTQQIAHAAHAIELATGR 472

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            PT EEIAKK+ MP   V  +     EP+    PI D D   L       N V+     I
Sbjct: 473 MPTIEEIAKKMEMPASKVAPLALAIPEPL----PIHDVDVDSLIAIDAQDNYVARDPMDI 528

Query: 606 --QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              + L  +  R LA+L P++E+VLR+RFGIG +   TLEE+G +  VTRERIRQIEAKA
Sbjct: 529 VSDSQLIGSIDRFLATLKPKDEQVLRLRFGIGAHEAMTLEEIGTRLEVTRERIRQIEAKA 588

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           I  LKHP+R ++L   L+G
Sbjct: 589 ICHLKHPARLERLLRDLNG 607



 Score = 65.2 bits (157), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 59/165 (35%), Gaps = 12/165 (7%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           ++     ++        D+     +DP+R+Y +E  +  LL+ + E+A+ + +E G    
Sbjct: 161 EMTPDEEDTVTEALAFIDNLAERRNDPLRIYQKEFQNATLLTADEEVALGQGMERGVQQA 220

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLR--------EIIDLEACIGPESKGGFFHGTEG 205
           + +L   P    A++     +      LR        E+ D+E     E         EG
Sbjct: 221 LDALAVWPSGIGAVLDAVHMVKSEAKPLRWLSSGPRAELQDIEISSNAEPAADSVLSVEG 280

Query: 206 HSYQKREDS----SQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                  DS       +  D++ E   + E  + +  D     D 
Sbjct: 281 IGTDDESDSQFGHDAHESTDELSELLSNAELLSGLDFDGALSSDG 325


>gi|237757189|ref|ZP_04585608.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690651|gb|EEP59840.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 285

 Score =  160 bits (403), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 87/275 (31%), Positives = 145/275 (52%), Gaps = 9/275 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KSI     +S  E   ++  V+        A ++++ +NLR VI++AK+Y   G+ F 
Sbjct: 13  YLKSIYKIPLLSKEEEESLLKKVK---EGDKEALQKLIISNLRFVINIAKRYAGYGIPFS 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  GN+GL++AA+KFD   G +F +YA+WW++Q+I  +I  +S  I+ P  M     K
Sbjct: 70  DLISAGNVGLIEAAKKFDTSKGVRFISYAVWWIRQSIINTIQHESEIIKKPNRMYAYASK 129

Query: 532 VVRTARRMSNKIKREPTPEEIA---KKLAMPVEG--VRKVLKITKEPISLETPIG-DEDT 585
           +      + + + REP+ +EI    K   + VE   V          +SL+TPI   ++ 
Sbjct: 130 INNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLDTPIEGTDND 189

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D I   N +       + +L+     +L +L+ RE  +L  RFG+      TL EV
Sbjct: 190 LVLEDTISVYNTLDIEKDINEEDLKRAIETLLDTLSQRERTILIHRFGLNGEEPKTLNEV 249

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+   ++RER+RQIE + ++KL+  ++ KKL   +
Sbjct: 250 GEIVGLSRERVRQIENRVLKKLRKIAKIKKLEDLI 284



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           V  YL+ +  I LLS+E E ++ K+++ G    +  L  S L F  +I            
Sbjct: 10  VDFYLKSIYKIPLLSKEEEESLLKKVKEGDKEALQKLIISNLRF--VINIAKRYAGYGIP 67

Query: 181 LREII 185
             ++I
Sbjct: 68  FSDLI 72


>gi|88808921|ref|ZP_01124430.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786863|gb|EAR18021.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 322

 Score =  160 bits (403), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 95/282 (33%), Positives = 162/282 (57%), Gaps = 7/282 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVI 457
           E+  +  +  E++       +  +E      +    +++       AK+ MV ANLRLV+
Sbjct: 40  ELMELESVEAELQEKRGGEAVLAAELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVV 99

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 100 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 159

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P + V++++   ++P+SLE
Sbjct: 160 TIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEDEVKELMCRARQPVSLE 219

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L D +     +          L+     +L  L   +ERVLRMR+G+   
Sbjct: 220 MKVGDGDDTELLDLLAGDGELPSE-QVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGE 278

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              +L  + K   ++R+R R++E + ++ L+      +LR +
Sbjct: 279 EPMSLTGIAKTLKMSRDRTRRLEREGLQSLRQAPL--ELRDY 318



 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS + EI + ++++ 
Sbjct: 11  DLVRSYLRDIGRVPLLSHQQEITLGRQVQE 40


>gi|225429414|ref|XP_002275831.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score =  160 bits (403), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 74/297 (24%), Positives = 146/297 (49%), Gaps = 4/297 (1%)

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV--SMVRKGECEASIA 444
           AK+  E      +   ++ I     E   I     +S       V   ++++        
Sbjct: 266 AKNEAEMSKGVKLVANLERIRATLEE--EIGHVASLSNWAEAAGVDKKVLQQQLQFGWYC 323

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++ +   LV+ +A+ Y   G+ F D++Q GN+G+++ AE+FD   GY+FSTY  +W+
Sbjct: 324 RDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYWI 383

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +++++  +A  +  ++IP  +   I ++ +  + +     R P   EIAK   + +  +R
Sbjct: 384 RKSMSTLVARHARGVKIPFTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGLSLAKIR 443

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
                 +   S +    D   + + +F  D +  SP +  +Q   R+    +L  L PRE
Sbjct: 444 SAGNCLRVVGSTDQSFQDCWGATILEFTPDTSIKSPEEGFMQQCKRKDIHNLLKGLDPRE 503

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            ++L +R+G G     +LEE+G++F V++E IR++E  A+  L+     + LR ++D
Sbjct: 504 RQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRDEEICQNLRHYVD 560


>gi|313837139|gb|EFS74853.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA2]
 gi|314927839|gb|EFS91670.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL044PA1]
 gi|314971910|gb|EFT16008.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA3]
 gi|328907302|gb|EGG27068.1| sigma-70 region 2 [Propionibacterium sp. P08]
          Length = 312

 Score =  160 bits (403), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 156/272 (57%), Gaps = 6/272 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +++ +  R  ++  +  T  + +E  H      +   +   A    V ANLRLV+
Sbjct: 39  ALARRIEAGVFARAVLEGQAETTSDATTEELH------QIAADGDEAMAHFVRANLRLVV 92

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVA+KY    +  LDL+QEGN GL++A EKFD+  G+KFSTYA WWV+QAI+R IA Q  
Sbjct: 93  SVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFSTYATWWVRQAISRGIAQQGR 152

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +R+PVH+ +++++V    R +  ++ REP   EIA +L +  E V ++++  ++ +SL+
Sbjct: 153 IVRLPVHVAEQVNQVSAARRNLERQLGREPETSEIADELEITEERVIELIRFGRDHVSLD 212

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            P+ D+  + LGD I  + +  P D  + A  R     +L +L  R   V+R R+G+   
Sbjct: 213 APVEDDGDTSLGDLIARETSPGPDDIVLDAEDRGRLEGLLDNLDERSADVVRRRYGLVDG 272

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L ++GK + +T ER+RQIE  A+  ++ 
Sbjct: 273 RQAKLADIGKVWGITAERVRQIERAALDSMRQ 304


>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 560

 Score =  160 bits (403), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 142/252 (56%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V ++++        + E++++   LV+  A+ Y   G+   DL+Q GN+G+++ AE+FD 
Sbjct: 309 VKVLQQQLSFGWYCRDELIKSTRSLVLYFARNYRGTGIALEDLLQAGNLGVLEGAERFDH 368

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTY  +W+++++++ ++  +  I+IP  +   I+++ +  + ++    + P  +
Sbjct: 369 TRGYRFSTYVQYWIRKSMSKIVSRLARGIQIPCTLSRAIYQIQKARKALTTSNGKYPDDD 428

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIAK   + +  +    +  +   S++  IG+   +   +F+ D +  SP +  ++ ++ 
Sbjct: 429 EIAKYTGLSLAKIESASRCLRVVGSIDQKIGESLNAKYLEFLPDTSVQSPEEVVMRQHMI 488

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +    +L SL  RE +VL +RFG+      +LEE+G+ F V++E +R++E + + +L++ 
Sbjct: 489 QDMHNLLRSLDSRERQVLILRFGLNDYQPKSLEEIGRHFHVSKEWVRRLEKRVMTRLRNE 548

Query: 671 SRSKKLRSFLDG 682
              + LR +++ 
Sbjct: 549 ETCRNLRHYINS 560


>gi|91978893|gb|ABE66422.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 289

 Score =  160 bits (403), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 131/331 (39%), Gaps = 44/331 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     I P             +         E +  D  E E + +     S DD +  
Sbjct: 61  I--SGFIDPNE-----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDDEADT 113

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L    + +  ++                                   
Sbjct: 114 GPDPEVAREKFGELRAQYEVTRLSI----------------------------------- 138

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           Q + ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +  
Sbjct: 139 QNNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQA 198

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E D  W  Y K   +      V  + D +L+   +++ I VETG+S
Sbjct: 199 KMPKKTFVAAFTNNECDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVETGLS 257

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           I++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 IAQIKDINRRMSIGEAKARRAKKEMVEANLR 288


>gi|33862729|ref|NP_894289.1| RNA polymerase sigma-70 factor family protein [Prochlorococcus
           marinus str. MIT 9313]
 gi|33634645|emb|CAE20631.1| Sigma-70 factor family [Prochlorococcus marinus str. MIT 9313]
          Length = 308

 Score =  160 bits (403), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 139/248 (56%), Gaps = 7/248 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R        AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 57  RLTIRRGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+       PT E++AK
Sbjct: 117 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKSRLMQNNGLPPTAEQLAK 176

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + +P+  V  +L        +SL+  +    D S L D +  +       + + +    
Sbjct: 177 TMRLPMAEVEDLLACELRSVTVSLQGVVKSKSDPSELADVLPSEEIPPMERAEM-SERTA 235

Query: 612 TTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +L  A+LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 236 SVWTLLNRANLTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVLQRALRKLR 295

Query: 669 HPSRSKKL 676
                  L
Sbjct: 296 KAGMQSGL 303


>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera]
          Length = 611

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 74/297 (24%), Positives = 146/297 (49%), Gaps = 4/297 (1%)

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV--SMVRKGECEASIA 444
           AK+  E      +   ++ I     E   I     +S       V   ++++        
Sbjct: 316 AKNEAEMSKGVKLVANLERIRATLEE--EIGHVASLSNWAEAAGVDKKVLQQQLQFGWYC 373

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++ +   LV+ +A+ Y   G+ F D++Q GN+G+++ AE+FD   GY+FSTY  +W+
Sbjct: 374 RDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYWI 433

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +++++  +A  +  ++IP  +   I ++ +  + +     R P   EIAK   + +  +R
Sbjct: 434 RKSMSTLVARHARGVKIPFTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGLSLAKIR 493

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
                 +   S +    D   + + +F  D +  SP +  +Q   R+    +L  L PRE
Sbjct: 494 SAGNCLRVVGSTDQSFQDCWGATILEFTPDTSIKSPEEGFMQQCKRKDIHNLLKGLDPRE 553

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            ++L +R+G G     +LEE+G++F V++E IR++E  A+  L+     + LR ++D
Sbjct: 554 RQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRDEEICQNLRHYVD 610


>gi|254432550|ref|ZP_05046253.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627003|gb|EDY39562.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 319

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 100/279 (35%), Positives = 163/279 (58%), Gaps = 10/279 (3%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVI 457
           E+ ++ ++  E+   +  T  S +E         ++++K       AK+ MV ANLRLV+
Sbjct: 33  ELMALEEMEQELTMRAGGTAPSAAELAKAAGLSPAVLKKRLQAGRRAKERMVAANLRLVV 92

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 93  SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 152

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V+ +L   ++P+SLE
Sbjct: 153 TIRLPIHITETLNKLKKGQRELSQELGRTPTVTELAGYVELPEEEVKDLLCRARQPVSLE 212

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           T +GD + + L D +     + P +      L+     +L  L   + RVL+MR+GI   
Sbjct: 213 TKVGDGEDTELLDLLAGDGEL-PEERVDGECLKGDLRALLEQLPELQGRVLKMRYGIDPQ 271

Query: 638 -----TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                   +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 272 SAEMAEPMSLTGIGRILGISRDRVRNLERDGLAGLRRLS 310



 Score = 41.4 bits (95), Expect = 0.57,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA--GRAMMMASL 157
           D VR YLR++G + LL+ E EI + ++++       M   L
Sbjct: 4   DLVRSYLRDIGRVPLLTHEQEITLGRQVQELMALEEMEQEL 44


>gi|326512474|dbj|BAJ99592.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 98/303 (32%), Positives = 163/303 (53%), Gaps = 15/303 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +K   +G W      ++  IL      K ++    IS  E R   S +R+      +
Sbjct: 210 VHLSKKIKDGIWLQQQRSKLTEILGNEPSYKQMAQSLRISTPELR---SRMRESF----L 262

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N+RLVIS+A+KY   G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 263 AREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 322

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S T R+P +M +++  +      + ++    PT + IA+ L +  + V
Sbjct: 323 IRQGVSRALADNSRTFRLPTYMHERLIAIRAAKYALEDQ-GVSPTTQNIAELLNISEKKV 381

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+           GD    +IED+N A  P     +  L+E    +L 
Sbjct: 382 HNATEAVNKALSLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEEWYLKEEVNNLLI 441

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LT RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R KKL 
Sbjct: 442 SNLTERERHIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKKLD 500

Query: 678 SFL 680
           + L
Sbjct: 501 ALL 503


>gi|283780188|ref|YP_003370943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438641|gb|ADB17083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 320

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 95/274 (34%), Positives = 162/274 (59%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ I+    +S  + R + + +         A+  MV ANLRLV+++A+ YT +GL
Sbjct: 43  LESYLREINETALLSARDERELAAAI---ADGDVRARDRMVRANLRLVVNIARGYTGKGL 99

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +G +FSTYA +W+KQ+I R++ + + TIRIP +M + 
Sbjct: 100 SLQDLIEEGNLGLLRAVEGFDPAVGTRFSTYASYWIKQSIKRALINSAKTIRIPAYMVEL 159

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  R   R++ ++ R PTPEE+A+ L +  + +  + K  +   S       E    L
Sbjct: 160 LSKWRRATARLTEELGRGPTPEEVARVLGLAKKKLPIIKKAIRIYNSTPQTDQSEAGWSL 219

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ + D+   +P D  ++ ++ +    +L ++  RE  VLRMRFG+G  T HTL+E+G+ 
Sbjct: 220 GEIVMDERLKNPEDELVEQDVLKHVMEMLHTMDSREATVLRMRFGLGDTTPHTLKEIGES 279

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             +TRER+RQIE +A+ KL    +  + R +L+ 
Sbjct: 280 LGLTRERVRQIETEALGKLADGLKDPRER-YLES 312



 Score = 37.5 bits (85), Expect = 8.7,   Method: Composition-based stats.
 Identities = 20/118 (16%), Positives = 36/118 (30%), Gaps = 2/118 (1%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
            E       +     ++S   +        S   P+  YLRE+    LLS   E  +A  
Sbjct: 8   PESKHAMTSVKRKVGSTSGKARGVAPRKAISLQTPLESYLREINETALLSARDERELAAA 67

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           I  G       +  + L    ++            L+++I+        +  GF    
Sbjct: 68  IADGDVRARDRMVRANLRL--VVNIARGYTGKGLSLQDLIEEGNLGLLRAVEGFDPAV 123


>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
 gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
          Length = 568

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/298 (23%), Positives = 153/298 (51%), Gaps = 5/298 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           + A+     +    +      + +   ++ S+S     +    +    ++ +        
Sbjct: 274 NEAEMSTGVKIVADMERIRTQLEEESGKVASLSCWAEAAGMNEK----LLMRNLHYGWYC 329

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W+
Sbjct: 330 RDELLKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWI 389

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-IAKKLAMPVEGV 563
           +++++  ++  +  + IP  +   I+++ +  + +      +   +E I+K  ++ V+ +
Sbjct: 390 RKSMSMMVSRHARGVHIPSSIIRTINQIQKARKTLKTSHGIKYPADEDISKLTSLSVKKI 449

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R   +  K   S+E  +GD  ++   +F  D    SP ++ ++ + R     +L  L PR
Sbjct: 450 RAANQCLKVVGSIEKKVGDCFSTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPR 509

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           E++V+ +R+G+      +LEE+GK   V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 510 EKQVMVLRYGLQNYRPKSLEEIGKLLRVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 567


>gi|167515034|gb|ABZ81801.1| RpoD [Aeromonas aquariorum]
          Length = 292

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 83/335 (24%), Positives = 140/335 (41%), Gaps = 46/335 (13%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +II     I P                         E DDV  T   I S         
Sbjct: 61  SDII--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLAD 94

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-N 300
              D   +   + + + D+ +      ++                  E + ELR+  +  
Sbjct: 95  EDEDEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVT 137

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            ++ Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L 
Sbjct: 138 RLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLC 197

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  E
Sbjct: 198 VEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEE 256

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           TG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 TGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|26665386|dbj|BAC44904.1| principal sigma factor [Fischerella major NIES-592]
          Length = 203

 Score =  159 bits (402), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 112/204 (54%), Positives = 152/204 (74%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R ++K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIVK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|170692344|ref|ZP_02883507.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
 gi|170142774|gb|EDT10939.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
          Length = 359

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 81  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 137

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 138 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 197

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 198 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 257

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 258 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 317

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 318 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 354



 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 31/97 (31%), Gaps = 1/97 (1%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             E       +A         R       T D ++ YL  +    LL+ E E   ++  +
Sbjct: 48  AEEGGDAREGAAEVVPDADDFRALLQAELTADTIQHYLNRISVKPLLTVEEEQKYSRLAK 107

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           AG       + E  L     I     LN G  LL  I
Sbjct: 108 AGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 143


>gi|186682180|ref|YP_001865376.1| SigH/RpoD family RNA polymerase sigma factor [Nostoc punctiforme
           PCC 73102]
 gi|186464632|gb|ACC80433.1| RNA polymerase, sigma 70 subunit SigH, RpoD family [Nostoc
           punctiforme PCC 73102]
          Length = 321

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 88/262 (33%), Positives = 151/262 (57%), Gaps = 5/262 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E + +        ++S          + ++  +     +   AK +M+ ANLRLV+S
Sbjct: 53  ILAESEKLTIELKRTPTLSEWANQMQLSEQELLQQL----NQGKKAKHKMITANLRLVVS 108

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  R L+ +DLIQEG +GL +  EKF+  LGY+FSTYA WW++Q ITR+IA Q   
Sbjct: 109 IAKQYQRRNLELMDLIQEGTLGLERGVEKFNPALGYRFSTYAYWWIRQGITRAIAQQGRA 168

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+ +K++K+ R  R +S  + R PT  EIA  L++    +R+ L +    ISL+ 
Sbjct: 169 IRLPIHINEKLNKIKRVQRELSQTLGRIPTSTEIANALSLKPSQIREFLLLATRTISLDI 228

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +  E    L D IED    S      + +L +    +L++L+ +++ +L + FG+    
Sbjct: 229 RVSSEKDLRLQDLIEDYKYSSNSY-ITEESLNQEVNSLLSNLSRQQQEILNLHFGLTDGE 287

Query: 639 DHTLEEVGKQFCVTRERIRQIE 660
           + +L+++G++  ++RER+RQIE
Sbjct: 288 ELSLQQIGQRLGISRERVRQIE 309



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 27/42 (64%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +  + +++T D VR YL+E+G I LL++E EI  A+ ++ 
Sbjct: 8   DTKASNTNKATTDTVRAYLKEIGRIPLLTQEQEIIFAQEVQQ 49


>gi|158336372|ref|YP_001517546.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158306613|gb|ABW28230.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 100/281 (35%), Positives = 176/281 (62%), Gaps = 6/281 (2%)

Query: 403 VDSILKIRNEIKSI--SVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISV 459
           + ++ +++ E++       T    +E   + V+ ++K       A ++MVE+NLRLV+S+
Sbjct: 39  LTALQEMKQELQDHLDREPTQKEWAEKAQVSVAQLQKELKLGHKANRKMVESNLRLVVSI 98

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY    ++FLDLIQEG IGL +  EKFD   GY+FSTYA WW++QA+TR+IA+Q  TI
Sbjct: 99  AKKYNKAKVEFLDLIQEGTIGLQRGVEKFDPMKGYRFSTYAYWWIRQAMTRAIAEQERTI 158

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+ +K+ K+ +  R++S K+ R+PT +E+A ++ +  + +   L   +  ISL+  
Sbjct: 159 RLPIHINEKLSKLRKVRRQLSQKLHRDPTVQELAVEMDLAPKKIEDYLNYARRSISLDIQ 218

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IGD+  + L + +ED N  SP   A  ++LR    ++L  L+P++  V+ +R+G+     
Sbjct: 219 IGDQQNTELWELLEDPN-ESPDTYATASSLRSDLAKLLQDLSPQQREVITLRYGLIDQNP 277

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            TL +VG++  V+RE +R++E +A + L+  S+   L+ ++
Sbjct: 278 LTLAKVGERLNVSREWVRRVEREAFKILR--SQKVMLQEYM 316


>gi|33241240|ref|NP_876182.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238770|gb|AAQ00835.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 328

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 98/291 (33%), Positives = 165/291 (56%), Gaps = 8/291 (2%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
            +   ++  +   E      +  E++S    +   + ++++ GIS+ E    +       
Sbjct: 35  TNEQEITLGRQVQELISLEKLERELESTNGKKPSKEDLAIDAGISVRELSKRLKR----- 89

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFST
Sbjct: 90  --GVRAKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFST 147

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++Q ITR+IA++S  IR+P+H+ + ++K+ +  R +S  ++R PT +E++  + +
Sbjct: 148 YAYWWIRQGITRAIAEKSRIIRLPIHITELLNKLKKGQRELSQHLERTPTMQELSAYVEI 207

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V+ ++    +P+SLE+ +GD + + L D +     + P        ++     +L 
Sbjct: 208 PVEEVKDLMFRASQPVSLESKVGDGEDTSLLDLLAIDTDL-PDQQIELDCMKGDLEVLLQ 266

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L   + RVLRMRFGI      TL  +G+   ++R+R+R +    ++ L+ 
Sbjct: 267 KLPELQNRVLRMRFGINGEEPMTLTGIGRMLGISRDRVRNLLRDGLKGLRQ 317



 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 12/31 (38%), Positives = 21/31 (67%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 18  IDLVRSYLRDIGRVPLLTNEQEITLGRQVQE 48


>gi|149277811|ref|ZP_01883951.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149231499|gb|EDM36878.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 288

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 90/274 (32%), Positives = 153/274 (55%), Gaps = 4/274 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  IS    +++ E   + S+VR        A  ++V ANLR V+SVAK Y + GL
Sbjct: 18  LEKYLSEISKIELLNVEEEVRLASIVR---EGDRAALDKLVSANLRFVVSVAKNYQDMGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLI EGN+GL+KAA ++D   G+KF ++A+WW++Q+IT +IADQ   IR+P +    
Sbjct: 75  RLADLISEGNLGLIKAASRYDHTKGFKFISFAVWWIRQSITYAIADQHRMIRLPGNQIVG 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSH 587
           I ++ RT+  +  K++R P+ EE+A+ L +P   V        +  SL+ PI   E  + 
Sbjct: 135 ITRLNRTSDLLEQKLERRPSLEEVAEALDLPETKVVDYQMSALKTTSLDMPILLGEPGTT 194

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            G  I +    +      + +L E   R+L+ L PRE+++L + +G+G      LE++  
Sbjct: 195 FGHMIRNSEVEAADAVLDRQSLAENVRRLLSILPPREQKILSLYYGLGGMPQTRLEDMVP 254

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F +++ER+RQ++ KA++ LK       +  F +
Sbjct: 255 VFHLSKERLRQLKDKAVKTLKACCSEVPMSGFFN 288



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 2/78 (2%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           +   S      D +  YL E+  IELL+ E E+ +A  +  G    +  L  + L F  +
Sbjct: 5   RISKSITDRGGDSLEKYLSEISKIELLNVEEEVRLASIVREGDRAALDKLVSANLRF--V 62

Query: 168 IIWRDELNDGTTLLREII 185
           +       D    L ++I
Sbjct: 63  VSVAKNYQDMGLRLADLI 80


>gi|148239880|ref|YP_001225267.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 7803]
 gi|147848419|emb|CAK23970.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 322

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 96/282 (34%), Positives = 161/282 (57%), Gaps = 7/282 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVI 457
           E+  +     E++       +  +E      +    +++       AK+ MV ANLRLV+
Sbjct: 40  ELMDLEATEAELQEKRGGEAVPAAELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVV 99

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 100 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 159

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S  + R P+  E+A  + +P + V++++   ++P+SLE
Sbjct: 160 TIRLPIHITEMLNKLKKGQRELSQDLGRTPSVTELAAFVELPEDEVKELMCRARQPVSLE 219

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L D +     + P +      L+     +L  L   +ERVLRMR+G+   
Sbjct: 220 MKVGDGDDTELLDLLAGDGEL-PSEQVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGE 278

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              +L  + K   ++R+R R++E + +  L+      +LR +
Sbjct: 279 DPMSLTGIAKTLKMSRDRTRRLEREGLESLRQAPL--ELRDY 318



 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS + EI + ++++ 
Sbjct: 11  DLVRSYLRDIGRVPLLSHQQEITLGRQVQE 40


>gi|170735771|ref|YP_001777031.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169817959|gb|ACA92541.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 511

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 105/241 (43%), Positives = 157/241 (65%), Gaps = 1/241 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A + M+EANLRLV+S+A+KY NRG+   DL+Q+G +GLM+A EKF++  G+KFSTYA 
Sbjct: 272 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYAT 331

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QAI R++AD+S TIR+PVH+ D+  +V R A R   +  R  TP E+A +  +   
Sbjct: 332 WWIRQAIARAVADRSRTIRVPVHVGDQYQRVQRHALRFRQRTGRRATPAELAAETGLDEG 391

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R VL +  EP+SL+TP+ D DT  L + IED+ + SP +      +RE    +L S+T
Sbjct: 392 KLRAVLALPAEPVSLDTPLPDADTG-LVELIEDQASASPFEQLADTRMRECVRALLRSVT 450

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           P E  VLR RFG+G     T + + +   ++RER+RQIE +A+  L+  + ++  +SFLD
Sbjct: 451 PTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTAAEAENAQSFLD 510

Query: 682 G 682
            
Sbjct: 511 A 511



 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 38/151 (25%), Positives = 75/151 (49%)

Query: 21  SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80
           +   D   D   +++ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D 
Sbjct: 7   TPRADTPLDPIIQLLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDE 66

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
             +         +++   A +    +         ++ DP+ +Y+R M ++ LL+REGEI
Sbjct: 67  PAVPAPFAGAAPVEVDRDALDEGRAMLGDLARGTSASTDPLALYMRRMHAVPLLTREGEI 126

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            +A+ IE GR  ++ ++   P     L+   
Sbjct: 127 VLAREIETGRHQVLHAIAGYPPAVDVLLERH 157


>gi|330938479|gb|EGH42082.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 183

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/181 (31%), Positives = 88/181 (48%), Gaps = 3/181 (1%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M ++   P T   ++     +      L ++  L   I P+           
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVTQ 182

Query: 206 H 206
            
Sbjct: 183 P 183


>gi|74316856|ref|YP_314596.1| RNA polymerase sigma factor RpoS [Thiobacillus denitrificans ATCC
           25259]
 gi|74056351|gb|AAZ96791.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 316

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 93/283 (32%), Positives = 153/283 (54%), Gaps = 4/283 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +     +A      E  + +  E   +   +  +  I     ++ +E    V++ R+ 
Sbjct: 16  ETEADEERHAASDSNEELASAILDE-PQVDVTQLYLNEIGQAPLLTAAEE---VALARRT 71

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A++ M+E NLRLV+++AK Y NRGL  LDL++EGN+GL+ A EKFD   G++FS
Sbjct: 72  VLGDFEARQTMIERNLRLVVNIAKHYANRGLTLLDLVEEGNLGLIHALEKFDPERGFRFS 131

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +QS TIR+PVH+  +++  +R  R +      + T ++IA    
Sbjct: 132 TYATWWIRQNIERAIMNQSRTIRLPVHIIKELNIYLRAQRHLETHGVTDATSDDIAALTG 191

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            PV  VR+++++ +   SL+ P+  + T  LG+ I D NA  P +      +       L
Sbjct: 192 HPVADVRRIMQLNERIASLDAPLDVDPTLSLGEAIADDNAHLPDEMLQLEEIENHVQEWL 251

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             L  ++  V+  RFG+      TLE++  +  VTRER+RQI+
Sbjct: 252 TQLNDKQRWVIERRFGLNGCEACTLEDLALELEVTRERVRQIQ 294



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/106 (22%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  D  D+   +++       + S    +      D    D  ++YL E+G   LL+   
Sbjct: 4   EHSDESDDLTPDETEADEERHAASDSNEELASAILDEPQVDVTQLYLNEIGQAPLLTAAE 63

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+A+A+R   G      ++ E  L     I      N G TLL  +
Sbjct: 64  EVALARRTVLGDFEARQTMIERNLRLVVNIAKHYA-NRGLTLLDLV 108


>gi|159904297|ref|YP_001551641.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889473|gb|ABX09687.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 335

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 93/268 (34%), Positives = 159/268 (59%), Gaps = 10/268 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  ++   G+++   +    +          AK+ MV ANLRLV+S+AKKYT R ++ LD
Sbjct: 76  LDELASAAGLTVGALKKKFRL-------GERAKERMVAANLRLVVSIAKKYTKRNMELLD 128

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S  IR+P+H+ + ++K+
Sbjct: 129 LIQEGTIGLVRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEMLNKL 188

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +  R +S ++ R P+  E+A+ + +  E V+ ++    +P+SLE  +GD+D + L D +
Sbjct: 189 KKGQRDLSQQLSRTPSVAELAEYIDVSEEEVKDLMLKASQPVSLEMKVGDKDDTVLLDLL 248

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
              N  SP        ++     +L  L   + RVLRMR+GI      +L  +G+   ++
Sbjct: 249 STDND-SPQQQIELDCMKGDLEILLEKLPELQYRVLRMRYGIDGEEPMSLTGIGRVLGIS 307

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           R+R+R +E   +R L+  S+ + + +++
Sbjct: 308 RDRVRNLERSGLRGLR--SKGEAVEAYV 333



 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 12/37 (32%), Positives = 22/37 (59%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
               S +D +R YLR++G + LLS + EI + + ++ 
Sbjct: 19  EKSTSDNDLIRSYLRDIGRVPLLSNDQEITLGRHVQE 55


>gi|297518949|ref|ZP_06937335.1| RNA polymerase sigma factor RpoD [Escherichia coli OP50]
          Length = 183

 Score =  159 bits (401), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/172 (33%), Positives = 89/172 (51%), Gaps = 1/172 (0%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
               K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D+ 
Sbjct: 6   QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDL 65

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
              ++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI IAKRIE
Sbjct: 66  MLAENTADEDAAEAAAQVLSSVE-SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 124

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
            G   +  S+ E P     L+   D +      L ++I        E     
Sbjct: 125 DGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAP 176


>gi|325109992|ref|YP_004271060.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
 gi|324970260|gb|ADY61038.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
          Length = 286

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 88/259 (33%), Positives = 151/259 (58%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+  + +S  E + + + +         A+  MV ANLRLV+++A+ Y ++GL
Sbjct: 24  LETYLREINETSLLSADEEKELANRI---AMGDLEARDRMVRANLRLVVNIARGYASKGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +  +FSTYA +W+KQ+I RS+ + + TIRIP +M + 
Sbjct: 81  PLQDLIEEGNLGLLRAVEGFDPNMNTRFSTYASYWIKQSIKRSLVNCAKTIRIPAYMVEL 140

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  +   R+ +++ R PT EE+A +L +P + +  V K  +   S      +E    L
Sbjct: 141 LSKWRKATARLQDELNRTPTAEEVAAELGLPKKKLNIVKKAIQLYNSTPQSDDEESGWSL 200

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ + D+ A+ P +  +  +      R+L  +  RE  +LRMRFG+      TL+E+G+ 
Sbjct: 201 GEMVADERAIGPEEELVNNDNLNHVYRMLDDMDDRESTILRMRFGLDHEEPKTLKEIGES 260

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE +A+ +L
Sbjct: 261 LGLTRERVRQIEQEALNRL 279



 Score = 44.4 bits (103), Expect = 0.062,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
             +  +P+  YLRE+    LLS + E  +A RI  G       +  + L    ++     
Sbjct: 17  SAAVQNPLETYLREINETSLLSADEEKELANRIAMGDLEARDRMVRANLRL--VVNIARG 74

Query: 174 LNDGTTLLREIIDLEACIGPESKGGF 199
                  L+++I+        +  GF
Sbjct: 75  YASKGLPLQDLIEEGNLGLLRAVEGF 100


>gi|312281919|dbj|BAJ33825.1| unnamed protein product [Thellungiella halophila]
          Length = 562

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 72/286 (25%), Positives = 153/286 (53%), Gaps = 4/286 (1%)

Query: 400 ACEVDSILKIRNEIKSIS--VETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLV 456
           A  V  + +IR +++  S  V +    +E   +   ++ +        + E++++   LV
Sbjct: 276 AKIVADMERIRTKLEEESGKVASMSCWAEAAGMNEILLMRNLHYGWYCRDELLKSTRSLV 335

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +++ Y   G+   DLIQ GN+G+++ AE+FD   GYKFSTY  +W++++++  ++  +
Sbjct: 336 LFLSRNYRGLGIAHEDLIQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSMMVSRHA 395

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREP-TPEEIAKKLAMPVEGVRKVLKITKEPIS 575
             + IP  +   + ++ +  + +      +    EEI+K+    ++ +R   +  K   S
Sbjct: 396 RGVYIPSSVIRTMSQIQKARKTLKTSHGIKYPADEEISKETGYSLKKIRAANQCLKVVGS 455

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++  +GD  T+   +F  D    SP ++ ++ +       +L  L PRE++V+ +R+G+ 
Sbjct: 456 IDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAWRDVHDLLQGLEPREKQVMVLRYGLQ 515

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                +LEE+GK   V++E IR+IE +A+ KL+  + ++ LR +L+
Sbjct: 516 GFRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQANAENLRFYLN 561


>gi|307107488|gb|EFN55731.1| hypothetical protein CHLNCDRAFT_35462 [Chlorella variabilis]
          Length = 267

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 91/252 (36%), Positives = 146/252 (57%), Gaps = 6/252 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR+       A++ MV  N+RLV+S+AKKY  RGL   DL+ EG +GL +A +KFD    
Sbjct: 16  VRRRLALGLQAREHMVNCNMRLVVSIAKKYVGRGLALQDLVAEGMVGLQRAVDKFDASTR 75

Query: 494 YKF-STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
            +    YA WW++Q++TR+I+DQ+  +R+PVH+ + + KV R  + + ++    P P+ +
Sbjct: 76  LQVTPAYAHWWIRQSVTRAISDQARVVRLPVHLHEAMGKVRRAEQALWDETGLLPAPQAV 135

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIG-----DEDTSHLGDFIEDKNAVSPLDSAIQA 607
           A +  +    +  + K  + P S +          +  +    ++E+     P + A   
Sbjct: 136 ADRCGLTHSKLMALYKSFRAPTSRDGVPTLGAGSVDAKAPGEQWVEEVGEEDPAELAHHR 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            ++E    VL +LT RE  +++MR+G+    + TLEEVG+ F VTRERIRQIEAKAIRKL
Sbjct: 196 MMKEDLNHVLLTLTERECGIIKMRYGLDDGEEKTLEEVGRAFNVTRERIRQIEAKAIRKL 255

Query: 668 KHPSRSKKLRSF 679
           + PSR  +L ++
Sbjct: 256 RSPSRVGQLVTY 267


>gi|289676146|ref|ZP_06497036.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 178

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/175 (32%), Positives = 88/175 (50%), Gaps = 3/175 (1%)

Query: 26  FSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                 K++I L R++ Y+T  E+N  LP D    EQ+ED + M+++MGI V +     D
Sbjct: 6   QQQSRIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDAD 65

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
                D+    ++A  ++  L   +      T DPVRMY+REMG++ELL+REGEI IAKR
Sbjct: 66  ALMLADADTDEAAAEEAAAALAAVETDI-GRTTDPVRMYMREMGTVELLTREGEIEIAKR 124

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
           IE G   +M ++   P T   ++     +      L ++  L   I P+      
Sbjct: 125 IEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPP 177


>gi|23978365|dbj|BAC21147.1| principal sigma factor [Leptolyngbya sp. PCC 7375]
          Length = 203

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 110/204 (53%), Positives = 151/204 (74%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL++L+P E  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDEVSKSLLREDLEGVLSTLSPSERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|54302639|ref|YP_132632.1| DNA-directed RNA polymerase sigma factor [Photobacterium profundum
           SS9]
 gi|90412658|ref|ZP_01220660.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
 gi|46916063|emb|CAG22832.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum SS9]
 gi|90326466|gb|EAS42878.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
          Length = 291

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 98/269 (36%), Positives = 158/269 (58%), Gaps = 4/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+  ++ I+++  ++  E    +   RK       AKK M+E+NLRLV+S+AKKY   G+
Sbjct: 16  IQLYLREIALKPLLTKHEE---ILYSRKSLTGDKEAKKVMIESNLRLVVSIAKKYRGSGM 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q  DLI EGNIGL+ + EKFD   G++FSTYA WW+KQ I R I +Q+ TIR+PVH+  +
Sbjct: 73  QLSDLIDEGNIGLITSVEKFDPERGFRFSTYATWWIKQTIERCIHNQARTIRLPVHVSKE 132

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-H 587
           I+ ++RT +++  K  +EPT EE+A+KL   V+ +  VL      +S +  I D+  S  
Sbjct: 133 INTIIRTHKQLMKKNNQEPTREEVAEKLERSVDDISSVLAYDAPIVSFDQTINDDANSQS 192

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +  FI D ++  P     + +++     +L +L  R+  +L  RFG+      TL++V  
Sbjct: 193 ISVFIADDSSDKPESQVDKDDIKGLALAMLENLNQRDREILCRRFGLLGYEVQTLQQVAN 252

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  +TRERIRQ++  +++KLK+       
Sbjct: 253 EVGLTRERIRQLQVSSLKKLKNTLERDNY 281



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 3/88 (3%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D +++YLRE+    LL++  EI  +++   G       + ES L    ++    +     
Sbjct: 14  DVIQLYLREIALKPLLTKHEEILYSRKSLTGDKEAKKVMIESNLRL--VVSIAKKYRGSG 71

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGH 206
             L ++ID E  IG  +    F    G 
Sbjct: 72  MQLSDLID-EGNIGLITSVEKFDPERGF 98


>gi|158337702|ref|YP_001518878.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158307943|gb|ABW29560.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 97/250 (38%), Positives = 162/250 (64%), Gaps = 3/250 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           VS ++K       A ++MVE+NLRLV+S+AKKY    ++FLDLIQEG IGL +  EKFD 
Sbjct: 70  VSQLQKELKLGHKANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGLQRGVEKFDP 129

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA WW++QA+TR+IA+Q  TIR+P+H+ +K+ K+ +  R++S K+ R+PT +
Sbjct: 130 MKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEKLSKLRKVRRQLSQKLHRDPTVQ 189

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A ++ +  + +   L   +  ISL+  IGD+  + L + +ED N  SP      ++LR
Sbjct: 190 ELAVEMDLAPKKIEDYLNYARRSISLDIQIGDQQNTELWELLEDPN-ESPDTYVTASSLR 248

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               ++L  L+P++  V+ +R+G+      TL +VG++  V+RE +R++E +A + L+  
Sbjct: 249 SDLAKLLQDLSPQQREVITLRYGLIDQNPLTLAKVGERLNVSREWVRRVEREAFKILR-- 306

Query: 671 SRSKKLRSFL 680
           S+   L+ ++
Sbjct: 307 SQKVMLQEYM 316


>gi|260436019|ref|ZP_05789989.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260413893|gb|EEX07189.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 335

 Score =  158 bits (400), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 91/238 (38%), Positives = 149/238 (62%), Gaps = 1/238 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +++       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD  
Sbjct: 88  MQLKRKLQHGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 147

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E
Sbjct: 148 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTE 207

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ + +P + V+ ++   ++P+SLE  +GD D + L + +     + P D   +  L+ 
Sbjct: 208 LAEFVELPEDDVKDLMCRARQPVSLEMKVGDGDDTELLELLSGDGDL-PSDQVEEDCLKG 266

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +L  L   +E+VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+ 
Sbjct: 267 DLRSLLGQLPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRR 324



 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 26  DLVRSYLRDIGRVPLLTHEQEITLGRQVQE 55


>gi|124026787|ref|YP_001015902.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961855|gb|ABM76638.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 335

 Score =  158 bits (400), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 98/276 (35%), Positives = 167/276 (60%), Gaps = 10/276 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E++S L  + +I   + + G+S  + +  +            AK+ MV ANLRLV+S
Sbjct: 62  LETELESDLGEKPDINFFADKAGLSPIQLKKKLK-------SGRRAKERMVAANLRLVVS 114

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S +
Sbjct: 115 VAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRS 174

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+ + ++K+ +  R +S ++ R PT +E+++ + +P   V+ ++    +P+SLET
Sbjct: 175 IRLPIHITEMLNKLKKGQRELSQELSRTPTLKELSEYVELPETDVKDLMSRAGQPVSLET 234

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMN 637
            IGD + + L D +   N +      I+++ ++     +L  L   + RVLRMR+G+  +
Sbjct: 235 KIGDGEDTILLDLL--SNEIDMPSEQIESDCMKGDLETLLEQLPELQNRVLRMRYGMDGD 292

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +L  +G+   ++R+R+R +E   +R L+    S
Sbjct: 293 DPMSLTGIGRVLGISRDRVRNLERDGLRGLRKTGDS 328



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  + +      +   +  D VR YLR++G + LLS E EI + ++++ 
Sbjct: 6   EAPKTKYSSSAASARSVTDIDLVRSYLRDIGRVPLLSHEQEITLGRQVQD 55


>gi|72383045|ref|YP_292400.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002895|gb|AAZ58697.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 335

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 100/276 (36%), Positives = 167/276 (60%), Gaps = 10/276 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E++S L  + +I   + + GIS  + +  +            AK+ MV ANLRLV+S
Sbjct: 62  LETELESDLGEKPDINFFADKAGISPIQLKKKLK-------SGRRAKERMVAANLRLVVS 114

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S +
Sbjct: 115 VAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRS 174

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+ + ++K+ +  R +S ++ R PT +E+++ + +P   V+ ++    +P+SLET
Sbjct: 175 IRLPIHITEMLNKLKKGQRELSQELSRTPTLKELSEYVELPETDVKDLMSRAGQPVSLET 234

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTPREERVLRMRFGIGMN 637
            IGD + + L D +   N +      I+++ ++     +L  L   + RVLRMR+GI  +
Sbjct: 235 KIGDGEDTILLDLL--SNEIDMPSEQIESDCMKGDLETLLEQLPELQNRVLRMRYGIDGD 292

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +L  +G+   ++R+R+R +E   +R L+    S
Sbjct: 293 DPMSLTGIGRVLGISRDRVRNLERDGLRGLRKTGDS 328



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            +  +        +   +  D VR YLR++G + LLS E EI + ++++ 
Sbjct: 6   EAPKTKNSSSAASARSVTDIDLVRSYLRDIGRVPLLSHEQEITLGRQVQD 55


>gi|325264732|ref|ZP_08131461.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030024|gb|EGB91310.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 292

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 98/261 (37%), Positives = 151/261 (57%), Gaps = 4/261 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I   + +S  E   +   +         AK ++ E+ L LV+S+A +Y+ RGL F+
Sbjct: 32  YLKEIGQISPLSSGEELELGKKI---AEGDEGAKLKLEESALCLVVSIAGQYSGRGLLFM 88

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLM+AAEK+D+     FS YA  W++ AI  ++ +QS  IR+P ++ + + K
Sbjct: 89  DLIQEGNIGLMQAAEKYDYTKDGGFSGYARRWIEDAIKHAVDEQSREIRVPAYVAENMKK 148

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLA-MPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           V + A  +  ++ RE T  EIA KL     E +  +L   K P+SL+ P+ D D  +L D
Sbjct: 149 VQKAAYELQQELGREATAGEIAGKLGDKSEEEIESILTFLKNPVSLDAPVEDGDDENLED 208

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D+   +P D+      +E    +L SL+ +E +V+  RFG+     HTLEEVG++  
Sbjct: 209 TIADREEKTPEDAVNSLIQKEEVLHLLESLSEKERQVISKRFGLEDGRVHTLEEVGQELN 268

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           V+RERI QIE  A++KL+  +
Sbjct: 269 VSRERISQIEEHAMKKLRQAA 289



 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 89/261 (34%), Gaps = 4/261 (1%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           + +   +    +P+++YL+E+G I  LS   E+ + K+I  G       L ES L     
Sbjct: 16  EIQIPDNVELTEPLKIYLKEIGQISPLSSGEELELGKKIAEGDEGAKLKLEESALCLVVS 75

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           I    + +    L  ++I        ++   + +  +G          ++  +  V E  
Sbjct: 76  IAG--QYSGRGLLFMDLIQEGNIGLMQAAEKYDYTKDGGFSGYARRWIEDAIKHAVDEQS 133

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
            +I   A V+++ +    +  E  +   R     E   A  L    ++    ++  L   
Sbjct: 134 REIRVPAYVAENMKKVQKAAYELQQELGREATAGE--IAGKLGDKSEEEIESILTFLKNP 191

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
             +   +    D  +     ++     +     L++    L L +S  +   + +     
Sbjct: 192 VSLDAPVEDGDDENLEDTIADREEKTPEDAVNSLIQKEEVLHLLESLSEKERQVISKRFG 251

Query: 348 RIMHNEGELLRLAQSYGIKRD 368
                   L  + Q   + R+
Sbjct: 252 LEDGRVHTLEEVGQELNVSRE 272


>gi|168036108|ref|XP_001770550.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
 gi|14669828|dbj|BAB62006.1| PpSIG1 [Physcomitrella patens]
 gi|14669830|dbj|BAB62007.1| PpSIG1 [Physcomitrella patens]
 gi|162678258|gb|EDQ64719.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
          Length = 677

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 131/598 (21%), Positives = 262/598 (43%), Gaps = 56/598 (9%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G +EL SR+ + ++A R        ++ +    +         DEL+  +++L +   L 
Sbjct: 86  GRVELPSRDQQQSVA-RALTVLHEHISGVALQNIALSE-----DELSRYSSILPDASTLL 139

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                E++         H  +  E  +  +     +    ++           +  D   
Sbjct: 140 RRSMLEAQWALTLKELMHEQKMEEQKNSRRAGKGKKSFSLEVTEDVSPGSTSTATGDLAV 199

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKV---------MCALDEIAEVYRELRSLQD 299
           E+  ++E+  +             + + +                +E+ + +R    L+D
Sbjct: 200 EDLTDEEKVTERKVTRRRGKGKLKQVERKQDTSLQETGNVHTEGSEEVVDYFRSGEQLKD 259

Query: 300 -NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE---------QLYDISKRI 349
            N      + K +   + L   LV+     S +    +L+V+         +L    +R+
Sbjct: 260 LNTARRGGEGKLTKFERKLDSSLVEDACPESTSTMTTELVVKSGSPSARTRRLESRQRRV 319

Query: 350 ------------------MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                              + +GE +R  +  G+    +L  +       + ++  ++  
Sbjct: 320 AIAGKPTSPDALTIHPLKKYQKGERVRRVKFDGV--QDYLTTYLREITKINLLTKQEEVF 377

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             +        ++   K+  E+  +      +      +  +VRK    A  A+ +MV A
Sbjct: 378 LSKKLRIGLNLLEERKKLAAELGYVPSNEEWAPHMNLSVGDLVRKLGE-AEWARDKMVMA 436

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+SVAK+Y + GL+  DLIQEG+IGL++  EKFD   GYK STY  WW++Q +TR+
Sbjct: 437 NLRLVVSVAKQYHSFGLEMADLIQEGSIGLLRGVEKFDHTRGYKLSTYVHWWIRQGVTRA 496

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           IAD S T+R+PVH+ D + ++ +    + ++     + +EI++   +    ++  L++TK
Sbjct: 497 IADHSRTVRLPVHVHDTLGRIRKAKSTLLSE-GCTASVQEISEATNLTGTKIKNTLQVTK 555

Query: 572 EPISLETPIGDE-----DTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVL-ASLTPRE 624
           + +SL+  IG       D   L   + D++  +   + ++  L ++   ++L + L PRE
Sbjct: 556 KLVSLDKEIGRNTLQSGDGETLHSLVADRDIENQPWTIVERMLMKDDVDKLLTSQLGPRE 615

Query: 625 ERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++R+ +G+G       +LE +  ++ V+RER+RQ+E  A+RKL+  SR + L  +L
Sbjct: 616 RDIVRLHYGVGREDGSVMSLESISYRYGVSRERVRQLETAAMRKLQIKSREQGLDRYL 673


>gi|116074383|ref|ZP_01471645.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069688|gb|EAU75440.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 90/239 (37%), Positives = 146/239 (61%), Gaps = 1/239 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +++       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   
Sbjct: 95  QLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTR 154

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+
Sbjct: 155 GYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTEL 214

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + +P E V+ ++   ++P+SLE  +GD D + L + +     +          L+  
Sbjct: 215 AEFVELPEEEVKDLMCRARQPVSLEMKVGDGDDTELLELLAGDGELPSE-QVEGECLKGD 273

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              +L  L   + +VLRMR+G+      +L  +G+   ++R+R+R +E   +  L+  S
Sbjct: 274 LRDLLEQLPELQRKVLRMRYGMNGEDPMSLTGIGRIIGISRDRVRNLERDGLAGLRRLS 332



 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS + EI + ++++ 
Sbjct: 31  DLVRSYLRDIGRVPLLSHQQEITLGRQVQD 60


>gi|290796544|gb|ADD64842.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 284

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 134/328 (40%), Gaps = 49/328 (14%)

Query: 51  AFLPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNSSVFL 106
             LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +   
Sbjct: 1   DHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAAA 60

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
               D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + 
Sbjct: 61  LTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEM 120

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           L+   +   +G   L EI+            GF    E         ++      D    
Sbjct: 121 LLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAV 169

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
           + D +        +     + P+  E                           V   ++ 
Sbjct: 170 DEDDDEDGDDDAAEEEAGPTGPDPVE---------------------------VATRMEN 202

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           +A  Y + + +        K+          +E +  +  +L L     D LV QL  + 
Sbjct: 203 LANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVV 256

Query: 347 KRIMHNEGELLRLAQS-YGIKRDVFLER 373
             I  +E ++L LA +   + R  F+  
Sbjct: 257 NGIKDHERKVLHLATTVARMPRKDFIRS 284


>gi|219111033|ref|XP_002177268.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411803|gb|EEC51731.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 324

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 98/282 (34%), Positives = 158/282 (56%), Gaps = 19/282 (6%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+  +   G + ++F  +V         +  AK+ MV++N+RLV+S+A+KY+N G+   D
Sbjct: 47  IEEWAAACGGTATDFVEMV-------MTSREAKQRMVQSNMRLVVSIARKYSNVGVSLQD 99

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEG++GL +AAEKF+   G+KFSTYA WW++QA+ RSIA  S TIR+PVH+ + +++V
Sbjct: 100 LVQEGSLGLSRAAEKFEPKKGFKFSTYASWWIQQAVFRSIAYHSRTIRLPVHVHNLLNRV 159

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--- 589
            +    +  ++ R PT EE+A++L M ++   K+L++TK  ISLETP    +   LG   
Sbjct: 160 RKVRNNLQRELSRTPTNEEMAEELGMTLQKYNKMLRLTKRSISLETPKYQSNPKDLGHES 219

Query: 590 -DFIEDK--------NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            D + D         +  +P     +    E    +L  L   E RV+  R+G+      
Sbjct: 220 HDLLGDTISASSALFDESTPEKRVDRGIFHEDLHEMLEILDEDERRVICSRYGLSDGLTR 279

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           T+  V  Q   ++  +R  E +A+RKL+ P   KKL+   D 
Sbjct: 280 TVTAVASQMKQSKAWVRSQECRALRKLRRPWYEKKLKEHQDA 321


>gi|23978360|dbj|BAC21145.1| principal sigma factor [Pleurocapsa sp. PCC 7314]
          Length = 203

 Score =  158 bits (399), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 111/204 (54%), Positives = 149/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V +NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKSLLREDLESVLDTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|23978350|dbj|BAC21142.1| principal sigma factor [Xenococcus sp. PCC 7307]
          Length = 203

 Score =  158 bits (398), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 111/204 (54%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKSLLREDLESVLDTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|320104603|ref|YP_004180194.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319751885|gb|ADV63645.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 277

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 93/259 (35%), Positives = 150/259 (57%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    +S  E + + + + K       A++ MV ANLRLV+++A+ Y  +GL
Sbjct: 16  LETYLREINEMALLSAEEEKELAARIAK---GDKTARERMVRANLRLVVNIARGYVGKGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +G +FSTYA +W+KQ+I R++ + +  IRIP +M + 
Sbjct: 73  ALQDLIEEGNLGLLRAVEGFDPKVGTRFSTYASYWIKQSIKRALVNTAKPIRIPAYMVEL 132

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  R A  + +++ R PT +EIA +L +P + +  V K  K    +      E    L
Sbjct: 133 LCKWRRAAIELQDRLGRTPTTDEIAHELRIPKKKLAIVKKAIKVYNLVPQSDQPESGWSL 192

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD + D+    P    ++A+  +   R L  +  RE  VLRMRFG+      TL+E+G+Q
Sbjct: 193 GDMLMDERTRPPDVEMVEADNLKLVMRRLEEMDKREATVLRMRFGLDDQPPCTLKEIGEQ 252

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE +A+ KL
Sbjct: 253 LGLTRERVRQIENEALNKL 271



 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 2/94 (2%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
           + + +     +   P+  YLRE+  + LLS E E  +A RI  G       +  + L   
Sbjct: 1   MARIRRHRRDTVQSPLETYLREINEMALLSAEEEKELAARIAKGDKTARERMVRANLRLV 60

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
             I     +  G   L+++I+        +  GF
Sbjct: 61  VNIARGY-VGKG-LALQDLIEEGNLGLLRAVEGF 92


>gi|113953662|ref|YP_731106.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113881013|gb|ABI45971.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 307

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 141/248 (56%), Gaps = 7/248 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 56  KRTIKRGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 115

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ ++     R+       P+ E++A+
Sbjct: 116 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARLMQSNGLAPSAEQLAE 175

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + +P+  V  +L        +SL+  +    D S L D +          + I A   +
Sbjct: 176 CMKLPISEVEDLLGCELRSVTVSLQGVVKSKSDPSELVDVLPSDEIPPMERAEI-AERTD 234

Query: 612 TTTRVLA--SLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +L   +LTP+E  ++ +RFG+ G +   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 235 SAWNLLDNSNLTPKERTIVMLRFGLDGSHEWRTLAEVARQMNCSREYCRQVVQRALRKLR 294

Query: 669 HPSRSKKL 676
             S    L
Sbjct: 295 KTSIQHGL 302


>gi|253701007|ref|YP_003022196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775857|gb|ACT18438.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 325

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 101/284 (35%), Positives = 168/284 (59%), Gaps = 5/284 (1%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
              + + + E K   +   D  +K+   +  I     +   + + +   + +       A
Sbjct: 29  EEVEGWADVEAKLPASEHFDDAIKL--YLIEIRKHALLDAVQEKELALKISQ---GDGDA 83

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +K M+ +NLRLV+ +AK+Y NRG+  LD+I+EGNIGL+KA E+F      +FSTYA WW+
Sbjct: 84  RKRMILSNLRLVVKIAKRYRNRGMPLLDIIEEGNIGLIKAVERFKLSKECRFSTYATWWI 143

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q+I R++ +Q  TIR+PVH+ D+I+++ R  R +  K+ REPT +E+A  L + V+ +R
Sbjct: 144 RQSIERALINQVRTIRLPVHVSDEINRMFRENRVLELKLNREPTAKEVADNLGITVQRLR 203

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +++ + K+  S+E P+G+     L D I+D + V P +     N  E  + +L  L+  E
Sbjct: 204 ELMVVLKKTFSIEQPMGERGDFCLTDTIQDTSTVLPTELLENQNRYELISNLLEFLSETE 263

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++L +RFG+      TL+ +G+ F VTRERIRQIE KA+ KL+
Sbjct: 264 RKILTLRFGLEDKAPQTLDTIGQGFGVTRERIRQIEVKALEKLR 307



 Score = 46.0 bits (107), Expect = 0.019,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 36/107 (33%), Gaps = 2/107 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D    E   E +    +          + K  A    DD +++YL E+    LL    E
Sbjct: 10  EDASLLEVEPEVAAHDEAGEEVEGWADVEAKLPASEHFDDAIKLYLIEIRKHALLDAVQE 69

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
             +A +I  G       +  S L    ++       +    L +II+
Sbjct: 70  KELALKISQGDGDARKRMILSNLRL--VVKIAKRYRNRGMPLLDIIE 114


>gi|146164070|gb|ABQ08718.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
          Length = 292

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 82/335 (24%), Positives = 133/335 (39%), Gaps = 45/335 (13%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       
Sbjct: 1   VRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P                         E +D+  T   I S        
Sbjct: 61  LSDII--SGFIDPN------------------------EAEDMAPTATHIGSELGEDDLA 94

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               +   E+ + D  + D D             +LR +       I             
Sbjct: 95  DEDEEDEDEDEDGDSSDDDGDGGPDPEVAREKFAELRAQYEVTRLSI------------- 141

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               QK+ ++    +     L  +     L   + D LV  + ++ +R+   E  +++L 
Sbjct: 142 ----QKNGRAHDDTQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLC 197

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E +  W  Y K   +      V  + + + +   +++ I  E
Sbjct: 198 VEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVQRAIGKLQQIEEE 256

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           TG+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 257 TGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|148239078|ref|YP_001224465.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847617|emb|CAK23168.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 308

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 140/248 (56%), Gaps = 7/248 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 57  KRTIKRGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FS YA WW++Q + R+++ QS TIRIPV++ +K+ K+  +  R+  +    P+ E++A 
Sbjct: 117 RFSNYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRASKARLMQRNGLSPSTEQLAD 176

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            L +P+  V  +L        +SL+  +    D S L D +  +       + I A    
Sbjct: 177 DLNLPISEVEDLLGCELRSVTVSLQGVVKSKSDPSELVDVLPSEEVPPMERAEI-AERTA 235

Query: 612 TTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  ++L    LTP+E  V+ +RFG+ G N   TL EV +Q   +RE  RQ+  +A+RKL+
Sbjct: 236 SAWKLLDKSNLTPKERTVVMLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLR 295

Query: 669 HPSRSKKL 676
                  L
Sbjct: 296 KTGIQHGL 303


>gi|302746280|gb|ADL62730.1| RpoD [Morganella morganii subsp. morganii]
          Length = 274

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 117/314 (37%), Gaps = 47/314 (14%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            ++I     + P +        E        +   E   +++ + + D +   +   D  
Sbjct: 61  SDLIT--GFVDPNA--------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDSD 110

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                 PE A      L    + +                                Q   
Sbjct: 111 DDNSIDPELARQKFEALRVQHEKAR-------------------------------QQIK 139

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
           ++G+    ++ + + L E    +     L   + D LV  + ++  R+   E  +++L  
Sbjct: 140 IHGRDHPNTNAEIQQLSE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLCV 195

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +   + +  F+    G E    W + A    +  W   +    + + +    ++ I  ET
Sbjct: 196 EQSKMPKKNFITLFTGNETSDSWFTAAVAMNKP-WSEKLQDVAEEVERSLQRLRQIEEET 254

Query: 421 GISISEFRHIVSMV 434
           G++I + + I   +
Sbjct: 255 GLTIEQVKDINRRM 268


>gi|326523529|dbj|BAJ92935.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score =  158 bits (398), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 98/303 (32%), Positives = 163/303 (53%), Gaps = 15/303 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +K   +G W      ++  IL      K ++    IS  E R   S +R+      +
Sbjct: 210 VHLSKKIKDGIWLQQQRSKLTEILGNEPSYKQMAQSLRISTPELR---SRMRESF----L 262

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N+RLVIS+A+KY   G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 263 AREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 322

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S T R+P +M +++  +      + ++    PT + IA+ L +  + V
Sbjct: 323 IRQGVSRALADNSKTFRLPTYMHERLIAIRAAKYALEDQ-GVSPTTQNIAELLNISEKKV 381

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+           GD    +IED+N A  P     +  L+E    +L 
Sbjct: 382 HNATEAVNKALSLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEEWYLKEEVNNLLI 441

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++LT RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R KKL 
Sbjct: 442 SNLTERERHIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKKLD 500

Query: 678 SFL 680
           + L
Sbjct: 501 ALL 503


>gi|6175930|gb|AAF05342.1|AF182106_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 303

 Score =  157 bits (397), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 92/252 (36%), Positives = 158/252 (62%), Gaps = 3/252 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTRERIR 657
           G++  +TRER+R
Sbjct: 292 GREIGLTRERVR 303



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|12045103|ref|NP_072914.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|255660251|ref|ZP_05405660.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|1350862|sp|P47491|RPOD_MYCGE RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1045940|gb|AAC71469.1| RNA polymerase sigma factor RpoD [Mycoplasma genitalium G37]
 gi|166078711|gb|ABY79329.1| RNA polymerase sigma factor RpoD [synthetic Mycoplasma genitalium
           JCVI-1.0]
          Length = 497

 Score =  157 bits (397), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 122/362 (33%), Positives = 206/362 (56%), Gaps = 13/362 (3%)

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
           ++L+   I  ++ +       I++   EL           +  +   +  + D   +   
Sbjct: 133 ITLSNKEIISVLAKFELPEDEIIYVLDELRDKGIQLQHDVEEHIHEFRANQ-DLSIIDED 191

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS-IAKK 446
            +    +  +      D++   R  + S+     +     + I  ++   + E+   A  
Sbjct: 192 IEELTSKNISNRDKVDDNV---RFFLGSLDFSKMLDFESEQRIAKVLNSTDEESRKYAIN 248

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V +NLRLV+S+AKK+  RGL F DLIQEGN+GL+KA  KF+W LG KFSTYA WW+KQ
Sbjct: 249 QLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWWIKQ 308

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL-----AMPVE 561
           AITR+IADQ+ T+RIPVHM + I+++ +  R +  ++ REPT EE+A+K+        V+
Sbjct: 309 AITRAIADQARTVRIPVHMVETINRLAKAERALYQELGREPTDEELAEKMGGQAEGFNVK 368

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASL 620
            + ++ +++ +P+SL+  +G ++ S  GDF++D +A +P +     +  E    +L  +L
Sbjct: 369 KIAEIKRLSLDPVSLDKTVGHDEESQFGDFVKDTDAQTPDEFTESRSNSEKIDELLNNNL 428

Query: 621 TPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL-RS 678
           + +EE ++RMR G+   N   TL+EVG++  + RE+IRQIE KAIRKL+H  R+  +  S
Sbjct: 429 SEQEELIVRMRIGMPPYNEPKTLDEVGQKILIPREKIRQIENKAIRKLRHAVRNNPISMS 488

Query: 679 FL 680
           FL
Sbjct: 489 FL 490


>gi|91783466|ref|YP_558672.1| RNA polymerase sigma factor RpoS [Burkholderia xenovorans LB400]
 gi|296157776|ref|ZP_06840610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
 gi|91687420|gb|ABE30620.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia xenovorans
           LB400]
 gi|295892022|gb|EFG71806.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
          Length = 360

 Score =  157 bits (397), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 198

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 199 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 258

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 259 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 318

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 319 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 355



 Score = 40.6 bits (93), Expect = 0.96,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 38/105 (36%), Gaps = 3/105 (2%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQK--RKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           DL++ +G  D    A   ++         R       T D ++ YL  +    LL+ E E
Sbjct: 41  DLDERQGGADEAGDAREGASEVAPDADDFRALLQAELTADTIQHYLNRISVKPLLTVEEE 100

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 101 QKYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 144


>gi|225621460|ref|YP_002722719.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225216281|gb|ACN85015.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 309

 Score =  157 bits (397), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 103/305 (33%), Positives = 179/305 (58%), Gaps = 12/305 (3%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSIS------------VETGISISEFRHIVSMVR 435
           K     E+K  V+  +  I +IR   K                   +  ++    +  + 
Sbjct: 3   KKDINQEYKGPVSVYLKQIGEIRRLTKEEELDLWQRLEVCRNDRALLENNDDEESLKKIE 62

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           + + E    + ++V++NLRLVIS+AK+Y N G+ F+D+I EGNIGL++A ++F++  G+K
Sbjct: 63  EIDKEIDSIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYKKGFK 122

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTY +WW+KQ+I + I+ +   IR P+H+   I K ++T++ ++ K+ R+PT +EI+K+
Sbjct: 123 FSTYGVWWIKQSIVKEISSKRHIIRFPMHIARLIKKSIQTSKTLTQKLGRDPTIDEISKE 182

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +  + +  ++  T++  S+++   + D + +   IEDKN  SP   A   +LR+T T 
Sbjct: 183 MKIDRKTLSYIMIFTQDTASVDSFFRNSDNNDMTSIIEDKNFPSPHQKAFMDSLRDTLTE 242

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L  +E  V+  R+G+      TLE+ GK+  +TRER+RQI+ KAI+KL   + SK+
Sbjct: 243 ALKCLDEKERTVIISRYGLYGKEAKTLEDTGKELNITRERVRQIQIKAIKKLAGLNLSKE 302

Query: 676 LRSFL 680
           L+SFL
Sbjct: 303 LKSFL 307


>gi|297811483|ref|XP_002873625.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297319462|gb|EFH49884.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 273

 Score =  157 bits (397), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 78/217 (35%), Positives = 129/217 (59%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  +GL   DLIQEG+IGL++ AE+FD   GYK STY  WW+KQAI R+IA +S  +++P
Sbjct: 52  YQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLP 111

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             M +   KV   +  ++ K++R+P+ EEIA+ L + V  VR  ++ ++ P+SL+  +  
Sbjct: 112 GSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLHVSAVRLAVERSRSPVSLDRVVSQ 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                L + +   +   P +   + +++    ++L SLT RE RVL + FG+   T  + 
Sbjct: 172 NGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLNGETPMSF 231

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           EE+GK   ++RER+RQI   A++KL++      L+ +
Sbjct: 232 EEIGKSLKLSRERVRQINGIALKKLRNVHNVNDLKIY 268


>gi|258592807|emb|CBE69116.1| RNA polymerase sigma factor RpoS [NC10 bacterium 'Dutch sediment']
          Length = 286

 Score =  157 bits (397), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 136/247 (55%), Gaps = 1/247 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +     A K++VEANLR V+ VA +Y   GL   DLI EGNIGL++AA ++      
Sbjct: 41  KATQRGDEKALKQLVEANLRFVVKVALRYRGCGLSLPDLINEGNIGLLEAARRYSPDYNV 100

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KF TYA+WW++QAI +++A     +R+P+       ++      +S +++ EPT  E+ +
Sbjct: 101 KFITYAVWWIRQAIMQALAISGGAVRLPLRKARLASQLDDVRADLSQQLQAEPTDSEVTE 160

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L +    +   L    +   L   IG E      +  E K         I+ +LRE   
Sbjct: 161 ELDLSASDLEGALHRAGQLAFLSDEIGLEQRIG-MELYESKQLPPADYELIRRSLREEVE 219

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           R+L SL  RE  ++ +RFG+G     TL+EVGK+  ++RER+RQIE +A +KL   ++S+
Sbjct: 220 RMLRSLNDRERLIVELRFGLGKEEAMTLKEVGKRLKLSRERVRQIEERAKQKLCVWAKSR 279

Query: 675 KLRSFLD 681
            L+ +L+
Sbjct: 280 HLKDYLN 286


>gi|90577776|ref|ZP_01233587.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440862|gb|EAS66042.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 291

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 95/260 (36%), Positives = 152/260 (58%), Gaps = 4/260 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K IS +  ++  +    +   RK  C  + +K  ++E+NLRLV+S+AKKY    +   
Sbjct: 20  YLKEISEKPLLTKEDE---ILYSRKSLCGDACSKNVLIESNLRLVVSIAKKYRGSSIHIS 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLM A EKFD   G++FSTYA WW+KQ I R+I +Q  TIR+PVH+  +I+ 
Sbjct: 77  DLIDEGNIGLMTAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQGRTIRLPVHVSKEINT 136

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGD 590
           ++RT +++  K  +EP+ E +A+ L   ++ V   L      +S +  I  E TS  +  
Sbjct: 137 IIRTHKQLVKKNNQEPSTELVAEVLNKTLDDVSTTLSYDTPIVSYDQSITSEATSQSIAV 196

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D+N+  P +      +++ T  VL  L  R++ ++  RFG+      TL+EV ++  
Sbjct: 197 LIADENSAKPDELVDDLAIQKITANVLKCLNNRDKEIICRRFGLLGYEAQTLQEVAEEVG 256

Query: 651 VTRERIRQIEAKAIRKLKHP 670
           +TRERIRQ++  ++ KLK+ 
Sbjct: 257 LTRERIRQLQVTSLAKLKNS 276



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 43/98 (43%), Gaps = 3/98 (3%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +K+       D V +YL+E+    LL++E EI  +++   G A     L ES L    ++
Sbjct: 5   KKEEQFSHGGDIVHLYLKEISEKPLLTKEDEILYSRKSLCGDACSKNVLIESNLRL--VV 62

Query: 169 IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
               +    +  + ++ID E  IG  +    F   +G 
Sbjct: 63  SIAKKYRGSSIHISDLID-EGNIGLMTAVEKFDPEKGF 99


>gi|26665382|dbj|BAC44902.1| principal sigma factor [Anabaena planctonica TAC421]
          Length = 203

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 112/204 (54%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE +   +P D   +  LRE   +VL SL PRE  VL
Sbjct: 121 SAQSPISLETPIGKEEDSRLGDFIESE-GETPEDQVSKNLLREDLEKVLDSLGPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|124023525|ref|YP_001017832.1| type II alternative sigma factor, sigma70 family [Prochlorococcus
           marinus str. MIT 9303]
 gi|123963811|gb|ABM78567.1| Putative type II alternative sigma factor, sigma70 family protein
           [Prochlorococcus marinus str. MIT 9303]
          Length = 308

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 138/248 (55%), Gaps = 7/248 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R        AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 57  RLTIRRGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+       PT E++ K
Sbjct: 117 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKSRLMQSNGLPPTAEQLVK 176

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + +P+  V  +L        +SL+  +    D S L D +  +       + + A    
Sbjct: 177 TMRLPMAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPSEEIPPMERAEM-AERTA 235

Query: 612 TTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +L  A+LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 236 SVWTLLNRANLTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALRKLR 295

Query: 669 HPSRSKKL 676
                  L
Sbjct: 296 KTGIQSGL 303


>gi|106895864|gb|ABF82640.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|106895884|gb|ABF82644.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC285]
 gi|106895888|gb|ABF82646.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 292

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 135/334 (40%), Gaps = 44/334 (13%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +II            GF    E                          E  A  +    
Sbjct: 61  SDII-----------SGFIDPNE-------------------------TEDMAPTATHIG 84

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           S++       E++E   DEDED  +                   E+   Y          
Sbjct: 85  SELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TR 138

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
           ++ QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  
Sbjct: 139 LSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCV 198

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +   + +  F+      E +  W  Y K   +      V  + + I +   +++ I  ET
Sbjct: 199 EQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEET 257

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           G+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 GLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|186475727|ref|YP_001857197.1| RNA polymerase sigma factor RpoS [Burkholderia phymatum STM815]
 gi|184192186|gb|ACC70151.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phymatum
           STM815]
          Length = 364

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 86  IQHYLNRISVKPLLTVEEEQRYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 142

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 143 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 202

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 203 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 262

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 263 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 322

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 323 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 359



 Score = 41.4 bits (95), Expect = 0.55,   Method: Composition-based stats.
 Identities = 26/114 (22%), Positives = 41/114 (35%), Gaps = 4/114 (3%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSA---SNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
            ++ +D  +  DE GS    +  S      ++      R       T D ++ YL  +  
Sbjct: 36  NVDELDNSNDADERGSRGDEEPDSREGANDSAPDADDFRALLQAELTADTIQHYLNRISV 95

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             LL+ E E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 96  KPLLTVEEEQRYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 148


>gi|124025343|ref|YP_001014459.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123960411|gb|ABM75194.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 307

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 89/254 (35%), Positives = 143/254 (56%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
              S  +K       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+
Sbjct: 50  EYSSAEKKRFKAGERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKY 109

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  ++   P+
Sbjct: 110 DPKRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSRLMQELGVHPS 169

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
             +IA ++ +P+E V ++L        +SL+  +    D S L D +  +       + +
Sbjct: 170 TNQIAIQMKIPLEEVEELLACELRSITVSLQGAVKSKADPSELVDILPSEEVPPMELAEL 229

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +   +L    LTP+E  +L +RFG+ G N   TL EV +Q   +RE  RQ+  +
Sbjct: 230 -AERSASAWSLLDKSNLTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQR 288

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 289 ALRKLRKTGIQSGL 302


>gi|253582113|ref|ZP_04859337.1| RNA polymerase [Fusobacterium varium ATCC 27725]
 gi|251836462|gb|EES64999.1| RNA polymerase [Fusobacterium varium ATCC 27725]
          Length = 275

 Score =  157 bits (396), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 88/257 (34%), Positives = 148/257 (57%), Gaps = 5/257 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +   E  +++   +        +K +++ +NLRLV+++AK Y N+GL F+
Sbjct: 12  YLADIRKYKILDKDEELNLLIKAK---AGDEESKNQLILSNLRLVVNIAKGYINKGLSFI 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+ A EKFD   G++FSTYA+WW+KQ+I++++  +   IRIP +  D ++K
Sbjct: 69  DLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRIPSYKYDLLNK 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V R            P  EEIA +L + V+ ++ ++   ++P+SL T IG  D  +L D 
Sbjct: 129 VNRYVMSRLKDEGNYPPVEEIAAELNIDVDKIQDIIMDFQDPMSLSTQIG--DDIYLEDT 186

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +  +   S  +       R+    ++  L  RE+ +L++R+G+     HTLEE+G    +
Sbjct: 187 LAQQEDFSMEEEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIHTLEEIGNTLNI 246

Query: 652 TRERIRQIEAKAIRKLK 668
           TRER+RQIE K ++KL+
Sbjct: 247 TRERVRQIEKKTLQKLR 263


>gi|218442621|ref|YP_002380941.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
 gi|218174979|gb|ACK73711.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
          Length = 308

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 95/302 (31%), Positives = 162/302 (53%), Gaps = 9/302 (2%)

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI-KSISVETGISISEF 427
            FL+ +         ++ +++   G+            ++ + +  K  SV    S  + 
Sbjct: 9   SFLDSYLKNFTRYELLNSSQEIDLGQKIQKWQKLKHQFVQFQKKTGKKTSVFDFCSDFQL 68

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
               +       E   AK ++V+ NLRLVI++AKKY  RGL F DL+QEGNIGL++AAE 
Sbjct: 69  EE--AEFYLVYEEGQQAKNQLVQGNLRLVINLAKKYLGRGLSFEDLLQEGNIGLIRAAEL 126

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+   GYKFSTYA WW++Q I R+I + + TIR+PVH+  +++++ +T  +++ ++ R P
Sbjct: 127 FEPSKGYKFSTYAYWWIRQQIIRAINNSARTIRLPVHIIARLNRIKKTQHKLAAQLGRTP 186

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T +EIA  L M  + + K  ++ ++ ISL T + ++    L D I D N        + +
Sbjct: 187 TVQEIATSLQMSAQEIEKYREVAQKTISLSTIVDEQGRETLQDLIADPNPQPDFLERVFS 246

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E     + +L PR + +L+ R       + TLE +G    +++ER+RQI  KA+ +L
Sbjct: 247 --YEQILEKMETLPPRYQDILKKRI----YEEQTLEAIGTSTKLSKERVRQIFQKALSRL 300

Query: 668 KH 669
           + 
Sbjct: 301 RE 302


>gi|91978907|gb|ABE66429.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 291

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 135/334 (40%), Gaps = 44/334 (13%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +II            GF    E                          E  A  +    
Sbjct: 61  SDII-----------SGFIDPNE-------------------------TEDMAPTATHIG 84

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           S++       E++E   DEDED  +                   E+   Y          
Sbjct: 85  SELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TR 138

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA- 360
           ++ QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  
Sbjct: 139 LSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCV 198

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           +   + +  F+      E +  W  Y K   +      V  + + I +   +++ I  ET
Sbjct: 199 EQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEET 257

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           G+SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 GLSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 291


>gi|307729587|ref|YP_003906811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
 gi|307584122|gb|ADN57520.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
          Length = 362

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMNSGDAAERRDASIDDIAYLTGKTADEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357


>gi|224000633|ref|XP_002289989.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220975197|gb|EED93526.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 321

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 93/263 (35%), Positives = 149/263 (56%), Gaps = 12/263 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            + R+    A  AK+ MV+ N+RLV+S+A++Y   G+   DL+QEG++GL +AAEKFD  
Sbjct: 50  RLFREMMLTAKEAKQRMVQCNMRLVVSIARRYHGVGVNVQDLVQEGSLGLARAAEKFDPK 109

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+KFSTYA WW++QA+ RSIA  S TIR+PVH+ + ++KV R  + +  ++ R PT EE
Sbjct: 110 KGFKFSTYASWWIQQAVFRSIAYHSRTIRLPVHVHNLLNKVRRARQVLQQELGRTPTNEE 169

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETP--------IGDEDTSHLGDFIEDK----NAVS 599
           +A ++ M +E   K+++ T+  ISLE P        +G E  + +GD ++      +  +
Sbjct: 170 MAVEMDMTIEKYNKMIRTTRNAISLERPKYKNNPKDLGHESEALVGDMVDSSAVIFDEKT 229

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P  +     L      +L  L   E  VL +R+GI      T+  V  +   T+  +R  
Sbjct: 230 PEQNVDHGLLHNDIEYMLGKLGEDERSVLCLRYGINDGITRTVTLVASEMRQTKSWVRSQ 289

Query: 660 EAKAIRKLKHPSRSKKLRSFLDG 682
           E +A+RKL+ P   K+L+   + 
Sbjct: 290 ECRALRKLRRPWYEKRLKEHRES 312


>gi|149200222|ref|ZP_01877244.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149136664|gb|EDM25095.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 279

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 154/274 (56%), Gaps = 5/274 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             I++ ++SI+    +S+ +   +  ++      +  A+++++ ANL+LV+ +A  Y + 
Sbjct: 6   ESIKSYMQSIATLPLVSVEDEIELAKLIE---AGSEDAREKLIIANLKLVVKIAHDYKSL 62

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLI EGNIGLMKA EKF    G KFS+Y  WW+KQAI R++A+Q   IRIPV   
Sbjct: 63  GVPLADLISEGNIGLMKAVEKFRPGHGAKFSSYGAWWIKQAIRRAVAEQGRVIRIPVQSA 122

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDT 585
            KI K+   A  ++ K+ R P+ EE+A+     V  VR +   +  P +SL T +   + 
Sbjct: 123 VKIRKIHHEAMLLAEKLGRVPSMEEVAEATGFSVRSVRGMSVASTAPAVSLNTTLKTGEE 182

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEE 644
             L D I D     P D+  + ++++    V+   LT RE+ +++MR+G+  +   TLEE
Sbjct: 183 GVLEDVIPDTLLKLPGDNMNETDVKQVLLEVIDSKLTEREQMIIKMRYGLDGHQQKTLEE 242

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +      TRER+RQI+ +A+RKL     S  L S
Sbjct: 243 LSDMVGRTRERVRQIQYQALRKLYAHLDSDILAS 276



 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++ Y++ + ++ L+S E EI +AK IEAG       L  + L  + ++    +       
Sbjct: 8   IKSYMQSIATLPLVSVEDEIELAKLIEAGSEDAREKLIIANL--KLVVKIAHDYKSLGVP 65

Query: 181 LREII 185
           L ++I
Sbjct: 66  LADLI 70


>gi|161899381|ref|XP_001712917.1| sigma 2 transcription factor [Bigelowiella natans]
 gi|75756411|gb|ABA27305.1| sigma 2 transcription factor [Bigelowiella natans]
          Length = 389

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 102/288 (35%), Positives = 174/288 (60%), Gaps = 3/288 (1%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
           EW   +    D  LK+ N++         +      + S +++      I+K+ +++ +L
Sbjct: 101 EWVKDLLRWEDLFLKLENKLGFYPTIDFFTKG-IIDLTSEIKERLAIGKISKEILIKRSL 159

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           +L+IS+AK+Y   GL F DLI EG +GLMK   K+D+  G+KFSTYA WW++Q+I+RSI 
Sbjct: 160 KLIISIAKRYNGCGLSFEDLIAEGILGLMKGIRKYDFSKGHKFSTYAHWWIRQSISRSID 219

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           DQS  IR+PV++++ + K+ +   +     KR PT EEI+  + +P++ +RK+L    + 
Sbjct: 220 DQSRIIRLPVYVKEILSKINKIKNKFYEDKKRYPTEEEISLLIGIPLKKLRKLLLSCNDL 279

Query: 574 ISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           ISL++ I ++  D++ L D IED   ++    AI+ +L++   + L +L+ RE  V+R+R
Sbjct: 280 ISLDSLIENDSNDSNMLNDSIEDSKVINSEVYAIEKSLKQDLNKALLTLSDRESAVIRLR 339

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +G+    + TLEE+G+   VTRER RQIE KA++KL+  + +     +
Sbjct: 340 YGLDDGNERTLEEIGEYLNVTRERARQIEIKALKKLQFNTSNYLFSDY 387


>gi|15558898|dbj|BAB64922.1| chloroplast RNA polymerase sigma factor [Chlamydomonas reinhardtii]
          Length = 250

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 88/241 (36%), Positives = 147/241 (60%), Gaps = 8/241 (3%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK+ ++++N +LV++V K +  +G    DL+ EG  GL+K  EK+D   G++F TYA WW
Sbjct: 7   AKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGFRFGTYAHWW 66

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++QA++RS+A+    +R+P+HM +++ ++   + ++  ++ REPT  E+AK   +PV  V
Sbjct: 67  IRQAVSRSLAETGRAVRLPMHMIEQLTRLKNLSAKLQTQLAREPTLPELAKAAGLPVTRV 126

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ---ANLRETTTRVLASL 620
           + +++  +   SL+TPI     + LG  ++D        +  +    +LR     +L  L
Sbjct: 127 QMLMETARSAASLDTPI---GGNELGPTVKDSVEDEREAADEEFGSDSLRNDMEAMLLEL 183

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS--RSKKLRS 678
             RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL+  +   S KL  
Sbjct: 184 PEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKLRVKTIDVSGKLME 243

Query: 679 F 679
           +
Sbjct: 244 Y 244


>gi|89074640|ref|ZP_01161105.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89049578|gb|EAR55138.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 284

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 95/265 (35%), Positives = 152/265 (57%), Gaps = 4/265 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I  I   +K IS +  ++  +  H     RK     + AK++++E+NLRLV+S+AKKY 
Sbjct: 5   EIDMIGLYMKDISSKPLLTKMDEIHYS---RKYLRGDNKAKEKLIESNLRLVVSIAKKYR 61

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              L   D+I EGN+GL+ A EKFD   G++FSTYA WW+KQ I R+I +Q+  IR+PVH
Sbjct: 62  AAHLLLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQNRAIRLPVH 121

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +I+ ++RT R +  K   EPT E+IA +L    + +  +L      +SL+  IGD++
Sbjct: 122 VSKEINALLRTHRDLMKKQNHEPTHEDIALQLNKETQDISTLLSYELNIVSLDQTIGDDE 181

Query: 585 T-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   +   + D+   SP     + ++      +L  + PRE  +L  RFG+      TL+
Sbjct: 182 SKGTIASLVVDEQIPSPSHIVEENSMVNLAEGLLNKIKPREREILCRRFGMMGYEPQTLQ 241

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           EV     +TRER+RQ++ K++ +LK
Sbjct: 242 EVASALGLTRERVRQLQMKSLERLK 266



 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 9/93 (9%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D + +Y++++ S  LL++  EI  +++   G       L ES L     I  +      
Sbjct: 6   IDMIGLYMKDISSKPLLTKMDEIHYSRKYLRGDNKAKEKLIESNLRLVVSIAKKYRAAH- 64

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             LL ++ID       E   G     E    +K
Sbjct: 65  -LLLGDMID-------EGNLGLITAVEKFDPEK 89


>gi|239993653|ref|ZP_04714177.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 231

 Score =  157 bits (396), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/177 (33%), Positives = 91/177 (51%), Gaps = 3/177 (1%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           +        K +I   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V +   
Sbjct: 1   MAQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAP 60

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
             DE   +++     +A  ++  L   + S    T DPVRMY+REMG++ELL+REGEI I
Sbjct: 61  DADELLMQEANADEDAAEAAAQALATVE-SEIGRTTDPVRMYMREMGTVELLTREGEIEI 119

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           AKRIE G   +  S+ E P     L+   D        L +II     + P  +   
Sbjct: 120 AKRIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDII--SGFVDPNDEQDL 174


>gi|323526138|ref|YP_004228291.1| RNA polymerase sigma-70 subunit RpoD subfamily [Burkholderia sp.
           CCGE1001]
 gi|323383140|gb|ADX55231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1001]
          Length = 358

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 103/315 (32%), Positives = 170/315 (53%), Gaps = 11/315 (3%)

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L+  QG E        A+  P+ +    +     +   I++ +  ISV+  +++ E +  
Sbjct: 42  LDDRQGAEEGEAREGAAEAVPDADDFRALLQAELTADTIQHYLNRISVKPLLTVEEEQKY 101

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
             + + GE E   A++ M+E NLRLV+S+AK Y NRG+  LDLI+EGN+GLM A EKFD 
Sbjct: 102 SRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGVPLLDLIEEGNLGLMHAIEKFDP 158

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR----- 545
             G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +           
Sbjct: 159 TRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEKNSMNSGEAA 218

Query: 546 ---EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
              + + ++IA       + V  +L + +   SL+ P+  +  S L D + D  + SP  
Sbjct: 219 ERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPLDLDPASSLLDLLSDDQSQSPDA 278

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                 L   T   LA L+ +   V+  RFG+      TLEE+  +  +TRER+RQI+ +
Sbjct: 279 EVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPATLEELADEMGLTRERVRQIQQE 338

Query: 663 AIRKLKHPSRSKKLR 677
           A+ +LK    S  +R
Sbjct: 339 ALVRLKRFFASNGVR 353



 Score = 41.4 bits (95), Expect = 0.48,   Method: Composition-based stats.
 Identities = 25/102 (24%), Positives = 38/102 (37%), Gaps = 1/102 (0%)

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           L+D +G+E+      +A         R       T D ++ YL  +    LL+ E E   
Sbjct: 42  LDDRQGAEEGEAREGAAEAVPDADDFRALLQAELTADTIQHYLNRISVKPLLTVEEEQKY 101

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 102 SRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 142


>gi|78212534|ref|YP_381313.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78196993|gb|ABB34758.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 309

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 86/254 (33%), Positives = 138/254 (54%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 +        AK +M+ +NLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+
Sbjct: 52  EYSDEEKGVIRRGERAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKY 111

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +    P+
Sbjct: 112 DPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNGLSPS 171

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            E++A+ + +P+  V  +L        +SL+  +    D S L D +          + I
Sbjct: 172 GEQLAEFMEIPIAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPSDELPPMERAEI 231

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +   +LA   LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 232 -AERTASVWSLLAKANLTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQR 290

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 291 ALRKLRKTGIQSGL 304


>gi|72381853|ref|YP_291208.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL2A]
 gi|72001703|gb|AAZ57505.1| possible type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
          Length = 307

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 91/284 (32%), Positives = 151/284 (53%), Gaps = 12/284 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  EV +++ +    +                 S  +K       AK +M+ ANLRLV++
Sbjct: 25  LGREVQAMVALNERCQQAGGHGP-----ECEYSSAEKKKFKAGERAKNQMITANLRLVVN 79

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q + R+++ QS T
Sbjct: 80  LAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAYWWIRQGLNRALSTQSRT 139

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISL 576
           IRIPV++ +K+ K+     R+  ++   P+  +IA ++ +P+E V ++L        +SL
Sbjct: 140 IRIPVNINEKLTKLRAAKSRLMQELGVHPSTNQIAIQMKIPLEEVEELLACELRSITVSL 199

Query: 577 ETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--LTPREERVLRMRFG 633
           +  +    D S L D +  +       + + A    +   +L    LTP+E  +L +RFG
Sbjct: 200 QGAVKSKADPSELVDILPSEEVPPMELAEL-AERSASAWSLLDKSNLTPKERTILSLRFG 258

Query: 634 I-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + G N   TL EV +Q   +RE  RQ+  +A+RKL+       L
Sbjct: 259 LDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLRKTGIQSGL 302


>gi|23978340|dbj|BAC21139.1| principal sigma factor [Stanieria cyanosphaera str. PCC 7437]
          Length = 203

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 110/204 (53%), Positives = 150/204 (73%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   ++ LRE    VL +L+P E  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDQVSKSLLREDLENVLDTLSPSERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|295676469|ref|YP_003604993.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
 gi|295436312|gb|ADG15482.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
          Length = 362

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 200

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 201 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 260

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 261 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 321 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 357



 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 41/107 (38%), Gaps = 5/107 (4%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKD----SADRSTDDPVRMYLREMGSIELLSRE 137
           DL++ +G  D  + A +  ++   L    D         T D ++ YL  +    LL+ E
Sbjct: 41  DLDERQGGLDDSEGADARESTGDALPDADDFRALLQAELTADTIQHYLNRISVKPLLTVE 100

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 101 EEQKYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 146


>gi|215270885|emb|CAR48120.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
 gi|215270889|emb|CAR48122.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
 gi|215270891|emb|CAR48123.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
          Length = 291

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 135/332 (40%), Gaps = 43/332 (12%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+REMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L +
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTD 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I     + P++           +     + S+ +  ++ +E   D E +   S D    
Sbjct: 61  LI--SGFVDPDAD----DTAAPTATHIGSELSETQLEEEDEEDLEDDEESDDDSDDSEED 114

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           V   PE A                             +   +++   Y+ L+      + 
Sbjct: 115 VGIDPELA-----------------------------LEKFNQLRSTYQNLQ------LA 139

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             +    S K  V  E ++ +     L   + D LV +L     R+   E  +++    Y
Sbjct: 140 INEYGYDSPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEY 199

Query: 364 G-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           G + +  F+    G E    W+       +  +   +    + I +   ++K I  ET +
Sbjct: 200 GKMPKKSFIALFTGNESSDAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSL 258

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 259 NVQNIKDISRRMSIGEAKARRAKKEMVEANLR 290


>gi|149183340|ref|ZP_01861778.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
 gi|148848937|gb|EDL63149.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
          Length = 330

 Score =  156 bits (395), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 117/221 (52%), Positives = 157/221 (71%), Gaps = 3/221 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     +S  E   + + +         AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 113 VRMYLKEIGRVDLLSAQEEISLANRIE---EGDEEAKRRLAEANLRLVVSIAKRYVGRGM 169

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 170 LFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 229

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REP+PEEIA+++ +  E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 230 INKLIRVQRQLLQDLGREPSPEEIAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHL 289

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           GDFIED  A SP + A    L+E    VL +LT REE VLR
Sbjct: 290 GDFIEDAEAQSPSEHAAYELLKEQLEDVLDTLTDREENVLR 330



 Score =  116 bits (291), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 110/262 (41%), Gaps = 13/262 (4%)

Query: 28  DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
           D   +++++L ++RG +T E++   L   E+ S+ M++    L   G+ +++    E+EE
Sbjct: 24  DQVKEQLMELGKKRGVLTYEDIAEKLANFELESDTMDEFYEQLGEQGVEIIN----ENEE 79

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             + ++   + A +    L           +DPVRMYL+E+G ++LLS + EI++A RIE
Sbjct: 80  DDDPNIQQLNKADDEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAQEEISLANRIE 139

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G       L E+ L     I  R  +  G   L  I         E   G     E   
Sbjct: 140 EGDEEAKRRLAEANLRLVVSIAKRY-VGRGMLFLDLI--------QEGNMGLIKAVEKFD 190

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           Y+K    S        Q     I   A+  +     V++  +      + L +   + + 
Sbjct: 191 YRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSP 250

Query: 268 TLSAMEDQLRPKVMCALDEIAE 289
              A E  L P+ +  + +IA+
Sbjct: 251 EEIAEEMDLTPEKVREILKIAQ 272


>gi|296535367|ref|ZP_06897567.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
 gi|296264309|gb|EFH10734.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
          Length = 1063

 Score =  156 bits (395), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 91/261 (34%), Positives = 147/261 (56%), Gaps = 12/261 (4%)

Query: 417  SVETGISISEFRHIVSMVRKG---------ECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            S   G  ++  R   S  ++                A++E+VE NL+ V+ +A++Y    
Sbjct: 791  SNHAGHELAALRRPASRAQQRAGLAGLSDAFQRYIDARQEIVEGNLKRVVWLARRYARAA 850

Query: 468  LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
            + FLDL+QEG IGL++A ++FD   G++F TYA WW++Q+++R + DQ  T+R+PVHM +
Sbjct: 851  VPFLDLVQEGQIGLLRAIDRFDPDRGFRFGTYATWWIRQSMSRYVQDQGRTVRVPVHMLE 910

Query: 528  KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTS 586
            +I K  R +  +  K    PTP+E+A  L   V  V + L    E IS +      ++ +
Sbjct: 911  RIAKAKRASEALRAKTGVVPTPQELAAALEADVVSVERALAADLEGISFDDMGSLPDEDA 970

Query: 587  HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             L   + D+   +PL + +  +LR      L  L  R+ R++ +RFG+      TLEEVG
Sbjct: 971  ALVAPLVDE--ATPLTALLHHDLRRLLAASLRRLDARQARIIDLRFGLTDGNPLTLEEVG 1028

Query: 647  KQFCVTRERIRQIEAKAIRKL 667
            + + VTRERIRQIEAK++++L
Sbjct: 1029 QFYGVTRERIRQIEAKSLKRL 1049


>gi|290796534|gb|ADD64837.1| RNA polymerase sigma factor [Xanthomonas dyei]
          Length = 283

 Score =  156 bits (395), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 134/327 (40%), Gaps = 49/327 (14%)

Query: 53  LPPDEVSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           LP D V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +     
Sbjct: 1   LPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAAALT 60

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
             D+    T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+
Sbjct: 61  ALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLL 120

Query: 169 IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG 228
              +   +G   L EI+            GF    E         ++      D    + 
Sbjct: 121 ADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDE 169

Query: 229 DIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
           D +        +     + P+  E                           V   ++ +A
Sbjct: 170 DDDEDGDDDAAEEEAGPTGPDPVE---------------------------VATRMENLA 202

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
             Y + + +        K+          +E +  +  +L L     D LV QL  +   
Sbjct: 203 NEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNG 256

Query: 349 IMHNEGELLRLAQS-YGIKRDVFLERH 374
           I  +E ++L LA +   + R  F+   
Sbjct: 257 IKDHERKVLHLATTVARMPRKDFIRSW 283


>gi|148241197|ref|YP_001226354.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849507|emb|CAK27001.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 324

 Score =  156 bits (395), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 96/242 (39%), Positives = 156/242 (64%), Gaps = 1/242 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +++R+       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD  
Sbjct: 77  AVLRRRLINGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 136

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E
Sbjct: 137 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITETLNKLKKGQRELSQELGRTPTVGE 196

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ L +P   V+ +L   ++P+SLE  +GD D + L + +++ +A  P +      L+ 
Sbjct: 197 LAEFLELPEPEVKDLLSRARQPVSLEMKVGDSDDTELCELLQN-DAPMPHELVDGDCLKG 255

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L P + RVL+MR+GI +    +L  +G++  ++R+R+R +E   +  L+  S
Sbjct: 256 DMRSLLEQLPPLQGRVLKMRYGIDVEEPMSLTGIGRELGMSRDRVRNLERDGLAGLRRLS 315

Query: 672 RS 673
            +
Sbjct: 316 EA 317



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS E EI + ++++ 
Sbjct: 15  DLVRSYLRDIGRVPLLSHEQEITLGRQVQE 44


>gi|89073765|ref|ZP_01160279.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89050540|gb|EAR56032.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 291

 Score =  156 bits (395), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 94/260 (36%), Positives = 151/260 (58%), Gaps = 4/260 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K IS +  ++  +    +   RK     + +K  ++E+NLRLV+S+AKKY    +   
Sbjct: 20  YLKDISEKPLLTKDDE---ILYSRKSLSGDAYSKNVLIESNLRLVVSIAKKYRGSSIHIS 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGLM A EKFD   G++FSTYA WW+KQ I R+I +Q  TIR+PVH+  +I+ 
Sbjct: 77  DLIDEGNIGLMTAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQGRTIRLPVHVSKEINT 136

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGD 590
           ++RT +++  K  +EP+ E +A+ L   ++ +   L      +S +  I  E +S  +  
Sbjct: 137 IIRTHKQLVKKNNQEPSTELVAEVLNKTLDDISTTLSYDTPIVSYDQSITSEASSQSIAV 196

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D+N+  P D      +++ TT VL  L  R++ ++  RFG+      TL+EV  +  
Sbjct: 197 LIADENSAKPDDLVDDLAIQKITTNVLNCLNNRDKEIICRRFGLLGYEAQTLQEVADEVG 256

Query: 651 VTRERIRQIEAKAIRKLKHP 670
           +TRERIRQ++  ++ KLK+ 
Sbjct: 257 LTRERIRQLQVTSLAKLKNS 276



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/98 (22%), Positives = 44/98 (44%), Gaps = 3/98 (3%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +K+       D V +YL+++    LL+++ EI  +++  +G A     L ES L    ++
Sbjct: 5   KKEEQFSHGGDIVHLYLKDISEKPLLTKDDEILYSRKSLSGDAYSKNVLIESNLRL--VV 62

Query: 169 IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
               +    +  + ++ID E  IG  +    F   +G 
Sbjct: 63  SIAKKYRGSSIHISDLID-EGNIGLMTAVEKFDPEKGF 99


>gi|260219679|emb|CBA26524.1| RNA polymerase sigma factor rpoS [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 340

 Score =  156 bits (394), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 91/277 (32%), Positives = 149/277 (53%), Gaps = 11/277 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ +      +  +   + +  R        A++ M+E NLRLVIS+AK Y  RG+   
Sbjct: 66  YLRGVRRTPLFTPEQEFEVATRAR---AGDFAARQSMIEHNLRLVISIAKGYAGRGVPMS 122

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GLM A +KF+   G++FSTYA WW++Q++ R++  Q   +R+PV++  ++ +
Sbjct: 123 DLIEEGNLGLMHAIDKFEPERGFRFSTYATWWIRQSVDRALMYQGRAVRLPVNVVREVQQ 182

Query: 532 VVRTARRMSN------KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DED 584
           V+R  R + N      +       E+IA  L      V  +L + + P SL+       D
Sbjct: 183 VLRARRLLENDAVLLAQRPEGIRVEDIAALLGRDAVDVTDLLAMAEAPRSLDARNDAGGD 242

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              LGD + D  A +P  +A+   +     + +A+L PRE+ VL  RFG+      TLE 
Sbjct: 243 EHSLGDSLADTLAAAPDSTALAHEVDALLEQWIATLNPREQEVLEARFGLHDRDPETLET 302

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHP-SRSKKLRSFL 680
           + ++  +TRER+RQI+ +A+ KLK   +R    R FL
Sbjct: 303 LSERLGLTRERVRQIQNEALFKLKRYLARRGIKREFL 339



 Score = 46.0 bits (107), Expect = 0.019,   Method: Composition-based stats.
 Identities = 25/122 (20%), Positives = 40/122 (32%), Gaps = 10/122 (8%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD-RSTDDPVRMYLREMGSIELLSR 136
           V+ D   +   + D     +    +   L   +D +      D + +YLR +    L + 
Sbjct: 19  VEQDLEPNNPLAPDPCARTAPDFIAKEALIAEEDPSTLEQGPDALSVYLRGVRRTPLFTP 78

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALII---------WRDELNDGTTLLREIIDL 187
           E E  +A R  AG      S+ E  L     I            D + +G   L   ID 
Sbjct: 79  EQEFEVATRARAGDFAARQSMIEHNLRLVISIAKGYAGRGVPMSDLIEEGNLGLMHAIDK 138

Query: 188 EA 189
             
Sbjct: 139 FE 140


>gi|301320481|gb|ADK69124.1| putative RNA polymerase sigma factor RpoD [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 506

 Score =  156 bits (394), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 128/335 (38%), Positives = 184/335 (54%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     I     ++  +      M V     +    + +++E+NL+LVISVA+K+ NRG
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 290

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP  +EIA +    +  + V ++ K++ EP+SLE P GDED 
Sbjct: 291 TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPFGDEDD 350

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI----------- 634
           +H GDF+EDK+ VSP +   +  L+E   +V   + PREE+V+RMR+GI           
Sbjct: 351 THFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRL 410

Query: 635 ----GMNTDHTLEEVGKQF---------------------------------------CV 651
                      L++  ++                                         V
Sbjct: 411 TQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEEVGKELNV 470

Query: 652 TRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
           TRERIRQIEAK IRKLK PS + K    L+ F  G
Sbjct: 471 TRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|209522220|ref|ZP_03270857.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
 gi|209497349|gb|EDZ97567.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
          Length = 363

 Score =  156 bits (394), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 85  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 141

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 142 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 201

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 202 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 261

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 262 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 321

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 322 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 358



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 39/107 (36%), Gaps = 5/107 (4%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKD----SADRSTDDPVRMYLREMGSIELLSRE 137
           DL++ +   D  + A +   +   L    D         T D ++ YL  +    LL+ E
Sbjct: 42  DLDERQSGLDDSEGADAREGTGDALPDADDFRALLQAELTADTIQHYLNRISVKPLLTVE 101

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E   ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 102 EEQKYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 147


>gi|23978372|dbj|BAC21150.1| principal sigma factor [Synechococcus sp. PCC 7001]
          Length = 203

 Score =  156 bits (394), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 109/204 (53%), Positives = 147/204 (72%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++  RLV+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSKFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S +  R+PT EEIA+ + M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P     +  LRE    VLA+L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-ADIENPEQDVAKNLLREDLEGVLATLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFDVT 203


>gi|26665384|dbj|BAC44903.1| principal sigma factor [Gloeobacter violaceus PCC 8105]
          Length = 203

 Score =  156 bits (394), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 109/204 (53%), Positives = 148/204 (72%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+A KY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIALKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVHLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDF E  +  +P D   +  LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFSE-ADGETPEDKVAKNLLREDLEAVLNTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQLFNVT 203


>gi|223994539|ref|XP_002286953.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220978268|gb|EED96594.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 298

 Score =  156 bits (394), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 79/287 (27%), Positives = 148/287 (51%), Gaps = 10/287 (3%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRH----IVSMVRKGECEASIAKKEMVEANLRLV 456
               S+L++R+++  I   +  S +++       V  +     +   ++ +++  N+ LV
Sbjct: 15  KSFRSVLRVRDQLVGIRQLSEPSEAQWASACSLTVEQLNDIMNKGQESRTKLITGNVGLV 74

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
             +AK+Y N      +LIQEG +G+M+AAE++D   G++FSTY   W++Q I R+IA+ S
Sbjct: 75  TLIAKRYYN---MLRNLIQEGYMGIMEAAERYDPSKGFRFSTYGTHWIRQRIVRAIAESS 131

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             IR+PVH++  I  + +        I R P+  E+A ++ + ++ +     +++  ISL
Sbjct: 132 RMIRLPVHVQATIRNINKKHEEFEATIGRSPSLPELAHEMGVSLDKLHLYQHLSRNVISL 191

Query: 577 E---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           E        ED   LGD I      +P + A+   LR     +L +L   E  VL  RFG
Sbjct: 192 ERAVDQHSPEDNRTLGDRIACTELPTPDEDAMSEALRGEVHSMLDALRDNERIVLTHRFG 251

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +      TL+E      ++ + +R +EAKA+ +L+ P  + +++ ++
Sbjct: 252 LDDGRPKTLKETAYGMGISIDSVRAVEAKALNRLRQPQLNYRVKDYV 298


>gi|237653675|ref|YP_002889989.1| RNA polymerase sigma factor RpoS [Thauera sp. MZ1T]
 gi|237624922|gb|ACR01612.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thauera sp. MZ1T]
          Length = 312

 Score =  156 bits (393), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 91/254 (35%), Positives = 149/254 (58%), Gaps = 3/254 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++  E   I   VR        A++ M+E NLRLV+++AK Y NRG+ 
Sbjct: 43  QLYLNEIGANPLLTAEEELVIARRVR---MGDFDARQTMIERNLRLVVNIAKHYLNRGIP 99

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDL++EGN+GLM A EKFD   G++FSTYA WW++Q I R+I +QS TIR+PVH+  ++
Sbjct: 100 LLDLVEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKEL 159

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           ++V+R  R +      E + E+IA +L   +E VR +L + +   SL+ P+  + +  +G
Sbjct: 160 NQVLRAQRHIEADCNGESSLEQIANRLGKTIEEVRSILALGEHTASLDAPLDIDPSLSIG 219

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + + D+  +S       + + +     LA L  ++  V+R R+GI      TLEE+ ++ 
Sbjct: 220 ESLADEQHISADLRIQCSEVEQLVREWLAILNDKQRMVIRHRYGIDECELLTLEELAERL 279

Query: 650 CVTRERIRQIEAKA 663
            +TRER+RQI+ +A
Sbjct: 280 ELTRERVRQIQLEA 293



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/130 (16%), Positives = 47/130 (36%), Gaps = 9/130 (6%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           ++  + +  E   +            Q      +    D  ++YL E+G+  LL+ E E+
Sbjct: 2   EEPVNLDELESQQEPDLPPEVEVFSFQAPPVVENEFFSDVTQLYLNEIGANPLLTAEEEL 61

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IA+R+  G      ++ E  L    ++       +    L ++++       E   G  
Sbjct: 62  VIARRVRMGDFDARQTMIERNLRL--VVNIAKHYLNRGIPLLDLVE-------EGNLGLM 112

Query: 201 HGTEGHSYQK 210
           H  E    ++
Sbjct: 113 HALEKFDPER 122


>gi|215270887|emb|CAR48121.1| RNA polymerase sigma factor [Vibrio parahaemolyticus]
          Length = 291

 Score =  156 bits (393), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 134/332 (40%), Gaps = 43/332 (12%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+REMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L +
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTD 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I     + P++           +     + S+ +  ++ +E   D E +   S D    
Sbjct: 61  LI--SGFVDPDAD----DTAAPTATHIGSELSETQLEEEDEEDLEDDEESDDDSDDSEED 114

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           V   PE A                             +   +++   Y+ L+      + 
Sbjct: 115 VGIDPELA-----------------------------LEKFNQLRSTYQNLQ------LA 139

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             +    S K  V  E ++ +     L   + D LV +L     R+   E  ++     Y
Sbjct: 140 INEYGYDSPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMNSVVEY 199

Query: 364 G-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           G + +  F+    G E    W+       +  +   +    + I +   ++K I  ET +
Sbjct: 200 GKMPKKSFIALFTGNESSDAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSL 258

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 259 NVQNIKDISRRMSIGEAKARRAKKEMVEANLR 290


>gi|149921691|ref|ZP_01910139.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149817429|gb|EDM76901.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 384

 Score =  156 bits (393), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 92/252 (36%), Positives = 146/252 (57%), Gaps = 1/252 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR      R+          +  +ANLRLV+S+A++ +N  L   DLIQEGNIGL+KA E
Sbjct: 133 FRIFHERCRRTAGRVRKYTNDFAKANLRLVVSLARRLSNGRLPLQDLIQEGNIGLLKAIE 192

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G++FSTYA WW++ +I+R+I ++   +R+PVH+ D   K+ R  RR   +I RE
Sbjct: 193 RFDHRKGFRFSTYASWWIRHSISRAIYNKGRQVRLPVHVYDVHQKITRVRRRYEAQIGRE 252

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           PT EEIA ++ +P+  V K+  I   P +SL+ P+   D     D +ED+ +  P     
Sbjct: 253 PTHEEIANEIGVPLAKVEKIAAIELGPIVSLDAPLSRNDDRSGVDLLEDQVSPGPGFELE 312

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L E     L++L P E  +LR R+G+      TL E+G+++ ++RERIRQ++ +A+ 
Sbjct: 313 LGELEEGLEDALSALRPMEADILRRRYGLDGVEKETLREIGERYALSRERIRQLQERAVS 372

Query: 666 KLKHPSRSKKLR 677
           +++     + L 
Sbjct: 373 RMREEFARRSLM 384


>gi|328480117|gb|EGF49090.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus MTCC
           5462]
          Length = 206

 Score =  156 bits (393), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 110/193 (56%), Positives = 146/193 (75%), Gaps = 3/193 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I   + ++  E    V++  K E     AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 16  VRMYLKEIGRVSLLTADEE---VALALKIEQGDQEAKQRLAEANLRLVVSIAKRYVGRGM 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 73  QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 132

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K++R  R++   + REPTPEEI  ++ MP E VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 133 INKLIRIQRQLLQDLGREPTPEEIGAEMDMPTEKVREILKIAQEPVSLETPIGEEDDSHL 192

Query: 589 GDFIEDKNAVSPL 601
           GDFIED++A SP 
Sbjct: 193 GDFIEDQDATSPE 205



 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/110 (28%), Positives = 45/110 (40%), Gaps = 9/110 (8%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
           +      +    +DPVRMYL+E+G + LL+ + E+A+A +IE G       L E+ L   
Sbjct: 1   MSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKIEQGDQEAKQRLAEANLRLV 60

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
             I  R  +  G   L  I         E   G     E   Y+K    S
Sbjct: 61  VSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVEKFDYRKGFKFS 101


>gi|13508091|ref|NP_110040.1| RNA polymerase sigma factor [Mycoplasma pneumoniae M129]
 gi|2500786|sp|P78022|RPOD_MYCPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1674175|gb|AAB96132.1| Sigma-70 Factor Family [Mycoplasma pneumoniae M129]
 gi|301633308|gb|ADK86862.1| RNA polymerase sigma factor RpoD [Mycoplasma pneumoniae FH]
          Length = 499

 Score =  156 bits (393), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 109/272 (40%), Positives = 174/272 (63%), Gaps = 8/272 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEAS-IAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           + S+     +     + I  ++   + E+   A  ++V +NLRLV+S+AKK+  RGL F 
Sbjct: 216 LGSLDSSKMLDFESEQRIAKVLNSTDEESRKYAINQLVTSNLRLVVSIAKKHLERGLDFN 275

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL+KA  KF+W LG KFSTYA WW+KQAITR+IADQ+ T+RIPVHM + I++
Sbjct: 276 DLIQEGNLGLLKAISKFNWSLGNKFSTYATWWIKQAITRAIADQARTVRIPVHMVETINR 335

Query: 532 VVRTARRMSNKIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           + +  R ++ ++ REPT EE+A+K+        V+ + ++ +++ +P+SL+  +G ++ S
Sbjct: 336 LAKAERALNQELGREPTAEELAEKMGGQAEGFTVKKIAEIKRLSLDPVSLDKTVGHDEES 395

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGI-GMNTDHTLEE 644
             GDF+ D +A  P +     +  E    +L + L+ +EE ++RMR G+   N   TL+E
Sbjct: 396 QFGDFVRDTDAQMPDEFTESRSNYEKIDELLNNCLSEQEELIVRMRIGMPPYNETKTLDE 455

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           V ++  + RE+IRQIE KAIRKL+   R+  +
Sbjct: 456 VSQKIKIPREKIRQIETKAIRKLRQAVRNNHM 487


>gi|156975281|ref|YP_001446188.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
 gi|156526875|gb|ABU71961.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
          Length = 287

 Score =  156 bits (393), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 89/279 (31%), Positives = 149/279 (53%), Gaps = 4/279 (1%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            K  +      +         I     +S  + R      +      + A+  M+ +NLR
Sbjct: 4   KKIKINNNSSELTAELIYFNDIGKYALLSADDEREYARRAK---MGDADARTRMINSNLR 60

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV+++AK+Y  RGL FLDLI EGNIGLM+A EKFD   G++FSTYA  W++Q+I R + +
Sbjct: 61  LVVNIAKRYKGRGLTFLDLISEGNIGLMRAVEKFDPEKGFRFSTYATHWIRQSIERELMN 120

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ T+R+PVH+  ++ + V+  + +S K  +  TP +IA  L +PV  V K L+  K  I
Sbjct: 121 QARTVRLPVHINKELKRYVKATKELSQKT-QTITPRDIADHLEIPVSSVLKHLEFDKSTI 179

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL++    E+   L + +       P     + N      + +  L P  + +L  R+G+
Sbjct: 180 SLDSYQDKEEAKPLAETMACHRLRCPELELEEDNAFLMLLQWIEELEPDLKLILTRRYGL 239

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             NT  +L+ VG +   +RERIR ++ + I+KL++ +++
Sbjct: 240 DGNTPTSLDTVGTELGYSRERIRHLQMQGIKKLQNLAKN 278



 Score = 38.3 bits (87), Expect = 4.8,   Method: Composition-based stats.
 Identities = 22/88 (25%), Positives = 31/88 (35%), Gaps = 9/88 (10%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +Y  ++G   LLS + E   A+R + G A     +  S L     I  R +   G T L 
Sbjct: 20  IYFNDIGKYALLSADDEREYARRAKMGDADARTRMINSNLRLVVNIAKRYK-GRGLTFLD 78

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQK 210
            I         E   G     E    +K
Sbjct: 79  LI--------SEGNIGLMRAVEKFDPEK 98


>gi|187923827|ref|YP_001895469.1| RNA polymerase sigma factor RpoS [Burkholderia phytofirmans PsJN]
 gi|187715021|gb|ACD16245.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phytofirmans
           PsJN]
          Length = 360

 Score =  156 bits (393), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 97/277 (35%), Positives = 158/277 (57%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I++ +  ISV+  +++ E +    + + GE E   A++ M+E NLRLV+S+AK Y NRG+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQKYSRLAKAGEFE---ARQVMIERNLRLVVSIAKGYLNRGV 138

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GLM A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  +
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRE 198

Query: 529 IHKVVRTARRMSNKIKR--------EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +++V+R  R +              + + ++IA       + V  +L + +   SL+ P+
Sbjct: 199 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 258

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +  S L D + D  + SP        L   T   LA L+ +   V+  RFG+      
Sbjct: 259 DLDPASSLLDLLSDDQSQSPDAEVQHRELETLTRAWLARLSDKHRHVIERRFGLNHIEPA 318

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLEE+  +  +TRER+RQI+ +A+ +LK    S  +R
Sbjct: 319 TLEELADEMGLTRERVRQIQQEALVRLKRFFASNGVR 355



 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 24/105 (22%), Positives = 39/105 (37%), Gaps = 3/105 (2%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQK--RKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           DL++ +G  D       +++ +       R       T D ++ YL  +    LL+ E E
Sbjct: 41  DLDERQGGADEAGETRESASEAAPDADDFRALLQAELTADTIQHYLNRISVKPLLTVEEE 100

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              ++  +AG       + E  L     I     LN G  LL  I
Sbjct: 101 QKYSRLAKAGEFEARQVMIERNLRLVVSIAKGY-LNRGVPLLDLI 144


>gi|32472693|ref|NP_865687.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
 gi|32443930|emb|CAD73372.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
          Length = 355

 Score =  156 bits (393), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 87/232 (37%), Positives = 143/232 (61%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +      +A+ +MV ANLRLV+++++ YT +GL   DLI+EGN+GL++A E FD   G +
Sbjct: 112 RIAQGDVMARDQMVRANLRLVVNISRGYTGKGLGLQDLIEEGNLGLLRAVEGFDPIHGTR 171

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA +W+KQ+I R++ + + TIRIP +M + + K  R   R++ ++ R PT EE+A+ 
Sbjct: 172 FSTYASYWIKQSIKRALINSAKTIRIPAYMVELLSKWRRATARLNEELGRTPTNEEVARV 231

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +P + +  + K  K   S       E    LGD ++D+   +P +  +  ++ +    
Sbjct: 232 LGLPKKKLPIIRKAIKINNSTPQSDQTEAGWSLGDMVQDERLKAPDEEMLDHDILKHAMS 291

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L  L  RE  VL++RFG+G     TL+E+G +  +TRER+RQIE +A+R+L
Sbjct: 292 LLGDLEERESTVLKLRFGLGGVEPMTLKEIGAELGLTRERVRQIETEALRRL 343


>gi|15828925|ref|NP_326285.1| RNA polymerase sigma factor [Mycoplasma pulmonis UAB CTIP]
 gi|14089868|emb|CAC13627.1| DNA-DIRECTED RNA POLYMERASE SIGMA FACTOR (SIGMA-A) [Mycoplasma
           pulmonis]
          Length = 461

 Score =  156 bits (393), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 110/270 (40%), Positives = 175/270 (64%), Gaps = 9/270 (3%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ++ +E + +   ++KG  +  IAK +++  NLRLVI+ AKKY NRGL F+DLI EGN 
Sbjct: 190 TLLTAAEEKQLAIDMKKGGLKGKIAKDKLINRNLRLVINNAKKYKNRGLSFIDLISEGNA 249

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           G++KA +KFD   G+KFSTYA WW++Q+ITR++ADQ+ TIRIPVHM + I+K+++  R +
Sbjct: 250 GIIKAVQKFDESKGFKFSTYATWWIRQSITRAVADQARTIRIPVHMVETINKIIKIEREL 309

Query: 540 SNKIKREPTPEEIAKKLAMPVE--GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
             ++   PT E+IA++     +   VR + K+  +PISL+  +G E+ S   DF++D++ 
Sbjct: 310 QQELGVNPTDEQIAERYGNDYDAKKVRYIRKMNIDPISLDKTVGKENDSFFSDFVKDESV 369

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRM-RFGIGMNTD------HTLEEVGKQFC 650
           +SP+D A + +L E    +L      EERVL M R+GIG + +      HT +++  +  
Sbjct: 370 ISPIDHAAKEDLNEHLLELLNEQLTEEERVLIMKRYGIGEDENGVPYQVHTFDQLATEKN 429

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++E+IRQ E K +R+LK   + K L+ +L
Sbjct: 430 TSKEKIRQWENKILRRLKATKKRKILKEYL 459


>gi|87124019|ref|ZP_01079869.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168588|gb|EAQ69845.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 308

 Score =  156 bits (393), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 140/248 (56%), Gaps = 7/248 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 57  KRVIKRGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +  +   PE++A+
Sbjct: 117 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQQHGQPANPEQLAE 176

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + +P+  V  +L        +SL+  +  + D S L D +          + I A    
Sbjct: 177 AMKIPLSEVEDLLACELRSVTVSLQGIVKSKADPSELVDVLPSDELPPMERAEI-AERTA 235

Query: 612 TTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +L    LTP+E  V+ +RFG+ G +   TL EV +    +RE  RQ+  +A+RKL+
Sbjct: 236 SAWTLLEKANLTPKERTVVMLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALRKLR 295

Query: 669 HPSRSKKL 676
                + L
Sbjct: 296 KTGIQQGL 303


>gi|144575120|gb|AAZ43865.2| DNA-directed RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 798

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 101/313 (32%), Positives = 164/313 (52%), Gaps = 22/313 (7%)

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E+D       K              V   ++   +   +     ++  E + +  
Sbjct: 472 NFSPDEIDLQIDEENKKQDLSNKLTETTDIVKWYMRWIGKYGKL-----LTPQEEKDLAE 526

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + KG      A+  +++ NLRLV++ AKKY NRGL F+DL+ EGN GL+KAA+KFD   
Sbjct: 527 EMDKGGSRGKRARDLIIKRNLRLVVNAAKKYKNRGLSFIDLVSEGNAGLLKAAQKFDIKK 586

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++Q+I+R++ADQ+  IR+PVHM + I+K+ +  R +  +   E   EEI
Sbjct: 587 GFKFSTYATWWIRQSISRAVADQARIIRVPVHMVETINKIYKIEREIQQENGGEIIDEEI 646

Query: 553 AKKLA-----MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           A +L           +R + KI   PISL+  +G E+ S  GDF++D++ +SP++ A + 
Sbjct: 647 AARLGGKSKKYDASYIRYIRKINTSPISLDKQVGKENDSFFGDFVKDESIISPVEFADKE 706

Query: 608 NLRETTTRVLAS-LTPREERVLRMRFGIGMN------TDHTLEEVGKQF-----CVTRER 655
            L       +   L+  E  +++   GIG +         TL+E+ K F      +++ER
Sbjct: 707 ELITKINYYVEKLLSEAEADLIKRYHGIGYDAKGNPVRSATLDEISKDFRGEGKKISKER 766

Query: 656 IRQIEAKAIRKLK 668
           +RQI  K  +KL+
Sbjct: 767 VRQIITKIYKKLR 779



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREGEIAIAKRIE 147
           S D +DL     N    L  +       T D V+ Y+R +G   +LL+ + E  +A+ ++
Sbjct: 474 SPDEIDLQIDEENKKQDLSNKLTE----TTDIVKWYMRWIGKYGKLLTPQEEKDLAEEMD 529

Query: 148 AGRAMMMAS 156
            G +    +
Sbjct: 530 KGGSRGKRA 538


>gi|317051905|ref|YP_004113021.1| sigma-70 family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946989|gb|ADU66465.1| RNA polymerase sigma factor, sigma-70 family [Desulfurispirillum
           indicum S5]
          Length = 305

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 91/301 (30%), Positives = 161/301 (53%), Gaps = 4/301 (1%)

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
             +        +   +      + S   +R+ ++ IS  T ++  E + +   +      
Sbjct: 7   EEFSEDLSMREDVLKQTATENYIPSGDSLRDYLRRISRITLLTAEEEKELARRI---SAG 63

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A + +VE+NLR V+ +A KY + G+  LDLI EGNIGL++AA +FD   G +F TYA
Sbjct: 64  DEQAFRVLVESNLRFVVKIAMKYRDIGINLLDLINEGNIGLLEAARRFDPERGNRFITYA 123

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMP 559
           +WW+KQ+I ++I   S T+R+P        K+    R  +     REPT +E+  +  + 
Sbjct: 124 VWWIKQSIIQAIISSSNTVRLPGKQARFASKLNSARREFARDHDGREPTEQELRDEYGLD 183

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +  +  +L+ T+  ISL+TPIG++D   L D +E     S  +  ++  +      ++A 
Sbjct: 184 ISNIEDILRATRSYISLDTPIGEDDERTLKDVLESPEESSTEEQYVRQKISTEIRSIIAE 243

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  R+  V+ +RFGI      TL+EVG +  +++ER+RQIE +A+++L+  + ++KL  +
Sbjct: 244 LESRDALVVDLRFGISEGIPQTLDEVGTRLGLSKERVRQIEERALKRLQRKAMNRKLSEY 303

Query: 680 L 680
           L
Sbjct: 304 L 304



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 43/190 (22%), Positives = 67/190 (35%), Gaps = 7/190 (3%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             + +   S     L++        + D +R YLR +  I LL+ E E  +A+RI AG  
Sbjct: 6   QEEFSEDLSMREDVLKQTATENYIPSGDSLRDYLRRISRITLLTAEEEKELARRISAGDE 65

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
                L ES L F   I    +  D    L ++I+ E  IG       F    G+ +   
Sbjct: 66  QAFRVLVESNLRFVVKIAM--KYRDIGINLLDLIN-EGNIGLLEAARRFDPERGNRFITY 122

Query: 212 E----DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                  S  +       T       A+ +    S       + +  E    E  D+   
Sbjct: 123 AVWWIKQSIIQAIISSSNTVRLPGKQARFASKLNSARREFARDHDGREPTEQELRDEYGL 182

Query: 268 TLSAMEDQLR 277
            +S +ED LR
Sbjct: 183 DISNIEDILR 192


>gi|291280296|ref|YP_003497131.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754998|dbj|BAI81375.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 313

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 85/254 (33%), Positives = 150/254 (59%), Gaps = 4/254 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++N +  IS    +S  E   +   +++       A +++V +NL+ V+S+A +Y N GL
Sbjct: 45  LKNYLNRISQFQPLSREEEYELGKRIQQ---GDKKALEKLVLSNLKFVVSIANRYKNTGL 101

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+I +GN+GL++AA++FD   G KF +YA+WW++QAI +++A+QS T+++P+     
Sbjct: 102 PLADIINQGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIIQALAEQSGTVKLPLKQASI 161

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++K+      +S ++ REPTP+EIA  L M    +  VL++++  +SLE PI D +    
Sbjct: 162 LYKINEAIEVLSKELGREPTPDEIAVYLDMDPADIENVLRVSRNYLSLEAPIKDGEDRAF 221

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +E     S  +      L+     ++  L  RE ++++ RFG+   T  TLEE+G+ 
Sbjct: 222 IDLLE-SGGKSVEEEIFLNTLKANIEEIVDELNEREAQIIKWRFGLEGETPKTLEEIGEI 280

Query: 649 FCVTRERIRQIEAK 662
             ++RER+RQIEA+
Sbjct: 281 LNISRERVRQIEAR 294



 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 26/124 (20%), Positives = 50/124 (40%), Gaps = 3/124 (2%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            V++G  +ED    ++   +    S       +     D  ++D ++ YL  +   + LS
Sbjct: 1   MVINGGGMEDINTDKNKELVEIDESLDEKDFVEIPLITDI-SEDGLKNYLNRISQFQPLS 59

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           RE E  + KRI+ G    +  L  S L  + ++   +   +    L +II+       E+
Sbjct: 60  REEEYELGKRIQQGDKKALEKLVLSNL--KFVVSIANRYKNTGLPLADIINQGNLGLLEA 117

Query: 196 KGGF 199
              F
Sbjct: 118 AKRF 121


>gi|319792729|ref|YP_004154369.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus EPS]
 gi|315595192|gb|ADU36258.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus EPS]
          Length = 340

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 85/294 (28%), Positives = 143/294 (48%), Gaps = 13/294 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V      P G     +  E    L I   ++ +      +  E        R        
Sbjct: 39  VELNAALPRGAKAELIGGEGADALTI--YLRQVRRTELFTPDEEFQAACAAR---SGDFA 93

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ M+E NLRLV+++AK Y  RG+   DLI+EGN+GLM A  KF+   G++FSTYA WW
Sbjct: 94  ARQSMIEHNLRLVVNIAKGYLGRGVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWW 153

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS------NKIKREPTPEEIAKKLA 557
           ++Q++ R++  Q+  IR+PVH+  ++ +V+R  R +        +       E+IA  L 
Sbjct: 154 IRQSVERAVMTQARAIRLPVHVVRELQQVLRARRALEGDAEFVARRPDGVRVEDIAALLG 213

Query: 558 MPVEGVRKVLKITKEPISLET-PIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTR 615
             V+ V  +L +++ P SL+      ++   L D +  D    +P        +     +
Sbjct: 214 RDVQEVADLLALSEAPRSLDAGDARGDEGFTLADTVASDDEQGNPSGVTQAHEVERLLDQ 273

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            + +L  RE  VL  R+G+      TLE +  +  +TRER+RQI+ +A+ K++ 
Sbjct: 274 WIHALDAREREVLEGRYGLHDREPETLEVLSVRLGLTRERVRQIQNEALAKMRR 327



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 40/103 (38%), Gaps = 2/103 (1%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
           + E   ++++       N+++    + +       D + +YLR++   EL + + E   A
Sbjct: 25  DKEISPDENIPADPVELNAALPRGAKAELIGGEGADALTIYLRQVRRTELFTPDEEFQAA 84

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
               +G      S+ E  L     I     L  G   L ++I+
Sbjct: 85  CAARSGDFAARQSMIEHNLRLVVNIAKGY-LGRG-VPLSDLIE 125


>gi|330946768|gb|EGH47674.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 184

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 95/184 (51%), Positives = 127/184 (69%), Gaps = 1/184 (0%)

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + R  FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+
Sbjct: 1   ARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGL 59

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            I+E + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLM
Sbjct: 60  KIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 119

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  +
Sbjct: 120 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 179

Query: 543 IKRE 546
           + RE
Sbjct: 180 MGRE 183


>gi|22135904|gb|AAM91534.1| sigma factor SigC [Arabidopsis thaliana]
          Length = 291

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 72/284 (25%), Positives = 146/284 (51%), Gaps = 5/284 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +      + +   ++ S+S     +    +    ++ +        + E+V++   LV+ 
Sbjct: 11  MERIRTQLEEESGKVASLSCWAAAAGMNEK----LLMRNLHYGWYCRDELVKSTRSLVLF 66

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ Y   G+   DLIQ G +G+++ AE+FD   GYKFSTY  +W++++++  ++  +  
Sbjct: 67  LARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARG 126

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPT-PEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           + IP  +   I+ + +  + +      +    EEIAK     V+ +R   +  K   S++
Sbjct: 127 VHIPSSIIRTINHIQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRAANQCLKVVGSID 186

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD  T+   +F  D    SP ++ ++ + R     +L  L PRE++V+ +R+G+   
Sbjct: 187 KKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDY 246

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              +LEE+GK   V++E IR+IE +A+ KL+    ++ LR +L+
Sbjct: 247 RPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 290


>gi|168700059|ref|ZP_02732336.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 272

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 85/256 (33%), Positives = 143/256 (55%), Gaps = 3/256 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S +E R + + V         A+  MV ANLRLV+++A+ YT +GL   
Sbjct: 14  YLSEIDHTPLLSAAEERDLGARV---LTGDPQARDRMVRANLRLVVNIARGYTGKGLALD 70

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+ EGN+GL++A E F+  +  +FSTYA +W+KQ+I R+I + + TIRIP +M + + K
Sbjct: 71  DLVSEGNMGLLRAVEGFEPSMNTRFSTYASYWIKQSIKRAIVNTAKTIRIPAYMAELLTK 130

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R   ++S+++ R PT +EIAK L +  + +  + K  +   +       +    + + 
Sbjct: 131 WRRATNQLSDELGRPPTHDEIAKFLGLSKKKLAIIKKAIRVANAGTQSDQSDAGWSIEET 190

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D    +P     +++  +    +L  +  RE  VLRMRFG+      TL+E+G+   +
Sbjct: 191 LMDSRGDAPDTELGKSDDLKQVLHLLDRMDQREATVLRMRFGLNDEEPRTLKEIGECLGL 250

Query: 652 TRERIRQIEAKAIRKL 667
           TRER+RQIE +A+ KL
Sbjct: 251 TRERVRQIENEALAKL 266


>gi|238786819|ref|ZP_04630620.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
 gi|238725187|gb|EEQ16826.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
          Length = 306

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 87/220 (39%), Positives = 149/220 (67%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +  A++Y+NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+
Sbjct: 79  VYFARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQT 138

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S+
Sbjct: 139 RTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSV 198

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +TP+G +    L D + D+N   P D+    +++++  + L  L  ++  VL  RFG+  
Sbjct: 199 DTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG 258

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 259 YEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 298



 Score = 44.1 bits (102), Expect = 0.090,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 82/236 (34%), Gaps = 18/236 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L       +     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENSTETEIFDEKALVEDEPTESELAEDELLAQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKR-----------IEAGRAMMMASLC----ESPLTFQALIIWRDE--LNDGTTL 180
            E+  A+R           IE G   ++ ++     E    F     W     +      
Sbjct: 77  EEVYFARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 136

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
               I L   I  E         E       E S++E   + + +   D+    ++++  
Sbjct: 137 QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEI-AEQLDKPVDDVSRMLRLNERI 195

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            S       ++E    ++  DE+++    +  +D ++  ++  L E+    RE+ +
Sbjct: 196 TSVDTPLGGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLA 251


>gi|67920853|ref|ZP_00514372.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856970|gb|EAM52210.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 297

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 96/286 (33%), Positives = 167/286 (58%), Gaps = 17/286 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVR----------------KGECEASIAKK 446
              +  +R+ ++SI     +S +E   +   ++                K   +   A++
Sbjct: 4   KKKVDTVRHYLQSIGKTPLLSSAEEIKLAEEIQAMLPLLEKEQLSREEEKIVAKGQKARE 63

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+EANLRLV+S+AKKY N GL  LDLIQEG++GL++  EKFD   GYKFSTYA WW++Q
Sbjct: 64  RMIEANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPARGYKFSTYAYWWIRQ 123

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            ITR+IA+QS TIR+P+H+ + ++K  ++ R ++ K+ R+PT  EIA+ + + V+ ++ +
Sbjct: 124 GITRAIAEQSRTIRLPIHINENLNKYRKSIRELTLKLGRKPTQREIAENMEISVDRLQFL 183

Query: 567 LKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            +   +  S    +  ++  + LG  + D+ ++SP D   Q         +L SLTPR++
Sbjct: 184 QQAAFKTKSRSLNVVIDENQTELGQLLPDEESISPSDFVKQEEKISQINNLLESLTPRQK 243

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+ +RFG+      + + +G++  V+ ER RQI ++A++ L+  +
Sbjct: 244 EVIILRFGLRDGKQMSYKAIGEKCGVSHERARQIYSRALKILRKQT 289



 Score = 37.9 bits (86), Expect = 6.4,   Method: Composition-based stats.
 Identities = 14/30 (46%), Positives = 19/30 (63%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YL+ +G   LLS   EI +A+ I+A
Sbjct: 8   DTVRHYLQSIGKTPLLSSAEEIKLAEEIQA 37


>gi|67925817|ref|ZP_00519113.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
 gi|67852341|gb|EAM47804.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
          Length = 386

 Score =  155 bits (392), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 97/256 (37%), Positives = 153/256 (59%), Gaps = 11/256 (4%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +  E GIS+ E + I+            AK++M++ANLRLV++V+KKY  +GL+F+DL+
Sbjct: 1   MLGKEIGISVRELQLILKR-------GKRAKEKMIQANLRLVVAVSKKYQGKGLEFMDLV 53

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
            EGN+GL++A EKF++  GYKFSTYA  W++QA+ R+I D+  TIR+PVH+ ++I K+ +
Sbjct: 54  SEGNLGLIRAVEKFEYDKGYKFSTYAYHWIRQALVRAICDKGRTIRVPVHINEEISKLKK 113

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDEDTSHLGDFIE 593
               +  K  R  T  E++++L +  E +R +  +    +SL+  + GDED S L  F+ 
Sbjct: 114 VQLEIRQKYGRSATVRELSERLEISPEKIRVLRSVNNPMLSLDQKVLGDEDNSTLLSFLA 173

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D N           N +E   + L  L P+E+RVLR  +        TL E+GK+  ++R
Sbjct: 174 DPNGDLQKFLDNLGN-KELVEQCLCGLKPQEQRVLREYYLE--TPSLTLNEIGKKMNLSR 230

Query: 654 ERIRQIEAKAIRKLKH 669
           ER+R I+  A+ KLK 
Sbjct: 231 ERVRHIKNNALDKLKQ 246


>gi|288917890|ref|ZP_06412250.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
 gi|288350679|gb|EFC84896.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score =  155 bits (391), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 122/246 (49%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +VS+       A++ + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 151 FARLVSLPEGDPERAAL-RDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 209

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 210 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQSLGRS 269

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  EIA+ L M  E V + L+       +SL+ P   +D +  + D +  ++      S
Sbjct: 270 PTVSEIARHLEMTEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDE-----S 324

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L PRE+R+L +RF        T  ++  +  +++  + ++ A+ 
Sbjct: 325 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN----MTQSQIANELGISQMHVSRLLART 380

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 381 LAQLRR 386


>gi|106895882|gb|ABF82643.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 291

 Score =  155 bits (391), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 134/333 (40%), Gaps = 44/333 (13%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L 
Sbjct: 1   MYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLS 60

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           +II            GF    E                          E  A  +    S
Sbjct: 61  DII-----------SGFIDPNE-------------------------TEDMAPTATHIGS 84

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
           ++       E++E   DEDED  +                   E+   Y          +
Sbjct: 85  ELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRL 138

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           + QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 139 SIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 198

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG
Sbjct: 199 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETG 257

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           +SI++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 LSIAQIKDINRRMSIGEAKARRAKKEMVEANLR 290


>gi|23978293|dbj|BAC21127.1| principal sigma factor [Arthrospira platensis]
          Length = 203

 Score =  155 bits (391), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 109/204 (53%), Positives = 148/204 (72%), Gaps = 1/204 (0%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V++NLRLV+S+AKKY NRGL F DLIQEG++GL++AAEK D   GYKFSTYA WW++QAI
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           TR+IADQS TIR+PV + + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K
Sbjct: 61  TRAIADQSRTIRLPVLLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAK 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             + PISLETPIG E+ S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VL
Sbjct: 121 SAQLPISLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLESVLDTLSPRERDVL 179

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT 652
           R+R+G+      TLEE+G+ F VT
Sbjct: 180 RLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|116075407|ref|ZP_01472667.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116067604|gb|EAU73358.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 310

 Score =  155 bits (391), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 138/247 (55%), Gaps = 5/247 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++   +   AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G+
Sbjct: 57  KRTIKKGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGH 116

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +  +  TP ++A+
Sbjct: 117 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNGQAATPAQLAE 176

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            + +    V  +L        +SL+  +    D S L D +  +       + I      
Sbjct: 177 AMQISRAEVDDLLGCELRSVTVSLQGIVKSKSDPSELVDVLPSEELPPMEQAEIDERTAS 236

Query: 612 TTTRV-LASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             T +  ++LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+ 
Sbjct: 237 AWTLLDRSNLTPKERTVVMLRFGLDGSNEWRTLAEVARHMGCSREYCRQVVQRALRKLRK 296

Query: 670 PSRSKKL 676
                 L
Sbjct: 297 SGIQNGL 303


>gi|242078297|ref|XP_002443917.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
 gi|241940267|gb|EES13412.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
          Length = 500

 Score =  155 bits (391), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 91/304 (29%), Positives = 161/304 (52%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +  ++   +G W      ++   L      K ++    IS  E R   + +R+      +
Sbjct: 204 IQLSRKIKDGIWLQHQRSKLKEKLGNEPSYKQLAQSLHISPPELR---ARMRESF----L 256

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N+RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 257 AREMLTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 316

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S   R+P ++ +++  +      + ++    PT E IA+ L +  + V
Sbjct: 317 IRQGVSRALADNSKAFRLPTYLHERLIAIRGAKYALEDQ-GIAPTVENIAESLNISEKKV 375

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+           GD    +IED+N A  P     +  L+E    ++ 
Sbjct: 376 HNATEAVNKVLSLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEERYLKEEVNNLIN 435

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 436 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLVAMEKLKHAARRKHLD 494

Query: 678 SFLD 681
           + L+
Sbjct: 495 ALLE 498


>gi|260435993|ref|ZP_05789963.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260413867|gb|EEX07163.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 309

 Score =  155 bits (391), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 86/254 (33%), Positives = 139/254 (54%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 +        AK +M+ +NLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+
Sbjct: 52  EYSDEEKGVIRRGERAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKY 111

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     R+  +    P+
Sbjct: 112 DPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRAAKARLMQRNGLSPS 171

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            E++A+ + +P+  V  +L        +SL+  +    D S L D +  +       + I
Sbjct: 172 GEQLAEFMEIPIAEVEDLLACELRSVTVSLQGVVKSKSDPSELVDVLPSEELPPLERAEI 231

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +   +LA   LTP+E  V+ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 232 -AERTASAWSLLAKANLTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQR 290

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 291 ALRKLRKTGIQSGL 304


>gi|296121869|ref|YP_003629647.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296014209|gb|ADG67448.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 290

 Score =  155 bits (391), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 84/259 (32%), Positives = 152/259 (58%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    ++  + R + + +  GE     A+  MV ANLRLV+++A+ Y  +GL
Sbjct: 28  LETYLREINETALLTARDERELANRIANGE---KEARDRMVRANLRLVVNIARAYVGKGL 84

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +  +FSTYA +W+KQ+I R++ +   TIRIP +M + 
Sbjct: 85  PLQDLIEEGNLGLLRAVEGFDPDMNTRFSTYASYWIKQSIKRALINCGKTIRIPAYMVEL 144

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  +   ++ ++ KR PT EE+A +L +P + +  V K      S      +E    +
Sbjct: 145 LSKWRKATAKLEDQFKRPPTQEEVAIELGLPKKKLSIVKKAIHLYSSTPQTDDEESGWMM 204

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D + D+    P D  +  +  +    +L ++  RE ++LR+RFG+  +   TL+E+G++
Sbjct: 205 SDMVADERVKGPDDELLDVDNLKHVYAMLETMDEREAKILRLRFGLDDSEPKTLKEIGEE 264

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE++A++++
Sbjct: 265 MGLTRERVRQIESEALKRI 283



 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 2/91 (2%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           S   +   P+  YLRE+    LL+   E  +A RI  G       +  + L     I  R
Sbjct: 19  SGSSAVQTPLETYLREINETALLTARDERELANRIANGEKEARDRMVRANLRLVVNIA-R 77

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHG 202
             +  G   L+++I+        +  GF   
Sbjct: 78  AYVGKG-LPLQDLIEEGNLGLLRAVEGFDPD 107


>gi|115521899|gb|ABJ09417.1| RNA polymerase sigma factor [Brevundimonas diminuta]
          Length = 275

 Score =  154 bits (390), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 109/312 (34%), Positives = 151/312 (48%), Gaps = 42/312 (13%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           +GEIAIAKRIEAGR  M++ LCES LTF+A+++WR+EL +   LLRE+IDL+A  G  + 
Sbjct: 1   KGEIAIAKRIEAGRDAMISGLCESALTFEAIMVWREELANNRILLREVIDLDATYGILNP 60

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
               H     +    E     +E DD    +G   S + +                    
Sbjct: 61  SSLPHNQPAPAQPTGEPDGDGEEDDDEDFDDGGAMSISALE------------------- 101

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE-----KSS 311
                             +LR  VM  LD IA  + E R LQD  V  +        K  
Sbjct: 102 -----------------AELRDGVMEVLDAIAVDFGEFRKLQDKLVEARLKGEVLTAKDQ 144

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
              + L   +   + ++ LN +RI+ LVEQLY I+KR++  EG LLRLA  YGI R  FL
Sbjct: 145 KTYEALTASISDRLKTMKLNNARIEALVEQLYAINKRLIGQEGRLLRLADGYGISRPEFL 204

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           + + G E+DP W    K+     W  F   E   I  IR +I +++ E G+ I ++R IV
Sbjct: 205 KAYFGSEMDPTWAERIKEMGVR-WTKFSENEAAQIDTIRTQIAAVATEAGVPIDDYRRIV 263

Query: 432 SMVRKGECEASI 443
            MV+KGE E   
Sbjct: 264 QMVQKGEREXRQ 275


>gi|116073053|ref|ZP_01470315.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068358|gb|EAU74110.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 321

 Score =  154 bits (390), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 89/237 (37%), Positives = 146/237 (61%), Gaps = 1/237 (0%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +++       AK+ MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   
Sbjct: 75  QLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTR 134

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           GYKFSTYA WW++Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+
Sbjct: 135 GYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQELGRTPTVTEL 194

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ + +P E V+ ++   ++P+SLE  +GD D + L + +     +          L+  
Sbjct: 195 AEFVELPEEEVKDLMCRARQPVSLEMKVGDGDDTELLELLSGDGELPSE-QVESECLKGD 253

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +L  L   + +VLRMR+G+      +L  + K   ++R+R R++E + +  L++
Sbjct: 254 LRDLLEQLPELQRKVLRMRYGMNGEDPMSLTGIAKTLKMSRDRTRRLEREGLEMLRN 310


>gi|114327512|ref|YP_744669.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
 gi|114315686|gb|ABI61746.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
          Length = 375

 Score =  154 bits (390), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 70/278 (25%), Positives = 123/278 (44%), Gaps = 13/278 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 84  LSRYLQEIRKYPMLTPEEELDLSRRWRDTEDMG--AAHRLVTSHLRLVAKIAMGYRGYGL 141

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A  +FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 142 PVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 201

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA  L +P  + V+   +++    SL  P+  
Sbjct: 202 KLFFNLRRLKGQMQAIDDGDLKPEQVSKIATSLNVPEQDVVQMNRRMSAPDHSLNAPLRQ 261

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E      D++ D         A    L   +      L +L  RE  +L        +  
Sbjct: 262 EGEGEWQDWLVDDAETQETVLADTEELGGRKTLLANALKTLNDRERHILTE--RRLKDEP 319

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            TLE++ + + ++RER+RQIE +A  KL+   +++ + 
Sbjct: 320 TTLEDLSQHYNISRERVRQIEVRAFEKLQKAMKAEVIE 357


>gi|42561001|ref|NP_975452.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492498|emb|CAE77094.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
          Length = 522

 Score =  154 bits (390), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 128/335 (38%), Positives = 184/335 (54%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     I     ++  +      M V     +    + +++E+NL+LVISVA+K+ NRG
Sbjct: 187 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 246

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 247 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 306

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP  +EIA +    +  + V ++ K++ EP+SLE P GDED 
Sbjct: 307 TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPFGDEDD 366

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI----------- 634
           +H GDF+EDK+ VSP +   +  L+E   +V   + PREE+V+RMR+GI           
Sbjct: 367 THFGDFVEDKDMVSPNEYTEKKILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRL 426

Query: 635 ----GMNTDHTLEEVGKQF---------------------------------------CV 651
                      L++  ++                                         V
Sbjct: 427 TQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEEVGKELNV 486

Query: 652 TRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
           TRERIRQIEAK IRKLK PS + K    L+ F  G
Sbjct: 487 TRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 521


>gi|2624403|emb|CAA74653.1| plastid RNA polymerase sigma factor [Sorghum bicolor]
          Length = 500

 Score =  154 bits (390), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 160/304 (52%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +  ++   +G W      ++   L      K ++    IS  E R   + +R+      +
Sbjct: 204 IQLSRKIKDGIWLQHQRSKLKEKLGNEPSYKQLAQSLHISPPELR---ARMRESF----L 256

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N+RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 257 AREMLTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 316

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S   R+P ++ +++  +      + ++    PT E IA+ L +  + V
Sbjct: 317 IRQGVSRALADNSKAFRLPTYLHERLIAIRGAKYALEDQ-GIAPTVENIAESLNISEKKV 375

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVLA 618
               +   + +SL+           GD    +IED+N A  P     +  L+E    ++ 
Sbjct: 376 HNATEAVNKVLSLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEERYLKEEVNNLIN 435

Query: 619 S-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           S L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 436 SNLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLVAMEKLKHAARRKHLD 494

Query: 678 SFLD 681
           + L+
Sbjct: 495 ALLE 498


>gi|215270833|emb|CAR48094.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270835|emb|CAR48095.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 291

 Score =  154 bits (389), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 69/332 (20%), Positives = 126/332 (37%), Gaps = 43/332 (12%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+ EMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L +
Sbjct: 1   YMSEMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTD 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I        +          G    + +   +++E  D  E   D     +       +
Sbjct: 61  LISGFVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDTEEDVGIDPE 120

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +                                    +   +++   Y+ L+      + 
Sbjct: 121 L-----------------------------------ALEKFNQLRSTYQNLQ------LA 139

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             +    S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  Y
Sbjct: 140 INEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEY 199

Query: 364 G-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           G + +  F+    G E    W+       +  +   +    + I +   ++K I  ET +
Sbjct: 200 GKMPKKSFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSL 258

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ++   + I   +  GE +A  AK EMVEA+LR
Sbjct: 259 NVQNIKDISRRMSIGEAKARRAKNEMVEAHLR 290


>gi|215270831|emb|CAR48093.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270837|emb|CAR48096.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 291

 Score =  154 bits (389), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 69/332 (20%), Positives = 127/332 (38%), Gaps = 43/332 (12%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+ EMG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L +
Sbjct: 1   YMSEMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTD 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I        +          G    + +   +++E  D  E   D    ++       +
Sbjct: 61  LISGFVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPE 120

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +                                    +   +++   Y+ L+      + 
Sbjct: 121 L-----------------------------------ALEKFNQLRSTYQNLQ------LA 139

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             +    S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  Y
Sbjct: 140 INEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEY 199

Query: 364 G-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           G + +  F+    G E    W+       +  +   +    + I +   ++K I  ET +
Sbjct: 200 GKMPKKSFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSL 258

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ++   + I   +  GE +A  AK EMVEA+LR
Sbjct: 259 NVQNIKDISRRMSIGEAKARRAKNEMVEAHLR 290


>gi|87124760|ref|ZP_01080608.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86167639|gb|EAQ68898.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 321

 Score =  154 bits (389), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 94/272 (34%), Positives = 157/272 (57%), Gaps = 5/272 (1%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSM----VRKGECEASIAKKEMVEANLRLVI 457
           E+  +  +  E++       +  +E      +    +++       AK+ MV ANLRLV+
Sbjct: 40  ELMELEALEAELRDQRGGEAVPAAELATAAGLSALQLKRKLQAGRRAKERMVAANLRLVV 99

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 100 SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 159

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A  + +P E V+ ++   ++P+SLE
Sbjct: 160 TIRLPIHITEMLNKLKKGQRELSQELGRTPTVTELAGFVELPEEEVKDLMCRARQPVSLE 219

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L + +     + P +      L+     +L  L   + RVLRMR+G+   
Sbjct: 220 MKVGDGDDTELLELLAGDGEL-PEEQVEVECLKGDLRDLLEQLPDLQRRVLRMRYGMDGE 278

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +L  + K   ++R+R R++E + +  L+ 
Sbjct: 279 EPMSLTGIAKSLRMSRDRTRRLEREGLEMLRR 310



 Score = 37.5 bits (85), Expect = 7.7,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS + EI + ++++ 
Sbjct: 11  DLVRSYLRDIGRVPLLSHQQEITLGRQVQE 40


>gi|159903122|ref|YP_001550466.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159888298|gb|ABX08512.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 312

 Score =  154 bits (389), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 89/257 (34%), Positives = 146/257 (56%), Gaps = 7/257 (2%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E      + R+   +   AK +M+ +NLRLV+++AK+Y  +GL  LDLIQEG +GL +A 
Sbjct: 47  EACEYTDLERRTIRQGERAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAV 106

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK+D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     ++      
Sbjct: 107 EKYDPKRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSQLMQANGL 166

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            P+ E +AKK+ +  E V ++L+       +SL+  +    D S LGD +  +       
Sbjct: 167 TPSSEMLAKKMHLSKEEVEELLECELRSITVSLQGVVQSKSDPSELGDVLPSEEIPPMEV 226

Query: 603 SAIQANLRETTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQI 659
           + + A   ++   +L  A+LTP+E  ++ +RFG+ G N   TL EV K    +RE  RQ+
Sbjct: 227 AEL-AERNDSAWSLLNKANLTPKERTIVSLRFGLDGSNEWRTLAEVAKHMNCSREYCRQV 285

Query: 660 EAKAIRKLKHPSRSKKL 676
             +A+RKL+       L
Sbjct: 286 VQRALRKLRKTGIQSGL 302


>gi|26665380|dbj|BAC44901.1| principal sigma factor [Chlorogloeopsis fritschii PCC 6912]
          Length = 198

 Score =  154 bits (389), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 108/199 (54%), Positives = 146/199 (73%), Gaps = 1/199 (0%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           +V+S+AKKY NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IAD
Sbjct: 1   MVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIAD 60

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           QS TIR+PVH+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PI
Sbjct: 61  QSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI 120

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETPIG E+ S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+
Sbjct: 121 SLETPIGKEEDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGL 179

Query: 635 GMNTDHTLEEVGKQFCVTR 653
                 TLEE+G+ F VTR
Sbjct: 180 DDGRMKTLEEIGQIFNVTR 198


>gi|110004382|emb|CAK98720.1| probable rna polymerase sigma-a factor protein [Spiroplasma citri]
          Length = 445

 Score =  154 bits (389), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 131/335 (39%), Positives = 187/335 (55%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     +     ++  E      M+      E    + +++ +NL+LV+SVA+K+ NRG
Sbjct: 111 IKAYFNILGTSKILTREEEIKYAKMLESSDPEEIRFGRDKLITSNLKLVVSVARKHLNRG 170

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KFD+  G+KFSTYA WW++QA TR+IADQ+ TIRIPVHM +
Sbjct: 171 LDFSDLIEEGNIGLMKAVDKFDYKRGFKFSTYATWWIRQATTRAIADQARTIRIPVHMVE 230

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP+  EIA+K+   M  E VR++ +++ EP+SLE PIGDED 
Sbjct: 231 TINKLTRIERQLTQELGREPSYNEIAEKMGQGMVGEKVREIKRLSIEPVSLEKPIGDEDD 290

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGM-------- 636
           +H GDF++DK+  +P +   + +LRE    V    L+ REE+V+RMRFG+          
Sbjct: 291 THFGDFVDDKDIFTPDEYTEKESLREVIDEVFHEILSAREEKVIRMRFGLLPTKLRTVLR 350

Query: 637 ----NTDHTLEEV------------------------------------------GKQFC 650
                 D T  E+                                          GK+F 
Sbjct: 351 LAKECEDETFPELVQTVKALDIHYDTPIEKVQSQKHALIDKHLSKYDSPKTLEEVGKEFK 410

Query: 651 VTRERIRQIEAKAIRKLK---HPSRSKKLRSFLDG 682
           VTRERIRQIEAK IRK K     S++K L+ F  G
Sbjct: 411 VTRERIRQIEAKTIRKFKPNQANSKAKVLKDFFKG 445



 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 28/156 (17%), Positives = 55/156 (35%), Gaps = 17/156 (10%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL-DLASSASNSSVFLQ 107
           +N     D+     +E+    L   G+   D +  E EE        +     +  +  +
Sbjct: 41  INDHFEVDDND---VEEYFEELVTNGVEFSDVNLEELEENEVPEPEKVTKKQPDEKLRYK 97

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA----SLCESPLT 163
               S +    D ++ Y   +G+ ++L+RE EI  AK +E+     +      L  S L 
Sbjct: 98  VGGISNETKIQDIIKAYFNILGTSKILTREEEIKYAKMLESSDPEEIRFGRDKLITSNLK 157

Query: 164 FQAL---------IIWRDELNDGTTLLREIIDLEAC 190
                        + + D + +G   L + +D    
Sbjct: 158 LVVSVARKHLNRGLDFSDLIEEGNIGLMKAVDKFDY 193


>gi|238926534|ref|ZP_04658294.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
 gi|238885480|gb|EEQ49118.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
          Length = 352

 Score =  154 bits (389), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 106/246 (43%), Positives = 154/246 (62%), Gaps = 9/246 (3%)

Query: 443 IAKKEMVEANLRLVISVA----KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            A++++   N +LV   A    K+Y +R L F D+ Q G IGL+ AA+KFD  +GY FST
Sbjct: 109 QAEQDLCVKNKKLVDKYALGYEKRYRHR-LDFDDIEQAGFIGLITAAKKFDISMGYSFST 167

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA+WW+KQAITR I D    IRIPVHM ++I KV      M +++ RE    ++  +   
Sbjct: 168 YAVWWIKQAITREIMDHGFVIRIPVHMMEQIIKVAGVEN-MFSELNREERIVKVMDETGY 226

Query: 559 PVEGVRKVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             E VR+ + + +  +   SL   +G+++T  LG+F+ D  A+S  +      LR     
Sbjct: 227 KEERVRECMMLKEYVLTYSSLNVTVGEDETVELGEFLSDDGAISIEEMIENKELRRMLDD 286

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL +LT +E++V+++RFG+  N   TLEEVGK F VTRERIRQIE+KA+RKL+HPSR   
Sbjct: 287 VLNTLTEKEKKVIKLRFGLEDNRQWTLEEVGKLFNVTRERIRQIESKALRKLRHPSRLHN 346

Query: 676 LRSFLD 681
           ++SFL+
Sbjct: 347 IKSFLE 352


>gi|3769432|gb|AAC78468.1| RNA polymerase sigma factor 2 [Zea mays]
          Length = 349

 Score =  154 bits (389), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 94/304 (30%), Positives = 160/304 (52%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +  ++   +G W      ++   L      K ++    IS  E R   + +R+      +
Sbjct: 53  IQLSRKIKDGIWLQHQRSKLKEKLGNEPSYKQLAQSLRISAPELR---ARMRESF----L 105

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N+RLVIS+A KY N G+   DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 106 AREMLTMSNIRLVISIAHKYDNLGVDLADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 165

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S T R+P ++ +++  +      + ++    PT E IA+ L + V+ V
Sbjct: 166 IRQGVSRALADNSKTFRLPTYLHERLLAIRGAKYALEDQ-GIAPTIENIAESLNISVKKV 224

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVLA 618
               +   + +SL+           GD    +IED+N A  P     +  L+E    ++ 
Sbjct: 225 HNATEAVHKVLSLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEEMYLKEEVNNLIN 284

Query: 619 S-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           S L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 285 SNLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVRLVAMEKLKHAARRKHLN 343

Query: 678 SFLD 681
           + L+
Sbjct: 344 ALLE 347


>gi|1542976|gb|AAB08043.1| sigma factor [Thermoanaerobacterium thermosulfurigenes]
          Length = 261

 Score =  154 bits (388), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 93/261 (35%), Positives = 150/261 (57%), Gaps = 7/261 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + +   +R        AK  +VE N+RLV  VA  +   G++F DL+QEG IGL
Sbjct: 5   LTKEEEKILFERLR---NGDESAKDVLVECNIRLVDKVAAGFLKSGVEFDDLVQEGLIGL 61

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A +KFD   GYKFSTYA W+++Q++ R I +    IR+P+H+ +KI+++++    +  
Sbjct: 62  LTAIDKFDHTKGYKFSTYATWYIQQSMRRYIGNYGKIIRLPIHINEKINRILKARYLIEQ 121

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSP 600
           K     T EEI++      E +   L    + ISL   + DE   + L +FI+D + +  
Sbjct: 122 KKGSLATTEEISRLTGYTEEEIEGYLSYATDVISLNQYVNDERVDAELINFIQD-DTIDV 180

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            + AI+  +++   ++L SL  RE  +L+MRFG G N   TL E+G  F +TRERIRQI+
Sbjct: 181 EEMAIEKEIKKEIRKILDSLPERERMILKMRFGFGCN-LKTLTEIGNIFGLTRERIRQIQ 239

Query: 661 AKAIRKLKHPSRSK-KLRSFL 680
              I++L+H  + K +LR  +
Sbjct: 240 NNTIKELRHNRKVKDRLREIM 260


>gi|257055481|ref|YP_003133313.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256585353|gb|ACU96486.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 315

 Score =  153 bits (387), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 85/241 (35%), Positives = 143/241 (59%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK  M+ ANLRLV++ A+K  +  L  LD IQEGN+GL++A EKFD+  G+KFST
Sbjct: 73  RDGQRAKDHMIRANLRLVVTAARKNRHTNLPLLDAIQEGNLGLIRAVEKFDYAKGFKFST 132

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YAMWW++QAI R  A QS  IR+P+H+ +++ K+ R  R + ++   E T EE+A    M
Sbjct: 133 YAMWWIRQAIQRGNAFQSNAIRLPMHVSEQVAKLDRLERTLQSRSNHELTVEELAAAAEM 192

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           PVE V  + +  +  +SL+  + ++   +L D + D    +  +   +  + +     + 
Sbjct: 193 PVERVEALRQAGRSTVSLDMSLDEDGELYLRDLVADGTVPAVGEGIERQAMVDQVRATID 252

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SL P E  V+ +R+G+     HT+ E+ ++  ++R+R+R +E +A+  L+ P RS+ L  
Sbjct: 253 SLPPMEAAVVSLRYGLRDGHQHTIPEISQRLGLSRKRVRTLEQRAMAMLREPQRSEPLLD 312

Query: 679 F 679
           +
Sbjct: 313 W 313



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR--AMMMASLCESPLT 163
           +  ++D       D VR YL E+G   LL+   E+ +AKRIEAG   A ++    E  +T
Sbjct: 1   MGSQRDRPVSEEPDIVRYYLDEVGETPLLTANQEVELAKRIEAGVYAAELLRRADEGEIT 60

Query: 164 FQALIIWRDELNDGTTLLRE 183
                   + +       ++
Sbjct: 61  LDYDRRDLEIVARDGQRAKD 80


>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba]
          Length = 567

 Score =  153 bits (387), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 136/251 (54%), Gaps = 1/251 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++          + E+V++   LV+ +A+ Y   G+   DLIQ G +G+++ AE+FD  
Sbjct: 316 KLLMHNLHFGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHT 375

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP-TPE 550
            GYKFSTY  +W++++++  ++  +  + IP  +   + ++ +  + +      +    E
Sbjct: 376 RGYKFSTYVRYWIRKSMSTMVSRHARGVHIPASIIRTMSQIQKARKTLKTSQGIKYPADE 435

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI+K     ++ +R   +  K   S++  +GD  T+   +F  D    SP ++ ++ + R
Sbjct: 436 EISKLTGYSLKKIRAANQCLKVVGSIDKKVGDCFTTRFLEFTPDPTMESPEEAVMRQSAR 495

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +L  L PRE++V+ +R+G+   +  +LEE+GK   V++E IR+IE +A+ KL+  
Sbjct: 496 GEVHNLLEGLEPREKQVMVLRYGLQDYSPKSLEEIGKILRVSKEGIRKIERRAMAKLRDQ 555

Query: 671 SRSKKLRSFLD 681
            ++  LR +L+
Sbjct: 556 PKADNLRYYLN 566


>gi|326801849|ref|YP_004319668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326552613|gb|ADZ80998.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 285

 Score =  153 bits (387), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 87/269 (32%), Positives = 146/269 (54%), Gaps = 4/269 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  +S    IS  E   +   +R       +A + + +ANLR VISVAK+Y ++GL   
Sbjct: 21  YLNEVSKFELISADEEVSLAEKIR---EGDQLALERLTKANLRFVISVAKQYQHQGLVLE 77

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN GL+KAA +FD   G+KF +YA+WW++Q+I  +I+ QS  +R+P +    + K
Sbjct: 78  DLINEGNAGLVKAARRFDETKGFKFISYAVWWIRQSIMSAISIQSRAVRLPGNQISNLIK 137

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + R+   M  +++REP+ EE+A +L    + +       +  +S++ P    +   L D 
Sbjct: 138 LRRSQAEMEQRLEREPSVEELAVELGTTTDRIIASFTNAERQLSIDAPSVFSEEERLLDS 197

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +   +  +     IQ +L      VL  L+ RE ++L M +G+  +   TL+E+  Q  +
Sbjct: 198 LASSD-PATDQQLIQDSLFLRIDLVLKKLSSRERQILTMFYGLSNSEPQTLDEIAYQLKL 256

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           T ERIRQ++ KA+  +K+ S  + L   L
Sbjct: 257 TPERIRQLKTKALLHIKNSSSGRDLLQHL 285



 Score = 44.4 bits (103), Expect = 0.069,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K  DS     +  + +YL E+   EL+S + E+++A++I  G  + +  L ++ L F  +
Sbjct: 5   KISDSITNRNNRSLSLYLNEVSKFELISADEEVSLAEKIREGDQLALERLTKANLRF--V 62

Query: 168 IIWRDELNDGTTLLREIID 186
           I    +      +L ++I+
Sbjct: 63  ISVAKQYQHQGLVLEDLIN 81


>gi|86605925|ref|YP_474688.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
 gi|86554467|gb|ABC99425.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
          Length = 318

 Score =  153 bits (387), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 97/255 (38%), Positives = 145/255 (56%), Gaps = 10/255 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +    ++  S   GI + E + I+            AKK MVE NLRLV+S+AK+Y NR
Sbjct: 46  RRQHESLEDWSRRLGIPLEELQQILRQ-------GEAAKKRMVECNLRLVVSIAKRYRNR 98

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL FLDLIQEG IGL +A EKFD   GYKFSTYA WW++Q++ R I ++   IR+P HM 
Sbjct: 99  GLPFLDLIQEGTIGLTRAVEKFDPTRGYKFSTYATWWIRQSVNRGIQNKGRLIRLPAHMY 158

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDT 585
           +K+ +V R  R +S +    P  EE+   L +  +  R+++      I SL   +GDED 
Sbjct: 159 EKVSQVKRRYRELSAEKGSRPAAEEVFDSLDIG-DNYRELITRHMAEIRSLNVGVGDEDG 217

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           + L  FI D++         +    E    +++ L+ RE++V+  R+G+  +   TL E+
Sbjct: 218 TELQHFIPDEDNDPIEHLN-RVAHCEEVRALVSQLSEREQQVIVARYGLDGSKGLTLREI 276

Query: 646 GKQFCVTRERIRQIE 660
           G+   ++RER+RQIE
Sbjct: 277 GEHIGLSRERVRQIE 291


>gi|167515040|gb|ABZ81804.1| RpoD [Aeromonas aquariorum]
          Length = 285

 Score =  153 bits (387), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 134/329 (40%), Gaps = 46/329 (13%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +II     I P                         E DDV  T   I S         
Sbjct: 61  SDII--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLAD 94

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-N 300
              D   +   + + + D+ +      ++                  E + ELR+  +  
Sbjct: 95  EDDDEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVT 137

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            ++ Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L 
Sbjct: 138 RLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLC 197

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  E
Sbjct: 198 VEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEE 256

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEM 448
           TG+SI++ + I   +  GE +A  AKKEM
Sbjct: 257 TGLSIAQIKDINRRMSIGEAKARRAKKEM 285


>gi|167515036|gb|ABZ81802.1| RpoD [Aeromonas aquariorum]
          Length = 285

 Score =  153 bits (387), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 134/329 (40%), Gaps = 46/329 (13%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L
Sbjct: 1   RMYMREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +II     I P                         E DDV  T   I S         
Sbjct: 61  SDII--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLAD 94

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-N 300
              D   +   + + + D+ +      ++                  E + ELR+  +  
Sbjct: 95  EDEDEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVT 137

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            ++ Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L 
Sbjct: 138 RLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLC 197

Query: 361 -QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
            +   + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  E
Sbjct: 198 VEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEE 256

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEM 448
           TG+SI++ + I   +  GE +A  AKKEM
Sbjct: 257 TGLSIAQIKDINRRMSIGEAKARRAKKEM 285


>gi|318041016|ref|ZP_07972972.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 323

 Score =  153 bits (387), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 85/251 (33%), Positives = 145/251 (57%), Gaps = 3/251 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             +++    A  A ++MV ANLRLV+S+A++ ++R L   DLIQEG +GL++A ++FD  
Sbjct: 76  RQLQRQLRLAERASEQMVTANLRLVVSLARRISHRRLDLDDLIQEGTLGLIRAVQRFDPS 135

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GYKFSTYA WW+++ + R++  QS TIR+P HM+D++ ++ R    +   + REP  EE
Sbjct: 136 RGYKFSTYATWWIREGMGRALQQQSRTIRLPAHMQDRLQRLRRCQMELRQMLGREPNLEE 195

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+   +    +R+ L   +EP+SL++  G ED   L D +    A  P D    A+L+ 
Sbjct: 196 LAEATELKPLDIREALFRAQEPLSLDSGHGPEDDLRLLDTLRC-GAQLPSDQLTAAHLQT 254

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  +E  +LR+R+GI       L  V +Q  ++R++ R +E +A   ++   
Sbjct: 255 DLVALLDELPEKEAELLRLRYGIDQPAPMNLSAVARQMGLSRDQARGMERRANAAIRRL- 313

Query: 672 RSKKLRSFLDG 682
            S ++  +L+ 
Sbjct: 314 -SDRVIDYLEA 323


>gi|297608012|ref|NP_001061065.2| Os08g0163400 [Oryza sativa Japonica Group]
 gi|255678168|dbj|BAF22979.2| Os08g0163400 [Oryza sativa Japonica Group]
          Length = 520

 Score =  153 bits (387), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 158/304 (51%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +    +G W      ++   L      K ++    IS  E R           E+ +
Sbjct: 224 VHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELR-------SRMHESFL 276

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 277 AREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 336

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++A+ S T R+P ++ +++  +      + ++    PT E IA  L +  + V
Sbjct: 337 IRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYELEDQ-GIAPTIENIAGSLNISEKKV 395

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+              L  +IED+N A  P     +  L+E   ++L 
Sbjct: 396 LNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 455

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 456 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLE 514

Query: 678 SFLD 681
           + L+
Sbjct: 515 ALLE 518


>gi|194699556|gb|ACF83862.1| unknown [Zea mays]
 gi|223944677|gb|ACN26422.1| unknown [Zea mays]
          Length = 496

 Score =  153 bits (386), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 91/304 (29%), Positives = 160/304 (52%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  ++   +G W      ++   L      K ++    I   E R   + +R+      +
Sbjct: 200 VQLSRKIKDGIWLQHQRSKLKEKLGNEPSYKQLAQSLRIPAPELR---ARMRESF----L 252

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 253 AREMLAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 312

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S + R+P ++ +++  +      + ++    PT E IA+ L +  + V
Sbjct: 313 IRQGVSRALADNSRSFRLPTYLHERLVAIRGAKYALEDQ-GIAPTVENIAESLNISEKKV 371

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + ISL+           GD    +IED+N A  P     +  L+E    ++ 
Sbjct: 372 HNATEAVHKVISLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEERYLKEEVNSLIN 431

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R + L 
Sbjct: 432 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLVAMEKLKHAARREHLD 490

Query: 678 SFLD 681
           + L+
Sbjct: 491 ALLE 494


>gi|148242708|ref|YP_001227865.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851018|emb|CAK28512.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 301

 Score =  153 bits (386), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 89/269 (33%), Positives = 146/269 (54%), Gaps = 7/269 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + +     +       +    ++       AK +M+ ANLRLV+++AK+Y  +GL+ LDL
Sbjct: 29  RKVQAMVPLQDKPVESLSEDEKRALRLGERAKNQMITANLRLVVNLAKRYQGKGLELLDL 88

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG +GL +A EKFD   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+ 
Sbjct: 89  IQEGTLGLTRAVEKFDPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLR 148

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGD 590
               R+     R+P  EE+A  L +P++ V  +L        +SL+  +    D S L D
Sbjct: 149 AAKARLFQSTGRQPIAEELADYLKLPLDEVEDLLGCELRSVTVSLQGVVKSKSDPSELVD 208

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGK 647
            +  +       + +     +T  ++L    LTP+E  V+ +RFG+ G N   TL EV +
Sbjct: 209 VLPSEEMPPMERAELDER-TQTVWKLLDQANLTPKERTVVMLRFGLDGTNEWRTLAEVAR 267

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           Q   +RE  RQ+  +++RKL+       L
Sbjct: 268 QMSCSREYCRQVVQRSLRKLRRAGIQSGL 296


>gi|46241495|gb|AAS82950.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 311

 Score =  153 bits (386), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 89/254 (35%), Positives = 150/254 (59%), Gaps = 8/254 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  ++        AK+ ++++N +LV++V K +  +G    DL+ EG  GL+K  EK+D 
Sbjct: 36  VESLKLRYDAGLKAKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDA 95

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++F TYA WW++QA++RS+A+    +R+P+HM +++ ++   + ++  ++ REPT  
Sbjct: 96  TKGFRFGTYAHWWIRQAVSRSLAETGRAVRLPMHMIEQLTRLKNLSAKLQTQLAREPTLP 155

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ---A 607
           E+AK   +PV  V+ +++  +   SL+TPI     + LG  ++D        +  +    
Sbjct: 156 ELAKAAGLPVTRVQMLMETARSAASLDTPI---GGNELGPTVKDSVEDEREAADEEFGSD 212

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +LR     +L  L  RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL
Sbjct: 213 SLRNDMEAMLLELPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKL 272

Query: 668 KHPS--RSKKLRSF 679
           +  +   S KL  +
Sbjct: 273 RVKTIDVSGKLMEY 286


>gi|254430393|ref|ZP_05044096.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197624846|gb|EDY37405.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 302

 Score =  153 bits (386), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 89/278 (32%), Positives = 155/278 (55%), Gaps = 12/278 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  +V ++  ++   +    +      + R      ++       AK +M+ ANLRLV++
Sbjct: 22  LGRKVQAMAVLQERCREAGGQGPACEYDDRE-----KRVLRLGERAKNQMITANLRLVVN 76

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y N+GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q + R+++ QS T
Sbjct: 77  LAKRYQNKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQGLNRALSTQSRT 136

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISL 576
           IRIPV++ +K+ ++     R        P+P+ +A ++ +P+  V ++L        +SL
Sbjct: 137 IRIPVNVNEKLTRLRAAKARYLQSHGVSPSPKALAGEMQLPLAEVEELLGCELRSITVSL 196

Query: 577 ETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--LTPREERVLRMRFG 633
           +  +    D S L D +     ++P++ A  A    +  ++L S  LTP+E  V+ +RFG
Sbjct: 197 QGVVKSKADPSELVDVLPSPE-LAPMERAELAERSASVWKLLESSNLTPKERTVVMLRFG 255

Query: 634 I-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           + G +   TL EV +Q   +RE  RQ+  +A+RKL+  
Sbjct: 256 LDGSHEWRTLAEVARQLDCSREYCRQVVQRALRKLRKT 293


>gi|54401876|gb|AAV34623.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401880|gb|AAV34625.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401882|gb|AAV34626.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401884|gb|AAV34627.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401886|gb|AAV34628.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401888|gb|AAV34629.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score =  153 bits (386), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 89/241 (36%), Positives = 152/241 (63%), Gaps = 3/241 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 1   LGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLD 57

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 58  LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L D +
Sbjct: 118 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDIL 177

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++  +T
Sbjct: 178 ADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLT 237

Query: 653 R 653
           R
Sbjct: 238 R 238



 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           L E+G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 1   LGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 59


>gi|317060654|ref|ZP_07925139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
 gi|313686330|gb|EFS23165.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 276

 Score =  153 bits (385), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 93/243 (38%), Positives = 147/243 (60%), Gaps = 4/243 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K +     AK +++  NLRLV++VAK Y ++G+  +DLI EGN+GL++A EKFD   G++
Sbjct: 35  KAQSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVEKGFR 94

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA+WW+KQ+I+++I  +   IRIP +  D ++K+ R            P+ EE+A+ 
Sbjct: 95  FSTYAVWWIKQSISKAIIFKGREIRIPSYRYDILNKINRYVTEEIKLYGVYPSVEEVAEY 154

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L MPV  V +++   +EP+SL T IG  +  +L D +         +      +++    
Sbjct: 155 LNMPVNKVEEIMIEFQEPMSLSTEIG--EDIYLEDTLS-GTEEHFEEKVYYKMMQQRLKD 211

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  L  RE+ +L++RFG+     HTLEE+GK F +TRER+RQIE   ++KLK    +K+
Sbjct: 212 ILNRLDTREQEILKLRFGLDGYEIHTLEEIGKNFNITRERVRQIEKNTLKKLKR-KYTKE 270

Query: 676 LRS 678
           LR 
Sbjct: 271 LRE 273


>gi|330447824|ref|ZP_08311472.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492015|dbj|GAA05969.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 286

 Score =  153 bits (385), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 96/269 (35%), Positives = 150/269 (55%), Gaps = 4/269 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +  IS +  ++  +    +   RK     + AKK +VE+NLRLV+S+AKKY    L
Sbjct: 11  VRLYLNDISNKPLLTKEDE---IQYSRKFLMGDTNAKKILVESNLRLVVSIAKKYRASKL 67

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGLM A +KFD   G++FSTYA WW+KQ I R+I +Q+ TIR+PVH+  +
Sbjct: 68  SLSDLIDEGNIGLMTAVDKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVHVSKE 127

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-H 587
           I+ ++RT R +      EPT ++IA+ L   +  +  +L      +SLE  +GD++ S  
Sbjct: 128 INTLLRTHRELMKVNNNEPTQDDIARVLNRDINEISSLLASEVNVVSLEQTLGDDENSNT 187

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           +   + D+   SP       ++ + T  +L  L  R+  ++  R+G+     HTL+EV  
Sbjct: 188 VAYLVADEQIASPSAEVDSDDIMKVTNMILHKLPSRDREIMCRRYGLMGYEPHTLQEVAD 247

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              +TRERIRQ++ K +  LK     +  
Sbjct: 248 SVGLTRERIRQLQIKTLNTLKRSLERENY 276



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 3/88 (3%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VR+YL ++ +  LL++E EI  +++   G       L ES L    ++    +     
Sbjct: 9   DVVRLYLNDISNKPLLTKEDEIQYSRKFLMGDTNAKKILVESNLRL--VVSIAKKYRASK 66

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGH 206
             L ++ID E  IG  +    F   +G 
Sbjct: 67  LSLSDLID-EGNIGLMTAVDKFDPEKGF 93


>gi|149197872|ref|ZP_01874921.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139093|gb|EDM27497.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  153 bits (385), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 95/272 (34%), Positives = 151/272 (55%), Gaps = 6/272 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +R+ +K+I+    IS  +   +  ++      +  A+++++  NLRLV+ +A  + + 
Sbjct: 6   ESVRSYMKNIAELPLISRDDEVELAELI---NNGSESAREQLIVGNLRLVVKIAHDFKSL 62

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLI EGNIGLMKA EKF   +G KFS+Y  WW+KQAI R +A+QS  IRIPV   
Sbjct: 63  GVPLADLISEGNIGLMKAVEKFKPGMGAKFSSYGAWWIKQAIRRCVAEQSRVIRIPVQSA 122

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDT 585
            K++K+ R A  ++ ++ R P+ +EIA+   M    V  +      P ISL T + D + 
Sbjct: 123 VKMYKIQRVAMHLAEELGRVPSEKEIAEAADMSQRSVHNLKVAATSPTISLSTSLKDGED 182

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEE 644
             L D + D  A  P       +++      +   LT RE+ ++ MR+G+     HTL+E
Sbjct: 183 GVLEDMLPDLMAKMPGGEMDDRDVKSLLQDCVDQHLTEREKLIINMRYGLNGGEQHTLDE 242

Query: 645 VGKQFCVTRERIRQIEAKAIRKL-KHPSRSKK 675
           + +    TRER+RQI+ KA++KL +H    KK
Sbjct: 243 ISELIGRTRERVRQIQHKALKKLSRHLDEIKK 274



 Score = 41.7 bits (96), Expect = 0.40,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            D+ VR Y++ +  + L+SR+ E+ +A+ I  G       L    L    ++    +   
Sbjct: 4   IDESVRSYMKNIAELPLISRDDEVELAELINNGSESAREQLIVGNLRL--VVKIAHDFKS 61

Query: 177 GTTLLREII 185
               L ++I
Sbjct: 62  LGVPLADLI 70


>gi|124021877|ref|YP_001016184.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962163|gb|ABM76919.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 350

 Score =  153 bits (385), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 93/288 (32%), Positives = 158/288 (54%), Gaps = 9/288 (3%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-------MVRKGECEASIAK 445
            E +  +  +V  ++ +      +  +TG + +  + +          ++K       AK
Sbjct: 58  HEQEITLGRQVQELMSLEQLESELEGKTG-APASRKELAKAAGLSELQLKKKLQIGRRAK 116

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++
Sbjct: 117 ERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIR 176

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V+ 
Sbjct: 177 QGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEVKD 236

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++   ++P+SLE  +  +        +       P +      ++     +L  L   + 
Sbjct: 237 LMCRARQPMSLEMKV-GDGDETELLELLAGEEELPSEKVEVDCMKGDLRTLLEKLPELQG 295

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           RVLRMR+GI       L  +G+   ++R+R+R +E   +  L+  S +
Sbjct: 296 RVLRMRYGIDGGEPMNLTGIGRILDISRDRVRNLERHGLNGLRQLSET 343



 Score = 41.0 bits (94), Expect = 0.77,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS E EI + ++++ 
Sbjct: 41  DLVRSYLRDIGRVPLLSHEQEITLGRQVQE 70


>gi|2780746|dbj|BAA24364.1| plastid RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 519

 Score =  153 bits (385), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 158/304 (51%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +    +G W      ++   L      K ++    IS  E R           E+ +
Sbjct: 223 VHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELR-------SRMHESFL 275

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 276 AREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 335

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++A+ S T R+P ++ +++  +      + ++    PT E IA  L +  + V
Sbjct: 336 IRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYELEDQ-GIAPTIENIAGSLNISEKKV 394

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+              L  +IED+N A  P     +  L+E   ++L 
Sbjct: 395 LNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 454

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 455 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLE 513

Query: 678 SFLD 681
           + L+
Sbjct: 514 ALLE 517


>gi|239814806|ref|YP_002943716.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus S110]
 gi|239801383|gb|ACS18450.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus S110]
          Length = 331

 Score =  153 bits (385), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 136/266 (51%), Gaps = 11/266 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ +      +  E        R        A++ M+E NLRLV+++AK Y  RG+   
Sbjct: 56  YLRQVRRTELFTPEEEYQAACAAR---AGDFAARQSMIEHNLRLVVNIAKAYLGRGVPLS 112

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+EGN+GLM A  KF+   G++FSTYA WW++Q++ R++  Q+  IR+PVH+  ++ +
Sbjct: 113 DLIEEGNLGLMHAITKFEPERGFRFSTYATWWIRQSVERAVLTQARAIRLPVHVVRELQQ 172

Query: 532 VVRTARRMSNKIKREPTP------EEIAKKLAMPVEGVRKVLKITKEPISLET-PIGDED 584
           V+R  R +    +           E++A  L + V+ V ++L + + P SL+      ++
Sbjct: 173 VLRARRTLEGDAEFLAHRPDGVRVEDVAAFLGLEVQAVAELLALAEAPRSLDAGDAHGDE 232

Query: 585 TSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              L D +  ++             +     + + +L  RE  VL  R+G+      TLE
Sbjct: 233 GFTLADTVASEDEQGDPTDVTHTHEVARLLDQWVHALDAREREVLEGRYGLHDREPETLE 292

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  +  +TRER+RQI+ +A+ K++ 
Sbjct: 293 VLSVRLGLTRERVRQIQNEALAKMRR 318



 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 2/90 (2%)

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
           S A+ ++  +    D       D + +YLR++   EL + E E   A    AG      S
Sbjct: 29  SPAAPAADLIAATTDLPGGEGADALTIYLRQVRRTELFTPEEEYQAACAARAGDFAARQS 88

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIID 186
           + E  L    ++            L ++I+
Sbjct: 89  MIEHNLRL--VVNIAKAYLGRGVPLSDLIE 116


>gi|148793336|gb|ABR12732.1| RNA polymerase sigma factor [Photobacterium phosphoreum]
 gi|148793338|gb|ABR12733.1| RNA polymerase sigma factor [Photobacterium phosphoreum]
          Length = 285

 Score =  152 bits (384), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 124/328 (37%), Gaps = 44/328 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     + P         T   +         E + +D  +   D +       ++    
Sbjct: 61  I--SGFVDPNE-----EATAAPTATHIGSELSETDLEDEDKDLEDGDDDDDAEDEEEDDG 113

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L    +  A  ++                                  
Sbjct: 114 SIDPELAREKFLELRHSYEKMALAINT--------------------------------- 140

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
             + +     +V  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 141 --NGRQHATTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 198

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 199 KMPKKTFISLFGGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRATLKLRILEQETGLS 257

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEA 451
           I   + I   +  GE +A  AKKEMVEA
Sbjct: 258 IERIKDISRRMSIGEAKARRAKKEMVEA 285


>gi|257463050|ref|ZP_05627452.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 272

 Score =  152 bits (384), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 93/243 (38%), Positives = 147/243 (60%), Gaps = 4/243 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K +     AK +++  NLRLV++VAK Y ++G+  +DLI EGN+GL++A EKFD   G++
Sbjct: 31  KAQSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVEKGFR 90

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA+WW+KQ+I+++I  +   IRIP +  D ++K+ R            P+ EE+A+ 
Sbjct: 91  FSTYAVWWIKQSISKAIIFKGREIRIPSYRYDILNKINRYVTEEIKLYGVYPSVEEVAEY 150

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L MPV  V +++   +EP+SL T IG  +  +L D +         +      +++    
Sbjct: 151 LNMPVNKVEEIMIEFQEPMSLSTEIG--EDIYLEDTLS-GTEEHFEEKVYYKMMQQRLKD 207

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  L  RE+ +L++RFG+     HTLEE+GK F +TRER+RQIE   ++KLK    +K+
Sbjct: 208 ILNRLDTREQEILKLRFGLDGYEIHTLEEIGKNFNITRERVRQIEKNTLKKLKR-KYTKE 266

Query: 676 LRS 678
           LR 
Sbjct: 267 LRE 269


>gi|54401878|gb|AAV34624.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score =  152 bits (384), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 89/241 (36%), Positives = 152/241 (63%), Gaps = 3/241 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y NRGL  LD
Sbjct: 1   LGEIGYSPLLTAEEK---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLD 57

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  
Sbjct: 58  LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L D +
Sbjct: 118 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDIL 177

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++  +T
Sbjct: 178 ADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLT 237

Query: 653 R 653
           R
Sbjct: 238 R 238


>gi|215270901|emb|CAR48128.1| RNA polymerase sigma factor [Vibrio cholerae]
 gi|223635919|emb|CAQ03761.1| RNA polymerase sigma factor [Vibrio cholerae]
          Length = 292

 Score =  152 bits (384), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 126/332 (37%), Gaps = 42/332 (12%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+REMG++ELL+REGEI IAKRIE G   + +++ E P T   ++   D +      L +
Sbjct: 1   YMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTD 60

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I     + P             ++   E S  +   +D    E + E     S D   +
Sbjct: 61  LI--SGFVDPND---METEAPTATHIGSELSEADLADEDDAVVEDEDEDGDGESSDSEEE 115

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           V   PE A      L                                       Q+  + 
Sbjct: 116 VGIDPELAREKFNELR-----------------------------------GKFQNLQLA 140

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS- 362
             +  + S +     + ++ +     L   + D LVE L     R+   E  +++     
Sbjct: 141 VNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEV 200

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+    G E +  W+       +  +   V  + + I +   +++ I  ET +
Sbjct: 201 AKMPKKSFIALFTGNESNEEWLDKVLA-SDKPYVAKVREQEEEIRRSIQKLQMIEQETSL 259

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           S+   + I   +  GE +A  AKKEMVEANLR
Sbjct: 260 SVERIKDISRRMSIGEAKARRAKKEMVEANLR 291


>gi|327538655|gb|EGF25307.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica WH47]
          Length = 330

 Score =  152 bits (384), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 87/232 (37%), Positives = 143/232 (61%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +      +A+ +MV ANLRLV+++++ YT +GL   DLI+EGN+GL++A E FD   G +
Sbjct: 87  RIAQGDVMARDQMVRANLRLVVNISRGYTGKGLGLQDLIEEGNLGLLRAVEGFDPIHGTR 146

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA +W+KQ+I R++ + + TIRIP +M + + K  R   R++ ++ R PT EE+A+ 
Sbjct: 147 FSTYASYWIKQSIKRALINSAKTIRIPAYMVELLSKWRRATARLNEELGRTPTNEEVARV 206

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +P + +  + K  K   S       E    LGD ++D+   +P +  +  ++ +    
Sbjct: 207 LGLPKKKLPIIRKAIKINNSTPQSDQTEAGWSLGDMVQDERLKAPDEEMLDHDILKHAMS 266

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L  L  RE  VL++RFG+G     TL+E+G +  +TRER+RQIE +A+R+L
Sbjct: 267 LLGDLEERESTVLKLRFGLGGVEPMTLKEIGAELGLTRERVRQIETEALRRL 318


>gi|2564653|gb|AAC45358.1| group 2 alternative sigma factor [Nostoc punctiforme PCC 73102]
          Length = 321

 Score =  152 bits (384), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 85/262 (32%), Positives = 149/262 (56%), Gaps = 5/262 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +  E + +        ++S          + ++  +     +   AK +M+ ANLRLV+S
Sbjct: 53  ILAESEKLTIELKRTPTLSEWANQMQLSEQELLQQL----NQGKKAKHKMITANLRLVVS 108

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y  R L+ +DLIQEG +GL +  EKF+  LGY+ +TYA WW++Q ITR+IA Q   
Sbjct: 109 IAKQYQRRNLELMDLIQEGTLGLERGVEKFNPALGYRKTTYAYWWIRQGITRAIAQQGRA 168

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P+H+ +K++K+ R  R +S  + R PT  EIA  L++    +R+ L +    ISL+ 
Sbjct: 169 IRLPIHINEKLNKIKRVQRELSQTLGRIPTSTEIANALSLKPSQIREFLLLATRTISLDI 228

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       L D IED    S      + +L +    +L++L+ +++ +L + FG+    
Sbjct: 229 RVSSAKDLRLQDLIEDYKYSSNSY-ITEESLNQEVNSLLSNLSRQQQEILNLHFGLTDGE 287

Query: 639 DHTLEEVGKQFCVTRERIRQIE 660
           + +L+++G++  ++RER+RQIE
Sbjct: 288 ELSLQQIGQRLGISRERVRQIE 309



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 27/42 (64%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
             +  + +++T D VR YL+E+G I LL++E EI  A+ ++ 
Sbjct: 8   DTKASNTNKATTDTVRAYLKEIGRIPLLTQEQEIIFAQEVQQ 49


>gi|295133351|ref|YP_003584027.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294981366|gb|ADF51831.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 284

 Score =  152 bits (383), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 76/265 (28%), Positives = 141/265 (53%), Gaps = 3/265 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     IS  E    V + RK +     A   +V +NLR V+SVAK+Y  +GL   
Sbjct: 21  YLKDIGPIARISSEEE---VELTRKIKAGDKKALHTLVTSNLRFVVSVAKQYQFKGLSLS 77

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA +FD   G+KF +YA+WW++QA+ +SI++ +  +R+P++    I+K
Sbjct: 78  DLIAEGNLGLIKAANRFDETRGFKFISYAVWWIRQAMVQSISENARVVRLPLNKLTLINK 137

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +    +   ++RE + EE++  L +P+  + +  K     +SL+ P+ +++     + 
Sbjct: 138 IRKANSALQQLLQREASLEEVSNFLNLPLTEIEEAGKSNATYLSLDKPLSNDNDDFTLNQ 197

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +       P    +  +      +++  L  RE+ V+ + FG+      +L ++     +
Sbjct: 198 LITSKIEDPDQGLLNVSTSHEINQLMTILEKREKEVIILLFGLNGGEAKSLRDISTLLGL 257

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           T ER+RQI+   + KL+   ++  L
Sbjct: 258 TSERVRQIKEMGLIKLRRSPKAAIL 282



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++G I  +S E E+ + ++I+AG    + +L  S L F   +  + +       L +
Sbjct: 21  YLKDIGPIARISSEEEVELTRKIKAGDKKALHTLVTSNLRFVVSVAKQYQFKG--LSLSD 78

Query: 184 II 185
           +I
Sbjct: 79  LI 80


>gi|330448286|ref|ZP_08311934.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328492477|dbj|GAA06431.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 291

 Score =  152 bits (383), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 94/266 (35%), Positives = 145/266 (54%), Gaps = 4/266 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+ +  ++  +    V   RK       +KK ++E+NLRLV+S+AKKY    +   
Sbjct: 20  YLKDIAEKDLLTKEDE---VLYSRKSLAGDENSKKVLIESNLRLVVSIAKKYRGSPMHIS 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+ A EKFD   G++FSTYA WW+KQ I R+I +Q  TIR+PVH+  +I+ 
Sbjct: 77  DLIDEGNIGLITAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQGRTIRLPVHVSKEINT 136

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGD 590
           +VR  +++  K   EP+ E+IA  L   +  V   L      IS +  +  E +   +  
Sbjct: 137 IVRAHKQLVKKNNEEPSKEQIANILNKSLHDVSTTLSYETPIISYDQSVNGEVNAQSMAV 196

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D+    P        + + TT VL  L  R++ ++  RFG+      TL+EV ++  
Sbjct: 197 LIADETMAKPDQHVDDLAIEKITTNVLNCLNKRDKEIICRRFGLLGYEAQTLQEVAEEVG 256

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKL 676
           +TRERIRQ++  ++ KLK+     K 
Sbjct: 257 LTRERIRQLQVTSLSKLKNSLTRDKY 282



 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           KD       D V +YL+++   +LL++E E+  +++  AG       L ES L    ++ 
Sbjct: 6   KDDLLSHGGDIVHLYLKDIAEKDLLTKEDEVLYSRKSLAGDENSKKVLIESNLRL--VVS 63

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
              +       + ++ID E  IG  +    F   +G 
Sbjct: 64  IAKKYRGSPMHISDLID-EGNIGLITAVEKFDPEKGF 99


>gi|238684475|gb|ACR54289.1| RNA polymerase sigma 70 factor [Aeromonas tecta]
          Length = 283

 Score =  152 bits (383), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 126/327 (38%), Gaps = 45/327 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           LREMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +I
Sbjct: 1   LREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     I P          +         S   ++    ++ E + E       +D    
Sbjct: 61  I--SGFIDPN------EADDVAPTATHIGSELSEDDLADEDEEDEDEDGDGDDAEDEGDG 112

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L    + +  ++                                   
Sbjct: 113 GPDPEVAREKFGELRAQYEVTRLSI----------------------------------- 137

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSY 363
           QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +  
Sbjct: 138 QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQA 197

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+      E +  W  Y K   +      +  + D +L+   +++ I  ETG+S
Sbjct: 198 KMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMDED-VLRAIGKLQQIEEETGLS 256

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVE 450
           I++ + I   +  GE +A  AKKEMVE
Sbjct: 257 IAQIKDINRRMSIGEAKARRAKKEMVE 283


>gi|113954287|ref|YP_730230.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881638|gb|ABI46596.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 318

 Score =  152 bits (383), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 95/283 (33%), Positives = 166/283 (58%), Gaps = 7/283 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIV----SMVRKGECEASIAKKEMVEANLRLVI 457
           E+  +  +  E+K       ++  E+        + +++       AK+ MV ANLRLV+
Sbjct: 37  ELMDLEALEAELKDQRGGEEVARDEWAKAAGMSAAQLKRKLQAGRRAKERMVAANLRLVV 96

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++Q ITR+IA++S 
Sbjct: 97  SVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSR 156

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           TIR+P+H+ + ++K+ +  R +S ++ R P+  E+A  + +P E V+ ++   ++P+SLE
Sbjct: 157 TIRLPIHITEMLNKLKKGQRELSQELGRTPSVTELASFVELPEEEVKDLMCRARQPVSLE 216

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             +GD D + L + +     + P D      L+     +L+ L   + +VLRMR+G+   
Sbjct: 217 MKVGDGDDTELLELLAGDGEL-PSDQVEGECLKGDLRDLLSQLPELQGKVLRMRYGMDGE 275

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              +L  + K   ++R+R R++E + +  L+     ++L++++
Sbjct: 276 EPMSLTGIAKSMKMSRDRTRRLEREGLEMLRRGD--EQLQAYV 316



 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS + EI + ++++ 
Sbjct: 8   DLVRSYLRDIGRVPLLSHQQEITLGRQVQE 37


>gi|257452079|ref|ZP_05617378.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|257466122|ref|ZP_05630433.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917279|ref|ZP_07913519.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|317058628|ref|ZP_07923113.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313684304|gb|EFS21139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313691154|gb|EFS27989.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 272

 Score =  152 bits (383), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 96/267 (35%), Positives = 154/267 (57%), Gaps = 7/267 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     +   E   +V   +        AK +++  NLRLV++VAK Y ++G+  +
Sbjct: 10  YLKDIRQYRTLEKEEELDLVIKAQ---SGDEEAKNQLILCNLRLVVNVAKGYRSKGMNLI 66

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL++A EKFD   G++FSTYA+WW+KQ+I+++I  +   IRIP +  D ++K
Sbjct: 67  DLISEGNLGLIRAIEKFDVGKGFRFSTYAVWWIKQSISKAIIFKGREIRIPSYRYDILNK 126

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +            PT EE+A+ L MPV  V +V+   +EP+SL T IG  +  +L D 
Sbjct: 127 INKYVTETVKLCGIYPTVEEVAEYLKMPVNKVEEVMIEFQEPMSLSTEIG--EDIYLEDT 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +         +      +++    +L+ L  RE+ +L++RFG+     HTLE++GK F +
Sbjct: 185 LSGAE-EHFEEKVYYKMMQQRLKDILSRLESREQEILKLRFGLDGYEIHTLEDIGKNFNI 243

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRS 678
           TRER+RQIE   ++KLK    +K+LR 
Sbjct: 244 TRERVRQIEKNTLKKLKR-KYTKELRE 269


>gi|164415557|gb|ABY53195.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415559|gb|ABY53196.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415561|gb|ABY53197.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415563|gb|ABY53198.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415565|gb|ABY53199.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415567|gb|ABY53200.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415569|gb|ABY53201.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415571|gb|ABY53202.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415573|gb|ABY53203.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415575|gb|ABY53204.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415577|gb|ABY53205.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415579|gb|ABY53206.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415581|gb|ABY53207.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415583|gb|ABY53208.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415585|gb|ABY53209.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415587|gb|ABY53210.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415589|gb|ABY53211.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415591|gb|ABY53212.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415593|gb|ABY53213.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 166

 Score =  151 bits (382), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 110/162 (67%), Positives = 133/162 (82%)

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+K+ KEPIS+ETP
Sbjct: 3   RIPVHMMETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKVAKEPISMETP 62

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IGD++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTD
Sbjct: 63  IGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTD 122

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 123 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 164


>gi|123968168|ref|YP_001009026.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123198278|gb|ABM69919.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 307

 Score =  151 bits (382), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 86/254 (33%), Positives = 140/254 (55%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 RK       AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+
Sbjct: 50  EYSEAERKKIKIGEKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKY 109

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     ++       PT
Sbjct: 110 DPSRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRSAKSKLMQLKGIPPT 169

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+A+++ +  E V ++L        +SL+  +    D S L D +          + +
Sbjct: 170 SDELAEEMKITKEEVDELLSCELRSITVSLQGTVKSKSDPSELVDILPSDQTPPMELAEL 229

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +  ++L    LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 230 -AERTASAWKLLDKANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQR 288

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 289 ALRKLRKAGIQNGL 302


>gi|148793342|gb|ABR12735.1| RNA polymerase sigma factor [Photobacterium iliopiscarium]
          Length = 285

 Score =  151 bits (382), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 124/328 (37%), Gaps = 44/328 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     + P         T   +         E + +D  +   D +       ++    
Sbjct: 61  I--SGFVDPNE-----EATAAPTATHIGSELSETDLEDEDKDLEDGDDDDDAEDEEEDDG 113

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L    +  A  ++                                  
Sbjct: 114 SIDPELAREKFLELRHSYEKMALAINT--------------------------------- 140

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
             + +     ++  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 141 --NGRQHATTEIAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 198

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 199 KMPKKTFISLFAGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLS 257

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEA 451
           I   + I   +  GE +A  AKKEMVEA
Sbjct: 258 IERIKDISRRMSIGEAKARRAKKEMVEA 285


>gi|33240031|ref|NP_874973.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33237557|gb|AAP99625.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 310

 Score =  151 bits (382), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 142/248 (57%), Gaps = 7/248 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R+       AK  M+ ANLRLV+++AKKY  +GL  LDLIQEG IGL +A EK+D   G+
Sbjct: 56  RRTIKIGEKAKNHMITANLRLVVNLAKKYQGKGLDLLDLIQEGTIGLTRAVEKYDPKRGH 115

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+      +  +    P+ E++AK
Sbjct: 116 RFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRAAKSELMQEYGTPPSAEQLAK 175

Query: 555 KLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           KL++  + +  +L+       +SL+  I    D S LGD +          + + A   +
Sbjct: 176 KLSVSKQIIGDLLECEMRSITVSLQGVIQSKTDPSELGDVLPSDEIPPMELAEL-AERND 234

Query: 612 TTTRVL--ASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   +L  A+LTP+E  ++ +RFG+ G N   TL EV K    +RE  RQ+  +A+RKL+
Sbjct: 235 SAWSLLNKANLTPKERTIVSLRFGLDGTNEWRTLAEVAKHMNCSREYCRQVVQRALRKLR 294

Query: 669 HPSRSKKL 676
                  L
Sbjct: 295 KTGIQSGL 302


>gi|47777365|gb|AAT37999.1| putative RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 882

 Score =  151 bits (382), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 140/281 (49%), Gaps = 5/281 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    +++LK  +E+   S      I E     +++R    E    ++ ++     LV  
Sbjct: 604 LEKIRENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKY 658

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  
Sbjct: 659 IAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGV 718

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T
Sbjct: 719 IQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYT 778

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            IG    +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+    
Sbjct: 779 EIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGK 838

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             +LE++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 839 CRSLEQIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 879


>gi|222632746|gb|EEE64878.1| hypothetical protein OsJ_19735 [Oryza sativa Japonica Group]
          Length = 1012

 Score =  151 bits (382), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 140/281 (49%), Gaps = 5/281 (1%)

Query: 399  VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
            +    +++LK  +E+   S      I E     +++R    E    ++ ++     LV  
Sbjct: 734  LEKIRENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKY 788

Query: 459  VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
            +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  
Sbjct: 789  IAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGV 848

Query: 519  IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
            I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T
Sbjct: 849  IQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYT 908

Query: 579  PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
             IG    +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+    
Sbjct: 909  EIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGK 968

Query: 639  DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              +LE++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 969  CRSLEQIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 1009


>gi|168704138|ref|ZP_02736415.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 280

 Score =  151 bits (382), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 85/256 (33%), Positives = 134/256 (52%), Gaps = 7/256 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     +S +E R +   +         A+  MV ANLRLV+++A+ YT RGL   
Sbjct: 24  YLREIDRTPLLSATEERELGGRI---LDGDPAARDRMVRANLRLVVNLARGYTGRGLSLD 80

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+ EGN+GL++A E FD  +  +FSTYA +W+KQ+I R+I + + TIR+P +M   + +
Sbjct: 81  DLVAEGNMGLLRAVEGFDPGMSTRFSTYASFWIKQSIQRAIVNTARTIRVPTYMAALVAR 140

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R    + +++ R P PEE+A  L +    +  V    K  ++      D+    L   
Sbjct: 141 WRRATAALGDELGRAPAPEEVAGHLGLSRRKLAMVQLALK--VAGAGTQADDAEGGLEGL 198

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D         A +    +     L  L PR+  VLR+RFG+      TL+EVG+   +
Sbjct: 199 IPDTRDSGSDADAAEQL--KLVFEQLDRLNPRDADVLRLRFGLSGEEPKTLKEVGEALGL 256

Query: 652 TRERIRQIEAKAIRKL 667
           T+ER+RQIE+ A+  L
Sbjct: 257 TKERVRQIESAALSAL 272



 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/85 (20%), Positives = 26/85 (30%), Gaps = 9/85 (10%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLRE+    LLS   E  +  RI  G       +  + L    ++            L +
Sbjct: 24  YLREIDRTPLLSATEERELGGRILDGDPAARDRMVRANLRL--VVNLARGYTGRGLSLDD 81

Query: 184 IIDLEACIGPESKGGFFHGTEGHSY 208
           ++        E   G     EG   
Sbjct: 82  LV-------AEGNMGLLRAVEGFDP 99


>gi|148793344|gb|ABR12736.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 284

 Score =  151 bits (381), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 129/328 (39%), Gaps = 45/328 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I        E+         G    + +   ++K+ +D  + + + E     S D     
Sbjct: 61  ISGFVDPNEEATAAPTATHIGSELSETDLEDEDKDLEDDDDEDAENEEEDDGSID----- 115

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L +  +  A  ++                                  
Sbjct: 116 ---PELAREKFLELRQSYEKMALAIN---------------------------------- 138

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
            +  +     +V  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 139 -QHGRQHATTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 197

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 198 KMPKKTFISLFAGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLS 256

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEA 451
           I   + I   +  GE +A  AKKEMVEA
Sbjct: 257 IERIKDISRRMSIGEAKARRAKKEMVEA 284


>gi|254526924|ref|ZP_05138976.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
 gi|221538348|gb|EEE40801.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
          Length = 307

 Score =  151 bits (381), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 86/254 (33%), Positives = 141/254 (55%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 RK       AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+
Sbjct: 50  EYSEAERKKIKIGEKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKY 109

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     ++       PT
Sbjct: 110 DPSRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRSAKSKLMQLKGIPPT 169

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+A+++ +  E + ++L        +SL+  +    D S L D +    A     + +
Sbjct: 170 SDELAEEMKITKEEIDELLSCELRSITVSLQGTVKSKSDPSELVDILPSDQAPPMELAEL 229

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +  ++L    LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 230 -AERTASAWKLLDKANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQR 288

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 289 ALRKLRKAGIQNGL 302


>gi|125602291|gb|EAZ41616.1| hypothetical protein OsJ_26150 [Oryza sativa Japonica Group]
          Length = 420

 Score =  151 bits (381), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 158/304 (51%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +    +G W      ++   L      K ++    IS  E R           E+ +
Sbjct: 124 VHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELR-------SRMHESFL 176

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 177 AREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 236

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++A+ S T R+P ++ +++  +      + ++    PT E IA  L +  + V
Sbjct: 237 IRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYELEDQ-GIAPTIENIAGSLNISEKKV 295

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+              L  +IED+N A  P     +  L+E   ++L 
Sbjct: 296 LNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 355

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 356 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLE 414

Query: 678 SFLD 681
           + L+
Sbjct: 415 ALLE 418


>gi|328947378|ref|YP_004364715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328447702|gb|AEB13418.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 283

 Score =  151 bits (381), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 93/284 (32%), Positives = 158/284 (55%), Gaps = 10/284 (3%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A ++D +    NEIK I     ++  E   + +           A+ +++ +N+R VI +
Sbjct: 6   AKDLDVVRIHLNEIKKIP---LLTNDEEIQLATRA---AAGDKAARDKLLTSNMRFVIKI 59

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A +Y N+GL++ DLI EG +GLMKA + FD   GY F +YA+WW++Q+I ++I D    I
Sbjct: 60  ASQYLNKGLEYEDLISEGYLGLMKALDHFDVSKGYHFISYAVWWIRQSIMKAIVDFGRPI 119

Query: 520 RIPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           R+PV+   ++ ++ R    +    K   E   EE+A KL M    +R++L I++E ISL+
Sbjct: 120 RLPVNKDAELTEIKRACHSVNPHGKKSEEEELEEVALKLGMTKHHIREMLNISQEMISLD 179

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +PI  +  + L D +      +P D+AI A+L+    +    L  +   VL MR+G+   
Sbjct: 180 SPISGDSDTALVDTVS-AGTFTPEDAAIDASLKTEIDKAFVGLDKKSVEVLNMRYGLNGQ 238

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK-KLRSFL 680
            + TL+EVG++  ++RER+RQIE  AI K++        L+ ++
Sbjct: 239 GERTLKEVGEKMNLSRERVRQIEKHAIAKIRANKICDISLKDYV 282



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           D VR++L E+  I LL+ + EI +A R  AG       L  S + F
Sbjct: 10  DVVRIHLNEIKKIPLLTNDEEIQLATRAAAGDKAARDKLLTSNMRF 55


>gi|83592446|ref|YP_426198.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575360|gb|ABC21911.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 299

 Score =  151 bits (381), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 123/270 (45%), Gaps = 13/270 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++I     ++  E   +   +R  +   S A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLQNIRKFPMLAPEEEYTLAQRLR--DSGDSEAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PMGEVISEGNVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 133

Query: 529 IHKVVRTARRMSNKIKREPTPE-----EIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                    +   ++  E         +IA KL +P + V     +++    SL  P+  
Sbjct: 134 KLFFNLRKMKGQLQLMDEGDMHPDKVTQIATKLGVPEQDVINMNRRLSSPDHSLNAPVRM 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D++       A    +   R   +  L SL  RE  +L  R        
Sbjct: 194 DGDGEWQDWLVDESDDQETTLAESQEMGQRRALLSGALKSLNERERHILTQRRLRD--DP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TLE++ + + ++RER+RQIE +A  KL+ 
Sbjct: 252 VTLEDLSQHYGISRERVRQIEVRAFEKLQK 281


>gi|327399101|ref|YP_004339970.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
 gi|327181730|gb|AEA33911.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
          Length = 289

 Score =  151 bits (380), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 91/276 (32%), Positives = 147/276 (53%), Gaps = 4/276 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             ++     + + +K IS    +S  E + +   ++K       A K++V+ NLR V+SV
Sbjct: 17  EVDLAESSALTSYLKEISKIPVLSAEEEKELGRRIKK---GDKEALKKLVKHNLRFVVSV 73

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKY N G+  LDLI EGN+GL+KAA+KFD     KF +YA WW+KQ+I + I +QS  I
Sbjct: 74  AKKYKNLGIPLLDLINEGNLGLIKAAKKFDPDRNTKFISYAAWWIKQSIMKYITEQSTPI 133

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIP+  + +I K+         K   EP   EI++   +    ++          SL+  
Sbjct: 134 RIPLKAKSRISKIDTIKEDYRQKFDEEPMNGEISEISDLSEREIKNAELARFYFDSLDDY 193

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           + D+     GD I  K   S  D  IQ +L E   + L+ L  RE+ ++++R+G+     
Sbjct: 194 VSDDKDILKGDLISLKEQ-SIEDEHIQKSLIEEVNKFLSELPEREQDIIKLRYGLYDGRP 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            TL E+G+++ +++ER+RQ+E   + KLK   +  K
Sbjct: 253 RTLREIGEKYGISKERVRQLENNILNKLKKRFKEYK 288



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 82/248 (33%), Gaps = 12/248 (4%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+E+  I +LS E E  + +RI+ G    +  L +  L F  ++    +  +    L +
Sbjct: 29  YLKEISKIPVLSAEEEKELGRRIKKGDKEALKKLVKHNLRF--VVSVAKKYKNLGIPLLD 86

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I+       ++   F                ++     + E    I    K        
Sbjct: 87  LINEGNLGLIKAAKKFDPDRNTKFISYAAWWIKQSIMKYITEQSTPIRIPLKAKSRISKI 146

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAME---DQLRPKVMCALDEIAEVYRELRSLQDN 300
                +  +  +      E      LS  E    +L      +LD+     +++    D 
Sbjct: 147 DTIKEDYRQKFDEEPMNGEISEISDLSEREIKNAELARFYFDSLDDYVSDDKDILKG-DL 205

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
               ++  +     K L E++ K +  L   +  I  L   LYD           L  + 
Sbjct: 206 ISLKEQSIEDEHIQKSLIEEVNKFLSELPEREQDIIKLRYGLYD------GRPRTLREIG 259

Query: 361 QSYGIKRD 368
           + YGI ++
Sbjct: 260 EKYGISKE 267


>gi|116070855|ref|ZP_01468124.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116066260|gb|EAU72017.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 239

 Score =  151 bits (380), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 85/235 (36%), Positives = 136/235 (57%), Gaps = 7/235 (2%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++Q 
Sbjct: 1   MITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQG 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R+++ QS TIRIPV++ +K+ K+     R+  +     T E++A+ + +P+  V  +L
Sbjct: 61  LNRALSTQSRTIRIPVNVNEKLTKLRAAKARVMQRNGLTATAEQLAEFMNLPLTEVEDLL 120

Query: 568 KI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTP 622
                   +SL+  +    D S L D +  +       + I A    +   +L  A+LTP
Sbjct: 121 ACELRSVTVSLQGIVKSKSDPSELVDILPSEEIPPMERAEI-AERSASVWALLSKANLTP 179

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +E +V+ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+       L
Sbjct: 180 KEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKTGIQSGL 234


>gi|58696753|ref|ZP_00372293.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
 gi|58537061|gb|EAL60191.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
          Length = 183

 Score =  151 bits (380), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 107/179 (59%), Positives = 142/179 (79%), Gaps = 1/179 (0%)

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WV+Q+ITR+I +QS  +RIP+HM + I K+ R  R+M++++ REPT EE++ +L MP+E 
Sbjct: 5   WVRQSITRAIPEQSKVVRIPLHMVEIISKINRALRKMTHEMGREPTLEELSVELTMPLER 64

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +RKV+KI ++P+SLE P G +D+S  GD IEDK    P D+AI A+LR  TT VLA+LTP
Sbjct: 65  IRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAAILADLRGITTNVLATLTP 124

Query: 623 REERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +EER+LRMRFG+G +  +HTLEEVGK F VTRERIRQIEAKA+RKLKHPSR++KLR F 
Sbjct: 125 KEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPSRARKLRGFF 183


>gi|87306425|ref|ZP_01088572.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
 gi|87290604|gb|EAQ82491.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
          Length = 296

 Score =  151 bits (380), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 92/259 (35%), Positives = 154/259 (59%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    +S  + + +  ++         A+  MV ANLRLV+++A+ YT +GL
Sbjct: 18  LETYLREINETALLSAKDEKDLAKLI---GEGDVNARDRMVRANLRLVVNIARGYTGKGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +G +FSTYA +W+KQ+I R++ + + TIRIP +M + 
Sbjct: 75  GLQDLIEEGNLGLLRAVEGFDPAMGTRFSTYASYWIKQSIKRALINCAKTIRIPAYMVEL 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  R   R++ ++ R PTPEEIA+ L +P + +  + K  K   S       +    L
Sbjct: 135 LSKWRRATNRLTEELGRTPTPEEIARVLGLPKKKLPIIKKAIKIYNSTPQTDQADSGWSL 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G+ + D    +P D  ++ +  +   ++L ++  RE  VLRMRFG+     HTL+E+G++
Sbjct: 195 GEMVMDDRLKNPEDEMVEHDDLKNVMQMLKTMDGREATVLRMRFGLEGMDPHTLKEIGEK 254

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE +A+ KL
Sbjct: 255 LGLTRERVRQIETEALGKL 273



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 28/67 (41%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
             Q++K+  + S   P+  YLRE+    LLS + E  +AK I  G       +  + L  
Sbjct: 2   ATQQKKEIKEESVQSPLETYLREINETALLSAKDEKDLAKLIGEGDVNARDRMVRANLRL 61

Query: 165 QALIIWR 171
              I   
Sbjct: 62  VVNIARG 68


>gi|89072392|ref|ZP_01158971.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89051924|gb|EAR57376.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 286

 Score =  150 bits (379), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 98/267 (36%), Positives = 149/267 (55%), Gaps = 4/267 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I  +R  +  IS +  +S  +    +   RK       +KK ++E+NLRLV+S+AKKY 
Sbjct: 7   EIDVVRLYLNDISNKPLLSKDDE---IQYSRKSLTGDPASKKILIESNLRLVVSIAKKYR 63

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              L   DLI EGNIGLM A EKFD   G++FSTYA WW+KQ I R+I +Q+ TIR+PV+
Sbjct: 64  AANLSLSDLIDEGNIGLMTAVEKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVN 123

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +  +I+ ++RT R +      EPT E+IA+ L    + +  +       +SL+  IGD +
Sbjct: 124 ISKEINTLLRTHRELMKLNNNEPTHEDIAQALNKESKEISALFSNEVNVVSLDQTIGDNE 183

Query: 585 TSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            SH +   + D+   SP       ++ + T  VL  +  R+  ++  RFG+     HTL+
Sbjct: 184 NSHTIAYLVADEQITSPSAEVDNDDMIKITNLVLNGINKRDREIICRRFGLMGYEPHTLQ 243

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHP 670
           EV     +TRERIRQ++ K++  LK  
Sbjct: 244 EVADAVGLTRERIRQLQIKSLNSLKRS 270



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            D VR+YL ++ +  LLS++ EI  +++   G       L ES L     I  +    + 
Sbjct: 8   IDVVRLYLNDISNKPLLSKDDEIQYSRKSLTGDPASKKILIESNLRLVVSIAKKYRAAN- 66

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGH 206
              L ++ID E  IG  +    F   +G 
Sbjct: 67  -LSLSDLID-EGNIGLMTAVEKFDPEKGF 93


>gi|255531368|ref|YP_003091740.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344352|gb|ACU03678.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 77/272 (28%), Positives = 145/272 (53%), Gaps = 3/272 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    +   E   +   +++G+     A + +V +NLR V++VAKKY +  L
Sbjct: 18  LARYLQEISKYPLLDAEEEIVLGKRIKEGDW---DALQRLVSSNLRFVVTVAKKYESPDL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI +GNIGL+KAAE+FD   G+KF +YA+WW++Q+I + +      + +P+     
Sbjct: 75  SLADLISDGNIGLIKAAERFDEKRGFKFISYAVWWIRQSILQGMNTSKRMVHLPMSQISG 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I +V R+  ++  +++R P  EE+A  +    E V   L I+   +SL+ P   +D   +
Sbjct: 135 IRQVKRSEIKLEQELQRIPCREELAGFMKTAEEVVYDYLYISGSQVSLDAPTEGQDGVLI 194

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              ++     +P  S  + +L +   R++  L+PRE  +L + +G+G N     +++   
Sbjct: 195 PCIVQYDKGPAPDASLERESLEKDVQRMMDILSPRERSILFLAYGMGNNRPLQNDDISTL 254

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++ E IR+ + KA+ +L+     K +R +L
Sbjct: 255 LGLSTETIRRSKNKALDRLRGLKEIKMMRRYL 286



 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           + + S    + D +  YL+E+    LL  E EI + KRI+ G    +  L  S L F  +
Sbjct: 5   RIERSITNRSQDSLARYLQEISKYPLLDAEEEIVLGKRIKEGDWDALQRLVSSNLRF--V 62

Query: 168 IIWRDELNDGTTLLREII 185
           +    +       L ++I
Sbjct: 63  VTVAKKYESPDLSLADLI 80


>gi|189916709|gb|ACE62865.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 107/159 (67%), Positives = 130/159 (81%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+K+ KEPIS+ETPIGD
Sbjct: 1   VHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKVAKEPISMETPIGD 60

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 61  DEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTL 120

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 159


>gi|189916717|gb|ACE62869.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 108/159 (67%), Positives = 131/159 (82%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM++ I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD
Sbjct: 1   VHMKETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGD 60

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 61  DEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTL 120

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 159


>gi|11079035|dbj|BAB17522.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 126/315 (40%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDDEEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ+            E+ R+            K  + 
Sbjct: 109 I------------IAAQRFGAVSDQM------------ELARKALK---------KHGRG 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 SKQATAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRFQPDIVRCQQKLTALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|301601122|dbj|BAJ13249.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601124|dbj|BAJ13250.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 106/232 (45%), Positives = 132/232 (56%), Gaps = 21/232 (9%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD 
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQ 218


>gi|302554830|ref|ZP_07307172.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472448|gb|EFL35541.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
          Length = 481

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 99/247 (40%), Positives = 135/247 (54%), Gaps = 11/247 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I ++ R  E     A + +V  N RLV  +A  Y  RGL   DL+Q G IGLM+A  KF
Sbjct: 233 EIAALPRGSERW--RAYECLVLHNQRLVWKIALGYQGRGLDTEDLVQHGTIGLMRAVRKF 290

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G+KFSTYA WW+KQAITR+IAD+   IR+P H+ +K+ KV    R++ N+  R  T
Sbjct: 291 DATKGFKFSTYATWWIKQAITRAIADEGTLIRLPAHVHEKVSKVAVAERKLLNE-GRPRT 349

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQA 607
            + +A    +    V KV +I++   SL+  IG  D + LGD I   +    P    I+ 
Sbjct: 350 VDNVAYVSGLTFAEVEKVRRISRSTDSLDRIIG--DDTALGDLIIGPSRLPGPDVVLIRK 407

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK- 666
             +     V+  L+ RE  VL  R G+  +   TLE++G  F VTRERIRQIE KA  K 
Sbjct: 408 EFQARLRHVVEHLSERERHVLVRRTGLDGDEPDTLEDIGVVFGVTRERIRQIEPKAKAKF 467

Query: 667 ----LKH 669
               L+H
Sbjct: 468 EGQLLRH 474


>gi|256371989|ref|YP_003109813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008573|gb|ACU54140.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 302

 Score =  150 bits (379), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 87/266 (32%), Positives = 140/266 (52%), Gaps = 4/266 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           IR  +  ++     S +E   +   VR        AK EMV ANLRLV+  A++Y +RG+
Sbjct: 37  IRLFLDDLAKHPLPSAAEQVELAKRVR---EGDEDAKAEMVAANLRLVVHWARRYQDRGV 93

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLIQEG  GL++A EKFDW  G+KFSTYA WWV+Q++ R++ +    IR+P+   ++
Sbjct: 94  ELADLIQEGTFGLIRAVEKFDWRRGFKFSTYATWWVRQSLQRAVHNHGQAIRLPMEAAER 153

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             +V    R ++  + R PT EEIA    +    +  V    +   SL+  +G E  + L
Sbjct: 154 SRRVDNVTRELAADLGRAPTEEEIAMAANLSASQLADVRHAARVVASLDQAVGPEGETSL 213

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD +  ++  S  +   ++  RE   R +  L   E +V+ +RFG+  +   +LE   + 
Sbjct: 214 GDLVVAQDT-SFEEEVDESISREMLRRAVEELDELERQVVTLRFGLQGDRPASLEATARI 272

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             +   R R++EA A+ KL    R +
Sbjct: 273 LGIGPRRARRLEASALAKLAENPRLR 298



 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 2/97 (2%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S+ +L  +S    S          A     D +R++L ++    L S   ++ +AKR+  
Sbjct: 5   SDSALKQSSRKRRSVQAEVDSALQAAGLGADSIRLFLDDLAKHPLPSAAEQVELAKRVRE 64

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           G     A +  + L    ++ W     D    L ++I
Sbjct: 65  GDEDAKAEMVAANLRL--VVHWARRYQDRGVELADLI 99


>gi|310815187|ref|YP_003963151.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
 gi|308753922|gb|ADO41851.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
          Length = 809

 Score =  150 bits (379), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 110/445 (24%), Positives = 173/445 (38%), Gaps = 42/445 (9%)

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           N E    +LD+     A    A+ D     +  A++        L   Q   ++   +  
Sbjct: 391 NMEAAGFDLDQATGHDAGLWDAVSDTSSDDLADAIEAALTRRTRLPGTQRFVMDKSDE-- 448

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                  L E +++    L L     +  V+ + D+   I     + +       +    
Sbjct: 449 -----LQLLEPMMRAKQELQLGILGSETAVQTILDVMDSIRAGVRDPVS------VSLKT 497

Query: 370 FLERHQGR-ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            +    G  E        A       W            +           +     E  
Sbjct: 498 IIPSRPGHAETSEV---MAAVEALRSWHTTGRVMDGKRRREALAALEALDLSLAFHKELV 554

Query: 429 HIVSMVRKGECEASI----------AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
             +      + EAS           A + ++  +L  V   A +  + G    D+ Q   
Sbjct: 555 RRLEQFPACQAEASQLEAEILISESATEHLIREHLPYVRRFASRNVDEGEDPEDVFQVAF 614

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL ++  +FD   GY+F  YA +W++QAITR  AD+   IRIPVH  +KI K+ R   R
Sbjct: 615 MGLQRSTRRFDPERGYRFLIYATYWMRQAITRWRADEGAAIRIPVHRNEKITKLDRALER 674

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI---TKEPISLETPIGDEDTSHLGDFIEDK 595
           +  ++    +  E+A++L   ++ V++   I    + P SL+            D     
Sbjct: 675 LDVRVGGAVSDLELAEELEWTIDEVKQFRGIPREAEYPASLDDWDNLLPEPSEADV---- 730

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                     Q          LA L  R+  VLRMRFGIG  TD TLEEVG+ + VTRER
Sbjct: 731 --------FDQTETERILADALAELPERQADVLRMRFGIGRETDMTLEEVGQIYGVTRER 782

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680
           IRQIEAKA+  L HP R ++L++ L
Sbjct: 783 IRQIEAKALDHLSHPGRKRRLQALL 807


>gi|189916711|gb|ACE62866.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916713|gb|ACE62867.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916715|gb|ACE62868.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  150 bits (379), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 108/159 (67%), Positives = 130/159 (81%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           VHM + I+K+ R +R+M  +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD
Sbjct: 1   VHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGD 60

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ SHLGDFIED N  SP+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTL
Sbjct: 61  DEDSHLGDFIEDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTL 120

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVGKQF VTRERIRQIEAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 159


>gi|33862400|ref|NP_893960.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640513|emb|CAE20302.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 335

 Score =  150 bits (378), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 93/288 (32%), Positives = 157/288 (54%), Gaps = 9/288 (3%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-------MVRKGECEASIAK 445
            E +  +  +V  ++ +      +  +TG   +  + +          ++K       AK
Sbjct: 43  HEQEITLGRQVQELMSLEQLESELEGQTG-EPASRKELAKAAGLSELQLKKKLQSGRRAK 101

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++
Sbjct: 102 ERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIR 161

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V+ 
Sbjct: 162 QGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEVKD 221

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++   ++P+SLE  +  +        +       P +      ++     +L  L   + 
Sbjct: 222 LMCRARQPMSLEMKV-GDGDETELLELLAGEEELPSEKVEVDCMKGDLRTLLEKLPELQG 280

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           RVLRMR+GI       L  +G+   ++R+R+R +E   +  L+  S +
Sbjct: 281 RVLRMRYGIDGGEPMNLTGIGRILDISRDRVRNLERHGLNGLRQLSET 328



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            S+AS S V           +  D VR YLR++G + LLS E EI + ++++ 
Sbjct: 3   DSAASKSLVKPAVVPARQLPADVDLVRSYLRDIGRVPLLSHEQEITLGRQVQE 55


>gi|126695941|ref|YP_001090827.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126542984|gb|ABO17226.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 307

 Score =  150 bits (378), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 84/254 (33%), Positives = 140/254 (55%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 RK       AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+
Sbjct: 50  EYSEAERKKIKIGEKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKY 109

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     ++       P+
Sbjct: 110 DPSRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRSAKSKLMQLKGIPPS 169

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+A+++ +  E + ++L        +SL+  +    D S L D +          + +
Sbjct: 170 TDELAEEMKITKEEIDELLSCELRSITVSLQGTVKSKSDPSELVDILPSDQTPPMELAEL 229

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +  ++L    LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 230 -AERTASAWKLLDKANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQR 288

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 289 ALRKLRKAGIQNGL 302


>gi|315185550|gb|EFU19319.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 281

 Score =  150 bits (378), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 86/274 (31%), Positives = 154/274 (56%), Gaps = 8/274 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +    ++ I     +S  E R +   +R+      +A++ ++ ANLRLV+ +A +++  
Sbjct: 13  REETAYLREIKRYKLLSPEEERELGKRIRR---GDPVARERLITANLRLVVKIALQFSVP 69

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            +  LDLIQEGNIGL++A EKFD+    +FSTYA WW++QAI R++ ++   IR+P    
Sbjct: 70  DIPLLDLIQEGNIGLIRAVEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRLPNRKE 129

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D + K+ +  R +  ++ REP+ EEIA  L M  E V +++ + +E +SLET I ++ + 
Sbjct: 130 DVLRKIEKARRLLEQRLMREPSTEEIADLLGMESEEVEELINLGQEVVSLETQI-NDGSM 188

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D      +        +A   +T T +  +L  RE  V+  R+ +     +TL+ + 
Sbjct: 189 DLHDVCPGGASPEEEVCR-KACREDTLTLIQRTLDSRESEVVLHRYAL-TGPRYTLKTLS 246

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +Q  ++ E +RQIE +A+RKL+   R++ +  ++
Sbjct: 247 EQMGISPETVRQIEIRALRKLRE--RAEVVGDYV 278


>gi|54401868|gb|AAV34620.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401871|gb|AAV34621.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401874|gb|AAV34622.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 299

 Score =  150 bits (378), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 154/248 (62%), Gaps = 3/248 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+V
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDV 291

Query: 646 GKQFCVTR 653
           G++  +TR
Sbjct: 292 GREIGLTR 299



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|269123355|ref|YP_003305932.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
 gi|268314681|gb|ACZ01055.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
          Length = 280

 Score =  150 bits (378), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 100/274 (36%), Positives = 144/274 (52%), Gaps = 5/274 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           ++I  I   I  +     ++  E   +   VR  E     AK  ++ +NLRLV+S AKK 
Sbjct: 11  NNINLISLYISDLQNHELLTSEEEVELFKRVR--EENDEQAKHLLILSNLRLVVSEAKKL 68

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              G+  +DLI EGN+GL+K+ +KFD+  G +FSTYA+WW+KQ I +SI +    IRIP 
Sbjct: 69  LGNGMPLIDLISEGNLGLIKSIDKFDYTKGLRFSTYAVWWIKQTIKKSIVNLGRDIRIPS 128

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           +  +++ KV +      N+    PT E IA+ L M    V  +    +E ISL   IG  
Sbjct: 129 YKYEQLSKVNKVIESYQNEFGDIPTAEYIAEVLGMKPSKVVLLQNEFQEIISLNDAIG-- 186

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   L D I   + V          L E       +L PRE+ +L +R+G+  N  HTL+
Sbjct: 187 DNIFLEDVIGQSDNVEDDIIR-NDQLSEMYNLFDKTLNPREKEILELRYGLANNKIHTLK 245

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           E+G++  +TRER+RQIE KAI KLK      K  
Sbjct: 246 EIGEKLSITRERVRQIEKKAITKLKKNLEEYKYM 279


>gi|312194695|ref|YP_004014756.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
 gi|311226031|gb|ADP78886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score =  149 bits (377), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 121/246 (49%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +V +       A+I + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 152 FARLVELPEGDAERAAI-RDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 210

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S K+ R 
Sbjct: 211 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQKLGRS 270

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  EIA  L M  E V + L+       +SL+ P   +D S  + D +  ++      S
Sbjct: 271 PTVAEIAAHLEMTEEEVLEGLESANAYSAVSLDAPDSGDDESPAVADTLGVQDE-----S 325

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L PRE+R+L +RF        T  ++  +  +++  + ++ A+ 
Sbjct: 326 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN----MTQSQIAIELGISQMHVSRLLART 381

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 382 LAQLRR 387


>gi|71894468|ref|YP_278576.1| RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 490

 Score =  149 bits (377), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 101/313 (32%), Positives = 164/313 (52%), Gaps = 22/313 (7%)

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E+D       K              V   ++   +   +     ++  E + +  
Sbjct: 164 NFSPDEIDLQIDEENKKQDLSNKLTETTDIVKWYMRWIGKYGKL-----LTPQEEKDLAE 218

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + KG      A+  +++ NLRLV++ AKKY NRGL F+DL+ EGN GL+KAA+KFD   
Sbjct: 219 EMDKGGSRGKRARDLIIKRNLRLVVNAAKKYKNRGLSFIDLVSEGNAGLLKAAQKFDIKK 278

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFSTYA WW++Q+I+R++ADQ+  IR+PVHM + I+K+ +  R +  +   E   EEI
Sbjct: 279 GFKFSTYATWWIRQSISRAVADQARIIRVPVHMVETINKIYKIEREIQQENGGEIIDEEI 338

Query: 553 AKKLA-----MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           A +L           +R + KI   PISL+  +G E+ S  GDF++D++ +SP++ A + 
Sbjct: 339 AARLGGKSKKYDASYIRYIRKINTSPISLDKQVGKENDSFFGDFVKDESIISPVEFADKE 398

Query: 608 NLRETTTRVLAS-LTPREERVLRMRFGIGMN------TDHTLEEVGKQF-----CVTRER 655
            L       +   L+  E  +++   GIG +         TL+E+ K F      +++ER
Sbjct: 399 ELITKINYYVEKLLSEAEADLIKRYHGIGYDAKGNPVRSATLDEISKDFRGEGKKISKER 458

Query: 656 IRQIEAKAIRKLK 668
           +RQI  K  +KL+
Sbjct: 459 VRQIITKIYKKLR 471



 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSI-ELLSREGEIAIAKRIE 147
           S D +DL     N    L  +       T D V+ Y+R +G   +LL+ + E  +A+ ++
Sbjct: 166 SPDEIDLQIDEENKKQDLSNKLTE----TTDIVKWYMRWIGKYGKLLTPQEEKDLAEEMD 221

Query: 148 AGRAMMMAS 156
            G +    +
Sbjct: 222 KGGSRGKRA 230


>gi|312114652|ref|YP_004012248.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
 gi|311219781|gb|ADP71149.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
          Length = 308

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 75/279 (26%), Positives = 129/279 (46%), Gaps = 13/279 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   +   +    R  E E + A +++V ++LRLV  +A  Y   GL
Sbjct: 13  LARYLEEIRRFPMLEPQQEYMLAK--RWQEHEDAKAAQKLVTSHLRLVARIAMGYRGYGL 70

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 71  PIGEVISEGNVGLMQAVKRFDPDKGFRLATYAMWWIRAAIQEYILRSWSLVKMGTTASQK 130

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++    + +  P++   IA  L +P E V  + +      SL  P+  +
Sbjct: 131 KLFFNLRKAKSQLQALEEGDLRPDQVKTIATNLGVPEEDVVSMNRRLGGDASLNAPLRAD 190

Query: 584 DTS-HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             S    D++ D+        A    L   RE     + SL  RE R+   R        
Sbjct: 191 SESGEWQDWLVDEGPNQETQLAESEELSRRREYLGAAMDSLNERERRIFTARRLAD--DP 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            TLEE+  +F V+RERIRQIE +A  K++   +   L++
Sbjct: 249 LTLEELSSEFNVSRERIRQIEVRAFEKVQKAVQKAALKA 287


>gi|125560253|gb|EAZ05701.1| hypothetical protein OsI_27933 [Oryza sativa Indica Group]
          Length = 372

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 158/304 (51%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +    +G W      ++   L      K ++    IS  E R           E+ +
Sbjct: 76  VHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELR-------SRMHESFL 128

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 129 AREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 188

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++A+ S T R+P ++ +++  +      + ++    PT E IA  L +  + V
Sbjct: 189 IRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYELEDQ-GIAPTIENIAGSLNISEKKV 247

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+              L  +IED+N A  P     +  L+E   ++L 
Sbjct: 248 LNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 307

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 308 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLE 366

Query: 678 SFLD 681
           + L+
Sbjct: 367 ALLE 370


>gi|37806471|dbj|BAC99906.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 342

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 158/304 (51%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +    +G W      ++   L      K ++    IS  E R           E+ +
Sbjct: 46  VHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELR-------SRMHESFL 98

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 99  AREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 158

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++A+ S T R+P ++ +++  +      + ++    PT E IA  L +  + V
Sbjct: 159 IRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYELEDQ-GIAPTIENIAGSLNISEKKV 217

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+              L  +IED+N A  P     +  L+E   ++L 
Sbjct: 218 LNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 277

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 278 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLE 336

Query: 678 SFLD 681
           + L+
Sbjct: 337 ALLE 340


>gi|114155166|dbj|BAF31033.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 142/263 (53%), Gaps = 27/263 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGG-- 168

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
                     +EDED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 169 --DMPMPEEEEEDEDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVKLV 325
            G        + + LK++L+  V
Sbjct: 227 AGTLSSGQERRYRRLKDQLITAV 249


>gi|11079023|dbj|BAB17516.1| DNA-directed RNA polymerase subunit D [Pseudomonas mucidolens]
          Length = 268

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 117/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E  +    +    + + D + A     DD  +    P  
Sbjct: 56  ------SGYIDPDDGITPPAAEVPAPVDPKAAKADDDSDDDEADASDDDDEVESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVSDQMELARKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 135 SKQATAELLALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRTD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|114155172|dbj|BAF31036.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|160358237|dbj|BAF93439.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601118|dbj|BAJ13247.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601144|dbj|BAJ13260.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 113/263 (42%), Positives = 142/263 (53%), Gaps = 27/263 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGG-- 168

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
                     +EDED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 169 --DMPMPEEEEEDEDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVKLV 325
            G        + K LK++L+  V
Sbjct: 227 AGTLSSGQERRYKELKDQLITAV 249


>gi|260773542|ref|ZP_05882458.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
 gi|260612681|gb|EEX37884.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
          Length = 297

 Score =  149 bits (377), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 94/274 (34%), Positives = 155/274 (56%), Gaps = 7/274 (2%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVD----SILKIRNEIKSISVETGISISEFRHIVSMVR 435
           DP  ++ A+   E      +  E D    S+   +  +  I     ++  E    V   R
Sbjct: 16  DPEVINAAESDVEQLSAINLKEEYDASSKSLDATQMYLSEIGFSPLLTAEEE---VLYAR 72

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   G++
Sbjct: 73  RALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFR 132

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S ++  EPT EEIA +
Sbjct: 133 FSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTAEEIAAE 192

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L  PVE V K+L++ +   S++TPIG +    L D + D N   P  S    ++R +   
Sbjct: 193 LDKPVEDVNKMLRLNERISSVDTPIGGDGDKALLDILPDSNHSDPEVSTQDEDIRLSLLN 252

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            L  L P+++ VL  R    +      ++ G++ 
Sbjct: 253 WLDELNPKQKEVLARRLDYWVMNLQRWKKSGEKL 286



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/89 (30%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
            S     S    K +  A   + D  +MYL E+G   LL+ E E+  A+R   G      
Sbjct: 24  ESDVEQLSAINLKEEYDASSKSLDATQMYLSEIGFSPLLTAEEEVLYARRALRGDEAARK 83

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREI 184
            + ES L     I  R   N G  LL  I
Sbjct: 84  RMIESNLRLVVKISRRYS-NRGLALLDLI 111


>gi|307718430|ref|YP_003873962.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532155|gb|ADN01689.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 281

 Score =  149 bits (376), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 85/274 (31%), Positives = 154/274 (56%), Gaps = 8/274 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
            +    ++ I     +S  E R +   +R+       A++ ++ ANLRLV+ +A +++  
Sbjct: 13  REEIAYLREIKRYKLLSPEEERELGKRIRR---GDPEARERLITANLRLVVKIALQFSVP 69

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            +  LDLIQEGNIGL++AAEKFD+    +FSTYA WW++QAI R++ ++   IR+P    
Sbjct: 70  DIPLLDLIQEGNIGLIRAAEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRLPNRKE 129

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D + K+ +  + +  ++ REP+ EEIA+ L M  E V +++ + +E +SLET I ++ + 
Sbjct: 130 DVLRKIEKAKQLLEQRLMREPSTEEIAELLGMETEEVEELINLGQEVVSLETQI-NDGSM 188

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D      +        +A   +T T +  +L  RE  V+  R+ +     +TL+ + 
Sbjct: 189 DLHDVCPGGASPEEEVCR-KACREDTLTLIQRTLDSRESEVVLHRYAL-TGPRYTLKTLS 246

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   ++ E +RQIE +A+RKL+   R++ +  ++
Sbjct: 247 EHLGISPETVRQIEIRALRKLRE--RAEVVGDYV 278



 Score = 37.5 bits (85), Expect = 7.6,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLRE+   +LLS E E  + KRI  G       L  + L     I  +  + D    L +
Sbjct: 18  YLREIKRYKLLSPEEERELGKRIRRGDPEARERLITANLRLVVKIALQFSVPD--IPLLD 75

Query: 184 II 185
           +I
Sbjct: 76  LI 77


>gi|330993273|ref|ZP_08317209.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
 gi|329759675|gb|EGG76183.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
          Length = 298

 Score =  149 bits (376), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 122/275 (44%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +S  E   +    R  +   + A  ++V ++LRLV  +A  Y   GL
Sbjct: 14  LSKYLRDIRKFPMLSPEEELRLSR--RWKDKGDTEAAHKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A  +FD   G++ +TYAMWW++ AI   I      ++I      K
Sbjct: 72  PVGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKIGTTAAQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA+ L +P + V     ++     SL  P+  
Sbjct: 132 KLFFNLRRLKGQMQAIDDGDLRPEQVNKIAQSLGVPEQDVVNMNRRLAAPDHSLNAPLRM 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D N       A        +      L +L  RE  +L        +  
Sbjct: 192 DGEGEWQDWLVDDNDNQEETLAQSEEYSGRQALLANALKTLNERERHILTE--RRLKDEP 249

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLE++   + ++RER+RQIE +A  KL+   +++
Sbjct: 250 ATLEDLSHVYNISRERVRQIEVRAFEKLQAAMKAE 284


>gi|148242910|ref|YP_001228067.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851220|emb|CAK28714.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 293

 Score =  149 bits (376), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 93/281 (33%), Positives = 156/281 (55%), Gaps = 23/281 (8%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECE--------------ASIAKKEMVEANLRLVIS 458
           +  I     +S  E   +   VR  +                   A+  +V+ANLRLV+ 
Sbjct: 13  LNGIGRHALLSPEEEVSLGRQVRAWQDHPGGPGQAPAAVQKRGLRARGRLVQANLRLVVH 72

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AKK   RGL   DL+QEG+IGL +AAEK+D   GY+FSTYA WW+KQA+ R+I  Q+  
Sbjct: 73  LAKKQHLRGLAMEDLVQEGSIGLQRAAEKYDPSTGYRFSTYAYWWIKQALHRAIQLQTPA 132

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISL 576
           +R+P  + +++ ++  T +R+S ++ R+P PEE+A+ +   ++ ++++ +        SL
Sbjct: 133 LRLPCRVSERLGRLRSTRQRLSQELGRQPRPEELAEAMGERIDQLQELERAQVISRGCSL 192

Query: 577 ETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--LTPREERVLRMRFG 633
           +TP+G + D   L D +ED    SP+D   QA   E    +L+S  L+ RE  V++ R  
Sbjct: 193 DTPMGSDPDHGSLVDLLEDDRT-SPMDQLEQALRSEQLAELLSSAGLSEREATVVQARHS 251

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
                    +++  +F ++RER RQ+E  A+RKL+H + ++
Sbjct: 252 EEHI---PYQQLADRFGISRERTRQLEHNALRKLRHCAEAQ 289


>gi|160358239|dbj|BAF93440.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601099|dbj|BAJ13238.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  149 bits (376), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 107/254 (42%), Positives = 141/254 (55%), Gaps = 20/254 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +   +  D +   +S     + + ++     +K      TDDPVRMYLREMGS+ELLSRE
Sbjct: 10  IPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREMGSVELLSRE 69

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE         
Sbjct: 70  GEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAK 129

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                      +    +++EKE+              + S+DD + V    +  E +E +
Sbjct: 130 AAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDMQMPEEEEED 179

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSS 311
            DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G       
Sbjct: 180 EDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQE 235

Query: 312 VKCKVLKEKLVKLV 325
            + K LK++L+  V
Sbjct: 236 RRYKELKDQLITAV 249


>gi|310778262|ref|YP_003966595.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
 gi|309747585|gb|ADO82247.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
          Length = 263

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 99/267 (37%), Positives = 139/267 (52%), Gaps = 8/267 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + I N +K IS    ++  E        +        A +++V +NLRLV+S+AKKY N 
Sbjct: 1   MNISNYLKEISHYPLLTKEEEIEFALKAQ---NGDESAHEKLVTSNLRLVVSIAKKYINI 57

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+  LDLIQEGNIGL+KA  KFD  +  +FSTYA +W+KQ+I R I+     IR P ++ 
Sbjct: 58  GIPVLDLIQEGNIGLIKAVSKFDTTMDKRFSTYATFWIKQSILRYISSNKGVIRYPTYIY 117

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDT 585
           D I K+ +  R   NK    P+ E IA  L    + V K L I ++ + SLE   G+   
Sbjct: 118 DNISKINKFIRDYKNKYGSVPSIEVIATGLEFKKKDVEKYLNIFEQSLNSLEESYGENGD 177

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            H    I   +     +  I  ++ E     L  L  +E  V+  RFG+      TLEE+
Sbjct: 178 LH--SIIPSDDL--FEEQIITDSVNEELISNLKILNSKERDVIIHRFGLFNKNVLTLEEI 233

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    +TRERIRQI+ KAI KL+   R
Sbjct: 234 GNHLNLTRERIRQIQLKAIDKLRDKFR 260



 Score = 45.2 bits (105), Expect = 0.040,   Method: Composition-based stats.
 Identities = 14/46 (30%), Positives = 20/46 (43%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           YL+E+    LL++E EI  A + + G       L  S L     I 
Sbjct: 6   YLKEISHYPLLTKEEEIEFALKAQNGDESAHEKLVTSNLRLVVSIA 51


>gi|301601142|dbj|BAJ13259.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 113/263 (42%), Positives = 143/263 (54%), Gaps = 27/263 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVKLV 325
            G        + K LK++L+  V
Sbjct: 227 AGTLSSGQERRYKELKDQLITSV 249


>gi|239934548|emb|CAR94588.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 231

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 101/231 (43%), Positives = 147/231 (63%), Gaps = 3/231 (1%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI- 191
           LLSREGEIAIAKRIEAGR  M++ LCESPL+FQA+IIWRDELN+G  LLR+IIDLEA   
Sbjct: 1   LLSREGEIAIAKRIEAGREAMISGLCESPLSFQAIIIWRDELNEGKILLRDIIDLEATYA 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           GP++K       E    +++E    E ++ +    E   +S ++    D        E A
Sbjct: 61  GPDAKKVEAPTPEERERKEKEARKAEADKREKAAEEMRAKSRSRRGGGDDVLSADDFEPA 120

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN--AVNGQKDEK 309
           E  + + D++++++  +L+AME +L+P V+   D IA+ Y+ LR LQD   +        
Sbjct: 121 EQPDDDDDDEDEEANVSLAAMEAELKPHVLETFDRIAKTYKSLRKLQDQEVSEKTALSPS 180

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
              + + L+E++++ V SLSLN +RI+ LVEQLYDI++R++  EG LLRLA
Sbjct: 181 QGRRYRKLREEIIEDVKSLSLNAARIEALVEQLYDINRRLISLEGRLLRLA 231


>gi|50365086|ref|YP_053511.1| RNA polymerase sigma factor [Mesoplasma florum L1]
 gi|50363642|gb|AAT75627.1| RNA polymerase sigma factor [Mesoplasma florum L1]
          Length = 471

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 126/335 (37%), Positives = 180/335 (53%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV-RKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+    +I     ++  +      +   +   E    +  ++ +NL+LVISVA+K+ NRG
Sbjct: 137 IKTYFSTIGQTKILTKDQEIVYAKLANSEDPEERKEGRDMLITSNLKLVISVARKHLNRG 196

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGL+KA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 197 LDFADLIEEGNIGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 256

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP+ +E+A+++   M  E V ++ KI  EP+SLE P GDED 
Sbjct: 257 TINKLSRIERQLTQELGREPSSKEVAERMGGDMTAEKVVEIKKIAVEPVSLEKPFGDEDD 316

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRE---------------------------------- 611
           +H GDF+EDK+ +SP D   +  LRE                                  
Sbjct: 317 THFGDFVEDKDMISPTDFTEKEILREVIDKVFEDMPAREEKVIRMRYGIVPTKVRTLIRL 376

Query: 612 ----------TTTRVLASLT-----PREE-----RVLRMRFGIGMNTDHTLEEVGKQFCV 651
                        + +  L      P E+       +     +      TLEEVGK+  V
Sbjct: 377 AEECNDETAGELAKAINKLDIHLETPVEKIRTVDSKIIQDHLLKYEASKTLEEVGKELNV 436

Query: 652 TRERIRQIEAKAIRKLKHPSRSKK----LRSFLDG 682
           TRERIRQIEAK IRKLK P+ + K    L+ F  G
Sbjct: 437 TRERIRQIEAKTIRKLKQPANANKSGKVLKEFYKG 471


>gi|114155170|dbj|BAF31035.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 112/262 (42%), Positives = 142/262 (54%), Gaps = 27/262 (10%)

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREMG 129
           VV+ +D ED    E   D  + +                +K      TDDPVRMYLREMG
Sbjct: 2   VVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREMG 61

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           S+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE 
Sbjct: 62  SVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLET 121

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                              +    +++EKE+              + S+DD + V    +
Sbjct: 122 TYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDMQ 171

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVN 303
             E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  
Sbjct: 172 MPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACA 227

Query: 304 GQKDEKSSVKCKVLKEKLVKLV 325
           G        + K LK++L+  V
Sbjct: 228 GTLSSGQERRYKELKDQLITAV 249


>gi|258543198|ref|YP_003188631.1| RNA polymerase factor sigma-32 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256634276|dbj|BAI00252.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637336|dbj|BAI03305.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640388|dbj|BAI06350.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643445|dbj|BAI09400.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646500|dbj|BAI12448.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649553|dbj|BAI15494.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652539|dbj|BAI18473.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655597|dbj|BAI21524.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 319

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 68/275 (24%), Positives = 123/275 (44%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +  + R  +     A  ++V ++LRLV  +A  Y   GL
Sbjct: 37  LSRYLQEIRKYPLLTPEEELSLSRLWR--DKGDVKAAHQLVTSHLRLVAKIAMGYRGYGL 94

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 95  PINELISEGNIGMMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 154

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA  L +  + V     ++     SL  P+  
Sbjct: 155 KLFFNLRRLKGQMQAIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSLNAPMRA 214

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +  S   D + D +       A    L   +   +  + +L  RE R+         +  
Sbjct: 215 DQDSEWQDRLVDDHTNQEDVYAENEELSGRKALLSSAMENLNERERRIFTE--RRLKDDP 272

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLEE+  ++ ++RER+RQIE +A  K++   + +
Sbjct: 273 STLEELAHEYGISRERVRQIEVRAFEKVQAAMKKE 307


>gi|313665390|ref|YP_004047261.1| RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
 gi|312949647|gb|ADR24243.1| putative RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
          Length = 498

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 127/335 (37%), Positives = 181/335 (54%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     I     ++  +      M V     +    + +++E+NL+LVISVA+K+ NRG
Sbjct: 163 IKTYFYKIGQAPILTKDQEIMYAKMAVSDDPEDVKEGRNKLIESNLKLVISVARKHLNRG 222

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 223 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 282

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP  EEIA +    +  + V ++ K++ EP+SLE P GDED 
Sbjct: 283 TINKLARVERQLTQELGREPNAEEIANRVGEGITSDKVIEIKKLSIEPVSLEKPFGDEDD 342

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL--- 642
           +H GDF+EDK+ VSP +   +  L+E   +V   + PREE+V+RMR+GI      TL   
Sbjct: 343 THFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRL 402

Query: 643 ----------------EEVGKQFCVTRERI------------------------------ 656
                           EE+        E++                              
Sbjct: 403 AQECNDSSAKELKQAIEELDIHLDTPIEKVRKFNNEIINNNLAKYDSARTLEEVGKELNV 462

Query: 657 -----RQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                RQIEAK IRKLK PS + K    L+ F  G
Sbjct: 463 TRERIRQIEAKTIRKLKQPSLNNKSGKTLKEFYKG 497


>gi|58038976|ref|YP_190940.1| RNA polymerase factor sigma-32 [Gluconobacter oxydans 621H]
 gi|58001390|gb|AAW60284.1| Heat shock sigma factor RpoH [Gluconobacter oxydans 621H]
          Length = 297

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 122/275 (44%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +    RK E   + A   +V ++LRLV  +A  Y   GL
Sbjct: 15  LTRYLQEIRKFPLLTPQEELDLSRRWRKDE--DTSAAHRLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A  +FD   G++ +TYAMWW++ A+   I      +++      K
Sbjct: 73  PVNELISEGNIGMMQAVRRFDPERGFRLATYAMWWIRAAMQEYILHSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA  L +P + V     ++     SL  P+  
Sbjct: 133 KLFFNLRRLKGQMQAIDDGDLKPEQVNSIATTLGVPEQDVVSMNQRLAAPDHSLNAPLRI 192

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D +       A        +    + L +L  RE  +L           
Sbjct: 193 DGEGEWQDWLVDDHENQEQTYAASEEFTGRKALLDQALMTLNERERHILSE--RRLKEEP 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLEE+   + V+RERIRQIEA+A+ KL+    ++
Sbjct: 251 STLEELSHHYNVSRERIRQIEARAMEKLQKAMAAE 285


>gi|158312828|ref|YP_001505336.1| FliA/WhiG family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108233|gb|ABW10430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Frankia sp.
           EAN1pec]
          Length = 376

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 122/246 (49%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +VS+       A++ + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 135 FVRLVSLPEGDPERAAL-RDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 193

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 194 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQSLGRS 253

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  EIA+ L M  E V + L+       +SL+ P   +D +  + D +  ++      S
Sbjct: 254 PTVSEIARHLEMSEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDE-----S 308

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L PRE+R+L +RF        T  ++  +  +++  + ++ A+ 
Sbjct: 309 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN----MTQSQIANELGISQMHVSRLLART 364

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 365 LAQLRR 370


>gi|114155168|dbj|BAF31034.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|114155684|dbj|BAF31028.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|114155686|dbj|BAF31029.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|114155688|dbj|BAF31030.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|118562877|dbj|BAF37806.1| RNA polymerase major sigma factor [Agrobacterium vitis]
 gi|118562879|dbj|BAF37807.1| RNA polymerase major sigma factor [Agrobacterium vitis]
 gi|301601097|dbj|BAJ13237.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601101|dbj|BAJ13239.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601103|dbj|BAJ13240.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601112|dbj|BAJ13244.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601114|dbj|BAJ13245.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601116|dbj|BAJ13246.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601120|dbj|BAJ13248.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601126|dbj|BAJ13251.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601128|dbj|BAJ13252.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601130|dbj|BAJ13253.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601132|dbj|BAJ13254.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
 gi|301601138|dbj|BAJ13257.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 113/263 (42%), Positives = 143/263 (54%), Gaps = 27/263 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVKLV 325
            G        + K LK++L+  V
Sbjct: 227 AGTLSSGQERRYKELKDQLITAV 249


>gi|115394497|gb|ABI97158.1| RNA polymerase sigma factor [Fusobacterium necrophorum]
          Length = 185

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 97/181 (53%), Positives = 132/181 (72%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR+IADQ  TIRIPVHM + I+K+ + AR    +  ++ TPE +A++L M
Sbjct: 2   YAPWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEILAERLGM 61

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V+ + ++ ++PISLETP+G E+ S LGDF+ED+  ++P +   ++ LRE    VL 
Sbjct: 62  EVEKVKSIQEMNQDPISLETPVGSEEDSELGDFVEDQKMLTPYELTNRSLLREQLDSVLG 121

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           SL+ REE+VLR R+G+   +  TLEEVGK F VTRERIRQIE KA+RKL+HPSR KKL  
Sbjct: 122 SLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLED 181

Query: 679 F 679
           F
Sbjct: 182 F 182


>gi|329114085|ref|ZP_08242849.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
 gi|326696624|gb|EGE48301.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
          Length = 319

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 68/275 (24%), Positives = 123/275 (44%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +  + R  +     A  ++V ++LRLV  +A  Y   GL
Sbjct: 37  LSRYLQEIRKYPLLTPEEELSLSRLWR--DKGDVKAAHQLVTSHLRLVAKIAMGYRGYGL 94

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 95  PINELISEGNIGMMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 154

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA  L +  + V     ++     SL  P+  
Sbjct: 155 KLFFNLRRLKGQMQAIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSLNAPMRA 214

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +  S   D + D +       A    L   +   +  + +L  RE R+         +  
Sbjct: 215 DQDSEWQDRLVDDHTNQEDVYAENEELSGRKALLSSAMENLNERERRIFTE--RRLKDDP 272

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLEE+  ++ ++RER+RQIE +A  K++   + +
Sbjct: 273 STLEELAHEYGISRERVRQIEVRAFEKVQAAMKKE 307


>gi|11079073|dbj|BAB17541.1| DNA-directed RNA polymerase subunit D [Pseudomonas corrugata]
          Length = 268

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       + +  + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGTTPPAAEVPPPIDAKAEKADDDSDDDDAEASDDEEEAESGPDPIV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVAEQMEITRKAL-----------------------------------KKHGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 195 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLGALETETGLSIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|162148038|ref|YP_001602499.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161786615|emb|CAP56197.1| putative RNA polymerase sigma-32 factor [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 325

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 124/275 (45%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +S  + + +    R  +   + A   +V ++LRLV  +A  Y   GL
Sbjct: 44  LSRYLQDIRKFPMLSPEDEQRLSR--RWKDKGDTEAAHALVTSHLRLVAKIAMGYRGYGL 101

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A  +FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 102 PLGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 161

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA+ L +P + V     +++    SL  P+  
Sbjct: 162 KLFFNLRRLKGQMQAIDDGDLKPEQVNKIAESLGVPEQDVINMNRRLSAPDHSLNAPLRA 221

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D++       A        +      + +L  RE  +L        +  
Sbjct: 222 DSEGEWQDWLVDEHDNQEQTLAENEEFSGRKALLDNAMKTLNDRERHILTE--RRLKDDP 279

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLEE+   + ++RER+RQIE +A  K++   +++
Sbjct: 280 ATLEELSHTYNISRERVRQIEVRAFEKVQAAMKAE 314


>gi|78778962|ref|YP_397074.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78712461|gb|ABB49638.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 307

 Score =  149 bits (375), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 85/254 (33%), Positives = 139/254 (54%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 RK       AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+
Sbjct: 50  EYSEAERKKIKIGEKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKY 109

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+     ++       P 
Sbjct: 110 DPSRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEKLTKLRSAKSKLMQLKGITPN 169

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+A++L +  E + ++L        +SL+  +    D S L D +          + +
Sbjct: 170 SDELAEELKITKEEIDELLSCELRSITVSLQGTVKSKSDPSELVDILPSDQTPPMELAEL 229

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +  ++L    LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 230 -AERTASAWKLLDKANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQR 288

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 289 ALRKLRKAGIQNGL 302


>gi|258648463|ref|ZP_05735932.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851219|gb|EEX71088.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 283

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 85/269 (31%), Positives = 146/269 (54%), Gaps = 4/269 (1%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  IS E  I++ E   +    +        A + +V ANLR V+SVAK+Y  +
Sbjct: 17  ESLERYLSEISREPRITVEEEVELGRRAK---NGDEAAVERLVRANLRFVVSVAKQYQGQ 73

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+  +DLI EGN+GL++AA +FD   G+KF +YA+WW++Q+I  +I ++S  IR+P +  
Sbjct: 74  GISLIDLINEGNLGLIQAAHRFDDTRGFKFISYAVWWIRQSILLAITEKSRLIRLPQNQM 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             I K++R   +     +R P+ EEI +++ +  E VR  L++  +P+S++ P+ +++  
Sbjct: 134 SSIQKILRFYNQYMQDYERPPSIEEICEQMQVTEERVRLALQLQNKPLSIDAPLTEDEAR 193

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L + +      S     ++   R    R+L  L P E  V+    G       +LEE+G
Sbjct: 194 TLSERLRSDKGSSADGPLLKEAERWKVERMLNLLPPLERSVIEYYLGF-KGQGISLEEIG 252

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            +  ++RER+RQI+ KAI  L+    S K
Sbjct: 253 NRIGLSRERVRQIKVKAIMILRRHHESTK 281


>gi|157412994|ref|YP_001483860.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157387569|gb|ABV50274.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 307

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 83/254 (32%), Positives = 140/254 (55%), Gaps = 7/254 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 RK       AK EM+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+
Sbjct: 50  EYSEAERKKIKIGEKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKY 109

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + ++++ QS TIRIPV++ +K+ K+     ++       PT
Sbjct: 110 DPSRGHRFSTYAYWWIRQGLNKALSTQSRTIRIPVNINEKLTKLRSAKSKLMQLKGIPPT 169

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+++++ +  E + ++L        +SL+  +    D S L D +          + +
Sbjct: 170 SDELSEEMKITKEEIEELLSCELRSITVSLQGTVKSKSDPSELVDILPSDQTPPMELAEL 229

Query: 606 QANLRETTTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    +  ++L    LT +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +
Sbjct: 230 -AERTASAWKLLDKANLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQR 288

Query: 663 AIRKLKHPSRSKKL 676
           A+RKL+       L
Sbjct: 289 ALRKLRKAGIQNGL 302


>gi|11079063|dbj|BAB17536.1| DNA-directed RNA polymerase subunit D [Pseudomonas corrugata]
 gi|11079079|dbj|BAB17544.1| DNA-directed RNA polymerase subunit D [Pseudomonas corrugata]
          Length = 268

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       + +  + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGTTPPAAEVPPPIDAKAEKADDDSDDDDAEASDDEEEAESGPDPVV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVAEQMEITRKAL-----------------------------------KKHGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 195 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALETETGLSIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|33322905|gb|AAQ07189.1|AF496497_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 167

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 98/167 (58%), Positives = 127/167 (76%)

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           Q+ TIRIPVHM + I+K++R  R++   + R+P PEEIA ++ +PV+ VR+VLK+ +EP+
Sbjct: 1   QARTIRIPVHMVETINKLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQEPV 60

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SLETPIG+ED SHLGDFIEDK+A SP   A    L++    VL +LT REE VLR+RFG+
Sbjct: 61  SLETPIGEEDDSHLGDFIEDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGL 120

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                 TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRS +LR FL+
Sbjct: 121 DDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFLE 167


>gi|83319868|ref|YP_424476.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|83283754|gb|ABC01686.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 505

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 127/335 (37%), Positives = 180/335 (53%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     I     ++  +      M V     +    + +++E+NL+LVISVA+K+ NRG
Sbjct: 171 IKTYFYKIGQAPILTKDQEIMYAKMAVSDDPEDVKEGRNKLIESNLKLVISVARKHLNRG 230

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KF++  G+KFSTYA WW+ QAITR+IADQ+ TIRIPVHM +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWISQAITRAIADQARTIRIPVHMVE 290

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP  EEIA +    +  + V ++ K++ EP+SLE P GDED 
Sbjct: 291 TINKLARVERQLTQELGREPNAEEIANRVGEGITSDKVIEIKKLSIEPVSLEKPFGDEDD 350

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL--- 642
           +H GDF+EDK+ VSP +   +  L+E   +V   + PREE+V+RMR+GI      TL   
Sbjct: 351 THFGDFVEDKDMVSPSEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRL 410

Query: 643 ----------------EEVGKQFCVTRERI------------------------------ 656
                           EE+        E++                              
Sbjct: 411 AQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNEIINNNLAKYDSARTLEEVGKELNV 470

Query: 657 -----RQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                RQIEAK IRKLK PS + K    L+ F  G
Sbjct: 471 TRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|11078999|dbj|BAB17504.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 126/315 (40%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDEEEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ+            E+ R+            K  + 
Sbjct: 109 I------------IAAQRFGAVSDQM------------ELARKALK---------KHGRG 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 SKQATAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|15237896|ref|NP_197800.1| SIGE (SIGMA FACTOR E); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|4033838|emb|CAA77213.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972299|dbj|BAA78109.1| RNA polymerase sigma subunit SigE [Arabidopsis thaliana]
 gi|10178160|dbj|BAB11572.1| sigma-like factor [Arabidopsis thaliana]
 gi|222423237|dbj|BAH19595.1| AT5G24120 [Arabidopsis thaliana]
 gi|332005876|gb|AED93259.1| RNA polymerase sigma factor [Arabidopsis thaliana]
          Length = 517

 Score =  148 bits (374), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 97/392 (24%), Positives = 177/392 (45%), Gaps = 22/392 (5%)

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL-LVEQLYDISKRIMHNEGELLR 358
                 +++K  V+  V KEK + L   ++L ++  +  +V  +     +    E ++ R
Sbjct: 136 KRKESGEEKKVVVRNNVKKEKRMSLDKRIALKRNVQEKPVVASVDKKVTKRQQEEEKIER 195

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSY----AKDFPEGEWKNFVACEVDSILKIRNEIK 414
           L + Y    D+         +   W            E  W   +   + ++L++++ ++
Sbjct: 196 LVRDYSASNDI---------VSLDWKKMKIPPVLSSTEHAWLFKLMQPMKALLEVKDVLQ 246

Query: 415 S---ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGL 468
                         E       V+K       A+ ++++ NLRLV+ V  KY +    G 
Sbjct: 247 KSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFVMNKYFHEFTNGP 306

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +F DL Q G  GL+ A ++F+    ++ STY ++W++ AI RS    S   R+P  +   
Sbjct: 307 KFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRS-MTTSNFTRVPFGLESV 365

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             ++ +    +  ++ R PT +E+ ++L +  E  R+VL+  K  +SL +          
Sbjct: 366 RVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQE-EF 424

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + I D + V   +S   A LR     VL SL P+E  V+R R+G+    D TL E+   
Sbjct: 425 INGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGN 484

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++RE +R+ E KA+ KLKH +R   LR ++
Sbjct: 485 LNISREMVRKHEVKALMKLKHQARVDYLRQYI 516


>gi|11078995|dbj|BAB17502.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  148 bits (374), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 126/315 (40%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +  V+  +   +  A+ S DD  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDEEEVESGPDP 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ+            E+ R+            K  + 
Sbjct: 109 I------------IAAQRFGAVSDQM------------ELARKALK---------KHGRG 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 SKQATAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|114155174|dbj|BAF31037.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  148 bits (374), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 112/257 (43%), Positives = 139/257 (54%), Gaps = 27/257 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGG-- 168

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
                     +EDED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 169 --DMPMPEEEEEDEDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKE 319
            G        + KVLK+
Sbjct: 227 AGTLSSGQERRYKVLKD 243


>gi|329895346|ref|ZP_08270971.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
 gi|328922359|gb|EGG29703.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
          Length = 424

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 130/245 (53%), Gaps = 1/245 (0%)

Query: 425 SEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
            E +  +   +         A+ ++V  N+RLV  +A++  NRG+   DL+QEG IGL++
Sbjct: 166 FERKEALRRGLMGPVQGYLAARDKLVMHNVRLVYKLAREKQNRGIAVRDLVQEGIIGLVR 225

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD+ LG++FSTYA  W  Q I R        +  P H+  +++ + R      ++ 
Sbjct: 226 AAEKFDYRLGFRFSTYAYNWTNQHIQRVCEGNGSLVTYPTHVTQEVNALYRVRNEWMDRR 285

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP+  E+A+     +E VR++ ++T   +S+++   ++  +     + D+ A   L+ 
Sbjct: 286 GEEPSLAELAEHSGFTLERVRELTQLTNLTVSIQSDDDEDTNALPESALVDEAANPALEQ 345

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           A   +L+    + L  L  RE+ ++  R+G+      TL ++  Q  V+RE +RQ+E  A
Sbjct: 346 AQSRSLKRLLEQQLKQLDRREQMIVTARWGLDGRPSRTLAQLADQLEVSRELVRQLEKSA 405

Query: 664 IRKLK 668
           +RKL+
Sbjct: 406 LRKLQ 410


>gi|307592489|ref|YP_003900080.1| RNA polymerase sigma-32 factor RpoH [Cyanothece sp. PCC 7822]
 gi|306986134|gb|ADN18014.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7822]
          Length = 307

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 87/281 (30%), Positives = 159/281 (56%), Gaps = 19/281 (6%)

Query: 394 EWKNFVACEVDSILKIRNEI--KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +W+  +    +   +  + I  +       +S +E+  I+        +   A   +V A
Sbjct: 37  KWQKLLKLFHELGQQYGSSISPEQFCQHYRLSKAEYDRIL-------YQGKKAADTLVRA 89

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NL+ VI +A +Y  RGL+  DLIQEG++GL++AAE+FD  LGY+FSTYA WWV+  +TR+
Sbjct: 90  NLKFVIFIANRYVGRGLELSDLIQEGSLGLIRAAERFDPSLGYQFSTYANWWVRAFMTRA 149

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +A+QS TIR+P  + DK++K+ +T   ++  + R P+  E+A+ L + V  +  + ++ K
Sbjct: 150 LANQSRTIRLPSQVNDKLNKIKKTRHNLAQLLGRSPSSSELAQALGISVLQLHSLAQLDK 209

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRM 630
           + ISL   + ++    L D I   +  S     +   L+ +   ++L +L+PR + ++R+
Sbjct: 210 KTISLSVWVDEQGRETLQDLIPSSDEPS-----LDETLKPDEIEQLLQTLSPRNQEIVRL 264

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           R   G     TL E+G+ F ++RER+R+I  +++  L+  +
Sbjct: 265 RILEG----KTLSEIGQSFHLSRERVRKICLRSLTILRQNA 301


>gi|106895880|gb|ABE66433.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC78]
          Length = 288

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 131/330 (39%), Gaps = 44/330 (13%)

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II
Sbjct: 1   REMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII 60

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
                       GF    E                          E  A  +    S++ 
Sbjct: 61  -----------SGFIDPNE-------------------------TEDMAPTATHIGSELG 84

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
                 E++E   DEDED  +                   E+   Y          ++ Q
Sbjct: 85  EDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQ 138

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYG 364
           K+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   
Sbjct: 139 KNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAK 198

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+SI
Sbjct: 199 MPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSI 257

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           ++ + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 AQIKDINRRMSIGEAKARRAKKEMVEANLR 287


>gi|11079117|dbj|BAB17563.1| DNA-directed RNA polymerase subunit D [Pseudomonas asplenii]
 gi|11079119|dbj|BAB17564.1| DNA-directed RNA polymerase subunit D [Pseudomonas asplenii]
          Length = 268

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 116/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   + +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILDEYNRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +   +    D +  +    +D  +    P  
Sbjct: 56  ------SGYIDPDDGIALPAAEVPPPVDAKTGKENATDDEDEESDSDDEDEVESGPDPIV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQLEIARKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + ++LVE++    +R+   E  +++L      + R  
Sbjct: 135 NKATIAELLLLAELFMPIKLVPKQFEVLVERVRSALERLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEIDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|300870272|ref|YP_003785143.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
 gi|300687971|gb|ADK30642.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
          Length = 284

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 86/261 (32%), Positives = 145/261 (55%), Gaps = 6/261 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +   ++K     S A+ +++ +NLR VIS+AK+Y N GL   DLI EGN+GL
Sbjct: 29  LTREEEIELTQRLKK---GDSQARAKLIRSNLRFVISIAKQYKNSGLLLEDLIGEGNLGL 85

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A ++FD   GY F +YA++W++Q+I R+I ++S  IR+P++    +  + R   +   
Sbjct: 86  IIATDRFDPDKGYHFISYAVYWIRQSILRAINEKSRLIRLPLNKAMDLVDLERAVHQCYY 145

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSP 600
           K    P  E++A  L      +R ++ +  E +SLE     +     L D +EDKN+ + 
Sbjct: 146 KTGHMPDVEDLAAILKKEPREIRNIMSMNNEYVSLEKDFNMDGVKDRLADVVEDKNSKTV 205

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            D      L E     +  L+  E+ ++  R+G+      TL+EVG+++  T+ERIRQIE
Sbjct: 206 EDILSDKELTEELKIAMEELSDIEKEIINARYGLDQ-EKKTLKEVGEKYSFTKERIRQIE 264

Query: 661 AKAIRKLKHPSRSKKLRSFLD 681
            KA++K+ H  R   L+ FL+
Sbjct: 265 KKALKKM-HSKRYSSLKDFLN 284



 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +Y  +    +LL+RE EI + +R++ G +   A L  S L F  +I    +  +   L
Sbjct: 16  ISLYFADAKREKLLTREEEIELTQRLKKGDSQARAKLIRSNLRF--VISIAKQYKNSGLL 73

Query: 181 LREII 185
           L ++I
Sbjct: 74  LEDLI 78


>gi|300023529|ref|YP_003756140.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525350|gb|ADJ23819.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 296

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 124/271 (45%), Gaps = 13/271 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++ +E   +    R  + E S A +++V ++LRLV  +A  Y   GL
Sbjct: 17  LSRYLEEIRKFPMLAPNEEYMLAK--RWQQHEDSDAAEKLVTSHLRLVARIAMGYRGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 75  PIGEVISEGNVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 134

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + R   ++      +  PE    IA KL +P E V  + +      SL  PI  E
Sbjct: 135 KLFFNLRRAKSQLQALDDGDLRPEHVKAIATKLGVPEEDVVSMNRRLGGDASLNAPIRAE 194

Query: 584 DTS-HLGDFIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIGMNTD 639
             S    D++ D              LR      +  L+ L  RE RV   R        
Sbjct: 195 SESGEWQDWLVDDTPTQEDRLVEDEELRRRKSYLSSALSVLNDRERRVFEQRRLAE--EP 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            TLEE+  +F V+RERIRQIE +A  K++  
Sbjct: 253 ATLEELSAEFGVSRERIRQIEVRAFEKVQKA 283


>gi|114155176|dbj|BAF31038.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 110/259 (42%), Positives = 139/259 (53%), Gaps = 27/259 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           +VV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   HVVEDEDAEDPAAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGG-- 168

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
                     +EDED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 169 --DMPMPEEEEEDEDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKL 321
            G        + K LK+ +
Sbjct: 227 AGTLSSGQERRYKNLKDSV 245


>gi|49328110|gb|AAT58808.1| hypothetical protein [Oryza sativa Japonica Group]
          Length = 799

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 140/281 (49%), Gaps = 5/281 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    +++LK  +E+   S      I E     +++R    E    ++ ++     LV  
Sbjct: 521 LEKIRENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKY 575

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  
Sbjct: 576 IAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGV 635

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T
Sbjct: 636 IQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYT 695

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            IG    +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+    
Sbjct: 696 EIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGK 755

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             +LE++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 756 CRSLEQIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 796


>gi|148793340|gb|ABR12734.1| RNA polymerase sigma factor [Photobacterium iliopiscarium]
          Length = 281

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 120/324 (37%), Gaps = 44/324 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     + P         T   +         E + +D  +   D +       ++    
Sbjct: 61  I--SGFVDPNE-----EATAAPTATHIGSELSETDLEDEDKDLEDGDDDDDAEDEEEDDG 113

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L    +  A  ++                                  
Sbjct: 114 SIDPELAREKFLELRHSYEKMALAINT--------------------------------- 140

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
             + +     ++  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 141 --NGRQHATTEIAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 198

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 199 KMPKKTFISLFAGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLS 257

Query: 424 ISEFRHIVSMVRKGECEASIAKKE 447
           I   + I   +  GE +A  AKKE
Sbjct: 258 IERIKDISRRMSIGEAKARRAKKE 281


>gi|76799605|ref|ZP_00781725.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
 gi|76585040|gb|EAO61678.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
          Length = 278

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 99/183 (54%), Positives = 138/183 (75%), Gaps = 3/183 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I V   ++  E + +   V        +AK+ + EANLRLV+S+AK+Y  RG+
Sbjct: 99  VRMYLKEIGVVPLLTNEEEKELAVAV---AEGDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           QFLDLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           I+K+VR  R +  ++ ++PTPE+IA+++ M  + VR++LKI +EP+SLETPIG+ED SHL
Sbjct: 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHL 275

Query: 589 GDF 591
           GDF
Sbjct: 276 GDF 278



 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 97/260 (37%), Gaps = 16/260 (6%)

Query: 31  WKKMIKLARQRGYVTIEELNAFL-PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGS 89
               I+  +++G    +E+   L  P  + ++Q++D +  L++ GI++ D      +EG+
Sbjct: 14  VADFIRNHKKQGTAIDDEVTEKLVIPFVLDADQIDDLLERLTDGGISITD------KEGN 67

Query: 90  EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
             +  +        +  ++   S     +DPVRMYL+E+G + LL+ E E  +A  +  G
Sbjct: 68  PSTKYVVEGPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAVAVAEG 127

Query: 150 RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
             M    L E+ L     I  R  +  G   L  I         E   G     +   Y 
Sbjct: 128 DLMAKQRLAEANLRLVVSIAKRY-VGRGMQFLDLI--------QEGNMGLMKAVDKFDYS 178

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K    S        Q     I   A+  +     V++  +        L E   D     
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQ 238

Query: 270 SAMEDQLRPKVMCALDEIAE 289
            A    + P  +  + +IA+
Sbjct: 239 IAERMDMTPDKVREILKIAQ 258


>gi|37806470|dbj|BAC99905.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 388

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 158/304 (51%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +    +G W      ++   L      K ++    IS  E R           E+ +
Sbjct: 92  VHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELR-------SRMHESFL 144

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +NLRLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 145 AREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 204

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++A+ S T R+P ++ +++  +      + ++    PT E IA  L +  + V
Sbjct: 205 IRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYELEDQ-GIAPTIENIAGSLNISEKKV 263

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + +SL+              L  +IED+N A  P     +  L+E   ++L 
Sbjct: 264 LNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 323

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R K L 
Sbjct: 324 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLE 382

Query: 678 SFLD 681
           + L+
Sbjct: 383 ALLE 386


>gi|301601134|dbj|BAJ13255.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  148 bits (373), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 142/263 (53%), Gaps = 27/263 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVKLV 325
            G        + K L ++L+  V
Sbjct: 227 AGTLSSGQERRYKELTDQLITAV 249


>gi|331703466|ref|YP_004400153.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802021|emb|CBW54175.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 506

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 126/335 (37%), Positives = 181/335 (54%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     I     ++  +      M V     +    + +++E+NL+LVISVA+K+ NRG
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 290

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP  +EIA +    +  + V ++ K++ EP+SLE P GDED 
Sbjct: 291 TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPFGDEDD 350

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL--- 642
           +H GDF+EDK+ VSP +   +  L+E   +V   + PREE+V+RMR+GI      TL   
Sbjct: 351 THFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRL 410

Query: 643 ----------------EEVGKQFCVTRERI------------------------------ 656
                           EE+        E++                              
Sbjct: 411 AQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEEVGKELNV 470

Query: 657 -----RQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                RQIEAK IRKLK PS + K    L+ F  G
Sbjct: 471 TRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|297737220|emb|CBI26421.3| unnamed protein product [Vitis vinifera]
          Length = 555

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 85/363 (23%), Positives = 173/363 (47%), Gaps = 12/363 (3%)

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEG---ELLRLAQSYGIKRDVFLERHQGRELDPHW 383
           S    Q R ++         +RI   +    E  +      +  +  L+ +    +    
Sbjct: 193 SFKARQKRREVTCSGTSARQRRISGRKRVMNEKSKSRVRAALGVENRLKGYVKGVVSEEL 252

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +++A+               D   +++  I S   +  ++ S  R   + ++    E S+
Sbjct: 253 LTHAQVVLLSNKIKAGLLLEDHKSRLKERIGSEPTDEQVAAS-LRMSRAELQSKLIECSL 311

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G+K STY  WW
Sbjct: 312 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 371

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++ + S T+R+P H+ +++  +     R+  K    P+ + IA+ L M  + V
Sbjct: 372 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEK-GITPSIDRIAECLNMSQKKV 430

Query: 564 RKVLKITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLA 618
           R   +   +  SL+              L  +I D    +     +    L++   +++ 
Sbjct: 431 RNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENNPWHGVDEWALKDEVNKLIN 490

Query: 619 -SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KLK+ +R  ++ 
Sbjct: 491 TTLGERERDIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVGLVALEKLKNAARKGRME 549

Query: 678 SFL 680
           + L
Sbjct: 550 AML 552


>gi|256383860|gb|ACU78430.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384691|gb|ACU79260.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455677|gb|ADH21912.1| RNA polymerase sigma-A factor [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 506

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 126/335 (37%), Positives = 181/335 (54%), Gaps = 61/335 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSM-VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I+     I     ++  +      M V     +    + +++E+NL+LVISVA+K+ NRG
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L F DLI+EGNIGLMKA +KF++  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 290

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKK--LAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            I+K+ R  R+++ ++ REP  +EIA +    +  + V ++ K++ EP+SLE P GDED 
Sbjct: 291 TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPFGDEDD 350

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL--- 642
           +H GDF+EDK+ VSP +   +  L+E   +V   + PREE+V+RMR+GI      TL   
Sbjct: 351 THFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRL 410

Query: 643 ----------------EEVGKQFCVTRERI------------------------------ 656
                           EE+        E++                              
Sbjct: 411 AQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEEVGKELNV 470

Query: 657 -----RQIEAKAIRKLKHPSRSKK----LRSFLDG 682
                RQIEAK IRKLK PS + K    L+ F  G
Sbjct: 471 TRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKG 505


>gi|114155164|dbj|BAF31032.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 143/263 (54%), Gaps = 27/263 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRXLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVKLV 325
            G        + + LK++L+  V
Sbjct: 227 AGTLSSGQERRYRRLKDQLITAV 249


>gi|302876403|ref|YP_003845036.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307687066|ref|ZP_07629512.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579260|gb|ADL53272.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 427

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 139/441 (31%), Positives = 217/441 (49%), Gaps = 45/441 (10%)

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK---- 318
           D+ +  +  + D LR      ++++ E++++   + D+ +     E +S+  +++     
Sbjct: 3   DNLSIIIDYINDNLRFGSKLNIEKVEELFKK-YRVSDSEMESVFTELNSLNIEIVHSKGA 61

Query: 319 --EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG------IKRD-- 368
             EK+ +L   +  N+   +  + + ++  K     +  +       G      + RD  
Sbjct: 62  FNEKISRLFKYIGPNKELRETKLNKWFETEKIDRDMQKRIRHSLNISGYTIINEVHRDIN 121

Query: 369 ----VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
                FL+     ELD                  V  + DS     +++K++  ++    
Sbjct: 122 FEDFDFLDEFNFEELD------------------VVLDNDSFNDEVSKLKNVVDKS--HN 161

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGL 481
            E+   +   ++   +   A   +V AN +LV  +A +Y   +       D+ Q G +GL
Sbjct: 162 LEYLVDLHSSKEDFRKREQALDNLVNANKKLVWEIALRYKQFSTVSFDNSDMYQAGVLGL 221

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKAAEKFD   G +FSTYA WWV+Q+ITRSIAD S TIRIPVHMR+KI K V T  +  N
Sbjct: 222 MKAAEKFDISKGNQFSTYATWWVRQSITRSIADYSTTIRIPVHMREKIIKYVSTENKFWN 281

Query: 542 KIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           +  R  + EE+A  L +  E V   +V +      SL+ PIG ++ S LG+FI D    S
Sbjct: 282 ENGRVASKEELANLLGISSEEVNYLQVYQDVANLTSLDIPIGADEGSFLGEFIPDDKHRS 341

Query: 600 PLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           P  SA +  L+     +    LTP+E R+L  RFG      HTLEE+G    VTRERIRQ
Sbjct: 342 PEKSAEEGELKRELKEICEGRLTPKETRILNFRFGFIDGRTHTLEEIGHVENVTRERIRQ 401

Query: 659 IEAKAIRKLKHPSRSKKLRSF 679
           IEAKAI KL++P   ++LR F
Sbjct: 402 IEAKAISKLQNPKILERLRDF 422


>gi|3893860|gb|AAC78467.1| RNA polymerase sigma factor 1 [Zea mays]
          Length = 398

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 91/304 (29%), Positives = 160/304 (52%), Gaps = 15/304 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  ++   +G W      ++   L      K ++    I   E R   + +R+      +
Sbjct: 102 VQLSRKIKDGIWLQHQRSKLKEKLGNEPSYKQLAQSLRIPAPELR---ARMRESF----L 154

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N RLVIS+A+KY N G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 155 AREMLAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 214

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S + R+P ++ +++  +      + ++    PT E IA+ L +  + V
Sbjct: 215 IRQGVSRALADNSRSFRLPTYLHERLVAIRGAKYALEDQ-GIAPTVENIAESLNISEKKV 273

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVL- 617
               +   + ISL+           GD    +IED+N A  P     +  L+E    ++ 
Sbjct: 274 HNATEAVHKVISLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEERYLKEEVNSLIN 333

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           ++L  RE  ++R+  GIG    HT E++ +QF ++RER+RQ+   A+ KLKH +R + L 
Sbjct: 334 STLNERERDIIRLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLVAMEKLKHAARREHLD 392

Query: 678 SFLD 681
           + L+
Sbjct: 393 ALLE 396


>gi|323144152|ref|ZP_08078788.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
 gi|322416060|gb|EFY06758.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
          Length = 311

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 81/275 (29%), Positives = 151/275 (54%), Gaps = 12/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I S+     +S  +   +  +V++       A+  M+ +NLRLVI VA+ Y  RG+
Sbjct: 43  LVSYISSVRRYPLLSQEDEVRLGRLVQQ---GDVKARNSMITSNLRLVIKVARDYRTRGV 99

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLI+EGN+GL+ A  KFD   G++FSTYA WW++Q I  ++ +QS  +R+P H+   
Sbjct: 100 PMLDLIEEGNLGLIHAVNKFDPERGFRFSTYATWWIRQGIEHAVMNQSRLVRLPFHVIKD 159

Query: 529 IHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS- 586
           +++V++  +++  K   +    ++IAK+L +  + VR +L + +     +  + ++D+  
Sbjct: 160 LNQVLKVKKKLQEKAHGQAVAVKDIAKELDIDEDKVRSMLVVAEGISISDLNVKNKDSEK 219

Query: 587 --HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D + D+   +  +      + +     + SL  R++ ++  RFGI  N   TLEE
Sbjct: 220 NVSLLDLLADEKTPTLEEQFGNTEIEKLLRSWIDSLNERQKIIVIHRFGINDNDIKTLEE 279

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +G+   +TRER+RQ++   +  LK     K L+++
Sbjct: 280 IGEMLHLTRERVRQLQKTVLISLK-----KFLKNY 309



 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 46/308 (14%), Positives = 106/308 (34%), Gaps = 25/308 (8%)

Query: 86  EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR 145
           E    +   +       S   +++       + D +  Y+  +    LLS+E E+ + + 
Sbjct: 8   EPSDLELNRIQEEEQEVSSSFEEKDIPVPSFSGDLLVSYISSVRRYPLLSQEDEVRLGRL 67

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI-------IDLEACIGPES--- 195
           ++ G      S+  S L    + + RD    G  +L  I       I       PE    
Sbjct: 68  VQQGDVKARNSMITSNLRL-VIKVARDYRTRGVPMLDLIEEGNLGLIHAVNKFDPERGFR 126

Query: 196 ---------KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                    + G  H     S   R      K+ + V + +  ++  A         +  
Sbjct: 127 FSTYATWWIRQGIEHAVMNQSRLVRLPFHVIKDLNQVLKVKKKLQEKAHGQAVAVKDIAK 186

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
             +  E+  R++    +  + +   ++++   K +  LD +A+        Q      +K
Sbjct: 187 ELDIDEDKVRSMLVVAEGISISDLNVKNKDSEKNVSLLDLLADEKTPTLEEQFGNTEIEK 246

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
             +S +     ++K++ ++    +N + I  L E++ ++         +L +      I 
Sbjct: 247 LLRSWIDSLNERQKII-VIHRFGINDNDIKTL-EEIGEMLHLTRERVRQLQKTVL---IS 301

Query: 367 RDVFLERH 374
              FL+ +
Sbjct: 302 LKKFLKNY 309


>gi|167950928|ref|ZP_02538002.1| RNA polymerase sigma factor RpoS [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 216

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 78/201 (38%), Positives = 123/201 (61%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  
Sbjct: 1   MALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVK 60

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+  +R AR+++  +  EPT EEIA  L  P+  V+++L + +   S++TP G +    
Sbjct: 61  EINVYLRAARQLAQSLDHEPTSEEIADLLDKPISEVKRMLGLNERVTSVDTPFGKDADKP 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D I D+    P  +     L       L  L  ++  V+  RFG+    + TLE+V  
Sbjct: 121 LLDTIPDERVQDPTVNIQNDGLNTNLDTWLLKLNDKQREVVERRFGLHGYENSTLEQVAN 180

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  VTRER+RQI+  A+R+L+
Sbjct: 181 ELGVTRERVRQIQMDALRRLR 201


>gi|269102892|ref|ZP_06155589.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162790|gb|EEZ41286.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 282

 Score =  148 bits (372), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 85/265 (32%), Positives = 147/265 (55%), Gaps = 6/265 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K +     ++  E   +   V+        A+ +++E+NLRLV+S+AKK  +RGL   
Sbjct: 10  YLKQLRSRALLTKEEEIELSIKVQ---AGDQKARAKLIESNLRLVVSIAKKMQHRGLDLD 66

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+ A EKF+   GY+FSTYA WW+KQA+ R+I + S  +R+PVH+  ++  
Sbjct: 67  DLINEGNIGLITAVEKFNPDYGYRFSTYATWWIKQAMDRAIHNHSREVRLPVHISKELCT 126

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +    + MS K ++  T ++++     P E + K+LK  +   SL+     ++ +   + 
Sbjct: 127 IYSAFKEMSTKSEQ-VTIDQVSALTGSPKEEIEKILKYERRYSSLDD--QFDEGAKFSEI 183

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D + +   +   + +  E    +LA L PR++ ++  RFG+     HTL+EV     +
Sbjct: 184 IPDHSKLDHTELLNEEDQTEVLAMLLAELKPRDQEIIARRFGLFGYEPHTLQEVATAVNL 243

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
           TRER+RQ++  A ++L    R + +
Sbjct: 244 TRERVRQLQILAQQRLAAKMRDRNI 268



 Score = 44.1 bits (102), Expect = 0.076,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +YL+++ S  LL++E EI ++ +++AG     A L ES L    ++    ++      L 
Sbjct: 9   IYLKQLRSRALLTKEEEIELSIKVQAGDQKARAKLIESNLRL--VVSIAKKMQHRGLDLD 66

Query: 183 EIID 186
           ++I+
Sbjct: 67  DLIN 70


>gi|318060769|ref|ZP_07979492.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078700|ref|ZP_07986032.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025872|ref|ZP_08453936.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332745724|gb|EGJ76165.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 367

 Score =  147 bits (371), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + F  + ++ +     A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 121 LSRALFLRLATLAQDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 179

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +T+  ++ 
Sbjct: 180 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQ 239

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+AK L +  + V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 240 KLDRSPTVPELAKALGVSEDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 299

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 300 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 350

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 351 RLLTRTLAQLRE 362


>gi|329890478|ref|ZP_08268821.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
 gi|328845779|gb|EGF95343.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
          Length = 294

 Score =  147 bits (371), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 126/274 (45%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLTEIRKFPMLTKDEEFMLAK--RWSEHQDPEAAHRLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  PE    IA KL +  E V  + +      SL  P+  +
Sbjct: 133 KLFFNLRKAKSQISAFEEGDLHPEHLTAIATKLGVSEEEVTNMNRRLGGDASLNAPLRAD 192

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNTD 639
             S   D++ D +AVS      +   +          +  LT RE+ +L        +  
Sbjct: 193 GESEWQDWLADDDAVSQETQLAENEEKSIRMSLLQEAMEELTDREKHILTE--RRLKDDP 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLEE+  Q+ V+RER+RQIE +A  KL+   R+
Sbjct: 251 VTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRA 284


>gi|301601140|dbj|BAJ13258.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  147 bits (371), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 112/261 (42%), Positives = 141/261 (54%), Gaps = 27/261 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGG-- 168

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
                     +EDED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 169 --DMPMPEEEEEDEDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKEKLVK 323
            G        + K LK++L+ 
Sbjct: 227 AGTLSSGQERRYKELKDQLIS 247


>gi|123965877|ref|YP_001010958.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123200243|gb|ABM71851.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 307

 Score =  147 bits (371), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 80/235 (34%), Positives = 133/235 (56%), Gaps = 7/235 (2%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ ANLRLV+++AK+Y  +GL+ LDLIQEG +GL +A EK+D   G++FSTYA WW++Q 
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R+++ QS TIRIPV++ +K+ K+     ++       PT  E+A+++ +  E + ++L
Sbjct: 129 LNRALSTQSRTIRIPVNINEKLTKLRAAKSKLMQLKGFPPTSFELAEEMKITKEEIDELL 188

Query: 568 KI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--LTP 622
                   +SL+  +    D S L D +          + + A    +   +L    LT 
Sbjct: 189 SCELRSITVSLQGTVKSKSDPSELVDILPSDQTPPMELAEL-AERTASAWTLLDKANLTE 247

Query: 623 REERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+       L
Sbjct: 248 KERKIVSLRFGLDGSNEWKTLAEVARHMSCSREYCRQVVQRALRKLRKAGIQNGL 302


>gi|58583919|ref|YP_202935.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58428513|gb|AAW77550.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 329

 Score =  147 bits (370), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 61  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 118

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 119 PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 178

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 179 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 236

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 237 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRW-LDSDSK 295

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 296 VTLQELADEYGVSAERIRQIEANALKKMK 324


>gi|33861134|ref|NP_892695.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33639866|emb|CAE19036.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 307

 Score =  147 bits (370), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 132/237 (55%), Gaps = 7/237 (2%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            EM+ ANLRLV++++K+Y  +GL  LDLIQEG +GL +A EK+D   G++FSTYA WW++
Sbjct: 67  NEMITANLRLVVNLSKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIR 126

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q + R+++ QS TIRIPV++ +K+ K+     ++       PT  E+A +L +  E + +
Sbjct: 127 QGLNRALSTQSRTIRIPVNINEKLTKLRAAKSKLMQLKGFPPTSIELANELKITKEEIDE 186

Query: 566 VLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--L 620
           +L        +SL+  +    D S L D +          + + A    +   +L    L
Sbjct: 187 LLSCELRSITVSLQGTVKSKSDPSELVDILPSDQTPPMELAEL-AERTASAWTLLDKANL 245

Query: 621 TPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           T +E +++ +RFG+ G N   TL EV +    +RE  RQ+  +A+RKL+       L
Sbjct: 246 TEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKAGIQNGL 302


>gi|148793350|gb|ABR12739.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 271

 Score =  147 bits (370), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 60/311 (19%), Positives = 113/311 (36%), Gaps = 44/311 (14%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     + P         T   +         E + +D  +   D +       ++    
Sbjct: 61  I--SGFVDPNE-----EATAAPTATHIGSELSETDLEDEDKDLEDDDDDEDAENEEEDDG 113

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L +  +  A  ++                                  
Sbjct: 114 SIDPELAREKFLELRQSYEKMALAIN---------------------------------- 139

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
            +  +     +V  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 140 -QHGRQHATTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 198

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 199 KMPKKTFISLFAGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLS 257

Query: 424 ISEFRHIVSMV 434
           I   + I   +
Sbjct: 258 IERIKDISRRM 268


>gi|296125976|ref|YP_003633228.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
 gi|296017792|gb|ADG71029.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
          Length = 285

 Score =  147 bits (370), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 88/253 (34%), Positives = 146/253 (57%), Gaps = 3/253 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + + ++ +   + A+ +++ +NLR VI++AK+Y N GL   DLI EGN+GL+ AA++F
Sbjct: 34  EEIELTKRLKEGDAEARSKLIRSNLRFVITIAKQYKNSGLLLEDLISEGNMGLIIAADRF 93

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GY F +YA++W++Q+I R+I ++S  IR+P++    +  + RT  +   K    P 
Sbjct: 94  DPDKGYHFISYAVYWIRQSILRAINEKSRLIRLPLNKAMDLVDLERTVHQYYYKSGYTPD 153

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQA 607
             E+A  L      +  ++ ++ E ISLE     +     L D IEDK + +  ++AI  
Sbjct: 154 VNELAAILNKDPNDILHIMSMSTEHISLEGEYNYDGMKDRLIDTIEDKTSKNVEETAINK 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L E     + SL+  E++++  R+GI      TL+EVG+ F  T+ERIRQIE KA+RK+
Sbjct: 214 ELMEELKTAIESLSDIEKQIINARYGIDQ-ERKTLKEVGEMFSFTKERIRQIEKKALRKM 272

Query: 668 KHPSRSKKLRSFL 680
            H  +   L+ FL
Sbjct: 273 -HSQKYSSLKDFL 284



 Score = 37.9 bits (86), Expect = 6.0,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +Y  +    +LL+RE EI + KR++ G A   + L  S L F  +I    +  +   L
Sbjct: 17  ISLYFADAKKEKLLTREEEIELTKRLKEGDAEARSKLIRSNLRF--VITIAKQYKNSGLL 74

Query: 181 LREII 185
           L ++I
Sbjct: 75  LEDLI 79


>gi|225620189|ref|YP_002721446.1| DNA-directed RNA polymerase sigma-70/sigma-32 subunit RpoD
           [Brachyspira hyodysenteriae WA1]
 gi|225215008|gb|ACN83742.1| RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Brachyspira hyodysenteriae WA1]
          Length = 287

 Score =  147 bits (370), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 90/283 (31%), Positives = 150/283 (53%), Gaps = 6/283 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    +    I         E  ++  E   +   ++      + A+ +++ +NLR VI+
Sbjct: 9   LRTNTEEQNNISLYFADAKKEKLLTREEEIELTKRLK---EGDAEARSKLIRSNLRFVIT 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK+Y N GL   DLI EGN+GL+ AA++FD   GY F +YA++W++Q+I R+I ++S  
Sbjct: 66  IAKQYKNSGLLLEDLISEGNLGLIIAADRFDPDKGYHFISYAVYWIRQSILRAINEKSRL 125

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P++    +  + R   +   K    P   E+A  L      +  ++ ++ E ISLE 
Sbjct: 126 IRLPLNKAMDLVDLERAVHQYYYKSGYTPDVNELATILNKDPNDILHIMSMSTEHISLEG 185

Query: 579 PIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
               +     L D IEDK + +  ++AI   L E     + SL+  E++++  R+GI   
Sbjct: 186 EYNYDGMKDRLIDTIEDKTSKNVEETAINKELMEELKTAIESLSDIEKQIINARYGIDQ- 244

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              TL+EVG+ F  T+ERIRQIE KA+RK+ H  +   L+ FL
Sbjct: 245 ERKTLKEVGEMFSFTKERIRQIEKKALRKM-HSQKYSSLKDFL 286



 Score = 37.5 bits (85), Expect = 6.8,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           + +Y  +    +LL+RE EI + KR++ G A   + L  S L F  +I    +  +   L
Sbjct: 19  ISLYFADAKKEKLLTREEEIELTKRLKEGDAEARSKLIRSNLRF--VITIAKQYKNSGLL 76

Query: 181 LREII 185
           L ++I
Sbjct: 77  LEDLI 81


>gi|295837881|ref|ZP_06824814.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826719|gb|EDY46528.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score =  147 bits (370), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + F  + ++ +     A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 40  LSRALFLRLATLAQDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 98

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +T+  ++ 
Sbjct: 99  IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQ 158

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+AK L +  + V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 159 KLDRSPTVPELAKALGVSEDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 218

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 219 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 269

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 270 RLLTRTLAQLRE 281


>gi|15639996|ref|NP_219449.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189026235|ref|YP_001934007.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
 gi|3323340|gb|AAC65963.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018810|gb|ACD71428.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 311

 Score =  147 bits (370), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 84/299 (28%), Positives = 143/299 (47%), Gaps = 28/299 (9%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             + +++    N++K I       +   +   +         + AK  +V AN+R VISV
Sbjct: 22  RHDENTLTAYLNDLKRI------PLMNEKEEYACACAAYAGDAQAKNALVRANVRFVISV 75

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y   GL   DLI EGNIGL+ AAE+F+   G +F +YA  W++Q+I +++ +++  I
Sbjct: 76  ARHYRTCGLPLADLISEGNIGLLTAAERFNPARGCRFISYAACWIRQSILKALNEKARII 135

Query: 520 RIPVHMRDKIHK-------VVRTARRMSNKIKREPTPEEIAKKLAM--PVEGVRKVLKIT 570
           R+PV               V      +S         +  A        VE V     I 
Sbjct: 136 RLPVSRIRAAKSTYEYIPPVTSVNVGISKTQGGNRYGKRRATMCRAVPTVEEV----HIW 191

Query: 571 KEPISLETPIGDE---------DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             P+SL+ P+G           D   +GD + D     P +  +   L+    ++L  L 
Sbjct: 192 HTPLSLDAPLGASGSRGESGDVDGLRIGDCVPDDLYAQPEEHMLACALQADIAKILRLLP 251

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            R+ +V+R RFG+G     +L+E+G+ F +T+ER+RQIE KA+ +++  +R  +L S++
Sbjct: 252 ARDAQVIRYRFGLGGYERRSLQEIGEIFQITKERVRQIEKKALLRIRSCARQHRLDSYI 310


>gi|297812573|ref|XP_002874170.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297320007|gb|EFH50429.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 517

 Score =  147 bits (370), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 99/392 (25%), Positives = 179/392 (45%), Gaps = 22/392 (5%)

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL-LVEQLYDISKRIMHNEGELLR 358
                 +++K  V+  V+KEK + L   ++L ++  +  +V        +    E ++ R
Sbjct: 136 KRKQSGEEKKVVVRNNVMKEKRLSLDKRIALKRNVQEKPVVISAEKKVTKKQQEEEKIER 195

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSY----AKDFPEGEWKNFVACEVDSILKIRNEIK 414
           L + Y    D+         +   W            E  W   +   + ++L++++E++
Sbjct: 196 LVRDYSASNDI---------VSLDWKKMKIPPVLSSTEHAWLFKLMQPMKALLEVKDELQ 246

Query: 415 S---ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGL 468
                         E       V+K       A+ ++++ NLRLV+ V  KY +    G 
Sbjct: 247 KSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFVMNKYFHDFTNGP 306

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +F DL Q G  GL+ A ++F+    ++ STY ++W++ AI RS    S   R+P  +   
Sbjct: 307 KFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRS-MTTSNFTRVPFGLESV 365

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             ++ +T   +  ++ R PT +E+ ++L +  E  R+VL+  K  +SL +          
Sbjct: 366 RVEIFKTKTELLFELGRLPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQE-EF 424

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + I D + V   +S   A LR     VL SL P+E  V+R R+G+    D TL E+   
Sbjct: 425 INGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGN 484

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++RE +R+ E KA+ KLKH +R   LR ++
Sbjct: 485 LNISREMVRKHEVKALMKLKHQARVDYLRQYI 516


>gi|144897893|emb|CAM74757.1| RNA polymerase sigma-32 factor [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 288

 Score =  147 bits (370), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 68/274 (24%), Positives = 125/274 (45%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +  +E   +    R  E     A   ++ ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLQEIRKFPMLEPTEEYQLAKRYR--EHGDFEAADRLITSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A ++FD   G++ +TYAMWW++ A+   I      +++      K
Sbjct: 74  PLGELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAVQEYILHSWSLVKMGTTAAQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                  K+    + M      + T   IA KL +P  + +    ++     SL  P+  
Sbjct: 134 KLFFNLRKLKGQMQAMDEGDLPQETVTSIATKLNVPENDVINMNRRLASPDHSLNAPVRM 193

Query: 583 EDTSHLGDFIEDK--NAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D+  +  + L    +  +R +  +  L +L  RE  +L           
Sbjct: 194 DGEGEWQDWLVDESDDQETELADRQERGIRSKLLSTALDTLNERERSILSQ--RRLTEDP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++ +Q+ ++RER+RQIE +A  KL+   R+
Sbjct: 252 ATLEDLSQQYGISRERVRQIEVRAFEKLQKSIRA 285


>gi|302520387|ref|ZP_07272729.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302429282|gb|EFL01098.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 338

 Score =  147 bits (370), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + F  + ++ +     A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 92  LSRALFLRLATLAQDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 150

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +T+  ++ 
Sbjct: 151 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQ 210

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+AK L +  + V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 211 KLDRSPTVPELAKALGVSEDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 270

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 271 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 321

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 322 RLLTRTLAQLRE 333


>gi|301601109|dbj|BAJ13243.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  146 bits (369), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 107/252 (42%), Positives = 140/252 (55%), Gaps = 20/252 (7%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +  D +   +S     + + ++     +K      TDDPVRMYLREMGS+ELLSREGE
Sbjct: 12  AAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREMGSVELLSREGE 71

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE           
Sbjct: 72  IAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAA 131

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                    +    +++EKE+              + S+DD + V    +  E +E + D
Sbjct: 132 PQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDMQMPEEEEEDED 181

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVK 313
           E    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G        +
Sbjct: 182 E----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQERR 237

Query: 314 CKVLKEKLVKLV 325
            K LK++L+  V
Sbjct: 238 YKELKDQLITAV 249


>gi|291060369|gb|ADD73104.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           str. Chicago]
          Length = 296

 Score =  146 bits (369), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 84/299 (28%), Positives = 143/299 (47%), Gaps = 28/299 (9%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             + +++    N++K I       +   +   +         + AK  +V AN+R VISV
Sbjct: 7   RHDENTLTAYLNDLKRI------PLMNEKEEYACACAAYAGDAQAKNALVRANVRFVISV 60

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y   GL   DLI EGNIGL+ AAE+F+   G +F +YA  W++Q+I +++ +++  I
Sbjct: 61  ARHYRTCGLPLADLISEGNIGLLTAAERFNPARGCRFISYAACWIRQSILKALNEKARII 120

Query: 520 RIPVHMRDKIHK-------VVRTARRMSNKIKREPTPEEIAKKLAM--PVEGVRKVLKIT 570
           R+PV               V      +S         +  A        VE V     I 
Sbjct: 121 RLPVSRIRAAKSTYEYIPPVTSVNVGISKTQGGNRYGKRRATMCRAVPTVEEV----HIW 176

Query: 571 KEPISLETPIGDE---------DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             P+SL+ P+G           D   +GD + D     P +  +   L+    ++L  L 
Sbjct: 177 HTPLSLDAPLGASGSRGESGDVDGLRIGDCVPDDLYAQPEEHMLACALQADIAKILRLLP 236

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            R+ +V+R RFG+G     +L+E+G+ F +T+ER+RQIE KA+ +++  +R  +L S++
Sbjct: 237 ARDAQVIRYRFGLGGYERRSLQEIGEIFQITKERVRQIEKKALLRIRSCARQHRLDSYI 295


>gi|83589704|ref|YP_429713.1| sporulation sigma factor SigG [Moorella thermoacetica ATCC 39073]
 gi|83572618|gb|ABC19170.1| RNA polymerase, sigma subunit, RpsG/SigG [Moorella thermoacetica
           ATCC 39073]
          Length = 272

 Score =  146 bits (369), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 80/265 (30%), Positives = 138/265 (52%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + +   I  + ++ +   + A+++++  NLRLV+SV +++TNRG
Sbjct: 17  MLNKVEICGVNTSKLPLLKSDEIRQLFQQMQAGETGAREKLITGNLRLVLSVIQRFTNRG 76

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 77  EHVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRD 135

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++    + NK+ REP+  E+A++L +P E V   L   +EP+SL  PI  +  D 
Sbjct: 136 VAYKALQIRDTLVNKLAREPSLAEVAQQLDLPQEEVIFALDAIQEPVSLFEPIYHDGGDP 195

Query: 586 SHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             + D I D+ N  S     I           +  L PRE  +L +RF  G     T  E
Sbjct: 196 IFVMDQIGDEKNQDSSWLENI------AIKEAMNKLNPRERLILSLRFFEG----KTQME 245

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 246 VADEIGISQAQVSRLEKAALQHMRK 270


>gi|301601107|dbj|BAJ13242.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 107/252 (42%), Positives = 139/252 (55%), Gaps = 20/252 (7%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +  D +   +S     + + ++     +K      TDDPVRMYLREMGS+ELLSREGE
Sbjct: 12  AAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREMGSVELLSREGE 71

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE           
Sbjct: 72  IAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAA 131

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                    +    +++EKE+              + S+DD + V              +
Sbjct: 132 PQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGG----DMPMPEEEE 177

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVK 313
           EDED+S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G        +
Sbjct: 178 EDEDESNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQERR 237

Query: 314 CKVLKEKLVKLV 325
            K LK++L+  V
Sbjct: 238 YKELKDQLITAV 249


>gi|301601136|dbj|BAJ13256.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 111/257 (43%), Positives = 139/257 (54%), Gaps = 27/257 (10%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AV 302
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A 
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLAC 226

Query: 303 NGQKDEKSSVKCKVLKE 319
            G        + K LK+
Sbjct: 227 AGTLSSGQERRYKELKD 243


>gi|296536196|ref|ZP_06898318.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
 gi|296263478|gb|EFH09981.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
          Length = 295

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 127/278 (45%), Gaps = 13/278 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +       E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLQEIRKFPMLTPEEEFRLAK--DWKEHGDQKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A  +FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                  ++      +     +    E+IA+ L +P + V     ++     SL  P+  
Sbjct: 134 KLFFNLRRLKGQMAALEEGDLQPEQVEKIARVLQVPEQDVVSMNRRLASPDNSLNAPVRA 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D++     + A + ++   RE     L +L  RE  +L        +  
Sbjct: 194 DSEGEWQDWLVDESESQETEIAERQDMSNRRELLGEALKTLNERERHILIE--RRLKDEP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            TLEE+ +Q+ ++RER+RQIE +A  KL+   +S+ + 
Sbjct: 252 TTLEELSQQYNISRERVRQIEVRAFEKLQKSMKSQIME 289


>gi|114155162|dbj|BAF31031.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 250

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 129/229 (56%), Gaps = 21/229 (9%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSS-------VFLQKRKDSADRSTDDPVRMYLREM 128
           NVV+ +D ED    E   D  + +                +K      TDDPVRMYLREM
Sbjct: 1   NVVEDEDAEDPAAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREM 60

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           GS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE
Sbjct: 61  GSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLE 120

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                               +    +++EKE+              + S+DD + V    
Sbjct: 121 TTYSGPEAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDM 170

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
           +  E +E + DE    S  +L+AME +LRP+VM  LD IA+ Y++L  +
Sbjct: 171 QMPEEEEEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLLQV 215


>gi|253583872|ref|ZP_04861070.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
 gi|251834444|gb|EES63007.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
          Length = 260

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 87/264 (32%), Positives = 141/264 (53%), Gaps = 6/264 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +L I   IK IS    ++  E R I    R        A++++V +NLRLVIS+A+KYTN
Sbjct: 1   MLDISEYIKDISTYPLLTPKEEREIAVKAR---SGDREAQEKLVTSNLRLVISIARKYTN 57

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G+  LDLIQEGN+GL++A EK++     +FSTY+ +W+KQ+I R I      IR P ++
Sbjct: 58  MGIPILDLIQEGNMGLIRAVEKYEPDKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSYV 117

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            D I ++ +  +   NK    P+ +EI + L M  +   + + + ++   +   +  E  
Sbjct: 118 YDGISRMKKYVQDYKNKNSHCPSIDEICRSLDMKKKEAERYIDVLEKGNGIGNEMYGEMV 177

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            +    I D    +  D  I  +      + +  L PRE  VL  R+G+      TL E+
Sbjct: 178 EYCSSIIYDD---TFEDEVIAKSSNIDLMKKVNKLPPREREVLIYRYGLLDEKVLTLGEI 234

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
           G++  +T+ERIRQI+ +AI +L+ 
Sbjct: 235 GQRMNLTKERIRQIQLEAIDRLRE 258



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 9/87 (10%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y++++ +  LL+ + E  IA +  +G       L  S L    +I    +  +    + +
Sbjct: 7   YIKDISTYPLLTPKEEREIAVKARSGDREAQEKLVTSNLRL--VISIARKYTNMGIPILD 64

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQK 210
           +I        E   G     E +   K
Sbjct: 65  LI-------QEGNMGLIRAVEKYEPDK 84


>gi|301601105|dbj|BAJ13241.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 110/257 (42%), Positives = 140/257 (54%), Gaps = 24/257 (9%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNS----SVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           D +D   EE   D    +     +    +     +K      TDDPVRMYLREMGS+ELL
Sbjct: 7   DAEDPAAEESDGDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREMGSVELL 66

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           SREGEIAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE      
Sbjct: 67  SREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGP 126

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                         +    +++EKE+              + S+DD + V    +  E +
Sbjct: 127 EAKAAPQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDMQMPEEE 176

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDE 308
           E + DE    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G    
Sbjct: 177 EEDEDE----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSS 232

Query: 309 KSSVKCKVLKEKLVKLV 325
               + K LK++L+  V
Sbjct: 233 GQERRYKELKDQLITAV 249


>gi|323704529|ref|ZP_08116107.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535991|gb|EGB25764.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 339

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 94/253 (37%), Positives = 141/253 (55%), Gaps = 11/253 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +     A + +V+ N +LV+S A K   R    +   DL+Q G  GL+KAAE+FD    
Sbjct: 87  YQQGNKWALEALVDRNKKLVMSRAYKCFKRYKLNIDEDDLVQYGYFGLIKAAERFDIKRE 146

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF TYA WW+ QAI RSI D    IR+PVH  D+I+KV+       +    +    +I 
Sbjct: 147 TKFVTYATWWIDQAIKRSICDYGFIIRLPVHYFDEINKVLNILS--IHFDLSKEAIIKIL 204

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGD------EDTSHLGDFIEDKNAVSPLDSAIQA 607
           ++  +  +    ++ + +  +S+++          +  + L D I DK   +  +     
Sbjct: 205 EENGISKDKYDDIMFVIENVLSIDSLNKYVNPNSGDGDTELLDLIVDKTNPTVEEEIDLK 264

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L+ET   +L +L  RE+ V+RMRFG+    + TLE +GK+F +TRERIRQIE KAI+KL
Sbjct: 265 LLKETINNILDTLKSREKEVIRMRFGLDGGDEMTLERIGKEFNITRERIRQIEEKAIKKL 324

Query: 668 KHPSRSKKLRSFL 680
           +HPSRSKKLR F+
Sbjct: 325 RHPSRSKKLRDFI 337


>gi|23429441|gb|AAM94468.1| RNA polymerase sigma factor D [Aeromonas sobria]
          Length = 281

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 122/325 (37%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P             +         E +  D  E E + E     + DD   
Sbjct: 60  II--SGFIDPNETE-----DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGD 112

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
               PE A      L    + +  ++                                  
Sbjct: 113 SGPDPEVAREKFGELRAQYEVTRLSI---------------------------------- 138

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +L+L  + 
Sbjct: 139 -QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E D  W  Y K   +  W   +    + +L+   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKARRAKKE 281


>gi|332297914|ref|YP_004439836.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181017|gb|AEE16705.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 269

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 128/264 (48%), Gaps = 5/264 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
             + +  I     ++  + + + + +       + AK ++V++NLRLV+S+A KY +  +
Sbjct: 6   YASYMAQIQRYPLLTPEQEKKLSADI---HNGDTSAKLKLVQSNLRLVVSIANKYVSDRI 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLIQEGN+GL+ AA KF +    +FSTYA  W+ Q I R I ++   I +P    + 
Sbjct: 63  GVMDLIQEGNLGLLTAASKFHYSFNTRFSTYAYSWITQYILRFIQNKIPYITLPHRKEEM 122

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K+      +  +++ EPT  EIA  + +    +   L       S++  I        
Sbjct: 123 LRKIHMAKIDLMQQLQSEPTLREIASYMDVSESDISGALMHEYVYSSIDAEIDGTSNLTC 182

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGK 647
            D I D +  SP    ++    E    ++ +L  RE +V+  RF    +    TL ++ +
Sbjct: 183 ADMIADPS-PSPEQLCLKNLEAEDIRSLVETLPDRERQVIYYRFNFDNSRKPWTLRQISE 241

Query: 648 QFCVTRERIRQIEAKAIRKLKHPS 671
              ++ E +RQ+E +A++ L+  +
Sbjct: 242 MLGISAETVRQMELRALQFLRTAA 265



 Score = 41.4 bits (95), Expect = 0.52,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y+ ++    LL+ E E  ++  I  G       L +S L    ++   ++       + +
Sbjct: 9   YMAQIQRYPLLTPEQEKKLSADIHNGDTSAKLKLVQSNLRL--VVSIANKYVSDRIGVMD 66

Query: 184 II 185
           +I
Sbjct: 67  LI 68


>gi|168704590|ref|ZP_02736867.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 278

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 83/259 (32%), Positives = 149/259 (57%), Gaps = 3/259 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    ++  + + +   + +     + A+ +MV ANLRLV+++A+ YT +GL
Sbjct: 16  LETYLREINETALLTADQEKSLARAIAQ---GDTEARDQMVRANLRLVVNIARGYTGKGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI+EGN+GL++A E FD  +  +FSTYA +W+KQ+I R++ + + TIRIP +M + 
Sbjct: 73  ALQDLIEEGNLGLLRAVEGFDPTMNTRFSTYASYWIKQSIKRALVNTAKTIRIPAYMVEL 132

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + K  R   ++S+++ R PT EE+ K L +P + +  + K  +   +       +    +
Sbjct: 133 LAKWRRATNKLSDELGRPPTHEEVGKLLGLPKKKLAIIKKAIRVYNAAPQADQGDQGWSI 192

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + + D  A +P    ++ +  +    +L  +  RE  VLRMRFG+      TL+E+G+ 
Sbjct: 193 EEMLMDNRAKTPDTEMVETDDLKQVLILLEKMDQREATVLRMRFGLNDEEPKTLKEIGEC 252

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +TRER+RQIE +A+ KL
Sbjct: 253 LGLTRERVRQIEGEALAKL 271



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           P+  YLRE+    LL+ + E ++A+ I  G       +  + L     I   
Sbjct: 15  PLETYLREINETALLTADQEKSLARAIAQGDTEARDQMVRANLRLVVNIARG 66


>gi|269120610|ref|YP_003308787.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268614488|gb|ACZ08856.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 270

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 93/259 (35%), Positives = 147/259 (56%), Gaps = 9/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I     ++  E   +   +++ + +   A+ E++ +NLRLVIS+AKK    GL  +
Sbjct: 11  YLKDIQKYELLNREEEYELFRRIKEDDSQD--ARHELILSNLRLVISIAKKSLGNGLPLI 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+KA  KFD+  G++FSTYA+WW+KQ+I ++I ++   IRIP +  +++ K
Sbjct: 69  DLISEGNIGLIKAINKFDYTKGHRFSTYAVWWIKQSIKKAIINKGRDIRIPSYKYEQLAK 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +      N     P+   IA++L +    V  ++   ++ ISL   IG  D   L D 
Sbjct: 129 VNKVMVNYINDHGETPSVAYIAEQLEIKEYKVSLLINEFQDIISLNDVIG--DNIFLEDV 186

Query: 592 I--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           I  ED      + +     +RE    +   L+ RE  ++ +R+G+  N  HTL+E+G + 
Sbjct: 187 IGNEDNIEEKIIKNDQINKMRELLDNI---LSEREREIIELRYGLYNNKMHTLKEIGDEL 243

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +TRER+RQIE KAI KLK
Sbjct: 244 NITRERVRQIEKKAITKLK 262


>gi|312282679|dbj|BAJ34205.1| unnamed protein product [Thellungiella halophila]
          Length = 511

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 95/375 (25%), Positives = 170/375 (45%), Gaps = 22/375 (5%)

Query: 317 LKEKLVKLVGSLSLNQSRIDL-LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
           +KEK + L   ++L ++  +  LV        +    E ++ RL + Y    D+      
Sbjct: 147 MKEKRLSLDKRIALKRNIQEKPLVPSAQKKVTKKQQEEEKIERLVRDYSASHDI------ 200

Query: 376 GRELDPHWVSY----AKDFPEGEWKNFVACEVDSILKIRNEIKS---ISVETGISISEFR 428
              +   W            E  W   +   + ++L++++E++              E  
Sbjct: 201 ---VSLDWKKMKIPPVLPSTEHAWLFKLMQPMKALLQVKDELQKSLGREPRETEIAGEIN 257

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
              + V++       A+ ++++ NLRLV+ V  KY      G +F DL Q G  GL+ A 
Sbjct: 258 MSAAEVKRKIEIGRAARNKLIKHNLRLVLFVMNKYFQDFTNGPKFQDLCQAGMRGLITAI 317

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+    ++ STY ++W++ AI RS    S   R+P  +     ++ +T   +  ++ R
Sbjct: 318 DRFEPKRKFRLSTYGLFWIRHAIIRS-MTTSNFTRVPFGLESVRVEIYKTKMELLFELGR 376

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            PT +E+ ++L +  E  R+VL+  K   SL +           + I D + V   +   
Sbjct: 377 LPTEDEVVERLKISPERYREVLRAAKPVFSLNSKHSVTQE-EFINGITDVDGVGADNRRQ 435

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A LR     VL SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ 
Sbjct: 436 PAILRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALM 495

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R   LR ++
Sbjct: 496 KLKHQARVDYLRQYI 510


>gi|148261701|ref|YP_001235828.1| RNA polymerase factor sigma-32 [Acidiphilium cryptum JF-5]
 gi|326405194|ref|YP_004285276.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
 gi|146403382|gb|ABQ31909.1| RNA polymerase, sigma 32 subunit, RpoH [Acidiphilium cryptum JF-5]
 gi|325052056|dbj|BAJ82394.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
          Length = 296

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 125/275 (45%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +S  E   +    R  + E   A  ++V ++LRLV  +A  Y   GL
Sbjct: 8   LARYLQEIRKFPMLSPEEEDRLARAWR--DNEDQAAAHKLVTSHLRLVAKIAMGYRGYGL 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 66  PLGELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 125

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA+ L +P + V     ++T    SL  PI  
Sbjct: 126 KLFFNLRRLKGQMQAIEDGDMQPEQVEKIARVLGVPEQDVVSMNRRLTAPDHSLNAPIRM 185

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D              +   R      L +L  RE  +L        +  
Sbjct: 186 DGEGEWQDWLVDDADSQEEAIGDHEEMTGRRALLATALKTLNDRERHILIQ--RRLKDDP 243

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLE++ +Q+ ++RER+RQIE +A  KL+   +++
Sbjct: 244 TTLEDLSQQYNISRERVRQIEVRAFEKLQKSMKAQ 278


>gi|148793320|gb|ABR12724.1| RNA polymerase sigma factor [Aliivibrio fischeri]
          Length = 279

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 129/328 (39%), Gaps = 50/328 (15%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     + P    G    T  H   +  ++  + E D+  E E + E  A +  +     
Sbjct: 61  I--SGFVDPNDD-GSSAPTATHIGSELSEAELDDEDDEDDEGETEEEEDAGIDPE----- 112

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
                                                 AL++  E+     ++Q      
Sbjct: 113 -------------------------------------LALEKFTELRTSYHNMQLAFEEF 135

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
            +D+    K +    +L  +     L   + D LV+++ D   R+   E  ++R+   YG
Sbjct: 136 GRDD---AKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYG 192

Query: 365 -IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E    W +      +  +   +    + I +   ++ SI  ETG+ 
Sbjct: 193 KMPKKSFIALFTGNESSDEWFNEIMA-SDKPYVERLQRYEEDIRRSIAKLDSIEKETGLP 251

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEA 451
           +   + I   +  GE +A  AKKEMVEA
Sbjct: 252 VENIKDISRRMSIGEAKARRAKKEMVEA 279


>gi|90577256|ref|ZP_01233067.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440342|gb|EAS65522.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 286

 Score =  146 bits (368), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 94/267 (35%), Positives = 147/267 (55%), Gaps = 4/267 (1%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  +R  +  IS +  ++  +    +   RK       +KK ++E+NLRLV+S+AKKY 
Sbjct: 7   EVDVVRLYLNDISNKPLLNKDDE---IQYSRKSLTGDLASKKILIESNLRLVVSIAKKYR 63

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              L   DLI EGNIGLM A EKFD   G++FSTYA WW+KQ I R+I +Q+ TIR+PVH
Sbjct: 64  ASNLSLSDLIDEGNIGLMTAVEKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVH 123

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI-GDE 583
           +  +I+ ++RT R +      EPT E+IA+ L    + +  +       ISL+  I   E
Sbjct: 124 ISKEINTLLRTHRELMKLNNNEPTHEDIAQALNKDSKEISALFSNEVNVISLDQTIGDTE 183

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +  +   + D+   SP       ++ + T  +L  +  R++ ++  RFG+     HTL+
Sbjct: 184 KSQTIAYLVADEQITSPSAEVDNDDMVKITNLILNGINARDKEIICRRFGLMGYEPHTLQ 243

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHP 670
           EV     +TRERIRQ++ K++  LK  
Sbjct: 244 EVADAVGLTRERIRQLQIKSLSSLKRS 270



 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 3/88 (3%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D VR+YL ++ +  LL+++ EI  +++   G       L ES L    ++    +     
Sbjct: 9   DVVRLYLNDISNKPLLNKDDEIQYSRKSLTGDLASKKILIESNLRL--VVSIAKKYRASN 66

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGH 206
             L ++ID E  IG  +    F   +G 
Sbjct: 67  LSLSDLID-EGNIGLMTAVEKFDPEKGF 93


>gi|302382389|ref|YP_003818212.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302193017|gb|ADL00589.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 295

 Score =  146 bits (367), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 78/274 (28%), Positives = 130/274 (47%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R  E + S +   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLTEIRKFPMLTKDEEFMLAK--RWSEHQDSESAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  PE    IA KL +  E V  + +      SL  P+  +
Sbjct: 134 KLFFNLRKAKSQISAFEEGDLRPEHLAAIATKLGVSEEEVTNMNRRLGGDASLNAPLRVD 193

Query: 584 DTSHLGDFIEDKNAVSPLD---SAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTD 639
             S   D++ D NAVS       + + +LR       +  LT RE+ +L        +  
Sbjct: 194 GESEWQDWLSDDNAVSQETALADSEEKSLRMGLLQEAMGELTEREKHILTE--RRLKDDP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLEE+  Q+ V+RER+RQIE +A  KL+   R+
Sbjct: 252 VTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRA 285


>gi|301601095|dbj|BAJ13236.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis]
          Length = 249

 Score =  146 bits (367), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 107/252 (42%), Positives = 140/252 (55%), Gaps = 20/252 (7%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
             +  D +   +S     + + ++     +K      TDDPVRMYLREMGS+ELLSREGE
Sbjct: 12  AAEESDNDEEAESEGGELAPAGNTAVATAKKKEPTDRTDDPVRMYLREMGSVELLSREGE 71

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           IAIAKRIEAGR  M+A LCESPLTFQALIIWRDELN+GTTLLREIIDLE           
Sbjct: 72  IAIAKRIEAGRETMIAGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAA 131

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                    +    +++EKE+              + S+DD + V    +  E +E + D
Sbjct: 132 PQFQSPEKIEADRKAAEEKEK----------TRRVRSSEDDITNVGGDMQMPEEEEEDED 181

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVK 313
           E    S  +L+AME +LRP+VM  LD IA+ Y++LR LQD       A  G        +
Sbjct: 182 E----SNLSLAAMEAELRPQVMETLDLIADTYKKLRKLQDQQVEARLACAGTLSSGQERR 237

Query: 314 CKVLKEKLVKLV 325
            K LK++L+  V
Sbjct: 238 YKELKDQLITAV 249


>gi|189423258|ref|YP_001950435.1| RNA polymerase, sigma 70 family subunit [Geobacter lovleyi SZ]
 gi|189419517|gb|ACD93915.1| putative RNA polymerase, sigma 70 family subunit [Geobacter lovleyi
           SZ]
          Length = 280

 Score =  146 bits (367), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 74/263 (28%), Positives = 126/263 (47%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     ++  E R     V+  E +   A   ++ +NLR V+ VA +Y + GL+ L
Sbjct: 15  YLSEIRKFNLLTEDEERDYA--VKFFEEKDLEAAHTLITSNLRYVVKVASEYRHYGLKML 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLM A  KF+   G +  +YA+WW++  I   I      ++I      R   
Sbjct: 73  DLIQEGNIGLMMAVRKFNPYRGVRLISYAVWWIRAYIQNYIVSAWSLVKIGTTQAQRKLF 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           + + +T   +     R+    E++  L +P   V ++ +  K  +SL   I + D   + 
Sbjct: 133 YGLRKTKEALLKLTGRDSDAFEVSSMLHVPDHEVVEMEQRLKGEVSLNEEIIEGDGLTIL 192

Query: 590 DFIEDK--NAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           + I D   N    L    Q  +L++     L  L  +E+ ++     I  +   TL+++ 
Sbjct: 193 ETIADDRMNQEEMLGEYQQEHSLKKAIAHALQGLNEKEKYIVEH--RITNDDPLTLQDIA 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
             F ++RER+RQIE +A+ KLK+
Sbjct: 251 DHFSISRERVRQIEERALVKLKN 273


>gi|91978905|gb|ABE66428.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 286

 Score =  146 bits (367), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 129/328 (39%), Gaps = 44/328 (13%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II  
Sbjct: 1   MGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-- 58

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                     GF    E                          E  A  +    S++   
Sbjct: 59  ---------SGFIDPNE-------------------------TEDMAPTATHIGSELGED 84

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
               E++E   DEDED  +                   E+   Y          ++ QK+
Sbjct: 85  DLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKN 138

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + 
Sbjct: 139 GRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMP 198

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++
Sbjct: 199 KKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQ 257

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLR 454
            + I   +  GE +A  AKKEMVEANLR
Sbjct: 258 IKDINRRMSIGEAKARRAKKEMVEANLR 285


>gi|167515030|gb|ABZ81799.1| RpoD [Aeromonas aquariorum]
          Length = 282

 Score =  146 bits (367), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 131/326 (40%), Gaps = 46/326 (14%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I     I P                         E DDV  T   I S            
Sbjct: 61  I--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLADEDE 94

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVN 303
           D   +   + + + D+ +      ++                  E + ELR+  +   ++
Sbjct: 95  DEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLS 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 IQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + + +L+   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKEM 448
           SI++ + I   +  GE +A  AKKEM
Sbjct: 257 SIAQIKDINRRMSIGEAKARRAKKEM 282


>gi|148793324|gb|ABR12726.1| RNA polymerase sigma factor [Photobacterium angustum]
 gi|148793326|gb|ABR12727.1| RNA polymerase sigma factor [Photobacterium angustum]
          Length = 284

 Score =  146 bits (367), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 128/328 (39%), Gaps = 45/328 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I        E+         G    + +   ++K+ +D ++ E   E     S D     
Sbjct: 61  ISGFVDPNEEATAAPTATHIGSELSESDLEDEDKDLEDDEDAEDSDEEEDDGSID----- 115

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L +  D  A  +                                   
Sbjct: 116 ---PELAREKFLELRQAYDKMALAIET--------------------------------- 139

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
             + + +   +V  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 140 --NGRQNATTEVAVEELSEVFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 197

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E    W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 198 KMPKKTFVSLFAGNESSQDWIDEALNSGKP-YAERLKVYEEDLRRSSLKLRMLEEETGLS 256

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEA 451
           I   + I   +  GE +A  AKKEMVEA
Sbjct: 257 IERIKDISRRMSIGEAKARRAKKEMVEA 284


>gi|242089037|ref|XP_002440351.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
 gi|241945636|gb|EES18781.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
          Length = 501

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 73/270 (27%), Positives = 131/270 (48%), Gaps = 11/270 (4%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQF 470
             ++  TG+++ + R  +            A+ ++++ NLRLV     KY        +F
Sbjct: 240 AELAEATGMTVHQLRRRLD-------VGRAARNKLIKHNLRLVPYAINKYYPDMGTDERF 292

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G  GL+ A ++F+   G++ STYA++W++ +I R+    S   R P  M  +  
Sbjct: 293 DDLCQAGANGLITAIDRFEPKRGFRISTYALFWIRHSIVRA-MTLSSFTRFPFAMESERQ 351

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           ++ +    ++ ++ R  T EE+ +K+ +  +  R VL++T+   SL           + +
Sbjct: 352 EIGKAREELAFELGRPATDEEVRRKVGISPQRYRDVLRMTRPTYSLHARNRVTQEELINE 411

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             +D              LR     +L SL P+E  V+R RFG+      TL E+     
Sbjct: 412 VTDDDAIGVDAGGRHNTLLRLAIDDLLDSLKPKESLVIRQRFGLDGRGKRTLSEIAGNLS 471

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++RE +R+ E KA+ KLKHP+R + LR ++
Sbjct: 472 ISREMVRKYELKALMKLKHPTRVEYLRRYM 501


>gi|124022691|ref|YP_001016998.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962977|gb|ABM77733.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 320

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 92/286 (32%), Positives = 157/286 (54%), Gaps = 9/286 (3%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-------MVRKGECEASIAK 445
            E +  +  +V  ++ +      +  +TG + +  + +          ++K       AK
Sbjct: 28  HEQEITLGRQVQELMSLEQLESELEGKTG-APASRKELAKAAGLSELQLKKKLQSGRRAK 86

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++
Sbjct: 87  ERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIR 146

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V+ 
Sbjct: 147 QGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEVKD 206

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++   ++P+SLE  +  +        +       P +      ++     +L  L   + 
Sbjct: 207 LMCRARQPMSLEMKV-GDGDETELLELLAGEEELPSEKVEVDCMKGDLRTLLEKLPELQG 265

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RVLRMR+GI       L  + K   ++R+R R++E + +  ++  S
Sbjct: 266 RVLRMRYGIDGGEPMNLTGIAKTLGMSRDRTRRLEREGLALMRTSS 311



 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS E EI + ++++ 
Sbjct: 11  DLVRSYLRDIGRVPLLSHEQEITLGRQVQE 40


>gi|242281118|ref|YP_002993247.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio salexigens
           DSM 2638]
 gi|242124012|gb|ACS81708.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           salexigens DSM 2638]
          Length = 322

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 81/274 (29%), Positives = 140/274 (51%), Gaps = 11/274 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ IS    +   E   +   V+  E     A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 45  YLQEISRFPLLEPDEEFRLAKQVQ--ENGDQQAAFRLVSSHLRLVVKIAMDFQRRWMQNV 102

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKI 529
           LDLIQEGN+GLMKA  KFD   G KFS YA +W+K  I + I D    ++I     + K+
Sbjct: 103 LDLIQEGNVGLMKAVNKFDPDKGIKFSYYAAFWIKAYILKYIMDNWRMVKIGTTQTQRKL 162

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHL 588
              +   R+    +  +PT  E++KKL +  E +     ++ K  +SL    G++  +  
Sbjct: 163 FYNLNKERQRLQALGFDPTTSELSKKLNVSEEEITEMDQRLAKNDLSLNLKFGEDSEATR 222

Query: 589 GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            DF+ D       +  +  I   L +    ++ +L  +E+ +L     +  ++  TL E+
Sbjct: 223 MDFLPDLGPGVEETLANKEISTLLLDQLRAIVPNLNEKEQVILND--RLLSDSPRTLREI 280

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G++F VTRER+RQIEA+ ++KL+    ++ ++ F
Sbjct: 281 GEEFGVTRERVRQIEARLLKKLREHL-AESVKDF 313



 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAM 152
           +          FL   +   + +T DP+ +YL+E+    LL  + E  +AK++ E G   
Sbjct: 15  NEEVKLPPKDDFLPTPRAKGEVATKDPLHLYLQEISRFPLLEPDEEFRLAKQVQENGDQQ 74

Query: 153 MMASLCESPLTFQALIIW 170
               L  S L     I  
Sbjct: 75  AAFRLVSSHLRLVVKIAM 92


>gi|106895886|gb|ABF82645.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC364]
          Length = 284

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 128/327 (39%), Gaps = 44/327 (13%)

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II 
Sbjct: 1   EMGTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII- 59

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                      GF    E                          E  A  +    S++  
Sbjct: 60  ----------SGFIDPNE-------------------------TEDMAPTATHIGSELGE 84

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
                E++E   DEDED  +                   E+   Y          ++ QK
Sbjct: 85  DDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQK 138

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGI 365
           + ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   +
Sbjct: 139 NGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKM 198

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+SI+
Sbjct: 199 PKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIA 257

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEAN 452
           + + I   +  GE +A  AKKEMVEAN
Sbjct: 258 QIKDINRRMSIGEAKARRAKKEMVEAN 284


>gi|306031830|gb|ADM83576.1| RNA polymerase sigma-70 factor [Pseudomonas sp. M1(2010b)]
          Length = 275

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 121/322 (37%), Gaps = 48/322 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +   +  + + +      +++  +    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDPKVKAEGDDEEDDKEESTEEEEEVESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVSDQMELARKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 135 SKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    G E+D  W   A    + ++   +      I++ + ++ ++  ETG+ I+E + 
Sbjct: 195 FLRLFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEIKD 253

Query: 430 IVSMVRKGECEASIAKKEMVEA 451
           I   +  GE +A  AKKEMVEA
Sbjct: 254 INRRMSIGEAKARRAKKEMVEA 275


>gi|4218586|emb|CAA10725.1| chloroplast sigma factor [Triticum aestivum]
          Length = 461

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 96/303 (31%), Positives = 161/303 (53%), Gaps = 15/303 (4%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           V  +K   +G W      ++   L      K ++    IS  E R   S +R+      +
Sbjct: 165 VHLSKKIKDGIWLQQQRSKLKEKLGNEPSYKQMAQSLRISTPELR---SRMRESF----L 217

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A++ +  +N+RLVIS+A+KY   G++  DLIQ G IGL++  EKFD   G++ STY  WW
Sbjct: 218 AREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTYVYWW 277

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++Q ++R++AD S T R+P ++ +++  +      + ++    PT + IAK L +  + V
Sbjct: 278 IRQGVSRALADNSKTFRLPTYLHERLIAIRGAKYALEDQ-GVSPTTQNIAKLLNISEKKV 336

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQANLRETTTRVLA 618
               +   + +SL+           GD    +IED+N A  P     +  L+E   ++L 
Sbjct: 337 HNATEAVNKALSLDQQAFPSLNGLPGDTLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLN 396

Query: 619 S-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           S LT RE  ++++  GIG    HT E++ +QF ++RER+RQ+   A+ KLK  +R KKL 
Sbjct: 397 SNLTERERDIIQLYHGIGK-QCHTWEDISRQFGLSRERVRQVGLIAMEKLKQRARRKKLD 455

Query: 678 SFL 680
           + L
Sbjct: 456 ALL 458


>gi|119384818|ref|YP_915874.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
 gi|119374585|gb|ABL70178.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 728

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 103/410 (25%), Positives = 172/410 (41%), Gaps = 35/410 (8%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           D++A+      + +      Q+      + + L E +++    L L     +  VE + D
Sbjct: 338 DDLADAIEAALTRRTRLPGTQRFVMDKSEERQLLEPMMRAKQELQLGILASETAVETILD 397

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR-ELDPHWVSYAKDFPEGEWKNFVACEV 403
           + + I     +   ++    I          G  E        A       W        
Sbjct: 398 VMESIRDGSRDPGSVSLRTIIP------SRPGHAETSEV---MAAADTLRSWHTTGRVMD 448

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI----------AKKEMVEANL 453
               +           +     E    +  +   + EAS           A + ++  +L
Sbjct: 449 GKRRREALAALEALDLSLAFHKELVRTLEQLPACQAEASQLEAELLLSESATEHLIREHL 508

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
             V   A +    G    D+ Q   +GL ++  +FD   GY+F  YA +W++QAITR  +
Sbjct: 509 PYVRRFASRNVEEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATYWMRQAITRWRS 568

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV---RKVLKIT 570
           D+   IRIPVH  +KI K+ R   R+  ++    +  E+AK+L   ++ V   R + +  
Sbjct: 569 DEGAAIRIPVHRNEKITKLDRALERLDVRVGGAVSDLELAKELEWTIDEVTQFRSIPREA 628

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           + P SL+            D + + + V       +A      T  LA L  R+  V+RM
Sbjct: 629 EYPESLDDW---------DDLLPEPSGVDV---FDEAETERIVTDALADLPERQADVIRM 676

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RFGIG ++D TLEE+G+ + VTRERIRQIEAK + +L HP R ++L+  L
Sbjct: 677 RFGIGRDSDMTLEEIGQIYGVTRERIRQIEAKGLDRLSHPGRKRRLQELL 726


>gi|83312286|ref|YP_422550.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82947127|dbj|BAE51991.1| DNA-directed RNA polymerase, sigma subunit [Magnetospirillum
           magneticum AMB-1]
          Length = 296

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 123/274 (44%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLQDIRKFPMLPPEEEYLLAKRFR--EHGDLPAANRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A  +FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PLGELISEGNVGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + +   +M    + + + E    IA KL +  + V     +++    SL  P+  
Sbjct: 134 KLFFNLRKLKGQMQAIEEGDMSAENVAKIATKLEVTEDEVVTMNRRLSSPDHSLNAPVRA 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E      D++ D +     +   +  L   R+  T  L +L  RE  +L           
Sbjct: 194 EGEGEWQDWLVDDHEDQETELGEREELGQRRQMLTSALEALNDRERAILIQ--RRLTEDP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++ +++ ++RER+RQIE +A  KL+   +S
Sbjct: 252 ATLEDLSQRYGISRERVRQIEVRAFEKLQKSVKS 285


>gi|95929333|ref|ZP_01312076.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134449|gb|EAT16105.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
          Length = 282

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 71/264 (26%), Positives = 132/264 (50%), Gaps = 9/264 (3%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +  IS    +       + +  RK       A  ++V ANLR V+ +A +Y   GL+ 
Sbjct: 13  HYMAQISQFEPLDRETEYELANRYRKNN--DLDAAHKLVCANLRFVVKIAYEYQAYGLKM 70

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKI 529
           +DL+QEGNIGLMKA +KFD     +  +YA+WW++  I   I +    ++I     R K+
Sbjct: 71  IDLVQEGNIGLMKAIKKFDPDRNIRLISYAVWWIRAYIHNYIINAWSLVKIGTTQARKKL 130

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
              ++  R    K+  +    EIA++L +  + V ++ +++     SL+  +  + T+  
Sbjct: 131 FFKLKQTRDALQKMGNDADHAEIARQLNVSTDEVAEMSVRLGGRDSSLDGQLTPDSTTSH 190

Query: 589 GDFIE--DKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            D +   DK+    L      +L      + L+ L  RE+ ++     I  +   TL+++
Sbjct: 191 LDTLVDHDKDQEQRLIELEHESLTTHRVQQALSHLNEREQHIV--HSRILQDDKATLQDL 248

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             Q+ +++ER+RQ+E +A+ KLK+
Sbjct: 249 ADQYGISKERVRQLEKRALEKLKN 272


>gi|254419521|ref|ZP_05033245.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
 gi|196185698|gb|EDX80674.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
          Length = 286

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 124/274 (45%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 7   LSRYLTEIRKFPMLTKDEEFMLAK--RWSEHQDPEAAHRLVTSHLRLVAKIAMGYRGYGL 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 65  PIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 124

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  PE    IA KL +  E V  + +      SL  P+  +
Sbjct: 125 KLFFNLRKAKSQISAFEEGDLHPEHLAAIATKLGVSEEEVTNMNRRLGGDASLNAPLRAD 184

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNTD 639
             S   D++ D  AVS          +          +  LT RE+ +L        +  
Sbjct: 185 GESEWQDWLADDTAVSQETQLADDEEKGIRMSLLQEAMEELTDREKHILTE--RRLKDDP 242

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLEE+  Q+ V+RER+RQIE +A  KL+   R+
Sbjct: 243 VTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRA 276


>gi|187251192|ref|YP_001875674.1| DNA-directed RNA polymerase sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
 gi|186971352|gb|ACC98337.1| DNA-directed RNA polymerase, sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
          Length = 380

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 96/278 (34%), Positives = 155/278 (55%), Gaps = 8/278 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           ++  VDSI +   +I  +S +  +S  E   +   ++K     + AK+ M+E NLRLVI 
Sbjct: 1   MSENVDSINQYFKKISEVSED--LSREEMEKLWKRIKK---GDTAAKQRMMELNLRLVIP 55

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
            AK++  + +  LDLI+EGN+GL++A EKFD   G++FSTYA++W+ QAI + I +QS  
Sbjct: 56  AAKRFMRKDIDLLDLIEEGNLGLLQAIEKFDPSKGFRFSTYAIYWIDQAIRKYIDEQSGA 115

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR---KVLKITKEPIS 575
           I+IP H    I K  RT   + + ++REP+  E++++L      ++   + +   K   S
Sbjct: 116 IKIPSHAWGDIKKWTRTWNALKDSLEREPSLTEMSRELDWSARKIKSILETINAAKGIDS 175

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L   IG+ED   L D + D    +P D   +++        L  L PR++ +L MR G+ 
Sbjct: 176 LALAIGEEDEVTLEDTLTDDGKGNPDDVFSRSSSNSALLAALEELNPRDKEILMMRNGLK 235

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            N   TL EV K   ++RER+RQIE +AI  ++  +  
Sbjct: 236 TNEPMTLSEVSKIMGLSRERVRQIEERAISHIRKKAHK 273


>gi|323454681|gb|EGB10551.1| hypothetical protein AURANDRAFT_23034 [Aureococcus anophagefferens]
          Length = 388

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 81/262 (30%), Positives = 139/262 (53%), Gaps = 16/262 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R        A+  +  ANLRLV+S+AK+Y   GL   DL+QEG  GL +A E+FD   G
Sbjct: 123 LRAARSRGVDARSTLTSANLRLVVSIAKRYRFCGLAQEDLLQEGAFGLSRAVERFDPERG 182

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA +W++QA+ R+ A+QS  IR+P H+ D++  + + +  +S ++ R+ T +E+A
Sbjct: 183 FRFSTYATFWIRQAVLRACAEQSRVIRLPAHVHDQLASMRKASAELSRRLGRDATDDELA 242

Query: 554 KKLAMP-VEGVRK-VLKITKEPISLETPIGDE-------------DTSHLGDFIEDKNAV 598
             L +   E +        ++P SL+                     + + + + D   +
Sbjct: 243 DHLELEKPEKLAFLRRCAAQDPSSLDEKHAIHAGRGSSVGGGGAAGATTIAESLSDDTIL 302

Query: 599 SPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            P +   +A  RE    +LA+    RE  VL MRFG+  N   +  ++ ++  V+RER+R
Sbjct: 303 VPDEFVAEAASREYVGDLLATVCNDRERDVLGMRFGLYGNAPISKTKIAERLAVSRERVR 362

Query: 658 QIEAKAIRKLKHPSRSKKLRSF 679
           QIE +A+ KL+   R+ +   +
Sbjct: 363 QIEVRALTKLRQTHRANRNEEY 384


>gi|219124053|ref|XP_002182327.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406288|gb|EEC46228.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 317

 Score =  145 bits (366), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 101/287 (35%), Positives = 155/287 (54%), Gaps = 29/287 (10%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---------T 464
           +  +   G+S  E R ++        E   A+  +V ANL LV ++AK+           
Sbjct: 40  QEWAAACGVSAVELRRVLD-------EGQQARAALVAANLGLVTALAKRQLSTLQTATEA 92

Query: 465 NRG----LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
            RG    L   DLIQEG +GLMKAAE+F+   G++FSTYA WWV+Q I +S++D S TIR
Sbjct: 93  GRGVGTILTLQDLIQEGTLGLMKAAERFEPERGWRFSTYATWWVRQRILKSVSDSSRTIR 152

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P H+   + ++ +           E T   +A+ L +PVE VR     ++  +SLETP+
Sbjct: 153 LPAHVHGTLQRIQKAKA-WFQAHGEEATLSSLAQYLELPVEKVRLYTDSSRNVMSLETPL 211

Query: 581 G------DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFG 633
                  DE+T  LGD +   +  +P +      LR     V+   LT  E+ VLR RFG
Sbjct: 212 KGRSAFKDENTRTLGDTLA-SDEKTPEEDVEAQALRLDLEHVMTQVLTDVEQNVLRRRFG 270

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   T  ++EE  +Q  V+R+RIR +E +A+ KL+HP ++ KL+S++
Sbjct: 271 LEDGTCWSVEETARQLGVSRDRIRLVETRALNKLRHPQQNYKLQSYV 317


>gi|75812393|ref|YP_320012.1| sigma-70 [Anabaena variabilis ATCC 29413]
 gi|75705149|gb|ABA24823.1| Sigma-70 [Anabaena variabilis ATCC 29413]
          Length = 314

 Score =  145 bits (365), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 93/278 (33%), Positives = 161/278 (57%), Gaps = 10/278 (3%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++  L  +  I+ ++ + G S +E   I+ +          AK++M+ ANLRLV+++AKK
Sbjct: 46  LEEQLHQQLNIQQLAADMGKSETEVFQILRL-------GQKAKEKMIAANLRLVVAIAKK 98

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y    L+FLDL+QEG+IGL KA E+FD   GYKFST A WW++Q IT++IA++S TIR P
Sbjct: 99  YRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTP 158

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
            HM D++ K+ +  R +   + REP   EIA+   +    VR+ L   + P+SL+ P+G 
Sbjct: 159 SHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQ 218

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ED     + +   +  SP +   +  LR+     L +L P +++VL +RFG+G     + 
Sbjct: 219 EDEVDFLEILP-ADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLST 277

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +++ ++  + + ++   + +AI+ L    +  ++R +L
Sbjct: 278 KQIAERLNIKQAKVGTTQKQAIKVLHR--QQPQMREYL 313



 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 11/30 (36%), Positives = 20/30 (66%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D V +YLRE+    +L+ E EI +A++++ 
Sbjct: 6   DSVGIYLREISKYPMLTPEQEITLARQVKQ 35


>gi|23429487|gb|AAM97311.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 281

 Score =  145 bits (365), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 119/320 (37%), Gaps = 44/320 (13%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II   
Sbjct: 5   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--S 62

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P             +         E +  D  E E + E     + DD       P
Sbjct: 63  GFIDPNE-----ADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDEGDGGPDP 117

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           E A      L    + +  ++                                   QK+ 
Sbjct: 118 EVAREKFGELRAQYEVTRLSI-----------------------------------QKNG 142

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKR 367
           ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +
Sbjct: 143 RAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 202

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F+      E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ 
Sbjct: 203 KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQI 261

Query: 428 RHIVSMVRKGECEASIAKKE 447
           + I   +  GE +A  AKKE
Sbjct: 262 KDINRRMSIGEAKARRAKKE 281


>gi|209407286|emb|CAP72528.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 284

 Score =  145 bits (365), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 127/325 (39%), Gaps = 46/325 (14%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I
Sbjct: 1   ELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTSEGGRLSDI--LSGYI 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P+  G         + Q+ E  + +     V + + D +     S+++       PE A
Sbjct: 59  DPDDDGAA-------APQEVEPQTPQTTSKPVDDDKDDEDEDDSDSEEEEGDGGPDPEVA 111

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                 + E  + +   L                                   +K  ++S
Sbjct: 112 RVRFGAVAEQLEKANKAL-----------------------------------KKHGRAS 136

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVF 370
            +     E L  L   + L   + D LVE++ +   +I   E  +++L      + R  F
Sbjct: 137 QQATEELEALATLFMPIKLVPKQYDALVERVRNALNQIRAQERAIMQLCVRDARMPRADF 196

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L +    E +  W     +  + ++   ++   + I + + ++  +  E  ++I++ + I
Sbjct: 197 LRQFPNNETNLSWADELAN-GKSKYAEAISNRKEDIQRCQQKLVELEQECALAIADIKDI 255

Query: 431 VSMVRKGECEASIAKKEMVEANLRL 455
              +  GE +A  AKKEMVEA    
Sbjct: 256 NRRMSIGEAKARRAKKEMVEATYVW 280


>gi|15419944|gb|AAK97216.1|AF300644_1 sigma factor RpoD [Lactobacillus acidophilus]
          Length = 162

 Score =  145 bits (365), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 96/162 (59%), Positives = 120/162 (74%)

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           RIPVHM + I+K++R  R++   + REPTPEEI  ++ MP   VR +L+I +E +SLETP
Sbjct: 1   RIPVHMVETINKLIRIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDILRIAQERVSLETP 60

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IG+ED SHLGDFIEDK+A SP   A    L+E   +VL +LT REE VLR+RFG+     
Sbjct: 61  IGEEDDSHLGDFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLRLRFGLEYGRT 120

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            TLEEVGK F VTRERIRQIEAKA+RKL+HPSRS +LR F+D
Sbjct: 121 RTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSNQLRDFMD 162


>gi|33863339|ref|NP_894899.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640788|emb|CAE21243.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 320

 Score =  145 bits (365), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 92/286 (32%), Positives = 156/286 (54%), Gaps = 9/286 (3%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-------MVRKGECEASIAK 445
            E +  +  +V  ++ +      +  +TG   +  + +          ++K       AK
Sbjct: 28  HEQEITLGRQVQELMSLEQLESELEGQTG-EPASRKELAKAAGLSELQLKKKLQSGRRAK 86

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + MV ANLRLV+SVAKKYT R ++ LDLIQEG IGL++  EKFD   GYKFSTYA WW++
Sbjct: 87  ERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIR 146

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q ITR+IA++S TIR+P+H+ + ++K+ +  R +S ++ R PT  E+A+ + +P E V+ 
Sbjct: 147 QGITRAIAEKSRTIRLPIHITEMLNKLKKGQRELSQEMGRTPTVSELAEFVELPEEEVKD 206

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           ++   ++P+SLE  +  +        +       P +      ++     +L  L   + 
Sbjct: 207 LMCRARQPMSLEMKV-GDGDETELLELLAGEEELPSEKVEVDCMKGDLRTLLEKLPELQG 265

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RVLRMR+GI       L  + K   ++R+R R++E + +  ++  S
Sbjct: 266 RVLRMRYGIDGGEPMNLTGIAKTLGMSRDRTRRLEREGLALMRTSS 311



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 21/30 (70%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D VR YLR++G + LLS E EI + ++++ 
Sbjct: 11  DLVRSYLRDIGRVPLLSHEQEITLGRQVQE 40


>gi|148793330|gb|ABR12729.1| RNA polymerase sigma factor [Photobacterium leiognathi]
 gi|148793332|gb|ABR12730.1| RNA polymerase sigma factor [Photobacterium leiognathi subsp.
           mandapamensis]
 gi|148793334|gb|ABR12731.1| RNA polymerase sigma factor [Photobacterium leiognathi subsp.
           mandapamensis]
          Length = 284

 Score =  145 bits (365), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 128/328 (39%), Gaps = 45/328 (13%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      + +I
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRITDI 60

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           I        E+         G    + +   ++K+ +D  + + D E     S D     
Sbjct: 61  ISGFVDPNEEATAAPTATHIGSELSETDLEDEDKDLEDDDDEDADSEDEDDGSID----- 115

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              PE A      L    D  A  +                                   
Sbjct: 116 ---PELAREKFLELRNAYDKMALAIDT--------------------------------- 139

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
             + +   + ++  E+L ++     L   + D LV  L D   ++  NE  ++R+     
Sbjct: 140 --NGRQDKQTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDAMDKVRTNERLIMRMCVDNS 197

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+S
Sbjct: 198 KMPKKTFVTLFAGNEANQDWIDEALNSGKP-YAERLKTYEEDLRRSAIKLRMLEEETGLS 256

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEA 451
           I   + I   +  GE +A  AKKEMVEA
Sbjct: 257 IERIKDISRRMSIGEAKARRAKKEMVEA 284


>gi|85859725|ref|YP_461927.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
 gi|85722816|gb|ABC77759.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
          Length = 289

 Score =  145 bits (365), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 79/263 (30%), Positives = 137/263 (52%), Gaps = 10/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I  I+    ++  E       +   + +   A +++V +NLR V+ +A +Y N G++  
Sbjct: 13  YIAEINRFPILTAEEEFRYA--IEWKKNQNMEAAEKLVVSNLRFVVKIAHEYRNYGVKLA 70

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLM A +KFD   GY+  +YA+WW++  I   I      ++I      R   
Sbjct: 71  DLIQEGNIGLMHAVKKFDPYKGYRLISYAVWWIRAYIQNYIIKTWSLVKIGTTQAQRKLF 130

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
            K+ +T + +     + P   EIA+ L +    V ++ ++++   +SL+  IGD+  S  
Sbjct: 131 FKLNKTKKDIQALSLKNPEFSEIAESLGVREGEVEEMDVRMSNRDLSLDMAIGDDGGSSH 190

Query: 589 GDFI--EDKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            DF+    ++  + L    +A L R+  T  LA L  +E  ++R    +  +   TL+E+
Sbjct: 191 MDFLTYAGEDQETALIRKEEAELVRKNITGALAVLNEKEMYIIR--NRVMADDPKTLQEI 248

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G  + +TRER RQIE +A++KL+
Sbjct: 249 GDIYNITRERARQIEKQALKKLR 271


>gi|11079194|dbj|BAB17588.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score =  144 bits (364), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 120/315 (38%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G         + Q+ E  + +     V + + D +     ++++       PE 
Sbjct: 59  IDPDDDGAA-------APQEVEPETPQTTAKPVVDDKDDDDEEESDTEEEEGDGGPDPEV 111

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  ++
Sbjct: 112 ARVRFGAVAEQLEKANKAL-----------------------------------KKHGRA 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     E L  L   + L   + D LVE++ D   +I   E  +++L      + R  
Sbjct: 137 SQQATEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E +  W        + ++   +    + I + + ++  +  +  ++I++ + 
Sbjct: 197 FLRQFPSNETNLDWAEQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKD 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRRMSIGEAKARRA 270


>gi|11079161|dbj|BAB17585.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 270

 Score =  144 bits (364), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 120/315 (38%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G         + Q+ E  + +     V + + D E     ++++       PE 
Sbjct: 59  IDPDDDGAA-------APQEVEPETPQTTAKPVVDDKDDDEEEESDTEEEEGDGGPDPEV 111

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  ++
Sbjct: 112 ARVRFGAVAEQLEKANKAL-----------------------------------KKHGRA 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     E L  L   + L   + D LVE++ D   +I   E  +++L      + R  
Sbjct: 137 SQQATEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E +  W        + ++   +    + I + + ++  +  +  ++I++ + 
Sbjct: 197 FLRQFPSNETNLDWAEQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKD 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRRMSIGEAKARRA 270


>gi|302746284|gb|ADL62732.1| RpoD [Morganella morganii subsp. sibonii]
          Length = 267

 Score =  144 bits (364), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 57/307 (18%), Positives = 111/307 (36%), Gaps = 47/307 (15%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I   
Sbjct: 1   GTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLIT-- 58

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             + P +        E        +   E   +++ + + D +   +   D        P
Sbjct: 59  GFVDPNA--------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDP 110

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           E A      L    + + H +                                ++G+   
Sbjct: 111 ELARQKFEALRVQHEKARHQI-------------------------------KIHGRDHP 139

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKR 367
            ++ + + L E    +     L   + D LV  + ++  R+   E  +++L  +   + +
Sbjct: 140 STNAEIQQLSE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLCVEQSKMPK 195

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F+    G E    W + A    +  W   +    + I +    ++ I  ETG++I + 
Sbjct: 196 KNFITLFTGNETSDSWFTAAVAMNKP-WSEKLQDMAEEIERSLQRLRQIEEETGLTIKQV 254

Query: 428 RHIVSMV 434
           + I   +
Sbjct: 255 KDINRRM 261


>gi|257126034|ref|YP_003164148.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
 gi|257049973|gb|ACV39157.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
          Length = 273

 Score =  144 bits (364), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 96/260 (36%), Positives = 145/260 (55%), Gaps = 9/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E   ++  +R+       A++ ++ +NLRLVIS AKK    GL  +
Sbjct: 12  YLSDIQKFDLLSKEEEYELLRRIRED--NDEQARQLLILSNLRLVISTAKKSLGNGLPLI 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+KA  KFD+  G++FSTYA+WW+KQAI ++I +    IRIP +  +++ K
Sbjct: 70  DLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQAIKKAIINIGRDIRIPSYKYEQLSK 129

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +  +  +      P+ E IAKK+ +    +  +L   ++ +SL   IG  D  +L D 
Sbjct: 130 VNKAIKDYTAIHGEAPSTEYIAKKVDLKESKIILLLGEFQDIMSLNETIG--DNIYLEDV 187

Query: 592 IE--DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           I   D      +       +RE   R+   L  RE ++L  R+G+  N  HTL+E+G+Q 
Sbjct: 188 IGKNDDVEDKIIKEDQLLEMRELLERI---LNERERKILEYRYGLYDNKIHTLKEIGEQM 244

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +TRER+RQIE KAI KLK 
Sbjct: 245 GITRERVRQIEKKAITKLKE 264


>gi|209965020|ref|YP_002297935.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958486|gb|ACI99122.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 294

 Score =  144 bits (364), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 125/276 (45%), Gaps = 17/276 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E   + A   +V ++LRLV  +A  Y   GL
Sbjct: 17  LARYLQEIRKFPMLEAEEEYMLAK--SWREHGDTDAAHRLVTSHLRLVAKIAMGYRGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 75  PLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 134

Query: 529 IHKVVRTARRMSNKIK-------REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPI 580
             K+    R++  +++          T  +IA+ L +P   V     ++     SL  P+
Sbjct: 135 --KLFFNLRKLKGQMQAIDEGDLHPETVRKIAETLDVPESDVVNMNRRLASPDHSLNAPL 192

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
             +      D++ D++    +    +  L   +      + +L  RE  +L  R      
Sbjct: 193 RVDGEGEWQDWLVDESESQEIRLGEREELGKRKALLAEAMKTLNDRERHILVERRLRDN- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLE++ +Q+ ++RER+RQIE +A  KL+   RS
Sbjct: 252 -PTTLEDLSQQYGISRERVRQIEVRAFEKLQKAIRS 286


>gi|288962535|ref|YP_003452830.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914801|dbj|BAI76286.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 296

 Score =  144 bits (364), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 76/277 (27%), Positives = 132/277 (47%), Gaps = 13/277 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +     R  +   R  + E S A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLQEIRKFPMLEP--EREYMLAKRWQQHEDSGAAHQLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M    + + +PE+   IA KL +P + V     ++     SL  P+  
Sbjct: 134 KLFFNLRRLKGQMQAIEEGDLSPEQVQAIATKLDVPEQDVVNMNRRLASPDHSLNAPLRA 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E      DF+ D++A   +  A +  L   R+     +  L  RE  +L  R        
Sbjct: 194 ESEGEWQDFLVDESASQEIALADREELGKRRKLLVEAMTGLNERERDILTERRLREA--P 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLE++ +++ ++RER+RQIE +A  KL+   ++  L
Sbjct: 252 TTLEDLSQKYGISRERVRQIEVRAFEKLQKAIKAAAL 288


>gi|326319203|ref|YP_004236875.1| RpoD subfamily RNA polymerase sigma-70 subunit [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323376039|gb|ADX48308.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 878

 Score =  144 bits (364), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 101/242 (41%), Positives = 149/242 (61%), Gaps = 5/242 (2%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +      IA+  M  ANL+L    A+KY   G    DL QEGN+GL+KA ++++W  G++
Sbjct: 513 RAMKSFRIARDRMTAANLKLAFFHARKYLYSGETLDDLAQEGNVGLLKAVDRYNWRRGFR 572

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA WWV+Q I+R +AD++ TIR+PVH+ +K  +  R A+R      R P+ +E+A++
Sbjct: 573 FSTYATWWVRQQISRYVADKARTIRMPVHIYEKAQRAERIAQRFEMLADRAPSLDELAER 632

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP   +  +L+I  EP  ++      D     D  +      P D+     +R    R
Sbjct: 633 MEMPRHKLAALLRIAPEPSRIDESPV--DELISLDARDAYWLPDPADAVETHQVRAALDR 690

Query: 616 VLASLTPR---EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            ++SL+ R   EE VLR+R+GIG++   TL+EVG++F VTRERIRQIEAKAIRKLKH +R
Sbjct: 691 YISSLSTRDRKEEHVLRLRYGIGVHEALTLDEVGQRFGVTRERIRQIEAKAIRKLKHHAR 750

Query: 673 SK 674
           S+
Sbjct: 751 SE 752



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 71/205 (34%), Gaps = 3/205 (1%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
                + E       +++++G  V +  +  D   S +        ++    L +   + 
Sbjct: 276 EDRSANPEAEAFLTMVINDLGAEVDERFEYVDASESFEVFVAPEETTDEETALDEAFAAI 335

Query: 114 DRSTD---DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           DR+     DP+R+Y  E   + LL+ E E+ +AK +EA     + +L          +  
Sbjct: 336 DRAASPRHDPLRIYQHEFQRLRLLTAEEELQLAKEMEASLEAALDALAAWSEGLALTLAA 395

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
              +  G  +   I    A   PE         +  + ++ E+    +  D      GD 
Sbjct: 396 GAAVIAGDRVPSSIWISGADADPEPTTTESLEADAPTQEEPEEVVDYESTDQTPTDAGDA 455

Query: 231 ESAAKVSKDDRSKVDSPPENAENDE 255
             A  + +         P+ A  +E
Sbjct: 456 TFAEALQRVATLVERDAPQRASPEE 480


>gi|23429449|gb|AAM94472.1| RNA polymerase sigma factor D [Aeromonas veronii]
          Length = 281

 Score =  144 bits (364), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 122/325 (37%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P             +         E +  D  E E + E     + DD   
Sbjct: 60  II--SGFIDPNE-----ADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDEGD 112

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
               PE A      L    + +  ++                                  
Sbjct: 113 GGPDPEVAREKFGELRAQYEVTRLSI---------------------------------- 138

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 139 -QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + + +L+   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKARRAKKE 281


>gi|6682871|dbj|BAA88922.1| sigma factor [Nicotiana tabacum]
          Length = 502

 Score =  144 bits (364), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 142/253 (56%), Gaps = 8/253 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R    E S+A++++  +N+RLV+S+A++Y   G +  DLIQ G IGL++  EKFD   G
Sbjct: 249 LRSTLIECSLAREKLAMSNVRLVMSIAQRYDTNGTEMADLIQGGLIGLLRGIEKFDHSRG 308

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +K STY  WW++Q ++R++ + S T+R+P+H+ +++  +     ++  +    P+ E+IA
Sbjct: 309 FKISTYVYWWIRQGVSRALVENSRTLRLPIHLHERLSLIRNAKIKL-KENGITPSIEKIA 367

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLDSAIQA-N 608
           + L M  + VR   + + +  SL+              L  +I D    +     +    
Sbjct: 368 ECLNMSQKKVRNATEASSKVFSLDREAFPSLNGLPGETLHSYIADNRLENIPWHGVDEWM 427

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L++    ++ ++L  RE  ++R+ +G+  N   T E++ ++  ++RER+RQ+   A+ KL
Sbjct: 428 LKDEVNNLISSTLREREREIVRLYYGLD-NECLTWEDISRRIGLSRERVRQVGLVALEKL 486

Query: 668 KHPSRSKKLRSFL 680
           KH +R ++L + L
Sbjct: 487 KHAARKRRLDAML 499


>gi|320103352|ref|YP_004178943.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319750634|gb|ADV62394.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 287

 Score =  144 bits (364), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 83/260 (31%), Positives = 143/260 (55%), Gaps = 8/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    +S +E R +   V         A+  +V+ANLRLV+S+A+ Y  +GL   
Sbjct: 19  YLKQINETPLLSAAEERELGRRV---SEGDYFARDHLVKANLRLVVSIARGYNGKGLGLD 75

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI+E N+GL++A E FD+    +FSTYA +W+KQ+I R++ +    IR+P +M   + K
Sbjct: 76  DLIEERNLGLIRAVETFDYSQNIRFSTYASYWIKQSIRRAVMNNGKPIRLPAYMVTLLAK 135

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
             +   +++ ++ R PTPEE+ K+L +    +  ++    E   L+     ++ +   L 
Sbjct: 136 WRQATTKLTARLGRPPTPEEVGKELRLSPRKI-PIVSKAMEVSKLQPYSEGDEDTGVPLD 194

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN--TDHTLEEVGK 647
           D + D N  SP +     + +     +L  L  RE  V+R+RFG+  +     TL ++G+
Sbjct: 195 DVLIDGNNRSPDELMAHDDDQARMKILLDELDERESAVIRLRFGLDESVPEAMTLRQIGE 254

Query: 648 QFCVTRERIRQIEAKAIRKL 667
           +  +TRER+RQ+E  A+ KL
Sbjct: 255 RLGLTRERVRQLEQAALTKL 274


>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea]
          Length = 548

 Score =  144 bits (364), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 132/250 (52%), Gaps = 1/250 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++         + E++++   LV+ +++ Y   G+   DL+Q GNIG+++ AE+FD  
Sbjct: 299 KVLQHDLHFGWYCRDELLKSGRSLVLYLSRYYRGLGVAHEDLMQAGNIGILQGAERFDHT 358

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTY  +W+++A+++ ++     I++P  +   I++V +  + +     + P   E
Sbjct: 359 RGYQFSTYVQYWIRKAMSQLVSRHGRGIKVPTTLSTTINRVQKARKILKRSQGKHPDDVE 418

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++K   + ++ ++      +   SL+  +G        +   D     P  + ++ ++R 
Sbjct: 419 VSKSTGLSLDKIKSADNCLRIVGSLDQKVGHFINMKYLECTPDTALEMPEKTVMKQHMRN 478

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              ++L  L P+E RVL  R+G+  +   +L EVGK F V++E IR++E +A+ KL+   
Sbjct: 479 DVHKLLQELDPKERRVLIHRYGLEGHC-MSLHEVGKVFDVSKEWIRKMEKRALTKLRTEQ 537

Query: 672 RSKKLRSFLD 681
               L+ +L+
Sbjct: 538 NQTNLKHYLN 547


>gi|59859799|gb|AAX09621.1| DNA-directed RNA polymerase subunit D [Pseudomonas entomophila L48]
          Length = 269

 Score =  144 bits (363), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   +I   D +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYIISEYDRVTAEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +  +    E      +    +E E + +  A+ S D+      P   
Sbjct: 56  ------SGYIDPDDNIAAPTEEVPIPGAKAAAAKEEEDEDDENAESSDDEEEAESGP--- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQL    +  L  +                  K  ++
Sbjct: 107 ----------DPVVAAQRFGAVNDQL----VITLKVLK-----------------KHGRT 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + D LVE++     R+   E  +++L      + R  
Sbjct: 136 HAESIGAMQALADLFMPIKLVPKQFDALVERVRSALDRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRLFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKE 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|3021658|dbj|BAA25349.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079091|dbj|BAB17550.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  144 bits (363), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+            +  +       K     +E++ + E A     ++ ++    P  
Sbjct: 59  IDPDDNIA--------APTEEVPIPGAKAAAAKEESDDEEEEAENSDDEEETESGPDPVV 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +                                    LQ      +K  ++
Sbjct: 111 AAQRFGAVSD-----------------------------------QLQATFKVVKKHGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIAALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|11079103|dbj|BAB17556.1| DNA-directed RNA polymerase subunit D [Pseudomonas fulva]
          Length = 268

 Score =  144 bits (363), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 110/315 (34%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +  +    E      +    +E   D E  +    ++ ++    P  
Sbjct: 56  ------SGYIDPDDNIAAPTEEVPIPGAKTAAAKEESEDEEEESDSDDEEETESGPDPVV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +                                    LQ      +K+ + 
Sbjct: 110 AAQRFGAVSD-----------------------------------QLQATNKVLKKNGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++     R+   E  +++L      + R  
Sbjct: 135 HKESIAALQALADLFMPIKLVPKQFEVLVERVRGALSRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG+++SE + 
Sbjct: 195 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVSEIKE 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|114798150|ref|YP_762122.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
 gi|114738324|gb|ABI76449.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
          Length = 295

 Score =  144 bits (363), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 121/270 (44%), Gaps = 13/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  +K+      +  +    +    R  E E   A  E+  A +RLVIS+A K+ + GL 
Sbjct: 13  RQFVKTAMKAPLLDPAHEASLARRWR--EAEDEAALHELTTAYMRLVISMAAKFRHYGLP 70

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+ EGN+GLM+AA +F+     +FSTYA WW++ +I   +      +R       K 
Sbjct: 71  MADLVSEGNVGLMQAAARFEPEREVRFSTYASWWIRSSIQDYVLRNWSIVRTGTTSAQKS 130

Query: 530 -----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
                 ++      + +        + ++  L +P+  V     +++    SL  P+  +
Sbjct: 131 LFFNLRRLRARISDLGDGTMTRENKQWVSTHLGVPLRDVEIMSARLSGSDRSLNAPLTMD 190

Query: 584 DTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +   D I D+ A    + + S   A   E  +  + +LTPRE     +          
Sbjct: 191 GDAEWQDMIADEGAPPEEAVMRSHDTARRHEWISEAMEALTPRE--TYIITRRRLSEEPQ 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLE +G +  V++ER+RQIE +A+ KLK  
Sbjct: 249 TLEALGHELGVSKERVRQIEHQALSKLKRA 278


>gi|3021664|dbj|BAA25352.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079099|dbj|BAB17554.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  144 bits (363), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 116/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   + +E + D+ +   GD E  A+   D        PE 
Sbjct: 59  IDPDDNIAAPTEEVPIPGTKAAAAKEESDDDEEESESGDDEEEAESGPD--------PEV 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      +++                                    LQ      +K+ ++
Sbjct: 111 ARQRFGAVND-----------------------------------QLQATNKVLKKNGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIEALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKE 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|3021654|dbj|BAA25347.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079093|dbj|BAB17551.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|11079095|dbj|BAB17552.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|11079123|dbj|BAB17566.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  144 bits (362), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +  +    E      +    +E   D E  A+ S D+      P   
Sbjct: 56  ------SGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDEEEEAESSDDEEETESGP--- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQL                     Q      +K  ++
Sbjct: 107 ----------DPVVAAQRFGAVSDQL---------------------QATFKVVKKHGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIAALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|296445492|ref|ZP_06887449.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296257058|gb|EFH04128.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 294

 Score =  144 bits (362), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 70/275 (25%), Positives = 127/275 (46%), Gaps = 12/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E E   A +++V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLAEIRRFPMLEPEQEYMLAKRWR--EHEDPNAAQKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 72  PIGEIVSEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWSLVKMGTTASQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S     + TPE   EIA++L +  + V ++ +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKSKISAFEDGDLTPEHVGEIARRLGVTNQDVIEMNRRMSGDASLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D ++        Q    N  +     L  L PRE R+             
Sbjct: 192 GEGEWQDWLVDDSSDQERILVDQEEAGNRLDALRGALTVLNPRERRIFEA--RRLSEDPV 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           TLE++  +F V+RER+RQIE +A  K++   R+  
Sbjct: 250 TLEDLSTEFGVSRERVRQIEVRAFEKVQSAVRAGM 284


>gi|3021650|dbj|BAA25345.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079105|dbj|BAB17557.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  144 bits (362), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +  +    E      +    +E   D E  A+ S D+      P   
Sbjct: 56  ------SGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDEEEEAESSDDEEETESGP--- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQL                     Q      +K  ++
Sbjct: 107 ----------DPVVAAQRFGAVSDQL---------------------QATFKVVKKHGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIAALQALADLFMPIKLVPKQFEVLVERVRDSLNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|110084474|gb|ABG49394.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 285

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 131/326 (40%), Gaps = 46/326 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     
Sbjct: 3   VELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGF 60

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P                         E DDV  T   I S            D   + 
Sbjct: 61  IDPN------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDE 96

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEK 309
             + +   DE +      ++                  E + ELR+  +   ++ QK+ +
Sbjct: 97  DGDGDDADDEGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGR 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
           +  + +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + + 
Sbjct: 140 AHDETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+      E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ +
Sbjct: 200 TFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EDVLRAIGKLQQIEEETGLSIAQIK 258

Query: 429 HIVSMVRKGECEASIAKKEMVEANLR 454
            I   +  GE +A  AKKEMVEANLR
Sbjct: 259 DINRRMSIGEAKARRAKKEMVEANLR 284


>gi|11079125|dbj|BAB17567.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 268

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 112/315 (35%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T  +++     +      L E++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDSILSEYTRVTTEGGRLAEVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +          K+    +    D E+      ++       PE 
Sbjct: 56  ------SGYIDPDDGIAAPAEVPVPVIKDGAAAEPETEDEEADGDSEDEEEGDGGPDPEV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 ARVRFGAVADQLEKAKKVL-----------------------------------KKHGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +      +L  L   + L   + D LV ++ D   R+   E  +++L      + R  
Sbjct: 135 SKQGMAELAELASLFMPIKLVPKQFDALVTRVRDALDRLRAQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E+D  W        + ++   +      IL+ + ++ ++  ETG+ +SE + 
Sbjct: 195 FLRQFPSHEIDESWAEQLSK-GKSKYAEAIGRLQADILRCQQKLVALEAETGLKLSEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|23015588|ref|ZP_00055360.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 296

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 69/274 (25%), Positives = 123/274 (44%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLQDIRKFPMLPPEEEYLLAKRFR--EHGDLPAANRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A  +FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PLGELISEGNVGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + +   +M    + + + E    IA KL +  + V     +++    SL  P+  
Sbjct: 134 KLFFNLRKLKGQMQAIEEGDMSAENVAKIATKLEVTEDEVITMNRRLSSPDHSLNAPVRT 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E      D++ D +     +   +  +   R   T  LA+L  RE  +L           
Sbjct: 194 EGEGEWQDWLVDDHEDQETELGEREEMGQRRGMLTSALAALNDRERAILIQ--RRLTEDP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++ +++ ++RER+RQIE +A  KL+   ++
Sbjct: 252 ATLEDLSQRYGISRERVRQIEVRAFEKLQKSVKT 285


>gi|315498780|ref|YP_004087584.1| RNA polymerase, sigma 32 subunit, rpoh [Asticcacaulis excentricus
           CB 48]
 gi|315416792|gb|ADU13433.1| RNA polymerase, sigma 32 subunit, RpoH [Asticcacaulis excentricus
           CB 48]
          Length = 344

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 74/274 (27%), Positives = 118/274 (43%), Gaps = 15/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 69  LNRYLSEIRKFPMLAKDEEFMLAK--RWAEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 126

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW+K AI   +      +++      K
Sbjct: 127 PIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIKAAIQEYVLRSWSLVKMGTTAAQK 186

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                  KV      +     R     +IA KL +  + V     +++    SL  P+  
Sbjct: 187 KLFFNLRKVKSEISALEEGDMRHEQVAQIATKLGVSEDDVISMNRRMSSPDSSLNAPLRV 246

Query: 583 -EDTSHLGDFIEDKNAVSPLDSAIQAN---LRE-TTTRVLASLTPREERVLRMRFGIGMN 637
            E  S   D++ D +  S       +    LR       +  L  RE  +L  R      
Sbjct: 247 SEGDSEWQDWLADDSTPSQETVLADSEEYKLRMSLLEEAMGELNERERAILTARRLQEN- 305

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              TLE++  +F V+RER+RQIE +A  KL+   
Sbjct: 306 -PTTLEDLADRFGVSRERVRQIEVRAFEKLQKAM 338


>gi|167515038|gb|ABZ81803.1| RpoD [Aeromonas aquariorum]
          Length = 285

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 127/322 (39%), Gaps = 46/322 (14%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II   
Sbjct: 8   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--S 65

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P                         E DDV  T   I S            D   
Sbjct: 66  GFIDPN------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDE 101

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKD 307
           +   + + + D+ +      ++                  E + ELR+  +   ++ Q++
Sbjct: 102 DEDGDGDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQN 144

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + 
Sbjct: 145 GRAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMP 204

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++
Sbjct: 205 KKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQ 263

Query: 427 FRHIVSMVRKGECEASIAKKEM 448
            + I   +  GE +A  AKKEM
Sbjct: 264 IKDINRRMSIGEAKARRAKKEM 285


>gi|167770711|ref|ZP_02442764.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
 gi|167667306|gb|EDS11436.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
          Length = 263

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 79/257 (30%), Positives = 138/257 (53%), Gaps = 14/257 (5%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   + T  +++ + +  + +++K       A++EM+  NLRLV+SV +K+TNRG  
Sbjct: 11  NKVEICGINTSKLTVLKEKEKIELLKKIRQGDQKARQEMINGNLRLVLSVVQKFTNRGEN 70

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +RD  
Sbjct: 71  LDDLFQVGCIGLIKAIDNFDPNQNVRFSTYGVPMIIGEIRRHLRDNNS-VRVSRSLRDLA 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++    + N+  +EPT EEIAK++    E V   L+   EP+SL  P+  +  DT +
Sbjct: 130 YKAMQAKEALINRNSKEPTVEEIAKEMGAKKEDVVLALEAIVEPMSLYDPVYSDGGDTIY 189

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I DKN+ S     I           + +L  RE+++L +RF  G     T  EV K
Sbjct: 190 VMDQIGDKNSESDWMDEI------VFREAMKNLGDREKQILSLRFFGG----KTQMEVAK 239

Query: 648 QFCVTRERIRQIEAKAI 664
           +  +++ ++ ++E  A+
Sbjct: 240 EIGISQAQVSRLEKGAL 256


>gi|218961053|ref|YP_001740828.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
 gi|167729710|emb|CAO80622.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
          Length = 292

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 138/264 (52%), Gaps = 6/264 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             ++N +  IS    +S  E   +    +        A  ++++ANL+ V+ +A +Y NR
Sbjct: 11  KALQNYLNEISKFKTLSREEEHDLAIKAK---NGDMDAMNKLIQANLKFVVKIASRYQNR 67

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   +LI EGNIGL+KA EKFD     K  +YA+WW+KQ I  +++++S  IR+P+   
Sbjct: 68  GLSLSELISEGNIGLIKAIEKFDPDKDIKLISYAIWWIKQRIMLAVSEKSSLIRVPMGKS 127

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-- 584
              H+V  T  R   +  +  TP+E+++K+ +  + + ++     E  S +  I   D  
Sbjct: 128 SAAHRVKLTQDRYFTETGKIATPDELSEKMNIAEKTIEQLQNKLPETSSFDDIITTSDSQ 187

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM-NTDHTLE 643
                D +EDK+ + P     Q  ++E     ++ L  RE  ++R  FG+   +      
Sbjct: 188 DFTAKDLLEDKDTLDPQSLYYQERMQEKIQNAISKLDAREAEIIRNYFGLNESHESRNFA 247

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           ++ ++  ++RER+RQI+ +A++K+
Sbjct: 248 QIAEKLGLSRERVRQIQKEALKKI 271


>gi|3021656|dbj|BAA25348.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079097|dbj|BAB17553.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|11079101|dbj|BAB17555.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|11079111|dbj|BAB17560.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 117/315 (37%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   + +E + D+ +   GD E  A+   D           
Sbjct: 59  IDPDDNIAAPTEEVPIPGAKAAAAKEESDDDEEESESGDDEEEAESGPDPVV-------- 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ                     LQ  +   +K+ ++
Sbjct: 111 --------------AAQRFGAVSDQ---------------------LQATSKVLKKNGRN 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIEALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKNAAIVACQQKLIDLETETGLTVAEIKE 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|197103875|ref|YP_002129252.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
 gi|196477295|gb|ACG76823.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
          Length = 295

 Score =  144 bits (362), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 123/275 (44%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLTEIRKFPMLAKDEEFMLAK--RWQEHQDPEAAHRLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRM----SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +    +       ++ E   +   K   +  E +    ++     SL +P+  
Sbjct: 133 KLFFNLRKAKSEISALEEGDLRPEQVRQIATKLGVLDEEVISMNRRLAGGDASLNSPLRA 192

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  S   D++ D++  S      +A  R    E     +A LT RE  +L        + 
Sbjct: 193 DSESEWQDWLVDEDTPSQESVVAEAEERGIRMELLQEAMAELTDRERHILTE--RRLKDE 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+  Q+ V+RER+RQIE +A  KL+   R+
Sbjct: 251 PTTLEELASQYGVSRERVRQIEVRAFEKLQKSMRA 285


>gi|330961077|gb|EGH61337.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 167

 Score =  143 bits (361), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 109/166 (65%), Positives = 135/166 (81%)

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ MP + +RKVLKI KEPIS
Sbjct: 1   ARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPIS 60

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRMRFGI 
Sbjct: 61  METPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGID 120

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HP+RS+ LRSFLD
Sbjct: 121 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 166


>gi|23978307|dbj|BAC21130.1| principal sigma factor [Calothrix brevissima]
          Length = 188

 Score =  143 bits (361), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 101/189 (53%), Positives = 136/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+ V
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLSV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+G     TLE
Sbjct: 121 EDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLGDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|148793328|gb|ABR12728.1| RNA polymerase sigma factor [Photobacterium leiognathi]
          Length = 283

 Score =  143 bits (361), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 127/327 (38%), Gaps = 45/327 (13%)

Query: 126 REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      + +II
Sbjct: 1   REMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRITDII 60

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
                   E+         G    + +   ++K+ +D  + + D E     S D      
Sbjct: 61  SGFVDPNEEATAAPTATHIGSELSETDLEDEDKDLEDDDDEDADSEDEDDGSID------ 114

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
             PE A      L    D  A  +                                    
Sbjct: 115 --PELAREKFLELRNAYDKMALAIDT---------------------------------- 138

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
            + +   + ++  E+L ++     L   + D LV  L D   ++  NE  ++R+      
Sbjct: 139 -NGRQDKQTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDAMDKVRTNERLIMRMCVDNSK 197

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + +  F+    G E +  W+  A +  +  +   +    + + +   +++ +  ETG+SI
Sbjct: 198 MPKKTFVTLFAGNEANQDWIDEALNSGKP-YAERLKTYEEDLRRSAIKLRMLEEETGLSI 256

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEA 451
              + I   +  GE +A  AKKEMVEA
Sbjct: 257 ERIKDISRRMSIGEAKARRAKKEMVEA 283


>gi|85706634|ref|ZP_01037726.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
 gi|85668692|gb|EAQ23561.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
          Length = 830

 Score =  143 bits (361), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 107/470 (22%), Positives = 183/470 (38%), Gaps = 42/470 (8%)

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
           +    + +  + + D      +   N E    +L +  +  A    A+ D     +  A+
Sbjct: 285 DDIDRLVAHCEGNGDLEELRSNLQRNMEAAGFDLAKATEHDADIWDAVSDTSSDDLADAI 344

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           +        L   Q   ++         +   L E +++    L L     +  VE + D
Sbjct: 345 EAALTRRTRLPGTQRFVMDKS-------EELQLLEPMMRAKQELQLGILASETAVETILD 397

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR-ELDPHWVSYAKDFPEGEWKNFVACEV 403
           +  R+     +   ++    I          G  E        A       W        
Sbjct: 398 VMNRLRDGSRDPGSVSLRTIIP------SRPGHAETSEV---MAAADALRSWNTTGRVMD 448

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI----------AKKEMVEANL 453
               +           +     E    +      + EAS           A + ++  +L
Sbjct: 449 GKRRREALAALEALELSLAFHKELVRRLEQFPACQAEASQLEAEILISESATEHLIREHL 508

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
             V   A +    G +  D+ Q   +GL ++  +FD   GY+F  YA +W++QAI R  A
Sbjct: 509 PYVRRFASRNVEEGEEPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATYWMRQAIMRWRA 568

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI---T 570
           D+   IRIPVH  +K+ K+ R   R+  ++    +  ++A++L   ++ VR+   I    
Sbjct: 569 DEGAAIRIPVHRNEKVTKLDRALDRLDVRVGGAVSDLDLAEELEWAIDEVRQFRCIPRKA 628

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           + P SL+            D ++            QA      T  LA L  R+  V+RM
Sbjct: 629 EYPASLDDWDNLLPEPSEVDVLD------------QAETERIVTEALADLPERQADVIRM 676

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           RFGIG +++ TLEE+G+ + VTRERIRQIEAK +  L HP R ++L+  L
Sbjct: 677 RFGIGHDSEMTLEEIGQIYGVTRERIRQIEAKGLDLLSHPGRKRRLQELL 726


>gi|3021652|dbj|BAA25346.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079089|dbj|BAB17549.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  143 bits (361), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                             +E        A    D+    D     
Sbjct: 59  IDPDDSIAAP----------------------TEEVPVPGAKTAAAKDDEDEDEDGEESG 96

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            + +E     D   +A    A+ DQ                     LQ      +K+ +S
Sbjct: 97  DDEEEGESGPDPWVAAQRFGAVNDQ---------------------LQATNKVLKKNGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIDALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKE 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|327438872|dbj|BAK15237.1| DNA-directed RNA polymerase [Solibacillus silvestris StLB046]
          Length = 425

 Score =  143 bits (360), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 102/260 (39%), Positives = 154/260 (59%), Gaps = 10/260 (3%)

Query: 431 VSMVRKGECEASIAKKE----MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMK 483
           +  +++   E    + +    +VEAN +LV  + K Y+     G    D+ Q G IGL+K
Sbjct: 163 IEYLKQIHSEDEFKRNKSLSNLVEANRKLVWKIVKHYSGLATVGFDENDMYQVGFIGLLK 222

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AAEKFD  LGY+FSTYA WW++QAITR IAD S  IRIPVH R+K++K ++    + N++
Sbjct: 223 AAEKFDVSLGYQFSTYATWWIRQAITRGIADYSTLIRIPVHYREKMNKFIKIENELWNEL 282

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            R  T  EI+K++  P   + ++     +    SL+  +GD++ + LG+ + D N   P 
Sbjct: 283 ARPATTFEISKEMEEPTNVIEELRFYISQSNLDSLDRLVGDDENTSLGELVLDDNLKMPD 342

Query: 602 DSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +   +  LR T   +  ++LT RE +VL  RFG   +   TLEEVG+ + +TRERIRQIE
Sbjct: 343 EEYYKIELRNTIGEIFQSNLTEREMQVLYYRFGFKNDETKTLEEVGQIYNLTRERIRQIE 402

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
           AKA+RKL+    +  L+ +L
Sbjct: 403 AKALRKLRKQKTTTVLKEYL 422


>gi|317121713|ref|YP_004101716.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591693|gb|ADU50989.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score =  143 bits (360), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 138/266 (51%), Gaps = 11/266 (4%)

Query: 408 KIRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           ++ N+++   V T  + +     +  + R+       A++++V+ NLRLV+SV +++ +R
Sbjct: 5   RMINKVEICGVNTAELPVLTNEQMRVLFRRMRQGDEEARQQLVQGNLRLVLSVIQRFNHR 64

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +R
Sbjct: 65  GEPVDDLFQVGCIGLMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLR 123

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D  +K ++   +++++  REPT EEIA++L +P E V   L   ++P+SL  PI  +   
Sbjct: 124 DVAYKALQVRDQLTHRHGREPTLEEIARELGLPREEVVHALDAIQDPVSLFEPIYQDG-- 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             GD I   + VS      +  L        +A L  RE+ ++  RF  G     T  EV
Sbjct: 182 --GDPIYVVDQVSDDKQRDEQWLETIAVREAMARLDEREQLIITKRFYQG----KTQMEV 235

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPS 671
             +  +++ ++ ++E  A+++++   
Sbjct: 236 ANEIGISQAQVSRLEKAALQRMRKYM 261


>gi|302746278|gb|ADL62729.1| RpoD [Morganella morganii subsp. morganii]
          Length = 267

 Score =  143 bits (360), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 56/306 (18%), Positives = 109/306 (35%), Gaps = 47/306 (15%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I    
Sbjct: 2   TVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLIT--G 59

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            + P +        E        +   E   +++ + + D +   +   D        PE
Sbjct: 60  FVDPNA--------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDPE 111

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A      L    + +                                Q   ++G+    
Sbjct: 112 LARQKFEALRVQHEKAR-------------------------------QQIKIHGRDHPN 140

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
           ++ + + L E    +     L   + D LV  + ++  R+   E  +++L  +   + + 
Sbjct: 141 TNAEIQQLSE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLCVEQSKMPKK 196

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W + A    +  W   +    + + +    ++ I  ETG++I E +
Sbjct: 197 NFITLFTGNETSDSWFTAAVAMNKP-WSEKLQDVAEEVERSLQRLRQIEEETGLTIKEVK 255

Query: 429 HIVSMV 434
            I   +
Sbjct: 256 DINRRM 261


>gi|215270839|emb|CAR48097.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score =  143 bits (360), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 119/322 (36%), Gaps = 43/322 (13%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I  
Sbjct: 1   MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISG 60

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 +          G    + +   +++E  D  E   D    ++       ++   
Sbjct: 61  FVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL--- 117

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
                                            +   +++   Y+ L+      +   + 
Sbjct: 118 --------------------------------ALEKFNQLRSTYQNLQ------LAINEH 139

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
              S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + 
Sbjct: 140 GYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMP 199

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W+       +  +   +    + I +   ++K I  ET +++  
Sbjct: 200 KKSFIALFTGNESSEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQS 258

Query: 427 FRHIVSMVRKGECEASIAKKEM 448
            + I   +  GE +A  AKKEM
Sbjct: 259 IKDISRRMSIGEAKARRAKKEM 280


>gi|20808499|ref|NP_623670.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
 gi|20517120|gb|AAM25274.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 265

 Score =  143 bits (360), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 81/259 (31%), Positives = 139/259 (53%), Gaps = 5/259 (1%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMK 483
            E      +  +       A+ E+VE N+ LV+S+A  ++   G++  DLIQEG IGL+ 
Sbjct: 7   KEKTDEFELFERLRNGDKKARDEIVEKNIGLVVSIAANFSKAYGVELDDLIQEGFIGLLA 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A E FD   GY+FSTYA++++KQ I R I  +S TI +PV    K+++V+    ++    
Sbjct: 67  AIEGFDHTKGYRFSTYAVFYIKQKIQRYIWGRSRTIHLPVKTYQKLNQVLSAQLKLEQVK 126

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS-PLD 602
             E  PEEIA++  +  E V  +L +    +SL   + + D + L D I D+ + +    
Sbjct: 127 G-EAFPEEIAEETGIKTEEVVNLLSLKNPTVSLNQQLYENDNTELIDVILDEQSENEIDR 185

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +     LR+     L  L  +E  VL MR+G+   T  TL+++ +   ++++R  QIE +
Sbjct: 186 NYSLEELRKILKECLEVLPEKERSVLEMRYGLN-GTPMTLKQIAEILNISKQRAGQIEKR 244

Query: 663 AIRKLKHPSRSKK-LRSFL 680
           A+++L++  + +  L  FL
Sbjct: 245 ALQRLRNSRKIRNALLDFL 263


>gi|23978347|dbj|BAC21141.1| principal sigma factor [Oscillatoria sp. PCC 7112]
          Length = 188

 Score =  143 bits (360), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 100/189 (52%), Positives = 135/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-SDGETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|13377878|gb|AAK20883.1|AF334761_4 RNA polymerase sigma-32 [Aeromonas hydrophila]
          Length = 284

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 132/271 (48%), Gaps = 9/271 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    ++  E R +   +++G      A +++V ++LR V+ VAK Y   GL
Sbjct: 17  LEGYIQAVNSIPVLTADEERELAERLQQGG--DLEAARQLVMSHLRFVVHVAKSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DL+QEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++     + 
Sbjct: 75  PQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKADIHEYVLRNWRMVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   +R +++       +      A+    P +      +++    + +    DED   
Sbjct: 135 KLFFNLRKSKKRLGWFSHDEVQAVAAELGVSPTDVTEMEARMSNYDQAFDLVGDDEDEGG 194

Query: 588 LGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++EDK+   A +  +     +     +  LA+L  R + ++R R+ +  ++  TL
Sbjct: 195 FAPVHYLEDKSSDLAATIENDNWDDHATRRLSSALATLDERSQHIIRARW-LDDDSKTTL 253

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +E+   + V+ ER+RQ+E  A++KLK    +
Sbjct: 254 QELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|329939708|ref|ZP_08289009.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329301278|gb|EGG45173.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 387

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + S+       A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 147 FVELRSLAAGSPEYAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 205

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R 
Sbjct: 206 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRS 265

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 266 PTVHELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY 325

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 326 -----RESLKPLLEDLPPREKRILLLRFFANMTQSQIAQEV----GISQMHVSRLLARTL 376

Query: 665 RKLKH 669
            +L+ 
Sbjct: 377 AQLRE 381


>gi|215270843|emb|CAR48099.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270853|emb|CAR48104.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 119/322 (36%), Gaps = 43/322 (13%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IA+RIE G   + +S+ E P T   ++   D++      L ++I  
Sbjct: 1   MGTVELLTREGEIDIAQRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISG 60

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 +          G    + +   +++E  D  E   D    ++       ++   
Sbjct: 61  FVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL--- 117

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
                                            +   +++   Y+ L+      +   + 
Sbjct: 118 --------------------------------ALEKFNQLRSTYQNLQ------LAINEH 139

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
              S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + 
Sbjct: 140 GYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMP 199

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W+       +  +   +    + I +   ++K I  ET +++  
Sbjct: 200 KKSFIALFTGNESSEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQN 258

Query: 427 FRHIVSMVRKGECEASIAKKEM 448
            + I   +  GE +A  AKKEM
Sbjct: 259 IKDISRRMSIGEAKARRAKKEM 280


>gi|215270841|emb|CAR48098.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270847|emb|CAR48101.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 119/322 (36%), Gaps = 43/322 (13%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IA+RIE G   + +S+ E P T   ++   D++      L ++I  
Sbjct: 1   MGTVELLTREGEIDIAQRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISG 60

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 +          G    + +   +++E  D  E   D    ++       ++   
Sbjct: 61  FVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDDDEESDDDSDESEEDVGIDPEL--- 117

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
                                            +   +++   Y+ L+      +   + 
Sbjct: 118 --------------------------------ALEKFNQLRSTYQNLQ------LAINEH 139

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
              S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + 
Sbjct: 140 GYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMP 199

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W+       +  +   +    + I +   ++K I  ET +++  
Sbjct: 200 KKSFIALFTGNESSEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQN 258

Query: 427 FRHIVSMVRKGECEASIAKKEM 448
            + I   +  GE +A  AKKEM
Sbjct: 259 IKDISRRMSIGEAKARRAKKEM 280


>gi|3021674|dbj|BAA25357.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079113|dbj|BAB17561.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|11079121|dbj|BAB17565.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 117/315 (37%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   + +E + D+ +   GD E  A+   D           
Sbjct: 59  IDPDDNIAAPTEEVPIPGAKAAAAKEESDDDEEESESGDDEEEAESGPDPVV-------- 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ                     LQ  +   +K+ +S
Sbjct: 111 --------------AAQRFGAVSDQ---------------------LQVTSKVLKKNGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIEALQALADLFMPIKLVPKQFEVLVERVRDALSRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKNAAIVACQQKLIDLETETGLTVAEIKE 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|106895878|gb|ABF82642.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 278

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 121/321 (37%), Gaps = 44/321 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + +     S DD +     PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDDEADTGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L    + +  ++                                   Q + ++    
Sbjct: 114 FGELRAQYEVTRLSI-----------------------------------QNNGRAHDDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E D  W  Y K   +      V  + D +L+   +++ I VETG+SI++ + I   
Sbjct: 199 FTNNECDTAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEVETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEMVEANLR 454
           +  GE +A  AKKEMVEANLR
Sbjct: 258 MSIGEAKARRAKKEMVEANLR 278


>gi|125553511|gb|EAY99220.1| hypothetical protein OsI_21178 [Oryza sativa Indica Group]
          Length = 500

 Score =  143 bits (360), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 132/251 (52%), Gaps = 5/251 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +R+       A+ ++++ NLRLV+    KY    +   +F D+ Q G  GL+ A ++F+
Sbjct: 252 QMRRHLEVGRAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDRFE 311

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++ STYA++W++ +I R+I   S   R P  M  +  ++ R    ++ ++ R PT 
Sbjct: 312 PKRGFRISTYALFWIRHSIVRAITL-SNFTRFPFAMESERQEIHRAREELAFELGRAPTE 370

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+ KK+ +     R V+++T+   SL           L + + D +A+    S+    L
Sbjct: 371 EEVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQE-ELINEVTDDDAIGVDTSSHNTLL 429

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R     +L SL P+E  V+R RFG+      TL E+     ++RE +R+ E KA+ KLKH
Sbjct: 430 RLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYELKALMKLKH 489

Query: 670 PSRSKKLRSFL 680
           P+R + LR ++
Sbjct: 490 PTRVEYLRRYM 500


>gi|215270851|emb|CAR48103.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 119/322 (36%), Gaps = 43/322 (13%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I  
Sbjct: 1   MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISG 60

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 +          G    + +   +++E  D  E   D    ++       ++   
Sbjct: 61  FVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL--- 117

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
                                            +   +++   Y+ L+      +   + 
Sbjct: 118 --------------------------------ALEKFNQLRSTYQNLQ------LAINEH 139

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
              S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + 
Sbjct: 140 GYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMP 199

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W+       +  +   +    + I +   ++K I  ET +++  
Sbjct: 200 KKSFIALFTGNESSEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQN 258

Query: 427 FRHIVSMVRKGECEASIAKKEM 448
            + I   +  GE +A  AKKEM
Sbjct: 259 IKDISRRMSIGEAKARRAKKEM 280


>gi|215270845|emb|CAR48100.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270849|emb|CAR48102.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 280

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 119/322 (36%), Gaps = 43/322 (13%)

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           MG++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I  
Sbjct: 1   MGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISG 60

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
                 +          G    + +   +++E  D  E   D    ++       ++   
Sbjct: 61  FVDPDADDTAAPTATHIGSELTESQLEEEDEEDVDDDEESDDDSDESEEDVGIDPEL--- 117

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
                                            +   +++   Y+ L+      +   + 
Sbjct: 118 --------------------------------ALEKFNQLRSTYQNLQ------LAINEH 139

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IK 366
              S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + 
Sbjct: 140 GYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMP 199

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+    G E    W+       +  +   +    + I +   ++K I  ET +++  
Sbjct: 200 KKSFIALFTGNESSEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQN 258

Query: 427 FRHIVSMVRKGECEASIAKKEM 448
            + I   +  GE +A  AKKEM
Sbjct: 259 IKDISRRMSIGEAKARRAKKEM 280


>gi|108762657|ref|YP_634340.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
 gi|585929|sp|Q07083|RPSC_MYXXA RecName: Full=RNA polymerase sigma-C factor
 gi|293866|gb|AAA25408.1| sigma factor [Myxococcus xanthus]
 gi|108466537|gb|ABF91722.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
          Length = 295

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 84/266 (31%), Positives = 135/266 (50%), Gaps = 14/266 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    ++  + + +    R        A  ++V ANLR V+ VA +Y + GL+  
Sbjct: 16  YLSEINQYPLLTQPQEQELSKRFR---AGDLAAGHQLVTANLRFVVKVAYEYRSYGLKMS 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQE NIGLMKA +KFD   G +  +YA+WW++  I   I      +++      R   
Sbjct: 73  DLIQEANIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNCILKNWSLVKLGTTQAQRRLF 132

Query: 530 HKVVRTARRMSNKIKRE---PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT 585
             + RT R +      +      EEIA+KL +    VR++  ++    +SL+ P+G++  
Sbjct: 133 FSLARTRRELEKMGAGDANVVNAEEIARKLNVKASEVREMEQRMGGRDLSLDAPMGEDGD 192

Query: 586 SHLGDFIEDK--NAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +   DF+E +  +AV  +    QANL RE   R L  L PRE  ++     +  + + TL
Sbjct: 193 ATHLDFVESESVSAVDEVADRQQANLTRELVQRALRRLDPRERFIIEQ--RVMGDAEMTL 250

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+G+ F  +RER RQ+E +A  KLK
Sbjct: 251 SELGEHFGFSRERARQLEIRAKDKLK 276


>gi|3021670|dbj|BAA25355.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079115|dbj|BAB17562.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILSEYDRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+            +  +       K     +E++ + E +     ++ ++    P  
Sbjct: 59  IDPDDNIA--------APTEEVPIPGAKAAAAKEESDDEEEESEGSDDEEETESGPDPVV 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +                                    LQ      +K+ ++
Sbjct: 111 AAQRFGAVSD-----------------------------------QLQATVKVVKKNGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D   R+   E  +++L      + R  
Sbjct: 136 HKESIEALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|11079031|dbj|BAB17520.1| DNA-directed RNA polymerase subunit D [Pseudomonas synxantha]
          Length = 269

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                      + +     +   D E+ A   ++D  +    P  
Sbjct: 59  IDPDDGI--------APPAAEVPPPVDPKAPKADDDTDDDEAEASSDEEDEVESGPDPVV 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRG 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|115465727|ref|NP_001056463.1| Os05g0586600 [Oryza sativa Japonica Group]
 gi|30698488|dbj|BAC76601.1| Sig5 [Oryza sativa Japonica Group]
 gi|30698518|dbj|BAC76607.1| plastid sigma factor SIG5 [Oryza sativa Japonica Group]
 gi|113580014|dbj|BAF18377.1| Os05g0586600 [Oryza sativa Japonica Group]
          Length = 500

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 132/251 (52%), Gaps = 5/251 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +R+       A+ ++++ NLRLV+    KY    +   +F D+ Q G  GL+ A ++F+
Sbjct: 252 QMRRHLEVGRAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDRFE 311

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++ STYA++W++ +I R+I   S   R P  M  +  ++ R    ++ ++ R PT 
Sbjct: 312 PKRGFRISTYALFWIRHSIVRAITL-SNFTRFPFAMESERQEIHRAREELAFELGRAPTE 370

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+ KK+ +     R V+++T+   SL           L + + D +A+    S+    L
Sbjct: 371 EEVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQE-ELINEVTDDDAIGVDTSSHNTLL 429

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R     +L SL P+E  V+R RFG+      TL E+     ++RE +R+ E KA+ KLKH
Sbjct: 430 RLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYELKALMKLKH 489

Query: 670 PSRSKKLRSFL 680
           P+R + LR ++
Sbjct: 490 PTRVEYLRRYM 500


>gi|23978358|dbj|BAC21144.1| principal sigma factor [Nodularia sp. PCC 73104]
          Length = 188

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 100/189 (52%), Positives = 136/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GY+FSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYRFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|23978298|dbj|BAC21128.1| principal sigma factor [Anabaena variabilis]
 gi|23978312|dbj|BAC21131.1| principal sigma factor [Nostoc linckia]
 gi|23978323|dbj|BAC21134.1| principal sigma factor [Anabaena variabilis]
 gi|23978327|dbj|BAC21135.1| principal sigma factor [Anabaenopsis circularis]
 gi|23978343|dbj|BAC21140.1| principal sigma factor [Chlorogloeopsis sp. PCC 6718]
 gi|23978354|dbj|BAC21143.1| principal sigma factor [Fischerella muscicola]
 gi|23978367|dbj|BAC21148.1| principal sigma factor [Chroococcidiopsis sp. PCC 7431]
 gi|26665388|dbj|BAC44905.1| principal sigma factor [Tolypothrix sp. IAM M-259]
 gi|26665392|dbj|BAC44907.1| principal sigma factor [Fischerella sp. IAM M-263]
 gi|26665394|dbj|BAC44908.1| principal sigma factor [Hapalosiphon sp. IAM M-264]
 gi|26665396|dbj|BAC44909.1| principal sigms factor [Hapalosiphon delicatulus IAM M-266]
 gi|26665398|dbj|BAC44910.1| principal sigma factor [Nostoc entophytum IAM M-267]
          Length = 188

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 101/189 (53%), Positives = 136/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|218197356|gb|EEC79783.1| hypothetical protein OsI_21197 [Oryza sativa Indica Group]
          Length = 557

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 140/281 (49%), Gaps = 5/281 (1%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    +++LK  +E+   S      I E     +++R    E    ++ ++     LV  
Sbjct: 279 LEKIRENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKY 333

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  
Sbjct: 334 IAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGV 393

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T
Sbjct: 394 IQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYT 453

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            IG    +   +   D +  +P ++  +  LRE    VL  L PRE  VL++R G+    
Sbjct: 454 EIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGK 513

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             +LE++G  + V++E IR+IE  A+ KL++     +L+ F
Sbjct: 514 CRSLEQIGSIYHVSKEWIRKIEKSAMSKLRNDDVHNELKDF 554


>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [Arabidopsis thaliana]
          Length = 502

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 143/255 (56%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYNNLGAEMSDLVQGGLIGLLRGIEKFDSS 306

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 307 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 365

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D     +P      
Sbjct: 366 IAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDD 425

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L+E  ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ 
Sbjct: 426 LALKEEVSKLISATLGEREKEIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 484

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 485 KLKHAARKRKMEAMI 499


>gi|269961508|ref|ZP_06175871.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
 gi|269833737|gb|EEZ87833.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
          Length = 285

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 131/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTPEEERGLAERLHYNGEID--AAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        S      D+D S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPMDDDDS 191

Query: 587 -----HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++EDK+   A +   +  + +        LASL  R +R++R R+      
Sbjct: 192 ANSYTAPMVYLEDKSSDVADNIEAANWETHTNNRLGHALASLDERSQRIVRSRWLDD--E 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 250 KATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|322384112|ref|ZP_08057830.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151192|gb|EFX44501.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 272

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 82/276 (29%), Positives = 143/276 (51%), Gaps = 18/276 (6%)

Query: 404 DSILKIRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           + I   RN+++   V+T     ++ +E R + ++++     A  A++++V  NLRLV+SV
Sbjct: 9   EVITVTRNKVEICGVDTAKLPVLTNTEMRELFALLQTKNERA--AREKLVNGNLRLVLSV 66

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            +++ NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  I
Sbjct: 67  IQRFNNRGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PI 125

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+   +RD  +K ++   +++N+  REPT  EI++ L +P E V   L   ++P+SL  P
Sbjct: 126 RVSRSLRDIAYKALQVRDQLTNRNSREPTIYEISEVLNVPKEDVVFALDAIQDPVSLFEP 185

Query: 580 IGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           I  +  D  ++ D I D+           A         +  L  RE+ +L MRF  G  
Sbjct: 186 IYHDGGDPIYVMDQISDERNKDLFWIEGIA-----LREAMRKLGSREKMILSMRFFEG-- 238

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              T  EV  +  +++ ++ ++E  AI +++   ++
Sbjct: 239 --KTQMEVADEIGISQAQVSRLEKSAINQMQKHVKT 272


>gi|86742435|ref|YP_482835.1| sigma 28 subunit [Frankia sp. CcI3]
 gi|86569297|gb|ABD13106.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Frankia sp. CcI3]
          Length = 338

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 119/246 (48%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +       +++ + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 97  FVRLAELPEDDPERSAV-RDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 155

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 156 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQTLGRS 215

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  EIA+ L M  + V + L+       +SL+ P   +D +  + D +  ++      S
Sbjct: 216 PTVSEIARHLQMSEDDVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDE-----S 270

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L  RE+R+L +RF        T  ++  +  +++  + ++ A+ 
Sbjct: 271 LEGVEYRESLKPLLEKLPAREKRILLLRFFGN----MTQSQIATELGISQMHVSRLLART 326

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 327 LAQLRR 332


>gi|26665390|dbj|BAC44906.1| principal sigma factor [Scytonema sp. IAM M-262]
          Length = 188

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 101/189 (53%), Positives = 137/189 (72%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  ++ +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-SDSETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|254514436|ref|ZP_05126497.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
 gi|219676679|gb|EED33044.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
          Length = 432

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 79/282 (28%), Positives = 135/282 (47%), Gaps = 3/282 (1%)

Query: 404 DSILKIRNEIKSISVETGISISEFR--HIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           DS+     +  +    T     E     +   +       S A+  +   NLRLV S+A 
Sbjct: 149 DSVADALQQWSTFWSHTEKRPKEALNPEVRDALVSHLERYSDARDTLTMHNLRLVYSIAG 208

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y  +G+ +LDLIQEG +GL++AAEK+D   G++FSTY   W+ QAI R + D    IR 
Sbjct: 209 RYRGKGVNYLDLIQEGTLGLIRAAEKYDHNKGFRFSTYCFNWITQAIRRHVGDTGGLIRY 268

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
           P H++++++K+ R       +   EP    +A+   + +E  R++L++    ISL+ P  
Sbjct: 269 PTHVQEQVNKLYRLRITEKQRTGEEPGDAALAEAAGLSLEKTRELLQLRNLGISLDAPQY 328

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D+D   L D +      +    A   +L +     +  L   E  V+  R+G+      +
Sbjct: 329 DDDDGTLLDTMSGGPFEACEAEAETESLHDRLLVEMQGLDQAEREVVIARWGLHDGPPLS 388

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK-KLRSFLDG 682
             E+  +  V+RE +RQ+E  A+ KL    R +     ++D 
Sbjct: 389 RAEIADRMSVSREWVRQLERAALTKLSGNERIRAAFADYIDA 430


>gi|239934516|emb|CAR94572.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 266

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 123/326 (37%), Gaps = 62/326 (19%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   +  +L   P T+ AL+   + ++ G   L++II    
Sbjct: 1   TVELLTREGEIRIAKRIEDGLNQVRGALGVFPGTYGALLGIYEPVSRGEGRLQDIIT--G 58

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I P            +S    +D   E                          VD+ P+
Sbjct: 59  FIDPNMPDEIAQPNAKNSDDDDDDDDDEP-------------------------VDTGPD 93

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             E                           V+     I ++Y  ++       + +K   
Sbjct: 94  PQE---------------------------VIDRFTSIGKLYAAIQQ------SIEKHGS 120

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRD 368
              K   L+++L      L L     DLLVE L     +I   E ++++      G+ R 
Sbjct: 121 QDEKTTKLRKQLSSEFMELKLAPKMFDLLVETLRGNIGKIRALERQVMQFCIRQAGMPRK 180

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+      E +  W++             ++   D I   + ++  I   T +SISE +
Sbjct: 181 EFISSFPENETNLDWINKHIRAKRKHSSQ-LSKLRDDITCAQRKLIEIEHSTSLSISEIK 239

Query: 429 HIVSMVRKGECEASIAKKEMVEANLR 454
            I   +  GE +A  AKKEMV+ANLR
Sbjct: 240 EINRQMSIGEAKARRAKKEMVDANLR 265


>gi|209542656|ref|YP_002274885.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209530333|gb|ACI50270.1| RNA polymerase, sigma 32 subunit, RpoH [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 295

 Score =  143 bits (359), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 124/275 (45%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +S  + + +    R  +   + A   +V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLQDIRKFPMLSPEDEQRLSR--RWKDKGDTEAAHALVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A  +FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 72  PLGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IA+ L +P + V     +++    SL  P+  
Sbjct: 132 KLFFNLRRLKGQMQAIDDGDLKPEQVNKIAESLGVPEQDVINMNRRLSAPDHSLNAPLRA 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D++       A        +      + +L  RE  +L        +  
Sbjct: 192 DSEGEWQDWLVDEHDNQEQTLAENEEFSGRKALLDNAMKTLNDRERHILTE--RRLKDDP 249

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLEE+   + ++RER+RQIE +A  K++   +++
Sbjct: 250 ATLEELSHTYNISRERVRQIEVRAFEKVQAAMKAE 284


>gi|261416342|ref|YP_003250025.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261372798|gb|ACX75543.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326200|gb|ADL25401.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 282

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 84/279 (30%), Positives = 146/279 (52%), Gaps = 17/279 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVR--KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             + ++    ++  E   ++ +++  + E     A + ++  NLR V+SVA+KY  RGL 
Sbjct: 9   YFRDLNRYPTLTPQEESALLKIIKNGETEEIRKSALQRLIRGNLRFVVSVARKYQGRGLS 68

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI EGN+GL KAA++FD     KF +YA+WW++Q+I +++ +Q   +RIP +    +
Sbjct: 69  LLDLINEGNLGLFKAAKRFDMDKDVKFISYAVWWIRQSIQKALFEQVGAVRIPPNKLALV 128

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD------- 582
           ++  R   +      +  + EE A      VE + K        ISL+ PIGD       
Sbjct: 129 NRFKRALMQNGGDYDKTISMEEFAPYERDIVEVMEK-----IVDISLDAPIGDDAGVSSA 183

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +  S L D +      +  +   +   ++     L+SL  REE +LRM +G+    D TL
Sbjct: 184 DSVSTLMDVLGSDG--NQDEDMEREERKKLIQETLSSLPQREEEILRMFYGLDTVEDTTL 241

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPS-RSKKLRSFL 680
           +++G+   ++RER+RQI+ K +R+L+      +KL  +L
Sbjct: 242 KDIGEDLKLSRERVRQIKNKTLRRLQKSKEHKEKLADYL 280


>gi|296114957|ref|ZP_06833602.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978475|gb|EFG85208.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
          Length = 299

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 70/275 (25%), Positives = 124/275 (45%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +S  E   +  +    E   + A  ++V ++LRLV  +A  Y   GL
Sbjct: 15  LSKYLRDIRKFPMLSPEEELKLSRL--WKEKGDTEAAHKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIG+M+A  +FD   G++ +TYAMWW++ AI   I      ++I      K
Sbjct: 73  PVGELISEGNIGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKIGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   +M      +  PE+   IAK L +P + V     +++    SL  P+  
Sbjct: 133 KLFFNLRRLKGQMQAIDDGDLQPEQVDKIAKSLGVPEQDVVNMNRRLSAPDHSLNAPLRT 192

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D +       A        +      + SL  RE  +L        +  
Sbjct: 193 DSEGEWQDWLVDDHDNQEQTLAENEEYSGRKALLANAMQSLNERERHILTE--RRLKDDP 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLE++   + ++RER+RQIE +A  K+++  +++
Sbjct: 251 ATLEDLSHVYNISRERVRQIEVRAFEKVQNAMKAE 285


>gi|149907981|ref|ZP_01896649.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
 gi|149808987|gb|EDM68918.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
          Length = 284

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 133/233 (57%), Gaps = 2/233 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A++ M+++NLRLVI++AK+Y +  L  +D+IQEGN GL+ A EKFD   G++FS
Sbjct: 37  HEGDQKARQRMIQSNLRLVINIAKRYQHTSLSLVDIIQEGNTGLIHAVEKFDATKGFRFS 96

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+WW+K  I R I +QS TIR+P+H+     ++++ AR     +K     ++IA  L 
Sbjct: 97  TYAVWWIKNNIERFIMNQSRTIRVPIHIGKTYKRILKNAREKVLDLKCNNDLKKIAINLE 156

Query: 558 MPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +  + V  VL       SL+  I   ++  + L D IED +   P D   + +       
Sbjct: 157 LEFDDVVNVLSYYFTEASLDKTIATKNDSNTALVDLIEDSSICKPNDEIEKTDTSSYLIT 216

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           VL  L  R+  ++ +RFG+G     TL  +G++  ++RER+RQI   +++K+K
Sbjct: 217 VLNHLCDRDREIIELRFGLGREEPQTLNAIGERLFMSRERVRQIITASLQKIK 269


>gi|288962386|ref|YP_003452681.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914652|dbj|BAI76137.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 293

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/282 (25%), Positives = 118/282 (41%), Gaps = 14/282 (4%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              D+   +   I        ++  +   +       E     A   +V ++LRLV+ +A
Sbjct: 8   RSPDAGESLSRYINDTHRYPVLTAEDEYMLAK--AWTEHGDVDAAHRLVTSHLRLVVKIA 65

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
             Y   GL   DLI EGN+GLM A +KF+   G++ STYAMWW+K +I   I      ++
Sbjct: 66  GGYRGYGLPLSDLIAEGNLGLMTAVKKFEPERGFRLSTYAMWWIKASIQDYILRSWSLVK 125

Query: 521 IPVHMRDKIH-----KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI- 574
           I      K       ++ R             +   IA  LA+P + V  + +    P+ 
Sbjct: 126 IGTTAAQKKLFFSLGRLKRKLGEYGGGDLHPDSVTSIATDLAVPEDDVVAMNRRLSAPVA 185

Query: 575 SLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRM 630
           SL  P+  E D+    D + D           +   R+        +  L  RE  +L  
Sbjct: 186 SLNAPMSAEGDSGEWQDLLADDRPSVEESLVERGEARQRSALLHEAMGVLNDRERDILTS 245

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
                 ++  TLE++  ++ V+RERIRQIE +A  K+   +R
Sbjct: 246 --RRLSDSPLTLEDLSVRYGVSRERIRQIEERAFEKVARQTR 285


>gi|317132579|ref|YP_004091893.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470558|gb|ADU27162.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 256

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 84/261 (32%), Positives = 143/261 (54%), Gaps = 14/261 (5%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +       +++++ +     A++E++  NLRLV+SV +++TNRG  
Sbjct: 4   NKVEICGVNTSKLKVLTESQKTALLKRVKQGDLAAREELISGNLRLVLSVIQRFTNRGEN 63

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 64  LDDLFQVGCIGLMKSIDNFDISQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIA 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   R+ N  +REPT EE+AK++ MP E +   L+   EP+SL  P+  +  DT +
Sbjct: 123 YKAMQCKERLMNANQREPTIEEMAKEMDMPKEEIVMALESVVEPVSLYEPVYSDGGDTIY 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I DK   S     I      T    + +L+ RE+R+L +RF  G    HT  EV  
Sbjct: 183 VMDQIGDKTVDSDWLDEI------TLKEAVGALSEREKRILYLRFFEG----HTQMEVAS 232

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  +++ ++ ++E  A+ K+K
Sbjct: 233 EIGISQAQVSRLEKGALSKIK 253


>gi|297837779|ref|XP_002886771.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
 gi|297332612|gb|EFH63030.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
          Length = 503

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 141/255 (55%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 248 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 307

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 308 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 366

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDS-AIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D    +        
Sbjct: 367 IAESLNMSQKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRVENNPWHGYDD 426

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L+E  ++++ A+L  RE  ++R+ +G+      T E++ K+  ++RER+RQ+   A+ 
Sbjct: 427 LALKEEVSKLISATLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 485

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 486 KLKHAARKRKMEAMI 500


>gi|6682869|dbj|BAA88921.1| sigma factor [Nicotiana tabacum]
          Length = 508

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 139/253 (54%), Gaps = 8/253 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++    E S+A++ +  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD   G
Sbjct: 255 LQSTLIECSLARERLAMSNVRLVMSIAQRYDNVGAEMADLVQGGLIGLLRGIEKFDPSKG 314

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YK STY  WW++Q ++R++ + S T+R+P ++ +++  +     R+  K    P+   IA
Sbjct: 315 YKISTYVYWWIRQGVSRALVENSRTLRLPTYLHERLSLIRNAKARLEEK-GITPSVNNIA 373

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLDSAIQAN- 608
             L M  + VR   + + +  SL+              L  +I D +  +     +    
Sbjct: 374 ASLNMSQKKVRNATEASSKMYSLDREAFPSLNGLPGETLHSYIADNHLENNPWHGVDVWA 433

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L++    ++ ++L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ KL
Sbjct: 434 LKDEVNNLISSTLRDREREIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVGLVALEKL 492

Query: 668 KHPSRSKKLRSFL 680
           KH +R ++L + L
Sbjct: 493 KHAARKRQLDAML 505


>gi|88705109|ref|ZP_01102821.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
 gi|88700804|gb|EAQ97911.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
          Length = 439

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 125/247 (50%), Gaps = 1/247 (0%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                S A+  +   NLRLV S+A +Y  +G+ +LDLIQEG +GL++AAEK+D   G++F
Sbjct: 191 HMESYSDARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHSKGFRF 250

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STY   W+ QAI R + D    IR P H++++++K+ R       +   EP    +A+  
Sbjct: 251 STYCFNWITQAIRRHVGDTGGLIRYPTHVQEQVNKLYRLRVTEKQRTGEEPGDAALAEAA 310

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + +E  R +L++    +SL+ P  D+D   L D +      +    A   +L +     
Sbjct: 311 GLTLEKTRDLLQLRNLGVSLDAPQFDDDDGTLLDTMSGGPFDASESEAETESLHDRLLLE 370

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK- 675
           +  L   E  V+  R+G+      +  E+  +  V+RE +RQ+E  A+ KL    R +  
Sbjct: 371 MEELDKAEREVVIARWGLHDGPPLSRAEIADRMSVSREWVRQLERAALTKLSGNERIRSA 430

Query: 676 LRSFLDG 682
              +++ 
Sbjct: 431 FADYMEA 437


>gi|209809124|ref|YP_002264662.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
 gi|208010686|emb|CAQ81073.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
          Length = 293

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 90/280 (32%), Positives = 155/280 (55%), Gaps = 6/280 (2%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
               +SI      +K I+    ++ SE        R        ++  ++E+NLRLV+ +
Sbjct: 10  EEPRNSIDAYSLYLKEINKYKLLTASEELEHS---RNYLSGDLKSRNVLIESNLRLVVKI 66

Query: 460 AKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           A KY +R    L  LD+I+EGN+GLMKA  KFD  LGY+FSTYA+WW+K++I  ++ + S
Sbjct: 67  ANKYRHRNQRELAPLDIIEEGNLGLMKAVNKFDPELGYRFSTYAVWWIKESIESALFNHS 126

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            T+R+PVH+  +++  +R AR +S  +K+EP+  EI+       + V K+L +     + 
Sbjct: 127 RTVRLPVHITKELNVYLRAARDLSRTLKKEPSISEISVHCNKDYKKVNKILGLVPSSSTC 186

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
            +   D+ +S+L +   D +   P  S  ++NL    +  L  L  RE++++  R+G+  
Sbjct: 187 HSASSDDMSSNLIELCADDHEQEPAQSLSKSNLESNLSSWLNLLQCREKQIIINRYGLFG 246

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLEE+G+   +++ER+RQI+ + + KL    +  KL
Sbjct: 247 TDVKTLEELGQDLQLSKERVRQIQTETLTKLNTIFKKNKL 286



 Score = 41.4 bits (95), Expect = 0.50,   Method: Composition-based stats.
 Identities = 21/100 (21%), Positives = 37/100 (37%)

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
           ++  K    R++ D   +YL+E+   +LL+   E+  ++   +G       L ES L   
Sbjct: 4   IECSKKEEPRNSIDAYSLYLKEINKYKLLTASEELEHSRNYLSGDLKSRNVLIESNLRLV 63

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
             I  +    +   L    I  E  +G       F    G
Sbjct: 64  VKIANKYRHRNQRELAPLDIIEEGNLGLMKAVNKFDPELG 103


>gi|196019865|ref|XP_002119058.1| hypothetical protein TRIADDRAFT_63024 [Trichoplax adhaerens]
 gi|190577137|gb|EDV18456.1| hypothetical protein TRIADDRAFT_63024 [Trichoplax adhaerens]
          Length = 349

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 92/394 (23%), Positives = 175/394 (44%), Gaps = 52/394 (13%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
             + E +++ ++ L   GI +++ +       +E  ++  +                +  
Sbjct: 1   NTNHEIVKEVISFLKESGIAIINKE-------AESEINAQAEQEEEFESTSTENIINNFG 53

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
            DDPVRMYL+EMG   LL+R+GE+ +AKRIE  R   +  + ++P+  + +  W D++  
Sbjct: 54  NDDPVRMYLKEMGYRLLLTRDGEVEVAKRIEKSRINKLFYIIQTPMALKKMQDWYDDILT 113

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G  LLRE+ID++A    E                                          
Sbjct: 114 GKKLLREVIDIDATASNEQFF--------------------------------------- 134

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            ++     D   +N E+   + D D+D  + ++SA+E+ L+PK++  L +I+E  + L  
Sbjct: 135 DENSEKTDDFNTKNTESGNDDFDNDDDSDSTSISAIENDLKPKILDILLKISENCKSLLQ 194

Query: 297 LQDNAVNGQKDEKSSVKCKV-----LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
           L D   + +    +  K +          +  L+G L LN   I+ +  QL +I+K I+ 
Sbjct: 195 LYDIKKDKKISSPNQSKTEKKLLDNKINDIANLLGELKLNDQFINEIFYQLKEINKDIIQ 254

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E EL +LA +  + R  F++ ++  +L+ +W+   K+     +   V        K + 
Sbjct: 255 IESELFKLASNSKLNRTKFIDVYRTIDLEKNWIDLLKNRGVK-YTKLVDENSSFFTKSQL 313

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
           + + I V+ G+SI++F+ I   ++K E E    K
Sbjct: 314 KFEKIKVKAGLSITQFKKIFQDIQKWEREVQKLK 347


>gi|149908225|ref|ZP_01896889.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
 gi|149808767|gb|EDM68700.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
          Length = 284

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 85/263 (32%), Positives = 143/263 (54%), Gaps = 4/263 (1%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ ++ ++ +   E  + +++          AK  M+EANLRLVISVAK+Y    
Sbjct: 9   ALDAYLQQVNKKSKLLTKEEEYDIAVA--VANGDLRAKNRMIEANLRLVISVAKRYQYSV 66

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +  +D+IQEGN GL++A EKFD   G++FSTYA+WW+K  I RSI +   TIRIP+H+  
Sbjct: 67  IPLVDIIQEGNTGLIRAVEKFDPNKGFRFSTYAVWWIKNNIERSIMNSDRTIRIPIHVGK 126

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS- 586
               + + A+ +   +  +     IAK L   V+ V  VL      +SL+  I  ++ S 
Sbjct: 127 MHKSIAKVAKELGLDVGSDNDLVVIAKVLETDVDEVMDVLSYYFSELSLDKGIVTDNESV 186

Query: 587 -HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D IED++  +P       + R+    +L +L   E +V+ +RFG+      +L  +
Sbjct: 187 TTLVDIIEDQSIRTPSAEIEGGSTRDYLLALLENLPAYERQVVELRFGLTGEEPLSLSRI 246

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G++  ++RE++R I    +R+LK
Sbjct: 247 GERLSMSREKVRIIIRTTLRRLK 269


>gi|23978331|dbj|BAC21136.1| principal sigma factor [Synechococcus leopoliensis]
          Length = 188

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 100/189 (52%), Positives = 136/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL++L+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-ADGETPEDEVAKNLLREDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQLFNVT 188


>gi|2398851|dbj|BAA22214.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 502

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 143/255 (56%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 306

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 307 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 365

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D     +P      
Sbjct: 366 IAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDD 425

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L+E  ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ 
Sbjct: 426 LALKEEVSKLISATLGEREKEIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 484

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 485 KLKHAARKRKMEAMI 499


>gi|78049505|ref|YP_365680.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|294626531|ref|ZP_06705130.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|294665098|ref|ZP_06730402.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|78037935|emb|CAJ25680.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|292599221|gb|EFF43359.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292605140|gb|EFF48487.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 294

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E + +    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 26  LDAYIGAVHQIPVLSVDEEQDLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 83

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 84  PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 143

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 144 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 201

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 202 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRRW-LDSDSK 260

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 261 VTLQELADEYGVSAERIRQIEANALKKMK 289


>gi|304404022|ref|ZP_07385684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347000|gb|EFM12832.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 272

 Score =  142 bits (358), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 143/276 (51%), Gaps = 18/276 (6%)

Query: 404 DSILKIRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           + I   RN+++   V+T     ++ +E R + + ++     A  A++++V  NLRLV+SV
Sbjct: 9   EVITLTRNKVEICGVDTSKLPVLTNAEMRELFTALQTRNERA--AREKLVNGNLRLVLSV 66

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            +++ NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  I
Sbjct: 67  IQRFNNRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PI 125

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+   +RD  +K ++    ++N   REPT  EI++ L +P E V   L   ++P+SL  P
Sbjct: 126 RVSRSLRDIAYKALQVRDSLTNANSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEP 185

Query: 580 IGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           I  +  D  ++ D I D    +   S I+          +  L  RE+ +L MRF  G  
Sbjct: 186 IYHDGGDPIYVMDQISDDK--NKDISWIEEI---ALREAMHKLNDREKMILSMRFFEG-- 238

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              T  EV  +  +++ ++ ++E  AI++++   ++
Sbjct: 239 --KTQMEVADEIGISQAQVSRLEKSAIQQMQKHVKT 272


>gi|167644630|ref|YP_001682293.1| RNA polymerase factor sigma-32 [Caulobacter sp. K31]
 gi|167347060|gb|ABZ69795.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter sp. K31]
          Length = 295

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 126/274 (45%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E + S A  +MV ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLTEIRKFPMLPKDEEFMLAQ--RWKEHQDSEAAHKMVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIA----KKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   +++     +  P++++    K   +  E +    ++     SL  P+  
Sbjct: 133 KLFFNLRKAKSQIAAFQDGDLHPDQVSYIATKLGVLDSEVISMNRRLGGPDASLNAPLRA 192

Query: 583 EDTSHLGDFIEDKNAVSPLD---SAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNT 638
           +  S   D++ D N VS         + ++R T     +  LT RE  +L        + 
Sbjct: 193 DGESEWQDWLADDNQVSQETVVAENQEKSMRMTLLEEAMVELTDRERHILTE--RRLKDD 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLE++  ++ V+RER+RQIE +A  KL+   R
Sbjct: 251 PTTLEDLATEYGVSRERVRQIEVRAFEKLQKSMR 284


>gi|158833995|gb|ABW81803.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 80/227 (35%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+  C    +++ M+E+NLRLV+ +A++Y N
Sbjct: 45  LDATQLYLGEIGYSPLLTAEEE---VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGN 101

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 102 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 161

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+ EEIA++L  PV+ V ++L++ +   S+++P+G +  
Sbjct: 162 VKELNVYLRTARELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSE 221

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D +   P D+    +++ +  + L  L  ++  VL  RF
Sbjct: 222 KALLDILSDDSENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRF 268



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 34/96 (35%), Gaps = 1/96 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E S        +          +  +   D  ++YL E+G   LL+ E E+  A+R   
Sbjct: 16  DEKSSMEDEILEDELEEDDLLLQNVTQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALC 75

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       + ES L     I  R   N G  LL  I
Sbjct: 76  GDQQSRRRMIESNLRLVVKIARRYG-NRGLALLDLI 110


>gi|2385344|emb|CAA74896.1| sigma factorB [Arabidopsis thaliana]
          Length = 500

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 143/255 (56%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 245 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 304

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 305 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 363

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D     +P      
Sbjct: 364 IAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDD 423

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L+E  ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ 
Sbjct: 424 LALKEEVSKLISATLGEREKEIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 482

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 483 KLKHAARKRKMEAMI 497


>gi|23978302|dbj|BAC21129.1| principal sigma factor [Oscillatoria agardhii]
          Length = 188

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 99/189 (52%), Positives = 135/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKF+   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFEHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-SDGETPEDQVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|118579103|ref|YP_900353.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501813|gb|ABK98295.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 282

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 120/262 (45%), Gaps = 9/262 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I   T +S  E       +   E +   A   ++ +NLR V+ VA +Y + GL+ L
Sbjct: 15  YLAEIRKFTLLSEEEEHRTA--IAFYEKKDLRAAHTLITSNLRFVVRVAYEYRHYGLKML 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLM A +K++   G +  +YA+WW++  I   +      ++I      R   
Sbjct: 73  DLIQEGNIGLMMAVKKYNPFKGVRLISYAVWWIRAYIQNHVISAWSLLKIGTTQAQRKLF 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+      + +    E   +  A+ L +    V ++ +  +   SL+  +   +     
Sbjct: 133 FKLREARNAIRHLNGGEDDLQSTARSLNVSDSEVVEMEQRLRGECSLDAELPGGEGVTGL 192

Query: 590 DFIEDKNAVSPL---DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           D + D          +  +Q  LR      +++L  +E  V+  R      T  TL+E+ 
Sbjct: 193 DGLVDDRMNQEELLSECQLQRKLRTDVATAVSALNEKERFVIEHRVSAD--TPLTLQEIA 250

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
            +F ++RER+RQIE  A++KLK
Sbjct: 251 SRFSISRERVRQIEEAALKKLK 272


>gi|1184690|gb|AAB01724.1| RNA polymerase sigma 32 subunit [Caulobacter crescentus CB15]
          Length = 295

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 68/274 (24%), Positives = 120/274 (43%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +S  E   +    R  E +   A  +MV ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLTEIRKFPMLSKDEEFMLAQ--RWKEHQDPQAAHKMVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRM----SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++       +  +   +   K   +  E +    +++    SL  P+  
Sbjct: 133 KLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRLSGPDASLNAPLRR 192

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  S   D++ D+  VS      +   +          +  LT RE  +L        + 
Sbjct: 193 DGESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTE--RRLKDD 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLEE+  Q+ V+RER+RQIE +A  KL+   R
Sbjct: 251 PTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMR 284


>gi|239977584|sp|P0CAW9|RP32_CAUCR RecName: Full=RNA polymerase sigma-32 factor
 gi|239977655|sp|B8H3C3|RP32_CAUCN RecName: Full=RNA polymerase sigma-32 factor
 gi|1262200|gb|AAC43981.1| RpoH [Caulobacter vibrioides]
 gi|1588870|prf||2209377A heat shock sigma factor 32
          Length = 295

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 68/274 (24%), Positives = 120/274 (43%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +S  E   +    R  E +   A  +MV ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLTEIRKFPMLSKDEEFMLAQ--RWKEHQDPQAAHKMVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRM----SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++       +  +   +   K   +  E +    +++    SL  P+  
Sbjct: 133 KLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRLSGPDASLNAPLRA 192

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  S   D++ D+  VS      +   +          +  LT RE  +L        + 
Sbjct: 193 DGESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTE--RRLKDD 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLEE+  Q+ V+RER+RQIE +A  KL+   R
Sbjct: 251 PTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMR 284


>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 508

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 142/255 (55%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++      S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 253 AELQSKSIACSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSS 312

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ + S T+R+P H+ +++  +     R+  K    P+ + 
Sbjct: 313 KGFRISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKIRLEEK-GVTPSIDR 371

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQA 607
           IA+ L +  + VR   +   +  SL+           G+    +I D    +     +  
Sbjct: 372 IAESLNISQKKVRNATEAVSKVFSLDREAFPSLNGLPGETHHSYIADNCLENNPWHGVDD 431

Query: 608 N-LRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L++   +++  +L  RE+ ++R+ +G+  N   T E++ K+  ++RER+RQ+   A+ 
Sbjct: 432 WALKDEVNKLINLTLQEREQEIIRLYYGLD-NESLTWEDISKRIGLSRERVRQVGLVALE 490

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R KKL + L
Sbjct: 491 KLKHAARKKKLEAML 505


>gi|296133647|ref|YP_003640894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032225|gb|ADG82993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 257

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 83/269 (30%), Positives = 135/269 (50%), Gaps = 19/269 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     +S SE R I   ++        A+ +++  NLRLV+SV +++T
Sbjct: 2   MINKVEICGVNTSKLPVLSSSEMRKIFEQMQ---AGDKSARTKLINGNLRLVLSVIQRFT 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    + NK  REP+  EIA +L MP E V   L   +EPISL  PI  + 
Sbjct: 118 LRDVAYKALQVRDALVNKYSREPSINEIASELKMPREEVVFALDAIQEPISLFEPIYHDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D  ++ D I D+  +        +         +  L  RE+ +L +RF  G     T 
Sbjct: 178 GDPIYVMDQIGDEKNLDGNWLEGIS-----VREAMRKLNEREKLILTLRFFEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            EV ++  +++ ++ ++E  A++ ++   
Sbjct: 229 MEVAEEIGISQAQVSRLEKAALKHMRKYM 257


>gi|219123705|ref|XP_002182160.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406121|gb|EEC46061.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 319

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 100/288 (34%), Positives = 154/288 (53%), Gaps = 27/288 (9%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-------- 463
           + +  +   G+S+   R ++        E   A+  +V ANL LV ++AK+         
Sbjct: 40  KHQEWAAACGVSVIVLRQVLD-------EGQQARAALVAANLGLVTALAKRQLSTLQTAT 92

Query: 464 -TNRG----LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
              RG    L   DLIQEG +GLMKAAE+F+   G++FSTYA WWV+Q I +S++D S T
Sbjct: 93  EAGRGVGTILTLQDLIQEGTLGLMKAAERFEPERGWRFSTYATWWVRQRILKSVSDSSRT 152

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P H+   + ++ +           E T   +A+ L +PVE VR     ++  +SLET
Sbjct: 153 IRLPAHVHGTLQRIQKAKAWFRA-HGEEATLSSLAQYLELPVEKVRLYTDSSRNVMSLET 211

Query: 579 PIG------DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P+       DE+T  LGD +         +   QA   +    ++  LT  E+ VLR RF
Sbjct: 212 PLKGRSAFKDENTRTLGDTLASDEKTPEENVEAQALRLDLEHVMIKVLTDVEQNVLRRRF 271

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+   T  +LEE  KQ  ++R+RIR +EA+A+ KL+ P ++ KLRS++
Sbjct: 272 GLEDGTSWSLEETAKQLGMSRDRIRLVEARALNKLRRPQQNYKLRSYM 319


>gi|15217767|ref|NP_176666.1| SIGA (SIGMA FACTOR A); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana]
 gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana]
 gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana]
 gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana]
 gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana]
 gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana]
          Length = 502

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 143/255 (56%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 306

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 307 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 365

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D     +P      
Sbjct: 366 IAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDD 425

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L+E  ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ 
Sbjct: 426 LALKEEVSKLISATLGEREKEIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 484

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 485 KLKHAARKRKMEAMI 499


>gi|16127328|ref|NP_421892.1| RNA polymerase factor sigma-32 [Caulobacter crescentus CB15]
 gi|221236131|ref|YP_002518568.1| RNA polymerase factor sigma-32 [Caulobacter crescentus NA1000]
 gi|13424754|gb|AAK25060.1| heat shock sigma factor RpoH [Caulobacter crescentus CB15]
 gi|220965304|gb|ACL96660.1| RNA polymerase sigma-32 factor [Caulobacter crescentus NA1000]
          Length = 298

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 68/274 (24%), Positives = 120/274 (43%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +S  E   +    R  E +   A  +MV ++LRLV  +A  Y   GL
Sbjct: 18  LSRYLTEIRKFPMLSKDEEFMLAQ--RWKEHQDPQAAHKMVTSHLRLVAKIAMGYRGYGL 75

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 76  PIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 135

Query: 529 --IHKVVRTARRM----SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++       +  +   +   K   +  E +    +++    SL  P+  
Sbjct: 136 KLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRLSGPDASLNAPLRA 195

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  S   D++ D+  VS      +   +          +  LT RE  +L        + 
Sbjct: 196 DGESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTE--RRLKDD 253

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLEE+  Q+ V+RER+RQIE +A  KL+   R
Sbjct: 254 PTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMR 287


>gi|167630136|ref|YP_001680635.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167592876|gb|ABZ84624.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 265

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 84/266 (31%), Positives = 134/266 (50%), Gaps = 21/266 (7%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     ++ +E R +   ++ GE     A+++++  NLRLV+SV +++TNR
Sbjct: 12  NKVEICGVNTSKLPVLTNAEMRTLFQAMQSGERS---AREKLISGNLRLVLSVIQRFTNR 68

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +R
Sbjct: 69  GEYVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLR 127

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--D 584
           D  +K ++    + N++ REPT  EIA  L  P E V   L   +EPISL  PI  +  D
Sbjct: 128 DIAYKALQVRDHLVNELSREPTVTEIADALGFPREEVVFALDAIQEPISLFEPIYHDGGD 187

Query: 585 TSHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              + D I D+ N  +     I           L  L  RE+ +L +RF  G     T  
Sbjct: 188 PIFVMDQIGDEKNQDAQWLEGI------AVREALRRLNDREKLILTLRFFEG----KTQM 237

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV  +  +++ ++ ++E  A+  ++ 
Sbjct: 238 EVADEIGISQAQVSRLEKAALTHMRK 263


>gi|158522485|ref|YP_001530355.1| RNA polymerase sigma 70 family subunit [Desulfococcus oleovorans
           Hxd3]
 gi|158511311|gb|ABW68278.1| putative RNA polymerase, sigma 70 family subunit [Desulfococcus
           oleovorans Hxd3]
          Length = 321

 Score =  142 bits (357), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 73/278 (26%), Positives = 138/278 (49%), Gaps = 13/278 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
               ++  +K +S    ++  +   +   V+  E     A   +  +NLRLV+ +A ++ 
Sbjct: 37  KYDPLQRYLKEVSRYNLLTREQEIELGKRVQ--EEGDEEAAYILATSNLRLVVKIALEFQ 94

Query: 465 NRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              +Q  LDLIQEGNIGLM A +KFD     KFS YA +W+K  I + + D    ++I  
Sbjct: 95  RVWMQNLLDLIQEGNIGLMHAVQKFDPYKNVKFSYYASFWIKAYILKFVMDNWRLVKIGT 154

Query: 524 --HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPI 580
             + R    ++ +  + + ++   EP P+ +A++L +P + V     ++    +SL+ P+
Sbjct: 155 TQNQRKLFFRLKKEKQALIDQ-GFEPRPKLLAERLGVPQKEVINMEQRLDMWDLSLDEPV 213

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGM 636
             +  +  GD ++  N     +      LR    E       +LTPRE  + +    I  
Sbjct: 214 SHDSDTQKGDLLDINNTQPVDEQVGDKALRQLVGEHLVEFKKTLTPRERDIFKT--RIYT 271

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +   TL+++G+++ ++RER+RQ+E   I+K++   + K
Sbjct: 272 DQPMTLQDIGERYAISRERVRQLEVNIIKKMRDFFKEK 309



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALII 169
           DP++ YL+E+    LL+RE EI + KR+ E G       L  S L     I 
Sbjct: 39  DPLQRYLKEVSRYNLLTREQEIELGKRVQEEGDEEAAYILATSNLRLVVKIA 90


>gi|305644360|gb|ADM53781.1| RNA polymerase sigma factor [Aeromonas hydrophila]
 gi|305644362|gb|ADM53782.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 115/176 (65%), Positives = 139/176 (78%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     
Sbjct: 61  LQEMGREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAL 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P D+A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRER
Sbjct: 121 PADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 176


>gi|260889708|ref|ZP_05900971.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260860314|gb|EEX74814.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 273

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 94/260 (36%), Positives = 145/260 (55%), Gaps = 9/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E   ++  +R+ +     A++ ++ +NLRLVIS AKK    GL  +
Sbjct: 12  YLSDIQKFDLLSKEEEYELLKRIREDD--DEQARQLLILSNLRLVISTAKKSLGNGLPLI 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGNIGL+KA  KFD+  G++FSTYA+WW+KQ+I ++I +    IRIP +  +++ K
Sbjct: 70  DLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQSIKKAIINIGRDIRIPSYKYEQLSK 129

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           V +  +  +      P+ E IAK++ +    V  +L   ++ +SL   IG  D  +L D 
Sbjct: 130 VNKVIKDYTAIHGEAPSTEYIAKEVDLKESKVILLLGEFQDIMSLNETIG--DNIYLEDI 187

Query: 592 IE--DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           I   D      +       +++   RV   L  RE  +L  R+G+  N  HTL+E+G+Q 
Sbjct: 188 IGKNDDVEDKIIKEDQLIEMKDLLERV---LNERERAILEYRYGLYDNKIHTLKEIGEQM 244

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +TRER+RQIE KAI KLK 
Sbjct: 245 GITRERVRQIEKKAITKLKE 264


>gi|225175484|ref|ZP_03729478.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168813|gb|EEG77613.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
          Length = 277

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 81/270 (30%), Positives = 133/270 (49%), Gaps = 19/270 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     +   E R + + +R        A++++V  NLRLV+SV +++ 
Sbjct: 21  VINKVEICGVNTAKLPVLKNDEMRRLFARLR---EGDESAREKLVNGNLRLVLSVIQRFN 77

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 78  NRGEYVDDLFQVGCIGLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 136

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +KV++    ++N+  REPT  EIAK+L +  E +   L   +EP+SL  PI  + 
Sbjct: 137 LRDIAYKVLQVRDSLANRFAREPTISEIAKELNLKREDIVFALDAIQEPVSLFEPIYHDG 196

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D   + D I D          + A         L  L  RE+ +L +RF  G     T 
Sbjct: 197 GDPIFVMDQISDDKNHDNKWLEVLA-----INEALHKLNEREKLILTLRFYRG----KTQ 247

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            EV  +  +++ ++ ++E  A+  L+   +
Sbjct: 248 MEVADEIGISQAQVSRLEKAALSHLRKHVQ 277


>gi|11079077|dbj|BAB17543.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A   + D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDPKAPKADDDTDEDEAEASTDDEEEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +   + +  L  +AE++                   
Sbjct: 110 VAAQRFGAVSDQMEITRKALKKHGRGNKQAIAELLALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDETWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|84625707|ref|YP_453079.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|289664834|ref|ZP_06486415.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vasculorum NCPPB702]
 gi|289671390|ref|ZP_06492465.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           musacearum NCPPB4381]
 gi|84369647|dbj|BAE70805.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 291

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 141 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 198

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 199 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRW-LDSDSK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|21244548|ref|NP_644130.1| RNA polymerase factor sigma-32 [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|21110222|gb|AAM38666.1| RNA polymerase sigma-32 factor [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 291

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E + +    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQDLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 141 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 198

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 199 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRRW-LDSDSK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|239934568|emb|CAR94598.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 224

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 102/270 (37%), Gaps = 47/270 (17%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLTF  ++   +++  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRHALSNYPLTFAFMLNQYEQVKA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L +II            GF             +               + E     
Sbjct: 61  GQGRLVDII-----------VGFIDPNAPDEIAAPVNPKLAAAAAPAAAEAEEEEEGEGT 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +++  +    PE A     +L                +L  +++ +L+E          
Sbjct: 110 EEEEALETGPDPEEAARRFASL---------------QKLHQQIVKSLEE---------- 144

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                        +  K + L++K  +    L L+    D L+ QL +    + + E  +
Sbjct: 145 ----------KGLADPKTQKLRKKAAQEFMELKLSPKMFDALILQLREHVSEVRNLEKSV 194

Query: 357 LRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           + L     G+ R  F+      E +  W+ 
Sbjct: 195 MMLCVRDAGMPRKDFIMTFPKNETNIKWLD 224


>gi|325924311|ref|ZP_08185855.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
 gi|325545176|gb|EGD16486.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
          Length = 291

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  PLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 141 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 198

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     L+ L  R   +++ R+ +  ++ 
Sbjct: 199 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGLSGLDTRSRDIVKRRW-LDSDSK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|58584688|ref|YP_198261.1| DNA-directed RNA polymerase sigma 32 subunit [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58419004|gb|AAW71019.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
           [Wolbachia endosymbiont strain TRS of Brugia malayi]
          Length = 297

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 75/281 (26%), Positives = 133/281 (47%), Gaps = 16/281 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I  +     +S  E   +       +C+   +  +++ ++L LV+ +A K+ N GL
Sbjct: 16  LTQYITEVRKFPMLSQEEEVRLAK--SWNQCKDISSAHKLITSHLNLVVKIAMKFKNYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
             +DLI EGN+GL+ A +KF+  LG++FSTYA+WW++ +I   I      ++I      R
Sbjct: 74  LLMDLIMEGNMGLIHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIGTTQAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-----EGVRKVLKITKEPISLETPIG 581
                + +  +R+     RE    E  K ++  +     + ++   ++  +  SL   I 
Sbjct: 134 RLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVIQMNYRLACKDQSLNNCIK 193

Query: 582 DEDTS--HLGDFIE--DKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGM 636
               S   L D I     N      +  +  L+ET     LASL  R   +   R+    
Sbjct: 194 VGGDSKKELQDMIPCNSVNQEVTYQNREEKELKETILNNALASLNERSRDIFISRYLSEN 253

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
               TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 254 TQ--TLDELSKKYCVSRERIRQLAEQAMSKVKQHIQSESLK 292


>gi|3219170|dbj|BAA28785.1| sigma-32 homolog [Hydrogenophilus thermoluteolus]
          Length = 309

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 72/266 (27%), Positives = 126/266 (47%), Gaps = 14/266 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I++++    +S +E   +    R  E     A +++V ANLR V+ +A++Y   GL  
Sbjct: 39  RYIQAVNRFPVLSEAEEHELAR--RFHETNDLDAARKLVLANLRYVVMIARQYFGYGLPE 96

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLIQEGN+GL+KA  +FD   G +F T+A +W+K  I   I      ++I      K  
Sbjct: 97  ADLIQEGNVGLLKAVRRFDPYKGVRFITFAAYWIKAEIHDYILRNWRLVKIATTKAQK-- 154

Query: 531 KVVRTARRMSN-KIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHL 588
           K+    R++   +       + IA+ LA+  E V ++  +     ++LE PI  ++ +  
Sbjct: 155 KLFFNLRKLLGSEPLTRAKADAIAETLAVKPEEVAEMHARFAGGDVALEAPIDSDEEADW 214

Query: 589 ---GDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ D +       A     R   E   + L  L  R   ++  R+        TL
Sbjct: 215 RAPLAYLPDPSGTPEEAVAEAEAERLSHEGLQQALTQLDERSRAIVTRRWL--TEKPATL 272

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ ++ ER+RQIEA A++KL+
Sbjct: 273 HELAAEYGISAERVRQIEAAALKKLR 298


>gi|112981046|gb|ABI29247.1| DNA-dependent RNA polymerase sigma factor D subunit [Comamonas
           denitrificans]
          Length = 268

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 121/315 (38%), Gaps = 56/315 (17%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   MM ++  SP T   ++    ++ +G  +
Sbjct: 1   VRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISTSPATIAEVLKMAADIREGKVI 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           +  ++D           GF +  E   Y   ED  +  E DD     G            
Sbjct: 61  ISTVVD-----------GFVNANENDDYVAEEDFDEYDEDDDDDGKGG------------ 97

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                                    +  ++ + ++L+   +   D +  ++ +LR   D 
Sbjct: 98  -------------------------SKAMTRLLEKLKTDALERFDRMGVLFEKLRKAYDK 132

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL- 359
              G      S     +++ + + + ++      I+ L +        +   E EL ++ 
Sbjct: 133 DGWG------SPTYVKVQKSITEELMTIRFTAKTIEKLCDMARAQVDDVRKKERELRKII 186

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
               G+ ++ F++      L+  WV       +  +   +   +  + +++  +  +   
Sbjct: 187 VDKCGMSQEQFIKDFPANLLNLQWVEKQAASNKP-YSAILGRNIPDVQELQQSLIDLQNR 245

Query: 420 TGISISEFRHIVSMV 434
             + + E + I   +
Sbjct: 246 VVVPLEELKRINKRM 260


>gi|42520871|ref|NP_966786.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|42410611|gb|AAS14720.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 297

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 77/287 (26%), Positives = 136/287 (47%), Gaps = 16/287 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           VDS   +   I  +     +S  E   +       + +   +  +++ ++L LV+ +A K
Sbjct: 10  VDSRTNLMQYIARVQKFPMLSQEEEVRLAK--NWNQYKDVSSAHKLITSHLNLVVKIAMK 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ +I   I      ++I 
Sbjct: 68  FKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIG 127

Query: 523 VH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-----EGVRKVLKITKEPIS 575
                R     + +  +R+     RE    E  K ++  +     + ++   ++  +  S
Sbjct: 128 TTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQS 187

Query: 576 LETPIGDEDTS--HLGDFIEDK--NAVSPLDSAIQANLRET-TTRVLASLTPREERVLRM 630
           L   I   D S   L D I     +      +  +  L+ET     LASL  R   +   
Sbjct: 188 LNDCIKIGDDSKRELQDMIPCNLVSQEVTYQNHEEKELKETILNNALASLNERARDIFIS 247

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           R+        TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 248 RYLSENIQ--TLDELSKKYCVSRERIRQLAEQAMAKVKQYIQSESLK 292


>gi|91202979|emb|CAJ72618.1| similar to DNA-directed RNA polymerase sigma subunit [Candidatus
           Kuenenia stuttgartiensis]
          Length = 256

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 88/248 (35%), Positives = 148/248 (59%), Gaps = 5/248 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I   V K     + A++++++ANLRLV+S+AK++ NRG  FLDLI+EGN+GL
Sbjct: 2   LTFEEELEIARKVAK---GDAEAREKLIKANLRLVVSIAKEFVNRGFSFLDLIEEGNLGL 58

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E FD   G +FSTYA WW+KQAI R+IA+++  IRIP +M  +I ++   +  +  
Sbjct: 59  IRAVEDFDITTGNRFSTYATWWIKQAIRRAIANKARIIRIPSYMLQRISQMKHASSGLLK 118

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVS 599
           K +R P+ +EIA ++ +  + V+ +    +   SL+ P+    +    L D   +   + 
Sbjct: 119 KHERSPSEQEIAAEIDITAQNVKNIELSLQSMTSLDAPLVSGADIIWALSDITPNGKTLP 178

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +   +   +ET  ++L +L  R   V+ MR+G+      TLE++ K   ++RER+RQI
Sbjct: 179 PEEGLEETYEKETLKKLLDTLDKRAATVITMRYGLVDGESRTLEDISKILKISRERVRQI 238

Query: 660 EAKAIRKL 667
           E + I+KL
Sbjct: 239 EKETIQKL 246


>gi|257095687|ref|YP_003169328.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257048211|gb|ACV37399.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 286

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 135/270 (50%), Gaps = 7/270 (2%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V ++  I   I++      ++  E   + +  R  +     A +++V ++LRLVIS+A+ 
Sbjct: 10  VSAVGSIDAYIQAARQFPMLTQEEEFRLATRFR--DDSDLDAARQLVLSHLRLVISIARG 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   +      +++ 
Sbjct: 68  YLGYGLPHADLIQEGNIGLMKAVKRFDPAHGVRLVSFAIHWIKAEIHEYVLKNWRMVKLA 127

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG 581
                +       + + +++        +IA +L++  E V ++  ++T   ++L+    
Sbjct: 128 TTKAQRKLFFNLRSMKANSEALSPGQVTDIAHRLSVKPEEVSEMEARLTGHDLALDGDSD 187

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
           D++      ++ D ++        +A  R   E     LASL PR  R++  R+ +   +
Sbjct: 188 DDEVFAPISYLADHSSEPVHVLEARARERLHNEGLQGALASLDPRSRRIVEARW-LTDES 246

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  +F V+ ERIRQ+E KA++K++
Sbjct: 247 PATLHELAAEFGVSAERIRQVEVKAMQKMR 276


>gi|23978316|dbj|BAC21132.1| principal sigma factor [Anabaena cylindrica]
          Length = 188

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 100/189 (52%), Positives = 135/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEK D   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S ++ R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE   +VL SL+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-SDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|158833991|gb|ABW81801.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 77/227 (33%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLGEICYSPLLTAAEEIYFARRV---LCGDGSSRRRMIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L  L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLFELSTKQREVLARRF 225



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+    LL+   EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLGEICYSPLLTAAEEIYFARRVLCGDGSSRRRMIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|156972625|ref|YP_001443532.1| RNA polymerase factor sigma-32 [Vibrio harveyi ATCC BAA-1116]
 gi|156524219|gb|ABU69305.1| hypothetical protein VIBHAR_00277 [Vibrio harveyi ATCC BAA-1116]
          Length = 285

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 131/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTPEEERGLAERLHYKGEID--AAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
                + ++ +R+      E   E +A++L +    VR++        S      D+D  
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPMDDDDN 191

Query: 586 ----SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
               +    ++EDK+   A +   +  + +        LASL  R +R++R R+      
Sbjct: 192 SNSYTAPMFYLEDKSSDVADNIEAANWETHTNNRLGHALASLDERSQRIVRSRWLDD--D 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 250 KATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
          Length = 502

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 143/255 (56%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 306

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 307 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 365

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D     +P      
Sbjct: 366 IAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDD 425

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L+E  ++++ A+L  RE+ ++R+ +G+      T E++ K+  ++RER+RQ+   A+ 
Sbjct: 426 LALKEEVSKLISATLGEREKEIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 484

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 485 KLKHAARKRKMEAMI 499


>gi|289642895|ref|ZP_06475030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
 gi|289507278|gb|EFD28242.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
          Length = 332

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 120/246 (48%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +V++    +  A I + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 91  FTQLVALPEGDQQRAEI-RDQLVRMHLPLVEYLARRFRNRGEPLDDLTQVATIGLIKSVD 149

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 150 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQTLGRS 209

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  EIA  L M  E V + L+       +SL+ P   +D +  + D +  ++      S
Sbjct: 210 PTVSEIAAHLQMSEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDE-----S 264

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L PRE+R+L +RF        T  ++  +  +++  + ++ A+ 
Sbjct: 265 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN----MTQSQIATELGISQMHVSRLLART 320

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 321 LAQLRR 326


>gi|90407357|ref|ZP_01215542.1| RpoD protein [Psychromonas sp. CNPT3]
 gi|90311508|gb|EAS39608.1| RpoD protein [Psychromonas sp. CNPT3]
          Length = 282

 Score =  141 bits (356), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 72/272 (26%), Positives = 130/272 (47%), Gaps = 14/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I+S++    +S SE + +   +         A K++V ++LR V  +AK Y   GL
Sbjct: 16  IEAYIQSVNKFAMLSASEEKALAERL--FYEGDLDAAKKLVMSHLRFVAYIAKSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  AIADLIQEGNVGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVIRNWRVVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+    K E   E +A  L +  + V     ++     S +    D+D 
Sbjct: 134 KLFFNLRKAKKRLGWFSKDE--VENVANNLNVSTKDVLEMESRLNGHDYSFDLTGDDDDE 191

Query: 586 SHLG--DFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +      ++EDKN   A+       Q+N++      L+SL  R + ++  R+        
Sbjct: 192 NCFAPVQYLEDKNADVALLVEVENSQSNMKRQLHSALSSLDERSQDIISSRWL--NEPKA 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           TL ++  ++ ++ ER+RQ+EA AI+KL+   +
Sbjct: 250 TLHDLAARYSISAERVRQLEANAIKKLQSNMQ 281


>gi|331028036|ref|YP_004421751.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
 gi|294805649|gb|ADF42487.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
          Length = 299

 Score =  141 bits (355), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 85/294 (28%), Positives = 141/294 (47%), Gaps = 28/294 (9%)

Query: 411 NEIKSISVETGISISEFRHIVSMV--------------------RKGECEASIAKKEMVE 450
           + +K I     ++ +E       +                    R        AK+ M+ 
Sbjct: 6   DYLKQIGRHPLLTATEEIEYSRQIQAMLAVQAEHPDSSTHTHQQRVIIRRGQRAKERMIV 65

Query: 451 ANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            NLRLV+++AKKY  R   L+ LDL+Q+GN+GL +A E FD   GYKFSTYA WW++Q+I
Sbjct: 66  RNLRLVVTIAKKYVKRCTSLEMLDLVQDGNMGLARATELFDPSRGYKFSTYAYWWIRQSI 125

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +R + D+   IR+P+H  +K+ K             + PT  E A  +      ++  L 
Sbjct: 126 SRGLQDRDRMIRLPIHRHEKVIKARAYMNHQLAMTGKMPTIAECAAAVDADPHELQASLV 185

Query: 569 ITKEPISLETP-IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           + ++  SL+    G +D S + D I D  ++   D  +    RE     +  L+  E+ +
Sbjct: 186 MAQDVCSLDAKASGRDDLSPILDLIPDPASLHKDDEYLIE--REILHDAINMLSEDEQDI 243

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP---SRSKKLRS 678
           +R   G+G     TL ++G++  V+RE IRQ   KA+ K++       +++LR 
Sbjct: 244 VRRHNGLGGAPKVTLGQLGQERGVSREAIRQKHTKAMNKVRQQIGRLTNERLRD 297



 Score = 41.7 bits (96), Expect = 0.37,   Method: Composition-based stats.
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPV  YL+++G   LL+   EI  +++I+A    M+A   E P +       R  +  G 
Sbjct: 2   DPVADYLKQIGRHPLLTATEEIEYSRQIQA----MLAVQAEHPDSSTHTHQQRVIIRRGQ 57

Query: 179 T 179
            
Sbjct: 58  R 58


>gi|213958518|gb|ACJ54680.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm3R]
          Length = 260

 Score =  141 bits (355), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 55/306 (17%), Positives = 110/306 (35%), Gaps = 47/306 (15%)

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++ 
Sbjct: 1   EMGTVELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL- 59

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                      G+    +G +    E       +    + + D + A   + D+      
Sbjct: 60  ----------SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDDDAEATTDDEEEAESG 109

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
           P             D+ +          +     +  L  +AE++               
Sbjct: 110 PDPVIAAQRFGAVSDQMEITRKALKKHGRGNKLAIAELVLLAELF--------------- 154

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
                                + L   + + LVE++     R+   E  +++L      +
Sbjct: 155 -------------------MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARM 195

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL +  G E+D  W        +G++   +      I++ + ++ ++  ETG++I+
Sbjct: 196 PRADFLRQFPGNEVDESWSDGLAK-GKGKYAEAIGRLQPDIIRCQQKLIALQTETGLTIA 254

Query: 426 EFRHIV 431
           E + I 
Sbjct: 255 EIKDIN 260


>gi|11078979|dbj|BAB17494.1| DNA-directed RNA polymerase subunit D [Pseudomonas cichorii]
 gi|11078981|dbj|BAB17495.1| DNA-directed RNA polymerase subunit D [Pseudomonas cichorii]
          Length = 269

 Score =  141 bits (355), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T + ++   D +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVEHILSEYDRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +     E++ D + +   S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPLDTKTAKADESDDDEDESGDASDDEEEAESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     ++ +          +     +  L  +AE++                   
Sbjct: 110 IAQQRFGAVAEQMEITRKALKKFGREDKNAIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRSALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIQRCQQKLTALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|282863440|ref|ZP_06272499.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561775|gb|EFB67318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 288

 Score =  141 bits (355), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 116/232 (50%), Gaps = 13/232 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM
Sbjct: 61  AYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAM 120

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V   I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+AK L +  E
Sbjct: 121 PTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVPELAKALGVSEE 180

Query: 562 GVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V   L +       SL++P  ++D     L D +  ++A            RE+   +L
Sbjct: 181 DVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGVEY-----RESLKPLL 235

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           A L PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 236 AKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLTQLRE 283


>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa]
 gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa]
          Length = 509

 Score =  141 bits (355), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 137/253 (54%), Gaps = 8/253 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++    + S+A++++  +N+RLV+S+A+KY N G +  DL+Q G IGL++  EKFD   G
Sbjct: 256 LQSKLIQCSLAREKLAMSNVRLVMSIAQKYDNMGAEMADLVQGGLIGLLRGIEKFDSSKG 315

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +K STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  K    P+ + IA
Sbjct: 316 FKISTYVYWWIRQGVSRALVDNSRTLRLPNHLHERLGLIRNAKIRLEEK-GVTPSIDRIA 374

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQAN- 608
           + L M    VR   +   +  SL+           G+    +I D    +     +    
Sbjct: 375 ESLNMSQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRPENNPWHGVDEWA 434

Query: 609 LRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+E   +++  +L  RE+ ++R+  G+      T E++ K+  ++RER+RQ+   A+ KL
Sbjct: 435 LKEEVNKLIDSTLQEREKEIIRLYHGLDQ-ECLTWEDISKRMGLSRERVRQVGLVALEKL 493

Query: 668 KHPSRSKKLRSFL 680
           KH +R +   + L
Sbjct: 494 KHAARKRNTEAML 506


>gi|257470234|ref|ZP_05634325.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064448|ref|ZP_07928933.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
 gi|313690124|gb|EFS26959.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
          Length = 260

 Score =  141 bits (355), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 85/263 (32%), Positives = 139/263 (52%), Gaps = 6/263 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +L I   IK IS    ++  E + I    +        A++++V +NLRLVIS+A+KYTN
Sbjct: 1   MLDISEYIKDISRYPLLTPEEEKDISIKAK---AGDKDAQEKLVTSNLRLVISIARKYTN 57

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G+  LDLIQEGN+GL++A EK++     +FSTY+ +W+KQ+I R I      IR P ++
Sbjct: 58  MGIPLLDLIQEGNMGLIRAVEKYEPEKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSYV 117

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            D I ++ +  +   NK    P+ EEI   L M  +   + +++ ++   +   +  E  
Sbjct: 118 YDGISRMKKYVQDYKNKNSHLPSIEEICSSLDMRKKEAERYIEVLEKGSCIGNEMYGEIA 177

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            +    I D      +   I  N      + +  L  +E  VL  R+G+      TL E+
Sbjct: 178 EYCSSIIFDDTFEDKV---IAKNSTIDLMKKVNKLPSKEREVLIYRYGLLDEKVLTLGEI 234

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G++  +T+ERIRQI+ +AI KL+
Sbjct: 235 GERMNLTKERIRQIQLEAIDKLR 257



 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 9/87 (10%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y++++    LL+ E E  I+ + +AG       L  S L    +I    +  +    L +
Sbjct: 7   YIKDISRYPLLTPEEEKDISIKAKAGDKDAQEKLVTSNLRL--VISIARKYTNMGIPLLD 64

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQK 210
           +I        E   G     E +  +K
Sbjct: 65  LI-------QEGNMGLIRAVEKYEPEK 84


>gi|11079049|dbj|BAB17529.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 116/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E  GD         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDTEDDDAEASGD--------DEDEVESGPDPVI 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  +S
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|295688294|ref|YP_003591987.1| RNA polymerase sigma 32 factor subunit RpoH [Caulobacter segnis
           ATCC 21756]
 gi|295430197|gb|ADG09369.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter segnis ATCC
           21756]
          Length = 295

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 125/274 (45%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +S  E   +    R  E +   A  +MV ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLTEIRKFPMLSKDEEFMLAQ--RWKEHQDPQAAHKMVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIA----KKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   +++   + +  PE+++    K   +  E +    +++    SL  P+  
Sbjct: 133 KLFFNLRKAKSQIAAFQEGDLRPEQVSAIATKLGVLDSEVISMNRRLSGPDASLNAPLRS 192

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR----ETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  S   D++ D+  VS      +   +          +  LT RE  +L        + 
Sbjct: 193 DSESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTE--RRLKDD 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLEE+  Q+ V+RER+RQIE +A  KL+   R
Sbjct: 251 PTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMR 284


>gi|251797866|ref|YP_003012597.1| sporulation sigma factor SigG [Paenibacillus sp. JDR-2]
 gi|247545492|gb|ACT02511.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. JDR-2]
          Length = 260

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 142/270 (52%), Gaps = 18/270 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + ++     A  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFTALQTQNEWA--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    ++N+  REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQVRDSLTNQNSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D    +   S I+          +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDDK--NKDVSWIEEI---ALREAMHKLNDREKMILSMRFFEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV  +  +++ ++ ++E  AI++++   ++
Sbjct: 231 EVADEIGISQAQVSRLEKSAIQQMQKHVKT 260


>gi|224007213|ref|XP_002292566.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971428|gb|EED89762.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 338

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 160/275 (58%), Gaps = 23/275 (8%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKK-----------YTNRGLQFLDLIQEG 477
           H V  +++    +  AK  ++EANLRLVI+VA++           +    +QF D  Q+G
Sbjct: 60  HTVPSLKQQIRRSQRAKAALIEANLRLVITVARQAVKKSPFRSSSHAASSVQFQDACQQG 119

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL +A EKFD  LG++FSTYA+WW+++ + +++ +QS T+R+P     KI+ +    R
Sbjct: 120 IIGLTRATEKFDPELGFRFSTYAIWWIQKEVAKNVNEQSRTVRVPGSAIKKINDIRIQER 179

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG------------DEDT 585
            + N++ R P+ +E+A+K  + VE +    +  KE  SL+  I             D+D 
Sbjct: 180 VLMNELGRRPSDDEVAEKCGLTVEKLNFYRQSAKEVKSLDKKIDSRTGKGSAASGGDDDG 239

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             +  F+ D    SP +   Q  +++   R++ +L+PRE+ V+R+RFG+      TL ++
Sbjct: 240 KTMEIFVRDTEHPSPSELIDQQMMQQDIRRLVKTLSPREQAVIRLRFGLDDGKPQTLGDI 299

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G++F V +ERI++IEA+A+ KL+ PSRS  ++ ++
Sbjct: 300 GEKFGVEKERIKKIEARALLKLRQPSRSSVVKCYV 334


>gi|332753462|gb|EGJ83842.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 215

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 139/207 (67%)

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  ++
Sbjct: 1   MLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKEL 60

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L 
Sbjct: 61  NVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALL 120

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D + D+    P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++ 
Sbjct: 121 DILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREI 180

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +TRER+RQI+ + +R+L+   +++ L
Sbjct: 181 GLTRERVRQIQVEGLRRLREILQTQGL 207


>gi|319408110|emb|CBI81763.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 308

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 67/278 (24%), Positives = 124/278 (44%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEIRRFPMLKPKEEYMLAKRYR--EHDDPKAAHKLVTSHLRLVAKIAIGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGNIGLM+A ++F+   G++ +TYAMWW+K +I   +      +++      K
Sbjct: 74  PIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + + N        +EIA +L +  + V  +        SL  P+  +
Sbjct: 134 RLFFNLRKLKNKLQALDNGDLNAEQVKEIATRLNVTEDEVVSMNHRLSGDTSLNAPLRTK 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +   +   D++ D +         Q  L   R      + +L  RE+ + +       + 
Sbjct: 194 EGEKTEWQDWLVDDSNSQEQILIEQDELENRRSMLIHAIDNLNEREKHIFKA--RRLSDE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+   F ++RER+RQIE +A  K+++  ++  L
Sbjct: 252 SLTLEELSNTFNISRERVRQIEMRAFEKVRNSIKAAIL 289


>gi|239934564|emb|CAR94596.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 95/270 (35%), Gaps = 46/270 (17%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
            DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  G
Sbjct: 1   TDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTYNFMLNQYEQVKAG 60

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
              L +II            GF             +          +E   D E      
Sbjct: 61  QGRLVDII-----------TGFIDPNAPDEIAAPVNPKLAAAAAPAEEESEDEEGEGGSE 109

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
            ++  +    PE A     ++ +        ++       P                   
Sbjct: 110 DEETLETGPDPEEAARRFLSISKQHQQVVKAMAEDRTGKDP------------------- 150

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                          K   L++K+      L L+    D L+ QL D    I + E +++
Sbjct: 151 ---------------KAVKLRKKVAGEFMELKLSPKMFDALIAQLRDNVAEIRNLEKQIM 195

Query: 358 RLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
            L     G+ R  F+      E +  W+  
Sbjct: 196 ILCVRDAGMPRKDFISTFPKNETNTKWLDK 225


>gi|115522843|ref|YP_779754.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisA53]
 gi|115516790|gb|ABJ04774.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           BisA53]
          Length = 299

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 122/273 (44%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLAEIRKFPMLEPQQEYMLAKRWR--EHDDRDAAHHLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IA +L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDMHPDQVKLIATRLGVTEQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +       A    L   R      +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDHSPSQEAVMAEHEELDHRRAALNGAIGVLNPRERRIFEARRLAD--DP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVK 284


>gi|294631337|ref|ZP_06709897.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292834670|gb|EFF93019.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 379

 Score =  141 bits (355), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 120/241 (49%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +++G  + +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 142 LRALKEGSPQYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 201

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 202 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 261

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 262 ELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 317

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 318 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 372

Query: 669 H 669
            
Sbjct: 373 E 373


>gi|2706544|emb|CAA75859.1| Sig1 [Sinapis alba]
          Length = 481

 Score =  141 bits (354), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 142/255 (55%), Gaps = 8/255 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 226 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNMGAEMSDLVQGGLIGLLRGIEKFDSS 285

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 286 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 344

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQA 607
           IA+ L M  + VR   +   +  SL+           G+    +I D    +       A
Sbjct: 345 IAESLNMSQKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRLENNPWHGYDA 404

Query: 608 N-LRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L++  +++++ +L  RE  ++R+ +G+      T E++ ++  ++RER+RQ+   A+ 
Sbjct: 405 LALKDEVSKLISVTLGEREREIIRLYYGLDK-ECLTWEDISQRIGLSRERVRQVGLVALE 463

Query: 666 KLKHPSRSKKLRSFL 680
           KLKH +R +K+ + +
Sbjct: 464 KLKHAARKRKMEAMI 478


>gi|118578560|ref|YP_899810.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501270|gb|ABK97752.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 292

 Score =  141 bits (354), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 73/263 (27%), Positives = 121/263 (46%), Gaps = 9/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E R     +R  E +   A   +V +NLR V+ +A +Y N G++ L
Sbjct: 15  YLAEIRKFNLLSEEEERSCA--IRFYEEKDLEAAHTLVTSNLRYVVKIASEYRNYGMKML 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLM A  KF+     +  +YA+WW++  I   I      I+I      R   
Sbjct: 73  DLIQEGNIGLMMAVRKFNPYRKIRLISYAVWWIRAYIQNYIVSAWSLIKIGTTQAQRKLF 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           + + +T   +      +    EIA  L +P   V  + +  K  +SL+  I + D     
Sbjct: 133 YGLRKTKEALLRMTGSDNDAAEIASMLQVPDHEVIDMEQRLKGEVSLDCQIVESDGLTFL 192

Query: 590 DFIEDK--NAVSPLDSAIQA-NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           + I D   N    L    Q   +++   + +  L  +E  ++     I  +   TL+++ 
Sbjct: 193 ETIADDRMNQEELLGENQQELQVKQRVIKAMEGLNEKERYIVEH--RITSDEPLTLQDIA 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
             F ++RER+RQ+E +A+ KLK 
Sbjct: 251 SHFSISRERVRQLEERALAKLKK 273


>gi|158833975|gb|ABW81793.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833979|gb|ABW81795.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  141 bits (354), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 76/227 (33%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLSEIGYSPLLTAAEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTY  WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHV 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L+ L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLSELSTKQREVLARRF 225



 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLSEIGYSPLLTAAEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|149908704|ref|ZP_01897365.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
 gi|149808246|gb|EDM68185.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
          Length = 284

 Score =  141 bits (354), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 134/233 (57%), Gaps = 2/233 (0%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A++ M+++NLRLVI++AK+Y +  L  +D+IQEGN GL+ A EKFD   G++FS
Sbjct: 37  NEGDEKARQRMIQSNLRLVINIAKRYQHTSLPLVDIIQEGNTGLIHAVEKFDATKGFRFS 96

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+WW+K  I R I +QS TIR+P+H+     ++++TAR     ++       +A+ L 
Sbjct: 97  TYAVWWIKNNIERFIMNQSRTIRVPIHIGKVYKRILKTAREQELDLQCNHDVMTLAEFLE 156

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTR 615
           M    V +VL       SL+  I  +  S   L D +ED +   P D    A+       
Sbjct: 157 MQYAQVNEVLSYYFNEASLDKTIVTDRDSSTALVDMLEDYSICKPNDELEDADTLCYLNE 216

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           VL  L+ R+ +++ +RFG+G     TL  +G++  ++RERIRQI   +++K++
Sbjct: 217 VLGHLSERDRKIIELRFGLGEEDPLTLHVIGERLSMSRERIRQIINLSLQKIQ 269


>gi|225462725|ref|XP_002268709.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|302143685|emb|CBI22546.3| unnamed protein product [Vitis vinifera]
          Length = 518

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 86/313 (27%), Positives = 148/313 (47%), Gaps = 14/313 (4%)

Query: 379 LDPHWVSY----AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM- 433
           +   W            E  W   +   +  +L++++ ++   +    +  E    +SM 
Sbjct: 208 VSLDWKKMKIPPVLPPSEHAWLFKLMQPMKGLLEVKDNLQK-DLGREPTDGELAEAMSMS 266

Query: 434 ---VRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEK 487
              VR+       A+ ++++ NLRLV+ V  KY      G +F DL Q G  GL+ A ++
Sbjct: 267 AVQVRRHMEVGQAARNKLIKHNLRLVLFVINKYFQEFANGPKFQDLCQAGVKGLITAIDR 326

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+    ++ STY ++W++ AI RS    S   R+   +     ++ R    +  K++R P
Sbjct: 327 FEPKRSFRLSTYGLFWIRHAIMRS-MTLSSFTRVSFGLESVRVEIQRAKLELLFKLQRLP 385

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EEI +K+ +  E   +V++ +K  +SL          ++ + I D   V        A
Sbjct: 386 TEEEIIEKVGISPERYHEVMRASKSVLSLHARHATTQEEYI-NGITDVEGVGGDRGRQLA 444

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR     VL SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KL
Sbjct: 445 LLRLALDDVLDSLKPKESLVMRQRYGLDGKGDRTLGEIAGNLSISREMVRKHEVKALMKL 504

Query: 668 KHPSRSKKLRSFL 680
           KHP+R   LR ++
Sbjct: 505 KHPARVDYLRQYI 517


>gi|3077738|dbj|BAA25787.1| SigB [Cyanidium caldarium]
          Length = 424

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 98/335 (29%), Positives = 165/335 (49%), Gaps = 49/335 (14%)

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
               ++   +    +   K+  E       T + +SE       VRK       A++ +V
Sbjct: 94  MATQDYCALMKQREELCAKLGREPTDTEWSTTVGVSEEE-----VRKRIERGRRARERLV 148

Query: 450 EANLRLVISVAKKY-------------TNRGLQFL----------------DLIQEGNIG 480
            +NLRLV+++A +Y             +  G+                   DLIQEG +G
Sbjct: 149 ASNLRLVLAIANRYKLRAVVCSAWKSRSKGGMDMPSHEKVRLQRQHNIFLGDLIQEGALG 208

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L++AAEKFD   G+KFSTYA WW++QAI R +++ S TIR+P H+ + + ++ R   R+ 
Sbjct: 209 LIRAAEKFDPSKGFKFSTYATWWIRQAIQRCVSEHSRTIRLPNHVTESLRQIYRMRARLQ 268

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-------------SLETPIGDEDTSH 587
           + +KR PT EE+A+   M ++ ++K+ +   E               SL      E    
Sbjct: 269 HVLKRPPTDEEVAEACNMTLKRLKKITQHAWETQTLSLEGPPNSEAHSLYKSQQGEAPLS 328

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVG 646
           +G  IE     +P ++  +  +RE    VL +L  +E  +LR+R+GI  +   H+ EE+ 
Sbjct: 329 IGSIIE-ATEETPEEALERNCMREDVECVLRTLPFQEREILRLRYGISDDERPHSTEELS 387

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            +F +    IR IE++A+RKL+HPS +  LR +++
Sbjct: 388 ARFQLPVHTIRLIESRALRKLRHPSLAAMLREYVN 422


>gi|288958414|ref|YP_003448755.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288910722|dbj|BAI72211.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 323

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 73/271 (26%), Positives = 123/271 (45%), Gaps = 13/271 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+       ++    R +   +   E     A +++V ++LRLVI +A+ +   GL
Sbjct: 40  LTRYIEESKRFPILAPDVERDLA--IAWRERGNPRALEQLVGSHLRLVIKIARGFGGYGL 97

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DL+ EGN+GLM+AA+KFD   G++F+TYA WW++ AI   I      +++      K
Sbjct: 98  SLVDLVAEGNVGLMQAAQKFDPQRGFRFATYATWWIRAAIQEYILHSWSLVKMGTTAAQK 157

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                  ++      +        T   IA +L +P  E V    ++     SL+  +  
Sbjct: 158 KLFFNLRRLKSQMAELEQGDLSPETVATIAAELDVPETEVVEMNRRLAANDSSLDATLST 217

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +  ++  + + D         A    L   R    + L  L PRE R+L        +  
Sbjct: 218 DGETNWLELLADDRPTQDAMLADADELALRRRLVGQALDRLDPRERRILFE--RRLKDDP 275

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            TLE + +QF V+RER+RQIE +A  KL+  
Sbjct: 276 STLEALSQQFSVSRERVRQIEVRAFEKLQKA 306


>gi|323456432|gb|EGB12299.1| hypothetical protein AURANDRAFT_12561 [Aureococcus anophagefferens]
          Length = 233

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 86/241 (35%), Positives = 128/241 (53%), Gaps = 11/241 (4%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A++ +V  N+RLV+SVAK+YT  GL   DL+QEG++GLM+AA KFD   G KFST
Sbjct: 2   RDGRSARQALVATNMRLVVSVAKRYTGLGLGLSDLVQEGSLGLMRAATKFDPARGCKFST 61

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAI R++A QS  IR+P+H+   + K+ R  R  +    REP+  E+A+ L M
Sbjct: 62  YACWWIQQAILRAVAFQSRLIRLPMHVHQDLAKLKRGTRDFTAAHGREPSDGELAELLEM 121

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               +RKV                 DT  L D +  K   +   +   A L E     + 
Sbjct: 122 TPAKLRKVRAAA----------RQGDTLKLEDTLASKE-PTGETAVELALLHEDLHAAMD 170

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L   E+RV+ +R+G+      T  +V      ++E +R+ E +AIRKL+ P     L  
Sbjct: 171 DLDADEKRVISLRYGLEDGVPCTPAQVAASCAESKEWVRRCEMRAIRKLRKPHHLMTLGH 230

Query: 679 F 679
           +
Sbjct: 231 Y 231


>gi|11078989|dbj|BAB17499.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 268

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDDDAEATDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +     A++   R   +   + IA                      
Sbjct: 110 AAQRFGAVADQMEITRK---ALKKHGRGNKLAIAELIA---------------------- 144

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 145 ----------LAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|158833951|gb|ABW81781.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833953|gb|ABW81782.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833955|gb|ABW81783.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833957|gb|ABW81784.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833961|gb|ABW81786.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833965|gb|ABW81788.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833981|gb|ABW81796.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833983|gb|ABW81797.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833985|gb|ABW81798.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833989|gb|ABW81800.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 77/227 (33%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLGEIGYSPLLTAAEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L  L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLFELSTKQREVLARRF 225



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLGEIGYSPLLTAAEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|239934586|emb|CAR94607.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 101/270 (37%), Gaps = 47/270 (17%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSNYPLTYTFMLNQYEQVKA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L +II            GF             +          +    + E     
Sbjct: 61  GQGRLVDII-----------VGFIDPNAPDEIAAPVNPKLAAAAAPAEPEAEEEEEGGDS 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             ++  +    PE A                   A   +L  +++ +L+E          
Sbjct: 110 EDEEALETGPDPEEAARRF---------------ASIQKLHQQIVKSLEE---------- 144

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                           K + L++K+ +    L L+    D L+ Q+ +    + + E  +
Sbjct: 145 ----------KGLDDPKTQKLRKKVAQEFMELKLSPKMFDALIVQMREHVAEVRNLEKSV 194

Query: 357 LRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           + L     G+ R  F+      E +  W+ 
Sbjct: 195 MMLCVRDAGMPRKDFITTFPKNETNIKWLD 224


>gi|29830729|ref|NP_825363.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607842|dbj|BAC71898.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 307

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 61  LSRSLFLRLAALDESSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 119

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 120 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 179

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 180 KLDRSPTVAELAAVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 239

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 240 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 290

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 291 RLLTRTLAQLRE 302


>gi|260906263|ref|ZP_05914585.1| RNA polymerase, sigma 32 subunit, RpoH [Brevibacterium linens BL2]
          Length = 903

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 92/306 (30%), Positives = 141/306 (46%), Gaps = 46/306 (15%)

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF------------------ 427
             KD  + E +  +    D+   +   +K I     +S +E                   
Sbjct: 556 LVKDADDDEPQELLRSVTDTDDLLGVYLKQIGQYPLLSAAEEVAVAKRIEAGMYATHVLS 615

Query: 428 ------RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
                 R     +   + + + A +EMV +NLRLV+S+AK++    L  LDLIQEGN+GL
Sbjct: 616 LGQYQTRRERRALEWVKADGAAAYEEMVTSNLRLVVSIAKRFNRSKLDLLDLIQEGNLGL 675

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A +KFD+  G KFSTYA WW++Q I R I D + TIR+P+H+ +K            +
Sbjct: 676 VRAVQKFDYTKGNKFSTYATWWIRQGIDRGIGDTAKTIRLPIHLFEKA-----------S 724

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-------LGDFIED 594
           +       +E           V + L++  +P+SLE  +  +   H         D I D
Sbjct: 725 EFWNCMRDDESRAACDHDHSKVEQALRM--QPVSLEGYLELQWDGHYAESLMSFDDRIAD 782

Query: 595 KN--AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +    +P    +   L ET   V+ SL  RE  ++R RFG       TL+ +G +F VT
Sbjct: 783 PDVFTDNPETKIVDGELLETVNSVVDSLPAREAEIIRRRFGWNGEPPQTLDAIGNRFAVT 842

Query: 653 RERIRQ 658
           RERIRQ
Sbjct: 843 RERIRQ 848



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
           +      DE+ +   + L   A +      +    +   TDD + +YL+++G   LLS  
Sbjct: 539 LPDQSGADEQPASKKIVLVKDADDDE---PQELLRSVTDTDDLLGVYLKQIGQYPLLSAA 595

Query: 138 GEIAIAKRIEAGR 150
            E+A+AKRIEAG 
Sbjct: 596 EEVAVAKRIEAGM 608


>gi|158833959|gb|ABW81785.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 75/227 (33%), Positives = 140/227 (61%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLSEIGYSPLLTAAEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI +P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIHLPIHI 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +++K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELAHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L  L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLFELSTKQREVLARRF 225



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLSEIGYSPLLTAAEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|154252606|ref|YP_001413430.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156556|gb|ABS63773.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 340

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 66/275 (24%), Positives = 128/275 (46%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E E + A  ++V ++LRLV  +A  Y   GL
Sbjct: 54  LSRYLQEIRKFPMLEPQEEYMLAKRWR--EHEDTEAAHQLVTSHLRLVAKIAMGYRGYGL 111

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 112 PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 171

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   ++    + +  PE+   I+ +L +  + V     +++    SL  P+  
Sbjct: 172 KLFFNLRKVKGQIQAIEEGDLHPEQVKVISDRLGVTEDEVISMNRRLSGPDNSLNAPLRQ 231

Query: 583 E-DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + +     D++ D  A           L   RE     +A+L  RE  +L        + 
Sbjct: 232 DSEGGEWQDWLVDDTADQEATLGEAEELDQRREMLAAAMATLNEREMHILTE--RRLKDE 289

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLE++ +++ ++RER+RQIE +A  KL+   ++
Sbjct: 290 PATLEDLSQEYGISRERVRQIEVRAFEKLQKAMKN 324


>gi|55274976|gb|AAV49287.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 83/204 (40%), Positives = 139/204 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCV 651
           L  RFG+      TLE+VG++  +
Sbjct: 181 LARRFGLLGYEAATLEDVGREIGL 204


>gi|11078993|dbj|BAB17501.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 121/315 (38%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + E D + A   + D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAAEIPPPVDPKAAKADDETDDDEAEASTDDEEEVESGP--- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R+            K  + 
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------ELARKALK---------KHGRG 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 SKQATAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|292398068|gb|ADE27982.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 272

 Score =  141 bits (354), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 117/318 (36%), Gaps = 48/318 (15%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II       
Sbjct: 1   LLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII------- 53

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                GF    E             +  +D    E + E     S DD       PE A 
Sbjct: 54  ----SGFIDPNEADDVAPTATHIGSELGEDDLADEDEDEDDDGDSSDDEGDGGPDPEVAR 109

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
               +L    + +  ++                                   QK+ ++  
Sbjct: 110 EKFGDLRAQYEVTRLSI-----------------------------------QKNGRAHE 134

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 135 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 194

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 195 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 253

Query: 432 SMVRKGECEASIAKKEMV 449
             +  GE +A  AKKEMV
Sbjct: 254 RRMSIGEAKARRAKKEMV 271


>gi|158833949|gb|ABW81780.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  141 bits (354), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 77/227 (33%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLGEIGYSPLLTAAEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVNRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L  L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLFELSTKQREVLARRF 225



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLGEIGYSPLLTAAEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|55274937|gb|AAV49269.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score =  141 bits (354), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 83/204 (40%), Positives = 138/204 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDNDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFC 650
           VL  RFG+      TLE+VG++  
Sbjct: 181 VLARRFGLLGYEAATLEDVGREIG 204


>gi|11079053|dbj|BAB17531.1| DNA-directed RNA polymerase subunit D [Pseudomonas tolaasii NCPPB
           2192]
 gi|11079061|dbj|BAB17535.1| DNA-directed RNA polymerase subunit D [Pseudomonas tolaasii]
          Length = 269

 Score =  141 bits (354), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 118/315 (37%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   + +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYNRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E+ GD         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDSEDDDAESSGD--------DEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  ++
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRT 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|3021678|dbj|BAA25359.1| RNA polymerase sigma-70 factor [Pseudomonas fluorescens]
 gi|11079001|dbj|BAB17505.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
 gi|11079013|dbj|BAB17511.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                      + +     +   D ++ A    +D  +    P  
Sbjct: 59  IDPDDGI--------APPAAEVPPPVDPKAVKADDDAEDDDAEASTDDEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  +S
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|319403703|emb|CBI77288.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 305

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 125/278 (44%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R+       A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEIRRFPVLEPQEEYMLAKRYREYN--DPKAAHKLVTSHLRLVAKIAIGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGNIGLM+A ++F+   G++ +TYAMWW+K +I   +      ++I      K
Sbjct: 74  PIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + + N        +EIA +L +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRLKVTEDEVVSMNRRLNGDASLNAPLLTN 193

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIGMNT 638
             ++    D++ D +         Q  L          + +L  RE+R+ + R       
Sbjct: 194 KGESYEWQDWLVDDSNNQEQTLIEQNELENRYSILIHAMDNLNEREKRIFKARRLRD--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIEA+A  K+++  ++  L
Sbjct: 252 PLTLEELSNEFNISRERVRQIEARAFEKIQNFIKTSAL 289


>gi|11079055|dbj|BAB17532.1| DNA-directed RNA polymerase subunit D [Pseudomonas tolaasii]
          Length = 269

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 118/315 (37%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   + +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYNRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E+ GD         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDSEDDDAESSGD--------DEDEFESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  ++
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRT 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|258488942|gb|ACV72477.1| RpoD [Xanthomonas campestris pv. campestris]
          Length = 260

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 115/299 (38%), Gaps = 46/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGTFPLSTELLLSDYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++      D    + D +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDADED 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                 +     + P+  E                           V   ++ +A  Y +
Sbjct: 110 GDDDAAEEEAGPTGPDPVE---------------------------VATRMENLANEYAK 142

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 143 FKKAYVKYGAEHKNVA------KAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 196

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 197 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIVSEQQ 254


>gi|73490229|dbj|BAE19789.1| sigma-70 factor [Pseudomonas fluorescens]
          Length = 269

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 55/316 (17%), Positives = 114/316 (36%), Gaps = 48/316 (15%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++    
Sbjct: 1   TVELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL---- 56

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                   G+    +G +    E       +   +  + + +       ++  +    P 
Sbjct: 57  -------SGYIDPDDGIAPPAAEVPPPVDTKVKAEGDDEEDDKEDSGEDEEEVESGPDPI 109

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A      + +  + +   L                                   +K  +
Sbjct: 110 IAAQRFGAVSDQMEIARKAL-----------------------------------KKHGR 134

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRD 368
            S +       L +L   + L   + + LVE++    +R+   E  +++L      + R 
Sbjct: 135 GSKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRT 194

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FL    G E+D  W   A    + ++   +      I++ + ++ ++  ETG+ I+E +
Sbjct: 195 DFLRLFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEIK 253

Query: 429 HIVSMVRKGECEASIA 444
            I   +  GE +A  A
Sbjct: 254 DINRRMSIGEAKARRA 269


>gi|166710450|ref|ZP_02241657.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 282

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 14  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 72  PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 132 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 189

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 190 HGPPSPVSYLVANEEDPSQAYERHDSEDNHLQLLREGMAGLDTRSRDIVKRRW-LDSDSK 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 249 VTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|323137119|ref|ZP_08072198.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322397477|gb|EFX99999.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 127/277 (45%), Gaps = 12/277 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E E   A +E+V ++LRLV  +A  Y   GL
Sbjct: 12  LARYLAEIRRFPMLEPQQEYMLAKRWR--EHEDPKAAQELVTSHLRLVAKIAMGYRGYGL 69

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 70  PIGEIISEGNVGLMQAVKRFEPDRGFRLATYAMWWIRASIQEYILRSWSLVKMGTTASQK 129

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R+S   + +  PE    IA +L +  + V ++ +      SL  P+ +E
Sbjct: 130 KLFFNLRKAKSRISAFEEGDMRPENVEKIATRLGVSQQDVIEMNRRMGGDASLNAPLREE 189

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +         Q    N  +     L  L PRE R+   R         
Sbjct: 190 GEGEWQDWLVDDSEDQERILVAQEENNNRLKALRGALDVLNPRERRIFEARRLAD--DPV 247

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLE++ ++F V+RER+RQIE +A  K++   RS   R
Sbjct: 248 TLEQLSEEFGVSRERVRQIEVRAFEKVQAAVRSGVAR 284


>gi|73490232|dbj|BAE19790.1| sigma-70 factor [Pseudomonas fluorescens]
          Length = 269

 Score =  140 bits (353), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 59/316 (18%), Positives = 119/316 (37%), Gaps = 48/316 (15%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++    
Sbjct: 1   TVELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL---- 56

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                   G+    +G +    E       +    + + D E A     ++ ++    P 
Sbjct: 57  -------SGYIDPDDGIAPPAAEVPPPIDAKAVKADDDTDDEDAEASDDEEEAESGPDPI 109

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A      + +  + +   L                                   +K  +
Sbjct: 110 IAAQRFGAVADQMEITRKAL-----------------------------------KKHGR 134

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRD 368
           ++ +       L +L   + L   + + LVE++     R+   E  +++L      + R 
Sbjct: 135 NNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRA 194

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI+E +
Sbjct: 195 DFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLSALEAETGLSIAEIK 253

Query: 429 HIVSMVRKGECEASIA 444
            I   +  GE +A  A
Sbjct: 254 DINRRMSIGEAKARRA 269


>gi|269958772|ref|YP_003328559.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
 gi|269848601|gb|ACZ49245.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
          Length = 307

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 68/278 (24%), Positives = 130/278 (46%), Gaps = 14/278 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + + I  +     +S  E + +          +     ++V ++LRLV+ VA  + N G
Sbjct: 31  DLVSYIAQVRTFPVLSEEEEKRLAE--NWYRRGSVADAHKLVTSHLRLVVKVAMGFKNYG 88

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  ++LI EGNIGLM+A ++F+  LG + +TYA+WW+K +I   I      IR+      
Sbjct: 89  LPLMELIMEGNIGLMQAVKRFNPDLGSRLATYAVWWIKASIKDYILRSWSCIRVGTTQAQ 148

Query: 528 K--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIG 581
           K     + +  +R+        T +E   IA++ A   E V R         +SL  P+ 
Sbjct: 149 KKLFFSLRKIKKRLLG-CGTSMTQKEVKTIAEECATSEEEVERMDRFFASRDVSLNEPVH 207

Query: 582 DEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNT 638
            E +  L D +     +  +   +  ++ ++++     L++L  R   +           
Sbjct: 208 GESSVELQDLVPSSLPSQEAMYLADEESAIKKSMFDAALSTLDHRHRDIF--TRRRLQER 265

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLE++ +++ V++ER+RQIE +A+ K+K    + ++
Sbjct: 266 PDTLEKLSEKYGVSKERVRQIELQALCKIKTFIEANRV 303


>gi|55274915|gb|AAV49259.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274917|gb|AAV49260.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274923|gb|AAV49263.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
 gi|55274925|gb|AAV49264.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274928|gb|AAV49265.1| RNA polymerase subunit sigma-38 [Shigella sonnei]
 gi|55274932|gb|AAV49267.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274939|gb|AAV49270.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274949|gb|AAV49274.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274955|gb|AAV49277.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274957|gb|AAV49278.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274959|gb|AAV49279.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274961|gb|AAV49280.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274974|gb|AAV49286.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274980|gb|AAV49289.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274991|gb|AAV49293.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274993|gb|AAV49294.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 83/204 (40%), Positives = 138/204 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFC 650
           VL  RFG+      TLE+VG++  
Sbjct: 181 VLARRFGLLGYEAATLEDVGREIG 204


>gi|34499661|ref|NP_903876.1| RNA polymerase factor sigma-32 [Chromobacterium violaceum ATCC
           12472]
 gi|34105511|gb|AAQ61866.1| RNA polymerase sigma-32 factor [Chromobacterium violaceum ATCC
           12472]
          Length = 287

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 135/264 (51%), Gaps = 7/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    ++  +   + +  ++       A ++MV ++LR+V+SV++ Y   GL
Sbjct: 16  LEQYIQAVNSIPMLTPEQETELATRFQQ--ENDLEAARQMVLSHLRVVVSVSRGYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q  DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   I      +RI      +
Sbjct: 74  QQADLIQEGNIGLMKAVKRFEPGRGVRLFSFAIHWIKAEIHEFILRNWRLVRIATTKPQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + +       E   + IA+ L +  E VR++ +++T + +SL     DED+  
Sbjct: 134 KLFFNLRSMKSGFSALSEQEAKSIAEDLGVKPEEVREMEIRMTGQDVSLLADSDDEDSYA 193

Query: 588 LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D++ D ++    +    A      E     L++L PR  R++  R+    ++  TL E
Sbjct: 194 PIDWLADSHSEPTRALERRAFDMLQSEGLEYALSTLDPRSRRIVEARWLAD-DSGATLHE 252

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +  +F V+ ERIRQIEAKA+ K+K
Sbjct: 253 LAAEFGVSAERIRQIEAKALSKMK 276


>gi|11079025|dbj|BAB17517.1| DNA-directed RNA polymerase subunit D [Pseudomonas azotoformans]
          Length = 269

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 116/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E  GD         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDSEDDDAEASGD--------DEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  ++
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|237809745|ref|YP_002894185.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
 gi|237502006|gb|ACQ94599.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
          Length = 284

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 133/268 (49%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    ++  + R +   ++        A +++V ++LR V+ +A+ Y+  GL
Sbjct: 17  LEGYIQAVNSIPMLTAEKERALAEQLQ--NDGDLEAARQLVMSHLRFVVHIARTYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 75  PQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWRMVKVATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +T +R+    + E     +A++L +  E V     +++    S +    D+  
Sbjct: 135 KLFFNLRKTKKRLGWFNQDEVRA--VAEELGVSPEDVTEMESRMSGLDHSFDGYDDDDSE 192

Query: 586 SHL--GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           S+     ++EDK+   A    ++    +        L  L  R ++++R R+ +  +   
Sbjct: 193 SNFAPAQYLEDKSSDLATVYENNNWDTHAEHRLAYALQGLDERSQQIVRARW-LDEDNKQ 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+  ++ V+ ER+RQ+E  A++KLK
Sbjct: 252 TLQELADRYGVSAERVRQLEKNALKKLK 279


>gi|23429485|gb|AAM97310.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 281

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 126/321 (39%), Gaps = 46/321 (14%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II   
Sbjct: 5   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--S 62

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P                         E DDV  T   I S            D   
Sbjct: 63  GFIDPN------------------------EADDVAPTATHIGSELSEDDLADEDEDEDE 98

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKD 307
           +   + +   DE +      ++                  E + ELR+  +   ++ QK+
Sbjct: 99  DEDGDGDDADDEGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKN 141

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            ++  + +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + 
Sbjct: 142 GRAHDETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMP 201

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E +  W  Y K   +      +  + D +L+   +++ I  ETG+SI++
Sbjct: 202 KKTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMDED-VLRAIGKLQQIEEETGLSIAQ 260

Query: 427 FRHIVSMVRKGECEASIAKKE 447
            + I   +  GE +A  AKKE
Sbjct: 261 IKDINRRMSIGEAKARRAKKE 281


>gi|289758832|ref|ZP_06518210.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714396|gb|EFD78408.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 170

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 83/170 (48%), Positives = 117/170 (68%)

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +  E V ++ +  +
Sbjct: 1   MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAR 60

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           EPISL+  IGDE  S LGDFIED  AV  +D+     L++    VL +L+ RE  V+R+R
Sbjct: 61  EPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLR 120

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           FG+      TL+E+G+ + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 121 FGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 170


>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa]
 gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa]
          Length = 499

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 135/253 (53%), Gaps = 8/253 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++    + S+A++++  +N+RLV+S+A+K  N G +  DL+Q G IGL++  EKFD   G
Sbjct: 246 LQSQLIQCSLAREKLAMSNVRLVMSIAQKNDNMGAEMADLVQAGLIGLLRGIEKFDSSKG 305

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           +K STY  WW++Q ++R++ +   T+R+P H+ +++  +     R+  K    P+ + IA
Sbjct: 306 FKISTYVYWWIRQGVSRALVENPRTLRLPNHLHERLGLIRNAKIRLEEK-GVTPSIDRIA 364

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQAN- 608
           + L M    VR   +   +  SL+           G+    +I D    +     +    
Sbjct: 365 ESLNMSQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRLENNPWHGVDEWA 424

Query: 609 LRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+E   +++ S L  RE  ++R+  G+      T E++ K+  ++RER+RQ+   A+ KL
Sbjct: 425 LKEEVNKLIDSALQEREREIIRLYHGLDK-ECLTWEDISKRMGLSRERVRQVGLVALEKL 483

Query: 668 KHPSRSKKLRSFL 680
           KH +R  KL + L
Sbjct: 484 KHAARKGKLEAML 496


>gi|147677561|ref|YP_001211776.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273658|dbj|BAF59407.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 259

 Score =  140 bits (353), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 68/259 (26%), Positives = 128/259 (49%), Gaps = 15/259 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++     +   E R ++   +      S A+ ++V  NL+LV ++ K++ NRG +  DL 
Sbjct: 9   NLPRFPLLKDREMRELLQKAK---AGDSYARDKLVNCNLKLVFNLVKRFQNRGYELEDLF 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G IGLMKA +KFD     KFSTYA+  +   I R + D    I++   +++K ++V +
Sbjct: 66  QIGCIGLMKAIDKFDVSYDVKFSTYAVPMIVGEIRRFLRD-DNPIKVSRSLKEKAYRVQQ 124

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
               ++ ++ REPT  E++ +L +  E V   L+  + P S+   +  +D    +L D I
Sbjct: 125 ARDLLTARLGREPTVGEVSAELGLSREEVVNALEAAQVPASIYETLHQDDGDPIYLLDQI 184

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           +                + T   +L  L  R+ ++L  RF      D T  ++ K+  ++
Sbjct: 185 KGSEEGDVPWLE-----KITVKELLNKLPERDRQILAWRFF----EDRTQSDIAKRLGLS 235

Query: 653 RERIRQIEAKAIRKLKHPS 671
           + ++ ++E +A++KLK   
Sbjct: 236 QVQVSRLERQALKKLKELM 254


>gi|319406710|emb|CBI80343.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 305

 Score =  140 bits (352), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 125/278 (44%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEIRRFPVLEPQEEYMLAK--RYHEYNDPKAAHKLVTSHLRLVAKIAIGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGNIGLM+A ++F+   G++ +TYAMWW+K +I   +      ++I      K
Sbjct: 74  PIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + + N        +EIA +L +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRLKVTEDEVVSMNRRLNGDASLNAPLLTN 193

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIGMNT 638
             ++    D++ D +         Q  L          + +L  RE+R+ + R       
Sbjct: 194 KGESYEWQDWLIDDSNNQEQTLIEQDELENRYSILIHAMDNLNEREKRIFKARRLRD--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIEA+A  K+K+  ++  L
Sbjct: 252 PLTLEELSNEFNISRERVRQIEARAFEKIKNFIKTSPL 289


>gi|156636391|gb|ABU92466.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  140 bits (352), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 66/196 (33%), Positives = 104/196 (53%), Gaps = 2/196 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +  + S +     E ++ +     L   + D LV +L     R+   E  ++
Sbjct: 8   QNLQLAVNEHGRDSAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIM 67

Query: 358 RLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           + A     + +  F+    G E +  W+       +  +   +    + I +   ++++I
Sbjct: 68  KSAVEIAKMPKKSFIALFTGNESNEEWLDQILA-SDKPYVEKIKLHEEDIRRSIAKLRAI 126

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET +S++  + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 127 EEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 186

Query: 477 GNIGLMKAAEKFDWCL 492
           GNIGLMKA +KF++  
Sbjct: 187 GNIGLMKAVDKFEYRR 202


>gi|158833993|gb|ABW81802.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 77/223 (34%), Positives = 140/223 (62%), Gaps = 3/223 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++ +E  +    V    C    +++ M+E+NLRLV+ ++++Y NRGL 
Sbjct: 6   QLYLGEIGYSPLLTAAEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYINRGLP 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  ++
Sbjct: 63  LLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKEL 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+     L 
Sbjct: 123 NVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAEKGLL 182

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           D + D+    P ++    +++++  + L  L+ ++  VL  RF
Sbjct: 183 DVLSDETDNDPENTTQNDDMKKSVVKWLFELSTKQREVLARRF 225



 Score = 43.7 bits (101), Expect = 0.095,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  +N G  LL
Sbjct: 6   QLYLGEIGYSPLLTAAEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY-INRGLPLL 64

Query: 182 REI 184
             I
Sbjct: 65  DLI 67


>gi|209407274|emb|CAP72522.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 277

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 63/320 (19%), Positives = 122/320 (38%), Gaps = 45/320 (14%)

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ELL+REGEI IAKRIE G   +M+++   P T   ++   + +      L +I  
Sbjct: 1   EMGTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYERVTTEGGRLSDI-- 58

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           L   I P+  G           Q+ E ++ +       + + D E     S+++      
Sbjct: 59  LSGYIDPDDDGA------AGPQQEVEPATPQTAAKPAADDKDDDEEDDSDSEEEEGDGGP 112

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
            PE A      + E  + +   L                                   +K
Sbjct: 113 DPEVARVRFGAVAEQLEAAKKAL-----------------------------------KK 137

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             + S +     ++L  L   + L   + D LVE++     ++   E  ++++      +
Sbjct: 138 HGRGSQQATDALQELATLFMPIKLIPKQYDALVERVRSALGQVRAQERAIMQICVRDARM 197

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL +    E D  W        + ++   +A   + I + + ++ ++  E  + I+
Sbjct: 198 PRADFLRQFPNNETDLGWADQLAG-GKSKYAEAIAARKEDIQRCQEKLLALEEECALLIT 256

Query: 426 EFRHIVSMVRKGECEASIAK 445
           + + I   +  GE +A  AK
Sbjct: 257 DIKDINRRMSIGEAKARRAK 276


>gi|325913818|ref|ZP_08176177.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325539893|gb|EGD11530.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 291

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  PLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 141 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 198

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +   + 
Sbjct: 199 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRW-LDSESK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|158833999|gb|ABW81805.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 81/227 (35%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+  C    +++ M+E+NLRLV+ +A++Y N
Sbjct: 45  LDATQLYLGEIGYSPLLTAEEE---VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGN 101

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +QS TIR+P+H+
Sbjct: 102 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTIRLPIHI 161

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+ EEIA++L  PV+ V ++L++ +   S+++P+G +  
Sbjct: 162 VKELNVYLRTARELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSE 221

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D +   P D+    +++ +  + L  L  ++  VL  RF
Sbjct: 222 KALLDILSDDSENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRF 268



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +        E S        +          +  +   D  ++YL E+G   LL+ E
Sbjct: 5   FDEESSVLGMFDEKSSMEDEILEDELEEDDLLLQNVTQRVLDATQLYLGEIGYSPLLTAE 64

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  EEVYFARRALCGDQQSRRRMIESNLRLVVKIARRYG-NRGLALLDLI 110


>gi|319405171|emb|CBI78776.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 305

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 71/280 (25%), Positives = 130/280 (46%), Gaps = 18/280 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEIRRFPILEPQEEYMLAK--RYHEHNDPKAAHKLVTSHLRLVAKIAIGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGNIGLM+A ++F+   G++ +TYAMWW+K +I   +      ++I      K
Sbjct: 74  PIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTANQK 133

Query: 529 IHKVVRTARRMSNKIKREPTPE-------EIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
             ++    R++ NK++   + +       EIA +L +  + V  + +      SL  P+ 
Sbjct: 134 --RLFFNLRKLKNKLQMLDSGDLNAQQVKEIATRLKVTEDEVVSMNRRLSGDASLNAPLL 191

Query: 582 DE--DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGM 636
               ++    D++ D +         Q  L        + + +L  RE+R+ + R     
Sbjct: 192 TNKGESYEWQDWLVDDSNNQEQILIEQDELENRYSLLIQAMDNLNEREKRIFKARRLRD- 250

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLEE+  +F ++RER+RQIEA+A  K+++  +   L
Sbjct: 251 -EPLTLEELSNEFNISRERVRQIEARAFEKVQNSIKISAL 289


>gi|91227498|ref|ZP_01261835.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262392915|ref|YP_003284769.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269968648|ref|ZP_06182645.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
 gi|91188522|gb|EAS74814.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262336509|gb|ACY50304.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269826735|gb|EEZ81072.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
          Length = 285

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 131/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        S      DED S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDEDDS 191

Query: 587 H-----LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++EDK+   A +   +  + +        LASL  R +R++R R+      
Sbjct: 192 SNAYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDD--E 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 250 KATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|54401900|gb|AAV34635.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 83/203 (40%), Positives = 137/203 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFC 650
           L  RFG+      TLE+VG++  
Sbjct: 181 LARRFGLLGYEAATLEDVGREIG 203


>gi|158833997|gb|ABW81804.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 80/227 (35%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+  C    +++ M+E+NLRLV+ +A++Y N
Sbjct: 45  LDATQLYLGEIGYSPLLTAEEE---VYFARRALCGDQQSRRRMIESNLRLVVKIARRYGN 101

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 102 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 161

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +++K+  EP+ EEIA++L  PV+ V ++L++ +   S+++P+G +  
Sbjct: 162 VKELNVYLRTARELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPLGGDSE 221

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D +   P D+    +++ +  + L  L  ++  VL  RF
Sbjct: 222 KALLDILSDDSENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRF 268



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +        E S        +          +  +   D  ++YL E+G   LL+ E
Sbjct: 5   FDEESSVLGMFDEKSSMEDEILEDELEEDDLLLQNVTQRVLDATQLYLGEIGYSPLLTAE 64

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  EEVYFARRALCGDQQSRRRMIESNLRLVVKIARRYG-NRGLALLDLI 110


>gi|158833967|gb|ABW81789.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833969|gb|ABW81790.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833971|gb|ABW81791.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833973|gb|ABW81792.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833977|gb|ABW81794.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833987|gb|ABW81799.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 75/227 (33%), Positives = 141/227 (62%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++ +E  +    V    C    +++ ++E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLSEIGYSPLLTAAEEIYFARRV---LCGDESSRRRVIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTY  WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHV 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L+ L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDNDPENTTQNDDMKKSVVKWLSELSTKQREVLARRF 225



 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+   EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLSEIGYSPLLTAAEEIYFARRVLCGDESSRRRVIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|262038022|ref|ZP_06011434.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747975|gb|EEY35402.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 258

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 93/264 (35%), Positives = 143/264 (54%), Gaps = 9/264 (3%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
            E +++  I   +  I     +S  E   ++  +R  E     A++ ++ +NLRLVIS A
Sbjct: 1   MEENNLNLISLYLSDIQKFNLLSKEEEYELLRRIR--EENDEQARQLLILSNLRLVISTA 58

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KK    GL  +DLI EGNIGL+KA  KFD+  G++FSTYA+WW+KQ+I ++I +    IR
Sbjct: 59  KKLLGNGLPLIDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQSIKKAIINTGRDIR 118

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           IP +  +++ KV +       K    P  E IAK++ +    V  +L   ++ ISL   I
Sbjct: 119 IPSYKYEQLSKVNKVITDYVAKYGESPPTEYIAKEVDLKESKVILLLNEFQDVISLNETI 178

Query: 581 GDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           G  D  +L D +   D      +     + +RE    +   LT RE  +L +R+G+  N 
Sbjct: 179 G--DNIYLEDIVGNTDDVEEKIIKEDQLSEMRELLENI---LTDREREILELRYGLYNNK 233

Query: 639 DHTLEEVGKQFCVTRERIRQIEAK 662
            HTL+E+G +  +TRER+RQIE K
Sbjct: 234 IHTLKEIGAKLNITRERVRQIEKK 257


>gi|55275000|gb|AAV49297.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 203

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 82/203 (40%), Positives = 137/203 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  L LI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFC 650
           L  RFG+      TLE+VG++  
Sbjct: 181 LARRFGLLGYEAATLEDVGREIG 203


>gi|111035800|emb|CAL29427.1| RNA polymerase sigma-32 factor [Wolbachia endosymbiont of
           Onchocerca volvulus]
          Length = 297

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 135/281 (48%), Gaps = 16/281 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I  +     +S  E   +     + +  +S    +++ ++L LV+ +A K+ N GL
Sbjct: 16  LMQYIAEVQKFPILSQEEETRLAKNWHQYKNISS--AHKLITSHLNLVVKIAMKFKNYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
             +DLI EGNIGLM A +KF+  LG++FSTYA+WW++ +I   I      I+I      R
Sbjct: 74  LLMDLIMEGNIGLMHAVKKFNPNLGFRFSTYAVWWIEASIKDFILKSWSFIKIGTTQAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-----EGVRKVLKITKEPISLETPIG 581
                + +  +R+     RE    E  K ++  +     + ++   ++  +  SL + + 
Sbjct: 134 KLFFSLRKIKKRILQYTNRETLSNEEIKAISNELAVSEGDVIQMSYRLAYKDQSLNSCLK 193

Query: 582 DEDTS--HLGDFIE--DKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGM 636
             D S   L D I     +      +  +  L+ET     LA+L  R   +   R+    
Sbjct: 194 VGDGSKKELQDMIPCNSVSQEVTYQNHEEKELKETILNNALANLNERSRDIFISRYLSEN 253

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
               TL+E+GK++ V+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 254 TQ--TLDELGKKYNVSRERIRQLAEQAMSKVKQYIQSESLK 292


>gi|225454597|ref|XP_002264928.1| PREDICTED: hypothetical protein isoform 1 [Vitis vinifera]
          Length = 507

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 141/260 (54%), Gaps = 8/260 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R   + ++    E S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  E
Sbjct: 247 LRMSRAELQSKLIECSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIE 306

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G+K STY  WW++Q ++R++ + S T+R+P H+ +++  +     R+  K    
Sbjct: 307 KFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEK-GIT 365

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLD 602
           P+ + IA+ L M  + VR   +   +  SL+              L  +I D    +   
Sbjct: 366 PSIDRIAECLNMSQKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENNPW 425

Query: 603 SAIQAN-LRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +    L++   +++  +L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+ 
Sbjct: 426 HGVDEWALKDEVNKLINTTLGERERDIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVG 484

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
             A+ KLK+ +R  ++ + L
Sbjct: 485 LVALEKLKNAARKGRMEAML 504


>gi|3021666|dbj|BAA25353.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079107|dbj|BAB17558.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 269

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRI+ G   +M ++   P T   ++   D +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIDEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   + +E + ++ +    D E  A+   D           
Sbjct: 59  IDPDDNIAAPTEEVPIPGAKAAAAKEESDDEEEESEGSDDEEEAESGPDPVV-------- 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ                     LQ  +   +K+ ++
Sbjct: 111 --------------AAQRFGAVSDQ---------------------LQATSKVLKKNGRT 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +     + L  L   + L   + ++LVE++ D    +   E  +++L      + R  
Sbjct: 136 HKESIEALQALADLFMPIKLVPKQFEVLVERVRDALNLLRQQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  W           W   +  +  +I+  + ++  +  ETG++++E + 
Sbjct: 196 FLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|28899727|ref|NP_799332.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260879104|ref|ZP_05891459.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|28807979|dbj|BAC61216.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|308089656|gb|EFO39351.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|328472446|gb|EGF43312.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus 10329]
          Length = 286

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 71/271 (26%), Positives = 131/271 (48%), Gaps = 17/271 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        S      D+D S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDDDDS 191

Query: 587 ------HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                     ++EDK+   A +   +  + +        LASL  R +R++R R+     
Sbjct: 192 ATSSYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDD-- 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 250 EKATLQDLADEFGVSAERIRQLEKNAMKKLK 280


>gi|258488864|gb|ACV72438.1| RpoD [Xanthomonas axonopodis pv. manihotis]
          Length = 261

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 116/299 (38%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +  L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDVAAIFTTFKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVXDQIISEQQ 255


>gi|11078975|dbj|BAB17492.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11079202|dbj|BAB17592.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  140 bits (352), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++   + +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYERVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +     +++ D E +   S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPLDAKAAKADDSDDDEEESGDASDDEEEAESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  L  +AE++                   
Sbjct: 110 IAQQRFGAVADQMEITRKALKKFGREDKNSIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRSALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIQRCQQKLTALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|55274951|gb|AAV49275.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 205

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 83/205 (40%), Positives = 139/205 (67%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V +
Sbjct: 61  QTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSR 120

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 121 MLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 180

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFC 650
            VL  RFG+      TLE+VG++  
Sbjct: 181 EVLARRFGLLGYEAATLEDVGREIG 205


>gi|258488878|gb|ACV72445.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488934|gb|ACV72473.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488986|gb|ACV72499.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489036|gb|ACV72524.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489040|gb|ACV72526.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489042|gb|ACV72527.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
          Length = 261

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 116/299 (38%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + +   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDDAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +  L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDVAAIFTTFKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|258488860|gb|ACV72436.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258488862|gb|ACV72437.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258488880|gb|ACV72446.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258488882|gb|ACV72447.1| RpoD [Xanthomonas axonopodis pv. manihotis]
 gi|258489014|gb|ACV72513.1| RpoD [Xanthomonas axonopodis pv. manihotis]
          Length = 261

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 116/299 (38%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +  L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDVAAIFTTFKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|328948870|ref|YP_004366207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328449194|gb|AEB14910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 272

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 86/271 (31%), Positives = 136/271 (50%), Gaps = 6/271 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I   +  + S+     +S  E   +   ++        A   +V +NLRLV+SVA ++ 
Sbjct: 2   EIDVAKGYLNSLKKYPLLSADEEIALAKRIK---SGDKEAFNLLVNSNLRLVVSVAGRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
                 +DLIQEGN+GLM AA+KFD   G +FSTYA  W+ Q I + I+  S  I +PVH
Sbjct: 59  KGAFCIMDLIQEGNLGLMVAAKKFDPAFGTRFSTYAYRWIVQRIMKFISANSSPILLPVH 118

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
               + ++ +       +  RE   +E+A    +  E +  VL+ +    SL+T + DE 
Sbjct: 119 RETLLRRIQKFQNIFFQQNGREAAVKELALFAGISEERLNDVLETSYTVASLDTEVADEG 178

Query: 585 TS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTL 642
            +  LGD I D  A SP + AI+ + +      + SLT  E+ VLR R+    +    +L
Sbjct: 179 KTVSLGDIIPDT-AFSPEELAIREDSKSCVNFFMDSLTGIEKSVLRHRYNFDYDLHSKSL 237

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            EVG+   +++E +RQ E +A + LK    S
Sbjct: 238 REVGRIVGLSQEAVRQAELRAKKHLKSAMES 268



 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL  +    LLS + EIA+AKRI++G       L  S L    ++      N G   + +
Sbjct: 9   YLNSLKKYPLLSADEEIALAKRIKSGDKEAFNLLVNSNLRL--VVSVAGRFNKGAFCIMD 66

Query: 184 II 185
           +I
Sbjct: 67  LI 68


>gi|224110206|ref|XP_002333134.1| predicted protein [Populus trichocarpa]
 gi|222834948|gb|EEE73397.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 88/358 (24%), Positives = 156/358 (43%), Gaps = 25/358 (6%)

Query: 344 DISKRIMHNEGELLRLAQSYGIKRD---------VFLERHQGRE--LDPHWVSY----AK 388
            + KRI        +L  S G ++D           +  +      +   W         
Sbjct: 158 SLEKRISLRIKNEEKLVSSAGKRKDRKNENEKIDDLVREYSASTDLVSLDWKKMKIPPVL 217

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS---MVRKGECEASIAK 445
              E  W   +   + ++L+++  ++         +   + I      VRK       A+
Sbjct: 218 TSSEHVWLFKLMQPMKALLQVKEHLQENLGGEPTDVELAKAINMDVLQVRKQIAVGRAAR 277

Query: 446 KEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++++ NLRLV+ V KKY      G +F D  Q G  GL+ A ++F+    ++ STY ++
Sbjct: 278 NKLIKHNLRLVLFVIKKYFQDFANGTKFQDFCQAGVKGLITAIDRFEPKRRFRLSTYGLF 337

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++ AI RS    S   R+   +     ++ +    +  ++KR+P  +EI +K+ +  E 
Sbjct: 338 WIRHAIIRS-MTLSSFTRVSFGLESIRSEIQKAKLELWFQLKRQPMEDEIIEKVRISPER 396

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             +V + +K  +SL +         +G   +         S   A LR     VL SL P
Sbjct: 397 YHEVTRASKPVLSLHSRHKTTQEEFIGGIADVDGGDDRRQS---ALLRLALDDVLDSLKP 453

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKHP+R   LR ++
Sbjct: 454 KESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHPTRVDYLRRYV 511


>gi|188574757|ref|YP_001911686.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188519209|gb|ACD57154.1| alternative sigma factor RpoH [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 282

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 14  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 72  PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 132 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 189

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 190 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRW-LDSDSK 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 249 VTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|325928799|ref|ZP_08189966.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
 gi|325540772|gb|EGD12347.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
          Length = 282

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E + +    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 14  LDAYIGAVHQIPVLSVDEEQDLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 72  PLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 132 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 189

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +  ++ 
Sbjct: 190 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRRW-LDSDSK 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 249 VTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|313901760|ref|ZP_07835186.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467966|gb|EFR63454.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 261

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 136/270 (50%), Gaps = 19/270 (7%)

Query: 408 KIRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           ++ N+++   V T     +S  + R +   +R        A++++V+ NLRLV+SV +++
Sbjct: 5   RMINKVEICGVNTAELPVLSNEQMRVLFRRMR---EGDEEARQQLVQGNLRLVLSVIQRF 61

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            +RG    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+  
Sbjct: 62  NHRGEPVDDLFQVGCIGLMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNT-PIRVSR 120

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            +RD  +K ++   +++++  REPT EEIA++L  P E V   L   ++P+SL  PI  +
Sbjct: 121 SLRDVAYKALQVRDQLTHRHGREPTLEEIAQELGQPREEVVHALDAIQDPVSLFEPIYQD 180

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D   + D + D            A         ++ L  RE+ ++  RF  G     T
Sbjct: 181 GGDPIFVVDQVSDDKQRDERWLETIA-----VREAMSRLDEREQLIITKRFYQG----KT 231

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             EV  +  +++ ++ ++E  A+++++   
Sbjct: 232 QMEVANEIGISQAQVSRLEKAALQRMRKYM 261


>gi|258488848|gb|ACV72430.1| RpoD [Xanthomonas axonopodis pv. glycines]
 gi|258489072|gb|ACV72542.1| RpoD [Xanthomonas axonopodis pv. glycines]
          Length = 260

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 116/299 (38%), Gaps = 46/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++      D    + D +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDED 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                 +     + P+  E                           V   ++ +A  Y +
Sbjct: 110 GDDDAAEEEAGPTGPDPVE---------------------------VATRMENLANEYAK 142

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 143 FKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 196

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 197 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIVSEQQ 254


>gi|49475181|ref|YP_033222.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49237986|emb|CAF27191.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 294

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 129/278 (46%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +     +   E   +    RK       A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLEEVRRFPMLEPQEEYMLAQRYRKH--NDLKAAHKLVTSHLRLVAKIAVGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLMKA ++F+   G++ +TYA+WW+K +I   +      +++    + +
Sbjct: 74  PIGEVISEGNVGLMKAVKRFEPERGFRLATYAIWWIKASIQEYVLRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R+      +   E   EIA +L +  + V  + +      SL  P+  +
Sbjct: 134 RLFFNLRKLKSRLQALDNGDLNAEQVKEIAIQLNVTEDEVVSMNRRLGGDTSLNAPLRTK 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +   S   D++ D +         Q  L   R   T  L +L  RE+R+ + R    +  
Sbjct: 194 EGENSEWQDWLVDDSNNQEQTLIEQNELENRRSMLTNALDNLNEREKRIFKARRLSDI-- 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIE +A  K+++  ++  L
Sbjct: 252 PLTLEELSSEFNISRERVRQIEMRAFEKIQNSIKASAL 289


>gi|197103427|ref|YP_002128805.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480703|gb|ACG80230.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 316

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 73/268 (27%), Positives = 121/268 (45%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +  I     +   E   +    R  E E   A   +V ++LRL   +A  Y   GL
Sbjct: 14  LRRYLTEIRKYPLLGKDEEYMLAKRWR--EHEDPEAAHRLVTSHLRLSAKIALSYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM A +KFD   G++ +TYA+WW++ AI   I      +++      K
Sbjct: 72  PLGEVISEGNLGLMHAVKKFDPDKGFRLATYAIWWIRAAIQEYILRSWSLVKLGTSAVQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   R+S     +  P++   IA +L +  E V     ++     SL +P+  
Sbjct: 132 KLFFNLRRAKARISALSDGDLKPDQVKAIASRLGVNEEEVVNMDRRLASRDASLNSPLAA 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +      D +ED+ AV P  +  +A       +   + + +L  RE R+         + 
Sbjct: 192 DAEQEWLDVLEDEAAVDPEAAVAEAEERALRMDLLAQAMQTLNARERRIFTA--RRLQDP 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              LE++ K F V+RER+RQIE +A  K
Sbjct: 250 PALLEDLAKDFGVSRERVRQIEVRAFEK 277


>gi|258488962|gb|ACV72487.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488964|gb|ACV72488.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
          Length = 260

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 116/299 (38%), Gaps = 46/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++      D    + D +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDED 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                 +     + P+  E                           V   ++ +A  Y +
Sbjct: 110 GDDDAAEEEAGPTGPDPVE---------------------------VATRMENLANEYAK 142

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 143 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 196

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 197 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 254


>gi|258488840|gb|ACV72426.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
          Length = 260

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 116/299 (38%), Gaps = 46/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++      D    + D +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDED 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                 +     + P+  E                           V   ++ +A  Y +
Sbjct: 110 GDDEAAEEEAGPTGPDPVE---------------------------VATRMENLANEYAK 142

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 143 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 196

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 197 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 254


>gi|158833963|gb|ABW81787.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 77/227 (33%), Positives = 140/227 (61%), Gaps = 3/227 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E  +    V    C    +++ M+E+NLRLV+ ++++Y N
Sbjct: 2   LDATQLYLGEIGYSPLLTAEEEIYFARRV---LCGDESSRRRMIESNLRLVVKISRRYIN 58

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 59  RGLPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +R AR +S+K+  +P+PEEIA++L  PV+ V ++L++ +   S++T  G+   
Sbjct: 119 VKELNVYLRAARELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDTSFGNAAE 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             L D + D+    P ++    +++++  + L  L+ ++  VL  RF
Sbjct: 179 KGLLDVLSDETDSDPENTTQNDDMKKSVVKWLFELSTKQREVLARRF 225



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+ E EI  A+R+  G       + ES L     I  R  +N G 
Sbjct: 3   DATQLYLGEIGYSPLLTAEEEIYFARRVLCGDESSRRRMIESNLRLVVKISRRY-INRGL 61

Query: 179 TLLREI 184
            LL  I
Sbjct: 62  PLLDLI 67


>gi|167730891|emb|CAJ29298.2| DNA-directed RNA polymerase subunit D [Pseudomonas thivervalensis]
          Length = 268

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPIDAKAAKADDDTDDDDAEASDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  ++
Sbjct: 110 AAQRFGAVADQMEITRKAL-----------------------------------KKHGRN 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 195 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|11078983|dbj|BAB17496.1| DNA-directed RNA polymerase subunit D [Pseudomonas cichorii]
          Length = 269

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++   + +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYERVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +     +++ D E +   S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPIDAKAAKADDSDDDEEESGDASDDEEEAESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  L  +AE++                   
Sbjct: 110 IAQQRFGAVADQMEITRKALKKFGREDKNSIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRSALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIQRCQQKLTALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|21233199|ref|NP_639116.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770141|ref|YP_244903.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|188993348|ref|YP_001905358.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. B100]
 gi|3046929|gb|AAC38329.1| heat shock sigma factor 32 [Xanthomonas campestris pv. campestris]
 gi|21115547|gb|AAM43471.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575473|gb|AAY50883.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|167735108|emb|CAP53320.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris]
          Length = 291

 Score =  140 bits (352), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E +++    R  +     A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFR--DELDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  PLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V ++  +++   I  +    ++D 
Sbjct: 141 KLFFNLRKSKTRLGWLNASEVTA--VAKDLNVSEREVMEMESRLSGRDIGFDASSDEDDD 198

Query: 586 ----SHLGDFIEDKNAVS--PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S +   + ++   S        + N  +     +A L  R   +++ R+ +   + 
Sbjct: 199 HGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRW-LDSESK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|258488874|gb|ACV72443.1| RpoD [Xanthomonas axonopodis pv. glycines]
          Length = 261

 Score =  140 bits (352), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 118/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVXDQIISEQQ 255


>gi|167730889|emb|CAJ29295.2| DNA-directed RNA polymerase subunit D [Pseudomonas
           frederiksbergensis]
          Length = 272

 Score =  140 bits (352), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/318 (18%), Positives = 115/318 (36%), Gaps = 47/318 (14%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++      
Sbjct: 1   ELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL------ 54

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                 G+    +G +    E       +    + + D + A   + D+      P    
Sbjct: 55  -----SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDDEAEASTDDEEEAESGPDPVI 109

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                    D+ +          +     +  L  +AE++                    
Sbjct: 110 AAQRFGAVADQMEITRKALKKHGRGNKLAIAELVLLAELF-------------------- 149

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVF 370
                           + L   + + LVE++     R+   E  +++L      + R  F
Sbjct: 150 --------------MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADF 195

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           L +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + I
Sbjct: 196 LRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDI 254

Query: 431 VSMVRKGECEASIAKKEM 448
              +  GE +A  AKKEM
Sbjct: 255 NRRMSIGEAKARRAKKEM 272


>gi|90422128|ref|YP_530498.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB18]
 gi|90104142|gb|ABD86179.1| sigma 32 (RpoH) [Rhodopseudomonas palustris BisB18]
          Length = 299

 Score =  140 bits (352), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 123/273 (45%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +        R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLAEIRKFPMLEPQQEYMFAKRWR--EHDDRDAAHHLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDMHPDQVKLIAKRLGVTEQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +       A    L   R   T  +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDHSPNQEAIMAEHEELDHRRAALTGAIGVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|258488856|gb|ACV72434.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488858|gb|ACV72435.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488884|gb|ACV72448.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488890|gb|ACV72451.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258488892|gb|ACV72452.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258488906|gb|ACV72459.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488936|gb|ACV72474.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488988|gb|ACV72500.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488990|gb|ACV72501.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258488992|gb|ACV72502.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489020|gb|ACV72516.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489022|gb|ACV72517.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489024|gb|ACV72518.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489026|gb|ACV72519.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489030|gb|ACV72521.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489032|gb|ACV72522.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489034|gb|ACV72523.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489046|gb|ACV72529.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489048|gb|ACV72530.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489050|gb|ACV72531.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489052|gb|ACV72532.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489054|gb|ACV72533.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489056|gb|ACV72534.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489058|gb|ACV72535.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489060|gb|ACV72536.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489062|gb|ACV72537.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489064|gb|ACV72538.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489066|gb|ACV72539.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489068|gb|ACV72540.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489070|gb|ACV72541.1| RpoD [Xanthomonas axonopodis pv. vignicola]
 gi|258489090|gb|ACV72551.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258489092|gb|ACV72552.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258489094|gb|ACV72553.1| RpoD [Xanthomonas citri pv. anacardii]
 gi|258489096|gb|ACV72554.1| RpoD [Xanthomonas citri pv. anacardii]
          Length = 261

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 118/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + +   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDDAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|258488838|gb|ACV72425.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488846|gb|ACV72429.1| RpoD [Xanthomonas axonopodis pv. glycines]
 gi|258488854|gb|ACV72433.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488866|gb|ACV72439.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
 gi|258488872|gb|ACV72442.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488876|gb|ACV72444.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
 gi|258488886|gb|ACV72449.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488910|gb|ACV72461.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488918|gb|ACV72465.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488944|gb|ACV72478.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488946|gb|ACV72479.1| RpoD [Xanthomonas axonopodis pv. citri]
 gi|258488972|gb|ACV72492.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
 gi|258488974|gb|ACV72493.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
          Length = 261

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 118/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|305644358|gb|ADM53780.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 114/176 (64%), Positives = 138/176 (78%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     
Sbjct: 61  LQEMGREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAL 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P D+A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VT ER
Sbjct: 121 PADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTVER 176


>gi|154500348|ref|ZP_02038386.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
 gi|150270853|gb|EDM98136.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
          Length = 256

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 138/264 (52%), Gaps = 11/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           ++ +++   V T  + + +    V+++++ +   + A++E++  NLRLV+SV +K++NRG
Sbjct: 1   MQGKVEICGVNTSKLKVLKNEETVALLKRTKEGDTAAREELIAGNLRLVLSVIQKFSNRG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + F+  L  +FSTY +  +   I R + D S   R+   MRD
Sbjct: 61  ENVDDLFQVGCIGLIKAIDNFNTDLDVRFSTYGVPMIVGEIRRYLRDNSSM-RVSRSMRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +KV++   +   + +REPT EEIAK L +  E V   +    +P+SL  P+  +    
Sbjct: 120 TAYKVLQAKEKFMAEHQREPTMEEIAKMLDLKREDVVFAMDAIMDPVSLYEPVYSDG--- 176

Query: 588 LGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            GD I   + V    +  ++ L        ++ L+ RE  +L +RF  G     T  EV 
Sbjct: 177 -GDAICVMDQVKDSKNTDESWLEHIALKEAISHLSDRERHILSLRFFEG----RTQMEVS 231

Query: 647 KQFCVTRERIRQIEAKAIRKLKHP 670
            +  +++ ++ ++E  AI K++  
Sbjct: 232 AEIGISQAQVSRLEKSAIWKIRKS 255


>gi|54401894|gb|AAV34632.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401896|gb|AAV34633.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274921|gb|AAV49262.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274982|gb|AAV49290.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 83/203 (40%), Positives = 138/203 (67%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQFC 650
           L  RFG+      TLE+VG++  
Sbjct: 181 LARRFGLLGYEAATLEDVGREIG 203


>gi|11079005|dbj|BAB17507.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
 gi|11079007|dbj|BAB17508.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 268

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 117/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDAKAAKADDDSDDDEAESSDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 135 NKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|92118359|ref|YP_578088.1| RNA polymerase factor sigma-32 [Nitrobacter hamburgensis X14]
 gi|91801253|gb|ABE63628.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter hamburgensis
           X14]
          Length = 299

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 125/274 (45%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +        R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLAEIRKFPMLEPHQEYMFAKRWR--EHDDREAAHHLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALEEGDMHPDQVKLIAKRLGVTEQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +       A    L   R+  T  +  L PRE R+   R        
Sbjct: 194 GEAGEWQDWLVDHSPTQEAIMAEHEELNHRRQALTGAMGVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++  +F V+RER+RQIE +A  K++   ++
Sbjct: 252 MTLEDLAAEFNVSRERVRQIEVRAFEKVQSAVKT 285


>gi|59714198|ref|YP_206973.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
 gi|59482446|gb|AAW88085.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
          Length = 294

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 85/268 (31%), Positives = 151/268 (56%), Gaps = 6/268 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---L 468
            +K I+    ++  E      + +K       A+  ++E+NLRLV+ VA KY  R    L
Sbjct: 23  YLKEINRYQLLTAEEELAYSRLYKK---GDVSARNTLIESNLRLVVKVANKYRKRNQTDL 79

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LD+I+EGN+GL+KA +KF+  LGY+FSTYA+WW++++I  ++ + S T+R+PVH+  +
Sbjct: 80  AILDIIEEGNLGLIKAIDKFNPELGYRFSTYAVWWIRESIESALFNHSRTVRLPVHITKE 139

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++  +R AR +S  +KREP+  +I+         V K++ +    ++  +   DE +   
Sbjct: 140 LNTYLRAARELSKSLKREPSIRDISTYCEEEQIKVSKIISLIPNQLTCHSACSDELSPKF 199

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            +   +  A+ P  S  Q NL    +  + SL  RE+ ++  R+G+      TLE++GK 
Sbjct: 200 FELSSNNKALEPDSSLSQNNLEMNLSSWIDSLNYREKEIIINRYGLFGCKVKTLEDLGKD 259

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             +++ER+RQI+++ + KL    +  KL
Sbjct: 260 LDLSKERVRQIQSETLIKLNTIFKKNKL 287



 Score = 41.4 bits (95), Expect = 0.57,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 2/94 (2%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT-FQALIIWR 171
            ++  +D   +YL+E+   +LL+ E E+A ++  + G      +L ES L     +    
Sbjct: 12  EEQGLNDSYSLYLKEINRYQLLTAEEELAYSRLYKKGDVSARNTLIESNLRLVVKVANKY 71

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
            + N     + +II+ E  +G       F+   G
Sbjct: 72  RKRNQTDLAILDIIE-EGNLGLIKAIDKFNPELG 104


>gi|291454068|ref|ZP_06593458.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291357017|gb|EFE83919.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 365

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++   G   A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 125 FIELRTLPAGGPEYAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 183

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 184 RFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQRHGRS 243

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+KL +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 244 PTVHELAEKLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 303

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 304 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 354

Query: 665 RKLKH 669
            +L+ 
Sbjct: 355 AQLRE 359


>gi|151413326|gb|ABS11159.1| RpoD [Pseudomonas oleovorans subsp. lubricantis]
          Length = 271

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/318 (18%), Positives = 116/318 (36%), Gaps = 48/318 (15%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   +M+++   P T   ++     +      L E++   
Sbjct: 1   GTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEVL--- 57

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                    G+    +G    +       KE    + ++ + E  +   +++       P
Sbjct: 58  --------SGYIDPDDGSVPDEAAAPVPVKEGAAAEASDEEEEDESGDDEEEEGDGGPDP 109

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           E A      + E +D     L                                   +K  
Sbjct: 110 EEAARRFTAVAEQQDKVLKAL-----------------------------------KKHG 134

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKR 367
           + S +       L +L   + L   + D LV ++ D   R+   E  +++L      + R
Sbjct: 135 RGSKQAIEELATLAELFMPIKLVPKQYDALVTKVRDALDRLRAQERAIMQLCVRDARMPR 194

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             FL    G E+D  W +      + ++   +      I + + ++  +  E  ++++E 
Sbjct: 195 ADFLRLFPGNEIDMDWAANLAK-GKAKYAEAIGALQADIQRCQQKLADLEAECNLTLAEI 253

Query: 428 RHIVSMVRKGECEASIAK 445
           + I   +  GE +A  AK
Sbjct: 254 KDINRRMSIGEAKARRAK 271


>gi|11079141|dbj|BAB17575.1| DNA-directed RNA polymerase subunit D [Pseudomonas balearica]
 gi|11079155|dbj|BAB17582.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp.]
          Length = 272

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 113/315 (35%), Gaps = 44/315 (13%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++   D +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYDRVVSEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G            +    +         + + + +  +  S ++       PE 
Sbjct: 59  IDPDDDGAAAPQEVEPVAPQVASKAAA-----DDKDDDEEDEESSDSDEEEGDGGPDPEV 113

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E    +   L                                   +K  + 
Sbjct: 114 ARIRFGAVAEQLAKAQKAL-----------------------------------KKFGRG 138

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     E L  L   + L   + D LVE++ D   RI   E  +++L      + R  
Sbjct: 139 SQQATDELEALAILFMPIKLVPKQYDALVERVRDALARIRAQERAIMQLCVRDARMPRAD 198

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E +  W   A    + ++   +A   D I   + ++  +  ETG+S+++ + 
Sbjct: 199 FLREFPNNETNLGWAE-AIASGKSKYAEAIAARKDDIRACQQKLVDLEQETGLSVADVKD 257

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 258 INRRMSIGEAKARRA 272


>gi|167465669|ref|ZP_02330758.1| sporulation sigma factor SigG [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 260

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 81/270 (30%), Positives = 141/270 (52%), Gaps = 18/270 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + ++++     A  A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNTEMRELFALLQTKNERA--AREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   +++N+  REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQVRDQLTNRNSREPTIYEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDERNKDLFWIEGIA-----LREAMRKLGSREKMILSMRFFEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV  +  +++ ++ ++E  AI +++   ++
Sbjct: 231 EVADEIGISQAQVSRLEKSAINQMQKHVKT 260


>gi|39933444|ref|NP_945720.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris CGA009]
 gi|192288802|ref|YP_001989407.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris TIE-1]
 gi|39647290|emb|CAE25811.1| RNA polymerase sigma 32 subunit, RpoH, stress response sigma factor
           [Rhodopseudomonas palustris CGA009]
 gi|192282551|gb|ACE98931.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 299

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 123/273 (45%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LARYLAEIRKFPMLEPQQEYMLAKRWR--EHGDRDAAHQLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IA +L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDLHPDQVKLIATRLGVTEQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D++       A    L   R      +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDQSPSQEAVMAEHEELDQRRAALNGAIQVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLASEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|328883832|emb|CCA57071.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 303

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 113/229 (49%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 79  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 138

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+A  L +  E V 
Sbjct: 139 VGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVTELAAVLGVSEEDVV 198

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 199 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 253

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 254 PPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 298


>gi|103487228|ref|YP_616789.1| RNA polymerase factor sigma-32 [Sphingopyxis alaskensis RB2256]
 gi|98977305|gb|ABF53456.1| RNA polymerase sigma factor RpoH [Sphingopyxis alaskensis RB2256]
          Length = 300

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 119/273 (43%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +   +    +  E   + A  ++V ++LRLV  +A  Y   GL
Sbjct: 20  LNRYLAEIRKFPLLTPEQEYMLAKRFQ--EHGDNEAAAQLVTSHLRLVAKIAMGYRGYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGLM+  +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 78  PVSELISEGNIGLMQGVKKFDPERGFRLATYAMWWIRASIQEFILRSWSLVKMGTTAAQK 137

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKL---AMPVEGVRKV--LKITKEPISLETPIG 581
                + R    +      + +PE +AK      +  + V  +          SL  P+G
Sbjct: 138 KLFFNLRRMKNNLEAFEDGDLSPEHVAKIATDLGVTEDEVVSMNRRMAMGGDTSLNVPMG 197

Query: 582 DEDTSHLGDFIEDKNAVSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++  S   D + D   +       +  +    +  T  L +L  RE  +L        + 
Sbjct: 198 EDGDSQWQDLLGDDGPLQDERVAEAQERDVRHDLLTEALETLNERERHILTE--RRLTDD 255

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TLE++ + + V+RER+RQIE +A  KL+   
Sbjct: 256 PKTLEDLSQLYDVSRERVRQIEVRAFEKLQKAM 288


>gi|239980906|ref|ZP_04703430.1| RNA polymerase sigma factor, sigma L [Streptomyces albus J1074]
 gi|291452768|ref|ZP_06592158.1| sigma L [Streptomyces albus J1074]
 gi|291355717|gb|EFE82619.1| sigma L [Streptomyces albus J1074]
          Length = 340

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 120/249 (48%), Gaps = 15/249 (6%)

Query: 427 FRHIVSMVRKGECEASIA--KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            R + +    G+     A  +  ++E NL LV   A ++ +R     D++Q G IGL+KA
Sbjct: 96  LRELAAEDSGGQDSPERAYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKA 155

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +T+  ++ K+ 
Sbjct: 156 IDRFDCERGVEFPTFAMPTVIGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLD 215

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSP 600
           R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++    
Sbjct: 216 RSPTVPELAHALGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALE 275

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                    RE+   +LA L PRE R++ +RF        T  ++G++  +++  + ++ 
Sbjct: 276 GVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVSRLL 326

Query: 661 AKAIRKLKH 669
            + + +L+ 
Sbjct: 327 TRTLAQLRE 335


>gi|11079206|dbj|BAB17594.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 268

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 117/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDAKAAKADDDSDDDEAESSDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 135 NKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|327190963|gb|EGE58017.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 332

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 126/279 (45%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 46  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 103

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 104 PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 163

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 164 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAA 223

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R   ++ ++ L  RE R+   R       
Sbjct: 224 EGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERERRIFEARRLAE--E 281

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R + L 
Sbjct: 282 PVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEALE 320


>gi|302792318|ref|XP_002977925.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
 gi|300154628|gb|EFJ21263.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
          Length = 326

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 89/305 (29%), Positives = 141/305 (46%), Gaps = 15/305 (4%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E+   W        +     F         +     +  +    +S+   R ++ +    
Sbjct: 34  EVRLAWFMAPAKRLQQVRLKFFEHLKREPSE-----EEWAKVAEMSVQTLRRLLQL---- 84

Query: 438 ECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                 A+ +M++ NLRLV   A+KY      L  LDL QEG  GLM A +KFD   GY+
Sbjct: 85  ---GQAARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPKKGYR 141

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA++WVK +I R+       +R+P ++  +   + R   ++S ++ REPT EE+  +
Sbjct: 142 FSTYAVYWVKNSILRAQTRLGHIVRVPYNVAAQKMTIQRKRAQLSLELDREPTHEEVITE 201

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L M      +VL+      SL           L   I D +          A LR     
Sbjct: 202 LKMDSRRYFEVLRTGAPRRSLNARSKVTGE-ELIHSISDPDENEAQYFNAGAQLRLGMDD 260

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL SL P+E  ++R R+G+    + +  E+G+   ++RE +R+ E + + KLKHP+R K 
Sbjct: 261 VLDSLKPKESLIIRQRYGLDGKGERSFTEIGRNLNLSREMVRKYEIRGMMKLKHPTRVKY 320

Query: 676 LRSFL 680
           LR FL
Sbjct: 321 LREFL 325


>gi|156636373|gb|ABU92457.1| RpoD [Vibrio vulnificus]
 gi|156636375|gb|ABU92458.1| RpoD [Vibrio vulnificus]
 gi|156636377|gb|ABU92459.1| RpoD [Vibrio vulnificus]
 gi|156636379|gb|ABU92460.1| RpoD [Vibrio vulnificus]
 gi|156636381|gb|ABU92461.1| RpoD [Vibrio vulnificus]
 gi|156636383|gb|ABU92462.1| RpoD [Vibrio vulnificus]
 gi|156636385|gb|ABU92463.1| RpoD [Vibrio vulnificus]
 gi|156636387|gb|ABU92464.1| RpoD [Vibrio vulnificus]
 gi|156636389|gb|ABU92465.1| RpoD [Vibrio vulnificus]
 gi|156636393|gb|ABU92467.1| RpoD [Vibrio vulnificus]
 gi|156636397|gb|ABU92469.1| RpoD [Vibrio vulnificus]
 gi|156636399|gb|ABU92470.1| RpoD [Vibrio vulnificus]
 gi|156636401|gb|ABU92471.1| RpoD [Vibrio vulnificus]
 gi|156636403|gb|ABU92472.1| RpoD [Vibrio vulnificus]
 gi|156636405|gb|ABU92473.1| RpoD [Vibrio vulnificus]
 gi|156636407|gb|ABU92474.1| RpoD [Vibrio vulnificus]
 gi|156636409|gb|ABU92475.1| RpoD [Vibrio vulnificus]
 gi|156636411|gb|ABU92476.1| RpoD [Vibrio vulnificus]
 gi|156636413|gb|ABU92477.1| RpoD [Vibrio vulnificus]
 gi|156636415|gb|ABU92478.1| RpoD [Vibrio vulnificus]
 gi|156636417|gb|ABU92479.1| RpoD [Vibrio vulnificus MO6-24/O]
 gi|156636419|gb|ABU92480.1| RpoD [Vibrio vulnificus]
 gi|156636421|gb|ABU92481.1| RpoD [Vibrio vulnificus]
 gi|156636423|gb|ABU92482.1| RpoD [Vibrio vulnificus]
 gi|156636425|gb|ABU92483.1| RpoD [Vibrio vulnificus]
 gi|156636427|gb|ABU92484.1| RpoD [Vibrio vulnificus]
 gi|156636429|gb|ABU92485.1| RpoD [Vibrio vulnificus]
 gi|156636435|gb|ABU92488.1| RpoD [Vibrio vulnificus]
 gi|156636437|gb|ABU92489.1| RpoD [Vibrio vulnificus]
 gi|156636439|gb|ABU92490.1| RpoD [Vibrio vulnificus]
 gi|156636441|gb|ABU92491.1| RpoD [Vibrio vulnificus]
 gi|156636443|gb|ABU92492.1| RpoD [Vibrio vulnificus]
 gi|156636445|gb|ABU92493.1| RpoD [Vibrio vulnificus]
 gi|156636447|gb|ABU92494.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  139 bits (351), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 66/196 (33%), Positives = 104/196 (53%), Gaps = 2/196 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +  + S +     E ++ +     L   + D LV +L     R+   E  ++
Sbjct: 8   QNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIM 67

Query: 358 RLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           + A     + +  F+    G E +  W+       +  +   +    + I +   ++++I
Sbjct: 68  KSAVEIAKMPKKSFIALFTGNESNEEWLDQILA-SDKPYVEKIKLHEEDIRRSIAKLRAI 126

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET +S++  + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 127 EEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 186

Query: 477 GNIGLMKAAEKFDWCL 492
           GNIGLMKA +KF++  
Sbjct: 187 GNIGLMKAVDKFEYRR 202


>gi|332982148|ref|YP_004463589.1| RNA polymerase sigma subunit RpsG/SigG [Mahella australiensis 50-1
           BON]
 gi|332699826|gb|AEE96767.1| RNA polymerase, sigma subunit, RpsG/SigG [Mahella australiensis
           50-1 BON]
          Length = 257

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 72/264 (27%), Positives = 134/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + +   + +  ++++ +     A++E +  NLRLV+S+ +++ NRG
Sbjct: 2   VINKVEICGVNTSKLPVLTDKQMKDLLKRIKEGDKAAREEFIRGNLRLVLSIIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EHVDDLFQVGCIGLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++  +  +EPT EEIAK + +P E V   +   ++PISL  P+  +  D 
Sbjct: 121 TAYKALQVREQLVAQNGKEPTVEEIAKAMELPAEEVVFAMDAIQDPISLFEPVYHDGGDA 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D + D            A         +  L+ RE+ +L MRF  G     T  EV
Sbjct: 181 IYVMDQVSDDKNQDDNWLETIA-----LKEAMQKLSEREKTILAMRFFQG----RTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            ++  +++ ++ ++E  A+  ++ 
Sbjct: 232 AEEIGISQAQVSRLEKSALSHMRK 255


>gi|311826281|emb|CBX60048.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 279

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/321 (19%), Positives = 118/321 (36%), Gaps = 43/321 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKAAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRSEEEIRRSITKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAKKEMV 449
            I   +  GE +A  AKKEMV
Sbjct: 259 DISRRMSIGEAKARRAKKEMV 279


>gi|258514354|ref|YP_003190576.1| sporulation sigma factor SigG [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778059|gb|ACV61953.1| RNA polymerase, sigma 28 subunit, SigG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 257

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 86/268 (32%), Positives = 136/268 (50%), Gaps = 21/268 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     I  S+ R +   +++     + A+ +++  NLRLV+SV +++T
Sbjct: 2   LINKVEICGVNTAKLPVIPNSKMRELFEAIQQ---GDTSARPQLINGNLRLVLSVIQRFT 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLMKAIDNFDLAQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    + NK  REP+  EIAK+L MP E V   L   +EPISL  PI  + 
Sbjct: 118 LRDVAYKALQVRDTLVNKHSREPSVNEIAKELKMPREEVVFALDAIQEPISLFEPIYHDG 177

Query: 584 -DTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            D   + D I +DKN        I           L  L+ RE+ +L +RF  G     T
Sbjct: 178 GDPIFVMDQISDDKNQDLNWLEGI------AIKDALRKLSDREKHILTLRFFDG----KT 227

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             EV  +  +++ ++ ++E  A+  ++ 
Sbjct: 228 QMEVADEIGISQAQVSRLEKAALHHMRK 255


>gi|149911320|ref|ZP_01899941.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
 gi|149805635|gb|EDM65637.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
          Length = 294

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 123/238 (51%), Gaps = 2/238 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+  M+++NLRLV+ VAKKY N  L + ++IQEGN GLM A +KFD   G +FSTYA
Sbjct: 39  DKAARDTMIQSNLRLVLMVAKKYQNYSLDWAEIIQEGNTGLMHAVDKFDPERGCRFSTYA 98

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +WW++  I + I + S TIRIP+H+     ++++ +  +   +       +IA++L +  
Sbjct: 99  VWWIRNNIEQYIMNHSRTIRIPIHVTRVYKQILKASSELGLDVDTNEGITKIAQELKISP 158

Query: 561 EGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             V  +L       SL+  I   D   + L D +  +    P     + +  E    +L 
Sbjct: 159 RKVLNILGHYFNEGSLDKEIHSGDNLLATLKDLVAAEVDCQPDIRYEKCDYYEYMDALLE 218

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            L  R + ++R+RFG       +L+ + +   ++RER+RQI    + +++    +  L
Sbjct: 219 YLPVRSQNIIRLRFGFKGQDPMSLQAIAQLMDISRERVRQIIRNGLSQVREQLCANDL 276


>gi|311898315|dbj|BAJ30723.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 360

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 111/227 (48%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V  ++ LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   +
Sbjct: 137 RNQLVRMHIPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDHERGVEFSTYATPTI 196

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S +  R PT  E+A+ L +  E V 
Sbjct: 197 VGEIKRHFRDKGWAVRVPRRLQELRLSLTTATSELSQRHGRSPTVHELAEHLGISEEDVL 256

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L+       +SL+ P  D+++  + D +   +             RE+   +LA L P
Sbjct: 257 EGLESANAYSTLSLDVPDSDDESPAVADTLGATDEALEGVEY-----RESLKPLLAQLPP 311

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+++L +RF   M       EV     +++  + ++ A+ + +L+ 
Sbjct: 312 REQKILVLRFFRNMTQSQIAAEV----GISQMHVSRLLARTLAQLRE 354


>gi|325983562|ref|YP_004295964.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
 gi|325533081|gb|ADZ27802.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
          Length = 281

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 126/264 (47%), Gaps = 7/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I + I+S++    ++  E   +   +         A ++++ ++LR V+++A+ Y   GL
Sbjct: 14  IESYIQSVNSFPILTQEEETSLARRL--WNRGDIEAAQQLIMSHLRFVVAIARGYKGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      ++I    + +
Sbjct: 72  PQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIMRNWRLVKIATTKQQR 131

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS- 586
                  + +           + +A +L +  E V ++  +     ISLE    DED + 
Sbjct: 132 KLFFNLRSMKHGLDTMNPQEVDAMAAQLGVKAEEVIEMEKRFNGSDISLEPVSEDEDDTF 191

Query: 587 HLGDFIEDKNAVSPLDSAIQ-ANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              +++ D    S L    Q  +LRE    + L  L  R   ++  R+    +T  TL +
Sbjct: 192 SPINYLTDGTEPSQLLEKEQITHLREKGLQKSLDCLDKRSRHIIEARWLREKDT-ATLHD 250

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +  +  V+ ER+RQIE KA++K++
Sbjct: 251 LADELGVSAERVRQIEVKALQKMR 274


>gi|254230128|ref|ZP_04923524.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
 gi|151937373|gb|EDN56235.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
          Length = 284

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 131/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        S      DED S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDEDDS 191

Query: 587 H-----LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++EDK+   A +   +  + +        LASL  R +R++R R+      
Sbjct: 192 SNAYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDD--E 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 250 KATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|23978319|dbj|BAC21133.1| principal sigma factor [Microcystis wesenbergii]
          Length = 188

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 101/189 (53%), Positives = 136/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S +++R+PT EEIA K+ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|23978363|dbj|BAC21146.1| principal sigma factor [Pleurocapsa sp. PCC 7327]
          Length = 188

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 100/189 (52%), Positives = 136/189 (71%), Gaps = 1/189 (0%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PV
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+ + I ++ +T + +S +++R+PT EEIA ++ M +E +R + K  + PISLETPIG E
Sbjct: 61  HLYETISRIKKTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKE 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           + S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLE
Sbjct: 121 EDSRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLE 179

Query: 644 EVGKQFCVT 652
           E+G+ F VT
Sbjct: 180 EIGQIFNVT 188


>gi|4100834|gb|AAD00999.1| RpoS [Escherichia coli]
          Length = 258

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 82/229 (35%), Positives = 143/229 (62%), Gaps = 3/229 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 31  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 87

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 88  RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 147

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 148 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 207

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 208 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 256



 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/96 (27%), Positives = 37/96 (38%), Gaps = 1/96 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E +L     + N     +     A +   D  ++YL E+G   LL+ E E+  A+R   
Sbjct: 2   DEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALR 61

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       + ES L     I  R   N G  LL  I
Sbjct: 62  GDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 96


>gi|3021676|dbj|BAA25358.1| RNA polymerase sigma-70 factor [Pseudomonas fluorescens]
 gi|11079021|dbj|BAB17515.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 116/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                      + +     +   D ++ A    +D  +    P  
Sbjct: 59  IDPDDGI--------APPAAEVPPPVDPKAPKADDDTDDDDAEASSDDEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +     A+E   R   +   + +A                      
Sbjct: 111 AAQRFGAVSDQMEITRK---ALEKHGRGNKLAIAELVA---------------------- 145

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 146 ----------LAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|239934572|emb|CAR94600.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 219

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/265 (22%), Positives = 99/265 (37%), Gaps = 49/265 (18%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLTFQ ++   + +  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTFQHILNSYESVKQ 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L +II     I P +             Q      +E+            E     
Sbjct: 61  GQGRLVDII--VGFIDPNAPDEIAAPVNPKLAQAAAPEVEEE-----------TEEGEST 107

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +++  +    PE A                   A   +L  + + A++           
Sbjct: 108 EEEEALETGPDPEEAARRF---------------ASIQKLHSQALKAIE----------- 141

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    +      K   +++K+      L L+    D L+ +L D    + + E ++
Sbjct: 142 ---------QHGIKDPKTVKIRKKVAGEFMELKLSPKMFDALIVRLRDHVAEVRNMEKQI 192

Query: 357 LRLAQS-YGIKRDVFLERHQGRELD 380
           +       G+ R  F+      E +
Sbjct: 193 MTFCVRDAGMPRKDFVTTFPKNETN 217


>gi|82703854|ref|YP_413420.1| RNA polymerase factor sigma-32 [Nitrosospira multiformis ATCC
           25196]
 gi|82411919|gb|ABB76028.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosospira multiformis
           ATCC 25196]
          Length = 281

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 133/276 (48%), Gaps = 12/276 (4%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A  V S   + N I+S++    ++  E   +   +R        A +++V ++LRLV+++
Sbjct: 4   ALTVPSAGSLENYIQSVNQFRILTQEEELQLARSLRDEGSID--AARQLVLSHLRLVVAI 61

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      +
Sbjct: 62  ARGYKGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFILRNWRLV 121

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAM-PVEGVRKVLKITKEPISL 576
           +I      +  K+    R +   +      E  E+A++L + P E V    + +   ISL
Sbjct: 122 KIATTKAQR--KLFFNLRSLKQALDTMSQKEVAEVAEQLGVKPEEVVEMETRFSGRDISL 179

Query: 577 ETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQANLR--ETTTRVLASLTPREERVLRMRF 632
           E    D+D        ++ D +  S +    Q      E   + L SL  R   ++  R+
Sbjct: 180 EPLSEDDDEETFSPIAYLTDGSEPSHVLEDEQTMRLRGEGLEQALESLDARSRHIIEARW 239

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +T  TL E+  +  V+ ER+RQIEAKA++KL+
Sbjct: 240 LREKDT-ATLHELADELGVSAERVRQIEAKAMQKLR 274


>gi|209407280|emb|CAP72525.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 271

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 120/315 (38%), Gaps = 45/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G           ++ E  + +       + + D E     S+++       PE 
Sbjct: 59  IDPDDDGA------AGPQEEVEPVTPQTTAKPAADDKDDEEEDDTDSEEEEGDGGPDPEV 112

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  + 
Sbjct: 113 ARVRFGAVAEQLEAAKKAL-----------------------------------KKHGRG 137

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     ++L  L   + L   + D LVE++ D   ++   E  ++++      + R  
Sbjct: 138 SQEATDALQELATLFMPIKLIPKQYDALVERVRDALSQVRAQERAIMQICVRDARMPRAD 197

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E +  W        + ++   +A   D I + + ++ ++  E  ++I++ + 
Sbjct: 198 FLRQFPNNETELSWADQLAS-GKSKYAEAIAARKDDIQRCQEKLLALEEECALAIADIKD 256

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 257 INRRMSIGEAKARRA 271


>gi|261405674|ref|YP_003241915.1| sporulation sigma factor SigG [Paenibacillus sp. Y412MC10]
 gi|315646040|ref|ZP_07899161.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|329922674|ref|ZP_08278226.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
 gi|261282137|gb|ACX64108.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. Y412MC10]
 gi|315278801|gb|EFU42115.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|328942016|gb|EGG38299.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
          Length = 260

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 81/270 (30%), Positives = 140/270 (51%), Gaps = 18/270 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++  E R +   +++       A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLTNVEMRELFHNLQQNNE--RSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   +++N   REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQVRDQLTNANSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D    +   S I+          +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDDK--NKDVSWIEEI---ALREAMHKLGQREKMILSMRFYEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV  +  +++ ++ ++E  AI++++   ++
Sbjct: 231 EVADEIGISQAQVSRLEKSAIKQMQKHVKT 260


>gi|258488842|gb|ACV72427.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488844|gb|ACV72428.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488850|gb|ACV72431.1| RpoD [Xanthomonas perforans]
 gi|258488868|gb|ACV72440.1| RpoD [Xanthomonas perforans]
 gi|258488904|gb|ACV72458.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488912|gb|ACV72462.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488924|gb|ACV72468.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
 gi|258488926|gb|ACV72469.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
 gi|258488928|gb|ACV72470.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488930|gb|ACV72471.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488932|gb|ACV72472.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
 gi|258488948|gb|ACV72480.1| RpoD [Xanthomonas perforans]
 gi|258488950|gb|ACV72481.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488952|gb|ACV72482.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488954|gb|ACV72483.1| RpoD [Xanthomonas axonopodis pv. begoniae]
 gi|258488956|gb|ACV72484.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488958|gb|ACV72485.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488960|gb|ACV72486.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
 gi|258488966|gb|ACV72489.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488968|gb|ACV72490.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488976|gb|ACV72494.1| RpoD [Xanthomonas axonopodis pv. vasculorum]
 gi|258488978|gb|ACV72495.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258488980|gb|ACV72496.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258488982|gb|ACV72497.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258488984|gb|ACV72498.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258488996|gb|ACV72504.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258488998|gb|ACV72505.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489000|gb|ACV72506.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489006|gb|ACV72509.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489008|gb|ACV72510.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489010|gb|ACV72511.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258489012|gb|ACV72512.1| RpoD [Xanthomonas axonopodis pv. ricini]
 gi|258489016|gb|ACV72514.1| RpoD [Xanthomonas perforans]
 gi|258489018|gb|ACV72515.1| RpoD [Xanthomonas perforans]
 gi|258489076|gb|ACV72544.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
 gi|258489078|gb|ACV72545.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
          Length = 261

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 117/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|153873537|ref|ZP_02002087.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152069997|gb|EDN67913.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 288

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 126/266 (47%), Gaps = 16/266 (6%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           ++I     +SI   R +    R    +   A + +V ++LR V+ +A  Y   GL   DL
Sbjct: 23  QAIKAIPLLSIEAERKLAE--RFIGEDDIEAARTLVMSHLRFVMHIAHNYRGYGLPQADL 80

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMRDKIHK 531
           IQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      ++       R     
Sbjct: 81  IQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIRAEIHEYILRNWRIVKVATTKSQRKLFFN 140

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS---- 586
           +    +R+    + E   E +AK L +  + VR++ L++    +S + P+  +D +    
Sbjct: 141 LRSAKKRLGWLTQDE--VETVAKDLGVSPKDVREMELRLNSYDLSFDMPVDADDDNAEIL 198

Query: 587 HLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               ++ED     A     S  + +      + LA L  R + +L+ R+     T  TL+
Sbjct: 199 SPVGYLEDNRYDPADLVEQSEWKTHGHRQLHQALAKLDVRSQDILQKRWLSENKT--TLQ 256

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+   + V+ ERIRQIE  A++KLK 
Sbjct: 257 ELANHYKVSAERIRQIENNALKKLKK 282


>gi|91974840|ref|YP_567499.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB5]
 gi|91681296|gb|ABE37598.1| RNA polymerase sigma factor RpoH [Rhodopseudomonas palustris BisB5]
          Length = 299

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 122/273 (44%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +        R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LARYLAEIRKFPMLEPQQEYMFAKRWR--EHDDRDAAHHLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IA +L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDMHPDQVKLIATRLGVTEQDVIDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D++       A    L   R      +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDQSPSQEAVMAEHEELDHRRAALNGAIGVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|258489038|gb|ACV72525.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
 gi|258489080|gb|ACV72546.1| RpoD [Xanthomonas perforans]
          Length = 261

 Score =  139 bits (350), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 117/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVXDQIISEQQ 255


>gi|144898533|emb|CAM75397.1| Sigma-70 region 2:Sigma-70 region 4 [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 290

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 76/277 (27%), Positives = 129/277 (46%), Gaps = 14/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   +   +    R  + E + A  ++V ++LRLV  +A  Y + GL
Sbjct: 15  LSKYLREIRDFPVLEPEQEYMLAK--RWVDYEDTAAAHQLVTSHLRLVAKIAMGYRHYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              DLI EGN+GLM+A +KF+   G++ STYAMWW+K ++   + +    ++I      +
Sbjct: 73  PMADLISEGNLGLMRAVKKFEPERGFRLSTYAMWWIKASLNEFVLNSWSLVKIGTLAAQK 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   ++      E  P +   IAK+L +   + V    ++     SL TP+  
Sbjct: 133 KLFFNLRKVKTKLRLLDATELAPADVRAIAKELGVSETDVVNMNRRMGGRDSSLNTPV-G 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E  + + + + D+        A    L   R+   + L SL  RE  +   R        
Sbjct: 192 ESGTEIIELLPDETDNQETGLAKHEELSKGRKLIAQALTSLNEREREIFVERRLRD--EP 249

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEE+G +F V+RERIRQIE KA  K++    +  L
Sbjct: 250 LTLEELGARFGVSRERIRQIEVKAFEKVRALVSAGFL 286


>gi|311826287|emb|CBX60051.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 279

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 62/321 (19%), Positives = 117/321 (36%), Gaps = 43/321 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D     +       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDTEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAKKEMV 449
            I   +  GE +A  AKKEMV
Sbjct: 259 DISRRMSIGEAKARRAKKEMV 279


>gi|311826271|emb|CBX60043.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|311826279|emb|CBX60047.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|311826283|emb|CBX60049.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 279

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 62/321 (19%), Positives = 118/321 (36%), Gaps = 43/321 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAKKEMV 449
            I   +  GE +A  AKKEMV
Sbjct: 259 DISRRMSIGEAKARRAKKEMV 279


>gi|118588309|ref|ZP_01545718.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118439015|gb|EAV45647.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 294

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 121/274 (44%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    +  E E   A + +V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLDEIRKFPMLQPQEEYMLAKRYK--EHEDPEAAERLVNSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 73  PIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  ++    + +     +     EIA KL +  E V  + +      SL  P+  E
Sbjct: 133 RLFFNLRRLKGKIQALDEGDLKPHQVSEIATKLGVSEEEVVSMNRRLGGDASLNAPVRAE 192

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
            D     D++ D++       A Q  L   R+     +  L  RE R+            
Sbjct: 193 ADAGEWQDWLVDESDSQETLLANQEELDMRRKMLNDAMDVLNERERRIFEA--RRLSEDP 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++  +F V+RER+RQIE +A  K++   R+
Sbjct: 251 MTLEDLSGEFGVSRERVRQIEVRAFEKVQKAVRN 284


>gi|319898405|ref|YP_004158498.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319402369|emb|CBI75908.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 305

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/280 (24%), Positives = 129/280 (46%), Gaps = 18/280 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLEEVRRFPVLEPQEEYMLAK--RYHEHNDPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGNIGLM+A ++F+   G++ +TYAMWW+K +I   +      ++I      K
Sbjct: 74  PIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTANQK 133

Query: 529 IHKVVRTARRMSNKIKREPTPE-------EIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
             ++    R++ NK++   + +       EIA +L +  + V  + +      SL  P+ 
Sbjct: 134 --RLFFNLRKLKNKLQMFDSGDLNAEQVKEIATRLKVTEDEVVSMNRRLSGDASLNAPLL 191

Query: 582 DE--DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGM 636
               ++    D++ D +         Q  L        + + +L  RE+R+ + R     
Sbjct: 192 TNKGESYEWQDWLVDDSNSQEQILIEQDELENRHSMLIQAMDNLNEREKRIFKARRLRD- 250

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
               TLEE+  +F ++RER+RQIE +A  K+++  +   L
Sbjct: 251 -EPMTLEELSNEFNISRERVRQIEMRAFEKIQNSIKLSAL 289


>gi|329938753|ref|ZP_08288149.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329302244|gb|EGG46136.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 291

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 45  LSRSLFLRLAALDEHSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 103

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 104 IKAIDRFDPDRGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 163

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 164 KLDRSPTVAELAVVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 223

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 224 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 274

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 275 RLLTRTLAQLRE 286


>gi|323702540|ref|ZP_08114203.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532514|gb|EGB22390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 260

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 127/244 (52%), Gaps = 8/244 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +  +++K +   + A++ +V  NL+LV ++ +++ NRG +  DL Q G IGLMKA +K
Sbjct: 20  KEMRDLIKKAQAGDADARERLVNCNLKLVFNLVQRFNNRGYELEDLFQIGCIGLMKAIDK 79

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D    +++   +++  +K+ +T  R++ ++ R+P
Sbjct: 80  FDLSYDVKFSTYAVPMIVGEIRRFLRD-DSPVKVSRSLKETAYKIQQTRDRLTARLGRDP 138

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +  EIA++L    E V   L+  + P S+   +  +D   +    +   A       ++ 
Sbjct: 139 SINEIAQELGCHREEVVSALEAAQTPTSIYETLHQDDGDPIYILDQLSGADDGDSPWLE- 197

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +    ++L  L  R+ ++L  RF      D T  EV  +  +++ ++ ++E +A+RKL
Sbjct: 198 --KLAVKQLLIELPERDRQILLWRFF----EDKTQSEVALRLGLSQVQVSRLERQALRKL 251

Query: 668 KHPS 671
           K   
Sbjct: 252 KELM 255


>gi|225454599|ref|XP_002264964.1| PREDICTED: hypothetical protein isoform 2 [Vitis vinifera]
          Length = 496

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 141/260 (54%), Gaps = 8/260 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R   + ++    E S+A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  E
Sbjct: 236 LRMSRAELQSKLIECSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIE 295

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G+K STY  WW++Q ++R++ + S T+R+P H+ +++  +     R+  K    
Sbjct: 296 KFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEK-GIT 354

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLD 602
           P+ + IA+ L M  + VR   +   +  SL+              L  +I D    +   
Sbjct: 355 PSIDRIAECLNMSQKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENNPW 414

Query: 603 SAIQAN-LRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +    L++   +++  +L  RE  ++R+ +G+  N   T E++ K+  ++RER+RQ+ 
Sbjct: 415 HGVDEWALKDEVNKLINTTLGERERDIIRLYYGLD-NECLTWEDISKRIGLSRERVRQVG 473

Query: 661 AKAIRKLKHPSRSKKLRSFL 680
             A+ KLK+ +R  ++ + L
Sbjct: 474 LVALEKLKNAARKGRMEAML 493


>gi|86747581|ref|YP_484077.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris HaA2]
 gi|86570609|gb|ABD05166.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 299

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 123/273 (45%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +        R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LARYLAEIRKFPMLEPQQEYMFAKRWR--EHDDRDAAHHLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDMHPDQVKLIAKRLGVTEQDVIDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D++       A    L   R      +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDQSPNQEAVMAEHEELDHRRAALNGAIGVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|170744871|ref|YP_001773526.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168199145|gb|ACA21092.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 296

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 123/274 (44%), Gaps = 12/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +  +E   +       E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLDEIRRFPMLEPTEEYMLAK--SWREHGDREAAHKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 72  PIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R+S   + +  PE   +IA +L +P + V ++ +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKGRISALDEGDLRPEQVKQIATRLGVPEQDVIEMNRRLSGDASLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +              N        L+ L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDDSPSQEAVLAREEEGQNRLAALRDALSVLNPRERRIFEARRLAE--EPI 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 250 TLEDLSSEFGVSRERVRQIEVRAFEKVQDAVKRN 283


>gi|305644356|gb|ADM53779.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  139 bits (350), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 114/176 (64%), Positives = 138/176 (78%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 60

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ REP PEE+A ++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED     
Sbjct: 61  LQEMGREPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAL 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P D+A   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VT ER
Sbjct: 121 PADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTWER 176


>gi|163803403|ref|ZP_02197278.1| RNA polymerase sigma factor [Vibrio sp. AND4]
 gi|159172807|gb|EDP57652.1| RNA polymerase sigma factor [Vibrio sp. AND4]
          Length = 285

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 132/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S +    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSANSYPMLTADEERGLAERLHYKGEID--AAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
                + ++ +R+      E   E +A++L +    VR++        S      D+D  
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPMDDDDN 191

Query: 586 ----SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
               +    ++EDK+   A +   +  +A+        LASL  R +R++R R+     +
Sbjct: 192 SNSYTAPMVYLEDKSSDVADNIEAANWEAHTNNRLGHALASLDERSQRIVRSRWLDDDKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  +F V+ ERIRQ+E  A++KLK
Sbjct: 252 --TLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|147678180|ref|YP_001212395.1| sporulation sigma factor SigG [Pelotomaculum thermopropionicum SI]
 gi|146274277|dbj|BAF60026.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 257

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 82/267 (30%), Positives = 134/267 (50%), Gaps = 19/267 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     ++ S+ + +   + K     + A+ +++  NLRLV+SV +++T
Sbjct: 2   LVNKVEICGVNTSKLPVLTGSQMKALFEAMHK---GDASARTKLINGNLRLVLSVIQRFT 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    + NK  REP+  EIA +L MP E +   L   +EPISL  PI  + 
Sbjct: 118 LRDVAYKALQVRDALVNKYSREPSINEIACELKMPREEIVFALDAIQEPISLFEPIYHDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D   + D I D+           A         L  L+ RE+ +L +RF  G     T 
Sbjct: 178 GDPIFVMDQISDEKNQDQNWLEGIA-----IRDALRKLSDREKLILTLRFYEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV ++  +++ ++ ++E  A+  +K 
Sbjct: 229 MEVAEEIGISQAQVSRLEKAALNHMKK 255


>gi|258488970|gb|ACV72491.1| RpoD [Xanthomonas axonopodis pv. malvacearum]
          Length = 261

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 117/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                 D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSGDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|190571331|ref|YP_001975689.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357603|emb|CAQ55044.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 297

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 77/287 (26%), Positives = 136/287 (47%), Gaps = 16/287 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V+S   +   I  +     +S  E   +       E +   +   ++ ++L LV+ +A K
Sbjct: 10  VNSSTNLMQYIAEVRKFPMLSQEEEVRLAK--NWQEYQDISSAHRLITSHLNLVVKIAMK 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ ++   I      ++I 
Sbjct: 68  FKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASMKDFILKSWSLVKIG 127

Query: 523 VH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA-----MPVEGVRKVLKITKEPIS 575
                R     + +  +R+     RE   +E  K ++        + V+   ++  +  S
Sbjct: 128 TTQAQRRLFFSLRKIKKRILQYTNRETLSKEEIKAISNELSVSEEDVVQMSYRLACKDQS 187

Query: 576 LETPIGDEDTS--HLGDFIEDK--NAVSPLDSAIQANLRET-TTRVLASLTPREERVLRM 630
           L   I   D S   L D I     +      +  +  L+ET  +  LASL  R   +   
Sbjct: 188 LNNCIKIGDDSKKELQDMIPCNLVSQEVAYQNHEEKALKETILSNALASLNERSRDIFIS 247

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           R+        TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 248 RYLSENTQ--TLDELSKKYCVSRERIRQLAEQAMSKVKQHIKSESLK 292


>gi|255545052|ref|XP_002513587.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223547495|gb|EEF48990.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 501

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 76/253 (30%), Positives = 127/253 (50%), Gaps = 7/253 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEK 487
           V  VRK       A+ ++++ NLRLV+ V  KY      G +F DL Q G  GL+ A ++
Sbjct: 252 VEKVRKQLEVGRAARNKLIKHNLRLVMFVMNKYFQDFANGPRFQDLCQAGVKGLITAIDR 311

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+    ++ STY+++W++ AI RS    S   ++   +     ++ +    +  +++R P
Sbjct: 312 FEPQRRFQLSTYSLFWIRHAIIRS-MTLSSFTKVSFGLESVRTEIQKAKLELLIELQRRP 370

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T EEI +++ +  E   +V++  K  +SL             + I D +          A
Sbjct: 371 TEEEIIERVGISAERYHEVIRAAKPALSLHARHAVTQE-EFINGITDIDGGDNRRQP--A 427

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR     VL SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KL
Sbjct: 428 LLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKYEVKALMKL 487

Query: 668 KHPSRSKKLRSFL 680
           KHP+R   LR ++
Sbjct: 488 KHPARVDYLRRYV 500


>gi|258488888|gb|ACV72450.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488914|gb|ACV72463.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488916|gb|ACV72464.1| RpoD [Xanthomonas axonopodis pv. aurantifolii]
 gi|258488920|gb|ACV72466.1| RpoD [Xanthomonas alfalfae subsp. citrumelonis]
          Length = 257

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 114/299 (38%), Gaps = 49/299 (16%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++         E   + +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDD 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
               ++       P E                              V   ++ +A  Y +
Sbjct: 110 DAAEEEAGPTGPDPVE------------------------------VATRMENLANEYAK 139

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 140 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 193

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 194 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 251


>gi|163867808|ref|YP_001609012.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161017459|emb|CAK01017.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 294

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 127/278 (45%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +     +   E   +    R  E     A   +V ++LRLV  VA  Y   GL
Sbjct: 16  LNRYLEEVRRFPMLEPKEEYMLAQRYR--EHNDLKAAHRLVTSHLRLVAKVAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGNIGLM+A ++F+   G++ +TYA+WW+K +I   +      +++      K
Sbjct: 74  PIGEVISEGNIGLMQAVKRFEPERGFRLATYAIWWIKASIQEYVLRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + + +        +EIA +L +  + V  + +      SL  P+  +
Sbjct: 134 RLFFNLRKLKNKLQALDSGDLNTEQVKEIATQLNVTEDEVVSMNRRLGGDTSLNAPLRTK 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +   S L D++ D++         ++ L   R      + +L  RE R+ + R    +  
Sbjct: 194 EGENSELQDWLVDESNNQEQILIEKSELENRRFMLVNAMNNLNDRERRIFKARRLNDI-- 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIE +A  K+++  R   L
Sbjct: 252 PLTLEELSSEFNISRERVRQIEMRAFEKVQNSIRDSAL 289


>gi|156636431|gb|ABU92486.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 66/196 (33%), Positives = 104/196 (53%), Gaps = 2/196 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +  + S +     E ++ +     L   + D LV +L     R+   E  ++
Sbjct: 8   QNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIM 67

Query: 358 RLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           + A     + +  F+    G E    W+       +  +   +    + I +  +++++I
Sbjct: 68  KSAVEIAKMPKKSFIALFTGNESSEEWLDKIL-VSDKPYAEKIKLHEEDIRRSISKLRAI 126

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET +S++  + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 127 EEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 186

Query: 477 GNIGLMKAAEKFDWCL 492
           GNIGLMKA +KF++  
Sbjct: 187 GNIGLMKAVDKFEYRR 202


>gi|316931591|ref|YP_004106573.1| RNA polymerase sigma 32 subunit RpoH [Rhodopseudomonas palustris
           DX-1]
 gi|315599305|gb|ADU41840.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           DX-1]
          Length = 299

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 122/273 (44%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LARYLAEIRKFPMLEPEQEYMLAKRWR--EHGDRDAAHQLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P+    IA +L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDLHPDHVKLIASRLGVTEQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D++       A    L   R      +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDQSPSQEAVLAEHEELDQRRAALNGAIQVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|297202300|ref|ZP_06919697.1| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
 gi|297148082|gb|EDY54214.2| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
          Length = 381

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 120/241 (49%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  ++ G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 144 LRAMKDGSPEYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 203

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  
Sbjct: 204 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVH 263

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 264 ELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 319

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 320 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 374

Query: 669 H 669
            
Sbjct: 375 E 375


>gi|164690667|dbj|BAF98617.1| putative DNA helicase [Streptomyces argenteolus]
          Length = 1064

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 80/228 (35%), Positives = 130/228 (57%), Gaps = 4/228 (1%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A   +V  N+RLV +    Y  +G+   DL+Q G +G+M+AAEKFD   G +FSTYA 
Sbjct: 150 RRAFDALVLHNIRLVHAAVAPYLGQGVDREDLVQHGVLGVMRAAEKFDPRAGTRFSTYAT 209

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           WW++QA++R++AD+  TIRIP H+RD + KV   A R S +    P P+++A +L +P +
Sbjct: 210 WWIRQAVSRAVADEGSTIRIPAHVRDVVLKVA-VACRRSRERGLRPRPQDLAAELDLPPD 268

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL-RETTTRVLASL 620
            V   L++++   SL+        + L   I  ++A+   +  ++A   R+    +L  L
Sbjct: 269 TVNLALRVSRPADSLDRVADGVRPAELA--ISLRDAIPGPEETLRAAFGRQWVDWLLEPL 326

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R   ++R R G+      TL+++G  + VTRERIRQ E +A+  L+
Sbjct: 327 PARNADIVRRRNGVIKGEPQTLKDIGVLYGVTRERIRQNEKRALAVLR 374


>gi|258488938|gb|ACV72475.1| RpoD [Xanthomonas axonopodis pv. axonopodis]
 gi|258488940|gb|ACV72476.1| RpoD [Xanthomonas axonopodis pv. axonopodis]
          Length = 261

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 118/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L++  + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLVDYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|156636395|gb|ABU92468.1| RpoD [Vibrio vulnificus]
 gi|156636449|gb|ABU92495.1| RpoD [Vibrio vulnificus]
 gi|156636451|gb|ABU92496.1| RpoD [Vibrio vulnificus]
 gi|156636453|gb|ABU92497.1| RpoD [Vibrio vulnificus]
 gi|156636459|gb|ABU92500.1| RpoD [Vibrio vulnificus]
 gi|156636463|gb|ABU92502.1| RpoD [Vibrio vulnificus]
 gi|156636465|gb|ABU92503.1| RpoD [Vibrio vulnificus]
 gi|156636467|gb|ABU92504.1| RpoD [Vibrio vulnificus]
 gi|156636469|gb|ABU92505.1| RpoD [Vibrio vulnificus]
 gi|156636471|gb|ABU92506.1| RpoD [Vibrio vulnificus]
 gi|156636473|gb|ABU92507.1| RpoD [Vibrio vulnificus]
 gi|156636477|gb|ABU92509.1| RpoD [Vibrio vulnificus]
 gi|156636479|gb|ABU92510.1| RpoD [Vibrio vulnificus]
 gi|156636481|gb|ABU92511.1| RpoD [Vibrio vulnificus]
 gi|156636483|gb|ABU92512.1| RpoD [Vibrio vulnificus]
 gi|156636485|gb|ABU92513.1| RpoD [Vibrio vulnificus]
 gi|156636487|gb|ABU92514.1| RpoD [Vibrio vulnificus]
 gi|156636489|gb|ABU92515.1| RpoD [Vibrio vulnificus]
 gi|156636491|gb|ABU92516.1| RpoD [Vibrio vulnificus]
 gi|156636493|gb|ABU92517.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 67/196 (34%), Positives = 104/196 (53%), Gaps = 2/196 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +  + S +     E ++ +     L   + D LV +L     R+   E  ++
Sbjct: 8   QNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIM 67

Query: 358 RLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           + A     + +  F+    G E    W+       +  +   +    + I +  +++++I
Sbjct: 68  KSAVEIAKMPKKSFIALFTGNESSEEWLDKIL-VSDKPYAEKIKLHEEDIRRSISKLRAI 126

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET +S+S  + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 127 EEETSLSVSNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 186

Query: 477 GNIGLMKAAEKFDWCL 492
           GNIGLMKA +KF++  
Sbjct: 187 GNIGLMKAVDKFEYRR 202


>gi|311826277|emb|CBX60046.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 279

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/321 (18%), Positives = 116/321 (36%), Gaps = 43/321 (13%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REG+I IAKRIE G   + +S+ E P T   ++   D++      L ++I   
Sbjct: 1   GTVELLTREGDIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGF 60

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                +          G    + +   +++E  D  E   D    ++       ++    
Sbjct: 61  VDPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL---- 116

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
                                           +   +++   Y+ L+      +   +  
Sbjct: 117 -------------------------------ALEKFNQLRSTYQNLQ------LAINEHG 139

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKR 367
             S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + +
Sbjct: 140 YESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPK 199

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F+    G E    W+       +  +   +    + I +   ++K I  ET +++   
Sbjct: 200 KSFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNI 258

Query: 428 RHIVSMVRKGECEASIAKKEM 448
           + I   +  GE +A  AKK  
Sbjct: 259 KDISRRMSIGEAKARRAKKRW 279


>gi|302810520|ref|XP_002986951.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
 gi|300145356|gb|EFJ12033.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
          Length = 326

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 89/305 (29%), Positives = 140/305 (45%), Gaps = 15/305 (4%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E+   W        +     F         +     +  +    +S+   R ++      
Sbjct: 34  EVRLAWFMAPAKRLQQVRLKFFEHLKREPSE-----EEWAKVAEMSVQTLRRLLQ----- 83

Query: 438 ECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                 A+ +M++ NLRLV   A+KY      L  LDL QEG  GLM A +KFD   GY+
Sbjct: 84  --SGQAARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPKKGYR 141

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA++WVK +I R+       +R+P ++  +   + R   ++S ++ REPT EE+  +
Sbjct: 142 FSTYAVYWVKNSILRAQTRLGHIVRVPYNVAAQKMTIQRKRAQLSLELDREPTHEEVITE 201

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L M      +VL+      SL           L   I D +          A LR     
Sbjct: 202 LKMDSRRYFEVLRTGAPRRSLNARSKVTGE-ELIHSISDPDENEAQYYNAGAQLRLGMDD 260

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           VL SL P+E  ++R R+G+    + +  E+G+   ++RE +R+ E + + KLKHP+R K 
Sbjct: 261 VLDSLKPKESLIIRQRYGLDGKGERSFTEIGRNLNLSREMVRKYEIRGMMKLKHPTRVKY 320

Query: 676 LRSFL 680
           LR FL
Sbjct: 321 LREFL 325


>gi|224116898|ref|XP_002331841.1| predicted protein [Populus trichocarpa]
 gi|222875079|gb|EEF12210.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 101/399 (25%), Positives = 171/399 (42%), Gaps = 24/399 (6%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
              +    +  + E      K++     K    LSL Q RI L   ++    K +     
Sbjct: 124 CRQRKRKTSECEKEDDGRTSKIIVRNQAKKAKRLSL-QKRIAL---RIKSDEKLVTSVGK 179

Query: 355 ELLRLAQSYGIKRDVFLERHQGRE--LDPHWVSY----AKDFPEGEWKNFVACEVDSILK 408
              R  ++  I  D  +  +          W            E  W   +   + + L+
Sbjct: 180 RKGRKNENEKI--DELVREYSSSTDLASLDWKKMKIPPVLTSAEHAWLFKLMQPMKASLQ 237

Query: 409 IRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVAKKY- 463
           ++  ++  S     +  E        V  VRK       A+ ++++ NLRLV+ V  KY 
Sbjct: 238 VKEHLQENSGREP-TEGELAEATDMDVLQVRKQIEVGRAARNKLIKHNLRLVLFVINKYF 296

Query: 464 --TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
                G ++ DL Q G  GLM A ++F+    ++ STY ++W++ AI RS    S   R+
Sbjct: 297 QDYANGPRYQDLCQAGVKGLMTAIDRFEPKRRFRLSTYGLFWIRHAIIRS-MTLSSFTRV 355

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
              +     ++ +    +  ++ R+PT EEI +K+ + +E   +V++ +K  +SL +   
Sbjct: 356 SFGLESIRSEIQKAKLELWFQLLRKPTGEEIIEKVGISIERYHEVMRASKPVLSLHSRHK 415

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 L   + D N     D    A LR     VL SL P+E  V+R RFG+    D T
Sbjct: 416 TTQE-ELISGVADVNGGD--DRRQSALLRLALDDVLDSLKPKESLVVRQRFGLDGKGDRT 472

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           L E+     ++RE +R+ EAKA+ KLKHP+R   L  ++
Sbjct: 473 LGEIAGNLNISREMVRKHEAKALMKLKHPTRVDYLCRYV 511


>gi|121602451|ref|YP_988610.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614628|gb|ABM45229.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 125/278 (44%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +V   R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLEEIRRFPILEPKEEYMLVK--RYNEHNDLKAAHKLVTSHLRLVAKIAIGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC--TIRIPVHMR 526
              ++I EGNIGLM+A ++F+   G++ +TYAMWW+K +I   +        I    + +
Sbjct: 74  PMGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTTNQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPI--G 581
                + +   ++      E   E   EIA +L +  + V  +        SL  P+   
Sbjct: 134 RLFFNLRKLKSKLQALDNGELNTEQVKEIATRLNVTEDEVVSMNHRLSGDTSLNAPLRTN 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +++ S   D + D+ +        +  L   R      +A+L  RE+R+         + 
Sbjct: 194 EDEHSEWQDCLVDEASSQEQVLIEKDELENRRSLLIHAMANLNEREKRIFEA--RRLSDE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIE +A  K++   R+  L
Sbjct: 252 VLTLEELSSEFNISRERVRQIEMRAFEKVQDFVRASAL 289


>gi|320009626|gb|ADW04476.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 288

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 117/232 (50%), Gaps = 13/232 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM
Sbjct: 61  AYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAM 120

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V   I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+AK L +  E
Sbjct: 121 PTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELAKALGVSEE 180

Query: 562 GVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V   L +       SL++P  ++D     L D +  ++A            RE+   +L
Sbjct: 181 DVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGVEY-----RESLKPLL 235

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           A L PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 236 AKLAPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLTQLRE 283


>gi|3021660|dbj|BAA25350.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079009|dbj|BAB17509.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 268

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPIDTKTAKADDDSDDDDAEASDDEEEAESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +     A++   R   +   + +A                      
Sbjct: 110 AAQRFGAVADQMEITRK---ALKKHGRHNKLAIAELLA---------------------- 144

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L  L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 145 ----------LSDLFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKSKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|311897125|dbj|BAJ29533.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 122/251 (48%), Gaps = 14/251 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + FR +  +   G  E +  +  ++E NL LV   + ++ +R     D++Q G IGL
Sbjct: 50  LSRALFRRLAGL-ESGSAEHTYVRDTLIELNLPLVRYASARFRSRNEPMEDIVQVGTIGL 108

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +    +S 
Sbjct: 109 IKAIDRFDPDRGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKAGDELSQ 168

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           ++ R PT  E+A  L +  + V + L +       SL++   ++D     L D +  ++ 
Sbjct: 169 RLDRSPTVPELAAYLGVTEDDVVEGLAVGNAYTASSLDSTPAEDDGGDGPLADRLGYED- 227

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                +      RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 228 ----LALEGVEYRESLKPLLAKLPPRERRIIMLRFFGN----LTQSQIGEEIGISQMHVS 279

Query: 658 QIEAKAIRKLK 668
           ++  K +  L+
Sbjct: 280 RLLTKTLAHLR 290


>gi|258489028|gb|ACV72520.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
          Length = 246

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 110/286 (38%), Gaps = 44/286 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + +   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDDAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            ++L LA +   + R  F+   +G + +  WV  A    +      
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQKWSSAL 243


>gi|209886261|ref|YP_002290118.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
 gi|209874457|gb|ACI94253.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
          Length = 299

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 124/274 (45%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +  I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSHYLAEIRKFPMLEPQEEYMLAKRWR--EHDDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   +   + +    E   + IAK+L +    V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALEDGDMHEDQVKLIAKRLGVTERDVIDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +        +S    + R   T  +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDTSPNQETIMAESEEYDHRRNALTGAMGVLNPRERRIFEARRLAE--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++  +F V+RER+RQIE +A  K++   +S
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKS 285


>gi|88799025|ref|ZP_01114606.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778252|gb|EAR09446.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 339

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 128/253 (50%), Gaps = 3/253 (1%)

Query: 418 VETGISISEFRHIVSMVRKGECEASI--AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
             TG  I E   + S              ++ ++ +N+RLV  VA ++T RGL  LDL Q
Sbjct: 80  RPTGSDIVELMRLESKPDLNPIFERWLSVREFLIASNIRLVFKVAHRHTERGLSLLDLAQ 139

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG  GL++A E+F      +FSTYA  W+ Q I  +I  Q+ T+ IP +++D + +  R 
Sbjct: 140 EGQFGLVRALERFRCDKELRFSTYATHWITQYIRLAIKKQTRTVPIPTNVQDDLARTNRA 199

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
             R   +  R  +  E A+      +    ++ +     SL+  + D+      D + D 
Sbjct: 200 LARAQQQQGRPVSVTEFARLSNQSTDAAEHLMSLNAPVQSLDERLSDDSEVSALDLL-DS 258

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +   P     +++ +E    +LA LT RE+++L MR+GIGM  ++   E+  Q  ++RER
Sbjct: 259 DLARPESEHERSDNQERVQALLAHLTSREQQILAMRYGIGMGAEYGYREIADQLNLSRER 318

Query: 656 IRQIEAKAIRKLK 668
           +RQ+E +A+  L+
Sbjct: 319 VRQLEKQALGFLR 331


>gi|241661869|ref|YP_002980229.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12D]
 gi|240863896|gb|ACS61557.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12D]
          Length = 309

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 139/279 (49%), Gaps = 13/279 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++  I   I+S++    +S  E + +    R  +     A + +V ++LRLV+S+A+ Y 
Sbjct: 32  NLGNIDAYIQSVNRVPMLSAEEEQRLAREYRDNDNLD--AARRLVLSHLRLVVSIARGYL 89

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  +YAM W+K  +   I      +++   
Sbjct: 90  GYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRMVKVATT 149

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ +         + +A +L +    VR++    +   I+LE  + D
Sbjct: 150 KAQRKLFFNLRSHKQDAQATFTSDEIDAVAAELNVKGTEVREMETRLSGGDIALEGQMDD 209

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S+    ++ D +         ++N R   E     LA L  R  R++  R+ + +N 
Sbjct: 210 GEESYAPIAYLADTHNEPTRVIEARSNDRMQSEGIEAALAKLDDRSRRIIEARW-LNVND 268

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           D     TL E+  +F V+ ERIRQIE+ A++K+K   ++
Sbjct: 269 DGSGGSTLHELADEFGVSAERIRQIESAAMKKMKGALQA 307


>gi|323701302|ref|ZP_08112977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533904|gb|EGB23768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 257

 Score =  139 bits (349), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 82/267 (30%), Positives = 138/267 (51%), Gaps = 19/267 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     ++ S+ R +   +++G      A+ +++  NLRLV+SV +++T
Sbjct: 2   LVNKVEICGVNTSKLPVLTNSQMRTLFEAMQQGN---KEARNQLINGNLRLVLSVIQRFT 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    + NK  REP+  EIA +L MP E +   L   +EPISL  PI  + 
Sbjct: 118 LRDVAYKALQVRDSLVNKFSREPSINEIAGELKMPREEIVFALDAIQEPISLFEPIYHDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D   + D I D+   +   S ++     +    L  L+ RE+ +L +RF  G     T 
Sbjct: 178 GDPIFVMDQISDEK--NMDLSWLEGI---SIRDALRRLSDREKHILTLRFFEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV  +  +++ ++ ++E  A+  ++ 
Sbjct: 229 MEVADEIGISQAQVSRLEKAALNHMRK 255


>gi|317447069|emb|CBX24518.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
          Length = 269

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEGSADASDDEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|51892360|ref|YP_075051.1| sporulation sigma factor SigG [Symbiobacterium thermophilum IAM
           14863]
 gi|51856049|dbj|BAD40207.1| RNA polymerase sigma factor similar to B. subtilis SigG
           [Symbiobacterium thermophilum IAM 14863]
          Length = 256

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 75/250 (30%), Positives = 132/250 (52%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ ++ R +   +R GE     A+ E++  NLRLV+SV +++ NRG    DL Q G IGL
Sbjct: 18  LTNAQMRELFVRMRSGE---KAARDELITGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 75  MKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDALVN 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           ++ REPT +EIA +L +P+E +   L   +EP+SL  P+ ++  D  ++ D + D++   
Sbjct: 134 RLSREPTVQEIADELGLPLEEIVYALDSIQEPVSLFEPLYNDGGDPIYVMDQVSDESQQD 193

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                  +       + L  L  RE  +L +RF  G     T  EV ++  +++ ++ ++
Sbjct: 194 SQWLEGIS-----IRQALHRLNERERLILTLRFFEG----KTQMEVAEEIGISQAQVSRL 244

Query: 660 EAKAIRKLKH 669
           E  A+  ++ 
Sbjct: 245 EKAALSHMRK 254


>gi|156636433|gb|ABU92487.1| RpoD [Vibrio vulnificus]
 gi|156636455|gb|ABU92498.1| RpoD [Vibrio vulnificus]
 gi|156636457|gb|ABU92499.1| RpoD [Vibrio vulnificus]
 gi|156636461|gb|ABU92501.1| RpoD [Vibrio vulnificus]
 gi|156636475|gb|ABU92508.1| RpoD [Vibrio vulnificus]
 gi|156636495|gb|ABU92518.1| RpoD [Vibrio vulnificus]
 gi|156636497|gb|ABU92519.1| RpoD [Vibrio vulnificus]
 gi|156636499|gb|ABU92520.1| RpoD [Vibrio vulnificus]
 gi|156636501|gb|ABU92521.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 67/196 (34%), Positives = 103/196 (52%), Gaps = 2/196 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +  + S +     E ++ +     L   + D LV +L     R+   E  ++
Sbjct: 8   QNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIM 67

Query: 358 RLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           + A     + +  F+    G E    W+       +  +   +    + I +   ++++I
Sbjct: 68  KSAVEIAKMPKKSFIALFTGNESSEEWLDKIL-VSDKPYAEKIKLHEEDIRRSIAKLRAI 126

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET +S+S  + I   +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQE
Sbjct: 127 EEETSLSVSNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 186

Query: 477 GNIGLMKAAEKFDWCL 492
           GNIGLMKA +KF++  
Sbjct: 187 GNIGLMKAVDKFEYRR 202


>gi|258488922|gb|ACV72467.1| RpoD [Xanthomonas axonopodis pv. alfalfae]
          Length = 261

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 117/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + +   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDDAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                                                         V   ++ +A  Y +
Sbjct: 121 GPTGPXPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|153953967|ref|YP_001394732.1| sporulation sigma factor SigG [Clostridium kluyveri DSM 555]
 gi|219854581|ref|YP_002471703.1| hypothetical protein CKR_1238 [Clostridium kluyveri NBRC 12016]
 gi|146346848|gb|EDK33384.1| SigG [Clostridium kluyveri DSM 555]
 gi|219568305|dbj|BAH06289.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 257

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 77/265 (29%), Positives = 138/265 (52%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + + + + +  ++ K +   + A+++ ++ NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTSKLPVLKEKEMKELLIKMQQGDNDAREKFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++  +  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALQVRDKLIRENNKEPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KN        I      +    +  L  RE+ +L +RF  G     T  E
Sbjct: 181 IYVMDQISDTKNVDENWLENI------SIKEAMKKLNDREKLILNLRFFDG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A+R ++ 
Sbjct: 231 VAHEIGISQAQVSRLEKTALRHMRK 255


>gi|258489044|gb|ACV72528.1| RpoD [Xanthomonas axonopodis pv. phaseoli]
          Length = 260

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 116/299 (38%), Gaps = 46/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGTFPLSTELLLSDYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++      D    + D +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDED 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                 +     + P+  E                           V   ++ +A  Y +
Sbjct: 110 GDDDAAEEEAGPTGPDPVE---------------------------VATRMENLANEYAK 142

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL ++   I  +E
Sbjct: 143 FKKAYVKYGAEHKN------VVKAREDMAAIFTTLKLPLPLTDSLVTQLREVVNGIKDHE 196

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 197 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIIAEQQ 254


>gi|4100836|gb|AAD01000.1| RpoS [Escherichia coli]
          Length = 259

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 82/229 (35%), Positives = 143/229 (62%), Gaps = 4/229 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 33  LDATQLYLGEIGYSPLLTAEE----VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 88

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 89  RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 149 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 208

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 209 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 257



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 26/96 (27%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E +L     + N     +     A +   D  ++YL E+G   LL+ E E+  A+R   
Sbjct: 4   DEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAE-EVYFARRALR 62

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           G       + ES L     I  R   N G  LL  I
Sbjct: 63  GDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 97


>gi|187927337|ref|YP_001897824.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12J]
 gi|309779962|ref|ZP_07674716.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
 gi|187724227|gb|ACD25392.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12J]
 gi|308921321|gb|EFP66964.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
          Length = 309

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++  I   I+S++    +S  E + +    R  +     A + +V ++LRLV+S+A+ Y 
Sbjct: 32  NLGNIDAYIQSVNRVPMLSAEEEQRLAREYRDNDNLD--AARRLVLSHLRLVVSIARGYL 89

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  +YAM W+K  +   I      +++   
Sbjct: 90  GYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRMVKVATT 149

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ +         + +A +L +    VR++    +   I+LE  + D
Sbjct: 150 KAQRKLFFNLRSHKQDAQATFTSDEIDAVAAELNVKGTEVREMETRLSGGDIALEGQMDD 209

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S     ++ D +         ++N R   E     LA L  R  R++  R+ + +N 
Sbjct: 210 GEESFAPIAYLADTHNEPTRVIEARSNDRMQSEGIEAALAKLDDRSRRIIEARW-LNVND 268

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           D     TL E+  +F V+ ERIRQIE+ A++K+K   ++
Sbjct: 269 DGSGGSTLHELADEFGVSAERIRQIESAAMKKMKGALQA 307


>gi|11078919|dbj|BAB17464.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   +    + ++        ESA    ++D  +    P  
Sbjct: 59  IDPDDGIAPPAEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVI 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L     + +  +   +                          
Sbjct: 111 AAQRFGAVSDQMEITRKALKKFGREDKHAIAEMV-------------------------- 144

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 145 ---------ALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    +G++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|209407278|emb|CAP72524.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 272

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/316 (19%), Positives = 120/316 (37%), Gaps = 46/316 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   D +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYDRVTSEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G         + Q+ E  + +       + + D E     S+++       PE 
Sbjct: 59  IDPDDDGAA-------APQEVEPVTPQTAAKPADDGKDDEEEDDSDSEEEEGDGGPDPEV 111

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  D +   L                                   +K  + 
Sbjct: 112 ARVRFGAVAEQLDAAKKAL-----------------------------------KKHGRG 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     ++L  L   + L   + D LVE++     ++   E  ++++      + R  
Sbjct: 137 SQQATEALQELATLFMPIKLIPKQYDALVERVRGALGQVRAQERAIMQICVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E D  W        + ++   +A   D I + + ++ ++  E  ++I++ + 
Sbjct: 197 FLRQFPSNETDLSWADQLAG-GKSKYAEAIAARKDDIQRCQQQLLALEEECVLAIADIKD 255

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 256 INRRMSIGEAKARRAK 271


>gi|83592357|ref|YP_426109.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575271|gb|ABC21822.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 306

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 129/276 (46%), Gaps = 17/276 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +   ++  +     A   +V ++LRLV  +A  Y + GL
Sbjct: 17  LSRYLTEIKRFPMLTPEEEFMLAKRLQ--DEGDRDAAHRLVTSHLRLVAKIAMGYRHYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+ EGN+GLMKA +KF+   G++ +TYAMWW+K +I   I +    +++      K
Sbjct: 75  PVSDLVAEGNMGLMKAVKKFEADRGFRLATYAMWWIKASINEYILNSWSLVKVGTVAAQK 134

Query: 529 IHKVVRTARRMSNKIKREPTPE-------EIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
             K+    RR+  K+      +        IA +L +    V  +  ++     SL  P+
Sbjct: 135 --KLFFNLRRLKAKLGVYEEGDLSPEDVKTIATQLKVTEADVVMMNRRLAGPDASLNVPV 192

Query: 581 GDEDTSHLGDFIEDK--NAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMN 637
           G++ +    D + D+  N      +  + +L        L++LT RE  ++        +
Sbjct: 193 GEDQSMDRMDLLMDEGDNQEEVYAAHEEQSLGNRLLKDALSTLTERERHIITA--RRLRS 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLEE+G ++ V+RER+RQIE +A  KL+   R 
Sbjct: 251 EPVTLEELGGEYGVSRERVRQIENRAFEKLQTAVRK 286


>gi|37784436|gb|AAO13111.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|37955130|gb|AAP76217.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 272

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 114/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     + DD       PE A   
Sbjct: 59  ETE-----DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L    + +  ++                                   QK+ ++    
Sbjct: 114 FGELRAQYEVTRLSI-----------------------------------QKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E D  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|258488870|gb|ACV72441.1| RpoD [Xanthomonas axonopodis pv. begoniae]
          Length = 261

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 117/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|209407288|emb|CAP72529.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 269

 Score =  138 bits (348), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 117/313 (37%), Gaps = 45/313 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   D +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYDRVTTEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G            + E  + +       + + D E     S ++       PE 
Sbjct: 59  IDPDDDGA------AGPQAEVEPVAPQAAAKPAGDDKDDEEEDDSDSDEEEGDGGPDPEV 112

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  D +   L                                   +K  + 
Sbjct: 113 ARVRFGAVAEQLDVAKKAL-----------------------------------KKHGRG 137

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     ++L  L   + L   + D LV+++ D   ++   E  ++++      + R  
Sbjct: 138 SQQATDALQELATLFMPIKLIPKQYDALVDRVRDALSQVRAQERAIMQICVRDARMPRAD 197

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E D  W     +  + ++   +A   + I + + ++ ++  E  ++I++ + 
Sbjct: 198 FLRQFPNNETDLDWAEKLAN-GKSKYAEAIAARKEDIQRCQQKLLALEEECILAIADIKD 256

Query: 430 IVSMVRKGECEAS 442
           I   +  GE +A 
Sbjct: 257 INRRMSIGEAKAR 269


>gi|149190801|ref|ZP_01869066.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
 gi|148835363|gb|EDL52335.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
          Length = 289

 Score =  138 bits (348), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 74/265 (27%), Positives = 145/265 (54%), Gaps = 6/265 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ- 469
             I  +     +S  +  H  ++ R+       A+  ++E+NLRLV+ +A+ YT RGL  
Sbjct: 22  KYIHDVVGIDLLSPEQEYHYATLARR---GDKAARDVLIESNLRLVVKIARNYTKRGLSN 78

Query: 470 --FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
              LDLI+EGN+GL+KA +KF+   G++FSTYA+WW++++I  S+ +   T+R+PVH+  
Sbjct: 79  HTILDLIEEGNLGLIKAIDKFEPEKGFRFSTYAVWWIRESIESSLMNTGRTVRLPVHVIK 138

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +I+++ +    +   ++R P+ +EIA+K A     +  ++ ++    S  +    +    
Sbjct: 139 EINRLSKQTNEIIADLQRPPSVKEIAEKTAKSQAQISDLIHMSGFIESSSSVDTIDKEFQ 198

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             +  + +    P D      L ++   V+ SL  +   ++  RFG+      TL+ +G+
Sbjct: 199 SLETCKSEAIPEPYDICHNEKLSQSLESVVLSLPEKYRDIVIHRFGLFGKEVLTLDNLGE 258

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSR 672
            F +++ER+RQ++ + I KL++  +
Sbjct: 259 MFGLSKERVRQLQQEGISKLQNKLK 283


>gi|220927320|ref|YP_002502622.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219951927|gb|ACL62319.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 296

 Score =  138 bits (348), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 122/274 (44%), Gaps = 12/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +  +E   +       E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLDEIRRFPMLEPTEEYMLAK--SWREHGDREAAHKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 72  PIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R+S   + +  PE   +IA +L +P + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKGRISALDEGDLRPEQVKQIATRLGVPEQDVIDMNRRLSGDASLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +              N        L+ L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDDSPSQEAVLAREEEGQNRLAALRDALSVLNPRERRIFEARRLAE--EPI 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 250 TLEDLSTEFGVSRERVRQIEVRAFEKVQDAVKRN 283


>gi|307328850|ref|ZP_07608020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885515|gb|EFN16531.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 276

 Score =  138 bits (348), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++  K   EA   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 30  LSRSLFLRLATL-DKDSAEAGYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 89  IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 148

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           ++ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  +++
Sbjct: 149 RLDRSPTVPELATALGVSEEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDS 208

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 209 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 259

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 260 RLLTRTLAQLRE 271


>gi|258488852|gb|ACV72432.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488894|gb|ACV72453.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488896|gb|ACV72454.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488898|gb|ACV72455.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488900|gb|ACV72456.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258488902|gb|ACV72457.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489082|gb|ACV72547.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489084|gb|ACV72548.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489086|gb|ACV72549.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
 gi|258489088|gb|ACV72550.1| RpoD [Xanthomonas campestris pv. mangiferaeindicae]
          Length = 261

 Score =  138 bits (348), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 118/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+                +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VAMRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            + +        K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|145300817|ref|YP_001143658.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853589|gb|ABO91910.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 284

 Score =  138 bits (348), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 117/239 (48%), Gaps = 7/239 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G +  ++A
Sbjct: 47  DLEAARQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFA 106

Query: 501 MWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           + W+K  I   +      +++     + K+   +R +++       +      A+    P
Sbjct: 107 VHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWFSHDEVQAVAAELGVSP 166

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTT 614
            +      +++    + +    DED        ++EDK+   A +  +     +     +
Sbjct: 167 TDVTEMEARMSNYDQAFDLVGDDEDEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLS 226

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             LA+L  R + ++R R+ +  ++  TL+E+   + V+ ER+RQ+E  A++KLK    +
Sbjct: 227 SALATLDERSQHIIRARW-LDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|258488994|gb|ACV72503.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489002|gb|ACV72507.1| RpoD [Xanthomonas axonopodis pv. allii]
 gi|258489004|gb|ACV72508.1| RpoD [Xanthomonas axonopodis pv. allii]
          Length = 261

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 118/299 (39%), Gaps = 45/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+     +  E+           +    +D + +++ D+  + E   E A
Sbjct: 61  HKEGKKRLAEIVVGFNDLIEEADAAAAALAAAGTVAVSDDEAVDEDDDEDGDDEAAEEEA 120

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                D                                        V   ++ +A  Y +
Sbjct: 121 GPTGPDPVE-------------------------------------VATRMENLANEYAK 143

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 144 FKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 197

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 255


>gi|260893400|ref|YP_003239497.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
 gi|260865541|gb|ACX52647.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
          Length = 256

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 71/262 (27%), Positives = 134/262 (51%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +   + +  +    +     A+ E+++ NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLTAQQMCRLFEAMKRGDGNARSELIKGNLRLVLSVVQRFANRGEH 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  LDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSLRDIA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++    ++++  REP+  EIA+ L +P E V   L+  ++P+SL  P+  +  D  +
Sbjct: 122 YKALQVRDVLASQYAREPSVAEIAEALKLPQEEVVMALEAIQDPVSLFEPVYHDGGDPIY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D+           A         +  L+ RE ++++MRF  G     T  EV +
Sbjct: 182 VMDQVGDEKNQDVNWLENIA-----IKEAMKRLSERERQIIKMRFFEG----KTQMEVAE 232

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+  ++ 
Sbjct: 233 EIGISQAQVSRLEKAALNHMRK 254


>gi|290959142|ref|YP_003490324.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
 gi|260648668|emb|CBG71781.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
          Length = 306

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 60  LSRSLFLRLAALDENSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 118

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 119 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 178

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 179 KLDRSPTVTELAAVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 238

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 239 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 289

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 290 RLLTRTLAQLRE 301


>gi|4100832|gb|AAD00998.1| RpoS [Escherichia coli]
          Length = 269

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 82/229 (35%), Positives = 143/229 (62%), Gaps = 3/229 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 42  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 98

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 99  RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 158

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 159 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 218

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
             L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 219 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 267



 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 2   AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 51

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 52  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 107


>gi|197336747|ref|YP_002158681.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
 gi|197313999|gb|ACH63448.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
          Length = 294

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 85/268 (31%), Positives = 152/268 (56%), Gaps = 6/268 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---L 468
            +K I+    ++  E      + +K       A+  ++E+NLRLV+ VA KY  R    L
Sbjct: 23  YLKEINRYQLLTAEEELVYSRLYKK---GDLSARNTLIESNLRLVVKVANKYRKRNQTDL 79

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LD+I+EGN+GL+KA +KF+  LGY+FSTYA+WW++++I  ++ + S T+R+PVH+  +
Sbjct: 80  AILDIIEEGNLGLIKAIDKFNPELGYRFSTYAVWWIRESIESALFNHSRTVRLPVHITKE 139

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           ++  +R AR +S  +KREP+  +I+         V K++ +    ++  +   DE +   
Sbjct: 140 LNTYLRAARELSKSLKREPSIRDISTYCEEEQIKVSKIISLIPNQLTCHSACSDELSPKF 199

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            +   +  A+ P +S  Q NL    +  + SL  RE+ ++  R+G+      TLE++GK 
Sbjct: 200 FELSSNNKALEPDNSLSQDNLEMNLSSWIDSLNYREKEIIINRYGLFGCKVKTLEDLGKD 259

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             +++ER+RQI+++ + KL    +  KL
Sbjct: 260 LDLSKERVRQIQSETLIKLNTIFKKNKL 287



 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 2/94 (2%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT-FQALIIWR 171
            ++   D   +YL+E+   +LL+ E E+  ++  + G      +L ES L     +    
Sbjct: 12  EEQGLKDSYSLYLKEINRYQLLTAEEELVYSRLYKKGDLSARNTLIESNLRLVVKVANKY 71

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
            + N     + +II+ E  +G       F+   G
Sbjct: 72  RKRNQTDLAILDIIE-EGNLGLIKAIDKFNPELG 104


>gi|11078977|dbj|BAB17493.1| DNA-directed RNA polymerase subunit D [Pseudomonas taetrolens]
          Length = 270

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 62/315 (19%), Positives = 118/315 (37%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +        D E     S D+  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDPKTAKAAEGDDEEEEKDDSTDEEEEVESGPDP 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ                     ++      +K  + 
Sbjct: 110 I------------IAAQRFGAVSDQ---------------------MEAARKALKKHGRD 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 137 SKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    G E+D  W   A    + ++   +      I++ + ++ ++  ETG+ ++E + 
Sbjct: 197 FLRLFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKVAEIKD 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRRMSIGEAKARRA 270


>gi|54401892|gb|AAV34631.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 83/200 (41%), Positives = 136/200 (68%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEVG 646
           VL  RFG+      TLE+VG
Sbjct: 181 VLARRFGLLGYEAATLEDVG 200


>gi|14994233|gb|AAK73284.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 144

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 100/142 (70%), Positives = 117/142 (82%)

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             +  RE TPEE+AK++ MP + +RKV+KI KEPIS+ETPIGD++ SHLGDFIED N  S
Sbjct: 1   LQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVES 60

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P+D+    NL ET   VLA LTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQI
Sbjct: 61  PVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 120

Query: 660 EAKAIRKLKHPSRSKKLRSFLD 681
           EAKA+RKL+HPSRS++LRSFLD
Sbjct: 121 EAKALRKLRHPSRSEQLRSFLD 142


>gi|182434526|ref|YP_001822245.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463042|dbj|BAG17562.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 300

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 124/246 (50%), Gaps = 8/246 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA 
Sbjct: 54  FFDRLQLLEEGTHEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAI 113

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D + ++ +P  +++    + +   ++S ++ R
Sbjct: 114 DRFDLSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLAKAKEQLSGELDR 173

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT +E+A  L +P E + + L         SL+TP  D D+        D    +    
Sbjct: 174 DPTVKELAAHLDLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYADVLGEADPGM 233

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               NL  T   +L  L  RE R+++MRFG     + T  ++G +  V++  + ++ ++ 
Sbjct: 234 ETVENLH-TLAPLLDQLDERERRIVQMRFGA----EMTQSQIGAELGVSQMHVSRLLSRI 288

Query: 664 IRKLKH 669
           +++L+ 
Sbjct: 289 VQQLRK 294


>gi|11079057|dbj|BAB17533.1| DNA-directed RNA polymerase subunit D [Pseudomonas agarici]
          Length = 268

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T + ++     +   +  L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHILGEYTRVTTESGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPIDAKAAKADDDSDDDEAEASDDEEEAESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQLEITTKAL-----------------------------------KKHGRH 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKAAIAELLALAELFMPIKLVPKQFEALVERVRGALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W + A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEIDESWTA-ALAKGKSKYAEAIGRLQPDIVRCQQKLSALEAETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|302746274|gb|ADL62727.1| RpoD [Morganella sp. RP-42]
          Length = 259

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 53/302 (17%), Positives = 105/302 (34%), Gaps = 47/302 (15%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I     + P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLIT--GFVDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
            +        E        +   E   +++ + + D +   +   D        PE A  
Sbjct: 59  NA--------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDPELARQ 110

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               L    + +                                Q   ++G+    ++ +
Sbjct: 111 KFEALRVQHEKAR-------------------------------QQIKIHGRDHPNTNAE 139

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            + L E    +     L   + D LV  + ++  R+   E  +++L  +   + +  F+ 
Sbjct: 140 IQQLSE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLCVEQSKMPKKNFIT 195

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
              G E    W + A    +  W   +    + + +    ++ I  ETG++I + + I  
Sbjct: 196 LFTGNETSDSWFTAAVAMNKP-WSEKLQDVAEEVERSLQGLRQIEEETGLTIKQVKDINR 254

Query: 433 MV 434
            +
Sbjct: 255 RM 256


>gi|78043932|ref|YP_360874.1| sporulation sigma factor SigG [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996047|gb|ABB14946.1| RNA polymerase sigma-G factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 76/262 (29%), Positives = 132/262 (50%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +   + +  +  K +     A+++++  NLRLV+S+ +++TNRG  
Sbjct: 4   NKVEICGVNTSKLPVLTNQEMKKLFLKVKEGDMEARQKLISGNLRLVLSIIQRFTNRGEY 63

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 64  VDDLFQVGCIGLIKAIDNFDLEQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDVA 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++    +  +  REPT  EIA++L +P E V   L   ++P+SL  PI  +  D   
Sbjct: 123 YKALQVRDNLVGRFSREPTVSEIAQELKVPQEEVVFALDAIQDPVSLFEPIYQDGGDPIF 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I+D+           A         L  L  RE  +L++RF  G     T  EV +
Sbjct: 183 VMDQIKDEKNTDHNWLQGIA-----LKEALERLNERERLILKLRFYEG----KTQMEVAE 233

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+  L+ 
Sbjct: 234 EIGISQAQVSRLEKAALNHLRK 255


>gi|226226008|ref|YP_002760114.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089199|dbj|BAH37644.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 302

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 97/274 (35%), Positives = 146/274 (53%), Gaps = 8/274 (2%)

Query: 411 NEIKSISVETGIS-ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
             +  I     I+  +E R +  + +K       A + +V ANLR VIS  KKY   GL 
Sbjct: 28  QYLHDIQKLPLITDAAEERRLARLAQK---GDEAAAERLVTANLRFVISYVKKYQGHGLD 84

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             +L+  GN GL+KA  KFD   G KF +YA+WWV+QA+ +++A+Q+ ++RIP++   ++
Sbjct: 85  LSELVAIGNEGLLKAVRKFDPDQGVKFISYAVWWVRQAVLKALAEQTRSVRIPLNQNSQL 144

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSH 587
            ++ R    +S  + REPT  E++K L  PVE VR   +I+   +SL+ PI  +D   S 
Sbjct: 145 IRMARGEMILSQVLNREPTDAELSKLLEEPVEQVRNARQISSTEVSLDAPIDRQDREAST 204

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMN-TDHTLEEV 645
           LG+    +      D      +RE   RV    LTPRE ++L + +G+       TLE +
Sbjct: 205 LGERFAGETHADIEDGTDFRLMREFIDRVFRKYLTPRERKILYLYYGLDEGAEAMTLERI 264

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           G    VTRERIRQI  +A  KL+     + L  F
Sbjct: 265 GALMGVTRERIRQIRERAFEKLRESPDGRALSGF 298


>gi|11078991|dbj|BAB17500.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 268

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 115/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDDDAEASDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQMEITRKAL-----------------------------------KKHGRY 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKAAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|317154823|ref|YP_004122871.1| sigma-70 family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316945074|gb|ADU64125.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 397

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 84/300 (28%), Positives = 145/300 (48%), Gaps = 14/300 (4%)

Query: 389 DFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
           D PE     FV      +     ++  +K I+    +   E   +   V+  +     A 
Sbjct: 94  DPPESRLPAFVVASSKEVRVRDPLQLYLKEIARFPLLDPEEEYALAKRVQ--DENDQDAA 151

Query: 446 KEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            ++V ++LRLV+ +A  +  R +Q  LDLIQEGN+GL+KA  KFD   G KFS YA +WV
Sbjct: 152 FKLVSSHLRLVVRIAMDFQRRWMQNALDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAFWV 211

Query: 505 KQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           K  I + I D    +++     + K+   +   R+    +  +PT E ++K L +    +
Sbjct: 212 KAYILKYIMDNWRMVKVGTTQTQRKLFYNLNKERQRLQAMGFDPTTEALSKSLGVSEAEI 271

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLAS 619
                ++++  +SL  P+G++  +   DF+         S     I   L E    +  +
Sbjct: 272 DEMDQRLSRNDMSLNAPLGEDSDATRMDFLPSLGPGIEESLASDQIVELLLENLKAIRPT 331

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  +E  +L     +  +   TL E+G++F VTRER+RQIEA+ I K++    ++K++ F
Sbjct: 332 LNDKELAILDH--RLLSDDPMTLREIGERFEVTRERVRQIEARLIAKIREHM-TEKIKGF 388



 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 35/91 (38%), Gaps = 1/91 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           DD   +  S  +L        S +       S +    DP+++YL+E+    LL  E E 
Sbjct: 77  DDSLGDPLSGTALPARLDPPESRLPAFVVASSKEVRVRDPLQLYLKEIARFPLLDPEEEY 136

Query: 141 AIAKRIE-AGRAMMMASLCESPLTFQALIIW 170
           A+AKR++          L  S L     I  
Sbjct: 137 ALAKRVQDENDQDAAFKLVSSHLRLVVRIAM 167


>gi|258488908|gb|ACV72460.1| RpoD [Xanthomonas axonopodis pv. dieffenbachiae]
          Length = 259

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 114/299 (38%), Gaps = 47/299 (15%)

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 1   GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 60

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++         E   + +  
Sbjct: 61  HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDG 109

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
              + ++ +    P                                V   ++ +A  Y +
Sbjct: 110 DDEAAEEEAGPTGPDPVE----------------------------VATRMENLANEYAK 141

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +          K+          +E +  +  +L L     D LV QL  +   I  +E
Sbjct: 142 FKKAY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHE 195

Query: 354 GELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            ++L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 196 RKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 253


>gi|3021682|dbj|BAA25361.1| RNA polymerase sigma-70 factor [Pseudomonas chlororaphis]
 gi|11079029|dbj|BAB17519.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. chlororaphis]
 gi|11079033|dbj|BAB17521.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. chlororaphis]
 gi|11079037|dbj|BAB17523.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. chlororaphis]
 gi|11079039|dbj|BAB17524.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. aureofaciens]
 gi|11079043|dbj|BAB17526.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. chlororaphis]
          Length = 268

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 116/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T + ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDAKAAKADDDTDDDDAEASDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQMEITRKAL-----------------------------------KKHGRE 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +       L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 HKQALAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|297158639|gb|ADI08351.1| RNA polymerase sigma factor, sigma L [Streptomyces bingchenggensis
           BCW-1]
          Length = 276

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++ R      +  +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 30  LSRSLFLRLAALDRDSVEH-TYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + +T+  +S 
Sbjct: 89  IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELSQ 148

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  +++
Sbjct: 149 KLDRSPTVTELATALGVSEEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDS 208

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 209 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 259

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 260 RLLTRTLAQLRE 271


>gi|49473931|ref|YP_031973.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49239434|emb|CAF25783.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 294

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 67/278 (24%), Positives = 129/278 (46%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +     +   E   +    R+       A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEVRRFPILEPKEEYMLAQRYRQH--NDLKAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A ++F+   G + +TYA+WW+K +I   +      ++I    + +
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGLRLATYAIWWIKASIQEYVLRSWSLVKIGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R+    K +   E   EIA +L +  + V  + +      SL  P+  +
Sbjct: 134 RLFFNLRKLKSRLQVLDKGDLNAEQVKEIATQLNVTEDEVISMNRRLCGDTSLNAPLRTQ 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +   S   D++ D +         Q+ L   R   T  +++L  RE+R+ +       + 
Sbjct: 194 EGENSEWQDWLVDDSNNQEQTLIEQSELENRRSMLTYAMSNLNEREKRIFKA--RRLSDK 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIE +A  K+++  ++  L
Sbjct: 252 PLTLEELSSEFNISRERVRQIEMRAFEKVQNSIKASAL 289


>gi|21222437|ref|NP_628216.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256786489|ref|ZP_05524920.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289770380|ref|ZP_06529758.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|13122198|emb|CAC32374.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289700579|gb|EFD68008.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 318

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 72  LSRSLFLRLAALGEDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 130

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 131 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 190

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 191 KLDRSPTVGELAAVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 250

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 251 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 301

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 302 RLLTRTLSQLRE 313


>gi|11079051|dbj|BAB17530.1| DNA-directed RNA polymerase subunit D [Pseudomonas agarici]
          Length = 268

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 118/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T + ++     +   +  L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHILGEYTRVTTESGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGVAPPAAEVPPPIDAKAVKADDDSDDDEAEASDDEEEAESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQLEITTKAL-----------------------------------KKHGRH 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKAAIAELLALAELFMPIKLVPKQFEALVERVRGALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W + A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEIDESWTA-ALAKGKSKYAEAIGRLQPDIVRCQQKLSALEAETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|158425877|ref|YP_001527169.1| RNA polymerase factor sigma-32 [Azorhizobium caulinodans ORS 571]
 gi|158332766|dbj|BAF90251.1| sigma-70 factor [Azorhizobium caulinodans ORS 571]
          Length = 300

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 67/272 (24%), Positives = 120/272 (44%), Gaps = 14/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--SWREHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   +   +     R    ++IA KL +  + V  + +      SL  P+ ++
Sbjct: 134 KLFFNLRKAKSQISALEEGDLRPDQVKQIATKLGVTEQDVVDMNRRLSGDASLNAPLRED 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
                   D+++D +     +      L   R   +  LA L PRE R+           
Sbjct: 194 GDGGGEWQDWLQDDHQDQETNLVESEELDNRRTALSSALAVLNPRERRIFEA--RRLSED 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TLEE+  +F V+RER+RQIE +A  K++  
Sbjct: 252 PVTLEELAAEFGVSRERVRQIEVRAFEKVQKA 283


>gi|300705271|ref|YP_003746874.1| RNA polymerase sigma h (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
 gi|299072935|emb|CBJ44291.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
          Length = 306

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  +   I+S++    ++  E + +             A + +V ++LRLV+S+A++Y 
Sbjct: 29  SLGNLDAYIQSVNRVPMLTAEEEQQLAR--DYHATGDLDAARRLVLSHLRLVVSIARQYL 86

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W+K  +   I      +++   
Sbjct: 87  GYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATT 146

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ ++        + +A++L +    VR++    +   I+LE  I D
Sbjct: 147 KAQRKLFFNLRSHKQDAHATFTSDEIDAVAQELNVKGAEVREMETRLSGGDIALEGHIDD 206

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S     ++ D +         + + R   E     LA L  R  R++  R+ + +N 
Sbjct: 207 GEESFAPIAYLADTHNEPTRVLETRGHDRLQSEGIETALAKLDDRSRRIIEARW-LNVND 265

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           D     TL E+  +F V+ ERIRQIE+ A++K+K   ++
Sbjct: 266 DGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQA 304


>gi|225055401|gb|ACN80687.1| Tsr7 [Streptomyces laurentii]
          Length = 336

 Score =  138 bits (347), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 107/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 108 EHQHVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTF 167

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 168 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLKIG 227

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 228 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 282

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 283 VQLPEREQRILMLRYYSN----LTQSQISQELGVSQMHVSRLLARSFARLRSANR 333


>gi|11079204|dbj|BAB17593.1| DNA-directed RNA polymerase subunit D [Pseudomonas cichorii]
          Length = 269

 Score =  138 bits (347), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++   + +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYERVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +     +++ D E + + S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPLDAKAAKADDSDDDEEESGEASDDEEEAESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     ++ +          +     +  L  +AE++                   
Sbjct: 110 VAQQRFGAVSEQMEITRKALKKFGREDKNAIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRSALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIQRCQQKLTALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|11078937|dbj|BAB17473.1| DNA-directed RNA polymerase subunit D [Pseudomonas caricapapayae]
 gi|11078945|dbj|BAB17477.1| DNA-directed RNA polymerase subunit D [Pseudomonas caricapapayae]
          Length = 269

 Score =  138 bits (347), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADGSDDEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    +G++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|160943880|ref|ZP_02091110.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444556|gb|EDP21560.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104729|emb|CBL02273.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii SL3/3]
          Length = 255

 Score =  138 bits (347), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 70/259 (27%), Positives = 132/259 (50%), Gaps = 14/259 (5%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V TG + +        ++         A+  MVE NLRLV+SV +++  RG  
Sbjct: 3   NKVELCGVNTGQLPVLTEAEKRQLLTLAHAGDKAARARMVEGNLRLVLSVVQRFAQRGEN 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +RD  
Sbjct: 63  LDDLFQVGCIGLIKAIDNFDPAQPVRFSTYGVPMIIGEIRRFLRDNN-ALRVSRTLRDTA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           ++ ++    +  ++ REPT +EIA    +    V   L+   EP+SL+ P+  +  D  +
Sbjct: 122 YRAMQARETLEKQLGREPTMDEIAAAAGLARREVTAALESVVEPLSLDEPVYTDGGDAMY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D ++     S +Q          +A+L+PRE+R++ +R+  G     T  EV +
Sbjct: 182 VIDQVRDPDSEESWISGLQ------FRDTVAALSPREKRIMELRYLRG----KTQMEVAQ 231

Query: 648 QFCVTRERIRQIEAKAIRK 666
           +  +++ ++ ++E  A+++
Sbjct: 232 EIGISQAQVSRLEKGALQQ 250


>gi|11079041|dbj|BAB17525.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. aureofaciens]
          Length = 268

 Score =  138 bits (347), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 116/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T + ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEIPPPVDAKAAKADDDTDDDDAEASDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQMEITRKAL-----------------------------------KKHGRE 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
             +       L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 HKQALAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|11079067|dbj|BAB17538.1| DNA-directed RNA polymerase subunit D [Pseudomonas agarici]
          Length = 268

 Score =  138 bits (347), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 117/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T + ++     +   +  L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVEHILGEYTRVTTESGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E            + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGVAPPAAEVPPPIDANAVKADDDSDDDEAEASDDEEEAESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQLEITTKAL-----------------------------------KKHGRH 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKAAIAELLALAELFMPIKLVPKQFEALVERVRGALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W + A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEIDESWTA-ALAKGKSKYAEAIGRLQPDIVRCQQKLSALEAETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|170752008|ref|YP_001758268.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170658530|gb|ACB27585.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 297

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 121/274 (44%), Gaps = 12/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +  SE   +    R  +     A   +V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLDEIRKFPMLEPSEEFTLAKAWR--DAGDREAAHRLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 72  PIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P+   +IA +L +P + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKGKISALDEGDLKPDQVKQIATRLGVPEQDVIDMNRRLSGDTSLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +              N        L  L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDNSPSQETVLAREQEGQNRLSALKDALGVLNPRERRIFEARRLAE--DPI 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 250 TLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 283


>gi|55274943|gb|AAV49271.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 204

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 82/204 (40%), Positives = 137/204 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+   ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDFSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFC 650
           VL  RFG+      TLE+VG++  
Sbjct: 181 VLARRFGLLGYEAATLEDVGREIG 204


>gi|226939164|ref|YP_002794235.1| RNA polymerase factor sigma-32 [Laribacter hongkongensis HLHK9]
 gi|226714088|gb|ACO73226.1| RpoH [Laribacter hongkongensis HLHK9]
          Length = 282

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 71/264 (26%), Positives = 130/264 (49%), Gaps = 7/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E + +   +++       A +++V ++LR+V+S+A+ Y   GL
Sbjct: 16  LDQYIAAVNSIPMLSQDEEQALARRLQQDN--DVEAARQLVMSHLRVVVSIARGYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   I      +R+      +
Sbjct: 74  PQADLIQEGNIGLMKAVKRFEPERGVRLFSFAIHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + +       +    +IA  L +  E VR++  +++ + ISL     +E+   
Sbjct: 134 KLFFNLRSMKQGFSALSDTEARQIADDLGVKPEEVREMETRMSGQDISLLAEDNEEEGFA 193

Query: 588 LGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             D++ D  +       +QA     RE   + L +L PR  R++  R+        TL +
Sbjct: 194 PIDWLADTRSEPTKQLEMQAYERLQREGIEQALQALDPRSRRIIEARWLADDGG-LTLHD 252

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +  +F V+ ERIRQIE KA++K+K
Sbjct: 253 LAAEFGVSAERIRQIEVKALKKMK 276


>gi|289169247|emb|CAX46383.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 271

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 114/315 (36%), Gaps = 45/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGF 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P          +         S   ++    ++ E + E       +D       PE 
Sbjct: 59  IDPN------EADDVAPTATHIGSELSEDDLADEDEEDEDEDGDGDDAEDEGDGGPDPEV 112

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L    + +  ++                                   QK+ ++
Sbjct: 113 AREKFGELRAQYEVTRLSI-----------------------------------QKNGRA 137

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
               +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  
Sbjct: 138 HDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKT 197

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F+      E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + 
Sbjct: 198 FVAAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EDVLRAIGKLQQIEEETGLSIAQIKD 256

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 257 INRRMSIGEAKARRA 271


>gi|11078997|dbj|BAB17503.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 268

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 115/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDDEADSSDDEEEAESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  +S
Sbjct: 110 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRS 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKAAIAELLLLAELFMPIKLVPKQFEALVERVRGALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPSNEVDESWSD-ALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|11078917|dbj|BAB17463.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078921|dbj|BAB17465.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078927|dbj|BAB17468.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078935|dbj|BAB17472.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078941|dbj|BAB17475.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078943|dbj|BAB17476.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|11078947|dbj|BAB17478.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|11078949|dbj|BAB17479.1| DNA-directed RNA polymerase subunit D [Pseudomonas amygdali]
 gi|11078951|dbj|BAB17480.1| DNA-directed RNA polymerase subunit D [Pseudomonas amygdali]
 gi|11078953|dbj|BAB17481.1| DNA-directed RNA polymerase subunit D [Pseudomonas amygdali]
 gi|11078955|dbj|BAB17482.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|11078959|dbj|BAB17484.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
 gi|146150873|gb|ABQ02693.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
 gi|315064861|emb|CBX20966.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
 gi|315064865|emb|CBX20968.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
 gi|317447071|emb|CBX24519.1| sigma factor 70 [Pseudomonas syringae pv. phaseolicola]
          Length = 269

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|297746567|emb|CAZ61001.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|297746569|emb|CAZ61002.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 267

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/304 (20%), Positives = 108/304 (35%), Gaps = 44/304 (14%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I
Sbjct: 1   ELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFI 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P             +         E +  D  E E + E     + DD       PE A
Sbjct: 59  DPNETE-----DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVA 113

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                 L    + +  ++                                   QK+ ++ 
Sbjct: 114 REKFGELRAQYEVTRLSI-----------------------------------QKNGRAH 138

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
              +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F
Sbjct: 139 EDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTF 198

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +      E D  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I
Sbjct: 199 VAAFTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLSIAQIKDI 257

Query: 431 VSMV 434
              +
Sbjct: 258 NRRM 261


>gi|163794484|ref|ZP_02188455.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
 gi|159180208|gb|EDP64731.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
          Length = 298

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 125/279 (44%), Gaps = 13/279 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E +   +  ++V ++LRLV  +A  Y   GL
Sbjct: 17  LSRYLQEIRKFPMLEPGEEYVLAK--SWREHDDVESAHKLVTSHLRLVAKIAMGYRGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGN+G+M+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 75  PLAELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRASIQEYILHSWSLVKMGTTAAQK 134

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + R   +M      + +PE    IA+KL +   + V    ++     SL  P+  
Sbjct: 135 KLFFNLRRLKGQMQAIEDGDLSPERVTAIAEKLDVSEADVVSMNRRLASPDHSLNAPLRQ 194

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D++ D+     +  A    L   R      + +L  RE  +L  R        
Sbjct: 195 DGEGEWQDWLVDEGQNQEVSFAEDEELSKRRRLLNVAMETLNDRERHILTERRLRDN--P 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            TLE++ +++ ++RER+RQIE +A  KL+   ++  +  
Sbjct: 253 TTLEDLSQEYDISRERVRQIEVRAFEKLQKAIKNAAIEE 291


>gi|3077740|dbj|BAA25788.1| SigC [Cyanidium caldarium]
          Length = 424

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 97/330 (29%), Positives = 163/330 (49%), Gaps = 49/330 (14%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           +   +    +   K+  E       T + +SE       VR        A+  +V +NLR
Sbjct: 99  YCALMKQREELCAKLGREPTDTEWSTTVGVSEEE-----VRNEIERGRRARARLVASNLR 153

Query: 455 LVISVAKKYTNR-------------GLQFL----------------DLIQEGNIGLMKAA 485
           LV+++A +Y +R             G+                   DLIQEG +GL++AA
Sbjct: 154 LVLAIANRYKSRAVVRSAWKSRSKGGMDMPSHEKVRLQRQHNIFLGDLIQEGALGLIRAA 213

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD   G+KFSTYA WW++QAI R +++ S TIR+P H+ + + ++ R   R+ + +KR
Sbjct: 214 EKFDPSKGFKFSTYATWWIRQAIQRCVSEHSRTIRLPNHVTESLRQIYRMRARLQHVLKR 273

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI-------------SLETPIGDEDTSHLGDFI 592
            PT EE+A+   M ++ ++K+ +   +               SL      E    +G  I
Sbjct: 274 PPTDEEVAEACNMTLKRLKKITQHAWKTQTLSLEGPPNNEAHSLYKSQQGEAPLSIGSII 333

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCV 651
           E     +P ++  +  +RE    VL +L  +E  +LR+R+GI  +   H+ EE+  +F +
Sbjct: 334 E-ATEETPEEALERNCMREDVECVLRTLPFQEREILRLRYGISDDERPHSTEELSARFQL 392

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
               IR IE++A+RKL+HPS +  LR +++
Sbjct: 393 PVHTIRLIESRALRKLRHPSLAAMLREYVN 422


>gi|77919976|ref|YP_357791.1| RNA polymerase, sigma (32) factor [Pelobacter carbinolicus DSM
           2380]
 gi|77546059|gb|ABA89621.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter carbinolicus DSM
           2380]
          Length = 286

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 70/264 (26%), Positives = 119/264 (45%), Gaps = 11/264 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I  I     ++  E   +     + +     A ++++ ANLR V+ +A +Y   GL+ L
Sbjct: 16  YIAQIRAFELLTKEEEFRLTQDYHRNQNI--EAAQQLICANLRFVVKIAHEYRGYGLKLL 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--I 529
           D+IQEGNIGLMKA +KFD   G +F TYA+WW++  I   I      ++I      K   
Sbjct: 74  DIIQEGNIGLMKAVKKFDPDRGLRFITYAVWWIRAYIHNFIIRNWSLVKIGTTQAQKKLF 133

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
            K+ +    +      E T   IA++L +  + V  +  ++     SL+  + + +   L
Sbjct: 134 FKLNQVRSAIQRMTGSEDTKA-IARELNVRDDEVEDMARRMAGRDTSLDMRLVEGEDFTL 192

Query: 589 GDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            D + D+          Q   +         L  L  RE R++     I      TL+ +
Sbjct: 193 LDSLADERESQEELLIKQQEKQITTSHIHGALQELNDRERRIVEE--RILQEEPRTLQAL 250

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
              F ++RER+RQ+E  A+ K++ 
Sbjct: 251 ADDFGISRERVRQLEKNALEKIRK 274


>gi|299134310|ref|ZP_07027503.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
 gi|298591057|gb|EFI51259.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
          Length = 299

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 123/274 (44%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +  I     +   E   +    R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSHYLAEIRKFPMLEPQEEYMLAKRWR--EHDDRDAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   +   +     RE   + IAK+L +    V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALEEGDMREDQVKLIAKRLGVTERDVIDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +        +S    + R   T  +  L PRE R+   R        
Sbjct: 194 GEPGEWQDWLVDTSPNQEAIMAESEEYDHRRNALTGAMGVLNPRERRIFEARRLAE--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++  +F V+RER+RQIE +A  K++   +S
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKS 285


>gi|239980907|ref|ZP_04703431.1| RNA polymerase sigma factor, sigma F [Streptomyces albus J1074]
 gi|291452769|ref|ZP_06592159.1| transcription initiation factor sigma F [Streptomyces albus J1074]
 gi|291355718|gb|EFE82620.1| transcription initiation factor sigma F [Streptomyces albus J1074]
          Length = 294

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 115/267 (43%), Gaps = 15/267 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             R         T +  S+ +     V  G  E +  +  ++EANL LV   A ++ +R 
Sbjct: 38  AARKRGADTRALTQLLFSQLKE----VEPGTAEHARVRSALIEANLPLVRYAAARFRSRN 93

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               D++Q G IGL+ A ++FD   G +F T+AM  V   I R   D   T+ +P  + +
Sbjct: 94  EPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHE 153

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDT 585
              +V      ++    R PT  EIA++L +  + V   ++   +    SLE     +  
Sbjct: 154 LWVQVTSATEDLTTAHGRSPTTAEIAERLRISEDEVLACIEAGRSYHATSLEAAQEGDGL 213

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D +  ++             R+    +L  L  RE+R+L +R+        T  ++
Sbjct: 214 PGLLDRLGYEDPALDGVEH-----RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQI 264

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +  V++  + ++ A++  +L+  +R
Sbjct: 265 SAELGVSQMHVSRLLARSFARLRSANR 291


>gi|167628452|ref|YP_001678951.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591192|gb|ABZ82940.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 264

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 66/244 (27%), Positives = 118/244 (48%), Gaps = 12/244 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
                 ++R  +     A++ +++ NLRLV ++ +++ +RG +  DL Q G IGL+KA +
Sbjct: 18  EEETTRLLRLAKDGDGDARERLIQCNLRLVFNLVQRFQHRGYELEDLFQIGVIGLIKAID 77

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     +FSTYA+  +   I R + D    +++    ++   ++ R  + ++  + RE
Sbjct: 78  KFDLSYNVRFSTYAVPMIVGEIRRFLRD-DSPVKVSRSYKEIAQRIHRVRQELNGSLGRE 136

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSA 604
           PT +EIA  + MPVE V + L+  + P S+   +  +D     L D +            
Sbjct: 137 PTVQEIAGAMNMPVEDVVEALEAVQLPTSIHETLYQDDGDPIFLLDQLASVGTEESAWFD 196

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                      VL+ L  RE  +L MRF      D T  EV     +++ +I +IE  A+
Sbjct: 197 -----HLALKDVLSRLAAREREILEMRFF----QDKTQTEVATLVGLSQVQISRIERAAL 247

Query: 665 RKLK 668
           +K++
Sbjct: 248 KKIR 251


>gi|38524289|emb|CAD57740.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri CLN100]
          Length = 275

 Score =  138 bits (346), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 61/318 (19%), Positives = 122/318 (38%), Gaps = 45/318 (14%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   +M+++   P T  +++   D +      L +I  L 
Sbjct: 1   GTVELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYDRVTTEGGRLSDI--LS 58

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P+  G           Q+ E ++ +       + + D       S+++       P
Sbjct: 59  GYIDPDDDGA------AGPQQEVEPAAPQAAAKPAGDGKDDENEDDSDSEEEEGDGGPDP 112

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           E A      + E  D +   L                                   +K  
Sbjct: 113 EVARVRFGAVAEQLDIAKKAL-----------------------------------KKHG 137

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKR 367
           + S +     + L  L   + L   + D LV+++ +   ++   E  ++++      + R
Sbjct: 138 RGSQQATDALQALATLFMPIKLIPKQYDALVDRVRNALSQVRAQERAIMQICVRDACMPR 197

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             FL +    E D  W     +  + ++   +A   + I + + ++ ++  E  ++I++ 
Sbjct: 198 AEFLRQFPNNETDLDWADRLAN-GKSKYAEAIAARKEDIQRCQQQLLALEEECILAIADI 256

Query: 428 RHIVSMVRKGECEASIAK 445
           + I   +  GE +A  AK
Sbjct: 257 KDINRRISIGEAKARRAK 274


>gi|330814385|ref|YP_004358624.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327487480|gb|AEA81885.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 300

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 121/271 (44%), Gaps = 14/271 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +  I     +  +E   +    R  E     A  ++V ++LRLV  +A  Y   GL  
Sbjct: 21  SYLSKIRKFPMLDAAEEYVLAKNWR--EQGDKDAAHKLVTSHLRLVAKIAMGYRGYGLPV 78

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI- 529
            +L+ EGNIGLM+A  KFD   G++ +TYAMWW+K +I   +      ++I      K  
Sbjct: 79  SELVSEGNIGLMQAVRKFDPEKGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTSAQKKL 138

Query: 530 ----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED 584
                K+                  EIA +L +  + V     ++     SL  P+G ED
Sbjct: 139 FFNLKKIKNQIFAAEQGNMLPEHITEIATQLDVREDEVVSMNQRLAGHEHSLNAPVGGED 198

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +   D++ D+NA   L  + +  L +        L  L  RE+ +L  R  I      
Sbjct: 199 SDAEWQDWVVDENADQELQISQKQELNQRQSLLKNALHVLDEREKEILHNRRLID--EPK 256

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TLEE+ ++  V+RERIRQIE +A  K++   
Sbjct: 257 TLEELSQKHKVSRERIRQIENRAFEKVQKAM 287


>gi|217969486|ref|YP_002354720.1| RNA polymerase factor sigma-32 [Thauera sp. MZ1T]
 gi|217506813|gb|ACK53824.1| RNA polymerase, sigma 32 subunit, RpoH [Thauera sp. MZ1T]
          Length = 283

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 71/265 (26%), Positives = 129/265 (48%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+S++    +S  +   + + +R  +     A +++V ++LR+V+++A+ Y   GL
Sbjct: 15  LDQYIQSVNRMPMLSEQQEVELATRLR--DEGDVDAARQLVMSHLRVVVAIARGYLGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      ++I     + 
Sbjct: 73  PHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHWIKAEIHEYILKNWRLVKIATTKAQR 132

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   +R  ++ S+ ++        A+    P E V    +++   I L+    DED   
Sbjct: 133 KLFFNLRGMKQDSSTLQPAEVRSIAAQLGVKPEEVVEMETRLSGRDIPLDAGSDDEDERF 192

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               ++ D +A            R         LASL  R   +++ R+ +      TL 
Sbjct: 193 APIAYLPDPHAEPSEQVEQAQLARLQDSGLRDALASLDERSRAIVQRRW-LAEGDSATLH 251

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  ++ V+ ERIRQIEAKA++K++
Sbjct: 252 ELAAEYGVSAERIRQIEAKAMQKMR 276


>gi|329910210|ref|ZP_08275256.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546240|gb|EGF31276.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 298

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 129/266 (48%), Gaps = 8/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I + I +++    ++  E   +   +R        A + MV ++LRLV+S+A+ Y   GL
Sbjct: 28  IDSYISAVNRLPMLTHEEEMSLARRLRDQNDLG--AAQGMVLSHLRLVVSIARGYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  +YAM W+K  +   I      +++      +
Sbjct: 86  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDT-- 585
                  + +           E +A+ L +  E V ++    +   I+LE P  DED   
Sbjct: 146 KLFFNLRSHKTGLDSMTPAQVEALAQTLNVKREEVIEMETRLSGRDIALEAPTDDEDDKF 205

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNTD-HTL 642
           + +     D+N  + +  A Q +  ++   ++ L  L  R  R++  R+    +    TL
Sbjct: 206 APIAYLSSDRNEPTNVLEAQQYDRLQSDGLSQALNKLDERSRRIVEARWLANDDGSGATL 265

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+ K+F V+ ERIRQIEA A++K+K
Sbjct: 266 HELAKEFGVSAERIRQIEAVALKKMK 291


>gi|54401890|gb|AAV34630.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274947|gb|AAV49273.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 203

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 83/203 (40%), Positives = 139/203 (68%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V +
Sbjct: 61  QTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSR 120

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 121 MLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 180

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQ 648
            VL  RFG+      TLE+VG++
Sbjct: 181 EVLARRFGLLGYEAATLEDVGRE 203


>gi|134298969|ref|YP_001112465.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134051669|gb|ABO49640.1| RNA polymerase, sigma subunit, RpoX/SigF [Desulfotomaculum reducens
           MI-1]
          Length = 260

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 130/247 (52%), Gaps = 12/247 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +  +++K +   S A++ +V  NL+LV ++ ++++NRG +  DL Q G IGLMKA +K
Sbjct: 20  KEMRGLLKKAQSGNSEARERLVNCNLKLVFNLVQRFSNRGYELEDLFQIGCIGLMKAIDK 79

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D    +++   +++  +K+ +T  R++ ++ REP
Sbjct: 80  FDLSYDVKFSTYAVPMIVGEIRRFLRD-DSPVKVSRSLKETAYKIQQTRDRLTARLGREP 138

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAI 605
           +  EIA++L+   E V   L+  + P S+   +  +D    ++ D +  ++         
Sbjct: 139 SINEIAEELSYSREEVVNALEAAQMPTSIYETLHQDDGDPIYILDQLSGEDEGDAPWLE- 197

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +    ++L  L  R+ ++L  RF      D T  EV  +  +++ ++ ++E +A+R
Sbjct: 198 ----KLAVKQILIQLPERDRQILLWRFF----EDKTQSEVALRLGLSQVQVSRLERQALR 249

Query: 666 KLKHPSR 672
           KLK    
Sbjct: 250 KLKELMH 256


>gi|222632729|gb|EEE64861.1| hypothetical protein OsJ_19718 [Oryza sativa Japonica Group]
          Length = 457

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 132/251 (52%), Gaps = 5/251 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +R+       A+ ++++ NLRLV+    KY    +   +F D+ Q G  GL+ A ++F+
Sbjct: 209 QMRRHLEVGRAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDRFE 268

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++ STYA++W++ +I R+I   S   R P  M  +  ++ R    ++ ++ R PT 
Sbjct: 269 PKRGFRISTYALFWIRHSIVRAITL-SNFTRFPFAMESERQEIHRAREELAFELGRAPTE 327

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+ KK+ +     R V+++T+   SL           L + + D +A+    S+    L
Sbjct: 328 EEVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQE-ELINEVTDDDAIGVDTSSHNTLL 386

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R     +L SL P+E  V+R RFG+      TL E+     ++RE +R+ E KA+ KLKH
Sbjct: 387 RLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYELKALMKLKH 446

Query: 670 PSRSKKLRSFL 680
           P+R + LR ++
Sbjct: 447 PTRVEYLRRYM 457


>gi|55274913|gb|AAV49258.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274972|gb|AAV49285.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 83/200 (41%), Positives = 137/200 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGK 647
           L  RFG+      TLE+VG+
Sbjct: 181 LARRFGLLGYEAATLEDVGR 200


>gi|55274911|gb|AAV49257.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274963|gb|AAV49281.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 202

 Score =  138 bits (346), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 83/202 (41%), Positives = 138/202 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQF 649
           L  RFG+      TLE+VG++ 
Sbjct: 181 LARRFGLLGYEAATLEDVGREI 202


>gi|91978913|gb|ABE66432.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|106895876|gb|ABF82641.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 272

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + +     S DD +     PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDDEADTGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L    + +  ++                                   Q + ++    
Sbjct: 114 FGELRAQYEVTRLSI-----------------------------------QNNGRAHDDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E D  W  Y K   +      V  + + +L+   +++ I VETG+SI++ + I   
Sbjct: 199 FTNNECDTAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEVETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|148793322|gb|ABR12725.1| RNA polymerase sigma factor [Photobacterium indicum]
          Length = 271

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 120/318 (37%), Gaps = 49/318 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDII--SGF 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P          E  +         E    D+ + + ++E+     +++ + +D  PE 
Sbjct: 59  IDPN--------EEQTAAPTATHIGSELSETDLADEDKNLETDEDDEEEEDTGID--PEL 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L    +  A  ++                                      + 
Sbjct: 109 AREKFLELRHSYEKMALAINT-----------------------------------HGRH 133

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +   +V   +L ++     L   + D LV  L D   ++  NE  ++R+      + +  
Sbjct: 134 NATTEVAVGELSEIFKQFRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCVDNSKMPKKT 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E  P W+  A +  +  +   +    + + +   +++ +  ETG+SI   + 
Sbjct: 194 FIKFFAGNESSPDWIDEALNSGKP-YAERLKIYEEDLRRSSLKLRILEKETGLSIERIKD 252

Query: 430 IVSMVRKGECEASIAKKE 447
           I   +  GE +A  AKKE
Sbjct: 253 ISRRMSIGEAKARRAKKE 270


>gi|33594607|ref|NP_882251.1| RNA polymerase factor sigma-32 [Bordetella pertussis Tohama I]
 gi|33598734|ref|NP_886377.1| RNA polymerase factor sigma-32 [Bordetella parapertussis 12822]
 gi|33603808|ref|NP_891368.1| RNA polymerase factor sigma-32 [Bordetella bronchiseptica RB50]
 gi|33564683|emb|CAE44005.1| RNA polymerase sigma-32 factor [Bordetella pertussis Tohama I]
 gi|33574864|emb|CAE39527.1| RNA polymerase sigma-32 factor [Bordetella parapertussis]
 gi|33577933|emb|CAE35198.1| RNA polymerase sigma-32 factor [Bordetella bronchiseptica RB50]
 gi|332384018|gb|AEE68865.1| RNA polymerase factor sigma-32 [Bordetella pertussis CS]
          Length = 307

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 72/265 (27%), Positives = 134/265 (50%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    ++  +   +   +R  +     A +E+V ++LRLV+SVA++Y   GL
Sbjct: 40  IDAYISAVNRLPILTAEQEGQLARRLR--DEGDLEAARELVVSHLRLVVSVARQYLGYGL 97

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++      +
Sbjct: 98  PHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIIRNWRLVKVATTKAQR 157

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R   +       + IA++L +  E V ++ ++++   +SLE+   D+D+  
Sbjct: 158 KLFFNLRSMRPDGQTLDPEQVDHIARELNVRREDVSEMEVRLSGRDLSLESQDDDDDSFA 217

Query: 588 LGDFIEDKNAVSP---LDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              ++ D+    P   LD     +L+     R L +L  R  R++  R+        TL 
Sbjct: 218 PIAYLSDEGRQEPSRVLDRMAHDDLQGAGLGRALEALDARSRRIIEARWLQDDGG-LTLH 276

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++F V+ ER+RQIEA A++K++
Sbjct: 277 ELAQEFGVSAERVRQIEAAALKKMR 301


>gi|25991939|gb|AAN76997.1|AF481773_1 putative sigma 70 transcription factor [Frankia sp. ACoN24d]
          Length = 185

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 80/166 (48%), Positives = 118/166 (71%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           + RG+  LDL+QEGN+GL++  +KFD+  GYKFSTYA WW++QAI R++ADQ  TIRIPV
Sbjct: 1   SGRGMTLLDLVQEGNLGLIRPVKKFDYAKGYKFSTYATWWIRQAIGRALADQGRTIRIPV 60

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            + ++I+K+ R  R++ + + REPT EE+A +L MP+E V ++ +  ++ +SLET +GD+
Sbjct: 61  XVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVVELRRYAQDTVSLETSVGDD 120

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
             S LGDFIED +A SP D+A    +++    VL  L PRE  V+R
Sbjct: 121 GDSVLGDFIEDSDATSPADAASYGAMQDEIENVLGGLNPREREVMR 166


>gi|311826273|emb|CBX60044.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 278

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 61/320 (19%), Positives = 116/320 (36%), Gaps = 43/320 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D     +       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDTEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAKKEM 448
            I   +  GE +A  AKKEM
Sbjct: 259 DISRRMSIGEAKARRAKKEM 278


>gi|311826269|emb|CBX60042.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 278

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 61/320 (19%), Positives = 117/320 (36%), Gaps = 43/320 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAKKEM 448
            I   +  GE +A  AKKEM
Sbjct: 259 DISRRMSIGEAKARRAKKEM 278


>gi|11078971|dbj|BAB17490.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   +    + ++        ESA    ++D  +    P  
Sbjct: 59  IDPDDGIAPPAEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVI 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L  +  + +  +   +                          
Sbjct: 111 AAQRFGAVSDQMEITRKALKKLGREDKHAIAEMV-------------------------- 144

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 145 ---------ALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|134298555|ref|YP_001112051.1| sporulation sigma factor SigG [Desulfotomaculum reducens MI-1]
 gi|134051255|gb|ABO49226.1| RNA polymerase, sigma subunit, RpsG/SigG [Desulfotomaculum reducens
           MI-1]
          Length = 257

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 132/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + +   + ++    +     A+ +++  NLRLV+SV +++TNRG
Sbjct: 2   LINKVEICGVNTSKLPVLKNTQMRTLFEAMQQGDKDARSQLINGNLRLVLSVIQRFTNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EYVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++    + NK  REP+  EIA +L MP E +   L   +EPISL  PI  +  D 
Sbjct: 121 VAYKALQVRDTLVNKYSREPSINEIAGELKMPREDIVFALDAIQEPISLFEPIYHDGGDP 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D I D+  +        +         L  L+ RE+ +L +RF  G     T  EV
Sbjct: 181 IFVLDQISDEKNLDLSWLEEIS-----IRDALRRLSDREKHILTLRFFEG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A+  +K 
Sbjct: 232 ADEIGISQAQVSRLEKAALNHMKK 255


>gi|149925644|ref|ZP_01913908.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
 gi|149825761|gb|EDM84969.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
          Length = 308

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 124/267 (46%), Gaps = 10/267 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +      +S  E   +   +++       A + +V ++LRLV++VA++Y   GL
Sbjct: 34  LDAYISATHQIPMLSPEEEVELGERLQRD--NDLEAARRLVLSHLRLVVAVARQYLGYGL 91

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRD 527
              DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      +++       
Sbjct: 92  PHADLIQEGNIGLMKAVKRFDPTRGVRLVSFALHWIKAEIHEYIIRNWRMVKMITTKAHR 151

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   + + ++    +  +   E  ++    P +      ++     SL+  +  +   +
Sbjct: 152 KLFFNLNSFKKYGQTLSPDQINEVASELNVRPEDVYDMERRMAGHEFSLDPVVDVDSEEN 211

Query: 588 LGD---FIEDKNAVSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +   ++  + A        + ++    E     LASL  R +R++  R+  G N   T
Sbjct: 212 SYNPVRYLAAEGAEPTEVLEGANMERLHSEGLDMALASLDERSQRIISSRWLAGEN-AKT 270

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  +  V+ ER+RQIE +A++K+K
Sbjct: 271 LHDLAAELGVSAERVRQIETQAMKKMK 297


>gi|291446269|ref|ZP_06585659.1| sigma L [Streptomyces roseosporus NRRL 15998]
 gi|291349216|gb|EFE76120.1| sigma L [Streptomyces roseosporus NRRL 15998]
          Length = 307

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 83  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 142

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L +  E V 
Sbjct: 143 VGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVSEEDVV 202

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 203 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 257

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 258 APRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 302


>gi|260434077|ref|ZP_05788048.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417905|gb|EEX11164.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 298

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 124/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E   + A  ++V ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEDHDTEAAHKLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   + +        ++IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEDGDLHPDNVKQIAHDLGVTEDEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ +L       M+
Sbjct: 194 EGEGTMQWQDWLEDESADQAGDYETREELEVRRELLAEALEVLNDREKDILTQ--RRLMD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QPVTLEELSSQYNVSRERIRQIEVRAFEKLQKKMR 286


>gi|300783890|ref|YP_003764181.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299793404|gb|ADJ43779.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 282

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 15/241 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDW 490
           +  +     ++  +V     LV  VA +    GL       DL+Q G  GL+ A EKFD 
Sbjct: 41  QFADSPDQASRDRLVLHYAPLVKYVAGR-VGTGLPTHIDVGDLVQSGIFGLVDAIEKFDP 99

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F TYAM  ++ AI   +  Q     +P  +R K  +  R   R+  ++ R PT  
Sbjct: 100 ERGLRFETYAMQRIRGAILDDLRSQDW---VPRAVRSKAKEAERAMERLGARLHRTPTDA 156

Query: 551 EIAKKLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           E+A +L + ++ +R     L++T      +     +D+  L D + D +AV P+   +  
Sbjct: 157 ELAAELGIGLDDLRDFYGQLQLTSVVALEDLVAAGKDSGSLVDTLPDDDAVDPVAVLVDQ 216

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R    + +A LT R++ V+ + +        TL E+GK   VT  R+ Q+  +A+ +L
Sbjct: 217 DNRRQLAQAIAQLTERDKIVVSLYYF----ESLTLAEIGKVLGVTESRVSQLHTRAVMRL 272

Query: 668 K 668
           +
Sbjct: 273 R 273


>gi|258489074|gb|ACV72543.1| RpoD [Xanthomonas axonopodis pv. glycines]
          Length = 259

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 69/297 (23%), Positives = 118/297 (39%), Gaps = 45/297 (15%)

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
            T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   +   
Sbjct: 1   RTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHK 60

Query: 176 DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
           +G   L EI+     +  E+                +D + +++ D+  + E   E A  
Sbjct: 61  EGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGP 120

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              D                                        V   ++ +A  Y + +
Sbjct: 121 TGPDPVE-------------------------------------VATRMENLANEYAKFK 143

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            +        K+          +E +  +  +L L     D LV QL  +   I  +E +
Sbjct: 144 KVY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERK 197

Query: 356 LLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           +L LA +   + R  F+   +G + +  WV  A    + +W + +    D I+  + 
Sbjct: 198 VLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSSALRDVKDQIISEQQ 253


>gi|23429435|gb|AAM94465.1| RNA polymerase sigma factor D [Aeromonas hydrophila]
          Length = 281

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 129/326 (39%), Gaps = 47/326 (14%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                         E DDV  T   I S           
Sbjct: 60  II--SGFIDPN------------------------ETDDVAPTATHIGSELSEEDLADED 93

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAV 302
            D   +   + + + D+ +      ++                  E + +LR+  +   +
Sbjct: 94  EDEDEDEDGDGDDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRL 136

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           + Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 137 SIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 196

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +      V  + + +L+   +++ I  ETG
Sbjct: 197 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETG 255

Query: 422 ISISEFRHIVSMVRKGECEASIAKKE 447
           +SI++ + I   +  GE +A  AKKE
Sbjct: 256 LSIAQIKDINRRMSIGEAKARRAKKE 281


>gi|188580210|ref|YP_001923655.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179343708|gb|ACB79120.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 297

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 69/274 (25%), Positives = 118/274 (43%), Gaps = 12/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +  +E   +       +     A   +V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLDEIRKFPMLEPAEEFTLAK--SWRDEGDREAAHRLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 72  PISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 131

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R   +     R    ++IA  L +P + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKGRISALDEGDLRPDQVQQIATSLGVPTQDVIDMNRRLSGDTSLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +       A +   R         L  L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRLAD--DPI 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 250 TLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 283


>gi|218528993|ref|YP_002419809.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|240137510|ref|YP_002961981.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254559688|ref|YP_003066783.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|218521296|gb|ACK81881.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|240007478|gb|ACS38704.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254266966|emb|CAX22766.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 297

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 69/274 (25%), Positives = 117/274 (42%), Gaps = 12/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +  +E   +       +     A   +V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLDEIRKFPMLEPAEEFTLAK--SWRDDGDREAAHRLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 72  PISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 131

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R   +     R    + IA  L +P + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKGRISALDEGDLRPDQVQHIATSLGVPAQDVIDMNRRLSGDTSLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +       A +   R         L  L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRLAD--DPI 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 250 TLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 283


>gi|297193425|ref|ZP_06910823.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
 gi|197723192|gb|EDY67100.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
          Length = 304

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 114/229 (49%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 80  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 139

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + + +  ++ K+ R PT  E+A  L +  E V 
Sbjct: 140 VGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQKLDRSPTVPELAAVLGVSEEDVV 199

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  +++            RE+   +LA L
Sbjct: 200 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDSALEGVEY-----RESLKPLLAKL 254

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 255 PPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 299


>gi|5911381|gb|AAD55771.1|AF177466_1 sigma-32 factor RpoH [Methylovorus sp. SS1]
          Length = 284

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 131/273 (47%), Gaps = 9/273 (3%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            V S+  +   +++I     +S+ E   + + +RKG      A K ++ ++LRLV S+A+
Sbjct: 9   SVSSLDSLDQYLRTIKAFPVLSVEEEYDLATRLRKGT--DIEAAKGLIVSHLRLVASIAR 66

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y+  GL   DLIQEGN+GLMKA  +FD   G +  ++AM W+K  I   I      +++
Sbjct: 67  GYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKV 126

Query: 522 PVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
                + K+   +R+ ++ S+ +      +   +    P E V    ++    ISLE   
Sbjct: 127 ATTKAQRKLFFNLRSMKKNSHTLSPAEVADIARELRVKPEEVVEMESRMGGHEISLEGNS 186

Query: 581 GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIG 635
            D+   +     ++ED+        A +             L SL  R  R+++ R+   
Sbjct: 187 DDDTEDNFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDERSRRIVQARWLQE 246

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            N   TL ++  +F V+ ERIRQIE KA++K+K
Sbjct: 247 NN-SATLHDLAAEFGVSAERIRQIEQKAMQKMK 278


>gi|311826275|emb|CBX60045.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 278

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 57/317 (17%), Positives = 114/317 (35%), Gaps = 43/317 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D +  ++       ++     
Sbjct: 61  DPDADDTTAPTATHIGSELTESQLEDEDEEDVDEDEDGDDSDDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESTDAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTVQNIK 258

Query: 429 HIVSMVRKGECEASIAK 445
            I   +  GE +A  AK
Sbjct: 259 DISRRMSIGEAKARRAK 275


>gi|302544114|ref|ZP_07296456.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461732|gb|EFL24825.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 293

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 123/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++  +   EA   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 47  LSRSLFLRLAAL-DRDSEEAGYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 105

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  ++ 
Sbjct: 106 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQ 165

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
            + R PT  E+A  L +  E V   L +       SL++P  +++     L D +  +++
Sbjct: 166 TLDRSPTVTELATALGVSEEDVVDGLAVGNAYTASSLDSPSPEDEGGEGSLADRLGYEDS 225

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 226 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 276

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 277 RLLTRTLAQLRE 288


>gi|54401898|gb|AAV34634.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274877|gb|AAV49241.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
 gi|55274996|gb|AAV49295.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 201

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 83/201 (41%), Positives = 138/201 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEVGKQ 648
           L  RFG+      TLE+VG++
Sbjct: 181 LARRFGLLGYEAATLEDVGRE 201


>gi|23014972|ref|ZP_00054764.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 292

 Score =  137 bits (345), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 131/277 (47%), Gaps = 14/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +    R  + E + A  ++V ++LRLV  +A  Y + GL
Sbjct: 15  LAKYLRDIKEFPVLAPEEEFMLAK--RWVDYEDTEAAHKLVTSHLRLVAKIALGYRHYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGLM+A +KF+   G++ +TYAMWW+K ++   + +    ++I      K
Sbjct: 73  PVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWWIKASLNEFVLNSWSMVKIGTLAAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + R   R+      +  PE    IA++L +    V     ++     SL TP+  
Sbjct: 133 KLFFNLRRIKSRLRLLESGDLAPEHVTTIARELDVDERDVVAMNRRMAGRDSSLNTPV-G 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E  + + D + D+        A +  L   R    R L SLT RE  V   R        
Sbjct: 192 EGGAEIQDLMADEADNQETSLAKREELSKGRTLIARALDSLTEREREVFVERRLRD--DP 249

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEE+G ++ V+RERIRQIE KA  K++   ++  L
Sbjct: 250 LTLEELGGRYGVSRERIRQIEVKAFEKVRDLVQAGFL 286


>gi|302389526|ref|YP_003825347.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
 gi|302200154|gb|ADL07724.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
          Length = 257

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 83/266 (31%), Positives = 139/266 (52%), Gaps = 17/266 (6%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     +S S+ + +   V++       A+++++  NLRLV+SV +++ NR
Sbjct: 4   NKVEICGVNTSKLPVLSNSKMKELFLRVKQ---GDKEAREKLIHGNLRLVLSVIQRFNNR 60

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +R
Sbjct: 61  GEYVDDLFQVGCIGLMKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLR 119

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           D  +K ++    + NK  REP+ EEIAK++ +P E +   L   +EPISL  PI  +   
Sbjct: 120 DIAYKALQVRDSLVNKNSREPSIEEIAKEMNIPSEEIVMALDAIQEPISLFEPIYHDG-- 177

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             GD I   + +S   +  +  LR  +    +  L  RE+ +L +RF  G     T  EV
Sbjct: 178 --GDPIFVMDQISDDKNNDENWLRSISIKEAMQKLNEREKLILTLRFFEG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPS 671
            ++  +++ ++ ++E  A++ LK   
Sbjct: 232 AQEIGISQAQVSRLEKAALKHLKKYM 257


>gi|182437345|ref|YP_001825064.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777955|ref|ZP_08237220.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465861|dbj|BAG20381.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658288|gb|EGE43134.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 288

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 116/229 (50%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L +  E V 
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVSEEDVV 183

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++A            RE+   +LA L
Sbjct: 184 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGVEY-----RESLKPLLAKL 238

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 239 APRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 283


>gi|111225338|ref|YP_716132.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
 gi|111152870|emb|CAJ64617.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
          Length = 299

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 120/246 (48%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +       A+I + ++V  +L LV  +A+++ NRG    DL+Q   IGL+K+ +
Sbjct: 58  FVRLAELPEGDAERAAI-RDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVD 116

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   IR+P  +++    + +    +S  + R 
Sbjct: 117 RFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLSLTKATSELSQTLGRS 176

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  EIA+ L M  E V + L+       +SL+ P   +D +  + D +  ++      S
Sbjct: 177 PTVSEIARHLQMSEEDVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDE-----S 231

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L PRE+R+L +RF        T  ++  +  +++  + ++ A+ 
Sbjct: 232 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN----MTQSQIATELGISQMHVSRLLART 287

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 288 LAQLRR 293


>gi|256823783|ref|YP_003147746.1| RNA polymerase sigma-32 subunit RpoH [Kangiella koreensis DSM
           16069]
 gi|256797322|gb|ACV27978.1| RNA polymerase, sigma 32 subunit, RpoH [Kangiella koreensis DSM
           16069]
          Length = 283

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 130/270 (48%), Gaps = 13/270 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   + ++S    +S+ + + +       +     A +++V A+LR V+ +A+ Y+  GL
Sbjct: 17  IDGYVSTVSAIPVLSVEQEQKLAH--EFHDNNDLEAARQLVMAHLRFVVYIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     + 
Sbjct: 75  PQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++  N +  +     +A+ L +  E VR++  ++     S + P   +D  
Sbjct: 135 KLFFNLRSKKKTLNWLNNDEVNA-VAQDLGVSEEEVRRMEGRLNAHDASFDAPNASDDDD 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            +     ++E  N   A +      Q          L +L  R + +L+ R+    +   
Sbjct: 194 AVYAPIHYLESPNSDPAQAIEQEDWQDQREVRLMSALKTLDERSQDILQQRWL--SDQKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TL ++  ++ ++ ERIRQ+E  A+ K+K+ 
Sbjct: 252 TLHDLADKYGISAERIRQLEKNAMNKIKNA 281


>gi|3021672|dbj|BAA25356.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079047|dbj|BAB17528.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 268

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 115/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPIDTKTAKADDDSDDDDAEASDDEEEAESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQMEITRKAL-----------------------------------KKHGRH 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L  L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKLAIAELLALADLFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARAA 268


>gi|302552550|ref|ZP_07304892.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470168|gb|EFL33261.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 301

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 55  LSRSLFLRLAALDEDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 113

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 114 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 173

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 174 KLDRSPTVTELASVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 233

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 234 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 284

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 285 RLLTRTLAQLRE 296


>gi|207743452|ref|YP_002259844.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
 gi|206594849|emb|CAQ61776.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
          Length = 203

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 71/198 (35%), Positives = 114/198 (57%), Gaps = 2/198 (1%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +  
Sbjct: 1   MHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEK 60

Query: 542 KI--KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
                R+ + E+IA  L    E V+ VL + +   SL+TP   +  + L DF+ D++  S
Sbjct: 61  SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDSGTSLLDFLSDEHGAS 120

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P        L +     LA L+ +   V+  RFG+      TLEE+  +  +TRER+RQI
Sbjct: 121 PDQEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELAAEMGLTRERVRQI 180

Query: 660 EAKAIRKLKHPSRSKKLR 677
           + +A+ KLK    S+ +R
Sbjct: 181 QQEALVKLKRHFASQGVR 198


>gi|23429459|gb|AAM94477.1| RNA polymerase sigma factor D [Aeromonas popoffii]
          Length = 281

 Score =  137 bits (345), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 128/326 (39%), Gaps = 47/326 (14%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++E L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVEFLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                         E DDV  T   I S    +      
Sbjct: 60  II--SGFIDPN------------------------ETDDVAPTATHIGSELGEADLADED 93

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAV 302
            D   +  ++ E + D+ +      ++                  E + ELR+  +   +
Sbjct: 94  EDEDEDEDDDGESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRL 136

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           + QK+ ++    +     +  +     L   + D LV  +  + +R+   E  +++L  +
Sbjct: 137 SIQKNGRAHEDTQAAIALMADVFRQFRLMPKQFDRLVNNMRGMMERVRVQERIIMKLCVE 196

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +      V  + D +L+   +++ I  ETG
Sbjct: 197 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRSIGKLQQIEEETG 255

Query: 422 ISISEFRHIVSMVRKGECEASIAKKE 447
           +SI++ + I   +  GE +A  AKKE
Sbjct: 256 LSIAQIKDINRRMSIGEAKAVRAKKE 281


>gi|326775053|ref|ZP_08234318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655386|gb|EGE40232.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 300

 Score =  137 bits (344), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 124/246 (50%), Gaps = 8/246 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA 
Sbjct: 54  FFDRLQVLEEGTHEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAI 113

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D + ++ +P  +++    + +   ++S ++ R
Sbjct: 114 DRFDLSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLAKAKEQLSGELDR 173

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT +E+A  L +P E + + L         SL+TP  D D+        D    +    
Sbjct: 174 DPTVKELAAHLDLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYADVLGEADPGM 233

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               NL  T   +L  L  RE R+++MRFG     + T  ++G +  V++  + ++ ++ 
Sbjct: 234 ETVENLH-TLAPLLDQLDERERRIVQMRFGA----EMTQSQIGAELGVSQMHVSRLLSRI 288

Query: 664 IRKLKH 669
           +++L+ 
Sbjct: 289 VQQLRK 294


>gi|254519266|ref|ZP_05131322.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
 gi|226913015|gb|EEH98216.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
          Length = 259

 Score =  137 bits (344), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 79/265 (29%), Positives = 134/265 (50%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + I + +    ++ K       A++  ++ NLRLV+SV +++ NRG
Sbjct: 4   IINKVEICGVNTSKLPILKEKEKRELLLKMRDGDKGARETFIKGNLRLVLSVIQRFNNRG 63

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 64  ENVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 122

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    R+  +  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 123 IAYKALLVRDRLIKENNKEPTVSQIAKELNLPREEVVFALDAIQDPVSLFEPIYHDGGDA 182

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KN+       I      +    +  L  RE+ +L +RF  G     T  E
Sbjct: 183 IYVMDQISDSKNSDESWLENI------SIKEAMKKLNDREKLILTLRFFNG----RTQME 232

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 233 VADEIGISQAQVSRLEKTALKHMRK 257


>gi|256379368|ref|YP_003103028.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923671|gb|ACU39182.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 268

 Score =  137 bits (344), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 114/230 (49%), Gaps = 12/230 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + E+V  +L +   +A+++ +RG    DL+Q   +GL+ A ++FD   G  F ++A+
Sbjct: 43  ERLRDELVTEHLPVARHIARRFGHRGEPHDDLVQVATVGLINAVDRFDPERGSDFLSFAV 102

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   + +   D S ++R+P  +++    +   + R+S ++ R PTP E+A+ L +  E
Sbjct: 103 PTIMGEVRKYFRDSSWSVRMPRRLKELHLAINAGSARLSQELGRAPTPSELAQHLGLSRE 162

Query: 562 GVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V + L         SL+  +  +D+S  LG  + +++             RE+   +L 
Sbjct: 163 EVHEGLAAGNAYHSASLDDLLVADDSSISLGSTLGEED-----PELEAIEQRESLHPLLE 217

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE R++ MRF        T  ++ ++  +++  + ++ AK +R+L+
Sbjct: 218 KLPERERRIVVMRFFGN----MTQTQIAQKVGISQMHVSRLLAKTLRQLR 263


>gi|163850434|ref|YP_001638477.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|163662039|gb|ABY29406.1| RNA polymerase sigma factor RpoH [Methylobacterium extorquens PA1]
          Length = 297

 Score =  137 bits (344), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 69/274 (25%), Positives = 117/274 (42%), Gaps = 12/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +  +E   +       +     A   +V ++LRLV  +A  Y   GL
Sbjct: 14  LSRYLDEIRKFPMLEPAEEFTLAK--SWRDDGDREAAHRLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 72  PISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 131

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R   +     R    + IA  L +P + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKGRISALDEGDLRPDQVQHIATSLGVPAQDVIDMNRRLSGDTSLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +       A +   R         L  L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRLAD--DPI 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 250 TLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 283


>gi|11079198|dbj|BAB17590.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  137 bits (344), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   +    + ++        ESA    ++D  +    P  
Sbjct: 59  IDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEE--------ESADASDEEDEVESGPDPVI 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L     + +  +   +                          
Sbjct: 111 AAQRFGAVSDQMEITRKALKKFGREDKHAIAEMV-------------------------- 144

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 145 ---------ALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|260574108|ref|ZP_05842113.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259023574|gb|EEW26865.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 292

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 125/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 26  ELRLAYAWRDQRDEAALHRLITAYMRLAISMAAKFRRYGAPMNDLIQEASLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +++    K+ R A + 
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLKRVQAKLEREAAQR 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              +      E +A+++ +P+  V  +  ++     SL      ED      D +ED   
Sbjct: 146 GESLDGHQLREMVAREVGVPLADVEMMEGRLAGSDFSLNATQSSEDEGREWIDALEDDGV 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +   +   A LR      +A+L PRE  ++  R   G     TLE +G +  +++E
Sbjct: 206 QAAEAVEGAHDAARLRGWLVVAMAALNPRERFIVTERKLRGDG--RTLESLGAELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  KL+     ++++L  FL
Sbjct: 264 RVRQLEAAAFAKLRRSLEGQTRELHHFL 291


>gi|253576139|ref|ZP_04853471.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844482|gb|EES72498.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 260

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 140/270 (51%), Gaps = 18/270 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R +   +++       A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFHSLQQD--HVRSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    ++N+  REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQMRDNLTNQNSREPTIFEISEALGLPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D    +   S I+          +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDDK--NKDVSWIEEI---ALREAMQRLGNREKMILSMRFFEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV  +  +++ ++ ++E  AI +++   +S
Sbjct: 231 EVADEIGISQAQVSRLEKSAILQMQKHVKS 260


>gi|323450165|gb|EGB06048.1| hypothetical protein AURANDRAFT_11909 [Aureococcus anophagefferens]
          Length = 325

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 87/259 (33%), Positives = 142/259 (54%), Gaps = 20/259 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R         ++E+++ NLRLV+SVAK+Y + GL F DL QEGN GL KA ++FD   G
Sbjct: 68  LRTRMGHMKACREELIQRNLRLVLSVAKRYGDCGLAFTDLCQEGNFGLAKACDRFDPSKG 127

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA+WW++QA+  ++A QS TIR+P H+ +K+ ++ +    +  +  R+ T +EIA
Sbjct: 128 FRFSTYAVWWIRQAVAHAVAHQSRTIRLPTHVHEKLRRMKKHKVALEKQTGRDATDDEIA 187

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIG------------------DEDTSHLGDFIEDK 595
           +++++  + +R++ +  +  +S +                          + L D + D 
Sbjct: 188 REMSLDADKLRRLRRAARGTVSTDVDAENLGSRRGAAPGNGRRGASYASGAQLADLLHDA 247

Query: 596 NAVSPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
               P   A ++ L++   R+    L  REE VL   FG+      TL E+  +F +TRE
Sbjct: 248 TQ-HPERDAAESLLKDEVRRMLDDDLEDREEDVLNRHFGLDGRRPETLAEIAVRFDLTRE 306

Query: 655 RIRQIEAKAIRKLKHPSRS 673
           RIRQIE  A  KL+ P RS
Sbjct: 307 RIRQIEKSAFAKLRQPHRS 325


>gi|114570847|ref|YP_757527.1| RNA polymerase sigma 32 subunit RpoH [Maricaulis maris MCS10]
 gi|114341309|gb|ABI66589.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 305

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 77/268 (28%), Positives = 121/268 (45%), Gaps = 13/268 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +KS      +S  +   +    R  +     A  E+ EA++RLVI+VA K+   GL 
Sbjct: 23  QRFVKSAMARDLLSREDEADLAR--RWKDDRDEKALHELTEAHMRLVIAVAAKFKRYGLP 80

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           F DLIQEGNIGLMKAA++FD     +FSTY  WW++  I   +      +R       K 
Sbjct: 81  FSDLIQEGNIGLMKAADRFDPERDVRFSTYVTWWIRSCIQDYVLRNWSIVRTGTTSAQKS 140

Query: 530 -----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
                 ++      +          ++IAK L +    V    L+++    SL  P+GD 
Sbjct: 141 LFFNLRRIRANIGDLDGSSITPDNRQKIAKDLRVRERDVENMALRLSASDRSLNAPVGDA 200

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDH 640
           + S   DF+ D  A    +   + +           L  L  RE+ ++R R      +  
Sbjct: 201 EDSQWQDFLVDDTAAPETEVMNRTDSERRSAWLGLALDGLNSREQFIIRERRLREDGS-- 258

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL  +G    +++ER+RQIE  A+ KL+
Sbjct: 259 TLASLGDSLGISKERVRQIENAALAKLR 286


>gi|296133159|ref|YP_003640406.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031737|gb|ADG82505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 260

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 64/256 (25%), Positives = 128/256 (50%), Gaps = 15/256 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++     +S  E + ++   +        A++++V  NL+LV ++ +++ NRG +  DL 
Sbjct: 9   NLPRFPLLSDKEMKELLIKAK---NGDQAAREKLVNCNLKLVFNLVQRFCNRGYEPEDLF 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G IGL+KA +KFD     KFSTYA+  +   I R + D    +++   +++  +K+ R
Sbjct: 66  QIGTIGLIKAIDKFDLSYDVKFSTYAVPLIIGEIRRFLRD-DNPVKVSRSVKETANKINR 124

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
              ++S  + R+PT  EIAK++ M  E +   ++ ++ P S+   +  +D    ++ D I
Sbjct: 125 AREKLSASLGRDPTISEIAKEVGMEREEIVNAMEASQLPTSIYETLYQDDGDPIYVMDAI 184

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
              +                   VL  L  RE++VL +RF      D T  +V +   ++
Sbjct: 185 TGSSGDEGQWFE-----HMALKDVLQKLPEREKKVLLLRFF----EDKTQTQVAEILGIS 235

Query: 653 RERIRQIEAKAIRKLK 668
           + ++ +IE +A++ ++
Sbjct: 236 QVQVSRIERQALKTIR 251


>gi|229525043|ref|ZP_04414448.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
 gi|229338624|gb|EEO03641.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
          Length = 286

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 135/272 (49%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    +S  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERL--HYKGDIDAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      ++D +
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDEN 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK+   A +      +A+  +  +  LASL  R + ++R R+ +  + 
Sbjct: 192 GMAYTAPVLYLEDKHSDLADNLAAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++ + + V+ ERIRQ+E  A+RKLK  
Sbjct: 251 KTTLQDLAEMYGVSAERIRQLEKNAMRKLKEA 282


>gi|37784442|gb|AAO13114.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|37784448|gb|AAO13117.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|37955128|gb|AAP76216.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|37955134|gb|AAP76219.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 272

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 114/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     + DD       PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDEGDGGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L    + +  ++                                   QK+ ++    
Sbjct: 114 FGELRAQYEVTRLSI-----------------------------------QKNGRAHDDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|288961334|ref|YP_003451673.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288913642|dbj|BAI75129.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 287

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 124/270 (45%), Gaps = 12/270 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++       ++      + +  R  + +   A   +V ++LRLV+ +A+ Y   GL
Sbjct: 1   MQLYLQDARKYQYLTPELELELAA--RWHDHQDPAALDRLVGSHLRLVVKMARGYLGYGL 58

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+ EGN+GLM+AA+KFD   G++F+TYA WWV+ AI   +      ++I      K
Sbjct: 59  PLADLVAEGNVGLMQAAQKFDPGKGFRFATYASWWVRAAIQEYVLHNWSLVKIGTTAGQK 118

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  ++    + + +        E IA +L +    V ++ +      SL   + ++
Sbjct: 119 KLFFSLRRLKARMQELDSGDLSPEAVESIATELNVSKAEVVEMNRRLGNDRSLNVGLSED 178

Query: 584 DTSHLGDFIEDK--NAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDH 640
             +   D + D   +  + L  + +   R+      L  L  RE R+L  R         
Sbjct: 179 GDAEWQDLLADDRPDQETVLADSEERRRRQQFLKLGLGVLDDRERRILVARRLRD--EPL 236

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLEE+ + F V+RER+RQ+E +A  KL+  
Sbjct: 237 TLEELSQTFQVSRERVRQLEVRAFEKLQKA 266


>gi|9621765|gb|AAF89531.1|AF160964_1 RNA polymerase sigma factor [Peanut witches'-broom phytoplasma]
          Length = 458

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 132/444 (29%), Positives = 211/444 (47%), Gaps = 47/444 (10%)

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE--KS 310
           N+E+++  +  +      A  + ++P++      + ++   L  L        K +  K 
Sbjct: 43  NEEKSVINEYQNKCDEYQAQLNSIQPQIENETKNLIKLKLTLEKLTKPKSKNSKLKIWKL 102

Query: 311 SVKCKVLKEKLVKLV-----GSLSLNQ-SRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
            VK    K K+ KL+         L    +     ++ Y + K    N    L+  ++  
Sbjct: 103 LVKSAKSKFKIWKLLVKSAKSKFKLVNYKQPKENTKKCYLMLKNTEKNLKNDLKKVKN-N 161

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           IK  +FL+       +              W       +  +++++ ++  +        
Sbjct: 162 IKIQLFLDLTSTNTSN--------------WGIIKKELLFKMMQVKKKLHLL-------- 199

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
             F      V   +  +    K++  +NLR+V+S+AKK + RG  FLDLI EGN+GLMK 
Sbjct: 200 --FNEFFRYVFNNQYSSHYGIKQL--SNLRIVVSIAKKQSERGQYFLDLIHEGNMGLMKT 255

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI- 543
            +KFD+  G+KFSTYA WW++QAITR++ADQS TIR PVH+ D ++K      +++  + 
Sbjct: 256 VDKFDYTKGFKFSTYATWWIRQAITRAVADQSRTIRCPVHVSDILNKNFAFKSKLTQDLA 315

Query: 544 --KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              R+    EIAK + +  + +     + +                   +   K ++   
Sbjct: 316 RKARKAENHEIAKAMNIETKKLMIYKWLKRNDFFRNIYSWWRWFFFRWFY---KRSLRYF 372

Query: 602 DSAIQ--ANLRETTTRVLAS-LTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERI 656
            S +    N ++T    L   LTPRE+ VL+MR+GI  G N  HTLEEVG +  VTRERI
Sbjct: 373 ASWLYVTRNFKKTLEESLEEALTPREQLVLKMRYGILEGDNRVHTLEEVGAKLGVTRERI 432

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFL 680
           RQIE KA+RKL+HPSRS  L SFL
Sbjct: 433 RQIETKALRKLRHPSRSNPL-SFL 455


>gi|91978901|gb|ABE66426.1| RNA polymerase sigma-70 factor [Aeromonas simiae]
 gi|91978903|gb|ABE66427.1| RNA polymerase sigma-70 factor [Aeromonas simiae]
          Length = 282

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 125/321 (38%), Gaps = 41/321 (12%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDIISGFVNPDEA 60

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            + G      G    + + + ++   D+ ++ + D   ++    D        PE A   
Sbjct: 61  DEMGPSATHIGSELGEDDLADEDSSDDEEEDEDEDGNDSSDDDSDGGPD----PEVAREK 116

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L    + +  ++                                   + + ++  + 
Sbjct: 117 FAELRTQYEVTRQSI-----------------------------------RTNGRAHDET 141

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    KL  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 142 QAEIAKLADIFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVSA 201

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      VA E + +L+   +++ I  ETG+SI++ + I   
Sbjct: 202 FTNNECETAWFEYQKQAGKAWSAPLVAME-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 260

Query: 434 VRKGECEASIAKKEMVEANLR 454
           +  GE +A  AKKEMVEANLR
Sbjct: 261 MSIGEAKARRAKKEMVEANLR 281


>gi|115372678|ref|ZP_01459985.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|310823838|ref|YP_003956196.1| RNA polymerase sigma-c factor [Stigmatella aurantiaca DW4/3-1]
 gi|115370399|gb|EAU69327.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|309396910|gb|ADO74369.1| RNA polymerase sigma-C factor [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 131/266 (49%), Gaps = 14/266 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    ++  E +   ++ R        A   +V +NLR V+ VA +Y + GL+  
Sbjct: 14  YLSEINQYPLLTQQEEQ---ALARSFRQGDLQAGHRLVTSNLRFVVKVAYEYRSYGLRMS 70

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQE NIGLMKA +KFD   G +  +YA+WW++  I   +      +++      R   
Sbjct: 71  DLIQEANIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQGYVLKNWSLVKLGTTQAQRRLF 130

Query: 530 HKVVRTARRMSNKI---KREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT 585
             + RT R +  +          EEIA+KL +    VR++  ++    +SL+ P+G++  
Sbjct: 131 FALARTRRELEKQGNTDGNIVNAEEIARKLNVKASEVREMEQRMGGRDLSLDAPMGEDGD 190

Query: 586 SHLGDFIEDK--NAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +   DF+     +    +    +A+L R    + L  L PRE  ++     +  +++ TL
Sbjct: 191 ATHMDFVASDSVSQADEVADRQEADLARTRIQQALQRLDPRERFIIEK--RVMSDSEMTL 248

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+G+ F  +RER RQ+E +A  KLK
Sbjct: 249 SELGEHFGFSRERARQLEIRAKDKLK 274



 Score = 41.4 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 3/94 (3%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
           A  ++ D +  YL E+    LL+++ E A+A+    G       L  S L F  ++    
Sbjct: 3   ASLTSTDSLSTYLSEINQYPLLTQQEEQALARSFRQGDLQAGHRLVTSNLRF--VVKVAY 60

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E       + ++I  EA IG       F   +G 
Sbjct: 61  EYRSYGLRMSDLIQ-EANIGLMKAVQKFDPDKGI 93


>gi|169245678|gb|ACA50885.1| RpoD [Agrobacterium tumefaciens]
 gi|169245698|gb|ACA50895.1| RpoD [Agrobacterium tumefaciens]
 gi|169245702|gb|ACA50897.1| RpoD [Agrobacterium rhizogenes]
 gi|169245712|gb|ACA50902.1| RpoD [Agrobacterium tumefaciens]
          Length = 174

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 95/173 (54%), Positives = 120/173 (69%), Gaps = 6/173 (3%)

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ
Sbjct: 1   QVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQ 60

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +   
Sbjct: 61  NRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSIANLAA 120

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             WK F   E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAK
Sbjct: 121 RGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAK 173


>gi|169831582|ref|YP_001717564.1| sporulation sigma factor SigG [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638426|gb|ACA59932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 255

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 133/264 (50%), Gaps = 18/264 (6%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           N+++   V T     ++ +E R +   ++        A+ +++  NLRLV+SV +++TNR
Sbjct: 3   NKVEICGVNTSKLPVLTAAEMRQLFQEMQ---AGDPSARSKLINGNLRLVLSVIQRFTNR 59

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G    DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +R
Sbjct: 60  GEFVDDLFQVGCIGLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLR 118

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DT 585
           D  +K ++    ++N+  REP+  EIA++L +P E +   L   +EPISL  PI  + D 
Sbjct: 119 DVAYKALQIRDNLANRFSREPSVSEIAQELNIPREEIVFALDSIQEPISLFEPIYHDGDP 178

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D + D+           A         +  L  RE+ +L +RF  G     T  EV
Sbjct: 179 IFVMDQVSDERNADANWLEDIA-----IRDAIRKLNEREKLILTLRFFEG----KTQMEV 229

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            ++  +++ ++ ++E  A+  ++ 
Sbjct: 230 AEEIGISQAQVSRLEKAALSHMRK 253


>gi|297746563|emb|CAZ60999.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|297746565|emb|CAZ61000.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 268

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 110/311 (35%), Gaps = 44/311 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     + DD       PE A   
Sbjct: 59  ETE-----DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              L    + +  ++                                   QK+ ++    
Sbjct: 114 FGELRAQYEVTRLSI-----------------------------------QKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E D  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIA 444
           +  GE +A  A
Sbjct: 258 MSIGEAKARRA 268


>gi|168700394|ref|ZP_02732671.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gemmata obscuriglobus UQM 2246]
          Length = 335

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 133/250 (53%), Gaps = 3/250 (1%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
            +E R  V  VR+        K  +  AN+RL   VAK++ +  L + DL+QE   GLM+
Sbjct: 79  CTEDRCDVIAVRRLRDRYVHYKHRLASANIRLAAHVAKRFRHHSLAYSDLLQEAVCGLMQ 138

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++FD   G + +TYA WW++Q +  ++A QS  + +  H   ++  + + +  +++  
Sbjct: 139 AIDRFDVSHGTRLATYATWWIRQTLQIAVARQSHLVSLSPHHLQELGLLQQESEALAHGG 198

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           K  P+P+E+A +    +E +  +   T+ P+SL   + D+    L + + D      L  
Sbjct: 199 KHLPSPQELASRTGSSLEHLTHLQTATRTPVSLNAVLDDDSDFKLTEAMPDTGT---LVM 255

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 +E  + ++ +L PRE +VL +RFG+  N  H+L ++G    +++ER+RQI+ +A
Sbjct: 256 QENNERQEALSFLMENLRPRERKVLDLRFGLTGNGTHSLRQIGHLLRISKERVRQIQNRA 315

Query: 664 IRKLKHPSRS 673
           + KLK  +  
Sbjct: 316 LEKLKANAER 325


>gi|11078967|dbj|BAB17488.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078973|dbj|BAB17491.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEKGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S ++      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  L  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W        +G++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGHEVDESWTDGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|11078939|dbj|BAB17474.1| DNA-directed RNA polymerase subunit D [Pseudomonas caricapapayae]
          Length = 269

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADGSDDEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|258622821|ref|ZP_05717838.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
 gi|258584882|gb|EEW09614.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
          Length = 286

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 135/272 (49%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    +S  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERL--HYKGDIDAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      ++D +
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDAAFEMSAEDDEN 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK+   A +      +A+  +  +  LASL  R + ++R R+ +  + 
Sbjct: 192 GMAYTAPVLYLEDKHSDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++ + + V+ ERIRQ+E  A+RKLK  
Sbjct: 251 KTTLQDLAEMYGVSAERIRQLEKNAMRKLKEA 282


>gi|258625092|ref|ZP_05720011.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
 gi|258582643|gb|EEW07473.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
          Length = 286

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 68/272 (25%), Positives = 135/272 (49%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    +S  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERL--HYKGDIDAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      ++D +
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDEN 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK+   A +      +A+  +  +  LASL  R + ++R R+ +  + 
Sbjct: 192 GMAYTAPVLYLEDKHSDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++ + + V+ ERIRQ+E  A+RKLK  
Sbjct: 251 KTTLQDLAEMYGVSAERIRQLEKNAMRKLKEA 282


>gi|66474711|gb|AAY46925.1| RpoD [Aeromonas molluscorum]
          Length = 272

 Score =  137 bits (344), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 114/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                        +         E +  D  E E + +     S DD +     PE A  
Sbjct: 59  NE-----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDDEADTGPDPEVARE 113

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               L    + +  ++                                   Q + ++   
Sbjct: 114 KFGELRAQYEVTRLSI-----------------------------------QNNGRAHDD 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E D  W  Y K   +      V  + + +L+   +++ I VETG+S ++ + I  
Sbjct: 199 AFTNNECDTAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEVETGLSRAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 258 RMSIGEAKARRAKKE 272


>gi|225175855|ref|ZP_03729848.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168779|gb|EEG77580.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 268

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 128/250 (51%), Gaps = 12/250 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + + +   +  + +K +     A++E++  NLRLV+SV +++ NRG    DL Q G IGL
Sbjct: 16  LPVLKSARMKELFKKMQSGDEHARQELINGNLRLVLSVLQRFKNRGENLDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + F       FSTYA+  +   I R + D +  +R+   ++   HK  ++   ++ 
Sbjct: 76  MKAVDNFSLDHNVHFSTYAVPMIIGEIKRYLRDNN-AVRVSRSLKMLAHKAQQSREELTR 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K+ REPT +EIA  L +  E V    +   +P+SL  P+  +  D   + D + D+++ +
Sbjct: 135 KLLREPTLKEIAADLDITPEEVVFAYQAINDPLSLHDPVFQDTTDPVFVMDLVSDQSSSA 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +          T  + +  L+ RE R+L  RF  G     T  E+  +  +++ ++ +I
Sbjct: 195 EIWVEDI-----TLRQAMEILSERERRILESRFFEG----RTQTEIANEIGISQAQVSRI 245

Query: 660 EAKAIRKLKH 669
           E  A+R+++H
Sbjct: 246 EKSALRQVRH 255


>gi|23429483|gb|AAM97309.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 281

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 127/321 (39%), Gaps = 46/321 (14%)

Query: 129 GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE 188
           G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II   
Sbjct: 5   GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--S 62

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             I P                         E DDV  T   I S            D   
Sbjct: 63  GFIDPN------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDE 98

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKD 307
           +  E+ + + D+ +      ++                  E + ELR+  +   ++ Q++
Sbjct: 99  DEDEDGDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQN 141

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIK 366
            ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + 
Sbjct: 142 GRAHDDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMP 201

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +  F+      E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++
Sbjct: 202 KKTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQ 260

Query: 427 FRHIVSMVRKGECEASIAKKE 447
            + I   +  GE +A  AKKE
Sbjct: 261 IKDINRRMSIGEAKARRAKKE 281


>gi|311826263|emb|CBX60039.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 275

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 58/317 (18%), Positives = 114/317 (35%), Gaps = 43/317 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKAAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRSEEEIRRSITKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAK 445
            I   +  GE +A  AK
Sbjct: 259 DISRRMSIGEAKARRAK 275


>gi|302536824|ref|ZP_07289166.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302445719|gb|EFL17535.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 332

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +       A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 92  FFELRRLPEGSPERAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 150

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 151 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 210

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 211 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 270

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 271 -----RESLKPLLEGLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 321

Query: 665 RKLKH 669
            +L+ 
Sbjct: 322 AQLRE 326


>gi|299068068|emb|CBJ39282.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum CMR15]
          Length = 306

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 133/278 (47%), Gaps = 11/278 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  +   I+S++    ++  E + +             A + +V ++LRLV+S+A++Y 
Sbjct: 29  SLGNLDAYIQSVNRVPMLTAEEEQQLAR--DYHATGDLDAARRLVLSHLRLVVSIARQYL 86

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  +   I      +++   
Sbjct: 87  GYGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATT 146

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ ++        + +A++L +    VR++    +   I+LE  I D
Sbjct: 147 KAQRKLFFNLRSHKQNAHATFTSDEIDAVAQELDVKGAEVREMETRLSGGDIALEGQIDD 206

Query: 583 EDTSH-LGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S     ++ D +           +     E     LA L  R  R++  R+    + 
Sbjct: 207 GEESFAPIAYLADTHNEPTRVLEGRGLDRLQSEGIETALAKLDDRSRRIIEARWLHVNDD 266

Query: 639 ---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                TL E+  +F V+ ERIRQIE+ A++K+K   +S
Sbjct: 267 GSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQS 304


>gi|54307376|ref|YP_128396.1| RNA polymerase factor sigma-32 [Photobacterium profundum SS9]
 gi|46911796|emb|CAG18594.1| putative RNA polymerase sigma-32 factor [Photobacterium profundum
           SS9]
          Length = 282

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 136/272 (50%), Gaps = 16/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++++    +S  + + +   +         A K +V +++R V+ VA+ Y+  GL
Sbjct: 12  LDSYIQTVNRHPMLSAEQEKELAERL--HYDGDIEAAKGLVMSHMRFVVHVARGYSGYGL 69

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 70  PIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 129

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++ +R+      E   E +A++L +    VR++  ++  +  + E P  D+D 
Sbjct: 130 KLFFNLRKSKKRLGWFNNAE--VEMVAEQLGVNPSEVREMESRLAAQDPAFELPNEDDDR 187

Query: 586 ----SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
               +    F+EDK+   A+S  ++  + +     +  LA L  R + ++R R+      
Sbjct: 188 DAGYTAPVYFLEDKSSDVALSYEENNWENHTNNRLSNALAGLDERSQHIVRSRWLDD--E 245

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++   + ++ ER+RQ+E  A++KLK  
Sbjct: 246 KTTLQDLANHYGISAERVRQLEKNAMKKLKEA 277


>gi|307944600|ref|ZP_07659940.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
 gi|307772349|gb|EFO31570.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
          Length = 294

 Score =  137 bits (344), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 74/281 (26%), Positives = 128/281 (45%), Gaps = 17/281 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    +  E     A + +V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLDEIRKFPLLQPQEEYMLAKRYK--EHADPEAAERLVNSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 73  PIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  ++    + +     +    +EIA KL +  E V  + +      SL +P+  E
Sbjct: 133 RLFFNLRRLKGKIQALEEGDLKPHQVQEIATKLGVSEEEVISMNRRLGGDTSLNSPVRAE 192

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
            D     D++ D+        A Q  L   RE  ++ +  L  RE R+            
Sbjct: 193 ADAGEWQDWLVDEADSQETLLANQEELDQRRELLSQAMDELNERERRIFTA--RRLSEDP 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRK----LKHPSRSKKL 676
            TLE++  +F V+RER+RQIE +A  K    +K+ +R+K+L
Sbjct: 251 ITLEDLSTEFGVSRERVRQIEVRAFEKVQKAVKNSARAKEL 291


>gi|326386899|ref|ZP_08208513.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326208579|gb|EGD59382.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 300

 Score =  136 bits (343), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 66/275 (24%), Positives = 117/275 (42%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 19  LNRYLTEIRKFPLLTAEQEYMLAK--RYQEHGDPQAAAQLVTSHLRLVAKIAMGYRGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGLM+  +KFD   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 77  PVSELISEGNIGLMQGVKKFDPDRGFRLATYAMWWIKASIQEFILRSWSLVKMGTTAAQK 136

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIG 581
                  ++ +      +        ++IA  L +P   V  + +        SL  P+ 
Sbjct: 137 KLFFNLRRMKKNLEAFEDSDLHPDDVKKIATDLGVPEADVVSMNRRMMMGGDASLNVPLR 196

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++      D++ D+  +     A         +     +  L  RE  +L       ++ 
Sbjct: 197 EDGEGSWQDWLADERPLQDEAVADAEEAQVRHDLLVEAMQDLNDRERHILID--RRLVDE 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+ + + V+RER+RQIE +A  KL+   + 
Sbjct: 255 PKTLEELSQVYHVSRERVRQIEVRAFEKLQKAIQR 289


>gi|1396060|dbj|BAA13043.1| part of principal sigma factor homolog [Synechocystis sp.]
          Length = 186

 Score =  136 bits (343), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 100/187 (53%), Positives = 136/187 (72%), Gaps = 1/187 (0%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL F DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS TIR+PVH+
Sbjct: 1   RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHL 60

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
            + I ++ +T + +S +++R+PT EEIA+K+ M +E +R + K  + PISLETPIG E+ 
Sbjct: 61  YETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEED 120

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S LGDFIE  +  +P D   +  LRE    VL +L+PRE  VLR+R+G+      TLEE+
Sbjct: 121 SRLGDFIE-ADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEI 179

Query: 646 GKQFCVT 652
           G+ F VT
Sbjct: 180 GQIFNVT 186


>gi|56477835|ref|YP_159424.1| RNA polymerase factor sigma-32 [Aromatoleum aromaticum EbN1]
 gi|56313878|emb|CAI08523.1| Sigma-32 factor RpoH (RNA polymerase sigma factor) [Aromatoleum
           aromaticum EbN1]
          Length = 283

 Score =  136 bits (343), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 76/268 (28%), Positives = 126/268 (47%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I+S++    ++  E   + + +R        A + +V ++LRLV+++++ Y   GL
Sbjct: 16  IDQYIQSVNRIPLLTEQEEVSLATRLR--NEGDLEAARGLVMSHLRLVVAISRGYLGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      ++I      +
Sbjct: 74  PHADLIQEGNIGLMKAVKRFDPDRGVRLVSFAIHWIKAEIHEYILKNWRLVKIATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAM---PVEGVRKVLKITKEPISLETPIGDEDT 585
             K+    R +          E +A    +   P E V    ++T   I LE    D+D 
Sbjct: 134 --KLFFNLRSLKQDTGTLNRDEVVAVAKQLGVKPEEVVEMETRLTGRDIQLE-GGPDDDE 190

Query: 586 SHLGD--FIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            H     ++ D NA            R   E  +  LASL  R   +++ R+ +      
Sbjct: 191 HHFAPIAYLPDPNAEPSEVLEQAQLARLQDEGLSDALASLDDRSRTIVKRRW-LTEGDSA 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQIEAKA++K++
Sbjct: 250 TLHELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|160933256|ref|ZP_02080645.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
 gi|156868330|gb|EDO61702.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
          Length = 260

 Score =  136 bits (343), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 80/266 (30%), Positives = 144/266 (54%), Gaps = 18/266 (6%)

Query: 411 NEIKSISVETG----ISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTN 465
           N+++   V T     ++  E R +++ ++     E   A++E++  NLRLV+SV +++TN
Sbjct: 4   NKVEICGVNTSKLKVLTEKEKRALLTQMKNGTPQEQKKAREELINGNLRLVLSVIQRFTN 63

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +
Sbjct: 64  RGENLDDLFQVGCIGLIKAIDNFDISQDVRFSTYGVPMIIGEIRRFLRDNNS-VRVSRSL 122

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R++ +  +EP+ EEIAK+L +P E V   L+   EP+SL  P+  +  
Sbjct: 123 RDTAYKAMQVKERLTTQNNKEPSIEEIAKELELPKEDVVLALEAIVEPVSLYEPVFSDGN 182

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           DT  + D + DKN  +     I           + +L PRE+++L +RF  G     T  
Sbjct: 183 DTIFVMDQVGDKNDDNNWLDEI------ALKEAIRNLGPREKKILNLRFFQG----KTQM 232

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV K+  +++ ++ ++E  ++ ++K+
Sbjct: 233 EVAKEIGISQAQVSRLEKGSLERIKN 258


>gi|302554065|ref|ZP_07306407.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302471683|gb|EFL34776.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 381

 Score =  136 bits (343), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++       A + + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 141 FLKLRALPDGSPEYAEL-RNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 199

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R 
Sbjct: 200 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRS 259

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+KL++  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 260 PTVHELAEKLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY 319

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 320 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 370

Query: 665 RKLKH 669
            +L+ 
Sbjct: 371 AQLRE 375


>gi|254390381|ref|ZP_05005598.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294813859|ref|ZP_06772502.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197704085|gb|EDY49897.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294326458|gb|EFG08101.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 314

 Score =  136 bits (343), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 113/228 (49%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 90  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 149

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + + +  ++ ++ R PT  E+A  L +  E V 
Sbjct: 150 VGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQRLDRSPTVPELAAVLGVSEEEVV 209

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 210 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 264

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+
Sbjct: 265 PPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLR 308


>gi|11078965|dbj|BAB17487.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078969|dbj|BAB17489.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S ++      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  L  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W        +G++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGHEVDESWTDGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|170718627|ref|YP_001783826.1| RNA polymerase factor sigma-32 [Haemophilus somnus 2336]
 gi|168826756|gb|ACA32127.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 2336]
          Length = 280

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 63/266 (23%), Positives = 125/266 (46%), Gaps = 12/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +      ++  E + +   +     +   A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEGYIHAAYDYPMLTAEEEKELAERL--YYHQDLDAAKTLILSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+   ++      E   +A +L +  E V     ++T   +  + P+ D+++
Sbjct: 134 --KLFFNLRKTKQRLGWFSDKEVDMVANELGVSKEDVLEMESRMTGSDVGFDLPVDDDES 191

Query: 586 SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++EDK+   A    +   +    +     LA L  R   +++ R+        TL
Sbjct: 192 YAPALYLEDKSSNFAAELENENFETQAADQVANALAELDERSRDIIKSRWLDD--EKATL 249

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 250 HDLAAKYNISAERVRQLETNALKKLK 275


>gi|83311906|ref|YP_422170.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82946747|dbj|BAE51611.1| RNA polymerase sigma-32 factor [Magnetospirillum magneticum AMB-1]
          Length = 292

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 76/277 (27%), Positives = 123/277 (44%), Gaps = 14/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +    R  + E + A   +V ++LRLV  +A  Y + GL
Sbjct: 15  LAKYLRDIKEFPVLAPEEEFMLAK--RWVDYEDTDAAHRLVTSHLRLVAKIALGYRHYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIGLM+A +KF+   G++ +TYAMWW+K ++   + +    ++I      K
Sbjct: 73  PVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWWIKASLNEFVLNSWSMVKIGTLAAQK 132

Query: 529 --IHKVVRTARRMS----NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + R   R+       +  E       +      + V    ++     SL  P+  
Sbjct: 133 KLFFNLRRIKSRLRLLEAGDLAPEHVATIARELDVDERDVVAMNRRMAGRDSSLNAPV-G 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E  + + D + D+          +  L   R    R L SLT RE  V   R        
Sbjct: 192 EGGTEIQDLMADEADNQETAYGKREELSKGRVLIARALDSLTEREREVFVERRLRD--DP 249

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            TLEE+G ++ V+RERIRQIE KA  K++   ++  L
Sbjct: 250 VTLEELGGRYGVSRERIRQIEVKAFEKVRDLVQAGFL 286


>gi|311826267|emb|CBX60041.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 275

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 58/317 (18%), Positives = 114/317 (35%), Gaps = 43/317 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAK 445
            I   +  GE +A  AK
Sbjct: 259 DISRRMSIGEAKARRAK 275


>gi|27364575|ref|NP_760103.1| RNA polymerase factor sigma-32 [Vibrio vulnificus CMCP6]
 gi|37678299|ref|NP_932908.1| RNA polymerase factor sigma-32 [Vibrio vulnificus YJ016]
 gi|320154977|ref|YP_004187356.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
 gi|29611852|sp|Q8DD54|RP32_VIBVU RecName: Full=RNA polymerase sigma-32 factor
 gi|27360694|gb|AAO09630.1| alternative sigma factor RpoH [Vibrio vulnificus CMCP6]
 gi|37197038|dbj|BAC92879.1| RNA polymerase sigma-32 factor [Vibrio vulnificus YJ016]
 gi|319930289|gb|ADV85153.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
          Length = 285

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 128/267 (47%), Gaps = 16/267 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 19  YIRSVNSYPMLTADEERDLAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R   
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLF 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
             + ++ +R+      E   E +A++L +    VR++        S      +ED S   
Sbjct: 137 FNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAVDSTFDLPNEEDDSSSV 194

Query: 590 D-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 ++EDK+   A +      +A+        LASL  R + ++R R+        T
Sbjct: 195 STAPVLYLEDKSSDVADNLEAQNWEAHTNNRLAMALASLDERSQHIVRSRWLDD--DKAT 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++ + + V+ ERIRQ+E  A++KLK
Sbjct: 253 LQDLAEMYGVSAERIRQLEKNAMKKLK 279


>gi|11078931|dbj|BAB17470.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078961|dbj|BAB17485.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTCVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|169245684|gb|ACA50888.1| RpoD [Agrobacterium tumefaciens]
 gi|169245688|gb|ACA50890.1| RpoD [Agrobacterium tumefaciens str. C58]
 gi|169245694|gb|ACA50893.1| RpoD [Agrobacterium tumefaciens]
          Length = 174

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 95/173 (54%), Positives = 120/173 (69%), Gaps = 6/173 (3%)

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ
Sbjct: 1   QVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVKSLSLNQ 60

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +RID LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +   
Sbjct: 61  NRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAA 120

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             WK F   E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAK
Sbjct: 121 RGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAK 173


>gi|20808063|ref|NP_623234.1| sporulation sigma factor SigG [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516644|gb|AAM24838.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 264

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 74/240 (30%), Positives = 125/240 (52%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ + +     A++E + +NLRLV+SV +++ NRG    DL Q G IGL+KA + FD  
Sbjct: 33  ELLIRMKNGDKKAREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGCIGLIKAIDNFDLD 92

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  E
Sbjct: 93  QNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGE 151

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANL 609
           IAK+L +P E V   L   +EP+SL  PI  +  D  ++ D + D   V  +        
Sbjct: 152 IAKELDLPSEEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQVSDDKNVDEVWLE----- 206

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L  L  RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++ 
Sbjct: 207 KIALKEALEKLNEREKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMRK 262


>gi|15640181|ref|NP_229808.1| RNA polymerase factor sigma-32 [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121591866|ref|ZP_01679036.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|147674371|ref|YP_001218271.1| RNA polymerase factor sigma-32 [Vibrio cholerae O395]
 gi|153214854|ref|ZP_01949662.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|153803613|ref|ZP_01958199.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|153818953|ref|ZP_01971620.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|153824136|ref|ZP_01976803.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|153826296|ref|ZP_01978963.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|153830006|ref|ZP_01982673.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|227080385|ref|YP_002808936.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|229508425|ref|ZP_04397929.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229508894|ref|ZP_04398384.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229515820|ref|ZP_04405278.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229517008|ref|ZP_04406454.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229520061|ref|ZP_04409489.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229527110|ref|ZP_04416504.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229606698|ref|YP_002877346.1| RNA polymerase factor sigma-32 [Vibrio cholerae MJ-1236]
 gi|254291956|ref|ZP_04962737.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|254851536|ref|ZP_05240886.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255743901|ref|ZP_05417856.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|262163699|ref|ZP_06031440.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262172906|ref|ZP_06040584.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262190731|ref|ZP_06048960.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262404885|ref|ZP_06081439.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297581813|ref|ZP_06943734.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|298501088|ref|ZP_07010888.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|12644296|sp|P50511|RP32_VIBCH RecName: Full=RNA polymerase sigma-32 factor
 gi|9654552|gb|AAF93327.1| RNA polymerase sigma-32 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121546267|gb|EAX56564.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|124115097|gb|EAY33917.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|124120852|gb|EAY39595.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|126510515|gb|EAZ73109.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|126518343|gb|EAZ75566.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|146316254|gb|ABQ20793.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|148874491|gb|EDL72626.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|149739964|gb|EDM54143.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|150422166|gb|EDN14132.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|227008273|gb|ACP04485.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|227011849|gb|ACP08059.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|229335341|gb|EEO00824.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229342849|gb|EEO07839.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229346071|gb|EEO11043.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229347083|gb|EEO12044.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229354011|gb|EEO18944.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229354698|gb|EEO19620.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229369353|gb|ACQ59776.1| RNA polymerase sigma factor RpoH [Vibrio cholerae MJ-1236]
 gi|254847241|gb|EET25655.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255738384|gb|EET93774.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|261893982|gb|EEY39968.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262027915|gb|EEY46579.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262033375|gb|EEY51884.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262348969|gb|EEY98108.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297533907|gb|EFH72747.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|297540122|gb|EFH76183.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|327483048|gb|AEA77455.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 286

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 135/272 (49%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    +S  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERL--HYKGDIDAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      ++D +
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDEN 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK+   A +      +A+  +  +  LASL  R + ++R R+ +  + 
Sbjct: 192 GMAYTAPVLYLEDKHSDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++ + + V+ ERIRQ+E  A+RKLK  
Sbjct: 251 KTTLQDLAEMYGVSAERIRQLEKNAMRKLKEA 282


>gi|87303841|ref|ZP_01086550.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87281651|gb|EAQ73647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 215

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 84/198 (42%), Positives = 127/198 (64%), Gaps = 1/198 (0%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            + +  R+       AK+ M++ANLRLV+SVAKKY  +GL+ LDLIQEG++GL +A EKF
Sbjct: 16  DLTTKQRRMLRIGRRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKF 75

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   GYKFSTYA WW++Q++TR+IA QS TIR+PVH+ +++  + + +  +++K+   P 
Sbjct: 76  DPTRGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPN 135

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQA 607
             EIA+ + +PVE +  +L+      SL+ P+  E+  S LGD I D +A  PLD   Q 
Sbjct: 136 RLEIAEAMDIPVEELDSLLRQALTTSSLDAPVNGEEGRSFLGDLIADSSADEPLDIVEQR 195

Query: 608 NLRETTTRVLASLTPREE 625
              E   R L+ L+ +E+
Sbjct: 196 IHHEQLGRWLSHLSEQEQ 213


>gi|27382448|ref|NP_773977.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1834373|emb|CAA70697.1| rpoH2 [Bradyrhizobium japonicum]
 gi|27355619|dbj|BAC52602.1| sigma32-like transcription factor [Bradyrhizobium japonicum USDA
           110]
          Length = 299

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 68/279 (24%), Positives = 129/279 (46%), Gaps = 13/279 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLAEIRKFPMLEPQQEYMLAKRWR--EHDDRDAAHQLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   +++   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKINALDEGDLRPDQVATIAKRLGVTDQDVIDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIED--KNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D   N  + +    +  + R+     +  L PRE R+   R        
Sbjct: 194 GEAGEWQDWLVDNTPNQEAMMAEHEEYDHRRDALNGAMGVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            TLE++  +F V+RER+RQIE +A  K++   +    R+
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGTIARA 290


>gi|11078987|dbj|BAB17498.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 268

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 57/315 (18%), Positives = 117/315 (37%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + + ESA    ++D  +    P  
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAAKAEGDDEEEESADASDEEDEVESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     + +  + +   L  +    +  +   +                          
Sbjct: 110 AQQRFGAVSDQMEITRKALKKLGRDDKHAIAEMV-------------------------- 143

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 144 ---------ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I + + ++ ++  ETG+ I+E + 
Sbjct: 195 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|29829555|ref|NP_824189.1| RNA polymerase sigma factor, sigH [Streptomyces avermitilis
           MA-4680]
 gi|29606663|dbj|BAC70724.1| putative RNA polymerase sigma factor, sigH [Streptomyces
           avermitilis MA-4680]
          Length = 391

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 119/241 (49%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + M+  G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 154 LRMLPDGSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 213

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  
Sbjct: 214 ERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQQHGRSPTVH 273

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 274 ELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 329

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 330 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 384

Query: 669 H 669
            
Sbjct: 385 E 385


>gi|89895640|ref|YP_519127.1| sporulation sigma factor SigG [Desulfitobacterium hafniense Y51]
 gi|89335088|dbj|BAE84683.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 266

 Score =  136 bits (343), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 80/270 (29%), Positives = 132/270 (48%), Gaps = 13/270 (4%)

Query: 403 VDSILKIRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           ++      N+++   V T  + +     +  +    +     A+++++  NLRLV+SV +
Sbjct: 5   LEGAQMALNKVEICGVNTSKLPVLSSAKMKELFVAYQSGEKEAREKLIYGNLRLVLSVIQ 64

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           ++TNRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+
Sbjct: 65  RFTNRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRV 123

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
              +RD  +K ++   ++ N+  REPT  EIA KL +P E V   L   +EPISL  PI 
Sbjct: 124 SRSLRDIAYKALQVRDQLVNECSREPTVSEIADKLTLPREEVIFALDAIQEPISLFEPIY 183

Query: 582 DE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
            +  D   + D I D+           A         L  L+ RE+ +L +RF  G    
Sbjct: 184 HDGGDPIFVMDQIGDEKHSDNSWLEGIA-----VREALRRLSEREKLILSLRFFHG---- 234

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  EV  +  +++ ++ ++E  A+  ++ 
Sbjct: 235 KTQMEVADEIGISQAQVSRLEKAALGHMRK 264


>gi|239942800|ref|ZP_04694737.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           15998]
          Length = 288

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L +  E V 
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVSEEDVV 183

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 184 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 238

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 239 APRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 283


>gi|27884311|dbj|BAC55891.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus]
          Length = 318

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 78  FFELRELPDGSAEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 136

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 137 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 196

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 197 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 256

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L +L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 257 -----RESLKPLLEALPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 307

Query: 665 RKLKH 669
            +L+ 
Sbjct: 308 AQLRE 312


>gi|291447660|ref|ZP_06587050.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291350607|gb|EFE77511.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 318

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 78  FFELRELPDGSPEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 136

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 137 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 196

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 197 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 256

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 257 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 307

Query: 665 RKLKH 669
            +L+ 
Sbjct: 308 AQLRE 312


>gi|323498063|ref|ZP_08103069.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
 gi|323316871|gb|EGA69876.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
          Length = 285

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 131/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+ ++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRKVNSYPMLTADEERELAERLHYDGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +AK+L +    VR++        S      D+D S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVAKELGVEPAEVREMESRLAAQDSTFEMPTDDDDS 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++EDK    A +   +  +A+     +  LASL  R + ++R R+     +
Sbjct: 192 VSSYTAPVLYLEDKASDVADNVEAANWEAHTNNRLSLALASLDERSQHIVRSRWLDDNKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 252 --TLQELAETYSVSAERIRQLEKNAMKKLK 279


>gi|169245674|gb|ACA50883.1| RpoD [Agrobacterium tumefaciens]
 gi|169245676|gb|ACA50884.1| RpoD [Agrobacterium tumefaciens]
 gi|169245680|gb|ACA50886.1| RpoD [Agrobacterium tumefaciens]
 gi|169245682|gb|ACA50887.1| RpoD [Agrobacterium tumefaciens]
 gi|169245686|gb|ACA50889.1| RpoD [Agrobacterium tumefaciens]
 gi|169245690|gb|ACA50891.1| RpoD [Agrobacterium tumefaciens]
 gi|169245692|gb|ACA50892.1| RpoD [Agrobacterium tumefaciens]
 gi|169245696|gb|ACA50894.1| RpoD [Agrobacterium tumefaciens]
 gi|169245700|gb|ACA50896.1| RpoD [Agrobacterium tumefaciens]
 gi|169245704|gb|ACA50898.1| RpoD [Agrobacterium tumefaciens]
 gi|169245706|gb|ACA50899.1| RpoD [Agrobacterium tumefaciens]
 gi|169245708|gb|ACA50900.1| RpoD [Agrobacterium tumefaciens]
 gi|169245710|gb|ACA50901.1| RpoD [Agrobacterium tumefaciens]
          Length = 174

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 94/173 (54%), Positives = 120/173 (69%), Gaps = 6/173 (3%)

Query: 279 KVMCALDEIAEVYRELRSLQDN------AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
           +VM  LD IA+ Y++LR LQD       A  G        + K LK++L+  V SLSLNQ
Sbjct: 1   QVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKDLKDQLITAVKSLSLNQ 60

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           +R+D LVEQLYDISKR+M NEG LLRLA+SYG+KRD FLE++ G ELDP+W+    +   
Sbjct: 61  NRVDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSIANLAA 120

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             WK F   E ++I +IR EI+++S ETGISI+EFR IVSMV+KGE EA IAK
Sbjct: 121 RGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAK 173


>gi|23429481|gb|AAM97308.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 281

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 129/326 (39%), Gaps = 47/326 (14%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                         E DDV  T   I S           
Sbjct: 60  II--SGFIDPN------------------------ETDDVAPTATHIGSELGEDDLADED 93

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV- 302
            D   +  E+ E + D+ +      ++                  E + ELR+  + A  
Sbjct: 94  EDEDEDEDEDGESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVARL 136

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           + QK+ ++    +     L  +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 137 SIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 196

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +      V  + + +L+   +++ I  ETG
Sbjct: 197 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETG 255

Query: 422 ISISEFRHIVSMVRKGECEASIAKKE 447
           +SI++ + I   +  GE +A  AKKE
Sbjct: 256 LSIAQIKDINRRMSIGEAKARRAKKE 281


>gi|3219168|dbj|BAA28784.1| sigma-32 homolog [Achromobacter xylosoxidans]
          Length = 306

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 73/265 (27%), Positives = 130/265 (49%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    +S      +   +R  E     A +E++ ++LRLV+SVA++Y   GL
Sbjct: 40  IDAYISAVNRLPVLSAERETELGRRLRDQEDLG--AARELILSHLRLVVSVARQYLGYGL 97

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++      +
Sbjct: 98  PHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRNWRLVKVATTKAQR 157

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R   +       E IA++L +  E V ++ ++++   +SLE    D+D+  
Sbjct: 158 KLFFNLRSMRPDGQTLDPEQVEHIARELNVRREDVSEMEVRLSGRDMSLENQDDDDDSYA 217

Query: 588 LGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              ++ D     P     +A   +      +  L +L PR  R++  R+        TL 
Sbjct: 218 PIAYLSDDGRQEPTRVLERAARDQLQGSGLSDALEALDPRSRRIVEARWLQDDGG-ATLH 276

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++F V+ ERIRQIEA A++K++
Sbjct: 277 ELAQEFGVSAERIRQIEAAALKKMR 301


>gi|90580452|ref|ZP_01236258.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90438361|gb|EAS63546.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 231

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 82/213 (38%), Positives = 128/213 (60%), Gaps = 1/213 (0%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AKKY    L   D+I EGN+GL+ A EKFD   G++FSTYA WW+KQ I R+I +Q+
Sbjct: 1   MSIAKKYRAAHLLLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQN 60

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+PVH+  +I+ ++RT R +  K   EPT E+IA++L      +  +    ++ +SL
Sbjct: 61  RTIRLPVHVSKEINGLLRTHRDLMKKQNHEPTHEDIAQQLNKETHDISILFSYEQKIVSL 120

Query: 577 ETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +  IGD++ T  +   I D+   SP     + ++      +L  + PRE  +L  RFG+ 
Sbjct: 121 DQTIGDDENTGTIASLIVDEQIPSPSHIVEENSMVNLAEDILNKIKPREREILCRRFGVM 180

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL+EV     +TRER+RQ++AK++ +LK
Sbjct: 181 GYEPQTLQEVALALGITRERVRQLQAKSLERLK 213


>gi|83746847|ref|ZP_00943894.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|207727816|ref|YP_002256210.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|207742220|ref|YP_002258612.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
 gi|83726432|gb|EAP73563.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|206591057|emb|CAQ56669.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206593608|emb|CAQ60535.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
          Length = 306

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  +   I+S++    ++  E + +             A + +V ++LRLV+S+A++Y 
Sbjct: 29  SLGNLDAYIQSVNRVPMLTAEEEQQLAR--DYHATGNLDAARRLVLSHLRLVVSIARQYL 86

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W+K  +   I      +++   
Sbjct: 87  GYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATT 146

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ ++        + +A++L +    VR++    +   I+LE  I D
Sbjct: 147 KAQRKLFFNLRSHKQDAHATFTSDEIDAVAQELNVKGAEVREMETRLSGGDIALEGQIDD 206

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S     ++ D +         + + R   E     LA L  R  R++  R+ + +N 
Sbjct: 207 GEESFAPIAYLADTHNEPTRVLETRGHDRLQSEGIETALAKLDDRSRRIIEARW-LNVND 265

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           D     TL E+  +F V+ ERIRQIE+ A++K+K   ++
Sbjct: 266 DGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQA 304


>gi|207723156|ref|YP_002253555.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
 gi|206588350|emb|CAQ35313.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
          Length = 229

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 70/196 (35%), Positives = 113/196 (57%), Gaps = 2/196 (1%)

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q+I R+I +Q+ T+R+PVH+  ++++V+R  R +    
Sbjct: 29  AIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHVIRELNQVLRAKRHLEKSG 88

Query: 544 --KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              R+ + E+IA  L    E V+ VL + +   SL+TP   +  + L DF+ D++  SP 
Sbjct: 89  IDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPFDLDPGTSLLDFLSDEHGASPD 148

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  L +     LA L+ +   V+  RFG+      TLEE+  +  +TRER+RQI+ 
Sbjct: 149 QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELAAEMGLTRERVRQIQQ 208

Query: 662 KAIRKLKHPSRSKKLR 677
           +A+ KLK    S+ +R
Sbjct: 209 EALVKLKRHFASQGVR 224


>gi|75676615|ref|YP_319036.1| RNA polymerase factor sigma-32 [Nitrobacter winogradskyi Nb-255]
 gi|74421485|gb|ABA05684.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter winogradskyi
           Nb-255]
          Length = 299

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 125/274 (45%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E       +R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLSEIRKFPMLEPHEEYMFAKRLR--EHDDRDAAHHLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDMRPDQVKLIAKRLGVTEQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D++       A        R   T  +  L PRE R+   R        
Sbjct: 194 GEAGEWQDWLVDQSPNQEAIMAEHEEFDHRRRALTGAMGVLNPRERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TLE++  +F V+RER+RQIE +A  K++   ++
Sbjct: 252 MTLEDLAAEFNVSRERVRQIEVRAFEKVQSAVKT 285


>gi|55274978|gb|AAV49288.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  136 bits (343), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 82/200 (41%), Positives = 137/200 (68%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L+
Sbjct: 61  ERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 121 LNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 180

Query: 629 RMRFGIGMNTDHTLEEVGKQ 648
             RFG+      TLE+VG++
Sbjct: 181 ARRFGLLGYEAATLEDVGRE 200


>gi|50871522|emb|CAF74851.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871528|emb|CAF74854.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871530|emb|CAF74855.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/301 (17%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +     V + + D E     ++++       PE A   
Sbjct: 59  DDGAA-------APQEVEPETPQTTAKPVADDKDDDEEEESDTEEEEGDGGPDPEVARVR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   +I   E  +++L      + R  FL +
Sbjct: 137 TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        + ++   +    + I + + ++  +  +  ++I++ + I   
Sbjct: 197 FPSNETNLDWAEQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
 gi|151280836|gb|ABR89246.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
          Length = 298

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 126/266 (47%), Gaps = 8/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    ++  E   +   +R  +     A +++V ++LRLV+S+A+ Y   GL
Sbjct: 28  IDAYISAVNRLPMLTHEEEMSLARRLR--DENDLGAAQKLVLSHLRLVVSIARGYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  +Y+M W+K  +   I      +++      +
Sbjct: 86  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDT-- 585
                  + +           +E+AK L +  E V ++    +   I+LE P  DED   
Sbjct: 146 KLFFNLRSHKTGLDSMTPDQVDELAKTLNVKREEVIEMETRLSGRDIALEAPTDDEDDKF 205

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTD-HTL 642
           + +     D    + +  + Q +    E  +  L  L  R  R++  R+    +    TL
Sbjct: 206 APIAYLSSDMQEPTKVLESQQFDRLQTEGLSNALGKLDARSRRIVEARWLANDDGSGATL 265

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  +F V+ ERIRQIEA A++K+K
Sbjct: 266 HELADEFGVSAERIRQIEAVALKKMK 291


>gi|148652168|ref|YP_001279261.1| RNA polymerase factor sigma-32 [Psychrobacter sp. PRwf-1]
 gi|148571252|gb|ABQ93311.1| RNA polymerase, sigma 32 subunit, RpoH [Psychrobacter sp. PRwf-1]
          Length = 372

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 120/270 (44%), Gaps = 9/270 (3%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   + S+     ++  + + +    R  +     A + +V ++LR VI +A+ Y+  
Sbjct: 94  INLGAYMNSVHQIPILTTEQEQELAH--RYYDDGDVEAARILVMSHLRFVIHIARSYSGY 151

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 152 GLPQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKA 211

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             K+   +R+ ++ +N++  E      A       + +    ++T    S E    D++ 
Sbjct: 212 HRKLFFNLRSLKKTNNQLTLEEADAIAADLNVTRKQVLEMESRLTSYDASFEAQSTDDED 271

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            H    +  ++ V P +    A+  E         + +L  R   ++  R+        T
Sbjct: 272 GHYAPQLFLEDGVDPAEMVEDADWEENNTNALMDAMDTLDERSRDIVEQRWL--SEQKST 329

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L E+   + ++ ER+RQIE  A+ K++   
Sbjct: 330 LHELAAVYNISAERVRQIEKNAMDKIREAM 359


>gi|78224050|ref|YP_385797.1| sigma 32 (RpoH) [Geobacter metallireducens GS-15]
 gi|78195305|gb|ABB33072.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter metallireducens
           GS-15]
          Length = 279

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 120/262 (45%), Gaps = 10/262 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     ++  E    +  V+  E +   A   ++ ANLR V+ VA +Y + G++ L
Sbjct: 15  YLAEIRKFPVLTPEE--EHLYAVKFYEEKDLEAAHRLITANLRFVVKVAAEYKSYGMKML 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--I 529
           DLIQEGNIGLM A  KFD   G +  +YA+WW++  I   I      ++I      K   
Sbjct: 73  DLIQEGNIGLMMAVRKFDPHKGIRLISYAVWWIRAYIQNYIISAWSLLKIGTTQAQKKLF 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+ +    +      + T E  A  L +    V ++ +  +   SL+  + D +   + 
Sbjct: 133 FKLNQAKNAIRRLTGGDDT-EATALSLHVKESEVIEMDQRMRGDYSLDAELVDGEGLTML 191

Query: 590 DFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           D + D+        A Q     L    T+ L  L  +E  V+     +  +   TL+E+ 
Sbjct: 192 DTLVDERQNQEEALAEQQEASRLHGQVTQALERLNEKERYVVE--NRVTADEPLTLQEIA 249

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
             F ++RER+RQIE  A++K+K
Sbjct: 250 DHFAISRERVRQIEEGALKKIK 271


>gi|11079059|dbj|BAB17534.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 121/315 (38%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + D + A   + D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDAKAAKADDDSDDDEAEASTDDEEEVESGP--- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            EV R+            K  +S
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------EVTRKALK---------KHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|332185869|ref|ZP_08387616.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
 gi|332014227|gb|EGI56285.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
          Length = 301

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 65/275 (23%), Positives = 116/275 (42%), Gaps = 14/275 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  +   +    +  E     A  ++V ++LRLV  +A  Y   
Sbjct: 18  QSLNRYLAEIKKFPILAPEQEYMLAKRFQ--EHGDPEAAAQLVTSHLRLVAKIAMGYRGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   +LI EGNIGLM+  +KF+   G++ +TYAMWW++ +I   I      +++     
Sbjct: 76  GLPTSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAA 135

Query: 527 DK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKV--LKITKEPISLETP 579
            K     + R   ++      +  PE+   IA  L +  + V  +          SL   
Sbjct: 136 QKKLFFNLRRMKSKLDAFEDGDLRPEDVTKIATDLGVNEDEVISMNRRMAMGGDTSLNVS 195

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGM 636
           + ++      D++ D   +     A Q       +     +  L  RE+ +L        
Sbjct: 196 MREDGEGQWQDWLADDAPLQDSVVAEQQEADVRHDMLVSAMDDLNDREKHILTE--RRLT 253

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +   TLEE+ + + V+RER+RQIE +A  KL+   
Sbjct: 254 DDPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAM 288


>gi|55274989|gb|AAV49292.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 199

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 82/199 (41%), Positives = 135/199 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEV 645
           VL  RFG+      TLE+V
Sbjct: 181 VLARRFGLLGYEAATLEDV 199


>gi|282861039|ref|ZP_06270104.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563697|gb|EFB69234.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 323

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 83  FVELRELPDGSAEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 141

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 142 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQYGRS 201

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 202 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 261

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 262 -----RESLKPLLEGLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 312

Query: 665 RKLKH 669
            +L+ 
Sbjct: 313 AQLRE 317


>gi|11079003|dbj|BAB17506.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E   D         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDTEDDDAEASTD--------DEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  +S
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGHEVDESWSD-ALAKGKAKYAEAIARLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|294813001|ref|ZP_06771644.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326441452|ref|ZP_08216186.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325600|gb|EFG07243.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 306

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 122/242 (50%), Gaps = 12/242 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ + +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+ 
Sbjct: 68  LARLEEGTHEHAYVRNTLVELNLSLVRFAAARFRSRSEPMDDIVQVGTIGLIKAIDRFEL 127

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D S ++R+P  +++    + R    ++ ++ R PT  
Sbjct: 128 SRGVEFPTFAMPTVIGEIKRFFRDTSWSVRVPRRLQELRLDLARAGDELTARLDRSPTVA 187

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQA 607
           E+A+ L +  + V + +       P SL+    +E+    L + I  ++        I  
Sbjct: 188 ELAEYLGIGADEVVEGMVASNAYTPSSLDARPQNEEHDGTLAERIGYEDGGLEGVEYI-- 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E+   ++A L  R+ R+L +RFG     D T  ++G++  +++ ++ ++ ++ + +L
Sbjct: 246 ---ESLKPLIAGLPDRDRRILSLRFGA----DMTQSDIGEELGISQMQVSRLLSRTLVRL 298

Query: 668 KH 669
           + 
Sbjct: 299 RR 300


>gi|323706111|ref|ZP_08117680.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534555|gb|EGB24337.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 256

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 134/262 (51%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++ + +     A++E +  NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLKGAKQKELLLRMKNGDKSAREEFINGNLRLVLSVIQRFNNRGEY 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  VDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDVA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   ++ N+  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D  +
Sbjct: 122 YKALQVRDKLVNENSKEPTVGDIAKELNIPREEVVFALDAIQDPVSLFEPIYHDGGDAIY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I D+  V  +     A         +  L  RE+ +L MRF  G     T  EV K
Sbjct: 182 VMDQIGDEKNVDEVWLEQIA-----LKEAIKKLNDREKMILTMRFFEG----KTQMEVAK 232

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+  ++ 
Sbjct: 233 EIGISQAQVSRLEKSALSHMRK 254


>gi|222053896|ref|YP_002536258.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
 gi|221563185|gb|ACM19157.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
          Length = 283

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 65/264 (24%), Positives = 118/264 (44%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E       VR  E +   A  +++ +NLR V+ +A +Y   G++ L
Sbjct: 15  YLAEIKRFPVLSPEEEHECA--VRFYEKKDLEAAHKLITSNLRFVVKIAGEYRAYGMKML 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGN+GLM A  KF+   G++  +YA+WW++  I   I      ++I      R   
Sbjct: 73  DLIQEGNVGLMMAVRKFNPHKGFRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQRKLF 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+ +    + N        +  A+ L +    V ++ +  +    L+  +   +   + 
Sbjct: 133 FKLNQAKSAIRNMTGGGEDFQATAEALDVKETEVAEMDQRMRGDFFLDAQVITGEGLTML 192

Query: 590 DFIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           + + D+         ++   A L +     L  L  +E  V+  R      +  TL+E+ 
Sbjct: 193 ESLPDERRNQEELLAEAQESALLEKQVASALTCLNEKERYVIEQRVSAE--SPLTLQEIA 250

Query: 647 KQFCVTRERIRQIEAKAIRKLKHP 670
             F ++RER+RQIE  A++K+K  
Sbjct: 251 DHFSISRERVRQIEEGALKKMKQA 274


>gi|55274919|gb|AAV49261.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 201

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 82/201 (40%), Positives = 137/201 (68%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EG++GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGSLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEVGK 647
           VL  RFG+      TLE+VG+
Sbjct: 181 VLARRFGLLGYEAATLEDVGR 201


>gi|187479755|ref|YP_787780.1| RNA polymerase factor sigma-32 [Bordetella avium 197N]
 gi|115424342|emb|CAJ50895.1| RNA polymerase sigma-32 factor [Bordetella avium 197N]
          Length = 307

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 72/283 (25%), Positives = 138/283 (48%), Gaps = 8/283 (2%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P G     V     ++  I   I +++    ++  +   +   +R  + +   + +E+V 
Sbjct: 22  PSGNALALVVANPGALGTIDAYITTVNRLPVLTAEQESTLARRLR--DSDDLESARELVL 79

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I  
Sbjct: 80  SHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHE 139

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKI 569
            I      +++      +       + R           + IA++L +  E V ++ +++
Sbjct: 140 YIIRNWRLVKVATTKAQRKLFFNLRSMRPDGHTLDTEQVDHIARELNVRREDVSEMEVRL 199

Query: 570 TKEPISLETPIGDEDTSHLGDFIED---KNAVSPLDSAIQANLR-ETTTRVLASLTPREE 625
           +   +SLE    D+D      ++ D   +     L+   + +L+ +  +  + +L PR  
Sbjct: 200 SGRDLSLENQDDDDDGYAPIAYLSDECREEPTRVLERKARDDLQGKGLSDAITALDPRSR 259

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R++  R+        TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 260 RIVEARWLQDEGG-ATLHELAAEFGVSAERIRQIEAAALKKMR 301


>gi|11078929|dbj|BAB17469.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11078963|dbj|BAB17486.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEKGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   +    + ++        ESA    ++D  +    P  
Sbjct: 59  IDPDDGIAPPAEVPPPVDPKAAKAEGADDDEE--------ESADASDEEDEVESGPDPVI 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     + +  + +   L                                   +K  + 
Sbjct: 111 AQQRFGAVSDQMEITRKAL-----------------------------------KKFGRD 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|320007063|gb|ADW01913.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 297

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 123/245 (50%), Gaps = 8/245 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA 
Sbjct: 51  FFDKLQVLEEGTHEYQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAI 110

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D + ++ +P  +++   ++ +   ++S K+ R
Sbjct: 111 DRFDLSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVELAKAKEQLSTKLDR 170

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT  E+A  L +P E + + L         SL+TP  D D+        D         
Sbjct: 171 DPTVAELAAHLDLPEEEIIEGLVAANGYSAGSLDTPNADSDSGSEQRAYADLLGEDDPGM 230

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               NL  T   +L  L  RE +++RMRFG     + T  ++G +  V++  + ++ ++ 
Sbjct: 231 ESVENLH-TLAPLLRQLDDRERKIVRMRFG----QEMTQAQIGAELGVSQMHVSRLLSRI 285

Query: 664 IRKLK 668
           +++L+
Sbjct: 286 VQRLR 290


>gi|315064845|emb|CBX20958.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|315064849|emb|CBX20960.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|315064853|emb|CBX20962.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|315064857|emb|CBX20964.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S ++      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  L  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAELVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W        +G++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGHEVDESWTDGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|218885581|ref|YP_002434902.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218756535|gb|ACL07434.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 474

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 143/276 (51%), Gaps = 14/276 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ IS    +   E   +   V+  E   S A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 198 YLREISRFPLLKPDEEFDLARRVQ--EQGDSDAAFRLVTSHLRLVVKIAMDFQRRWMQNV 255

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDLIQEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      R  
Sbjct: 256 LDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQAQRKL 315

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE-DTS 586
            + + +  +R+  +   +P    +++KL + VE V ++  ++    +SL+  +G++   +
Sbjct: 316 FYNLNKERQRLIAQ-GYDPDATILSEKLNVTVEQVIEMEQRLDSSDMSLDITVGEDSGGA 374

Query: 587 HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              DF+         +  +S I   +++    +L  L+ +E  +L+    +      TL 
Sbjct: 375 TRMDFLPALGPGIEETLANSEIARMVQDRVQTILPKLSDKEAYILQH--RLLSEQPVTLR 432

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+G+++ +TRER+RQIEA+ ++KL+     K++R F
Sbjct: 433 EIGEKYDITRERVRQIEARLLQKLRDHL-FKEIRDF 467



 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 54/311 (17%), Positives = 104/311 (33%), Gaps = 41/311 (13%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQK----RKDSADRSTDDPVRMYLREMGSIELLSRE 137
           D +      D+ D A ++  S+   +     R      ST D + +YLRE+    LL  +
Sbjct: 152 DDDSPPARHDAHDGADASDESAGRHRSLPVLRPAMPGASTRDSLHLYLREISRFPLLKPD 211

Query: 138 GEIAIAKRI-EAGRAMMMASLCESPLTF-------------QALIIWRDELNDGTTLLRE 183
            E  +A+R+ E G +     L  S L               Q ++    E N G      
Sbjct: 212 EEFDLARRVQEQGDSDAAFRLVTSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVN 271

Query: 184 IIDLEACIGPESKGGF-----------------FHGTEGHSYQKREDSSQEKERDDVQET 226
             D E  I       F                   GT     +   + ++E++R   Q  
Sbjct: 272 KFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQAQRKLFYNLNKERQRLIAQGY 331

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME--DQLRPKVMCAL 284
           + D    ++       +V    +  ++ + +LD    + +   + M+    L P +   L
Sbjct: 332 DPDATILSEKLNVTVEQVIEMEQRLDSSDMSLDITVGEDSGGATRMDFLPALGPGIEETL 391

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
                       +Q         E   ++ ++L E+ V    +L     + D+  E++  
Sbjct: 392 ANSEIARMVQDRVQTILPKLSDKEAYILQHRLLSEQPV----TLREIGEKYDITRERVRQ 447

Query: 345 ISKRIMHNEGE 355
           I  R++    +
Sbjct: 448 IEARLLQKLRD 458


>gi|11079027|dbj|BAB17518.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 117/315 (37%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+ EGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTAEGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E   D E   +   D           
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDSEDDDAEASSDDEDEVESGPDPI--------- 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                         +A    A+ DQ+            E+ R+            K  +S
Sbjct: 110 -------------IAAQRFGAVSDQM------------EITRKALK---------KHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + +       L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|148257972|ref|YP_001242557.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. BTAi1]
 gi|146410145|gb|ABQ38651.1| RNA polymerase, sigma 32 subunit, RpoH [Bradyrhizobium sp. BTAi1]
          Length = 299

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 125/273 (45%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E + S A +++V ++LRLV  +A  Y   GL
Sbjct: 16  LARYLAEIRKFPMLEPQEEYMLAKRWR--EHDDSDAAQKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   R+S   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSRISALDEGDLHPDQVKLIAKRLGVTDQDVVDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +       A        R+     +  L  RE R+   R        
Sbjct: 194 GEAGEWQDWLVDTSPNQEAIMAEHEEYDHRRQALNGAIGVLNARERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|18310743|ref|NP_562677.1| sporulation sigma factor SigG [Clostridium perfringens str. 13]
 gi|18145424|dbj|BAB81467.1| probable transcription initiation factor sigma G [Clostridium
           perfringens str. 13]
          Length = 270

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 76/267 (28%), Positives = 139/267 (52%), Gaps = 15/267 (5%)

Query: 407 LKIRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           + + N+++   V T  + + + + +  ++ + +   + A+++ ++ NLRLV+SV +++ N
Sbjct: 13  IMMINKVEICGVNTAKLPVLKEKEMKELLLQMQNGDTSAREKFIKGNLRLVLSVIQRFNN 72

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D + TIR+   +
Sbjct: 73  RGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-TIRVSRSL 131

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K +    ++ N+  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  
Sbjct: 132 RDIAYKALLVRDKLVNENNKEPTVSQIAKELKIPREDVVFALDAIQDPVSLFEPIYHDGG 191

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D I D KN        I           +  L  RE+ +L +RF  G     T 
Sbjct: 192 DAIYVMDQISDSKNQDDSWLENI------AIKEAMKKLNDREKLILNLRFFNG----RTQ 241

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV  +  +++ ++ ++E  A++ ++ 
Sbjct: 242 MEVADEIGISQAQVSRLEKIALKHMRK 268


>gi|30024623|dbj|BAC75680.1| sigma L [Streptomyces griseus]
          Length = 288

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+ + L +  E V 
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELVRALGVSEEDVV 183

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++A            RE+   +LA L
Sbjct: 184 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGVEY-----RESLKPLLAKL 238

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 239 APRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 283


>gi|259417918|ref|ZP_05741837.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
 gi|259346824|gb|EEW58638.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
          Length = 298

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 126/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+      +  PE   +IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEDGDLRPEAVKKIATDLGVTEDEVISMNRRMSGGDASLNAMVGG 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +  S     D++ED+ A    D   Q  L   RE     ++ L  RE+ +L  R      
Sbjct: 194 DGDSTMQWQDWLEDEGADQAGDYEAQDELQARRELLAEAMSVLNDREKDILTQRRLAD-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QAKTLEELSVQYDVSRERIRQIEVRAFEKLQKKMR 286


>gi|11079065|dbj|BAB17537.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
 gi|11079071|dbj|BAB17540.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
 gi|11079083|dbj|BAB17546.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
 gi|11079085|dbj|BAB17547.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
 gi|11079087|dbj|BAB17548.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E   D         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDTEDDDAEASTD--------DEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  +S
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGHEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|11079015|dbj|BAB17512.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginata]
 gi|11079017|dbj|BAB17513.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
 gi|11079069|dbj|BAB17539.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
 gi|11079081|dbj|BAB17545.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 114/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                +   + +   DD  E   D         +D  +    P  
Sbjct: 59  IDPDDGIAPPAAEVPPPVDAKAAKADDDTEDDEAEASTD--------DEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  +S
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGHEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|50871524|emb|CAF74852.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871526|emb|CAF74853.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/301 (17%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +     V + + D E     ++++       PE A   
Sbjct: 59  DDGAA-------APQEVEPETPQTTAKPVVDDKDDDEEEESDTEEEEGDGGPDPEVARVR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   +I   E  +++L      + R  FL +
Sbjct: 137 TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        + ++   +    + I + + ++  +  +  ++I++ + I   
Sbjct: 197 FPSNETNLDWAEQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|50871520|emb|CAF74850.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/301 (17%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +     V + + D +     ++++       PE A   
Sbjct: 59  DDGAA-------APQEVEPETPQTTAKPVVDDKDDDDEEESDTEEEEGDGGPDPEVARVR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   +I   E  +++L      + R  FL +
Sbjct: 137 TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        + ++   +    + I + + ++  +  +  ++I++ + I   
Sbjct: 197 FPSNETNLDWAEQLAA-GKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|320353914|ref|YP_004195253.1| RNA polymerase sigma 32 subunit RpoH [Desulfobulbus propionicus DSM
           2032]
 gi|320122416|gb|ADW17962.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfobulbus propionicus
           DSM 2032]
          Length = 328

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 74/282 (26%), Positives = 138/282 (48%), Gaps = 10/282 (3%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ IS    +S  E   +   VR  E     A   +V +NLRLV+ VA  +    
Sbjct: 36  ALHRYLQEISQYELLSREETEELA--VRFQETGDPDAAYRLVSSNLRLVVKVAMDFQKYW 93

Query: 468 LQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHM 525
           +Q F+DLIQEGN+GL++A +KFD   G KFS YA +W++  I + I D    ++I     
Sbjct: 94  MQNFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAYWIRAYILKFIMDNWRLVKIGTTQA 153

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDED 584
           + K+   +   +++      +P  + +A++L +    V ++  ++    +SLE P+  + 
Sbjct: 154 QRKLFFSLNKEKKLLESQGFKPEVKLLAERLNVKESEVIEMGQRMDNWDVSLEAPVRSDS 213

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR--EERVLRMRFGIGMNTDHTL 642
                +F+         +      +RE    +LA L+ R  E+  + +   +  +   TL
Sbjct: 214 EDEQKNFLP-HEGPGIEEMVASQEMRERLAGILADLSTRLNEKEQVILTTRLLSDEPKTL 272

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK--LRSFLDG 682
           + +  +F ++RER+RQIE+  ++KL+     +   ++ FL G
Sbjct: 273 QTIADEFNISRERVRQIESNLLKKLRKQFEKEMPDIQDFLSG 314


>gi|308069872|ref|YP_003871477.1| RNA polymerase sigma-G factor (stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
 gi|305859151|gb|ADM70939.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
          Length = 260

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 141/270 (52%), Gaps = 18/270 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + +++       A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFTSLQQNNE--RSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    ++N   REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQVRDSLTNLNSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D    +   S I+          +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDDR--NKDVSWIEEI---ALREAMHRLGQREKMILSMRFYEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV  +  +++ ++ ++E  AI++++   +S
Sbjct: 231 EVADEIGISQAQVSRLEKSAIQQMQKHVKS 260


>gi|23429457|gb|AAM94476.1| RNA polymerase sigma factor D [Aeromonas allosaccharophila]
          Length = 281

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 125/325 (38%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II            GF    E                          E  A  +    S+
Sbjct: 60  II-----------SGFIDPNE-------------------------TEDMAPTATHIGSE 83

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +       E++E   DEDED  +                   E+   Y          ++
Sbjct: 84  LGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLS 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 IQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + + I +   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A+ AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKAARAKKE 281


>gi|11078923|dbj|BAB17466.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 269

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   +    + ++        ESA    ++D  +    P  
Sbjct: 59  IDPDDGIAPPAEVPPPVDPKAAKTEGADDDEE--------ESADASDEEDEVESGPDPVI 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     + +  + +   L                                   +K  + 
Sbjct: 111 AQQRFGAVSDQMEITRKAL-----------------------------------KKFGRD 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|222150148|ref|YP_002551105.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221737130|gb|ACM38093.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 285

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 72/277 (25%), Positives = 129/277 (46%), Gaps = 15/277 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           ++S+   +  I+       +   E   +   VR       +A+ ++  A++RLVI++A K
Sbjct: 1   MNSLQADKKLIRIAMAAPYLERQEEHDLA--VRWKHGNDQVARNQIAHAHMRLVIAMASK 58

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +   GL   DLIQEG IGL++AA +F+     +FSTYA WW++ ++   I      +R  
Sbjct: 59  FRGFGLPLGDLIQEGYIGLLEAAARFEPTRDVRFSTYAGWWIRASMQDYILRNWSIVRGG 118

Query: 523 VHMRDKI-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISL 576
                K       ++     +   ++  +   +EIA  L + +  V+    +++    SL
Sbjct: 119 TSSSQKALFFNLRRLRAKLAQGDQRLTDQAIHQEIATALGVSLADVQSMDARLSSNDTSL 178

Query: 577 ETPIGD--EDTSHLGDFIEDKN--AVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMR 631
           + PI +  E+ +   D +          +   I    R +     +A L  RE R++R R
Sbjct: 179 QAPISNNGEEGAERLDMLASDEPTPDEQVTDMIDTERRLDWLRGAMAHLNEREMRIIRAR 238

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                    TLEE+G +  +++ER+RQIE +A+ KLK
Sbjct: 239 RLSEDG--ATLEELGCELGISKERVRQIETRAMEKLK 273


>gi|219670064|ref|YP_002460499.1| sporulation sigma factor SigG [Desulfitobacterium hafniense DCB-2]
 gi|219540324|gb|ACL22063.1| RNA polymerase, sigma 28 subunit, SigG [Desulfitobacterium
           hafniense DCB-2]
          Length = 257

 Score =  136 bits (342), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 80/264 (30%), Positives = 130/264 (49%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + +     +  +    +     A+++++  NLRLV+SV +++TNRG
Sbjct: 2   ALNKVEICGVNTSKLPVLSSAKMKELFVAYQSGEKEAREKLIYGNLRLVLSVIQRFTNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++ N+  REPT  EIA KL +P E V   L   +EPISL  PI  +  D 
Sbjct: 121 IAYKALQVRDQLVNECSREPTVSEIADKLTLPREEVIFALDAIQEPISLFEPIYHDGGDP 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D I D+           A         L  L+ RE+ +L +RF  G     T  EV
Sbjct: 181 IFVMDQIGDEKHSDNSWLEGIA-----VREALRRLSEREKLILSLRFFHG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A+  ++ 
Sbjct: 232 ADEIGISQAQVSRLEKAALGHMRK 255


>gi|332799104|ref|YP_004460603.1| RNA polymerase sigma-28 subunit SigG [Tepidanaerobacter sp. Re1]
 gi|332696839|gb|AEE91296.1| RNA polymerase, sigma 28 subunit, SigG [Tepidanaerobacter sp. Re1]
          Length = 257

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 138/268 (51%), Gaps = 21/268 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           I N+++   V+T     +S ++ + +   ++K       A+++++  NLRLV+SV +++ 
Sbjct: 2   IVNKVEICGVDTSKLPVLSNAKMKELFLQLQK---GDKSAREKLISGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-QIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    +  K  REP+  E+AK++ MP E V   L   +EP+SL  PI  + 
Sbjct: 118 LRDTAYKALQVRDSLVTKNSREPSINEVAKEMNMPSEEVVFALDAIQEPVSLFEPIYHDG 177

Query: 584 -DTSHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            D   + D I D+ N        I      +    +  L  RE+++L +RF  G     T
Sbjct: 178 GDPIFVMDQISDEKNQDDQWLQGI------SIKEAMQRLGEREKKILNLRFFEG----KT 227

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             EV ++  +++ ++ ++E  A++ ++ 
Sbjct: 228 QMEVAQEIGISQAQVSRLEKAALKHMRK 255


>gi|55274945|gb|AAV49272.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 82/204 (40%), Positives = 138/204 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRL++ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLMVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFC 650
           VL  RFG+      TLE+VG++  
Sbjct: 181 VLARRFGLLGYEAATLEDVGREIG 204


>gi|3021662|dbj|BAA25351.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079011|dbj|BAB17510.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 268

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 55/315 (17%), Positives = 116/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + + + A     ++ ++    P  
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPIDAKAAKADDDAEDDDAEASDDEEEAESGPDPII 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 AAQRFGAVADQMEITRKAL-----------------------------------KKHGRH 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 135 NKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 195 FLRQFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|11079075|dbj|BAB17542.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 269

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/315 (19%), Positives = 121/315 (38%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +    E       +    + + + + A   + D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAAEVPPPVDAKAAKADDDSEDDEAEASTDDEEEVESGP--- 106

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            E+ R+            K  +S
Sbjct: 107 ----------DPIIAAQRFGAVSDQM------------EITRKALK---------KHGRS 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|213621937|ref|ZP_03374720.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 197

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 78/190 (41%), Positives = 132/190 (69%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW+
Sbjct: 1   RRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V 
Sbjct: 61  RQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVS 120

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++
Sbjct: 121 RMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 180

Query: 625 ERVLRMRFGI 634
             VL  RFG+
Sbjct: 181 REVLARRFGL 190


>gi|169831385|ref|YP_001717367.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638229|gb|ACA59735.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 128/249 (51%), Gaps = 12/249 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R    ++R  +    +A++ ++ ANL+LV +V +++  RG    DL Q G IGL+KA +K
Sbjct: 18  RETRRLLRLSQQGDVLARETLINANLKLVCNVIRRFEGRGYDPDDLFQIGCIGLIKAIDK 77

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D    +R+   +++   K   T  ++  ++ R+P
Sbjct: 78  FDLRFKVKFSTYAVPMIIGEIRRFLRD-DTPLRVSRSLKELAWKAQSTREQLQVRLDRDP 136

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAI 605
           T  E+A++L +P E +   L+  + P SL   +  +  D  H+ D +++K          
Sbjct: 137 TIGELAEELGIPREELVGALEAAQSPTSLYEVLHQDEGDPIHVMDQVQNKEENEGAWVE- 195

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               R     +L SL  R+ R++  RF      D T  EV +   +++ ++ ++E +A+R
Sbjct: 196 ----RIALQELLDSLPERDRRIVVWRFF----EDKTQAEVARNLGLSQVQVSRLEREALR 247

Query: 666 KLKHPSRSK 674
           KLK  +R+K
Sbjct: 248 KLKSMARAK 256


>gi|297200783|ref|ZP_06918180.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197712353|gb|EDY56387.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 297

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 121/252 (48%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 51  LSRSLFLRLAALDENSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 109

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 110 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 169

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 170 KLDRSPTVAELASVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 229

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 230 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 280

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 281 RLLTRTLAQLRE 292


>gi|284990614|ref|YP_003409168.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
 gi|284063859|gb|ADB74797.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
          Length = 360

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 120/242 (49%), Gaps = 12/242 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ + K +      ++ +VE +L LV   A++++NRG  F DL+Q G +GL+ A ++FD 
Sbjct: 123 LATLDKDDPRRERLREVLVEEHLPLVRHFARRFSNRGEPFDDLLQVGTLGLIAAIDRFDP 182

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F ++A+  +   I R   DQ  ++R+P  +++    +      ++ K  R PTP 
Sbjct: 183 TRGVEFLSFAVPTITGEIKRHFRDQGWSVRVPRRLQELHLSLNAAVGELAQKNGRAPTPS 242

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQA 607
           E+A+ L +P   V + L +       SL+  +  ED S  L   + ++++          
Sbjct: 243 ELAEHLGIPRAEVLEGLAVANAYRSSSLDERLSGEDDSPTLAATLGEEDSALEGVEY--- 299

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+   +LA++  RE R+L +RF        T  ++     +++  + ++ ++ + KL
Sbjct: 300 --RESLQPLLATIPARERRILILRFFGN----MTQSQIAADIGISQMHVSRLLSQTLAKL 353

Query: 668 KH 669
           + 
Sbjct: 354 RE 355


>gi|86157496|ref|YP_464281.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774007|gb|ABC80844.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 300

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 121/272 (44%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    +++ E R +    R  +   + A   +VEANLR V+ VA +Y + GL
Sbjct: 11  LDQYLREINRVALLTVEEERRLARQFR--DEGNTRAGHRLVEANLRFVVKVAFEYRSYGL 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           +  DLIQEGNIGLMKA +KFD     +  +YA+WW++  I   I      ++I      R
Sbjct: 69  RMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQR 128

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE-------IAKKLAMPVEGVRKVLKITKEPISLETP 579
                + RT   +          EE         K    P + V    ++    +SL+ P
Sbjct: 129 KLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEGRDLSLDAP 188

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMN 637
           + D  ++HL     D        +  + +  L    +  +  L PRE  ++     I   
Sbjct: 189 VADGTSTHLEFTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERHIVEA--RIMGE 246

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TL ++G  F  +RER RQ+E +A+ KL+ 
Sbjct: 247 GKETLRDLGHHFGFSRERARQLEIRALEKLRR 278



 Score = 37.5 bits (85), Expect = 8.2,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 124 YLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           YLRE+  + LL+ E E  +A++  + G       L E+ L F  ++    E       + 
Sbjct: 14  YLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRF--VVKVAFEYRSYGLRMA 71

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           ++I        E   G     +     K 
Sbjct: 72  DLI-------QEGNIGLMKAVQKFDPDKE 93


>gi|292494331|dbj|BAI94508.1| RNA polymerase beta subunit D [Pseudomonas sp. HT-3]
          Length = 263

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 54/300 (18%), Positives = 101/300 (33%), Gaps = 48/300 (16%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   +M+++   P T   ++     +      L E++          
Sbjct: 5   REGEIEIAKRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEVL---------- 54

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             G+    +G    +       KE    +E++   E  +     +       PE A    
Sbjct: 55  -SGYIDPDDGCVPDEAAAPVPVKEGAAAEESDDXXEDESGDHXQEEGDGGPDPEEAARRF 113

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             + E +D     L                                   +K  + S +  
Sbjct: 114 TAVAEQQDKVLKAL-----------------------------------KKHGRGSKQAT 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
                L +L   + L   + D LV Q+ D   R+   E  +++L      + R  FL   
Sbjct: 139 EELATLAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRADFLRLF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E+D  W +      + ++   +      I + + ++  +  E  +S++E + I   +
Sbjct: 199 PGNEIDMDWAADLAK-GKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKDINRRM 257


>gi|256751992|ref|ZP_05492861.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749102|gb|EEU62137.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 256

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 136/261 (52%), Gaps = 11/261 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++++ +     A++E +  NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLKPSKQKELLQRMKNGDKKAREEFINGNLRLVLSVIQRFNNRGEY 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  VDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLRDIA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   ++ ++  +EPT  EIAK+L +P E V   L   +EP+SL  PI  +     G
Sbjct: 122 YKALQVRDKLVSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDG----G 177

Query: 590 DFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I   + VS   +  +  L +      +  L+ RE+ +L MRF  G     T  EV K+
Sbjct: 178 DAIYVMDQVSDDKNMDEVWLEKIALKEAIQKLSEREKMILTMRFFEG----KTQMEVAKE 233

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A+  ++ 
Sbjct: 234 IGISQAQVSRLEKAALNHMRK 254


>gi|190576084|ref|YP_001973929.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia K279a]
 gi|190014006|emb|CAQ47646.1| putative RNA polymerase sigma-32 factor [Stenotrophomonas
           maltophilia K279a]
          Length = 291

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 67/269 (24%), Positives = 128/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ + + +    R G      A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDDEQDLARRFRDG--NDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  ALGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E +   +AK L +    V ++  +++   I  + P  +++ 
Sbjct: 141 KLFFNLRKSKTRLGWMNAAEVSA--VAKDLNVSEREVMEMESRLSGRDIGFDAPTDEDNE 198

Query: 586 ----SHLGDFIEDKNAVSPLDSAI--QANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S     + D    S        + N  +     LA L  R   ++R R+ +  ++ 
Sbjct: 199 HAPPSPAAFLVADDEDPSMAYEREDSEDNQMQLLREGLAELDARSRDIIRRRW-LDADSK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQ+EA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|213958530|gb|ACJ54686.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 19-20cm5R]
          Length = 262

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/303 (17%), Positives = 105/303 (34%), Gaps = 47/303 (15%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++       
Sbjct: 1   LLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL------- 53

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                G+    +G +    E       +    + + D E A   + D+      P     
Sbjct: 54  ----SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIA 109

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                   D+ +          +     +  L  +AE++                     
Sbjct: 110 AQRFGAVSDQMEITRKALKKHGRGNKLAIAELVLLAELF--------------------- 148

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
                          + L   + + LVE++     R+   E  +++L      + R  FL
Sbjct: 149 -------------MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFL 195

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + I 
Sbjct: 196 RQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDIN 254

Query: 432 SMV 434
             +
Sbjct: 255 RRM 257


>gi|182436064|ref|YP_001823783.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776688|ref|ZP_08235953.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178464580|dbj|BAG19100.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326657021|gb|EGE41867.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 318

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 78  FFELRELPDGSAEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 136

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 137 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 196

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 197 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 256

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 257 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 307

Query: 665 RKLKH 669
            +L+ 
Sbjct: 308 AQLRE 312


>gi|23429451|gb|AAM94473.1| RNA polymerase sigma factor D [Aeromonas schubertii]
          Length = 283

 Score =  136 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 123/325 (37%), Gaps = 43/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II            GF +  E              E        G       ++ +D S 
Sbjct: 60  II-----------SGFVNPDEA------------DEMGPTATHIGSELGEDDLADEDSSD 96

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +   E+ E D  + D D             +LR +       I                
Sbjct: 97  EEEEDEDEEGDGNDDDGDGGPDPEVAREKFAELRAQYEITRQSIRS-------------- 142

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQS 362
              + ++  + +    +L  +     L   + D LV  + ++ +R+   E  +L+   + 
Sbjct: 143 ---NGRAHEETQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVEQ 199

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +       A E + +L+   +++ I  ETG+
Sbjct: 200 AKMPKKTFVSAFTNNECETAWFEYQKQAGKAWSAPLAAME-EEVLRSIGKLQQIEEETGL 258

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 259 SIAQIKDINRRMSIGEAKARRAKKE 283


>gi|126728120|ref|ZP_01743936.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
 gi|126711085|gb|EBA10135.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
          Length = 277

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/268 (27%), Positives = 128/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       + +   A   +++A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 11  ELRLAYAWRDEKDEAALHRLIQAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A+ +
Sbjct: 71  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKALFFNMRRVQARLEREAQAI 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
             ++        IA ++ +P+  V  +  +++    SL      ED      D +ED + 
Sbjct: 131 GAQLDSHQLRHMIASEIGVPLRDVEMMEGRLSGSDFSLNATQSVEDEGREWIDTLEDDSA 190

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A    +S     LR+   + + SL  RE  ++R R         TLE +G +  +++E
Sbjct: 191 HGAEIVENSHDTECLRDWLVQAMGSLNERERFIVRERKLRD--EPRTLESLGNELGLSKE 248

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S +++ FL
Sbjct: 249 RVRQLEAAAFGKMRKALEAQSGEVQHFL 276


>gi|302559791|ref|ZP_07312133.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477409|gb|EFL40502.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 301

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 120/252 (47%), Gaps = 14/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  +  +       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 54  LSRSLFLRLAVLGEDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 112

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 113 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 172

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  ++ 
Sbjct: 173 KLDRSPTVPELAAVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDT 232

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 233 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 283

Query: 658 QIEAKAIRKLKH 669
           ++  + + +L+ 
Sbjct: 284 RLLTRTLAQLRE 295


>gi|239989259|ref|ZP_04709923.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           11379]
          Length = 288

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + +T+  ++ K+ R PT  E+A+ L +  E V 
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELAQKLDRSPTVPELARALGVSEEDVI 183

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 184 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 238

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 239 APRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 283


>gi|297192165|ref|ZP_06909563.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197720190|gb|EDY64098.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 349

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +       A + + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 109 FIELRKLPDGSPQRAEL-RNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 167

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 168 RFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 227

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 228 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY 287

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 288 -----RESLKPLLEGLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 338

Query: 665 RKLKH 669
            +L+ 
Sbjct: 339 AQLRE 343


>gi|55274998|gb|AAV49296.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 198

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 82/198 (41%), Positives = 135/198 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNTDHTLEEV 645
           L  RFG+      TLE+V
Sbjct: 181 LARRFGLLGYEAATLEDV 198


>gi|254478776|ref|ZP_05092144.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035288|gb|EEB75994.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 258

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/240 (30%), Positives = 124/240 (51%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++   +     A++E + +NLRLV+SV +++ NRG    DL Q G IGL+KA + FD  
Sbjct: 27  ELLITMKNGDKKAREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGCIGLIKAIDNFDLD 86

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D +  IR+   +RD  +K ++   ++ ++  +EPT  E
Sbjct: 87  QNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLRDIAYKALQVRDKLVSENSKEPTVGE 145

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANL 609
           IAK+L +P E V   L   +EP+SL  PI  +  D  ++ D + D   V  +        
Sbjct: 146 IAKELDLPSEEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQVSDDKNVDEVWLE----- 200

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L  L  RE+ +L MRF  G     T  EV K+  +++ ++ ++E  A+  ++ 
Sbjct: 201 KIALKEALEKLNEREKMILTMRFFEG----KTQMEVAKEIGISQAQVSRLEKAALNHMRK 256


>gi|28199909|ref|NP_780223.1| RNA polymerase factor sigma-32 [Xylella fastidiosa Temecula1]
 gi|28058040|gb|AAO29872.1| RNA polymerase sigma-32 factor [Xylella fastidiosa Temecula1]
          Length = 293

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 28  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 86  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 145

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-D 584
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 146 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 203

Query: 585 TSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 204 PSPVGYLIANDGDPSQAYERGNSEETQLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 261

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 262 LQELAEEYGVSAERIRQIEANALKKMK 288


>gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas arsenicoxydans]
 gi|133739970|emb|CAL63021.1| RNA polymerase sigma-32 factor [Herminiimonas arsenicoxydans]
          Length = 298

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 72/266 (27%), Positives = 124/266 (46%), Gaps = 8/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    ++  E   +   +R        A +++V ++LRLV+S+A+ Y   GL
Sbjct: 28  IDAYISAVNRLPMLTHEEEISLAKRLRDDNDLG--AAQKLVLSHLRLVVSIARGYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  +Y+M W+K  +   I      +++      +
Sbjct: 86  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDT-- 585
                  + +           E +AK L +  E V ++    +   I+LE P  DED   
Sbjct: 146 KLFFNLRSHKTGLDAMTPDQVEALAKTLNVKREEVIEMETRLSGRDIALEAPTDDEDDKF 205

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTD-HTL 642
           + +     D    + +  + + +    E  +  L  L PR  R++  R+    +    TL
Sbjct: 206 APIAYLSSDSQEPTRVLESQRYDRLQTEGLSSALGKLDPRSRRIVEARWLANDDGSGATL 265

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  +F V+ ERIRQIE  A++K+K
Sbjct: 266 HELANEFGVSAERIRQIETVALKKMK 291


>gi|3021668|dbj|BAA25354.1| RNA polymerase sigma-70 factor [Pseudomonas putida]
 gi|11079109|dbj|BAB17559.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 270

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/316 (18%), Positives = 121/316 (38%), Gaps = 48/316 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++   D +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +     + + D E   + + D+  +V+S P+ 
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAPAKADADDDEEEEKEGASDEEDEVESGPDP 109

Query: 251 AENDER-NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
               +R  L  D+ ++   +     + +   +  L ++AE++                  
Sbjct: 110 FVAQQRFALVADQLEATAKVLKKHGRPKQASIAELLQLAELF------------------ 151

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRD 368
                             + L   + ++LVE++    +R+   E  +++L      + R 
Sbjct: 152 ----------------MPIKLVPKQFEVLVERVRSALERLRAQERAIMQLCVRDARMPRA 195

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            FL      E+D  W           W   +      I++ + ++  +  ETG++I+E +
Sbjct: 196 DFLRLFPSNEVDTTWSGDLSKRSAK-WAEALGRLDADIVRCQQKLIDLQEETGLTIAEIK 254

Query: 429 HIVSMVRKGECEASIA 444
            I   +  GE +A  A
Sbjct: 255 DINRRMSIGEAKARRA 270


>gi|11078933|dbj|BAB17471.1| DNA-directed RNA polymerase subunit D [Pseudomonas ficuserectae]
          Length = 269

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 113/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    + T+ D E +A  S D+      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + L+E++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLLERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|254384107|ref|ZP_04999452.1| sigma factor [Streptomyces sp. Mg1]
 gi|194342997|gb|EDX23963.1| sigma factor [Streptomyces sp. Mg1]
          Length = 301

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 122/251 (48%), Gaps = 14/251 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F+ + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 55  LSRSLFQRLAALDADSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 113

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  ++ 
Sbjct: 114 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQ 173

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  +++     L D +  ++ 
Sbjct: 174 KLDRSPTVPELAAVLGVSEEEVVDGLAVGNAYTASSLDSPSPEDEGGEGSLADRLGYEDT 233

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 234 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 284

Query: 658 QIEAKAIRKLK 668
           ++  + + +L+
Sbjct: 285 RLLTRTLAQLR 295


>gi|113461681|ref|YP_719750.1| RNA polymerase factor sigma-32 [Haemophilus somnus 129PT]
 gi|112823724|gb|ABI25813.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 129PT]
          Length = 280

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 63/266 (23%), Positives = 126/266 (47%), Gaps = 12/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +      ++  E + +   +     +   A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEGYIHAAYDYPMLTAEEEKELAERL--YYHQDLDAAKTLILSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+   ++      E   +A +L +  E V     ++T   +  + P+ D+++
Sbjct: 134 --KLFFNLRKTKQRLGWFSDKEVDMVANELGVSKEDVLEMESRMTGSDVGFDLPVDDDES 191

Query: 586 SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++EDK+   A    +   +    +     LA L  R + +++ R+        TL
Sbjct: 192 YAPALYLEDKSSNFAAELENENFETQAADQVANALAELDERSQDIIKSRWLDD--EKATL 249

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 250 HDLAAKYNISAERVRQLETNALKKLK 275


>gi|197121539|ref|YP_002133490.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196171388|gb|ACG72361.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 300

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 121/272 (44%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    +++ E R +    R  +   + A   +VEANLR V+ VA +Y + GL
Sbjct: 11  LDQYLREINRVALLTVEEERRLARQFR--DEGNTRAGHRLVEANLRFVVKVAFEYRSYGL 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           +  DLIQEGNIGLMKA +KFD     +  +YA+WW++  I   I      ++I      R
Sbjct: 69  RMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQR 128

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE-------IAKKLAMPVEGVRKVLKITKEPISLETP 579
                + RT   +          EE         K    P + V    ++    +SL+ P
Sbjct: 129 KLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEGRDLSLDAP 188

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMN 637
           + D  ++HL     D        +  + +  L    +  +  L PRE  ++     I   
Sbjct: 189 VADGTSTHLEFTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERHIVEA--RIMGE 246

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TL ++G  F  +RER RQ+E +A+ KL+ 
Sbjct: 247 GKETLRDLGHHFGFSRERARQLEIRALEKLRR 278



 Score = 37.5 bits (85), Expect = 8.2,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 124 YLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           YLRE+  + LL+ E E  +A++  + G       L E+ L F  ++    E       + 
Sbjct: 14  YLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRF--VVKVAFEYRSYGLRMA 71

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           ++I        E   G     +     K 
Sbjct: 72  DLI-------QEGNIGLMKAVQKFDPDKE 93


>gi|271502546|ref|YP_003335572.1| RNA polymerase sigma-32 subunit RpoH [Dickeya dadantii Ech586]
 gi|270346101|gb|ACZ78866.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech586]
          Length = 285

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K+++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTADEERALAERL--HYHGDLDAAKQLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIG 581
                + +T +R+    + E   E +A++L +  + VR++      +      S E    
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPSPEDDAQ 191

Query: 582 DEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    +++DK+   A    +   + +  +  T  L  L  R + ++R R+ +  + 
Sbjct: 192 PGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADHYGVSAERVRQLEKNAMKKLR 280


>gi|158320421|ref|YP_001512928.1| sporulation sigma factor SigG [Alkaliphilus oremlandii OhILAs]
 gi|158140620|gb|ABW18932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 257

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 133/262 (50%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +   +  +  +     + A++E ++ NLRLV+SV +++ NRG  
Sbjct: 4   NKVEICGVNTSELPVLKNSQMRVLFDRIHKGDNSAREEFIQGNLRLVLSVIQRFNNRGEH 63

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     +FSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 64  VDDLFQVGCIGLIKAIDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTA 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   ++ NK  +EPT  +IA++L +P E V   L   ++P+SL  PI  +  D   
Sbjct: 123 YKALQVREQLINKNSKEPTIAQIAEELNLPREDVVFALDAIQDPVSLFEPIYQDSGDAIF 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D+ +         A         +  L  RE+ +L +RF  G     T  EV  
Sbjct: 183 VMDQVCDEKSEDECWIDGIA-----LREAMRKLNSREKHILSLRFFEG----RTQMEVAD 233

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A++ ++ 
Sbjct: 234 EIGISQAQVSRLEKTALKHMRK 255


>gi|329849869|ref|ZP_08264715.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
 gi|328841780|gb|EGF91350.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
          Length = 299

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 75/278 (26%), Positives = 124/278 (44%), Gaps = 15/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 24  LNRYLSEIRKFPMLAKDEEFMLAK--RWQEHQDPKAAHKLVTSHLRLVAKIAMGYRGYGL 81

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW+K +I   +      +++      K
Sbjct: 82  PVGEVISEGNVGLMQAVKKFDADRGFRLATYAMWWIKASIQEYVLRSWSLVKMGTTAAQK 141

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIG- 581
                  KV      +     R    E+IA KL +   + +    +++    SL  PI  
Sbjct: 142 KLFFNLRKVKSEISALEEGDLRHEQVEQIATKLGVSETDVINMNRRMSSPDSSLNAPIRA 201

Query: 582 DEDTSHLGDFIEDKNAVSPL----DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            E  S   D++ D   VS      DS   +         +  L  RE  +L        +
Sbjct: 202 SEGESEWQDWLVDDKQVSQETVLADSEEYSQRMGLLEAAMGELNAREREILTE--RRLKD 259

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +  TLE++ ++F V+RER+RQIE +A  KL+    + K
Sbjct: 260 SPTTLEDLAERFGVSRERVRQIEVRAFEKLQKAMTASK 297


>gi|226484289|emb|CAQ03749.1| RNA polymerase sigma factor [Enterovibrio nigricans]
 gi|226484291|emb|CAQ03750.1| RNA polymerase sigma factor [Enterovibrio nigricans]
          Length = 265

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 57/313 (18%), Positives = 109/313 (34%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  GF   ++            E   + +++ + +     +   D    V   PE 
Sbjct: 56  ------SGFVDPSQDDIAPTATHIGSELTEEQLKDED-NDGDDDEDDDDSEEDVGIDPEL 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L    +     ++                                   K+ + 
Sbjct: 109 AREKFSELRLSYEGMQAAIN-----------------------------------KNGRF 133

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
                    +L ++     L   + D LV ++     R+   E  ++RL      + +  
Sbjct: 134 HDDTHAAIAELSEVFKQFRLVPKQFDRLVNEMRGTMDRVRTQERIVMRLCVDQAKMPKKT 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E   +W+  A    E  + + +    + + +   ++K I  ETG+++   + 
Sbjct: 194 FVQLFGGNESSDNWLDAALA-TEKPFVDRLKLYEEDLRRCVQKLKIIEDETGLNVERIKD 252

Query: 430 IVSMVRKGECEAS 442
           I   +  GE +A 
Sbjct: 253 ISRRMSIGEAKAR 265


>gi|126739146|ref|ZP_01754840.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
 gi|126719763|gb|EBA16471.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
          Length = 292

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 134/278 (48%), Gaps = 17/278 (6%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N +   +++  +  +E    ++   + +     A   +  A +RL IS+A K+   G   
Sbjct: 9   NPLPRKAMKAELLDAETERALAYAWRDQR-DVKALHRLTNAYMRLAISMAAKFNRYGAPM 67

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI--------- 521
            DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +I   +      +R          
Sbjct: 68  NDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKTL 127

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPI 580
             ++R    ++ R A    +++ R    ++IA ++ +P+  V  +  +++    SL    
Sbjct: 128 FFNLRRVQAQLERRAYADGHRLDRHQLHQKIASEIGVPLRDVEMMDGRLSGSDFSLNANQ 187

Query: 581 GDE-DTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
             + D     D +ED++   A     +  +  LR+     + SLT RE  ++  R     
Sbjct: 188 ASDNDGREWIDALEDEHAEGAEQVEGTHDRRQLRQWLVEAMQSLTERERFIIVARKLQEP 247

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
               TLE++G++  +++ER+RQ+EA A++K++    S 
Sbjct: 248 F--RTLEDLGQELNLSKERVRQLEAAALKKMRKALASH 283


>gi|167037237|ref|YP_001664815.1| sporulation sigma factor SigG [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040623|ref|YP_001663608.1| sporulation sigma factor SigG [Thermoanaerobacter sp. X514]
 gi|300914664|ref|ZP_07131980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307267689|ref|ZP_07549143.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724102|ref|YP_003903853.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115656|ref|YP_004185815.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854863|gb|ABY93272.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856071|gb|ABY94479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|300889599|gb|EFK84745.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|306917291|gb|EFN47611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581163|gb|ADN54562.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928747|gb|ADV79432.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 256

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 136/261 (52%), Gaps = 11/261 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++++ +     A++E +  NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLKPSKQKELLQRMKNGDKKAREEFINGNLRLVLSVIQRFNNRGEY 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  VDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLRDIA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   ++ ++  +EPT  EIAK+L +P E V   L   +EP+SL  PI  +     G
Sbjct: 122 YKALQVRDKLVSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDG----G 177

Query: 590 DFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I   + VS   +  +  L +      +  L+ RE+ +L MRF  G     T  EV K+
Sbjct: 178 DAIYVMDQVSDDKNMDEVWLEKIALKEAIQKLSEREKMILTMRFFEG----KTQMEVAKE 233

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A+  ++ 
Sbjct: 234 IGISQAQVSRLEKAALNHMRK 254


>gi|332289156|ref|YP_004420008.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
 gi|330432052|gb|AEC17111.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
          Length = 281

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 133/269 (49%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E + +   +     +   A K+++ ++LR VI +A+ Y+  GL
Sbjct: 16  LEGYIRAANEYPMLTAEEEKELAERL--YYHQDVDAAKKLILSHLRFVIHIARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 74  PQADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVL-KITKEPISLETPIGD-ED 584
             K+    R+   ++      E   +A +L +  E V+++  +++   ++ + P  D E+
Sbjct: 134 --KLFFNLRKTKQRLGWFNANEVDMVANELGVSAEDVQEMESRMSGIDMAFDLPTDDSEE 191

Query: 585 TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           T     ++EDK+   A    +   +    +  +  L  L  R   +++ R+        T
Sbjct: 192 TYSPALYLEDKSSNFAAELEEENFENQATDQLSEALEQLDERSRHIIQTRWLDDN--KAT 249

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           L+E+   + V+ ERIRQ+E+ A++KL++ 
Sbjct: 250 LQELADHYGVSAERIRQLESNALKKLRNA 278


>gi|11078925|dbj|BAB17467.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|11079200|dbj|BAB17591.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
 gi|146150865|gb|ABQ02689.1| sigma factor 70 [Pseudomonas avellanae]
 gi|146150867|gb|ABQ02690.1| sigma factor 70 [Pseudomonas avellanae]
 gi|315064841|emb|CBX20956.1| sigma factor 70 [Pseudomonas syringae pv. syringae]
          Length = 269

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/315 (17%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + D E +A  S ++      P   
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPV 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D+ +          +     +  +  +AE++                   
Sbjct: 110 IAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMVALAELF------------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                            + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 151 ---------------MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|251791618|ref|YP_003006339.1| RNA polymerase factor sigma-32 [Dickeya zeae Ech1591]
 gi|247540239|gb|ACT08860.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya zeae Ech1591]
          Length = 285

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K+++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYHGDLDAAKQLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIG 581
                + +T +R+    + E   E +A++L +  + VR++      +      S E    
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDPSPEDDAQ 191

Query: 582 DEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    +++DK+   A    +   + +  +  T  L  L  R + ++R R+ +  + 
Sbjct: 192 PGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADHYGVSAERVRQLEKNAMKKLR 280


>gi|119715950|ref|YP_922915.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536611|gb|ABL81228.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 270

 Score =  136 bits (341), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/224 (26%), Positives = 111/224 (49%), Gaps = 12/224 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L LV   A+++ NRG    DL+Q G IGL+K+ ++FD   G +FSTYA   +   
Sbjct: 49  LVHLHLPLVEHCARRFRNRGEPLEDLVQVGTIGLIKSVDRFDADRGVEFSTYATPTIIGE 108

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R   D+   IR+P  +++   ++   +  ++  + R PTP E+A  +   VE + + +
Sbjct: 109 IKRYFRDKGWAIRVPRRLQELRMQISTASAELTQSLGRSPTPRELAGAIGCTVEEIVEGI 168

Query: 568 K--ITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +       +SL+     +D T+ + D I   +            +RE+   +L  L PRE
Sbjct: 169 ESSNAYSTLSLDATDDGDDNTASMLDAIGVDDE-----GLEHVEIRESLKPLLDRLEPRE 223

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++L +RF   M      EE+     V++  + ++  + + +L+
Sbjct: 224 KKILLLRFFKNMTQSQIAEEI----GVSQMHVSRLLNRTLEQLR 263


>gi|311826265|emb|CBX60040.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 276

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 119/318 (37%), Gaps = 43/318 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I     +
Sbjct: 1   ELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFV 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P++       T   +     + ++ +  D+  E   + E       D    V   PE A
Sbjct: 59  DPDAD----DTTAPTATHIGSELTESQLEDEDDEDVDEDEDGDDSDDDAEEDVGIDPELA 114

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                        +   +++   Y+ L+      +   +    S
Sbjct: 115 -----------------------------LEKFNQLRSTYQNLQ------LAINEHGYES 139

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVF 370
            K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F
Sbjct: 140 PKATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYGKMPKKSF 199

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +    G E    W+       +  +   +    + I +   ++K I  ET +++   + I
Sbjct: 200 IALFTGNESTDAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTVQNIKDI 258

Query: 431 VSMVRKGECEASIAKKEM 448
              +  GE +A  AKKEM
Sbjct: 259 SRRMSIGEAKARRAKKEM 276


>gi|113866384|ref|YP_724873.1| RNA polymerase factor sigma-32 [Ralstonia eutropha H16]
 gi|113525160|emb|CAJ91505.1| DNA-directed RNA polymerase sigma subunit (RpoH) [Ralstonia
           eutropha H16]
          Length = 308

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 132/273 (48%), Gaps = 10/273 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+++     ++  E + +   +R  +     A ++MV ++LRLV+S+A++Y   GL
Sbjct: 36  LDSYIQAVHRIPLLTAEEEQRLARELRDHDSVD--AARQMVMSHLRLVVSIARQYLGYGL 93

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD   G +  +YAM W+K  I   +      +++     + 
Sbjct: 94  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQR 153

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS 586
           K+   +R+ ++ ++    E       +    P E +    +++   ++LE  I D E+  
Sbjct: 154 KLFFNLRSHKQGAHTFTPEQVEAVARELNVKPEEVMEMETRLSGGDLALEGQIDDGEEEF 213

Query: 587 HLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT---DH 640
               ++ D +         + + R   E     L  L  R  R++  R+    +      
Sbjct: 214 APIAYLADNHNEPTRVLEAKRHDRMQVEGLEEALGKLDERSRRIIEARWLHVEDDGSGGS 273

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL E+  +F V+ ERIRQIEA A++K+K   ++
Sbjct: 274 TLHELADEFGVSAERIRQIEAAAMKKMKGALQA 306


>gi|302793696|ref|XP_002978613.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
 gi|300153962|gb|EFJ20599.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
          Length = 458

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKF 488
              +R+       A+ +++E N RLV+ +A++Y          DL QEG  GL+ A + F
Sbjct: 206 FRTLRRRLQLGEAAQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLIDAMDHF 265

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +   G +FSTYA++W++ A+ R+I      IR+P     K  ++ +  R +  ++ R P+
Sbjct: 266 NPGKGTRFSTYAIFWIRTAMVRAITRTGQVIRLPFSFAAKKVEIRKARRELRVELGRNPS 325

Query: 549 PEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            EE+ ++  + PV+             SL   +   D   L    E  + VS       +
Sbjct: 326 DEEVMERTGLDPVQFWNIYYYSNFRVRSLNETVRGTDEEFLEYLPETGDIVS-----ESS 380

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTD--HTLEEVGKQFCVTRERIRQIEAKAIR 665
            +RE     L  L  +E  VL+ R+G+        +L EVG++  +++E +R+ EA A+ 
Sbjct: 381 EVREEIVTALQRLKDKERMVLQHRYGLEDGAIAVKSLREVGRRLNMSQEMVRRYEASALE 440

Query: 666 KLKHPSRSKKLRSFL 680
           +L+H   +K LRS L
Sbjct: 441 RLRHQEEAKSLRSCL 455


>gi|239934550|emb|CAR94589.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 225

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 89/223 (39%), Positives = 135/223 (60%), Gaps = 3/223 (1%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI-G 192
           L   G IAIAKRIEAGR  M++ LCESPL+FQA+IIWRDELN+G  LLR+IIDLEA   G
Sbjct: 3   LVARGRIAIAKRIEAGREAMISGLCESPLSFQAIIIWRDELNEGKILLRDIIDLEATYAG 62

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P++K       E    +++E    E ++ +    E   +S ++    D        E  E
Sbjct: 63  PDAKKVEAPTPEERERKEKEARKAEADKREKAAEEMRAKSGSRRGGSDDVLSADDFEPVE 122

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN--AVNGQKDEKS 310
             + + D++++++  +L+AME +L+P V+   D IA+ Y+ LR LQD   +         
Sbjct: 123 QPDDDDDDEDEEANVSLAAMEAELKPHVLETFDRIAKTYKSLRKLQDQEVSEKTALSPSQ 182

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
             + + L+E++++ V SLSLN +RI+ LVEQLYDI++R++  E
Sbjct: 183 GRRYRKLREEIIEDVKSLSLNAARIEALVEQLYDINRRLISLE 225


>gi|239934560|emb|CAR94594.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 101/269 (37%), Gaps = 47/269 (17%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  G 
Sbjct: 1   DPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALANYPLTYTFMLNQYEQVKMGQ 60

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
             L +II            GF             +         V+    + E A     
Sbjct: 61  GRLVDII-----------VGFIDPNAPDEIAAPVNPKLAAAAAPVEPEAEEEEEAGDSED 109

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           ++  +    PE A                   A   +L  +V+ +L+E            
Sbjct: 110 EEALETGPDPEEAARRF---------------ASIQKLHQQVVKSLEE------------ 142

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                         K + L++K+ +    L L+    D L+ Q+ +    + + E  ++ 
Sbjct: 143 --------KGLDDPKTQKLRKKVAQEFMELKLSPKMFDALIVQMREHVSEVRNLEKSVMM 194

Query: 359 LAQS-YGIKRDVFLERHQGRELDPHWVSY 386
           L     G+ R  F+      E +  W+  
Sbjct: 195 LCVRDAGMPRKDFITTFPKNETNIKWLDK 223


>gi|255525678|ref|ZP_05392611.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296185436|ref|ZP_06853846.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
 gi|255510664|gb|EET86971.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296050270|gb|EFG89694.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
          Length = 257

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/265 (27%), Positives = 135/265 (50%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + + + + +  ++          +++ +++NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTAKLPVLKEKEMKELLLSMRNGDVSCREKFIKSNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+K+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             ++ ++   R+ ++  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYRALQVRDRLISENNKEPTVSQIAKELKVPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KN        I           +  L  RE+ +L +RF  G     T  E
Sbjct: 181 IYVMDQISDNKNMDDSWLENI------AIKEAMKKLNDREKLILNLRFFDG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A+R ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALRHMRK 255


>gi|148552989|ref|YP_001260571.1| RNA polymerase factor sigma-32 [Sphingomonas wittichii RW1]
 gi|148498179|gb|ABQ66433.1| RNA polymerase sigma factor RpoH [Sphingomonas wittichii RW1]
          Length = 301

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 117/275 (42%), Gaps = 14/275 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  E   +    +  E     A   +V ++LRLV  +A  Y   
Sbjct: 18  QSLNRYLAEIRKFPLLTAEEEYMLAKRFQ--EHGDPEAATRLVTSHLRLVAKIAMGYRGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   +LI EGNIGLM+  +KF+   G++ +TYAMWW+K +I   I      +++     
Sbjct: 76  GLPASELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTTAA 135

Query: 527 DK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKE--PISLETP 579
            K     + R   ++      +  PE+   IA  L +  E V  + +        SL   
Sbjct: 136 QKKLFFNLRRMKSQLEAFEDGDLKPEDLKKIATDLGVSEEEVTSMNRRMSMGGDASLNVS 195

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGM 636
           + ++      D + D+  +     A               LA+L  RE+ +L       +
Sbjct: 196 MNEDGEGEWQDMLVDQGPLQDERLAEVEEKSVRHNMLNEALAALNDREKHILVE--RRLV 253

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +   TLEE+ + + V+RER+RQIE +A  KL+   
Sbjct: 254 DEPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAM 288


>gi|295399724|ref|ZP_06809705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978127|gb|EFG53724.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 271

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 139/261 (53%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++       A++++V  NLRLV+SV +++ NRG 
Sbjct: 15  RNKVEICGVDTSKLPVLKNEEMRELFKRMHEGDLEAREKLVNGNLRLVLSVIQRFNNRGE 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 75  FVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT EEIA  L +P E V   L   ++P+SL  PI ++  D  
Sbjct: 134 AYKALQVREKLMGEAAKEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPI 193

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+ +        +  L+E   R    L  RE+ ++R RF  G     T  EV 
Sbjct: 194 YVMDQLSDERSGDNQW-IEEIALKEGLCR----LNEREKMIIRKRFFQG----KTQMEVA 244

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AIR++
Sbjct: 245 EEIGISQAQVSRLEKAAIRQM 265


>gi|320008631|gb|ADW03481.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 320

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 80  FIELRALPEGSAEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 138

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 139 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 198

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 199 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 258

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 259 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 309

Query: 665 RKLKH 669
            +L+ 
Sbjct: 310 AQLRE 314


>gi|220916304|ref|YP_002491608.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954158|gb|ACL64542.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 300

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 121/272 (44%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    +++ E R +    R  +   + A   +VEANLR V+ VA +Y + GL
Sbjct: 11  LDQYLREINRVALLTVEEERRLARQFR--DEGNTRAGHRLVEANLRFVVKVAFEYRSYGL 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           +  DLIQEGNIGLMKA +KFD     +  +YA+WW++  I   I      ++I      R
Sbjct: 69  RMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQR 128

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE-------IAKKLAMPVEGVRKVLKITKEPISLETP 579
                + RT   +          EE         K    P + V    ++    +SL+ P
Sbjct: 129 KLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEGRDLSLDAP 188

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMN 637
           + D  ++HL     D        +  + +  L    +  +  L PRE  ++     I   
Sbjct: 189 VADGTSTHLEFTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERHIVEA--RIMGE 246

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TL ++G  F  +RER RQ+E +A+ KL+ 
Sbjct: 247 GKETLRDLGHHFGFSRERARQLEIRALEKLRR 278



 Score = 37.1 bits (84), Expect = 8.9,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 124 YLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           YLRE+  + LL+ E E  +A++  + G       L E+ L F  ++    E       + 
Sbjct: 14  YLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRF--VVKVAFEYRSYGLRMA 71

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           ++I        E   G     +     K 
Sbjct: 72  DLI-------QEGNIGLMKAVQKFDPDKE 93


>gi|46240842|dbj|BAD15074.1| RNA polymerase alternative sigma factor [Saccharopolyspora
           erythraea]
          Length = 280

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            + V + +      +  +V  +L +   +A+++++RG    DL Q   +GL+ A ++FD 
Sbjct: 27  FAKVERQDPRHEQLRDRLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDP 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F +YA+  +   + R   D    +R+P  +++    V     R+S +  R PTP 
Sbjct: 87  GRGVDFLSYAVPTIMGEVRRHFRDTGWAVRMPRRLQELHLSVSAAIARLSQEFGRAPTPS 146

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA+ L +    V   L+        SL+  + D D   LGD I   +A        +  
Sbjct: 147 EIAEHLGISTNDVYHGLEAGNAYRSASLDELLTDTDEIPLGDAIGSNDA-----ELDEVE 201

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RET   +LA L  RE R+L MRF  G     T  ++ +Q  +++  + ++ ++ +  L+
Sbjct: 202 NRETIRPLLAELEERERRILVMRFFRG----MTQTQIAEQVGISQMHVSRLLSRTLAWLR 257

Query: 669 H 669
            
Sbjct: 258 E 258


>gi|23429443|gb|AAM94469.1| RNA polymerase sigma factor D [Aeromonas veronii bv. sobria]
          Length = 281

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 123/325 (37%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II            GF    E                          E  A  +    S+
Sbjct: 60  II-----------SGFIDPNE-------------------------TEDMAPTATHIGSE 83

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +       E++E   DEDED  +                   E+   Y          ++
Sbjct: 84  LGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLS 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 IQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + + I +   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +   AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKGRRAKKE 281


>gi|307293092|ref|ZP_07572938.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
 gi|306881158|gb|EFN12374.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
          Length = 304

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 118/273 (43%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +   +    R  E   S A  ++V ++LRLV  +A  Y   GL
Sbjct: 19  LNRYLSEIRKFPILTPEQEYMLAK--RYAEHADSEAAAQLVTSHLRLVAKIAMGYRGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGLM+  +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 77  PVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEFILRSWSLVKMGTTAAQK 136

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIG 581
                  ++        +        ++IA  L +  E V  +          SL  P+ 
Sbjct: 137 KLFFNLRRMKNNIEAFEDGDLHPDDVKKIATDLGVTEEDVISMNRRMAMGGDTSLNVPMR 196

Query: 582 DEDTSHLGDFIEDKN--AVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++      D++ D +      +    ++ LR +     +  L  RE+ +L  R       
Sbjct: 197 EDGEGQWQDWLADTDPLQDERVADRQESELRHDMLVEAMDDLNDREKHILAERRLAE--E 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TLEE+ + + V+RER+RQIE +A  KL+   
Sbjct: 255 PKTLEELSQVYGVSRERVRQIEVRAFEKLQKAM 287


>gi|114797392|ref|YP_759060.1| RNA polymerase factor sigma-32 [Hyphomonas neptunium ATCC 15444]
 gi|114737566|gb|ABI75691.1| alternative sigma factor RpoH [Hyphomonas neptunium ATCC 15444]
          Length = 298

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 77/272 (28%), Positives = 128/272 (47%), Gaps = 13/272 (4%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  I     +  +E   +    R  E E + A ++MV ++LRLV  +A  Y   GL  
Sbjct: 20  RYLSEIRKFPMLEKNEEFMLAR--RWHEHEDTEAAEKMVTSHLRLVAKIAMGYRGYGLPM 77

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            ++I EGN+GLM+A +KFD   G++ +TYAMWW++ AI   I      +++      K  
Sbjct: 78  AEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTAAQKKL 137

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
              + R    M    + +  PE+   IA+KL +    V     +++    SL  P+G + 
Sbjct: 138 FFNLRRLKGEMQALEEGDLKPEQARLIAEKLNVTETEVYSMNGRMSGSDASLNVPMGTDG 197

Query: 585 TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                D++ D     A +  +S          T+ +  L+ RE  +L       ++   T
Sbjct: 198 DMEWQDWLADDEPGTAETFANSQELDARMTLLTQAMEDLSERERHILTE--RRLVDEPKT 255

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           LEE+ +Q+ V+RERIRQIE +A  KL+   + 
Sbjct: 256 LEELSEQYNVSRERIRQIEVRAFEKLQKAMKR 287


>gi|90412724|ref|ZP_01220725.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90326299|gb|EAS42718.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 286

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 65/272 (23%), Positives = 136/272 (50%), Gaps = 16/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++++    +++ + + +   +         A K +V +++R V+ VA+ Y+  GL
Sbjct: 16  LDSYIQTVNRHPMLTVEQEKELAERL--HYDGDIEAAKGLVMSHMRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++ +R+      E   E +A++L +    VR++  ++  +  + E P  D+D 
Sbjct: 134 KLFFNLRKSKKRLGWFNNAE--VEMVAEQLGVNPSEVREMESRLAAQDPAFELPNEDDDR 191

Query: 586 ----SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
               +    F+EDK    A+S  ++  + +     +  LA L  R + ++R R+      
Sbjct: 192 DAGYTAPVYFLEDKASDVALSYEENNWENHTNNRLSNALAGLDERSQHIVRSRWLDD--E 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++   + ++ ER+RQ+E  A++KLK  
Sbjct: 250 KTTLQDLANHYGISAERVRQLEKNAMKKLKEA 281


>gi|23429461|gb|AAM94478.1| RNA polymerase sigma factor D [Aeromonas veronii]
 gi|23429463|gb|AAM94479.1| RNA polymerase sigma factor D [Aeromonas veronii]
 gi|23429465|gb|AAM94480.1| RNA polymerase sigma factor D [Aeromonas veronii]
          Length = 281

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 124/325 (38%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II            GF    E                          E  A  +    S+
Sbjct: 60  II-----------SGFIDPNE-------------------------TEDMAPTATHIGSE 83

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +       E++E   DEDED  +                   E+   Y          ++
Sbjct: 84  LGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLS 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 IQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + D I +   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKARRAKKE 281


>gi|11079147|dbj|BAB17578.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
          Length = 270

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 120/315 (38%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++ + P T  +++   + +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G    +  +    K+     + + D E  +  + D   + D  P  
Sbjct: 56  ------SGYIDPDDGSLPAEEVEPVNLKDDSADSKEKDDEEEESDDNSDSDDEGDGGP-- 107

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D +++    +A+ +QL                            +K  + 
Sbjct: 108 ----------DPEEARLRFTAVSEQLDKA---------------------KKALKKHGRG 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++    + +   E  +++L      + R  
Sbjct: 137 SKQATAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  WV       + ++   +    D IL+ + ++ ++  E  ++++E + 
Sbjct: 197 FLRLFPNHETDEKWVDSVLK-SKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKE 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRAMSIGEAKARRA 270


>gi|304320253|ref|YP_003853896.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303299155|gb|ADM08754.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 304

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 72/277 (25%), Positives = 125/277 (45%), Gaps = 16/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    +  E E   A + ++ ++LRLV  +A  Y   GL
Sbjct: 19  LNRYLAEIRKFPLLERDEEYMLAKRFK--EHEDPDAAQRLITSHLRLVAKIAMGYRGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ STYAMWW++ +I   I      ++I      K
Sbjct: 77  PTGEVISEGNVGLMQAVKKFDPDKGFRLSTYAMWWIRASIQEYILRSWSLVKIGTTAAQK 136

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   ++    + +  PEE   IA +L +  + V     ++     SL +P+  
Sbjct: 137 KLFFNLRKLKGQIDAVDEGDMRPEEVELIATRLGVTEDEVISMNRRMAGSDNSLNSPMRS 196

Query: 583 EDTS--HLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGM 636
           +        D++ D+NAV+     ++ +      E     +  L  RE  +L        
Sbjct: 197 DGDGGAEWQDWLVDENAVNAESQLVKDDEFETRMELLQEAMVDLNDRERHILTE--RRLT 254

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
               TLEE+  ++ V+RERIRQIE +A  KL+   + 
Sbjct: 255 ENPKTLEELSGEYGVSRERIRQIEVRAFEKLQKAMKR 291


>gi|322421263|ref|YP_004200486.1| RNA polymerase sigma 32 subunit RpoH [Geobacter sp. M18]
 gi|320127650|gb|ADW15210.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M18]
          Length = 284

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 69/269 (25%), Positives = 119/269 (44%), Gaps = 10/269 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I  +   +  I+    +S  E   +    R  +     A  +++ +NLR V+ +A +Y +
Sbjct: 9   IDSLTLYLTEINRFPLLSADEEMDLAYRFR--DEGDLQAAHKLITSNLRFVVKIAGEYRS 66

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH- 524
            G++ LDLIQEGNIGLM A  KFD   G +  +YA+WW++  I   I      ++I    
Sbjct: 67  YGMKMLDLIQEGNIGLMMAVRKFDPAKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQ 126

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
             R    K+ +  + + N    E      A  L +     R++ +  +  +SL+  + D 
Sbjct: 127 AQRKLFFKLNQAKQAIINMTG-EGDLHAAAISLDVKDTEAREMEQRLRGELSLDVEMFDG 185

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +     + + D         A +     L +     L  L  +E  V+  R         
Sbjct: 186 EGGTFLETLPDLRQNQEEMLAERQETTILEQGVASALGHLNEKERFVIERRVAAE--EPL 243

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TL+E+   F ++RER+RQIE  A++K+K 
Sbjct: 244 TLQEIADHFSISRERVRQIEEGALKKMKR 272



 Score = 37.5 bits (85), Expect = 7.5,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWRDELND 176
            D + +YL E+    LLS + E+ +A R  + G       L  S L F  ++    E   
Sbjct: 9   IDSLTLYLTEINRFPLLSADEEMDLAYRFRDEGDLQAAHKLITSNLRF--VVKIAGEYRS 66

Query: 177 GTTLLREII 185
               + ++I
Sbjct: 67  YGMKMLDLI 75


>gi|292494333|dbj|BAI94509.1| RNA polymerase beta subunit D [Pseudomonas indoloxydans]
          Length = 264

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/305 (17%), Positives = 105/305 (34%), Gaps = 48/305 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL REGEI IA+RIE G   +M+++   P T   ++     +      L EI+     
Sbjct: 1   VELLYREGEIEIAQRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGGRLXEIL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G    +       KE    + ++   E  +    ++       PE 
Sbjct: 56  ------SGYIDPDDGCVPDEAAAPVPVKEGAAAEASDDXXEDESGDHXEEEGDGGPDPEE 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  + 
Sbjct: 110 AARRFTAVAEQLEKARKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++ D   R+   E  +++L      + R  
Sbjct: 135 SKQAIEELATLAELFMPIKLVPKQYDALVTKVRDALDRLRAQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    G E+D  W +      + ++   +      I + + ++  +  E  ++++E + 
Sbjct: 195 FLRLFPGNEIDMDWAANLAK-GKAKYAEAIGALQADIQRCQQKLADLEAECNLTLAEIKD 253

Query: 430 IVSMV 434
           I   +
Sbjct: 254 INRRM 258


>gi|326392135|ref|ZP_08213612.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325991822|gb|EGD50337.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 256

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 136/261 (52%), Gaps = 11/261 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++++ +     A++E +  NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLKPSKQKELLQRMKNGDEKAREEFINGNLRLVLSVIQRFNNRGEY 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  VDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLRDIA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   ++ ++  +EPT  EIAK+L +P E V   L   +EP+SL  PI  +     G
Sbjct: 122 YKALQVRDKLVSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDG----G 177

Query: 590 DFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D I   + VS   +  +  L +      +  L+ RE+ +L MRF  G     T  EV K+
Sbjct: 178 DAIYVMDQVSDDKNMDEVWLEKIALKEAIQKLSEREKMILTMRFFEG----KTQMEVAKE 233

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A+  ++ 
Sbjct: 234 IGISQAQVSRLEKAALNHMRK 254


>gi|310642978|ref|YP_003947736.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247928|gb|ADO57495.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 260

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 141/270 (52%), Gaps = 18/270 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++ +E R + + +++       A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLTNAEMRELFTSLQQNNE--RSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    ++N   REPT  EI++ L +P E V   L   ++P+SL  PI  +  
Sbjct: 120 RDIAYKALQVRDSLTNLNSREPTIFEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D    +   S I+          +  L  RE+ +L MRF  G     T  
Sbjct: 180 DPIYVMDQISDDR--NKDVSWIEEI---ALREAMHRLGQREKMILSMRFYEG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV  +  +++ ++ ++E  AI++++   +S
Sbjct: 231 EVADEIGISQAQVSRLEKSAIQQMQKHVKS 260


>gi|1143832|gb|AAA84899.1| RNA polymerase sigma C subunit [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 130/266 (48%), Gaps = 14/266 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    ++  E +   ++ R        A   +V +NLR V+ VA +Y + GL+  
Sbjct: 14  YLSEINQYPLLTQQEEQ---ALARSFRQGDLQAGHRLVTSNLRFVVKVAYEYRSYGLRMS 70

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQE NIGLMKA +KFD   G +  +YA+WW+   I   +      +++      R   
Sbjct: 71  DLIQEANIGLMKAVQKFDPDKGIRLISYAVWWILAYIQGYVLKNWSLVKLGTTQAQRRLF 130

Query: 530 HKVVRTARRMSNKI---KREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT 585
             + RT R +  +          EEIA+KL +    VR++  ++    +SL+ P+G++  
Sbjct: 131 FALARTRRELEKQGNTDGNIVNAEEIARKLNVKASEVREMEQRMGGRDLSLDAPMGEDGD 190

Query: 586 SHLGDFIEDK--NAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +   DF+     +    +    +A+L R    + L  L PRE  ++     +  +++ TL
Sbjct: 191 ATHMDFVASDSVSQADEVADRQEADLARTRIQQALQRLDPRERFIIEK--RVMSDSEMTL 248

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+G+ F  +RER RQ+E +A  KLK
Sbjct: 249 SELGEHFGFSRERARQLEIRAKDKLK 274



 Score = 41.4 bits (95), Expect = 0.58,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 3/94 (3%)

Query: 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
           A  ++ D +  YL E+    LL+++ E A+A+    G       L  S L F  ++    
Sbjct: 3   ASLTSTDSLSTYLSEINQYPLLTQQEEQALARSFRQGDLQAGHRLVTSNLRF--VVKVAY 60

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E       + ++I  EA IG       F   +G 
Sbjct: 61  EYRSYGLRMSDLIQ-EANIGLMKAVQKFDPDKGI 93


>gi|311826289|emb|CBX60052.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 278

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/320 (18%), Positives = 117/320 (36%), Gaps = 43/320 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REG+I IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGDIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEASIAKKEM 448
            I   +  GE +A  AKKEM
Sbjct: 259 DISRRMSIGEAKARRAKKEM 278


>gi|288957081|ref|YP_003447422.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288909389|dbj|BAI70878.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 298

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 76/288 (26%), Positives = 125/288 (43%), Gaps = 16/288 (5%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC-EASIAKKEMVEANLRLVISV 459
             +D     R  +  I       +    H   + RK        A  ++V A  RLV++ 
Sbjct: 2   AYIDDPETQRANLSFIKASMREPLLSRDHEFDLARKWREGSDERALHQLVRAYTRLVVAT 61

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A ++ N GL   DL+QEGN+GLM+AA +F+     +FSTYA WW++ A+   I      +
Sbjct: 62  ASRFRNYGLPMGDLVQEGNVGLMQAASRFEPDREVRFSTYAAWWIRSAMQDYILRNWSIV 121

Query: 520 RIPV---------HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKI 569
           R            ++R    K+    +  S     +   E IA +L + V  V    +++
Sbjct: 122 RTGTTAAQKSLFFNLRRLRAKIDSATQNGSGAPLTKEGREWIAGELRVEVAEVEAMEMRL 181

Query: 570 TKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLR-ETTTRVLASLTPREER 626
           +    SL TP+ D       DF+ D   +    +     AN R +     L  L+P    
Sbjct: 182 SGADQSLNTPVADGSDDDWQDFLADQRPSPEDVVIGMRDANTRSQWLAEALGELSP--RE 239

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
              +R         TLEE+G++  V++ER+RQ+E +A+ KL+     +
Sbjct: 240 RTIIRERRLREEGATLEELGRELGVSKERVRQLEHRALLKLRQSMLKR 287


>gi|189184203|ref|YP_001937988.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str. Ikeda]
 gi|189180974|dbj|BAG40754.1| heat shock sigma factor RpoH [Orientia tsutsugamushi str. Ikeda]
          Length = 299

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 134/275 (48%), Gaps = 15/275 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I+    ++  E   +       E     A   +V+++L+LV  +A  Y   GL  +
Sbjct: 22  YLQKINRIPSLTAEEEYMLAK--SYFEQNNLKAAHSLVKSHLKLVAKIALSYRGYGLPVV 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH- 530
           DL+ EGNIGL++A +K++  LG++ STYA+WW+K AI   I      +++      K   
Sbjct: 80  DLVSEGNIGLLQAVKKYNPELGFRLSTYAIWWIKAAIQDYILRSWSLVKLGTTAAQKKLF 139

Query: 531 ----KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKITKEPISLETPI--GDE 583
               K+     ++  +       ++IA +  + +  V +   +++   +SL TPI   ++
Sbjct: 140 FNLGKIKNKITKLHARAINSSDYKQIADESGVSIAEVSEVNQRLSNSDLSLNTPISYHED 199

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D + L + + +      +  A Q +L   +E     L +LT RE  ++R R         
Sbjct: 200 DATELVELVPEHRPNQEIILANQQDLNLKQEVLQNALQTLTQRELYIIRARKLQD--EPD 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           TLE++   F V++ERIRQIE+KA  KL+  + + K
Sbjct: 258 TLEKLSLHFNVSKERIRQIESKAFEKLQQYAMNTK 292


>gi|304317193|ref|YP_003852338.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778695|gb|ADL69254.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 256

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 76/262 (29%), Positives = 133/262 (50%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++ + +     A++E +  NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLKGAKQKELLIRMKNGDKNAREEFINGNLRLVLSVIQRFNNRGEY 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  VDDLFQVGCIGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDVA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   ++ N+  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D  +
Sbjct: 122 YKALQIRDKLVNENSKEPTVGDIAKELNIPREEVVFALDAIQDPVSLFEPIYHDGGDAIY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I D   V  +     A         +  L  RE+ +L MRF  G     T  EV +
Sbjct: 182 VMDQIGDDKNVDEVWLEQIA-----LKEAIKKLNDREKMILTMRFFEG----KTQMEVAR 232

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+  ++ 
Sbjct: 233 EIGISQAQVSRLEKSALTHMRK 254


>gi|284044896|ref|YP_003395236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949117|gb|ADB51861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 300

 Score =  135 bits (340), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 80/266 (30%), Positives = 147/266 (55%), Gaps = 6/266 (2%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D++  ++  ++  S    ++ +E   +   + +       AK+ +V  NLRLV+S+A+++
Sbjct: 26  DTLDALQLFLRRASRYPLLTPAEELALSRRIER---GDLAAKERLVNHNLRLVVSIARRF 82

Query: 464 TN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
                L  LDL+QEG +GL++AAEKFDW  G++FSTYA  W++QAI R IA    TIR+P
Sbjct: 83  QGVSELTLLDLVQEGVVGLIRAAEKFDWRRGFRFSTYATLWIRQAIQRGIATHGRTIRLP 142

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
           V++  +  KV   ARR+  ++ R PT EEI+    +P + V  + ++++   SL+  +  
Sbjct: 143 VNVAQRERKVAAAARRLEAELGRAPTVEEISSASDLPPDQVADLREVSRTLASLDQVVTA 202

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHT 641
           +  + LG+ +  + A    +        ET  R +  L   +  V+++RFG+  + T   
Sbjct: 203 DTDTTLGELLPSE-APEVEEQVDALLQAETVRRTVEHLPSPQRDVIKLRFGLEEDRTPLP 261

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
             ++G++  +   ++R IE +A+ +L
Sbjct: 262 HAQIGRRLALATAQVRAIEREALARL 287



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 79/256 (30%), Gaps = 9/256 (3%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             D +   +      Q   D     T D ++++LR      LL+   E+A+++RIE G  
Sbjct: 2   PADPSQRPAPERAPAQPPADHVADDTLDALQLFLRRASRYPLLTPAEELALSRRIERGDL 61

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
                L    L     I  R +     TLL  +   E  +G       F    G  +   
Sbjct: 62  AAKERLVNHNLRLVVSIARRFQGVSELTLLDLV--QEGVVGLIRAAEKFDWRRGFRFSTY 119

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
                 +       T G              KV +     E +       E+ S+ +   
Sbjct: 120 ATLWIRQAIQRGIATHGRTIRLPVNVAQRERKVAAAARRLEAELGRAPTVEEISSAS--- 176

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
               L P  +  L E++     L  +     +    E    +   ++E+ V  +      
Sbjct: 177 ---DLPPDQVADLREVSRTLASLDQVVTADTDTTLGELLPSEAPEVEEQ-VDALLQAETV 232

Query: 332 QSRIDLLVEQLYDISK 347
           +  ++ L     D+ K
Sbjct: 233 RRTVEHLPSPQRDVIK 248


>gi|17545093|ref|NP_518495.1| RNA polymerase factor sigma-32 [Ralstonia solanacearum GMI1000]
 gi|17427383|emb|CAD13902.1| probable rna polymerase sigma h (sigma-32) factor transcription
           regulator protein [Ralstonia solanacearum GMI1000]
          Length = 306

 Score =  135 bits (339), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 134/278 (48%), Gaps = 11/278 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  +   I+S++    ++  E + +             A + +V ++LRLV+S+A++Y 
Sbjct: 29  SLGNLDAYIQSVNRVPMLTAEEEQQLAR--DYHATGNLDAARRLVLSHLRLVVSIARQYL 86

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  +   I      +++   
Sbjct: 87  GYGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATT 146

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ ++        + +A++L +    VR++    +   I+LE  I D
Sbjct: 147 KAQRKLFFNLRSHKQDAHATFTSDEVDAVAQELNVKGAEVREMETRLSGGDIALEGQIDD 206

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S     ++ D +         +   R   E     LA L  R  R++  R+    + 
Sbjct: 207 GEESFAPIAYLADTHNEPTRVLEGRGRDRLQSEGIETALAKLDDRSRRIIEARWLHVNDD 266

Query: 639 ---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                TL E+  +F V+ ERIRQIE+ A++K+K   +S
Sbjct: 267 GSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQS 304


>gi|217978453|ref|YP_002362600.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
 gi|217503829|gb|ACK51238.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
          Length = 303

 Score =  135 bits (339), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 68/277 (24%), Positives = 121/277 (43%), Gaps = 12/277 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E   S A  ++V ++LRLV  +A  Y   GL
Sbjct: 14  LARYLNEIRRFPMLEPQQEYMLAKRWR--EHADSDAAHKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 72  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTASQK 131

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  KV      +     R    ++IA +L +  + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKVKSQISALEEGDLRPEHVDKIAHRLGVSKQDVIDMNRRMSGDASLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSP--LDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D +A     L    + + R       L  L  RE R+   R         
Sbjct: 192 GEGEWQDWLVDDSASQEKLLVDREETDNRLGALHTALNVLNDRERRIFEARRLAD--DPM 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLE +  +F ++RER+RQIE +A  K++   ++   R
Sbjct: 250 TLEALSDEFDISRERVRQIEVRAFEKVQSAVKAGVAR 286


>gi|71275285|ref|ZP_00651572.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71902025|ref|ZP_00684069.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71164094|gb|EAO13809.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71728204|gb|EAO30391.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score =  135 bits (339), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 81  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-D 584
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 141 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 198

Query: 585 TSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 199 PSPVGYLIANDGDPSQAYERGNSEETQLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 256

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 257 LQELAEEYGVSAERIRQIEANALKKMK 283


>gi|328542558|ref|YP_004302667.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326412304|gb|ADZ69367.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 296

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 126/275 (45%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    ++ +  A  A + +V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLDEIRRFPMLEPQEEYMLAKRYKEHDDPA--AAERLVNSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 73  PLGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  ++    + +     +    +EIA KL +P E V  + +      SL  PI   
Sbjct: 133 RLFFNLRRLKGRIQALEEGDLKPEQVQEIATKLGVPEEDVVSMNRRLAGDASLNAPIRAA 192

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D++       A Q  L   R+     +  LT RE R+   R       
Sbjct: 193 EADSGEWQDWLVDESESQETLLANQEELDIRRKLLGDAMDILTERERRIFEARRLAE--D 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+  +F V+RER+RQIE +A  K++   R 
Sbjct: 251 PITLEELSTEFGVSRERVRQIEVRAFEKIQKAVRK 285


>gi|239930292|ref|ZP_04687245.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291438640|ref|ZP_06578030.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341535|gb|EFE68491.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
          Length = 300

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 114/229 (49%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 76  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 135

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + +T+  +S K+ R PT  E+A  L +  E V 
Sbjct: 136 VGEIKRFFRDTSWSVRVPRRLQELRLALTKTSDELSQKLDRSPTVTELATALGVSEEDVV 195

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 196 DGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 250

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE R++ +RF        T  ++G++  +++  + ++  + + +L+ 
Sbjct: 251 PPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLRE 295


>gi|162454145|ref|YP_001616512.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161164727|emb|CAN96032.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 283

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 71/277 (25%), Positives = 126/277 (45%), Gaps = 9/277 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    D    +   I  +     +S  E   +    R  +     A   +  ANLR V+S
Sbjct: 1   MQTSRDQASAVSRYITHVRQIPELSREEEVELARRWR--DHGDEQAAAALALANLRHVVS 58

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A  Y   G+   DLI EGN G++ A  K+D   G +F TYA +W++  I   +      
Sbjct: 59  IAISYRRYGIPLADLIAEGNFGIVHAIRKYDPDRGNRFVTYAAYWIRAYILNHVIHSWSL 118

Query: 519 IRIPVH--MRDKIHKVVRTARRMSNKIKR-EPTPEEIAKKLAMPVEGVRKVLKITK-EPI 574
           + +           ++ R   R++  +   E     +A+K   P E V ++    +   +
Sbjct: 119 VGVGSGPLRSKMFFRLRRERARIAGLVGEGEEGDRLLAEKFGAPAEKVLEMAHRLEARDV 178

Query: 575 SLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQ-ANLRETTTRVLASLTPREERVLRMR 631
           SL+T + ++    L D +  +D++       A + A LRE  T+ + +L PRE  ++  R
Sbjct: 179 SLDTKVFEDGARSLVDTLPADDQDQEERFSRAEEGALLRERLTQAVENLDPRERYIVETR 238

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  + +L E+G++  V+RER RQ+EA+A +KL+
Sbjct: 239 MMADPEEELSLAEIGRRLGVSRERARQLEARAKKKLR 275


>gi|148793348|gb|ABR12738.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 263

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 55/303 (18%), Positives = 105/303 (34%), Gaps = 44/303 (14%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +II     + 
Sbjct: 1   LLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDII--SGFVD 58

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P         T   +         E + +D  +   D +       ++       PE A 
Sbjct: 59  PNE-----EATAAPTATHIGSELSETDLEDEDKDLEDDDDDEDAENEEEDDGSIDPELAR 113

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                L +  +  A  ++                                   +  +   
Sbjct: 114 EKFLELRQSYEKMALAIN-----------------------------------QHGRQHA 138

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
             +V  E+L ++     L   + D LV  L D   ++  NE  ++R+      + +  F+
Sbjct: 139 TTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFI 198

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E +  W+  A +  +  +   +    + + +   +++ +  ETG+SI   + I 
Sbjct: 199 SLFAGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLSIERIKDIS 257

Query: 432 SMV 434
             +
Sbjct: 258 RRM 260


>gi|108803518|ref|YP_643455.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764761|gb|ABG03643.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 274

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 74/247 (29%), Positives = 131/247 (53%), Gaps = 2/247 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDW 490
           +++ +       A++ ++E++L L  ++A++Y  R +  F DL+QEG + L+ A + +D 
Sbjct: 26  ALLERAASGDREARRRVIESHLGLAAALARRYARRWVVPFEDLLQEGALALVHAVDHYDP 85

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA WWVKQAI R+    +  +R+P        ++    R +  ++ RE    
Sbjct: 86  SRGMRFSTYATWWVKQAIRRAAMAYARPMRVPERTWRLSERLAEAERELRAELGREIEDR 145

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++   L    E + +V +     +SLE+P+G+E+   LGD + D+NA  P + A + + R
Sbjct: 146 DLRSGLGWSEEELSEVRRAMGPVVSLESPVGEEEEDVLGDLVADENAEDPAELAARNDAR 205

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 L++L  RE  VL  R+G+      T  ++G++  V+RER RQ+E  A  +L+  
Sbjct: 206 RRLAHALSALPRRERAVLAGRYGL-TGEPRTFVDLGRELGVSRERARQLERAAAERLREH 264

Query: 671 SRSKKLR 677
            R   L 
Sbjct: 265 GRRLGLE 271


>gi|56551645|ref|YP_162484.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241761228|ref|ZP_04759316.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752767|ref|YP_003225660.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|59803027|sp|P50512|RP32_ZYMMO RecName: Full=RNA polymerase sigma-32 factor
 gi|56543219|gb|AAV89373.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374135|gb|EER63632.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552130|gb|ACV75076.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 302

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 117/274 (42%), Gaps = 14/274 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + +  I     +   E   +    +  E +   A   +V ++LRLV  +A  Y   
Sbjct: 18  QSLNHYLADIRKFPILKPEEEYMLAKRFQ--EHQDPKAASRLVTSHLRLVAKIAMGYRGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   +LI EGNIGLM+  +KFD   G++ +TYA+WW+K +I   I      +++     
Sbjct: 76  GLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWWIKASIQEYILRSWSLVKMGTTAA 135

Query: 527 DK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKV--LKITKEPISLETP 579
            K     + R    M+     +  P+E   IA  L +  E V  +          SL   
Sbjct: 136 QKKLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNLGVSNEEVVNMNRRMAMGGDSSLNIT 195

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGM 636
           + ++    + D++ D+  +       +       +     +  L  RE+ +L        
Sbjct: 196 MREDGEGQMQDWLVDQEPLQDQQIEEEEESLVRHKLLIEAMDKLNDREKHILTE--RRLS 253

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +   TLEE+ + + V+RER+RQIE +A  KL+  
Sbjct: 254 DNPKTLEELSQVYGVSRERVRQIEVRAFDKLQKA 287


>gi|311103433|ref|YP_003976286.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
 gi|310758122|gb|ADP13571.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
          Length = 294

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 74/265 (27%), Positives = 131/265 (49%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I S++    +S      +   +R  E     A +E++ ++LRLV+SVA++Y   GL
Sbjct: 28  IDAYISSVNRLPVLSAERETELGRRLRDQEDLG--AARELILSHLRLVVSVARQYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++      +
Sbjct: 86  PHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R   +       + IA++L +  E V ++ ++++   +SLE    D+D+  
Sbjct: 146 KLFFNLRSMRPDGQTLDPDQVDHIARELNVRREDVSEMEVRLSGRDMSLENQDDDDDSYA 205

Query: 588 LGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              ++ D+    P     +A   +      T  L +L PR  R++  R+        TL 
Sbjct: 206 PIAYLSDEGRQEPTRVLERAARDQLQSAGLTDALQALDPRSRRIVEARWLQDDGG-ATLH 264

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++F V+ ERIRQIEA A++K++
Sbjct: 265 ELAQEFGVSAERIRQIEAAALKKMR 289


>gi|285019635|ref|YP_003377346.1| RNA polymerase sigma-32 factor protein [Xanthomonas albilineans GPE
           PC73]
 gi|283474853|emb|CBA17352.1| probable rna polymerase sigma-32 factor protein [Xanthomonas
           albilineans]
          Length = 292

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 127/270 (47%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     ++  E   +   VR  + E   A +E+V ++LR V+ VA+ Y   GL
Sbjct: 24  LDAYIGAVHQIPVLTSEEEHALA--VRYRDQEDLDAARELVHSHLRFVVHVARGYNGYGL 81

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 82  PLGDLVQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEYILKNWRIVKVATTKAQR 141

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + ++  R+      E T   +AK L +    V     +++   I  + P  ++D 
Sbjct: 142 KLFFNLRKSKTRLGWMNAAEVTA--VAKDLNVSEREVLEMESRLSGRDIGFDAPSDEDDD 199

Query: 586 -------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                  ++L    ED +      +    N  +     LA L  R   ++  R+ +  ++
Sbjct: 200 HAPPSPAAYLMANEEDPSQA-YERADSDDNQLQLLREGLAELDARSRDIIERRW-LDADS 257

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ERIRQIEA A++K+K
Sbjct: 258 KITLQELADEYGVSAERIRQIEANALKKMK 287


>gi|188591091|ref|YP_001795691.1| RNA polymerase factor sigma-32 [Cupriavidus taiwanensis LMG 19424]
 gi|170937985|emb|CAP62969.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Cupriavidus taiwanensis LMG
           19424]
          Length = 309

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 132/273 (48%), Gaps = 10/273 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+++     ++  E + +   +R  + ++  A + +V ++LRLV+S+A++Y   GL
Sbjct: 37  LDSYIQAVHRIPLLTAEEEQRLARELR--DHDSVEAARRLVMSHLRLVVSIARQYLGYGL 94

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD   G +  +YAM W+K  I   +      +++     + 
Sbjct: 95  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQR 154

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS 586
           K+   +R+ ++  +    E       +    P E +    +++   ++LE  + D E+  
Sbjct: 155 KLFFNLRSHKQGGHTFTPEQVEAVARELNVKPEEVMEMETRLSGGDLALEGQVDDGEEEF 214

Query: 587 HLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRF---GIGMNTDH 640
               ++ D +         +   R   E     LA L  R  R++  R+       +   
Sbjct: 215 APIAYLADNHNEPTRVMEAKRQDRMQVEGLEEALAKLDERSRRIIEARWLNVEDDGSGGA 274

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL E+  +F V+ ERIRQIEA A++K+K   ++
Sbjct: 275 TLHELADEFGVSAERIRQIEAAAMKKMKGALQA 307


>gi|146338455|ref|YP_001203503.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. ORS278]
 gi|146191261|emb|CAL75266.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Bradyrhizobium sp. ORS278]
          Length = 299

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 124/273 (45%), Gaps = 13/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E + S A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LARYLSEIRKFPMLEPQEEYMLAKRWR--EHDDSDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IAK+L +  + V  + +      SL  PI D+
Sbjct: 134 KLFFNLRKAKSKISALDEGDLRPDQVKLIAKRLGVTDQDVIDMNRRLGGDASLNAPIRDD 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  D++ D +       A        R+     +  L  RE R+   R        
Sbjct: 194 GEAGEWQDWLVDTSPNQEAIMAEHEEYDHRRQALNGAIGVLNARERRIFEARRLAD--EP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TLE++  +F V+RER+RQIE +A  K++   +
Sbjct: 252 MTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|307546422|ref|YP_003898901.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
 gi|307218446|emb|CBV43716.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
          Length = 288

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 127/273 (46%), Gaps = 15/273 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   I++++    +++ E R +    R  +     A + +V ++LR V+ +A+ Y+  
Sbjct: 15  HDLNGYIQAVNGIPMLTVDEERELA--FRLHDEGDLEAARRLVMSHLRFVVHIARSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-- 524
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 73  GLAQADLIQEGNVGLMKAVKRFDPNQGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKA 132

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
            R     +    +R++     E   E IAK L +  E VR++  +++      +   G++
Sbjct: 133 QRKLFFNLRGAKKRLAWLNSNE--VEAIAKDLDVKPEVVREMEGRLSAHDAGFDAAPGED 190

Query: 584 DTS------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           + S      H  D      A    DS  + +  +     L+ L  R   +L+ R+    +
Sbjct: 191 EESAYQAPVHYLDDASQDPATQLEDSDWEEDSTQRLQAALSELDERSRDILQRRWL--SD 248

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              TL ++   + V+ ERIRQ+E  A++K++  
Sbjct: 249 DKSTLHDLADVYGVSAERIRQLEKNAMKKIRQS 281


>gi|300692652|ref|YP_003753647.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
 gi|299079712|emb|CBJ52389.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
          Length = 306

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  +   I+S++    ++  E + +             A + +V ++LRLV+S+A++Y 
Sbjct: 29  SLGNLDAYIQSVNRVPMLTAEEEQQLAR--DYHATGNLDAARRLVLSHLRLVVSIARQYL 86

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W+K  +   I      +++   
Sbjct: 87  GYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATT 146

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++ ++        + +A++L +    VR++    +   I+LE  I D
Sbjct: 147 KAQRKLFFNLRSHKQDAHATFTSDEIDAVAQELNVKGTEVREMETRLSGGDIALEGQIDD 206

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT 638
            + S     ++ D +         + + R   E     LA L  R  R++  R+ + +N 
Sbjct: 207 GEESFAPIAYLADAHNEPTRVLEARGHDRLQSEGIETALAKLDDRSRRIIEARW-LNVND 265

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           D     TL E+  +F V+ ERIRQIE+ A++K+K   ++
Sbjct: 266 DGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQA 304


>gi|302525186|ref|ZP_07277528.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
 gi|302434081|gb|EFL05897.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
          Length = 282

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 110/241 (45%), Gaps = 15/241 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDW 490
           +  +     ++  +V     LV  VA +    GL       DL+Q G  GL+ A EKFD 
Sbjct: 41  QFADKPDQTSRDRLVLHYAPLVKYVAGR-VGTGLPTHVDVGDLVQSGIFGLVDAIEKFDP 99

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F TYAM  ++ AI   +  Q     +P  +R K  +  R   R+  ++ R PT  
Sbjct: 100 ERGLRFETYAMQRIRGAILDDLRSQDW---VPRAVRSKAKETARALERLGARLHRTPTDA 156

Query: 551 EIAKKLAMPVEGVRKV--LKITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           E+A ++ + ++ +R           ++LE  +   +D   L D + D  AV P+   +  
Sbjct: 157 ELAGEMGISLDDLRDFYGQLRLTSVVALEDLVAAGKDAGSLVDTLPDDGAVDPVAVLVDQ 216

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R      +A LT R++ V+ + +        TL E+GK   VT  R+ Q+  +A+ +L
Sbjct: 217 DNRRQLAEAIAQLTDRDKIVVSLYYF----ESLTLAEIGKVLGVTESRVSQLHTRAVMRL 272

Query: 668 K 668
           +
Sbjct: 273 R 273


>gi|319778863|ref|YP_004129776.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
 gi|317108887|gb|ADU91633.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
          Length = 292

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 72/265 (27%), Positives = 122/265 (46%), Gaps = 9/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I+ ++    ++  + R     ++K       A + ++  +LRLV+SVA++Y   GL
Sbjct: 25  IEAYIQEVNRIPILTAEQERDYAERLQK--SGDLKAAQALILPHLRLVVSVARQYLGYGL 82

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  T+AM W+K  I   +      ++I      +
Sbjct: 83  PHADLIQEGNIGLMKAVKRFDVSRGVRLVTFAMHWIKAEIHEYVIRNWRLVKIATTKAQR 142

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSH 587
                  + R   K         IAKKL + P + V    +++   I+L+T + ++D   
Sbjct: 143 KLFFNLNSLRPEGKSLDNDDIVGIAKKLNVRPEDVVEMEKRMSGHDIALDTLMDEDDDYA 202

Query: 588 LGDFIEDKNAVSPLDSAIQANL----RETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              ++ D  A  P +  +         +     L  L  R   ++  R+        TL 
Sbjct: 203 PIQYLADDEAYEPENVMLAQEHDKLENQGLKSALDQLDDRSRHIIESRWLSEDKP--TLH 260

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  Q+ V+ ERIRQIE  AI+K++
Sbjct: 261 DLAAQYNVSAERIRQIENAAIKKMR 285


>gi|11079019|dbj|BAB17514.1| DNA-directed RNA polymerase subunit D [Pseudomonas marginalis]
          Length = 267

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 62/315 (19%), Positives = 120/315 (38%), Gaps = 49/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+               K   +  + + D+ + ++ + E+ +                
Sbjct: 59  IDPDDGIAPPAEVPPPVEAKVAKADDDTDDDEAESSDDEEEAESGP-------------- 104

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                     D   +A    A+ DQ+            EV R+            K  +S
Sbjct: 105 ----------DPVIAAQRFGAVADQM------------EVTRKALK---------KHGRS 133

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++     R+   E  +++L      + R  
Sbjct: 134 NKAAIAELLALAELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDARMPRAD 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 194 FLRQFPSNEVDESWSD-ALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKD 252

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 253 INRRMSIGEAKARRA 267


>gi|110635485|ref|YP_675693.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286469|gb|ABG64528.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 308

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 120/275 (43%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  ++V ++LRLV  +A  Y   GL
Sbjct: 15  LTRYLEEIRRFPMLQPEEEYMLAKRYR--EHDDTDAAHKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K AI   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  KV    + +           EIA +L +  E V  + +      SL  PI   
Sbjct: 133 RLFFNLRKVKGKIQALDEGDLNPEQVSEIATRLNVSEEEVISMNRRLSGDASLNAPIRAT 192

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D++         Q  L   R      +  L  RE R+         + 
Sbjct: 193 EGESGEWQDWLVDEHENQEEMLVEQDELESRRRMLEDAMDVLNDRERRIFEA--RRLSDE 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+  +F ++RER+RQIE +A  K++   ++
Sbjct: 251 PMTLEELSGEFDISRERVRQIEVRAFEKVQEAVKA 285


>gi|146277611|ref|YP_001167770.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145555852|gb|ABP70465.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 298

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 66/275 (24%), Positives = 123/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + + + A   +V ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVDHQDNRAAHRLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRM----SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++       ++ E   +          E +    +++    SL   IG 
Sbjct: 134 KLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLSVTEAEVIDMNRRLSASDASLNATIGS 193

Query: 583 EDT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +    +   D++ED+++    D A +  L   RE   + ++ L  RE+ +L        +
Sbjct: 194 DGDGATQWQDWLEDEDSDQASDYAERDELEIRRELLAQAMSVLNDREKDILVQ--RRLTD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+   + V+RERIRQIE +A  KL+   R
Sbjct: 252 DPVTLEELSDGYGVSRERIRQIEVRAFEKLQARMR 286


>gi|125972969|ref|YP_001036879.1| sporulation sigma factor SigG [Clostridium thermocellum ATCC 27405]
 gi|256004766|ref|ZP_05429741.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281417180|ref|ZP_06248200.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713194|gb|ABN51686.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium thermocellum
           ATCC 27405]
 gi|255991216|gb|EEU01323.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281408582|gb|EFB38840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940795|gb|ADU74829.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 1313]
          Length = 257

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 137/266 (51%), Gaps = 17/266 (6%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     ++  + + +   + K     + A++E ++ NLRLV+SV +++ 
Sbjct: 2   LVNKVEICGVNTSKLPVLTNEQKKELFERMHK---GDTSAREEFIKGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLIKAIDNFDVTQNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +RD  +K ++   +++N+  +EPT EEIAK+L +P E V   L   ++PISL   +  + 
Sbjct: 118 LRDIAYKALQAKEKLTNQNSKEPTIEEIAKELGLPKEEVVFALDAIQDPISLFESVYHDG 177

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               GD I   + V    +  +  L     +  +  L  RE+ +L +RF  G     T  
Sbjct: 178 ----GDAIYVMDQVKDEKNNDENWLEGIALSEAMRKLNDREKLILNLRFFDG----RTQM 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV ++  +++ ++ ++E  A+  ++ 
Sbjct: 230 EVAEEIGISQAQVSRLEKTALMHMRK 255


>gi|326503440|dbj|BAJ86226.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326503904|dbj|BAK02738.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 81/297 (27%), Positives = 147/297 (49%), Gaps = 10/297 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKK 446
           P+      +   + +IL+++  ++S  +++  + +E        V  +R+       A+ 
Sbjct: 203 PQSARLFKIMQPMKAILEVQENMRS-ELQSEPTEAEVAEAMNMPVQRLRRLRDVGRAARN 261

Query: 447 EMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++ NLRLV+    KY        +F DL Q G  GL+ A ++F+   G++ STYA++W
Sbjct: 262 KLIKHNLRLVLYAINKYYPDMTGDERFADLCQAGANGLITAIDRFEPKRGFRISTYALFW 321

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ ++ R+    S   R P  M  +  ++ R    +S ++ R PT EE  KK+ +     
Sbjct: 322 IRHSVVRA-MTLSSFTRFPFAMESERQEINRAREELSFELGRTPTDEETMKKVGLSPARY 380

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R V+++T+   SL +         L + + D +A+          LR     +L SL P+
Sbjct: 381 RDVVRMTRPAYSLHSRNRVTQE-ELINEVTDVDAIGVDTHKHNRLLRLAIDDLLDSLKPK 439

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R RFG+      TL E+     ++RE +R+ E KA+ KLKHP+R   LR ++
Sbjct: 440 ESVVIRQRFGLDGRGRRTLSEIAGNLRISREMVRKYELKALMKLKHPTRVDYLRRYM 496


>gi|240850016|ref|YP_002971409.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240267139|gb|ACS50727.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 294

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 68/278 (24%), Positives = 127/278 (45%), Gaps = 14/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ +     +   E   +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEVRHFPMLDPKEEYMLAQRYR--EHNDLKAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYA+WW+K +I   +      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAIWWIKASIQEYVLRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + + N        +EIA +L +  + V  + +      SL  P+  +
Sbjct: 134 RLFFNLRKLKSKLQALDNGDLNAEQVKEIATQLNVSEDEVISMNRRLGGDTSLNAPLRTK 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +   S L D++ D++         ++ L   R      + +L  RE+R+ + R    +  
Sbjct: 194 EGENSELQDWLVDESNDQEQVLIEKSELENRRSMLINAMDNLNEREKRIFKARRLNDI-- 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLEE+  +F ++RER+RQIE +A  K++   R   L
Sbjct: 252 PLTLEELSGEFNISRERVRQIEMRAFEKVQDSIRDSAL 289


>gi|290959143|ref|YP_003490325.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
 gi|260648669|emb|CBG71782.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
          Length = 287

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 114/255 (44%), Gaps = 15/255 (5%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T +   E +H+      G  E +  +  ++EANL LV   A ++ +R     D++Q G I
Sbjct: 43  TQVLFGELKHLA----PGTPEHNRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTI 98

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A ++FD   G +F T+AM  V   I R   D   T+ +P  + +   +V      +
Sbjct: 99  GLINAIDRFDPDRGVQFPTFAMPTVIGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDL 158

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +    R P+  EIA++L +  E V   ++   +    SLE     +    L D +  ++ 
Sbjct: 159 TTAFGRTPSTAEIAERLRITEEEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDP 218

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       R+    +L  L  RE+R+L +R+        T  ++  +  V++  + 
Sbjct: 219 ELDGVEH-----RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVS 269

Query: 658 QIEAKAIRKLKHPSR 672
           ++ A++  +L+  +R
Sbjct: 270 RLLARSFARLRSANR 284


>gi|182682661|ref|YP_001830821.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M23]
 gi|182632771|gb|ACB93547.1| RNA polymerase, sigma 32 subunit, RpoH [Xylella fastidiosa M23]
          Length = 288

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 81  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-D 584
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 141 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 198

Query: 585 TSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 199 PSPVGYLIANDGDPSQAYERGNSEETQLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 256

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 257 LQELAEEYGVSAERIRQIEANALKKMK 283


>gi|23429447|gb|AAM94471.1| RNA polymerase sigma factor D [Aeromonas veronii bv. veronii]
          Length = 281

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 124/325 (38%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQIQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II            GF    E                          E  A  +    S+
Sbjct: 60  II-----------SGFIDPNE-------------------------TEDMAPTATHIGSE 83

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +       E++E   DEDED  +                   E+   Y          ++
Sbjct: 84  LGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLS 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 IQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + + I +   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKARRAKKE 281


>gi|1621026|gb|AAB17121.1| RpoS [Yersinia enterocolitica]
          Length = 277

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 77/219 (35%), Positives = 137/219 (62%), Gaps = 3/219 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+NRGL 
Sbjct: 60  QLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSNRGLA 116

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+ L++A EKFD   G++FSTY+ WW++Q I R+I +Q+ TIR+P+H+  ++
Sbjct: 117 LLDLIEEGNLCLIRAVEKFDPEPGFRFSTYSHWWIRQTIERAIMNQTRTIRLPIHIVKEL 176

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +    TAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L 
Sbjct: 177 NVYFGTARELSHKLDHEPSAEEIAEQLNKPVDDVSRMLRLNERITSVDTPLGGDSEKSLL 236

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           D + D+N   P D+    +++++  + L  L  ++  VL
Sbjct: 237 DILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 275



 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/115 (20%), Positives = 44/115 (38%), Gaps = 1/115 (0%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           ++ +  +V   ++  + E  ++   +    + +S    +             ++YL E+G
Sbjct: 8   VNELHEDVNFDENSTETEIFDEKQLVEDEPTEASSAEDELLAQGVTQRCWSTQLYLGEIG 67

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
              LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 68  YSPLLTAEEEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 121


>gi|297746543|emb|CAZ60989.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 267

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 112/304 (36%), Gaps = 46/304 (15%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I
Sbjct: 1   ELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFI 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P          +  +       SQ  + D   E E + E+    S DD       PE A
Sbjct: 59  DPNE-------ADDVAPTATHIGSQLGKDDLADEDENENENDDGDSSDDEGDGGPDPEVA 111

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                +L    + +  ++                                   QK+ ++ 
Sbjct: 112 REKFGDLRAQYEVTRLSI-----------------------------------QKNGRAH 136

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
              +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F
Sbjct: 137 EDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTF 196

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +      E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I
Sbjct: 197 VAAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDI 255

Query: 431 VSMV 434
              +
Sbjct: 256 NRRM 259


>gi|298292657|ref|YP_003694596.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296929168|gb|ADH89977.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 303

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/272 (24%), Positives = 121/272 (44%), Gaps = 14/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E E   A  ++V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLAEIRRFPMLEPQEEYMLAKRWR--EHEDPEAAHKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 73  PISEVISEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S     +      ++IA KL +  + V  + +      SL  P+  +
Sbjct: 133 KLFFNLRKAKSQISALEDGDLRPDQVQQIATKLGVTEQEVVDMNRRLSGDASLNAPLRGD 192

Query: 584 --DTSHLGDFIED--KNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNT 638
                   D++ D   +  + L    + + R       L+ L  RE R+         + 
Sbjct: 193 VEGGGEWQDWLADDRDDQETTLADLEETDNRRSALAGALSVLNERERRIFEA--RRLSDD 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TLE++  +F V+RER+RQIE +A  K++  
Sbjct: 251 PMTLEDLASEFGVSRERVRQIEVRAFEKVQKA 282


>gi|55274930|gb|AAV49266.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 81/198 (40%), Positives = 134/198 (67%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           + M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V +
Sbjct: 61  QTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSR 120

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 121 MLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 180

Query: 626 RVLRMRFGIGMNTDHTLE 643
            VL  RFG+      TLE
Sbjct: 181 EVLARRFGLLGYEAATLE 198


>gi|134102136|ref|YP_001107797.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291007613|ref|ZP_06565586.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133914759|emb|CAM04872.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 280

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            + V + +      +  +V  +L +   +A+++++RG    DL Q   +GL+ A ++FD 
Sbjct: 27  FAKVERQDPRHEQLRDRLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDP 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F +YA+  +   + R   D    +R+P  +++    V     R+S +  R PTP 
Sbjct: 87  GRGVDFLSYAVPTIMGEVRRHFRDTGWAVRMPRRLQELHLSVSAAIARLSQEFGRAPTPS 146

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA+ L +    V   L+        SL+  + D D   LGD I   +A        +  
Sbjct: 147 EIAEHLGISTNDVYHGLEAGNAYRSASLDELLTDTDEIPLGDAIGSNDA-----ELDEVE 201

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RET   +LA L  RE R+L MRF  G     T  ++ +Q  +++  + ++ ++ +  L+
Sbjct: 202 NRETIRPLLAELEERERRILVMRFFRG----MTQTQIAEQVGISQMHVSRLLSRTLAWLR 257

Query: 669 H 669
            
Sbjct: 258 E 258


>gi|66474685|gb|AAY46912.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 114/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+ +GEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTAQGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                        +         E +  D  E E + E     S DD       PE A  
Sbjct: 59  ND-----ADDVAPTATHIGSELGENDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVARE 113

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 114 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 258 RMSIGEAKARRAKKE 272


>gi|15894973|ref|NP_348322.1| sporulation sigma factor SigG [Clostridium acetobutylicum ATCC 824]
 gi|1350864|sp|P33658|RPSG_CLOAB RecName: Full=RNA polymerase sigma-G factor
 gi|15024660|gb|AAK79662.1|AE007679_8 Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|580960|emb|CAA80621.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|706854|gb|AAC43310.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|325509110|gb|ADZ20746.1| sporulation sigma factor SigG [Clostridium acetobutylicum EA 2018]
          Length = 257

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 76/263 (28%), Positives = 140/263 (53%), Gaps = 11/263 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++       + A+++ ++ NLRLV+SV +++ NRG
Sbjct: 2   VINKVEICGVNTSKLPVLKEKEMRELLISMRNGNTTAREKFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+K+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENADDLFQVGCIGLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             ++ ++   R+ +K  +EPT  +IAK+L +P E V   L   ++PISL  PI  +D   
Sbjct: 121 IAYRALQVRDRLISKNNKEPTVSQIAKELKIPREEVIFALDAIQDPISLFEPIYHDD--- 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            GD I   + +S   +   + L+  +    +  L+ RE+ +L MRF  G     T  EV 
Sbjct: 178 -GDAIYVMDQISDNKNLDDSWLQNISIKEAMKKLSDREKMILNMRFFDG----RTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
            +  +++ ++ ++E  A++ +K 
Sbjct: 233 DEIGISQAQVSRLEKTALKHMKK 255


>gi|55274970|gb|AAV49284.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 196

 Score =  135 bits (339), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 80/196 (40%), Positives = 132/196 (67%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQRE 180

Query: 627 VLRMRFGIGMNTDHTL 642
           VL  RFG+      TL
Sbjct: 181 VLARRFGLLGYEAATL 196


>gi|86747323|ref|YP_483819.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
 gi|86570351|gb|ABD04908.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 329

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 121/273 (44%), Gaps = 13/273 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ +++I     +   E   +    R  +     A   ++ ++LRL   +A+ +   G  
Sbjct: 23  KSYMRAIGRYPVLEPDEEARLWQ--RWLQHRDKAAADALITSHLRLAAKLARDFRRYGFP 80

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDK 528
             DLI E N+GLM A ++FD   G +FST A+WW++ AI   I      +RI     + K
Sbjct: 81  LGDLIAEANLGLMMALDRFDPERGARFSTCAVWWIRSAIYDHIIRSWSLVRIGRTPAQKK 140

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKL----AMPVEGVRKVLKITKEPISLETPIGD-E 583
           +   +R   R           +E+A+++     +P+  V ++ +      SL TP+ D +
Sbjct: 141 LFFRLRGEIRRLQPDHHGTLTKELAEQISATLDVPLREVIEMEQRLSGDRSLNTPLSDLD 200

Query: 584 DTSHLGDFIEDK--NAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           ++    D I D   NA + L    + +  R      L  L  RE  +             
Sbjct: 201 ESGEWQDLIADDAPNAEAVLAGHDELDHQRRALQDALVQLDARERYIFSA--RHLGERPA 258

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           + E +G+   ++ ER+RQIEA+A  K+ + +R 
Sbjct: 259 SFETIGQSLSISAERVRQIEARAFAKVANSARR 291


>gi|88607306|ref|YP_505338.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
 gi|88598369|gb|ABD43839.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
          Length = 289

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 68/278 (24%), Positives = 124/278 (44%), Gaps = 12/278 (4%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ +     ++  E +       K    A     ++V ++LRLV+ VA  + + G
Sbjct: 13  DLLAYMEQVRAFPMLTEREEKECAENWHKNRSVAD--AHKLVTSHLRLVVKVAMGFRSYG 70

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K +I   I      +RI      
Sbjct: 71  LPLMELIMEGNIGLMQAVKKFNPELGFRLSTYAIWWIKASIKDYILRSWSCMRIGTTQAQ 130

Query: 528 K--IHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
           K     + +  RR+        +     IA++     + V       +   ISL   +  
Sbjct: 131 KKLFFSLRKIKRRILGCSASASQSDIRAIAEECGTSEKEVESMDRFFSNRDISLSDKVCC 190

Query: 583 EDTSHLGDFIE--DKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTD 639
           E  + L D I     N      S  ++ +++      L++L  R   +   R        
Sbjct: 191 ESGTELQDLIPCSSPNQEVMYLSHEESVMKDQMVKEALSTLDERHRDIFSRRKLKEH--P 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            TLE + +++ V++ERIRQIE ++  K++    + + +
Sbjct: 249 DTLETLSEEYGVSKERIRQIELQSFSKVRSFVNANRYK 286


>gi|213418760|ref|ZP_03351826.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 162

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 96/162 (59%), Positives = 128/162 (79%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           + + +   +++ I  ETG++I + + I   +  GE +A  AKKEMVEANLRLVIS+AKKY
Sbjct: 1   EEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKY 60

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           TNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIRIPV
Sbjct: 61  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 120

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           HM + I+K+ R +R+M  ++ REPTPEE+A+++ MP + +RK
Sbjct: 121 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRK 162


>gi|302535694|ref|ZP_07288036.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444589|gb|EFL16405.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 300

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 123/251 (49%), Gaps = 14/251 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F+ + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 54  LSRSLFQRLAALDVDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 112

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  ++ 
Sbjct: 113 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQ 172

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  +++     L D +  +++
Sbjct: 173 KLDRSPTVPELAAVLGVTEEEVVDGLAVGNAYTASSLDSPSPEDEGGEGSLADRLGYEDS 232

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE +++ +RF        T  ++G++  +++  + 
Sbjct: 233 ALEGVEY-----RESLKPLLAKLPPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVS 283

Query: 658 QIEAKAIRKLK 668
           ++  + + +L+
Sbjct: 284 RLLTRTLAQLR 294


>gi|182677344|ref|YP_001831490.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633227|gb|ACB94001.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 299

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 70/277 (25%), Positives = 125/277 (45%), Gaps = 12/277 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E E   A + +V ++LRLV  +A  Y   GL
Sbjct: 14  LTRYLNEIRRFPMLEPQEEYMLAKRWR--EHEDPDAAQRLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 72  PIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTASQK 131

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S   + +  P++   IA +L +  + V  + +      SL  P+ +E
Sbjct: 132 KLFFNLRKAKSQISALDEGDLRPDQVALIATRLGVTGQEVIDMNRRMSGDASLNAPLREE 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQA---NLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 D++ D  A      A Q    N      + L  L PRE R+   R         
Sbjct: 192 GEGEWQDWLVDDQANQEHVLADQEESANRLGALRQALDVLNPRERRIFEARRLAD--DPV 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           TLE +  +F ++RER+RQIE +A  K++   ++   R
Sbjct: 250 TLEALSDEFDISRERVRQIEVRAFEKVQAAVKAGVAR 286


>gi|23429453|gb|AAM94474.1| RNA polymerase sigma factor D [Aeromonas sp. 'CDC 2478-85']
          Length = 281

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 130/326 (39%), Gaps = 47/326 (14%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                         E DDV  T   I S           
Sbjct: 60  II--SGFIDPN------------------------EVDDVAPTATHIGSELSEDDLADED 93

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAV 302
            D   +  E+ + + D+ +      ++                  E + ELR+  +   +
Sbjct: 94  EDEDEDEDEDGDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRL 136

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           + Q++ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 137 SIQQNGRAHDDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 196

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +      +  + + +L+   +++ I  ETG
Sbjct: 197 QAKMPKKTFVAAFTNNEWETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETG 255

Query: 422 ISISEFRHIVSMVRKGECEASIAKKE 447
           +SI++ + I   +  GE +A  AKKE
Sbjct: 256 LSIAQIKDINRRMSIGEAKARRAKKE 281


>gi|261210147|ref|ZP_05924444.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
 gi|260840687|gb|EEX67236.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
          Length = 286

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 136/272 (50%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +     E   A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNGYPMLTADEERELAERL--HYKEDIEAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      ++D +
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDAAFEMSAEDDEN 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK+   A +      +A+  +  +  LASL  R + ++R R+ +  + 
Sbjct: 192 GMAYTAPVLYLEDKHSDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++ + + V+ ERIRQ+E  A+RKLK  
Sbjct: 251 KTTLQDLAEMYGVSAERIRQLEKNAMRKLKEA 282


>gi|15839280|ref|NP_299968.1| RNA polymerase factor sigma-32 [Xylella fastidiosa 9a5c]
 gi|9107932|gb|AAF85488.1|AE004075_3 RNA polymerase sigma-32 factor [Xylella fastidiosa 9a5c]
          Length = 293

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 28  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 86  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 145

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-D 584
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 146 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 203

Query: 585 TSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 204 PSPVGYLIANDGDPSQAYERGNSEETKLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 261

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 262 LQELAEEYGVSAERIRQIEANALKKMK 288


>gi|1163231|gb|AAC45341.1| DNA polymerase sigma 32 subunit [Vibrio cholerae]
          Length = 286

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 68/272 (25%), Positives = 134/272 (49%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    +S  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERL--HYKGDIDAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      ++D +
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDEN 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK+   A +      +A+  +  +  LASL    + ++R R+ +  + 
Sbjct: 192 GMAYTAPVLYLEDKHSDLADNLEAENWEAHTTQRLSMALASLDDGSQHIVRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++  ++ V+ ERIRQ+E  A+RKLK  
Sbjct: 251 KTTLQDLAAKYGVSAERIRQLEKNAMRKLKEA 282


>gi|239990645|ref|ZP_04711309.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 309

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 69  FFELRELPDGSPEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 127

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 128 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 187

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 188 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 247

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 248 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 298

Query: 665 RKLKH 669
            +L+ 
Sbjct: 299 AQLRE 303


>gi|74316363|ref|YP_314103.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
 gi|74055858|gb|AAZ96298.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
          Length = 281

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 132/265 (49%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+++S    +S+ E + +       + +   A + +V ++LR+V+S+A+ Y   GL
Sbjct: 15  LDSYIQTVSHYPMLSLEEEQKLAR--AWHDEQDLEAARRLVLSHLRVVVSIARHYLGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMRD 527
              DLIQEGN+GLMKA ++FD   G +  ++A+ W++  I   +      ++      + 
Sbjct: 73  PHADLIQEGNVGLMKAVKRFDPDRGVRLVSFALHWIRAEIHEYVLKNYRMVKLATTKAQR 132

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS 586
           K+   +R+ ++  N +  +       +      + +    +++   +S++  + D ED  
Sbjct: 133 KLFFNLRSLKQSLNALTVQQADAMAQELNVSRKDVLEMETRLSGHDVSIDPMVDDGEDDY 192

Query: 587 HLGDFI--EDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               ++   ++N    L+      LRE+  T  L  L  R   +++ R+ +      TL 
Sbjct: 193 SPIAYLASAEENPAQRLEREQTERLRESGLTSALEELDERSRHIIQARW-LSEGDVATLH 251

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  Q+ V+ ERIRQIEA+A++K++
Sbjct: 252 ELAAQYGVSAERIRQIEARALQKMR 276


>gi|27904539|ref|NP_777665.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340406|sp|Q89B27|RP32_BUCBP RecName: Full=RNA polymerase sigma-32 factor
 gi|27903936|gb|AAO26770.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
          Length = 287

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 133/274 (48%), Gaps = 14/274 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  + + I+  +    +S  E +++   +         A K ++ ++LR VI V++ Y+
Sbjct: 13  SLGNLDSYIREANSWPMLSSQEEKYLSEKL--FYHGDLNAAKTLILSHLRFVIHVSRNYS 70

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IP 522
             GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++    
Sbjct: 71  GYGLLQADLIQEGNIGLMKAVRRFNPKIGVRLVSFAVHWIKSEIHEYVLRNWRIVKVATT 130

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISL-ETPI 580
              R     + +T +R+      E   E +A++L +  E VR++  +++ + I+L   P 
Sbjct: 131 KSQRKLFFNLRKTKQRLGWFNDHE--LELVAQELGVKREDVREMESRMSAQDIALHHVPD 188

Query: 581 GDEDTSHLGDFIED-KNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGI 634
              +  +    I   K+++S   + ++ +  E       +  L+SL  R   ++  R+  
Sbjct: 189 NFREEQNFSYTIPYLKDSLSDFANHVEEDNWEAHKTNKLSNALSSLDERSRNIIHARWLD 248

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +   TL E+   + ++ ER+RQ+E  A++KLK
Sbjct: 249 DSDHKMTLREIAHNYGISAERVRQLEKNAMKKLK 282


>gi|71901711|ref|ZP_00683785.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71728528|gb|EAO30685.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 81  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-D 584
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 141 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 198

Query: 585 TSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 199 PSPVGYLIANDGDPSQAYERGNSEETQLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 256

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 257 LQELAEEYGVSAERIRQIEANALKKMK 283


>gi|209965510|ref|YP_002298425.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958976|gb|ACI99612.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 295

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 124/274 (45%), Gaps = 18/274 (6%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IK+   E  +S      +    R  E     A  E+V +  RLV++ A ++ N GL   D
Sbjct: 17  IKASMKEPLLSRDHEFDLAKRWR--ERGDEAALHELVRSYTRLVVATAARFRNYGLPMGD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEGN+GLM+AA +F+     +FSTYA WW++ A+   I      +R       K   +
Sbjct: 75  LVQEGNVGLMQAAARFEPDREVRFSTYAAWWIRSAMQDYILRNWSIVRTGTTAAQKA--L 132

Query: 533 VRTARRMSNKIKREPT--------PEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               RR+  KI+  P+           IA++L +    V    +++     SL +P+ + 
Sbjct: 133 FFNLRRLRAKIEDSPSASALSPDGRRRIAEELNVDESDVESMEMRLAAADQSLNSPVAEG 192

Query: 584 DTSHLGDFIED--KNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 DF+ D   +    +       +R       L  L+PRE  ++  R         
Sbjct: 193 GDDEWQDFLSDQRPSPEDVVIGMRDGRMRSRWLAEALGELSPRERTIIAQRRLRDDG--A 250

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLEE+G+   V++ER+RQ+E +A+ KL+     +
Sbjct: 251 TLEELGRVLGVSKERVRQLEHRALMKLRASMIRR 284


>gi|254384657|ref|ZP_04999996.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194343541|gb|EDX24507.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 334

 Score =  134 bits (338), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +       A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 94  FFELRELPEGSVERAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 152

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 153 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 212

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 213 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 272

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 273 -----RESLKPLLEGLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 323

Query: 665 RKLKH 669
            +L+ 
Sbjct: 324 AQLRE 328


>gi|315121811|ref|YP_004062300.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313495213|gb|ADR51812.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 300

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 126/276 (45%), Gaps = 14/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  I  I     +   E   +    R  E     A  ++V ++LRLV+ +A  Y   GL
Sbjct: 16  LRRYIHEIKKIPMLEKQEEYMLAK--RYHEHHDLNAVHKLVTSHLRLVVKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGNIGLM+A +KFD   G++ +TY +WW+K AI   I      ++I    + +
Sbjct: 74  PISEVISEGNIGLMQAVKKFDPERGFRLATYGIWWIKAAIQEYILRSWSLVKIGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+         PE   EIA KL +    V  +        SL   +   
Sbjct: 134 RLFFNLRRLKGRLQAVNDTNLKPEQVVEIATKLNVSEAEVISMNCRLSGDESLNVLMNSS 193

Query: 582 DEDTSHLGDFIE---DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D+D+S   D +    D    + +D   + N R   TR +++L PRE R+           
Sbjct: 194 DKDSSQWQDLLVYNHDSQEQTLIDKEERKNRRNMLTRSMSTLNPRERRIFEA--RRLNEN 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             TLE +  +F V+RERIRQIEA+A  K++   + +
Sbjct: 252 PSTLENLSSEFAVSRERIRQIEARAFEKVQASVQKQ 287


>gi|121535240|ref|ZP_01667054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306125|gb|EAX47053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 257

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 80/267 (29%), Positives = 134/267 (50%), Gaps = 19/267 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           I N+++   V T     +S ++ R +  ++++G      A+++++  NLRLV+SV +++ 
Sbjct: 2   IVNKVEICGVNTAKLPVLSANKMRELFEIMQQGN---PEAREQLIYGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           MRD  +K ++    + +K  REP+  EIA +L +P E +   L   +EP+SL  PI  + 
Sbjct: 118 MRDIAYKALQVRDALVSKFSREPSINEIADELKIPREEIIFALDAIQEPVSLFEPIYHDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D   + D I D            A         L  L+ RE+ +L +RF  G     T 
Sbjct: 178 GDPIFVMDQISDDKNQDMNWLEGVA-----IKEALRKLSDREKHILTLRFFEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV  +  +++ ++ ++E  A+  ++ 
Sbjct: 229 MEVADEIGISQAQVSRLEKAALGHMRK 255


>gi|1143379|dbj|BAA09444.1| sigma-32 homolog [Zymomonas mobilis]
          Length = 302

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 117/274 (42%), Gaps = 14/274 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + +  I     +   E   +    +  E +   A   +V ++LRLV  +A  Y   
Sbjct: 18  QSLNHYLADIRKFPILKPEEEYMLAKRFQ--EHQDPKAASRLVTSHLRLVAKIAMGYRGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   +LI EGNIGLM+  +KFD   G++ +TYA+WW+K +I   I      +++     
Sbjct: 76  GLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWWIKASIQEYILRSWSLVKMGTTAA 135

Query: 527 DK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKV--LKITKEPISLETP 579
            K     + R    M+     +  P+E   IA  L +  E V  +          SL   
Sbjct: 136 QKKLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNLGVSNEEVVNMNRRMAMGGDSSLNIT 195

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGM 636
           + ++    + D++ D+  +       +       +     +  L  RE+ +L        
Sbjct: 196 MREDGEGQMQDWLVDQEPLQDQQIEEEEESLVRHKLLIEAMDRLNDREKHILTE--RRLS 253

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +   TLEE+ + + V+RER+RQIE +A  KL+  
Sbjct: 254 DNPKTLEELSQVYGVSRERVRQIEVRAFDKLQKA 287


>gi|302774234|ref|XP_002970534.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
 gi|300162050|gb|EFJ28664.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
          Length = 458

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKF 488
              +R+       A+ +++E N RLV+ +A++Y          DL QEG  GL+ A + F
Sbjct: 206 FRTLRRRLQLGEAAQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLIDAMDHF 265

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +   G +FSTYA++W++ AI R+I      IR+P     K  ++ +  R +  ++ R P+
Sbjct: 266 NPGKGTRFSTYAIFWIRTAIVRAITRTGQVIRLPFSFAAKKVEIRKARRELRVELGRNPS 325

Query: 549 PEEIAKKLAM-PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            EE+ ++  + PV+             SL   +   D   L    E  + VS       +
Sbjct: 326 DEEVMERTGLDPVQFWNIYYYSNFRVRSLNETVRGTDEEFLEYLPETGDIVS-----ESS 380

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMN--TDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            +RE     L  L  +E  VL+ R+G+        +L EVG++  +++E +R+ EA A+ 
Sbjct: 381 EVREEIVTALQRLKDKERMVLQHRYGLEDGALAVKSLREVGRRLNMSQEMVRRYEASALE 440

Query: 666 KLKHPSRSKKLRSFL 680
           +L+H   +K LRS L
Sbjct: 441 RLRHQEEAKSLRSCL 455


>gi|332703233|ref|ZP_08423321.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332553382|gb|EGJ50426.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 398

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 147/277 (53%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ IS    +   E   +   VR  +     A   +V ++LRLV+ +A  +  R +
Sbjct: 118 LHMYMQEISRFPILKPEEEVELARRVR--DTGDQDAAFRLVTSHLRLVVKIAMDFQRRWM 175

Query: 469 Q-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-R 526
           Q  LDL+QEGN+GLM+A +KFD   G KFS YA +W+K  I + I D    ++I     +
Sbjct: 176 QNVLDLVQEGNVGLMRAVQKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQTQ 235

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT 585
            K+   +   R+       +PT   ++K L + VE + ++  ++++  +SL+  IGD+ T
Sbjct: 236 RKLFYNLNKERQRLQSQGFDPTSSTLSKSLGVSVEDIEEMDQRLSRSDMSLDITIGDDTT 295

Query: 586 SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +   DF+         +  +S I A LRE    ++  L+ +E+ +L+    +  ++  TL
Sbjct: 296 ATRMDFLPALGPGIEETLANSEISALLREHLASIVPMLSDKEQDILQK--RLLSDSPVTL 353

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            E+G Q+ +TRER+RQIEA+ ++K++    + K+  F
Sbjct: 354 REIGDQYGITRERVRQIEARLLQKIREHL-TDKIEDF 389



 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 27/144 (18%), Positives = 49/144 (34%), Gaps = 19/144 (13%)

Query: 45  TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV 104
           T  EL      + +  E  ++        G +  D  ++E E    D  DL    +   +
Sbjct: 26  TAGELGDRSGAERLKPEDTDEDSPDTDLTGEDETDTPEMELE-AEPDLDDLVEELAPEGM 84

Query: 105 FLQKRKDSAD-----------------RSTDDPVRMYLREMGSIELLSREGEIAIAKRI- 146
              + K+  +                   T D + MY++E+    +L  E E+ +A+R+ 
Sbjct: 85  DQDEVKEPGETPLGPGAFRLPVLKAGRGGTADILHMYMQEISRFPILKPEEEVELARRVR 144

Query: 147 EAGRAMMMASLCESPLTFQALIIW 170
           + G       L  S L     I  
Sbjct: 145 DTGDQDAAFRLVTSHLRLVVKIAM 168


>gi|307128894|ref|YP_003880910.1| RNA polymerase sigma-32 (sigma H) factor [Dickeya dadantii 3937]
 gi|306526423|gb|ADM96353.1| RNA polymerase, sigma 32 (sigma H) factor [Dickeya dadantii 3937]
          Length = 285

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K+++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYHGDLDAAKQLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIG 581
                + +T +R+    + E   E +A++L +  + VR++      +      S E    
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPSPEDDAQ 191

Query: 582 DEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    +++DK+   A    +   + +  +  T  L  L  R + ++R R+ +  + 
Sbjct: 192 PGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADHYGVSAERVRQLEKNAMKKLR 280


>gi|289578664|ref|YP_003477291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544884|ref|YP_003677186.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528377|gb|ADD02729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842659|gb|ADH61175.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 256

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 133/262 (50%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++ + +     A++E +  NLRLV+SV +++ NRG  
Sbjct: 3   NKVEICGVNTSKLPVLKPSKQKELLIRMKNGDKKAREEFINGNLRLVLSVIQRFNNRGEY 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  
Sbjct: 63  VDDLFQVGCIGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSLRDIA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   ++ ++  +EPT  EIAK+L +P E V   L   +EP+SL  PI  +  D  +
Sbjct: 122 YKALQVRDKLVSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D   +  +        +      +  L  RE+ +L +RF  G     T  EV K
Sbjct: 182 VMDQVSDDKNIDEVWLE-----KIALKEAIQKLNEREKLILTLRFFEG----KTQMEVAK 232

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+  ++ 
Sbjct: 233 EIGISQAQVSRLEKAALNHMRK 254


>gi|94309217|ref|YP_582427.1| RNA polymerase factor sigma-32 [Cupriavidus metallidurans CH34]
 gi|93353069|gb|ABF07158.1| RNA polymerase sigma 32 (sigma H) factor [Cupriavidus metallidurans
           CH34]
          Length = 311

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 129/268 (48%), Gaps = 10/268 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+++     ++  E   +   +R  +     A + MV ++LRLV+S+A++Y   GL
Sbjct: 39  LDSYIQAVHRIPMLTPEEELSLARDLRDNDSVD--AARRMVMSHLRLVVSIARQYLGYGL 96

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD   G +  +YAM W+K  I   +      +++     + 
Sbjct: 97  PHADLIQEGNIGLMKAVKRFDPEQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQR 156

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS 586
           K+   +R+ ++ S+    E       +    P E +    +++   ++LE  I D E+  
Sbjct: 157 KLFFNLRSHKQGSHTFTPEQIEAVARELNVKPEEVMEMETRMSGGDMALEGQIEDGEEEF 216

Query: 587 HLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT---DH 640
               ++ D +         + + R   E     L  L PR  R++  R+    +      
Sbjct: 217 APIAYLADNHNEPTQVLEAKRHDRLQVEGLEEALTKLDPRSRRIIEARWLDVNDDGSGGA 276

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  +F V+ ERIRQIE+ A++K+K
Sbjct: 277 TLHELADEFGVSAERIRQIESAAMKKMK 304


>gi|302746291|gb|ADL62735.1| RpoD [Morganella psychrotolerans]
          Length = 261

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 51/302 (16%), Positives = 103/302 (34%), Gaps = 48/302 (15%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
            +REGEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I        
Sbjct: 1   WTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLI-------- 52

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
               GF              +   +   +    +   E   +  +++ +     PE A  
Sbjct: 53  ---TGFVDPNAEEDLAPTATNIGSELPAEELNKDDTDEDEDEEEEEEETDNSIDPELARQ 109

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               L    + +   +                                +NG+    S+ +
Sbjct: 110 KFDALRVQHEKTRKQI-------------------------------KLNGRDHPSSNAE 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            ++L +    +     L   + D LV ++ ++  R+   E  +++L  +   + +  F+ 
Sbjct: 139 IQLLSD----VFKEFRLVPKQFDYLVSKMREMMDRVRLQERFIMKLCVEQSKMPKKNFIT 194

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
              G E    W + A    +  W   +    + + +    ++ I  ETG++I E + I  
Sbjct: 195 LFTGNETSDTWFTAAIAMNKP-WSEKLQDVAEEVQRSLQRLRMIEEETGLTIKEVKDINR 253

Query: 433 MV 434
            +
Sbjct: 254 RM 255


>gi|294630218|ref|ZP_06708778.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833551|gb|EFF91900.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 302

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 122/251 (48%), Gaps = 14/251 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S S F  + ++       A   +  ++E NL LV   A ++ +R     D++Q G IGL
Sbjct: 56  LSRSLFLRLAALEEDSPERA-YVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 114

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD   G +F T+AM  V   I R   D S ++R+P  +++    + + +  +S 
Sbjct: 115 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELSQ 174

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNA 597
           K+ R PT  E+A  L +  E V   L +       SL++P  ++D     L D +  +++
Sbjct: 175 KLDRSPTVAELAAVLGVSEEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDS 234

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA L PRE R++ +RF        T  ++G++  +++  + 
Sbjct: 235 ALEGVEY-----RESLKPLLAKLPPRERRIIMLRFFAN----MTQSQIGEEVGISQMHVS 285

Query: 658 QIEAKAIRKLK 668
           ++  + + +L+
Sbjct: 286 RLLTRTLAQLR 296


>gi|242241268|ref|YP_002989449.1| RNA polymerase factor sigma-32 [Dickeya dadantii Ech703]
 gi|242133325|gb|ACS87627.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech703]
          Length = 285

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 67/270 (24%), Positives = 126/270 (46%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K+++ ++LR VI VA+ Y   GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYHGDLDAAKQLILSHLRFVIHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-- 584
                + +T RR+    + E   E +A++L +  + VR++            P  D+D  
Sbjct: 134 KLFFNLRKTKRRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTYDPTPDDDAQ 191

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
               +   +  ++  S     I+ +  ET         L  L  R + ++R R+ +  + 
Sbjct: 192 PGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLAYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+   + V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADYYGVSAERVRQLEKNAMKKLR 280


>gi|259910110|ref|YP_002650466.1| RNA polymerase factor sigma-32 [Erwinia pyrifoliae Ep1/96]
 gi|224965732|emb|CAX57264.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae Ep1/96]
 gi|283480207|emb|CAY76123.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae DSM 12163]
 gi|310765698|gb|ADP10648.1| RNA polymerase factor sigma-32 [Erwinia sp. Ejp617]
          Length = 284

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    ++  E + +   +    C    A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRAANAWPMLTAEEEKALAERLHYQGCL--EAAKTLILSHLRFVVHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R+    + E   E +A++L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKAKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDPTPDDEGE 191

Query: 586 S-HLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
              +   +  ++  S   + I+ +  E          +  L  R + ++R R+ +  +  
Sbjct: 192 GRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQGLDERSQHIIRARW-LDDDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 TTLQELADQYGVSAERVRQLEKNAMKKLR 279


>gi|110799379|ref|YP_696447.1| sporulation sigma factor SigG [Clostridium perfringens ATCC 13124]
 gi|168207288|ref|ZP_02633293.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210606|ref|ZP_02636231.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168214238|ref|ZP_02639863.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|168217048|ref|ZP_02642673.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
 gi|169342669|ref|ZP_02863710.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625828|ref|ZP_02953594.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|110674026|gb|ABG83013.1| RNA polymerase sigma-G factor [Clostridium perfringens ATCC 13124]
 gi|169299175|gb|EDS81245.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661342|gb|EDT14025.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711289|gb|EDT23471.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170714329|gb|EDT26511.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|177908862|gb|EDT71354.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380954|gb|EDT78433.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
          Length = 257

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 76/265 (28%), Positives = 138/265 (52%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ + +   + A+++ ++ NLRLV+SV +++ NRG
Sbjct: 2   MINKVEICGVNTAKLPVLKEKEMKELLLQMQNGDTSAREKFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D + TIR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-TIRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    ++ N+  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALLVRDKLVNENNKEPTVSQIAKELKIPREDVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KN        I           +  L  RE+ +L +RF  G     T  E
Sbjct: 181 IYVMDQISDSKNQDDSWLENI------AIKEAMKKLNDREKLILNLRFFNG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKIALKHMRK 255


>gi|253999699|ref|YP_003051762.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. SIP3-4]
 gi|253986378|gb|ACT51235.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. SIP3-4]
          Length = 284

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 75/273 (27%), Positives = 129/273 (47%), Gaps = 9/273 (3%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            V S+  +   +++I     +S  E   + + +RK       A K ++ ++LRLV S+A+
Sbjct: 9   SVSSLDSLDQYLRTIKAFPVLSAEEEYDLATRLRKDNDID--AAKGLIVSHLRLVASIAR 66

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y+  GL   DLIQEGN+GLMKA  +FD   G +  ++AM W+K  I   I      +++
Sbjct: 67  GYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKV 126

Query: 522 PVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
                + K+   +R+ ++ S+ +  +   +   +    P E V    ++    ISLE   
Sbjct: 127 ATTKAQRKLFFNLRSMKKNSHTLSPDEVADIARELKVKPEEVVEMESRMGGHEISLEGNS 186

Query: 581 GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIG 635
            D+         ++ED+        A +             L SL  R  R+++ R+   
Sbjct: 187 DDDSEDSFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDDRSRRIVQARWLQE 246

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            N   TL ++  +F V+ ERIRQIE KA++K+K
Sbjct: 247 NN-SATLHDLAAEFGVSAERIRQIEQKAMQKMK 278


>gi|238058450|gb|ACR39376.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 274

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 60/306 (19%), Positives = 116/306 (37%), Gaps = 46/306 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGF 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P                         E DDV  T   I S            D   + 
Sbjct: 59  IDPN------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDE 94

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEK 309
             + + + D+ +      ++                  E + +LR+  +   ++ Q++ +
Sbjct: 95  DGDGDDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGR 137

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
           +    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + + 
Sbjct: 138 AHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKK 197

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+      E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ +
Sbjct: 198 TFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIK 256

Query: 429 HIVSMV 434
            I   +
Sbjct: 257 DINRRM 262


>gi|77462968|ref|YP_352472.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126461842|ref|YP_001042956.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221638824|ref|YP_002525086.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332557843|ref|ZP_08412165.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|1769585|gb|AAC46050.1| RpoH [Rhodobacter sphaeroides]
 gi|77387386|gb|ABA78571.1| sigma factor RpoH1 (Sigma-32 group, heat shock) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126103506|gb|ABN76184.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221159605|gb|ACM00585.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332275555|gb|EGJ20870.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 298

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 130/275 (47%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + + + A  ++V ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVDHQDNRAAHKLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   ++    + +  PE   +IAK L +   E +    +++    SL   IG 
Sbjct: 134 KLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLGVSETEVIDMNRRLSGSDASLNATIGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED+++    D A +  L   RE   + ++ L  RE+ +L        +
Sbjct: 194 DGEGSTQWQDWLEDEDSDQAADYAERDELEIRRELLAQSMSVLNDREKDILVQ--RRLTD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+ + + V+RERIRQIE +A  KL+   R
Sbjct: 252 DPVTLEELSEGYGVSRERIRQIEVRAFEKLQAKMR 286


>gi|222475169|ref|YP_002563585.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
 gi|222419306|gb|ACM49329.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
          Length = 307

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 67/278 (24%), Positives = 125/278 (44%), Gaps = 14/278 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + + +  +     +S  E + +          +      +V ++LRLV+ +A  + + G
Sbjct: 31  DLVSYVAQVRTFPILSEEEEKRLAE--NWYRRGSVADAHRLVTSHLRLVVKIAMGFKSYG 88

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +I   I      IR+      
Sbjct: 89  LPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQAQ 148

Query: 528 K--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIG 581
           K     + +  +R+ +      T +E   IA++ A   E V R         +SL   + 
Sbjct: 149 KKLFFSLRKIKKRLLS-CGSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQVH 207

Query: 582 DEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            E +  L D +        +  L     A  +      LA+L  R   +           
Sbjct: 208 GESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIF--TRRRLQER 265

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLE++ +++ V++ER+RQIE +A+ K+K    + ++
Sbjct: 266 PDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEANRV 303


>gi|239941779|ref|ZP_04693716.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239988239|ref|ZP_04708903.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291445225|ref|ZP_06584615.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348172|gb|EFE75076.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 329

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D++Q G IGL+KA +
Sbjct: 87  LFERLESLEEGTHEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAID 146

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    +S ++ R 
Sbjct: 147 RFELSRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQQLDRA 206

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E++++L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 207 PTVAELSERLGITPDEVVEGMSASNAYTASSLDAKPEEDDSEGALADRIGYEDHGLEGIE 266

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A+L  R+  +L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 267 YV-----ESLKPLIAALPARDRMILSLRFVSN----MTQSEIGEELNISQMHVSRLLSRT 317

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 318 LTKLRK 323


>gi|148284686|ref|YP_001248776.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str.
           Boryong]
 gi|146740125|emb|CAM80313.1| RNA polymerase sigma-32 factor [Orientia tsutsugamushi str.
           Boryong]
          Length = 299

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 134/275 (48%), Gaps = 15/275 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I+    ++  E   +       E     A   +V+++L+LV  +A  Y   GL  +
Sbjct: 22  YLQKINRIPSLTAEEEYMLAK--SYFEQNNLKAAHSLVKSHLKLVAKIALSYRGYGLPVV 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH- 530
           DL+ EGNIGL++A +K++  LG++ STYA+WW+K AI   I      +++      K   
Sbjct: 80  DLVSEGNIGLLQAVKKYNPELGFRLSTYAIWWIKAAIQDYILRSWSLVKLGTTAAQKKLF 139

Query: 531 ----KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKITKEPISLETPI--GDE 583
               K+     +M  +       ++IA +  + +  V +   +++   +SL TPI   ++
Sbjct: 140 FNLGKIKNKITKMHARAINSSDYKQIADESGVSIAEVSEVNQRLSNSDLSLNTPISYHED 199

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           D + L + + +      +  A Q +L   +E     L +LT RE  ++R R         
Sbjct: 200 DATELVELVPEHRPNQEIILANQQDLNLKKEVLENALQTLTQRELYIIRARKLQD--EPD 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           TLE++   F V++ERIRQIE+KA  KL+  + + K
Sbjct: 258 TLEKLSLHFNVSKERIRQIESKAFEKLQQYAMNTK 292


>gi|23429445|gb|AAM94470.1| RNA polymerase sigma factor D [Aeromonas jandaei]
          Length = 281

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 124/325 (38%), Gaps = 45/325 (13%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                                   D E  A  +    S+
Sbjct: 60  II--SGFIDPN----------------------------------DTEDMAPTATHIGSE 83

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
           +       E+++ + DEDED                      E+   Y          ++
Sbjct: 84  LSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVAREKFAELRAQYEV------TRLS 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 IQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 197

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +  W   +    + + +   +++ I  ETG+
Sbjct: 198 AKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLMEMDEEVQRAIGKLQQIEEETGL 256

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 257 SIAQIKDINRRMSIGEAKARRAKKE 281


>gi|317403164|gb|EFV83689.1| RNA polymerase sigma factor [Achromobacter xylosoxidans C54]
          Length = 294

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 73/265 (27%), Positives = 132/265 (49%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    +S      +   +R  + E   A +E+V ++LRLV+SVA++Y   GL
Sbjct: 28  IDAYISAVNRLPVLSAERETELGRRLR--DSEDLGAARELVLSHLRLVVSVARQYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++      +
Sbjct: 86  PHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R   +       + IA++L +  E V ++ ++++   +SLE    D+D+  
Sbjct: 146 KLFFNLRSMRPDGQTLDPEQVDHIARELNVRREDVSEMEVRLSGRDMSLENQDDDDDSYA 205

Query: 588 LGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              ++ D+    P     +A   +      +  L +L PR  R++  R+        TL 
Sbjct: 206 PIAYLSDEGRQEPTRVLERAARDQLQSSGLSSALEALDPRSRRIVEARWLQDDGG-ATLH 264

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++F V+ ERIRQIEA A++K++
Sbjct: 265 ELAQEFGVSAERIRQIEAAALKKMR 289


>gi|300854419|ref|YP_003779403.1| putative RNA polymerase sigma-G factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434534|gb|ADK14301.1| predicted RNA polymerase sigma-G factor [Clostridium ljungdahlii
           DSM 13528]
          Length = 257

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 72/264 (27%), Positives = 136/264 (51%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + + + + +  ++ K +   + ++++ ++ NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTSKLPVLKGKEMKELLIKMQQGDNESREKFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++  +  +EPT  +IA++L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALQVRDKLIRENNKEPTISQIAEELNIPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I D   +        +         +  L  RE+ +L +RF  G     T  EV
Sbjct: 181 IYVMDQISDTKNLDENWLENIS-----IKEAMKKLNDREKLILNLRFFDG----RTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A+R ++ 
Sbjct: 232 ADEIGISQAQVSRLEKTALRHMRK 255


>gi|326490962|dbj|BAJ90342.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 81/297 (27%), Positives = 146/297 (49%), Gaps = 10/297 (3%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI----VSMVRKGECEASIAKK 446
           P+      +   + +IL+++  ++S  +++  + +E        V  +R+       A+ 
Sbjct: 203 PQSARLFKIMQPMKAILEVQENMRS-ELQSEPTEAEVAEAMNMPVQRLRRLRDVGRAARN 261

Query: 447 EMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++++ NLRLV+    KY        +F DL Q G  GL+ A ++F+   G++ STYA+ W
Sbjct: 262 KLIKHNLRLVLYAINKYYPDMTGDERFADLCQAGANGLITAIDRFEPKRGFRISTYALSW 321

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ ++ R+    S   R P  M  +  ++ R    +S ++ R PT EE  KK+ +     
Sbjct: 322 IRHSVVRA-MTLSSFTRFPFAMESERQEINRAREELSFELGRTPTDEETMKKVGLSPARY 380

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R V+++T+   SL +         L + + D +A+          LR     +L SL P+
Sbjct: 381 RDVVRMTRPAYSLHSRNRVTQE-ELINEVTDVDAIGVDTHKHNRLLRLAIDDLLDSLKPK 439

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E  V+R RFG+      TL E+     ++RE +R+ E KA+ KLKHP+R   LR ++
Sbjct: 440 ESVVIRQRFGLDGRGRRTLSEIAGNLRISREMVRKYELKALMKLKHPTRVDYLRRYM 496


>gi|313201748|ref|YP_004040406.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. MP688]
 gi|312441064|gb|ADQ85170.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. MP688]
          Length = 290

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 75/273 (27%), Positives = 129/273 (47%), Gaps = 9/273 (3%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            V S+  +   +++I     +S  E   + + +RK       A K ++ ++LRLV S+A+
Sbjct: 15  SVSSLDSLDQYLRTIKAFPVLSAEEEYDLATRLRKDNDID--AAKGLIVSHLRLVASIAR 72

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y+  GL   DLIQEGN+GLMKA  +FD   G +  ++AM W+K  I   I      +++
Sbjct: 73  GYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKV 132

Query: 522 PVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
                + K+   +R+ ++ S+ +  +   +   +    P E V    ++    ISLE   
Sbjct: 133 ATTKAQRKLFFNLRSMKKNSHTLSPDEVADIARELKVKPEEVVEMESRMGGHEISLEGNS 192

Query: 581 GDEDTSHLGD--FIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIG 635
            D+         ++ED+        A +             L SL  R  R+++ R+   
Sbjct: 193 DDDSEDSFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDDRSRRIVQARWLQE 252

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            N   TL ++  +F V+ ERIRQIE KA++K+K
Sbjct: 253 NN-SATLHDLAAEFGVSAERIRQIEQKAMQKMK 284


>gi|239930293|ref|ZP_04687246.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 305

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 111/244 (45%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +  G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD 
Sbjct: 68  LKELEPGTPEHTRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDP 127

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R P+  
Sbjct: 128 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAFGRSPSTA 187

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  E V   ++   +    SLE     +    L D +  ++            
Sbjct: 188 EIAERLRITEEDVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALDGVEH---- 243

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+
Sbjct: 244 -RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLR 298

Query: 669 HPSR 672
             +R
Sbjct: 299 SANR 302


>gi|239945848|ref|ZP_04697785.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239992317|ref|ZP_04712981.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291449304|ref|ZP_06588694.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291352251|gb|EFE79155.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 298

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 125/246 (50%), Gaps = 8/246 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA 
Sbjct: 52  FFDRLQVLEEGTHEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAI 111

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D + ++ +P  +++    + +   ++S ++ R
Sbjct: 112 DRFDLSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLAKAKEQLSAELDR 171

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT +E+A  L +P E + + L         SL+TP  D D+        D    +    
Sbjct: 172 DPTVKELATHLDLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYADVLGEADPGM 231

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               NL  T   +L  L  RE R+++MRFG     + T  ++G++  V++  + ++ ++ 
Sbjct: 232 ETVENLH-TLAPLLEQLDDRERRIVQMRFGA----EMTQSQIGEELGVSQMHVSRLLSRI 286

Query: 664 IRKLKH 669
           +++L+ 
Sbjct: 287 VQQLRK 292


>gi|218710915|ref|YP_002418536.1| RNA polymerase factor sigma-32 [Vibrio splendidus LGP32]
 gi|218323934|emb|CAV20295.1| RNA polymerase sigma-32 factor [Vibrio splendidus LGP32]
          Length = 303

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 132/272 (48%), Gaps = 16/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S +    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 34  LDSYIRSANSYPMLTPDEERGLAERLHYKGEID--AAKGLILSHLRFVVHVARGYSGYGL 91

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 92  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 151

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++ +R+      E   E +A++L +    VR++  ++  +  + E P+ D+D 
Sbjct: 152 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDATFEAPMDDDDG 209

Query: 586 SH----LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++EDK    A +   +  +++        L SL  R + ++R R+      
Sbjct: 210 GSAYTAPVYYLEDKASDVAETVEAANWESHTNNRLGLALKSLDERSQHIVRSRWLDDN-- 267

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++   + ++ ER+RQ+E  A++KLK  
Sbjct: 268 KATLQDLADTYSISAERVRQLEKNAMKKLKQA 299


>gi|167561467|ref|ZP_02354383.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis EO147]
 gi|167568698|ref|ZP_02361572.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis C6786]
          Length = 311

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 134/272 (49%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R G      A +++V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTPEEERQYATEYRDGNNLD--AARQLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +   +       + +A++L +  E V ++    +   I+LE  I D 
Sbjct: 153 KAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRF---GIGM 636
           + S+  +    +  N  + + +A Q ++ +T    R L SL  R  R++  R+   G   
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARWLNVGDDG 272

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|110802253|ref|YP_699047.1| sporulation sigma factor SigG [Clostridium perfringens SM101]
 gi|110682754|gb|ABG86124.1| RNA polymerase sigma-G factor [Clostridium perfringens SM101]
          Length = 257

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 76/265 (28%), Positives = 138/265 (52%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ + +   + A+++ ++ NLRLV+SV +++ NRG
Sbjct: 2   MINKVEICGVNTAKLPVLKEKEMKELLLQMQNGDTSAREKFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D + TIR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-TIRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    ++ N+  +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALLVRDKLVNENNKEPTVSQIAKELKIPREDVVFALDAIQDPVSLFEPIYYDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KN        I           +  L  RE+ +L +RF  G     T  E
Sbjct: 181 IYVMDQISDSKNQDDSWLENI------AIKEAMKKLNDREKLILNLRFFNG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKIALKHMRK 255


>gi|150390630|ref|YP_001320679.1| sporulation sigma factor SigG [Alkaliphilus metalliredigens QYMF]
 gi|149950492|gb|ABR49020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 257

 Score =  134 bits (338), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 127/245 (51%), Gaps = 15/245 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            RH+  ++++     + A++E ++ NLRLV+SV +++ NRG    DL Q G IGL+KA +
Sbjct: 24  MRHLFGLIKQ---GDNSAREEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGCIGLIKAID 80

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD     +FSTYA+  +   I R + D +  IR+   +RD  +K ++   +++N+  +E
Sbjct: 81  NFDLRHNVRFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAYKALQVRDQLTNQKSKE 139

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSA 604
           P+  EIA  L +P E V   L   ++P+SL  PI  +  D   + D I D+ +       
Sbjct: 140 PSVAEIAANLNIPREDVVFALDAIQDPVSLFEPIYHDSGDAIFVMDQIRDEKSEDETWID 199

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A         +  L  RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A+
Sbjct: 200 GIA-----LREAMRRLNNREKHILNLRFFEG----RTQMEVADEIGISQAQVSRLEKTAL 250

Query: 665 RKLKH 669
           + ++ 
Sbjct: 251 KHMRK 255


>gi|294011928|ref|YP_003545388.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
 gi|292675258|dbj|BAI96776.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
          Length = 304

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 119/273 (43%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +   +    R  E + S A  ++V ++LRLV  +A  Y   GL
Sbjct: 19  LNRYLSEIRKFPILTPEQEYMLAK--RYAEHQDSEAAAQLVTSHLRLVAKIAMGYRGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGLM+  +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 77  PVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEFILRSWSLVKMGTTAAQK 136

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIG 581
                  ++        +        ++IA  L +  E V  +          SL  P+ 
Sbjct: 137 KLFFNLRRMKNNIEAFEDGDLHPDDVKKIATDLGVTEEDVISMNRRMAMGGDTSLNVPMR 196

Query: 582 DEDTSHLGDFIEDKN--AVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++      D++ D +      +    ++ LR +     +  L  RE+ +L  R       
Sbjct: 197 EDGEGQWQDWLADSDPLQDERVADRQESELRHDMLVEAMDDLNDREKHILAERRLAE--E 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TLEE+ + + V+RER+RQIE +A  KL+   
Sbjct: 255 PKTLEELSQVYGVSRERVRQIEVRAFEKLQKAM 287


>gi|257054261|ref|YP_003132093.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256584133|gb|ACU95266.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 267

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 117/246 (47%), Gaps = 13/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F    ++       A + +  +V  +L L   +A++++ RG+   DL+Q   +GL+ A +
Sbjct: 23  FEEFAALDPDDPRRAEL-RDRLVTGHLPLAEHIAQRFSGRGVAKEDLVQVARVGLINAVD 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  V   + R   D    IR+P  +++    +   + ++S ++ R 
Sbjct: 82  RFDPSRGSDFLSFAVPTVMGEVRRHFRDTGWVIRVPRRLKELHLSINNASTQLSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDS 603
           PTP EIA  L + +E V + L+       +SL+  +  + +   LGD + +++A      
Sbjct: 142 PTPSEIADHLGLTLEEVFEGLEAGNAYHSMSLDEVLSADTENLALGDTLGEEDAALAGVE 201

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                  ET   ++  L  RE  +L +RF        T  ++ ++  +++  + ++ A+ 
Sbjct: 202 N-----HETLQPLVKQLPERERTILALRFVHN----MTQTQIAERIGISQMHVSRLLART 252

Query: 664 IRKLKH 669
           ++KL+ 
Sbjct: 253 LKKLRE 258


>gi|55274897|gb|AAV49250.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 78/197 (39%), Positives = 131/197 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  L LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGKQFC 650
           +      TLE+VG++  
Sbjct: 182 LLGYEAATLEDVGREIG 198


>gi|312111757|ref|YP_003990073.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
 gi|311216858|gb|ADP75462.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
          Length = 271

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 138/261 (52%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++       A++++V  NLRLV+SV +++ NRG 
Sbjct: 15  RNKVEICGVDTSKLPVLKNEEMRELFKRMHEGDLEAREKLVNGNLRLVLSVIQRFNNRGE 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 75  FVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT EEIA  L +P E V   L   ++P+SL  PI ++  D  
Sbjct: 134 AYKALQVREKLMGEAAKEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPI 193

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+          +  L+E   R    L  RE+ ++R RF  G     T  EV 
Sbjct: 194 YVMDQLSDERNGDSQW-IEEIALKEGLCR----LNEREKMIIRKRFFQG----KTQMEVA 244

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AIR++
Sbjct: 245 EEIGISQAQVSRLEKAAIRQM 265


>gi|66474719|gb|AAY46929.1| RpoD [Aeromonas sp. SF8-170]
          Length = 272

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                        +         E +  D  E E + E     S DD       PE A  
Sbjct: 59  NE-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVARE 113

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 114 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKK+
Sbjct: 258 RMSIGEAKARRAKKK 272


>gi|326442277|ref|ZP_08217011.1| RNA polymerase sigma factor, sigma L [Streptomyces clavuligerus
           ATCC 27064]
          Length = 292

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 113/228 (49%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NL LV   A ++ +R     D++Q G IGL+KA ++FD   G +F T+AM  V
Sbjct: 68  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 127

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D S ++R+P  +++    + + +  ++ ++ R PT  E+A  L +  E V 
Sbjct: 128 VGEIKRFFRDTSWSVRVPRRLQELRLALTKASDELAQRLDRSPTVPELAAVLGVSEEEVV 187

Query: 565 KVLKI--TKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             L +       SL++P  ++D     L D +  ++             RE+   +LA L
Sbjct: 188 DGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGVEY-----RESLKPLLAKL 242

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            PRE +++ +RF        T  ++G++  +++  + ++  + + +L+
Sbjct: 243 PPRERQIIMLRFFAN----MTQSQIGEEVGISQMHVSRLLTRTLAQLR 286


>gi|29830728|ref|NP_825362.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607841|dbj|BAC71897.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 309

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 111/244 (45%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +R G  E S  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD 
Sbjct: 72  LKDLRPGSPEHSRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDP 131

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  
Sbjct: 132 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTA 191

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  E V   ++   +    SLE     +    L D +  ++            
Sbjct: 192 EIAERLRITEEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH---- 247

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+
Sbjct: 248 -RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFARLR 302

Query: 669 HPSR 672
             +R
Sbjct: 303 SANR 306


>gi|254525091|ref|ZP_05137146.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
 gi|219722682|gb|EED41207.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
          Length = 291

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 128/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ + + +    R G      A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDDEQDLARRFRDG--NDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  ALGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E +   +AK L +    V ++  +++   I  + P  +++ 
Sbjct: 141 KLFFNLRKSKTRLGWMNAAEVSA--VAKDLNVSEREVMEMESRLSGRDIGFDAPTDEDNE 198

Query: 586 ----SHLGDFIEDKNAVSPLDSAI--QANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S     + +    S        + N  +     LA L  R   ++R R+ +  ++ 
Sbjct: 199 HAPPSPAAFLVANDEDPSMAYERADSEDNQMQLLREGLAELDARSRDIIRRRW-LDADSK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQ+EA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|307578942|gb|ADN62911.1| RNA polymerase factor sigma-32 [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 282

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 17  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 75  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-D 584
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 135 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 192

Query: 585 TSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 193 PSPVGYLIANDGDPSQAYERGNSEETQLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 250

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 251 LQELAEEYGVSAERIRQIEANALKKMK 277


>gi|239929001|ref|ZP_04685954.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291437340|ref|ZP_06576730.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291340235|gb|EFE67191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 374

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 119/241 (49%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  ++ G  E +  + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 137 LRSLQDGSPEYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 196

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 197 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 256

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 257 ELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 312

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 313 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 367

Query: 669 H 669
            
Sbjct: 368 E 368


>gi|239906748|ref|YP_002953489.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
 gi|239796614|dbj|BAH75603.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
          Length = 348

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 81/308 (26%), Positives = 144/308 (46%), Gaps = 12/308 (3%)

Query: 379 LDPH-WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           LDP   +  A  F     +      + +   ++  ++ I     +   E + +   VR  
Sbjct: 37  LDPDLEIDAADTFTLPAPRPRSEGSLSTRDPLQLYLREIGKFPMLKPEEEQELARRVR-- 94

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +     A   ++ ++LRLV+ +A  +  R +Q  LDLIQEGN+GLM+A  KFD   G KF
Sbjct: 95  DANDQKAAFRLISSHLRLVVKIAMDFQRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKF 154

Query: 497 STYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           S YA +W+K  I + I D    ++I     + K+   +   R+    +  +P+  ++++ 
Sbjct: 155 SYYAAYWIKAYILKYIMDNWRMVKIGTTQAQRKLFYNLNKERQRLQSLGFDPSAAQLSQA 214

Query: 556 LAMPVEG-VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRE 611
           L +     V    +++   +SL+  +GD+ TS   DF+               I   L +
Sbjct: 215 LNVTESDIVEMDQRLSGNDLSLDVSLGDDTTSTRLDFLPALTPGIEEILAGDEISHQLDK 274

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +   L  +E  +L     I  ++  TL E+G ++ +TRER+RQIE++ + KLK   
Sbjct: 275 HIQSIRPKLNEKEIELLD--NRILSDSPVTLREIGAKYGITRERVRQIESRLLEKLKDHL 332

Query: 672 RSKKLRSF 679
            SK++  F
Sbjct: 333 -SKRIEDF 339



 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 31/66 (46%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           E + D      +A   ++   + +     ST DP+++YLRE+G   +L  E E  +A+R+
Sbjct: 34  EPTLDPDLEIDAADTFTLPAPRPRSEGSLSTRDPLQLYLREIGKFPMLKPEEEQELARRV 93

Query: 147 EAGRAM 152
                 
Sbjct: 94  RDANDQ 99


>gi|254477747|ref|ZP_05091133.1| alternative sigma factor RpoH [Ruegeria sp. R11]
 gi|214031990|gb|EEB72825.1| alternative sigma factor RpoH [Ruegeria sp. R11]
          Length = 298

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 124/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + +  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEEQDANSAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   +        + ++IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLHPDSVKKIATDLGVTEDEVISMNRRMSGGDASLNATVGT 193

Query: 583 EDTS--HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ +L  R      
Sbjct: 194 EGEGAMQWQDWLEDEDADQAGDYEARDELEARRELLASALEVLNDREKDILTQRRLAD-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QAKTLEDLSTQYGVSRERIRQIEVRAFEKLQKKMR 286


>gi|220931759|ref|YP_002508667.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
 gi|219993069|gb|ACL69672.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
          Length = 260

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 74/256 (28%), Positives = 131/256 (51%), Gaps = 15/256 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +++G+     A+++++  NLRLV+SV +++ NRG    DL Q G IGL
Sbjct: 18  LSNEEMRKLFKKMQQGDWS---ARQKIINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     +FSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 75  IKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDTAYKALQMKESLKN 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K   EP+ +E++++L +P   +   L   ++PISL  PI  +  D   + D I D+    
Sbjct: 134 KKSEEPSLKEVSEELGIPRSEIIFALDAIQDPISLFEPIYHDGGDPIFVMDQISDEKTED 193

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                  A         L  L+PRE+ +L  RF  G     T  EV  +  +++ ++ ++
Sbjct: 194 ENWLEGIA-----VREGLRKLSPREKLILAYRFYEG----KTQMEVANEIGISQAQVSRL 244

Query: 660 EAKAIRKLKHPSRSKK 675
           E  A+++LK   +  +
Sbjct: 245 EKAALKRLKRHVKEDR 260


>gi|156936376|ref|YP_001440292.1| RNA polymerase factor sigma-32 [Cronobacter sakazakii ATCC BAA-894]
 gi|260599762|ref|YP_003212333.1| RNA polymerase factor sigma-32 [Cronobacter turicensis z3032]
 gi|156534630|gb|ABU79456.1| hypothetical protein ESA_04276 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218939|emb|CBA34294.1| RNA polymerase sigma-32 factor [Cronobacter turicensis z3032]
          Length = 285

 Score =  134 bits (337), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 133/270 (49%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K+++ ++LR V+ +A+ Y   GL
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKL--HYQGDLEAAKKLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIG 581
                + +T +R+    + E   E +A++L +  + VR++      +     +S +   G
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSPDDDAG 191

Query: 582 DEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D        F++DK+   A    D   + +  +  T  +  L  R ++++R R+ +  + 
Sbjct: 192 DSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERSQQIIRARW-LDEDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELANRYGVSAERVRQLEKNAMKKLR 280


>gi|189424394|ref|YP_001951571.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
 gi|189420653|gb|ACD95051.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
          Length = 285

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 74/264 (28%), Positives = 119/264 (45%), Gaps = 10/264 (3%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  I     +   E   +   VR  E     A + ++ +NLR V+ +A +Y N GL+ 
Sbjct: 14  KYLSEIKSFPLLDEQEEHRLA--VRLFEENDLSAAQTLITSNLRFVVKIAAEYRNYGLKM 71

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDLIQEGNIGLM A  KF+   G++  TYA+WW++  I   I      ++I      R  
Sbjct: 72  LDLIQEGNIGLMLAVRKFNPYRGFRLITYAVWWIRAQIQSYIVSSWSLLKIGTTQAQRKL 131

Query: 529 IHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             K+ +    + +     E      A  L +    V ++       +SL+      +   
Sbjct: 132 FFKLKQAKNAILSMNGGDEGDLPATALSLDVREAEVEEMELRLMGEVSLDAEQVAGEGGS 191

Query: 588 LGDFIEDK--NAVSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           L + + D   N  S L     Q  LR      ++ L  +E+ V++    I  +   TL+E
Sbjct: 192 LLETLVDDRPNQESQLADLQEQQALRVVVADAVSRLGEKEQFVVKQ--RIVADDPMTLQE 249

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +   F ++RER+RQIE  A+RK+K
Sbjct: 250 IADHFSISRERVRQIEENALRKIK 273


>gi|170731288|ref|YP_001776721.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M12]
 gi|167966081|gb|ACA13091.1| RNA polymerase sigma-32 factor [Xylella fastidiosa M12]
          Length = 288

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 129/267 (48%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++   + +S+ E + +    R  + +   A +E+V ++LR V+ VA+ Y+  GL
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYR--DQQDLDAARELVHSHLRFVVRVARGYSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++AM W++  +   I      +++      R
Sbjct: 81  SLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + ++  R+      E +   +A+ L +    V     +++   I  + P  D   
Sbjct: 141 KLFFNLRKSRTRLGWMNAEEVSA--VARDLNVSEREVLEMESRLSGRDIGFDAPEEDNAP 198

Query: 586 -SHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S +G  I +    S         +  LR      L+ L  R   +++ R+ +  +   T
Sbjct: 199 LSPVGYLIANDGDPSQAYERGNSEETQLR-LLQEGLSVLDTRSRDIIQRRW-LETDKKIT 256

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ +++ V+ ERIRQIEA A++K+K
Sbjct: 257 LQELAEEYGVSAERIRQIEANALKKMK 283


>gi|89094249|ref|ZP_01167191.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081504|gb|EAR60734.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 411

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 85/262 (32%), Positives = 144/262 (54%), Gaps = 11/262 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R ++  I      +  E   ++S   K        + +++E NLRLV  VA ++ + G+ 
Sbjct: 148 REKLVRILTSGLRTTEEVDSLISRYEKL-------RSKLIEKNLRLVYVVALRFKSSGVS 200

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLIQEGNIGL+KAA++F++  GY+FSTYA W ++  +  ++     TI  P ++++K+
Sbjct: 201 LDDLIQEGNIGLLKAADRFNFVHGYRFSTYAFWCIQNVLKTALQKNYHTISRPSYLQEKL 260

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI---GDEDTS 586
             + R + R  N+  R P   E+++  ++P   + K+     EP+SL  P+    + +  
Sbjct: 261 SVIKRESVRFLNQYGRYPGTTELSELTSIPEAMLEKIKSFPAEPLSLSQPVSRSQEGEDL 320

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            +   +ED NA++       A  R    R+   L  RE +VL+MRFGI  +T+HTLEE+ 
Sbjct: 321 TVESTLED-NAMAAEKETDIALKRRMLERMSLRLNEREYKVLKMRFGIDCHTEHTLEEIS 379

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
            Q  V+ ER+RQ++  A+ KL+
Sbjct: 380 HQLNVSVERVRQLQKIALEKLQ 401


>gi|117927772|ref|YP_872323.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117648235|gb|ABK52337.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 287

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 111/230 (48%), Gaps = 10/230 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + E+V+ +L LV  +A+++ NRG    DL+Q   IGL+KA ++FD   G +FSTYA 
Sbjct: 60  QEIRSELVQTHLPLVEYLARRFRNRGEPHDDLVQVATIGLIKAIDRFDVERGVEFSTYAT 119

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D+   IR+P  +++    + +    +S +  R PT  E+A  L M  +
Sbjct: 120 PTIVGEIKRYFRDRGWAIRVPRRLQELKMSLAKATSELSQQYGRAPTVSELADHLGMSED 179

Query: 562 GVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + + L+       ISL+TP    +T             +  ++      RE+   +L  
Sbjct: 180 EILEGLESANAYSTISLDTP----ETDDADALAVADTLGNIDEALEGVEYRESLKPLLEK 235

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L PRE+R+L +RF        T  ++  +  +++  + ++ A+ + +L+ 
Sbjct: 236 LPPREKRILLLRFFRN----MTQSQIAAELGISQMHVSRLLARTLARLRE 281


>gi|87201057|ref|YP_498314.1| RNA polymerase factor sigma-32 [Novosphingobium aromaticivorans DSM
           12444]
 gi|87136738|gb|ABD27480.1| RNA polymerase, sigma 32 subunit, RpoH [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 299

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 66/275 (24%), Positives = 117/275 (42%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +   +    +  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 19  LNRYLSEIRKFPVLTAEQEYMLAKRFQ--EHQDPEAAAQLVTSHLRLVAKIAMGYRGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGLM+  +KF+   G++ +TYAMWW+K ++   I      +++      K
Sbjct: 77  PVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIKASMQEFILRSWSLVKMGTTAAQK 136

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIG 581
                  ++ +      +         +IA  L +P + V  + +        SL   + 
Sbjct: 137 KLFFNLRRMKKNLEAFEDSDLHPDDVRKIATDLGVPEQEVVNMNRRMMMGGDASLNVSMR 196

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++      D++ D   +     A         E     + SL  RE  +L  R  I    
Sbjct: 197 EDGEGSWQDWLTDDRPLQDETVADAEEAQYRHELLVEAMESLNERERHILTDRRLID--D 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+ + + V+RER+RQIE +A  KL+   + 
Sbjct: 255 PKTLEELSQVYNVSRERVRQIEVRAFEKLQKAIQR 289


>gi|291544789|emb|CBL17898.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. 18P13]
          Length = 257

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 134/254 (52%), Gaps = 15/254 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T +  SE   ++  +++    +  A+ +++  NLRLV+SV +++  RG    DL Q 
Sbjct: 14  SKLTVLKESEKIELLREIQRTG--SKEARDKLINGNLRLVLSVIQRFAGRGEDIDDLFQI 71

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   FD     +FSTY +  +   + R + D +  I++   +RD  +K ++  
Sbjct: 72  GVIGLIKAINNFDLSKEVRFSTYCVPMISGELRRFLRDYN-HIKVSRSLRDLAYKAMQAK 130

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED 594
            +++ + ++EPT +EIAK++      V   L+   +P+SL  P+  +  DT ++ D I D
Sbjct: 131 EQLTAEQQKEPTMDEIAKRIDAKRSDVVLALESVTDPVSLYEPVYSDAGDTLYVLDQISD 190

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +N+V      I           + +L PRE+R+L +RF  G     T  EV ++  +++ 
Sbjct: 191 QNSVDSWLDEI------ALRDAIKALQPREKRILYLRFFQG----KTQVEVAQEIGISQA 240

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E  A+ ++K
Sbjct: 241 QVSRLEKGALNQIK 254


>gi|168180582|ref|ZP_02615246.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|168182609|ref|ZP_02617273.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|170757556|ref|YP_001782076.1| sporulation sigma factor SigG [Clostridium botulinum B1 str. Okra]
 gi|170761503|ref|YP_001787848.1| sporulation sigma factor SigG [Clostridium botulinum A3 str. Loch
           Maree]
 gi|187778872|ref|ZP_02995345.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226949887|ref|YP_002804978.1| sporulation sigma factor SigG [Clostridium botulinum A2 str. Kyoto]
 gi|237795971|ref|YP_002863523.1| sporulation sigma factor SigG [Clostridium botulinum Ba4 str. 657]
 gi|169122768|gb|ACA46604.1| RNA polymerase sigma-G factor [Clostridium botulinum B1 str. Okra]
 gi|169408492|gb|ACA56903.1| RNA polymerase sigma-G factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182668579|gb|EDT80558.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|182674221|gb|EDT86182.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|187772497|gb|EDU36299.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226842131|gb|ACO84797.1| RNA polymerase sigma-G factor [Clostridium botulinum A2 str. Kyoto]
 gi|229263792|gb|ACQ54825.1| RNA polymerase sigma-G factor [Clostridium botulinum Ba4 str. 657]
          Length = 257

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 75/265 (28%), Positives = 134/265 (50%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ +     +  ++E ++ NLRLV+SV K++ NRG
Sbjct: 2   VINKVEICGVNTSKLPVLKDKEMKKLLVRIRNGETECREEFIQGNLRLVLSVIKRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++     +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALQARDKLIKNNNKEPTVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             + D I D KN        I      +    +  L  RE+ +L +RF  G     T  E
Sbjct: 181 IFVMDQISDTKNVDENWIENI------SIKEAMKKLNDREKLILNLRFFDG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|261886011|ref|ZP_06010050.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 190

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 82/184 (44%), Positives = 124/184 (67%), Gaps = 1/184 (0%)

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
                +QA+ R+IADQ+ TIRIP+HM + I+++ +       K  + P    I  ++ + 
Sbjct: 6   CSLRARQAMCRAIADQALTIRIPIHMIETINRINKFIENFFQKKGKGPDVAFIPGEVGLS 65

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++ V++V+KITKEPISLE PIG ED    GDF+EDK  +SP++  ++ +L+E    VL  
Sbjct: 66  IDKVKQVIKITKEPISLEAPIGSEDDGKYGDFVEDKTNLSPMEQILKGDLKEQIDEVLDQ 125

Query: 620 LTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+ AI+KLKHP   +KL++
Sbjct: 126 LNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKN 185

Query: 679 FLDG 682
           +++G
Sbjct: 186 YIEG 189


>gi|297746561|emb|CAZ60998.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 271

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 66/313 (21%), Positives = 112/313 (35%), Gaps = 44/313 (14%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   + +S+ E P     L+   D+       L +II     I P       
Sbjct: 1   DIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNETE--- 55

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                 +         E +  D  E E + E     + DD       PE A      L  
Sbjct: 56  --DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREKFGELRA 113

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
             + +  ++                                   QK+ ++    +    +
Sbjct: 114 QYEVTRLSI-----------------------------------QKNGRAHEDTQAAIAQ 138

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGREL 379
           L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E 
Sbjct: 139 LADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAAFTNNEC 198

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  GE 
Sbjct: 199 DSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEA 257

Query: 440 EASIAKKEMVEAN 452
           +A  AKKEMVEAN
Sbjct: 258 KARRAKKEMVEAN 270


>gi|302558487|ref|ZP_07310829.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302476105|gb|EFL39198.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 281

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 118/241 (48%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  ++ G  E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 44  LRTLQDGTPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 103

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 104 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 163

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 164 ELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 219

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 220 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 274

Query: 669 H 669
            
Sbjct: 275 E 275


>gi|194367438|ref|YP_002030048.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia
           R551-3]
 gi|194350242|gb|ACF53365.1| RNA polymerase, sigma 32 subunit, RpoH [Stenotrophomonas
           maltophilia R551-3]
          Length = 291

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 128/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ + + +    R G      A +E+V ++LR V+ VA+ Y   GL
Sbjct: 23  LDAYIGAVHQIPVLSVDDEQDLARRFRDG--NDLDAARELVHSHLRFVVHVARGYNGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  +   I      +++      R
Sbjct: 81  ALGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQR 140

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++  R+      E +   +AK L +    V ++  +++   I  + P  +++ 
Sbjct: 141 KLFFNLRKSKTRLGWMNAAEVSA--VAKDLNVSEREVMEMESRLSGRDIGFDAPTDEDNE 198

Query: 586 ----SHLGDFIEDKNAVSPLDSAI--QANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               S     + +    S        + N  +     LA L  R   ++R R+ +  ++ 
Sbjct: 199 HAPPSPAAYLVANDEDPSMAYERADSEDNQMQLLREGLAELDARSRDIIRRRW-LDADSK 257

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ERIRQ+EA A++K+K
Sbjct: 258 VTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|30248598|ref|NP_840668.1| RNA polymerase factor sigma-32 [Nitrosomonas europaea ATCC 19718]
 gi|30180193|emb|CAD84495.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 280

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 70/265 (26%), Positives = 124/265 (46%), Gaps = 7/265 (2%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + + I++ S    +S  E   +   +R  E     A  ++V ++LR+V+++A+ Y   G
Sbjct: 14  DLDSYIRATSSFPVLSREEEASLAKRMR--EEGDVNAAHQLVLSHLRVVVTIARGYLGYG 71

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEGNIGLMKA  +FD   G +  ++A+ W++  I   I      ++I    + 
Sbjct: 72  LPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIRAEIHEFIMRNWRLVKIATTKQQ 131

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLE-TPIGDEDT 585
           +       + +       +     +A++L +  E V ++  + +   ISLE     DED 
Sbjct: 132 RKLFFNLRSMKKGLDTMSQAEVASMAEQLGVKAEEVVEMETRFSGRDISLEPVTDSDEDD 191

Query: 586 SHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
                ++ D +  S      Q            L SL  R  R++  R+ +  +   TL 
Sbjct: 192 FSPIAWLTDGSDPSRELEKEQLERLTHARLKNSLDSLDERSRRIIEARW-LREDKAATLH 250

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  +  V+ ER+RQIEAKA++K++
Sbjct: 251 ELADELGVSAERVRQIEAKAMKKMR 275


>gi|261377878|ref|ZP_05982451.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
 gi|269145731|gb|EEZ72149.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
          Length = 290

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 74/266 (27%), Positives = 134/266 (50%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +++ E  H+    RK       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNSIPMLTLDEETHLAERQRK---GDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      +EIA  L + +  V     ++T   I++     D++ S
Sbjct: 137 KLFFNLRSMRKNLNALSP-KEAQEIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|290473624|ref|YP_003466496.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
 gi|289172929|emb|CBJ79700.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
          Length = 285

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 127/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    +S  E + +   +         A K+++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LEGYVRASNAYPMLSAEEEKELAERL--HYQGDLDAAKKLILSHLRFVVHVARSYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
                + +  +R+    + E     +AK+L +  + VR++   +        + +     
Sbjct: 134 KLFFNLRKAKQRLGWFNQDEVDL--VAKELGVTSKDVREMESRMSAQDMAFDMSSNDDSH 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRFGIGMNT 638
           D+  +   +  ++  S     I+ +  E       +  +  L  R + ++R R+ +  + 
Sbjct: 192 DSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSMAIEGLDERSQDIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|283787904|ref|YP_003367769.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
 gi|282951358|emb|CBG91057.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
          Length = 284

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSPDDESD 191

Query: 586 SH-LGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           S  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKTSNFADGIEEDNWEDQAASKLTHAMEGLDERSQAIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|55274901|gb|AAV49252.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 79/197 (40%), Positives = 132/197 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGKQFC 650
           +      TLE+VG++  
Sbjct: 182 LLGYEAATLEDVGREIG 198


>gi|290957490|ref|YP_003488672.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260647016|emb|CBG70115.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 388

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++       A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 148 FIELRALPDGSVEYAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 206

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 207 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQQHGRS 266

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+KLA+  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 267 PTVHELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY 326

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 327 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 377

Query: 665 RKLKH 669
            +L+ 
Sbjct: 378 AQLRE 382


>gi|325288838|ref|YP_004265019.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964239|gb|ADY55018.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 135/264 (51%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + +     +  +  K +      ++++++ NLRLV+SV ++++NRG
Sbjct: 2   VLNKVEICGVNTSKLPVLSGAKMKELFTKMQAGDGTIREQLIKGNLRLVLSVIQRFSNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EHVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   +++ +  REPT +EIA KL  P E V   L   +EP+SL  PI  +  D 
Sbjct: 121 IAYKALQIRDKLATECSREPTIQEIAAKLETPQEEVILALDAIQEPVSLFEPIYHDGGDP 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I D      +     +         +  L  RE+R++ +RF  G     T  EV
Sbjct: 181 IYVMDQIGDHKQSDRIWLESLS-----IKEGIERLGEREKRIISLRFFQG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            ++  +++ ++ ++E  A++ ++ 
Sbjct: 232 AEEIGISQAQVSRLEKAALKHMRK 255


>gi|291438641|ref|ZP_06578031.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
 gi|291341536|gb|EFE68492.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
          Length = 303

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 111/244 (45%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +  G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD 
Sbjct: 66  LKELEPGTPEHTRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDP 125

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R P+  
Sbjct: 126 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAFGRSPSTA 185

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  E V   ++   +    SLE     +    L D +  ++            
Sbjct: 186 EIAERLRITEEDVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALDGVEH---- 241

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+
Sbjct: 242 -RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLR 296

Query: 669 HPSR 672
             +R
Sbjct: 297 SANR 300


>gi|213018727|ref|ZP_03334535.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995678|gb|EEB56318.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 281

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 75/279 (26%), Positives = 132/279 (47%), Gaps = 16/279 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I  +     +S  E   +       E +   +   ++ ++L LV+ +A K+ N GL  
Sbjct: 2   QYIAEVRKFPMLSQEEEVRLAK--NWQEYQDISSAHRLITSHLNLVVKIAMKFKNYGLLL 59

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ ++   I      ++I      R  
Sbjct: 60  MDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASMKDFILKSWSLVKIGTTQAQRRL 119

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLA-----MPVEGVRKVLKITKEPISLETPIGDE 583
              + +  +R+     RE   +E  K ++        + V+   ++  +  SL   I   
Sbjct: 120 FFSLRKIKKRILQYTNRETLSKEEIKAISNELSVSEEDVVQMSYRLACKDQSLNNCIKIG 179

Query: 584 DTS--HLGDFIEDK--NAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNT 638
           D S   L D I     +      +  +  L+ET  +  LASL  R   +   R+      
Sbjct: 180 DDSKKELQDMIPCNLVSQEVAYQNHEEKALKETILSNALASLNERSRDIFISRYLSENTQ 239

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 240 --TLDELSKKYCVSRERIRQLAEQAMSKVKQHIKSESLK 276


>gi|94497521|ref|ZP_01304090.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
 gi|94422938|gb|EAT07970.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
          Length = 310

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 118/273 (43%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 25  LNRYLSEIRKFPLLTPEQEYMLAK--RYQEHQDPEAAAQLVTSHLRLVAKIAMGYRGYGL 82

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LI EGNIGLM+  +KF+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 83  PVSELISEGNIGLMQGVKKFEADRGFRLATYAMWWIRASIQEFILRSWSLVKMGTTAAQK 142

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKV--LKITKEPISLETPIG 581
                + R    +      +  PE+   IA  L +  + V  +          SL  P+ 
Sbjct: 143 KLFFNLRRMKNNIEAFEDGDLRPEDVTKIATDLGVSEDDVISMNRRMAMGGDTSLNVPMR 202

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++      D++ D + +     A +       +     +  L  RE+ +L  R       
Sbjct: 203 EDGEGQWQDWLADTDPLQDERVADEQEKVQRHDMLVEAMDDLNDREKHILAERRLAE--E 260

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TLEE+ + + V+RER+RQIE +A  KL+   
Sbjct: 261 PKTLEELSQVYGVSRERVRQIEVRAFEKLQKAM 293


>gi|192289929|ref|YP_001990534.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
 gi|192283678|gb|ACF00059.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 326

 Score =  134 bits (337), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 117/274 (42%), Gaps = 13/274 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           ++ +++I     +   E   +    R        A   ++ ++LRL   +A+ Y   G  
Sbjct: 23  QDYMRAIGRYPVLEPDEEARLWQ--RWHTARDKAAADVLITSHLRLAAKLARNYRRYGFP 80

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRD 527
             DLI E N+GLM A +KFD   G +F+T A+WW++ AI   I      +RI      + 
Sbjct: 81  IGDLIAEANLGLMMALDKFDPTRGARFATCAVWWIRSAIYDHIVRSWSLVRIGRTPAQKK 140

Query: 528 KIHKVVRTARRMSNKIKREPTP---EEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-E 583
              ++    RR+        T    E+I+  L +P+  V ++ +     +SL  P+ D +
Sbjct: 141 LFFRLRGEIRRLRPDHHGALTKDLAEQISTSLDVPLREVIEMEQRLSGDLSLNAPLSDLD 200

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           ++    D I D +  +    A    L   R      L  L  RE  +         +   
Sbjct: 201 ESGEWQDLIADDSPNAEAILAGHDELDRQRGALRDALVQLDARERYIFSA--RHLGDRPA 258

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + E +G+   ++ ER+RQIEA+A  K+   +R  
Sbjct: 259 SFEAIGQSLSLSAERVRQIEARAFAKVATAARRH 292


>gi|66474697|gb|AAY46918.1| RpoD [Aeromonas sp. RK 70363]
          Length = 272

 Score =  134 bits (336), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                        +         E +  D  E E + E     S DD       PE A  
Sbjct: 59  ND-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVARE 113

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 114 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +++   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVMRSIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 258 RMSIGEAKARRAKKE 272


>gi|50123263|ref|YP_052430.1| RNA polymerase factor sigma-32 [Pectobacterium atrosepticum
           SCRI1043]
 gi|49613789|emb|CAG77240.1| RNA polymerase sigma-32 factor [Pectobacterium atrosepticum
           SCRI1043]
          Length = 285

 Score =  134 bits (336), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/270 (23%), Positives = 131/270 (48%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYQGDLEAAKHLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + +   R+    + E   E +A++L +  + VR++  ++  + ++ +    ++  
Sbjct: 134 KLFFNLRKAKTRLGWFNQDE--VELVARELGVTTKDVREMESRMAAQDMTFDPTPEEDSH 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   +   +  ++  S     I+ +  +T      T  L  L  R + ++R R+ +  + 
Sbjct: 192 DGKAMSPMLYLQDKSSDFADGIEEDNWDTHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|53718144|ref|YP_107130.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei K96243]
 gi|76812253|ref|YP_332145.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1710b]
 gi|126441976|ref|YP_001057600.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 668]
 gi|126453430|ref|YP_001064846.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1106a]
 gi|134279764|ref|ZP_01766476.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|167717993|ref|ZP_02401229.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei DM98]
 gi|167737009|ref|ZP_02409783.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 14]
 gi|167814118|ref|ZP_02445798.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 91]
 gi|167822644|ref|ZP_02454115.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 9]
 gi|167844214|ref|ZP_02469722.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei B7210]
 gi|167892724|ref|ZP_02480126.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 7894]
 gi|167901220|ref|ZP_02488425.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei NCTC
           13177]
 gi|167909437|ref|ZP_02496528.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 112]
 gi|167917468|ref|ZP_02504559.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei BCC215]
 gi|217419877|ref|ZP_03451383.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|226199497|ref|ZP_03795054.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237810751|ref|YP_002895202.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242316271|ref|ZP_04815287.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254181885|ref|ZP_04888482.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|254187820|ref|ZP_04894332.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|254196825|ref|ZP_04903249.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|254260127|ref|ZP_04951181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
 gi|254296064|ref|ZP_04963521.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|52208558|emb|CAH34494.1| RNA polymerase sigma-32 factor [Burkholderia pseudomallei K96243]
 gi|76581706|gb|ABA51181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710b]
 gi|126221469|gb|ABN84975.1| alternative sigma factor RpoH [Burkholderia pseudomallei 668]
 gi|126227072|gb|ABN90612.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106a]
 gi|134248964|gb|EBA49046.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|157805888|gb|EDO83058.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|157935500|gb|EDO91170.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|169653568|gb|EDS86261.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|184212423|gb|EDU09466.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|217397181|gb|EEC37197.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|225928378|gb|EEH24408.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237503746|gb|ACQ96064.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242139510|gb|EES25912.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254218816|gb|EET08200.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
          Length = 311

 Score =  134 bits (336), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 134/269 (49%), Gaps = 12/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++++    +S  E R   +  R+       A + +V ++LRLV+SVA+ Y   GL
Sbjct: 39  IDAYIQAVNRIPLLSAEEERQYATEYREQNNLD--AARRLVLSHLRLVVSVARNYLGYGL 96

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++      +
Sbjct: 97  PHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQR 156

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDTSH 587
                  + +   +       + +A++L +  E V ++    +   I+LE  I D + S+
Sbjct: 157 KLFFNLRSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDDGEESY 216

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNTD---- 639
             +    +  N  + + +A Q ++ +T    R L SL  R  R++  R+ + ++ D    
Sbjct: 217 APIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARW-LNVDDDGSGG 275

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 276 STLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|239934578|emb|CAR94603.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 233

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 55/271 (20%), Positives = 103/271 (38%), Gaps = 45/271 (16%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
            T  L +II            GF             +    +   +++    +     + 
Sbjct: 61  QTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAAAEIENEAEEEAEEGEG 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           + ++   +++ P+  E   R                            D +++ + +++ 
Sbjct: 110 ASEEEETLETGPDPEEAARR---------------------------FDSLSKTFVQVQK 142

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    +      K   L++KL      L L+    D+L+ Q+      I + E ++
Sbjct: 143 ------GMAEKGAXDPKVMKLRKKLADEFMELKLSPKMFDMLITQIRRSLTDIRNVEKQV 196

Query: 357 LRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
           + L     G+ R  F+      E +  W+  
Sbjct: 197 MLLCVRDSGMPRKDFISTFPSNETNLSWLDK 227


>gi|224827256|ref|ZP_03700350.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
 gi|224600545|gb|EEG06734.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
          Length = 287

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 71/265 (26%), Positives = 131/265 (49%), Gaps = 9/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+ ++    +S  E   + + +         A K++V ++LR+V+S+A+ Y   GL
Sbjct: 16  LEQYIQIVNSVPLLSAEEENELANRL--HAQNDLEAAKKLVLSHLRVVVSIARGYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  PQADLIQEGNIGLMKAVKRFEPNRGVRLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     IA  L +  E VR++  +++ + ++L     D++  
Sbjct: 134 KLFFNLRSMKKSFAAL-TDSEARVIADDLGVKPEEVREMETRMSGQDVALLADDNDDEGF 192

Query: 587 HLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              D++ D +          A          + L+SL  R  R++  R+    ++  TL 
Sbjct: 193 APIDWLADSDHEPTRQLEKKAFDHLQTAGLEQALSSLDARSRRIIEARWLAD-DSGATLH 251

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  +F V+ ERIRQIEAKA+ K+K
Sbjct: 252 ELAAEFGVSAERIRQIEAKALTKMK 276


>gi|190893168|ref|YP_001979710.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190698447|gb|ACE92532.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 302

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 126/279 (45%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R   ++ ++ L  RE R+   R       
Sbjct: 194 EGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R + L 
Sbjct: 252 PVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEALE 290


>gi|99080404|ref|YP_612558.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036684|gb|ABF63296.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 299

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 127/275 (46%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+      +  PE   +IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEDGDLRPEVVKKIATDLGVTEDEVISMNRRMSGGDASLNAMVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +  S     D++ED++A    D   +  L   RE     ++ L  RE+ +L  R      
Sbjct: 194 DGDSTMQWQDWLEDEDADQAGDYEARDELQARRELLAEAMSVLNDREKDILTQRRLAE-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QAKTLEELSVQYDVSRERIRQIEVRAFEKLQKKMR 286


>gi|319788352|ref|YP_004147827.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466864|gb|ADV28596.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 292

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 128/270 (47%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I ++     +S+ E + +    R  + E   A +E+V ++LR V+ VA+ Y   GL
Sbjct: 24  LEAYIGAVHQIPVLSVEEEQALARRYR--DQEDLDAARELVHSHLRFVVHVARGYNGYGL 81

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           Q  DLIQEGNIGLMKA ++FD  LG +  ++A+ W++  I   I      +++      R
Sbjct: 82  QLGDLIQEGNIGLMKAVKRFDPDLGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQR 141

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +   R+      E +   +AK L +    V     +++   I  + P  +++ 
Sbjct: 142 KLFFNLRKAKTRLGWMNAAEVSA--VAKDLNVSEREVLEMESRLSGRDIGFDAPADEDEE 199

Query: 586 -------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                  ++L    ED +         + +  +     LASL  R   ++  R+ +   +
Sbjct: 200 HAPPSPAAYLVSMDEDPSQA-LEREDSEGHKLDLLRDGLASLDARSRDIIARRW-LDDES 257

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ERIRQIEA A++K++
Sbjct: 258 KVTLQELADEYGVSAERIRQIEANAMKKMR 287


>gi|239982221|ref|ZP_04704745.1| RNA polymerase sigma factor, sigH [Streptomyces albus J1074]
          Length = 287

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++   G   A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 47  FIELRTLPAGGPEYAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 105

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 106 RFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQRHGRS 165

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+KL +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 166 PTVHELAEKLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 225

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 226 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 276

Query: 665 RKLKH 669
            +L+ 
Sbjct: 277 AQLRE 281


>gi|115378280|ref|ZP_01465448.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|310821082|ref|YP_003953440.1| RNA polymerase sigma-b factor [Stigmatella aurantiaca DW4/3-1]
 gi|401024|sp|Q01624|RPSB_STIAD RecName: Full=RNA polymerase sigma-B factor
 gi|46680|emb|CAA78693.1| sigma factor (SigB) [Stigmatella aurantiaca DW4/3-1]
 gi|115364722|gb|EAU63789.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|309394154|gb|ADO71613.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
          Length = 296

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 73/264 (27%), Positives = 125/264 (47%), Gaps = 14/264 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I+    +S+ E +   ++ RK       A   +V +NLR V+ V+ +Y + G+
Sbjct: 14  LTMYLSEINQYGLLSVEEEQ---ALARKFVKGDLAAGHRLVTSNLRFVVKVSYEYRSYGI 70

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           +  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  I   I      +++      R
Sbjct: 71  KMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQR 130

Query: 527 DKIHKVVRTARRMSNKI---KREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGD 582
                + RT R +             +EIA KL +    VR++  ++    +SL+ P+G+
Sbjct: 131 KLFFSLARTRRELEKFGAGDGAVVNVDEIANKLNVKASEVREMEQRMGGRDLSLDAPMGE 190

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   DF+    A    + A +     +       L  L PRE  ++     +     
Sbjct: 191 DGGNSHVDFVASAAAPQDDEFADKEEAGLINSRVHMALMRLDPRERFIIEQ--RVMNERP 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKA 663
            TL+E+G+ F  +RER RQ+E +A
Sbjct: 249 MTLKELGEHFGFSRERARQLEIRA 272



 Score = 37.5 bits (85), Expect = 6.8,   Method: Composition-based stats.
 Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 3/84 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL E+    LLS E E A+A++   G       L  S L F  ++    E       + 
Sbjct: 16  MYLSEINQYGLLSVEEEQALARKFVKGDLAAGHRLVTSNLRF--VVKVSYEYRSYGIKMS 73

Query: 183 EIIDLEACIGPESKGGFFHGTEGH 206
           ++I  E  IG       F   +G 
Sbjct: 74  DLIQ-EGNIGLMKAVQKFDPDKGI 96


>gi|319945291|ref|ZP_08019553.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
 gi|319741861|gb|EFV94286.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
          Length = 298

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 132/278 (47%), Gaps = 10/278 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           VA  V S+  +   I +++    +S  E   +    +  E +   A + +V ++LRLV+S
Sbjct: 16  VAPAVPSLGNLDAYISAVNRMPMLSAEEESSLARRFK--EHQDVDAARTLVTSHLRLVVS 73

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VA++Y   GL   DLIQEGNIGLMKA ++FD     +  ++A+ W+K  I   I      
Sbjct: 74  VARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDRSVRLVSFALHWIKAEIHEYILKNWRL 133

Query: 519 IRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           +++     + K+   +R+ ++  + +  E   +   +      +      ++T   I+LE
Sbjct: 134 VKVATTKAQRKLFFNLRSMKKDLDTLTPEAVTDIAEQLNVREKDVTEMETRMTGHEIALE 193

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRF 632
               DE+ +  G         S     I+   R+          LA+L  R   +++ R+
Sbjct: 194 PQGDDEEGAGFGPAAYLAAPGSEPTEIIEDRQRDWLQTEGLSNALATLDERSRNIVQSRW 253

Query: 633 GIGMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +     TL+++  ++ V+ ERIRQIEA+A++K+K
Sbjct: 254 LRDEDEGGSRTLQDLANEYGVSAERIRQIEAQAMKKMK 291


>gi|23429437|gb|AAM94466.1| RNA polymerase sigma factor D [Aeromonas hydrophila]
          Length = 270

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 117/315 (37%), Gaps = 46/315 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                     +  +       S+  E D   E E + E     S DD       PE A  
Sbjct: 59  NE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVARE 111

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 112 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 136

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 137 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 196

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 197 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 255

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 256 RMSIGEAKARRAKKE 270


>gi|332142899|ref|YP_004428637.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|332143056|ref|YP_004428794.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552921|gb|AEA99639.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327553078|gb|AEA99796.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 284

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 66/281 (23%), Positives = 136/281 (48%), Gaps = 14/281 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  V     I   I+++S    +S  E R +   +R+ E     A +++V ++LR V+ 
Sbjct: 8   MALSVPHSGSIEGYIQAVSSIDMLSAEEERELAVRLREDE--DLQAARKLVMSHLRFVVH 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      
Sbjct: 66  IAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRI 125

Query: 519 IRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPIS 575
           +++      R     + +  +R+      E     +A +L +  + V +   +++ +  +
Sbjct: 126 VKVATTKAQRKLFFNLRKAKKRLGWFTHDEVQT--VANELGVSTKEVLQMEARMSSQDQA 183

Query: 576 LETPIGDEDTSHLG--DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +    +++T +     F+EDK++      +++       +     + +L  R + ++  
Sbjct: 184 FDLSADEDETGNFAPVQFLEDKSSDVETDVINNDWDTAASKRLYSAIKTLDDRSQDIIET 243

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           R+        TL+++  ++ V+ ER+RQIE  A++KL+   
Sbjct: 244 RWLADN--KITLQDLADKYQVSAERVRQIEKNAMKKLQAAM 282


>gi|226484293|emb|CAQ03751.1| RNA polymerase sigma factor [Enterovibrio nigricans]
          Length = 265

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 56/313 (17%), Positives = 109/313 (34%), Gaps = 49/313 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  GF   ++            E   + +++ + +     +   D    V   PE 
Sbjct: 56  ------SGFVDPSQDDIAPTATHIGFELTEEQLKDED-NDGDDDEDDDDSEEDVGIDPEL 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L    +     ++                                   K+ + 
Sbjct: 109 AREKFSELRLSYEGMQAAIN-----------------------------------KNGRF 133

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
                    +L ++     L   + D LV ++     R+   E  ++RL      + +  
Sbjct: 134 HDDTHAAIAELSEVFKQFRLVPKQFDRLVNEMRGTMDRVRTQERIVMRLCVDQAKMPKKT 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E   +W+  A    E  + + +    + + +   ++K +  ETG+++   + 
Sbjct: 194 FVQLFGGNESSDNWLDAALA-TEKPFVDRLKLYEEDLRRCVQKLKIVEDETGLNVERIKD 252

Query: 430 IVSMVRKGECEAS 442
           I   +  GE +A 
Sbjct: 253 ISRRMSIGEAKAR 265


>gi|117618742|ref|YP_854903.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560149|gb|ABK37097.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 284

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 115/239 (48%), Gaps = 7/239 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G +  ++A
Sbjct: 47  DLEAARQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPSVGVRLVSFA 106

Query: 501 MWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           + W+K  I   +      +++     + K+   +R +++    +  E      A      
Sbjct: 107 VHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWLNHEEVQAVAADLGVSA 166

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTT 614
            +      +++    + +    DE+        ++EDK+   A +  +     +     +
Sbjct: 167 ADVTEMEARMSNYDQAFDLVGDDEEEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLS 226

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             LA+L  R + ++R R+ +   +  TL+E+   + V+ ER+RQ+E  A++KLK    +
Sbjct: 227 SALATLDERSQHIIRARW-LDDESKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|116254340|ref|YP_770178.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258988|emb|CAK10097.1| putative rpoH sigma factor [Rhizobium leguminosarum bv. viciae
           3841]
          Length = 304

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 135/287 (47%), Gaps = 15/287 (5%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F   E+ ++   R  IK       ++  E   + +  R  + +   A+ ++  A++RLVI
Sbjct: 13  FREIEMKNMSADRRMIKIAMAAPYLARQEEHDLAT--RWKDHDDRGARNQIAMAHMRLVI 70

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I     
Sbjct: 71  SMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWS 130

Query: 518 TIRIPVHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITK 571
            +R       K     + R   +++    ++  +   +EIA  L + +  V+    +++ 
Sbjct: 131 IVRGGTSSAQKALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLSDVQTMDARLSG 190

Query: 572 EPISLETPIGDED--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREER 626
              SL+ P    D  ++   DF+  +D      + + I    R       L  L  RE +
Sbjct: 191 NDASLQAPSVSGDAESAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMK 250

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           ++  R         TLEE+G    +++ER+RQIE++A+ KL+    S
Sbjct: 251 IISARRLAEDG--ATLEELGADLGISKERVRQIESRAMEKLRSALVS 295


>gi|311277614|ref|YP_003939845.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
 gi|308746809|gb|ADO46561.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
          Length = 285

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 134/270 (49%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K+++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKL--HYQGDLEAAKKLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    D+  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDLGPDDDAQ 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  + 
Sbjct: 192 DGQPMAPVLYLQDKSSNFADGIEDDNWEEQAANKLTDAMQGLDERSQDIIRARW-LDEDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADRYGVSAERVRQLEKNAMKKLR 280


>gi|148380489|ref|YP_001255030.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933176|ref|YP_001384712.1| sporulation sigma factor SigG [Clostridium botulinum A str. ATCC
           19397]
 gi|153936833|ref|YP_001388233.1| sporulation sigma factor SigG [Clostridium botulinum A str. Hall]
 gi|153938804|ref|YP_001391829.1| sporulation sigma factor SigG [Clostridium botulinum F str.
           Langeland]
 gi|148289973|emb|CAL84086.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929220|gb|ABS34720.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152932747|gb|ABS38246.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. Hall]
 gi|152934700|gb|ABS40198.1| RNA polymerase sigma-G factor [Clostridium botulinum F str.
           Langeland]
 gi|295319855|gb|ADG00233.1| RNA polymerase sigma-G factor [Clostridium botulinum F str. 230613]
 gi|322806802|emb|CBZ04371.1| RNA polymerase sporulation specific sigma factor SigG [Clostridium
           botulinum H04402 065]
          Length = 257

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 75/265 (28%), Positives = 134/265 (50%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ +     +  ++E ++ NLRLV+SV K++ NRG
Sbjct: 2   VINKVEICGVNTSKLPVLKDKEMKKLLVRIRNGETECREEFIQGNLRLVLSVIKRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++     +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALQARDKLIKNNNKEPTVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             + D I D KN        I      +    +  L  RE+ +L +RF  G     T  E
Sbjct: 181 IFVMDQISDTKNIDENWIENI------SIKEAMKKLNDREKLILNLRFFDG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|53724102|ref|YP_104622.1| RNA polymerase factor sigma-32 [Burkholderia mallei ATCC 23344]
 gi|121598782|ref|YP_991458.1| RNA polymerase factor sigma-32 [Burkholderia mallei SAVP1]
 gi|124383719|ref|YP_001027464.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10229]
 gi|126449925|ref|YP_001082430.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10247]
 gi|167001066|ref|ZP_02266867.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
 gi|238561338|ref|ZP_00442201.2| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|254175044|ref|ZP_04881705.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|254201710|ref|ZP_04908074.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|254207043|ref|ZP_04913394.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|254357524|ref|ZP_04973798.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|52427525|gb|AAU48118.1| RNA polymerase sigma-32 factor [Burkholderia mallei ATCC 23344]
 gi|121227592|gb|ABM50110.1| alternative sigma factor RpoH [Burkholderia mallei SAVP1]
 gi|124291739|gb|ABN01008.1| RNA polymerase sigma-32 factor [Burkholderia mallei NCTC 10229]
 gi|126242795|gb|ABO05888.1| alternative sigma factor RpoH [Burkholderia mallei NCTC 10247]
 gi|147747604|gb|EDK54680.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|147752585|gb|EDK59651.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|148026588|gb|EDK84673.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|160696089|gb|EDP86059.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|238524810|gb|EEP88241.1| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|243063136|gb|EES45322.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
          Length = 311

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 134/269 (49%), Gaps = 12/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++++    +S  E R   +  R+       A + +V ++LRLV+SVA+ Y   GL
Sbjct: 39  IDAYIQAVNRIPLLSAEEERQYATEYREQNNLD--AARRLVLSHLRLVVSVARNYLGYGL 96

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++      +
Sbjct: 97  PHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQR 156

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDTSH 587
                  + +   +       + +A++L +  E V ++    +   I+LE  I D + S+
Sbjct: 157 KLFFNLRSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDDGEESY 216

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNTD---- 639
             +    +  N  + + +A Q ++ +T    R L SL  R  R++  R+ + ++ D    
Sbjct: 217 APIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARW-LNVDDDGSGG 275

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 276 STLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|11078985|dbj|BAB17497.1| DNA-directed RNA polymerase subunit D [Pseudomonas syringae]
          Length = 268

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 115/315 (36%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L +++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G +         + +    +  + + E+A     ++  +    P  
Sbjct: 56  ------SGYIDPDDGIAPPAEVPPPVDPKAAKAEGDDEEEETAEATDDEEEVESGPDPVI 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     + +  + +   L                                   +K  + 
Sbjct: 110 AQQRFGAVSDQMEITRKAL-----------------------------------KKFGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 135 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +A     I + + ++ ++  ETG+ I+E + 
Sbjct: 195 FLRQFPGHEVDESWTD-ALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|84393530|ref|ZP_00992284.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84375809|gb|EAP92702.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 291

 Score =  134 bits (336), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 137/278 (49%), Gaps = 17/278 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S +    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSANSYPMLTPEEERGLAERLHYKGEID--AAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + ++ +R+      E   E +A++L +    VR++  ++  +  + E P+ D+D 
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDATFEAPMDDDDG 191

Query: 586 SH----LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++EDK    A +   +  +++        L SL  R + ++R R+     +
Sbjct: 192 GSAYTAPVYYLEDKASDVAETVEAANWESHTNNRLGLALKSLDERSQHIVRSRWLDDNKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TL+++   + ++ ER+RQ+E  A++KLK  SR + L
Sbjct: 252 --TLQDLADTYSISAERVRQLEKNAMKKLK-ASRWRFL 286


>gi|302542626|ref|ZP_07294968.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302460244|gb|EFL23337.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 351

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 112/226 (49%), Gaps = 11/226 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 128 RNNLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTV 187

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S +  R PT  E+A+ LA+  E V 
Sbjct: 188 VGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQRHGRAPTVHELAEHLAISEEEVL 247

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L+       +SL+ P  D+++  + D +  ++             RE+   +L  L P
Sbjct: 248 EGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY-----RESLKPLLEDLPP 302

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+++L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 303 REKKILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 344


>gi|327191758|gb|EGE58760.1| RNA polymerase factor sigma-32 [Rhizobium etli CNPAF512]
          Length = 319

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 135/287 (47%), Gaps = 15/287 (5%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F   E+ ++   R  IK       ++  E   + +  R  + +   A+ ++  A++RLVI
Sbjct: 28  FREIEMKNMSADRRMIKIAMAAPYLARQEEHDLAT--RWKDHDDRGARNQIAMAHMRLVI 85

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I     
Sbjct: 86  SMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWS 145

Query: 518 TIRIPVHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITK 571
            +R       K     + R   +++    ++  +   +EIA  L + +  V+    +++ 
Sbjct: 146 IVRGGTSSAQKALFFNLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSG 205

Query: 572 EPISLETPIGDED--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREER 626
              SL+ P    D  ++   DF+  +D      + + I    R       L  L  RE +
Sbjct: 206 NDASLQAPSVSGDAESAEKMDFLVSDDPLPDEQVSNMIDGERRRIWLASALKHLNEREMK 265

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           ++  R         TLEE+G    +++ER+RQIE++A+ KL+    S
Sbjct: 266 IISARRLAEDG--ATLEELGADLGISKERVRQIESRAMEKLRTALVS 310


>gi|292489953|ref|YP_003532845.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|292900984|ref|YP_003540353.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291200832|emb|CBJ47966.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291555392|emb|CBA23800.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|312174141|emb|CBX82394.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC BAA-2158]
          Length = 284

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    ++  E + +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRAANAWPMLTAEEEKALAERL--HYQGDLEAAKTLILSHLRFVVHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R+    + E   E +A++L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKAKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDPTPDDEGE 191

Query: 586 S-HLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
              +   +  ++  S   + I+ +  E       +  +  L  R + ++R R+ +  +  
Sbjct: 192 GRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLSDAMQGLDERSQHIIRARW-LDDDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 TTLQELADQYGVSAERVRQLEKNAMKKLR 279


>gi|146329254|ref|YP_001209773.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
 gi|146232724|gb|ABQ13702.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
          Length = 297

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 58/270 (21%), Positives = 126/270 (46%), Gaps = 9/270 (3%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I   I  +     +   E   + + +++    A  A + ++  +L+ V+ +A+ +   G
Sbjct: 26  DIDQYIAKVRQIPILDADEEFRLATELQQNHSLA--AAQTLIVHHLKFVVHIARGFLGYG 83

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   +      ++I      
Sbjct: 84  LPLGDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYVIRNWRLVKIATTKAQ 143

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDEDTS 586
           +       + + +     +   + IA+ L + V+ V ++      + I+ +    ++D  
Sbjct: 144 RKLFFNLRSMKKNMHWLSDAEAQTIAEDLNVSVKDVLEMESRIHGQDIAFDPLDENDDEE 203

Query: 587 HLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++    ++ D++   A+S      +  L+   T+ L  L  R   ++  R+ +  +   T
Sbjct: 204 NVAPAAWLTDESVDPALSTEHHEQKHLLQHQLTQGLNQLDARSREIIESRW-LNEHEKVT 262

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L+ +  ++ ++ ERIRQIE +A+ +LK+  
Sbjct: 263 LQTLASKYHISAERIRQIEQQALLQLKNSM 292


>gi|325579283|ref|ZP_08149239.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159518|gb|EGC71652.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 293

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 133/267 (49%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +         A K++V ++LR VI VA+ Y+  GL
Sbjct: 28  IEAYIRAANEYPMLTAEEEKSLAERL--YYDGDIEAAKKLVLSHLRFVIHVARGYSGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 86  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 145

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  ++T   +  + P  D+D 
Sbjct: 146 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMTGADVGFDLPTDDDDE 203

Query: 586 SHLGD-FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +++   ++EDK+   A        +    E     LA+L  R + +++ R+        T
Sbjct: 204 AYVPSLYLEDKSSNFAAELESENFEEQATEKLGTALANLDERSQDIIKARWLDD--EKAT 261

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  ++ V+ ERIRQ+EA A++KLK
Sbjct: 262 LHDLAAKYNVSAERIRQLEANALKKLK 288


>gi|255553456|ref|XP_002517769.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223543041|gb|EEF44576.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 389

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 129/253 (50%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V++  +   E +     +       R     V K  C+   +++ +     RLV+S+A +
Sbjct: 135 VEAARRRIAETQEHEPTSKQLAEALRMRKKNVDKILCKGRQSRERITGNYRRLVLSIANR 194

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y  +GL   DLIQEG+IGL++ AE+FD   G K STY  WW+K+AI  SI+  S  +R P
Sbjct: 195 YRGKGLSLQDLIQEGSIGLLRGAERFDPKRGNKLSTYVYWWIKEAIITSISINSRIVRQP 254

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             + D+  K+      ++ ++ R P+  EIAK+L + V  VR V   ++  +SL+  + D
Sbjct: 255 RSLWDRTTKIAEAKISLTERLGRLPSYREIAKELNVHVSTVRLVFSRSRSTVSLDQAVSD 314

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +    L + I     + P +   +  L++    ++ +L  RE   LR+ FG+   T  + 
Sbjct: 315 QGGMTLQEIIPGPEEMMPENMVKKQLLKKELEELIQTLGKREAHTLRLIFGLNGQTPQSC 374

Query: 643 EEVGKQFCVTRER 655
           +E+G+   + RER
Sbjct: 375 DEIGRSLKLCRER 387


>gi|11078957|dbj|BAB17483.1| DNA-directed RNA polymerase subunit D [Pseudomonas savastanoi]
          Length = 271

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 114/315 (36%), Gaps = 45/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T   ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+       G    +        +  + +   + E +   A+    +D  +    P  
Sbjct: 59  IDPD------DGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEDEVESGPDPVI 112

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     + +  + +   L                                   +K  + 
Sbjct: 113 AQQRFGAVSDQMEITRKAL-----------------------------------KKFGRD 137

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
                     L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 138 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 197

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I + + ++ ++  ETG+ I+E + 
Sbjct: 198 FLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKD 256

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 257 INRRMSIGEAKARRA 271


>gi|215270893|emb|CAR48124.1| RNA polymerase sigma factor [Vibrio alginolyticus]
 gi|215270895|emb|CAR48125.1| RNA polymerase sigma factor [Vibrio alginolyticus]
 gi|215270897|emb|CAR48126.1| RNA polymerase sigma factor [Vibrio alginolyticus]
 gi|215270899|emb|CAR48127.1| RNA polymerase sigma factor [Vibrio alginolyticus]
          Length = 271

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 55/313 (17%), Positives = 109/313 (34%), Gaps = 43/313 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   ++ E  D  E   D    ++       ++        
Sbjct: 61  ADDTAAPTATHIGSELTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +   +S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEYGYNSP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F+
Sbjct: 140 KATVANEMMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET +++   + I 
Sbjct: 200 ALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDIS 258

Query: 432 SMVRKGECEASIA 444
             +  GE +A  A
Sbjct: 259 RRMSIGEAKARRA 271


>gi|182438259|ref|YP_001825978.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326778910|ref|ZP_08238175.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178466775|dbj|BAG21295.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326659243|gb|EGE44089.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 323

 Score =  134 bits (336), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 57/246 (23%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D++Q G IGL+KA +
Sbjct: 81  LFERLECLEEGTHEYSYVRNTLVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAID 140

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    +S ++ R 
Sbjct: 141 RFELSRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQQLDRA 200

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E++++L +  E V + +         SL+    ++D    L D I  ++       
Sbjct: 201 PTVAELSERLGISPEEVVEGMSASNAYTASSLDAKPEEDDGEGALADRIGYEDHSLEGIE 260

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A+L  R+  +L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 261 YV-----ESLKPLIAALPARDRMILSLRFVSN----MTQSEIGEELNISQMHVSRLLSRT 311

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 312 LTKLRK 317


>gi|11079127|dbj|BAB17568.1| DNA-directed RNA polymerase subunit D [Pseudomonas
           pseudoalcaligenes]
 gi|11079133|dbj|BAB17571.1| DNA-directed RNA polymerase subunit D [Pseudomonas oleovorans]
 gi|11079135|dbj|BAB17572.1| DNA-directed RNA polymerase subunit D [Pseudomonas
           pseudoalcaligenes]
          Length = 268

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 113/315 (35%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T   ++     +      L EI+     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEIL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G    +       KE    + ++ + E  +   +++       PE 
Sbjct: 56  ------SGYIDPDDGSVPDEAAAPVPVKEGAAAEASDEEEEDESGDDEEEEGDGGPDPEE 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  + 
Sbjct: 110 AARRFTAVAEQLEKARKAL-----------------------------------KKHGRG 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++ D   R+   E  +++L      + R  
Sbjct: 135 SKQAIEELATLAELFMPIKLVPKQYDALVTKVRDALDRLRAQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    G E+D  W +      + ++   +      I + + ++  +  E  ++++E + 
Sbjct: 195 FLRLFPGNEIDMDWAANLAK-GKAKYAEAIGALQADIQRCQQKLADLEAECNLTLAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|258511274|ref|YP_003184708.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478000|gb|ACV58319.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 259

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 134/264 (50%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V T     ++ ++ R +   +R        A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVNTSQLPVLTNAQMRELFEQLR---AGDPSAREKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    +++K  REP+  EIA ++ +P E V   L   ++P+S+  PI  +  
Sbjct: 119 RDIAYKALQVRDMLASKNLREPSIVEIANEMNLPKEEVVFALDAIQDPVSMFEPIYHDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L+ RE+++L  RF  G     T  
Sbjct: 179 DPIYVMDQIHDEREKDSAWVEGIA-----LREAMRKLSDREKKILAKRFYEG----KTQM 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV  +  +++ ++ ++E  AI ++
Sbjct: 230 EVADEIGISQAQVSRLEKAAIHRM 253


>gi|311826285|emb|CBX60050.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 271

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 56/313 (17%), Positives = 112/313 (35%), Gaps = 43/313 (13%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I    
Sbjct: 1   TVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFV 60

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               +          G    + +   +++E  D  E   D    ++       ++     
Sbjct: 61  DPDADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL----- 115

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
                                          +   +++   Y+ L+      +   +   
Sbjct: 116 ------------------------------ALEKFNQLRSTYQNLQ------LAINEHGY 139

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRD 368
            S K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + + 
Sbjct: 140 ESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKK 199

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E    W+       +  +   +    + I +   ++K I  ET +++   +
Sbjct: 200 SFIALFTGNESSEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIK 258

Query: 429 HIVSMVRKGECEA 441
            I   +  GE +A
Sbjct: 259 DISRRMSIGEAKA 271


>gi|258404985|ref|YP_003197727.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
 gi|257797212|gb|ACV68149.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
          Length = 350

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 141/273 (51%), Gaps = 12/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ ++    +   E   +   VR  +     A   ++ ++LRLV+ +A ++  R +
Sbjct: 71  LKLYLREVNRFPLLEPDEEVELARRVR--DENDQSAAFRLISSHLRLVVKIAMEFQRRWM 128

Query: 469 -QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--M 525
              LDL+QEGN+GLMKA +KFD   G KFS YA +W++  I + I D    +++      
Sbjct: 129 KNVLDLVQEGNVGLMKAVQKFDPERGIKFSYYASFWIRAYILKFIMDNWRMVKLGTTQAQ 188

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDED 584
           R   + + R  +R+      +P    +++ L +  E V ++  ++    +SL+ P+G++ 
Sbjct: 189 RKLFYNLSREKQRL-QAQGFDPDASTLSENLDVSEESVVEMTQRLGGHDLSLDAPLGEDS 247

Query: 585 TSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +S   DF+    A      A Q     LR+    +L  L  +E+ +L     +  ++  T
Sbjct: 248 SSSRMDFLPALGAGIEESLAQQEMGSALRQHLQTILPKLNDKEKEILEH--RLLTDSPVT 305

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L E+G+++ +TRER+RQIE++ ++KLK    S+
Sbjct: 306 LREIGEKYGITRERVRQIESRLLQKLKTHLSSE 338



 Score = 44.8 bits (104), Expect = 0.051,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK-----RKDSADRSTDD 119
           +++    +  I + + +  E  + S      A S    +   +      +  S D +  D
Sbjct: 10  NSMEHEHDHDIELDEPEAGETLDDSTAEEASAESLPAPAAVTEHLPSLIQPSSNDVAIQD 69

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152
           P+++YLRE+    LL  + E+ +A+R+      
Sbjct: 70  PLKLYLREVNRFPLLEPDEEVELARRVRDENDQ 102


>gi|4514507|dbj|BAA75452.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
 gi|4514509|dbj|BAA75453.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 279

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 63/316 (19%), Positives = 117/316 (37%), Gaps = 38/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    +   G   L ++  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADL--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PES        E  +    +++  +K   DV+  + + E  A    +  +     PE 
Sbjct: 59  LDPESDEEIPEVLEEEAVLAEDETDSKKSTKDVKLDDDEEEEEADSDDESEADSGPDPEI 118

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+    ++  T+                                    K  + 
Sbjct: 119 AKARFTELENAWLNTKATIE-----------------------------------KHGRD 143

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S + +   + L  +           D++ E +     +I   E E++R A   G + R  
Sbjct: 144 SKQAEEALQALATVFMMFKFTPRLFDIISEMIRGTHDQIRGAEREVMRYAVRRGRMDRTQ 203

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F     G+E +P W+         + K ++      +L  + +I  I  E G+ +   + 
Sbjct: 204 FRTSFPGQESNPAWLDEQIAKTPADQKAYLEKVRPDVLAFQQKIADIEKELGLDVKGIKD 263

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 264 IAKRMAVGEAKARRAK 279


>gi|223635903|emb|CAQ03753.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635905|emb|CAQ03754.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635907|emb|CAQ03755.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635909|emb|CAQ03756.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635911|emb|CAQ03757.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635913|emb|CAQ03758.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|223635915|emb|CAQ03759.1| RNA polymerase sigma factor [Enterovibrio coralii]
 gi|226484295|emb|CAQ03752.1| RNA polymerase sigma factor [Enterovibrio coralii]
          Length = 267

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 56/314 (17%), Positives = 110/314 (35%), Gaps = 49/314 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS-PPE 249
                  GF   ++            E   + + + + D +  +    D   +     PE
Sbjct: 56  ------SGFVDPSQEDIAPTATHIGSELTEEQLDDEDDDGDDDSDDDDDSSEEDAGIDPE 109

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A      L +  +     ++                                   K  +
Sbjct: 110 LAREKFTELRQSYEVMQAAIN-----------------------------------KHGR 134

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRD 368
                     +L ++     L   + D LV ++ +   R+   E  ++RL      + + 
Sbjct: 135 FHDDTHTAIAELSEVFKQFRLVPKQFDRLVNEMRETMDRVRTQERIVMRLCVDQAKMPKK 194

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F++   G E   +W+  A    E  + + +    + + +   ++K +  ETG+++   +
Sbjct: 195 TFVQLFSGNESSDNWLDAALA-TEKPYVDRLKQYEEDLRRCIQKLKIVEDETGLNVERIK 253

Query: 429 HIVSMVRKGECEAS 442
            I   +  GE +A 
Sbjct: 254 DISRRMSIGEAKAR 267


>gi|291439213|ref|ZP_06578603.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342108|gb|EFE69064.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 304

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 120/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 62  LFERLEALEEGTLEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 121

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 122 RFEMSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRA 181

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 182 PTVAELAERLGITNDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGIE 241

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I     E+   ++A L PR+ ++L +RF  G     T  E+G++  +++  + ++ ++ 
Sbjct: 242 YI-----ESLKPLIAELPPRDRKILSLRFVAG----MTQSEIGEELGISQMHVSRLLSRT 292

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 293 LVKLRR 298


>gi|330831381|ref|YP_004394333.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806517|gb|AEB51716.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 284

 Score =  133 bits (335), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 115/239 (48%), Gaps = 7/239 (2%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A +++V ++LR V+ VAK Y   GL   DL+QEGNIGLMKA ++FD  +G +  ++A
Sbjct: 47  DLEAARQLVMSHLRFVVHVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFA 106

Query: 501 MWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           + W+K  I   +      +++     + K+   +R +++    +  E      A      
Sbjct: 107 VHWIKAEIHEYVLRNWRMVKVATTKAQRKLFFNLRKSKKRLGWLNHEEVQAVAADLGVSA 166

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKN---AVSPLDSAIQANLRETTT 614
            +      ++     + +    DE+        ++EDK+   A +  +     +     +
Sbjct: 167 ADVTEMEARMANYDQAFDLVGDDEEEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLS 226

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             LA+L  R + ++R R+ +  ++  TL+E+   + V+ ER+RQ+E  A++KLK    +
Sbjct: 227 SALATLDERSQHIIRARW-LDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254040288|gb|ACT57084.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 302

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 124/276 (44%), Gaps = 14/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I  I     +   E   +    R  E     A   +V ++LRLV+ +A  Y   GL
Sbjct: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGNIGLM+A +KFD   G++ +TY+MWW+K A+   I      ++I    + +
Sbjct: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + R    +         PE+   IAKKL +    V  +        SL   I   
Sbjct: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193

Query: 584 D--TSHLGDFIE---DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D  +S   D++    D      ++   + N R   TR ++ L PRE R+   R       
Sbjct: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             TLE +  +F V+RER+RQIEA+A +K++   + +
Sbjct: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287


>gi|167751709|ref|ZP_02423836.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|167655517|gb|EDR99646.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|291558002|emb|CBL35119.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum
           V10Sc8a]
          Length = 261

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 76/263 (28%), Positives = 133/263 (50%), Gaps = 14/263 (5%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++R+       A+++++  NLRLV+SV ++++ RG  
Sbjct: 9   NKVEISGVNTAKLKVLKESEKTELLRQMRSGDPTAREKLINGNLRLVLSVIQRFSGRGEN 68

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGLMKA + F      +FSTYA+  +   + R + D    IR+   MRD  
Sbjct: 69  PDDLFQVGCIGLMKAIDNFSTDFNVRFSTYAVPMIMGELRRYLRDSGS-IRVSRSMRDLA 127

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   +++N   +EPT E+IAK++    E V   L+   +PISL  P+  E  DT +
Sbjct: 128 YKAMQAREKLTNDNSKEPTIEQIAKEIDAKREDVVIALEAVSDPISLYEPVFSESGDTIY 187

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I D N        I           +  L  RE+ +L++RF  G     T  EV +
Sbjct: 188 MMDQIGDNNDDRNWLDEI------ALKEAIIGLDDREKNILKLRFFRG----KTQVEVAQ 237

Query: 648 QFCVTRERIRQIEAKAIRKLKHP 670
           +  +++ ++ ++E  A+ K+K  
Sbjct: 238 EIGISQAQVSRLEKGALGKIKKA 260


>gi|320539367|ref|ZP_08039036.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
 gi|320030492|gb|EFW12502.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
          Length = 285

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 67/270 (24%), Positives = 132/270 (48%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K+++ A+LR V  +A+ Y+  GL
Sbjct: 16  LEAYIRAANTYPMLTAEEERDLAERL--HYQGDLGAAKQLILAHLRFVAHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPAPDDETR 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   L   +  ++  S     I+ +  E+         L  L  R + ++R R+ +  + 
Sbjct: 192 DGQSLAPVLYLQDKSSDFAEDIEEDNWESNAADKLAYALEGLDERSQHIIRARW-LDNDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KLK
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLK 280


>gi|23429439|gb|AAM94467.1| RNA polymerase sigma factor D [Aeromonas media]
          Length = 280

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 128/326 (39%), Gaps = 48/326 (14%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                         E DDV  T   I S           
Sbjct: 60  II--SGFIDPN------------------------EADDVAPTATHIGSELSEDDLADED 93

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAV 302
            D   +  E+ + + D+ +      ++                  E + ELR+  +   +
Sbjct: 94  EDEDEDEDEDGDSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRL 136

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-Q 361
           + QK+ ++    +    +L  +     L   + D LV  + ++ +R+   E  +++L  +
Sbjct: 137 SIQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVE 196

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              + +  F+      E +  W  Y K   +  W   +    + +L+   +++ I    G
Sbjct: 197 QAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRLVKMDEEVLRSIGKLQQIEE-AG 254

Query: 422 ISISEFRHIVSMVRKGECEASIAKKE 447
           +SI++ + I   +  GE +A  AKKE
Sbjct: 255 LSIAQIKDINRRMSIGEAKARRAKKE 280


>gi|33946401|gb|AAQ55816.1| truncated stationary phase specific sigma factor [Pseudomonas
           syringae]
          Length = 252

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 75/224 (33%), Positives = 127/224 (56%), Gaps = 4/224 (1%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E  P   + +K     +   ++     ++   +  +  I     +S +E  H   +    
Sbjct: 33  ESTPTARTKSKKATATKQHKYID-YTRALDATQLYLNEIGFSPLLSPAEEVHFARL---S 88

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +      +K M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FS
Sbjct: 89  QSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFS 148

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+PEEIA  L 
Sbjct: 149 TYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLE 208

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            PV  V+++L + +   S++  +G +    L D + D     P 
Sbjct: 209 KPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPC 252



 Score = 46.8 bits (109), Expect = 0.011,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 54/136 (39%), Gaps = 13/136 (9%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           L+   P  ++  E +      L + GI      D +     ++S   A + S  +   ++
Sbjct: 3   LSKEAPGFDIDDEVL------LMDSGI------DSDLMSEDDESTPTARTKSKKATATKQ 50

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            K        D  ++YL E+G   LLS   E+  A+  ++G       + ES L     I
Sbjct: 51  HKYIDYTRALDATQLYLNEIGFSPLLSPAEEVHFARLSQSGDPAGRKRMIESNLRLVVKI 110

Query: 169 IWRDELNDGTTLLREI 184
             R  +N G +LL  I
Sbjct: 111 ARRY-VNRGLSLLDLI 125


>gi|253991200|ref|YP_003042556.1| RNA polymerase factor sigma-32 [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782650|emb|CAQ85814.1| component of rna polymerase, sigma 32 factor [Photorhabdus
           asymbiotica]
          Length = 285

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E + +   +         A K+++ ++LR V+ VA+ Y   GL
Sbjct: 16  LEGYIRASNAYPMLTAEEEKELAERL--HYQGDLDAAKKLILSHLRFVVHVARSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
                + +T +R+    + E   E +AK+L +  + VR++   +        +     ++
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVAKELGVTSKDVREMESRMSAQDMAFDMSADDDNQ 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRFGIGMNT 638
           +   +   +  ++  S     I+ +  E       +  +  L  R + ++R R+ +  + 
Sbjct: 192 EGQSVAPVLYLQDKASDFAGGIEEDNWENHAADKLSVAIEGLDERSQDIIRCRW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|291613119|ref|YP_003523276.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
 gi|291583231|gb|ADE10889.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
          Length = 289

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 126/267 (47%), Gaps = 9/267 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +++++    +S  E   + +  +        A +++V ++LR+V+SVA+ Y   GL
Sbjct: 16  LESYVQAVNRFPVLSHEEELSLANRFK--AHNDLDAARQLVLSHLRVVVSVARGYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA +++D   G +  ++A+ W++  I   +      ++I      +
Sbjct: 74  PQADLIQEGNIGLMKAVKRYDATRGVRLVSFALHWIRAEIHEYVVRNWRLVKIATTKSQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV------LKITKEPISLETPIGD 582
                  + +   +  +     EIA++L +    V ++       ++  EP+S E     
Sbjct: 134 KLFFNLRSMKQGLEPLKPQQVREIAQQLNVSERDVVEMEARFAGHEVALEPLSGEEDESY 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHT 641
              S+L D  E + +     +  +        + LASL  R  R++  R+         T
Sbjct: 194 APISYLADNAEHEPSYILEAAEREHLHTAGLAQALASLDERSRRIVEARWLRDEEEHAAT 253

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  +F V+ ERIRQIE KA+ K++
Sbjct: 254 LHELADEFKVSAERIRQIEQKALSKMQ 280


>gi|37784470|gb|AAO13128.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     S DD       PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 114 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    KL  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAKLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKA-WSPRLLVMDEEVLRSIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|10129883|dbj|BAB13517.1| sigma factor [Sinorhizobium meliloti]
          Length = 301

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 122/279 (43%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLAK--RYQEHDDRKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K AI   I      +++    + +
Sbjct: 74  PIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+    + +  PE   EIA  L +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEKVVSMNRRLSGDASLNAPIKAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R      +  L  RE R+           
Sbjct: 194 EGDSGQWQDWLVDDHDNQEQILIEQDELESRRGLLANAMKVLNDRERRIFEA--RRLTEE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R   L 
Sbjct: 252 PITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALE 290


>gi|317486415|ref|ZP_07945242.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
 gi|316922325|gb|EFV43584.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
          Length = 403

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 77/265 (29%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ +S    +   E   +   V+K     S A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 127 YLREVSRFPMLKPDEEFDLARRVQKTG--DSDAAFRLVSSHLRLVVKIAMDFQRRWMQNV 184

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDLIQEGN+GLM+A  KFD   G KFS YA +W++  I + I D    ++I      R  
Sbjct: 185 LDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIRAYILKFIMDNWRMVKIGTTQAQRKL 244

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDEDTS- 586
            + + R  +++  +   +P    +A++L +  + + ++ +      +SL+  +GDE  S 
Sbjct: 245 FYNLNRERQKLIAE-GFDPDAATLAERLGVGEDQIVEMQQRLDASDMSLDATVGDESGSA 303

Query: 587 HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              DF+         S     I   L+     +L SL+ +E  +L     +  +   TL 
Sbjct: 304 TRMDFLPALGPGIEESLAGMEIAELLQSKIRDILPSLSEKEAYILEH--RLLTDDPVTLR 361

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G+++ VTRER+RQ+EA+ ++KLK
Sbjct: 362 EIGERYNVTRERVRQLEARLLQKLK 386



 Score = 45.2 bits (105), Expect = 0.036,   Method: Composition-based stats.
 Identities = 22/107 (20%), Positives = 44/107 (41%), Gaps = 11/107 (10%)

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD----------SADRSTDDPVRMY 124
           ++V D +D + E+  +D  +   +A +    +    D           +  S+ D + +Y
Sbjct: 68  MDVTDAEDEDSEDIGDDLPEDDVAALDPDADILPEGDTLPAPSQQHLPSLSSSKDSLHLY 127

Query: 125 LREMGSIELLSREGEIAIAKRIE-AGRAMMMASLCESPLTFQALIIW 170
           LRE+    +L  + E  +A+R++  G +     L  S L     I  
Sbjct: 128 LREVSRFPMLKPDEEFDLARRVQKTGDSDAAFRLVSSHLRLVVKIAM 174


>gi|302558953|ref|ZP_07311295.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302476571|gb|EFL39664.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 282

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 125/247 (50%), Gaps = 14/247 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 38  FFRRLTVLEEGTHEYQYARNTLIEMNMSLVRYAAGRFRSRGPEEMEDIVQVGMIGLIKAI 97

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S ++ +P  +++   ++ R    + +++ R
Sbjct: 98  DRFELSREVEFTSFAIPYIVGEIKRFFRDTSWSVHVPRRLQEARVQLARATEELRSRLGR 157

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
            PT  E+A+ +++  E V +    +      SL+  I    +  S L DFI  ++A   L
Sbjct: 158 TPTVGELAQLMSLTEEEVNEARIASNGYNSASLDAAIGSEPDGESVLADFIGSEDAALEL 217

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  RE +++  RF      + T  E+G++   ++  + ++ +
Sbjct: 218 VEDFHA-----LAPMIADLDERERKIVHWRFV----EELTQAEIGQRLGCSQMHVSRLLS 268

Query: 662 KAIRKLK 668
           + +++L+
Sbjct: 269 RTLKRLR 275


>gi|213958522|gb|ACJ54682.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm5R]
          Length = 252

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 51/298 (17%), Positives = 103/298 (34%), Gaps = 47/298 (15%)

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
           EMG++ELL+ EGEI IA RIE G   +M ++   P T   ++     +      L +++ 
Sbjct: 1   EMGTVELLTLEGEIEIANRIEEGIREVMGAIAHFPGTVDPILSEYTRVTTEGGRLSDVL- 59

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                      G+    +G +    E       +    + + D E A   + D+      
Sbjct: 60  ----------SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESG 109

Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
           P             D+ +          +     +  L  +AE++               
Sbjct: 110 PDPVIAAQRFGAVSDQMEITRKALKKHGRGNKLAIAELVLLAELF--------------- 154

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
                                + L   + + LVE++     R+   E  +++L      +
Sbjct: 155 -------------------MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARM 195

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++
Sbjct: 196 PRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLT 252


>gi|163738663|ref|ZP_02146077.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|163742952|ref|ZP_02150335.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383635|gb|EDQ08021.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161387991|gb|EDQ12346.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 298

 Score =  133 bits (335), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 124/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + S +  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEEQDSASAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   R   +        + ++IA  L +   E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLHPDSVKKIATDLGVTETEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ +L  R      
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLASALEVLNDREKDILTQRRLAD-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QAKTLEDLSTQYGVSRERIRQIEVRAFEKLQKKMR 286


>gi|209965454|ref|YP_002298369.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958920|gb|ACI99556.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 307

 Score =  133 bits (335), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 69/277 (24%), Positives = 132/277 (47%), Gaps = 12/277 (4%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++   +SI  +R      +    +  +E + +       E +   A   +V +++RL +
Sbjct: 3   LMSVFSESIDVLRAYTAQANRHPMLDPAEEQMLAR--AWAERQDRKAFDRLVRSHMRLAV 60

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            +A KY   GL   DLI E NIGL+KA ++FD   G++ +TYA+WW++  +   +     
Sbjct: 61  KIASKYARSGLPMGDLISEANIGLVKAVQRFDPDRGFRLATYALWWIRAEVQTYVLHNWS 120

Query: 518 TIR--IPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            ++      ++     + +T RR+   ++I  +   + +A +L   V+ VR++      P
Sbjct: 121 MLKGGNTAALKRLFFNLRQTQRRLGIQDRIMSDEEADRVADELGASVDEVREMEHRFATP 180

Query: 574 I-SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLR 629
           + SL  P+G++      D + D+     +  A ++ L   +      L +L  RE  +  
Sbjct: 181 VTSLNVPVGEDGDHEALDLLADETETVEVRLAEKSELAVRKALMVDALGALGDRERHIFV 240

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            R     +   TLE + +Q+ V++ERIRQIE+ A +K
Sbjct: 241 SRNL--TDQPVTLETLAQQYGVSKERIRQIESGAYKK 275


>gi|239994826|ref|ZP_04715350.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 284

 Score =  133 bits (335), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 65/281 (23%), Positives = 136/281 (48%), Gaps = 14/281 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  V     I   I+++S    +S  E R +   +R+ E     A +++V ++LR V+ 
Sbjct: 8   MALSVPHSGSIEGYIQAVSSIDMLSAEEERELAVRLREDE--DLQAARKLVMSHLRFVVH 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      
Sbjct: 66  IAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRI 125

Query: 519 IRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPIS 575
           +++      R     + +  +R+      E     +A +L +  + V +   +++ +  +
Sbjct: 126 VKVATTKAQRKLFFNLRKAKKRLGWFTHDEVQT--VANELGVSTKEVLQMEARMSSQDQA 183

Query: 576 LETPIGDEDTSHLG--DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +    +++T +     ++EDK++      +++       +     + +L  R + ++  
Sbjct: 184 FDLTADEDETGNFAPVQYLEDKSSDVETDVINNDWDTAASKRLYSAIKTLDERSQDIIET 243

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           R+        TL+++  ++ V+ ER+RQIE  A++KL+   
Sbjct: 244 RWLADN--KITLQDLADKYQVSAERVRQIEKNAMKKLQAAM 282


>gi|55274967|gb|AAV49283.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score =  133 bits (335), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 79/194 (40%), Positives = 131/194 (67%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L+
Sbjct: 61  ERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 121 LNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 180

Query: 629 RMRFGIGMNTDHTL 642
             RFG+      TL
Sbjct: 181 ARRFGLLGYEAATL 194


>gi|66474735|gb|AAY46937.1| RpoD [Aeromonas popoffii]
          Length = 272

 Score =  133 bits (335), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S    +       D   +  ++
Sbjct: 59  N------------------------ETDDVAPTATHIGSELGEADLADEDEDEDEDEDDD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            E + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +     L  +     L   + D LV  +  + +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAVLADVFRQFRLMPKQFDRLVNNMRGMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKK+
Sbjct: 257 RRMSIGEAKARRAKKK 272


>gi|37784480|gb|AAO13133.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 274

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 117/315 (37%), Gaps = 42/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       ++   E    +   +D  E E + E     S DD       PE A   
Sbjct: 59  EAD---DVAPTATHIGSELGEDDLADEDEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 115

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 116 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 140

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 141 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 200

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 201 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 259

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 260 MSIGEAKARRAKKEM 274


>gi|89067929|ref|ZP_01155373.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046527|gb|EAR52583.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 297

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 72/271 (26%), Positives = 124/271 (45%), Gaps = 15/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + E + A  ++V ++LRL   +A  Y   GL
Sbjct: 15  LNRYLQEIRRFPMLEPEEEYMLAK--RWVDHEDTDAAHKLVTSHLRLAAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 132

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKLA----MPVEGVRKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE +A+          E +    +++    SL   IG 
Sbjct: 133 KLFFNLRKAKARIGALEEGDLRPENVAQIANDLGVTETEVISMNRRLSGGDASLNAMIGT 192

Query: 583 EDTS--HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E  S     D++ED++A    D   +  L   RE     +  L  RE+ +L        +
Sbjct: 193 EGDSATQWQDWLEDESADQAGDYEERDELSTRRELLGEAMDVLNDREKDILTQ--RRLQD 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TLEE+  Q+ V+RERIRQIE +A  KL+
Sbjct: 251 QAVTLEELSGQYGVSRERIRQIEVRAFDKLQ 281


>gi|2529267|gb|AAB81186.1| sigma factor [Paenibacillus polymyxa]
          Length = 251

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 63/254 (24%), Positives = 124/254 (48%), Gaps = 14/254 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T  S  E   +  ++   +   + A++ ++ +N+RLV SV +++ NRG +  DL Q 
Sbjct: 5   GKKTSHSYLEDTEVKRLIALSQSGDNDARETLINSNIRLVWSVVQRFMNRGYEPDDLFQI 64

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +  
Sbjct: 65  GCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKETANKVRKMK 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             +S  + R PT +E+A +L +  E V    +  K P S+   + + D     L D I D
Sbjct: 124 DELSKPLNRLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD 183

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++     D       +      +  L+ RE  ++     +    D T  EV  +  +++ 
Sbjct: 184 ESQERWFD-------KLALNEAIDGLSERERLIV----YLRYYRDQTQSEVASRLGISQV 232

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K +++++
Sbjct: 233 QVSRLEKKILQQIR 246


>gi|4514505|dbj|BAA75451.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 279

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 63/316 (19%), Positives = 117/316 (37%), Gaps = 38/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++    +   G   L ++  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADL--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PES        E  +    +++  +K   DV+  + + E  A    +  +     PE 
Sbjct: 59  LDPESDEEIPEVLEEEAVLAEDETDSKKSTKDVKLDDDEEEEEADSDDESEADSGPDPEI 118

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+    ++  T+                                    K  + 
Sbjct: 119 AKARFTELENAWLNTKTTIE-----------------------------------KHGRD 143

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S + +   + L  +           D++ E +     +I   E E++R A   G + R  
Sbjct: 144 SKQAEDALQALATVFMMFKFTPRLFDIISEMIRGTHDQIRGAEREVMRYAVRRGRMDRTQ 203

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F     G+E +P W+         + K ++      +L  + +I  I  E G+ +   + 
Sbjct: 204 FRSSFPGQESNPAWLDEQIAKTPADQKAYLEKVRPDVLAFQQKIADIEKELGLDVKGIKD 263

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 264 IAKRMAVGEAKARRAK 279


>gi|329936108|ref|ZP_08285907.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329304426|gb|EGG48305.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 310

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 116/241 (48%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  ++ G  E +  +  +V  +L LV  +A++Y NRG    DL Q   IGL+K+ ++FD 
Sbjct: 73  LRALKDGSPEYAELRNRLVRMHLPLVEHLARRYRNRGEPLDDLTQVATIGLIKSVDRFDP 132

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  
Sbjct: 133 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQQHGRSPTVH 192

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KLA+  E V + L+       +SL+ P  D+D   + D +    A           
Sbjct: 193 ELAEKLAISEEEVLEGLESANAYSTLSLDVPDTDDDAPAVADRLGADEAA-----LESVE 247

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R +   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + KL+
Sbjct: 248 YRASLRLLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAKLR 303

Query: 669 H 669
            
Sbjct: 304 E 304


>gi|23429455|gb|AAM94475.1| RNA polymerase sigma factor D [Aeromonas enteropelogenes]
          Length = 280

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 121/325 (37%), Gaps = 46/325 (14%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           Y RE G++ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +
Sbjct: 1   YERE-GTVELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSD 59

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     I P                         E +D+  T   I S           
Sbjct: 60  II--SGFIDPN------------------------EAEDMAPTATHIGSELGEDDLADED 93

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +   E+ + D  + D D             +LR +       I                
Sbjct: 94  EEDEDEDEDGDSSDDDGDGGPDPEVAREKFAELRAQYEVTRLSI---------------- 137

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QS 362
            QK+ ++    +     L  +     L   + D LV  + ++ +R+   E  +++L  + 
Sbjct: 138 -QKNGRAHDDTQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 196

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             + +  F+      E +  W  Y K   +      V  + + + +   +++ I  ETG+
Sbjct: 197 AKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVQRAIGKLQQIEEETGL 255

Query: 423 SISEFRHIVSMVRKGECEASIAKKE 447
           SI++ + I   +  GE +A  AKKE
Sbjct: 256 SIAQIKDINRRMSIGEAKALRAKKE 280


>gi|307328229|ref|ZP_07607407.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306886063|gb|EFN17071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 307

 Score =  133 bits (334), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 119/250 (47%), Gaps = 7/250 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   ++ + +G  E    +  ++E NL LV   A+++ NR ++  D++Q G IGL+KA +
Sbjct: 62  FLDRLTELEEGTHEYQYVRNTLIELNLSLVRYAARRFHNRSVEMEDIVQVGTIGLIKAID 121

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD     +F+T+A+ ++   I R   D S  + +P  +++    + +    +  ++ R 
Sbjct: 122 RFDLSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRIDLAKANEELFQRLDRS 181

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+ L +  + V   L  +   +  SL+ P   E  +       D+       + 
Sbjct: 182 PTTAELAEHLQLSEDEVVDGLVASNGYLTSSLDAPAEQESGATRVTTYADR-FGDVDPAM 240

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                      ++  L  R+ R+L++RFG     + T  E+G +  V++  + ++ ++A+
Sbjct: 241 EAVENLHALKPLVEELGERDRRILQLRFG----EEMTQSEIGAELGVSQMHVSRLLSRAL 296

Query: 665 RKLKHPSRSK 674
            +L+    ++
Sbjct: 297 SRLRRGMLAE 306


>gi|303248805|ref|ZP_07335056.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
 gi|302489817|gb|EFL49747.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
          Length = 344

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 136/278 (48%), Gaps = 13/278 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ I     +   E + +   VR  +     A   ++ ++LRLV+ +A  +  R +
Sbjct: 64  LQLYLREIGKFPMLKPEEEQELARRVR--DSGDEKAAFRLISSHLRLVVKIAMDFQRRWM 121

Query: 469 Q-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--M 525
           Q  LDLIQEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      
Sbjct: 122 QNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIGTTQAQ 181

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG-VRKVLKITKEPISLETPIGDED 584
           R   + + +   R+   +  +P+  ++++ L +     V    +++   +SL+  +G++ 
Sbjct: 182 RKLFYNLNKERNRL-QTLGFDPSASQLSEALNVTESDIVEMDQRLSGNDLSLDVSLGEDS 240

Query: 585 TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           TS   DF+               I   L +    +  SL  +E  +L     I  ++  T
Sbjct: 241 TSTRLDFLPALTPGIEEILAGDEISHQLEKHIQTIRPSLNEKELDLLD--NRILSDSPVT 298

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L E+G ++ +TRER+RQIEA+ + KLK    SK++  F
Sbjct: 299 LREIGAKYGITRERVRQIEARLLEKLKEHL-SKRIEDF 335



 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +  +  + +E+ +  A+   +  +   +   S   ST DP+++YLRE+G   +L  E E 
Sbjct: 24  EHNDAPDDAEEKVIDAAPVDDFRLPAPRAGSSGSLSTRDPLQLYLREIGKFPMLKPEEEQ 83

Query: 141 AIAKRI-EAGRAMMMASLCESPLTFQALIIW 170
            +A+R+ ++G       L  S L     I  
Sbjct: 84  ELARRVRDSGDEKAAFRLISSHLRLVVKIAM 114


>gi|148793346|gb|ABR12737.1| RNA polymerase sigma factor [Photobacterium kishitanii]
 gi|148793352|gb|ABR12740.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 262

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 57/303 (18%), Positives = 109/303 (35%), Gaps = 45/303 (14%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +II       
Sbjct: 1   LLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPN 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            E+         G    + +   ++K+ +D  + + + E     S D        PE A 
Sbjct: 61  EEATAAPTATHIGSELSETDLEDEDKDLEDDDDEDAENEEEDDGSID--------PELAR 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                L +  +  A  ++                                   +  +   
Sbjct: 113 EKFLELRQSYEKMALAIN-----------------------------------QHGRQHA 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
             +V  E+L ++     L   + D LV  L D   ++  NE  ++R+      + +  F+
Sbjct: 138 TTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFI 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E +  W+  A +  +  +   +    + + +   +++ +  ETG+SI   + I 
Sbjct: 198 SLFAGNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLSIERIKDIS 256

Query: 432 SMV 434
             +
Sbjct: 257 RRM 259


>gi|260774824|ref|ZP_05883726.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
 gi|260609249|gb|EEX35404.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
          Length = 285

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 133/270 (49%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRTVNGYPMLTAEEERGLAERLHYNGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        +      D+D S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDAAFEMQNDDDDS 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++EDK    A +   +  +A+     +  L+SL  R + ++R R+     +
Sbjct: 192 GVSYTAPMLYLEDKASDVADNVEAANWEAHTNNRLSLALSSLDERSQHIVRSRWLEDNKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 252 --TLQELAETYSVSAERIRQLEKNAMKKLK 279


>gi|239944189|ref|ZP_04696126.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 284

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +      +A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 44  FFELRELPDGSPEKAEL-RNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 102

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 103 RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRS 162

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L +  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 163 PTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVEY 222

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 223 -----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 273

Query: 665 RKLKH 669
            +L+ 
Sbjct: 274 AQLRE 278


>gi|295675387|ref|YP_003603911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
 gi|295435230|gb|ADG14400.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
          Length = 311

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 73/272 (26%), Positives = 131/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   + +R+ +     A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERKFATELREHDNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           E +AK+L +  E V ++    +   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKQGLGAFTPDEIEGLAKELNVKREEVAEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRF---GIGM 636
           + S+    ++ D ++      A +   R   +     L +L PR  R++  R+       
Sbjct: 213 EESYAPIAYLADSHSEPTAVLASRQRDRLQSDGIASALDALDPRSRRIIEARWLKVADDG 272

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|237747428|ref|ZP_04577908.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
 gi|229378779|gb|EEO28870.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
          Length = 299

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 76/271 (28%), Positives = 126/271 (46%), Gaps = 8/271 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  I   I  ++    +++ +   +   +R  E     A +E+V ++LRLV+S+A+ Y 
Sbjct: 25  SLGNIEAYIAEVNRLPILTLEQETDLA--LRYRERNDLSAAQELVLSHLRLVVSIARNYL 82

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G +  +YA+ W+K  I   I      ++I   
Sbjct: 83  GYGLPHADLIQEGNIGLMKAVKRFDPGMGVRLVSYAIHWIKAEIHEYILRNWRMVKIATT 142

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +             +A+KL +  E V ++        I+LET   D+
Sbjct: 143 KAQRKLFFNLRSHKNGLDSMTRAQIRSLAEKLNVKDEEVAEMETRLNGHDIALETQHDDD 202

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFG-IGMNT 638
           D +     ++  +          + N R   E     LA L PR  R++  R+       
Sbjct: 203 DDNFAPIAYLSSEQTEPASILEARQNDRMQSEGLAEALAKLDPRSRRIVEARWLNSDDGN 262

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             TL  +  +F V+ ERIRQIEA A++K+K+
Sbjct: 263 SATLHALAAEFGVSAERIRQIEAAALKKMKN 293


>gi|254384106|ref|ZP_04999451.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
 gi|194342996|gb|EDX23962.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
          Length = 302

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 110/241 (45%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 68  LQPGTSEHTRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 127

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 128 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNAATEDLTTLHGRTPTTPEIA 187

Query: 554 KKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  E V   ++   +    SLE     +    L D +  ++             R+
Sbjct: 188 ERLRITEEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPELAGVEH-----RD 242

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +
Sbjct: 243 LVRHLLVQLPEREQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSAN 298

Query: 672 R 672
           R
Sbjct: 299 R 299


>gi|55274986|gb|AAV49291.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 196

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 77/195 (39%), Positives = 130/195 (66%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 2   VVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 61

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S
Sbjct: 62  TRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITS 121

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+ 
Sbjct: 122 VDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLL 181

Query: 636 MNTDHTLEEVGKQFC 650
                TLE+VG++  
Sbjct: 182 GYEAATLEDVGREIG 196


>gi|213417289|ref|ZP_03350433.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 277

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 79/223 (35%), Positives = 139/223 (62%), Gaps = 3/223 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
             L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 274



 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|302559792|ref|ZP_07312134.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477410|gb|EFL40503.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 298

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 115/255 (45%), Gaps = 15/255 (5%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T +   + + +V     G  E +  +  ++EANL LV   A ++ +R     D++Q G I
Sbjct: 54  TQLLFGQLKELV----PGTPEHARVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTI 109

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+ A ++FD   G +F T+AM  V   I R   D   T+ +P  + +   +V      +
Sbjct: 110 GLINAIDRFDPERGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDL 169

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +    R P+  EIA++L +  + V   ++   +    SLE     +    L D +  ++ 
Sbjct: 170 TTAFGRSPSTAEIAERLRISEDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDP 229

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       R+    +L  L  RE+R+L +R+        T  ++  +  V++  + 
Sbjct: 230 ALDGVEH-----RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVS 280

Query: 658 QIEAKAIRKLKHPSR 672
           ++ A++ ++L+  +R
Sbjct: 281 RLLARSFQRLRSANR 295


>gi|301644085|ref|ZP_07244098.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|301077566|gb|EFK92372.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
          Length = 283

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 142/270 (52%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++      +S  E + + S ++    +   A K+++ ++LR VI +A++Y+  GL
Sbjct: 14  LDSYIRAAYACPMLSQEEEQQLASNLQ--IHDDLDAAKQLILSHLRFVIHIARQYSGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ WVK  I   +      +++      R
Sbjct: 72  PQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWVKSEIHEYVLRNWRIVKVATTKAQR 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   + +A++L + V+ VR++  +++ + ++ +    DE  
Sbjct: 132 KLFFNLRKTKQRLGWFNQDE--VDMVARELGVSVKDVREMESRMSAQDMAYDIYPDDETD 189

Query: 586 SHL----GDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +H       +++DK++       +    A   +     + +L PR + ++R R+ +  + 
Sbjct: 190 THHPVSPSLYLQDKSSDFAGMIEEDNWDAQATDHLVAAMETLDPRSQDIIRARW-LDDDN 248

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+ +++ ++ ER+RQ+E  A++KL+
Sbjct: 249 KATLHELAERYGISAERVRQLENNAMKKLR 278


>gi|215270883|emb|CAR48119.1| RNA polymerase sigma factor [Vibrio natriegens]
          Length = 273

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 117/312 (37%), Gaps = 40/312 (12%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I     + P
Sbjct: 1   LTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           +++      T  H   +  +S  E E D   + + + E     S+D    V   PE A  
Sbjct: 59  DAED-TAAPTATHIGSELSESQLEDEDDTDVDDDDEDEDGDDDSEDTEEDVGIDPELA-- 115

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
                                      +   +++   Y+ L+      +   +    S K
Sbjct: 116 ---------------------------LEKFNQLRSTYQNLQ------LAINEYGYESPK 142

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLE 372
             V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F+ 
Sbjct: 143 ATVANEMMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSVVEYGKMPKKSFIA 202

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
              G E    W+       +  +   +    + I +   ++K I  ET +S+   + I  
Sbjct: 203 LFTGNESSDAWLDEILA-SDKPYAEKIKRNEEEIRRSITKLKMIEEETSLSVQNVKDISR 261

Query: 433 MVRKGECEASIA 444
            +  GE +A  A
Sbjct: 262 RMSIGEAKARRA 273


>gi|113972098|ref|YP_735891.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-4]
 gi|114049328|ref|YP_739878.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-7]
 gi|117922401|ref|YP_871593.1| RNA polymerase factor sigma-32 [Shewanella sp. ANA-3]
 gi|113886782|gb|ABI40834.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-4]
 gi|113890770|gb|ABI44821.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-7]
 gi|117614733|gb|ABK50187.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. ANA-3]
          Length = 285

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 126/273 (46%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S++  T +       +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYIHSVTSMTMLDAETEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +   R+      E     +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNIRKAKTRLGWFSDDEVAM--VAENLGVSKADVTEMESRMAAQDPAFDLSSDNDDE 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   ++N +      + +L  R + +LR R+     T  
Sbjct: 195 QDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQHILRARWLDDDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL+E+ + + V+ ERIRQ+E  A+ KLK    +
Sbjct: 253 TLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|297193426|ref|ZP_06910824.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197723191|gb|EDY67099.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 282

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 111/241 (46%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E S  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 48  LQAGTAEHSRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRG 107

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 108 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRSPTTAEIA 167

Query: 554 KKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++   +    SLE     +    L D +  ++             R+
Sbjct: 168 ERLKIGEDEVLACIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALAGVEH-----RD 222

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+        T  ++ ++  V++  + ++ A++  +L+  +
Sbjct: 223 LVRHLLVQLPEREQRILMLRYYSN----LTQSQISQELGVSQMHVSRLLARSFARLRSAN 278

Query: 672 R 672
           R
Sbjct: 279 R 279


>gi|91978899|gb|ABE66425.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 279

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 122/321 (38%), Gaps = 44/321 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGIIQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEMVEANLR 454
           +  GE +A  AKKEMVEANLR
Sbjct: 258 MSIGEAKARRAKKEMVEANLR 278


>gi|10952458|gb|AAG24943.1|AF128845_2 RpoH [Sinorhizobium meliloti]
          Length = 301

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 122/279 (43%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLAK--RYQEHDDRKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K AI   I      +++    + +
Sbjct: 74  PIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+    + +  PE   EIA  L +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEEVVSMNRRLSGDASLNAPIKAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R      +  L  RE R+           
Sbjct: 194 EGDSGQWQDWLVDDHDNQEQILIEQDELESRRALLANAMKVLNDRERRIFEA--RRLTEE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R   L 
Sbjct: 252 PITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALE 290


>gi|303238906|ref|ZP_07325437.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593539|gb|EFL63256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 257

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/266 (27%), Positives = 136/266 (51%), Gaps = 17/266 (6%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     ++  + + +   + K     + A++E ++ NLRLV+SV +++ 
Sbjct: 2   LINKVEICGVNTSKLPVLTNDQKKVLFERMHK---GDTSAREEFIKGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLIKAIDNFDVSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +RD  +K ++   R++NK  +EPT ++I+K+L +P E +   L   ++PISL   +  + 
Sbjct: 118 LRDIAYKALQAKERLTNKNSKEPTVDDISKELGIPKEDIVFALDAIQDPISLFESVYHDG 177

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               GD I   + V    +  +  L        +  L  RE+ +L +RF  G     T  
Sbjct: 178 ----GDAIYVMDQVKDEKNHDENWLEGIALNEAMRKLNDREKLILNLRFFDG----RTQM 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV ++  +++ ++ ++E  A+  ++ 
Sbjct: 230 EVAEEIGISQAQVSRLEKTALMHMRK 255


>gi|238028681|ref|YP_002912912.1| RNA polymerase factor sigma-32 [Burkholderia glumae BGR1]
 gi|237877875|gb|ACR30208.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia glumae BGR1]
          Length = 311

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 134/273 (49%), Gaps = 12/273 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R  +   S   + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPEEERQYATEFRDQQNLES--ARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +A++L +  E V ++    +   I+LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKGMQAMTPE-EIDGLAQELNVKREDVAEMETRLSGGDIALEGQVED 211

Query: 583 EDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRF---GIG 635
            + S     ++ D +       A +   R   E  +  L SL  R  R++  R+   G  
Sbjct: 212 GEESFAPIAYLADSHNEPTAVLASRQRDRLQTEGISEALDSLDTRSRRIIEARWLNVGDD 271

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +   TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 272 GSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|226311983|ref|YP_002771877.1| sporulation sigma factor SigF [Brevibacillus brevis NBRC 100599]
 gi|226094931|dbj|BAH43373.1| RNA polymerase sigma-F factor [Brevibacillus brevis NBRC 100599]
          Length = 251

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 121/239 (50%), Gaps = 14/239 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +   + A++ +V +N+RLV SV +++ NRG +  DL Q G IGL+KA +KFD  
Sbjct: 20  ELIAKSQAGDTEARELLVNSNIRLVWSVVQRFINRGYEADDLFQIGCIGLLKAVDKFDLS 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D   T+++   +++  +KV RT   +  +  R PT  E
Sbjct: 80  YDVRFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKETANKVRRTKDELYKQFGRAPTIAE 138

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANL 609
           +A  + +  E V    +  + P S+   + + D     L D I D+      +       
Sbjct: 139 VADAVGITPEEVVFAQEANRAPSSIHETVFENDGDPITLIDQIADEGVNKWFE------- 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      ++ L+ RE+ ++ +R+      D T  EV ++  +++ ++ ++E + ++ +K
Sbjct: 192 KIALKDAISRLSEREQLIVYLRY----YKDQTQSEVAERLGISQVQVSRLEKRILQTIK 246


>gi|197122293|ref|YP_002134244.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196172142|gb|ACG73115.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 307

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 128/274 (46%), Gaps = 16/274 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    +++ + + +    +      + A   +V ANLR V+ VA +Y + G +  
Sbjct: 16  YLSEINRFPLLTVEDEQRLAR--QYCADRDTRAAHRLVTANLRFVVKVAYEYRSYGFRMA 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA +KFD   G +  +YA+WW++  I   I      +++      R   
Sbjct: 74  DLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKLF 133

Query: 530 HKVVRTARRM---SNKIKREPTPEE---IAKKLAMPVEGVRKV-LKITKEPISLETPIGD 582
             + RT R +   S +   +    +   +AKKL +    VR++  ++    +SL+ P+GD
Sbjct: 134 FSLARTKRELDKRSQEHGADSDGHDANKVAKKLRVKPGEVREMEQRMEGRDLSLDAPMGD 193

Query: 583 EDTSHLGDFIEDKNAVSPLDS---AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      DF+    A    +      Q  +       L  L  RE  ++     +  +  
Sbjct: 194 DGGYSHVDFLPSGTASQDDELSGVQEQKVVSGRVGEALGRLDQRERYIIE--MRVMSDRP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TL+E+G+ F  +RER RQ+E +A  KLK   R+
Sbjct: 252 LTLKELGEHFGFSRERARQLEIRAKEKLKEELRA 285


>gi|4102217|gb|AAD11814.1| sigma-like factor [Streptomyces sp. A21]
          Length = 343

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 119/245 (48%), Gaps = 8/245 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAA 485
           F   +  + +G  +   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA 
Sbjct: 97  FFDRLRTLEEGTHDYQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAI 156

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D + ++ +P  +++   ++ +    +S  + R
Sbjct: 157 DRFDLSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVELAKAKEALSADLDR 216

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT  E+A +L +  E + + L         SL+TP  D ++ +      D         
Sbjct: 217 DPTVAELAARLDLSEEEIIEGLVAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGM 276

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               NL      +L  L  RE  ++RMRFG     + T  ++G +  V++  + ++ ++ 
Sbjct: 277 ESVENLH-ALAPLLRQLDDRERAIVRMRFG----QEMTQAQIGAELGVSQMHVSRLLSRI 331

Query: 664 IRKLK 668
           +R+L+
Sbjct: 332 VRRLR 336


>gi|71892394|ref|YP_278128.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|71796500|gb|AAZ41251.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 282

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/266 (24%), Positives = 133/266 (50%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   IK  +  T ++  E + +   +         A K+++ ++LR V+ V++ Y+  GL
Sbjct: 17  LEAYIKVANAYTMLTAEEEKTLAKRL--YYNGDLDAAKKLIVSHLRFVVHVSRNYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  L  +  ++A+ W+K  I   +      ++I      R
Sbjct: 75  PQADLIQEGNIGLMKAVRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWRIVKIATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED- 584
                + +T +R+      E   E +AK L +  + VR++  +++ + ++ E    +++ 
Sbjct: 135 KLFFNLRKTKQRLGWFNAGEI--EIVAKALNVTSKDVREMESRMSAQDMTFEQSSDEDNR 192

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
             T     +++DK   S  +      + +     + +L  R + ++R R+ + ++   TL
Sbjct: 193 GITIAPILYLQDKIVSSNEEEEWIDQVSDKLNAAIKTLDERSQHIIRARW-LNVDNKSTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+  Q+ V+ ER+RQ+E  A++K+K
Sbjct: 252 QELANQYGVSAERVRQLEKNAMKKMK 277


>gi|220917075|ref|YP_002492379.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954929|gb|ACL65313.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 307

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 128/274 (46%), Gaps = 16/274 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    +++ + + +    +      + A   +V ANLR V+ VA +Y + G +  
Sbjct: 16  YLSEINRFPLLTVEDEQRLAR--QYCADRDTRAAHRLVTANLRFVVKVAYEYRSYGFRMA 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA +KFD   G +  +YA+WW++  I   I      +++      R   
Sbjct: 74  DLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKLF 133

Query: 530 HKVVRTARRM---SNKIKREPTPEE---IAKKLAMPVEGVRKV-LKITKEPISLETPIGD 582
             + RT R +   S +   +    +   +AKKL +    VR++  ++    +SL+ P+GD
Sbjct: 134 FSLARTKRELDKRSQEHGADSDGHDANKVAKKLRVKPGEVREMEQRMEGRDLSLDAPMGD 193

Query: 583 EDTSHLGDFIEDKNAVSPLDS---AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      DF+    A    +      Q  +       L  L  RE  ++     +  +  
Sbjct: 194 DGGYSHVDFLPSGTASQDDELSGVQEQKVVSGRVVEALGRLDQRERYIIE--MRVMSDRP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TL+E+G+ F  +RER RQ+E +A  KLK   R+
Sbjct: 252 LTLKELGEHFGFSRERARQLEIRAKEKLKEELRA 285


>gi|109900247|ref|YP_663502.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
 gi|109702528|gb|ABG42448.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
          Length = 289

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 135/271 (49%), Gaps = 14/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   ++++S    ++  E R +   +++   +  +A ++++ ++LR V+ +AK Y+  GL
Sbjct: 24  IETYVQAVSSINMLTAEEERGLAERLQQ--EDDLLAARKLIMSHLRFVVHIAKSYSGYGL 81

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 82  PQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 141

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E   +++A  L +  + V +   +++    + +    D+++
Sbjct: 142 KLFFNLRKNKKRLGWFTHAE--VQKVASDLGVSEKEVLQMEARMSSHDQAFDLSADDDES 199

Query: 586 SHLG--DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  F+EDK+A      +++   A   +     + +L  R + +++ R+     T  
Sbjct: 200 GSFAPVQFLEDKSADVETDVVNADWDATASQKLYSAIKTLDERSQHIIQTRWLSDDKT-- 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL+++  ++ V+ ER+RQIE  A++KL+   
Sbjct: 258 TLQDLADKYQVSAERVRQIEKNAMKKLQSAM 288


>gi|328884955|emb|CCA58194.1| RNA polymerase sigma factor [Streptomyces venezuelae ATCC 10712]
          Length = 344

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 112/227 (49%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 121 RNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTV 180

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S +  R PT  E+A++L +  E V 
Sbjct: 181 VGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQQHGRSPTVHELAERLGISEEEVL 240

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L+       +SL+ P  D+++  + D +  ++             RE+   +L  L P
Sbjct: 241 EGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY-----RESLKPLLEDLPP 295

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+R+L +RF   M      +EV     +++  + ++ A+ +  L+ 
Sbjct: 296 REKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLASLRE 338


>gi|307328849|ref|ZP_07608019.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885514|gb|EFN16530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 107/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++EANL LV   A ++ +R     D+IQ G IGL+ A ++FD   G +F T+
Sbjct: 49  EHTRVRAALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPDRGVQFPTF 108

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 109 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTVLHGRSPTTAEIAERLKLS 168

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            E V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 169 EEEVLACIEAGRSYHATSLEAAQEGDGLPGLVDRLGYEDPALAGVEH-----RDLVRHLL 223

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++  +  V++  + ++ +++  +L+  +R
Sbjct: 224 VQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLSRSFARLRSANR 274


>gi|55274875|gb|AAV49240.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 193

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 78/191 (40%), Positives = 130/191 (68%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q 
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  V
Sbjct: 121 RLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 180

Query: 628 LRMRFGIGMNT 638
           L  RFG+    
Sbjct: 181 LARRFGLLGYE 191


>gi|317494584|ref|ZP_07952997.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316917514|gb|EFV38860.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 283

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/268 (22%), Positives = 132/268 (49%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E + +   +         A K+++ ++LR V+ VA+ Y   GL
Sbjct: 16  LEAYVRAANTYPMLTAEEEKELGERL--HYEGDLDAAKQLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + V     ++  + ++ +    D+++
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVSEKDVLEMESRMAAQDMAFDMSNDDDES 191

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTDH 640
           S     +  ++  S   + I+ +  ++      T  +  L  R + ++R R+ +  +   
Sbjct: 192 SPAAPVLFLQDKSSDFANDIEDDNWDSHAADKLTLAMEGLDERSQHIIRARW-LDDDNKA 250

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 TLQELADQYGVSAERVRQLEKNAMKKLR 278


>gi|253686510|ref|YP_003015700.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251753088|gb|ACT11164.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 285

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 132/270 (48%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYQGDLDAAKHLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + +T  R+    + E   E +A++L +  + VR++  ++  + ++ +    ++  
Sbjct: 134 KLFFNLRKTKTRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDSH 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   +   +  ++  S     I+ +  +T      T  L  L  R + ++R R+ +  + 
Sbjct: 192 DGKAMSPMLYLQDKSSDFADGIEEDNWDTHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|94499982|ref|ZP_01306517.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
 gi|94427840|gb|EAT12815.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
          Length = 368

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/246 (30%), Positives = 140/246 (56%), Gaps = 2/246 (0%)

Query: 424 ISEFR-HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           I E +  +    +  +      + ++V+ANLRL + VA++YT +G++  +LIQEG +GL+
Sbjct: 117 IHELKGRLYKQAQVLKRRYEDYRNQLVQANLRLAMHVARQYTGKGMELEELIQEGTLGLI 176

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           K AE+++   GY+F+TYA WW++QAI  +++++   +RIP ++ D+I KV R        
Sbjct: 177 KGAERYNINKGYRFTTYAYWWIQQAIKGALSEKRGIVRIPTNVTDRIVKVERCKYEFFKA 236

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R P  +EI+  L M V+ +R  L +T    S++ PI  ++   + + +  ++  +P  
Sbjct: 237 NGRYPNAKEISSILGMDVDHIRSTLAVTNVGDSIDEPI-YDEGLTMQESMASESIATPSS 295

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              + +      +++  L  R++ ++R+  GIG+   +  +E+  Q  VT ER RQ+  +
Sbjct: 296 QLDEEDGEAFLEKLIGELPKRQQFIVRLYHGIGIGQTYPFKEIAPQIGVTLERTRQLYHE 355

Query: 663 AIRKLK 668
           +IR+LK
Sbjct: 356 SIRQLK 361


>gi|215270865|emb|CAR48110.1| RNA polymerase sigma factor [Vibrio rotiferianus]
 gi|215270867|emb|CAR48111.1| RNA polymerase sigma factor [Vibrio rotiferianus]
 gi|215270869|emb|CAR48112.1| RNA polymerase sigma factor [Vibrio rotiferianus]
 gi|215270871|emb|CAR48113.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 270

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/311 (17%), Positives = 110/311 (35%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   +++E  D  E   D +  ++       ++        
Sbjct: 61  ADDTTAPTATHIGSELTESQLEDEDEEDVDEDEDGDDSDDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET +++ + + I 
Sbjct: 200 ALFTGNESTDAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTVQKIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAQ 269


>gi|84688065|ref|ZP_01015924.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84663915|gb|EAQ10420.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 298

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 68/275 (24%), Positives = 125/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + + + A  ++V ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQDIRKFPMLEPEEEYMLAK--RWVDHQDTDAAHQLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKLA----MPVEGVRKVLKITKEPISLETPIGD 582
                + +   R+      +  PE +A+          E +    +++    SL   I +
Sbjct: 134 KLFFNLRKAKARIGALEDGDLRPENVAQIAHDLNVTEEEVISMNRRMSGGDASLNATITN 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +  S     D++ED++A    D   +  L   RE   + +  L  RE+ +L        +
Sbjct: 194 DGDSTMQWQDWLEDEDADQAGDYEQRDELTVRREMLAQAMDVLNDREKDILTQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   +
Sbjct: 252 ETVTLEDLSGQYDVSRERIRQIEVRAFEKLQKRMQ 286


>gi|21223610|ref|NP_629389.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|5912531|emb|CAB56114.2| SigH protein [Streptomyces coelicolor A3(2)]
 gi|9968693|emb|CAC05976.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 361

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 117/241 (48%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + K   E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 124 LRTLEKDSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 184 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 243

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KL++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 244 ELAEKLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 299

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 300 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 354

Query: 669 H 669
            
Sbjct: 355 E 355


>gi|260575497|ref|ZP_05843496.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259022417|gb|EEW25714.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 298

 Score =  133 bits (334), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 125/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVDHQDATAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKLA----MPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++    + +  PE +A+          E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKAKVGALEEGDLRPENVARIAHDLNVSETEVIDMNRRLSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED+++    D A +  L   R    + +A L  RE+ +L        +
Sbjct: 194 DGEGSTQWQDWLEDEDSDQANDYAERNELEMRRALLVQAMAVLNDREKDIL--MQRRLAD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++   + V+RERIRQIE +A  KL+   R
Sbjct: 252 EPVTLEDLSASYGVSRERIRQIEVRAFEKLQERMR 286


>gi|295696452|ref|YP_003589690.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412054|gb|ADG06546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 261

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 78/263 (29%), Positives = 135/263 (51%), Gaps = 13/263 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V T  + +     +  +  + +     A++ ++  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEISGVNTSQLPVLTNAEMRKLFAEFQAGDLSARERLIHGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  NVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   +++N+  REPT  EI+++L +P E V   L   ++P+SL  PI  +  D  
Sbjct: 122 AYKALQVRDQLTNERLREPTITEISEQLNLPKEDVVFALDAIQDPVSLFEPIYHDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D I D      L     A         +  L  RE+++L MRF  G     T  EV 
Sbjct: 182 YVMDQIRDDRNQDVLWVEEIA-----LREAMNKLGQREQKILAMRFFEG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
           ++  +++ ++ ++E  AI+ ++ 
Sbjct: 233 EEIGISQAQVSRLEKSAIQHMQK 255


>gi|301155494|emb|CBW14960.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 280

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 133/267 (49%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +         A K++V ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKSLAERL--YYDGDIEAAKKLVLSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  ++T   +  + P  D+D 
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMTGADVGFDLPTDDDDE 190

Query: 586 SHLGD-FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +++   ++EDK+   A        +    E     LA+L  R + +++ R+        T
Sbjct: 191 AYVPSLYLEDKSSNFAAELESENFEEQATEKLGTALANLDERSQEIIKARWLDD--EKAT 248

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  ++ V+ ERIRQ+EA A++KLK
Sbjct: 249 LHDLAAKYNVSAERIRQLEANALKKLK 275


>gi|255003152|ref|ZP_05278116.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Puerto Rico]
 gi|255004281|ref|ZP_05279082.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Virginia]
          Length = 296

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 67/278 (24%), Positives = 125/278 (44%), Gaps = 14/278 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + + +  +     +S  E + +          +      +V ++LRLV+ +A  + + G
Sbjct: 20  DLVSYVAQVRTFPILSEEEEKRLAE--NWYRRGSVADAHRLVTSHLRLVVKIAMGFKSYG 77

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +I   I      IR+      
Sbjct: 78  LPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQAQ 137

Query: 528 K--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIG 581
           K     + +  +R+ +      T +E   IA++ A   E V R         +SL   + 
Sbjct: 138 KKLFFSLRKIKKRLLS-CGSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQVH 196

Query: 582 DEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            E +  L D +        +  L     A  +      LA+L  R   +           
Sbjct: 197 GESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIF--TRRRLQER 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLE++ +++ V++ER+RQIE +A+ K+K    + ++
Sbjct: 255 PDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEANRV 292


>gi|209407282|emb|CAP72526.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 269

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/313 (19%), Positives = 116/313 (37%), Gaps = 45/313 (14%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +M+++   P T  +++   D +      L +I  L   I 
Sbjct: 1   LLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYDRVTSEGGRLSDI--LSGYID 58

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P+  G            + E  + +       + + D +     S+++       PE A 
Sbjct: 59  PDDDGA------AGPQAEVEPVTPQAAAKPAGDDKDDEDEDDSDSEEEEGDGGPDPEVAR 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                + E  D +   L                                   +K  + S 
Sbjct: 113 IRFGAVAEQLDVAKKAL-----------------------------------KKHGRGSQ 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
           +     ++L  L   + L   + D LVE++ D   +I   E  ++++      + R  FL
Sbjct: 138 QATDALQELAILFMPIKLIPKQYDALVERVRDALAQIRAQERAIMQICVRDARMPRADFL 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +    E D  W        + ++   +A   + I + + ++ ++  E  ++I++ + I 
Sbjct: 198 RQFPNNETDLDWADKLAS-GKSKYAEAIAARKEDIQRCQQKLLALEEECVLAIADIKDIN 256

Query: 432 SMVRKGECEASIA 444
             +  GE +A  A
Sbjct: 257 RRMSIGEAKARRA 269


>gi|182437344|ref|YP_001825063.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777954|ref|ZP_08237219.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465860|dbj|BAG20380.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658287|gb|EGE43133.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 106/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 64  EHRRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTF 123

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 124 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTAEIAERLKIS 183

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 184 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 238

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 239 VQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 289


>gi|302765387|ref|XP_002966114.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
 gi|300165534|gb|EFJ32141.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
          Length = 249

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 81/242 (33%), Positives = 133/242 (54%), Gaps = 12/242 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+ +NLRLV+++A++Y N G++  DLIQEG +GL+   EKFD   G+KFSTYA WW+ QA
Sbjct: 1   MILSNLRLVVAIARRYENMGVEIGDLIQEGTLGLIHGLEKFDVSRGFKFSTYAYWWIFQA 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + RS+  +   +R P H+ + I K+ +   R      R  + E + + L +P   +   L
Sbjct: 61  MIRSLDKRGKCVRYPFHLCEAIRKINQLRNR--QVDDRPVSVETMMQVLKLPRARIEIAL 118

Query: 568 KITKEPI-SLETPI----GDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLA-SL 620
           + +   + SL+  +      E+   L DFI D+N  +      + + ++E   R+L   L
Sbjct: 119 QASNYRLTSLDRHVANKRCFEEGDPLEDFIVDQNVENQPWLMAERDAVKEELDRLLESKL 178

Query: 621 TPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             RE  V+R RFG+  N     +  E+G+   ++RER+RQ+E  A+ KL+   +S+    
Sbjct: 179 DAREREVIRKRFGLHPNQTSPLSRHEIGRSCGISRERVRQLENDAMAKLR-ACKSRLSME 237

Query: 679 FL 680
           FL
Sbjct: 238 FL 239


>gi|251796351|ref|YP_003011082.1| sporulation sigma factor SigF [Paenibacillus sp. JDR-2]
 gi|247543977|gb|ACT00996.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. JDR-2]
          Length = 251

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 124/250 (49%), Gaps = 17/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  +E + ++++    +   +IA+  +V+ N+RLV SV +++ NRG +  DL Q G IGL
Sbjct: 13  LDDAEVKRLIAL---SQSGDTIARDTLVQCNIRLVWSVVQRFINRGYEPEDLFQIGCIGL 69

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    +S 
Sbjct: 70  LKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKETANKVRKMKDELSK 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVS 599
            + R PT  E+A +L +  E V    +  K P S+   + + D     L D I D +   
Sbjct: 129 TLGRLPTVSEVADRLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADDSQER 188

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D       +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++
Sbjct: 189 WFD-------KLALIEAIEGLSERERLIVYLRY----YRDKTQSEVASRLGISQVQVSRL 237

Query: 660 EAKAIRKLKH 669
           E K ++ ++ 
Sbjct: 238 EKKILQSIRE 247


>gi|289769170|ref|ZP_06528548.1| SigH protein [Streptomyces lividans TK24]
 gi|289699369|gb|EFD66798.1| SigH protein [Streptomyces lividans TK24]
          Length = 361

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 117/241 (48%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + K   E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 124 LRTLEKDSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 183

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 184 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 243

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KL++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 244 ELAEKLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 299

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 300 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 354

Query: 669 H 669
            
Sbjct: 355 E 355


>gi|148793354|gb|ABR12741.1| RNA polymerase sigma factor [Photobacterium kishitanii]
          Length = 263

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/303 (17%), Positives = 104/303 (34%), Gaps = 44/303 (14%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +  S+ E P     L+   D++      L +II     + 
Sbjct: 1   LLTREGEIDIAKRIEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDII--SGFVD 58

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P         T   +         E + +D  +   D +       ++       PE A 
Sbjct: 59  PNE-----EATAAPTATHIGSELSETDLEDEDKDLEDDDDDEDAENEEEDDGSIDPELAR 113

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                L +  +  A  ++                                   +  +   
Sbjct: 114 EKFLELRQSYEKMALAIN-----------------------------------QHGRQHA 138

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
             +V  E+L ++     L   + D LV  L D   ++  NE  ++R+      + +  F+
Sbjct: 139 TTEVAVEELSEIFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFI 198

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W+  A +  +  +   +    + + +   +++ +  ETG+SI   + I 
Sbjct: 199 SLFASNESNSDWIDTALNSGKP-YAERLKNYEEDLRRSTLKLRILEQETGLSIERIKDIS 257

Query: 432 SMV 434
             +
Sbjct: 258 RRM 260


>gi|15966479|ref|NP_386832.1| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307300484|ref|ZP_07580264.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307318349|ref|ZP_07597784.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|15075750|emb|CAC47305.1| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306896031|gb|EFN26782.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306904650|gb|EFN35234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 301

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 122/279 (43%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLAK--RYQEHDDRKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K AI   I      +++    + +
Sbjct: 74  PIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+    + +  PE   EIA  L +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEEVVSMNRRLSGDASLNAPIKAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R      +  L  RE R+           
Sbjct: 194 EGDSGQWQDWLVDDHDNQEQILIEQDELESRRALLANAMKVLNDRERRIFEA--RRLTEE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R   L 
Sbjct: 252 PITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALE 290


>gi|302560279|ref|ZP_07312621.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302477897|gb|EFL40990.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 304

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 120/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 62  LFERLESLEEGTPEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 121

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 122 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRS 181

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +  E V + +         SL+    ++D    L D I  ++       
Sbjct: 182 PTVAELAERLGITNEEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGIE 241

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L PR+ ++L +RF  G     T  E+G++  +++  + ++ ++ 
Sbjct: 242 YV-----ESLKPLIAELPPRDRKILSLRFVAG----MTQSEIGEELGISQMHVSRLLSRT 292

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 293 LVKLRK 298


>gi|150397812|ref|YP_001328279.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029327|gb|ABR61444.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 301

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 75/279 (26%), Positives = 123/279 (44%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLAK--RYQEHDDRKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K AI   I      +++    + +
Sbjct: 74  PIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+    + +  PE   EIA  L +  + V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEDEVISMNRRLSGDASLNAPIKAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D+N         Q  L   R      L  L  RE R+           
Sbjct: 194 EGDSGQWQDWLVDENDNQEQILIEQDELDNRRALLANALKVLNDRERRIFEA--RRLTED 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R   L 
Sbjct: 252 PITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALE 290


>gi|215270873|emb|CAR48114.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 270

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/311 (17%), Positives = 110/311 (35%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   +++E  D  E   D +  ++       ++        
Sbjct: 61  ADDTTAPTATHIGSELTESQLEDEDEEDVDEDEDGDDSDDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET +++ + + I 
Sbjct: 200 ALFTGNESTDAWLDEVLA-SDNPYAEKIKRNEEEIRRSIAKLKMIENETSLTVQKIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAQ 269


>gi|332763556|gb|EGJ93795.1| alternative sigma factor RpoH [Shigella flexneri 2930-71]
          Length = 280

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 12  LDSYIRAANAWPMLSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGL 69

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 70  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 129

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    D+  
Sbjct: 130 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSD 187

Query: 586 SH-LGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           S  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 188 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMHGLDERSQDIIRARW-LDEDNK 246

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 247 STLQELADRYGVSAERVRQLEKNAMKKLR 275


>gi|328883833|emb|CCA57072.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 281

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 107/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 53  EHHRVRGALIEANLPLVRYAADRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTF 112

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 113 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLRIG 172

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 173 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 227

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 228 VQLPEREQRILMLRYYSN----LTQSQISQELGVSQMHVSRLLARSFARLRSANR 278


>gi|205373280|ref|ZP_03226084.1| sporulation sigma factor SigG [Bacillus coahuilensis m4-4]
          Length = 258

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 76/261 (29%), Positives = 138/261 (52%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + RK +   + +++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFRKMQAGDTYSREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT EEIAK L +P E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQAREKLMGETSKEPTAEEIAKVLDVPHEDIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+   +   + I+          L  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLSDER--NRDVNWIEEI---ALKEGLRRLNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
            +  +++ ++ ++E  AI+ +
Sbjct: 233 DEIGISQAQVSRLEKAAIKHM 253


>gi|37784418|gb|AAO13102.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           smithia]
          Length = 270

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 117/315 (37%), Gaps = 46/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    +  +       S+  E D   E E + E     S DD       PE A   
Sbjct: 59  E-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDSDSSDDEGDGGPDPEVAREK 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 112 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 137 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 197 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 255

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 256 MSIGEAKARRAKKEM 270


>gi|37784404|gb|AAO13095.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           pectinolytica]
 gi|37784412|gb|AAO13099.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784414|gb|AAO13100.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           achromogenes]
 gi|242117652|dbj|BAH80098.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 270

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 117/315 (37%), Gaps = 46/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    +  +       S+  E D   E E + E     S DD       PE A   
Sbjct: 59  E-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 112 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 137 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 197 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 255

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 256 MSIGEAKARRAKKEM 270


>gi|261366888|ref|ZP_05979771.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
 gi|282571002|gb|EFB76537.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
          Length = 260

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 117/248 (47%), Gaps = 9/248 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +       +++R      + A+++M++ NLRLV+SV +K+ NRG    DL Q G IGL
Sbjct: 16  LPVLSETEKSALIRAARAGDAEARRKMIQGNLRLVLSVVQKFANRGENLDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD  L  +FSTY +  +   I R + D +  +R+   +RD  +  +R    +  
Sbjct: 76  IKAIDHFDPSLQVRFSTYGVPMIVGEIRRFLRDNN-AVRVSRSIRDLAYHSMRAREALQK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  R+P   EIA ++    E V   L+   EP SL  P+  +         +  +A    
Sbjct: 135 ENGRDPKISEIAARVGASPENVAMALESVVEPASLYEPVYSDGEDSFAIVDQLHDATGEE 194

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   R+T      SL+ RE R++ MR+  G        E+     +++ ++ ++E 
Sbjct: 195 SWISDIMFRDTV----KSLSARERRIIAMRYLGGKTQMQVAREI----GISQAQVSRLEK 246

Query: 662 KAIRKLKH 669
            A+ ++K 
Sbjct: 247 GALNRIKE 254


>gi|295696440|ref|YP_003589678.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412042|gb|ADG06534.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 256

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/255 (25%), Positives = 120/255 (47%), Gaps = 17/255 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S +  ++  + R +++     +   + A++ +V  N RLV SV +++  RG +  DL Q 
Sbjct: 9   STKAKLTDQQVRELIAQ---SQSGDAGARETLVLFNQRLVWSVVQRFLGRGYEPEDLFQI 65

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGLMKA +KFD     KFSTYA+  +   I R + D   T+++   +++    + R  
Sbjct: 66  GCIGLMKAIDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSVKETARHIRRAR 124

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIED 594
             ++ ++ R+P   E+A++L M    V       + P S+   + + D     L D I D
Sbjct: 125 DELAKRLGRQPHINELAEELGMDPAEVVFTQDAMRAPASIHETVFENDGDPILLMDQIAD 184

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +      D       R   T  L  L  RE  ++ +RF      D T  EV +   +++ 
Sbjct: 185 EEQEKWFD-------RLALTDALNRLPERERLIVFLRFF----RDKTQSEVAEVLGISQV 233

Query: 655 RIRQIEAKAIRKLKH 669
           ++ ++E K + +++ 
Sbjct: 234 QVSRLEKKILNRIRR 248


>gi|310642622|ref|YP_003947380.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247572|gb|ADO57139.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 251

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 124/254 (48%), Gaps = 14/254 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T  S  E   +  ++   +   + A++ +V +N+RLV SV +++ NRG +  DL Q 
Sbjct: 5   GKKTSHSYLEDTEVKRLIALSQSGDNDARETLVNSNIRLVWSVVQRFMNRGYEPDDLFQI 64

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +  
Sbjct: 65  GCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKETANKVRKMK 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             +S ++ R PT +E+A +L +  E V    +  K P S+   + + D     L D I D
Sbjct: 124 DELSKRLNRLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD 183

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++     D       +      +  L+ RE  ++     +    D T  EV  +  +++ 
Sbjct: 184 ESQERWFD-------KLALNEAIDGLSERERLIV----YLRYYRDQTQSEVASRLGISQV 232

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K ++ ++
Sbjct: 233 QVSRLEKKILQLIR 246


>gi|71064787|ref|YP_263514.1| RNA polymerase factor sigma-32 [Psychrobacter arcticus 273-4]
 gi|71037772|gb|AAZ18080.1| putative Sigma 32 (RpoH) [Psychrobacter arcticus 273-4]
          Length = 341

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 125/271 (46%), Gaps = 11/271 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++ ++ + +    R  +     A + +V ++LR VI +A+ Y+  
Sbjct: 64  VNLGAYINTVHQIPILTPTQEQELAH--RYYDEGDVEAARLLVMSHLRFVIHIARSYSGY 121

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 122 GLPQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKA 181

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ +N++  E   + IA  L +  + V     ++T    S E    D+D
Sbjct: 182 HRKLFFNLRSLKKTNNQLTIE-EADAIANDLNVTRKQVLEMESRLTSYDASFEAQSSDDD 240

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++ + P +   +++  E         + +L  R   ++  R+        
Sbjct: 241 DGRYAPQLFLEDGIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWL--SEQKS 298

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL E+   + ++ ER+RQIE  A+ K++   
Sbjct: 299 TLHELAAVYSISAERVRQIEKNAMDKIREAM 329


>gi|66474669|gb|AAY46904.1| RpoD [Aeromonas salmonicida subsp. salmonicida]
          Length = 270

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 117/315 (37%), Gaps = 46/315 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                     +  +       S+  E D   E E + E     S DD       PE A  
Sbjct: 59  NE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVARE 111

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 112 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 136

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 137 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 196

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 197 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 255

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 256 RMSIGEAKARRAKKE 270


>gi|37784424|gb|AAO13105.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784426|gb|AAO13106.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784456|gb|AAO13121.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784458|gb|AAO13122.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784466|gb|AAO13126.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784472|gb|AAO13129.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784474|gb|AAO13130.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784476|gb|AAO13131.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37784478|gb|AAO13132.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37784482|gb|AAO13134.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
 gi|37784492|gb|AAO13139.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     S DD       PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 114 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|282866278|ref|ZP_06275324.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282558864|gb|EFB64420.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 318

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA ++F+ 
Sbjct: 80  LETLEEGTHEYAYVRNTLVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFEL 139

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  
Sbjct: 140 SRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRAPTVV 199

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQA 607
           E+A++L +  E V + +         SL+    D+D    L D +  ++        I  
Sbjct: 200 ELAERLGITHEEVVEGMTASNAYTASSLDAKPEDDDNEGALADRLGYEDNGLEGIEYI-- 257

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E+   ++ASL  R+  +L +RF        T  E+G++  +++  + ++ ++ + KL
Sbjct: 258 ---ESLKPLIASLPLRDRTILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRTLVKL 310

Query: 668 KH 669
           + 
Sbjct: 311 RR 312


>gi|254428104|ref|ZP_05041811.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
 gi|196194273|gb|EDX89232.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
          Length = 287

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 128/271 (47%), Gaps = 13/271 (4%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   +++++    +S  E + +   +     +   A + +V ++LR V  +A+ YT  G
Sbjct: 19  DLDAYMRAVNAVPVLSAEEEQRLGERL--YYDQDLDAARSLVLSHLRFVAHIARSYTGYG 76

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MR 526
           L   DL+QEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     +
Sbjct: 77  LPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYVIKNWRIVKVATTKAQ 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
            K+   +R  ++   ++  E   + +A  L +    V+++  ++     S + P  D+D 
Sbjct: 137 RKLFFNLRGQKKRLGRLTME-EAQRVADDLGVTATQVKEMEGRLGAYDASFDGPTNDDDD 195

Query: 586 SHL----GDFIEDKNAVSPLDSAIQANLRE--TTTRVLASLTPREERVLRMRFGIGMNTD 639
           S +         D +  + L +      RE    +  L +L  R   +L  R+       
Sbjct: 196 STVVSPAAYLHSDNSDPADLLAEQDKQQRESRQLSSALMALDERSRDILERRWLAD--QK 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            TL+E+  ++ V+ ERIRQ+E  AI+KL++ 
Sbjct: 254 STLQELADEYGVSAERIRQLENNAIKKLRNA 284


>gi|183598031|ref|ZP_02959524.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
 gi|188022810|gb|EDU60850.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
          Length = 292

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 68/282 (24%), Positives = 135/282 (47%), Gaps = 16/282 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +++ +    ++  E + +   +         A K+++ ++LR VI VA+ Y   GL
Sbjct: 16  IEAYMRAANAYPMLTAEEEKELAERL--HYHGDLDAAKQLILSHLRFVIHVARSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + +  +R+    + E   + +AK+L +  + VR++               D+D+ 
Sbjct: 134 KLFFNLRKNKKRLGWFNQDE--VDMVAKELGVSTKDVREMESRMAAQDMAFDMSDDDDSG 191

Query: 587 HLGD------FIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            LG       F++DK++    S  +   +++  +     L SL  R + ++R R+ +  +
Sbjct: 192 DLGQPIAPVLFLQDKSSDFAGSIEEDNWESHATDRLADALDSLDERSQDIIRARW-LDDD 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              TL+E+  ++ V+ ER+RQ+E  A++KL+      +  S+
Sbjct: 251 NKTTLQELADKYGVSAERVRQLEKNAMKKLRAAMEEGEEESY 292


>gi|313810026|gb|EFS47747.1| sigma-70 region 2 [Propionibacterium acnes HL083PA1]
          Length = 464

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 88/198 (44%), Positives = 121/198 (61%), Gaps = 25/198 (12%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR-------------------------KGECEASI 443
           +++ +K I     ++  E   +   +                              +  +
Sbjct: 214 VKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDREDYEWIAEDGKV 273

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW
Sbjct: 274 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 333

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +KQAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPTPEE+A +L M  E V
Sbjct: 334 IKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELASELDMTAEKV 393

Query: 564 RKVLKITKEPISLETPIG 581
            +V K  +EPISL TP  
Sbjct: 394 IEVQKYGREPISLHTPHW 411



 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD------RSTDDPVRMYLREMGSI 131
           VD  D +  E ++D   +       S+      D  +       +T DPV+ YL+++G +
Sbjct: 165 VDERDYDPAEAAKDEQQINKETEAFSLSDNDDADEPEQTVMVAGATADPVKDYLKQIGKV 224

Query: 132 ELLSREGEIAIAKRIEAGR 150
            LL+   E+ +AKRIEAG 
Sbjct: 225 ALLNAVEEVDLAKRIEAGL 243


>gi|218132880|ref|ZP_03461684.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991753|gb|EEC57757.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
          Length = 259

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 76/253 (30%), Positives = 130/253 (51%), Gaps = 14/253 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  +E +    ++RK     S A+++ ++ NLRLV+SV +++   G    DL Q G IGL
Sbjct: 18  LLKNEEKD--ELLRKAIDGDSKAREKYIKGNLRLVLSVIQRFAGNGENADDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     +FSTYA+  +   + R + D +  IR+   +RD  +K +     ++ 
Sbjct: 76  MKAIDNFDVTQNVRFSTYAVPMIMGEVRRYMRDYNS-IRVSRSLRDTAYKAIHARDMLTK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K + EPT  EIA ++ +P E +   L   + P+SL  P+  E  DT ++ D I DK    
Sbjct: 135 KNQHEPTVMEIAAEVGLPKEEIVMALDAMQTPLSLYEPVFSEGGDTLYVMDQISDKKNRE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +      LRE  +R    L  RE  ++R+RF  G     T  EV +   +++ ++ ++
Sbjct: 195 -DNWVEDIALREAVSR----LPERERNIIRLRFFDG----RTQMEVARDVGISQAQVSRL 245

Query: 660 EAKAIRKLKHPSR 672
           E  A+R +K+  +
Sbjct: 246 EKNALRSMKNYLQ 258


>gi|255312697|gb|ACU01758.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 131/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  L+LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|91775055|ref|YP_544811.1| sigma 32 (RpoH) [Methylobacillus flagellatus KT]
 gi|91709042|gb|ABE48970.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacillus flagellatus
           KT]
          Length = 285

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 75/273 (27%), Positives = 131/273 (47%), Gaps = 10/273 (3%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + S   +   +++I     +S  E   + + ++K       A K +V ++LRLV S+A+ 
Sbjct: 10  ISSFDSLDQYLRAIKSFPVLSAEEELKLATRLKKY--NDLEAAKTLVVSHLRLVASIARN 67

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA  +FD   G +  ++AM W+K  I   I      +++ 
Sbjct: 68  YAGYGLPQADLIQEGNIGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKVA 127

Query: 523 VH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPI 580
               + K+   +R+ ++             IA++L +  E V     +++   ISLE   
Sbjct: 128 TTKAQRKLFFNLRSMKKGQTASLHSDEVAHIARELNVKPEEVLEMEARMSGHEISLEGNA 187

Query: 581 GDEDT---SHLGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIG 635
            D++    S +          S +  A +A+   T   +  LA L  R  R++  R+   
Sbjct: 188 DDDNEDMFSPISYLQASHAEPSEILEAQEADQLHTTGLSTALAKLDDRSRRIVEARWLQE 247

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +   TL ++ ++F V+ ERIRQIE KA+++++
Sbjct: 248 GHN-ATLHDLAEEFGVSAERIRQIEQKAMKQMR 279


>gi|146295967|ref|YP_001179738.1| sporulation sigma factor SigG [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409543|gb|ABP66547.1| RNA polymerase, sigma subunit, RpsG/SigG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 255

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 79/260 (30%), Positives = 132/260 (50%), Gaps = 9/260 (3%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +      + +++K +     A+K+ +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPMLSHEEKIELLKKMKNGDKEARKQFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNAM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   R  ++  REPT EEIA +L +  E +   L   +EPISL  PI  + T  + 
Sbjct: 121 YKALKIKERYISQNYREPTLEEIANELCISKEDLVFALDSIQEPISLYEPIFQDSTDTMY 180

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              +  +  S  +  ++     +    L+ LT RE+ +L +R+  G     T  EV    
Sbjct: 181 VVDQVSDQKSCENLWLEEI---SLKDALSRLTKREKEILYLRYYKG----KTQMEVATII 233

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ +IE  AI  +K 
Sbjct: 234 GISQAQVSRIEKSAIGHIKK 253


>gi|86358940|ref|YP_470832.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283042|gb|ABC92105.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 302

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 125/279 (44%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSAVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R    + ++ L  RE R+   R       
Sbjct: 194 EGDSGQWQDWLVDDHESQEDVLIEQDELETRRRMLAKAMSVLNERERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R + L 
Sbjct: 252 PVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEALE 290


>gi|254995008|ref|ZP_05277198.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Mississippi]
          Length = 296

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 68/278 (24%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + + +  +     +S  E + +          +      +V ++LRLV+ +A  + + G
Sbjct: 20  DLVSYVAQVRTFPILSEEEEKRLAE--NWYRRGSVADAHRLVTSHLRLVVKIAMGFKSYG 77

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +I   I      IR+      
Sbjct: 78  LPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQAQ 137

Query: 528 K--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIG 581
           K     + +  +R+ +      T +E   IA++ A   E V R         +SL   + 
Sbjct: 138 KKLFFSLRKIKKRLLS-CGSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQVH 196

Query: 582 DEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            E +  L D +        +  L     A  +      LA+L  R   +   R       
Sbjct: 197 GESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLRE--R 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLE++ +++ V++ER+RQIE +A+ K+K    + ++
Sbjct: 255 PDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEANRV 292


>gi|261819465|ref|YP_003257571.1| RNA polymerase factor sigma-32 [Pectobacterium wasabiae WPP163]
 gi|261603478|gb|ACX85964.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium wasabiae
           WPP163]
          Length = 285

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 132/270 (48%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYQGDLEAAKHLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + +T  R+    + E   E +A++L +  + VR++  ++  + ++ +    ++  
Sbjct: 134 KLFFNLRKTKTRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDSH 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   +   +  ++  S     I+ +  +T      T  L  L  R + ++R R+ +  + 
Sbjct: 192 DGKAMSPMLYLQDKSSDFAGGIEEDNWDTHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|239932973|ref|ZP_04689926.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441326|ref|ZP_06580716.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291344221|gb|EFE71177.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 295

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 118/251 (47%), Gaps = 8/251 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S   FR +  +  +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IG
Sbjct: 42  ELSRQFFRRLAEL-EEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDIVQTGMIG 100

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    ++
Sbjct: 101 LIKAIDRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELA 160

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +++ REPT  E+A  + +  + V +           SL+  +  +   +    + D   V
Sbjct: 161 SRLDREPTVAELATLMNITEDQVIEGQIAANGYNSSSLDAALTGDGPENGEAVLADFIGV 220

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                 +  +       ++A L+ R+ +++ MRF      + T  E+G++   ++  + +
Sbjct: 221 EEEGLRLVEDFH-ALAPLMAELSERDRQIIHMRFV----EEATQAEIGERLGCSQMHVSR 275

Query: 659 IEAKAIRKLKH 669
           +  + I +L+ 
Sbjct: 276 LIKRIIARLRE 286


>gi|37527948|ref|NP_931293.1| RNA polymerase factor sigma-32 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787384|emb|CAE16473.1| RNA polymerase sigma-32 factor [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 285

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E + +   +         A K+++ ++LR V+ VA+ Y   GL
Sbjct: 16  LEGYVRASNTYPMLTAEEEKELAERL--HYQGDLDAAKKLILSHLRFVVHVARSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
                + +T +R+    + E   E +AK+L +  + VR++   +        +      +
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVAKELGVTSKDVREMESRMSAQDMAFDMSADDDSQ 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRFGIGMNT 638
           +   +   +  ++  S     I+ +  E       +  + SL  R + ++R R+ +  + 
Sbjct: 192 EGQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSVAIESLDERSQDIIRCRW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|218289914|ref|ZP_03494104.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240054|gb|EED07240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 259

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 134/264 (50%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V T     ++ ++ R +   +R        A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVNTSQLPVLTNAQMRELFEQLR---AGDLSAREKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    +++K  REP+  EIA ++ +P E V   L   ++P+S+  PI  +  
Sbjct: 119 RDIAYKALQVRDMLASKNLREPSIVEIANEMNLPKEEVVFALDAIQDPVSMFEPIYHDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L+ RE+++L  RF  G     T  
Sbjct: 179 DPIYVMDQIHDEREKDSAWVEGIA-----LREAMRKLSDREKKILAKRFYEG----KTQM 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV  +  +++ ++ ++E  AI ++
Sbjct: 230 EVADEIGISQAQVSRLEKAAIHRM 253


>gi|209551384|ref|YP_002283301.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209537140|gb|ACI57075.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 287

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 130/275 (47%), Gaps = 15/275 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  IK       ++  E   +   +R  + +   A+ ++  A++RLVIS+A K+ N GL 
Sbjct: 8   RRMIKIAMAAPYLARQEEHDLA--IRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLP 65

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 66  MSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKA 125

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   +++    ++  +   +EIA  L + +  V+    +++    SL+ P    
Sbjct: 126 LFFNLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSG 185

Query: 584 D--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNT 638
           D  ++   DF+  +D      + + I    R       L  L  RE +++  R       
Sbjct: 186 DAESAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDG- 244

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+G    +++ER+RQIE++A+ KL+    S
Sbjct: 245 -ATLEELGADLGISKERVRQIESRAMEKLRSALVS 278


>gi|291619275|ref|YP_003522017.1| RpoH [Pantoea ananatis LMG 20103]
 gi|291154305|gb|ADD78889.1| RpoH [Pantoea ananatis LMG 20103]
 gi|327395604|dbj|BAK13026.1| RNA polymerase sigma-32 factor RpoH [Pantoea ananatis AJ13355]
          Length = 285

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +++ +    +S  E + +   +         A K ++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LESYVRAANTWPMLSAEEEKALAERL--HYQGDLDAAKTLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
                + +T +R+    + E   E +A++L +  + VR++   +        +       
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSADDESG 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           +   +   +  ++  S     I+ +  E+      T  +  L  R + ++R R+ +  + 
Sbjct: 192 EGKSMAPVLYLQDKTSDFADGIEEDNWESHAADKLTYAMEGLDERSQHIIRARW-LDEDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KTTLQELADRYGVSAERVRQLEKNAMKKLR 280


>gi|86158413|ref|YP_465198.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774924|gb|ABC81761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 307

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 74/274 (27%), Positives = 128/274 (46%), Gaps = 16/274 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    +++ E + +    +      + A   +V ANLR V+ VA +Y + G +  
Sbjct: 16  YLSEINRFPLLTVDEEQRLAR--QFCADRDTRAAHRLVTANLRFVVKVAYEYRSYGFRMA 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA +KFD   G +  +YA+WW++  I   I      +++      R   
Sbjct: 74  DLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKLF 133

Query: 530 HKVVRTARRMSNKIKRE------PTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGD 582
             + RT R +  + + +          ++AKKL +    VR++  ++    +SL+ P+GD
Sbjct: 134 FSLARTKRELDKRSQEQGADSDGHDANKVAKKLRVKPGEVREMEQRMEGRDLSLDAPMGD 193

Query: 583 EDTSHLGDFIEDKNAVSPLDS---AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      DF+   +     +      Q  +       L  L  RE  ++     +  +  
Sbjct: 194 DGGYSHVDFLASGSTSQDDELSGVQEQKVVSGRIVEALGRLDQRERYIIE--MRVMSDRP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TL+E+G+ F  +RER RQ+E +A  KLK   R+
Sbjct: 252 LTLKELGEHFGFSRERARQLEIRAKDKLKEELRA 285


>gi|308069565|ref|YP_003871170.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           (sporulation sigma factor) [Paenibacillus polymyxa E681]
 gi|305858844|gb|ADM70632.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Paenibacillus polymyxa E681]
          Length = 251

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 124/254 (48%), Gaps = 14/254 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T  S  E   +  ++   +   + A++ +V +N+RLV SV +++ NRG +  DL Q 
Sbjct: 5   GKKTSHSYLEDAEVKQLIALSQSGDNEARETLVNSNIRLVWSVVQRFMNRGYEPDDLFQI 64

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +  
Sbjct: 65  GCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKETANKVRKMK 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             +S ++ R PT +E+A +L +  E V    +  K P S+   + + D     L D I D
Sbjct: 124 DELSKRLNRLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD 183

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           ++     D       +      +  L+ RE  ++     +    D T  EV  +  +++ 
Sbjct: 184 ESQERWFD-------KLALNEAIGGLSERERLIV----YLRYYRDQTQSEVASRLGISQV 232

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K ++ ++
Sbjct: 233 QVSRLEKKILQLIR 246


>gi|3021680|dbj|BAA25360.1| RNA polymerase sigma-70 factor [Pseudomonas fluorescens]
 gi|11079045|dbj|BAB17527.1| DNA-directed RNA polymerase subunit D [Pseudomonas fluorescens]
          Length = 269

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 112/315 (35%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +E L+REGEI IAKRIE G   +M ++   P T    +     +      L ++  L   
Sbjct: 1   VESLTREGEIEIAKRIEEGIREVMGAIAHFPGTVDHTLSEYTRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                      + +     +   D ++ A    +D  +    P  
Sbjct: 59  IDPDDGI--------APPAAEVPPPVDPKAVKADDDAEDDDAEASSDDEDEVESGPDPII 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  ++
Sbjct: 111 AAQRFGAVSDQMEITRKAL-----------------------------------KKHGRA 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           +         L +L   + L   + + LVE++    +R+   E  +++L      + R  
Sbjct: 136 NKLAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 FLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 255 INRRMSIGEAKARRA 269


>gi|119899581|ref|YP_934794.1| RNA polymerase factor sigma-32 [Azoarcus sp. BH72]
 gi|119671994|emb|CAL95908.1| RNA polymerase sigma-32 factor [Azoarcus sp. BH72]
          Length = 284

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 135/265 (50%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++++    ++  +   + + +R  +     A +++V ++LR+V+++A+ Y   GL
Sbjct: 16  IDQYIQAVNRVPLLTEQQEVELATRLR--DDGDVDAARQLVMSHLRVVVAIARGYLGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD   G +  ++A+ W+K  I   I      ++I     + 
Sbjct: 74  PHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHWIKAEIHEYILKNWRLVKIATTKAQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   +R+ ++ +  + R+       +    P E V    +++   I ++    DED   
Sbjct: 134 KLFFNLRSLKQDTGTLNRDEVEAVATQLGVKPEEVVEMETRLSGRDIPIDGGNDDEDERF 193

Query: 588 -LGDFIEDKNAV--SPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               ++    A     L+ A +A+L++T   + L +L  R   ++  R+ +      TL 
Sbjct: 194 APIAYLPAPAAEPSEVLERAERAHLQDTGLKQALGALDERSRTIVERRW-LTDGDSATLH 252

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  ++ V+ ERIRQIEAKA++K++
Sbjct: 253 ELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|146410|gb|AAA23991.1| heat shock regulatory protein [Escherichia coli]
          Length = 284

 Score =  133 bits (333), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 133/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    D+  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLASDDDSD 191

Query: 586 SH-LGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           SH +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SHAMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|254501465|ref|ZP_05113616.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
 gi|222437536|gb|EEE44215.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
          Length = 269

 Score =  133 bits (333), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 70/261 (26%), Positives = 120/261 (45%), Gaps = 13/261 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +    +  E E   A + +V ++LRLV  +A  Y   GL   +++ EGN+GL
Sbjct: 2   LQPQEEYMLAKRYK--EHEDPEAAERLVNSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI-----HKVVRTA 536
           M+A ++F+   G++ +TYAMWW+K AI   I      +++      K       ++    
Sbjct: 60  MQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGKI 119

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDK 595
           + +     +    +EIA +L +  E V  + +      SL  PI  E D     D++ D+
Sbjct: 120 QALEEGDLKPHQVQEIATRLGVSEEEVVSMNRRLGGDASLNAPIRAEADAGEWQDWLVDE 179

Query: 596 NAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           +       A Q  L   R+  +  +  L  RE R+             TLE++  +F V+
Sbjct: 180 SDSQETLLANQEELDMRRKMLSDAMDVLNDRERRIFEA--RRLSEDPMTLEDLSGEFGVS 237

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
           RER+RQIE +A  K++   R+
Sbjct: 238 RERVRQIEVRAFEKVQKAVRN 258


>gi|126348115|emb|CAJ89836.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 295

 Score =  133 bits (333), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 117/247 (47%), Gaps = 7/247 (2%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA
Sbjct: 45  RQFFQRLTELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIGLIKA 104

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +S+++ 
Sbjct: 105 IDRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELSSRLD 164

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           REPT  E+A  + +    V +    +      SL+  +  +        + D   V    
Sbjct: 165 REPTVAELATLMNISENEVVEGQIASNGYNSSSLDAALTGDGPEGGESVLADFIGVEEDG 224

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  +   +   ++A L+ R+ +++ MRF      + T  E+G++   ++  + ++  +
Sbjct: 225 LRLVEDFH-SLAPLMAELSERDRQIIHMRFV----EEATQAEIGERLGCSQMHVSRLIKR 279

Query: 663 AIRKLKH 669
            I +L+ 
Sbjct: 280 IITRLRE 286


>gi|24376056|ref|NP_720099.1| RNA polymerase factor sigma-32 [Shewanella oneidensis MR-1]
 gi|24351072|gb|AAN57543.1|AE015890_4 RNA polymerase sigma-32 factor [Shewanella oneidensis MR-1]
          Length = 285

 Score =  133 bits (333), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 125/273 (45%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S++    +       +   ++  E     A K+++ ++LR V+ VAK Y   GL
Sbjct: 19  LEAYIHSVTSMNMLDAETEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYAGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +   R+      E T   +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNIRKAKTRLGWFSDDEVTM--VAENLGVSKADVTEMESRMAAQDPAFDLSSDNDDE 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   ++N +      + +L  R + +LR R+     T  
Sbjct: 195 HDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQHILRARWLDDDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL+E+ + + V+ ERIRQ+E  A+ KLK    +
Sbjct: 253 TLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|585927|sp|P37970|RPOF_STRAU RecName: Full=RNA polymerase sigma-F factor
 gi|153450|gb|AAA93050.1| minor sigma-like factor [Streptomyces aureofaciens]
          Length = 297

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 109/241 (45%), Gaps = 11/241 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++ G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G
Sbjct: 63  LQPGTREHERVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERG 122

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA
Sbjct: 123 VQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNAATEDLTTLHGRTPTTPEIA 182

Query: 554 KKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L +  + V   ++   +    SLE     +    L D +  ++             R+
Sbjct: 183 ERLRISEDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPELAGVEH-----RD 237

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +
Sbjct: 238 LVRHLLVQLPEREQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSAN 293

Query: 672 R 672
           R
Sbjct: 294 R 294


>gi|253681759|ref|ZP_04862556.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
 gi|253561471|gb|EES90923.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
          Length = 257

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 77/265 (29%), Positives = 136/265 (51%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ K       ++++ +  NLRLV+SV +++ NRG
Sbjct: 2   MINKVEICGVNTSKLPVLKDKEMKELLIKMRDGDYFSREKFIRGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   R+ NK  ++P   +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALQVRDRLINKDNKDPNVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KNA       I      +    +  L  RE+ +L MRF  G     T  E
Sbjct: 181 LYVMDQISDSKNADDSWIENI------SIKEAMKRLNKREKLILNMRFFQG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|294085881|ref|YP_003552641.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
 gi|292665456|gb|ADE40557.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 312

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 72/277 (25%), Positives = 123/277 (44%), Gaps = 15/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   +   +       E     +  ++V ++LRLV  +A  Y   GL
Sbjct: 21  LSRYLEQIRAFPMLEPKQEYMLAK--AWKEKGDVESAHQLVTSHLRLVAKIAMGYRGYGL 78

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLI EGN+G+M A +KF+   G++ +TYAMWW+K AI   I      ++I      +
Sbjct: 79  PVADLISEGNLGMMHAVKKFEPEKGFRLATYAMWWIKAAIQEYILRSWSLVKIGTTAGQK 138

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + R   ++    + +  PE+   IA +L +    V     ++     SL  P+  
Sbjct: 139 KLFFNLRRIKGQIQAIDEGDLKPEQVTHIADELNVTEAEVMSMNQRMAGNDRSLNVPLSR 198

Query: 583 EDT--SHLGDFIEDK--NAVSPLDSAIQANLRETT-TRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED   +  +      + + R       +  L  RE+R+L+ R      
Sbjct: 199 DGEGTGEWQDWLEDDTVDQETSFAEHEEYSARANLMMDAMKGLNEREQRILQARRLAEP- 257

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
              TLE++  +F V+RERIRQIE +A  KL+   R K
Sbjct: 258 -PLTLEDLAGEFNVSRERIRQIEVRAFEKLQKAVRDK 293


>gi|11079143|dbj|BAB17576.1| DNA-directed RNA polymerase subunit D [Pseudomonas alcaligenes]
          Length = 267

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/315 (19%), Positives = 117/315 (37%), Gaps = 49/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T  +++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAISLFPGTVDSILAEYQRVTTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+            S    E   + KE     + + + E       DD       PE 
Sbjct: 59  IDPDDG----------SLPAEEVVPELKEATAEAKDDEEEEEEGDSDSDDEGDGGPDPEE 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  D +   L                                   +K  + 
Sbjct: 109 AARRFGAVAEQLDKARKAL-----------------------------------KKHGRG 133

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S + +  ++ L +L   + L   + D LVE++    +++   E  +++L      + R  
Sbjct: 134 SKQAEKEQQALAELFMPIKLVPKQFDALVERVRGSLEQVRAQERAIMQLCVRDARMPRAD 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL+   G E+   W +      + ++   +   +  I + + ++ +I  + G+ I+E + 
Sbjct: 194 FLKLFPGNEVATDWAAGLAK-GKAKYAEAIGNLLADIQRCQEKMAAIEADAGLVIAEIKD 252

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 253 INRRMSIGEAKARRA 267


>gi|319781136|ref|YP_004140612.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167024|gb|ADV10562.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 303

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 124/275 (45%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E E + A  ++V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLEEIRRFPMLQPQEEYMLAK--RYAEHEDTSAAHKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  KV    + + +   +     EIA +L +    V  + +      SL  PI   
Sbjct: 133 RLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVSEAEVVSMNRRLSGDASLNAPIRAS 192

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R   +  LA L  RE R+   R       
Sbjct: 193 EGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNERERRIFEARRLAE--E 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+  +F ++RER+RQIE +A  K++   ++
Sbjct: 251 PLTLEELSSEFDISRERVRQIEVRAFEKVQDAVKA 285


>gi|225630797|ref|YP_002727588.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
 gi|225592778|gb|ACN95797.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
          Length = 270

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 129/268 (48%), Gaps = 16/268 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +       + +   +  +++ ++L LV+ +A K+ N GL  +DL+ EGN+GL
Sbjct: 2   LSQEEEVRLAK--NWNQYKDVSSAHKLITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRM 539
           M A +KF+  LG++FSTYA+WW++ +I   I      ++I      R     + +  +R+
Sbjct: 60  MHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIGTTQAQRRLFFSLRKIKKRI 119

Query: 540 SNKIKREPTPEEIAKKLAMPV-----EGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
                RE    E  K ++  +     + ++   ++  +  SL   I   D S   L D I
Sbjct: 120 LQYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMI 179

Query: 593 EDK--NAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                +      +  +  L+E      LASL  R   +   R+        TL+E+ K++
Sbjct: 180 PCNLVSQEVTYQNHEEKELKEAILNNALASLNERARDIFISRYLSENIQ--TLDELSKKY 237

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           CV+RERIRQ+  +A+ K+K   +S+ L+
Sbjct: 238 CVSRERIRQLAEQAMAKVKQYIQSESLK 265


>gi|13473215|ref|NP_104782.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14023963|dbj|BAB50568.1| sigma factor [Mesorhizobium loti MAFF303099]
          Length = 303

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 122/275 (44%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E E + A  ++V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLEEIRRFPMLQPQEEYMLAK--RYAEHEDTSAAHKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  KV    + + +   +     EIA +L +    V  + +      SL  PI   
Sbjct: 133 RLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVTEAEVVSMNRRLSGDASLNAPIRAT 192

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R   +  LA L  RE R+   R       
Sbjct: 193 EGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNERERRIFEARRLAE--E 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+  +F ++RER+RQIE +A  K++   ++
Sbjct: 251 PLTLEELSAEFDISRERVRQIEVRAFEKVQDAVKA 285


>gi|320103437|ref|YP_004179028.1| RpoD subfamily RNA polymerase sigma-70 factor [Isosphaera pallida
           ATCC 43644]
 gi|319750719|gb|ADV62479.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Isosphaera
           pallida ATCC 43644]
          Length = 286

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 82/251 (32%), Positives = 122/251 (48%), Gaps = 9/251 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R +   V       + A++ M+EANLRLV  VA +Y   GL + DL+ EGN+GL
Sbjct: 33  LTAEEERELARRV---LRGDASARRRMIEANLRLVAMVAARYRGLGLDWEDLVGEGNLGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A   +D   G +FSTYA  W++Q I  ++   + TIR+P HM  K+    R   R++ 
Sbjct: 90  IRAVSSYDPDRGVRFSTYAAHWIRQTIRVALTTTAATIRLPAHMVTKLALWRRAEARLTR 149

Query: 542 KIKREPTPEEIAKKLAMPVE-GVRKVLKITKEPISLETPIGDEDTSH----LGDFIEDKN 596
            + R PT EE+A +L       +     +    +  E P   E          D   D  
Sbjct: 150 NLGRSPTFEEVADELGWSSSTRLSMKRAMESGRVHHEEPGATEGRGSESRRPIDQAVDPR 209

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                +   +  L E   R L  L  RE  VL +R+G+G      L EV     VTRE +
Sbjct: 210 PEPAWEIERRDELLE-LRRSLQRLGERERLVLALRYGLGDIAPKPLREVATTLGVTREWV 268

Query: 657 RQIEAKAIRKL 667
           R+IEA+A+R+L
Sbjct: 269 RRIEARALRQL 279


>gi|304311558|ref|YP_003811156.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
 gi|301797291|emb|CBL45511.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
          Length = 285

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   + +++    +S  E R +    R    E   A +++V A+LR V+ VA+ Y   G
Sbjct: 16  DLNRYLSAVNSVAILSADEERALAE--RYYYNEDVDAARQLVLAHLRFVVHVARGYNGYG 73

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HM 525
           LQ  DL+QEGN+GLMKA ++FD  +G +  ++A+ W+K  I   I      ++I      
Sbjct: 74  LQLSDLVQEGNVGLMKAVKRFDPTMGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKSQ 133

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
           R     +    RR+      E     IA +L +  E VR++  ++     + + P+  +D
Sbjct: 134 RKLFFNLRSHKRRLGVLSGDEVNM--IATELNVSPEDVREMEGRLAAHDTAFDAPVDADD 191

Query: 585 TSHLG---DFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            S       ++ED     A    D+    N  +     + SL  R   +L+ R+    + 
Sbjct: 192 ESASQAPVYYLEDASMDPAHQLEDAQWTDNTTDRLQLAMNSLDERSRDILQQRWF--NDD 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL ++  Q+ V+ ERIRQ+EA A++K+K
Sbjct: 250 KATLHDLAAQYSVSAERIRQLEANAMKKIK 279


>gi|154245929|ref|YP_001416887.1| RNA polymerase factor sigma-32 [Xanthobacter autotrophicus Py2]
 gi|154160014|gb|ABS67230.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthobacter autotrophicus
           Py2]
          Length = 300

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 68/271 (25%), Positives = 121/271 (44%), Gaps = 13/271 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLEEIRRFPMLEPQEEYMLAK--SWREHGDRDAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++S     +  PE   +IA KL +  + V  + +      SL +PI ++
Sbjct: 134 KLFFNLRKAKSQISALEDGDLKPEHVKQIATKLGVTEQDVVDMNRRLSGDASLNSPIRED 193

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
            +     D++ D+        A    L   R   +  L+ L  RE R+            
Sbjct: 194 SEGGEWQDWLVDERLDQEEQLAESEELDNRRAALSGALSVLNDRERRIFEA--RRLSEDP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            TLE++  +F V+RER+RQIE +A  K++  
Sbjct: 252 MTLEDLASEFGVSRERVRQIEVRAFEKVQKA 282


>gi|321309570|ref|YP_004191899.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801414|emb|CBY92060.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 524

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 97/313 (30%), Positives = 158/313 (50%), Gaps = 46/313 (14%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           + ++     ++  E R +  ++   +     A K+++ +NLRLVIS+AKKY NRG    D
Sbjct: 205 LSTLHFSKMLTAEEERKLAKLMDNPDLR-PFAVKQLMTSNLRLVISIAKKYLNRGFSLGD 263

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+QEG  GLMK+ +KFD+  G KFSTYA WW++Q+ITR+IADQ+  IRIPVHM + I+K 
Sbjct: 264 LVQEGVFGLMKSIQKFDYKFGNKFSTYATWWIRQSITRAIADQARIIRIPVHMVEVINKF 323

Query: 533 VRTARRMSNKIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           V+  + +  K   EPT E++A+++        V+ V  + K+  + +SL+ PI   +TS+
Sbjct: 324 VKAEKDLILKNGEEPTIEQLAQEMQKYSPQYTVQKVSDIKKLNIDLVSLDKPIAHNETSN 383

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFG------------- 633
             DF++D+ A S  + A   +        L  +L   E  ++ M +G             
Sbjct: 384 FSDFVQDEEAASSEEVAASTHKSMVLQEFLESTLEDDELLMIHMHYGLMEYKSPHTIEQI 443

Query: 634 --------------------------IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                                     +  +   T EE  K+       +R+  ++A+RKL
Sbjct: 444 VSERLLNPKYKGILKNKAINFVINGMLEKHKVLTPEEWKKEKAKVENFVRKKISQALRKL 503

Query: 668 KHPSRSKKLRSFL 680
           K PS++ K R+  
Sbjct: 504 KKPSKNGKYRTIF 516


>gi|227823295|ref|YP_002827267.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342296|gb|ACP26514.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 301

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/279 (26%), Positives = 123/279 (44%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLAK--RYQEHDDRSAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KF+   G++ +TYAMWW+K AI   I      +++    + +
Sbjct: 74  PIGEVMSEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+    + +  PE   EIA  L +  + V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEDEVVSMNRRLSGDASLNAPIKAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D++         Q  L   R      +  L  RE R+           
Sbjct: 194 EGDSGQWQDWLVDEHDNQEEILIEQDELDSRRALLASAMKVLNDRERRIFEA--RRLTEE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLEE+  +F ++RER+RQIE +A  K++   R   L 
Sbjct: 252 PVTLEELSTEFDISRERVRQIEVRAFEKVQEAVRKAALE 290


>gi|254462386|ref|ZP_05075802.1| alternative sigma factor RpoH [Rhodobacterales bacterium HTCC2083]
 gi|206678975|gb|EDZ43462.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium HTCC2083]
          Length = 298

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 124/276 (44%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPMLEPEEEYMLAK--SWVEKQDTAAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ E N+GLM+A ++FD   G++ STYAMWW++ AI   I      +++      K
Sbjct: 74  PQAEVVSEANVGLMQAVKRFDPEKGFRLSTYAMWWIRAAIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKLA----MPVEGVRKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE +A+          E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNRIGALEEGDMRPENVARIAHDLGVTETEVISMNRRMSGGDASLNAQVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     +  L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARREMLADAMDVLNDREKDILVQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLE++  Q+ V+RERIRQIE +A  KL+   RS
Sbjct: 252 KPVTLEDLSGQYDVSRERIRQIEVRAFEKLQERMRS 287


>gi|182418893|ref|ZP_02950150.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237667291|ref|ZP_04527275.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377176|gb|EDT74744.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237655639|gb|EEP53195.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 257

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 75/265 (28%), Positives = 133/265 (50%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + I + +    ++ + +     A++  ++ NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTSKLPILKEKEKKQLLLQMKAGDKSARETFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENIDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    +      +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALIVREKFIKDNNKEPTISQIAKELELPREEVVFALDAIQDPVSLYEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D K+        I      +    +  L+ RE+ +L +RF  G     T  E
Sbjct: 181 IYVMDQISDSKDTDENWLENI------SIKEAMKKLSDREKLILNLRFFNG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|326571483|gb|EGE21498.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC7]
          Length = 371

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 125/270 (46%), Gaps = 11/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++  E R +    R        A + +V ++LR VI +A+ Y+  
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAE--RYYHDGDVEAARLLVMSHLRFVIHIARSYSGY 154

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 155 GLSQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKA 214

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ SN++  +     IA  L + V+ V     ++T    S E    D+D
Sbjct: 215 HRKLFFNLRSLKKSSNQLTLDEATA-IANDLNVTVKQVLEMESRLTSYDASFEAQDSDDD 273

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++AV+P D   +A+  E         + +L  R   ++  R+        
Sbjct: 274 EGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLAD--QKS 331

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TL E+   + ++ ER+RQIE  A+ K+K  
Sbjct: 332 TLHELAATYNISAERVRQIEKNAMNKIKEA 361


>gi|215270863|emb|CAR48109.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 269

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/311 (17%), Positives = 109/311 (35%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   +++E  D  E   D    ++       ++        
Sbjct: 61  ADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKAAVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET +++   + I 
Sbjct: 200 ALFTGNESSEAWLDEILS-SDKPYAEKIKRSEEEIRRSITKLKMIEQETSLNVQNIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAR 269


>gi|167585406|ref|ZP_02377794.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ubonensis Bu]
          Length = 311

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 140/301 (46%), Gaps = 13/301 (4%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             P+ +S A    E      +A        +  I   I++++    ++  E R   +  R
Sbjct: 6   TLPNTLSPASAKAESAGSLALATHSMLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFR 65

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +       A + +V ++LRLV+S+A+ Y   GL   DLIQEGNIGLMKA ++FD     +
Sbjct: 66  EQNNLD--AARRLVLSHLRLVVSIARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVR 123

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
             +YA+ W+K  I   I      +++      +       + +   +       + +A++
Sbjct: 124 LVSYAIHWIKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKKGMQAMTPEEIDGLAQE 183

Query: 556 LAMPVEGV-RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRET 612
           L +  E V     +++   I+LE  + D + S+  +    +  N  + + +A Q ++ +T
Sbjct: 184 LNVKREEVTEMETRLSGGDIALEGQVEDGEESYAPIAYLADSHNEPTAVLAARQRDMLQT 243

Query: 613 --TTRVLASLTPREERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               + L +L  R  R++  R+    +      TL ++  +F V+ ERIRQIEA A++K+
Sbjct: 244 DGIAQALDALDARSRRIIEARWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKM 303

Query: 668 K 668
           +
Sbjct: 304 R 304


>gi|163747420|ref|ZP_02154772.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
 gi|161379273|gb|EDQ03690.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
          Length = 298

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 127/275 (46%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A   MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      +
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   ++    + +  PE   EIA +L +   E V    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNKIGALEEGDLRPENVTEIATQLGVTEAEVVSMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D A +  L   RE     L  L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYAERDELETRREMLADALDVLNDREKDILTQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 ETVTLEDLSTQYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|5732893|gb|AAD49326.1|AF162936_2 RNA polymerase alternative sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 354

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 117/241 (48%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + K   E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 117 LRTLEKDSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 176

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 177 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 236

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KL++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 237 ELAEKLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 292

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 293 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 347

Query: 669 H 669
            
Sbjct: 348 E 348


>gi|55274953|gb|AAV49276.1| RNA polymerase subunit sigma-38 [Shigella flexneri 2a]
          Length = 193

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 77/190 (40%), Positives = 129/190 (67%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L+
Sbjct: 61  ERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 120

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           + +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL
Sbjct: 121 LNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 180

Query: 629 RMRFGIGMNT 638
             RFG+    
Sbjct: 181 ARRFGLLGYE 190


>gi|289808389|ref|ZP_06539018.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 148

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 101/144 (70%), Positives = 118/144 (81%)

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +M  ++ REPTPEE+A+++ MP + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED   
Sbjct: 4   QMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL 63

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIR
Sbjct: 64  ELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 123

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLD 681
           QIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 124 QIEAKALRKLRHPSRSEVLRSFLD 147


>gi|170691517|ref|ZP_02882682.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
 gi|170143722|gb|EDT11885.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
          Length = 311

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 129/272 (47%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+ +     A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           E +AK+L +  E V ++    +   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKQGLGSFTPDEIEGLAKELNVKREEVAEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+    ++ D ++      A +   +   +     L +L  R  R++  R+    +  
Sbjct: 213 EESYAPIAYLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIEARWLKVQDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|134100730|ref|YP_001106391.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006467|ref|ZP_06564440.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133913353|emb|CAM03466.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 268

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 116/245 (47%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +  +     ++ +  +V  +L +   +A+++ +RG    DL+Q   +GL+KA +
Sbjct: 19  FAELAELDEQDGRYQAL-RDRLVTEHLPVAEHIARRFRHRGETHDDLVQVATLGLIKAVD 77

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F +YA+  +   + R   D   ++R+P  M++    V      +S ++ R 
Sbjct: 78  RFDPGRGVGFMSYAVPTIMGEVRRHFRDAGWSVRMPRRMQELHLSVSAGISALSQELGRA 137

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PTP E+A  L + V+ V++ L+        SL+  +   D   LG+ I   ++       
Sbjct: 138 PTPSELAAHLKLSVDDVQQGLEAGNAYRSASLDDLLTGTDDVPLGEAIGFDDS-----EL 192

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +   RET   +LA L  RE R+L MRF  G     T  E+ +Q  V++  + ++  + +
Sbjct: 193 AEVEDRETIRPLLAELPERERRILVMRFFRG----MTQTEIAEQVGVSQMHVSRLLTRTL 248

Query: 665 RKLKH 669
             L+ 
Sbjct: 249 SWLRE 253


>gi|168186812|ref|ZP_02621447.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
 gi|169295146|gb|EDS77279.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
          Length = 256

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 77/265 (29%), Positives = 138/265 (52%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ K +   ++++++ V  NLRLV+SV +++ NRG
Sbjct: 1   MINKVEICGVNTSKLPVLKEKEMKELLLKMKDGDNLSREKFVRGNLRLVLSVIQRFNNRG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 61  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   R+  K  ++P   +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 120 IAYKALQVRDRIIKKENKDPNVSQIAKELDLPREEVVFALDAIQDPVSLFEPIYHDGGDA 179

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KNA       I      +    +  L  RE+ +L MRF  G     T  E
Sbjct: 180 LYVMDQISDNKNADESWIENI------SIKEAMKRLNEREKLILNMRFFQG----RTQME 229

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 230 VADEIGISQAQVSRLEKTALKHMRK 254


>gi|11079139|dbj|BAB17574.1| DNA-directed RNA polymerase subunit D [Pseudomonas citronellolis]
          Length = 269

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 58/315 (18%), Positives = 115/315 (36%), Gaps = 47/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++ + P     ++     +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAQFPGAVDGILDEYQRVVSEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+              ++ E   ++K  D   + + + +  +    +D       PE 
Sbjct: 59  IDPDDGS--------VPAEEVELDLKDKGGDAKAKDDEEEDEESDDDSEDEGDGGPDPEE 110

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  D +   L                                   +K  + 
Sbjct: 111 AARRFGLVADQLDKTKKAL-----------------------------------KKHGRG 135

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++ D   ++   E  +++L      + R  
Sbjct: 136 SKQADAEMLALAELFMPIKLVPKQFDALVTRVRDALDQVRRQERAIMQLCVRDARMPRAD 195

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    GRE D  WV       + ++   +    D +++ + ++ ++     + +SE + 
Sbjct: 196 FLRLFPGRETDEAWVDSVLK-AKPKYAEALERVKDDVVRNQQKLSALESNVDLKVSEIKD 254

Query: 430 IVSMVRKGECEASIA 444
           +   +  GE +A  A
Sbjct: 255 VNRAMSIGEAKARRA 269


>gi|239934544|emb|CAR94586.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 241

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 90/259 (34%), Positives = 143/259 (55%), Gaps = 29/259 (11%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
             GEIAIAKRIEAGR +M+  +CESPL  +++I W   L DG  LLRE+IDL+A    E 
Sbjct: 4   AXGEIAIAKRIEAGRELMIGGICESPLAIESIIAWYKALQDGDILLREVIDLDATYSGE- 62

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  + D  Q +  D E   + S++   +     E    + 
Sbjct: 63  -----------------------QEDFTQVSREDKEEEEEDSEESEDEEGEDGEEKGGES 99

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-----DEKS 310
              DEDEDD+A +LSAME++L P+V     +I + Y++++ +Q+  +   +     DEK+
Sbjct: 100 SEDDEDEDDNAMSLSAMEEELAPQVFEIFGKIQKTYKKMQKVQNERLELLQKGRKADEKA 159

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
             K + LK  +V+L+  + LN SRI+ L+++LY +++ ++  EG++LR+A    +KR+ F
Sbjct: 160 DKKYEKLKHDMVELMNEVRLNNSRIEQLIDRLYTMNRELVSLEGKMLRMAVDCKVKREDF 219

Query: 371 LERHQGRELDPHWVSYAKD 389
           LE + G ELDP W++  K 
Sbjct: 220 LEHYYGAELDPRWLTKVKK 238


>gi|317046493|ref|YP_004114141.1| RNA polymerase,sigma 32 subunit,RpoH [Pantoea sp. At-9b]
 gi|316948110|gb|ADU67585.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. At-9b]
          Length = 285

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 129/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +V   +S  E + +   +         A K ++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LESYIRAANVWPMLSAEEEKALAERL--HYQGDLDAAKTLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
                + +T +R+    + E   E +A++L +  + VR++   +        +     + 
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSADDENG 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           ++  +   +  ++  S     I+ +  +       T  +  L  R + ++R R+ +    
Sbjct: 192 ESKTMAPVLYLQDKTSDFADGIEEDNWDAHAADKLTDAMQGLDERSQHIIRARW-LDEEN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KTTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|297158638|gb|ADI08350.1| RNA polymerase sigma factor, sigma F [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 111/253 (43%), Gaps = 12/253 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++   F  +  +         + +  ++EANL LV   A ++ +R     D++Q G IGL
Sbjct: 32  LTQVLFAELSDLTPGTPEHGRV-RDALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A ++FD   G +F T+AM  V   I R   D   T+ +P  + +   +V      ++ 
Sbjct: 91  INAIDRFDPERGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTV 150

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              R PT  EIA++L +  + V   ++   +    SLE     +    L D +  ++   
Sbjct: 151 LHGRSPTTAEIAERLGLGEDEVLACIEAGRSYHATSLEAAQEGDGLPGLVDRLGYEDPAL 210

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                     R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++
Sbjct: 211 AGVEH-----RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRL 261

Query: 660 EAKAIRKLKHPSR 672
            +++  +L+  +R
Sbjct: 262 LSRSFARLRSANR 274


>gi|258515296|ref|YP_003191518.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779001|gb|ACV62895.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 259

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 66/257 (25%), Positives = 130/257 (50%), Gaps = 15/257 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++     +   E R +++  +      ++A++ +V  NL+LV ++ K++ NRG +  DL 
Sbjct: 9   NLPRFPLLKDEEMRQLLAKAK---LGDAVARERLVNCNLKLVFNLVKRFNNRGYELEDLF 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G+IGLMKA +KFD     KFSTYA+  +   I R + D    +++   +++  +KV +
Sbjct: 66  QIGSIGLMKAIDKFDLNYDVKFSTYAVPMIVGEIRRFLRD-DNPVKVSRSVKEIAYKVQQ 124

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
           T  R+  K+ REP+  E+A+++ +  E V   L+  + P S+   +  +D    +L D +
Sbjct: 125 TKERLIGKLGREPSIGEVAEEIGLSKEEVVIALEAAQSPTSIYETLHQDDGDPIYLLDQL 184

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
             K                    +L +L  R+ ++L  RF      D T  ++ ++  ++
Sbjct: 185 SSKEGNDLFWLDQIE-----VKELLNNLHERDRQILIWRFF----EDKTQSDIARRLGLS 235

Query: 653 RERIRQIEAKAIRKLKH 669
           + ++ ++E +A+ KLK 
Sbjct: 236 QVQVSRLERQALNKLKE 252


>gi|256785278|ref|ZP_05523709.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 354

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 117/241 (48%), Gaps = 11/241 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + K   E +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 117 LRTLEKDSPEYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 176

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 177 DRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVH 236

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A+KL++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 237 ELAEKLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 292

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 293 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 347

Query: 669 H 669
            
Sbjct: 348 E 348


>gi|71909448|ref|YP_287035.1| RNA polymerase factor sigma-32 [Dechloromonas aromatica RCB]
 gi|71849069|gb|AAZ48565.1| RNA polymerase, sigma 32 subunit, RpoH [Dechloromonas aromatica
           RCB]
          Length = 286

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 126/272 (46%), Gaps = 11/272 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  I   I++ +    ++ +E   +   +         A +++V ++LRLVIS+A+ Y 
Sbjct: 12  SVGNIDAYIQAANRYPMLTEAEESRLAERL--HNDGDVEAARQLVLSHLRLVISIARGYL 69

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  ++AM W+K  I   I      +++   
Sbjct: 70  GYGLPHADLIQEGNIGLMKAVKRFDPSRGVRLVSFAMHWIKAEIHEYILKNWRLVKVATT 129

Query: 525 MRDKIHKVVRTARRMSNKIKREPT---PEEIAKKLAMPVEGVRKVLKI-TKEPISLETPI 580
              +       + +   +     +     E+A +L +  + V ++    +   I+L+   
Sbjct: 130 KAQRKLFFNLRSMKSGYEGIDTLSGTQAAEVAARLGVKQDEVVEMETRLSGRDIALDGNP 189

Query: 581 GD-EDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGM 636
            D E+     D++ D           +A  R   E     L +L PR  R++  R+    
Sbjct: 190 DDGEEAFAPIDYLADSRYEPTRVLENKAIARLQDEGLHEALEALDPRSRRIIEARWLHD- 248

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL ++  +F V+ ERIRQIE KA++K++
Sbjct: 249 GETATLHDLADEFDVSAERIRQIEVKALQKMR 280


>gi|239930843|ref|ZP_04687796.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 308

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 120/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 66  LFERLEALEEGTLEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 125

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 126 RFEMSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRA 185

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 186 PTVAELAERLGITNDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGIE 245

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I     E+   ++A L PR+ ++L +RF  G     T  E+G++  +++  + ++ ++ 
Sbjct: 246 YI-----ESLKPLIAELPPRDRKILSLRFVAG----MTQSEIGEELGISQMHVSRLLSRT 296

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 297 LVKLRR 302


>gi|209519627|ref|ZP_03268417.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
 gi|209499913|gb|EDZ99978.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
          Length = 311

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 131/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   + +R+ +     A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATELREHDNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           + +A++L +  E V ++    +   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKQGLGAFTPDEIDGLARELNVKREEVAEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRF---GIGM 636
           + S+    ++ D ++      A +   R   +     L +L PR  R++  R+       
Sbjct: 213 EESYAPIAYLADSHSEPTAVLASRQRDRLHSDGIASALDALDPRSRRIIEARWLKVADDG 272

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|24114721|ref|NP_709231.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 301]
 gi|30065262|ref|NP_839433.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 2457T]
 gi|110807289|ref|YP_690809.1| RNA polymerase factor sigma-32 [Shigella flexneri 5 str. 8401]
 gi|24053937|gb|AAN44938.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|30043524|gb|AAP19244.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str.
           2457T]
 gi|110616837|gb|ABF05504.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|281602809|gb|ADA75793.1| Sigma(32) factor of RNA polymerase [Shigella flexneri 2002017]
 gi|313647240|gb|EFS11692.1| alternative sigma factor RpoH [Shigella flexneri 2a str. 2457T]
 gi|332749439|gb|EGJ79856.1| alternative sigma factor RpoH [Shigella flexneri K-671]
 gi|332750286|gb|EGJ80697.1| alternative sigma factor RpoH [Shigella flexneri 4343-70]
 gi|332751371|gb|EGJ81774.1| alternative sigma factor RpoH [Shigella flexneri 2747-71]
 gi|332996248|gb|EGK15875.1| alternative sigma factor RpoH [Shigella flexneri VA-6]
 gi|332996590|gb|EGK16215.1| alternative sigma factor RpoH [Shigella flexneri K-272]
 gi|332997356|gb|EGK16972.1| alternative sigma factor RpoH [Shigella flexneri K-218]
 gi|333012512|gb|EGK31893.1| alternative sigma factor RpoH [Shigella flexneri K-304]
 gi|333012998|gb|EGK32374.1| alternative sigma factor RpoH [Shigella flexneri K-227]
          Length = 284

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    D+  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSD 191

Query: 586 SH-LGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           S  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMHGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|326564381|gb|EGE14609.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 12P80B1]
          Length = 371

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 125/270 (46%), Gaps = 11/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++  E R +    R        A + +V ++LR VI +A+ Y+  
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAE--RYYHDGDVEAARLLVMSHLRFVIHIARSYSGY 154

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 155 GLSQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKA 214

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ SN++  +     IA  L + V+ V     ++T    S E    D+D
Sbjct: 215 HRKLFFNLRSLKKSSNQLTLDEATA-IANDLNVTVKQVLEMESRLTSYDASFEAQDSDDD 273

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++AV+P D   +A+  E         + +L  R   ++  R+        
Sbjct: 274 EGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLAD--QKS 331

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TL E+   + ++ ER+RQIE  A+ K+K  
Sbjct: 332 TLHELAATYNISAERVRQIEKNAMNKIKEA 361


>gi|85704163|ref|ZP_01035266.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
 gi|85671483|gb|EAQ26341.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
          Length = 277

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 116/260 (44%), Gaps = 16/260 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 11  ELALAYAWRDQRDEEALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 71  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAMAN 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
             ++      E IA ++ +P+  V  +  +++    SL      ED      D +ED+ A
Sbjct: 131 GQQLDGYQLREMIAHEVGVPLRDVEMMEGRLSGSDFSLNATQSAEDEGREWIDTLEDEGA 190

Query: 598 ---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         LR+     LA L  RE  ++R R         TLE +G++  +++E
Sbjct: 191 RGDEIVERHHDMHALRDWLADALARLNERERFIVRERKLRD--DPRTLESLGEELNLSKE 248

Query: 655 RIRQIEAKAIRKLKHPSRSK 674
           R+RQ+EA A +K++      
Sbjct: 249 RVRQLEAAAFQKMRKHLEKH 268


>gi|325518946|gb|EGC98485.1| RNA polymerase factor sigma-32 [Burkholderia sp. TJI49]
          Length = 311

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/273 (26%), Positives = 139/273 (50%), Gaps = 12/273 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  +   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNLDAYIQAVNRIPLLTAEEERQYATQFREDNNLD--AARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I     T+++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +AK+L +  E V     +++   I+LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKGVQAMTPE-EIDGLAKELNVKREEVTEMETRLSGGDIALEGQVED 211

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT 638
            + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+    + 
Sbjct: 212 GEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARWLHVDDD 271

Query: 639 ---DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 272 GSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|223975681|gb|ACN32028.1| unknown [Zea mays]
          Length = 565

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 77/283 (27%), Positives = 136/283 (48%), Gaps = 6/283 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + ++K   E+ S       +  +   +VS ++ G C     +  ++     LV  
Sbjct: 288 LEKIREKMVKEGQEV-SYHRWAEAAGVDEAELVSRLQAGYC----CRDRLLVTTEWLVRC 342

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ YT  G    DL+Q G +G++  AEKFD   G +FSTY  +W+++ +   +A+ S  
Sbjct: 343 IARTYTGMGTALDDLLQAGKMGVLDGAEKFDSRKGCRFSTYVKYWIRKGMLALLAENSGV 402

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
             +P  M   + KV    R +  +  R P+  E+A  + + V  VR   K ++  +SL +
Sbjct: 403 TLLPARMESIMRKVKEARRGIRYRQGRNPSDSEVAAAVGVSVANVRLARKCSRRAVSLYS 462

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +         + I D++A     +  +  LRE    VL  L  RE RVLR+R G+    
Sbjct: 463 EVAIGQDVKFAEVIPDESASPDEAALFRGQLRERLLLVLGRLPAREGRVLRLRHGLEDGR 522

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFL 680
             +LEE+G  + V++E IR+IE  A+ +L+   +  + L  F+
Sbjct: 523 CRSLEEIGGIYGVSKEWIRKIEKSAMARLRDDDAVRRDLHDFV 565


>gi|302147251|emb|CBL51747.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 262

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 104/300 (34%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                      +         E +  D  E E + E     + DD       PE A    
Sbjct: 59  TE-----DVAPTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREKF 113

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L    + +  ++                                   QK+ ++    +
Sbjct: 114 GELRAQYEVTRLSI-----------------------------------QKNGRAHEDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E D  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECDSAWFEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|66474635|gb|AAY46887.1| RpoD [Aeromonas hydrophila]
          Length = 272

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 117/316 (37%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S                +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEYEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +       ++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLCIHQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|55274894|gb|AAV49249.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 195

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 130/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  L LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|296133019|ref|YP_003640266.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031597|gb|ADG82365.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 262

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 110/251 (43%), Gaps = 17/251 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  +     A+++++     LV  VA +        +Q  DLI  G  GL+ A EKF+  
Sbjct: 16  RFKKERDLAAREQLILKYAPLVKYVAGRLAISLPPNVQQDDLISYGIFGLIDAIEKFEPE 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA+  +K AI   +            +R K  ++  T  R+ N++ R  T EE
Sbjct: 76  RNIKFETYAISRIKGAIWDGLRSMDWIPY---SIRQKAKELEETYARLENELGRPATDEE 132

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSH----LGDFIEDKNAVSPLDSAI 605
           + + L +  +    +L+ T     +SLE     +        + D I D     P+ + +
Sbjct: 133 MCETLGITKQQFYSLLQETSCTSLLSLEDLFVFDRDGTNGVKMIDTIADSRVPDPVAAVM 192

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               ++     +  L  RE+ V+ + +  G     TL+E+GK   VT  RI Q+  KAI 
Sbjct: 193 FEEQKKILGEAINKLPEREKMVIALYYYEG----LTLKEIGKVLGVTESRISQLHTKAIL 248

Query: 666 KLK-HPSRSKK 675
           +L+   SR KK
Sbjct: 249 RLRGRLSRVKK 259


>gi|238063793|ref|ZP_04608502.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
 gi|237885604|gb|EEP74432.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
          Length = 294

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 112/244 (45%), Gaps = 14/244 (5%)

Query: 430 IVSMVRKGECEASIA--KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +M        S A  +   +EA L L   +A +Y+ RG    DL Q   +GL+KA +K
Sbjct: 53  LNAMAALPANHPSRAAMRDRAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDK 112

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G  F+ YA+  +   + R   D++  IR+P  +++    +      +   + R P
Sbjct: 113 FDPSRGVDFAGYAIPTIIGELKRHFRDRTWDIRVPRRLQELRLAISDANSTLLQTLGRSP 172

Query: 548 TPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSA 604
           T  +IA  L +  E V + L+       +SL TP    +  + LGD +  ++        
Sbjct: 173 TVADIAAHLKLTEEEVLEGLEGARAYNAVSLSTPTGDGDRATELGDMLGGEDT-----EF 227

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A LR      LA+L  RE+++L +RF        T  ++  Q  V++  + ++ A+A+
Sbjct: 228 ELAELRVALGPALATLDEREQKILTLRFYGN----LTQSQIADQIGVSQMHVSRLLARAL 283

Query: 665 RKLK 668
            KL+
Sbjct: 284 TKLR 287


>gi|167835356|ref|ZP_02462239.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis MSMB43]
          Length = 311

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 136/273 (49%), Gaps = 12/273 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A +++V ++LRLV+SVA+ Y 
Sbjct: 35  QLGNIDAYIQAVNRVPLLTAEEERQYATEYREQNNLD--AARQLVLSHLRLVVSVARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +   +       + +A++L +  E V ++    +   I+LE  I D 
Sbjct: 153 KAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNTD 639
           + S+  +    +  N  + + +A Q ++ +T    R L SL  R  R++  R+ + ++ D
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARW-LNVDDD 271

Query: 640 ----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 272 GSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|255312665|gb|ACU01742.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312669|gb|ACU01744.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  132 bits (332), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 130/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ T R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTNRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|255068324|ref|ZP_05320179.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|261365915|ref|ZP_05978798.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
 gi|255047443|gb|EET42907.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|288565493|gb|EFC87053.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
          Length = 287

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 134/266 (50%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E   +    +K       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLTPEEESQLAERQQK---GDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V ++  ++T   I++     D++ S
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVMEMEQRMTGHDIAIMADNNDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +A      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|254515828|ref|ZP_05127888.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
 gi|219675550|gb|EED31916.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
          Length = 303

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 67/269 (24%), Positives = 131/269 (48%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++++    +S      +   +         A +E+V ++LR V  +A+ Y   GL
Sbjct: 36  LAAYVQAVARVPVLSPEREHMLAEKL--FYDGDVQAARELVMSHLRFVAHIARSYRGYGL 93

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      ++I     + 
Sbjct: 94  SEADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYILRNWRIVKIATTKAQR 153

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+A++    +  +   + +A  L + V+ V R   +++   ++ + P G +D  
Sbjct: 154 KLFFNLRSAKKSLAWLSAD-EAQAVANDLGVDVQEVHRMEGRLSSHDVAFDAPAGSDDDE 212

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED++   A+   DS  QA+ +      +A L  R   +L  R+    +   
Sbjct: 213 GWQAPQYYLEDRSADPAIDVEDSEWQADSQAQLHAAIADLDERSRNILAQRWL--TDDKA 270

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TL E+  ++ V+ ERIRQ+E  A++K++ 
Sbjct: 271 TLHELAAEYGVSAERIRQLEQAAMKKIRQ 299


>gi|332308280|ref|YP_004436131.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175609|gb|AEE24863.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 283

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/271 (22%), Positives = 134/271 (49%), Gaps = 14/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   ++++S    +S  E + +   +++   +  +A ++++ ++LR V+ +AK Y+  GL
Sbjct: 18  IETYVQAVSSIDMLSAEEEKGLAERLQQ--EDDLLAARKLIMSHLRFVVHIAKSYSGYGL 75

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 76  PQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E   +++A  L +  + V +   +++    + +    D+++
Sbjct: 136 KLFFNLRKNKKRLGWFTHAE--VQKVASDLGVSEKEVLQMEARMSSHDQAFDLSADDDES 193

Query: 586 SHLG--DFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  F+EDK+       +++   A   +     + +L  R + +++ R+     T  
Sbjct: 194 GSFAPVQFLEDKSPDVETEVVNADWDATASQKLYSAIKTLDERSQHIIQTRWLSDDKT-- 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL+++  ++ V+ ER+RQIE  A++KL+   
Sbjct: 252 TLQDLADKYQVSAERVRQIEKNAMKKLQSAM 282


>gi|257056691|ref|YP_003134523.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256586563|gb|ACU97696.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 266

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 109/226 (48%), Gaps = 11/226 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E++   L L   +A+++  RG    DL+Q   +GL+ A ++FD   G +F  +A+  +
Sbjct: 45  REEIITRCLPLAEHIARRFVGRGEPRDDLVQVARLGLLNAIDRFDASRGTEFVAFAVPTI 104

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S  +R+P  +++    + + + +++ ++ R PTP E+A +L +  E V 
Sbjct: 105 MGEVRRHFRDSSWAVRVPRRLKELHLSLSQASSKLAQRLGRAPTPSELAAELGLSPEDVW 164

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L      + +S++    DE T  L + +   +              E+   +LASL  
Sbjct: 165 DGLLAGNAYQSVSMDAAYDDEGTLPLAETVGHDD-----VELEHVEYHESLQPLLASLPE 219

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE RVL +RF        T  ++ ++  +++  + ++ A+ +  L+
Sbjct: 220 RERRVLILRFFGN----MTQTQIAERVGISQMHVSRLLARTLEFLR 261


>gi|297569322|ref|YP_003690666.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925237|gb|ADH86047.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 363

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 78/283 (27%), Positives = 144/283 (50%), Gaps = 14/283 (4%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ IS    +S +E   +  + +  E     A  ++V ANLRLV+ VA  +    
Sbjct: 79  ALHRYLQEISQYRLLSRAETDELARLFK--ETGDPEAAYKLVTANLRLVVKVAMDFQKYW 136

Query: 468 LQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHM 525
           +Q FLDLIQEGNIGL++A +KFD     KFS YA +W++  I + I D    ++I     
Sbjct: 137 MQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAYWIRAYILKFIMDNWRLVKIGTTQA 196

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDED 584
           + K+   +   +++      +P P+ +A++L +    V ++  ++    +SLE+P+ ++ 
Sbjct: 197 QRKLFFSLNKEKKLLESQGFKPEPKLLAQRLNVKESEVIEMSQRMDNWDMSLESPMREDS 256

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA----SLTPREERVLRMRFGIGMNTDH 640
                DF+      S  +      +RE    +L     +L  +E  +LR    +  +   
Sbjct: 257 GDERKDFLP-VAGPSVEERVAADEVREWMAGILDKMRRTLNEKELAILRE--RLLSDEPA 313

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK--LRSFLD 681
           TL+E+  +F ++RER+RQIEA  ++K++    ++   ++ FLD
Sbjct: 314 TLQEIADRFAISRERVRQIEANLLKKMRTYLENEVPDIKEFLD 356


>gi|227823777|ref|YP_002827750.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342779|gb|ACP26997.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 288

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 74/285 (25%), Positives = 131/285 (45%), Gaps = 19/285 (6%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + ++   R  IK       +   E   +    R        A+ ++  +++RLVI++A K
Sbjct: 1   MKTLTADRRLIKIAMDAPYLERDEEHALAEAWR--NDHDQEARNKIAMSHMRLVIAMAAK 58

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + + GL   DL+QEG+IGL++AA +F+     +FSTYA WW++ ++   +      +R  
Sbjct: 59  FRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDFVLRNWSIVRGG 118

Query: 523 VHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISL 576
                K     + R   R++    ++      +EIA  L + +  V+    +++    SL
Sbjct: 119 TSSAQKALFFNLRRLRARLAQGDRQLTSLAMHQEIAAALGVSLADVQTMDARLSGNDASL 178

Query: 577 ETPIGD--EDTSHLGDFIED-----KNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           + P+G    D     DF+          VS +    +A  R      L  LT RE +++R
Sbjct: 179 QAPVGHGDSDGGARLDFLPSDAPLPDEQVSDMIDGERA--RRWLQVALTQLTEREMKIIR 236

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            R         TLEE+G    +++ER+RQIE +A+ KL+    S+
Sbjct: 237 ARRLSEDG--ATLEELGLALGISKERVRQIETRALEKLRTALASR 279


>gi|39995761|ref|NP_951712.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|39982525|gb|AAR33985.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|298504771|gb|ADI83494.1| RNA polymerase sigma-32 factor RpoH [Geobacter sulfurreducens
           KN400]
          Length = 284

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 120/262 (45%), Gaps = 10/262 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     ++  E       V+  E +   A   ++ +NLR V+ +A +Y + GL+ L
Sbjct: 15  YLREIRKFPVLTPEEEYRFA--VKFYEDKDLEAAHSLITSNLRFVVKIAAEYRSYGLKML 72

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--I 529
           DLIQEGN+GLM A  KF+   G +  +YA+WW++  I   I      ++I      K   
Sbjct: 73  DLIQEGNVGLMMAVRKFNPYKGIRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQKKLF 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+ +    +      +   E  A  L +    V ++ +  +    L+  I + D   + 
Sbjct: 133 FKLNQAKNAIKGLTGTD-DIEATATSLHVKESEVLEMDQRMRGDFYLDAEIKNGDGLTIL 191

Query: 590 DFIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           + + D+      +  +      L++     L  L  +E  ++     +  +T  TL+E+ 
Sbjct: 192 ETLADERQNQEDTLAELQESELLKQHIAGALGKLNEKERFIVEQ--RVTADTPLTLQEIA 249

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
            +F ++RER+RQIE  A+RK+K
Sbjct: 250 DRFSISRERVRQIEEAALRKIK 271


>gi|110835430|ref|YP_694289.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
 gi|110648541|emb|CAL18017.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
          Length = 289

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 64/272 (23%), Positives = 128/272 (47%), Gaps = 13/272 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +++++    +S  E + +   +     +   A + +V ++LR V  +A+ YT  
Sbjct: 20  HDLDAYMRAVNAVPVLSAEEEQRLGERL--YYDQDLDAARSLVLSHLRFVAHIARSYTGY 77

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DL+QEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 78  GLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYVIKNWRIVKVATTKA 137

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
           + K+   +R  ++   ++  E   + +A  L +    V+++  ++     S + P  D+D
Sbjct: 138 QRKLFFNLRGQKKRLGRLTLE-EAQRVADDLGVTAAQVKEMEGRLGAYDASFDGPTNDDD 196

Query: 585 TSHL----GDFIEDKNAVSPLDSAIQANLRE--TTTRVLASLTPREERVLRMRFGIGMNT 638
            S +         D +  + L +      RE    +  L +L  R   +L  R+      
Sbjct: 197 DSTVVSPAAYLHSDNSDPADLLAEQDQQQRESRQLSSALMALDERSRDILERRWLAD--Q 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+E+  ++ V+ ERIRQ+E  AI+KL++ 
Sbjct: 255 KSTLQELADEYSVSAERIRQLENNAIKKLRNA 286


>gi|89092456|ref|ZP_01165410.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89083544|gb|EAR62762.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 284

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 130/269 (48%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +++++    +S+ E R +   +         A +++V ++LR V+ VAK Y+  
Sbjct: 15  QNLDAYVQNVTAIPVLSVEEERSLAERL--HFDGDVEAARQLVMSHLRFVVHVAKTYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ WVK  +   I      +++     
Sbjct: 73  GLPLGDLIQEGNVGLMKAVKRFDPTMGVRLVSFAVHWVKAEMHEFILRNWRIVKVATTKA 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
            +       +++ S           IA+ L +  + VR++  ++     + + P G +D 
Sbjct: 133 QRKLFFNLRSKKKSLSWMTNDEVNAIAEDLGVEAKVVRQMEGRMASVDTAFDAPEGADDE 192

Query: 586 ---SHLGDFIEDKNA---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   ++EDK+A   +   ++  + + +      ++ L  R + +L  R+    +  
Sbjct: 193 QAAWAPAHYLEDKSADPSMQLEEANWEQDSQRRLMSAMSELDERSKDILARRWL--TDDK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 251 ATLHELAAEYGVSAERIRQLEKNAMKKIR 279


>gi|73540031|ref|YP_294551.1| RNA polymerase factor sigma-32 [Ralstonia eutropha JMP134]
 gi|72117444|gb|AAZ59707.1| Sigma-70 region 2 [Ralstonia eutropha JMP134]
          Length = 309

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 139/302 (46%), Gaps = 10/302 (3%)

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D   ++        +  +F      ++  + + I+++     ++  E + +   +R+ + 
Sbjct: 8   DQTLMNSRLPTAPKQAGSFALTFPATVGNLESYIQAVHRIPMLTAEEEQRLARELREDDS 67

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
               A +++V ++LRLV+S+A++Y   GL   DLIQEGNIGLMKA ++FD   G +  +Y
Sbjct: 68  VD--AARQLVMSHLRLVVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPNQGVRLVSY 125

Query: 500 AMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           AM W+K  I   +      +++     + K+   +R+ ++ S+    E            
Sbjct: 126 AMHWIKAEIHEYVLKNWRMVKVATTKAQRKLFFNLRSHKQGSHTFTPEQIEAVARDLNVK 185

Query: 559 PVEGVRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTT 614
           P E +    +++   ++LE  + D E+      ++ D +         +   R   E   
Sbjct: 186 PEEVMEMETRMSGGDLALEGQVDDGEEEFAPIAYLADNHNEPTRVLEAKRQDRMQVEGLE 245

Query: 615 RVLASLTPREERVLRMRF---GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             LA L  R  R++  R+       +   TL E+  +F V+ ERIRQIE  A++K+K   
Sbjct: 246 EALARLDERSRRIIEARWLNVEDDGSGGATLHELADEFGVSAERIRQIEVAAMKKMKGAL 305

Query: 672 RS 673
           ++
Sbjct: 306 QA 307


>gi|284053375|ref|ZP_06383585.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 183

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 69/182 (37%), Positives = 120/182 (65%), Gaps = 1/182 (0%)

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++Q ITR+IA QS TIR+PVH+ +K++K+ +  R++S +  R  T ++IA +L M  
Sbjct: 1   YWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKSRTATIDDIATELKMTP 60

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           + +R+VL      +SLET +G +  + LGD +E + + +P +  ++ +L      +LA L
Sbjct: 61  DQIREVLLRVPRSVSLETKVGTDKDTELGDLLETEES-TPEELLMRESLYRELQHILADL 119

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           + +E  V++MR+G+G    ++L E+G+   ++RER+RQIEAKA++KL+ P R  ++R +L
Sbjct: 120 SGKERAVIQMRYGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRVRDYL 179

Query: 681 DG 682
           D 
Sbjct: 180 DS 181


>gi|116253507|ref|YP_769345.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258155|emb|CAK09256.1| putative RNA polymerase sigma-32 factor [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 302

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 124/279 (44%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D     D++ D +         Q  L   R    + ++ L  RE R+   R       
Sbjct: 194 EGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R + L 
Sbjct: 252 PVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEALE 290


>gi|254389000|ref|ZP_05004231.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294814936|ref|ZP_06773579.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702718|gb|EDY48530.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294327535|gb|EFG09178.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 358

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 124/257 (48%), Gaps = 12/257 (4%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +  S + G + + F  + ++       A + + ++V  +L LV  +A+++ NRG    DL
Sbjct: 105 QQESQDRGGARAMFVELRALPDGSRERAEL-RNQLVRMHLPLVEHLARRFRNRGEPLDDL 163

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q   IGL+K+ ++FD   G +FSTYA   V   I R   D+   +R+P  +++    + 
Sbjct: 164 TQVATIGLIKSVDRFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALT 223

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDF 591
                +S    R PT  E+A++L +  E V + L+       +SL+ P  D+++  + D 
Sbjct: 224 TATAELSQLHGRSPTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADT 283

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +  ++             RE+   +L  L PRE+R+L +RF   M      +EV     +
Sbjct: 284 LGAEDEALEGVEY-----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GI 334

Query: 652 TRERIRQIEAKAIRKLK 668
           ++  + ++ A+ + +L+
Sbjct: 335 SQMHVSRLLARTLAQLR 351


>gi|324998294|ref|ZP_08119406.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 258

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 113/228 (49%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V   L +   +A+++ +RG    DL+Q   +GL+ A ++FD   G +F ++A+  +
Sbjct: 31  RDRLVTGYLPVAQHIARRFNHRGEPLDDLVQVATVGLINAIDRFDPDKGGEFFSFAVPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   DQS ++R+P  ++D    +      +S  + R P P EIA+ L +PV  V 
Sbjct: 91  SGEVRRHFRDQSWSMRVPRRLKDMHVSINGAVSELSQTLGRSPRPSEIAEHLGLPVPEVL 150

Query: 565 KVLKI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+        SL+  +  ED    +G+ + D +A        + + RE+   +LA L 
Sbjct: 151 EGLEAAEAYRSSSLDEMLSSEDGGATVGELVGDADA-----ELDRVDYRESLRPLLAELA 205

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           PRE  ++ +RF        T  ++  +  +++  + ++ ++ + +L++
Sbjct: 206 PRERTIVMLRFFGN----RTQTQIANEVGISQMHVSRLLSQTLSRLRN 249


>gi|297746549|emb|CAZ60992.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 267

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 63/312 (20%), Positives = 114/312 (36%), Gaps = 46/312 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                     +  +       S+  E D   E E + E     S DD       PE A  
Sbjct: 59  NE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVARE 111

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 112 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 136

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 137 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 196

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 197 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 255

Query: 433 MVRKGECEASIA 444
            +  GE +A  A
Sbjct: 256 RMSIGEAKARRA 267


>gi|239942801|ref|ZP_04694738.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           15998]
 gi|239989260|ref|ZP_04709924.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           11379]
 gi|291446270|ref|ZP_06585660.1| sigma F [Streptomyces roseosporus NRRL 15998]
 gi|291349217|gb|EFE76121.1| sigma F [Streptomyces roseosporus NRRL 15998]
          Length = 285

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 106/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 57  EHRRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTF 116

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 117 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTAEIAERLKIS 176

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 177 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 231

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 232 VQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 282


>gi|254511947|ref|ZP_05124014.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
 gi|221535658|gb|EEE38646.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
          Length = 298

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 127/275 (46%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A +KFD   G++ +TYAMWW++ +I   +      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE    IA+ L +  E V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLRPENVARIAEDLGVTEEEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ +L       M+
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLAAALDVLNDREKDILTQ--RRLMD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QVVTLEELSTQYNVSRERIRQIEVRAFEKLQKKMR 286


>gi|261405990|ref|YP_003242231.1| sporulation sigma factor SigF [Paenibacillus sp. Y412MC10]
 gi|329929773|ref|ZP_08283449.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
 gi|261282453|gb|ACX64424.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. Y412MC10]
 gi|328935751|gb|EGG32212.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
          Length = 251

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 127/253 (50%), Gaps = 17/253 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T +  +E + ++++    +   ++A+  +V  N+RLV SV +++ NRG +  DL Q G 
Sbjct: 10  QTYLDDAEVKRLIAL---SQSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGC 66

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    
Sbjct: 67  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKEMANKVRKKRDE 125

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKN 596
           +S ++ R PT +E+A++L +  E V    +  K P S+   + + D     L D I D +
Sbjct: 126 LSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQIADDS 185

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                D       +      +  LT RE  ++     +    D T  EV  +  +++ ++
Sbjct: 186 QERWFD-------KLALNEAIGGLTERERLIV----YLRYYRDQTQSEVATRLGISQVQV 234

Query: 657 RQIEAKAIRKLKH 669
            ++E K ++ +++
Sbjct: 235 SRLEKKILQSIRN 247


>gi|152972335|ref|YP_001337481.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580698|ref|YP_002236168.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238896924|ref|YP_002921669.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae NTUH-K2044]
 gi|262040527|ref|ZP_06013768.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288933158|ref|YP_003437217.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|290511960|ref|ZP_06551328.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|329999131|ref|ZP_08303332.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
 gi|150957184|gb|ABR79214.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569756|gb|ACI11532.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238549251|dbj|BAH65602.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259042120|gb|EEW43150.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288887887|gb|ADC56205.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|289775750|gb|EFD83750.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|328538425|gb|EGF64546.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
          Length = 284

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 131/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K+++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LESYIRAANTWPMLSADEERELAEKL--HYQGDLEAAKKLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKTSNFADGIEDDNWEEQAANKLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|332653369|ref|ZP_08419114.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
 gi|332518515|gb|EGJ48118.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
          Length = 256

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 135/264 (51%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + +     +++R+ +     A++E++  NLRLV+SV  K+ NRG
Sbjct: 1   MLNKVELCGVNTAKLKVLKNEETQALLRRAKEGDKQAREELIAGNLRLVLSVIHKFANRG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD  L  KFSTY +  +   I R + D S   R+   MRD
Sbjct: 61  ENVDDLFQVGCIGLIKAIDNFDTSLDVKFSTYGVPMIVGEIRRYLRDNSAM-RVSRAMRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +KV++       + ++EP+ EEIA+ L +  E V   L    +P+SL  PI  +  DT
Sbjct: 120 TAYKVLQAKESYMAQHQKEPSVEEIAQMLGIKREEVVFALDAILDPVSLYEPIYSDSGDT 179

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D ++D      +               ++ L+ RE+++L MRF        T  EV
Sbjct: 180 VCVMDQVKDSRNTDEMWLE-----HIALKEAVSRLSEREQKILAMRF----YQSKTQVEV 230

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            ++  +++ ++ ++E  A+R+++ 
Sbjct: 231 SREIGISQAQVSRLEKNALRQIRK 254


>gi|254464548|ref|ZP_05077959.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
 gi|206685456|gb|EDZ45938.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
          Length = 298

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 125/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + +  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEEQDAASAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+      +  PE    IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEDGDLRPENVKRIATDLGVTEDEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ +L       M+
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLAEALDVLNDREKDILTQ--RRLMD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QAVTLEDLSAQYNVSRERIRQIEVRAFEKLQKKMR 286


>gi|119776597|ref|YP_929337.1| RNA polymerase factor sigma-32 [Shewanella amazonensis SB2B]
 gi|119769097|gb|ABM01668.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella amazonensis
           SB2B]
          Length = 285

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 126/268 (47%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S++    +   +   +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYIHSVNSMPMLEAEQEYQLAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKSYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E     +A+ L +  + V     ++  +  + +     +D 
Sbjct: 137 KLFFNLRKAKQRLGWFSDDEVAM--VAENLGVSKDDVTEMESRMAAQDQAFDLVNDHDDD 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   ++N +      + +L  R + +LR R+        
Sbjct: 195 EGFAPVHYLEDHSSDLAANIENDNWESNAQNRLIAAIKTLDERSQHILRARWLDD--DKV 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+ +Q+ V+ ERIRQ+E  A+ KLK
Sbjct: 253 TLQELAEQYQVSAERIRQLEKNAMNKLK 280


>gi|293602894|ref|ZP_06685333.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
 gi|292818688|gb|EFF77730.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
          Length = 294

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/265 (27%), Positives = 129/265 (48%), Gaps = 8/265 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    +S      +   +R  E     A +E++ ++LRLV+SVA++Y   GL
Sbjct: 28  IDAYISAVNRLPVLSAERETELGRRLRDQEDLG--AARELILSHLRLVVSVARQYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++      +
Sbjct: 86  PHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R   +       + IA++L +  E V ++ ++++   +SLE    D+D+  
Sbjct: 146 KLFFNLRSMRPDGQTLDPDQVDHIARELNVRREDVSEMEVRLSGREMSLENQDDDDDSFA 205

Query: 588 LGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              ++ D     P     +A   E      T  L +L  R  R++  R+        TL 
Sbjct: 206 PIAYLSDDGRQEPTRVLERAARDELQSTGLTTALEALDARSRRIVEARWLQDDGG-ATLH 264

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ ++F V+ ERIRQIEA A++K++
Sbjct: 265 ELAQEFGVSAERIRQIEAAALKKMR 289


>gi|260461535|ref|ZP_05809782.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032605|gb|EEW33869.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 303

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 122/275 (44%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E E + A  ++V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLEEIRRFPMLQPQEEYMLAK--RYAEHEDTSAAHKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 73  PIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  KV    + + +   +     EIA +L +    V  + +      SL  PI   
Sbjct: 133 RLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVSEAEVVSMNRRLSGDASLNAPIRAT 192

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R   +  LA L  RE R+   R       
Sbjct: 193 EGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNDRERRIFEARRLAE--E 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+  +F ++RER+RQIE +A  K++   ++
Sbjct: 251 PLTLEELSAEFDISRERVRQIEVRAFEKVQDAVKA 285


>gi|315646368|ref|ZP_07899486.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
 gi|315278011|gb|EFU41331.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
          Length = 251

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 128/253 (50%), Gaps = 17/253 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T +  +E + ++++    +   ++A+  +V  N+RLV SV +++ NRG +  DL Q G 
Sbjct: 10  QTYLDDAEVKRLIAL---SQSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGC 66

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +    
Sbjct: 67  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKEMANKVRKKRDE 125

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKN 596
           +S ++ R PT +E+A++L +  E V    +  K P S+   + + D     L D I D++
Sbjct: 126 LSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQIADES 185

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                D       +      +  LT RE  ++     +    D T  EV  +  +++ ++
Sbjct: 186 QERWFD-------KLALNEAIGGLTERERLIV----YLRYYRDQTQSEVASRLGISQVQV 234

Query: 657 RQIEAKAIRKLKH 669
            ++E K ++ +++
Sbjct: 235 SRLEKKILQSIRN 247


>gi|307728369|ref|YP_003905593.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
 gi|307582904|gb|ADN56302.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
          Length = 311

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 134/275 (48%), Gaps = 16/275 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+ +     A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEGVRKVLKI-TKEPISLETPI 580
              +  K+    R     +    TP+EI   AK+L +  E V ++    +   ++LE  +
Sbjct: 153 KAQR--KLFFNLRSHKQGLGA-FTPDEIDGLAKELNVKREEVAEMETRLSGGDVALEGQV 209

Query: 581 GDEDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGM 636
            D + S+    ++ D ++      A +   +   +     L +L  R  R++  R+    
Sbjct: 210 EDGEESYAPIAYLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIEARWLKVQ 269

Query: 637 NT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 270 DDGSGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|110679109|ref|YP_682116.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109455225|gb|ABG31430.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 298

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 122/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPQEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      +
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQK 133

Query: 527 DKIHKVVRTARR---MSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   +   +            IAK L +   E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNKIGALEEGDLHPDNVARIAKDLGVTETEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     ++ L  RE  +L+        
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLADAMSVLNDRERDILQQ--RRLSE 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  ++ V+RERIRQIE +A  KL+   R
Sbjct: 252 QTVTLEDLSAEYNVSRERIRQIEVRAFEKLQKKMR 286


>gi|83949442|ref|ZP_00958175.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837341|gb|EAP76637.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 298

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 68/276 (24%), Positives = 118/276 (42%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E + + A   MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--AWVEKQDTEAAHRMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   +          + IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDMHPDNVKRIATDLGVTEDEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A                E  T  +  L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEKRNEMETRLELLTEAMDVLNDREKDILSQ--RRLND 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLE++  ++ V+RERIRQIE +A  KL+   RS
Sbjct: 252 ETVTLEDLSTEYGVSRERIRQIEVRAFEKLQKRMRS 287


>gi|320537570|ref|ZP_08037508.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320145572|gb|EFW37250.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 274

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 76/268 (28%), Positives = 142/268 (52%), Gaps = 5/268 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +K I     ++  E   +   ++        A ++++ +NLRLV+ +AK  T      
Sbjct: 8   QYLKDIKRYPLLTAQEELCLADKIQ---NGDRGALQQLINSNLRLVVKMAKDRTPSENLL 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           +DLIQEGN+GLM AAEKF      +FS+YA WW++Q++ R +  +  TIR+P    D + 
Sbjct: 65  MDLIQEGNMGLMIAAEKFSSSFNARFSSYACWWIRQSLNRYLNGKHETIRLPFRKADLLR 124

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ +T      K +R P+ EEIA+ + +P++ V ++   T++PIS ++P+    +++L D
Sbjct: 125 KIEKTIDLFKEKYRRTPSYEEIAEIIQVPLKSVIQICVFTEKPISFDSPLQIHFSANLYD 184

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
             E+ +     +   +  +      +  +L  RE+ ++  R  I      +L  +G ++ 
Sbjct: 185 LTENNDYNPEKEYFRKVQIEAFRKFLQNTLKSREKDIIEERLPITDKNPKSLRSLGIKYG 244

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           ++ E +RQ E +A++KL+     K L+S
Sbjct: 245 ISAESVRQTEIRALKKLR--MHEKYLKS 270



 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+++    LL+ + E+ +A +I+ G    +  L  S L    ++    +      LL +
Sbjct: 9   YLKDIKRYPLLTAQEELCLADKIQNGDRGALQQLINSNLRL--VVKMAKDRTPSENLLMD 66

Query: 184 II 185
           +I
Sbjct: 67  LI 68


>gi|320009625|gb|ADW04475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 285

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 106/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 57  EHHRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTF 116

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 117 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTGEIAERLKIS 176

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 177 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 231

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 232 VQLPEREQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 282


>gi|227113845|ref|ZP_03827501.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 285

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 132/270 (48%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYQGDLEAAKHLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + ++  R+    + E   E +A++L +  + VR++  ++  + ++ +    ++  
Sbjct: 134 KLFFNLRKSKTRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDSH 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   +   +  ++  S     I+ +  ET      T  L  L  R + ++R R+ +  + 
Sbjct: 192 DGKAMSPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|55274885|gb|AAV49245.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|255312609|gb|ACU01714.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312611|gb|ACU01715.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312613|gb|ACU01716.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312615|gb|ACU01717.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312617|gb|ACU01718.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312619|gb|ACU01719.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312621|gb|ACU01720.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312623|gb|ACU01721.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312625|gb|ACU01722.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312627|gb|ACU01723.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312629|gb|ACU01724.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312631|gb|ACU01725.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312635|gb|ACU01727.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312637|gb|ACU01728.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312649|gb|ACU01734.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312651|gb|ACU01735.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312655|gb|ACU01737.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312657|gb|ACU01738.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312667|gb|ACU01743.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312673|gb|ACU01746.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312675|gb|ACU01747.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312677|gb|ACU01748.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312679|gb|ACU01749.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312681|gb|ACU01750.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312683|gb|ACU01751.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312685|gb|ACU01752.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312687|gb|ACU01753.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312691|gb|ACU01755.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312693|gb|ACU01756.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312695|gb|ACU01757.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312699|gb|ACU01759.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312701|gb|ACU01760.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312703|gb|ACU01761.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312705|gb|ACU01762.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 79/194 (40%), Positives = 131/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|83859721|ref|ZP_00953241.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852080|gb|EAP89934.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 301

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 11/243 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             E     A   +  A +RLVIS+A K+ + GL F DL+ EGNIGLM+AA +F+     +
Sbjct: 43  WKEKGDEEALHALTTAYMRLVISIAAKFRHYGLPFPDLVSEGNIGLMQAAARFEPEREVR 102

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPEE-- 551
           FSTYA WW++ +I   +      +R       K     + R    + +    + TPE   
Sbjct: 103 FSTYATWWIRASIQDYVLRNWSIVRTGTTAAQKSLFFNLRRLRALIKDTSSGQLTPENRA 162

Query: 552 -IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQ 606
            +A+ L +  + V K+  ++     SL  P  ++      D + D+N       ++   Q
Sbjct: 163 YVAQALRVGEDDVEKMASRLAAVDRSLNAPFSEDGEGEWQDLLADENPDPETQVMEDRDQ 222

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A   +     L+ L+ RE+ ++R           TLE++G++  +++ER+RQ+E +A+ K
Sbjct: 223 AQRAQWLGEALSRLSEREQLIIRE--RRLGEDSVTLEKLGERLGISKERVRQVEHQALNK 280

Query: 667 LKH 669
           LK 
Sbjct: 281 LKK 283


>gi|313901496|ref|ZP_07834946.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313468234|gb|EFR63698.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 258

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/254 (24%), Positives = 116/254 (45%), Gaps = 18/254 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKE----MVEANLRLVISVAKK---YTNRGLQFLDLIQEGN 478
           E +             + A  E    ++  +L LV  +A +   +    ++  DLI  G 
Sbjct: 4   ELKQRQERAELWRRYRTAADPESWEALIREHLPLVRYLAGRLVVHLPPQVELDDLISYGI 63

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            GLM+A +++D   G KF TYA   ++ A+   +       +    +R +  +V    RR
Sbjct: 64  FGLMEAIKRYDPSRGVKFETYAYTRIRGAMLDGLRAMDWVPQG---LRRRAREVEACYRR 120

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIG--DEDTSHLGDFIED 594
           + N++ R     E+A +L +  +   ++LK       ISL+  +    +D + + D + D
Sbjct: 121 LENRLGRPAEDAEVAAELGLTPDEFGELLKDLARTTVISLDDVLRSESDDPAAVLDRLAD 180

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A  PL +A  A+LR+   + LA L  RE  V+ + +  G     T++E+ +   V+  
Sbjct: 181 PGAADPLAAATLADLRQRLAQALAVLPERERLVITLYYYEG----LTVKEIAEVMGVSPS 236

Query: 655 RIRQIEAKAIRKLK 668
           R+ Q+  +AI +L+
Sbjct: 237 RVSQLHTRAILRLR 250


>gi|54401902|gb|AAV34636.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 80/194 (41%), Positives = 131/194 (67%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+
Sbjct: 1   NLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 60

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +
Sbjct: 61  IMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNE 120

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  R
Sbjct: 121 RITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARR 180

Query: 632 FGIGMNTDHTLEEV 645
           FG+      TLE+V
Sbjct: 181 FGLLGYEAATLEDV 194


>gi|21225555|ref|NP_631334.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256783425|ref|ZP_05521856.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767301|ref|ZP_06526679.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|4835317|emb|CAB42939.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289697500|gb|EFD64929.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 295

 Score =  132 bits (331), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 118/247 (47%), Gaps = 7/247 (2%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA
Sbjct: 45  RQFFRRLTELEEGTAEYQFARNTLIEMNMSLVRFAAGRFRGRGNDMEDIVQTGMIGLIKA 104

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ R    +S ++ 
Sbjct: 105 IDRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELARAREELSTRLD 164

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           REPT  E+A  + +  + V +    +      SL+  +  +   +    + D   V    
Sbjct: 165 REPTVAELATLMNIGEDQVIEGQIASNGYNSSSLDAALTGDGPENGESVLADFIGVEEDG 224

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  +   +   ++A L+ R+ +++ +RF      + T  E+G++   ++  + ++  +
Sbjct: 225 LRLVEDFH-SLAPLMAELSERDRQIIHLRFV----EEATQAEIGERLGCSQMHVSRLIKR 279

Query: 663 AIRKLKH 669
            I +L+ 
Sbjct: 280 IITRLRE 286


>gi|167508102|gb|ABZ81326.1| RpoD [Bowmanella pacifica]
          Length = 265

 Score =  132 bits (331), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 56/314 (17%), Positives = 105/314 (33%), Gaps = 50/314 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   +  S+ E P     L+   D+       L +I+          
Sbjct: 1   REGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQWDQFEAEEIRLSDIV---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E            E   +++ + + D +       D  S VD  PE A    
Sbjct: 51  -LGFIDPNETDVAPTATHIGSELSDEELDDEDDDEDEDEDDDDDADSGVD--PELARQKF 107

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L E    +   +++                                     +     K
Sbjct: 108 AALREQHFKTRDAIASK-----------------------------------GRDHADAK 132

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + D +V+ +  +  R+   E  +++       + +  F++  
Sbjct: 133 TEIAALSEIFKEFRLVPKQFDRMVKNMRGMMDRVRVQERIVMKHCVMHAKMPKKDFIKAF 192

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E    W++      +    + +    + + +   ++  +  ETG+SI++ + I   +
Sbjct: 193 AGNETSSEWLTTLLASGKPYVADLL-THKEELERCIAKMNQVEEETGLSIADIKDINRRM 251

Query: 435 RKGECEASIAKKEM 448
             GE +A  AKK  
Sbjct: 252 SIGEAKARRAKKRW 265


>gi|330466807|ref|YP_004404550.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328809778|gb|AEB43950.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 273

 Score =  132 bits (331), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/227 (26%), Positives = 109/227 (48%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +   +EA L L   +A +Y+ RG    DL Q   +GL+KA +KFD   G  F+ YA+  +
Sbjct: 49  RDRAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDKFDPTRGVDFAGYAIPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D++  IR+P  +++    +      +   + R PT  +IA  L +  E V 
Sbjct: 109 IGELKRHFRDRTWDIRVPRRLQELRLAISDANSSLLQTLGRSPTVADIAAHLKLTEEEVL 168

Query: 565 KVLK--ITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+       +SL TP    +  + LGD +  +++         A LR      LA+L 
Sbjct: 169 EGLEGARAYNAVSLSTPTGDGDRATELGDMLGGEDS-----EFELAELRVALGPALATLD 223

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+++L +RF        T  ++ +Q  V++  + ++ A+A+ KL+
Sbjct: 224 EREQKILTLRFYGN----LTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|186475070|ref|YP_001856540.1| RNA polymerase factor sigma-32 [Burkholderia phymatum STM815]
 gi|184191529|gb|ACC69494.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phymatum
           STM815]
          Length = 311

 Score =  132 bits (331), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 129/272 (47%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+     S   +++V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATEYREQNNLES--ARKLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD- 582
              +       + +   +       + +AK+L +  E V ++    +   ++LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKQGLQSFTPDEIDGLAKELNVKREEVAEMETRLSGGDVALEGQVEDG 212

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT- 638
           E+      ++ D ++      A +   R   +     L SL  R  R++  R+    +  
Sbjct: 213 EEAFAPIAYLADSHSEPTAVLAARQRDRLHSDGIASALESLDSRSRRIIEARWLQVEDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|15803973|ref|NP_290009.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 EDL933]
 gi|15833564|ref|NP_312337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           Sakai]
 gi|16131333|ref|NP_417918.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|26250076|ref|NP_756116.1| RNA polymerase factor sigma-32 [Escherichia coli CFT073]
 gi|74314061|ref|YP_312480.1| RNA polymerase factor sigma-32 [Shigella sonnei Ss046]
 gi|82545824|ref|YP_409771.1| RNA polymerase factor sigma-32 [Shigella boydii Sb227]
 gi|82778725|ref|YP_405074.1| RNA polymerase factor sigma-32 [Shigella dysenteriae Sd197]
 gi|89110551|ref|AP_004331.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|91212950|ref|YP_542936.1| RNA polymerase factor sigma-32 [Escherichia coli UTI89]
 gi|110643701|ref|YP_671431.1| RNA polymerase factor sigma-32 [Escherichia coli 536]
 gi|117625739|ref|YP_859062.1| RNA polymerase factor sigma-32 [Escherichia coli APEC O1]
 gi|157158396|ref|YP_001464926.1| RNA polymerase factor sigma-32 [Escherichia coli E24377A]
 gi|157162938|ref|YP_001460256.1| RNA polymerase factor sigma-32 [Escherichia coli HS]
 gi|168747045|ref|ZP_02772067.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|168753229|ref|ZP_02778236.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|168759499|ref|ZP_02784506.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|168765824|ref|ZP_02790831.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|168772630|ref|ZP_02797637.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|168779560|ref|ZP_02804567.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|168785282|ref|ZP_02810289.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|168797247|ref|ZP_02822254.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|170018307|ref|YP_001723261.1| RNA polymerase factor sigma-32 [Escherichia coli ATCC 8739]
 gi|170082975|ref|YP_001732295.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170683649|ref|YP_001745710.1| RNA polymerase factor sigma-32 [Escherichia coli SMS-3-5]
 gi|170766775|ref|ZP_02901228.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|187730400|ref|YP_001882152.1| RNA polymerase factor sigma-32 [Shigella boydii CDC 3083-94]
 gi|188495507|ref|ZP_03002777.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|191169502|ref|ZP_03031234.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|191170346|ref|ZP_03031899.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|193061907|ref|ZP_03043004.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|193068783|ref|ZP_03049743.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194427076|ref|ZP_03059628.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194431093|ref|ZP_03063386.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194435828|ref|ZP_03067931.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|195934955|ref|ZP_03080337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|208806017|ref|ZP_03248354.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814463|ref|ZP_03255792.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821158|ref|ZP_03261478.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209398124|ref|YP_002272905.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920920|ref|YP_002295004.1| RNA polymerase factor sigma-32 [Escherichia coli SE11]
 gi|215488736|ref|YP_002331167.1| RNA polymerase factor sigma-32 [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217325718|ref|ZP_03441802.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218550723|ref|YP_002384514.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ATCC 35469]
 gi|218556012|ref|YP_002388925.1| RNA polymerase factor sigma-32 [Escherichia coli IAI1]
 gi|218560529|ref|YP_002393442.1| RNA polymerase factor sigma-32 [Escherichia coli S88]
 gi|218691746|ref|YP_002399958.1| RNA polymerase factor sigma-32 [Escherichia coli ED1a]
 gi|218697144|ref|YP_002404811.1| RNA polymerase factor sigma-32 [Escherichia coli 55989]
 gi|218702206|ref|YP_002409835.1| RNA polymerase factor sigma-32 [Escherichia coli IAI39]
 gi|218707055|ref|YP_002414574.1| RNA polymerase factor sigma-32 [Escherichia coli UMN026]
 gi|227883607|ref|ZP_04001412.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|237703208|ref|ZP_04533689.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|238902552|ref|YP_002928348.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|253771710|ref|YP_003034541.1| RNA polymerase factor sigma-32 [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038629|ref|ZP_04872685.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|254163385|ref|YP_003046493.1| RNA polymerase factor sigma-32 [Escherichia coli B str. REL606]
 gi|254795381|ref|YP_003080218.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           TW14359]
 gi|256020809|ref|ZP_05434674.1| RNA polymerase factor sigma-32 [Shigella sp. D9]
 gi|256025815|ref|ZP_05439680.1| RNA polymerase factor sigma-32 [Escherichia sp. 4_1_40B]
 gi|260846245|ref|YP_003224023.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260857567|ref|YP_003231458.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260870186|ref|YP_003236588.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|261224744|ref|ZP_05939025.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261254361|ref|ZP_05946894.1| RNA polymerase, sigma 32 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284801|ref|YP_003501619.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293407042|ref|ZP_06650966.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|293412884|ref|ZP_06655552.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|293416865|ref|ZP_06659502.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|293453766|ref|ZP_06664185.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|297517521|ref|ZP_06935907.1| RNA polymerase factor sigma-32 [Escherichia coli OP50]
 gi|298382788|ref|ZP_06992383.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|300815334|ref|ZP_07095559.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300822733|ref|ZP_07102870.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300898837|ref|ZP_07117141.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300907388|ref|ZP_07125036.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300917205|ref|ZP_07133887.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300930998|ref|ZP_07146356.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300936478|ref|ZP_07151398.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300946790|ref|ZP_07161034.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300956796|ref|ZP_07169063.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300985247|ref|ZP_07177344.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300987360|ref|ZP_07178168.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|301018548|ref|ZP_07182926.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|301021811|ref|ZP_07185775.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|301050314|ref|ZP_07197203.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|301302348|ref|ZP_07208480.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301645904|ref|ZP_07245818.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|306816195|ref|ZP_07450333.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|307140144|ref|ZP_07499500.1| RNA polymerase factor sigma-32 [Escherichia coli H736]
 gi|307311872|ref|ZP_07591510.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|309794740|ref|ZP_07689162.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|312968227|ref|ZP_07782437.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|331644161|ref|ZP_08345290.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331649268|ref|ZP_08350354.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331655044|ref|ZP_08356043.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331659757|ref|ZP_08360695.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331665070|ref|ZP_08365971.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331670287|ref|ZP_08371126.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331674946|ref|ZP_08375703.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331679529|ref|ZP_08380199.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331685107|ref|ZP_08385693.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332282016|ref|ZP_08394429.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|84028120|sp|P0AGB5|RP32_ECO57 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028121|sp|P0AGB4|RP32_ECOL6 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028122|sp|P0AGB3|RP32_ECOLI RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|12518117|gb|AAG58570.1|AE005569_10 RNA polymerase, sigma(32) factor; regulation of proteins induced at
           high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|26110505|gb|AAN82690.1|AE016768_108 RNA polymerase sigma-32 factor [Escherichia coli CFT073]
 gi|147732|gb|AAA24587.1| RNA polymerase sigma-32 subunit [Escherichia coli]
 gi|466597|gb|AAB18436.1| RNA polymerase sigma-32 subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|1789871|gb|AAC76486.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13363784|dbj|BAB37733.1| RNA polymerase sigma32 factor [Escherichia coli O157:H7 str. Sakai]
 gi|73671328|gb|AAZ80075.1| RpoH [Escherichia coli LW1655F+]
 gi|73857538|gb|AAZ90245.1| RNA polymerase, sigma(32) factor [Shigella sonnei Ss046]
 gi|81242873|gb|ABB63583.1| RNA polymerase, sigma(32) factor [Shigella dysenteriae Sd197]
 gi|81247235|gb|ABB67943.1| RNA polymerase sigma(32) factor [Shigella boydii Sb227]
 gi|85676582|dbj|BAE77832.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|91074524|gb|ABE09405.1| component of RNA polymerase, sigma 32 factor [Escherichia coli
           UTI89]
 gi|110345293|gb|ABG71530.1| RNA polymerase sigma-32 factor [Escherichia coli 536]
 gi|115514863|gb|ABJ02938.1| RNA polymerase sigma factor [Escherichia coli APEC O1]
 gi|157068618|gb|ABV07873.1| alternative sigma factor RpoH [Escherichia coli HS]
 gi|157080426|gb|ABV20134.1| alternative sigma factor RpoH [Escherichia coli E24377A]
 gi|169753235|gb|ACA75934.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli ATCC 8739]
 gi|169890810|gb|ACB04517.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170124213|gb|EDS93144.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|170521367|gb|ACB19545.1| alternative sigma factor RpoH [Escherichia coli SMS-3-5]
 gi|187427392|gb|ACD06666.1| alternative sigma factor RpoH [Shigella boydii CDC 3083-94]
 gi|187771635|gb|EDU35479.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|188018405|gb|EDU56527.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|188490706|gb|EDU65809.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|189002511|gb|EDU71497.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|189359084|gb|EDU77503.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|189364663|gb|EDU83082.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|189369524|gb|EDU87940.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|189374649|gb|EDU93065.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|189380077|gb|EDU98493.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|190900463|gb|EDV60280.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|190909154|gb|EDV68740.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|192932697|gb|EDV85294.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|192957859|gb|EDV88302.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194415037|gb|EDX31307.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194420548|gb|EDX36624.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194425371|gb|EDX41355.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|208725818|gb|EDZ75419.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735740|gb|EDZ84427.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741281|gb|EDZ88963.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209159524|gb|ACI36957.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209756038|gb|ACI76331.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756040|gb|ACI76332.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756042|gb|ACI76333.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756044|gb|ACI76334.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756046|gb|ACI76335.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209914179|dbj|BAG79253.1| RNA polymerase sigma-32 factor [Escherichia coli SE11]
 gi|215266808|emb|CAS11249.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|217321939|gb|EEC30363.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353876|emb|CAV00268.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli 55989]
 gi|218358264|emb|CAQ90911.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia fergusonii
           ATCC 35469]
 gi|218362780|emb|CAR00406.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI1]
 gi|218367298|emb|CAR05076.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli S88]
 gi|218372192|emb|CAR20054.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI39]
 gi|218429310|emb|CAR10124.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli ED1a]
 gi|218434152|emb|CAR15069.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli UMN026]
 gi|222035167|emb|CAP77912.1| RNA polymerase sigma-32 factor [Escherichia coli LF82]
 gi|226839135|gb|EEH71158.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|226902472|gb|EEH88731.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|227839486|gb|EEJ49952.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|238863499|gb|ACR65497.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|242378982|emb|CAQ33780.1| RNA polymerase, sigma 32 (sigma H) factor, subunit of RNA
           polymerase sigma 32 [Escherichia coli BL21(DE3)]
 gi|253322754|gb|ACT27356.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975286|gb|ACT40957.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979442|gb|ACT45112.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|254594781|gb|ACT74142.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257756216|dbj|BAI27718.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257761392|dbj|BAI32889.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257766542|dbj|BAI38037.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|260447523|gb|ACX37945.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli DH1]
 gi|281180490|dbj|BAI56820.1| RNA polymerase sigma-32 factor [Escherichia coli SE15]
 gi|284923451|emb|CBG36546.1| RNA polymerase sigma-32 factor [Escherichia coli 042]
 gi|290764674|gb|ADD58635.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291321892|gb|EFE61323.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|291425853|gb|EFE98887.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|291431441|gb|EFF04426.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|291468531|gb|EFF11024.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|294492777|gb|ADE91533.1| alternative sigma factor RpoH [Escherichia coli IHE3034]
 gi|298276624|gb|EFI18142.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|299881444|gb|EFI89655.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|300297943|gb|EFJ54328.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|300306228|gb|EFJ60748.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|300316435|gb|EFJ66219.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300357522|gb|EFJ73392.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300399667|gb|EFJ83205.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|300400897|gb|EFJ84435.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300408118|gb|EFJ91656.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300415544|gb|EFJ98854.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300453547|gb|EFK17167.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300458400|gb|EFK21893.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300461176|gb|EFK24669.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300524733|gb|EFK45802.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300532226|gb|EFK53288.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300842511|gb|EFK70271.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301075893|gb|EFK90699.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|305850591|gb|EFM51048.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|306908016|gb|EFN38516.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|307555555|gb|ADN48330.1| component of RNA polymerase [Escherichia coli ABU 83972]
 gi|307628534|gb|ADN72838.1| RNA polymerase factor sigma-32 [Escherichia coli UM146]
 gi|308121790|gb|EFO59052.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|309703867|emb|CBJ03208.1| RNA polymerase sigma-32 factor [Escherichia coli ETEC H10407]
 gi|312287052|gb|EFR14962.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|312948014|gb|ADR28841.1| RNA polymerase factor sigma-32 [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062740|gb|ADT77067.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli W]
 gi|315138035|dbj|BAJ45194.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315256058|gb|EFU36026.1| alternative sigma factor RpoH [Escherichia coli MS 85-1]
 gi|315286128|gb|EFU45566.1| alternative sigma factor RpoH [Escherichia coli MS 110-3]
 gi|315291684|gb|EFU51040.1| alternative sigma factor RpoH [Escherichia coli MS 153-1]
 gi|315295969|gb|EFU55278.1| alternative sigma factor RpoH [Escherichia coli MS 16-3]
 gi|320175708|gb|EFW50796.1| RNA polymerase sigma factor RpoH [Shigella dysenteriae CDC 74-1112]
 gi|320187771|gb|EFW62446.1| RNA polymerase sigma factor RpoH [Shigella flexneri CDC 796-83]
 gi|320191521|gb|EFW66171.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194037|gb|EFW68670.1| RNA polymerase sigma factor RpoH [Escherichia coli WV_060327]
 gi|320199638|gb|EFW74228.1| RNA polymerase sigma factor RpoH [Escherichia coli EC4100B]
 gi|320639745|gb|EFX09339.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           G5101]
 gi|320645244|gb|EFX14260.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str.
           493-89]
 gi|320650555|gb|EFX19021.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str. H
           2687]
 gi|320655748|gb|EFX23671.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320661531|gb|EFX28946.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320666554|gb|EFX33537.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154300|gb|EFZ40503.1| alternative sigma factor RpoH [Escherichia coli EPECa14]
 gi|323174100|gb|EFZ59728.1| alternative sigma factor RpoH [Escherichia coli LT-68]
 gi|323376672|gb|ADX48940.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli KO11]
 gi|323934553|gb|EGB30953.1| sigma protein RpoH [Escherichia coli E1520]
 gi|323939321|gb|EGB35532.1| sigma proteinRpoH [Escherichia coli E482]
 gi|323944315|gb|EGB40390.1| sigma protein RpoH [Escherichia coli H120]
 gi|323950129|gb|EGB46012.1| sigma proteinRpoH [Escherichia coli H252]
 gi|323954785|gb|EGB50566.1| sigma proteinRpoH [Escherichia coli H263]
 gi|323959687|gb|EGB55338.1| sigma proteinRpoH [Escherichia coli H489]
 gi|323966125|gb|EGB61562.1| sigma proteinRpoH [Escherichia coli M863]
 gi|323970059|gb|EGB65334.1| sigma proteinRpoH [Escherichia coli TA007]
 gi|323974898|gb|EGB70009.1| sigma proteinRpoH [Escherichia coli TW10509]
 gi|324009349|gb|EGB78568.1| alternative sigma factor RpoH [Escherichia coli MS 57-2]
 gi|324014559|gb|EGB83778.1| alternative sigma factor RpoH [Escherichia coli MS 60-1]
 gi|324018638|gb|EGB87857.1| alternative sigma factor RpoH [Escherichia coli MS 117-3]
 gi|324111782|gb|EGC05762.1| sigma proteinRpoH [Escherichia fergusonii B253]
 gi|324116341|gb|EGC10260.1| sigma proteinRpoH [Escherichia coli E1167]
 gi|325499010|gb|EGC96869.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ECD227]
 gi|326337569|gb|EGD61404.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1044]
 gi|326344680|gb|EGD68429.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1125]
 gi|330909502|gb|EGH38016.1| RNA polymerase sigma factor RpoH [Escherichia coli AA86]
 gi|331036455|gb|EGI08681.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331041766|gb|EGI13910.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331047059|gb|EGI19137.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331052972|gb|EGI25005.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331057580|gb|EGI29566.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331062349|gb|EGI34269.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331067855|gb|EGI39253.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331072701|gb|EGI44026.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331077478|gb|EGI48690.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332085344|gb|EGI90516.1| alternative sigma factor RpoH [Shigella boydii 5216-82]
 gi|332085690|gb|EGI90854.1| alternative sigma factor RpoH [Shigella dysenteriae 155-74]
 gi|332090225|gb|EGI95323.1| alternative sigma factor RpoH [Shigella boydii 3594-74]
 gi|332104368|gb|EGJ07714.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|332345416|gb|AEE58750.1| alternative sigma factor RpoH [Escherichia coli UMNK88]
          Length = 284

 Score =  132 bits (331), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    D+  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSD 191

Query: 586 SH-LGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           S  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|215270877|emb|CAR48116.1| RNA polymerase sigma factor [Vibrio rotiferianus]
 gi|215270879|emb|CAR48117.1| RNA polymerase sigma factor [Vibrio rotiferianus]
 gi|215270881|emb|CAR48118.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 272

 Score =  132 bits (331), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 59/311 (18%), Positives = 112/311 (36%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I     + 
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVD 58

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P++       T   +     + ++ +  D+  E   + E       D    V   PE A 
Sbjct: 59  PDAD----DTTAPTATHIGSELTESQLEDEDDEDVDEDEDGDDSDDDAEEDVGIDPELA- 113

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 114 ----------------------------LEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET ++    + I 
Sbjct: 200 ALFTGNESTDAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTEQNIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAQ 269


>gi|241206826|ref|YP_002977922.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|86450985|gb|ABC96760.1| putative RNA polymerase sigma factor [Rhizobium leguminosarum bv.
           trifolii TA1]
 gi|240860716|gb|ACS58383.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 287

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 130/275 (47%), Gaps = 15/275 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  IK       ++  E   + +  R  + +   A+ ++  A++RLVIS+A K+ N GL 
Sbjct: 8   RRMIKIAMAAPYLARQEEHDLAT--RWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLP 65

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 66  MSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKA 125

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   +++    ++  +   +EIA  L + +  V+    +++    SL+ P    
Sbjct: 126 LFFNLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSG 185

Query: 584 D--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNT 638
           D  ++   DF+  +D      + + I    R       L  L  RE +++  R       
Sbjct: 186 DAESAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDG- 244

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+G    +++ER+RQIE++A+ KL+    S
Sbjct: 245 -ATLEELGADLGISKERVRQIESRAMEKLRSALVS 278


>gi|257886121|ref|ZP_05665774.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
 gi|257821977|gb|EEV49107.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
          Length = 383

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 94/250 (37%), Positives = 135/250 (54%), Gaps = 8/250 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                 + +   +V+AN RLV+ +A++Y       L   DL Q G IGL+KAA+KFD   
Sbjct: 121 YQRERDNSSLDALVKANRRLVLKIAQRYNKYLTSSLDIDDLEQFGMIGLLKAADKFDLSK 180

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
            Y FSTYA +W++Q+I+R I D S T+R+PVH+ +KI+K+ R   RM            I
Sbjct: 181 EYAFSTYATYWIRQSISRGIMDTSLTVRLPVHIFEKINKLNRLEARMM-TNSSTTDISSI 239

Query: 553 AKKLAMPVEGVRKVLKITKEPISL---ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            K++ +  E    +L I    +SL   +TPIG +  + +GD + D N     +      L
Sbjct: 240 LKEMDISEEQYYDLLAIRSTYLSLPSLDTPIGIDGDATIGDMLPDNN-YDIEEVIDLGFL 298

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE   + +  L  +E  VL +RFG       TLEE+G  F VTRERIRQIEAKAIRK+K 
Sbjct: 299 REDIKKSMTYLKEKEREVLYLRFGFDGEGRKTLEEIGNIFGVTRERIRQIEAKAIRKMKK 358

Query: 670 PSRSKKLRSF 679
               + +  +
Sbjct: 359 KVNRELISDY 368


>gi|66474725|gb|AAY46932.1| RpoD [Aeromonas sp. ym3]
          Length = 272

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKK+
Sbjct: 257 RRMSIGEAKARRAKKK 272


>gi|162463525|ref|NP_001105185.1| sigma factor protein [Zea mays]
 gi|20159761|gb|AAM12034.1| sigma factor protein [Zea mays]
          Length = 568

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 77/283 (27%), Positives = 136/283 (48%), Gaps = 6/283 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + ++K   E+ S       +  +   +VS ++ G C     +  ++     LV  
Sbjct: 291 LEKIREKMVKEGQEV-SYHRWAEAAGVDEAELVSRLQAGYC----CRDRLLVTTEWLVRC 345

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ YT  G    DL+Q G +G++  AEKFD   G +FSTY  +W+++ +   +A+ S  
Sbjct: 346 IARTYTGMGTALDDLLQAGKMGVLDGAEKFDSRKGCRFSTYVKYWIRKGMLALLAENSGV 405

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
             +P  M   + KV    R +  +  R P+  E+A  + + V  VR   K ++  +SL +
Sbjct: 406 TLLPARMESIMRKVKEARRGIRYRQGRNPSDSEVAAAVGVSVANVRLARKCSRRAVSLYS 465

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +         + I D++A     +  +  LRE    VL  L  RE RVLR+R G+    
Sbjct: 466 EVAIGQDVKFAEVIPDESASPDEAALFRGQLRERLLLVLGRLPAREGRVLRLRHGLEDGR 525

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKKLRSFL 680
             +LEE+G  + V++E IR+IE  A+ +L+   +  + L  F+
Sbjct: 526 CRSLEEIGGIYGVSKEWIRKIEKSAMARLRDDDAVRRDLHDFV 568


>gi|51599021|ref|YP_073209.1| RNA polymerase sigma factor [Borrelia garinii PBi]
 gi|51573592|gb|AAU07617.1| RNA polymerase sigma factor [Borrelia garinii PBi]
          Length = 266

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 77/260 (29%), Positives = 145/260 (55%), Gaps = 10/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   + S +++G    + AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIKLASQIQRGN---AQAKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQF 649
            ED N+ +P  +  Q +  +    VL + L  +E  +++ R+ +  N    TL+++  + 
Sbjct: 185 YED-NSFNPEITLEQDSTIKHLNYVLETKLNEKERYIIKKRYNLDNNPKKSTLKDISTEL 243

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            ++ E +RQIE + ++KLK 
Sbjct: 244 GISSETVRQIEKRVLKKLKE 263



 Score = 37.9 bits (86), Expect = 6.6,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           +YL+ +   +L++ E EI +A +I+ G A     +  + L    ++            + 
Sbjct: 11  IYLKSVREHKLITHEEEIKLASQIQRGNAQAKNKMINANLRL--VLKIIKRYAGKGLKIE 68

Query: 183 EII 185
           ++I
Sbjct: 69  DLI 71


>gi|282862754|ref|ZP_06271815.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282562440|gb|EFB67981.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 298

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 120/245 (48%), Gaps = 8/245 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQEGNIGLMKAA 485
           F   +  + +G  E   A+  ++E NL LV   A ++ NRG     D+IQ G IGL+KA 
Sbjct: 52  FFDRLQTLEEGTHEYQYARNTLIEMNLSLVRYAASRFRNRGGDDTEDIIQVGTIGLIKAI 111

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D + ++ +P  +++   ++ +    +S ++ R
Sbjct: 112 DRFDLSREVEFATFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVELAKAKETLSAQLDR 171

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT  E+A  L +P E + + L         SL+TP  D ++ +      D         
Sbjct: 172 DPTVAELATHLDLPEEEIIEGLVAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGM 231

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               NL      +L  L  RE  ++RMRFG     + T  ++G +  V++  + ++ ++ 
Sbjct: 232 ESVENLH-ALAPLLRQLDDRERTIVRMRFG----QEMTQAQIGAELGVSQMHVSRLLSRI 286

Query: 664 IRKLK 668
           +++L+
Sbjct: 287 VQRLR 291


>gi|255312639|gb|ACU01729.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312641|gb|ACU01730.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312643|gb|ACU01731.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312645|gb|ACU01732.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 77/192 (40%), Positives = 129/192 (67%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 4   VVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 63

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S
Sbjct: 64  TRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITS 123

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+ 
Sbjct: 124 VDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLL 183

Query: 636 MNTDHTLEEVGK 647
                TLE+VG+
Sbjct: 184 GYEAATLEDVGR 195


>gi|302544308|ref|ZP_07296650.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461926|gb|EFL25019.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 288

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 115/243 (47%), Gaps = 7/243 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   ++ + +G  +    +  ++E NL LV   A+++ NR ++  D++Q G IGL+KA +
Sbjct: 26  FLDRLTELEEGTHDYQYVRNTLIELNLSLVRYAARRFRNRSVEMEDVVQVGTIGLIKAID 85

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD     +F+T+A+ ++   I R   D S  + +P  +++    + +    +  +  R 
Sbjct: 86  RFDLSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRIDLAKANEELFQRFDRS 145

Query: 547 PTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+ L +  + V   L  +      SL+ P   E  +       D+         
Sbjct: 146 PTTTELAEHLNLSEDEVLDGLVASNGYSTSSLDAPADPETGTTRVTTYADRIGEVDPAME 205

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  NL      ++  L  R+ R+L+MRFG     + T  E+G +  V++  + ++  K++
Sbjct: 206 VVENLH-ALKPLVEQLGERDRRILQMRFG----EEMTQSEIGAELGVSQMHVSRLLTKSL 260

Query: 665 RKL 667
            +L
Sbjct: 261 TRL 263


>gi|145637130|ref|ZP_01792792.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145640200|ref|ZP_01795784.1| RNA polymerase sigma factor [Haemophilus influenzae R3021]
 gi|229846357|ref|ZP_04466465.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|145269575|gb|EDK09516.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145274786|gb|EDK14648.1| RNA polymerase sigma factor [Haemophilus influenzae 22.4-21]
 gi|229810450|gb|EEP46168.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|309972570|gb|ADO95771.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2846]
          Length = 281

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A +  +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPALYLEDKSSNFAAALENENFESQATEQLGAALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|261415107|ref|YP_003248790.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371563|gb|ACX74308.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326239|gb|ADL25440.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 270

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 67/270 (24%), Positives = 131/270 (48%), Gaps = 20/270 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ I     +S  E + +    +       IA+K+++ AN+R V+ VA +Y    +
Sbjct: 10  LKRYLEDIRRTAPLSREEEQILFQKAK---EGDKIARKKLISANMRFVLKVAIQYRGCPI 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+ EG +GL++A E F+   G KF +Y +WW+K  ITR+I +Q   IR+P +    
Sbjct: 67  PLPDLVSEGAMGLVRAIESFEHTRGLKFISYGVWWIKAYITRAINEQGNLIRLPANQ--- 123

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             +V +          +E              E +R++++I +  +S ++P+  +  +  
Sbjct: 124 HLRVRKALHE--QSRGKEIN------------EEIRELIQIGQRGVSFDSPLKADSKATY 169

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + + D  A +P   +   ++      ++  L  RE RV+   FGI      TL EVG+ 
Sbjct: 170 AEVLPDSGASNPEADSEIQSVEALARDLMEQLPEREARVITGIFGINQEAPQTLREVGES 229

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             ++ ER+RQ+  +A+R+++  +    L+ 
Sbjct: 230 MNISHERVRQLRDQALRRIRKYNSKDFLQE 259


>gi|61657177|emb|CAG17719.1| DNA-directed RNA polymerase subunit D [Pseudomonas balearica]
          Length = 263

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 57/301 (18%), Positives = 104/301 (34%), Gaps = 44/301 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T   ++   D +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYDRVVSEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G            +    +         + + + +  +  S ++       PE A   
Sbjct: 59  DDGAAAPQEVEPVAPQVASKAAA-----DDKDDDEEDEESSDSDEEEGDGGPDPEVARIR 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E    +   L                                   +K  + S + 
Sbjct: 114 FGAVAEQLAKAQKAL-----------------------------------KKFGRGSQQA 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   RI   E  +++L      + R  FL  
Sbjct: 139 TDELEALAILFMPIKLVPKQYDALVERVRDALARIRAQERAIMQLCVRDARMPRADFLRE 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W   A    + ++   +A   D I   + ++  +  ETG+S+++ + I   
Sbjct: 199 FPNNETNLGWAE-AIASGKSKYAQAIAARKDDIRACQQKLLDLEQETGLSVADVKDINRR 257

Query: 434 V 434
           +
Sbjct: 258 M 258


>gi|120600694|ref|YP_965268.1| RNA polymerase factor sigma-32 [Shewanella sp. W3-18-1]
 gi|146291400|ref|YP_001181824.1| RNA polymerase factor sigma-32 [Shewanella putrefaciens CN-32]
 gi|120560787|gb|ABM26714.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. W3-18-1]
 gi|145563090|gb|ABP74025.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           CN-32]
 gi|319428373|gb|ADV56447.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           200]
          Length = 285

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 128/273 (46%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S++  + +       +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYIHSVTSISMLDAEAEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E T   +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNIRKAKKRLGWFSDEEVTM--VAENLGVSKADVTEMESRMAAQDPAFDLTSDNDDE 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   ++N +      + +L  R + +LR R+     T  
Sbjct: 195 QDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQHILRARWLDDDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL+E+ + + V+ ERIRQ+E  A+ KLK    +
Sbjct: 253 TLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|224369499|ref|YP_002603663.1| RpoH [Desulfobacterium autotrophicum HRM2]
 gi|223692216|gb|ACN15499.1| RpoH [Desulfobacterium autotrophicum HRM2]
          Length = 322

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 75/308 (24%), Positives = 152/308 (49%), Gaps = 12/308 (3%)

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              + D  +V      P+ +     +  +     +++ +  I+    ++  E  ++ + +
Sbjct: 9   PVDDTDDTYVRRGYLVPKVKKNTSSSKALVKADPLQSYLAEINRYRLLTREEEVNLGTKI 68

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLG 493
           +  E   S A   MV +NLRLV+ +A  +    +Q  LDLIQEGNIGL+KA +KFD    
Sbjct: 69  Q--EENDSDAAYVMVTSNLRLVVKIALDFQRIWMQNLLDLIQEGNIGLVKAVKKFDPYKN 126

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEE 551
            KFS YA +W+K  I + I D    ++I      R    ++ +  +++ ++   +P P+ 
Sbjct: 127 VKFSYYASFWIKAYILKFIMDNWRLVKIGTTQGQRKLFFRLKKEKQKLIDE-GFDPGPKL 185

Query: 552 IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQA 607
           +++++ +  + + ++  ++    +SL+ P+ ++  +   +FI    D          I+ 
Sbjct: 186 LSERMGVSEQEIIEMDQRLDGWDLSLDEPLRNDSDTERIEFINVESDSTEDRVARKEIED 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L     +  A+L PRE  +      I  +   TL+E+G+++ ++RER+RQIE   I+K+
Sbjct: 246 ILHVRVKKFTATLNPREMEIFSK--RIFSDEPRTLQEIGEEYNISRERVRQIENNIIKKM 303

Query: 668 KHPSRSKK 675
           K   +++ 
Sbjct: 304 KEYFKNEM 311


>gi|297195554|ref|ZP_06912952.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197721376|gb|EDY65284.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 291

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 113/239 (47%), Gaps = 4/239 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ + +G  E    +  ++E NL LV   A ++ NR  Q  D+IQ G IGL+KA ++F+ 
Sbjct: 51  LASLEEGTHEYQYVRNTLIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGLIKAIDRFEL 110

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +F+T+A+ ++   I R   D S  + +P  +++    + +    +S K+   PT  
Sbjct: 111 SREVEFATFAVPYIIGEIKRFFRDTSWAVHVPRRLQELRIDLAKAVDELSQKLDHTPTTA 170

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ L M  E + + +  +    +    +  +D S  G         +P      A   
Sbjct: 171 ELAEHLGMDEEEIIEGVVASNGYTAGSIDMPMDDASDHGAVPLSDRLGAPDAELEIAENV 230

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    ++  L  R+ ++L+MRFG     + T  E+G +  V++  + ++ ++   +L+ 
Sbjct: 231 QALKPLIEELDERDRQILQMRFG----EEMTQSEIGAELGVSQMHVSRLLSRITARLRE 285


>gi|261415258|ref|YP_003248941.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371714|gb|ACX74459.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302327293|gb|ADL26494.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 283

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 136/278 (48%), Gaps = 5/278 (1%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              +        +  IS    ++  +      +++K       A   +V +NLR V+++A
Sbjct: 5   NNREQKDIYMQYLNDISRYPLLTREQE---TILLQKSAEGNKAALDMLVNSNLRFVVNIA 61

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
             Y  RGL  ++LI EGN+GL++AA +FD  L  KF +YA+WW++Q ITR+I+++   IR
Sbjct: 62  NLYKGRGLDIMELINEGNMGLIEAARRFDRSLKIKFISYAVWWIRQNITRAISEKGRMIR 121

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPT--PEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           I       + +  R A+ +   I    T   + +          + K+L +     SL+ 
Sbjct: 122 ISAEKELMLRRFNRHAKDVQQVIGGTFTINTQSLEGLSKYKASEIEKILMMGNSTSSLDA 181

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           P+ ++  + LGD I D  + +   +            +  +L+ +E+ ++++ +G  M++
Sbjct: 182 PVNEDGDATLGDTISDSQSRTDELADNNNRAEVFDKVLDKNLSNQEKEIIKLYYGFKMDS 241

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           D  L+E+     +++ER+RQ++  A+ KL+     + L
Sbjct: 242 DLNLKEIAPMVGLSKERVRQLKENALNKLRDAEVERLL 279


>gi|297200782|ref|ZP_06918179.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197712352|gb|EDY56386.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 285

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 112/244 (45%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  ++ G  E +  +  ++EANL LV   A ++ +R     D+IQ G IGL+ A ++FD 
Sbjct: 48  LKELQPGTPEHNRVRTALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDP 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  
Sbjct: 108 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAFGRTPTTA 167

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  + V   ++   +    SLE     +    L D +  ++            
Sbjct: 168 EIAQRLRITEDEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH---- 223

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+
Sbjct: 224 -RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLR 278

Query: 669 HPSR 672
             +R
Sbjct: 279 SANR 282


>gi|37784420|gb|AAO13103.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 270

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 117/315 (37%), Gaps = 46/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    +  +       S+  E D   E E + E     S DD       PE A   
Sbjct: 59  E-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 112 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 137 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 197 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 255

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 256 MSIGEAKARRAKKEM 270


>gi|1526450|dbj|BAA13238.1| RNA polymerase sigma subunit, truncated form of sigma-38
           [Escherichia coli W3110]
 gi|23306704|gb|AAN15271.1| C-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 269

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 77/218 (35%), Positives = 136/218 (62%), Gaps = 3/218 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
             L D + D+    P D+    +++++  + L  L  +
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L + E S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEYEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|150016005|ref|YP_001308259.1| sporulation sigma factor SigG [Clostridium beijerinckii NCIMB 8052]
 gi|149902470|gb|ABR33303.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 257

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 77/265 (29%), Positives = 132/265 (49%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + I + +    +  + +     A++  ++ NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTSKLPILKEKEKKQLFLQMQAGDKNARETFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENIDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    +      +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALIMREKFIKDNNKEPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            ++ D I D KN        I      +    +  LT RE+ +L +RF  G     T  E
Sbjct: 181 IYVMDQISDAKNTDEHWLENI------SIKEAMKKLTDREKLILNLRFFNG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|330375231|gb|AEC12842.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens]
          Length = 200

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 68/195 (34%), Positives = 117/195 (60%)

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+
Sbjct: 1   AVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKL 60

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             EP+PEEIA  L  PV  V+++L + +   S++  +G +    L D + D     P + 
Sbjct: 61  DHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGPDSDKTLLDTLTDDRPTDPCEL 120

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +L ++  + L+ LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + 
Sbjct: 121 LQDDDLSQSIDQWLSELTEKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEG 180

Query: 664 IRKLKHPSRSKKLRS 678
           +++L+       L S
Sbjct: 181 LKRLREILEKNGLSS 195


>gi|300718824|ref|YP_003743627.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
 gi|299064660|emb|CAX61780.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
          Length = 284

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +V   ++  E + +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRAANVWPMLTAEEEKALAERL--HYQGDLEAAKTLILSHLRFVVHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+    + E   E +A++L +  + V     ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKAKQRLGWFNQEE--VEMVARELGVTSKDVLEMESRMAAQDMTFDPTPDDEGE 191

Query: 586 S-HLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
              +   +  ++  S     I+ +  E+      +  +  L  R + ++R R+ +  +  
Sbjct: 192 GRSMAPMLYLQDKSSDFADGIEEDNWESHAADKLSDAMQGLDERSQNIIRARW-LDDDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 TTLQELADQYGVSAERVRQLEKNAMKKLR 279


>gi|227329284|ref|ZP_03833308.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 285

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 64/270 (23%), Positives = 132/270 (48%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E R +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERL--HYQGDLDAAKHLILSHLRFVIHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + ++  R+    + E   E +A++L +  + VR++  ++  + ++ +    ++  
Sbjct: 134 KLFFNLRKSKTRLGWFNQDE--VELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDSH 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D   +   +  ++  S     I+ +  ET      T  L  L  R + ++R R+ +  + 
Sbjct: 192 DGKAMSPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 KSTLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|311897124|dbj|BAJ29532.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 301

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/249 (22%), Positives = 107/249 (42%), Gaps = 12/249 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++   F  +  +       A + +  ++E N+ LV   A ++ +R     D++Q G IGL
Sbjct: 56  LTRVLFERLAELPPGTPERARV-RSALIEINIPLVRYAAIRFRSRNEPMEDVVQVGTIGL 114

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A ++FD   G +F TYA+  +   I R   D   T+ +P  +++   +V      ++ 
Sbjct: 115 INAIDRFDPDRGVQFPTYALPTILGEIKRYFRDNVRTMHVPRRLQELWVQVSGAMEELTV 174

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              R P   EIA  L +P E VR  L         SLE     E    L D +  +++  
Sbjct: 175 AHGRAPKVPEIAANLRIPEEDVRACLDAGRAYNAASLEAAQEHEGGLALLDRLGYEDSAL 234

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                     R+    +L  L  RE R++ +RF        T  ++  +  +++  + ++
Sbjct: 235 TDVEH-----RDMVRHLLVQLPERERRIIMLRFFAN----LTQSQISTELGMSQMHVSRL 285

Query: 660 EAKAIRKLK 668
            ++ + +L+
Sbjct: 286 LSRILSRLR 294


>gi|326204636|ref|ZP_08194492.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
 gi|325985203|gb|EGD46043.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
          Length = 257

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 70/264 (26%), Positives = 128/264 (48%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + +        +  +     + A+ E +  NLRLV+SV +++ NRG
Sbjct: 2   LINKVEICGVNTSKLPVLTNEQKKVLFERMHKGDNSARDEFINGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EYVDDLFQVGCIGLIKAIDNFDVSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   R++ +  +EPT  E+A++L +P E +   L   ++PISL   +  +  D 
Sbjct: 121 IAYKALQAKERLTTQNSKEPTIAELAQELQLPKEDIVFALDAIQDPISLFESVYHDGGDA 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D + D   +        +         +  L  RE+ +L +RF  G     T  EV
Sbjct: 181 IYVMDQVSDDKNIDENWLETIS-----LKEAMRKLNDREKLILNLRFFEG----RTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A+  +K 
Sbjct: 232 ADEIGISQAQVSRLEKTALMHMKK 255


>gi|153003975|ref|YP_001378300.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152027548|gb|ABS25316.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 299

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 122/272 (44%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I+    +++ E R +    R      + A  ++VEANLR V+ VA +Y + GL
Sbjct: 11  LDQYLREINKVALLTVEEERRLAREFRDEGK--TRAAHKLVEANLRFVVKVAFEYRSYGL 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           +  DLIQEGNIGLMKA +KFD     +  +YA+WW++  I   I      ++I      R
Sbjct: 69  RMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQR 128

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV-------EGVRKVLKITKEPISLETP 579
                + RT   +           E      +         + V    ++    +SL+ P
Sbjct: 129 KLFFSLARTRHEIERVTPGAGLDSEGIDVNLVAKKLRVRASDVVEMQQRMEGRDLSLDAP 188

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMN 637
           + D  ++HL     D +      +  + +  +       ++ L PRE  ++     I  +
Sbjct: 189 VADGTSTHLEFTPSDADPQDDELARAEEDAIVNRRVNDAMSRLDPRERHIVEA--RIMGD 246

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TL ++G+ F  +RER RQ+E +A+ KL+ 
Sbjct: 247 GKETLRDLGQHFGFSRERARQLEIRALEKLRR 278



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 124 YLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           YLRE+  + LL+ E E  +A+   + G+      L E+ L F  ++    E       + 
Sbjct: 14  YLREINKVALLTVEEERRLAREFRDEGKTRAAHKLVEANLRF--VVKVAFEYRSYGLRMA 71

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKR 211
           ++I        E   G     +     K 
Sbjct: 72  DLI-------QEGNIGLMKAVQKFDPDKE 93


>gi|323524659|ref|YP_004226812.1| RNA polymerase sigma-32 subunit RpoH [Burkholderia sp. CCGE1001]
 gi|323381661|gb|ADX53752.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1001]
          Length = 311

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 134/275 (48%), Gaps = 16/275 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+ +     A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEI---AKKLAMPVEGVRKVLKI-TKEPISLETPI 580
              +  K+    R     +    TP+EI   AK+L +  E V ++    +   I+LE  +
Sbjct: 153 KAQR--KLFFNLRSHKQGLGA-FTPDEIDGLAKELNVKREEVAEMETRLSGGDIALEGQV 209

Query: 581 GDEDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGM 636
            D + S+    ++ D ++      A +   +   +     L +L  R  R++  R+    
Sbjct: 210 EDGEESYAPIAYLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIEARWLKVQ 269

Query: 637 NT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 270 DDGSGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|37784416|gb|AAO13101.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           masoucida]
          Length = 270

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 116/314 (36%), Gaps = 46/314 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    +  +       S+  E D   E E + E     S DD       PE A   
Sbjct: 59  E-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 112 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 137 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 197 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 255

Query: 434 VRKGECEASIAKKE 447
           +  GE +A  AKKE
Sbjct: 256 MSIGEAKARRAKKE 269


>gi|74099847|gb|AAZ99132.1| RpoH [Rhizobium leguminosarum]
          Length = 302

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 125/279 (44%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R    + ++ L  RE R+   R       
Sbjct: 194 EGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R + L 
Sbjct: 252 PVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEALE 290


>gi|149198541|ref|ZP_01875585.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149138256|gb|EDM26665.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 282

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 79/277 (28%), Positives = 141/277 (50%), Gaps = 6/277 (2%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + N +K++S    I        +++  K       A +E+  ANLRLV+++AK++ NRG
Sbjct: 5   ALDNYLKNLSDYDLIDSD---REIALANKIAKGDESAIQELTLANLRLVVTIAKQFMNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   +LI EGN GL+KAA++F    G KF++YA WW+KQ I R+I D    +R+PV    
Sbjct: 62  VALGELIAEGNHGLVKAAQRFRPGHGAKFASYAAWWIKQNIRRAIRDDKRIVRVPVQSLL 121

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDED-T 585
           ++ K+     ++  +       + +AK++ +    VR   L +     S+   I  +   
Sbjct: 122 RMQKIKNARLKIQQETGDASNDKAVAKEVGISPRLVRTTSLHVDTSSFSINEQISQDGKA 181

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEE 644
           +  G+ I D  A +P +     +  +T   ++   LT RE ++L  RFG+      TL E
Sbjct: 182 TEKGELIPDSQAQTPGEVMEFHDGYKTLMEIVRQELTEREYKILSARFGLDDGEAKTLAE 241

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
             +   +T ER+RQ++ +A+R+L+      +L   ++
Sbjct: 242 TSELVGLTSERVRQLQQEALRRLRCKLAPHELEGLIN 278


>gi|86359605|ref|YP_471497.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283707|gb|ABC92770.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 287

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 128/275 (46%), Gaps = 15/275 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  IK       ++  E   + +  R  + +   A+ ++  A++RLVIS+A K+ N GL 
Sbjct: 8   RRMIKIAMAAPYLARQEEHDLAT--RWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLP 65

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 66  MSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKA 125

Query: 530 -----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
                 ++     R   ++  +   +EIA  L + +  V+    +++    SL+ P    
Sbjct: 126 LFFNLRRLRAKLARGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSG 185

Query: 584 D--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNT 638
           D  ++   DF+  +D      + + I    R       L  L  RE +++  R       
Sbjct: 186 DAESAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDG- 244

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+G    +++ER+RQIE++A+ KL+    S
Sbjct: 245 -ATLEELGADLGISKERVRQIESRAMEKLRSALVS 278


>gi|296135250|ref|YP_003642492.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
 gi|294339349|emb|CAZ87705.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Thiomonas sp. 3As]
 gi|295795372|gb|ADG30162.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
          Length = 302

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 128/276 (46%), Gaps = 10/276 (3%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + S+  +   I +++    +S  E   +    R  E     A  ++V ++LRLV+S A++
Sbjct: 24  LPSLGNLDAYISAVNRLPMLSAEEEARLARTWR--EQGDKDAAGKLVLSHLRLVVSTARQ 81

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD   G +  +YA+ W+K  I   I      +++ 
Sbjct: 82  YLGYGLPHADLIQEGNIGLMKAVKRFDPAHGVRLVSYALHWIKAEIHEYILRNWRLVKVA 141

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG 581
                +       + + +N    E   +++A+ L +  E V ++  ++    I+L+  + 
Sbjct: 142 TTKSQRKLFFNLRSMKTANAGMNEAQIDDMAQALNVKREDVIEMESRMGGADIALDPTVE 201

Query: 582 DEDTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMN 637
           D + S+    ++ D           +++ R   E     L  L  R   ++  R+    +
Sbjct: 202 DGEESYAPISYLADNTQEPMAVLEARSHDRLQVEGLENALELLDARSRAIVEQRWLQVND 261

Query: 638 T---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 TL E+  ++ V+ ERIRQIE  A++K++  
Sbjct: 262 DGSGGKTLHELAAEYGVSAERIRQIEVAAMKKMRKS 297


>gi|333024500|ref|ZP_08452564.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332744352|gb|EGJ74793.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 356

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 116/240 (48%), Gaps = 11/240 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +       +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 119 LRTLEPESAAYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 178

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  
Sbjct: 179 ERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQQHGRSPTVH 238

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A++L++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 239 ELAQRLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 294

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 295 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 349


>gi|299473209|emb|CBN78785.1| RNA polymerase [Ectocarpus siliculosus]
          Length = 627

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 91/263 (34%), Positives = 141/263 (53%), Gaps = 17/263 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKK--YTNRG----LQFLDLIQEGNIGLMKA 484
           V  + +       A+  M+  NLRLV+ +A++  Y        +   D+IQ+G  GL+KA
Sbjct: 222 VEGLEREIGIMKAARDRMISCNLRLVVHIARRKFYKGASGTLKVSLEDMIQDGTAGLVKA 281

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E+FD   G++FSTYA WWV Q I    AD    +R+P+ +   + KV+R    M +++ 
Sbjct: 282 VERFDPEKGFRFSTYATWWVHQGIHCGFADCGRVVRLPMSLHTMVCKVMRLQTAMVDQLG 341

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITK-EPISLE----------TPIGDEDTSHLGDFIE 593
           R+PT +E++ +  +    V K L++ + EPISL+                    +GD ++
Sbjct: 342 RQPTVQELSLESGLDERKVEKCLRVNQVEPISLDGYRKSKSGHLNFENSFRRERVGDSVK 401

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                 P+D A  + L+     +L  L+ RE  VLRMRFGIG ++  TLE VG++  VTR
Sbjct: 402 SVQETEPVDGADVSLLKTDVDTILGDLSEREAYVLRMRFGIGGSSPSTLETVGQELQVTR 461

Query: 654 ERIRQIEAKAIRKLKHPSRSKKL 676
           ER+RQI+  AI+KL+  S S  L
Sbjct: 462 ERVRQIQIAAIQKLRGRSPSHDL 484


>gi|15615117|ref|NP_243420.1| sporulation sigma factor SigG [Bacillus halodurans C-125]
 gi|10175174|dbj|BAB06273.1| RNA polymerase sporulation forespore-specific (late) sigma-G factor
           [Bacillus halodurans C-125]
          Length = 261

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 81/272 (29%), Positives = 140/272 (51%), Gaps = 21/272 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R + + ++      + A++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNQEMRELFARLQ---SGDTSARETLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++   ++  + +R  EPT +EIAK+L +P E V   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDQLMGEKQREKEPTVQEIAKELGVPKEDVVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D  ++ D I D            A         +  L  RE+ +L MRF  G     T
Sbjct: 179 GGDPIYVMDQISDDRNKDVQWVDEIA-----LKEAMVRLNDREKLILNMRFYQG----KT 229

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             EV ++  +++ ++ ++E  AI+++   ++S
Sbjct: 230 QMEVAEEIGISQAQVSRLEKAAIQQMSKHAQS 261


>gi|302544115|ref|ZP_07296457.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461733|gb|EFL24826.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 284

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 107/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++EANL LV   A ++ +R     D+IQ G IGL+ A ++FD   G +F T+
Sbjct: 54  EHNRVRDALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPGRGVQFPTF 113

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 114 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTVLHGRSPTTAEIAERLGLG 173

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 174 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLVDRLGYEDPALAGVEH-----RDLVRHLL 228

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++  +  V++  + ++ +++  +L+  +R
Sbjct: 229 VQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLSRSFARLRSANR 279


>gi|206559184|ref|YP_002229944.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia J2315]
 gi|198035221|emb|CAR51095.1| RNA polymerase sigma-32 factor [Burkholderia cenocepacia J2315]
          Length = 311

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 132/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R        A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERRYATEFRDDNNLD--AARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE 583
              +       + + S +       + +A++L +  E V     +++   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKREEVTEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+    +  
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARWLHVDDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|66474729|gb|AAY46934.1| RpoD [Aeromonas sp. CCRC 13881]
          Length = 272

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + +LR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKK+
Sbjct: 257 RRMSIGEAKARRAKKK 272


>gi|310815299|ref|YP_003963263.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
 gi|308754034|gb|ADO41963.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
          Length = 298

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 124/272 (45%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   +   +       +   + A  ++V ++LRL   +A  Y   GL
Sbjct: 16  LSRYLQEIRKFPMLEPEQEYMLAR--NWVDHGDTQAAHKLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + +   R+    + +  PE    IA  L +P E V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLRPEHVQRIAHDLGVPEEEVVNMNRRLSGGDASLNAMVGG 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +D S     D++ED+++    D   +  L   R      +  L  RE  VL        +
Sbjct: 194 DDDSSTQWQDWLEDEDSDQAADFEARDELDARRVLLEAAMEDLNDRERDVL--MMRRLQD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TLEE+ +++ V+RERIRQIE +A  KL+ 
Sbjct: 252 PPVTLEELSEKYSVSRERIRQIEVRAFEKLQK 283


>gi|281355585|ref|ZP_06242079.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281318465|gb|EFB02485.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 248

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 83/223 (37%), Positives = 130/223 (58%), Gaps = 3/223 (1%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV  +A  +  RGL + DL+ EGN GLM AA ++D   G +FSTY+ WW+KQA
Sbjct: 18  LIEENLRLVQKIANDFLGRGLPWEDLVSEGNRGLMTAARRYDPSRGARFSTYSAWWIKQA 77

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I ++IA+Q+  +R+P+  +    K+ R    ++  +   P+ EE+A+   +P+  V ++ 
Sbjct: 78  IRQAIAEQAQMVRVPIGTQTHWRKIRRIVNELTEALGHAPSDEEVAEAANLPLATVNRLR 137

Query: 568 KITKEPI-SLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              +  + SL  PI D   D     DF +D    +P    I+    E    +L +LT RE
Sbjct: 138 GSRQIDVQSLNAPISDGDPDGGEFQDFFQDDTEPAPDQQLIKLEDVENLLSLLETLTERE 197

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++VLR+RFG+      TL+EVG +   T ER+RQI+ +A+RKL
Sbjct: 198 QKVLRLRFGLDGEPIRTLDEVGTELNCTNERVRQIQNQALRKL 240


>gi|1710646|sp|P50509|RP32_PROMI RecName: Full=RNA polymerase sigma-32 factor
 gi|1143374|dbj|BAA09441.1| sigma-32 homolog [Proteus mirabilis]
          Length = 284

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 68/269 (25%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANSYPMLTAEEEKELAERL--HYEGDLEAAKTLILSHLRFVIHVARSYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA   F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  PQADLIQEGNIGLMKAVRHFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R+    + E   E +AK+L +    VR++  +++ + ++ +    D D 
Sbjct: 134 KLFFNLRKNKKRLGWFNQDE--VELVAKELGVSESDVREMESRMSAQDMAFDMSADDSDD 191

Query: 586 SHLGD---FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
            H      F+EDK+   A    +     +  +  T  + +L  R + ++R R+    N  
Sbjct: 192 PHPVAPVLFLEDKSSDFADGIEEDNWDNHAADRLTLAIKTLDERSQDIIRARWLEDDNKS 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 252 -TLQELADKYGVSAERVRQLEKNAMKKLR 279


>gi|226313413|ref|YP_002773307.1| sporulation sigma factor SigG [Brevibacillus brevis NBRC 100599]
 gi|226096361|dbj|BAH44803.1| RNA polymerase sigma-G factor [Brevibacillus brevis NBRC 100599]
          Length = 259

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 83/270 (30%), Positives = 138/270 (51%), Gaps = 19/270 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     ++  E R +   ++ GE     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLTNKEMRDLFERLQSGEL---AAREKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEFVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++    ++NK  REPT  EI+++L +  E V   L   ++P+SL  PI  +  
Sbjct: 119 RDIAYKALQVRDNLTNKHSREPTIIEISQELNVAKEDVVFALDAIQDPVSLFEPIYQDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +L MRF  G     T  
Sbjct: 179 DPIYVMDQISDEKNKDVTWVEEIA-----LREGMQRLGDREKMILSMRFYEG----KTQM 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           EV ++  +++ ++ ++E  AI  ++   +S
Sbjct: 230 EVAEEIGISQAQVSRLEKAAIAHMQKHVQS 259


>gi|300926841|ref|ZP_07142609.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|301329786|ref|ZP_07222521.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
 gi|300417191|gb|EFK00502.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|300844135|gb|EFK71895.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
          Length = 284

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LDSYIRAANAWPMLSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++    ++   D D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDQSSDDDSD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|66474713|gb|AAY46926.1| RpoD [Aeromonas media]
          Length = 272

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IA+RIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAERIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GDSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHN 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|312622917|ref|YP_004024530.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203384|gb|ADQ46711.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 255

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 79/262 (30%), Positives = 136/262 (51%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +      + ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKLELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   +  NK ++EPT EEIAK+L++  E +   L   +EPISL  P+  +  DT +
Sbjct: 121 YKALKIKEKYINKNQKEPTLEEIAKELSITKEDLVFALDSIQEPISLYEPVFQDSTDTMY 180

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + + + D  +   +     +         L+ LT RE+ +L +R+  G     T  EV K
Sbjct: 181 VVERLCDHKSCESVWLEEIS-----LKDALSKLTKREKEILYLRYYKG----KTQMEVAK 231

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              +++ ++ +IE  AI  +K 
Sbjct: 232 IVGISQAQVSRIEKSAIGHIKK 253


>gi|56416805|ref|YP_153879.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
 gi|56388037|gb|AAV86624.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
          Length = 290

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 67/278 (24%), Positives = 125/278 (44%), Gaps = 14/278 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + + +  +     +S  E + +          +      +V ++LRLV+ +A  + + G
Sbjct: 14  DLVSYVAQVRTFPILSEEEEKRLAE--NWYRRGSVADAHRLVTSHLRLVVKIAMGFKSYG 71

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  ++LI EGNIGLM+A ++F+  LG++ +TYA+WW+K +I   I      IR+      
Sbjct: 72  LPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQAQ 131

Query: 528 K--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIG 581
           K     + +  +R+ +      T +E   IA++ A   E V R         +SL   + 
Sbjct: 132 KKLFFSLRKIKKRLLS-CGSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQVH 190

Query: 582 DEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            E +  L D +        +  L     A  +      LA+L  R   +           
Sbjct: 191 GESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIF--TRRRLQER 248

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             TLE++ +++ V++ER+RQIE +A+ K+K    + ++
Sbjct: 249 PDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEANRV 286


>gi|220917834|ref|YP_002493138.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955688|gb|ACL66072.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 322

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 139/296 (46%), Gaps = 15/296 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
             GE ++     +     +R  +  ++    +S  E   +   V+  E     A   +V 
Sbjct: 18  SAGEARDRSEGGLVRYDPLRAYMAEVARHPVLSRDEEHALA--VQYRETGDVDAAYRLVA 75

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G K S+YA WW++  I R
Sbjct: 76  SNLRLVVKIAHEYRRTAFQLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIR 135

Query: 511 SIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL- 567
            I +    +++      R     + +   ++  +   EPTP  +AK L +  + V ++  
Sbjct: 136 FIMENWRLVKLGTTQAQRKLFFNLSKEREKLLAR-GIEPTPRLLAKNLQVEEKDVEEMSA 194

Query: 568 KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANL----RETTTRVLASL 620
           ++  + +SL+ P+G E      +  D + D    SP  +     L    RE       +L
Sbjct: 195 RMAADDLSLDAPVGTEGDDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLDAFSGTL 254

Query: 621 TPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           T  +ER +     +        TL+EVG  F +TRER RQIEAK   +L+   R++
Sbjct: 255 TDEKERYIFEHRLLPPDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAE 310



 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCES 160
            S    + +        DP+R Y+ E+    +LSR+ E A+A +  E G       L  S
Sbjct: 17  PSAGEARDRSEGGLVRYDPLRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYRLVAS 76

Query: 161 PLTFQALIIWRDE 173
            L     I     
Sbjct: 77  NLRLVVKIAHEYR 89


>gi|239926901|ref|ZP_04683854.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
 gi|291435248|ref|ZP_06574638.1| HasL [Streptomyces ghanaensis ATCC 14672]
 gi|291338143|gb|EFE65099.1| HasL [Streptomyces ghanaensis ATCC 14672]
          Length = 281

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 57/283 (20%), Positives = 130/283 (45%), Gaps = 21/283 (7%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC-------EASIAKKEMVE 450
            +A       +I  E+  +     ++  + R +  +  +          E   A+  ++E
Sbjct: 1   MMAMTTARADEIITELPEVVDPGQVAPKDARELSRLFFRQLAVLEEGTPEYQYARNTLIE 60

Query: 451 ANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
            N+ LV   A ++ +RG  +  D++Q G IGL+KA ++F+     +F+++A+ ++   + 
Sbjct: 61  MNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELSREVEFTSFAIPYIVGEMK 120

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R   D S ++ +P  +++   ++ R    +  ++ R PT  E+A+ +++  E V +    
Sbjct: 121 RFFRDTSWSVHVPRRLQEARVQLARATEELRTRLGRTPTTRELAQLMSLTEEEVNEARIA 180

Query: 570 T--KEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                  SL+  I    +  S L DFI  ++A   L     A        ++A L  RE 
Sbjct: 181 ANGYNSASLDAAIGSEPDGESVLADFIGSEDAALELVEDFHA-----LAPMIAELDERER 235

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++  RF      + T  E+G++   ++  + ++ ++ +++L+
Sbjct: 236 KIIHWRFV----EELTQAEIGERLGCSQMHVSRLISRILKRLR 274


>gi|149915381|ref|ZP_01903908.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149810670|gb|EDM70511.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 292

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 117/260 (45%), Gaps = 16/260 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELKLAYAWRDQRDEEALHRLITAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARIEREAMAK 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
             ++      E IA ++ +P+  V  +  +++    SL      ED      D IED+  
Sbjct: 146 GEQLDGHQLREMIAHEVGVPLRDVEMMEGRLSGTDFSLNATQSVEDEGREWIDTIEDEGP 205

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                     +   LRE     ++ L  RE  ++R R    +    TLE +G++  +++E
Sbjct: 206 RGDQLVEQDHDLMALREWLGDAMSKLNDRERFIVRERKLRDV--PRTLESLGEELNLSKE 263

Query: 655 RIRQIEAKAIRKLKHPSRSK 674
           R+RQ+EA A +K++      
Sbjct: 264 RVRQLEAAAFQKMRKHLERH 283


>gi|284033085|ref|YP_003383016.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283812378|gb|ADB34217.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 264

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 119/232 (51%), Gaps = 12/232 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           + S+A+  +V  ++ LV  +A+++ NRG  + DL+Q   IGL+KA ++FD   G +FSTY
Sbjct: 36  QHSLARDGLVSLHMPLVEHLARRFRNRGEPYDDLVQVATIGLIKAIDRFDSDRGVEFSTY 95

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   +   I R   D+   IR+P  +++    +      ++ ++ R PT  E++ +L + 
Sbjct: 96  ATPTILGEIKRYFRDKGWAIRVPRRLQELRLSLTAATAELTQELGRAPTVAELSTRLGLS 155

Query: 560 VEGVRKVLK--ITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + V + L+       +SL+ P  +E D + + D +  ++             RE+   +
Sbjct: 156 QDLVIEGLESANAYNTLSLDAPDQNEADATTVLDGLGGEDEA-----LESVEFRESLKPL 210

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LA L  RE+R+L +RF  GM      EE+     +++  + ++ A+ + +L+
Sbjct: 211 LAQLETREKRILTLRFFRGMTQSQIAEEI----GISQMHVSRLLARTLTELR 258


>gi|212703179|ref|ZP_03311307.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
 gi|212673445|gb|EEB33928.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
          Length = 364

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 73/269 (27%), Positives = 134/269 (49%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ +S    +   E   +   VR  +     A   +V ++LRLV+ +A  +  R +
Sbjct: 86  LQLYLREVSRFPMLKPEEEHELAVRVR--DHNDPDAAFRLVSSHLRLVVRIAMDFQRRWM 143

Query: 469 Q-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--M 525
           Q  LDL+QEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      
Sbjct: 144 QNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQVQ 203

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE- 583
           R   + + R  +++  +   +P    ++++L +  E +     ++    +SL   +G++ 
Sbjct: 204 RKLFYNLNRERQKLIAQ-GFDPDAAMLSERLGVSEEQITEMDQRLAANDLSLNAQVGEDA 262

Query: 584 DTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +   DF+         S  DS +   LRE    +L  L  +E  +L  +  +  +   
Sbjct: 263 GGATRMDFLPALGPGIEDSLGDSEVAELLREKLKTILPKLNEKELYIL--QNRLLTDDPV 320

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TL E+G+++ VTRER+RQ+EA+ + K++ 
Sbjct: 321 TLREIGERYNVTRERVRQLEARLLEKIRQ 349



 Score = 43.7 bits (101), Expect = 0.096,   Method: Composition-based stats.
 Identities = 17/94 (18%), Positives = 36/94 (38%)

Query: 56  DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR 115
           + + +   + ++  L  +  + +D  ++ D       L    S   SS+           
Sbjct: 21  EVLDAADEDSSLDSLEELDEDSLDQGEILDVGDDGPMLLTEGSHDESSLPAPSMPRLPST 80

Query: 116 STDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
              D +++YLRE+    +L  E E  +A R+   
Sbjct: 81  GGRDSLQLYLREVSRFPMLKPEEEHELAVRVRDH 114


>gi|119944398|ref|YP_942078.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
 gi|119863002|gb|ABM02479.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
          Length = 283

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 66/266 (24%), Positives = 118/266 (44%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   ++S++  + +S    + +   +         A K++V ++LR V+ +AK Y   GL
Sbjct: 16  IGAYVQSVNQFSMLSAEAEKELAERL--FHEGDLAAAKKLVMSHLRFVVYIAKSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  AQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVIRNWRMVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREP-TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
                + R  +R+      E  T  E        V  +   L    +   L     DE  
Sbjct: 134 KLFFNLRRAKKRLGWFSHDEVATVAENLNVSTKDVLEMESRLNAQDQSFDLSDSDDDESG 193

Query: 586 SHLGDFIEDKNAVSPL---DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++EDK+A           Q + +      L++L  R + ++  R+        TL
Sbjct: 194 FAPVQYLEDKSADVFQVVATENTQLHTKNKLYSALSTLDERSQDIVSSRWL--SEPKATL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ ++ ERIRQ+E  A++KL+
Sbjct: 252 HDLAARYGISAERIRQLEENAMKKLQ 277


>gi|83718896|ref|YP_441014.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|167579742|ref|ZP_02372616.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis TXDOH]
 gi|167617818|ref|ZP_02386449.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis Bt4]
 gi|257140333|ref|ZP_05588595.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|83652721|gb|ABC36784.1| RNA polymerase sigma-32 factor [Burkholderia thailandensis E264]
          Length = 311

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 73/273 (26%), Positives = 135/273 (49%), Gaps = 12/273 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERQYATEYREQNSLD--AARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +   +       + +A++L +  E V ++    +   I+LE  I D 
Sbjct: 153 KAQRKLFFNLRSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNTD 639
           + S+  +    +  N  + + +A Q ++ +T    R L SL  R  R++  R+ + ++ D
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALDSLDARSRRIIEARW-LNVDDD 271

Query: 640 ----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 272 GSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|37784450|gb|AAO13118.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37784454|gb|AAO13120.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37784490|gb|AAO13138.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956251|gb|AAO73796.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956253|gb|AAO73797.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956255|gb|AAO73798.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|37956257|gb|AAO73799.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
          Length = 272

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S    +       D   +  ++ 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELGEADLADEDEDEDEDEDDDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           E + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  ESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +     L  +     L   + D LV  +  + +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIALLADVFRQFRLMPKQFDRLVNNMRGMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|259416055|ref|ZP_05739975.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
 gi|259347494|gb|EEW59271.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
          Length = 292

 Score =  131 bits (330), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 74/268 (27%), Positives = 126/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       + +   A   ++ A +RL +S+A K+   G    DLIQE  +GLMKAAEKF
Sbjct: 26  ELALAYAWRDHQDVQALHRLITAYMRLAVSMASKFRRYGAPMNDLIQEAGLGLMKAAEKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLEREAESD 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET-PIGDEDTSHLGDFIEDKNA 597
             ++ R    + +A+++ +P+  V  +  ++     SL      DED     D +ED + 
Sbjct: 146 GVELDRHKLHQMVAEEIGVPLRDVEMMDGRLAGADFSLNAVQSADEDGREWIDALEDDSE 205

Query: 598 VSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +         +  LRE     L  L  RE  ++R R         TLE +G +  +++E
Sbjct: 206 QAAERVAADHDRRQLREWLVTALNGLNERERFIVRERKLRE--ESRTLESLGNELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  K++     +S+++++FL
Sbjct: 264 RVRQLEAAAFLKMRKSLEGQSREVQNFL 291


>gi|307102796|gb|EFN51063.1| hypothetical protein CHLNCDRAFT_33233 [Chlorella variabilis]
          Length = 288

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 81/255 (31%), Positives = 140/255 (54%), Gaps = 29/255 (11%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           ++ N+RLVI++AK+Y   G+  +DLI EG +GL K+ ++FD   G+KFSTYA WW++Q+I
Sbjct: 1   MQYNVRLVINIAKRYVGNGIDIVDLIPEGLVGLSKSLDRFDASKGFKFSTYAHWWIRQSI 60

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
           +R++ DQ+  +R+P H+ + ++++ R    M+ +    P+ EEIA  + +PV  V   L+
Sbjct: 61  SRAVCDQARVVRLPSHVCETLYRINRAITSMTEQRDEMPSYEEIAAAVDLPVRRVIHYLR 120

Query: 569 ITKEP----ISLETPIGDEDTSHLGDF----IED------KNAVSPLDSAIQANLRETTT 614
           ++K P     + + P      S L +     +ED             + A   ++R+ T 
Sbjct: 121 LSKLPGGAASARDRPTQYLSGSSLKEVTYEALEDCAEDEDPGEEGEEEEAQHESIRQMTD 180

Query: 615 RVLASLTPREERVLRMRFGIG---------------MNTDHTLEEVGKQFCVTRERIRQI 659
            +L++L  RE  +LR+R+G+                     +L EV   + +++ERIRQI
Sbjct: 181 LLLSTLEKRERNILRLRYGLLGWGPAAGGLSWDDNVDGGSMSLGEVASAYGLSKERIRQI 240

Query: 660 EAKAIRKLKHPSRSK 674
           E KA+R L+ P R +
Sbjct: 241 EDKAMRALRKPWRQQ 255


>gi|157149048|ref|YP_001456366.1| RNA polymerase factor sigma-32 [Citrobacter koseri ATCC BAA-895]
 gi|157086253|gb|ABV15931.1| hypothetical protein CKO_04887 [Citrobacter koseri ATCC BAA-895]
          Length = 284

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ VA+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKL--HYQGDLEAAKTLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|107023748|ref|YP_622075.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia AU 1054]
 gi|116690835|ref|YP_836458.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia HI2424]
 gi|170734160|ref|YP_001766107.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia MC0-3]
 gi|254247164|ref|ZP_04940485.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|105893937|gb|ABF77102.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia AU
           1054]
 gi|116648924|gb|ABK09565.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           HI2424]
 gi|124871940|gb|EAY63656.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|169817402|gb|ACA91985.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 311

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 133/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLD--AARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE 583
              +       + + S +       + +A++L +  E V     +++   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKKSMQAMTPEEIDGLAQELNVKREEVTEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+    +  
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARWLHVDDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|145639818|ref|ZP_01795419.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|145271036|gb|EDK10952.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|309750314|gb|ADO80298.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2866]
          Length = 281

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E  +  L SL  R + +++ R+        
Sbjct: 191 ETYSPSLYLEDKSSNFAAELENENFESQATEQLSAALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|304415276|ref|ZP_07395971.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304282866|gb|EFL91334.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 285

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 127/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E + +   +         A K+++ ++LR V  VA+ Y+  GL
Sbjct: 16  LDAYIRTSNTYPMLTAEEEQELAERL--HYHGDLSAAKQLILSHLRFVTHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPAIGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-----RKVLKITKEPISLETPIG 581
                + ++ +R+    + E   E +AK+L +  + V     R   +     +S +    
Sbjct: 134 KLFFNLRKSKQRLGWFNQDE--VEMVAKELGVSKKDVHEMESRMSAQDMTFDLSPDDDTR 191

Query: 582 DEDTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D        +++D+N+       +     +  +  +  L  L  R + ++R R+ +  + 
Sbjct: 192 DGQLVAPVLYLQDRNSDFAGDVEEDNWDNHAVDKLSFALEKLDERSQHIIRARW-LNDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KATLQELANQYGVSAERVRQLEKNAMKKLR 280


>gi|190893879|ref|YP_001980421.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190699158|gb|ACE93243.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 287

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 130/275 (47%), Gaps = 15/275 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  IK       ++  E   + +  R  + +   A+ ++  A++RLVIS+A K+ N GL 
Sbjct: 8   RRMIKIAMAAPYLARQEEHDLAT--RWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLP 65

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 66  MSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKA 125

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   +++    ++  +   +EIA  L + +  V+    +++    SL+ P    
Sbjct: 126 LFFNLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSG 185

Query: 584 D--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNT 638
           D  ++   DF+  +D      + + I    R       L  L  RE +++  R       
Sbjct: 186 DAESAEKMDFLVSDDPLPDEQVSNMIDGERRRIWLASALKHLNEREMKIISARRLAEDG- 244

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLEE+G    +++ER+RQIE++A+ KL+    S
Sbjct: 245 -ATLEELGADLGISKERVRQIESRAMEKLRTALVS 278


>gi|164686360|ref|ZP_02210390.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
 gi|164601962|gb|EDQ95427.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
          Length = 257

 Score =  131 bits (329), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 78/264 (29%), Positives = 134/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + + +   +  ++ K +     A+++ V+ NLRLV+SV +K+ NRG
Sbjct: 2   IINKVEICGVNTSELPVFKADQMRELLVKIKQGDEDARQKFVKGNLRLVLSVIQKFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G +GL+KA + FD     +FSTYA+  +   I R + D +  IR+   ++D
Sbjct: 62  ENVDDLFQIGCVGLIKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLKD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   R+     +EPT  EIAK+L M VE V   L   ++PISL  P+  +  D 
Sbjct: 121 IAYKALQVRERLIRTNSKEPTISEIAKELDMEVESVVMALDAIQDPISLFDPVYQDNGDA 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D ++DK           A         +  L+ RE+ VL +RF  G     T  EV
Sbjct: 181 IFVMDQVQDKKDTDENWLEEIA-----LKEAIKKLSSREKLVLDLRFYKG----RTQIEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ +IE  A++ ++ 
Sbjct: 232 ADEIGISQAQVSRIEKNALKNMRK 255


>gi|269103879|ref|ZP_06156576.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163777|gb|EEZ42273.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 287

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 64/272 (23%), Positives = 132/272 (48%), Gaps = 16/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++++    ++  + + +   +         A K +V ++LR V+ +A+ Y+  GL
Sbjct: 16  LDSYIQAVNRYPMLTAEQEKELAERL--HFDGDIDAAKALVMSHLRFVVHIARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIG 581
                + ++ +R+      E     +A +L +    VR++      +     +S +    
Sbjct: 134 KLFFNLRKSKKRLGWFNNEEINM--VADQLGVEPSEVREMESRLAAQDATFEMSNDDDDR 191

Query: 582 DEDTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D   +    ++EDK++    S  +S  + +     ++ LA L  R + ++R R+     +
Sbjct: 192 DFTPTAPAYYLEDKSSDVARSYEESNWETHATNRLSQALAGLDERSQFIVRSRWLDEDKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL+++  +F V+ ERIRQ+E  A++KLK  
Sbjct: 252 --TLQDLADRFGVSAERIRQLEKNAMKKLKEA 281


>gi|312128104|ref|YP_003992978.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778123|gb|ADQ07609.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 255

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 78/260 (30%), Positives = 134/260 (51%), Gaps = 9/260 (3%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +      + ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKLELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   +  NK  REPT EEIAK+L++  E +   L   +EPISL  P+  + T  + 
Sbjct: 121 YKALKIKEKYINKNHREPTLEEIAKELSITKEELVFALDSIQEPISLYEPVFQDSTDTMY 180

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              +  +  S  +  ++     +    L+ LT RE+ +L +R+  G     T  EV +  
Sbjct: 181 VVEKLCDHKSCENVWLEEI---SLKDALSKLTKREKEILYLRYYKG----KTQMEVARIV 233

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ +IE  AI  +K 
Sbjct: 234 GISQAQVSRIEKSAIGHIKK 253


>gi|171320177|ref|ZP_02909239.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171094591|gb|EDT39643.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 311

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 74/274 (27%), Positives = 141/274 (51%), Gaps = 14/274 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+     S   + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDS--ARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +A++L +  E V     +++   I+LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKSMQAMTPE-EIDGLAQELNVKREDVTEMETRLSGGDIALEGQVDD 211

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT 638
            + S+  +    +  N  S + +A Q ++ +T    + L +L  R  R++  R+ + ++ 
Sbjct: 212 GEESYAPIAYLADSHNEPSAVLAARQRDMLQTDGIAQALEALDARSRRIIEARW-LNVDD 270

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           D     TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 271 DGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|328882855|emb|CCA56094.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 296

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 116/250 (46%), Gaps = 8/250 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S   F  +  +  +G  + +  +  +VE NL LV   A ++  R     D++Q G IGL
Sbjct: 47  LSKQLFARLAEL-EEGTHDHAYVRNTLVELNLALVRFAAARFGTRSEPMEDIVQVGTIGL 105

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++F+   G +F T+AM  +   I R   D S ++ +P  +++    + R    ++ 
Sbjct: 106 IKAIDRFELTRGVEFPTFAMPTIIGEIKRFFRDTSWSVHVPRRLQELRLDLARAGDTLAQ 165

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++ R PT  E+A++L +  E V + +         SL+    +E+       + D+    
Sbjct: 166 RLDRAPTVAELAEELGIAPEEVVEGMAASNAYTASSLDAQPDEEEGGGGEATLADRLGYE 225

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                       +   ++ASL  RE ++L +RF  G     T  E+G +  +++  + ++
Sbjct: 226 -DHGLTGIEYIASLKPMIASLPARERQILSLRFVSG----LTQSEIGTELGISQMHVSRL 280

Query: 660 EAKAIRKLKH 669
            A+ + +L+ 
Sbjct: 281 LARTLARLRR 290


>gi|215270857|emb|CAR48106.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 269

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/311 (17%), Positives = 109/311 (35%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   +++E  D  E   D    ++       ++        
Sbjct: 61  ADDTAAPTATHIGSELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKAAVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET +++   + I 
Sbjct: 200 ALFTGNESSEAWLDEILS-SDKPYAEKIKRSEEEIRRSITKLKMIEEETSLNVQNIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAR 269


>gi|215270855|emb|CAR48105.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270859|emb|CAR48107.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|215270861|emb|CAR48108.1| RNA polymerase sigma factor [Vibrio campbellii]
 gi|311826261|emb|CBX60038.1| RNA polymerase sigma factor [Vibrio campbellii]
          Length = 269

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/311 (17%), Positives = 109/311 (35%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   +++E  D  E   D    ++       ++        
Sbjct: 61  ADDTAAPTATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKAAVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET +++   + I 
Sbjct: 200 ALFTGNESSEAWLDEILS-SDKPYAEKIKRSEEEIRRSITKLKMIEEETSLNVQNIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAR 269


>gi|91794849|ref|YP_564500.1| RNA polymerase factor sigma-32 [Shewanella denitrificans OS217]
 gi|91716851|gb|ABE56777.1| RNA polymerase sigma factor RpoH [Shewanella denitrificans OS217]
          Length = 284

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 130/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+S++    +   + + +   ++  E     A K+++ ++LR V+ VAK Y   GL
Sbjct: 19  LEAYIQSVTSINMLGAEDEQALAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYAGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + ++ +R+      E T   +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNIRKSKKRLGWFSDAEVTM--VAENLGVSKADVTEMESRMAAQDPAFDIASDNDDE 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +      ++ED +   A    ++  ++N +      + +L  R + +L+ R+     T  
Sbjct: 195 TDFSPVHYLEDHSSDVAQQVENANWESNSQSRLFSAIKTLDERSQHILQARWLDDDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+ + + V+ ERIRQ+E  A+ KLK
Sbjct: 253 TLQELAETYQVSAERIRQLEKNAMNKLK 280


>gi|304397877|ref|ZP_07379753.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308188475|ref|YP_003932606.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
 gi|304354588|gb|EFM18959.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308058985|gb|ADO11157.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
          Length = 285

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 127/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +++ +    +S  E + +   +         A K ++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LESYVRAANTWPMLSAEEEKALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLVQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
                + +T +R+    + E   E +A++L +  + VR++   +        +       
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSADDESS 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           +   +   +  ++  S     I+ +  +       +  +  L  R + ++R R+ +  + 
Sbjct: 192 EGRSMAPVLYLQDKTSDFADGIEEDNWDAHAADKLSYAMEGLDERSQHIIRARW-LDEDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KTTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|37784460|gb|AAO13123.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIEPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     S DD       PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 114 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|289207353|ref|YP_003459419.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
 gi|288942984|gb|ADC70683.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
          Length = 289

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 115/271 (42%), Gaps = 17/271 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++++S    +     R +   +   E     A ++++  NLR V+ VA+ Y   GL
Sbjct: 20  LDHYMQAVSRIEVLDPEHERELARSL--HERNDLDAARQLILHNLRFVVHVARGYQGYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGN+GLMKA  +FD   G +  ++A+ W++  I   I      +++      R
Sbjct: 78  PLGDLIQEGNVGLMKAVRRFDPNQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQR 137

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                +    +R+      E +   +A+ L +    V     +++ +  S +     +D 
Sbjct: 138 KLFFNLRSAKQRLGWMSNDEVSA--VARDLGVSENDVWEMERRLSSQDASFDPAPDSDDE 195

Query: 586 SHL--------GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                       + + D  A    D     + +E     L  L  R   +L  R+     
Sbjct: 196 HTYLAPAQRLSIEDMSDDPAQVAEDEDWDRHYQERLASTLGELDERSRDILARRY--MSE 253

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL E+  ++ V+ ERIRQIE  AI++++
Sbjct: 254 PKATLHELAAEYGVSAERIRQIENNAIKRIR 284


>gi|54025575|ref|YP_119817.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017083|dbj|BAD58453.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 315

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 118/252 (46%), Gaps = 12/252 (4%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +    ++ V  G  E +  + E++   + L   +A+K++ RG  F DL Q   +GL+
Sbjct: 70  DLPDLFDRLAAVEPGTAEHAALRDELISRCVPLADHIARKFSGRGEPFDDLTQVARVGLV 129

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A ++FD   G  F ++A+  +   + R   D +  +R+P  +++   ++      +S  
Sbjct: 130 HAVDRFDPARGSNFLSFAVPTIMGEVRRYFRDHTWAMRVPRRVKETHLRIGAAIDTLSQS 189

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLE-TPIGDEDTSHLGDFIEDKNAVS 599
           + R PT +EIA +L +  + V + +      +P S++   +G E  + L D + ++ A  
Sbjct: 190 LGRSPTAKEIAAELRVDPDEVTQAVIAGNAYQPSSIDAAALGRESDASLLDTLGEEEA-- 247

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 +         +LA L  RE R+L MRF        T  ++ KQ  +++  + +I
Sbjct: 248 ---QFERVEEYVAIRPLLAGLPERERRILTMRFF----ESMTQTQIAKQMGISQMHVSRI 300

Query: 660 EAKAIRKLKHPS 671
            AK + +L+  S
Sbjct: 301 LAKTLARLRELS 312


>gi|302389825|ref|YP_003825646.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
 gi|302200453|gb|ADL08023.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
          Length = 241

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 121/239 (50%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++K +     AK E+V  NL LV S+ K++TNRG +  DL Q G+IGL+KA EKFD+
Sbjct: 7   MELLKKAKEGDQEAKSELVSLNLGLVWSIVKRFTNRGYEIEDLFQIGSIGLLKAIEKFDF 66

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R I D    I++   +RD   K+     R++ ++ REPT  
Sbjct: 67  SYNVKFSTYAVPMIIGEIRRYIRD-DRPIKMTRSLRDFSIKIQNAKERLAKELNREPTIA 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A++L    E +   L+  +  ISL      ED S +    +  +     +  +     
Sbjct: 126 ELAEELGATPEELVVGLEAAQPIISLNDVAFQEDGSPIYYMDQLNSDEHHQNQWLDTI-- 183

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L+ L   E +++ +R+      D T  EV K   +T+ ++ ++E K + K+++
Sbjct: 184 -ALKEALSKLDKLERQIIILRYF----KDKTQTEVAKILGITQVQVSRLERKILAKIRN 237


>gi|168235161|ref|ZP_02660219.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194737973|ref|YP_002116503.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194713475|gb|ACF92696.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197291332|gb|EDY30684.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 284

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +T 
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDTK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|66474659|gb|AAY46899.1| RpoD [Aeromonas veronii]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GDSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|119384948|ref|YP_916004.1| RNA polymerase factor sigma-32 [Paracoccus denitrificans PD1222]
 gi|119374715|gb|ABL70308.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 301

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 120/276 (43%), Gaps = 16/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       + + + A + +V ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--AWVDHQDAEAAQRLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTSAQK 133

Query: 529 --IHKVVRTARRM----SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++       ++ E   +          E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKSKLGALEEGDLRPENVTQIAHDLNVTEQEVIDMNRRLSSGDASLNATVGS 193

Query: 583 EDTSH---LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGM 636
            D        D++ED++A      A    L   RE     +  L  RE+ +L  R     
Sbjct: 194 GDGESTAQWQDWLEDEDANQAEAFAEADELSARREMLIAAMDVLNDREKDILMERRLRD- 252

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               TLE++  ++ V+RERIRQIE +A  KL++  R
Sbjct: 253 -DPMTLEDLSTRYGVSRERIRQIEVRAFEKLQNRIR 287


>gi|298369543|ref|ZP_06980860.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282100|gb|EFI23588.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 287

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 131/266 (49%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +    +K       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLSAEEESSLAERQQK---GDLEAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      +EIA  L + +  V     ++T   I +     D++ S
Sbjct: 134 KLFFNLRSMRKSLNALSP-KEAQEIADDLGVKLSEVLEMEQRMTSHDIGIMADNSDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +A      A QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDAEPSRQLAKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HELADEYGVSAERIRQIEAKAMQKLR 277


>gi|197123044|ref|YP_002134995.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|196172893|gb|ACG73866.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
          Length = 322

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 139/296 (46%), Gaps = 15/296 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
             GE ++     +     +R  +  ++    +S  E   +   V+  E     A   +V 
Sbjct: 18  AAGEARDRSEGGLVRYDPLRAYMAEVARHPVLSRDEEHALA--VQYRETGDVDAAYRLVA 75

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G K S+YA WW++  I R
Sbjct: 76  SNLRLVVKIAHEYRRTAFQLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIR 135

Query: 511 SIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL- 567
            I +    +++      R     + +   ++  +   EPTP  +AK L +  + V ++  
Sbjct: 136 FIMENWRLVKLGTTQAQRKLFFNLSKEREKLLAR-GIEPTPRLLAKNLQVEEKDVEEMSA 194

Query: 568 KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANL----RETTTRVLASL 620
           ++  + +SL+ P+G E      +  D + D    SP  +     L    RE       +L
Sbjct: 195 RMAADDLSLDAPVGTEGDDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLDAFSGTL 254

Query: 621 TPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           T  +ER +     +        TL+EVG  F +TRER RQIEAK   +L+   R++
Sbjct: 255 TDEKERYIFEHRLLPPDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAE 310



 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCES 160
            +    + +        DP+R Y+ E+    +LSR+ E A+A +  E G       L  S
Sbjct: 17  PAAGEARDRSEGGLVRYDPLRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYRLVAS 76

Query: 161 PLTFQALIIWRDE 173
            L     I     
Sbjct: 77  NLRLVVKIAHEYR 89


>gi|93005058|ref|YP_579495.1| RNA polymerase factor sigma-32 [Psychrobacter cryohalolentis K5]
 gi|92392736|gb|ABE74011.1| sigma 32 (RpoH) [Psychrobacter cryohalolentis K5]
          Length = 287

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 125/271 (46%), Gaps = 11/271 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++ ++ + +    R  +     A + +V ++LR VI +A+ Y+  
Sbjct: 10  VNLGAYINTVHQIPILTPTQEQELAH--RYYDEGDVEAARLLVMSHLRFVIHIARSYSGY 67

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 68  GLPQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKA 127

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ +N++  E   + IA  L +  + V     ++T    S E    D+D
Sbjct: 128 HRKLFFNLRSLKKTNNQLTLE-EADAIANDLNVTRKQVLEMESRLTSYDASFEAQSSDDD 186

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++ + P +   +++  E         + +L  R   ++  R+        
Sbjct: 187 DGRYAPQLFLEDGIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWL--SEQKS 244

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL E+   + ++ ER+RQIE  A+ K++   
Sbjct: 245 TLHELAAVYSISAERVRQIEKNAMDKIREAM 275


>gi|2384764|gb|AAC97123.1| heat shock sigma factor [Rhodobacter capsulatus]
          Length = 299

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 67/277 (24%), Positives = 119/277 (42%), Gaps = 16/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       + +   A   +V ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--AWVDHQDPKAAHRLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKLA----MPVEGVRKVLKITKEPISLETPIGD 582
                + +   ++    + +  P+ +AK          + +    ++     SL   +G 
Sbjct: 134 KLFFNLRKAKSKIGAFEEGDLRPDAVAKIAHDLNVSEGDVIEMNRRLAGSDASLNAQVGA 193

Query: 583 EDT---SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGM 636
            D    +   D++ED++A      A    L   R      +  L  RE  +L  R     
Sbjct: 194 GDGESATQWQDWLEDEDADQAEAYAEADELQARRAMLVAAMDVLNERERDILMARRLRD- 252

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
               TLEE+  Q+ V+RERIRQIE +A  KL+   ++
Sbjct: 253 -EPVTLEELSSQYDVSRERIRQIEVRAFEKLQGRMKA 288


>gi|296112758|ref|YP_003626696.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|295920452|gb|ADG60803.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|326561004|gb|EGE11369.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 7169]
 gi|326566767|gb|EGE16906.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 103P14B1]
 gi|326567391|gb|EGE17506.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC1]
 gi|326575234|gb|EGE25162.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis CO72]
 gi|326576679|gb|EGE26586.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 101P30B1]
 gi|326577646|gb|EGE27523.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis O35E]
          Length = 371

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 125/270 (46%), Gaps = 11/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++  E R +    R        A + +V ++LR VI +A+ Y+  
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAE--RYYHDGDVEAARLLVMSHLRFVIHIARSYSGY 154

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 155 GLSQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKA 214

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ SN++  +     IA  L + V+ V     ++T    S E    D+D
Sbjct: 215 HRKLFFNLRSLKKSSNQLTLDEATA-IANDLNVTVKQVLEMESRLTSYDASFEAQDSDDD 273

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++AV+P D   +A+  E         + +L  R   ++  R+        
Sbjct: 274 EGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLAD--QKS 331

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TL E+   + ++ ER+RQIE  A+ K+K  
Sbjct: 332 TLHELAATYNISAERVRQIEKNAMNKIKEA 361


>gi|315503089|ref|YP_004081976.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|315409708|gb|ADU07825.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 273

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 108/227 (47%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +   +EA L L   +A +Y+ RG    DL Q   IGL+KA +KFD   G  F+ YA+  +
Sbjct: 49  RDRAIEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAIPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D++  IR+P  +++    +      +   + R PT  +IA  L +  E V 
Sbjct: 109 IGELKRHFRDRTWDIRVPRRLQELRLAISDANSTLLQTLGRSPTVADIAAHLKLTEEEVL 168

Query: 565 KVLK--ITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+       +SL TP    E  + LGD +  ++          A +R      LA+L 
Sbjct: 169 EGLEGARAYNAVSLSTPTGDGERATELGDLLGGEDG-----EFELAEMRVALGPALATLD 223

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+++L +RF        T  ++ +Q  V++  + ++ A+A+ KL+
Sbjct: 224 QREQKILTLRFYGN----LTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|255312647|gb|ACU01733.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312653|gb|ACU01736.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 77/192 (40%), Positives = 129/192 (67%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 4   VVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 63

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S
Sbjct: 64  TRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITS 123

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+ 
Sbjct: 124 VDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLL 183

Query: 636 MNTDHTLEEVGK 647
                TLE+VG+
Sbjct: 184 GYEAATLEDVGR 195


>gi|3249719|gb|AAC26662.1| RNA polymerase sigma-like factor [Streptomyces lividans TK24]
          Length = 162

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 79/162 (48%), Positives = 116/162 (71%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EPTP+E+A  L +
Sbjct: 1   YATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGCEPTPQEVAAHLDL 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V +VL++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LR+    VL+
Sbjct: 61  APERVGEVLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLRQHLEAVLS 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 121 TLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIE 162


>gi|254459542|ref|ZP_05072958.1| sigma 32 [Rhodobacterales bacterium HTCC2083]
 gi|206676131|gb|EDZ40618.1| sigma 32 [Rhodobacteraceae bacterium HTCC2083]
          Length = 292

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 78/279 (27%), Positives = 133/279 (47%), Gaps = 20/279 (7%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +       +    R   CEAS+ +  ++ A +RL IS+A K+   G    DLIQE 
Sbjct: 17  KAEMLDAETELKLAYAWRDERCEASLHR--LINAYMRLAISMASKFRRYGAPLNDLIQEA 74

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDK 528
            +GLMKAA+KFD   G +FSTYA+WW+K +I   +      +R            +MR  
Sbjct: 75  GLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRV 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
             ++ R A++    + R    + I+ ++ +P+  V  +  +++    SL      ED   
Sbjct: 135 QARLEREAQQRGEALDRHQLHQMISTEIGVPLNDVEMMHGRLSGSDFSLNATQSVEDEGR 194

Query: 587 HLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              D +ED  A +     +    A +RE     + +L  RE  ++R R  +      TLE
Sbjct: 195 EWIDALEDDGAQAEEIVENEHDTAQMREWLLGAMNALNERERFIVRERKLLD--EPRTLE 252

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHP--SRSKKLRSFL 680
            +G +  +++ERIRQ+EA A +K++    + S ++ +FL
Sbjct: 253 SLGNELGLSKERIRQLEAAAFQKMRKTLEANSSEVHAFL 291


>gi|291087795|ref|ZP_06347503.2| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
 gi|291073935|gb|EFE11299.1| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
          Length = 291

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/286 (23%), Positives = 134/286 (46%), Gaps = 19/286 (6%)

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKK 446
             + E +         +    N+++   V T    +  +E +    +  +       A++
Sbjct: 16  CKKPEGRTAANNVRRILFMALNKVEICGVNTAKLPLLTNEEKE--ELFARILKGDREARE 73

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           + ++ NLRLV+SV ++++       DL Q G IGL+KA + FD     +FSTYA+  +  
Sbjct: 74  QYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPMILG 133

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            + R + D +  IR+   +RD  +K +     +  K  +EPT  EIA+++ +  E +   
Sbjct: 134 EVKRYLRDNNS-IRVSRSLRDTAYKAIYARESLMKKNLKEPTLCEIAEEVGVSKEDITYA 192

Query: 567 LKITKEPISLETPIGDE--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPR 623
           L   + P+SL  P+  +  D  ++ D + D KN+       I      + +  +  L  R
Sbjct: 193 LDAIQSPVSLYEPVYTDGGDPLYVMDQLSDKKNSEENWIEDI------SLSEAMRRLPER 246

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E  ++ MRF  G     T  EV ++  +++ ++ ++E  A++ +K+
Sbjct: 247 ERHIIGMRFFEG----KTQTEVAEEIHISQAQVSRLEKNALKAMKN 288


>gi|145631055|ref|ZP_01786830.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148827424|ref|YP_001292177.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittGG]
 gi|144983340|gb|EDJ90822.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148718666|gb|ABQ99793.1| RNA polymerase sigma factor [Haemophilus influenzae PittGG]
 gi|301168923|emb|CBW28517.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus influenzae
           10810]
          Length = 281

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E  +  L SL  R + +++ R+        
Sbjct: 191 ETYSPALYLEDKSSNFAAELENENFESQATEQLSAALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|50262051|gb|AAT72766.1| putative sigma factor 32 [Dichelobacter nodosus]
          Length = 283

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 58/270 (21%), Positives = 126/270 (46%), Gaps = 9/270 (3%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I   I  +     +   E   + + +++    A  A + ++  +L+ V+ +A+ +   G
Sbjct: 12  DIDQYIAKVRQIPILDADEEFRLATELQQNHSLA--AAQTLIVHHLKFVVHIARGFLGYG 69

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   +      ++I      
Sbjct: 70  LPLGDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYVIRNWRLVKIATTKAQ 129

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDEDTS 586
           +       + + +     +   + IA+ L + V+ V ++      + I+ +    ++D  
Sbjct: 130 RKLFFNLRSMKKNMHWLSDAEAQTIAEDLNVSVKDVLEMESRIHGQDIAFDPLDENDDEE 189

Query: 587 HLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++    ++ D++   A+S      +  L+   T+ L  L  R   ++  R+ +  +   T
Sbjct: 190 NVAPAAWLTDESVDPALSTEHHEQKHLLQHQLTQGLNQLDARSREIIESRW-LNEHEKVT 248

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L+ +  ++ ++ ERIRQIE +A+ +LK+  
Sbjct: 249 LQTLASKYHISAERIRQIEQQALLQLKNSM 278


>gi|66474661|gb|AAY46900.1| RpoD [Aeromonas media]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GDSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +++   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVVRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|170750108|ref|YP_001756368.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170656630|gb|ACB25685.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 291

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 129/270 (47%), Gaps = 11/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  I++      ++  E R +   VR  +     A   ++ A++RLVI++A ++ + GL 
Sbjct: 9   RQFIRTAMEAPFLAREEERGLA--VRWKDERDERALHRLISAHMRLVIALAGRFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG++GLM+AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  MADLVQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   R+     +   +     IA  + +  + V     +++   +SL  P+G++
Sbjct: 127 LFFNLRRLRARLMQSTEEHVGDEIHRRIASAIGVSRDDVALMDARLSGPDMSLNAPVGED 186

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH- 640
               S   DF+ D   +     +   +     + +  +LT   ER LR+     +  D  
Sbjct: 187 SDASSERMDFLVDGADLPDETVSATVDGERRLSWLQQALTVLSERELRILRERRLAEDQA 246

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLE +G++  +++ER+RQIE +A+ KL+  
Sbjct: 247 TLEALGQRLGISKERVRQIENRALEKLRRA 276


>gi|145628599|ref|ZP_01784399.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|145632513|ref|ZP_01788247.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148825451|ref|YP_001290204.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittEE]
 gi|144979069|gb|EDJ88755.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|144986708|gb|EDJ93260.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148715611|gb|ABQ97821.1| RNA polymerase sigma factor [Haemophilus influenzae PittEE]
          Length = 281

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 131/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPSLYLEDKSSNFAAELENENFESQATEQLGVALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|315635212|ref|ZP_07890490.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
 gi|315476174|gb|EFU66928.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
          Length = 283

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E + +   +     E   A K++V ++LR VI VA+ Y+  GL
Sbjct: 17  LEAYIRAANEYPMLTAEEEKELAERL--YYNEDIEAAKKLVLSHLRFVIHVARGYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 75  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  + V ++  ++T   ++ + P  D D 
Sbjct: 135 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSPQDVVEMESRMTGADVAFDLPTDDHDE 192

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK    A    +   +A   +     L +L  R + +++ R+     T  
Sbjct: 193 ETYAPALYLEDKGSNFAAELENENYEAQATDQLVVALNNLDARSQDIIKARWLDE--TKA 250

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 251 TLQDLAAKYNISAERVRQLETNALKKLK 278


>gi|160871836|ref|ZP_02061968.1| alternative sigma factor RpoH [Rickettsiella grylli]
 gi|159120635|gb|EDP45973.1| alternative sigma factor RpoH [Rickettsiella grylli]
          Length = 290

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 75/276 (27%), Positives = 126/276 (45%), Gaps = 18/276 (6%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I      I  +     +S  E   +    R  +     A K+++  NLR V+ +A+ Y  
Sbjct: 14  INSTDAYITRLKQIPVLSAEEEIELAE--RYYQHHDLDAAKKLIITNLRFVVHIAQTYMG 71

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   I      ++I    
Sbjct: 72  YGLALADLIQEGNIGLMKAVKRFDPKVGVRLISFAVHWIKAEIQEFILRNWRIVKIATTK 131

Query: 526 RDKIHKVVRTARRMSNKIKREPTP--EEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             +  K+    R+M  ++        E +A  L +  E VR++        +SL+    D
Sbjct: 132 AQR--KLFFNLRKMKKRLGWFNQNEIEAVAHDLGVKPETVREMEFRLASNDMSLDISHDD 189

Query: 583 EDTS-----HLGDFIEDKNAVSP----LDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            + +      L D   + N   P      S    +  +   + L  L  RE+ ++R R+ 
Sbjct: 190 PNEAKSTRYPLLDIHFEDNRYDPARLLEASNSTESNHDNLYKALTQLDEREQNIIRDRWL 249

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             M    TL+E+ +++ V+ ERIRQ+E KA++ L+H
Sbjct: 250 --MEPKMTLQELAQRYHVSAERIRQLEQKAMKALRH 283


>gi|88705470|ref|ZP_01103181.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
 gi|88700560|gb|EAQ97668.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
          Length = 338

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 131/269 (48%), Gaps = 13/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++++    +S      +   +         A +E+V ++LR V  +A+ Y   GL
Sbjct: 71  LAAYVQAVAKVPVLSADREHELAEKL--FYDGDVQAARELVMSHLRFVAHIARSYRGYGL 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      ++I     + 
Sbjct: 129 AEADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYILRNWRIVKIATTKAQR 188

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+A++    +  +     +A  L + V+ V R   +++   ++ + P+G +D  
Sbjct: 189 KLFFNLRSAKKSLAWLSADEAKA-VADDLGVDVQEVHRMEGRLSSHDVAFDAPVGADDEE 247

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED++   A +  +S  QA+ +      +A L  R   +L  R+    +   
Sbjct: 248 GWQAPQYYLEDQSVDPATNVENSEWQADSQAQLHAAIAELDERSRNILAQRWL--TDDKA 305

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TL E+  ++ V+ ERIRQ+E  A++K++ 
Sbjct: 306 TLHELAAEYDVSAERIRQLEQAAMKKIRK 334


>gi|84499725|ref|ZP_00998013.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84392869|gb|EAQ05080.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 292

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 70/264 (26%), Positives = 120/264 (45%), Gaps = 16/264 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   +V A +RL IS+A KY   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELSLAYSWRDDRDERALHRLVTAYMRLAISMASKYRRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    K+ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAKLEREALGR 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              + +    + +A ++ +P+  V+ +  +++    SL      ++      D IED   
Sbjct: 146 GETLDKHQLHQLVAMEVGVPLRDVQMMDGRLSGSDFSLNATQSVDEEGREWIDTIEDDGV 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +      +  LR      ++ L  RE  ++  R         TLE +G++  +++E
Sbjct: 206 QAAEAVEADHDRETLRLWLAEAMSDLNDRETLIVTERKLRDA--PRTLESLGQELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRS 678
           R+RQ+EA A +K++    S+ + +
Sbjct: 264 RVRQLEAAAFKKMRRHLESQGVEA 287


>gi|237728776|ref|ZP_04559257.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|283835854|ref|ZP_06355595.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
 gi|226909398|gb|EEH95316.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|291068027|gb|EFE06136.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
          Length = 284

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ VA+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKL--HYQGDLEAAKTLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|15889716|ref|NP_355397.1| RNA polymerase factor sigma-32 [Agrobacterium tumefaciens str. C58]
 gi|15157628|gb|AAK88182.1| RNA polymerase sigma-32 factor [Agrobacterium tumefaciens str. C58]
          Length = 300

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 74/280 (26%), Positives = 123/280 (43%), Gaps = 14/280 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLGK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRLHGDASLNAPIKAS 193

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R    + +  L  RE R+   R       
Sbjct: 194 EGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNERERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             TLEE+  +F ++RER+RQIE +A  K++   + + L +
Sbjct: 252 PVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEA 291


>gi|323699411|ref|ZP_08111323.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           ND132]
 gi|323459343|gb|EGB15208.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans ND132]
          Length = 375

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 141/277 (50%), Gaps = 11/277 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I+    +   E   +   V++       A  ++V ++LRLV+ +A  +  R +
Sbjct: 95  LQLYLKEIARFPMLEPEEEYALAKRVQED--NDQDAAFKLVSSHLRLVVKIAMDFQRRWM 152

Query: 469 QF-LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-R 526
           Q  LDLIQEGN+GL+KA  KFD   G KFS YA +W+K  I + I D    ++I     +
Sbjct: 153 QNGLDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAFWIKAYILKYIMDNWRMVKIGTTQTQ 212

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
            K+   +   R+    +  +P+ E ++++L +    +     +++K  +SL TP+GD+  
Sbjct: 213 RKLFYNLNKERQRLQTLGFDPSTEALSERLGVSEAEIDEMDQRLSKNDMSLNTPLGDDSD 272

Query: 586 SHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +   DF+         S  +  I   L      + ASL  +E  +L     +  +   TL
Sbjct: 273 TTRMDFLPSLAPGVEESIANDQIVDLLLNNIREIRASLNDKEVAILD--RRLLSDDPVTL 330

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            E+G++F VTRER+RQIEA+ + K++    + K++ F
Sbjct: 331 REIGEEFGVTRERVRQIEARLMAKIREHL-TDKVKDF 366



 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLT 163
            L+    S      DP+++YL+E+    +L  E E A+AKR+ E         L  S L 
Sbjct: 79  ALKLAPPSKAVRIRDPLQLYLKEIARFPMLEPEEEYALAKRVQEDNDQDAAFKLVSSHLR 138

Query: 164 FQALIIW 170
               I  
Sbjct: 139 LVVKIAM 145


>gi|302871380|ref|YP_003840016.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574239|gb|ADL42030.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 255

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 77/260 (29%), Positives = 133/260 (51%), Gaps = 9/260 (3%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +        ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKFELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   +  NK  REPT EEIAK+L++  E +   L   +EPISL  P+  + +  + 
Sbjct: 121 YKALKIKEKYINKNHREPTLEEIAKELSITKEELVFALDSIQEPISLYEPVFQDSSDTMY 180

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              +  +  S  +  ++     +    L+ LT RE+ +L +R+  G     T  EV +  
Sbjct: 181 VVEKLCDQKSCENVWLEEI---SLKDALSKLTKREKEILYLRYYKG----KTQMEVARIV 233

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ +IE  AI  +K 
Sbjct: 234 GISQAQVSRIEKSAIGHIKK 253


>gi|215270875|emb|CAR48115.1| RNA polymerase sigma factor [Vibrio rotiferianus]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 54/311 (17%), Positives = 108/311 (34%), Gaps = 43/311 (13%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            +          G    + +   +++E  D  E   D +  ++       ++        
Sbjct: 61  ADDTTAPTATHIGSELTESQLEDEDEEDVDEDEDGDDSDDDSEEDVGIDPEL-------- 112

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +   +++   Y+ L+      +   +    S 
Sbjct: 113 ---------------------------ALEKFNQLRSTYQNLQ------LAINEHGYESP 139

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           K  V  E ++ +     L   + D LV +L     R+   E  +++    YG + +  F+
Sbjct: 140 KATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYGKMPKKSFI 199

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    + I +   ++K I  ET ++    + I 
Sbjct: 200 ALFTGNESTDAWLDEVLA-SDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTEQNIKDIS 258

Query: 432 SMVRKGECEAS 442
             +  GE +A 
Sbjct: 259 RRMSIGEAKAQ 269


>gi|260582846|ref|ZP_05850631.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
 gi|260094059|gb|EEW77962.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
          Length = 281

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 131/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPSLYLEDKSSNFAAELENENFESQATEQLGVALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|161505889|ref|YP_001573001.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867236|gb|ABX23859.1| hypothetical protein SARI_04068 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 284

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 128/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +  +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKAKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|325293796|ref|YP_004279660.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
 gi|1710644|sp|P50507|RP32_AGRTU RecName: Full=RNA polymerase sigma-32 factor
 gi|1143324|dbj|BAA09439.1| sigma-32 homolog [Agrobacterium tumefaciens]
 gi|325061649|gb|ADY65340.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
          Length = 300

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 74/280 (26%), Positives = 123/280 (43%), Gaps = 14/280 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLGK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRLHGDASLNAPIKAS 193

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R    + +  L  RE R+   R       
Sbjct: 194 EGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             TLEE+  +F ++RER+RQIE +A  K++   + + L +
Sbjct: 252 PVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEA 291


>gi|302127761|emb|CBL51734.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 262

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 105/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                      +         E +  D  E E + +     S DD +     PE A    
Sbjct: 59  -----ADDVAPTATHIGSELSEDDLADEDEEEDEEDDDDGDSSDDEADTGPDPEVAREKF 113

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L    + +  ++                                   Q + ++    +
Sbjct: 114 GELRAQYEVTRLSI-----------------------------------QNNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRIQERIILKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E D  W  Y K   +      V  + + +L+   +++ I VETG+SI++ + I   +
Sbjct: 199 TNNECDTAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEVETGLSIAQIKDINRRM 257


>gi|66474629|gb|AAY46884.1| RpoD [Aeromonas sp. AE-51]
 gi|66474631|gb|AAY46885.1| RpoD [Aeromonas hydrophila]
 gi|66474643|gb|AAY46891.1| RpoD [Aeromonas sp. AN-24]
 gi|66474679|gb|AAY46909.1| RpoD [Aeromonas bestiarum]
 gi|66474695|gb|AAY46917.1| RpoD [Aeromonas sp. RK 217215]
 gi|66474699|gb|AAY46919.1| RpoD [Aeromonas sp. 1m]
 gi|66474709|gb|AAY46924.1| RpoD [Aeromonas sp. 19m]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|126700256|ref|YP_001089153.1| sporulation sigma factor SigG [Clostridium difficile 630]
 gi|254976235|ref|ZP_05272707.1| sporulation sigma factor SigG [Clostridium difficile QCD-66c26]
 gi|255093622|ref|ZP_05323100.1| sporulation sigma factor SigG [Clostridium difficile CIP 107932]
 gi|255101810|ref|ZP_05330787.1| sporulation sigma factor SigG [Clostridium difficile QCD-63q42]
 gi|255307677|ref|ZP_05351848.1| sporulation sigma factor SigG [Clostridium difficile ATCC 43255]
 gi|255315370|ref|ZP_05356953.1| sporulation sigma factor SigG [Clostridium difficile QCD-76w55]
 gi|255518035|ref|ZP_05385711.1| sporulation sigma factor SigG [Clostridium difficile QCD-97b34]
 gi|255651151|ref|ZP_05398053.1| sporulation sigma factor SigG [Clostridium difficile QCD-37x79]
 gi|255656619|ref|ZP_05402028.1| sporulation sigma factor SigG [Clostridium difficile QCD-23m63]
 gi|260684217|ref|YP_003215502.1| sporulation sigma factor SigG [Clostridium difficile CD196]
 gi|260687876|ref|YP_003219010.1| sporulation sigma factor SigG [Clostridium difficile R20291]
 gi|296449925|ref|ZP_06891689.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296878307|ref|ZP_06902315.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
 gi|306521001|ref|ZP_07407348.1| sporulation sigma factor SigG [Clostridium difficile QCD-32g58]
 gi|115251693|emb|CAJ69528.1| RNA polymerase sigma-G factor [Clostridium difficile]
 gi|260210380|emb|CBA64761.1| RNA polymerase sigma-G factor [Clostridium difficile CD196]
 gi|260213893|emb|CBE05925.1| RNA polymerase sigma-G factor [Clostridium difficile R20291]
 gi|296261195|gb|EFH08026.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296430605|gb|EFH16444.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
          Length = 257

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 76/262 (29%), Positives = 132/262 (50%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + + + +  ++ + +     A+++ V  NLRLV+SV KK+ NRG  
Sbjct: 4   NKVEICGVNTSELPVLKNKQMKELLLQIKNGDEEARQQFVRGNLRLVLSVIKKFNNRGEN 63

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     +FSTYA+  +   I R + D +  IR+   ++D  
Sbjct: 64  IDDLFQIGCIGLIKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLKDIA 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   R+     +EPT  EIAK+L + VE V   L   ++PISL  P+  +  D   
Sbjct: 123 YKALQVRERLIRTNSKEPTVSEIAKELELEVESVVMALDAIQDPISLFDPVYQDNGDAIF 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D ++DK           +         +  L  RE+ VL +RF  G     T  EV  
Sbjct: 183 VMDQVQDKKDTDENWLQEIS-----LKEAIKKLNSREKLVLDLRFYKG----RTQIEVAD 233

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ +IE  A++ ++ 
Sbjct: 234 EIGISQAQVSRIEKNALKNMRK 255


>gi|11079192|dbj|BAB17587.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|11079196|dbj|BAB17589.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 117/315 (37%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G           Q+ E  + +       + + D E     S+++       PE 
Sbjct: 59  IDPDDDGAA-------GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEV 111

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +                                       +K  ++
Sbjct: 112 ARMRFGAVAEQLEKAKKA-----------------------------------LKKHGRA 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     E L  L   + L   + D LVE++ +   +I   E  +++L      + R  
Sbjct: 137 SQQAVEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E +  W        +G++   +    + I++ + ++  +  E  + I++ + 
Sbjct: 197 FLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADIKD 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRRMSIGEAKARRA 270


>gi|302520386|ref|ZP_07272728.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318060770|ref|ZP_07979493.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078699|ref|ZP_07986031.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025873|ref|ZP_08453937.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|302429281|gb|EFL01097.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|332745725|gb|EGJ76166.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 274

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 106/232 (45%), Gaps = 11/232 (4%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
             +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM 
Sbjct: 49  RVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMP 108

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V   I R   D   T+ +P  + +   +V   A  ++    R PT  EIA++L +  + 
Sbjct: 109 TVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSAAEDLTTAHGRSPTTAEIAERLRIGEDE 168

Query: 563 VRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           V   ++   +    SLE     +    L D +  ++             R+    +L  L
Sbjct: 169 VLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH-----RDLVRHLLVQL 223

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 224 PEREQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 271


>gi|16272227|ref|NP_438438.1| RNA polymerase factor sigma-32 [Haemophilus influenzae Rd KW20]
 gi|68248876|ref|YP_247988.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 86-028NP]
 gi|260580848|ref|ZP_05848673.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|319896604|ref|YP_004134797.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
 gi|1173123|sp|P44404|RP32_HAEIN RecName: Full=RNA polymerase sigma-32 factor
 gi|1573235|gb|AAC21935.1| RNA polymerase sigma-32 factor (rpoH) [Haemophilus influenzae Rd
           KW20]
 gi|68057075|gb|AAX87328.1| RNA polymerase sigma-32 factor [Haemophilus influenzae 86-028NP]
 gi|260092471|gb|EEW76409.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|317432106|emb|CBY80457.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
          Length = 281

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 131/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|66474703|gb|AAY46921.1| RpoD [Aeromonas sp. 13m]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGLNQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + +LR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|15022434|dbj|BAB62255.1| RNA polymerase sigma 70 factor [Treponema medium]
          Length = 155

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 81/152 (53%), Positives = 106/152 (69%)

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +KV R +R++  K  REPT EEIA +L   VE V++V  + +EPISLETPIG+E+ S LG
Sbjct: 3   NKVTRESRQLMQKFGREPTDEEIAAQLGWNVERVKQVKNVAREPISLETPIGEEEDSSLG 62

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           DFIEDK+  +P +      L+E    VL+ L  RE+ VL+MRFG+      TLEEVG  F
Sbjct: 63  DFIEDKDVENPSNLTEYILLQEQLRGVLSCLPLREQEVLKMRFGLDEGYALTLEEVGLYF 122

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            VTRERIRQIEAKA+R+L+HP +S KL+ +LD
Sbjct: 123 NVTRERIRQIEAKALRRLRHPKQSCKLKDYLD 154


>gi|282863441|ref|ZP_06272500.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561776|gb|EFB67319.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 285

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 105/232 (45%), Gaps = 11/232 (4%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
             +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM 
Sbjct: 60  RVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMP 119

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L +  E 
Sbjct: 120 TVVGEIKRYFRDNVRTVHVPRRLHELWVQVTGATEDLTTAHGRSPTTAEIAQRLKISEEE 179

Query: 563 VRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           V   ++   +    SLE     +    L D +  ++             R+    +L  L
Sbjct: 180 VLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLLVQL 234

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 235 PEREQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 282


>gi|295399044|ref|ZP_06809026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110351|ref|YP_003988667.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
 gi|294978510|gb|EFG54106.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215452|gb|ADP74056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
          Length = 250

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/253 (26%), Positives = 125/253 (49%), Gaps = 17/253 (6%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
           +T +   E +    ++R+ +     A+ E+++ N+RLV SV +++ NRG +  DL Q G 
Sbjct: 9   QTLLKDHEMK---KLIRRSQEGDQQARNEIIQKNMRLVWSVVQRFLNRGYEPDDLFQIGC 65

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K+ +    
Sbjct: 66  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKETGNKIRKARDE 124

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKN 596
           +S K  R PT  EIA  L +  E V    +  + P S+   + + D     L D I D +
Sbjct: 125 LSKKHGRAPTVTEIADYLEISPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIADAD 184

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D       +    + +  L  RE  ++ +R+      D T  EV  +  +++ ++
Sbjct: 185 EASWFD-------KIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQV 233

Query: 657 RQIEAKAIRKLKH 669
            ++E K ++++K 
Sbjct: 234 SRLEKKILQQIKE 246


>gi|66474633|gb|AAY46886.1| RpoD [Aeromonas hydrophila]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAISQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|238899138|ref|YP_002924820.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466898|gb|ACQ68672.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 285

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 118/242 (48%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A ++++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HSHGDLNAARQLILSHLRFVAHIARHYSGYGLPQADLIQEGNIGLMKAVRRFNPNMGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +  +R+    + E   + +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFSQNE--VDMVAK 159

Query: 555 KLAMPVEGVRKVLKITK-----EPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQ 606
           +L +  + VR++            + LE    +  +     ++EDKN   A +   +   
Sbjct: 160 ELGVTSKDVREMESRMSAQDMAFELPLEDESREGQSPAPVMYLEDKNSDFADNIEKNNWG 219

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +  ++    L  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 DHAADSLWVALKGLDERSQDIIRARW-LDDDNKSTLQELADRYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|66474637|gb|AAY46888.1| RpoD [Aeromonas hydrophila]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 120/316 (37%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAHLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|37784434|gb|AAO13110.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
 gi|37955126|gb|AAP76215.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 272

 Score =  131 bits (329), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           +   DE +      ++                  E + ELR+  +   ++ QK+ ++  +
Sbjct: 95  DDADDEGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDE 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + D +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMDED-VLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|332977407|gb|EGK14184.1| DNA-directed RNA polymerase sigma subunit RpoH [Psychrobacter sp.
           1501(2011)]
          Length = 362

 Score =  131 bits (328), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 63/299 (21%), Positives = 129/299 (43%), Gaps = 10/299 (3%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDS-ILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
               WVS+  D    +    +   + +  + +   + S+     ++  + + +    R  
Sbjct: 55  TTEEWVSHYPDTSTRDLVPAMPVNLSAPGINLGAYMNSVHQIPILTTEQEQELAH--RYY 112

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +     A + +V ++LR VI +A+ Y+  GL   DLIQEGN+GLMKA ++FD   G +  
Sbjct: 113 DEGDVEAARILVMSHLRFVIHIARSYSGYGLPQADLIQEGNLGLMKAVKRFDPNKGVRLV 172

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           ++A+ W+K  I   +      +++       K+   +R+ ++ +N++  E      A   
Sbjct: 173 SFAVHWIKAEIHEFVIRNWRIVKVATTKAHRKLFFNLRSLKKTNNQLTLEEADAIAADLN 232

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE----T 612
               + +    ++T    S E    D++  H    +  ++ V P +    A+  E     
Sbjct: 233 VTRKQVLEMESRLTSYDASFEAQSSDDEDGHYAPQLFLEDGVDPAEMVEDADWEENNTNA 292

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               + +L  R   ++  R+        TL E+   + ++ ER+RQIE  A+ K++   
Sbjct: 293 LMDAMDTLDDRSRDIVEQRWL--SEQKSTLHELAAVYNISAERVRQIEKNAMDKIREAM 349


>gi|61657175|emb|CAG17718.1| DNA-directed RNA polymerase subunit D [Pseudomonas balearica]
          Length = 263

 Score =  131 bits (328), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 57/301 (18%), Positives = 105/301 (34%), Gaps = 44/301 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T   ++   D +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYDRVVSEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G            +    +   ++      + + +  +  S ++       PE A   
Sbjct: 59  DDGAAAPQEVEPVAPQVASKAAADDK-----DDDEEDEESSDSDEEEGDGGPDPEVARIR 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E    +   L                                   +K  + S + 
Sbjct: 114 FGAVAEQLAKAQKAL-----------------------------------KKFGRGSQQA 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   RI   E  +++L      + R  FL  
Sbjct: 139 TDELEALAILFMPIKLVPKQYDALVERVRDALARIRAQERAIMQLCVRDARMPRADFLRE 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W   A    + ++   +A   D I   + ++  +  ETG+S+++ + I   
Sbjct: 199 FPNNETNLGWAE-AIASGKSKYAEAIAARKDDIRACQQKLVDLEQETGLSVADVKDINRR 257

Query: 434 V 434
           +
Sbjct: 258 M 258


>gi|21222438|ref|NP_628217.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|585925|sp|P37971|RPOF_STRCO RecName: Full=RNA polymerase sigma-F factor
 gi|153455|gb|AAA93052.1| sigma factor [Streptomyces coelicolor A3(2)]
 gi|13122128|emb|CAC32306.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 287

 Score =  131 bits (328), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 106/230 (46%), Gaps = 11/230 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM  V
Sbjct: 64  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D   T+ +P  + +   +V      ++    R PT  EIA++L +  E V 
Sbjct: 124 VGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRITEEEVL 183

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++   +    SLE     +    L D +  ++             R+    +L  L  
Sbjct: 184 SCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH-----RDLVRHLLVQLPE 238

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 239 REQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLRSANR 284


>gi|239934524|emb|CAR94576.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 252

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 55/303 (18%), Positives = 100/303 (33%), Gaps = 54/303 (17%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +  S+ E P     L+   D        L +II       
Sbjct: 2   LLTREGEIKIAKRIEDGINQVQCSVAEYPEAITYLLEQWDAFEAEEVRLTDII------- 54

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                GFF   E  +                + ++ ++E       DD       PE A 
Sbjct: 55  ----SGFFDPDEVDNAPVAA------THVGSELSKEELEDEDDDDDDDEEDTGIDPEFAR 104

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                L    + +   ++                                   K  ++  
Sbjct: 105 EKFDMLRTQYETTRGVIA-----------------------------------KHGRADA 129

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
           K K     L ++     L   + D LV  +  +  ++   E  +++       + ++ F+
Sbjct: 130 KAKTTIHDLSEVFRQFRLVPKQFDRLVGNMRGMMNKVRVQECLIMKHCVQMAKLPKETFV 189

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           +   G E    W   A      ++   +      + +  N++ +I +ETG++IS  + I 
Sbjct: 190 KAFSGNETTNAWFE-ALISKNKKYAVALEEHRGEVERSINKLNNIEIETGLNISNIKDIN 248

Query: 432 SMV 434
             +
Sbjct: 249 RRM 251


>gi|114763110|ref|ZP_01442536.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114544163|gb|EAU47172.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 298

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 124/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E + + +   +V ++LRL   +A  Y   GL
Sbjct: 16  LSRYLSEIRKFPLLEPEEEYMLAK--RWVEDQDAESAHRLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   + +   R    E IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKSRIGALEDGDLRPEHVERIATDLGVTHDEVISMNRRLSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +D S     D++ED++A    D A +  L   RE  T  +  L  RE  +L  R      
Sbjct: 194 DDESSMQWQDWLEDESADQAGDYAERNELEARRELLTEAMDVLNERERDILTQRRLAE-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+   + V+RERIRQIE +A  KL+   R
Sbjct: 252 QPVTLEELSGVYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|3249729|gb|AAC26667.1| RNA polymerase sigma-like factor [Streptomyces bluensis]
          Length = 161

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 83/161 (51%), Positives = 111/161 (68%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R +R+M   + REPTPEE+AK+L M
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVSRQMLQDLGREPTPEELAKELDM 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V +V K  +EPISL TP+G++  +  GD IED  AV P D+     L+E    VL 
Sbjct: 61  TPEKVIEVQKYGREPISLHTPLGEDGDTQFGDLIEDSEAVVPADAVSFTLLQEQLHSVLD 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +L+ RE  V+ MRFG+      TL+E+GK + VTRERIRQI
Sbjct: 121 TLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQI 161


>gi|115352926|ref|YP_774765.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria AMMD]
 gi|170701101|ref|ZP_02892077.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|172061774|ref|YP_001809426.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria MC40-6]
 gi|115282914|gb|ABI88431.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           AMMD]
 gi|170134002|gb|EDT02354.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|171994291|gb|ACB65210.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MC40-6]
          Length = 311

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 74/274 (27%), Positives = 141/274 (51%), Gaps = 14/274 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+     S   + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDS--ARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +A++L +  E V     +++   I+LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKSMQAMTPE-EIDGLAQELNVKREDVTEMETRLSGGDIALEGQVDD 211

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT 638
            + S+  +    +  N  S + +A Q ++ +T    + L +L  R  R++  R+ + ++ 
Sbjct: 212 GEESYAPIAYLADSHNEPSAVLAARQRDMLQTDGIAQALEALDARSRRIIEARW-LNVDD 270

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           D     TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 271 DGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|255312663|gb|ACU01741.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 130/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+ L++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|66474671|gb|AAY46905.1| RpoD [Aeromonas sp. A1-Manipal]
          Length = 272

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI +AKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDLAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAISQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|260431476|ref|ZP_05785447.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260415304|gb|EEX08563.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 292

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 125/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELRLAYAWRDERDEQALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAASD 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET-PIGDEDTSHLGDFIEDKNA 597
             ++ R    + IA ++ +P+  V  +  ++     SL      DED     D +ED +A
Sbjct: 146 GVELDRHQLHQMIAAEIGVPLRDVEMMHGRLAGSDFSLNAVQSADEDGREWIDALEDDSA 205

Query: 598 VS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +            LRE     + +L  RE  ++R R         TLE +G++  +++E
Sbjct: 206 QAAELVEHGHDTRQLREWLITAMQALNERERFIVRERKLRDP--ARTLESLGQELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  K++     +S++++ FL
Sbjct: 264 RVRQLEAAAFAKMRKSLEGQSREVQHFL 291


>gi|241206034|ref|YP_002977130.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859924|gb|ACS57591.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 302

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 124/279 (44%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D     D++ D +         Q  L   R    + ++ L  RE R+   R       
Sbjct: 194 EGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   R + L 
Sbjct: 252 PVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEALE 290


>gi|332995320|gb|AEF05375.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 284

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 65/281 (23%), Positives = 138/281 (49%), Gaps = 14/281 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  V     I   ++++S    ++  E R +   +R+ E     A +++V ++LR V+ 
Sbjct: 8   LALSVPHSGSIEGYVQAVSRIDMLTAEEERALAVRLREDE--DLEAARKLVMSHLRFVVH 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      
Sbjct: 66  IAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRI 125

Query: 519 IRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPIS 575
           +++      R     + +  +R+      E     +A +L +  + V +   +++ +  +
Sbjct: 126 VKVATTKAQRKLFFNLRKAKKRLGWFTHEEVQT--VASELGVSTKEVLQMEARMSSQDQA 183

Query: 576 LETPIGDEDTSHLG--DFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +    +++T +     F+EDK+    +  +++    N  +     + +L  R + ++  
Sbjct: 184 FDLSADEDETGNFAPVQFLEDKSTDVEMDVINNDWDTNASKRLYSAIKTLDDRSQDIIET 243

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           R+     +  TL+++  ++ V+ ER+RQIE  A++KL+   
Sbjct: 244 RWLAD--SKITLQDLADKYEVSAERVRQIEKNAMKKLQAAM 282


>gi|153008567|ref|YP_001369782.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560455|gb|ABS13953.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 303

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 64/267 (23%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHTDPKAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLKVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D ++        Q  L   R    + + +L  RE R+         + 
Sbjct: 194 EGESGEWQDWLVDDSSSQEQVLIEQDELENRRSMLEQAMDTLNDRERRIFEA--RRLSDD 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSSEFGISRERVRQIEVRAFE 278


>gi|254439883|ref|ZP_05053377.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255329|gb|EDY79643.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 292

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 74/268 (27%), Positives = 127/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 26  ELALAYAWRDERDEQALHRLITAYMRLAISMASKFRRYGAPMNDLIQEASLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            ++R    ++ R A + 
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAMKR 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              + R    + IA ++ +P+  V  +  +++    SL      ED      D +ED   
Sbjct: 146 GETLDRHDMRQMIATEVGVPLRDVEMMEGRLSGSDFSLNATQSSEDEGREWIDALEDDGE 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +  +S     LR+     L +L+ RE+ ++R R         TLE +G +  +++E
Sbjct: 206 QAAETVQNSHDTDTLRQWLLTALTALSDREQFIVRERKLRDA--PRTLESLGTELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  K++     +S ++ +FL
Sbjct: 264 RVRQLEAAAFGKMRKSLEGQSHEVHNFL 291


>gi|118443097|ref|YP_878334.1| sporulation sigma factor SigG [Clostridium novyi NT]
 gi|118133553|gb|ABK60597.1| Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           novyi NT]
          Length = 256

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 73/264 (27%), Positives = 134/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + + + +  ++ K +   ++++++ V  NLRLV+SV +++ NRG
Sbjct: 1   MINKVEICGVNTSKLPVLKEKEMKELLLKMKDGDNLSREKFVRGNLRLVLSVIQRFNNRG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 61  ENVDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++  K  ++P    IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 120 IAYKALQVRDKIIKKENKDPNVSRIAKELDLPREEVVFALDAIQDPVSLFEPIYHDGGDA 179

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I D   V             +    +  L  RE+ +L MRF  G     T  EV
Sbjct: 180 LYVMDQISDSKNVDESWIE-----NISIKEAMKRLNEREKMILNMRFFQG----RTQMEV 230

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A++ ++ 
Sbjct: 231 ADEIGISQAQVSRLEKTALKHMRK 254


>gi|126172428|ref|YP_001048577.1| RNA polymerase factor sigma-32 [Shewanella baltica OS155]
 gi|153002659|ref|YP_001368340.1| RNA polymerase factor sigma-32 [Shewanella baltica OS185]
 gi|217975235|ref|YP_002359986.1| RNA polymerase factor sigma-32 [Shewanella baltica OS223]
 gi|304412289|ref|ZP_07393897.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|307306073|ref|ZP_07585818.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
 gi|125995633|gb|ABN59708.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS155]
 gi|151367277|gb|ABS10277.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS185]
 gi|217500370|gb|ACK48563.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS223]
 gi|304349324|gb|EFM13734.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|306910946|gb|EFN41373.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
          Length = 285

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 65/273 (23%), Positives = 127/273 (46%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S++  + +       +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYIHSVTSISMLDAEAEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E T   +A+ L +    V     ++  +  + +     ++ 
Sbjct: 137 KLFFNIRKAKKRLGWFSDAEVTM--VAENLGVSKADVTEMESRMAAQDPAFDLTNDQDEE 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   ++N +      + +L  R + +LR R+     T  
Sbjct: 195 HDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQHILRARWLDDDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL+E+ + + V+ ERIRQ+E  A+ KLK    +
Sbjct: 253 TLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|332977445|gb|EGK14221.1| DNA-directed RNA polymerase sigma subunit SigF [Desmospora sp.
           8437]
          Length = 254

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 127/254 (50%), Gaps = 17/254 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S +E + +   ++K +   + A+  +V+ N+RLV SV +++ NRG +  DL Q 
Sbjct: 8   SRHKHLSDTEVKEL---IQKSQKGDTEARDRLVQHNIRLVWSVVQRFLNRGYEAEDLFQI 64

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA +KFD     KFSTYA+  +   I R + D    +++   +++  +++ +  
Sbjct: 65  GCIGLLKAVDKFDLAYDVKFSTYAVPMIIGEIQRFLRD-DGMVKVSRSLKELSNRIRKVK 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             M+  + R PT +E+++++ +  E +    +  + P S+   + + D     L D I D
Sbjct: 124 DEMTKGLGRSPTIQELSEEMGVTPEEIVFAQEANRTPTSIHETVYENDGDPITLMDQIAD 183

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +      D       R      +  L  RE  ++ +RF      D T  EV ++  +++ 
Sbjct: 184 EEEEGWFD-------RMALKEAIRQLEERERLIVYLRFF----KDQTQSEVAQRLGISQV 232

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K IR+++
Sbjct: 233 QVSRLEKKIIRRMR 246


>gi|297157938|gb|ADI07650.1| SigL-like sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 322

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 119/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               + ++ +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA +
Sbjct: 80  LFERLEILEEGTHEYAYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAID 139

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 140 RFELSRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 199

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +    V + +         SL+    ++D    L D I  ++       
Sbjct: 200 PTAGELAERLGLTTAEVIEGMAASNAYTASSLDAQPEEDDTEGALADRIGYEDHGLEGIE 259

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L+PR+ ++L +RF        T  E+G +  +++  + ++ ++ 
Sbjct: 260 YV-----ESLKPLIADLSPRDRKILSLRFVAN----MTQSEIGDELGISQMHVSRLLSRT 310

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 311 LVRLRR 316


>gi|188535384|ref|YP_001909181.1| RNA polymerase factor sigma-32 [Erwinia tasmaniensis Et1/99]
 gi|188030426|emb|CAO98320.1| RNA polymerase sigma-32 factor [Erwinia tasmaniensis Et1/99]
          Length = 284

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 131/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    ++  E + +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRAANARPMLTAEEEKALAERL--HYQGDLEAAKTLILSHLRFVVHVARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R+    + E   E +A++L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKAKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDPAPDDEGE 191

Query: 586 S-HLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
              +   +  ++  S   + I+ +  E          +  L  R + ++R R+ +  +  
Sbjct: 192 GRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQGLDERSQHIIRARW-LDDDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 TTLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|329295846|ref|ZP_08253182.1| RNA polymerase factor sigma-32 [Plautia stali symbiont]
          Length = 285

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 129/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +++ +    ++  E + +   +         A K ++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LESYVRAANNWPVLTAEEEKALAERL--HYQGDLDAAKTLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKAATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-----RKVLKITKEPISLETPIG 581
                + +T +R+    + E   E +A++L +  + V     R   +     +S +   G
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVLEMESRMAAQDMTFDMSSDDDAG 191

Query: 582 DEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +        +++DK    A    +    A+  +  +  + SL  R + ++R R+ +  + 
Sbjct: 192 EGKPMAPVLYLQDKTSDFADGIEEDNWDAHAADKLSDAMLSLDERSQHIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 251 KTTLQELADQYGVSAERVRQLEKNAMKKLR 280


>gi|261855188|ref|YP_003262471.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
 gi|261835657|gb|ACX95424.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
          Length = 291

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 64/270 (23%), Positives = 123/270 (45%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +  +     ++  E + +   ++        A ++++ ++LR V+ +A+ Y   GL
Sbjct: 20  LQQYLAEVRRIPLLTADEEQKLAEQLK--STGDIDAAQKLIMSHLRFVVHIARGYRGYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+     +  T+A+ W++  I   I      ++I      +
Sbjct: 78  PLADLIQEGNIGLMKAVKRFEPEQKVRLVTFAVHWIRAEIHEYILKNWRIVKIATTKAQR 137

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT 585
             K+    R+M + +      E   IA +L +P   V     ++    I+++ P+ D + 
Sbjct: 138 --KLFFKMRQMKSGLGWLTADETRAIAAELNVPEREVVTMESRLYSHDIAIDAPVYDSEQ 195

Query: 586 S----HLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNT 638
                     + D++ VS  D   Q +  +     T  L  L  R   +L  R+      
Sbjct: 196 EGSGPSYEQILVDQHQVSVEDMTAQRDEDDRVTAMTHALHDLDARSRDILERRWLQEP-- 253

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+ +  ++ V+ ER+RQIE  A++KL+
Sbjct: 254 KATLQTLADEYQVSAERVRQIENAALKKLR 283


>gi|326443307|ref|ZP_08218041.1| sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 351

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 124/257 (48%), Gaps = 12/257 (4%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +  S + G + + F  + ++       A + + ++V  +L LV  +A+++ NRG    DL
Sbjct: 98  QQESQDRGGARAMFVELRALPDGSRERAEL-RNQLVRMHLPLVEHLARRFRNRGEPLDDL 156

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q   IGL+K+ ++FD   G +FSTYA   V   I R   D+   +R+P  +++    + 
Sbjct: 157 TQVATIGLIKSVDRFDPERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLALT 216

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDF 591
                +S    R PT  E+A++L +  E V + L+       +SL+ P  D+++  + D 
Sbjct: 217 TATAELSQLHGRSPTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADT 276

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +  ++             RE+   +L  L PRE+R+L +RF   M      +EV     +
Sbjct: 277 LGAEDEALEGVEY-----RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GI 327

Query: 652 TRERIRQIEAKAIRKLK 668
           ++  + ++ A+ + +L+
Sbjct: 328 SQMHVSRLLARTLAQLR 344


>gi|221199969|ref|ZP_03573012.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
 gi|221206876|ref|ZP_03579888.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221173531|gb|EEE05966.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221180208|gb|EEE12612.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
          Length = 311

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 132/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE 583
              +       + +   +       + +A++L +  E V     +++   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKREEVTEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+    +  
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARWLHVDDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|215254262|gb|ACJ64130.1| RNA polymerase sigma 70 factor [Vibrio sp. cn83]
          Length = 268

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 57/312 (18%), Positives = 100/312 (32%), Gaps = 45/312 (14%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + +S+ E P T   ++   D++      L ++I       
Sbjct: 1   LLTREGEIDIAKRIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDVISGFVDPN 60

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            E          G    + +   ++ E  D  E     +       D             
Sbjct: 61  EEETAAPTATHIGSELSEADLEDEDDEDVDEDEDSDSEDEEEDTGIDPEL---------- 110

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                       +     +   Y      QD  +   +    S 
Sbjct: 111 ---------------------------ALEKFTALRNTY------QDLQLAVNEFGYDSP 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFL 371
           +     E + ++     L   + D LV +L     R+   E  ++R A  YG + +  F+
Sbjct: 138 QVAKSHELVQEVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMRQAVEYGKMPKKSFI 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               G E    W+       +  +   +    D I +   ++  I  ET +S+   + I 
Sbjct: 198 ALFTGNESSEAWLDEVLA-SDKPYAEKIKRYEDDIRRSIQKLNIIEDETSLSVQNIKDIS 256

Query: 432 SMVRKGECEASI 443
             +  GE +A  
Sbjct: 257 RRMSIGEAKARR 268


>gi|219684379|ref|ZP_03539323.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219685569|ref|ZP_03540385.1| RNA polymerase sigma factor [Borrelia garinii Far04]
 gi|219672368|gb|EED29421.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219672847|gb|EED29870.1| RNA polymerase sigma factor [Borrelia garinii Far04]
          Length = 266

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 76/260 (29%), Positives = 144/260 (55%), Gaps = 10/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   +++G    + AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIKLAGQIQRGN---AQAKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQF 649
            ED N+ +P  +  Q +  +    VL + L  +E  +++ R+ +  N    TL+++  + 
Sbjct: 185 YED-NSFNPEITLEQDSTIKHLNYVLETKLNEKERYIIKKRYNLDNNPKKSTLKDISTEL 243

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            ++ E +RQIE + ++KLK 
Sbjct: 244 GISSETVRQIEKRVLKKLKE 263


>gi|126727088|ref|ZP_01742925.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126703516|gb|EBA02612.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 289

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 123/276 (44%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E + S A   +V ++LRL   +A  Y   GL
Sbjct: 10  LNRYMQEIRKFPMLEPEEEYMLAK--NWVEHQDSGAAHRLVTSHLRLAAKIAMGYRGYGL 67

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ E N+GLM+A +KFD   G++ STYAMWW++ +I   +      +++      K
Sbjct: 68  PQAEVVSEANVGLMQAVKKFDPEKGFRLSTYAMWWIRASIQEYVLRSWSLVKLGTTSAQK 127

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAK----KLAMPVEGVRKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE +AK          E +    +++    SL   +G 
Sbjct: 128 KLFFNLRKAKNRIGALEEGDLRPENVAKIASDLNVTETEVISMNRRMSGGDASLNVQVGG 187

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ D +A    D   Q  L   RE   + +A L  RE+ +L        +
Sbjct: 188 DGEGTAQWQDWLADDSADQAGDYEKQDELDTRRELMAQAMAVLNDREKEILME--RRLQD 245

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLEE+ + F V+RERIRQIE +A  KL+   RS
Sbjct: 246 KPKTLEELSEVFSVSRERIRQIEVRAFEKLQTEMRS 281


>gi|114561466|ref|YP_748979.1| RNA polymerase factor sigma-32 [Shewanella frigidimarina NCIMB 400]
 gi|114332759|gb|ABI70141.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella frigidimarina
           NCIMB 400]
          Length = 285

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 68/269 (25%), Positives = 126/269 (46%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+S++    +       I   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYIQSVTSINMLDADTEYDIAKRLQ--ENGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + ++ +R+      E T   +A+ L +    V     ++  +  + +     +D 
Sbjct: 137 KLFFNIRKSKKRLGWFSDAEVTM--VAENLGVSKADVTEMESRMAAQDPAFDLTNDSDDD 194

Query: 586 SH---LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
            H      ++ED +   A     +  +A+ +      + +L  R + +LR R+     T 
Sbjct: 195 HHDFAPALYLEDHSSDVADQVEHANWEADSQTRLLSAIKTLDERSQHILRARWLDD--TK 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 253 VTLQELASTYEVSAERIRQLEKNAMNKLK 281


>gi|161523666|ref|YP_001578678.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|189351565|ref|YP_001947193.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|160341095|gb|ABX14181.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia multivorans
           ATCC 17616]
 gi|189335587|dbj|BAG44657.1| RNA polymerase sigma-32 factor [Burkholderia multivorans ATCC
           17616]
          Length = 311

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 132/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE 583
              +       + +   +       + +A++L +  E V     +++   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKREDVTEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+    +  
Sbjct: 213 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARWLHVDDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|2529275|gb|AAB81194.1| sigma factor [Geobacillus stearothermophilus]
          Length = 250

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 68/256 (26%), Positives = 126/256 (49%), Gaps = 14/256 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            + V+ G S  + + +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL 
Sbjct: 2   DVDVKQGQSPIKDQEMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLF 61

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +
Sbjct: 62  QIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKEMGNKIRK 120

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
               +S    R PT  EIA  L +  E V    +  + P S+   + + D     L D I
Sbjct: 121 AKDELSKTRGRSPTITEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQI 180

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +  S  D       +    + +  L  RE  ++ +R+      D T  EV  +  ++
Sbjct: 181 ADADEASWFD-------KIALKKAIEELDERERLIVYLRY----YRDRTQSEVASRLGIS 229

Query: 653 RERIRQIEAKAIRKLK 668
           + ++ ++E K ++ +K
Sbjct: 230 QVQVSRLEKKILQHIK 245


>gi|302867457|ref|YP_003836094.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|315506134|ref|YP_004085021.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|302570316|gb|ADL46518.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
 gi|315412753|gb|ADU10870.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 269

 Score =  131 bits (328), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 118/227 (51%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + +++EA L L   +A +Y+ RG    DL Q   +GL+KA ++FD   G  F+ +A+  +
Sbjct: 46  RNQVIEAWLPLANHLAARYSGRGEPAGDLAQTAALGLIKAVDRFDASRGVDFAGFAIPTI 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  +++   ++      ++  + R PT  +IA  L +  E V 
Sbjct: 106 LGEIKRHFRDRTWNIRVPRRLQELRLRISEANSTLTQTLNRAPTVADIAAHLDVTEEEVL 165

Query: 565 KVLK--ITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+       +SL TPIGD D+ + LGD +  ++     +    A+LR +    LA+L 
Sbjct: 166 EGLEGARAYNAVSLSTPIGDGDSATELGDTLGTED-----NEYELADLRASLGPALATLD 220

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+++L +RF        T  E+  +  V++  + ++ A+A+ KL+
Sbjct: 221 EREQKILTLRFYGN----LTQSEIAARVGVSQMHVSRLLARALTKLR 263


>gi|302127751|emb|CBL51729.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 262

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 57/300 (19%), Positives = 104/300 (34%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                      +         E +  D  E E + E     + DD       PE A    
Sbjct: 59  -----ADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDEGDGGPDPEVAREKF 113

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L    + +  ++                                   QK+ ++    +
Sbjct: 114 GELRAQYEVTRLSI-----------------------------------QKNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|66474723|gb|AAY46931.1| RpoD [Aeromonas sp. ym2]
          Length = 272

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DD+  T   I S            +   +  E+
Sbjct: 59  N------------------------ETDDMAPTATHIGSELGEDDLADEDEEDEEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKK+
Sbjct: 257 RRMSIGEAKARRAKKK 272


>gi|86137868|ref|ZP_01056444.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85825460|gb|EAQ45659.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 298

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 124/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E E S A   MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--AWVEKEDSGAAHRMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   +      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKL---AMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE +AK      +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLRPENVAKIAHDLGVTEDEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE   + L  L  RE+ +L  R      
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLGQALEVLNDREKDILTKRRLAENV 253

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 254 Q--TLEELSAQYSVSRERIRQIEVRAFEKLQKKMR 286


>gi|55274909|gb|AAV49256.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 78/193 (40%), Positives = 129/193 (66%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E+NLRLV+ +A++Y NRGL  LDLI+EGN+ L++A EKFD   G++FSTYA WW++Q I 
Sbjct: 1   ESNLRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIE 60

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++
Sbjct: 61  RAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRL 120

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL 
Sbjct: 121 NERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLA 180

Query: 630 MRFGIGMNTDHTL 642
            RFG+      TL
Sbjct: 181 RRFGLLGYEAATL 193


>gi|229844972|ref|ZP_04465109.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
 gi|229812106|gb|EEP47798.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
          Length = 281

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 131/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPSLYLEDKSSNFAAELENENFESQATEQLGVALQSLDVRSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|111115602|ref|YP_710220.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
 gi|110890876|gb|ABH02044.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
          Length = 266

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 146/260 (56%), Gaps = 10/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +V  +++    ++ AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIQLVGQIQR---GSAKAKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQF 649
            ED N+ +P  +  Q +  +    +L + LT +E  +++ R+ +  +    TL+++  + 
Sbjct: 185 YED-NSFNPEITLEQDSTLQHLNYILETKLTEKERYIIKKRYNLDNSPKKSTLKDISTEL 243

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            ++ E +RQIE + ++KLK 
Sbjct: 244 GISSETVRQIEKRVLKKLKE 263


>gi|138894663|ref|YP_001125116.1| sporulation sigma factor SigG [Geobacillus thermodenitrificans
           NG80-2]
 gi|134266176|gb|ABO66371.1| Sporulation-specific sigma factor [Geobacillus thermodenitrificans
           NG80-2]
          Length = 264

 Score =  131 bits (328), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 77/261 (29%), Positives = 136/261 (52%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++       A++++V  NLRLV+SV +++ NRG 
Sbjct: 8   RNKVEICGVDTSKLPVLKNEEMRELFQRMHEGDLEAREKLVNGNLRLVLSVIQRFNNRGE 67

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 68  FVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   R+  +  +EP+ EEIAK+L +  E V   L   ++P+SL  PI ++  D  
Sbjct: 127 AYKALQVRERLMGETAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGGDPI 186

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+           A         L  L  RE+ ++R RF  G     T  EV 
Sbjct: 187 YVMDQLSDERNRDSQWIEEIA-----LKEGLRRLNEREKMIIRKRFFQG----KTQMEVA 237

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AIR++
Sbjct: 238 EEIGISQAQVSRLEKAAIRQM 258


>gi|330447179|ref|ZP_08310829.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491370|dbj|GAA05326.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 286

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 68/283 (24%), Positives = 135/283 (47%), Gaps = 16/283 (5%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K   A  + S   + + I++++    ++    + +   +     +   A K +V ++LR 
Sbjct: 3   KEMSAMALVSTDSLDSYIQTVNRYPMLTPEREKELAERL--HYDDDINAAKALVMSHLRF 60

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A+ Y+  GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +   
Sbjct: 61  VVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 516 SCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
              +++      R     + ++ +R+      E     +A++L +  E VR++       
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNNEEVNM--VAEQLGVEPEEVREMESRLAAQ 178

Query: 574 ISLETPIGDEDT-----SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREE 625
                   D+D           F+EDK+   A++  ++  + +     ++ LASL  R +
Sbjct: 179 DPTFEMQNDDDDRDAAPMAPAYFLEDKSSDVALTYEENNWENHANNRLSQALASLDERSQ 238

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++R R+        TL+++   + V+ ERIRQ+E  A++KLK
Sbjct: 239 HIVRSRWLDD--DKSTLQDLADSYGVSAERIRQLEKNAMKKLK 279


>gi|326569916|gb|EGE19966.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC8]
          Length = 371

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 125/270 (46%), Gaps = 11/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++  E R +    R        A + +V ++LR VI +A+ Y+  
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAE--RYYHDGDVEATRLLVMSHLRFVIHIARSYSGY 154

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 155 GLSQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKA 214

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ SN++  +     IA  L + V+ V     ++T    S E    D+D
Sbjct: 215 HRKLFFNLRSLKKSSNQLTLDEATA-IANDLNVTVKQVLEMESRLTSYDASFEAQDSDDD 273

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++AV+P D   +A+  E         + +L  R   ++  R+        
Sbjct: 274 EGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLAD--QKS 331

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TL E+   + ++ ER+RQIE  A+ K+K  
Sbjct: 332 TLHELAATYNISAERVRQIEKNAMNKIKEA 361


>gi|326775534|ref|ZP_08234799.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655867|gb|EGE40713.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 122/252 (48%), Gaps = 8/252 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G      A+  ++E NL LV   AK++ NRG  +  D+IQ G IGL+KA 
Sbjct: 46  FFDQLQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIIQVGTIGLIKAI 105

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +T   +S ++ R
Sbjct: 106 DRFELSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKTREALSTRLDR 165

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EPT  E+A  L +  E V + L         SL+ PIG +  S       D         
Sbjct: 166 EPTVAELAHHLELTEEEVIEGLIAANGYTAGSLDLPIGADQNSAETVTYGDIKGDVDPAM 225

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  +L  T   +L  L  RE  ++ MRFG     + T  ++G+   +++  + ++ ++ 
Sbjct: 226 ELVEDLH-TLAPLLEQLDEREREIVAMRFG----REMTQAQIGEHLGISQMHVSRLLSRL 280

Query: 664 IRKLKHPSRSKK 675
           + KL+    ++K
Sbjct: 281 LTKLRKDMLTEK 292


>gi|198284457|ref|YP_002220778.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667652|ref|YP_002427124.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198248978|gb|ACH84571.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519865|gb|ACK80451.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 286

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 59/267 (22%), Positives = 118/267 (44%), Gaps = 8/267 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ ++ +  +   E R +   +R  +     A K++V ++LR V+ VA+ Y   GL
Sbjct: 17  LAGYLRFVNAQPLLRPEEERDLARRLR--DHGDVDAAKDLVLSHLRFVVRVARGYRGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
           Q  DLIQEGNIGLMKA +++D   G +  ++A+ WVK  I   I      +++     + 
Sbjct: 75  QEADLIQEGNIGLMKAVKRYDPDHGVRLVSFAVHWVKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   +R++R  +  +  E +            + +    +++    SL     +E    
Sbjct: 135 KLFFNLRSSRSHTGWMSGEESAAMADDLGVTQAQVLEMEGRMSGYDYSLNLEPDEEREGG 194

Query: 588 LGDFIEDKNA---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
               + D         ++              L++L  R+  ++  R+    +   TL+ 
Sbjct: 195 RAPDLADPTGSPIEQLVERDWDQQQHRALHTALSALPQRDRYIIENRWL--SDDPKTLQV 252

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +G +  V+ ER+RQ+E  ++ KL+   
Sbjct: 253 LGDELGVSAERVRQLEKSSMGKLRQQM 279


>gi|229543947|ref|ZP_04433006.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
 gi|229325086|gb|EEN90762.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
          Length = 252

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 130/260 (50%), Gaps = 17/260 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K    +T +   E +++   +R+ +     A+  +VE N+RLV SV +++ NRG +  
Sbjct: 4   ELKKAEKKTRLKDEEVKNL---IRRSQEGDQGARDLIVEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  ++
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKETGNR 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +T   ++ K+ R PT  EIA +L MPVE V    +  K P S+   + + D     L 
Sbjct: 120 IRKTRDELTKKLGRSPTVHEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+N     D              +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQISDQNDQKWFDQI-------ALQEAIRGLEERERLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ ++E K +  +K 
Sbjct: 229 GISQVQVSRLEKKILEVMKE 248


>gi|283852956|ref|ZP_06370215.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
 gi|283571646|gb|EFC19647.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
          Length = 342

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 133/275 (48%), Gaps = 13/275 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ I     +   E + +   VR  +     A   ++ ++LRLV+ +A  +  R +Q  
Sbjct: 65  YLREIGKFPMLKPEEEQELARRVR--DLGDQKAAFRLISSHLRLVVKIAMDFQRRWMQNV 122

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDLIQEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      R  
Sbjct: 123 LDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIGTTQAQRKL 182

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG-VRKVLKITKEPISLETPIGDEDTSH 587
            + + +   R+   +  +P+  ++++ L +     V    +++   +SL+  +GD+ TS 
Sbjct: 183 FYNLNKERHRL-QTLGFDPSASQLSQALNVTESDIVEMDQRLSGNDLSLDMTLGDDSTST 241

Query: 588 LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             DF+               I   L +    +   L  +E  +L     I  ++  TL E
Sbjct: 242 RLDFLPALTPGIEEILAGDEISHQLDKHIQTIRPKLNEKELDLLD--NRILSDSPATLRE 299

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           +G ++ +TRER+RQIEA+ + KLK    S+++  F
Sbjct: 300 IGAKYGITRERVRQIEARLLEKLKEHL-SRRIEDF 333



 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 1/93 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +  +L+D E  ++         +  +   K   +   ST DP+ +YLRE+G   +L  E 
Sbjct: 20  ETLELDDPEALDEEAVEIEPVDDFRLPTPKTSGAGSLSTRDPLHLYLREIGKFPMLKPEE 79

Query: 139 EIAIAKRI-EAGRAMMMASLCESPLTFQALIIW 170
           E  +A+R+ + G       L  S L     I  
Sbjct: 80  EQELARRVRDLGDQKAAFRLISSHLRLVVKIAM 112


>gi|302866675|ref|YP_003835312.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302569534|gb|ADL45736.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 273

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 108/227 (47%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +   +EA L L   +A +Y+ RG    DL Q   IGL+KA +KFD   G  F+ YA+  +
Sbjct: 49  RDRAIEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAIPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D++  IR+P  +++    +      +   + R PT  +IA  L +  E V 
Sbjct: 109 IGELKRHFRDRTWDIRVPRRLQELRLAISDANSTLLQTLGRSPTVADIAAHLKLTEEEVL 168

Query: 565 KVLK--ITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L+       +SL TP    E  + LGD +  ++          A +R      LA+L 
Sbjct: 169 EGLEGARAYNAVSLSTPTGDGERATELGDLLGGEDG-----EFELAEMRVALGPALATLD 223

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+++L +RF        T  ++ +Q  V++  + ++ A+A+ KL+
Sbjct: 224 QREQKILTLRFYGN----LTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|255312671|gb|ACU01745.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 130/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|254384440|ref|ZP_04999781.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
 gi|194343326|gb|EDX24292.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
          Length = 1094

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 133/248 (53%), Gaps = 6/248 (2%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S      I ++          A+   V  N  L   +A ++  +GL   DL+Q G +GL+
Sbjct: 242 SRPTEAEIAALAATDLRV--RARNCFVVHNQGLAHGIALRHAGQGLDHEDLLQHGALGLI 299

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           +AA KFD   GYKFSTYA WW++Q+++R++AD+   IRIPVH  ++I KV    RR+ ++
Sbjct: 300 RAAVKFDPVKGYKFSTYATWWIRQSMSRAVADEGAVIRIPVHFHEQIRKVAAAERRLQSE 359

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPL 601
             R  +   +A    + V+ V ++ ++++   SL+  IG  D  HLGD +  D+   S  
Sbjct: 360 -GRPWSAVHVAVACDLSVQRVEEIRRVSRRTDSLDRVIG--DGVHLGDLVALDRPLPSAE 416

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             A++    +    +L     R+ R+L  R G+      TL+++GK+F VTRERIRQ+E 
Sbjct: 417 HLAMEEMGHKHLLSLLTRFDARDARILLRRTGLDGGDRSTLDDLGKEFGVTRERIRQVEV 476

Query: 662 KAIRKLKH 669
           KA    + 
Sbjct: 477 KAFAAFRE 484


>gi|134297011|ref|YP_001120746.1| RNA polymerase factor sigma-32 [Burkholderia vietnamiensis G4]
 gi|134140168|gb|ABO55911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia vietnamiensis
           G4]
          Length = 331

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 73/274 (26%), Positives = 142/274 (51%), Gaps = 14/274 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    +S  E R   +  R+       A +++V ++LRLV+S+A+ Y 
Sbjct: 55  QLGNIDAYIQAVNRIPLLSAEEERRYATEFREDNNLD--AARKLVLSHLRLVVSIARNYL 112

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 113 GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 172

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +A++L +  E V     +++   I+LE  + D
Sbjct: 173 KAQRKLFFNLRSHKKSMQAMTPE-EIDGLAQELNVKREEVTEMETRLSGGDIALEGQVED 231

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT 638
            + ++  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+ + ++ 
Sbjct: 232 GEEAYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALEALDARSRRIIEARW-LNVDD 290

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           D     TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 291 DGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 324


>gi|264685610|dbj|BAI49154.1| RNA polymerase beta subunit [Aeromonas sp. AC9804]
 gi|264685612|dbj|BAI49155.1| RNA polymerase beta subunit [Aeromonas sp. AC0202]
          Length = 272

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEHYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + +LR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|261250002|ref|ZP_05942579.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
 gi|260939506|gb|EEX95491.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
          Length = 285

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 67/270 (24%), Positives = 130/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S +    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSANSYPMLTPEEERDLAERLHYDGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT- 585
                + ++ +R+      E   E +A++L +    VR++        +      D+D  
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAQDATFEMPTDDDET 191

Query: 586 --SHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
             S+    +  ++  S +   ++A+  E       +  L SL  R + ++R R+     +
Sbjct: 192 GTSYTAPMVYLEDKASDVADHVEASNWEAHTNNRLSLALKSLDDRSQHIVRSRWLDDNKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 252 --TLQELAETYSVSAERIRQLEKNAMKKLK 279


>gi|241758558|ref|ZP_04756675.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
 gi|241321301|gb|EER57461.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
          Length = 287

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 131/266 (49%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E   +    +K       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLTAEEETQLAERQQK---GDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      +EIA  L + +  V     ++T   I +     D++ +
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQEIANDLGVKLSEVLEMEQRMTGHDIGIMAENNDDEDN 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +A      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|238921550|ref|YP_002935065.1| RNA polymerase factor sigma-32 [Edwardsiella ictaluri 93-146]
 gi|238871119|gb|ACR70830.1| alternative sigma factor RpoH, putative [Edwardsiella ictaluri
           93-146]
          Length = 284

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E R +   +         A K+++ ++LR V+ VA+ Y   GL
Sbjct: 16  LEAYVRAANAYPMLTAEEERALGERL--HYKGDLDAAKQLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + V     ++  + ++ + P  DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVSEKDVLEMESRMAAQDMAFDLPGDDEQE 191

Query: 586 SHLGD---FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   F++DK+   A    D   +++  +  +  L  L  R + ++R R+ +  +  
Sbjct: 192 GAPAAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDERSQHIIRARW-LDSDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 ATLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|318060190|ref|ZP_07978913.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actG]
 gi|318078835|ref|ZP_07986167.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actF]
          Length = 356

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 116/240 (48%), Gaps = 11/240 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +       +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 119 LRTLEPESAAYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 178

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R PT  
Sbjct: 179 ERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQQHGRSPTVH 238

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A++L++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 239 ELAQRLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 294

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 295 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 349


>gi|315127793|ref|YP_004069796.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
 gi|315016307|gb|ADT69645.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
          Length = 287

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 129/271 (47%), Gaps = 17/271 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++++S    + + + + +   ++  E     A K+++ ++LR V  +AK Y+  GL   
Sbjct: 22  YLQAVSTIPMLKVEQEQELAKKLQ--EEGDLSAAKQLIMSHLRFVAHIAKSYSGYGLPQA 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R   
Sbjct: 80  DLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKLF 139

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-- 586
             + +  +R+    + E +   +A +L +  + VR++  +++ + +  +    D D +  
Sbjct: 140 FNLRKNKKRLGWFNQAEVST--VASELGVSEKEVREMESRMSGQDMGFDLTGDDNDDAPT 197

Query: 587 ---HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ D +   A        Q          L +L  R + ++  R+    +   
Sbjct: 198 STYSPVQYLTDGSADLADDIEQQQWQEQSHTRLFSALKTLDERSQDIVSARWL--SDDKA 255

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL+E+ +++ V+ ER+RQ+E  A++KL+   
Sbjct: 256 TLQELAEKYSVSAERVRQLEKTAMKKLQSAM 286


>gi|16762736|ref|NP_458353.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|16766854|ref|NP_462469.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|29144223|ref|NP_807565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62182067|ref|YP_218484.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161616616|ref|YP_001590580.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167549215|ref|ZP_02342974.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167990783|ref|ZP_02571882.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168232714|ref|ZP_02657772.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168241719|ref|ZP_02666651.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168260704|ref|ZP_02682677.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|168465152|ref|ZP_02699044.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168818616|ref|ZP_02830616.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443524|ref|YP_002042813.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194449082|ref|YP_002047593.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194469731|ref|ZP_03075715.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|197250526|ref|YP_002148491.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197265856|ref|ZP_03165930.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198244039|ref|YP_002217526.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387614|ref|ZP_03214226.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204928638|ref|ZP_03219837.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205354814|ref|YP_002228615.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858806|ref|YP_002245457.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213426834|ref|ZP_03359584.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213619347|ref|ZP_03373173.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213649997|ref|ZP_03380050.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|213857359|ref|ZP_03384330.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|224585360|ref|YP_002639159.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238910431|ref|ZP_04654268.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|289829445|ref|ZP_06547057.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|25288476|pir||AB0992 RNA polymerase sigma-32 factor [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16422128|gb|AAL22428.1| sigma H factor of RNA polymerase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|16505042|emb|CAD08062.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139860|gb|AAO71425.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62129700|gb|AAX67403.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock proteins induced by cytoplasmic stress [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|161365980|gb|ABX69748.1| hypothetical protein SPAB_04433 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194402187|gb|ACF62409.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194407386|gb|ACF67605.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194456095|gb|EDX44934.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195632472|gb|EDX50956.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197214229|gb|ACH51626.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197244111|gb|EDY26731.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197938555|gb|ACH75888.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199604712|gb|EDZ03257.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204322071|gb|EDZ07269.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205274595|emb|CAR39645.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205325609|gb|EDZ13448.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205330694|gb|EDZ17458.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205333102|gb|EDZ19866.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205338892|gb|EDZ25656.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205344405|gb|EDZ31169.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205350317|gb|EDZ36948.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710609|emb|CAR34967.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224469888|gb|ACN47718.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|261248721|emb|CBG26559.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995798|gb|ACY90683.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301160107|emb|CBW19627.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312914591|dbj|BAJ38565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|320087978|emb|CBY97740.1| RNA polymerase sigma-32 factor Heat shock regulatory protein F33.4
           [Salmonella enterica subsp. enterica serovar Weltevreden
           str. 2007-60-3289-1]
 gi|321226618|gb|EFX51668.1| RNA polymerase sigma factor RpoH [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614066|gb|EFY11002.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617958|gb|EFY14851.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625428|gb|EFY22254.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322629893|gb|EFY26666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322632218|gb|EFY28969.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636431|gb|EFY33138.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643092|gb|EFY39666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322644713|gb|EFY41249.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322651265|gb|EFY47649.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322652822|gb|EFY49161.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659124|gb|EFY55376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322663174|gb|EFY59378.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322668661|gb|EFY64814.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322674536|gb|EFY70629.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322678259|gb|EFY74320.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322682485|gb|EFY78506.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322684198|gb|EFY80204.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716555|gb|EFZ08126.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131927|gb|ADX19357.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323192247|gb|EFZ77479.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196326|gb|EFZ81478.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323201872|gb|EFZ86935.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323206415|gb|EFZ91376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212008|gb|EFZ96835.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323216913|gb|EGA01636.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222313|gb|EGA06696.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323224327|gb|EGA08616.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323228255|gb|EGA12386.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233477|gb|EGA17570.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237061|gb|EGA21128.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323243724|gb|EGA27740.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323246034|gb|EGA30021.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323250810|gb|EGA34688.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323255821|gb|EGA39571.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323261903|gb|EGA45470.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267705|gb|EGA51187.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323268585|gb|EGA52052.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326625307|gb|EGE31652.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629958|gb|EGE36301.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990419|gb|AEF09402.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 284

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|284053747|ref|ZP_06383957.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 179

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 66/180 (36%), Positives = 110/180 (61%), Gaps = 3/180 (1%)

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            WW++QAITR+IA  S TIR+P+H+ +K++K+ R  R +  +  R  TP EIAK L +  
Sbjct: 1   YWWIRQAITRAIAQNSRTIRLPIHITEKLNKIKRVQRELFQQYGRNATPTEIAKALDLEP 60

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             +R  L  ++ P+SL+  +GD   + L D +ED++A S      Q  LR+    ++A L
Sbjct: 61  SQIRDYLLASRHPVSLDLRVGDNQDTELQDLLEDESA-SADSYVTQQLLRQDLKDMMADL 119

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TP++  VL +R+G+    + +L +VG Q  ++RER+RQ+E +A+  L+   R  ++R +L
Sbjct: 120 TPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRERVRQLENQALNHLRR--RKAQVREYL 177


>gi|254251367|ref|ZP_04944685.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
 gi|124893976|gb|EAY67856.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
          Length = 311

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 72/274 (26%), Positives = 141/274 (51%), Gaps = 14/274 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTAEEERQYATEFRENNNL--EAARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +A++L +  E V ++    +   ++LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKSMQAMTPE-EIDGLAQELNVKREEVAEMETRLSGGDVALEGQVED 211

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT 638
            + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+ + ++ 
Sbjct: 212 GEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARW-LNVDD 270

Query: 639 D----HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           D     TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 271 DGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|257055039|ref|YP_003132871.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
 gi|256584911|gb|ACU96044.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
          Length = 295

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 104/240 (43%), Gaps = 19/240 (7%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDWCLGYK 495
            +   +  +V     LV  VA +    GL       DLIQ G  GL+ A EKFD   G +
Sbjct: 55  PSQRVRDRLVLHYAPLVKYVAGR-VGTGLPTHIDVADLIQSGIFGLVDAIEKFDPERGLR 113

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F TYAM  ++ AI   +  Q     +P  +R +  ++ R   R+  +++R PT  E+A +
Sbjct: 114 FETYAMQRIRGAILDDLRSQDW---VPRAVRSRAREIERAHERLGARLRRTPTDAEVAAE 170

Query: 556 LAMPVEGVRK--VLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           L + +  +R           ++L+  +         T    D + D  AV P    +  +
Sbjct: 171 LGITLRELRDLYGQLRLTSVLALDDLMGASKDNGNGTGSPADTLPDDGAVDPAAVLVDQD 230

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R      +A L  R+  V+ + +        TL E+GK   VT  R+ Q+  +A+ +L+
Sbjct: 231 NRRQLAEAIAQLNERDRIVVSLYYFEN----LTLAEIGKVLGVTESRVSQLHTRAVLRLR 286


>gi|172087778|ref|YP_205833.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197336399|ref|YP_002157235.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
 gi|171902364|gb|AAW86945.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197317889|gb|ACH67336.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
          Length = 286

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 71/288 (24%), Positives = 133/288 (46%), Gaps = 19/288 (6%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
              E  +      DSI    + ++S++    ++++E R +   +   E     A KE++ 
Sbjct: 1   MSKEMYSMAVVSQDSID---SYLRSVNSYPMLTVAEERELAERLHYKEEI--EAAKELIL 55

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ++LR V+ VA+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I  
Sbjct: 56  SHLRFVVHVARGYSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHE 115

Query: 511 SIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            +      +++      R     + +  +R+      E   E +AK L +    VR++  
Sbjct: 116 YVLRNWRIVKVATTKAQRKLFFNLRKNKKRLGWFNNGE--VEAVAKDLGVAPSEVREMEA 173

Query: 569 ITKEPISLETPIGDEDTSHLG-----DFIEDKN---AVSPLDSAIQANLRETTTRVLASL 620
                 S      ++D   +       ++EDK    A S  +   +          +A+L
Sbjct: 174 RLAAQDSTFEAPAEDDDRDMAFTAPVYYLEDKQSDVAYSLEEDNWEDYTNNRLANAIATL 233

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + +++ R+        TL+E+   + V+ ERIRQ+E  A++KLK
Sbjct: 234 DERSQHIVQSRWLAD--EKATLQELADTYQVSAERIRQLEKNAMKKLK 279


>gi|66474733|gb|AAY46936.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKK+
Sbjct: 257 RRMSIGEAKARRAKKK 272


>gi|121611388|ref|YP_999195.1| RNA polymerase sigma-32 subunit RpoH [Verminephrobacter eiseniae
           EF01-2]
 gi|121556028|gb|ABM60177.1| RNA polymerase, sigma 32 subunit, RpoH [Verminephrobacter eiseniae
           EF01-2]
          Length = 313

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 70/290 (24%), Positives = 131/290 (45%), Gaps = 24/290 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V ++  +   I +++    ++  + +      +  E     A   +V ++LRLV+S+A++
Sbjct: 21  VPALGNLDAYIAAVNRLPLLTYEQEQSYARQFK--EHNDLDAAGRLVLSHLRLVVSIARQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VH-MRDKIHKVVRTARRMSNKIKR------------EPTPEEIAKKLAMPVEGVRKV-LK 568
               + K+   +R+ ++                   E   + +A +L +  E V ++  +
Sbjct: 139 TTKAQRKLFFNLRSMKQGFKADAGATDAATYRDTLSEHEIDAVAAQLHVKREEVIEMETR 198

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPR 623
           ++   + L+    D+     G      +A     + I++  R+        + LASL  R
Sbjct: 199 MSGGDVLLDPAPSDDGEQAFGPIAYLADASHEPTALIESRQRDALATDGIAKALASLDER 258

Query: 624 EERVLRMRFG---IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             R+++ R+           TL ++   + V+ ERIRQIE  A++K+K  
Sbjct: 259 SRRIVQERWLKVNDDGTGGMTLHDLAAIYGVSAERIRQIEVAAMKKMKQA 308


>gi|255312633|gb|ACU01726.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 130/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEI ++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEITEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTEDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|66474701|gb|AAY46920.1| RpoD [Aeromonas sp. 12m]
 gi|66474705|gb|AAY46922.1| RpoD [Aeromonas sp. 15m]
          Length = 272

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGIYQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|52424080|ref|YP_087217.1| RNA polymerase factor sigma-32 [Mannheimia succiniciproducens
           MBEL55E]
 gi|52306132|gb|AAU36632.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 282

 Score =  130 bits (327), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 129/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    +S  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANEYPMLSAEEEKELAERL--YYQEDLEAAKKLILSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E     +A +L +  E V ++  ++T   +  + P  D + 
Sbjct: 134 KLFFNLRKTKQRLGWFSDNELDL--VANELGVTKEDVIEMESRMTGADVGFDLPTDDSEE 191

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A        +    +  +  + +L  R + +++ R+     T  
Sbjct: 192 ETFAPSMYLEDKSSNFAAELESENFETQAIDQLSNAMENLDERSKDIIQARWLDD--TKA 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ ++ ER+RQ+E  A++KLK
Sbjct: 250 TLHELAAKYNISAERVRQLETNALKKLK 277


>gi|212639646|ref|YP_002316166.1| sporulation sigma factor SigG [Anoxybacillus flavithermus WK1]
 gi|212561126|gb|ACJ34181.1| DNA-directed RNA polymerase specialized sigma subunit sigG
           [Anoxybacillus flavithermus WK1]
          Length = 259

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 138/262 (52%), Gaps = 13/262 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            RN+++   V+T  + + +   +  + R+ +     A+++++  NLRLV+SV +++ NRG
Sbjct: 2   ARNKVEICGVDTSKLPVLKNEEMRELFRQMQAGDISAREKLITGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   +M ++  +EPT EEIAK L +P E +   L   ++P+SL  PI ++  D 
Sbjct: 121 IAYKALQVREKMMSETAKEPTAEEIAKILDVPHEEIVFALDAIQDPVSLFEPIYNDGGDP 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D + D+           A         L  L  RE+ ++R RF  G     T  EV
Sbjct: 181 IYVMDQLSDEKNRDTNWIEEIA-----LKEGLRRLNEREKMIIRKRFFQG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
            ++  +++ ++ ++E  AI+++
Sbjct: 232 AEEIGISQAQVSRLEKAAIKQM 253


>gi|239826533|ref|YP_002949157.1| sporulation sigma factor SigG [Geobacillus sp. WCH70]
 gi|239806826|gb|ACS23891.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. WCH70]
          Length = 259

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 76/261 (29%), Positives = 137/261 (52%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++       A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFKRMHEGDLEAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++ ++  +EP+ EEIAK L +P E V   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLMSETAKEPSAEEIAKVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 YVMDQLSDERNRDSQWIEEIA-----LKEGMRRLNEREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AIR++
Sbjct: 233 EEIGISQAQVSRLEKAAIRQM 253


>gi|302746286|gb|ADL62733.1| RpoD [Morganella morganii subsp. sibonii]
          Length = 258

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 51/298 (17%), Positives = 102/298 (34%), Gaps = 47/298 (15%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +  S+ E P     L+   D +  G   L ++I     + P +  
Sbjct: 1   GEIDIAKRIEDGIFQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLIT--GFVDPNA-- 56

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 E        +   E   +++ + + D +   +   D        PE A      
Sbjct: 57  ------EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDPELARQKFEA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L    + + H +                                ++G+    ++ + + L
Sbjct: 111 LRVQHEKARHQI-------------------------------KIHGRDHPSTNAEIQQL 139

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQG 376
            E    +     L   + D LV  + ++  R+   E  +++L  +   + +  F+    G
Sbjct: 140 SE----VFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLCVEQSKMPKKNFITLFTG 195

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            E    W + A    +  W   +    + I +    ++ I  ETG++I + + I   +
Sbjct: 196 NETSDSWFTAAVAMNKP-WSEKLQDMAEEIERSLQRLRQIEEETGLTIKQVKDINRRM 252


>gi|317423774|emb|CBI85534.1| RNA polymerase sigma factor [Aeromonas bestiarum]
          Length = 273

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  ++
Sbjct: 59  N------------------------EADDVAPTATHIGSELGEDDLADEDEDEDEDEDDD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            E + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKA-WSPRLVDMDEEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|187763324|gb|ACD35539.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 123/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    EG               DDV  T   I S            D   +  E+ 
Sbjct: 52  --SGFIDPNEG---------------DDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|253576354|ref|ZP_04853684.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844247|gb|EES72265.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 251

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 130/259 (50%), Gaps = 18/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K IS E  +  +E + ++++    +   + A+  +V  N+RLV SV +++ NRG +  
Sbjct: 4   EVKQISREF-LDDTEVKRLIAL---SQSGDNAARDRLVNCNIRLVWSVVQRFMNRGYEPE 59

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K
Sbjct: 60  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKEMANK 118

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           V +    +S ++ R PT +E+A +L +  E V    +  K P S+   + + D     L 
Sbjct: 119 VRKKKDELSKQLGRLPTVKEVADELGVTPEDVVFAQEANKPPASIHETVFENDGDPITLM 178

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+      D       +      +  LT RE  ++ +R+      D T  EV  + 
Sbjct: 179 DQIADETQERWFD-------KLALHEAIDGLTDRERLIVYLRY----YRDQTQSEVATRL 227

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++ ++
Sbjct: 228 GISQVQVSRLEKKILQSIR 246


>gi|241764416|ref|ZP_04762441.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
 gi|241366206|gb|EER60777.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
          Length = 312

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 70/287 (24%), Positives = 127/287 (44%), Gaps = 23/287 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    ++  E +     +R  +     A   +V ++LRLV+S+A++
Sbjct: 21  VPPLGNLDAYISAVNRLPLLTHEEEQTYARKLR--DHNDVDAAGRLVMSHLRLVVSIARQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VH-MRDKIHKVVRTARR-----------MSNKIKREPTPEEIAKKLAMPVEGVRKV-LKI 569
               + K+   +R+ ++                  E   + +A +L +  E V ++  ++
Sbjct: 139 TTKAQRKLFFNLRSMKQGFKADAAVDAATHRDTLSEQEIDAVATQLNVKREEVIEMETRM 198

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPRE 624
               + L+    D+     G      +A     + I++  R+          LA L  R 
Sbjct: 199 AGGDVLLDPAPSDDGEQAFGPIGYLADASHEPTAMIESRQRDALATDGIAMALARLDDRS 258

Query: 625 ERVLRMRFG---IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R++  R+           TL E+   + V+ ERIRQIE  A++K+K
Sbjct: 259 RRIVEERWLKVNDDGTGGMTLHELAAVYGVSAERIRQIEVAAMKKMK 305


>gi|238755238|ref|ZP_04616583.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
 gi|238706579|gb|EEP98951.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
          Length = 285

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 123/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKKLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQEE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  +++ + ++ +    D+  D   +   +  ++  S     I+ +  E
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPTPDDDVRDGQSMAPVLYLQDKTSDFADGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +      +  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SHAADKLSYALEGLDERSQHIIRARW-LDDDNKTTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|312134672|ref|YP_004002010.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774723|gb|ADQ04210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 255

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 77/260 (29%), Positives = 134/260 (51%), Gaps = 9/260 (3%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +        ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKFELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   +  NK +REPT EEIAK+L++  E +   L   +EPISL  P+  + +  + 
Sbjct: 121 YKALKIKEKYINKNQREPTLEEIAKELSITKEELVFALDSIQEPISLYEPVFQDSSDTMY 180

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              +  +  S  +  ++     +    L+ LT RE+ +L +R+  G     T  EV +  
Sbjct: 181 VVEKLCDQKSCENVWLEEI---SLKDALSKLTKREKEILYLRYYKG----KTQMEVARIV 233

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ +IE  AI  +K 
Sbjct: 234 GISQAQVSRIEKSAIGHIKK 253


>gi|297157365|gb|ADI07077.1| putative sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 242

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 119/245 (48%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + S+       A + +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 2   FVELRSLPEGSTARAEL-RNTLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S +  R 
Sbjct: 61  RFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQRHGRA 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A++L++  E V + L+       +SL+ P  D+++  + D +  ++        
Sbjct: 121 PTVHELAEQLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY 180

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE+   +L  L PRE+++L +RF   M      +EV     +++  + ++ A+ +
Sbjct: 181 -----RESLKPLLEDLPPREKKILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTL 231

Query: 665 RKLKH 669
            +L+ 
Sbjct: 232 AQLRE 236


>gi|114764201|ref|ZP_01443439.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114543353|gb|EAU46369.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 292

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 124/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELQLAYAWRDHRDEAALHRLINAYMRLAISMAAKFKRYGAPMGDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAAAE 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLE-TPIGDEDTSHLGDFIEDKNA 597
              ++R      IAK++ +P+  V  +  +++    SL  T   DED     D +ED   
Sbjct: 146 GRALERHSLHAAIAKEVGVPLHDVEMMDGRLSGSDFSLNATQSTDEDGREWIDTLEDDGE 205

Query: 598 VS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            S            LRE     L  L  RE  ++R R         TLE +G++  +++E
Sbjct: 206 QSASLVEGKLDNDQLREWLVVALTGLNDRERFIVRERKLRD--ETRTLESLGQELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S+++  FL
Sbjct: 264 RVRQLEAAAFVKMRKSLEAQSREVAQFL 291


>gi|37784410|gb|AAO13098.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida subsp.
           salmonicida]
          Length = 270

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 116/314 (36%), Gaps = 46/314 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    +  +       S+  E D   E E + E     S DD       PE A   
Sbjct: 59  E-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 112 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 137 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 197 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 255

Query: 434 VRKGECEASIAKKE 447
           +  GE +A  AKKE
Sbjct: 256 MSIGEAKARRAKKE 269


>gi|11079157|dbj|BAB17583.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 119/315 (37%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+  G           Q+ E  + +       + + D E     S+++       PE 
Sbjct: 59  IDPDDDGAA-------GPQEVEPEAPKAPAKAATDDKDDEEEDDSDSEEEEGDGGPDPEV 111

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  + +   L                                   +K  ++
Sbjct: 112 ARLRFGAVAEQLEKANKAL-----------------------------------KKHGRA 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +     E L  L   + L   + D LVE++ +   +I   E  +++L      + R  
Sbjct: 137 SQQAVEELEALAILFMPIKLVPKQYDALVERVRNALNQIRIQERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +    E++  W        +G++   +    + I + + ++  +  E  ++I++ + 
Sbjct: 197 FLRQFPNNEINLDWADQLAS-GKGKYAEAIGNRKEDIQRCQQKLIELQQECNLAIADIKD 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRRMSIGEAKARRA 270


>gi|86139299|ref|ZP_01057869.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85824143|gb|EAQ44348.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 292

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 72/283 (25%), Positives = 132/283 (46%), Gaps = 20/283 (7%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K+      +     + +       +     A   +  A +RL IS+A K+   G    DL
Sbjct: 13  KTAMKAEMLDAETEKRLA--YAWRDHRDVEALHRLTNAYMRLAISMAVKFKRYGAPMNDL 70

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVH 524
           IQE  +GLMKAA+KFD   G +FSTYA+WW+K ++   +      +R            +
Sbjct: 71  IQEAGLGLMKAADKFDPDRGVRFSTYAIWWIKASVQDYVMRNWSMVRTGSTSSQKSLFFN 130

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
           MR    ++ R A     ++ +    ++IA ++ +P+  V  +  +++    SL      E
Sbjct: 131 MRRVQTQLERQANAQGQRLDKHQLHQQIASEIGVPIRDVEMMDGRLSGADFSLNAARSTE 190

Query: 584 -DTSHLGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
            +     + +ED +A +      S     LR+     +  L+ RE+R++  R     N  
Sbjct: 191 AEGQEWIEILEDDSAQAAELVERSHDHRKLRKWLVEAMQGLSGREQRIVVARKL--SNPP 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP--SRSKKLRSFL 680
            TLE +G++  +++ER+RQ+EA A +K++    +RS+++   L
Sbjct: 249 RTLEALGRELSLSKERVRQLEAGAFQKMRKTLDTRSREVHKLL 291


>gi|37784432|gb|AAO13109.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|37955122|gb|AAP76213.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|37955124|gb|AAP76214.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763298|gb|ACD35526.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 272

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|160877394|ref|YP_001556710.1| RNA polymerase factor sigma-32 [Shewanella baltica OS195]
 gi|160862916|gb|ABX51450.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS195]
 gi|315269598|gb|ADT96451.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS678]
          Length = 285

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 64/273 (23%), Positives = 126/273 (46%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S++  + +       +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYIHSVTSISMLDAEAEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E T   +A+ L +    V     ++  +  + +     ++ 
Sbjct: 137 KLFFNIRKAKKRLGWFSDAEVTM--VAENLGVSKADVTEMESRMAAQDPAFDLTNDQDEE 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   ++N +      + +L  R + +L  R+     T  
Sbjct: 195 HDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQHILHARWLDDDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL+E+ + + V+ ERIRQ+E  A+ KLK    +
Sbjct: 253 TLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|66474639|gb|AAY46889.1| RpoD [Aeromonas hydrophila]
          Length = 272

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   + S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHMGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|302874724|ref|YP_003843357.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
 gi|302577581|gb|ADL51593.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
          Length = 256

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 74/264 (28%), Positives = 134/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + +   +  ++ K +    I++++ +  NLRLV+SV +++ NRG
Sbjct: 1   MINKVEICGVNTSKLPVLKEHEMRELLDKMKAGDYISREKFIRGNLRLVLSVIQRFNNRG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 61  ENADDLFQVGCIGLIKALDNFDLTQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             ++ ++   ++  +  +EPT  +IAK+L +  E V   L   +EP+SL  PI  +  D 
Sbjct: 120 IAYRALQVRDKLLTENNKEPTVYQIAKELDVAKEEVIFALDAIQEPVSLFEPIYHDGGDA 179

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I D   +        A         +  L+ RE+ +L MRF  G     T  EV
Sbjct: 180 IYVMDQISDSKNLDESWLENIA-----IKEAMKRLSDREKLILNMRFFDG----RTQMEV 230

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A+R ++ 
Sbjct: 231 ADEIGISQAQVSRLEKNALRHMRK 254


>gi|50871552|emb|CAF74867.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871554|emb|CAF74868.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 51/301 (16%), Positives = 109/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +       + + D +     ++++       PE A   
Sbjct: 59  DDGAA-------APQEVEPEAPQTTAKAAADEKDDEDEDDSDTEEEEGDGGPDPEVARLR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + + LVE++     +I   E  +++L      + R  FL +
Sbjct: 137 VEELEALAILFMPIKLVPKQYEALVERVRSALGQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        +G++   +    + I + + ++  +  E  ++I++ + I   
Sbjct: 197 FPSNETNLDWAEQLAS-GKGKYAEAIGNRKEDIQRCQQKLIELEQECDLAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|3249733|gb|AAC26669.1| RNA polymerase sigma-like factor [Streptomyces peucetius]
          Length = 162

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 107/162 (66%), Positives = 131/162 (80%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ REPTPEE+ +++ M
Sbjct: 1   YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEM 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P + +RKVLKI KEPIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+
Sbjct: 61  PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDVLS 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIE
Sbjct: 121 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 162


>gi|77359323|ref|YP_338898.1| RNA polymerase factor sigma-32 [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874234|emb|CAI85455.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Pseudoalteromonas haloplanktis TAC125]
          Length = 287

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 132/272 (48%), Gaps = 19/272 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++++S    + + + + + + ++  E     A K+++ ++LR V  +AK Y+  GL   
Sbjct: 22  YLQAVSTIPMLKVEQEQELATRLQ--EEGDLSAAKQLIMSHLRFVAHIAKGYSGYGLPQA 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R   
Sbjct: 80  DLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKLF 139

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-- 586
             + +  +R+    + E +   +A +L +  + VR++  +++ + +  +    D+D++  
Sbjct: 140 FNLRKNKKRLGWFNQAEVST--VASELGVSEKEVREMESRMSGQDMGFDLTGDDDDSAPS 197

Query: 587 -------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                  +L D   D  A        Q          L +L  R + ++  R+    +  
Sbjct: 198 STYSPVQYLTDGTADL-ADDIEQQQWQEQSHTRLFSALKTLDERSQDIVSARWL--TDDK 254

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TL+E+ +++ V+ ER+RQ+E  A++KL+   
Sbjct: 255 ATLQELAEKYSVSAERVRQLEKTAMKKLQAAM 286


>gi|108798252|ref|YP_638449.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119867348|ref|YP_937300.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126433912|ref|YP_001069603.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108768671|gb|ABG07393.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119693437|gb|ABL90510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126233712|gb|ABN97112.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 263

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 112/231 (48%), Gaps = 13/231 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+
Sbjct: 38  QRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVDAGSDFVSFAV 97

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   + R   D S ++++P  +++   ++      +S ++ R PT  E+A++L M  +
Sbjct: 98  PTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGSATAELSQRLGRAPTASELAEELGMDRD 157

Query: 562 GVRKVLKI--TKEPISLET--PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V + L    +   +S+++    G+ED   + D + D +         Q   RE    +L
Sbjct: 158 EVVEGLVAGSSYNTLSIDSGGNSGNEDAPAIADTLGDVD-----LGLDQIENREALRPLL 212

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           A+L  RE  VL +RF        T  ++ ++  +++  + ++ AK++ +L+
Sbjct: 213 AALPERERMVLLLRFFEN----LTQTQIAERVGISQMHVSRLLAKSLTRLR 259


>gi|269140667|ref|YP_003297368.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|267986328|gb|ACY86157.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|304560452|gb|ADM43116.1| RNA polymerase sigma factor RpoH [Edwardsiella tarda FL6-60]
          Length = 284

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 133/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E R +   +         A K+++ ++LR V+ VA+ Y   GL
Sbjct: 16  LEAYVRAANAYPMLTAEEERALGERL--HYKGDLDAAKQLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + V     ++  + ++ + P  DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVSEKDVLEMESRMAAQDMAFDLPGDDEQE 191

Query: 586 ---SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
              +    F++DK+   A    D   +++  +  +  L  L  R + ++R R+ +  +  
Sbjct: 192 GAPTAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDERSQHIIRARW-LDSDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 ATLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|229541192|ref|ZP_04430252.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
 gi|229325612|gb|EEN91287.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
          Length = 258

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 74/261 (28%), Positives = 139/261 (53%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  +++K     + A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRDLLKKMHAGDASAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLNQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++ +   +EPT EEIA++L +P E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLMSATSKEPTTEEIARELDVPHEDIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 YVMDQVSDEKNKDSQWIEEIA-----LQEGMRRLNEREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 233 EEIGISQAQVSRLEKAAIKQM 253


>gi|114569135|ref|YP_755815.1| RNA polymerase factor sigma-32 [Maricaulis maris MCS10]
 gi|114339597|gb|ABI64877.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 295

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 126/276 (45%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +  I     +   E   +    R+ E     A +++V ++LRLV  +A  Y   GL
Sbjct: 15  LSSYLSEIRRFPMLEKDEEFMLGKRWREHEDGG--AAEKLVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 73  PIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 132

Query: 529 --IHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIG- 581
                + R   +M    + +      E IA KL +  + V     +++    SL  P+  
Sbjct: 133 KLFFNLRRMKSQMQALDEGDLKPDQVEAIATKLGVTNDEVMSMNGRLSGPDASLNAPLRG 192

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMN 637
            E      D++ D  A S  D   +++      +     +  L  RE+ +L+        
Sbjct: 193 TEGEGQWQDWLSDDTAESQEDELAESDEFDTRMQLLQSAMGELNEREQHILQE--RRLSE 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLEE+ + + V+RERIRQIE +A  KL+   ++
Sbjct: 251 DPKTLEELAEHYGVSRERIRQIEVRAFEKLQKAMKA 286


>gi|262273588|ref|ZP_06051402.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
 gi|262222566|gb|EEY73877.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
          Length = 287

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ ++    ++  E R +   +     E   A K ++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LDSYLQQVNSYPMLTADEERELAERL--HYEEDLDAAKSLILSHLRFVVHIARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 74  PISDLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
             K+    R+   ++      E   +A++L +    VR++        +       +D  
Sbjct: 134 --KLFFNLRKSKKRLGWFNAEEVNMVAEQLGVDAAEVREMESRLAAQDAGFDAGVGDDER 191

Query: 587 HLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
             G      ++EDK+   A +      + +      + ++ L  R + ++R R+ +  + 
Sbjct: 192 EGGAVAPVFYLEDKSSDIATNLESQNWEDHTNRRLAQAMSGLDARSQHIIRSRW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+   + V+ ERIRQ+E  A+RKLK
Sbjct: 251 KVTLQELADHYQVSAERIRQLEKNAMRKLK 280


>gi|302549129|ref|ZP_07301471.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466747|gb|EFL29840.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 295

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 115/247 (46%), Gaps = 7/247 (2%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA
Sbjct: 45  RQFFQRLTELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMEDIVQTGMIGLIKA 104

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +    +++++ 
Sbjct: 105 IDRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVDLAKAREELASRLD 164

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           REPT  E+A  + +    V +           SL+  +  +        + D   V    
Sbjct: 165 REPTVAELATLMNISENQVVEGQIAANGYNSSSLDAALTGDGPEGGEAVLADFIGVEEDG 224

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  +   +   ++A L+ R+ +++ MRF      + T  E+G++   ++  + ++  +
Sbjct: 225 LRLVEDFH-SLAPLMAELSERDRQIIHMRFV----EEATQAEIGERLGCSQMHVSRLIKR 279

Query: 663 AIRKLKH 669
            I +L+ 
Sbjct: 280 IITRLRQ 286


>gi|254703436|ref|ZP_05165264.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261754065|ref|ZP_05997774.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743818|gb|EEY31744.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 300

 Score =  130 bits (327), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 13  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 70

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 71  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 130

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 131 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 190

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 191 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 248

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 249 PMTLEDLSGEFGISRERVRQIEVRAFE 275


>gi|264685606|dbj|BAI49152.1| RNA polymerase beta subunit [Aeromonas sp. 67P24]
          Length = 272

 Score =  130 bits (327), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|126738732|ref|ZP_01754428.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
 gi|126719913|gb|EBA16620.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
          Length = 298

 Score =  130 bits (327), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 126/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E E + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--AWVEKEDTGAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE   +IA  L +  E V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLRPENVAQIAHDLGVTEEEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE   + +  L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLVQAMEVLNDREKDILTQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  ++ V+RERIRQIE +A  KL+   R
Sbjct: 252 QATTLEDLSGEYGVSRERIRQIEVRAFEKLQKKMR 286


>gi|225024603|ref|ZP_03713795.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
 gi|224942617|gb|EEG23826.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
          Length = 283

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 76/267 (28%), Positives = 133/267 (49%), Gaps = 12/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E     S+  +       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 16  LEQYIHTVNSIPLLTAEEE---HSLAVRQLQGDLEAAKKLILSHLRVVVSIARGYDGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 73  NQADLIQEGNIGLMKAVKRYEPNRGARLFSFAVHWIKAEIHEFILRNWRMVRVATTKPQR 132

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISL--ETPIGDED 584
           K+   +R+ R+  N +  E   + IA  L + ++ V     ++T + I+L  +    DED
Sbjct: 133 KLFFNLRSMRKSMNALSPE-EAQTIADDLGVKMDEVLEMEQRMTGKDIALLPDNSDSDED 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    D++ D  +      A +   A   E     LA L  R  R++  R+        T
Sbjct: 192 SYAPIDWLADTRSEPTQQIAQKARYAMQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LT 250

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  ++ V+ ERIRQIEAKAI+KL+
Sbjct: 251 LHELAAEYGVSAERIRQIEAKAIQKLR 277


>gi|145635177|ref|ZP_01790882.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
 gi|145267598|gb|EDK07597.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
          Length = 281

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 131/268 (48%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 EIYSPSLYLEDKSSNFAAELENENFESQATEQLNTALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|220929478|ref|YP_002506387.1| sporulation sigma factor SigG [Clostridium cellulolyticum H10]
 gi|219999806|gb|ACL76407.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulolyticum
           H10]
          Length = 257

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 132/267 (49%), Gaps = 19/267 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           + N+++   V T     ++  + + +   + K     + A+ E ++ NLRLV+SV +++ 
Sbjct: 2   LINKVEICGVNTSKLPVLTNEQKKELFERMHK---GDNSARDEFIKGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+K+ + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEYVDDLFQVGCIGLIKSIDNFDVTQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++   R++ +  +EPT  E+A++L +P E +   L   ++PISL   +  + 
Sbjct: 118 LRDIAYKALQAKERLTTQNSKEPTIVELAQELQLPKEDIVFALDAIQDPISLFESVYHDG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D  ++ D + D   +        +         +  L  RE+ +L +RF  G     T 
Sbjct: 178 GDAIYVMDQVSDDKNIDENWLETIS-----LKEAMRKLNDREKLILNLRFFEG----RTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV  +  +++ ++ ++E  A+  +K 
Sbjct: 229 MEVADEIGISQAQVSRLEKTALMHMKK 255


>gi|153004710|ref|YP_001379035.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028283|gb|ABS26051.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
          Length = 307

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 77/270 (28%), Positives = 132/270 (48%), Gaps = 16/270 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I+    +++ E + +  + R  +   + A   +V ANLR V+ V+ +Y + G +  
Sbjct: 16  YLSEINRFPLLTVDEEQRLARLFR--DEGDTRAAHRLVTANLRFVVKVSYEYRSYGFKMA 73

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA +KFD   G +  +YA+WW++  I   I      +++      R   
Sbjct: 74  DLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKLF 133

Query: 530 HKVVRTARRMSN---KIKREPTPEE---IAKKLAMPVEGVRKV-LKITKEPISLETPIGD 582
             + RT R +     +  R+   ++   IAKKL +    V ++  ++    +SL+ P+GD
Sbjct: 134 FSLARTKRELDKMSVEHGRDSDAQDKGKIAKKLRVKPAEVEEMEQRMDGRDLSLDAPMGD 193

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      DF+  K+A    + +     +      T  LA L  RE  ++     +  +  
Sbjct: 194 DGGYSHIDFVAAKSAAQDDELSDAEEQQIVSAKVTAALARLDQRERYIIEQ--RVMSDRP 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+E+G+ F  +RER RQ+E +A  KLK 
Sbjct: 252 LTLKELGEHFGFSRERARQLEIRAKEKLKQ 281


>gi|56696293|ref|YP_166650.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56678030|gb|AAV94696.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 298

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 126/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + +  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVEEQDAESAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   ++    + +  PE    IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKAKIGALEEGDLRPENVARIAHDLGVSEDDVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ VL  R  +   
Sbjct: 194 EGEGTMQWQDWLEDEDADQAADYEARDELEARRELLASALDVLNEREKDVLTQRRLLD-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QTVTLEDLSAQYNVSRERIRQIEVRAFEKLQKRMR 286


>gi|329123705|ref|ZP_08252265.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
 gi|327469904|gb|EGF15369.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
          Length = 281

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G + +++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|294678332|ref|YP_003578947.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294477152|gb|ADE86540.1| RNA polymerase sigma-32 factor-2 [Rhodobacter capsulatus SB 1003]
          Length = 299

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 69/277 (24%), Positives = 123/277 (44%), Gaps = 16/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       + +   A   +V ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--AWVDHQDPKAAHRLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ AI   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKV-LKITKEPISLETPIGD 582
                + +   ++    + +  P+   +IA  L +  + V ++  ++     SL   +G 
Sbjct: 134 KLFFNLRKAKSKIGALDEGDLRPDAVAKIAHDLNVSEDDVIEMNRRLAGSDASLNAQVGA 193

Query: 583 EDT---SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGM 636
            D    +   D++ED++A      A    L   R      +  L  RE  +L  R     
Sbjct: 194 SDGESATQWQDWLEDEDADQAEAYAEADELQARRAMLVAAMDVLNERERDILMARRLRD- 252

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
               TLEE+  Q+ V+RERIRQIE +A  KL+   ++
Sbjct: 253 -EPVTLEELSSQYDVSRERIRQIEVRAFEKLQGRMKA 288


>gi|260425792|ref|ZP_05779772.1| alternative sigma factor RpoH [Citreicella sp. SE45]
 gi|260423732|gb|EEX16982.1| alternative sigma factor RpoH [Citreicella sp. SE45]
          Length = 298

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 124/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E + + +  ++V ++LRL   +A  Y   GL
Sbjct: 16  LSRYLSEIRKFPLLEPEEEYMLAK--RWVEDQDAPSAHKLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   +     R    E+IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKSRIGALEEGDLRPEHVEKIATDLGVSKDEVISMNRRLSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +D S     D++ED+ A    D A +  L   R    + +  L  RE+ +L  R      
Sbjct: 194 DDDSSMQWQDWLEDEGADQASDYAERNELEARRALLAQAMDVLNDREKDILTQRRLAE-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++   + V+RERIRQIE +A  KL+   R
Sbjct: 252 QPVTLEDLSSVYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|55274883|gb|AAV49244.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274899|gb|AAV49251.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 193

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 78/192 (40%), Positives = 129/192 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEV 645
           +      TLE+V
Sbjct: 182 LLGYEAATLEDV 193


>gi|297614626|gb|ADI48615.1| RNA polymerase sigma-70 factor [Shewanella sp. KJW27]
          Length = 263

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 56/305 (18%), Positives = 111/305 (36%), Gaps = 51/305 (16%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+    I IAKRIE G   + +S+ E P     ++   D+       L +II       
Sbjct: 1   LLTA-RRIQIAKRIEEGINTVQSSVAEYPQAIAMILEQFDQFEAEEIRLSDII------- 52

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV--DSPPEN 250
                GF +  E +          E   +D+ + +   +       D   +      PE 
Sbjct: 53  ----SGFVNPDEDNVGPSATHIGSELSDEDLDDEDDMDDDDEDDDSDSEDEGSKGPDPEE 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L    + ++  L  ++ +  P+ + AL  I E+++E                 
Sbjct: 109 ARERFGQLRAVYE-NSLKLIELKGRDHPESVAALFHIGEIFKE----------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
                              L   + D LV+ +  +  ++   E  +L+L  +   + +  
Sbjct: 151 -----------------FRLVPKQFDRLVKSMRSMMDKVRVQERLILKLCVEQAKMPKKN 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E D  W + A+      +   +    + +L+ R ++++I  ETG+SI+  + 
Sbjct: 194 FVKLFTGNETDISWFN-AEMNSGKPYAEGLKMVEEDVLRCRAKLEAIEAETGLSIASIKD 252

Query: 430 IVSMV 434
           I   +
Sbjct: 253 INRRM 257


>gi|58579073|ref|YP_197285.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417699|emb|CAI26903.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 320

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 76/282 (26%), Positives = 129/282 (45%), Gaps = 16/282 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  +     +S+ E   +       E        ++V ++LRLV+ VA  + N GL
Sbjct: 38  LMSYINEVQSFQVLSLEEEEKLAK--NWYEHGVIADAHKLVTSHLRLVVKVALSFKNYGL 95

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K +I   I      I+I      +
Sbjct: 96  PLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCIKIGTTQAQR 155

Query: 529 IHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
                    +           +E    IA + +   + V ++    T    SL   +   
Sbjct: 156 KLFFSLRKIKKKLLKYHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRDKSLNDVVFSN 215

Query: 584 DTSH---LGDFI--EDKNAVSPLDSAIQANLRETT-TRVLASLTPREERVLRMRFGIGMN 637
            + +   L D I  ED N         + +++++  T+ LA+L  R   +   R  I   
Sbjct: 216 GSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDIFIRRKLIE-- 273

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              TLE + K++ +++ERIRQIE  A  K+K+   SK+ + F
Sbjct: 274 EPDTLEILSKKYNISKERIRQIETHAFLKVKNFVISKR-KEF 314


>gi|89099621|ref|ZP_01172496.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
 gi|89085774|gb|EAR64900.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
          Length = 259

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 77/267 (28%), Positives = 138/267 (51%), Gaps = 13/267 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++     + A++ +V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFKQMHEGDTYARECLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   R+ ++  +EPT EEIA+ L +P E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVRERLMSETSKEPTAEEIARVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ +LR RF  G     T  EV 
Sbjct: 182 FVMDQLSDERNKDIQWIEEIA-----LKEGMRRLNEREKLILRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRS 673
           ++  +++ ++ ++E  AI+++    +S
Sbjct: 233 EEIGISQAQVSRLEKAAIKQMNKNIQS 259


>gi|222528794|ref|YP_002572676.1| sporulation sigma factor SigG [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455641|gb|ACM59903.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 255

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 135/262 (51%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +      + ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKLELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   +  N  ++EPT EEIAK+L++  E +   L   +EPISL  P+  +  DT +
Sbjct: 121 YKALKIKEKYINNNQKEPTLEEIAKELSITKEDLVFALDSIQEPISLYEPVFQDSTDTMY 180

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + + + D  +   +     +         L+ LT RE+ +L +R+  G     T  EV K
Sbjct: 181 VVERLCDHKSCESVWLEEIS-----LKDALSKLTKREKEILYLRYYKG----KTQMEVAK 231

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              +++ ++ +IE  AI  +K 
Sbjct: 232 IVGISQAQVSRIEKSAIGHIKK 253


>gi|254473077|ref|ZP_05086475.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
 gi|211957798|gb|EEA93000.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
          Length = 297

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 121/274 (44%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R+ +     A +++V ++LRLV  +A  Y   GL
Sbjct: 15  LSRYLDEIRKFPMLQPQEEYMLAKRYREHDEP--KAAEKLVNSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 73  PLGEVISEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRTWSLVKMGTTANQK 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + R   ++      +  PE   +IA  L +    V  + +      SL  P+   
Sbjct: 133 RLFFNLRRVKGKIQAFEDGDLRPEQVQQIATTLGVTENEVVSMNRRLGGDSSLNAPLRSS 192

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +   S   D++ D +       A Q      R+     ++ L  RE R+           
Sbjct: 193 EGESSEWQDWLVDDSESQEAVLAEQEEYDVRRDMLKNAMSVLNERETRIFEA--RRLSEN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLEE+  +F V+RER+RQIE +A  K++   +
Sbjct: 251 PITLEELSTEFGVSRERVRQIEVRAFEKVQKAVQ 284


>gi|290962991|ref|YP_003494173.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652517|emb|CBG75650.1| sigma factor [Streptomyces scabiei 87.22]
          Length = 283

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 57/248 (22%), Positives = 123/248 (49%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG     D++Q G IGL+KA 
Sbjct: 39  FFEQLTVLEEGTREYQYARNTLIEMNISLVRYAAGRFRSRGADEMEDIVQVGMIGLIKAI 98

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+T+A+ ++   I R   D S  + +P  +++   ++ R    +S+++ R
Sbjct: 99  DRFELSREVEFTTFAVPYIVGEIRRFFRDTSWAVHVPRRLKEARVELARATDELSSRLGR 158

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH--LGDFIEDKNAVSPL 601
            PT +E+A+ + +  + V +           SL+  IG ++T    L DFI  ++A   L
Sbjct: 159 SPTVKELAELMNLSEDEVIEARLAANGYNSSSLDAAIGGDETGEAALADFIGSEDAGMEL 218

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        +L+ L  R+ R++ MRF      + T  ++ +    ++  + ++ +
Sbjct: 219 VEDFHA-----LAPLLSELGDRDRRIIHMRFV----EELTQAQIAEHLGCSQMHVSRLLS 269

Query: 662 KAIRKLKH 669
           + + +L+ 
Sbjct: 270 RTLARLRR 277


>gi|332531759|ref|ZP_08407644.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038735|gb|EGI75177.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 287

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 59/271 (21%), Positives = 128/271 (47%), Gaps = 17/271 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++++S    + + + + +   ++  E     A K+++ ++LR V  +AK Y+  GL   
Sbjct: 22  YLQAVSTIPMLKVEQEQELAKRLQ--EEGDLSAAKQLIMSHLRFVAHIAKSYSGYGLPQA 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R   
Sbjct: 80  DLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKLF 139

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-- 586
             + +  +R+    + E +   +A +L +  + VR++  +++ + +  +    D D +  
Sbjct: 140 FNLRKNKKRLGWFNQAEVST--VASELGVSEKEVREMESRMSGQDMGFDLTGDDNDDAPT 197

Query: 587 ---HLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ D     A        +          L +L  R + ++  R+    +   
Sbjct: 198 STYSPVQYLTDGAADLADDVEQEQWKEQAHTRLFSALKTLDERSQDIVSARWL--SDDKA 255

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL+E+ +++ V+ ER+RQ+E  A++KL+   
Sbjct: 256 TLQELAQKYSVSAERVRQLEKTAMKKLQSAM 286


>gi|52080862|ref|YP_079653.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|52786234|ref|YP_092063.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|319645181|ref|ZP_07999414.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
 gi|52004073|gb|AAU24015.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus licheniformis ATCC 14580]
 gi|52348736|gb|AAU41370.1| SigF [Bacillus licheniformis ATCC 14580]
 gi|317392990|gb|EFV73784.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
          Length = 255

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 127/262 (48%), Gaps = 17/262 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  +  T +   E + +   ++  +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKENQNTQLKDHEVKEL---IKNSQNGDQKARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S    R PT +EIA  L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRAKDELSKSNGRIPTVQEIADYLEISSEEVVMAQEAVRSPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE+ ++ +R+      D T  EV  + 
Sbjct: 180 DQIADQSEEKWFD-------KIALKEAIKDLDEREKLIVYLRY----YKDKTQSEVADRL 228

Query: 650 CVTRERIRQIEAKAIRKLKHPS 671
            +++ ++ ++E K ++++K+  
Sbjct: 229 GISQVQVSRLEKKILKQIKNQM 250


>gi|319775860|ref|YP_004138348.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
 gi|317450451|emb|CBY86667.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
          Length = 281

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 15  IEGYIRAANEYPMLTAEEEKELAERL--YYHEDLDAAKKLILSHLRFVIHVARGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G + +++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T
Sbjct: 133 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAET 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   ++   E     L SL  R + +++ R+        
Sbjct: 191 ETYSPALYLEDKSSNFAAELENENFESQATEQLGVALQSLDARSQDIIKARWLDDN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 249 TLHDLAAKYNVSAERIRQLETNALKKLK 276


>gi|302877701|ref|YP_003846265.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
 gi|302580490|gb|ADL54501.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
          Length = 284

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 131/266 (49%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  +     +S  E   + +  R        A +++V ++LR+V+SVA+ Y   GL
Sbjct: 16  LDSYIHLVRRYAVLSQEEEFDLATRFR--NDNDLDAARQLVLSHLRVVVSVARGYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA + +D   G +  ++A+ W++  I   +      ++I      +
Sbjct: 74  PQADLIQEGNIGLMKAVKHYDPEFGVRLVSFALHWIRAEINEFVVRNWRMVKIATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
                  + +   +  +     EIA++L +    V ++  +     ++L+    D+D + 
Sbjct: 134 KLFFNLRSLKQGLESLKPKQISEIAEQLNVSEHDVIEMEARFAGHEVALDPAGSDDDDTY 193

Query: 587 ----HLGDFIEDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
               +L D  E+    + L+S+   +LR +   R LASL  R  R++  R+ +  + + T
Sbjct: 194 APIQYLADS-EEHEPSNILESSEGLSLRTQGLARALASLDDRSRRIVEARW-LSEDQNAT 251

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
           L ++  +F V+ ERIRQIE KA+ K+
Sbjct: 252 LHDLAAEFKVSAERIRQIEQKAMSKM 277


>gi|289770379|ref|ZP_06529757.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
 gi|289700578|gb|EFD68007.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
          Length = 287

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 106/230 (46%), Gaps = 11/230 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM  V
Sbjct: 64  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D   T+ +P  + +   +V      ++    R PT  EIA++L +  E V 
Sbjct: 124 VGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRITEEEVL 183

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++   +    SLE     +    L D +  ++             R+    +L  L  
Sbjct: 184 SCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH-----RDLVRHLLVQLPE 238

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 239 REQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLRSANR 284


>gi|66474675|gb|AAY46907.1| RpoD [Aeromonas hydrophila]
          Length = 272

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGIIQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + +LR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|326773499|ref|ZP_08232782.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636729|gb|EGE37632.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 147

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 73/146 (50%), Positives = 96/146 (65%)

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
            R+M   + REPTPEE+A +L M  E V +V K  +EPISL TP+G++  S  GD IED 
Sbjct: 2   QRQMLQDLGREPTPEELAVELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEFGDLIEDS 61

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            AV P D+     L+E    VL +L+ RE  V+ MRFG+      TL+E+GK + VTRER
Sbjct: 62  EAVVPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRER 121

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLD 681
           IRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 122 IRQIESKTMSKLRHPSRSQVLRDYLD 147


>gi|297746547|emb|CAZ60991.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 268

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 59/304 (19%), Positives = 109/304 (35%), Gaps = 46/304 (15%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I
Sbjct: 1   ELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFI 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P          +  +       S+  E D   E E + E     S DD       PE A
Sbjct: 59  DPNE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVA 111

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                +L    + +  ++                                   QK+ ++ 
Sbjct: 112 REKFGDLRAQYEVTRLSI-----------------------------------QKNGRAH 136

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
              +    +L  +     L   +   L   + ++ +R+   E  +++L  +   + +  F
Sbjct: 137 EDTQAAIAQLADVFRQFRLMPKQFGRLFNNMREMMERVRVQERIIMKLCVEQAKMPKKTF 196

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +      E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I
Sbjct: 197 VAAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDI 255

Query: 431 VSMV 434
              +
Sbjct: 256 NRRM 259


>gi|225019126|ref|ZP_03708318.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
 gi|224948099|gb|EEG29308.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
          Length = 288

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 139/267 (52%), Gaps = 16/267 (5%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEA--SIAKKEMVEANLRLVISVAKKYTN 465
             N+++   + T  + + + +  + ++ + +       A+++++  NL+LV+SV +++TN
Sbjct: 32  YLNKVEICGINTATLKVLKEKEKIELLTRIKNNDRPEQAREKLISGNLKLVLSVIQRFTN 91

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGL+KA + FD     +FSTYA+  +   I R + D +  +R+   +
Sbjct: 92  RGENLDDLFQVGCIGLIKAIDNFDISQNVRFSTYAVPMIIGEIRRYLRDNNS-VRVSRSL 150

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           +D  +K ++   +++    +EPT +EI++++ +  E V   L+   +P+SL  P+  +  
Sbjct: 151 KDTAYKAMQAKEKLTTAHLKEPTIDEISQEMGVRREDVVLALESIVDPVSLYEPVYSDGG 210

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           DT ++ D I DK+        I           + +L  RE+++L +RF  G     T  
Sbjct: 211 DTIYVMDQIGDKSDDKNWLDEI------AIKEAIKNLNEREKKILSLRFFNG----KTQV 260

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHP 670
           EV +   +++ ++ ++E  A+ ++K  
Sbjct: 261 EVAEDIGISQAQVSRLEKGALDRIKKS 287


>gi|213425678|ref|ZP_03358428.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 304

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 74/201 (36%), Positives = 132/201 (65%)

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           E N+ L++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RT
Sbjct: 96  ESNLRLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRT 155

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           AR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +    L D + D+
Sbjct: 156 ARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADE 215

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               P D+    +++++  + L  L  ++  VL  RFG+      TLE+VG++  +TRER
Sbjct: 216 KENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRER 275

Query: 656 IRQIEAKAIRKLKHPSRSKKL 676
           +RQI+ + +R+L+   +++ L
Sbjct: 276 VRQIQVEGLRRLREILQTQGL 296



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/94 (23%), Positives = 36/94 (38%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172
           E+  A+R   G       + ES L     +   D
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLIRAVEKFD 109


>gi|56419663|ref|YP_146981.1| sporulation sigma factor SigG [Geobacillus kaustophilus HTA426]
 gi|261419325|ref|YP_003253007.1| sporulation sigma factor SigG [Geobacillus sp. Y412MC61]
 gi|297530705|ref|YP_003671980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766141|ref|YP_004131642.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
 gi|56379505|dbj|BAD75413.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-G) [Geobacillus kaustophilus HTA426]
 gi|261375782|gb|ACX78525.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC61]
 gi|297253957|gb|ADI27403.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111007|gb|ADU93499.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
          Length = 259

 Score =  130 bits (326), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 137/261 (52%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+       A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFRRMHEGDLEAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   R+ ++  +EP+ EEIAK+L +  E V   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVRERLMSETAKEPSTEEIAKELGVAHEEVVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+           A         L  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 YVMDQLSDERNRDSQWIEEIA-----LKEGLRRLNEREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AIR++
Sbjct: 233 EEIGISQAQVSRLEKAAIRQM 253


>gi|291561536|emb|CBL40335.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SS3/4]
          Length = 258

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 128/260 (49%), Gaps = 13/260 (5%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + +        + R+ +   + A++  ++ NLRLV+SV ++++      
Sbjct: 5   KVEICGVNTSKLPLLTNEEKTDLFRRIQNGDTDARETYIKGNLRLVLSVIQRFSGSSENL 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+KA + FD     KFSTYA+  +   + R + D +  IR+   +RD  +
Sbjct: 65  DDLFQIGCIGLIKAIDNFDLSQNVKFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL-- 588
           K +     ++ +  REPT  EIA ++ +  E +   +   + P+SL  P+  +    L  
Sbjct: 124 KALSARELLTKRNLREPTIMEIADEVGISKEEITYAMDAIQSPVSLYEPVYTDGGDPLCV 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I DK   +  ++ ++     + +  +  L  RE R++ MRF  G     T  EV  +
Sbjct: 184 MDQISDKK--NREENWVEQL---SLSEAMKRLPARERRIIDMRFFEG----KTQTEVAGE 234

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +++ ++ ++E  A++ +K
Sbjct: 235 VGISQAQVSRLEKNALKAMK 254


>gi|58617131|ref|YP_196330.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
 gi|58416743|emb|CAI27856.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
          Length = 319

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 76/282 (26%), Positives = 129/282 (45%), Gaps = 16/282 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  +     +S+ E   +       E        ++V ++LRLV+ VA  + N GL
Sbjct: 38  LMSYINEVQSFQVLSLEEEEKLAK--NWYEHGVIADAHKLVTSHLRLVVKVALSFKNYGL 95

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K +I   I      I+I      +
Sbjct: 96  PLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCIKIGTTQAQR 155

Query: 529 IHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
                    +           +E    IA + +   + V ++    T    SL   +   
Sbjct: 156 KLFFSLRKIKKKLLKYHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRDKSLNDVVFSN 215

Query: 584 DTSH---LGDFI--EDKNAVSPLDSAIQANLRETT-TRVLASLTPREERVLRMRFGIGMN 637
            + +   L D I  ED N         + +++++  T+ LA+L  R   +   R  I   
Sbjct: 216 GSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDIFIRRKLIE-- 273

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
              TLE + K++ +++ERIRQIE  A  K+K+   SK+ + F
Sbjct: 274 EPDTLEILSKKYNISKERIRQIETHAFLKVKNFVISKR-KEF 314


>gi|254719685|ref|ZP_05181496.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|265984700|ref|ZP_06097435.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306840038|ref|ZP_07472825.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
 gi|264663292|gb|EEZ33553.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306404852|gb|EFM61144.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
          Length = 303

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|261380105|ref|ZP_05984678.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
 gi|284797325|gb|EFC52672.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
          Length = 287

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 131/266 (49%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E   +    +K       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLTAEEETQLAERQQK---GDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      +EIA  L + +  V     ++T   I +     D++ +
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQEIADDLGVKLSEVLEMEQRMTGHDIGIMAENNDDEDN 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +A      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|56415467|ref|YP_152542.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364396|ref|YP_002144033.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129724|gb|AAV79230.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095873|emb|CAR61447.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 284

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 129/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSVERVRQLEKNAMKKLR 279


>gi|23502510|ref|NP_698637.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619585|ref|YP_001593472.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|163845234|ref|YP_001622889.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|225628222|ref|ZP_03786256.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|254708479|ref|ZP_05170307.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708670|ref|ZP_05170481.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714517|ref|ZP_05176328.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717415|ref|ZP_05179226.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030196|ref|ZP_05443810.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256061694|ref|ZP_05451831.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|256160370|ref|ZP_05458060.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255578|ref|ZP_05461114.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167873|ref|ZP_05754684.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|260568745|ref|ZP_05839213.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|261219245|ref|ZP_05933526.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222781|ref|ZP_05937062.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315977|ref|ZP_05955174.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316160|ref|ZP_05955357.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322306|ref|ZP_05961503.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261325699|ref|ZP_05964896.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261757310|ref|ZP_06001019.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|265987224|ref|ZP_06099781.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998739|ref|ZP_06111296.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|23348506|gb|AAN30552.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336396|gb|ABX62701.1| alternative sigma factor RpoH [Brucella canis ATCC 23365]
 gi|163675957|gb|ABY40067.1| alternative sigma factor RpoH [Brucella suis ATCC 23445]
 gi|225616068|gb|EEH13116.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|260154129|gb|EEW89211.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|260921365|gb|EEX88018.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924334|gb|EEX90902.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261294996|gb|EEX98492.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295383|gb|EEX98879.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261301679|gb|EEY05176.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261305003|gb|EEY08500.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261737294|gb|EEY25290.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|262553428|gb|EEZ09197.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659421|gb|EEZ29682.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 303

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|294501013|ref|YP_003564713.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|295706362|ref|YP_003599437.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
 gi|294350950|gb|ADE71279.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|294804021|gb|ADF41087.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
          Length = 259

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 77/267 (28%), Positives = 140/267 (52%), Gaps = 13/267 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFKQMQAGDGTAREKLVSGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   R+ ++  +EPT EEI+K L +P E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVRERLMSETSKEPTAEEISKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+           A         +  L  RE+ +LR RF  G     T  EV 
Sbjct: 182 YVMDQLSDERNRDSTWIEEIA-----LQEGMRRLNEREKLILRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRS 673
           ++  +++ ++ ++E  AI+++    +S
Sbjct: 233 EEIGISQAQVSRLEKAAIKQMNKNIQS 259


>gi|167462564|ref|ZP_02327653.1| sporulation sigma factor SigF [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 251

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 124/250 (49%), Gaps = 17/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E + ++++    +   +IA+  +V  N+RLV SV +++ NRG +  DL Q G IGL
Sbjct: 13  LDDQEVKRLIAL---SQSGDTIARDTLVNCNIRLVWSVVQRFLNRGYEADDLFQIGCIGL 69

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ +KF+     KFSTYA+  +   I R + D   T+++   +++  +KV +T   +S 
Sbjct: 70  LKSVDKFNLSYEVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKELANKVRKTKDELSK 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVS 599
            ++R PT +E+A  L +  E V    +  K   S+   +   D D   L D I D +   
Sbjct: 129 NLERLPTLKEVANALGITPEEVVFAQEANKPLSSIHETVFENDWDPITLMDQIADDSQEK 188

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D       +      +  L+ RE  ++ +R+      D T  EV  +  +++ ++ ++
Sbjct: 189 WFD-------KLALNEAIEGLSERERLIVYLRYF----KDQTQSEVANRLGISQVQVSRL 237

Query: 660 EAKAIRKLKH 669
           E K ++ +++
Sbjct: 238 EKKILQSIRN 247


>gi|170742915|ref|YP_001771570.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168197189|gb|ACA19136.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 293

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 126/270 (46%), Gaps = 11/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  ++       +   E R +   VR  +     A   ++ A++RLVI++A ++ + GL 
Sbjct: 9   RQFVRMAMDAPFLEREEERGLA--VRWKDKRDEQALHRLISAHMRLVIALAGRFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG++GLM+AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  MADLVQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   R+     +   +     IA  + +  E V     +++   +SL  PI DE
Sbjct: 127 LFFNLRRLRARLMQSTDERVGDEIHRRIATAIGVSREDVALMDARLSGPDMSLNAPITDE 186

Query: 584 DTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH- 640
             +     DF+ D + +     +   +     T +  +LT   ER LR+     +  D  
Sbjct: 187 GDASAERVDFLVDTSPLPDEAVSDAVDGERRLTWLRQALTVLSERELRILHERRLAEDQA 246

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLE +G +  +++ER+RQIE +A+ KL+  
Sbjct: 247 TLEALGHRLGISKERVRQIENRALEKLRRA 276


>gi|34822013|gb|AAQ82815.1| RNA polymerase sigma-70 factor [Aeromonas sp. 239]
 gi|34822032|gb|AAQ82816.1| RNA polymerase sigma-70 factor [Aeromonas sp. 480]
 gi|34822063|gb|AAQ82817.1| RNA polymerase sigma-70 factor [Aeromonas sp. 57]
 gi|34822087|gb|AAQ82818.1| RNA polymerase sigma-70 factor [Aeromonas sp. 280]
 gi|34822107|gb|AAQ82819.1| RNA polymerase sigma-70 factor [Aeromonas sp. 610]
 gi|187763294|gb|ACD35524.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763296|gb|ACD35525.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763318|gb|ACD35536.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|187763362|gb|ACD35558.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|264685616|dbj|BAI49157.1| RNA polymerase beta subunit [Aeromonas sp. GMA0361]
          Length = 272

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|317423770|emb|CBI85532.1| RNA polymerase sigma factor [Aeromonas bestiarum]
          Length = 272

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 119/316 (37%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            +   D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GDDADDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|260425737|ref|ZP_05779717.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
 gi|260423677|gb|EEX16927.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
          Length = 292

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 74/268 (27%), Positives = 127/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     +   ++ A +RL IS+A K+   G    DL+QE  +GLMKAA+KF
Sbjct: 26  ELRLAYAWRDQRDEASLHRLINAYMRLAISMASKFKRYGAPMGDLVQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAAAE 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLE-TPIGDEDTSHLGDFIEDKNA 597
              ++R      IA+++ +P+  V  +  +++    SL  T   DED     D +ED   
Sbjct: 146 GKTLERHMLHAAIAQEIGVPLSDVEMMEGRLSGSDFSLNATQSSDEDGREWIDTLEDDGE 205

Query: 598 VS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                       A LRE     +++L  RE  ++R R         TLE +G++  +++E
Sbjct: 206 QGSSVVEGRLDNAQLREWLVVAMSALNDRERFIVRERKLRD--ETRTLESLGQELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S++++ FL
Sbjct: 264 RVRQLEAAAFAKMRKSLEAQSREVQHFL 291


>gi|66474665|gb|AAY46902.1| RpoD [Aeromonas bestiarum]
 gi|66474667|gb|AAY46903.1| RpoD [Aeromonas bestiarum]
 gi|66474681|gb|AAY46910.1| RpoD [Aeromonas bestiarum]
          Length = 272

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            E + D+ +      ++                  E + ELR+  +   ++ QK+ ++  
Sbjct: 95  GESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|216263458|ref|ZP_03435453.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
 gi|215980302|gb|EEC21123.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
          Length = 266

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 145/260 (55%), Gaps = 10/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   +++    ++ AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIQLAGQIQR---GSAKAKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQF 649
            ED N+ +P  +  Q +  +    +L + LT +E  +++ R+ +  +    TL+++  + 
Sbjct: 185 YED-NSFNPEITLEQDSTLQHLNYILETKLTEKERYIIKKRYNLDNSPKKSTLKDISTEL 243

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            ++ E +RQIE + ++KLK 
Sbjct: 244 GISSETVRQIEKRVLKKLKE 263


>gi|297616994|ref|YP_003702153.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144831|gb|ADI01588.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 256

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 73/264 (27%), Positives = 133/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + + +   +  +  + +     A++E++  NLRLV+SV +++ +RG
Sbjct: 1   MLNKVEICGVNTSNLPVLKNERMRDLFLRVKQNDRQAREELIRGNLRLVLSVIQRFNHRG 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     +FSTYA+  +   I R + D +  +R+   +RD
Sbjct: 61  EYVDDLFQVGCIGLIKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNN-PVRVSRSLRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++   ++  +  REPT  EIA +L +  E V   L   +EP+SL  PI ++  D 
Sbjct: 120 VAYKALQVREQLLAEKSREPTIAEIADRLEVSQEEVVFALDAIQEPVSLFEPIYNDGGDP 179

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D I D      L     +         L  L+ RE+ +L +RF  G     T  EV
Sbjct: 180 ILVMDQISDDKTTDELWLEGIS-----IREALKKLSEREKLILTLRFFEG----KTQMEV 230

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            ++  +++ ++ ++E  A++ +K 
Sbjct: 231 AEEIGISQAQVSRLEKAALKHMKK 254


>gi|259479061|dbj|BAI40078.1| RNA polymerase sigma-70 factor [Aeromonas sp. Kochi]
 gi|326682074|emb|CBL30928.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682076|emb|CBL30929.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682078|emb|CBL30930.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682082|emb|CBL30932.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682084|emb|CBL30933.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682086|emb|CBL30934.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682088|emb|CBL30935.1| RNA polymerase sigma factor [Aeromonas aquariorum]
          Length = 272

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|297614628|gb|ADI48616.1| RNA polymerase sigma-70 factor [Shewanella sp. KJW23]
          Length = 263

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 57/305 (18%), Positives = 110/305 (36%), Gaps = 51/305 (16%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+    I IAKRIE G   + +S+ E P     ++   D+       L +II       
Sbjct: 1   LLTA-RRIQIAKRIEEGINTVQSSVAEYPQAIAMILEQFDQFEAEEIRLSDII------- 52

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV--DSPPEN 250
                GF +  E            E   DD+ + +   +       D   +      PE 
Sbjct: 53  ----SGFVNPDEDDVGPSATHIGSELSDDDLDDEDDMDDDDEDDDSDSEDEGSKGPDPEE 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L    + ++  L  ++ +  P+ + AL  I E+++E                 
Sbjct: 109 ARERFGQLRAVYE-NSLKLIELKGRDHPESVAALFHIGEIFKE----------------- 150

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
                              L   + D LV+ +  +  ++   E  +L+L  +   + +  
Sbjct: 151 -----------------FRLVPKQFDRLVKSMRSMMDKVRVQERLILKLCVEQAKMPKKN 193

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E D  W + A+      +   +    + +L+ R ++++I  ETG+SI+  + 
Sbjct: 194 FVKLFTGNETDISWFN-AEMNSGKPYAEGLKMVEEDVLRCRAKLEAIEAETGLSIASIKD 252

Query: 430 IVSMV 434
           I   +
Sbjct: 253 INRRM 257


>gi|294638156|ref|ZP_06716412.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
 gi|291088723|gb|EFE21284.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
          Length = 284

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 131/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E R +   +         A K+++ ++LR V+ VA+ Y   GL
Sbjct: 16  LEAYVRAANAYPMLTAEEERALGERL--HYQGDLDAAKQLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + V     ++  + ++ + P  DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VELVARELGVSEKDVLEMESRMAAQDMAFDLPNDDEQE 191

Query: 586 SHLGD---FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   F++DK+   A    D   +++  +  +  L  L  R + ++R R+ +     
Sbjct: 192 GAPAAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDERSQHIIRARW-LDSENK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 ATLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|239832766|ref|ZP_04681095.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
 gi|239825033|gb|EEQ96601.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
          Length = 303

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 64/267 (23%), Positives = 119/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHTDPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D ++        Q  L   R    + + +L  RE R+         + 
Sbjct: 194 EGESGEWQDWLVDDSSSQEQILIEQDELDNRRSMLEQAMDTLNDRERRIFEA--RRLSDD 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSSEFSISRERVRQIEVRAFE 278


>gi|304320154|ref|YP_003853797.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
 gi|303299057|gb|ADM08656.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
          Length = 283

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 123/275 (44%), Gaps = 11/275 (4%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
             +D+   ++  I+       +SI E R ++   R  + +   A  ++  A++R+ +S A
Sbjct: 1   MVIDNDEYLKATIRQAMSAPLLSIEEERSLMR--RWVDDQDERALGKLTRAHMRMAVSTA 58

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
            K+   GL   DLIQEG IGL++AA++FD     +F TYA WW++ ++   I      +R
Sbjct: 59  IKFRGYGLPLADLIQEGAIGLLEAAKRFDPDREVRFCTYAGWWIRASMQDYILRNWSIVR 118

Query: 521 IPVHMRDK--IHKVVRTARRMSNKIKREPTPE-EIAKKLAMPVEGVR-KVLKITKEPISL 576
           +      K     + R    + +      T   + A++  +    +     ++ +   SL
Sbjct: 119 VGSKSAHKTIFFNLSRIRSMIEDADTAPRTARIKAAERFNVSESDIEFMTSRLGRRDQSL 178

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
              + D+      D I D+          +  QA  +    + L +L+ RE  ++  RF 
Sbjct: 179 NAMLTDDGDIERQDLIPDEREGPDSLAEGTLDQARRKSWIGKALKTLSNRERMIIEHRFF 238

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  TL  +G    +++ER+RQIE +A+ KLK
Sbjct: 239 --TEEKMTLSRLGDDLSLSKERVRQIEKQAMGKLK 271


>gi|297250602|ref|ZP_06934149.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
 gi|296838520|gb|EFH22458.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
          Length = 290

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 72/266 (27%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      +EIA  L + +  V     ++T   I++     D++ S
Sbjct: 137 KLFFNLRSMRKNLNALSP-KEAQEIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|220921709|ref|YP_002497010.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219946315|gb|ACL56707.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 293

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 126/270 (46%), Gaps = 11/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  ++       +   E R +   VR  +     A   ++ A++RLVI++A ++ + GL 
Sbjct: 9   RQFVRMAMDAPFLEREEERGLA--VRWKDERDEQALHRLISAHMRLVIALAGRFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG++GLM+AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  MADLVQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   R+     +   +     IA  + +  E V     +++   +SL  PI DE
Sbjct: 127 LFFNLRRLRARLMQSTDERVGDEIHSRIATAIGVSREDVALMDARLSGPDMSLNAPITDE 186

Query: 584 DTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH- 640
             +     DF+ D + +     +   +     T +  +LT   ER LR+     +  D  
Sbjct: 187 GDASAERVDFLVDTSPLPDEAVSDAVDGERRLTWLRQALTVLSERELRILHERRLAEDQA 246

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLE +G +  +++ER+RQIE +A+ KL+  
Sbjct: 247 TLEALGHRLGISKERVRQIENRALEKLRRA 276


>gi|293391201|ref|ZP_06635535.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951735|gb|EFE01854.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 282

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 67/268 (25%), Positives = 134/268 (50%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K++V ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANEYPMLTAEEEKELAERL--YYKEDIEAAKKLVLSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  + V ++  ++T   ++ + P  + D 
Sbjct: 134 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSPQDVMEMESRMTGADVAFDLPGDEHDE 191

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   +A   +     L +L  R + +++ R+     T  
Sbjct: 192 ETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDARSQDIIKARWLDE--TKA 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+++  ++ ++ ER+RQ+EA A++KLK
Sbjct: 250 TLQDLAAKYNISAERVRQLEANALKKLK 277


>gi|306844673|ref|ZP_07477258.1| alternative sigma factor RpoH [Brucella sp. BO1]
 gi|306274845|gb|EFM56615.1| alternative sigma factor RpoH [Brucella sp. BO1]
          Length = 303

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSSEFGISRERVRQIEVRAFE 278


>gi|295836990|ref|ZP_06823923.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
 gi|197697450|gb|EDY44383.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
          Length = 312

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 59/246 (23%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 70  LFERLEDLDEGTHAHSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 129

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 130 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 189

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PTP E+A +L +  E V + +         SL+    ++D  S L D +  ++       
Sbjct: 190 PTPSELADRLGIEREEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGIE 249

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I     E+   ++A L  R+ ++L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 250 YI-----ESLKPMIARLPQRDRKILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRT 300

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 301 LVKLRK 306


>gi|182435018|ref|YP_001822737.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463534|dbj|BAG18054.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 292

 Score =  130 bits (326), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 122/252 (48%), Gaps = 8/252 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G      A+  ++E NL LV   AK++ NRG  +  D+IQ G IGL+KA 
Sbjct: 46  FFDQLQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIIQVGTIGLIKAI 105

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +T   +S ++ R
Sbjct: 106 DRFELSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKTREALSTRLDR 165

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           EPT  E+A  L +  E V + L         SL+ PIG +  S       D         
Sbjct: 166 EPTVAELAHHLELTEEEVIEGLIAANGYTAGSLDLPIGADQNSAETVTYGDIKGDVDPAM 225

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  +L  T   +L  L  RE  ++ MRFG     + T  ++G+   +++  + ++ ++ 
Sbjct: 226 ELVEDLH-TLAPLLERLDEREREIVAMRFG----REMTQAQIGEHLGISQMHVSRLLSRL 280

Query: 664 IRKLKHPSRSKK 675
           + KL+    ++K
Sbjct: 281 LTKLRKDMLTEK 292


>gi|256786488|ref|ZP_05524919.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 291

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 106/230 (46%), Gaps = 11/230 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM  V
Sbjct: 68  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 127

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D   T+ +P  + +   +V      ++    R PT  EIA++L +  E V 
Sbjct: 128 VGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRITEEEVL 187

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++   +    SLE     +    L D +  ++             R+    +L  L  
Sbjct: 188 SCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH-----RDLVRHLLVQLPE 242

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+  +R
Sbjct: 243 REQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLRSANR 288


>gi|187918623|ref|YP_001884188.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
 gi|119861471|gb|AAX17266.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
          Length = 267

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/259 (26%), Positives = 135/259 (52%), Gaps = 8/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   ++        AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHRLITHEEEIELAKQIK---LGDLKAKNKMINANLRLVLKIIKRYAGKGLKVE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  E+I ++  +      K++   ++  SL+  +   + S L + 
Sbjct: 129 INK----YLMEEEKSPKKEDIMERFNLTTAQYVKIIPYLEKEYSLDKKLEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
            ED +          + L+     +   L  +E  ++R R+ +  N    TL+++  +  
Sbjct: 185 YEDNSFNPESTLEQNSTLKHLNHILETKLNDKERYIIRKRYNLDNNDKKSTLKDISSELG 244

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++ E +RQIE + ++KL+ 
Sbjct: 245 ISSETVRQIEKRVLKKLRE 263


>gi|302552549|ref|ZP_07304891.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470167|gb|EFL33260.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 289

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 111/244 (45%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  ++ G  E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD 
Sbjct: 52  LKELQPGTSEHDRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDP 111

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  
Sbjct: 112 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTSFGRTPTTA 171

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  + V   ++   +    SLE     +    L D +  ++            
Sbjct: 172 EIAERLRITEDEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH---- 227

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+
Sbjct: 228 -RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLR 282

Query: 669 HPSR 672
             +R
Sbjct: 283 SANR 286


>gi|255312689|gb|ACU01754.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 79/194 (40%), Positives = 131/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKSLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|15616654|ref|NP_239866.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681412|ref|YP_002467797.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219681968|ref|YP_002468352.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|257471086|ref|ZP_05635085.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|7994684|sp|O05385|RP32_BUCAI RecName: Full=RNA polymerase sigma-32 factor
 gi|25288470|pir||H84932 DNA-directed RNA polymerase (EC 2.7.7.6) sigma-32 factor [imported]
           - Buchnera sp. (strain APS)
 gi|1929472|gb|AAB51433.1| heat shock sigma factor 32 [Buchnera aphidicola]
 gi|10038717|dbj|BAB12752.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219621701|gb|ACL29857.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219624255|gb|ACL30410.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311085774|gb|ADP65856.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086927|gb|ADP67007.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 284

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 127/269 (47%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+  ++   +SI E + +   +R        A K ++ ++LR VI +++ Y+  GL
Sbjct: 16  LDAYIRIANLWPMLSIEEEKKLTKRLRYNG--DLDAAKTLILSHLRFVIHISRNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  LQSDLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHWIKSEIHEYVLRNWRIVKVATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLE---TPIGD 582
                + +T +R+      E   + +A++L +    VR++  +++ + ++         D
Sbjct: 134 KLFFNLRKTKKRLG--WFNEEEIQIVARELGVSSRDVREMESRMSAQDVAFNPSPEEHCD 191

Query: 583 EDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             T+    +++DK    A        + +     +  L  L  R   ++  R+ +  N  
Sbjct: 192 SKTNSSIQYLQDKTSNFANGVEQDNWEEHAANKLSSALLRLDERSRHIIHARW-LDKNKK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +TL+ +   + ++ ER+RQ+E  A++KLK
Sbjct: 251 NTLQNIANNYGISAERVRQLEKNAMKKLK 279


>gi|325266382|ref|ZP_08133060.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
 gi|324982175|gb|EGC17809.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
          Length = 332

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 127/273 (46%), Gaps = 11/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 57  LEQYIHTVNNIPMLSAEEETRLAER---QIKGDLEAAKQLILSHLRVVVSIARGYDGYGL 113

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   I      +R+      +
Sbjct: 114 NQADLIQEGNIGLMKAVKRFEPHHGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 173

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R S K       ++IA  L + V  V ++  ++T   I L     D+D ++
Sbjct: 174 KLFFNLRSMRNSLKALSPKEAQDIADDLGVKVSEVMEMEQRMTGHDIGLLADNQDDDENN 233

Query: 588 ---LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                D++ D         A +A+     E     LA L  R  R++  R+        T
Sbjct: 234 AFAPIDWLSDSQHEPSHQLAQKAHYALQTEGLQAALAQLDERSRRIVETRWLHD-GQAAT 292

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L E+  +F V+ ERIRQIEAKAI+KL+    ++
Sbjct: 293 LHELAAEFGVSAERIRQIEAKAIQKLRAIMENQ 325


>gi|66474617|gb|AAY46878.1| RpoD [Aeromonas caviae]
 gi|66474621|gb|AAY46880.1| RpoD [Aeromonas caviae]
 gi|66474641|gb|AAY46890.1| RpoD [Aeromonas hydrophila]
 gi|66474683|gb|AAY46911.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  130 bits (326), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|302535695|ref|ZP_07288037.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
 gi|302444590|gb|EFL16406.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
          Length = 355

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 106/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 127 EHHRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTF 186

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 187 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNAATEDLTTLHGRTPTTPEIAERLRIS 246

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 247 EDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPELAGVEH-----RDLVRHLL 301

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 302 VQLPEREQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 352


>gi|326318574|ref|YP_004236246.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375410|gb|ADX47679.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 313

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 119/290 (41%), Gaps = 24/290 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  +  +   I +++    ++  E R     ++  E     A   MV ++LRLV+S+A++
Sbjct: 21  IPPLGNLDAYISAVNRLPMLTAEEERTYARRLK--EHNDVEAAGRMVMSHLRLVVSIARQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD     +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VHMRDKIHKVV----RTARRMSNKIKREPTPEEIAKKLAMP----------VEGVRKVLK 568
                +         +   +  +      T  E   +  +            E +    +
Sbjct: 139 TTKSQRKLFFNLRSMKQGFKADSAAGNTGTHRETLSEQEIDVVAQQLNVKREEVIEMETR 198

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPR 623
           ++   + L+    D+     G      +      + I++  R+          LA+L  R
Sbjct: 199 LSGGDVMLDPAPSDDGEQAYGPIAYLADGTHEPTAMIESRQRDVLATDGIANALATLDDR 258

Query: 624 EERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             R++  R+    +      TL E+   + V+ ERIRQIE  A++K+K  
Sbjct: 259 SRRIVEERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKA 308


>gi|37784406|gb|AAO13096.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784468|gb|AAO13127.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784484|gb|AAO13135.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784486|gb|AAO13136.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|37784488|gb|AAO13137.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|259479057|dbj|BAI40076.1| RNA polymerase sigma-70 factor [Aeromonas sp. GV16]
 gi|264685604|dbj|BAI49151.1| RNA polymerase beta subunit [Aeromonas sp. A10]
 gi|264685608|dbj|BAI49153.1| RNA polymerase beta subunit [Aeromonas sp. Y62]
 gi|264685614|dbj|BAI49156.1| RNA polymerase beta subunit [Aeromonas sp. GF1]
 gi|264685618|dbj|BAI49158.1| RNA polymerase beta subunit [Aeromonas sp. ATCC 19570]
 gi|264685620|dbj|BAI49159.1| RNA polymerase beta subunit [Aeromonas sp. ATCC 14715]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + +LR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|304393314|ref|ZP_07375242.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
 gi|303294321|gb|EFL88693.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
          Length = 300

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 122/273 (44%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ I     +   E   +    R  E + + A  +MV ++LRLV  +A  Y   GL
Sbjct: 15  LQRYMEEIRKFPMLKPDEEYMLGK--RYSEHDDTEAAHKMVTSHLRLVAKIAMGYRGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW+K +I   +      +++      K
Sbjct: 73  PVSEVISEGNVGLMQAVKKFDPEKGFRLATYAMWWIKASIQEYVLRSWSLVKMGTTANQK 132

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + +     ++   E+IA  L +  + VR + +      SL  PI   
Sbjct: 133 RLFFNLRKLKGKLKALEEGELKQENVEKIASTLGVSHDEVRSMNQRLSGDASLNAPIKAA 192

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R+     +  L  RE+R+   R       
Sbjct: 193 EGESGQWQDWLVDDSESQEQMLIKQDELDVRRDMLAEAMDVLNDREKRIFMARRLEE--D 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TLE +  +F ++RER+RQIE +A  K++   
Sbjct: 251 PLTLEVLSGEFDISRERVRQIEVRAFEKVQKAM 283


>gi|66474613|gb|AAY46876.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQSAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|284008659|emb|CBA75293.1| RNA polymerase sigma-32 factor [Arsenophonus nasoniae]
          Length = 292

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 134/270 (49%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   ++S +    ++  E +     +         A K+++ ++LR VI +A+ Y+  GL
Sbjct: 23  IEAYVRSANAYPMLTAEEEQEYAKRL--HYHGDLNAAKQLILSHLRFVIHIARNYSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 81  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 140

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
             K+    R+   +I      E   +AK+L +  + VR++  ++  + ++ +    D+  
Sbjct: 141 --KLFFNLRKNKKRIGWFNQNEVDMVAKELGVTSKDVREMESRMAAQDMAFDMNDDDDSG 198

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRFGIGMNT 638
           + + +   +  ++  S    +I+ +  E       T+ L++L  R + ++R R+ +    
Sbjct: 199 ENTTIAPVLYLQDKSSDFADSIEEDNWENHATDKLTQALSTLDERSQDIIRARW-LDDEN 257

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+++  ++ V+ ER+RQ+E  A++KL+
Sbjct: 258 KTTLQDLADKYSVSAERVRQLEKNAMKKLR 287


>gi|119503515|ref|ZP_01625598.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119460577|gb|EAW41669.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 282

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 65/265 (24%), Positives = 119/265 (44%), Gaps = 11/265 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++++S    +S+   + +   +    C  S   +E+V A+LR V+ +A+ Y+  GL   
Sbjct: 18  YVQAVSGIPILSVDREQALAEKLYYEGCVDS--ARELVLAHLRFVVHIARSYSGYGLAEG 75

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIH 530
           DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  +   I      +++     + K+ 
Sbjct: 76  DLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKLF 135

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG- 589
             +R+A++    +  E T    A       E  R   +++   I+ + P   +D      
Sbjct: 136 FNLRSAKKSLGWLNAEETQAIAADLGVDEAEVQRMEGRLSSRDIAFDLPTDADDEDAWQS 195

Query: 590 -----DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
                D I    A          +        L+ L  R   ++  R+        TL E
Sbjct: 196 PQAYLDDISTDPARCIEAEDSARDGENRLRAALSDLDERSRNIVTQRWLAE--QKATLHE 253

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           +  ++ V+ ERIRQ+E  A++KLK+
Sbjct: 254 LAAEYGVSAERIRQLEVNAMKKLKN 278


>gi|57996876|emb|CAI45886.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 76/190 (40%), Positives = 127/190 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  L+LI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLE 643
           +      TLE
Sbjct: 182 LLGYEAATLE 191


>gi|297746545|emb|CAZ60990.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 267

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 110/304 (36%), Gaps = 46/304 (15%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I
Sbjct: 1   ELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFI 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P          +  +       S+  E D   E E + E     S DD       PE A
Sbjct: 59  DPNE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVA 111

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                +L    + +  ++                                   QK+ ++ 
Sbjct: 112 REKFGDLRAQYEVTRLSI-----------------------------------QKNGRAH 136

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVF 370
              +    +L  +     L   +   LV  + ++ +R+   E  +++L  +   + +  F
Sbjct: 137 EDTQAAIAQLADVFRQFRLMPKQFYRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTF 196

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           +      E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I
Sbjct: 197 VAAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDI 255

Query: 431 VSMV 434
              +
Sbjct: 256 NRRM 259


>gi|37784462|gb|AAO13124.1| RNA polymerase sigma-70 factor [Aeromonas cf.
           bestiarum/salmonicida]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 114/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE     + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDRINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       +         E +  D  E E + E     S DD       PE A   
Sbjct: 59  E-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREK 113

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             +L    + +  ++                                   QK+ ++    
Sbjct: 114 FGDLRAQYEVTRLSI-----------------------------------QKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|72160963|ref|YP_288620.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71914695|gb|AAZ54597.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 267

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 117/248 (47%), Gaps = 10/248 (4%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +  +     E    + E+VE +L LV  +A+++ NRG    DL Q   IGL+K+
Sbjct: 23  RELFERLGELDPDSPERQRIRDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKS 82

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++FD   G +FSTYA   +   I R   D+   +R+P  +++    + +    +S +  
Sbjct: 83  IDRFDLSRGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAVSELSQRHG 142

Query: 545 REPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           R PT  E+A+ L M  E V + L+       +SL+ P   ++ +     + D   +   +
Sbjct: 143 RAPTVAELAEYLKMSEEEVLEGLESANAYSTVSLDAPDNGDEDAP---AVADSLGI-MDE 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           S      RE+   +L  L PRE+++L +RF        T  ++  +  +++  + ++ A+
Sbjct: 199 SLEGVEYRESLKPLLERLPPREKKILLLRFFGN----MTQSQIAAELGISQMHVSRLLAR 254

Query: 663 AIRKLKHP 670
            + +L+  
Sbjct: 255 TLAQLRQA 262


>gi|321116382|emb|CBN73608.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 270

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/313 (18%), Positives = 116/313 (37%), Gaps = 45/313 (14%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   +M+++   P T   ++   + +      L +I  L   I 
Sbjct: 2   LLTREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYERVTTEGGRLSDI--LSGYID 59

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P+  G           ++ E  + +       + + D E     S+++       PE A 
Sbjct: 60  PDDDGA------AGPQEEVEPVAPQTAAKPAGDDKDDDEEDDSDSEEEEGDGGPDPEVAR 113

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                + E  + +   L                                   +K  + S 
Sbjct: 114 VRFGAVAEQLEVAKKAL-----------------------------------KKHGRGSQ 138

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
           +     ++L  L   + L   + D LV+++ D   ++   E  ++++      + R  FL
Sbjct: 139 QATDALQELATLFMPIKLIPKQYDALVDRVRDALSQVRAQERAIMQICVRDARMPRADFL 198

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
            +    E D  W     +  + ++   +A   + I + + ++ ++  E  + I++ + I 
Sbjct: 199 RQFPNNETDLGWADKLAN-GKSKYAEAIAERKEDIQRCQEKLLALEEECALLITDIKDIN 257

Query: 432 SMVRKGECEASIA 444
             +  GE +A  A
Sbjct: 258 RRMSIGEAKARRA 270


>gi|291522675|emb|CBK80968.1| RNA polymerase, sigma subunit, RpsG/SigG [Coprococcus catus GD/7]
          Length = 259

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 129/266 (48%), Gaps = 15/266 (5%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + + +      ++++ +     A++  +  NLRLV+SV ++++      
Sbjct: 5   KVEICGVNTAKLPLLKEDEKEMLMKRIKSHDLRARERFINGNLRLVLSVIQRFSGTNENV 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+KA + FD   G +FSTYA+  +   I R + D S  IR+   +RD  +
Sbjct: 65  NDLFQVGCIGLIKAIDNFDLTQGVRFSTYAVPMIVGEIRRFLRDNS-AIRVSRSLRDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL-- 588
           K +     +  +  REPT  EIA++  +P E +   L   + P+SL  P+  +    L  
Sbjct: 124 KAIYAREALITRNNREPTVMEIAEETGIPKEDIVFALDAIQSPMSLYEPVYTDGGDALCI 183

Query: 589 GDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            D + D KN  +     +           +  L+ RE R+++MRF  G     T  EV  
Sbjct: 184 MDQVSDRKNGENSWVENL------ALNDAMKRLSHRENRIIKMRFYEG----KTQMEVAD 233

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
           +  +++ +I +IE  A++ ++   R+
Sbjct: 234 ELAISQAQISRIEKSALQNMRTYLRA 259


>gi|323099956|gb|ADX23556.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 134/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 36  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 95

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 96  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 154

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 155 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 214

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 215 FVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 265

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 266 EEIGISQAQVSRLEKSAIKQM 286


>gi|66474717|gb|AAY46928.1| RpoD [Aeromonas veronii]
 gi|66474737|gb|AAY46938.1| RpoD [Aeromonas veronii bv. sobria]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 116/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II        
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-------- 52

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
               GF    E                          E  A  +    S++       E+
Sbjct: 53  ---SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADED 84

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           +E   DEDED  +                   E+   Y          ++ QK+ ++   
Sbjct: 85  EEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKK+
Sbjct: 258 RMSIGEAKARRAKKK 272


>gi|66474721|gb|AAY46930.1| RpoD [Aeromonas sp. ym1]
 gi|66474727|gb|AAY46933.1| RpoD [Aeromonas sp. ym4]
 gi|66474731|gb|AAY46935.1| RpoD [Aeromonas sp. CCRC 13980]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II        
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-------- 52

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
               GF    E                          E  A  +    S++       E+
Sbjct: 53  ---SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADED 84

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           +E   DEDED                      E+   Y          ++ QK+ ++   
Sbjct: 85  EEDEEDEDEDGDNSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKK+
Sbjct: 258 RMSIGEAKARRAKKK 272


>gi|66474677|gb|AAY46908.1| RpoD [Aeromonas bestiarum]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 113/315 (35%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+ E EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTHEREIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                        +         E +  D  E E + E     S DD       PE A  
Sbjct: 59  NE-----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVARE 113

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 114 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 258 RMSIGEAKARRAKKE 272


>gi|150398305|ref|YP_001328772.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029820|gb|ABR61937.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 288

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 76/285 (26%), Positives = 134/285 (47%), Gaps = 19/285 (6%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + ++   R  IK       +   E   +    R        A+ ++  +++RLVIS+A K
Sbjct: 1   MKTLTADRRMIKIAMEAPYLERDEEHALAEAWR--NDNDQEARNKIAMSHMRLVISMAAK 58

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + + GL   DL+QEG+IGL++AA +F+     +FSTYA WW++ ++   +      +R  
Sbjct: 59  FRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGG 118

Query: 523 VHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISL 576
                K     + R   R++    ++  +   EEIA  + + +  V+    +++    SL
Sbjct: 119 TSSAQKALFFNLRRLRARLAQGDRQLTSQAVHEEIAAAIGVSLADVQTMDARLSGNDASL 178

Query: 577 ETPI--GDEDTSHLGDFIEDK-----NAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           + PI  GD D     DF+  +       VS L    +A  R      L  L+ RE +++R
Sbjct: 179 QAPIGGGDPDAGARLDFLASEAPLPDEQVSDLIDGERA--RRWLHVALGELSEREMKIIR 236

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            R         TLEE+G    +++ER+RQIE +A+ KL+    ++
Sbjct: 237 ARRLSEDG--ATLEELGVALGISKERVRQIETRALEKLRAALTAR 279


>gi|15595116|ref|NP_212905.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|195941591|ref|ZP_03086973.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 80a]
 gi|216264706|ref|ZP_03436698.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218249170|ref|YP_002375269.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221217974|ref|ZP_03589441.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223889406|ref|ZP_03623992.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224532620|ref|ZP_03673242.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225548870|ref|ZP_03769847.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225550031|ref|ZP_03770992.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225551867|ref|ZP_03772810.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226320640|ref|ZP_03796199.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|226321470|ref|ZP_03796997.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|2688700|gb|AAC67109.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|215981179|gb|EEC21986.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218164358|gb|ACK74419.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221192280|gb|EEE18500.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223885092|gb|EEF56196.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224512476|gb|EEF82855.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225369490|gb|EEG98942.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225370473|gb|EEG99909.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225371662|gb|EEH01089.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226233266|gb|EEH32018.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|226233963|gb|EEH32685.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|312148432|gb|ADQ31091.1| RNA polymerase sigma factor [Borrelia burgdorferi JD1]
 gi|312149704|gb|ADQ29775.1| RNA polymerase sigma factor [Borrelia burgdorferi N40]
          Length = 266

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 139/259 (53%), Gaps = 8/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   +++G  +   AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIKLAGQIQRGNAK---AKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
            ED +    +     + L+     +   L  +E  +++ R+ +  +    TL+++  +  
Sbjct: 185 YEDNSFNPEITLEQDSTLKHLNYILETKLNEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++ E +RQIE + ++KLK 
Sbjct: 245 ISSETVRQIEKRVLKKLKE 263


>gi|218670385|ref|ZP_03520056.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 266

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 120/253 (47%), Gaps = 12/253 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E     A  ++V ++LRLV  +A  Y   GL   +++ EGN+GLM+A +KFD   G+
Sbjct: 4   RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGF 63

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPE-- 550
           + +TYAMWW+K +I   I      +++    + +     + R   R+      +  PE  
Sbjct: 64  RLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHV 123

Query: 551 -EIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQA 607
            EIA KL +  E V  + +      SL  PI   + D+    D++ D +         Q 
Sbjct: 124 SEIATKLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQD 183

Query: 608 NL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            L   R   ++ ++ L  RE R+   R         TLE++  +F ++RER+RQIE +A 
Sbjct: 184 ELETRRRMLSKAMSVLNERERRIFEARRLAE--EPVTLEDLSAEFDISRERVRQIEVRAF 241

Query: 665 RKLKHPSRSKKLR 677
            K++   R + L 
Sbjct: 242 EKVQDAVRKEALE 254


>gi|83941135|ref|ZP_00953597.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83846955|gb|EAP84830.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 298

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 121/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A   MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      +
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQK 133

Query: 527 DKIHKVVRTARR---MSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   R   +          + IA  L +   E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNRIGALEEGDLHPDNVKRIATDLGVTETEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     L  L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQATDYEERDELETRREMLAEALDVLNDREKDILTQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QTVTLEDLSSQYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|306841398|ref|ZP_07474101.1| alternative sigma factor RpoH [Brucella sp. BO2]
 gi|306288583|gb|EFM59932.1| alternative sigma factor RpoH [Brucella sp. BO2]
          Length = 303

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|163733965|ref|ZP_02141406.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
 gi|161392501|gb|EDQ16829.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
          Length = 298

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 122/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPQEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      +
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQK 133

Query: 527 DKIHKVVRTARR---MSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   +   +            IAK L +   E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNKIGALEEGDLHPDNVARIAKDLGVTETEVISMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED+ A    D   +  L   RE     ++ L  RE+ +L+        
Sbjct: 194 EGEGTMQWQDWLEDEGADQAGDYEARDELEARRELLADAMSVLNDREKDILQQ--RRLSE 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  ++ V+RERIRQIE +A  KL+   R
Sbjct: 252 KTVTLEDLSAEYNVSRERIRQIEVRAFEKLQKKMR 286


>gi|312797371|ref|YP_004030293.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
 gi|312169146|emb|CBW76149.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
          Length = 319

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 126/272 (46%), Gaps = 10/272 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    +S ++   +    R+       A +++V ++LRLV+S+A+ Y   GL
Sbjct: 47  LDAYIQAVNRIPLLSQADETRLAIEYREQNKLD--AARQLVLSHLRLVVSIARNYLGYGL 104

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++      +
Sbjct: 105 PHADLIQEGNIGLMKAVKRFDPRQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQR 164

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSH 587
                  + +   +         +AK+L +  E V     ++    I+LE    D + S 
Sbjct: 165 KLFFNLRSHKQGMQAFTPDEIAGLAKELNVKREEVTEMETRLAGGDIALEGQFEDGEESF 224

Query: 588 -LGDFIEDKNAV--SPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNT---DH 640
               ++ D      + L S  +  L+ E     L SL  R  R++  R+    +      
Sbjct: 225 APIAYLADSRTEPTTVLASRQRDLLQTEGLAEALESLDARSRRIIEARWLQVQDDGSGGA 284

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           TL E+  +F V+ ERIRQIEA A++K++   +
Sbjct: 285 TLHELADEFGVSAERIRQIEASAMKKMRSALQ 316


>gi|260913469|ref|ZP_05919947.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
 gi|260632409|gb|EEX50582.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
          Length = 281

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 131/267 (49%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 16  LEGYIRAANEYPMLTAEEEKELAERL--YYQEDLEAAKKLILSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGD-ED 584
                + +T +R+      E   E +A +L +  E V ++  ++T   ++ + P  D E+
Sbjct: 134 KLFFNLRKTKQRLG--WFNENEVEMVANELGVTPEDVMEMESRMTGSDVAFDLPTDDSEE 191

Query: 585 TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           T     ++EDK    A    D   +    E  +  L  L  R   +++ R+        T
Sbjct: 192 TYSPALYLEDKGSNFAAELEDENYETQATEQLSVALEGLDERSLDIIKSRWLDDN--KAT 249

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 250 LQDLAAKYNISAERVRQLETNALKKLK 276


>gi|94499830|ref|ZP_01306366.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
 gi|94428031|gb|EAT13005.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
          Length = 288

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 126/269 (46%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   + +I     +S  E R +   +         A + +V ++LR V+ +AK Y   
Sbjct: 17  RDLDGYLNAIGGIAVLSAEEERELADRL--YYESDLEAARRLVLSHLRFVVHIAKSYNGY 74

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     
Sbjct: 75  GLNQSDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKA 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
            +       + +  N    E    +IA+ L +  + V ++  +++    + ++P+ D++ 
Sbjct: 135 QRKLFFNLRSAKKRNGWLNEAEAHKIAEDLGVSAKEVYEMEGRLSSHDSTFDSPVADDED 194

Query: 586 SHL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           S      +++ED +   A++  +   + +        L  L  R + +L  R+       
Sbjct: 195 SAYQAPANYLEDHSFDPALAVENENYEQDSTARLQDALVQLDDRSKDILMRRWL--GEHK 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A++K+K
Sbjct: 253 ATLHELADEYGVSAERIRQLEKNAMKKIK 281


>gi|163736875|ref|ZP_02144293.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|161389479|gb|EDQ13830.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 292

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/288 (25%), Positives = 136/288 (47%), Gaps = 19/288 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I N +   +++  +  +E   +       +     A   ++ A +RL IS+A K+   G 
Sbjct: 7   IENPLPKRAMKAELLDAET-ELQLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGA 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI------- 521
              DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +I   +      +R        
Sbjct: 66  PMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQK 125

Query: 522 --PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET 578
               +MR    ++ R A+    ++ +    ++IA ++ +P+  V+ +  ++     SL  
Sbjct: 126 SLFFNMRRVQAQLERQAQSDGARLDKHQLHQQIATEIGVPLRDVQMMDGRLAGSDFSLNA 185

Query: 579 PIGDEDTS-HLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGI 634
               ED      + +ED +A +        +   LR+     + +L  RE  ++  R   
Sbjct: 186 VQSSEDEGREWIEALEDDSAQAAELVEESHDTRQLRDWLVEAMQALNERERFIITERKLR 245

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR--SKKLRSFL 680
                 TLE +G +  +++ER+RQ+EA A +K++      S+++++FL
Sbjct: 246 E--KPRTLESLGNELDLSKERVRQLEAGAFQKMRKSLETCSREVQNFL 291


>gi|323492929|ref|ZP_08098069.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
 gi|323312822|gb|EGA65946.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
          Length = 285

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 130/270 (48%), Gaps = 16/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYDGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-----KITKEPISLETPIG 581
                + ++ +R+      E   E +A++L +    VR++      +     +  +    
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPAEVREMESRLAAQDATFEMPSDDDDS 191

Query: 582 DEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
               +    ++EDK    A +   +  +A+     +  L +L  R + ++R R+     +
Sbjct: 192 ASSYTAPMVYLEDKASDVADNVEAANWEAHTNNRLSLALKTLDDRSQHIVRSRWLDDNKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 252 --TLQELAETYSVSAERIRQLEKNAMKKLK 279


>gi|270158013|ref|ZP_06186670.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|289163720|ref|YP_003453858.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
 gi|269990038|gb|EEZ96292.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|288856893|emb|CBJ10704.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
          Length = 284

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 122/275 (44%), Gaps = 17/275 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I  ++    +S+ E   I    R        A + +V A+LR V+ VA+ Y   GL
Sbjct: 17  IDAYIHRVNQIPMLSLEE--EIACAERFHSEGDLEAARRLVLAHLRYVVRVARGYLGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I      +
Sbjct: 75  PLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKIATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             K+    R+M N++      E  A    + V     VL + +   +++TP    D    
Sbjct: 135 --KLFFNLRQMKNRLGWMSHEEVSAVANDLGVSR-EDVLVMEQRLNAMDTPYDAPDADDH 191

Query: 589 GDFIE----------DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +F            D  +V   + +     RE     L  L  R + +L+ R+      
Sbjct: 192 DEFYTAPERYLFNTNDDPSVMLENDSASDQGREKLMFALEQLDERSQDILQQRWL--SEE 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TL ++ K++ V+ ER+RQ+E  A++KLK    S
Sbjct: 250 KLTLHDLAKKYGVSAERVRQLEKNAMKKLKQYIES 284


>gi|21219133|ref|NP_624912.1| RNA polymerase sigma factor sig8 [Streptomyces coelicolor A3(2)]
 gi|256789847|ref|ZP_05528278.1| RNA polymerase sigma factor sig8 [Streptomyces lividans TK24]
 gi|289773730|ref|ZP_06533108.1| SigB [Streptomyces lividans TK24]
 gi|6670923|gb|AAF23070.1|AF068267_4 SigB [Streptomyces coelicolor A3(2)]
 gi|6448735|emb|CAB61294.1| RNA polymerase sigma factor sig8 [Streptomyces coelicolor A3(2)]
 gi|289703929|gb|EFD71358.1| SigB [Streptomyces lividans TK24]
          Length = 281

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 55/270 (20%), Positives = 132/270 (48%), Gaps = 21/270 (7%)

Query: 412 EIKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++  I+  + ++  + R +  +       + +G  E   A+  ++E N+ LV   A ++ 
Sbjct: 15  DMPEIADPSKVAPRDARELSKLFFEQLTVLEEGTPEHQYARNTLIEMNMSLVRFAAGRFR 74

Query: 465 NRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +RG  +  D++Q G IGL+KA ++F+     +F+++A+ ++   I R   D S  + +P 
Sbjct: 75  SRGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPR 134

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIG 581
            +++   ++ R    + +++ R PT  E+++ +++P + V +           SL+  I 
Sbjct: 135 RLQEARVQLARATEELRSRLGRTPTTAELSELMSLPEDEVVEARLAANGYNSASLDAAIN 194

Query: 582 --DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             ++  S L DFI   +A   L     A        ++A L  R+ +++  RF      +
Sbjct: 195 GSEDGESALADFIGADDAALALVDDFHA-----LAPMIAELDERDRQIIHWRFV----EE 245

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T +++G++  V++  + ++ ++ + +L+ 
Sbjct: 246 LTQKDIGERLGVSQMHVSRLISRLLARLRE 275


>gi|253699229|ref|YP_003020418.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
 gi|251774079|gb|ACT16660.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
          Length = 285

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/270 (24%), Positives = 115/270 (42%), Gaps = 11/270 (4%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I  +   +  I+    ++  E   +    R+       A   ++ +NLR V+ +A +Y +
Sbjct: 9   IDNLTLYLTEINRFPLLTADEEMDLACRFRR--EGDLEAAHRLITSNLRFVVKIAGEYRS 66

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH- 524
            G++ LDLIQEGNIGLM A  KFD   G +  +YA+WW++  I   I      ++I    
Sbjct: 67  YGMKMLDLIQEGNIGLMMAVRKFDPDKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQ 126

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIGD 582
             R    K+ +  + + N    E      A  L +     +++ +  +  +SL+      
Sbjct: 127 AQRKLFFKLNQAKQAIVNMTG-EGDLHAAAISLDVKDHEAQEMEQRLRGELSLDVEMFEG 185

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E      + + D         A +     L       L  L  +E  V+  R        
Sbjct: 186 EGGGTFLESLPDLRQNQEEMLAERQETTILERNVASALEDLNEKERFVIEQRVAAEN--P 243

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+E+   F ++RER+RQIE  A++K+K 
Sbjct: 244 MTLQEIADHFSISRERVRQIEEGALKKMKR 273


>gi|133473|sp|P26764|RPSF_BACLI RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|304173|gb|AAA22797.1| sporulation protein [Bacillus licheniformis]
          Length = 255

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 127/262 (48%), Gaps = 17/262 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  +  T +   E + +   ++  +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKENQNTQLKDHEVKEL---IKNSQNGDQKARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S    R PT +EIA  L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRAKEELSKSNGRIPTVQEIADYLEISSEEVVMAQEAVRSPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE+ ++ +R+      D T  EV  + 
Sbjct: 180 DQIADQSEEKWFD-------KIALKEAIKDLDEREKLIVYLRY----YKDKTQSEVADRL 228

Query: 650 CVTRERIRQIEAKAIRKLKHPS 671
            +++ ++ ++E K ++++K+  
Sbjct: 229 GISQVQVSRLEKKILKQIKNQM 250


>gi|66474623|gb|AAY46881.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIEIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|37784446|gb|AAO13116.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
          Length = 274

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 42/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF +  E              E        G       ++ +D S  +   E+ E D
Sbjct: 52  --SGFVNPDEA------------DEMGPTATHIGSELGEDDLADEDSSDEEEEDEDEEGD 97

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             + D D             +LR +       I                   + ++  + 
Sbjct: 98  GNDDDGDGGPDPEVAREKFAELRAQYEITRQSIRS-----------------NGRAHEET 140

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+   +   + +  F+  
Sbjct: 141 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVEQAKMPKKTFVSA 200

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +       A E D +L+   +++ I  ETG+SI++ + I   
Sbjct: 201 FTNNECETAWFEYQKQAGKAWSAPLAAME-DEVLRSIGKLQQIEEETGLSIAQIKDINRR 259

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 260 MSIGEAKARRAKKEM 274


>gi|182440445|ref|YP_001828164.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326781114|ref|ZP_08240379.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178468961|dbj|BAG23481.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326661447|gb|EGE46293.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 293

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/274 (20%), Positives = 121/274 (44%), Gaps = 26/274 (9%)

Query: 412 EIKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           E+  I     ++  + R +  +       + +G      A+  ++E NL LV   A ++ 
Sbjct: 22  ELPWIEDAGKVAPMDARRLSRLFFDRLQTLEEGTHAYQYARNTLIEMNLSLVRFAANRFR 81

Query: 465 NRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           NRG     D++Q G IGL+KA ++FD     +F+++A+ ++   I R   D S  + +P 
Sbjct: 82  NRGSGDMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPR 141

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIG 581
            +++    + +    ++  + R+PT +E+A+ L +    V + +  +      SL+ P  
Sbjct: 142 RLQELRVDLAKAKEALAGVLDRDPTAKELAEYLGIEESEVTEGIVASNGYTAGSLDMPTD 201

Query: 582 DEDTS-------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
             +            D + D +      +            +L  L  RE R++ MRFG 
Sbjct: 202 TAEAGPGQTAGRTFADVLGDPD-----PAMEAVENLHALAPLLDELDERERRIIDMRFG- 255

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + T  ++G +  +++  + ++ ++ + KL+
Sbjct: 256 ---QEMTQAQIGAELGISQMHVSRLLSRMLGKLR 286


>gi|261866928|ref|YP_003254850.1| RNA polymerase factor sigma-32 [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412260|gb|ACX81631.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 282

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 133/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K++V ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANEYPMLTAEEEKELAERL--YYKEDIEAAKKLVLSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  + V ++  ++T   ++ + P  + D 
Sbjct: 134 KLFFNLRKTKQRLG--WFNENEVDMVANELGVSPQDVMEMESRMTGADVAFDLPGDEHDE 191

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   +A   +     L +L  R + +++ R+     T  
Sbjct: 192 ETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDARSQDIIKARWLDE--TKA 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 250 TLQDLAAKYNISAERVRQLETNALKKLK 277


>gi|295837882|ref|ZP_06824815.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|197699594|gb|EDY46527.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 274

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 106/230 (46%), Gaps = 11/230 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM  V
Sbjct: 51  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 110

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D   T+ +P  + +   +V   A  ++    R PT  EIA++L +  + V 
Sbjct: 111 VGEIKRYFRDNVRTVHVPRRLHELWVQVNSAAEDLTTAHGRSPTTAEIAERLRIAEDEVL 170

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++   +    SLE     +    L D +  ++             R+    +L  L  
Sbjct: 171 ACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH-----RDLVRHLLVQLPE 225

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 226 REQRILLLRYYNN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 271


>gi|209696299|ref|YP_002264230.1| RNA polymerase factor sigma-32 [Aliivibrio salmonicida LFI1238]
 gi|208010253|emb|CAQ80584.1| RNA polymerase sigma-32 factor [Aliivibrio salmonicida LFI1238]
          Length = 286

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 69/288 (23%), Positives = 133/288 (46%), Gaps = 19/288 (6%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
              E  +      DSI    + ++S++    +++ + R +   +   E     A KE++ 
Sbjct: 1   MSKEMYSMAVVSQDSID---SYLRSVNRYPMLTVEKERDLAERLHYKEEI--EAAKELIL 55

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ++LR V+ VA+ Y+  GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I  
Sbjct: 56  SHLRFVVHVARGYSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHE 115

Query: 511 SIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            +      +++      R     + +  +R+      E   E +AK L +    VR++  
Sbjct: 116 YVLRNWRIVKVATTKAQRKLFFNLRKNKKRLGWFNNGE--VEAVAKDLGVSPSEVREMES 173

Query: 569 ITKEPISLETPIGDEDTSHLG-----DFIEDKNAV---SPLDSAIQANLRETTTRVLASL 620
                 S      ++D   +       ++EDK +    S  +   +          +A+L
Sbjct: 174 RLAAQDSTFEAPTEDDDRDMAFTAPVYYLEDKQSDIAHSLEEDNWEDYTNNRLANAIATL 233

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R + +++ R+    +   TL+E+   + V+ ERIRQ+E  A++KLK
Sbjct: 234 DDRSQHIVQSRWL--TDEKTTLQELANTYSVSAERIRQLEKNAMKKLK 279


>gi|304387988|ref|ZP_07370160.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
 gi|304337987|gb|EFM04125.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
          Length = 290

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 137 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|188585937|ref|YP_001917482.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350624|gb|ACB84894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 269

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 128/250 (51%), Gaps = 13/250 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ SE + +   +R G+ E   A+++++  NLRLV+SV +++ NRG    DL Q G +GL
Sbjct: 19  LNNSEMKELFEKMRVGDDEDE-ARQKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCVGL 77

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    +  
Sbjct: 78  IKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALQIRDELVE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K  REP   EIA+KL +  E V   L   ++P+SL  PI  +  D   + D I D+    
Sbjct: 137 KNSREPAISEIAEKLDVSEEQVVFALDAIQDPVSLFEPIYHDGGDPIFVMDQISDEKNQD 196

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                  A         L  L+ RE+ ++ +RF  G     T  EV ++  +++ ++ ++
Sbjct: 197 RTWLEEIA-----IKEGLHRLSSREKLIVNLRFFKG----KTQMEVAEEIGISQAQVSRL 247

Query: 660 EAKAIRKLKH 669
           E  A+ +LK 
Sbjct: 248 EKAALSQLKK 257


>gi|332976340|gb|EGK13196.1| DNA-directed RNA polymerase sigma subunit SigG [Desmospora sp.
           8437]
          Length = 259

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 81/265 (30%), Positives = 138/265 (52%), Gaps = 18/265 (6%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            RN+++   V+T     +   E R +   ++  E     A++++V  NLRLV+SV +++ 
Sbjct: 2   ARNKVEICGVDTSKLPVLKNEEMRALFRSLQ--EEGDRSAREKLVNGNLRLVLSVIQRFN 59

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGLMKA + FD     KFSTYA+  +   I R + D +  IR+   
Sbjct: 60  NRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS 118

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K ++    ++ +  REPT +EI+++L +  E V   L   ++P+SL  PI  + 
Sbjct: 119 LRDIAYKALQVRDSLTYRHSREPTIQEISEELNVSKEEVVFALDAIQDPVSLFEPIYQDG 178

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D  ++ D + D      L    +  LRE     +  L  RE+ +L MRF  G     T 
Sbjct: 179 GDPIYVMDQLADDENKD-LHWVEEIALRE----AMGRLNDREKMILSMRFFEG----KTQ 229

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
            EV ++  +++ ++ ++E  AI+++
Sbjct: 230 MEVAEEIGISQAQVSRLEKAAIQQM 254


>gi|91205341|ref|YP_537696.1| RNA polymerase factor sigma-32 [Rickettsia bellii RML369-C]
 gi|91068885|gb|ABE04607.1| RNA polymerase sigma-32 factor [Rickettsia bellii RML369-C]
          Length = 294

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 125/270 (46%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEEFLLAK--SYLEQNDLQAAHKLVTSHLKLVAKIATGYRTYGLPV 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 531 -----KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED 584
                K+      + ++        +IA +L + V  V    ++++   +SL   I ++D
Sbjct: 136 FFSLSKIKNKITNLYSRAITSDDFVQIADELGVSVSEVSDMNIRLSGSDLSLNNTINNDD 195

Query: 585 TS--HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
            S   L + + +        +  + ++   R   +  +  L  RE R+L  R      T 
Sbjct: 196 ASSGELIELLPETRPSPEAIAISKEDMTHKRALLSSAMKVLNARELRILTERKLQD--TP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDVLSSEYNISKERIRQIENTAFEKIKK 283


>gi|255312659|gb|ACU01739.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 79/194 (40%), Positives = 131/194 (67%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDLERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEVGK 647
           +      TLE+VG+
Sbjct: 182 LLGYEAATLEDVGR 195


>gi|224531828|ref|ZP_03672460.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
 gi|224511293|gb|EEF81699.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
          Length = 266

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 70/259 (27%), Positives = 139/259 (53%), Gaps = 8/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   +++    ++ AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIKLAGQIQR---GSAQAKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
            ED +    +     + L+     +   L  +E  +++ R+ +  +    TL+++  +  
Sbjct: 185 YEDNSFNPEITLEQDSTLKHLNYVLETKLNEKERYIIKKRYNLDNSPKKSTLKDISMELG 244

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++ E +RQIE + ++KLK 
Sbjct: 245 ISSETVRQIEKRVLKKLKE 263


>gi|52080136|ref|YP_078927.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|52785510|ref|YP_091339.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|319646086|ref|ZP_08000316.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
 gi|52003347|gb|AAU23289.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus licheniformis ATCC 14580]
 gi|52348012|gb|AAU40646.1| SigG [Bacillus licheniformis ATCC 14580]
 gi|317391836|gb|EFV72633.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
          Length = 259

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 139/264 (52%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +   + A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFKQMQ--DEGDTTAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  REPT +EIAK+L +  E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSREPTAQEIAKELEVSHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+   +     I+          +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDER--NKDSQWIEEL---ALKEGMRRLNEREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV  +  +++ ++ ++E  AI+++
Sbjct: 231 EVADEIGISQAQVSRLEKAAIKQM 254


>gi|326563747|gb|EGE13998.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 46P47B1]
          Length = 371

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/270 (25%), Positives = 124/270 (45%), Gaps = 11/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++  E R +    R        A + +V ++LR VI +A+ Y+  
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAE--RYYHDGDVEAARLLVMSHLRFVIHIARSYSGY 154

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 155 GLSQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKA 214

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ SN++  +     IA  L + V+ V     ++T    S E    D+D
Sbjct: 215 HRKLFFNLRSLKKSSNQLTLDEATA-IANDLNVTVKQVLEMESRLTSYDASFEAQDSDDD 273

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  +  ++AV+P D   +A+  E         +  L  R   ++  R+        
Sbjct: 274 EGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMEILDERSRDIITQRWLAD--QKS 331

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TL E+   + ++ ER+RQIE  A+ K+K  
Sbjct: 332 TLHELAATYNISAERVRQIEKNAMNKIKEA 361


>gi|239934518|emb|CAR94573.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 257

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/317 (17%), Positives = 117/317 (36%), Gaps = 61/317 (19%)

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
           ++ELL+REGEI IAKRIE G   +M ++   P T + ++     ++     L ++I    
Sbjct: 1   TVELLTREGEIVIAKRIEEGLRELMKAMALFPGTVEHILNEYALIDSEERRLNDLI---- 56

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
                                    + + +           + A     +D +     PE
Sbjct: 57  --------------------TGYPDTADDDIPPPAPQVTAADKADSDDDEDEAATGPDPE 96

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A+                                 E+ + Y++       + +  ++ +
Sbjct: 97  EAK-----------------------------IRFTELKKQYQK------TSNSVNRNGR 121

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRD 368
              + +   EKL +L  S  L   + + L++ +  +  R+  +E  ++ LA     + R 
Sbjct: 122 DHPRAEAELEKLGELFKSFKLTPRQFEPLLQHIRAVLTRLRRHEKTVMSLAVRGAKMPRK 181

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            F+    G E +  W+       +  +   +      +++ + +IK +  ETG++++E +
Sbjct: 182 EFITSFPGNETNEKWIDKHI-RAKKPYSELLVNVKTEVIRAQKKIKLLEEETGLTVTEIK 240

Query: 429 HIVSMVRKGECEASIAK 445
            I   +  GE ++  AK
Sbjct: 241 DINRQMSIGEAKSRRAK 257


>gi|56695321|ref|YP_165669.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56677058|gb|AAV93724.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 292

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 70/268 (26%), Positives = 124/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELALAYAWRDHRDEAALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAATD 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              + R    + IA ++ +P+  V  +  +++    SL      ++      + +ED++ 
Sbjct: 146 GLALDRHQLHQMIASEIGVPLRDVEMMEGRLSGSDFSLNATQASDEEGREWIEALEDESE 205

Query: 598 VSPL---DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +            LR+     + +L  RE  ++R R         TLE +G +  +++E
Sbjct: 206 QAAELVAHRHDTEQLRDWLIEAMQALNERERFIVRERKLRD--EPRTLESLGDELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    +RS++++ FL
Sbjct: 264 RVRQLEAAAFAKMRKSLEARSREVQHFL 291


>gi|85714568|ref|ZP_01045555.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85698453|gb|EAQ36323.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 272

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 122/261 (46%), Gaps = 13/261 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E       +R  E +   A   +V ++LRLV  +A  Y   GL   +++ EGN+GL
Sbjct: 2   LEPHEEYMFAKRLR--EHDDRDAAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           M+A ++F+   G++ +TYAMWW+K +I   I      +++      K     + +   ++
Sbjct: 60  MQAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKKLFFNLRKAKSKI 119

Query: 540 SNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDK 595
           S   + +  P++   IA++L +  + V  + +      SL  PI D+       D++ D+
Sbjct: 120 SALDEGDMRPDQVKLIARRLGVTEQDVVDMNRRLGGDASLNAPIRDDGEAGEWQDWLVDQ 179

Query: 596 NAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           +       A        R   T  +  L PRE R+   R         TLE++  +F V+
Sbjct: 180 SPTQEAVMAEHEEFDHRRRALTGAMGVLNPRERRIFEARRLAD--EPMTLEDLAAEFNVS 237

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
           RER+RQIE +A  K++   ++
Sbjct: 238 RERVRQIEVRAFEKVQSAVKT 258


>gi|294813860|ref|ZP_06772503.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326442278|ref|ZP_08217012.1| RNA polymerase sigma factor, sigma F [Streptomyces clavuligerus
           ATCC 27064]
 gi|294326459|gb|EFG08102.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 335

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 108/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 107 EHTRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTF 166

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 167 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRIPTTAEIAERLRIG 226

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 227 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 281

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 282 VQLPEREQRILMLRYYSN----LTQSQISQELGVSQMHVSRLLARSFARLRSANR 332


>gi|121535758|ref|ZP_01667560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121305657|gb|EAX46597.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 243

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 128/249 (51%), Gaps = 10/249 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   +   +++ +     AK+ ++E N+ LV S+  ++ NRG ++ DL Q G IGLMKA 
Sbjct: 3   EDAELKEWIKRAQAGDKQAKEYILEHNVNLVRSIVHRFLNRGYEWDDLFQIGCIGLMKAI 62

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           E+FD     KFSTYA+  V   I R I D     ++   +++  ++V RT  R+ + + R
Sbjct: 63  ERFDLNFNVKFSTYAVPMVIGEIRRFIRD-DNPTKVSRPVKELAYRVYRTQERLQSLLGR 121

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EPT  E+AK+LA+  + +   L+  + P SL      +D    GD I   + ++  D   
Sbjct: 122 EPTIHEVAKELALAPQEIVSALEAMQPPASLFEQAYHDD----GDPISRLDQIAQCDGQD 177

Query: 606 QANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            A   +     VL+ L P+E  V+ +RF      D T  E+     +++ ++ +IE +A+
Sbjct: 178 NAYFEKLALREVLSRLPPKERYVIHLRFF----EDKTQAEIANMIGLSQVQVSRIEKQAL 233

Query: 665 RKLKHPSRS 673
           R ++   ++
Sbjct: 234 RLIRDLMQT 242


>gi|114331030|ref|YP_747252.1| RNA polymerase factor sigma-32 [Nitrosomonas eutropha C91]
 gi|114308044|gb|ABI59287.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas eutropha C91]
          Length = 280

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 121/264 (45%), Gaps = 7/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E   +   ++  E     A  ++V ++LR V+ +A+ Y   GL
Sbjct: 15  LESYIRAANSFPVLSREEEISLAKKMQ--ENGDINAAHQLVLSHLRTVVMIARGYLGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA  +FD   G +  ++A+ W+K  I   I      ++I     + 
Sbjct: 73  PHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIKAEIHEFIMRNWRLVKIATTKPQR 132

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTS 586
           K+   +R+ +   + + +        +      E V    + +   ISLE     DE+  
Sbjct: 133 KLFFNLRSMKEGLDTMNQAEVATMAEQLGVKAEEVVEMETRFSGRDISLEPLTDSDEEDF 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
               ++ D +  S      Q            L SL  R  R++  R+ +  +   TL E
Sbjct: 193 SPIAYLTDGSDPSRELEKEQLERLTHAKLKDSLDSLDERSRRIIEARW-LREDKAATLHE 251

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           + K+  V+ ER+RQIEAKA++K++
Sbjct: 252 LAKELGVSAERVRQIEAKAMKKMR 275


>gi|330818365|ref|YP_004362070.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
 gi|327370758|gb|AEA62114.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
          Length = 311

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/273 (26%), Positives = 136/273 (49%), Gaps = 12/273 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I+S++    +++ E R   +  R      S   + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQSVNRIPMLTLEEERQYATEFRDQNNLES--ARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPNQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +A++L +  E V ++    +   I+LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKGMQAMTPE-EIDGLAQELNVKREDVAEMETRLSGGDIALEGQVDD 211

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRF---GIG 635
            + S   +    +  N  + + ++ Q +  +T   +  L SL  R  R++  R+      
Sbjct: 212 GEESFAPIAYLADSHNEPTAVIASRQRDRLQTDGISEALESLDARSRRIIEARWLNVEDD 271

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +   TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 272 GSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|218848158|ref|YP_002454701.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
 gi|218546289|gb|ACK98682.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
          Length = 295

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 88/293 (30%), Positives = 141/293 (48%), Gaps = 14/293 (4%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F       I K  NEI +  + T     E      +++  E     +++ ++ +NLRLV+
Sbjct: 3   FNKRNSSEIGKYLNEICNYDILTDEQSME-----HIIKYKEKGDIDSRELLICSNLRLVV 57

Query: 458 SVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           SVAK +   G    +++IQEG IGLMK  E +D+  G K STY  WW++Q I++ ++   
Sbjct: 58  SVAKSFPCYGNCDLMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINR 117

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +R+   M+ KI +V         +     T  E+A++L      V   L   +   ++
Sbjct: 118 SDVRVATTMQKKITEVKNCYYENMGEKGTNLTTMEVAERLGYKESIVIDALVTDRITNTI 177

Query: 577 ETPIGDEDTSHLGD-------FIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVL 628
                 ++   L D        + +KNA +P +       +     ++  +L PREE VL
Sbjct: 178 SIEDDVQNEKTLLDRQQSTLAILANKNAPNPSEVMATEEEKFEFDELMFVTLNPREESVL 237

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           R RFG     + TLE+  +   VTRER++QIE KAI K+K    SKK+ SF +
Sbjct: 238 RYRFGFDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQRLSSKKINSFQE 290


>gi|161869654|ref|YP_001598821.1| RNA polymerase factor sigma-32 [Neisseria meningitidis 053442]
 gi|161595207|gb|ABX72867.1| RNA polymerase sigma-32 factor [Neisseria meningitidis 053442]
 gi|316983693|gb|EFV62674.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
 gi|325140133|gb|EGC62662.1| alternative sigma factor RpoH [Neisseria meningitidis CU385]
 gi|325200603|gb|ADY96058.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
          Length = 287

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 70/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNRIPMLTQEEETRLAER---QHKGDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HQLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|295836570|ref|ZP_06823503.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826098|gb|EDY44232.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 338

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 115/240 (47%), Gaps = 11/240 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +       +  +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD 
Sbjct: 101 LRTLEPESAAYAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDP 160

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA   V   I R   D+   +R+P  +++    +      +S    R PT  
Sbjct: 161 ERGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLSLTSATAELSQLHGRSPTVH 220

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A++L++  E V + L+       +SL+ P  D+++  + D +  ++            
Sbjct: 221 ELAQRLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY---- 276

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+   +L  L PRE+R+L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 277 -RESLKPLLEDLPPREKRILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 331


>gi|254294740|ref|YP_003060763.1| RNA polymerase factor sigma-32 [Hirschia baltica ATCC 49814]
 gi|254043271|gb|ACT60066.1| RNA polymerase, sigma 32 subunit, RpoH [Hirschia baltica ATCC
           49814]
          Length = 295

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 70/275 (25%), Positives = 122/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   + +  R  + E   A ++MV ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLTEIRKYPLLEKDQEFMLANRWR--DHEDPEAAEKMVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTAAQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPI-G 581
                  ++    + +     R     EIA +L +   E +    ++T    SL  PI G
Sbjct: 134 KLFFNLRRLKGEIQALEEGDLRPENVAEIATRLNVSETEVISMNRRMTGGDASLNAPIGG 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMN 637
            +      D++ D N  +  +   Q +            +  L  RE+ ++        +
Sbjct: 194 ADGDGEWMDWLSDDNQQNQAEEYEQNDEFSTRMSLLETAMEGLNEREKHIIAE--RRLKD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+   + V+RERIRQIE +A  KL+   +
Sbjct: 252 EPSTLEELSAVYNVSRERIRQIEVRAFEKLQKAMK 286


>gi|239934562|emb|CAR94595.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 217

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 97/263 (36%), Gaps = 47/263 (17%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLT+  ++   +++  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSNYPLTYTFMLNQYEQVKA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L +II            GF             +          +    + E     
Sbjct: 61  GQGRLVDII-----------VGFIDPNAPDEIAAPVNPKLAAAAAPAEPEAEEEEEGGDS 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             ++  +    PE A                   A   +L  +V+ +L+E          
Sbjct: 110 EDEEALETGPDPEEAARRF---------------ASIQKLHQQVVKSLEE---------- 144

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                           K + L++K+ +    L L+    D L+ Q+ +    + + E  +
Sbjct: 145 ----------KGLDDPKTQKLRKKVAQEFMELKLSPKMFDALIVQMREHVAEVRNLEKSV 194

Query: 357 LRLAQS-YGIKRDVFLERHQGRE 378
           + L     G+ R  F+      E
Sbjct: 195 MMLCVRDAGMPRRDFITTFPKNE 217


>gi|153840380|ref|ZP_01993047.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
 gi|149745954|gb|EDM57084.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/265 (25%), Positives = 125/265 (47%), Gaps = 17/265 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + ++ +R+      E   E +A++L +    VR++        S      D+D S
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE--VETVARELGVEPSEVREMESRLAAVDSTFDMPTDDDDS 191

Query: 587 ------HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                     ++EDK+   A +   +  + +        LASL  R +R++R R+     
Sbjct: 192 ATSSYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDD-- 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAK 662
              TL+++  +F V+ ERIRQ+E  
Sbjct: 250 EKATLQDLADEFGVSAERIRQLEKN 274


>gi|229586560|ref|YP_002845061.1| RNA polymerase factor sigma-32 [Rickettsia africae ESF-5]
 gi|228021610|gb|ACP53318.1| RNA polymerase sigma-32 factor [Rickettsia africae ESF-5]
          Length = 293

 Score =  129 bits (325), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 130/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEELLLAK--SYLEGNDLQAAHKLVTSHLKLVAKIASGYRTYGLPM 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRTITTDDFVQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 196 AESGELIELLPETRPTPETMAINKQNSTSKRQLLSNAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|300721688|ref|YP_003710964.1| sigma H (sigma 32) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297628181|emb|CBJ88736.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus nematophila ATCC
           19061]
          Length = 285

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 115/242 (47%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLDAAKKLILSHLRFVVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +  +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFNQDEI--ELVAK 159

Query: 555 KLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++   +        +     + D+  +   +  ++  S     I+ +  E
Sbjct: 160 ELGVTSKDVREMESRMSAQDMAFDMSADDDNHDSQPVAPVLYLQDKASDFADGIEEDNWE 219

Query: 612 -----TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  +  +  L  R + ++R R+ +      TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 NHAADKLSVAMEGLDERSQDIIRARW-LDDENKTTLQELADKYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|284156787|gb|ACM45450.2| RNA polymerase sigma-70 factor [Aeromonas fluvialis]
          Length = 271

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 115/315 (36%), Gaps = 45/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E +D+  T   I S       D    +   E+ + D
Sbjct: 59  ------------------------ETEDMAPTATHIGSELSEEDLDDEDEEEEDEDEDGD 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             + D D             +LR +       I                 QK+ ++    
Sbjct: 95  NSDDDGDGGPDPEVAREKFGELRAQYEVTRLSI-----------------QKNGRAHQDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 257 MSIGEAKARRAKKEM 271


>gi|320010407|gb|ADW05257.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 326

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 113/241 (46%), Gaps = 8/241 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +G  E +  +  +VE NL LV   A ++  R     D++Q G IGL+KA ++F+ 
Sbjct: 86  LEALEEGTHEYAYVRNTLVELNLALVKFAASRFRTRSEPMEDIVQVGTIGLIKAIDRFEL 145

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  +   I R   D S ++R+P  +++    + +    +S ++ R PT  
Sbjct: 146 SRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELSQQLDRAPTVA 205

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L +  + V + +         SL+    D    + G   +           I+  
Sbjct: 206 ELADRLGLSRDEVVEGMAASNAYTASSLDAKPDDHGDGNEGALADRLGYEDNGLEGIE-- 263

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E+   ++ASL  R+  +L MRF        T  E+G++  +++  + ++ ++ + KL+
Sbjct: 264 YIESLKPLIASLPLRDRTILSMRFVSN----MTQSEIGEELGISQMHVSRLLSRTLVKLR 319

Query: 669 H 669
            
Sbjct: 320 K 320


>gi|157964378|ref|YP_001499202.1| RNA polymerase factor sigma-32 [Rickettsia massiliae MTU5]
 gi|157844154|gb|ABV84655.1| RNA polymerase sigma-32 factor [Rickettsia massiliae MTU5]
          Length = 310

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 130/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 35  SYLQKINKIPSLTQEEELLLAK--SYLEGNDLQAAHKLVTSHLKLVAKIASGYRTYGLPI 92

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 93  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 152

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 153 FFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 212

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 213 AESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTERKL--TDTP 270

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 271 KTLDILSNEYNISKERIRQIENTAFEKIKK 300


>gi|121730259|ref|ZP_01682638.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
 gi|121627991|gb|EAX60548.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
          Length = 259

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 128/259 (49%), Gaps = 15/259 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +         A K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGL
Sbjct: 2   LSADEERELAERL--HYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRM 539
           MKA ++F+  +G +  ++A+ W+K  I   +      ++I      R     + ++ +R+
Sbjct: 60  MKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-----FIED 594
                 E   E +A++L +    VR++        +      ++D + +       ++ED
Sbjct: 120 GWFNNGE--VETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYLED 177

Query: 595 KN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           K+   A +      +A+  +  +  LASL  R + ++R R+ +  +   TL+++ + + V
Sbjct: 178 KHSDLADNLEAENWEAHTTQRLSMALASLDERSQHIVRARW-LDDDNKTTLQDLAEMYGV 236

Query: 652 TRERIRQIEAKAIRKLKHP 670
           + ERIRQ+E  A+RKLK  
Sbjct: 237 SAERIRQLEKNAMRKLKEA 255


>gi|99080297|ref|YP_612451.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036577|gb|ABF63189.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 292

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 126/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       + +   A   ++ A +RL +S+A K+   G    DLIQE  +GLMKAAEKF
Sbjct: 26  ELALAYAWRDEKDVQALHRLITAYMRLAVSMASKFRRYGAPMNDLIQEAGLGLMKAAEKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQAQLEREAAGE 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET-PIGDEDTSHLGDFIEDKN- 596
             ++ R    + +A+++ +P+  V  +  ++     SL      DED     D +ED + 
Sbjct: 146 GVELDRHKLMQMVAEEIGVPLRDVEMMDGRLAGADFSLNAVQSADEDGREWIDALEDDSE 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A        +  LRE     L  L  RE  ++R R         TLE +G +  +++E
Sbjct: 206 QAADRVEADHDRRQLREWLLSALNGLNERERFIVRERKLRE--EARTLESLGNELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  K++     +S+++++FL
Sbjct: 264 RVRQLEAAAFSKMRKSLEGQSREVQNFL 291


>gi|254818833|ref|ZP_05223834.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 242

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 110/243 (45%), Gaps = 10/243 (4%)

Query: 430 IVSMVRKGECEASIAKKE--MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            V++ R        A++   +V   L L   VA  +  RG    DLIQ   +GLM A  +
Sbjct: 2   FVALHRMPAESHEYARQREYIVARCLPLADHVASHFARRGEGLEDLIQVARLGLMNAVNR 61

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G  F  +A+  +   + R   D S  +R+P  +R+   ++ R    ++ ++ R P
Sbjct: 62  FDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHVQISRATADLAQQLGRAP 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
              E+++ L +P E + + L         SL+ P+G + +       +    + P    I
Sbjct: 122 NAGELSQMLEVPREEIVECLVAGDAYRLDSLDAPLGADSSGTPRSVADSVGDIDPQIEHI 181

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               RE    ++A+L PRE  VLRMRF        T  ++ ++  V++ ++ +I A  +R
Sbjct: 182 TN--REALRALVATLPPRERDVLRMRFF----ESMTQSQIAERIGVSQMQVSRILANTLR 235

Query: 666 KLK 668
            L+
Sbjct: 236 CLR 238


>gi|33520062|ref|NP_878894.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia floridanus]
 gi|33504408|emb|CAD83301.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia floridanus]
          Length = 283

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 135/267 (50%), Gaps = 12/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ ++   +++ E + +   +         A K+++ ++LR VI VA+ Y+  GL
Sbjct: 17  LEAYIRAANLYPMLTVEEEQKLAKNL--YYNGDLNAAKKLIVSHLRFVIHVARNYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMK+  +F+  L  +  ++A+ W+K  I   +      ++I      R
Sbjct: 75  SQADLIQEGNIGLMKSIRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWRIVKIATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   E +AK L +  + VR++  ++  + ++LE P  DED 
Sbjct: 135 KLFFNLRKTKQRLG--WFNEGEIEMVAKTLHVTCKDVREMESRMAAQDMTLEQPYLDEDD 192

Query: 586 SHLGD----FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            ++      +++DK  +   +      +       L +L  R + ++R R+ +  +   T
Sbjct: 193 KNILSIPMLYLQDKITIIDDEEEWIDQVSNKLNIALNTLDKRSQHIIRARW-LNADNKTT 251

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+  Q+ ++ ERIRQ+E  A++K+K
Sbjct: 252 LQELANQYGISAERIRQLEKNAMKKMK 278


>gi|328948495|ref|YP_004365832.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
 gi|328448819|gb|AEB14535.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
          Length = 349

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 74/267 (27%), Positives = 119/267 (44%), Gaps = 12/267 (4%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLI 474
           ++    I   + R   +++ + +     A   M E  LR V+ ++  +       F +  
Sbjct: 93  VAHIKSIKPPQHREWKNLIYEAQSGNVYAFNRMTEMYLRGVLRISYNFAKENYCDFEEAF 152

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G IGL++A + FD      F++Y    V   + R  + ++    +PVH   K  + + 
Sbjct: 153 QNGTIGLIRAIKNFDVTSPNSFASYYSLSVLSEMQRKYSVKNSFFDLPVHFSQKTFEFLG 212

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +   K K       I       +E   K+       + L+    +     +   IED
Sbjct: 213 IISKYLAKGKTPEESIGIIS-DDFYLEINPKLKMYFLPYLDLDAISYENFAFDI--HIED 269

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                     I  +L+E    VL +L  RE +VL MRFG+      TLEEVGK + V+RE
Sbjct: 270 D--------IIYESLKEQLNEVLHTLPERERKVLEMRFGLNNLKQMTLEEVGKYYNVSRE 321

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RIRQIE KA+R+L+HP R+  LR ++D
Sbjct: 322 RIRQIEKKALRRLRHPHRASGLRDYID 348


>gi|224534531|ref|ZP_03675107.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
 gi|224514208|gb|EEF84526.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
          Length = 266

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 145/260 (55%), Gaps = 10/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   +++G    + AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIQLAGQIQRGN---AQAKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQF 649
            ED N+ +P  +  Q +  +    +L + LT +E  +++ R+ +  +    TL+++  + 
Sbjct: 185 YED-NSFNPEITLEQDSTIKHLNYILETKLTEKERYIIKKRYNLDNSPKKSTLKDISTEL 243

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            ++ E +RQIE + ++KLK 
Sbjct: 244 GISSETVRQIEKRVLKKLKE 263


>gi|302551910|ref|ZP_07304252.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302469528|gb|EFL32621.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 304

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/246 (23%), Positives = 120/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 62  LFERLESLEEGTHEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 121

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R 
Sbjct: 122 RFELSRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRA 181

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 182 PTVTELAERLGISNDEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGIE 241

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L PR+ ++L +RF  G     T  E+G++  +++  + ++ ++ 
Sbjct: 242 YV-----ESLKPLIAELPPRDRKILSLRFVAG----LTQSEIGEELGISQMHVSRLLSRT 292

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 293 LVRLRK 298


>gi|57996878|emb|CAI45887.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 77/190 (40%), Positives = 126/190 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL +A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLE 643
           +      TLE
Sbjct: 182 LLGYEAATLE 191


>gi|251793696|ref|YP_003008426.1| RNA polymerase factor sigma-32 [Aggregatibacter aphrophilus NJ8700]
 gi|247535093|gb|ACS98339.1| alternative sigma factor RpoH [Aggregatibacter aphrophilus NJ8700]
          Length = 282

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  E + +   +     E   A K++V ++LR VI VA+ Y+  GL
Sbjct: 16  LEAYIRAANEYPMLTAEEEKELAERL--YYQEDIDAAKKLVLSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R       E   + +A +L +  + V ++  ++T   ++ + P  D D 
Sbjct: 134 KLFFNLRKTKQRFG--WFSENEVDMVANELGVSPQDVVEMESRMTGADVAFDLPTDDHDE 191

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK    A    +   +A   +     L +L  R + +++ R+     T  
Sbjct: 192 ETYAPALYLEDKGSNFAAELENENYEAQATDRLAVALDNLDARSQDIIKARWLDE--TKA 249

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+++ +++ ++ ER+RQ+E  A++KLK
Sbjct: 250 TLQDLAEKYNISAERVRQLETNALKKLK 277


>gi|333022810|ref|ZP_08450874.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332742662|gb|EGJ73103.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 275

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 111/245 (45%), Gaps = 14/245 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              +  +VE  L +   +A +Y  RG    DL Q   +GL+KA ++FD  +   F +YA+
Sbjct: 37  ERQRSRLVETWLPMAHRIAGRYRERGENLEDLCQVAALGLVKAVDRFDPEVSDAFESYAV 96

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPV 560
             ++  + R   D +  + +P  +++  + V    + ++ +   R P+  E+A+   +  
Sbjct: 97  PTIRGELKRHFRDNTWGVHVPRRVQELRNAVRTALQELAPRTAPRTPSVAELAESAKLGE 156

Query: 561 EGVRKVLKI--TKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVL 617
           E VR+ L+   +  P+SL+     E    L D +  D  A + +        RE+    L
Sbjct: 157 EEVRRGLEALDSYRPVSLDGTPTPEGEHPLRDRLGADDPAYAIVVD------RESVRPAL 210

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
           A L  RE  +L +RF        T   +  +  +++  + ++  +A  ++KH   ++  R
Sbjct: 211 AELPERERYILYLRFFH----ARTQRAIAAELGLSQMHVSRLITQACAQVKHRVEARPPR 266

Query: 678 SFLDG 682
           + L G
Sbjct: 267 AVLTG 271


>gi|261414351|gb|ACX83584.1| RNA polymerase sigma-70 factor [Aeromonas taiwanensis]
          Length = 272

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + IL+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEILRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|163941643|ref|YP_001646527.1| sporulation sigma factor SigG [Bacillus weihenstephanensis KBAB4]
 gi|229134713|ref|ZP_04263522.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|163863840|gb|ABY44899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228648759|gb|EEL04785.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|322510150|gb|ADX05464.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 135/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 36  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 95

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 96  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 154

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 155 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 214

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D ++D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 215 FVMDQLKDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 265

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 266 EEIGISQAQVSRLEKSAIKQM 286


>gi|146313497|ref|YP_001178571.1| RNA polymerase factor sigma-32 [Enterobacter sp. 638]
 gi|145320373|gb|ABP62520.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter sp. 638]
          Length = 285

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 117/242 (48%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K ++ ++LR V+ VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKTLILSHLRFVVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +  +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFNQEE--VEMVAR 159

Query: 555 KLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++   +        + +    +D+  +   +  ++  S     I+ +  E
Sbjct: 160 ELGVSSKDVREMESRMAAQDMTFDMSSDDDAQDSQPMAPVLYLQDKTSNFADGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  T  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 DQAANKLTHAMEGLDERSQAIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|159045518|ref|YP_001534312.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157913278|gb|ABV94711.1| RNA polymerase sigma 32 factor [Dinoroseobacter shibae DFL 12]
          Length = 293

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/268 (27%), Positives = 120/268 (44%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 27  ELRLAYAWRDQRDEEALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKF 86

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 87  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAASA 146

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              + R    + IA ++ +P+  V  +  ++     SL      ED      D +ED  A
Sbjct: 147 GEPLDRHQLRQMIATEVGVPLHDVEMMEGRLAGSDYSLNATQSTEDEGREWIDTLEDTGA 206

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +        +   LR      + +L  RE  ++R R         TLE +G++  +++E
Sbjct: 207 QAAELVEQDHDIETLRGWLITAMDALNERERFIVRERKLRD--QPRTLESLGQELGLSKE 264

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  K++     +S ++R F 
Sbjct: 265 RVRQLEAAAFGKMRKNLMNQSSEVRQFF 292


>gi|1552544|emb|CAA90874.1| sigma factor [Bacillus coagulans]
          Length = 252

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 128/260 (49%), Gaps = 17/260 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K    +  +   E +++   +R+ E     A+  +VE N+RLV SV  ++ NRG +  
Sbjct: 4   ELKKAENKARLKDEEVKNL---IRRTEEGDQEARDLIVEKNIRLVWSVVHRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  ++
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKETGNR 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    ++ K+ R PT  EIA +L MPVE V    +  K P S+   + + D     L 
Sbjct: 120 IRKIRDELTKKLGRSPTVHEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+N     D              +  L  RE  ++ +R+      D T  E G++ 
Sbjct: 180 DQISDQNDQKWFDQI-------ALQEAIRGLEERERLIVYLRY----YKDQTQSEAGERL 228

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ ++E K +R +K 
Sbjct: 229 GISQVQVSRLEKKILRVMKE 248


>gi|307824191|ref|ZP_07654417.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734571|gb|EFO05422.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 391

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 129/230 (56%), Gaps = 2/230 (0%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              +++M+  N+RL   VA K+    L F DL+QEG +GL+KA ++FD   GY+FSTYA+
Sbjct: 146 QRLRQQMIAGNVRLAAFVAHKHKTTVLSFDDLLQEGVVGLIKAVDRFDPYRGYQFSTYAI 205

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
            W+KQAI+R I  Q   +R+PV + ++   V    R    + +R P+ E++     +  +
Sbjct: 206 PWIKQAISRLIVKQEKIVRLPVALAERACAVFEAMRNAYLQTERWPSIEQLKSLCDLSED 265

Query: 562 GVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            ++ +    +   SL+     E+     L   ++ +    PLD  I  NL     +V+A+
Sbjct: 266 EIKTIRNYYQATHSLDAVGDAEEDEGQALMARMKQRQFALPLDELIDRNLGRYLDQVVAT 325

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  +E  +L MRFG+  +T+ TL+ +  Q  V+RER+RQI+  A++KLK+
Sbjct: 326 LPDKEAAILNMRFGLKNHTEMTLQAIADQLQVSRERVRQIQNDALKKLKN 375


>gi|290962881|ref|YP_003494063.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652407|emb|CBG75540.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 275

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 119/250 (47%), Gaps = 15/250 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   ++++ +G       +  ++E NL LV   A ++  R     D++Q G IGL+KA
Sbjct: 26  RQFFDRLAVLDEGTHTYQYVRNTLIEMNLSLVRYAASRFRGREDSLEDIVQVGTIGLIKA 85

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+T+A+ ++   I R   D S  + +P  +++   ++ R    + +++ 
Sbjct: 86  IDRFELSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELARATDELQSRLG 145

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIG----DEDTSHLGDFIEDKNAV 598
           R PT  E+++ +++  E V +  K +      SL+  +     D+  + LGD I +++  
Sbjct: 146 RMPTTRELSELMSLSEEEVIEARKASNGYNTSSLDAALTSDGGDDGDAVLGDLIGEEDHA 205

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             L     +        ++A L  RE R++ +RF          EE      V++  + +
Sbjct: 206 LQLVEDFHS-----LAPLIAQLDDRERRIIHLRFVEEWTQSQIAEE----LGVSQMHVSR 256

Query: 659 IEAKAIRKLK 668
           + ++ I++L+
Sbjct: 257 LISRIIKRLR 266


>gi|326791514|ref|YP_004309335.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
 gi|326542278|gb|ADZ84137.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
          Length = 249

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/255 (21%), Positives = 117/255 (45%), Gaps = 15/255 (5%)

Query: 425 SEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIG 480
            E + + +          +  K  ++E  + LV  VA +   Y N+ +   DL+  G +G
Sbjct: 1   MEKKDMNAVWAEYVGTRDTALKSSLIEHYVYLVKLVAGRLGIYLNQYVDSDDLVGYGVLG 60

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+ A +KFD     KF TYA   ++ AI  +I        +P  +R K   + +    + 
Sbjct: 61  LIDAVDKFDPGKNVKFETYASLRIRGAILDAIRKLDW---VPRTLRKKQKDIDKAYIELE 117

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
            ++ R+P  EE+A  L + +E   ++L    + +++ + I  ++  +  + ++D +A  P
Sbjct: 118 GRLGRQPLDEEVADFLEISIEEYNELL----KEVNISSLISIDEYMYQFESVKDPSAPIP 173

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            +      ++E     + SL  RE++V+ + +      + TL+E+     V+  R+ Q+ 
Sbjct: 174 ENYIEDTEVKEMLAEFIDSLPEREKKVIFLYY----YEELTLKEISHVLEVSESRVSQLH 229

Query: 661 AKAIRKLKHPSRSKK 675
            KA+ +L+   +   
Sbjct: 230 TKAVSRLRAYMQKHH 244


>gi|187763322|gb|ACD35538.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    EG                DV  T   I S            D   +  E+ 
Sbjct: 52  --SGFIDPNEGX---------------DVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|196047982|ref|ZP_03115160.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
 gi|196021238|gb|EDX59967.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
          Length = 289

 Score =  129 bits (324), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 86/272 (31%), Positives = 146/272 (53%), Gaps = 6/272 (2%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             +  ++    +  I   + ++  E +  +   +  E     A++ ++E NLRLV+SV  
Sbjct: 3   NRNDSVEYNLYLNEIGQHSLLTEEEEKMYLRKYK--ENGDMEARRILIECNLRLVVSVVN 60

Query: 462 KYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
            Y   G  + +D+IQ GN+GL++  E F+     K +TY  WW++  I+R I      IR
Sbjct: 61  SYPRVGNCEKMDMIQVGNVGLIRGIEAFEISKNCKLATYVTWWIRHEISRFITFNKNDIR 120

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLET 578
             V +++K+ K+ +     + K KR+   E+IA++L   VE V +++   + KE +SL+ 
Sbjct: 121 CSVTIQNKMDKLKKYFSNENGKAKRKLNIEQIAEELGYSVETVLQIMDTLMLKESVSLDA 180

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMN 637
           P  DED+  + + +++  A +P++             +L + L  +EE V+R RFG    
Sbjct: 181 PSSDEDSRPVMNSVKNAKAPNPVELITSEEQLYQIEELLFTVLNEKEESVIRYRFGFDTE 240

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            D TLEEV + F +TRERI+QIE KAI KLK+
Sbjct: 241 KDLTLEEVARIFGITRERIQQIEKKAIGKLKN 272



 Score = 37.9 bits (86), Expect = 5.7,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 123 MYLREMGSIELLSREGEIAIAKR-IEAGRAMMMASLCESPLT-FQALIIWRDELNDGTTL 180
           +YL E+G   LL+ E E    ++  E G       L E  L    +++     + +   +
Sbjct: 12  LYLNEIGQHSLLTEEEEKMYLRKYKENGDMEARRILIECNLRLVVSVVNSYPRVGNCEKM 71


>gi|329937605|ref|ZP_08287124.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329303004|gb|EGG46892.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 292

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 123/249 (49%), Gaps = 14/249 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   +S++ +G  E   A+  ++E N+ LV   A ++ NRG    D++Q G IGL+KA
Sbjct: 39  RQFFQRLSVLEEGTHEYQYARNTLIEMNMSLVRFAAGRFRNRGDDMEDIVQVGMIGLIKA 98

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +S+++ 
Sbjct: 99  IDRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELSSRLD 158

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDED---TSHLGDFIEDKNAVS 599
           R+PT  E+A  + +P + V +           SL+  +  ED    + L DFI  ++   
Sbjct: 159 RDPTVAELATLMNLPEKDVVEAQIAANGYNSSSLDAALSGEDQDGEAVLSDFIGAEDEAM 218

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L          T   ++A L+ R+ R++ MRF      + T  ++G Q   ++  + ++
Sbjct: 219 GLVEDFH-----TLAPLVAELSERDRRIIHMRFV----EEATQADIGAQLGCSQMHVSRL 269

Query: 660 EAKAIRKLK 668
             + I +L+
Sbjct: 270 IKRIIEQLR 278


>gi|297197353|ref|ZP_06914750.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197714848|gb|EDY58882.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 263

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 106/244 (43%), Gaps = 13/244 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E +A   + E+VE  L +   +A ++  RG    DL Q   +GL+KA +
Sbjct: 22  FERLAQLPDGTERKAL--RDELVELWLPMAERIAVRFRGRGESLEDLYQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F  YA+  V   I R   D   T+ +P  ++D  ++V + ++ +S    R 
Sbjct: 80  HYDPARGSAFEAYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRQASKELSQTPGRA 139

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  EIA++  +  + VR   +  +    +SLE  +   D   LGD +   +    +   
Sbjct: 140 PTVAEIAERAHLTEDEVRAGAEALECFSALSLEAEMPGTDGYALGDALGVPDPGYDVVVD 199

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                R      L +L  RE  +L +RF  GM      EE      +++  + ++ +   
Sbjct: 200 -----RVAVGPCLKALPERERTILYLRFFRGMTQSCIAEE----LGISQMHVSRLLSTCF 250

Query: 665 RKLK 668
            +L+
Sbjct: 251 AQLR 254


>gi|15676610|ref|NP_273754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis MC58]
 gi|7225940|gb|AAF41127.1| RNA polymerase sigma-32 factor [Neisseria meningitidis MC58]
          Length = 290

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 70/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNRIPMLTQEEETRLAER---QHKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 137 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|187763306|gb|ACD35530.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 272

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEGEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVRERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|126729201|ref|ZP_01745015.1| RNA polymerase sigma factor [Sagittula stellata E-37]
 gi|126710191|gb|EBA09243.1| RNA polymerase sigma factor [Sagittula stellata E-37]
          Length = 298

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 125/275 (45%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   +   +    R  E E + A  ++V ++LRL   +A  Y   GL
Sbjct: 16  LSRYLQEIRKFPLLEPEQEYMLAK--RWVEDEDTQAAHQLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   + +   R    E+IA  L +  + V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKSRIGALEDGDLRPEHVEKIATDLGVTQDEVISMNRRLSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    + A +  L   R    + +  L  RE  +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGEYAERNELEARRALLEQAMDVLNDRERDILSQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 QAVTLEELSGQYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|66474693|gb|AAY46916.1| RpoD [Aeromonas veronii bv. sobria]
          Length = 272

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II        
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-------- 52

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
               GF    E                          E  A  +    S++       E+
Sbjct: 53  ---SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADED 84

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           +E   DEDED                      E+   Y          ++ QK+ ++   
Sbjct: 85  EEDEEDEDEDGDNSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 258 RMSIGEAKARRAKKE 272


>gi|66474615|gb|AAY46877.1| RpoD [Aeromonas veronii bv. sobria]
 gi|66474625|gb|AAY46882.1| RpoD [Aeromonas veronii bv. sobria]
 gi|66474663|gb|AAY46901.1| RpoD [Aeromonas veronii]
 gi|66474691|gb|AAY46915.1| RpoD [Aeromonas veronii bv. sobria]
          Length = 272

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 116/315 (36%), Gaps = 44/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II        
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-------- 52

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
               GF    E                          E  A  +    S++       E+
Sbjct: 53  ---SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADED 84

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           +E   DEDED  +                   E+   Y          ++ QK+ ++   
Sbjct: 85  EEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHED 138

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 139 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 198

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I  
Sbjct: 199 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINR 257

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 258 RMSIGEAKARRAKKE 272


>gi|121999080|ref|YP_001003867.1| RNA polymerase sigma-32 subunit RpoH [Halorhodospira halophila SL1]
 gi|121590485|gb|ABM63065.1| RNA polymerase, sigma 32 subunit, RpoH [Halorhodospira halophila
           SL1]
          Length = 287

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/266 (24%), Positives = 120/266 (45%), Gaps = 15/266 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+++S    +   E   +    R        A +++V ++LR V+ VA+ Y   GL   
Sbjct: 23  YIQAVSQIPVLDADEEYELAR--RCQYEGDLDAARQLVLSHLRFVVHVARGYRGYGLALG 80

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      +++      +  K
Sbjct: 81  DLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQR--K 138

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAM---PVEGVRKVLKITKEPISLETPIGDEDTSH- 587
           +    R    ++      E  A    +   P   +    +++ + +  +  + +ED    
Sbjct: 139 LFFNLRGAKKRLGWMTREEVNAVAEDLGVQPETVLEMESRLSGQDLGFDPLVSEEDEEQA 198

Query: 588 --LGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED     A     S    +  ++  + L  L  R + +LR R+        TL
Sbjct: 199 RAPVAYLEDRRFDPAEVVESSDWGTHQDDSLHQALGQLDERSQNILRARWLEE--ERQTL 256

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+ +++ V+ ERIRQ+E  AI KL+
Sbjct: 257 QELAERYGVSAERIRQLEKNAISKLR 282


>gi|77464172|ref|YP_353676.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126463015|ref|YP_001044129.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221640041|ref|YP_002526303.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332559048|ref|ZP_08413370.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|77388590|gb|ABA79775.1| sigma factor RpoH2 (Sigma-32 group [Rhodobacter sphaeroides 2.4.1]
 gi|126104679|gb|ABN77357.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221160822|gb|ACM01802.1| RNA polymerase, sigma 32 subunit, RpoH precursor [Rhodobacter
           sphaeroides KD131]
 gi|332276760|gb|EGJ22075.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 292

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 123/268 (45%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A KY   G    DLIQE ++GLMKAA+KF
Sbjct: 26  ELRLAYAWRDQRDERALHRLITAYMRLAISMASKYRRYGAPMNDLIQEASLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQS---------CTIRIPVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +                 +  +MR    ++ R A + 
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSLVRTGSTSSQKALFFNMRRVQARLEREASQR 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              +      E +A  + +P+  V  +  +++    SL      +D      D +ED +A
Sbjct: 146 GEALDAHQLREMVAHDVGVPLSDVEMMEGRLSGSDFSLNATQSADDEGREWIDALEDDSA 205

Query: 598 VS---PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +      S   A LR      +  L  RE  ++  R    +    TLE +G++  +++E
Sbjct: 206 QAAEVVEGSLDAARLRGWLVSAMQQLNARERFIVTERKLRDV--PRTLESLGEELKLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S+++  FL
Sbjct: 264 RVRQLEAAAFAKMRRSLEAQSREVHHFL 291


>gi|197116970|ref|YP_002137397.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
 gi|197086330|gb|ACH37601.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
          Length = 285

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 117/270 (43%), Gaps = 11/270 (4%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I  +   +  I+    ++  E   +    R+       A   ++ ANLR V+ +A +Y +
Sbjct: 9   IDNLTLYLAEINRFPLLTADEEMDLAGRFRR--EGDLEAAHRLITANLRFVVKIAGEYRS 66

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH- 524
            G++ LDLIQEGNIGLM A  KFD   G +  +YA+WW++  I   I      ++I    
Sbjct: 67  YGMKMLDLIQEGNIGLMMAVRKFDPDKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQ 126

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIGD 582
             R    K+ +  + + N    E      A  L +     R++ +  +  +SL+      
Sbjct: 127 AQRKLFFKLNQAKQAIVNMTG-EGDLHAAAISLDVKDNEAREMEQRLRGELSLDVEMFEG 185

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E      + + D         A +     L       L +L  +E+ V+  R        
Sbjct: 186 EGGGTFLESLPDLRQNQEEMLAERQETTILERNVASALENLNEKEKFVIEQRVAAE--DP 243

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+E+   F ++RER+RQIE  A++K+K 
Sbjct: 244 MTLQEIADHFSISRERVRQIEEGALKKMKR 273


>gi|308051462|ref|YP_003915028.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
 gi|307633652|gb|ADN77954.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
          Length = 286

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 124/273 (45%), Gaps = 16/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++++    +S  E +++   V +       A K ++ A+LR V+ VA+ Y   GL
Sbjct: 20  LESYIQAVNAIPMLSAEEEQYLARQVEQ---GDLDAAKHLIMAHLRFVVHVARSYAGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPNIGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R+      E +   +A +L +    V ++  ++     + +     +D 
Sbjct: 137 KLFFNLRKAKKRLGWFSAEEVST--VADELGVSESEVMEMEARMAAVDAAFDIAPERDDD 194

Query: 586 S---HLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   F+ED    +A +          ++     L +L  R   +L  R+       
Sbjct: 195 EGAFAPALFLEDKQSDHAEALEQEDWDRQSQQRLHAALNTLDERSRDILMARWLDEP--K 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TL+E+  ++ V+ ERIRQ+E  AI+KLK    
Sbjct: 253 ATLQELADRYQVSAERIRQLEKNAIKKLKSAME 285


>gi|256390724|ref|YP_003112288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
 gi|256356950|gb|ACU70447.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
          Length = 411

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 104/239 (43%), Gaps = 16/239 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ ++     LV  VA +        L   D +  G  GL+ A E+F+     KF TYA+
Sbjct: 179 RERLILHYSPLVKYVAGRVRVGLPGALDSADFVSSGIFGLIDAIERFEPHRHVKFETYAI 238

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +        IP  +R K  ++ + + R+  +  R P+  EIA++L + + 
Sbjct: 239 ARIRGAIIDELRALDW---IPRSLRQKAREIEQASVRLEQEFGRTPSESEIARELGIGLG 295

Query: 562 GVRKVL------KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +R++        +      L  P    D   L + +ED +A  P+        R    R
Sbjct: 296 ELRQIFSKLSLVNVAALDELLALPTQSGDRIPLMETLEDGDAPDPVALFEVQETRALLAR 355

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            + SL  R++ V+ + +  G     TL ++G+   V+  R+ QI  KA+  L+    +K
Sbjct: 356 AVNSLPERDKTVVTLYYFEG----MTLAQIGEVLGVSESRVCQIHTKAVLTLRGKLSAK 410


>gi|264685622|dbj|BAI49160.1| RNA polymerase beta subunit [Aeromonas sp. ATCC 15467]
          Length = 273

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 119/315 (37%), Gaps = 46/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AK+ 
Sbjct: 257 RMSIGEAKARRAKER 271


>gi|66474689|gb|AAY46914.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +++   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVMRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|146276534|ref|YP_001166693.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145554775|gb|ABP69388.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 292

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/268 (26%), Positives = 123/268 (45%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A KY   G    DLIQE ++GLMKAA+KF
Sbjct: 26  ELRLAYAWRDQRDERALHRLITAYMRLAISMASKYRRYGAPMNDLIQEASLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQS---------CTIRIPVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +                 +  +MR    ++ R A + 
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSLVRTGSTSSQKALFFNMRRVQARLEREASQR 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
             ++      E +A  + +P+  V  +  +++    SL      +D      D +ED +A
Sbjct: 146 GEQLDAHQLRELVAHDVGVPLSDVEMMEGRLSGSDFSLNATQSADDEGREWIDALEDDSA 205

Query: 598 VSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +      S     LR      +  L  RE  ++  R    +    TLE +G++  +++E
Sbjct: 206 QASEVVEGSLDAERLRGWLVVAMQQLNARERFIVTERKLRDV--PRTLESLGEELKLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S+++  FL
Sbjct: 264 RVRQLEAAAFAKMRRSLEAQSREVHHFL 291


>gi|332286014|ref|YP_004417925.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
 gi|330429967|gb|AEC21301.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
          Length = 293

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 117/264 (44%), Gaps = 7/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I +++    ++  E   +   +R  + +   A ++++ ++LRLV+S+A++Y   GL
Sbjct: 28  IEAYISAVNRLPMLTQEEETSLGKRLR--DHDDLDAARQLITSHLRLVVSIARQYLGYGL 85

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++      +
Sbjct: 86  AHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIVRNWRLVKVATTKAQR 145

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
                    R   +        EIA++L +  E V ++               DED    
Sbjct: 146 KLFFNLRRMRPDGQTLDTEQVNEIARELNVRPEDVSEMEVRMSGREFALESNDDEDGYAP 205

Query: 589 GDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             ++ D+    P     +              L  L  R  R+++ R+        TL E
Sbjct: 206 IAYLSDEGQQEPSRVLERRAYDALQGSGLADALDVLDERSRRIVQARWLQDEGG-ATLHE 264

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +  +F V+ ERIRQIEA A +KL+
Sbjct: 265 LAAEFGVSAERIRQIEAAAFKKLR 288


>gi|297614624|gb|ADI48614.1| RNA polymerase sigma-70 factor [Shewanella chilikensis]
          Length = 262

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 53/299 (17%), Positives = 107/299 (35%), Gaps = 50/299 (16%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            I IAKRIE G   + +S+ E P     ++   D+       L +II            G
Sbjct: 5   RIQIAKRIEEGINTVQSSVAEYPQAIAMILEQFDQFEAEEIRLSDII-----------SG 53

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV--DSPPENAENDER 256
           F +  E +          E   +D+ + +   +       D   +      PE A     
Sbjct: 54  FVNPDEDNVGPSATHIGSELSDEDLDDEDDMDDDDDDDDSDSEDEGSKGPDPEEARERFG 113

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            L    + ++  L  ++ +  P+ +  L  I E+++E                       
Sbjct: 114 QLRTVYE-NSLKLIELKGRDHPESVATLFHIGEIFKE----------------------- 149

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
                        L   + D LV+ +  +  ++   E  +L+L  +   + +  F++   
Sbjct: 150 -----------FRLVPKQFDRLVKSMRSMMDKVRVQERLILKLCVEQAKMPKKNFVKLFT 198

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E D  W + A+      +   +    + +L+ R ++++I  ETG+SI+  + I   +
Sbjct: 199 GNETDISWFN-AEMNSGKPYAEGLKMVEEDVLRCRAKLEAIEAETGLSIASIKDINRRM 256


>gi|222086841|ref|YP_002545375.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221724289|gb|ACM27445.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 302

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 73/279 (26%), Positives = 121/279 (43%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQEEYMLAK--RYAEHADREAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + R   R+    + +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDEGDLKPEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAS 193

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R    R ++ L  RE R+           
Sbjct: 194 EGESGQWQDWLVDDHESQEAVLIEQDELDTRRRMLARAMSVLNDRERRIFEA--RRLSED 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLE++  +F ++RER+RQIE +A  K++   +   L 
Sbjct: 252 PVTLEDLSSEFDISRERVRQIEVRAFEKVQEAVQKDALE 290


>gi|167508100|gb|ABZ81325.1| RpoD [Bowmanella denitrificans]
          Length = 266

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/314 (17%), Positives = 104/314 (33%), Gaps = 49/314 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   +  S+ E P     L+   D+       L +I+          
Sbjct: 1   REGEIDIAKRIEDGINQVQCSVAEYPEAITYLLDQWDQYEAEEIRLSDIV---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E            E   +++ + + D +     + DD      P        
Sbjct: 51  -LGFIDPNETDVAPTATHIGSELSEEELDDEDDDEDEDDDNNDDDGDSGVDP-------- 101

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                          A    LR +     D IA                    +     K
Sbjct: 102 -----------EVARAKFSALREQYTKTRDAIASK-----------------GRDHADAK 133

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERH 374
                L ++     L   + D +V+ +  +  R+   E  +++       + +  F++  
Sbjct: 134 TEIAALSEVFKEFRLVPKQFDRMVKNMRSMMDRVRVQERIVMKHCVMHAKMPKKDFIKAF 193

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E    W+       +    + +    + + +  +++  +  ETG++I++ + I   +
Sbjct: 194 AGNETTTAWLEILLKSGKAYVNDLL-THKEELERCISKMNQVEEETGLTIADIKDINRRM 252

Query: 435 RKGECEASIAKKEM 448
             GE +A  AKK+ 
Sbjct: 253 SIGEAKARRAKKKW 266


>gi|319639187|ref|ZP_07993938.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
 gi|317399371|gb|EFV80041.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
          Length = 287

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/266 (27%), Positives = 131/266 (49%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E   +    +K       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLTAEEETQLAERQQK---GDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  + +      +EIA  L + +  V     ++T   I +     D++ +
Sbjct: 134 KLFFNLRSMRKNLSALSP-KEAQEIADDLGVKLSEVLEMEQRMTGHDIGIMAENNDDEDN 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +A      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HELAAEYGVSAERIRQIEAKAMQKLR 277


>gi|4514503|dbj|BAA75450.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter lwoffii]
          Length = 278

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 115/316 (36%), Gaps = 39/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   ++ S+   P   + ++    +   G   L ++  L   
Sbjct: 1   VELLTREGEIGIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADL--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PES        E       + +  +K   DV+  + + E A      +      P   
Sbjct: 59  LDPESDEEIPEVLEEEVEIAEDKTDSKKSTKDVKLDDDEEEEAETEDDSEADSGPDP--- 115

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            E  +    E E+   +T +A+E                                K  + 
Sbjct: 116 -EIAKARFTELENAWLNTKTAIE--------------------------------KHGRD 142

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S + +   E L  +           D++ E +     +I   E E++R A   G + R  
Sbjct: 143 SEESEAALEALATVFMMFKFTPRLFDIISEMIRGTHDQIRGAEREVMRYAVRRGRMDRTQ 202

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F     G+E +P W+         + K ++      +L  + +I  I  E G+ +   + 
Sbjct: 203 FRTSFPGQESNPAWLDEQIAKTPADQKAYLEKVRPDVLAFQQKIADIEKELGLDVKGIKD 262

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 263 IAKRMAVGEAKARRAK 278


>gi|312876365|ref|ZP_07736350.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796859|gb|EFR13203.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 255

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 75/262 (28%), Positives = 134/262 (51%), Gaps = 13/262 (4%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +      + ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKLELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   +  +  ++EPT EEIAK+L++  E +   L   +EPISL  P+  +  DT +
Sbjct: 121 YKALKIKEKYISNNQKEPTLEEIAKELSITKEELVFTLDSIQEPISLYEPVFQDSTDTMY 180

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + + + D  +   +     +         L+ LT RE+ +L + +  G     T  EV +
Sbjct: 181 VVEKLYDHKSSENVWLEEIS-----LKDALSRLTKREKEILYLHYYKG----KTQMEVAR 231

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              +++ ++ +IE  AI  +K 
Sbjct: 232 IVGISQAQVSRIEKSAIGHIKK 253


>gi|15603449|ref|NP_246523.1| RNA polymerase factor sigma-32 [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|12721979|gb|AAK03668.1| RpoH [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 281

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/267 (24%), Positives = 131/267 (49%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +     E   A K+++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANEYPMLTAEEEKELAERL--YYQEDLEAAKKLILSHLRFVIHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   E +A +L +    V ++  ++T   ++ + P  D + 
Sbjct: 134 KLFFNLRKTKQRLG--WFNENEVEMVANELGVSPADVMEMESRMTGADVAFDLPTDDNEE 191

Query: 586 SHLGD-FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++    ++EDK    A    +   +A   E  +  L  L  R   +++ R+        T
Sbjct: 192 TYSPSLYLEDKGSNFAAELENENYEAQATEQLSVALEGLDERSLDIIKARWLDEN--KAT 249

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+++  ++ ++ ER+RQ+E  A++KLK
Sbjct: 250 LQDLAAKYNISAERVRQLETNALKKLK 276


>gi|157692208|ref|YP_001486670.1| sporulation sigma factor SigG [Bacillus pumilus SAFR-032]
 gi|194014766|ref|ZP_03053383.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
 gi|157680966|gb|ABV62110.1| DNA-directed RNA polymerase sigma subunit SigG [Bacillus pumilus
           SAFR-032]
 gi|194013792|gb|EDW23357.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
          Length = 259

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 78/264 (29%), Positives = 137/264 (51%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNDEMRKLFRQLQ--DEGDDTAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EPT E+IAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDERNKDTQWVEELA-----LKEGMRRLNDREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 231 EVAEEIGISQAQVSRLEKAAIKQM 254


>gi|302876248|ref|YP_003844881.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307686980|ref|ZP_07629426.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579105|gb|ADL53117.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 281

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 132/259 (50%), Gaps = 15/259 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAK-KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
               +   A+  ++  N RLV   A  K     L + DL+QEG IGLM   EKF+     
Sbjct: 20  YQTNKDITARDYLIINNKRLVYKAASLKKDTSLLAYDDLVQEGLIGLMIGIEKFNADYNS 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTY  +W+KQ I R+I +   +IR+P+H+ +KI+KV+    + + K     + +    
Sbjct: 80  KFSTYIYYWIKQRIDRAIYNTGTSIRLPIHLINKINKVMYVENKNNVKSLDNDSTDLCTD 139

Query: 555 KLAMPV--EGVRKVLKITKEPISLETPI---GDEDTSHLGDFIEDKNA---------VSP 600
                   +  + ++K  K  ISL + +     E    L DFI++ ++          S 
Sbjct: 140 LDITDKQYDYYKFLVKQFKNIISLNSALLSDNSEGDEELIDFIDENSSNFGDPGSKNYSI 199

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             + I+  L      VL +L  RE+ VLRMRFG+      TLE++G  F VTRERIRQIE
Sbjct: 200 DSNIIKEELSHDLNEVLKTLNEREQHVLRMRFGLDDGEMKTLEQIGNHFNVTRERIRQIE 259

Query: 661 AKAIRKLKHPSRSKKLRSF 679
           +KA++KL++P    +L  +
Sbjct: 260 SKALKKLRNPKILMRLEGY 278


>gi|55274934|gb|AAV49268.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 191

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 76/190 (40%), Positives = 127/190 (66%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 2   VVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 61

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S
Sbjct: 62  TRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITS 121

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+ 
Sbjct: 122 VDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLL 181

Query: 636 MNTDHTLEEV 645
                TLE+V
Sbjct: 182 GYEAATLEDV 191


>gi|195970121|ref|NP_387362.2| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307302477|ref|ZP_07582234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307316193|ref|ZP_07595637.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|8131943|gb|AAF73147.1|AF149031_2 sigma factor RpoH2 [Sinorhizobium meliloti]
 gi|10129889|dbj|BAB13518.1| sigma factor [Sinorhizobium meliloti]
 gi|187904236|emb|CAC47835.2| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306898033|gb|EFN28775.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306903147|gb|EFN33737.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 288

 Score =  129 bits (324), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 130/275 (47%), Gaps = 18/275 (6%)

Query: 414 KSISVETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           + I +       E     ++ +         A+ ++  +++RLVIS+A K+ + GL   D
Sbjct: 9   RMIKIAMEAPYLERDEEHALAQAWRNDNDQEARNKIAMSHMRLVISMAAKFRSFGLPMGD 68

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           L+QEG+IGL++AA +F+     +FSTYA WW++ ++   +      +R       K    
Sbjct: 69  LVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFF 128

Query: 531 KVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   R++    ++  +   EEIA  L + +  V+    +++    SL+ PIG  D  
Sbjct: 129 NLRRLRARLAQGDRQLTSQAMHEEIAAALGVSLADVQTMDARLSGNDASLQAPIGSGDPD 188

Query: 586 -SHLGDFIEDK-----NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                DF+  +       VS L    +A  R      L  L+ RE +++R R        
Sbjct: 189 AGARLDFLASEAPLPDEQVSDLIDGERA--RRWLQVALGELSEREMKIIRARRLTEDG-- 244

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLEE+G    +++ER+RQIE +A+ KL+    +K
Sbjct: 245 ATLEELGVALGISKERVRQIETRALEKLRAALTAK 279


>gi|187763292|gb|ACD35523.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 116/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYGV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|114321809|ref|YP_743492.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
 gi|114228203|gb|ABI58002.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 285

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/264 (24%), Positives = 128/264 (48%), Gaps = 12/264 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I +++    +S  E   +    R        A + +V ++LR V+ +A+ Y   GL   
Sbjct: 23  YIHAVNQIPVLSAEEEHELAERYR--LQGDLDAARALVLSHLRFVVHIARSYRGYGLPLG 80

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIH 530
           D+IQEGN+GLMKA ++FD   G +  ++A+ W++  I   +      +++     + K+ 
Sbjct: 81  DIIQEGNVGLMKAVKRFDPAQGVRLVSFAVHWIRAEIHEYVLRNWRIVKVATTKAQRKLF 140

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLG 589
             +R+ R+    +  E   + +A+ L +  E VR++  ++T    + +   G +D     
Sbjct: 141 FNLRSGRKHLGWLTSE-EVDAMARDLGVKPETVREMEARMTGNDTTFDPTPGQDDEGIHA 199

Query: 590 D--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              ++EDK    A +  ++  + +  +   + LA L  R + +L  R+        TL+E
Sbjct: 200 PVAYLEDKRYDPATAVEEADWEQHRDQNLHQALAGLDERSQDILARRWL--SERKATLKE 257

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           + + + V+ ERIRQ+E  A+ +LK
Sbjct: 258 LAEHYQVSAERIRQLEKNAMGRLK 281


>gi|197103189|ref|YP_002128567.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480465|gb|ACG79992.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 310

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 118/271 (43%), Gaps = 14/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  + ++     ++  E   +   VR  +     A   ++ ++LRL   +A  Y   GL
Sbjct: 19  LRQYLSAVRRYPVLTRDEEYALARRVR--DEVDLAAAHRLMTSHLRLAAKIACGYRGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              D+I E N+GL+ A  KFD     + STYA WW++ A+   I      +++      +
Sbjct: 77  PLEDMISEANVGLLHAIYKFDLERDCRLSTYAAWWIRAALQDYILRHWSIVKLGTSATQK 136

Query: 527 DKIHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                  R   R     +++    +  ++A+   +P   +     ++    +SL    GD
Sbjct: 137 RLFFGFRRARARVEACPSELLAGDSIAKMAELFHVPPGDITGMEARLGWRDLSLSALHGD 196

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNT 638
           E      + + D+NA  P  +  +A+ R+      T+ L+ L  RE R+   R       
Sbjct: 197 EGEPDRLERLADENAQDPETALSEADERDYRTRLLTQALSPLGSREHRIFVARRLRDP-- 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              L E+ +++ V+ ERIRQIE +A  K++ 
Sbjct: 255 PAPLAELAQEYGVSCERIRQIEMRAFEKVQR 285


>gi|148560551|ref|YP_001259508.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|294850906|ref|ZP_06791582.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
 gi|148371808|gb|ABQ61787.1| alternative sigma factor RpoH [Brucella ovis ATCC 25840]
 gi|294821549|gb|EFG38545.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
          Length = 303

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 118/267 (44%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  SIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|296164736|ref|ZP_06847300.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295899907|gb|EFG79349.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 288

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 107/241 (44%), Gaps = 8/241 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +     E +  ++ +V   L L   VA  +  RG    DL+Q   +GLM A  +FD 
Sbjct: 51  LRTMPAESHEYARQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDP 110

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   + R   D S  +R+P  +R+   ++ RT   ++ K+ R PT  
Sbjct: 111 DKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHVQISRTTGDLAQKLGRAPTAG 170

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+++ L +P E + + L         SL+ P+G + +      +                
Sbjct: 171 ELSRALEVPHEEIVECLVAGDAYRLDSLDAPMGTDSSGT--PRLVADAVGGIDPQIEHIT 228

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE    ++A+L  RE  VLRMRF        T  ++ ++  V++ ++ +I A  +R L+
Sbjct: 229 NREALRVLVAALPEREREVLRMRFF----ESMTQSQIAERIGVSQMQVSRILAGTLRCLR 284

Query: 669 H 669
            
Sbjct: 285 E 285


>gi|163758761|ref|ZP_02165848.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
 gi|162284051|gb|EDQ34335.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
          Length = 300

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 123/275 (44%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   E   +    R  + E + A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLAEIRRFPMLEPQEEYMLAK--RFLQHEDTKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              ++I EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVISEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                + +   ++      +  P+   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRKVKSKIQAVEDGDLRPDQVAEIATKLNVSEEEVISMNRRLSGDASLNAPIKAS 193

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D++         Q  L   R      L  L  RE+R+   R       
Sbjct: 194 EGESGQWQDWLVDESDSQEDMLVEQDELESRRAMLKSALEVLNEREKRIFEARRLRD--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLE++  +F ++RER+RQIE +A  K++   + 
Sbjct: 252 PITLEDLSGEFDISRERVRQIEVRAFEKVQDAVQK 286


>gi|17986661|ref|NP_539295.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|62290526|ref|YP_222319.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700442|ref|YP_415016.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|189024748|ref|YP_001935516.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|225853116|ref|YP_002733349.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|237816032|ref|ZP_04595028.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|254689824|ref|ZP_05153078.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254694316|ref|ZP_05156144.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|254697972|ref|ZP_05159800.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254730858|ref|ZP_05189436.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256045266|ref|ZP_05448160.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114225|ref|ZP_05454970.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|256258077|ref|ZP_05463613.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256263396|ref|ZP_05465928.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|260547226|ref|ZP_05822964.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260565841|ref|ZP_05836324.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260755355|ref|ZP_05867703.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758577|ref|ZP_05870925.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260762409|ref|ZP_05874746.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884371|ref|ZP_05895985.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214622|ref|ZP_05928903.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|265991691|ref|ZP_06104248.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995528|ref|ZP_06108085.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|297248928|ref|ZP_06932636.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|17982279|gb|AAL51559.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
 gi|62196658|gb|AAX74958.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616543|emb|CAJ11621.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|189020320|gb|ACD73042.1| Sigma-70 factor family [Brucella abortus S19]
 gi|225641481|gb|ACO01395.1| alternative sigma factor RpoH [Brucella melitensis ATCC 23457]
 gi|237788695|gb|EEP62907.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|260095591|gb|EEW79469.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260151214|gb|EEW86309.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260668895|gb|EEX55835.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260672835|gb|EEX59656.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675463|gb|EEX62284.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260873899|gb|EEX80968.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916229|gb|EEX83090.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|262766812|gb|EEZ12430.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|263002647|gb|EEZ15050.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263093393|gb|EEZ17462.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|297174061|gb|EFH33418.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|326409662|gb|ADZ66727.1| Sigma-70 factor family [Brucella melitensis M28]
 gi|326539369|gb|ADZ87584.1| alternative sigma factor RpoH [Brucella melitensis M5-90]
          Length = 303

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/267 (23%), Positives = 117/267 (43%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE  +   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERHIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|312794092|ref|YP_004027015.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181232|gb|ADQ41402.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 255

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 76/260 (29%), Positives = 134/260 (51%), Gaps = 9/260 (3%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +      + ++++ +     A++  +E NLRLV+SV +K+ NRG  
Sbjct: 2   NKVEICGVNTSTLPVLSHEEKLELLKRMKEGDKEARRIFIEGNLRLVLSVVQKFANRGEN 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     KFSTYA+  +   I R + D +   RI   ++D  
Sbjct: 62  LDDLFQVGCIGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSLKDTA 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K ++   +  N  ++EPT EEIAK+L++  E +   L   +EPISL  P+  + T  + 
Sbjct: 121 YKALKIKEKYINNNQKEPTLEEIAKELSVTKEELVFALDSIQEPISLYEPVFQDSTDTMY 180

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              +  +  S  +  ++     +    L+ LT RE+ +L +R+  G     T  EV +  
Sbjct: 181 VVEKLCDHKSCENVWLEEI---SLKDALSRLTKREKEILYLRYYKG----KTQMEVARIV 233

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +++ ++ +IE  AI  +K 
Sbjct: 234 GISQAQVSRIEKSAIGHIKK 253


>gi|304407011|ref|ZP_07388665.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343998|gb|EFM09838.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 251

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 120/253 (47%), Gaps = 14/253 (5%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            +T     E   +  ++   +   ++++  +V  N+RLV SV +++ NRG +  DL Q G
Sbjct: 6   KQTAQPYLEDAEVKRLIALSQSGDNVSRDTLVHCNIRLVWSVVQRFMNRGYEPEDLFQIG 65

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +KV +   
Sbjct: 66  CIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTLKVSRSLKETANKVRKMKD 124

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDK 595
            +S  + R PT  E+A+ L +  E V    +  K P S+   + + D     L D I D 
Sbjct: 125 ELSKTLGRLPTITEVAEGLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIADD 184

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +     D       +      +  L  RE  ++ +R+      D T  EV  +  +++ +
Sbjct: 185 SQERWFD-------KLALAEAIEGLAERERLIVYLRY----YRDQTQSEVASRLGISQVQ 233

Query: 656 IRQIEAKAIRKLK 668
           + ++E K ++ +K
Sbjct: 234 VSRLEKKILQLIK 246


>gi|57996874|emb|CAI45885.1| negative response regulator [Escherichia coli]
 gi|57996882|emb|CAI45889.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 77/190 (40%), Positives = 127/190 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLE 643
           +      TLE
Sbjct: 182 LLGYEAATLE 191


>gi|20151162|pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
           Sigma Factor Spoiiab With The Sporulation Sigma Factor
           Sigmaf
          Length = 243

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 124/254 (48%), Gaps = 14/254 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S   G S  + + +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q 
Sbjct: 2   SHMQGQSPIKDQEMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI 61

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K+ +  
Sbjct: 62  GCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKEMGNKIRKAK 120

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             +S    R PT  EIA  L +  E V    +  + P S+   + + D     L D I D
Sbjct: 121 DELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIAD 180

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +  S  D       +    + +  L  RE  ++ +R+      D T  EV  +  +++ 
Sbjct: 181 ADEASWFD-------KIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQV 229

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K ++ +K
Sbjct: 230 QMSRLEKKILQHIK 243


>gi|121634509|ref|YP_974754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis FAM18]
 gi|218767834|ref|YP_002342346.1| RNA polymerase factor sigma-32 [Neisseria meningitidis Z2491]
 gi|120866215|emb|CAM09955.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           FAM18]
 gi|121051842|emb|CAM08148.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           Z2491]
 gi|261392916|emb|CAX50501.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           8013]
          Length = 290

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 137 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|329120658|ref|ZP_08249321.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327460882|gb|EGF07216.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 287

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 128/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E  ++             A K ++ ++LR+V+S+A+ Y   GL
Sbjct: 18  LEQYIHTVNSIPLLTPEEEHNLAER---KMGGDVEAAKRLILSHLRVVVSIARGYDGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 75  NQADLIQEGNIGLMKAVKRYEPDRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  + +      + IA  L + +  V ++  ++T   I+L     D++ S
Sbjct: 135 KLFFNLRSMRKSLSALSP-KEAQAIADDLGVKLSEVMEMEQRMTGRDIALLADNSDDEDS 193

Query: 587 H-LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +          A  A   E     LA L  R  R++  R+        TL
Sbjct: 194 FAPIDWLADHDNEPTRQIERKAHHALQTEGLQNALAKLDERSRRIVETRWLQDDGG-LTL 252

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 253 HELAAEYGVSAERIRQIEAKAMQKLR 278


>gi|269127892|ref|YP_003301262.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312850|gb|ACY99224.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermomonospora curvata DSM 43183]
          Length = 276

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 120/250 (48%), Gaps = 20/250 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G+ E    + E+VE +L LV  +A+++ NRG    DLIQ   IGL+K+ +
Sbjct: 34  LFERLHQLPEGDPERQRVRDELVELHLPLVEYLARRFRNRGEWLDDLIQVATIGLIKSID 93

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   +R+P  +++    + +    ++ +  R 
Sbjct: 94  RFDLDRGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAISDLAQREGRA 153

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+ L M  E V + L+       +SL+ P   +         ED  AV+     
Sbjct: 154 PTVSELAEHLQMSEEEVLEGLESANAYSTVSLDAPDSGD---------EDAPAVADSLGM 204

Query: 605 IQANL-----RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +  +L     RE+   +L  L  RE+R+L +RF        T  ++  +  +++  + ++
Sbjct: 205 VDDSLEGVEYRESLKPLLEKLPAREKRILLLRFFGN----MTQSQIANELGISQMHVSRL 260

Query: 660 EAKAIRKLKH 669
            A+ + +L+ 
Sbjct: 261 LARTLAQLRE 270


>gi|159045149|ref|YP_001533943.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157912909|gb|ABV94342.1| RNA polymerase [Dinoroseobacter shibae DFL 12]
          Length = 298

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 127/275 (46%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + E + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPMLEPEEEYMLAK--RWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE    IA  L +  + V     +++    SL   IG 
Sbjct: 134 KLFFNLRKAKNRIGALEEGDLRPENVARIANDLNVTEDEVISMNRRMSGGDASLNAMIGS 193

Query: 583 EDT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +    +   D++ED++A    D A +  L   RE     +  L  RE+ +L  R      
Sbjct: 194 DGEGATEWQDWLEDEDADQADDFAEKDELMVRRELLAEAMGVLNDREKDILMKRRLED-- 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+ + + V+RERIRQIE +A  KL+   R
Sbjct: 252 KPATLEELSEVYGVSRERIRQIEVRAFEKLQKAMR 286


>gi|254804595|ref|YP_003082816.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254668137|emb|CBA04749.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254669711|emb|CBA03845.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha153]
 gi|308388900|gb|ADO31220.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           alpha710]
 gi|319410084|emb|CBY90418.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           WUE 2594]
 gi|325127782|gb|EGC50690.1| alternative sigma factor RpoH [Neisseria meningitidis N1568]
 gi|325129864|gb|EGC52669.1| alternative sigma factor RpoH [Neisseria meningitidis OX99.30304]
 gi|325131835|gb|EGC54535.1| alternative sigma factor RpoH [Neisseria meningitidis M6190]
 gi|325133774|gb|EGC56430.1| alternative sigma factor RpoH [Neisseria meningitidis M13399]
 gi|325136066|gb|EGC58676.1| alternative sigma factor RpoH [Neisseria meningitidis M0579]
 gi|325137885|gb|EGC60460.1| alternative sigma factor RpoH [Neisseria meningitidis ES14902]
 gi|325141969|gb|EGC64407.1| alternative sigma factor RpoH [Neisseria meningitidis 961-5945]
 gi|325144085|gb|EGC66393.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240013]
 gi|325197931|gb|ADY93387.1| alternative sigma factor RpoH [Neisseria meningitidis G2136]
 gi|325203799|gb|ADY99252.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240355]
 gi|325206445|gb|ADZ01898.1| alternative sigma factor RpoH [Neisseria meningitidis M04-240196]
          Length = 287

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HQLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|110224833|emb|CAJ29294.1| DNA-directed RNA polymerase subunit D [Pseudomonas brassicacearum]
          Length = 258

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/300 (17%), Positives = 108/300 (36%), Gaps = 48/300 (16%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   +M ++   P T   ++     +      L +++          
Sbjct: 1   REGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             G+    +G +    E       +    + + D + A     ++ ++    P  A    
Sbjct: 51  -SGYIDPDDGIAPPAAEVPPPIDAKAVKADDDTDDDEAEASDDEEEAESGPDPVIAAQRF 109

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             + +  + +   L                                   +K  +++ +  
Sbjct: 110 GAVADQMEITRKAL-----------------------------------KKHGRNNKQAI 134

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
                L +L   + L   + + LVE++     R+   E  +++L      + R  FL + 
Sbjct: 135 AELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 194

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI+E + I   +
Sbjct: 195 PGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKDINRRM 253


>gi|260771645|ref|ZP_05880565.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
 gi|260613422|gb|EEX38621.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
          Length = 285

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 115/244 (47%), Gaps = 14/244 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 42  HYSGDIEAAKTLILSHLRFVVHVARGYSGYGLPIADLVQEGNIGLMKAVKRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAR 159

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-----FIEDKN---AVSPLDSAIQ 606
           +L +    VR++        S      ++D +         ++EDK    A +      +
Sbjct: 160 ELGVEPAEVREMESRLAALDSTFEFSAEDDDNPNAYTAPVLYLEDKQSDLAENIEAQNWE 219

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +     +  LASL  R + ++R R+        TL+E+   + V+ ERIRQ+E  A++K
Sbjct: 220 NHTNHRLSLALASLDERSQHIVRSRWLDD--QKATLQELADLYQVSAERIRQLEKNAMKK 277

Query: 667 LKHP 670
           LK  
Sbjct: 278 LKEA 281


>gi|302556969|ref|ZP_07309311.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474587|gb|EFL37680.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 295

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 119/250 (47%), Gaps = 8/250 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S   FR +  +  +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IG
Sbjct: 42  ELSRQFFRRLAEL-EEGTREYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIG 100

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    ++
Sbjct: 101 LIKAIDRFELAREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELA 160

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +++ REPT  E+A  + +  + V +           SL+  +  +   +    + D   V
Sbjct: 161 SRLDREPTVAELATLMNITEQQVVEGQIAANGYNSSSLDAALTGDGPEYGEAVLADFIGV 220

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                 +  +   +   ++A L+PR+  +L +RF      + T  E+G++   ++  + +
Sbjct: 221 EEEGLRLVEDFH-SLAPLMAELSPRDREILHLRFV----EEATQAEIGERLGCSQMHVSR 275

Query: 659 IEAKAIRKLK 668
           +  + I +L+
Sbjct: 276 LIKRIIARLR 285


>gi|297197437|ref|ZP_06914834.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197716285|gb|EDY60319.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 298

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 118/247 (47%), Gaps = 7/247 (2%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   ++ + +G  E   A+  ++E N+ LV   A ++  RG    D++Q G IGL+KA
Sbjct: 48  RQFFQRLTELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMEDIVQTGMIGLIKA 107

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +++++ 
Sbjct: 108 IDRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELASRLD 167

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           R+PT  E+A  + +  + V +    +      SL+  +  +        + D   V    
Sbjct: 168 RDPTVAELATLMNISEKEVIEAQIASNGYNSSSLDAALTGDGPEGGEAVLADFIGVEEDG 227

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  +   +   ++A L+ R+ +++ MRF      + T  E+G++   ++  + ++  +
Sbjct: 228 LRLVEDFH-SLAPLMAELSERDRQIIHMRFV----EEATQSEIGERLGCSQMHVSRLIKR 282

Query: 663 AIRKLKH 669
            I +L+ 
Sbjct: 283 IITRLRE 289


>gi|120612533|ref|YP_972211.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax citrulli AAC00-1]
 gi|120590997|gb|ABM34437.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax citrulli
           AAC00-1]
          Length = 313

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 119/290 (41%), Gaps = 24/290 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  +  +   I +++    ++  E R     ++  E     A   MV ++LRLV+S+A++
Sbjct: 21  IPPLGNLDAYISAVNRLPMLTAEEERTYARRLK--EHNDVEAAGRMVMSHLRLVVSIARQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD     +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VHMRDKIHKVV----RTARRMSNKIKREPTPEEIAKKLAMP----------VEGVRKVLK 568
                +         +   +         T  E   +  +            E +    +
Sbjct: 139 TTKSQRKLFFNLRSMKQGFKADAAAGDAGTHRETLSEQEIDVVAQQLNVKREEVIEMETR 198

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPR 623
           ++   + L+    D+     G      + +    + I++  R+          LA+L  R
Sbjct: 199 LSGGDVMLDPAPSDDGEQAYGPIAYLADGMHEPTAMIESRQRDVLATDGIANALATLDDR 258

Query: 624 EERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             R++  R+    +      TL E+   + V+ ERIRQIE  A++K+K  
Sbjct: 259 SRRIVEERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKA 308


>gi|163740703|ref|ZP_02148097.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161386561|gb|EDQ10936.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 292

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/288 (25%), Positives = 135/288 (46%), Gaps = 19/288 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I N +   +++  +  +E   +       +     A   ++ A +RL IS+A K+   G 
Sbjct: 7   IENPLPKRAMKAELLDAET-ELQLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGA 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI------- 521
              DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +I   +      +R        
Sbjct: 66  PMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQK 125

Query: 522 --PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET 578
               +MR    ++ R A+    ++ +    ++IA ++ +P+  V+ +  ++     SL  
Sbjct: 126 SLFFNMRRVQAQLERQAQSEGTRLDQHQLHQQIATEIGVPLRDVQMMDGRLAGADFSLNA 185

Query: 579 PIGDEDTS-HLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGI 634
               E+      + +ED +A +        +   LR      + +L  RE  ++  R   
Sbjct: 186 VQSAEEEGREWIEALEDDSAQAAELVEESHDTRQLRTWLVEAMQALNDRERFIITERKLR 245

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR--SKKLRSFL 680
                 TLE +G +  +++ER+RQ+EA A +K++      S+++++FL
Sbjct: 246 E--KPRTLESLGTELGLSKERVRQLEAGAFQKMRKSLETCSREVQNFL 291


>gi|331269711|ref|YP_004396203.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126261|gb|AEB76206.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 242

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 126/250 (50%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E + ++  +R        ++++ +  NLRLV+SV +++ NRG    DL Q G IGL
Sbjct: 4   LKDKEMKELLIKMR---DGDYFSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGCIGL 60

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++   R+ N
Sbjct: 61  IKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALQVRDRLIN 119

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K  ++P   +IAK+L +P E V   L   ++P+SL  PI  +  D  ++ D I D  +V 
Sbjct: 120 KDNKDPNVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDALYVMDQISDNKSVD 179

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                       +    +  L  RE+ +L MRF  G     T  EV  +  +++ ++ ++
Sbjct: 180 DSWIE-----NISIKEAMKRLNEREKLILNMRFFQG----RTQMEVADEIGISQAQVSRL 230

Query: 660 EAKAIRKLKH 669
           E  A++ ++ 
Sbjct: 231 EKTALKHMRK 240


>gi|239934580|emb|CAR94604.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 223

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/267 (20%), Positives = 102/267 (38%), Gaps = 45/267 (16%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
            T  L +II            GF             +    +   +++    +     + 
Sbjct: 61  QTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAAAEIENEAEEEAEEGEG 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           + ++   +++ P+  E   R                            D +++ + +++ 
Sbjct: 110 ASEEEETLETGPDPEEAARR---------------------------FDSLSKTFVQVQK 142

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    +      +   L++KL      L L+    D+L+ Q+      I + E ++
Sbjct: 143 ------GMAEKGADDPRVMKLRKKLADEFTELKLSPKMFDMLITQIRRSLTDIRNVEKQV 196

Query: 357 LRLAQS-YGIKRDVFLERHQGRELDPH 382
           + L     G+ R  F+      E +  
Sbjct: 197 MLLCVRDSGMPRKDFISTFPSNETNLS 223


>gi|89099055|ref|ZP_01171934.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
 gi|89086185|gb|EAR65307.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
          Length = 252

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/259 (25%), Positives = 126/259 (48%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +T +   E + +   ++K +     A+  +V+ N+RLV SV +++ NRG +  
Sbjct: 4   EVKTDKTQTYLKDHEVKEL---IQKSQAGDQGARDTIVQKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKEMGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    ++    R PT  E++  L +P E +    +  + P S+   + + D     L 
Sbjct: 120 IRKAKDELTKTFGRIPTVTELSAYLEIPPEDIILAQEAGRTPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I+D N     D              +  L  RE  ++ +R+      D T  EV  + 
Sbjct: 180 DQIDDGNDGKWFDQI-------ALKEAIRELDERERLIVYLRY----YKDQTQSEVAARL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILQQMK 247


>gi|319764144|ref|YP_004128081.1| RNA polymerase sigma factor rpoh [Alicycliphilus denitrificans BC]
 gi|330826499|ref|YP_004389802.1| RNA polymerase sigma-32 subunit RpoH [Alicycliphilus denitrificans
           K601]
 gi|317118705|gb|ADV01194.1| RNA polymerase sigma factor RpoH [Alicycliphilus denitrificans BC]
 gi|329311871|gb|AEB86286.1| RNA polymerase, sigma 32 subunit, RpoH [Alicycliphilus
           denitrificans K601]
          Length = 311

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 69/288 (23%), Positives = 130/288 (45%), Gaps = 22/288 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ E +      +K       A   +V ++LRLV+S++++
Sbjct: 21  VPPLGNLDAYISAVNRLPLLTLEEEQRYAQQFKKD--NDLEAAGRLVLSHLRLVVSISRQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VH-MRDKIHKVVRTARR----------MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-T 570
               + K+   +R+ ++             +   +   + +A++L +  E V ++     
Sbjct: 139 TTKAQRKLFFNLRSMKQGFKADAIDADTHRETLSDHEIDMVAEQLNVKREEVIEMETRLA 198

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPREE 625
              + L+    D+     G      +      + I++  R+       T  LASL  R  
Sbjct: 199 GGDVLLDPAPSDDGEQAFGPIAYLADTAHEPTAMIESRQRDALATDGITSALASLDARSR 258

Query: 626 RVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K  
Sbjct: 259 RIVEQRWLQVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKA 306


>gi|238763647|ref|ZP_04624607.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238789414|ref|ZP_04633200.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238793542|ref|ZP_04637166.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
 gi|238698125|gb|EEP90882.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238722557|gb|EEQ14211.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238727132|gb|EEQ18662.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
          Length = 285

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +   
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWD 219

Query: 611 ----ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               +  +  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 NHAADKLSYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|238798006|ref|ZP_04641495.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
 gi|238718109|gb|EEQ09936.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
          Length = 285

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S    +I+ +   
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWD 219

Query: 611 ----ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               +     L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 GHAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|294676015|ref|YP_003576630.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294474835|gb|ADE84223.1| RNA polymerase sigma-32 factor-1 [Rhodobacter capsulatus SB 1003]
          Length = 292

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 16/253 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             +     A   +V A +RL IS+A K+   G    DLIQE ++GLMKAA+KFD   G +
Sbjct: 33  WRDHRDEAALHRLVSAYMRLAISMASKFRRYGAPMNDLIQEASLGLMKAADKFDPDRGVR 92

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKRE------- 546
           FSTYA+WW+K +I   +      +R       K     + R   ++  + + E       
Sbjct: 93  FSTYAVWWIKASIQEFVMRNWSMVRTGSTSSQKALFFNLKRVQAQIQREAEAEGVVLDGA 152

Query: 547 PTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSA 604
              E++A  + + +  V  +  +++   +SL  P   ++      D +ED+         
Sbjct: 153 QLREKVAISIGVSMADVEMMEGRLSGSDLSLNAPQSHDEDGREWVDTLEDEGGSPETRVT 212

Query: 605 IQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +   +R+   + +  L+ RE  ++  R  I      TLE +G++  +++ERIRQ+EA
Sbjct: 213 EAHDGAKMRDWLGQAMGQLSARERYIVAQRRLID--EPRTLESLGEELGLSKERIRQLEA 270

Query: 662 KAIRKLKHPSRSK 674
           +A  K++    S+
Sbjct: 271 QAFSKMRKSLESR 283


>gi|229490177|ref|ZP_04384024.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229322925|gb|EEN88699.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 264

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 104/244 (42%), Gaps = 12/244 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             +  +     E    +  ++   L L   +A+++  RG    DL+Q   +GL+ A ++F
Sbjct: 27  EELRTLEPHSPEYERVRTALITRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNAVDRF 86

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G  F ++A+  V   + R   D    +R+P  M++   ++ +    +S ++   PT
Sbjct: 87  DSTRGSDFVSFAVPTVMGEVRRHFRDTGWALRVPRRMKELHFQLGQAISELSQQLGHAPT 146

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+A+ L +  E V + L      + +S++       D   L + + D +A        
Sbjct: 147 VDELAETLGIEREEVAQALIAGNAYQTVSVDGAASNHTDDLPLVETLGDYDAA-----LE 201

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                E    +L  L  RE  VL +RF        T  ++ ++  V++  + ++ AK + 
Sbjct: 202 NVENHEALRPLLDKLPERERTVLMLRFFGN----LTQTQIAEKVGVSQMHVSRLLAKTLS 257

Query: 666 KLKH 669
            L+ 
Sbjct: 258 NLRE 261


>gi|313799121|gb|ADR82155.1| RNA polymerase sigma factor [Mycoplasma sp. 1220]
 gi|313799126|gb|ADR82156.1| RNA polymerase sigma factor [Mycoplasma anatis]
 gi|313799129|gb|ADR82157.1| RNA polymerase sigma factor [Mycoplasma anatis]
          Length = 183

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 80/173 (46%), Positives = 114/173 (65%), Gaps = 2/173 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +   +  G      A+ ++++ NLRLVI+ AKKY NRGL F+DLI EGN G+
Sbjct: 10  LSADEEVELAKTMNLGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNAGI 69

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KAA+K++   G+KFSTYA WW++QAITR++ADQ+ TIR+PVHM + I+K+ +  R +  
Sbjct: 70  LKAAQKYNVDKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQQ 129

Query: 542 KIKREPTPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
           ++ REP  EEIA K       E VR + KI  +PISL+  IG E+ S   DF+
Sbjct: 130 ELGREPLDEEIAAKFGNAYTAEKVRYIRKINIDPISLDKQIGKENDSSFSDFV 182


>gi|187763314|gb|ACD35534.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKE 
Sbjct: 257 RMSIGEAKARRAKKEW 272


>gi|21221509|ref|NP_627288.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289771198|ref|ZP_06530576.1| SigI protein [Streptomyces lividans TK24]
 gi|5911753|emb|CAB55836.1| SigI protein [Streptomyces coelicolor A3(2)]
 gi|7672251|emb|CAB89440.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701397|gb|EFD68826.1| SigI protein [Streptomyces lividans TK24]
          Length = 304

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 62  LFERLESLEEGTHEHAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 121

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 122 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 181

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A+ L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 182 PTVSELAEHLGLSKDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGIE 241

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L  R+ ++L +RF  G     T  E+G++  +++  + ++ ++ 
Sbjct: 242 YV-----ESLKPLIAELPSRDRKILSLRFVAG----MTQSEIGEELGISQMHVSRLLSRT 292

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 293 LVRLRK 298


>gi|4514517|dbj|BAA75457.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 279

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 120/316 (37%), Gaps = 38/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++   ++   G   L +I  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PES        E  +  + ED     +  DV+  + D E  ++   D        PE 
Sbjct: 59  LDPESDEEIPEVLEEEAELEEEDEKSPSKAKDVKLDDDDEEEESEGDDDSEGDSGPDPEI 118

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+   +++   ++                                   K  ++
Sbjct: 119 AKARFTELENAWNETKAIIA-----------------------------------KHGRN 143

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S +     E L  +           +++ E +    ++I  NE E++R A   G + R+ 
Sbjct: 144 SAEADAALESLAAVFMMFKFTPRLFEIISEMIRGTHEQIRSNEREIMRYAVRRGRMDRNQ 203

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F      +E +  W+         E K  +      +L  + +I  I  + G+++ + + 
Sbjct: 204 FRLSFPEQESNLAWLDEQIAKAPAETKGHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 263

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 264 ISKRMTVGEAKARRAK 279


>gi|5360738|dbj|BAA82139.1| sigma factor of sigB family [Streptomyces griseus]
          Length = 259

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 114/252 (45%), Gaps = 19/252 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   +  + +G      A+  ++E NL LV   A ++ NRG     D++Q G IGL+KA 
Sbjct: 10  FFDRLQTLEEGTHAYQYARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAI 69

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D S  + +P  +++    + +    ++  + R
Sbjct: 70  DRFDLSREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDLAKAKEALAGVLDR 129

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS-------HLGDFIEDKN 596
           +PT +E+A+ L +    V + +  +      SL+ P    +            D + D +
Sbjct: 130 DPTAKELAEYLGIEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQTAGRTFADVLGDPD 189

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                 +            +L  L  RE R++ MRFG     + T  ++G +  +++  +
Sbjct: 190 -----PAMEAVENLHALAPLLDELDERERRIIDMRFG----QEMTQAQIGAELGISQMHV 240

Query: 657 RQIEAKAIRKLK 668
            ++ ++ + KL+
Sbjct: 241 SRLLSRMLGKLR 252


>gi|149187051|ref|ZP_01865358.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
 gi|148829340|gb|EDL47784.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
          Length = 319

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 134/309 (43%), Gaps = 20/309 (6%)

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E+D   V    +         +  E  S+ +  +EIK   + T     + +  +   R 
Sbjct: 8   HEVDARKVRDYVNTTRSLSVPALGGE-QSLNRYLSEIKKFPILT-----QEQEYMLAKRY 61

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E   S A  ++V ++LRLV  +A  Y   GL   DLI EGN+GLM+  +KF+   G++ 
Sbjct: 62  EEHGDSEAAAQLVTSHLRLVSKIAMGYRGYGLPVSDLISEGNVGLMQGVKKFEADRGFRL 121

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKI-----HKVVRTARRMSNKIKREPTPEE 551
           +TYAMWW+K +I   I      +++      K       ++ +      +        ++
Sbjct: 122 ATYAMWWIKASIQEYILRSWSLVKMGTTAAQKKLFFNLRRMKKNLDAYEDTDLHPDDVQK 181

Query: 552 IAKKLAMPVEGVRKVLKITKE--PISLETPIGD--EDTSHLGDFIEDK---NAVSPLDSA 604
           IA  L +P + V  + +        SL  P+ +  E +    D++ D       +  D+ 
Sbjct: 182 IATDLGVPEQEVVNMNRRMMMGGDGSLNVPMRNGEEGSGEWMDWLTDDRPLQDETVADAE 241

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +    E     + +L  RE+ +L            TLEE+ + + V+RERIRQIE +A 
Sbjct: 242 EKEVRHEMLGEAMEALNEREQHILTE--RRLTENPQTLEELSQVYNVSRERIRQIEVRAF 299

Query: 665 RKLKHPSRS 673
            KL+   ++
Sbjct: 300 EKLQKAMKA 308


>gi|254390382|ref|ZP_05005599.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
 gi|197704086|gb|EDY49898.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
          Length = 326

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 108/235 (45%), Gaps = 11/235 (4%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 98  EHTRVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTF 157

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           AM  V   I R   D   T+ +P  + +   +V      ++    R PT  EIA++L + 
Sbjct: 158 AMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNGATEDLTTAHGRIPTTAEIAERLRIG 217

Query: 560 VEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            + V   ++   +    SLE     +    L D +  ++             R+    +L
Sbjct: 218 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHLL 272

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             L  RE+R+L +R+        T  ++ ++  V++  + ++ A++  +L+  +R
Sbjct: 273 VQLPEREQRILMLRYYSN----LTQSQISQELGVSQMHVSRLLARSFARLRSANR 323


>gi|37784430|gb|AAO13108.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|37955142|gb|AAP76221.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|37956263|gb|AAO73802.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763276|gb|ACD35515.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763278|gb|ACD35516.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763280|gb|ACD35517.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763282|gb|ACD35518.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763288|gb|ACD35521.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763290|gb|ACD35522.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763300|gb|ACD35527.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763320|gb|ACD35537.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763326|gb|ACD35540.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763332|gb|ACD35543.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763334|gb|ACD35544.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763336|gb|ACD35545.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763338|gb|ACD35546.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763340|gb|ACD35547.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763342|gb|ACD35548.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763344|gb|ACD35549.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763352|gb|ACD35553.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763356|gb|ACD35555.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|187763358|gb|ACD35556.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|53802588|ref|YP_112675.1| RNA polymerase factor sigma-32 [Methylococcus capsulatus str. Bath]
 gi|53756349|gb|AAU90640.1| RNA polymerase sigma-32 factor [Methylococcus capsulatus str. Bath]
          Length = 286

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 123/272 (45%), Gaps = 16/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I +   +++    +   E R +   +R  + +   A + +V ANLR V  +A+ Y   GL
Sbjct: 16  IDDYFAAVNRLPRLDADEERELA--IRFRDEQDLEAARRLVLANLRFVAYIARGYLGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA +++D  +G +  ++A+ W++  I   I      ++I      +
Sbjct: 74  PLADLIQEGNIGLMKAVKRYDPDVGVRLVSFAVHWIRAEIHEFIIQNWRIVKIATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+M N++          +A +L + VE V +   ++    ++LE    D+  
Sbjct: 134 --KLFFNLRKMKNRLGWLTPEEAAAVAAELGVDVEDVYKMENRLNNPDMALEAHGEDDGD 191

Query: 586 S-------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                   H         A+    S  +   +E     +  L  R   ++  R+      
Sbjct: 192 DRESHAPIHYLQQEGGDPALLIEHSEWENRQQEKLQEAIGQLDERSRDIVASRWL--SED 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TL ++  ++ V+ ERIRQ+E+ A++KL++ 
Sbjct: 250 KLTLHDLAARYNVSAERIRQLESSAMKKLRNA 281


>gi|254476880|ref|ZP_05090266.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
 gi|214031123|gb|EEB71958.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
          Length = 292

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 73/288 (25%), Positives = 135/288 (46%), Gaps = 19/288 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I N +   +++  +  +E   +       +     A   ++ A +RL IS+A K+   G 
Sbjct: 7   IENPLPKRAMKAELLDAET-ELKLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGA 65

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI------- 521
              DLIQE  +GLMKAA+KFD   G +FSTYA+WW+K +I   +      +R        
Sbjct: 66  PMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQK 125

Query: 522 --PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET 578
               +MR    ++ R A     ++ +    ++IA ++ +P+  V+ +  +++    SL  
Sbjct: 126 SLFFNMRRVQAQLEREAAASGEQLDQHQLHQKIATEIGVPLRDVQMMDGRLSGADFSLNA 185

Query: 579 PIGDEDTS-HLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGI 634
               ED      + +ED +A +        +   LR      + +L  RE  ++  R   
Sbjct: 186 VQSAEDEGREWIEALEDDSAQAAELVEESHDTRQLRTWLVEAMQALNDRERFIITERKLR 245

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR--SKKLRSFL 680
                 TLE +G +  +++ER+RQ+EA A +K++      S+++++FL
Sbjct: 246 D--KPRTLESLGDELGLSKERVRQLEAAAFQKMRKSLETCSREVQNFL 291


>gi|197287411|ref|YP_002153283.1| RNA polymerase factor sigma-32 [Proteus mirabilis HI4320]
 gi|227358346|ref|ZP_03842687.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
 gi|194684898|emb|CAR47059.1| RNA polymerase sigma-32 factor [Proteus mirabilis HI4320]
 gi|227161682|gb|EEI46719.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
          Length = 284

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 69/269 (25%), Positives = 132/269 (49%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +         A K ++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANSYPMLTAEEEKELAERL--HYEGDLEAAKTLILSHLRFVIHVARSYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R+    + E   E +AK+L +    VR++  +++ + ++ +    D D 
Sbjct: 134 KLFFNLRKNKKRLGWFNQDE--VELVAKELGVSESDVREMESRMSAQDMAFDMSADDSDD 191

Query: 586 SHLGD---FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           SH      F+EDK+   A    +     +  +  T  + +L  R + ++R R+    N  
Sbjct: 192 SHPVAPVLFLEDKSSDFADGIEEDNWDNHAADRLTLAIKTLDERSQDIIRARWLEDDNKS 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 252 -TLQELADKYGVSAERVRQLEKNAMKKLR 279


>gi|149202416|ref|ZP_01879389.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
 gi|149144514|gb|EDM32545.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
          Length = 277

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 114/260 (43%), Gaps = 16/260 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 11  ELALAYAWRDQRDEEALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGLGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 71  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREALAN 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
             ++      E IA ++ +P+  V  +  +++    SL      ED      D +ED  A
Sbjct: 131 GEQLDGYQLREMIAHEVGVPLRDVEMMEGRLSGSDFSLNATQSSEDEGRQWIDTLEDDGA 190

Query: 598 ---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         LR      L+ L  RE  ++R R         TLE +G++  +++E
Sbjct: 191 RGDEIVERDHDMHALRTWLADALSRLNDRERFIVRERKLRD--DPRTLESLGEELNLSKE 248

Query: 655 RIRQIEAKAIRKLKHPSRSK 674
           R+RQ+EA A +K++      
Sbjct: 249 RVRQLEAAAFQKMRKHLEKH 268


>gi|84500884|ref|ZP_00999119.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84390951|gb|EAQ03369.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 298

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 123/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   +          ++IA  L +    V     +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLHPDNVKQIANDLGVTEAEVISMNRRMSGGDASLNATVGM 193

Query: 583 EDTS--HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +  S     D++ED+ A    D A +  +   RE     +A L  RE  +L         
Sbjct: 194 DAESAMEWQDWLEDEEADQAGDYAERDEMDSRRELLAEAMAVLNDRERDILTQ--RRLSE 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++ +Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 ETITLEDLSEQYGVSRERIRQIEVRAFEKLQLQMR 286


>gi|302521363|ref|ZP_07273705.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302430258|gb|EFL02074.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 312

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 119/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 70  LFERLEDLDEGTHAHSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 129

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 130 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 189

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PTP E+A+KL +  E V + +         SL+    ++D  S L D +  ++       
Sbjct: 190 PTPSELAEKLGIEREEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGIE 249

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I     E+   ++A L  R+ ++L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 250 YI-----ESLKPMIARLPQRDRKILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRT 300

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 301 LVKLRK 306


>gi|55274965|gb|AAV49282.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 77/192 (40%), Positives = 128/192 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLEEV 645
           +      TLE+V
Sbjct: 182 LLGYEAATLEDV 193


>gi|303304828|emb|CBL59288.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304830|emb|CBL59289.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304832|emb|CBL59290.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304834|emb|CBL59291.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304836|emb|CBL59292.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304838|emb|CBL59293.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304840|emb|CBL59294.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304842|emb|CBL59295.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304844|emb|CBL59296.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304846|emb|CBL59297.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304848|emb|CBL59298.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
 gi|303304850|emb|CBL59299.1| RNA polymerase sigma-70 factor [Xanthomonas arboricola pv. pruni]
          Length = 246

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 70/290 (24%), Positives = 117/290 (40%), Gaps = 48/290 (16%)

Query: 58  VSSEQMEDTVAMLSNMGINVV----DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           V  EQ+ED ++M++ MGI+V     D + L   +G+  + ++  +A+  +       D+ 
Sbjct: 1   VDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVDDTAAEEAAAALTALDTE 60

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
              T DPVRMY+REMG++ELL+REGEIAIAKRIE G + + A+L   PL+ + L+   + 
Sbjct: 61  GGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEA 120

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
             +G   L EI+            GF    E         ++      D    + D +  
Sbjct: 121 HKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDED 169

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
                 +     + P+  E                           V   ++ +A  Y +
Sbjct: 170 GDDDAAEEEAGPTGPDPVE---------------------------VATRMENLANEYAK 202

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            + +        K+          +E +  +  +L L     D LV QL 
Sbjct: 203 FKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLR 246


>gi|55274892|gb|AAV49248.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 190

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 76/189 (40%), Positives = 126/189 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTL 642
           +      TL
Sbjct: 182 LLGYEAATL 190


>gi|37956271|gb|AAO73806.1| RNA polymerase sigma-70 factor [Aeromonas sp. 117P]
 gi|37956275|gb|AAO73808.1| RNA polymerase sigma-70 factor [Aeromonas sp. 40]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 119/316 (37%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           +   D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DDADDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|37784408|gb|AAO13097.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37956249|gb|AAO73795.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|37956265|gb|AAO73803.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37956267|gb|AAO73804.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|37956269|gb|AAO73805.1| RNA polymerase sigma-70 factor [Aeromonas sp. LMG 13662]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           E + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  ESSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|238784413|ref|ZP_04628423.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
 gi|238714705|gb|EEQ06707.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
          Length = 285

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 121/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +   
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWD 219

Query: 611 ----ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               +     L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 NHAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|34580656|ref|ZP_00142136.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
 gi|28262041|gb|EAA25545.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
          Length = 293

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 130/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEELLLAK--SYLEGNDLQAAHKLVTSHLKLVAKIASGYRTYGLPM 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPALGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 196 AESGELIELLPETRPTPETMAINKQNSTSKRQLLSNAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|196247722|ref|ZP_03146424.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196212506|gb|EDY07263.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 259

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 77/261 (29%), Positives = 136/261 (52%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + ++       A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRELFQRMHEGDLEAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   R+  +  +EP+ EEIAK+L +  E V   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVRERLMGETAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D + D+           A         L  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 YVMDQLSDERNRDSQWIEEIA-----LKEGLRRLNEREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AIR++
Sbjct: 233 EEIGISQAQVSRLEKAAIRQM 253


>gi|254369205|ref|ZP_04985217.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122155|gb|EDO66295.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 292

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 134/274 (48%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   +E+A++L +  E V ++ K   +   SL+ P  D+D  
Sbjct: 141 KLFFNLRSSKDKIGWLSSEN-IKELAEELGVKEETVIEMEKRMCQGDASLDLPYTDDDGE 199

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     VL+    R + ++  R+ +      
Sbjct: 200 QTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--KA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 258 TLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|262277481|ref|ZP_06055274.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
 gi|262224584|gb|EEY75043.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
          Length = 300

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 123/269 (45%), Gaps = 14/269 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I     +  +E   +    R  E     +  ++V ++LRLV  +A  Y   GL  
Sbjct: 21  SYLQKIRKFPMLDAAEEYILAKNWR--EKGDKESAHKLVTSHLRLVAKIATGYRGYGLPM 78

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI- 529
            +L+ EGNIGLM A +KFD   G++ +TYAMWW+K ++   I      ++I      K  
Sbjct: 79  SELVSEGNIGLMTAVKKFDPERGFRLATYAMWWIKASMQEYILRSWSLVKIGTTAAQKKL 138

Query: 530 ----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDED 584
                K+     R            EIA +L +  + V  + +  K P  SL   I  E+
Sbjct: 139 FFNLRKMKNQIMRSDQTDLLPEQVTEIANRLDVTEDEVNSMDQRMKGPEASLNATISGEE 198

Query: 585 -TSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             S   D++ D+NA   L  A +      +    + ++ L  RE+ +L            
Sbjct: 199 GESEWQDWVVDENADQELQIAHRQETNKRKALLDKAMSILNEREKEILFD--RRLNEEPK 256

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TLEE+ +++ ++RERIRQIE +A  KL+ 
Sbjct: 257 TLEELSQKYNISRERIRQIENRAFEKLQK 285


>gi|123440620|ref|YP_001004614.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332159850|ref|YP_004296427.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122087581|emb|CAL10362.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318607604|emb|CBY29102.1| RNA polymerase sigma factor RpoH [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664080|gb|ADZ40724.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330862604|emb|CBX72757.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica W22703]
          Length = 285

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +   
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPTPDDEVRDGQSMAPVLYLQDKTSDFADGIEEDNWD 219

Query: 611 ----ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               +  T  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 NHAADKLTYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|323452445|gb|EGB08319.1| hypothetical protein AURANDRAFT_5759 [Aureococcus anophagefferens]
          Length = 239

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 118/246 (47%), Gaps = 15/246 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTN-----RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           AK  +V AN  LV+S+A+ Y             DL+QEG +GL++A EK++   G +F T
Sbjct: 1   AKHALVRANGGLVVSIARGYQRLRTGAGVEALDDLVQEGTLGLIRAVEKYEPERGIRFGT 60

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA  W+K +I+  +      I++P  + D   +  R++  + N + R+ T EE+A+ L  
Sbjct: 61  YATAWIKASISAWLKRGDAMIKVPSRVADLGLRAARSSSALQNDLGRDATAEEVARDLGA 120

Query: 559 PVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               V            +S +   G +  S+    + D++           +L+   T  
Sbjct: 121 STAAVEAAASALHGSRVVSYDASAGGDSESNFVACLADED-------CAVGDLKADLTNA 173

Query: 617 LAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           LA+ L  RE RV+R+R+G+   T  +  E      + +E +RQI  KA RKL+  ++   
Sbjct: 174 LAAVLDDRELRVVRLRYGLDDGTQRSTRECAAALGIGKESVRQICLKAFRKLRGTAQGSA 233

Query: 676 LRSFLD 681
           L S +D
Sbjct: 234 LLSHMD 239


>gi|294788977|ref|ZP_06754217.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
 gi|294483079|gb|EFG30766.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
          Length = 289

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 76/267 (28%), Positives = 135/267 (50%), Gaps = 12/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S+ E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 16  LEQYIHTVNAIPMLSLEEETKLAER---QLRGDIEAAKQLILSHLRVVVSIARGYDGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++F+   G +  ++A+ W+K  I   I      +RI     + 
Sbjct: 73  NQADLIQEGNIGLMKAVKRFEPVHGARLFSFAVHWIKAEIHEFILRNWRLVRIATTKPQR 132

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISL--ETPIGDED 584
           K+   +R+ R+  N +      +EIA  L + +  V ++  ++T   ++L  E+   +ED
Sbjct: 133 KLFFNLRSMRKSLNALSP-KEAQEIADDLGVKLTEVMEMEQRMTGNDVALLAESDDDNED 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    D++ D ++      A QA+     E     LA L  R  R++  R+        T
Sbjct: 192 SFAPIDWLADNDSEPSQQIAKQAHYALQTEGLQNALAQLDERSRRIVETRWLADDGG-LT 250

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 251 LHDLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|240013602|ref|ZP_04720515.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI18]
 gi|240112396|ref|ZP_04726886.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|240120672|ref|ZP_04733634.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID24-1]
 gi|268598456|ref|ZP_06132623.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|268582587|gb|EEZ47263.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
          Length = 290

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/266 (27%), Positives = 131/266 (49%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++ T   D++ S
Sbjct: 137 KLFFNLRSMRKNLNVLSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMTDNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|294501135|ref|YP_003564835.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|295706482|ref|YP_003599557.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|464690|sp|P35145|RPSF_BACME RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|39654|emb|CAA45288.1| spoIIAC [Bacillus megaterium]
 gi|294351072|gb|ADE71401.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|294804141|gb|ADF41207.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|383708|prf||1904152C spoIIAC gene
          Length = 253

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 126/259 (48%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K    E  +   E + +   +++ +    IA+  +V+ N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNKNEPYLKDHEVKDL---IKRSQQGDQIARDTIVQKNMRLVWSVVQRFINRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKEMSNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S  + R PT  E+A+ L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRKAKDELSKLLGRVPTVAEVAEHLDLTPEEVVLAQEANRAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D       D       +      +  L  RE+ ++ +R+      D T  EV  + 
Sbjct: 180 DQIADHTEAKWFD-------KIALKEAIEELDEREKLIVYLRY----YKDQTQSEVAARL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|238650752|ref|YP_002916605.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
 gi|238624850|gb|ACR47556.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
          Length = 293

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 130/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEELLLAK--SYLEGNDLQAAHKLVTSHLKLVAKIASGYRTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 196 AESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|187763348|gb|ACD35551.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 123/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            ++   +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQIAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|187763310|gb|ACD35532.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  +  + +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMRQMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|237749576|ref|ZP_04580056.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
 gi|229380938|gb|EEO31029.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
          Length = 299

 Score =  129 bits (323), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 74/271 (27%), Positives = 127/271 (46%), Gaps = 8/271 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  I   I  I+    ++      +    R  E     A +E+V ++LRLV S+A+ Y 
Sbjct: 25  SLGNIEAYIAEINRLPMLTQERETELAQ--RYHENNDLAAAQELVLSHLRLVASIARNYL 82

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G +  +YA+ W+K  I   I      +++   
Sbjct: 83  GYGLPHADLIQEGNIGLMKAVKRFDPKMGVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 142

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +  N+         +A+KL +  E V ++    +   I+LET   D+
Sbjct: 143 KAQRKLFFNLRSHKSGNEAMTREQIRSLAEKLNVKDEEVSEMETRLSGHDIALETQHDDD 202

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTD 639
           D +     ++  +          + + R   E     L  L  R +R++  R+    +  
Sbjct: 203 DDNFAPIAYLSSEQTEPTRVLEAKQHDRLQSEGLAEALDKLDDRSKRIIEARWLKNDDGS 262

Query: 640 -HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             TL ++ ++F V+ ERIRQIEA A++K+K+
Sbjct: 263 GATLHDLAEEFGVSAERIRQIEAAALKKMKN 293


>gi|259479067|dbj|BAI40081.1| RNA polymerase sigma-70 factor [Aeromonas sp. TT2]
 gi|259479069|dbj|BAI40082.1| RNA polymerase sigma-70 factor [Aeromonas sp. TT5]
          Length = 272

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E +D+  T   I S            +   +  E+ 
Sbjct: 59  ------------------------ETEDIAPTATHIGSELGEDDLADEDEEDEEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DSSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|294670676|ref|ZP_06735551.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307564|gb|EFE48807.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 287

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 69/266 (25%), Positives = 127/266 (47%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    ++  E  ++             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 18  LDQYIHTVNSIPLLTPEEEHNLAER---KMRGDVEAAKQLILSHLRVVVSIARGYDGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 75  NQADLIQEGNIGLMKAVKRYEPDRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  + +      + IA  L + +  V     ++T + ++L     D+D +
Sbjct: 135 KLFFNLRSMRKSLSALSP-KEAQAIADDLGVKLSEVLEMEQRMTGKDVALLADNSDDDDN 193

Query: 587 H-LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D +          A      E     LA L  R  R++  R+        TL
Sbjct: 194 FAPIDWLADHDNEPTRQIERKAHYTLQTEGLQNALAKLDDRSRRIVETRWLQDDGG-LTL 252

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 253 HELAAEYGVSAERIRQIEAKAMQKLR 278


>gi|238759635|ref|ZP_04620796.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
 gi|238702178|gb|EEP94734.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
          Length = 285

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 123/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +  +
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGHSMAPVLYLQDKSSDFADGIEEDNWD 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +      +  +  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SHAADKLSYAMEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|284030454|ref|YP_003380385.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
 gi|283809747|gb|ADB31586.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
          Length = 301

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 85/235 (36%), Positives = 136/235 (57%), Gaps = 16/235 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ M+E NLRLV+S+AK+YT +GL  LDLIQEGNIGLM+A E+FD+ LG++FSTYA+WW+
Sbjct: 80  RRRMIEGNLRLVVSLAKRYTGKGLSLLDLIQEGNIGLMRAVERFDYKLGHRFSTYAIWWI 139

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +QA+ R+I+D+S  +R+P        +V    R +  +++REPT EE+A+  ++ V  V 
Sbjct: 140 RQALGRAISDRSRLVRMPAQAYVDAGRVAVVQRELIQRLEREPTIEELARATSLTVARVE 199

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L     P  L+         H  D + D   +       +A LR      L  L   +
Sbjct: 200 RALAWKLRPEPLD--------GHDSDQVIDDETL-----LQRAALRRDLHCQLEFLDDLK 246

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           + VLR+R+G+      +LEE  +   +   R+R +E +A+R L+   ++  LR +
Sbjct: 247 QDVLRLRYGLHNTPQSSLEETAEYLSLPPARVRSLELEALRHLR---KAPGLREY 298


>gi|254453216|ref|ZP_05066653.1| sigma 32 [Octadecabacter antarcticus 238]
 gi|198267622|gb|EDY91892.1| sigma 32 [Octadecabacter antarcticus 238]
          Length = 292

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 128/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 26  ELALAYAWRDERDEQALHRLITAYMRLAISMASKFRRYGAPMNDLIQEASLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            ++R    ++ R A + 
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAMKR 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              + R    + IA ++ +P+  V  +  +++    SL      ED      D +ED   
Sbjct: 146 GETLDRHDMRQMIATEVGVPLRDVEMMEGRLSGSDFSLNATQSSEDEGREWIDALEDDGE 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +  +S     LR+     L +L+ RE+ ++R R         TLE +G +  +++E
Sbjct: 206 QAADAVQNSHDTDTLRQWLLTALTALSDREQFIVRERKLRDA--PRTLESLGTELSLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           R+RQ+EA A  K++     +S+++ SFL
Sbjct: 264 RVRQLEAAAFGKMRKSLEGQSQEVHSFL 291


>gi|208779746|ref|ZP_03247090.1| alternative sigma factor RpoH [Francisella novicida FTG]
 gi|208744201|gb|EDZ90501.1| alternative sigma factor RpoH [Francisella novicida FTG]
          Length = 292

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/275 (23%), Positives = 133/275 (48%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++      +
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDT 585
             K+    R + +KI    + +  E+A++L +  E V ++ K   +   SL+ P  D+D 
Sbjct: 141 --KLFFNLRSIKDKIGWLSSEDIKELAEELGVKEETVIEMEKRMCQGDASLDLPYTDDDG 198

Query: 586 SHLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   ++EDK++        Q    N +     VL+    R + ++  R+ +     
Sbjct: 199 EQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--K 256

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 257 ATLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|213958512|gb|ACJ54677.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 3-3.5cm5R]
          Length = 264

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 53/310 (17%), Positives = 107/310 (34%), Gaps = 47/310 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           R+GEI IAKRIE G   +M ++   P T   ++     +      L +++          
Sbjct: 1   RDGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             G+    +G +    E       +    + + D + A   + D+      P        
Sbjct: 51  -SGYIDPDDGIAPPAAEVPPPVDPKAVKADDDTDDDDAEATTDDEEEAESGPDPVIAAQR 109

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                D+ +          +     +  L  +AE++                        
Sbjct: 110 FGAVSDQMEITRKALKKHGRGNKLAIAELVLLAELF------------------------ 145

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
                       + L   + + LVE++     R+   E  +++L      + R  FL + 
Sbjct: 146 ----------MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 195

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E+D  W   A    + ++   +A     I+  + ++ ++  ETG++I+E + I   +
Sbjct: 196 PGNEVDESWSD-ALAKAKSKYAEAIAPLQPDIICCQQKLIALQTETGLTIAEIKDINRRM 254

Query: 435 RKGECEASIA 444
             GE +A  A
Sbjct: 255 SIGEAKARRA 264


>gi|37784428|gb|AAO13107.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
          Length = 274

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 115/315 (36%), Gaps = 42/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF +  E              E        G       ++ +D S  +   E+ E D
Sbjct: 52  --SGFVNPDEA------------DEMGPTATHIGSELGEDDLADEDSSDEEEEDEDEEGD 97

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             + D D             +LR +       I                   + ++  + 
Sbjct: 98  GNDDDGDGGPDPEVAREKFAELRAQYEITRQSIRS-----------------NGRAHEET 140

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+   +   + +  F+  
Sbjct: 141 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERLILKMCVEQAKMPKKTFVSA 200

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +       A E + +L+   +++ I  ETG+SI++ + I   
Sbjct: 201 FTNNECETAWFEYQKQAGKAWSAPLAAME-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 259

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 260 MSIGEAKARRAKKEM 274


>gi|153947554|ref|YP_001399239.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           31758]
 gi|152959049|gb|ABS46510.1| alternative sigma factor RpoH [Yersinia pseudotuberculosis IP
           31758]
          Length = 285

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +  +
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWD 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           T      +  L  L  R + ++R R+    N   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 THAADKLSYALEGLDERSQHIIRARWLDDENKS-TLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|154685949|ref|YP_001421110.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens FZB42]
 gi|154351800|gb|ABS73879.1| SigG [Bacillus amyloliquefaciens FZB42]
          Length = 260

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 81/264 (30%), Positives = 137/264 (51%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFRQLQ--DEGDDSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  REPT EEIAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSREPTAEEIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDERNKDTQWIEELA-----LKEGMRRLNEREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 231 EVAEEIGISQAQVSRLEKAAIKQM 254


>gi|51892950|ref|YP_075641.1| sporulation sigma factor SigF [Symbiobacterium thermophilum IAM
           14863]
 gi|51856639|dbj|BAD40797.1| RNA polymerase sigma factor similar to B. subtilis
           sporulation-specific sigma-F [Symbiobacterium
           thermophilum IAM 14863]
          Length = 255

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/255 (26%), Positives = 120/255 (47%), Gaps = 14/255 (5%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           G    E R +V++ R        A+  +VE NLRLV S+  +++  G    DL Q G IG
Sbjct: 11  GWPDEEVRRLVALAR---AGDKEARDRLVEGNLRLVRSLVSRFSASGADPEDLFQIGCIG 67

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++FD     +FSTYA+  +   I R + D    +R+   ++    +  R   R++
Sbjct: 68  LLKAIDRFDLNYDVRFSTYAVPLIMGEIRRHLRD-DGPMRVSRSLKQLAQQARRVRERLA 126

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAV 598
            +++R+PT  E+A +L +  E V   L   + P S+   + + D    +L D +   +  
Sbjct: 127 AQMERDPTVAEVAAELGVSPEEVVAALDGVRPPTSIHQTVHEGDGDPIYLLDQLAADDGQ 186

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +  LRE     L  L  RE  V+ +RF      D T  EV      ++ ++ +
Sbjct: 187 REGVWLDRVALRE----GLNQLDERERTVILLRFF----RDKTQTEVASILGCSQVQVSR 238

Query: 659 IEAKAIRKLKHPSRS 673
           +E +A+ ++++   +
Sbjct: 239 LERRALERIRNYVNA 253


>gi|221133912|ref|ZP_03560217.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola sp. HTCC2999]
          Length = 283

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 63/286 (22%), Positives = 137/286 (47%), Gaps = 15/286 (5%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
               +A  +     I + I+S+S    +S  E + +   +         A +E+V ++LR
Sbjct: 3   KSMQMALTIPQSGSIESYIQSVSNIPMLSADEEKSLAERL--FNEGDLTAARELVMSHLR 60

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
            V+ +AK Y+  GL   DL+QEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +  
Sbjct: 61  FVVHIAKSYSGYGLAQADLVQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEFVLK 120

Query: 515 QSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITK 571
               +++      R     + ++ +R+     +E   +++A++L +  + V +   ++  
Sbjct: 121 NWRIVKVATTKAQRKLFFNLRKSKKRLGWFTHKE--VQKVAEELGVSEKEVLQMEARMGS 178

Query: 572 EPISLETPIGDEDT---SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  + +    D D         ++EDK+     + +++   +N        + +L  R +
Sbjct: 179 QDTAFDLSSDDGDDNSNFSPAQYLEDKSENVEAAVINADYDSNASARLYSAIKTLDERSQ 238

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            ++  R+    +   TL+++  ++ V+ ER+RQIE  A++K++   
Sbjct: 239 YIIETRWL--NDNKMTLQDLAAKYEVSAERVRQIEKNAMKKIQAAM 282


>gi|296270865|ref|YP_003653497.1| Sig B/F/G subfamily RNA polymerase sigma-28 [Thermobispora bispora
           DSM 43833]
 gi|296093652|gb|ADG89604.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermobispora bispora DSM 43833]
          Length = 259

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 117/250 (46%), Gaps = 21/250 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +           + E+VE ++ LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 18  FAELAQLPPDDPRR-QRIRDELVELHMPLVEYLARRFRNRGEWLDDLTQVATIGLIKSID 76

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   +   I R   D+   +R+P  +++    + +    +S +  R 
Sbjct: 77  RFDLSRGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAISELSQRESRA 136

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A+ L M  E V + L+       +SL+ P   +         ED  AVS     
Sbjct: 137 PTVAELAEHLQMSEEEVLEGLESANAYSTVSLDAPDSGD---------EDAPAVSDSLGI 187

Query: 605 IQANL-----RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           +  +L     RE+   +L  L PRE+R+L +RF        T  ++  +  +++  + ++
Sbjct: 188 VDESLEGVEYRESLKPLLERLPPREKRILLLRFFGN----MTQSQIANELGISQMHVSRL 243

Query: 660 EAKAIRKLKH 669
            A+ + +L+ 
Sbjct: 244 LARTLAQLRE 253


>gi|148241530|ref|YP_001226687.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849840|emb|CAK27334.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 280

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 80/269 (29%), Positives = 137/269 (50%), Gaps = 21/269 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK----------------GECEASIAKKEMVEAN 452
           +R  ++ I     +   +   +  +V++                       A++ M++AN
Sbjct: 5   VRAYLEQIGRYALLRPEQEVELARLVQRAQQLEQQLQLSPTEQRELRRGRRARERMIQAN 64

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV++VAK Y  RGL  +DL+QEG++GL++A EKFD  LGY+FSTYA  W++QAI+R +
Sbjct: 65  LRLVVTVAKTYQGRGLDLMDLVQEGSLGLIRAVEKFDPTLGYRFSTYAWNWIRQAISRGL 124

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
             +  T+R+P+H+  ++  + R   R+  +         +A +  + ++     L++   
Sbjct: 125 ETKGRTLRLPIHVTQQLRALRRAHERLWQQ-GLSTDLVAVAAEAGVDLKAASLALRMAPG 183

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +SL+TP    ++  L   +      SPLD A + +  E   R L  L  R+++VL+ R+
Sbjct: 184 TLSLDTPAAGSESDLLQ--LLPSAEPSPLDEAERHDGWERMGRQLRHLPERDQQVLQWRY 241

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                    L  VG+Q   +RER RQIE 
Sbjct: 242 L--TPERQKLSVVGEQLGCSRERARQIEQ 268



 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             +PVR YL ++G   LL  E E+ +A+ ++
Sbjct: 1   MAEPVRAYLEQIGRYALLRPEQEVELARLVQ 31


>gi|85373062|ref|YP_457124.1| RNA polymerase factor sigma-32 [Erythrobacter litoralis HTCC2594]
 gi|84786145|gb|ABC62327.1| RNA polymerase sigma-32 factor [Erythrobacter litoralis HTCC2594]
          Length = 301

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 70/279 (25%), Positives = 125/279 (44%), Gaps = 16/279 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  +   +    R  E E   A  ++V ++LRLV  +A  Y   
Sbjct: 16  QSLNRYLSEIKKYPVLTAEQEYMLAK--RYQEHEDPEAAAQLVSSHLRLVAKIAMGYRGY 73

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GLM+  +KF+   G++ +TYAMWW+K ++   I      +++     
Sbjct: 74  GLPVSDLISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASMQEFILRSWSLVKMGTTAA 133

Query: 527 DK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKE--PISLETP 579
            K     + R  +++      + +PE+   IA  L +P + V  + +        SL TP
Sbjct: 134 QKKLFFNLRRMKKQLEAYEDTDLSPEDVTKIATDLGVPEQEVINMNRRMMMGGDGSLNTP 193

Query: 580 IGD--EDTSHLGDFIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           + +  + +    D++ D       +  ++       E     + +L  RE+ +L      
Sbjct: 194 MRNGEDGSGEWQDWLTDDRPLQDETVANAEEAQVRHEMLVEAMDALNEREQHILTE--RR 251

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                 TLEE+ + + V+RERIRQIE +A  KL+   + 
Sbjct: 252 LTENPQTLEELSQVYDVSRERIRQIEVRAFEKLQKAMQR 290


>gi|56708190|ref|YP_170086.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670661|ref|YP_667218.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134302102|ref|YP_001122071.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|187931929|ref|YP_001891914.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|224457293|ref|ZP_03665766.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370677|ref|ZP_04986682.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254875002|ref|ZP_05247712.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604682|emb|CAG45745.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320994|emb|CAL09128.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134049879|gb|ABO46950.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151568920|gb|EDN34574.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|187712838|gb|ACD31135.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|254841001|gb|EET19437.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159406|gb|ADA78797.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 292

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 134/274 (48%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   +E+A++L +  E V ++ K   +   SL+ P  D+D  
Sbjct: 141 KLFFNLRSSKDKIGWLSSEN-IKELAEELGVKEETVIEMEKRMCQGDASLDLPYTDDDGE 199

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     VL+    R + ++  R+ +      
Sbjct: 200 QTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--KA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 258 TLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|3249731|gb|AAC26668.1| RNA polymerase sigma-like factor [Streptomyces spectabilis]
          Length = 161

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 81/162 (50%), Positives = 116/162 (71%), Gaps = 1/162 (0%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RRM  +   EP+PEE+A  L +
Sbjct: 1   YATWWIRQAMSRAMADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPSPEEVAAHLDL 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P E VR  L++ +EP+SL  P+G+ED   LGD IED +A SP++SA    LRE    VL+
Sbjct: 61  PHERVR-GLRLAQEPVSLHAPVGEEDDVALGDLIEDGDAASPVESAAFLLLREHLEAVLS 119

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 120 TLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIE 161


>gi|300508138|dbj|BAJ10901.1| RNA polymerase subunit D [Pseudomonas tuomuerensis]
          Length = 265

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/301 (17%), Positives = 105/301 (34%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           SREGEI IAKRIE G   +M+++   P     ++     +      L +   L   I P+
Sbjct: 4   SREGEIEIAKRIEEGLREVMSAIAHFPGAVDGILAEYQRVVSEGGRLSD--GLSGYIDPD 61

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    E    +    +++        + + + ES+     +  +     PE A   
Sbjct: 62  DGTLPAEEVEPVIVKSGTPAAK-------DDEDEEEESSESSDDETETDGGPDPEEAARR 114

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E    +   L A   +  P  +  L  +AE++                       
Sbjct: 115 FNAVAEQLAVAKKAL-AKHGRSHPTSVAELLALAELF----------------------- 150

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
                        + L   + D LVE++    +R+   E  +++L      + R  FL+ 
Sbjct: 151 -----------MPIKLVPKQFDALVEKVRSALERVRQQERAIMQLCVRDARMPRTDFLKL 199

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
             G E+D  W +      + ++   +    D I + +  +  +  E  ++I+E + +   
Sbjct: 200 FPGNEVDLDWSTQIAK-GKAKYAEAIGNLQDDIKRNQQVLIDLQNEVDLTIAEIKDVNRR 258

Query: 434 V 434
           +
Sbjct: 259 M 259


>gi|255312661|gb|ACU01740.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 77/192 (40%), Positives = 128/192 (66%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 4   VVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 63

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S
Sbjct: 64  TRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITS 123

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            +TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+ 
Sbjct: 124 EDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLL 183

Query: 636 MNTDHTLEEVGK 647
                TLE+VG+
Sbjct: 184 GYEAATLEDVGR 195


>gi|302532223|ref|ZP_07284565.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302441118|gb|EFL12934.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 307

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/272 (23%), Positives = 126/272 (46%), Gaps = 21/272 (7%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  +     I+ ++ R +  +       + +G  E   A+  ++E NL LV   A+++  
Sbjct: 35  LPRVEQAREIAPADARELSRLFFARLRSLEEGTREYQYARNTLIEMNLSLVHYAARRFRA 94

Query: 466 R----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           R    GL   D+IQ G IGL+KA ++FD     +FST A+ ++   I R   D +  + +
Sbjct: 95  RVSGGGLDMDDVIQVGTIGLIKAIDRFDLDREVEFSTLALPYITGEIKRHFRDTTWAVHV 154

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETP 579
           P  +++   ++ +    ++  + R PT +E+A+ L +  E V   L         SL+T 
Sbjct: 155 PRRLQELRSELAKAQESLTEALHRAPTVKEVAQHLGLSEEEVIDGLVAANGYTSGSLDTA 214

Query: 580 IGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
              E+   T      + +K   S     +  +   T   +L  L PRE  +L MRFG   
Sbjct: 215 DEAEEARGTGRPARALAEKLGESDPAMELFEDFH-TLAPLLRELQPRERLILSMRFG--- 270

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + T  E+G +  +++ ++ ++ ++ + +L+
Sbjct: 271 -QEKTQAEIGAELHISQMQVSRLLSRTLARLR 301


>gi|189024846|ref|YP_001935614.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|189020418|gb|ACD73140.1| Sigma-70 factor family [Brucella abortus S19]
          Length = 306

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 77/296 (26%), Positives = 134/296 (45%), Gaps = 15/296 (5%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +S +   P       V     +    ++ I+S      +   E R +   +R  E +   
Sbjct: 1   MSSSSTVPANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQD 58

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW
Sbjct: 59  ALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWW 118

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           ++ ++   I      +R       K     + R   +++         E   EI+ +L +
Sbjct: 119 IRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGV 178

Query: 559 PVEGVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ET 612
               V     +++    SL  P+  E+T  S   DF+ D + +    +    ++      
Sbjct: 179 STSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRW 238

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TR L +L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 239 LTRALDTLNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 292


>gi|209550663|ref|YP_002282580.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536419|gb|ACI56354.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 302

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 124/276 (44%), Gaps = 14/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + D+    D++ D +         Q  L   R    + ++ L  RE R+   R       
Sbjct: 194 EGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             TLE++  +F ++RER+RQIE +A  K++   R +
Sbjct: 252 PVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKE 287


>gi|167630319|ref|YP_001680818.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
 gi|167593059|gb|ABZ84807.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
          Length = 266

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 114/253 (45%), Gaps = 17/253 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
                + +   A++E++     LV  VA +        ++  DLI  G  GLM A EKFD
Sbjct: 18  WASYKDHKDPAAREELILIYAPLVKFVAGRLAISLPPNVEREDLISYGVFGLMDAIEKFD 77

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G KF TYA+  ++ ++   +        +PV +R K  ++ +T   +S ++ RE T 
Sbjct: 78  LARGLKFETYAIARIRGSMLDGLRAMDW---VPVSVRQKTRELEKTYATLSQRLGREATD 134

Query: 550 EEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPLDS 603
           EE+A+ L + +    K+L+       +SL+     +    D   L D + D+    P  +
Sbjct: 135 EEVAQALGLTLNEFAKLLQDVQATTIMSLDEYWLTDSDKGDPVRLIDSLADEQVEEPTAA 194

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R    + +  L  +E  V+ + +  G     TL+E+G    V+  RI Q+  KA
Sbjct: 195 LEFEETRLLLAQAIDKLPEKERTVIALYYYEG----LTLKEIGAVIGVSESRISQLHTKA 250

Query: 664 IRKLK-HPSRSKK 675
           I +L+   +R KK
Sbjct: 251 ILRLRGQLARQKK 263


>gi|326682080|emb|CBL30931.1| RNA polymerase sigma factor [Aeromonas aquariorum]
 gi|326682090|emb|CBL30936.1| RNA polymerase sigma factor [Aeromonas aquariorum]
          Length = 272

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVPEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|222149598|ref|YP_002550555.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221736580|gb|ACM37543.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 300

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 71/279 (25%), Positives = 117/279 (41%), Gaps = 14/279 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +       +    R  E     A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQVEYMLAK--RYAEHGDRDAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  ++    + +     +     EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGKIQAIEEGDLKPDQVTEIATKLKVSEEEVISMNRRLSGDASLNAPIRAS 193

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +         Q  L   R   +R +  L  RE R+   R       
Sbjct: 194 EGESGQWQDWLVDDHDSQEDTLIEQDELETRRNMLSRAMGVLNDRERRIFAARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             TLEE+  +F ++RER+RQIE +A  K++   +   L 
Sbjct: 252 PVTLEELSSEFDISRERVRQIEVRAFEKVQDAVQKDALE 290


>gi|86157650|ref|YP_464435.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85774161|gb|ABC80998.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 322

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 82/296 (27%), Positives = 140/296 (47%), Gaps = 15/296 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
             GE ++     +     +R  +  ++    +S  E   +   V+  E     A  ++V 
Sbjct: 18  AAGEARDRSEGGLVRYDPLRAYMAEVARHPVLSRDEEHALA--VQYRETGDVDAAYKLVA 75

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           +NLRLV+ +A +Y     Q LDL+QEGN+GLM+A +K+D   G K S+YA WW++  I R
Sbjct: 76  SNLRLVVKIAHEYRRTAFQLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIR 135

Query: 511 SIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL- 567
            I +    +++      R     + +   ++  +   EPTP  +AK L +  + V ++  
Sbjct: 136 FIMENWRLVKLGTTQAQRKLFFNLSKEREKLLAR-GIEPTPRLLAKNLQVEEKDVEEMSA 194

Query: 568 KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANL----RETTTRVLASL 620
           ++  + +SL+ P+G E      +  D + D    +P  +     L    RE       +L
Sbjct: 195 RMAADDLSLDAPVGTEGDDGRQNRLDRLADDGGQAPDAALGDEQLRRIFREKLDAFSGTL 254

Query: 621 TPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           T  +ER +     +        TL+EVG  F +TRER RQIEAK   +L+   R++
Sbjct: 255 TDEKERYIFEHRLLPPDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAE 310



 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCES 160
            +    + +        DP+R Y+ E+    +LSR+ E A+A +  E G       L  S
Sbjct: 17  PAAGEARDRSEGGLVRYDPLRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYKLVAS 76

Query: 161 PLTFQALIIWRDE 173
            L     I     
Sbjct: 77  NLRLVVKIAHEYR 89


>gi|16079402|ref|NP_390226.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221310263|ref|ZP_03592110.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314586|ref|ZP_03596391.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319509|ref|ZP_03600803.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323785|ref|ZP_03605079.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321311821|ref|YP_004204108.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
 gi|133474|sp|P07860|RPSF_BACSU RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|143611|gb|AAA22788.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|1304000|dbj|BAA12655.1| SpoIIAC [Bacillus subtilis]
 gi|2634780|emb|CAB14277.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484775|dbj|BAI85850.1| sporulation sigma factor SigF [Bacillus subtilis subsp. natto
           BEST195]
 gi|320018095|gb|ADV93081.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
          Length = 255

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 66/259 (25%), Positives = 127/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K       +   E + +   +++ +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNGKNAQLKDHEVKEL---IKQSQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S  + R PT +EIA  L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRAKDELSKTLGRVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D +     D       +      ++ L  RE+ ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADNSEEKWFD-------KIALKEAISDLEEREKLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQIK 247


>gi|157828283|ref|YP_001494525.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165932987|ref|YP_001649776.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. Iowa]
 gi|157800764|gb|ABV76017.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165908074|gb|ABY72370.1| RNA polymerase sigma-32 factor [Rickettsia rickettsii str. Iowa]
          Length = 293

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 131/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEELLLAK--SYLEGNDLQAAHKLVTSHLKLVAKIASGYRTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      +  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTTAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I ++D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLSLNNSINNDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 196 AESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|118497682|ref|YP_898732.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           novicida U112]
 gi|194323654|ref|ZP_03057430.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|254373048|ref|ZP_04988537.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|254374500|ref|ZP_04989981.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|118423588|gb|ABK89978.1| RNA polymerase sigma-32 factor [Francisella novicida U112]
 gi|151570775|gb|EDN36429.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3549]
 gi|151572219|gb|EDN37873.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|194322018|gb|EDX19500.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|332678395|gb|AEE87524.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida Fx1]
          Length = 292

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 134/274 (48%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   +E+A++L +  E V ++ K   +   SL+ P  D+D  
Sbjct: 141 KLFFNLRSSKDKIGWLSSE-DIKELAEELGVKEETVIEMEKRMCQGDASLDLPYTDDDGE 199

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     VL+    R + ++  R+ +      
Sbjct: 200 QTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--KA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 258 TLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|89053397|ref|YP_508848.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88862946|gb|ABD53823.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 292

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 125/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     +   +V A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 25  ELRLAYAWRDDRCEESLHRLVTAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKF 84

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A + 
Sbjct: 85  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAMKS 144

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
            + + +    + IA ++ +P+  V  +  ++     SL      ED      D +ED   
Sbjct: 145 GDTLDKHQLRQMIATEVGVPLHDVEMMEGRLAGSDYSLNATQSAEDEGREWIDTLEDDGE 204

Query: 598 VSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +          A LR+     + +L  RE  ++R R         TLE +G +  +++E
Sbjct: 205 QAEHIVEHFHDTAQLRDWLIASMNALNDRERFIVRERKLRE--DPRTLESLGTELGLSKE 262

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++SK++RSFL
Sbjct: 263 RVRQLEAAAFGKMRKTLEAQSKEVRSFL 290


>gi|15892330|ref|NP_360044.1| RNA polymerase factor sigma-32 [Rickettsia conorii str. Malish 7]
 gi|15619475|gb|AAL02945.1| RNA polymerase sigma-32 factor [Rickettsia conorii str. Malish 7]
          Length = 293

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 130/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEELLLAK--SYLEGNDLQAAHKLVTSHLKLVAKIASGYRTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 196 AESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|238750715|ref|ZP_04612214.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
 gi|238711105|gb|EEQ03324.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
          Length = 285

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 123/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S    +I+ +  +
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWD 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  +  L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 DHAADKLSYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|61657179|emb|CAG17720.1| DNA-directed RNA polymerase subunit D [Pseudomonas mendocina]
          Length = 259

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/301 (17%), Positives = 106/301 (35%), Gaps = 48/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T   ++   + +      L E++         
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILAEYNRVTTEGGRLAEVL--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              G+    +G    +       KE    +E++ + E  +   +++       PE A   
Sbjct: 52  --SGYIDPDDGSVPDEAAAPVPVKEGAAAEESDDEEEDESGDDEEEEGDGGPDPEEAARR 109

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E ++     L                                   +K  + S + 
Sbjct: 110 FTAVAEQQEKVQKAL-----------------------------------KKHGRGSKQA 134

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
                 L +L   + L   + D LV Q+ D   R+   E  +++L      + R  FL  
Sbjct: 135 IEELATLAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRADFLRL 194

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
             G E+D  W +      + ++   +      I + + ++  +  E  +S++E + I   
Sbjct: 195 FPGNEIDMDWAADLAK-GKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKDINRR 253

Query: 434 V 434
           +
Sbjct: 254 M 254


>gi|261414353|gb|ACX83585.1| RNA polymerase sigma-70 factor [Aeromonas sanarellii]
          Length = 272

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DD+  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EVDDMAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + IL+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEILRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|222087729|ref|YP_002546266.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221725177|gb|ACM28333.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 286

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 78/272 (28%), Positives = 131/272 (48%), Gaps = 19/272 (6%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  IK       ++  E   +   +R  + E   A+ ++  A++RLVIS+A K+ N GL 
Sbjct: 7   RRMIKMAMAAPYLARDEEHDLA--IRWKDHEDRGARNKIATAHMRLVISMAGKFRNFGLP 64

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 65  MSDLVQEGYVGLLEAAARFEPEREVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKA 124

Query: 530 HKVVRTARRMSNKIKREPT-------PEEIAKKLAMPVEGVR-KVLKITKEPISLETPIG 581
             +    RR+  K+ R  T        EEIA  L + +  V+    +++    SL+ P  
Sbjct: 125 --LFFNLRRLRAKLARGNTGVTVQSIHEEIAVALGVSLSDVQTMDARLSSNDASLQAPSI 182

Query: 582 DED--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGM 636
             D  ++   DF+  ++      + + I    R       L  L  RE +++R R  +  
Sbjct: 183 SGDAESAERMDFLISDEPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIIRARRLVED 242

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TLEE+G    +++ER+RQIE++A+ KL+
Sbjct: 243 G--ATLEELGADLGISKERVRQIESRAMEKLR 272


>gi|239827600|ref|YP_002950224.1| sporulation sigma factor SigF [Geobacillus sp. WCH70]
 gi|239807893|gb|ACS24958.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. WCH70]
          Length = 250

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 126/255 (49%), Gaps = 17/255 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T I   E + +   +R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q 
Sbjct: 7   QDQTPIKDQEMKEL---IRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEPDDLFQI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K+ +  
Sbjct: 64  GCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKEMGNKIRKAK 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             +S K  R PT  EIA  L +  E V    +  + P S+   + + D     L D I D
Sbjct: 123 DELSKKQGRAPTVTEIADYLEISPEDVVLAQEAIRSPASIHETVYENDGDPITLLDQIAD 182

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            + VS  D       +    + +  L  RE  ++ +R+      D T  EV  +  +++ 
Sbjct: 183 SDEVSWFD-------KIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQV 231

Query: 655 RIRQIEAKAIRKLKH 669
           ++ ++E K ++++K 
Sbjct: 232 QVSRLEKKILQQIKE 246


>gi|56963560|ref|YP_175291.1| sporulation sigma factor SigF [Bacillus clausii KSM-K16]
 gi|56909803|dbj|BAD64330.1| DNA-directed RNA polymerase sigma factor sigma-F [Bacillus clausii
           KSM-K16]
          Length = 254

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 64/262 (24%), Positives = 125/262 (47%), Gaps = 17/262 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +S  + + +   + K +   + A+  +V  N RLV SV +++ NRG +  
Sbjct: 4   EVKNGGKKKPLSDKQVKEL---IAKSQEGDTEARDSIVNHNTRLVWSVVQRFLNRGYEAD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSIKELSNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    ++  ++R PT  EIA+ L +  E +       +   S+   + + D     L 
Sbjct: 120 IRKAKDELTKTLRRAPTINEIAEHLGVTPEEIVFAGDANRSLSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D + V   D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADHSQVKWFD-------KIALKEAICDLGERERLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLKHPS 671
            +++ ++ ++E K + ++K   
Sbjct: 229 GISQVQVSRLEKKILEQMKETM 250


>gi|239934574|emb|CAR94601.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 223

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 54/267 (20%), Positives = 101/267 (37%), Gaps = 45/267 (16%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
            T  L +II            GF             +    +   +++    +     + 
Sbjct: 61  QTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAAAEIENEAEEEAEEGEG 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           + ++   +++ P+  E   R                            D +++ + +++ 
Sbjct: 110 ASEEEETLETGPDPEEAARR---------------------------FDSLSKTFVQVQK 142

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    +      K   L++KL      L L+    D+L+ Q+      I + E ++
Sbjct: 143 ------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLITQIRRSLTDIRNVEKQV 196

Query: 357 LRLAQS-YGIKRDVFLERHQGRELDPH 382
           + L     G+ R  F+      E +  
Sbjct: 197 MLLCVRDSGMPRKDFISTFPSNETNLS 223


>gi|22124334|ref|NP_667757.1| RNA polymerase factor sigma-32 [Yersinia pestis KIM 10]
 gi|45442990|ref|NP_994529.1| RNA polymerase factor sigma-32 [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51594579|ref|YP_068770.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           32953]
 gi|108806209|ref|YP_650125.1| RNA polymerase factor sigma-32 [Yersinia pestis Antiqua]
 gi|108810319|ref|YP_646086.1| RNA polymerase factor sigma-32 [Yersinia pestis Nepal516]
 gi|145600678|ref|YP_001164754.1| RNA polymerase factor sigma-32 [Yersinia pestis Pestoides F]
 gi|153997132|ref|ZP_02022265.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162418961|ref|YP_001605171.1| RNA polymerase factor sigma-32 [Yersinia pestis Angola]
 gi|165926363|ref|ZP_02222195.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165939186|ref|ZP_02227737.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166011667|ref|ZP_02232565.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166213537|ref|ZP_02239572.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167401873|ref|ZP_02307361.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167420986|ref|ZP_02312739.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167426241|ref|ZP_02317994.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|170026187|ref|YP_001722692.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis YPIII]
 gi|186893581|ref|YP_001870693.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis PB1/+]
 gi|218930813|ref|YP_002348688.1| RNA polymerase factor sigma-32 [Yersinia pestis CO92]
 gi|229837138|ref|ZP_04457303.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|229839498|ref|ZP_04459657.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229900061|ref|ZP_04515198.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229900493|ref|ZP_04515622.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|270488848|ref|ZP_06205922.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294505476|ref|YP_003569538.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957109|gb|AAM84008.1|AE013642_9 RNA polymerase, sigma(32) factor [Yersinia pestis KIM 10]
 gi|45437857|gb|AAS63406.1| RNA polymerase sigma-32 factor [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51587861|emb|CAH19464.1| RNA polymerase sigma-32 factor [Yersinia pseudotuberculosis IP
           32953]
 gi|108773967|gb|ABG16486.1| RNA polymerase sigma-32 factor [Yersinia pestis Nepal516]
 gi|108778122|gb|ABG12180.1| RNA polymerase sigma-32 factor [Yersinia pestis Antiqua]
 gi|115349424|emb|CAL22397.1| RNA polymerase sigma-32 factor [Yersinia pestis CO92]
 gi|145212374|gb|ABP41781.1| RNA polymerase sigma-32 factor [Yersinia pestis Pestoides F]
 gi|149289438|gb|EDM39516.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162351776|gb|ABX85724.1| alternative sigma factor RpoH [Yersinia pestis Angola]
 gi|165912959|gb|EDR31585.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165921887|gb|EDR39084.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165989436|gb|EDR41737.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166205210|gb|EDR49690.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166961115|gb|EDR57136.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167048766|gb|EDR60174.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167054760|gb|EDR64564.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169752721|gb|ACA70239.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           YPIII]
 gi|186696607|gb|ACC87236.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           PB1/+]
 gi|229682512|gb|EEO78599.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|229686841|gb|EEO78920.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695864|gb|EEO85911.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229706081|gb|EEO92090.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|262363541|gb|ACY60262.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367470|gb|ACY64027.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337352|gb|EFA48129.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294355935|gb|ADE66276.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320013591|gb|ADV97162.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 285

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  VA+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLGAAKQLILSHLRFVAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +AK
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAK 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  +++ + ++ +    DE  D   +   +  ++  S     I+ +  +
Sbjct: 160 ELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWD 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +      +  L  L  R + ++R R+    N   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SHAADKLSYALEGLDERSQHIIRARWLDDENKS-TLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|312139980|ref|YP_004007316.1| sigma-70 factor sigf [Rhodococcus equi 103S]
 gi|311889319|emb|CBH48635.1| sigma-70 factor SigF [Rhodococcus equi 103S]
          Length = 259

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 112/242 (46%), Gaps = 13/242 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + + E   +  ++ ++   L L   +A+++  RG  F DL+Q  +IGL+ A +++D 
Sbjct: 22  LQALDENEPGHAELRESIITRCLPLAQHIARRFDRRGEPFEDLVQVASIGLVNAVDRYDV 81

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   + R   D    +R+P  +++    +V+T+ ++S ++ R PT  
Sbjct: 82  ERGSDFLAFAVPTIMGEVRRHFRDTGWAVRVPRRLKELHLDLVKTSAQLSQRLGRSPTTR 141

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE----TPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           E+A++L + VE V + L+      +L        G +  S LGD + D ++         
Sbjct: 142 EMAEELGIEVEEVAQGLQAANGYQALSVDAAAGSGPDTGSTLGDLLGDNDS-----DIAG 196

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               ET   VL  L  RE  VL +RF           ++     V++  + +I +  + +
Sbjct: 197 VEDHETLRVVLEGLPERERTVLLLRFFGNQTQS----QIAAHVGVSQMHVSRILSDTLAR 252

Query: 667 LK 668
           L+
Sbjct: 253 LR 254


>gi|325674546|ref|ZP_08154234.1| RNA polymerase sigma-F factor [Rhodococcus equi ATCC 33707]
 gi|325554806|gb|EGD24480.1| RNA polymerase sigma-F factor [Rhodococcus equi ATCC 33707]
          Length = 259

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 112/242 (46%), Gaps = 13/242 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + + +   +  ++ ++   L L   +A+++  RG  F DL+Q  +IGL+ A +++D 
Sbjct: 22  LQALDENDPGHAELRESIITRCLPLAEHIARRFDRRGEPFEDLVQVASIGLVNAVDRYDV 81

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   + R   D    +R+P  +++    +V+T+ ++S ++ R PT  
Sbjct: 82  ERGSDFLAFAVPTIMGEVRRHFRDTGWAVRVPRRLKELHLDLVKTSAQLSQRLGRSPTTR 141

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE----TPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           E+A++L + VE V + L+      +L        G +  S LGD + D ++         
Sbjct: 142 EMAEELGIEVEEVAQGLQAANGYQALSVDAAAGSGPDTGSTLGDLLGDNDSDIAGVED-- 199

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               ET   VL  L  RE  VL +RF           ++     V++  + +I +  + +
Sbjct: 200 ---HETLRVVLEGLPERERTVLLLRFFGNQTQS----QIAAHVGVSQMHVSRILSDTLAR 252

Query: 667 LK 668
           L+
Sbjct: 253 LR 254


>gi|239981813|ref|ZP_04704337.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 328

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 111/231 (48%), Gaps = 12/231 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +F T+AM
Sbjct: 101 AYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAM 160

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A +L +  E
Sbjct: 161 PTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVRELADRLGLSQE 220

Query: 562 GVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V + +         SL+    ++D    L D I  ++        +     E+   ++A
Sbjct: 221 EVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGIEGIEYV-----ESLKPLIA 275

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R+ R+L +RF        T  E+G++  +++  + ++  + + +L+ 
Sbjct: 276 ELPARDRRILSLRFTAN----MTQSEIGEELGISQMHVSRLLTRTLNRLRK 322


>gi|203284664|ref|YP_002222404.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
 gi|201084107|gb|ACH93698.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
          Length = 267

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 136/259 (52%), Gaps = 8/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   ++     +  AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHRLITHEEEIELAKQIK---LGSLKAKNQMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  E+I ++  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLMEEEKSPKKEDIMERFNLTTAQYVKIIPYLEKEYSLDKKIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
            ED +          + L+     +   L  +E  +++ R+ +  +    TL+++  +  
Sbjct: 185 YEDNSFNPESTLEQNSTLKHLNYILETKLNEKERYIIKKRYNLDNSDKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++ E +RQIE + ++KL+ 
Sbjct: 245 ISSETVRQIEKRVLKKLRE 263


>gi|315506253|ref|YP_004085140.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
 gi|315412872|gb|ADU10989.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
          Length = 377

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 110/237 (46%), Gaps = 12/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F
Sbjct: 35  PPERRQEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SF 93

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           + YA   +   I R   D++  + +P  +RD I +V +    +++++ R PT  E++ +L
Sbjct: 94  TAYAAITIVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATATLTSELSRAPTVAELSARL 153

Query: 557 AMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             P E +   L+      P SL  P+G E ++  GD + + +      +    + R T +
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPVGGESSAEFGDLVGESD-----HALESVDDRVTVS 208

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +L  L  RE R+L MRF           E+  +F +++  + ++ ++A+  L+   
Sbjct: 209 GLLHRLPWRERRILAMRFYGNQTQ----AEIAARFGISQMHVSRLLSRALTWLRQAM 261


>gi|302867341|ref|YP_003835978.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302570200|gb|ADL46402.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 377

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 110/237 (46%), Gaps = 12/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F
Sbjct: 35  PPERRQEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SF 93

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           + YA   +   I R   D++  + +P  +RD I +V +    +++++ R PT  E++ +L
Sbjct: 94  TAYAAITIVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATATLTSELSRAPTVAELSARL 153

Query: 557 AMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             P E +   L+      P SL  P+G E ++  GD + + +      +    + R T +
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPVGGESSAEFGDLVGESD-----HALESVDDRVTVS 208

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +L  L  RE R+L MRF           E+  +F +++  + ++ ++A+  L+   
Sbjct: 209 GLLHRLPWRERRILAMRFYGNQTQ----AEIAARFGISQMHVSRLLSRALTWLRQAM 261


>gi|187763308|gb|ACD35531.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 271

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 114/315 (36%), Gaps = 45/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E +D+  T   I S            D   E+ + D
Sbjct: 59  ------------------------ETEDMAPTATHIGSELGEDDLADEDEDEEDEDEDGD 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             + D D             +LR +       I                 QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVAREKFGELRAQYEVTRLSI-----------------QKNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 257 MSIGEAKARRAKKEM 271


>gi|45643442|gb|AAC79984.2| HasL [Streptomyces ambofaciens]
 gi|126347729|emb|CAJ89446.1| putative sigma factor [Streptomyces ambofaciens ATCC 23877]
          Length = 281

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 54/248 (21%), Positives = 126/248 (50%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAA 485
           F   +S++ +G  E   A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 37  FFQQLSVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 97  DRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVQLARATEELRSRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
            PT +E+++ +++P + V +           SL+  I   ++  S L DFI  ++    L
Sbjct: 157 NPTTKELSELMSLPEDEVVEARLAANGYNSASLDAAISGSEDGESALADFIGAEDTALAL 216

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  R+ +++  RF      + T +++G++  V++  + ++ +
Sbjct: 217 VEDFHA-----LAPMIAELDERDRQIIHWRFV----EELTQKDIGERLGVSQMHVSRLIS 267

Query: 662 KAIRKLKH 669
           + + +L+ 
Sbjct: 268 RLLARLRE 275


>gi|298293645|ref|YP_003695584.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296930156|gb|ADH90965.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 293

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 125/261 (47%), Gaps = 18/261 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  +E   +    R  E     A   ++ A++RL I++A+++ N GL   DLIQEG+IGL
Sbjct: 21  LDRTEEYELAR--RWAEQHDEKALHALIHAHMRLAIAIARRFRNYGLPMPDLIQEGHIGL 78

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRM 539
           M+AA +F+     +F+TYA WW++ AI   +      +R       +     + R   R+
Sbjct: 79  MEAASRFETTHEVRFATYASWWIRAAIQDYVLRNWSIVRGGTSSGQKALFFNLRRVRARL 138

Query: 540 SNKIK--REPTPEE----IAKKLAMPVEGV-RKVLKITKEPISLETPIGD--EDTSHLGD 590
                   E T EE    IA+KL +    V R   ++    +SL  P+    ED +   D
Sbjct: 139 ERANGGAGETTREEMHRSIAEKLGVSEIEVARMDARLNVPDLSLNAPLSFGEEDGAERMD 198

Query: 591 FIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            +   + +     +++ +    R      L  L  RE R++  R     +   TLE +G+
Sbjct: 199 QLVAADPLPDEQVSMEIDGERRRRWLQGALRGLNEREFRIIEARRLTEDSE--TLEVLGE 256

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  +++ER+RQIE++AI KL+
Sbjct: 257 RLGISKERVRQIESRAIEKLR 277


>gi|11079163|dbj|BAB17586.1| DNA-directed RNA polymerase subunit D [Marinobacterium georgiense]
          Length = 270

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 59/317 (18%), Positives = 117/317 (36%), Gaps = 50/317 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M +L   P +   ++   +++      L +I      
Sbjct: 1   VELLTREGEIDIAKRIEEGIREVMMALSRFPGSVDIILNAYNQVLQEEGRLSDI--FSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+++                D   + +     + + D +S    S  D  +    PE 
Sbjct: 59  IDPDAE------VPEDETDAPVDIDDDDDDRSDDDDDDDDDSDNSDSSTDEKERGPDPEE 112

Query: 251 AENDERNLDE--DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           A      + E  D  ++A   +A +D++   VM                           
Sbjct: 113 ARQRFGLIQECLDNLNAARERNASKDEISEAVMA-------------------------- 146

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKR 367
                       L      + L+    +LLVE++ +  + I   E  ++R+  Q   + R
Sbjct: 147 ------------LCNAFAPIKLSPRYYELLVERVRNCIEGIRKQERSIMRICTQKAKMPR 194

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             F++   G E    W+    +  +  +   +   +  + + + ++  I    G+S+++ 
Sbjct: 195 PAFIKSFPGNETSSEWLESLANGNKP-YAAAINRNLYDLQRAQRKLIQIEETIGLSLADI 253

Query: 428 RHIVSMVRKGECEASIA 444
           + +   +  GE  A  A
Sbjct: 254 KEVNRAMSIGEAHARRA 270


>gi|157825543|ref|YP_001493263.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
 gi|157799501|gb|ABV74755.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
          Length = 293

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 129/270 (47%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   G+  
Sbjct: 18  NYLQKINNIPSLTQEEEFLLAK--SYLEENDLQAAHKLVTSHLKLVAKIASGYRTYGIPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFAKIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+     +  L  RE R+L  R     +T 
Sbjct: 196 AASGELIELLPETRPTPEAMAINKQNFTSKRKLLANAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 TTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|325202493|gb|ADY97947.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240149]
 gi|325207756|gb|ADZ03208.1| alternative sigma factor RpoH [Neisseria meningitidis NZ-05/33]
          Length = 287

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 129/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA +++    G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYKPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HQLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|297614622|gb|ADI48613.1| RNA polymerase sigma-70 factor [Shewanella algae]
          Length = 261

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 55/299 (18%), Positives = 107/299 (35%), Gaps = 50/299 (16%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            I IAKRIE G   + +S+ E P     ++   D+       L +II            G
Sbjct: 4   RIQIAKRIEEGINTVQSSVAEYPQAIAMILEQFDQFEAEEIRLSDII-----------SG 52

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV--DSPPENAENDER 256
           F +  E            E   DD+ + +   +       D   +      PE A     
Sbjct: 53  FVNPDEDDVGPSATHIGSELSDDDLDDEDDMDDDDEDDDSDSEDEGSKGPDPEEARERFG 112

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            L    + ++  L  ++ +  P+ + AL  I E+++E                       
Sbjct: 113 QLRAVYE-NSLKLIELKGRDHPESVAALFHIGEIFKE----------------------- 148

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
                        L   + D LV+ +  +  ++   E  +L+L  +   + +  F++   
Sbjct: 149 -----------FRLVPKQFDRLVKSMRSMMDKVRVQERLILKLCVEQAKMPKKNFVKLFT 197

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E D  W + A+      +   +    + +L+ R ++++I  ETG+SI+  + I   +
Sbjct: 198 GNETDISWFN-AEMNSGKPYAEGLKMVEEDVLRCRAKLEAIEAETGLSIASIKDINRRM 255


>gi|157803973|ref|YP_001492522.1| RNA polymerase factor sigma-32 [Rickettsia canadensis str. McKiel]
 gi|157785236|gb|ABV73737.1| hypothetical protein A1E_04050 [Rickettsia canadensis str. McKiel]
          Length = 296

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEEFLLAK--SYLEENDLKAAHKLVTSHLKLVAKIASGYRTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 T--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           T    L + + +        +  + N    +      +  L  RE R+L  R     +T 
Sbjct: 196 TESGELIELLPETRPTPEAMAINKQNYTTKKHLLASAMKILNDRELRILTERKL--KDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSSEYNISKERIRQIENTAFEKIKK 283


>gi|59800736|ref|YP_207448.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|194098013|ref|YP_002001061.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae NCCP11945]
 gi|239998477|ref|ZP_04718401.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|240016041|ref|ZP_04722581.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA6140]
 gi|240080183|ref|ZP_04724726.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|240115137|ref|ZP_04729199.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|240117420|ref|ZP_04731482.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|240122976|ref|ZP_04735932.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|240125228|ref|ZP_04738114.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|240127682|ref|ZP_04740343.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|254493195|ref|ZP_05106366.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|260441046|ref|ZP_05794862.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI2]
 gi|268594335|ref|ZP_06128502.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268596331|ref|ZP_06130498.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268600810|ref|ZP_06134977.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268603115|ref|ZP_06137282.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268681596|ref|ZP_06148458.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268683824|ref|ZP_06150686.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268686066|ref|ZP_06152928.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291044379|ref|ZP_06570088.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|293399564|ref|ZP_06643717.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
 gi|59717631|gb|AAW89036.1| putative RNA polymerase sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|193933303|gb|ACF29127.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512235|gb|EEH61580.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|268547724|gb|EEZ43142.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268550119|gb|EEZ45138.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268584941|gb|EEZ49617.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268587246|gb|EEZ51922.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268621880|gb|EEZ54280.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268624108|gb|EEZ56508.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268626350|gb|EEZ58750.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291011273|gb|EFE03269.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|291610133|gb|EFF39255.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
          Length = 290

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 137 KLFFNLRSMRKNLNVLSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|3929539|gb|AAC79983.1| HasR [Streptomyces ambofaciens]
 gi|117164812|emb|CAJ88361.1| putative sigma factor [Streptomyces ambofaciens ATCC 23877]
          Length = 281

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 126/248 (50%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAA 485
           F   +S++ +G  E   A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 37  FFQQLSVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    + +++ R
Sbjct: 97  DRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVQLARATEELRSRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
            PT +E+++ +++P + V +           SL+  I   ++  S L DFI   +A   L
Sbjct: 157 NPTTKELSELMSLPEDEVVEARLAANGYNSASLDAAISGSEDGESALADFIGADDATLAL 216

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  R+ +++  RF      + T +++G++  V++  + ++ +
Sbjct: 217 VDDFHA-----LAPMIAELDERDRQIIHWRFV----EELTQKDIGERLGVSQMHVSRLIS 267

Query: 662 KAIRKLKH 669
           + + +L+ 
Sbjct: 268 RLLARLRE 275


>gi|16078597|ref|NP_389416.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309407|ref|ZP_03591254.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313732|ref|ZP_03595537.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318656|ref|ZP_03599950.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322929|ref|ZP_03604223.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321315298|ref|YP_004207585.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
 gi|133475|sp|P19940|RPSG_BACSU RecName: Full=RNA polymerase sigma-G factor; AltName: Full=Stage
           III sporulation protein G
 gi|143430|gb|AAA22703.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|580764|emb|CAA40771.1| sigma-G factor [Bacillus subtilis subsp. subtilis str. 168]
 gi|2633906|emb|CAB13407.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|320021572|gb|ADV96558.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
          Length = 260

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 137/264 (51%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFRQLQ--DEGDDSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EPT E+IAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDERNTDSQWIEELA-----LKEGMRRLNDREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 231 EVAEEIGISQAQVSRLEKAAIKQM 254


>gi|85707639|ref|ZP_01038705.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85689173|gb|EAQ29176.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 298

 Score =  128 bits (322), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 72/279 (25%), Positives = 123/279 (44%), Gaps = 16/279 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +  I     ++  +   +    R  E E   A  ++V ++LRLV  +A  Y   
Sbjct: 13  QSLNRYLSEIKKYPVLTAEQEYMLAK--RYAEHEDPEAASQLVSSHLRLVAKIAMGYRGY 70

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLI EGN+GLM+  +KF+   G++ +TYAMWW+K +I   I      +++     
Sbjct: 71  GLPVSDLISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTTAA 130

Query: 527 DK--IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKE--PISLETP 579
            K     + R  +++      +  P++   IA  L +P + V  + +        SL TP
Sbjct: 131 QKKLFFNLRRMKKQLEAYEDSDLHPDDVTKIATDLGVPEQEVVNMNRRMMMGGDGSLNTP 190

Query: 580 IGD--EDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGI 634
           + +  + +    D++ D   +     A         E     + SL  RE+ +L      
Sbjct: 191 MRNGEDGSGEWQDWLTDDRPLQDETVADAEEAEVRHEMLVEAMDSLNEREQHILTE--RR 248

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                 TLEE+ + + V+RERIRQIE +A  KL+   + 
Sbjct: 249 LTEKPQTLEELSQVYDVSRERIRQIEVRAFEKLQKAMQR 287


>gi|66474655|gb|AAY46897.1| RpoD [Aeromonas veronii bv. sobria]
          Length = 271

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 115/314 (36%), Gaps = 44/314 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                             D E  A  +    S++       E++
Sbjct: 59  ----------------------------------DTEDMAPTATHIGSELSEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           + + DEDED                      E+   Y          ++ QK+ ++    
Sbjct: 85  DEDEDEDEDGDNSDDDGDGGPDPEVAREKFAELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKE 447
           +  GE +A  AKKE
Sbjct: 258 MSIGEAKARRAKKE 271


>gi|5911749|emb|CAB55833.1| SigJ protein [Streptomyces coelicolor A3(2)]
          Length = 266

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 55/269 (20%), Positives = 131/269 (48%), Gaps = 21/269 (7%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I+  + ++  + R +  +       + +G  E   A+  ++E N+ LV   A ++ +
Sbjct: 1   MPEIADPSKVAPRDARELSKLFFEQLTVLEEGTPEHQYARNTLIEMNMSLVRFAAGRFRS 60

Query: 466 RG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           RG  +  D++Q G IGL+KA ++F+     +F+++A+ ++   I R   D S  + +P  
Sbjct: 61  RGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRR 120

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIG- 581
           +++   ++ R    + +++ R PT  E+++ +++P + V +           SL+  I  
Sbjct: 121 LQEARVQLARATEELRSRLGRTPTTAELSELMSLPEDEVVEARLAANGYNSASLDAAING 180

Query: 582 -DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            ++  S L DFI   +A   L     A        ++A L  R+ +++  RF      + 
Sbjct: 181 SEDGESALADFIGADDAALALVDDFHA-----LAPMIAELDERDRQIIHWRFV----EEL 231

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T +++G++  V++  + ++ ++ + +L+ 
Sbjct: 232 TQKDIGERLGVSQMHVSRLISRLLARLRE 260


>gi|92115102|ref|YP_575030.1| RNA polymerase factor sigma-32 [Chromohalobacter salexigens DSM
           3043]
 gi|91798192|gb|ABE60331.1| RNA polymerase, sigma 32 subunit, RpoH [Chromohalobacter salexigens
           DSM 3043]
          Length = 288

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 65/272 (23%), Positives = 124/272 (45%), Gaps = 15/272 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   I++++    +S  E R +    R  E     A + +V ++LR V+ +A+ Y+  
Sbjct: 15  HDLNGYIQAVNRIAVLSSEEERELG--FRLYEQGDLEAARRLVMSHLRFVVHIARSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-- 524
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      ++I     
Sbjct: 73  GLPQADLIQEGNVGLMKAVKRFDPTQGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKA 132

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
            R     +    +R++     E   + IAK L +  + VR++  +++      +    +E
Sbjct: 133 QRKLFFNLRGAKKRLAWLNNDE--VDAIAKDLDVKPQVVREMEGRLSAFDAGYDATPSEE 190

Query: 584 DT---SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +         +++D+    A     +  + +        L  L  R   +L+ R+     
Sbjct: 191 EDQGYQAPAHYLDDERFDPAAQLEAADWEEDSTHRLQAALGELDERSRDILQRRWLAE-- 248

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  TL E+   + V+ ERIRQ+E  A++K+K 
Sbjct: 249 SKATLHELADVYGVSAERIRQLEKNAMKKIKQ 280


>gi|328880412|emb|CCA53651.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 283

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 125/248 (50%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG +  D++Q G IGL+KA +
Sbjct: 39  FFQELTVLEEGTHEYQYARNTLIEMNMSLVRYAAGRFRHRGDEMEDIVQVGMIGLIKAID 98

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+T+A+ ++   I R   D S  + +P  +++   ++ +    +S ++ R 
Sbjct: 99  RFELSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELAKATEELSTRLGRT 158

Query: 547 PTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI---GDEDTSHLGDFIEDKNAVSPL 601
           PT +E+A+ +++  E V +    +      SL+  +    ++  + L DFI  ++    L
Sbjct: 159 PTSKELAELMSLTEEEVNEARLASNGYHSSSLDAALSGENEDSEASLADFIGSEDPAMEL 218

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A L  R+ +++ +RF      + T  ++G++   ++  + ++ +
Sbjct: 219 VEDFHA-----LAPLIAELDERDRQIIHLRFV----EELTQAQIGERLGCSQMHVSRLLS 269

Query: 662 KAIRKLKH 669
           + I+ L+ 
Sbjct: 270 RTIKSLRQ 277


>gi|302556259|ref|ZP_07308601.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302473877|gb|EFL36970.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 281

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 127/250 (50%), Gaps = 14/250 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMK 483
            +F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+K
Sbjct: 35  RQFFDRLAVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIK 94

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++FD     +F+++A+ ++   I R   D +  + +P  +++   ++ R    + +++
Sbjct: 95  AIDRFDLSREAEFTSFAVPYIVGEIKRFFRDTTWAVHVPRRLQEARVQLARATEELRSRL 154

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
            R PT +E+++ +++P + VR+           SL+  I   D     L DFI  ++   
Sbjct: 155 GRTPTVKELSELMSLPEQEVREARIAANGYNSSSLDATISGSDDGEAALQDFIGAEDQAM 214

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L     A        +LA L  R+  ++RMRF      + T  ++G++  V++ ++ ++
Sbjct: 215 ELVEDFHA-----LAPLLAELDERDRHIIRMRFV----EELTQAQIGERLGVSQMQVSRL 265

Query: 660 EAKAIRKLKH 669
            ++ + +L+ 
Sbjct: 266 LSRTLARLRE 275


>gi|188588400|ref|YP_001920536.1| sporulation sigma factor SigG [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778549|ref|ZP_04821469.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498681|gb|ACD51817.1| RNA polymerase sigma-G factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082864|gb|EES48754.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 257

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 77/265 (29%), Positives = 131/265 (49%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + + + +    ++   +     A++  ++ NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTSKLPMLKEKEKKQLLLALKKGDLSARETFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    +      REPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALIVRDKFIKDNNREPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             + D I D KN        I      +    +  LT RE+ +L +RF  G     T  E
Sbjct: 181 IFVMDQISDSKNTDESWLENI------SIKEAMKKLTDREKLILNLRFFRG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|317163755|gb|ADV07296.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 287

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 134 KLFFNLRSMRKNLNVLSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HQLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|311029938|ref|ZP_07708028.1| sporulation sigma factor SigG [Bacillus sp. m3-13]
          Length = 259

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 81/267 (30%), Positives = 139/267 (52%), Gaps = 13/267 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFREMQGGELSAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   R+ ++  REPT EEIAK L +P E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVRERLMSETSREPTAEEIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++ D I D+           A         +  L  RE+ +LR RF  G     T  EV 
Sbjct: 182 YVLDQISDEKNKDIQWIEEIA-----LKEGMRRLNDREKLILRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +  +++ ++ ++E  AI+++    +S
Sbjct: 233 DEIGISQAQVSRLEKAAIKQMNKNIQS 259


>gi|308173495|ref|YP_003920200.1| RNA polymerase sporulation-specific sigma factor sigma-G [Bacillus
           amyloliquefaciens DSM 7]
 gi|307606359|emb|CBI42730.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553575|gb|AEB24067.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens TA208]
 gi|328911632|gb|AEB63228.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens LL3]
          Length = 260

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 81/264 (30%), Positives = 137/264 (51%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFKQLQ--DEGDDSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  REPT EEIAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSREPTAEEIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDERNKDTQWIEELA-----LKEGMRRLNEREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 231 EVAEEIGISQAQVSRLEKAAIKQM 254


>gi|302391629|ref|YP_003827449.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
 gi|302203706|gb|ADL12384.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
          Length = 260

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 77/248 (31%), Positives = 123/248 (49%), Gaps = 15/248 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   ++        A++ +V  NL+LV+SV +++ NRG    DL Q G IGL
Sbjct: 18  LSNEEMRELFKKMQ---NGDREARQTIVGGNLKLVLSVLQRFNNRGEPIDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     KFSTYA+  +   I R + D +  IR+   +RD  +K ++    + N
Sbjct: 75  MKAIDNFDLSRNVKFSTYAVPMIIGEIRRHLRDHN-PIRVSRSLRDTAYKALQMKESLEN 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K   EPT  EIA++L +P E + + L   ++PISL  PI  +  D  ++ D + D ++  
Sbjct: 134 KTSEEPTLTEIAQELGIPREEIVQALDAIQDPISLFEPIYQDGGDPIYVMDQVSDDDSED 193

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                  A         L  L  RE+ +L MRF  G     T  EV     +++ ++ ++
Sbjct: 194 ESWLEGIA-----VREALRQLEDREKLILSMRFYKG----KTQMEVADNIGISQAQVSRL 244

Query: 660 EAKAIRKL 667
           E  A+  L
Sbjct: 245 EKAALENL 252


>gi|167627742|ref|YP_001678242.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597743|gb|ABZ87741.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 292

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/274 (22%), Positives = 136/274 (49%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +  ++    +S+ E + +    +  +     A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LNSYLNFVNSLPILSVEEEQELARRYKYQK--DLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   + +A++L +  E V ++ K   +   SL+ P  D++  
Sbjct: 141 KLFFNLRSSKDKIGWLSSEDIKQ-LAEELGVKEETVIEMEKRMCQGDASLDLPYTDDEGG 199

Query: 587 HL---GDFIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     V++    R + ++  R+ +   T  
Sbjct: 200 QSNQQSFYLEDKSSDIEHQIVQQDYYDNFKAIVKDVISGFDTRTKDIIMSRYLLD--TKA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE +A+ KL+   ++K
Sbjct: 258 TLQDLAAKYNISAERVRQIEEEALVKLRKAIKNK 291


>gi|50871556|emb|CAF74869.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/301 (17%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +     V + + D +     S+++       PE A   
Sbjct: 59  DDGAA-------APQEVEPQTPQSTSKPVDDDKDDEDEEESESEEEEGDGGPDPEVARLR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   +I   E  +++L      + R  FL +
Sbjct: 137 TEELEALAILFMPIKLVPKQYDALVERVRDALSQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        + ++   +    + I + + ++  +  +  ++I++ + I   
Sbjct: 197 FPNNETNLDWAEQLAA-GKSKYAEAIGNRKEDIQRCQQKLIELEQQCELAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|187935615|ref|YP_001885389.1| sporulation sigma factor SigG [Clostridium botulinum B str. Eklund
           17B]
 gi|187723768|gb|ACD24989.1| RNA polymerase sigma-G factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 257

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 76/265 (28%), Positives = 131/265 (49%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           I N+++   V T  + + + +    ++   +     A++  ++ NLRLV+SV +++ NRG
Sbjct: 2   IINKVEICGVNTSKLPMLKEKEKKQLLLALKKGDLSARETFIKGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    +      +EPT  +IAK+L +P E V   L   ++P+SL  PI  +  D 
Sbjct: 121 IAYKALIVRDKFIKDNNKEPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDA 180

Query: 586 SHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             + D I D KN        I      +    +  LT RE+ +L +RF  G     T  E
Sbjct: 181 IFVMDQISDSKNTDESWLENI------SIKEAMKKLTDREKLILNLRFFRG----RTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ ++ 
Sbjct: 231 VADEIGISQAQVSRLEKTALKHMRK 255


>gi|47028349|gb|AAT09107.1| RpoH-like sigma factor [Rhizobium sp. TAL11145]
          Length = 289

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 77/281 (27%), Positives = 133/281 (47%), Gaps = 19/281 (6%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
             + ++   R  IK       +   E   +   +R  + +   A+ ++  A++RLVIS+A
Sbjct: 1   MHMKNMSADRRMIKIAMAAPYLGRDEEHDLA--IRWKDHDDRGARNKIATAHMRLVISMA 58

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
            K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I      +R
Sbjct: 59  GKFRNFGLPMSDLVQEGYVGLLEAAARFEPEREVRFSTYASWWIRASIQDYILRNWSIVR 118

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPT-------PEEIAKKLAMPVEGVR-KVLKITKE 572
                  K   +    RR+  K+ R  T        EEIA  L + +  V+    +++  
Sbjct: 119 GGTSSAQKA--LFFNLRRLRAKLARGNTGVTVQSIHEEIAVALGVSLADVQTMDARLSSN 176

Query: 573 PISLETPIGDED--TSHLGDFI--EDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERV 627
             SL+ P    D  ++   DF+  ++      + + I    R       L  L  RE ++
Sbjct: 177 DASLQAPSISGDAESAERMDFLISDEPLPDEQVSNMIDGERRRVWLASALKHLNEREMKI 236

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R R  +      TLEE+G    +++ER+RQIE++A+ KL+
Sbjct: 237 IRARRLVEDG--ATLEELGADLGISKERVRQIESRAMEKLR 275


>gi|291453672|ref|ZP_06593062.1| SigI protein [Streptomyces albus J1074]
 gi|291356621|gb|EFE83523.1| SigI protein [Streptomyces albus J1074]
          Length = 285

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 111/231 (48%), Gaps = 12/231 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+   G +F T+AM
Sbjct: 58  AYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAM 117

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D S ++R+P  +++    + +    ++ K+ R PT  E+A +L +  E
Sbjct: 118 PTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVRELADRLGLSQE 177

Query: 562 GVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V + +         SL+    ++D    L D I  ++        +     E+   ++A
Sbjct: 178 EVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGIEGIEYV-----ESLKPLIA 232

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  R+ R+L +RF        T  E+G++  +++  + ++  + + +L+ 
Sbjct: 233 ELPARDRRILSLRFTAN----MTQSEIGEELGISQMHVSRLLTRTLNRLRK 279


>gi|85058065|ref|YP_453767.1| RNA polymerase factor sigma-32 [Sodalis glossinidius str.
           'morsitans']
 gi|84778585|dbj|BAE73362.1| RNA polymerase sigma-32 factor RpoH [Sodalis glossinidius str.
           'morsitans']
          Length = 285

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 133/270 (49%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E R +   +         A K+++ ++LR V+ +A+ Y+  GL
Sbjct: 16  LEAYVRAANAYPMLTAEEERALAERL--HYQGDLEAAKKLILSHLRFVVHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE-- 583
                + +T +R+    + E   E +AK+L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVAKELGVTSKDVREMESRMAAQDMTFDPTPEDEAR 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           +   +   +  ++  S     I+ +  +       +  L  L  R + ++R R+ +  + 
Sbjct: 192 EGQPMAPMLYLQDKSSDFADGIEEDNWDDHAADKLSAALEGLDERSQDIIRARW-LDDDN 250

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++K++
Sbjct: 251 KSTLQELADRYGVSAERVRQLEKNAMKKMR 280


>gi|133286|sp|P11539|RP32_CITFR RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein
 gi|40469|emb|CAA33083.1| unnamed protein product [Citrobacter freundii]
          Length = 284

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ VA+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAEKL--HYQGDLEAAKTLILSHLRFVVHVARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           +  DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  RQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+ +  +  
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEEDNWEDQAANKLTHAMEGLDERSQDIIRARW-LDEDNK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 STLQELADRYGVSAERVRQLEKNAMKKLR 279


>gi|296332278|ref|ZP_06874740.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674979|ref|YP_003866651.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150592|gb|EFG91479.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305413223|gb|ADM38342.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 255

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 66/259 (25%), Positives = 127/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K       +   E + +   +++ +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNGKNAQLKDHEVKEL---IKQSQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S  + R PT +EIA  L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRAKDELSKTLGRVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D +     D       +      ++ L  RE+ ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADNSEEKWFD-------KIALKEAISDLEEREKLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQIK 247


>gi|259479065|dbj|BAI40080.1| RNA polymerase sigma-70 factor [Aeromonas sp. TT1]
          Length = 271

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 113/315 (35%), Gaps = 45/315 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E +D+  T   I S            +   E+ + 
Sbjct: 59  N------------------------EAEDMAPTATHIGSELGEDDLADEDEEDEDEDEDG 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           D  + D D             +LR +       I                 QK+ ++   
Sbjct: 95  DSSDDDGDGGPDPEVAREKFAELRAQYEVTRLSI-----------------QKNGRAHND 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D + +   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VQRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 257 RISIGEAKARRAKKE 271


>gi|302552488|ref|ZP_07304830.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470106|gb|EFL33199.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 285

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 123/248 (49%), Gaps = 14/248 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           +F   ++++ +G  E   A+  ++E N+ LV   A+++ + G    D++Q G IGL+KA 
Sbjct: 40  QFLDRLAVLEEGTPEHQYARNTLIEMNMSLVRFAARRFRSSGQAMEDVVQVGVIGLIKAI 99

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ +    +++++ R
Sbjct: 100 DRFEVSREVQFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARTELAKATEELASRLGR 159

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPI---GDEDTSHLGDFIEDKNAVSP 600
            P   E+A  + +  E V +        +  SL+  I    ++  S L +FI +++    
Sbjct: 160 APRVAELAALMNLSEEEVVEAQVAANGYLSSSLDATISGDSEDSDSTLSEFIGEEDPGLE 219

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           L     A        ++A L  R+  +L +RF      + T  E+GK+  +++  + ++ 
Sbjct: 220 LVEDFHA-----LAPLIAELDERQRLILHLRFV----EELTQAEIGKRLGISQMHVSRLI 270

Query: 661 AKAIRKLK 668
           A+ + +L+
Sbjct: 271 ARTVARLR 278


>gi|209407276|emb|CAP72523.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 267

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 57/312 (18%), Positives = 116/312 (37%), Gaps = 46/312 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   +M+++   P T  +++   + + +    L +I  L   I P
Sbjct: 1   LTREGEIEIAKRIEEGIREVMSAVAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
           +  G         + Q+ E  + +       + + D E     S+++       PE A  
Sbjct: 59  DDDGAA-------APQEVEPVAPQTTAKPAADDKDDDEEDESDSEEEEGDGGPDPEVARV 111

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               + E  + +   L                                   +K  + S +
Sbjct: 112 RFGAVAEQLEAAKKAL-----------------------------------KKHGRGSQQ 136

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLE 372
                ++L  L   + L   + D LVE++     ++   E  ++++      + R  FL 
Sbjct: 137 ATDALQELATLFMPIKLIPKQYDALVERVRGALGQVRAQERAIMQICVRDARMPRADFLR 196

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           +    E D  W        + ++   +A   + I + + ++ ++  E  + I++ + I  
Sbjct: 197 QFPSNETDLGWADQLAS-SKSKYAEAIAARKEDIQRCQEKLLALEEECALVIADIKDINR 255

Query: 433 MVRKGECEASIA 444
            +  GE +A  A
Sbjct: 256 RMSIGEAKARRA 267


>gi|78067614|ref|YP_370383.1| RNA polymerase factor sigma-32 [Burkholderia sp. 383]
 gi|77968359|gb|ABB09739.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. 383]
          Length = 311

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 140/273 (51%), Gaps = 12/273 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    +++ E R   +  R+G    S   + +V ++LRLV+S+++ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPLLTVEEERQYATEFREGNNLDS--ARRLVLSHLRLVVSISRNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I     T+++   
Sbjct: 93  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTVKVATT 152

Query: 525 -MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
             + K+   +R+ ++    +  E   + +AK+L +  E V     +++   I+LE  + D
Sbjct: 153 KAQRKLFFNLRSHKKGLQAMTPE-EIDGLAKELNVKREDVTEMETRLSGGDIALEGQVED 211

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT 638
            + S+  +    +  N  + + +A Q +  +T    + L +L  R  R++  R+    + 
Sbjct: 212 GEESYAPIAYLADSHNEPTAVLAARQRDTLQTDGIAQALDALDARSRRIIEARWLHVDDD 271

Query: 639 ---DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 272 GSGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304


>gi|89256211|ref|YP_513573.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314678|ref|YP_763401.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502270|ref|YP_001428335.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167009752|ref|ZP_02274683.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367537|ref|ZP_04983563.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290952961|ref|ZP_06557582.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295313833|ref|ZP_06804405.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144042|emb|CAJ79290.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129577|gb|ABI82764.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253353|gb|EBA52447.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156252873|gb|ABU61379.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 292

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/274 (22%), Positives = 133/274 (48%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   +E+A++L +  E V ++ K   +   SL+    D+D  
Sbjct: 141 KLFFNLRSSKDKIGWLSSEN-IKELAEELGVKEETVIEMEKRMCQGDASLDLSYTDDDGE 199

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     VL+    R + ++  R+ +      
Sbjct: 200 QTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--KA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 258 TLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|226305067|ref|YP_002765025.1| RNA polymerase sigma factor SigF [Rhodococcus erythropolis PR4]
 gi|226184182|dbj|BAH32286.1| RNA polymerase sigma factor SigF [Rhodococcus erythropolis PR4]
          Length = 264

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 104/244 (42%), Gaps = 12/244 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             +  +     E    +  ++   L L   +A+++  RG    DL+Q   +GL+ A ++F
Sbjct: 27  EEMRTLEPHSPEYERVRTALITRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNAVDRF 86

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G  F ++A+  V   + R   D    +R+P  M++   ++ +    +S ++   PT
Sbjct: 87  DSTRGSDFVSFAVPTVMGEVRRHFRDTGWALRVPRRMKELHFQLGQAISELSQQLGHAPT 146

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
            +E+A+ L +  E V + L      + +S++       D   L + + D +A        
Sbjct: 147 VDELAETLGIEREEVAQALIAGNAYQTVSVDGAASNHTDDLPLVETLGDYDAA-----LE 201

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                E    +L  L  RE  VL +RF        T  ++ ++  V++  + ++ AK + 
Sbjct: 202 NVENHEALRPLLDKLPERERTVLMLRFFGN----LTQTQIAEKVGVSQMHVSRLLAKTLS 257

Query: 666 KLKH 669
            L+ 
Sbjct: 258 NLRE 261


>gi|37784422|gb|AAO13104.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
 gi|37784440|gb|AAO13113.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. veronii]
 gi|37784452|gb|AAO13119.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|37784464|gb|AAO13125.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. veronii]
 gi|37956259|gb|AAO73800.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|37956261|gb|AAO73801.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|91978895|gb|ABE66423.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|91978909|gb|ABE66430.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|91978911|gb|ABE66431.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763270|gb|ACD35512.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763272|gb|ACD35513.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763284|gb|ACD35519.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763312|gb|ACD35533.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763328|gb|ACD35541.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763330|gb|ACD35542.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763350|gb|ACD35552.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|187763360|gb|ACD35557.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 116/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|148833421|gb|ABR14580.1| DNA-dependent RNA polymerase sigma factor D subunit [Pseudomonas
           xiamenensis]
          Length = 270

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 61/309 (19%), Positives = 105/309 (33%), Gaps = 40/309 (12%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +MA++   P T    +     + +    L +I      I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMAAISMFPGTVDGFLGDYQRITEEGGRLSDI--FSGYIDPDDD- 57

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           G           +      +K+     E E + +       ++ S     PE A      
Sbjct: 58  GMSGTDNAIVPGEAAKPKSDKKASADDEDEDEEDEEDDTEAEEESDGGPDPEVARQRFGA 117

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + E  D     L                                   +K E+SS +    
Sbjct: 118 IQEQLDKLNKAL-----------------------------------KKHERSSPEVVAE 142

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQG 376
            + L  L   + L   + D LVE++      I   E  +++L      + R  FL    G
Sbjct: 143 LDALALLFMPIKLVPKQYDALVERVRSTQDHIRAQERAIMQLCVRDARMPRADFLRSFPG 202

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E +  W+           +   A + D IL+ + ++ ++  +  +SI++ + I   +  
Sbjct: 203 NETNEQWIDDLLAKGPAYAEALQAVKAD-ILRAQKQLIALEQDAQLSIADVKDINRRMSI 261

Query: 437 GECEASIAK 445
           GE  A  AK
Sbjct: 262 GEARARRAK 270


>gi|66474707|gb|AAY46923.1| RpoD [Aeromonas sp. 17m]
          Length = 272

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 120/316 (37%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + +LR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A   KKE
Sbjct: 257 RRMSIGEAKARRRKKE 272


>gi|55274903|gb|AAV49253.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 192

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 76/192 (39%), Positives = 129/192 (67%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+
Sbjct: 1   VKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQT 60

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S+
Sbjct: 61  RTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSV 120

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+  
Sbjct: 121 DTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG 180

Query: 637 NTDHTLEEVGKQ 648
               TLE+VG++
Sbjct: 181 YEAATLEDVGRE 192


>gi|257453679|ref|ZP_05618966.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
 gi|257448913|gb|EEV23869.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
          Length = 393

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 68/271 (25%), Positives = 125/271 (46%), Gaps = 11/271 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I ++     ++  + + +    R  +     A + +V ++LR VI +A+ Y+  
Sbjct: 119 VNLGAYINAVHQIPILTAEQEQELAH--RYTDEGDVEAARLLVMSHLRFVIHIARSYSGY 176

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      +++     
Sbjct: 177 GLPQGDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKA 236

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
             K+   +R+ ++ +N++  E   E IAK L + V+ V     ++T    S E    DED
Sbjct: 237 HRKLFFNLRSLKKTNNQLTLE-EAEAIAKDLNVTVKQVLEMESRLTSYDASFEAQSDDED 295

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNTDH 640
                     ++A  P D    A+  E         +  L  R   +++ R+        
Sbjct: 296 EGRYAPQYFLEDAADPADMVEDADWEENNNSALMEAMEDLDDRSRDIVQQRWL--NEQKA 353

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL E+  ++ ++ ER+RQIE  A+ K+K   
Sbjct: 354 TLHELAAEYNISAERVRQIEKNAMDKIKEAM 384


>gi|187763316|gb|ACD35535.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE  A  AKKEM
Sbjct: 258 MSIGEARARRAKKEM 272


>gi|2832900|emb|CAA04387.1| Sigma A [Lysinibacillus sphaericus]
          Length = 140

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 86/139 (61%), Positives = 106/139 (76%)

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + REP+PEEI +++ +  E VR++LKI +EP+SLETPIG+ED SHLGDFIED  A SP D
Sbjct: 2   LGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDSEAQSPSD 61

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A    L+E    VL +LT REE VLR+RFG+      TLEEVGK F VTRERIRQIEAK
Sbjct: 62  HAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAK 121

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+RKL+HPSRSK+L+ FL+
Sbjct: 122 ALRKLRHPSRSKRLKDFLE 140


>gi|91787153|ref|YP_548105.1| sigma 32 (RpoH) [Polaromonas sp. JS666]
 gi|91696378|gb|ABE43207.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas sp. JS666]
          Length = 322

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/286 (22%), Positives = 127/286 (44%), Gaps = 21/286 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ + +     +++     S    ++V ++LRLV+S+++K
Sbjct: 33  VPPLGNLDAYISAVNRLPMLTLEQEQEFAKKLKENNDLDS--AGKLVLSHLRLVVSISRK 90

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILKNWRMVKVA 150

Query: 523 VH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----------VEGVRKVLKITK 571
               + K+   +R+ ++         T  +   +  +            E +    +++ 
Sbjct: 151 TTKAQRKLFFNLRSMKQGFKDDADVATHRDTLTEGQIDSMAKTLNVKREEVIEMEQRMSG 210

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASLTPREER 626
             + L+    D+     G      +A     + +++  R++         L  L PR  R
Sbjct: 211 GDVLLDPSPSDDGEDAFGPIAYLADATQEPTALMESRQRDSLASDGISAALQELDPRSRR 270

Query: 627 VLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++  R+    +      TL ++  ++ V+ ERIRQIE  A++K+K 
Sbjct: 271 IVEERWLKVNDDGSGGMTLHDLADEYQVSAERIRQIEVSAMKKMKK 316


>gi|320105081|ref|YP_004180672.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319752363|gb|ADV64123.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 322

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 68/225 (30%), Positives = 130/225 (57%), Gaps = 10/225 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++  AN+RLV  VAK++ +RG+ + DL+QEG  GL++A ++FD   G K +TYA WW+
Sbjct: 92  RSKLALANMRLVAHVAKRFRDRGVSYSDLLQEGFCGLLEAIDRFDLAHGTKLATYATWWI 151

Query: 505 KQAITRSIADQSCTIR-IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +QA+ R++A  +  +R  P H+R          +    +  +  T ++ + + ++  E +
Sbjct: 152 RQAMQRAVAATAYPVRLSPRHLRQLARN-----QEEIERGGQPRTRKKASDEESVSPEMI 206

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++   T+  +SL+  +  + +  L   + D           + ++ ET  +++ +L PR
Sbjct: 207 QRIHAATRPTVSLDATVDSDSSFSLLHTMSDPEGDRTG----EVDMDETIVKLMENLRPR 262

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E +VL +RFG+   T H+L +VGK   V++ER+RQI+ +A+ KL+
Sbjct: 263 EIQVLSLRFGLNGATRHSLSQVGKVLDVSKERVRQIQDRALEKLR 307


>gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
 gi|300076221|gb|ADJ65620.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
          Length = 299

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 130/275 (47%), Gaps = 8/275 (2%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           S+  I   I +++    ++  E   +   +R+       A ++MV ++LRLV+S+A+ Y 
Sbjct: 25  SLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDLG--AAQKMVLSHLRLVVSIARGYL 82

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 83  GYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLVKVATT 142

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           E +AK L +  E V ++    +   I+LE+P  DE
Sbjct: 143 KAQRKLFFNLRSHKEGLDAMTPAQVEALAKTLDVKREEVIEMETRLSGRDIALESPTDDE 202

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           D   + +     D +  + +  A Q +    E     L+ L  R  R++  R+    +  
Sbjct: 203 DDKFAPIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDERSRRIVEARWLANDDGS 262

Query: 640 -HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TL E+  +F V+ ERIRQIEA A++K+K   ++
Sbjct: 263 GATLHELADEFGVSAERIRQIEAVALKKMKTSLQA 297


>gi|239934584|emb|CAR94606.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 230

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 95/270 (35%), Gaps = 48/270 (17%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +M +L   P   Q ++     +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIVIAKRIEEGVRELMHALAYWPGAVQQILDEYALVAK 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L ++I            G+    E       E+  +       +    D +     
Sbjct: 61  EERRLADVI-----------IGWLDPVEEIPTAVIEEIEELPVVAGAKVAGDDDDEEGGA 109

Query: 237 SKDDRSKVDS-PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           ++D+   V    PE A      L + +D +   L+                         
Sbjct: 110 TEDEEEAVSGVDPEEARVRFEALQQQQDKAQKALT------------------------- 144

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                     K    S + +     L  L     L   + D +  +     + I   E  
Sbjct: 145 ----------KYGYGSKQAEKELTALGDLFKFFKLPTRQFDPIYSKARATLENIRKQERT 194

Query: 356 LLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
           ++ L      ++R  F++   G E++  W+
Sbjct: 195 IMDLCTRKAQMQRKTFIKEFPGNEINEEWL 224


>gi|67458885|ref|YP_246509.1| RNA polymerase factor sigma-32 [Rickettsia felis URRWXCal2]
 gi|67004418|gb|AAY61344.1| RNA polymerase sigma-32 factor [Rickettsia felis URRWXCal2]
          Length = 293

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 127/270 (47%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEEFLLAK--SYLEENDLQAAHKLVTSHLKLVAKIASGYRTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI- 529
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 530 ----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
               +K+      + ++        +IA +L + V  V ++  +I+   +SL  PI  +D
Sbjct: 136 FFSLNKIKHKITNLYSRAITADDFIQIADELGVSVNEVSEMNTRISGPDLSLNNPINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + +    R+  +  +  L  RE R+   R     +T 
Sbjct: 196 AESGELIELLPETRPTPETIAINKQDSTGKRKLLSNAMKILNDRELRIFTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSNEYNISKERIRQIENTAFEKIKK 283


>gi|23502620|ref|NP_698747.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619688|ref|YP_001593575.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|254703536|ref|ZP_05165364.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|260568841|ref|ZP_05839309.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|23348625|gb|AAN30662.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336499|gb|ABX62804.1| RNA polymerase sigma factor, sigma-70 family [Brucella canis ATCC
           23365]
 gi|260154225|gb|EEW89307.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
          Length = 311

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 76/289 (26%), Positives = 131/289 (45%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNCWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|268590799|ref|ZP_06125020.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
 gi|291313578|gb|EFE54031.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
          Length = 292

 Score =  128 bits (321), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 65/271 (23%), Positives = 130/271 (47%), Gaps = 16/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +++ +    ++  E + +   +         A K+++ ++LR VI VA+ Y   GL
Sbjct: 16  IEAYVRAANSYPMLTAEEEKELAERL--HYHGDLDAAKQLILSHLRFVIHVARSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + +  +R+    + E   + +A++L +  + VR++               D+D+S
Sbjct: 134 KLFFNLRKNKKRLGWFNQDE--VDMVAQELGVSTKDVREMESRMAAQDMAFDMSDDDDSS 191

Query: 587 HLGD------FIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             G       +++DK +    S  D   +++  +     L SL  R + ++R R+ +  +
Sbjct: 192 DFGGPVAPVLYLQDKASDFAGSIEDDNWESHATDRLADALDSLDERSQDIIRARW-LDDD 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 NKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|298243403|ref|ZP_06967210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
 gi|297556457|gb|EFH90321.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
          Length = 294

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 118/242 (48%), Gaps = 15/242 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E ++S  + E++     LV     +        +   DLI  G IGL+ A +++D  
Sbjct: 13  RYQEHKSSELRNELITMYAPLVRLAVGRLGIPPTSIMDSEDLIGYGMIGLINAIDRYDLS 72

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F  +A   ++ A+   I   +    +P     +I ++ RT   +  ++ R  T  E
Sbjct: 73  RGVRFEAFATPRIRGAVIDQIRQLNW---LPRSSVSRIRQIERTHAELEQQLGRPATEAE 129

Query: 552 IAKKLAMPVEGVRKVLK-ITKEPISLETP----IGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            AK L + VE  R++L  ++   +SL+ P    I +++++ LGD +ED++   P ++   
Sbjct: 130 AAKALDVSVERYRQMLTEMSVSVLSLDAPMGSSIQEDESASLGDMLEDESQQDPGEAVEH 189

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L ++ +  L  L PRE+ +L + +      + T++E+ +   V+  R+ Q+  +A+ +
Sbjct: 190 EELIQSLSAALQHLPPREQLLLSLYY----KEELTMKEISRIMNVSESRVCQLRMQALVR 245

Query: 667 LK 668
           L+
Sbjct: 246 LR 247


>gi|187763354|gb|ACD35554.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +   AKKEM
Sbjct: 258 MSIGEAKGRRAKKEM 272


>gi|261417856|ref|YP_003251538.1| sporulation sigma factor SigF [Geobacillus sp. Y412MC61]
 gi|297529524|ref|YP_003670799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319767332|ref|YP_004132833.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
 gi|261374313|gb|ACX77056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC61]
 gi|297252776|gb|ADI26222.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317112198|gb|ADU94690.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
          Length = 252

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 119/242 (49%), Gaps = 14/242 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q G IGL+K+ +KF
Sbjct: 18  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D   T+++   +++  +K+ +    +S    R PT
Sbjct: 78  DLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPT 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA  L +  E V    +  + P S+   + + D     L D I D +  S  D    
Sbjct: 137 VTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADADEASWFD---- 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    + +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K ++ 
Sbjct: 193 ---KIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQVSRLEKKILQH 245

Query: 667 LK 668
           +K
Sbjct: 246 IK 247


>gi|111017120|ref|YP_700092.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110816650|gb|ABG91934.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 111/232 (47%), Gaps = 12/232 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EAS  + E++   L L   +A+++  RG    DL+Q   +GL+KA ++FD   G+ F +Y
Sbjct: 37  EASALRDEVITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSY 96

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A+  +   + R   D   ++R+P  M++    + +    +S ++ R P+  EIA +L + 
Sbjct: 97  AVPTIMGEVRRYFRDTGWSMRVPRRMQELHALITKAVDELSQELGRSPSASEIAAQLELD 156

Query: 560 VEGVRKVLKI--TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           V  V + L      + +S++  +GD+ D   L + + +++                    
Sbjct: 157 VREVSEGLLAKNAYQTLSMDAAMGDDPDDLPLAETLGEED-----PELANVESHAAVRPA 211

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L P E RVL +RF        T  E+ ++  V++ ++ +I A+ +  L+
Sbjct: 212 LQKLPPLERRVLMLRFF----GSMTQTEIAQRVGVSQMQVSRILARTLSGLR 259


>gi|4514521|dbj|BAA75459.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 279

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 119/316 (37%), Gaps = 38/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++   ++   G   L +I  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PES        E  +  + ED     +  DV+  + D E  ++   D        PE 
Sbjct: 59  LDPESDEEIPEVLEEETELEEEDEKSPSKAKDVKLDDDDEEEESEGDDDSEGDSGPDPEI 118

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+   +++   +                                    K  ++
Sbjct: 119 AKARFTELENAWNETKAII-----------------------------------VKHGRN 143

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S +     E L  +           +++ E +    ++I  NE E++R A   G + R+ 
Sbjct: 144 SAEADAALESLAAVFMMFKFTPRLFEIISEMIRGTHEQIRSNEREIMRYAVRRGRMDRNQ 203

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F      +E +  W+         E K  +      +L  + +I  I  + G+++ + + 
Sbjct: 204 FRLSFPEQESNLAWLDEQIAKAPAETKGHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 263

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 264 ISKRMTVGEAKARRAK 279


>gi|295102494|emb|CBL00039.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii L2-6]
          Length = 255

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 132/247 (53%), Gaps = 16/247 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +++  R        A++ M+E NLRLV+SV ++++ RG    DL Q G IGL
Sbjct: 18  LSEQEKRDLLTRAR---AGDKKARQSMIEGNLRLVLSVVQRFSQRGENMDDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     +FSTY +  +   I R + D +  +R+   +RD  ++ +++   +  
Sbjct: 75  IKAIDNFDPAQQVRFSTYGVPMIIGEIRRFLRDNN-ALRVSRSLRDTAYRAMQSREELEK 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           ++ REPT +EIA+K  +    V   L+   EP+SLE P+  +  D  ++ D + D +   
Sbjct: 134 QLGREPTVDEIAQKTGLSRREVSAALESVVEPLSLEEPVYADGGDAVYVIDQVRDPDGED 193

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              S +Q        + +A LTPRE+R++ +R+  G     T  EV ++  +++ ++ ++
Sbjct: 194 SWISGLQ------FRQTVAGLTPREKRIMELRYLKG----KTQMEVAREIGISQAQVSRL 243

Query: 660 EAKAIRK 666
           E  A+ +
Sbjct: 244 EKAALEQ 250


>gi|262195735|ref|YP_003266944.1| RNA polymerase, sigma 70 family subunit [Haliangium ochraceum DSM
           14365]
 gi|262079082|gb|ACY15051.1| putative RNA polymerase, sigma 70 family subunit [Haliangium
           ochraceum DSM 14365]
          Length = 389

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 81/275 (29%), Positives = 137/275 (49%), Gaps = 13/275 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+       +S  E   +   V+  E E + A + ++EANLRLV+ ++ +Y     
Sbjct: 106 LSAYIQETKRYPLLSREEEHDLA--VKLVENEDADAARRLIEANLRLVVKISYEYRRAYR 163

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRD 527
             LDLIQEGNIGLM+A  K+D   G K S+YA WW++  I + I +    ++I     + 
Sbjct: 164 NLLDLIQEGNIGLMQAVRKYDPYRGVKLSSYAAWWIRAYILKFILNNWRLVKIGTTQAQR 223

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDTS 586
           K+   +R  R    ++   PTP  +A+ L +  + V ++ K  +    SL+ P+  E+  
Sbjct: 224 KLFFNLRKERERLEQLGFTPTPALLAENLDVTEKEVVEMEKRLSAPDASLDAPMQGEEDG 283

Query: 587 ---HLGDFIE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                 D++     D+       S  Q  LRE   R   +L  REE + R R+    +T 
Sbjct: 284 APRTRMDYLPTEETDRPDRQVAQSQFQELLREKLERFAETLEGREETIFRERWL--TDTP 341

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TL+++G Q+ V+RER RQ+E + + +L+    ++
Sbjct: 342 STLQQIGDQYGVSRERARQLEKRLLGRLRKYLEAE 376



 Score = 37.5 bits (85), Expect = 8.4,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKR-IEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DP+  Y++E     LLSRE E  +A + +E   A     L E+ L    + I  +     
Sbjct: 104 DPLSAYIQETKRYPLLSREEEHDLAVKLVENEDADAARRLIEANLRL-VVKISYEYRRAY 162

Query: 178 TTLLREI 184
             LL  I
Sbjct: 163 RNLLDLI 169


>gi|297196939|ref|ZP_06914336.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197715922|gb|EDY59956.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 281

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 129/248 (52%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAA 485
           F   ++++ +G  E S A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 37  FFDQLAVLEEGTPEYSYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 96

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ R    + +++ R
Sbjct: 97  DRFELTREVEFTSFAIPYIVGEIKRFFRDTTWAVHVPRRLQEARVQLARATEELRSRLGR 156

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
            PT +E+++ +++  E VR+      +    SL+  I   ++  S L DFI  ++    L
Sbjct: 157 TPTVKELSELMSLSEEEVREARLASNSYNSSSLDAAISGSEDGESALADFIGAEDRALEL 216

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A        ++A+L  R+ +++ MRF      + T  ++G++  V++  + ++ +
Sbjct: 217 VEDFHA-----LAPLIAALDDRDRQIIHMRFV----EELTQAQIGERLGVSQMHVSRLLS 267

Query: 662 KAIRKLKH 669
           + + +L+ 
Sbjct: 268 RTLARLRE 275


>gi|297614620|gb|ADI48612.1| RNA polymerase sigma-70 factor [Shewanella haliotis]
          Length = 259

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 55/299 (18%), Positives = 107/299 (35%), Gaps = 50/299 (16%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            I IAKRIE G   + +S+ E P     ++   D+       L +II            G
Sbjct: 2   RIQIAKRIEEGINTVQSSVAEYPQAIAMILEQFDQFEAEEIRLSDII-----------SG 50

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV--DSPPENAENDER 256
           F +  E            E   DD+ + +   +       D   +      PE A     
Sbjct: 51  FVNPDEDDVGPSATHIGSELSDDDLDDEDDMDDDDEDDDSDSEDEGSKGPDPEEARERFG 110

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            L    + ++  L  ++ +  P+ + AL  I E+++E                       
Sbjct: 111 QLRTVYE-NSLKLIELKGRDHPESVAALFHIGEIFKE----------------------- 146

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
                        L   + D LV+ +  +  ++   E  +L+L  +   + +  F++   
Sbjct: 147 -----------FRLVPKQFDRLVKSMRSMMDKVRVQERLILKLCVEQAKMPKKNFVKLFT 195

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E D  W + A+      +   +    + +L+ R ++++I  ETG+SI+  + I   +
Sbjct: 196 GNETDISWFN-AEMNSGKPYAEGLKMVEEDVLRCRAKLEAIEAETGLSIASIKDINRRM 253


>gi|228973923|ref|ZP_04134498.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980512|ref|ZP_04140822.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228779332|gb|EEM27589.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228785789|gb|EEM33793.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
          Length = 289

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 134/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 33  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 92

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 93  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 151

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 152 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 211

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 212 FVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 262

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 263 EEIGISQAQVSRLEKSAIKQM 283


>gi|88813090|ref|ZP_01128332.1| RpoH [Nitrococcus mobilis Nb-231]
 gi|88789723|gb|EAR20848.1| RpoH [Nitrococcus mobilis Nb-231]
          Length = 292

 Score =  128 bits (321), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 126/268 (47%), Gaps = 16/268 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + I++++    +S  E   +    R  +     A + +V ++LR V+ +A+ Y   GL  
Sbjct: 24  HYIQAVNRLPTLSAEEEYQLARRYR--DHNDLKAARGLVLSHLRFVVHIARGYKGYGLPL 81

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
            DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      +++      R  
Sbjct: 82  TDLIQEGNIGLMKAVKRFDPAVGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKL 141

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
              +    +R+    + E     +A  L +  E V+++ L+++ + +S +      +   
Sbjct: 142 FFNLRGAKKRLGWLNRAEVDA--VANDLGVKPETVQEMELRLSGQEVSFDPGPDAAEDDD 199

Query: 588 L----GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +      ++ D+    A        Q +  E+    LA L  R   ++  R+        
Sbjct: 200 IVRAPAAYLRDQRPNPAEEIESHDWQTHQSESLATALAHLDERSRAIVHERWL--NEPKA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+ +++ V+ ERIRQ+E  A++KL+
Sbjct: 258 TLQELAERYAVSAERIRQLEKNALKKLR 285


>gi|89895050|ref|YP_518537.1| hypothetical protein DSY2304 [Desulfitobacterium hafniense Y51]
 gi|89334498|dbj|BAE84093.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 260

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 129/257 (50%), Gaps = 15/257 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++     +S  E   ++   +      + A++ ++  NL+L+ ++ +++++RG +  DL 
Sbjct: 9   NLPRFPLLSDEEMMDLLHRAQ---NGDAEARERLINCNLKLIFNLVQRFSHRGYELEDLF 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G IGL+KA +KFD+  G KFSTYA+  +   I R + D    +++P   ++ ++KV +
Sbjct: 66  QIGTIGLIKAIDKFDFTYGVKFSTYAVPMIIGEIRRFLRD-DHPVKVPRSYKELVYKVNK 124

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
               +S  + R+PT  EIA+ + +  E +   L+  + P S+   +  +D+   ++ D +
Sbjct: 125 ARESLSATLGRDPTIGEIAESIGVDREDIVSALEAVQSPTSIHDTLYQDDSDPIYILDQL 184

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
             +  +           +     VL  L  RE+RVL MRF      D T  E+     ++
Sbjct: 185 PMEKDLEAGWFE-----KIALKEVLDKLPEREKRVLMMRF----YEDKTQSEIAALLNLS 235

Query: 653 RERIRQIEAKAIRKLKH 669
           + +I +IE  A+ +++ 
Sbjct: 236 QVQISRIERAALHRIRQ 252


>gi|89076088|ref|ZP_01162448.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048240|gb|EAR53822.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 286

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 129/272 (47%), Gaps = 16/272 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + I++++    ++    + +   +   +   S     +V ++LR V+ +A+ Y+  
Sbjct: 14  ESLDSYIQTVNRYPMLTPEREKELAERLHYDDDINSAKA--LVMSHLRFVVHIARGYSGY 71

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-- 524
           GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++     
Sbjct: 72  GLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKA 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
            R     + ++ +R+      E     +A++L +    VR++               D+D
Sbjct: 132 QRKLFFNLRKSKKRLGWFNNDEVNM--VAEQLGVEPSDVREMESRLAAQDPTFEMQNDDD 189

Query: 585 TS-----HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                      ++EDK+   A++  ++  + +     ++ LASL  R + ++R R+    
Sbjct: 190 ERDTTPVAPAYYLEDKSSDVALTYEENNWENHANNRLSQALASLDERSQHIVRSRWLDD- 248

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL+++   + V+ ERIRQ+E  A++KLK
Sbjct: 249 -EKSTLQDLANNYGVSAERIRQLEKNAMKKLK 279


>gi|313901877|ref|ZP_07835297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
 gi|313467870|gb|EFR63364.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
          Length = 251

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 110/238 (46%), Gaps = 13/238 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +  +       A++ +V  ++ LV  VA+++ + G    DLIQ G IGL++A + FD  
Sbjct: 4   RLWERARQGDGEARERLVALHMPLVRHVARRFASFGHDLDDLIQAGTIGLLQAIDGFDPS 63

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA+  +   I R +        +   MR ++ ++ R A  M  ++ R P    
Sbjct: 64  RGYQFSTYAVPVILGEIRRWLRASD-PAGLSRAMRARVAEIRRVADAMEQELGRRPPAAA 122

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +A++LA  V  V   L+  + P+SL+ P+  E D +  GD +         D+       
Sbjct: 123 VAQRLACDVADVTFALEAAQSPVSLDEPLSAEPDAACRGDRLPAPGDPDWSDTV------ 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 LA L PR    LR    +    D T  EV     +++ ++ ++E  A+ +L+
Sbjct: 177 -AVRAALAQLPPR----LRTIIALRFFRDLTQAEVAAAVGLSQPQVSRLEKMALARLR 229


>gi|229593148|ref|YP_002875267.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens SBW25]
 gi|312963636|ref|ZP_07778117.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
 gi|229365014|emb|CAY53168.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens SBW25]
 gi|311282145|gb|EFQ60745.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
          Length = 284

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLGAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  E     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDADWSDNSNHNLHEALEVLDDRSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|148265963|ref|YP_001232669.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
 gi|146399463|gb|ABQ28096.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
          Length = 280

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 114/264 (43%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +S  E   +   V+  E +   A   ++ +NLR V+ +A +Y + G++ L
Sbjct: 11  YLAEIRRFPVLSAEEEHGLA--VKLYEEKDLEAAHRLITSNLRFVVKIAGEYRSYGMKML 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLM A  KF+   G++  +YA+WW++  I   I      ++I      R   
Sbjct: 69  DLIQEGNIGLMMAVRKFNPYKGFRLISYAVWWIRAYIQNHIVSTWSLLKIGTTQAQRKLF 128

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
            K+ +    + +        +  A  L +     +++ +  +    L+  +   +   + 
Sbjct: 129 FKLNQAKSAIRSMTGGGDDLQAAALSLDVKESEAQEMDQRMRGDYFLDAEVVTGEGLTML 188

Query: 590 DFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
           + + D+                L       L  L  +E  V+  R     +   TL+E+ 
Sbjct: 189 ESLPDERRNQEELLGEAEESAILEREVAAALTCLNEKERYVIEQRVS--SDEPLTLQEIA 246

Query: 647 KQFCVTRERIRQIEAKAIRKLKHP 670
             F ++RER+RQIE  A++K+K  
Sbjct: 247 DHFSISRERVRQIEEGALKKMKRA 270


>gi|325475291|gb|EGC78476.1| region 2 family RNA polymerase sigma-70 factor [Treponema denticola
           F0402]
          Length = 275

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 86/262 (32%), Positives = 141/262 (53%), Gaps = 6/262 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   IK       +S  +   +   V+KG    + A + +V +NLRLVI +AKK+++   
Sbjct: 6   LLQYIKDSKKYPLLSAEQEAELADEVKKGN---TEAIEVLVTSNLRLVIKMAKKFSSNEN 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q L+LIQEGN+GLMKAA KF      +FS+YA WW+KQ+  R +      I++PV     
Sbjct: 63  QILELIQEGNMGLMKAASKFSKSFKVRFSSYAAWWIKQSFIRYLNSADKVIKLPVRKEAL 122

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSH 587
           I +V +       K    P+  ++A+ +   V+ + +V       I SL+ P+ +E +++
Sbjct: 123 IRQVNKEEENYKIKYGILPSYSQLAEIMKEKVDIIAQVKSFNYTDICSLDDPVDNERSAN 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVG 646
           L DFI   N  +P +  I    +E   + L  L  RE+ VLR R+G+ G  T  T   +G
Sbjct: 183 LYDFIPC-NTYNPEEEFIDNEFKEKLNKCLEILNDREKDVLRNRYGLDGTMTSTTFAVLG 241

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K++ ++ E IRQ + +A++KL+
Sbjct: 242 KKYSISAESIRQTQLRALKKLR 263


>gi|256370062|ref|YP_003107573.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|256000225|gb|ACU48624.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
          Length = 303

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 117/267 (43%), Gaps = 14/267 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D + D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDRLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIR 665
             TLE++  +F ++RER+RQIE +A  
Sbjct: 252 PMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|119474993|ref|ZP_01615346.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119451196|gb|EAW32429.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 491

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 77/256 (30%), Positives = 125/256 (48%), Gaps = 5/256 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V  +   + E    +  MV  NLRLV  +AK+Y +  L  L+LIQEG  GL++A EKF
Sbjct: 234 ERVKELGALKKEYVDYRNVMVNHNLRLVYHIAKRYNSGTLPMLELIQEGVFGLVRAVEKF 293

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
               G +FSTYA  W++  +  +    +  +R+P      + K+ R+  + S       +
Sbjct: 294 QPASGNRFSTYAYLWIEAKVRLTHEKLNSLVRLPSSNFQDVIKLRRSMEQ-SRSTGERFS 352

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
              +A KL M    V  +L+   +P+SL+ P+G ED                    + ++
Sbjct: 353 TRNVAAKLDMTQAHVELLLRTKSQPLSLDQPVGGEDNDLSLSGTLQLEQPPVSSLVLNSD 412

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++   T +L+ LT RE  +L+ RFG+G     + E +GK   ++RER+RQIE  A+  LK
Sbjct: 413 MQRQVTELLSELTSREAYILQHRFGLGDMEPMSRESIGKNIGLSRERVRQIEKAALISLK 472

Query: 669 ----HPSRSKKLRSFL 680
               +  R   L+ +L
Sbjct: 473 ELLDNTERGDDLKLYL 488


>gi|328675965|gb|AEB28640.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida 3523]
          Length = 292

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 134/274 (48%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPEQGVRLVSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   +E+A++L +  E V ++ K   +   SL+ P  D+D  
Sbjct: 141 KLFFNLRSSKDKIGWLSSE-DIKELAEELGVKEETVIEMEKRMCQGDASLDLPYTDDDGE 199

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     VL+    R + ++  R+ +      
Sbjct: 200 QTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--KA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE  A+ KLK   +++
Sbjct: 258 TLQDLAAKYNISAERVRQIEEDALAKLKKAIKNR 291


>gi|254456610|ref|ZP_05070039.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
 gi|207083612|gb|EDZ61038.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
          Length = 297

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 126/272 (46%), Gaps = 14/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +             A +++V ++LRLV  +A  Y   GL
Sbjct: 18  LSAYLEQIKKFPMLAAEEEYMLAK--NWKTTGNVKAAEKLVTSHLRLVAKIAMGYKGYGL 75

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW+K +I   I      ++I      +
Sbjct: 76  PVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKIGTTTAQK 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
                + +   +++ + + +   E   EIA KL +  E V     +++ +  SL   +  
Sbjct: 136 KLFFNLKKIKNQIAPQTEGDLRNEHVNEIANKLDVSKEEVVSMNRRLSGKEFSLNAQV-G 194

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           ED     D++ DK     L  A Q  +   ++     +  L  RE  +L        +  
Sbjct: 195 EDGDEWQDWLVDKELDHDLKFAHQEEMEQRKDLLKNSIKVLNDREREILYS--RRLNDDP 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TLE++ K++ ++RER+RQIE KA  KL+   
Sbjct: 253 TTLEDLSKKYKISRERVRQIENKAFEKLQKHM 284


>gi|241668310|ref|ZP_04755888.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254876843|ref|ZP_05249553.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254842864|gb|EET21278.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 292

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 63/274 (22%), Positives = 136/274 (49%), Gaps = 13/274 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +  ++    +S+ E + +    +  +     A +++V ++LR V  +A+ ++  GL
Sbjct: 23  LNSYLNFVNSLPILSVEEEQELARRYKYQK--DLDAAQQLVLSHLRFVTKIARNFSGYGL 80

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 81  SIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 140

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   + +A++L +  E V ++ K   +   SL+ P  D++  
Sbjct: 141 KLFFNLRSSKDKIGWLSSEDIKQ-LAEELGVKEETVIEMEKRMCQGDASLDLPYTDDEGG 199

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     V++    R + ++  R+ +   T  
Sbjct: 200 QSNQQSLYLEDKSSDIEHQIVQQDYYDNFKAIVKDVISGFDTRTKDIIMSRYLLD--TKA 257

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TL+++  ++ ++ ER+RQIE +A+ KL+   ++K
Sbjct: 258 TLQDLATKYNISAERVRQIEEEALVKLRKAIKNK 291


>gi|312135430|ref|YP_004002768.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775481|gb|ADQ04968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 240

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD  
Sbjct: 8   ELISKAKNGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPS 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  E
Sbjct: 68  FNVRFSTYAVPMIIGEIKRYLRDDGR-IKVSRKIKENQGKIKKLRNQFVSSNGREPTISE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           I++   +  + +   L  + E  SL   +  E+     L D   D+   S     + A  
Sbjct: 127 ISQLTGLSSDEILLCLDASSEVASLNEVVNQEEGKPITLMDIASDEEDYSTKLLDLMA-- 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L  RE  ++ MR+        T  E+ KQ  +++  + +IE +A+ ++K 
Sbjct: 185 ---LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKQLNISQVHVSRIEKRALERIKR 237


>gi|167622231|ref|YP_001672525.1| RNA polymerase factor sigma-32 [Shewanella halifaxensis HAW-EB4]
 gi|167352253|gb|ABZ74866.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella halifaxensis
           HAW-EB4]
          Length = 285

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/275 (23%), Positives = 123/275 (44%), Gaps = 20/275 (7%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            ++S +   + I  +  +T         +   ++  E     A K+++ ++LR V+ VAK
Sbjct: 18  SLESYVHSAHNIPMLEADTEY------ELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAK 69

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++
Sbjct: 70  GYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKV 129

Query: 522 PVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLET 578
                 R     + +  +R+      E     +A  L +    V     ++  +  + + 
Sbjct: 130 ATTKAQRKLFFNLRKAKKRLGWFSDSEVGM--VADSLGVSKADVTEMESRMAAQDPAFDL 187

Query: 579 PIGDED--TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
              ++D        ++ED +   A        + N +      + +L  R + +L+ R+ 
Sbjct: 188 ASDNDDEHDYAPMHYLEDHSSDLASQVESDNWEQNNQARLLSAIKTLDERSQHILKARWL 247

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               T  TL+++   + V+ ERIRQ+E  A+ KLK
Sbjct: 248 DEDKT--TLQDLASTYQVSAERIRQLEKNAMSKLK 280


>gi|188583534|ref|YP_001926979.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179347032|gb|ACB82444.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 290

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 128/270 (47%), Gaps = 11/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  I++      ++  E R +   V   E     A   ++ A++RLVI++A ++ + GL 
Sbjct: 9   RQFIRTAMEAPFLAREEERGLA--VAWKEARDERALHRLISAHMRLVIALAGRFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG++GLM+AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  MADLVQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126

Query: 529 -IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   R+    + +   E    IA  + +  E V     +++   +SL  P+G+E
Sbjct: 127 LFFNLRRLRARLMQSTEEQVGSEIHGRIASAIGVSREDVALMDARLSGPDMSLNAPVGEE 186

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH- 640
               S   DF+ D  A+     +   +       +  +LT   ER LR+     +  D  
Sbjct: 187 SEASSERMDFLVDNAALPDETVSALVDGERRLVWLRQALTVLSERELRILRERRLAEDQA 246

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLE +G +  +++ER+RQIE +A+ KL+  
Sbjct: 247 TLEALGHRLGISKERVRQIENRALEKLRRA 276


>gi|329936708|ref|ZP_08286415.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
 gi|329303938|gb|EGG47821.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
          Length = 279

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 108/241 (44%), Gaps = 25/241 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               +++++     LV  VA +  + GL       D +  G  GL+ A EK+D     KF
Sbjct: 43  DERLREQLILHYSPLVKYVAGR-VSVGLPPNVEQADFVSSGVFGLIDAIEKYDIGREIKF 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A +L
Sbjct: 102 ETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYTTLEARLRRTPTESEVAAEL 158

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSH---------LGDFIEDKNAVSPLDSAIQA 607
            + V+     L      +SL   +  E+  H         L D +ED +A +P++ A   
Sbjct: 159 GIRVDD----LHAVFSQLSLANVVALEEILHIGGEGGGLSLMDTLEDTSADNPVEVAEDR 214

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 215 ELRRFLARAINTLPEREKTVVTLYYFEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 270

Query: 668 K 668
           +
Sbjct: 271 R 271


>gi|317121837|ref|YP_004101840.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591817|gb|ADU51113.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 112/254 (44%), Gaps = 18/254 (7%)

Query: 426 EFRHIVSMVRKGECEASIAKKE----MVEANLRLVISVAKK---YTNRGLQFLDLIQEGN 478
           E +             + A  E    ++  +L LV  +A +   +    ++  DLI  G 
Sbjct: 4   ELKQRADRAELWRRYRTTADPESWEALIREHLPLVRYLAGRMIIHLPPQVELDDLISYGI 63

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            GLM+A  ++D   G KF TYA   ++ A+   +       +    +R +   V    RR
Sbjct: 64  FGLMEAIRRYDPARGVKFETYAYTRIRGAMLDGLRAMDWVPQ---TLRRRARDVEACYRR 120

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIG--DEDTSHLGDFIED 594
           + N++ R    +E+A +L +  E    +L+       +SL+  +    +D + + D + D
Sbjct: 121 LENRLGRPANDDEVAAELGLKPEEFAGLLQELARTTVVSLDDVLPSDSDDPAAVLDRLAD 180

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A  PL +A  A+LR      LA L  RE  V+ + +  G     T++E+ +   V+  
Sbjct: 181 PGATDPLQAATLADLRRRLADALAGLPERERLVVSLYYYEG----LTVKEIAEVMGVSPS 236

Query: 655 RIRQIEAKAIRKLK 668
           R+ Q+  +AI +L+
Sbjct: 237 RVSQLHTRAILRLR 250


>gi|296129329|ref|YP_003636579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Cellulomonas flavigena
           DSM 20109]
 gi|296021144|gb|ADG74380.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Cellulomonas flavigena
           DSM 20109]
          Length = 328

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 105/247 (42%), Gaps = 16/247 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           R      + A++ ++   + LV +VA +   R    ++  DL+  G  GL+ A EK+   
Sbjct: 84  RFTASRCAKAREVLILHYVPLVTAVAGRIGMRLPSTVEHADLVSYGMFGLIDAIEKYCTD 143

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF +YA   ++ AI   +        +P  +R K   V R    +   + R PT  E
Sbjct: 144 RAVKFESYASSRIRGAIIDELRAMDW---VPRSVRTKARAVDRAYGELEATLHRAPTEAE 200

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDT----SHLGDFIEDKNAVSPLDSAI 605
           +A++L +PV  +R       +    +L+  +   D     + L D + D+ A  P  S  
Sbjct: 201 VAQRLELPVSELRAVYSQLASVNIAALDEMLAGSDDRPGAATLADTLGDRRADDPAGSVE 260

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +   +R +  L  RE  V+ + +        TL E+G+   VT  RI QI   A+ 
Sbjct: 261 AQETKYLLSRAIECLGERERLVVVLYY----YESMTLAEIGRVLGVTESRISQIHTAAMG 316

Query: 666 KLKHPSR 672
           +L+   R
Sbjct: 317 RLRTRLR 323


>gi|182440616|ref|YP_001828335.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178469132|dbj|BAG23652.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 290

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 57/248 (22%), Positives = 118/248 (47%), Gaps = 8/248 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G      A+  ++E NL LV   AK++ NRG  +  D++Q G IGL+KA 
Sbjct: 44  FFERLQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIVQVGTIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +    ++ ++ R
Sbjct: 104 DRFELSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKAKEELAGRLDR 163

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT  E+A  L +  E V + L  +      SL+ PIG E  S       D         
Sbjct: 164 DPTVGELAAHLGLTDEEVVEGLIASNGYTAGSLDLPIGTEQNSAETITYGDIKGDLDPAI 223

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  NL      +L  L  R+  ++ MRFG     + T  ++G++  +++  + ++  + 
Sbjct: 224 ELVENLH-ALAPLLEGLGDRDREIVAMRFG----QELTQAQIGERLGISQMHVSRLLNRL 278

Query: 664 IRKLKHPS 671
           + +L+   
Sbjct: 279 LTQLRKNM 286


>gi|203288197|ref|YP_002223212.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
 gi|201085417|gb|ACH94991.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
          Length = 267

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 70/260 (26%), Positives = 143/260 (55%), Gaps = 10/260 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   ++     +  AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHRLITHEEEIELAKQIK---LGSLKAKNQMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  E+I ++  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLMEEEKSPKKEDIMERFNLTTAQYVKIIPYLEKEYSLDKKIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDH-TLEEVGKQF 649
            ED N+++P  +  Q +  +    +L + L  +E  +++ R+ +  +    TL+++  + 
Sbjct: 185 YED-NSLNPESTLEQNSTLKHLNYILETKLNEKERYIIKKRYNLDNSDKKSTLKDISTEL 243

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            ++ E +RQIE + ++KL+ 
Sbjct: 244 GISSETVRQIEKRVLKKLRE 263


>gi|270264290|ref|ZP_06192557.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
 gi|270041939|gb|EFA15036.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
          Length = 285

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 121/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAR 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  ++  + ++ +    D+  D   +   +  ++  S     I+ +  E
Sbjct: 160 ELGVTSKDVREMESRMAAQDMTFDPTPDDDARDGQSMAPVLYLQDKSSDFAEGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +         L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SNAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           LK
Sbjct: 279 LK 280


>gi|290959865|ref|YP_003491047.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
 gi|260649391|emb|CBG72506.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
          Length = 304

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 62  LFERLESLEEGTYEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 121

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R 
Sbjct: 122 RFELSRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRA 181

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 182 PTVGELAERLGLTNDEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGIE 241

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L PR+ ++L +RF        T  E+G +  +++  + ++ ++ 
Sbjct: 242 YV-----ESLKPLIAGLPPRDRQILSLRFVAN----MTQSEIGDELGISQMHVSRLLSRT 292

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 293 LVRLRK 298


>gi|259479059|dbj|BAI40077.1| RNA polymerase sigma-70 factor [Aeromonas sp. GV20]
          Length = 272

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 115/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +R GEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TRAGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYQAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|110224843|emb|CAJ29299.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. OX1]
          Length = 258

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 52/300 (17%), Positives = 109/300 (36%), Gaps = 48/300 (16%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   +M ++   P T + ++     +      L +++          
Sbjct: 1   REGEIEIAKRIEEGIREVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVL---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             G+    +G +    E       +    + + D E A     ++ ++    P  A    
Sbjct: 51  -SGYIDPDDGIAPPAAEVPPPIDAKAAKADDDTDDEDAEASDDEEEAESGPDPVIAAQRF 109

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             + +  + +   L                                   +K  +++ +  
Sbjct: 110 GAVADQMEITRKAL-----------------------------------KKHGRNNKQAI 134

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
                L +L   + L   + + LVE++     R+   E  +++L      + R  FL + 
Sbjct: 135 AELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 194

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI+E + I   +
Sbjct: 195 PGHEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLSALEAETGLSIAEIKDINRRM 253


>gi|229031535|ref|ZP_04187535.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
 gi|228729824|gb|EEL80804.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
          Length = 289

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 133/264 (50%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE     A++++V  NLRLV+SV +++ N
Sbjct: 33  RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEIS---AREKLVNGNLRLVLSVIQRFNN 89

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D    IR+   +
Sbjct: 90  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDND-PIRVSRSL 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 149 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 208

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+           A         +  L  RE+ ++R RF  G     T  
Sbjct: 209 DPIFVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQM 259

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 260 EVAEEIGISQAQVSRLEKSAIKQM 283


>gi|331697274|ref|YP_004333513.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951963|gb|AEA25660.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 296

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 124/251 (49%), Gaps = 20/251 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  + +     + +  + ++E +L L   +AK+++ RG    DL Q   +GL+ A +
Sbjct: 11  FTELACLPKGHRRRSRLRDRLIIE-HLPLARHIAKRFSQRGEPLQDLEQVAVLGLINAVD 69

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +F  +A+  +   + R   D++ TIR+P  +++    +   A R++ ++ R 
Sbjct: 70  RFDPARGPEFLAFAIPTITGEVLRWFRDRAWTIRVPRRLKELDMSISTAADRLTQELGRA 129

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PTP EIA +L + +  V + ++       +SL+ P+  E         ED++  + + + 
Sbjct: 130 PTPSEIAARLDVALSDVVESIQAREAYRCVSLDVPLSTES--------EDESVHNGILAR 181

Query: 605 IQ-----ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                     RE  + ++ +LT RE+R++ +RF      D T  E+G++  +++  + ++
Sbjct: 182 TDPGVALVEDREVLSPLVDALTEREQRIVLLRFF----EDMTQNEIGQEIGISQMHVSRV 237

Query: 660 EAKAIRKLKHP 670
              A+ +L+  
Sbjct: 238 LTAALERLRQA 248


>gi|311068942|ref|YP_003973865.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
 gi|310869459|gb|ADP32934.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
          Length = 255

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 128/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  S    +   E + +   +++ +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNSKNAQLKDHEVKDL---IKRSQDGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S    R PT +EIA+ L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRAKDELSKTYGRVPTVQEIAEHLEIDAEDVVLAQEAVRAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D +     D       +      ++ L  RE+ ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADHSEEKWFD-------KIALKEAISDLEEREKLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQIK 247


>gi|291454422|ref|ZP_06593812.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
 gi|291357371|gb|EFE84273.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 279

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 105/242 (43%), Gaps = 25/242 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
            +  +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEKFDPERSIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  ++ R PT  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYASLEAELHRTPTEAEVAAEMG 157

Query: 558 MPVEGVRKVLKITKEPISL-----------ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           + VE     L      +SL               G  D   + D +ED +A +P++ A  
Sbjct: 158 IAVED----LHAVFSQLSLANVVALEELLHGGGEGGGDRLSIMDTLEDTSADNPVELAED 213

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR    R +  L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +
Sbjct: 214 RELRRLLARAINLLPEREKTVVTLYYYEG----LTLAEIGHVLGVTESRVSQIHTKSVLQ 269

Query: 667 LK 668
           L+
Sbjct: 270 LR 271


>gi|253997181|ref|YP_003049245.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera mobilis JLW8]
 gi|253983860|gb|ACT48718.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera mobilis JLW8]
          Length = 285

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 123/273 (45%), Gaps = 9/273 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +    ++I     +S  E   + +  +K       A ++++ ++LRLV S+A+ Y   GL
Sbjct: 16  LDQYTRAIKAYPILSAEEELTLANRFKK--ENDLEAARQLIVSHLRLVASIARGYMGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD   G +  ++AM W+K  I   I      ++I      +
Sbjct: 74  PQADLIQEGNIGLMKAVKRFDPERGVRLVSFAMHWIKAEIHEYIVRNWRLVKIATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSH 587
                  + +      +    + IA++L +  E V     ++    ISLE+ I D+   H
Sbjct: 134 KLFFNLRSMKTGINTMQTSEIDHIARELNVKPEEVLEMESRLNGHEISLESNIDDDSEEH 193

Query: 588 LGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                  ++       A++A   E          L  L  R  RV+  R+    +   TL
Sbjct: 194 YSPIAYLQDESLTPPEALEAKQFEMAETTGLASALNHLDERSRRVVEARWLQE-DASKTL 252

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            E+  +F V+ ERIRQIE KA+ K+K    + +
Sbjct: 253 HELADEFGVSAERIRQIEQKAMLKMKTLMLASR 285


>gi|118465934|ref|YP_882149.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118167221|gb|ABK68118.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 269

 Score =  128 bits (320), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 109/248 (43%), Gaps = 8/248 (3%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + E    +  +     E    ++ +V   L L   VA  +  RG    DL+Q   +GLM
Sbjct: 24  DVVEMFLELRRMPAESHEYRRQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLM 83

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F  +A+  +   + R   D S  +R+P  +R+   ++ RT   ++ +
Sbjct: 84  NAVNRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHVQISRTTADLAQQ 143

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           + R P   E+++ L +P E + + L         SL+ P G + +       +    + P
Sbjct: 144 LGRAPNAGELSQVLEVPREEIVECLVAGDAYRLDSLDAPQGADSSGTPRSVADSVGDIDP 203

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               I    RE    ++A+L  RE  VLRMRF        T  ++ ++  V++ ++ +I 
Sbjct: 204 QIEHITN--REALRVLVATLPHREREVLRMRFF----ESMTQSQIAERIGVSQMQVSRIL 257

Query: 661 AKAIRKLK 668
           A  +R L+
Sbjct: 258 ANTLRCLR 265


>gi|256787303|ref|ZP_05525734.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 308

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 66  LFERLESLEEGTHEHAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 125

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 126 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 185

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A+ L +  + V + +         SL+    ++D    L D I  ++       
Sbjct: 186 PTVSELAEHLGLSKDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGIE 245

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L  R+ ++L +RF  G     T  E+G++  +++  + ++ ++ 
Sbjct: 246 YV-----ESLKPLIAELPSRDRKILSLRFVAG----MTQSEIGEELGISQMHVSRLLSRT 296

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 297 LVRLRK 302


>gi|254441831|ref|ZP_05055324.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
 gi|198251909|gb|EDY76224.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
          Length = 298

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 126/276 (45%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + E + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPMLEPDEEYMLAK--RWVDHEDTDAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   +      +++      K
Sbjct: 74  PTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE    IA  L +   E V    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNRIGALEEGDLRPENVQRIANDLGVTEAEVVSMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED++A    D   +  L   RE     +  L  RE+ +L  R      
Sbjct: 194 DGEGTMQWQDWLEDESADQAGDYEDRDELQQRRELMAEAMDVLNDREKDILMQRRLAEKT 253

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLE++  Q+ V+RERIRQIE +A  KL+   ++
Sbjct: 254 V--TLEDLSGQYSVSRERIRQIEVRAFEKLQKKMQT 287


>gi|219669461|ref|YP_002459896.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
 gi|219539721|gb|ACL21460.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
          Length = 261

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 129/257 (50%), Gaps = 15/257 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           ++     +S  E   ++   +      + A++ ++  NL+L+ ++ +++++RG +  DL 
Sbjct: 10  NLPRFPLLSDEEMMDLLHRAQ---NGDAEARERLINCNLKLIFNLVQRFSHRGYELEDLF 66

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G IGL+KA +KFD+  G KFSTYA+  +   I R + D    +++P   ++ ++KV +
Sbjct: 67  QIGTIGLIKAIDKFDFTYGVKFSTYAVPMIIGEIRRFLRD-DHPVKVPRSYKELVYKVNK 125

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
               +S  + R+PT  EIA+ + +  E +   L+  + P S+   +  +D+   ++ D +
Sbjct: 126 ARESLSATLGRDPTIGEIAESIGVDREDIVSALEAVQSPTSIHDTLYQDDSDPIYILDQL 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
             +  +           +     VL  L  RE+RVL MRF      D T  E+     ++
Sbjct: 186 PMEKDLEAGWFE-----KIALKEVLDKLPEREKRVLMMRF----YEDKTQSEIAALLNLS 236

Query: 653 RERIRQIEAKAIRKLKH 669
           + +I +IE  A+ +++ 
Sbjct: 237 QVQISRIERAALHRIRQ 253


>gi|302746289|gb|ADL62734.1| RpoD [Morganella morganii subsp. sibonii]
          Length = 256

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 45/296 (15%), Positives = 94/296 (31%), Gaps = 47/296 (15%)

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
           I IAKRIE G   +  S+ E P     L+   D +  G   L ++I     + P +    
Sbjct: 1   IDIAKRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLIT--GFVDPNA---- 54

Query: 200 FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
               E        +   E   +++ + + D +   +   D        PE A      L 
Sbjct: 55  ----EEDLAPTATNIGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDPELARQKFEALR 110

Query: 260 EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
              + +   +                                       +         +
Sbjct: 111 VQHEKARQQIKI-----------------------------------HGRDHPSTNAEIQ 135

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRE 378
           +L ++     L   + D LV  + ++  R+   E  +++L  +   + +  F+    G E
Sbjct: 136 QLFEVFKEFRLVPKQFDHLVNNMREMMDRVRQQERYIMKLCVEQSKMPKKNFITLFTGNE 195

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
               W + A    +  W   +    + I +    ++ I  ETG++ ++ + I   +
Sbjct: 196 TSDSWFTAAIAMNKP-WSEKLQDMAEEIERSLQRLRQIEEETGLTFNDVKDINRRM 250


>gi|229075660|ref|ZP_04208642.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
 gi|229098374|ref|ZP_04229319.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|229117400|ref|ZP_04246776.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228666010|gb|EEL21476.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228684991|gb|EEL38924.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|228707436|gb|EEL59627.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
          Length = 289

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 134/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 33  RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 92

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 93  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 151

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 152 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 211

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 212 FVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 262

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 263 EEIGISQAQVSRLEKSAIKQM 283


>gi|119716157|ref|YP_923122.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536818|gb|ABL81435.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 282

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 68/257 (26%), Positives = 117/257 (45%), Gaps = 17/257 (6%)

Query: 420 TGISISEFRHIVSMVRKGECEASIA------KKEMVEANLRLVISVAKKYTNRGLQFLDL 473
            G++  E     + +      +  A         +V  N  +  +VA ++ NRG+   DL
Sbjct: 28  CGLTRPERAEHTARLLDEAQHSDDAGEREEVLGRVVVINRGVADAVAARFRNRGIPQEDL 87

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q    GL KA  +FD  L     TYA+  ++  + R   DQ  T+R P  +++   +V 
Sbjct: 88  RQVAYEGLTKAVHRFDPELRNDLLTYAVPTIRGELQRYFRDQGWTVRPPRRIQELQWRVN 147

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDF 591
           +   R++ +  REP+ +EIA +L   VE  R         +P SL+ P+G E  + +G+ 
Sbjct: 148 QVIERLTQERGREPSEDEIAAELDTTVEEYRDAASAFGCFQPTSLDQPVGHEGETPVGEL 207

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I   +A  P   A     R     V+  L  R  R+L +RF      D T EE+G+   V
Sbjct: 208 IAGADADGPATEA-----RMLLAPVVRRLPERHRRILYLRFF----EDLTQEEIGRDLGV 258

Query: 652 TRERIRQIEAKAIRKLK 668
           T+ ++ ++ ++ +  L+
Sbjct: 259 TQMQVSRLLSRILGDLR 275


>gi|83950005|ref|ZP_00958738.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837904|gb|EAP77200.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 277

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 117/260 (45%), Gaps = 16/260 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A KY   G    DLIQE  +GLMKAA+KF
Sbjct: 11  ELALAYAWRDQRDEEALHRLINAYMRLAISMASKYRRYGAPLNDLIQEAGLGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K  I   +      +R            +MR    ++ R A   
Sbjct: 71  DPDRGVRFSTYAVWWIKAGIQDYVMRNWSMVRTGSTSSQKALFFNMRRVRAQIEREAEAS 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
             ++      E IA ++ +P+  V  +  +++   +SL      ED      D +ED   
Sbjct: 131 GTRLDGHQLREMIATEVGVPLRDVEMMEGRLSGSDLSLNATQSTEDEGREWIDALEDDGP 190

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +        +   LR      LA+L  RE  +LR R         TLE +G++  +++E
Sbjct: 191 RAEEMVEEDHDQRVLRLWLRDALAALNDRERFILRHRKL--SEEVRTLESLGEELGLSKE 248

Query: 655 RIRQIEAKAIRKLKHPSRSK 674
           R+RQ+EA A+ K++     +
Sbjct: 249 RVRQLEAAALVKMRKRLERE 268


>gi|11079145|dbj|BAB17577.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
 gi|11079149|dbj|BAB17579.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
 gi|11079151|dbj|BAB17580.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
 gi|11079153|dbj|BAB17581.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
          Length = 270

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 121/315 (38%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++ + P T  +++   + +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAQFPGTVDSILADYNRIVAEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+         E  + +                     + +A   + D  + +S   +
Sbjct: 59  IDPDDGSLPAEEVEPVNLK---------------------DDSADSKEKDDEEEESDDSS 97

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             +DE +   D +++    +A+ +QL                            +K  + 
Sbjct: 98  DSDDEGDGGPDPEEARLRFTAVSEQLDKA---------------------KKALKKHGRG 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++    + +   E  +++L      + R  
Sbjct: 137 SKQATAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL      E D  WV       + ++   +    D IL+ + ++ ++  E  ++++E + 
Sbjct: 197 FLRLFPNHETDEKWVDSVLK-SKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKE 255

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 256 INRAMSIGEAKARRA 270


>gi|297202660|ref|ZP_06920057.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197713235|gb|EDY57269.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 280

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 105/242 (43%), Gaps = 26/242 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               +++++     LV  VA +  + GL       D +  G  GL+ A EKFD     KF
Sbjct: 43  DERLREQLILHYSPLVKYVAGR-VSVGLPPNVEQADFVSSGVFGLIDAIEKFDLDREIKF 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A +L
Sbjct: 102 ETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPTEGEVAGEL 158

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQ 606
            + V+     L      +SL   +  E          D     D +ED  A +P++ A  
Sbjct: 159 GIAVDD----LHAVFSQLSLANVVALEELLHVGGEGGDGLSFMDTLEDPAADNPVEVAED 214

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +
Sbjct: 215 RELRRFLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQ 270

Query: 667 LK 668
           L+
Sbjct: 271 LR 272


>gi|41407572|ref|NP_960408.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395925|gb|AAS03791.1| SigF_1 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 269

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 109/248 (43%), Gaps = 8/248 (3%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + E    +  +     E    ++ +V   L L   VA  +  RG    DL+Q   +GLM
Sbjct: 24  DVVEMFLELRRMPAESHEYRRQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLM 83

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F  +A+  +   + R   D S  +R+P  +R+   ++ RT   ++ +
Sbjct: 84  NAVNRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHVQISRTTADLAQQ 143

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           + R P   E+++ L +P E + + L         SL+ P G + +       +    + P
Sbjct: 144 LGRAPNAGELSQVLEVPREEIVECLVAGDAYRLDSLDAPQGADSSGTPRSVADSVGDIDP 203

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               I    RE    ++A+L  RE  VLRMRF        T  ++ ++  V++ ++ +I 
Sbjct: 204 QIEHITN--REALRVLVATLPHREREVLRMRFF----ESMTQSQIAERIGVSQMQVSRIL 257

Query: 661 AKAIRKLK 668
           A  +R L+
Sbjct: 258 ANTLRCLR 265


>gi|52546492|dbj|BAD51629.1| DNA-directed RNA polymerase subunit D [Burkholderia cepacia]
          Length = 278

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 118/316 (37%), Gaps = 39/316 (12%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD----- 55

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                                    +    D  +T+G     A+  +++  + +   E  
Sbjct: 56  ----------------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEE 93

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
           E +E +       +A  L A    L+   +    +I+E + ++R   +      K+   S
Sbjct: 94  EEEEDDGAAQASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKS 143

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + ++      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 144 KAYLKAQETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 203

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   ++  V +I + +  +  +     + + + +  
Sbjct: 204 IARFPGSETDLDWAEKITAEGHP-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKET 262

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 263 NRQMAAGELKARQAKR 278


>gi|307330885|ref|ZP_07610018.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883426|gb|EFN14479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 263

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 113/226 (50%), Gaps = 11/226 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V  +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA   V
Sbjct: 40  RNHLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTV 99

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +S +  R PT  E+A++L++  E V 
Sbjct: 100 VGEIKRHFRDKGWAVRVPRRLQELRLSLTTATAELSQRHGRAPTVHELAEQLSISEEEVL 159

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L+       +SL+ P  D+++  + D +  ++             RE+   +L  L P
Sbjct: 160 EGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVEY-----RESLKPLLEDLPP 214

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+++L +RF   M      +EV     +++  + ++ A+ + +L+
Sbjct: 215 REKKILLLRFFGNMTQSQIAQEV----GISQMHVSRLLARTLAQLR 256


>gi|77461555|ref|YP_351062.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf0-1]
 gi|77385558|gb|ABA77071.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas fluorescens
           Pf0-1]
          Length = 284

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLGAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  E     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDADWSDNSNHNLHEALEVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|71737989|ref|YP_276878.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|257482996|ref|ZP_05637037.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289624653|ref|ZP_06457607.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289648492|ref|ZP_06479835.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|289672442|ref|ZP_06493332.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           FF5]
 gi|298485264|ref|ZP_07003357.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|302187226|ref|ZP_07263899.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           642]
 gi|71558542|gb|AAZ37753.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|298160252|gb|EFI01280.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320326376|gb|EFW82429.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320331634|gb|EFW87572.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330871135|gb|EGH05844.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330872356|gb|EGH06505.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891333|gb|EGH23994.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. mori str.
           301020]
 gi|330898959|gb|EGH30378.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330954977|gb|EGH55237.1| RNA polymerase factor sigma-32 [Pseudomonas syringae Cit 7]
 gi|330982560|gb|EGH80663.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
 gi|330985905|gb|EGH84008.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
 gi|331011765|gb|EGH91821.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 284

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 128/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    DS    N      + L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDSDWTDNSTANLHQALDVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|295092809|emb|CBK78916.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium cf.
           saccharolyticum K10]
          Length = 258

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 130/267 (48%), Gaps = 19/267 (7%)

Query: 409 IRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
             N+++   V T    +  +E +    +  +       A+++ ++ NLRLV+SV ++++ 
Sbjct: 2   ALNKVEICGVNTAKLPLLTNEEKE--ELFARILKGDREAREQYIKGNLRLVLSVIQRFSG 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                 DL Q G IGL+KA + FD     +FSTYA+  +   + R + D +  IR+   +
Sbjct: 60  SSENVDDLFQIGCIGLIKAIDNFDITQNVRFSTYAVPMILGEVKRYLRDNNS-IRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K +     +  K  +EPT  EIA+++ +  E +   L   + P+SL  P+  +  
Sbjct: 119 RDTAYKAIYARESLMKKNLKEPTLCEIAEEVGVSKEDITYALDAIQSPVSLYEPVYTDGG 178

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           D  ++ D + D KN+       I      + +  +  L  RE  ++ MRF  G     T 
Sbjct: 179 DPLYVMDQLSDKKNSEENWIEDI------SLSEAMRRLPERERHIIGMRFFEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            EV ++  +++ ++ ++E  A++ +K+
Sbjct: 229 TEVAEEIHISQAQVSRLEKNALKAMKN 255


>gi|163853281|ref|YP_001641324.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|218532097|ref|YP_002422913.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|254563204|ref|YP_003070299.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|163664886|gb|ABY32253.1| RNA polymerase sigma factor, sigma-70 family [Methylobacterium
           extorquens PA1]
 gi|218524400|gb|ACK84985.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|254270482|emb|CAX26482.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 290

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 128/270 (47%), Gaps = 11/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  I++      ++  E R +   V   E     A   ++ A++RLVI++A ++ + GL 
Sbjct: 9   RQFIRTAMEAPFLARDEERGLA--VAWKEARDERALHRLISAHMRLVIALAGRFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG++GLM+AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  MADLVQEGHVGLMEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126

Query: 529 -IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   R+    + +   E    IA  + +  E V     +++   +SL  P+G+E
Sbjct: 127 LFFNLRRLRARLMQSTEEQVGSEIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEE 186

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH- 640
               S   DF+ D  A+     +   +       +  +LT   ER LR+     +  D  
Sbjct: 187 SEASSERMDFLVDNAALPDETVSALVDGERRLIWLRQALTVLSERELRILRERRLAEDQA 246

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           TLE +G +  +++ER+RQIE +A+ KL+  
Sbjct: 247 TLEALGHRLGISKERVRQIENRALEKLRRA 276


>gi|154686587|ref|YP_001421748.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens FZB42]
 gi|308174131|ref|YP_003920836.1| RNA polymerase sporulation-specific sigma factor sigma-F [Bacillus
           amyloliquefaciens DSM 7]
 gi|63146682|emb|CAG28933.1| Sigma F [Bacillus amyloliquefaciens FZB42]
 gi|154352438|gb|ABS74517.1| SigF [Bacillus amyloliquefaciens FZB42]
 gi|307606995|emb|CBI43366.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328552736|gb|AEB23228.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens TA208]
 gi|328912466|gb|AEB64062.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 255

 Score =  128 bits (320), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 68/259 (26%), Positives = 127/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  S    +   E + +   ++K +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNSKNAQLKDHEVKEL---IKKSQEGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S    R PT +EIA  L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRAKDELSKTYGRVPTVQEIADHLEIDAEDVVLAQEAVRAPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D +     D       +      ++ L  RE+ ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADHSEEKWFD-------KIALKEAISDLEEREKLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQIK 247


>gi|332529979|ref|ZP_08405929.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
 gi|332040452|gb|EGI76828.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
          Length = 326

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 69/295 (23%), Positives = 133/295 (45%), Gaps = 31/295 (10%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    ++  E +      R  +     A  ++V ++LRLV++ A++
Sbjct: 27  VPPLGNLDAYITAVNRMPMLTAEEEQEFARKFR--DNNDLEAAGKLVLSHLRLVVATARQ 84

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  I   I      +++ 
Sbjct: 85  YMGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHWIKAEIHEYILKNWRMVKVA 144

Query: 523 VH-MRDKIHKVVRTARR-------------------MSNKIKREPTPEEIAKKLAMPVEG 562
               + K+   +R+ ++                      +   E   +++A++L +  E 
Sbjct: 145 TTKAQRKLFFNLRSKKQGYKAASAADSSLHDGLDAATHRETLSEHEIDQMARELNVKREE 204

Query: 563 VRKVLKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRV 616
           V ++    +   + L+   G++     G      +A     + I+A  R+        + 
Sbjct: 205 VIEMETRLSGGDVMLDPGPGEDGEDSFGPIAYLTDAGHEPTAMIEARQRDRLATDGIAKA 264

Query: 617 LASLTPREERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +L PR  R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K
Sbjct: 265 LDALDPRSRRIVEERWLKVNDDASGGMTLHELAAEYGVSAERIRQIEVAAMKKMK 319


>gi|56420843|ref|YP_148161.1| sporulation sigma factor SigF [Geobacillus kaustophilus HTA426]
 gi|56380685|dbj|BAD76593.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-F) (stage II sporulation protein AC) [Geobacillus
           kaustophilus HTA426]
          Length = 250

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 119/242 (49%), Gaps = 14/242 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q G IGL+K+ +KF
Sbjct: 16  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKF 75

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D   T+++   +++  +K+ +    +S    R PT
Sbjct: 76  DLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPT 134

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA  L +  E V    +  + P S+   + + D     L D I D +  S  D    
Sbjct: 135 VTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADADEASWFD---- 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    + +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K ++ 
Sbjct: 191 ---KIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQVSRLEKKILQH 243

Query: 667 LK 668
           +K
Sbjct: 244 IK 245


>gi|1710647|sp|P50510|RP32_SERMA RecName: Full=RNA polymerase sigma-32 factor
 gi|1143376|dbj|BAA09442.1| sigma-32 homolog [Serratia marcescens]
          Length = 285

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 121/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLDAAKQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAR 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  ++  + ++ +    DE  D   +   +  ++  S     I+ +  E
Sbjct: 160 ELGVTSKDVREMESRMAAQDMTFDPTPDDEARDGQSMAPVLYLQDKSSDFAEGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +         L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SNAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           LK
Sbjct: 279 LK 280


>gi|311068054|ref|YP_003972977.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
 gi|310868571|gb|ADP32046.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
          Length = 260

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 137/264 (51%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFRQLQ--DEGDDSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EPT E+IAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+           A         +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDERNKDTQWIEELA-----LKEGMRRLNDREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 231 EVAEEIGISQAQVSRLEKAAIKQM 254


>gi|299534115|ref|ZP_07047467.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
 gi|298718024|gb|EFI59029.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
          Length = 314

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 65/291 (22%), Positives = 122/291 (41%), Gaps = 25/291 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ E +     ++  E     A   +V ++LRLV+S++++
Sbjct: 21  VPPLGNLDAYISAVNRMPMLTLEEEQDYARKLK--EHNDLDAAGRLVMSHLRLVVSISRQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---------------VEGVRKVL 567
                +       + +   K       EE+A +  +                 E +    
Sbjct: 139 TTKAQRKLFFNLRSMKHDLKSDAAMADEELALRETLTSNEIDAVAAKLNVKREEVIEMET 198

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTP 622
           ++    + L+    D+     G      +A     + +++  R+          L  L  
Sbjct: 199 RLAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDD 258

Query: 623 REERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R  R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K  
Sbjct: 259 RSRRIVEERWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKA 309


>gi|66474687|gb|AAY46913.1| RpoD [Aeromonas caviae]
          Length = 272

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 121/316 (38%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+ EGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTHEGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +  E+
Sbjct: 59  N------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDED 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHD 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      +  + + +++   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVMRSIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|37956273|gb|AAO73807.1| RNA polymerase sigma-70 factor [Aeromonas sp. 116P]
          Length = 272

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 118/315 (37%), Gaps = 46/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           +   D+ +      ++                  E + ELR+  +   ++ QK+ ++   
Sbjct: 95  DDADDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 257 RMSIGEAKARRAKKE 271


>gi|114566373|ref|YP_753527.1| sporulation sigma factor SigG [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337308|gb|ABI68156.1| RNA polymerase sigma-G factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 234

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 127/238 (53%), Gaps = 10/238 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +  +     + A++++++ N+RLV+SV +++TNRG    DL Q G IGL+K+ + FD   
Sbjct: 4   LFTEMHQGKTQAREKLIQGNIRLVLSVIQRFTNRGEYVDDLFQVGCIGLIKSIDNFDLSQ 63

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D +  +R+   +RD  +K ++   ++ N    EPT  +I
Sbjct: 64  NVRFSTYAVPMIIGEIRRYLRDNN-AVRVSRSLRDIAYKALQVREKLINDNSAEPTVSQI 122

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE- 611
           A+ L +  E V   L   +EP+SL  PI ++     GD I   + +S   S  +  L E 
Sbjct: 123 AQHLDVSREEVVFALDAIQEPVSLFEPIYNDG----GDPILVMDQLSDERSGDEQWLEEI 178

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    +  L  RE+ ++ +RF  G     T  EV ++  +++ ++ ++E  A+++L+ 
Sbjct: 179 SIKEAMKKLNDREKHIVSLRFFAG----KTQMEVAEEIGISQAQVSRLEKAALKQLRK 232


>gi|23098931|ref|NP_692397.1| sporulation sigma factor SigG [Oceanobacillus iheyensis HTE831]
 gi|22777159|dbj|BAC13432.1| stage III sporulation protein G (RNA polymerase
           sporulation-specific sigma G factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 260

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 77/264 (29%), Positives = 134/264 (50%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           R++++   V+T     +   E + +   VR  E     A++E+V  NLRLV+SV +++ N
Sbjct: 3   RHKVEICGVDTSKLPVLKNEEMKKLF--VRMQEDGDITAREELVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++ +K  +EP+P EIAK++ +P   V   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVREKLISKTSKEPSPAEIAKEMDIPQTDVVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D I D+              + +    +  L  RE+ +L  RF  G     T  
Sbjct: 180 DPIFVMDQISDEKDKDSSWVD-----KLSLKEGMHQLNEREKMILNKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV  +  +++ ++ ++E  AI ++
Sbjct: 231 EVADEIGISQAQVSRLEKAAISQM 254


>gi|262273681|ref|ZP_06051494.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
 gi|262222096|gb|EEY73408.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
          Length = 246

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 76/205 (37%), Positives = 125/205 (60%), Gaps = 3/205 (1%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A    ++   +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ +
Sbjct: 42  ATSTKALDATQLYLSEIGYSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKI 98

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           +++Y+NRGL  LDL++EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 99  SRRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 158

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR ++ K+  EPT E+IA +L  PVE V ++L++ +   S++ P
Sbjct: 159 RLPIHVVKELNVYLRTARELAQKLDHEPTAEDIAFQLDKPVEDVNRMLRLNERISSVDNP 218

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSA 604
           IG +    L D I D+    P    
Sbjct: 219 IGGDSEKALLDIIPDEKEGGPEREY 243



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 25/104 (24%), Positives = 40/104 (38%), Gaps = 1/104 (0%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +DL  ++   + L + S         +    +      D  ++YL E+G   LL+ E E+
Sbjct: 11  EDLGVDDVDMEQLAIESEDEVVEEVEESVSFATSTKALDATQLYLSEIGYSPLLTAEEEV 70

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             A+R   G       + ES L     I  R   N G  LL  +
Sbjct: 71  LYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGLALLDLV 113


>gi|237816135|ref|ZP_04595131.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
 gi|237788798|gb|EEP63010.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
          Length = 319

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 79/305 (25%), Positives = 138/305 (45%), Gaps = 15/305 (4%)

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           Q  ++ P  +S +   P       V     +    ++ I+S      +   E R +   +
Sbjct: 5   QENQMKPSSMSSSSTVPANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--I 62

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     
Sbjct: 63  RWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDV 122

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE-- 550
           +FSTYA WW++ ++   I      +R       K     + R   +++         E  
Sbjct: 123 RFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIY 182

Query: 551 -EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQ 606
            EI+ +L +    V     +++    SL  P+  E+T  S   DF+ D + +    +   
Sbjct: 183 REISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESS 242

Query: 607 ANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            ++       TR L +L  RE  ++R R         TLE +G++  +++ER+RQIE++A
Sbjct: 243 IDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRA 300

Query: 664 IRKLK 668
           + KLK
Sbjct: 301 MEKLK 305


>gi|255262130|ref|ZP_05341472.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
 gi|255104465|gb|EET47139.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
          Length = 292

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 126/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     +   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 26  ELKLAYAWRDERCEQSLHRLITAYMRLAISMASKFKRYGAPMNDLIQEASLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            ++R    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAATA 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
             ++ R    + IA ++ +P+  V  +  +++    SL      ED      D +ED + 
Sbjct: 146 GEELDRHQMRQMIATEVGVPLHDVEMMEGRLSGSDYSLNATQSSEDEGREWIDALEDDSD 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +  +      LR      L++L+ RE+ ++  R     +   TLE +G +  +++E
Sbjct: 206 QAAENVENDHDTETLRSWLVTALSALSHREQYIVTERKI--KDQTRTLESLGHELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFL 680
           RIRQ+EA A  K++     +S++L  F 
Sbjct: 264 RIRQLEAAAFIKMRKSLEGQSRELHHFF 291


>gi|110635708|ref|YP_675916.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286692|gb|ABG64751.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 284

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 73/280 (26%), Positives = 126/280 (45%), Gaps = 14/280 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +R ++   +++      E  H +++ +  E +   A   M+ A++RLVI++A K+ N 
Sbjct: 3   EDVRRKLIKAAMKAPYLGREEEHELAL-QWKERQDQQALHRMIMAHMRLVIAMAGKFRNF 61

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEG++GL++AA +FD     +FSTYA WW++ ++   I      +R      
Sbjct: 62  GLSMSDLIQEGHVGLLEAAARFDPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSA 121

Query: 527 DK--IHKVVRTARRMSNKIKR---EPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPI 580
            K     + R   ++         E    E+A+ L +    V  +  ++     SL  P+
Sbjct: 122 QKALFFNLRRLRMKLQKAGGTTPSEDVYREVAQALRVSESDVAMMDSRLAAADASLNAPL 181

Query: 581 GDEDT--SHLGDF-IEDKNAVSPLDSAIQANLR--ETTTRVLASLTPREERVLRMRFGIG 635
             +    S   DF I DK     L        R  +   + L +L  RE  ++R      
Sbjct: 182 RSDSDPTSERIDFLICDKPQPDELVREAIDGERKAQWLHQALGTLNGRELTIVRE--RRL 239

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
                TLE +G    +++ER+RQIE++A+ KL+       
Sbjct: 240 SEEGATLEALGASLGISKERVRQIESRALEKLRTALVKHH 279


>gi|254453399|ref|ZP_05066836.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
 gi|198267805|gb|EDY92075.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
          Length = 298

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 126/276 (45%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + E + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPMLEPDEEYMLAK--RWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   +      +++      K
Sbjct: 74  PTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE    IA  L +   E V    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNRIGALEEGDLRPENVQRIATDLGVTEAEVVSMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED++A    D   +  L   RE     +  L  RE+ +L  R      
Sbjct: 194 DGEGTMQWQDWLEDESADQAGDYEARDELTQRRELMAEAMEVLNDREKDILMQRRLAEKT 253

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLE++  Q+ V+RERIRQIE +A  KL+   ++
Sbjct: 254 V--TLEDLSGQYSVSRERIRQIEVRAFEKLQKKMQT 287


>gi|110224837|emb|CAJ29296.1| DNA-directed RNA polymerase subunit D [Pseudomonas kilonensis]
          Length = 258

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 49/300 (16%), Positives = 107/300 (35%), Gaps = 48/300 (16%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   +M ++   P T   ++     +      L +++          
Sbjct: 1   REGEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             G+    +G +    E       +    + + D + A     ++ ++    P  A    
Sbjct: 51  -SGYIDPDDGIAPPAAEVPPPIDAKAVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRF 109

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             + +  + +   L                                   +K  +++ +  
Sbjct: 110 GAVADQMEITRKAL-----------------------------------KKHGRNNKQAI 134

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
                L +L   + L   + + LVE++     R+   E  +++L      + R  FL + 
Sbjct: 135 AELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 194

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I+E + I   +
Sbjct: 195 PGHEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRM 253


>gi|333024988|ref|ZP_08453052.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332744840|gb|EGJ75281.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 316

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 119/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 74  LFERLEDLDEGTHAHSYVRHTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 133

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 134 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 193

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PTP E+A+KL +  E V + +         SL+    ++D  S L D +  ++       
Sbjct: 194 PTPSELAEKLGIEREEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHSLEGIE 253

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I     E+   ++A L  R+ ++L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 254 YI-----ESLKPMIARLPQRDRKILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRT 304

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 305 LVKLRK 310


>gi|90581423|ref|ZP_01237218.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90437400|gb|EAS62596.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 286

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 129/272 (47%), Gaps = 16/272 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + I++++    ++    + +   +   +   S     +V ++LR V+ +A+ Y+  
Sbjct: 14  ESLDSYIQTVNRYPMLTPEREKELAERLHYDDDINSAKA--LVMSHLRFVVHIARGYSGY 71

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-- 524
           GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++     
Sbjct: 72  GLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKA 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
            R     + ++ +R+      E     +A++L +    VR++               D+D
Sbjct: 132 QRKLFFNLRKSKKRLGWFNNDEVNM--VAEQLGVEPSDVREMESRLAAQDPTFEMQNDDD 189

Query: 585 TS-----HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                      ++EDK+   A++  ++  + +     ++ LASL  R + ++R R+    
Sbjct: 190 ERDTTPVAPAYYLEDKSSDLALTYEENNWENHANNRLSQALASLDERSQHIVRSRWLDD- 248

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL+++   + V+ ERIRQ+E  A++KLK
Sbjct: 249 -EKSTLQDLADNYGVSAERIRQLEKNAMKKLK 279


>gi|306021726|gb|ADM80299.1| RNA-polymerase sigma subunit [Geobacillus pallidus]
          Length = 256

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 113/246 (45%), Gaps = 13/246 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
             V   +        A   +V+  + LV     + +    + +   DLI  G +GL  A 
Sbjct: 10  ERVYWDKWFRHRDQDAGNMLVKKYMPLVRYHVSRISVGLPKNVDKDDLISFGLMGLYDAL 69

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD     KF TYA + ++ AI   +  +     +P   R+K  KV     R+  K  R
Sbjct: 70  EKFDPTRDLKFDTYASFRIRGAILDGLRKEDW---LPRSFREKAKKVEAAIERLEQKYHR 126

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDF-IEDKNAVSPLD 602
             TP E+A++L M  E V  V+        +S++  + D++     +  ++D   ++P +
Sbjct: 127 NVTPNEVAEELGMTPEEVVHVVNENFFANVLSIDEQLHDQEEGEQMNIVLKDDKTLTPEE 186

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++  L E  T++++ L  +E+ VL + +      + TL E+G    ++  RI QI +K
Sbjct: 187 HLLKEELFEHLTKLISQLNDKEQLVLSLFY----KEELTLTEIGNVLNLSTSRISQIHSK 242

Query: 663 AIRKLK 668
           A+ KLK
Sbjct: 243 ALYKLK 248


>gi|119953545|ref|YP_945755.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
 gi|119862316|gb|AAX18084.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
          Length = 267

 Score =  127 bits (319), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 68/259 (26%), Positives = 134/259 (51%), Gaps = 8/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   ++        AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHRLITHEEEIELAKQIK---LGDLKAKNKMINANLRLVLKIIKRYAGKGLKVE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  E+I ++  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLMEEEKSPKKEDIMERFNLTTAQYIKIIPYLEKEYSLDKKIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
            ED +          + L+     +   L  +E  ++  R+ +  +    TL+++  +  
Sbjct: 185 YEDNSFNPESTLEQNSTLKHLNHILETKLNEKERYIIIKRYNLDNSDKKSTLKDISNELG 244

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++ E +RQIE + ++KLK 
Sbjct: 245 ISSETVRQIEKRVLKKLKE 263


>gi|66474673|gb|AAY46906.1| RpoD [Aeromonas sp. ABJ]
          Length = 272

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 119/316 (37%), Gaps = 46/316 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+RE  I IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTRERRIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E DDV  T   I S            D   +   +
Sbjct: 59  N------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGD 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSV 312
            + + D+ +      ++                  E + ELR+  +   ++ Q++ ++  
Sbjct: 95  GDDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHE 137

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFL 371
             +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+
Sbjct: 138 DTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFV 197

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I 
Sbjct: 198 AAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDIN 256

Query: 432 SMVRKGECEASIAKKE 447
             +  GE +A  AKKE
Sbjct: 257 RRMSIGEAKARRAKKE 272


>gi|294630217|ref|ZP_06708777.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833550|gb|EFF91899.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 314

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 111/244 (45%), Gaps = 11/244 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +  G  E +  +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD 
Sbjct: 77  LKELEPGTSEHARVRGALIEANLPLVRYAAGRFRSRNEPMEDVVQVGTIGLINAIDRFDP 136

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  V   I R   D   T+ +P  + +   +V      ++    R PT  
Sbjct: 137 DRGVQFPTFAMPTVVGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTA 196

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA++L +  E V   ++   +    SLE     +    L D +  ++            
Sbjct: 197 EIAERLRITEEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH---- 252

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+    +L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++ ++L+
Sbjct: 253 -RDLVRHLLVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFQRLR 307

Query: 669 HPSR 672
             +R
Sbjct: 308 SANR 311


>gi|254490572|ref|ZP_05103758.1| alternative sigma factor RpoH [Methylophaga thiooxidans DMS010]
 gi|224464316|gb|EEF80579.1| alternative sigma factor RpoH [Methylophaga thiooxydans DMS010]
          Length = 287

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 63/257 (24%), Positives = 116/257 (45%), Gaps = 12/257 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   + + +++       A + +V ++LR V+ +AK Y+  GL   DLIQEGNIGL
Sbjct: 31  LTAEEEYDLATRLQQDG--DLEAAQRLVLSHLRFVVRIAKGYSGYGLPVADLIQEGNIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMS 540
           MKA ++F+   G +  ++A+ WV+  I   +      ++I     + K+   +R+A++  
Sbjct: 89  MKAVKRFNPEKGVRLVSFAVHWVRAEIHEYVIRNWRIVKIATTKAQRKLFFNLRSAKQRL 148

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH----LGDFIEDKN 596
             + +E            P   +    ++ +   S + P    D          ++    
Sbjct: 149 GWLNQEEVEAVAEDLGVTPANVMDMERRLAQPDASFDLPADSNDDEETHFSPVAYLAGPE 208

Query: 597 AVSPLDSAIQANL----RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
              P     Q N     ++  T  LA+L  R   ++  R+ +  +   TL  +  Q+ V+
Sbjct: 209 NSDPSQQLEQENYSDYQQQKLTNALATLDDRSRDIIMQRW-LNEDDKATLHTLADQYQVS 267

Query: 653 RERIRQIEAKAIRKLKH 669
            ERIRQIE  A++KLK 
Sbjct: 268 AERIRQIENNAMKKLKK 284


>gi|254510133|ref|ZP_05122200.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
 gi|221533844|gb|EEE36832.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
          Length = 292

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 124/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELQLAYAWRDNRDEQALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAATE 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET-PIGDEDTSHLGDFIEDKN- 596
              + R    + IA ++ +P+  V  +  ++     SL      DED     D +ED   
Sbjct: 146 GLDLDRHQLHQMIAAEIGVPLRDVEMMEGRLAGSDFSLNAVQSADEDGREWIDALEDDRE 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A S   S     LR+     + +L  RE  ++R R         TLE +G++  +++E
Sbjct: 206 QAAESVEHSHDTQQLRDWLVTAMQALNDRERFIVRERKLREP--ARTLESLGQELGLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S++++ F 
Sbjct: 264 RVRQLEAAAFTKMRKNLEAQSREVQHFF 291


>gi|42782996|ref|NP_980243.1| sporulation sigma factor SigG [Bacillus cereus ATCC 10987]
 gi|49186753|ref|YP_030005.1| sporulation sigma factor SigG [Bacillus anthracis str. Sterne]
 gi|49478441|ref|YP_037965.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141585|ref|YP_085244.1| sporulation sigma factor SigG [Bacillus cereus E33L]
 gi|118479123|ref|YP_896274.1| sporulation sigma factor SigG [Bacillus thuringiensis str. Al
           Hakam]
 gi|196038711|ref|ZP_03106019.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|222097349|ref|YP_002531406.1| sporulation sigma factor sigg [Bacillus cereus Q1]
 gi|228928952|ref|ZP_04091984.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935219|ref|ZP_04098045.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228947623|ref|ZP_04109913.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987048|ref|ZP_04147173.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229092950|ref|ZP_04224083.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|229123417|ref|ZP_04252621.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|229186144|ref|ZP_04313313.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|254683387|ref|ZP_05147247.1| sporulation sigma factor SigG [Bacillus anthracis str. CNEVA-9066]
 gi|254739809|ref|ZP_05197502.1| sporulation sigma factor SigG [Bacillus anthracis str. Kruger B]
 gi|254750999|ref|ZP_05203038.1| sporulation sigma factor SigG [Bacillus anthracis str. Vollum]
 gi|254757943|ref|ZP_05209970.1| sporulation sigma factor SigG [Bacillus anthracis str. Australia
           94]
 gi|301055394|ref|YP_003793605.1| RNA polymerase sigma-G factor [Bacillus anthracis CI]
 gi|42738923|gb|AAS42851.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10987]
 gi|49180680|gb|AAT56056.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Sterne]
 gi|49329997|gb|AAT60643.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51975054|gb|AAU16604.1| RNA polymerase sigma-G factor [Bacillus cereus E33L]
 gi|118418348|gb|ABK86767.1| RNA polymerase, sigma subunit, RpsG/SigG [Bacillus thuringiensis
           str. Al Hakam]
 gi|196030434|gb|EDX69033.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|221241407|gb|ACM14117.1| RNA polymerase sigma-G factor [Bacillus cereus Q1]
 gi|228597320|gb|EEK54971.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|228660193|gb|EEL15829.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|228690454|gb|EEL44238.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|228772642|gb|EEM21083.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228812143|gb|EEM58474.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824384|gb|EEM70190.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830759|gb|EEM76364.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|300377563|gb|ADK06467.1| RNA polymerase sigma-G factor [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327802|gb|ADY23062.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 289

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 134/264 (50%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE     A++++V  NLRLV+SV +++ N
Sbjct: 33  RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEIS---AREKLVNGNLRLVLSVIQRFNN 89

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 90  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 148

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 149 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 208

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+           A         +  L  RE+ ++R RF  G     T  
Sbjct: 209 DPIFVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQM 259

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 260 EVAEEIGISQAQVSRLEKSAIKQM 283


>gi|30024622|dbj|BAC75679.1| sigma F [Streptomyces griseus]
          Length = 293

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 104/236 (44%), Gaps = 12/236 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           E    +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+
Sbjct: 64  EHRRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTF 123

Query: 500 AMWWVKQAITRSIA-DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           AM  V   I R    + +     P  + +   +V      ++    R PT  EIA++L +
Sbjct: 124 AMPTVVGEIKRYFRDNCAHPSTSPDRLHELWVQVTGATEDLTTAHGRSPTTAEIAERLKI 183

Query: 559 PVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             + V   ++   +    SLE     +    L D +  ++             R+    +
Sbjct: 184 SEDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEH-----RDLVRHL 238

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  L  RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 239 LVQLPEREQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 290


>gi|296331109|ref|ZP_06873583.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674264|ref|YP_003865936.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151753|gb|EFG92628.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412508|gb|ADM37627.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 260

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 139/264 (52%), Gaps = 18/264 (6%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++  +     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNEEMRKLFRQLQ--DEGDDSAREKLVNGNLRLVLSVIQRFNN 60

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 61  RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 119

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   R+ ++  +EPT E+IAK L +P E +   L   ++P+SL  PI ++  
Sbjct: 120 RDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGG 179

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D+   +     I+          +  L  RE+ +LR RF  G     T  
Sbjct: 180 DPIYVMDQISDER--NKDSQWIEEL---ALKEGMRRLNDREKMILRKRFFQG----KTQM 230

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 231 EVAEEIGISQAQVSRLEKAAIKQM 254


>gi|326332872|ref|ZP_08199129.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
 gi|325949230|gb|EGD41313.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
          Length = 265

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 114/233 (48%), Gaps = 9/233 (3%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + E + A++E+V  N+ LV   A ++  RG    DL+Q G +GL+ A +++D     +FS
Sbjct: 38  DAERTAAREELVHLNMALVEYCASQFYGRGEPHEDLVQVGVVGLLNAVDRYDLARDVEFS 97

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  +   I R   D    + +P  +RD    +      +S ++ R PT  ++A +L 
Sbjct: 98  TYAVPTILGEIKRYFRDSRWAVSVPRRLRDLQQNLRDATAELSQELGRSPTARDLATRLG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + +E V + L+ +    +L      ++T+ + D +      +         +RE+   VL
Sbjct: 158 VSLETVVEGLESSNAYAALSLDSESDETAPMLDSL-----TAHDLRLDDVEVRESIKPVL 212

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            SL+  E++VL ++F        T  E+  +  V++ ++ ++  +++ +L+  
Sbjct: 213 DSLSAHEKQVLMLKFFRN----KTQTEIAGELGVSQMQVSRLLNRSLAQLRKA 261


>gi|302554440|ref|ZP_07306782.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472058|gb|EFL35151.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 280

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 43  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIDREIKFE 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 103 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPTEGEVAAEMG 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E          D   + D +ED  A +P++ A   
Sbjct: 160 IGVEE----LHAVFSQLSLANVVALEELLHAGGEGGDGLSVMDTLEDTAADNPVEVAEDR 215

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 216 ELRRLLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 271

Query: 668 K 668
           +
Sbjct: 272 R 272


>gi|149202313|ref|ZP_01879286.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
 gi|149144411|gb|EDM32442.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
          Length = 298

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 68/276 (24%), Positives = 120/276 (43%), Gaps = 15/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWAEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   +   +     R    ++IA  L +    V     ++     SL   +G 
Sbjct: 134 KLFFNLRKAKAKIGALEEGDMRPDVVKKIATDLGVTEAEVISMNQRMAGADASLNATVGA 193

Query: 583 EDTSH--LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A               RE   + +  L  RE  +L        +
Sbjct: 194 EGEGSMQWQDWLEDEDADQAGDYERRDELDARRELLVQAMDVLNERERDILTQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TLE++  ++ V+RERIRQIE +A  KL+   R+
Sbjct: 252 ETVTLEDLSAEYDVSRERIRQIEVRAFEKLQKRMRA 287


>gi|62258694|gb|AAX77814.1| unknown protein [synthetic construct]
          Length = 327

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  ++    +S+ + + +    +    +   A +++V ++LR V  +A+ ++  GL
Sbjct: 49  LSAYLNFVNTLPVLSLEQEQELARRYKY--KKDLDAAQQLVLSHLRFVTKIARNFSGYGL 106

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA  KFD   G +  ++A+ W+K  +   +      +++     + 
Sbjct: 107 SIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKIVKVATTKAQR 166

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTS 586
           K+   +R+++     +  E   +E+A++L +  E V ++ K   +   SL+ P  D+D  
Sbjct: 167 KLFFNLRSSKDKIGWLSSEN-IKELAEELGVKEETVIEMEKRMCQGDASLDLPYTDDDGE 225

Query: 587 HLGD---FIEDKNAVSPLDSAIQ---ANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK++        Q    N +     VL+    R + ++  R+ +      
Sbjct: 226 QTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKDIIMSRYLLDN--KA 283

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           TL+++  ++ ++ ER+RQIE  A+ KLK   +++  
Sbjct: 284 TLQDLAAKYNISAERVRQIEEDALAKLKKAIKNRSY 319


>gi|239934576|emb|CAR94602.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 103/270 (38%), Gaps = 43/270 (15%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   ++  L   P T Q ++   +    
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGIYQVLKPLAHYPETTQLVLDDYERYLA 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L EII            GF    E  +      S  E++++++  T  D +   + 
Sbjct: 61  QEIRLNEII-----------SGFADTDEQVAPASNIGSMLEEQQENILTTAEDEDEDGEG 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +     +           +                            D++ + Y ++  
Sbjct: 110 GEGGEGVIGDEDGPNPELAKEY-------------------------FDDLRDHYNKVMR 144

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           L        +  +   K   L E++      L L   ++D L      +   I   E  +
Sbjct: 145 LIK------EHGRDHAKTLKLLEEMSDCFLKLKLTSRQVDRLTRHFKLLRNHIREFERGI 198

Query: 357 LRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
           +RL  +   I R +F+E   G+E D HW+ 
Sbjct: 199 MRLCIEKARIPRKLFIETFPGQETDLHWLD 228


>gi|254283645|ref|ZP_04958613.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
 gi|219679848|gb|EED36197.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
          Length = 291

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 127/266 (47%), Gaps = 15/266 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+++     +S    + +   +  GEC AS   +E+V A+LR V+ +A+ Y+  GL   
Sbjct: 27  YIQAVGTIPMLSAEREQALAEKLYYGECVAS--ARELVLAHLRFVVHIARSYSGYGLAEA 84

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIH 530
           DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  +   I      +++     + K+ 
Sbjct: 85  DLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKLF 144

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--------LKITKEPISLETPIGD 582
             +R+A++  + +    T   IA+ L +P   V+++        +       + +     
Sbjct: 145 FNLRSAKKNLSWLTHSETQA-IAEDLGVPEAEVQRMEGRLSCRDMAFDAPSDADDDDAWQ 203

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               +L D   D  AV+   +   A+        LA L  R + +L  R+        TL
Sbjct: 204 APQHYLQDLSSDP-AVAVEAANSSADDETRLHAALAQLDARSQDILARRWLAE--KKATL 260

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  +  V+ ERIRQ+EA A++KL+
Sbjct: 261 HELAAEHGVSAERIRQLEANAMKKLR 286


>gi|119476594|ref|ZP_01616904.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119449850|gb|EAW31086.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 194

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 67/189 (35%), Positives = 118/189 (62%)

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +R AR ++ K+  EPTP
Sbjct: 1   PERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTQKLDHEPTP 60

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEIA+ L  PV  V+++L++ +   S++TP+G +    L D I D +   P +     ++
Sbjct: 61  EEIAELLDRPVADVKRMLRLNERVASVDTPLGADSDKSLLDTIPDTHVSDPAEMLQDDDM 120

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + + +  +  LT ++  V+  RFG+      TLEEVG++  +TRER+RQI+ +A+++L+ 
Sbjct: 121 KASISEWIGELTEKQREVVARRFGLRGYETSTLEEVGREIGLTRERVRQIQVEALKRLRD 180

Query: 670 PSRSKKLRS 678
               + L S
Sbjct: 181 ILEKQGLSS 189


>gi|293393954|ref|ZP_06638260.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
 gi|291423514|gb|EFE96737.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
          Length = 285

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 121/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAR 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  ++  + ++ +    DE  D   +   +  ++  S     I+ +  E
Sbjct: 160 ELGVTSKDVREMESRMAAQDMTFDPTPDDEARDGQSMAPVLYLQDKTSDFAEGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +         L  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SNAADKLAYALEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           LK
Sbjct: 279 LK 280


>gi|187763286|gb|ACD35520.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 116/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFKDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|52546494|dbj|BAD51630.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546496|dbj|BAD51631.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546498|dbj|BAD51632.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546500|dbj|BAD51633.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546502|dbj|BAD51634.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546504|dbj|BAD51635.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546506|dbj|BAD51636.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546508|dbj|BAD51637.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546510|dbj|BAD51638.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546512|dbj|BAD51639.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546514|dbj|BAD51640.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546516|dbj|BAD51641.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546518|dbj|BAD51642.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546520|dbj|BAD51643.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546522|dbj|BAD51644.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546524|dbj|BAD51645.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546526|dbj|BAD51646.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546528|dbj|BAD51647.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546530|dbj|BAD51648.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546532|dbj|BAD51649.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546534|dbj|BAD51650.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546536|dbj|BAD51651.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546538|dbj|BAD51652.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546540|dbj|BAD51653.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546542|dbj|BAD51654.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546544|dbj|BAD51655.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546546|dbj|BAD51656.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546548|dbj|BAD51657.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546550|dbj|BAD51658.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546552|dbj|BAD51659.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546554|dbj|BAD51660.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546556|dbj|BAD51661.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546558|dbj|BAD51662.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546560|dbj|BAD51663.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546562|dbj|BAD51664.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546564|dbj|BAD51665.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546566|dbj|BAD51666.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546568|dbj|BAD51667.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546570|dbj|BAD51668.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546572|dbj|BAD51669.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|52546574|dbj|BAD51670.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506775|dbj|BAD91134.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506778|dbj|BAD91135.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506781|dbj|BAD91136.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506784|dbj|BAD91137.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506788|dbj|BAD91138.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506791|dbj|BAD91139.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506795|dbj|BAD91140.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506798|dbj|BAD91141.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506801|dbj|BAD91142.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506804|dbj|BAD91143.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506807|dbj|BAD91144.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506810|dbj|BAD91145.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506813|dbj|BAD91146.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506816|dbj|BAD91147.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506819|dbj|BAD91148.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506822|dbj|BAD91149.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506825|dbj|BAD91150.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506828|dbj|BAD91151.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506831|dbj|BAD91152.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506834|dbj|BAD91153.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506838|dbj|BAD91154.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506841|dbj|BAD91155.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506844|dbj|BAD91156.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506847|dbj|BAD91157.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506850|dbj|BAD91158.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
 gi|61506853|dbj|BAD91159.1| DNA-directed RNA polymerase subunit D [Burkholderia glumae]
          Length = 275

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 53/316 (16%), Positives = 115/316 (36%), Gaps = 42/316 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDP 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   GF       + +  E+  +  E ++ ++ +G  ++ A  ++ +           
Sbjct: 61  NAEDTDGFNAKEAEEAEEAEEEEEEANEDEEEEDDDGAAQATANAAQLEA---------- 110

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                   L+   +     I+E + ++R   +      K+   S
Sbjct: 111 ------------------------LKRASLEKFALISEWFDKMRRAFE------KEGYKS 140

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + S+      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 141 KSYLKAQETIQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 200

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   +   + +I + +  +  +     + + + +  
Sbjct: 201 IARFPGSETDLTWAEKVAAESHS-YSAILVRNIPAIHEQQQRLLDLQARVVLPLKDLKET 259

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 260 NRQMAAGELKARQAKR 275


>gi|254694416|ref|ZP_05156244.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
          Length = 311

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 74/267 (27%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 35  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 92

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 93  LIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 152

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 153 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETG 212

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 213 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 270

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 271 LEALGEKLGISKERVRQIESRAMEKLK 297


>gi|94265020|ref|ZP_01288789.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|94270029|ref|ZP_01291635.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93450968|gb|EAT01953.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93454509|gb|EAT04794.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
          Length = 337

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 74/280 (26%), Positives = 139/280 (49%), Gaps = 10/280 (3%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ IS    +S  E   +    +  E     A  ++V ANLRLV+ VA  +    
Sbjct: 49  ALHRYLQEISQYRLLSREETDELARRFQ--ESGDPDAAYQLVTANLRLVVKVAMDFQKYW 106

Query: 468 LQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHM 525
           +Q FLDLIQEGNIGL++A +KFD     KFS YA +W++  I + I D    ++I     
Sbjct: 107 MQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAYWIRAYILKFIMDNWRLVKIGTTQA 166

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDED 584
           + K+   +   +++      EP P+ +A++L +    + ++  ++    +SLE+P+ ++ 
Sbjct: 167 QRKLFFNLNKEKKLLEAQGFEPEPKLLAQRLNVKESEIIEMGQRLEHGDMSLESPLREDS 226

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--LTPREERVLRMRFGIGMNTDHTL 642
                DF+             +  +R+    +L    LT  E+ +  +   +  +   TL
Sbjct: 227 DEQRKDFLP-MLGPGVEQRVAEDEIRQWMAAMLDKLRLTLNEKELAILDQRLLNDDPRTL 285

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK--LRSFL 680
           +E+  +F ++RER+RQIEA  ++K++    ++   ++ FL
Sbjct: 286 QEIADRFTISRERVRQIEANLLKKMRLYLENEVPDVKDFL 325


>gi|259479063|dbj|BAI40079.1| RNA polymerase sigma-70 factor [Aeromonas sp. Rameshwaram]
          Length = 271

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 115/314 (36%), Gaps = 44/314 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKE 447
           +  GE +A  AKKE
Sbjct: 258 MSIGEAKARRAKKE 271


>gi|37784438|gb|AAO13112.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|37955132|gb|AAP76218.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
          Length = 272

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 116/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                             D E  A  +    S++       E++
Sbjct: 59  ----------------------------------DTEDMAPTATHIGSELSEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           + + DEDED                      E+   Y          ++ QK+ ++    
Sbjct: 85  DEDEDEDEDGDNSDDDGDGGPDPEVAREKFAELRAQYEV------TRLSIQKNGRAHDDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +  W   +    + + +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKA-WSPRLMEMDEEVQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|66474619|gb|AAY46879.1| RpoD [Aeromonas enteropelogenes]
 gi|66474627|gb|AAY46883.1| RpoD [Aeromonas schubertii]
 gi|66474645|gb|AAY46892.1| RpoD [Aeromonas hydrophila]
          Length = 271

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 113/315 (35%), Gaps = 45/315 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                                    E +D+  T   I S            +   E+ + 
Sbjct: 59  N------------------------EAEDMAPTATHIGSELGEDDLADEDEEDEDEDEDG 94

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           D  + D D             +LR +       I                 QK+ ++   
Sbjct: 95  DSSDDDGDGGPDPEVAREKFAELRAQYEVTRLSI-----------------QKNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      V  + D + +   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLVEMDED-VQRAIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 257 RMSIGEAKARRAKKE 271


>gi|62290634|ref|YP_222427.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700548|ref|YP_415122.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|148559493|ref|YP_001259609.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|254689924|ref|ZP_05153178.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254700417|ref|ZP_05162245.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|254719758|ref|ZP_05181569.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|254730958|ref|ZP_05189536.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256258178|ref|ZP_05463714.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256370169|ref|YP_003107680.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260547128|ref|ZP_05822866.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297249027|ref|ZP_06932735.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306839453|ref|ZP_07472261.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
 gi|62196766|gb|AAX75066.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616649|emb|CAJ11731.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|148370750|gb|ABQ60729.1| RNA polymerase sigma-70 factor family protein [Brucella ovis ATCC
           25840]
 gi|256000332|gb|ACU48731.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260095493|gb|EEW79371.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297174160|gb|EFH33517.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306405398|gb|EFM61669.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
          Length = 311

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 76/289 (26%), Positives = 131/289 (45%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|57239125|ref|YP_180261.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|57161204|emb|CAH58118.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 296

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 75/278 (26%), Positives = 127/278 (45%), Gaps = 15/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  +     +S+ E   +       E        ++V ++LRLV+ VA  + N GL
Sbjct: 14  LMSYINEVQSFQVLSLEEEEKLAK--NWYEHGVIADAHKLVTSHLRLVVKVALSFKNYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K +I   I      I+I      +
Sbjct: 72  PLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCIKIGTTQAQR 131

Query: 529 IHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
                    +           +E    IA + +   + V ++    T    SL   +   
Sbjct: 132 KLFFSLRKIKKKLLKYHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRDKSLNDVVFSN 191

Query: 584 DTSH---LGDFI--EDKNAVSPLDSAIQANLRETT-TRVLASLTPREERVLRMRFGIGMN 637
            + +   L D I  ED N         + +++++  T+ LA+L  R   +   R  I   
Sbjct: 192 GSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDIFIRRKLIE-- 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
              TLE + K++ +++ERIRQIE  A  K+K+   SK+
Sbjct: 250 EPDTLEILSKKYNISKERIRQIETHAFLKVKNFVISKR 287


>gi|159037890|ref|YP_001537143.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
 gi|157916725|gb|ABV98152.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
          Length = 374

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 112/237 (47%), Gaps = 12/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F
Sbjct: 35  PPERRQEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SF 93

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           + YA   +   I R   D++  + +P  +RD I +V +    +++++ R PT  E+A++L
Sbjct: 94  TAYAAITIVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATAALTSELSRAPTVAELARRL 153

Query: 557 AMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             P E +   L+      P SL  P+G E ++  GD + + +     ++    + R T +
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPVGGESSAEFGDLVGESD-----NALESVDDRVTVS 208

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +L  L  RE R+L MRF           E+  +F +++  + ++ ++A+  L+   
Sbjct: 209 GLLHRLPWRERRILAMRFYGNQTQ----AEIAARFGISQMHVSRLLSRALTWLRQAM 261


>gi|297539272|ref|YP_003675041.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera sp. 301]
 gi|297258619|gb|ADI30464.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera sp. 301]
          Length = 285

 Score =  127 bits (319), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 119/266 (44%), Gaps = 9/266 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I     +S  E   +   V+        A ++++ ++LRLV S+A+ Y   GL   DLIQ
Sbjct: 23  IKAYPVLSAEEEYSLA--VKFRADNDLEAARQLIVSHLRLVASIARGYNGYGLPQSDLIQ 80

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVR 534
           EGNIGLMKA ++FD   G +  ++AM W+K  +   I      ++I     + K+   +R
Sbjct: 81  EGNIGLMKAVKRFDPERGVRLVSFAMHWIKAEMHEYIVRNWRMVKIATTKAQRKLFFNLR 140

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD--FI 592
           + +   N ++         +    P E +    ++    ISLE  I D+         ++
Sbjct: 141 SMKTGLNSLQPAEVAHIAKELNVKPEEVLEMEARLNGHEISLEANIDDDSDEQYSPIAYL 200

Query: 593 EDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
            D+      +     I+          L +L  R  RV+  R+        TL E+  +F
Sbjct: 201 PDEGLEPLEALESKQIEIAETTGLANALQNLDDRSRRVVEARWLQDQGG-KTLHELADEF 259

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKK 675
            V+ ERIRQIE KA++K+K    + +
Sbjct: 260 GVSAERIRQIEQKAMQKMKSLMLASR 285


>gi|326781290|ref|ZP_08240555.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326661623|gb|EGE46469.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 290

 Score =  127 bits (318), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 57/248 (22%), Positives = 118/248 (47%), Gaps = 8/248 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G      A+  ++E NL LV   AK++ NRG  +  D++Q G IGL+KA 
Sbjct: 44  FFERLQVLEEGTHAYQYARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIVQVGTIGLIKAI 103

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   I R   D +  + +P  +++    + +    ++ ++ R
Sbjct: 104 DRFELSREVEFTSFAIPYIVGEIKRFFRDSTWAVHVPRRLQELRVTLAKAKEELAGRLDR 163

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT  E+A  L +  E V + L  +      SL+ PIG E  S       D         
Sbjct: 164 DPTVGELAAHLGLTDEEVIEGLIASNGYTAGSLDLPIGTEQNSAETITYGDIKGDLDPAI 223

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  NL      +L  L  R+  ++ MRFG     + T  ++G++  +++  + ++  + 
Sbjct: 224 ELVENLH-ALAPLLEGLGDRDREIVAMRFG----QELTQAQIGERLGISQMHVSRLLNRL 278

Query: 664 IRKLKHPS 671
           + +L+   
Sbjct: 279 LTQLRKNM 286


>gi|55274907|gb|AAV49255.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 189

 Score =  127 bits (318), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 76/189 (40%), Positives = 127/189 (67%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 1   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 60

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 61  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 120

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+     
Sbjct: 121 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEA 180

Query: 640 HTLEEVGKQ 648
            TLE+VG++
Sbjct: 181 ATLEDVGRE 189


>gi|320012478|gb|ADW07328.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 290

 Score =  127 bits (318), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 54/246 (21%), Positives = 112/246 (45%), Gaps = 9/246 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   +  + +G  E   A+  ++E NL LV   A ++ NRG     D++Q G IGL+KA 
Sbjct: 41  FFDRLQALDEGTPEHQYARNTLIEMNLSLVRFAAGRFRNRGSGDMEDIVQVGTIGLIKAI 100

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D +  + +P  +++    + +    ++ ++ R
Sbjct: 101 DRFDLAREVEFTSFAVPYIVGEIKRFFRDTTWAVHVPRRLQELRVDLAKAKEALAVELDR 160

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS-- 603
           +PT +E+A  L +  E + + L       +    +  +   H G     +     L    
Sbjct: 161 DPTVQELAGYLDLEEEEITEGLVAANGYTAGSLEMPADAGDHAGRTTAGRTYADVLGEPD 220

Query: 604 --AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                         +L  L  RE R++ MRFG     + T  ++G +  +++  + ++ +
Sbjct: 221 PAMETVENLHALAPLLGELDARERRIIDMRFG----QEMTQAQIGDELGISQMHVSRLLS 276

Query: 662 KAIRKL 667
           + +RKL
Sbjct: 277 RILRKL 282


>gi|302558130|ref|ZP_07310472.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
 gi|302475748|gb|EFL38841.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
          Length = 280

 Score =  127 bits (318), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 104/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      +   D +  G  GL+ A EKFD     KF 
Sbjct: 43  DERLREQLILHYSPLVKYVAGRVSVGLPPNVDQGDFVSSGVFGLIDAIEKFDVDREIKFE 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A +L 
Sbjct: 103 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPSESEVAGELG 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + V+     L      +SL   +  E          D   L D +ED  A  P++ A   
Sbjct: 160 IAVDE----LHAVFSQLSLANVVALEELLHVGGESGDRLSLMDTLEDTAADDPVEVAEDR 215

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 216 ELRRFLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 271

Query: 668 K 668
           +
Sbjct: 272 R 272


>gi|226359630|ref|YP_002777408.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226238115|dbj|BAH48463.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 265

 Score =  127 bits (318), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ +   EAS  + E++   L L   +A+++  RG    DL+Q   +GL+KA ++FD 
Sbjct: 28  LRILEESSGEASALRDEIITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDP 87

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G+ F +YA+  +   + R   D   ++R+P  M++    + +    +S ++ R P+  
Sbjct: 88  DRGFDFVSYAVPTIMGEVRRYFRDTGWSMRVPRRMQELHALIAKAVDELSQELGRSPSAS 147

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQA 607
           EIA +L + V  V + L      + +S++  +GD+ D   L + + +++           
Sbjct: 148 EIAAELELDVREVSEGLLAKNAYQTLSMDAAMGDDPDDLPLAETLGEED-----PELANV 202

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               +    L  L P E RVL +RF        T  E+ ++  V++ ++ +I A+ +  L
Sbjct: 203 ESHASVRPALEKLPPLERRVLMLRFF----GSMTQTEIAQRVGVSQMQVSRILARTLSGL 258

Query: 668 KH 669
           + 
Sbjct: 259 RE 260


>gi|157373363|ref|YP_001471963.1| RNA polymerase factor sigma-32 [Shewanella sediminis HAW-EB3]
 gi|157315737|gb|ABV34835.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sediminis
           HAW-EB3]
          Length = 285

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 123/268 (45%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + S    + +   +   +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LEAYVHSAHNISMLQPEQEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+   ++      E   +A  L +    V     ++  +  + +    ++D 
Sbjct: 137 --KLFFNLRKSKKRLGWFSDEEVGMVADNLGVSKADVTEMESRMAAQDPAFDLASDNDDD 194

Query: 586 SHL--GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A    +  ++A+ +      + +L  R + +L+ R+        
Sbjct: 195 HDFAPMHYLEDHSSDLASQVENDNLEASNQARLLSAIKTLDERSQHILQARWL--NEDKT 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 253 TLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|83859148|ref|ZP_00952669.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852595|gb|EAP90448.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 296

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 123/275 (44%), Gaps = 14/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E E S A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLAEIRKFPMLEKDQEFMLAK--RWQEHEDSDAAHQLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A +KFD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQK 133

Query: 529 --IHKVVRTARRMSNKIKRE---PTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + R   +M    + +      EEIA KL +  + V     +++    SL  P+  
Sbjct: 134 KLFFNLRRMKSQMRALDEGDLRPDQVEEIATKLGVTDDDVISMNRRLSGPDASLNAPMRA 193

Query: 583 EDTSHLGDF----IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +  +   D+      D       +S   +         + +L  RE+ +++         
Sbjct: 194 DGEAEWQDWLADDDADDAEDELAESDEFSMRMTLLQEAMGALNEREQNIIQE--RRLTEE 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TLE++ + + V+RERIRQIE +A  KL++  + 
Sbjct: 252 PKTLEDLAQVYGVSRERIRQIEVRAFEKLQNEMKR 286


>gi|302147249|emb|CBL51746.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 262

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 56/300 (18%), Positives = 103/300 (34%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                      +         E +  D  E E + E       +D       PE A    
Sbjct: 59  -----ADDVAPTATHIGSELSEDDLADEDEEEDEDEDGDGDDAEDEGDGGPDPEVAREKF 113

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             L    + +  ++                                   QK+ ++    +
Sbjct: 114 GELRAQYEVTRLSI-----------------------------------QKNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      +  + D +L+   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLLEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|239934554|emb|CAR94591.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 210

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 97/257 (37%), Gaps = 49/257 (19%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G   +  +L   PLTFQ ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTFQHILNSYESVKQ 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
           G   L +II     I P +             Q      +E+            E     
Sbjct: 61  GQGRLVDII--VGFIDPNAPDEIAAPVNPKLAQAAAPEVEEE-----------TEEGEST 107

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            +++  +    PE A                   A   +L  + + A++           
Sbjct: 108 EEEEALETGPDPEEAARRF---------------ASIQKLHSQALKAIE----------- 141

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    +      K   +++K+      L L+    D L+ QL D    + + E ++
Sbjct: 142 ---------QHGIKDPKTVKIRKKVAGEFMELKLSPKMFDALIVQLRDHVAEVRNMEKQI 192

Query: 357 LRLAQS-YGIKRDVFLE 372
           + L     G+ R  F+ 
Sbjct: 193 MTLCVRDAGMPRKDFVT 209


>gi|163845340|ref|YP_001622995.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|163676063|gb|ABY40173.1| RNA polymerase sigma factor, sigma-70 family [Brucella suis ATCC
           23445]
          Length = 311

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 75/289 (25%), Positives = 130/289 (44%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLV S+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVTSMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKALFFNLCRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNCWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|254392909|ref|ZP_05008077.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294811525|ref|ZP_06770168.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326440088|ref|ZP_08214822.1| putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|197706564|gb|EDY52376.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294324124|gb|EFG05767.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 289

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 118/248 (47%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   ++ + +G  +    +  ++E NL LV   A ++ NR  Q  D+IQ G IGL+KA +
Sbjct: 45  FFERLAHLDEGTRDHQYVRNTLIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGLIKAID 104

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+     +F+T+A+ ++   I R   D S  + +P  +++    + +    +S ++ R 
Sbjct: 105 RFELSREVEFATFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRIDLAKATDDLSQRLDRS 164

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-----TSHLGDFIEDKNAVSPL 601
           PT  E+A+ L +  + V + +       +    +  ED     TS L D +   +A   +
Sbjct: 165 PTTRELAEHLGIDEQEVIEGVVAANGYTAGSIDMPLEDSSDHTTSSLSDRLGAPDAGLEI 224

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +QA        ++  L  R+ R+LRMRFG     + T  E+G +  V++  + ++  
Sbjct: 225 AENVQA-----LKPLIEELGERDRRILRMRFG----EELTQSEIGAELGVSQMHVSRLLT 275

Query: 662 KAIRKLKH 669
           +   +L+ 
Sbjct: 276 RITTRLRE 283


>gi|66474715|gb|AAY46927.1| RpoD [Aeromonas veronii]
          Length = 275

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 116/315 (36%), Gaps = 41/315 (13%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REG I IAKRIE G   + +S+ E       L+   D+       L +II        
Sbjct: 1   LTREGGIDIAKRIEDGINQVQSSVAEYTEAITYLLEQYDKFEAEQLRLSDIISGFVNPDE 60

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
             + G      G    + + + ++       + E D +     S DD S     PE A  
Sbjct: 61  ADEMGPSATHIGSELGEDDLADEDSSD----DEEEDEDEDGNDSSDDDSDGGPDPEVARE 116

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               L    + +  ++                                   + + ++  +
Sbjct: 117 KFAELRTQYEVTRQSI-----------------------------------RTNGRAHDE 141

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    KL  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+ 
Sbjct: 142 TQAEIAKLADIFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVS 201

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      VA E + +L+   +++ I  ETG+SI++ + I  
Sbjct: 202 AFTNNECETAWFEYQKQAGKAWSAPLVAME-EEVLRSIGKLQQIEEETGLSIAQIKDINR 260

Query: 433 MVRKGECEASIAKKE 447
            +  GE +A  AKKE
Sbjct: 261 RMSIGEAQARRAKKE 275


>gi|144899360|emb|CAM76224.1| Sigma-70 region 2:Sigma-70 region 4:Sigma-70 region 1.2
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 291

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 69/271 (25%), Positives = 123/271 (45%), Gaps = 14/271 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
             K++     +S  +   ++   R  +     A+  ++ A+LRLV+  A ++   GL   
Sbjct: 14  YYKAMRETALLSGEDEAELIR--RWKDEGDEKARTRLLSAHLRLVVKTAGQFKGYGLSGA 71

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM--RDKI 529
           DL+ EGN+GL++A E FD     +FSTYA WWV+ A+   +   S  +   +    +   
Sbjct: 72  DLVAEGNLGLVRALESFDPGRNLRFSTYAQWWVRAAMFEYVLKFSTPVNFGLSAERKKLF 131

Query: 530 HKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDT 585
            K+     R++       +  E   +A +L +  + V ++   +T+ P SL+ P+  E  
Sbjct: 132 FKLRGIKARLTGPSGNALSVAETAQVADELGVRDQRVAEMERLLTQSPRSLDAPV-GESG 190

Query: 586 SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              G+ + D           +  L   RE        LT RE  ++  R          L
Sbjct: 191 IPFGELLADDRPSVEETLGERQELMYRRELLKHAWEGLTERERDIVAQRTLREN--PLRL 248

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E++ +++ ++RER+RQIE  A+ KLK   R+
Sbjct: 249 EDLAQRYSISRERVRQIEGSALTKLKALVRA 279


>gi|318056726|ref|ZP_07975449.1| SigL-like sigma factor [Streptomyces sp. SA3_actG]
 gi|318075360|ref|ZP_07982692.1| SigL-like sigma factor [Streptomyces sp. SA3_actF]
          Length = 316

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 119/246 (48%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G    S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 74  LFERLEDLDEGTHAHSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 133

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 134 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 193

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PTP E+A+KL +  E V + +         SL+    ++D  S L D +  ++       
Sbjct: 194 PTPSELAEKLGIEREEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGIE 253

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I     E+   ++A L  R+ ++L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 254 YI-----ESLKPMIARLPQRDRKILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRT 304

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 305 LVKLRK 310


>gi|157692844|ref|YP_001487306.1| sporulation sigma factor SigF [Bacillus pumilus SAFR-032]
 gi|194016850|ref|ZP_03055463.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
 gi|157681602|gb|ABV62746.1| DNA-directed RNA polymerase sigma subunit SigF [Bacillus pumilus
           SAFR-032]
 gi|194011456|gb|EDW21025.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
          Length = 255

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 129/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K  + +  +S  E + +   ++K +     A+  +VE N+RLV SV +++ NRG +  
Sbjct: 4   EVKKQAKKAQLSNDEVKEL---IKKSQDGDQQARDLLVEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + R    +S    R PT +EIA+ L +  E V    +  + P S+   + + D     L 
Sbjct: 120 IRRARDELSKSHGRMPTVQEIAEYLDITPEDVVLAQEAVRTPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D +     D       +      +  L  RE+ ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADHSEERWFD-------KIALKEAIKELEEREKLIVYLRY----YKDQTQSEVAERL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K +++++
Sbjct: 229 GISQVQVSRLEKKILKQIQ 247


>gi|260589168|ref|ZP_05855081.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
 gi|260540249|gb|EEX20818.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
          Length = 266

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 134/273 (49%), Gaps = 19/273 (6%)

Query: 406 ILKIRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +    N+++   V T    I  +E +   ++  + +     A+++ ++ NLRLV+SV K+
Sbjct: 6   LAMALNKVEICGVNTSRLPILTNEEKD--ALFVRIKEGDPEAREQYIKGNLRLVLSVIKR 63

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +++      DL Q G +GL+KA + FD  L  KFSTYA+  +   I R + D +  IR+ 
Sbjct: 64  FSSSNENADDLFQIGCVGLIKAIDNFDTTLNVKFSTYAVPMIIGEIRRYLRDNN-AIRVS 122

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +RD  +K +        +  +EPT  EIA+++ +  E +   L   + P+SL  P+  
Sbjct: 123 RSLRDVAYKAIYAKENYVKQNLKEPTINEIAEEIGIDKEEIVYALDAIQSPVSLYEPVYT 182

Query: 583 E--DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           E  DT ++ D I D KN        I           L  L  RE+ ++ MRF  G    
Sbjct: 183 EGGDTLYVMDQISDKKNKEDNWIENI------ALKEALKKLDDREQHIVTMRFYEG---- 232

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            T  EV ++  +++ ++ ++E  A++ +++  R
Sbjct: 233 KTQMEVAEEIGISQAQVSRLEKHALKTMRNYLR 265


>gi|40787125|gb|AAR90090.1| WhiG-like protein [Streptomyces ambofaciens]
          Length = 280

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 107/242 (44%), Gaps = 26/242 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               +++++     LV  VA +  + GL       D +  G  GL+ A EKFD     KF
Sbjct: 43  DERLREQLILHYSPLVKYVAGR-VSVGLPPNVEQADFVSSGVFGLIDAIEKFDVDREIKF 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++
Sbjct: 102 ETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYTTLEARLRRTPSESEVAVEM 158

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLDSAIQ 606
            + VE     L      +SL   +  E+  H          L D +ED  A +P++ A  
Sbjct: 159 GIAVED----LHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTLEDTAADNPVEVAED 214

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +
Sbjct: 215 RELRRLLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQ 270

Query: 667 LK 668
           L+
Sbjct: 271 LR 272


>gi|240140689|ref|YP_002965169.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|240010666|gb|ACS41892.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
          Length = 262

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 119/246 (48%), Gaps = 9/246 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V   E     A   ++ A++RLVI++A ++ + GL   DL+QEG++GLM+AA +F+    
Sbjct: 3   VAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPERE 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE- 550
            +FSTYA WW++ +I   I      +R       K     + R   R+    + +   E 
Sbjct: 63  VRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLMQSTEEQVGSEI 122

Query: 551 --EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAI 605
              IA  + +  E V     +++   +SL  P+G+E    S   DF+ D  A+     + 
Sbjct: 123 HGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEESEASSERMDFLVDNAALPDETVSA 182

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAKAI 664
             +       +  +LT   ER LR+     +  D  TLE +G +  +++ER+RQIE +A+
Sbjct: 183 LVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLEALGHRLGISKERVRQIENRAL 242

Query: 665 RKLKHP 670
            KL+  
Sbjct: 243 EKLRRA 248


>gi|222112015|ref|YP_002554279.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax ebreus TPSY]
 gi|221731459|gb|ACM34279.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax ebreus TPSY]
          Length = 311

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 67/288 (23%), Positives = 129/288 (44%), Gaps = 22/288 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    ++  E +     ++        A   +V ++LRLV+S++++
Sbjct: 21  VPPLGNLDAYISAVNRIPLLTQEEEQRYARQLKDDNNV--EAAGRLVLSHLRLVVSISRQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VH-MRDKIHKVVRTARR----------MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-T 570
               + K+   +R+ ++             +   +   + +A++L +  E V ++    +
Sbjct: 139 TTKAQRKLFFNLRSMKQGFKADALDADTHRETLSDHEIDLVAEQLNVKREEVIEMETRLS 198

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPREE 625
              + L+    D+     G      +A     + I++  R+          L SL  R  
Sbjct: 199 GGDVLLDPAPSDDGEQAFGPIAYLADAGHEPTAMIESRQRDALATDGIATALDSLDARSR 258

Query: 626 RVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K  
Sbjct: 259 RIVEQRWLQVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKA 306


>gi|52546490|dbj|BAD51628.1| DNA-directed RNA polymerase subunit D [Burkholderia cepacia]
          Length = 278

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 118/316 (37%), Gaps = 39/316 (12%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVD----- 55

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                                    +    D  +T+G     A+  +++  + +   E  
Sbjct: 56  ----------------------GLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEE 93

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
           E +E +       +A  L A    L+   +    +I+E + ++R   +      K+   S
Sbjct: 94  EEEEDDGAAQASANAAQLEA----LKRASLEKFSQISEWFDKMRRAFE------KEGYKS 143

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + ++      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 144 KAYLKAQETIQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 203

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   ++  V +I + +  +  +     + + + +  
Sbjct: 204 IARFPGSETDLDWAEKIMAEGHS-YSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKET 262

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 263 NRQMAAGELKARQAKR 278


>gi|330944706|gb|EGH46637.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 284

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 128/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    DS    N      + L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDSDWTDNSPANLHQALDVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|297746551|emb|CAZ60993.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 268

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 63/313 (20%), Positives = 114/313 (36%), Gaps = 46/313 (14%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P
Sbjct: 1   LTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDP 58

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                     +  +       S+  E D   E E + E     S DD       PE A  
Sbjct: 59  NE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDEGDSSDDEGDGGPDPEVARE 111

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
              +L    + +  ++                                   QK+ ++   
Sbjct: 112 KFGDLRAQYEVTRLSI-----------------------------------QKNGRAHED 136

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     L   + D L   + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 137 TQAAIAQLADVFRQFRLMPKQFDRLDNNMPEMMERVRVQERIIMKLCVEQAKMPKKTFVA 196

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 197 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 255

Query: 433 MVRKGECEASIAK 445
            +  GE +A  AK
Sbjct: 256 RMSIGEAKARRAK 268


>gi|42525589|ref|NP_970687.1| sigma-70 family RNA polymerase sigma factor [Treponema denticola
           ATCC 35405]
 gi|41815600|gb|AAS10568.1| RNA polymerase sigma-70 factor, region 2 family [Treponema
           denticola ATCC 35405]
          Length = 275

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 85/262 (32%), Positives = 141/262 (53%), Gaps = 6/262 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   IK       +S  +   +   V+KG    + A + +V +NLRLVI +AKK+++   
Sbjct: 6   LLQYIKDSKKYPLLSAEQEAELADEVKKGN---TEAIEVLVTSNLRLVIKMAKKFSSNEN 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           Q L+LIQEGN+GLMKAA KF      +FS+YA WW+KQ+  R +      I++PV     
Sbjct: 63  QILELIQEGNMGLMKAASKFSKSFKVRFSSYAAWWIKQSFIRYLNSADKVIKLPVRKEAL 122

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSH 587
           I +V +       K    P+  ++A+ +   V+ + ++       I SL+ P+ +E +++
Sbjct: 123 IRQVHKEEENYKIKYGILPSYSQLAEIMKEKVDIIAQIKSFNYTDICSLDDPVDNERSAN 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVG 646
           L DFI   N  +P +  I    +E   + L  L  RE+ VLR R+G+ G  T  T   +G
Sbjct: 183 LYDFIPC-NTYNPEEEFIDNEFKEKLNKCLEILNDREKDVLRNRYGLDGTMTSTTFAVLG 241

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
           K++ ++ E IRQ + +A++KL+
Sbjct: 242 KKYSISAESIRQTQLRALKKLR 263


>gi|187763304|gb|ACD35529.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 114/315 (36%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IA  IE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAIWIEDGTNQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|126734879|ref|ZP_01750625.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126715434|gb|EBA12299.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 277

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 121/260 (46%), Gaps = 16/260 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 11  ELALAYAWRDERDEKALHRLITAYMRLAISMASKFKRYGAPMNDLIQEASVGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 71  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAAAE 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              + ++   E IA ++ +P+  V  +  +++    SL      ED      D +ED   
Sbjct: 131 GRVMDKQEMRELIAIEVGVPLHDVEMMEGRLSGSDFSLNATQSVEDEGREWIDALEDDGP 190

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +   +     LR+     L++L  RE+ ++R R         TLE +G +  +++E
Sbjct: 191 QAAETVEHTHDNDTLRQWLLTALSNLNDREQFIVRERKLRE--DPRTLESLGTELGLSKE 248

Query: 655 RIRQIEAKAIRKLKHPSRSK 674
           R+RQ+EA A  K++    S+
Sbjct: 249 RVRQLEAAAFGKMRKSLESQ 268


>gi|292492240|ref|YP_003527679.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
 gi|291580835|gb|ADE15292.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
          Length = 287

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 60/273 (21%), Positives = 127/273 (46%), Gaps = 15/273 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           ++  +    +++     +S  +  ++   +R  +     A +++V ++LR V+ +A+ Y+
Sbjct: 16  AVGDLDTYCQTVHSIPILSADQEHNLALRLR--DHHDLDAARQLVLSHLRFVVRIARGYS 73

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD   G +  ++A+ W++  I   I      +++   
Sbjct: 74  GYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATT 133

Query: 525 --MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLE---T 578
              R     +    +R+    ++E   +E+A+ L +  + V     +++ +    E    
Sbjct: 134 KAQRKLFFNLRSAKKRLGWLNRKE--VDEVARDLGVSPKQVLEMEARLSSQDTPFEGPNA 191

Query: 579 PIGDEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
              ++D      ++ D     A        + +  +   + L +L PR   ++  R+   
Sbjct: 192 ENSEDDIPAPIAYLFDPTTDPARQMERLDQENHYGQRLQQALEALDPRSRAIIHRRWLQE 251

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  TL E+  ++ ++ ERIRQ+E  AI+KL+
Sbjct: 252 SKS--TLHELAAEYQISAERIRQLENNAIKKLR 282


>gi|302386721|ref|YP_003822543.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197349|gb|ADL04920.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 120/247 (48%), Gaps = 14/247 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + +  + ++       A+++ ++ NLRLV+SV ++++       DL Q G IGL+KA
Sbjct: 21  NEEKEV--LFKRILNGDKKAREDYIKGNLRLVLSVIQRFSGSNENVDDLFQIGCIGLIKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     +FSTYA+  +   + R + D +  IR+   +RD  +K +     +  K  
Sbjct: 79  IDNFDITQNVRFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAYKAIYAKENLMKKNL 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLD 602
           +EPT  EIA+++ +  E +   L   + P+SL  P+  +    L   D I DK  +    
Sbjct: 138 KEPTLMEIAEEIGVSKEDITYALDAIQSPVSLYEPVYSDGGDPLFVMDQISDKKNLEENW 197

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
               +         +  L  RE  ++ MRF  G     T  EV ++  +++ ++ ++E  
Sbjct: 198 VEDIS-----LNEAMRRLPERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRLEKN 248

Query: 663 AIRKLKH 669
           A++ +K+
Sbjct: 249 ALKTMKN 255


>gi|294634103|ref|ZP_06712658.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829917|gb|EFF88271.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 294

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 117/251 (46%), Gaps = 8/251 (3%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S   FR +  +  +G  E   A+  ++E N+ LV   A ++ NR     D++Q G IG
Sbjct: 41  ELSRHFFRRLTEL-EEGTHEYQYARNTLIEMNMSLVRFAAGRFRNRSDDMEDIVQTGMIG 99

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ R    +S
Sbjct: 100 LIKAIDRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELARAREELS 159

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAV 598
           +++ R+PT  E+A  + +    V +    +      SL+  +  +        + D   V
Sbjct: 160 SRLDRDPTVAELATLMNLSESEVVEAQIASNGYNSSSLDAALTGDGPEGGEAVLADFIGV 219

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                 +  +       ++A L+ R+ R++ +RF      + T  E+G+Q   ++  + +
Sbjct: 220 EEHGIRLVEDFH-ALAPLVADLSERDRRIIHLRFV----EEATQAEIGEQLGCSQMHVSR 274

Query: 659 IEAKAIRKLKH 669
           +  + I +L+ 
Sbjct: 275 LIKRIITQLRQ 285


>gi|288927103|ref|ZP_06420991.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|288336130|gb|EFC74523.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
          Length = 287

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 137/273 (50%), Gaps = 41/273 (15%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   +  I  E+ ++  + + + + ++        A +++  ANL+ V+++A+++  RG
Sbjct: 54  ALNTYLDEIGQESPLTPEKEQDLAACIQ---AGDRGALEQLTRANLKFVVAMARRFRGRG 110

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGNIGLM+AA KFD   G +F  YA  +V++A+ R++               
Sbjct: 111 LAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPYVRKAMERAV--------------- 155

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                                 E+ A    +P + +R+  +   +P S++ P+ + +   
Sbjct: 156 ----------------------EQQAGLYRVPRDIMRQKSRHEVQPASVDAPLSEGNKFT 193

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +E+K+A+ P D      + E    ++A+L  RE+RV+R  +G+G     +L E+ +
Sbjct: 194 LLDILENKDAIHPDDDYNVQAMIEALESLVATLDEREQRVVRGFYGLGTGRI-SLAEIAE 252

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           Q  + RER RQI  +A+RK+   ++++ L+ F+
Sbjct: 253 QMGIKRERARQIRDRALRKIARSTQNRALKIFI 285


>gi|188587460|ref|YP_001919005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179352147|gb|ACB86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 273

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 65/253 (25%), Positives = 122/253 (48%), Gaps = 8/253 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + +        +  + E     AK+E++  NLRLV+SV  K+ NRG    DL Q G +GL
Sbjct: 16  LPVISSEETQKLFERLEQGDEQAKQELINGNLRLVLSVINKFKNRGENLDDLFQVGCLGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD   G KFSTYA+  +   I R + D    +R+   ++    +  +   ++  
Sbjct: 76  VKAVDNFDPKQGVKFSTYAVPMIMGEIKRYLRD-DSPMRVSRSLKLLGQEAAKAKEKLRK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +   EPT EE+A +L +  E + + L  + EP+SL  P+  + T  +    + K+    L
Sbjct: 135 EKPYEPTIEELASELNISREELVEALNSSSEPLSLYDPVYSDSTDPVLLVDQIKDEEERL 194

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ ++     T    +A L  R+  ++  RF  G        EV  +  +++ ++ ++E 
Sbjct: 195 ENWVENM---TLKEAIAKLPERQRNIVNRRFFKGQTQV----EVSDELNISQAQVSRLEK 247

Query: 662 KAIRKLKHPSRSK 674
            A+ +L+   + +
Sbjct: 248 SALLQLRKLVKEE 260


>gi|27380342|ref|NP_771871.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1613784|gb|AAC44755.1| sigma32-like factor RpoH1 [Bradyrhizobium japonicum]
 gi|27353506|dbj|BAC50496.1| sigma32-like factor [Bradyrhizobium japonicum USDA 110]
          Length = 308

 Score =  127 bits (318), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 124/274 (45%), Gaps = 9/274 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  +        R  E     A   +V ++LRLV  +A +Y   GL
Sbjct: 16  LSKYLVEIRKFPLLTPEQELAYARRWR--EHRDRDAAYHLVTSHLRLVAKIAMRYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGNIGLM+A  +FD   G + +TYAMWW++ +I   I      ++I      K
Sbjct: 74  PIAEIVSEGNIGLMQAVRRFDPDRGVRLATYAMWWIRASIQEYILRSWSLVKIAASASQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
               K+ R    +S     +  PE+   IA++L +    V  + +  +   SL  PI DE
Sbjct: 134 KLFFKLRRAKSAISALQDGDLRPEQVRLIAERLKVAERDVVAMDRRLRGDASLNVPIHDE 193

Query: 584 DT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HT 641
           D      D++ D      +  A +   ++    +  +L     R   +     +N +  T
Sbjct: 194 DEGGQTLDWLVDPAPTCEITLAEEQEAKQRRLALANALANLNARERNIFTARWLNEESTT 253

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           LEE+  ++ V+RER+RQIE +A +K+K    + +
Sbjct: 254 LEELAAEYGVSRERVRQIEERAFQKVKAAMLTSR 287


>gi|212638845|ref|YP_002315365.1| sporulation sigma factor SigF [Anoxybacillus flavithermus WK1]
 gi|212560325|gb|ACJ33380.1| Stage II sporulation protein AC, DNA-directed RNA polymerase
           sporulation-specific sigma factor (sigma-F)
           [Anoxybacillus flavithermus WK1]
          Length = 247

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 120/242 (49%), Gaps = 15/242 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q G IGLMK+ +KF
Sbjct: 14  EIKELIRRSQQGDQQARDEIIEKNMRLVWSVVQRFLNRGYEPEDLFQIGCIGLMKSVDKF 73

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R I D    +++   +++  +K+ +    +S +  R PT
Sbjct: 74  DLSYDVKFSTYAVPMILGEIQRFIRDDGS-VKVSRSLKEIGNKIRKAKDELSKQNGRVPT 132

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA+ L +  E V    +  + P S+   + + D     L D I D+  V        
Sbjct: 133 VNEIAQFLQISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADEQDVWFD----- 187

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    + +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K +++
Sbjct: 188 ---KIALKKAMEELDERERLIVYLRY----YKDQTQSEVAARLGISQVQVSRLEKKILQQ 240

Query: 667 LK 668
           +K
Sbjct: 241 MK 242


>gi|187922577|ref|YP_001894219.1| RNA polymerase factor sigma-32 [Burkholderia phytofirmans PsJN]
 gi|187713771|gb|ACD14995.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phytofirmans
           PsJN]
          Length = 311

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 130/272 (47%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+ +   S   + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLES--ARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           +++AK+L +  E V ++    +   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKQGLGAFTPDQIDDLAKELNVKREEVSEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT- 638
           + ++    ++ D ++      A +   +   +     L +L  R  R++  R+    +  
Sbjct: 213 EEAYAPIAYLADSHSEPTAVLASRQRDKLHSDGIASALDALDARSRRIIEARWLKVEDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|11079137|dbj|BAB17573.1| DNA-directed RNA polymerase subunit D [Pseudomonas mendocina]
          Length = 270

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 59/315 (18%), Positives = 118/315 (37%), Gaps = 46/315 (14%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M+++ + P     ++     +      L ++  L   
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMSAIAQFPGAVDGILDEYKRIVTEGGRLSDV--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+                              E  G  + A    K+   + +    +
Sbjct: 59  IDPDDGSLPAEEV---------------------EPVGLKDDAEAKDKEKDEEDEESDGD 97

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           +E +E +   D +++A    A+ +QL                            +K  + 
Sbjct: 98  SEEEEGDGGPDPEEAARRFGAVSEQLEKA---------------------KKALKKHGRG 136

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D+LV ++ D    +   E  +++L      + R  
Sbjct: 137 SKQATEELVALAELFMPIKLVPKQFDVLVAKVRDSLDSVRRGERAIMQLCVRDARMPRAD 196

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL +  G E D  WV       + ++   +    D IL+ + ++  +   + ++++E + 
Sbjct: 197 FLRQFPGHETDTAWVDAVLK-GKPKYAEAIERLRDDILRNQQKLVDLEASSQLTVAEIKD 255

Query: 430 IVSMVRKGECEASIA 444
           +   +  GE +A  A
Sbjct: 256 VNRAMSIGEAKARRA 270


>gi|21223976|ref|NP_629755.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|256784937|ref|ZP_05523368.1| RNA polymerase sigma factor WhiG [Streptomyces lividans TK24]
 gi|289768830|ref|ZP_06528208.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
 gi|133480|sp|P17211|RPSW_STRCO RecName: Full=RNA polymerase sigma factor whiG
 gi|153486|gb|AAA26828.1| sigma factor (whiG) (put. alt.); putative [Streptomyces coelicolor]
 gi|3192014|emb|CAA19413.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|289699029|gb|EFD66458.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
          Length = 280

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 107/242 (44%), Gaps = 26/242 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               +++++     LV  VA +  + GL       D +  G  GL+ A EKFD     KF
Sbjct: 43  DERLREQLILHYSPLVKYVAGR-VSVGLPPNVEQADFVSSGVFGLIDAIEKFDVDREIKF 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++
Sbjct: 102 ETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPSESEVAVEM 158

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLDSAIQ 606
            + VE     L      +SL   +  E+  H          L D +ED  A +P++ A  
Sbjct: 159 GIAVED----LHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTLEDTAADNPVEVAED 214

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +
Sbjct: 215 RELRRLLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQ 270

Query: 667 LK 668
           L+
Sbjct: 271 LR 272


>gi|323486723|ref|ZP_08092043.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692138|ref|ZP_08106382.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399942|gb|EGA92320.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503825|gb|EGB19643.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 258

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 66/255 (25%), Positives = 123/255 (48%), Gaps = 15/255 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E   +   +         A+++ ++ NLRLV+SV ++++N      DL Q 
Sbjct: 14  SKLPLLSNDEKEELFKRI---LDGDMDAREQYIKGNLRLVLSVIQRFSNSSENVDDLFQI 70

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA + FD     +FSTYA+  +   + R + D +  IR+   +RD  +K +   
Sbjct: 71  GCIGLIKAIDNFDITQNVRFSTYAVPMILGEVKRYLRDNNS-IRVSRSLRDTAYKAIYAR 129

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED 594
             +  +  +EPT  EIA ++ +  E +   L   + P+SL  P+  +  D  ++ D + D
Sbjct: 130 EGLMKRNLKEPTICEIADEIGVSKESITYALDAIQSPVSLYEPVYTDGGDPLYVMDQLSD 189

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           K   S        +L E     +  L  RE  ++ MRF  G     T  EV ++  +++ 
Sbjct: 190 KK-CSEEHWIEDISLNE----AMKRLPERERHIIDMRFFEG----KTQTEVAEEIHISQA 240

Query: 655 RIRQIEAKAIRKLKH 669
           ++ ++E  A++ +++
Sbjct: 241 QVSRLEKSALKNMRN 255


>gi|307330048|ref|ZP_07609199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306884309|gb|EFN15344.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 107/233 (45%), Gaps = 16/233 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF TYA+
Sbjct: 44  REQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDPERAIKFETYAI 103

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++ + +E
Sbjct: 104 TRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPSEAEVAAEMDISIE 160

Query: 562 GV--RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +            ++LE  +       D   L D +ED  A +P++ A    LR    R
Sbjct: 161 ELHGVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDRELRRLLAR 220

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE+ V+ + +  G     TL E+G+   VT  R+ QI  K++ +L+
Sbjct: 221 AINTLPEREKTVVTLYYYEG----LTLAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|157963788|ref|YP_001503822.1| RNA polymerase factor sigma-32 [Shewanella pealeana ATCC 700345]
 gi|157848788|gb|ABV89287.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella pealeana ATCC
           700345]
          Length = 285

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/273 (22%), Positives = 123/273 (45%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + + S      +   +   +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 19  LESYVHSAHNIPMLEADKEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED- 584
                + +  +R+      E     +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNLRKAKKRLGWFSDSEVGM--VAESLGVSKADVTEMESRMAAQDPAFDLASDNDDE 194

Query: 585 -TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A    +   + N +      + +L  R + +L+ R+     T  
Sbjct: 195 QDYAPMHYLEDHSSDLASQVENDNWEQNNQARLLSAIKTLDERSQHILKARWLDEDKT-- 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TL+++   + V+ ERIRQ+E  A+ KLK    +
Sbjct: 253 TLQDLAATYQVSAERIRQLEKNAMNKLKGCMEA 285


>gi|66047972|ref|YP_237813.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           B728a]
 gi|237802354|ref|ZP_04590815.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|63258679|gb|AAY39775.1| Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas syringae pv.
           syringae B728a]
 gi|330957082|gb|EGH57342.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. maculicola
           str. ES4326]
 gi|330970950|gb|EGH71016.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aceris
           str. M302273PT]
 gi|331025211|gb|EGI05267.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 284

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 128/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++++    ++    R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVQTVNSIPLLTPERERELAESL--YYEQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    DS    N      + L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDSDWTDNSTANLHQALDVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|83590339|ref|YP_430348.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83573253|gb|ABC19805.1| RNA polymerase, sigma subunit, RpoX/SigF [Moorella thermoacetica
           ATCC 39073]
          Length = 270

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 122/245 (49%), Gaps = 12/245 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R+ +     A++ ++  NL+LV ++ +++  R  +  DL Q G IGL+KA +KFD  
Sbjct: 21  ELLRRAKAGDKEARERLINCNLKLVFNLVQRFEKRNYELEDLFQIGTIGLIKAIDKFDLS 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    +++   +++   KV RT   ++ K  REP   E
Sbjct: 81  YKVRFSTYAVPMILGEIRRFLRD-DSAVKVSRSLKETAFKVNRTREELAKKFGREPAIGE 139

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANL 609
           IA+ L +  E +   L+  + P S+   +  +D    ++ D +  ++   P         
Sbjct: 140 IAEALDLSREEIIAALEAVQMPSSIHDTVYQDDGDPIYVLDQLASEDGEEPEWLD----- 194

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     VL  L  +  RVL +RF      D T  EV  +  +++ +I +IE +A+++++ 
Sbjct: 195 KIALKEVLRQLPEKHRRVLVLRFF----QDKTQAEVAARMGLSQVQISRIERQALQRIRE 250

Query: 670 PSRSK 674
             +++
Sbjct: 251 LLQAE 255


>gi|239933042|ref|ZP_04689995.1| RNA polymerase secondary sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291441393|ref|ZP_06580783.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344288|gb|EFE71244.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 263

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 102/246 (41%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E  A   + ++V+A L +   +A ++  RG    DL Q   +GL+KA +
Sbjct: 22  FARLARLPEGPERRAL--RDDLVQAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
            +D   G  F  YA+  +   I R   D   T+ +P  ++D  ++V   AR ++     R
Sbjct: 80  HYDPVRGNAFEAYAVPTITGEIKRHFRDHMWTLHVPRRVQDLRNRVRHAARELAQTTVGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EIA    +    VR  ++  +    +SLE  +   D   LGD +   +       
Sbjct: 140 APTVPEIAAYARLTESEVRTGMEALECFSALSLEAEMPGTDGYALGDSVGGPDPAFDTVV 199

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R T    L +L  RE  +L +RF  GM      E       +++  + ++ +  
Sbjct: 200 D-----RVTVRPFLEALPERERLILYLRFFRGMTQSTIAE----HLGISQMHVSRLLSSC 250

Query: 664 IRKLKH 669
             +L+ 
Sbjct: 251 FAQLRE 256


>gi|46143484|ref|ZP_00135165.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|126209296|ref|YP_001054521.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           L20]
 gi|126098088|gb|ABN74916.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 316

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 129/266 (48%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+  +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGL 106

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +
Sbjct: 107 PLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQR 166

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
                    +       E   +++A+ L +  E VR++  ++T + +  + P+G++D   
Sbjct: 167 KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDDDEV 226

Query: 587 -HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED +   A    D              LA+L  R + +++ R+        TL
Sbjct: 227 YTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDE--EKATL 284

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 285 QDLAEKYGISAERVRQLENAALKKIK 310


>gi|187763346|gb|ACD35550.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 272

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 122/316 (38%), Gaps = 46/316 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +  E+ 
Sbjct: 59  ------------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DNSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDD 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLE 372
            +    +L  +     +   + D LV  + ++ +R+   E  +++L  +   + +  F+ 
Sbjct: 138 TQNAIAQLADVFRQFRVMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 197

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
                E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I  
Sbjct: 198 AFTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINR 256

Query: 433 MVRKGECEASIAKKEM 448
            +  GE +A  AKKEM
Sbjct: 257 RMSIGEAKARRAKKEM 272


>gi|297180174|gb|ADI16396.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured bacterium HF130_12L15]
          Length = 288

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 72/258 (27%), Positives = 120/258 (46%), Gaps = 15/258 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +   VR  +     A   +  A++RLVIS+A K+   GL   DL+QEG++GL
Sbjct: 20  LDRVEEHDLA--VRWRDDRDQEALHRITMAHMRLVISMAGKFRYFGLPMSDLVQEGHVGL 77

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           ++AA +F+     +FSTYA WW++ ++   I      +R       K     + R   R+
Sbjct: 78  LEAAARFEPERDVRFSTYATWWIRASMQDHILRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 540 SN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGD--EDTSHLGDFI- 592
           +     +K     +EIA  + + V  V     +++    SL  P+ D  E TS   DF+ 
Sbjct: 138 AQGTEPLKGAAVYQEIADAIGVSVADVALMDSRLSGPDSSLNAPVADGGESTSERMDFLV 197

Query: 593 -EDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            ED      + ++I    R     R L  L      +  +R     +   TLE +G +  
Sbjct: 198 SEDPTPDEVVSASIDDERRTMWLNRALGVLND--RELRIIRERRLRDEGATLESLGAKLG 255

Query: 651 VTRERIRQIEAKAIRKLK 668
           +++ER+RQIE +A+ KL+
Sbjct: 256 ISKERVRQIENRALEKLR 273


>gi|306844750|ref|ZP_07477335.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
 gi|306274922|gb|EFM56692.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
          Length = 311

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 75/289 (25%), Positives = 131/289 (45%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL  P+  E++  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEESGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|296161515|ref|ZP_06844320.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
 gi|295888159|gb|EFG67972.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
          Length = 311

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 129/272 (47%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+ +   S   + +V ++LRLV+S+A+ Y 
Sbjct: 35  QLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLES--ARRLVLSHLRLVVSIARNYL 92

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 93  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 152

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           E +AK+L +  E V ++    +   I+LE  + D 
Sbjct: 153 KAQRKLFFNLRSHKQGLGAFTPDEIEGLAKELNVKREEVSEMETRLSGGDIALEGQVEDG 212

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+    ++ D ++      A +   +   +     L +L  R  R++  R+    +  
Sbjct: 213 EESYAPIAYLADSHSEPTAVLASRQRDKLQSDGIASALDALDARSRRIIEARWLKVEDDG 272

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 273 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 304


>gi|153005405|ref|YP_001379730.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152028978|gb|ABS26746.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 357

 Score =  127 bits (318), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 78/282 (27%), Positives = 131/282 (46%), Gaps = 15/282 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
               +R  +  I+    +S  E   +   VR  E     A   +V +NLRLV+ +A +Y 
Sbjct: 67  RYDPLRAYMAEIARHPLLSREEEHELA--VRYRETGDVDAAYRLVASNLRLVVKIAHEYR 124

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
               Q LDL+QEGN+GLM+A +K+D   G K S+YA WW++  I R I +    +++   
Sbjct: 125 RTAFQLLDLVQEGNMGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRMVKLGTT 184

Query: 525 --MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG 581
              R     + +   ++  +   EPTP  +AK L +  + V ++  ++  E +SL+ P+ 
Sbjct: 185 QAQRKLFFNLAKEREKLLAR-GIEPTPRLLAKNLDVEEKDVEEMTARMAGEDLSLDAPLR 243

Query: 582 DEDTSHLG---DFIEDKNAVSPLDSAIQANLRETTTRVLASL-----TPREERVLRMRFG 633
            ++        D +    A +P +      LR      L +        +E  +   R  
Sbjct: 244 GDEDGSRQTRLDRVAGDGADAPDERLGDEQLRRLFREKLETFSKTIRDEKERYIFDKRLL 303

Query: 634 IGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
                   TL+E+G +F +TRER RQIEAK   +L+   R++
Sbjct: 304 PAGGEAPLTLQEIGDRFKLTRERARQIEAKLTARLRDYLRAE 345



 Score = 44.1 bits (102), Expect = 0.089,   Method: Composition-based stats.
 Identities = 42/277 (15%), Positives = 78/277 (28%), Gaps = 50/277 (18%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWR------ 171
           DP+R Y+ E+    LLSRE E  +A R  E G       L  S L     I         
Sbjct: 69  DPLRAYMAEIARHPLLSREEEHELAVRYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAF 128

Query: 172 ---DELNDGTTLLRE----------------------------------IIDLEACIGPE 194
              D + +G   L +                                  ++ L       
Sbjct: 129 QLLDLVQEGNMGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRMVKLGTTQAQR 188

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                          +  + +      ++   E D+E        +   +D+P    E+ 
Sbjct: 189 KLFFNLAKEREKLLARGIEPTPRLLAKNLDVEEKDVEEMTARMAGEDLSLDAPLRGDEDG 248

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
            R    D        +  E     ++     E  E + +  +++D       D++     
Sbjct: 249 SRQTRLDRVAGDGADAPDERLGDEQLRRLFREKLETFSK--TIRDEKERYIFDKRLLPAG 306

Query: 315 KVLKEKLVKLVGSLSLNQ---SRID-LLVEQLYDISK 347
                 L ++     L +    +I+  L  +L D  +
Sbjct: 307 GEAPLTLQEIGDRFKLTRERARQIEAKLTARLRDYLR 343


>gi|238064463|ref|ZP_04609172.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237886274|gb|EEP75102.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 305

 Score =  126 bits (317), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 112/237 (47%), Gaps = 12/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F
Sbjct: 58  PPERRQEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SF 116

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           + YA   +   I R   D++  + +P  +RD I +V +    +++++ R PT  E+A++L
Sbjct: 117 TAYAAITIVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATATLTSELSRAPTVAELAERL 176

Query: 557 AMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             P E +   L+      P SL  P+G E ++  GD + + +     ++    + R T +
Sbjct: 177 ETPQEEILAALESAAGYSPASLNAPVGGESSAEFGDLVGESD-----NALESVDDRVTIS 231

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +L  L  RE R+L MRF           E+  +F +++  + ++ ++A+  L+   
Sbjct: 232 GLLHRLPWRERRILAMRFYGNQTQ----AEIAARFGISQMHVSRLLSRALTWLRQAM 284


>gi|254382042|ref|ZP_04997404.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194340949|gb|EDX21915.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 278

 Score =  126 bits (317), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 106/237 (44%), Gaps = 16/237 (6%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLRQQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDIDRSIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPTECEVADEMG 157

Query: 558 MPVEGV--RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + VE +            ++L+  +       D   L D +ED  A +P++ A    LR 
Sbjct: 158 IAVEELHTVFSQLSLANVVALDELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEGRELRR 217

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L+
Sbjct: 218 LLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|302871563|ref|YP_003840199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574422|gb|ADL42213.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 240

 Score =  126 bits (317), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD  
Sbjct: 8   ELISKAKNGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPS 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  E
Sbjct: 68  FNVRFSTYAVPMIIGEIKRYLRDDGR-IKVSRKIKENQSKIKKLRNQFVSDNGREPTISE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           I++   +  E +   +  + E  SL   I  E+     L D   D+   S     + A  
Sbjct: 127 ISQLTGLSSEEILLCMDASSEVASLSEVINQEEGKPITLMDLASDEEDYSTKLLDLMA-- 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L  RE  ++ MR+        T  E+ KQ  +++  + +IE +A+ ++K 
Sbjct: 185 ---LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKQLNISQVHVSRIEKRALERIKR 237


>gi|262204122|ref|YP_003275330.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily [Gordonia
           bronchialis DSM 43247]
 gi|262087469|gb|ACY23437.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily [Gordonia
           bronchialis DSM 43247]
          Length = 276

 Score =  126 bits (317), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 109/243 (44%), Gaps = 13/243 (5%)

Query: 431 VSMVRKGECEASIAKKE--MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           +  +      A+ AKK   ++E  L L   VA ++++RG  F DL+Q   IG++ A ++F
Sbjct: 32  LRELSAETDAAAHAKKRDNIIERCLPLAEHVAWRFSDRGEPFDDLLQVARIGVVNAVDRF 91

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G  F ++A+  V   + R   D    IR+P   ++    + +    +  ++ R P 
Sbjct: 92  DGERGDSFLSFAVPTVMGEVRRHFRDSMWAIRVPRRAKETSLSIGKATDELVQRLGRSPR 151

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P E+A  L +PV+ V   L      +  S++    D+D   + D + D +A        Q
Sbjct: 152 PSELAAHLGLPVDEVIDGLLARSAYQARSIDATPEDDDGRSIRDTLGDDDA-----RLAQ 206

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +   T   VL  L  RE  ++ +RF        +  E+  +  +++  + ++ ++ +  
Sbjct: 207 IDEFVTLRPVLDQLPDREREIVTLRFFH----AMSQSEIAARVGISQMHVSRLLSRTLET 262

Query: 667 LKH 669
           L+ 
Sbjct: 263 LRE 265


>gi|160897140|ref|YP_001562722.1| RNA polymerase sigma 32 subunit RpoH [Delftia acidovorans SPH-1]
 gi|160362724|gb|ABX34337.1| RNA polymerase, sigma 32 subunit, RpoH [Delftia acidovorans SPH-1]
          Length = 314

 Score =  126 bits (317), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 125/293 (42%), Gaps = 29/293 (9%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ E +     ++  E     A   +V ++LRLV+S++++
Sbjct: 21  VPPLGNLDAYISAVNRLPMLTLEEEQDYARKLK--EHSDLDAAGRLVMSHLRLVVSISRQ 78

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD     +  +YAM W+K  I   I      +++ 
Sbjct: 79  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEE----------------IAKKLAMPVEGVRKV 566
                +  K+    R M   +K +    E                +A+KL +  E V ++
Sbjct: 139 TTKAQR--KLFFNLRSMKQGLKSDAAMAEDGAMLRDTLTSGEIDAVAEKLNVKREEVMEM 196

Query: 567 LKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASL 620
                   + L+    D+     G      +      + I++  R+          L SL
Sbjct: 197 ETRLAGGDVLLDPSPSDDGEQAFGPIAYLADGAHEPTAMIESRQRDHLATDGIAMALDSL 256

Query: 621 TPREERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             R  R++  R+    +      TL E+   + V+ ERIRQIE  A++K+K  
Sbjct: 257 DDRSRRIVEERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKA 309


>gi|300689719|ref|YP_003750714.1| RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
 gi|299076779|emb|CBM09897.1| putative RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
          Length = 907

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 131/247 (53%), Gaps = 7/247 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            S  R    E    +  M++ANLRLV+ +A+   + GL+  DLIQEGN+GL+KA ++FDW
Sbjct: 536 ASAYRSAIAELIRYRDHMMQANLRLVMDIARHRMHSGLRVEDLIQEGNLGLLKAVDRFDW 595

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FST A+WW+KQ I R I D +  IR+PVH+  KI +  R      +   +  +  
Sbjct: 596 RRGFRFSTMAIWWIKQQIGRGIFDTALEIRLPVHIHQKISRGRRETESFEHVRGKPASLS 655

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E A    M ++      +   EP+S+E             + + + +  P     + +  
Sbjct: 656 ERATICNMTLDKFELAARALSEPLSIEGAQQVG-------YFKSEESDEPFARMSEDDDA 708

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                VL  L  ++  VLR+RFGIG+    TLE++G+   VTRER+RQIEA A++KL  P
Sbjct: 709 RLVEEVLTKLKTKDAEVLRLRFGIGVLEALTLEQIGEILGVTRERVRQIEAAAMQKLSSP 768

Query: 671 SRSKKLR 677
              + L 
Sbjct: 769 FSREALM 775



 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 71/191 (37%), Gaps = 10/191 (5%)

Query: 70  LSNMGINVVDGDDLEDEEGSED---SLDLASSASNSSVFLQKRKDSADRSTD--DPVRMY 124
           L +MG  V +  +      SE+    +D   +    +   +      D  +D  DP+R+Y
Sbjct: 313 LGDMGAEVDERLEFPSAIPSENFKVIVDPVETEDEEAEVDKAILHFEDLLSDKNDPLRIY 372

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            R      LLS E EI  A+++E   A  + +L + PL    L+    +    T+ L  I
Sbjct: 373 HRAAVKHSLLSAEQEIDYARKMENAIARALDALAKWPLGLNRLLAETHK-AASTSYLSTI 431

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQE----KERDDVQETEGDIESAAKVSKDD 240
           + +      +            +    +   QE     E  D +E+ G ++    +    
Sbjct: 432 VVMRGDDSDDIDQDADLDELADAIPDLKVDLQEIHAPAELMDKEESPGAVDDPIGILASI 491

Query: 241 RSKVDSPPENA 251
           ++      E+A
Sbjct: 492 QAMATESMEDA 502


>gi|260767580|ref|ZP_05876516.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|260617480|gb|EEX42663.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|315178774|gb|ADT85688.1| RNA polymerase sigma-32 factor [Vibrio furnissii NCTC 11218]
          Length = 258

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 117/242 (48%), Gaps = 14/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G + 
Sbjct: 15  HYSGDIEAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRL 74

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A+
Sbjct: 75  VSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAR 132

Query: 555 KLAMPVEGVRKVL-----KITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQ 606
           +L +    VR++      +     +S +        +    ++EDK    A +      +
Sbjct: 133 ELGVEPSEVREMESRLAAQDATFEMSNDDDDNPNAYTAPVLYLEDKQSDLAENVEAQNWE 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A+  +     L+SL  R + ++R R+        TL+E+ + + V+ ERIRQ+E  A++K
Sbjct: 193 AHTNQRLALALSSLDERSQHIVRSRWLDD--QKATLQELAEMYNVSAERIRQLEKNAMKK 250

Query: 667 LK 668
           LK
Sbjct: 251 LK 252


>gi|170724574|ref|YP_001758600.1| RNA polymerase factor sigma-32 [Shewanella woodyi ATCC 51908]
 gi|169809921|gb|ACA84505.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella woodyi ATCC
           51908]
          Length = 283

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 123/268 (45%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + S    + +   +   +   ++  E     A K+++ ++LR V+ VAK Y+  GL
Sbjct: 17  LEAYVHSAHNISMLEPEQEYELAKRLQ--ETGDLQAAKQLIMSHLRFVVHVAKGYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 75  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+   ++      E   +A  L +    V     ++  +  + +    ++D 
Sbjct: 135 --KLFFNLRKSKKRLGWFSDEEVGMVADNLGVSKADVTEMESRMAAQDPAFDLASDNDDD 192

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A    +  +++N +      + +L  R + +L+ R+        
Sbjct: 193 QDFSPVHYLEDHSSDLASQVENDNLESNNQARLLSAIKTLDERSQHILQARWL--NEDKT 250

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 251 TLQELAATYQVSAERIRQLEKNAMNKLK 278


>gi|171464209|ref|YP_001798322.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|171193747|gb|ACB44708.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 307

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 130/268 (48%), Gaps = 10/268 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +S +E  H+    R  E     A K +V ++LRLV+SVA++Y   G+
Sbjct: 36  LDSYIAYVNRVPMLSAAEELHLAQEFRCTENVD--AAKTLVLSHLRLVVSVARQYLGYGI 93

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA +++D   G + ++YA+ W+K  I   I      ++       +
Sbjct: 94  PHADLIQEGNIGLMKAVKRYDPSNGARLASYAIHWIKAEIHEYILKNWRLVKTATTKAQR 153

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + + +         + +AK L +    V+++ +++    ++LE    DED+++
Sbjct: 154 KLFFNLRSNKPTLSALTPNEVDALAKTLDVKGSDVKEMEMRLAGGDVALEGDDSDEDSAY 213

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRE--TTTRVLASLTPREERVLRMRFGIGMNT---DH 640
             +    +     +   ++ +AN  +     + L +L  R   +++ R+           
Sbjct: 214 APIQWLADSSQEPTARIASAEANALQGPKLDQALMALDERSRNIVQSRWLAMDAEGNGTK 273

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ ++ ER+RQIE  A++K++
Sbjct: 274 TLHDLADEYGISAERVRQIETAALKKMR 301


>gi|239982297|ref|ZP_04704821.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291454142|ref|ZP_06593532.1| sigma factor [Streptomyces albus J1074]
 gi|291357091|gb|EFE83993.1| sigma factor [Streptomyces albus J1074]
          Length = 298

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 119/248 (47%), Gaps = 11/248 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   +  + +G  E   A+  ++E NL LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 49  FFDRLQTLEEGTPEHQYARNTLIEMNLSLVRYAAGRFRHRGPGEMEDIVQVGTIGLIKAI 108

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+T+A+ ++   I R   D S  + +P  +++    + +    ++ ++ R
Sbjct: 109 DRFDLSREVEFTTFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDMAKAKESLAAELDR 168

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLG---DFIEDKNAVSP 600
           EPT +E+A KL    E V + L         SL+ P    D +  G     + D      
Sbjct: 169 EPTVKELAAKLERTEEEVVEGLVAANGYTAGSLDVPTESGDDNRAGGSPRSLADTLGAPD 228

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               +  +L      +L +L  RE R++ MRFG     + T  ++G +  +++  + ++ 
Sbjct: 229 PAQELVEDLH-ALAPLLETLDERERRIVEMRFG----QELTQSQIGAELGISQMHVSRLL 283

Query: 661 AKAIRKLK 668
           ++ + +L+
Sbjct: 284 SRILTRLR 291


>gi|145224454|ref|YP_001135132.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216940|gb|ABP46344.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium gilvum
           PYR-GCK]
          Length = 270

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 113/253 (44%), Gaps = 8/253 (3%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +      +  +     E     + ++   L L    A+++  RG    DL Q  ++GL+
Sbjct: 10  DVPNMIRALRQLDPASPEYRRLHERIIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLV 69

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A ++FD   G  F  YA+  +   + R   D S  +++P  ++D   ++ +    ++ +
Sbjct: 70  NAVKRFDPDSGSDFLAYAVPTIMGEVRRYFRDCSWAVKVPRRLKDLNSQLAKARAELTQQ 129

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + R PTP E+A  L +  E V +    +    +L T          GDF+  +  +   D
Sbjct: 130 LGRAPTPSEVAAHLGIDREEVVQATIASSNYATLSTDSTSGPD---GDFVALRETLGEPD 186

Query: 603 SAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           + + A +  ET   ++  L PRE+ VL++RF      + T  ++ ++   ++  + ++ A
Sbjct: 187 ARLDAVVDNETIRPLIEKLPPREQAVLKLRFF----DEMTQTQIAERMGYSQMHVSRLLA 242

Query: 662 KAIRKLKHPSRSK 674
           KA+  L+  + S 
Sbjct: 243 KALATLRDQALSD 255


>gi|138895880|ref|YP_001126333.1| sporulation sigma factor SigF [Geobacillus thermodenitrificans
           NG80-2]
 gi|134267393|gb|ABO67588.1| RNA polymerase sigma-F factorr [Geobacillus thermodenitrificans
           NG80-2]
          Length = 252

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 119/245 (48%), Gaps = 14/245 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q G IGL+K+ +KF
Sbjct: 18  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D   T+++   +++  +K+ +    +S    R PT
Sbjct: 78  DLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPT 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA  L +  E V    +  + P S+   + + D     L D I D +  S  +    
Sbjct: 137 ITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIADADEASWFE---- 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    + +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K ++ 
Sbjct: 193 ---KIALKKAIEELDERERLIVYLRY----YKDQTQSEVAARLGISQVQVSRLEKKILQH 245

Query: 667 LKHPS 671
           +K   
Sbjct: 246 IKEKM 250


>gi|91781700|ref|YP_556906.1| RNA polymerase factor sigma-32 [Burkholderia xenovorans LB400]
 gi|91685654|gb|ABE28854.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia xenovorans
           LB400]
          Length = 307

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 129/272 (47%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++ +E R   +  R+ +   S   + +V ++LRLV+S+A+ Y 
Sbjct: 31  QLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLES--ARRLVLSHLRLVVSIARNYL 88

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++   
Sbjct: 89  GYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATT 148

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +       + +           E +AK+L +  E V ++    +   I+LE  + D 
Sbjct: 149 KAQRKLFFNLRSHKQGLGAFTPDEIEGLAKELNVKREEVSEMETRLSGGDIALEGQVEDG 208

Query: 584 DTSH-LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+    ++ D ++      A +   +   +     L +L  R  R++  R+    +  
Sbjct: 209 EESYAPIAYLADSHSEPTAVLASRQRDKLQSDGIASALDALDARSRRIIEARWLKVEDDG 268

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL E+  +F V+ ERIRQIEA A++K++
Sbjct: 269 SGGSTLHELADEFGVSAERIRQIEASAMKKMR 300


>gi|145594674|ref|YP_001158971.1| sigma-70 region 2 domain-containing protein [Salinispora tropica
           CNB-440]
 gi|145304011|gb|ABP54593.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 284

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 112/232 (48%), Gaps = 12/232 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA 
Sbjct: 40  QEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAA 98

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D++  + +P  +RD I +V +    +++++ R PT  E+A++L  P E
Sbjct: 99  ITIVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATAALTSELSRAPTVAELARRLETPEE 158

Query: 562 GVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +   L+      P SL  P+G E ++  GD + + +     ++    + R T + +L  
Sbjct: 159 EILAALESAAGYSPASLNAPVGGESSAEFGDLVGESD-----NALESVDDRVTVSGLLHR 213

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L  RE R+L MRF           E+  +F +++  + ++ ++A+  L+   
Sbjct: 214 LPWRERRILAMRFYGNQTQ----AEIAARFGISQMHVSRLLSRALTWLRQAM 261


>gi|254708375|ref|ZP_05170203.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708771|ref|ZP_05170582.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714614|ref|ZP_05176425.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717512|ref|ZP_05179323.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030297|ref|ZP_05443911.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256160470|ref|ZP_05458159.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255677|ref|ZP_05461213.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167971|ref|ZP_05754782.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|261757411|ref|ZP_06001120.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|261737395|gb|EEY25391.1| sigma-70 factor family [Brucella sp. F5/99]
          Length = 311

 Score =  126 bits (317), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 76/289 (26%), Positives = 131/289 (45%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSVPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|293375845|ref|ZP_06622113.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325844994|ref|ZP_08168319.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
 gi|292645524|gb|EFF63566.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325488967|gb|EGC91357.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
          Length = 331

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 96/274 (35%), Positives = 151/274 (55%), Gaps = 21/274 (7%)

Query: 425 SEFRHIVSMVRKGE-CEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIG 480
           +E++H +  ++K        A + ++  N  LV  +  +YT   +  L + DL   G  G
Sbjct: 59  NEYQHNLEYLKKYRLENDETALEWLIFNNTNLVHKIIGRYTKFYHHKLDYDDLFSVGLEG 118

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA EKFD+     FSTYA +WVKQA+TR+IAD+  TIRIPVHM + I++V+R  ++  
Sbjct: 119 LMKAIEKFDFTFDNNFSTYATYWVKQAVTRTIADEGFTIRIPVHMFESINQVMRYEQKAD 178

Query: 541 NKIKREPTPEEIAKKLAMPVEG---VRKVLKITKEPISLETPIGDED-TSHLGDFIEDKN 596
            +       + +  +L +P+E    V++V     +P SL   +  ED  + L D I ++N
Sbjct: 179 QE-DEPVDVDNLCGELKIPIEKYEAVKRVQTYMLKPTSLNGFVSKEDEDTELQDLISNEN 237

Query: 597 AV----------SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            +          +P   A+  +L+    +++ SL PRE+ V+  RFG+      TLEE+G
Sbjct: 238 EMLVEGMSRIYDNPEKQAMDEDLKAYMDKMILSLNPREQFVIIHRFGLNGEEKKTLEEIG 297

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +   VTRERIRQIEAKA+RKL+      + + +L
Sbjct: 298 EIEGVTRERIRQIEAKAMRKLRTLLM--RYKEYL 329


>gi|160935677|ref|ZP_02083052.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441421|gb|EDP19131.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 123/246 (50%), Gaps = 14/246 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E +    + ++       A+++ ++ NLRLV+SV ++++N      DL Q G IGL+KA
Sbjct: 21  NEEKE--ELFQRILDGDKEAREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCIGLIKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   + R + D +  IR+   +RD  +K +    +++    
Sbjct: 79  IDNFDITQNVKFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAYKALYAREQLTRTNS 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLD 602
           +EPT  EIA+++ +  E +   L   + P+SL  P+  +    L   D I DK     L+
Sbjct: 138 KEPTLMEIAQEIGVSKEDITYALDAIQTPVSLYEPVYTDGGDPLFVMDQISDKK---NLE 194

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                +L  +    +  L  RE  ++ MRF  G     T  EV ++  +++ ++ ++E  
Sbjct: 195 ENWVEDL--SLVEAMKRLPERERHIIDMRFFEG----KTQTEVAQEIHISQAQVSRLEKN 248

Query: 663 AIRKLK 668
           A++ +K
Sbjct: 249 ALKSMK 254


>gi|71083311|ref|YP_266030.1| RNA polymerase factor sigma-32 [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71062424|gb|AAZ21427.1| RNA polymerase sigma-32 factor (rpoH) RP303 [Candidatus
           Pelagibacter ubique HTCC1062]
          Length = 293

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 127/272 (46%), Gaps = 14/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +             A +++V ++LRLV  +A  Y   GL
Sbjct: 14  LSAYLEQIKKFPMLAAEEEYMLAK--NWKATGNVKAAEKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      ++I      +
Sbjct: 72  PVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKIGTTTAQK 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   +++ + + +  PE   EIA KL +  + V     +++ +  SL   +  
Sbjct: 132 KLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKLDVNKDEVISMNRRLSGKEFSLNAQV-G 190

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           ED     D++ DK     L  A Q  +   +      +  L  RE+ +L        +  
Sbjct: 191 EDGDEWQDWLVDKELDHDLKFAHQEEMGQRQNLLKDSIKILNEREKEILYS--RRLNDEP 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TLE++ K++ ++RER+RQIE KA  KL+   
Sbjct: 249 TTLEDLSKKYKISRERVRQIENKAFEKLQKHM 280


>gi|169629597|ref|YP_001703246.1| RNA polymerase sigma factor SigF [Mycobacterium abscessus ATCC
           19977]
 gi|169241564|emb|CAM62592.1| Alternative sigma factor SigF [Mycobacterium abscessus]
          Length = 272

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/253 (24%), Positives = 115/253 (45%), Gaps = 13/253 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +    ++ + +         +E+V   L L  +VA+ +  RG    DLIQ   +GL+
Sbjct: 28  DVPDMFRSLAGLAEHSDAYQRKHEEIVTRCLPLADNVARHFDRRGEDLEDLIQVARVGLL 87

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F  +A+  +   + R   D   ++ +P  +RD+  ++ R    ++ +
Sbjct: 88  NAVNRFDPEKGASFLGFAVPTMMGEVRRHFRDHGWSLHVPRAIRDRHAQISRATAELTQE 147

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAV 598
           ++R PT  E+A +L +  E V + L      +P S+E P+   D    HL D + +++  
Sbjct: 148 LQRAPTAGELAAELGIDREEVVESLIAADAYQPQSIEAPLSHGDQESKHLSDLLGNED-- 205

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               +      RE    +LA+L  RE  VL +RF  G     T  ++  Q  V++  + +
Sbjct: 206 ---PALEHVTNREAVRPLLANLPLRERTVLELRFFKG----MTQSQIAAQIGVSQMHVSR 258

Query: 659 IEAKAIRKLKHPS 671
           I +  +R L+   
Sbjct: 259 ILSDTLRYLREQM 271


>gi|84515395|ref|ZP_01002757.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510678|gb|EAQ07133.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 303

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 72/271 (26%), Positives = 124/271 (45%), Gaps = 15/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  + E + A  +MV ++LRL   +A  Y   GL
Sbjct: 21  LNRYMQEIRKFPMLEPEEEYMLAK--RWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYGL 78

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 79  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTSAQK 138

Query: 529 --IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE   +IA  L +  + V     +++    SL   IG 
Sbjct: 139 KLFFNLRKAKNRIGALEEGDLRPENVKQIANDLGVTEDEVISMNRRLSGGDASLNAQIGS 198

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED +A +  D      L   R      +  L PRE+ +L  R      
Sbjct: 199 DGEGSMQWQDWLEDDSANTAADYEEHDELDARRALLVEAMTLLNPREKDILVQRRLAE-- 256

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TLE++  ++ V+RERIRQIE +A  KL+
Sbjct: 257 ETVTLEDLSARYEVSRERIRQIEVRAFEKLQ 287


>gi|294631664|ref|ZP_06710224.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
 gi|292834997|gb|EFF93346.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
          Length = 280

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 105/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 43  DERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDIDREIKFE 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 103 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPTETEVAGEMG 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + V+     L      +SL   +  E          D     D +ED  A +P++ A   
Sbjct: 160 IAVDE----LHAVFSQLSLANVVALEELLHVGGEDGDGLSFMDTLEDTAADNPVEVAEDR 215

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 216 ELRRFLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 271

Query: 668 K 668
           +
Sbjct: 272 R 272


>gi|294629742|ref|ZP_06708302.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292833075|gb|EFF91424.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 305

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 116/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E +  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA +
Sbjct: 63  LFERLESLEEGTHEHAYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAID 122

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 123 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 182

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDS 603
           PT  E+A+ L +  E V + +         SL+     +E    L D I  ++       
Sbjct: 183 PTVSELAEHLGLSAEEVVEGMAASNAYTASSLDAQPEENESEGALADRIGYEDHGIEGIE 242

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L  R+ ++L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 243 YV-----ESLKPLIAELPSRDRKILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRT 293

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 294 LVRLRK 299


>gi|256832234|ref|YP_003160961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
 gi|256685765|gb|ACV08658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
          Length = 283

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/252 (26%), Positives = 106/252 (42%), Gaps = 19/252 (7%)

Query: 429 HIVSMVRKGECEASIA--KKEMVEANLRLVISVAKKYTNRGLQF----LDLIQEGNIGLM 482
             V  +         A  ++E++     LV  +A +     L       DL+  G  GL+
Sbjct: 31  RTVRQLWDAYKANPTALGREELILHYAPLVTMIAGR-VGMKLPNTVEAADLVSYGMFGLI 89

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A +KFD     KF TYA   V+ AI   +        IP  +R +  +  R    + N 
Sbjct: 90  DAIDKFDPSRDIKFETYASTRVRGAIIDELRALDW---IPRSVRSRAREYDRACEHLENT 146

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDE---DTSHLGDFIEDKNA 597
           + REPT  EIA+ L +P + V ++     +   I+L+  +      D     D +++  A
Sbjct: 147 LHREPTSGEIAQHLGVPEKDVWQLQWQVSSGHVIALDEVVSTGDRVDQISAMDSVQETLA 206

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V P  S  Q  +RE   + +  L  RE  V+ + +        TL E+GK   VT  R+ 
Sbjct: 207 VDPAQSFAQGEMREILAQAVDHLNERERAVVTLYYF----RSMTLSEIGKLLGVTESRVS 262

Query: 658 QIEAKAIRKLKH 669
           Q+ +  I KL+ 
Sbjct: 263 QMHSAIIVKLRK 274


>gi|328880523|emb|CCA53762.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 325

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/242 (21%), Positives = 113/242 (46%), Gaps = 5/242 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G    S  +  +VE NL LV   A ++ +    + DL+Q G +GL+KA  
Sbjct: 53  LFERLRSLEEGTASYSYVRNTLVELNLSLVKYAATRFRHSSENWEDLVQVGTVGLIKAIN 112

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +F ++A+  V   I R + D S ++ +P  +++    V +    +  ++ R 
Sbjct: 113 RFDPARGNEFMSFALPTVLGEIRRHLRDTSWSVHVPRRLQELRLDVAKANDALEQELGRP 172

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E++ +L +  + +R+         S    +  +D       +  +   S  D+  +
Sbjct: 173 PTAAELSDRLHITEDELREGRIAANGFASRSLDVPVDDEDAGPGMLA-RCLGSDDDAFEK 231

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               E    ++A+L+ R+  +L +RFG     + T  E+G++  +++  + ++ ++ +  
Sbjct: 232 VLNLEALKPLVAALSERDRTILALRFG----GELTQAEIGERLGLSQMHVSRLLSRILGG 287

Query: 667 LK 668
           L+
Sbjct: 288 LR 289


>gi|239947881|ref|ZP_04699634.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239922157|gb|EER22181.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 293

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 130/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEEFLLAK--SYLEENDLQAAHKLVTSHLKLVAKIASGYRTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K AI   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + +  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFAQIADELGVSINEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L  R     +T 
Sbjct: 196 AESGELIELLPETRPTPEAMAINKQNSTSKRKLLSNAMKILNDRELRILTERKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSSEYNISKERIRQIENTAFEKIKK 283


>gi|254482649|ref|ZP_05095887.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
 gi|214037008|gb|EEB77677.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
          Length = 284

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 130/268 (48%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++++     +S    R +   +     +   A +E+V ++LR V+ +A+ Y+  GL
Sbjct: 17  LAAYVQAVGSIPVLSPERERELAEDL--FYNDNLTAARELVMSHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  +   I      +++     + 
Sbjct: 75  AEADLIQEGNVGLMKAIKRFDPEKGVRLVSFAVHWIKAEMHEYILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ ++  + +  +     +A+ L + V+ V R   ++T   ++ +     +D  
Sbjct: 135 KLFFNLRSKKKSLSWLSADEAKA-VAEDLGVDVKEVHRMEGRLTSRDLAYDMSTDSDDDD 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A +  +   + N +      LA L  R   +L  R+     +  
Sbjct: 194 AWQAPQYYLEDHSSDPAQTVEEGDWKQNSQAQLHSALADLDERSRNILAQRWLAEDKS-- 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  Q+ V+ ERIRQ+EA A++KLK
Sbjct: 252 TLHELADQYGVSAERIRQLEANAMKKLK 279


>gi|253578148|ref|ZP_04855420.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850466|gb|EES78424.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39BFAA]
          Length = 259

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 132/267 (49%), Gaps = 13/267 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + +        + R+ +     A++  ++ NLRLV+SV +++ N  
Sbjct: 2   ALNKVEICGVNTSKLPVLTAEEKAELFRRIKNGDEQARELYIKGNLRLVLSVIRRFQNSS 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENADDLFQIGCIGLIKAIDNFDTTLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K + T      +  +EPT  EIA+++ +  E +   L   + P+SL  P+  E  DT
Sbjct: 121 IAYKAIYTRENYMKQHLKEPTVTEIAQEIGIEKEMIVYALDAIQNPVSLFEPVYTEGGDT 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I DK   +  +  I+          +  L  RE+ ++ +RF  G     T  EV
Sbjct: 181 LYVMDQISDKK--NKEERWIENL---ALREAMQRLNSREKHIIELRFYEG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
            ++  +++ ++ ++E  A++ +++  R
Sbjct: 232 AQEIGISQAQVSRLEKNALKSMRNYLR 258


>gi|300787087|ref|YP_003767378.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299796601|gb|ADJ46976.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 263

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 48/224 (21%), Positives = 104/224 (46%), Gaps = 6/224 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V   L L   +A +++ RG    DL+Q   IGL+ A ++FD   G+ F ++A+  +
Sbjct: 39  RSKLVTELLPLAEHIATRFSGRGEPREDLVQVARIGLINAVDRFDPARGHDFLSFAVPTI 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D   ++R+P  +++    + + +  +S ++ R PTP E+A+ L + V+ VR
Sbjct: 99  MGEVRRHFRDTGWSVRVPRRLKELHLSLSQGSAVLSQRLGRAPTPTELAEHLNLDVDEVR 158

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L       +L       D +      +         + ++    E    +L  L  RE
Sbjct: 159 EGLLAGNAYQALSVDKPVHDDAEALSLADTMGEPDHEMAMVEN--HEALQPLLQELPKRE 216

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +L MRF  G     T  ++  +  +++  + ++ ++ + +L+
Sbjct: 217 RAILVMRFFGG----LTQTQIADRVGISQMHVSRLLSQTLEQLR 256


>gi|239623454|ref|ZP_04666485.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521485|gb|EEQ61351.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 258

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 125/246 (50%), Gaps = 14/246 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E +    + ++       A+++ ++ NLRLV+SV ++++N      DL Q G IGL+KA
Sbjct: 21  NEEKE--ELFKRILNGDKDAREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCIGLIKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   + R + D +  IR+   +RD  +K +    +++    
Sbjct: 79  IDNFDITQNVKFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAYKALYAREQLTRVNS 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLD 602
           +EPT  EIA+++ +  E +   L   + P+SL  P+  +  D  ++ D I DK     L+
Sbjct: 138 KEPTLVEIAQEIGVSKEDITYALDAIQTPVSLYEPVYTDGGDPLYVMDQISDKK---NLE 194

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                +L  +    +  L  RE  ++ MRF  G     T  EV ++  +++ ++ ++E  
Sbjct: 195 ENWVEDL--SLVEAMKRLPERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRLEKN 248

Query: 663 AIRKLK 668
           A++ +K
Sbjct: 249 ALKSMK 254


>gi|163854463|ref|YP_001628761.1| RNA polymerase factor sigma-32 [Bordetella petrii DSM 12804]
 gi|163258191|emb|CAP40490.1| RNA polymerase sigma-32 factor [Bordetella petrii]
          Length = 295

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 65/227 (28%), Positives = 116/227 (51%), Gaps = 6/227 (2%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+V ++LRLV+SVA++Y   GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K 
Sbjct: 64  ELVLSHLRLVVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKA 123

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I   I      +++      +       + R   +       + IA++L +  E V ++
Sbjct: 124 EIHEFIIRNWRMVKVATTKAQRKLFFNLRSMRPDGQTLDPEQVDRIAQELNVRREDVSEM 183

Query: 567 -LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLT 621
            ++++   +SLE    DE+      ++ D+    P     + +  E         L +L 
Sbjct: 184 EVRLSGRDLSLEKQDDDEEAFAPISYLSDEGRQEPTRVLDRRDHDELQGAGLAHALQALD 243

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R  R++  R+        TL+E+ ++F V+ ERIRQIE+ A++K++
Sbjct: 244 ARSRRIIEARWLQDDGGV-TLQELAQEFGVSAERIRQIESAALKKMR 289


>gi|149181668|ref|ZP_01860161.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
 gi|148850646|gb|EDL64803.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
          Length = 253

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 116/243 (47%), Gaps = 14/243 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++++ +     A+  +V+ N+RLV SV +++ NRG +  DL Q G IGL+K+ +KF
Sbjct: 18  EVKELIKRSQEGDQSARDTIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R I D   T+++   +++  +++ R    +S    R PT
Sbjct: 78  DLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKEMGNRIRRAKDELSKTFGRVPT 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA  L +  E V    + ++ P S+   + + D     L D I D +     D    
Sbjct: 137 VNEIAAHLELSPEEVVMAQEASRSPSSIHETVYENDGDPITLLDQISDTSDQKWFD---- 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +      +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K +  
Sbjct: 193 ---KIALKEAIRELDERERLIVYLRY----YKDQTQSEVADRLGISQVQVSRLEKKILHN 245

Query: 667 LKH 669
           +K 
Sbjct: 246 MKE 248


>gi|51246044|ref|YP_065928.1| RNA polymerase sigma-B factor [Desulfotalea psychrophila LSv54]
 gi|50877081|emb|CAG36921.1| probable RNA polymerase sigma-B factor [Desulfotalea psychrophila
           LSv54]
          Length = 332

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 69/283 (24%), Positives = 136/283 (48%), Gaps = 12/283 (4%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   ++ IS    ++  E   + +  +  E     A   +V +NLRLV+ VA  +    
Sbjct: 46  ALHRYLQEISQYELLTREETDALATRYK--ESGDQDAAYTLVSSNLRLVVKVAMDFQKYW 103

Query: 468 LQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHM 525
           +Q F+DLIQEGN+GL++A +KFD   G KFS YA +W++  + + I D    ++I     
Sbjct: 104 MQNFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAYWIRAYVLKFIMDNWRLVKIGTTQA 163

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDED 584
           + K+   +   +++      +P P+ +A++L +  + V ++  ++    +SLE+P+  + 
Sbjct: 164 QRKLFFSLNKEKKLLESQGFDPKPKLLAERLNVREKEVIEMGQRMDNWDVSLESPVRSDS 223

Query: 585 TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 F+               I+  L E    +  +L  +E  +L     +  +   T
Sbjct: 224 DDEQKSFLPSNGPGIESVVAGKEIKVKLTELIDVLKVNLNDKERMILEK--RLLTDEPLT 281

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK--LRSFLDG 682
           L+ +  +F ++RER+RQIE   ++K+K    ++   +  + DG
Sbjct: 282 LQNIADKFGISRERVRQIEVNLLKKMKKYFEAEMPDIIDYFDG 324


>gi|302147235|emb|CBL51739.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|302147237|emb|CBL51740.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 262

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/300 (19%), Positives = 105/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                      +         E +  D  E E + E     S DD       PE A    
Sbjct: 59  -----ADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREKF 113

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            +L    + +  ++                                   QK+ ++    +
Sbjct: 114 GDLRAQYEVTRLSI-----------------------------------QKNGRAHEDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|239817346|ref|YP_002946256.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
 gi|239803923|gb|ACS20990.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
          Length = 313

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 127/291 (43%), Gaps = 30/291 (10%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +D+ +   N +        +++ E +     +R  +     A   ++ ++LRLV+S+++
Sbjct: 26  NLDAYISAANRLPM------LTLEEEQGFARRLR--DHNDLEAAGALILSHLRLVVSISR 77

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++
Sbjct: 78  QYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKV 137

Query: 522 PVH-MRDKIHKVVRTARR-------------MSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
                + K+   +R+ ++               + +  +   +   +    P E +    
Sbjct: 138 ATTKAQRKLFFNLRSMKQGFKADSAAADNGTHRDTLSPDEVSQMATRLNVKPEEVLEMET 197

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASLTP 622
           +++   + L+    D+     G      +A     + +++  R+  +       L +L  
Sbjct: 198 RLSGGDVLLDPGPSDDGDEAFGPIAYLADATQEPTALLESQQRDRLSSDGIATALEALDD 257

Query: 623 REERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R  R++  R+    +      TL ++   + V+ ERIRQIE  A++K+K  
Sbjct: 258 RSRRIVEERWLKVNDDGSGGMTLHDLAAVYGVSAERIRQIEVAAMKKMKKA 308


>gi|271969498|ref|YP_003343694.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270512673|gb|ACZ90951.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 266

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 112/230 (48%), Gaps = 10/230 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + E+VE +L LV  +A+++ NRG    DL Q   IGL+K+ ++FD   G +FSTYA 
Sbjct: 39  QRIRDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLGRGVEFSTYAT 98

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D+   +R+P  +++    + +    +S +  R PT  E+A  L M  E
Sbjct: 99  PTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAISELSQREGRAPTVGELAAFLKMSEE 158

Query: 562 GVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V + L+       +SL+ P   +D +     + D   +   DS      RE+   +L  
Sbjct: 159 EVLEGLESANAYSTVSLDAPDSGDDDAP---AVADSLGI-VDDSLEGVEYRESLKPLLER 214

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L PRE+R+L +RF        T  ++  +  +++  + ++ A+ + +L+ 
Sbjct: 215 LPPREKRILLLRFFGN----MTQSQIATELGISQMHVSRLLARTLAQLRE 260


>gi|240171602|ref|ZP_04750261.1| RNA polymerase sigma factor SigF [Mycobacterium kansasii ATCC
           12478]
          Length = 262

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 117/250 (46%), Gaps = 13/250 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + E    ++       +    + ++VE  L L   +A+++  RG    DLIQ   +GL+
Sbjct: 18  DVPEMFRELAGFDPDSPDFQRHRDKIVERCLPLADHIARRFEGRGEPRDDLIQVARVGLV 77

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S +
Sbjct: 78  NAVVRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATAELSQR 137

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAV 598
           + R PT  E+A +L M    V + L    +   +S+++  G+ED     + D + D +A 
Sbjct: 138 LGRAPTATELAAELGMDRGEVVEGLVAGSSYNTLSIDSGGGNEDDDARAIADTLGDMDA- 196

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +   RE+   +L +L  RE  VL +RF        T  ++ ++  +++  + +
Sbjct: 197 ----GLDRIEDRESLRPLLEALPERERTVLILRFF----ESMTQTQIAERVGISQMHVSR 248

Query: 659 IEAKAIRKLK 668
           + AK++ +L+
Sbjct: 249 LLAKSLARLR 258


>gi|254363063|ref|ZP_04979122.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261492837|ref|ZP_05989384.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
 gi|261494798|ref|ZP_05991276.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|153094728|gb|EDN75518.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261309509|gb|EEY10734.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261311519|gb|EEY12675.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
          Length = 319

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 67/301 (22%), Positives = 135/301 (44%), Gaps = 18/301 (5%)

Query: 378 ELDPHWVSYAKDFPE--GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           E+D    S     P             +DS +++ N+         ++  + + +    R
Sbjct: 24  EIDEEETSVEAMHPALVSGSMPVPQGNLDSYIRMANQYPI------LTAEQEKELAE--R 75

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
               E   A K+++ +++R VI +A+ Y   GL   DLIQEGNIGLMKA ++FD  +G +
Sbjct: 76  YYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVR 135

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
             ++A+ WVK  I   +      +++      +         +       E   +++A  
Sbjct: 136 LVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKLFFNLRKNKNRLAWFNEEEIKKVADD 195

Query: 556 LAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE--- 611
           L + VE VR++  ++T + +  + P GD+D       +  +++ S     ++        
Sbjct: 196 LGVSVEEVREMESRMTGQDLGFDLPAGDDDEDSYAPSMYIEDSSSNFADDLEDEQHNGQA 255

Query: 612 --TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  LA+L  R + +++ R+        TL+++  ++ ++ ER+RQ+E  A++K+K 
Sbjct: 256 TAQLAYALATLDERSQDIIKTRWLDDN--KATLQDLADKYNISAERVRQLENAALKKIKE 313

Query: 670 P 670
            
Sbjct: 314 A 314


>gi|221211178|ref|ZP_03584157.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
 gi|221168539|gb|EEE01007.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
          Length = 281

 Score =  126 bits (317), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 132/272 (48%), Gaps = 10/272 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  I   I++++    ++  E R   +  R+       A + +V ++LRLV+S+A+ Y 
Sbjct: 5   QLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNL--EAARRLVLSHLRLVVSIARNYL 62

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++   
Sbjct: 63  GYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATT 122

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE 583
              +       + +   +       + +A++L +  E V     +++   I+LE  + D 
Sbjct: 123 KAQRKLFFNLRSHKKGMQAMTPEEIDGLAQELNVKREEVTEMETRLSGGDIALEGQVEDG 182

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNT- 638
           + S+  +    +  N  + + +A Q ++ +T    + L +L  R  R++  R+    +  
Sbjct: 183 EESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEARWLHVDDDG 242

Query: 639 --DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 243 SGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 274


>gi|283796413|ref|ZP_06345566.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|291075823|gb|EFE13187.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|295091441|emb|CBK77548.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Clostridium cf.
           saccharolyticum K10]
 gi|295114800|emb|CBL35647.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily
           [butyrate-producing bacterium SM4/1]
          Length = 245

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 116/240 (48%), Gaps = 11/240 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++         A+  +VE N+ LV S+ +++  RG +  DL Q G+IGL+KA +KFD 
Sbjct: 11  IRLIMLAHGGDKAARDRLVEENMGLVWSIVRRFAGRGCETEDLFQIGSIGLIKAIDKFDT 70

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R + D    I++   +++   KV     +++  + REPT E
Sbjct: 71  SYDVRFSTYAVPMIAGEIRRFLRD-DGMIKVSRSVKEMGIKVSAAREKLAGTLGREPTLE 129

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANL 609
           EIA  +    E V   L+   +  SL  P G +DT+  L D +  ++         +   
Sbjct: 130 EIAGSVGASREEVAASLEAGAQVESLYAPAGGDDTNLSLLDRLSQES-----RENEEVLD 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    ++L SL  +E  ++  R+  G         +  Q  +++ ++ ++E + ++K++ 
Sbjct: 185 RMVLKKLLGSLGEKERELIVRRYFYGQTQTK----IAGQMGISQVQVSRMEKRILKKMRE 240


>gi|258546170|ref|ZP_05706404.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
 gi|258518595|gb|EEV87454.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
          Length = 287

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 129/268 (48%), Gaps = 11/268 (4%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I   I  I     +   E R +   +   E     A + ++  +L+ V+ +A+ +T  G
Sbjct: 19  DIDQYIAKIRQIPALDAEEERKLA--IALQETNDINAAQTLIVHHLKFVVHIARGFTGYG 76

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MR 526
           L   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      ++I     +
Sbjct: 77  LPLGDLIQEGNVGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYIIRNWRMVKIATTKAQ 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDEDT 585
            K+   +R+ ++  N +  E   + IA +L +  + V ++      + I+ E    DED 
Sbjct: 137 RKLFFNLRSMKKSLNWLN-EAEAKAIADELNVSTKDVFEMESRIHGQDIAFELNDDDEDN 195

Query: 586 SHL--GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            H     ++ D +   A     +  +  ++    + L +L PR   +++ R+ +  ++  
Sbjct: 196 DHFSPSQWLADDSIDPAEHTEHAEHENLMQRKLAKGLQALDPRSRAIVQARW-LNEDSKA 254

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+ +  ++ V+ ERIRQIE +A+ +L+
Sbjct: 255 TLQTLASEYNVSAERIRQIEQQAMHQLR 282


>gi|261754167|ref|ZP_05997876.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743920|gb|EEY31846.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 293

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 74/267 (27%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNCWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKERVRQIESRAMEKLK 279


>gi|127514531|ref|YP_001095728.1| RNA polymerase factor sigma-32 [Shewanella loihica PV-4]
 gi|126639826|gb|ABO25469.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella loihica PV-4]
          Length = 285

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 122/268 (45%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S      +  +E   +   ++  E     A K+++ ++LR VI VAK Y   GL
Sbjct: 19  LEAYIHSAHNIPMLEANEEYELAKRLQ--ETGDIQAAKQLIMSHLRFVIHVAKGYAGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E T   +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNLRKAKKRLGWFSDEEVTM--VAENLGVSKSDVTEMESRMAAQDPAFDLASDNDDD 194

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A    +   +A+ +      + +L  R + +L+ R+        
Sbjct: 195 QDYAPVHYLEDHSSDIASQVENDNFEADNQTRLLAAIKTLDERSQHILQARWLDE--EKT 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 253 TLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|329938754|ref|ZP_08288150.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329302245|gb|EGG46137.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 305

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 105/230 (45%), Gaps = 11/230 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EANL LV   A ++ +R     D++Q G IGL+ A ++FD   G +F T+AM  V
Sbjct: 82  RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 141

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D   T+ +P  + +   +V      ++    R PT  EIA++L +  E V 
Sbjct: 142 VGEIKRYFRDNVRTVHVPRRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIGEEEVL 201

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             ++   +    SLE     +    L D +  ++             R+    +L  L  
Sbjct: 202 SCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGVEH-----RDLVRHLLVQLPE 256

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE+R+L +R+        T  ++  +  V++  + ++ A++  +L+  +R
Sbjct: 257 REQRILLLRYYSN----LTQSQISAELGVSQMHVSRLLARSFARLRSANR 302


>gi|315444787|ref|YP_004077666.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263090|gb|ADT99831.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 270

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 113/253 (44%), Gaps = 8/253 (3%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +      +  +     E     + ++   L L    A+++  RG    DL Q  ++GL+
Sbjct: 10  DVPNMIRALRQLDPASPEYRRLHERIIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLV 69

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A ++FD   G  F  YA+  +   + R   D S  +++P  ++D   ++ +    ++ +
Sbjct: 70  NAVKRFDPDSGSDFLAYAVPTIMGEVRRYFRDCSWAVKVPRRLKDLNSQLAKARAELTQQ 129

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + R PTP E+A  L +  E V +    +    +L T          GDF+  +  +   D
Sbjct: 130 LGRAPTPSEVAAHLGIDREEVVQATIASSNYATLSTDSTSGPD---GDFVALRETLGEPD 186

Query: 603 SAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           + + A +  ET   ++  L PRE+ VL++RF      + T  ++ ++   ++  + ++ A
Sbjct: 187 ARLDAVVDNETIRPLIEKLPPREQAVLKLRFF----DEMTQTQIAERMGYSQMHVSRLLA 242

Query: 662 KAIRKLKHPSRSK 674
           KA+  L+  + S 
Sbjct: 243 KALATLRDQALSD 255


>gi|302549049|ref|ZP_07301391.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466667|gb|EFL29760.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 263

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 103/246 (41%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E +A   + E+VEA L +   +A ++  RG    DL Q   +GL+KA +
Sbjct: 22  FDRLARLPEGPERKAL--RDELVEAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN-KIKR 545
            +D   G  F  YA+  V   I R   D   T+ +P  ++D  ++V    + +S   + R
Sbjct: 80  HYDPARGNAFEAYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRHAVKELSQTTLGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EIA+   +    VR   +  +    +SLE  +   D   LGD I   +      +
Sbjct: 140 APTVAEIAEYAHLTEGEVRTGTEALECFSALSLEAEMPGTDGYALGDAIGGPD-----PA 194

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      L +L  RE  +L +RF  GM      E    Q  +++  + ++ +  
Sbjct: 195 FDTVVNRVAVKPCLEALPERERIILYLRFFKGMTQSRIAE----QLGISQMHVSRLLSSC 250

Query: 664 IRKLKH 669
              L+ 
Sbjct: 251 FAHLRE 256


>gi|29830033|ref|NP_824667.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607143|dbj|BAC71202.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 306

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+ 
Sbjct: 68  LESLEEGTHEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEL 127

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R PT  
Sbjct: 128 SRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRAPTVS 187

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQA 607
           E+A++L +    V + +         SL+    ++D    L D I  ++        +  
Sbjct: 188 ELAERLGISNGEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGIEFV-- 245

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E+   ++A L  R+ ++L +RF        T  E+G +  +++  + ++ ++ + +L
Sbjct: 246 ---ESLKPLIAQLPSRDRKILSLRFVAN----MTQSEIGDELGISQMHVSRLLSRTLVRL 298

Query: 668 KH 669
           + 
Sbjct: 299 RK 300


>gi|284028883|ref|YP_003378814.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283808176|gb|ADB30015.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 287

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 101/226 (44%), Gaps = 11/226 (4%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            +++  N  +  S+A +Y ++G+   DL Q   +GL+KAA  +       F  YA+  ++
Sbjct: 62  DQVILLNSPIARSIASRYRSKGVDSDDLEQVAYLGLVKAANGYRPSESTAFLAYAVPTIR 121

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R   D + T+R P  +++    +      ++ K+   PT  E A+ L      + +
Sbjct: 122 GELKRYFRDCAWTVRPPRRVQEMQGSIAAAEPELTQKLGHLPTDRETAEALGTEPGEIAE 181

Query: 566 VL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
               +     +SL+ P   E  + L D + D      L   +      T T  +A L  R
Sbjct: 182 ATAVRACFSTLSLDAPGSGEGGASLMDTVADAEDGYDLVENVH-----TLTPAVADLDDR 236

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + R+L++RF  G       EE+G++  V++ ++ ++    + +L+ 
Sbjct: 237 DRRILQLRFCHGYTQ----EEIGQELGVSQMQVSRLLRGILDRLRE 278


>gi|256061796|ref|ZP_05451931.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 311

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 75/289 (25%), Positives = 131/289 (45%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYAFWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    +  
Sbjct: 131 YILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDIEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|313115569|ref|ZP_07801028.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622084|gb|EFQ05580.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 255

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 71/261 (27%), Positives = 136/261 (52%), Gaps = 14/261 (5%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   + T  + +        ++ +     + A+++MVE NLRLV+SV +++  RG  
Sbjct: 3   NKVELCGMNTAKLPVLTEAEKRELLARAHAGDAAAREQMVEGNLRLVLSVVQRFAQRGEN 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +RD  
Sbjct: 63  LDDLFQVGCIGLIKAIDHFDPAQPVRFSTYGVPMIIGEIRRFLRDNN-ALRVSRSLRDTA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           ++ +++   +  ++ REPT +EIA+   +    V   L+   EPISLE P+  +  D  +
Sbjct: 122 YRAMQSREALEKQLGREPTMDEIAQAAGLARREVTAALESVVEPISLEEPVYTDGGDAMY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D +      S +Q        + +A LTPRE+R++ +R+  G     T  EV +
Sbjct: 182 VIDQVRDPDGEDSWISGLQ------FRQTVAGLTPREKRIMELRYLQG----KTQMEVAR 231

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  +++ ++ ++E  A+ + +
Sbjct: 232 EIGISQAQVSRLEKGALSQFR 252


>gi|330812379|ref|YP_004356841.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327380487|gb|AEA71837.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 284

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLEAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  E     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDADWSDNSNTNLHEALEVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|196248769|ref|ZP_03147469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196211645|gb|EDY06404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 250

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 119/245 (48%), Gaps = 14/245 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++R+ +     A+ E++E N+RLV SV +++ NRG +  DL Q G IGL+K+ +KF
Sbjct: 16  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKF 75

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D   T+++   +++  +K+ +    +S    R PT
Sbjct: 76  DLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPT 134

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIA  L +  E V    +  + P S+   + + D     L D I D +  S  +    
Sbjct: 135 ITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIADADEASWFE---- 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    + +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K ++ 
Sbjct: 191 ---KIALKKAIEELDERERLIVYLRY----YKDQTQSEVAARLGISQVQVSRLEKKILQH 243

Query: 667 LKHPS 671
           +K   
Sbjct: 244 IKEKM 248


>gi|197247378|ref|YP_002147821.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197211081|gb|ACH48478.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 269

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 77/210 (36%), Positives = 134/210 (63%), Gaps = 3/210 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             L D + D+    P D+    +++++T R
Sbjct: 232 KALLDILADEKENGPEDTTQDDDMKQSTER 261



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|37784444|gb|AAO13115.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
 gi|37955136|gb|AAP76220.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
          Length = 271

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 113/315 (35%), Gaps = 45/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E +D+  T   I S            +   E+ + D
Sbjct: 59  ------------------------EAEDMAPTATHIGSELGEDDLADEDEEDEDEDEDGD 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             + D D             +LR +       I                 QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVAREKFAELRAQYEVTRLSI-----------------QKNGRAHDDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + + +   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVQRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 257 MSIGEAKARRAKKEM 271


>gi|319651418|ref|ZP_08005547.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396949|gb|EFV77658.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 252

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 65/259 (25%), Positives = 131/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +T +  +E + +   +++ +     A+ ++V+ N+RLV SV +++ NRG +  
Sbjct: 4   EVKAEKGQTYLKDNEVKEL---IKQSQSGDQGARDKIVQKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKEMGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S  + R PT  E+++ L +  E +    + ++ P S+   + + D     L 
Sbjct: 120 IRKAKDELSKTLGRIPTVTELSEFLEISPEDIILAQEASRIPSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I+D N     D       +      +  L  RE  ++ +R+      D T  EV  + 
Sbjct: 180 DQIDDGNEGKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAARL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILQQMK 247


>gi|224533396|ref|ZP_03673990.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
 gi|224513561|gb|EEF83918.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
          Length = 266

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 70/259 (27%), Positives = 138/259 (53%), Gaps = 8/259 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +KS+     I+  E   +   +++G  +   AK +M+ ANLRLV+ + K+Y  +GL+  
Sbjct: 12  YLKSVREHKLITHEEEIKLAGQIQRGNAK---AKNKMINANLRLVLKIIKRYAGKGLKIE 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GL++AAEK+D     KFSTYA +W+KQ++ R++  ++  +++P    + I +
Sbjct: 69  DLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLILQ 128

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +       + ++ P  EEI K+  +      K++   ++  SL+  I   + S L + 
Sbjct: 129 INK----YLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSENSTLLNL 184

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFC 650
            ED +    +     + L+     +      +E  +++ R+ +  +    TL+++  +  
Sbjct: 185 YEDNSFNPEITLEQDSTLKHLNYILETKSNEKERYIIKKRYNLDNSPKKSTLKDISTELG 244

Query: 651 VTRERIRQIEAKAIRKLKH 669
           ++ E +RQIE + ++KLK 
Sbjct: 245 ISSETVRQIEKRVLKKLKE 263


>gi|315608976|ref|ZP_07883948.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|315249356|gb|EFU29373.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 287

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 137/273 (50%), Gaps = 41/273 (15%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   +  I  E+ ++  + + + + ++        A +++  ANL+ V+++A+++  RG
Sbjct: 54  ALNTYLDEIGQESPLTPEKEQDLAACIQ---AGDRGALEQLTRANLKFVVAMARRFRGRG 110

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLI EGNIGLM+AA KFD   G +F  YA  +V++A+ R++               
Sbjct: 111 LAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPYVRKAMERAV--------------- 155

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                                 E+ A    +P + +R+  +   +P S++ P+ + +   
Sbjct: 156 ----------------------EQQAGLYRVPRDIMRQKSRHEVQPASVDAPLSEGNKFT 193

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +E+K+A+ P D      + E    ++A+L  RE+RV+R  +G+G     +L E+ +
Sbjct: 194 LLDILENKDAIHPDDDYNVQAMIEALESLVATLDEREQRVVRGFYGLGTGRI-SLAEIAE 252

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           Q  + RER RQI  +A+RK+   ++++ L+ F+
Sbjct: 253 QMGIKRERARQIRDRALRKIARSTQNRALKIFI 285


>gi|91762259|ref|ZP_01264224.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718061|gb|EAS84711.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 293

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 127/272 (46%), Gaps = 14/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     ++  E   +             A +++V ++LRLV  +A  Y   GL
Sbjct: 14  LSAYLEQIKKFPMLAAEEEYMLAK--NWKATGNVKAAEKLVTSHLRLVAKIAMGYRGYGL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I EGN+GLM+A +KF+   G++ +TYAMWW++ +I   I      ++I      +
Sbjct: 72  PVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKIGTTTAQK 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   +++ + + +  PE   EIA KL +  + V     +++ +  SL   +  
Sbjct: 132 KLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKLDVNKDEVISMNRRLSGKEFSLNAQV-G 190

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
           ED     D++ DK     L  A Q  +   +      +  L  RE+ +L        +  
Sbjct: 191 EDGDEWQDWLVDKELDHDLKFAHQEEMGQRQNLLKDSIKILNEREKEILYS--RRLNDEP 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TLE++ K++ ++RERIRQIE KA  KL+   
Sbjct: 249 TTLEDLSKKYKISRERIRQIENKAFEKLQKHM 280


>gi|195940831|ref|ZP_03086213.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|1710645|sp|P50508|RP32_ENTCL RecName: Full=RNA polymerase sigma-32 factor
 gi|1143326|dbj|BAA09440.1| sigma-32 homolog [Enterobacter cloacae]
 gi|295097059|emb|CBK86149.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 285

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 115/242 (47%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K ++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVAR 159

Query: 555 KLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++   +        +       D+  +   +  ++  S     I+ +  E
Sbjct: 160 ELGVSSKDVREMESRMAAQDMTFDMSADDDASDSQPMAPVLYLQDKTSNFADGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  T  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 DQAANKLTFAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|57996884|emb|CAI45890.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 76/190 (40%), Positives = 126/190 (66%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  +    L  ++  VL  RFG
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWRFELNAKQREVLARRFG 181

Query: 634 IGMNTDHTLE 643
           +      TLE
Sbjct: 182 LLGYEAATLE 191


>gi|117925612|ref|YP_866229.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117609368|gb|ABK44823.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 290

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 68/266 (25%), Positives = 131/266 (49%), Gaps = 10/266 (3%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR- 466
           ++   ++ +     +S  E   +   VR  E     A  ++V + LR V S+AK+Y    
Sbjct: 14  QLAGYMQQVDSYPMLSAEEEFELA--VRYREQNDLEAAHKLVTSYLRYVASIAKEYQGYY 71

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G++F+DL+QEG++GLM+A ++FD   G++ +TYAMWW+K +I   +      ++I     
Sbjct: 72  GIKFMDLVQEGSVGLMQAVKRFDPHKGFRLATYAMWWIKASIQEFVLHHWSLVKIGTTAA 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
            +         + + +       EE+ ++  +  E V     +++    SL   +  E  
Sbjct: 132 QRKLFFNLRKSKDTLERLDATQAEEMGQRFGVSGEAVLEMDARLSGPDDSLNRCL-VEGG 190

Query: 586 SHLGDFIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
             + + + D      +  L S  +   ++   + L+ L+ RE+ ++R    I      TL
Sbjct: 191 EEIQNMLADSAPNQEMRLLASESERLQQQMIKQALSFLSEREQMIVRA--RIMCAEPVTL 248

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           E +G++  V+RERIRQ+E +A++KL+
Sbjct: 249 EVLGERLGVSRERIRQLETRALKKLR 274


>gi|197302592|ref|ZP_03167647.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
 gi|197298490|gb|EDY33035.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
          Length = 259

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 128/263 (48%), Gaps = 11/263 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + N+++   V T  + +        + R+ +     A++E ++ NLRLV+SV K++ +  
Sbjct: 1   MMNKVELCGVNTSKLPLLREDEKEELFRRIQKGDEKAREEYIKGNLRLVLSVIKRFDSSS 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G +GLMKA + FD     +FSTYA+  +   I R + D S  IR+   +RD
Sbjct: 61  ESADDLFQIGCVGLMKAVDNFDPERLVRFSTYAVPMIVGEIRRYLRDNSS-IRVSRSLRD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K +        +  +EPT +EIA ++ +  E V   L   + P+SL  P+ ++    
Sbjct: 120 TAYKAIYAKEGYVRRYMKEPTVQEIADEIGIAKEDVVFALDAVQTPMSLHEPVYNDG--- 176

Query: 588 LGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            GD +   + VS   +  +  + E +    +  L  RE  ++ +RF  G     T  EV 
Sbjct: 177 -GDALYVMDQVSDKKNREENWVEELSLEAAMERLNERERYIISLRFFEG----KTQTEVA 231

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
            Q  +++ ++ ++E  A++ ++ 
Sbjct: 232 GQIGISQAQVSRLEKNALKTMRQ 254


>gi|153811113|ref|ZP_01963781.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
 gi|149833001|gb|EDM88084.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
          Length = 259

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 78/267 (29%), Positives = 134/267 (50%), Gaps = 11/267 (4%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + I +     ++ +K +   S A+++ ++ NLRLV+SV K++ N  
Sbjct: 2   ALNKVEICGVNTSSLPILKSDEKEALFQKIKKGDSEAREQYIKGNLRLVLSVIKRFQNSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENADDLFQIGCIGLMKAVDNFDDTLNVKFSTYAVPMIIGEIRRYLRDYNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K + T   M  K  +EPT +EIA ++ +  E +   L   + P+SL  P+  E    
Sbjct: 121 IAYKAIYTKENMIKKNLKEPTIDEIADEIGIEKEMIVYALDAIQSPVSLFEPVYSEG--- 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            GD +   + +S   +     L   +    +  L  RE+ ++ MRF  G     T  EV 
Sbjct: 178 -GDTLYVMDQISDQKNKEDHWLENLSLREAMNRLNQREKHIIEMRFYEG----RTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +  +++ ++ ++E  A++ +K+  RS
Sbjct: 233 DEIGISQAQVSRLEKNALKTMKNYLRS 259


>gi|326791409|ref|YP_004309230.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
 gi|326542173|gb|ADZ84032.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
          Length = 257

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 75/265 (28%), Positives = 135/265 (50%), Gaps = 15/265 (5%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + I       ++ +  E   + A++E +  NLRLV+SV +++ NRG
Sbjct: 2   AINKVEICGVNTAKLPILTNEQKETLFKLIEQGDNKAREEYIRGNLRLVLSVIQRFNNRG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD     +FSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  EHVDDLFQVGCIGLIKAIDNFDVTQNVRFSTYAVPMIIGEIRRYLRDNN-AIRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K ++T  +++ K  +EPT +EIA +L +  E +   L   ++PISL  P+  +++  
Sbjct: 121 TAYKALQTKEQLTRKNAKEPTVQEIADELGIKKEDIVFALDAIQDPISLFEPVYHDESDT 180

Query: 588 L--GDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           L   D + +DKN        I           +  +  RE+++L +RF  G     T  E
Sbjct: 181 LYIMDQVSDDKNQDDVWLENI------ALKEAMKRINDREKQILMLRFFAG----KTQME 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           V  +  +++ ++ ++E  A++ +K 
Sbjct: 231 VANEIGISQAQVSRLEKTALKHMKK 255


>gi|254486865|ref|ZP_05100070.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
 gi|214043734|gb|EEB84372.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
          Length = 298

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 121/272 (44%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E + + A   MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      +
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   R+    + +  PE    IA  L +   E V    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKNRIGALEEGDMRPENVSRIATDLGVTEAEVVSMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A       +       RE     L  L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEEREELETRREMLAEALEVLNDREKDILTQ--RRLSD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TLE++  Q+ V+RERIRQIE +A  KL+ 
Sbjct: 252 ETITLEDLSSQYDVSRERIRQIEVRAFEKLQK 283


>gi|90418989|ref|ZP_01226900.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
 gi|90337069|gb|EAS50774.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
          Length = 303

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 68/274 (24%), Positives = 116/274 (42%), Gaps = 14/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E +   A   +V ++LRLV  +A  Y   GL
Sbjct: 16  LSRYLEEIRRFPMLEPQEEYMLAK--RYAEHDDRDAAHRLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + +     R     +IA  L +  E V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSRIQALDEGDLRPDQVSQIATNLGVSDEEVVSMNRRLSGDASLNAPLRAT 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D +       A    L   R    + +  L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSETQEDLLARNDELDQRRGMLQQAMGVLNDRERRIFEARRLAE--D 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             TLE +  +F ++RER+RQIE +A  K++   R
Sbjct: 252 PLTLETLSGEFEISRERVRQIEVRAFEKVQKAVR 285


>gi|51473499|ref|YP_067256.1| RNA polymerase factor sigma-32 [Rickettsia typhi str. Wilmington]
 gi|51459811|gb|AAU03774.1| RNA polymerase sigma 32 subunit (heat shock sigma factor)
           [Rickettsia typhi str. Wilmington]
          Length = 293

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 131/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEEFLLAK--SYLEENDLQAAHKLVTSHLKLVAKIASGYKTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K +I   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVHEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L+ R     +T 
Sbjct: 196 VESGELIELLPETRPTPEAMAINKQNYTSKRKLLSNAMQILNDRELRILKDRKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSSEYNISKERIRQIENTAFEKIKK 283


>gi|70733139|ref|YP_262912.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf-5]
 gi|68347438|gb|AAY95044.1| transcription initiation factor sigma 32 [Pseudomonas fluorescens
           Pf-5]
          Length = 284

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 129/268 (48%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLEAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  E     +A+ L +    VR++  ++T + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A+   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPALQLEDADWSDNSTSNLHEALEVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|685227|dbj|BAA04283.1| sigma factor [Streptomyces setonii]
          Length = 259

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 116/253 (45%), Gaps = 19/253 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E NL LV   A ++ NRG     D++Q G IGL+KA 
Sbjct: 10  FFDRLQVLEEGTHEYQYARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAI 69

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D S  + +P  +++    + +    ++  + R
Sbjct: 70  DRFDLSREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQELRVDLAKAKESLAGDLDR 129

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS-------HLGDFIEDKN 596
           +PT  E+A+ L +    V + +  +      SL+ P    +            D + + +
Sbjct: 130 DPTVRELAQDLGIEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQHSGRTFADVLGEPD 189

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                 +            +L  L  RE R++ MRFG     + T  ++G +  +++  +
Sbjct: 190 -----PAMETVENLHALAPLLGELDERERRIIDMRFG----QEMTQAQIGAELGISQMHV 240

Query: 657 RQIEAKAIRKLKH 669
            ++ ++ + KL++
Sbjct: 241 SRLLSRMLGKLRN 253


>gi|296105152|ref|YP_003615298.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059611|gb|ADF64349.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 285

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 117/242 (48%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKKLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVAR 159

Query: 555 KLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++   +        + +     D+  +   +  ++  S     I+ +  E
Sbjct: 160 ELGVSSKDVREMESRMAAQDMTFDMSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  +  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 DQAANKLSYAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|192362020|ref|YP_001983950.1| RNA polymerase factor sigma-32 [Cellvibrio japonicus Ueda107]
 gi|190688185|gb|ACE85863.1| alternative sigma factor RpoH [Cellvibrio japonicus Ueda107]
          Length = 286

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/271 (24%), Positives = 121/271 (44%), Gaps = 20/271 (7%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++++S    +S+ E + +   +         A +++V A+LR V+ +A+ Y   GL
Sbjct: 19  LNAYVQAVSSFAILSVEEEQQLARDLHDNGNLD--AARKLVMAHLRFVVHIARSYNGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      ++I      R
Sbjct: 77  PLGDLIQEGNVGLMKAVKRFDPDKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                +    +R++     E   E +A  L + V+ VR++        S +      D  
Sbjct: 137 KLFFNLRGAKKRLAWLSNDE--AEAVALDLGVDVKQVREMEGRL---ASYDAGFDASDDD 191

Query: 587 HLGDFIE-----DKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMN 637
              +++      + N   P     +AN  E         +  L  R   +L+ R+    +
Sbjct: 192 EDDNYVAPANYLEDNRYDPAARLEEANWEEASVNGLEMAMEKLDDRSRVILQRRWL--ND 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL ++  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 250 DKATLHDLAAEYGVSAERIRQLEKNAMNKVK 280


>gi|323138995|ref|ZP_08074055.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322395749|gb|EFX98290.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 126/273 (46%), Gaps = 16/273 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  +K+ +    +   E + +   V   +     A  ++  A++RLVI++A K+ + GL 
Sbjct: 9   RELMKAAAEAPFLERDEEKALA--VAWRDHGDRRALHKLTAAHMRLVIALAAKFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+QEG++GL++AA +F      +FSTYA WW++ +I   +      +R       K 
Sbjct: 67  IADLVQEGHVGLLEAAARFAPERDVRFSTYATWWIRASIQDYVLRNWSIVRGGTSSSQKA 126

Query: 530 HKVVRTARRMSNK-----IKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE 583
                   R                + IAK L +    V  +  +++   +SL   + D+
Sbjct: 127 LFFNLRRLRARLARDPDAYGSGDAYQAIAKALGVSRADVEMMDSRLSGSDVSLNAQLVDD 186

Query: 584 DTS---HLGDFIEDKN--AVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMN 637
           D+S      DF+ D +      +   + ++ R       LA L+ RE R+++       +
Sbjct: 187 DSSGSAQRMDFLVDDHPLPDEAVQETMDSDRRARWLKDALAILSERELRIVQE--RRLTD 244

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              TLE +G +  +++ER+RQIE++A+ KL+  
Sbjct: 245 NLVTLETLGDKLGISKERVRQIESRALIKLRKA 277


>gi|319649652|ref|ZP_08003808.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
 gi|317398814|gb|EFV79496.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
          Length = 236

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 128/244 (52%), Gaps = 12/244 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            + ++       A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD  
Sbjct: 3   ELFKQMHKGDITAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMKSIDNFDLS 62

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D +  IR+   +RD  +K ++   R+ +K  REPT EE
Sbjct: 63  QNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLMSKTSREPTAEE 121

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANL 609
           IAK+L +P E +   L   ++P+SL  PI ++  D  ++ D + D+           A  
Sbjct: 122 IAKELDVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQLSDERNKDIQWIEEIA-- 179

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  +  L  RE+ +LR RF  G     T  EV ++  +++ ++ ++E  AI+++  
Sbjct: 180 ---LKEGMRRLNEREKLILRKRFFQG----KTQMEVAEEIGISQAQVSRLEKAAIKQMNK 232

Query: 670 PSRS 673
             +S
Sbjct: 233 NIQS 236


>gi|284045116|ref|YP_003395456.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283949337|gb|ADB52081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 68/266 (25%), Positives = 122/266 (45%), Gaps = 18/266 (6%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
           +ET +   E + +    +        A++ +V A   LV  VA +  +     ++  DLI
Sbjct: 1   METNVKAIELKDLWRRYK--ASGDGRARERLVVAYSPLVKYVAGRMASGLPAHVEEADLI 58

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+ A E+FD     KF TYA+  ++ AI   +        +P  +R K  ++ R
Sbjct: 59  SYGLIGLISAIERFDLGREIKFETYAIPRIRGAIIDELRSLDW---VPRSVRAKAREIER 115

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS----HL 588
              ++ +K++R PT EE+A +L M ++  +  L         +L+      D S     L
Sbjct: 116 ANAKLEHKLQRAPTDEEMAHELDMSMDEFQDALIQISNSTIAALDELWTVSDASGDQISL 175

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D ++D +A  P      + L++     +A L  RE+ V+     +    + TL E+G+ 
Sbjct: 176 LDTLQDPDAPDPEKIVDASELKDRVADAIARLPEREKLVI----ALYYYENLTLREIGEV 231

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             VT  RI Q+  KA+ +L+   +++
Sbjct: 232 LGVTESRISQLHTKAVLRLRSRLQNE 257


>gi|255263634|ref|ZP_05342976.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
 gi|255105969|gb|EET48643.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
          Length = 298

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 122/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E E S +  ++V ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPMLEPEEEYMLAK--SWVENEDSKSAHKLVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A +KFD   G++ STYAMWW++ AI   +      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKKFDPEKGFRLSTYAMWWIRAAIQEYVLRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARRMSNKIKREPTPEEIAKKLA----MPVEGVRKVLKITKEPISLETPIGD 582
                + +   R+      +  PE + +          E +    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKSRIGALEDGDLRPEHVERIANDLGVNEQEVINMNRRLSGGDASLNAQVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           E        D++ED++A    D   +  L   RE     ++ L  RE+ +L        +
Sbjct: 194 EGEGTMQWQDWLEDEDADQAGDYEAKDELDSRRELLADAMSVLNDREKDIL--MQRRLQD 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLEE+  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 252 KAITLEELSGQYDVSRERIRQIEVRAFEKLQKKMR 286


>gi|44662845|gb|AAS47504.1| major sigma factor 70 [Meiothermus ruber DSM 1279]
          Length = 168

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 91/167 (54%), Positives = 116/167 (69%), Gaps = 2/167 (1%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA- 557
           YA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTARRM  ++ REP+ EEIA  +  
Sbjct: 2   YATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARRMQQELGREPSYEEIADAMGP 61

Query: 558 -MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E   + 
Sbjct: 62  GWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDSAAQSMLSEELEKA 121

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           L  L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 122 LGKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 168


>gi|42566466|gb|AAS21045.1| major sigma factor 70 [Meiothermus silvanus DSM 9946]
          Length = 168

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 90/167 (53%), Positives = 117/167 (70%), Gaps = 2/167 (1%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA- 557
           YA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR+M  ++ REPT EEI++ +  
Sbjct: 2   YATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQMQQELGREPTYEEISEAMGP 61

Query: 558 -MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
               + V +  KI +EP+SLETPIGDE  S  GDFI D++  SP+DSA Q+ L E   + 
Sbjct: 62  GWDAKKVEETFKIAQEPVSLETPIGDEKDSFYGDFIPDEHMASPVDSAAQSMLSEELEKA 121

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           L  L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA
Sbjct: 122 LGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 168


>gi|328880278|emb|CCA53517.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 290

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 120/253 (47%), Gaps = 16/253 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S    R + +   +G       +  ++E N+ LV+  A ++  RG +  D++Q G IGL
Sbjct: 38  LSKVFLRELAAR-EEGTEGHQYVRNTLIEMNMSLVVYAAGRFRARGDEMEDIVQVGMIGL 96

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA ++FD     +F+T+A+ ++   I R   D +  + +P  +++   ++ +    +S+
Sbjct: 97  IKAIDRFDLSREVEFATFAVPYIVGEIKRFFRDSTWAVHVPRRLQEARVELAKATDELSS 156

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI----GDEDTSHLGDFIEDK 595
           ++ R P   E+A  + +  E V +           SL+  +     ++D + L D I  +
Sbjct: 157 RLGRAPRVAELAPAMDLSEEQVVEAQVAANGYHSTSLDAAVAGGDSEDDDAALADLIGQE 216

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +    L          T   ++ +L PR+  +L +RF      + T  E+G++  V++  
Sbjct: 217 DPAIELFEDFH-----TLAPLVEALGPRDRLLLHLRFV----EELTQSEIGERLGVSQMH 267

Query: 656 IRQIEAKAIRKLK 668
           + ++ A+ I +L+
Sbjct: 268 VSRLLARNIERLR 280


>gi|114707401|ref|ZP_01440298.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114537282|gb|EAU40409.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 304

 Score =  126 bits (316), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 122/280 (43%), Gaps = 14/280 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E +   A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLEEIRRFPMLQPDEEYMLAK--RYAEHDDRNAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +++ EGN+GLM+A ++FD   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                  K+    + + +        ++IA +L +  + V  + +      SL +P+   
Sbjct: 134 RLFFNLRKMKSRIQALEDGDLNPDQVKQIATQLGVSDDEVISMNRRLSGDASLNSPLRAT 193

Query: 584 DT--SHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       D++ D+N       A Q  L   R    R +  L  RE R+           
Sbjct: 194 EGESGEWQDWLVDENESQEDVLAQQDELDQRRGMLKRAMGILNDRERRIFEA--RRLSED 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
             TLE +  +F ++RER+RQIE +A  K++   +   +  
Sbjct: 252 PITLEALSGEFDISRERVRQIEVRAFEKVQKAVQENVVAD 291


>gi|297562622|ref|YP_003681596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296847070|gb|ADH69090.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 267

 Score =  126 bits (315), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 117/248 (47%), Gaps = 10/248 (4%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +  +     E    + E+VE +L LV  +A+++ NRG    DL Q   IGL+K+
Sbjct: 23  RELFERLGELEADSEERRRIRDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKS 82

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++FD   G +FSTYA   +   I R   D+   +R+P  +++    + +    +S +  
Sbjct: 83  IDRFDLERGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLSLTKAVSDLSQREG 142

Query: 545 REPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           R PT  E+A  L M  E V + L+       +SL+ P   ++ +     + D   +   +
Sbjct: 143 RSPTVAELAAHLQMTEEEVLEGLESANAYSTVSLDAPDSGDEDAP---AVADSLGI-VDE 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           S      RE+   +L  L PRE+R+L +RF        T  ++ ++  +++  + ++ A+
Sbjct: 199 SLEGVEYRESLKPLLEQLPPREKRILLLRFFGN----MTQSQIAQELGISQMHVSRLLAR 254

Query: 663 AIRKLKHP 670
            + +L+  
Sbjct: 255 TLAQLRQA 262


>gi|218777994|ref|YP_002429312.1| RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
 gi|218759378|gb|ACL01844.1| putative RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
          Length = 328

 Score =  126 bits (315), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 79/297 (26%), Positives = 141/297 (47%), Gaps = 10/297 (3%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E      S     P    K      + S   ++  +  IS    ++  E R +   VR  
Sbjct: 11  EKQKKEKSAKAKPPAVVSKASKERALVSYDPLQRYLSEISKYPLLTREEERELA--VRVQ 68

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           E +   A   +V ANLRLV+ +A ++    +Q  LDLIQEGNIGLM+AA KFD     KF
Sbjct: 69  EFDDPDAAYRLVTANLRLVVKIALEFQRVWMQNLLDLIQEGNIGLMQAARKFDPYKNVKF 128

Query: 497 STYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           S Y+ +W+K  I + I D    ++I     + K+   ++  ++   +   +P P+ +++K
Sbjct: 129 SYYSSFWIKAYILKFIMDNWRLVKIGTTQAQRKLFFKLKKEKQKLLEEGFDPKPKLLSEK 188

Query: 556 LAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD---SAIQANLRE 611
           L +    +     ++    +SL+ P+ D+  S   +F+   +  +        ++  LRE
Sbjct: 189 LGVSERDIIDMDQRLNNWDLSLDAPVKDDSDSERIEFLSTPSESAEDQVARKEMETILRE 248

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +L  RE  +   R     ++  TL+++G +  ++RER+RQ+E+  ++KLK
Sbjct: 249 KIDIFRKTLKERELEIFDERVF--SDSPVTLQQIGDRHGISRERVRQVESGVVKKLK 303



 Score = 44.1 bits (102), Expect = 0.091,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 26/63 (41%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
            E      S+ +     + K        + DP++ YL E+    LL+RE E  +A R++ 
Sbjct: 10  EEKQKKEKSAKAKPPAVVSKASKERALVSYDPLQRYLSEISKYPLLTREEERELAVRVQE 69

Query: 149 GRA 151
              
Sbjct: 70  FDD 72


>gi|154252145|ref|YP_001412969.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156095|gb|ABS63312.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 298

 Score =  126 bits (315), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 72/272 (26%), Positives = 118/272 (43%), Gaps = 17/272 (6%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  +K       +       +    R  +     A  E+  A +RLVIS+A ++ N GL 
Sbjct: 14  RRYMKQAMTVPLLDEQHEFDLAR--RWKDHGDEQALHELTCAYMRLVISLATRFRNYGLP 71

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
           + DLIQEGN+GLM+AA +F+   G +FSTYA WW++ AI   I      +R       K 
Sbjct: 72  YGDLIQEGNVGLMQAAARFEPERGVRFSTYASWWIRAAIQDYILRNWSIVRTGTTAAHKS 131

Query: 530 -----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGD- 582
                 ++       + +   E     IAK+L +    V  +         SL   + D 
Sbjct: 132 LFFNLRRLRALIANGTRQNLTEDDRIFIAKRLGVGASDVATIDARLMTGDRSLNATVSDS 191

Query: 583 ---EDTSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGM 636
              E+ +   D +  +  +   +     + ++        L SL  RE  ++R R     
Sbjct: 192 TSSENLTEWQDLLPCERPLPEEEVMENHDSKQRSRWIEGALESLNERELTIIRERRLRDD 251

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TLE +G +  +++ER+RQIE  A++KL+
Sbjct: 252 V--ATLETLGVRLGISKERVRQIEHMALKKLR 281


>gi|261341953|ref|ZP_05969811.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
 gi|288315861|gb|EFC54799.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
          Length = 285

 Score =  126 bits (315), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 116/242 (47%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K ++ ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKTLILSHLRFVVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVAR 159

Query: 555 KLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++   +        + +     D+  +   +  ++  S     I+ +  E
Sbjct: 160 ELGVSSKDVREMESRMAAQDMTFDMSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  +  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A++K
Sbjct: 220 DQAANKLSFAMEGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           L+
Sbjct: 279 LR 280


>gi|165977273|ref|YP_001652866.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|190151190|ref|YP_001969715.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|303252711|ref|ZP_07338873.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307248906|ref|ZP_07530917.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307262328|ref|ZP_07543976.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307264539|ref|ZP_07546123.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|165877374|gb|ABY70422.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|189916321|gb|ACE62573.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|302648450|gb|EFL78644.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854601|gb|EFM86793.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306867991|gb|EFM99819.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306870138|gb|EFN01898.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 316

 Score =  126 bits (315), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 129/266 (48%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+  +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGL 106

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +
Sbjct: 107 PLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQR 166

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
                    +       E   +++A+ L +  E VR++  ++T + +  + P+G++D   
Sbjct: 167 KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDDDEV 226

Query: 587 -HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED +   A    D              LA+L  R + +++ R+        TL
Sbjct: 227 YTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDE--EKATL 284

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 285 QDLAEKYGISAERVRQLENAALKKIK 310


>gi|291531212|emb|CBK96797.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum 70/3]
          Length = 255

 Score =  126 bits (315), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 129/255 (50%), Gaps = 14/255 (5%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + + +      ++R+       A+++++  NLRLV+SV ++++ RG  
Sbjct: 9   NKVEISGVNTAKLKVLKESEKTELLRQMRSGDPTAREKLINGNLRLVLSVIQRFSGRGEN 68

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGLMKA + F      +FSTYA+  +   + R + D    IR+   MRD  
Sbjct: 69  PDDLFQVGCIGLMKAIDNFSTDFNVRFSTYAVPMIMGELRRYLRDSGS-IRVSRSMRDLA 127

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++   +++N   +EPT E+IAK++    E V   L+   +PISL  P+  E  DT +
Sbjct: 128 YKAMQAREKLTNDNSKEPTIEQIAKEIDAKREDVVIALEAVSDPISLYEPVFSESGDTIY 187

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D I D N        I           +  L  RE+ +L++RF  G     T  EV +
Sbjct: 188 MMDQIGDNNDDRNWLDEI------ALKEAIIGLDDREKNILKLRFFRG----KTQVEVAQ 237

Query: 648 QFCVTRERIRQIEAK 662
           +  +++ ++ ++E +
Sbjct: 238 EIGISQAQVSRLEKR 252


>gi|329896515|ref|ZP_08271573.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
 gi|328921732|gb|EGG29105.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
          Length = 286

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 126/270 (46%), Gaps = 12/270 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+++S    +S+   R +   +     +   A +++V ++LR V+ +A+ Y+  GL
Sbjct: 17  LAAYIQTVSSIPVLSVERERELAEDL--YYNDNLEAARQLVMSHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  +   I      +++     + 
Sbjct: 75  AEADLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTS 586
           K+   +R++++    +  E   + +A  L + V  V     +++   ++ + P   +D  
Sbjct: 135 KLFFNLRSSKKALAWLSAE-EAQAVADDLGVDVREVATMEARMSSRDVAFDAPSDSDDDD 193

Query: 587 HLGD--FIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 ++ED  A        +  Q +        L  L  R   +L  R+    +   T
Sbjct: 194 VYAPQYYLEDHRADPAQQVESTNWQEDSESRLHYALEQLDERSRDILAQRWL--NDEKAT 251

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L ++  Q+ V+ ERIRQ+E  A++K++   
Sbjct: 252 LHDLAAQYGVSAERIRQLEQNAMQKVRKLM 281


>gi|325289982|ref|YP_004266163.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965383|gb|ADY56162.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 133/249 (53%), Gaps = 12/249 (4%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + + + +  ++ K +     A+++++  NL+L+ ++ +++T+RG +  DL Q G IGL+
Sbjct: 14  PLLKEQEMTELLHKAQAGDHDAREQLINCNLKLIFNLIQRFTHRGYELEDLFQIGTIGLI 73

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KFD+  G KFSTYA+  +   I R + D    I++P   ++ ++K+ R+  ++S +
Sbjct: 74  KAIDKFDFSYGVKFSTYAVPMIIGEIRRFLRD-DHPIKVPRSYKELVYKIHRSREKLSLE 132

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSP 600
           + REPT  EIA+ L +  E +   L   + P S+   +  +D+   ++ D I  +  + P
Sbjct: 133 LNREPTVNEIAQDLNVGSEEIVTALDAVQSPTSINDTLYQDDSDPIYILDQIPVEKDLVP 192

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                 A        VL  L  RE++VL MRF      D T  E+ K+  +++ +I +IE
Sbjct: 193 AWFEEVA-----LKDVLNKLPEREKQVLVMRF----YEDKTQSEIAKRLNLSQVQISRIE 243

Query: 661 AKAIRKLKH 669
             A+  LK 
Sbjct: 244 RAALLHLKQ 252


>gi|152976264|ref|YP_001375781.1| sporulation sigma factor SigG [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025016|gb|ABS22786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 259

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 135/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +   + A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGETSAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IA+ L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLIAENSKEPTAMDIAQVLDVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 233 EEIGISQAQVSRLEKSAIKQM 253


>gi|84515923|ref|ZP_01003284.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510365|gb|EAQ06821.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 277

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 121/260 (46%), Gaps = 16/260 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 11  ELRLAYAWRDQRDEEALHRLITAYMRLAISMASKFKRYGAPMNDLIQEASVGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A   
Sbjct: 71  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAAAE 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDK-- 595
              ++     E+IA ++ +P+  V+ +  +++    SL      ED      D +ED   
Sbjct: 131 GLHLETHELHEKIAIEVGVPLHDVQMMDGRLSGSDFSLNATQSMEDEGREWIDALEDDAP 190

Query: 596 -NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A    +S     LR+     L +L  RE+ ++R R         TLE +G +  +++E
Sbjct: 191 QAAEKVENSHDTDTLRQWLVTALTALNDREQFIVRERKLRD--DPRTLESLGSELGLSKE 248

Query: 655 RIRQIEAKAIRKLKHPSRSK 674
           R+RQ+EA A  K++    ++
Sbjct: 249 RVRQLEAAAFGKMRKSLEAQ 268


>gi|37362432|gb|AAO23112.1| sigma factor S [Vibrio vulnificus]
          Length = 167

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 75/164 (45%), Positives = 116/164 (70%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             R+       A+K M+E+NLRLV+ ++++Y+NRGL  LDLI+EGN+GL++A EKFD   
Sbjct: 2   YARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPER 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  +++  +RTAR +S K+  EPT EEI
Sbjct: 62  GFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYLRTARELSQKLDHEPTAEEI 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           A +L +PV+ V K+L++ +   S++TPIG +    L D I D N
Sbjct: 122 AAQLDIPVDDVGKMLRLNERISSVDTPIGGDGEKALLDIIRDAN 165


>gi|167765669|ref|ZP_02437722.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
 gi|167712644|gb|EDS23223.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
          Length = 271

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 72/273 (26%), Positives = 135/273 (49%), Gaps = 13/273 (4%)

Query: 400 ACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
             + + ++  R +++   V T  + +        +  + E    +A++  ++ NLRLV+S
Sbjct: 6   ESQTEELIMARKKVEICGVNTSSLPLLSEEEKEDLFERIEQGDLLAREHYIKGNLRLVLS 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           + ++++       DL Q G IGLMKA + FD  L  KFSTYA+  +   + R + D    
Sbjct: 66  IIQRFSGSNENADDLFQVGCIGLMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM 125

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
            R+   +RD  +K +     ++ K+  EPT + IAK++ M  E V   L     P+SL  
Sbjct: 126 -RVSRSLRDTAYKAINAREVLTKKLNHEPTIDVIAKEIDMKKEDVLFALDAIATPLSLYE 184

Query: 579 PIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           P+  +  DT +L D ++DK   +  DS +++         +  L  RE  +++MRF  G 
Sbjct: 185 PVYQDGGDTLYLMDQVKDKK--NKEDSWVESI---ALKEAMEHLPDREYDIIKMRFFEG- 238

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               T  EV  +  +++ ++ ++E  A++ +K+
Sbjct: 239 ---KTQTEVADEIAISQAQVSRLEKNALKHMKN 268


>gi|239928675|ref|ZP_04685628.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291436999|ref|ZP_06576389.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291339894|gb|EFE66850.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
          Length = 280

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 43  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGIFGLIDAIEKFDVDREIKFE 102

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A +L 
Sbjct: 103 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPSESEVAGELG 159

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 160 IAVEE----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDR 215

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 216 ELRRFLVRAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 271

Query: 668 K 668
           +
Sbjct: 272 R 272


>gi|297200169|ref|ZP_06917566.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197713380|gb|EDY57414.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 304

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + +G  E S  +  +VE NL LV   A ++ +R     D+IQ G IGL+KA ++F+ 
Sbjct: 66  LESLEEGTYEYSYVRNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEL 125

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ K+ R PT  
Sbjct: 126 SRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQKLDRAPTVA 185

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQA 607
           E+A +L +  E V + +         SL+    ++D    L D I  ++        +  
Sbjct: 186 ELADRLGLSKEEVVEGMAASNAYTAASLDAQPEEDDSEGALADRIGYEDHGLEGIEYV-- 243

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              E+   ++A L  R+ ++L +RF  G     T  E+G++  +++  + ++ ++ + +L
Sbjct: 244 ---ESLKPLIAELPSRDRQILSLRFVAG----MTQSEIGEELGISQMHVSRLLSRTLVRL 296

Query: 668 KH 669
           + 
Sbjct: 297 RK 298


>gi|28867660|ref|NP_790279.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213967796|ref|ZP_03395943.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382433|ref|ZP_07230851.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           Max13]
 gi|302061175|ref|ZP_07252716.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           K40]
 gi|302132032|ref|ZP_07258022.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|28850895|gb|AAO53974.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213927572|gb|EEB61120.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|330965442|gb|EGH65702.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. actinidiae
           str. M302091]
 gi|331014973|gb|EGH95029.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 284

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++    R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPERERELAESL--YYEQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 +++ED     A    D+    N      + L  L  R   +L  R+        
Sbjct: 194 AFQSPANYLEDHRYDPARQLEDADWTDNSTANLHQALDVLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 252 TLHDLAQKYNVSAERIRQLEKSAMNKLK 279


>gi|29829172|ref|NP_823806.1| RNA polymerase sigma factor WhiG [Streptomyces avermitilis MA-4680]
 gi|29606278|dbj|BAC70341.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 280

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 106/242 (43%), Gaps = 26/242 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               +++++     LV  VA +  + GL       D +  G  GL+ A EKFD     KF
Sbjct: 43  DERLREQLILHYSPLVKYVAGR-VSVGLPPNVEQADFVSSGVFGLIDAIEKFDIGREIKF 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++
Sbjct: 102 ETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPTEGEVATEM 158

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQ 606
            + V+     L      +SL   +  E          D   L D +ED  A +P++ A  
Sbjct: 159 GIAVDE----LHSVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAED 214

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +
Sbjct: 215 RELRRFLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQ 270

Query: 667 LK 668
           L+
Sbjct: 271 LR 272


>gi|83643468|ref|YP_431903.1| RNA polymerase factor sigma-32 [Hahella chejuensis KCTC 2396]
 gi|83631511|gb|ABC27478.1| RNA polymerase sigma-32 factor RpoH [Hahella chejuensis KCTC 2396]
          Length = 284

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 116/241 (48%), Gaps = 13/241 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            + E   A +++V A+LR V+ +AK Y+  GL   DL+QEGNIGLMKA ++F+   G + 
Sbjct: 43  HQNEDLYAARQLVMAHLRFVVHIAKSYSGYGLSQADLVQEGNIGLMKAVKRFNPEFGVRL 102

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   I      +++      R     +    +R++     E     +A+
Sbjct: 103 VSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKLFFNLRSAKKRLAWLTNDEAKA--VAE 160

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHL---GDFIED---KNAVSPLDSAIQA 607
            L +    VR++  ++  +  S +    ++D +      +++ED     A+   +   + 
Sbjct: 161 DLGVDTHVVREMESRLAGQDTSFDAGADEDDETAFKAPANYLEDRRYDPAMMLENENWEE 220

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +        L  L  R + +++ R+        TL E+  ++ V+ ERIRQ+E  A++K+
Sbjct: 221 DSNSRLHDALTQLDERSKDIIQKRWLAEN--KATLHELADEYGVSAERIRQLEKNAMKKV 278

Query: 668 K 668
           K
Sbjct: 279 K 279


>gi|330468593|ref|YP_004406336.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
 gi|328811564|gb|AEB45736.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
          Length = 292

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 111/230 (48%), Gaps = 12/230 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+ ++V   L     +A++Y  RG    DL Q   +GL+ A +++D   G  F+ YA   
Sbjct: 42  ARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERG-SFTAYAAIT 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D++  + +P  +RD I +V +    +++++ R PT  E++K+L  P E +
Sbjct: 101 IVGEIKRHFRDRTWGVHVPRRLRDLILEVGQATAALTSELSRAPTVAELSKRLDTPEEEI 160

Query: 564 RKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              L+      P SL  P+G E ++  GD + + +      +    + R T + +L  L 
Sbjct: 161 LAALESAAGYSPASLNAPVGGESSAEFGDLVGESD-----IALESVDDRVTVSGLLHRLP 215

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            RE R+L MRF           E+  +F +++  + ++ ++A+  L+   
Sbjct: 216 WRERRILAMRFYGNQTQ----AEIAARFGISQMHVSRLLSRALTWLRQAM 261


>gi|288553150|ref|YP_003425085.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
 gi|288544310|gb|ADC48193.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
          Length = 261

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 81/272 (29%), Positives = 137/272 (50%), Gaps = 21/272 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +  +E R + + ++        A++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSKLPVLKNTEMRELFTQLQ---SGDDSAREVLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMS--NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++   ++    K + EPT +EIAK L +P E V   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDQLMAEKKRENEPTVQEIAKVLDVPKEDVVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D   + D I D+           A         +  L  RE+ +L MRF  G     T
Sbjct: 179 GGDPIFVMDQISDERNKDVNWVEEIA-----LKEAMIRLNDREKMILNMRFFQG----KT 229

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             EV  +  +++ ++ ++E  AI+++   ++S
Sbjct: 230 QMEVADEIGISQAQVSRLEKAAIQQMNKHAQS 261


>gi|299141532|ref|ZP_07034668.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298576868|gb|EFI48738.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 252

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 88/286 (30%), Positives = 136/286 (47%), Gaps = 41/286 (14%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K     E +S+    NEI     ET +S  E + +   +  G   A  A  ++  ANLR 
Sbjct: 8   KPLSERESESLNIYLNEI---GKETILSDDEEKQLSQQIMAGGAAAERAIGKLTSANLRF 64

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y +RG+  LDLI EGNIGLMKAA  FD   G +F  YA  +V++A+  ++ +Q
Sbjct: 65  VVSIAKQYVDRGVAILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNEQ 124

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S   R+P H                     E + EE A   A                 S
Sbjct: 125 SGIFRLPKH---------------------EHSAEEKANSRAF----------------S 147

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++ P+ +    +L   + D  A  P   A++ +++E     +  L  RE  V+   +GIG
Sbjct: 148 VDAPLQNGKNVNLLSILSDPTAARPDQEALETSVKEELLEAMNILDNRERNVVEAFYGIG 207

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                T  E+G++  + RER+RQI  KA+RKL   + S  L+++L+
Sbjct: 208 QPH-LTFAEIGEKMGLKRERVRQIRNKAVRKLNRNTTSDMLKAYLE 252



 Score = 37.9 bits (86), Expect = 5.3,   Method: Composition-based stats.
 Identities = 32/187 (17%), Positives = 75/187 (40%), Gaps = 10/187 (5%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTF 164
           K          + + +YL E+G   +LS + E  ++++I AG       +  L  + L F
Sbjct: 5   KTGKPLSERESESLNIYLNEIGKETILSDDEEKQLSQQIMAGGAAAERAIGKLTSANLRF 64

Query: 165 QALIIWRDELNDGTTLLREIID-----LEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
              I  +  ++ G  +L  I +     ++A    +   G         + ++   +   E
Sbjct: 65  VVSIA-KQYVDRGVAILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNE 123

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN-DERNLDEDEDDSAHTLSAMEDQLRP 278
           +  +        SA + +      VD+P +N +N +  ++  D   +     A+E  ++ 
Sbjct: 124 QSGIFRLPKHEHSAEEKANSRAFSVDAPLQNGKNVNLLSILSDPTAARPDQEALETSVKE 183

Query: 279 KVMCALD 285
           +++ A++
Sbjct: 184 ELLEAMN 190


>gi|94987055|ref|YP_594988.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731304|emb|CAJ54667.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 385

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 78/273 (28%), Positives = 140/273 (51%), Gaps = 14/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  ++ +S    +   E   +   V+K  C  S A   ++ ++LRLV+ +A  +  R +
Sbjct: 106 LQLYLREVSRFPMLKPEEELRLAQDVQKKGC--SKAAFRLISSHLRLVVKIAMDFQRRWM 163

Query: 469 Q-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--M 525
           Q  LDLIQEGN+GLM+A  KFD   G KFS YA +W++  I + I D    ++I      
Sbjct: 164 QNVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIRAYILKFIMDNWRMVKIGTTQAQ 223

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDE- 583
           R   + + R  +++  +   +P    +A +L +  E + ++ +      +SL+  +G+E 
Sbjct: 224 RKLFYNLNRERQKLLAE-GFDPDTSSLALRLGVGEEQIIEMQQRLDASDMSLDVTVGEET 282

Query: 584 DTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +   DF+   N     S     I   L++    +L  L+ +E  +L     +  +   
Sbjct: 283 GNASRIDFLPAINPGIEESLAGQEIAILLQDRIKDILPLLSEKEVYIL--HNRLLTDDPV 340

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSR 672
           TL E+G+++ VTRER+RQ+EA+ ++KL+ H SR
Sbjct: 341 TLREIGEKYSVTRERVRQLEARLLQKLRTHLSR 373


>gi|322834883|ref|YP_004214910.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
 gi|321170084|gb|ADW75783.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
          Length = 285

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 127/270 (47%), Gaps = 15/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++ +    ++  E R +   +         A KE++ ++LR V  +A+ Y+  GL
Sbjct: 16  LEAYVRAANAYPMLTAEEERALAERL--HYNGDLEAAKELILSHLRFVAHIARNYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDE-- 583
             K+    R+   ++        E +A++L +  + V     ++  + ++ +    DE  
Sbjct: 134 --KLFFNLRKNKQRLGWFSHDEVEHVARELGVTSKDVLEMESRMAAQDMTFDPTPDDEPR 191

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           D + +   +  ++  S     I+ +  +       +  +  L  R + ++R R+    N 
Sbjct: 192 DGAAMAPMLYLQDKSSDFAETIEEDNWDQDATDKLSSAMEGLDERSQDIIRARWLDDENK 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 252 S-TLQELADKYGVSAERVRQLEKNAMKKLR 280


>gi|126650128|ref|ZP_01722361.1| sporulation sigma factor SigF [Bacillus sp. B14905]
 gi|126593300|gb|EAZ87262.1| sporulation sigma factor SigF [Bacillus sp. B14905]
          Length = 263

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 125/249 (50%), Gaps = 17/249 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +++  +KG+ E   A+K MVE N RLV S+ +++T RG++  DL Q G IGL
Sbjct: 12  LSQEEMRDLIARAQKGDHE---ARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGL 68

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK+ +KFD     KFSTYA+  +   I R + D    +++   +R+   K+         
Sbjct: 69  MKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGMVKVSRSIRELNFKIRHATDEFIK 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K +  PT +E+A+ L +  E +       ++P SL   + +   D+  L D ++D+ +  
Sbjct: 128 KNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDEKSEQ 187

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D             VL  L PRE+ ++ +R+           E+  +  +++ ++ ++
Sbjct: 188 PFDYI-------PLKEVLTRLEPREQSIIYLRYFSDCTQ----TEIANRLGISQVQVSRL 236

Query: 660 EAKAIRKLK 668
           E K + +LK
Sbjct: 237 EKKILAQLK 245


>gi|3249725|gb|AAC26665.1| RNA polymerase sigma-like factor [Streptomyces glauceuces]
          Length = 162

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 76/162 (46%), Positives = 113/162 (69%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QA++R++ADQ+ TIR+PVH+ + I++VVR  RR+  +   EPT E+I   L +
Sbjct: 1   YATWWIRQAMSRALADQADTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIGVDLDL 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V  +L++ +EP+SL  P+G+ED    GD IED +A SP++SA+   LRE    VL+
Sbjct: 61  TPERVTDILRLGQEPVSLHAPVGEEDDVSFGDLIEDGDAASPVESAVFLLLREHLEAVLS 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L  RE +V+++R+G+      TLEE+G+ F VTRERIRQIE
Sbjct: 121 TLGERERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIE 162


>gi|307251409|ref|ZP_07533324.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306856577|gb|EFM88718.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 316

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 129/266 (48%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+  +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGL 106

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +
Sbjct: 107 PLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAIHWVKAEIHEYVLKNWRIVKVATTKAQR 166

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
                    +       E   +++A+ L +  E VR++  ++T + +  + P+G++D   
Sbjct: 167 KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDDDEV 226

Query: 587 -HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED +   A    D              LA+L  R + +++ R+        TL
Sbjct: 227 YTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDE--EKATL 284

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 285 QDLAEKYGISAERVRQLENAALKKIK 310


>gi|120556648|ref|YP_960999.1| RNA polymerase factor sigma-32 [Marinobacter aquaeolei VT8]
 gi|120326497|gb|ABM20812.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 286

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 131/268 (48%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ S    +S+ E R +   +         A +++V ++LR VI +A+ Y   GL
Sbjct: 17  LESYIQAASRIPVLSVDEERELAERL--HYHGDVEAARQLVLSHLRFVIHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A  L +    VR++  ++  +  + + P+ D++ +
Sbjct: 135 KLFFNLRSQKKKLAWLNHDELKA-VANDLGVEPHVVREMEGRLASQDTAFDGPMDDDEDN 193

Query: 587 HL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   ++    +      + L  L  R + +LR R+     +  
Sbjct: 194 AYQAPAYYLEDRRSDPAVQLENADWSEDSNGRLMQALEQLDERSQDILRERWL--SESKS 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 252 TLHELADKYGVSAERIRQLEKNAMKKIR 279


>gi|264680055|ref|YP_003279964.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
 gi|262210570|gb|ACY34668.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
          Length = 324

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 65/291 (22%), Positives = 122/291 (41%), Gaps = 25/291 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ E +     ++  E     A   +V ++LRLV+S++++
Sbjct: 31  VPPLGNLDAYISAVNRMPMLTLEEEQDYARKLK--EHNDLDAAGRLVMSHLRLVVSISRQ 88

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 89  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 148

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---------------VEGVRKVL 567
                +       + +   K       EE+A +  +                 E +    
Sbjct: 149 TTKAQRKLFFNLRSMKHDLKSDAAMADEELALRETLTSNEIDAVAAKLNVKREEVIEMET 208

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTP 622
           ++    + L+    D+     G      +A     + +++  R+          L  L  
Sbjct: 209 RLAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDD 268

Query: 623 REERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R  R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K  
Sbjct: 269 RSRRIVEERWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKA 319


>gi|307246764|ref|ZP_07528832.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307255748|ref|ZP_07537551.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307257933|ref|ZP_07539687.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307260200|ref|ZP_07541909.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306852339|gb|EFM84576.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306861308|gb|EFM93299.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306863580|gb|EFM95509.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865745|gb|EFM97624.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 316

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 130/266 (48%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+  +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGL 106

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +
Sbjct: 107 PLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQR 166

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
                    +       E   +++A+ L + +E VR++  ++T + +  + P+G++D   
Sbjct: 167 KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSLEEVREMESRMTGQDLGFDLPVGEDDDEV 226

Query: 587 -HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED +   A    D              LA+L  R + +++ R+        TL
Sbjct: 227 YTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDE--EKATL 284

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 285 QDLAEKYGISAERVRQLENAALKKIK 310


>gi|281425346|ref|ZP_06256259.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
 gi|281400509|gb|EFB31340.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
          Length = 252

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 88/286 (30%), Positives = 136/286 (47%), Gaps = 41/286 (14%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K     E +S+    NEI     ET +S  E + +   +  G   A  A  ++  ANLR 
Sbjct: 8   KPLSERESESLNIYLNEI---GKETILSDDEEKQLSQQIMAGGAAAEQAIGKLTSANLRF 64

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+S+AK+Y +RG+  LDLI EGNIGLMKAA  FD   G +F  YA  +V++A+  ++ +Q
Sbjct: 65  VVSIAKQYVDRGVAILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNEQ 124

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           S   R+P H                     E + EE A   A                 S
Sbjct: 125 SGIFRLPKH---------------------EHSAEEKANSRAF----------------S 147

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           ++ P+ +    +L   + D  A  P   A++ +++E     +  L  RE  V+   +GIG
Sbjct: 148 VDAPLQNGKNVNLLSILSDPTAARPDQEALETSVKEELLEAMNILDNRERNVVEAFYGIG 207

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
                T  E+G++  + RER+RQI  KA+RKL   + S  L+++L+
Sbjct: 208 QPH-LTFAEIGEKMGLKRERVRQIRNKAVRKLNRNTTSDMLKAYLE 252



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 32/187 (17%), Positives = 75/187 (40%), Gaps = 10/187 (5%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTF 164
           K          + + +YL E+G   +LS + E  ++++I AG       +  L  + L F
Sbjct: 5   KTGKPLSERESESLNIYLNEIGKETILSDDEEKQLSQQIMAGGAAAEQAIGKLTSANLRF 64

Query: 165 QALIIWRDELNDGTTLLREIID-----LEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
              I  +  ++ G  +L  I +     ++A    +   G         + ++   +   E
Sbjct: 65  VVSIA-KQYVDRGVAILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNE 123

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN-DERNLDEDEDDSAHTLSAMEDQLRP 278
           +  +        SA + +      VD+P +N +N +  ++  D   +     A+E  ++ 
Sbjct: 124 QSGIFRLPKHEHSAEEKANSRAFSVDAPLQNGKNVNLLSILSDPTAARPDQEALETSVKE 183

Query: 279 KVMCALD 285
           +++ A++
Sbjct: 184 ELLEAMN 190


>gi|302556917|ref|ZP_07309259.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
 gi|302474535|gb|EFL37628.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
          Length = 263

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 104/246 (42%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E    + + E+V A L +   +A ++  RG    DL Q   +GL+KA +
Sbjct: 22  FARLARLPEGPER--RMLRDELVTAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
            +D   G  F  YA+  V   I R   D   T+ +P  ++D  ++V ++A+ ++     R
Sbjct: 80  HYDPARGNAFEAYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRQSAKELAQTTPGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EIA    +  + VR  ++       +SL+  +   D   LGD +   +       
Sbjct: 140 APTVAEIAAHARLTEDEVRTGMEALECFTALSLDAEMPGTDGYALGDALGGPD-----PG 194

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      L +L  RE  +L +RF  G     T   + +Q  +++  + ++ +  
Sbjct: 195 YDTVVDRVAVRPCLEALPERERLILYLRFFRG----MTQSGIAEQLGISQMHVSRLLSGC 250

Query: 664 IRKLKH 669
             +L+ 
Sbjct: 251 FARLRE 256


>gi|157368473|ref|YP_001476462.1| RNA polymerase factor sigma-32 [Serratia proteamaculans 568]
 gi|157320237|gb|ABV39334.1| RNA polymerase, sigma 32 subunit, RpoH [Serratia proteamaculans
           568]
          Length = 285

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 121/242 (50%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V  +A+ Y+  GL   DLIQEGNIGLMKA  +F+  +G + 
Sbjct: 42  HYQGDLEAAKQLILSHLRFVAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRL 101

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      +++      R     + +T +R+    + E   E +A+
Sbjct: 102 VSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VELVAR 159

Query: 555 KLAMPVEGVRKVL-KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +L +  + VR++  ++  + ++ +    D+  +   +   +  ++  S     I+ +  E
Sbjct: 160 ELGVTSKDVREMESRMAAQDMTFDPTPDDDAREGQSMAPVLYLQDKSSDFAEGIEEDNWE 219

Query: 612 T-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +         +  L  R + ++R R+ +  +   TL+E+  Q+ V+ ER+RQ+E  A++K
Sbjct: 220 SNAADKLAYAMEGLDERSQHIIRARW-LDDDNKSTLQELADQYGVSAERVRQLEKNAMKK 278

Query: 667 LK 668
           LK
Sbjct: 279 LK 280


>gi|309378784|emb|CBX22610.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 287

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIRTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILKNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      + IA  L + +  V     ++T   I++     D+D +
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQSIADDLGVKLSEVLEMEQRMTGRDIAIMADNNDDDDN 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 252 HQLAAEYGVSAERIRQIEAKAMQKLR 277


>gi|257438785|ref|ZP_05614540.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
 gi|257198753|gb|EEU97037.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
          Length = 254

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 70/262 (26%), Positives = 137/262 (52%), Gaps = 14/262 (5%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V+T  + +        ++ +     + A++ M+E NLRLV+SV +++  RG  
Sbjct: 3   NKVELCGVDTAQLPVLSEAEKRQLLTRARAGDAAARQAMIEGNLRLVLSVVQRFAQRGEN 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G IGL+KA + FD     +FSTY +  +   I R + D +  +R+   +RD  
Sbjct: 63  LDDLFQVGCIGLIKAIDNFDPAQPVRFSTYGVPMIIGEIRRFLRDNN-ALRVSRSLRDAA 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSH 587
           +K ++    +  ++ REPT +E+A++  +    V   L+   EPISLE P+  +  D  +
Sbjct: 122 YKAMQAREALEKQLGREPTVDEVARQAGLSRREVNAALESVVEPISLEEPLYTDGGDAMY 181

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + D ++     S ++        + +A LTPRE+R++ +R+  G        EV +
Sbjct: 182 VIDQVRDPDSEDSWISGLE------FRQTVAGLTPREKRIMELRYLKGETQM----EVAR 231

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+ + +H
Sbjct: 232 EIGISQAQVSRLEKAALEQFRH 253


>gi|288942274|ref|YP_003444514.1| RNA polymerase sigma-32 subunit RpoH [Allochromatium vinosum DSM
           180]
 gi|288897646|gb|ADC63482.1| RNA polymerase, sigma 32 subunit, RpoH [Allochromatium vinosum DSM
           180]
          Length = 279

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/266 (24%), Positives = 124/266 (46%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I S      +++ E R +   +R  +     A K +V ++LR VI +A+ Y   GL
Sbjct: 13  IEAYINSAYQIPVLTLEEERSLAVRLR--DQNDMEAAKRLVTSHLRFVIRIARGYLGYGL 70

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEG +GLMKA  +F+  +G +  ++A+ W++  I   I      +++     + 
Sbjct: 71  PLPDLIQEGTVGLMKAVRRFEPDMGVRLVSFAVHWIRAEIHEYILRNWRIVKVATTKAQR 130

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE--TPIGDEDT 585
           K+   +R++++    + ++   E  A     P   ++   +++ + +S +      D+  
Sbjct: 131 KLFFNLRSSKKRLGWLTKQEVDEVAADLGVKPEVVLQMESRLSNQDLSFDGLEDDDDDSP 190

Query: 586 SHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +    ++ D   + +          + RE     LA L  R + +L  R+        TL
Sbjct: 191 AAPSTYLPDVRMEPSRLLEHEDTDRDQRERLYAALADLDERSKTILFERWLSEKKQ--TL 248

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+ ++F V+ ERIRQIE  A++K++
Sbjct: 249 HELAEKFGVSAERIRQIEKNAMKKVR 274


>gi|167507905|gb|ABZ81273.1| RpoD [Thalassospira sp. MCCC 1A00385]
 gi|167507921|gb|ABZ81281.1| RpoD [Thalassospira sp. MCCC 1A01109]
 gi|167507961|gb|ABZ81301.1| RpoD [Thalassospira sp. MCCC 1A02059]
          Length = 253

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 124/251 (49%), Gaps = 12/251 (4%)

Query: 179 TLLREIIDLEACIG--PESKGGFFHGTEGH-----SYQKREDSSQEKERDDVQETEGDIE 231
            LLR++IDLE   G  P+++ G   G +         +  + ++ +++ D   ET   I 
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIGAPEGEDEDVDAEADVESFDSANDDEDEDAETETPDAIG 60

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                 ++D    DS  E     +   +++ +    +LS ME++L  +V+   + IA+ Y
Sbjct: 61  GEEAEEEEDDESEDSEGEEGGEGDDEDEDENEQVNVSLSKMEEELTEQVLEKFELIAKTY 120

Query: 292 RELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            +L   Q+  +      ++       +   LK ++V+L+  + LN  RI+ L++ L  ++
Sbjct: 121 EKLHKAQEQRLVALNKGETVPAATEKRYTKLKNEMVELMEDVHLNNFRIEELLDHLTGLN 180

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
            R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK F+    + I
Sbjct: 181 NRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPNWMERVAGLPGKGWKTFIERYPEEI 240

Query: 407 LKIRNEIKSIS 417
            K+R +I  +S
Sbjct: 241 AKLREDIGGVS 251


>gi|32490821|ref|NP_871075.1| RNA polymerase factor sigma-32 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166027|dbj|BAC24218.1| rpoH [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 281

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 132/267 (49%), Gaps = 12/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + IK  +  + +SI E + +   +        +A K+++ ++LR V+ +++ Y+  GL
Sbjct: 15  LESYIKKANSYSMLSIEEEKILTERL--HYNGDLLAAKKLILSHLRFVVHISRNYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
           Q  DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  QRADLIQEGNVGLMKAVKRFNPAIGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + +  +++    + E   + +AK L +  + VR++               +ED  
Sbjct: 133 KLFFNLRKAKKKLGWFNQYE--VDMLAKSLGVTSKDVREMESRMSAKDMAFDFNSEEDKH 190

Query: 587 HLGDFIEDKNAVSPLDSAIQANLR-----ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                +  K+  S     I+ +       +  +  L++L  R + ++R R+ +  +   T
Sbjct: 191 KNNAILYLKDKTSDFADTIEEDNWDIHATDKLSAALSNLDLRSQEIIRSRW-LRYDNKST 249

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+ K++ ++ ERIRQ+E  A++K++
Sbjct: 250 LKELAKKYGISAERIRQLEKNAMKKIR 276


>gi|118470482|ref|YP_886176.1| RNA polymerase sigma factor SigF [Mycobacterium smegmatis str. MC2
           155]
 gi|25396413|dbj|BAC24795.1| alternative sigma factor SigF [Mycobacterium smegmatis]
 gi|118171769|gb|ABK72665.1| RNA polymerase sigma-F factor [Mycobacterium smegmatis str. MC2
           155]
          Length = 250

 Score =  126 bits (315), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 115/227 (50%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++++VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+  +
Sbjct: 29  REKIVERCLPLADHIARRFDGRGEPREDLVQVARVGLVNAVNRFDVEAGSDFVSFAVPTI 88

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D S ++++P  +++   ++      +S ++ R PT  E+A +L M  E V 
Sbjct: 89  MGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRAPTASELAHELDMDREEVV 148

Query: 565 KVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L    +   +S+++  G ++ +  + D + D +         Q + RE+   +LASL 
Sbjct: 149 EGLIAGSSYNTLSIDSGGGGDEEAPAIVDTLGDLD-----MGLDQIDNRESLRPLLASLP 203

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL +RF        T  ++ ++  +++  + ++ AK++ +L+
Sbjct: 204 ERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKSLARLR 246


>gi|303251140|ref|ZP_07337324.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253519|ref|ZP_07535389.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649991|gb|EFL80163.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859020|gb|EFM91063.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 316

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 129/266 (48%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+  +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGL 106

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +
Sbjct: 107 PLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQR 166

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS- 586
                    +       E   +++A+ L +  E VR++  ++T + +  + P+G++D   
Sbjct: 167 KLFFNLRKNKNRLAWFNEEEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDDDEV 226

Query: 587 -HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED +   A    D              LA+L  R + +++ R+        TL
Sbjct: 227 YTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDKRSQDIIKTRWLDE--EKATL 284

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++ +++ ++ ER+RQ+E  A++K+K
Sbjct: 285 QDLAEKYGISAERVRQLENAALKKIK 310


>gi|302537203|ref|ZP_07289545.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
 gi|302446098|gb|EFL17914.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
          Length = 278

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDIERSIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPTEGEVAGEMG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 158 IAVEE----LHTVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDR 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 214 ELRRLLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 269

Query: 668 K 668
           +
Sbjct: 270 R 270


>gi|153854687|ref|ZP_01995937.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
 gi|149752791|gb|EDM62722.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
          Length = 258

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 129/262 (49%), Gaps = 9/262 (3%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + +++   V T  + I   +   ++  + +     AK+E ++ NLRLV+SV +++   G
Sbjct: 2   AQGKVEICGVNTAKLPILNEKEKEALFVRIKAGDQEAKEEYIKGNLRLVLSVIRRFGASG 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA   F+  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAINNFNTELEVKFSTYAVPMIIGEIRRYMRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K +        K ++EPT +EIA+++ +  E +   L   + P+SL+ P+ ++    
Sbjct: 121 TAYKAIYAKENYMKKNQKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDA 180

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L    +  +  +  +  I+     +    +  L  RE  ++++RF  G     T  EV  
Sbjct: 181 LYVMDQLSDQTNKEEKWIEDL---SLEEAMKHLGERERYIIKLRFFQG----KTQMEVAD 233

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A++ ++ 
Sbjct: 234 EIQISQAQVSRLEKNALKTMRQ 255


>gi|312793875|ref|YP_004026798.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181015|gb|ADQ41185.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD  
Sbjct: 8   ELISKAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPS 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  E
Sbjct: 68  FNVRFSTYAVPMIIGEIKRYLRD-DGKIKVSRKIKENQSKIKKLRNQFVSSNGREPTISE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           I++   +  + +   +  T E  SL   +  E+     L D   D+   S     + A  
Sbjct: 127 ISQLTGLSSDEILLCMDATSEVASLNDVVNQEEGKPITLMDIASDEEDYSTKLLDLMA-- 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L  RE  ++ MR+        T  E+ K+  +++  + +IE +A+ ++K 
Sbjct: 185 ---LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKELNISQVHVSRIEKRALERIKR 237


>gi|115374575|ref|ZP_01461855.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823765|ref|YP_003956123.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|115368445|gb|EAU67400.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396837|gb|ADO74296.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 366

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 131/273 (47%), Gaps = 12/273 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +  ++    +   E   +    ++       A   +V +NLRLV+ +A +Y    L
Sbjct: 87  LQAYMAEVTRHPLLKREEEYALAKQYQQTG--DVRAAYRLVASNLRLVVKLAHEYHRNPL 144

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
             LDL+QEGNIGLM+A +K+D   G K S+YA WW++  I R I D    +++      R
Sbjct: 145 SLLDLVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQR 204

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDT 585
               K+ +   ++  +   EP P+ +A++L +  + V ++ +      +S++ P+GDE  
Sbjct: 205 KLFFKLRQEQDKLIAQ-GFEPNPKLLAERLNVTEQDVVEMDQRLGHDEVSIDAPVGDESR 263

Query: 586 SHLGDFIEDKNAVSPLDSAIQANL----RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +   D +   +AV   +      L    RE       +L  +E         +  +   T
Sbjct: 264 ASRADRLLPSSAVGAEERLGNEELKELFREKLAEFAQTLEGKER--FIFESRLTADEPLT 321

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L+++G ++ V+RER RQIEA  I +++   R +
Sbjct: 322 LQDIGDKYGVSRERARQIEAALINRMREFMRER 354



 Score = 43.7 bits (101), Expect = 0.096,   Method: Composition-based stats.
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 1/91 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           +   +E    D+      A  + V      +    +  DP++ Y+ E+    LL RE E 
Sbjct: 47  EPAPEELAEADAEVEELEAPTAPVRALVPVEDTGLARKDPLQAYMAEVTRHPLLKREEEY 106

Query: 141 AIAKRIEA-GRAMMMASLCESPLTFQALIIW 170
           A+AK+ +  G       L  S L     +  
Sbjct: 107 ALAKQYQQTGDVRAAYRLVASNLRLVVKLAH 137


>gi|302127753|emb|CBL51730.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 262

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +   + +
Sbjct: 58  -----------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDGDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
              DE +      ++                  E + ELR+  +   ++ QK+ ++  + 
Sbjct: 95  DADDEGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDET 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + D +L+   +++ I  +TG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLLEMDED-VLRAIGKLQQIEEKTGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|153440|gb|AAC36891.1| minor sigma-like factor [Streptomyces aureofaciens]
 gi|743686|prf||2013252A RNA polymerase:SUBUNIT=sigma factor
          Length = 278

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 105/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDIERSIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPTEGEVAGEMG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E          D   L D +ED  A  P++ A   
Sbjct: 158 IGVEE----LHTVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDHAADDPVEVAEDR 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 214 ELRRLLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 269

Query: 668 K 668
           +
Sbjct: 270 R 270


>gi|299783172|gb|ADJ41170.1| RNA polymerase sigma factor [Lactobacillus fermentum CECT 5716]
          Length = 287

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 92/261 (35%), Positives = 137/261 (52%), Gaps = 28/261 (10%)

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           +  +++   L EK+ +      LN   +D L++ + D    ++   G+    A       
Sbjct: 35  KAKNIQYDELTEKIAE---PFGLNADGMDALLQNVEDAGVSVVDENGDPDLRALKA---- 87

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                               K   +          +     +R  +K I     ++  E 
Sbjct: 88  ------------------TEKLSSKALKDTTAPSSIKINDPVRMYLKEIGRVNLLTADEE 129

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             +   + K       AK+E+ EANLRLV+S+AK+Y  RG+QFLDLIQEGN+GLMKA EK
Sbjct: 130 VALALRIEK---GDETAKQELAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEK 186

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R++   + REP
Sbjct: 187 FDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREP 246

Query: 548 TPEEIAKKLAMPVEGVRKVLK 568
            PEEI  ++ M  + VR +L 
Sbjct: 247 LPEEIGAEMDMDTQKVRDILN 267



 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 55/217 (25%), Positives = 92/217 (42%), Gaps = 23/217 (10%)

Query: 1   MTIGKKRNR-DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFL-PPDEV 58
           M    K+NR  S+ E  +  +       D +   +I+  ++   +  +EL   +  P  +
Sbjct: 1   MAKSSKKNRVISNLEDFNQAE------YDKAVGALIRNYKKAKNIQYDELTEKIAEPFGL 54

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
           +++ M+  +  + + G++VVD      E G  D   L ++   SS  L+     +    +
Sbjct: 55  NADGMDALLQNVEDAGVSVVD------ENGDPDLRALKATEKLSSKALKDTTAPSSIKIN 108

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPVRMYL+E+G + LL+ + E+A+A RIE G       L E+ L     I  R  +  G 
Sbjct: 109 DPVRMYLKEIGRVNLLTADEEVALALRIEKGDETAKQELAEANLRLVVSIAKRY-VGRGM 167

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
             L  I         E   G     E   Y+K    S
Sbjct: 168 QFLDLI--------QEGNMGLMKAVEKFDYRKGFKFS 196


>gi|238021049|ref|ZP_04601475.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
 gi|237868029|gb|EEP69035.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
          Length = 290

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 133/267 (49%), Gaps = 12/267 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +++ E     S+ ++       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 16  LEQYIHTVNSIPMLTLEEE---TSLAQRQLRGDLEAAKQLILSHLRVVVSIARGYDGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +RI     + 
Sbjct: 73  NQADLIQEGNVGLMKAVKRFEPTHGARLFSFAVHWIKAEIHEFILRNWRLVRIATTKPQR 132

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  + +      ++IA  L + +  V     ++T   ++L     D+D +
Sbjct: 133 KLFFNLRSMRKSLSALSP-KEAQDIADDLGVKLSDVLEMEQRMTGNDVALLADNSDDDDN 191

Query: 587 HLG--DFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    D++ D ++         A  A   E     L+ L  R  R++  R+        T
Sbjct: 192 NFAPIDWLSDDSSEPSQQLAKKAHYALQTEGLRNALSQLDERSRRIVETRWLQDDGG-LT 250

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E+  +F V+ ERIRQIEAKA++KL+
Sbjct: 251 LHELAAEFGVSAERIRQIEAKAMQKLR 277


>gi|319407753|emb|CBI81400.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 303

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R        A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD   G
Sbjct: 46  LRWKNKRDDNAMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRG 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI-----HKVVRTARRMSNKIKREPT 548
            +FSTYA WW++ +I   I      +R       K       ++     +  N + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLAQDDNTLTKQEI 165

Query: 549 PEEIAKKLAMPVEGVRKVLKI---TKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDS 603
              I++KL + V  V K+      T   +SL      E      D + D + +  S ++ 
Sbjct: 166 FRAISEKLGVSVNDVEKMDFRFSGTDNSLSLSISENGETPIAKMDSLIDDHPLPDSVIEQ 225

Query: 604 AIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           AI    R +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 AIDGQRRAQWLHEALQILNERELEIIR--FRRLNEEGTTLEVLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|261344963|ref|ZP_05972607.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
 gi|282567106|gb|EFB72641.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
          Length = 291

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 65/271 (23%), Positives = 132/271 (48%), Gaps = 16/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    +S  E + +   +         A K+++ ++LR VI +A+ Y   GL
Sbjct: 16  IEAYIRAANTYPMLSAEEEKELAERL--HYDGDLEAAKQLILSHLRFVIHIARSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                + +  +R+    + E   + +A++L +  + V ++               D+D+ 
Sbjct: 134 KLFFNLRKNKKRLGWFNQDE--VDMVAQELGVSTKDVLEMESRMAAQDMAFDMSDDDDSG 191

Query: 587 HLGD------FIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
             G       +++DK++    S  D   +++  +  +  LASL  R + ++R R+ +  +
Sbjct: 192 DFGGPIAPVLYLQDKSSDFAGSIEDDNWESHATDRLSDALASLDERSQDIIRARW-LDDD 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 SKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|261400394|ref|ZP_05986519.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313668808|ref|YP_004049092.1| RNA polymerase sigma-32 factor [Neisseria lactamica ST-640]
 gi|269209833|gb|EEZ76288.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313006270|emb|CBN87733.1| putative RNA polymerase sigma-32 factor [Neisseria lactamica
           020-06]
          Length = 290

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 20  LEQYIRTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 77  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILKNWRLVRVATTKPQR 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      + IA  L + +  V     ++T   I++     D+D +
Sbjct: 137 KLFFNLRSMRKNLNALSP-KEAQSIADDLGVKLSEVLEMEQRMTGRDIAIMADNNDDDDN 195

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 196 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 254

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQIEAKA++KL+
Sbjct: 255 HQLAAEYGVSAERIRQIEAKAMQKLR 280


>gi|312884403|ref|ZP_07744108.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367925|gb|EFP95472.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 285

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 120/236 (50%), Gaps = 14/236 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A K ++ ++LR V+ VA+ Y+  GL   DL+QEGNIGLMKA ++F+  +G +  ++A+ 
Sbjct: 48  DAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVH 107

Query: 503 WVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           W+K  I   +      ++I      R     + ++ +R+    + E   E +A++L +  
Sbjct: 108 WIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNQGE--VETVARELGVEP 165

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSH-----LGDFIEDKN---AVSPLDSAIQANLRET 612
             VR++        +      D+D +H        ++EDK    A +   +  +A+    
Sbjct: 166 SEVREMESRLAAQDATFEVPSDDDDAHTSYVAPMVYLEDKASDIADNIEAANWEAHTNNR 225

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L SL  R + ++R R+     +  TL+E+ + + V+ ERIRQ+E  A++KLK
Sbjct: 226 LSLALKSLDERSQHIVRSRWLDDNKS--TLQELAETYQVSAERIRQLEKNAMKKLK 279


>gi|309785782|ref|ZP_07680413.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|308926902|gb|EFP72378.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|315614730|gb|EFU95370.1| alternative sigma factor RpoH [Escherichia coli 3431]
 gi|323162701|gb|EFZ48540.1| alternative sigma factor RpoH [Escherichia coli E128010]
 gi|323164790|gb|EFZ50582.1| alternative sigma factor RpoH [Shigella sonnei 53G]
 gi|323179012|gb|EFZ64586.1| alternative sigma factor RpoH [Escherichia coli 1180]
 gi|323182926|gb|EFZ68327.1| alternative sigma factor RpoH [Escherichia coli 1357]
 gi|323188948|gb|EFZ74232.1| alternative sigma factor RpoH [Escherichia coli RN587/1]
 gi|327251097|gb|EGE62790.1| alternative sigma factor RpoH [Escherichia coli STEC_7v]
          Length = 257

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 126/256 (49%), Gaps = 14/256 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL   DLIQEGNIGL
Sbjct: 2   LSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRM 539
           MKA  +F+  +G +  ++A+ W+K  I   +      +++      R     + +T +R+
Sbjct: 60  MKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSH-LGDFIEDKNA 597
               + E   E +A++L +  + VR++  ++  + ++ +    D+  S  +   +  ++ 
Sbjct: 120 GWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQDK 177

Query: 598 VSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            S     I+ +  E       T  +  L  R + ++R R+ +  +   TL+E+  ++ V+
Sbjct: 178 SSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNKSTLQELADRYGVS 236

Query: 653 RERIRQIEAKAIRKLK 668
            ER+RQ+E  A++KL+
Sbjct: 237 AERVRQLEKNAMKKLR 252


>gi|52546480|dbj|BAD51623.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|52546482|dbj|BAD51624.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|52546484|dbj|BAD51625.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
          Length = 281

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/316 (17%), Positives = 118/316 (37%), Gaps = 36/316 (11%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEEGLKHMVQAISACPTTIADILGMAERVANDEIRVDELVD----- 55

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                 G        +     + + E   D  +E E + + A     ++     +     
Sbjct: 56  ------GLLDAEAAEAAANEAELASEDSDDMDEEEEEEEDDAEDDEDEEDGDEGA----- 104

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                         A   +A  + L+   +    +I+  +  +R   +      K+   S
Sbjct: 105 ------------RQASANAAQLEALKRAALEKFGKISTEFSAMRDAYE------KEGYQS 146

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVF 370
                 +E + + + S+      ++ L + L    + +   E +LL  +    G+ R  F
Sbjct: 147 PAYLHAQEAIQQELTSIRFTARTVERLCDTLRAQVEEVRSVERQLLATVVDRCGMSRAEF 206

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           ++R  G E +  W + A       +   +   + +I + + ++  +     + + + +  
Sbjct: 207 IQRFPGNETNLEW-AQAIVDERHPYSAVLERNIPAIREQQQKLIDLQARVVLPLGDLKET 265

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 266 NRQMASGELKARQAKR 281


>gi|221195774|ref|ZP_03568827.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
 gi|221184248|gb|EEE16642.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
          Length = 276

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 124/240 (51%), Gaps = 12/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  E   S  + +++ ++L LV  +A K+ NRG    DLIQ G IGL+KA ++FD   G
Sbjct: 36  AQYQETHDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGTIGLIKAIDRFDPSRG 95

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F+TYA   +   I R   D+  ++R+P  +++   KV +    ++ +++R P+ EEIA
Sbjct: 96  LEFTTYATPTIMGEIKRHFRDKGWSVRVPRRLQELSAKVNQITDELTTELQRSPSIEEIA 155

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA----NL 609
           KKL + V+ V + ++ +    S    +  E      D  E  + +    +  +A    + 
Sbjct: 156 KKLGVSVDEVLEAMESSGAYSS----VPLEGGGSSVDGDEAPSIIDQYITEDEALAGSDD 211

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R      +A  +PRE+ ++RMRF  G     T  E+ ++  +++ ++ ++  + +++++ 
Sbjct: 212 RIVLEDAIADFSPREQEIIRMRFVEG----LTQVEIAEKLGISQVQVSRLLRRTLKRIQE 267


>gi|282861385|ref|ZP_06270450.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
 gi|282564043|gb|EFB69580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
          Length = 278

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDLERAIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQLRRTPTEAEVAAEMG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 158 IALEE----LHSVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEIAEDR 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 214 ELRRMLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 269

Query: 668 K 668
           +
Sbjct: 270 R 270


>gi|254775435|ref|ZP_05216951.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
          Length = 242

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 107/240 (44%), Gaps = 8/240 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +     E    ++ +V   L L   VA  +  RG    DL+Q   +GLM A  +FD 
Sbjct: 5   LRRMPAESHEYRRQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDP 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   + R   D S  +R+P  +R+   ++ RT   ++ ++ R P   
Sbjct: 65  AKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHVQISRTTADLAQQLGRAPNAG 124

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+++ L +P E + + L         SL+ P G + +       +    + P    I   
Sbjct: 125 ELSQVLEVPREEIVECLVAGDAYRLDSLDAPQGADSSGTPRSVADSVGDIDPQIEHITN- 183

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE    ++A+L  RE  VLRMRF        T  ++ ++  V++ ++ +I A  +R L+
Sbjct: 184 -REALRVLVATLPHREREVLRMRFF----ESMTQSQIAERIGVSQMQVSRILANTLRCLR 238


>gi|167748837|ref|ZP_02420964.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
 gi|167651807|gb|EDR95936.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
          Length = 275

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 76/269 (28%), Positives = 131/269 (48%), Gaps = 17/269 (6%)

Query: 406 ILKIRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           I+   N+++   V T    +  +E +    +  + E     A+++ ++ NLRLV+SV ++
Sbjct: 16  IIMALNKVEICGVNTASLPLLTNEEKE--ELFIRIEQGDQEAREQYIKGNLRLVLSVIQR 73

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           ++       DL Q G IGLMKA + FD  L  KFSTYA+  +   + R + D +   R+ 
Sbjct: 74  FSGSNENADDLFQVGCIGLMKAIDNFDRSLNVKFSTYAVPMIIGEVRRYLRDNNSM-RVS 132

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +RD  +K +     ++ K  +EPT E IA+++ M  E V   L     P+SL  P+  
Sbjct: 133 RSLRDIAYKAITAKEALTKKFNKEPTIEAIAEEIEMKKEDVLFALDAIATPLSLYEPVYQ 192

Query: 583 E--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           +  DT  L D ++DK     L     A         +  L  RE  ++R+RF  G     
Sbjct: 193 DGGDTLFLMDQVKDKKNKEELWVESIA-----LKDAMEHLPEREYNIIRLRFFDG----K 243

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T  EV  +  +++ ++ ++E  A++ +KH
Sbjct: 244 TQTEVADEISISQAQVSRLEKNALKHMKH 272


>gi|182435659|ref|YP_001823378.1| RNA polymerase sigma factor WhiG [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326776293|ref|ZP_08235558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
 gi|178464175|dbj|BAG18695.1| putative RNA polymerase sigma factor WhiG [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656626|gb|EGE41472.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
          Length = 278

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 105/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERAIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  + +R P+  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQFRRTPSEAEVASEMG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 158 IALEE----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDR 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 214 ELRRLLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 269

Query: 668 K 668
           +
Sbjct: 270 R 270


>gi|328542017|ref|YP_004302126.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326411767|gb|ADZ68830.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 289

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 125/272 (45%), Gaps = 15/272 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  +K+      ++  E   + +  R+ +  A  A + +  A++RLVI+VA ++ N GL 
Sbjct: 9   RQLVKAAMNAPYLTREEELELATRWRQDKDVA--ALERLSLAHMRLVIAVASRFRNFGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DLIQEG++GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  MNDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSTQKA 126

Query: 529 -IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   ++S+    +       +IA+ + +    V     +++    SL  PI D 
Sbjct: 127 LFFNLRRLRAKLSSNRVDLPETELHRQIAEAIGVKTADVDLMNARLSGPDTSLNAPIIDS 186

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D S     DF+     +     +   +    R      +  LT RE +++          
Sbjct: 187 DGSSADRQDFLISDAPLPDETVSENIDSERQRRWLRSAMNVLTERERKIVSE--RRLTEE 244

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             TLE +G +  +++ER+RQIE +A+ KL+  
Sbjct: 245 GATLEALGAKMGISKERVRQIENRALEKLREA 276


>gi|121603798|ref|YP_981127.1| RNA polymerase sigma-32 subunit RpoH [Polaromonas naphthalenivorans
           CJ2]
 gi|120592767|gb|ABM36206.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas
           naphthalenivorans CJ2]
          Length = 322

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 65/287 (22%), Positives = 129/287 (44%), Gaps = 23/287 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ + +     +++     S    ++V ++LRLV+S+++K
Sbjct: 33  VPPLGNLDAYISAVNRLPMLTLEQEQEFSKKLKENNDLDS--AGKLVLSHLRLVVSISRK 90

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGNIGLMKA ++FD     +  +YAM W+K  I   I      +++ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVA 150

Query: 523 VH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----------VEGVRKVLKITK 571
               + K+   +R+ ++         T  +   +  +            E +    +++ 
Sbjct: 151 TTKAQRKLFFNLRSMKQGYKDDADVATHRDTLTESQIDSMARTLNVKREEVIEMEQRMSG 210

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREER 626
             + L+    D+     G      +A     + +++  R+          L  L PR  R
Sbjct: 211 GDVLLDPSPNDDGDDAFGPIAYLADAAQEPTALMESRERDDLMTDGLSTALQELDPRARR 270

Query: 627 VLRMRFGIGMNTD----HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++  R+ + +N D     TL ++  ++ V+ ERIRQIE  A++K+K 
Sbjct: 271 IVEERW-LNVNDDGSGGMTLHDLAAEYKVSAERIRQIEVAAMKKMKK 316


>gi|266624907|ref|ZP_06117842.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
 gi|288863210|gb|EFC95508.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
          Length = 258

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 119/249 (47%), Gaps = 14/249 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  +E +   ++ ++       A++E ++ NLRLV+SV ++++       DL Q G IGL
Sbjct: 18  LLNNEEKE--ALFKRILDGDMEAREEYIKGNLRLVLSVIQRFSGSNENVDDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     +FSTYA+  +   + R + D +  IR+   +RD  +K +     +  
Sbjct: 76  IKAIDNFDITQNVRFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAYKAIYAKENLMK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVS 599
           K  +EPT  EIA ++ +  E +   L   + P+SL  P+  +    L   D I DK  + 
Sbjct: 135 KNLKEPTIMEIADEIGVSKEDITYALDAIQNPVSLYEPVYSDGGDPLFVMDQISDKKNLE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                  +         +  L  RE  ++ MRF  G     T  EV ++  +++ ++ ++
Sbjct: 195 ENWVEDIS-----LNEAMKRLPERERHIIDMRFFEG----KTQTEVAEEIHISQAQVSRL 245

Query: 660 EAKAIRKLK 668
           E  A++ +K
Sbjct: 246 EKNALKSMK 254


>gi|21672319|ref|NP_660386.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|25091196|sp|Q8KA76|RP32_BUCAP RecName: Full=RNA polymerase sigma-32 factor
 gi|21622919|gb|AAM67597.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 285

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/277 (22%), Positives = 134/277 (48%), Gaps = 15/277 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            V ++  +   I+  ++   +SI E + +   +R  +     A K ++ ++LR VI +++
Sbjct: 9   SVTALGNLDAYIRIANLWPMLSIKEEKLLTKRLRYHD--DLDAAKTLILSHLRFVIHISR 66

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR- 520
            Y+  GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++ 
Sbjct: 67  NYSGYGLLQADLIQEGNIGLMKAVRRFNPDIGVRLVSFAVHWIKSEIHEYVLRNWRIVKV 126

Query: 521 -IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET 578
                 R     + +  +R+    + E   E +A++L +  E VR++  +++ + I+   
Sbjct: 127 ATTKSQRKLFFNLRKNKKRLGWFNQEEI--EIVARELGVSSEDVREMESRMSAQDITFNP 184

Query: 579 PIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMR 631
              ++  D    G+    ++  S   + ++ +          +  L  L  R   ++R R
Sbjct: 185 FPEEDLKDGKINGNMFYLQDKTSNFANGLEQDNWNKHTTSKLSNALLRLDERSRNIIRAR 244

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +     +TL+++   + ++ ER+RQ+E  A++KLK
Sbjct: 245 W-LDKKEKNTLQKIANNYGISAERVRQLEKNAMKKLK 280


>gi|325674621|ref|ZP_08154308.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
 gi|325554207|gb|EGD23882.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
          Length = 262

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 120/248 (48%), Gaps = 12/248 (4%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ++E    ++    G+   +  +  +V  +L L  ++A+++++RG +  DL Q   +GL+ 
Sbjct: 19  VAELFAELANCDPGDERGTALRDRIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLIN 78

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++FD   G  F+ YA+  +   + R   D +   R+P  ++D    V +    +S ++
Sbjct: 79  AVDRFDPAQGSSFAAYAVPTIMGEVRRYFRDHAWAARVPRRLKDLTLDVGKATEALSQRL 138

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSP 600
            R PT  E+A +L    + V + +      +  SL++P+G +  S  L D +   +    
Sbjct: 139 GRSPTAHELATELGTDPDSVMEAIAAAGAYQTHSLDSPVGRDGESATLADTLATDD---- 194

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                Q  L      ++  L PRE+R++ MRF      + T  E+ ++  V++ +I ++ 
Sbjct: 195 -VDLEQTELHLALQPLIDQLEPREKRIVVMRFF----EERTQTEIAREIGVSQVQISRLL 249

Query: 661 AKAIRKLK 668
           +K + +++
Sbjct: 250 SKILARIR 257


>gi|260755457|ref|ZP_05867805.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758679|ref|ZP_05871027.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260884475|ref|ZP_05896089.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214728|ref|ZP_05929009.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261750913|ref|ZP_05994622.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|265984775|ref|ZP_06097510.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294851008|ref|ZP_06791684.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
 gi|260668997|gb|EEX55937.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260675565|gb|EEX62386.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260874003|gb|EEX81072.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916335|gb|EEX83196.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261740666|gb|EEY28592.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|264663367|gb|EEZ33628.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294821651|gb|EFG38647.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
          Length = 293

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 74/267 (27%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKERVRQIESRAMEKLK 279


>gi|291545415|emb|CBL18523.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. SR1/5]
          Length = 259

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 133/268 (49%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + + +      + ++ +     A++  ++ NLRLV+SV +++ N  
Sbjct: 2   ALNKVEICGVNTSTLPVLDQEEKAELFKRIKAGDEEARELYIKGNLRLVLSVIRRFQNSS 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAIDNFDTTLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K + T      +  +EPT  EIA ++ +  E +   +   + P+SL  P+  E  DT
Sbjct: 121 IAYKTIYTRENYMRQHLKEPTIAEIADEIGIDKEMIVYAMDAIQSPVSLFEPVYSEGGDT 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I DK  +   +     +LR+     +  L  RE  ++ +RF  G     T  EV
Sbjct: 181 LYVMDQISDKKNLE-ENWVEDISLRD----AMNRLGERERHIIDLRFYEG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +  +++ ++ ++E  A+R +++  R+
Sbjct: 232 ADEIGISQAQVSRLEKHALRSMRNYLRN 259


>gi|187763274|gb|ACD35514.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 271

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 113/315 (35%), Gaps = 45/315 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                             + E  A  +    S++       E++
Sbjct: 52  ----------------------------SGNDPNETEDMAPTATHIGSELGEDDLADEDE 83

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 84  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W    K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFENQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 257 MSIGEAKALRAKKEM 271


>gi|126664542|ref|ZP_01735526.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
 gi|126630868|gb|EBA01482.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
          Length = 286

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 131/268 (48%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ S    +++ E R +   +         A ++++ ++LR VI +A+ Y+  GL
Sbjct: 17  LESYIQAASRIPILTVDEERALSERL--YYEGDVDAARQLILSHLRFVIHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DL+QEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  NQSDLVQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R  ++    +  +     +A  L +    VR++  +++    + + P+ D++ S
Sbjct: 135 KLFFNLRGQKKKLAWLSHDELNA-VAADLGVEARVVREMEGRLSSHDTAFDGPMNDDEDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     A     S    +      + L+SL  R + +LR R+     T  
Sbjct: 194 AYQAPAYYLEDHRSNPATQLERSNWTEDSNGRLMQALSSLDDRSQDILRERWL--SETKS 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQ+E  A++K++
Sbjct: 252 TLHQLADRYGVSAERIRQLEKNAMKKIR 279


>gi|145590108|ref|YP_001156705.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048514|gb|ABP35141.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 309

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 131/268 (48%), Gaps = 10/268 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +S +E  H+    R+ E     A K +V ++LRLV+SVA++Y   G+
Sbjct: 36  LDSYIAYVNRVPMLSAAEELHLAQEFRRTENVD--AAKTLVLSHLRLVVSVARQYLGYGI 93

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA +++D   G +  +YA+ W+K  I   I      ++       +
Sbjct: 94  PHADLIQEGNIGLMKAVKRYDPNNGARLVSYAIHWIKAEIHEYILKNWRLVKTATTKAQR 153

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + + +         + +AK L +    V+++ +++    I+LE    D+++++
Sbjct: 154 KLFFNLRSNKPTLSALTPSEVDALAKALDVKGSDVKEMEMRLAGGDIALEGDDSDDESAY 213

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRE--TTTRVLASLTPREERVLRMRFGIGMNT---DH 640
             +    ++    +   ++ +A+  +     + L SL  R   +++ R+           
Sbjct: 214 APIQWLADNTQEPTARIASAEADALQGPRLDQALMSLDERSRNIVQSRWLAMDAEGNGTK 273

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ ++ ER+RQIE  A++K++
Sbjct: 274 TLHDLAAEYGISAERVRQIETAALKKMR 301


>gi|300114350|ref|YP_003760925.1| RNA polymerase sigma 32 subunit RpoH [Nitrosococcus watsonii C-113]
 gi|299540287|gb|ADJ28604.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus watsonii
           C-113]
          Length = 287

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 123/269 (45%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +    ++      +S  + R +   +R+       A +++V ++LR VI +A+ Y   GL
Sbjct: 20  LNTYCQNAHSIPVLSADQERSLALRLRQY--NDLEAARQLVLSHLRFVIRIARGYNGYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD   G +  ++A+ W++  I   I      +++      R
Sbjct: 78  PLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQR 137

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                +    +R+    ++E    E+A+ L +  + V ++  +++ +    +    +E  
Sbjct: 138 KLFFNLRSAKKRLGWLNRKE--VNEVAQDLGISPKQVMEMEARLSSQDTPFDGTNTEESE 195

Query: 586 SHL---GDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           + L     ++ D +A           +    +   + L  L  R   ++  R+     + 
Sbjct: 196 NSLPAPMAYLADPSADPAQKMELLDQENYYGQRLRQALEVLDLRSRTIINRRWLQENKS- 254

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ ++ ERIRQ+E  AI+K++
Sbjct: 255 -TLHELAAEYQISAERIRQLENNAIKKMR 282


>gi|312127292|ref|YP_003992166.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311777311|gb|ADQ06797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++FD  
Sbjct: 8   ELISKAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPS 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  E
Sbjct: 68  FNVRFSTYAVPMIIGEIKRYLRD-DGKIKVSRKIKENQGKIKKLRNQFVSNHGREPTISE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           I++   +  + +   L  + E  SL   I  E+     L D   D+   S     + A  
Sbjct: 127 ISQLTGLSSDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA-- 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L  RE  ++ MR+        T  E+ K+  +++  + +IE +A+ ++K 
Sbjct: 185 ---LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKELNISQVHVSRIEKRALERIKR 237


>gi|254465185|ref|ZP_05078596.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
 gi|206686093|gb|EDZ46575.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
          Length = 292

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 68/275 (24%), Positives = 123/275 (44%), Gaps = 18/275 (6%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +       +     R +       +     +   ++ A +RL IS+A K+   G    DL
Sbjct: 13  RQAMKAELLDADTERRLA--YAWRDDRDVESLHRLINAYMRLAISMAAKFKRYGAPMNDL 70

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVH 524
           IQE  +GLMKAA+KFD   G +FSTYA+WW+K +I   +      +R            +
Sbjct: 71  IQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFN 130

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDE 583
           MR    ++ R AR     + +    ++IA ++ +P+  V  +  +++    SL      +
Sbjct: 131 MRRVQAQLEREARSSGVPLDQHQLHQKIATEIGVPLRDVEMMEGRLSGADFSLNAVQSTD 190

Query: 584 DTS-HLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +      D +ED  + +      + +   LR+     L +L  RE  ++  R        
Sbjct: 191 EEGREWIDALEDDASQAEDLVQERHDRRQLRKWLVTALQALNDRERFIITERKLRD--RP 248

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TLE +G +  +++ER+RQ+EA A +K++    S+
Sbjct: 249 RTLESLGTELGLSKERVRQLEAGAFQKMRKSLESQ 283


>gi|293609550|ref|ZP_06691852.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828002|gb|EFF86365.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 288

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 121/272 (44%), Gaps = 11/272 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + E    D+D 
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 195

Query: 586 SHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       ++ED     A    +   +          +  L  R   +L+ R+     + 
Sbjct: 196 TPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDDKS- 254

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TL E+  ++ V+ ERIRQ+E  A+ K+K   
Sbjct: 255 -TLHELAAEYNVSAERIRQLEKNAMEKIKTAM 285


>gi|312138386|ref|YP_004005722.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311887725|emb|CBH47037.1| putative sigma-70 factor [Rhodococcus equi 103S]
          Length = 262

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 120/248 (48%), Gaps = 12/248 (4%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           ++E    ++    G+   +  +  +V  +L L  ++A+++++RG +  DL Q   +GL+ 
Sbjct: 19  VAELFAELANCDPGDERGTALRDRIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLIN 78

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A ++FD   G  F+ YA+  +   + R   D +   R+P  ++D    V +    +S ++
Sbjct: 79  AVDRFDPAQGSSFAAYAVPTIMGEVRRYFRDHAWAARVPRRLKDLTLDVGKATEALSQRL 138

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSP 600
            R PT  E+A +L    + V + +      +  SL++P+G +  S  L D +   +    
Sbjct: 139 GRSPTAHELATELGTDPDSVMEAIAAAGAYQTHSLDSPVGRDGESATLADTLATDD---- 194

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                Q  L      ++  L PRE+R++ MRF      + T  E+ ++  V++ +I ++ 
Sbjct: 195 -VDLEQTELHLALRPLIDQLEPREKRIVVMRFF----EERTQTEIAREIGVSQVQISRLL 249

Query: 661 AKAIRKLK 668
           +K + +++
Sbjct: 250 SKILARIR 257


>gi|212637488|ref|YP_002314013.1| RNA polymerase factor sigma-32 [Shewanella piezotolerans WP3]
 gi|212558972|gb|ACJ31426.1| RNA polymerase sigma-32 factor [Shewanella piezotolerans WP3]
          Length = 285

 Score =  125 bits (314), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 123/268 (45%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I S    + +   +   +   ++  E     A KE++ ++LR V+ VAK Y+  GL
Sbjct: 19  LESYIHSAHSISMLDAEKEHELAKRLQ--ETGDLSAAKELIMSHLRFVVHVAKGYSGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDED- 584
                + +T +R+      E     +A+ L +    V     ++  +  + +    ++D 
Sbjct: 137 KLFFNLRKTKKRLGWFSDNEVGM--VAESLGVSKADVTEMESRMAAQDPAFDLASDNDDE 194

Query: 585 -TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED +   A    +   + + +      + +L  R + +L+ R+        
Sbjct: 195 QDYAPMHYLEDHSSDLASQVENDNWEQSNQTRLLSAIKTLDERSQHILQARWL--NEDKT 252

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 253 TLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|254381148|ref|ZP_04996513.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194340058|gb|EDX21024.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 306

 Score =  125 bits (313), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/280 (21%), Positives = 131/280 (46%), Gaps = 28/280 (10%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVA 460
           ++   +  I     ++ ++ R +  +       + +G  +   A+  ++E N+ LV   A
Sbjct: 30  QLAGPLPRIDNAREVTPADARELSRLFLVRLRELEEGTRDYQYARNTLIEMNISLVRFAA 89

Query: 461 KKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           +++T R   G++  D+IQ G IGL+KA ++FD     +FST A+ ++   I R   D + 
Sbjct: 90  RRFTARINAGIELDDVIQVGTIGLIKAIDRFDPDREVEFSTLALPYITGEIKRYFRDTTW 149

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPIS 575
            + +P  +++   ++ +    ++  + R P+ +EIA+ L +  E V + L         S
Sbjct: 150 AVHVPRRLQELRVELAKCQETLTEVLGRAPSVKEIAEHLELSEEEVIEGLVAANGYSSAS 209

Query: 576 LETPIGDED-------TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           L++  G  D          L D + D +    L   +      T   +L+ L  R+ ++L
Sbjct: 210 LDSTAGTTDRPAALSEGRPLADTVGDIDPAMVLFEDVH-----TLAPLLSELDERDLQIL 264

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RMRF      + T  E+G +  +++ ++ ++  + + +L+
Sbjct: 265 RMRFA----REMTQAEIGTELGISQMQVSRLLTRILTRLR 300


>gi|229075781|ref|ZP_04208758.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
 gi|229098543|ref|ZP_04229484.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|229104680|ref|ZP_04235342.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|229117569|ref|ZP_04246941.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228665889|gb|EEL21359.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228678744|gb|EEL32959.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|228684865|gb|EEL38802.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|228707333|gb|EEL59529.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
          Length = 252

 Score =  125 bits (313), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVKNEKKKPQLKDHELK---ALIQKSQGGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMRDELSKEFGRAPTINEVAEALELTPEEVVLAQEASRPPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|291004131|ref|ZP_06562104.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 328

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 111/238 (46%), Gaps = 15/238 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWCLG 493
           +      +  +V     LV  VA +    GL       DLIQ G  GL+ A EKF+   G
Sbjct: 92  QQRDQELRDRLVLHYAPLVKYVAGR-VGTGLPSHVEVSDLIQSGIFGLVDAIEKFEPERG 150

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF TYAM  ++ AI   +  Q     +P  +R +   V R   R+  K++R  +  E+A
Sbjct: 151 LKFETYAMQRIRGAILDDLRAQDW---VPRSVRSRARDVERALERLEAKLQRTASDAELA 207

Query: 554 KKLAMPVEGVRKVLKITKE--PISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++L + V+ +R++    +    ++L+  IG    TS L + + D  A  P+ + +  + R
Sbjct: 208 EELELSVDELRELFAQLQMTSVVALDDLIGAGQTTSSLAETLPDDRAEDPVATLVDRDSR 267

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +  L+ R+  V+ + +        TL E+GK   VT  R+ Q+  +A+ +L+
Sbjct: 268 RQLAEAVERLSDRDRIVVTLYYFEN----LTLAEIGKVLGVTESRVCQLHTRAVLRLR 321


>gi|221065333|ref|ZP_03541438.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
 gi|220710356|gb|EED65724.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
          Length = 324

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/291 (21%), Positives = 122/291 (41%), Gaps = 25/291 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    +++ E +     ++  E     A   +V ++LRLV+S++++
Sbjct: 31  VPPLGNLDAYISAVNRMPMLTLEEEQDYARKLK--EHNDLDAAGRLVMSHLRLVVSISRQ 88

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 89  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 148

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP---------------VEGVRKVL 567
                +       + +   K       +E+A +  +                 E +    
Sbjct: 149 TTKAQRKLFFNLRSMKHELKSDAAMADDELALRETLTSNEIDAVAAKLNVKREEVIEMET 208

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTP 622
           ++    + L+    D+     G      +A     + +++  R+          L  L  
Sbjct: 209 RLAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDD 268

Query: 623 REERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R  R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K  
Sbjct: 269 RSRRIVEERWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKA 319


>gi|222529665|ref|YP_002573547.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456512|gb|ACM60774.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 232

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 116/239 (48%), Gaps = 12/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+ + +    +A+++++E NL LV SV KK+  +G++  DL Q G+IGL+KA ++FD   
Sbjct: 1   MISRAKNGDKLARQQLIENNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPSF 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  EI
Sbjct: 61  NVRFSTYAVPMIIGEIKRYLRD-DGKIKVSRKIKENQGKIKKLRNQFVSNHGREPTISEI 119

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   L  + E  SL   I  E+     L D   D+   S     + A   
Sbjct: 120 SQLTGLSNDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA--- 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L  L  RE  ++ MR+        T  E+ KQ  +++  + +IE +A+ ++K 
Sbjct: 177 --LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKQLNISQVHVSRIEKRALERIKR 229


>gi|29827692|ref|NP_822326.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604792|dbj|BAC68861.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 295

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 53/249 (21%), Positives = 122/249 (48%), Gaps = 14/249 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            +F   +S + +G  +   A+  ++E N+ LV   A ++ NRG    D++Q G IGL+KA
Sbjct: 43  RQFFRRLSELEEGTHDYQYARNTLIEMNMSLVRFAAGRFRNRGDDMEDIVQVGMIGLIKA 102

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+     +F+++A+ ++   I R   D +  + +P  +++   ++ +    +S+++ 
Sbjct: 103 IDRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAREELSSRLD 162

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDED---TSHLGDFIEDKNAVS 599
           REP+  E+A  + +    V +    +      SL+  +  +D    + L DFI +++   
Sbjct: 163 REPSVAELATLMNLSENEVVEAQIASNGYNSSSLDAALSGDDQEGEAVLADFIGEEDDGM 222

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L          T   ++A L+ R+ +++ MRF      + T  ++G +   ++  + ++
Sbjct: 223 QLVEDFH-----TLAPLVAELSDRDRQIIHMRFV----EEATQADIGARLGCSQMHVSRL 273

Query: 660 EAKAIRKLK 668
             + I +L+
Sbjct: 274 IKRIIEQLR 282


>gi|325275633|ref|ZP_08141532.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
 gi|313501084|gb|ADR62450.1| RpoH [Pseudomonas putida BIRD-1]
 gi|324099220|gb|EGB97167.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
          Length = 284

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERL--YYQQDVEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|284046869|ref|YP_003397209.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951090|gb|ADB53834.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 276

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 121/249 (48%), Gaps = 19/249 (7%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
                      A+K MVE +L L   +A++Y++RG    DL+Q  ++GL+KA ++FD   
Sbjct: 39  RPADYPRSGHDARKAMVEQHLGLAHHLARRYSDRGEPLDDLVQVASLGLLKAVDRFDPAR 98

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F++YA+  +   + R   D+   I +P  +++   +V      ++    R PTP ++
Sbjct: 99  GVSFASYAVPTILGELRRHFRDRGWAIHVPRDLKEAALRVESA---LAGHAGRSPTPSQL 155

Query: 553 AKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQ 606
            K+  + VE V + L++      +SL+ P G+E+       ++    D + +        
Sbjct: 156 GKETGLDVEAVLEALEVAGAHRALSLDAPAGNEEEGTTATLVDRLGRDDDELDRAGD--- 212

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R T  R+ + L PRE  +LR+RF      D T  E+G +  V++  + ++   A+ +
Sbjct: 213 ---RATIERLASVLEPREREILRLRFV----EDMTQSEIGARVGVSQMHVSRLIRTALTR 265

Query: 667 LKHPSRSKK 675
           ++  S++ +
Sbjct: 266 MRLASQTSR 274


>gi|312622111|ref|YP_004023724.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202578|gb|ADQ45905.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ + +    +A+++++E+NL LV SV KK+  +G++  DL Q G+IGL+KA ++FD  
Sbjct: 8   ELISRAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPS 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  E
Sbjct: 68  FNVRFSTYAVPMIIGEIKRYLRD-DGKIKVSRKIKENQGKIKKLRNQFVSNHGREPTISE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           I++   +  + +   L  + E  SL   I  E+     L D   D+   S     + A  
Sbjct: 127 ISQLTGLSNDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA-- 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L  RE  ++ MR+        T  E+ KQ  +++  + +IE +A+ ++K 
Sbjct: 185 ---LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKQLNISQVHVSRIEKRALERIKR 237


>gi|322513377|ref|ZP_08066496.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
 gi|322120867|gb|EFX92727.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
          Length = 318

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 143/322 (44%), Gaps = 16/322 (4%)

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
               +R    + I+    +E     EL                       +DS +++ N+
Sbjct: 1   MRNEMRKFNEHEIEDAEVIESDDVAELGNEPSEAMHPALVQGGMPVPQGNLDSYIRMANQ 60

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
                    +S  + + +    R    E   A K+++ +++R VI +A+ Y   GL   D
Sbjct: 61  YPI------LSAEQEKELAE--RYYYDEDLEAAKQLILSHMRFVIHIARGYLGYGLPLAD 112

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +    
Sbjct: 113 LIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKLFF 172

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGD- 590
                +       E   +++A+ L + VE VR++  ++T + +  + P G++D       
Sbjct: 173 NLRKNKNRLAWFNEDEIKKVAEDLGVSVEEVREMESRMTGQDLGFDLPAGEDDDEAYAPS 232

Query: 591 -FIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            +IED ++    +   + +  E        LA+L  R + +++ R+        TL+++ 
Sbjct: 233 MYIEDNSSNFADELEDEEHTGEATAQLAYALATLDERSQDIIKTRWLDE--DKATLQDLA 290

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
            ++ ++ ER+RQ+E  A++K+K
Sbjct: 291 DKYGISAERVRQLENAALKKIK 312


>gi|319760734|ref|YP_004124672.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318039448|gb|ADV33998.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 284

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 113/238 (47%), Gaps = 8/238 (3%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A K+++ ++LR V+ +A+ Y+  GL   DLIQEGNIGLMK+  +F+  L  + 
Sbjct: 44  YYNSDLNAAKKLIVSHLRFVVHIARNYSGYGLAQADLIQEGNIGLMKSVRRFNPELDVRL 103

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + +T +R+      E   E +AK
Sbjct: 104 VSFAVHWIKSEIHEYVLKNWRIVKIATTKAQRKLFFNLRKTKQRLG--WFNEEEIEMVAK 161

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKNAVSPLDSAIQANLR 610
            L +  + VR++               D+D  ++      +++DK  +   +      + 
Sbjct: 162 TLHVTCKDVREMESRMAAQDMTFEQSSDDDEKNILSIPMLYLQDKVTMIDEEEEWINQVS 221

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 L SL  R + ++R R+    +   TL+E+  Q+ V+ ERIRQ+E  A++K+K
Sbjct: 222 NKLNIALNSLDKRSQHIIRARWLNTNDNKTTLQELANQYGVSAERIRQLEKNAMKKMK 279


>gi|225389920|ref|ZP_03759644.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
 gi|225044021|gb|EEG54267.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
          Length = 258

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 125/246 (50%), Gaps = 14/246 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E + +  + ++       A+++ ++ NLRLV+SV ++++       DL Q G IGL+KA
Sbjct: 21  NEEKEV--LFKRILDGDKEAREQYIKGNLRLVLSVIQRFSGNQENIDDLFQIGCIGLIKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD     KFSTYA+  +   + R + D +  IR+   +RD  +K +    +++    
Sbjct: 79  IDNFDITQNVKFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAYKAIYAREQLTRLNS 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLD 602
           +EPT  EIA+++ +  E +   L   + P+SL  P+  +  D  ++ D I DK     L+
Sbjct: 138 KEPTLAEIAQEIGVSKEDITYALDAIQTPVSLYEPVYTDGGDPLYVMDQISDKK---NLE 194

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                +L  +    +  L  RE  ++ +RF  G     T  EV ++  +++ ++ ++E  
Sbjct: 195 ENWVEDL--SLGEAMKRLPERERHIIDLRFFEG----KTQTEVAEEIHISQAQVSRLEKN 248

Query: 663 AIRKLK 668
           A++ +K
Sbjct: 249 ALKTMK 254


>gi|254380542|ref|ZP_04995908.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339453|gb|EDX20419.1| sigma factor [Streptomyces sp. Mg1]
          Length = 304

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 122/256 (47%), Gaps = 23/256 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLM 482
           F   +  + +G  E    +  ++E +L LV   A+++  R    GL   D+IQ G IGL+
Sbjct: 52  FFRRLRTLEEGTREYQYTRNTLIEMSLSLVQFAARRFRARVLGGGLDMDDIIQVGTIGLI 111

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++FD     +FST A+ ++   I R   D + ++ +P  +++   ++ +    +++ 
Sbjct: 112 KAIDRFDPEREVEFSTLALPYIVGEIKRHFRDTTWSVHVPRRLQELRSELAKAQEALTDV 171

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS--------HLGDFI 592
           + R PT +E+A+ L +  E V   L         SL+   G+ +TS         L D +
Sbjct: 172 LGRAPTVKEVAEHLELTEEQVIDGLVAANGYTSGSLDAAAGESETSPSTGRSTRPLADLV 231

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D +    L   +      T   +L  L  R+  +L+MRFG     D T  E+G +  ++
Sbjct: 232 GDVDPAMELFEDLH-----TLAPLLRQLDERDRLILQMRFG----QDRTQAEIGSELGIS 282

Query: 653 RERIRQIEAKAIRKLK 668
           + ++ ++ ++ + +L+
Sbjct: 283 QMQVSRLLSRTLARLR 298


>gi|83589646|ref|YP_429655.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83572560|gb|ABC19112.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Moorella
           thermoacetica ATCC 39073]
          Length = 255

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 113/253 (44%), Gaps = 20/253 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                 ++ ++E+V   L LV     +   +    L   DL+  G +GL++A +++D   
Sbjct: 12  YMAGRDALRRQELVLKYLPLVKYHVNRLAVKPPPHLDQEDLLGYGIVGLLEAVDRYDPSR 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F T+A   ++ AI  ++         P  + +K+ +  +  R++  +   E +   +
Sbjct: 72  GVNFETFASQRIRGAILDALRRAHW---APRSLIEKLRRASQVYRQLEQEQGGEVSDGAV 128

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           A+ L +    +R++++       +SLE  +     E+ +  G+ + D  +  P+    Q 
Sbjct: 129 ARALGITEAELRELMERGSQMAILSLEDFLLDQEGEEGTTRGELLADPGSPDPVGIYEQG 188

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR      L +L  ++  VL + +  G     TL+E+GK   ++  R+ Q+  +AI  L
Sbjct: 189 ELRRALAAALENLKEKDRLVLTLYYYEG----LTLKEIGKVLGISESRVCQLHGRAILNL 244

Query: 668 KHPSRSKKLRSFL 680
           +     ++L  F+
Sbjct: 245 R-----RQLADFI 252


>gi|302127747|emb|CBL51727.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
          Length = 262

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 112/301 (37%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKFEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ +
Sbjct: 58  -----------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ Q + ++  + 
Sbjct: 95  SSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQNNGRAHDET 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +L+L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  +  ++L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKSWSPRLVEMDR-NVLRAIGKLQQIEEETGLSITQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|302542195|ref|ZP_07294537.1| RNA polymerase sigma factor WhiG [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459813|gb|EFL22906.1| RNA polymerase sigma factor WhiG [Streptomyces himastatinicus ATCC
           53653]
          Length = 277

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 16/233 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF TYA+
Sbjct: 44  REQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDPERAIKFETYAI 103

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        IP  +R K   V R    +   ++R PT  E+A ++ + V+
Sbjct: 104 TRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAALRRTPTEVEVAAEMDISVD 160

Query: 562 GV--RKVLKITKEPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +            ++LE  +       D   L D +ED  A +P++ A    LR    R
Sbjct: 161 ELHGVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDRELRRLLAR 220

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE+ V+ + +  G     TL E+G+   VT  R+ QI  K++ +L+
Sbjct: 221 AINTLPEREKTVVTLYYYEG----LTLAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|228992638|ref|ZP_04152564.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
 gi|228998684|ref|ZP_04158271.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|229006186|ref|ZP_04163872.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228755027|gb|EEM04386.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228761152|gb|EEM10111.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|228766970|gb|EEM15607.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
          Length = 259

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 133/261 (50%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D            A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLSDDKQRDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 233 EEIGISQAQVSRLEKSAIKQM 253


>gi|152978131|ref|YP_001343760.1| RNA polymerase factor sigma-32 [Actinobacillus succinogenes 130Z]
 gi|150839854|gb|ABR73825.1| RNA polymerase, sigma 32 subunit, RpoH [Actinobacillus succinogenes
           130Z]
          Length = 281

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 127/268 (47%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++ +    ++  + +     +     +   A K ++ ++LR VI VA+ Y   GL
Sbjct: 15  LEGYIRAANEYPMLTAEQEKDYAERL--YYQDDLDAAKALILSHLRFVIHVARGYAGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 73  PQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+      E   + +A +L +  E V ++  ++T   I  + P  D + 
Sbjct: 133 KLFFNLRKTKQRLG--WFSENEVDLVANELGVSKEDVIEMESRMTGADIGFDLPADDAEE 190

Query: 586 SHLGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK+   A    +   +    +  T  + +L  R + +++ R+        
Sbjct: 191 ETFAPSMYLEDKSSNFAAELENENFETQAVDQLTVAMETLDARSQDIIKTRWLDEN--KA 248

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ ++ ER+RQ+E+ A++KLK
Sbjct: 249 TLHDLAAKYNISAERVRQLESNALKKLK 276


>gi|126733180|ref|ZP_01748927.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126716046|gb|EBA12910.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 298

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 122/275 (44%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   +   +    R  + E + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYMQEIRKFPMLEPEQEYMLAK--RWVDHEDTDAAHQMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGD 582
                + +   R   + +   R    E IA  L +  + V     +++    SL   +  
Sbjct: 134 KLFFNLRKAKNRIGALEDGDLRPENVERIANDLGVTEQEVISMNRRLSGGDASLNATVSA 193

Query: 583 EDTS--HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           +        D++ED++A +  D      L   RE     +  L  RE+ +L         
Sbjct: 194 DGEGAAQWQDWLEDESANTAADYEASDELTARRELLAEAMEVLNDREKDIL--MQRRLSE 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++  Q+ V+RERIRQIE +A  KL+   +
Sbjct: 252 ETVTLEDLSGQYDVSRERIRQIEVRAFEKLQAKMQ 286


>gi|163748787|ref|ZP_02156039.1| RNA polymerase sigma factor [Shewanella benthica KT99]
 gi|161331561|gb|EDQ02366.1| RNA polymerase sigma factor [Shewanella benthica KT99]
          Length = 286

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 120/269 (44%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + S    + +   +   +   ++  E     A K+++ ++LR V+ VAK Y   GL
Sbjct: 19  LEAYVHSAHNISMLEADQEYELAKRLQ--ETGDIQAAKQLIMSHLRFVVHVAKGYAGYGL 76

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 77  PQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
                + +  +R+      E     +A+ L +    V     ++  +  + +     +D 
Sbjct: 137 KLFFNLRKAKKRLGWFSDAEVGM--VAENLGVSKADVTEMESRMAAQDPAFDLVSDSDDD 194

Query: 586 SH---LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   ++ED +   A       ++A+ +      + +L  R + +L+ R+       
Sbjct: 195 IQDYAPALYLEDHSSDLASQVETDNLEASNQTRLLAAIKTLDERSQHILQARWL--NEDK 252

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL+E+   + V+ ERIRQ+E  A+ KLK
Sbjct: 253 TTLQELAATYQVSAERIRQLEKNAMNKLK 281


>gi|163759996|ref|ZP_02167080.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
 gi|162282954|gb|EDQ33241.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
          Length = 278

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 72/259 (27%), Positives = 119/259 (45%), Gaps = 16/259 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +   V     +   A  ++  A++RLVIS+A K+ N GL   DL+QEG++GL
Sbjct: 11  LERDEEHDLA--VAWKNNKDQDALHKITMAHMRLVISMAAKFRNFGLPMGDLVQEGHVGL 68

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           ++AA +FD     +FSTYA WW++ +I   I      +R       K     + R   R+
Sbjct: 69  LEAAARFDPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 128

Query: 540 SN---KIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHLGDFIE-- 593
           +     +       +IA  L + V+ V     +++    SL  P+ D ++    D ++  
Sbjct: 129 AQDDPTLTDSAIHIQIADSLGVHVKDVAVMDARLSGPDSSLNAPMSDGESGASSDRMDFL 188

Query: 594 --DKNAVSPLDSAIQANLRE--TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
             D+       S I    R        L +L PRE  ++R R         TLE +G   
Sbjct: 189 KSDEPLPDEQVSTIIDEERRNTWLGDALNTLNPRELLIIRKRRLAE--EGATLEALGATL 246

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ER+RQIE +A+ KL+
Sbjct: 247 GISKERVRQIENRALEKLR 265


>gi|302147247|emb|CBL51745.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
          Length = 262

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S    +       D   +  ++ E
Sbjct: 58  -----------------------ETDDVAPTATHIGSELGEADLADEDEDEDEDEDDDGE 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +     L  +     L   + D LV  +  + +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIALLADVFRQFRLMPKQFDRLVNNMRGMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|223635917|emb|CAQ03760.1| RNA polymerase sigma factor [Enterovibrio coralii]
          Length = 242

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 54/313 (17%), Positives = 103/313 (32%), Gaps = 72/313 (23%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +  S+ E P +   L+   D++      L +II     
Sbjct: 1   VELLTREGEIDIAKRIEDGINQVQISVAEYPGSISYLLDQFDKVEAEELRLTDII----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  GF   ++            E++                            PE 
Sbjct: 56  ------SGFVDPSQEDIAPTATHIGSEEDA------------------------GIDPEL 85

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      L +  +     ++                                   K  + 
Sbjct: 86  AREKFTELRQSYEVMQAAIN-----------------------------------KHGRF 110

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
                    +L ++     L   + D LV ++ +   R+   E  ++RL      + +  
Sbjct: 111 HDDTHTAIAELSEVFKQFRLVPKQFDRLVNEMRETMDRVRTQERIVMRLCVDQAKMPKKT 170

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E   +W+  A    E  + + +    + + +   ++K +  ETG+++   + 
Sbjct: 171 FVQLFSGNESSDNWLDAALA-TEKPYVDRLKQYEEDLRRCIQKLKIVEDETGLNVERIKD 229

Query: 430 IVSMVRKGECEAS 442
           I   +  GE +A 
Sbjct: 230 ISRRMSIGEAKAR 242


>gi|139436946|ref|ZP_01771106.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
 gi|133776593|gb|EBA40413.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
          Length = 263

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 122/241 (50%), Gaps = 7/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +    +  E     A++++V +++ LV  +A K+ NRG    DL+Q G +GL+KA ++
Sbjct: 18  RELFRRYK--ETGDPDAREQLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKAIDR 75

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G +F+T+A   +   I R   D+  ++R+P  +++   KV +   +++N+++R P
Sbjct: 76  FDPERGLEFTTFATPTILGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDKLTNELQRSP 135

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             EEIA+ L + V+ V + ++ +    S+         S     I D+ A    +     
Sbjct: 136 KVEEIAEYLDVTVDEVLEAMESSSAYTSVPIEAPGASDSDDAPSILDRYADD-DNELDFT 194

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R      +   +PRE  V+ +RF  G     T  E+ K+  +++ ++ ++  + ++K+
Sbjct: 195 DDRLVIEEAIRDFSPREREVIELRFVKG----MTQIEIAKKLGISQVQVSRLLRRTLKKI 250

Query: 668 K 668
           +
Sbjct: 251 Q 251


>gi|119715629|ref|YP_922594.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536290|gb|ABL80907.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 260

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 110/230 (47%), Gaps = 12/230 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + E+V  N+ +    A++Y  RG+   DL Q   +GL+KA   F+   G+ F ++A+
Sbjct: 24  RRIRDEIVRLNMGVASDCARRYRQRGIATEDLDQVAYLGLVKAVRGFEPGRGHDFLSFAV 83

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  + R   D    +R P  +++   ++      +S ++ R P P ++A+ L + +E
Sbjct: 84  PTIRGEVRRHFRDLGWALRPPRSIQELQSRIHAAEGDLSQELGRSPRPSDLARHLGVDLE 143

Query: 562 GVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V   L  T    P SL+  +G +    LGD +      +   +  QA  R T   VL  
Sbjct: 144 QVLDALGATGCFAPASLD-VVGADGDDSLGDRLG-----TADPAFDQAEARITLAAVLRG 197

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LTPRE R+L +RF       HT  E+G    VT+ ++ ++  + + +L+ 
Sbjct: 198 LTPRERRILELRFFGN----HTQAEIGADIGVTQMQVSRLLNRILARLRE 243


>gi|291448094|ref|ZP_06587484.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|1655819|gb|AAB41960.1| sporulation sigma factor [Streptomyces filamentosus]
 gi|291351041|gb|EFE77945.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 278

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 105/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERAIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  + +R P+  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQFRRTPSEAEVASEMG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 158 IALEE----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDR 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 214 ELRRLLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 269

Query: 668 K 668
           +
Sbjct: 270 R 270


>gi|297560730|ref|YP_003679704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845178|gb|ADH67198.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 287

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 108/251 (43%), Gaps = 7/251 (2%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            I   E    +  +   +  A   ++E+V     LV  +A++Y  RG    DL Q   +G
Sbjct: 32  EIPAEELLAELHGLDDDDPRAVRLREEVVVRYQPLVNKLARRYNGRGEPLEDLKQTAMVG 91

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA   +    G  F +Y M  V   I R   D +  IR+P   ++   K+ +      
Sbjct: 92  LVKAIRGYRPDRGKPFISYLMPTVTGEIKRHFRDHTWAIRVPRRHQENRIKLRQVLNTFQ 151

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAV 598
               R PT  EIAK++ +  E V ++++   +   +SL+ P   +     G  +ED    
Sbjct: 152 QTHARVPTNAEIAKEMGLDEEEVVELVQASESYRSLSLDAPDSSDSDGQEGSRLEDHLG- 210

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           S  +   +   RE+    LA L  RE  +L++RF      DHT  E+  +   ++  + +
Sbjct: 211 SEDEGLERVVQRESLKPALARLPEREREILKLRFF----GDHTQTEIADRMGYSQMHVSR 266

Query: 659 IEAKAIRKLKH 669
           +    + +L+ 
Sbjct: 267 LLKNTLEQLRE 277


>gi|66474657|gb|AAY46898.1| RpoD [Aeromonas jandaei]
          Length = 270

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 63/313 (20%), Positives = 114/313 (36%), Gaps = 44/313 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                            D E  A  +    S++       E+++
Sbjct: 58  ---------------------------------DTEDMAPTATHIGSELSEDDLADEDED 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            + DEDED                      E+   Y          ++ QK+ ++    +
Sbjct: 85  EDEDEDEDGDNSDDDGDGGPDPEVAREKFAELRAQYEV------TRLSIQKNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +  W   +    + + +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKA-WSPRLMEMDEEVQRAIGKLQQIEEETGLSIAQIKDINRRM 257

Query: 435 RKGECEASIAKKE 447
             GE +A  AKK+
Sbjct: 258 SIGEAKARRAKKK 270


>gi|30021992|ref|NP_833623.1| sporulation sigma factor SigG [Bacillus cereus ATCC 14579]
 gi|206971353|ref|ZP_03232304.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218899057|ref|YP_002447468.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228902409|ref|ZP_04066563.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|228909729|ref|ZP_04073552.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228922656|ref|ZP_04085956.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228940992|ref|ZP_04103550.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954180|ref|ZP_04116208.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960121|ref|ZP_04121785.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966857|ref|ZP_04127901.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|229019106|ref|ZP_04175941.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|229025350|ref|ZP_04181768.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|229047588|ref|ZP_04193178.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|229071403|ref|ZP_04204625.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|229081156|ref|ZP_04213666.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|229104466|ref|ZP_04235133.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|229111373|ref|ZP_04240926.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|229129181|ref|ZP_04258154.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|229146475|ref|ZP_04274846.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|229162839|ref|ZP_04290796.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|229180179|ref|ZP_04307523.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|229192073|ref|ZP_04319042.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|296504397|ref|YP_003666097.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|29897548|gb|AAP10824.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 14579]
 gi|206734125|gb|EDZ51296.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218543268|gb|ACK95662.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228591399|gb|EEK49249.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|228603388|gb|EEK60865.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|228620721|gb|EEK77590.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|228637108|gb|EEK93567.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|228654418|gb|EEL10283.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|228672149|gb|EEL27440.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|228678908|gb|EEL33118.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|228702200|gb|EEL54676.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|228711694|gb|EEL63647.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|228723835|gb|EEL75190.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|228735935|gb|EEL86512.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|228742206|gb|EEL92371.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|228792956|gb|EEM40514.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799637|gb|EEM46590.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805500|gb|EEM52091.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818671|gb|EEM64738.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228837085|gb|EEM82426.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228850018|gb|EEM94849.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228857153|gb|EEN01659.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|296325449|gb|ADH08377.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|326941673|gb|AEA17569.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 259

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 134/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 233 EEIGISQAQVSRLEKSAIKQM 253


>gi|78357159|ref|YP_388608.1| sigma 70 family protein [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78219564|gb|ABB38913.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 360

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 79/280 (28%), Positives = 142/280 (50%), Gaps = 22/280 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ IS    +   E   +   V+      S A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 84  YLREISRFPMLKPDEEFELARRVQ--LHNDSDAAFRLVSSHLRLVVKIAMDFQRRWMQNV 141

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDLIQEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      R  
Sbjct: 142 LDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIKAYILKFIMDNWRLVKIGTTQAQRKL 201

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS- 586
            + + +  +++  +   +P    ++++L +  E V ++  ++    +SL+  +GDE+ S 
Sbjct: 202 FYNLNKERQKLIAQ-GYDPDAAMLSERLDVTTEQVVEMEQRLDASDMSLDVQVGDENGSA 260

Query: 587 -------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   LG  IED  A + + + +Q  +R+        L  +E  +L     +     
Sbjct: 261 SRMDFLPALGPGIEDTLANNEIAAMVQERIRDIVPL----LNDKELDILNS--RLLSEDP 314

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            TL E+G+++ +TRER+RQIEA+ ++K++     K+++ F
Sbjct: 315 VTLREIGEKYDITRERVRQIEARLLQKIRDHL-FKEIKDF 353



 Score = 37.5 bits (85), Expect = 6.7,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 23/48 (47%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             S   L       ++ T D + +YLRE+    +L  + E  +A+R++
Sbjct: 60  DVSDTDLPAPLPPGNKPTRDSLHLYLREISRFPMLKPDEEFELARRVQ 107


>gi|260550924|ref|ZP_05825130.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
 gi|260406051|gb|EEW99537.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
          Length = 288

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 121/269 (44%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + E    D+D 
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 195

Query: 586 SHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       ++ED     A    +   +          +  L  R   +L+ R+     + 
Sbjct: 196 TPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDDKS- 254

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 255 -TLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|30424475|dbj|BAC76410.1| heat shock sigma-32 factor [Colwellia maris]
          Length = 285

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 122/256 (47%), Gaps = 15/256 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +      R        A +E++ ++LR VI VAK Y+  GL   DL+QEGN+GLMKA +
Sbjct: 31  EKEHNLATRLYNENDLSAAQELIMSHLRFVIHVAKGYSGYGLPHADLVQEGNVGLMKAVK 90

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+  +G +  ++A+ W+K  I   +      +++      +  K+    R+   ++   
Sbjct: 91  RFNPEVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKNKKRLGWF 148

Query: 547 PTPE--EIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED-----TSHLGDFIEDKN-- 596
            T E   +A+ L +  + V ++  +++    + E    D+D           +++DK   
Sbjct: 149 STEEVNTVAENLGVTTKDVMEMESRMSSYDQAFELSKDDDDNLGASNFSPAQYLQDKQSD 208

Query: 597 -AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
            AV   +     +  +  +  L +L  R + +++ R+     T  TL+E+  ++ ++ ER
Sbjct: 209 LAVEVENDNWDNHANKRLSTALVTLDERSQDIIKTRWLTEDKT--TLQELANKYQISAER 266

Query: 656 IRQIEAKAIRKLKHPS 671
           +RQ+E  A+ KLK+  
Sbjct: 267 VRQLEKNALSKLKNTM 282


>gi|302147261|emb|CBL51752.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 262

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPGAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ E
Sbjct: 58  -----------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGE 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|258511711|ref|YP_003185145.1| sporulation sigma factor SigF [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257478437|gb|ACV58756.1| RNA polymerase, sigma 28 subunit, SigF [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 256

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 119/258 (46%), Gaps = 17/258 (6%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +S  E R ++          + A++ ++  N RLV +V +++  RG +  DL
Sbjct: 11  HHVDEYEKLSDEEVRELLER---SHNGDAEARERLIVHNQRLVWAVVQRFLGRGYEAEDL 67

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q G IGLMKA +KFD     KFSTYA+  +   I R + D   T+++   +++   ++ 
Sbjct: 68  FQIGCIGLMKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DSTVKVSRSLKETAKQIR 126

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDF 591
               R++ ++ R+P   EIA+ + M    +    +  + P S+   + + D    +L D 
Sbjct: 127 HVRDRLAKELGRQPHITEIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYLMDQ 186

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I D+      D             ++  L  RE  ++ MRF      D T  +V +   +
Sbjct: 187 IADEETEGKFDKVE-------LHEIIGRLPERERFIVYMRFF----RDKTQSDVARVLGI 235

Query: 652 TRERIRQIEAKAIRKLKH 669
           ++ ++ ++E + +++++ 
Sbjct: 236 SQVQVSRLEKRILQQIRQ 253


>gi|120402666|ref|YP_952495.1| RNA polymerase sigma factor SigF [Mycobacterium vanbaalenii PYR-1]
 gi|119955484|gb|ABM12489.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 262

 Score =  125 bits (313), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 58/245 (23%), Positives = 118/245 (48%), Gaps = 13/245 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G       +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 24  FRELAEL-EEGTAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVI 82

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 83  RFDVNAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRA 142

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDS 603
           PT  E+A +L M  + V + L    +   +S+++   G+ED   + D + D +      S
Sbjct: 143 PTATELAAELEMDRDEVVEGLVAGSSYNTLSIDSGGSGNEDAPAIADTLGDVD-----LS 197

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   RE    +LA+L  RE  VL +RF        T  ++ ++  +++  + ++ AK+
Sbjct: 198 LDQIENREALRPLLAALPERERTVLALRFF----ESMTQTQIAERVGISQMHVSRLLAKS 253

Query: 664 IRKLK 668
           + +L+
Sbjct: 254 LARLR 258


>gi|312972274|ref|ZP_07786448.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
 gi|310334651|gb|EFQ00856.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
          Length = 257

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 123/256 (48%), Gaps = 14/256 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL   DLIQEGNIGL
Sbjct: 2   LSADEERALAEKL--HYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRM 539
           MKA  +F+  +G +  ++A+ W+K  I   +      +++      R     + +T +R+
Sbjct: 60  MKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
               + E   E +A++L +  + VR++      ++     +   D D+  +   +  ++ 
Sbjct: 120 GWFNQDE--VEMVARELGVTSKDVREMESRMAAQDMTFDLSSNDDSDSQPMAPVLYLQDK 177

Query: 598 VSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            S     I+ +  E       T  +  L  R + ++R R+ +  +   TL+E+  ++ V+
Sbjct: 178 SSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNKSTLQELADRYGVS 236

Query: 653 RERIRQIEAKAIRKLK 668
            ER+RQ+E  A++KL+
Sbjct: 237 AERVRQLEKNAMKKLR 252


>gi|170719544|ref|YP_001747232.1| RNA polymerase factor sigma-32 [Pseudomonas putida W619]
 gi|169757547|gb|ACA70863.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida W619]
          Length = 284

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLAERL--YYEQDLEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|50871538|emb|CAF74860.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 109/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G           Q+ E  + +       + + D E     S+++       PE A   
Sbjct: 59  DDGAA-------GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKAKTAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ +   +I   E  +++L      + R  FL +
Sbjct: 137 VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        +G++   +    + I++ + ++  +  E  + I++ + I   
Sbjct: 197 FPNNETNLDWAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|229086468|ref|ZP_04218640.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
 gi|228696785|gb|EEL49598.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
          Length = 259

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 133/261 (50%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  FVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D            A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLSDDKQRDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 233 EEIGISQAQVSRLEKSAIKQM 253


>gi|47570318|ref|ZP_00240965.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
 gi|47553027|gb|EAL11431.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
          Length = 257

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 134/264 (50%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE     A++++V  NLRLV+SV +++ N
Sbjct: 1   RNKVEICGVDTAKLPVLXNDEMRKLFREMQSGEIS---AREKLVNGNLRLVLSVIQRFNN 57

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 58  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 116

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 117 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 176

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+           A         +  L  RE+ ++R RF  G     T  
Sbjct: 177 DPIFVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQM 227

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 228 EVAEEIGISQAQVSRLEKSAIKQM 251


>gi|307943602|ref|ZP_07658946.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
 gi|307773232|gb|EFO32449.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
          Length = 291

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 123/270 (45%), Gaps = 15/270 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  ++       ++  E   +   VR  +     A +++  ++ RLVISVA K+ N GL 
Sbjct: 9   RELVRKAMKAPYLTREEEHDLA--VRWRDNRDEKALEKLSLSHTRLVISVASKFRNFGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DLIQEG++GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 67  LGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKA 126

Query: 529 -IHKVVRTARRM---SNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
               + R   ++      +      ++IA  + +    V     +++    SL  P+ D 
Sbjct: 127 LFFNLRRLRAKLSGNQQNLTDSELHQKIADAIGVKPADVATMNARLSGPDTSLNAPVTDS 186

Query: 584 DTSHL--GDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           + S     DF+           +   +    R+     +  LT RE +++R         
Sbjct: 187 EGSSSDRQDFLVSDAPQPDDIVSESIDTERRRKWLASAMTVLTDRELKIVRE--RRLTEE 244

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 245 GATLESLGQKLGISKERVRQIESRAMEKLK 274


>gi|320008281|gb|ADW03131.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces
           flavogriseus ATCC 33331]
          Length = 278

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 105/237 (44%), Gaps = 24/237 (10%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF TYA+
Sbjct: 45  REQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERAIKFETYAI 104

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++ + +E
Sbjct: 105 TRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQLRRTPSEAEVASEMGVALE 161

Query: 562 GVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                L      +SL   +  E          D   L D +ED  A  P++ A    LR 
Sbjct: 162 E----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADDPVEVAEDRELRR 217

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L+
Sbjct: 218 LLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|240144182|ref|ZP_04742783.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
 gi|257203785|gb|EEV02070.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
          Length = 259

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 134/261 (51%), Gaps = 13/261 (4%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + I +     ++  + +   + A++  ++ NLRLV+SV K+++      
Sbjct: 5   KVEICGVNTAKLPILKEEEKDALFARIKQGDTAARETYIKGNLRLVLSVIKRFSGNHENV 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+K+ + FD  +G KFSTYA+  +   I R + D +  IR+   +RD  +
Sbjct: 65  DDLFQIGCIGLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           K + T   +S    +EPT +EIA +  +  E +   L   + P+SL  P+  +  DT ++
Sbjct: 124 KAIHTKEILSKTENKEPTLDEIAAESGISKEDIVFALDAIQSPLSLYDPVYTDGGDTLYV 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I DK   +  ++ I+     +    L  L  RE  +L++RF  G     T  EV  +
Sbjct: 184 MDQISDKK--NREENWIEEL---SLNDALDRLNERENYILKLRFFEG----KTQMEVADE 234

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A++ ++H
Sbjct: 235 IHISQAQVSRLEKSALKSIRH 255


>gi|299538362|ref|ZP_07051645.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
 gi|298725949|gb|EFI66541.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
          Length = 247

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 117/238 (49%), Gaps = 14/238 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ + +     A+K MVE N RLV S+ +++T RG++  DL Q G IGLMK+ +KFD   
Sbjct: 4   LIARAQQGDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLMKSVDKFDLTY 63

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R + D    +++   +R+   K+         K +  PT +E+
Sbjct: 64  DVKFSTYAVPMIIGEIQRFLRD-DGMVKVSRSIRELNFKIRHATDEFIKKNEHPPTIQEL 122

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ L +  E +       ++P SL   + +   D+  L D ++D+ +  P D        
Sbjct: 123 AQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDEKSEQPFDYI------ 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                VL  L PRE+ ++ +R+           E+  +  +++ ++ ++E K + +LK
Sbjct: 177 -PLKEVLTRLEPREQSIIYLRYFSDCTQ----TEIANRLGISQVQVSRLEKKILAQLK 229


>gi|52546628|dbj|BAD51697.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546630|dbj|BAD51698.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546632|dbj|BAD51699.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546636|dbj|BAD51701.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546638|dbj|BAD51702.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546640|dbj|BAD51703.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546642|dbj|BAD51704.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546644|dbj|BAD51705.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546646|dbj|BAD51706.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546648|dbj|BAD51707.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546650|dbj|BAD51708.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546652|dbj|BAD51709.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546656|dbj|BAD51714.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546658|dbj|BAD51715.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546662|dbj|BAD51717.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546672|dbj|BAD51731.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|71040346|dbj|BAE16170.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
          Length = 275

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 54/316 (17%), Positives = 115/316 (36%), Gaps = 42/316 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDP 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   GF       + +  ED  +  E ++ ++ +G  ++ A  ++ +           
Sbjct: 61  NAEDTDGFNAKEAEEAEEADEDEEEASEDEEAEDDDGAAQATANAAQLEA---------- 110

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                   L+   +     I+E + ++R   +      K+   S
Sbjct: 111 ------------------------LKRASLEKFAMISEWFDKMRRAFE------KEGYKS 140

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + S+      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 141 KSYLKAQETIQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 200

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   +   + +I + +  +  +     + + + +  
Sbjct: 201 IARFPGSETDLTWAEKVASESHS-YSAILVRNIPAIHEQQQRLLDLQARVVLPLKDLKET 259

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 260 NRQMAAGELKARQAKR 275


>gi|296168913|ref|ZP_06850582.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896382|gb|EFG76035.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 262

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  +FD   G  F ++A+
Sbjct: 37  QRQRDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAV 96

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   + R   D S ++++P  +++   ++      +S ++ R PT  E+A +L M  E
Sbjct: 97  PTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATAELSQRLGRAPTATELAAELGMDRE 156

Query: 562 GVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V + L    +   +S+++  G ++     + D + D +         +   +E+   +L
Sbjct: 157 EVVEGLVAGSSYNTLSIDSGGGSDEDEARAIADTLGDVDT-----GLDRIEDQESLRPLL 211

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  RE  VL +RF        T  ++ ++  +++  + ++ AK++ +L+
Sbjct: 212 EALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKSLTRLR 258


>gi|54401904|gb|AAV34637.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 183

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 71/179 (39%), Positives = 121/179 (67%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q
Sbjct: 2   VVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 61

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+P+H+  +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +   S
Sbjct: 62  TRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERITS 121

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           ++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 122 VDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 180


>gi|307824539|ref|ZP_07654764.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734523|gb|EFO05375.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 285

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 123/269 (45%), Gaps = 21/269 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  +     +++ + R +   ++  +     A +E+V  NLR VI VA+ Y+  GL   
Sbjct: 19  YLNVVRQMPKLTVEQERELA--LKFRDDGDLEAARELVMTNLRFVIHVARGYSGYGLSMP 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           D+IQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +  K
Sbjct: 77  DIIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVIKNWGIVKVATTKAQR--K 134

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVE---GVRKVLKITKEPISLETPIGDEDTSHL 588
           +    R+    +      E +A    + V+         ++    +S + P+   D S  
Sbjct: 135 LFFNLRKSKQDLGWLSNDEAVAIAKDLDVDVSTVYEMEKRLGSRDMSFDMPV---DESTE 191

Query: 589 GDFIE---------DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             ++             AV   +S  + + ++     +A L  R   +L  R+   M+  
Sbjct: 192 ESYVAPASYLHQHGGDPAVLLENSDWEGHEQDLLADAMAELDERSLDILSSRWL--MDKK 249

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+ +++ V+ ERIRQ+E  A++KL+
Sbjct: 250 ATLHELAERYNVSAERIRQLEQNAMKKLR 278


>gi|30263905|ref|NP_846282.1| sporulation sigma factor SigG [Bacillus anthracis str. Ames]
 gi|47778237|ref|YP_020684.2| sporulation sigma factor SigG [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|165872304|ref|ZP_02216941.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167641114|ref|ZP_02399369.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170688856|ref|ZP_02880059.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|170708817|ref|ZP_02899253.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|177654919|ref|ZP_02936636.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190565736|ref|ZP_03018655.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035947|ref|ZP_03103349.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196045922|ref|ZP_03113151.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206976720|ref|ZP_03237624.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217961324|ref|YP_002339892.1| sporulation sigma factor SigG [Bacillus cereus AH187]
 gi|218233406|ref|YP_002368703.1| sporulation sigma factor SigG [Bacillus cereus B4264]
 gi|218905033|ref|YP_002452867.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225865885|ref|YP_002751263.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227813187|ref|YP_002813196.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228916541|ref|ZP_04080107.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229140552|ref|ZP_04269107.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|229152101|ref|ZP_04280296.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|229157482|ref|ZP_04285559.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|229174570|ref|ZP_04302100.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|229198015|ref|ZP_04324729.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|229602177|ref|YP_002868139.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
 gi|254721437|ref|ZP_05183226.1| sporulation sigma factor SigG [Bacillus anthracis str. A1055]
 gi|30258549|gb|AAP27768.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Ames]
 gi|47551942|gb|AAT33159.2| RNA polymerase sigma-G factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164711980|gb|EDR17520.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167510894|gb|EDR86285.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170126302|gb|EDS95193.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|170667211|gb|EDT17971.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|172080430|gb|EDT65517.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190562655|gb|EDV16621.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991596|gb|EDX55562.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196023362|gb|EDX62040.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206745030|gb|EDZ56433.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217067470|gb|ACJ81720.1| RNA polymerase sigma-G factor [Bacillus cereus AH187]
 gi|218161363|gb|ACK61355.1| RNA polymerase sigma-G factor [Bacillus cereus B4264]
 gi|218537241|gb|ACK89639.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225788717|gb|ACO28934.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227002358|gb|ACP12101.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228585494|gb|EEK43598.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|228608875|gb|EEK66167.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|228625932|gb|EEK82682.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|228631450|gb|EEK88084.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|228643113|gb|EEK99389.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|228843120|gb|EEM88202.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229266585|gb|ACQ48222.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
          Length = 259

 Score =  124 bits (312), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 134/264 (50%), Gaps = 19/264 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEIS---AREKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   + D + D+           A         +  L  RE+ ++R RF  G     T  
Sbjct: 179 DPIFVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQM 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           EV ++  +++ ++ ++E  AI+++
Sbjct: 230 EVAEEIGISQAQVSRLEKSAIKQM 253


>gi|261219345|ref|ZP_05933626.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222881|ref|ZP_05937162.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315875|ref|ZP_05955072.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316262|ref|ZP_05955459.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322406|ref|ZP_05961603.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|265987326|ref|ZP_06099883.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998840|ref|ZP_06111397.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|260921465|gb|EEX88118.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924434|gb|EEX91002.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261295096|gb|EEX98592.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295485|gb|EEX98981.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261304901|gb|EEY08398.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|262553529|gb|EEZ09298.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659523|gb|EEZ29784.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 293

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 74/267 (27%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKERVRQIESRAMEKLK 279


>gi|297199468|ref|ZP_06916865.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197712989|gb|EDY57023.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 282

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 52/270 (19%), Positives = 126/270 (46%), Gaps = 21/270 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGEC-------EASIAKKEMVEANLRLVISVAKKYT 464
           E+ ++   + ++  + R +  +  +          E   A+  ++E N+ LV   A ++ 
Sbjct: 16  ELPAVPDPSKVAPKDARELTRLFFQQLTVLDEGTPEYQYARNTLIEMNISLVRYAASRFR 75

Query: 465 NRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +R   +  D++Q G IGL+KA ++F+     +F+++++ ++   I R   D +  + +P 
Sbjct: 76  SRDPEEMEDIVQVGVIGLIKAIDRFELSREVEFTSFSIPYIVGEIKRFFRDTTWAVHVPR 135

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIG 581
            +++   ++ R    +S ++ R PT  E+A+ + +  + V +    +      SL+  IG
Sbjct: 136 RLQEARVQLARATEELSTRLGRTPTVAELAQLMNLEEKEVIEARLASNGYRSSSLDAAIG 195

Query: 582 DEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           + D     L DFI   +    L     A        ++A+L  R  ++L  RF      +
Sbjct: 196 NGDDGETALADFIGTDDGALELVEDFHA-----LAPMIAALDERSRKILHWRFV----EE 246

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  ++G++  +++  + ++ ++ + +L+ 
Sbjct: 247 ATQAQIGERLGISQMHVSRLLSRTLAQLRE 276


>gi|145225367|ref|YP_001136045.1| RNA polymerase sigma factor SigF [Mycobacterium gilvum PYR-GCK]
 gi|145217853|gb|ABP47257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 262

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 119/246 (48%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G       +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELAEL-EEGSAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVI 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVTAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLET--PIGDEDTSHLGDFIEDKNAVSPLD 602
           PTP E+A +L M  + V + L    +   +S+++    G+ED   + D + D +      
Sbjct: 142 PTPSELAAELEMDRDEVVEGLVAGSSYNTLSIDSGGGSGNEDAPAIADTLGDVD-----L 196

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  Q   RE    +LA+L  RE  VL +RF        T  ++ ++  +++  + ++ AK
Sbjct: 197 TLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAK 252

Query: 663 AIRKLK 668
           ++ +L+
Sbjct: 253 SLTRLR 258


>gi|125972644|ref|YP_001036554.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125712869|gb|ABN51361.1| RNA polymerase, sigma subunit, RpoX/SigF [Clostridium thermocellum
           ATCC 27405]
          Length = 246

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 129/246 (52%), Gaps = 7/246 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + ++   +     A+  +VE N+ LV S+ +++ NRG +  D+ Q G IGL+KA  
Sbjct: 6   EKETLELIAAAKAGDKDAQSLLVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAIN 65

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R I D    I++   +++  +K   T   MS ++ RE
Sbjct: 66  KFDCSYDVKFSTYAVPMIIGEIKRFIRD-DGMIKVSRSLKELANKARITKEIMSKELGRE 124

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  EI+++L +PVE V   ++ +  P SL + +G+ D S     + DK A    +  + 
Sbjct: 125 PTVGEISEQLGIPVEEVVMAMEASCTPESLYSTLGEGDNSS--TLLIDKIANESENQEVD 182

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R    +VL +L PRE++++ +R+      + T  ++ K   +++ ++ +IE K + +
Sbjct: 183 IVDRIDLRKVLDTLKPREKQIIVLRYF----KEKTQVQIAKMLGISQVQVSRIEKKILEE 238

Query: 667 LKHPSR 672
           ++   +
Sbjct: 239 IRKKIK 244


>gi|169632997|ref|YP_001706733.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii SDF]
 gi|169795347|ref|YP_001713140.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AYE]
 gi|184158784|ref|YP_001847123.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii ACICU]
 gi|213158666|ref|YP_002319964.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|215482881|ref|YP_002325084.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|239502880|ref|ZP_04662190.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB900]
 gi|301346949|ref|ZP_07227690.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB056]
 gi|301513493|ref|ZP_07238730.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB058]
 gi|301596794|ref|ZP_07241802.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB059]
 gi|332850459|ref|ZP_08432779.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332871911|ref|ZP_08440323.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
 gi|169148274|emb|CAM86139.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii AYE]
 gi|169151789|emb|CAP00610.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii]
 gi|183210378|gb|ACC57776.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii ACICU]
 gi|193077812|gb|ABO12685.2| EsvH [Acinetobacter baumannii ATCC 17978]
 gi|213057826|gb|ACJ42728.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|213986534|gb|ACJ56833.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|322507403|gb|ADX02857.1| rpoH [Acinetobacter baumannii 1656-2]
 gi|323518699|gb|ADX93080.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332730730|gb|EGJ62041.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332731125|gb|EGJ62426.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
          Length = 288

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 121/269 (44%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + E    D+D 
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 195

Query: 586 SHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       ++ED     A    +   +          +  L  R   +L+ R+     + 
Sbjct: 196 TPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNILQRRWLDDDKS- 254

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 255 -TLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|331082586|ref|ZP_08331709.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
 gi|330400205|gb|EGG79847.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 259

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 75/271 (27%), Positives = 133/271 (49%), Gaps = 19/271 (7%)

Query: 409 IRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
             N+++   V T    I  +E +   ++  + +     A+++ ++ NLRLV+SV K++++
Sbjct: 2   ALNKVEICGVNTSRLPILTNEEKD--ALFVRIKEGDPEAREQYIKGNLRLVLSVIKRFSS 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                 DL Q G +GL+KA + FD  L  KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  SNENADDLFQIGCVGLIKAIDNFDTTLNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K +        +  +EPT  EIA+++ +  E +   L   + P+SL  P+  E  
Sbjct: 119 RDVAYKAIYAKENYVKQNLKEPTINEIAEEIGIDKEEIVYALDAIQSPVSLYEPVYTEGG 178

Query: 584 DTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           DT ++ D I D KN        I           L  L  RE+ ++ MRF  G     T 
Sbjct: 179 DTLYVMDQISDKKNKEDNWIENI------ALKEALKKLDDREQHIVTMRFYEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            EV ++  +++ ++ ++E  A++ ++   RS
Sbjct: 229 MEVAEEIGISQAQVSRLEKHALKTMRTYLRS 259


>gi|331696957|ref|YP_004333196.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951646|gb|AEA25343.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 288

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 112/248 (45%), Gaps = 12/248 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+      T   ++     ++ +   +   +  ++ +V  +L +V  +A+++  RG    
Sbjct: 34  EVPETGSSTYDHLAPLFDELAAMTADDPRRTTLRERLVTGHLPVVRHIARRFAGRGEPVD 93

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G +GL+ A ++FD   G  F +YA+  +   + R   D++ ++R+P  +++    
Sbjct: 94  DLEQAGTVGLINAVDRFDPARGVDFLSYAVPTITGEVRRHFRDRTWSMRVPRRLKELQSS 153

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLG 589
           +      ++ ++ R P P EIA ++   V+ V + L+        SL+  +  +  + L 
Sbjct: 154 INSAVGGLAQELGRAPRPSEIADRIGRDVDEVIEGLEARQVYRSTSLDELV-ADSDAMLS 212

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           + +   +A        + + R+T   +L  L  RE  +L +RF  G     T  ++  + 
Sbjct: 213 ETLGIADA-----ELEKVDYRQTLAPLLDELPTRERTILVLRFFAG----MTQTQIADEV 263

Query: 650 CVTRERIR 657
            V++  + 
Sbjct: 264 GVSQMHVS 271


>gi|256004731|ref|ZP_05429707.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281416836|ref|ZP_06247856.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|255991324|gb|EEU01430.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281408238|gb|EFB38496.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|316941118|gb|ADU75152.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 1313]
          Length = 248

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 129/246 (52%), Gaps = 7/246 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + ++   +     A+  +VE N+ LV S+ +++ NRG +  D+ Q G IGL+KA  
Sbjct: 8   EKETLELIAAAKAGDKDAQSLLVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAIN 67

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R I D    I++   +++  +K   T   MS ++ RE
Sbjct: 68  KFDCSYDVKFSTYAVPMIIGEIKRFIRD-DGMIKVSRSLKELANKARITKEIMSKELGRE 126

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  EI+++L +PVE V   ++ +  P SL + +G+ D S     + DK A    +  + 
Sbjct: 127 PTVGEISEQLGIPVEEVVMAMEASCTPESLYSTLGEGDNSS--TLLIDKIANESENQEVD 184

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R    +VL +L PRE++++ +R+      + T  ++ K   +++ ++ +IE K + +
Sbjct: 185 IVDRIDLRKVLDTLKPREKQIIVLRYF----KEKTQVQIAKMLGISQVQVSRIEKKILEE 240

Query: 667 LKHPSR 672
           ++   +
Sbjct: 241 IRKKIK 246


>gi|332875153|ref|ZP_08442986.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
 gi|332736597|gb|EGJ67591.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
          Length = 280

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 121/269 (44%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 10  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 67

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 68  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 127

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + E    D+D 
Sbjct: 128 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 187

Query: 586 SHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       ++ED     A    +   +          +  L  R   +L+ R+     + 
Sbjct: 188 TPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNILQRRWLDDDKS- 246

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 247 -TLHELAAEYNVSAERIRQLEKNAMEKIK 274


>gi|291536437|emb|CBL09549.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           M50/1]
          Length = 259

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 71/261 (27%), Positives = 134/261 (51%), Gaps = 13/261 (4%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + I +     ++  + +   + A++  ++ NLRLV+SV K+++      
Sbjct: 5   KVEICGVNTAKLPILKEEEKDALFARIKQGDTAARETYIKGNLRLVLSVIKRFSGNHENV 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+K+ + FD  +G KFSTYA+  +   I R + D +  IR+   +RD  +
Sbjct: 65  DDLFQIGCIGLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           K + T   +S    +EPT +EIA +  +  E +   L   + P+SL  P+  +  DT ++
Sbjct: 124 KAIHTKEILSKTENKEPTLDEIAAESGISKEDIVFALDAIQSPLSLYDPVYTDGGDTLYV 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I DK   +  ++ ++     +    L  L  RE  +L++RF  G     T  EV  +
Sbjct: 184 MDQISDKK--NREENWVEEL---SLNDALDRLNERENYILKLRFFEG----KTQMEVADE 234

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A++ ++H
Sbjct: 235 IHISQAQVSRLEKSALKSIRH 255


>gi|146284301|ref|YP_001174454.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri A1501]
 gi|145572506|gb|ABP81612.1| sigma factor RpoH [Pseudomonas stutzeri A1501]
 gi|327482685|gb|AEA85995.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri DSM 4166]
          Length = 284

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 63/275 (22%), Positives = 122/275 (44%), Gaps = 17/275 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVQTVNSLPLLTVEQERELAERL--FYHQDLEAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W++  I   I      +++      R
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                +    +R++     E T   +A  L +    VR++            P  D D  
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVTA--VADSLGVEPHEVREMESRLTGHDMAFDPAADADDD 192

Query: 587 ----HLGDFIEDKNAVSPLDSAIQANLRE----TTTRVLASLTPREERVLRMRFGIGMNT 638
                   ++ED     P      A+  +    +    L  L  R   +L+ R+      
Sbjct: 193 SAYQSPAHYLEDHR-YDPARQLEDADWSDSSTSSLHAALEGLDERSRDILQQRWL--NED 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TL ++  ++ V+ ERIRQ+E  A+ KLK   ++
Sbjct: 250 KATLHDLAAKYNVSAERIRQLEKNAMNKLKGSIQA 284


>gi|228988887|ref|ZP_04148936.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228770801|gb|EEM19317.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 295

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 85/288 (29%), Positives = 138/288 (47%), Gaps = 14/288 (4%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F       + K  NEI +  + T     E      +++  E     ++  ++ +NLRLV+
Sbjct: 3   FNKRNSSEMGKYLNEICNYDILTDEQSME-----HIIKYKEKGDIDSRDLLICSNLRLVV 57

Query: 458 SVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           SVAK +   G    +++IQEG IGLMK  E +D+  G K STY  WW++Q I++ ++   
Sbjct: 58  SVAKSFPCYGNCDLMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINR 117

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +R+   M+ KI +V         +     T +E+A++L      V   L   +   ++
Sbjct: 118 SDVRVATTMQKKITEVKNCYYENMGEKGTNLTTKEVAERLGYKESIVIDALVTDRITNTI 177

Query: 577 ETPIGDEDTSHLGD-------FIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVL 628
                 ++   L D        + +KNA +P +       +     ++  +L PREE VL
Sbjct: 178 SIEDDVQNEKTLLDKQQSTLAILANKNAPNPSEVIATEEEKFEFDELMFVTLNPREESVL 237

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           R RFG     + TLE+  +   VTRER++QIE KAI K+K    SKK+
Sbjct: 238 RYRFGFDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQRLSSKKI 285


>gi|161898865|gb|ABX80422.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 110/241 (45%), Gaps = 4/241 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S          A    D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVAGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|228949811|ref|ZP_04112021.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228809869|gb|EEM56280.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 295

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 138/288 (47%), Gaps = 14/288 (4%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F       + K  NEI +  + T     E      +++  E     ++  ++ +NLRLV+
Sbjct: 3   FNKRNSSEMGKYLNEICNYDILTDEQSME-----HIIKYKEKGDIDSRDLLICSNLRLVV 57

Query: 458 SVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           SVAK +   G    +++IQEG IGLMK  E +D+  G K STY  WW++Q I++ ++   
Sbjct: 58  SVAKSFPCYGNCDLMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINR 117

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
             +R+   M+ KI +V         +     T +E+A+KL      V   L   +   ++
Sbjct: 118 SDVRVATTMQKKITEVKNCYYENMGEKGTNLTTKEVAEKLGYKESIVIDALVTDRITNTI 177

Query: 577 ETPIGDEDTSHLGD-------FIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVL 628
                 ++   L D        + +KNA +P +       +     ++  +L PREE VL
Sbjct: 178 SIEDDVQNEKTLLDKQQSTLAILANKNAPNPSEVIATEEEKFEFDELMFVTLNPREESVL 237

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           R RFG     + TLE+  +   VTRER++QIE KAI K+K    SKK+
Sbjct: 238 RYRFGFDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQRLSSKKI 285


>gi|148550183|ref|YP_001270285.1| RNA polymerase factor sigma-32 [Pseudomonas putida F1]
 gi|148514241|gb|ABQ81101.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida F1]
          Length = 284

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERL--YYEQDVEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|152967736|ref|YP_001363520.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151362253|gb|ABS05256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 326

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 15/227 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+   +L L   +A ++  RG    DL+Q   IGL+KA ++FD   G  F  YA+  +
Sbjct: 106 REELTRRHLPLADHLAARFLGRGEPQDDLVQVATIGLLKALDRFDPSRGVPFGAYAVPTM 165

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   +R+P  +++    +      +++++ R PT  E+A++     E V 
Sbjct: 166 LGEIKRHFRDRGWAMRVPRRIQEAGRALGDAREALTHELGRAPTVAELAERTGYDPEDVV 225

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            VL+       + L+T       + LG    D +A+  +        RE    +LA L  
Sbjct: 226 DVLESANAYSTLPLDTGSPTSLVASLG---ADDDALQNV------ENREALRPLLAGLPA 276

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE R+L +RF  GM+      EV     +++  + ++  + + +L+ 
Sbjct: 277 RERRILALRFVRGMSQSQIAAEV----GISQMHVSRLLTRTLAQLRE 319


>gi|291464148|gb|ADE05599.1| RNA polymerase sigma factor [Thalassospira tepidiphila]
          Length = 262

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 115/260 (44%), Gaps = 21/260 (8%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR++IDLE   G   +                D+  + E  +    + D E+  +   
Sbjct: 1   LLLRDVIDLETTYGGGPEAEIAAAEGEDEEDTDVDAEADVESFESANDDDDEEAETETPA 60

Query: 239 D----------------DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                            ++S  +      E D+ + D++ +    +LS ME++L  +V+ 
Sbjct: 61  GLTDEAEEDEDEEDDESEKSDDEEGEATGEGDDDDDDDENEQVNVSLSKMEEELTEQVLE 120

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDL 337
             + IA+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ 
Sbjct: 121 KFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNNFRIEE 180

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK 
Sbjct: 181 LLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKT 240

Query: 398 FVACEVDSILKIRNEIKSIS 417
           FV    + I  +R  I  +S
Sbjct: 241 FVERYSEEIANLREGIGGVS 260


>gi|153209360|ref|ZP_01947367.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212217703|ref|YP_002304490.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuK_Q154]
 gi|120575393|gb|EAX32017.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212011965|gb|ACJ19345.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuK_Q154]
          Length = 288

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 121/276 (43%), Gaps = 13/276 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI  I + I  ++    +S  E   + +  R+       A +++V ++LR V+ +A+ Y+
Sbjct: 14  SIGSIGSYISLVNRIPLLSAEEEHDLANKFRQ--SNDLEAARKLVLSHLRFVVRIARGYS 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      ++I   
Sbjct: 72  GYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATT 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +                 +     +A++L +  + VR++ +       + +    + 
Sbjct: 132 KAQRKLFFNLRKHAKKRGWFSDHEAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEES 191

Query: 584 DTSHLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           D+          ++EDK    A+    S    +        + SL  R   +L  R+   
Sbjct: 192 DSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRWL-- 249

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                TL E+  Q+ V+ ERIRQ+E  A++K++   
Sbjct: 250 SEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|15604172|ref|NP_220687.1| RNA polymerase factor sigma-32 [Rickettsia prowazekii str. Madrid
           E]
 gi|3860864|emb|CAA14764.1| RNA POLYMERASE SIGMA-32 FACTOR (rpoH) [Rickettsia prowazekii]
 gi|292571903|gb|ADE29818.1| RNA polymerase sigma-32 factor [Rickettsia prowazekii Rp22]
          Length = 293

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 131/270 (48%), Gaps = 15/270 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + ++ I+    ++  E   +       E     A  ++V ++L+LV  +A  Y   GL  
Sbjct: 18  SYLQKINKIPSLTQEEEFLLAK--SYLEENDLQAAHKLVTSHLKLVAKIASSYKTYGLPI 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-- 528
            +L+ EGNIGLM+A +KF+  LG++ STYAMWW+K +I   I      +++      K  
Sbjct: 76  TELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKSWSLVKMGTTAAQKKL 135

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
              + +   +++N   R  T ++   IA +L + V  V ++  +I+   +SL   I  +D
Sbjct: 136 FFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRISGPDLSLNNSINSDD 195

Query: 585 --TSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTD 639
             +  L + + +        +  + N    R+  +  +  L  RE R+L+ R     +T 
Sbjct: 196 VESGELIELLPELRPTPEAMAINKQNYTSKRKLLSNAMQILNDRELRILKDRKL--TDTP 253

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            TL+ +  ++ +++ERIRQIE  A  K+K 
Sbjct: 254 KTLDILSSEYNISKERIRQIENTAFEKIKK 283


>gi|319795672|ref|YP_004157312.1| RNA polymerase, sigma 32 subunit, rpoh [Variovorax paradoxus EPS]
 gi|315598135|gb|ADU39201.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus EPS]
          Length = 313

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 126/291 (43%), Gaps = 30/291 (10%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +D+ +   N +        +++ E +     +R  +     A   ++ ++LRLV+S+++
Sbjct: 26  NLDAYISAANRLP------LLTLEEEQGFARKLR--DQNDLDAAGALILSHLRLVVSISR 77

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++
Sbjct: 78  QYLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKV 137

Query: 522 PVH-MRDKIHKVVRTARR-------------MSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
                + K+   +R+ ++                 +  +   +   +    P E +    
Sbjct: 138 ATTKAQRKLFFNLRSMKQGFKADSAASDNGTHRETLSPDEVSQMATRLNVKPEEVLEMET 197

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASLTP 622
           +++   + L+    D+     G      +A     + +++  R+  +       L +L  
Sbjct: 198 RLSGGDVLLDPGPSDDGDEAFGPIAYLADATQEPTALLESQQRDRLSSDGIATALEALDA 257

Query: 623 REERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R  R++  R+    +      TL ++   + V+ ERIRQIE  A++K+K  
Sbjct: 258 RSRRIVEERWLKVNDDGSGGMTLHDLAAVYGVSAERIRQIEVAAMKKMKKA 308


>gi|187763302|gb|ACD35528.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 272

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 117/315 (37%), Gaps = 44/315 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G + + +S+ E P     L+   D+       L +II         
Sbjct: 1   TREGEIDIAKRIEDGISQVQSSVAEYPEAITYLLEQDDKYEAEQLRLSDII--------- 51

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              GF    E                          E  A  +    S++       E++
Sbjct: 52  --SGFIDPFE-------------------------TEDMAPTATHIGSELGEDDLADEDE 84

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E   DEDED  +                   E+   Y          ++ QK+ ++    
Sbjct: 85  EDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDT 138

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 139 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 198

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   
Sbjct: 199 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRR 257

Query: 434 VRKGECEASIAKKEM 448
           +  GE +A  AKKEM
Sbjct: 258 MSIGEAKARRAKKEM 272


>gi|56964115|ref|YP_175846.1| sporulation sigma factor SigG [Bacillus clausii KSM-K16]
 gi|56910358|dbj|BAD64885.1| DNA-directed RNA polymerase sigma factor sigma-G [Bacillus clausii
           KSM-K16]
          Length = 261

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 80/266 (30%), Positives = 135/266 (50%), Gaps = 21/266 (7%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +  +E R + + ++        A++ +V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTSTLPVLKNAEMRELFTKLQ---AGYEPARETLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMS--NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           RD  +K ++   +M    K ++EPT +EIA  L +P E V   L   ++P+SL  PI ++
Sbjct: 119 RDIAYKALQVRDQMMAEKKREKEPTVQEIAAVLEVPKEDVVFALDAIQDPVSLFEPIYND 178

Query: 584 --DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             D   + D I D+           A         +  L  RE+ +L MRF  G     T
Sbjct: 179 GGDPIFVMDQISDERNKDINWVEEIA-----LKEAMVRLNDREKTILNMRFFQG----KT 229

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
             EV ++  +++ ++ ++E  AI+++
Sbjct: 230 QMEVAEEIGISQAQVSRLEKGAIQQM 255


>gi|325265256|ref|ZP_08131981.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
 gi|324029435|gb|EGB90725.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
          Length = 259

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 130/263 (49%), Gaps = 11/263 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + + +     ++  + +     A++E ++ NLRLV+SV K+++N  
Sbjct: 2   ALNKVELCGVNTAKLPLLKEEEKEALFTRIKAGDEEAREEYIKGNLRLVLSVIKRFSNSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G +GLMKA + FD     KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENADDLFQIGCVGLMKAVDHFDPNRLVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K +        K  +EPT +EIA+++ +  E +   L   + P+SL  P+  +    
Sbjct: 121 TAYKAIYAKEGYMKKHLKEPTVQEIAEEIGISKEDIVFALDAIQMPMSLHEPVYSDG--- 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            GD +   + VS   +  +  + E +    +  L  RE  ++ +RF  G     T  EV 
Sbjct: 178 -GDTLYVMDQVSDKKNKEENWVEELSLEAAMERLNERERYIITLRFFEG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
           ++  +++ ++ ++E  A++ +K 
Sbjct: 233 EEIKISQAQVSRLEKNALKVMKQ 255


>gi|161898855|gb|ABX80417.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  124 bits (312), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 110/241 (45%), Gaps = 4/241 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S          A    D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVAGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|261325797|ref|ZP_05964994.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261301777|gb|EEY05274.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 293

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEAAARFDPDRDVRFSTYAFWWIRASMQDYILRNWSIVRGGTSSAQKALFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    +     +++    SL  P+  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDIEFMDSRLSGPDSSLSAPMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKERVRQIESRAMEKLK 279


>gi|121595815|ref|YP_987711.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax sp. JS42]
 gi|120607895|gb|ABM43635.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax sp. JS42]
          Length = 321

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 67/288 (23%), Positives = 129/288 (44%), Gaps = 22/288 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  +  +   I +++    ++  E +     ++        A   +V ++LRLV+S++++
Sbjct: 31  VPPLGNLDAYISAVNRLPLLTQEEEQRYARQLKDDNNV--EAAGRLVLSHLRLVVSISRQ 88

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   I      +++ 
Sbjct: 89  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 148

Query: 523 VH-MRDKIHKVVRTARR----------MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-T 570
               + K+   +R+ ++             +   +   + +A++L +  E V ++    +
Sbjct: 149 TTKAQRKLFFNLRSMKQGFKADALDADTHRETLSDHEIDLVAEQLNVKREEVIEMETRLS 208

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPREE 625
              + L+    D+     G      +A     + I++  R+          L SL  R  
Sbjct: 209 GGDVLLDPAPSDDGEQAFGPIAYLADAGHEPTALIESRQRDALATDGIATALDSLDARSR 268

Query: 626 RVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K+K  
Sbjct: 269 RIVEQRWLQVNDDGSGGMTLHELATEYGVSAERIRQIEVAAMKKMKKA 316


>gi|82949200|dbj|BAE53364.1| sigma factor [Streptomyces sp. AJ9463]
          Length = 195

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 85/152 (55%), Positives = 113/152 (74%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 43  KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 102

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R+M   + REPT
Sbjct: 103 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 162

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           PEE+AK+L M  E V +V K  +EPISL TP+
Sbjct: 163 PEELAKELDMTPEKVIEVQKYGREPISLHTPL 194



 Score = 44.8 bits (104), Expect = 0.049,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL+++G + LL+ E E+ +AKRIEAG       L  S      L    + + +    
Sbjct: 2   YLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANSDKLAPKLKRELEIIAEDGRR 57


>gi|260554461|ref|ZP_05826682.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
 gi|260411003|gb|EEX04300.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
          Length = 288

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 121/269 (44%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + E    D+D 
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVMEMEGRLTAYDAAFEAQGDDDDD 195

Query: 586 SHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       ++ED     A    +   +          +  L  R   +L+ R+     + 
Sbjct: 196 TPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNILQRRWLDDDKS- 254

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 255 -TLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|50084493|ref|YP_046003.1| RNA polymerase factor sigma-32 [Acinetobacter sp. ADP1]
 gi|49530469|emb|CAG68181.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp.
           ADP1]
          Length = 289

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 64/270 (23%), Positives = 122/270 (45%), Gaps = 12/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + ET   D+D 
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFETQGDDDDD 195

Query: 586 SH----LGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           S        ++ED     A    +   +          +  L  R   +L+ R+     +
Sbjct: 196 SSTHVAPALYLEDNRYDPARLAENDDYEEQSSTALHEAMNQLDDRSRNILQRRWLDDDKS 255

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 256 --TLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|52546634|dbj|BAD51700.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546654|dbj|BAD51712.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546660|dbj|BAD51716.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546664|dbj|BAD51720.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546666|dbj|BAD51721.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546668|dbj|BAD51724.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
 gi|52546670|dbj|BAD51726.1| DNA-directed RNA polymerase subunit D [Burkholderia plantarii]
          Length = 275

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 54/316 (17%), Positives = 115/316 (36%), Gaps = 42/316 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELVDGLLDP 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   GF       + +  ED  +  E ++ ++ +G  ++ A  ++ +           
Sbjct: 61  NAEDTDGFNAKEAEEAEEADEDEEEASEDEEAEDDDGAAQATANAAQLEA---------- 110

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                   L+   +     I+E + ++R   +      K+   S
Sbjct: 111 ------------------------LKRASLEKFAMISEWFDKMRRAFE------KEGYKS 140

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + S+      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 141 KSYLKAQETIQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 200

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   +   + +I + +  +  +     + + + +  
Sbjct: 201 IARFPGSETDLAWAEKVASESHS-YSAILVRNIPAIHEQQQRLLDLQARVVLPLKDLKET 259

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 260 NRQMAAGELKARQAKR 275


>gi|318075685|ref|ZP_07983017.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actF]
          Length = 259

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 67/252 (26%), Positives = 113/252 (44%), Gaps = 27/252 (10%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAE 486
           +  + K   +A + +++++     LV  VA +  + GL       D +  G  GL+ A E
Sbjct: 13  LWRMYKTTGDARL-REQLILHYSPLVKYVAGR-VSVGLPPNVEQADFVSSGVFGLIDAIE 70

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KF TYA+  ++ A+   +        IP  +R K   V R    +  K+ R 
Sbjct: 71  KFDIERSIKFETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAKLHRT 127

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED----------TSHLGDFIEDKN 596
           PT  E+A ++ + VE     L      +SL   +  E+             + D +ED  
Sbjct: 128 PTEVEVASEMGVGVED----LHAVFSQLSLANVVALEELLSVGSEGGGRLSIMDTLEDTG 183

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A +P++ A    LR+  +R + SL  RE+ V+ + +  G     TL E+G    VT  R+
Sbjct: 184 ADNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYYEG----LTLAEIGHVLGVTESRV 239

Query: 657 RQIEAKAIRKLK 668
            QI  K++ +L+
Sbjct: 240 SQIHTKSVLQLR 251


>gi|215254264|gb|ACJ64131.1| RNA polymerase sigma 70 factor [Vibrio agarivorans]
          Length = 261

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 52/305 (17%), Positives = 102/305 (33%), Gaps = 45/305 (14%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   + +++ E P T   ++   D++      L +II     + P   G   
Sbjct: 1   DIAKRIEDGINQVQSAVTEYPGTIPYILEQFDKVQAEELRLTDII--SGFVDPNDDGT-- 56

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                        S   +   + ++ EG+ +   +   D+       PE A         
Sbjct: 57  ----AAPTATHIGSELAEADLEDEDDEGNEQDGDESEDDEEEDTGIDPELA--------- 103

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                               +    E+   +      Q+  +   +    S + K   E 
Sbjct: 104 --------------------LEKFTELRNTF------QNRQLAINEHGPDSAQAKQTGEL 137

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           + ++     L   + D LV +L     R+   E  ++R    YG + +  F+    G E 
Sbjct: 138 VKEVFAEFRLTPKQFDHLVNELRTSMDRVRTQERLIMRSVVEYGKMPKKSFIALFTGNES 197

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  + + +    D I +   ++  I  ET +++   + I   +  GE 
Sbjct: 198 TEAWLDEVLA-SDKPYADKIRRSEDDIRRCIQKLSIIEEETSLTVQSIKDISRRMSIGEA 256

Query: 440 EASIA 444
           +A  A
Sbjct: 257 KARRA 261


>gi|52842873|ref|YP_096672.1| RNA polymerase factor sigma-32 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52629984|gb|AAU28725.1| RNA polymerase sigma-32 factor RpoH [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 292

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 65/273 (23%), Positives = 122/273 (44%), Gaps = 15/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +++ E        R        A +++V A+LR V+ VA+ Y   GL
Sbjct: 25  LDSYIHRVNQIPMLTLEEEIAYAE--RFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 82

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 83  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 142

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+M N++      E   +AK L +  E V     ++     S + P  D++ 
Sbjct: 143 --KLFFNLRQMKNRLGWFSNEEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDND 200

Query: 586 ------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                       + D  AV   +       RE     +  L  R + +L+ R+       
Sbjct: 201 DAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAE--EK 258

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TL ++ +++ V+ ER+RQ+E  A++K++    
Sbjct: 259 LTLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 291


>gi|26991784|ref|NP_747209.1| RNA polymerase factor sigma-32 [Pseudomonas putida KT2440]
 gi|8885996|gb|AAF80334.1|AF157048_1 heat shock sigma factor RpoH [Pseudomonas putida]
 gi|24986895|gb|AAN70673.1|AE016711_1 RNA polymerase sigma-32 factor [Pseudomonas putida KT2440]
          Length = 284

 Score =  124 bits (311), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERL--YYEQDVEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|150389982|ref|YP_001320031.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949844|gb|ABR48372.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 258

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 124/242 (51%), Gaps = 11/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             +++++  +     A++++V  NL L+ SV K+++NRG    DL Q G+IGL+KA  KF
Sbjct: 19  ETMTLIQMAQKGDLQAQEKLVSHNLGLIRSVIKRFSNRGYDREDLFQLGSIGLIKAIRKF 78

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   I R + D    I++   ++    +V  T  ++  +  REPT
Sbjct: 79  DISFNVRFSTYAVPMIIGEIKRFLRD-DGIIKVSRSLKQTASRVKVTKEKLFKEFGREPT 137

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             EIAK L +  E +   L     P  L   I  +D S  HL D I + +++   +   +
Sbjct: 138 LHEIAKVLEITKEEIVMALDSNMYPEYLYEVIHQDDGSPIHLIDKISETDSLDDSEVIDK 197

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    V+  L PRE +++ +R+      D T  E+ K   +++ ++ +IE K ++ 
Sbjct: 198 IMLKE----VIGRLEPRERQIIILRYF----KDKTQTEIAKVLGISQVQVSRIEKKVLQT 249

Query: 667 LK 668
           +K
Sbjct: 250 MK 251


>gi|282864142|ref|ZP_06273199.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561220|gb|EFB66765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 290

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 116/252 (46%), Gaps = 19/252 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  ++E NL LV   A ++ +RG     D++Q G +GL+KA 
Sbjct: 41  FFDRLQLLDEGTPEHQYARNTLIEMNLSLVRFAAGRFRSRGSGDMEDIVQVGTVGLIKAI 100

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD     +F+++A+ ++   I R   D + ++ +P  +++    + R    ++  + R
Sbjct: 101 DRFDLAREVEFTSFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVDLARAKETLAVGLDR 160

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS-------HLGDFIEDKN 596
           +PT +E+A  L +  + V   +         SL+ P    D +          D + + +
Sbjct: 161 DPTVQELAAHLGLDEQEVTDGIVAANGYTAGSLDMPAEAGDPAGRATGGRTFADVLGEPD 220

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                 +            +L  L  RE R++ MRFG     + T  ++G +  +++  +
Sbjct: 221 -----PAMETVENLHALAPLLEDLDARERRIIEMRFG----QELTQAQIGDELGISQMHV 271

Query: 657 RQIEAKAIRKLK 668
            ++  + +RKL+
Sbjct: 272 SRLLGRTLRKLR 283


>gi|315445714|ref|YP_004078593.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315264017|gb|ADU00759.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 262

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 119/246 (48%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +  +G       +  +VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELAEL-EEGSAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVI 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVNAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLET--PIGDEDTSHLGDFIEDKNAVSPLD 602
           PTP E+A +L M  + V + L    +   +S+++    G+ED   + D + D +      
Sbjct: 142 PTPSELAAELEMDRDEVVEGLVAGSSYNTLSIDSGGGSGNEDAPAIADTLGDVD-----L 196

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  Q   RE    +LA+L  RE  VL +RF        T  ++ ++  +++  + ++ AK
Sbjct: 197 TLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAK 252

Query: 663 AIRKLK 668
           ++ +L+
Sbjct: 253 SLTRLR 258


>gi|220929692|ref|YP_002506601.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
 gi|220000020|gb|ACL76621.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
          Length = 249

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 124/241 (51%), Gaps = 10/241 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           + +++ K +     A+  +VE N+ LV S+ K++ NRG +  DL Q G+IGL+KA  KFD
Sbjct: 9   VFTLIIKAKAGDKQAQSVLVEKNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFD 68

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R I D    I++   +++   K   T   MS ++ REPT 
Sbjct: 69  TSYDVKFSTYAVPMIIGEIKRFIRD-DGIIKVSRSLKEVSSKARITKEIMSKELGREPTI 127

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
            EIA+ + +  E +   ++    P SL + IGD + S   L D I+  N  S     I  
Sbjct: 128 NEIAQHMNISPEELVMAIEAGCTPESLYSTIGDGENSPILLIDRIDAANNNSCEVDLID- 186

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +    ++L +L  RE +++ +R+      + T  ++ K   +++ ++ +IE K +R +
Sbjct: 187 --KIAIRQILDTLDTRERQIIILRYF----KEKTQVQIAKLLGISQVQVSRIEKKILRDI 240

Query: 668 K 668
           K
Sbjct: 241 K 241


>gi|110678526|ref|YP_681533.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109454642|gb|ABG30847.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 292

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 71/269 (26%), Positives = 123/269 (45%), Gaps = 18/269 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     +   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELELAYAWRDERCEKSLHRLITAYMRLAISMASKFKRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R +   
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLERESAAS 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              + R    + I+ ++ +P+  V  +  +++    SL      ED      D +ED + 
Sbjct: 146 GEPLDRHQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNATQSTEDEGREWIDALEDDSA 205

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +         LR    + +  L  RE  ++R R         TLE +G++  +++E
Sbjct: 206 QAAETVEHHHDTEQLRAWLLQAMNDLNERERFIVRERKLRDA--PRTLESLGQELNLSKE 263

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFLD 681
           R+RQ+EA A  K++     +S+++  FLD
Sbjct: 264 RVRQLEAAAFGKMRKSLENQSREVLYFLD 292


>gi|52546578|dbj|BAD51672.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546582|dbj|BAD51674.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546586|dbj|BAD51676.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546588|dbj|BAD51677.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546590|dbj|BAD51678.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546592|dbj|BAD51679.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546594|dbj|BAD51680.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546600|dbj|BAD51683.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546604|dbj|BAD51685.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546606|dbj|BAD51686.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546608|dbj|BAD51687.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546610|dbj|BAD51688.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546614|dbj|BAD51690.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546616|dbj|BAD51691.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546620|dbj|BAD51693.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546622|dbj|BAD51694.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042248|dbj|BAE46943.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042250|dbj|BAE46944.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042252|dbj|BAE46945.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
          Length = 275

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 115/316 (36%), Gaps = 42/316 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRIDELVDGLNDP 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   GF       + Q  ED  +  E ++ ++ +G  ++ A  ++ +           
Sbjct: 61  NAEDADGFNAKEAEEAEQADEDEEEAAEDEEEEDDDGAAQATANAAQLEA---------- 110

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                   L+   +     I+E + ++R   +      K+   S
Sbjct: 111 ------------------------LKRTSLEKFALISEWFDKMRRAFE------KEGYKS 140

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + S+      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 141 KSYLKAQETIQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 200

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   +   V +I + +  +  +     + + + +  
Sbjct: 201 ISRFPGSETDLAWAEKIATESHS-YSAILQRNVPAIHEQQQRLLDLQARVVLPLKDLKET 259

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 260 NRQMAAGELKARQAKR 275


>gi|52546576|dbj|BAD51671.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546580|dbj|BAD51673.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546584|dbj|BAD51675.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546596|dbj|BAD51681.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546598|dbj|BAD51682.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546602|dbj|BAD51684.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546612|dbj|BAD51689.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546618|dbj|BAD51692.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546624|dbj|BAD51695.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|52546626|dbj|BAD51696.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040326|dbj|BAE16160.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040328|dbj|BAE16161.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040330|dbj|BAE16162.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040332|dbj|BAE16163.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040334|dbj|BAE16164.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040336|dbj|BAE16165.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040338|dbj|BAE16166.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040340|dbj|BAE16167.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|71040342|dbj|BAE16168.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli pv.
           cocovenerans]
 gi|71040344|dbj|BAE16169.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli pv.
           agaricicola]
 gi|78042254|dbj|BAE46946.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042256|dbj|BAE46947.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
 gi|78042258|dbj|BAE46948.1| DNA-directed RNA polymerase subunit D [Burkholderia gladioli]
          Length = 275

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 115/316 (36%), Gaps = 42/316 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   ++   + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRIDELVDGLNDP 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   GF       + Q  ED  +  E ++ ++ +G  ++ A  ++ +           
Sbjct: 61  NAEDADGFNAKEAEEAEQADEDEEEAGEDEEEEDDDGAAQATANAAQLEA---------- 110

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                   L+   +     I+E + ++R   +      K+   S
Sbjct: 111 ------------------------LKRTSLEKFALISEWFDKMRRAFE------KEGYKS 140

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + S+      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 141 KSYLKAQETIQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEF 200

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R  G E D  W           +   +   V +I + +  +  +     + + + +  
Sbjct: 201 ISRFPGSETDLAWAEKIATESHS-YSAILQRNVPAIHEQQQRLLDLQARVVLPLKDLKET 259

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 260 NRQMAAGELKARQAKR 275


>gi|317423772|emb|CBI85533.1| RNA polymerase sigma factor [Aeromonas bestiarum]
          Length = 269

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 115/312 (36%), Gaps = 46/312 (14%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P    
Sbjct: 1   GEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN--- 55

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                                E DDV  T   I S            D   +   + +  
Sbjct: 56  ---------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDGDGDDA 94

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKV 316
            D+ +      ++                  E + ELR+  +   ++ QK+ ++    + 
Sbjct: 95  DDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHEDTQA 137

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
               L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    
Sbjct: 138 AIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFT 197

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   + 
Sbjct: 198 NNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMS 256

Query: 436 KGECEASIAKKE 447
            GE +A  AKKE
Sbjct: 257 IGEAKARRAKKE 268


>gi|89055891|ref|YP_511342.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88865440|gb|ABD56317.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 298

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 120/275 (43%), Gaps = 15/275 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +       E E + A  +MV ++LRL   +A  Y   GL
Sbjct: 16  LNRYLQEIRKFPMLEPEEEYMLAK--AWAEKEDTEAAHKMVTSHLRLAAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I E N+GLM+A +KFD   G++ +TYAMWW++ AI   +      +++      K
Sbjct: 74  PQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWWIRAAIQEYVLRSWSMVKLGTTSAQK 133

Query: 529 --IHKVVRTARR---MSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGD 582
                + +   R   +     R    E IA  L +   E V    +++    SL   +G 
Sbjct: 134 KLFFNLRKAKARIGALEEGDLRPENVERIANDLGVTEAEVVSMNRRMSGGDASLNATVGS 193

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMN 637
           ED       D++ED++A    D A +   +         +  L  RE+ +L         
Sbjct: 194 EDEGSAQWQDWLEDEDADQATDYAERDEFQSRMALMAEAMEVLNDREKDILTQ--RRLQE 251

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              TLE++   + V+RER+RQIE +A  KL+   R
Sbjct: 252 KAVTLEDLSGVYNVSRERVRQIEVRAFEKLQKRMR 286


>gi|153008471|ref|YP_001369686.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560359|gb|ABS13857.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 311

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 35  IRSAMSAPYLEREEERALA--IRWKELKDQDALHRITSAHMRLVISMAGRFRKFKLPMND 92

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 93  LIQEGYVGLLEAAARFDPEREVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 152

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTS 586
            + R   +++         E   EI+ +L +    V     +++    SL  P+ +E++ 
Sbjct: 153 NLRRLRSKLAQSDDNMTKAEMYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNNEESG 212

Query: 587 HL--GDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            +   DF+ D + +    +    ++    +     L +L  RE  ++R R         T
Sbjct: 213 AVRRMDFLVDDHPLQDEIAESSIDMERRNQWLNVALDTLNERELHIIRERRLDDDGV--T 270

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 271 LEALGEKLGISKERVRQIESRAMEKLK 297


>gi|325122820|gb|ADY82343.1| RNA polymerase factor sigma-32 [Acinetobacter calcoaceticus PHEA-2]
          Length = 276

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 120/272 (44%), Gaps = 11/272 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 6   VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 63

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 64  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 123

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S K+  E            P + +    ++T    + E    D+D 
Sbjct: 124 QRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 183

Query: 586 SHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       ++ED     A    +   +          +  L  R   +L+ R+       
Sbjct: 184 TPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDD--DK 241

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            TL E+  ++ V+ ERIRQ+E  A+ K+K   
Sbjct: 242 STLHELAAEYNVSAERIRQLEKNAMEKIKTAM 273


>gi|163735266|ref|ZP_02142701.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
 gi|161391480|gb|EDQ15814.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
          Length = 284

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 71/269 (26%), Positives = 123/269 (45%), Gaps = 18/269 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     +   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 18  ELRLAYAWRDERCEKSLHRLITAYMRLAISMASKFKRYGAPMNDLIQEAGLGLMKAADKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R +   
Sbjct: 78  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQARLERESAAS 137

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              + R    + I+ ++ +P+  V  +  +++    SL      ED      D +ED + 
Sbjct: 138 GEPLDRHQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNATQSTEDEGREWIDALEDDSA 197

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +         LR    + +  L  RE  ++R R         TLE +G++  +++E
Sbjct: 198 QAAETVEHHHDTEQLRAWLLQAMNDLNERERFIVRERKLRDA--PRTLESLGQELSLSKE 255

Query: 655 RIRQIEAKAIRKLKHPS--RSKKLRSFLD 681
           R+RQ+EA A  K++     +S+++  FLD
Sbjct: 256 RVRQLEAAAFGKMRKNLENQSREVLYFLD 284


>gi|162457339|ref|YP_001619706.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
 gi|161167921|emb|CAN99226.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
          Length = 443

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 74/305 (24%), Positives = 145/305 (47%), Gaps = 9/305 (2%)

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           G +L+   +  +     GE +      +     ++  ++ +     ++  E + +     
Sbjct: 134 GVDLNDIELPRSARASGGEGRGSGDVALSRTDPLQAYLREVQRHALLTPDEEKELTIKYT 193

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K +  A+ A+  +V ANLRLV+ +A +Y       +DLIQEGNIGLM+A +++D   G K
Sbjct: 194 KTQDVATAAR--LVTANLRLVVKLAYEYRRAYKNIMDLIQEGNIGLMQAVKRYDPYRGVK 251

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            S+YA WW++  I R I +    +++      R     + +   ++S  +  EPT  EIA
Sbjct: 252 LSSYAAWWIRAYILRFILNNWRLVKLGTTQAQRKLFFNLNKEKAKLSA-MGIEPTAAEIA 310

Query: 554 KKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLGDF-IEDKNAVSPLDSAIQANLRE 611
           K+L++  + V  +  ++     SL+ P+GD +   +    +   +  SP  +   + +  
Sbjct: 311 KRLSVEEKEVVDMDRRLASGEASLDAPVGDLEGRTIPRVELLVSSGASPDTAFEASEMGM 370

Query: 612 TTTRVLASLTP--REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                L+      + + V+     +      TL+E+G +F ++RER+RQ+EA+   KL+ 
Sbjct: 371 LVHDRLSKFRETLKGKDVIIFDKRMAAEDPLTLQELGNEFGISRERVRQLEARLQSKLRT 430

Query: 670 PSRSK 674
             + +
Sbjct: 431 YLQEE 435


>gi|124268355|ref|YP_001022359.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
 gi|124261130|gb|ABM96124.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
          Length = 319

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 66/289 (22%), Positives = 131/289 (45%), Gaps = 25/289 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V S+  +   I +++    +++ E + +   +R  +     A   +V ++LRLV+SV+++
Sbjct: 30  VPSLGDLNAYIAAVNRLPMLTLEEEQSLGQRLR--DEHDLEAAGRLVLSHLRLVVSVSRQ 87

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  I   +      +++ 
Sbjct: 88  YLGYGLPHGDLIQEGNVGLMKAVKRFDPSQGVRLVSYALHWIKAEIHEYVLRNWRMVKLA 147

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP--------------VEGVRKVLK 568
                +  K+    R M    K + T  ++ +                    E +    +
Sbjct: 148 TTKAQR--KLFFNLRSMKQGFKGDATDSDLHRSTLTDAEIDIVASELKVKREEVIEMETR 205

Query: 569 ITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLR--ETTTRVLASLTPRE 624
           ++   ++L+    D D S+  +    +D++  + +  A + +    +     L  L  R 
Sbjct: 206 LSGGDVALDPQTDDGDESYAPIAYLADDRHEPTRVLDAQRRDALAGDGIGEALDVLDARS 265

Query: 625 ERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K++  
Sbjct: 266 RRIVEERWLKVNDNGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMRKA 314


>gi|297156863|gb|ADI06575.1| RNA polymerase sigma factor WhiG [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 107/237 (45%), Gaps = 24/237 (10%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF TYA+
Sbjct: 44  REQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDPERAIKFETYAI 103

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        IP  +R K   V R    +   ++R P+  E+A ++ + ++
Sbjct: 104 TRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAALRRTPSEAEVAAEMDIGLD 160

Query: 562 GVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLDSAIQANLRE 611
                L      +SL   +  ED  H          L D +ED  A +P++ A    LR 
Sbjct: 161 E----LHGVFSQLSLANVVALEDLLHASGEGGERLSLMDTLEDTAADNPVEVAEDRELRR 216

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R + +L  RE+ V+ + +  G     TL E+G+   VT  R+ QI  K++ +L+
Sbjct: 217 LLARAINTLPEREKTVVTLYYYEG----LTLAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|262195942|ref|YP_003267151.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262079289|gb|ACY15258.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 298

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 112/266 (42%), Gaps = 9/266 (3%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  + S+     +   E   +    R  E     A   +V + LR V+ +A+KY   G+ 
Sbjct: 12  QTYVDSVERIAALEREEELALARRWR--EHGDRAAADALVSSQLRSVLKIARKYRGYGIY 69

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD-- 527
             DL+ EGN+GL++A  +F+   G +F TYA  WV+  I   +      + +    +   
Sbjct: 70  LSDLVAEGNLGLLEAVNRFEPERGLRFFTYARHWVRAFILAHVLKHWSIVDLGTTAQQSK 129

Query: 528 KIHKVVRTARRMSNKIKREPTPEE--IAKKLAMPVEGVRKVLKI-TKEPISLETPIGDED 584
              ++     R+   +  +    E  +A       E VR  L+   +   SL+ P+ D  
Sbjct: 130 MFFRLQSEHARLLTTLGDQSDQVERQLADTFKTSPEQVRANLQRLARRDASLDVPVVDGG 189

Query: 585 TSHLGDFIEDKNAVSPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            + L     D        +A + +  +R   + +  +L  RE  ++  R         TL
Sbjct: 190 ITFLDMLQADTTDQETQTAAAELSSVVRNAVSELWPTLDCRERLIVDERLLPADGDPRTL 249

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
             +G+Q  +TRER+RQ+EA    +L+
Sbjct: 250 AALGRQLGLTRERVRQLEAGVKDRLR 275


>gi|89900482|ref|YP_522953.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
 gi|89345219|gb|ABD69422.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
          Length = 313

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 71/292 (24%), Positives = 127/292 (43%), Gaps = 34/292 (11%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +D+ +   N +        +++ E +      R+    A  A  ++V ++LRLV+SV++
Sbjct: 26  NLDAYISAANRLPM------LTLEEEQEFSRKFRQDNDLA--AAGKLVLSHLRLVVSVSR 77

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  I   I      +++
Sbjct: 78  QYLGYGLPHGDLIQEGNVGLMKAVKRFDPDHGVRLVSYALHWIKAEIHEYILKNWRMVKV 137

Query: 522 PVHMRDKIHKVVRTARRMSNKIK---------------REPTPEEIAKKLAMPVEGVRKV 566
                 +  K+    R M  + K                E   + +A +L +  E V ++
Sbjct: 138 ATTKAQR--KLFFNLRSMKQRYKSDDAAADLGTHRDTLNEDQIDAMALELRVKREEVMEM 195

Query: 567 LKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-----VLASL 620
               +   + L+    D+     G      +        I+A+ R+          L +L
Sbjct: 196 ETRLSGGDVLLDPSPTDDGDDAFGPIAYLTDTRHEPTEMIEAHQRDLLASDGIATALEAL 255

Query: 621 TPREERVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             R  R++  R+    + +    TL E+   + V+ ERIRQIE  A++K+K 
Sbjct: 256 DERSRRIVEERWLKVNDDNSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKK 307


>gi|167507973|gb|ABZ81307.1| RpoD [Thalassospira sp. MCCC 1A02450]
          Length = 258

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 67/256 (26%), Positives = 116/256 (45%), Gaps = 17/256 (6%)

Query: 179 TLLREIIDLEACIGPESKGGFFH------------GTEGHSYQKREDSSQEKERDDVQET 226
            LLR++IDLE   G                       +    +   D   E E +  + +
Sbjct: 1   LLLRDVIDLETTFGGGPDAAAIGEEEGEATEEDSASEDFEPTESDADEDDEAETETPEPS 60

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
            GD         DD        E+ E D+ + D++ +    +LS ME++L  +V+   ++
Sbjct: 61  AGDHGDDEDDEDDDEETDGEGSEDGEGDDDDEDDENEQVNVSLSKMEEELTEQVLEKFEK 120

Query: 287 IAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA+ Y +L   Q+  +      +S       +   LK+++V L+  + LN  RI+ L++ 
Sbjct: 121 IAKTYEKLHKAQEQRLAALNKGESVPAATEKRYGKLKQEMVDLMEDVHLNNFRIEELLDH 180

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           L  ++ R++  EG+LLR A    IKR  F++ +QG ELDP+W+    + P   WK FV  
Sbjct: 181 LTGLNNRLLGLEGKLLRFADRVKIKRPDFIKHYQGNELDPNWMEKVGNLPGKGWKLFVER 240

Query: 402 EVDSILKIRNEIKSIS 417
             + I  +R  +  +S
Sbjct: 241 YPEEIANLREGVGGVS 256


>gi|29827282|ref|NP_821916.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604380|dbj|BAC68451.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 279

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/269 (20%), Positives = 128/269 (47%), Gaps = 21/269 (7%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I+  +G++  + R +  +       + +G  E   A+  ++E N+ LV   A ++ +
Sbjct: 14  LPEIADPSGVAPKDARQLSRLFFDRLAVLEEGTPEYQYARNTLIEMNVTLVRFAAARFRS 73

Query: 466 RGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           R      D++Q G IGL+KA ++F+     +F+++A+ ++   I R   D S  + +P  
Sbjct: 74  RSQDEMEDIVQVGTIGLIKAIDRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRR 133

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI-- 580
           +++   ++ +    + +++ R PT +E+++ + +  E V +    +      SL+  I  
Sbjct: 134 LQEARIQLAKATEELQSRLDRMPTVKELSELMCLSEEEVNEARLASNGYTSSSLDATISS 193

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            ++  + L DFI   +    L     A        ++A L  RE R++ MRF      + 
Sbjct: 194 SNDGEAALADFIGTDDNALELVEDFNA-----LAPMIAELDDRERRIIHMRFV----DEL 244

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T  ++G+   V++  + ++ ++ + KL+ 
Sbjct: 245 TQAQIGEHLGVSQMHVSRLLSRTLAKLRE 273


>gi|260892756|ref|YP_003238853.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
 gi|260864897|gb|ACX52003.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
          Length = 245

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 128/253 (50%), Gaps = 14/253 (5%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
             G  + + +   +++ + +     A++ +V ANL LV  V +++  +G +  DL Q G 
Sbjct: 1   MPGKDLLDQKTTRALLLRAQEGDPQARELLVRANLGLVGKVVRRFAGQGREGEDLFQIGC 60

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA ++FD   G  FSTYA+  +   I R + D    +++   +++   +V+RT   
Sbjct: 61  IGLLKAIDRFDPQRGTCFSTYAVATILGEIRRFLRD-DGMLKVSRSLKETSRRVIRTRAS 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKN 596
           +   + REP+  EIA+ L + VE V   L+  K P  L+ P+  E    L   D +  + 
Sbjct: 120 LKMALGREPSVAEIAESLGIAVEEVVMALEAGKAPAFLQEPLAGEGEEALCWEDCLSSEK 179

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S L++    +LRE+  R    L  RE  ++  RF  G       EEV KQ  +++ ++
Sbjct: 180 EESWLETL---SLRESLRR----LPAREREIIWWRFFAGYTQ----EEVAKQLGISQAQV 228

Query: 657 RQIEAKAIRKLKH 669
            ++E  A++KL+ 
Sbjct: 229 SRLERNALQKLRE 241


>gi|161898895|gb|ABX80437.1| SigB [Listeria monocytogenes]
 gi|161898903|gb|ABX80441.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKINNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|160892497|ref|ZP_02073287.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
 gi|156865538|gb|EDO58969.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
          Length = 258

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 77/253 (30%), Positives = 127/253 (50%), Gaps = 15/253 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +   + +       A++  ++ NLRLV+SV ++++N      DL Q G IGL
Sbjct: 19  LTDKEKDELFDRIEQ---GDMAARETFIKGNLRLVLSVIQRFSNSNENPDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD  L  KFSTYA+  +     R + D +  IR+   +RD  +K + T   +  
Sbjct: 76  IKAIDNFDRSLNVKFSTYAVPMILGECRRYLRDNNS-IRVSRSLRDIAYKAIYTKDALLK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K+ REPT +EIAK++ +  E +   L     P+SL  P+  E  DT ++ D + DK    
Sbjct: 135 KLDREPTVDEIAKEIDVAPEDITTALDAISTPVSLYEPVYQEGGDTLYIVDQLSDKKNKE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +     +L+E     +  L  RE  +LR+RF  G     T  EV  +  +++ ++ +I
Sbjct: 195 -ENWVENISLKE----AMKKLNEREYNILRLRFFEG----KTQTEVASEIAISQAQVSRI 245

Query: 660 EAKAIRKLKHPSR 672
           E  AI+ LK   R
Sbjct: 246 EKSAIKSLKGYLR 258


>gi|2529271|gb|AAB81191.1| sigma factor [Lysinibacillus sphaericus]
          Length = 263

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 68/249 (27%), Positives = 125/249 (50%), Gaps = 17/249 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +++  ++G+ E   A+K MVE N RLV S+ +++T RG++  DL Q G IGL
Sbjct: 12  LSQEEMRDLIARAQQGDHE---ARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGL 68

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK+ +KFD     KFSTYA+  +   I R + D    +++   +R+   K+         
Sbjct: 69  MKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGMVKVSRSIRELNFKIRHATDEFIK 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           + +  PT +E+A+ L +  E +       ++P SL   + +   D+  L D ++D+ +  
Sbjct: 128 RNEHRPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDEKSEQ 187

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D             VL  L PRE+ ++ +R+           E+  +  +++ ++ ++
Sbjct: 188 PFDYI-------PLKEVLTRLEPREQSIIYLRYFSDCTQ----TEIANRLGISQVQVSRL 236

Query: 660 EAKAIRKLK 668
           E K + +LK
Sbjct: 237 EKKILAQLK 245


>gi|215432251|ref|ZP_03430170.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           EAS054]
 gi|289755409|ref|ZP_06514787.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis EAS054]
 gi|289695996|gb|EFD63425.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis EAS054]
          Length = 261

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 117/245 (47%), Gaps = 13/245 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +V +           + ++V+  L L   +A+++  RG    DLIQ   +GL+ AA 
Sbjct: 23  FRELVGLPAGSPEF-QRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDMKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           P+  E+A +L M    V + L    +   +S+++  G +D +  + D + D +A      
Sbjct: 142 PSASELAAELGMDRAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA-----G 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   RE    +L +L  RE  VL +RF        T  ++ ++  +++  + ++ AK+
Sbjct: 197 LDQIENREVLRPLLEALPERERTVLVLRFF----DSMTQTQIAERVGISQMHVSRLLAKS 252

Query: 664 IRKLK 668
           + +L+
Sbjct: 253 LARLR 257


>gi|90023234|ref|YP_529061.1| RNA polymerase factor sigma-32 [Saccharophagus degradans 2-40]
 gi|89952834|gb|ABD82849.1| CheW protein [Saccharophagus degradans 2-40]
          Length = 284

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 64/275 (23%), Positives = 128/275 (46%), Gaps = 13/275 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   I++++    ++  E + +   +   +     A ++MV A+LR V+ +AK Y+  
Sbjct: 15  QNLNAYIQTVNGVAVLTAEEEKALAEDLYYRDNLD--AARKMVMAHLRFVVHIAKSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      ++I     
Sbjct: 73  GLSQSDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKA 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
            +        ++           E +A+ L + V+ VR++  ++     + +    ++D 
Sbjct: 133 QRKLFFNLRGQKKRLAWLTNSEAEAVAQDLNVDVKHVREMEGRLASFDATFDAGADEDDD 192

Query: 586 S-------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +       +L D   D + +   +   + ++    T  L SL  R   +L+ R+    + 
Sbjct: 193 TAYQAPANYLEDRRYDPSTLLEDEDWTENSV-SGLTTALESLDDRSRDILQQRWL--SDD 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TL ++  Q+ V+ ERIRQ+E  A++K+K    +
Sbjct: 250 KSTLHDLAAQYGVSAERIRQLEKNAMKKVKTYLEA 284


>gi|199601686|dbj|BAG70954.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens]
          Length = 153

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 91/188 (48%), Positives = 107/188 (56%), Gaps = 35/188 (18%)

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
           +K      TDDPVRMYLREMGS+ELLSREGEIAIAKRIEAGR  M+A LCESPLTFQALI
Sbjct: 1   KKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALI 60

Query: 169 IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG 228
           IWRDELN+GTTLLREIIDLE                     K     Q    DD+    G
Sbjct: 61  IWRDELNEGTTLLREIIDLETTYS-------------GPEAKAAPQFQSSSEDDITNVGG 107

Query: 229 DIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
           D+    +  +D+                        S  +L+AME +LRP+VM  LD IA
Sbjct: 108 DMPMPEEEEEDEDE----------------------SNLSLAAMEAELRPQVMETLDLIA 145

Query: 289 EVYRELRS 296
           + Y++LR 
Sbjct: 146 DTYKKLRK 153


>gi|149909450|ref|ZP_01898105.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149807560|gb|EDM67509.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 287

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 55/274 (20%), Positives = 125/274 (45%), Gaps = 19/274 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I+ ++    ++  + + +   ++        A ++++ ++LR V+ VA+ Y   GL
Sbjct: 16  IEAYIQGVNNIPMLTAEQEKELGERLQ--NEGDVDAARQLIMSHLRFVVHVARGYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+  +G +  ++A+ WVK  I   +      +++      +
Sbjct: 74  AQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWVKAEIHEFVLRNWRVVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVL-KITKEPISLETP------ 579
             K+    R+   ++    + E   +A+ L +  + V ++  +++    + +        
Sbjct: 134 --KLFFNLRKSKKRLGWFTSAEVKTVAETLGVSTKDVVEMESRMSYSDQAFDLYADDDSD 191

Query: 580 -IGDEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
                 +     ++ED     A+         +   + T  ++ L  R + +++ R+   
Sbjct: 192 KDSGSTSFSPAQYLEDNASDVALQVERENWDKSASLSLTNAISELDERSQDIVKSRWLAE 251

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                TL+ +  ++ V+ ER+RQ+E  A++KL+ 
Sbjct: 252 --DKATLQYLADRYGVSAERVRQLEKNAMKKLRE 283


>gi|153487|gb|AAA26829.1| sigma factor (whiG) (put. alt.) (gtg start codon); putative
           [Streptomyces coelicolor]
          Length = 258

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 107/241 (44%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 21  DERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDVDREIKFE 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++ 
Sbjct: 81  TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEARLRRTPSESEVAVEMG 137

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E+  H          L D +ED  A +P++ A   
Sbjct: 138 IAVED----LHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTLEDTAADNPVEVAEDR 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 194 ELRRLLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 249

Query: 668 K 668
           +
Sbjct: 250 R 250


>gi|291538695|emb|CBL11806.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           XB6B4]
          Length = 259

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 133/261 (50%), Gaps = 13/261 (4%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + I +     ++  + +   + A++  ++ NLRLV+SV K+++      
Sbjct: 5   KVEICGVNTAKLPILKEEEKDALFARIKQGDTAARETYIKGNLRLVLSVIKRFSGNHENV 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+K+ + FD  +G KFSTYA+  +   I R + D +  IR+   +RD  +
Sbjct: 65  DDLFQIGCIGLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           K + T   +S    +EPT +EIA +  +  E +   L   + P+SL  P+  +  DT ++
Sbjct: 124 KAIHTKEILSKTENKEPTLDEIAAESGISKEDIVFALDAIQSPLSLYDPVYTDGGDTLYV 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I DK   +  ++ I+     +    L  L  RE  +L++RF  G     T  EV  +
Sbjct: 184 MDQISDKK--NREENWIEEL---SLNDALDRLNERENYILKLRFFEG----KTQMEVADE 234

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A+  ++H
Sbjct: 235 IHISQAQVSRLEKSALNSIRH 255


>gi|167949417|ref|ZP_02536491.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 128

 Score =  124 bits (311), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 92/127 (72%), Positives = 106/127 (83%)

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP + VRKVLKI KEPIS+ETPIGD++ SHLGDFIED   VSP+DSA    LRE T  
Sbjct: 1   MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVVSPVDSATSEGLREATQN 60

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS++
Sbjct: 61  MLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSER 120

Query: 676 LRSFLDG 682
           +RSFLD 
Sbjct: 121 MRSFLDN 127


>gi|284028684|ref|YP_003378615.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283807977|gb|ADB29816.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 275

 Score =  124 bits (310), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 115/230 (50%), Gaps = 10/230 (4%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            E +E NL +  S+A ++  RG++  DL Q   +GL+KAA  ++   G  F  YA+  ++
Sbjct: 47  NEAIELNLGIAHSIASRFRGRGVESDDLDQVAYLGLLKAARSYNPSTGTPFLAYAVPTIR 106

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R   D S T+RIP  +++    +     ++   ++R+PT EE+A +L   V  V  
Sbjct: 107 GEVKRYFRDCSWTVRIPRRLQELQGSIASVRPQLVQDLQRDPTLEELAAELGTDVAEVEA 166

Query: 566 VLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            +        +SL+ P+  + T++L D I D+   S   +   A L      VL  LTPR
Sbjct: 167 AIAADGCFSVLSLDRPVDGDSTANLADTIADEEDTSFERTEAVAML----EPVLNDLTPR 222

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E ++L +RF  G    HT  ++G +  V++ ++ ++    + +L+    S
Sbjct: 223 ERKILELRFIEG----HTQADIGAEIGVSQMQVSRLLRGILDRLREQIES 268


>gi|256784015|ref|ZP_05522446.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 266

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 113/247 (45%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E +    +  +VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 21  FRRLATLPDGPEHD--ELRDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVD 78

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           ++D   G  F +YA+  +   I R   D   T+ +P  +++  ++V    + +S  I  R
Sbjct: 79  RYDPERGNAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQELRNRVRFAGQDLSQTIPGR 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            PT  EIA++  +  E VR  L+   +   +SL+  +   ED   LGD +   +      
Sbjct: 139 RPTVAEIAERAELSEEDVRVGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPALDTV 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE     LA+L PRE  +L MRF   M      E    Q  +++  + ++  +
Sbjct: 199 VD-----REAVKDRLAALPPRERAILYMRFFDDMTQSRIAE----QLGISQMHVSRLITR 249

Query: 663 AIRKLKH 669
              +++ 
Sbjct: 250 CCDRVRE 256


>gi|325973333|ref|YP_004250397.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
 gi|325989768|ref|YP_004249467.1| RNA polymerase sigma factor [Mycoplasma suis KI3806]
 gi|323574853|emb|CBZ40513.1| RNA polymerase sigma factor [Mycoplasma suis]
 gi|323651935|gb|ADX98017.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
          Length = 530

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 96/267 (35%), Positives = 149/267 (55%), Gaps = 9/267 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           + ++     ++  E + I  ++     + S A+K+++ +NLRLVISVAKKY N G    D
Sbjct: 206 LSTLCFSRMLTADEEKKIAQLM-DIPEKRSFAEKQLMTSNLRLVISVAKKYLNCGFNLGD 264

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQEG  GL KA  KFD+  G KFSTYA WW++QAITRSIADQS  IRIPVHM + I+K+
Sbjct: 265 LIQEGVFGLRKAITKFDYKFGNKFSTYATWWIRQAITRSIADQSKIIRIPVHMMEVINKM 324

Query: 533 VRTARRMSNKIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            +  + +  K    PT EE++ ++           + ++ KI  + +SL+ PI + ++S+
Sbjct: 325 TKAEKELVLKTGNPPTLEELSSEMQKYGTQFTPIKISEIKKINVDLVSLDKPILNNESSN 384

Query: 588 LGDFI-EDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEV 645
             DF+ ED +  +P   A +    E    +L  +L   E  +L + FG+     HT+E++
Sbjct: 385 FADFVREDGDEANPEWIASKNIYEEKLKSLLQETLKKDEYLILALHFGLNNQESHTVEQI 444

Query: 646 GKQFCVTRERIRQIE-AKAIRKLKHPS 671
            + F    +    I   K I+KL  P+
Sbjct: 445 SQLFAKNSDYFSGILTNKKIKKLLTPT 471


>gi|239982580|ref|ZP_04705104.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 259

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 105/242 (43%), Gaps = 25/242 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
            +  +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 21  DARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEKFDPERSIKFE 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  ++ R PT  E+A ++ 
Sbjct: 81  TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYASLEAELHRTPTEAEVAAEMG 137

Query: 558 MPVEGVRKVLKITKEPISL-----------ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           + VE     L      +SL               G  D   + D +ED +A +P++ A  
Sbjct: 138 IAVED----LHAVFSQLSLANVVALEELLHGGGEGGGDRLSIMDTLEDTSADNPVELAED 193

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             LR    R +  L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +
Sbjct: 194 RELRRLLARAINLLPEREKTVVTLYYYEG----LTLAEIGHVLGVTESRVSQIHTKSVLQ 249

Query: 667 LK 668
           L+
Sbjct: 250 LR 251


>gi|225853213|ref|YP_002733446.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|256263296|ref|ZP_05465828.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|225641578|gb|ACO01492.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis ATCC 23457]
 gi|263093265|gb|EEZ17362.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409772|gb|ADZ66837.1| RNA polymerase factor sigma-32 [Brucella melitensis M28]
          Length = 311

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 76/289 (26%), Positives = 131/289 (45%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V C   +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRCFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++ A +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|167036147|ref|YP_001671378.1| RNA polymerase factor sigma-32 [Pseudomonas putida GB-1]
 gi|166862635|gb|ABZ01043.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida GB-1]
          Length = 284

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERL--YYEQDVEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPAVQLEDADWSDNSASNLHEALQGLDERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|15614101|ref|NP_242404.1| sporulation sigma factor SigF [Bacillus halodurans C-125]
 gi|10174155|dbj|BAB05257.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           [Bacillus halodurans C-125]
          Length = 252

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 65/259 (25%), Positives = 125/259 (48%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K    E   +  E + +++     +     A+ ++V  N RLV SV +++ NRG +  
Sbjct: 4   EVKQNEKEQPFTDEEIKQLIAQ---SQAGDQEARDQIVSRNTRLVWSVVQRFLNRGYEAD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSIKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    M+  + R PT  EIA++L +  E V      ++   S+   + + D     L 
Sbjct: 120 IRKLKDDMTKTLGRTPTVNEIAEQLEITPEEVVFAGDASRSLSSIHETVYENDGDPITLL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +ED++     D       +      + +L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQLEDQSETRWFD-------KIALKEAIHNLEERERLIVYLRY----YKDQTQSEVAQRL 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K +  +K
Sbjct: 229 GISQVQVSRLEKKILETMK 247


>gi|229013088|ref|ZP_04170253.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
 gi|229061509|ref|ZP_04198853.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|229168644|ref|ZP_04296366.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228614800|gb|EEK71903.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228717743|gb|EEL69393.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|228748342|gb|EEL98202.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
          Length = 259

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 135/261 (51%), Gaps = 13/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 122 AYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D ++D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 182 FVMDQLKDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 233 EEIGISQAQVSRLEKSAIKQM 253


>gi|294138987|ref|YP_003554965.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
 gi|293325456|dbj|BAJ00187.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
          Length = 286

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 122/257 (47%), Gaps = 14/257 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
           IS+ E +    + ++ +    I A K+++ ++LR V+ VAK Y+  GL   DLIQEGNIG
Sbjct: 29  ISMLEAKQEHELAKRLQETGDIQAAKQLIMSHLRFVVHVAKGYSGYGLPQADLIQEGNIG 88

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LMKA ++FD  +G +  ++A+ W+K  I   +      +++      +  K+    R+  
Sbjct: 89  LMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQR--KLFFNLRKSK 146

Query: 541 NKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSH---LGDFIED 594
            ++      E   +A+ L +    V     ++  +  + +    ++D         ++ED
Sbjct: 147 KRLGWFSDAEVGMVAENLGVSKADVTEMESRMAAQDPAFDLASDNDDDIQDYAPALYLED 206

Query: 595 KN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            +   A        +A+ +      + +L  R + +L+ R+        TL+E+   + V
Sbjct: 207 HSSDLANQVETDNFEADNQTRLLAAIKTLDERSQHILQARWL--NEDKTTLQELAATYQV 264

Query: 652 TRERIRQIEAKAIRKLK 668
           + ERIRQ+E  A+ KLK
Sbjct: 265 SAERIRQLEKNAMNKLK 281


>gi|238917256|ref|YP_002930773.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872616|gb|ACR72326.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 258

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 132/262 (50%), Gaps = 15/262 (5%)

Query: 412 EIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + + +      ++ K +   + A++  ++ NLRLV+S+ ++++  G   
Sbjct: 5   KVEICGVNTSDLPLLKPAQAKELLVKIKSGDTQARETFIKGNLRLVLSIVQRFSQSGENL 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IG++KA + FD  L  +FSTYA+  +   I R + D S TIR+   ++D  +
Sbjct: 65  DDLFQIGCIGMIKAIDNFDISLNVQFSTYAVPMIIGEIKRFLRDNS-TIRVSRSLKDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           K + T   +  K  +EP+  EIA+++ +    +   L+     ISL  P+ ++  DT ++
Sbjct: 124 KAITTRETLMKKNLKEPSITEIAEEIGISKADIVIALEAVTPSISLYEPVFNDGGDTLYV 183

Query: 589 GDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            D ++D KN        I           +  L+PRE +++ +RF        T  EV K
Sbjct: 184 IDQVKDKKNTEDRWVRNI------ALQEAINRLSPRERQIIILRFF----DCLTQTEVAK 233

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              +++ ++ ++E  A+R +K 
Sbjct: 234 GLGISQAQVSRLEKCALRDMKR 255


>gi|167507953|gb|ABZ81297.1| RpoD [Thalassospira sp. MCCC 1A02039]
 gi|167507955|gb|ABZ81298.1| RpoD [Thalassospira sp. MCCC 1A02040]
          Length = 257

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 67/255 (26%), Positives = 120/255 (47%), Gaps = 16/255 (6%)

Query: 179 TLLREIIDLEACIG-------PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI- 230
            LLR++IDLE   G         ++G     T+  +    E      + DD  ETE    
Sbjct: 1   LLLRDVIDLETTYGGGPEAEIAAAEGEDEEDTDVDAEADVESFESANDDDDEAETETPAG 60

Query: 231 ---ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
              E+  +   ++ S+     E   + + + D++ +    +LS ME++L  +V+   + I
Sbjct: 61  ITDEAEEEEDDEEESEKSEGEEGEGDGDDDDDDENEQVNVSLSKMEEELTEQVLEKFELI 120

Query: 288 AEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           A+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ +
Sbjct: 121 AKTYEKLHKAQEQRLVALNKGEAVPVATEKRYNKLKNEMVDLMEDVHLNNFRIEELLDHM 180

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK FV   
Sbjct: 181 TGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKTFVERY 240

Query: 403 VDSILKIRNEIKSIS 417
            D I  +R  +  +S
Sbjct: 241 SDEIANLREGVGGVS 255


>gi|83955694|ref|ZP_00964274.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83839988|gb|EAP79164.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 279

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 71/271 (26%), Positives = 120/271 (44%), Gaps = 15/271 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I     +   E   +    R  E + + A   MV ++LRL   +A  Y   GL   +
Sbjct: 1   MQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYGLPQAE 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIH 530
           +I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      +    
Sbjct: 59  VISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQKKLFF 118

Query: 531 KVVRTARR---MSNKIKREPTPEEIAKKLAMPV-EGVRKVLKITKEPISLETPIGDEDTS 586
            + +   R   +          + IA  L +   E +    +++    SL   +G E   
Sbjct: 119 NLRKAKNRIGALEEGDLHPDNVKRIATDLGVTETEVISMNRRMSGGDASLNATVGSEGEG 178

Query: 587 H--LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                D++ED++A    D   +  L   RE     L  L  RE+ +L        +   T
Sbjct: 179 TMQWQDWLEDEDADQATDYEERDELETRREMLAEALDVLNDREKDILTQ--RRLSDQTVT 236

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           LE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 237 LEDLSSQYDVSRERIRQIEVRAFEKLQKRMR 267


>gi|50871566|emb|CAF74874.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 262

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 109/301 (36%), Gaps = 45/301 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T   ++   + + +    L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYERVTNEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +     V + + D E     S+++       PE A   
Sbjct: 59  DDGA------AGAPQEVEPVAPQVAAKPVADDKDDDEEEESDSEEEEGDGGPDPEVARVR 112

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +                                       +K  ++S + 
Sbjct: 113 FGAVAEQLEKAKKA-----------------------------------LKKHGRASQQA 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   +I   E  +++L      + R  FL +
Sbjct: 138 IDELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAVMQLCVRDARMPRADFLRQ 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        + ++   +    + I + + ++  +  E  ++I++ + I   
Sbjct: 198 FPSNETNLAWAEELAA-GKSKYAEAIGARKEDIQRCQQKLIELEQECELAIADIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|21224822|ref|NP_630601.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|3559995|emb|CAA20617.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 266

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 113/247 (45%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E +    +  +VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 21  FRRLATLPDGPEHD--ELRDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVD 78

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           ++D   G  F +YA+  +   I R   D   T+ +P  +++  ++V    + +S  I  R
Sbjct: 79  RYDPERGNAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQELRNRVRFAGQDLSQTIPGR 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            PT  EIA++  +  E VR  L+   +   +SL+  +   ED   LGD +   +      
Sbjct: 139 RPTVAEIAERAELSEEDVRVGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPALDTV 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE     LA+L PRE  +L MRF   M      E    Q  +++  + ++  +
Sbjct: 199 VD-----REAVKDRLAALPPRERAILYMRFFNDMTQSRIAE----QLGISQMHVSRLITR 249

Query: 663 AIRKLKH 669
              +++ 
Sbjct: 250 CCDRVRE 256


>gi|152998320|ref|YP_001343155.1| RNA polymerase factor sigma-32 [Marinomonas sp. MWYL1]
 gi|150839244|gb|ABR73220.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas sp. MWYL1]
          Length = 288

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 118/269 (43%), Gaps = 11/269 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + I+++S    ++  E + +   +     E   A + +V ++LR V+ +AK Y+  
Sbjct: 15  QNLESYIQAVSRIPILTADEEKALAERL--YYQEDLEAARTLVMSHLRFVVHIAKSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     
Sbjct: 73  GLAQGDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKA 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI----TKEPISLETPIGD 582
            +       + + S         E +A  L +  E VR++            +      D
Sbjct: 133 QRKMFFNLRSAKKSLSWFSNSEVESVASDLGVTPEVVRQMEGRLSSSDMAFDASADDDDD 192

Query: 583 EDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   ++ED     A    +   + +  +     +A L  R   +L  R+     + 
Sbjct: 193 SAFQAPSQYLEDHRSDPATLLENGNWEEDSNQRLEVAMADLDERSRNILVQRWLSDAKS- 251

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 252 -TLHELADEYGVSAERIRQLEKNAMKKIR 279


>gi|165922507|ref|ZP_02219678.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212211687|ref|YP_002302623.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuG_Q212]
 gi|165916712|gb|EDR35316.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212010097|gb|ACJ17478.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuG_Q212]
          Length = 288

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 121/276 (43%), Gaps = 13/276 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI  I + I  ++    +S  E   + +  R+       A +++V ++LR V+ +A+ Y+
Sbjct: 14  SIGSIGSYISWVNRIPLLSAEEEHDLANKFRQ--SNDLEAARKLVLSHLRFVVRIARGYS 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      ++I   
Sbjct: 72  GYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATT 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +                 +     +A++L +  + VR++ +       + +    + 
Sbjct: 132 KAQRKLFFNLRKHAKKRGWFSDHEAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEES 191

Query: 584 DTSHLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           D+          ++EDK    A+    S    +        + SL  R   +L  R+   
Sbjct: 192 DSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRWL-- 249

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                TL E+  Q+ V+ ERIRQ+E  A++K++   
Sbjct: 250 SEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|56459340|ref|YP_154621.1| RNA polymerase factor sigma-32 [Idiomarina loihiensis L2TR]
 gi|56178350|gb|AAV81072.1| DNA-directed RNA polymerase sigma 32 subunit [Idiomarina loihiensis
           L2TR]
          Length = 286

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 65/281 (23%), Positives = 136/281 (48%), Gaps = 17/281 (6%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +A  V     +   I+S++    ++  + + + + +   E     A KE++ ++LR V+ 
Sbjct: 8   MALSVPQGAGLDGYIQSVNRIPMLTAEKEKALATRL--YENSDLDAAKELIMSHLRFVVH 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           VA+ Y+  GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      
Sbjct: 66  VARSYSGYGLPQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVLRNWRV 125

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKR--EPTPEEIAKKLAMPVEGV-RKVLKITKEPIS 575
           +++      +  K+    R+M  ++    +   E +A +L +  + V     +++    +
Sbjct: 126 VKVATTKAQR--KLFFNLRKMKKRLGWFSQKEVETVANELGVSTKEVLEMETRMSAHDQA 183

Query: 576 LETPIGDEDT-----SHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERV 627
            E    D+D+          ++EDK    A        + + ++     ++ L  R + +
Sbjct: 184 FELSSDDDDSKEGSAYSPAMYLEDKRSDLAAEIEAKDYENHTQQKLLGAMSHLDERSQDI 243

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++ R+     T  TL ++ +++ V+ ER+RQ+E  A++KL+
Sbjct: 244 VQSRWLSEDKT--TLHDLAEKYEVSAERVRQLEQNAMKKLR 282


>gi|302539934|ref|ZP_07292276.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302457552|gb|EFL20645.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 274

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 114/256 (44%), Gaps = 15/256 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + +EFR +  +    E EA   ++ +VEA + +   +A++Y NRG    DL Q   +GL+
Sbjct: 26  TDAEFREMARLPEGPEKEAL--RQRVVEAWMPMAQRLARQYRNRGESLEDLEQVAALGLV 83

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +++D   G  F+ +A+  V   I R   D    + +P  +++  ++V    R +S+ 
Sbjct: 84  KAVKRYDPEHGTAFAGFAVPTVVGEIKRHFRDHLWVLHVPRRVQELRNRVRAAHRELSHS 143

Query: 543 IKREPTPEE-IAKKLAMPVEGVR--KVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAV 598
           +     P E IA++  +  + VR       +  P+SL+  +   +D   L D +      
Sbjct: 144 LDDATVPTEAIAERTGLSEKEVRIGMEAMGSFTPLSLDAQLTGADDGYSLADTLG----- 198

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               +  +   RE     L  L  RE ++L MRF   M      E    Q  +++  + +
Sbjct: 199 GQEPAYDRVVDREAVRPGLGRLPARERQILYMRFFCDMTQSRIAE----QLGISQMHVSR 254

Query: 659 IEAKAIRKLKHPSRSK 674
           +  +    L+  + ++
Sbjct: 255 LINRTCSTLRAQALAE 270


>gi|145224453|ref|YP_001135131.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216939|gb|ABP46343.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 342

 Score =  124 bits (310), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 112/247 (45%), Gaps = 6/247 (2%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +    ++++ +        ++ ++   L L   +A+++  RG    DL+Q   +GL+
Sbjct: 90  DVLDMFRELAVLDRDSAAFRRQREAIIARCLPLADHIARRFRGRGEGHEDLVQVARVGLL 149

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD      F  +A+  +   + R   D   ++++P  +++   ++      ++ +
Sbjct: 150 NAVNRFDVDSANDFLAFAVPTMMGEVRRYFRDHGWSLKVPRRLKELNVRLNAARADLTQE 209

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + R PTP E+AK L +  E V + L       +  T      +   G+ +  ++     D
Sbjct: 210 LNRAPTPSELAKYLGIDREEVVEGLVAANAYSTRSTEQPTTFSGD-GEGLSLQDTFGAPD 268

Query: 603 SAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             IQ  +   T   +LA+L  R+  VL++RF      D T  ++ +Q  V++  + ++ A
Sbjct: 269 DNIQKVIDVNTVQPLLAALPERDRLVLKLRFF----EDRTQSQIAEQIGVSQMHVSRLLA 324

Query: 662 KAIRKLK 668
           +A+  L+
Sbjct: 325 RALATLR 331


>gi|302147239|emb|CBL51741.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 262

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 112/301 (37%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ +
Sbjct: 58  -----------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|51894120|ref|YP_076811.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
 gi|51857809|dbj|BAD41967.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
          Length = 253

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            +H+    R  +   + A+  +V+  L LV  VA +        +   D+   G  GL++
Sbjct: 1   MQHLELWQRWRQSHDTAARDALVQHYLWLVRYVAGRLMVGMPDHVDQGDVEGHGCFGLLE 60

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  ++D   G +F T+A+ W++ A    +            +R ++ ++ R    +   +
Sbjct: 61  AIARYDPDRGVRFETFAIPWIRGACLEGLRAMQWAPA----LRRRVRQLERVRDELMAVL 116

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDED--TSHLGDFIEDKNAVS 599
            REP+  E+A+++ + VE   + L+       +SL+  +  +D  T+ L D + D+ AV 
Sbjct: 117 GREPSAAELAEQMGISVEEAERRLQEAGTLAVLSLDEALAFDDGETTALADRVADEEAVD 176

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P   + +A  RE   R +ASLT +E+ V+ + +  G       +EV +   +++ RI Q+
Sbjct: 177 PELESQRAERREVLARAIASLTEQEQLVIALIYQEG----LIAKEVSEILGLSQARISQV 232

Query: 660 EAKAIRKLK-HPSRSKK 675
            +KAI +L+   SR K+
Sbjct: 233 HSKAILRLRGKLSRMKR 249


>gi|291559903|emb|CBL38703.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SSC/2]
          Length = 258

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 72/264 (27%), Positives = 131/264 (49%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            R +++   V T  + +        +  + E    +A++  ++ NLRLV+S+ ++++   
Sbjct: 2   ARKKVEICGVNTSSLPLLSEEEKEDLFERIEQGDLLAREHYIKGNLRLVLSIIQRFSGSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD  L  KFSTYA+  +   + R + D     R+   +RD
Sbjct: 62  ENADDLFQVGCIGLMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM-RVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +     ++ K+  EPT + IAK++ M  E V   L     P+SL  P+  +  DT
Sbjct: 121 TAYKAINAREVLTKKLNHEPTIDVIAKEIDMKKEDVLFALDAIATPLSLYEPVYQDGGDT 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            +L D ++DK   +  DS +++         +  L  RE  +++MRF  G     T  EV
Sbjct: 181 LYLMDQVKDKK--NKEDSWVESI---ALKEAMEHLPDREYDIIKMRFFEG----KTQTEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E  A++ +K+
Sbjct: 232 ADEIAISQAQVSRLEKNALKHMKN 255


>gi|88858433|ref|ZP_01133075.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
 gi|88820050|gb|EAR29863.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
          Length = 288

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 132/269 (49%), Gaps = 17/269 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++++S    +S  + + +   V+  +     A ++++ ++LR V  +AK Y+  GL   
Sbjct: 22  YLQAVSGIAMLSAEDEQALA--VKLQQDGDLDAARQLIMSHLRFVAHIAKGYSGYGLPQA 79

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKI 529
           DLIQEGNIGLMKA ++FD  +G +  ++A+ W+K  I   +      +++      R   
Sbjct: 80  DLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQRKLF 139

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-- 586
             + +  +R+      E +   +A +L +  + VR++  +++ + +  +    D+D++  
Sbjct: 140 FNLRKNKKRLGWFNPEEVST--VANELGVTEKDVREMEARMSSQDMVFDLTTDDDDSTSA 197

Query: 587 ---HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ D +   A    +   +          L SL  R + +++ R+    +   
Sbjct: 198 TQYSPVQYLTDNSVDLADKIEEEQWEEQTHNRLFHALKSLDERSQDIVQTRWL--SDDKA 255

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           TL+++  ++ V+ ER+RQ+E  A++KL+H
Sbjct: 256 TLQDLAVKYDVSAERVRQLEKTAMKKLQH 284


>gi|332524130|ref|ZP_08400360.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
 gi|332107469|gb|EGJ08693.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
          Length = 306

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 71/291 (24%), Positives = 131/291 (45%), Gaps = 23/291 (7%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V SI  +   I +++    +S  E   +   +R  E     A   +V ++LRLV+SV+++
Sbjct: 17  VPSIGHLDAYITAVNRLPMLSAQEEVALGKRLR--EHGDLEAAGRLVLSHLRLVVSVSRQ 74

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  I   I      +++ 
Sbjct: 75  YLGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHWIKAEIHEYILKNWRMVKVA 134

Query: 523 VH-MRDKIHKVVRTARR----------MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-T 570
               + K+   +R+ ++          +          E +A++L +  + V ++     
Sbjct: 135 TTKAQRKLFFNLRSMKQGLKGEAAEADLHRSTLTPAEVETVARELNVKPDEVVEMETRLA 194

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT-----TRVLASLTPREE 625
              ++LE P  D+            +  S     ++A  R+        + L+ L  R  
Sbjct: 195 GGDVALE-PQTDDSEESFAPIAYLADEASEPTRLLEARRRDWLSGDGIAQALSVLDARSR 253

Query: 626 RVLRMRFGIGMNTD---HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++  R+    +      TL E+  ++ V+ ERIRQIE  A++K++    +
Sbjct: 254 RIVEERWLKVNDDSSGGMTLHELAAEYGVSAERIRQIEVAAMKKMRKALEA 304


>gi|331695379|ref|YP_004331618.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950068|gb|AEA23765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 259

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 56/255 (21%), Positives = 118/255 (46%), Gaps = 18/255 (7%)

Query: 423 SISEFRHIVSMVRKGECEA------SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +  E+ H+V ++ +    A         + E+V   L +   +A+++ +RG    DL Q 
Sbjct: 4   TDPEYGHLVPLLEEYAGLAPDDPRREALRDELVRGYLPVAQHIARRFAHRGEPLDDLTQV 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
             +GL+ A ++F    G  F ++A+  +   + R   D   ++R+P  ++D    +    
Sbjct: 64  ATVGLINAIDRFAPDKGSDFFSFAVPTISGEVRRHFRDLGWSMRVPRRLKDLHVSLNGAV 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIE 593
             +S ++ R P P EIA+ L MPV  V + L+        SL+  +  E  S  +G+ + 
Sbjct: 124 SDLSQRLGRAPKPTEIAEYLGMPVADVLEGLEAADAYRSSSLDEMLSSEQGSATVGELVG 183

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           + +A        + + R+    VLA L  RE  ++ +RF        T  ++ ++  +++
Sbjct: 184 EADA-----ELDRVDTRQALRPVLAELGERERTIVMLRFFGN----MTQTQIAEKVGISQ 234

Query: 654 ERIRQIEAKAIRKLK 668
             + ++ A+ + +L+
Sbjct: 235 MHVSRLLAQTLDRLR 249


>gi|256396809|ref|YP_003118373.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256363035|gb|ACU76532.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 353

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 13/245 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +         I + E+V+ +L LV  +A+++ NRG    DL Q   IGL+K+ +
Sbjct: 112 FARLNELPEGSTERKQI-RDELVQMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVD 170

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +FSTYA   V   I R   D+   +R+P  +++    +      +S + +R 
Sbjct: 171 RFDTERGVEFSTYATPTVIGEIKRHFRDKGWAVRVPRRLQELRLSLTSATSELSQRNRRS 230

Query: 547 PTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           PT  E+A+ L +  E V + L+       +SL+   G ++ S  + D +  ++       
Sbjct: 231 PTVAELAEYLKISEEEVLEGLESANAYSTLSLDVSEGGDEDSPAVADSLGSEDEALEGVE 290

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 RE+   +L  L PRE+++L +RF   M      EE+     +++  + ++ A+ 
Sbjct: 291 Y-----RESLKPLLEQLPPREKKILLLRFFGNMTQSQIAEEI----GISQMHVSRLLART 341

Query: 664 IRKLK 668
           + +L+
Sbjct: 342 LEQLR 346


>gi|167507899|gb|ABZ81270.1| RpoD [Thalassospira sp. MCCC 1A00350]
 gi|167507915|gb|ABZ81278.1| RpoD [Thalassospira sp. MCCC 1A01057]
 gi|167507925|gb|ABZ81283.1| RpoD [Thalassospira sp. MCCC 1A01148]
 gi|167507933|gb|ABZ81287.1| RpoD [Thalassospira sp. MCCC 1A01275]
 gi|167507969|gb|ABZ81305.1| RpoD [Thalassospira sp. MCCC 1A02096]
          Length = 257

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 120/255 (47%), Gaps = 16/255 (6%)

Query: 179 TLLREIIDLEACIG-------PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI- 230
            LLR++IDLE   G         ++G     T+  +    E      + DD  ETE    
Sbjct: 1   LLLRDVIDLETTYGGGPEAEIAAAEGEDEEDTDVDAEADVESFESANDDDDEAETETPAG 60

Query: 231 ---ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
              E+  +   ++ S+     E   + E + D++ +    +LS ME++L  +V+   + I
Sbjct: 61  ITDEAEEEEDDEEESEKSEGEEGEGDGEDDDDDENEQVNVSLSKMEEELTEQVLEKFELI 120

Query: 288 AEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           A+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ +
Sbjct: 121 AKTYEKLHKAQEQRLVALNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNNFRIEELLDHM 180

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK FV   
Sbjct: 181 TGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKTFVERY 240

Query: 403 VDSILKIRNEIKSIS 417
            D I  +R  +  +S
Sbjct: 241 SDEIANLREGVGGVS 255


>gi|317056324|ref|YP_004104791.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315448593|gb|ADU22157.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ruminococcus
           albus 7]
          Length = 256

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 74/261 (28%), Positives = 129/261 (49%), Gaps = 14/261 (5%)

Query: 411 NEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V TG + I        ++++       A++++++ NLRLV+SV +KY+     
Sbjct: 4   NKVEISGVNTGDLKILTESEKQELLKRSADGDKTAREKLIKGNLRLVLSVLQKYSGGKEN 63

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G +GL+KA + FD  L  +FSTYA+  +   I R + D    IR+   MRD  
Sbjct: 64  PDDLFQVGVVGLIKAIDNFDVGLNVRFSTYAVPMILGEIKRYMRDF-RPIRVSRSMRDLA 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL- 588
           ++V++   R   + +REP+ +EIA+        +   L+   +P+S+  P+  +    L 
Sbjct: 123 YRVMQAKERFIAEKQREPSIDEIAEITNEKRADIVTALESVTDPVSIYEPVYTDGGDPLC 182

Query: 589 -GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D I D    S     +      T    L  L PRE+ +L +RF  G    HT  EV  
Sbjct: 183 IADQICDSTDDSSWLEEL------TMKEALKELRPREKNILFLRFFKG----HTQVEVAH 232

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           +  +++ ++ ++E  A+ K+K
Sbjct: 233 EIGISQAQVSRLEKNALNKIK 253


>gi|260438829|ref|ZP_05792645.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
 gi|292808819|gb|EFF68024.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
          Length = 260

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 71/265 (26%), Positives = 127/265 (47%), Gaps = 13/265 (4%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + +   +    ++ K +     A++  ++ NLRLV+SV K+++  G   
Sbjct: 5   KVEICGVNTSKLPLLSTKEKEELIIKVKNGDKAARERYIKCNLRLVLSVVKRFSGNGENM 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+KA + FD  L  KFSTYA+  +   I R + D S  IR+   ++D   
Sbjct: 65  DDLFQIGCIGLIKAIDNFDMSLNVKFSTYAVPMIIGEIRRFLRDNS-QIRVSRSLKDVAF 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           + +    R+    K EPT  E+A ++ +  E +   L   + P+SL  PI  +  D  ++
Sbjct: 124 RAIYAKERIMKTGKDEPTVNELATEIGVSKEELVMALDAIQTPVSLYEPIYTDGGDMLYV 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I DK           A         +  L  RE+ ++++R+  G     T  EV K 
Sbjct: 184 MDQIGDKKNTEENWVNEMA-----LKDAIKRLPDREKEIIKLRYFDG----KTQMEVSKM 234

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             +++ ++ ++E  AI+ +++  R 
Sbjct: 235 VRISQAQVSRLEKSAIKNMENYLRR 259


>gi|297191780|ref|ZP_06909178.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197721703|gb|EDY65611.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 278

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 105/233 (45%), Gaps = 16/233 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF TYA+
Sbjct: 45  REQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERSIKFETYAI 104

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++ + V+
Sbjct: 105 TRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPSESEVAAEMGITVD 161

Query: 562 GV--RKVLKITKEPISLETPIGDEDTS----HLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            +            ++LE  +           L D +ED  A +P++ A    LR    R
Sbjct: 162 ELHSVFSQLSLANVVALEELLHVGGEGGERLSLMDTLEDTAADNPVEVAEGRELRRLLAR 221

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L+
Sbjct: 222 AINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQLR 270


>gi|90415296|ref|ZP_01223230.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90332619|gb|EAS47789.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 278

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 124/268 (46%), Gaps = 12/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I+  +    ++I E R +   +     E   A + MV A+LR V+ +A+ Y   GL
Sbjct: 10  LNAYIQGTATVPILTIDEERALGESL--YYQEDLDAARRMVMAHLRFVVHIARSYNGYGL 67

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA  +F+   G +  ++A+ W+K  I   I      ++I     + 
Sbjct: 68  PLADLIQEGNVGLMKAVRRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQR 127

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   +R+A++    +  +              + +   +++T    + + P G++D S 
Sbjct: 128 KLFFNLRSAKKQLQWLSADEAKAVADDLGVQVKDVMEMEMRLTSRDPAFDAPAGEDDESS 187

Query: 588 ----LGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  F+EDK+   A    +   + +        ++ L  R   +L+ R+    +   
Sbjct: 188 SFQAPVYFLEDKSMDPAQLAENDDWEVDNNTRLIAAVSDLDDRSRDILQRRWL--NDAKA 245

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 246 TLHELAAEYGVSAERIRQLEKNAMKKVR 273


>gi|50871564|emb|CAF74873.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 262

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 108/301 (35%), Gaps = 45/301 (14%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T   ++   + + +    L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDGILADYERVTNEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +     V + + D E     S+++       PE A   
Sbjct: 59  DDGA------AGAPQEVEPVAPQVAAKPVADDKDDDEEEESDSEEEEGDGGPDPEVARAR 112

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +                                       +K  ++S   
Sbjct: 113 FGAVAEQLEKAKKA-----------------------------------LKKHGRASQHA 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ D   +I   E  +++L      + R  FL +
Sbjct: 138 IDELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAVMQLCVRDARMPRADFLRQ 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        + ++   +    + I + + ++  +  E  ++I++ + I   
Sbjct: 198 FPSNETNLAWAEELAA-GKSKYAEAIGARKEDIQRCQQKLIELEQECELAIADIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|167507965|gb|ABZ81303.1| RpoD [Thalassospira sp. MCCC 1A02093]
          Length = 257

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 67/255 (26%), Positives = 120/255 (47%), Gaps = 16/255 (6%)

Query: 179 TLLREIIDLEACIG-------PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI- 230
            LLR++IDLE   G         ++G     T+  +    E      + DD  ETE    
Sbjct: 1   LLLRDVIDLETTYGGGPEAEIAAAEGEDEEDTDVDAEADVESFESANDDDDEAETETPAG 60

Query: 231 ---ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
              E+  +   ++ S+     E   + + + D++ +    +LS ME++L  +V+   + I
Sbjct: 61  ITDEAEEEEDDEEESEKSEGEEGEGDGDDDDDDENEQVNVSLSKMEEELTEQVLEKFELI 120

Query: 288 AEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           A+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ +
Sbjct: 121 AKTYEKLHKAQEQRLVALNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNNFRIEELLDHM 180

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK FV   
Sbjct: 181 TGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKTFVERY 240

Query: 403 VDSILKIRNEIKSIS 417
            D I  +R  +  +S
Sbjct: 241 ADEIANLREGVGGVS 255


>gi|262278444|ref|ZP_06056229.1| EsvH [Acinetobacter calcoaceticus RUH2202]
 gi|262258795|gb|EEY77528.1| EsvH [Acinetobacter calcoaceticus RUH2202]
          Length = 288

 Score =  124 bits (310), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 127/270 (47%), Gaps = 13/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
           + K+   +R+ ++ S K+  E   + IA  L +  E V ++  ++T    + E    D+D
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLE-EAQSIANDLNVTAEQVLEMEGRLTAYDAAFEAQGDDDD 194

Query: 585 TSHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++ED     A    +   +          +  L  R   +L+ R+     +
Sbjct: 195 DTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHNAMDQLDDRSRNILQRRWLDDDKS 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 255 --TLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|50871558|emb|CAF74870.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871560|emb|CAF74871.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 110/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G         + Q+ E  + +       + + D E     S+++       PE A   
Sbjct: 59  DDGAA-------APQEVEPVTPQATAKPADDDKDDEEEDDSDSEEEEGDGGPDPEVARVR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  D +   L                                   +K  + S + 
Sbjct: 112 FGAVAEQLDVAKKAL-----------------------------------KKHGRGSQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               ++L  L   + L   + D LV+++ D   +I   E  ++++      + R  FL +
Sbjct: 137 TDALQELATLFMPIKLIPKQYDALVQRVRDALSQIRAQERAIMQICVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E D  W        + ++   +A   + I   + ++ ++  E  ++I++ + I   
Sbjct: 197 FPNHETDLDWADQLAA-GKSKYAEAIAARKEDIQSCQQKLIALEEECVLAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|317121977|ref|YP_004101980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
 gi|315591957|gb|ADU51253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
          Length = 250

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 109/240 (45%), Gaps = 13/240 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
             +  +     + A++ +V  ++ LV  VA+++   G +  DL+Q G IGL++A + FD 
Sbjct: 3   AELWARARRGDAEARERLVALHMPLVRHVARRFAGFGHEMDDLVQAGTIGLLQAIDGFDP 62

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY+FSTYA+  +   I R +        +   MR ++  + R A  M  ++   P   
Sbjct: 63  ARGYQFSTYAVPAILGEIRRWLRASD-PAGLTRAMRARVAAIRRVAEAMEQELGHRPPAA 121

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANL 609
            +A++L   V  V   L+ ++ P+SL+ P+  + D S  G  +         D+      
Sbjct: 122 AVAERLGCDVADVTFALEASQVPVSLDEPLSSDPDASARGQRLAAPAEPDWSDAV----- 176

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L PR   ++ +RF      D T  EV     +++ ++ ++E  A+ +L+ 
Sbjct: 177 --AVRAALTQLPPRLRTIVTLRFF----RDMTQAEVAAAVGLSQPQVSRLEKLALGQLRQ 230


>gi|11079159|dbj|BAB17584.1| DNA-directed RNA polymerase subunit D [Marinobacterium stanieri]
          Length = 266

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 113/315 (35%), Gaps = 50/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M +L   P +   ++   + +      L +I      
Sbjct: 1   VELLTREGEIDIAKRIEEGIREVMMALSRFPGSVDIILDAYNSVLQEEGRLSDI--FSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P+S                 ++  E E D+  E + D +       ++  +    PE 
Sbjct: 59  IDPDSDI----------PAPEAEAPVEIEEDEDDEDDDDDKEKGDDDSNEEKERGPDPEE 108

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + E  D+   T+                                    +   S
Sbjct: 109 ARQRFGLIQESLDNLNATI------------------------------------ERGGS 132

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDV 369
           + + +     L      + L+    DLLV+++ D    I   E  ++R+  Q   + R +
Sbjct: 133 ADEVEFAAMSLANAFAPIKLSPRYYDLLVQRVRDCIDSIRKQERTIMRICTQRAKMPRPL 192

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F++   G E    W+    +  +  +   +   +  + + +  ++ +    G+ +++ + 
Sbjct: 193 FIKSFPGNETSQEWLDELVN-SDKPFAAPIKRSMPDLQRAQRRLRQVEENIGLRLADIKE 251

Query: 430 IVSMVRKGECEASIA 444
           +   +  GE  A  A
Sbjct: 252 VNRDLSIGEARARRA 266


>gi|302127743|emb|CBL51725.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|302147241|emb|CBL51742.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|302147243|emb|CBL51743.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|328802587|emb|CBL54075.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|328802589|emb|CBL54076.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|328802591|emb|CBL54077.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|328802593|emb|CBL54078.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|329111882|emb|CBL59323.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|329111884|emb|CBL59324.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|329111886|emb|CBL59325.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 262

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +   + +
Sbjct: 58  -----------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ Q++ ++    
Sbjct: 95  DSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|225574955|ref|ZP_03783565.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037802|gb|EEG48048.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
          Length = 259

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 136/268 (50%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + I        + R+ +     A++E ++ NLRLV+SV K+++N  
Sbjct: 2   ALNKVEICGVNTAKLPILSNEEKEELFRRIKQGDQQAREEYIKGNLRLVLSVIKRFSNSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENADDLFQIGCIGLIKAIDNFDTTLDVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +    R+  +  +EPT EEI+K++ +  E +   L   + P+SL  P+  E  D 
Sbjct: 121 IAYKAIYAKERIVKEELKEPTIEEISKEIGIEKEMIVYALDAIQNPVSLFEPVYTEGGDA 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I DK          + +LRE     +  L  RE+ ++ +RF  G     T  EV
Sbjct: 181 LYVMDQISDKKNKE-EHWVEELSLRE----AMDRLGEREKHIIDLRFYEG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            ++  +++ ++ ++E  A++ ++   RS
Sbjct: 232 AREIGISQAQVSRLEKNALKTMRTYLRS 259


>gi|161898923|gb|ABX80451.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 108/239 (45%), Gaps = 4/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|30022159|ref|NP_833790.1| sporulation sigma factor SigF [Bacillus cereus ATCC 14579]
 gi|30264150|ref|NP_846527.1| sporulation sigma factor SigF [Bacillus anthracis str. Ames]
 gi|42783188|ref|NP_980435.1| sporulation sigma factor SigF [Bacillus cereus ATCC 10987]
 gi|47529588|ref|YP_020937.1| sporulation sigma factor SigF [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47568126|ref|ZP_00238830.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49186981|ref|YP_030233.1| sporulation sigma factor SigF [Bacillus anthracis str. Sterne]
 gi|49478518|ref|YP_038132.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141420|ref|YP_085409.1| sporulation sigma factor SigF [Bacillus cereus E33L]
 gi|65321467|ref|ZP_00394426.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|75762406|ref|ZP_00742276.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118479276|ref|YP_896427.1| sporulation sigma factor SigF [Bacillus thuringiensis str. Al
           Hakam]
 gi|165871124|ref|ZP_02215774.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167633745|ref|ZP_02392069.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|167639441|ref|ZP_02397712.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|170687128|ref|ZP_02878346.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|170705887|ref|ZP_02896350.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|177652593|ref|ZP_02935009.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190565830|ref|ZP_03018749.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035002|ref|ZP_03102409.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196045861|ref|ZP_03113090.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206971277|ref|ZP_03232228.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206977400|ref|ZP_03238296.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217961566|ref|YP_002340136.1| sporulation sigma factor SigF [Bacillus cereus AH187]
 gi|218234550|ref|YP_002368877.1| sporulation sigma factor SigF [Bacillus cereus B4264]
 gi|218899234|ref|YP_002447645.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|218905210|ref|YP_002453044.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|222097523|ref|YP_002531580.1| sporulation sigma factor sigf [Bacillus cereus Q1]
 gi|225866059|ref|YP_002751437.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227816852|ref|YP_002816861.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228902583|ref|ZP_04066734.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|228909904|ref|ZP_04073725.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228916713|ref|ZP_04080278.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922825|ref|ZP_04086123.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228929122|ref|ZP_04092149.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935394|ref|ZP_04098212.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941224|ref|ZP_04103777.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947793|ref|ZP_04110080.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954358|ref|ZP_04116384.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960339|ref|ZP_04121992.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228967106|ref|ZP_04128142.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974156|ref|ZP_04134726.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980748|ref|ZP_04141053.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228987264|ref|ZP_04147385.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229019284|ref|ZP_04176110.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|229025528|ref|ZP_04181938.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|229047765|ref|ZP_04193345.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|229071577|ref|ZP_04204795.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|229081330|ref|ZP_04213833.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|229093131|ref|ZP_04224253.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|229111546|ref|ZP_04241097.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|229123596|ref|ZP_04252791.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|229129353|ref|ZP_04258324.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|229140809|ref|ZP_04269354.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|229146647|ref|ZP_04275014.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|229152275|ref|ZP_04280468.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|229157657|ref|ZP_04285732.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|229186319|ref|ZP_04313484.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|229192285|ref|ZP_04319250.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|229198196|ref|ZP_04324905.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|229603990|ref|YP_002868374.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|254683842|ref|ZP_05147702.1| sporulation sigma factor SigF [Bacillus anthracis str. CNEVA-9066]
 gi|254721677|ref|ZP_05183466.1| sporulation sigma factor SigF [Bacillus anthracis str. A1055]
 gi|254736189|ref|ZP_05193895.1| sporulation sigma factor SigF [Bacillus anthracis str. Western
           North America USA6153]
 gi|254744078|ref|ZP_05201761.1| sporulation sigma factor SigF [Bacillus anthracis str. Kruger B]
 gi|254754142|ref|ZP_05206177.1| sporulation sigma factor SigF [Bacillus anthracis str. Vollum]
 gi|254758168|ref|ZP_05210195.1| sporulation sigma factor SigF [Bacillus anthracis str. Australia
           94]
 gi|296504567|ref|YP_003666267.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|301055569|ref|YP_003793780.1| sporulation sigma factor SigF [Bacillus anthracis CI]
 gi|29897716|gb|AAP10991.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 14579]
 gi|30258795|gb|AAP28013.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Ames]
 gi|42739116|gb|AAS43043.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10987]
 gi|47504736|gb|AAT33412.1| RNA polymerase sigma-F factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47555116|gb|EAL13463.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49180908|gb|AAT56284.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Sterne]
 gi|49330074|gb|AAT60720.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974889|gb|AAU16439.1| RNA polymerase sigma-F factor [Bacillus cereus E33L]
 gi|74490099|gb|EAO53445.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118418501|gb|ABK86920.1| RNA polymerase, sigma subunit, RpoX/SigF [Bacillus thuringiensis
           str. Al Hakam]
 gi|164713043|gb|EDR18570.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167512500|gb|EDR87875.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|167531151|gb|EDR93838.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|170129427|gb|EDS98291.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|170668745|gb|EDT19490.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|172081928|gb|EDT66996.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190562749|gb|EDV16715.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992541|gb|EDX56502.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196023301|gb|EDX61979.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206734049|gb|EDZ51220.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206744391|gb|EDZ55802.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217063378|gb|ACJ77628.1| RNA polymerase sigma-F factor [Bacillus cereus AH187]
 gi|218162507|gb|ACK62499.1| RNA polymerase sigma-F factor [Bacillus cereus B4264]
 gi|218540139|gb|ACK92537.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|218540957|gb|ACK93351.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|221241581|gb|ACM14291.1| RNA polymerase sigma-F factor [Bacillus cereus Q1]
 gi|225790809|gb|ACO31026.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227007915|gb|ACP17658.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228585356|gb|EEK43465.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|228591235|gb|EEK49089.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|228597113|gb|EEK54768.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|228625614|gb|EEK82366.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|228631237|gb|EEK87873.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|228636817|gb|EEK93280.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|228642599|gb|EEK98885.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|228653958|gb|EEL09825.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|228659731|gb|EEL15376.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|228671928|gb|EEL27221.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|228690280|gb|EEL44073.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|228701952|gb|EEL54435.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|228711513|gb|EEL63470.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|228723557|gb|EEL74922.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|228735810|gb|EEL86395.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|228741969|gb|EEL92143.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|228772493|gb|EEM20938.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228778917|gb|EEM27179.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228785496|gb|EEM33505.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792475|gb|EEM40041.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799363|gb|EEM46327.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805290|gb|EEM51883.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228811780|gb|EEM58114.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818383|gb|EEM64455.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824146|gb|EEM69960.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830412|gb|EEM76022.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228836880|gb|EEM82223.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228842900|gb|EEM87983.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849739|gb|EEM94572.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228857024|gb|EEN01533.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|229268398|gb|ACQ50035.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|296325619|gb|ADH08547.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|300377738|gb|ADK06642.1| sporulation sigma factor SigF [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327980|gb|ADY23240.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941847|gb|AEA17743.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 252

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVKNEKKKPQLKDHELK---ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMRDELSKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|317128506|ref|YP_004094788.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473454|gb|ADU30057.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
          Length = 252

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 124/244 (50%), Gaps = 14/244 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +  ++++ +  A  A+ ++V AN RLV SV +++ NRG +  DL Q G IGL+K+ +K
Sbjct: 18  KEVKRLIKEAQDGAQEARDQIVNANTRLVWSVVQRFLNRGYEADDLFQIGCIGLIKSVDK 77

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    +S  + R P
Sbjct: 78  FDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSIKESANKIRKMKEELSKTLGRTP 136

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAI 605
           T  EIA+KL +  E V    + +++  S+   + + D     L D I D   +   D   
Sbjct: 137 TVNEIAEKLDLTPEEVVFAQEASRQLTSIHETVYENDGDPITLLDQISDDGDMKWFD--- 193

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +      +  L  RE+ ++ +R+      D T  +V ++  +++ ++ ++E K ++
Sbjct: 194 ----KIALRDEIDKLDEREKLIVYLRY----YKDQTQSQVAERLGISQVQVSRLEKKILK 245

Query: 666 KLKH 669
            LK 
Sbjct: 246 VLKE 249


>gi|167507971|gb|ABZ81306.1| RpoD [Thalassospira sp. MCCC 1A02411]
          Length = 258

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 70/256 (27%), Positives = 120/256 (46%), Gaps = 17/256 (6%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTE------GHSYQKREDSSQEKERDDVQETEGDIES 232
            LLR++IDLE   G           E        + +  E +  + + DD  ETE    S
Sbjct: 1   LLLRDVIDLETTFGGGPDAAAIGEEEGEATEEDSASEDFEPTESDADEDDEAETETPEPS 60

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDS------AHTLSAMEDQLRPKVMCALDE 286
           A     D+  + D    + E  E    +D+++         +LS ME++L  +V+   ++
Sbjct: 61  AGDHGDDEEDEDDDEETDGEGSEDGEGDDDEEDDENEQVNVSLSKMEEELTEQVLEKFEK 120

Query: 287 IAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA+ Y +L   Q+  +      +S       +   LK+++V L+  + LN  RI+ L++ 
Sbjct: 121 IAKTYEKLHKAQEQRLAALNKGESVPAATEKRYGKLKQEMVDLMEDVHLNNFRIEELLDH 180

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           L  ++ R++  EG+LLR A    IKR  F++ +QG ELDP+W+    + P   WK FV  
Sbjct: 181 LTGLNNRLLGLEGKLLRFADRVKIKRPDFIKHYQGNELDPNWMEKVGNLPGKGWKLFVER 240

Query: 402 EVDSILKIRNEIKSIS 417
             + I  +R  +  +S
Sbjct: 241 YPEEIANLREGVGGVS 256


>gi|302527791|ref|ZP_07280133.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
 gi|302436686|gb|EFL08502.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
          Length = 243

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 50/223 (22%), Positives = 97/223 (43%), Gaps = 12/223 (5%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V   L +   +A ++T RG    DL+Q   IGL+ A ++F    G  F ++A+  +   I
Sbjct: 23  VTEFLPVAEHIATRFTGRGEPREDLVQVARIGLINAIDRFTPDRGPDFLSFAVPTIMGEI 82

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
            R   D   ++R+P  +++    + R +  +S  + R PTP E+A+ L + +  V + L 
Sbjct: 83  RRYFRDTGWSVRVPRRLKELHLSLSRGSATLSQTLGRAPTPTELAEHLGLELSEVHEGLV 142

Query: 569 ITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                 +L       D +    L D +   +              E    +L  L  RE 
Sbjct: 143 AGHAYQTLSVDKPVHDDAEPLLLADTLGSDD-----PEIEHIENHEALQPLLRELPKRER 197

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L MRF  G     T  ++ +Q  +++  + ++ ++ + +L+
Sbjct: 198 AILVMRFFGG----LTQTQIAEQVGISQMHVSRLLSQTLEQLR 236


>gi|15613092|ref|NP_241395.1| RNA polymerase sigma factor SigB [Bacillus halodurans C-125]
 gi|10173142|dbj|BAB04248.1| RNA polymerase general stress sigma factor(sigma B) [Bacillus
           halodurans C-125]
          Length = 261

 Score =  123 bits (309), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 112/234 (47%), Gaps = 4/234 (1%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
               + ++V+    LV S+A+K++       DLIQ G +GL+ A E++D   G  F ++A
Sbjct: 27  DEEIQTKLVKHYEPLVHSLARKFSRSRAHDDDLIQVGMVGLLAAFERYDPKYGRSFESFA 86

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +   I R I D++ ++ +P  +++   K+ + A  ++++++R P  EEIA  L +  
Sbjct: 87  VPTIIGEIKRFIRDKTWSVHVPRRIKELGPKIKKAADELASELQRSPRVEEIADFLGVSE 146

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V + +++ K   +L      E     G+               +A+ +    +    L
Sbjct: 147 EEVLETMEMGKSYQALSVDRSLEADPEGGEVTLLDLVGQEDGGYEKADQQMLLEKAFQVL 206

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             RE+++L   +        + +E G +  +++  + +++ +A++KL+   R +
Sbjct: 207 DEREKQILLCTYF----EHLSQKETGHRLGISQMHVSRLQRRALKKLRDSIRVE 256


>gi|297746557|emb|CAZ60996.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 266

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 59/311 (18%), Positives = 108/311 (34%), Gaps = 46/311 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            EGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   PEGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   +  +       S+  E D   E E + E     S DD       PE A    
Sbjct: 59  -------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKF 111

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            +L    + +  ++                                   QK+ ++    +
Sbjct: 112 GDLRAQYEVTRLSI-----------------------------------QKNGRAHEDTQ 136

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D L     ++ +R+   E  +++L  +   + +  F+   
Sbjct: 137 AAIAQLADVFRQFRLMPKQFDRLGNNTCEMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 196

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 197 TNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 255

Query: 435 RKGECEASIAK 445
             GE +    K
Sbjct: 256 SIGEAKGPPCK 266


>gi|161898889|gb|ABX80434.1| SigB [Listeria monocytogenes]
 gi|161898893|gb|ABX80436.1| SigB [Listeria monocytogenes]
 gi|161898909|gb|ABX80444.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 108/239 (45%), Gaps = 4/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+
Sbjct: 182 RMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|328802585|emb|CBL54074.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 262

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +   + +
Sbjct: 58  -----------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ Q++ ++    
Sbjct: 95  DSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QNAISQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|118618107|ref|YP_906439.1| RNA polymerase sigma factor SigF [Mycobacterium ulcerans Agy99]
 gi|183981270|ref|YP_001849561.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
 gi|118570217|gb|ABL04968.1| alternate RNA polymerase sigma factor SigF [Mycobacterium ulcerans
           Agy99]
 gi|183174596|gb|ACC39706.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
          Length = 262

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 114/250 (45%), Gaps = 13/250 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + E    ++            +  +VE  L L   +A+++  RG    DL+Q   +GL+
Sbjct: 18  DVPEMFRELATFDADSPNFQRHRDTIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLV 77

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S +
Sbjct: 78  NAVVRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGAATAELSQR 137

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAV 598
           + R PT  E+A +L M    V + L    +   +S+++  G ED     + D + D +A 
Sbjct: 138 LGRAPTATELAAELEMDRAEVVEGLVAGSSYNTLSIDSGSGSEDDDARAIADTLGDMDA- 196

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +   RE+   +L +L  RE  VL +RF        T  ++ ++  +++  + +
Sbjct: 197 ----GLDRIEDRESLRPLLEALPERERTVLVLRFF----DSMTQTQIAERVGISQMHVSR 248

Query: 659 IEAKAIRKLK 668
           + AK++ +L+
Sbjct: 249 LLAKSLARLR 258


>gi|293376228|ref|ZP_06622471.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325845152|ref|ZP_08168461.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
 gi|292645120|gb|EFF63187.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325488817|gb|EGC91217.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
          Length = 259

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 131/247 (53%), Gaps = 12/247 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  + +  +     A++ +++ NLRLV+S+ KK+ +RG    DL Q G +GLMKA + F
Sbjct: 23  EMTELFKSFQNGNVEARESLIKGNLRLVLSIIKKFNHRGENLDDLFQVGCLGLMKAIDHF 82

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D +  +R+   +RD  +KV++   ++S +++R+PT
Sbjct: 83  DLSHEVKFSTYAVPMIIGEIRRYLRDNNS-LRVSRSLRDTAYKVLQVKDQLSIELQRDPT 141

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQ 606
            EEIA  + +    V   ++   +P+S+ +PI ++  DT HL D I+D +      S   
Sbjct: 142 NEEIAAAIGVEPIDVVLSVEAISDPVSIFSPIYNDGGDTIHLIDQIKDDSITDDKWSV-- 199

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +         L  RE+R++  R+ +G     T  E+  +  +++ ++ ++E  A++ 
Sbjct: 200 ---KLMLEEGFKRLGKREKRIIHDRYFMG----KTQMEIAAEIGISQAQVSRLEKNALQV 252

Query: 667 LKHPSRS 673
           ++   +S
Sbjct: 253 MEEMMKS 259


>gi|66474653|gb|AAY46896.1| RpoD [Aeromonas sp. AN-46]
          Length = 269

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 114/312 (36%), Gaps = 44/312 (14%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEI IAKRIE G   + +S+ E P     L+   D+       L +II           
Sbjct: 1   EGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII----------- 49

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
            GF    E                          E  A  +    S++       E++E 
Sbjct: 50  SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDEED 84

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
             DEDED  +                   E+   Y          ++ QK+ ++    + 
Sbjct: 85  EEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQA 138

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
              +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    
Sbjct: 139 AIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFT 198

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   + 
Sbjct: 199 NNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMS 257

Query: 436 KGECEASIAKKE 447
            GE +A  AKKE
Sbjct: 258 IGEAKARRAKKE 269


>gi|328802603|emb|CBL54083.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 262

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINPVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +   + +
Sbjct: 58  -----------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ Q++ ++    
Sbjct: 95  DSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|255017998|ref|ZP_05290124.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-515]
          Length = 209

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 47/170 (27%), Positives = 79/170 (46%), Gaps = 7/170 (4%)

Query: 16  EDSDDSLVFDFSDDSWKK-MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           +  +   V + S +  K+ +I+  +++G +T  ++ A L P  + S+QM++ +  +   G
Sbjct: 4   KTKNTKPVAELSVEQVKEALIEEGKKKGILTYAKIAARLAPFTLDSDQMDEYLEHVGEAG 63

Query: 75  INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
           I V      +D +  +            S  L           +DPVRMYL+E+G ++LL
Sbjct: 64  IEV-----SDDADDEDPDETELVKEETESFDLTDMSVPPGVKINDPVRMYLKEIGRVDLL 118

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           + + EIA+AKRIEAG       L E+ L     I  R  +  G   L  I
Sbjct: 119 TADEEIALAKRIEAGDIEAKGRLAEANLRLVVSIAKRY-VGRGMLFLDLI 167



 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 56/108 (51%), Positives = 77/108 (71%), Gaps = 3/108 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  +K I     ++  E    +++ ++ E     AK  + EANLRLV+S+AK+Y  RG+
Sbjct: 105 VRMYLKEIGRVDLLTADEE---IALAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
            FLDLIQEGN+GLMKA EKFD+  G+KFSTYA WW++QAITR+IADQ+
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209


>gi|161898913|gb|ABX80446.1| SigB [Listeria monocytogenes]
 gi|161898915|gb|ABX80447.1| SigB [Listeria monocytogenes]
 gi|161898939|gb|ABX80459.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|161898845|gb|ABX80412.1| SigB [Listeria monocytogenes]
 gi|161898851|gb|ABX80415.1| SigB [Listeria monocytogenes]
 gi|161898853|gb|ABX80416.1| SigB [Listeria monocytogenes]
 gi|161898861|gb|ABX80420.1| SigB [Listeria monocytogenes]
 gi|161898863|gb|ABX80421.1| SigB [Listeria monocytogenes]
 gi|161898867|gb|ABX80423.1| SigB [Listeria monocytogenes]
 gi|161898869|gb|ABX80424.1| SigB [Listeria monocytogenes]
 gi|161898873|gb|ABX80426.1| SigB [Listeria monocytogenes]
 gi|161898875|gb|ABX80427.1| SigB [Listeria monocytogenes]
 gi|161898877|gb|ABX80428.1| SigB [Listeria monocytogenes]
 gi|161898879|gb|ABX80429.1| SigB [Listeria monocytogenes]
 gi|161898887|gb|ABX80433.1| SigB [Listeria monocytogenes]
 gi|161898891|gb|ABX80435.1| SigB [Listeria monocytogenes]
 gi|161898901|gb|ABX80440.1| SigB [Listeria monocytogenes]
 gi|161898911|gb|ABX80445.1| SigB [Listeria monocytogenes]
 gi|161898919|gb|ABX80449.1| SigB [Listeria monocytogenes]
 gi|161898925|gb|ABX80452.1| SigB [Listeria monocytogenes]
 gi|161898927|gb|ABX80453.1| SigB [Listeria monocytogenes]
 gi|161898929|gb|ABX80454.1| SigB [Listeria monocytogenes]
 gi|161898935|gb|ABX80457.1| SigB [Listeria monocytogenes]
 gi|161898941|gb|ABX80460.1| SigB [Listeria monocytogenes]
 gi|161898943|gb|ABX80461.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|300728464|ref|ZP_07061824.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
 gi|299774265|gb|EFI70897.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
          Length = 251

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 85/273 (31%), Positives = 133/273 (48%), Gaps = 41/273 (15%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +  I  E  +S  E + + + ++        A +++  ANLR V+S+AK+Y +RGL
Sbjct: 18  LQTYLSEIGKENLLSEQEEQELSAKIQ---NGDESAIEKLTTANLRFVVSIAKRYQDRGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGN GL+KAA KFD   G +F  YA+ +++QAI  +I +QS    +P  M   
Sbjct: 75  GINDLISEGNFGLIKAARKFDAAKGQRFVQYAVHFIRQAIENAIQEQSGIYTLPHSM--- 131

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
                               P E+ +  A                 S++ P+    T+ L
Sbjct: 132 ------------------DDPVELKQSKAF----------------SVDAPLVQGKTASL 157

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGK 647
              + D NAV P    +   LR+   R L+ L  RE RV+ M +G+   N   T EE+G 
Sbjct: 158 LHVLSDPNAVIPDKPYLDDVLRQGLIRSLSVLNDRERRVVSMFYGLNDQNAGLTYEEIGT 217

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           Q  + RER+R I  KA RK+K  +++ +L+S+L
Sbjct: 218 QLGLKRERVRDIRKKAERKMKKYTKNDQLKSYL 250



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 29/66 (43%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K         +D ++ YL E+G   LLS + E  ++ +I+ G    +  L  + L F   
Sbjct: 5   KTGKPLSEQENDSLQTYLSEIGKENLLSEQEEQELSAKIQNGDESAIEKLTTANLRFVVS 64

Query: 168 IIWRDE 173
           I  R +
Sbjct: 65  IAKRYQ 70


>gi|89068061|ref|ZP_01155478.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046300|gb|EAR52357.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 281

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 116/255 (45%), Gaps = 16/255 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE ++GLMKAA+KF
Sbjct: 16  ELRLAYAWRDQRDERALHRLITAYMRLAISMAAKFRRYGAPMNDLIQEASLGLMKAADKF 75

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            ++R    ++ R A   
Sbjct: 76  DPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLRRVQARLEREAAAS 135

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKN- 596
              I R+   E IA ++ +P+  V  +  +++    SL      ED      + +ED   
Sbjct: 136 GAPIDRQKMREMIAAEVGVPLHDVEMMEGRLSGSDYSLNATQSAEDEGREWIEALEDDGM 195

Query: 597 --AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A    +S     LR      L+ L  RE  +++ R         TLE +G +  +++E
Sbjct: 196 QAAEKVENSHDIDTLRHWLLNALSQLNERERFIVKERKLRD--DPRTLESLGDELGLSKE 253

Query: 655 RIRQIEAKAIRKLKH 669
           R+RQ+EA A  K++ 
Sbjct: 254 RVRQLEAAAFGKMRK 268


>gi|302127755|emb|CBL51731.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|328802597|emb|CBL54080.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 262

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 58/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +   + +
Sbjct: 58  -----------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + +LR+  +   ++ Q++ ++    
Sbjct: 95  DSDDDGDGGPDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + D +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|289767896|ref|ZP_06527274.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289698095|gb|EFD65524.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 270

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 113/247 (45%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E +    +  +VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 25  FRRLATLPDGPEHD--ELRDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVD 82

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           ++D   G  F +YA+  +   I R   D   T+ +P  +++  ++V    + +S  I  R
Sbjct: 83  RYDPERGNAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQELRNRVRFAGQDLSQTIPGR 142

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            PT  EIA++  +  E VR  L+   +   +SL+  +   ED   LGD +   +      
Sbjct: 143 RPTVAEIAERAELSEEDVRVGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPALDTV 202

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE     LA+L PRE  +L MRF   M      E    Q  +++  + ++  +
Sbjct: 203 VD-----REAVKDRLAALPPRERAILYMRFFDDMTQSRIAE----QLGISQMHVSRLITR 253

Query: 663 AIRKLKH 669
              +++ 
Sbjct: 254 CCDRVRE 260


>gi|104779584|ref|YP_606082.1| RNA polymerase factor sigma-32 [Pseudomonas entomophila L48]
 gi|95108571|emb|CAK13265.1| sigma H (sigma 32) factor of RNA polymerase RpoH [Pseudomonas
           entomophila L48]
          Length = 284

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 127/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERDLGERL--YYEQDLEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPASEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     A+   D+    N        L  L  R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPALQLEDADWSDNSSSNLHEALQGLDDRSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+ +++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELAEKYSVSAERIRQLEKNAMNKVK 279


>gi|319899398|ref|YP_004159495.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319403366|emb|CBI76925.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 303

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 112/246 (45%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD    
Sbjct: 46  LRWKDKRDDNAMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRE 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN------KIKR 545
            +FSTYA WW++ +I   I      +R       K     + R   +++       K + 
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLAQDDSTLTKQEI 165

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN--AVSPLDS 603
             T  E        VE +          +SL      E+     D + D +    + ++ 
Sbjct: 166 FRTISEKLGVSVSDVEKMDFRFSAADNSLSLSVSENGENPIAKMDSLVDDHPLPDAVIEQ 225

Query: 604 AIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           AI    R +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 AIDGQRRTKWLYEALKILNERELEIIR--FRRLNEEGATLEVLGQKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|225375609|ref|ZP_03752830.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
 gi|225212588|gb|EEG94942.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
          Length = 259

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 66/261 (25%), Positives = 127/261 (48%), Gaps = 13/261 (4%)

Query: 412 EIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + I +     ++  +       A++  ++ NLRLV+SV K+++      
Sbjct: 5   KVEICGVNTAKLPILKETEKEALFARIRQGDQEAREMYIKGNLRLVLSVIKRFSGSHENL 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+K+ + F+  L  KFSTYA+  +   I R + D +  IR+   +RD  +
Sbjct: 65  DDLFQIGCIGLIKSIDNFNPDLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHL 588
           K +     +S    +EPT +EIA++  +  E +   L   + P+SL  P+  +  DT ++
Sbjct: 124 KAIHAKEVLSKNSFKEPTLQEIAEESGVAAEDILYALDAIQSPVSLYDPVYTDGGDTLYV 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I DK              + + +  +  L+ RE  ++ +RF  G     T  EV  +
Sbjct: 184 MDQISDKKNKEENWVE-----KLSLSDAMNHLSERENFIINLRFFEG----KTQMEVADE 234

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A++ ++ 
Sbjct: 235 IHISQAQVSRLEKSALKTIRQ 255


>gi|148358598|ref|YP_001249805.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
 gi|148280371|gb|ABQ54459.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
          Length = 284

 Score =  123 bits (309), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 66/274 (24%), Positives = 123/274 (44%), Gaps = 15/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +++ E        R        A +++V A+LR V+ VA+ Y   GL
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAE--RFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+M N++      E   +AK L +  E V     ++     S + P  D++ 
Sbjct: 135 --KLFFNLRQMKNRLGWFSNEEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDND 192

Query: 586 ------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                       + D  AV   +       RE     +  L  R + +L+ R+       
Sbjct: 193 DAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TL ++ +++ V+ ER+RQ+E  A++K++    S
Sbjct: 251 LTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMES 284


>gi|330719751|gb|EGG98273.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC2047]
          Length = 283

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 129/275 (46%), Gaps = 13/275 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   + S+S    ++  + + +   +     E   A ++++ ++LR V+ +AK Y+  
Sbjct: 14  QNLAAYVTSVSSIPVLTAEQEKELAERL--YYQEDLEAARQLIMSHLRFVVHIAKSYSGY 71

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++FD   G +  ++A+ W+K  I   I      +++     
Sbjct: 72  GLPQGDLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKA 131

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
            +         + S         + IA+ L +  + VR++  +++      +    D+D 
Sbjct: 132 QRKLFFNLRGAKKSLAWLSNDEVDAIAEDLGVDAKVVRQMEGRLSAHDAPFDMGADDDDD 191

Query: 586 SHL---GDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNT 638
           S      +++EDK    P+D   Q N +ET        +A L  R + +L  R+      
Sbjct: 192 SAYQAPANYLEDKR-CDPVDLLEQQNWQETSNRKLFEAMADLDERSKDILNARWL--SEQ 248

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             TL ++  ++ V+ ERIRQ+E  A++K+K   ++
Sbjct: 249 KSTLHDLADKYGVSAERIRQLEKNAMKKIKVAMQA 283


>gi|15610422|ref|NP_217803.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Rv]
 gi|15842877|ref|NP_337914.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           CDC1551]
 gi|31794466|ref|NP_856959.1| RNA polymerase sigma factor SigF [Mycobacterium bovis AF2122/97]
 gi|121639175|ref|YP_979399.1| RNA polymerase sigma factor SigF [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148663149|ref|YP_001284672.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|148824488|ref|YP_001289242.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis F11]
 gi|167968918|ref|ZP_02551195.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|215405299|ref|ZP_03417480.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           02_1987]
 gi|215413164|ref|ZP_03421865.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           94_M4241A]
 gi|215428770|ref|ZP_03426689.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T92]
 gi|215447591|ref|ZP_03434343.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|218755069|ref|ZP_03533865.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis GM
           1503]
 gi|219559346|ref|ZP_03538422.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T17]
 gi|224991668|ref|YP_002646357.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253800329|ref|YP_003033330.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           1435]
 gi|254233896|ref|ZP_04927221.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis C]
 gi|254365909|ref|ZP_04981954.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis str. Haarlem]
 gi|254552388|ref|ZP_05142835.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260188335|ref|ZP_05765809.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|260202448|ref|ZP_05769939.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T46]
 gi|260206638|ref|ZP_05774129.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis K85]
 gi|289444868|ref|ZP_06434612.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T46]
 gi|289448975|ref|ZP_06438719.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|289555564|ref|ZP_06444774.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           605]
 gi|289571513|ref|ZP_06451740.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T17]
 gi|289576006|ref|ZP_06456233.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis K85]
 gi|289747104|ref|ZP_06506482.1| sigma factor SigF [Mycobacterium tuberculosis 02_1987]
 gi|289751981|ref|ZP_06511359.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T92]
 gi|289759427|ref|ZP_06518805.1| sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|289763474|ref|ZP_06522852.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis GM 1503]
 gi|294993773|ref|ZP_06799464.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis 210]
 gi|297635940|ref|ZP_06953720.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           4207]
 gi|297732937|ref|ZP_06962055.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           R506]
 gi|298526762|ref|ZP_07014171.1| sigma factor SigF [Mycobacterium tuberculosis 94_M4241A]
 gi|306777615|ref|ZP_07415952.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu001]
 gi|306782337|ref|ZP_07420674.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu002]
 gi|306786159|ref|ZP_07424481.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu003]
 gi|306790527|ref|ZP_07428849.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu004]
 gi|306795048|ref|ZP_07433350.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu005]
 gi|306799245|ref|ZP_07437547.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu006]
 gi|306805094|ref|ZP_07441762.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu008]
 gi|306809281|ref|ZP_07445949.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu007]
 gi|306969383|ref|ZP_07482044.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu009]
 gi|306973735|ref|ZP_07486396.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu010]
 gi|307081445|ref|ZP_07490615.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu011]
 gi|307086048|ref|ZP_07495161.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu012]
 gi|313660269|ref|ZP_07817149.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           V2475]
 gi|5917771|gb|AAD56032.1|AF181975_3 sigma factor SigF [Mycobacterium bovis]
 gi|1877341|emb|CAB07069.1| ALTERNATE RNA POLYMERASE SIGMA FACTOR SIGF [Mycobacterium
           tuberculosis H37Rv]
 gi|13883208|gb|AAK47728.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis CDC1551]
 gi|31620062|emb|CAD95406.1| PROBABLE RNA POLYMERASE SIGMA FACTOR SIGF [Mycobacterium bovis
           AF2122/97]
 gi|121494823|emb|CAL73304.1| Probable rna polymerase sigma factor sigF [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|124599425|gb|EAY58529.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis C]
 gi|134151422|gb|EBA43467.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis str. Haarlem]
 gi|148507301|gb|ABQ75110.1| sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|148723015|gb|ABR07640.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis F11]
 gi|224774783|dbj|BAH27589.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253321832|gb|ACT26435.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           1435]
 gi|289417787|gb|EFD15027.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T46]
 gi|289421933|gb|EFD19134.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|289440196|gb|EFD22689.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           605]
 gi|289540437|gb|EFD45015.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis K85]
 gi|289545267|gb|EFD48915.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T17]
 gi|289687632|gb|EFD55120.1| sigma factor SigF [Mycobacterium tuberculosis 02_1987]
 gi|289692568|gb|EFD59997.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T92]
 gi|289710980|gb|EFD74996.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis GM 1503]
 gi|289714991|gb|EFD79003.1| sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|298496556|gb|EFI31850.1| sigma factor SigF [Mycobacterium tuberculosis 94_M4241A]
 gi|308214036|gb|EFO73435.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu001]
 gi|308325087|gb|EFP13938.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu002]
 gi|308329308|gb|EFP18159.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu003]
 gi|308333139|gb|EFP21990.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu004]
 gi|308336826|gb|EFP25677.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu005]
 gi|308340659|gb|EFP29510.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu006]
 gi|308344393|gb|EFP33244.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu007]
 gi|308348397|gb|EFP37248.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu008]
 gi|308353234|gb|EFP42085.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu009]
 gi|308356974|gb|EFP45825.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu010]
 gi|308360831|gb|EFP49682.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu011]
 gi|308364515|gb|EFP53366.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu012]
 gi|323718155|gb|EGB27337.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CDC1551A]
 gi|326902486|gb|EGE49419.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis W-148]
 gi|328460063|gb|AEB05486.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           4207]
          Length = 261

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 117/245 (47%), Gaps = 13/245 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +V +           + ++V+  L L   +A+++  RG    DLIQ   +GL+ AA 
Sbjct: 23  FRELVGLPAGSPEF-QRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           P+  E+A +L M    V + L    +   +S+++  G +D +  + D + D +A      
Sbjct: 142 PSASELAAELGMDRAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA-----G 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   RE    +L +L  RE  VL +RF        T  ++ ++  +++  + ++ AK+
Sbjct: 197 LDQIENREVLRPLLEALPERERTVLVLRFF----DSMTQTQIAERVGISQMHVSRLLAKS 252

Query: 664 IRKLK 668
           + +L+
Sbjct: 253 LARLR 257


>gi|288555973|ref|YP_003427908.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
 gi|288547133|gb|ADC51016.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
          Length = 256

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 117/244 (47%), Gaps = 14/244 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + +  ++ + +     A+  +V  N RLV SV +++ NRG +  DL Q G IGL+K+ +K
Sbjct: 19  KEVKELIARSQEGDQQARDLIVNRNTRLVWSVVQRFMNRGYEADDLFQIGCIGLIKSVDK 78

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KFSTYA+  +   I R + D   T+++   +++  +K+ +    ++  + R P
Sbjct: 79  FDLSYDVKFSTYAVPMIIGEIQRFLRD-DGTVKVSRSIKELGNKIRKMKDELTKSLGRVP 137

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAI 605
           T  EIA++L +  E V    + ++   S+   + + D     L D I D+      D   
Sbjct: 138 TVNEIAEQLEITPEEVVFAGEASRSLTSIHETVYENDGDPITLLDQIADQTETKWFD--- 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +      +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++E K + 
Sbjct: 195 ----KIALKEAIRDLDERERLIVFLRY----YKDQTQSEVATRLGISQVQVSRLEKKILE 246

Query: 666 KLKH 669
           ++K 
Sbjct: 247 QMKE 250


>gi|228992811|ref|ZP_04152736.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
 gi|228998857|ref|ZP_04158442.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|229006374|ref|ZP_04164053.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228754873|gb|EEM04239.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228760873|gb|EEM09834.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|228766860|gb|EEM15498.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
          Length = 252

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 129/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+++   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVRNEKKKPQLKDHELK---ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMKDELSKEYGRAPTINEVAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+      D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQTETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|330959691|gb|EGH59951.1| putative RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 291

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 69/268 (25%), Positives = 115/268 (42%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +S  E R +    R  E     A +++V + LR V+ +A++Y+  GL
Sbjct: 22  LDAYLTVIHSLPKMSAEEERRLSE--RHFEHNDMDAARQLVTSQLRFVVHIARRYSGYGL 79

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGL+KA ++F+     +  T+A+  +K  I   I      +R+     + 
Sbjct: 80  PLSDLIQEGNIGLIKAVKRFNPAAQVRLITFAVHGIKAEINEYILRNCRMVRMATTKAQR 139

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R   R    +  + T   IA  L + V  V+++  ++     S +     +D S
Sbjct: 140 KLLFNLRKQPRSRTWLTADETKH-IADILNVSVRDVKEMETRMAGNDTSFDPAADADDDS 198

Query: 587 HL---GDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            L      + D           + +           L SL  R   +L  RF        
Sbjct: 199 ALLTPAHQLGDHRYDPAHLYETENDADTSSYDLHTALNSLDERSRDILAQRFL--SERKA 256

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL ++  ++ V+ ERIRQIE  A+ KLK
Sbjct: 257 TLHDLATKYKVSAERIRQIEKLALAKLK 284


>gi|323449639|gb|EGB05525.1| hypothetical protein AURANDRAFT_60247 [Aureococcus anophagefferens]
          Length = 399

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 75/268 (27%), Positives = 133/268 (49%), Gaps = 27/268 (10%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYT--------------NRGLQFLDLIQEGNIGLMKA 484
            E   A++ M+ +N+RLV+++A++                       DL+ EG +GL KA
Sbjct: 132 AECREAREVMMLSNMRLVVAMARRMQRSLPQASRLAVDRDGGSYALDDLVAEGTLGLAKA 191

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++F+   G++FSTYA WWV+QAI R+I  ++  + +PVH++    K     + + ++  
Sbjct: 192 VDRFEPDRGFRFSTYATWWVRQAIQRAIRRRA-VVAVPVHVQQLAKKCENATQELRDEYG 250

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED---TSHLGDF--------IE 593
           R PT  E+A ++    + ++   +      SL+ P+        SH+ DF        I 
Sbjct: 251 RPPTSAELAARVGASEKRLKLAGRAALATFSLDVPLSAARGGKGSHVADFAEAATLNEIV 310

Query: 594 DKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           + +  +P ++A    LR+     + A+L P E  VLR+R G+      T  +VG+    T
Sbjct: 311 ESDEPAPEEAATFHELRDAIDYAMHANLQPSERDVLRLRLGLDDGETRTRRQVGEICGQT 370

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++IR IE  A+ KL+H     +LR ++
Sbjct: 371 EKKIRAIERAALTKLRHTRDCVQLREYV 398


>gi|229180352|ref|ZP_04307695.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
 gi|228603099|gb|EEK60577.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
          Length = 252

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVKNEKKKPQLKDHELK---ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMRDELSKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSEAKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|167507931|gb|ABZ81286.1| RpoD [Thalassospira sp. MCCC 1A01172]
          Length = 253

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 124/251 (49%), Gaps = 12/251 (4%)

Query: 179 TLLREIIDLEACIG--PESKGGFFHGTEGH-----SYQKREDSSQEKERDDVQETEGDIE 231
            LLR++IDLE   G  P+++ G   G +         +  + ++ +++ D   ET   I 
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIGAEEGEDEDVDAEADVESFDSANDDEDEDAETETPDAIG 60

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                 ++D    DS  E     +   +++ +    +LS ME++L  +V+   + IA+ Y
Sbjct: 61  GEETEEEEDDESEDSEGEEGGEGDDEDEDENEQVNVSLSKMEEELTEQVLEKFELIAKTY 120

Query: 292 RELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            +L   Q+  +      ++       +   LK ++V+L+  + LN  RI+ L++ L  ++
Sbjct: 121 EKLHKAQEQRLVALNKGETVPAATEKRYTKLKNEMVELMEDVHLNNFRIEELLDHLTGLN 180

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
            R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK F+    + I
Sbjct: 181 NRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPNWMERVAGLPGKGWKTFIERYPEEI 240

Query: 407 LKIRNEIKSIS 417
            K+R +I  +S
Sbjct: 241 AKLREDIGGVS 251


>gi|167507901|gb|ABZ81271.1| RpoD [Thalassospira sp. MCCC 1A00370]
 gi|167507963|gb|ABZ81302.1| RpoD [Thalassospira sp. MCCC 1A02060]
          Length = 253

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 124/251 (49%), Gaps = 12/251 (4%)

Query: 179 TLLREIIDLEACIG--PESKGGFFHGTEGH-----SYQKREDSSQEKERDDVQETEGDIE 231
            LLR++IDLE   G  P+++ G   G +         +  + ++ +++ D   ET   I 
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIGAEEGEDEDVDAEADVESFDSANDDEDEDAETETPDAIG 60

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                 ++D    DS  E     +   +++ +    +LS ME++L  +V+   + IA+ Y
Sbjct: 61  GEEAEEEEDDESEDSEGEEGGEGDDEDEDENEQVNVSLSKMEEELTEQVLEKFELIAKTY 120

Query: 292 RELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            +L   Q+  +      ++       +   LK ++V+L+  + LN  RI+ L++ L  ++
Sbjct: 121 EKLHKAQEQRLVALNKGETVPAATEKRYTKLKNEMVELMEDVHLNNFRIEELLDHLTGLN 180

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
            R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK F+    + I
Sbjct: 181 NRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPNWMERVAGLPGKGWKTFIERYPEEI 240

Query: 407 LKIRNEIKSIS 417
            K+R +I  +S
Sbjct: 241 AKLREDIGGVS 251


>gi|148266118|ref|YP_001232824.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter
           uraniireducens Rf4]
 gi|146399618|gb|ABQ28251.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           uraniireducens Rf4]
          Length = 251

 Score =  123 bits (309), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 117/254 (46%), Gaps = 18/254 (7%)

Query: 433 MVRKGECEASIA----KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAA 485
           +++  E EA  A    + E+V ++L LV  +  +  +     L   DL     IGL+ AA
Sbjct: 4   LLKAYEQEAQRAVIPDRDELVVSHLPLVKFLVDRIASALPPHLDRDDLRSAAVIGLISAA 63

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           E+FD   G  F T+A   ++  I   +  Q     +   +RDK  ++ R    +  ++ R
Sbjct: 64  ERFDPSRGVMFKTFAEQRIRGTIMDELRSQDW---LTRSLRDKFKRLEREFSCLEQRLGR 120

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLG--DFIEDKNAVSPL 601
            PT EE+A  + + +EG   +L+       +SL+    DED S LG  D +EDK   SP 
Sbjct: 121 NPTSEEVAAAMGLELEGYFHLLEEIHFLSFVSLDDAWMDEDGSPLGLLDVLEDKGVESPQ 180

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  I     E     +  L  +E  V+ + +      +  L+E+G    +T  RI Q+ +
Sbjct: 181 NQLIARQTVENLAEAIDGLPEKERIVITLYY----YEELNLKEIGSVLSLTESRISQLHS 236

Query: 662 KAIRKLKHPSRSKK 675
           +A+ +L+   +  K
Sbjct: 237 QALLRLRGRMKLHK 250


>gi|269963639|ref|ZP_06177962.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269831652|gb|EEZ85788.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 279

 Score =  123 bits (308), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 74/264 (28%), Positives = 133/264 (50%), Gaps = 7/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-- 466
             + +K I     +S  +  H   + R        A++ M+E+NLRLV+ +AK Y  R  
Sbjct: 12  YAHYLKDIVGIDLLSREDELHYAKLNR---AGDKEAREVMIESNLRLVVKIAKSYLKRTG 68

Query: 467 -GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                LDLI+EGNIGL+KA +K+D   GY+FSTYA+WW+++ I  ++ +   T+R+P H+
Sbjct: 69  NNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPAHV 128

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +I+ +       S  + ++ +  E++    + VE V + L      I + T +     
Sbjct: 129 CKEINSLASKKHDASKTMSKDISISELSHCSGVKVERVDE-LVALSGFIDVSTTVDLNHA 187

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + +  E +    P          +    V+ +L  + ++VL  RFG+  +   TL EV
Sbjct: 188 PFVLEQCESEYTTDPQQDCEDHCFTQALEHVVNTLPVKLQQVLIHRFGLFEHNVKTLAEV 247

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
           G    V+ ER+RQ++ +A+ +++ 
Sbjct: 248 GDLLNVSNERVRQMQKEAVERIQK 271



 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 26/96 (27%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
                +  DP   YL+++  I+LLSRE E+  AK   AG       + ES L     I  
Sbjct: 2   KETFSAGKDPYAHYLKDIVGIDLLSREDELHYAKLNRAGDKEAREVMIESNLRLVVKIAK 61

Query: 171 RDELNDGTTL-LREIIDLEACIGPESKGGFFHGTEG 205
                 G    L ++I+ E  IG       +    G
Sbjct: 62  SYLKRTGNNFTLLDLIE-EGNIGLIKAIDKYDPEPG 96


>gi|303327038|ref|ZP_07357480.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
 gi|302863026|gb|EFL85958.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score =  123 bits (308), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 67/266 (25%), Positives = 131/266 (49%), Gaps = 13/266 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ +S    +   E   +   VR  +     A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 76  YLREVSRFPMLKPEEEHELALRVR--DHNDPDAAFRLVSSHLRLVVRIAMDFQRRWMQNV 133

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDL+QEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      R  
Sbjct: 134 LDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQVQRKL 193

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE-DTS 586
            + + R  +++  +   +P    ++++L +  + + ++  ++    +SL   +G++   +
Sbjct: 194 FYNLNRERQKLIAQ-GYDPDAAMLSERLGVTEDQINEMDQRLASTDLSLNVQVGEDSGGA 252

Query: 587 HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              DF+         +     I   +R     ++  L  +E  +L  +  +  +   TL 
Sbjct: 253 SRMDFLPALGPGIEDTLASDEIAGLVRSRLKTIMPKLNEKEVYIL--QNRLLTDEPVTLR 310

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+G+++ VTRER+RQ+EA+ + K++ 
Sbjct: 311 EIGERYNVTRERVRQLEARLLEKIRQ 336



 Score = 41.4 bits (95), Expect = 0.48,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 39/91 (42%)

Query: 59  SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
             EQ  +T+ +L    +   +  D++D++ +E  L L   +  +       +  +     
Sbjct: 11  DEEQNLETLDLLDGEELAAGEVLDVDDDKDAEPELALEEGSDGALPAPSVPRLPSPAGAR 70

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
           D + +YLRE+    +L  E E  +A R+   
Sbjct: 71  DSLHLYLREVSRFPMLKPEEEHELALRVRDH 101


>gi|299769389|ref|YP_003731415.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
 gi|298699477|gb|ADI90042.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
          Length = 288

 Score =  123 bits (308), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 127/270 (47%), Gaps = 13/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
           + K+   +R+ ++ S K+  E   + IA  L +  E V ++  ++T    + E    D+D
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLE-EAQSIANDLNVTAEQVLEMEGRLTAYDAAFEAQGDDDD 194

Query: 585 TSHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++ED     A    +   +          +  L  R   +L+ R+     +
Sbjct: 195 DTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDDKS 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 255 --TLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|262372449|ref|ZP_06065728.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
 gi|262312474|gb|EEY93559.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
          Length = 289

 Score =  123 bits (308), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 122/270 (45%), Gaps = 13/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 19  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKLLVMSHLRFVVHIARSYAGY 76

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 77  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 136

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           + K+   +R+ ++ S ++  E            P + +    ++T    + E    D+D 
Sbjct: 137 QRKLFFNLRSLKKSSKRLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 196

Query: 586 SHL---GDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNT 638
           +       ++ED N   P     + +  E         +  L  R   +L+ R+      
Sbjct: 197 TPHTAPALYLED-NRYDPARLIEEEDYEEQSTSALHEAMDQLDDRSRNILQRRWLDD--D 253

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 254 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|302338101|ref|YP_003803307.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635286|gb|ADK80713.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 262

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 112/258 (43%), Gaps = 16/258 (6%)

Query: 420 TGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQ 475
            G  + E +    +            +   +E    LV  VA K      + ++F DL+ 
Sbjct: 1   MGDQLLEEKTEAELWELYRNSRDPKIRDRFIEQYSPLVKYVAGKVAIGMPQNVEFDDLVG 60

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G  GL  A EKFD     KF TYA+  ++ AI   +        +P  +R K  ++  T
Sbjct: 61  FGVFGLFDAIEKFDPEKHVKFKTYAVTRIRGAIYDELRSIDW---VPRSVRQKAREIEET 117

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGD 590
             R+   + R  + +EIA +L + V   +K++        +SL       D +    + D
Sbjct: 118 IHRLEASLGRAASDKEIADELGISVADFQKLMLKISGTSVLSLNDVWYTGDENDTVAIVD 177

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE   +++P     +  +R    + ++ L  +E++VL + +      D TL+E+GK   
Sbjct: 178 GIESPQSLNPDIIIEKEEIRRVIVQAISELPEKEKKVLVLYY----YEDLTLKEIGKVLD 233

Query: 651 VTRERIRQIEAKAIRKLK 668
           VT  R+ Q+  KAI +L+
Sbjct: 234 VTESRVSQLHTKAIMRLR 251


>gi|161898883|gb|ABX80431.1| SigB [Listeria monocytogenes]
          Length = 235

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 108/239 (45%), Gaps = 4/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 1   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 120

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 121 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+
Sbjct: 181 RMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLR 235


>gi|212711019|ref|ZP_03319147.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
 gi|212686187|gb|EEB45715.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
          Length = 291

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 59/271 (21%), Positives = 124/271 (45%), Gaps = 16/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +++ +    ++  E + +   +         A K+++ ++LR VI +A+ Y   GL
Sbjct: 16  IEAYMRAANAYPMLTAEEEKELAERL--HYDGDLEAAKQLILSHLRFVIHIARSYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      ++       R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKSQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT----KEPISLETPIGD 582
                + +  +R+    + E     +A++L +  + V ++              +     
Sbjct: 134 KLFFNLRKNKKRLGWFNQDEVNM--VAQELGVSTKDVLEMESRMAAQDMAFDMSDDDDSG 191

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMN 637
           +    +   +  ++  S   + I+ +  E+         LASL  R + ++R R+ +  +
Sbjct: 192 DFGGPVAPVLYLQDKASDFANTIEDDNWESHATDRLADALASLDERSQDIIRARW-LDDD 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL+E+  ++ V+ ER+RQ+E  A++KL+
Sbjct: 251 NKTTLQELADKYGVSAERVRQLEKNAMKKLR 281


>gi|197723821|gb|ACH72690.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 238

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 108/241 (44%), Gaps = 4/241 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+ 
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLRE 237

Query: 670 P 670
            
Sbjct: 238 A 238


>gi|317129288|ref|YP_004095570.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474236|gb|ADU30839.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
          Length = 261

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 82/268 (30%), Positives = 138/268 (51%), Gaps = 15/268 (5%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + + + +  +  K +     A++E+V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTSKLPVLKNKEMRVLFEKMQNGDEFAREELVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--D 584
            +K ++    M N+ K  REPT +EIAK L +P E +   L   ++P+SL  PI ++  D
Sbjct: 122 AYKALQVRDNMMNEKKREREPTVQEIAKVLDVPKEDIVFALDAIQDPVSLFEPIYNDGGD 181

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             ++ D I D            A         +  L  RE+ +L MRF  G     T  E
Sbjct: 182 PIYVMDQISDDKQKDIQWIEEIA-----LKEAMIRLNDREKMILDMRFFQG----KTQME 232

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           V  +  +++ ++ ++E  AI+++   ++
Sbjct: 233 VADEIGISQAQVSRLEKAAIQQMNKHAK 260


>gi|75764482|ref|ZP_00743967.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488029|gb|EAO51760.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 260

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 69/261 (26%), Positives = 128/261 (49%), Gaps = 12/261 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +         R  
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNPIRFCAFLGRYA 122

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
           +   ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  D  
Sbjct: 123 LINXLQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPI 182

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            + D + D+           A         +  L  RE+ ++R RF  G     T  EV 
Sbjct: 183 FVMDQLSDEKQKDEQWVEELA-----LKEGMKRLNDREKMIIRKRFFQG----KTQMEVA 233

Query: 647 KQFCVTRERIRQIEAKAIRKL 667
           ++  +++ ++ ++E  AI+++
Sbjct: 234 EEIGISQAQVSRLEKSAIKQM 254


>gi|108799863|ref|YP_640060.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119868973|ref|YP_938925.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126435506|ref|YP_001071197.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108770282|gb|ABG09004.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119695062|gb|ABL92135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126235306|gb|ABN98706.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 269

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/251 (23%), Positives = 116/251 (46%), Gaps = 15/251 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +   ++S++  G  +    ++ +V   L L   +A +Y  +G    DL+Q   +GLM
Sbjct: 25  DVPDMFRLLSVLSPGTPDHDRQRERIVTRCLPLADHIAFRYHRKGENLDDLVQIARVGLM 84

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F ++A+  +   I R   D    + +P  ++D   ++ R   R++  
Sbjct: 85  HAVNRFDPENGANFLSFAVPTMLGEIRRHFRDNGWAMHVPRRLKDLHVQITRATPRLTQS 144

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL-----ETPIGDEDTSHLGDFIEDKNA 597
           + R PTP ++A +L    + V + L +  +  SL          D+ T  L D + + + 
Sbjct: 145 LGRPPTPTDLAAELGADRQEVVECL-VAGDAYSLRSIDSPISSSDDTTRSLADTLGEVDG 203

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                       RE+   +LA+LT RE  V+ +RF        T  ++ ++  V++ ++ 
Sbjct: 204 -----EMEHITDRESLRPLLAALTERERTVISLRFFA----SMTQTQIAERIGVSQMQVS 254

Query: 658 QIEAKAIRKLK 668
           +I AK +++L+
Sbjct: 255 RILAKTLQQLR 265


>gi|73667010|ref|YP_303026.1| sigma-70 region 2:sigma-70 region 4 [Ehrlichia canis str. Jake]
 gi|72394151|gb|AAZ68428.1| RNA polymerase, sigma 32 subunit, RpoH [Ehrlichia canis str. Jake]
          Length = 300

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 69/271 (25%), Positives = 123/271 (45%), Gaps = 14/271 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + +  +     +S  E   +       E         +V ++LRLV+ +A  + N GL
Sbjct: 20  LMSYMNEVHTFPILSPEEEDRLAK--NWYENGIVEDAHRLVTSHLRLVVKIALSFKNYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
             ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K +I   I      I+I      R
Sbjct: 78  PLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKASIKDYILKSWSCIKIGTTQAQR 137

Query: 527 DKIHKVVRTARRMSNKIKREPTPEE-IAKKLAMPVEGV-RKVLKITKEPISLETPIGDED 584
                + +  +++           + IA + +   + V +     T    SL   +   D
Sbjct: 138 KLFFSLRKIKQKLFKYNNITQDDIKLIANECSTSEQEVEQMNRYFTYRDRSLNEVVFSND 197

Query: 585 ---TSHLGDFI--EDKNAVSPLDSAIQANLRETT-TRVLASLTPREERVLRMRFGIGMNT 638
                 L + I  +  N         +A+L+ET  T+ L++L  R   +   R  I    
Sbjct: 198 NQKGIELQEIIKCDTPNQEDTYLLNEEASLKETLITQALSTLNERYRDIFIRRRLIEN-- 255

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             TL+ + +++ +++ER+RQIE  A  K+K+
Sbjct: 256 PDTLDTLSQEYKISKERVRQIEMHAFTKVKN 286


>gi|154707560|ref|YP_001423635.1| RNA polymerase factor sigma-32 [Coxiella burnetii Dugway 5J108-111]
 gi|154356846|gb|ABS78308.1| RNA polymerase sigma-32 factor [Coxiella burnetii Dugway 5J108-111]
          Length = 288

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 122/276 (44%), Gaps = 13/276 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI  I + I  ++    +S  E   + +  R+       A +++V ++LR V+ +A+ Y+
Sbjct: 14  SIGSIGSYISWVNRIPLLSAEEEHDLANKFRQ--SNDLEAARKLVLSHLRFVVRIARGYS 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G + +++A+ W++  I   I      ++I   
Sbjct: 72  GYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLASFAVHWIRAEIHEFILKNWRIVKIATT 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +                 +     +A++L +  + VR++ +       + +    + 
Sbjct: 132 KAQRKLFFNLRKHAKKRGWFSDHEAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEES 191

Query: 584 DTSHLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           D+          ++EDK    A+    S    +        + SL  R   +L  R+   
Sbjct: 192 DSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRWL-- 249

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                TL E+  Q+ V+ ERIRQ+E  A++K++   
Sbjct: 250 SEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|229031716|ref|ZP_04187709.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
 gi|228729600|gb|EEL80587.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
          Length = 252

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +   E +   +++++ +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVKNEKKKPQLKDHELK---ALIQQSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMRDELSKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|302522171|ref|ZP_07274513.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318056578|ref|ZP_07975301.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actG]
 gi|302431066|gb|EFL02882.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
          Length = 279

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 113/251 (45%), Gaps = 25/251 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +  + K   +A + +++++     LV  VA + +      ++  D +  G  GL+ A EK
Sbjct: 33  LWRMYKTTGDARL-REQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 91

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF TYA+  ++ A+   +        IP  +R K   V R    +  K+ R P
Sbjct: 92  FDIERSIKFETYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAKLHRTP 148

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED----------TSHLGDFIEDKNA 597
           T  E+A ++ + VE     L      +SL   +  E+             + D +ED  A
Sbjct: 149 TEVEVASEMGVGVED----LHAVFSQLSLANVVALEELLSVGSEGGGRLSIMDTLEDTGA 204

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            +P++ A    LR+  +R + SL  RE+ V+ + +  G     TL E+G    VT  R+ 
Sbjct: 205 DNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYYEG----LTLAEIGHVLGVTESRVS 260

Query: 658 QIEAKAIRKLK 668
           QI  K++ +L+
Sbjct: 261 QIHTKSVLQLR 271


>gi|256114330|ref|ZP_05455068.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 311

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 75/289 (25%), Positives = 130/289 (44%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++ A +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 297


>gi|229163011|ref|ZP_04290967.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
 gi|229174749|ref|ZP_04302273.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228608739|gb|EEK66037.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228620417|gb|EEK77287.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
          Length = 252

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +   E +   +++++ +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVKNEKKKPQLKDHELK---ALIQQSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMRDELSKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSETKWFD-------KIALKEAIRELDDRERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|152976482|ref|YP_001375999.1| sporulation sigma factor SigF [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025234|gb|ABS23004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 252

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 128/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+++      +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVRNEKKNPQLKDHELK---ALIQKSQDGDQGARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMKDELSKEYGRAPTINEVAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+      D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQAETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|311696378|gb|ADP99251.1| RNA polymerase, sigma 32 subunit, RpoH [marine bacterium HP15]
          Length = 286

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 131/270 (48%), Gaps = 13/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + I++ S    +++ E R +   +         A +++V ++LR VI +A+ Y+  
Sbjct: 15  QNLESYIQAASRIPVLTVDEERELAERL--HYEGDVEAARQLVMSHLRFVIHIARSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +++     
Sbjct: 73  GLAQADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKA 132

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
           + K+   +R+ ++    +  +     +A+ L +    VR++  ++  +  + + P  D+D
Sbjct: 133 QRKLFFNLRSQKKKLAWLSHDELNA-VAEDLGVEPRVVREMEGRLASQDTAFDGPQDDDD 191

Query: 585 TSHL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++ED     A    ++    +      + L  L  R + +LR R+     +
Sbjct: 192 DNAYQAPAYYLEDARSNPATQLENADWSDDSNGRLMQALGQLDERSQDILRERWL--SES 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 250 KSTLHELADRYGVSAERIRQLEKNAMKKIR 279


>gi|254468686|ref|ZP_05082092.1| alternative sigma factor RpoH [beta proteobacterium KB13]
 gi|207087496|gb|EDZ64779.1| alternative sigma factor RpoH [beta proteobacterium KB13]
          Length = 281

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 69/277 (24%), Positives = 137/277 (49%), Gaps = 14/277 (5%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           ++  +DS    + ++++I + T     E  ++   +   E     A ++++ ++LRLVI 
Sbjct: 9   LSPSLDSFDLYQQQVQAIPLLTE---HEEMNLAKKL--HEENDLNAARQLIMSHLRLVIK 63

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC- 517
           +A+ Y+  GL   DL+QEGNIGLMKA ++FD   G +  ++AM+W+K  I   +      
Sbjct: 64  IARSYSGYGLNQADLVQEGNIGLMKAVKRFDPSRGVRLVSFAMYWIKAEIQEFVVRNWRL 123

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI---TKEPI 574
                   + K+   +R+ ++    +K+E   +EIAK+L +    V+++       +  +
Sbjct: 124 VKTATTKAQRKLFFNLRSMKKTLQPLKQE-EIKEIAKELNVKESDVKEMEYRFNGNEIAL 182

Query: 575 SLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             +    +++      +++D+NA      +    ++N     +  + S+  R   +L  R
Sbjct: 183 DYQDEDNEDEVFRPISYLQDENADPVKQLISKESESNNLSALSNAIKSIDERSRYILESR 242

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +      TL E+  +  V+ ERIRQIE  A++KLK
Sbjct: 243 W-LNEEKSKTLHELADELGVSAERIRQIEQNALKKLK 278


>gi|83944334|ref|ZP_00956789.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83844878|gb|EAP82760.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 295

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 71/268 (26%), Positives = 124/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 29  ELKLAYAWRDERDEEALHRLITAYMRLAISMAGKFKRYGASMNDLIQEAGLGLMKAADKF 88

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A+  
Sbjct: 89  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQAA 148

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              + +    + I+ ++ +P+  V  +  +++    SL      ED      D + D +A
Sbjct: 149 GETLDKHQLRQMISTEIGVPMHDVEMMEGRLSGSDFSLNATQSAEDEGREWIDALVDDSA 208

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +        +   LR      + +L  RE+ ++R R         TLE +G +  +++E
Sbjct: 209 QAAERVEESHDTLTLRSWLLSAMQALNEREQFIVRERKLRD--QPRTLESLGAELSLSKE 266

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S ++R FL
Sbjct: 267 RVRQLEAAAFGKMRKTLETQSSEVRHFL 294


>gi|220936149|ref|YP_002515048.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997459|gb|ACL74061.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 281

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 122/266 (45%), Gaps = 15/266 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I++I+    +   E + +   +R  + +   A +++V  NLR V+ +A+ Y+  GL   
Sbjct: 17  YIQAITRLPVLDAEEEQRLARDLR--DRQDLEAARKLVMHNLRFVVHIARGYSGYGLGLG 74

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      +++      +  K
Sbjct: 75  DLIQEGNIGLMKAVKRFDPEMGVRLISFAVHWIRAEIHEFILRNWRIVKVATTKAQR--K 132

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAM---PVEGVRKVLKITKEPISLETPIGDEDTS-- 586
           +    R    ++    + E  A    +   P + +    ++  + +S +     ++    
Sbjct: 133 LFFNLRSAKQRLGWFNSEEVNAVADDLGVTPAQVLEMESRLAGQDVSFDPAPASDEDGPS 192

Query: 587 -HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               + + D++   A         A+        L +L PR   ++  R+        TL
Sbjct: 193 LSPAETLIDESGDPAERLEADDWAAHHETRLHSGLEALDPRSRDIVARRWL--TEQKATL 250

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ ++ ER+RQ+E+ A+RKL+
Sbjct: 251 HELAAEYGISAERVRQLESNAMRKLR 276


>gi|146296669|ref|YP_001180440.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410245|gb|ABP67249.1| RNA polymerase, sigma subunit, RpoX/SigF [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 231

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 115/239 (48%), Gaps = 13/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M+ K +     A++E++E NL LV S+ KK+  +G++  DL Q G IGL+KA ++FD   
Sbjct: 1   MISKAKNGDKKARQELIENNLALVWSIVKKFVVKGIEADDLFQIGCIGLIKAVDRFDLSF 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA+  +   I R + D    I+I   +++  +K+ R       +  REPT  EI
Sbjct: 61  NVRFSTYAVPMIIGEIKRYLRD-DGKIKISRKIKENQNKLKRFRDEFLFQNGREPTISEI 119

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR 610
           ++   +  + +   +  + +  SL   I  E+     L D   D++  S L   +     
Sbjct: 120 SEATGLSQDDILLCIDASLDVTSLNEVINQEEGKPITLMDIAADEDYSSRLLDIM----- 174

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L  L  RE  ++ MR+        T  E+ K+  +++  + +IE KA+ ++K 
Sbjct: 175 -ALKEGLRKLKGRERYIIFMRYFKN----KTQSEIAKELNISQVHVSRIEKKALERIKR 228


>gi|229492054|ref|ZP_04385868.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229321078|gb|EEN86885.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 259

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 111/247 (44%), Gaps = 12/247 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               ++ +   +      + +++E  L L   +A +Y  RG    DL+Q  ++GL+ A  
Sbjct: 12  LLEELASLPGDDARCERLRTQIIELCLPLTRHIALRYRGRGQALDDLVQAASVGLVSAVN 71

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F  +A+  +   + +   D+   +R+P  +++    + +    ++  + RE
Sbjct: 72  RFDLAKGKDFLAFAIPTMMGEVRKHFRDRGWDVRVPRSLQENCLALNKARTALTQDLGRE 131

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+AK+L +    V +++    +    SL+      D   + D + + +A       
Sbjct: 132 PTVPELAKELGVEPAEVAEIVAAGDSYHAASLDAAAVG-DGRSIADALGEFDAALDGI-- 188

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + +ET    L +L  RE  ++  RF      + T  E+ ++  V++  + ++ A+++
Sbjct: 189 ---DNQETLRPALLALPERERIIVIYRFF----GELTQAEIAEKIGVSQMHVSRLLAQSL 241

Query: 665 RKLKHPS 671
            KL+  S
Sbjct: 242 AKLRASS 248


>gi|47122|emb|CAA48660.1| whiG-Stv [Streptomyces griseocarneus]
          Length = 278

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 106/237 (44%), Gaps = 16/237 (6%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEKFDPARAIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R PT  E+A ++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAELRRTPTEAEVAAEMG 157

Query: 558 MPVEGV--RKVLKITKEPISLETPIGDEDTS----HLGDFIEDKNAVSPLDSAIQANLRE 611
           + +E +            ++LE  +   D       L D +ED  A  P++ A    LR 
Sbjct: 158 IALEELHSVFSQLSLANVVALEDLLHAGDEGGERLSLMDTLEDTAADDPVEVAEDHELRR 217

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R + +L  RE+ V+ + +  G     TL E+G+   VT  R+ QI  K++ +L+
Sbjct: 218 LLARAINTLPEREKTVVTLYYYEG----LTLAEIGQVLGVTESRVSQIHTKSVLQLR 270


>gi|239934556|emb|CAR94592.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 207

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 95/255 (37%), Gaps = 49/255 (19%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           VRMY+REMG++ELL+REGEI IAKRIE G   +  +L   PLTFQ ++   + +  G   
Sbjct: 1   VRMYMREMGTVELLTREGEIRIAKRIEEGLDAVRTALSSYPLTFQHILNSYELVKQGQGR 60

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L +II     I P +             Q      +E+            E      +++
Sbjct: 61  LVDII--VGFIDPNAPDEIAAPVNPKLAQAAAPEVEEE-----------TEEGESTEEEE 107

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             +    PE A                   A   +L  + + A++               
Sbjct: 108 ALETGPDPEEAARRF---------------ASISKLHQQALKAIE--------------- 137

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                +      K   +++K+      L L+    D L+ QL D    + + E +++ L 
Sbjct: 138 -----QHGIKDPKTVKIRKKVAGEFMELKLSPKMFDALIVQLRDHVAEVRNMEKQIMTLC 192

Query: 361 QS-YGIKRDVFLERH 374
               G+ R  F+   
Sbjct: 193 VRDAGMPRKDFVTTF 207


>gi|71280363|ref|YP_266929.1| RNA polymerase factor sigma-32 [Colwellia psychrerythraea 34H]
 gi|71146103|gb|AAZ26576.1| RNA polymerase sigma-32 factor [Colwellia psychrerythraea 34H]
          Length = 285

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/274 (22%), Positives = 131/274 (47%), Gaps = 17/274 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   ++S      ++  +   + + +         A +E++ ++LR VI VAK Y+  GL
Sbjct: 15  IEAYMQSAYSIPMLTAEKEHDLATRL--YNENDLQAAQELIMSHLRFVIHVAKGYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+QEGN+GLMKA ++F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 73  PHADLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQR 132

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED- 584
             K+    R+   ++    T E   +A+ L +  + V ++  +++    + E    D+D 
Sbjct: 133 --KLFFNLRKNKKRLGWFSTEEVNTVAENLGVTTKDVMEMESRMSSHDQAFELSKDDDDN 190

Query: 585 ----TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
               +     +++DK    AV   +     +  +  +  L +L  R + +++ R+     
Sbjct: 191 LGSSSFSPAQYLQDKQSDLAVEVENDNWDNHANKRLSTALVTLDERSQDIIKTRWLTEDK 250

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           T  TL+E+  ++ ++ ER+RQ+E  A+ KLK+  
Sbjct: 251 T--TLQELANKYQISAERVRQLEKNALSKLKNTM 282


>gi|329941096|ref|ZP_08290375.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329299627|gb|EGG43526.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 319

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 116/246 (47%), Gaps = 12/246 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               +  + +G  E +  +  +VE NL LV   A ++  R     D+IQ G IGL+KA +
Sbjct: 77  LFQRLESLEEGTYEHAYVRHTLVELNLALVKFAAARFRTRSEPMEDIIQVGTIGLIKAID 136

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 137 RFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQQLDRA 196

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A +L +  E V + +         SL+    ++D    L D I  ++       
Sbjct: 197 PTVTELADRLGLSNEEVVEGMVASNAYTASSLDAQPEEDDSEGALADRIGYEDHELEGVE 256

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     E+   ++A L  R+ ++L +RF        T  E+G++  +++  + ++ ++ 
Sbjct: 257 YV-----ESLKPLIAGLPQRDRKILSLRFVAN----MTQSEIGEELGISQMHVSRLLSRT 307

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 308 LVRLRK 313


>gi|303232785|ref|ZP_07319470.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
 gi|302481271|gb|EFL44346.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
          Length = 287

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 121/238 (50%), Gaps = 7/238 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++        A+ ++V  +L L   +A K+ NRG    DLIQ   IGL+KA ++FD   G
Sbjct: 49  IKFKRHGDEEARNQLVLNHLNLARFLASKFKNRGESLDDLIQVATIGLIKAIDRFDIDRG 108

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F+T+A   +   I R   D+S ++R+P  +++   KV +    ++ K++  P+ EEIA
Sbjct: 109 LEFTTFATPTILGEIKRHFRDRSWSVRVPRRLQELSSKVSQATDMLTEKLQHSPSVEEIA 168

Query: 554 KKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L + V+ V + ++       +SL+ P  D D       + D  A S  D     + + 
Sbjct: 169 RELDVSVDEVLEAMESSRAYSSVSLDVPTVDNDDGSAATSVLDTYA-SVDDDLESCDDKL 227

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               ++ + T RE++++RMRF  G     T  E+  +  V++ ++ ++    +RKL+ 
Sbjct: 228 VLQEIIKNCTEREQQIIRMRFLDG----MTQVEIADKLQVSQVQVSRLLRNTLRKLQE 281


>gi|154503856|ref|ZP_02040916.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
 gi|153795455|gb|EDN77875.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
          Length = 259

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 123/236 (52%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           + +     A+++ ++ NLRLV+SV K++++      DL Q G +GLMKA + FD     K
Sbjct: 30  RIKEGDEDAREQYIKGNLRLVLSVIKRFSSSSENADDLFQIGCVGLMKAVDHFDPSRLVK 89

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA+  +   I R + D +  IR+   +RD  +K +        K  +EPT +EIA++
Sbjct: 90  FSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAYKAIYAKEGFVKKYSKEPTVQEIAEE 148

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + +  E +   L   + P+SL  P+  +  DT ++ D + DK   +  ++ ++     + 
Sbjct: 149 IGISKEDIVFALDAIQMPVSLHEPVYSDGGDTLYIMDQVSDKK--NREENWVEEL---SL 203

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +  L  RE  ++++RF  G     T  EV +Q  +++ ++ ++E  A++ +K 
Sbjct: 204 EAAMERLNERERFIIQLRFFEG----KTQMEVAEQIQISQAQVSRLEKNALKIMKQ 255


>gi|163941815|ref|YP_001646699.1| sporulation sigma factor SigF [Bacillus weihenstephanensis KBAB4]
 gi|229013283|ref|ZP_04170424.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
 gi|229061746|ref|ZP_04199079.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|229134882|ref|ZP_04263689.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|229168817|ref|ZP_04296536.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|163864012|gb|ABY45071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614665|gb|EEK71771.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|228648557|gb|EEL04585.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|228717492|gb|EEL69156.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|228748050|gb|EEL97914.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
          Length = 252

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+++   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVRNEKKKPQLKDHELK---ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           V +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 VRKMRDELSKEFGRAPTINEVAQALELTPEEVVLAQEASRAPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|311030733|ref|ZP_07708823.1| sporulation sigma factor SigF [Bacillus sp. m3-13]
          Length = 251

 Score =  123 bits (308), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 124/254 (48%), Gaps = 17/254 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T +   E + +   +++ +     A+  +V+ N+RLV SV +++ NRG +  DL Q 
Sbjct: 8   QTQTYLKDHEVKEL---IKRSQSGEQEARDTIVQKNMRLVWSVVQRFMNRGYEPDDLFQI 64

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K+ +KFD     KFSTYA+  +   I R I D    +++   +++  +K+ +  
Sbjct: 65  GCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDGS-VKVSRSLKEVANKIRKAK 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIED 594
             +S +  R PT  EIA+ L +  E V    +  + P S+   + + D     L D I D
Sbjct: 124 DELSKRYGRVPTINEIAEFLEITAEEVVLAQEAARAPSSIHETVYENDGDPITLLDQIAD 183

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +     D       +      +  L  RE+ ++ +R+      D T  EV ++  +++ 
Sbjct: 184 HSEHRWFD-------KIALKEAIEELDEREKLIVYLRY----YKDQTQTEVAQRLGISQV 232

Query: 655 RIRQIEAKAIRKLK 668
           ++ ++E K ++++K
Sbjct: 233 QVSRLEKKILQQMK 246


>gi|196038743|ref|ZP_03106051.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
 gi|196030466|gb|EDX69065.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
          Length = 252

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 130/259 (50%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K+   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVKNEKKKPQLKDQELK---ALIQKSQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMRDELSKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D++     D       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQSETKWFD-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|326201325|ref|ZP_08191197.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
 gi|325988893|gb|EGD49717.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
          Length = 248

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 126/239 (52%), Gaps = 7/239 (2%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +++++ K +     A+  +VE N+ LV S+ K++ NRG +  DL Q G+IGL+KA  KFD
Sbjct: 9   VLTLIIKAKAGDKQAQSVLVERNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFD 68

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KFSTYA+  +   I R I D    I++   +++   K   T   MS ++ REPT 
Sbjct: 69  TSYDVKFSTYAVPMIIGEIKRFIRD-DGIIKVSRSLKEISSKARITKEIMSKELGREPTI 127

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA+++ +  E +   ++    P SL + IGD D S +   + D+   +  +  +    
Sbjct: 128 NEIAQRMNISPEELVMAIEAGCTPESLYSTIGDGDNSPI--LLIDRIDAADNNCEVDLID 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    ++L +L  RE +++ +R+      + T  ++ K   +++ ++ +IE K +R +K
Sbjct: 186 KIAIRQILDTLDTRERQIIILRYF----KEKTQVQIAKLLGISQVQVSRIEKKILRDIK 240


>gi|167854819|ref|ZP_02477597.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219871694|ref|YP_002476069.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
 gi|167854117|gb|EDS25353.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219691898|gb|ACL33121.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
          Length = 315

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 132/268 (49%), Gaps = 14/268 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+  +    ++  + + +    R    E   A K+++ ++LR V+ +A+ Y   GL
Sbjct: 46  LDSYIRMANQYPVLTAEQEKELAE--RFYYDEDLDAAKQLIMSHLRFVVYIARGYLGYGL 103

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR--IPVHMR 526
              DLIQEGNIGLMKA ++F+  +G + +++A+ WVK  I   +      ++       R
Sbjct: 104 PLADLIQEGNIGLMKAVKRFNPEIGVRLASFAVHWVKAEIHEYVLKNWRIVKVATTKSQR 163

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +  +R++     E    ++A++L +  + V+++  ++  + I  +T +GD+D 
Sbjct: 164 KLFFNLRKNKQRLA--WFNEEEIRKVAEELGVSTDDVKEMESRMVGQDIGFDTSVGDDDD 221

Query: 586 SHLGD--FIEDKNA---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            +     ++ED+++                      LA L  R + +++ R+        
Sbjct: 222 DNYVPSMYLEDESSNFVDELEYEEYSGRATAQLAYALAQLDERSQNIIKTRWLDEN--KA 279

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  Q+ ++ ER+RQ+E +A++K+K
Sbjct: 280 TLHELAAQYNISAERVRQLENQALKKIK 307


>gi|55274905|gb|AAV49254.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 182

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 71/179 (39%), Positives = 119/179 (66%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 2   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 62  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 121

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           +G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+    
Sbjct: 122 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYE 180


>gi|66474651|gb|AAY46895.1| RpoD [Aeromonas enteropelogenes]
          Length = 269

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 63/313 (20%), Positives = 116/313 (37%), Gaps = 46/313 (14%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P   
Sbjct: 1   EGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLCLSDII--SGFIDPN-- 56

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                 E DDV  T   + S            D   +   + + 
Sbjct: 57  ----------------------ETDDVAPTATHMGSELSEEDLADEDEDEDEDEDGDGDD 94

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCK 315
           + D+ +      ++                  E + ELR+  +   ++ QK+ ++    +
Sbjct: 95  SDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDDTQ 137

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
                L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 138 AAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 197

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      V  + + + +   +++ I  ETG+SI++ + I   +
Sbjct: 198 TNNECETAWFEYQKQAGKAWSPRLVEMD-EDVQRAIGKLQQIEEETGLSIAQIKDINRRM 256

Query: 435 RKGECEASIAKKE 447
             GE +A  AKKE
Sbjct: 257 SIGEAKARRAKKE 269


>gi|54295507|ref|YP_127922.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Lens]
 gi|53755339|emb|CAH16835.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Lens]
          Length = 284

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/274 (23%), Positives = 123/274 (44%), Gaps = 15/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +++ E        R        A +++V A+LR V+ VA+ Y   GL
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAE--RFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+M N++      E   +AK L +  E V     ++     S + P  D++ 
Sbjct: 135 --KLFFNLRQMKNRLGWFSNEEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDND 192

Query: 586 ------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                       + D  AV   +       RE     +  L  R + +L+ R+       
Sbjct: 193 DAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TL ++ +++ V+ ER+RQ+E  A++K++    +
Sbjct: 251 LTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMEA 284


>gi|254487022|ref|ZP_05100227.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
 gi|214043891|gb|EEB84529.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
          Length = 277

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 70/268 (26%), Positives = 123/268 (45%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 11  ELKLAYAWRDERDEEALHRLITAYMRLAISMAGKFKRYGAPMNDLIQEAGLGLMKAADKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A+  
Sbjct: 71  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQAA 130

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              + +    + I+ ++ +P+  V  +  +++    SL      ED      D + D  A
Sbjct: 131 GETLDKHQLRQMISTEIGVPMHDVEMMEGRLSGSDYSLNATQSSEDEGREWIDALVDDTA 190

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +        +   LR      + +L  RE+ ++R R         TLE +G++  +++E
Sbjct: 191 QAAERVEESHDIVTLRNWLLGAMQALNDREQFIVRERKLRD--QPRTLESLGQELNLSKE 248

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S ++  FL
Sbjct: 249 RVRQLEAAAFAKMRKTLETQSAEVHHFL 276


>gi|149924702|ref|ZP_01913051.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
 gi|149814429|gb|EDM74021.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
          Length = 371

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 77/305 (25%), Positives = 140/305 (45%), Gaps = 14/305 (4%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           ELD    S +   P    +   A  +     +   +  +     ++  +   +   VR  
Sbjct: 61  ELDAIEASLSARRPRAAPEGTTALALRD--PMAAYMAEVRRHPLLTREQEHELA--VRWV 116

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E     A K +V +NLRLV+ +A +Y       LDL+QEGN+GL+KA +KFD   G K S
Sbjct: 117 EHGDQEAAKRLVTSNLRLVVKIANEYRRGYQNLLDLVQEGNVGLLKAVQKFDPYRGVKLS 176

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           TY+ WW++  + + I +    ++I     + K+   +R  R    +   +PT E IAK+L
Sbjct: 177 TYSGWWIRAYVLKHILNNWRLVKIGTTQNQRKLFFNLRKQREALIRAGIDPTAENIAKEL 236

Query: 557 AMPVEGVRKVL-KITKEPISLETPIGDEDT---SHLGDFIEDKNAV---SPLDSAIQANL 609
            +  E V ++  ++     SL  P+G  +        D +ED+             +  L
Sbjct: 237 DVSTEEVVEMQKRMGAPDASLNAPLGSGEEPGARTRLDMLEDETTDPEGEVSGEEFKRLL 296

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +      A+L+ RE  +      +  +   TL+ +G+++ V+RER RQ+E + + +L+ 
Sbjct: 297 HDKLRTFGATLSGREAEIFGE--RLIADEPITLQALGERWGVSRERARQVEKRMVLRLRK 354

Query: 670 PSRSK 674
             +++
Sbjct: 355 YLQAE 359



 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 3/99 (3%)

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR-I 146
            ++  LD   ++ ++       + +   +  DP+  Y+ E+    LL+RE E  +A R +
Sbjct: 57  ATDAELDAIEASLSARRPRAAPEGTTALALRDPMAAYMAEVRRHPLLTREQEHELAVRWV 116

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185
           E G       L  S L    ++   +E   G   L +++
Sbjct: 117 EHGDQEAAKRLVTSNLRL--VVKIANEYRRGYQNLLDLV 153


>gi|331090618|ref|ZP_08339469.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330401058|gb|EGG80653.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 259

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 72/264 (27%), Positives = 134/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + + +     ++  + +     AK+E ++ NLRLV+SV K+++N  
Sbjct: 2   ALNKVEICGVNTAKLPLLKEEEKEALFVRIKAGDEEAKEEYIKGNLRLVLSVIKRFSNSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA   F+  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAINNFNTELNVKFSTYAVPMIIGEIRRYMRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +           +EPT +EIA ++ +  E + + L   + P+SL  PI ++  DT
Sbjct: 121 TAYKAIYAKEGYMKTHLKEPTIQEIASEIGISKEEIVQALDAIQMPMSLHEPIYNDGGDT 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I DK   +  ++ ++     +    +  L  RE ++++MRF  G     T  E+
Sbjct: 181 LYVMDQISDKK--NKEENWVEEL---SLAEAMERLGERERKIIQMRFFEG----KTQMEI 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K+  +++ ++ ++E  A+  +K 
Sbjct: 232 AKEIHISQAQVSRLEKNALEFMKQ 255


>gi|307611543|emb|CBX01223.1| RNA polymerase sigma-32 factor [Legionella pneumophila 130b]
          Length = 284

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/274 (23%), Positives = 123/274 (44%), Gaps = 15/274 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +++ E        R        A +++V A+LR V+ VA+ Y   GL
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAE--RFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+M N++      E   +AK L +  E V     ++     S + P  D++ 
Sbjct: 135 --KLFFNLRQMKNRLGWFSNEEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDND 192

Query: 586 ------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                       + D  AV   +       RE     +  L  R + +L+ R+       
Sbjct: 193 DAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            TL ++ +++ V+ ER+RQ+E  A++K++    +
Sbjct: 251 LTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMEA 284


>gi|4514513|dbj|BAA75455.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
 gi|4514515|dbj|BAA75456.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 278

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 121/316 (38%), Gaps = 39/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++   ++   G   L +I  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PE+        E  +  + ++ S   +  DV+  + D E  ++   D   +    PE 
Sbjct: 59  LDPETDEDIPEVLEEEAELEEDEDSS-PKAKDVKLDDDDEEEESEGDDDSEGESGPDPEV 117

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+   +++   ++                                   K  + 
Sbjct: 118 AKVRFSELEAAWNETKTVVA-----------------------------------KHGRD 142

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S + K   E L  +           +++ E +     +I  NE E++R A   G + R  
Sbjct: 143 SDEAKAALEALAAVFMMFKFTPRLFEIISEMIRGTHDQIRSNEREIMRYAVRRGRMDRTQ 202

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F      +E +P W+         E K  +      +L  + +I  I  + G+++ + + 
Sbjct: 203 FRTTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 262

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 263 ISKRMAVGEAKARRAK 278


>gi|83953376|ref|ZP_00962098.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83842344|gb|EAP81512.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 295

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 71/268 (26%), Positives = 124/268 (46%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 29  ELKLAYAWRDERDEEALHRLITAYMRLAISMAGKFKRYGASMNDLIQEAGLGLMKAADKF 88

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A+  
Sbjct: 89  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREAQAA 148

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              + +    + I+ ++ +P+  V  +  +++    SL      ED      D + D +A
Sbjct: 149 GETLDKHQLRQMISTEIGVPMHDVEMMEGRLSGSDFSLNATQSAEDEGREWIDALVDDSA 208

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +        +   LR      + +L  RE+ ++R R         TLE +G +  +++E
Sbjct: 209 QAAERIEESHDTLTLRSWLLSAMQALNEREQFIVRERKLRD--QPRTLESLGAELSLSKE 266

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++    ++S ++R FL
Sbjct: 267 RVRQLEAAAFGKMRKTLETQSSEVRHFL 294


>gi|114566413|ref|YP_753567.1| RNA polymerase sigma factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337348|gb|ABI68196.1| putative RNA polymerase sigma factor [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 260

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 117/251 (46%), Gaps = 15/251 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +R  E E   A+ +++     LV  VA +   + +  ++  +LI  G  GL+ A EKFD
Sbjct: 13  WIRLKENEDIEARDQLIIHFAHLVKYVASRLAIHLSSLVELDELISYGIEGLIDAIEKFD 72

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF TYA+  ++ ++   +        IPV +R K  ++ +    +  ++ R  + 
Sbjct: 73  HKRNIKFETYAITRIRGSMIDGLRSMDW---IPVSLRQKSKELEKAYMNVEARLGRSASD 129

Query: 550 EEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSA 604
            E+A++L + ++   V          ISL+  +  ED      + D +ED N++S  +  
Sbjct: 130 AEVAEELGLNLDEFAVLLRDVAATTIISLDDFLPGEDGEQKKRMLDLLEDHNSISASEIV 189

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               +++   + ++ L  +E+ V+ + +  G     TL+E+G    ++  RI Q+  KAI
Sbjct: 190 EFNEVKDLLAKAISRLPDKEKLVVYLYYYEG----LTLKEIGATISLSESRISQLHTKAI 245

Query: 665 RKLKHPSRSKK 675
            +L+     KK
Sbjct: 246 LRLRGSLSKKK 256


>gi|114705882|ref|ZP_01438785.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114538728|gb|EAU41849.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 300

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 74/246 (30%), Positives = 119/246 (48%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR  E     A  ++  A++RLVIS+A K+ + GL   DLIQEG++GL++AA +F+    
Sbjct: 43  VRWKENRDQEALHKITSAHMRLVISMASKFRHFGLAMNDLIQEGHVGLLEAAARFEPERE 102

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---KIKREPT 548
            +FSTYA WW++ +I   I      +R       K     + R   R+S     I     
Sbjct: 103 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLSQGAEPISGNAM 162

Query: 549 PEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSH--LGDFI--EDKNAVSPLDS 603
             EIA  L +    V     +++    SL  P+ D+++      DF+  +D      +  
Sbjct: 163 YREIAGALKVSESDVALMDSRLSGPDSSLNAPLLDDESGSADRQDFLVADDPLPDETVSV 222

Query: 604 AIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +I    R    T  L  L+ RE +++R R         TLE +G +  +++ER+RQIE +
Sbjct: 223 SIDDERRVTWLTSALDVLSERELKIIRERRLQDDG--ATLEALGTKLGISKERVRQIETR 280

Query: 663 AIRKLK 668
           A+ KL+
Sbjct: 281 ALEKLR 286


>gi|297746555|emb|CAZ60995.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 266

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/311 (18%), Positives = 108/311 (34%), Gaps = 46/311 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            EGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   PEGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE 58

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   +  +       S+  E D   E E + E     S DD       PE A    
Sbjct: 59  -------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKF 111

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            +L    + +  ++                                   Q++ ++    +
Sbjct: 112 GDLRAQYEVTRLSI-----------------------------------QQNGRAHEDTQ 136

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D L     ++ +R+   E  +++L  +   + +  F+   
Sbjct: 137 AAIAQLADVFRQFRLMPKQFDRLGNNTCEMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 196

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 197 TNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 255

Query: 435 RKGECEASIAK 445
             GE +    K
Sbjct: 256 SIGEAKGPPCK 266


>gi|255030138|ref|ZP_05302089.1| RNA polymerase sigma factor SigB [Listeria monocytogenes LO28]
          Length = 245

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 113/248 (45%), Gaps = 4/248 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+ 
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLRE 237

Query: 670 PSRSKKLR 677
             +++++ 
Sbjct: 238 ALQNEEVE 245


>gi|197723817|gb|ACH72688.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 256

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 112/248 (45%), Gaps = 4/248 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 12  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 71

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 72  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 131

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 132 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 191

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 192 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 247

Query: 667 LKHPSRSK 674
           L+   +++
Sbjct: 248 LREALQNE 255


>gi|296501716|ref|YP_003663416.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
 gi|296322768|gb|ADH05696.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
          Length = 257

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 121/261 (46%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIADFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|161898857|gb|ABX80418.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 108/239 (45%), Gaps = 4/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+
Sbjct: 182 RMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLR 236


>gi|114776846|ref|ZP_01451889.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114552932|gb|EAU55363.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 274

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/265 (21%), Positives = 122/265 (46%), Gaps = 9/265 (3%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + +     +  +E   +  +    +     A +++V ANL  V ++A++Y + GL  +DL
Sbjct: 15  REMRKTPRLDRAEETRLARL--WHDQGDREAARQLVVANLGGVAAIAREYRHFGLPEMDL 72

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEG +GLM A ++FD   G++  TYA WWV+ AI   I      +++  +   +     
Sbjct: 73  IQEGTLGLMHAVKRFDPERGFRLMTYASWWVRAAIHDFILHSWSIVKLGTNKLQRRVFAG 132

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT-KEPISLETPIGDEDTSHLGDFI 592
               + +         +++A    +     ++      +  +SL+    DE    +   +
Sbjct: 133 LQKAKNAIAAFDGSRADDVAADFGITAGEYQEAAGAFLQRDLSLD-CACDEGGDAMVHNL 191

Query: 593 E--DKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           E  D +    +     +  R+      L++L  R+  +L  +     +   TL+++ ++F
Sbjct: 192 ESMDASPEQIVTDNNWSEHRQAGLYHALSTLPERDRLIL--QRRHLSDEPATLKDLSEEF 249

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSK 674
            V+ ERIRQ+EA+A+++L+    ++
Sbjct: 250 GVSMERIRQLEARAMKQLRESLVNQ 274


>gi|77165402|ref|YP_343927.1| RpoH [Nitrosococcus oceani ATCC 19707]
 gi|254433859|ref|ZP_05047367.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
 gi|76883716|gb|ABA58397.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus oceani ATCC
           19707]
 gi|207090192|gb|EDZ67463.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
          Length = 287

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 123/270 (45%), Gaps = 17/270 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +    ++      +S  + R +   +R+       A +++V ++LR VI +A+ Y   GL
Sbjct: 20  LNTYCQNAHSIPVLSAEQERSLALRLRQH--NDLEAARQLVLSHLRFVIRIARGYNGYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA ++FD   G +  ++A+ W++  I   I      +++      R
Sbjct: 78  PLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQR 137

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                +    +R+    ++E   +E+A+ L +  + V ++  +++ +    +    +E  
Sbjct: 138 KLFFNLRSAKKRLGWLNRKE--VDEVAQDLGVSPKQVMEMEARLSSQDAPFDGSNAEESE 195

Query: 586 -------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                  ++L D   D  A        +    +   + L  L  R   ++  R+     +
Sbjct: 196 NGIPAPMAYLADPSADP-AQKMELLDQENYYGQRLQQALEVLDLRSRTIINRRWLQENKS 254

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ ++ ERIRQ+E  AI+K++
Sbjct: 255 --TLHELAAEYQISAERIRQLENNAIKKMR 282


>gi|54298657|ref|YP_125026.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Paris]
 gi|296108313|ref|YP_003620014.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
 gi|53752442|emb|CAH13874.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Paris]
 gi|295650215|gb|ADG26062.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
          Length = 284

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/273 (23%), Positives = 122/273 (44%), Gaps = 15/273 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  ++    +++ E        R        A +++V A+LR V+ VA+ Y   GL
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAE--RFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDT 585
             K+    R+M N++      E   +AK L +  E V     ++     S + P  D++ 
Sbjct: 135 --KLFFNLRQMKNRLGWFSNEEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDND 192

Query: 586 ------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                       + D  AV   +       RE     +  L  R + +L+ R+       
Sbjct: 193 DAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            TL ++ +++ V+ ER+RQ+E  A++K++    
Sbjct: 251 LTLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 283


>gi|300788069|ref|YP_003768360.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299797583|gb|ADJ47958.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 273

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 124/247 (50%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F     +  +    A++ ++ ++  +L L   +A++++ RG  F DL+Q    GL++A +
Sbjct: 33  FAERSRLDAEDPRRAAL-RERLITEHLPLAEHIARRFSGRGEPFEDLLQVARTGLIRAVD 91

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G  F ++A+  +   + R   D   ++R+P  ++D   K+ + +  +++++ R 
Sbjct: 92  RYAADRGSDFVSFAVPTIMGEVRRHFRDVGWSMRVPRALKDLKQKLAKASDVLAHELGRA 151

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLD 602
           PTP E+A+ L + +E VR+ L         SL+TP    ++D +  G   ED +     +
Sbjct: 152 PTPSELARHLDLDIETVREGLLAAQAYRATSLDTPAREGEDDFAAAGRLAEDDSGFERFE 211

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           + I           +A+L PRE  +++MRF      + T  ++ ++  V++  + ++ AK
Sbjct: 212 NHI------ALRAAMATLEPRERAIVKMRFA----DELTQSQIAQRIGVSQMHVSRLLAK 261

Query: 663 AIRKLKH 669
            + +L+ 
Sbjct: 262 TLEQLRQ 268


>gi|256829638|ref|YP_003158366.1| RNA polymerase sigma-32 subunit RpoH [Desulfomicrobium baculatum
           DSM 4028]
 gi|256578814|gb|ACU89950.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfomicrobium baculatum
           DSM 4028]
          Length = 356

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 74/280 (26%), Positives = 127/280 (45%), Gaps = 10/280 (3%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             EV ++  +   ++ I     +   E   +    R  +     A   ++ +NLRLV+ +
Sbjct: 67  RREVATLDPLHIYLQEIKKFKPLEQDEEFDLARRYRDEKE--EQAAFILITSNLRLVVKI 124

Query: 460 AKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           A  +  R +   LDLIQEGN+GLMKA +KFD   G KFS YA +W+K  I + I D    
Sbjct: 125 AMDFQRRWMKNVLDLIQEGNVGLMKAVQKFDPDKGIKFSYYASFWIKAYILKFIMDNWRM 184

Query: 519 IRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
           ++I      R   + + +  +R+  +     T            + V    ++ +  +SL
Sbjct: 185 VKIGTTQAQRKLFYNLGKERQRLQAQGFDPTTSTLSKNLQVSEADIVEMGQRLGQHDVSL 244

Query: 577 ETPIGDEDTSHLGDFIEDKNA---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +  IGD+ +    DFI    A          I   + +    +   L  +E  +L     
Sbjct: 245 DMKIGDDSSFTPMDFIPALEAGIEEQMAADEISVLIHDNIDAIRDGLNEKELDILEQ--R 302

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +  ++  TL E+G ++ +TRER+RQIEA+ ++K+K    S
Sbjct: 303 LLADSPITLREIGDKYGITRERVRQIEARLLQKIKAQMSS 342


>gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
 gi|151280463|gb|ABR88873.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
          Length = 243

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 54/244 (22%), Positives = 102/244 (41%), Gaps = 12/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                    K  +V  +  LV  +A +   +    ++  DLIQ G IGL+ A  +++   
Sbjct: 1   MYTAAGKSDKNHLVGEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVSRYEETH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA+  ++ A+   +         P  MR  + K+      +  ++ R P   E+
Sbjct: 61  GAQFETYAVQRIRGAMLDELRSSDWM---PRSMRQNMRKIEVAMNTLQQRLGRPPNESEV 117

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK+L + +   + +L      + +  E     ED  H  D      +  PL + +    R
Sbjct: 118 AKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFLDRYCTDESPDPLQNLMNTGFR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 + +L  RE+    +  G+    +  L+E+G    VT  R+ Q+ ++AI +++  
Sbjct: 178 AAVIEAIQALPEREK----ILMGLYYEQEMNLKEIGAVMGVTESRVSQLHSQAIARMRAN 233

Query: 671 SRSK 674
            R K
Sbjct: 234 LREK 237


>gi|268608170|ref|ZP_06141897.1| sporulation sigma factor SigG [Ruminococcus flavefaciens FD-1]
          Length = 259

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 72/263 (27%), Positives = 138/263 (52%), Gaps = 17/263 (6%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRGL 468
           N+++   + T  + + +    ++++R+ +   S  A+ ++++ NLRLV+SV +++T RG 
Sbjct: 4   NKVEIAGINTSELKVMKEDEKMALLREIKATGSKEARDKLIKGNLRLVLSVIQRFTGRGE 63

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGL+KA   FD     +FSTY +  +   + R + D S  +++   +RD 
Sbjct: 64  DIDDLFQIGVIGLIKAINNFDLTKEVRFSTYCVPMISGELRRHLRDYS-HVKVSRSLRDL 122

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            +K +++  R++ +++REP+ +EIA+ +      +   L+   +P+SL  P+  +    L
Sbjct: 123 AYKAIQSKERLTVRLQREPSIDEIAEDIGEKRSEIVIALESISDPVSLYEPVYSDSDDTL 182

Query: 589 --GDFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
              D I D+N        I++ L E T    +  L  RE  +L +RF  G     T  EV
Sbjct: 183 FIMDQISDRND-------IESRLNELTIRDAINQLGQRERNILYLRFFRG----KTQTEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
             +  +++ ++ ++E  AIR +K
Sbjct: 232 AGEIGISQAQVSRLEKSAIRTVK 254


>gi|149378434|ref|ZP_01896128.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
 gi|149357284|gb|EDM45812.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
          Length = 289

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 67/268 (25%), Positives = 128/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ S    +S+ E R +   +         A +E+V ++LR VI +A+ Y   GL
Sbjct: 17  LESYIQAASRIPVLSVEEERKLAERL--HYDGDVDAARELVLSHLRFVIHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  SQADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A  L +    VR++  ++     + + P  D+D +
Sbjct: 135 KLFFNLRSQKKRLAWLSHDEVNA-VASDLGVEPRVVREMEGRLASHDTAFDGPQDDDDDN 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++EDK    A     S    +        L  L  R + +LR R+    ++  
Sbjct: 194 AYQAPAYYLEDKRSNPATQLEQSDWTDDSNGRLMAALEQLDERSQDILRERWL--SDSKS 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 252 TLHELADRYGVSAERIRQLEKNAMKKIR 279


>gi|23099294|ref|NP_692760.1| sporulation sigma factor SigF [Oceanobacillus iheyensis HTE831]
 gi|22777523|dbj|BAC13795.1| stage II sporulation protein AC (RNA polymerase sigma-F factor)
           [Oceanobacillus iheyensis HTE831]
          Length = 250

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 119/242 (49%), Gaps = 15/242 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R  +     A+  +VE N+RLV SV +++ NRG    DL Q G+IGL+K+ +KFD  
Sbjct: 19  ELIRLSQQGDQSARDRLVEKNIRLVWSVVQRFINRGYDPDDLFQIGSIGLIKSIDKFDLS 78

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R I D    I++   +++  +K+ R    M+ +  R PT  E
Sbjct: 79  YDVKFSTYAVPMIIGEIQRFIRDDGS-IKVSRSLKEIGNKIRRKKDEMTKQYGRSPTVNE 137

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANL 609
           +A+ L +  E V    +  K P S+   + + D     L D I D+++            
Sbjct: 138 LAEALELQPEEVVHAQEAAKSPQSIYETVFENDGDPITLLDQIADQDSKWFE-------- 189

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +    + SLT RE  ++ +R+      D T  EV ++  +++ ++ ++E K +  +K 
Sbjct: 190 KLSLQEAIRSLTERERLIIYLRY----YKDKTQTEVAERLGISQVQVSRLEKKILEDMKK 245

Query: 670 PS 671
             
Sbjct: 246 NM 247


>gi|134102478|ref|YP_001108139.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
 gi|133915101|emb|CAM05214.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 311

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 111/238 (46%), Gaps = 15/238 (6%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWCLG 493
           +      +  +V     LV  VA +    GL       DLIQ G  GL+ A EKF+   G
Sbjct: 75  QQRDQELRDRLVLHYAPLVKYVAGR-VGTGLPSHVEVSDLIQSGIFGLVDAIEKFEPERG 133

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF TYAM  ++ AI   +  Q     +P  +R +   V R   R+  K++R  +  E+A
Sbjct: 134 LKFETYAMQRIRGAILDDLRAQDW---VPRSVRSRARDVERALERLEAKLQRTASDAELA 190

Query: 554 KKLAMPVEGVRKVLKITKE--PISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++L + V+ +R++    +    ++L+  IG    TS L + + D  A  P+ + +  + R
Sbjct: 191 EELELSVDELRELFAQLQMTSVVALDDLIGAGQTTSSLAETLPDDRAEDPVATLVDRDSR 250

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +  L+ R+  V+ + +        TL E+GK   VT  R+ Q+  +A+ +L+
Sbjct: 251 RQLAEAVERLSDRDRIVVTLYYFEN----LTLAEIGKVLGVTESRVCQLHTRAVLRLR 304


>gi|319406278|emb|CBI79915.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 303

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 116/246 (47%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD    
Sbjct: 46  LRWKDKRDDDAMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPERE 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI-----HKVVRTARRMSNKIKREPT 548
            +FSTYA WW++ +I   I      +R       K       ++     +  N + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLAQDDNTLTKQEI 165

Query: 549 PEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG---DFIEDKNAVSPLDSA 604
              I++KL + V  V K+  + +    SL   I +   + +      I+D      +   
Sbjct: 166 FSAISEKLGVSVNDVEKMDFRFSGTDNSLSLSISESGETPIAKMDSLIDDHPLPDAVIEQ 225

Query: 605 IQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +    R  +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 VIDGQRRAQWLYEALQILNERELEIIR--FRRLKEEGATLEVLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|163744692|ref|ZP_02152052.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
 gi|161381510|gb|EDQ05919.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
          Length = 292

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 70/268 (26%), Positives = 126/268 (47%), Gaps = 18/268 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +       +     A   ++ A +RL IS+A K+   G    DLIQE  +GLMKAA+KF
Sbjct: 26  ELKLAYAWRDQRDEAALHRLITAYMRLAISMAGKFKRYGAPMNDLIQEAGLGLMKAADKF 85

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI---------PVHMRDKIHKVVRTARRM 539
           D   G +FSTYA+WW+K +I   +      +R            +MR    ++ R A  +
Sbjct: 86  DPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQARLEREASAV 145

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDKNA 597
              + +    + I+ ++ +P+  V  +  +++    SL      ED      + + D++A
Sbjct: 146 GETLDKHQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNATQSAEDEGREWIEALADESA 205

Query: 598 VSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +      Q +   LR      +  L+ RE+ ++R R         TLE +G +  +++E
Sbjct: 206 QAAERVEEQHDTAQLRNWLLTAMQGLSDREQFIVRERKLRDP--SRTLESLGDELSLSKE 263

Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
           R+RQ+EA A  K++     +S+++ +FL
Sbjct: 264 RVRQLEAAAFGKMRKSLEMQSREVFAFL 291


>gi|291436144|ref|ZP_06575534.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291339039|gb|EFE65995.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 282

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 107/229 (46%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+VEA L +   +A ++ +RG  F DL Q   +GL+KA +++D  LG  F +YA+  +
Sbjct: 53  RGEIVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTI 112

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM-SNKIKREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  +++  ++V   ++ +  +   R PT  EIA+   +  E V
Sbjct: 113 TGEIKRHFRDHMWTLHVPRRVQELRNRVRSASQDLSLSGSGRPPTVAEIAEHADLSEEDV 172

Query: 564 RKVLKI--TKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           R       +   +SL+  +   +D   LGD +   +             RE     LA+L
Sbjct: 173 RTGQGALDSFTALSLDAELTSGDDGYSLGDTLGAPDPALDTVVD-----REAVRERLAAL 227

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE+ +L MRF      D T   +  +  +++  + ++ ++   +++ 
Sbjct: 228 PEREQAILYMRFF----GDMTQSSIAAELGISQMHVSRLISRCCGRIRE 272


>gi|87121174|ref|ZP_01077065.1| sigma factor RpoH [Marinomonas sp. MED121]
 gi|86163666|gb|EAQ64940.1| sigma factor RpoH [Marinomonas sp. MED121]
          Length = 291

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 56/273 (20%), Positives = 119/273 (43%), Gaps = 13/273 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + I+++S    ++  +   +   +         A +++V ++LR V+ +AK Y+  
Sbjct: 15  QNLESYIQAVSTIPILTAEDENKLAERL--YYDGDLEAARQLVMSHLRFVVHIAKSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     
Sbjct: 73  GLNQGDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKA 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--------KEPISLET 578
            +       + + +         E +A  L +  E VR++                  + 
Sbjct: 133 QRKMFFNLRSAKKTLSWFSNDEVESVAGDLGVSPEVVRQMEGRMSSSDTTFDASSDDDDD 192

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                  ++L D   D  +++   +  + + R      ++ L  R   +L  R+    ++
Sbjct: 193 SAYQAPANYLEDHRYDPASLTENGNWEEDSNRR-LQEAMSELDERSRNILVQRWL--SDS 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TL ++  ++ V+ ERIRQ+E  A+ K++   
Sbjct: 250 KSTLHDLADEYGVSAERIRQLEKNAMAKIRTSM 282


>gi|225628325|ref|ZP_03786359.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
 gi|225616171|gb|EEH13219.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
          Length = 278

 Score =  123 bits (307), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 74/267 (27%), Positives = 126/267 (47%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 2   IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 60  LIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 119

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 120 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETG 179

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 180 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 237

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 238 LEALGEKLGISKERVRQIESRAMEKLK 264


>gi|11079129|dbj|BAB17569.1| DNA-directed RNA polymerase subunit D [Pseudomonas fulva]
          Length = 268

 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 113/315 (35%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T  +++     +      L E++     
Sbjct: 1   VELLTREGEIEIAKRIEKGIREVMGAVAHFPGTVDSILAEYTRVTTEGGRLVEVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G    +          D  ++ + D E      +++       PE 
Sbjct: 56  ------SGYIDPDDGSVPAEAAAPVPAASDDKAEDKDDDEEDGDSDDEEEEGDGGPDPEE 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 ALRRFTAVSDQLEVAKKAL-----------------------------------KKHGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++ +   R+   E  +++L      + R  
Sbjct: 135 SKQAIEELRLLAELFMPIKLVPKQYDALVVRVREALDRLRGQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    G E+D  W +      + ++   +      I + + ++ ++  ET ++++E + 
Sbjct: 195 FLRLFPGNEVDLDWAASLAK-GKAKYAEAIGNLQADIQRCQQKLIALQDETDLTLAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|118594538|ref|ZP_01551885.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440316|gb|EAV46943.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 286

 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 124/262 (47%), Gaps = 11/262 (4%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           ++I     ++  E   + S +++       A K+++ ++L+LV+ +A+ Y+   L   DL
Sbjct: 20  ETIRKIPSLTAEEEYELASRLKRD--NDLEAAKKLILSHLKLVMKIARSYSGYNLPHADL 77

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDKIHKV 532
           +QEGNIGLMKA +KFD   G +  +YA++W+K  I   +              + K+   
Sbjct: 78  VQEGNIGLMKAVKKFDPDRGVRLVSYAIYWIKAEIQEYVVKNWRLVKTATTKAQRKLFFN 137

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDEDTSHLG 589
           +R+ R+    +K E   + IA +L +    VR++   L   +  I       +ED     
Sbjct: 138 LRSLRKTLQPLKPE-EIKSIANELNVKESEVREMEFRLNGKETTIDYSDDESEEDHFRPI 196

Query: 590 DFIEDKNA---VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            ++ED+             ++N+       L+ L  R   V+  R+ +  N   TL E+ 
Sbjct: 197 SYLEDETPSPLEKIEMDQAESNVSAELQHALSELDSRSRSVVEARW-LNDNKSETLNELA 255

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
            +F V+ ERIRQIE  A +K++
Sbjct: 256 SKFKVSAERIRQIEKNAFKKIR 277


>gi|302535451|ref|ZP_07287793.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444346|gb|EFL16162.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 288

 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 111/242 (45%), Gaps = 4/242 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             H ++ + +G  + S  +  +VE NL LV   A+++  R     D++Q G IGL+KA  
Sbjct: 44  LFHRLAELDEGTADYSYVRNTLVELNLSLVKYAARRFRGRSEPMEDIVQVGTIGLIKAIN 103

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +F+T+AM  +   I R   D S  +++P  +++      +    +   + RE
Sbjct: 104 RFDPERGVEFTTFAMPTISGEIKRFFRDTSWAVKVPRRLQELRIDSAKAHDALEQDLGRE 163

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E+A++L +  E   +  K      +       ++ S      E  +      +  +
Sbjct: 164 PTDTEMARELDVTPEEFSEGRKAASAYSARSLDAPVQEDSERDPAAERASLGEEEPAYDR 223

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               E+   +LA L  RE  +L +RFG     + T  E+G +  +++  + ++  + + +
Sbjct: 224 IECLESLKPMLAVLPERERELLSLRFG----QELTQSEIGARLGLSQMHVSRLLNRTLTR 279

Query: 667 LK 668
           L+
Sbjct: 280 LR 281


>gi|197723819|gb|ACH72689.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 257

 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 112/248 (45%), Gaps = 4/248 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSK 674
           L+   +++
Sbjct: 249 LREALQNE 256


>gi|302127745|emb|CBL51726.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 262

 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ E
Sbjct: 58  -----------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGE 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHEDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +     L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|50871562|emb|CAF74872.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  123 bits (307), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 109/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++     +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYQRVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G           Q+ E  + +       + + D E     S+++       PE A   
Sbjct: 59  DDGAA-------GPQEVEPEAPKAAAKTATDDKDDEEEDDSDSEEEEGDGGPDPEVARLR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ +   +I   E  +++L      + R  FL +
Sbjct: 137 IEELEALAILFMPIKLVPKQYDALVERVRNALNQIRIQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E++  W        +G++   +    + I + + ++  +  E  ++I++ + I   
Sbjct: 197 FPSNEINLDWADQLAG-GKGKYAEAIGNRKEDIQRCQQKLIELQQECNLAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|331007677|ref|ZP_08330813.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
 gi|330418520|gb|EGG93050.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
          Length = 288

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 65/277 (23%), Positives = 123/277 (44%), Gaps = 18/277 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +++++    +++ E + +   +     E   A + +V A+LR V+ +AK Y   GL
Sbjct: 17  INAYMQAVNSFAVLTVEEEKDLGERL--YYHEDLDAARGLVMAHLRFVVHIAKSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  +   I      +++      +
Sbjct: 75  SQSDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQR 134

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             K+    R    ++      E  A    + VE   K +   +  +S      D D    
Sbjct: 135 --KLFFNLRGQKKRLGWLSYDEATAVAADLNVE--VKHVHEMESRLSAYDASFDADNDDD 190

Query: 589 --------GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                    +++ED     A     S    +        LA+L  R + +++ R+ +  +
Sbjct: 191 DESAYKAPANYLEDHRYNPAQELEASDWSDDNASRLRTALATLDERSQVIIQRRW-LNDD 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
              TL E+  +F V+ ERIRQ+E  A++K+K    ++
Sbjct: 250 NKSTLHELAAEFGVSAERIRQLEKNAMKKVKTAMETE 286


>gi|30019159|ref|NP_830790.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 14579]
 gi|29894702|gb|AAP07991.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 14579]
          Length = 258

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 121/261 (46%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 2   MEIQSQPTNLTKEDVIKLIADFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 60  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 120 KLAIEELTDHLQRSPRIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 180 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 233

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 234 ISQMHVSRIKRQAISKLKQAA 254


>gi|296101730|ref|YP_003611876.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295056189|gb|ADF60927.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 239

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 112/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V     ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAHAMGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRET 612
           ++L +PVE  R++L  T            E+     + + D++   +PL   ++ NLR+ 
Sbjct: 122 ERLGIPVEEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDEHQQENPLHHLMEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIEALPEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|1276889|gb|AAC44103.1| stress response/stationary phase sigma factor [Mycobacterium
           tuberculosis H37Rv]
 gi|1589717|prf||2211432A RNA polymerase sigma factor
          Length = 261

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 117/245 (47%), Gaps = 13/245 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +V +           + ++V+  L L   +A+++  RG    DLIQ   +GL+ AA 
Sbjct: 23  FRELVGLPAGSPEF-QRHRDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVKTGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDS 603
           P+  E+A +L M    V + L    +   +S+++  G +D +  + D + D +A      
Sbjct: 142 PSASELAAELGMDRAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA-----G 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   RE    +L +L  RE  VL +RF        T  ++ ++  +++  + ++ AK+
Sbjct: 197 LDQIENREVLRPLLEALPERERTVLVLRFF----DSMTQTQIAERVGISQMHVSRVLAKS 252

Query: 664 IRKLK 668
           + +L+
Sbjct: 253 LARLR 257


>gi|167507937|gb|ABZ81289.1| RpoD [Thalassospira sp. MCCC 1A01300]
 gi|167507941|gb|ABZ81291.1| RpoD [Thalassospira sp. MCCC 1A01330]
          Length = 255

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 65/253 (25%), Positives = 115/253 (45%), Gaps = 14/253 (5%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR++IDLE   G                   E ++ E + D+  E E +         
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAEEADAEGDDFEAAAVETDDDEDDEAETETPEPTGAPA 60

Query: 239 DDRSKVDSPPENAENDERNLDED---------EDDSAHTLSAMEDQLRPKVMCALDEIAE 289
            D  + D   E+ ++ E    E           +    +LS ME++L  +V+   + IA+
Sbjct: 61  SDEEEEDDDEESDDDSEGEEGEGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKFELIAK 120

Query: 290 VYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ L  
Sbjct: 121 TYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELLDHLTG 180

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK F+    D
Sbjct: 181 LNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVGELPGKGWKAFIERYPD 240

Query: 405 SILKIRNEIKSIS 417
            I ++R ++  +S
Sbjct: 241 EIAQLREQVGGVS 253


>gi|50871536|emb|CAF74859.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871542|emb|CAF74862.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871544|emb|CAF74863.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871546|emb|CAF74864.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871548|emb|CAF74865.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871550|emb|CAF74866.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|85815555|emb|CAI54233.1| DNA-directed RNA polymerase subunit D [Pseudomonas
           chloritidismutans]
          Length = 261

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/301 (17%), Positives = 108/301 (35%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G           Q+ E  + +       + + D E     S+++       PE A   
Sbjct: 59  DDGAA-------GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +                                       +K  ++S + 
Sbjct: 112 FGAVAEQLEKAKKA-----------------------------------LKKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ +   +I   E  +++L      + R  FL +
Sbjct: 137 VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        +G++   +    + I++ + ++  +  E  + I++ + I   
Sbjct: 197 FPNNETNLDWAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|229086642|ref|ZP_04218811.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
 gi|228696724|gb|EEL49540.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
          Length = 252

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 129/259 (49%), Gaps = 17/259 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+++   +  +   E +   ++++K +     A+  +V++N+RLV SV +++ NRG +  
Sbjct: 4   EVRNEKKKPQLKDHELK---ALIQKSQDGDQGARDTIVQSNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     KFSTYA+  +   I R + D    +++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLSFEVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKETGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLG 589
           + +    +S +  R PT  E+A+ L +  E V    + ++ P S+   + + D     + 
Sbjct: 120 IRKMKDELSKEYGRAPTINEVAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITIL 179

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D+      +       +      +  L  RE  ++ +R+      D T  EV ++ 
Sbjct: 180 DQIADQTETKWFE-------KIALKEAIRELDERERLIVYLRY----YKDQTQSEVAERI 228

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247


>gi|328802595|emb|CBL54079.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 262

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/301 (19%), Positives = 112/301 (37%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ +
Sbjct: 58  -----------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ Q++ ++    
Sbjct: 95  NSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|290956130|ref|YP_003487312.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645656|emb|CBG68747.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 1033

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 89/235 (37%), Positives = 141/235 (60%), Gaps = 4/235 (1%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            A+  +V  N RLV S+ +   ++GL++ DL+Q G +GLM+AA KFD   GYKFSTYA W
Sbjct: 249 RARDCLVLHNQRLVHSLIRSCLDQGLEYEDLVQHGVLGLMRAARKFDPAKGYKFSTYATW 308

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WV+Q+++R+IAD+   IR+PVHM +++ KV    R ++ +  R     ++A +  M ++ 
Sbjct: 309 WVRQSVSRAIADEGALIRVPVHMHEQMRKVAAAERALAAQ-GRPAGNVDVAVQCDMTLDR 367

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLT 621
           V ++ K+T+   SL+  IG  D + LGDF+  + A  S  +  +   L E    V+ + +
Sbjct: 368 VEEIRKLTRRTDSLDRIIG--DGATLGDFVGKRQALPSVENDVLHVLLMEDVMGVVGTFS 425

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            R  R+L  R G+      TL+E+G++F VTRERIRQ+E KA  + +   R+  L
Sbjct: 426 ERSARILVRRLGLDGEEPSTLDELGREFGVTRERIRQLEGKARSEFRCRLRAAGL 480


>gi|47564960|ref|ZP_00236004.1| sigma-B [Bacillus cereus G9241]
 gi|47558333|gb|EAL16657.1| sigma-B [Bacillus cereus G9241]
          Length = 257

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 121/261 (46%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIAEFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|256392583|ref|YP_003114147.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256358809|gb|ACU72306.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 262

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 110/239 (46%), Gaps = 13/239 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +   + E    ++ ++   +     VA ++  RG    DL Q   +GL+KA + FD   G
Sbjct: 27  MAPDDAEYEGLREFVIGEYMSYARYVAGRFRQRGESQADLEQVAYLGLVKAVDNFDPDYG 86

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   +   + R   D +  + +P  +++    V    R ++ ++   P+  +IA
Sbjct: 87  AAFLTYATPMIAGEVRRHFRDTTWDVHVPRRVQENALAVRAAERELTQQLGHAPSAAQIA 146

Query: 554 KKLAMPVEGVRKVLK--ITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANL 609
           ++L +  + V +  +        SL+ P+     D + +G+ + D +    L        
Sbjct: 147 ERLDLSADEVAEAYEASAAHHTASLDVPVAMADGDGASMGELMGDDDPGYDLVVD----- 201

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE    +LA L+PR++R+L M+F        +  ++G +  V++ ++ ++ ++ + +L+
Sbjct: 202 REALKPLLAELSPRDKRILLMKFFRN----MSQAQIGAELGVSQMQVSRLLSQILGRLR 256


>gi|332981002|ref|YP_004462443.1| RNA polymerase sigma-28 subunit SigF [Mahella australiensis 50-1
           BON]
 gi|332698680|gb|AEE95621.1| RNA polymerase, sigma 28 subunit, SigF [Mahella australiensis 50-1
           BON]
          Length = 256

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 114/246 (46%), Gaps = 12/246 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I  ++ K       A + + E NL LV +V +K+ NRG ++ DL Q G++GL+KA   +
Sbjct: 21  EIEDLIVKVRQGNKQAAEILAERNLGLVHNVVRKFMNRGYEYDDLFQVGSMGLVKAINNY 80

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   ++   +K+     R+  ++ REP+
Sbjct: 81  DLSYNVKFSTYAVPMIMGEIKRFLRDDGS-IKVSRSVKIAAYKIHNAQDRIKKELGREPS 139

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
            +E+A  L M    V   ++    P+SL     ++  S   L D I D + +        
Sbjct: 140 VQELATALDMEPADVVYAMEADTVPVSLYDSAYEDGESSISLIDRISDGDELDTDVID-- 197

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R      +A L  +  +V+ +R+      D T  EV +   +T+ ++ +IE K +  
Sbjct: 198 ---RVALKECIAQLDAKGRQVILLRYF----KDKTQSEVAQMLGITQVQVCRIEKKVLEF 250

Query: 667 LKHPSR 672
           ++   +
Sbjct: 251 MRQYIK 256


>gi|12744861|gb|AAK06822.1|AF326688_1 RNA polymerase sigma-32 factor [Burkholderia pseudomallei]
          Length = 281

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 133/269 (49%), Gaps = 12/269 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++++    +S  E R   +  R+       A + +V ++LRLV+SVA+ Y   GL
Sbjct: 9   IDAYIQAVNRIPLLSAEEERQYATEYREQNNLD--AARRLVLSHLRLVVSVARNYLGYGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++FD     +  +YA+ W+K  I   I      +++       
Sbjct: 67  PHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVGDDEGAA 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDTSH 587
                  + +   +       + +A++L +  E V ++    +   I+LE  I D + S+
Sbjct: 127 QAFFNLRSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDDGEESY 186

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRET--TTRVLASLTPREERVLRMRFGIGMNTD---- 639
             +    +  N  + + +A Q ++ +T    R L SL  R  R++  R+ + ++ D    
Sbjct: 187 APIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARW-LNVDDDGSGG 245

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  +F V+ ERIRQIEA A++K++
Sbjct: 246 STLHDLAAEFGVSAERIRQIEASAMKKMR 274


>gi|52546486|dbj|BAD51626.1| DNA-directed RNA polymerase subunit D [Burkholderia caryophylli]
 gi|52546488|dbj|BAD51627.1| DNA-directed RNA polymerase subunit D [Burkholderia caryophylli]
          Length = 274

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 52/316 (16%), Positives = 111/316 (35%), Gaps = 43/316 (13%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   M+ ++   P T   +++  + + +    + E++D     
Sbjct: 1   ELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILVMAERVANDDLRIDELVDGLIDP 60

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             E   GF          + E + +E E ++ ++      +A     +            
Sbjct: 61  NAEDTDGFSAQEAESIENENEAAEEEDEEEEEEDDGAAQATANAAQLEA----------- 109

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                                   L+   +     I+E + ++R   +      K+   S
Sbjct: 110 ------------------------LKRTSLDKFALISEWFDKMRRAFE------KEGYKS 139

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVF 370
                 +E +   + S+      ++ L + L      +   E ++L +     G+ R  F
Sbjct: 140 KSYLKAQEAIQNELMSIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRAEF 199

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           + R    E D  W           +   ++  + +I + +  +  +     + + + +  
Sbjct: 200 IARFPSNETDLDWAEKIVAESHP-YSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKET 258

Query: 431 VSMVRKGECEASIAKK 446
              +  GE +A  AK+
Sbjct: 259 NRQMAAGELKARQAKR 274


>gi|11079131|dbj|BAB17570.1| DNA-directed RNA polymerase subunit D [Pseudomonas straminea]
          Length = 268

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/315 (17%), Positives = 113/315 (35%), Gaps = 48/315 (15%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI IAKRIE G   +M ++   P T  +++     +      L E++     
Sbjct: 1   VELLTREGEIEIAKRIEEGIREVMGAVAHFPGTVDSILAEYTRVTTEGGRLVEVL----- 55

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                  G+    +G    +          D  ++ + D E      +++       PE 
Sbjct: 56  ------SGYIDPDDGSVPAEAAAPVPAASDDKAEDKDDDEEDGDSDDEEEEGDGGPDPEE 109

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A      + +  + +   L                                   +K  + 
Sbjct: 110 ALRRFTAVSDQLEVAKKAL-----------------------------------KKHGRD 134

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           S +       L +L   + L   + D LV ++ +   R+   E  +++L      + R  
Sbjct: 135 SKQAIEELRLLAELFMPIKLVPKQYDALVVRVREALDRLRGQERAIMQLCVRDARMPRAD 194

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           FL    G E+D  W +      + ++   +      I + + ++ ++  ET ++++E + 
Sbjct: 195 FLRLFPGNEVDLDWAASLAK-GKAKYAEAIGNLQADIQRCQQKLIALQDETDLTLAEIKD 253

Query: 430 IVSMVRKGECEASIA 444
           I   +  GE +A  A
Sbjct: 254 INRRMSIGEAKARRA 268


>gi|78221650|ref|YP_383397.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78192905|gb|ABB30672.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           metallireducens GS-15]
          Length = 250

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 118/246 (47%), Gaps = 14/246 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++ +  ++ ++ E++  +L LV  +  +   +    L   DL+    IGL+ AAE+FD  
Sbjct: 10  QEAQRSSAQSRDELIVTHLPLVKFLVGRIATQLPPHLDQDDLMSAAVIGLITAAERFDPS 69

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F T+A   ++  I   +  Q     +   +RDK  K+ R    + +++ R PT EE
Sbjct: 70  RGVQFKTFAEQRIRGTIIDELRSQDW---LTRSLRDKFKKLEREFVMLEHRLGRNPTSEE 126

Query: 552 IAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA 607
           +AK L + V+    +L+       +SL+    DED S  G  D +EDK   +P    +  
Sbjct: 127 VAKSLEISVDDYHHMLEEIHLLSFVSLDESWEDEDGSPFGLLDILEDKGVENPQSQLMAR 186

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            + +T T  +  L  +E  V+   +      +  L+E+G    ++  RI Q+ ++AI +L
Sbjct: 187 QMLDTLTEAIEGLPEKERLVITFYY----YEELNLKEIGAVLDLSESRISQLHSQAIVRL 242

Query: 668 KHPSRS 673
           +   ++
Sbjct: 243 RAKMKN 248


>gi|255020686|ref|ZP_05292748.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
 gi|254969922|gb|EET27422.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
          Length = 285

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 8/234 (3%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +   A K++V ++LR V+ VA+ Y   GL   DLIQEGNIGLMKA ++FD   G +  ++
Sbjct: 46  DDVDAAKQLVLSHLRFVVRVARAYRGYGLPEADLIQEGNIGLMKAVKRFDPEQGVRLVSF 105

Query: 500 AMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           A+ W+K  +   I      +++     + K+   +R+AR+ S  + +E +   IA+ L +
Sbjct: 106 AVHWIKAEMHEFILRNWRIVKVATTKAQRKLFFNLRSARQSSGWLGQEESAA-IAEDLGV 164

Query: 559 PVEGVRKVL-KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL---DSAIQANLRETTT 614
             E V ++  ++  +  SL+    DE+       +ED    S     D       +    
Sbjct: 165 SQEAVLEMEGRMAGQDYSLQYESDDEEGHGRTLELEDPGESSVEALIDRDWDQQRQRGLR 224

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L SL+ R+  +++ R+    +   TL+ +G++  V+ ER+RQ+E   + KL+
Sbjct: 225 AALQSLSERDRYIIQNRWL--SDDPKTLQALGEELGVSAERVRQLEKSGMEKLR 276


>gi|50871540|emb|CAF74861.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/301 (17%), Positives = 108/301 (35%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G           Q+ E  + +       + + D E     S+++       PE A   
Sbjct: 59  DDGAA-------GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +                                       +K  ++S + 
Sbjct: 112 FGAVAEQLEKAKKA-----------------------------------LKKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ +   +I   E  +++L      + R  FL +
Sbjct: 137 VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W        +G++   +    + I++ + ++  +  E  + I++ + I   
Sbjct: 197 FPNNETNLDWAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEKECDLVIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|297560171|ref|YP_003679145.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844619|gb|ADH66639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 313

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 111/246 (45%), Gaps = 10/246 (4%)

Query: 429 HIVSMVRKGECEASIA---KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
            ++S +R+   +   A   ++ +V     L+  +A++Y  RG    DL Q   +GL+KA 
Sbjct: 63  ELISQLRELAEDDPRADELRERVVVLYQPLINKIARRYGGRGEPLEDLKQTAMVGLVKAV 122

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
             +D   G  F +Y +  V   I R   D +  +R+P   ++   K+ R          R
Sbjct: 123 RGYDPARGKPFISYLLPTVTGEIKRHFRDHTWAVRVPRRHQENRVKLRRVTGEFQQAHAR 182

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  E+++++ +P   V +++++  +   +SL+ P   +     G  +ED        +
Sbjct: 183 TPTVHELSEEMGLPEAEVGELIQVSESYRSLSLDAPDSSDSEGQEGTRLEDHLGCE-DAA 241

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   RE+    LA L  RE  +LR+RF      DHT  E+  +   ++  + ++ +  
Sbjct: 242 LDRVVERESLKPALARLPAREREILRLRFF----GDHTQSEIADRLGYSQMHVSRLLSGV 297

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 298 LEQLRE 303


>gi|30266015|gb|AAN16085.1| SigB [Listeria welshimeri]
          Length = 259

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+ +L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQMILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|16802936|ref|NP_464421.1| RNA polymerase sigma factor SigB [Listeria monocytogenes EGD-e]
 gi|47094902|ref|ZP_00232516.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499433|ref|ZP_03667782.1| RNA polymerase sigma factor SigB [Listeria monocytogenes Finland
           1988]
 gi|224503136|ref|ZP_03671443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           R2-561]
 gi|254827839|ref|ZP_05232526.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|254832139|ref|ZP_05236794.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 10403S]
 gi|254898932|ref|ZP_05258856.1| RNA polymerase sigma factor SigB [Listeria monocytogenes J0161]
 gi|254911580|ref|ZP_05261592.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|254935906|ref|ZP_05267603.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284801225|ref|YP_003413090.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284994367|ref|YP_003416135.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289434163|ref|YP_003464035.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|315281577|ref|ZP_07870178.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
 gi|22770508|gb|AAN06629.1|AF497201_1 sigma factor B [Listeria monocytogenes]
 gi|22770512|gb|AAN06631.1|AF497203_1 sigma factor B [Listeria monocytogenes]
 gi|22770532|gb|AAN06641.1|AF497213_1 sigma factor B [Listeria monocytogenes]
 gi|3298587|gb|AAC38791.1| Sigma B [Listeria monocytogenes]
 gi|16410298|emb|CAC98973.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           EGD-e]
 gi|47016784|gb|EAL07703.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|66968488|gb|AAY59623.1| SigB [Listeria seeligeri]
 gi|112363462|gb|ABI16056.1| sigma B [Listeria monocytogenes]
 gi|153582303|emb|CAO79793.1| sigma factor B [Listeria monocytogenes]
 gi|153582305|emb|CAO79794.1| sigma factor B [Listeria monocytogenes]
 gi|223700498|gb|ACN20365.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700502|gb|ACN20368.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700506|gb|ACN20371.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700514|gb|ACN20377.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700518|gb|ACN20380.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700522|gb|ACN20383.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700526|gb|ACN20386.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700530|gb|ACN20389.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700534|gb|ACN20392.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700538|gb|ACN20395.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700542|gb|ACN20398.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700546|gb|ACN20401.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700550|gb|ACN20404.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700554|gb|ACN20407.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700558|gb|ACN20410.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700562|gb|ACN20413.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700566|gb|ACN20416.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700570|gb|ACN20419.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700574|gb|ACN20422.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700578|gb|ACN20425.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700582|gb|ACN20428.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700586|gb|ACN20431.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700590|gb|ACN20434.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700594|gb|ACN20437.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700598|gb|ACN20440.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700602|gb|ACN20443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700606|gb|ACN20446.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700610|gb|ACN20449.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700614|gb|ACN20452.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700618|gb|ACN20455.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700622|gb|ACN20458.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700626|gb|ACN20461.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700630|gb|ACN20464.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700634|gb|ACN20467.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700638|gb|ACN20470.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700642|gb|ACN20473.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700646|gb|ACN20476.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700650|gb|ACN20479.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700654|gb|ACN20482.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700658|gb|ACN20485.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700662|gb|ACN20488.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700666|gb|ACN20491.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700670|gb|ACN20494.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700674|gb|ACN20497.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700678|gb|ACN20500.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700682|gb|ACN20503.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700686|gb|ACN20506.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700690|gb|ACN20509.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700694|gb|ACN20512.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700698|gb|ACN20515.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700702|gb|ACN20518.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700706|gb|ACN20521.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700710|gb|ACN20524.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700714|gb|ACN20527.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700718|gb|ACN20530.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700722|gb|ACN20533.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700726|gb|ACN20536.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700730|gb|ACN20539.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700734|gb|ACN20542.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700738|gb|ACN20545.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700742|gb|ACN20548.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700746|gb|ACN20551.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700750|gb|ACN20554.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700754|gb|ACN20557.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700758|gb|ACN20560.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700762|gb|ACN20563.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700766|gb|ACN20566.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700770|gb|ACN20569.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700774|gb|ACN20572.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700778|gb|ACN20575.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700782|gb|ACN20578.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700786|gb|ACN20581.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700790|gb|ACN20584.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700794|gb|ACN20587.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700798|gb|ACN20590.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700802|gb|ACN20593.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700806|gb|ACN20596.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700810|gb|ACN20599.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700814|gb|ACN20602.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700818|gb|ACN20605.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700822|gb|ACN20608.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700826|gb|ACN20611.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700830|gb|ACN20614.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700834|gb|ACN20617.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700838|gb|ACN20620.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700842|gb|ACN20623.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700846|gb|ACN20626.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700850|gb|ACN20629.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700854|gb|ACN20632.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700858|gb|ACN20635.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700862|gb|ACN20638.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700866|gb|ACN20641.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700870|gb|ACN20644.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700874|gb|ACN20647.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700878|gb|ACN20650.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700882|gb|ACN20653.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700886|gb|ACN20656.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700890|gb|ACN20659.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700894|gb|ACN20662.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700898|gb|ACN20665.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700902|gb|ACN20668.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700906|gb|ACN20671.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700910|gb|ACN20674.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700914|gb|ACN20677.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700918|gb|ACN20680.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700922|gb|ACN20683.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700926|gb|ACN20686.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700930|gb|ACN20689.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700934|gb|ACN20692.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700938|gb|ACN20695.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700942|gb|ACN20698.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700946|gb|ACN20701.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700950|gb|ACN20704.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700954|gb|ACN20707.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700958|gb|ACN20710.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700962|gb|ACN20713.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700966|gb|ACN20716.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700970|gb|ACN20719.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700974|gb|ACN20722.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700978|gb|ACN20725.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700982|gb|ACN20728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700986|gb|ACN20731.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700990|gb|ACN20734.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700994|gb|ACN20737.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700998|gb|ACN20740.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|258600220|gb|EEW13545.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|258608494|gb|EEW21102.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284056787|gb|ADB67728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284059834|gb|ADB70773.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289170407|emb|CBH26947.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|293589526|gb|EFF97860.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|302034427|gb|ADK92367.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034429|gb|ADK92368.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034431|gb|ADK92369.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034433|gb|ADK92370.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034439|gb|ADK92373.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034441|gb|ADK92374.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034443|gb|ADK92375.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034445|gb|ADK92376.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|313614786|gb|EFR88329.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
          Length = 259

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|291484084|dbj|BAI85159.1| sporulation sigma factor SigG [Bacillus subtilis subsp. natto
           BEST195]
          Length = 237

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 124/235 (52%), Gaps = 12/235 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +     A++++V  NLRLV+SV +++ NRG    DL Q G IGLMK+ + FD     
Sbjct: 7   QLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNV 66

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTYA+  +   I R + D +  IR+   +RD  +K ++   R+ ++  +EPT E+IAK
Sbjct: 67  KFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAK 125

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L +P E +   L   ++P+SL  PI ++  D  ++ D I D+           A     
Sbjct: 126 VLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNTDSQWIEELA----- 180

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               +  L  RE+ +LR RF  G     T  EV ++  +++ ++ ++E  AI+++
Sbjct: 181 LKEGMRRLNDREKMILRKRFFQG----KTQMEVAEEIGISQAQVSRLEKAAIKQM 231


>gi|30266009|gb|AAN16082.1| SigB [Listeria ivanovii]
 gi|30266011|gb|AAN16083.1| SigB [Listeria ivanovii]
          Length = 259

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|171060212|ref|YP_001792561.1| RNA polymerase sigma-32 subunit RpoH [Leptothrix cholodnii SP-6]
 gi|170777657|gb|ACB35796.1| RNA polymerase, sigma 32 subunit, RpoH [Leptothrix cholodnii SP-6]
          Length = 313

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 127/289 (43%), Gaps = 25/289 (8%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V S+  +   I +++    ++  E       +R  + +   A   +V ++LRLV+SVA++
Sbjct: 24  VPSLGNLDAYISAVNRLPLLTHEEEVSFARRLR--DSQDVEAAGRLVLSHLRLVVSVARQ 81

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y   GL   DLIQEGN+GLMKA ++FD   G +  +YAM W+K  I   +      +++ 
Sbjct: 82  YLGYGLPHGDLIQEGNVGLMKAVKRFDPEQGVRLVSYAMHWIKAEIHEYVLKNWRVVKLA 141

Query: 523 VH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP----------VEGVRKVLKIT 570
                R     +    R++  +     T      +  +            E +    +  
Sbjct: 142 TTKAQRKLFFNLRSMKRQLKGEAADGDTHRSSLTEAEIDTVARELNVKREEVIEMEARFA 201

Query: 571 KEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPRE 624
              ++LE    ++D S+    ++ D+        A++A  R+        R L +L  R 
Sbjct: 202 GGDVALEPGSDEDDESYTPIAYLADERQE--PTRALEAAHRDELAGPGLLRALDALDARS 259

Query: 625 ERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            R++  R+    +      TL ++  ++ V+ ERIRQIE  A++K++  
Sbjct: 260 RRIVEERWLKVNDDGSGGLTLHDLAAEYGVSAERIRQIEVAAMKKMRKA 308


>gi|163938900|ref|YP_001643784.1| RNA polymerase sigma factor SigB [Bacillus weihenstephanensis
           KBAB4]
 gi|163861097|gb|ABY42156.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
          Length = 257

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 121/261 (46%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +V     LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTDLTKEDVIKLIAEFQQNQCD--EAQERLVNHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  + +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGVHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++      +  SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYQVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEQTERRLVLDDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|30266005|gb|AAN16080.1| SigB [Listeria seeligeri]
 gi|30266007|gb|AAN16081.1| SigB [Listeria seeligeri]
 gi|66968476|gb|AAY59617.1| SigB [Listeria seeligeri]
 gi|66968478|gb|AAY59618.1| SigB [Listeria seeligeri]
 gi|66968480|gb|AAY59619.1| SigB [Listeria seeligeri]
 gi|66968482|gb|AAY59620.1| SigB [Listeria seeligeri]
 gi|66968484|gb|AAY59621.1| SigB [Listeria seeligeri]
 gi|66968486|gb|AAY59622.1| SigB [Listeria seeligeri]
 gi|313634111|gb|EFS00776.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL N1-067]
 gi|313638716|gb|EFS03817.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL S4-171]
          Length = 259

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 115/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V    +LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|85704966|ref|ZP_01036066.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670288|gb|EAQ25149.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 279

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 120/272 (44%), Gaps = 15/272 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ I     +   E   +    R  E + + A  +MV ++LRL   +A  Y   GL   +
Sbjct: 1   MQEIRKFPLLEPEEEYMLAK--RWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGLPQAE 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           +I E N+GLM+A ++FD   G++ +TYAMWW++ +I   I      +++      K    
Sbjct: 59  VISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFF 118

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
            + +   ++      +  PE   +IA  L +    V     ++     SL   +G E   
Sbjct: 119 NLRKAKAKIGALEDGDMRPEVVKKIATDLGVTEAEVISMNQRMAGADASLNATVGSEGEG 178

Query: 587 H--LGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                D++ED++A               RE  T  +  L  RE  +L        +   T
Sbjct: 179 SMQWQDWLEDEDADQAGDYERRDEMDARRELLTMAMDVLNERERDILTQ--RRLSDETVT 236

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           LE++  ++ V+RERIRQIE +A  KL+   R+
Sbjct: 237 LEDLSAEYDVSRERIRQIEVRAFEKLQKRMRA 268


>gi|46907127|ref|YP_013516.1| RNA polymerase sigma factor SigB [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092103|ref|ZP_00229896.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|217965008|ref|YP_002350686.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|226223514|ref|YP_002757621.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           Clip81459]
 gi|254823836|ref|ZP_05228837.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|254852389|ref|ZP_05241737.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|254931278|ref|ZP_05264637.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|254994246|ref|ZP_05276436.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-064]
 gi|255521165|ref|ZP_05388402.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-175]
 gi|290892914|ref|ZP_06555904.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|300764104|ref|ZP_07074099.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|22770514|gb|AAN06632.1|AF497204_1 sigma factor B [Listeria monocytogenes]
 gi|22770518|gb|AAN06634.1|AF497206_1 sigma factor B [Listeria monocytogenes]
 gi|22770520|gb|AAN06635.1|AF497207_1 sigma factor B [Listeria monocytogenes]
 gi|22770522|gb|AAN06636.1|AF497208_1 sigma factor B [Listeria monocytogenes]
 gi|22770524|gb|AAN06637.1|AF497209_1 sigma factor B [Listeria monocytogenes]
 gi|22770526|gb|AAN06638.1|AF497210_1 sigma factor B [Listeria monocytogenes]
 gi|22770528|gb|AAN06639.1|AF497211_1 sigma factor B [Listeria monocytogenes]
 gi|22770530|gb|AAN06640.1|AF497212_1 sigma factor B [Listeria monocytogenes]
 gi|3298584|gb|AAC38789.1| sigma B [Listeria monocytogenes]
 gi|3298589|gb|AAC38792.1| Sigma B [Listeria monocytogenes]
 gi|26000673|gb|AAN75465.1| SigB [Listeria monocytogenes]
 gi|46880394|gb|AAT03693.1| RNA polymerase sigma-B factor [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47019543|gb|EAL10283.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|112960117|gb|ABI27557.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960121|gb|ABI27560.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960125|gb|ABI27563.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960129|gb|ABI27566.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960133|gb|ABI27569.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960137|gb|ABI27572.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960141|gb|ABI27575.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960145|gb|ABI27578.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960149|gb|ABI27581.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960153|gb|ABI27584.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960157|gb|ABI27587.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960161|gb|ABI27590.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960165|gb|ABI27593.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960169|gb|ABI27596.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960173|gb|ABI27599.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960177|gb|ABI27602.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960181|gb|ABI27605.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960185|gb|ABI27608.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960189|gb|ABI27611.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960193|gb|ABI27614.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960197|gb|ABI27617.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960201|gb|ABI27620.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960205|gb|ABI27623.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960209|gb|ABI27626.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960213|gb|ABI27629.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960217|gb|ABI27632.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960221|gb|ABI27635.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960225|gb|ABI27638.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960229|gb|ABI27641.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960233|gb|ABI27644.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960237|gb|ABI27647.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960241|gb|ABI27650.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960245|gb|ABI27653.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960249|gb|ABI27656.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960253|gb|ABI27659.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960257|gb|ABI27662.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960261|gb|ABI27665.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960265|gb|ABI27668.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960269|gb|ABI27671.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960273|gb|ABI27674.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960277|gb|ABI27677.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960281|gb|ABI27680.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960285|gb|ABI27683.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960289|gb|ABI27686.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960293|gb|ABI27689.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960297|gb|ABI27692.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960301|gb|ABI27695.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960305|gb|ABI27698.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960309|gb|ABI27701.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960313|gb|ABI27704.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960317|gb|ABI27707.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960321|gb|ABI27710.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960325|gb|ABI27713.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960329|gb|ABI27716.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960333|gb|ABI27719.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960337|gb|ABI27722.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960341|gb|ABI27725.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960345|gb|ABI27728.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960349|gb|ABI27731.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960353|gb|ABI27734.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960357|gb|ABI27737.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960361|gb|ABI27740.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962434|gb|ABI28932.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962439|gb|ABI28936.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962444|gb|ABI28940.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962449|gb|ABI28944.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962454|gb|ABI28948.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962459|gb|ABI28952.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962464|gb|ABI28956.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962469|gb|ABI28960.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962474|gb|ABI28964.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962479|gb|ABI28968.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962484|gb|ABI28972.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962489|gb|ABI28976.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962494|gb|ABI28980.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962499|gb|ABI28984.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962504|gb|ABI28988.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962509|gb|ABI28992.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962514|gb|ABI28996.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962519|gb|ABI29000.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962524|gb|ABI29004.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962529|gb|ABI29008.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962534|gb|ABI29012.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962539|gb|ABI29016.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962544|gb|ABI29020.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962549|gb|ABI29024.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962554|gb|ABI29028.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962559|gb|ABI29032.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962564|gb|ABI29036.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962569|gb|ABI29040.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962574|gb|ABI29044.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962579|gb|ABI29048.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962584|gb|ABI29052.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962589|gb|ABI29056.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962594|gb|ABI29060.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962599|gb|ABI29064.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962604|gb|ABI29068.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962609|gb|ABI29072.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962614|gb|ABI29076.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962619|gb|ABI29080.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962624|gb|ABI29084.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962629|gb|ABI29088.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962634|gb|ABI29092.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962644|gb|ABI29100.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962649|gb|ABI29104.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962654|gb|ABI29108.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962659|gb|ABI29112.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962664|gb|ABI29116.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962669|gb|ABI29120.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962674|gb|ABI29124.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962679|gb|ABI29128.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962684|gb|ABI29132.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962689|gb|ABI29136.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962694|gb|ABI29140.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962699|gb|ABI29144.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962704|gb|ABI29148.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962709|gb|ABI29152.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962714|gb|ABI29156.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962719|gb|ABI29160.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962724|gb|ABI29164.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962729|gb|ABI29168.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962734|gb|ABI29172.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962739|gb|ABI29176.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962744|gb|ABI29180.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|118084623|gb|ABI16055.2| sigma B [Listeria monocytogenes]
 gi|118084625|gb|ABI16057.2| sigma B [Listeria monocytogenes]
 gi|153582301|emb|CAO79792.1| sigma factor B [Listeria monocytogenes]
 gi|153582307|emb|CAO79795.1| sigma factor B [Listeria monocytogenes]
 gi|217334278|gb|ACK40072.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|225875976|emb|CAS04680.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258605695|gb|EEW18303.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|290557490|gb|EFD91014.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|293582827|gb|EFF94859.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|293593059|gb|EFG00820.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|300515094|gb|EFK42146.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|302034435|gb|ADK92371.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034437|gb|ADK92372.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|307570432|emb|CAR83611.1| RNA polymerase sigma-B factor [Listeria monocytogenes L99]
 gi|313609777|gb|EFR85233.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL F2-208]
 gi|328467051|gb|EGF38146.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 1816]
 gi|328475458|gb|EGF46224.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 220]
 gi|332311302|gb|EGJ24397.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. Scott A]
          Length = 259

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|332970514|gb|EGK09503.1| RNA polymerase sigma factor SigB [Desmospora sp. 8437]
          Length = 261

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 118/240 (49%), Gaps = 8/240 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E      ++ +V+    LV ++A K+T     F DL+Q G IGL+ A +++D   G 
Sbjct: 21  RYQEESDEEIQEVLVDHFTPLVETLASKFTKGSEPFEDLVQVGMIGLLAALKRYDPDFGK 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F ++A+  +   I R I D++ ++ +P  +++   ++ + A  ++ + +R P+ +EIA+
Sbjct: 81  SFESFAVPTIVGEIKRHIRDKTWSVHVPRRIKELGPRIKKAAEELTIRYQRSPSVDEIAQ 140

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L +  E V + +++  +   +S+++PI   +       ++           +   L   
Sbjct: 141 YLDVTPEEVLETMEMGRSYNAVSVDSPIEANNEGSQVTLLDLVGNRDAGFEKVDQQL--L 198

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             +    LT RE+ ++RM F        + ++VG +  +++  + +++ +A+ KL+   R
Sbjct: 199 LQKAFQVLTDREQAIIRMTFFDN----LSQKQVGDELGISQMHVSRLQRRALGKLREAIR 254


>gi|66474649|gb|AAY46894.1| RpoD [Aeromonas hydrophila]
          Length = 268

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 63/312 (20%), Positives = 112/312 (35%), Gaps = 45/312 (14%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P   
Sbjct: 1   EGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN-- 56

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                 E +D+  T   I S            +   E+ + D  
Sbjct: 57  ----------------------EAEDMAPTATHIGSELGEDDLADEDEEDEDEDEDGDSS 94

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
           + D D             +LR +       I                 Q++ ++    + 
Sbjct: 95  DDDGDGGPDPEVAREKFAELRAQYEVTRLSI-----------------QQNGRAHEDTQN 137

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
              +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    
Sbjct: 138 AIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFT 197

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   + 
Sbjct: 198 NNECETAWFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRMS 256

Query: 436 KGECEASIAKKE 447
            GE +A  AKKE
Sbjct: 257 IGEAKARRAKKE 268


>gi|119475401|ref|ZP_01615754.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451604|gb|EAW32837.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 282

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 120/271 (44%), Gaps = 10/271 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +++++    ++      +   +   E   S   +E+V A+LR V+ +A+ Y   GL
Sbjct: 16  LNAYMQTVNNFPVLTAEREHELAEALYYHENLES--ARELVMAHLRFVVHIARSYNGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++F+   G +  ++A+ WVK  +   I      +++      +
Sbjct: 74  PLADLIQEGNIGLMKAVKRFNPEKGVRLVSFAVHWVKAEMHEYILRNWRIVKVATTKAQR 133

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDEDT 585
                    +       E     IA+ L + V+ VR++   L  +           D+  
Sbjct: 134 KLFFNLRGAKKKLAWLNEKEAHAIAEDLNVDVKEVRRMESRLTASDLGFDAGADDEDDGF 193

Query: 586 SHLGDFIEDKNAVSP---LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++ED +A       D+  + N  +     L  L  R   +++ R+    ++  TL
Sbjct: 194 VAPAHYLEDHSANPAMLLEDADWEQNSNQHLQLALEQLDERSRDIIQARWL--SDSKSTL 251

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            ++  ++ V+ ER+RQ+E  A++K++    +
Sbjct: 252 HDLAGKYGVSAERVRQLEKNAMKKVRATMEA 282


>gi|254454176|ref|ZP_05067613.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
 gi|198268582|gb|EDY92852.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
          Length = 715

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 123/255 (48%), Gaps = 14/255 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVE----ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           ++ + R    E+   ++ ++E    + L  +  +A ++   GL+  DL QEG  GL ++ 
Sbjct: 471 VLEVARMKLQESVSLRRSLIEAASISQLTQLRRLATRFPTEGLEEDDLFQEGYFGLTRSV 530

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           E F    G + +TY+ + ++Q I R++ D    +RIPVH   K+  + R   R+S  I R
Sbjct: 531 EMFHAGRGNRLTTYSQYRIRQTIARAVDDHRSVVRIPVHFASKVRLIERFGERVSGNISR 590

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                 + K   + +  ++K+  I +  I  +  +  +    L  F             +
Sbjct: 591 SDYHCALGKAFQIELAEIQKIENIPRLSIEFDENLYSDADIELEPF----------QRVL 640

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   +      L  L  R   ++  RFG+  N + TLE+ G+ + VTRERIRQ+EAKAI 
Sbjct: 641 EQQRQAIIKDFLEDLPERHADIIVRRFGLDGNDEMTLEQCGQVYGVTRERIRQLEAKAID 700

Query: 666 KLKHPSRSKKLRSFL 680
            L+HP R+K LR  L
Sbjct: 701 WLRHPVRAKFLRELL 715


>gi|22770510|gb|AAN06630.1|AF497202_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      +  +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELXRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|327441148|dbj|BAK17513.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score =  122 bits (306), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 70/253 (27%), Positives = 126/253 (49%), Gaps = 16/253 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E + +   +++GE    I ++++V  NLRLV+S+  +Y  RG Q  DL Q G IGL
Sbjct: 18  LKPDEMKDLFIRLQQGEW---IVREQLVFCNLRLVLSIVGRYAYRGEQADDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +   
Sbjct: 75  LKAIDNFDLKHNVRFSTYAVPMIMGEIRRHLRDHH-ALRVSRSLRDIAYKAMKAKEQFIA 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           +   EPT E++A+ + M  E V   L   ++P+SL+ PI  +  D   + D I+DK    
Sbjct: 134 EHLTEPTIEQLAQAIEMKKEDVLFALDAIQDPMSLQEPIYSDGGDAIFMIDQIKDKVTEE 193

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
               +I      +    +  L  R++ ++  RF +G     T  E+ +   +++ +I ++
Sbjct: 194 HWVGSI------SLQESMKKLNSRQKMIIEKRFFLG----ETQTEIAQSLGISQAQISRL 243

Query: 660 EAKAIRKLKHPSR 672
           E  A+  +K   R
Sbjct: 244 EKSAVELMKRDFR 256


>gi|295698248|ref|YP_003602903.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|295698251|ref|YP_003602906.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157186|gb|ADD79631.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157289|gb|ADD79734.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
          Length = 286

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 67/276 (24%), Positives = 135/276 (48%), Gaps = 16/276 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   IK+      +++ E +  +++      +   A K+++ ++LR VI ++K Y+  GL
Sbjct: 15  LSAYIKTAYSYPVLTMEEEKKYINL--FYHHQDLRAAKKLILSHLRFVIHISKNYSGYGL 72

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGN+GLMKA +KF+     +  ++A+ W+K  I   I      +++      +
Sbjct: 73  LQADLIQEGNVGLMKAVQKFNPNASVRLVSFAIHWIKAEIHEYILRNWRIVKVATTKAQR 132

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVL-KITKEPISLE---TPIGD 582
             K+    RR   KI      E   +AKKL +  + VR++  ++  + +  +        
Sbjct: 133 --KLFFNLRRNKKKIGWFDQTEIDSVAKKLGVSKKDVREMESRMVAKDMVFDINEEENRM 190

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRFGIGMN 637
           +D   L   +  ++  S    +++ +  E       T+ L+ L  R + +++ R+ +  +
Sbjct: 191 KDDFFLIPALYLEDKSSTFFESLEKDNWENHTIKRLTQALSKLDKRSQEIIKKRW-LNQS 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              TL+++ KQ+ V+ ERIRQ+E  A++K++    S
Sbjct: 250 GRETLQDLAKQYKVSAERIRQLEKNAMKKIRSLIES 285


>gi|29833942|ref|NP_828576.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29611067|dbj|BAC75111.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/251 (23%), Positives = 111/251 (44%), Gaps = 15/251 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + ++F  +  +    E +A   + E+V A L +   +A +Y  RG    DL Q   +GL+
Sbjct: 18  TAADFERLFGLPDGRERQAL--RDEIVRAWLPMAERIAWRYRGRGESTEDLCQVAAVGLV 75

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +++D   G  F +YA+  +   I R   D    + +P  ++D  ++V   A+ +S  
Sbjct: 76  KAVDRYDPARGNAFESYAVPTITGEIKRHFRDHMWVLHVPRRVQDLRNRVRVAAKELSQT 135

Query: 543 I-KREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH-LGDFIEDKNAV 598
           +   EPT  EIA+   +  + V+  L    T   +SL+  +   D  + L D +   ++ 
Sbjct: 136 VPGHEPTVTEIAEHAQLSEDDVQIGLEAMDTFTALSLDAELPGSDDGYALSDALGGPDSG 195

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             L        RE     L +L  RE  +L +R+  GM      E    Q  +++  + +
Sbjct: 196 YDLVVD-----REAVKPSLRALPERERTILYLRYFRGMTQSSIAE----QLGISQMHVSR 246

Query: 659 IEAKAIRKLKH 669
           + +    +++ 
Sbjct: 247 LISGCCARMRE 257


>gi|312877562|ref|ZP_07737521.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795637|gb|EFR12007.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 240

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +    +A+++++E+NL LV SV KK+  +G++  DL Q G IGL+KA ++F   
Sbjct: 8   ELISKAKNGDKLARQQLIESNLALVWSVVKKFAAKGVELDDLFQIGCIGLIKAVDRFAPS 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I R + D    I++   +++   K+ +   +  +   REPT  E
Sbjct: 68  FNLRFSTYAVPMIIGEIKRYLRD-DGKIKVSRKIKENQSKIKKLRNQFVSSNGREPTISE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           I++   +  + +   +  + E  SL   +  E+     L D   D+   S     + A  
Sbjct: 127 ISQLTGLSSDEILLCMDASSEVASLNEVVNQEEGKPITLMDIASDEEDYSTKLLDLMA-- 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  L  L  RE  ++ MR+        T  E+ K+  +++  + +IE +A+ ++K 
Sbjct: 185 ---LKEGLKKLKGRERYIIFMRYFKN----KTQSEIAKELNISQVHVSRIEKRALERIKR 237


>gi|493078|gb|AAA92723.1| RpoH (sigma 32) [Pseudomonas aeruginosa]
          Length = 284

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 122/269 (45%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + S++    +S  + R +   +     +   A ++MV A+LR V+ +AK Y+  GL
Sbjct: 17  LEAYVHSVNSIPLLSPEQERELAERL--FYQQDLEAARQMVLAHLRFVVHIAKSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS- 586
           K+   +R+ ++    +  E     +A+ L +    VR++            P  D D   
Sbjct: 135 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGQDMAFDPAADADDES 193

Query: 587 ---HLGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTD 639
                  ++ED     P      A+  ++        L  L  R   +L+ R+       
Sbjct: 194 AYQSPAHYLEDHR-YDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWL--SEEK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 251 ATLHDLAEKYNVSAERIRQLEKNAMSKLK 279


>gi|167507897|gb|ABZ81269.1| RpoD [Thalassospira xiamenensis]
          Length = 255

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 118/253 (46%), Gaps = 14/253 (5%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGT---------EGHSYQKREDSSQEKERDDVQETEGD 229
            LLR++IDLE   G                    +       E  + E E  + +  E  
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAAEGDEAEETEGDDFEAAAVETDADEDEEAETETPEPT 60

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
              A+   ++D  + +S   +  + +   D++ +    +LS ME++L  +V+   + IA+
Sbjct: 61  GAPASDEEEEDDDEEESDEGSEGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKFELIAK 120

Query: 290 VYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            Y +L   Q+  +      +S       +   LK ++V L+  + LN  RI+ L++ L  
Sbjct: 121 TYEKLHKAQEQRLVAMNKGESVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELLDHLTG 180

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK F+    D
Sbjct: 181 LNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVSELPGKGWKAFIERYPD 240

Query: 405 SILKIRNEIKSIS 417
            I ++R ++  +S
Sbjct: 241 EIAQLREQVGGVS 253


>gi|302147231|emb|CBL51737.1| RNA polymerase sigma-70 factor [Aeromonas sp.]
          Length = 262

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 112/301 (37%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DD+  T   I S            D   +  E+ +
Sbjct: 58  -----------------------EVDDMAPTATHIGSELSEDDLADEDEDEDEDEDEDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ QK+ ++    
Sbjct: 95  NSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + IL+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEILRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|290957086|ref|YP_003488268.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
 gi|260646612|emb|CBG69709.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
          Length = 258

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 21  DERLREQLILHYSPLVKYVAGRVSVGLPANVEQADFVSSGVFGLIDAIEKFDIDREIKFE 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    + ++++R P+  E+A ++ 
Sbjct: 81  TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLESRLRRTPSEGEVAAEMG 137

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + V+     L      +SL   +  E          D   L D +ED  A  P++ A   
Sbjct: 138 IAVDE----LHAVFSQLSLANVVALEELLHAGGEGGDRLSLMDTLEDTAADDPVEVAEDR 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 194 ELRRFLARAINTLPEREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 249

Query: 668 K 668
           +
Sbjct: 250 R 250


>gi|226952985|ref|ZP_03823449.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|294650567|ref|ZP_06727924.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
 gi|226836306|gb|EEH68689.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|292823564|gb|EFF82410.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
          Length = 289

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 129/273 (47%), Gaps = 13/273 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 19  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKLLVMSHLRFVVHIARSYAGY 76

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 77  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 136

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED 584
           + K+   +R+ ++ S ++  E   + IA  L +  E V ++  ++T    + E    D+D
Sbjct: 137 QRKLFFNLRSLKKSSKRLTLE-EAQAIANDLNVTAEQVLEMEGRLTAYDAAFEAQGDDDD 195

Query: 585 TSHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       ++ED     A    +   +A       + +  L  R   +L+ R+     +
Sbjct: 196 DTPHTAPALYLEDNRYDPARLAEEEDYEAQSTAALHQAMDQLDDRSRNILQRRWLDDDKS 255

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
             TL E+  ++ V+ ERIRQ+E  A+ K+K   
Sbjct: 256 --TLHELAAEYNVSAERIRQLEKNAMEKIKTAM 286


>gi|161898881|gb|ABX80430.1| SigB [Listeria monocytogenes]
 gi|161898907|gb|ABX80443.1| SigB [Listeria monocytogenes]
          Length = 233

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 106/235 (45%), Gaps = 4/235 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 3   AAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 63  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 122

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 123 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 182

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+
Sbjct: 183 EKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLR 233


>gi|226310092|ref|YP_002769986.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
 gi|226093040|dbj|BAH41482.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/258 (21%), Positives = 129/258 (50%), Gaps = 10/258 (3%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S  E + ++ +   GE +    ++++V A   LV S+AKK+    + + DL+Q G IGL+
Sbjct: 11  SPEELKELIHL--YGETKDPTIQEQLVRAYTPLVESLAKKFVRGQVMYEDLVQVGLIGLL 68

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            +  +FD      F ++A+  +   I R I D++ ++ +P  +++   K+ R    ++ K
Sbjct: 69  ASFRRFDPSFERTFESFAIPTIVGEIKRYIRDKTWSVYVPRRVKELSPKIKRVVDELTIK 128

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           ++R P   +IA  L +  E + + L++  +   +S+++ +  +   +    ++    +  
Sbjct: 129 LQRSPQIADIANSLGVSEEAILETLEMGRSYHSLSMDSELEADLDGNTISLLDLVGTMEE 188

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
              A++ NL     R L  L  RE+ ++++ F      + + ++ G    +++  I +++
Sbjct: 189 GYGAVEQNL--MLERALQILDHREKEIIQLTF----YQNLSQKQAGDIMGMSQMHISRLQ 242

Query: 661 AKAIRKLKHPSRSKKLRS 678
            +A+ KL+   R ++L +
Sbjct: 243 RRALGKLREALRVEQLET 260


>gi|218133795|ref|ZP_03462599.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991170|gb|EEC57176.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
          Length = 256

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/252 (23%), Positives = 118/252 (46%), Gaps = 16/252 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   ++ +       A+  +V  N+ L+ S+ K++T RG +  DL Q G+IGL+KA +KF
Sbjct: 7   HTKELIEQAHRGDKEARNRLVTENMGLIWSIVKRFTGRGHELEDLFQIGSIGLIKAIDKF 66

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   + R + D    I++   +++ + KV R   ++  ++  EP+
Sbjct: 67  DTSYDVRFSTYAVPMITGEVKRFLRD-DGMIKVSRSLKEIVVKVQRAREQLQKEMGEEPS 125

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVS------- 599
            E IA+ + +P E +   L+   E  S+   I   D     L D + D+ +         
Sbjct: 126 MEMIARAIDVPEEDIVMALEAGSEIESIYKTIYQSDGNEITLIDRVADRGSSGAGIVPEC 185

Query: 600 --PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                   Q        ++L  L   E+ ++ +R+      D T  +V K+  +++ ++ 
Sbjct: 186 EWTDYEKEQLINHMVLKQILDELPENEKNLILLRYF----RDQTQTQVAKEMGISQVQVS 241

Query: 658 QIEAKAIRKLKH 669
           +IE + + +L+ 
Sbjct: 242 RIEKRILLRLRE 253


>gi|226304764|ref|YP_002764722.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
 gi|226183879|dbj|BAH31983.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
          Length = 272

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 49/224 (21%), Positives = 105/224 (46%), Gaps = 12/224 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L L   VA++Y  RG  F DL Q   +GL++A ++FD   G  F ++A+  V   
Sbjct: 51  IIELCLPLATHVARRYQGRGQPFEDLEQVARVGLVQAVQRFDVDKGSDFLSFAVPTVMGE 110

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + +   D   ++R+P  ++++   + R    +S  + R PT  E+A +L +  + V + L
Sbjct: 111 VRKHFRDHGWSVRVPRSLQERHLALNRALTSLSQTLGRAPTVAELATELDIEPDEVEQGL 170

Query: 568 KI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
               +     L+T    + +   L D +         ++  + +  ET    L +L  RE
Sbjct: 171 TAGNSYRTTPLDTASAGDGSGLTLIDTLG-----QYDEAISRIDNHETLRPALLALPERE 225

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +RF        T  ++ ++  +++  + +I  + +++L+
Sbjct: 226 RTIVVLRFFGH----LTQSQIAEKIGISQMHVSRILTQTLKQLR 265


>gi|328948392|ref|YP_004365729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
 gi|328448716|gb|AEB14432.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
          Length = 262

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 113/256 (44%), Gaps = 19/256 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEG 477
           +  +E   +    +K +  A   +  ++   + LV  VA +  + G+     F DL+  G
Sbjct: 6   LDENEEAELWHEYKKSKSVA--IRDRLIRQYMPLVKWVAGR-VSTGMPDSVEFDDLVGFG 62

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
             GL+ A  KFD   G KF TYA   ++ AI   + +      +P  +R K  ++  T  
Sbjct: 63  QFGLLDAINKFDIDKGVKFKTYATTRIRGAIFDELRELDW---VPRSVRQKSREIEDTIV 119

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH---LGDFI 592
            + +K+ R  +  EIAK + M     +  +        +SL       D S    +GD I
Sbjct: 120 ELESKLGRTASDAEIAKAMNMTEAEYQSAVMKVSGTSVLSLNDVWYSGDESEHVSIGDSI 179

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E  N+++P     +  +R    + +  L   E+ V+ + +    + D + +E+G+   V+
Sbjct: 180 EAPNSLNPDVIVEREEIRRVIIQAINELPKNEKMVIVLYY----HEDLSFKEIGQVLNVS 235

Query: 653 RERIRQIEAKAIRKLK 668
             RI Q+ +KA  +L+
Sbjct: 236 ESRISQLHSKANLRLR 251


>gi|218896055|ref|YP_002444466.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
 gi|218544560|gb|ACK96954.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
          Length = 257

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 120/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTTLTKEDVIKLIAEFQQNQCN--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEQTERRLVLEDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|308233741|ref|ZP_07664478.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Atopobium vaginae DSM
           15829]
 gi|328943730|ref|ZP_08241195.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
 gi|327491699|gb|EGF23473.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
          Length = 286

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 126/234 (53%), Gaps = 7/234 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E     A++++V A+L L   +A K+ NRG    DL+Q   IGL+KA ++FD   G 
Sbjct: 39  RYKETGDEQAREQLVLAHLNLARFLASKFKNRGESLDDLVQVATIGLIKAIDRFDISRGL 98

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+T+A   +   I R   D+  ++R+P  +++   KV + + +++ K++R P+ +EIA+
Sbjct: 99  EFTTFATPTIMGEIKRHFRDKGWSVRVPRRLQELSAKVTQVSDKLTEKLQRSPSVDEIAQ 158

Query: 555 KLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L + V+ V + ++       +SL+ P GD+D       + DK A+   +    ++ R  
Sbjct: 159 ALGVSVDEVLEAMESAHAYSSVSLDVPQGDDDDGTQSSTVIDKYAL-VDEDLESSDDRIV 217

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             + +   + RE++++RMRF  G        E+ ++  +++ ++ ++  K ++K
Sbjct: 218 LEQAIKDFSEREQQIIRMRFLEGFTQV----EIAQKLQISQVQVSRLLRKTLQK 267


>gi|322496011|emb|CBJ55210.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 261

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/306 (18%), Positives = 108/306 (35%), Gaps = 46/306 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P     
Sbjct: 1   EIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE--- 55

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                +  +       S+  E D   E E + E     S DD       PE A     +L
Sbjct: 56  ----ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDL 111

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
               + +  ++                                   QK+ ++    +   
Sbjct: 112 RAQYEVTRLSI-----------------------------------QKNGRAHEDTQAAI 136

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
            +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      
Sbjct: 137 AQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNN 196

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +  G
Sbjct: 197 ECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIG 255

Query: 438 ECEASI 443
           E +A  
Sbjct: 256 EAKARR 261


>gi|262369666|ref|ZP_06062994.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
 gi|262315734|gb|EEY96773.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
          Length = 289

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 66/271 (24%), Positives = 122/271 (45%), Gaps = 14/271 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKLLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
            +       + + S+K       + IA  L +  E V ++  ++T    + E    D+D 
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLKEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDE 195

Query: 586 SH----LGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMN 637
                    ++ED N   P   A + +  E         +  L  R   +L+ R+     
Sbjct: 196 GSTHVAPALYLED-NRYDPARLAEEEDYEEQSTNALHDAMEQLDDRSRNILQRRWLDD-- 252

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 253 EKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|302538372|ref|ZP_07290714.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302447267|gb|EFL19083.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 323

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 120/280 (42%), Gaps = 27/280 (9%)

Query: 413 IKSISVETGISISEFRHI-------VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I     ++ ++ R +       +  + +G  E    +  ++E N  LV    +++  
Sbjct: 39  LPRIDEPREVAPADARELSKVFFARLRELPEGTAERQYVRNTLIEMNASLVQYAVRRFRG 98

Query: 466 RGL----QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           R         DL+Q G IGL+KA ++FD     +F+T AM ++   I R   D +  + +
Sbjct: 99  RAEGAAGDVDDLVQVGTIGLIKAIDRFDPARENEFATLAMPYITGEIKRHFRDTAWAVHV 158

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETP 579
           P  +++    + +    ++ ++ R PT  ++A  L +  E V + L         SL+ P
Sbjct: 159 PRRLQELRIDIAKAKEELTIRLDRSPTVRDLAAYLDLTEEQVIEGLVAANGHTSGSLDAP 218

Query: 580 IGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
             +          L + + ++     L   IQ     T   +L  L+ RE  +LRMRFG 
Sbjct: 219 HAEHGDGPAEGHTLAEVLGEEEPALELVEDIQ-----TLAPLLERLSERERTMLRMRFG- 272

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
               + T  ++G    +++ ++ ++ ++ +  L+    S 
Sbjct: 273 ---EELTQAQMGAALGISQMQVSRLLSRLLAHLRTSMLSD 309


>gi|330505413|ref|YP_004382282.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
 gi|328919699|gb|AEB60530.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
          Length = 284

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 118/269 (43%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHAVNSIPLLTPEQERELAENL--FYQQDLEAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W++  I   I      +++      R
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                +    +R++     E T   +A+ L +    VR++            P  D D  
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVTA--VAESLGVEPHEVREMESRLTGQDMAFDPAADADDD 192

Query: 587 ----HLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   ++ED     A    D+    +        L SL  R   +L  R+       
Sbjct: 193 SAFQSPAHYLEDHRYDPARQLEDADWSDSSSSNLHEALESLDERSRDILYQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  ++ V+ ERIRQ+E  A+ KLK
Sbjct: 251 ATLHDLAAKYNVSAERIRQLEKNAMNKLK 279


>gi|229815207|ref|ZP_04445543.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
 gi|229809217|gb|EEP44983.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
          Length = 261

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 120/243 (49%), Gaps = 11/243 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +    +  E     A++++V ++L LV  +A K+ NRG    DLIQ G +GL+KA ++
Sbjct: 17  RELFRRFK--EEGDMDAREKLVMSHLNLVRFIANKFKNRGEPIDDLIQVGYLGLLKAIDR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G +F+T+A   +   I R   D+  ++R+P  +++   KV +    ++++++R P
Sbjct: 75  FDPSRGLEFTTFATPTIMGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDTLTSQLQRSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           T  EIA  L   V+ V + +        +SLE P G +D              +      
Sbjct: 135 TIAEIADYLDATVDEVLEAMESSSAYSSVSLEAPSGADDDDTPSVI---DRYATEDSDLA 191

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             + R      LAS +PRE  V+ MRF  G     T  E+ ++  +++ ++ ++  + ++
Sbjct: 192 FTDDRIIIEEALASFSPRERDVIEMRFLKG----MTQIEIAEKLGISQVQVSRLLRRTLK 247

Query: 666 KLK 668
           K++
Sbjct: 248 KIQ 250


>gi|116872297|ref|YP_849078.1| RNA polymerase sigma factor SigB [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|55535652|gb|AAV52891.1| SigB [Listeria welshimeri]
 gi|116741175|emb|CAK20295.1| RNA polymerase sigma-37 (sigma-B) [Listeria welshimeri serovar 6b
           str. SLCC5334]
          Length = 259

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+ +L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQMILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|302147255|emb|CBL51749.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
          Length = 262

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 107/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II          
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E                          E+ A  +    S++       E++E
Sbjct: 51  -SGFIDPNE-------------------------TENMAPTATHIGSELGEDDLADEDEE 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
              DEDED  +                   E+   Y          ++ QK+ ++    +
Sbjct: 85  DEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|254503566|ref|ZP_05115717.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
 gi|222439637|gb|EEE46316.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
          Length = 287

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 73/272 (26%), Positives = 131/272 (48%), Gaps = 19/272 (6%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R+ +K+      ++  E   +   ++  + +   A +++  +++RLVI+VA ++ N GL 
Sbjct: 5   RHLVKTAMKAPYLTREEELELA--IQWRDNKDEKALEKLSLSHMRLVIAVASRFKNFGLN 62

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLIQEG++GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 63  IGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKA 122

Query: 530 HKVVRTARRMSNKIKREPT-------PEEIAKKLAMPVEGV-RKVLKITKEPISLETPIG 581
             +    RR+  K+    T        ++IA  + +    V     +++    SL  P+ 
Sbjct: 123 --LFFNLRRLRAKLSSNQTPLTDSELHQKIADAIGVKQSDVAVMNARLSGPDTSLNAPVT 180

Query: 582 DEDTSH--LGDFIEDK--NAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGM 636
           D + S     DF+          +   I A  R       L  L+ RE +++R R     
Sbjct: 181 DTEGSSADRQDFLVSDAPQPDEIVTENIDAERRNTWLASALDVLSERELKIVRERRLSED 240

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TLE +GK+  +++ER+RQIE++A++KLK
Sbjct: 241 G--ATLESLGKKLGISKERVRQIESRALQKLK 270


>gi|167507903|gb|ABZ81272.1| RpoD [Thalassospira lucentensis]
          Length = 267

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 66/265 (24%), Positives = 115/265 (43%), Gaps = 26/265 (9%)

Query: 179 TLLREIIDLEACIG--PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
            LLR++IDLE   G  P+++          +  +  D   + E  D    + D E+  + 
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAQESDGEEADAEEVDPEADVESFDSANDDDDDEAETET 60

Query: 237 S-------------------KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
                               K D    +        D    D++ +    +LS ME++L 
Sbjct: 61  PHTIGEEEEEDDEDESETSEKSDDDDEEEEQAQGPRDSDEDDDENEQVNVSLSKMEEELT 120

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQ 332
            +V+   + IA+ Y +L   Q+  +      ++       +   LK ++V L+  + LN 
Sbjct: 121 EQVLEKFELIAKTYEKLHKAQEQRLVAHNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNN 180

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
            RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P 
Sbjct: 181 FRIEELLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGNELDPNWMERVSGLPG 240

Query: 393 GEWKNFVACEVDSILKIRNEIKSIS 417
             WK F+    D I  +R  I  +S
Sbjct: 241 KGWKAFIERYPDEIANLREGIGGVS 265


>gi|55274887|gb|AAV49246.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 199

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 76/198 (38%), Positives = 128/198 (64%), Gaps = 3/198 (1%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL---AMPVEGVRKVLKIT 570
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EE  +       PV+ V ++L++ 
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEAEEIAEQLDKPVDDVSRMLRLN 121

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  
Sbjct: 122 ERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLAR 181

Query: 631 RFGIGMNTDHTLEEVGKQ 648
           RFG+      TLE+VG++
Sbjct: 182 RFGLLGYEAATLEDVGRE 199


>gi|217958581|ref|YP_002337129.1| RNA polymerase sigma factor SigB [Bacillus cereus AH187]
 gi|217065197|gb|ACJ79447.1| RNA polymerase sigma-B factor [Bacillus cereus AH187]
          Length = 257

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 122/261 (46%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTTLTKEDVIKLIAEFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 ++++++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|158320823|ref|YP_001513330.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158141022|gb|ABW19334.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 256

 Score =  122 bits (305), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 121/252 (48%), Gaps = 7/252 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + I E    + ++ + +     A++ +V  NL LV SV +++ NRG +  DL Q G IGL
Sbjct: 11  VEILEHDRTIELILQAQSGNMEAQEILVNHNLGLVRSVIRRFANRGYEREDLFQLGCIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +KFD     +FSTYA+  +   I R + D    I++   ++    +V  T  ++  
Sbjct: 71  IKAIKKFDTSFDVRFSTYAVPMIIGEIKRFLRD-DGIIKVSRSLKQTAARVKMTKEKLQK 129

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           +  REPT +EIA  +    E +   L  +  P  L   I  +D S +   + DK + +  
Sbjct: 130 ENGREPTLQEIADDMGATKEEIVMALDSSASPEYLYDVIHQDDGSPI--HLIDKISENDT 187

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
               +   R      ++ L PRE +++ +R+      D T  ++ +   +++ ++ +IE 
Sbjct: 188 LEDSEVIDRIVLQEAISKLEPRERQIIFLRYF----KDQTQTQIAQVLGISQVQVSRIEK 243

Query: 662 KAIRKLKHPSRS 673
           K ++ +K   + 
Sbjct: 244 KVLQNMKDIMKK 255


>gi|317470325|ref|ZP_07929717.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
 gi|316902189|gb|EFV24111.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
          Length = 258

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 75/266 (28%), Positives = 129/266 (48%), Gaps = 17/266 (6%)

Query: 409 IRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
             N+++   V T    +  +E +    +  + E     A+++ ++ NLRLV+SV ++++ 
Sbjct: 2   ALNKVEICGVNTASLPLLTNEEKE--ELFIRIEQGDQEAREQYIKGNLRLVLSVIQRFSG 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                 DL Q G IGLMKA + FD  L  KFSTYA+  +   + R + D +   R+   +
Sbjct: 60  SNENADDLFQVGCIGLMKAIDNFDRSLNVKFSTYAVPMIIGEVRRYLRDNNSM-RVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K +     ++ K  +EPT E IA+++ M  E V   L     P+SL  P+  +  
Sbjct: 119 RDIAYKAITAKEALTKKFNKEPTIEAIAEEIEMKKEDVLFALDAIATPLSLYEPVYQDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           DT  L D ++DK     L     A         +  L  RE  ++R+RF  G     T  
Sbjct: 179 DTLFLMDQVKDKKNKEELWVESIA-----LKDAMEHLPEREYNIIRLRFFDG----KTQT 229

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV  +  +++ ++ ++E  A++ +KH
Sbjct: 230 EVADEISISQAQVSRLEKNALKHMKH 255


>gi|160880600|ref|YP_001559568.1| sporulation sigma factor SigG [Clostridium phytofermentans ISDg]
 gi|160429266|gb|ABX42829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 260

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 127/246 (51%), Gaps = 14/246 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E +   ++  + +     A++  ++ NLRLV+S+ ++++N      DL Q G IGLMKA 
Sbjct: 22  EEKD--ALFERIKQGDKEARELYIKGNLRLVLSIIQRFSNSNENVDDLFQIGCIGLMKAI 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD   G KFSTYA+  +   I R + D +  IR+   +RD  +K +     +  K  +
Sbjct: 80  DNFDITQGVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSLRDTAYKAIYAKEMLLKKNDK 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDS 603
           EPT  EIA ++ +  E +   L   + P+SL  P+  E  DT ++ D + DK      + 
Sbjct: 139 EPTVCEIANEVGISQEDIVAALDAIQSPVSLYEPVYSEGGDTLYIMDQVSDKKNKE-ENW 197

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             + +L+E     +A L+PRE  ++ +RF  G       EE+     +++ ++ ++E  A
Sbjct: 198 VEEISLKE----AMARLSPRENNIINLRFFQGKTQMEVAEEIQ----ISQAQVSRLEKNA 249

Query: 664 IRKLKH 669
           ++ +++
Sbjct: 250 LKNMRN 255


>gi|167507919|gb|ABZ81280.1| RpoD [Thalassospira sp. MCCC 1A01103]
 gi|167507957|gb|ABZ81299.1| RpoD [Thalassospira sp. MCCC 1A02041]
 gi|167507959|gb|ABZ81300.1| RpoD [Thalassospira sp. MCCC 1A02042]
          Length = 261

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 65/259 (25%), Positives = 115/259 (44%), Gaps = 20/259 (7%)

Query: 179 TLLREIIDLEACIG--PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK- 235
            LLR++IDLE   G  PE++     G E  +    E   +  E  +  + E       + 
Sbjct: 1   LLLRDVIDLETTYGGGPEAEIAAAEGDEEDTDVDPEADVESFESANDDDDEEAETETPEG 60

Query: 236 ------------VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
                          ++    D         + + D++ +    +LS ME++L  +V+  
Sbjct: 61  ITDDAEEEEDEDDESEESEGEDGESTGEREGDDDDDDENEQVNVSLSKMEEELTEQVLEK 120

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            + IA+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L
Sbjct: 121 FELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNNFRIEEL 180

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
           ++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK F
Sbjct: 181 LDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKAF 240

Query: 399 VACEVDSILKIRNEIKSIS 417
           V    D I  +R  +  +S
Sbjct: 241 VERYPDEIANLREGVGGVS 259


>gi|161898917|gb|ABX80448.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 108/240 (45%), Gaps = 4/240 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKINNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 236


>gi|3386359|gb|AAC34827.1| RNA polymerase sigma B [Listeria monocytogenes]
          Length = 266

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 20  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 80  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 139

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 140 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 199

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 200 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 255

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 256 LREALQNEEVE 266


>gi|238800552|gb|ACR56097.1| RNA polymerase sigma factor SigB [Listeria innocua]
          Length = 248

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 2   EKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 61

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 62  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 121

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 122 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 181

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 182 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 237

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 238 LREALQNEEVE 248


>gi|74317198|ref|YP_314938.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056693|gb|AAZ97133.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 236

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 100/229 (43%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E +     LV  +A     R    ++  DLIQ G IGLM A  +FD   G +F +YA 
Sbjct: 8   QDEQITKYAPLVKRIAYHMMARLPASVEVDDLIQVGLIGLMDAVSRFDGTQGAQFESYAT 67

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + +      +P H+R K  ++     ++  +  + P+  EI+ +L +P++
Sbjct: 68  QRIRGAMLDELREADW---LPRHVRQKSRQIEAAIHKLEQRHGKAPSESEISAELGIPID 124

Query: 562 GVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             + +L   K    L      ++ S   L  ++ D  +  PL        R +    +  
Sbjct: 125 QYQSMLGDVKCSQLLYYEDFSDEDSASFLERYLVD-GSNDPLAVLEDEGFRASLIAAIHH 183

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE        G+    D  L+E+G    V+  R+ Q+ ++A+ +L+
Sbjct: 184 LPERER----SMMGMYYEQDMNLKEIGAVLGVSESRVCQLHSQAVARLR 228


>gi|326539488|gb|ADZ87703.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis M5-90]
          Length = 293

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 125/267 (46%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++ A +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKERVRQIESRAMEKLK 279


>gi|222094730|ref|YP_002528790.1| RNA polymerase sigma factor sigb [Bacillus cereus Q1]
 gi|221238788|gb|ACM11498.1| RNA polymerase sigma-B factor [Bacillus cereus Q1]
          Length = 257

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 122/261 (46%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTTLTKEDVMKLIAEFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 ++++++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|218232670|ref|YP_002365766.1| RNA polymerase sigma factor SigB [Bacillus cereus B4264]
 gi|218160627|gb|ACK60619.1| RNA polymerase sigma-B factor [Bacillus cereus B4264]
          Length = 257

 Score =  122 bits (305), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 120/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +V     LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIADFQQNQCD--EAQERLVNHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 ++++ +R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|326938732|gb|AEA14628.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 257

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 120/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTTLTKEDVIKLIAEFQQNQCN--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|302147257|emb|CBL51750.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. veronii]
 gi|302147263|emb|CBL51753.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|328802599|emb|CBL54081.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
 gi|328802601|emb|CBL54082.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
          Length = 262

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 60/300 (20%), Positives = 106/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II          
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E                          E  A  +    S++       E++E
Sbjct: 51  -SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDEE 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
              DEDED  +                   E+   Y          ++ QK+ ++    +
Sbjct: 85  DEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|206968111|ref|ZP_03229067.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
 gi|206737031|gb|EDZ54178.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
          Length = 257

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 120/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +V     LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIADFQQNQCD--EAQERLVNHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 ++++ +R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   FG  +N     ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGENLNQ----KDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|50871532|emb|CAF74856.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|50871534|emb|CAF74858.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 261

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 110/301 (36%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
             G           Q+ E  + +       + + D E     S+++       PE A   
Sbjct: 59  DDGAA-------GPQEVEPEAPKAPAKAATDDKDDEEEDDSDSEEEEGDGGPDPEVARLR 111

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              + E  + +   L                                   +K  ++S + 
Sbjct: 112 FGAVAEQLEKANKAL-----------------------------------KKHGRASQQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
               E L  L   + L   + D LVE++ +   +I   E  +++L      + R  FL +
Sbjct: 137 VEELEALAILFMPIKLVPKQYDALVERVRNALNQIRIQERAIMQLCVRDARMPRADFLRQ 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E++  W        +G++   +    + I + + ++  +  E  ++I++ + I   
Sbjct: 197 FPNNEINLDWADQLAS-GKGKYAEAIGNRKEDIQRCQQKLIELQQECNLAIADIKDINRR 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|90420276|ref|ZP_01228184.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90335610|gb|EAS49360.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 289

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 72/271 (26%), Positives = 125/271 (46%), Gaps = 16/271 (5%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  I++      +   E   +   VR  E     A  ++  A++RLVIS+A K+ + GL 
Sbjct: 8   RTLIRAAMSAPYLQREEEYELA--VRWKEKRDQEALHKITSAHMRLVISMAAKFRHFGLA 65

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DLIQEG++GL++AA +F+     +FSTYA WW++ +I   I      +R       K 
Sbjct: 66  MNDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 125

Query: 529 -IHKVVRTARRMSNKIKREPT----PEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
               + R   R+S       T     +EIA  L +    V     +++    SL  P+ +
Sbjct: 126 LFFNLRRLRARLSQGADGGVTGSAMYKEIATALKVSEGDVALMDSRLSGPDSSLNAPLME 185

Query: 583 EDTSH--LGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMN 637
           +++      DF+   + +     ++  +           L  L+ RE +++R R      
Sbjct: 186 DESGSADRQDFLVSNSPLPDEMVSVSIDDERRVTWLHSALDVLSERELKIIRERRLQDDG 245

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              TLE +G +  +++ER+RQIE +A+ KL+
Sbjct: 246 --ATLEALGTKLGISKERVRQIETRALEKLR 274


>gi|284992377|ref|YP_003410931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
 gi|284065622|gb|ADB76560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
          Length = 266

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 110/237 (46%), Gaps = 16/237 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYK 495
            A   +  ++     LV  VA +    GL       DL+  G  GL+ A  ++      K
Sbjct: 31  RAPELRDRLILHYAPLVKYVAGR-VGSGLPAHVEQADLVSYGTFGLIDAITRYQPSREVK 89

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F +YAM  ++ AI   +        IP  +R K  +  RT   + ++++R P+ EE+A +
Sbjct: 90  FESYAMARIRGAIIDELRSTDW---IPRSVRMKARQFERTVALLESRLQRSPSEEEVAAE 146

Query: 556 LAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRE 611
           + M VE VRK L        ++L+  + D++     L D ++D +A+ P   A  +  R+
Sbjct: 147 MDMDVEDVRKFLGQLSLVNVVALDELLSDDEGGAPRLVDTLQDTSALDPQAMAEHSEARQ 206

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R +  L  RE+ V+ + +  G     TL ++G+   VT  RI Q+  KA+  L+
Sbjct: 207 LLARAVEQLPEREKVVVSLYYFEG----LTLADIGRVLGVTESRICQLHTKAVLHLR 259


>gi|329940311|ref|ZP_08289592.1| putative RNA polymerase sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329300372|gb|EGG44269.1| putative RNA polymerase sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 270

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 115/251 (45%), Gaps = 15/251 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + ++FR + ++    E +A   +  +VEA L +   +A ++ NRG  + DL Q   +GL+
Sbjct: 18  TAADFRRLAALPDGPERDAL--RSRVVEAWLPMAERLAGRFRNRGESYEDLRQVAALGLV 75

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++++  LG  F +YA+  V   I R   D   T+ +P  ++D  ++V    + +S  
Sbjct: 76  KAVDRYEPDLGNAFESYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRFATQDLSQT 135

Query: 543 I-KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAV 598
           I  R PT  EIA    +  E V+   +   +   +SL+  +   ED   L D +   +  
Sbjct: 136 ISGRRPTVAEIAAHAHLSEEDVKAGQEALESFTALSLDAELPGSEDGYSLSDALGSADPA 195

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                      RE+    LA+L  RE  +L MRF   M      E    Q  +++  + +
Sbjct: 196 LDTVVD-----RESVKPRLAALPERERAILYMRFFGDMTQSRIAE----QLGISQMHVSR 246

Query: 659 IEAKAIRKLKH 669
           + ++   +L+ 
Sbjct: 247 LISRCCARLRE 257


>gi|291550016|emb|CBL26278.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus torques
           L2-14]
          Length = 260

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 73/266 (27%), Positives = 136/266 (51%), Gaps = 11/266 (4%)

Query: 411 NEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           N+++   V T  + +   +    + R+      +A++E ++ NLRLV+SV K++ +    
Sbjct: 4   NKVELCGVNTSKLPLLREKEKEELFRRIRQGDKLAREEYIKGNLRLVLSVMKRFDSSNEN 63

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL Q G +GL+KA + FD     KFSTYA+  +   I R + D S  +R+   +RD  
Sbjct: 64  ADDLFQIGCVGLVKAVDNFDPDRQVKFSTYAVPMIIGEIRRYLRDNSS-LRVSRSLRDIA 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +KV+ T      K  +EP+ +EIA+++ +  E V   L   + P+SL+ P+ ++     G
Sbjct: 123 YKVIYTREGYIRKNMKEPSIQEIAEEIGLSKEEVVYALDAVQTPMSLQEPVYNDG----G 178

Query: 590 DFIEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           D +   + VS   +  +  + E +    +  L  RE R++R+RF  G     T  EV +Q
Sbjct: 179 DALYVMDQVSDKKNREENWVEELSLEAAMERLNERERRLIRLRFFEG----KTQMEVSEQ 234

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             +++ ++ ++E  A++ ++     K
Sbjct: 235 IGISQAQVSRLEKNALKTMRQYLLGK 260


>gi|313619763|gb|EFR91370.1| RNA polymerase sigma-B factor [Listeria innocua FSL S4-378]
          Length = 259

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 115/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|168986243|dbj|BAG11803.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986245|dbj|BAG11804.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986247|dbj|BAG11805.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986249|dbj|BAG11806.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986251|dbj|BAG11807.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986253|dbj|BAG11808.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986255|dbj|BAG11809.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986259|dbj|BAG11811.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|168986261|dbj|BAG11812.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|258642983|gb|ACV86055.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 177

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 119/175 (68%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 2   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 62  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 121

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           +G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 122 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 176


>gi|166031695|ref|ZP_02234524.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
 gi|166028672|gb|EDR47429.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
          Length = 244

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 124/244 (50%), Gaps = 12/244 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++++       A+  +VE N  LV  + K++ NRG++  DL Q GNIGL+KA +KF
Sbjct: 3   HTIALIQRSHEGDEEARARLVEENAGLVWCIVKRFHNRGVETEDLFQIGNIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K       + N+  REPT
Sbjct: 63  DLSYDVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELAYKAYLLKEDLQNQWGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQ 606
             E++++L +  E +   L    +  SL  PI  +D     L D +E+K+         Q
Sbjct: 122 VGELSERLGVEQEELVMALDAGGDVESLHKPIYQKDGQEIRLMDKLEEKSE-----EHEQ 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                  T +L  L   E+R++ +R+      + T  +VG++  +++ ++ ++E K + +
Sbjct: 177 VLNHIVLTELLGVLNQDEKRLIYLRYFA----EQTQSQVGRELGISQVQVSRMEKKILGQ 232

Query: 667 LKHP 670
           LK+ 
Sbjct: 233 LKNA 236


>gi|4514511|dbj|BAA75454.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 278

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 118/316 (37%), Gaps = 39/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++   ++   G   L +I  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PE+             +  ED     +  DV+  + D E  ++   D   +    PE 
Sbjct: 59  LDPETDEDIPE-VLEEEAELEEDEDASPKAKDVKLDDDDEEEESEGDDDSEGESGPDPEV 117

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+   +++   ++                                   K  + 
Sbjct: 118 AKVRFSELEAAWNETKSVVA-----------------------------------KHGRD 142

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S + K   E L  +           D++ E +     +I  NE E++R A   G + R  
Sbjct: 143 SDEAKAALEALAAVFMMFKFTPRLFDIISEMIRGTHDQIRSNEREIMRYAVRRGRMDRTQ 202

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F      +E +P W+         E K  +      +L  + +I  I  + G+++ + + 
Sbjct: 203 FRMTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 262

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 263 ISKRMAVGEAKARRAK 278


>gi|301059188|ref|ZP_07200126.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
 gi|300446678|gb|EFK10505.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
          Length = 329

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 128/276 (46%), Gaps = 12/276 (4%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
              ++  +  I     ++  E   + + ++  E     A   +V +NLRLV+ +A  +  
Sbjct: 46  YDPLQIYLLEIKQYHLLTREEEIELATRIQ--ENNDDDAAFRLVTSNLRLVVKIAMDFHR 103

Query: 466 RGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV- 523
                 LDLIQEGN+GL++A  KFD   G KFS YA +W+K  I + I D    ++I   
Sbjct: 104 YWTKNLLDLIQEGNLGLLQAVRKFDPYRGIKFSYYASFWIKAYILKFIMDNWKMVKIGTT 163

Query: 524 -HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIG 581
              R     + +   ++  +    P P  +A+KL +    V ++  ++    ISL  P+G
Sbjct: 164 QSQRKLFFNLAKERDKLIAQ-GFTPEPRLLAEKLDVKESEVVEMTQRLGGWEISLSAPVG 222

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNT 638
           ++     G F+ D    +    +   +   L ++      +L+ +E  +      I    
Sbjct: 223 EDSRESYGSFLPDPAMAADDLLSNDESKNVLTKSLQEFRKTLSGKEADIFD--NRILAEK 280

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             TL+++G ++ ++RERIRQI+ K I+ ++   + K
Sbjct: 281 PLTLQDLGDKYKISRERIRQIQEKIIKNIRKWLKEK 316



 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           DP+++YL E+    LL+RE EI +A RI E         L  S L     I         
Sbjct: 47  DPLQIYLLEIKQYHLLTREEEIELATRIQENNDDDAAFRLVTSNLRLVVKIAMDFHRYWT 106

Query: 178 TTLLREI 184
             LL  I
Sbjct: 107 KNLLDLI 113


>gi|15595573|ref|NP_249067.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAO1]
 gi|116054106|ref|YP_788549.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|152989115|ref|YP_001345866.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PA7]
 gi|218889117|ref|YP_002437981.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa LESB58]
 gi|254243475|ref|ZP_04936797.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|296386874|ref|ZP_06876373.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAb1]
 gi|313112005|ref|ZP_07797792.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
 gi|2507390|sp|P42378|RP32_PSEAE RecName: Full=RNA polymerase sigma-32 factor
 gi|9946228|gb|AAG03765.1|AE004475_7 sigma factor RpoH [Pseudomonas aeruginosa PAO1]
 gi|765096|dbj|BAA08769.1| heat-shock sigma factor [Pseudomonas aeruginosa]
 gi|998760|gb|AAB33935.1| heat-shock sigma factor sigma 32 [Pseudomonas aeruginosa]
 gi|115589327|gb|ABJ15342.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126196853|gb|EAZ60916.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|150964273|gb|ABR86298.1| alternative sigma factor RpoH [Pseudomonas aeruginosa PA7]
 gi|218769340|emb|CAW25100.1| sigma factor RpoH [Pseudomonas aeruginosa LESB58]
 gi|310884294|gb|EFQ42888.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
          Length = 284

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 122/269 (45%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + S++    +S  + R +   +     +   A ++MV A+LR V+ +AK Y+  GL
Sbjct: 17  LEAYVHSVNSIPLLSPEQERELAERL--FYQQDLEAARQMVLAHLRFVVHIAKSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS- 586
           K+   +R+ ++    +  E     +A+ L +    VR++            P  D D   
Sbjct: 135 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGQDMAFDPAADADDES 193

Query: 587 ---HLGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTD 639
                  ++ED     P      A+  ++        L  L  R   +L+ R+       
Sbjct: 194 AYQSPAHYLEDHR-YDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWL--SEEK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 251 ATLHDLAEKYNVSAERIRQLEKNAMSKLK 279


>gi|326443735|ref|ZP_08218469.1| RNA polymerase sigma factor WhiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 258

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 21  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERSIKFE 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A+++ 
Sbjct: 81  TYAITRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPSEGEVAEEMG 137

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E          D   L D +ED  A  P++ A   
Sbjct: 138 IAVEE----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADDPVEVAEGR 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 194 ELRRLLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 249

Query: 668 K 668
           +
Sbjct: 250 R 250


>gi|170780849|ref|YP_001709181.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155417|emb|CAQ00524.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 337

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 103/229 (44%), Gaps = 11/229 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
                ++V  +L L   +A++++ R   + DL Q G +GL+KAA ++D   G  F ++A+
Sbjct: 85  RRLHDQIVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAI 144

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R + D    +R P  +++  H ++     ++ ++ R PT  E+A     P E
Sbjct: 145 PTISGEIKRHLRDNGWMVRPPRQIQELRHALLAVVPALTQRLGRTPTDAELAAHTGHPRE 204

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V + L    +  P SL+  + + +   L D +   +         +A            
Sbjct: 205 EVMEALAAHSSLRPASLDHTVHEHEGISLADTLGADD-----PGYARAERTVLLDAARGV 259

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ R+ R+L +RF    +      E+  +  VT+ ++ ++ A+ +  L+
Sbjct: 260 LSERDRRILHLRFVDECSQS----EIAAELGVTQMQVSRLLARILGALR 304


>gi|226946813|ref|YP_002801886.1| RNA polymerase factor sigma-32 [Azotobacter vinelandii DJ]
 gi|226721740|gb|ACO80911.1| RNA polymerase sigma-32 factor [Azotobacter vinelandii DJ]
          Length = 284

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 124/269 (46%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHAVNSIPLLTAEQERELADRL--YYQQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W++  I   I      ++I     + 
Sbjct: 75  AQSDLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILRNWRIVKIATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K+   +R+ ++    +  E   + +A+ L +    VR++            P  D D   
Sbjct: 135 KLFFNLRSQKKRLAWLNNE-EVDAVAESLGVEPHEVREMESRLSGQDMAFDPAADADDDS 193

Query: 588 L----GDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTD 639
           +      ++ED+    P     +A+  ++        L  L  R   +L  R+       
Sbjct: 194 VFQAPAHYLEDQR-YDPARQLEEADWSDSAAANLHEALEGLDERSRDILYQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  ++ V+ ERIRQ+E  A+ KLK
Sbjct: 251 ATLHDLAAKYKVSAERIRQLEKSALNKLK 279


>gi|255022641|ref|ZP_05294627.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-208]
 gi|22770504|gb|AAN06627.1|AF497199_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|5821404|dbj|BAA83808.1| sigma factor 32 [Pseudomonas putida]
          Length = 284

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 126/268 (47%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    +++ + R +   +     +   A ++MV A+LR V+ +A+ Y   GL
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERL--YYEQDVEAARQMVMAHLRFVVHIARSYAGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIPEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  +++ + ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLSGQDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  ++ED     AV   D+    N        L     R   +L  R+        
Sbjct: 194 AFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGWNERSRDILYQRWLAE--EKA 251

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVK 279


>gi|255280674|ref|ZP_05345229.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
 gi|255268611|gb|EET61816.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
          Length = 258

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 136/270 (50%), Gaps = 19/270 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
             N+++   V T     ++  E   +   +R+       A++  ++ NLRLV+SV K+++
Sbjct: 2   ALNKVEICGVNTSKLPVLTNEEKEELFERIRQ---GDMEARELYIKGNLRLVLSVIKRFS 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
                  DL Q G IGLMKA + F+  +  KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  ASNENADDLFQIGCIGLMKAIDNFNTEMDVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE- 583
           +RD  +K + T      K  +EPT  E+A+++ +  E +   +   + P+SL  P+  E 
Sbjct: 118 LRDTAYKALYTREAYMKKHLKEPTINELAEEIGISREDIVFAMDAIQSPLSLYDPVYSEG 177

Query: 584 -DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            DT ++ D I DK   +  ++ +++         +  L+ RE +++ MRF  G     T 
Sbjct: 178 GDTLYVMDQISDKK--NKEENWVESL---ALQEAMKRLSDRERKIINMRFFEG----KTQ 228

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            EV  + C+++ ++ ++E  A++ +++  R
Sbjct: 229 MEVAAEICISQAQVSRLEKSALKSMRNFLR 258


>gi|118591280|ref|ZP_01548678.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118435952|gb|EAV42595.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 287

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 67/272 (24%), Positives = 128/272 (47%), Gaps = 15/272 (5%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + R  +++      ++  E   +   +R  +     A +++  +++RLVI+VA ++ N G
Sbjct: 5   EKRQLVRAAMKAPYLTREEELELA--IRWRQERDEKALEKLSLSHMRLVIAVASRFRNFG 62

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DLIQEG++GL++AA +F+     +FSTYA WW++ +I   I      +R       
Sbjct: 63  LSLGDLIQEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQ 122

Query: 528 K--IHKVVRTARRMSNK---IKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIG 581
           K     + R   ++S     +      ++IA  + +    V     +++    SL  P+ 
Sbjct: 123 KALFFNLRRLRAKLSGNQTPLTDSELHQKIADAIGVKQSDVALMNARLSGPDTSLNAPVT 182

Query: 582 DEDTSH--LGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGM 636
           D + S     DF+     +      +  +    +   +  L  L+ RE +++R R     
Sbjct: 183 DSEGSSADRQDFLVSDAPLPDEIVTVSIDTERRQRWLSSALEVLSERELKIVRERRLSED 242

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               TLE +G +  +++ER+RQIE++A+ KLK
Sbjct: 243 G--ATLESLGVKLGISKERVRQIESRAMEKLK 272


>gi|114770145|ref|ZP_01447683.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114548982|gb|EAU51865.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 294

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 118/250 (47%), Gaps = 16/250 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +   + +   A   ++ A +RL IS+A K+   G+   DLIQE  +GLMKAA+KFD   G
Sbjct: 31  IAWRDHKDEDALHRLINAYMRLAISMASKFRRYGVSQQDLIQEAGMGLMKAADKFDPDKG 90

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRI--PVHMRDKIHKVVRTARRMS-------NKIK 544
            +FSTYA WWVK +I   +      +R     + +     + R   ++          + 
Sbjct: 91  VRFSTYAQWWVKASIQDFVMRNYSMVRTGSTTNQKSLFFNIKRVKAQLERDAVQNNQTVT 150

Query: 545 REPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS-HLGDFIEDK---NAVS 599
                E+++ +L +P+  V  +  +++   +SL     ++D      + + D+    A  
Sbjct: 151 PAQILEQVSTELGVPMRDVMMMNGRMSGGDMSLNAIQSNDDEGREWIETLADEAPGGAEI 210

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              S  +  L+    + +  L  RE+ ++  R  I   +  TLE +G +  +++ERIRQI
Sbjct: 211 VEQSFDEEKLKIWIGQSMEVLNEREKYIVIQRKMID--SPRTLESIGVELKLSKERIRQI 268

Query: 660 EAKAIRKLKH 669
           E  A+ KLK 
Sbjct: 269 ENAALEKLKK 278


>gi|302127759|emb|CBL51733.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 262

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI I KRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIXKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ +
Sbjct: 58  -----------------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ QK+ ++    
Sbjct: 95  SSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|317505016|ref|ZP_07962964.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
 gi|315663898|gb|EFV03617.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
          Length = 260

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 89/297 (29%), Positives = 140/297 (47%), Gaps = 41/297 (13%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +   K       K     E +S+    NEI     E  +S  E   +   +++G   +  
Sbjct: 5   IKQEKMKKIKTGKPLSERESESLNLYLNEI---GKEELLSDDEENKLSQQIQQGGASSER 61

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A  ++  ANLR V+++AK+YT+RG+  LDLI EGNIGLMKAA  FD   G +F  YA  +
Sbjct: 62  AINKLTSANLRFVVAIAKQYTDRGVAILDLISEGNIGLMKAAMSFDGSRGLRFVGYAEPF 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V++AI  ++ +QS   R+P H                     E +PEE A   A      
Sbjct: 122 VRRAIEAAVNEQSGIFRLPKH---------------------ENSPEEKANSRAF----- 155

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                      S++ P+ +     L   + D NA  P    ++A+++E   + +  L  R
Sbjct: 156 -----------SVDAPLENGKNMSLLSVLSDPNAARPDQEVLEASVKEELMQAMNILNQR 204

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E+ V+   +GIG     T  E+ ++  + RER+RQI  KA+RKL   + S  L+++L
Sbjct: 205 EKNVVEAFYGIGQPH-LTFAEIAEKMGLKRERVRQIRNKAVRKLNRNTTSDMLKAYL 260



 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 34/191 (17%), Positives = 76/191 (39%), Gaps = 10/191 (5%)

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTF 164
           K          + + +YL E+G  ELLS + E  ++++I+ G       +  L  + L F
Sbjct: 14  KTGKPLSERESESLNLYLNEIGKEELLSDDEENKLSQQIQQGGASSERAINKLTSANLRF 73

Query: 165 QALIIWRDELNDGTTLLREIID-----LEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
              I  +   + G  +L  I +     ++A +  +   G         + +R   +   E
Sbjct: 74  VVAIA-KQYTDRGVAILDLISEGNIGLMKAAMSFDGSRGLRFVGYAEPFVRRAIEAAVNE 132

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN-DERNLDEDEDDSAHTLSAMEDQLRP 278
           +  +        S  + +      VD+P EN +N    ++  D + +      +E  ++ 
Sbjct: 133 QSGIFRLPKHENSPEEKANSRAFSVDAPLENGKNMSLLSVLSDPNAARPDQEVLEASVKE 192

Query: 279 KVMCALDEIAE 289
           ++M A++ + +
Sbjct: 193 ELMQAMNILNQ 203


>gi|66474647|gb|AAY46893.1| RpoD [Aeromonas sp. AN-30]
          Length = 268

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 63/312 (20%), Positives = 118/312 (37%), Gaps = 46/312 (14%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P    
Sbjct: 1   GEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN--- 55

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                                E DDV  T   I S            D   +  E+ + +
Sbjct: 56  ---------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNS 94

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKV 316
            D+ +      ++                  E + ELR+  +   ++ Q++ ++    + 
Sbjct: 95  DDDGDGGPDPEVA-----------------REKFGELRAQNEVTRLSIQQNGRAHDDTQN 137

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
              +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+    
Sbjct: 138 AIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFT 197

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
             E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   + 
Sbjct: 198 NNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMS 256

Query: 436 KGECEASIAKKE 447
            GE +A  AKKE
Sbjct: 257 IGEAKARRAKKE 268


>gi|29828415|ref|NP_823049.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29605518|dbj|BAC69584.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 109/229 (47%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+VEA L +   +A ++ NRG  + DL Q  ++GL+KA +++D  LG  F +YA+  +
Sbjct: 38  REEIVEAWLPMAERLAGRFRNRGENYEDLRQVASLGLVKAVDRYDPELGNAFESYAVPTI 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V   ++ +S  I  R PT  EIA+   M  E V
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRFASQDLSQTISGRRPTVAEIAEHANMSEEDV 157

Query: 564 RKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           R  L+   +   +SL+  +   ED   L D +   +    +        RE     L +L
Sbjct: 158 RAGLEALESFTALSLDAELPGSEDGYSLSDALGSADPALDIVVD-----REAVKPRLQAL 212

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE  +L MRF   M      E    Q  +++  + +I ++   +L+ 
Sbjct: 213 PERERDILYMRFFGDMTQSRIAE----QLGISQMHVSRIISRCCDRLRE 257


>gi|119718035|ref|YP_925000.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119538696|gb|ABL83313.1| sigma-70 region 2 domain protein [Nocardioides sp. JS614]
          Length = 257

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 106/226 (46%), Gaps = 11/226 (4%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            +++  N+ + +   +++  RG+   DL Q   +GL+KA + FD   G+ F ++A+  ++
Sbjct: 33  DQLIRLNMAVAVDATRRFRGRGIATDDLEQVAYVGLVKAVKGFDPDRGHDFLSFAIPTIR 92

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R   D   T+R P  +++   K++     +  ++ R P P EIA+ L +  + V +
Sbjct: 93  GEVRRHFRDLGWTVRPPRSIQEAQTKIIACEGELYQQLGRAPRPSEIAEHLGLDRDLVVE 152

Query: 566 VLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            L  +    P SL+ P  + D   +G  +   +          A  R     VLA L+ R
Sbjct: 153 ALGASGCFAPASLDAPAHEGDDDPIGRRLGFTDE-----GFDVAEARAVLAPVLAKLSKR 207

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E  ++ MRF  G        ++G+   VT+ ++ ++  + + +L+ 
Sbjct: 208 ERIIVEMRFFRGCTQ----AQIGEAIGVTQMQVSRLLTRLMARLRE 249


>gi|315302306|ref|ZP_07873197.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
 gi|313629329|gb|EFR97571.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
          Length = 259

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 115/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|30266017|gb|AAN16086.1| SigB [Listeria welshimeri]
          Length = 259

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGNQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+ +L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQMILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|332670026|ref|YP_004453034.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Cellulomonas
           fimi ATCC 484]
 gi|332339064|gb|AEE45647.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cellulomonas
           fimi ATCC 484]
          Length = 296

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 102/247 (41%), Gaps = 16/247 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
            +        +  A++ ++     LV +VA +   R    ++  DL+  G  GL+ A EK
Sbjct: 48  AAWADFKSTGSRAAREHLILHYAPLVAAVAGRVGMRLPSTVEQADLVSYGMFGLIDAIEK 107

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           ++     KF +YA   ++ AI   +        +P  +R K   V R    +   + R P
Sbjct: 108 YETDRAVKFESYASSRIRGAIIDELRAMDW---VPRSVRTKARSVDRAYAELEATLHRAP 164

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH----LGDFIEDKNAVSPL 601
           T  E+A+ L + V  +R       T    +L+  +G  +       L D + D+    P 
Sbjct: 165 TEAEVARHLEISVGELRATFSQLSTVNIAALDELLGGGEDRQAGVCLVDTLGDERTQDPA 224

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            S   A  +    R +  L  RE  V+ + +  G     TL E+G+   VT  RI Q+  
Sbjct: 225 GSLDAAETKYLLARAIEQLGDRERMVVVLYYYEG----MTLAEIGRVLGVTESRISQMHT 280

Query: 662 KAIRKLK 668
            A+ +L+
Sbjct: 281 AAMLRLR 287


>gi|29827628|ref|NP_822262.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604728|dbj|BAC68797.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 295

 Score =  121 bits (304), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 59/271 (21%), Positives = 128/271 (47%), Gaps = 23/271 (8%)

Query: 412 EIKSISVETGISISEFRHI-------VSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           E+ +I+    +S  + R +       +S++ +G  +    +  ++E NL LV   A ++ 
Sbjct: 25  ELDAIADPLAVSPKDARELSRHFFARLSVLEEGTQDYQYVRNTLIEMNLTLVRYAASRFR 84

Query: 465 NRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +RG  +  D++Q G IGL+KA ++F+     +F+++A+ ++   I R   D S  + +P 
Sbjct: 85  SRGSGEMEDIVQVGTIGLIKAIDRFELSREVEFASFAVPYIVGEIKRFFRDTSWAVHVPR 144

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE------PISLE 577
            +++   ++ +    +S +  R PT  E+A+ +++  E V +  K            SL 
Sbjct: 145 RLQEARVELAQATDELSRRTGRTPTVRELAELMSLTEEEVIEARKAANAYRSSSLDASLS 204

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                ++ S L DFI  +     L   + +        ++A L  R+ R+L +RF     
Sbjct: 205 GDGSADNESVLADFIGREETALELIEDMHS-----LAPLVAQLDERDRRILHLRFV---- 255

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + T  ++G++  +++  + ++  K I  L+
Sbjct: 256 DELTQAQIGERLGISQMHVSRLINKIITTLR 286


>gi|148833419|gb|ABR14579.1| DNA-dependent RNA polymerase sigma factor D subunit [Pseudomonas
           pertucinogena]
          Length = 269

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 54/309 (17%), Positives = 107/309 (34%), Gaps = 41/309 (13%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +MA++   P T   ++     + +    L +I      I P+  G
Sbjct: 1   GEIEIAKRIEEGIREVMAAISMFPGTVDGILTEYQRIAEEGGRLTDI--FNGYIDPDDDG 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                         +   ++K      + + + E   +   ++ +     PE A      
Sbjct: 59  LSGTDNAVVPAAAAKPKDEKK----ASDDDEEEEEDTEDDTEEETDGGPDPEIARQRFGA 114

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + E  +     L A +                                  ++S       
Sbjct: 115 VQEQLEKVRKVLKAKKG---------------------------------DRSHPDVVAE 141

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQG 376
            E L +L   + L   + D LV ++  +   I   E  +++L      + R  FL    G
Sbjct: 142 METLAQLFMPIKLVPKQYDALVARVRGVQDDIRARERAIMQLCVRDARMPRADFLRSFPG 201

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E +  W+       +  + + +A     IL+ + ++ ++  +  ++I++ + I   +  
Sbjct: 202 NETNEKWIDEVLA-KKPAYADALAALQPDILRQQQQLIALEQDAQLTIAQVKDINRRMSI 260

Query: 437 GECEASIAK 445
           GE  A  AK
Sbjct: 261 GEARARRAK 269


>gi|292696907|dbj|BAI99626.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696911|dbj|BAI99628.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696925|dbj|BAI99635.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 253

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/291 (17%), Positives = 96/291 (32%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNETE-----DV 53

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +         E +  D  E E + E     + DD       PE A      L    + 
Sbjct: 54  APTATHIGSELSEDDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREKFGELRAQYEV 113

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +  ++                                   QK+ ++    +    +L  +
Sbjct: 114 TRLSI-----------------------------------QKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +L+L  +   + +  F+      E D  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAAFTNNECDSAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKA-WSPRLVEMAEDVLRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|265995632|ref|ZP_06108189.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|262766916|gb|EEZ12534.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 293

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 125/267 (46%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++ A +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKERVRQIESRAMEKLK 279


>gi|262376306|ref|ZP_06069536.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
 gi|262308907|gb|EEY90040.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
          Length = 289

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 118/270 (43%), Gaps = 12/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKITKEPISLETPIGDE 583
            +       + + S+K       + IA  L +  E V ++   L          +   DE
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLAEAQSIANDLNVTPEQVLEMEGRLTAYDAAFDASSDDDDE 195

Query: 584 DTSHLGDFIE-DKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNT 638
            ++H+   +  + N   P       +  E         +  L  R   +L+ R+      
Sbjct: 196 GSTHVAPALYLEDNRYDPARLIENEDYEEQSTSALHEAMDQLDDRSRNILQRRWLDD--E 253

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 254 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|220927856|ref|YP_002504765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
 gi|219998184|gb|ACL74785.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
          Length = 249

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 111/230 (48%), Gaps = 11/230 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L L   ++KK+ NRG+ F D+ Q   + L+ A E+F    G KF ++A   +
Sbjct: 29  RNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALINAVERFSPDKGVKFISFATPTI 88

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+S TI+IP  + +    V +    ++ K+ R P  +EIA+ + +PVE V 
Sbjct: 89  LGEIKRFFRDKSTTIKIPRRIYESRQGVNKARDELTQKLSRVPRADEIAEYMGIPVETVL 148

Query: 565 KVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           ++++     I  SL+  I  ++ + LGD +          +    + ++   +VL S   
Sbjct: 149 EIIEAGSSTIVKSLDQTINQDNDAELGDTLGYDE-----KTYEMIDNKDFLEKVLISFND 203

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            E + +  R+      + T +++ +   V++  + ++E K + K +   +
Sbjct: 204 VERQFVTYRY----IQNKTQKQIAEILGVSQMYVSRMERKILDKFRKYLK 249


>gi|311894139|dbj|BAJ26547.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 281

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + FR +  +    +   S  +  ++E N+ LV  VA ++ +R  +  D++Q G +GL
Sbjct: 9   LSDALFRRLAGL-NPEDPVHSYVRGTVIELNMPLVRFVASRFRHRPEELDDIVQVGTVGL 67

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD   G +F TYA+  +   I R   D S  +R+P  ++++    VR + R+  
Sbjct: 68  IKAVDGFDPDRGVEFVTYAIPTISGEIKRFFRDTSWPLRVPRSVQERYLAAVRASDRLEQ 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + R P   E+A +L +  +   + L+  +           +D S               
Sbjct: 128 ALGRLPDTAELAAELHVTEDEAAEGLEAGRLCRCDSLDSLRDDGSDDAGSALINRLGGCD 187

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                A LR   T  L+ L  RE  VL +RF  G     T  E+  +  V++  + +I A
Sbjct: 188 PELEVAELRVMATPFLSRLPERERTVLLLRFWGG----LTQSEIAARIGVSQMHVSRILA 243

Query: 662 KAIRKLKH 669
             +  L+ 
Sbjct: 244 ATLAGLRE 251


>gi|322496001|emb|CBJ55205.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 259

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 57/304 (18%), Positives = 108/304 (35%), Gaps = 46/304 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P     
Sbjct: 1   EIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE--- 55

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                +  +       S+  E D   E E + E     S DD       PE A     +L
Sbjct: 56  ----ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDL 111

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
               + +  ++                                   Q++ ++    +   
Sbjct: 112 RAQYEVTRLSI-----------------------------------QQNGRAHEDTQAAI 136

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
            +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      
Sbjct: 137 AQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNN 196

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +  G
Sbjct: 197 ECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIG 255

Query: 438 ECEA 441
           E +A
Sbjct: 256 EAKA 259


>gi|17986563|ref|NP_539197.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|17982171|gb|AAL51461.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
          Length = 319

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 76/305 (24%), Positives = 136/305 (44%), Gaps = 15/305 (4%)

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           Q  ++ P  +S +   P       V     +    ++ I+S      +   E R +   +
Sbjct: 5   QENQMKPSSMSSSSTVPANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--I 62

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++ A +FD     
Sbjct: 63  RWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDV 122

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE-- 550
           +FSTYA WW++ ++   I      +R       K     + R   +++         E  
Sbjct: 123 RFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIY 182

Query: 551 -EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQ 606
            EI+ +L +    V     +++    SL   +  E+T  S   DF+ D + +    +   
Sbjct: 183 REISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIAESS 242

Query: 607 ANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            ++       TR L +L  RE  ++R R         TLE +G++  ++++R+RQIE++A
Sbjct: 243 IDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--TLEALGEKLGISKQRVRQIESRA 300

Query: 664 IRKLK 668
           + KLK
Sbjct: 301 MEKLK 305


>gi|322496009|emb|CBJ55209.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 261

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 57/306 (18%), Positives = 108/306 (35%), Gaps = 46/306 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P     
Sbjct: 1   EIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE--- 55

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                +  +       S+  E D   E E + E     S DD       PE A     +L
Sbjct: 56  ----ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDL 111

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
               + +  ++                                   Q++ ++    +   
Sbjct: 112 RAQYEVTRLSI-----------------------------------QQNGRAHEDTQAAI 136

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
            +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      
Sbjct: 137 AQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNN 196

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +  G
Sbjct: 197 ECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIG 255

Query: 438 ECEASI 443
           E +A  
Sbjct: 256 EAKARR 261


>gi|161829709|ref|YP_001597727.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 331]
 gi|161761576|gb|ABX77218.1| alternative sigma factor RpoH [Coxiella burnetii RSA 331]
          Length = 288

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 121/276 (43%), Gaps = 13/276 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI  I + I  ++    +S  E   + +  R+       A +++V ++LR V+ +A+ Y+
Sbjct: 14  SIGSIGSYISWVNRIPLLSAEEEHDLANKFRQ--SNDLEAARKLVLSHLRFVVRIARGYS 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      ++I   
Sbjct: 72  GYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATT 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +                 +     +A++L +  + VR++ +       + +    + 
Sbjct: 132 KAQRKLFFNLRKHAKKRGWFSDHEAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEES 191

Query: 584 DTSHLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           D+          ++EDK    A+    S    +        + S+  R   +L  R+   
Sbjct: 192 DSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSMDDRSRDILYQRWL-- 249

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                TL E+  Q+ V+ ERIRQ+E  A++K++   
Sbjct: 250 SEKKSTLHELAAQYSVSAERIRQLEKNAMQKIRTAM 285


>gi|161898931|gb|ABX80455.1| SigB [Listeria monocytogenes]
 gi|161898937|gb|ABX80458.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 110/241 (45%), Gaps = 4/241 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|3298591|gb|AAC38793.1| Sigma B [Listeria innocua]
          Length = 259

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 115/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|322496007|emb|CBJ55208.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 261

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 58/306 (18%), Positives = 107/306 (34%), Gaps = 46/306 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P     
Sbjct: 1   EIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE--- 55

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                +  +       S+  E D   E E + E     S DD       PE A     +L
Sbjct: 56  ----ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDL 111

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
               + +  ++                                   QK+ ++    +   
Sbjct: 112 RAQYEVTRLSI-----------------------------------QKNGRAHEDTQAAI 136

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
            +L  +     L   + D LV  + ++ + +   E  +++L  +   + +  F+      
Sbjct: 137 AQLADVFRQFRLMPKQFDRLVNNMREMMEPVRVQERIIMKLCVEQAKMPKKTFVAAFTNN 196

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W  Y K   +  W   +    + +L+   +++ I  ETG+SI++ + I   +  G
Sbjct: 197 ECETAWFEYQKQAGKA-WSPRLLVLDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIG 255

Query: 438 ECEASI 443
           E +A  
Sbjct: 256 EAKARR 261


>gi|239944630|ref|ZP_04696567.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           15998]
 gi|239991094|ref|ZP_04711758.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           11379]
          Length = 247

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 105/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 10  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERAIKFE 69

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  + +R P+  E+A ++ 
Sbjct: 70  TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQFRRTPSEAEVASEMG 126

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 127 IALEE----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDR 182

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 183 ELRRLLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 238

Query: 668 K 668
           +
Sbjct: 239 R 239


>gi|297561355|ref|YP_003680329.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845803|gb|ADH67823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 101/238 (42%), Gaps = 7/238 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + + +  A    + +V     LV  +A++Y  RG    DL Q   +GL+KA   F+   G
Sbjct: 43  LDRDDPRADDLCERVVVLYQPLVNKLARRYNGRGEPLDDLQQTAMLGLVKAIHGFNPDRG 102

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F +Y +  V   I R   D +  +R+    ++   K+ +          R PT  E++
Sbjct: 103 KPFISYLLPTVTGEIKRHFRDHTWAVRVSRRHQENRIKLRQALNDFQQAHARTPTVHELS 162

Query: 554 KKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +++ +P   V +++++  +   +SL+ P   +     G  +ED          +    RE
Sbjct: 163 EEMGLPEAEVGELIQVSESYRSLSLDAPDTSDSDGQEGTRLEDHLGSEDEGLELVVQ-RE 221

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    LA L  RE  +L +RF      DHT  E+      ++  + ++    + +L+ 
Sbjct: 222 SLKPALARLPEREREILMLRFF----GDHTQSEIADCLGYSQMHVSRLLNGVLGQLRE 275


>gi|220904711|ref|YP_002480023.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219869010|gb|ACL49345.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 433

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 70/275 (25%), Positives = 135/275 (49%), Gaps = 21/275 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ +S    +   E   +   VR  +   + A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 157 YLREVSRFPMLKPEEEHELAVRVR--DHNDADAAFRLVSSHLRLVVRIAMDFQRRWMQNV 214

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDL+QEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      R  
Sbjct: 215 LDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQVQRKL 274

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS- 586
            + + R  +++  +   +P    ++++L +  E + ++  ++    +SL   +G++    
Sbjct: 275 FYNLNRERQKLIMQ-GYDPDAAMLSERLGVTEEQINEMDQRLASTDMSLNAQVGEDSGGA 333

Query: 587 -------HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   LG  IED  A + +   +    R     ++  L  +E+ +L     +  +  
Sbjct: 334 TRMDFLPALGPGIEDSLASTEIAGIV----RSKLKTIMPKLNEKEQYIL--HNRLLSDEP 387

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            TL E+G+++ +TRER+RQ+EA+ + K+    ++ 
Sbjct: 388 ITLREIGERYNITRERVRQLEARLVEKIGQHMKND 422



 Score = 42.5 bits (98), Expect = 0.23,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 40/118 (33%), Gaps = 5/118 (4%)

Query: 57  EVSSEQMEDTVAMLSNMGINVVDGDD---LEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
            +  +++E        + I   D ++     D +  ++         + SV         
Sbjct: 88  VLDVDELEHERDT-DELDIESPDSEEELLDSDMDEDDEPRLTDEDEQDRSVPAPSSSRVP 146

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIW 170
              T D + +YLRE+    +L  E E  +A R+ +   A     L  S L     I  
Sbjct: 147 AVGTRDSLHLYLREVSRFPMLKPEEEHELAVRVRDHNDADAAFRLVSSHLRLVVRIAM 204


>gi|255319457|ref|ZP_05360671.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262378519|ref|ZP_06071676.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
 gi|255303397|gb|EET82600.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262299804|gb|EEY87716.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
          Length = 289

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 123/270 (45%), Gaps = 12/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           + +   I +++    ++  + + +    R    +   A K +V ++LR V+ +A+ Y   
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAE--RYYYDQDLDAAKMLVMSHLRFVVHIARSYAGY 75

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I     
Sbjct: 76  GLPQGDLIQEGNLGLMKAVKRFDPSMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKA 135

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP--IGDE 583
           + K+   +R+ ++ S K+  E            P + +    ++T    + E      D+
Sbjct: 136 QRKLFFNLRSLKKSSKKLTLEEARSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDDDDD 195

Query: 584 DTSHLGDFIEDKNA-VSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNT 638
            +SH+   +  +++   P       +  E         +  L  R   +L+ R+     +
Sbjct: 196 SSSHVAPVLYLEDSRYDPARLVEDEDWEEQSNSALHNAMDQLDDRSRNILQRRWLDDDKS 255

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 256 --TLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|29655194|ref|NP_820886.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 493]
 gi|6716381|gb|AAF26609.1|AF120928_1 heat-shock sigma factor [Coxiella burnetii]
 gi|29542466|gb|AAO91400.1| RNA polymerase sigma-32 factor [Coxiella burnetii RSA 493]
          Length = 288

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 121/276 (43%), Gaps = 13/276 (4%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI  I + I  ++    +S  E   + +  R+       A +++V ++LR V+ +A+ Y+
Sbjct: 14  SIGSIGSYISWVNRIPLLSAEEEHDLANKFRQ--SNDLEAARKLVLSHLRFVVRIARGYS 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      ++I   
Sbjct: 72  GYGLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATT 131

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDE 583
              +                 +     +A++L +  + VR++ +       + +    + 
Sbjct: 132 KAQRKLFFNLRKHAKKRGWFSDHEAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEES 191

Query: 584 DTSHLGD-----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           D+          ++EDK    A+    S    +        + S+  R   +L  R+   
Sbjct: 192 DSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSMDDRSRDILYQRWL-- 249

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                TL E+  Q+ V+ ERIRQ+E  A++K++   
Sbjct: 250 SEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|294815383|ref|ZP_06774026.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
 gi|294327982|gb|EFG09625.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 278

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 41  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDIERSIKFE 100

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A+++ 
Sbjct: 101 TYAITRIRGAMIDELRALDW---IPRSVRQKARAVERAYATLEAQLRRTPSEGEVAEEMG 157

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + VE     L      +SL   +  E          D   L D +ED  A  P++ A   
Sbjct: 158 IAVEE----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADDPVEVAEGR 213

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 214 ELRRLLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVLGVTESRVSQIHTKSVLQL 269

Query: 668 K 668
           +
Sbjct: 270 R 270


>gi|161898871|gb|ABX80425.1| SigB [Listeria monocytogenes]
          Length = 229

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 106/233 (45%), Gaps = 4/233 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G  
Sbjct: 1   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 60

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  
Sbjct: 61  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIADF 120

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +  E V + +++ K   +L      E  S               D   + N R    +
Sbjct: 121 IGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLLEK 180

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL+
Sbjct: 181 VLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKLR 229


>gi|229492301|ref|ZP_04386108.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229320710|gb|EEN86524.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 260

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/224 (22%), Positives = 106/224 (47%), Gaps = 12/224 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E  L L   VA++Y  RG  F DL Q   +GL++A ++FD   G  F ++A+  V   
Sbjct: 39  IIELCLPLATHVARRYQGRGQPFEDLEQVARVGLIQAVQRFDVDKGSDFLSFAVPTVMGE 98

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + +   D   ++R+P  ++++   + R    +S  + R PT  E+AK+L +  + V + L
Sbjct: 99  VRKHFRDHGWSVRVPRSLQERHLALNRALTTLSQTLGRAPTVAELAKELDIEPDEVEQGL 158

Query: 568 KI--TKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
               +     L+T    + +   L D +         ++  + +  ET    L +L  RE
Sbjct: 159 TAGNSYRTTPLDTASAGDGSGLTLIDTLG-----QYDEAISRIDNHETLRPALLALPERE 213

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +RF   +      E+V     +++  + +I  +++++L+
Sbjct: 214 RTIVVLRFFGHLTQSQIAEKV----GISQMHVSRILTQSLKQLR 253


>gi|205352349|ref|YP_002226150.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205272130|emb|CAR36983.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|326627399|gb|EGE33742.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 239

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 111/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  K+ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQKLGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           ++L +PV   R++L  T            E+     + + E+    +PL   ++ +LR+ 
Sbjct: 122 ERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIESLPEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|167758779|ref|ZP_02430906.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
 gi|167663519|gb|EDS07649.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
          Length = 258

 Score =  121 bits (303), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 64/262 (24%), Positives = 128/262 (48%), Gaps = 9/262 (3%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + +++   V T  + I +     ++  + +   + AK+E ++ NLRLV+SV K++    
Sbjct: 2   AQGKVEICGVNTAKLPILKEEEKEALFARIKAGDAEAKEEYIKGNLRLVLSVIKRFGGSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA   F+  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K +        +  +EPT +EIA+++ +  E +   L   + P+SL+ P+ ++    
Sbjct: 121 TAYKAIYAKENYIKQNLKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDA 180

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L    +  +  +  +  ++     +    +  L  RE  ++++RF  G     T  EV  
Sbjct: 181 LYVMDQISDTKNKEEKWVEDL---SLEAAMQHLGERERYIIKLRFFEG----KTQMEVAD 233

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  +++ ++ ++E  A+R ++ 
Sbjct: 234 EIKISQAQVSRLEKNALRLMRQ 255


>gi|322496005|emb|CBJ55207.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 261

 Score =  121 bits (303), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 57/306 (18%), Positives = 108/306 (35%), Gaps = 46/306 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P     
Sbjct: 1   EIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE--- 55

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                +  +       S+  E D   E E + E     S DD       PE A     +L
Sbjct: 56  ----ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDL 111

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
               + +  ++                                   Q++ ++    +   
Sbjct: 112 RAQYEVTRLSI-----------------------------------QQNGRAHEDTQAAI 136

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
            +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      
Sbjct: 137 AQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNN 196

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +  G
Sbjct: 197 ECETAWFEYQKQAGKAWSPRLLDMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIG 255

Query: 438 ECEASI 443
           E +A  
Sbjct: 256 EAKARR 261


>gi|46579995|ref|YP_010803.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120602593|ref|YP_966993.1| sigma-70 region 2 domain-containing protein [Desulfovibrio vulgaris
           DP4]
 gi|46449411|gb|AAS96062.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120562822|gb|ABM28566.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio vulgaris DP4]
 gi|311234006|gb|ADP86860.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           vulgaris RCH1]
          Length = 356

 Score =  121 bits (303), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 75/276 (27%), Positives = 140/276 (50%), Gaps = 14/276 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            ++ IS    +   E   +   VR+       A   +V ++LRLV+ +A  +  R +Q  
Sbjct: 80  YLREISRFPMLKPEEEYELAKRVRETGDGD--AAFRLVSSHLRLVVKIAMDFQRRWMQNV 137

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           LDLIQEGN+GLM+A  KFD   G KFS YA +W+K  I + I D    ++I      R  
Sbjct: 138 LDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQAQRKL 197

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS- 586
            + + +  +++  +   +P    ++++L +  E V ++  ++    +SL+ P+GDE    
Sbjct: 198 FYNLNKERQKLILQ-GYDPDAATLSERLNVTKEQVVEMEQRLDASDVSLDIPVGDEGGGA 256

Query: 587 HLGDFIE--DKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
              DF+          L +   A++ +     ++  L+ +E  +L  +  +      TL 
Sbjct: 257 SRMDFLPALGPGIEDALSNHEIASMVQNRLQSIIPKLSDKEVDIL--QNRLLSEEPVTLR 314

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           E+G+++ +TRER+RQIEA+ ++K++     K+++ F
Sbjct: 315 EIGEKYDITRERVRQIEARLLQKIRDHL-FKEIKDF 349



 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 21/105 (20%), Positives = 36/105 (34%), Gaps = 8/105 (7%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS-------ADRSTDDPVRMYLR 126
            + ++DG D   ++  +    +               D+          +  D + +YLR
Sbjct: 23  DVEIIDGPDDSADDTEDTEDFVDEDDVIDIGDDDHAPDTFHLNAPATVSTGKDSLHLYLR 82

Query: 127 EMGSIELLSREGEIAIAKRI-EAGRAMMMASLCESPLTFQALIIW 170
           E+    +L  E E  +AKR+ E G       L  S L     I  
Sbjct: 83  EISRFPMLKPEEEYELAKRVRETGDGDAAFRLVSSHLRLVVKIAM 127


>gi|302147253|emb|CBL51748.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
          Length = 262

 Score =  121 bits (303), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 105/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II          
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E                          E  A  +    S++       E++E
Sbjct: 51  -SGFIDPNEA-------------------------EDMAPTATHIGSELGEDDLADEDEE 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
              DEDED  +                   E+   Y          ++ QK+ ++    +
Sbjct: 85  MREDEDEDGDSSDDDGDGGPDPEVAREKFAELRAQYEV------TRLSIQKNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
                L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      V  + D + +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLVEMDED-VQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|121602584|ref|YP_988464.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614761|gb|ABM45362.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 121/254 (47%), Gaps = 13/254 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +     +R  +     A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +
Sbjct: 40  KEYDLALRWKDKRDDEAMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAAR 99

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNK--- 542
           F+     +FSTYA WW++ +I   I      +R       K     + R   ++  +   
Sbjct: 100 FEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAQLVQEDST 159

Query: 543 IKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTSHL--GDFIEDKN--- 596
           + ++     IA+KL++PV  V R   + +    SL   I + + S +   D + D++   
Sbjct: 160 LTKQDIFRSIAEKLSVPVSDVERMDFRFSGADNSLSVSISENEESPVTKIDNLVDEHPLP 219

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            +    +       +     L  L  RE  ++R  F    +   TLE +G++  +++ER+
Sbjct: 220 DILIEKAIDGQRRTQWLYDALQILNEREMEIIR--FRRLNDESATLESLGERLGISKERV 277

Query: 657 RQIEAKAIRKLKHP 670
           RQIE +A++KL+  
Sbjct: 278 RQIEVRALQKLRRA 291


>gi|161898897|gb|ABX80438.1| SigB [Listeria monocytogenes]
          Length = 235

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 109/239 (45%), Gaps = 4/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 1   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 120

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 121 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 181 RMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 235


>gi|295095481|emb|CBK84571.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 229

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 110/228 (48%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V     ++  ++ R  T  E+A++L +PVE
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAHAMGQLEQELGRNATETEVAERLGIPVE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D++   +PL   ++ NLR+     + +L
Sbjct: 120 EYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDEHQQENPLHHLLEGNLRQRVMEAIEAL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|291300290|ref|YP_003511568.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290569510|gb|ADD42475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Stackebrandtia nassauensis DSM 44728]
          Length = 267

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 113/243 (46%), Gaps = 11/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             +  ++K +      +  +V+  L L   +A+++ +RG    DL Q   +GL+ A + F
Sbjct: 30  ERMERLKKTDPRRRALRNTVVQRALPLADRLARRFEHRGQPLEDLTQVARLGLINAVDNF 89

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
               G  F+ +A+  +   + R   D+   +R+P  +++        ++ +S ++ R PT
Sbjct: 90  KCGRGGGFTHFAVPSILGELKRHFRDKGWLVRVPRRLQETRLAFNEASKDLSQRLGRSPT 149

Query: 549 PEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E+ A+ L+MPVE VR  +      E +SL TP   E +  L D +   +      +   
Sbjct: 150 LEDYAEYLSMPVEQVRAGINCVGAYEGVSLHTPAHRESSEELIDSLGGSD-----PAMAS 204

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A  R      +  LTPRE R+L +RF   ++      E+ ++  +++  + ++  + + K
Sbjct: 205 AEARMLLRPAIKELTPRECRILSLRFVDDLHQS----EIAREVGLSQMHVSRLLRQTLTK 260

Query: 667 LKH 669
           L+ 
Sbjct: 261 LRE 263


>gi|169351116|ref|ZP_02868054.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
 gi|169292178|gb|EDS74311.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
          Length = 239

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 120/240 (50%), Gaps = 14/240 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ K  C   IAK+ +V  NL LV S+  ++ N      DL Q G IGLMKA   FD 
Sbjct: 7   IELIEKARCGDEIAKELVVNQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAINNFDT 66

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA+  +   I R   D   TI++   +++   K+ +    + N+  ++PT E
Sbjct: 67  NYGVQFSTYAVPIIMGEIKRYFRD-DGTIKVSRSLKELNLKINKVKELLINQTGQDPTVE 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQAN 608
            IAK L + V+ V + +  +  P SL  PI ++D S +   + +EDK+     +      
Sbjct: 126 AIAKYLNIDVQDVVEAIDSSYYPTSLSEPIYEKDGSSISMEERVEDKHNKMWFE------ 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +  L  +E+ +L +R+ +  N +     V K+  +++ ++ ++E K I KL+
Sbjct: 180 -KIALKMEIDKLDEKEKLILYLRYQLDFNQEK----VAKRLNISQVQVSRLEKKIIAKLR 234


>gi|256045366|ref|ZP_05448260.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260565741|ref|ZP_05836224.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260151114|gb|EEW86209.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
          Length = 311

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 73/289 (25%), Positives = 129/289 (44%), Gaps = 15/289 (5%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           P       V     +    ++ I+S      +   E R +   +R  E +   A   +  
Sbjct: 13  PANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQDALHRITS 70

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           A++RLVIS+A ++    L   DLIQEG +GL++ A +FD     +FSTYA WW++ ++  
Sbjct: 71  AHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQD 130

Query: 511 SIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR- 564
            I      +R       K     + R   +++         E   EI+ +L +    V  
Sbjct: 131 YILRNWSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEF 190

Query: 565 KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLAS 619
              +++    SL   +  E+T  S   DF+ D + +    +    ++       TR L +
Sbjct: 191 MDSRLSGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDT 250

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  ++R R         TLE +G++  ++++R+RQIE++A+ KLK
Sbjct: 251 LNERELHIIRERRLDDDGV--TLEALGEKLGISKQRVRQIESRAMEKLK 297


>gi|153814532|ref|ZP_01967200.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|317500575|ref|ZP_07958796.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089324|ref|ZP_08338225.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848026|gb|EDK24944.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|316898008|gb|EFV20058.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330405505|gb|EGG85037.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 260

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 120/241 (49%), Gaps = 12/241 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           + +     A+++ ++ NLRLV+SV K++ N      DL Q G +GLMKA + FD     K
Sbjct: 30  RIKAGDEEAREKYIKGNLRLVLSVIKRFENSSENADDLFQIGCVGLMKAVDHFDPGRMVK 89

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA+  +   I R + D S  IR+   +RD  +K +        +  +EPT +EIA++
Sbjct: 90  FSTYAVPMIIGEIRRYLRDNS-PIRVSRSLRDTAYKAIYAKEGYIKRHMKEPTVQEIAEE 148

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + +  E +   L   + P+SL  P+  +  D   + D + DK   +  ++ I+     + 
Sbjct: 149 IGIAKEEIVYALDAIQMPMSLHEPVYSDGQDALFVMDQVSDKK--NKEENWIEEL---SL 203

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +  L  RE  ++ +RF  G     T  EV +Q  +++ ++ ++E  A++ ++     
Sbjct: 204 EAAMERLNERERYIITLRFFEG----KTQMEVAEQINISQAQVSRLEKNALKIMRKYLLG 259

Query: 674 K 674
           K
Sbjct: 260 K 260


>gi|328885347|emb|CCA58586.1| RNA polymerase sigma factor for flagellar operon [Streptomyces
           venezuelae ATCC 10712]
          Length = 258

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF 
Sbjct: 21  DERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFDVERAIKFE 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  ++ A+   +        IP  +R K   V R    +  +++R P+  E+A ++ 
Sbjct: 81  TYAITRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQLRRTPSETEVAAEMD 137

Query: 558 MPVEGVRKVLKITKEPISLETPIGDE----------DTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E     L      +SL   +  E          D   L D +ED  A +P++ A   
Sbjct: 138 ISLED----LHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTLEDTAADNPVEVAEDR 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            LR    R + +L  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L
Sbjct: 194 ELRRLLARAINTLPEREKTVVTLYYYEG----LTLAEIGHVLGVTESRVSQIHTKSVLQL 249

Query: 668 K 668
           +
Sbjct: 250 R 250


>gi|302544852|ref|ZP_07297194.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302462470|gb|EFL25563.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 315

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 62/297 (20%), Positives = 133/297 (44%), Gaps = 29/297 (9%)

Query: 379 LDPHWVSYA---------KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR- 428
            DP W + A         +  P+ + +       D + ++ +++  I     +S  + R 
Sbjct: 10  TDPSWSTRATVSSAHVPEQFVPDADAQALAGYSFDELTEL-SDLPEIPSFETVSPVDARA 68

Query: 429 ------HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
                   + ++ +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+
Sbjct: 69  LSKTLFERIEVLEEGTHEYAYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLI 128

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ +
Sbjct: 129 KAIDRFEPGRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQR 188

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVS 599
           + R PT  E+A++L +    V + +         SL+    ++D    L D I  ++   
Sbjct: 189 LDRAPTVHELAQRLDITTAEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGL 248

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                +     E+   ++A L  R++++L +RF        T  E+G++  +++  +
Sbjct: 249 EGIEYV-----ESLKPLIADLPARDKQILSLRFVAN----MTQSEIGEELGISQMHV 296


>gi|295836278|ref|ZP_06823211.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
 gi|197697357|gb|EDY44290.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
          Length = 279

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 67/268 (25%), Positives = 120/268 (44%), Gaps = 29/268 (10%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQF 470
           +S+      S+ E       + K   +A + +++++     LV  VA + +      ++ 
Sbjct: 20  ESVQRRAPQSVDEL----WRMYKTTGDARL-REQLILHYSPLVKYVAGRVSVGLPPNVEQ 74

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            D +  G  GL+ A EKFD     KF TYA+  ++ A+   +        IP  +R K  
Sbjct: 75  ADFVSSGVFGLIDAIEKFDIERSIKFETYAITRIRGAMIDELRALDW---IPRSVRQKAR 131

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED------ 584
            V R    +  K++R P+  E+A+++ + VE     L      +SL   +  E+      
Sbjct: 132 NVERAYATLEAKLRRTPSEAEVAREMGVGVED----LHAVFSQLSLANVVALEELLSVGS 187

Query: 585 ----TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                  + D +ED +A +P++ A    LR   +R + SL  RE+ V+ + +  G     
Sbjct: 188 EGGGRLSIMDTLEDTDADNPVEVAEGRELRRLLSRAINSLPEREKTVVMLYYYEG----L 243

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TL E+G    VT  R+ QI  K++ +L+
Sbjct: 244 TLAEIGHVLGVTESRVSQIHTKSVLQLR 271


>gi|154485093|ref|ZP_02027541.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
 gi|149734046|gb|EDM50165.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
          Length = 258

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 73/259 (28%), Positives = 128/259 (49%), Gaps = 17/259 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E + +   ++KG     +A+++ +  NLRLV+S+ ++++N      DL Q 
Sbjct: 14  SKLPLLTEDEKKELFKEIKKGN---EVAREKYIRGNLRLVLSILQRFSNSNENVDDLFQI 70

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA + FD  L  KFSTYA+  +   + R + D +  IR+   ++D  +K +   
Sbjct: 71  GCIGLIKAVDNFDDTLNVKFSTYAVPMISGELKRYLRDNA-AIRVSRSIKDIAYKAIYCK 129

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED 594
             +     REPT  EIAK++ +  E V   L   + P+SL  P+ D+  DT ++ D I D
Sbjct: 130 ENIIKTTHREPTVVEIAKEIGVEPEDVVYALDAIQSPVSLYDPVYDQGGDTLYVMDQISD 189

Query: 595 -KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            KN        I           L  L+ RE +++ MRF  G     T  E+  +  +++
Sbjct: 190 KKNKEEKWVENI------VLNEALKGLSERERKIIDMRFFNG----KTQMEIADEIGISQ 239

Query: 654 ERIRQIEAKAIRKLKHPSR 672
            ++ ++E  A++ +K    
Sbjct: 240 AQVSRLEKNALKAMKKYME 258


>gi|256393983|ref|YP_003115547.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256360209|gb|ACU73706.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 265

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 108/240 (45%), Gaps = 13/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +   + E    ++ ++   +     VA ++  RG    DL Q   +GL+KA + FD   
Sbjct: 27  KMSPDDSEYEALREYVIGEYMSYARFVAARFRLRGETQADLEQVAYLGLVKAVDNFDPDY 86

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   +   + R   D +  + +P   ++    V    R ++ ++ R P+  EI
Sbjct: 87  GATFLTYATPMIAGEVRRHFRDTTWHVHVPRRAQENALAVRAVERELTQQLGRAPSAAEI 146

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQAN 608
            ++L +  + V +  +        SL+ P+     D + LGD + D++            
Sbjct: 147 GRRLDLSADEVAEAYEASAAHHTASLDVPVAMADGDGASLGDLLGDED-----PGFDSVV 201

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE    +LA L+PR++R+L M+F        +  ++G +  V++ ++ ++ ++ I  L+
Sbjct: 202 DREALKPLLAELSPRDKRILLMKFFRN----MSQAQIGAEIGVSQMQVSRLLSQIIGSLR 257


>gi|319409355|emb|CBI82999.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 303

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 118/246 (47%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +F+    
Sbjct: 46  LRWKDKRDDKAMHQIAAAHMRLVISIASRFKRFKMPLSDLVQEGYVGLLEAAARFEPDRD 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---KIKREPT 548
            +FSTYA WW++ +I   I      +R       K     + R   ++      + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAQLVQDDSTMSKQDI 165

Query: 549 PEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHL--GDFIEDKN--AVSPLDS 603
              I++KL + V  V     + +    SL   + + D + +   D + D+     S ++ 
Sbjct: 166 FRVISEKLGVSVSDVETMDFRFSGTDNSLSMSVSENDDNSVTKLDTLVDEKPLPDSLIEK 225

Query: 604 AIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            I    R +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 VIDGQRRTQWLYDALQILNERELEIIR--FRRLNEESATLEFLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|283785667|ref|YP_003365532.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
 gi|282949121|emb|CBG88728.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
          Length = 239

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           ++L +PVE  R++L  T            E+     + + E+    +PL   +++NLR+ 
Sbjct: 122 ERLGIPVEEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLESNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIEALPEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|302147245|emb|CBL51744.1| RNA polymerase sigma-70 factor [Aeromonas sp.]
          Length = 262

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 105/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II          
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E                          E  A  +    S++       E++E
Sbjct: 51  -SGFVDPNEA-------------------------EDMAPTATHIGSELSEDDLADEDEE 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
              DEDED  +                   E+   Y          ++ QK+ ++    +
Sbjct: 85  EEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
                L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +  W   +    + I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKA-WSPRLTEMDEDIQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|302147229|emb|CBL51736.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
          Length = 262

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 57/300 (19%), Positives = 106/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                            D E  A  +    S++       E+++
Sbjct: 58  ---------------------------------DTEDMAPTATHIGSELSEDDLADEDED 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            + DEDED                      E+   Y          ++ QK+ ++    +
Sbjct: 85  EDKDEDEDGDNSDDDGDGGPDPEVAREKFAELRAQYEV------TRLSIQKNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +  W   +    + + +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKA-WSPRLMEMDEEVQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|302127757|emb|CBL51732.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|302147227|emb|CBL51735.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|302147233|emb|CBL51738.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
          Length = 262

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 57/300 (19%), Positives = 106/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                            D E  A  +    S++       E+++
Sbjct: 58  ---------------------------------DTEDMAPTATHIGSELSEDDLADEDED 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
            + DEDED                      E+   Y          ++ QK+ ++    +
Sbjct: 85  EDEDEDEDGDNSDDDGDGGPDPEVAREKFAELRAQYEV------TRLSIQKNGRAHDDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +  W   +    + + +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKA-WSPRLMEMDEEVQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|296448000|ref|ZP_06889906.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296254510|gb|EFH01631.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 289

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 61/274 (22%), Positives = 128/274 (46%), Gaps = 17/274 (6%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           R  +K+      +   E + +   +   +    +A  ++  A++RLVI++A ++ + GL 
Sbjct: 9   RELVKAAMEAPFLEREEEKQLA--IAWKDRRDGVALHKLASAHMRLVIALAVRFRHYGLP 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK- 528
             DL+QEG++GL++AA +F      +FSTYA WW++ +I   +      +R       K 
Sbjct: 67  VADLVQEGHVGLLEAAARFAPERDVRFSTYATWWIRASIQDYVLRNWSIVRGGTSSSQKA 126

Query: 529 -IHKVVRTARRMSNKIKREPT----PEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGD 582
               + R   ++++  +         + IA  + +    V     ++    +SL + + +
Sbjct: 127 LFFNLRRLRAKLAHAPQTAAESGDAFDAIAGAIGVSRADVELMNSRLAGSDVSLNSQLIE 186

Query: 583 ED---TSHLGDFIEDKN--AVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGM 636
           +D   ++   DF+ D        ++  + ++ R       L  L+ RE R+++       
Sbjct: 187 DDSASSAERMDFLVDDRPLPDEIVEDRLDSDRRARWLADALKLLSERELRIVQE--RRLS 244

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +  TLE +G +  +++ER+RQIE +A+ KL+  
Sbjct: 245 ESLVTLESLGDRLGISKERVRQIENRALCKLRKA 278


>gi|133478|sp|P12254|RPSK_BACSU RecName: Full=RNA polymerase sigma-K factor; AltName:
           Full=Sigma-27; AltName: Full=Stage IV sporulation
           protein CB; Flags: Precursor
          Length = 294

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 64/275 (23%), Positives = 117/275 (42%), Gaps = 7/275 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 8   ALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I  +      
Sbjct: 65  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEIVITKGGCIH 124

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
              I  ++               N              +   +    + LK TK+ +SL 
Sbjct: 125 PSLIRFNIYGVRIHNGNFFHDKVNNCFFIFKSMPPLFVMNNEILMHLRALKKTKKDVSLH 184

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +N        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 185 DPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKQYIDILDDREKEVIVGRFGL 243

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 244 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 278


>gi|209407284|emb|CAP72527.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 265

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 56/308 (18%), Positives = 112/308 (36%), Gaps = 46/308 (14%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M+++   P T  +++   + +      L +I  L   I P+  G
Sbjct: 3   GEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDG 60

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                      Q+ E  + +       + + D E     S+++       PE A      
Sbjct: 61  AA-------GPQEVEPEAPKAPAKAATDDKDDEEEDDSDSEEEEGDGGPDPEVARLRFGA 113

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + E  + +   L                                   +K  ++S +    
Sbjct: 114 VAEQLEKANKAL-----------------------------------KKHGRASQQAVEE 138

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQG 376
            E L  L   + L   + D LVE++ +   +I   E  +++L      + R  FL +   
Sbjct: 139 LEALAILFMPIKLVPKQYDALVERVRNALNQIRIQERAIMQLCVRDARMPRADFLRQFPS 198

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
            E++  W        +G++   +    + I + + ++  +  E  ++I++ + I   +  
Sbjct: 199 NEINLDWADQLAS-GKGKYAEAIGNRKEDIQRCQQKLIELQQECNLAIADIKDINRRMSI 257

Query: 437 GECEASIA 444
           GE +A  A
Sbjct: 258 GEAKARRA 265


>gi|260598417|ref|YP_003210988.1| flagellar biosynthesis sigma factor [Cronobacter turicensis z3032]
 gi|260217594|emb|CBA31853.1| RNA polymerase sigma factor for flagellar operon [Cronobacter
           turicensis z3032]
          Length = 239

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTADGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATELEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           ++L++P+E  R++L  T            E+     + + ED    +PL   ++ NLRE 
Sbjct: 122 ERLSIPLEEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEDNQNENPLHQLLEGNLRER 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIESLPEREQMVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|153876074|ref|ZP_02003579.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152067462|gb|EDN66421.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 242

 Score =  121 bits (302), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 110/232 (47%), Gaps = 9/232 (3%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           ++V ++LR V+ +A  Y   GL   DLIQEGNIGLMKA ++F+  +G +  ++A+ W++ 
Sbjct: 9   KLVISHLRFVLYIAHGYRGYGLPLADLIQEGNIGLMKAVKRFNPNVGVRLVSFAVHWIRA 68

Query: 507 AITRSIADQSCTIR-IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            I   I      ++ +    + K+   +R+ ++    + +    +          + +  
Sbjct: 69  EIHEFILRNWRIVKVVTTKAQRKLFFNLRSMKKRLGWLSQAEVDKVAQDLGVSSKDVLEM 128

Query: 566 VLKITKEPISLETPIGDEDTSHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLAS 619
             +++ + ++ + P+  +D   +     ++ED     A        +A+  +        
Sbjct: 129 EKRLSMQDVAFDAPVDSDDDDEVFAPAAYLEDNRYDPAALVEQDEWEAHGHKQLLHAFKK 188

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L  R + +L+ R+        TL+E+   + V+ ERIRQIE+ A++KLK   
Sbjct: 189 LDVRSQDILQQRWL--SEDKATLQELANHYKVSAERIRQIESNALKKLKKNM 238


>gi|4514519|dbj|BAA75458.1| RNA polymerase sigma subunit (SIGMA-70) [Acinetobacter sp.]
          Length = 278

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 118/316 (37%), Gaps = 39/316 (12%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+REGEI+IAKRIE G   ++ S+   P   + ++   ++   G   L +I  L   
Sbjct: 1   VELLTREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLQEYNDFLTGERRLADI--LSGY 58

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           + PE+             +  ED     +  DV+  + D E  ++   D   +    PE 
Sbjct: 59  LDPETDEDIPE-VLEEEAELEEDEDASPKAKDVKLDDDDEEEESEGDDDSEGESGPDPEV 117

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
           A+     L+   +++   ++                                   +  + 
Sbjct: 118 AKVRFSELEAAWNETKSVVA-----------------------------------RHGRD 142

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDV 369
           S + K   E L  +           D++ E +     +I  NE E++R A   G + R  
Sbjct: 143 SDEAKAALEALAAVFMMFKFTPRLFDIISEMIRGTHDQIRSNEREIMRYAVRRGRMDRTQ 202

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
           F      +E +P W+         E K  +      +L  + +I  I  + G+++ + + 
Sbjct: 203 FRMTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 262

Query: 430 IVSMVRKGECEASIAK 445
           I   +  GE +A  AK
Sbjct: 263 ISKRMAVGEAKARRAK 278


>gi|161898847|gb|ABX80413.1| SigB [Listeria monocytogenes]
          Length = 233

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 107/235 (45%), Gaps = 4/235 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 3   AAYQENGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 63  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 122

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 123 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 182

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL+
Sbjct: 183 EKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKLR 233


>gi|222053730|ref|YP_002536092.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. FRC-32]
 gi|221563019|gb|ACM18991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. FRC-32]
          Length = 251

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/253 (24%), Positives = 116/253 (45%), Gaps = 14/253 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAE 486
           + +  ++ +  A   + E+V ++L LV  +  +  +     L   DL     IGL+ AAE
Sbjct: 5   LKAYEQEAQRTAIPDRDELVVSHLPLVKFLVDRIASALPPHLDRDDLRSAAVIGLISAAE 64

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F T+A   ++  I   +  Q     +   +RDK  ++ R    +  ++ R 
Sbjct: 65  RFDPTRGVMFKTFAEQRIRGTIMDELRSQDW---LTRSLRDKFKRLEREFSALEQRLGRN 121

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLG--DFIEDKNAVSPLD 602
           P+ +E+A  + + +E    +L+       +SL+    DED S LG  D +EDK   SP +
Sbjct: 122 PSSDEVAAAMGLDLEAYFHLLEEIHFLSFVSLDDAWMDEDGSPLGLLDVLEDKGIESPQN 181

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             I     E     + +L  +E  V+ + +      +  L+E+G    +T  RI Q+ ++
Sbjct: 182 QLIARQTVENLAEAIDNLPEKERIVITLYY----YEEMNLKEIGAVLHLTESRISQLHSQ 237

Query: 663 AIRKLKHPSRSKK 675
           A+ +L+   +  +
Sbjct: 238 ALLRLRGRMKLHR 250


>gi|85710830|ref|ZP_01041891.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
 gi|85695234|gb|EAQ33171.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
          Length = 286

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 135/271 (49%), Gaps = 17/271 (6%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+S++    +S  + + +   +++ +     A KE++ ++LR V+ +A+ Y+  GL   
Sbjct: 21  YIQSVNRIPMLSAEKEKALAKRLQEDK--DLDAAKELIMSHLRFVVHIARGYSGYGLPQA 78

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      +++      +  K
Sbjct: 79  DLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRVVKVATTKAQR--K 136

Query: 532 VVRTARRMSNKIKREPTP--EEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDED---- 584
           +    R+M  ++        E +AK+L +  + V ++  +++    + E    D+D    
Sbjct: 137 LFFNLRKMKKRLGWFNQDEVETVAKELGVSSKEVMEMEARMSAHDQAFELSSDDDDSKEG 196

Query: 585 -TSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            T     ++EDK    A        +A+ ++     ++ L  R + +++ R+     +  
Sbjct: 197 STYSPAMYLEDKRSDLAEEIETEDYEAHTQKKLFSAMSELDERSQDIVQSRWL--SESKV 254

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           TL ++  ++ V+ ER+RQ+E  A++KL+   
Sbjct: 255 TLHDLAAKYEVSAERVRQLEQNAMKKLRAAM 285


>gi|167507977|gb|ABZ81309.1| RpoD [Thalassospira sp. MCCC 1A02758]
 gi|167507979|gb|ABZ81310.1| RpoD [Thalassospira sp. MCCC 1A02767]
 gi|167507981|gb|ABZ81311.1| RpoD [Thalassospira sp. MCCC 1A02785]
 gi|167507985|gb|ABZ81313.1| RpoD [Thalassospira sp. MCCC 1A02843]
 gi|167507987|gb|ABZ81314.1| RpoD [Thalassospira sp. MCCC 1A02866]
 gi|167507989|gb|ABZ81315.1| RpoD [Thalassospira sp. MCCC 1A02873]
 gi|167507997|gb|ABZ81319.1| RpoD [Thalassospira sp. MCCC 1A02935]
          Length = 257

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 63/255 (24%), Positives = 115/255 (45%), Gaps = 16/255 (6%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGT-----------EGHSYQKREDSSQEKERDDVQETE 227
            LLR++IDLE   G                      E  + +   D  +E E +  + T 
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAEEGEEADAEGDDFEAAAVETDADEDEEAETETPEPTG 60

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
                  +   ++        E   + +   D++ +    +LS ME++L  +V+   + I
Sbjct: 61  APASDEEEEDDEESDDDSEGEEGEGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKFELI 120

Query: 288 AEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           A+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ L
Sbjct: 121 AKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELLDHL 180

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK FV   
Sbjct: 181 TGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVGELPGKGWKAFVERY 240

Query: 403 VDSILKIRNEIKSIS 417
            D I ++R ++  +S
Sbjct: 241 PDEIAQLREQVGGVS 255


>gi|119514602|gb|ABL76113.1| SigB [Listeria monocytogenes]
 gi|119514606|gb|ABL76115.1| SigB [Listeria monocytogenes]
 gi|119514608|gb|ABL76116.1| SigB [Listeria monocytogenes]
 gi|119514610|gb|ABL76117.1| SigB [Listeria monocytogenes]
 gi|119514614|gb|ABL76119.1| SigB [Listeria monocytogenes]
 gi|119514618|gb|ABL76121.1| SigB [Listeria monocytogenes 690]
 gi|119514626|gb|ABL76125.1| SigB [Listeria monocytogenes]
 gi|119514630|gb|ABL76127.1| SigB [Listeria monocytogenes]
 gi|119514632|gb|ABL76128.1| SigB [Listeria monocytogenes]
          Length = 249

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 L 667
           L
Sbjct: 249 L 249


>gi|193222293|emb|CAL61487.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Herminiimonas arsenicoxydans]
          Length = 243

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 101/244 (41%), Gaps = 12/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                    +  +V  +  LV  +A +   +    ++  DLIQ G IGL+ A  +++   
Sbjct: 1   MYTAAGRSDRDHLVSEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVGRYEETH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA+  ++ A+   +         P  MR  + K+      +  K+ R P   E+
Sbjct: 61  GAQFETYAVQRIRGAMLDELRSSDWM---PRSMRQNMRKIEVAMNSLQQKLGRPPNESEV 117

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK+L + +   + +L      + +  E     ED  H  D      +  PL + +    R
Sbjct: 118 AKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFLDRYCTDESPDPLQNLMNTGFR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 + +L  RE+    +   +    +  L+E+G    VT  R+ Q+ ++AI +++  
Sbjct: 178 SAVIAAIEALPEREK----ILMSLYYEQEMNLKEIGAVMGVTESRVSQLHSQAIARMRAN 233

Query: 671 SRSK 674
            R K
Sbjct: 234 LREK 237


>gi|119514598|gb|ABL76111.1| SigB [Listeria monocytogenes]
 gi|119514600|gb|ABL76112.1| SigB [Listeria monocytogenes]
 gi|119514604|gb|ABL76114.1| SigB [Listeria monocytogenes]
 gi|119514612|gb|ABL76118.1| SigB [Listeria monocytogenes]
 gi|119514616|gb|ABL76120.1| SigB [Listeria monocytogenes]
 gi|119514620|gb|ABL76122.1| SigB [Listeria monocytogenes]
 gi|119514622|gb|ABL76123.1| SigB [Listeria monocytogenes]
 gi|119514624|gb|ABL76124.1| SigB [Listeria monocytogenes]
 gi|119514628|gb|ABL76126.1| SigB [Listeria monocytogenes]
 gi|119514634|gb|ABL76129.1| SigB [Listeria monocytogenes]
 gi|119514636|gb|ABL76130.1| SigB [Listeria monocytogenes]
 gi|119514638|gb|ABL76131.1| SigB [Listeria monocytogenes]
          Length = 249

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 L 667
           L
Sbjct: 249 L 249


>gi|223635921|emb|CAQ03762.1| RNA polymerase sigma factor [Grimontia hollisae]
          Length = 252

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 50/299 (16%), Positives = 101/299 (33%), Gaps = 50/299 (16%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            I IAKRIE G   +  S+ E P +  +L+   D++      L +II            G
Sbjct: 1   RIDIAKRIEDGINQVQVSVAEYPGSISSLLDQFDKVEAEELRLTDII-----------SG 49

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS--PPENAENDER 256
           F    +            E   + + + + D++       +D ++ D+   PE A     
Sbjct: 50  FVDPNQDDIAPTATHIGSELTDEQLDDEDDDVDDDDDEDSEDEAEEDTGIDPELAREKFN 109

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            L    +    ++                                   QK  +   +  V
Sbjct: 110 ELRVAYEGMQQSI-----------------------------------QKYGRFHEQTTV 134

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQ 375
              +L ++     L   + D LV ++ D   R+   E  ++RL      + +  F++   
Sbjct: 135 AIAELSEVFKQFRLVPKQFDRLVNEMRDTMDRVRTQERIIMRLCVDQAKMPKKTFVQLFA 194

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E    W+  A    +  +   +    + + +   ++K +  ETG+S+   + I   +
Sbjct: 195 GNESSDAWLDKALA-SDKPYAERLKQHEEDLRRCIQKLKIVEDETGLSVERVKDISRRM 252


>gi|218548541|ref|YP_002382332.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ATCC
           35469]
 gi|218356082|emb|CAQ88699.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia fergusonii
           ATCC 35469]
 gi|324113640|gb|EGC07615.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           fergusonii B253]
 gi|325496958|gb|EGC94817.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ECD227]
          Length = 238

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 109/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +   ++  ++ R  +  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAQAIGQLEQELGRNASETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           K+L +  E  R++L  T            E+     + I E+    +PL   ++++LR+ 
Sbjct: 122 KRLGISTEEYRQMLLDTNNSQLFSYDEWREEHGDSAELITEEHQQANPLHQLLESDLRQQ 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIERLPEREKLVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|237653596|ref|YP_002889910.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
 gi|237624843|gb|ACR01533.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
          Length = 257

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 110/238 (46%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             +    + K  +VE    LV  +A +  +R    +   DLIQ G +GL+ A  +++  L
Sbjct: 1   MYDAHGKLDKGGLVENYAPLVKRIAYQLMSRLPASVDVDDLIQNGMMGLLDALGRYEQGL 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA+  ++ A+   + +      +P  +R  + ++      +  +  R P+  E+
Sbjct: 61  GAQFETYAVQRIRGAMLDGLRENDW---LPRSLRRDMRRIEAAIHSLEQQNGRPPSESEL 117

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L +P+E  +++L+     + + LE    +ED  +L   +  +    PL      +LR
Sbjct: 118 AAALDLPLEDYQRMLQDARGHQLVYLEDFNREEDDDYLDRHLA-QEGNDPLTLLEDTDLR 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +  L  RE+ V+     +  + +  L E+G+   VT  R+ Q+ ++A+ +L+
Sbjct: 177 RRLVGAIEHLPEREQLVM----ALYYDEELNLREIGEVLGVTESRVCQLHSQAVARLR 230


>gi|223041647|ref|ZP_03611844.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
 gi|223017511|gb|EEF15925.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
          Length = 321

 Score =  121 bits (302), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 64/320 (20%), Positives = 140/320 (43%), Gaps = 10/320 (3%)

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++    + I+    +E       +   +   K           A    +   + + I+  
Sbjct: 1   MKNFDEHEIEDAEIVEAESIEPDEVELLDEDKHIEATHPALLSANMPVTTGNLESYIRMA 60

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL   DLIQE
Sbjct: 61  NQYPILTADQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPLADLIQE 118

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +        
Sbjct: 119 GNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRK 178

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS--HLGDFIE 593
            +       E   + +A  L +  E VR++  ++T + +  + P GD++        ++E
Sbjct: 179 NKNRLAWFNEEEIKRVAHDLGVSEEEVREMESRMTGQDLGFDLPSGDDEDEAYTPSMYLE 238

Query: 594 DKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           D ++    +   + +  E        L++L  R + +++ R+        TL ++  ++ 
Sbjct: 239 DNSSNFADELEDEEHTGEATAQLAYALSTLDERSQDIIKTRWLDEN--KLTLHDLAAKYQ 296

Query: 651 VTRERIRQIEAKAIRKLKHP 670
           ++ ER+RQ+E  A++K+K+ 
Sbjct: 297 ISAERVRQLENAALKKIKNA 316


>gi|148273835|ref|YP_001223396.1| putative RNA polymerase sigma factor SigF [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
 gi|147831765|emb|CAN02734.1| putative RNA polymerase sigma factor, SigF-homolog (stress
           response/stationary phase sigma factor) [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
          Length = 335

 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 104/229 (45%), Gaps = 11/229 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
                ++V  +L L   +A++++ R   + DL Q G +GL+KAA ++D   G  F ++A+
Sbjct: 83  RRLHDQIVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAI 142

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R + D    +R P H+++  H ++     ++ ++ R PT  E+A       E
Sbjct: 143 PTISGEIKRHLRDNGWVVRPPRHVQELRHALLAVVPALTQRLGRTPTDAELAAHTGHARE 202

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V + L    +  P SL+  + +++   L D I   +         +A            
Sbjct: 203 EVVEALAAHSSLRPASLDFTVHEDEGISLADTIGADD-----PGYARAERTVLLDAARGV 257

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+ R+ R+L +RF    +      E+  +  VT+ ++ ++ A+ +  L+
Sbjct: 258 LSDRDRRILHLRFVDECSQS----EIAAELGVTQMQVSRLLARILGALR 302


>gi|167507983|gb|ABZ81312.1| RpoD [Thalassospira sp. MCCC 1A02803]
 gi|167507993|gb|ABZ81317.1| RpoD [Thalassospira sp. MCCC 1A02898]
          Length = 262

 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 63/260 (24%), Positives = 115/260 (44%), Gaps = 21/260 (8%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR++IDLE   G   +                D+  + E  +    + D E+  +   
Sbjct: 1   LLLRDVIDLETTYGGGPEAEIAAAEGEDEEDTDVDAEADVESFESANDDDDEEAETETPA 60

Query: 239 D----------------DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                            ++S+ +        D+ + D++ +    +LS ME++L  +V+ 
Sbjct: 61  GLTDEAEEDEDEEDDESEKSEDEEGEGEGRGDDDDDDDENEQVNVSLSKMEEELTEQVLE 120

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDL 337
             + IA+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ 
Sbjct: 121 KFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNNFRIEE 180

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK 
Sbjct: 181 LLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKT 240

Query: 398 FVACEVDSILKIRNEIKSIS 417
           FV    + I  +R  I  +S
Sbjct: 241 FVERYSEEIANLREGIGGVS 260


>gi|42566462|gb|AAS21043.1| major sigma factor 70 [Deinococcus grandis]
 gi|42566464|gb|AAS21044.1| major sigma factor 70 [Deinococcus proteolyticus]
          Length = 168

 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 88/167 (52%), Positives = 118/167 (70%), Gaps = 2/167 (1%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA- 557
           YA WW++QAI R+IADQ+ TIRIPVHM + I+K+ RTAR++  ++ RE T EEIA+ +  
Sbjct: 2   YATWWIRQAINRAIADQARTIRIPVHMVETINKLTRTARQLQQELSREATYEEIAEAMGP 61

Query: 558 -MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                 V +V K+++EP+SLETPIGDE  S  GDFI D+N  SP+++A +  L E   + 
Sbjct: 62  GWDAAKVEEVQKVSQEPVSLETPIGDEKDSFYGDFIPDENLDSPVENAAKTLLSEELEKA 121

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           L+ LT RE  VL+ R G+    +HTLEEVG++F VTRERIRQIE KA
Sbjct: 122 LSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKA 168


>gi|290769931|gb|ADD61700.1| putative protein [uncultured organism]
          Length = 259

 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 131/268 (48%), Gaps = 13/268 (4%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + +        + ++ +     A++  ++ NLRLV+SV +++ N  
Sbjct: 2   ALNKVEICGVNTSTLPVLNQEEKEELFKRIKAGDEEARELYIKGNLRLVLSVIRRFQNSS 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAIDNFDTTLQVKFSTYAVPMIVGEIRRYLRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K + T      +  +EPT  EIA ++ +  E +   +   + P+SL  P+  E  DT
Sbjct: 121 IAYKTIYTRENYMRQHLKEPTIAEIADEIGIDKEMIVYAMDAIQSPVSLFEPVYSEGGDT 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I DK      +     +LR+     +  L  RE  ++ +RF  G     T  EV
Sbjct: 181 LYVMDQISDKKNRE-ENWVEDISLRD----AMNRLGERERHIIDLRFYEG----KTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +  +++ ++ ++E  A+R +++  R+
Sbjct: 232 ADEIGISQAQVSRLEKHALRSMRNYLRN 259


>gi|210608669|ref|ZP_03287946.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
 gi|210152926|gb|EEA83932.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
          Length = 259

 Score =  120 bits (301), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 70/264 (26%), Positives = 134/264 (50%), Gaps = 13/264 (4%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V+T  + + +     ++  K +     AK++ ++ NLRLV+SV K++TN  
Sbjct: 2   ALNKVEICGVDTSKLPLLKEEEKNALFAKIKAGDEGAKEQYIKGNLRLVLSVIKRFTNSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA   F+  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K +        +  REPT +EI++++ +  E +   +   + P+SL  P+ ++  D 
Sbjct: 121 TAYKAIYAKEGYMKRNLREPTLQEISEEIGIAKEDIVFAMDAIQAPMSLNEPVYNDGGDA 180

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            ++ D I DK   +  ++ I+          +  L  RE+ ++R+RF  G     T  EV
Sbjct: 181 LYVMDQISDKK--NKEENWIEEL---ALQAAMEHLGEREKYIIRLRFFEG----RTQMEV 231

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            +   +++ ++ ++E  A++ ++ 
Sbjct: 232 AEDIDISQAQVSRLEKHALKVMRQ 255


>gi|298250481|ref|ZP_06974285.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
 gi|297548485|gb|EFH82352.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
          Length = 313

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 79/302 (26%), Positives = 138/302 (45%), Gaps = 43/302 (14%)

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           + +   F     D ++ +   I+    + G +  +FR + +       +   AK  +VEA
Sbjct: 21  KRDIAGFSLLSPDEVVGLAQRIEGAGKQRG-TRLQFRTVSA--DGANPDVQQAKNRLVEA 77

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           NLRLV SVA +Y   G+  +DLIQEGNIGL+ A EKFD   GY+FSTYA  W++Q I R 
Sbjct: 78  NLRLVRSVAYQYRGFGVDIMDLIQEGNIGLIHAVEKFDPTKGYRFSTYATHWIRQYICRE 137

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +A Q   IRIP+++++++  +         +  ++    ++                   
Sbjct: 138 LARQIHKIRIPLYLQEQLRHLPEAPTTPDGQAMQDQAHAKLMVAYERSKA---------- 187

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--ASLTPREERVLR 629
             +S +    + +            A +P    +Q   R+   ++   A LT RE +VL 
Sbjct: 188 THVSFDAVPFEFEDP----------APTPEQYCMQGAQRQLLHQLFLRAGLTQRERQVLV 237

Query: 630 MRFGIGMNTDHTLE------------------EVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +R+G+    +  LE                  ++G Q  ++ E +RQIE +A+ KL++  
Sbjct: 238 LRYGLQQQREEGLEALLSGAISDQKQDESTYPQIGTQLGLSHEAVRQIEMRALLKLRYQV 297

Query: 672 RS 673
           ++
Sbjct: 298 QA 299


>gi|297154338|gb|ADI04050.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 268

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 112/249 (44%), Gaps = 15/249 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + +EF  I  +    + EA   ++++VEA + +   +A +Y NRG    DL Q   +GL+
Sbjct: 22  TSAEFERIAELPDGPQKEAL--RQQVVEAWIPMADRLAGQYRNRGESLEDLRQVAALGLV 79

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA  ++D   G  F ++A+  V   I R   D    + +P  +++  ++V    R +S+ 
Sbjct: 80  KAVNRYDPGRGSAFESFAVPTVVGEIKRHFRDHLWALHVPRRVQELRNRVRTAHRELSHS 139

Query: 543 I-KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAV 598
           +  R P  EEIA +  +  E VR  +    +  P+SL+ P+   D  + L D +      
Sbjct: 140 LDDRAPDVEEIADRTGLSEEDVRTGVAALDSFAPLSLDAPLTGTDDGYALRDTLG----- 194

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               +  +   RE     L  L  RE R+L MRF   M      E    Q  +++  + +
Sbjct: 195 EQEPAYDRVVDREAVRSGLCRLPERERRILYMRFFCDMTQSRIAE----QLGISQMHVSR 250

Query: 659 IEAKAIRKL 667
           +  +   +L
Sbjct: 251 LINRTCSRL 259


>gi|146309186|ref|YP_001189651.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina ymp]
 gi|145577387|gb|ABP86919.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas mendocina ymp]
          Length = 284

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 116/269 (43%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHAVNSIPLLTPEQERELAESL--YYQQDLEAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W++  I   I      +++      R
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQR 134

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI----TKEPISLETPIGD 582
                +    +R++     E T   +A+ L +    VR++                   D
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVTA--VAESLGVEPHEVREMESRLTGQDMAFDPASDADDD 192

Query: 583 EDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   ++ED     A    D+    +        L SL  R   +L  R+       
Sbjct: 193 SAFQSPAHYLEDHRYDPARQLEDADWSDSSSSNLHEALESLDERSRDILYQRWLAE--EK 250

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++  ++ V+ ERIRQ+E  A+ KLK
Sbjct: 251 ATLHDLAAKYNVSAERIRQLEKNAMNKLK 279


>gi|108760621|ref|YP_631554.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
 gi|108464501|gb|ABF89686.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
          Length = 246

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 116/229 (50%), Gaps = 10/229 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ANLR V+ VA +Y + G++  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 508 ITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKRE--PTPEEIAKKLAMPVEGV 563
           I   I      +++      R     + RT R +      +     ++IA++L +    V
Sbjct: 61  IQNYILKSWSLVKLGTTQAQRKLFFSLARTRRELEKFGSGDAAVNVDDIARRLHVKPGEV 120

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLAS 619
           R++  ++    +SL+ P+G++  +   DF+    A    + A +     +       L  
Sbjct: 121 REMEQRMGGRDLSLDAPMGEDGGNSHVDFVVSAAAPQDDEFADKEEAGLINARVRTALMR 180

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PRE  ++     +      TL+E+G+ F  +RER RQ+E +A  KLK
Sbjct: 181 LDPRERFIIEQ--RVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLK 227


>gi|16760902|ref|NP_456519.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765294|ref|NP_460909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29141406|ref|NP_804748.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|62180530|ref|YP_216947.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|161936245|ref|YP_150204.2| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|194736051|ref|YP_002114988.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195873263|ref|ZP_02696436.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197263158|ref|ZP_03163232.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197301170|ref|ZP_02664251.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204931059|ref|ZP_03221885.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205357293|ref|ZP_02346566.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|207856530|ref|YP_002243181.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|224583543|ref|YP_002637341.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|289810757|ref|ZP_06541386.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
 gi|61224055|sp|P0A2E8|FLIA_SALTY RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|61224057|sp|P0A2E9|FLIA_SALTI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|25331353|pir||AF0750 RNA polymerase sigma transcription factor for flagellar operon fliA
           [imported] - Salmonella enterica subsp. enterica serovar
           Typhi (strain CT18)
 gi|556579|dbj|BAA00389.1| sigma factor [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|4115509|dbj|BAA36397.1| FliA [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16420491|gb|AAL20868.1| sigma F (sigma 28) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503199|emb|CAD05705.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137033|gb|AAO68597.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi str.
           Ty2]
 gi|62128163|gb|AAX65866.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|194711553|gb|ACF90774.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195634506|gb|EDX52858.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197241413|gb|EDY24033.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197288040|gb|EDY27427.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204320103|gb|EDZ05308.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205322652|gb|EDZ10491.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|206708333|emb|CAR32636.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|224468070|gb|ACN45900.1| flagellar biosynthesis sigma factor FliA [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|261247122|emb|CBG24945.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|267993942|gb|ACY88827.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158470|emb|CBW17980.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|320085426|emb|CBY95207.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|322715006|gb|EFZ06577.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130234|gb|ADX17664.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323250213|gb|EGA34105.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|332988845|gb|AEF07828.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 239

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 111/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           ++L +PV   R++L  T            E+     + + E+    +PL   ++ +LR+ 
Sbjct: 122 ERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIESLPEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|222151972|ref|YP_002561132.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
 gi|222121101|dbj|BAH18436.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
          Length = 255

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 118/248 (47%), Gaps = 9/248 (3%)

Query: 429 HIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I + ++   + +   A+KE+V    +LV S+A +Y+       DL+Q G +GL+ A  +
Sbjct: 13  EINAWIKLYQDTQDEFAQKELVLHYQKLVESLAYRYSKGQSHHEDLVQVGMVGLLGAINR 72

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   K+ R    ++N++ R P
Sbjct: 73  FDVTFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPKIKRATDELTNELGRSP 132

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
              EIA+++    E V + +++  +   +S++  I  +        ++            
Sbjct: 133 KIIEIAQRIEATEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDVMGNTEEGYDLT 192

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    +VL  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 193 EK--RMILEKVLPILSDREREIIQCTFLDG----LSQKETGEKIGLSQMHVSRLQRTAIK 246

Query: 666 KLKHPSRS 673
           KL+   ++
Sbjct: 247 KLRDAVQN 254


>gi|2660755|gb|AAC29510.1| sigma-B general stress transcription factor [Bacillus
           licheniformis]
          Length = 265

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 122/258 (47%), Gaps = 6/258 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   S  T ++ +E   ++   +  + +   A+  +V+    LV ++AKKY+       D
Sbjct: 3   MAQPSKTTKLTKTEVDTLIK--KYQDSQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHED 60

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G +GL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++
Sbjct: 61  LCQVGMLGLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRI 120

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                 ++N+ +R P  +EIA+ L +  E V + +++ K   +L      E  +      
Sbjct: 121 KMAVDHLTNETQRSPKVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEADADGSTVT 180

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S  +   + N +     VL  L+ RE++++ + +      + + +E G    ++
Sbjct: 181 ILDIVGSQEEGYEKVNQKLMLESVLHVLSDREKQIIELTY----IQNKSQKETGDMLGIS 236

Query: 653 RERIRQIEAKAIRKLKHP 670
           +  + +++ KA++KL+  
Sbjct: 237 QMHVSRLQRKAVKKLREA 254


>gi|291196338|emb|CBG22641.1| DNA-directed RNA polymerase subunit D [Pseudomonas meridiana]
          Length = 238

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 50/284 (17%), Positives = 105/284 (36%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +  V+  +   +  A+ S DD  +V+S P+               
Sbjct: 50  GITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDDEEVESGPDPI------------I 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  + S +       L +L
Sbjct: 97  AAQRFGAVSDQM------------ELARKALK---------KHGRGSKQATAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEI 238


>gi|78043803|ref|YP_360778.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77995918|gb|ABB14817.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 121/244 (49%), Gaps = 10/244 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + I  ++ K +     A+++++  NL+LV  V +++ +RG +  DL Q G IGL+KA +
Sbjct: 18  EQEIKELIEKAQKGDVAAREKLINCNLKLVFKVVERFLHRGYEVEDLFQIGTIGLIKAID 77

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R + D    IRI    ++   K+++    ++ K+ RE
Sbjct: 78  KFDLKQQVKFSTYAVPMIVGEIRRFLRD-DQAIRISRSTKELGVKILKEKEALTVKLGRE 136

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E+ + L    E + + L+  +   SL   +  +D    GD I   + +       Q
Sbjct: 137 PTIAELEETLGYSREAIVEALEAGQSLASLFETVHQDD----GDPIYLLDQIKQEGDEEQ 192

Query: 607 ANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L   +   VL+ L PRE  +L  RF      + T  E+ +   +++ ++ ++E +A+ 
Sbjct: 193 TLLENISIKEVLSKLEPRERYILINRFF----KEKTQMEIARTLGISQVQVSRLERQALL 248

Query: 666 KLKH 669
           KLK 
Sbjct: 249 KLKR 252


>gi|240948113|ref|ZP_04752523.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
 gi|240297593|gb|EER48085.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
          Length = 321

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 64/320 (20%), Positives = 140/320 (43%), Gaps = 10/320 (3%)

Query: 357 LRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           ++    + I+    +E       +   +   K           A    +   + + I+  
Sbjct: 1   MKNFDEHEIEDAEIVEAESIEPDEVELLDEDKHIEATHPALLSANMPVTTGNLESYIRMA 60

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +    ++  + + +    R    E   A K+++ +++R VI +A+ Y   GL   DLIQE
Sbjct: 61  NQYPILTADQEKELAE--RYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPLADLIQE 118

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++      +        
Sbjct: 119 GNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRK 178

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS--HLGDFIE 593
            +       E   + +A  L +  E VR++  ++T + +  + P GD++        ++E
Sbjct: 179 NKNRLAWFNEEEIKRVAHDLGVSEEEVREMESRMTGQDLGFDLPSGDDEDEAYTPSMYLE 238

Query: 594 DKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           D ++    +   + +  E        L++L  R + +++ R+        TL ++  ++ 
Sbjct: 239 DNSSNFADELEDEEHTGEATAQLAYALSTLDERSQDIIKTRWLDEN--KLTLHDLAAKYQ 296

Query: 651 VTRERIRQIEAKAIRKLKHP 670
           ++ ER+RQ+E  A++K+K+ 
Sbjct: 297 ISAERVRQLENAALKKIKNA 316


>gi|270265483|emb|CBI68359.1| DNA-directed RNA polymerase subunit D [Pseudomonas fulva]
          Length = 241

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 45/288 (15%), Positives = 93/288 (32%), Gaps = 48/288 (16%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++   D +      L +++            
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVL-----------S 49

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
           G+    +  +    E      +    +E   D E  +    ++ ++    P  A      
Sbjct: 50  GYIDPDDNIAAPTDEVPIPGAKTAAAKEESEDEEEESDSDDEEETESGPDPVVAAQRFGA 109

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +                                    LQ      +K+ +   +    
Sbjct: 110 VSD-----------------------------------QLQATNKVLKKNGREHKESVAA 134

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQG 376
            + L  L   + L   + ++LVE++     R+   E  +++L      + R  FL     
Sbjct: 135 LQALADLFMPIKLVPKQFEVLVERVRSALSRLRQQERAIMQLCVRDARMPRADFLRMFPS 194

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            E D  W           W   +  +  +I+  + ++  +  ETG+++
Sbjct: 195 NETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTV 241


>gi|256783362|ref|ZP_05521793.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289767236|ref|ZP_06526614.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289697435|gb|EFD64864.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
          Length = 263

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 105/246 (42%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E +A   +  ++   L +   +A ++  RG    DL Q   +GL+KA +
Sbjct: 22  FERLAGLPEGPERKAL--RDNLIRVWLPMAERIAVRFRGRGENLEDLYQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
            +D   G+ F  YA+  V   I R   D   T+ +P  ++D  ++V ++A+ ++     R
Sbjct: 80  HYDPERGHAFEAYAVPTVTGEIKRHFRDHMWTLHVPRRIQDLRNRVRKSAKELAQTTPGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT EEIA+   +    VR  ++  +    +SLE  +   D   LGD +   +       
Sbjct: 140 APTVEEIAEHAQLTTAEVRTGMEALECFSALSLEAEMPGTDGYALGDALGGPDPAFDAVV 199

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      L +L  RE  +L +RF  GM        + +Q  +++  + ++    
Sbjct: 200 D-----RVAVRPCLEALPERERTILYLRFFGGMTQSR----IAQQLGISQMHVSRLLTGC 250

Query: 664 IRKLKH 669
             +++ 
Sbjct: 251 FDRIRE 256


>gi|307327205|ref|ZP_07606393.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306887096|gb|EFN18094.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 272

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 115/250 (46%), Gaps = 15/250 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + +EF  +  +    E EA   ++ +VEA + +   +A++Y NRG    DL Q   +GL+
Sbjct: 26  TSAEFAEMARLPDGPEKEAL--RRRVVEAWMPMAERLARQYRNRGESLEDLEQVAALGLV 83

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN- 541
           KA +++D   G  F+ +A+  +   I R   D    + +P  ++D  ++V    R +S+ 
Sbjct: 84  KAVKRYDPEHGTAFAGFAVPTIVGEIKRHFRDHLWVLHVPRRVQDLRNRVRAAHRELSHS 143

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAV 598
              R P  ++IA++  +  + VR  ++   +  P+SL+  +   +D   L D +  + A 
Sbjct: 144 ADDRPPRTQDIAERTGLTEKEVRAGMEAMGSFTPLSLDAQLTGSDDGYSLADTLGAQEAA 203

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +   RE     L+ L  RE ++L MRF   M      E    Q  +++  + +
Sbjct: 204 -----YDRVVDREAVRPGLSRLPERERQILYMRFFCDMTQSRIAE----QLGISQMHVSR 254

Query: 659 IEAKAIRKLK 668
           +  +    L+
Sbjct: 255 LINRTCSTLR 264


>gi|167507935|gb|ABZ81288.1| RpoD [Thalassospira sp. MCCC 1A01288]
 gi|167507939|gb|ABZ81290.1| RpoD [Thalassospira sp. MCCC 1A01318]
 gi|167507943|gb|ABZ81292.1| RpoD [Thalassospira sp. MCCC 1A01423]
 gi|167507947|gb|ABZ81294.1| RpoD [Thalassospira sp. MCCC 1A01449]
          Length = 266

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 65/264 (24%), Positives = 117/264 (44%), Gaps = 25/264 (9%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS--------------------SQEK 218
            LLR++IDLE   G                +   ++                    S E+
Sbjct: 1   LLLRDVIDLETTYGGGPDAAAIGEEGEGDDEDDVEAVFSPLESSDDEEEDDEKEVESPEQ 60

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
                   E  + S  +  +DD  + D   E    ++ + D++ +    +LS ME++L  
Sbjct: 61  PLSASPARERKVSSDDEDDEDDDDEEDGDGEEGSGEDDDEDDENEQVNVSLSKMEEELTE 120

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQS 333
           +V+   ++IA+ Y +L   Q+  +      ++       +   LK+++V L+  + LN  
Sbjct: 121 QVLEKFEKIAKTYEKLHKAQEQRLAAMNKGETVPAATEKRYGKLKQEMVDLMEDVHLNNF 180

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
           RI+ L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+         
Sbjct: 181 RIEELLDHLTGLNNRLLGLEGKLLRYADRCKIKRPDFVKQYQGNELDPNWMERVGALSGK 240

Query: 394 EWKNFVACEVDSILKIRNEIKSIS 417
            WK FV    D I ++R  I  +S
Sbjct: 241 GWKLFVERYPDEIAQLREGIGGVS 264


>gi|16799967|ref|NP_470235.1| RNA polymerase sigma factor SigB [Listeria innocua Clip11262]
 gi|16413344|emb|CAC96126.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria innocua
           Clip11262]
 gi|30266013|gb|AAN16084.1| SigB [Listeria monocytogenes]
          Length = 259

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 114/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|213958514|gb|ACJ54678.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm1R]
          Length = 257

 Score =  120 bits (301), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 46/303 (15%), Positives = 100/303 (33%), Gaps = 47/303 (15%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   +M ++   P T   ++     +      L +++            G+ 
Sbjct: 1   EIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYI 49

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              +G +    E       +    + + D + A   + D+      P             
Sbjct: 50  DPDDGIAPPAAEVPPPVDPKAVKADDDTDDDDAEATTDDEEEAESGPDPVIAAQRFGAVS 109

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+ +          +     +  L  +AE++                             
Sbjct: 110 DQMEITRKALKKHGRGNKLAIAELVLLAELF----------------------------- 140

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGREL 379
                  + L   + + LVE++     R+   E  +++L      + R  FL +  G E+
Sbjct: 141 -----MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 195

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
           D  W        + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE 
Sbjct: 196 DESWSDGLAK-GKSKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEIKDINRRMSIGEA 254

Query: 440 EAS 442
           +A 
Sbjct: 255 KAR 257


>gi|226361251|ref|YP_002779029.1| RNA polymerase sigma factor SigF [Rhodococcus opacus B4]
 gi|226239736|dbj|BAH50084.1| RNA polymerase sigma factor SigF [Rhodococcus opacus B4]
          Length = 265

 Score =  120 bits (301), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 107/254 (42%), Gaps = 18/254 (7%)

Query: 424 ISEFRHIVSMVRKGECEAS------IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
             E++ + ++ R+              +  +V   L L   +A+++  RG    DL+Q  
Sbjct: 15  PDEYQDVTALFRQMAALDEDDPRRSRLRDAVVTRCLPLAEHIARRFDGRGEAHDDLVQVA 74

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+ + ++FD   G  F ++A+  +   + R   D    +R+P  M++    + +   
Sbjct: 75  RLGLVNSVDRFDVERGSDFVSFAVPTIMGEVRRHFRDTGWAVRVPRRMKELHLALSQAVA 134

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLE-TPIGDEDTSHLGDFIED 594
            +S  +   PT  E+A+ L +  E V + L      + +S++ T         + + + D
Sbjct: 135 ELSQSLGHAPTVSELAEHLDLEQEEVAQGLLAGNAYQTVSVDNTSSDRAGELSMVETLGD 194

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +A             ET   +L SL  RE  VL +RF        T  ++  +  +++ 
Sbjct: 195 YDAA-----MDDVENHETLRPLLQSLPERERTVLMLRFFGN----MTQTQIADRVGISQM 245

Query: 655 RIRQIEAKAIRKLK 668
            + ++ AK +  L+
Sbjct: 246 HVSRLLAKTLASLR 259


>gi|239832848|ref|ZP_04681177.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
 gi|239825115|gb|EEQ96683.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
          Length = 278

 Score =  120 bits (301), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 125/267 (46%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 2   IRSAMSAPYLEREEERDLA--IRWRELKDQEALHRITSAHMRLVISMAGRFRKFKLPMND 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++AA +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 60  LIQEGYVGLLEAAARFDPEREVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFF 119

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL  P+  E++ 
Sbjct: 120 NLRRLRSKLAQSDDTMSKAEIYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNSEESG 179

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++    +     L +L  RE  ++R R         T
Sbjct: 180 ASRRMDFLVDDHPLQDEIAESSIDMERRNQWLNVALDTLNERELHIIRERRLDDDGV--T 237

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  +++ER+RQIE++A+ KLK
Sbjct: 238 LEALGEKLGISKERVRQIESRAMEKLK 264


>gi|134036998|gb|ABO47837.1| truncated sigma 38 factor [Escherichia coli]
 gi|134037001|gb|ABO47839.1| truncated sigma 38 factor [Escherichia coli]
          Length = 240

 Score =  120 bits (301), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 73/189 (38%), Positives = 123/189 (65%), Gaps = 3/189 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIED 594
             L D + D
Sbjct: 232 KALLDILAD 240



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|198284078|ref|YP_002220399.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218665176|ref|YP_002426733.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248599|gb|ACH84192.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218517389|gb|ACK77975.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 285

 Score =  120 bits (301), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 123/243 (50%), Gaps = 6/243 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + ++R+       A+  ++ A++ LV +VA+ Y N+GL   DL+QEG +GL++A ++
Sbjct: 41  KQELQLIRRLRRGDECARATLISAHMPLVRAVARGYRNKGLSQEDLLQEGYMGLLRAVDR 100

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F   LG +FS+YA WW+++A+ R++  +S  IR+P ++   +H  +++     +      
Sbjct: 101 FQEGLGTRFSSYATWWIREAMQRAL-IRSRFIRLPDYLAKSLHAYMQSGAEEDSDAGV-- 157

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             E+  + L +    +R +        SL+  I  +    +     D    SP     + 
Sbjct: 158 RREQRREALGVRESTMRALDFADIRVFSLDEEI-SDGPGRIEQVTGD--VASPDSDYDRD 214

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            + +     L  L  ++  V+  R+G+  +   TLE V ++  V+RE +RQ++ +A+ +L
Sbjct: 215 AICKALREHLTELNEKQREVMVFRYGMHGDAPMTLEAVAERMGVSREAVRQLQVRALTRL 274

Query: 668 KHP 670
           +  
Sbjct: 275 RQS 277


>gi|332799331|ref|YP_004460830.1| RNA polymerase sigma-28 subunit SigF [Tepidanaerobacter sp. Re1]
 gi|332697066|gb|AEE91523.1| RNA polymerase, sigma 28 subunit, SigF [Tepidanaerobacter sp. Re1]
          Length = 240

 Score =  120 bits (301), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 132/240 (55%), Gaps = 8/240 (3%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I+ ++++ +     A+ E+V  NL LV S+ K++ NRG +  DL Q G+IGL+KA EKFD
Sbjct: 6   IMELLKEAKRGEKKARDELVSLNLGLVWSIVKRFNNRGYEPEDLFQIGSIGLLKAIEKFD 65

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +    KFSTYA+  +   I R I D    I++   +++  +K+ +T   ++N + REPT 
Sbjct: 66  FSYDVKFSTYAVPMIMGEIRRYIRD-DKPIKVSRSLKELGYKIQKTQEELTNTLDREPTI 124

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EI+ ++ +PVE +   ++ ++  +SL   +  +D S +  ++ D+   +     +  + 
Sbjct: 125 NEISDEMEVPVEEIVMAMEASQSLVSLNDVVYQDDGSPI--YLIDQLNENEYQENLLHD- 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L+ L   E +++ +R+      D T  +V K+  +T+ ++ ++E K + K+K+
Sbjct: 182 KIALKEALSKLDRDERQIITLRYF----KDMTQIDVAKKLNMTQVQVSRLERKVLTKVKN 237


>gi|290956233|ref|YP_003487415.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645759|emb|CBG68850.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 262

 Score =  120 bits (301), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 59/228 (25%), Positives = 106/228 (46%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++EA L +   +A ++ +RG  + DL Q  ++GL+KA +++D  LG  F +YA+  +
Sbjct: 36  RDRIIEAWLPMAERLAGRFRSRGESYEDLRQVASLGLVKAVDRYDPELGNAFESYAVPTI 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V    + +S  I  R PT  EIA+   M  E V
Sbjct: 96  TGEIKRHFRDHMWTLHVPRRVQDLRNRVRFATQDLSQTISGRRPTVAEIAEHANMSEEDV 155

Query: 564 RKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           R  L+   +   +SL+  +   ED   L D +   +             RE     LA+L
Sbjct: 156 RVGLEALESFTALSLDAELPGSEDGYSLSDALGSADPALDTVVD-----REAVKPRLAAL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L MRF   M      +E      +++  + ++ ++   +L+
Sbjct: 211 PERERAILYMRFFGDMTQSRIADE----LGISQMHVSRLISRCCDRLR 254


>gi|291196378|emb|CBG22661.1| DNA-directed RNA polymerase subunit D [Pseudomonas proteolytica]
          Length = 238

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 50/284 (17%), Positives = 105/284 (36%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +  V+  +   +  A+ S DD  +V+S P+               
Sbjct: 50  GITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDEEEVESGPDPI------------I 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  + S +       L +L
Sbjct: 97  AAQRFGAVSDQM------------ELARKALK---------KHGRGSKQATAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEI 238


>gi|322421664|ref|YP_004200887.1| RNA polymerase sigma 28 subunit FliA/WhiG [Geobacter sp. M18]
 gi|320128051|gb|ADW15611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M18]
          Length = 250

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 111/236 (47%), Gaps = 14/236 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V ++L LV  +  +  +     L   DL     IGL+ AAE+FD   G +F T+A 
Sbjct: 20  RDELVVSHLPLVKFIVDRIASSLPPHLDRDDLRSAAVIGLISAAERFDPSRGVQFKTFAE 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +  Q     +   +RDK  K+ +   ++  ++ R P+ +E+A  + + ++
Sbjct: 80  QRIRGTIMDELRAQDW---LTRSLRDKFKKLEKEFSQLEQRLGRNPSSDEVATAMGLELK 136

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVL 617
              ++L+       +SL+    DED +  G  D +EDK   SP +  I     E     +
Sbjct: 137 DYFRLLEEIHLLSFVSLDDAWHDEDGAPFGLLDVLEDKGTESPQNQLIARQTVERLAEAI 196

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +L  +E  V+ + +      +  L+E+G    +T  RI Q+ ++AI +L+   + 
Sbjct: 197 DTLPEKERIVITLYY----YEELNLKEIGAVLDLTESRISQLHSQAIIRLRGKMKR 248


>gi|291196304|emb|CBG22624.1| DNA-directed RNA polymerase subunit D [Pseudomonas gessardii]
          Length = 238

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 50/284 (17%), Positives = 105/284 (36%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +  V+  +   +  A+ S DD  +V+S P+               
Sbjct: 50  GITPPAAEIPPPVDPK-AVKADDETDDDEAEASTDDEEEVESGPDPI------------I 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  + S +       L +L
Sbjct: 97  AAQRFGAVSDQM------------ELARKALK---------KHGRGSKQATAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEI 238


>gi|255026033|ref|ZP_05298019.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-003]
          Length = 259

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +A +K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAXKK 248

Query: 667 LKHPSRSKKLR 677
           L+   +++++ 
Sbjct: 249 LREALQNEEVE 259


>gi|311900244|dbj|BAJ32652.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 310

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 112/244 (45%), Gaps = 10/244 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               ++ + +G  E S  +  ++E NL LV    +++ +    + DL+Q G++GL+KA +
Sbjct: 68  LLRRLAGLEEGTREFSYVRTTLIELNLTLVRFAIRRFGHSKEPYEDLLQVGSVGLIKAID 127

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD  LG +F+TYA+  +   I R   D + ++ +P  +++    + +    ++  + RE
Sbjct: 128 RFDPSLGVEFTTYAVPTIIGEIRRHFRDTTWSVHVPRRLQELRLDLAKAQDALAQTLDRE 187

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  ++A+ L++  E V + L         SL+     E           +         
Sbjct: 188 PTVADLAEYLSISEEEVIEGLAAANAHTAGSLDLTSPGEGDGQQ----PAERLGRVDGRF 243

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                      ++A L  R+ ++L MRF      D T  ++G +  +++  + ++ ++ +
Sbjct: 244 ALVENLVALKPLIAQLPERDRQILAMRFS----EDLTQSQIGARLGLSQMHVSRLLSRTL 299

Query: 665 RKLK 668
            +L+
Sbjct: 300 ARLR 303


>gi|288287|emb|CAA39117.1| unnamed protein product [Myxococcus xanthus]
          Length = 246

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 70/229 (30%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ANLR V+ VA +Y + G++  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 508 ITRSIADQSCTIRIPVHMR--DKIHKVVRTARRMSNKIKRE--PTPEEIAKKLAMPVEGV 563
           I   I      +++            + RT R +      +     ++IA++L +    V
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKFGSGDAAVNVDDIARRLHVKPGEV 120

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLAS 619
           R++  ++    +SL+ P+G++  +   DF+    A    + A +     +       L  
Sbjct: 121 REMEQRMGGRDLSLDAPMGEDGGNSHVDFVVSAAAPQDDEFADKEEAGLINARVRTALMR 180

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PRE  ++     +      TL+E+G+ F  +RER RQ+E +A  KLK
Sbjct: 181 LDPRERFIIEQ--RVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLK 227


>gi|270668763|ref|ZP_06222551.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
 gi|270316653|gb|EFA28454.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
          Length = 151

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 90/150 (60%), Positives = 113/150 (75%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              D I +  N +      T ++I++ R I   V +GE +A  AKKEMVEANLRLVIS+A
Sbjct: 2   KYEDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIA 61

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           KKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITRSIADQ+ TIR
Sbjct: 62  KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 121

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
           IPVHM + I+K+ R +R++  ++ RE TPE
Sbjct: 122 IPVHMIETINKLNRISRQLLQEMGREATPE 151


>gi|117926357|ref|YP_866974.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117610113|gb|ABK45568.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 297

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 125/270 (46%), Gaps = 11/270 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +K  +    +S  E   + +  R+       A   +V A+LRLV+ +A++Y      
Sbjct: 24  QRFLKQAAQAPMLSADEEYQLATNYRRHN--DLEAAHRLVHAHLRLVLKIAREYLYYRSS 81

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRD 527
             DL+QEG+IGLM A +KFD   G + +TYA+WW++ AI   I + +  +++      R 
Sbjct: 82  LPDLVQEGSIGLMHAVKKFDAQRGNRLATYAVWWIRAAIHDFILNTAHMVKVATTKLKRH 141

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              K+ +    ++   ++E   EE+A K A   + + ++        S       ++   
Sbjct: 142 LFFKLRQAKSSLAPLNQQE--AEELAVKFATDAQTILEMDSRLAGADSSLNQPLFDEGGE 199

Query: 588 LGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           L + +ED+     L        +       + L  L  RE+ ++  RF          E+
Sbjct: 200 LIELLEDERPNQELQLQSAQQQQRLGRLVKQGLKQLNEREQAIIISRFMGEHAEPR--EQ 257

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + ++F ++ ER+RQIE +A+ KL+   +S+
Sbjct: 258 LAQRFQISGERVRQIEQRAMAKLRSYFQSQ 287


>gi|146312155|ref|YP_001177229.1| flagellar biosynthesis sigma factor [Enterobacter sp. 638]
 gi|145319031|gb|ABP61178.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter sp.
           638]
          Length = 239

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 111/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTADGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V     ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAHAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + V+  R++L  T            E+     + + D+N   +PL   ++ NLR+ 
Sbjct: 122 ERLGIAVQDYRQMLLDTNNSQLFSYDEWREEHGDSVELVTDENQHENPLHQLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIEALPEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|30261116|ref|NP_843493.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Ames]
 gi|47526271|ref|YP_017620.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|65318395|ref|ZP_00391354.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165871654|ref|ZP_02216299.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167635453|ref|ZP_02393766.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|167638886|ref|ZP_02397160.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|170687593|ref|ZP_02878809.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|170707965|ref|ZP_02898414.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|177653505|ref|ZP_02935679.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190566700|ref|ZP_03019617.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196037492|ref|ZP_03104803.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227816152|ref|YP_002816161.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229604478|ref|YP_002865547.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
 gi|254682827|ref|ZP_05146688.1| RNA polymerase sigma factor SigB [Bacillus anthracis str.
           CNEVA-9066]
 gi|254725613|ref|ZP_05187395.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. A1055]
 gi|254734239|ref|ZP_05191952.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Western
           North America USA6153]
 gi|254740112|ref|ZP_05197804.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Kruger B]
 gi|254753453|ref|ZP_05205489.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Vollum]
 gi|254758550|ref|ZP_05210577.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Australia
           94]
 gi|17369088|sp|Q9K5J6|RPSB_BACAN RecName: Full=RNA polymerase sigma-B factor
 gi|8670945|emb|CAB95034.1| sigB [Bacillus anthracis]
 gi|30254730|gb|AAP24979.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Ames]
 gi|47501419|gb|AAT30095.1| RNA polymerase sigma-B factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164712555|gb|EDR18087.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167513016|gb|EDR88388.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|167529071|gb|EDR91825.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|170127125|gb|EDS96003.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|170668406|gb|EDT19153.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|172081309|gb|EDT66383.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190562252|gb|EDV16220.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196031734|gb|EDX70330.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227003869|gb|ACP13612.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229268886|gb|ACQ50523.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
          Length = 257

 Score =  120 bits (300), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 118/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEQTERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|324997618|ref|ZP_08118730.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 277

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 102/227 (44%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++++      +V  +A +Y +RG    DL Q G IGL+ A ++FD   G  F  YA+  +
Sbjct: 43  REQLARGFHPVVRHIAGRYRHRGEPADDLEQVGAIGLLNALDRFDPEQGTPFLAYAVPTI 102

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++ ++R+P  ++D   ++ R    ++ +  R P   E+A+ L    E V 
Sbjct: 103 TGEIRRHFRDRTWSMRVPRRLKDFQTRMTRAQEELAVRHGRAPKVSELAEHLGTSREEVI 162

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L+   +    SL+  +  +  S LG+ +   +A            RE     L  L  
Sbjct: 163 EGLQAQDSYRSDSLD-RLAGDTESPLGEIVGGADAGIGTVED-----REALRPALRRLPE 216

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE  +L +RF          EEV     +++  + ++ A+++  L+ 
Sbjct: 217 RERTILLLRFFGNRTQTQIAEEV----GLSQMHVSRLLARSLATLRR 259


>gi|126348048|emb|CAJ89768.1| putative RNA polymerase secondary sigma factor [Streptomyces
           ambofaciens ATCC 23877]
          Length = 264

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 101/227 (44%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+++  L +   +A ++  RG    DL Q   +GL+KA + +D   G+ F  YA+  V
Sbjct: 39  RDELIQVWLPMSERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPRRGHAFEAYAVPTV 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN-KIKREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V ++A+ ++     R PT EEIA    +    V
Sbjct: 99  TGEIKRHFRDHMWTLHVPRRIQDLRNRVRKSAKELAQVTPGRAPTVEEIADHAHLTTVEV 158

Query: 564 RKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R  ++  +    +SLE  +   D   LGD +   +             R      L +L 
Sbjct: 159 RTGMEALECFSALSLEAEMPGTDGYALGDALGGPDPAFDAVVD-----RVAVRPCLEALP 213

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  +L +RF  GM        + +Q  +++  + ++ +    +++
Sbjct: 214 ERERTILYLRFFGGMTQSR----IAQQLGISQMHVSRLLSGCFDRIR 256


>gi|114332399|ref|YP_748621.1| RNA polymerase, sigma 28 subunit [Nitrosomonas eutropha C91]
 gi|114309413|gb|ABI60656.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosomonas
           eutropha C91]
          Length = 236

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 109/243 (44%), Gaps = 11/243 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                 +I K + V     LV  +A     R    +Q  DLIQ G IGL+ A  +++   
Sbjct: 1   MYTEAGTIDKDQFVIEFTPLVKRIAYHMMARLPASVQVDDLIQAGMIGLLDAINRYEGSY 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F +YA   ++ ++   + +      +P  +R K+ ++    R +  ++   P+ +EI
Sbjct: 61  GRQFESYAAQRIRGSMLDELREADW---LPRSLRRKMRQIETAMRTLEQRLGCPPSEQEI 117

Query: 553 AKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A +L +P+   +++L+      +        ++  H  D + +     PLD  ++ NLRE
Sbjct: 118 ADELNLPLAEYQEMLQEAGGGQLIYYEDFQVDEEDHFLDHLCNDQGNEPLDQLLEKNLRE 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                +  L  +E+ V+    G+    +  L E+G    V+  RI Q+  +AI +L+   
Sbjct: 178 LLVAAIEKLPAKEKLVM----GMYYEQEMNLREIGDVLGVSESRICQLHTQAISRLRTRL 233

Query: 672 RSK 674
           R K
Sbjct: 234 RDK 236


>gi|6010732|gb|AAF01232.1|AF184101_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 242

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 73/190 (38%), Positives = 124/190 (65%), Gaps = 3/190 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP+G +  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231

Query: 586 SHLGDFIEDK 595
             L D + D+
Sbjct: 232 KALLDILADE 241



 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|225862940|ref|YP_002748318.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
 gi|225786058|gb|ACO26275.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
          Length = 257

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 117/261 (44%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V     LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVNHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|146344240|ref|YP_001202096.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
 gi|146188052|emb|CAM96382.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
          Length = 291

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 111/260 (42%), Gaps = 13/260 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +S  E R +   + +       A +E+V + LR V+ +A+ Y+  GL
Sbjct: 22  LDAYLTVIHSIPNMSAEEERRLSERLVEHNDMD--AARELVTSQLRFVVHIARSYSGYGL 79

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR-IPVHMRD 527
              DLIQEGNIGL+KA ++F+     +  T+ + W++  I   I      +R      + 
Sbjct: 80  PLSDLIQEGNIGLIKAVKRFNPAAQVRLITFGVHWIRAEINEFIIRNGRMVRLATTKAQR 139

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
           K+   +R   R  N +  + T   IA  L + V  V+++  ++     S +     +D S
Sbjct: 140 KLFFNLRKQPRSRNWLTADETRH-IADTLNVSVLDVKEMETRMAGNDTSFDPAADADDES 198

Query: 587 ---HLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                   I D           +A+     +     L +L  R   +L  RF     +  
Sbjct: 199 AYITPSHQIGDHRYDPAYQYETEADAGTSTDDLHAALNNLDERSRDILAQRFL--SESKA 256

Query: 641 TLEEVGKQFCVTRERIRQIE 660
           TL ++  ++ V+ ERIRQIE
Sbjct: 257 TLNDLASKYNVSAERIRQIE 276


>gi|225028119|ref|ZP_03717311.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
 gi|224954589|gb|EEG35798.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
          Length = 278

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 75/276 (27%), Positives = 136/276 (49%), Gaps = 17/276 (6%)

Query: 399 VACEVDSILKIRNEIKSISVET---GISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           V   +  I    N+++   V T    +   E +   ++  + E     A+++ V+ NLRL
Sbjct: 11  VHVHLRRIAMFLNKVEICGVNTSELPLLSDEEKE--NLFIQIEQGNMDAREQYVKGNLRL 68

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+SV +++++      DL Q G IGLMKA + FD  L  KFSTYA+  +   + R + D 
Sbjct: 69  VLSVIQRFSSNHEHADDLFQVGCIGLMKAIDNFDRTLNVKFSTYAVPMILGEVRRYLRDN 128

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +  IR+   +RD  +K +    +++  + R PT EE++KK  +P E +   L     P+S
Sbjct: 129 NS-IRVSRSLRDTAYKAIYAKEQLTKSMNRTPTIEEVSKKTEIPEEDIIYALDAIATPMS 187

Query: 576 LETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           L  P+  +  D   L D I DK   +  D+ I+     +    +  L+ RE  ++  RF 
Sbjct: 188 LFEPVYQDGNDPLFLMDQICDKK--NKEDTWIEHL---SLQEAMNQLSGREYHIIEKRFF 242

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            G     T  EV  +  +++ ++ ++E  A++ +++
Sbjct: 243 EG----KTQTEVADEISISQAQVSRLEKNALKSIRN 274


>gi|284043529|ref|YP_003393869.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947750|gb|ADB50494.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 261

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 105/237 (44%), Gaps = 13/237 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E      +   +E+ + LV  +A++Y        DL+Q   +GL+KA ++FD   G 
Sbjct: 32  RYRETGDPRCRTRAIESFMPLVHKLARRYHPGPEPLDDLVQVACVGLVKAIDRFDPDAGP 91

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+++A+  +   + R   D + ++ +P  +++   ++      +S +  R PT  E++ 
Sbjct: 92  RFASFAIPTITGELRRHFRDTTWSVHVPRRVQEDALRLRHAMTELSERPGRSPTIHELSA 151

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLR 610
              +  E + + L     K   SL+ P+  +D     +GD +              A  R
Sbjct: 152 ATGLDDEQITEALHATTAKAASSLDRPVPGQDDGSATIGDTLGCDE-----YGFALAEHR 206

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            T    L +L  R+  +L +RF      D T  E+ ++   ++ ++ ++  +A+  L
Sbjct: 207 TTIGPRLRALPLRDREILYLRFA----EDMTQHEIAQRIGCSQMQVSRLLRRALDAL 259


>gi|298529795|ref|ZP_07017198.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511231|gb|EFI35134.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 336

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 133/314 (42%), Gaps = 10/314 (3%)

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
                +R       +G+  +       +     E           +  +R  ++ +    
Sbjct: 9   TQRKKERQDIKAPEEGQLDEKKVAEKLESAVGKEVSPLPGNTPMPMDALRIYLRQVGNFP 68

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNI 479
            +S  E   +    R    +   A   ++ +NLRLV+ +A ++  + +   LDLIQEGN+
Sbjct: 69  TMSAEEEFELARKFRDEGNQD--AAFMLITSNLRLVVKIAMEFQRKWMKNVLDLIQEGNV 126

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTAR 537
           GLMKA +KFD   G KFS YA +W++  I + I D    +++      R   + + +  +
Sbjct: 127 GLMKALKKFDPDKGIKFSYYASFWIRAYILKFIMDNWRMVKVGTTQAQRKLFYNLSKEKQ 186

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE---D 594
           R+ +                   + V    ++ +  +SL+ P  ++      + I    D
Sbjct: 187 RLESMGITADADAISQSLDVSETDVVEMGQRLGQHDLSLDMPYNEDSDVTPMNVIPALGD 246

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                 L       L++    ++  L+ +E+ ++     +   +  TL E+G+++ +TRE
Sbjct: 247 GAEEILLQGETAQLLQQNIKELMPKLSDKEKDIIE--MRLLAESPVTLREIGEKYGITRE 304

Query: 655 RIRQIEAKAIRKLK 668
           R+RQIE++ + K+K
Sbjct: 305 RVRQIESRLLGKIK 318



 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 21/92 (22%), Positives = 34/92 (36%), Gaps = 1/92 (1%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
            D    EEG  D   +A    ++                D +R+YLR++G+   +S E E
Sbjct: 16  QDIKAPEEGQLDEKKVAEKLESAVGKEVSPLPGNTPMPMDALRIYLRQVGNFPTMSAEEE 75

Query: 140 IAIAKRI-EAGRAMMMASLCESPLTFQALIIW 170
             +A++  + G       L  S L     I  
Sbjct: 76  FELARKFRDEGNQDAAFMLITSNLRLVVKIAM 107


>gi|168986257|dbj|BAG11810.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
          Length = 177

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 118/175 (67%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW++Q I R+I +Q+ TI
Sbjct: 2   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFLFSTYATWWIRQTIERAIMNQTRTI 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 62  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 121

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           +G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG+
Sbjct: 122 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 176


>gi|168335364|ref|ZP_02693458.1| sporulation sigma factor SigG [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 243

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 125/255 (49%), Gaps = 19/255 (7%)

Query: 409 IRNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
             N+++   V T     ++  +  H+  ++       ++A++E +  NLRLV+SV +++ 
Sbjct: 2   AINKVEICGVNTAKLPTLTNQQKEHLFELI---GAGDNMAREEYIRGNLRLVLSVIQRFN 58

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           NRG    DL Q G IGL+KA + FD   G KFSTYA+  +   I R + D +  IR+   
Sbjct: 59  NRGEHVDDLFQVGCIGLIKAIDNFDTTQGVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRS 117

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +RD  +K ++   ++  +  +EPT EEIA  L +  E +   L   ++PISL  P+  +D
Sbjct: 118 LRDTAYKALQVKEKLLRQNSKEPTIEEIAAVLEIATENIVFALDAIQDPISLFEPVYHDD 177

Query: 585 TSHL--GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              L   D + D+ +   +     A         +  L  RE+ +L +RF  G     T 
Sbjct: 178 GDALFIMDQVSDEKSQDDIWLENIA-----LKEAMKRLNDREKHILTLRFFAG----KTQ 228

Query: 643 EEVGKQFCVTRERIR 657
            EV  +  +++ ++ 
Sbjct: 229 MEVADEIGISQAQVS 243


>gi|108757418|ref|YP_634007.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
 gi|108461298|gb|ABF86483.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
          Length = 278

 Score =  120 bits (300), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 68/271 (25%), Positives = 131/271 (48%), Gaps = 14/271 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  +     ++  E   +    +  E     A   +V +NLRLV+ +A +Y    L  LD
Sbjct: 1   MAEVQRHPLLTREEELQLARHYK--ESGDVNAAYRLVASNLRLVVKLAHEYHRNPLSLLD 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIH 530
           L+QEGNIGLM+A +K+D   G K S+YA WW++  I R I D    +++      R    
Sbjct: 59  LVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQRKLFF 118

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTS--- 586
           K+ +   ++  +   E +P+ +A++L +  + V ++ +      +S++ P+G++D S   
Sbjct: 119 KLRQEQEKLIAQ-GFEASPKLLAERLNVTEQDVVEMDQRLGHDEMSIDAPLGNDDDSRTT 177

Query: 587 HLGDFIEDKNAVSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               ++   +  +        ++A  RE  +    +L  +E         +  +   TL+
Sbjct: 178 RADRYLPSNSMPADERLGAEQLKALFREKLSEFARTLEGKER--FIFESRLVSDEPLTLQ 235

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           ++G ++ V+RER RQIEA  I +++   R +
Sbjct: 236 DIGDKYGVSRERARQIEAALINRMRDFMREQ 266


>gi|88658518|ref|YP_507464.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
 gi|88599975|gb|ABD45444.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 297

 Score =  120 bits (300), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 120/272 (44%), Gaps = 15/272 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I  +     +S  E   +       E         +V ++LRLV+ VA  + N  L
Sbjct: 14  LMSYINEVHAFPILSPEEEDRLAR--NWYENGIVADAHRLVTSHLRLVVKVALSFKNYEL 71

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRD 527
             ++LI EGNIGLM+A +KF+  LG++ STYA+WW+K  I   I      I+I     + 
Sbjct: 72  PLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKAFIKDYILKSWSCIKIGTTQAQR 131

Query: 528 KIHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGV-RKVLKITKEPISLETPIGDE 583
           K+   +R  ++   K     T E+   IA K +   + V +          SL   +   
Sbjct: 132 KLFFSLRKIKKKLFKYNHNITKEDIKLIANKCSTSEQEVEQMNRYFLYRDRSLNELVFSN 191

Query: 584 DTS---HLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMN 637
           D      L + I+           +   L   +   ++ L++L  R   +   R  I   
Sbjct: 192 DNQNGVELQEIIKCDTPNQEDTYLLNEELNIKKALISQALSTLNERYRDIFIRRRLIE-- 249

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TL+++ +++ +++ER+RQIE  A  K+K+
Sbjct: 250 EPDTLDKLSQEYNISKERVRQIEMHAFTKVKN 281


>gi|33151352|ref|NP_872705.1| RNA polymerase factor sigma-32 [Haemophilus ducreyi 35000HP]
 gi|33147572|gb|AAP95094.1| RNA polymerase sigma-32 factor [Haemophilus ducreyi 35000HP]
          Length = 319

 Score =  120 bits (300), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 65/273 (23%), Positives = 128/273 (46%), Gaps = 16/273 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +DS +++ N+   ++ E   +++E        R    E   A K+++ +++R VI +A+
Sbjct: 50  NLDSYIRMANQYPILTAEQEKTLAE--------RYYYDEDVDAAKQLILSHMRFVIHIAR 101

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y   GL   DLIQEGNIGLMKA ++FD  +G +  ++A+ WVK  I   +      +++
Sbjct: 102 GYMGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKV 161

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
                 +         +       E   +++A+ L +  E VR++               
Sbjct: 162 ATTKAQRKLFFNLRKNKHRLAWFNEDEIQQVAQDLGVSTEEVREMESRMTGQDVGFDISA 221

Query: 582 DEDTSHL---GDFIEDKNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIG 635
           +ED S +     ++ED ++    +   + +  E        LA+L  R + +++ R+   
Sbjct: 222 NEDESEVYVPSMYLEDNSSNFADELEEEQHTGEATAKLAYALATLDERSQDIIKTRWLDE 281

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                TL E+  ++ ++ ER+RQ+E  A++K+K
Sbjct: 282 N--KATLHELAAKYSISAERVRQLENAALKKIK 312


>gi|49183950|ref|YP_027202.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Sterne]
 gi|49177877|gb|AAT53253.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Sterne]
          Length = 258

 Score =  120 bits (300), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 118/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 2   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 60  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 120 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 180 RIE--SVGEVEQGYEQTERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 233

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 234 ISQMHVSRIKRQAISKLKQAA 254


>gi|297559507|ref|YP_003678481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296843955|gb|ADH65975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score =  120 bits (300), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 111/249 (44%), Gaps = 7/249 (2%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           +  E   ++  + +G+ +A+  ++ ++     L+  +A++Y  RG    DL Q   +GL 
Sbjct: 32  TAEELLSVLVRLGEGDPQANGLRERVMVLYQPLINKIARRYGGRGEPLEDLKQTAMVGLA 91

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA   +D   G  F +Y +  V   I R   D +  +R+P   ++   K+ R       +
Sbjct: 92  KAVRGYDPARGKPFISYLLPTVTGEIKRHFRDHTWAVRVPRRHQENRVKLRRVTSEFQQR 151

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
             R PT  E+A  + +P   V ++ ++  +   +SL+ P   +     G  +ED      
Sbjct: 152 HARTPTIAELAHDMGLPEAEVSELTQVSESYRSLSLDAPDSSDSEGQEGTRLEDHLGCE- 210

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +  +   RE+    LA L  RE  +LR+RF      DHT  E+  +   ++  + ++ 
Sbjct: 211 DAALDRVVERESLKPALARLPAREREILRLRFF----GDHTQSEIADRLGYSQMHVSRLL 266

Query: 661 AKAIRKLKH 669
           +  + +L+ 
Sbjct: 267 SGVLEQLRE 275


>gi|294669660|ref|ZP_06734727.1| hypothetical protein NEIELOOT_01561 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308573|gb|EFE49816.1| hypothetical protein NEIELOOT_01561 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 146

 Score =  120 bits (300), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 49/141 (34%), Positives = 69/141 (48%), Gaps = 2/141 (1%)

Query: 7   RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
            N     E ED +  L  +      +++I   + RGY+T  E+N  LP D   +EQ+++ 
Sbjct: 2   SNPQDYEEQEDDNRPLTAEEQRARLRQLILQGKDRGYITYAEINDALPDDMSDAEQIDNI 61

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDL--ASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           V M+  +GI V +     D     DS        A   +       DS    T DPVRMY
Sbjct: 62  VNMIQGLGIQVTEEAPDADSLLMNDSGTGMTDDDAVEEAEAALSNADSEFGRTTDPVRMY 121

Query: 125 LREMGSIELLSREGEIAIAKR 145
           +REMG +ELL+RE EI IAK+
Sbjct: 122 MREMGQVELLTREDEIIIAKK 142


>gi|161898933|gb|ABX80456.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  120 bits (300), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 110/241 (45%), Gaps = 5/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+ +G  F +  Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYS-QGKSFHEDSQVGNIGLLGAIRR 59

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 60  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 119

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 120 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 179

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+KL
Sbjct: 180 NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKKL 235

Query: 668 K 668
           +
Sbjct: 236 R 236


>gi|295109704|emb|CBL23657.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus obeum
           A2-162]
          Length = 259

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 72/266 (27%), Positives = 130/266 (48%), Gaps = 11/266 (4%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
             N+++   V T  + I +      + R+ +   + A+++ ++ NLRLV+SV +++ N  
Sbjct: 2   ALNKVEICGVNTSSLPILKQEEKDELFRRIKQGDTKAREQYIKGNLRLVLSVIRRFQNSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGLMKA + FD  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLMKAVDNFDDTLMVKFSTYAVPMIIGEIRRYLRDYNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K +        +  +EPT EEIA+++ +  E +   L   + P+SL  P+  E    
Sbjct: 121 IAYKAIYAKENYIRQNLKEPTMEEIAEEIGIEKEMIVYALDAIQSPVSLYEPVYSEG--- 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            GD +   + +S   +  +  L        +  L  RE  ++ MRF  G     T  EV 
Sbjct: 178 -GDTLYVMDQISDRKNKEEHWLENLSLKEAMNRLGSRERHIIEMRFYEG----KTQMEVA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSR 672
            +  +++ ++ ++E  A++ +++  R
Sbjct: 233 DEIGISQAQVSRLEKNALKTMRNYLR 258


>gi|218676616|ref|YP_002395435.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
 gi|218324884|emb|CAV26646.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
          Length = 298

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 77/266 (28%), Positives = 137/266 (51%), Gaps = 9/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-- 466
             + +K I     +S  +  +   + R        A+  M+E+NLRLV+ +AK Y  R  
Sbjct: 29  YAHYLKDIVGIDLLSREDELYYAKLNR---AGDKQARDIMIESNLRLVVKIAKSYLKRKG 85

Query: 467 -GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                LDLI+EGNIGL+KA +K+D   GY+FSTYA+WW+++ I  ++ ++  T+R+P H+
Sbjct: 86  NNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHV 145

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +I+ +      +S K+++E +  E++    +  E V   L      I + T +G    
Sbjct: 146 CKEINSLASKKLDVSKKMRKEISISELSNSSGVKAERV-DQLVALSGFIDVTTTVGISHA 204

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + D  E +    P       +      +++ +L P+ ++VL  RFG   N   TL EV
Sbjct: 205 PLVLDQCESEYIPDPQQDCEDQSFTHALEQIINTLPPKLQKVLIHRFGFFDNKVKTLSEV 264

Query: 646 GKQF--CVTRERIRQIEAKAIRKLKH 669
           G+     V+ ER+RQ++ +A+ +++ 
Sbjct: 265 GQMLDVNVSNERVRQMQKEAVERIQK 290



 Score = 41.7 bits (96), Expect = 0.42,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 39/100 (39%), Gaps = 2/100 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +     +  +  +P   YL+++  I+LLSRE E+  AK   AG       + ES L    
Sbjct: 15  ETPIKESFTTATEPYAHYLKDIVGIDLLSREDELYYAKLNRAGDKQARDIMIESNLRLVV 74

Query: 167 LIIWRDELNDGTTL-LREIIDLEACIGPESKGGFFHGTEG 205
            I        G    L ++I+ E  IG       +    G
Sbjct: 75  KIAKSYLKRKGNNFTLLDLIE-EGNIGLIKAIDKYDPEPG 113


>gi|333003010|gb|EGK22564.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           VA-6]
          Length = 239

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVCHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|166031183|ref|ZP_02234012.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
 gi|166029030|gb|EDR47787.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
          Length = 278

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 70/266 (26%), Positives = 132/266 (49%), Gaps = 13/266 (4%)

Query: 407 LKIRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
            K++ +++   V T  + I +     ++  + +     AK+E ++ NLRLV+SV K++ +
Sbjct: 18  EKMQGKVEICGVNTAKLPILKEEEKEALFARIKAGDDEAKEEYIKGNLRLVLSVIKRFHS 77

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                 DL Q G IGL+KA   F+  L  KFSTYA+  +   I R + D S  IR+   +
Sbjct: 78  SNENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNSS-IRVSRSL 136

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K +        +  REPT +EIA+++ +  E +   L   + P+SL+ P+  +  
Sbjct: 137 RDTAYKAIYAKENYVKQNMREPTVQEIAQEIGIAKEDIVYALDAIQAPMSLQEPVYSDGG 196

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D    +  +  +++    +    +  L  RE  ++ +RF  G     T  
Sbjct: 197 DALYVMDQISDHK--NKEEKWVESL---SLQAAMEHLNERERYIISLRFFDG----RTQM 247

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV +   +++ ++ ++E  A+R ++ 
Sbjct: 248 EVARDVGISQAQVSRLEKNALRIMRQ 273


>gi|27375413|ref|NP_766942.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
 gi|1834377|emb|CAA70861.1| RNA polymerase subunit [Bradyrhizobium japonicum]
 gi|27348550|dbj|BAC45567.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
          Length = 307

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 116/265 (43%), Gaps = 15/265 (5%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I     +   + + +    R  E     A   +V ++LRL   +A+ Y   GL  +DLI 
Sbjct: 32  IRRYELLEPGQEQQLAR--RWHETRDRGAADALVTSHLRLAAKLARGYKGYGLPMVDLIA 89

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH----- 530
           E N+GL+ AA +F+   G +FSTYA+WW+K AI   I      ++I      K       
Sbjct: 90  EANLGLVIAASRFEPGRGARFSTYAIWWIKAAIHEYILRSWSLVKIGTTAAQKKLFFKLR 149

Query: 531 -KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHL 588
            ++ +    + + +  +   E IA KL +    V ++       +SL   +G E+  + L
Sbjct: 150 SEIRKATGSVMSGLTPDV-AELIAGKLDVTAREVIEMDARLNGDMSLNARVGGEESGTEL 208

Query: 589 GDFIEDK--NAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
              + D   +A + L    Q   R +     L  L  RE  V   R         TL+++
Sbjct: 209 EALLVDGAVDAETMLADHEQTERRAKALRVALGGLAARERHVFEARRLTEC--PVTLDQL 266

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHP 670
            ++  ++ ER+RQIE +A  K+K  
Sbjct: 267 ARELSISSERVRQIEIRAFAKVKRA 291


>gi|84872788|gb|ABC67485.1| RpoH2 [Sinorhizobium sp. BL3]
          Length = 286

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 65/285 (22%), Positives = 126/285 (44%), Gaps = 15/285 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + ++   R  IK       +   E   +    R        A+ ++  +++RLV+++A K
Sbjct: 1   MKTLTADRRLIKIAMDAPYLERDEEHALAEAWRYD--HDQEARNKIAMSHMRLVVAMAAK 58

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + + GL   DL+QEG+IGL++AA +F+     +FSTYA WW++ ++   +      +R  
Sbjct: 59  FRSFGLPMGDLVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGG 118

Query: 523 VHMRDK--IHKVVRTARRMSN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISL 576
                K     + R   R++    ++  +   EEIA  L + +  V+    +++    SL
Sbjct: 119 TSSAQKALFFNLRRLRARLAQGDRQLTSQAMHEEIAAALGVSLADVQTMDARLSGNDASL 178

Query: 577 ETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMR 631
           + P+G  D       DF+     +     +   +    R      L  L+ RE +++R R
Sbjct: 179 QAPVGHGDAESGARLDFLPSDAPLPDEQVSEMIDGERARRWLHSALRELSEREMKIIRAR 238

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
                    TLEE+G    +++ER+R    ++   ++   R+  L
Sbjct: 239 RLSEDG--ATLEELGVALGISKERVRSKRGRSKSCVRRSPRAPAL 281


>gi|197723815|gb|ACH72687.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 242

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 6   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 65

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 66  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 125

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 126 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 185

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+K
Sbjct: 186 VNQRMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDISQMHVSRIQRQAIKK 241

Query: 667 L 667
           L
Sbjct: 242 L 242


>gi|324325029|gb|ADY20289.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 257

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 119/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVMKLIAEFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|34496477|ref|NP_900692.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
 gi|34102331|gb|AAQ58697.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
          Length = 248

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 105/239 (43%), Gaps = 19/239 (7%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           VEA   LV  +A     R    ++  DL+Q G IGL++AA +FD   G +F T+A   ++
Sbjct: 22  VEAYAPLVRKLASIMIARLPASVELGDLVQVGMIGLIEAARQFDPAQGVQFETFASQRIR 81

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   +  +     +P   R    ++     ++  ++ R P   EIA ++ + +E  + 
Sbjct: 82  GAMLDELRREDW---LPRQARRNSRQIEEAISKLEQRLGRAPLESEIAAEMGVELEQYQD 138

Query: 566 VL--KITKEPISLETPIGDEDTSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +L        +  E   G +D         I D ++  PL +    + R      +  L 
Sbjct: 139 MLGDCKGTTLLHFEDFGGGDDEGSHNPVTNIADDDSPDPLAALSDDSFRRQLVSAIKFLP 198

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            R++ V+     +    +  L+E+G    VT  R+ Q+ ++AI +L+      KL+ +L
Sbjct: 199 ERDQLVM----ALYYEQELNLKEIGAVLGVTESRVCQLHSQAIARLR-----AKLKDWL 248


>gi|294497070|ref|YP_003560770.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|295702435|ref|YP_003595510.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
 gi|294347007|gb|ADE67336.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|294800094|gb|ADF37160.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
          Length = 264

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 48/262 (18%), Positives = 122/262 (46%), Gaps = 6/262 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+ S    ++  + +  +   +K   +   A+ ++V     LV S+A++Y+       D
Sbjct: 1   MKTQSQPMKLTKEQVQERIERFQKT--QDEEAQSDLVVHYKNLVESIARRYSKGRSLHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           ++Q G +GL+ A  ++D   G  F ++A+  +   I R + D++ ++ +P  +++   K+
Sbjct: 59  IVQVGMLGLLGAIRRYDASFGRSFESFAVPTIIGEIKRFLRDKTWSVHVPRRIKELGPKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                 ++ +++R P  +EIA  + +  E + + +++ +   +L      E  S      
Sbjct: 119 KAAVEELTTRLQRSPQVKEIADHIGVTEEEILETMEMGQSYQALSVDHSIEADSDGSTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                        + + R    ++L  L+ RE+ V+R  F        + ++ G++  ++
Sbjct: 179 ILDLVGEQESGYEKTDQRLVLEKILHVLSDREKEVIRYTFIEN----LSQKDAGEKLGIS 234

Query: 653 RERIRQIEAKAIRKLKHPSRSK 674
           +  + +++ +A+ KL+  +RS 
Sbjct: 235 QMHVSRLQRRALDKLRTAARSD 256


>gi|215254266|gb|ACJ64132.1| RNA polymerase sigma 70 factor [Vibrio campbellii]
          Length = 263

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 49/305 (16%), Positives = 102/305 (33%), Gaps = 43/305 (14%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   + +S+ E P T   ++   D++      L ++I        +      
Sbjct: 1   DIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPT 60

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
               G    + +   +++E  D  E   D    ++       ++                
Sbjct: 61  ATHIGSELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL---------------- 104

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                               +   +++   Y+ L+      +   +    S K  V  E 
Sbjct: 105 -------------------ALEKFNQLRSTYQNLQ------LAINEHGYESPKATVANEL 139

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+    G E 
Sbjct: 140 MLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNES 199

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +    + I +   ++K I  ET +++   + I   +  GE 
Sbjct: 200 SEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEA 258

Query: 440 EASIA 444
           +A  A
Sbjct: 259 KARRA 263


>gi|196035080|ref|ZP_03102486.1| RNA polymerase sigma-B factor [Bacillus cereus W]
 gi|195992144|gb|EDX56106.1| RNA polymerase sigma-B factor [Bacillus cereus W]
          Length = 257

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 118/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEQTERRLVLEDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|254819525|ref|ZP_05224526.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 262

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 107/242 (44%), Gaps = 6/242 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + S+           + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 23  FRELASVAADSMEL-QRQRDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVV 81

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 82  RFDVDAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQRLGRA 141

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E+A +L M  E V + L       +L    G          I D           +
Sbjct: 142 PTATELAAELEMDREEVVEGLVAGSSYNTLSIDSGGGGEEEEARAIADTLG-DVDTGLDR 200

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +E+   +L +L  RE  VL +RF        T  ++ ++  +++  + ++ AK++ +
Sbjct: 201 IEDQESLRPLLEALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKSLTR 256

Query: 667 LK 668
           L+
Sbjct: 257 LR 258


>gi|261419446|ref|YP_003253128.1| RNA polymerase sigma factor SigD [Geobacillus sp. Y412MC61]
 gi|319766261|ref|YP_004131762.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
 gi|261375903|gb|ACX78646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC61]
 gi|317111127|gb|ADU93619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
          Length = 251

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 101/247 (40%), Gaps = 12/247 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLM 482
           E R               A +E+V+  + LV    ++ +      +   +L+  G +GL 
Sbjct: 8   EERKYWD--EWIHGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLY 65

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A EKFD     KF TYA + ++ AI   +  +     +P  MRDK  K+     R+  +
Sbjct: 66  DALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSMRDKAKKIEGAIERLEQR 122

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R  T +EIA +L M  E V+     T     L       D       + D  A  P +
Sbjct: 123 HMRSVTAKEIAAELGMTEEEVQAAASETFFSHWLPLGQTTVDEDEGLLSVRDDRAPLPEE 182

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++  + E     +  L  +E+ V+ + +      + T  E+G    ++  RI QI AK
Sbjct: 183 QIVKQEMIEKLAEAIGQLNEKEQLVISLFY----KEELTFTEIGSLLHLSTSRISQIHAK 238

Query: 663 AIRKLKH 669
           A+ KL+ 
Sbjct: 239 ALWKLRR 245


>gi|319404792|emb|CBI78393.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 247

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 13/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
             ++  A++RLVIS+A ++    +   DL+QEG +GL++AA +FD   G +FSTYA WW+
Sbjct: 1   MHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWWI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKI-----HKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           + +I   I      +R       K       ++     +  N + ++     I++KL + 
Sbjct: 61  RASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLAQDDNTLTKQEIFRAISEKLGVS 120

Query: 560 VEGVRKVLKI---TKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLR-ETT 613
           V  V K+      T   +SL      E      D + D + +  S ++ AI    R +  
Sbjct: 121 VNDVEKMDFRFSGTDNSLSLSISENGETPIAKMDSLIDDHPLPDSVIEQAIDGQRRAQWL 180

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              L  L  RE  ++R  F        TLE +G++  +++ER+RQIE +A++KL+
Sbjct: 181 HEALQILNERELEIIR--FRRLNEEGTTLEVLGEKLGISKERVRQIEVRALQKLR 233


>gi|21225616|ref|NP_631395.1| RNA polymerase secondary sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|2687404|gb|AAC01582.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
 gi|8246836|emb|CAB92887.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
          Length = 263

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 106/246 (43%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E +A   + +++   L +   +A ++  RG    DL Q   +GL+KA +
Sbjct: 22  FERLAGLPEGPERKAL--RDDLIRVWLPMAERIAVRFRGRGENLEDLYQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
            +D   G+ F  YA+  V   I R   D   T+ +P  ++D  ++V ++A+ ++     R
Sbjct: 80  HYDPERGHAFEAYAVPTVTGEIKRHFRDHMWTLHVPRRIQDLRNRVRKSAKELAQTTPGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT EEIA+   +    VR  ++  +    +SLE  +   D   LGD +   +       
Sbjct: 140 APTVEEIAEHAQLTTAEVRTGMEALECFSALSLEAEMPGTDGYALGDALGGPDPAFDAVV 199

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      L +L  RE  +L +RF  GM        + +Q  +++  + ++    
Sbjct: 200 D-----RVAVRPCLEALPERERTILYLRFFGGMTQSR----IAQQLGISQMHVSRLLTGC 250

Query: 664 IRKLKH 669
             +++ 
Sbjct: 251 FDRIRE 256


>gi|319935952|ref|ZP_08010376.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809066|gb|EFW05562.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 241

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 115/240 (47%), Gaps = 10/240 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++ K       AK+++V+ NL LV S+  ++ N      DL Q G IGLMKA   F
Sbjct: 5   KTLDLLVKVRSGDEQAKEQVVKDNLGLVWSIVHRFKNSYYDKEDLFQIGCIGLMKAINHF 64

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   I R   D   TI++   +++   KV +    +  +   EPT
Sbjct: 65  DPSYNVQFSTYAVPIIMGEIKRYFRD-DGTIKVSRSLKELNIKVTKAKEILQAENNEEPT 123

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A+ L + V  V + +  +  P SL  PI ++D S +   +ED+          +  
Sbjct: 124 VEEVARYLEVDVHDVVEAIDSSYYPTSLSEPIYEKDGSTIS--MEDRLIDKSDHMWFE-- 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +  L  +E+ ++ MR+ +  N     E + ++  +++ ++ ++E K + KL+
Sbjct: 180 -KIALEMEMEKLDEKEKMIIYMRYQLDYNQ----EAIAQRLGISQVQVSRLEKKIVTKLR 234


>gi|291196302|emb|CBG22623.1| DNA-directed RNA polymerase subunit D [Pseudomonas fuscovaginae]
          Length = 237

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 95/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   + +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDYILDEYNRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +   +    D +  +    +D  +    P  A      + +  + 
Sbjct: 50  GIALPAAEVPPPVDAKTGKENATDDEDEESDSDDEDEVESGPDPIVAAQRFGAVADQLEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L +L
Sbjct: 110 ARKAL-----------------------------------KKHGRGNKATIAELLLLAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + ++LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEVLVERVRSALERLRQQERAIMQLCVRDARMPRADFLRQFPGNEIDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 TD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEI 237


>gi|154684976|ref|YP_001420137.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens FZB42]
 gi|126363073|emb|CAM35801.1| RNA polymerase sigma-B factor [Bacillus amyloliquefaciens FZB42]
 gi|154350827|gb|ABS72906.1| SigB [Bacillus amyloliquefaciens FZB42]
          Length = 262

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 118/258 (45%), Gaps = 6/258 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   S  T ++  E   ++        +   A++ +VE    LV  +AKKY+       D
Sbjct: 1   MAQPSKTTKLTKDEVDRLIR--DFQTHDNKEAQETLVEVYTNLVEMLAKKYSKGKSFHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++
Sbjct: 59  LRQVGMIGLLGAIKRYDPEVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +++ + +R P  EEIA  L +  E V + +++ K   +L      E  +      
Sbjct: 119 KMAVDQLTTETQRSPKVEEIAAFLDVSEEEVLETMEMGKSYQALSVDHSIEADADGSTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S  +   + N +     VL  L+ RE++++ + F      + + +E G    ++
Sbjct: 179 ILDIVGSQEEGYERVNQQMMIKSVLHVLSDREKQIIDLTFV----QNKSQKETGDILGIS 234

Query: 653 RERIRQIEAKAIRKLKHP 670
           +  + +++ KA++KL+  
Sbjct: 235 QMHVSRLQRKAVKKLREA 252


>gi|167507975|gb|ABZ81308.1| RpoD [Thalassospira sp. MCCC 1A02753]
 gi|167507991|gb|ABZ81316.1| RpoD [Thalassospira sp. MCCC 1A02878]
 gi|167507995|gb|ABZ81318.1| RpoD [Thalassospira sp. MCCC 1A02921]
          Length = 257

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 114/255 (44%), Gaps = 16/255 (6%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ-----------EKERDDVQETE 227
            LLR++IDLE   G              +  + +D              E E +  + T 
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAEEGEQADAQGDDFEAAAVETDADEDEEAETETPEPTG 60

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
                  +   ++        E   + +   D++ +    +LS ME++L  +V+   + I
Sbjct: 61  APASDEEEEDDEESDDDSEGEEGEGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKFELI 120

Query: 288 AEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           A+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ L
Sbjct: 121 AKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELLDHL 180

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK F+   
Sbjct: 181 TGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVSELPGKGWKAFIERY 240

Query: 403 VDSILKIRNEIKSIS 417
            D I ++R ++  +S
Sbjct: 241 PDEIAQLREQVGGVS 255


>gi|315133339|emb|CAJ29297.2| DNA-directed RNA polymerase subunit D [Pseudomonas mediterranea]
          Length = 237

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 43/284 (15%), Positives = 97/284 (34%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       + +  + + D + A     ++ ++    P  A      + E  + 
Sbjct: 50  GTTPPAAEVPPPIDAKAEKADDDSDDDDAEASEDEEEAESGPDPIVAAQRFGAVAEQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + + +       L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRDNKQAIAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +A     I++ + ++ ++  ETG+SI+E 
Sbjct: 195 TD-ALAKGKTKYAEAIARLQPDIVRCQQKLSALETETGLSIAEI 237


>gi|302127749|emb|CBL51728.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 262

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 57/301 (18%), Positives = 111/301 (36%), Gaps = 46/301 (15%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE     + +S+ E P     L+   D+       L +II     I P  
Sbjct: 1   REGEIDIAKRIEDRINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN- 57

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                                  E DDV  T   I S            D   +  E+ +
Sbjct: 58  -----------------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGD 94

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKC 314
            + D+ +      ++                  E + ELR+  +   ++ Q++ ++    
Sbjct: 95  NSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDT 137

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLER 373
           +    +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+  
Sbjct: 138 QNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAA 197

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E +  W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   
Sbjct: 198 FTNNECETAWFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRR 256

Query: 434 V 434
           +
Sbjct: 257 M 257


>gi|254387389|ref|ZP_05002636.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346181|gb|EDX27147.1| sigma factor [Streptomyces sp. Mg1]
          Length = 266

 Score =  119 bits (299), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 113/247 (45%), Gaps = 18/247 (7%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKF 488
           +  + +G  E    +  ++E N  LV    +++ +R  G    D++Q G IGL+KA ++F
Sbjct: 17  LRELTEGTPEHQYVRNTLIEMNASLVQYAVRRFRSRCDGGDIEDVVQVGTIGLIKAIDRF 76

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FST AM ++   I R   D S  +R+P  +++    + +    ++ ++ R PT
Sbjct: 77  DPARENEFSTLAMPYITGEIKRHFRDTSWAVRVPRRLQELRIDIAKAKEELTVRLDRSPT 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS-----HLGDFIEDKNAVSPL 601
             ++A  L +  E V + L         SL+ P  D          L D + ++     L
Sbjct: 137 VTDLAGHLGLTDEEVVEGLVAANGHTSGSLDAPHSDHGDGPTTGHTLADVMGEEEPALAL 196

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +QA        +L  L+ RE  +LRMRFG     + T  ++G    +++ ++ ++  
Sbjct: 197 VEDVQA-----LAPLLQRLSERERSMLRMRFG----EELTQAQIGTALGISQMQVSRLLN 247

Query: 662 KAIRKLK 668
           + +  L+
Sbjct: 248 RILAHLR 254


>gi|194016072|ref|ZP_03054687.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
 gi|194012427|gb|EDW21994.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
          Length = 262

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/252 (21%), Positives = 115/252 (45%), Gaps = 6/252 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E   ++        +   A+  +VE    LV  +AKKY+       DL Q 
Sbjct: 5   SKTMKLTKDEVDRLIQ--SYQSNQDEQAQLTLVECYTNLVDMLAKKYSKGKSFHEDLRQV 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++    
Sbjct: 63  GMIGLLGAIKRYDPLVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAV 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             ++ + ++ P  +EIA+ L +  E V + +++ K   +L    G E  S          
Sbjct: 123 DHLTTETQKSPQVQEIAEYLDVTEEEVLETMEMGKSYQALSVDQGVEADSEGSTVTILDV 182

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  +   + N +     VL  LT RE+ ++ + +      + + +E G    +++  +
Sbjct: 183 VGSQEEGYERVNQKMMLESVLHVLTDREKEIINLTYL----QNKSQKETGDLLGISQMHV 238

Query: 657 RQIEAKAIRKLK 668
            +++ KA++KL+
Sbjct: 239 SRLQRKAVKKLR 250


>gi|196044126|ref|ZP_03111362.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218902186|ref|YP_002450020.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
 gi|196024765|gb|EDX63436.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218534787|gb|ACK87185.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
          Length = 257

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 118/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|32423705|gb|AAP81248.1| sigma-32 subunit of RNA polymerase [Candidatus Portiera
           aleyrodidarum]
          Length = 280

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 72/268 (26%), Positives = 126/268 (47%), Gaps = 12/268 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   IK++     IS  +   +   +R        A + +V +NLR VI +A+ Y+  GL
Sbjct: 10  IEGYIKTVLGFPIISAQDEYDLARRLR--NKGDLDAARCLVISNLRFVIHIARSYSGYGL 67

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
           Q  D+IQEGN+GLMKA ++FD   G +  ++A+ W+K  I   +      ++I     + 
Sbjct: 68  QNSDIIQEGNVGLMKAVKRFDPAHGVRLVSFAIHWIKAEIHEYVLRNWRIVKIATTKSQR 127

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDTS 586
           K+   +R A+   N + RE   + IAK L +    VR++    +      +    +E  +
Sbjct: 128 KLFFSLRCAKTSLNWLNRE-EIKSIAKDLNVKPTVVREMECRLSSTDYGFDNKQKEEKNN 186

Query: 587 H--LGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +    +++ED     A+   +   +          L  L  R   +L+ R+        T
Sbjct: 187 YKNPSNYLEDSRFDPALQFENFDFERYSYRRLYVALNKLDERVRDILKQRWL--NEPKAT 244

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L E+   + V+ ERIRQ+E +AI+K+K+
Sbjct: 245 LHELADIYGVSAERIRQLEQRAIKKIKN 272


>gi|52144331|ref|YP_082499.1| RNA polymerase sigma factor SigB [Bacillus cereus E33L]
 gi|51977800|gb|AAU19350.1| RNA polymerase sigma-B factor [Bacillus cereus E33L]
          Length = 258

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 118/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 2   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 60  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 120 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 180 RIE--SVGEVEQGYEQTERRLVLEDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 233

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 234 ISQMHVSRIKRQAISKLKQAA 254


>gi|254973932|ref|ZP_05270404.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-66c26]
 gi|255091318|ref|ZP_05320796.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CIP 107932]
 gi|255312976|ref|ZP_05354559.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-76w55]
 gi|255515735|ref|ZP_05383411.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-97b34]
 gi|255648829|ref|ZP_05395731.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-37x79]
 gi|260682047|ref|YP_003213332.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260685645|ref|YP_003216778.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
 gi|306518943|ref|ZP_07405290.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-32g58]
 gi|260208210|emb|CBA60565.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260211661|emb|CBE01928.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
          Length = 233

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 123/232 (53%), Gaps = 11/232 (4%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++E+++ N+ LV S+A+K+    +G ++ DL+  G IGL+ A  KFD   G KFS+Y+  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYI 62

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +K AI   I +QS    I  H   K++K  R   ++ +K+ REPT  EIAK+L +  + 
Sbjct: 63  KIKSAILDEIRNQS---PISKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELNVSEKE 119

Query: 563 VR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +   +        +SL   I ++    + D I D+   +P +   +    E  ++ +++L
Sbjct: 120 LHDIESNIDMLNIVSLNYVIFEDTNETVQDVISDREEEAPENIIEEEEKLEILSKAISNL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RE+ +L + +      D  L+E+GK   V+  R+ Q+  K+IR L++  +
Sbjct: 180 NEREKLILSLYY----YEDLNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227


>gi|326203397|ref|ZP_08193262.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325986655|gb|EGD47486.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 249

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + E+V   L L   ++KK+ NRG+ F D+ Q   + L+KA E+F    G KF ++A 
Sbjct: 26  QDYRNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALIKAVERFSPEKGVKFISFAT 85

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   I R   D+S TI+IP  + +    V +    ++ K+ R P  +EIA+ + + V+
Sbjct: 86  PTILGEIKRFFRDKSTTIKIPRRIYESRQGVNKARDELTQKLSRVPRADEIAEYMGISVD 145

Query: 562 GVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V ++L+     I  SL+  I  E+ S LGD +          +    + ++   + L S
Sbjct: 146 TVLEILEAGSSSIVKSLDQSINQENDSELGDTLGYDE-----KTYEMIDNKDFLEKALTS 200

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               E+  ++ R+      + T +++ +   V++  I ++E K + K +   +
Sbjct: 201 FNDIEKEFIKYRY----IQNMTQKQIAEILGVSQMYISRMEKKILDKFRTYLK 249


>gi|325981885|ref|YP_004294287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Nitrosomonas sp.
           AL212]
 gi|325531404|gb|ADZ26125.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Nitrosomonas sp.
           AL212]
          Length = 238

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           +I K + +     LV  +A     R    +Q  DLIQ G IGL+ A  +++   G +F +
Sbjct: 9   AIDKDQFIAEFTPLVKRIAYHMMTRLPASVQVDDLIQAGMIGLLDAINRYEGSYGRQFES 68

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++ +I   + +      +P  +R K+ ++      +  +    P   ++AK+L M
Sbjct: 69  YAAQRIRGSILDELREADW---LPRSIRKKMRRIEAAVNLLEQRNGCAPNELDLAKELDM 125

Query: 559 PVEGVRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            ++   + L+  +   +        +D     D +   +   PL++ +  N R      +
Sbjct: 126 SLDEYHETLQSARGAQLIYYEDFQQDDEEPFLDRLFIDSEGDPLNALLDENFRNQLIAAI 185

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +L PRE++++ M +      +  L E+G+   V+  R+ Q+  +A+ +L+   R+
Sbjct: 186 DNLPPREKQMMGMHY----EQEMNLREIGEVLGVSESRVCQLHTQAVARLRSRLRN 237


>gi|331086150|ref|ZP_08335232.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406309|gb|EGG85823.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 259

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 125/247 (50%), Gaps = 14/247 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E +   ++  K +     A++  ++ NLRLV+SV K++ +      DL Q G +GLMKA
Sbjct: 21  NEEKE--ALFVKIKEGDEAARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCVGLMKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + F+  L  KFSTYA+  +   I R + D +  IR+   +RD  +K +        +  
Sbjct: 79  IDNFNTDLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAYKAIYAKEGYMKRHL 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLD 602
           +EPT EEIA+++ +  E +   L   + P+SL  P+ ++  D  ++ D I DK   +  +
Sbjct: 138 KEPTVEEIAEEIGIAKEDIIFALDAIQAPMSLNEPVYNDSGDALYVMDQISDKK--NREE 195

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++     +    +  L  RE  ++++RF  G     T  EV  Q  +++ ++ ++E  
Sbjct: 196 YWVEGL---SLEAAMERLNERERFIIQLRFFEG----KTQMEVASQVKISQAQVSRLEKN 248

Query: 663 AIRKLKH 669
           A++ ++ 
Sbjct: 249 ALKTMRQ 255


>gi|284043274|ref|YP_003393614.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947495|gb|ADB50239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 258

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 116/235 (49%), Gaps = 9/235 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R  E     A++ ++E  + LV S+A++Y NRG    DL Q G +GL+KA ++FD   
Sbjct: 21  LRRWHEERDEDARRALIERMMPLVRSLARRYANRGEPLDDLEQVGCVGLIKAVDRFDLSR 80

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FST+A+  +   I R   D++ ++R+   +++   +V R A R+S K+ R PT E++
Sbjct: 81  ELRFSTFAVPTILGEIKRHFRDRAWSVRVSRGLQELSARVTREADRLSTKLGRSPTIEDL 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+      E V + L+  +   ++       D       I  ++          A  R  
Sbjct: 141 AEATNSTPEQVLEALQGAQAYSTVPLEEPLGDDGEPVARIGAED-----PEFELAEERIE 195

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +R L  L+ RE R++ +RF  G     T  E+ ++  +++  + ++  +++ ++
Sbjct: 196 LSRGLHVLSERERRIVLLRFFAG----LTQREIAERVGISQMHVSRLLRRSLERM 246


>gi|167507913|gb|ABZ81277.1| RpoD [Thalassospira sp. MCCC 1A01051]
 gi|167507917|gb|ABZ81279.1| RpoD [Thalassospira sp. MCCC 1A01072]
 gi|167507945|gb|ABZ81293.1| RpoD [Thalassospira sp. MCCC 1A01448]
 gi|167507967|gb|ABZ81304.1| RpoD [Thalassospira sp. MCCC 1A02094]
          Length = 260

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 113/258 (43%), Gaps = 19/258 (7%)

Query: 179 TLLREIIDLEACIGPESKG--------------GFFHGTEGHSYQKREDSSQEKERDDVQ 224
            LLR++IDLE   G                   G             ED   E E  +  
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAAEGDEAEETEGDDFEAAAVETDADEDEEAETETPEPT 60

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                 E      +++  +     E   + +   D++ +    +LS ME++L  +V+   
Sbjct: 61  GAPASDEEEQDDDEEESDEDSEGSEGDGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKF 120

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           + IA+ Y +L   Q+  +      +S       +   LK ++V L+  + LN  RI+ L+
Sbjct: 121 ELIAKTYEKLHKAQEQRLVAMNKGESVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELL 180

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           + L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK F+
Sbjct: 181 DHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVSELPGKGWKAFI 240

Query: 400 ACEVDSILKIRNEIKSIS 417
               D I ++R ++  +S
Sbjct: 241 ERYPDEIAQLREQVGGVS 258


>gi|167507911|gb|ABZ81276.1| RpoD [Thalassospira sp. MCCC 1A01041]
 gi|167507923|gb|ABZ81282.1| RpoD [Thalassospira sp. MCCC 1A01140]
 gi|167507999|gb|ABZ81320.1| RpoD [Thalassospira sp. MCCC 1A03005]
 gi|167508001|gb|ABZ81321.1| RpoD [Thalassospira sp. MCCC 1A03052]
 gi|167508003|gb|ABZ81322.1| RpoD [Thalassospira sp. MCCC 1A03093]
          Length = 260

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 113/258 (43%), Gaps = 19/258 (7%)

Query: 179 TLLREIIDLEACIGPESKG--------------GFFHGTEGHSYQKREDSSQEKERDDVQ 224
            LLR++IDLE   G                   G             ED   E E  +  
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAAEGDEAEETEGDDFEAAAVETDADEDEEAETETPEPT 60

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                 E      +++  +     E   + +   D++ +    +LS ME++L  +V+   
Sbjct: 61  GAPASDEEEEDDDEEESDEDSEGSEGEGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKF 120

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           + IA+ Y +L   Q+  +      +S       +   LK ++V L+  + LN  RI+ L+
Sbjct: 121 ELIAKTYEKLHKAQEQRLVAMNKGESVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELL 180

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           + L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK F+
Sbjct: 181 DHLTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVSELPGKGWKAFI 240

Query: 400 ACEVDSILKIRNEIKSIS 417
               D I ++R ++  +S
Sbjct: 241 ERYPDEIAQLREQVGGVS 258


>gi|161502922|ref|YP_001570034.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160864269|gb|ABX20892.1| hypothetical protein SARI_00981 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 229

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 111/228 (48%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L +PVE
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVAERLGIPVE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + E+    +PL   ++++LR+     + SL
Sbjct: 120 EYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQKENPLHQLLESDLRQRVMGAIESL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|256396292|ref|YP_003117856.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256362518|gb|ACU76015.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 263

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 111/242 (45%), Gaps = 13/242 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  +   + E    ++ ++   +     VA K+  RG    DL Q   +GL+KA + FD 
Sbjct: 24  LRRMAPDDAEYEGLREFVIGEYMSYARYVAGKFRQRGESQADLEQVAYLGLVKAVDNFDP 83

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   +   + R   D +  + +P  +++    V    R ++ ++   P+  
Sbjct: 84  DYGAAFLTYATPMIAGEVRRHFRDTTWDVHVPRRVQENALAVRAAERELTQQLGHAPSAA 143

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQ 606
           +IA++L +  + V +  +        SL+ P+     D + +G+ + D++    L     
Sbjct: 144 QIAERLDLSADEVAEAYEASAAHHTASLDVPVAMADGDGASMGELMGDEDPGFELVVD-- 201

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              RE    +LA L+ R++R+L M+F        +  ++G +  V++ ++ ++ ++ + +
Sbjct: 202 ---REALKPLLAELSTRDKRILLMKFFRN----MSQAQIGAELGVSQMQVSRLLSQILGR 254

Query: 667 LK 668
           L+
Sbjct: 255 LR 256


>gi|326790567|ref|YP_004308388.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
 gi|326541331|gb|ADZ83190.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
          Length = 239

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 121/241 (50%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H + ++++ +    IAK  +V+ NL LV S+ ++++NRG    DL Q G+IGL+K+ +KF
Sbjct: 3   HTLELIQRAQQGDEIAKNILVQENLGLVWSLVRRFSNRGYDMEDLFQIGSIGLLKSIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +KV      +  ++ REPT
Sbjct: 63  DLSFNVKFSTYAVPMIVGEIKRFLRD-DGMIKVSRSLKETAYKVRILKDELIRELNREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EIA  L + VE V + L+   E  SL   I   D   +   + DK    P       +
Sbjct: 122 ISEIAAGLDLQVEEVVEALESNAEIESLNAVIYQGDGKPI--TLSDKIDEVPTLQNSLVD 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +   T ++  L P E  ++ MR+      D T  E+     +++ ++ +IE + ++K++
Sbjct: 180 -KMILTELIERLLPIEREIIHMRYF----EDRTQTEIASALDISQVQVSRIEKRILKKMR 234

Query: 669 H 669
            
Sbjct: 235 E 235


>gi|290962882|ref|YP_003494064.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652408|emb|CBG75541.1| probable sigma factor [Streptomyces scabiei 87.22]
          Length = 280

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 110/235 (46%), Gaps = 15/235 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ NRG    DL Q   +GL+KA ++F+   G  F +YA+  +
Sbjct: 51  RDELVRAWLPMAHRIASRFRNRGESLEDLRQVAAMGLVKAVDRFEPERG-AFESYAVPTI 109

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK--REPTPEEIAKKLAMPVEG 562
              I R   D+  T+R+P  ++D  +KV    R +S       EP+  +IA    +  E 
Sbjct: 110 TGEIKRHFRDRMWTLRVPRRVQDLRNKVRVARRELSQTSGGSAEPSVADIAALAGLTEEE 169

Query: 563 VRKVLKI--TKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           V   ++   +   +SL+  +   +D  +L D +   +A   +        RE+  + L+ 
Sbjct: 170 VHAGMEALDSFSALSLDAEMASGDDGYNLADTLGAPDAAYDVVVD-----RESVKQGLSR 224

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  RE  +L MRF      D T   +  +  +++  + ++ +++  +++  +  +
Sbjct: 225 LPERERAILYMRFF----EDMTQNRIADRLGISQMHVSRLISRSCARVREEALGR 275


>gi|229131899|ref|ZP_04260765.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
 gi|228651574|gb|EEL07543.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
          Length = 224

 Score =  119 bits (298), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 103/226 (45%), Gaps = 8/226 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D++Q G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  + +P  ++D   K+      +++ ++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGVHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIM 120

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                 +  SL+  + +         IE  +         Q   R     +   L   E+
Sbjct: 121 DAKNNYQVSSLDDVVENSSDGSSVARIE--SVGEVEQGYEQTERRLVLKDIFNVLNDTEK 178

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+   FG  +N     ++ G++  +++  + +I+ +AI KLK  +
Sbjct: 179 SVIHYIFGENLNQ----KDTGERLGISQMHVSRIKRQAISKLKQAA 220


>gi|297530579|ref|YP_003671854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297253831|gb|ADI27277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 251

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 101/247 (40%), Gaps = 12/247 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLM 482
           E R               A +E+V+  + LV    ++ +      +   +L+  G +GL 
Sbjct: 8   EERKYWD--EWIHGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLY 65

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A EKFD     KF TYA + ++ AI   +  +     +P  MRDK  K+     R+  +
Sbjct: 66  DALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSMRDKAKKIEEAIERLEQR 122

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R  T +EIA +L M  E V+     T     L       D       + D  A  P +
Sbjct: 123 HMRSVTAKEIAAELGMTEEEVQAAASETFFSHWLPLGQTTVDEDEGLLSVRDDRAPLPEE 182

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++  + E     +  L  +E+ V+ + +      + T  E+G    ++  RI QI AK
Sbjct: 183 QIVKQEMIEKLAEAIGQLNEKEQLVISLFY----KEELTFTEIGSLLHLSTSRISQIHAK 238

Query: 663 AIRKLKH 669
           A+ KL+ 
Sbjct: 239 ALWKLRR 245


>gi|107099361|ref|ZP_01363279.1| hypothetical protein PaerPA_01000373 [Pseudomonas aeruginosa PACS2]
          Length = 274

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 66/269 (24%), Positives = 122/269 (45%), Gaps = 15/269 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + S++    +S  + R +   +     +   A ++MV A+LR V+ +AK Y+  GL
Sbjct: 7   LEAYVHSVNSIPLLSPEQERELAERL--FYQQDLEAARQMVLAHLRFVVHIAKSYSGYGL 64

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 65  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 124

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS- 586
           K+   +R+ ++    +  E     +A+ L +    VR++            P  D D   
Sbjct: 125 KLFFNLRSQKKRLAWLNNEEVHR-VAESLGVEPREVREMESRLTGQDMAFDPAADADDES 183

Query: 587 ---HLGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGIGMNTD 639
                  ++ED     P      A+  ++        L  L  R   +L+ R+       
Sbjct: 184 AYQSPAHYLEDHR-YDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWL--SEEK 240

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 241 ATLHDLAEKYNVSAERIRQLEKNAMSKLK 269


>gi|13473307|ref|NP_104874.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14024055|dbj|BAB50660.1| RpoH-like sigma factor C [Mesorhizobium loti MAFF303099]
          Length = 287

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 120/257 (46%), Gaps = 14/257 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +  + ++       A   +  A++RLVIS+A K+ + GL   DLIQEG++GL
Sbjct: 20  LERDEEHRLALLWKQD--NDQNALHSITVAHMRLVISMASKFRHYGLPLGDLIQEGHVGL 77

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           ++AA +F+     +FSTYA WW++ ++   I      +R       K     + R   R+
Sbjct: 78  LEAAARFEPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 540 SN---KIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE-DTSHLGDFIED 594
           +N    +       E++  L +    V  +  +++    SL  P+ D+   +   DF+  
Sbjct: 138 ANGAEPLSNTTLYREVSVALGVSEADVAMMDSRLSAPDSSLNMPLADDAGATERMDFLVS 197

Query: 595 KNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            + +       + ++          L +L  RE R++        +   TLE +G+   +
Sbjct: 198 DDPLPDEIVGDKIDVARRSLWLKEALHALNARELRIIEE--RRLNDEGATLEALGETLGI 255

Query: 652 TRERIRQIEAKAIRKLK 668
           ++ER+RQIEA+A+ KLK
Sbjct: 256 SKERVRQIEARAMEKLK 272


>gi|297203565|ref|ZP_06920962.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|297148443|gb|EFH28990.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 265

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 120/256 (46%), Gaps = 19/256 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E +    + ++VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 22  FRRLAALPPGPERDTL--RGQVVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           ++D  LG+ F +YA+  +   I R   D   T+ +P  ++D  ++V   ++ ++  I  R
Sbjct: 80  RYDPALGHAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQDLRNRVRIASQDLAQTIPGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            PT  EIA+  +M  E V   L+   +   +SL+  +   ED   L D +      S   
Sbjct: 140 RPTVAEIAEHASMSEEDVLVGLEALESFSALSLDAELPGSEDGYSLADALG-----SFDP 194

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +      RE+    LA+L  RE  +L MRF   M      E    Q  +++  + ++ ++
Sbjct: 195 ALDTVVDRESVKPRLAALPERERAILYMRFFGDMTQSRIAE----QLGISQMHVSRLISR 250

Query: 663 AIRKLKHPSRSKKLRS 678
              +++     + LR 
Sbjct: 251 CCGRMRE----QILRD 262


>gi|318061849|ref|ZP_07980570.1| sigma factor [Streptomyces sp. SA3_actG]
          Length = 295

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 105/240 (43%), Gaps = 12/240 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              +  +VEA L +   +A +Y  RG    DL Q   +GL++A ++FD  +   F TYA+
Sbjct: 35  ERQRALLVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAV 94

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPV 560
             ++  + R   D +  + +P  +++    V    + ++ +   R P+  E+A+   +  
Sbjct: 95  PTMQGELKRHFRDNTWGVHVPRRVQELRSAVRAALQELAPRPALRAPSVGELARCAKLSE 154

Query: 561 EGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             VR+ L+   +   +SL++    E    L D +  ++      +      RE+    LA
Sbjct: 155 AEVRQGLEALDSYRSVSLDSAAPSEGEHPLRDRLGAED-----PAYETVVDRESVRPALA 209

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  RE  +L +RF        T   +  +  +++  + ++   A  +++H   ++  R 
Sbjct: 210 ELPERERYILYLRFFH----ARTQRAIAAELGLSQMHVSRLITHACAQVRHRVEARPPRG 265


>gi|118476614|ref|YP_893765.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis str. Al
           Hakam]
 gi|301052635|ref|YP_003790846.1| sigma factor B [Bacillus anthracis CI]
 gi|118415839|gb|ABK84258.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Bacillus thuringiensis
           str. Al Hakam]
 gi|300374804|gb|ADK03708.1| sigma factor B [Bacillus cereus biovar anthracis str. CI]
          Length = 258

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 118/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 2   MEIQSQPTNLTKEDVIKLIAEFQQNQCG--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 60  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 120 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 180 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 233

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 234 ISQMHVSRIKRQAISKLKQAA 254


>gi|54022121|ref|YP_116363.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54013629|dbj|BAD54999.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 266

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 117/243 (48%), Gaps = 8/243 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + + +      ++E++E  L L   +A+K++ RG  F DL+Q   +G++ A ++FD 
Sbjct: 27  LRALAEDDPRRRALREELIERCLPLAEHIARKFSGRGENFEDLLQIARVGMVAAVDRFDP 86

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   + R   D + ++R+P  +++    +      ++ ++ R P   
Sbjct: 87  TQGAPFLGFAVPTIMGEVRRHFRDHTWSVRVPRRLKELQATLNPAIETLTQRLGRMPKAR 146

Query: 551 EIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A++L + +  V + L      +  S++   GD+  S      +   A  P    ++  
Sbjct: 147 ELAEELGVDIAEVTQALVARNAYQTSSIDGSSGDDGESSAPALADTLGAEDPEFGTVENY 206

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L      ++A+L  RE+RVL MRF        + E++ +Q   ++ ++ +I ++ ++ L+
Sbjct: 207 L--AVKPLIAALPEREQRVLVMRFFH----SMSQEQIAQQIGCSQMQVSRILSRTLKSLR 260

Query: 669 HPS 671
             +
Sbjct: 261 EQA 263


>gi|225569422|ref|ZP_03778447.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
 gi|225161630|gb|EEG74249.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
          Length = 237

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 119/243 (48%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A+ ++VE N  LV  + K++ NRG +  DL Q GNIGL+KA +KF
Sbjct: 3   HTIALIKKSHQGDEKARAQLVEENAGLVWCIVKRFYNRGAEAEDLFQVGNIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      ++   + REPT
Sbjct: 63  DMSYEVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELSYKAYLCQEKLQEALGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQ 606
             EIA+ L +  E +   L  + +  SL  PI  ++     L D + +K          +
Sbjct: 122 ITEIAEYLEVDREELTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGE-----EK 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                   ++L  L   E +++ +R+           +VG++  +++ ++ ++E K +++
Sbjct: 177 ILNHMLLQQLLEYLNKDERQLIYLRYFANQTQS----QVGQELGISQVQVSRLEKKILKR 232

Query: 667 LKH 669
           L+ 
Sbjct: 233 LRE 235


>gi|157161393|ref|YP_001458711.1| flagellar biosynthesis sigma factor [Escherichia coli HS]
 gi|157067073|gb|ABV06328.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           HS]
          Length = 239

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 111/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +VV+   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVVQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|22770516|gb|AAN06633.1|AF497205_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L    +++++ 
Sbjct: 249 LLEALQNEEVE 259


>gi|157691239|ref|YP_001485701.1| RNA polymerase sigma factor SigB [Bacillus pumilus SAFR-032]
 gi|157679997|gb|ABV61141.1| DNA-directed RNA polymerase sigma subunit SigB [Bacillus pumilus
           SAFR-032]
          Length = 262

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 53/252 (21%), Positives = 115/252 (45%), Gaps = 6/252 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E   ++        +   A+  +VE    LV  +AKKY+       DL Q 
Sbjct: 5   SKTMKLTKDEVDRLIQ--SYQSNQDEQAQLTLVECYTNLVDMLAKKYSKGKSFHEDLRQV 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++    
Sbjct: 63  GMIGLLGAIKRYDPLVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAV 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             ++ + ++ P  +EIA+ L +  E V + +++ K   +L    G E  S          
Sbjct: 123 DHLTTETQKSPKVQEIAEYLDVTEEEVLETMEMGKSYQALSVDQGVEADSEGSTVTILDV 182

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  +   + N +     VL  LT RE+ ++ + +      + + +E G    +++  +
Sbjct: 183 VGSQEEGYERVNQKMMLESVLHVLTDREKEIINLTYL----QNKSQKETGDLLGISQMHV 238

Query: 657 RQIEAKAIRKLK 668
            +++ KA++KL+
Sbjct: 239 SRLQRKAVKKLR 250


>gi|239934536|emb|CAR94582.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 259

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/298 (16%), Positives = 102/298 (34%), Gaps = 48/298 (16%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G + ++ +L   P     L+   + +  G   L +II            
Sbjct: 7   GEIQIAKRIEEGVSQVLYALASYPSVVAQLLAEYEIVERGEARLSDII-----------I 55

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
            F    +       E ++     +   + + D +     ++D    +   PE A      
Sbjct: 56  SFNEFDDTSDTAANETTTASSGVNSAADEDSDDDEDEAETEDTVVDLGPDPEEAAR---- 111

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
                                       E+ E+Y ++ +      N +K   +    KVL
Sbjct: 112 -------------------------RFAEMRELYGQMLA------NIEKFGINHADNKVL 140

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQG 376
           ++++ +    L L    ++ L+E L     +I   E  ++ +      + R +F+     
Sbjct: 141 RQRMAECFMDLKLTPKVLECLIETLRHTVDQIRTQERIIMNICVGKAQMPRKIFINSFPE 200

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            E +  W      +   ++   +A     I K ++ +  +  E  + I E + I   +
Sbjct: 201 NETNLDWTDEHI-YVGKKYSTALAKYRYDIRKTQSRLLDLQYEESLPIHELKDINRYM 257


>gi|42528183|ref|NP_973281.1| RNA polymerase sigma factor WhiG [Treponema denticola ATCC 35405]
 gi|41819453|gb|AAS13200.1| RNA polymerase sigma-27 factor [Treponema denticola ATCC 35405]
 gi|325474612|gb|EGC77798.1| RNA polymerase sigma-27 factor [Treponema denticola F0402]
          Length = 262

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 106/243 (43%), Gaps = 17/243 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDW 490
           +  +      ++  +     LV  VA K    G+     F DL+  G  GL+ A EK+D 
Sbjct: 17  KYKKTSDPKIREYFILKYAPLVKYVAGK-VGIGMPTNVEFDDLVGYGVFGLLDAIEKYDL 75

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KF+TYA+  ++ AI   +        +P  +R K  ++  T   +  ++ R  + E
Sbjct: 76  DKNVKFNTYAVNRIRGAIFDELRSIDW---VPRSVRQKSREIEETIADLEARLGRSASNE 132

Query: 551 EIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
           EIA  + + +E    +L        ISL       D S    +GD IE  ++++P     
Sbjct: 133 EIAYAMGLDIEEYNSLLLKISATSVISLTDLRFSNDDSEEFSVGDIIEAPSSLNPDVIVE 192

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + +++      +  L  RE++VL M +      D TL E+G+   VT  R+ QI   A  
Sbjct: 193 REDIKRVIVEAIKELPDREKKVLIMYY----YEDMTLREIGEVLHVTESRVSQIHTSANI 248

Query: 666 KLK 668
           KL+
Sbjct: 249 KLR 251


>gi|301029374|ref|ZP_07192470.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
 gi|299877729|gb|EFI85940.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
          Length = 239

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNSTETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|225568653|ref|ZP_03777678.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
 gi|225162581|gb|EEG75200.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
          Length = 259

 Score =  119 bits (298), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 65/266 (24%), Positives = 129/266 (48%), Gaps = 9/266 (3%)

Query: 409 IRNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            + +++   V T  + I +     ++  + +     AK+E ++ NLRLV+SV K++    
Sbjct: 2   AQGKVEICGVNTAKLPILKEEEKEALFARIKAGDEEAKEEYIKGNLRLVLSVIKRFGGSN 61

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA   F+  L  KFSTYA+  +   I R + D +  IR+   +RD
Sbjct: 62  ENPDDLFQIGCIGLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNS-IRVSRSLRD 120

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
             +K +        +  +EPT +EIA+++ +  E +   L   + P+SL+ P+ ++    
Sbjct: 121 TAYKAIYAKENYVKRNLKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDA 180

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L    +  +  +  +  ++     +    +  L  RE  ++++RF  G     T  EV +
Sbjct: 181 LYVMDQISDTKNKEEKWVEDL---SLEAAMEHLGERERYIIKLRFFEG----KTQMEVAE 233

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673
           +  +++ ++ ++E  A+R +K    +
Sbjct: 234 EINISQAQVSRLEKNALRVMKQYLEN 259


>gi|265991792|ref|ZP_06104349.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263002748|gb|EEZ15151.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 293

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 124/267 (46%), Gaps = 15/267 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I+S      +   E R +   +R  E +   A   +  A++RLVIS+A ++    L   D
Sbjct: 17  IRSAMSAPYLEREEERALA--IRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSD 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IH 530
           LIQEG +GL++ A +FD     +FSTYA WW++ ++   I      +R       K    
Sbjct: 75  LIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFF 134

Query: 531 KVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT- 585
            + R   +++         E   EI+ +L +    V     +++    SL   +  E+T 
Sbjct: 135 NLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETG 194

Query: 586 -SHLGDFIEDKNAVSPLDSAIQANLR---ETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            S   DF+ D + +    +    ++       TR L +L  RE  ++R R         T
Sbjct: 195 ASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--T 252

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LE +G++  ++++R+RQIE++A+ KLK
Sbjct: 253 LEALGEKLGISKQRVRQIESRAMEKLK 279


>gi|56419781|ref|YP_147099.1| RNA polymerase sigma factor SigD [Geobacillus kaustophilus HTA426]
 gi|56379623|dbj|BAD75531.1| DNA-directed RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           kaustophilus HTA426]
          Length = 251

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 101/247 (40%), Gaps = 12/247 (4%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLM 482
           E R               A +E+V+  + LV    ++ +      +   +L+  G +GL 
Sbjct: 8   EERKYWD--EWIHGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLY 65

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A EKFD     KF TYA + ++ AI   +  +     +P  MRDK  K+     R+  +
Sbjct: 66  DALEKFDPSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSMRDKAKKIEEAIERLEQR 122

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
             R  T +EIA +L M  E V+     T     L       D       + D  A  P +
Sbjct: 123 HMRSVTAKEIAAELGMTEEEVQAAASETFFSHWLPLGQTTVDEDEGLLAVRDDRAPLPEE 182

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++  + E     +  L  +E+ V+ + +      + T  E+G    ++  RI QI AK
Sbjct: 183 QIVKQEMIEKLAEAIGQLNEKEQLVISLFY----KEELTFTEIGSLLHLSTSRISQIHAK 238

Query: 663 AIRKLKH 669
           A+ KL+ 
Sbjct: 239 ALWKLRR 245


>gi|296332841|ref|ZP_06875301.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673187|ref|YP_003864859.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150121|gb|EFG91010.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411431|gb|ADM36550.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 262

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/254 (21%), Positives = 118/254 (46%), Gaps = 6/254 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T ++  E   ++S       +   A++ +V     LV  +AKKY+       DL Q 
Sbjct: 5   SKTTKLTKDEVDRLIS--DYQTNQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQV 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++    
Sbjct: 63  GMIGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAV 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            +++ + +R P  EEIA+ L +  E V + +++ K   +L      E  +          
Sbjct: 123 DQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEADADGSTVTILDI 182

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D   + N +     VL  L+ RE++++ + +      + + +E G    +++  +
Sbjct: 183 VGSQEDGYERVNQQMMLQSVLHVLSDREKQIIDLTY----IQNKSQKETGDILGISQMHV 238

Query: 657 RQIEAKAIRKLKHP 670
            +++ KA++KL+  
Sbjct: 239 SRLQRKAVKKLREA 252


>gi|88797598|ref|ZP_01113187.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88779770|gb|EAR10956.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 290

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 111/272 (40%), Gaps = 15/272 (5%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   I +++    +S  E + +   +     +   + + +V ++LR V+ +AK Y+  
Sbjct: 19  QNLEAYITTVNGFELLSAEEEKDLAERL--YYHDDLESARRLVMSHLRFVVHIAKSYSGY 76

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA  +F+  +G +  ++A+ W+K  I   I      ++I     
Sbjct: 77  GLNQGDLIQEGNVGLMKAIRRFNPEVGVRLVSFAVHWIKAEIHEYILKNWRIVKIATTKA 136

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS------LETPI 580
            +  K+    R    ++      E  A    + VE         +   S           
Sbjct: 137 QR--KLFFNLRSSKKRLGWLNEREAQAIADDLGVEKKIVYDMEGRLTASDAAFDGFNDDD 194

Query: 581 GDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            D    H  D++    D  A +   +    +        L  L  R   +++ R+     
Sbjct: 195 DDGAAFHPSDYLMNEADDPAAAVEQANYTDDAHGQLFSALEDLDDRSRDIIQQRWL--NE 252

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              TL E+  ++ V+ ERIRQ+E  A+ K+K 
Sbjct: 253 EKATLHELADKYGVSAERIRQLEKNAMNKVKK 284


>gi|296284608|ref|ZP_06862606.1| RNA polymerase factor sigma-32 [Citromicrobium bathyomarinum JL354]
          Length = 280

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 120/273 (43%), Gaps = 16/273 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  I     ++  +   +    R  E E   A  ++V ++LRLV  +A  Y   GL   D
Sbjct: 1   MSEIKKFPVLTAEQEYMLAK--RYEEHEDPEAAAQLVSSHLRLVAKIAMGYRGYGLPVSD 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI--- 529
           LI EGN+GLM+  +KF+   G++ +TYAMWW+K +I   I      +++      K    
Sbjct: 59  LISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTTAAQKKLFF 118

Query: 530 --HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV----RKVLKITKEPISLETPIGDE 583
              ++ +      +        ++IA  L +P + V    R++L      +++     +E
Sbjct: 119 NLRRMKKNLDAYEDTDLHPDDVKKIATDLGVPEQEVINMNRRMLMGGDSSLNVSMRGDEE 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           + S   D++ D   +    +A               + SL  RE+ +L            
Sbjct: 179 NASQWQDWLTDDRPLQDETTADTQEAQVRHAMLLEAMDSLNDREKHILTE--RRLTEDPQ 236

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           TLEE+ K + V+RERIRQIE +A  KL+   + 
Sbjct: 237 TLEELSKVYDVSRERIRQIEVRAFEKLQKAMQR 269


>gi|229165937|ref|ZP_04293702.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
 gi|228617490|gb|EEK74550.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
          Length = 224

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/226 (22%), Positives = 103/226 (45%), Gaps = 8/226 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  + +P  ++D   K+      +++ ++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGVHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                 +  SL+  + +         IE  +         Q   R     +   L   E+
Sbjct: 121 DAKNNYQVSSLDDVVENSSDGSSVARIE--SVGEVEQGYEQTERRLVLDDIFNVLNDTEK 178

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+   FG  +N     ++ G++  +++  + +I+ +AI KLK  +
Sbjct: 179 SVIHYIFGENLNQ----KDTGERLGISQMHVSRIKRQAISKLKQAA 220


>gi|167507895|gb|ABZ81268.1| RpoD [Thalassospira profundimaris]
          Length = 262

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 117/260 (45%), Gaps = 21/260 (8%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            LLR++IDLE   G   +                D+  + E  +    + D E+  +   
Sbjct: 1   LLLRDVIDLETTYGRGLEAEIAAAEGEDEEDTDVDAEADVESFESANDDDDEEAETETPA 60

Query: 239 D----------------DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                            ++S+ +     A+ D+ + D++ +    +LS ME++L  +V+ 
Sbjct: 61  GLTDEAEEDEDEEDDESEKSEDEEGEAGADGDDDDDDDENEQVNVSLSKMEEELTEQVLE 120

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDL 337
             + IA+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ 
Sbjct: 121 KFELIAKTYEKLHKAQEQRLVAMNKGEAVPAATEKRYNKLKNEMVDLMEDVHLNNFRIEE 180

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           L++ L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK 
Sbjct: 181 LLDHLTGLNNRLLGLEGKLLRFADRCKIKRPDFIKQYQGHELDPNWMERVGGLPGKGWKT 240

Query: 398 FVACEVDSILKIRNEIKSIS 417
           FV    + I  +R  I  +S
Sbjct: 241 FVERYSEEIASLREGIGGVS 260


>gi|298715063|emb|CBJ27770.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Ectocarpus siliculosus]
          Length = 737

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 80/338 (23%), Positives = 153/338 (45%), Gaps = 33/338 (9%)

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
            G+ R     +    E +       + +  G  +     E DS  + R  ++ ++   G+
Sbjct: 408 QGVHRQSGGRKFLNHEEEMELGETVQRY-RGLIEAQEKAEKDSGRRPR--LRDVARSAGL 464

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNI 479
           S   F  ++            A++++V  NL LV+S+A KY            LIQEG I
Sbjct: 465 SEEAFASVMQ-------AGMEARQKLVVCNLALVVSLANKYKRSHFDCGCLQTLIQEGTI 517

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL++AAE++D   G++F+TYA+WW++  +  S+  +   I +P+ ++++ + V R+  ++
Sbjct: 518 GLIRAAERYDPSKGFRFTTYAIWWIEARLRVSVQTEERFIHVPMWVKNQYNTVHRSVPKL 577

Query: 540 SNKIKREPTPEEIAKKLAMP-----------VEGVRKVLKITKEPISLETPIG-----DE 583
              + REPT EE+A ++ +            VE +   +   ++  SL+ P+        
Sbjct: 578 RKSLGREPTSEELAAQVEIDTNSKVVVTPKRVEELETWVSFHRKHESLDVPLEVSTPVPA 637

Query: 584 DTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D S + D +   D +  S  +  IQ +  E+   +   L+  + ++LRM+ G+G      
Sbjct: 638 DCSTIEDGVKAPDPSTESTSELEIQRDFLES--CLCQDLSKIQRKILRMKVGLGGEKGKN 695

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            +E+ +   +    +   E KA  KL+   R     SF
Sbjct: 696 RQEISRALKMPFNNVISEERKAFYKLRGLQRGGGYPSF 733


>gi|331663420|ref|ZP_08364330.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
 gi|331059219|gb|EGI31196.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
          Length = 239

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGSVLEVGESRVSQLHSQAIKRLR 233


>gi|328955594|ref|YP_004372927.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
 gi|328455918|gb|AEB07112.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
          Length = 262

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 119/234 (50%), Gaps = 5/234 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E     A++++V +++ LV  +A K+ NRG    DL+Q G +GL+KA ++F+   G 
Sbjct: 23  RYKEDGDDDAREKLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKAIDRFEPARGL 82

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F+TYA   +   I R   D+  ++R+P  +++   KV +    ++ +++R P  EEIA+
Sbjct: 83  EFTTYATPTILGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDLLTTELQRSPKVEEIAE 142

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L   V+ V + ++ +    S+         +     I D+ A+   +     + R    
Sbjct: 143 YLDATVDEVLEAMESSSAYSSVPLEGTGSSENDDAPSIIDRYAID-DNVLSFTDDRLIIE 201

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L S +PRE  V+ +RF  G     T  E+ +Q  +++ ++ ++  + ++K++
Sbjct: 202 DALESFSPREREVVNLRFLKG----MTQIEIAEQLGISQVQVSRLLRRTLKKIQ 251


>gi|161613481|ref|YP_001587446.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167993526|ref|ZP_02574620.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168234127|ref|ZP_02659185.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168244804|ref|ZP_02669736.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168259759|ref|ZP_02681732.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168822997|ref|ZP_02834997.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194445382|ref|YP_002041220.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194450090|ref|YP_002046006.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471287|ref|ZP_03077271.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197251137|ref|YP_002146068.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197362055|ref|YP_002141692.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242943|ref|YP_002215131.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200390898|ref|ZP_03217509.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|213053507|ref|ZP_03346385.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213650343|ref|ZP_03380396.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855803|ref|ZP_03384043.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|238912471|ref|ZP_04656308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289824078|ref|ZP_06543676.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|56127386|gb|AAV76892.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. ATCC 9150]
 gi|161362845|gb|ABX66613.1| hypothetical protein SPAB_01198 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194404045|gb|ACF64267.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194408394|gb|ACF68613.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194457651|gb|EDX46490.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197093532|emb|CAR58994.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. AKU_12601]
 gi|197214840|gb|ACH52237.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197937459|gb|ACH74792.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199603343|gb|EDZ01889.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205328422|gb|EDZ15186.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205331884|gb|EDZ18648.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205336383|gb|EDZ23147.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205340661|gb|EDZ27425.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350810|gb|EDZ37441.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|312912946|dbj|BAJ36920.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321224599|gb|EFX49662.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322616949|gb|EFY13857.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322618189|gb|EFY15081.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322625859|gb|EFY22678.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626311|gb|EFY23121.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322632726|gb|EFY29471.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322639068|gb|EFY35761.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640509|gb|EFY37162.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647255|gb|EFY43754.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649897|gb|EFY46318.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322655505|gb|EFY51813.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322660283|gb|EFY56521.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662964|gb|EFY59171.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668149|gb|EFY64308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322674091|gb|EFY70185.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675556|gb|EFY71630.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322683032|gb|EFY79048.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686726|gb|EFY82704.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195385|gb|EFZ80565.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199276|gb|EFZ84371.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204441|gb|EFZ89447.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323207531|gb|EFZ92479.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323211856|gb|EFZ96687.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323217516|gb|EGA02235.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323219591|gb|EGA04075.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223594|gb|EGA07909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231538|gb|EGA15651.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235981|gb|EGA20060.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240551|gb|EGA24594.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245443|gb|EGA29443.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323253976|gb|EGA37800.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323255497|gb|EGA39258.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262094|gb|EGA45657.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323266217|gb|EGA49707.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270674|gb|EGA54115.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326622879|gb|EGE29224.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
          Length = 229

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 109/228 (47%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L +PV 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVAERLGIPVA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + E+    +PL   ++ +LR+     + SL
Sbjct: 120 EYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVMDAIESL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|238917528|ref|YP_002931045.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872888|gb|ACR72598.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 249

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 124/240 (51%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K       A++++V  NL L+ ++ K++  RG +  DL Q G IGL+KA + F+  
Sbjct: 16  ELIAKAHNNDKEAREKLVTDNLGLIWNIIKRFKGRGTEQEDLFQIGCIGLIKAIDNFNLD 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           +   FSTYA+  +   I R + D    +++   +++   K ++ A ++ + +  EPT E+
Sbjct: 76  MDVAFSTYAVPMITGEIRRFLRD-DGMVKVSRSIKENAVKSMKAAGQLRDTLGCEPTVEQ 134

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANL 609
           IA    + VE +   +  + E  S+   I   D S   L D +EDK  +        A+ 
Sbjct: 135 IAAACELSVEDITLSMSASMEVESIYKTIYQGDGSEVMLMDKLEDKADIG-----ETASS 189

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    +++ +L+ RE+ ++RMR+      D+T  +V K+F +++ ++ ++E K +  ++ 
Sbjct: 190 KVALVQLMETLSQREKELIRMRY----YDDYTQMQVAKEFGISQVQVSRMEKKILSGMRK 245


>gi|61657181|emb|CAG17721.1| DNA-directed RNA polymerase subunit D [Pseudomonas aeruginosa]
          Length = 261

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/301 (17%), Positives = 112/301 (37%), Gaps = 46/301 (15%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   +M+++ + P T  +++   + +      L ++  L   I P+
Sbjct: 1   TREGEIEIAKRIEEGIREVMSAIAQFPGTVDSILADYNRIVAEGGRLSDV--LSGYIDPD 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                    E  + +                     + +A   + D  + +S   +  +D
Sbjct: 59  DGSLPAEEVEPVNLK---------------------DDSADSKEKDDEEEESDDSSDSDD 97

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
           E +   D +++    +A+ +QL                            +K  + S + 
Sbjct: 98  EGDGGPDPEEARLRFTAVSEQLDKA---------------------KKALKKHGRGSKQA 136

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLER 373
                 L +L   + L   + D LV ++    + +   E  +++L      + R  FL  
Sbjct: 137 TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 196

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
               E D  WV       + ++   +    D IL+ + ++ ++  E  ++++E + I   
Sbjct: 197 FPNHETDEKWVDSVLK-SKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRA 255

Query: 434 V 434
           +
Sbjct: 256 M 256


>gi|308172341|ref|YP_003919046.1| RNA polymerase sigma-37 factor sigma B [Bacillus amyloliquefaciens
           DSM 7]
 gi|307605205|emb|CBI41576.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328552153|gb|AEB22645.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens TA208]
 gi|328910426|gb|AEB62022.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens LL3]
          Length = 262

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 119/258 (46%), Gaps = 6/258 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   S  T ++  E   ++  +     +   A++ +VE    LV  +AKKY+       D
Sbjct: 1   MAQPSKTTKLTKDEVDRLI--LDFQIHDNKEAQETLVEVYTNLVEMLAKKYSKGKSFHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++
Sbjct: 59  LRQVGMIGLLGAIKRYDPEVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                +++ + +R P  EEIA  L +  E V + +++ K   +L      E  +      
Sbjct: 119 KMAVDQLTTETQRSPKVEEIAAFLDVSEEEVLETMEMGKSYQALSVDHSIEADADGSTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S  +   + N +     VL  L+ RE++++ + F      + + +E G    ++
Sbjct: 179 ILDIVGSQEEGYERVNQQMMIKSVLHVLSDREKQIIDLTFV----QNKSQKETGDILGIS 234

Query: 653 RERIRQIEAKAIRKLKHP 670
           +  + +++ KA++KL+  
Sbjct: 235 QMHVSRLQRKAVKKLREA 252


>gi|251795840|ref|YP_003010571.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
 gi|247543466|gb|ACT00485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
          Length = 258

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 120/259 (46%), Gaps = 15/259 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDL 473
             S  + +   +   ++   ++  C    A   +++    LV     K   NR   + DL
Sbjct: 1   MKSQSSCLDQQQIADLLQRYKEMSCND--AATALLQHFESLVRMAVSKISRNRPDLYEDL 58

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q G + +++  +++D   G  F  YAM  V   +   + D+S  I++P +M++K   + 
Sbjct: 59  YQVGQMSMLRLFKQYDSDKGVPFEGYAMKSVIGQLKNYLRDKSWYIQVPRNMKEKGLLIQ 118

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDE-DTSHLGD 590
           +    ++ K++R P  +EIA  L + VE   +VL  + + + +SL+TP+  E D++ +GD
Sbjct: 119 KAIDELTTKLERSPKMDEIAAYLGLSVEETIEVLSSRESYQYVSLDTPLSSEGDSATIGD 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D +           + +   +  +A L   E +VL + +  G     +  E+  Q  
Sbjct: 179 VISDHSD-----KYSHVDNQIALSDAMAQLKEEERKVLVLVYQHGQ----SQREIADQLG 229

Query: 651 VTRERIRQIEAKAIRKLKH 669
           V++  + + + +A+ KL+ 
Sbjct: 230 VSQMSVSRFQKRALDKLRQ 248


>gi|315444786|ref|YP_004077665.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263089|gb|ADT99830.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 284

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 112/247 (45%), Gaps = 6/247 (2%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +    ++++ +        ++ ++   L L   +A+++  RG    DL+Q   +GL+
Sbjct: 32  DVLDMFRELAVLDRDSAAFRRQREAIIARCLPLADHIARRFRGRGEGHEDLVQVARVGLL 91

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD      F  +A+  +   + R   D   ++++P  +++   ++      ++ +
Sbjct: 92  NAVNRFDVDSANDFLAFAVPTMMGEVRRYFRDHGWSLKVPRRLKELNVRLNAARADLTQE 151

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           + R PTP E+AK L +  E V + L       +  T      +   G+ +  ++     D
Sbjct: 152 LNRAPTPSELAKYLGIDREEVVEGLVAANAYSTRSTEQPTTFSGD-GEGLSLQDTFGAPD 210

Query: 603 SAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             IQ  +   T   +LA+L  R+  VL++RF      D T  ++ +Q  V++  + ++ A
Sbjct: 211 DNIQKVIDVNTVQPLLAALPERDRLVLKLRFF----EDRTQSQIAEQIGVSQMHVSRLLA 266

Query: 662 KAIRKLK 668
           +A+  L+
Sbjct: 267 RALATLR 273


>gi|15802357|ref|NP_288383.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7
           EDL933]
 gi|15831915|ref|NP_310688.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           Sakai]
 gi|26248189|ref|NP_754229.1| flagellar biosynthesis sigma factor [Escherichia coli CFT073]
 gi|49176170|ref|NP_416432.3| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|74311731|ref|YP_310150.1| flagellar biosynthesis sigma factor [Shigella sonnei Ss046]
 gi|89108757|ref|AP_002537.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|110642027|ref|YP_669757.1| flagellar biosynthesis sigma factor [Escherichia coli 536]
 gi|157158016|ref|YP_001463226.1| flagellar biosynthesis sigma factor [Escherichia coli E24377A]
 gi|170019740|ref|YP_001724694.1| flagellar biosynthesis sigma factor [Escherichia coli ATCC 8739]
 gi|170081570|ref|YP_001730890.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170684004|ref|YP_001743321.1| flagellar biosynthesis sigma factor [Escherichia coli SMS-3-5]
 gi|187776391|ref|ZP_02802353.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188025223|ref|ZP_02776870.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|189010650|ref|ZP_02808323.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189402557|ref|ZP_02783240.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189403603|ref|ZP_02796533.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189404441|ref|ZP_02789463.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189405427|ref|ZP_02815329.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189406256|ref|ZP_02827273.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|191168296|ref|ZP_03030089.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|191173335|ref|ZP_03034865.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|193066383|ref|ZP_03047431.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|193071158|ref|ZP_03052082.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194429934|ref|ZP_03062444.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194439580|ref|ZP_03071653.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208810387|ref|ZP_03252263.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209399914|ref|YP_002271036.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209919344|ref|YP_002293428.1| flagellar biosynthesis sigma factor [Escherichia coli SE11]
 gi|215487127|ref|YP_002329558.1| flagellar biosynthesis sigma factor [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218554506|ref|YP_002387419.1| flagellar biosynthesis sigma factor [Escherichia coli IAI1]
 gi|218689915|ref|YP_002398127.1| flagellar biosynthesis sigma factor [Escherichia coli ED1a]
 gi|218695529|ref|YP_002403196.1| flagellar biosynthesis sigma factor [Escherichia coli 55989]
 gi|218699514|ref|YP_002407143.1| flagellar biosynthesis sigma factor [Escherichia coli IAI39]
 gi|218705417|ref|YP_002412936.1| flagellar biosynthesis sigma factor [Escherichia coli UMN026]
 gi|238901131|ref|YP_002926927.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253773125|ref|YP_003035956.1| flagellar biosynthesis sigma factor [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254793572|ref|YP_003078409.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           TW14359]
 gi|260844326|ref|YP_003222104.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260855902|ref|YP_003229793.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260868514|ref|YP_003234916.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|291283099|ref|YP_003499917.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|293405408|ref|ZP_06649400.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|293410281|ref|ZP_06653857.1| conserved hypothetical protein [Escherichia coli B354]
 gi|293446304|ref|ZP_06662726.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|298381052|ref|ZP_06990651.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|307314171|ref|ZP_07593781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|312967123|ref|ZP_07781341.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|312973866|ref|ZP_07788038.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|331642544|ref|ZP_08343679.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331668616|ref|ZP_08369464.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331673440|ref|ZP_08374208.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331677807|ref|ZP_08378482.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331683474|ref|ZP_08384075.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332278907|ref|ZP_08391320.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|84028136|sp|P0AEM8|FLIA_ECO57 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028137|sp|P0AEM7|FLIA_ECOL6 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028138|sp|P0AEM6|FLIA_ECOLI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|12516023|gb|AAG56937.1|AE005415_2 flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli O157:H7 str. EDL933]
 gi|26108593|gb|AAN80796.1|AE016762_49 RNA polymerase sigma factor for flagellar operon [Escherichia coli
           CFT073]
 gi|556180|gb|AAC37011.1| sigma factor 28 [Escherichia coli]
 gi|687650|gb|AAC43543.1| sigma F [Escherichia coli]
 gi|1736581|dbj|BAA15742.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|1788231|gb|AAC74989.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13362129|dbj|BAB36084.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli O157:H7 str. Sakai]
 gi|73855208|gb|AAZ87915.1| alternative sigma factor 28 [Shigella sonnei Ss046]
 gi|110343619|gb|ABG69856.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           536]
 gi|157080046|gb|ABV19754.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E24377A]
 gi|169754668|gb|ACA77367.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli ATCC
           8739]
 gi|169889405|gb|ACB03112.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170521722|gb|ACB19900.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SMS-3-5]
 gi|187767374|gb|EDU31218.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014157|gb|EDU52279.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|188999325|gb|EDU68311.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354876|gb|EDU73295.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359713|gb|EDU78132.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189365564|gb|EDU83980.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370194|gb|EDU88610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189375693|gb|EDU94109.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|190901668|gb|EDV61424.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|190906452|gb|EDV66061.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|192925968|gb|EDV80614.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|192955553|gb|EDV86032.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194412023|gb|EDX28335.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194421489|gb|EDX37503.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208724903|gb|EDZ74610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209161314|gb|ACI38747.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209748392|gb|ACI72503.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748394|gb|ACI72504.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748396|gb|ACI72505.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209912603|dbj|BAG77677.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE11]
 gi|215265199|emb|CAS09588.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|218352261|emb|CAU98017.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli 55989]
 gi|218361274|emb|CAQ98858.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI1]
 gi|218369500|emb|CAR17267.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI39]
 gi|218427479|emb|CAR08375.2| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli ED1a]
 gi|218432514|emb|CAR13407.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli UMN026]
 gi|222033663|emb|CAP76404.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LF82]
 gi|238863498|gb|ACR65496.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253324169|gb|ACT28771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254592972|gb|ACT72333.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257754551|dbj|BAI26053.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257759473|dbj|BAI30970.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257764870|dbj|BAI36365.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|260448961|gb|ACX39383.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli DH1]
 gi|284921835|emb|CBG34908.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           042]
 gi|290762972|gb|ADD56933.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|291323134|gb|EFE62562.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|291427616|gb|EFF00643.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|291470749|gb|EFF13233.1| conserved hypothetical protein [Escherichia coli B354]
 gi|298278494|gb|EFI20008.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|306906140|gb|EFN36658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|307553936|gb|ADN46711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ABU 83972]
 gi|309702217|emb|CBJ01534.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ETEC H10407]
 gi|310332461|gb|EFP99696.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|312288587|gb|EFR16489.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|315061222|gb|ADT75549.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli W]
 gi|315617855|gb|EFU98453.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           3431]
 gi|320191897|gb|EFW66544.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC1212]
 gi|320194366|gb|EFW68997.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           WV_060327]
 gi|320198616|gb|EFW73216.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EC4100B]
 gi|323158594|gb|EFZ44608.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E128010]
 gi|323165278|gb|EFZ51066.1| RNA polymerase sigma factor for flagellar operon [Shigella sonnei
           53G]
 gi|323180827|gb|EFZ66367.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1180]
 gi|323186802|gb|EFZ72122.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           RN587/1]
 gi|323378201|gb|ADX50469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli KO11]
 gi|323937197|gb|EGB33477.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1520]
 gi|323940415|gb|EGB36606.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E482]
 gi|323948197|gb|EGB44185.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H120]
 gi|323961971|gb|EGB57570.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H489]
 gi|323968339|gb|EGB63746.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli M863]
 gi|323972715|gb|EGB67916.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TA007]
 gi|323977897|gb|EGB72983.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TW10509]
 gi|324118976|gb|EGC12865.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1167]
 gi|326342331|gb|EGD66112.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1044]
 gi|326344837|gb|EGD68584.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1125]
 gi|327253053|gb|EGE64707.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           STEC_7v]
 gi|331039342|gb|EGI11562.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331063810|gb|EGI35721.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331069638|gb|EGI41025.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331074267|gb|EGI45587.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331079689|gb|EGI50886.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332089656|gb|EGI94758.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           5216-82]
 gi|332101259|gb|EGJ04605.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|332343648|gb|AEE56982.1| RNA polymerase sigma factor for flagellar operon protein
           [Escherichia coli UMNK88]
 gi|332756073|gb|EGJ86426.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           4343-70]
 gi|333003239|gb|EGK22785.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-218]
 gi|333004180|gb|EGK23712.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-272]
 gi|333017792|gb|EGK37099.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-227]
          Length = 239

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|156933482|ref|YP_001437398.1| flagellar biosynthesis sigma factor [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531736|gb|ABU76562.1| hypothetical protein ESA_01300 [Cronobacter sakazakii ATCC BAA-894]
          Length = 229

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 58/228 (25%), Positives = 112/228 (49%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L++P+E
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATELEVAERLSIPLE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + ED    +PL   +++NLRE     + SL
Sbjct: 120 EYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEDNQNENPLHQLLESNLRERVMEAIESL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREQMVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|302528260|ref|ZP_07280602.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302437155|gb|EFL08971.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 261

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 118/253 (46%), Gaps = 18/253 (7%)

Query: 425 SEFRHIVSMVRKGECEASIA------KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            ++RH  ++  +    A         ++ ++E +L L   +A+++  RG    DL+Q   
Sbjct: 7   DDYRHYAALFEEISHLAEDTDEHSRLRRRLIEEHLPLAEHIARRFARRGQPTEDLLQVAR 66

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+ A +++D      F  +A+  V   + R   D + ++R+P  +++    V + A  
Sbjct: 67  IGLINAVDRYDPARQTDFVAFAVPTVMGEVRRYFRDHTWSVRVPRRLKELHLTVGQAATE 126

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIEDK 595
           +  ++ R PT  E+A  L + ++ V + L      +  S++ P  D+  S  L D + D+
Sbjct: 127 LGQRLGRAPTARELADHLDLDLDEVAEALHAGNAYQASSIDYPAHDDSGSVALADTLGDE 186

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +         +   RET   +L SL  RE  +L MRF        T  ++ ++  +++ +
Sbjct: 187 D-----PEIEKLEDRETLKPLLRSLPERERAILVMRFFSN----MTQSQIAERVGLSQMQ 237

Query: 656 IRQIEAKAIRKLK 668
           + ++ A+ +  L+
Sbjct: 238 VSRLLARTLSTLR 250


>gi|239934514|emb|CAR94571.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 255

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 64/313 (20%), Positives = 109/313 (34%), Gaps = 64/313 (20%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGE+ IAKRIE G   ++A+L + P T   +      L+ G   L ++  L   I P 
Sbjct: 4   TREGELEIAKRIEDGLNQVLAALSQYPRTMHIVHQAGARLSVGELRLGDV--LSGFIDPA 61

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
           S+       + +   +  D                         D    VD+ P+     
Sbjct: 62  SETAPPVPHQNNGENRNGD-------------------------DSEEAVDTGPD----- 91

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD-EKSSVK 313
                                        L+E+      L  L   A+   K   +    
Sbjct: 92  -----------------------------LEEVCARIAALVELHKRALAAVKRYGRDHKT 122

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLE 372
            +   E+L + +          DLLV  L  + +RI   E  ++    +   + R  F+ 
Sbjct: 123 ARRRYEELAEQIVQFKFVPRFFDLLVGNLRQVIQRIRSKERAIMEICVRQTQMPRREFVS 182

Query: 373 RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               RE DP W+    +     +   +   +D I +++ ++ SI  E  +SI E + I  
Sbjct: 183 TFPKRETDPQWLQDQLN-AGRAYSAGLREHIDEITRLQQKLVSIEKEACLSIGEIKEINR 241

Query: 433 MVRKGECEASIAK 445
            +  GE +A  AK
Sbjct: 242 RMSIGEAKARRAK 254


>gi|326797246|ref|YP_004315066.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
 gi|326548010|gb|ADZ93230.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
          Length = 288

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 58/270 (21%), Positives = 125/270 (46%), Gaps = 13/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             + + ++ +S    ++  E + +   +         A + +V ++LR V+ +AK Y+  
Sbjct: 15  QHLESYVQGVSTIPILTAEEEQKLAERL--YYDGDLEAARALVMSHLRFVVHIAKSYSGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-M 525
           GL   DL+QEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     
Sbjct: 73  GLSQGDLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKA 132

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT----KEPISLETPIG 581
           + K+   +R+A++  + +      + +A  L +  + VR++            +      
Sbjct: 133 QRKMFFNLRSAKKTLSWLNN-SEVDAVANDLGVSPDVVRQMEGRMSSTDMAFDATTDDDD 191

Query: 582 DEDTSHLGDFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D        ++ED     A+   D   +A+      + ++ L  R   +L  R+     +
Sbjct: 192 DSAFQAPASYLEDGRYDPAMLLEDGNWEADSNRRLQQAMSDLDERSRNILVQRWLSENKS 251

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL ++  ++ V+ ERIRQ+E  A++K++
Sbjct: 252 --TLHDLADEYGVSAERIRQLEKNAMKKIR 279


>gi|210633875|ref|ZP_03297890.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
 gi|210159044|gb|EEA90015.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
          Length = 261

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 122/244 (50%), Gaps = 11/244 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +    +  E     A++++V ++L LV  +A K+ NRG    DL+Q G +GL+KA ++
Sbjct: 17  RELFRRFK--EEGDMDAREKLVMSHLNLVRFIANKFKNRGEPIDDLVQVGYLGLLKAIDR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G +F+T+A   +   I R   D+  ++R+P  +++   KV +    ++++++R P
Sbjct: 75  FDPARGLEFTTFATPTIMGEIKRHFRDKGWSVRVPRRLQELSAKVNQATDTLTSQLQRSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           T  EIA+ L   V+ V + +        +SLE P G ED              +  +   
Sbjct: 135 TIAEIAEYLDATVDEVLEAMESSSAYSSVSLEAPSGMEDDDAPSVI---DRYATEDEELA 191

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             + R      LAS +PRE  V+ MRF  G     T  E+ ++  +++ ++ ++  + ++
Sbjct: 192 FTDDRIIIEEALASFSPREREVIEMRFLQG----MTQIEIAEKLGISQVQVSRLLRRTLK 247

Query: 666 KLKH 669
           K++ 
Sbjct: 248 KIQE 251


>gi|221308296|ref|ZP_03590143.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221312618|ref|ZP_03594423.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221317541|ref|ZP_03598835.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221321817|ref|ZP_03603111.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767137|ref|NP_388354.2| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|321314147|ref|YP_004206434.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
 gi|133469|sp|P06574|RPSB_BACSU RecName: Full=RNA polymerase sigma-B factor; AltName: Full=General
           stress protein 84; Short=GSP84; AltName: Full=Sigma-37
 gi|143538|gb|AAA22754.1| sigma-37 RNA polymerase [Bacillus subtilis]
 gi|225184764|emb|CAB12280.2| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291482882|dbj|BAI83957.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. natto
           BEST195]
 gi|320020421|gb|ADV95407.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
          Length = 262

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/254 (21%), Positives = 118/254 (46%), Gaps = 6/254 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T ++  E   ++S       +   A++ +V     LV  +AKKY+       DL Q 
Sbjct: 5   SKTTKLTKDEVDRLIS--DYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQV 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++    
Sbjct: 63  GMIGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAV 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            +++ + +R P  EEIA+ L +  E V + +++ K   +L      E  S          
Sbjct: 123 DQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEADSDGSTVTILDI 182

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D   + N +     VL  L+ RE++++ + +      + + +E G    +++  +
Sbjct: 183 VGSQEDGYERVNQQLMLQSVLHVLSDREKQIIDLTY----IQNKSQKETGDILGISQMHV 238

Query: 657 RQIEAKAIRKLKHP 670
            +++ KA++KL+  
Sbjct: 239 SRLQRKAVKKLREA 252


>gi|332297782|ref|YP_004439704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
 gi|332180885|gb|AEE16573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
          Length = 262

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/256 (21%), Positives = 107/256 (41%), Gaps = 18/256 (7%)

Query: 423 SISEFR-HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEG 477
           SI E +      +   + ++   +   +   + LV  VA K    G+     F DL+  G
Sbjct: 4   SIFEEKTEDELWLEYKKTKSPALRDAFIRQYMPLVKYVAGK-VATGMPGSVEFDDLVGFG 62

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
             GL+ A  K+D     KF TYA+  ++ +I   +        +P  +R K  ++     
Sbjct: 63  QFGLLDAINKYDPDKNVKFKTYAVTRIRGSIFDELRQLDW---VPRSVRQKAREIEDAIV 119

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTS---HLGDFI 592
            + +++ R  +  E+A  + +     ++ +        +SL       D S    +GD I
Sbjct: 120 ALESRLGRPASDAEVAGSMGISEAEFQQTVMRVSGTSVLSLNDVWYSGDDSDHVSIGDSI 179

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E   +++P     +  +R      +  L  +E+ VL + +    + D T +E+G+   V+
Sbjct: 180 ESPASLNPDVIVEREEIRRVIAEAITELPEKEKMVLVLYY----HEDLTFKEIGQVLNVS 235

Query: 653 RERIRQIEAKAIRKLK 668
             RI Q+  KA  +L+
Sbjct: 236 ESRISQLHTKANMRLR 251


>gi|167507927|gb|ABZ81284.1| RpoD [Thalassospira sp. MCCC 1A01166]
 gi|167507929|gb|ABZ81285.1| RpoD [Thalassospira sp. MCCC 1A01167]
          Length = 255

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 121/253 (47%), Gaps = 14/253 (5%)

Query: 179 TLLREIIDLEACIG--PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA--- 233
            LLR++IDLE   G  P+++ G   G +     + +  + +   ++  E           
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIGAEEGEDEDVDAEADVENFDSANEEDDEDAETETPENIG 60

Query: 234 ----AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
                +   DD    DS  +   + E   +++ +    +LS ME++L  +V+   + IA+
Sbjct: 61  GEEAEEEEDDDEESEDSEGDEEGDGEDEDEDENEQVNVSLSKMEEELTEQVLEKFELIAK 120

Query: 290 VYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            Y +L   Q+  +      ++       +   LK ++V+L+  + LN  RI+ L++ L  
Sbjct: 121 TYEKLHKAQEQRLVALNKGETVPAATEKRYAKLKNEMVELMEDVHLNNFRIEELLDHLTG 180

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
           ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK F+    +
Sbjct: 181 LNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVAGLPGKGWKAFIERYPE 240

Query: 405 SILKIRNEIKSIS 417
            I K+R ++  +S
Sbjct: 241 EIAKLREDVGGVS 253


>gi|291529642|emb|CBK95228.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 340

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 88/293 (30%), Positives = 145/293 (49%), Gaps = 25/293 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIA--KKEMVEANLRLVISVAKKYTN- 465
           +   +  +S     +  E + +   + + E E      K E+   N+RLV+ VAK+Y   
Sbjct: 44  LSMYMYEMSKWQPFTEEEEKQVFKELSETESEDKKKQLKDEIFSRNIRLVVYVAKRYYKN 103

Query: 466 -RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            + ++ +DLI E ++GL+KA +++D+  GYKFSTYA WW+ QA TRSIA+ +  IR PVH
Sbjct: 104 LKHMEPIDLIDEASLGLLKAIDRYDYTTGYKFSTYAYWWINQACTRSIANDNDLIRQPVH 163

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP---ISLETPIG 581
           + + I KV +  R+           + IAK+L +  E VR +L I       ISL+  + 
Sbjct: 164 IHEFIIKVKKAQRKWGQTHDNNAPVDYIAKELNVSEEKVRNILIIIDCQSNYISLDCTMS 223

Query: 582 DE----DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS--------------LTPR 623
                   + +G+ + D       +       +     +L+                T R
Sbjct: 224 KGSEEPGDTEVGEIVLDPKGNVDFEKVEVNQFQNRIIEILSKANNKTSAKSNRSVEQTKR 283

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              V++ RFG       TLEE+ + + V+RERIRQIEA+A++ L++P   ++L
Sbjct: 284 MIDVIKRRFGFDNCRIETLEEIAQSYGVSRERIRQIEAQALKILRNPKYKREL 336


>gi|112962639|gb|ABI29096.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
          Length = 258

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 115/252 (45%), Gaps = 7/252 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           P   +IA  + +  E +    +  + + +S++  I  +        ++           +
Sbjct: 133 PQISDIADFIGVTEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 192

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+
Sbjct: 193 --NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIK 246

Query: 666 KLKHPSRSKKLR 677
           KL+   +++++ 
Sbjct: 247 KLREALQNEEVE 258


>gi|237731968|ref|ZP_04562449.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
 gi|226907507|gb|EEH93425.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
          Length = 239

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 112/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
            +LA+PV+  R++L  T            E+     + + E+    +PL   ++ NLR+ 
Sbjct: 122 ARLAIPVQEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|295840299|ref|ZP_06827232.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295827905|gb|EDY46913.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 56/272 (20%), Positives = 127/272 (46%), Gaps = 14/272 (5%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I+    ++  + R +  +       + +G  E   A+  ++E N+ LV   A+++ +
Sbjct: 20  LPEIAEPHKVAPRDARELTRLFFDRLDTLEEGTREFQDARNTLIEMNMSLVRFAARRFRS 79

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    D++Q G IGL+KA ++F+     +F+T+A+ ++   I R   D +  + +P  +
Sbjct: 80  RGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAVPYIVGEIKRFFRDTTWAVHVPRRL 139

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDE 583
           ++   ++ +    +S ++ R P   E+A  + +  + V +           SL+  IG E
Sbjct: 140 QEARVELAKANEELSTRLGRAPRVSELAALMNLSEQQVVEAQIAANGYSSSSLDATIGGE 199

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D+      + D          +  +L      +LA L PR+ ++L +RFG     + T  
Sbjct: 200 DSGEGEAVLSDFIGADDPGMELVEDLH-ALAPLLAGLEPRDRQILELRFG----QELTQA 254

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++G++  V++  + ++  + +  L+    S++
Sbjct: 255 QIGERLGVSQMHVSRLLNRTLGTLRAGLMSER 286


>gi|120403519|ref|YP_953348.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium
           vanbaalenii PYR-1]
 gi|119956337|gb|ABM13342.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium
           vanbaalenii PYR-1]
          Length = 242

 Score =  119 bits (297), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 108/248 (43%), Gaps = 15/248 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  ++ +G       +  ++E  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 2   FRELA-LLDEGSAPYRRQRDAIIERCLPLADHIARRFRGRGEAHEDLVQVARVGLLNAVN 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD      F  +A+  +   + R   D   ++++P  +++   ++      +++++ R 
Sbjct: 61  RFDVDSANDFLAFAVPTMMGEVRRYFRDHGWSLKVPRRLKELNVRLNSARSELTHQLNRA 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-----DTSHLGDFIEDKNAVSPL 601
           PTP E+A+ L M  + + + L       +  T          D   L D I   +     
Sbjct: 121 PTPSELAEFLGMERDEIVEGLVAANAYSTRSTEQETMRTGDGDGLTLLDTIGGPDEGIQR 180

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              IQ     T   +LA L  R+  VL++RF        T  ++ ++  V++  + ++ A
Sbjct: 181 VIDIQ-----TVQPLLAKLPARDRLVLQLRFFDN----LTQSQIAERIGVSQMHVSRLLA 231

Query: 662 KAIRKLKH 669
           +A+  L+ 
Sbjct: 232 RALATLRE 239


>gi|111019111|ref|YP_702083.1| RNA polymerase sigma factor SigF [Rhodococcus jostii RHA1]
 gi|110818641|gb|ABG93925.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 106/254 (41%), Gaps = 18/254 (7%)

Query: 424 ISEFRHIVSMVRKGECEAS------IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
             E++ + ++  +              +  +V   L L   +A+++  RG    DL+Q  
Sbjct: 15  PDEYQDVTALFEQMAALDEDDPRRSRLRDAVVTRCLPLAEHIARRFDGRGEAHDDLVQVA 74

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+ + ++FD   G  F ++A+  +   + R   D    +R+P  M++    + +   
Sbjct: 75  RLGLVNSVDRFDVERGSDFVSFAVPTIMGEVRRHFRDTGWAVRVPRRMKELHLALSQAVA 134

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLE-TPIGDEDTSHLGDFIED 594
            +S  +   PT  E+A+ L +  E V + L      + +S++ T         + + + D
Sbjct: 135 ELSQSLGHAPTVSELAEHLDLEQEEVAQGLLAGNAYQTVSVDNTSSDRTGELSMVETLGD 194

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +A             ET   +L SL  RE  VL +RF        T  ++  +  +++ 
Sbjct: 195 YDAA-----MDDVENHETLRPLLQSLPERERTVLMLRFFGN----MTQTQIADRVGISQM 245

Query: 655 RIRQIEAKAIRKLK 668
            + ++ AK +  L+
Sbjct: 246 HVSRLLAKTLASLR 259


>gi|143460|gb|AAA22713.1| 37 kd minor sigma factor (rpoF, sigB; ttg start codon) [Bacillus
           subtilis]
 gi|143463|gb|AAA22715.1| 37 kd minor sigma factor (ttg start codon) [Bacillus subtilis]
 gi|1881283|dbj|BAA19310.1| RNA POLYMERASE SIGMA-B FACTOR (SIGMA-37) [Bacillus subtilis]
          Length = 264

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/254 (21%), Positives = 118/254 (46%), Gaps = 6/254 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T ++  E   ++S       +   A++ +V     LV  +AKKY+       DL Q 
Sbjct: 7   SKTTKLTKDEVDRLIS--DYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQV 64

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++    
Sbjct: 65  GMIGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAV 124

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            +++ + +R P  EEIA+ L +  E V + +++ K   +L      E  S          
Sbjct: 125 DQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEADSDGSTVTILDI 184

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             S  D   + N +     VL  L+ RE++++ + +      + + +E G    +++  +
Sbjct: 185 VGSQEDGYERVNQQLMLQSVLHVLSDREKQIIDLTY----IQNKSQKETGDILGISQMHV 240

Query: 657 RQIEAKAIRKLKHP 670
            +++ KA++KL+  
Sbjct: 241 SRLQRKAVKKLREA 254


>gi|75761672|ref|ZP_00741618.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490828|gb|EAO54098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 258

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 119/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C    A++ +V+    LV S+A +Y+  G    D
Sbjct: 2   MEIQSQPTTLTKEDVIKLIAEFQQNQCN--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 60  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 120 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVA 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         Q   R     +   L   E+ V+   FG  +N     ++  ++  
Sbjct: 180 RIE--SVGEVEQGYEQTERRLVLEDIFNVLNDMEKSVIHYIFGENLNQ----KDTRERLG 233

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 234 ISQMHVSRIKRQAISKLKQAA 254


>gi|229010401|ref|ZP_04167605.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
 gi|228750821|gb|EEM00643.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
          Length = 224

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 103/226 (45%), Gaps = 8/226 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  I +P  ++D   K+      +++ ++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                 +  SL+  + +         IE  +         Q   R     +   L   E+
Sbjct: 121 DAKNNYQVSSLDDVVENSSDGSSVARIE--SVGEVEQGYEQTERRLVLDDIFNVLNDTEK 178

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+   FG  +N     ++ G++  +++  + +I+ +AI KLK  +
Sbjct: 179 SVIHYIFGENLNQ----KDTGERLGISQMHVSRIKRQAISKLKQAA 220


>gi|255305293|ref|ZP_05349465.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile ATCC 43255]
          Length = 233

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 123/232 (53%), Gaps = 11/232 (4%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++E+++ N+ LV S+A+K+    +G ++ DL+  G IGL+ A  KFD   G KFS+Y+  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDTEKGAKFSSYSYI 62

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +K AI   I +QS    I  H   K++K  R   ++ +K+ REPT  EIAK+L +  + 
Sbjct: 63  KIKSAILDEIRNQS---PISKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELKVSEKE 119

Query: 563 VR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +   +        +SL   I ++    + D I D+   +P +   +    E  ++ +++L
Sbjct: 120 LHDIESNIDMLNIVSLNYVIFEDTNETVQDVISDREEEAPENIIEEEEKLEILSKAISNL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RE+ +L + +      D  L+E+GK   V+  R+ Q+  K+IR L++  +
Sbjct: 180 NEREKLILSLYY----YEDLNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227


>gi|331653330|ref|ZP_08354335.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
 gi|323174562|gb|EFZ60183.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LT-68]
 gi|331049428|gb|EGI21500.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
          Length = 239

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYIPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|91223562|ref|ZP_01258827.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269965686|ref|ZP_06179799.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
 gi|91191648|gb|EAS77912.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269829754|gb|EEZ83990.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
          Length = 244

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 103/244 (42%), Gaps = 15/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKAITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   +        +P  +     ++ +    +  ++ R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDMRKGDW---VPRSVHKNNREINQAIAELEGELNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A  L M ++     L        + +E     +D     D  +D N   P    
Sbjct: 118 PTDSEVATHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSN---PFKGV 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           +  + R+     +  L  RE  VL + +    + +  L+E+G    V+  R+ QI ++A+
Sbjct: 175 VDESFRKALVESIKQLPEREALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQAM 230

Query: 665 RKLK 668
           ++L+
Sbjct: 231 QRLR 234


>gi|41409504|ref|NP_962340.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|254776692|ref|ZP_05218208.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|41398335|gb|AAS05956.1| SigF_2 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 262

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 116/250 (46%), Gaps = 13/250 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +    ++       E    + ++VE  L L   +A+++  RG    DL+Q   +GL+
Sbjct: 18  DVPDMFRELATAEPDSMEFQRQRDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLV 77

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A  +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S +
Sbjct: 78  NAVVRFDVDAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQR 137

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAV 598
           + R PT  E+A +L M  E V + L    +   +S+++  G E+     + D + D +  
Sbjct: 138 LGRAPTATELAAELEMDREEVVEGLVAGSSYNTLSIDSGGGSEEEEVRAIADTLGDVDT- 196

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +   +E+   +L +L  RE  VL +RF        T  ++ ++  +++  + +
Sbjct: 197 ----GLDRIEDQESLRPLLEALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSR 248

Query: 659 IEAKAIRKLK 668
           + AK++ +L+
Sbjct: 249 LLAKSLTRLR 258


>gi|302335912|ref|YP_003801119.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
 gi|301319752|gb|ADK68239.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
          Length = 276

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 121/250 (48%), Gaps = 7/250 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +    +        A++++V ++L LV  +A K+ NRG    DL+Q G IGL+KA ++
Sbjct: 33  RELFRRYK--VEGDEDAREQLVMSHLNLVRFLASKFKNRGEPLDDLVQVGTIGLIKAIDR 90

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G +F+T+A   +   I R   D+  ++R+P  +++   KV +    ++  ++R P
Sbjct: 91  FDPERGLEFTTFATPTIMGEIKRHFRDKGWSVRVPRRLQELSAKVNQVTDELTKDLQRSP 150

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           + EEIA  L   V+ V + ++ +    S+               + D  A +  +    +
Sbjct: 151 SVEEIAAALDTTVDEVLEAMESSSAYSSVPLEGTGPGADDDAPSVIDHYA-TVDEDLAAS 209

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R      +   +PRE+ ++RMRF  G     T  E+ ++  +++ ++ ++  + ++K+
Sbjct: 210 DDRMVIEETVRDFSPREQEIIRMRFIEG----LTQVEIARRLGISQVQVSRLLRRTLQKV 265

Query: 668 KHPSRSKKLR 677
           +     + L 
Sbjct: 266 QEKIDPEGLM 275


>gi|54024680|ref|YP_118922.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54016188|dbj|BAD57558.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 261

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 108/236 (45%), Gaps = 12/236 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+++  L L   +A+++  RG  F DL+Q   +GL++AA++FD   G  F  +A+  +
Sbjct: 36  RAEVIDRALPLAEHIARRFAGRGESFDDLLQVARLGLVQAADRFDVGRGSSFLAFAVPTI 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D +  +R+P   ++    +  T   +S ++ R P   EIA +L + V  V 
Sbjct: 96  MGEVRRHFRDNTWAVRVPRRTKEIQGSIGATVEELSQRLGRMPRAREIAAELGIDVVEVT 155

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L      +  SL++  GD+  +      E   A  P    +   L      ++A L  
Sbjct: 156 QALIAGNAYQSSSLDSTAGDDGENTPLPLSESLGAEEPSFEFVDDYL--AVRPLIAELPE 213

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           RE +VL MRF  G     T  ++     V++  + +I +K +    H  R + LR 
Sbjct: 214 RERQVLVMRFFEG----KTQTQIADVLGVSQMHVSRILSKTL----HALREQALRD 261


>gi|302037625|ref|YP_003797947.1| flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
 gi|300605689|emb|CBK42022.1| Flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
          Length = 247

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 109/234 (46%), Gaps = 13/234 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A   ++ +++    +V ++A +   R    +   DLI  G +GLM A +K+D     KF 
Sbjct: 13  AEADRERVIQEFTHVVKAMAHRLAFRLPAYMDAEDLISVGIMGLMDAMDKYDPTREAKFK 72

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA + ++ A+   I        IP  + ++I  + +T   + +++ R PT +E+ K+L 
Sbjct: 73  TYAEFRIRGAMLDEIRSMDW---IPRSVHERITLLQKTYSELLHRLGRPPTDQEVGKELK 129

Query: 558 MPVEGVRKVLKITK--EPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTT 614
           M  E + + L  ++    ISL+     +   H +   + D N   PL   +    R    
Sbjct: 130 MSAEELDEFLTRSRGAVVISLDDLGVQDADGHKIISVLTDSNQPDPLSVLVNERARHVLE 189

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  +E  VL + +      + T++E+G+   VT  R+ QI +KAI  LK
Sbjct: 190 AAIHDLPEKERLVLSLYYF----EELTMKEIGQALKVTESRVCQIHSKAILHLK 239


>gi|39998144|ref|NP_954095.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
 gi|39985090|gb|AAR36445.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
          Length = 250

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 58/251 (23%), Positives = 120/251 (47%), Gaps = 14/251 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           + +  ++ +   +  + E++  +L LV  +  +  ++    L   DL+    IGL+ AAE
Sbjct: 5   LKAYEQEAQRSVAQTRDELIVNHLPLVKFLVGRIASQLPPHLDQEDLMSAAIIGLITAAE 64

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +F T+A   ++  I   +  Q     +   +RDK  K+ +    + +++ R 
Sbjct: 65  RFDPTRGVQFKTFAEQRIRGTIIDELRSQDW---LTRSLRDKFKKLEKEFVLLEHQLGRN 121

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLD 602
           PT EE+A  L M V+   ++L+       +SL+    D+D S  G  D + D +  +P  
Sbjct: 122 PTSEEVATALKMSVDEYYQMLEEIHLLSFVSLDESWEDDDGSPFGLLDILADTSIENPQS 181

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +   + ++ T  + SL  +E  V+ + +      +  L+E+G    ++  RI Q+ ++
Sbjct: 182 QLMARQMLDSLTESIESLPEKERLVITLYY----YEELNLKEIGAVLELSESRISQLHSQ 237

Query: 663 AIRKLKHPSRS 673
           AI +L+   ++
Sbjct: 238 AIVRLRAKMKN 248


>gi|289810010|ref|ZP_06540639.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 227

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 53/254 (20%), Positives = 83/254 (32%), Gaps = 46/254 (18%)

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMA 155
              A  ++  +    +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  
Sbjct: 20  DEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQC 79

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           S+ E P     L+   D +      L ++I            GF                
Sbjct: 80  SVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNAEEEMAPTATHV 128

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
             +   +  + + D +                PE A                       +
Sbjct: 129 GSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKF------------------AE 170

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           LR + +   D I                     +S    +    KL ++     L   + 
Sbjct: 171 LRAQYVVTRDTIKAK-----------------GRSHAAAQEEILKLSEVFKQFRLVPKQF 213

Query: 336 DLLVEQLYDISKRI 349
           D LV  +  +  R+
Sbjct: 214 DYLVNSMRVMMDRV 227


>gi|261340320|ref|ZP_05968178.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
 gi|288317411|gb|EFC56349.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
          Length = 229

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 109/228 (47%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V     ++  ++ R  T  E+A++L + VE
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAHAMGQLEQELGRNATETEVAERLGIAVE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D++   +PL   ++ NLR+     + +L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDEHQQENPLHHLMEGNLRQRVMEAIEAL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|157692327|ref|YP_001486789.1| RNA polymerase sigma factor SigD [Bacillus pumilus SAFR-032]
 gi|157681085|gb|ABV62229.1| DNA-directed RNA polymerase sigma subunit D [Bacillus pumilus
           SAFR-032]
          Length = 255

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 111/243 (45%), Gaps = 13/243 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD 489
             R  E +   A  +++   + LV     + +    + +   DLI  G +GL  A EKFD
Sbjct: 12  WARWKEWKDPAAGDDLMRRYMPLVTYHVGRISIGLPKSVHKEDLISLGMLGLYDALEKFD 71

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF TYA + ++ AI   +  +     +P   R+K  KV     ++  +  R  TP
Sbjct: 72  PGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKKVEAAIEKLEQRYLRNVTP 128

Query: 550 EEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E+A++L M  + V   +        +S++  +   ED  ++   I D+  V+P +  ++
Sbjct: 129 TEVAEELGMSEQDVVTTMNEGFFANLLSIDEKLHDQEDGENVQVMIRDEKTVTPEEKMLK 188

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L E     +  L+ +E+ V+ + +      + TL E+G    ++  RI QI +KA+ K
Sbjct: 189 DELIEQLAEKMTELSEKEKLVISLFY----KEELTLTEIGHVLNLSTSRISQIHSKALFK 244

Query: 667 LKH 669
           LKH
Sbjct: 245 LKH 247


>gi|157145286|ref|YP_001452605.1| flagellar biosynthesis sigma factor [Citrobacter koseri ATCC
           BAA-895]
 gi|157082491|gb|ABV12169.1| hypothetical protein CKO_01023 [Citrobacter koseri ATCC BAA-895]
          Length = 229

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 112/228 (49%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++LA+PVE
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVAERLAIPVE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + E+    +PL   +++NLR+     + SL
Sbjct: 120 EYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLESNLRQRVMDAIESL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREQLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|239934588|emb|CAR94608.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 220

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 95/263 (36%), Gaps = 44/263 (16%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IAKRIE G    M ++   P + Q ++     +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIVIAKRIEEGVREFMHAVAYWPGSVQKILDEYALVAK 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               L ++I     + P  +       E    +    +  +   DD +E        A  
Sbjct: 61  EERRLADVI--IGWLDPVEEIPATLIDEDAEIEVAPVAGAKPAGDDDEE------EGAAT 112

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             ++ +     PE A+     L + +D    TL+                          
Sbjct: 113 EDEEEAVSGVDPEEAKVRFEALQKQQDKVNKTLA-------------------------- 146

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    K    S + +    +L  L     +   + + L  +  +  + +   E  +
Sbjct: 147 ---------KYGYGSKQAEKELSELGDLFKFFKIPARQFEPLYTKARETLENVRKAERLV 197

Query: 357 LRLAQS-YGIKRDVFLERHQGRE 378
           + L      ++R  F++   G E
Sbjct: 198 MDLCTRKAQMQRKTFIKEFPGNE 220


>gi|188495466|ref|ZP_03002736.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|293415233|ref|ZP_06657876.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|331647515|ref|ZP_08348607.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
 gi|188490665|gb|EDU65768.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|281178984|dbj|BAI55314.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE15]
 gi|291432881|gb|EFF05860.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|330911730|gb|EGH40240.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           AA86]
 gi|331043239|gb|EGI15377.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
          Length = 239

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 109/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   +  NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDNNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|311900799|dbj|BAJ33207.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 56/267 (20%), Positives = 127/267 (47%), Gaps = 16/267 (5%)

Query: 412 EIKSISVETGISISEFRHIVSMV-------RKGECEASIAKKEMVEANLRLVISVAKKYT 464
           E+  +   T ++ ++ R +  ++        +G  E S  +  +VE NL LV    +++ 
Sbjct: 32  ELAELGDLTEVAPTDARDLTRVLLARLAGLEEGTREYSYVRASLVELNLSLVRFALRRFG 91

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           +      DL+Q G +GL+KA ++F+   G +F+T+A+  +   + R   D +  + +P  
Sbjct: 92  SHRESTEDLMQVGAVGLIKAIDRFETERGLEFTTFAIPTILGELRRHFRDTTWAVHVPRR 151

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGD 582
           +++    +V+    +S  + R PT  E+++ L +  E V + L+        SL+ P G 
Sbjct: 152 LQELRLALVKAQDALSQALDRAPTVAELSEHLGITQEEVIEGLQAANAHSTDSLDLPAGP 211

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +D       +  K   +     +  +L  +   ++A+L  R+  +L MRF      + T 
Sbjct: 212 DDDGPGA--LAAKIGGTDERLGMVEDLV-SLQPLIAALPERDRLILSMRF----TEELTQ 264

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ++G++  +++  + ++ ++ + KL+ 
Sbjct: 265 SQIGERLGLSQMHVSRLLSRTLAKLRQ 291


>gi|30250410|ref|NP_842480.1| RNA polymerase sigma-70 factor family protein [Nitrosomonas
           europaea ATCC 19718]
 gi|30181205|emb|CAD86403.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 236

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 109/234 (46%), Gaps = 11/234 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K + +     LV  +A     R    +Q  DLIQ G IGL+ A  +++   G +F +YA 
Sbjct: 10  KDQFITEFTPLVKRIAHHMMARLPASVQVDDLIQAGMIGLLDAINRYEGSYGRQFESYAA 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ +I   + +      +P  +R K+ ++    R +  ++   P+ +EIA ++ +P+ 
Sbjct: 70  QRIRGSILDELREADW---LPRSLRRKMRQIETAMRALEQRLGYPPSEQEIANEMNLPLV 126

Query: 562 GVRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             +++L+      +       +++  H  D +    +  PLD  ++ NLRE     +  L
Sbjct: 127 EYQEMLQEAGGGQLIYYEDFQEDEEDHFLDRLRGDQSNEPLDRLLEKNLRELLVAAIEKL 186

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             +E+ V+    G+    +  L E+GK   V+  R+ Q+  +AI +L+   R K
Sbjct: 187 PAKEKLVM----GMYYEQEMNLREIGKVLGVSESRVCQLHTQAISRLRTHLRDK 236


>gi|322496003|emb|CBJ55206.1| RNA polymerase sigma factor [Aeromonas bestiarum]
          Length = 259

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 58/298 (19%), Positives = 108/298 (36%), Gaps = 46/298 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   + +S+ E P     L+   D+       L +II     I P     
Sbjct: 1   EIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---- 54

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                               E DDV  T   I S            D   +  E+ E + 
Sbjct: 55  --------------------ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGESSD 94

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVL 317
           D+ +      ++                  E + ELR+  +   ++ QK+ ++    +  
Sbjct: 95  DDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHEDTQAA 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQG 376
              L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+     
Sbjct: 138 IALLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTN 197

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            E +  W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 NECETAWFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 254


>gi|323144379|ref|ZP_08078987.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
 gi|322415832|gb|EFY06558.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
          Length = 295

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 67/277 (24%), Positives = 130/277 (46%), Gaps = 16/277 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +K+I+    +   + R +   +R        A +++V ++LRLV+S+A+ Y   GL
Sbjct: 20  IDAYVKAINKFPMLEEEDERTLAKRLRDYG--DLDAARKLVLSHLRLVVSIARGYLGYGL 77

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA + FD  +G + + +A+ W+K  I   +      +++      +
Sbjct: 78  PISDLIQEGNIGLMKAVKHFDPDVGGRLAAFAVHWIKAEIHDYVIKNWRVVKVATTKAQR 137

Query: 529 IHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKI-TKEPISLETPIGDEDT 585
             K+    R+   ++      E  ++A  L +  + V ++      + I  +    D+  
Sbjct: 138 --KLFFKLRQNKQRLGWFSDSERNKVADDLGVSADDVAEMETRLAGQDIGFDADSDDDSD 195

Query: 586 SHLGD----FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                    ++ED+N   A +  +   +     +  + L SL  R   +++ R+      
Sbjct: 196 KGSSFSPSAYLEDENSNFANTFENIDYENYELSSLRKALDSLDERSRYIVQRRWLDEN-- 253

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
             TL+E+ ++  V+ ER+RQIE +A++K+K    + K
Sbjct: 254 KATLQELSEKLNVSIERVRQIENQALKKIKSNILADK 290


>gi|49480184|ref|YP_035252.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49331740|gb|AAT62386.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 258

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 119/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +V+    LV S+A +Y+  G    D
Sbjct: 2   MEIQSQPTNLTKEDVIKLIAEFQQNQCD--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 60  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 120 KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 180 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 233

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 234 ISQMHVSRIKRQAISKLKQAA 254


>gi|260875653|gb|ACX53633.1| RNA polymerase sigma factor [Pseudomonas alcaliphila]
          Length = 253

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 51/295 (17%), Positives = 101/295 (34%), Gaps = 48/295 (16%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   +M+++   P T   ++     +      L E++            G+ 
Sbjct: 3   RIAKRIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEVL-----------SGYI 51

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              +G    +       KE    +E++ + E  +   +++       PE A      + E
Sbjct: 52  DPDDGSVPDEAAAPVPVKEGAAAEESDDEEEDESGDDEEEEGDGGPDPEEAARRFNAVAE 111

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            +D               KV+ AL                     K  + S +       
Sbjct: 112 QQD---------------KVLKALK--------------------KHGRGSKQAIEELAT 136

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGREL 379
           L +L   + L   + D LV Q+     R+   E  +++L      + R  FL    G E+
Sbjct: 137 LAELFMPIKLVPKQYDALVTQVRGALDRLRAQERAIMQLCVRDARMPRADFLRLFPGNEI 196

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           D  W +      + ++   +      I + + ++  +  E  +S++E + I   +
Sbjct: 197 DMDWAADLAK-GKAKYAEALGNLQADIQRCQQKLADLEAECSLSLAEIKDINRRM 250


>gi|205373764|ref|ZP_03226566.1| sporulation sigma factor SigF [Bacillus coahuilensis m4-4]
          Length = 244

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 114/236 (48%), Gaps = 14/236 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I  ++++ +     A+  +V  N+RLV SV +++ NRG +  DL Q G+IGL+K+ +KF
Sbjct: 18  EIKQLIKRSQDGDVDARDMIVNRNMRLVWSVVQRFLNRGYEPDDLFQIGSIGLLKSVDKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R I D   T+++   +++  +K+ R    +S  + R PT
Sbjct: 78  DLSYDVKFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKETGNKIRRAKEELSKTLNRVPT 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQ 606
             E+A  L +  E V    + ++ P S+   + + D     L D I D+N     D    
Sbjct: 137 ISELADFLEITPEEVVLAQEASRTPSSIHETVYENDGDPITLLDQIADQNDQKWFD---- 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              +      +  L  RE  ++ +R+      D T  EV  +  +++ ++ ++  K
Sbjct: 193 ---KIALKEAIRELDERERLIVFLRY----YKDQTQSEVADRLGISQVQVSRLRKK 241


>gi|229016304|ref|ZP_04173251.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
 gi|229022543|ref|ZP_04179074.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228738763|gb|EEL89228.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228744996|gb|EEL95051.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
          Length = 224

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 104/226 (46%), Gaps = 8/226 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVDHYKNLVHSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  I +P  ++D   K+      ++++++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                    SL+  + +         IE  +         Q   R     +   L   E+
Sbjct: 121 DAKNNYRVSSLDDVVENSSDGSSVARIE--SVGEVEQGYEQTERRLILDDIFNVLNDTEK 178

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+   FG  +N     ++ G++  +++  + +I+ +AI KLK  +
Sbjct: 179 SVIHYIFGENLNQ----KDTGERLGISQMHVSRIKRQAISKLKQAA 220


>gi|126697838|ref|YP_001086735.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile 630]
 gi|255099435|ref|ZP_05328412.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-63q42]
 gi|115249275|emb|CAJ67088.1| RNA polymerase sigma-28factor for flagellar operon [Clostridium
           difficile]
          Length = 233

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 123/232 (53%), Gaps = 11/232 (4%)

Query: 445 KKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++E+++ N+ LV S+A+K+    +G ++ DL+  G IGL+ A  KFD   G KFS+Y+  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYI 62

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +K AI   I +QS    I  H   K++K  R   ++ +K+ REPT  EIAK+L +  + 
Sbjct: 63  KIKSAILDEIRNQS---PISKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELKVSEKE 119

Query: 563 VR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +   +        +SL   I ++    + D I D+   +P +   +    E  ++ +++L
Sbjct: 120 LHDIESNIDMLNIVSLNYVIFEDTNETVQDVISDREEEAPENIIEEEEKLEILSKAISNL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             RE+ +L + +      D  L+E+GK   V+  R+ Q+  K+IR L++  +
Sbjct: 180 NEREKLILSLYY----YEDLNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227


>gi|22770506|gb|AAN06628.1|AF497200_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 113/251 (45%), Gaps = 4/251 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 192

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+K
Sbjct: 193 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIKK 248

Query: 667 LKHPSRSKKLR 677
           L    +++++ 
Sbjct: 249 LLEALQNEEVE 259


>gi|228919826|ref|ZP_04083184.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839842|gb|EEM85125.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 224

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 51/226 (22%), Positives = 103/226 (45%), Gaps = 8/226 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV     LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G  F  +A+  +   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I + + D++  I +P  ++D   K+      ++++++R P   EIA  L +  E V +++
Sbjct: 61  IKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIM 120

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                    SL+  + +         IE  +         +   R     +   L   E+
Sbjct: 121 DAKNNYRVSSLDDVVENSSDGSSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNETEK 178

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            V+   FG  +N     ++ G++  +++  + +I+ +AI KLK  +
Sbjct: 179 SVIHYIFGENLNQ----KDTGERLGISQMHVSRIKRQAISKLKQAA 220


>gi|167507907|gb|ABZ81274.1| RpoD [Thalassospira sp. MCCC 1A01013]
 gi|167507909|gb|ABZ81275.1| RpoD [Thalassospira sp. MCCC 1A01017]
          Length = 258

 Score =  118 bits (296), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 108/252 (42%), Gaps = 17/252 (6%)

Query: 179 TLLREIIDLEACIGPESKGGFFHG------------TEGHSYQKREDSSQEKERDDVQET 226
            LLR++IDLE   G                               ++  + +        
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAEEGEEADAEGDDFEAAAVETDADEDEEAETETPEPTG 60

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
               +   +   ++        E   + +   D++ +    +LS ME++L  +V+   + 
Sbjct: 61  APASDEEEEDDDEESDDDSEGEEGEGDGDDEDDDENEQVNVSLSKMEEELTEQVLEKFEL 120

Query: 287 IAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA+ Y +L   Q+  +      ++       +   LK ++V L+  + LN  RI+ L++ 
Sbjct: 121 IAKTYEKLHKAQEQRLVAMNKGETVPAATEKRYAKLKGEMVDLMEDVHLNNFRIEELLDH 180

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+    + P   WK F+  
Sbjct: 181 LTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVGELPGKGWKAFIER 240

Query: 402 EVDSILKIRNEI 413
             D I ++R ++
Sbjct: 241 YPDEIAQLREQV 252


>gi|229542547|ref|ZP_04431607.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
 gi|229326967|gb|EEN92642.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
          Length = 259

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 124/257 (48%), Gaps = 5/257 (1%)

Query: 419 ETGISISEFRHIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            + +   +   +  +++   +     A++ +V    +LV S+A+KY+       D+ Q G
Sbjct: 1   MSKLPQPDQIDVNQLIQSFQQNGDKEAQEILVAHYQKLVESLARKYSKGRAYQEDIFQVG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL+ A ++FD  +G  F ++A+  +   I R + D++ ++ +P  +++   ++  T  
Sbjct: 61  IIGLLGAIQRFDPNIGKSFESFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKSTVE 120

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           +++N+++R P   EIA  L +  E V + ++++K   +L      E  S           
Sbjct: 121 KLTNELQRSPKIAEIAAHLEISEEEVLEAMEMSKSYHALSVDHSIESDSDGSTVTLLDMV 180

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S  D   + N R    +VL  L+ RE +V+   +      + + ++ G++  +++  + 
Sbjct: 181 GSEDDGYEKVNQRLVLEKVLHVLSERERQVIHYTY----IENLSQKDTGEKLGISQMHVS 236

Query: 658 QIEAKAIRKLKHPSRSK 674
           +++ +AI+KL+     +
Sbjct: 237 RLQRRAIKKLRDAIEGE 253


>gi|307718622|ref|YP_003874154.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
 gi|306532347|gb|ADN01881.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
          Length = 262

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 109/247 (44%), Gaps = 15/247 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              +      ++  ++    LV  VA K        ++F DLI  G  GL+ A EKFD  
Sbjct: 17  EYQKTRDPQIREYFIKQYAPLVKYVAGKIAVGLPSSVEFDDLIGFGTFGLLDAIEKFDPE 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA+  ++ AI   +        +P  +R K  ++     R+ + + R  T EE
Sbjct: 77  KHVKFKTYAVTRIRGAIYDELRAMDW---VPRSVRQKSREIEDALHRLESSLGRAATDEE 133

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQ 606
           +A+++ M    ++K L+   +   +SL+      D +    + D +E   A  P     +
Sbjct: 134 LAREMNMSSRELQKTLQKISSTSILSLQELWYTGDENDRVAIADMLEAPQAYDPAARVER 193

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             ++      +  L  +E++VL + +      D TL+E+G    VT  R+ Q+  KAI +
Sbjct: 194 EEIKRVVAEAIKELPEKEKKVLVLYY----YEDLTLKEIGAILNVTESRVSQLHTKAISR 249

Query: 667 LKHPSRS 673
           L+   R+
Sbjct: 250 LRVKLRN 256


>gi|55274872|gb|AAV49239.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 179

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 76/204 (37%), Positives = 126/204 (61%), Gaps = 25/204 (12%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            M+E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++
Sbjct: 61  TIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM 120

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L++ +   S++T                             +++++  + L  L  ++  
Sbjct: 121 LRLNERITSVDT-------------------------PQDDDMKQSIVKWLFELNAKQRE 155

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFC 650
           VL  RFG+      TLE+VG++  
Sbjct: 156 VLARRFGLLGYEAATLEDVGREIG 179


>gi|311279128|ref|YP_003941359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
 gi|308748323|gb|ADO48075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
          Length = 243

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRET 612
           ++L + VE  R++L  T            E+     + + ++N   +PL   +++NLR+ 
Sbjct: 122 QRLGIAVEEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEENQQENPLHQLMESNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREQLVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|257457436|ref|ZP_05622606.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
 gi|257445165|gb|EEV20238.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
          Length = 262

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 102/244 (41%), Gaps = 15/244 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +     +    ++  +     LV  VA K        ++F DL+  G  GL+ A +K+D
Sbjct: 15  WLEYKHTQDPQLREFFIVKYAPLVKYVAGKVAVGMPNNVEFDDLVGYGVFGLLDAIDKYD 74

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF+TYA+  ++ AI   +        +P  +R +  ++      +  ++    T 
Sbjct: 75  PEKNVKFNTYAVTRIRGAIFDELRSIDW---VPRSVRQQSREIEEVIADLEARLGHAATD 131

Query: 550 EEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSA 604
            EIA+ L M VE   +VL        ISL       D S    + D IE   +++P    
Sbjct: 132 SEIAEALGMSVEEFHQVLLKISGTSIISLTDLRFGADDSEQTPVADSIEAPTSLNPDVIV 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  ++      +  L  RE++VL M +      D TL E+GK   VT  R+ QI   A 
Sbjct: 192 EREEMKRIIVDAINELPDREKKVLIMYY----YEDMTLREIGKVLEVTESRVSQIHTSAN 247

Query: 665 RKLK 668
            KLK
Sbjct: 248 LKLK 251


>gi|254784503|ref|YP_003071931.1| RNA polymerase factor sigma-32 [Teredinibacter turnerae T7901]
 gi|237687248|gb|ACR14512.1| alternative sigma factor RpoH [Teredinibacter turnerae T7901]
          Length = 284

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 117/270 (43%), Gaps = 13/270 (4%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +   +++++    +S  E + +   +     +   A + +V A+LR V+ +AK Y   
Sbjct: 15  QNLNAYMQAVNNFAVLSAEEEKQLAEDL--YYRQDLDAARRLVMAHLRFVVHIAKSYAGY 72

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DLIQEGN+GLMKA ++F+   G +  ++A+ W+K  I   I      +++     
Sbjct: 73  GLAQGDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKA 132

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--------LKITKEPISLET 578
            +        ++             +A+ L + V+ VR++                  + 
Sbjct: 133 QRKLFFNLRGQKKRLAWLTNDEANAVAQDLNVDVKNVREMESRLSAYDAAFDAGADDDDE 192

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                  ++L D   D + +       + ++     R +  L  R   +L+ R+    ++
Sbjct: 193 TAYQAPANYLEDRRYDPSTMLENADWTENSV-AGLERAMDQLDDRSRDILQQRWL--SDS 249

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             TL E+  ++ V+ ERIRQ+E  A++K++
Sbjct: 250 KATLHELADKYGVSAERIRQLEKNAMKKMR 279


>gi|297617167|ref|YP_003702326.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297145004|gb|ADI01761.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 258

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 112/250 (44%), Gaps = 16/250 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           R  +     A+ E++     LV  +A +     ++  ++  +LI  G  GL+ A  +FD 
Sbjct: 12  RYKDEGDIEARDELILHYAGLVKYIAARLFPNLSSHQVELDELISYGIEGLIDAVHRFDP 71

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KF TYA+  +K AI   +        IPV +R K  ++ +    + +++ R  T E
Sbjct: 72  KRKVKFETYALARIKGAIIDGLRAMDW---IPVSLRHKAKELEKAYCLLEHRLGRAATDE 128

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAI 605
           E+A +L M +   + +LK       I LE  I  ++      + D I+D+ A   L+   
Sbjct: 129 EMACELGMSIPEFQNLLKEVNLATIIYLEDLIPGDEGDKNKRIADVIKDERAEDGLELIE 188

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +      +A L  +E  V+ + +  G     TL+E+G+   ++  RI Q+  KAI 
Sbjct: 189 FEESKRLLAEAIALLPEKERTVVTLYYYEG----LTLKEIGEVLGLSESRISQLHTKAIL 244

Query: 666 KLKHPSRSKK 675
           +L+     KK
Sbjct: 245 RLRGRLGKKK 254


>gi|167755690|ref|ZP_02427817.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|237734438|ref|ZP_04564919.1| sporulation sigma factor sigF [Mollicutes bacterium D7]
 gi|167704629|gb|EDS19208.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|229382668|gb|EEO32759.1| sporulation sigma factor sigF [Coprobacillus sp. D7]
          Length = 240

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 119/240 (49%), Gaps = 14/240 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ +       AK+ +V  NL LV S+  ++ N      DL Q G IGLMKA   FD 
Sbjct: 7   IELIEQAHRGDDRAKELVVSQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAVNNFDT 66

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FSTYA+  +   I R   D   TI++   +++   K+ +    ++N+  ++PT E
Sbjct: 67  NYGVQFSTYAVPIIMGEIKRYFRD-DGTIKVSRSLKELNLKINKARELLTNQTGQDPTVE 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQAN 608
           +IA  L + V+ V + +  +  P SL  PI ++D S +   + IE+K+     +      
Sbjct: 126 QIAAYLDVDVQDVVEAIDSSYYPTSLSEPIYEKDGSSISMEERIENKHNKMWFE------ 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +  L  +E+ +L MR+ +  N +     V ++  +++ ++ ++E K I KL+
Sbjct: 180 -KIALEMEIDKLDEKEKLILYMRYQLDFNQER----VAQRLNISQVQVSRLEKKIIAKLR 234


>gi|20151056|pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
 gi|20151057|pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
          Length = 241

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 89/239 (37%), Positives = 147/239 (61%), Gaps = 20/239 (8%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           E+  D+++++      + +L+++ G+ +++  E  + + L    +       E       
Sbjct: 21  EEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEK------ 74

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
             +  ++ ++  ++KS+         E +  + + R    E   A++ ++EANLRLV+S+
Sbjct: 75  -PDPKTVEEVDGKLKSL-------PKELKRYLHIAR----EGEAARQHLIEANLRLVVSI 122

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           AKKYT RGL FLDLIQEGN GL++A EKF++   +KFSTYA WW++QAI R+IADQ+ TI
Sbjct: 123 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTI 182

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL--AMPVEGVRKVLKITKEPISL 576
           RIPVHM + I+K+ RTAR++  ++ REP+ EEIA+ +      + V + LKI +EP+SL
Sbjct: 183 RIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241



 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN- 175
           T DPVR YL E+G + LL+ E EI +A+++E G    +  L E+    Q LI        
Sbjct: 1   TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG-MEAIKKLSEATGLDQELIREVVRAKI 59

Query: 176 DGTTLLREIIDLEACIGP 193
            GT  +++I  L+    P
Sbjct: 60  LGTARIQKIPGLKEKPDP 77


>gi|322833177|ref|YP_004213204.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
 gi|321168378|gb|ADW74077.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
          Length = 240

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  I K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E+FD   G
Sbjct: 5   YTADGVIDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +       K+ R P+  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVSQAMHSAEQKLGRPPSEGEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           + L +P+E  R++L  T            E+     + + E     +PL   ++ NLR  
Sbjct: 122 QVLDIPIEEYRQILMDTNSSQLFSYDEWREEHGDTAEALMEGHEEANPLHHLLEGNLRHR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIDALPEREKLVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|91227014|ref|ZP_01261551.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|91188816|gb|EAS75102.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|210148643|gb|ACJ09227.1| RpoS-like sigma factor [Vibrio alginolyticus]
          Length = 279

 Score =  118 bits (295), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 131/267 (49%), Gaps = 7/267 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-- 466
             + +K I     +S  E  H   + R        A++ ++E+NLRLV+ +AK Y  R  
Sbjct: 12  YAHYLKDIVGIDLLSREEELHYAKLNR---AGDEEAREMLIESNLRLVVKIAKGYLKRPG 68

Query: 467 -GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                LDLI+EGNIGL+KA +KFD   GY+FSTYA+WW+++ I  ++ +   T+R+P H+
Sbjct: 69  NNFTLLDLIEEGNIGLIKAVDKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPAHV 128

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +I+ +       S    +E +  E+++   +  E + + L      I + T       
Sbjct: 129 CKEINSLALKKLDASKSESKELSISELSRCSGVKAERIDE-LVALSGFIDVSTTADLHRV 187

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + +  E +    P          +    ++ +L  + ++VL  RFG+      TL E+
Sbjct: 188 PFVLELCESEYTPDPQQDCENQCFTQAIENIIKTLPTKLQKVLIHRFGLFDQRVKTLSEI 247

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+ ER+RQ++ +A+ +++   R
Sbjct: 248 GLLLNVSNERVRQMQIEAVERVQKRLR 274



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 28/88 (31%), Positives = 36/88 (40%), Gaps = 2/88 (2%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DP   YL+++  I+LLSRE E+  AK   AG       L ES L     I        G 
Sbjct: 10  DPYAHYLKDIVGIDLLSREEELHYAKLNRAGDEEAREMLIESNLRLVVKIAKGYLKRPGN 69

Query: 179 TL-LREIIDLEACIGPESKGGFFHGTEG 205
              L ++I+ E  IG       F    G
Sbjct: 70  NFTLLDLIE-EGNIGLIKAVDKFDPEPG 96


>gi|210617641|ref|ZP_03291672.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
 gi|210149188|gb|EEA80197.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
          Length = 237

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 123/243 (50%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++R+       A++++VE N+ L+  + K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIRQSHDGDEKAREQLVEENIGLIWCIVKRFYGRGAEPEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      ++  K+ R+PT
Sbjct: 63  DMTYDVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELSYKAYFAKEKLQEKLGRDPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQ 606
            EE+A+ + +  E +   ++ + E  SL  PI  +D     L D +E+  A        +
Sbjct: 122 LEELAETMEVEKEELVMAMESSGEVESLHKPIYQKDGNEIQLMDKLEETGAQE-----EK 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    ++L  L   E +++ +R+           +VGK   +++ ++ ++E K ++ 
Sbjct: 177 VLNQMLLAQLLEGLEKEERQLIYLRYFANQTQS----QVGKTLGISQVQVSRLEKKILKN 232

Query: 667 LKH 669
           L+ 
Sbjct: 233 LRQ 235


>gi|52079008|ref|YP_077799.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|319648688|ref|ZP_08002899.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52002219|gb|AAU22161.1| RNA polymerase sigma-37 factor (sigma-B) [Bacillus licheniformis
           ATCC 14580]
 gi|317389107|gb|EFV69923.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 263

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 122/258 (47%), Gaps = 6/258 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   S  T ++ +E   ++   +  E +   A+  +V+    LV ++AKKY+       D
Sbjct: 1   MAQPSKTTKLTKTEVDTLIK--KYQENQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G +GL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++
Sbjct: 59  LCQVGMLGLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                 ++ + +R P  +EIA+ L +  E V + +++ K   +L      E  +      
Sbjct: 119 KMAVDHLTTETQRSPRVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEADADGSTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S  +   + N +     VL  L+ RE++++ + +      + + +E G+   ++
Sbjct: 179 ILDIVGSQEEGYEKVNQKLMLESVLHVLSDREKQIIELTY----IQNKSQKETGEMLGIS 234

Query: 653 RERIRQIEAKAIRKLKHP 670
           +  + +++ KA+++L+  
Sbjct: 235 QMHVSRLQRKAVKRLREA 252


>gi|325263641|ref|ZP_08130375.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
 gi|324031350|gb|EGB92631.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
          Length = 238

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 126/241 (52%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A++++VE N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIKKSHDGDKKAREQLVEENVGLVWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K+ +T   ++  + REPT
Sbjct: 63  DLSYEVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELSYKIFQTREALTGSLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A  + +  E + + ++   E  SL  PI  ++ + +    + +      +  +   
Sbjct: 122 LEELANTMNVDKEEIVQAMEAGGEVESLYKPIHQKEGNEIRLVDKLEEKERKEEKILDHM 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L     ++L SL   E +++ +R+      D T  +VGK+  +++ ++ ++E + I  L+
Sbjct: 182 L---LAQLLESLDKEERQLIYLRYFA----DETQSQVGKKLGISQVQVSRMEKRIIENLR 234

Query: 669 H 669
            
Sbjct: 235 R 235


>gi|291563747|emb|CBL42563.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SS3/4]
          Length = 239

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 117/245 (47%), Gaps = 12/245 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
                 ++++       A+  +V  N  LV S+ +++  RG +  DL Q GNIGL+KA +
Sbjct: 1   MADTAELLKRSHAGDKEARDRLVMENAGLVWSIVRRFIGRGPEPDDLFQIGNIGLIKAID 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD  LG +FSTYA+  +   I R + D    I++   +++   KV     ++   + RE
Sbjct: 61  HFDTELGVRFSTYAVPMITGEIRRFLRD-DGMIKVSRPLKELAGKVGAAREKLEADLGRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSA 604
           PT EE+A+ +    E V   ++      S+  P    D S   L D I +K + +     
Sbjct: 120 PTVEELARSVGASREEVAASMEAGARVGSIYEPFDAGDESGGCLADKIAEKTSEN----- 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +   R     +L+ L  +E+++++MR+        T   +  +  +++ ++ ++E K +
Sbjct: 175 DRVLDRIVLAELLSGLGEKEQQIIKMRYFEN----MTQTVIAGRLGISQVQVSRMEKKIL 230

Query: 665 RKLKH 669
           R+++ 
Sbjct: 231 REMRE 235


>gi|219125233|ref|XP_002182890.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217405684|gb|EEC45626.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 312

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 137/281 (48%), Gaps = 23/281 (8%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA-KKY----TNRGL 468
           +  + + G+S  E R +V+  R+       AK ++V ANL LV +V  ++Y    T+ G+
Sbjct: 37  QEWADKVGLSNKELRRVVNDYRR-------AKHDLVTANLGLVHAVVNQQYGSLKTHTGI 89

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +LIQEG++GL++AAE FD   G +FSTYA+ W+K  ++ S   +   +R+P   + K
Sbjct: 90  TKEELIQEGSLGLLRAAELFDPERGLRFSTYAVVWIKGVLSNSHLPE--LVRLPAREKTK 147

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK---VLKITKEPISLETPIGDE-- 583
            +K+    R +       PT EE+A    M V+ V +    ++  +  +SL+        
Sbjct: 148 WNKIQTIQREVETANGVVPTVEELATLTGMTVQEVVQTTRRMQQARSILSLDFEYSSHSR 207

Query: 584 ---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTD 639
              DT+     + ++        A +  L+      +A +L  RE R+LR+R+G+     
Sbjct: 208 SGADTATSSAALANQECPEDAKLAARTQLQADVIAAMARNLDAREARLLRLRYGLADGQT 267

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +L E      ++  R +QI    + KL+  + ++ L  +L
Sbjct: 268 RSLAECADAMGLSPTRTQQIAQTCLSKLRQAAEAESLEEYL 308


>gi|270262372|ref|ZP_06190644.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
 gi|270044248|gb|EFA17340.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
          Length = 240

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  +    + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWLRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +  R++  ++ R  +  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRHAREVAQVMRQLEQRLGRPASEVEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L +P++  R++L  T            E+     +  +E     +PL   ++ NLR+ 
Sbjct: 122 QTLNIPLDEYRQILLDTNNSQLFSYDEWREEHGESAEPLLEGHEEANPLHHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIDALPEREKMVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|161898849|gb|ABX80414.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 108/241 (44%), Gaps = 5/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI KL
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAI-KL 235

Query: 668 K 668
           +
Sbjct: 236 R 236


>gi|260222460|emb|CBA32046.1| RNA polymerase sigma factor for flagellar operon [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 273

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/266 (21%), Positives = 115/266 (43%), Gaps = 15/266 (5%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLD 472
           +   T  +I + R+          +  + +  +++    LV  +A     +    ++  D
Sbjct: 16  LCPSTQQTIFQHRNARRETLMYTAKGQLDRSALIKQYQPLVRRLAHHMMAKLPPSVEVDD 75

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LIQ G IGL  A  +++   G +F T+A   ++ A+   + +           R    ++
Sbjct: 76  LIQVGLIGLSDALSRYEASQGVQFETFATQRIRGAMLDELRENDWM---SRGSRKSQKEI 132

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHL 588
               R++ +K+ R P   EIA +L M +   + +L      + + LE       +D ++L
Sbjct: 133 ETALRKLEHKLGRSPAESEIATELGMSLSDYQSLLGKVRGTQLVYLEDMARRNEDDDTYL 192

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              + D++A  PL+      LR++    +  L  RE+ ++ M +      D  L+E+   
Sbjct: 193 DRHVADQDA-DPLNMLRDQRLRQSLVDAIKCLPEREQYIMSMYY----EQDMNLKEIAAV 247

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             VT  R+ Q+ +++I +L+   RS 
Sbjct: 248 LDVTESRVCQLHSQSIARLRAKMRSH 273


>gi|225389231|ref|ZP_03758955.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
 gi|225044710|gb|EEG54956.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
          Length = 239

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++ +       A+ ++V  N+ L+ S+ +++  RG +  DL Q G+IGLMKA +KF
Sbjct: 3   ETLKLILRAHEGDKTARDQLVMDNVGLIWSIVRRFAGRGYEMEDLFQIGSIGLMKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++   KV      M+ ++ REPT
Sbjct: 63  DTTFEVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSIKELGLKVKCAREEMTYELGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            EEIA  + +  E V   ++   E  SL  P+G  D +   L D +E++N     +    
Sbjct: 122 IEEIAGSVGVSREEVAASMEAGAEVESLYRPVGGSDDNQLCLMDRLEEEN-----NEHEA 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     +L+SL   E  ++  R+           ++ +   +++ ++ ++E + ++ 
Sbjct: 177 LINRMVLKELLSSLEEGEREIIVRRYFHNQTQ----TQIAQDLGISQVQVSRLEKRILKA 232

Query: 667 LKHPSRS 673
           ++    S
Sbjct: 233 MRKRFES 239


>gi|254381060|ref|ZP_04996425.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339970|gb|EDX20936.1| sigma factor [Streptomyces sp. Mg1]
          Length = 302

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 115/253 (45%), Gaps = 15/253 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +  + +G  E    +  ++E N+ LV   A+++ +R   G+   D++Q G IGL+KA ++
Sbjct: 56  LRSLEEGTREYQYTRNTLIEMNISLVNFAARRFRSRAGGGVDIEDIVQVGTIGLIKAIDR 115

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     +FST A+ ++   I R   D +  + +P  +++   ++ ++   ++    R P
Sbjct: 116 FDPDREVEFSTLALPYISGEIKRFFRDTTWAVHVPRRLQELRSELAKSQDALTEVFGRAP 175

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISL------ETPIGDEDTSHLGDFIEDKNAVSPL 601
           T +EIA+ L +  + V + L       S        +       +      E    V P 
Sbjct: 176 TVKEIAEHLELSEDDVIEGLVAANGYTSGSIDAATSSRQRTSGETEGRSLAETVGEVDPD 235

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
               +     T   +L SL  R+ R+L MRFG     + T  E+G +  +++ ++ ++  
Sbjct: 236 MELFEEF--HTLAPLLQSLKERDRRILAMRFG----EEMTQAEIGTELGISQMQVSRLLT 289

Query: 662 KAIRKLKHPSRSK 674
           + + +L+    ++
Sbjct: 290 RVLTRLRTAMLAE 302


>gi|315186365|gb|EFU20125.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Spirochaeta
           thermophila DSM 6578]
          Length = 262

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 109/247 (44%), Gaps = 15/247 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              +      ++  ++    LV  VA K        ++F DLI  G  GL+ A EKFD  
Sbjct: 17  EYQKTRDPQIREYFIKQYAPLVKYVAGKIAVGLPSSVEFDDLIGFGTFGLLDAIEKFDPE 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA+  ++ AI   +        +P  +R K  ++     R+ + + R  T EE
Sbjct: 77  KHVKFKTYAVTRIRGAIYDELRAMDW---VPRSVRQKSKEIEDALHRLESSLGRAATDEE 133

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQ 606
           +A+++ M    ++K L+   +   +SL+      D +    + D +E   A  P     +
Sbjct: 134 LAREMNMSSRELQKTLQKISSTSILSLQELWYTGDENDRVAIADMLEAPQAYDPAARVER 193

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             ++      +  L  +E++VL + +      D TL+E+G    VT  R+ Q+  KAI +
Sbjct: 194 EEIKRVVAEAIKELPEKEKKVLVLYY----YEDLTLKEIGAILNVTESRVSQLHTKAISR 249

Query: 667 LKHPSRS 673
           L+   R+
Sbjct: 250 LRVKLRN 256


>gi|302522454|ref|ZP_07274796.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
 gi|302431349|gb|EFL03165.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
          Length = 297

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 113/247 (45%), Gaps = 20/247 (8%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCL 492
           + +G      A+  ++E N  LV   A+++ NRG     D++Q G IGL+KA ++FD   
Sbjct: 54  LEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAIDRFDLTR 113

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F+++A+ ++   I R   D +  + +P  +++    + R   R++ ++ R+P  +E+
Sbjct: 114 EAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELRVDLARAKERLAVELDRDPGVKEL 173

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLD 602
           A +L +  E V   L      +S    +  + ++             DF+ D        
Sbjct: 174 AAELGISEEEVIDGLIAANGYMSDSLDLPADSSTSGKPDQKTATTYADFLGD-----WDP 228

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +            +L +L  RE  +L +RFG     + T  ++G +  V++  + ++ ++
Sbjct: 229 AMELVENFTALRPLLGTLDDRERYLLELRFG----QELTQAQIGAELGVSQMHVSRLLSR 284

Query: 663 AIRKLKH 669
            + KL+ 
Sbjct: 285 TLGKLRE 291


>gi|161898837|gb|ABX80408.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 108/238 (45%), Gaps = 4/238 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+    + ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVKELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|206975667|ref|ZP_03236579.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
 gi|206746129|gb|EDZ57524.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
          Length = 257

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 119/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +V+    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTTLTKEDVIKLIAEFQQNQCD--EAQERLVDHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 +++ ++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDCLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|91211141|ref|YP_541127.1| flagellar biosynthesis sigma factor [Escherichia coli UTI89]
 gi|117624064|ref|YP_852977.1| flagellar biosynthesis sigma factor [Escherichia coli APEC O1]
 gi|218558780|ref|YP_002391693.1| flagellar biosynthesis sigma factor [Escherichia coli S88]
 gi|237705878|ref|ZP_04536359.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|91072715|gb|ABE07596.1| flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli UTI89]
 gi|115513188|gb|ABJ01263.1| flagellar biosynthesis sigma factor FliA [Escherichia coli APEC O1]
 gi|218365549|emb|CAR03276.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli S88]
 gi|226900635|gb|EEH86894.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|294492788|gb|ADE91544.1| flagellar operon sigma factor FliA [Escherichia coli IHE3034]
 gi|323952417|gb|EGB48290.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H252]
 gi|323956319|gb|EGB52062.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H263]
          Length = 239

 Score =  118 bits (295), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMETIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|52784380|ref|YP_090209.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|52346882|gb|AAU39516.1| SigB [Bacillus licheniformis ATCC 14580]
          Length = 264

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 122/258 (47%), Gaps = 6/258 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   S  T ++ +E   ++   +  E +   A+  +V+    LV ++AKKY+       D
Sbjct: 2   MAQPSKTTKLTKTEVDTLIK--KYQENQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G +GL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++
Sbjct: 60  LCQVGMLGLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                 ++ + +R P  +EIA+ L +  E V + +++ K   +L      E  +      
Sbjct: 120 KMAVDHLTTETQRSPRVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEADADGSTVT 179

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S  +   + N +     VL  L+ RE++++ + +      + + +E G+   ++
Sbjct: 180 ILDIVGSQEEGYEKVNQKLMLESVLHVLSDREKQIIELTY----IQNKSQKETGEMLGIS 235

Query: 653 RERIRQIEAKAIRKLKHP 670
           +  + +++ KA+++L+  
Sbjct: 236 QMHVSRLQRKAVKRLREA 253


>gi|133470|sp|P19433|RPSB_MYXXA RecName: Full=RNA polymerase sigma-B factor
          Length = 246

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 70/229 (30%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           MV ANLR V+ VA +Y + G++  DLIQEGNIGLMKA +KFD   G +  +YA+WW++  
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 508 ITRSIADQSCTIRIPVHMR--DKIHKVVRTARRMSNKIKRE--PTPEEIAKKLAMPVEGV 563
           I   I      +++            + RT R +      +     ++IA++L +    V
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKFGSGDAAVNVDDIARRLHVKPGEV 120

Query: 564 RKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLAS 619
           R++  ++    +SL+ P+G++  +   DF+    A    + A +     +       L  
Sbjct: 121 REMEQRMGGRDLSLDAPMGEDGGNSHVDFVVSAAAPQDDEFADKEEAGLINARVRAALMR 180

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PRE  ++     +      TL+E+G+ F  +RER RQ+E +A  KLK
Sbjct: 181 LDPREPFIIEQ--RVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLK 227


>gi|329937639|ref|ZP_08287158.1| RNA polymerase sigma factor sig8 [Streptomyces griseoaurantiacus
           M045]
 gi|329303038|gb|EGG46926.1| RNA polymerase sigma factor sig8 [Streptomyces griseoaurantiacus
           M045]
          Length = 287

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 120/256 (46%), Gaps = 17/256 (6%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNI 479
            +S   F  + ++  +G  E    +  ++E NL LV   A ++ +RG     D++Q G I
Sbjct: 36  ELSRHFFARLATL-EEGTPEYQYVRNTLIEMNLSLVRYAASRFRSRGADEMEDIVQVGTI 94

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+KA ++F+     +F+++A+ ++   I R   D S  + +P  +++   ++ R    +
Sbjct: 95  GLIKAIDRFELTREVEFTSFAVPYIVGEIKRFFRDTSWAVHVPRRLQEARVELARATEEL 154

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE------PISLETPIGDEDTSHLGDFIE 593
           S +  R+PT  E++  +++P E V +  K +          SL    G +  S L DFI 
Sbjct: 155 SRRTGRQPTVRELSALMSLPEEEVIEARKASNAYRSSSLDASLSGDGGLDGESALADFIG 214

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +     L   + +        ++A L  R+  +L +RF      + T  ++G++  +++
Sbjct: 215 VEERGLELIEDLHS-----LAPLVAGLPERDRTILHLRFV----EELTQAQIGERLGISQ 265

Query: 654 ERIRQIEAKAIRKLKH 669
             + ++  + +  L+ 
Sbjct: 266 MHVSRLLNRIVTGLRE 281


>gi|254383401|ref|ZP_04998753.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194342298|gb|EDX23264.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 311

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 111/247 (44%), Gaps = 5/247 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S + FR +  +        S  +  +VE NL LV   A+++  R     D++Q G IGL
Sbjct: 36  LSATLFRRLAELHEGSPEY-SYVRNTLVELNLSLVRYAARRFRARSEPMEDIVQVGTIGL 94

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA  +FD   G +F+++AM  +   I R   D S  +++P  +++      +    +  
Sbjct: 95  IKAINRFDPGRGVEFTSFAMPTITGEIKRFFRDTSWAVKVPRRLQELRIDAAKAHDALEQ 154

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            + R P+  E+A +L +  E + +  K      +       ++   L  +          
Sbjct: 155 DLGRPPSDVELAGRLHVSPEELAEGQKAAHGYSARSLDAPSQEEGDLASYSGAPAIGEEE 214

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +  +    E+   +LA+L  RE  +L +RFG     + T  E+G +  +++  + ++ +
Sbjct: 215 PAYDRIECLESLKPILAALPDRERTLLSLRFG----QELTQAEIGDRLGLSQMHVSRLLS 270

Query: 662 KAIRKLK 668
           + + +L+
Sbjct: 271 RTLARLR 277


>gi|218133693|ref|ZP_03462497.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991068|gb|EEC57074.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
          Length = 254

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 109/263 (41%), Gaps = 18/263 (6%)

Query: 425 SEFRHIVSMVRKGECEASIA-KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIG 480
            +      +  +     S A + +++    +LV  VA +   Y    +++ DL   G  G
Sbjct: 1   MDEAARNKLWSEYSRTRSTALRDQLIIEYSQLVKLVAGRLGMYLGYSVEYDDLCGYGIFG 60

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+ A +KFD     KF TYA   ++ AI   I        IP  +R K  K+     ++ 
Sbjct: 61  LIDAIDKFDCNKNVKFETYASLRIRGAILDQIRKMDW---IPRSLRQKQKKIDAAMSKIE 117

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
            +     T EE+A++L + ++              ISL+     + T    D + +    
Sbjct: 118 AQKGSVATDEELAQELGITLDEFNDWQGKTKATNLISLDEYTETQGTEAKMDSVTNARFD 177

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            P D   +  L++     ++ LT +E  V+ + +      + TL+E+     V+  R+ Q
Sbjct: 178 QPEDVVEKEELKKMIVEAISLLTDKERSVVTLYY----YEEMTLKEISLVLDVSESRVSQ 233

Query: 659 IEAKAIRKLKHPSRSKKLRSFLD 681
           +  KA+ K+K      KL  +L+
Sbjct: 234 LHTKALLKMK-----SKLGPYLN 251


>gi|298507081|gb|ADI85804.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           sulfurreducens KN400]
          Length = 250

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 120/251 (47%), Gaps = 14/251 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           + +  ++ +   +  + E++  +L LV  +  +  ++    L   DL+    IGL+ AAE
Sbjct: 5   LKAYEQEAQRSVAQTRDELIVNHLPLVKFLVGRIASQLPPHLDQEDLMSAAIIGLITAAE 64

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G +F T+A   ++  I   +  Q     +   +RDK  K+ +    + +++ R 
Sbjct: 65  RFDPTRGVQFKTFAEQRIRGTIIDELRSQDW---LTRSLRDKFKKLEKEFVLLEHQLGRN 121

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLD 602
           PT +E+A  L M V+   ++L+       +SL+    D+D S  G  D + D +  +P  
Sbjct: 122 PTSDEVATALKMSVDEYYRMLEEIHLLSFVSLDESWEDDDGSPFGLLDILADTSIENPQS 181

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +   + ++ T  + SL  +E  V+ + +      +  L+E+G    ++  RI Q+ ++
Sbjct: 182 QLMARQMLDSLTESIESLPEKERLVITLYY----YEELNLKEIGAVLELSESRISQLHSQ 237

Query: 663 AIRKLKHPSRS 673
           AI +L+   ++
Sbjct: 238 AIVRLRAKMKN 248


>gi|303282119|ref|XP_003060351.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226457822|gb|EEH55120.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 425

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 85/267 (31%), Positives = 134/267 (50%), Gaps = 29/267 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAK------KYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLG 493
              A++++V  N+ L  S+A+       + +RGL    DL QEG  GL +AA+KFD   G
Sbjct: 62  GQNARRQLVVKNVGLAYSIARDVFEKLNHADRGLLSVSDLAQEGCAGLAQAADKFDPSRG 121

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA  W ++ +  +I +   TIR+P+HM + + +  +  R ++ K  R PT EE++
Sbjct: 122 YKFSTYAYNWTRKYVVNAIQNNGRTIRLPIHMHEIMQRAKKATRELTQKHGRAPTDEEMS 181

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-------LGDFI-------EDKNAVS 599
           + L +PV  V+++    +  +SL+   G   +         + D I       + K+ + 
Sbjct: 182 RTLGVPVSRVQEINDWARSTLSLDVGGGGRSSDDGDGGAEGMMDGIVFALGSKDGKDGML 241

Query: 600 PLDSAIQAN-----LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
               A +A+     LR       A+L PRE  VLR RFG+       L   G    V+ E
Sbjct: 242 SPHEAAEADMEADLLRRDLEEAFATLLPREAFVLRHRFGLAAAASTAL---GTLLGVSHE 298

Query: 655 RIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            IR  E +A+ KLK PSR+ +   +LD
Sbjct: 299 TIRTYERRALEKLKQPSRAARFVRYLD 325


>gi|302541605|ref|ZP_07293947.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459223|gb|EFL22316.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 292

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 55/249 (22%), Positives = 113/249 (45%), Gaps = 15/249 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + ++FR I S+      EA   ++++V A + +   +A ++ NRG    DL Q   +GL+
Sbjct: 46  TTADFRRIASLPEGAPKEAL--RQDVVRAWMPMAERLAGQFRNRGESAEDLRQVAMLGLV 103

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA  ++D   G  F +YA+  V   + R   D    + +P  +++  ++V    + ++  
Sbjct: 104 KAVNRYDPDRGTAFESYAVPTVVGEVKRHFRDHLWGLHVPRRVQELRNRVRTAVQDLTRT 163

Query: 543 -IKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAV 598
              R P+  ++A+   +  E VR  ++   +   +SL+  +   D  + L D +      
Sbjct: 164 PDGRTPSVADVAEHTGLSEEEVRSGMEALESYSTLSLDAELRGADDGYALVDTLG----- 218

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP  S  +   RE     LA+L  RE R+L +RF            +  +  +++  + +
Sbjct: 219 SPEPSYDRVVQREALKPCLAALPERERRILYLRFFCDETQGR----IADRMGISQMHVSR 274

Query: 659 IEAKAIRKL 667
           + ++   +L
Sbjct: 275 LISRTCERL 283


>gi|167464139|ref|ZP_02329228.1| DNA-directed RNA polymerase sigma subunit D [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322382365|ref|ZP_08056272.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321153718|gb|EFX46093.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 262

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 67/252 (26%), Positives = 120/252 (47%), Gaps = 12/252 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             E     AK+ ++E  L LV  V+ + +N   R +   DL   G +GLM A EKFD   
Sbjct: 18  WKEAGCLEAKQSLLEQYLPLVDYVSSRMSNGLPRNVAKEDLASFGVLGLMDAVEKFDHTR 77

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA W +  A+   +        +P  +R+K  K+    +++     R  T  EI
Sbjct: 78  GLQFETYASWRILGAVIDGLRQGDW---VPRSLREKAKKIEDAYQKLEQHYLRTVTDAEI 134

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++ L +  E  R++L+        S++ PI +E++      + D+ A +P     +  L+
Sbjct: 135 SEYLGVEEEEFRQMLQEINVTSICSVDDPIKEEESETRLSLLIDEKAKNPEYKVNEFYLK 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           ET  R +  LT +E+ V+ + +      + +L E+ +   ++  RI Q+ +KAI +L+  
Sbjct: 195 ETLARAIEKLTEKEKIVVSLFYF----EELSLSEIAEVMSLSPSRISQLHSKAILRLRGT 250

Query: 671 SRSKKLRSFLDG 682
               K++ F D 
Sbjct: 251 LNKYKIQLFQDS 262


>gi|291442923|ref|ZP_06582313.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291345870|gb|EFE72774.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 265

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 102/228 (44%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + + L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F TYA+  V
Sbjct: 39  RDETIRSWLPMAHRIATRFRNRGEAMDDLRQVAAMGLVKAVDRYDPERGKAFETYAVPTV 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              + R   D +  + +P  ++D  ++V    R ++       PT  EIA    +  E V
Sbjct: 99  TGELKRHFRDHTWDVHVPRRVQDLRNRVRVARRELAQTSGGGSPTCAEIASATGLGEEDV 158

Query: 564 RKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+   +   +SL+  P G E  S L D +      S   +   A  RE     L  L
Sbjct: 159 LLGLEALESYSALSLDAEPAGVEGGSPLVDRLG-----SCDAALDTAVDREAVKPELRGL 213

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L +R+      D T   + ++  +++  + ++ +++  +++
Sbjct: 214 PERERTILYLRYF----QDMTQVRIAERLGISQMHVSRLLSRSCERVR 257


>gi|303241077|ref|ZP_07327586.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302591337|gb|EFL61076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 246

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 126/244 (51%), Gaps = 7/244 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + +++K +     A+  +VE N+ LV S+ K++ NRG +  D+ Q G IGL+KA +KF
Sbjct: 8   ETLELIKKAKSGDKQAQSILVERNVGLVWSIVKRFQNRGYETDDIYQIGCIGLIKAIKKF 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R I D    I++   +++  +K+  T   M  ++ REP+
Sbjct: 68  DDSFDVKFSTYAVPMIIGEIKRFIRD-DGIIKVSRSLKELSNKIRVTKEIMMKELGREPS 126

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EI+ ++ +  E +   ++    P SL   +GD DTS +   + DK      D  +   
Sbjct: 127 ISEISLRMDVAAEELVMAMEANCSPESLYNTVGDSDTSTV--LLIDKLNNESNDEEVDLV 184

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     VL +L PRE++++ +R+      + T  ++ K   +++ ++ +IE K + ++K
Sbjct: 185 DKIDLRLVLNTLKPREKQIIILRYF----KEKTQVQIAKMLGISQVQVSRIEKKILDEIK 240

Query: 669 HPSR 672
              +
Sbjct: 241 KKIK 244


>gi|42524687|ref|NP_970067.1| RNA polymerase sigma factor for flagellar operon [Bdellovibrio
           bacteriovorus HD100]
 gi|39576897|emb|CAE78126.1| RNA polymerase sigma factor for flagellar operon [Bdellovibrio
           bacteriovorus HD100]
          Length = 261

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 115/246 (46%), Gaps = 14/246 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +     +    A   K +++     L+  +A+K   R    ++  DLI  G IGLM A E
Sbjct: 8   LKKYKEEPRKLAPTQKDDLIREYAPLIKFIAQKIAVRLPSNIELDDLISAGVIGLMDAIE 67

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           K+D     KF TYA + ++ AI   +  Q     +P  +RDK   + +T  ++   + R 
Sbjct: 68  KYDSTRDNKFKTYAEFRIRGAILDELRAQDW---VPRSIRDKAKLLDKTMVQLEADLGRT 124

Query: 547 PTPEEIAKKLAMPVEG----VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           P+ EE+AK L + ++     V +V  ++  PI   T   + D   + D +E     SP +
Sbjct: 125 PSDEEVAKALNVSIDEFHDLVNQVRPVSLLPIDQATSFSNTDKKSIMDILEGSRTNSPFN 184

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                N++E   + +  L  R+  VL + +      D  L+E+G+   VT  R+ Q+ A+
Sbjct: 185 QLNVKNIKEVVAQAIEELPERQRLVLSLYY----YEDLNLKEIGQVLRVTESRVSQLHAQ 240

Query: 663 AIRKLK 668
           A+ +L+
Sbjct: 241 AVARLR 246


>gi|223986354|ref|ZP_03636363.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
 gi|223961703|gb|EEF66206.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
          Length = 257

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 133/261 (50%), Gaps = 13/261 (4%)

Query: 412 EIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           +++   V T  + + + + +  +  + +     AK++++  NL+LV+S+ +++ +R    
Sbjct: 5   KVEICGVNTATLPVLKSQQMTELFIQLQDGDLSAKEKLINGNLKLVLSIVQRFAHRTENM 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL Q G IGL+KA + FD     +FSTYA+  +   I R + D    IR+  H++D  +
Sbjct: 65  DDLFQIGCIGLIKAIDNFDLSHEVRFSTYAVPMIIGEIKRYLRDNQ-MIRVSRHLKDLAY 123

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HL 588
           KV++      +  +REP+  E+A+ + +  + + + L+  +  +S+  PI ++D    +L
Sbjct: 124 KVLKEKEAFIHANQREPSLAELAEIMGVKEKDIAESLESLQSVVSIFEPIYNDDGDTLYL 183

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I+D +      S++ A         +  L+ +E +++  R+  G        E+  +
Sbjct: 184 LDQIKDDHDEIGKLSSLIA-----LKESMKHLSDKEAQIINKRYYQGQTQ----TEIASE 234

Query: 649 FCVTRERIRQIEAKAIRKLKH 669
             +++ ++ ++E  A++ LK 
Sbjct: 235 LGISQAQVSRLEKSALQCLKK 255


>gi|197303315|ref|ZP_03168355.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
 gi|197297599|gb|EDY32159.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
          Length = 237

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 123/245 (50%), Gaps = 12/245 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +S++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTISLIRKSHHGDKEAREQLVKENVGLVWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   I R + D    I++   ++   +K  +    ++ ++ REPT
Sbjct: 63  DLSYDVQFSTYAVPMISGEIRRFLRD-DGMIKVSRSLKKLSYKCGKKKEELTERMGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQ 606
            EE+A  L    E + + ++   E  S+  PI  E  S L   D +E+K+          
Sbjct: 122 MEELATSLGTEKEELVQAMEAATEVESIYRPIHQEGDSQLSILDRLEEKSRPE-----EH 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R   +++L  L   E +++ +R+      + T   VG+   +++ ++ ++E K + +
Sbjct: 177 LLNRMMLSQILDGLDKEERQLIYLRYF----QEKTQAAVGEILGISQVQVSRMEKKILER 232

Query: 667 LKHPS 671
           ++   
Sbjct: 233 MRKQM 237


>gi|239939493|ref|ZP_04691430.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239985982|ref|ZP_04706646.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
          Length = 262

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 102/228 (44%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + + L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F TYA+  V
Sbjct: 36  RDETIRSWLPMAHRIATRFRNRGEAMDDLRQVAAMGLVKAVDRYDPERGKAFETYAVPTV 95

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              + R   D +  + +P  ++D  ++V    R ++       PT  EIA    +  E V
Sbjct: 96  TGELKRHFRDHTWDVHVPRRVQDLRNRVRVARRELAQTSGGGSPTCAEIASATGLGEEDV 155

Query: 564 RKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+   +   +SL+  P G E  S L D +      S   +   A  RE     L  L
Sbjct: 156 LLGLEALESYSALSLDAEPAGVEGGSPLVDRLG-----SCDAALDTAVDREAVKPELRGL 210

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L +R+      D T   + ++  +++  + ++ +++  +++
Sbjct: 211 PERERTILYLRYF----QDMTQVRIAERLGISQMHVSRLLSRSCERVR 254


>gi|269836601|ref|YP_003318829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
 gi|269785864|gb|ACZ38007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
          Length = 264

 Score =  118 bits (294), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 102/237 (43%), Gaps = 10/237 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R         ++ ++     LV  V  +        L   DL+  G IGL++A ++FD  
Sbjct: 20  RYAIERDGSTREALIRQYAPLVKYVVDRLRVALTATLDRDDLLGYGTIGLIEAIDRFDPE 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF T+A+  ++ AI  ++        +P   R +   + +  R +     R P  EE
Sbjct: 80  RGVKFETFAIQRIRGAIIDAVRTLD---LVPRTARQRARAIEQAYREIFAATGRMPPEEE 136

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A  L M ++  R+ L+     I        +    L D + D  A  PLD+A++++L  
Sbjct: 137 VAAHLGMTIDAFRQALQDAACAILPLQQSDRDGEGTLEDTLPDAQATEPLDAAVRSDLVH 196

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                L  L  R+  ++ + +      + TL E+ +   +T  R+ Q+ ++A  +L+
Sbjct: 197 RLAAALERLPERDRLIVTLYY----YEELTLREISEVLGITESRVSQLLSRARLQLR 249


>gi|317051537|ref|YP_004112653.1| FliA/WhiG family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946621|gb|ADU66097.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfurispirillum
           indicum S5]
          Length = 250

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 105/245 (42%), Gaps = 15/245 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R         + +++E    L+  +A +        ++  DLI  G +GL+ A +KFD  
Sbjct: 10  RAELKNTPAIRNQIIEEYAPLIKYIATRIHAGLPSNIELDDLISIGALGLIDAIDKFDMN 69

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++  I   +        +P  +R K   + R   ++     RE +  E
Sbjct: 70  RGVLFKTYAESRIRGKILDELRKLDW---LPRGLRQKNKALDRAYSKLGINEGREVSDGE 126

Query: 552 IAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQ 606
           +A +L +    V++ +        +SL+  + D D S    L D I D+    P +    
Sbjct: 127 LAAELGIDEAEVQQYISQAGGYTMLSLDEQMYDRDGSESGTLSDLIPDRENAGPEEHLEI 186

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +E   + +  L+ +E+++L     +    + T++E+G    +T  R+ QI ++A+ K
Sbjct: 187 TQNQEFLKKHIRLLSEKEQQML----ALYYYEELTMKEIGTVLGITESRVSQIHSQALFK 242

Query: 667 LKHPS 671
           LK   
Sbjct: 243 LKKAM 247


>gi|318075206|ref|ZP_07982538.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 293

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 104/236 (44%), Gaps = 12/236 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              +  +VEA L +   +A +Y  RG    DL Q   +GL++A ++FD  +   F TYA+
Sbjct: 35  ERQRALLVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAV 94

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPV 560
             ++  + R   D +  + +P  +++    V    + ++ +   R P+  E+A+   +  
Sbjct: 95  PTMQGELKRHFRDNTWGVHVPRRVQELRSAVRAALQELAPRPALRAPSVGELARCAKLSE 154

Query: 561 EGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             VR+ L+   +   +SL++    E    L D +  ++      +      RE+    LA
Sbjct: 155 AEVRQGLEALDSYRSVSLDSAAPSEGEHPLRDRLGAED-----PAYETVVDRESVRPALA 209

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            L  RE  +L +RF        T   +  +  +++  + ++   A  +++H   ++
Sbjct: 210 ELPERERYILYLRFFH----ARTQRAIAAELGLSQMHVSRLITHACAQVRHRVEAR 261


>gi|117928753|ref|YP_873304.1| RNA polymerase sigma factor WhiG [Acidothermus cellulolyticus 11B]
 gi|117649216|gb|ABK53318.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 289

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 65/252 (25%), Positives = 110/252 (43%), Gaps = 20/252 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLM 482
            R +    +  E      ++ ++     LV  VA +    GL       DL+  G  GL+
Sbjct: 39  LRDLWRRFK--ETGDPELRERLILHYSPLVKYVAGR-VGVGLPPNIEQADLVSYGIFGLI 95

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A EKFD     KF TYA+  +K AI   +        IP  +R K  +V +    + +K
Sbjct: 96  DAIEKFDLDRAIKFETYAINRIKGAIIDELRAIDW---IPRSVRYKAREVEKAYAALEHK 152

Query: 543 IKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIG----DEDTSHLGDFIEDKN 596
           + R PT  E+A +L + ++ +            I+L+  +       D   L D +ED  
Sbjct: 153 LHRTPTEAEVAAELGISLDELHAIFSQVSFVNVIALDELLNVGGDRGDRLSLVDTLEDTK 212

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A  P+++      +   +R + +L  RE+ V+ + +  G     TL E+G+   VT  RI
Sbjct: 213 AEDPVEAFETEETKYLLSRAINALPEREKIVITLYYYEG----LTLAEIGQVLGVTESRI 268

Query: 657 RQIEAKAIRKLK 668
            Q+  KA+ +L+
Sbjct: 269 CQMHTKAVLQLR 280


>gi|318059283|ref|ZP_07978006.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075250|ref|ZP_07982582.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 294

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 113/247 (45%), Gaps = 20/247 (8%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCL 492
           + +G      A+  ++E N  LV   A+++ NRG     D++Q G IGL+KA ++FD   
Sbjct: 51  LEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAIDRFDLTR 110

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F+++A+ ++   I R   D +  + +P  +++    + R   R++ ++ R+P  +E+
Sbjct: 111 EAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELRVDLARAKERLAVELDRDPGVKEL 170

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLD 602
           A +L +  E V   L      +S    +  + ++             DF+ D        
Sbjct: 171 AAELGISEEEVIDGLIAANGYMSDSLDLPADSSTSGKPDQKTATTYADFLGD-----WDP 225

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +            +L +L  RE  +L +RFG     + T  ++G +  V++  + ++ ++
Sbjct: 226 AMELVENFTALRPLLGTLDDRERYLLELRFG----QELTQAQIGAELGVSQMHVSRLLSR 281

Query: 663 AIRKLKH 669
            + KL+ 
Sbjct: 282 TLGKLRE 288


>gi|317499023|ref|ZP_07957304.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|291560723|emb|CBL39523.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SSC/2]
 gi|316893673|gb|EFV15874.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 241

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 123/240 (51%), Gaps = 8/240 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R  +     A+++++  N+ L+ SV +++TNRG +  DL Q G+IGLMKA +KFD  
Sbjct: 6   ELLRLTKEGNEAAREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLS 65

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++   +++ ++K+++   +   + +RE T EE
Sbjct: 66  YDVKFSTYAVPMITGEIRRFLRD-DGMIKVSRSLKENVYKIMKAREKFCQQYQREATIEE 124

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           I++   +  E +   L+ + E  S+      +D S +    +     +  +  +   L  
Sbjct: 125 ISEITKITREEIVTSLEASNEVESIHQSAYQKDGSEISLLDKLSKGENESEKVVDHVL-- 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                +  L  +E++++  R+  G     T +E+ K F +++ ++ +IE + ++KL+   
Sbjct: 183 -LKEAMKHLEQKEQQMIYYRYFEG----KTQQEIAKIFHISQVQVSRIEKRILKKLRRQM 237


>gi|212709528|ref|ZP_03317656.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
 gi|212687866|gb|EEB47394.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
          Length = 242

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 108/242 (44%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + E    L+   A K   R    +   DLIQ G IGL+ A E+FD  LG
Sbjct: 9   YTAEGVINKNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDASLG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +     +P  +R +  ++ +    +   + R  T  EIA
Sbjct: 69  ASFATYAVQRIRGSMLDELRSRDW---VPRSVRRQAREMTKAIGELEQSLGRSATEPEIA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K L + +   R+VL  T      S +        S      ED    +PL   ++++L++
Sbjct: 126 KALDIDLAEYRQVLLDTNNSQLFSYDEWHEVHGESCEPSMDEDDGG-NPLSLLMESSLKD 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+   
Sbjct: 185 QIVAAIEQLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSKL 240

Query: 672 RS 673
           RS
Sbjct: 241 RS 242


>gi|253998499|ref|YP_003050562.1| flagellar biosynthesis sigma factor [Methylovorus sp. SIP3-4]
 gi|313200585|ref|YP_004039243.1| RNA polymerase sigma-28 subunit FliA/WhiG [Methylovorus sp. MP688]
 gi|253985178|gb|ACT50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           SIP3-4]
 gi|312439901|gb|ADQ84007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           MP688]
          Length = 244

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 107/235 (45%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  ++  +  LV  +A +   +    ++  DL+Q G +GL+ A  +++   G +F TYA 
Sbjct: 11  KDSLLHQHATLVKKLAYQLKAKLPPSVELDDLVQAGMMGLLDAINRYEDTHGAQFETYAA 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + +      +P  +R  +  V     ++   + R PT  E+AK+L M ++
Sbjct: 71  QRIRGAMIDELRNADW---LPRSIRKNMRDVEGAINQLEQVLGRPPTEGEVAKQLKMSLD 127

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      + +  E     E   H  D     ++ +P+   + +N RET    + +
Sbjct: 128 DYYDMLGECSGHQLLYYEDFHESEGGDHFLDRFLQDDSGNPIKGLLDSNFRETLIEAIEN 187

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  RE+    +  G+    +  L+E+G    V+  R+ Q+ ++AI +L+   + +
Sbjct: 188 LPEREQ----ILMGLYYEQELNLKEIGAVMNVSESRVCQLHSQAIARLRAYMKEQ 238


>gi|54023854|ref|YP_118096.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54015362|dbj|BAD56732.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 273

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 120/252 (47%), Gaps = 9/252 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++       A + ++E++   L L  ++A+++TNRG++F DL+Q   +GL+ A +
Sbjct: 26  FEKLAALDADDPHRAVV-REEILHRCLPLAHNIARRFTNRGVEFEDLLQIARLGLVHAVD 84

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F  +A+  +   + R   D    +R+P  M++    +     R+++++ R+
Sbjct: 85  RFDLEHGDSFLGFAVPTIMGEVRRYFRDHGWAVRVPRRMKELHQLLGPATDRLTHQLGRQ 144

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A +L + +  V + L         SL+      +        +   AV P    
Sbjct: 145 PTARELASELGVELTEVTQALVARNAFTTESLDGGERTGEEGGALPIADRLGAVEPCYGL 204

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++  +      ++A+L  RE +VL +RF        T  E+G+    ++ ++ +I AK +
Sbjct: 205 LEDAM--AVRPLIAALPERERQVLILRFYDN----KTQAEIGRLLGCSQMQVSRILAKTL 258

Query: 665 RKLKHPSRSKKL 676
             L+  + ++ +
Sbjct: 259 TMLREKALAEPV 270


>gi|82776398|ref|YP_402747.1| flagellar biosynthesis sigma factor [Shigella dysenteriae Sd197]
 gi|81240546|gb|ABB61256.1| alternative sigma factor 28 [Shigella dysenteriae Sd197]
          Length = 239

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQCIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D     +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDYQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G +  V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAELEVGESRVSQLHSQAIKRLR 233


>gi|304559365|gb|ADM42029.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda FL6-60]
          Length = 237

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 111/244 (45%), Gaps = 11/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               E  I K  + +    LV   A +   R    ++  DL+Q G IGL+ A E++D   
Sbjct: 1   MYTAEGVIDKNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+TYA+  ++ A+   +  +     +P  +R     V    +R   ++ R P   EI
Sbjct: 61  GTAFTTYAIQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRTPGDSEI 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRE 611
           A+++ +P+E  +++L  T            ED     +  +E     +PL   ++++LR 
Sbjct: 118 AQEMGIPLEEYQQILLDTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRG 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+   
Sbjct: 178 RVIAAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTRL 233

Query: 672 RSKK 675
            S++
Sbjct: 234 LSQR 237


>gi|161898859|gb|ABX80419.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  118 bits (294), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 111/241 (46%), Gaps = 5/241 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+ +G  F +  Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYS-QGKSFHEDSQVGNIGLLGAIRR 59

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 60  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 119

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 120 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 179

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+KL
Sbjct: 180 NQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIKKL 235

Query: 668 K 668
           +
Sbjct: 236 R 236


>gi|226484287|emb|CAQ03748.1| RNA polymerase sigma factor [Enterovibrio calviensis]
          Length = 253

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 49/304 (16%), Positives = 96/304 (31%), Gaps = 52/304 (17%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +  S+ E P +  +L+   D++      L +II            GF   
Sbjct: 1   AKRIEDGINQVQVSVAEYPGSIASLLDQFDKVEAEELRLTDII-----------SGFVDP 49

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
           ++            E       E   D +       ++       PE A      L    
Sbjct: 50  SQEDIAPTATHIGSELT----NEQLADEDKNDDDDDEEEEDTGIDPELAREKFNELRVAY 105

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           D     ++                                   K+ +          +L 
Sbjct: 106 DTMQSAIN-----------------------------------KNGRFHKDTAESVAELS 130

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDP 381
           ++     L   + D LV ++     R+   E  ++RL      + +  F++   G E   
Sbjct: 131 EVFKQFRLIPKQFDRLVNEMRSTMDRVRTQERLVMRLCVDQAKMPKKTFVQLFAGNESSD 190

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           +W+  A    E  + + +    + + +   ++K I  ETG+++   + I   +  GE +A
Sbjct: 191 NWLD-AAMASEKPFVDRLKLYEEDLRRCVQKLKIIEDETGLNVERIKDISRRMSIGEAKA 249

Query: 442 SIAK 445
              +
Sbjct: 250 RPCR 253


>gi|262358316|gb|ACY56763.1| RpoD [Vibrio harveyi]
          Length = 260

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 48/302 (15%), Positives = 101/302 (33%), Gaps = 43/302 (14%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   + +S+ E P T   ++   D++      L ++I        +      
Sbjct: 1   DIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPT 60

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
               G    + +   +++E  D  E   D    ++       ++                
Sbjct: 61  ATHIGSELTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPEL---------------- 104

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                               +   +++   Y+ L+      +   +    S K  V  E 
Sbjct: 105 -------------------ALEKFNQLRSTYQNLQ------LAINEHGYESPKATVANEL 139

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+    G E 
Sbjct: 140 MLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNES 199

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +    + I +   ++K I  ET +++   + I   +  GE 
Sbjct: 200 SEAWLDEILA-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEA 258

Query: 440 EA 441
           +A
Sbjct: 259 KA 260


>gi|333023850|ref|ZP_08451914.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332743702|gb|EGJ74143.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 294

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 56/272 (20%), Positives = 121/272 (44%), Gaps = 27/272 (9%)

Query: 416 ISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I     I+ ++ R +  +       + +G      A+  ++E N  LV   A+++ NRG 
Sbjct: 26  IEDAGKIAPTDARELSRLFFDQLVVLEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGN 85

Query: 469 -QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               D++Q G IGL+KA ++FD     +F+++A+ ++   I R   D +  + +P  +++
Sbjct: 86  GDMEDILQVGTIGLIKAIDRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQE 145

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               + R   R++ ++ R+P  +E+A +L +  E V   L      +S    +  + ++ 
Sbjct: 146 LRVDLARAKERLAVELDRDPGVKELAAELNISEEEVIDGLIAANGYMSDSLDLPADSSTS 205

Query: 588 ----------LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                       DF+ D        +            +L +L  RE  +L +RFG    
Sbjct: 206 GKPDQKTATTYADFLGD-----WDPAMELVENFTALRPLLGTLDDRERYLLELRFG---- 256

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            + T  ++G +  V++  + ++ ++ + KL+ 
Sbjct: 257 QELTQAQIGAELGVSQMHVSRLLSRTLGKLRE 288


>gi|326319090|ref|YP_004236762.1| RNA polymerase sigma-28 subunit FliA/WhiG [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375926|gb|ADX48195.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 237

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 102/244 (41%), Gaps = 12/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  +  LV  +A     +    ++  DLIQ G IGL +A  +++   
Sbjct: 1   MYTAKGQLNRDALIRQHAPLVRRIAHHMIAKLPPNVELDDLIQVGMIGLSEALSRYEVTQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R    ++     R+  K+ R P   EI
Sbjct: 61  GVQFETFASQRIRGAMLDELREGDWM---SRSSRKSQKEIEHAVTRLEQKLGRSPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + +   + +L      + + LE     +D     D     +A  P+       LR
Sbjct: 118 ATELELSLAEYQSLLSKVRGTQLVYLEDMTHGDDDDGFLDRHVADSAADPMAMLRDQRLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +    + +L  RE++++    G+    D  L+E+     VT  RI Q+ +++I +L+  
Sbjct: 178 ASLVAAIKALPEREQQIM----GMYYEHDMNLKEIAAVLGVTESRICQLHSQSIARLRAK 233

Query: 671 SRSK 674
            RS 
Sbjct: 234 MRSH 237


>gi|269139471|ref|YP_003296172.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
 gi|267985132|gb|ACY84961.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
          Length = 240

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 111/243 (45%), Gaps = 11/243 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + +    LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVIDKNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R     V    +R   ++ R P   EIA
Sbjct: 65  TAFTTYAIQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRTPGDSEIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           +++ +P+E  +++L  T            ED     +  +E     +PL   ++++LR  
Sbjct: 122 QEMGIPLEEYQQILLDTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRGR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+    
Sbjct: 182 VIAAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLL 237

Query: 673 SKK 675
           S++
Sbjct: 238 SQR 240


>gi|161898841|gb|ABX80410.1| SigB [Listeria monocytogenes]
          Length = 234

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 108/238 (45%), Gaps = 4/238 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+    + ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVKELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|78486471|ref|YP_392396.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
 gi|78364757|gb|ABB42722.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
          Length = 283

 Score =  117 bits (293), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 59/273 (21%), Positives = 122/273 (44%), Gaps = 9/273 (3%)

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
           A  +     I + ++++     +S  E R +   +     +   A ++++ ++LR V+ +
Sbjct: 9   ANNLTPGQNIESYLRTVQTLPQLSADEERELAEKL--YHDKDLNAARQLILSSLRYVVPI 66

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+ Y   GL   DLIQEGNIGLMKA ++F+     +  T+A+ WV+  I   +      +
Sbjct: 67  ARSYNGYGLPLNDLIQEGNIGLMKAVKRFNPAEKVRLMTFAVHWVRAEINEYVIKNWRIV 126

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLET 578
           +       +       + + S +   +   + IAK+L +  + V ++      + +S++ 
Sbjct: 127 KTATTKAQRKLFFKLRSTKKSLEWLGDKDADTIAKELGVTRKDVLEMETRLYGQDMSVDL 186

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET----TTRVLASLTPREERVLRMRFGI 634
              +E+ +     +     + P       +  +       + L  L  R   +L+ R+  
Sbjct: 187 SPDEEEANSKTYPVLVSQELDPETQLANDSQSDHELGKMHQALKQLDQRSRDILQQRWLS 246

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T   L+ + +++ V+ ERIRQIE +AI+ L
Sbjct: 247 EDKT--GLKALSEKYGVSMERIRQIEQQAIKTL 277


>gi|110805895|ref|YP_689415.1| flagellar biosynthesis sigma factor [Shigella flexneri 5 str. 8401]
 gi|195939226|ref|ZP_03084608.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           EC4024]
 gi|208816591|ref|ZP_03257711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208820391|ref|ZP_03260711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217328583|ref|ZP_03444664.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227885651|ref|ZP_04003456.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|256017880|ref|ZP_05431745.1| flagellar biosynthesis sigma factor [Shigella sp. D9]
 gi|256022420|ref|ZP_05436285.1| flagellar biosynthesis sigma factor [Escherichia sp. 4_1_40B]
 gi|261227583|ref|ZP_05941864.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261255813|ref|ZP_05948346.1| RNA polymerase, sigma 28 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|300818654|ref|ZP_07098862.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300822306|ref|ZP_07102447.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300899176|ref|ZP_07117454.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300904809|ref|ZP_07122636.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300917364|ref|ZP_07134033.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300925015|ref|ZP_07140938.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300951546|ref|ZP_07165380.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300956562|ref|ZP_07168843.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300982291|ref|ZP_07176001.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300993927|ref|ZP_07180602.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|301018228|ref|ZP_07182743.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|301050723|ref|ZP_07197582.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|301305263|ref|ZP_07211360.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|301327712|ref|ZP_07220918.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301645559|ref|ZP_07245489.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|306814254|ref|ZP_07448420.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|307138589|ref|ZP_07497945.1| flagellar biosynthesis sigma factor [Escherichia coli H736]
 gi|309795968|ref|ZP_07690381.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|110615443|gb|ABF04110.1| flagellar biosynthesis sigma factor FliA [Shigella flexneri 5 str.
           8401]
 gi|208730934|gb|EDZ79623.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208740514|gb|EDZ88196.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217317930|gb|EEC26357.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227837224|gb|EEJ47690.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|300297591|gb|EFJ53976.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|300307268|gb|EFJ61788.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300316625|gb|EFJ66409.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300357213|gb|EFJ73083.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300399815|gb|EFJ83353.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|300403277|gb|EFJ86815.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300406428|gb|EFJ89966.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|300415410|gb|EFJ98720.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300418834|gb|EFK02145.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300449221|gb|EFK12841.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300525189|gb|EFK46258.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300528826|gb|EFK49888.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300839469|gb|EFK67229.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|300845756|gb|EFK73516.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301076168|gb|EFK90974.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|305852413|gb|EFM52864.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|308120418|gb|EFO57680.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|312946514|gb|ADR27341.1| flagellar biosynthesis sigma factor [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|315136559|dbj|BAJ43718.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315257247|gb|EFU37215.1| flagellar biosynthesis sigma factor [Escherichia coli MS 85-1]
 gi|315290288|gb|EFU49666.1| flagellar biosynthesis sigma factor [Escherichia coli MS 153-1]
 gi|315296505|gb|EFU55802.1| flagellar biosynthesis sigma factor [Escherichia coli MS 16-3]
 gi|320641770|gb|EFX11158.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           G5101]
 gi|320658015|gb|EFX25777.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320658587|gb|EFX26281.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320668485|gb|EFX35312.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323152745|gb|EFZ39017.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EPECa14]
 gi|323186302|gb|EFZ71652.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1357]
 gi|324007273|gb|EGB76492.1| flagellar biosynthesis sigma factor [Escherichia coli MS 57-2]
 gi|324013514|gb|EGB82733.1| flagellar biosynthesis sigma factor [Escherichia coli MS 60-1]
 gi|324017957|gb|EGB87176.1| flagellar biosynthesis sigma factor [Escherichia coli MS 117-3]
          Length = 229

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 108/228 (47%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D +   +PL   + +NLR+     + +L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|215270827|emb|CAR48091.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270829|emb|CAR48092.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 260

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 48/302 (15%), Positives = 100/302 (33%), Gaps = 43/302 (14%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   + +S+ E P T   ++   D++      L ++I        +      
Sbjct: 1   DIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPT 60

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
               G    + +   +++E  D  E   D     +       ++                
Sbjct: 61  ATHIGSELTESQLEEEDEEDVDEDEESDDDSDDTEEDVGIDPEL---------------- 104

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                               +   +++   Y+ L+      +   +    S K  V  E 
Sbjct: 105 -------------------ALEKFNQLRSTYQNLQ------LAINEHGYESPKATVANEL 139

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+    G E 
Sbjct: 140 MLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNES 199

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +    + I +   ++K I  ET +++   + I   +  GE 
Sbjct: 200 SEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEA 258

Query: 440 EA 441
           +A
Sbjct: 259 KA 260


>gi|215270819|emb|CAR48087.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270821|emb|CAR48088.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270823|emb|CAR48089.1| RNA polymerase sigma factor [Vibrio harveyi]
 gi|215270825|emb|CAR48090.1| RNA polymerase sigma factor [Vibrio harveyi]
          Length = 260

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 48/302 (15%), Positives = 101/302 (33%), Gaps = 43/302 (14%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   + +S+ E P T   ++   D++      L ++I        +      
Sbjct: 1   DIAKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPT 60

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
               G    + +   +++E  D  E   D    ++       ++                
Sbjct: 61  ATHIGSELTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPEL---------------- 104

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                               +   +++   Y+ L+      +   +    S K  V  E 
Sbjct: 105 -------------------ALEKFNQLRSTYQNLQ------LAINEHGYESPKATVANEL 139

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           ++ +     L   + D LV +L     R+   E  +++ A  YG + +  F+    G E 
Sbjct: 140 MLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSAVEYGKMPKKSFIALFTGNES 199

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +    + I +   ++K I  ET +++   + I   +  GE 
Sbjct: 200 SEAWLDEILS-SDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEA 258

Query: 440 EA 441
           +A
Sbjct: 259 KA 260


>gi|167759902|ref|ZP_02432029.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
 gi|167662521|gb|EDS06651.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
          Length = 237

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 118/243 (48%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A+  +VE N  LV  + K++ NRG++  DL Q GNIGL+KA +KF
Sbjct: 3   HTIALIQKSHDGDEEARARLVEENAGLVWCIVKRFYNRGVEAEDLFQVGNIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      R+  +  R+PT
Sbjct: 63  DMSYDVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELAYKAYLCQERLQEQWGRDPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQ 606
             EIA+ L +  E +   L  + +  SL  PI  ++     L D + +K          +
Sbjct: 122 ITEIAESLNVEREELTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGE-----DK 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                   ++L  L   E +++ +R+           +VG++  +++ ++ ++E K ++ 
Sbjct: 177 ILNHMLLQQLLNYLDKDERQLIYLRYFANQTQ----TQVGRELGISQVQVSRMEKKILKN 232

Query: 667 LKH 669
           L+ 
Sbjct: 233 LRE 235


>gi|311898622|dbj|BAJ31030.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 276

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 103/238 (43%), Gaps = 18/238 (7%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               + +++     LV  VA +    GL       D +  G  GL+ A EKFD     KF
Sbjct: 40  DHRLRDQLILHYSPLVKYVAGR-VGVGLPANVEQADFVSSGVFGLIDAIEKFDIDRAIKF 98

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA+  ++ AI   +        IP  +R K   V R    +  +++R P   E+A ++
Sbjct: 99  ETYAISRIRGAIIDELRALDW---IPRSVRQKAKAVERAYATLEARLRRTPYDPEVAAEM 155

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGD----EDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            + ++ +  +         ++L+  +       D   L + + D  A +P++ A    LR
Sbjct: 156 GISLDDLHTIFSQLSLANVVALDELLHSAGEGGDRLTLMETLPDSGADNPVEIAEDRELR 215

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 + +L  RE+ V+ + +  G     TL E+G+   VT  R+ QI  K++ +L+
Sbjct: 216 RLLASAVNTLPEREKTVVTLYYYEG----LTLAEIGQVLGVTESRVSQIHTKSVLQLR 269


>gi|320647130|gb|EFX15963.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           493-89]
 gi|320652413|gb|EFX20711.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           H 2687]
          Length = 228

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 108/228 (47%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D +   +PL   + +NLR+     + +L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|150019061|ref|YP_001311315.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
 gi|149905526|gb|ABR36359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
          Length = 242

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 115/244 (47%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +    K+++++  + LV  +A +     N+ +++ DL+  G +GLM A  KFD   
Sbjct: 1   MHALKDVDGKEQIIQEYIPLVKYIASRVMFGKNKYMEYEDLVSYGMVGLMDALNKFDDTK 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G KFS+YA   +K A+   +        I     DK++K  +    +  ++ REPT +EI
Sbjct: 61  GMKFSSYASIRIKGAMIDELR---RNRPISKGAMDKLNKYNKAVDTLQLELLREPTNDEI 117

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANL 609
           AK L + +  V ++         +SLE  I  +D   +L   IEDKN+ SP         
Sbjct: 118 AKYLGISMSEVAEIENYINYISMVSLENVIFSDDEDVNLIGIIEDKNSPSPDAYLQDKEQ 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E  T+ +  L  ++  VL + +  G     TL+E+G    V+  R+ Q+ ++AI  L+ 
Sbjct: 178 LEILTKAIDLLKEKDRIVLNLYYYEG----LTLKEIGTVLSVSESRVCQLHSRAISSLRE 233

Query: 670 PSRS 673
             R 
Sbjct: 234 CMRK 237


>gi|161898905|gb|ABX80442.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 107/238 (44%), Gaps = 4/238 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           N R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ +AI+
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQRQAIK 234


>gi|86145220|ref|ZP_01063551.1| RpoS-like sigma factor [Vibrio sp. MED222]
 gi|85836797|gb|EAQ54917.1| RpoS-like sigma factor [Vibrio sp. MED222]
          Length = 298

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 137/266 (51%), Gaps = 9/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-- 466
             + +K I     +S  +  +   + R        A+  M+E+NLRLV+ +AK Y  R  
Sbjct: 29  YAHYLKDIVGIDLLSREDELYYAKLNR---AGDKHARDIMIESNLRLVVKIAKSYLKRKG 85

Query: 467 -GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                LDLI+EGNIGL+KA +K+D   GY+FSTYA+WW+++ I  ++ ++  T+R+P H+
Sbjct: 86  NNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHV 145

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +I+ +      +S K+++E +  E++    +  E V   L      I + T +G    
Sbjct: 146 CKEINSLASKKLDVSKKMRKEISISELSNISGVKAERV-DQLVALSGFIDVTTTVGISHA 204

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + +  E +    P       +      +++ +L P+ ++VL  RFG   N   TL EV
Sbjct: 205 PLVLEQCESEYIPDPQQDCEDQSFTHALEQIINTLPPKLQKVLIHRFGFFDNKVKTLSEV 264

Query: 646 GKQF--CVTRERIRQIEAKAIRKLKH 669
           G+     V+ ER+RQ++ +A+ +++ 
Sbjct: 265 GQMLDVNVSNERVRQMQKEAVERIQK 290



 Score = 41.0 bits (94), Expect = 0.68,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 39/100 (39%), Gaps = 2/100 (2%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +     +  +  +P   YL+++  I+LLSRE E+  AK   AG       + ES L    
Sbjct: 15  ETPIKESFSTATEPYAHYLKDIVGIDLLSREDELYYAKLNRAGDKHARDIMIESNLRLVV 74

Query: 167 LIIWRDELNDGTTL-LREIIDLEACIGPESKGGFFHGTEG 205
            I        G    L ++I+ E  IG       +    G
Sbjct: 75  KIAKSYLKRKGNNFTLLDLIE-EGNIGLIKAIDKYDPEPG 113


>gi|312621597|ref|YP_004023210.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202064|gb|ADQ45391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 246

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 125/253 (49%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 9   KFTKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   + +Q     +P  +R K  ++ R    +  +  + PT +E
Sbjct: 69  KGVKFETYAYTRIKGAIIDCVRNQDF---LPRSIRQKAKEIERAYIEIEKE-GKTPTNQE 124

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK++ + VE ++K+     +   ISLE+ +     S +G     ++ VS  +  I+   
Sbjct: 125 VAKRIGISVEELQKLQDRISSGMIISLESFLEQNYESKIGGL---EDFVSQPEHFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR+   + + +L   E  V+ + +      D +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 182 LRKVLRQQIDNLMENERMVIVLYY----YEDLSIKEIAKVLGVSESRVSQLHTRALLKLR 237

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 238 SA-----LQKYLE 245


>gi|163815157|ref|ZP_02206538.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
 gi|158449566|gb|EDP26561.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
          Length = 260

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 75/255 (29%), Positives = 126/255 (49%), Gaps = 12/255 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +          +  + E     A+ E +E NLRLV+SV +++ +      DL Q G IGL
Sbjct: 16  LPYLTEDEKNKLFDRMEQGDESARDEFIEGNLRLVLSVIQRFGSSNENPDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD  L  KFSTYA+  +     R + D +  IR+   +RD  +K +     +  
Sbjct: 76  IKALDNFDRSLNVKFSTYAVPMIIGECRRYLRDNN-AIRVSRSLRDIAYKAIYAKENLQK 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
              +EPT EEIA+++++P E +   L     P+SL  P+  E  DT ++ D I+D  +  
Sbjct: 135 TRDKEPTIEEIAEEISIPKEDIVMSLDAISAPLSLYEPVYQEGGDTLYIMDQIKDGKSRE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L      +LRE     +  L  RE+ ++R+RF  G     T  EV ++  +++ ++ ++
Sbjct: 195 ELW-VENLDLRE----AMGRLCDREKNIVRLRFFEG----KTQTEVAEEISISQAQVSRL 245

Query: 660 EAKAIRKLKHPSRSK 674
           E  AI+ L+     K
Sbjct: 246 EKNAIKSLRRYLEDK 260


>gi|291196292|emb|CBG22617.1| DNA-directed RNA polymerase subunit D [Pseudomonas cremoricolorata]
          Length = 237

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 91/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   + +   +  L ++             G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYERVTTDSGRLSDVF-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +    +      +     + E + ES    S+++ ++    P  A      + E  D 
Sbjct: 50  NIAAPNDDLPVPGAKPAAKADDEEEEESDDSDSEEEETESGPDPVLAAQRFGAVAEQRDA 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  ++          L +L
Sbjct: 110 TLKVL-----------------------------------KKHGRAHKDSIAAMLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL    G E D  W
Sbjct: 135 FMPIKLVPKQFEALVERVRGALERLRAQERAIMQLCVRDARMPRADFLRLFPGNETDQTW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                      W   +  +  +I+  + ++  +  ETG+++ E 
Sbjct: 195 SGDLSKRSTK-WAAALGEKDAAIVACQQKLIDLETETGLTVLEI 237


>gi|197120125|ref|YP_002140552.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           bemidjiensis Bem]
 gi|253702434|ref|YP_003023623.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M21]
 gi|197089485|gb|ACH40756.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           bemidjiensis Bem]
 gi|251777284|gb|ACT19865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M21]
          Length = 250

 Score =  117 bits (293), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 109/236 (46%), Gaps = 14/236 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V  +L LV  +  +  +     L   DL     IGL+ AAE+FD   G +F T+A 
Sbjct: 20  RDELVVTHLPLVKFIVDRIASSLPPHLDRDDLRSAAVIGLISAAERFDPARGVQFKTFAE 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +  Q     +   +RDK  K+ R   ++  ++ R P+ +E+A  + + ++
Sbjct: 80  QRIRGTIMDELRAQDW---LTRSLRDKFKKLEREFSQLEQRLGRNPSSDEVALAMGLELK 136

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLRETTTRVL 617
              ++L+       +SL+    DED +  G  D +EDK   SP    I     E     +
Sbjct: 137 DYFRLLEEIHLLSFVSLDDAWHDEDGAPFGLLDVLEDKGTESPQSQLIARQTVERLAEAI 196

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            +L  +E  V+ + +      +  L+E+G    +T  RI Q+ ++AI +L+   + 
Sbjct: 197 DALPEKERIVVTLYY----YEELNLKEIGAVLDLTESRISQLHSQAIIRLRGKMKR 248


>gi|71906382|ref|YP_283969.1| sigma-70 region 4 [Dechloromonas aromatica RCB]
 gi|71846003|gb|AAZ45499.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Dechloromonas
           aromatica RCB]
          Length = 248

 Score =  117 bits (293), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 109/238 (45%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                    ++++V+  + LV  +A     R    +QF DL+Q G IGL+ A ++F    
Sbjct: 1   MYTAAGQPDREQLVQRFVPLVKRIAYHLMARLPPSVQFDDLVQNGMIGLLDAIDRFQEGF 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   + +      +P ++R ++ ++     ++ ++  R P+ +E+
Sbjct: 61  GAQFETYATQRIRGAMLDGLRENDW---LPRNLRRELRRIETAINQLEHEHGRVPSEKEL 117

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ L M +   +K L+     + +  +   G+ D   L     D NA  P       +++
Sbjct: 118 AEALGMSLADYQKTLQDARGHQLVYFDDLAGEGDEGFLERHFTD-NAADPAAILEDKSVK 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            T    +  L  RE+ ++     +    D  L E+G+   VT  R+ Q+  +AI +L+
Sbjct: 177 ATLITAIGELPEREKMMM----ALYYEQDLNLREIGEVMGVTESRVCQLHTQAIARLR 230


>gi|294811026|ref|ZP_06769669.1| Putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|326439632|ref|ZP_08214366.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294323625|gb|EFG05268.1| Putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
          Length = 277

 Score =  117 bits (293), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 105/229 (45%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+V A L +   +A+++ +RG    DL Q   +GL+KA +++D   G  F+++A+  +
Sbjct: 51  RQELVNAWLPMSERLARRFRDRGESLEDLRQVAALGLVKAVDRYDPARGCAFASFAVPTI 110

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGV 563
              + R   D   T+ +P  ++D+ ++V    + ++     R PT  EIA++  +     
Sbjct: 111 TGEVKRHFRDHMWTLHVPRRVQDQRNRVRAAQQELAQTVTGRAPTEAEIAERAGLTPAQT 170

Query: 564 RKVLKI--TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           R+ L    +   +SL+     + D   + D +   +    +        RE     L  L
Sbjct: 171 REGLAAIGSYRTLSLDAEAPGDGDGCTMADALGGPDPALDVVID-----REAVRPRLREL 225

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE R+L MRF  GM      E+      +++  + ++ + +  +L+ 
Sbjct: 226 PERERRILYMRFFRGMTQSRIAED----LGISQMHVSRLISHSCDRLRQ 270


>gi|302555286|ref|ZP_07307628.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472904|gb|EFL35997.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 264

 Score =  117 bits (293), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 117/247 (47%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E +A   + E+VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 22  FRRLATLPAGPERDAL--RDEIVEAWLPMADRLAGRFRSRGESFEDLRQVAALGLVKAVD 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           ++D  LG  F +YA+  V   I R   D   T+ +P  ++D  ++V   ++ +S  I  R
Sbjct: 80  RYDPELGNAFESYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLRNRVRVASQDLSQTISGR 139

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            PT  EIA+   M  + V+  L+   +   +SL+  +   ED   L D +   +      
Sbjct: 140 RPTIAEIAEHAKMSEDDVKAGLEALESFTALSLDAELPGSEDGYSLSDALGSVDPALDTV 199

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE+    LA+L  RE  +L MRF   M      EE      +++  + ++ ++
Sbjct: 200 VD-----RESVKARLAALPERERAILYMRFFGDMTQSRIAEE----LGISQMHVSRLISR 250

Query: 663 AIRKLKH 669
           +  +++ 
Sbjct: 251 SCGRVRE 257


>gi|311071144|ref|YP_003976067.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
 gi|310871661|gb|ADP35136.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
          Length = 262

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 119/258 (46%), Gaps = 6/258 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +   S  T ++  E   +++       +   A++ +V+    LV  +AKKY+       D
Sbjct: 1   MAQPSKTTKLTKDEVDRLIN--EYQTNQDDSAQETLVQVYTNLVEVLAKKYSKGKSFHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G IGL+ A +++D  +G  F  +A+  +   I R + D++ ++ +P  +++   ++
Sbjct: 59  LRQVGMIGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                 ++ + +R P  EEIA+ L +  E V + +++ K   +L      E  +      
Sbjct: 119 KMAVDTLTTETQRSPKVEEIAEYLDVSEEEVLETMEMGKSYQALSVDHSIEADADGSTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S  D   + N +     VL  L+ RE++++ + +      + + +E G    ++
Sbjct: 179 ILDIVGSQEDGYERVNQQMMLKSVLHVLSEREKQIIDLTY----IQNKSQKETGDILGIS 234

Query: 653 RERIRQIEAKAIRKLKHP 670
           +  + +++ KA++KL+  
Sbjct: 235 QMHVSRLQRKAVKKLREA 252


>gi|303240258|ref|ZP_07326777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302592168|gb|EFL61897.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 108/251 (43%), Gaps = 11/251 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGN 478
           +S S  +      +  + +    K++++     ++  VA +   Y    +++ DLI  G 
Sbjct: 1   MSTSTIKQQEMWRQYSDTKDPAIKEKLIIEYSHIIKYVAGRLSIYFGSNVEYDDLIGYGV 60

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            GL+ A  KFD   G KF TYA   ++ AI  SI +      +P  +R K  ++ R    
Sbjct: 61  FGLIDAINKFDINKGVKFETYASLRIRGAIIDSIRELDW---VPRSLRQKNKELERVYTE 117

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + N++    T +E+A+KL + V+   K+L        +      E     G  I      
Sbjct: 118 VENELGHSATDQEVAQKLGVSVDEFYKLLNEVNLSSLISLEEFLEQNYEAGVNIAGGCKE 177

Query: 599 SPLDSAIQ-ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              +  ++   LRE     +  L  +E+ V+   +      D TL+E+ +   V+  RI 
Sbjct: 178 DRPEGYMEITELREILVDAIGKLPEKEKTVVSFYYF----EDLTLKEISEIMKVSESRIS 233

Query: 658 QIEAKAIRKLK 668
           Q+  KAI +L+
Sbjct: 234 QLHTKAILRLR 244


>gi|49474699|ref|YP_032741.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49240203|emb|CAF26671.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 303

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 116/246 (47%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+    
Sbjct: 46  LRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDRE 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI-----HKVVRTARRMSNKIKREPT 548
            +FSTYA WW++ +I   I      +R       K       ++     +  N + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLVQDDNALTKQDI 165

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNA-VSPLDSA 604
              IA++L + V  V  +        +  +    E++ +     D + D +     L   
Sbjct: 166 FRTIAERLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPIAKMDALVDDSPLPDALIEQ 225

Query: 605 IQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  + R  +     L SL  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 VIDSQRRTQWLHDALQSLNERELEIIR--FRRLNEEGATLEVLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|302036735|ref|YP_003797057.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
 gi|300604799|emb|CBK41131.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
          Length = 340

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 137/311 (44%), Gaps = 11/311 (3%)

Query: 375 QGRELDPHWVSYAKDFPEGEWKNF-VACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
              E        A   P  E +   ++  +  +  ++  +  I     +S  E   +   
Sbjct: 30  PTDEEVTEEHEAADHQPSKEPQEAPLSTSLVPVTTLQQYLTEIRRYPYLSKEEELRLFE- 88

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                  +  A  +++ ANLR+ +S+A +Y + G   +DLIQEGN+GL++A +KFD    
Sbjct: 89  -EYQLRGSRDAAMKLILANLRVSVSIASEYLHTGADHMDLIQEGNVGLLQAIKKFDPTKN 147

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEE 551
            +F  YA WW +  I R + +    I++      R   + + +   ++  +     +   
Sbjct: 148 VRFYAYAAWWARAYILRYLLNTYRLIKVGTTQDQRKLFYNLKKEKAKLEREGFAPDSKLL 207

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD---SAIQAN 608
             +      + +    ++    +SL+ PIG E+   L D +      +      + ++A 
Sbjct: 208 ADRLNVRERDVIEMDQRLGSWELSLDQPIGQENDGTLMDILPAHEQPADERLADTQLKAL 267

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R        +L  REE +LR    I   T  TLE++G ++ +T+ER RQ+EA+ I++L+
Sbjct: 268 FRRKLAEFTKTLDEREEDILR--NRILSETPLTLEDMGAKYGITKERTRQLEARIIKRLR 325

Query: 669 HPSRSKKLRSF 679
              + K ++ F
Sbjct: 326 DYIK-KDVKDF 335


>gi|283832678|ref|ZP_06352419.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
 gi|291072353|gb|EFE10462.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
          Length = 229

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 111/228 (48%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++LA+PV+
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVAERLAIPVQ 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + E+    +PL   ++ NLR+     + +L
Sbjct: 120 EYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLEGNLRQRVMDAIEAL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|302147259|emb|CBL51751.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|329111880|emb|CBL59322.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 262

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 58/300 (19%), Positives = 105/300 (35%), Gaps = 44/300 (14%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEI IAKRIE G   + +S+ E       L+   D+       L +II          
Sbjct: 1   REGEIDIAKRIEDGINQVQSSVAEYLKAITYLLEQYDKYEAEQLRLSDII---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E                          E  A  +    S++       E++E
Sbjct: 51  -SGFIDPNE-------------------------TEDMAPTATHIGSELGEDDLADEDEE 84

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
              DEDED  +                   E+   Y          ++ QK+ ++    +
Sbjct: 85  DEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQ 138

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERH 374
               +L  +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+   
Sbjct: 139 AAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAF 198

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E +  W  Y K   +      V  + + I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 TNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRRM 257


>gi|331657967|ref|ZP_08358929.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
 gi|331056215|gb|EGI28224.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
          Length = 239

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 109/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIEMLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|84385871|ref|ZP_00988901.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
 gi|84379187|gb|EAP96040.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
          Length = 262

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 75/255 (29%), Positives = 133/255 (52%), Gaps = 6/255 (2%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQE 476
            GI +      V   +        A+  M+E+NLRLV+ +AK Y  R       LDLI+E
Sbjct: 1   MGIDLLSREDEVYYAKLNRAGDKQARDIMIESNLRLVVKIAKSYLKRKGNNFTLLDLIEE 60

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           GNIGL+KA +K+D   GY+FSTYA+WW+++ I  ++ ++  T+R+P H+  +I+ +    
Sbjct: 61  GNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHVCKEINSLASKK 120

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             +S K+ +E +  E++    +  + V   L      I + T +G      + D  E + 
Sbjct: 121 LDVSKKMSKEISISELSDSSGVKAKRV-DQLVALSGFIDVTTTVGTNHAPMVLDQCESEY 179

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF--CVTRE 654
              P       +  +   +++++L P+ ++VL  RFG   N   TL EVG+     V+ E
Sbjct: 180 IPDPQRDCEDQSFTQALEQIISTLPPKLQKVLIHRFGFFDNKVKTLSEVGQMLDVNVSSE 239

Query: 655 RIRQIEAKAIRKLKH 669
           R+RQ++ +A+ +++ 
Sbjct: 240 RVRQMQKEAVERIQK 254


>gi|332531601|ref|ZP_08407498.1| RNA polymerase sigma-28 subunit FliA/WhiG [Hylemonella gracilis
           ATCC 19624]
 gi|332038964|gb|EGI75393.1| RNA polymerase sigma-28 subunit FliA/WhiG [Hylemonella gracilis
           ATCC 19624]
          Length = 245

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 53/243 (21%), Positives = 103/243 (42%), Gaps = 12/243 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  + +  ++   + LV  +A     +    +Q  DLIQ G IGL +A  +++   G
Sbjct: 10  YTAQGQLDRDALIRQYVPLVRRLAHHMMAKLPPSIQVDDLIQVGLIGLSEALTRYEATQG 69

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F T+A   ++ A+   + +           R    ++     R+ +++ R P+  EIA
Sbjct: 70  VQFETFATQRIRGAMIDELRENDWM---SRGSRKSQKEIESALTRLEHQLGRSPSESEIA 126

Query: 554 KKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L M +   + +L   K    + LE   G +D     D         P+       LR 
Sbjct: 127 EELGMELAEYQALLYKVKGTQLVYLEDMSGGDDEEGFLDRHMVDGESDPMALLRNQRLRA 186

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +    + +L  RE+ V+ M +      D  L+E+     VT  R+ Q+ +++I +L+   
Sbjct: 187 SLVDAIKALPEREQYVMSMYY----EQDMNLKEIAAVLGVTESRVCQLHSQSIARLRAKM 242

Query: 672 RSK 674
           RS 
Sbjct: 243 RSH 245


>gi|302531661|ref|ZP_07284003.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302440556|gb|EFL12372.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 258

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 118/244 (48%), Gaps = 16/244 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +  +      I +  +V  +L L  ++A+K+ NR     DL+Q   +GL+ A +
Sbjct: 17  FHELTQLPDRSPRREEI-RDILVREHLELARNLARKFRNRDEAMDDLVQIATVGLIHAVD 75

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   +     D S ++R+P  +++    +      ++ ++ R 
Sbjct: 76  RYDPTQGTDFLAFAVPTISGELRHHFRDNSWSVRVPRRLKELNATISAAREELTVRLSRA 135

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           P P EIA+ L +P+E V + L+  +     SL+  + +   +  G         +P  + 
Sbjct: 136 PKPSEIARHLDVPIEDVYEGLRAGQGRYGASLDNLLENSAHTRFG---------APDANL 186

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            QA LRE    +L SL  RE +++ +RFG G     +  ++ ++  V++ ++ ++ A  +
Sbjct: 187 GQAELREALRPMLDSLPERERKIVALRFGSG----MSQSDIARRVGVSQMQVSRLLAATL 242

Query: 665 RKLK 668
           +KL+
Sbjct: 243 KKLR 246


>gi|297196321|ref|ZP_06913719.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722899|gb|EDY66807.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 307

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 125/265 (47%), Gaps = 17/265 (6%)

Query: 413 IKSISVETGISISEFRHI-------VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I     +S  + R +       ++++ +G  E S  +  +VE NL LV   A ++ N
Sbjct: 37  LPEIPDPRAVSPMDARALSTTLFARLAVLEEGTPEYSYVRNTLVELNLSLVKFAALRFAN 96

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           R     D+IQ G IGL+KA  +FD     +F+++A+  V   I R   D S ++R+P  +
Sbjct: 97  RAEPMEDIIQVGTIGLIKAINRFDLEREVEFASFALPTVIGEIKRFFRDSSWSVRVPRRL 156

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDE 583
           ++    + +    +  ++ R PT  E+A  L +  E V +  + +      SL+  + DE
Sbjct: 157 QELRIDLAKALDVLEQRLGRRPTTAELAAYLGVSEEEVVEGERASNGYTAQSLDATVNDE 216

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D S+      ++       +    +  E    ++A+L  R+  +L +RF      + T  
Sbjct: 217 DASN----AVNRRLGIDDPAFDIIDSLEALKPLIATLDERDRLILSLRFR----EELTQS 268

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G++  +++  + ++ A+ + KL+
Sbjct: 269 EIGERLGISQMHVSRLLARILEKLR 293


>gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase sigma factor [Herbaspirillum
           seropedicae SmR1]
 gi|300074130|gb|ADJ63529.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           protein [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 106/245 (43%), Gaps = 13/245 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +    K +++E +  LV  +A +   +    ++  DLIQ G +GL+ A  +++   
Sbjct: 1   MYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA+  ++ A+   +        +P  +R    KV    + +  ++ R+P   E+
Sbjct: 61  GAQFETYAVQRIRGAMLDELRSSDW---LPRSIRQNARKVEEAMQTLLQQLGRQPKEAEL 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANL 609
           A+ + + +E  + +L        +      +D     H  D  +  ++  PL + I    
Sbjct: 118 AQHMQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGF 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE     + +L  RE+    +   +    +  L+E+G    V+  R+ Q+ ++AI +++ 
Sbjct: 178 REAVVDSIKALPEREQ----ILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRS 233

Query: 670 PSRSK 674
             R  
Sbjct: 234 YLREH 238


>gi|82543610|ref|YP_407557.1| flagellar biosynthesis sigma factor [Shigella boydii Sb227]
 gi|81245021|gb|ABB65729.1| alternative sigma factor 28 [Shigella boydii Sb227]
 gi|320176074|gb|EFW51142.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae CDC 74-1112]
 gi|320184751|gb|EFW59543.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           CDC 796-83]
          Length = 239

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 109/235 (46%), Gaps = 11/235 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L
Sbjct: 182 VMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|213958508|gb|ACJ54675.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 3-3.5cm2R]
          Length = 252

 Score =  117 bits (292), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 42/298 (14%), Positives = 96/298 (32%), Gaps = 47/298 (15%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G   +M ++   P T   ++     +      L +++            G+    +G +
Sbjct: 1   EGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIA 49

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
               E       +    + + D + A   + D+      P             D+ +   
Sbjct: 50  PPAAEVPPPVDPKAVKADDDTDDDDAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITR 109

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                  +     +  L  +AE++                                    
Sbjct: 110 KALKKHGRGNKLAIAELVLLAELF----------------------------------MP 135

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSY 386
           + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   
Sbjct: 136 IKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD- 194

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           A    + ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  A
Sbjct: 195 ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRA 252


>gi|291547959|emb|CBL21067.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus sp.
           SR1/5]
          Length = 260

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 125/249 (50%), Gaps = 12/249 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++ +       A+  + E N  L+ SVAK++  RG++  DL Q G+IGL+KA +KF
Sbjct: 3   RTLVLIGRAHQGDKAARDLLFEENTGLIYSVAKRFLGRGVEMEDLFQIGSIGLLKAVDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++   +++  +++ +    ++ +++REPT
Sbjct: 63  DMSYDVKFSTYAVPMIIGEIKRYLRD-DGILKVSRSLKENHYRIYQVREALTRRLEREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
             E+A+++ + +E +   ++   E  SL   I   + +   L D + +K      +   +
Sbjct: 122 TGEMAEEMGISIEELVMTMESGAEVESLHKTIYQGEGTEISLMDKLPEKE-----NRQEK 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     +L +L  +E R++ MR+      + T  E+  +  V++ ++ ++E + +R 
Sbjct: 177 VLDRIFLEEILGTLEAKERRLIYMRYF----QNMTQMEIAHELGVSQVQVSRMEKRILRS 232

Query: 667 LKHPSRSKK 675
           L+  +   K
Sbjct: 233 LQESAEKNK 241


>gi|291196374|emb|CBG22659.1| DNA-directed RNA polymerase subunit D [Pseudomonas plecoglossicida]
          Length = 238

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 93/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   D +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAP---- 54

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                              +E       AA   ++   + +    + + +E     D   
Sbjct: 55  ------------------TEEVPVPGTKAAAAKEESDDEEEESESSDDEEETESGPDPVV 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQL    +  L                     K  ++  +     + L  L
Sbjct: 97  AAQRFGAVSDQL-AITLKVLK--------------------KHGRTHAESIGAMQALADL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D+LVE++ D   R+   E  +++L      + R  FL      E D  W
Sbjct: 136 FMPIKLVPKQFDVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRLFPSNETDQTW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                      W   +  +  +I+  + ++  +  ETG++++E 
Sbjct: 196 SGDLAKRSTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEI 238


>gi|222530110|ref|YP_002573992.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456957|gb|ACM61219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 246

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 124/253 (49%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 9   KFTKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   +  Q     +P  +R K  ++ R    +  +  + PT +E
Sbjct: 69  KGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQKAKEIERVYIEIEKE-GKTPTNQE 124

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK++ + VE ++K+     +   ISLE+ +     S +G     ++ VS  +  I+   
Sbjct: 125 VAKRIGISVEELQKLQDRISSGMIISLESFLEQNYESKIGGL---EDFVSQPEHFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE   + + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 182 LREVLRQQIDNLLENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLR 237

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 238 SA-----LQKYLE 245


>gi|121596110|ref|YP_988006.1| FliA/WhiG family RNA polymerase sigma factor [Acidovorax sp. JS42]
 gi|222112265|ref|YP_002554529.1| RNA polymerase, sigma 28 subunit, flia/whig [Acidovorax ebreus
           TPSY]
 gi|120608190|gb|ABM43930.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidovorax sp.
           JS42]
 gi|221731709|gb|ACM34529.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax ebreus
           TPSY]
          Length = 237

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 96/244 (39%), Gaps = 12/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  +   ++ LV  +A     +    ++  DLIQ G IGL  A  +++   
Sbjct: 1   MYTAKGQLDRDALFHQHVPLVRRIAHHMIAKLPPNVELDDLIQVGMIGLNDALSRYEVAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R     +     R+  ++ R P   EI
Sbjct: 61  GVQFETFASQRIRGAMLDELREGDWM---SRSSRKSQKDIEHALHRVEQRLGRSPIESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L M +E  + +L      + + LE    D++     D         P+       LR
Sbjct: 118 AAELGMSLEDYQALLSKVRGTQLVYLEDFHHDDEDEGFLDRHVADEGADPMAVLRDQRLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +    + +L  RE+       G+    D  L+E+     VT  R+ Q+ ++AI +L+  
Sbjct: 178 ASLVEAIKALPEREQ----YIMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTK 233

Query: 671 SRSK 674
            R  
Sbjct: 234 MRGH 237


>gi|152997431|ref|YP_001342266.1| RNA polymerase sigma-28 subunit FliA/WhiG [Marinomonas sp. MWYL1]
 gi|150838355|gb|ABR72331.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas sp. MWYL1]
          Length = 245

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 101/235 (42%), Gaps = 10/235 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +A+++   +VE    LV  +A     R    +   DLIQ G +GL++A ++F+   G
Sbjct: 10  YSKKATLSIDAIVEQYGYLVKKIAYHLLARLPDSVDVDDLIQAGMMGLIEAYKRFESTKG 69

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ +I   +         P  +R     V    + +  K+ RE +  E+A
Sbjct: 70  ASFETYAGIRIRGSIMDEVRKTDW---APRSVRRNGRAVATAIKELEAKLGREVSDMEVA 126

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + + ++   +++  +            +  ++  D IE +   +P     +   +   
Sbjct: 127 SHMNISMDEYHEMIHSSMSTQLFSYEEMLDSDTNNLDSIESEVENAPYSLVEEGGFQNQL 186

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +  L  RE+ VL + +    N +  L+E+G    V+  R+ QI ++A  +L+
Sbjct: 187 AKEIDDLPEREKLVLSLYY----NEELNLKEIGAVLGVSESRVSQIHSQAAMRLR 237


>gi|300782223|ref|YP_003762514.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299791737|gb|ADJ42112.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 259

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 113/239 (47%), Gaps = 15/239 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              +  +V  +L L  ++A+K+ NR     DL+Q   +GL+ A ++FD   G  F  +A+
Sbjct: 32  ERIRDTLVRTHLELARNLARKFRNRDEAMEDLVQIATVGLIHAVDRFDPAQGTDFLAFAV 91

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   +     D S ++R+P  +++    +      ++ ++ R P P EIA +L +P+E
Sbjct: 92  PTISGELRHHFRDNSWSVRVPRRLKELNANISAAREELTVQLSRAPKPSEIAARLGVPIE 151

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V + L+  +     SL+         HL +        +P     QA LRE    +L S
Sbjct: 152 DVYEGLRAGQGRYGASLD---------HLLENAAHTRFGAPDAELGQAELREALRPMLES 202

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  RE +++ +RFG G     +  ++ ++  V++ ++ ++ A  ++KL+      +L  
Sbjct: 203 LPERERKIVALRFGSG----MSQSDIARRVGVSQMQVSRLLAATLKKLRSGLDESELAD 257


>gi|134300227|ref|YP_001113723.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134052927|gb|ABO50898.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfotomaculum
           reducens MI-1]
          Length = 251

 Score =  117 bits (292), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 59/246 (23%), Positives = 117/246 (47%), Gaps = 14/246 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWC 491
           +        A+++++  +L LV  +A +   +   F    DL   G IGLM+A +K+D  
Sbjct: 9   KYITLRDPEARQKIILLHLPLVKHLAGRVAVKLPSFILREDLESYGVIGLMEALDKYDPA 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           +G+ F +YA   ++ A+   +  Q+    +P     K   +  T  R+  +     T E 
Sbjct: 69  MGHSFDSYAYHRIRGAMLDEVRRQNW---LPRTAWQKNQLLKNTRERLEREQGEVITNEV 125

Query: 552 IAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA 607
           +AK++ +PVE VR+++         SL+  +   D S +   + +ED N+  PL    + 
Sbjct: 126 LAKEMGIPVEEVRQLIFNANKMYIQSLDEEVAGHDGSQMSKLELLEDTNSPDPLSIVEEK 185

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +      + +L+ RE+ +L + +  G     TL+E+G+   V+  R+ Q+ ++ +++L
Sbjct: 186 ESKRLLAEAIETLSEREKLILALYYSEG----LTLKEIGQVLEVSESRVCQLHSQVMKRL 241

Query: 668 KHPSRS 673
           K    S
Sbjct: 242 KKTLES 247


>gi|157371179|ref|YP_001479168.1| flagellar biosynthesis sigma factor [Serratia proteamaculans 568]
 gi|157322943|gb|ABV42040.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Serratia
           proteamaculans 568]
          Length = 240

 Score =  117 bits (292), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 109/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  +    + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWLRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +  R++  ++ R  +  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRHAREVAQVMRQLEQQLGRPASEVEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + ++  R++L  T            E+     +  +E     +PL   ++ NLR+ 
Sbjct: 122 QTLNLSLDEYRQILLDTNNSQLFSYDEWREEHGESAEPLLEGHEEANPLHHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIEALPEREKMVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|23098085|ref|NP_691551.1| RNA polymerase sigma factor SigB [Oceanobacillus iheyensis HTE831]
 gi|22776310|dbj|BAC12586.1| RNA polymerase general stress sigma factor (sigma B)
           [Oceanobacillus iheyensis HTE831]
          Length = 263

 Score =  116 bits (291), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 115/250 (46%), Gaps = 5/250 (2%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +  ++K      I ++++V     LV S+A+KY+       DL+Q G IGL+ A
Sbjct: 13  DEVYQWIEYLQKDPTNEEI-QEKIVLKYQDLVGSIARKYSKNSAIHEDLVQVGMIGLLAA 71

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++D   G  F ++A+  +   I R I D++ ++ +P  +++   K+ +    ++   +
Sbjct: 72  VRRYDPTYGKSFESFAIPTIIGEIKRFIRDKTWSVHVPRRIKELGPKIRKGVDELTTDNQ 131

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           + PT  EIAK +    E V + +++ +   +L      E  S            +  D  
Sbjct: 132 KSPTVAEIAKYIGTSEEEVLETMEMGQSYKALSVDRKIEADSDGSTVAILDLVGNSEDGY 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                R    ++L  L+ RE+++L   +        + +E G+   +++  + +++ +++
Sbjct: 192 DNVEQRMMLEKILPILSEREQQILECTYFKN----MSQKETGELLGISQMHVSRLQRRSL 247

Query: 665 RKLKHPSRSK 674
           RKL+   +S+
Sbjct: 248 RKLREAIQSE 257


>gi|331698492|ref|YP_004334731.1| RNA polymerase sigma 28 subunit FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953181|gb|AEA26878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
          Length = 429

 Score =  116 bits (291), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 108/239 (45%), Gaps = 13/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
            + +G       +  +V     LV +VA +        ++  DL+Q G  GL+ A  +FD
Sbjct: 192 WLDRGGPRDRTVRDLLVAHYGPLVRAVAARMAVGLPASVEVSDLVQAGVFGLLDAIARFD 251

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +F TYA   ++ A+   +  Q     +P  +R +I ++ RT  ++  ++ R P  
Sbjct: 252 PTRGIRFETYAAQRIRGAMLDELRAQDW---VPRTVRSRIREIERTREQLERRLGRAPDR 308

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA +L +P+  + +  +  +  +S+E     E  S + + + D++A  P +       
Sbjct: 309 REIAAELGLPLRELVRAGQR-RRLVSVEALA--ESASSVAESVVDESAPDPAEVFALQET 365

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +  L  R+  V+++ +        TL E+G+   VT  R+ Q+ A+ + +L+
Sbjct: 366 HRELAAAVRLLDERDRLVVQLYYVEN----RTLAEIGRLLGVTESRVCQLHARMVVRLR 420


>gi|317123623|ref|YP_004097735.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Intrasporangium calvum DSM 43043]
 gi|315587711|gb|ADU47008.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Intrasporangium calvum DSM 43043]
          Length = 282

 Score =  116 bits (291), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 109/244 (44%), Gaps = 13/244 (5%)

Query: 429 HIVSMVRKGECEASIAK--KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            ++  + +    A   +   E+V  +L L   VA +Y  R +   DL+Q   + L+ A +
Sbjct: 32  ELLLELSRTTNCAERERLTDEIVRLHLDLCDGVAARYAGRSIPTEDLVQVARLALLVAIK 91

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G  F  YA+  +   + R   D    +R P  +++    +         +    
Sbjct: 92  RYQPGPGSSFIGYALPTISGELKRHFRDHGWMVRPPRRLQELGPVLRLAREHWEQEHGTS 151

Query: 547 PTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT +++A+++ +  E V + L  + +  P+SL+   GD+++  L + + +          
Sbjct: 152 PTTQDLAEEVGVDPEQVSECLSAEHSYHPLSLDLTFGDDESRSLAESLAEPQD-----EL 206

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             A  R +    L+SL+ ++  +L+MRF  G     T +E+G    V++ ++ ++    +
Sbjct: 207 ESAADRVSLGTALSSLSQKDRELLQMRFVDG----MTQKEIGLALGVSQMQVSRLVRAVL 262

Query: 665 RKLK 668
            +L+
Sbjct: 263 DRLR 266


>gi|118464372|ref|YP_883398.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118165659|gb|ABK66556.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 241

 Score =  116 bits (291), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 115/246 (46%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + +       E    + ++VE  L L   +A+++  RG    DL+Q   +GL+ A  
Sbjct: 2   FRELAT-AEPDSMEFQRQRDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVV 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   + R   D S ++++P  +++   ++      +S ++ R 
Sbjct: 61  RFDVDAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGTATADLSQRLGRA 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLD 602
            T  E+A +L M  E V + L    +   +S+++  G E+     + D + D +      
Sbjct: 121 HTATELAAELEMDREEVVEGLVAGSSYNTLSIDSGGGSEEEEVRAIADTLGDVDT----- 175

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              +   +E+   +L +L  RE  VL +RF        T  ++ ++  +++  + ++ AK
Sbjct: 176 GLDRIEDQESLRPLLEALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAK 231

Query: 663 AIRKLK 668
           ++ +L+
Sbjct: 232 SLTRLR 237


>gi|290475011|ref|YP_003467895.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
 gi|289174328|emb|CBJ81122.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
          Length = 240

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E+FD   G
Sbjct: 5   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +T R++  ++ R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVTQTIRKLEQELGRPASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           K+L + +   R++L  T            E         IED++  +PL   ++ +LR+ 
Sbjct: 122 KELKINLIEYRQILLDTNNSQLFSYDEWHEIHGESCEPVIEDEHETNPLQQLLEGDLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              V+ SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDVIESLPEREKMVLTLYY----QEELNLKEIGAVLNVGESRVSQLHSQAIKRLR 233


>gi|259908158|ref|YP_002648514.1| flagellar biosynthesis sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963780|emb|CAX55281.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           pyrifoliae Ep1/96]
 gi|283478078|emb|CAY73994.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
 gi|310767931|gb|ADP12881.1| flagellar biosynthesis sigma factor [Erwinia sp. Ejp617]
          Length = 240

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                 + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTANGVMDKHSLWQRYIPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     ++   + R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHQVEQALGRTATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
            +L +P+E  R++L  T            E+     + + E     +PL   ++ +LR+ 
Sbjct: 122 AQLDVPLEEYRQILLDTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRDR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIDGLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|319781051|ref|YP_004140527.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317166939|gb|ADV10477.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 287

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 121/257 (47%), Gaps = 14/257 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +  +    E     A   +  A++RLVIS+A K+ + GL   DL+QEG++GL
Sbjct: 20  LERDEEHRLALL--WKEDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLVQEGHVGL 77

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           ++AA +F+     +FSTYA WW++ ++   I      +R       K     + R   R+
Sbjct: 78  LEAAARFEPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 540 SN---KIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE-DTSHLGDFIED 594
           +N    +       E+++ L +    V  +  +++    SL  P+ D+  ++   +F+  
Sbjct: 138 ANGAEPLSNATLYREVSEALGVSEADVAMMDSRLSAPDSSLNMPVADDAGSTERMEFLVS 197

Query: 595 KNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            + +       + ++          L +L  RE R++        +   TLE +G+   +
Sbjct: 198 DDPLPDEIVGDKIDVARRSLWLREALRALNARELRIIEE--RRLNDEGATLEALGETLGI 255

Query: 652 TRERIRQIEAKAIRKLK 668
           ++ER+RQIEA+A+ KLK
Sbjct: 256 SKERVRQIEARAMEKLK 272


>gi|300935898|ref|ZP_07150854.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|300458917|gb|EFK22410.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|307626601|gb|ADN70905.1| flagellar biosynthesis sigma factor [Escherichia coli UM146]
 gi|315286624|gb|EFU46057.1| flagellar biosynthesis sigma factor [Escherichia coli MS 110-3]
          Length = 229

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 108/228 (47%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D +   +PL   + +NLR+     + +L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMETIETL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|56962590|ref|YP_174316.1| RNA polymerase sigma factor SigB [Bacillus clausii KSM-K16]
 gi|56908828|dbj|BAD63355.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Bacillus clausii KSM-K16]
          Length = 261

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 116/240 (48%), Gaps = 4/240 (1%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +  +  A+ ++V     LV S+++K++       DL Q G +GL+ A ++++   G 
Sbjct: 21  QYQKTGSEEAQIKLVNHFEALVRSLSRKFSKGREYDEDLYQVGMVGLLAAMKRYNEDYGR 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F ++A+  V   I R I D++ ++ +P  +++   K+ + A  ++ +++R P   EIA+
Sbjct: 81  SFESFAVPTVVGEIKRFIRDKTWSVHVPRRIKELGPKIKKAADTLTIELQRSPYVHEIAE 140

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            L +  E V + ++++K   +L      E     G+        +      QA+ +    
Sbjct: 141 YLQVTEEEVLETMEMSKSYQALSVNRPLEADQEGGEVTLLDLVGNEEAGYEQADQKLLLE 200

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +    L  RE+ +L+  +        + +E G++  +++  + +++ +A++KL+   R +
Sbjct: 201 KAFEVLNEREKDILQCTYYEN----LSQKETGEKLGISQMHVSRLQRRALQKLRDSIRVE 256


>gi|327438482|dbj|BAK14847.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 261

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 106/239 (44%), Gaps = 4/239 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +  +          ++  +V    +LV S+A+KY++    + D++Q G +GL+ A  +FD
Sbjct: 16  LNWIAEYQASGCEESQTNLVLHYQQLVESIARKYSHGKSYYDDIVQVGMLGLLGAIRRFD 75

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++  + +P  +++   ++      ++  ++R P+ 
Sbjct: 76  PSFGRSFEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKELGPRIKAAVEALTTSLQRSPSI 135

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            EIA  L +  E V + +++ +   +L      E  S                     N 
Sbjct: 136 TEIATYLEVQDEDVLEAMEMGRSYQALSMDHSIESDSDGSTVTLFDVVGREDTGYEVTNR 195

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      +  L  RE +++++ +        + +E G++  +++  + +I+ KAI+KL+
Sbjct: 196 RMIVADAMNVLNERERQIIQLTYL----EQLSQKEAGERLGISQMHVSRIQRKAIKKLQ 250


>gi|226364233|ref|YP_002782015.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226242722|dbj|BAH53070.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 285

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/225 (22%), Positives = 100/225 (44%), Gaps = 10/225 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++E  L L   +A+++  RG    DLIQ   +GL+KA ++FD   G  F +YA+  +
Sbjct: 59  RQRLIERCLPLAEHIARRFLGRGEPLDDLIQVARLGLVKAVDRFDARCGASFVSYAVPTI 118

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    + +P  M++    +      ++  + R PT  E+A+ L +  + V 
Sbjct: 119 TGEVRRHFRDTGWAMHVPRSMQELHLSLTNATTELTTTLGRAPTASELAEALGIDKDEVA 178

Query: 565 KVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           + L+++    +L       ED   L + I D +      S            +L SL   
Sbjct: 179 RGLRVSDAYSTLSVDFPLGEDERPLSETIGDVD-----PSLAHVEDHVVLEPLLGSLPDL 233

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  VL +RF        T  ++  +  V++ ++ ++ +K +  L+
Sbjct: 234 ERTVLVLRFFGN----MTQSQIAARVGVSQMQVSRLLSKTLADLR 274


>gi|269968333|ref|ZP_06182353.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
 gi|269827051|gb|EEZ81365.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
          Length = 296

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 131/267 (49%), Gaps = 7/267 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-- 466
             + +K I     +S  E  H   + R        A++ ++E+NLRLV+ +AK Y  R  
Sbjct: 29  YAHYLKDIVGIDLLSREEELHYAKLNR---VGDEEAREMLIESNLRLVVKIAKGYLKRPG 85

Query: 467 -GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                LDLI+EGNIGL+KA +KFD   GY+FSTYA+WW+++ I  ++ +   T+R+P H+
Sbjct: 86  NNFTLLDLIEEGNIGLIKAVDKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPAHV 145

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +I+ +       S    +E +  E+++   +  E + + L      I + T       
Sbjct: 146 CKEINSLALKKLDASKSESKELSISELSRCSGVKAERIDE-LVALSGFIDVSTTADLHRV 204

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             + +  E +    P          +    ++ +L  + ++VL  RFG+      TL E+
Sbjct: 205 PFVLELCESEYTPDPQQDCENQCFTQAIENIIKTLPIKLQKVLIHRFGLFDQRVKTLSEI 264

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+ ER+RQ++ +A+ +++   R
Sbjct: 265 GLLLNVSNERVRQMQIEAVERVQKRLR 291



 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 28/104 (26%), Positives = 39/104 (37%), Gaps = 2/104 (1%)

Query: 103 SVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPL 162
           +V  +     +     DP   YL+++  I+LLSRE E+  AK    G       L ES L
Sbjct: 11  AVTDELSMKESLSVGKDPYAHYLKDIVGIDLLSREEELHYAKLNRVGDEEAREMLIESNL 70

Query: 163 TFQALIIWRDELNDGTTL-LREIIDLEACIGPESKGGFFHGTEG 205
                I        G    L ++I+ E  IG       F    G
Sbjct: 71  RLVVKIAKGYLKRPGNNFTLLDLIE-EGNIGLIKAVDKFDPEPG 113


>gi|297196439|ref|ZP_06913837.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197722266|gb|EDY66174.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 292

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 115/233 (49%), Gaps = 8/233 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   +  + +G  E   A+  ++E N+ LV  VA+++ NR     D++Q G IGL+KA +
Sbjct: 50  FFDRLQHLEEGTPEYQYARNTLIEMNISLVRYVARRFRNRAESDEDIVQVGTIGLIKAID 109

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD     +F+T+A+ ++   I R   D S  + +P  +++   ++V+    +S K+ R 
Sbjct: 110 RFDLSREVEFATFAVPYILGEIKRFFRDTSWAVHVPRRLQELRLELVQAVNELSGKLHRA 169

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+++ L +PVE V + L      +  S + P  +   +    F E    + P    
Sbjct: 170 PTAAELSEHLEIPVEEVTEGLVAMNGYVASSFDVPNTEGGPNAEAPFAERFGDLDPALGL 229

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           ++    +    ++  L  R+  +LR+RFG     +    E+G++  +++ ++ 
Sbjct: 230 VEDL--QALKPLIEELDDRDRLILRLRFG----DELKQAEIGERLGISQMQVS 276


>gi|2338708|gb|AAC46374.1| sigma factor RpoS [Vibrio cholerae]
          Length = 168

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 69/168 (41%), Positives = 113/168 (67%), Gaps = 3/168 (1%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  +  I     ++  E    V   R+       A+K M+E+NLRLV+ ++++Y+NRGL 
Sbjct: 4   QLYLSEIGFSPLLTAEEE---VLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLA 60

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
            LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R++ +Q+ TIR+P+H+  ++
Sbjct: 61  LLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVVKEL 120

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           +  +RTAR +S ++  EPTPEEIA +L  PV+ V K+L++ +   S++
Sbjct: 121 NIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERITSVD 168



 Score = 45.2 bits (105), Expect = 0.039,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D  ++YL E+G   LL+ E E+  A+R   G       + ES L     I  R   N G 
Sbjct: 1   DATQLYLSEIGFSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYS-NRGL 59

Query: 179 TLLREI 184
            LL  I
Sbjct: 60  ALLDLI 65


>gi|194014777|ref|ZP_03053394.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
 gi|194013803|gb|EDW23368.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
          Length = 255

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 110/242 (45%), Gaps = 13/242 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD 489
             R  E +   A  +++   + LV     + +    + +   DLI  G +GL  A EKFD
Sbjct: 12  WARWKEWKDPAAGDDLMRRYMPLVTYHVGRISIGLPKSVHKEDLISLGMLGLYDALEKFD 71

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF TYA + ++ AI   +  +     +P   R+K  KV     ++  +  R  TP
Sbjct: 72  PGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKKVEAAIEKLEQRYLRNVTP 128

Query: 550 EEIAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQ 606
            E+A++L M  + V   +        +S++  +   ED  ++   I D+  V+P +  ++
Sbjct: 129 TEVAEELGMSEQDVVTTMNEGFFANLLSIDEKLHDQEDGENVQVMIRDEKTVTPEEKMLK 188

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L E     +  L+ +E+ V+ + +      + TL E+G    ++  RI QI +KA+ K
Sbjct: 189 DELIEQLAEKMTELSEKEKLVISLFY----KEELTLTEIGHVLNLSTSRISQIHSKALFK 244

Query: 667 LK 668
           LK
Sbjct: 245 LK 246


>gi|217967697|ref|YP_002353203.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
 gi|217336796|gb|ACK42589.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
          Length = 413

 Score =  116 bits (291), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 112/346 (32%), Positives = 166/346 (47%), Gaps = 78/346 (22%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     ++  E   +   V +       AKK ++EANLRLV+SVAK+Y  RGL
Sbjct: 72  VKMYLKEIGKIPLLTPEEEIELAKRVEQ---GDEDAKKRLIEANLRLVVSVAKRYIGRGL 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 SFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAM------------PVEGVRKVLKITKEPISL 576
           ++K+ +  R ++  + R+PT E+IAK L +              E +     +    +SL
Sbjct: 189 MNKIHKITRLLTQSLGRKPTEEDIAKFLVIQQKLQEFEVYQESGEKISDDEIVEISMLSL 248

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPREERV-------L 628
           +         HL    + K  ++      +A  LR      +   T +   +       L
Sbjct: 249 DEIAKKLVELHLK--TKGKKELTKEKINEEAKELRHVLEEEIKQQTEKVREISMMGQEPL 306

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVT-----------------------RER---------- 655
            +   +G + D+ L +  +   ++                       RER          
Sbjct: 307 SLEMPVGEDEDNRLADFVENKDLSPADIAVQKSLKKDIEELLNELSEREREILKLRFGLE 366

Query: 656 --------------------IRQIEAKAIRKLKHPSRSKKLRSFLD 681
                               IRQIEAKA+R+L+HPSRSKK++ +L+
Sbjct: 367 DNQPRTLEEVGKLFNVTRERIRQIEAKALRRLRHPSRSKKIKDYLE 412



 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 74/377 (19%), Positives = 134/377 (35%), Gaps = 32/377 (8%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +  +   +ED               ++ +   +   DDPV+MYL+E+G I LL+ E EI 
Sbjct: 33  ESHELVDNEDLYVDVKEDKLPESVEEEVEIPEEIELDDPVKMYLKEIGKIPLLTPEEEIE 92

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWR---------DELNDGTTLLREIIDLEACIG 192
           +AKR+E G       L E+ L     +  R         D + +G   L + ++      
Sbjct: 93  LAKRVEQGDEDAKKRLIEANLRLVVSVAKRYIGRGLSFLDLIQEGNLGLIKAVEKFDWRK 152

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                 +       +  +         R  V   E   +         +S    P E   
Sbjct: 153 GYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETMNKIHKITRLLTQSLGRKPTEEDI 212

Query: 253 NDE----RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
                  + L E E          +D++    M +LDEIA+   EL              
Sbjct: 213 AKFLVIQQKLQEFEVYQESGEKISDDEIVEISMLSLDEIAKKLVEL------------HL 260

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
           K+  K ++ KEK+ +    L      ++  ++Q  +  + I     E L L    G   D
Sbjct: 261 KTKGKKELTKEKINEEAKELR---HVLEEEIKQQTEKVREISMMGQEPLSLEMPVGEDED 317

Query: 369 VFLERH-QGRELDPHWVSYAKDFPEG--EWKNFVACEVDSILKIRNEIKSISVETGISIS 425
             L    + ++L P  ++  K   +   E  N ++     ILK+R  ++     T   + 
Sbjct: 318 NRLADFVENKDLSPADIAVQKSLKKDIEELLNELSEREREILKLRFGLEDNQPRTLEEVG 377

Query: 426 EFRHIVS-MVRKGECEA 441
           +  ++    +R+ E +A
Sbjct: 378 KLFNVTRERIRQIEAKA 394


>gi|6952813|gb|AAF32414.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus]
          Length = 245

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 95/226 (42%), Gaps = 15/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 20  FIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSKGASFETYAGIRI 79

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +        +P  +     ++ +    +   + R+PT  E+A  L M ++   
Sbjct: 80  RGAMLDDMRKGDW---VPRSVHKNNREINQAVAELEGVLNRDPTDSEVAAHLGMSLDQYH 136

Query: 565 KVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L        + +E     +D     D  +D N   P       + R+     +  L  
Sbjct: 137 SALTDINCSRLVGIEDLGVSDDVISPADETDDSN---PFKGVADESFRKALVESIKQLPE 193

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  VL + +    + +  L+E+G    V+  R+ QI ++A+++L+
Sbjct: 194 REALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQAMQRLR 235


>gi|295109465|emb|CBL23418.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus
           obeum A2-162]
          Length = 238

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 111/240 (46%), Gaps = 8/240 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++++ +       A++ +   N  L+   AK++  RG+   DL Q G+IGL+KA +KF
Sbjct: 4   DTLALIGRAHQGDKEARERLFHENTGLIYCAAKRFLGRGVDMEDLFQIGSIGLLKAVDKF 63

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++   +++  +++ R    +   + REPT
Sbjct: 64  DTSYDVKFSTYAVPMIIGEIKRFLRD-DGILKVSRSVKENQYRIGRKREELEKTLGREPT 122

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A+ + M  E +   +    +  S+   I   + + L             +   +  
Sbjct: 123 LGELAESVQMLPEELAMTMDAANDVESIYQIIYQGEGNELRLL---DKIPEKENLHDRLL 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     +L SL   E ++L MR+      + T  EV  +F V++ +I ++E K + +L+
Sbjct: 180 NKIFLEELLRSLNAEERKLLYMRYF----REMTQTEVADEFGVSQVQISRMEKKILNRLR 235


>gi|293395614|ref|ZP_06639897.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
 gi|291421933|gb|EFE95179.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
          Length = 240

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  + K  +    + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTADGVMDKHSLWLRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R     V +  +R+  ++ R     E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRHARDVAQAMQRLEQQLGRPAGELEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + + M +   R++L  T            E+     +  +E     +PL   ++ +LR+ 
Sbjct: 122 QAMNMSLADYRQILMDTNNSQLFSYDEWREEQGESAEPLLEGHAEANPLHQLLEGSLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|303256291|ref|ZP_07342307.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|330998988|ref|ZP_08322713.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
 gi|302861020|gb|EFL84095.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|329575730|gb|EGG57256.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
          Length = 306

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 69/282 (24%), Positives = 124/282 (43%), Gaps = 16/282 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            ++  ++  N+   +S          R     VR  E     A  E+V ++LRLVIS+A+
Sbjct: 31  SLEEYIRAANKAPILSA--------EREHELAVRLQEHGDMEAAGELVMSHLRLVISIAR 82

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y   GL F DLIQEGNIGLMKA ++F+   G +  T+AM W+K  I   +      +++
Sbjct: 83  QYQGYGLPFGDLIQEGNIGLMKAVKRFNPNNGARLVTFAMTWIKSEIQEYVLRNWRLVKV 142

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPI 580
                 +         +   K+      E+IA+ L +    V     ++    + ++ P 
Sbjct: 143 ATTKSQRKLFFNLRKLKDDTKLLGTSEAEKIAETLDVKPSEVFEMEKRMLGSDVEIDEPS 202

Query: 581 -GDEDTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERVLRMRF---G 633
            G ++     +++ D+      +    A +  +       +  L  R  R++  R+    
Sbjct: 203 GGTDEGMAPSEWLTDERDTPENTIARGAYENTIENRLPEAVKKLDDRSRRIIEARWLYND 262

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
              +   TL ++ K+  V++ER+RQ+E KA   LK   +  K
Sbjct: 263 QDGSKGATLADLAKEMGVSQERVRQLEKKAFATLKTYLKEDK 304


>gi|117926317|ref|YP_866934.1| FliA/WhiG family RNA polymerase sigma factor [Magnetococcus sp.
           MC-1]
 gi|117610073|gb|ABK45528.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Magnetococcus sp.
           MC-1]
          Length = 260

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 110/251 (43%), Gaps = 19/251 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           E   S++++E++     LV  VA + +    + +   DL Q G +GL+ A  KFD   G 
Sbjct: 19  EAWKSLSREEIILKYAPLVRYVAGRISMKLPQSVDLDDLYQVGVMGLIDAVSKFDPDRGI 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KF TYA + ++ AI   +        +P  +R    ++     ++  K  R     E+A+
Sbjct: 79  KFQTYAEFRIRGAILDELRAIDW---VPRQLRQNASQMQEAYNQLEAKFGRPAEDVEVAE 135

Query: 555 KLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANLR 610
            L + +    + +   +    +S E    + D       + + D +   P+++     LR
Sbjct: 136 HLGISLNEYHEQIDQVRGISIVSFEDIRPNNDDEEWDVLEVLADPSVQDPVEAIGLMELR 195

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 + +L  +E  V+ + +      + T+ E+G+   +T  RI Q+ +KA  +++  
Sbjct: 196 HAMADAIETLPEKERLVVTLYYF----EELTMSEIGEVLGLTESRISQLHSKAALRMR-- 249

Query: 671 SRSKKLRSFLD 681
               +++ FL+
Sbjct: 250 ---ARIKRFLN 257


>gi|138894766|ref|YP_001125219.1| RNA polymerase sigma factor SigD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247611|ref|ZP_03146313.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
 gi|134266279|gb|ABO66474.1| RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           thermodenitrificans NG80-2]
 gi|196212395|gb|EDY07152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
          Length = 253

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 109/239 (45%), Gaps = 14/239 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
                   A +E+V+  + LV    ++ +      +   +L+  G +GL  A EKFD   
Sbjct: 18  WVNGRDRHAAEELVQRYMPLVSYHVQRLSATLPSSVPKEELVSLGLVGLYDALEKFDPSR 77

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA + ++ AI   +  +     +P  +RDK+ K+  TA R+  +  R  T +E+
Sbjct: 78  DLKFDTYASFRIRGAILDGLRKEDW---LPRSVRDKVKKIEETAERLEQRYMRSVTAKEV 134

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L M  E V+  +  T     +SL     +ED   L   I D  AV P +  ++  + 
Sbjct: 135 AAELGMTEEEVQAAVNETFFSNWLSLGQTACEEDDEPLA--IRDDRAVLPEEQVVKQEMI 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E     +  L  +E+ V+ + +      + T  E+G    ++  RI QI AKA+ KL+ 
Sbjct: 193 EKLAVGIGQLNEKEQLVISLFY----KEELTFTEIGSILQLSTSRISQIHAKALWKLRR 247


>gi|164687591|ref|ZP_02211619.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
 gi|164603365|gb|EDQ96830.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
          Length = 255

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 119/242 (49%), Gaps = 11/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + +++K +     AK  ++ +NL LV SV  K++N G +  DL Q G+IGL+KA  KF
Sbjct: 18  ETLDLIQKVQNGDEEAKALLISSNLGLVRSVIGKFSNIGYERDDLFQLGSIGLIKAIYKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++   ++    KV      +S K+ R+PT
Sbjct: 78  DPSYNVKFSTYAVPMILGEIKRYLRD-DGMVKVSRSLKQLAIKVKMQGEMLSKKLGRDPT 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            EE+A+ + +  E V   ++       L+  I +E+ S   L D I  K           
Sbjct: 137 IEELAEAIGVEKEDVVMAIESNFSVEYLQGVIHEEEGSPICLIDKISQKGEAEEDKVVDN 196

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E    VL  L  RE +++ +R+      D T  E+G+   +++ ++ +IE K + K
Sbjct: 197 ILLKE----VLGKLDKRERQIIMLRYF----EDKTQSEIGELLNISQVQVSRIEKKVLHK 248

Query: 667 LK 668
           LK
Sbjct: 249 LK 250


>gi|329904712|ref|ZP_08273913.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327547856|gb|EGF32614.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 244

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 105/236 (44%), Gaps = 13/236 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  ++  +  LV  +A +   +    ++  DLIQ G IGL  A  +++   G +F TYA+
Sbjct: 10  KNHLLVQHAPLVKRLAHQMKAKLPPSVEVDDLIQAGMIGLFDAINRYEDTHGAQFETYAV 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +        +P  MR  + K+    + +  K+ R P   E+AK + + + 
Sbjct: 70  QRIRGSMLDELRSSDW---LPRSMRQNMRKIEVAMQALQQKLGRAPLEAEVAKHMKLSLA 126

Query: 562 GVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             + +L      + +  E      E   H  D      + +PL S + A  R+   R + 
Sbjct: 127 EYQNLLGEGGGHQLVYYEDFHDSSEGNEHFLDRYCTDLSDNPLQSLLNAGFRDAVIRAIE 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +L  RE+    +  G+    +  L+E+G    VT  RI Q+ ++AI +++   R K
Sbjct: 187 ALPEREK----ILMGLYYEQEMNLKEIGAVLGVTESRISQLHSQAIARMRAFLREK 238


>gi|295835999|ref|ZP_06822932.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295825822|gb|EFG64505.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 297

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 56/278 (20%), Positives = 122/278 (43%), Gaps = 24/278 (8%)

Query: 413 IKSISVETGISISEFRHI----VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I+           E   +    ++++ +G      A+  ++E N  LV   A+++ NRG 
Sbjct: 29  IEDAGKIAPQDARELSRLFFDQLTVLEEGTHAYQYARNTLIEMNQSLVRFAARRFRNRGN 88

Query: 469 -QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               D++Q G +GL+KA ++FD     +F+++A+ ++   I R   D +  + +P  +++
Sbjct: 89  GDMEDILQVGTVGLIKAIDRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQE 148

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               + R   R++  + R+P  +E+A +L +  + V   L      +S    +  + T+ 
Sbjct: 149 LRVDLARAKERLAVDLDRDPGVKELAAELGISEDEVIDGLIAANGYMSDSLDLPADSTTS 208

Query: 588 ----------LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                       DF+ D        +            +L +L  RE  +L +RFG    
Sbjct: 209 GKPDQKTATTYADFLGD-----WDPAMELVEDFTALRPLLGTLDDRERYLLELRFG---- 259

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            + T  ++G +  V++  + ++ ++ + KL+    S+K
Sbjct: 260 QELTQAQIGAELGVSQMHVSRLLSRTLGKLREGLLSEK 297


>gi|89073430|ref|ZP_01159953.1| flagellar biosynthesis sigma factor FliA [Photobacterium sp. SKA34]
 gi|89050694|gb|EAR56175.1| flagellar biosynthesis sigma factor FliA [Photobacterium sp. SKA34]
          Length = 240

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 105/235 (44%), Gaps = 17/235 (7%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +   + +  +E    LV  +A     R        DLIQ G IGL++A + +D   G  F
Sbjct: 9   QYQQSPQAFIERYSSLVKRIAHHLMVRLPPSVLVEDLIQSGMIGLLEAQQNYDPTKGASF 68

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+A   ++ A+   I        +P  +     K+      + N++ R+P  +EIA+ L
Sbjct: 69  ETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRKISEAISHLENELGRDPNDQEIAQYL 125

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQANLRETT 613
            MP+E   + L      ++    +G  D     D + ++ ++   SP    +  N R + 
Sbjct: 126 DMPLEQYHQALN----DVNCGRLVGISDLGVAEDTVANEESIGENSPFQGVVDDNFRASL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + +L  RE  VL + +    + +  L+E+G    V+  RI QI ++A+++L+
Sbjct: 182 AEAIKTLPEREALVLSLYY----DEELNLKEIGAVIGVSESRICQIHSQAMQRLR 232


>gi|323490578|ref|ZP_08095784.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
 gi|323395844|gb|EGA88684.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
          Length = 260

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 109/235 (46%), Gaps = 4/235 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             + E   A+  +V    RLV S+A+KY+N      D+ Q G +GL+ A  ++D   G  
Sbjct: 22  YQKTEDEEAQTNLVLNYKRLVESIARKYSNGKSYHEDIAQVGMLGLLGAIRRYDPSYGRS 81

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A+  +   I R + D++  I +P  +++   ++  T   ++ +++R P   EIA+ 
Sbjct: 82  FEAFAVPTIIGEIKRFLRDKTWAIHVPRRIKELGPRIKATVEVLTTELQRSPQVWEIAEY 141

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           L +  + + + +++ K   +L      E  S               D   +A+ R     
Sbjct: 142 LDVEEDDILEAMEMGKSYQALSMDHSLEADSDGSTITLFDVVGQEDDGYEKADQRMLVAE 201

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +  L+ RE+++++  +        + +E G +  +++  + +++ KAI+KL+  
Sbjct: 202 AMNVLSEREKQIIQFTY----IEQLSQKEAGDKLGISQMHVSRLQRKAIKKLQEA 252


>gi|229195303|ref|ZP_04322075.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
 gi|228588158|gb|EEK46204.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
          Length = 242

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 106/240 (44%), Gaps = 8/240 (3%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               + +   A++ +V+    LV S+A +Y+  G    D+IQ G +GL+ A  ++D+ +G
Sbjct: 5   AEFQQNQCDEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I + + D++  I +P  ++D   K+      +++ ++R P   EIA
Sbjct: 65  NAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIA 124

Query: 554 KKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             L +  E V +++         SL+  + +         IE  +         +   R 
Sbjct: 125 DHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIE--SVGEVEQGYEETERRL 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               +   L   E+ V+   F      +   ++ G++  +++  + +I+ +AI KLK  +
Sbjct: 183 VLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLGISQMHVSRIKRQAISKLKQAA 238


>gi|293401521|ref|ZP_06645664.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305159|gb|EFE46405.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 259

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 128/250 (51%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + +    +K +     AK+++++ NL+LV+S+ ++++NR     DL Q G IGL
Sbjct: 19  LSNEEMKELF---KKYQSGDEQAKEDLIQGNLKLVLSIVQRFSNRCENMDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ + FD     +FSTYA+  +   I R + D    IR+  H++D  +KV R      +
Sbjct: 76  VKSIDNFDLKHEVRFSTYAVPMIMGEIKRYLRDNQ-VIRVSRHLKDLAYKVFRLKEEYIH 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVS 599
           + ++EPT   +A++L +  + V   L  T+  +S+  P+ + D    +L D I+D     
Sbjct: 135 EHQKEPTIHWLAEQLQVKEKDVVDALDSTQSVVSIFEPVYNTDGDELYLLDQIKDDKD-- 192

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 + +   T  + + +L  +E+ +++ R+      D T  E+  +  +++ ++ ++
Sbjct: 193 ---EIERLSNYMTLKKSMRNLKGKEKDIIQKRY----YQDKTQTEIANELGISQAQVSRL 245

Query: 660 EAKAIRKLKH 669
           E  AI  LK 
Sbjct: 246 EKNAIALLKK 255


>gi|309789348|ref|ZP_07683938.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
 gi|308922742|gb|EFP68259.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
          Length = 229

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 108/228 (47%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QCIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D     +PL   + +NLR+     + +L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDYQRENPLQQLLDSNLRQRVMEAIETL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G +  V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAELEVGESRVSQLHSQAIKRLR 223


>gi|167507949|gb|ABZ81295.1| RpoD [Thalassospira sp. MCCC 1A02030]
 gi|167507951|gb|ABZ81296.1| RpoD [Thalassospira sp. MCCC 1A02031]
          Length = 258

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 114/256 (44%), Gaps = 17/256 (6%)

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV-- 236
            LLR++IDLE   G                   E   +  +  +  E E       +   
Sbjct: 1   LLLRDVIDLETTYGGGPDAEIAAEEGEEEEVDAEADVESFDSANDDEDEEAETETPEPIG 60

Query: 237 ----------SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                       D+ S      E  + D+ + +++ +    +LS ME++L  +V+   + 
Sbjct: 61  GDDAEEEEEDEDDEESGDSDGEEGGDGDDDDDEDENEQVNVSLSKMEEELTEQVLEKFEL 120

Query: 287 IAEVYRELRSLQDNAVNGQKDEKS-----SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
           IA+ Y +L   Q+  +      ++       +   LK ++V+L+  + LN  RI+ L++ 
Sbjct: 121 IAKTYEKLHKAQEQRLVALNKGEAVPAATEKRYAKLKNEMVELMEDVHLNNFRIEELLDH 180

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           L  ++ R++  EG+LLR A    IKR  F++++QG ELDP+W+      P   WK F+  
Sbjct: 181 LTGLNNRLLGLEGKLLRFADRCKIKRPDFVKQYQGHELDPNWMERVAGLPGKGWKAFIER 240

Query: 402 EVDSILKIRNEIKSIS 417
             + I K+R ++  +S
Sbjct: 241 YPEEIAKLREDVGGVS 256


>gi|319654668|ref|ZP_08008747.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
 gi|317393584|gb|EFV74343.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
          Length = 264

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 114/247 (46%), Gaps = 5/247 (2%)

Query: 429 HIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
              ++++     +   A+  +V     LV ++A+KY+       D++Q G IGL+ A  +
Sbjct: 14  ETNALIKAYQLHQDEDAQNTLVLQYQNLVEAIARKYSKGRSYHEDIVQVGIIGLLGAIRR 73

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+  T   ++ ++ R P
Sbjct: 74  YDESFGKTFEAFAVPTIIGEIKRFLRDKTWSVHVPRRIKELGPKIKATVEELTTELHRSP 133

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             +EIA  L +  E V + +++ K   +L      E  S  G         +  +   + 
Sbjct: 134 RVDEIADVLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGGTVTLLDIVGNEDEGYEKV 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           N      +VL  L+ RE+ +++  +        + +E G +  +++  + +++ +AI+KL
Sbjct: 194 NQMLVLDKVLHVLSEREKLIIQYTYLEN----MSQKEAGDKLGISQMHVSRLQRRAIKKL 249

Query: 668 KHPSRSK 674
           +    S+
Sbjct: 250 QEAIHSE 256


>gi|239934532|emb|CAR94580.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 238

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 110/301 (36%), Gaps = 65/301 (21%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G   + A+LC  P TF  L I  + +  G   L ++  L   + 
Sbjct: 2   LLTREGEIRIAKRIEEGLNQVKAALCLFPPTFDHLRISYEIIRAGEARLTDL--LTGFVD 59

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
           P +                                       +  KD     D+ P+ AE
Sbjct: 60  PNAPDEIAQPNAKT----------------------------QEEKDKEKAEDTGPDPAE 91

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
            D+R                              +  ++R  + L       + D + + 
Sbjct: 92  ADKR------------------------------LKSIFRRQKRL---MSTIETDGREAK 118

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
           K    ++KL   +  ++L     + L   L      I   E +++ +     G+ R  F+
Sbjct: 119 KVINAQQKLTGELAEINLAPKLFEALCNNLRGTIGSIRQLEKQVMVICIREAGMARKEFI 178

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E + +WV       + ++ + ++     I + + ++++I VETG+SI+E + + 
Sbjct: 179 ASFPKNETNLNWVDKHI-RAKRKYSSILSKMKPDIQRAQRKLQAIKVETGMSIAEIKDVN 237

Query: 432 S 432
            
Sbjct: 238 R 238


>gi|28899006|ref|NP_798611.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153836996|ref|ZP_01989663.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|260365248|ref|ZP_05777805.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|260878798|ref|ZP_05891153.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|260899951|ref|ZP_05908346.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|28807225|dbj|BAC60495.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149749769|gb|EDM60514.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|308094185|gb|EFO43880.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|308107226|gb|EFO44766.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|308115412|gb|EFO52952.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|328474457|gb|EGF45262.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus 10329]
          Length = 244

 Score =  116 bits (290), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 101/244 (41%), Gaps = 15/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKAITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   +        +P  +     ++ +    +   + R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDMRKGDW---VPRSVHKNNREINQAVAELEGVLNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A  L M ++     L        + +E     +D     D  +D N   P    
Sbjct: 118 PTDSEVAAHLGMSLDQYHSALTDINCSRLVGIEDLGVSDDVISPADETDDSN---PFKGV 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + R+     +  L  RE  VL + +    + +  L+E+G    V+  R+ QI ++A+
Sbjct: 175 ADESFRKALVESIKQLPEREALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQAM 230

Query: 665 RKLK 668
           ++L+
Sbjct: 231 QRLR 234


>gi|302385959|ref|YP_003821781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302196587|gb|ADL04158.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 240

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 117/243 (48%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + +++        A+ ++V  N  LV S+ +++T RG +  DL Q G+IGLMKA +KF
Sbjct: 6   ETMRLIQMAHEGDKAARDQLVTDNFGLVWSIVRRFTGRGYEAEDLFQIGSIGLMKAIDKF 65

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++   KV      +  ++ REPT
Sbjct: 66  DLSYEVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSIKEMGLKVKNVREELIYRLGREPT 124

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            EEIA ++    E V   ++   E  SL   +   D +   L D IE++++        +
Sbjct: 125 VEEIAGEIGASKEEVAASIEAGAEVESLYRSVNKNDENSILLIDKIEEESSA-----QEE 179

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     +L +L+ ++  ++  R+           ++  +  +++ ++ ++E K +++
Sbjct: 180 LLNRMVLRELLTALSDKDREIIIRRYYYNETQS----QIAAKLGISQVQVSRLEKKILKQ 235

Query: 667 LKH 669
           ++ 
Sbjct: 236 MRE 238


>gi|291196368|emb|CBG22656.1| DNA-directed RNA polymerase subunit D [Pseudomonas parafulva]
          Length = 237

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 90/284 (31%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   D +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +    E      +    +E   D E  +    ++ ++    PE A      + +    
Sbjct: 50  NIAAPTEEVPVPGAKAAATKEESEDEEEESDSDDEEETESGPDPEVARQRFGAVSD---- 105

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                                           LQ      +K  +   +     + L  L
Sbjct: 106 -------------------------------QLQATNKVVKKHGRGHKESVAALQALADL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + ++LVE++ D   R+   E  +++L      + R  FL      E D  W
Sbjct: 135 FMPIKLVPKQFEVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                      W   +  +  +I+  + ++  +  E+G++++E 
Sbjct: 195 SGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLENESGLTVAEI 237


>gi|188592109|ref|YP_001796707.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; sigma-f factor; sigma-27; sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
 gi|170938483|emb|CAP63470.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; Sigma-F factor; Sigma-27; Sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
          Length = 238

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 112/242 (46%), Gaps = 12/242 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + + ++V+A+  LV  +A +   R    +Q  DLIQ G IGL+ AA++++   
Sbjct: 1   MYTIQGKLEQADVVKAHAPLVRRIALQLAARLPASVQIDDLIQAGMIGLLDAAKRYEDTH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +            +R    ++ RT R +  K+ R P   E+
Sbjct: 61  GARFETYASQRIRGAMLDEVRANDW---QSRSLRQFTRRIERTQRNLEQKLGRTPIDSEV 117

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ + MP++  + +L      + +  E      +   L   +   +  +PL   +++ +R
Sbjct: 118 AEAMEMPLDEYQLLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGSDDGNPLTVLMESGMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   R +  L  RE+ VL + +    + +  L E+G    VT  R+ QI  +AI +L+  
Sbjct: 178 EALVRAIERLPEREKLVLSLCY----DQELNLREIGAVLDVTESRVCQIRGQAINRLRTQ 233

Query: 671 SR 672
            R
Sbjct: 234 LR 235


>gi|239934570|emb|CAR94599.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 229

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/264 (19%), Positives = 96/264 (36%), Gaps = 44/264 (16%)

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           RMY+ EMG++ELL+REGEI IAKRIE G   +M ++   P + Q ++     +      L
Sbjct: 1   RMYMSEMGTVELLTREGEIVIAKRIEEGVRELMHAVAYWPGSVQKILDEYALVAKEERRL 60

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            ++I     + P  +       E    +    +  +   DD +E        A    ++ 
Sbjct: 61  ADVI--IGWLDPVEEIPATLIDEDAEIEVAPVAGAKPAGDDDEE------EGAATEDEEE 112

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
           +     PE A+     L + +D    TL+                               
Sbjct: 113 AVSGVDPEEAKVRFEALQKQQDKVNKTLA------------------------------- 141

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
               K    S + +    +L  L     +   + + L  +  +  + +   E  ++ L  
Sbjct: 142 ----KYGYGSKQAEKELSELGDLFKFFKIPARQFEPLYTKARETLENVRKAERLVMDLCT 197

Query: 362 S-YGIKRDVFLERHQGRELDPHWV 384
               ++R  F++   G E++  W+
Sbjct: 198 RKAQMQRKTFIKEFPGNEINEEWL 221


>gi|160896045|ref|YP_001561627.1| RNA polymerase sigma 28 subunit FliA/WhiG [Delftia acidovorans
           SPH-1]
 gi|160361629|gb|ABX33242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Delftia acidovorans
           SPH-1]
          Length = 237

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 98/244 (40%), Gaps = 12/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  ++ LV  +A     +    ++  DLIQ G IGL +A  +F+   
Sbjct: 1   MYTAKGQLDRDALIRRHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R     +     R+  ++ R P   EI
Sbjct: 61  GVQFETFASQRIRGAMLDELREGDWM---SRSSRKSQKDIEHALHRLEQRLGRTPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L M ++  + +L      + + LE   G ++     +     +   P        LR
Sbjct: 118 ADELGMDLDDYQSLLGKVRGTQLVYLEDMSGGDEGEDFLERHVADSGADPFALLRDHRLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 + +L  RE+       G+    D  L+E+     VT  R+ Q+ ++AI +L+  
Sbjct: 178 VALVEAIKALPEREQ----YIMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTK 233

Query: 671 SRSK 674
            R+ 
Sbjct: 234 MRAH 237


>gi|332969043|gb|EGK08083.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Kingella kingae
           ATCC 23330]
          Length = 287

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 70/266 (26%), Positives = 124/266 (46%), Gaps = 10/266 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S+ E    V +  +       A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 14  LEQYIHTVNNIPMLSLEEE---VGLAERQIKGDLEAAKKLILSHLRVVVSIARGYDGYGL 70

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+      +
Sbjct: 71  NQADLIQEGNIGLMKAVKRYEPNHGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 130

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
                  + R S         + IA  L + +  V ++  ++T   I L     D+D + 
Sbjct: 131 KLFFNLRSMRSSLSALSPKEAQSIADDLGVKLSEVMEMEQRMTGRDIGLLADNNDDDDAA 190

Query: 588 LG--DFIED---KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               +++ D   + +      A  A   +     LA L  R  R++  R+        TL
Sbjct: 191 FAPIEWLSDASHEPSQQLERKAHYALQTDGLQAALAQLDERSRRIVETRWLQDEG-ALTL 249

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+  ++ V+ ERIRQIE KA++KLK
Sbjct: 250 HELAAEYGVSAERIRQIEVKAMQKLK 275


>gi|95929871|ref|ZP_01312612.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95134167|gb|EAT15825.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 243

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 106/230 (46%), Gaps = 14/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E+V++++ LV  V  +   +   F    D+     +GLM AA +FD   G  F T+A 
Sbjct: 15  KNELVKSHMSLVHLVVDRMRAQVPGFVTKDDMTSAAMMGLMDAATRFDPSRGIMFKTFAE 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I            +R+K  ++ +T  +M +++ R P  EE+A+ + M ++
Sbjct: 75  RRIRGAIYDEIRKMDW---FSRSLREKQGRIGKTITQMEHRLGRTPEEEEVAEAMDMTLD 131

Query: 562 GVRKVLKITKE--PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             R +L        +SL   +   +D  +  D + D ++ S      ++ L       L 
Sbjct: 132 EYRHMLGQVCHLGCVSLNETLDDRDDGRNFLDLLTD-DSPSVQQRIEESELASELAGQLD 190

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ +E  V+ + +      + T +E+ +   +T  RI Q+ ++A+ KLK
Sbjct: 191 KLSEKERLVISLYY----YEELTQKEIAEVLDLTEGRISQLHSQALVKLK 236


>gi|50120672|ref|YP_049839.1| flagellar biosynthesis sigma factor [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611198|emb|CAG74644.1| RNA polymerase sigma factor for flagellar operon [Pectobacterium
           atrosepticum SCRI1043]
          Length = 240

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R    +V +  ++   ++ R PT +E+A
Sbjct: 65  TAFTTYAVQRIRGSMLDELRSRDW---APRSVRRNAREVAQAMQQTEQQLGRTPTEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL   ++ NLR  
Sbjct: 122 QTLNITLEDYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRHR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIENLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|90579944|ref|ZP_01235752.1| flagellar biosynthesis sigma factor FliA [Vibrio angustum S14]
 gi|90438829|gb|EAS64012.1| flagellar biosynthesis sigma factor FliA [Vibrio angustum S14]
          Length = 240

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 106/235 (45%), Gaps = 17/235 (7%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +   + +  +E    LV  +A     R        DLIQ G IGL++A + +D   G  F
Sbjct: 9   QYQQSPQAFIERYSSLVKRIAHHLMVRLPPSVLVEDLIQAGMIGLLEAQQNYDPTKGASF 68

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+A   ++ A+   I        +P  +     K+      + N++ R+P  +EIA+ L
Sbjct: 69  ETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRKISEAISHLENELGRDPNDQEIAQYL 125

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQANLRETT 613
            MP+E   + L      ++    +G  D     D + ++ ++   +PL   +  N R + 
Sbjct: 126 DMPLEQYHQALN----DVNCGRLVGISDLGVAEDTVANEESIGENTPLQGVVDDNFRASL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + +L  RE  VL + +    + +  L+E+G    V+  RI QI ++A+++L+
Sbjct: 182 AEAIETLPEREALVLSLYY----DEELNLKEIGAVIGVSESRICQIHSQAMQRLR 232


>gi|161898921|gb|ABX80450.1| SigB [Listeria monocytogenes]
          Length = 231

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 105/235 (44%), Gaps = 4/235 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D 
Sbjct: 1   IWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDA 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   
Sbjct: 61  TFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQIS 120

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +IA  + +  E V + +++ K   +L      E  S               D   + N R
Sbjct: 121 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQR 180

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +AI+
Sbjct: 181 MLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQAIK 231


>gi|188586048|ref|YP_001917593.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350735|gb|ACB85005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 250

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 109/247 (44%), Gaps = 13/247 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             +       ++++     LV     K    +  GL   DLI  G IGL+ A +KFD   
Sbjct: 9   YQDSGDRQQLEKLISEYSYLVKKQVDKVNYPSISGLNRDDLISFGVIGLIDAIKKFDINR 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
              F  YA   ++ AI   +        +P ++R+++  +    R++  K+ R PT  E+
Sbjct: 69  NVPFEAYANIRIRGAILDGLRKFDF---VPRNLREEMKTLHSEYRKLEQKLGRTPTNNEL 125

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANL 609
           A ++++    + K+ + T    P  L   I  E+    L D   D N+  P     +   
Sbjct: 126 AYQMSISEAELDKLWQATNCVIPSYLSDYITAEEGELTLEDIYPDSNSPDPQSRIDEKTT 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + + +L  +E+ VL + +      + TL+E+ K   +T  RI Q+ +KA+ +L+ 
Sbjct: 186 KQELGQAIDTLPQKEKLVLSLYY----YEELTLKEIAKILELTESRISQLHSKAVLRLRG 241

Query: 670 PSRSKKL 676
               KKL
Sbjct: 242 KLAKKKL 248


>gi|313647807|gb|EFS12253.1| RNA polymerase sigma factor rpoS [Shigella flexneri 2a str. 2457T]
          Length = 254

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 69/175 (39%), Positives = 116/175 (66%), Gaps = 3/175 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP 
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPW 226



 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|292696831|dbj|BAI99588.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696833|dbj|BAI99589.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696979|dbj|BAI99662.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC2]
 gi|292696981|dbj|BAI99663.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC3]
          Length = 253

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/291 (16%), Positives = 97/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-----ADDV 53

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +         E +  D  E E + E     S DD       PE A     +L    + 
Sbjct: 54  APTATHIGSELGEDDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEV 113

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +  ++                                   QK+ ++    +    +L  +
Sbjct: 114 TRLSI-----------------------------------QKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|54308132|ref|YP_129152.1| flagellar biosynthesis sigma factor [Photobacterium profundum SS9]
 gi|46912558|emb|CAG19350.1| Putative flagellar-specific RNA polymerase sigma factor, FliA
           [Photobacterium profundum SS9]
          Length = 240

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 102/227 (44%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F T+A   +
Sbjct: 17  FIERYSSLVKRIAYHLMGRLPPSVQVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGIRI 76

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++     ++ NK+ R+PT  EIA+ L M ++   
Sbjct: 77  RGAMLDDIRRGDW---VPRSVYKNNRRITEAMAQLENKLGRDPTDTEIAEHLEMTLDQYH 133

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L      ++    +G +D     D +     +    P    +  N R++    + +L 
Sbjct: 134 QALN----DVNCGRLVGMDDLGVSEDAVTTEASREENLPFQGVVDDNFRQSLADAIKTLP 189

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G    V+  RI QI ++A+++L+
Sbjct: 190 EREALVLSLYY----DEELNLKEIGVVVGVSESRICQIHSQAMQRLR 232


>gi|94676476|ref|YP_588537.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94219626|gb|ABF13785.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 286

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 129/276 (46%), Gaps = 16/276 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +D    + + +K+ +    ++  E   +   +         A K ++ ++LR VI++A+ 
Sbjct: 11  IDKKGSLEDYVKAANAYPMLTAEEELKLAEKL--HYQGDIEAAKLLILSHLRFVINIART 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y+   L   DLIQEGNIGLMKA  KF+  +G +  ++A+ W+K  I   +      +++ 
Sbjct: 69  YSGYNLPQADLIQEGNIGLMKAVRKFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 128

Query: 523 VH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETP 579
                R     + +  +R+    + E   E +AK+L +  + VR++  ++  + I+ +  
Sbjct: 129 TTKAQRRLFFNLRKIKQRLGWFNQEE--VEMVAKELGVTSKDVREMESRMAAQDIAFDPI 186

Query: 580 IGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRE-----TTTRVLASLTPREERVLRMRF 632
             DE  D   +   +  ++  S     I+    E          L  L  R + ++  R+
Sbjct: 187 PNDEVPDKLLMAPILYLQDKGSDFADRIEEQNWEYHAADKLNIALDKLDERSKNIIAARW 246

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               N   TL+++  ++ V+ ERIRQ+E  A++K++
Sbjct: 247 L--DNKKSTLQDLANKYGVSAERIRQLEKNAMKKIR 280


>gi|312126848|ref|YP_003991722.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311776867|gb|ADQ06353.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 248

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 123/253 (48%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 11  KFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   +  Q     +P  +R K  ++ +    +  +  + PT +E
Sbjct: 71  KGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQKAKEIEKAYIEIEKE-GKTPTDQE 126

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK++ + V+ ++K+     +   ISL++ +     S +G     ++ VS  +  I+   
Sbjct: 127 VAKRIGISVDELQKLQDRISSGMIISLDSFLEQNYESKIGGL---EDFVSQPEHFIENEE 183

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+    + + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 184 LKTVLRQQIDNLMENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLR 239

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 240 SA-----LQKYLE 247


>gi|302557289|ref|ZP_07309631.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302474907|gb|EFL38000.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 269

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 112/247 (45%), Gaps = 15/247 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR + ++    E EA   + E+VEA L +   +A ++ +RG  F DL Q   +GL+KA +
Sbjct: 26  FRRLTALPACPEREAL--RDEIVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVD 83

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           ++D  LG  F +YA+  +   I R   D   T+ +P  +++  ++V   ++ +S     R
Sbjct: 84  RYDSELGNAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQELRNRVRYASQDLSGTTPGR 143

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLD 602
            PT  EIA+   +  E VR   +   +   +SL+  +   +D   LGD +   +      
Sbjct: 144 RPTVTEIAEHAHLSEEDVRTGQEALESFSALSLDAELPGSDDGYSLGDALGAPDPALDTV 203

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE     LA L  RE  +L MRF          EE      +++  + ++ ++
Sbjct: 204 VD-----REAVKERLAELPERERAILYMRFFDDRTQSSIAEE----LGISQMHVSRLISR 254

Query: 663 AIRKLKH 669
              +++ 
Sbjct: 255 CCGRVRE 261


>gi|89099505|ref|ZP_01172381.1| sigma factor B [Bacillus sp. NRRL B-14911]
 gi|89085891|gb|EAR65016.1| sigma factor B [Bacillus sp. NRRL B-14911]
          Length = 264

 Score =  116 bits (289), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 122/262 (46%), Gaps = 6/262 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S     S  E   ++   +  E +   A++ +V     LV ++A+KY+       D
Sbjct: 1   MQKQSQPNQRSKEEINELIKAYQ--ENQDEEAQEILVRNYKALVETIARKYSKGRSYHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           + Q G IGL+ A  ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+
Sbjct: 59  IAQVGIIGLLGAIRRYDETFGKSFEAFAVPTIIGEIKRFLRDKTWSVHVPRRIKELGPKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
             T   ++ ++ R P  +EIA ++ +  E V + +++ K   +L      E  S  G   
Sbjct: 119 KTTVEELTTQLHRSPRVDEIADEIGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGGTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 +  +   + N R    RVL  LT RE+++++  +        + ++ G +  ++
Sbjct: 179 LLDIVGNVDEGFEKVNQRMVLERVLHVLTDREKQIIQYTYLEN----MSQKDAGDKLGIS 234

Query: 653 RERIRQIEAKAIRKLKHPSRSK 674
           +  + +++ +AI+KL+    ++
Sbjct: 235 QMHVSRLQRRAIKKLQEAINAE 256


>gi|332096706|gb|EGJ01697.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           3594-74]
          Length = 229

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 107/227 (47%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D +   +PL   + +NLR+     + +L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRL 222


>gi|321309571|ref|YP_004191900.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801415|emb|CBY92061.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 424

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 82/304 (26%), Positives = 136/304 (44%), Gaps = 48/304 (15%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +  ++       + A K +   NLRLV S A+KY N G    DL+QEG  GL
Sbjct: 115 LTFEEETALFKLLE-NPETRNFAVKRLTIFNLRLVWSSARKYLNYGFPMEDLVQEGIFGL 173

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA  KFD   G +FSTYA WW++QA+ R++ D+S  IR+PVHM   I+ + R  + +  
Sbjct: 174 VKAIHKFDCAFGNRFSTYATWWIRQAMLRAVEDKSRIIRVPVHMVPVINNLARIEKALIL 233

Query: 542 KIKREPTPEEIAKKL-----AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +   EPT E++ +++        V+ V  + K+  + +SL+  I  ++  +  D + D+ 
Sbjct: 234 ENGEEPTIEQLTQEMQKYDSQYTVQKVSDIKKLNIDWVSLDKLIDYDE--NFLDSVPDEE 291

Query: 597 AVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTD---------------- 639
            +S  + AI  +        L  +L   E  VL M +G+                     
Sbjct: 292 VISSEEEAILTHKSMVLQEFLESTLEDDELLVLDMHYGLMEFESPNTIEQIVSEILFNPE 351

Query: 640 -----------------------HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
                                     EE  K+       +R+  ++A+RKLK PS++ K 
Sbjct: 352 YRDVIKNKAINFVINEMLGKQDVLAPEEWKKEKAKVENFVRKKISQALRKLKKPSKNGKY 411

Query: 677 RSFL 680
           R+  
Sbjct: 412 RTIF 415


>gi|300928953|ref|ZP_07144457.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
 gi|300463107|gb|EFK26600.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
          Length = 229

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 107/228 (46%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + D +   +PL   + +NLR+     +  L
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIEML 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|292488613|ref|YP_003531497.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292899773|ref|YP_003539142.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291199621|emb|CBJ46740.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291554044|emb|CBA21132.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|312172755|emb|CBX81011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 240

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                 + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTANGVMDKHSLWQRYIPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     ++   + R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHQVEQALGRTATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
            +L +P+E  R++L  T            E+     + + E     +PL   ++ +LR+ 
Sbjct: 122 AQLDVPLEEYRQILLDTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRDR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIDGLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|256379908|ref|YP_003103568.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
 gi|255924211|gb|ACU39722.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
          Length = 272

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 106/235 (45%), Gaps = 19/235 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +  +V     LV  VA +    GL       DLIQ G  GL+ A EKF+   G KF TYA
Sbjct: 37  RDRLVLHYAPLVKYVAGR-VGTGLPAHVDVADLIQSGIFGLVDAIEKFEPERGLKFETYA 95

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           M  ++ AI   +  Q     +P  +R +   V R   R+  +++R PT  E+A +L + +
Sbjct: 96  MQRIRGAILDDLRSQDW---VPRSVRSRARDVERALERLGGRLQRTPTDRELAAELKIGL 152

Query: 561 EGVRK--VLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             +R+          ++L+  I          S L + + D+ A  P+ S +  + R   
Sbjct: 153 GELRELYAQFQLTSVVALDELIAAGRAAGSAGSSLAESLPDEGAEDPVASLVDQDSRRQL 212

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +A L  R+  V+ + +        TL E+GK   VT  R+ Q+  +A+ +L+
Sbjct: 213 ADAIAQLAERDRVVVTLYYFEN----LTLAEIGKVLGVTESRVCQLHTRAVLRLR 263


>gi|213958520|gb|ACJ54681.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm4R]
          Length = 242

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 45/291 (15%), Positives = 95/291 (32%), Gaps = 50/291 (17%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IAKRIE G   +M ++   P T   ++     +      L +++            G+ 
Sbjct: 1   EIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYI 49

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              +G +    E       +    + + D E A   + D+      P             
Sbjct: 50  DPDDGIAPPAAEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVS 109

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+ +          +     +  L  +AE++                             
Sbjct: 110 DQMEITRKALKKHGRGNKLAIAELVLLAELF----------------------------- 140

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGREL 379
                  + L   + + LVE++     R+   E  +++L      + R  FL +  G E+
Sbjct: 141 -----MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 195

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
           D  W    K     ++   +      I++ + ++ ++  ETG++I+E + I
Sbjct: 196 DESWTDALK----SKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDI 242


>gi|256004813|ref|ZP_05429788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 2360]
 gi|281417227|ref|ZP_06248247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|255991263|gb|EEU01370.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 2360]
 gi|281408629|gb|EFB38887.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940748|gb|ADU74782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 1313]
          Length = 256

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 110/252 (43%), Gaps = 11/252 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKA 484
           + +    +  + +    K++++     +V  +A +   Y    +++ DLI  G  GL+ A
Sbjct: 7   KQLELWKQYADTKNPAIKEQLIIEYSNIVKYIAGRLSIYFGSNVEYDDLIGYGIFGLIDA 66

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD   G KF TYA   ++ +I  SI +      +P  +R K  ++ +    + N++ 
Sbjct: 67  IEKFDINKGVKFETYASLRIRGSIIDSIRELDW---VPRSLRQKNKELEKVYAEIENELG 123

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-DFIEDKNAVSPLDS 603
           R  + +E+A KL + V+ + K+L        +      E    +G     +     P   
Sbjct: 124 RSASDKEVADKLGITVDELNKLLNEVNLSSMISLEEFLEQNYEIGVTTAPESRDEKPEGY 183

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              A LRE     ++ L  +E+ V+ + +      D TL+E+     V+  RI Q+  KA
Sbjct: 184 IEMAELREILADAISKLPEKEKMVITLYYF----EDLTLKEISAIMKVSESRISQLHTKA 239

Query: 664 IRKLKHPSRSKK 675
           I +L+      K
Sbjct: 240 ILRLRGKLARHK 251


>gi|255019642|ref|ZP_05291721.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970865|gb|EET28348.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
          Length = 285

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 125/288 (43%), Gaps = 15/288 (5%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           + AK  P+   K     +   I      ++       +S  +   +++ +R        A
Sbjct: 3   ARAKAKPQRLPKILPHAQEPDIPADLLPLQESGPF--LSPEQESAVIAQIR---SGDEAA 57

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +V A++ LV ++A+ Y N+GL   DL+QEG +GLM+A ++F   LG +FS+YA WW+
Sbjct: 58  RATLVSAHMPLVRAIARSYRNKGLSQEDLVQEGYMGLMRAMDRFQEGLGTRFSSYATWWI 117

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           ++A+ R++        I          + ++   +  K   E    +  +       GVR
Sbjct: 118 REAMQRAL--------IRARFIRLPDYLAKSLHALQQKSLDEVDGHDAQRAQRREALGVR 169

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTRVLASLTP 622
                  +   +     DE+ +     IE    N  SP     +          L  L  
Sbjct: 170 DSTMRALDFADVRVCSLDEEMADGPSRIEQVVGNVASPAQDYDRDASVRALREHLKLLNE 229

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           ++  V+  RFG+  +   TLE + ++  V+RE +RQ++ +A+ +L+  
Sbjct: 230 KQREVMIYRFGLHGDAPMTLEAIAERLGVSREAVRQLQVRALLRLRQA 277


>gi|83647839|ref|YP_436274.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
 gi|83635882|gb|ABC31849.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
          Length = 275

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 61/261 (23%), Positives = 110/261 (42%), Gaps = 16/261 (6%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQ 469
           ++ I    G++        + +   E  A  A   +V     LV  +A     R    +Q
Sbjct: 17  VEIIRFIAGLARKFMSLANTYMMYSETRAERA-DTLVRQYAPLVKRIAHHLIARLPASVQ 75

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLIQ G IGL++AA+K+D   G KF TYA   ++ A+   I        +P  +    
Sbjct: 76  VEDLIQAGMIGLLEAAQKYDAGKGAKFETYAGIRIRGAMVDEIRKGDW---VPRSVHRNA 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSH 587
             +      +  +  R+ +  E+A +L +P+E     L+     +  SLE      +   
Sbjct: 133 RNIAEAIHTIEARTGRDASDAEVAAELGVPLEQYHASLRDASSGKLFSLEELGFHGEGGS 192

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             + +    A +PL    Q    E  +  +  L  RE+ VL + +    + +  L+E+G+
Sbjct: 193 DDETL---TADNPLSDIEQNAFLEKLSAAIDGLPEREKLVLSLYY----DEELNLKEIGQ 245

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI ++A  +L+
Sbjct: 246 VLSVSESRVSQIHSQATLRLR 266


>gi|302343327|ref|YP_003807856.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301639940|gb|ADK85262.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 346

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 121/267 (45%), Gaps = 12/267 (4%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            ++  +        +S  E   +    R  E +   A   +V +NLRLV+ +A ++    
Sbjct: 63  ALQRYLWEARQYPLLSREEEDALAR--RFVEEQDPEAAAMLVTSNLRLVVKIAMEHQRYW 120

Query: 468 L-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-- 524
           +   LDLIQEGN+GL++A +KFD   G KFS YA +W+K  I + I D    +R+     
Sbjct: 121 MRNLLDLIQEGNMGLLQAVQKFDPFRGIKFSYYASFWIKAYILKFIMDNWRLVRVGTTQA 180

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE 583
            R   +K+ R   ++       P P  + ++L +  + V  +  ++    +SL+ P+ D+
Sbjct: 181 QRKLFYKLRREKEKL-QAQGVTPGPRLLGQRLGVSEKDVVDMEQRLDSWELSLDAPVRDD 239

Query: 584 DTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
                 + +            DS ++            +L  +E+ +L     +      
Sbjct: 240 SDDTHKNLLPSPRPTAEQDLADSELRQLFHRKLMEFRQTLDDKEQDILD--NRLLAENPQ 297

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKL 667
           TL EVG +  V+RERIRQ++ + + KL
Sbjct: 298 TLSEVGDRHGVSRERIRQLQVRLMEKL 324


>gi|154686064|ref|YP_001421225.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens FZB42]
 gi|308173610|ref|YP_003920315.1| RNA polymerase sigma-28 factor sigma-D [Bacillus amyloliquefaciens
           DSM 7]
 gi|154351915|gb|ABS73994.1| SigD [Bacillus amyloliquefaciens FZB42]
 gi|307606474|emb|CBI42845.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328553458|gb|AEB23950.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens TA208]
 gi|328911751|gb|AEB63347.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 254

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 109/241 (45%), Gaps = 13/241 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E +   A  +++   + LV     + +    + +   DL+  G +GL  A EKFD  
Sbjct: 14  RWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDALEKFDPG 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +  +     +P   R+K  KV     ++  +  R  TP E
Sbjct: 74  RDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKKVEAAIEKLEQRYLRNVTPSE 130

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           IA++L M  + V   +        +S++  +   +D  ++   I D   V P +  ++  
Sbjct: 131 IAEELGMTEQDVVSTMNEGFFANLLSIDEKLHDQDDGENIQVMIRDDKNVPPEEKIMKDE 190

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L       +  L+ +E+ V+ + +      + TL E+G+   ++  RI QI +KA+ KLK
Sbjct: 191 LIAQLAGKIHELSEKEQLVVSLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246

Query: 669 H 669
           H
Sbjct: 247 H 247


>gi|160878636|ref|YP_001557604.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427302|gb|ABX40865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 238

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++R  +    +A+  +V  N+ LV S+ +++  RG +  DL Q G+IGLMKA +KF
Sbjct: 2   DTLDLIRLSKQGDKVARDRVVTENVGLVWSIVRRFMGRGHEAEDLFQIGSIGLMKAIDKF 61

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++   K+      + +K  REPT
Sbjct: 62  DLSYDVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSLKETAGKIRLMRETLESKNGREPT 120

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQ 606
            EEI + L +  E V   L+   E  SL   I   D     L D IE  +  S       
Sbjct: 121 IEEIGEALELAKEEVVMALESGAEVESLYKTIYQGDGNAIFLIDKIEQTDDASDEMID-- 178

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                    V+ SL  +E+ ++R+R+      D T  E+ KQ  +++ ++ ++E K +R 
Sbjct: 179 ---HMALREVMDSLDEKEKDIIRLRYF----KDKTQTEIAKQLGISQVQVSRLERKILRT 231

Query: 667 LKH 669
           ++ 
Sbjct: 232 MRE 234


>gi|116514965|ref|YP_802594.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256819|gb|ABJ90501.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 291

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 59/276 (21%), Positives = 129/276 (46%), Gaps = 16/276 (5%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I  +   I+  +  + ++  + + +   +         + K ++ +NLR VI VAK Y+
Sbjct: 15  NIGSLEAYIRLANSFSILTSEKEKSLAKKL--FFYSDIESAKLLILSNLRFVIHVAKNYS 72

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
             GL   DLIQEGNIGLMKA  +F+  +  +  ++A+ W+K  I   +      ++I   
Sbjct: 73  GYGLPQADLIQEGNIGLMKAIRRFNPNINVRLVSFAVHWIKSEIHEYVLRNWRIVKIATT 132

Query: 525 --MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG 581
              R     + ++ +R+    + E     ++++L +  + V+++  +++ + I+ +    
Sbjct: 133 KAQRKLFFNLRKSKKRLGWFNRHEIDT--VSQELGVSTQEVKEMEARMSAQDITFDLSAK 190

Query: 582 DEDTSHLGD------FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           D     + +       +EDK    ++         +     T  L  L  R +++++ R+
Sbjct: 191 DSHLDSITNNLRTSFHLEDKKSNFSIKIEKDNWALHATNKLTNALLILDKRSQQIIKRRW 250

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                   TL+ + + + ++ ER+RQ+E  A++KLK
Sbjct: 251 LDDDKPKITLQAIARDYGISAERVRQLEKNAMKKLK 286


>gi|111021699|ref|YP_704671.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110821229|gb|ABG96513.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 249

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/241 (21%), Positives = 109/241 (45%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             +  +   +    + ++ ++E  L L   +A+++  RG    DLIQ   +GL+KA ++F
Sbjct: 6   EAIGRLAASDPRREVLRQRLIERCLPLAEHIARRFHGRGEPLDDLIQVARLGLVKAVDRF 65

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G  F +YA+  +   + R   D    +R+P  M++    +      ++  + R PT
Sbjct: 66  DARCGANFVSYAVPTITGEVRRHFRDTGWAMRVPRSMQELHLSLTNATTELTTTLGRAPT 125

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQA 607
             E+A+ + +  + V + L++     +L T     E+   L + I D   V P  + ++ 
Sbjct: 126 ASELAEAVGIDKDEVVQGLRVADAYSTLSTDFPLGENERPLSETIGD---VDPALAHVED 182

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++      +L SL   E  VL +RF        T  ++  +  V++ ++ ++  K +  L
Sbjct: 183 HV--VLAPLLESLPDLERTVLVLRFFGN----MTQSQIAARVGVSQMQVSRLLTKTLADL 236

Query: 668 K 668
           +
Sbjct: 237 R 237


>gi|291196350|emb|CBG22647.1| DNA-directed RNA polymerase subunit D [Pseudomonas mosselii]
          Length = 238

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/284 (17%), Positives = 95/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   D +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDYILGEYDRVTSEGGRLSDV--LSGYIDPDDNIAAPTEEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                K   + +E++ +D +  +GD E  A+   D                         
Sbjct: 59  PIPGAKAAAAKEEEDEEDEENADGDDEEEAESGPDPVV---------------------- 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A++DQL    +  L  +                  K  +S        + L  L
Sbjct: 97  AAQRFGAVKDQL----IDTLKVLK-----------------KHGRSHKDSIGAMQALADL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++     R+   E  +++L      + R  FL      E D  W
Sbjct: 136 FMPIKLVPKQFDALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLFPSNETDQTW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                      W   +  +  +I+  + ++  +  ETG++++E 
Sbjct: 196 SGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEI 238


>gi|72161738|ref|YP_289395.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915470|gb|AAZ55372.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 308

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 115/250 (46%), Gaps = 18/250 (7%)

Query: 427 FRHIVSMV--RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            R + ++   +  E  ++  + E+V   + LV   A++Y NRG    DL Q G +GLMKA
Sbjct: 66  ERLLAALADHQDDEETSARIRDELVRLYMPLVRREARRYRNRGEPMDDLYQVGMLGLMKA 125

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + FD   G  F  Y +  V   + R   D +  +R+P   +++  ++ R     + K  
Sbjct: 126 IKGFDPSYGKPFVAYLLPMVTGELKRHFRDTTWAVRVPRVHQERRSELNRVIAEFTQKHG 185

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPI-GDEDTSHLGDFI--EDKNAVS 599
           R PT  EIA  L M +E   +++        +SL+TP    ED S LGD +   D +  +
Sbjct: 186 RTPTTREIADALEMDLESAIELIDASSAYSALSLDTPFGDTEDESALGDTLGVADGDLET 245

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +D       + +    L  L  RE RV+ +RF        T  E+     +++  + ++
Sbjct: 246 VVD-------KTSLKDALDRLPERERRVILLRFFGN----KTQSEIAADVGLSQMHVSRL 294

Query: 660 EAKAIRKLKH 669
            ++ +R+L+ 
Sbjct: 295 LSQTLRQLRR 304


>gi|74317267|ref|YP_315007.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056762|gb|AAZ97202.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 246

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 104/233 (44%), Gaps = 12/233 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A   K +++E  + +V  +A     R    ++  DL+Q G IGL+ A  ++D     +F 
Sbjct: 9   AKSEKNDLLEQYMPMVKRLAHHMMGRLPPSVEEDDLVQAGMIGLLDAVSRYDEAQSAQFE 68

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA+  ++ ++   +         P   R  + K+ +    + +++ R+P+  EIA+ + 
Sbjct: 69  AYAIQRIRGSMIDELRQSDWM---PRSARQSMRKIEQAIAALQHQLGRQPSEGEIAEAMK 125

Query: 558 MPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +P+   + +L      + +  E     ++     D      A  PL   + ANLR     
Sbjct: 126 IPLADYQSMLGDARGHQLLYFEDFGESDEDDSFLDKQSADEATMPLPQLLDANLRACIIA 185

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +L  RE+ ++ + +      +  L E+ + F V+  RI Q+  +AI +L+
Sbjct: 186 GIENLPEREQLLMSLYY----EQELNLREIAEVFGVSESRICQLHGQAIARLR 234


>gi|54025772|ref|YP_120014.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017280|dbj|BAD58650.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 281

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 115/250 (46%), Gaps = 9/250 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  + ++ +      ++ ++ ++   L L   +A++++ RG  F DL Q   +GL++A +
Sbjct: 33  FAELAALDKHDPRRRAL-REHIIGLCLPLADHIARRFSGRGEAFDDLHQTARLGLVQAVD 91

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F  +A+  +   + R   D +  +R+P   ++    +     ++S +  R 
Sbjct: 92  RFDVRRGSSFLAFAVPTIMGEVRRHFRDHTWALRVPRRAKELQAMIGPATEKLSQRHGRM 151

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDFIEDK-NAVSPLDSA 604
           PT  EIA +L + +  V + L       +     +G +D  ++G  I D      P    
Sbjct: 152 PTAREIAAELDVELVEVTRALVAANAYSTNTLHAVGRDDDGNVGLSIGDSLGTEEPCYRL 211

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++  +      ++A+L  RE +VL  RF        T  ++ ++  V++ ++ +I  + +
Sbjct: 212 MEDAM--AVRPLIAALPERERQVLIWRF----YDSLTQSQIAERLGVSQMQVSRILNRTL 265

Query: 665 RKLKHPSRSK 674
            +L+  + ++
Sbjct: 266 TRLREEALAE 275


>gi|257784260|ref|YP_003179477.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
 gi|257472767|gb|ACV50886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
          Length = 284

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 123/240 (51%), Gaps = 12/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  E + S  + +++ ++L LV  +A K+ NRG    DLIQ G IGL+KA ++F+   G
Sbjct: 44  AQYKETKDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGTIGLIKAIDRFEPDRG 103

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F+TYA   +   I R   D+  ++R+P  +++   K+ +    ++ +++R P+ EEIA
Sbjct: 104 LEFTTYATPTIMGEIKRHFRDKGWSVRVPRRLQELSSKINQVTDDLTKELQRSPSIEEIA 163

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA----NL 609
           ++L   VE + + ++ +    S  + +  E      D  E  + +    +  +     + 
Sbjct: 164 QRLDTNVEEILEAMESS----SAYSSVPLEGGGSGADGDETPSIIDQYVTEDEDLAGSDD 219

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R      +   +PRE+ ++RMRF  G     T  E+ ++  +++ ++ ++  + +++++ 
Sbjct: 220 RIVLDEAIRDFSPREQEIIRMRFVEG----LTQVEIAEKLNISQVQVSRLLRRTLKRIQE 275


>gi|163801862|ref|ZP_02195759.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
 gi|159174370|gb|EDP59174.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
          Length = 244

 Score =  115 bits (288), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/226 (22%), Positives = 95/226 (42%), Gaps = 15/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 19  FIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAKQNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +   + R+P   E+A+ L M ++   
Sbjct: 79  RGAMLDDIRKGDW---VPRSVHKNNRQINQAIAELEGALNRDPFDSEVAEHLGMTLDQYH 135

Query: 565 KVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             L        + +E     +D     D  +D N   P       + ++     +  L  
Sbjct: 136 SALTDINCSKLVGIEDLGVSDDVISPADETDDSN---PFKGVADDSFKKALVESIKQLPE 192

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  VL + +    + +  L+E+G    V+  R+ QI ++A+++L+
Sbjct: 193 REALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQAMQRLR 234


>gi|225574676|ref|ZP_03783286.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038103|gb|EEG48349.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
          Length = 239

 Score =  115 bits (288), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 123/244 (50%), Gaps = 12/244 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             H ++++ +       A+  + E N+ L+ S+ K++ NRG++  DL Q G+IGL+KA +
Sbjct: 3   MEHTLALIARAHQGDKEARDTIFEENIGLIWSIVKRFQNRGVELEDLFQIGSIGLLKAVD 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R + D    I++   +++  +K      ++  ++ R+
Sbjct: 63  KFDLSYDVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKEVCYKAYLAREKLEKELGRD 121

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSA 604
           P   E+A ++ +P E +   L    E  SL+  I   +     L D +E+K      +  
Sbjct: 122 PQIAEMAGEIGIPQEELMMALDSNVEIESLQKTIYQGEGNDIRLIDKLEEKK-----NRQ 176

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            ++  R     +L  LT  E R++ MR+      + T  E+ ++  V++ ++ ++E K +
Sbjct: 177 EESLNRILLEEILGQLTVSERRLIYMRYF----QERTQTEIARELGVSQVQVSRMEKKIL 232

Query: 665 RKLK 668
           ++L+
Sbjct: 233 KRLR 236


>gi|163869170|ref|YP_001610422.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161018869|emb|CAK02427.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 303

 Score =  115 bits (288), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 114/246 (46%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+    
Sbjct: 46  LRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDRE 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNK---IKREPT 548
            +FSTYA WW++ +I   I      +R       K     + R   ++      + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLVQDDSALSKQDI 165

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNA-VSPLDSA 604
              IA+KL + V  V  +        +  +    E++       D + D++     L   
Sbjct: 166 FRTIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDSPVAKMDVLVDESPLPDALIEQ 225

Query: 605 IQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +    R  +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 VIDGQRRTQWLYDALQILNERELEIIR--FRRLNEEGATLEVLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|118602568|ref|YP_903783.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
 gi|118567507|gb|ABL02312.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 280

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 128/268 (47%), Gaps = 10/268 (3%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +     I  SE  H ++ V+  E     A +++V +++R V  +A  Y   GL+  DL+
Sbjct: 17  EVQKYPPILNSEQEHELA-VKLYENHDLSAARKLVLSHMRFVAFIAHGYKGYGLEQADLV 75

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKV 532
           QEG IGLMKA ++F+     + +++A++W++  I   I      +++      R    K+
Sbjct: 76  QEGTIGLMKAVKRFNPNRNVRLASFAVYWIRAEIHEFIFKNWKIVKVATTKAQRKLFFKL 135

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +    + + +  E   ++IA  L +  + V ++    +          DED+     ++
Sbjct: 136 KQAKAHIYSSLNEEQ-ADKIANDLGVRRKDVLEMESRLQFNDVTFEVSDDEDSLAPEQYL 194

Query: 593 EDKNAVSPLD----SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            ++N  +P      +  + N ++   + L+SL  R   +L+ R+        TL  +  +
Sbjct: 195 TNENVQTPEQLLLINDSKQNQQQQLYKALSSLDERSLDILQSRYL--KEEKTTLHTLADK 252

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           + +++ER+RQ+E KA++KLK   + + L
Sbjct: 253 YGISKERVRQLETKAMQKLKSNLQEQSL 280


>gi|49476176|ref|YP_034217.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49238984|emb|CAF28284.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 303

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 114/246 (46%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+    
Sbjct: 46  LRWKDKRDDEAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDRE 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNK---IKREPT 548
            +FSTYA WW++ +I   I      +R       K     + R   ++      + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLVQDDSALSKQDI 165

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNA-VSPLDSA 604
              IA+KL + V  V  +        +  +    E++ +     D + D +     L   
Sbjct: 166 FRSIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPVAKMDALVDDSPLPDALIEQ 225

Query: 605 IQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +    R  +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 VIDGQRRTQWLYDALQILNERELEIIR--FRRLNEEGATLEVLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|253580606|ref|ZP_04857870.1| RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847977|gb|EES75943.1| RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 237

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 121/243 (49%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++ K +     A+  + + N  LV S+AK++  R ++  D++Q G+IGL+KA ++F
Sbjct: 3   HTLALIMKSQQGDKEARDTVFKENAGLVYSMAKRFAGRSVEMEDIVQIGSIGLLKAIDRF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++  ++++   ++      +  ++ REP 
Sbjct: 63  DISYDVKFSTYAVPMIIGEIRRYLRD-DGMLKVSRNLKENCARIYSAREALEKELGREPI 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQ 606
            EE+AK   + V+ V   ++   E  SL   I   D     L D +++K      +    
Sbjct: 122 LEEVAKATELSVDEVVMSMESGAEVESLHKIIYQGDGNDISLMDRLQEKE-----NGQDA 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A  R     +L  L  RE +++ MR+      D T  E+  +  +++ ++ ++E + +++
Sbjct: 177 ALNRIFLDEILKKLDARERQLIGMRYF----KDMTQTEIAAEMGISQVQVSRMEKRILKE 232

Query: 667 LKH 669
           LK 
Sbjct: 233 LKK 235


>gi|320537994|ref|ZP_08037899.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
 gi|320145151|gb|EFW36862.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
          Length = 262

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 66/244 (27%), Positives = 113/244 (46%), Gaps = 15/244 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFD 489
            +   +   +  ++  +     LV  VA K        ++F DL+  G  GL  A +K+D
Sbjct: 15  WLEYKKTGNAKIREFFIIQYAPLVKYVASKIAVGKPGSIEFDDLVSYGIFGLFDAIDKYD 74

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+TYA+  ++ AI   +        +P  +R +I ++  T   +  K+ R  T 
Sbjct: 75  PEKNIRFNTYAVTRIRGAIYDELRSIDW---VPRSVRQQIKQIEDTIAAIEAKLGRSATD 131

Query: 550 EEIAKKLAMPVEGVRKVL--KITKEPISL-ETPIGDEDTSHL--GDFIEDKNAVSPLDSA 604
           EEIA +L + +E   ++L        ISL +T  G ED+  +  GD IE   +++P    
Sbjct: 132 EEIAFELNISLEEYHQLLLKISGTSVISLADTKFGGEDSGQIAVGDSIEAPASLNPDVIV 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  ++      +  L+ RE++VL + +      D TL+E+GK   VT  R+ QI   A 
Sbjct: 192 EREEIKRVIVEAIKELSEREQQVLILYY----YEDMTLKEIGKVLKVTESRVSQIHTSAN 247

Query: 665 RKLK 668
            KLK
Sbjct: 248 LKLK 251


>gi|333028638|ref|ZP_08456702.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332748490|gb|EGJ78931.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 310

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/272 (20%), Positives = 128/272 (47%), Gaps = 14/272 (5%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I+    ++  + R +  +       + +G  E   A+  ++E N+ LV   A+++ +
Sbjct: 44  LPEIAEPHKVAPRDARELTRLFFDRLDTLEEGTREFQDARNTLIEMNMSLVRFAARRFRS 103

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    D++Q G IGL+KA ++F+     +F+T+A+ ++   I R   D +  + +P  +
Sbjct: 104 RGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAVPYIVGEIKRFFRDTTWAVHVPRRL 163

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDE 583
           ++   ++ +    +S ++ R P   E+A  +++  + V +           SL+  IG E
Sbjct: 164 QEARVELAKANEELSTRLGRAPKVSELAALMSLSEQQVVEAQIAANGYSSSSLDATIGGE 223

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D+      + D          +  +L      +LA L PR+ ++L +RFG     + T  
Sbjct: 224 DSGEGEAALSDFIGAEDPGMELVEDLH-ALAPLLAGLEPRDRQILELRFG----QELTQA 278

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++G++  V++  + ++  + +  L+    S++
Sbjct: 279 QIGERLGVSQMHVSRLLNRTLGTLRAGLMSER 310


>gi|328951994|ref|YP_004369328.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452318|gb|AEB08147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
          Length = 258

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 107/242 (44%), Gaps = 15/242 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +   E       + +V     ++  +A +   R    +   DLI  G IGL+ A +KFD 
Sbjct: 16  IDWPEKIDPETHERLVLQYAPMIKYIAARLALRLPSHISLDDLISSGMIGLLDAIKKFDP 75

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F TYA + +K AI   +        IP  +R K  ++ +   ++  ++ R    E
Sbjct: 76  QKNISFKTYAEFRIKGAILDELRALDW---IPRSIRKKTSQLEKAYTKLEKELGRPAEAE 132

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLET-----PIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           E+A  + + +E    ++  TK    L+       + +   + L + ++D+++ SP  S  
Sbjct: 133 EVAHSMGLSMEEFYHLIDETKGVSLLDIDAVRRNLNEFSEAELYEILQDESSRSPFISVH 192

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A LR+   R L  L  +E+ ++ + +      + T++E+G+    T  RI QI  +AI 
Sbjct: 193 FAELRDLLMRALEDLPDKEKLLISLYY----YEELTMKEIGEIMGYTESRISQIHTQAIF 248

Query: 666 KL 667
            L
Sbjct: 249 HL 250


>gi|167932999|ref|ZP_02520086.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7b]
          Length = 211

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 81/161 (50%), Positives = 112/161 (69%), Gaps = 3/161 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +R  ++ I     +S  E   +   V         AK +M EAN+RLV+S+AK+Y+ RGL
Sbjct: 51  VRLYLREIGKIPLLSAEEEMELAHRV---VQGDKKAKDKMAEANMRLVVSIAKRYSGRGL 107

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN GL++A EKFD   G+KFSTYA WW++QAITR+IADQ+  IRIPVHM + 
Sbjct: 108 DFLDLIQEGNTGLLRAVEKFDPDKGFKFSTYATWWIRQAITRAIADQARVIRIPVHMVET 167

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           I+K++RT RRM+ ++ REPT EE++K+L M  + +  V+KI
Sbjct: 168 INKLLRTQRRMTQELNREPTIEELSKELDMEPDKIEYVMKI 208



 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
           ++VD     D +             +      +  D     +DD VR+YLRE+G I LLS
Sbjct: 9   DIVDATLQVDFDEPNIDDLADEEEPDEQTLNGQYLDDV---SDDSVRLYLREIGKIPLLS 65

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
            E E+ +A R+  G       + E+ +     I  R
Sbjct: 66  AEEEMELAHRVVQGDKKAKDKMAEANMRLVVSIAKR 101


>gi|229917800|ref|YP_002886446.1| RNA polymerase sigma factor SigB [Exiguobacterium sp. AT1b]
 gi|229469229|gb|ACQ71001.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Exiguobacterium sp. AT1b]
          Length = 266

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 49/260 (18%), Positives = 113/260 (43%), Gaps = 5/260 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           + + S +   S  E    +   ++ +    + +  ++     LV ++A+K++       D
Sbjct: 1   MPAKSQQRHHSDDEVLEWIERYQQDDQNEEV-QMLLINRYSDLVEALARKFSRGRAIHDD 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+Q G IGL+ A  +FD   G  F ++A+  +   I R I D++ ++ +P  +++   K+
Sbjct: 60  LVQVGMIGLLAALRRFDPEFGRSFESFAVPTIIGEIKRFIRDKTWSVHVPRRIKELGPKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +T   ++ +++R P  +EIA  L +  E + + L++ K   +L      E  +      
Sbjct: 120 KKTVEELTTELQRSPRIDEIADHLGVSDEEILETLEMGKSYQALSVDSSIEADNEGSTVT 179

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 S        + R    +    L  RE  +L   +        + +E G+   ++
Sbjct: 180 LLDLVGSQERGYESVDQRLILEKAFNVLNERERAILECAYYKN----MSQKETGELLGIS 235

Query: 653 RERIRQIEAKAIRKLKHPSR 672
           +  + +++ +A+ KL+   +
Sbjct: 236 QMHVSRLQRRALEKLREAIK 255


>gi|326780902|ref|ZP_08240167.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326661235|gb|EGE46081.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 264

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 100/228 (43%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + A L +   +A ++ +RG    DL Q   +GL+KA +++D   G  F +YA+  V
Sbjct: 38  RDETICAWLPMAHRIATRFRDRGEAMDDLRQVAAMGLVKAVDRYDPDRGKAFESYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              + R   D +  + +P  ++D  ++V    R ++       PT  +IA    +  E V
Sbjct: 98  TGELKRHFRDHTWDVHVPRRVQDLRNRVRVARRELAQSSGGAAPTCADIASATGLGEEDV 157

Query: 564 RKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+   +   +SL+  P G E  S L D +      S   +   A  RE     L  L
Sbjct: 158 LLGLEALESYSALSLDAGPAGVEGGSPLADRLG-----SCDGALDVAIDREAVKPGLRGL 212

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L +R+   M      E    Q  +++  + ++ +++  +++
Sbjct: 213 PERERTILYLRYFRDMTQSRIAE----QLGISQMHVSRLLSQSCERVR 256


>gi|158320542|ref|YP_001513049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
 gi|158140741|gb|ABW19053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
          Length = 245

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 111/238 (46%), Gaps = 17/238 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKK-YTNRG--LQFLDLIQEGNIGLMKAAEKFDWCL 492
                 S AK  ++E  +RLV  +A + Y + G  +++ DL+  G  GL+ A EKFD   
Sbjct: 11  YKNNNDSQAKALLIEEYIRLVKFIAGRLYISYGSNIEYDDLVSYGIFGLIDAIEKFDLNK 70

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA   ++ AI  S+        +P  +R K  K+      + NK+ R  T  E+
Sbjct: 71  QVKFETYAQIRIRGAIIDSLRSLDW---VPRSIRQKSKKIEEAYSSLENKLGRSATDVEV 127

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           ++ L + V+ ++++L    +   ISLE  I   +   +G+  E++     +      N  
Sbjct: 128 SEALDISVKELQEILLNTASFNVISLEEVIF--EVGLIGNTAEEQLTEDLICRRETYNN- 184

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +  L  RE +V+ + +        T +E+GK   ++  R+ Q+ +KAI +LK
Sbjct: 185 --LKDTIVQLPERERQVISLYYYNN----LTYKEIGKVLDISESRVSQLHSKAISRLK 236


>gi|213958516|gb|ACJ54679.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 6-6.5cm2R]
          Length = 243

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 43/289 (14%), Positives = 95/289 (32%), Gaps = 47/289 (16%)

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           IAKRIE G   +M ++   P T   ++     +      L +++            G+  
Sbjct: 1   IAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYID 49

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             +G +    E       +    + + D + A   + D+      P             D
Sbjct: 50  PDDGIAPPAAEVPPPVDPKAVKADDDTDDDDAEAATDDEEEAESGPDPVIAAQRFGAVSD 109

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
           + +          +     +  L  +AE++                              
Sbjct: 110 QMEITRKALKKHGRGNKLAIAELVLLAELF------------------------------ 139

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELD 380
                 + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D
Sbjct: 140 ----MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVD 195

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
             W   A    + ++   +      I++ + ++ ++  ETG++I+E + 
Sbjct: 196 ESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKD 243


>gi|254228448|ref|ZP_04921874.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262393605|ref|YP_003285459.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
 gi|151939036|gb|EDN57868.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262337199|gb|ACY50994.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
          Length = 244

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 102/244 (41%), Gaps = 15/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKAITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   +        +P  +     ++ +    +  ++ R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDMRKGDW---VPRSVHKNNREINQAIAELEGELNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+A  L M ++     L        + +E     +D     D  +D N   P    
Sbjct: 118 PTDSEVATHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSN---PFKGV 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + R+     +  +  RE  VL + +    + +  L+E+G    V+  R+ QI ++A+
Sbjct: 175 ADESFRKALVESIKQIPEREALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQAM 230

Query: 665 RKLK 668
           ++L+
Sbjct: 231 QRLR 234


>gi|291196322|emb|CBG22633.1| DNA-directed RNA polymerase subunit D [Pseudomonas libanensis]
          Length = 238

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 93/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A   S D+      P             D+ +
Sbjct: 50  GIAPPAAEVPPPVDPKAPKADDDTDDDEAEASSDDEDEVESGPDPVVAAQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +   + +  L  +AE++                                 
Sbjct: 110 ITRKALKKHGRGNKQAIAELVALAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEI 238


>gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Herminiimonas
           arsenicoxydans]
          Length = 216

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 91/209 (43%), Gaps = 9/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DLIQ G IGL+ A  +++   G +F TYA+  ++ A+   +         P  MR 
Sbjct: 9   VEVDDLIQAGMIGLLDAVGRYEETHGAQFETYAVQRIRGAMLDELRSSDWM---PRSMRQ 65

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDT 585
            + K+      +  K+ R P   E+AK+L + +   + +L      + +  E     ED 
Sbjct: 66  NMRKIEVAMNSLQQKLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDN 125

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            H  D      +  PL + +    R      + +L  RE+    +   +    +  L+E+
Sbjct: 126 EHFLDRYCTDESPDPLQNLMNTGFRSAVIAAIEALPEREK----ILMSLYYEQEMNLKEI 181

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    VT  R+ Q+ ++AI +++   R K
Sbjct: 182 GAVMGVTESRVSQLHSQAIARMRANLREK 210


>gi|229082715|ref|ZP_04215161.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
 gi|228700606|gb|EEL53146.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
          Length = 323

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 132/264 (50%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-- 469
           EIK I     +S  E    + + ++ +      +  +   N+ LV+S+A+KY N+     
Sbjct: 39  EIKEIGNYKVLSKQES---LKLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI-TRSIADQSCTIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+K+++       +S   +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIKKSMLGIICRKKSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS 586
             + V    +      R P+ EE+AK+L +  E V K     K    ++L+    +ED  
Sbjct: 156 NLRYVELEDKYLQMYNRTPSVEEVAKELNVTSETVIKYNVYYKRATTMTLDVDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            L  F +D + +   +  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 ILNPFYDDSSTIPSTNEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K   +T ER+ QI+ +AI+KLK 
Sbjct: 276 AKALMITTERVSQIKDEAIKKLKK 299


>gi|260589293|ref|ZP_05855206.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|331082700|ref|ZP_08331823.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540374|gb|EEX20943.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|330400319|gb|EGG79961.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 237

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 120/241 (49%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I++++ +       A+  + E N+ LV S+A+++ NRG +  DL+Q G IGL+KA +KF
Sbjct: 3   DILALIGRAHQGDKSARDILTEKNMGLVHSIARRFQNRGAELEDLVQIGCIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   I R + D    +++   +++   K       +  K  +EP+
Sbjct: 63  DLSYEVRFSTYAVPMITGEIKRFLRD-DGMVKVSRSLKEAAGKAYAVREELLMKTGQEPS 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIAK+L++  E +   ++ + +  SL+  I   D S +   +EDK          +  
Sbjct: 122 MEEIAKELSVSEEELIMAMESSAQVESLQKTIYQSDGSDIA--LEDKLPYEKD-EQEEVL 178

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     +L SL  RE  ++ +RF      + T   + K   +++ ++ ++E K ++ L+
Sbjct: 179 DKLLLEDILGSLNARERELIYLRFF----KEKTQTSIAKMMGMSQVQVSRLEKKILKALR 234

Query: 669 H 669
            
Sbjct: 235 E 235


>gi|108743436|dbj|BAE95539.1| putative RNA polymerase sigma factor [Streptomyces kanamyceticus]
          Length = 278

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 105/228 (46%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E+VE  L +   +A ++ NRG    DL Q   +GL+KA +++D   G  F +YA+  V
Sbjct: 52  RQEVVEVWLPMSERLAGRFRNRGESLDDLRQVAALGLVKAVDRYDPRRGTAFESYAVPTV 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGV 563
              I R   D   T+ +P  ++D  ++V    + ++     R PT  EIA++  M  E  
Sbjct: 112 TGEIKRHFRDHMWTLHVPRRVQDLRNRVRFARQDLAQTVSGRAPTTAEIAERAQMSEEDA 171

Query: 564 RKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +  L+   +   +SL+  +   ED   L D +   +    +        RE+    +A L
Sbjct: 172 KAGLEALDSFTALSLDAELPGSEDGYSLSDALGGPDPALDVVID-----RESVKPRIAQL 226

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L MRF   M      +E+     +++  + ++ ++   +L+
Sbjct: 227 PERERTILYMRFFGDMTQSRIADEM----GISQMHVSRLISRCCDRLR 270


>gi|255526140|ref|ZP_05393061.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296187150|ref|ZP_06855547.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
 gi|255510189|gb|EET86508.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296048185|gb|EFG87622.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
          Length = 251

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 58/239 (24%), Positives = 118/239 (49%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++        A  +++E NL LV +++KK+ NRG ++ D+ Q G +GL+KA   FD 
Sbjct: 17  LELIKYARNGNKDALNKLIEVNLPLVSAISKKFLNRGYEYEDIFQIGCMGLVKAVNNFDE 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R I D    I++   +++   K+      ++ +I REPT E
Sbjct: 77  KYNVKFSTYAVPMILGEIKRFIRD-DGMIKVSRSVKNTAKKLHYAKEALTKQISREPTIE 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+++   + VE +   ++ +     L   I  +D + +   + DK + S    +   + R
Sbjct: 136 ELSEYSGIGVEDIIFAMESSNSLQYLYDTIHQDDGAPV--LLIDKLSESSDRDSEIVD-R 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L +L  +  +++ +R+      D T  +V K   +++ ++ +IE K ++ ++ 
Sbjct: 193 IALKEALKNLDVKSRQIIMLRYF----KDKTQIQVAKMLGISQVQVSRIEKKVLKVMRE 247


>gi|241763670|ref|ZP_04761720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax delafieldii
           2AN]
 gi|241367145|gb|EER61511.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax delafieldii
           2AN]
          Length = 246

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 101/245 (41%), Gaps = 13/245 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  ++ LV  +A     +    ++  DLIQ G +GL  A  +++   
Sbjct: 9   MYTAKGQLDRDALIRQHVPLVRRIAHHMIAKLPPNVELDDLIQVGMMGLADALSRYEATQ 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R     +  + RR+  K+ R P   EI
Sbjct: 69  GVQFETFATQRIRGAMLDELREGDWM---SRSSRKSQKDIEHSLRRLEQKLGRPPLESEI 125

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANL 609
           A  + M +   + +L      + + LE     ++      D     ++  PL+      L
Sbjct: 126 AADMGMSLAEYQSLLGKVRGTQLVYLEDMTHGDEGDEGFLDRHVADSSADPLELLRDHRL 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R +  + + SL  RE+       G+    D  L+E+     VT  R+ Q+ +++I +L+ 
Sbjct: 186 RASLVQAIQSLPEREQ----HIMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQSIARLRA 241

Query: 670 PSRSK 674
             RS 
Sbjct: 242 KMRSH 246


>gi|88608622|ref|YP_506230.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600791|gb|ABD46259.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
          Length = 288

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 127/264 (48%), Gaps = 19/264 (7%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + I     +   E R ++   R        A + +VEA LRLV+ V  ++ N G   +DL
Sbjct: 18  RKILAIPILQEEEERELID--RWFVHRDISAAQRLVEAYLRLVVKVTVRFRNYGFPLMDL 75

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
             EGNIGLMKA + F+  LG+  +TYA+WW+K AI   +      ++I      +  ++ 
Sbjct: 76  ASEGNIGLMKAIKNFNPTLGHGIATYAIWWIKAAINEYVIRSWSMVKIGTTAAQR--RLF 133

Query: 534 RTARRMSN--------KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
              R++ N        + +      EI       VE + ++L      +SL   +G++D+
Sbjct: 134 FNLRKLKNSGSVAGLDENQVVKRISEILAVSKNDVEEMERILNA--RDVSLNMQLGEDDS 191

Query: 586 SHLGDFI--EDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           S + D +   + N  + L    +  ++ +     + +L  R + +   R    +    TL
Sbjct: 192 SEVHDLVPFPEANQEAVLLETQERQMKSQLLYEAVEALEARHKEIFVARSLSAV--PRTL 249

Query: 643 EEVGKQFCVTRERIRQIEAKAIRK 666
           +E+G++F +++ER+RQI A+A++K
Sbjct: 250 KELGEKFSISQERVRQIHARAMKK 273


>gi|291196398|emb|CBG22671.1| DNA-directed RNA polymerase subunit D [Pseudomonas trivialis]
          Length = 238

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 49/284 (17%), Positives = 100/284 (35%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + E D E     S D+      P             D   
Sbjct: 50  GIAPPAAEVPPPVDPKAPKADDETDDEETEGSSDDEDEVESGP-------------DPVI 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  +S+ +       L +L
Sbjct: 97  AAQRFGAVSDQM------------EITRKALK---------KHGRSNKQAIAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 238


>gi|299535877|ref|ZP_07049197.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
 gi|298728629|gb|EFI69184.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
          Length = 257

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 125/250 (50%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E + +   ++      +  ++E+V  NLRLV+S+  ++  RG Q  DL Q G IGL
Sbjct: 18  LKHEEMKELFIRLQ---AGETEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +   
Sbjct: 75  MKAIDHFDLKHNVRFSTYAVPMIIGEIRRHLRDHH-ALRVSRSLRDIAYKAMQAKEQWIT 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
              REPT EEIA+ + M  E V   L   ++P+SL+ PI  +  D  ++ D + D + VS
Sbjct: 134 DNLREPTIEEIAEMIDMKKEDVLFALDAIQDPVSLQEPIYSDGGDAVYMMDQLRDDD-VS 192

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                   +++E+       L  R++ ++  RF  G     T  E+ K+  +++ +I ++
Sbjct: 193 EDQWVAYVSVKESLQ----KLDERQQMIVAKRFYYG----ETQTEIAKELGISQAQISRL 244

Query: 660 EAKAIRKLKH 669
           E  AI  ++ 
Sbjct: 245 EKNAIETMQK 254


>gi|240851254|ref|YP_002972657.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240268377|gb|ACS51965.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 303

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 114/246 (46%), Gaps = 13/246 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R  +     A  ++  A++RLVI++A ++    +   DL+QEG +GL++AA +F+    
Sbjct: 46  LRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDRE 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNK---IKREPT 548
            +FSTYA WW++ +I   I      +R       K     + R   ++      + ++  
Sbjct: 106 VRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLIQDDSALSKQDI 165

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNA-VSPLDSA 604
              IA+KL + V  V  +        +  +    E++ +     D + D +     L   
Sbjct: 166 FRTIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPIAKMDVLVDDSPLPDALIEQ 225

Query: 605 IQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +    R  +     L  L  RE  ++R  F        TLE +G++  +++ER+RQIEA+
Sbjct: 226 VIDGQRRTQWLYDALQILNERELEIIR--FRRLNEEGATLEVLGEKLGISKERVRQIEAR 283

Query: 663 AIRKLK 668
           A++KL+
Sbjct: 284 ALQKLR 289


>gi|282599758|ref|ZP_05971750.2| motility sigma factor FliA [Providencia rustigianii DSM 4541]
 gi|282567697|gb|EFB73232.1| motility sigma factor FliA [Providencia rustigianii DSM 4541]
          Length = 242

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 108/242 (44%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + E    L+   A K   R    +   DLIQ G IGL+ A E+FD  LG
Sbjct: 9   YTAEGVINKNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDASLG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +     +P  +R +  ++ +    +  K+ R  +  EIA
Sbjct: 69  ASFATYAVQRIRGSMLDELRSRDW---VPRSVRRQAREMTKAIGELEQKLGRSASEPEIA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + L + +   R+VL  T      S +        S      ED    +PL   ++++LR+
Sbjct: 126 QSLDIELSEYRQVLLDTNNSQLFSYDEWHEIHGESCEPSMDEDDGG-NPLSLLMESSLRD 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                +  L  RE  VL + +      +  L+E+G    V   R+ Q+ ++AI++L+   
Sbjct: 185 QIMGAIEQLPEREMLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSKL 240

Query: 672 RS 673
           +S
Sbjct: 241 KS 242


>gi|261407955|ref|YP_003244196.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|329929288|ref|ZP_08283041.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
 gi|261284418|gb|ACX66389.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|328936657|gb|EGG33100.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
          Length = 262

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 116/238 (48%), Gaps = 12/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             E     AKK+++E +L +V  V+ +      + +   DL   G +GL+ A EKFD+  
Sbjct: 18  WKEDGDHEAKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLASNGVMGLIDAIEKFDYKR 77

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA W V+ AI  S+        +P  +R+K  K+    +++  K  R  +  E+
Sbjct: 78  GLQFETYASWRVRGAILDSLRQGDW---VPRSVREKAKKIETAYQQLEQKYLRSVSDSEM 134

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +  L +  +  R +L+        SLE PI +E++      + D+ A +P     +  LR
Sbjct: 135 SDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNPDHKVHEFYLR 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   + +  LTP+E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 195 EALMKGIGKLTPKERTVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|226325489|ref|ZP_03801007.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
 gi|225206232|gb|EEG88586.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
          Length = 239

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 123/244 (50%), Gaps = 8/244 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++R+       A+ ++VE N  L+  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIRRAHEGDENARAQLVEENTGLIWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    +++   +++  +K  +    ++ K+ REP 
Sbjct: 63  DLGYDVKFSTYAVPMITGEIKRFLRD-DGMLKVSRSLKEIAYKAYQAKEALTEKLGREPL 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEIA++  +  E +   ++   E  SL  P+G +D + +      +       +  +  
Sbjct: 122 LEEIAEETGVEKEELVMAMEAAGEVESLHRPVGMKDGNEVMLL---EKIADTGGAEEKIL 178

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                T ++  L   E ++L +R+      D T  E+G++  +++ ++ ++E K ++ ++
Sbjct: 179 DHLLLTELIKELKKDERKLLYLRYFA----DKTQTEIGEELGISQVQVSRMEKKILKTMR 234

Query: 669 HPSR 672
             ++
Sbjct: 235 EHAK 238


>gi|253996640|ref|YP_003048704.1| flagellar biosynthesis sigma factor [Methylotenera mobilis JLW8]
 gi|253983319|gb|ACT48177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylotenera mobilis
           JLW8]
          Length = 244

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 46/209 (22%), Positives = 95/209 (45%), Gaps = 9/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DLIQ G +GL+ A  +++   G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VELDDLIQAGMMGLLDAVNRYEDTHGAQFETYAAQRIRGAMLDELRSSDW---LPRSIRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT 585
            +  V     ++  ++ + PT  ++AKKL M +    ++L      + I  E     +  
Sbjct: 94  NMRDVENAISQLEQQLGQSPTENDVAKKLNMSLAEYHEMLGDCSGHQLIYYEDFHEADSG 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            H  D  +  +   P+   +  + ++     + SL  RE+ +L    G+    +  L+E+
Sbjct: 154 EHFLDRFQTDHDNDPIKGLLIGDFKDALIGAIDSLPEREKILL----GLYYEQELNLKEI 209

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R K
Sbjct: 210 GAVMSVSESRVCQLHSQAVARLRANLREK 238


>gi|42524684|ref|NP_970064.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
 gi|39576894|emb|CAE78123.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
          Length = 373

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 131/264 (49%), Gaps = 6/264 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     ++  E   +    +  E +   A + +V+ANLR V+ VA +Y+  G 
Sbjct: 103 LVMYLNEIRRYKVLTREEEMALAK--KYFESKDPEAAQALVKANLRFVVKVAAEYSKFGS 160

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           + +DLIQEGN+GLM A  +F+   G +  TYA+WW++  I   +  Q   +RI      +
Sbjct: 161 KMIDLIQEGNVGLMHAVREFNPYKGARLITYAVWWIRGYIQEFLMRQYSMVRIGTTQNQR 220

Query: 529 IHKV-VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS 586
                ++  +   + +  EP    I+ +L +P + VR + ++++   +SL+ P+ DE  +
Sbjct: 221 KLFYQLQKEKEALDAMGIEPNIGLISSRLGIPEDEVRDMTMRMSGRDVSLDRPVDDESGT 280

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR--EERVLRMRFGIGMNTDHTLEE 644
            LGD     +     ++       E   + +  + P   E   + +   I  +   TL+E
Sbjct: 281 TLGDLQRGPSDQPLDEALAHNEQLEILKQKIEEIRPELSEREKIILDERILNDDPLTLQE 340

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G++  +TRE +RQ+EA+ ++K+K
Sbjct: 341 IGEKHGITREAVRQMEARLMKKIK 364



 Score = 44.8 bits (104), Expect = 0.043,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
           ++ E         D        +  L     S   ++ DP+ MYL E+   ++L+RE E+
Sbjct: 63  EEAEKAYAVPSVEDDLPDVEEDTKTLAVADTSKALTSADPLVMYLNEIRRYKVLTREEEM 122

Query: 141 AIAKR-IEAGRAMMMASLCESPLTF 164
           A+AK+  E+       +L ++ L F
Sbjct: 123 ALAKKYFESKDPEAAQALVKANLRF 147


>gi|328952031|ref|YP_004369365.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452355|gb|AEB08184.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
          Length = 328

 Score =  115 bits (287), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 63/276 (22%), Positives = 124/276 (44%), Gaps = 10/276 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  ++  +  I+    +   E + + ++    E     A   ++ +NLRLV+ +A  + 
Sbjct: 42  EVDALQRYMGEINRYPLLQPEEEKRLATL--YHETADQDAAYTLITSNLRLVVKIALDFQ 99

Query: 465 NRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-P 522
              +   LDLIQEGNIGLM+A +KFD   G K S YA +W+K  I + I D    ++I  
Sbjct: 100 KFWMRNLLDLIQEGNIGLMQAIKKFDPYRGIKLSYYASFWIKAYILKFIMDNWKLVKIGT 159

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIG 581
              + K+   ++  +        E  P+ I+ +L +    V ++  ++     SL+ P+ 
Sbjct: 160 TQAQRKLFFSLKKEKERLRAQGYEADPKLISTRLNVKEAEVIEMDQRLGSWEFSLDAPLK 219

Query: 582 DEDTSHLGDFIEDKNAVSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +      +F+      +        ++            +L   E  +L +   +    
Sbjct: 220 SDSEELHINFLTSGETAADEHLAREEMKDIFLMRLAEFRNTLKDNERDILDL--RLLAEH 277

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             TL+E+G +  ++RER+RQIE + ++KL+    ++
Sbjct: 278 PLTLQEIGARHNISRERVRQIEERLLKKLRQFMHNE 313


>gi|331696322|ref|YP_004332561.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951011|gb|AEA24708.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 283

 Score =  114 bits (286), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 106/246 (43%), Gaps = 15/246 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAA 485
            R + +         ++ + E++ A L +V  +A +++      + DL+Q G +GL+ A 
Sbjct: 42  MRELAATPPSDPRRDAL-RSELILAFLPIVRHLALRHSAGYPGGYDDLVQVGTVGLISAI 100

Query: 486 EKFDWCL-GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           +++D    G     Y +  V+  + R   D++  +R+P  ++D    + +    +S ++ 
Sbjct: 101 DRWDPDRAGADLLGYLVPCVRGEMLRYFRDRTWAVRVPRRLKDLAVAINKATGPLSQQLG 160

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPIS--LETPIGDEDTSHLGDFIEDKNAVSPLD 602
           R P P E+A  L + V  V + L       S  LE    +   S      E    +  + 
Sbjct: 161 RAPRPSELAAHLGVDVSEVVEALTAKAGHHSDPLEPVDPETGESSHERLGELDGELDHV- 219

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  R     +L SL  RE  +L +RF      D T  ++ ++  +++  + ++ A+
Sbjct: 220 -----EYRHALRPLLESLPERERTILMLRFF----RDMTQTQIAEEIGISQMHVSRLLAR 270

Query: 663 AIRKLK 668
           ++  L+
Sbjct: 271 SLTTLR 276


>gi|182440239|ref|YP_001827958.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178468755|dbj|BAG23275.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 264

 Score =  114 bits (286), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 100/228 (43%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + A L +   +A ++ +RG    DL Q   +GL+KA +++D   G  F +YA+  V
Sbjct: 38  RDETICAWLPMAHRIATRFRDRGEAMDDLRQVAAMGLVKAVDRYDPDRGKAFESYAVPTV 97

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREPTPEEIAKKLAMPVEGV 563
              + R   D +  + +P  ++D  ++V    R ++       PT  +IA    +  E V
Sbjct: 98  TGELKRHFRDHTWDVHVPRRVQDLRNRVRVARRELAQSSGGAAPTCADIASATGLGEEDV 157

Query: 564 RKVLKI--TKEPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              L+   +   +SL+  P G E  S L D +      S   +   A  RE     L  L
Sbjct: 158 LLGLEALESYSALSLDAGPAGVEGGSPLADRLG-----SCDGALDVAIDREAVKPGLRGL 212

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  +L +R+   M      E    Q  +++  + ++ +++  +++
Sbjct: 213 PERERTILYLRYFRDMTQSRIAE----QLGISQMHVSRLLSQSCERVR 256


>gi|116328490|ref|YP_798210.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116331220|ref|YP_800938.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116121234|gb|ABJ79277.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124909|gb|ABJ76180.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 266

 Score =  114 bits (286), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 107/241 (44%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +    +  +VE    LV  VA +      + ++F DL+  G  GL+ A EKFD   
Sbjct: 20  YRDTKDQDIRSYLVEKYSPLVKHVAGRIAIGMPQNVEFDDLVSYGVFGLLDAIEKFDPDR 79

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYAM  ++ +I   +        IP  +R K  ++ +    + NK  ++   + I
Sbjct: 80  LIKFKTYAMTRIRGSIFDELRSIDW---IPRSIRQKAKQLEQIIGMLENKEGQQVDDDAI 136

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQA 607
           AK+L + +E    +L        +SL        + D     + +E    ++P     + 
Sbjct: 137 AKELGISMEEYNSLLTKISGTSLVSLNDIWFLGDENDEVSFMETLESPMNMNPDTIIEKE 196

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            ++      + +L  +E++V+ + +      D TL+E+G+   VT  RI Q+  +A+ +L
Sbjct: 197 EIKNVIVEAIKTLPEKEKKVIVLYY----YEDLTLKEIGEVLEVTESRISQLHTRAVSRL 252

Query: 668 K 668
           +
Sbjct: 253 R 253


>gi|28211847|ref|NP_782791.1| sporulation sigma factor SigF [Clostridium tetani E88]
 gi|28204289|gb|AAO36728.1| RNA polymerase sigma-F factor [Clostridium tetani E88]
          Length = 255

 Score =  114 bits (286), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +     A  ++VE NL LV +++KK+ NRG  + D+ Q G +GL+KA   FD   
Sbjct: 22  LLEKAKNGDKKATDKLVELNLPLVSAISKKFLNRGYDYEDIYQIGCMGLVKAINNFDSSY 81

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R I D    I++   ++    K+      +  K+ REP+ EE+
Sbjct: 82  NVKFSTYAVPMIMGEIKRFIRD-DGIIKVSRSLKIMARKLYYHRETLCKKLGREPSIEEL 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           ++   + +E +   ++ +     L   I  +D + +   + DK + +  + +   N +  
Sbjct: 141 SEYTGLEIEEIVYAMESSSNLQYLHDVIHQDDGAPIM--LIDKISENYSEDSDIIN-KLA 197

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L  L  +  +++ +R+      D T  EV K   +++ ++ +IE + ++ +K 
Sbjct: 198 LKEALGKLDAKSRQIIMLRYF----KDKTQIEVAKMLGISQVQVSRIEKRVLKTMKE 250


>gi|182418318|ref|ZP_02949613.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237666658|ref|ZP_04526643.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|182377700|gb|EDT75244.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237657857|gb|EEP55412.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 243

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 115/235 (48%), Gaps = 13/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K++++E  + LV  +A +     N+ +++ DL+  G IGL+ A  KFD   G KFS+YA 
Sbjct: 11  KEQIIEEYIPLVKYIASRVMFAKNKYMEYEDLVSYGMIGLIDAINKFDNSKGMKFSSYAS 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K A+   +        I     DK+++  +    +  ++ REPT +EI+  L +   
Sbjct: 71  IRIKGAMIDELRK---NRPISKGAMDKLNRYNKAIEELQGRLLREPTTQEISNYLGISSS 127

Query: 562 GVRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE+ I  +D   +L   IEDKN+ SP          E  T+ + 
Sbjct: 128 EVAEIENYINYISMVSLESVIFSDDEDVNLMGVIEDKNSPSPHSYLEDKEKLEILTQAIE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  ++  +L + +  G     TL+E+GK   V+  R+ Q+ +++IR L+   + 
Sbjct: 188 LLKEKDRMILNLYYYEG----LTLKEIGKILEVSESRVCQLHSRSIRNLRECMKK 238


>gi|160946612|ref|ZP_02093815.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
 gi|158446996|gb|EDP23991.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
          Length = 254

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 121/251 (48%), Gaps = 17/251 (6%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + +       E      + +++E NL +   +AKKY NRG+ + DL Q  ++GL+ A
Sbjct: 11  EEIKSLFR--EYFENPTPELRDKLIEKNLYMAEILAKKYVNRGIDYDDLFQVASLGLIYA 68

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +++D   G++FS++AM  +   I R   D+   IR+P  +++   KV      ++ ++ 
Sbjct: 69  IDRYDISKGFEFSSFAMPTIVGEIKRYFRDKGWVIRVPRRIQENSKKVNNAKYHLTQELG 128

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKE------PISLETPIGDEDTSHLGDFIEDKNAV 598
           R PT ++IA  + +  E V ++++ +K         S E    ++  ++L D + +++  
Sbjct: 129 RTPTIKDIADYVELSEEEVLEIMEASKVYTPQSLDQSFENSDSEDKDTNLIDIVGEED-- 186

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                    + ++   + L  LT  E++++  R+        T   + K+  +++  + +
Sbjct: 187 ---KEFDFIDNQDFIRKTLDKLTEVEKQIILGRYF----EQKTQVALAKELNISQMTVSR 239

Query: 659 IEAKAIRKLKH 669
           +E KA+ K + 
Sbjct: 240 LEKKALAKFRE 250


>gi|255505890|ref|ZP_05348671.3| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
 gi|255265373|gb|EET58578.1| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
          Length = 238

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 125/248 (50%), Gaps = 12/248 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             H   ++ +       A++++VE NL LV ++AK++T RG    DL Q G+IGL+KA +
Sbjct: 1   MEHTHWLIERAHQGDKAAREQLVEENLGLVFTIAKRFTGRGTDVEDLFQIGSIGLLKAID 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F+     KFSTYA+  +   I R + D    +++   +++   +      ++  K+ RE
Sbjct: 61  NFNLSYDVKFSTYAVPMIAGEIRRFLRD-DGMLKVSRSLKETAGRAAAAREQLEKKLGRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSA 604
           PT EE++ ++ +  E +   ++   E  SL  P+   D +  +L D IE+K +++     
Sbjct: 120 PTMEELSGEVGITREEIVLAMEAAAEVESLHRPVYQGDGTAIYLEDRIEEKESMN----- 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +       T V+  L P E+ ++ MR+      D T  +V +    T+ ++ ++E K +
Sbjct: 175 EKVLDNMVLTEVMEKLEPEEQFLIIMRYF----KDKTQSQVAELLGRTQVQVSRMEKKIL 230

Query: 665 RKLKHPSR 672
           +K++   +
Sbjct: 231 KKMRDALQ 238


>gi|169827020|ref|YP_001697178.1| sporulation sigma factor SigG [Lysinibacillus sphaericus C3-41]
 gi|168991508|gb|ACA39048.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Lysinibacillus sphaericus C3-41]
          Length = 257

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 125/250 (50%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E + +   ++      +  ++E+V  NLRLV+S+  ++  RG Q  DL Q G IGL
Sbjct: 18  LKHEEMKELFIRLQ---AGETEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +   
Sbjct: 75  MKAIDHFDLKHNVRFSTYAVPMIIGEIRRHLRDHH-ALRVSRSLRDIAYKAMQAKEQWIT 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           +  REPT EEIA  + M  E V   L   ++P+SL+ PI  +  D  ++ D + D + VS
Sbjct: 134 ENLREPTIEEIADMIDMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLRDDD-VS 192

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                   +++E+       L  R++ ++  RF  G     T  E+ K+  +++ +I ++
Sbjct: 193 EDQWVAYVSVKESLQ----KLDERQQMIVAKRFYYG----ETQTEIAKELGISQAQISRL 244

Query: 660 EAKAIRKLKH 669
           E  AI  ++ 
Sbjct: 245 EKNAIETMQK 254


>gi|291196344|emb|CBG22644.1| DNA-directed RNA polymerase subunit D [Pseudomonas monteilii]
          Length = 238

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 93/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   D +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAP---- 54

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                              +E       AA   ++   + +      + +E     D   
Sbjct: 55  ------------------TEEVPIPGTKAAAAKEESDDEEEESEGGDDEEEAESGPDPVV 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ +Q                     LQ      +K+ ++  +     + L  L
Sbjct: 97  AAQRFGAVSEQ---------------------LQATTKVLKKNGRTHKESVEALQALADL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + ++LVE++ D   R+   E  +++L      + R  FL      E D  W
Sbjct: 136 FMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                      W   +  +  +I+  + ++  +  ETG++++E 
Sbjct: 196 SGDLAKRNTK-WAAALGEKDAAIVACQQKLIDLETETGLTVAEI 238


>gi|260461453|ref|ZP_05809700.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032523|gb|EEW33787.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 287

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 64/255 (25%), Positives = 118/255 (46%), Gaps = 10/255 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +  +    E     A   +  A++RLVIS+A K+ + GL   DLIQEG++GL
Sbjct: 20  LERDEEHRLALL--WKEDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLIQEGHVGL 77

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           ++AA +F+     +FSTYA WW++ ++   I      +R       K     + R   R+
Sbjct: 78  LEAAARFEPERDVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 540 SN---KIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDE-DTSHLGDFIED 594
           +N    +  E    E++  L +    V  +  +++    SL  P+ D+   +   DF+  
Sbjct: 138 ANGAEPLSNETLYREVSVALGVSEADVAMMDSRLSAPDSSLNVPLADDAGATERMDFLVS 197

Query: 595 KNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            + +     + + ++ R +     A        +  +      +   TLE +G+   +++
Sbjct: 198 DDPLPDEVVSDRIDVARRSVWLKAALAALNARELRIIEERRLSDEGATLEALGETLGISK 257

Query: 654 ERIRQIEAKAIRKLK 668
           ER+RQIEA+A+ KLK
Sbjct: 258 ERVRQIEARAMEKLK 272


>gi|153835421|ref|ZP_01988088.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156975413|ref|YP_001446320.1| flagellar biosynthesis sigma factor [Vibrio harveyi ATCC BAA-1116]
 gi|148868042|gb|EDL67225.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156527007|gb|ABU72093.1| hypothetical protein VIBHAR_03144 [Vibrio harveyi ATCC BAA-1116]
          Length = 244

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 101/244 (41%), Gaps = 15/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKAITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++ +    +   + R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDIRKGDW---VPRSVHKNNREINQAIAELEGVLNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           P+  E+A  L M ++     L        + +E     +D     D  +D N   P    
Sbjct: 118 PSDSEVAAHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSN---PFKGV 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + ++     +  L  RE  VL + +    + +  L+E+G    V+  R+ QI ++A+
Sbjct: 175 ADESFKKALVESIKQLPEREALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQAM 230

Query: 665 RKLK 668
           ++L+
Sbjct: 231 QRLR 234


>gi|304404273|ref|ZP_07385935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347251|gb|EFM13083.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 262

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 114/255 (44%), Gaps = 12/255 (4%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQ 475
            T        +I    +    +   AKK+++E  L LV  V  +      + +   DL  
Sbjct: 1   MTEPKTPHLSNIEKWRKWKTEKDIEAKKQLIEQYLPLVDYVTSRMAIGLPKTVSKDDLYS 60

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G +GL+ A EKFD+  G +F TYA W ++  I   +        +P  +RDK  ++   
Sbjct: 61  NGVMGLIDAIEKFDYERGLQFETYASWRIRGGIIDGLRQGDW---VPRSVRDKAKRIEEA 117

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIE 593
            + +  K  R  T  EI+  L +  +    +L+        SLE PI +E++      + 
Sbjct: 118 YQLLEQKYLRSVTDAEISDYLNVSEKEFTGILQEIAVTTICSLEDPIREEESETRLSLLV 177

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D+ A +P     +  L+E+  + +  LT +E  V+ + +      + +L E+ +   ++ 
Sbjct: 178 DEKAKNPDYKVHEFYLKESLVKGIERLTEKERTVVSLFY----YEELSLSEIAEVMSLSP 233

Query: 654 ERIRQIEAKAIRKLK 668
            RI Q+ +KAI +L+
Sbjct: 234 SRISQLHSKAILRLR 248


>gi|297582861|ref|YP_003698641.1| LuxR family transcriptional regulator [Bacillus selenitireducens
           MLS10]
 gi|297141318|gb|ADH98075.1| transcriptional regulator, LuxR family [Bacillus selenitireducens
           MLS10]
          Length = 268

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 121/255 (47%), Gaps = 8/255 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R +  +    E      + ++V     LV ++A+K++       DL+Q G IGL+ A  
Sbjct: 20  ERQLKMIAEFQETGDDEIQTQLVLEYENLVHALARKFSRGQRHDEDLVQVGMIGLLAALR 79

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F ++A+  +   I R I D++ ++ +P  +++   K+      ++ +++R 
Sbjct: 80  RFDPSFGRSFESFAVPTIVGEIKRFIRDKTWSVHVPRRIKELGPKIKSAVENLTTELQRS 139

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           P  EEIA  L +  E + + +++  + + +S++  I  +D       ++   +V      
Sbjct: 140 PQVEEIADYLEVSEEEILETMEMGKSYQALSVDRSIEADDEGSAVTLLDLVGSVESGYEQ 199

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L     +    LT RE+++L++ +        + +E G+Q  +++  + +++ +A+
Sbjct: 200 TDQQL--LLEKAFQVLTDREKQILQLTYFEN----MSQKETGEQLGISQMHVSRLQRRAL 253

Query: 665 RKLKHPSRSKKLRSF 679
           +KLK   R +   +F
Sbjct: 254 QKLKDSIRIEATEAF 268


>gi|301165903|emb|CBW25476.1| RNA polymerase sigma factor WhiG [Bacteriovorax marinus SJ]
          Length = 260

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 107/247 (43%), Gaps = 13/247 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKA 484
           + + ++           K E++     L+  +A++  +R    ++  DLI  G IGLM A
Sbjct: 6   KKLKNLKDYRSTVDPKVKDEIIIEYAPLIKYIAQRIASRLPSNVELDDLISCGVIGLMDA 65

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD     KF TYA + ++ +I   +  Q     +P  +R+K   V R   ++     
Sbjct: 66  IEKFDPSRDNKFKTYAEFRIRGSILDELRAQDW---VPRSVREKAKLVERAYAKIEAAEG 122

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISL---ETPIGDEDTSHLGDFIEDKNAVSPL 601
           R  T EE+  +L +  E    +L   K    L   ++   ++    L   +ED    +P 
Sbjct: 123 RPATDEEMCAELGVNQEEFYDLLNKAKSVSVLNIDDSASFNKGDKKLIAGLEDNRNSNPF 182

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +      R+     +A L  ++  VL + +      D  L+E+G+   VT  R+ Q+  
Sbjct: 183 HAVANKGSRDKIKEGIAQLPEKQRLVLSLYY----YEDLNLKEIGQVLNVTESRVSQLHT 238

Query: 662 KAIRKLK 668
           +AI KLK
Sbjct: 239 QAIMKLK 245


>gi|297194001|ref|ZP_06911399.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152057|gb|EFH31507.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 305

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 117/239 (48%), Gaps = 13/239 (5%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +S + F  + S+  +G  E +  +  +VE NL LV   A ++  R     D+IQ G IG
Sbjct: 58  ELSKTLFARLASL-EEGTHEYAYVRNTLVELNLALVKFAASRFRTRSEPMEDIIQVGTIG 116

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA ++F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    +S
Sbjct: 117 LIKAIDRFELSRGVEFPTFAMPTIIGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELS 176

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNA 597
            ++ R PT +E+A++L +  + V + +         SL+    ++D    L + I  ++ 
Sbjct: 177 QQLDRAPTVDELAQRLDIGRDEVVEGMAASNAYTASSLDAQPEEDDSEGALANRIGYEDH 236

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  I     E+   ++ASL PR+ ++L +RF        T  E+G++  +++  +
Sbjct: 237 GLEGIEYI-----ESLRPMIASLPPRDRKILSLRFVAN----MTQSEIGEELGISQMHV 286


>gi|3249723|gb|AAC26664.1| RNA polymerase sigma-like factor [Micromonospora olivasterospora]
          Length = 162

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 80/162 (49%), Positives = 113/162 (69%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R     + REPTPEE+AK++ +
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQREFFQDLGREPTPEELAKEMDI 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   + L++   +VL 
Sbjct: 61  TPEKVLEIQQYAREPISLDQTIGDEGDSSLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQ 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE
Sbjct: 121 TLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIE 162


>gi|320107038|ref|YP_004182628.1| RNA polymerase sigma 28 subunit FliA/WhiG [Terriglobus saanensis
           SP1PR4]
 gi|319925559|gb|ADV82634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Terriglobus saanensis
           SP1PR4]
          Length = 294

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 101/229 (44%), Gaps = 12/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + +++  +   V  VA++   R    ++  DLI  G IGL+ A  KFD     +F +YA 
Sbjct: 59  RDQLLVEHFPTVRYVARRIHERLPQHMELDDLIAAGMIGLIDAFSKFDHSKKVQFKSYAQ 118

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + ++ AI  S+         P  +R K   V    R ++ +    P  +EIA+++ + + 
Sbjct: 119 FRIRGAILDSLRTLDW---SPRELRRKGRAVEEAIRAVTQRFGCVPAEQEIAREMNLSLS 175

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             + +L   K  E  SL    G++       ++       PL   ++  L++     +  
Sbjct: 176 EYQGLLGELKGLEIGSLHAERGEDSGEEELAYVPGSPEDGPLFRCLKGELKQHLMEAIDD 235

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  VL + +      + T++EVG    V   R+ QI + A+ +L+
Sbjct: 236 LPERERMVLTLYY----YEELTMKEVGLTLGVVESRVSQIHSSAVARLR 280


>gi|307330561|ref|ZP_07609702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883810|gb|EFN14855.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 315

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 111/233 (47%), Gaps = 12/233 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               + ++ +G  E +  +  +VE NL LV   A ++ +R     D++Q G IGL+KA +
Sbjct: 73  LFERLEVLEEGTHEYAYVRNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAID 132

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +F+   G +F T+AM  +   I R   D S ++R+P  +++    + +    ++ ++ R 
Sbjct: 133 RFETGRGVEFPTFAMPTIVGEIKRFFRDTSWSVRVPRRLQELRLDLAKAGDELAQRLDRA 192

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
           PT  E+A++L +    V + +         SL+    ++D    L D I  ++       
Sbjct: 193 PTVSELAQRLDISQSEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGIE 252

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            +     E+   ++A L+ R+ ++L +RF        T  E+G++  +++  +
Sbjct: 253 YV-----ESLKPLIADLSARDRKILSLRFVAN----MTQSEIGEELGISQMHV 296


>gi|6010720|gb|AAF01226.1|AF184095_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 254

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 68/175 (38%), Positives = 115/175 (65%), Gaps = 3/175 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++T  
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTRW 226



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|323487067|ref|ZP_08092375.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694575|ref|ZP_08108741.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399568|gb|EGA91958.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501343|gb|EGB17239.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 237

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 118/241 (48%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++         A++ +V  N+ LV S+ +++T RG +  DL Q G+IGL+KA +KF
Sbjct: 3   ETMKLIEMAHSGDKAARERLVMDNVGLVWSIVRRFTGRGCETEDLFQIGSIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +FSTYA+  +   I R + D    I++   +++   KV      +S  + REPT
Sbjct: 63  DTSYDVRFSTYAVPMITGEIKRFLRD-DGMIKVSRSIKELGFKVSAVRESLSGSLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEI++ L +  E V   L+   +  SL  P G  + + L   + DK A    ++ +  +
Sbjct: 122 LEEISEALEVSKEEVAASLEAGCQVESLYAPSGSGEDNTLS--LIDKVAEEKEENEMLLD 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R     +L SL  ++  ++  R+           ++ +   +++ ++ ++E K +R+++
Sbjct: 180 -RMVLGELLKSLEKKQREIIVRRYFYNQTQ----TQIAEILGISQVQVSRMERKILREMR 234

Query: 669 H 669
            
Sbjct: 235 E 235


>gi|319893019|ref|YP_004149894.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162715|gb|ADV06258.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 256

 Score =  114 bits (286), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 116/246 (47%), Gaps = 5/246 (2%)

Query: 429 HIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   ++     E   A++++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIQAYQNDEDHEAQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N++ R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELGRSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +  EIA++L +  E V + +++ +   +L      E                  D+    
Sbjct: 135 SISEIAERLEVSDEDVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQHDDNYELT 194

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    R+L  LT RE  +++  F  G     + +E G++  +++  + +++  AI+KL
Sbjct: 195 EKRMILERILPILTDREREIIQCTFIDG----LSQKETGERIGLSQMHVSRLQRTAIKKL 250

Query: 668 KHPSRS 673
           +  +R 
Sbjct: 251 QEAARK 256


>gi|188025882|ref|ZP_02960155.2| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
 gi|188020848|gb|EDU58888.1| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
          Length = 246

 Score =  114 bits (285), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 106/242 (43%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + E    L+   A K   R    +   DLIQ G IGL+ A E+FD   G
Sbjct: 9   YTAEGVINKNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDASQG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R +  ++ +    +   + R  T  EIA
Sbjct: 69  ASFATYAVQRIRGSMLDELRSRDW---APRSVRRQAREMAKVIGELEQSLSRSATESEIA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           + L + V   R+ L  T      S +        S     I++ +  +PL   +++NLR 
Sbjct: 126 QALNIDVTEYRQALLDTNNSQLYSYDEWHEIHGES-CEPAIDESDGGNPLSLLMESNLRA 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+   
Sbjct: 185 QIIEAIEQLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRGRL 240

Query: 672 RS 673
           +S
Sbjct: 241 KS 242


>gi|224477054|ref|YP_002634660.1| RNA polymerase sigma factor SigB [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421661|emb|CAL28475.1| sigma factor B [Staphylococcus carnosus subsp. carnosus TM300]
          Length = 256

 Score =  114 bits (285), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 124/248 (50%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +R+ + +  + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINEWIRQHQNDENTDAQDKLVKHYQKLIESLAFKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G KF  + +  V   I R + D++ ++ +P  +++   ++ +T   ++N+++R P
Sbjct: 75  FDINFGRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKTTDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAERLEVTDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGEQEGGYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  LT RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILTDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRNAIK 248

Query: 666 KLKHPSRS 673
           KL+  ++ 
Sbjct: 249 KLQQAAKK 256


>gi|318060086|ref|ZP_07978809.1| sigma factor [Streptomyces sp. SA3_actG]
 gi|318076269|ref|ZP_07983601.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 286

 Score =  114 bits (285), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 56/272 (20%), Positives = 128/272 (47%), Gaps = 14/272 (5%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I+    ++  + R +  +       + +G  E   A+  ++E N+ LV   A+++ +
Sbjct: 20  LPEIAEPHKVAPRDARELTRLFFDRLDTLEEGTREFQDARNTLIEMNMSLVRFAARRFRS 79

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    D++Q G IGL+KA ++F+     +F+T+A+ ++   I R   D +  + +P  +
Sbjct: 80  RGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAVPYIVGEIKRFFRDTTWAVHVPRRL 139

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDE 583
           ++   ++ +    +S ++ R P   E+A  +++  + V +           SL+  IG E
Sbjct: 140 QEARVELAKANEELSTRLGRAPKVSELAALMSLSEQQVVEAQIAANGYSSSSLDATIGGE 199

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D+      + D          +  +L      +LA L PR+ ++L +RFG     + T  
Sbjct: 200 DSGEGEAALSDFIGAEDPGMELVEDLH-ALAPLLAGLEPRDRQILELRFG----QELTQA 254

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++G++  V++  + ++  + +  L+    S++
Sbjct: 255 QIGERLGVSQMHVSRLLNRTLGTLRAGLMSER 286


>gi|300722632|ref|YP_003711922.1| sigma F (sigma 28) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297629139|emb|CBJ89735.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           nematophila ATCC 19061]
          Length = 240

 Score =  114 bits (285), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E+FD   G
Sbjct: 5   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDSMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +T R++  ++ R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVTQTIRKLEQELGRPASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           K+L + +   R++L  T            E         IE+++  +PL   ++ +LR+ 
Sbjct: 122 KELKINLIEYRQILLDTNNSQLFSYDEWHEIHGESCEPVIEEEHETNPLQQLLEGDLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++ SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VINIIESLPEREKMVLTLYY----QEELNLKEIGAVLNVGESRVSQLHSQAIKRLR 233


>gi|317129180|ref|YP_004095462.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
 gi|315474128|gb|ADU30731.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
          Length = 254

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 109/246 (44%), Gaps = 13/246 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E    +A   +V+A L LV    ++      R +Q  DL   G +GL  A EKFD  
Sbjct: 16  RWSEDRDEVACDRLVQAYLPLVDYHVQRIGANLPRNVQLDDLRSNGMLGLYDALEKFDEK 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +        +P  +R+K  K+ +   ++  +  R   P+E
Sbjct: 76  RELKFDTYASFRIRGAIIDGLRQMDW---LPRSVREKTKKIDQATEKLEQQYGRYVNPKE 132

Query: 552 IAKKLAMPVEGVRKVLKITK--EPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQAN 608
           +A  L M  E V K +  +     +S++ P  D E        I D+  ++P     +  
Sbjct: 133 VADYLGMNEEDVYKTINESYLAHQLSIDEPAQDSEKEDSFTATIMDEKTLTPEQHIDKKG 192

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             E    ++ +   +E+ ++ + +      + TL E+G+   V+  R+ QI +K I KL+
Sbjct: 193 QMEELAEIIKTFNEKEQLIISLFYF----EELTLTEIGEILNVSTSRVSQIHSKTIFKLQ 248

Query: 669 HPSRSK 674
               SK
Sbjct: 249 QKLLSK 254


>gi|162449128|ref|YP_001611495.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159710|emb|CAN91015.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 275

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 66/257 (25%), Positives = 126/257 (49%), Gaps = 15/257 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            ++    +S    R +    R        A + ++EA L  V+++A +Y   GL   D++
Sbjct: 16  ELANYATLSPEAERELALRWR---AGDRDAGRRLIEACLPFVMTIALEYRRWGLPMEDIV 72

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEGNIGL+KAAE+FD   G + +TYA +W++  I   +A     +R+     ++  + +R
Sbjct: 73  QEGNIGLLKAAERFDPDRGCRLATYAAYWIRAEIREHVARGYRIVRLGSSKSER--RALR 130

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-EPISLETPIGDEDTSHLGDFIE 593
             R+       E  P  +A+   +  E   ++L +     +SLE    ++  + +     
Sbjct: 131 IYRK-----THEKDPAVLAELSGLSEERAAELLPLLMARDVSLERSPTEDGIAPVERLAS 185

Query: 594 DKNAVSPL--DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             +       D+  +A L     +V+  L+PRE  ++  R+    ++  TLE++G  F V
Sbjct: 186 SAHTPEDEACDADERAQLSRALLQVVNELSPRERSIMNQRWL--TDSPVTLEQLGADFGV 243

Query: 652 TRERIRQIEAKAIRKLK 668
           ++ER+RQIE +A ++++
Sbjct: 244 SKERVRQIEERAKKRMR 260


>gi|311030102|ref|ZP_07708192.1| RNA polymerase sigma factor SigD [Bacillus sp. m3-13]
          Length = 254

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 111/241 (46%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDWC 491
               +   A   +V+  + LV    ++ +  GL       +L     +GL  A EKFD  
Sbjct: 16  WKTKKDPDAGDFLVKKYMPLVHYHVQRIS-TGLPKSVKREELKSLAFVGLFDAIEKFDPS 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ +I   +  +     +P  +R+K  ++  T   +  K+ R  T EE
Sbjct: 75  RDLKFDTYASFRIRGSIIDGLRKEDW---LPRSVREKAKRIESTLENLEQKLMRNATLEE 131

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQAN 608
           +A  L MP E V  V+        +S++    + D  SH    ++D+  +SP +  I++ 
Sbjct: 132 VAAHLDMPEEEVSTVMHEVFYSNILSMDEMPKENDEQSHGAYVLKDEKVISPEEELIKSE 191

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +     + +LT  E+ V+ + +      + TL E+G+   +T  RI QI +KAI KL+
Sbjct: 192 LIQLLGEQIENLTENEQIVISLFY----KEELTLTEIGQVLGLTTSRISQIHSKAIFKLR 247

Query: 669 H 669
            
Sbjct: 248 K 248


>gi|15639696|ref|NP_219146.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025934|ref|YP_001933706.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum SS14]
 gi|3323011|gb|AAC65675.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018509|gb|ACD71127.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 262

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 104/244 (42%), Gaps = 15/244 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFD 489
            +      ++  ++  V     LV  VA K        ++F DL+  G  GL  A +K+D
Sbjct: 15  WLEYRRTRSAKIREYFVVQYAPLVKYVASKIAVGKPGNVEFDDLVSYGIFGLFDAIDKYD 74

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+TYA+  ++ AI   +        +P  +R +  ++      +  ++ R  T 
Sbjct: 75  PEKNIRFNTYAVTRIRGAIFDELRSIDW---VPRSVRQQTRQIEEAIADLEARLGRXATD 131

Query: 550 EEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSA 604
            EIA  L + +E   ++L        ISL       D      +GD IE   +++P    
Sbjct: 132 TEIACALNIELEEYHQLLLKVSGTSVISLADSKFGGDERDHVSVGDSIEAPASLNPDVIV 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  ++      +  L+ RE++VL + +      + TL+E+GK   VT  RI QI   A 
Sbjct: 192 EREEIKRIIAEAIRELSQREQQVLILYY----YEEMTLKEIGKVLKVTESRISQIHTSAN 247

Query: 665 RKLK 668
            KLK
Sbjct: 248 LKLK 251


>gi|16078710|ref|NP_389529.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309525|ref|ZP_03591372.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313849|ref|ZP_03595654.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318772|ref|ZP_03600066.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323044|ref|ZP_03604338.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|296330862|ref|ZP_06873337.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674380|ref|YP_003866052.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315414|ref|YP_004207701.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
 gi|1350863|sp|P10726|RPSD_BACSU RecName: Full=RNA polymerase sigma-D factor; AltName: Full=Sigma-28
 gi|289304|gb|AAA61470.1| sigma factor 28 [Bacillus subtilis]
 gi|2634019|emb|CAB13520.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291484202|dbj|BAI85277.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151867|gb|EFG92741.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412624|gb|ADM37743.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021688|gb|ADV96674.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
          Length = 254

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 110/241 (45%), Gaps = 13/241 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E +   A  +++   + LV     + +    + +   DL+  G +GL  A EKFD  
Sbjct: 14  RWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDALEKFDPS 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +  +     +P   R+K  KV     ++  +  R  +P E
Sbjct: 74  RDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKKVEAAIEKLEQRYLRNVSPAE 130

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           IA++L M V+ V   +        +S++  +   +D  ++   I D   V P +  ++  
Sbjct: 131 IAEELGMTVQDVVSTMNEGFFANLLSIDEKLHDQDDGENIQVMIRDDKNVPPEEKIMKDE 190

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L       +  L+ +E+ V+ + +      + TL E+G+   ++  RI QI +KA+ KLK
Sbjct: 191 LIAQLAEKIHELSEKEQLVVSLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246

Query: 669 H 669
           +
Sbjct: 247 N 247


>gi|293366035|ref|ZP_06612723.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|291319758|gb|EFE60116.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
          Length = 256

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 123/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V+   +L+ S+A +Y+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEVFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQEAAR 255


>gi|323463926|gb|ADX76079.1| RNA polymerase sigma-B factor [Staphylococcus pseudintermedius
           ED99]
          Length = 256

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 115/246 (46%), Gaps = 5/246 (2%)

Query: 429 HIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   ++     E   A++++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIQAYQNDEDHEAQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N++ R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELGRSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           +  EIA +L +  E V + +++ +   +L      E                  D+    
Sbjct: 135 SISEIADRLEVSDEDVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQHDDNYELT 194

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    R+L  LT RE  +++  F  G     + +E G++  +++  + +++  AI+KL
Sbjct: 195 EKRMILERILPILTDREREIIQCTFIDG----LSQKETGERIGLSQMHVSRLQRTAIKKL 250

Query: 668 KHPSRS 673
           +  +R 
Sbjct: 251 QEAARK 256


>gi|319399556|gb|EFV87811.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis FRI909]
          Length = 256

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 124/247 (50%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S+A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQEAAR 255


>gi|311068169|ref|YP_003973092.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
 gi|310868686|gb|ADP32161.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
          Length = 254

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 109/241 (45%), Gaps = 13/241 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E +   A  +++   + LV     + +    + +   DL+  G +GL  A EKFD  
Sbjct: 14  RWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDALEKFDPS 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +  +     +P   R+K  KV     ++  +  R  +P E
Sbjct: 74  RDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKKVEAAIEKLEQRYLRNVSPAE 130

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           IA++L M  + V   +        +S++  +   +D  ++   I D   V P +  ++  
Sbjct: 131 IAEELGMTEQDVVSTMNEGFFANLLSIDEKLHDQDDGENIQVMIRDDKNVPPEEKIMKDE 190

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L       +  L+ +E+ V+ + +      + TL E+G+   ++  RI QI +KA+ KLK
Sbjct: 191 LIAQLAEKIHELSEKEQLVVSLFY----KEELTLTEIGQVLSLSTSRISQIHSKALFKLK 246

Query: 669 H 669
           H
Sbjct: 247 H 247


>gi|239826640|ref|YP_002949264.1| RNA polymerase sigma factor SigD [Geobacillus sp. WCH70]
 gi|239806933|gb|ACS23998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp. WCH70]
          Length = 254

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 106/250 (42%), Gaps = 15/250 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLM 482
           E R      R        A  ++V+  + LV    ++      + +   +LI  G +GL 
Sbjct: 8   EERKYWD--RWIYHRDPQAGDKLVQTYMPLVHYHVQRIAASLPKTISKQELISLGLMGLY 65

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A EKFD     KF TYA + ++ AI   +  +     +P  +R+K  K+  T  ++  +
Sbjct: 66  DALEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDW---LPRSVREKAKKIEETIEKLEQR 122

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF---IEDKNAVS 599
             R  T +E+A +L +  E V   +        L       +     +    I D+   S
Sbjct: 123 YMRSVTAKEVADELGITEEEVYMAVNENFFANVLSFQHVITENKEEENALLAIRDEKTPS 182

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +  ++  L E    V+  L+ +E+ V+ + +      + T  E+G+   ++  RI Q+
Sbjct: 183 PEEEVLKQELYEKLAEVIQQLSEKEQLVISLFY----KEELTFTEIGEILGLSTSRISQL 238

Query: 660 EAKAIRKLKH 669
            +KAI KL+ 
Sbjct: 239 HSKAIFKLRK 248


>gi|187926255|ref|YP_001892600.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12J]
 gi|241665743|ref|YP_002984102.1| flagellar biosynthesis sigma factor [Ralstonia pickettii 12D]
 gi|309778948|ref|ZP_07673718.1| RNA polymerase sigma factor for flagellar operon [Ralstonia sp.
           5_7_47FAA]
 gi|187728009|gb|ACD29173.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12J]
 gi|240867770|gb|ACS65430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12D]
 gi|308922295|gb|EFP67922.1| RNA polymerase sigma factor for flagellar operon [Ralstonia sp.
           5_7_47FAA]
          Length = 253

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 103/245 (42%), Gaps = 11/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +          K + +     LV  +A +   +    ++  DLIQ G +GL+ A  +++ 
Sbjct: 9   MDMYTATGRKTKSDEMATYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEE 68

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  
Sbjct: 69  TQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTET 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA  L M +   +K L   +    L       ED     +    +N  +PLD  +  +L
Sbjct: 126 EIAVALGMSLAEYQKQLVDLQGSQLLYYEDFDREDADAFIENRAPENDATPLDQLLDHDL 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+    +  L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++ 
Sbjct: 186 RESVVAAIEGLPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRS 241

Query: 670 PSRSK 674
             R +
Sbjct: 242 RLRDR 246


>gi|300854227|ref|YP_003779211.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
 gi|300434342|gb|ADK14109.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
          Length = 241

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 112/233 (48%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  L LV  +A +      + +++ DL+  G +GL+ A  KFD   G KFSTYA 
Sbjct: 10  KEELVKKYLPLVKYIASRVIIGKTKYIEYEDLVSYGMLGLIDAINKFDKDRGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK++K       +  K+ REP+ EEIA +L MP++
Sbjct: 70  IRIKGSMIDELR---RNSPISKGAMDKLNKYNAAMDSLRTKLGREPSSEEIANELGMPLK 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++         +SLE  I  ++D   L   +ED  + SP  S  +  + E   + L 
Sbjct: 127 KMMEIENYINYISIVSLEDLIFSEDDDIPLMGTVEDTKSPSPEKSLEKKEMLEYLAKALD 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  V+ + +        TL+E+G    V+  R+ Q+ ++AI  L+   
Sbjct: 187 LLNEKDNLVITLYY----YEKLTLKEIGHILNVSESRVCQLHSRAILHLRKNM 235


>gi|291060074|gb|ADD72809.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 262

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 104/244 (42%), Gaps = 15/244 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFD 489
            +      ++  ++  V     LV  VA K        ++F DL+  G  GL  A +K+D
Sbjct: 15  WLEYRRTRSAKIREYFVVQYAPLVKYVASKIAVGKPGNVEFDDLVSYGIFGLFDAIDKYD 74

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                +F+TYA+  ++ AI   +        +P  +R +  ++      +  ++ R  T 
Sbjct: 75  PEKNIRFNTYAVTRIRGAIFDELRSIDW---VPRSVRQQTRQIEEAIADLEARLGRAATD 131

Query: 550 EEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSA 604
            EIA  L + +E   ++L        ISL       D      +GD IE   +++P    
Sbjct: 132 TEIACALNIELEEYHQLLLKVSGTSVISLADSKFGGDERDHVSVGDSIEAPASLNPDVIV 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  ++      +  L+ RE++VL + +      + TL+E+GK   VT  RI QI   A 
Sbjct: 192 EREEIKRIIAEAIRELSQREQQVLILYY----YEEMTLKEIGKVLKVTESRISQIHTSAN 247

Query: 665 RKLK 668
            KLK
Sbjct: 248 LKLK 251


>gi|116749546|ref|YP_846233.1| sigma-70 region 2 domain-containing protein [Syntrophobacter
           fumaroxidans MPOB]
 gi|116698610|gb|ABK17798.1| sigma-70 region 2 domain protein [Syntrophobacter fumaroxidans
           MPOB]
          Length = 326

 Score =  114 bits (285), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 71/263 (26%), Positives = 127/263 (48%), Gaps = 10/263 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-F 470
            +  I     +S  E   +   +R  E     A  +++ ANLRLV+ +A  +    +Q  
Sbjct: 48  YLDEIKRYPLLSREEETDLA--IRYREKGDIEAGYKLITANLRLVVKIAMDFQRYWMQNL 105

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKI 529
           +DLIQEGN+GLM+A +KFD   GYKFS YA +W+K  I + I D    ++I     + K+
Sbjct: 106 MDLIQEGNVGLMQAVKKFDPYRGYKFSYYASFWIKAYIIKFIMDNWKLVKIGTTQAQRKL 165

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHL 588
              +R  +        E +P+ ++ +L +    + ++  ++    ISL++P+ ++     
Sbjct: 166 FFNLRKEKERLEAQGIEASPKLLSHRLDVKESEIIEMDQRLNSWEISLDSPLKEDSEDTH 225

Query: 589 GDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             F+   +        D   +A L +        L  +E   +     +      TL+E+
Sbjct: 226 KSFLPSDDLPVDDQIADREAKAILHDKLLLFREQLKGKEA--VIFDKRLLTEEPMTLQEI 283

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G +F ++RER+RQIE++  +KLK
Sbjct: 284 GDRFGISRERVRQIESRLKKKLK 306



 Score = 44.8 bits (104), Expect = 0.050,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 30/83 (36%), Gaps = 1/83 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI-E 147
           S D  D   +   S        +     + DP R+YL E+    LLSRE E  +A R  E
Sbjct: 13  SPDRGDPHEAGEESRSGSTFPAERPQAVSFDPFRIYLDEIKRYPLLSREEETDLAIRYRE 72

Query: 148 AGRAMMMASLCESPLTFQALIIW 170
            G       L  + L     I  
Sbjct: 73  KGDIEAGYKLITANLRLVVKIAM 95


>gi|325288800|ref|YP_004264981.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964201|gb|ADY54980.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 254

 Score =  114 bits (285), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 107/257 (41%), Gaps = 19/257 (7%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-------GLQFLDLIQEGNIGLMK 483
           +  +       ++A+  + E  +   + + K+   R        ++  DLI  G  GL+ 
Sbjct: 1   MKKIMYNNQYHAMARGNLSEEYIDQYLPLVKRLAGRLAMSLPSHIEEEDLIGYGVFGLID 60

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +K++   G KF TYA   ++ A+   +             R K+ KV +    + N  
Sbjct: 61  ALQKYEPSRGVKFETYASLRIRGAMIDGLRSMDWVPH---SARQKVKKVRQAYIDLENLQ 117

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLE---TPIGDEDTSHLGDFIEDKNAV 598
            R P+ EE+A  L + +E +   L   +    +S++        +      D I D  A 
Sbjct: 118 GRTPSIEEVAGFLEIQLEELHTTLLHGQYMTLVSMDQLLDGHSGDSGISPVDLIIDAEAQ 177

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              ++  +   ++   R +  L+ +E+ V+ M +      + TL+E+     ++  RI Q
Sbjct: 178 ESFNNIEKEEQKQILAREIEKLSEKEKLVIAMYYR----EEMTLKEIAAVMNLSESRISQ 233

Query: 659 IEAKAIRKLKHPSRSKK 675
           I ++AI +L+     +K
Sbjct: 234 IHSQAILRLRGYLGRQK 250


>gi|299822364|ref|ZP_07054250.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
 gi|299815893|gb|EFI83131.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
          Length = 259

 Score =  114 bits (285), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 109/241 (45%), Gaps = 4/241 (1%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             E     A+  +V     LV S+A+KY+       DL+Q G IGL+ A +++D   G  
Sbjct: 22  YQETADDDAQTNLVLHYHNLVESIARKYSQGKSFHEDLVQVGVIGLLGAIKRYDPDFGKS 81

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA  
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIANF 141

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +    E + + +++ K   +L      E  S               +   Q N R    +
Sbjct: 142 IGATEEEILEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGVDEGFEQVNQRMILEK 201

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  L  RE+++L+  F        + +E G+   +++  + +++ +AI+KL+    +++
Sbjct: 202 ILPVLDEREQKILQYTFIEN----RSQKETGELLDISQMHVSRVQRQAIKKLREALLNEE 257

Query: 676 L 676
           +
Sbjct: 258 V 258


>gi|27468586|ref|NP_765223.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis ATCC
           12228]
 gi|57867587|ref|YP_189242.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis RP62A]
 gi|251812213|ref|ZP_04826686.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876523|ref|ZP_06285389.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|27316133|gb|AAO05267.1|AE016749_213 sigma factor B [Staphylococcus epidermidis ATCC 12228]
 gi|57638245|gb|AAW55033.1| RNA polymerase sigma-37 factor [Staphylococcus epidermidis RP62A]
 gi|251804310|gb|EES56967.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281294775|gb|EFA87303.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|329726159|gb|EGG62631.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU144]
 gi|329734176|gb|EGG70494.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU045]
          Length = 256

 Score =  114 bits (285), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 123/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V+   +L+ S+A +Y+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQEAAR 255


>gi|332981462|ref|YP_004462903.1| RNA polymerase sigma-28 subunit FliA/WhiG [Mahella australiensis
           50-1 BON]
 gi|332699140|gb|AEE96081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Mahella australiensis
           50-1 BON]
          Length = 247

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 104/231 (45%), Gaps = 15/231 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++ E    ++  +A +    N G    DLI  G  GL+ A E++D     KF TYA  
Sbjct: 24  RNKLAEHYAPMIKYIASRLMVYNTGDDLDDLIGYGVFGLLDAIERYDPSRDVKFETYASH 83

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI  ++  +     IP  +RDK+  +    +++     +  + E++ + L + +E 
Sbjct: 84  RIRGAIIDNLRKKD---VIPRSVRDKVKHLDAVYKQLEATSDKPVSDEDVCRYLGISIEQ 140

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +  +         +       D  ++GD        S      +  L++  +  ++ L+ 
Sbjct: 141 LDALYADINRFNCISLDEIFVDEWNIGD------TESSESVYDRIELKQVLSEAVSKLSD 194

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           RE+++L++ +  G     TL+E+GK   ++  R+ Q+  KA+ +L+   R 
Sbjct: 195 REKQLLQLYYYDG----LTLKEIGKVLGISESRVSQLHTKALLQLRSRLRK 241


>gi|261880927|ref|ZP_06007354.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
 gi|270332314|gb|EFA43100.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
          Length = 243

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 124/274 (45%), Gaps = 40/274 (14%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   +  I     +S  E   +   ++      S A +E+  ANL  VI++A +Y  RGL
Sbjct: 10  INRYLNDIGHHNLLSNEEELQLADRIQ---AGDSQAIEELTSANLTYVITLANQYVKRGL 66

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI EGNIG+++AA KF    G +F  +A  +++ A+ ++I  Q+   R+P +    
Sbjct: 67  ALEDLISEGNIGMLQAATKFSRDAGKRFVAFAAPYIRDAMEQAIEQQAGLYRVPRNA--D 124

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            +K+ +   +                                   +S++ P+       L
Sbjct: 125 NNKLEKKRSK----------------------------------ALSIDEPLCGSHELSL 150

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           G  I D+NA  P +   +  L    T ++A L  RE++V+R  +GIG     T+ E G  
Sbjct: 151 GHVIPDRNATVPDEDLEKDMLLGELTELIADLDQREQQVIRALYGIG-TEAKTMLETGMA 209

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
             + RER+RQI  KAIRK+   ++S  L+ +L  
Sbjct: 210 MGLKRERVRQIRNKAIRKICRLTKSSDLKDYLKS 243



 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           D +  YL ++G   LLS E E+ +A RI+AG +  +  L  + LT   +I   ++     
Sbjct: 8   DSINRYLNDIGHHNLLSNEEELQLADRIQAGDSQAIEELTSANLT--YVITLANQYVKRG 65

Query: 179 TLLREII 185
             L ++I
Sbjct: 66  LALEDLI 72


>gi|24215303|ref|NP_712784.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45657258|ref|YP_001344.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24196402|gb|AAN49802.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45600496|gb|AAS69981.1| RNA polymerase sigma-28 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 266

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 107/241 (44%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             E +    +  +VE    LV  VA +      + ++F DL+  G  GL+ A EKFD   
Sbjct: 20  YRETKDQDIRSYLVEKYSPLVKHVAGRIAIGMPQNVEFDDLVSYGVFGLLDAIEKFDPER 79

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYAM  ++ +I   +        IP  +R K  ++ +    + NK  ++   + I
Sbjct: 80  LIKFKTYAMTRIRGSIFDELRSIDW---IPRSIRQKAKQLEQIIGMLENKEGQQVDDDAI 136

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQA 607
           AK+L + +E    +L        +SL        + D     + +E    ++P     + 
Sbjct: 137 AKELGISMEEYNSLLTKISGTSLVSLNDIWFLGDENDEVSFMETLESPMNMNPDTIIEKE 196

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            ++      + +L  +E++V+ + +      D TL+E+G+   VT  RI Q+  +A+ +L
Sbjct: 197 EIKNVIVEAIKTLPEKEKKVIVLYY----YEDLTLKEIGEVLEVTESRISQLHTRAVSRL 252

Query: 668 K 668
           +
Sbjct: 253 R 253


>gi|4103482|gb|AAD01786.1| sigma-E factor [Myxococcus xanthus]
          Length = 280

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 130/273 (47%), Gaps = 16/273 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  +     ++  E   +    +  E     A   +V  NLRLV+ +A +Y    L  LD
Sbjct: 1   MAEVQRHPLLTREEELQLARHYK--ESGDVNAAYRLVAWNLRLVVKLAHEYHRNPLSLLD 58

Query: 473 LI--QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDK 528
           L+  QEGNIGLM+A +K+D   G K S+YA WW++  I R I D    +++      R  
Sbjct: 59  LVLVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQRKL 118

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-ISLETPIGDEDTS- 586
             K+ +   ++  +   E +P+ +A++L +  + V ++ +      +S++ P+G++D S 
Sbjct: 119 FFKLRQEQEKLIAQ-GFEASPKLLAERLNVTEQDVVEMDQRLGHDEMSIDAPLGNDDDSR 177

Query: 587 --HLGDFIEDKNAVSPLD---SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 ++   +  +        ++A  RE  +    +L  +E         +  +   T
Sbjct: 178 TTRADRYLPSNSMPADERLGAEQLKALFREKLSEFARTLEGKER--FIFESRLVSDEPLT 235

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L+++G ++ V+RER RQIEA  I +++   R +
Sbjct: 236 LQDIGDKYGVSRERARQIEAALINRMRDFMREQ 268


>gi|209408344|emb|CAP19915.1| DNA-directed RNA polymerase subunit D [Pseudomonas xanthomarina]
          Length = 244

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 46/288 (15%), Positives = 98/288 (34%), Gaps = 45/288 (15%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +M+++   P T  +++   D +      L +I  L   I P+  G     
Sbjct: 1   AKRIEEGIREVMSAIAHFPGTVDSILADYDRVTTEGGRLSDI--LSGYIDPDDDGA---- 54

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                  + E  + +       + + D E     S ++       PE A      + E  
Sbjct: 55  --AGPQAEVEPVTPQAAAKPAGDDKDDEEEDDSDSDEEEGDGGPDPEVARVRFGAVAEQL 112

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           D +   L                                   +K  + S +     ++L 
Sbjct: 113 DVAKKAL-----------------------------------KKHGRGSQQATDALQELA 137

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            L   + L   + D LV ++ D   ++   E  ++++      + R  FL +    E D 
Sbjct: 138 TLFMPIKLIPKQYDALVLRVRDALSQVRAQERAIMQICVRDARMPRADFLRQFPTNETDL 197

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRH 429
            W        + ++   +A   + I + + ++ ++  E  ++I++ + 
Sbjct: 198 GWADQLAS-GKSKYAEAIAARKEDIQRCQQKLLALEEECILAIADIKD 244


>gi|147678403|ref|YP_001212618.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146274500|dbj|BAF60249.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 256

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 102/248 (41%), Gaps = 16/248 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
            +    R+        K E+V + L LV  +A +   +    +   DL   G +GL++A 
Sbjct: 6   ELWREYRR--SRDEKLKHEIVMSYLPLVKYLAGRLAVKLPACIGQEDLESFGILGLLEAV 63

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK++   G  F  YA   ++ AI       +    IP  M  KI  +  T  R+  +   
Sbjct: 64  EKYNPDYGVSFKAYAYNRIRGAIIDEFRKLNW---IPRTMWQKIQSLNNTRERLQGEAGE 120

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS--HLGDFIEDKNAVSPL 601
             T E +A  + + +  + K+          SL+  +   D      GD I+D  +  PL
Sbjct: 121 TVTSETLAGAMGISLPELHKLAWHASRLSLSSLDETVALADGELVRWGDMIQDPESPDPL 180

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D   +   R    + +  L  ++  VL + +  G     TL+E+G    V+  R+ Q+  
Sbjct: 181 DIIEKEEGRRLLVQAIEELPEKDRLVLSLYYQEG----LTLKEIGAVMEVSESRVCQLHT 236

Query: 662 KAIRKLKH 669
           +AI +L+ 
Sbjct: 237 RAINRLRK 244


>gi|90411040|ref|ZP_01219054.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
 gi|90328253|gb|EAS44564.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
          Length = 240

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 101/227 (44%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F T+A   +
Sbjct: 17  FIERYSSLVKRIAYHLMGRLPSSVQVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGIRI 76

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++      + NK+ R+PT  EIA+ L M ++   
Sbjct: 77  RGAMLDDIRRGDW---VPRSVYKNNRRITEAMALLENKLGRDPTDTEIAEHLEMTLDQYH 133

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + L      ++    +G +D     D +     +    P    +  N R++    + +L 
Sbjct: 134 QALN----DVNCGRLVGMDDLGVSEDAVTTEASREENLPFQGVVDDNFRQSLADAIKTLP 189

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G    V+  RI QI ++A+++L+
Sbjct: 190 EREALVLSLYY----DEELNLKEIGAVVGVSESRICQIHSQAMQRLR 232


>gi|92114133|ref|YP_574061.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797223|gb|ABE59362.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Chromohalobacter
           salexigens DSM 3043]
          Length = 232

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 103/237 (43%), Gaps = 14/237 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I +  ++E  + LV   A     R    ++  DLIQ G +GL+ A E+FD   
Sbjct: 1   MYTAQGKIDQHALLEQYMPLVRRHALALQVRLPASVELDDLIQAGMVGLLDALERFDATQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  FST+A   V+ A+   +  +      P  +R     + +   ++   + R P   EI
Sbjct: 61  GASFSTFANQRVRGAMIDELRSRDWM---PRSVRRSARALDQAVHKLEQTLGRAPDEREI 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRE 611
           A  L M VE   ++L        L     D+  S LG+    D    +P D+ +Q + R 
Sbjct: 118 ANALGMSVEEYHQLLLDANNGYLL---GFDDVVSELGEPPGGDTAPATPHDALLQGDART 174

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE+ +L    G+    +  L+E+G    V+  R+ Q+ ++A+ +L+
Sbjct: 175 HLVAAIEHLPEREKLLL----GLYYQEELNLKEIGAVLGVSESRVCQLHSQAVARLR 227


>gi|15614994|ref|NP_243297.1| RNA polymerase sigma factor SigD [Bacillus halodurans C-125]
 gi|10175051|dbj|BAB06150.1| RNA polymerase sigma-D factor [Bacillus halodurans C-125]
          Length = 256

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 118/247 (47%), Gaps = 14/247 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
                 +  A   ++   L LV    ++ +    R +   DLI  G +GL+ A EKF+  
Sbjct: 15  EWLTERSQEACDALIRQYLPLVHYHVQRISVGLPRSVSKDDLISHGMLGLLDALEKFNPD 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + V+ AI   +  +     +P  MR+KI K+     ++  K+ R  + EE
Sbjct: 75  RDLKFDTYASFRVRGAILDGLRKEDW---LPRSMREKIKKIEAATEKLEQKLGRNVSVEE 131

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQAN 608
           +AK++ +    V + +  +     +S++    D D        I DK ++SP +  ++  
Sbjct: 132 VAKEVGISENEVSQTMTESLVANLLSMDEKTNDSDREETYTATIIDKQSLSPEEKLLEEA 191

Query: 609 LRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +E  ++++A+ L  +E+ V+    G+    + TL E+G+   ++  RI QI +KA+ +L
Sbjct: 192 QKEELSQLIANILNEKEQLVI----GLFYFEELTLTEIGQILKLSTSRISQIHSKALFRL 247

Query: 668 KHPSRSK 674
           +   + +
Sbjct: 248 QQALKKR 254


>gi|329735692|gb|EGG71975.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU028]
          Length = 256

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 123/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQEAAR 255


>gi|149183717|ref|ZP_01862127.1| sigma factor B [Bacillus sp. SG-1]
 gi|148848576|gb|EDL62816.1| sigma factor B [Bacillus sp. SG-1]
          Length = 265

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 52/263 (19%), Positives = 120/263 (45%), Gaps = 6/263 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  +S     +  + +  +   ++       A+  +V     LVIS+A+KY+       D
Sbjct: 1   MPKLSQPNQQTKEQVKKWIKAYQEDN--DDEAQSNLVLHYENLVISIARKYSKGKSFHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           ++Q G IGL+ A  ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+
Sbjct: 59  IVQVGMIGLLGAIRRYDDSFGKTFEAFAIPTIVGEIKRFLRDKTWSVHVPRRIKELGPKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
             T   ++N ++R P  EEIA  + +  E V + +++ K   +L      E  S      
Sbjct: 119 KSTVEELTNTLERSPKVEEIADYIGVTEEEVLEAMEMGKSYQALSVDHSIEADSEGSTVT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 +  +   + N +    +VL  L+ RE  +++  +        + ++ G++  ++
Sbjct: 179 LLDIVGNVDEGYERINQKLVLEKVLHVLSERERLIIQYTYLDN----LSQKDAGEKLGIS 234

Query: 653 RERIRQIEAKAIRKLKHPSRSKK 675
           +  + +++ +AI+KLK    ++ 
Sbjct: 235 QMHVSRLQRRAIKKLKEAIDAEM 257


>gi|17226799|gb|AAL37943.1|AF359562_4 SigB [Staphylococcus epidermidis]
          Length = 256

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 123/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQEAAR 255


>gi|124516296|gb|EAY57804.1| putative RNA polymerase sigma 28 subunit, FliA/WhiG [Leptospirillum
           rubarum]
          Length = 251

 Score =  114 bits (284), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 102/229 (44%), Gaps = 14/229 (6%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++     V   A +Y++R    L   DLI  G  GL+ AA +FD   G KF T A   ++
Sbjct: 10  LKEFAVTVKFFALRYSHRLPPELDVDDLISAGMGGLLDAARRFDPSRGIKFKTLAEHRIR 69

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   I         P  +R+K+  V +    +  + KREPT +EIA ++ M  E   +
Sbjct: 70  GAMLDEIRAADWM---PRSVREKLTHVQQVKTELIARYKREPTRQEIAARMDMTEEEFDR 126

Query: 566 VLKIT--KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +         +SLE  +  ED     L D +       PL S +Q+ + E   + L  L 
Sbjct: 127 LSVDIEPHHLVSLEDLMDPEDGDSPSLLDRLSAPQEGDPLASLLQSEVSEKLCQALDRLP 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            ++  VL + +      + T++EV +   V+  R+ QI  +A+  LK  
Sbjct: 187 EKQRLVLSLYY----YEELTMKEVARVVGVSESRVSQIHGQALAALKQS 231


>gi|300717210|ref|YP_003742013.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
 gi|299063046|emb|CAX60166.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
          Length = 240

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTADGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     ++   + R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHKVEQSLGRTATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLRET 612
             L + ++  R++L  T            E+     + + D     +PL   ++ NLRE 
Sbjct: 122 ASLDVSLQEYRQILLDTNNSQLFSYDEFREEHGDTAELVTDGHEEANPLHQLMEGNLRER 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPDREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|220929439|ref|YP_002506348.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
 gi|219999767|gb|ACL76368.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
          Length = 254

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 106/247 (42%), Gaps = 11/247 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  E + + AK++++     L+  VA +   Y    ++F DL+  G  GL+ A EK+D  
Sbjct: 12  QYIETKDAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEKYDLA 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   ++ +I  SI D      +P  +R K  ++ +    + N+     T +E
Sbjct: 72  KGVKFETYASLRIRGSIIDSIRDMDW---VPRSLRQKNKELEKVYVEIENEKGHTATDKE 128

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-DFIEDKNAVSPLDSAIQANLR 610
           +A+K+ + +    K+L        +      E     G +   +     P  S     ++
Sbjct: 129 VAEKMGLSMSDFYKLLNDVNVSSMMSLDEFMEQNYERGLEIFSESTEDKPEASLEFNEMK 188

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     +  L  +E+ V+   +      + TL+E+     VT  RI Q+  KA+ ++K  
Sbjct: 189 QLLADCIDKLPEKEKAVITFYYF----EELTLKEISAIMNVTESRISQLHTKALLRMKGK 244

Query: 671 SRSKKLR 677
               ++ 
Sbjct: 245 LFRHRIM 251


>gi|331696199|ref|YP_004332438.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950888|gb|AEA24585.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 303

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 115/262 (43%), Gaps = 18/262 (6%)

Query: 417 SVETGISISEFRHIVSMVRKGEC------EASIAKKEMVEANLRLVISVAKKYTN--RGL 468
           +  T +  SE+   + ++++         E    ++++V + L +V  +A++Y N  R  
Sbjct: 39  ADATELGPSEYADQMPLLQRYAALPADDPERERIREQLVLSFLPVVEHLARRYGNGYRVA 98

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGY-KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
            + DL+Q G +GL+ A +++D      +F  Y +  V+  I R   D++ ++R+P  ++D
Sbjct: 99  AYDDLVQTGTVGLITAIDRWDPERAKGEFLGYLIPCVRGEILRYFRDRTWSMRVPRRLKD 158

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               + + +  ++ ++ R P P E+A  L +  E V + L    +  +        D   
Sbjct: 159 LGVAIGKASGPLTQELGRAPRPSELAAHLGVDREEVIEALAAAADRRATPLFPVTHDDDA 218

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                 ++   +   +            ++  L  RE  +L +RF      D T  ++  
Sbjct: 219 -----PEERVGTVEKAYDHVEYAIALKPLIEQLPERERLILTLRFF----GDQTQSQIAA 269

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  V++  + ++ A+ + +L+ 
Sbjct: 270 RVGVSQMHVSRLLARTLERLRE 291


>gi|297588048|ref|ZP_06946692.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
 gi|297574737|gb|EFH93457.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
          Length = 258

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 68/266 (25%), Positives = 129/266 (48%), Gaps = 19/266 (7%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           KSIS E   +I E       ++  E      +  +VE NL +   +AKKYT RG+++ DL
Sbjct: 4   KSISKEEQENIKEL-----FLKFQETRDKKTRDTLVEKNLYIAEILAKKYTGRGIEYDDL 58

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q   IGL+ A +++D   GY+FS+YA   +   I +   D+   IR+P  +++   KV 
Sbjct: 59  YQVACIGLIYAIDRYDPSKGYEFSSYATPTIVGEIKKYFRDKGWVIRVPRRIQELNKKVA 118

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGD---EDTSHL 588
                ++  +++ PT E+IA  L++  E V +VL+      P SL+  I     +  ++L
Sbjct: 119 NAKIHLAQTMQKSPTVEDIADYLSISNEEVLEVLEGAKVYAPQSLDQSIDQSSDDRDTNL 178

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I +++        ++   R+   R +  L   E+++L  R+        T   + ++
Sbjct: 179 SDLIGEED-----KDMLKFENRDLINRCMEDLNEVEKKILLGRYF----DKKTQIVIAEE 229

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             +++  + ++E K ++K K   + +
Sbjct: 230 LDISQMTVSRMEKKILKKFKASLKEQ 255


>gi|302517710|ref|ZP_07270052.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302426605|gb|EFK98420.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 286

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 56/272 (20%), Positives = 128/272 (47%), Gaps = 14/272 (5%)

Query: 413 IKSISVETGISISEFRHIVSM-------VRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +  I+    ++  + R +  +       + +G  E   A+  ++E N+ LV   A+++ +
Sbjct: 20  LPEIAEPHKVAPRDARELTRLFFDRLDTLEEGTREFQDARNTLIEMNMSLVRFAARRFRS 79

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    D++Q G IGL+KA ++F+     +F+T+A+ ++   I R   D +  + +P  +
Sbjct: 80  RGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAVPYIVGEIKRFFRDTTWAVHVPRRL 139

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDE 583
           ++   ++ +    +S ++ R P   E+A  +++  + V +           SL+  IG E
Sbjct: 140 QEARVELAKANEELSTRLGRAPKVSELAALMSLSEQQVVEAQIAANGYSSSSLDATIGGE 199

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D+      + D          +  +L      +LA L PR+ ++L +RFG     + T  
Sbjct: 200 DSGEGEAALSDFIGAEDPGMELVEDLH-ALAPLLADLEPRDRQILELRFG----QELTQA 254

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++G++  V++  + ++  + +  L+    S++
Sbjct: 255 QIGERLGVSQMHVSRLLNRTLGTLRAGLMSER 286


>gi|15604780|ref|NP_219564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D/UW-3/CX]
 gi|76788774|ref|YP_327860.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           A/HAR-13]
 gi|237802495|ref|YP_002887689.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/Jali20/OT]
 gi|237804410|ref|YP_002888564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/TZ1A828/OT]
 gi|255310863|ref|ZP_05353433.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276]
 gi|255317163|ref|ZP_05358409.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276s]
 gi|255348424|ref|ZP_05380431.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70]
 gi|255502966|ref|ZP_05381356.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70s]
 gi|255506635|ref|ZP_05382274.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D(s)2923]
 gi|3328455|gb|AAC67652.1| Sigma-28/WhiG Family [Chlamydia trachomatis D/UW-3/CX]
 gi|76167304|gb|AAX50312.1| FliA [Chlamydia trachomatis A/HAR-13]
 gi|231272710|emb|CAX09614.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273729|emb|CAX10508.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|289525106|emb|CBJ14577.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296434648|gb|ADH16826.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis E/150]
 gi|296435578|gb|ADH17752.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9768]
 gi|296436502|gb|ADH18672.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11222]
 gi|296437438|gb|ADH19599.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11074]
 gi|296438365|gb|ADH20518.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           E/11023]
 gi|297139937|gb|ADH96695.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9301]
 gi|297748191|gb|ADI50737.1| FliA [Chlamydia trachomatis D-EC]
 gi|297749071|gb|ADI51749.1| FliA [Chlamydia trachomatis D-LC]
          Length = 253

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 107/241 (44%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +    +  ++E+ L LV +VA +  +     ++  DL   G  GL++A E+FD   
Sbjct: 13  YWSTKEIHHRDVLIESYLPLVKNVAHRLASGMPSHVKMEDLYALGVEGLIRAVERFDPEK 72

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F +YA++ +K AI   +  Q     +P  +  + +++      +   + +EPT  E+
Sbjct: 73  SKRFESYALFIIKAAIIDGLRKQDW---VPRSVYQRANRLADAMDSLRQTLGKEPTDGEL 129

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQA 607
            + L +  + +      ++    +SL      +D      L + I D+ A +  D   + 
Sbjct: 130 CEYLNISQQELSHWFSSSRPALVLSLHDDFSCQDDDEGLALEERIADERAETGYDVIRKK 189

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 T  L +L  +E +V+     +    D  L+E+GK   V+  R+ QI +KA+ KL
Sbjct: 190 EAISILTEALLALDEKERQVM----ALYYYDDLVLKEIGKILGVSESRVSQIHSKALLKL 245

Query: 668 K 668
           +
Sbjct: 246 R 246


>gi|260438776|ref|ZP_05792592.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
 gi|292808765|gb|EFF67970.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
          Length = 255

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 103/243 (42%), Gaps = 13/243 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            +   +      +++++     LV  VA +   Y    +++ DL+  G  GL+ A +KFD
Sbjct: 10  WMSYSKNRTPELREQIIIEYAPLVKLVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFD 69

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +    KF TYA   ++  I   I        IP  +R+K  K+     R+  +  +  T 
Sbjct: 70  YGKNVKFETYASLRIRGEILDQIRKMDW---IPRSVREKQKKIDSARTRLETENGKNATD 126

Query: 550 EEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EE+A  L + ++ +      TK    +SL+  +         +   + +   P     + 
Sbjct: 127 EELAAALDLSLDELNNWQGQTKVSNLVSLDEFVEQGSELS-METAGNSHFEQPERVVEKE 185

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L    +  L+ LT +E+ V+ + +      + TL+E+     V+  R+ Q+  KA+ KL
Sbjct: 186 ELAVKISEALSHLTEKEKMVVTLYY----YEEMTLKEISNVMEVSESRVSQLHTKALVKL 241

Query: 668 KHP 670
           K  
Sbjct: 242 KKS 244


>gi|160914281|ref|ZP_02076502.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
 gi|158433908|gb|EDP12197.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
          Length = 260

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 124/252 (49%), Gaps = 15/252 (5%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ++ ++ + +   ++K       AK+E++  NL+LV+S+ +++ NR     DL Q G I
Sbjct: 17  TVLNNTQMKELFLRMQK---GDQNAKEELINGNLKLVLSIVQRFANRCENMDDLFQVGCI 73

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+K+ + FD     +FSTYA+  +   I R + D    +R+  H++D  +K  R     
Sbjct: 74  GLVKSIDHFDLKHEVRFSTYAVPMIMGEIKRYLRDNQ-VLRVSRHLKDLAYKCFRLKEEY 132

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNA 597
            ++ ++EP+   +A++L +  + +   L  T+  +S+  P+ + D    +L D I D+  
Sbjct: 133 VHQHQKEPSITWLAEQLEVREKDIVDALDSTQNVLSIFEPVYNSDGDELYLLDQIRDEKD 192

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              L + + +         L  L  +E  +L  R+      D T  E+  +  +++ ++ 
Sbjct: 193 EIDLLNNVLS-----LRSSLKQLKEKELEILDKRY----YQDMTQTEIANELGISQAQVS 243

Query: 658 QIEAKAIRKLKH 669
           ++E  AI  L+ 
Sbjct: 244 RLEKSAISTLRK 255


>gi|166154282|ref|YP_001654400.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 434/Bu]
 gi|166155157|ref|YP_001653412.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335533|ref|ZP_07223777.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis L2tet1]
 gi|165930270|emb|CAP03756.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931145|emb|CAP06710.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 253

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 107/241 (44%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +    +  ++E+ L LV +VA +  +     ++  DL   G  GL++A E+FD   
Sbjct: 13  YWSTKEIHHRDVLIESYLPLVKNVAHRLASGMPSHVKMEDLYALGVEGLIRAVERFDPEK 72

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F +YA++ +K AI   +  Q     +P  +  + +++      +   + +EPT  E+
Sbjct: 73  SKRFESYALFIIKAAIIDGLRKQDW---VPRSVYQRANRLADAMDSLRQTLGKEPTDGEL 129

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQA 607
            + L +  + +      ++    +SL      +D      L + I D+ A +  D   + 
Sbjct: 130 CEYLNISQQELSHWFSSSRPALVLSLNDDFSCQDDDEGLALEERIADERAETGYDVIRKK 189

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 T  L +L  +E +V+     +    D  L+E+GK   V+  R+ QI +KA+ KL
Sbjct: 190 EAISILTEALLALDEKERQVM----ALYYYDDLVLKEIGKILGVSESRVSQIHSKALLKL 245

Query: 668 K 668
           +
Sbjct: 246 R 246


>gi|5327289|emb|CAB46360.1| FliA, sigma 28 [Xenorhabdus nematophila]
 gi|139522465|gb|ABO77651.1| FliA [Xenorhabdus nematophila]
          Length = 230

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 111/228 (48%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E+FD   G  F+TYA+
Sbjct: 3   KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDSMQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +      P  +R    +V +T R++  ++ R  + +E+AK+L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---APRSVRRNAREVTQTIRKLEQELGRPASEQEVAKELKINLI 119

Query: 562 GVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E         IE+++  +PL   ++ +LR+    ++ SL
Sbjct: 120 EYRQILLDTNNSQLFSYDEWHEIHGESCEPVIEEEHETNPLQQLLEGDLRQRVINIIESL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKMVLTLYY----QEELNLKEIGAVLNVGESRVSQLHSQAIKRLR 223


>gi|317127083|ref|YP_004093365.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315472031|gb|ADU28634.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 262

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 116/247 (46%), Gaps = 8/247 (3%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +  +           + ++V     LV ++A+K++       DLIQ G IGL+ A  +FD
Sbjct: 17  LQWIAEYQSTGNKEIQTKLVLEFESLVHALARKFSRGQRHDEDLIQVGMIGLLAAIRRFD 76

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             +G  F ++A+  +   I R I D++ ++ +P  +++   KV      ++ +++R P  
Sbjct: 77  PTIGKSFESFAVPTIIGEIKRFIRDKTWSVHVPRRIKEMGPKVKNAVDTLTTQLQRSPKV 136

Query: 550 EEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EEIA  +    E V + +++  + + +S++  I  +D       +      S      + 
Sbjct: 137 EEIAAHIDASEEEVLETMEMGKSYQALSVDRSIEADDEGSAVTLL--DLVGSTEGGYEKT 194

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + +    +    L+ RE+++L + +        + ++ G++  +++  + +++ +A++KL
Sbjct: 195 DQQMLLEKAFTVLSDREKQILHLTYFEN----LSQKDTGEKLGISQMHVSRLQRRALQKL 250

Query: 668 KHPSRSK 674
           +   + +
Sbjct: 251 RESLKVE 257


>gi|183220350|ref|YP_001838346.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910466|ref|YP_001962021.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167775142|gb|ABZ93443.1| RNA polymerase sigma subunit [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167778772|gb|ABZ97070.1| RNA polymerase sigma factor for flagellar operon [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 266

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 109/242 (45%), Gaps = 15/242 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +    + +  +  +VE    LV  VA +      + ++F DL+  G  GL+ A EKFD  
Sbjct: 19  QYRVKKDAEIRSYLVEKYSPLVKHVAGRIAIGMPQNVEFEDLVSYGVFGLLDAIEKFDPS 78

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYAM  ++ +I   +        IP  +R K  ++      + NK  ++   EE
Sbjct: 79  REIKFKTYAMTRIRGSIFDELRSVDW---IPRSIRQKAKQLENIIAMLENKEGKKVDDEE 135

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQ 606
           IAK+L + +E    +L        +SL        + D     + +E    ++P +   +
Sbjct: 136 IAKELGVSMEEYNSLLAKLSGTSLVSLNDIWFLGDENDEVSFMETLESPMNMNPDNIIEK 195

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             ++      + SL  +E++V+ + +      D TL+E+G+   VT  RI Q+  KA+ +
Sbjct: 196 EEIKNVIVEAIQSLPEKEKKVIVLYY----YEDLTLKEIGEVLEVTESRISQLHTKAVAR 251

Query: 667 LK 668
           L+
Sbjct: 252 LR 253


>gi|301166786|emb|CBW26363.1| RNA polymerase sigma-32 factor [Bacteriovorax marinus SJ]
          Length = 350

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 78/283 (27%), Positives = 137/283 (48%), Gaps = 15/283 (5%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           K+ V  +      +   ++ IS    ++I E R +   +   E       K++V ANLRL
Sbjct: 65  KDLVKYDSKIGDPLTAYLREISKYELLTIEEERELTQKL--VETGDIEVAKKLVAANLRL 122

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A +Y +     +DLIQEGNIGLMKA  K+D   G K S YA WW+K  I + I D 
Sbjct: 123 VVKIAMEYRSSFQNVMDLIQEGNIGLMKAVSKYDPDKGAKLSYYASWWIKSYILKYILDN 182

Query: 516 SCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV---LKIT 570
              ++I      +   + +++   R+  K   EP  + +++ L +  + V  +   +  +
Sbjct: 183 FRLVKIGTTNEQKKLFYNLMKEKDRL-AKQGIEPDHKLLSENLGVSEKAVALMDGRMSSS 241

Query: 571 KEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREE 625
              +SLETP+G +  S  L D + D++     +    A     L+E     ++ L  R+ 
Sbjct: 242 GGELSLETPLGHDSGSGVLSDILVDQDESDISEKIADAQGLEILQENLRDFVSGLKERDR 301

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +    +      +L+ +  ++ V+RERIRQIE + ++ LK
Sbjct: 302 DIFKK--RLLSEVPPSLQNIADEYGVSRERIRQIEERLLKNLK 342



 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 22/96 (22%), Positives = 36/96 (37%), Gaps = 1/96 (1%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           +   L D E S    +  +     ++   K     D    DP+  YLRE+   ELL+ E 
Sbjct: 36  ESKTLADIEISLKKSNEDAQDLLPALTSSKDLVKYDSKIGDPLTAYLREISKYELLTIEE 95

Query: 139 EIAIAKR-IEAGRAMMMASLCESPLTFQALIIWRDE 173
           E  + ++ +E G   +   L  + L     I     
Sbjct: 96  ERELTQKLVETGDIEVAKKLVAANLRLVVKIAMEYR 131


>gi|237683088|gb|ACR10585.1| DNA-dependent RNA polymerase sigma factor [Diaphorobacter sp.
           R-26815]
          Length = 236

 Score =  114 bits (284), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 47/291 (16%), Positives = 102/291 (35%), Gaps = 56/291 (19%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
           EI IAKRIE G   MM ++  SP T   ++   +E+ +G  ++  ++D           G
Sbjct: 1   EIEIAKRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVIINTVVD-----------G 49

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
           F +  E   Y   ED  +  E DD     G                              
Sbjct: 50  FSNPEEADDYVAEEDFDEYDEEDDDDGKGG------------------------------ 79

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                  +  ++ + ++L+   +   DE+  ++ ++  + D    G      +     ++
Sbjct: 80  -------SKAMTRLLEKLKNDALERFDELRALFEKMHKIYDKEGYG------TPAYMKVQ 126

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSYGIKRDVFLERHQGR 377
            ++   + ++      I+ L + +      +   E EL R+     G+ ++ F++     
Sbjct: 127 HEISAKLMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVDKCGMPQETFIKEFPPN 186

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
            LD  WV          W   +   +  I +++  +  +     + + E +
Sbjct: 187 LLDRTWVEKQAA-AAKPWSTVMQRNIPPIQELQQHLIDLQSRVVVPLGELK 236


>gi|239933011|ref|ZP_04689964.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441364|ref|ZP_06580754.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344259|gb|EFE71215.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 287

 Score =  113 bits (283), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 107/234 (45%), Gaps = 12/234 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 50  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPGRG-AFESYAVPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              + R   D+   +R+P  +++  +KV    R ++      EP+  +IA    +  E V
Sbjct: 109 TGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELTQNPGSPEPSVADIAAHTGLTEEEV 168

Query: 564 RKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              ++   +   +SL+  +  +D  +    + D    S     I  + RE+    L  L 
Sbjct: 169 GAGMEALESFSTLSLDAELSADDDGY---SLADTLGASDASYDIVID-RESAKEGLRRLP 224

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            RE  +L MRF      D T   +  +  +++  + ++ +++  +++  +  ++
Sbjct: 225 ERERAILYMRFF----EDMTQSRIADRLGISQMHVSRLISRSCARVRAEAMGQR 274


>gi|266620503|ref|ZP_06113438.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
 gi|288867868|gb|EFD00167.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
          Length = 237

 Score =  113 bits (283), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++         A+  +V  N+ L+ S+ +++T RG    DL Q G+IGLMKA +KF
Sbjct: 3   ETMRLIEMAHEGDKEARDRLVTENMGLIWSIVRRFTGRGYDPEDLFQIGSIGLMKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++   +V      +   + REPT
Sbjct: 63  DMSFDVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSIKEMGTRVKCVREALGFTLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            EEIA +L    E V   ++   E  SL   +   D +   L D IE++++        +
Sbjct: 122 IEEIAGELGASKEEVAASIEAGAEVESLYRTVNKNDENSILLIDKIEEESSA-----QEE 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     +L  L+ ++  ++  R+           ++     +++ ++ ++E K +++
Sbjct: 177 LLNRMVLRELLTGLSDKDREIIIRRYYYNETQS----QIASHLGISQVQVSRLEKKILKQ 232

Query: 667 LKH 669
           ++ 
Sbjct: 233 MRE 235


>gi|254473016|ref|ZP_05086414.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
 gi|211957737|gb|EEA92939.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
          Length = 289

 Score =  113 bits (283), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 122/260 (46%), Gaps = 14/260 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++            A  ++  ++ RLVI+ A ++ + G+   DLIQEG+IGL
Sbjct: 23  LSKEEEYKLLE--GWITKRDHRALDKLSLSHSRLVIAQALRFKSYGVPLSDLIQEGHIGL 80

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI----HKVVRTAR 537
           M+AA +F      +FSTYA WW+K  I   +      +R     R K+     K +R   
Sbjct: 81  MEAANRFKLSKDVRFSTYASWWIKSFIQDYVLRNQSIVRGGTSSRQKMLFFGFKRMRAEL 140

Query: 538 RMSN-KIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTS-HLGDFIED 594
              + ++  +   ++I+ +    +  ++ +  ++ +   SL   +   +T+  L D +  
Sbjct: 141 ASKHPELSEDQLHQQISNQTGANMRDIKMMSSRLGRSDTSLNATLKGSETNLQLQDTLAA 200

Query: 595 KNAVSPLDSAIQANLRET---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
              +      +  +           + +L PRE+RV+R R         TLE +GK+  V
Sbjct: 201 DEPLPDEIVEVHLDSERAERRLFDAIKTLPPREQRVIRDRKLREDGV--TLEALGKKLGV 258

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           ++ER+RQIE++A++KLK   
Sbjct: 259 SKERVRQIESRAMQKLKDAM 278


>gi|297538886|ref|YP_003674655.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Methylotenera
           sp. 301]
 gi|297258233|gb|ADI30078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylotenera sp. 301]
          Length = 244

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 105/235 (44%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K E++  +  LV  +A +   +    ++  DLIQ G +GL+ A  +++   G +F TYA 
Sbjct: 11  KDELLNKHAVLVKKLAYQLKAKLPPSVELDDLIQAGMMGLLDAINRYEDTHGAQFETYAA 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +        +P  +R  +  V     ++  ++ + PT  E+AKKL + + 
Sbjct: 71  QRIRGSMLDELRSADW---LPRSVRKSMRDVEIAISQLEQQLGKPPTENEVAKKLQLSLS 127

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      + I  E     E+  H  D         P+ S ++ + RE     + +
Sbjct: 128 DYYDMLGDCSGHQLIYYEDFHESENGEHFLDRFNADTTGDPIKSLLEGDFREALVGAITA 187

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  RE+    +  G+    +  L+E+G    V+  R+ Q+ ++A+ +L+   + K
Sbjct: 188 LPEREK----ILMGLYYEQELNLKEIGAVMNVSESRVCQLHSQAVARLRSNLKEK 238


>gi|150390456|ref|YP_001320505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
 gi|149950318|gb|ABR48846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
          Length = 243

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 111/238 (46%), Gaps = 15/238 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKK-YTNRG--LQFLDLIQEGNIGLMKAAEKFDWCL 492
             +      K E++E  + LV  +A + YT+ G  + + DL+  G  GL+ A EKFD   
Sbjct: 10  YKQNHDLQTKNELIEKYIALVKIIAGRLYTSYGSNVDYDDLVSYGIFGLIDAIEKFDINK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA   ++ AI   + +      +P  +R K  K+     +  N++ R     E+
Sbjct: 70  NVKFETYAQIRIRGAIIDQLRNLDW---VPRSIRQKSKKIEDAYAKAENRLGRSVLDFEV 126

Query: 553 AKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++L M +    + L+   +   +SLE  +   DT H    I D+N +       +   R
Sbjct: 127 AQELEMSIGDFHRTLQQINSFNIVSLEERLS--DTHHNQIPIGDENDLPEQIICNKEE-R 183

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 + SL+ RE+ V+ + +  G     T +E+G+   V+  R+ Q+ +KAI +LK
Sbjct: 184 LLLRSSIESLSEREKTVVTLYYYEGF----TYKEIGQVLDVSESRVSQLHSKAIVRLK 237


>gi|315648111|ref|ZP_07901212.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
 gi|315276757|gb|EFU40100.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
          Length = 262

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 116/238 (48%), Gaps = 12/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             E     AKK+++E +L +V  V+ +      + +   DL   G +GL+ A EKFD+  
Sbjct: 18  WKEDGDHEAKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLASNGVMGLIDAIEKFDYKR 77

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA W V+ AI  S+        +P  +R+K  ++    +++  K  R  +  E+
Sbjct: 78  GLQFETYASWRVRGAILDSLRQGDW---VPRSVREKAKRIETAYQQLEQKYLRSVSDSEM 134

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +  L +  +  R +L+        SLE PI +E++      + D+ A +P     +  LR
Sbjct: 135 SDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNPDHKVHEFYLR 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   + +  LTP+E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+
Sbjct: 195 EALMKGIGKLTPKERTVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLR 248


>gi|94968665|ref|YP_590713.1| sigma 28 [Candidatus Koribacter versatilis Ellin345]
 gi|94550715|gb|ABF40639.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Candidatus
           Koribacter versatilis Ellin345]
          Length = 262

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 112/237 (47%), Gaps = 12/237 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            +  +V   +  V  +A++      R +   DLI  G +GL+ AA K+D     +F +YA
Sbjct: 17  HRDRLVMEQMSQVKYIARRIHERLPRHVPIEDLINAGILGLIDAAGKYDSEKNVQFQSYA 76

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            + ++ AI  S+ D       P  +R K   +     R++++    P  +E+A++L M +
Sbjct: 77  KFRIRGAILDSLRDLDW---SPRDLRRKARALEAAELRLTSETGHPPLEDELARELGMDL 133

Query: 561 EGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +G R++ +  +     SL+  +  E      + + + +  SPLD+ +++   E     + 
Sbjct: 134 DGFRELTRELEGLGISSLQEGLPAEGFGEEREVVVESHEESPLDAFLRSENHELLVEAIE 193

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  RE +VL     +    + T++EVG    V   R+ QI ++A+ +++   +S+ 
Sbjct: 194 QLPARERQVL----ALYYFEELTMKEVGDVLGVGESRVSQIHSQALTRVRARLQSRH 246


>gi|291437789|ref|ZP_06577179.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
 gi|291340684|gb|EFE67640.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
          Length = 285

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 107/236 (45%), Gaps = 17/236 (7%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGEC-------EASIAKKEMVEANLRLVISVAKKYT 464
           E+  +     ++  + R +  +  +          E   A+  ++E N+ LV   A ++ 
Sbjct: 52  ELPEVVDPGQVAPKDARELSRLFFRQLAVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFR 111

Query: 465 NRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +RG  +  D++Q G IGL+KA ++F+     +F+++A+ ++   + R   D S ++ +P 
Sbjct: 112 SRGPEEMEDIVQVGMIGLIKAIDRFELSREVEFTSFAIPYIVGEMKRFFRDTSWSVHVPR 171

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI- 580
            +++   ++ R    +  ++ R PT  E+A+ +++  E V +           SL+  I 
Sbjct: 172 RLQEARVQLARATEELRTRLGRTPTTRELAQLMSLTEEEVNEARIAANGYNSASLDAAIG 231

Query: 581 -GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
              +  S L DFI  ++A   L     A        ++A L  RE +++  RF   
Sbjct: 232 SEPDGESVLADFIGSEDAALELVEDFHA-----LAPMIAELDERERKIIHWRFVEE 282


>gi|212639538|ref|YP_002316058.1| RNA polymerase sigma factor SigD [Anoxybacillus flavithermus WK1]
 gi|212561018|gb|ACJ34073.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anoxybacillus flavithermus WK1]
          Length = 243

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 106/240 (44%), Gaps = 12/240 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  +     A  +++E  + LV    ++  +   + ++  DL     +GL  A EKFD  
Sbjct: 5   KWIDTRDREAGDQLIEKYMPLVDYHVQRIASSLPKSVKKEDLKSLALLGLYDALEKFDPS 64

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +  +     +P  +R+K  K+  T  R+     R+ + +E
Sbjct: 65  RDLKFDTYASFRIRGAILDGLRKEDW---LPRSVREKAKKIEATIERLQQMHMRDVSAKE 121

Query: 552 IAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +A  L +  + V      +     +SL+    D+D       I D ++ SP +  ++   
Sbjct: 122 VADALNISEDEVYAVMNEQFFANVLSLDERPFDDDDDQPSFTIRDDHSPSPEEHMLREEQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                +V+  L  +E+ V+ + +      + T  E+G    ++  RI QI AKA+ K++ 
Sbjct: 182 IAQLAQVIQQLNEKEQLVISLFY----KEELTFTEIGHIMGLSTSRISQIHAKALFKMRK 237


>gi|17549609|ref|NP_522949.1| flagellar biosynthesis sigma factor [Ralstonia solanacearum
           GMI1000]
 gi|17431863|emb|CAD18541.1| probable rna polymerase sigma factor for flagellar operon (sigma-f
           factor) transcription regulator protein [Ralstonia
           solanacearum GMI1000]
          Length = 253

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 106/245 (43%), Gaps = 11/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +          K + + A   LV  +A +   +    ++  DLIQ G +GL+ A  +++ 
Sbjct: 9   MDMYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEE 68

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  
Sbjct: 69  TQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTET 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA  L M +   +K+L   +    L       ED     +    +N  +PLD  +  +L
Sbjct: 126 EIAAALNMSLADYQKLLVELQGSQLLYYEDFDREDADAFIENRAPENDATPLDQLLDHDL 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+    + +L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++ 
Sbjct: 186 RESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRS 241

Query: 670 PSRSK 674
             R +
Sbjct: 242 RLRER 246


>gi|37522237|ref|NP_925614.1| RNA polymerase sigma factor SigF [Gloeobacter violaceus PCC 7421]
 gi|35213237|dbj|BAC90609.1| glr2668 [Gloeobacter violaceus PCC 7421]
          Length = 254

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 98/227 (43%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + E+V  NL LV  +A +          DL+Q G IGLM+A E+FD  LG+ FS++A   
Sbjct: 27  RNELVCRNLGLVRKIAHQLARGSSEPLEDLVQVGAIGLMRAVERFDPSLGHAFSSFATPC 86

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ A+   + D   ++R+P  + +   +  R A  +S +    P+  ++A  L +  E  
Sbjct: 87  IRGAMQHYLRDHGHSVRLPRRLLELDSRARRAAHALSQRHGCTPSERQVASALDISAEEW 146

Query: 564 RKVL--KITKEPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            ++   +  +  +SL+ P     DT  L + +   +         +   R    R LA L
Sbjct: 147 LQMRLARANRTLVSLDAPAGPHPDTPPLVELLPGPDTPEVSPEGQE---RAHLARALAQL 203

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
               + V+R  +        T  E  ++  V+   + +   K   +L
Sbjct: 204 EAATQVVVRQVYF----EKRTQSETARRLGVSPMTVSRRLKKGTGQL 246


>gi|229827370|ref|ZP_04453439.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
 gi|229788308|gb|EEP24422.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
          Length = 268

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 66/259 (25%), Positives = 116/259 (44%), Gaps = 28/259 (10%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  +      +++++     LV  +A +   Y    +++ DL+  G  GL+ A +KFD  
Sbjct: 20  QYAKKPTQELREKLIIEYANLVKIIAGRMSIYLGYNVEYDDLVGYGIFGLIDAIDKFDHV 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   I        IP  MR +  K+    R +  K  R  T EE
Sbjct: 80  KGVKFETYASLRIKGAILDQIRKMDW---IPRTMRQRQKKLEAAERAIEEKYGRMATDEE 136

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-DFIEDKNA--------VSPLD 602
           IA +L + V+         +  +S+   I  +D    G D + DK+           P +
Sbjct: 137 IAAELGISVDEY----GSWQSQVSMSGIISLDDYLEQGSDLVADKSGSKLGISGFEQPEE 192

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +  +  L+E+    +  LT +E++V+     +    + TL+E+ +   V+  R+ Q+  K
Sbjct: 193 AVEKEELKESLAVAIEGLTEKEQKVI----ALYYYEELTLKEISRVLSVSESRVSQLHTK 248

Query: 663 AIRKLKHPSRSKKLRSFLD 681
           A+ KLK     +KL  ++D
Sbjct: 249 ALTKLK-----EKLGDYID 262


>gi|47565382|ref|ZP_00236424.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
 gi|208742286|ref|YP_002267738.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus]
 gi|47557736|gb|EAL16062.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
          Length = 325

 Score =  113 bits (283), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 131/264 (49%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-- 469
           EIK I     +S  E    + + ++ +      +  +   N+ LV+S+A+KY N+     
Sbjct: 41  EIKGIGNYKVLSKQES---LKLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIE 97

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I  +     +IP  +   
Sbjct: 98  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNSVNQF 157

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS 586
             + V    +      R P+ EE+ K+L +  E V K     K    ++L+    +ED  
Sbjct: 158 NLRYVELEDKYLQMYNRPPSVEEVVKELNVTSETVIKHNVYYKRATTMTLDVDTINEDIG 217

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
            L  F +D +A+   +  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 218 ILNPFYDDSSAIPSTNEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 277

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K   +T ER+ QI+ +AI+KLK 
Sbjct: 278 AKALMITTERVSQIKDEAIKKLKK 301


>gi|292698270|dbj|BAI99679.1| RNA polymerase sigma-70 factor [Aeromonas sp. MU1]
          Length = 253

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 52/292 (17%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDSSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ QK+ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDDTQAAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|242241477|ref|ZP_04795922.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
 gi|242235020|gb|EES37331.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
          Length = 256

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 124/247 (50%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S+A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  A++
Sbjct: 195 EK--RMILERILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAVK 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQEAAR 255


>gi|294636855|ref|ZP_06715188.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
 gi|291089930|gb|EFE22491.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
          Length = 240

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + +    LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVIDKNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R     V    +R   ++ R P+  EIA
Sbjct: 65  TAFTTYAIQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRVPSDGEIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           +++ +P+   +++L  T            E+     + +  ++ + +PL   ++++LR  
Sbjct: 122 QEMGIPLAEYQQILLDTNSSQLFSYDEWREEHGDNAEPVWGEEESANPLRQLLESDLRGR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIAAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|171058305|ref|YP_001790654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptothrix cholodnii
           SP-6]
 gi|170775750|gb|ACB33889.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptothrix cholodnii
           SP-6]
          Length = 238

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 98/232 (42%), Gaps = 13/232 (5%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++    LV  +A +   +    ++  DLIQ G IGL  A  +FD   G  F T+A   +
Sbjct: 13  LLKQYSPLVRRLAHQMIAKLPANVEIDDLIQVGMIGLTDALSRFDIGQGVMFETFATQRI 72

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +       R     +     +     R+  K+ R P   EIAK++ + +   +
Sbjct: 73  RGAMLDELRGSDWMSRGNRKHQR---DIEGAVHRLEQKLGRTPQESEIAKEMGITLLEYQ 129

Query: 565 KVLKITKEP--ISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +L   +    I LE   G + D  +L   +       PL       +R+     + +L 
Sbjct: 130 DLLNRVRGTQLIYLEDMGGADGDNDYLDRHVAADTGGDPLARLNDHRMRQALVDAIKNLP 189

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            RE+ V+ M +      D  L+E+     VT  R+ Q+ +++I +L+   R+
Sbjct: 190 EREQYVMSMYY----EEDMNLKEIAAVLGVTESRVCQLHSQSIARLRAKLRT 237


>gi|238920292|ref|YP_002933807.1| flagellar biosynthesis sigma factor [Edwardsiella ictaluri 93-146]
 gi|238869861|gb|ACR69572.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           ictaluri 93-146]
          Length = 240

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 55/243 (22%), Positives = 109/243 (44%), Gaps = 11/243 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + +    LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVIDKNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R     V    +R   ++ R P   EIA
Sbjct: 65  TAFTTYAIQRIRGAMLDELRSRDW---VPRSVRRNARGVSAAMQRAEQRLGRVPGDSEIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           +++ + +   +++L  T            E+     +  +E     +PL   ++++LR  
Sbjct: 122 QEMGISLAEYQQILLDTNTSQLFSYDEWREEHGDSAEPVVEQSEESNPLHQLLESDLRGR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+    
Sbjct: 182 VIAAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLL 237

Query: 673 SKK 675
           S++
Sbjct: 238 SQR 240


>gi|307131576|ref|YP_003883592.1| RNA polymerase sigma-28 (sigma F) factor [Dickeya dadantii 3937]
 gi|306529105|gb|ADM99035.1| RNA polymerase, sigma 28 (sigma F) factor [Dickeya dadantii 3937]
          Length = 240

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +  ++    + R PT +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAQAMQQAEQSLGRAPTEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL+  +  NLR+ 
Sbjct: 122 QTLNISLEEYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEEANPLNQLMDVNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIESLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|291196324|emb|CBG22634.1| DNA-directed RNA polymerase subunit D [Pseudomonas lini]
          Length = 237

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 42/284 (14%), Positives = 96/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +      + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDPKAAPAADDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +     A++   R   +   + IA                                L +L
Sbjct: 110 TRK---ALKKHGRGNKLAIAELIA--------------------------------LAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 TD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|317048579|ref|YP_004116227.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Pantoea sp.
           At-9b]
 gi|316950196|gb|ADU69671.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           At-9b]
          Length = 240

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 107/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTADGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     ++   + R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHQVEQAMGRAATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
            +L + +E  R++L  T            E+     + + E     +PL   ++ NLRE 
Sbjct: 122 DQLNVSLEEYRQILLDTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGNLRER 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|318041080|ref|ZP_07973036.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 131/276 (47%), Gaps = 29/276 (10%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGE----------CEASIAKKEMVEANLRLVISVA 460
           + +++I     ++  E  H+ ++V+                  A + +V ANLRLV++VA
Sbjct: 7   DYLRTIGRIPLLTAQEEVHLGTIVKDWMESNDPSPALQRRGRRALQRIVTANLRLVVTVA 66

Query: 461 KKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
            +Y  R        +DL+Q GN+GL++AAEK+D   GYKFSTY  WW++Q+I R + + S
Sbjct: 67  LRYIRRLKHLAHDPMDLVQAGNLGLLRAAEKYDPTRGYKFSTYGYWWIRQSINRYLQEHS 126

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG--VRKVLKITKEPI 574
            +IRIPV++    ++    A  + +      + E++A+ L    +       ++     +
Sbjct: 127 GSIRIPVNLVSLANR----ADSLQSLRSHPMSVEQLAEALQESPQRLLYAMAIQHRSNTV 182

Query: 575 SLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           SL+  +   D    L D + D +     D              L  L+  E  V+++R+G
Sbjct: 183 SLDQQLSGSDGDMTLLDTVTDDHQPLITDDY------RWMHSQLQHLSTPELTVIQLRYG 236

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  +  EV +    ++++++++E  A+ KL+ 
Sbjct: 237 EDKQ--RSFAEVARLIGRSKDQVQRLERHALTKLRR 270


>gi|292698316|dbj|BAI99702.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 103/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGIHQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +   + + + D+ +  
Sbjct: 49  --------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|238916778|ref|YP_002930295.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
 gi|238872138|gb|ACR71848.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
          Length = 252

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 102/230 (44%), Gaps = 13/230 (5%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++    +LV  VA +   Y    +++ DL+  G  GL+ A +KFD+    KF TYA 
Sbjct: 22  RDELIVEYAQLVKLVAGRLNMYLGYNVEYDDLVGYGIFGLIDAIDKFDYGKNVKFETYAS 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I        IP  +R K  ++     ++ ++     + EE+A +L +  +
Sbjct: 82  LRIRGAILDQIRKMDW---IPRSLRQKQKRIEAAMTKIESETGHIASDEELAAELGITQD 138

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +            ISL+            + + + +   P D+  +  L++   + + S
Sbjct: 139 ELSDWQGKMKASNLISLDEYTEAGSEVK-MESVGNSHFDQPEDAMEKEELKKMMVKAIDS 197

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LT +E  V+ + +      + TL+E+     V+  R+ Q+  KA+ K+K 
Sbjct: 198 LTEKERSVVVLYY----YEEMTLKEISLTLEVSESRVSQLHTKALNKMKK 243


>gi|224826337|ref|ZP_03699439.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601438|gb|EEG07619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 248

 Score =  113 bits (283), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 53/218 (24%), Positives = 99/218 (45%), Gaps = 18/218 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DL Q G IGL++AA +FD   G +F T+A   ++ A+   +  +     +P   R 
Sbjct: 44  VELDDLAQVGIIGLIEAARQFDPTQGVQFETFASQRIRGAMLDELRREDW---LPRQARR 100

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              ++     ++  +  R P   EIA  L +P+   + +L   K  +SL+     +D   
Sbjct: 101 HSKQIEDAIHQLEQREGRPPQESEIADFLGLPLAEYQTMLGECKG-VSLQHFSDFDDEDG 159

Query: 588 LG-----DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +G       + D NAV P  S    + R      + +L  R++ V+     +    +  L
Sbjct: 160 VGAEAAVANVADDNAVDPFASLADGDFRGALVDAIKALPERDQLVM----ALYYEQELNL 215

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           +E+G    V+  R+ Q+ ++AI +++      KLR +L
Sbjct: 216 KEIGAVLGVSESRVSQLHSQAIARVR-----SKLREWL 248


>gi|291196404|emb|CBG22674.1| DNA-directed RNA polymerase subunit D [Pseudomonas veronii]
          Length = 238

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/284 (15%), Positives = 93/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGI------- 51

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       + +     +   D ++ A    DD  +    P  A      + +  + 
Sbjct: 52  -APPAAEVPPPVDPKAVKADDDAEDDDAEASTDDDDEVESGPDPIIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +S+         L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRSNKLAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEI 238


>gi|291196262|emb|CBG22602.1| DNA-directed RNA polymerase subunit D [Pseudomonas abietaniphila]
          Length = 236

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/284 (15%), Positives = 97/284 (34%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T + ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         +++ +     + D E +    +++      P   A    +      D 
Sbjct: 50  GIAPPAEVPPPIDQKAEKADAADDDDEESDSDDEEEAESGPDPVVAA----QRFGAVSDQ 105

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            A TL A++                                K  + S +       L +L
Sbjct: 106 MAITLKALK--------------------------------KHGRGSKQANEELLALAEL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 134 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDQSW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I + + ++ ++  ETG+++ E 
Sbjct: 194 TD-ALAKGKSKYAEAIGRLQADIQRCQQKLTALEEETGLTVLEI 236


>gi|302872543|ref|YP_003841179.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302575402|gb|ADL43193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 246

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 123/253 (48%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 9   KFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   +  Q     +P  +R K  ++ +    +  +  R PT +E
Sbjct: 69  KGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQKAKEIEKAYIEIERE-GRTPTDDE 124

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK++ + +  ++K+     +   +SL++ +     S +G     ++ VS  +  I+   
Sbjct: 125 VAKRVGLSISELQKLQEKISSGMIVSLDSFLEQNYESKIGGL---EDFVSQPEHFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 182 LKEVLRQQIDNLLENERMVIVLYY----YEELSIKEIAKILGVSESRVSQLHTRALLKLR 237

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 238 SA-----LQKYLE 245


>gi|149923127|ref|ZP_01911542.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
 gi|149816035|gb|EDM75549.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
          Length = 304

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 109/265 (41%), Gaps = 15/265 (5%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  +S    I     R +    R       +A + ++EA+LR V+++A+ Y N G   
Sbjct: 23  RYVAHVSSFEEIDGERERELA---RAYHEGDRLAGQRLIEAHLRDVVAIARGYRNYGHPM 79

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR--DK 528
            +L+ EGN+GL++A E FD   G +F TY  +WV+  I   +      +R+         
Sbjct: 80  AELVAEGNVGLVRALESFDPERGLRFMTYGRYWVRARILAHVQRSWSLVRVGSSSAHTRL 139

Query: 529 IHKVVRTARRMSNKIKREPTPEE---IAKKLAMPVEGVR-KVLKITKEPISLETPIGDED 584
            + + R   R            E   +A+        V     +I    +SL+       
Sbjct: 140 FYGLHRARGRFQATAGERDGAAERAALAEYFGCSEAHVEAMAARIDGRDLSLD------H 193

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            S      E     +  +  +   +RE    V+  L PRE  +LR R      +  +L E
Sbjct: 194 PSSAALVSESTVEATIFEREVGELVRERIAAVIRELDPRERVILRRRLLDESGSPPSLVE 253

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           VG++  ++RER RQ+E +   KL+ 
Sbjct: 254 VGRELGLSRERTRQLEQRVKTKLRR 278


>gi|271500098|ref|YP_003333123.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Dickeya
           dadantii Ech586]
 gi|270343653|gb|ACZ76418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dickeya
           dadantii Ech586]
          Length = 240

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +  ++    + R PT +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAQAMQQAEQSLGRAPTEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL+  +  NLR+ 
Sbjct: 122 QTLNISLEEYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLNLLMDVNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIENLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|126649718|ref|ZP_01721954.1| sporulation sigma factor SigG [Bacillus sp. B14905]
 gi|126593437|gb|EAZ87382.1| sporulation sigma factor SigG [Bacillus sp. B14905]
          Length = 257

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 127/250 (50%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E + +   ++ GE E    ++E+V  NLRLV+S+  ++  RG Q  DL Q G IGL
Sbjct: 18  LKHEEMKELFIRLQAGEIE---IREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIGL 74

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA + FD     +FSTYA+  +   I R + D    +R+   +RD  +K ++   +   
Sbjct: 75  MKAIDHFDLKHNVRFSTYAVPMIIGEIRRHLRDHH-ALRVSRSLRDIAYKAMQAKEQWIT 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           +  REPT EEIA  + M  E V   L   ++P+SL+ PI  +  D  ++ D + D + VS
Sbjct: 134 ENLREPTIEEIADMIEMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLRDDD-VS 192

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                   +++E+       L  R++ ++  RF  G     T  E+ K+  +++ +I ++
Sbjct: 193 EDQWVAYVSVKESLQ----KLDERQQMIVAKRFYYG----ETQTEIAKELGISQAQISRL 244

Query: 660 EAKAIRKLKH 669
           E  AI  ++ 
Sbjct: 245 EKNAIETMQK 254


>gi|299069774|emb|CBJ41053.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CMR15]
          Length = 253

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 106/245 (43%), Gaps = 11/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +          K + + A   LV  +A +   +    ++  DLIQ G +GL+ A  +++ 
Sbjct: 9   MDMYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEE 68

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  
Sbjct: 69  TQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTET 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA  L M +   +K+L   +    L       ED     +    +N  +PLD  +  +L
Sbjct: 126 EIAAFLNMSLADYQKLLVELQGSQLLYYEDFDREDADAFIENRAPENDATPLDQLLDHDL 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+    + +L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++ 
Sbjct: 186 RESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRS 241

Query: 670 PSRSK 674
             R +
Sbjct: 242 RLRER 246


>gi|313887713|ref|ZP_07821395.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312846322|gb|EFR33701.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 261

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 58/252 (23%), Positives = 116/252 (46%), Gaps = 15/252 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + +       E +    +  ++E +L +   ++KKYT RG+ + D+ Q  +IGL
Sbjct: 13  LTKEERKDLFK--EYHETKDQEIRDILIEEHLYIAEILSKKYTGRGIDYDDIYQVASIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A E++D   G++FS++A   +   I +   D   TIR+P  +++   K+      +S 
Sbjct: 71  IYAIERYDPEKGFEFSSFATPTIIGEIKKYFRDNGWTIRVPRRIQELSKKISNATVSLSQ 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH--LGDFIEDKNA 597
           K ++ PT +EIA+ L    E V + ++ +    P SL+      D S   L D I  + A
Sbjct: 131 KYQKTPTIDEIAEYLDSTPEEVMEAMEASKVYTPQSLDVTYESGDESEVNLSDLIGVEEA 190

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                   +    +   + + +L   E  +L  R+        T   + K+  +++  + 
Sbjct: 191 -----YFDKIESNDFFKKAMENLDEVERTILIDRYF----NKKTQVVIAKKLNISQMTVS 241

Query: 658 QIEAKAIRKLKH 669
           +IE K + K++ 
Sbjct: 242 RIEKKVLEKMRK 253


>gi|290879068|emb|CBK39758.1| sigma factor of RNA polymerase [Pseudomonas sp. a390]
 gi|290879070|emb|CBK39759.1| sigma factor of RNA polymerase [Pseudomonas sp. a391]
 gi|290879072|emb|CBK39760.1| sigma factor of RNA polymerase [Pseudomonas sp. a393]
 gi|290879076|emb|CBK39762.1| sigma factor of RNA polymerase [Pseudomonas sp. a399]
          Length = 247

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/293 (14%), Positives = 99/293 (33%), Gaps = 48/293 (16%)

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           M+++   P T   ++     +      L +++            G+    +G +    E 
Sbjct: 1   MSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEV 49

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                 +    +   D + A     ++ ++    P  A      + +  + +   L    
Sbjct: 50  PPPVDPKAAKADDAEDDDEAESSDDEEEAESGPDPVIAAQRFGAVSDQMEITRKAL---- 105

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                          +K  +S+         L +L   + L   
Sbjct: 106 -------------------------------KKHGRSNKAAIAELLALAELFMPIKLVPK 134

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A    +
Sbjct: 135 QFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD-ALAKGK 193

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
            ++   +      I++ + ++ ++  ETG++I+E + I   +  GE +A  AK
Sbjct: 194 SKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAKARRAK 246


>gi|168333394|ref|ZP_02691674.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family protein
           [Epulopiscium sp. 'N.t. morphotype B']
          Length = 249

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 121/255 (47%), Gaps = 12/255 (4%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           ++T  +  +      ++ K +     AK+ +VE NL LV S+ K++TNRG    DL Q G
Sbjct: 1   MDTQTTNEQMEKTRLLILKAQGGDISAKELLVEQNLGLVWSLVKRFTNRGYDLDDLFQVG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           +IGL+K+ EKFD      FSTYA+  +   I R + D    I++   ++D   K      
Sbjct: 61  SIGLLKSIEKFDLKYPVAFSTYAVPMIVGEIKRFLRD-DGLIKVSRSLKDLASKARNVKE 119

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED--TSHLGDFIEDK 595
               +  REPT +EI+  L +P E +   L+   E  SL   +      T  L + I D+
Sbjct: 120 DFQRQENREPTLKEISDILNVPCEEIAVSLEANMEVESLNAVVNPNSSATITLAEKI-DQ 178

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +     +      L+E    ++ +L+  E +++  R+      D T  E+  +  V++ +
Sbjct: 179 SPDEQKNIFENIYLKE----IIKTLSSVERQIVNYRYF----EDLTQLEIANRLGVSQVQ 230

Query: 656 IRQIEAKAIRKLKHP 670
           I +IE + + KL+  
Sbjct: 231 ISRIEKRVLEKLRQS 245


>gi|292696871|dbj|BAI99608.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 103/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +   + + + D+ +  
Sbjct: 49  --------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDTQAAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|86605313|ref|YP_474076.1| RNA polymerase sigma factor SigF [Synechococcus sp. JA-3-3Ab]
 gi|86553855|gb|ABC98813.1| RNA polymerase sigma factor, group 3 [Synechococcus sp. JA-3-3Ab]
          Length = 299

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGY 494
             +      +  +VE NL LV   A  + N+    + DL+Q G IGL++A E+FD   G 
Sbjct: 62  YHQTRDPALRNRLVEINLGLVRKEAHHWRNQCDEGYDDLVQVGCIGLIQAIERFDISRGL 121

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FS++AM +++  I   + D+S TIRIP        +  +   R+  ++ R P+  E+ +
Sbjct: 122 AFSSFAMPYIRGEIQHYLRDKSPTIRIPRRWATLQRQAKKVIARLRQELGRSPSEAEVRE 181

Query: 555 KLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRE 611
            L +  +  R++    +    +SL+ P+  E+ S  LGD I D+   S     +    R 
Sbjct: 182 ALQLTEQEWRELELAQQNSLLLSLDAPVQVEEDSVALGDTIPDQRYRSF---QLAEEDRI 238

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                LA L  R  ++L   F      D T +E  ++  ++   + +   K + +L
Sbjct: 239 RLQNALAKLEERTRQILEFVFF----YDLTQKETAERLGISAVTVSRQVKKGLERL 290


>gi|312792676|ref|YP_004025599.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179816|gb|ADQ39986.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 246

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 61/253 (24%), Positives = 124/253 (49%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 9   KFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   +  Q     +P  +R K  ++ +    +  +  + PT +E
Sbjct: 69  KGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQKAKEIEKAYVEIERE-GKTPTDQE 124

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK++ + V  ++K+ +   +   ISL++ +     S +G     ++ VS  +  I+   
Sbjct: 125 VAKRVGISVNELQKLQERISSGMIISLDSFLEQNYESKIGGL---EDFVSQPEHFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KLK
Sbjct: 182 LKEVLRQQIENLMENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLK 237

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 238 AA-----LQKYLE 245


>gi|126642303|ref|YP_001085287.1| EsvH [Acinetobacter baumannii ATCC 17978]
          Length = 233

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 58/228 (25%), Positives = 105/228 (46%), Gaps = 9/228 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V ++LR V+ +A+ Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  
Sbjct: 2   LVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAE 61

Query: 508 ITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           I   +      ++I     + K+   +R+ ++ S K+  E            P + +   
Sbjct: 62  IHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLTLEEAQSIANDLNVTPEQVLEME 121

Query: 567 LKITKEPISLETPIGDEDTSHL---GDFIED---KNAVSPLDSAIQANLRETTTRVLASL 620
            ++T    + E    D+D +       ++ED     A    +   +          +  L
Sbjct: 122 GRLTAYDAAFEAQGDDDDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQL 181

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R   +L+ R+        TL E+  ++ V+ ERIRQ+E  A+ K+K
Sbjct: 182 DDRSRNILQRRWLDD--DKSTLHELAAEYNVSAERIRQLEKNAMEKIK 227


>gi|291196354|emb|CBG22649.1| DNA-directed RNA polymerase subunit D [Pseudomonas orientalis]
          Length = 238

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/284 (15%), Positives = 95/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEI 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + ++  DD  E   D        ++D  +    P  A      + +  + 
Sbjct: 59  PPPVDPKAPKADDETEDDDAEASSD--------EEDEVESGPDPIIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + + +       L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRGNKQAIAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDETW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 SD-ALAKGKAKYAEAIGRLQPDIIRCQQKLSALEAETGLTIAEI 238


>gi|291617817|ref|YP_003520559.1| FliA [Pantoea ananatis LMG 20103]
 gi|291152847|gb|ADD77431.1| FliA [Pantoea ananatis LMG 20103]
          Length = 240

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     ++   + R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHQVEQMLGRAASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           ++L + +E  R++L  T            E+     + + E     +PL   ++ +LRE 
Sbjct: 122 QQLNVSIEEYRQILLDTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGSLRER 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|160915290|ref|ZP_02077503.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
 gi|158433089|gb|EDP11378.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
          Length = 240

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 117/240 (48%), Gaps = 14/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +++         A ++ VEAN  LV ++ K++ NR +   DL Q G IGLMKA   FD  
Sbjct: 8   ALLAAIRYGDEEALEQFVEANQPLVYAIVKRFHNRRISQEDLFQIGCIGLMKAIHNFDAA 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R   D    IRI   +++   ++++   +++  + +EPT  +
Sbjct: 68  YEVKFSTYAVPIIMGEIKRFFRDDGS-IRISRSLKEGYLQMLKIKEQLTQTLGKEPTYAQ 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANL 609
           IA+ + + V  V    +  +   SL+ PI + D S   L D +ED      +       +
Sbjct: 127 IAQAMNIEVGEVILAFEANQFMYSLDEPIYENDGSAIVLEDRVEDPKQTDIV-------M 179

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +  +  A L  RE+ +L  R+ +        E++ K+  +++ ++ ++E K + KLK 
Sbjct: 180 KLSLRKEFARLEQREQLILHYRYDLN----MKQEDIAKRLHISQVQVSRLEKKILWKLKE 235


>gi|292696977|dbj|BAI99661.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC1]
 gi|292696999|dbj|BAI99672.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC8]
          Length = 253

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 51/292 (17%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EADDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDSSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ QK+ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHDDTQAAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|291196290|emb|CBG22616.1| DNA-directed RNA polymerase subunit D [Pseudomonas costantinii]
          Length = 238

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 95/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + +   DD  E  GD         +D  +    P  A      + +  + 
Sbjct: 59  PPPVDAKAAKADDDSEDDDAEASGD--------DEDEVESGPDPIIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +++ +       L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRANKQAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   +G++   +      IL+ + ++ ++  ETG++I+E 
Sbjct: 196 SDGLAK-GKGKYAEAIGRLQPDILRCQQKLIALQTETGLTIAEI 238


>gi|225376836|ref|ZP_03754057.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
 gi|225211332|gb|EEG93686.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 57/240 (23%), Positives = 114/240 (47%), Gaps = 7/240 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
             ++R+ +     A+ ++V  NL LV ++ +++  RG    +L Q G IGL+KA + FD 
Sbjct: 5   AELIRQAQDGDKKARDKVVSDNLGLVHAIVRRFEKRGHDREELFQIGCIGLIKAIDHFDL 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            L   FSTYA+  +   I R + D    +++   +++  +K+ R    ++ ++ R+P+  
Sbjct: 65  SLNLAFSTYAVPMITGEIRRFLRD-DGMVKVSRSLKENGYKISRAKEVLTTELGRDPSLL 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN 608
           E++    +  E +   L   +   S+  P+   D     L D I D++ V          
Sbjct: 124 ELSAMTELGTEEIVMALDANRGVESIYQPVCGSDGDELLLIDQIGDQSDVYEEPEKEAVL 183

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +    +++ +L   E++++R+R+        T  EV     VT+ +I + E K + KL+
Sbjct: 184 NKMVIRQLMDTLDETEQQIIRLRYFEN----KTQCEVAGILAVTQVQISRNERKILAKLR 239


>gi|304398826|ref|ZP_07380696.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308187260|ref|YP_003931391.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
 gi|304353530|gb|EFM17907.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308057770|gb|ADO09942.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
          Length = 240

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     R+   + R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHRVEQSLGRSASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
           ++L + +E  R++L  T            E+     + + E     +PL   ++ +LRE 
Sbjct: 122 QQLNVSMEEYRQILLDTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLLEGSLRER 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPDREKMVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|239934512|emb|CAR94570.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 240

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 57/300 (19%), Positives = 106/300 (35%), Gaps = 64/300 (21%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EGEI IAKRIE G    + SL   PLT    +    ++  G   L ++  L A I P + 
Sbjct: 1   EGEIKIAKRIEKGLNQALRSLSGFPLTIATTLEEFAKVQAGEMKLTDL--LTAYIDPNAV 58

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                   D+V   +           D+  +VD+ P+  E   R
Sbjct: 59  ------------------------DEVAIPKPRQAGDNNDDDDEEEEVDTGPDPEEARVR 94

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCK 315
                                             Y +++ L   A+N   K    + + K
Sbjct: 95  ----------------------------------YEKMKRLNTRALNASAKHGSDAPQAK 120

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
            L+E+L +    L L   ++D L   L  + +RI  +E  ++ L      + R  F+   
Sbjct: 121 KLREQLTEQFLELKLTPKQVDKLTLGLRQVVERIRSHERAIIDLCVRSAKMPRKEFIASF 180

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              E + +W+          +   +  + + I + + ++ ++  E  ++I+E + I   +
Sbjct: 181 PENETNVNWIDGYLK--GKRYSASLKPQAEEIRRHQTKLIALEKEAKLTIAEIKEINRKM 238


>gi|291196380|emb|CBG22662.1| DNA-directed RNA polymerase subunit D [Pseudomonas psychrophila]
          Length = 237

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 39/284 (13%), Positives = 93/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +   +  + + +      +++  +    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDPKVKAEGDDEEDDKEESTEEEEEVESGPDPIIAAQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + S +       L +L
Sbjct: 110 ARKAL-----------------------------------KKHGRGSKQAIAELVALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL    G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRLFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG+ I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEI 237


>gi|155061095|gb|ABS90485.1| RNA polymerase sigma factor [Streptomyces albus]
          Length = 282

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 19/253 (7%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           +  EF  + S+    E EA  A  E+VEA L +   +A ++ N+G    DL Q   +GL+
Sbjct: 26  TAVEFARLASLGSGPEREALCA--EIVEAWLPMAHRIAGRFRNKGESLEDLQQVAAMGLV 83

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA  +++   G  F +YA+  +   + R   D+   +R+P  +++  +KV    R + ++
Sbjct: 84  KAVNRYEPGRG-AFESYAVPTITGELRRHFRDRMWDVRVPRRVQELRNKVRAARRELLDR 142

Query: 543 ---IKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIG--DEDTSHLGDFIEDK 595
                REPT  EI ++  +    VR  ++       +SL+  +   + D   L D +   
Sbjct: 143 PGGSGREPTLAEIGEQAELTEAEVRDGMEAMEGYSALSLDAEVSSAEPDGFSLADTLGAP 202

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +      +    N RE     L  L  RE  +L +R+   M      EE      +++  
Sbjct: 203 D-----PAYDHINDREAAKAGLRRLPERERTILYLRYFEDMTQSRIAEE----LGISQMH 253

Query: 656 IRQIEAKAIRKLK 668
           + ++ +++  +++
Sbjct: 254 VSRLISRSCARVR 266


>gi|3249721|gb|AAC26663.1| RNA polymerase sigma-like factor [Micromonospora echinospora]
          Length = 161

 Score =  113 bits (282), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 79/162 (48%), Positives = 110/162 (67%), Gaps = 1/162 (0%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDI 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V ++ +  +EPISL+  IGDE  S LGDFIED  AV  +D+   + L++   +VL 
Sbjct: 61  TPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFSLLQDQLQQVLQ 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +P   RV  MRFG+      TL+E+G+ + VTRERIRQIE
Sbjct: 121 G-SPSVRRVWSMRFGLTDGQPRTLDEIGQVYGVTRERIRQIE 161


>gi|292696839|dbj|BAI99592.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 32]
 gi|292696867|dbj|BAI99606.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696869|dbj|BAI99607.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696873|dbj|BAI99609.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696879|dbj|BAI99612.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696881|dbj|BAI99613.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696883|dbj|BAI99614.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696885|dbj|BAI99615.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696931|dbj|BAI99638.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696949|dbj|BAI99647.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO562]
 gi|292696961|dbj|BAI99653.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696985|dbj|BAI99665.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC5]
 gi|292698296|dbj|BAI99692.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698298|dbj|BAI99693.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698310|dbj|BAI99699.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698314|dbj|BAI99701.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698328|dbj|BAI99708.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698338|dbj|BAI99713.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698342|dbj|BAI99715.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698350|dbj|BAI99719.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698354|dbj|BAI99721.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698360|dbj|BAI99724.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 103/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +   + + + D+ +  
Sbjct: 49  --------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|213419842|ref|ZP_03352908.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 115

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 85/113 (75%), Positives = 93/113 (82%)

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
           I KEPIS+ETPIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VL
Sbjct: 2   IAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVL 61

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 62  RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 114


>gi|172038499|ref|YP_001805000.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171699953|gb|ACB52934.1| group 3 sigma-70 RNA polymerase sigma factor J [Cyanothece sp. ATCC
           51142]
          Length = 282

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 106/228 (46%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE NL LV  VA + + +    + DL Q G +GL++A E+FD   G  FS++A+ +
Sbjct: 53  RNQLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFDPQQGCAFSSFAIPY 112

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+   +RIP   ++  +K  +  ++++  +KR P+  EIA  L +P+E  
Sbjct: 113 IRGEMLHYLRDKGSVMRIPRRWQELYNKAKKIRKQLTVSLKRPPSDWEIADALGVPLEEW 172

Query: 564 RKVLKI--TKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +       +  +SL+  I    + +   GD + D+   +          R    R L  
Sbjct: 173 NECQLALQNRLLVSLDATISHNVDCSISFGDTLPDQEYQAKQKLEED---RLQLQRALGQ 229

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  + +  +   F      +   +E  KQ  ++   + +   K I++L
Sbjct: 230 LEEKTKAAIECVFLH----ELPRKEAAKQIGISPMTVTRHLKKGIQQL 273


>gi|160939297|ref|ZP_02086648.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438260|gb|EDP16020.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
          Length = 240

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 115/243 (47%), Gaps = 12/243 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++         A+ ++V  N+ L+ S+ ++++ RG +  DL Q G+IGL+KA +KF
Sbjct: 6   ETMKLINMAHEGDKAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKAIDKF 65

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++   KV      M+  + REPT
Sbjct: 66  DTGFDVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSIKELGVKVRAAREEMTYALGREPT 124

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLE--TPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            EEIA +L    E V   L+   E  SL      GDE++++L D +   N     +    
Sbjct: 125 IEEIAGRLGTSREEVAASLEAAAEVESLYRPADSGDENSTYLMDRLAQDN-----NDHED 179

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     ++  L   +  ++  R+        T  ++  +  +++ ++ ++E + +++
Sbjct: 180 LLNRMVLKDLMEGLEEEQREIILRRYFYN----ETQTQIAGELGISQVQVSRLEKRILKE 235

Query: 667 LKH 669
           ++ 
Sbjct: 236 MRK 238


>gi|152965379|ref|YP_001361163.1| RNA polymerase sigma factor WhiG [Kineococcus radiotolerans
           SRS30216]
 gi|151359896|gb|ABS02899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 312

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 66/257 (25%), Positives = 112/257 (43%), Gaps = 21/257 (8%)

Query: 425 SEFRHIVSMVRKGECEAS---IAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEG 477
            E           E +AS   + +++++     LV  VA +    GL       DL+  G
Sbjct: 57  QEQAEAALRAMWEEYKASGDGVVREKLIMHYSPLVKYVAGR-VGVGLPPNIEQADLVSYG 115

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
             GL+ A EKFD     KF TYA+  ++ AI   +        IP  +R K  +V RT  
Sbjct: 116 IFGLIDAIEKFDIERAIKFETYAISRIRGAIIDELRSIDW---IPRSVRSKAREVERTYA 172

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPI----GDEDTSHLGDF 591
            +  ++ R PT  E+A ++ + +  +  +         ++L+  +       D   L D 
Sbjct: 173 ALEAELHRTPTEVEVAARMEIKLSELHHIFSQVSYVNVVALDELLSVSGEKGDKLSLVDT 232

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +ED  A  P+ S  +   +   +R +  L  RE+ V+ + +  G     TL E+G+   V
Sbjct: 233 LEDTKAEDPVQSFEKEETKFLLSRAINQLPEREKIVVTLYYYEG----LTLAEIGRVLGV 288

Query: 652 TRERIRQIEAKAIRKLK 668
           T  RI Q+  KA+ +L+
Sbjct: 289 TESRICQMHTKAVLQLR 305


>gi|320012666|gb|ADW07516.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 294

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 120/250 (48%), Gaps = 17/250 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAA 485
           F   + ++ +G  E   A+  +VE N+ LV   A+++ NRG     D+ Q G IGL+KA 
Sbjct: 49  FFERLQVLEEGTHEYQYARNTLVEMNISLVRFAARRFRNRGSGDMEDITQVGTIGLIKAI 108

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+T+A+ ++   I R   D +  + +P  +++   ++ +    ++ ++ R
Sbjct: 109 DRFELSREVEFATFAVPYIVGEIKRFFRDTTWAVHVPRRLQELRVELAKAKDELAVRLDR 168

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTS-----HLGDFIEDKNAV 598
           +PT +E+A  L    + V + +  +      SL+ P    +T+        D + + ++ 
Sbjct: 169 DPTVKELAAHLDRTEDEVIEGIIASNGYTAGSLDMPTDTGETTGTASRTFADILGEPDSA 228

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                 + A        +L  L  RE R++ MRFG     + T  ++G +  V++  + +
Sbjct: 229 METVENLHA-----LAPLLEQLDDRERRLIEMRFG----QEMTQSQIGAELDVSQMHVSR 279

Query: 659 IEAKAIRKLK 668
           +  + + KL+
Sbjct: 280 LLTRTLGKLR 289


>gi|169823706|ref|YP_001691317.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302380124|ref|ZP_07268597.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|303234447|ref|ZP_07321085.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
 gi|167830511|dbj|BAG07427.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302312066|gb|EFK94074.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|302494402|gb|EFL54170.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
          Length = 258

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 68/266 (25%), Positives = 128/266 (48%), Gaps = 19/266 (7%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           KSIS E   +I E       ++  E      +  +VE NL +   +AKKYT RG+++ DL
Sbjct: 4   KSISKEEQENIKEL-----FLKFQETRDKKTRDTLVEKNLYIAEILAKKYTGRGIEYDDL 58

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q   IGL+ A +++D   GY+FS+YA   +   I +   D+   IR+P  +++   KV 
Sbjct: 59  YQVACIGLIYAIDRYDPSKGYEFSSYATPTIVGEIKKYFRDKGWVIRVPRRIQELNKKVA 118

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLE---TPIGDEDTSHL 588
                +S  +++ PT E+IA  L++  E V +VL+      P SL+       ++  ++L
Sbjct: 119 TAKVHLSQTMQKSPTVEDIADYLSISNEEVLEVLEGAKVYAPQSLDQSIDQSNEDRETNL 178

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I +++        ++   R+   R +  L   E ++L  R+        T   + ++
Sbjct: 179 SDLIGEED-----KDMLKFENRDLINRCMQDLNKVERKILLGRYF----DKKTQIVIAEE 229

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
             +++  + ++E K ++K K   + +
Sbjct: 230 LDISQMTVSRMEKKILKKFKAALKEQ 255


>gi|312876527|ref|ZP_07736510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796738|gb|EFR13084.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 246

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 61/253 (24%), Positives = 122/253 (48%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 9   KFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K AI   +  Q     +P  +R K  ++ +    +  +  + PT +E
Sbjct: 69  KGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQKAKEIEKAYVEIERE-GKTPTDQE 124

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK++ + V  ++K      +   ISL++ +     S +G     ++ VS  +  I+   
Sbjct: 125 VAKRVGISVNELQKLKERISSGMIISLDSFLEQNYESKIGGL---EDFVSQPEHFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + + +L   E  V+ + +      + +++E+ K   V+  R+ Q+  +A+ KLK
Sbjct: 182 LKEVLRQQIENLMENERMVIVLYY----YEELSIKEIAKVLGVSESRVSQLHTRALLKLK 237

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 238 AA-----LQKYLE 245


>gi|108804196|ref|YP_644133.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765439|gb|ABG04321.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 258

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 111/240 (46%), Gaps = 9/240 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R        A++++++  L L   +A+K+  RG    DL+Q  ++GL+KA ++FD   
Sbjct: 17  LERYHREGDRQAREQVIQEQLPLAEFLARKFAGRGEPLEDLVQVASVGLIKAVDRFDVDR 76

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +FSTYA   +   I R   D+   +R+P  +++    V    R  + +  R PT +E+
Sbjct: 77  NIEFSTYATPNILGEIKRHFRDKGWAMRVPRGLQELRQAVKEAIREETVRTGRSPTMDEL 136

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++L   VE V + L         SL+ PI  +D    GD I D  A          + +
Sbjct: 137 AERLDTDVESVAEALTLGRAYNTTSLDAPISQDDAE--GDTIMDLQADENQPIEGIED-K 193

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +  L  ++  +LR+RF  G     T  E+ ++  V++  + ++  +AI  L+  
Sbjct: 194 LLLQEAMRGLREQQREILRLRFNEG----KTQTEIAERIGVSQMHVSRLLRRAIADLRRS 249


>gi|292696863|dbj|BAI99604.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696891|dbj|BAI99618.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696959|dbj|BAI99652.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 103/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +   + + + D+ +  
Sbjct: 49  --------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHEDTQNAISQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|228474927|ref|ZP_04059656.1| RNA polymerase sigma-B factor [Staphylococcus hominis SK119]
 gi|228271159|gb|EEK12539.1| RNA polymerase sigma-B factor [Staphylococcus hominis SK119]
          Length = 256

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 115/247 (46%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGE-CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +      A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQDNINPYAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ +    ++N++ R P
Sbjct: 75  FDISFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVGDELTNELGRSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SILEIANRLEVNEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE  +++  F  G     + +E G++  +++  + +++  AIR
Sbjct: 195 EK--RMILERILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIR 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQQAAR 255


>gi|168187412|ref|ZP_02622047.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
 gi|169294714|gb|EDS76847.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
          Length = 251

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++K +     A  E+VE NL LV +++KK+ NRG ++ D+ Q G++GL+KA   FD 
Sbjct: 17  LELIKKAKLGDKKALDELVEKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R I D    I++   ++    K+     +++ K+ REPT E
Sbjct: 77  SYNVQFSTYAVPMIMGEIRRFIRD-DGLIKVSRSVKYTARKLHFDKEKLTKKLHREPTLE 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K   +  E +   ++   EP  L   I  +D S +  ++ DK  V       + + +
Sbjct: 136 ELSKFSGIEKEQIIFAMEAINEPKYLYDTIHQDDGSPI--YLIDKVVVKDESEVDELD-K 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L  L  R  +++ +R+   +        V K   +++ ++ +IE K ++ +K 
Sbjct: 193 IALKEALNKLDQRSRQIIILRYFKDITQVK----VAKMLGISQVQVSRIEKKVLKTMKE 247


>gi|284041831|ref|YP_003392171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283946052|gb|ADB48796.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 110/249 (44%), Gaps = 17/249 (6%)

Query: 430 IVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
           +    R+ +     A + ++V A   +V  VA +   R    +   DLI +G  GL+ A 
Sbjct: 10  LAERWRRYKGTGERAARDDLVLAYSPIVKYVAGRVAARMPAHVDVADLISDGFKGLLDAV 69

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           E+F+   G +F  YA   ++ AI   +        +P  +R +  ++ R    ++ +++R
Sbjct: 70  ERFEPVRGVRFEAYADTRIRGAIFDGLRSLDW---VPRAVRAEAREIERATAELAMRLQR 126

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGD----EDTSHLGDFIEDKNAVS 599
            PT  E+A  L+M    +   L+   +   ++L+ P G          L D + D +AV 
Sbjct: 127 MPTDPELAGALSMSRRQLAASLQRVSDSRIVALDEPWGPVLADGRPVALLDTLPDLDAVD 186

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P   + +    E     +  L  RE+ VL    G+  + D TL ++G+   ++  R  Q+
Sbjct: 187 PAADSDETERSERIGAAVRQLPAREQVVL----GLRYHHDLTLLQIGEVLGISESRTSQL 242

Query: 660 EAKAIRKLK 668
             KA  +LK
Sbjct: 243 HTKAALQLK 251


>gi|256391118|ref|YP_003112682.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256357344|gb|ACU70841.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 366

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 52/246 (21%), Positives = 103/246 (41%), Gaps = 16/246 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +++            + E++  ++     VA +++       DL Q   + L+KA + F
Sbjct: 113 ELLADCESDSVRHRTLRDELIAEHMNYARYVASRFSVPADTAEDLEQVAYLALIKAVDNF 172

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT-ARRMSNKIKREP 547
           D   G  F  Y    V   I R   D +  + +P  M++    +    A ++  ++ R P
Sbjct: 173 DPARGTAFLGYLTPMVAGEIKRYFRDSTWDVHVPRRMQELSLALHGAPAEQLERRLGRSP 232

Query: 548 TPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDT--SHLGDFI-EDKNAVSPLD 602
           T  E+A+ L    E + +           SLE P+   D   + LG+ +  D +A   + 
Sbjct: 233 TIAELAEHLGAQPEEIVEAFDASAAYSATSLERPLVPGDEQGASLGETLGGDDDAYEWVV 292

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE    +LA+L  +++R+L MRF  G     T  ++G +  V++ ++ +   +
Sbjct: 293 D------REALKPLLAALPEKDKRILLMRFFRG----MTQSQIGTELGVSQMQVSRYLTR 342

Query: 663 AIRKLK 668
            +  L+
Sbjct: 343 ILSTLR 348


>gi|292696837|dbj|BAI99591.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 14]
 gi|292696851|dbj|BAI99598.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 503]
 gi|292696853|dbj|BAI99599.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 20]
 gi|292696865|dbj|BAI99605.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696875|dbj|BAI99610.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696877|dbj|BAI99611.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696887|dbj|BAI99616.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696921|dbj|BAI99633.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp.
           hydrophila]
 gi|292696927|dbj|BAI99636.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp.
           hydrophila]
 gi|292696929|dbj|BAI99637.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila subsp.
           hydrophila]
 gi|292696933|dbj|BAI99639.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696939|dbj|BAI99642.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696947|dbj|BAI99646.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO1235]
 gi|292696951|dbj|BAI99648.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO1080]
 gi|292696965|dbj|BAI99655.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696989|dbj|BAI99667.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696993|dbj|BAI99669.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698266|dbj|BAI99677.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC13]
 gi|292698272|dbj|BAI99680.1| RNA polymerase sigma-70 factor [Aeromonas sp. MU2]
 gi|292698274|dbj|BAI99681.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698280|dbj|BAI99684.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698284|dbj|BAI99686.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698288|dbj|BAI99688.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698290|dbj|BAI99689.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698294|dbj|BAI99691.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698320|dbj|BAI99704.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698322|dbj|BAI99705.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698324|dbj|BAI99706.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698352|dbj|BAI99720.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 49/292 (16%), Positives = 103/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +   + + + D+ +  
Sbjct: 49  --------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + +LR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|291196300|emb|CBG22621.1| DNA-directed RNA polymerase subunit D [Pseudomonas fragi]
          Length = 237

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 39/284 (13%), Positives = 92/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +   +  + + +       ++  +    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDPKVKAEGDDEEDDKEESSEDEEEVESGPDPIIAAQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + S +       L +L
Sbjct: 110 ARKAL-----------------------------------KKHGRGSKQAIAELVALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL    G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRLFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG+ I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEI 237


>gi|167040197|ref|YP_001663182.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           sp. X514]
 gi|300914281|ref|ZP_07131597.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|307265137|ref|ZP_07546696.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307724483|ref|YP_003904234.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|326391064|ref|ZP_08212611.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166854437|gb|ABY92846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889216|gb|EFK84362.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|306919759|gb|EFN49974.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307581544|gb|ADN54943.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|325992849|gb|EGD51294.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score =  113 bits (281), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 115/241 (47%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++R  +     + ++++  N  L+ S+ KK++NRG +  DL Q G IG +KA +KF
Sbjct: 11  ENLELIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVKAIQKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K STYA+  +   I R + D    I++   +++   K       +SN++ REPT
Sbjct: 71  DESYNVKLSTYAVPIIMGEIKRFLRD-DGLIKVSRSLKELSTKAFYVKEILSNELNREPT 129

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EIA++L +  E +    +      SL      ++   L         VS  +  +  +
Sbjct: 130 INEIAERLNVSPEEIAMAFESAATAESLYDNATHDEDDRLL-----IEMVSEEEKEVDID 184

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     V+  L PRE++++ +R+      D T  EV     +++ ++ +IE K ++KL+
Sbjct: 185 DKLALQMVINKLKPREKQIIFLRYF----KDMTQMEVASVLGISQVQVSRIEKKVLQKLR 240

Query: 669 H 669
            
Sbjct: 241 K 241


>gi|67078088|ref|YP_245708.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
 gi|66970394|gb|AAY60370.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
          Length = 323

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 133/264 (50%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-- 469
           EIK I     +S  E    +++ ++ +      +  +   N+ LV+S+A+KY N+     
Sbjct: 39  EIKEIGNYQVLSKQES---LNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+K+ +   I  +     +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIKKRMLGIICKKRSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS 586
             K V    +      R P+ EE+ K+L +  E V +     K    ++L+    +ED  
Sbjct: 156 NLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRVTTMTLDIDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
               F +DK+A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 ISNSFYDDKSAIPSINEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K   +T ER+ QI+ +AI+KLK 
Sbjct: 276 AKALMITTERVSQIKEEAIKKLKK 299


>gi|284007149|emb|CBA72430.1| flagellar biosynthesis sigma factor [Arsenophonus nasoniae]
          Length = 243

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 111/237 (46%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  I K  + E  + LV   A K   R    ++  DL+Q G IGL+ A E+FD   G
Sbjct: 8   YTQDGVIEKDVLWERYIPLVRHEALKLQVRLPASVELDDLVQAGGIGLLDALERFDASQG 67

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  V+ A+   +  +     +P  +R +  +  +  +++   + R  T +EIA
Sbjct: 68  TAFTTYAVQRVRGAMLDELRARDW---VPRSVRRQAREATKVMQQLEQALGRPATEQEIA 124

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
            KL + +   +++L+ T      S +        S     IE  +  +PL + I  ++R+
Sbjct: 125 DKLHIGLLEYQQLLQDTNNSQLCSYDEWHEVHGES-CEPIIEVDDERNPLQTLIATDIRK 183

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + +  L  RE+ VL + +      D  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 184 NIIKAIECLPEREKMVLTLYY----QEDLNLKEIGAVLNVGESRVSQLHSQAIKRLR 236


>gi|291196394|emb|CBG22669.1| DNA-directed RNA polymerase subunit D [Pseudomonas simiae]
          Length = 238

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 95/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + +   DD  E  GD         +D  +    P  A      + +  + 
Sbjct: 59  PPPVDAKAAKADDDTEDDDAEASGD--------DEDEVESGPDPIIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +++ +       L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRANKQAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 238


>gi|254498663|ref|ZP_05111381.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
 gi|254352111|gb|EET10928.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
          Length = 280

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 71/280 (25%), Positives = 129/280 (46%), Gaps = 27/280 (9%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +D+ +   N+I  +++E  I+ +E        R        A + +V A+LR V+ VA+
Sbjct: 12  SLDAYIHRVNQIPMLTMEEEIACAE--------RFHSEGDIEAARRLVLAHLRYVVRVAR 63

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            Y   GL   DLIQEGN+GLMKA ++FD  +G +  ++A+ W+K  I   +      ++I
Sbjct: 64  GYLGYGLPLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKI 123

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPE--EIAKKLAMPVEGVRKVLKITKEPISLETP 579
                 +  K+    R+M N++      E   +AK L +  + V   L + +   +++ P
Sbjct: 124 ATTKAQR--KLFFNLRQMKNRLGWFSNEEVAAVAKDLGVSTDEV---LVMEQRLNAMDAP 178

Query: 580 IGDEDTSHLGDF----------IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
               D     DF          + D  A+     +     RE     L  L  R + +L+
Sbjct: 179 YDAPDADDNDDFHMAPERYLFNVNDDPALVLEKESTGDRGREQLLLALEQLDERSQDILQ 238

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R+        TL ++ +++ ++ ER+RQ+E  A++KL+ 
Sbjct: 239 QRWLAD--DKLTLHDLAEKYAISAERVRQLEKNAMKKLRQ 276


>gi|254796721|ref|YP_003081557.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
 gi|254589969|gb|ACT69331.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
          Length = 288

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 126/262 (48%), Gaps = 15/262 (5%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + I     +   E R ++   R        A + +VEA LRLV+ V  ++ N G   +DL
Sbjct: 18  RKILAIPILQEEEERDLID--RWFLHRDISAAQRLVEAYLRLVVKVTVRFRNYGFPLMDL 75

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
             EGNIGLMKA + F+  LG+  +TYA+WW+K AI   +      ++I      +  K+ 
Sbjct: 76  ASEGNIGLMKAIKNFNPTLGHGIATYAIWWIKAAINEYVIRSWSIVKIGTTAAQR--KLF 133

Query: 534 RTARRMSNK-----IKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH 587
              R++ N      +       +I++ L +    V ++   +    +SL   +G++ +S 
Sbjct: 134 FNLRKLKNSGSVAGLDEHQVVGKISEMLEVSKNDVEEMERILNVRDVSLNMQLGEDGSSE 193

Query: 588 LGDFI--EDKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           + D I   + N  + L    +  ++       + SL  R + +   R    +    TL+E
Sbjct: 194 VHDLIPFPEANQEAVLSETRERQMKNRLLYEAVESLEARHKEIFVARSLSAV--PRTLKE 251

Query: 645 VGKQFCVTRERIRQIEAKAIRK 666
           +G++F +++ER+RQI A+A++K
Sbjct: 252 LGEKFSISQERVRQIHARAMKK 273


>gi|169351193|ref|ZP_02868131.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
 gi|169292255|gb|EDS74388.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
          Length = 258

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 127/248 (51%), Gaps = 13/248 (5%)

Query: 428 RHIVSMV-RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           +   +++    + +    K+++V  N++LVIS+ K++ NR     DL Q G IGL+KA E
Sbjct: 21  KETYALIDEYQKTKDERIKEKLVNDNIKLVISMTKRFYNRSDGCDDLFQVGMIGLIKAIE 80

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F+     KFSTYA+  +   + R + D    I+I   ++D  +K+++      NK +RE
Sbjct: 81  NFNTSYDLKFSTYAVPLIIGEMKRYLRDNH-QIKISRSLKDIAYKILKIKDEYLNKFQRE 139

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSA 604
           PT +E+AKKL +    + + L  T    SL+  + + D + L   D + D+ A       
Sbjct: 140 PTIKELAKKLDIDQSVIVEALLSTNSVASLQEEVKNSDGNSLKMIDSLSDEKA-----GV 194

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
           ++ N R      L SL+ +E  V++ R+  G     +  E+ K+  +++ ++ +IE KA+
Sbjct: 195 LKTNERIDLYDALKSLSQKEHDVIKQRYFEG----LSQSEIAKELFISQAQVSRIEKKAL 250

Query: 665 RKLKHPSR 672
             L +  +
Sbjct: 251 NTLHNYLK 258


>gi|308273291|emb|CBX29894.1| RNA polymerase sigma-32 factor [uncultured Desulfobacterium sp.]
          Length = 298

 Score =  113 bits (281), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 70/271 (25%), Positives = 129/271 (47%), Gaps = 10/271 (3%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
               ++  +  +S    +S    R     V+  + +   A  E+V +NLRLV+ +A ++ 
Sbjct: 18  KYDPLQRYMMEVSNHNLLSR--EREYALAVKVFDHDDKDAAYEIVTSNLRLVVKIALEFQ 75

Query: 465 NRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              +Q  LDLIQEGNIGLM+A  KFD     KFS YA +W+K  I + I D    ++I  
Sbjct: 76  RIWMQNLLDLIQEGNIGLMQAVRKFDPYKNVKFSYYASFWIKAYILKFIMDNWRLVKIGT 135

Query: 524 HM-RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIG 581
              + K+   ++  ++       +P P+ ++++L +  + +  +  ++    +SL TP+ 
Sbjct: 136 TQGQRKLFFKLKKEKQDLIDQGFDPKPKLLSERLGVTEKEIVDMDQRLDGWDVSLNTPLS 195

Query: 582 DEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           D+  S   +FI    D          +   +          +T RE  +  +   I  + 
Sbjct: 196 DDSDSEKIEFISYDSDSAEEQVAKKQMDNLIYSKIDEFRKLMTKRENEIFDL--RIFSDN 253

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             TL+E+G ++ ++RER+RQ+E   I K++ 
Sbjct: 254 PVTLQEIGDRYGISRERVRQLEKNIITKMRE 284


>gi|116694211|ref|YP_728422.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
 gi|113528710|emb|CAJ95057.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
          Length = 238

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 113/242 (46%), Gaps = 12/242 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + + ++V+A+ +LV  +A +   R    +Q  DLIQ G IGL+ AA++++   
Sbjct: 1   MYTIQGKLEQADVVKAHAQLVRRIALQLAARLPASVQIDDLIQAGMIGLLDAAKRYEDTH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +            +R    ++ RT R +  K+ R P   E+
Sbjct: 61  GARFETYASQRIRGAMLDEVRANDW---QSRSLRQFTRRIERTQRGLEQKLGRAPLDSEV 117

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ + M ++  + +L      + +  E      +   L   +   +  +PL   +++ +R
Sbjct: 118 AEAMEMALDEYQLLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGSDDGNPLTVLMESGMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   R +  L  RE+ VL + +    + +  L E+G    VT  R+ QI  +AI +L++ 
Sbjct: 178 EALIRAIDRLPEREKLVLSLCY----DQELNLREIGAVLDVTESRVCQIRGQAITRLRNQ 233

Query: 671 SR 672
            R
Sbjct: 234 LR 235


>gi|55274889|gb|AAV49247.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 180

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 68/185 (36%), Positives = 115/185 (62%), Gaps = 8/185 (4%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  L LI        +A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLGLI--------RAVEKFDPERGFRFSTYATWWIRQTIERAIM 53

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 54  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 113

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RFG
Sbjct: 114 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 173

Query: 634 IGMNT 638
           +    
Sbjct: 174 LLGYE 178


>gi|291196282|emb|CBG22612.1| DNA-directed RNA polymerase subunit D [Pseudomonas brenneri]
          Length = 238

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/284 (16%), Positives = 100/284 (35%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + E D + A   + D+      P             D   
Sbjct: 50  GIAPPAAEIPPPVDPKAAKADDETDDDEAEASTDDEEEVESGP-------------DPII 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  + S +       L +L
Sbjct: 97  AAQRFGAVSDQM------------ELARKALK---------KHGRGSKQATAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEI 238


>gi|291196268|emb|CBG22605.1| DNA-directed RNA polymerase subunit D [Pseudomonas antarctica]
          Length = 238

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 92/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + E D + A   + D+      P             D+ +
Sbjct: 50  GIAPPAAEVPPPVDPKAAKADDETDDDDAEASTDDEDEVESGPDPIVAAQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +     +  L  +AE++                                 
Sbjct: 110 ITRKALKKHGRGNKLAIAELVVLAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEI 238


>gi|238784716|ref|ZP_04628720.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238714395|gb|EEQ06403.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 240

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVIDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQQVEQRVGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           K L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 KILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|311031146|ref|ZP_07709236.1| RNA polymerase sigma factor SigB [Bacillus sp. m3-13]
          Length = 261

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 112/238 (47%), Gaps = 4/238 (1%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R  +    +++ ++VE    LV S+A+KY+       DL Q G IGL+ A ++FD   
Sbjct: 16  LERYQQDGCEVSQLQLVEHYTALVESIARKYSRGKAFHEDLSQVGMIGLLGAMKRFDASF 75

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++N+++R P   EI
Sbjct: 76  GRSFEAFAVPTIIGEIKRFLRDKTWSVHVPRRIKEIGPKIKSAVEELTNELQRSPKVFEI 135

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  L +  E V + +++++   +L      E  S            +      Q + +  
Sbjct: 136 ADYLEVTEEEVLEAMEMSQNYQALSVDNAIEADSDGSTVTILDIVGNQDAGFDQVDQQLL 195

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             ++   L+ RE++++   F        + +E G++  +++  + +++ KA+ KLK  
Sbjct: 196 LQKIFHVLSEREKQIIECTFFKN----MSQKETGEKLGISQMHVSRLQRKALTKLKQA 249


>gi|291537993|emb|CBL11104.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis XB6B4]
          Length = 248

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 55/241 (22%), Positives = 112/241 (46%), Gaps = 8/241 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++++       A+  ++  NL LV ++A ++ +RG +  +L Q G IGLMKA +KFD  
Sbjct: 6   ELMQQAHGGDKGARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLS 65

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           L   FSTYA+  +   I R + D    +++   +++  +K  R    +  ++ REP   E
Sbjct: 66  LNLAFSTYAVPVIMGEIRRFLRD-DGMVKVSRTLKENAYKAGRAKEELWGELGREPGLLE 124

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQAN 608
           IA++  +    +   ++  ++  S+  P+ ++D   L       E +             
Sbjct: 125 IAERTGLSSGEIIMAMESARDVESIYQPVYEKDGDELLMVDQLCEKEENGKDEPEKEAVL 184

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    +++  L  RE+ ++R R+        T  E  K+  +T+ ++ ++E K +  L+
Sbjct: 185 NRMVIEQLMELLDEREQNLIRCRYFEN----RTQSETAKELGMTQVQVSRLEKKILLCLR 240

Query: 669 H 669
            
Sbjct: 241 K 241


>gi|308048769|ref|YP_003912335.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
 gi|307630959|gb|ADN75261.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
          Length = 237

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 101/233 (43%), Gaps = 15/233 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE +  LV  +A     R    +Q  DL+Q G +GL++AA  FD   G  F T+A 
Sbjct: 13  RAALVERHTPLVKRIAHHLLARLPASVQLDDLLQSGMVGLLEAARNFDGSKGASFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I         P  +     +V     ++  ++ R+PT  E+A  L + V+
Sbjct: 73  IRIRGAMLDEIRRGDW---TPRSVHRNSRRVTDAMEQLERQLGRDPTGTEVADYLELSVD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
               +L      +S    +G +D     D I   + +    D       +      + +L
Sbjct: 130 EYHHILH----DVSAGKLVGLDDLGVSEDAIGPGEESSEHFDHLADGRFQSALVEAIKTL 185

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             RE  VL + +    + +  L+E+G+   V+  R+ QI ++++ +LK   R+
Sbjct: 186 PEREALVLSLYY----DEELNLKEIGQVLGVSESRVSQIHSQSMVRLKTKLRA 234


>gi|256371428|ref|YP_003109252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008012|gb|ACU53579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 254

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 64/255 (25%), Positives = 103/255 (40%), Gaps = 17/255 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           +S  E        R        A+  ++E    LV  VA +        +   DL   G 
Sbjct: 1   MSDDEVIESAWR-RFKHDGDLEARNRLLEHYASLVRFVASRVAVGLPASVDPNDLASYGT 59

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            GL+ A EKF+   G KF TYA+  +K AI   +        +P  +R K   V +    
Sbjct: 60  FGLIDALEKFEPERGIKFETYAITRIKGAIIDELRAIDW---VPRSVRAKAKSVEQAYAA 116

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIG---DEDTSHLGDFIE 593
           +  ++ R PT  E+A +L M  + +  +         + L+  +      +   LGD + 
Sbjct: 117 LEARLHRPPTDAEVASELGMSEDELLAIYSKISFLGLVGLDEVVMSGERGEGMTLGDTLA 176

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D+   S   +  +   R      +  L  RE+ VL + +  G     TL E+G+   VT 
Sbjct: 177 DRRQ-SAGGAFEEQERRRMLADSINQLADREKTVLVLYYYEGF----TLAEIGRILGVTE 231

Query: 654 ERIRQIEAKAIRKLK 668
            RI QI +KA+  L+
Sbjct: 232 SRICQIHSKAVLALR 246


>gi|332527910|ref|ZP_08403946.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
 gi|332112486|gb|EGJ12279.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
          Length = 237

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 100/242 (41%), Gaps = 12/242 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  +    ++     LV  +A +   +    ++  DLIQ G IGL  A  +FD   
Sbjct: 1   MYTAKGQLDANALLRQYSPLVRRLAHQMIAKLPANVELDDLIQVGMIGLSDALSRFDAAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   +       R     +     +     ++  K+ R P   EI
Sbjct: 61  GVQFETFATQRIRGAMLDELRGNDWMSRGDRRHQR---SIEAAVHKLEQKLHRAPNESEI 117

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK++ + +   +++L      + I LE   GD+      D     +  +PL       +R
Sbjct: 118 AKEMGLSLAEYQELLTKVRGTQLIYLEDMSGDDGDEDYLDRHVHDDEANPLGRLQDQRMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     + +L  RE+ V+ M +      D  L+E+     VT  R+ Q+ +++I +L+  
Sbjct: 178 QALVDAIKNLPEREQYVMSMYY----EHDMNLKEIAAVLKVTESRVCQLHSQSIARLRTR 233

Query: 671 SR 672
            R
Sbjct: 234 LR 235


>gi|22298280|ref|NP_681527.1| RNA polymerase sigma factor SigF [Thermosynechococcus elongatus
           BP-1]
 gi|22294459|dbj|BAC08289.1| group 3 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 261

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/245 (23%), Positives = 111/245 (45%), Gaps = 12/245 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +    +  A   +  +VE N+ LV   A ++       F DL+Q G +GL++A E+FD  
Sbjct: 18  LQAYRDNPAPELRNRLVELNIGLVRKEAHRWVQCTQESFDDLMQVGTLGLIRAIERFDPT 77

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D+S  IR+P   +    +  R  + +  +++R PT  E
Sbjct: 78  KGVAFSSFAIPYIRGEIQHYLRDKSPQIRLPRRWQTLQSQGKRVIQELRQQLERPPTDSE 137

Query: 552 IAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
           IA+ L +P+E  +     +    P+SL+ P  + +     LGD + D+   S   +    
Sbjct: 138 IAQALDVPLEEWQAAKFASYHTTPVSLDAPTFEGEEESVALGDILPDQRYQSFQLAEED- 196

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    + L  L  R  ++L   F      D + +E  +   ++   + +   K ++ L
Sbjct: 197 --RIRLQQCLRKLEARTCQILEFVFL----RDLSQKETAELLGLSAVTVSRQIKKGLQAL 250

Query: 668 KHPSR 672
           +   R
Sbjct: 251 QQMMR 255


>gi|332701290|ref|ZP_08421378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332551439|gb|EGJ48483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 264

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 111/243 (45%), Gaps = 13/243 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + E  AS  ++E+V      +  +A +      + ++  +L+  G++GLM+A +KF+  L
Sbjct: 27  RWENFASQDREEIVRHYGPKIKIMALRLKAKLPQTVELGELMSAGSLGLMEALQKFNPEL 86

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA   +K A+   +            +R ++  +  T R +  +  R  T +EI
Sbjct: 87  RIKFETYAESRIKGAMLDELRRMDWY---SRGLRQRLRLMEHTVREIEQETGRPATVQEI 143

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK+  +  + V   L++ +  + L      E  + + D   D +   P  SA    L + 
Sbjct: 144 AKRTGLSEKDVDMGLEMLQNQLCLSLDAISECVASVSDAGVDGD---PYQSAAFQELIDK 200

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            T ++  LTPRE+ VL + +G     +  + E      +T  R+ Q+ ++A+ KL+   +
Sbjct: 201 ITLLIDELTPREKLVLSLYYG----EELNMRETANVMEITEGRVSQLHSQALGKLRKLFK 256

Query: 673 SKK 675
            + 
Sbjct: 257 DQY 259


>gi|253990087|ref|YP_003041443.1| flagellar biosynthesis sigma factor [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253781537|emb|CAQ84700.1| rna polymerase sigma factor for flagellar operon (sigma-f factor
           (sigma-27) (sigma-28) [Photorhabdus asymbiotica]
          Length = 244

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 113/237 (47%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E+FD   G
Sbjct: 9   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPACVELDDLLQAGGIGLLNAVERFDSLQG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +T R++   + R  + +E+A
Sbjct: 69  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVTQTIRKLEQDLGRPASEQEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K+L + +   R++L  T      S +        S     IE+ +  +PL   +++++R+
Sbjct: 126 KELKIDLVEYRQILLDTNNSQLFSYDEWHEMHGES-CEPVIEEGHETNPLQQLLESDVRQ 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + SL  RE+ VL + +      +  L+E+G    V   RI Q+ ++AI++L+
Sbjct: 185 RVIDAIDSLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRISQLHSQAIKRLR 237


>gi|291196296|emb|CBG22619.1| DNA-directed RNA polymerase subunit D [Pseudomonas
           extremorientalis]
          Length = 238

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 95/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + +   DD  E  GD         +D  +    P  A      + +  + 
Sbjct: 59  PPPVDAKAAKADDDSEDDDAEASGD--------DEDEVESGPDPIIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +++ +       L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRANKQAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 238


>gi|325660705|ref|ZP_08149334.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331085570|ref|ZP_08334654.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325473012|gb|EGC76221.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330407457|gb|EGG86959.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 240

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 118/240 (49%), Gaps = 8/240 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++++       A++++VE N  LV  + K++  RG    DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIQRSHDGDEKAREQLVEENTGLVWCIVKRFFGRGTDSEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K      R+  K  REPT
Sbjct: 63  DLNYDVKFSTYAVPMISGEIRRFLRD-DGMIKVSRSLKETAYKAFLARERLQKKYNREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+A +L +  E +   L  + E  SL  PI  +D + +   + DK            N
Sbjct: 122 MEELAAELEVEKEELAMALDASGEVESLHKPIYQKDGNEIQ--LLDKLEEEEGQEETILN 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 ++L  L   E +++ +R+           E+GK+  +++ ++ ++E K ++ ++
Sbjct: 180 -HMLIRQLLEELDREERQLIYLRYFANQTQS----EIGKKLGISQVQVSRLEKKILKNMR 234


>gi|254246774|ref|ZP_04940095.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
 gi|124871550|gb|EAY63266.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
          Length = 306

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 106/253 (41%), Gaps = 13/253 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            RH          +  +++ +++     LV  +  +   +    +   DLIQ G IGLM 
Sbjct: 55  ERHPKERATMYNAQGKMSQADVLAQYAPLVRRLGLQLVAKMPASVDLDDLIQAGMIGLMD 114

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AA ++    G +F TYA   ++ A+   +        +P  +R    +V     ++   +
Sbjct: 115 AAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSREVEHAVHQVEQHL 171

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            R  +  EIA+ L MP++  + +L+       I  E      D     D     +A  PL
Sbjct: 172 GRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDRAADDEPFLDRYRVDHA-DPL 230

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            + +  +LRE     +  L  RE+ ++ + +  G      L E+G    V+  R+ Q+ +
Sbjct: 231 SALLDDHLREALVEAIERLPEREKLLMSLYYERG----LNLREIGAVLEVSESRVCQLHS 286

Query: 662 KAIRKLKHPSRSK 674
           +A+ +L+   R +
Sbjct: 287 QAVARLRARLREQ 299


>gi|314935979|ref|ZP_07843329.1| RNA polymerase sigma-B factor [Staphylococcus hominis subsp.
           hominis C80]
 gi|313655985|gb|EFS19727.1| RNA polymerase sigma-B factor [Staphylococcus hominis subsp.
           hominis C80]
          Length = 256

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 115/247 (46%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGE-CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +      A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQDNINPHAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ +    ++N++ R P
Sbjct: 75  FDISFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVGDELTNELGRSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SILEIANRLEVNEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE  +++  F  G     + +E G++  +++  + +++  AIR
Sbjct: 195 EK--RMILERILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIR 248

Query: 666 KLKHPSR 672
           KL+  +R
Sbjct: 249 KLQQAAR 255


>gi|118443643|ref|YP_877879.1| sporulation sigma factor SigF [Clostridium novyi NT]
 gi|118134099|gb|ABK61143.1| RNA polymerase sigma-F factor [Clostridium novyi NT]
          Length = 251

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 119/239 (49%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++K +     A  E+VE NL LV +++KK+ NRG ++ D+ Q G++GL+KA   FD 
Sbjct: 17  LELIKKAKLGDKKALDELVEKNLPLVTAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R I D    I++   ++    K+     +++ K+ REPT E
Sbjct: 77  SYNVQFSTYAVPMIMGEIRRFIRD-DGLIKVSRSVKYTARKLHFDKEKLTKKLNREPTVE 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K   +  E +    +   EP  L   I  +D S +  ++ DK  V   +S I    +
Sbjct: 136 ELSKFSGIDKEQIIFATEAINEPKYLYDTIHQDDGSPI--YLIDK-VVLKDESEIDELDK 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L+ L  R  +++ +R+   +        V K   +++ ++ +IE K ++ +K 
Sbjct: 193 IALKEALSKLDQRSRQIIILRYFKDITQVK----VAKMLGISQVQVSRIEKKVLKTMKE 247


>gi|327394234|dbj|BAK11656.1| RNA polymerase sigma factor for flagellar operon FliA [Pantoea
           ananatis AJ13355]
          Length = 230

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 106/228 (46%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +      P  +R    +V     ++   + R  + +E+A++L + +E
Sbjct: 63  QRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHQVEQMLGRAASEQEVAQQLNVSIE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     + + E     +PL   ++ +LRE     + +L
Sbjct: 120 EYRQILLDTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGSLRERVIEAIEAL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKMVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 223


>gi|167770367|ref|ZP_02442420.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
 gi|167667689|gb|EDS11819.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
          Length = 225

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 54/225 (24%), Positives = 107/225 (47%), Gaps = 14/225 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  N+ LV S A ++  RG+++ DL Q G +GL KA + FD   G K STYA+  +
Sbjct: 12  REQTISENIGLVHSCAHRFKGRGIEYDDLFQAGCMGLCKAVDAFDPQRGVKLSTYAVPVI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    +++   +++   ++ R   +++  + REP+  E+A+ + +P E V 
Sbjct: 72  LGEMRRLFRDGG-AVKVSRTLKELSLRIGRAREQLALALGREPSVSELAQAMELPEEQVV 130

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L     P+SL     DED     D   D +    L   I      +  +V+  L  ++
Sbjct: 131 EALCAAAPPLSLTE--SDEDGGGQIDLPAD-SPEDQLADVI------SLNQVVEKLEDKD 181

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ +R+  G     T  +   +  +T+ ++ + E K +  L+ 
Sbjct: 182 RALIELRYYSG----MTQVQTAARLGMTQVQVSRREKKILGILRQ 222


>gi|240146182|ref|ZP_04744783.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|257201716|gb|EEV00001.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|291536709|emb|CBL09821.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis M50/1]
          Length = 248

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 118/241 (48%), Gaps = 8/241 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++++       A+  ++  NL LV ++A ++ +RG +  +L Q G IGLMKA +KFD  
Sbjct: 6   ELMQQAHGGDKGARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLS 65

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           L   FSTYA+  +   I R + D    +++   +++  +K  R    +  ++ REP   E
Sbjct: 66  LNLAFSTYAVPVIMGEIRRFLRD-DGMVKVSRTLKENAYKAGRAKEELWGELGREPGLLE 124

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQANL 609
           IA++  +    +   ++  ++  S+  P+ ++D   L   D + +K      +   +A L
Sbjct: 125 IAERTGLSSGEIIMAMESARDVESIYQPVYEKDGDELLMVDQLCEKEENGRDEPEKEAVL 184

Query: 610 -RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    +++  L  RE+ ++R R+        T  E  K+  +T+ ++ ++E K +  L+
Sbjct: 185 NRMVIEQLMELLDEREQNLIRCRYFEN----RTQSETAKELGMTQVQVSRLEKKILLCLR 240

Query: 669 H 669
            
Sbjct: 241 K 241


>gi|291196286|emb|CBG22614.1| DNA-directed RNA polymerase subunit D [Pseudomonas cedrina]
          Length = 238

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 42/284 (14%), Positives = 94/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGI------- 51

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       + +     +   D ++ A    +D  +    P  A      + +  + 
Sbjct: 52  -APPAAEVPPPVDPKAVKADDETEDDDAEASSDDEDEVESGPDPVVAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +S+ +       L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRSNKQAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEI 238


>gi|282861223|ref|ZP_06270288.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563881|gb|EFB69418.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 296

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 54/267 (20%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 412 EIKSISVETGISISEFRHI-------VSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           E+  I     I+  + R +       + ++ +G  E   A+  ++E N+ LV   A+++ 
Sbjct: 29  ELPWIEDAGKIAPKDARELSTLFFAQLQVLEEGTHEYQYARNTLIEMNISLVRFAARRFR 88

Query: 465 NRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           NRG     D+ Q G +GL+KA ++F+     +F+T+A+ ++   I R   D +  + +P 
Sbjct: 89  NRGSGDMEDITQVGIVGLIKAIDRFELSREVEFATFAVPYIVGEIKRFFRDTTWAVHVPR 148

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIG 581
            +++   ++ +    ++ ++ R+PT +E+A+ L +  + V + +  +      SL+ P  
Sbjct: 149 RLQELRVELAKAKEELAVRLDRDPTVKELAEYLGLTEDEVVEGIVASNGYTAGSLDLPTD 208

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             + +             P  +            +L  L  RE R++ MRFG     + T
Sbjct: 209 ANEATATATRTFADILGEPDAAMETVENLHALAPLLEELDDRERRIIEMRFG----QEMT 264

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++G +  +++  + ++ ++ + KL+
Sbjct: 265 QAQIGAELGISQMHVSRLLSRTLGKLR 291


>gi|188589198|ref|YP_001920238.1| sporulation sigma factor SigF [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778416|ref|ZP_04821336.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499479|gb|ACD52615.1| RNA polymerase sigma-F factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082731|gb|EES48621.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 251

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 112/239 (46%), Gaps = 12/239 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++   +   + A   ++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD  
Sbjct: 18  QLLPLAKDGDTEAMNRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLS 77

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++  +++    ++  T   ++ K+ R PT EE
Sbjct: 78  YNVKFSTYAVPMIIGEIKRFLRD-DGMIKVSRNVKSLAKRIHFTKEELTKKLNRSPTIEE 136

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANL 609
           +A+   +  E +   ++       L   I  +D +   L D + +K              
Sbjct: 137 LAEYSGVDKEEIIFAIESATSLQYLYDTIHQDDGAPVLLIDKLSEKGEDDIGMIN----- 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      L SL  +  +++ +R+      D T  +V K   +++ ++ +IE K + K++
Sbjct: 192 KIALKEALRSLDEKARQIIVLRYF----KDKTQVQVAKLLGISQVQVSRIEKKVLLKMR 246


>gi|251797416|ref|YP_003012147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
 gi|247545042|gb|ACT02061.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
          Length = 256

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 112/246 (45%), Gaps = 14/246 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF----LDLIQEGNIGLMKAAEKFDWC 491
             E     AKK ++E  L LV  V  +    GL       DL   G +GL+ A EKFD+C
Sbjct: 13  WKEEGDLEAKKRLIEQFLPLVDYVTNRMAI-GLPKNVLKDDLASNGVMGLIDAIEKFDYC 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F TYA W ++ +I   +        +P  +R+K  ++    + +  K  R  +  E
Sbjct: 72  RGLQFETYASWRIRGSIIDGLRQGDW---VPRSVREKAKRIEEAYQSLEQKYLRSVSDAE 128

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           I++ L +  +    +L         SLE PI +E++      + D+ A +P   A +  L
Sbjct: 129 ISQYLNVSEKEFTTMLHEIAITTVCSLEDPIREEESETRLSLLIDERAKNPDHKAHEFFL 188

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +++    +  LT +E  V+ + +      + +L E+ +   ++  RI Q+ +KAI +L+ 
Sbjct: 189 KDSLISGIEKLTEKERTVISLFY----YEELSLSEIAEVMSLSPSRISQLHSKAILRLRG 244

Query: 670 PSRSKK 675
                K
Sbjct: 245 ALAKHK 250


>gi|292698292|dbj|BAI99690.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
          Length = 253

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/292 (17%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      +  + + IL+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLLEMD-EEILRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|289578314|ref|YP_003476941.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544594|ref|YP_003676896.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528027|gb|ADD02379.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842369|gb|ADH60885.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 116/239 (48%), Gaps = 10/239 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           ++++R  +     + ++++  N  L+ S+ KK++NRG +  DL Q G +G +KA +KFD 
Sbjct: 13  LTLIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCMGFVKAVQKFDE 72

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               K STYA+  +   I R + D    I++   +++   K       +S+++ REPT  
Sbjct: 73  SYNVKLSTYAVPIIMGEIKRFLRD-DGLIKVSRSLKELSTKAFYLKEVLSSELNREPTIN 131

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA++L +  E V    +      SL      ++   L         VS  +  +  + +
Sbjct: 132 EIAERLKVSPEEVAMAFESAATAESLYDNATHDEDDRLL-----IEMVSEEEKEVDIDDK 186

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                V+  L PRE++++ +R+      D T  E+     +++ ++ +IE K ++KL+ 
Sbjct: 187 LALQMVINKLKPREKQIIFLRYF----KDMTQMEIASILGISQVQVSRIEKKVLQKLRK 241


>gi|242238998|ref|YP_002987179.1| flagellar biosynthesis sigma factor [Dickeya dadantii Ech703]
 gi|242131055|gb|ACS85357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya dadantii
           Ech703]
          Length = 240

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    R+    + R PT +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAHAMRQAEQLLGRAPTEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL   +  NLR+ 
Sbjct: 122 QSLNISLEEYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEEANPLHQLMDVNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMEAIENLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|238924598|ref|YP_002938114.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
 gi|238876273|gb|ACR75980.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
          Length = 259

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 121/248 (48%), Gaps = 15/248 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +   ++K       A+++ +  NLRLV+SV ++++N      DL Q G IGL
Sbjct: 19  LKDDEKEELFEKIKK---GDKAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK+ + FD  +G KFSTYA+  +   + R + D S   RIP  +RD  ++ +++  ++S 
Sbjct: 76  MKSIDNFDPTIGVKFSTYAVPMIIGEVRRYLRDNS-AYRIPRSLRDTAYQAIKSKEKLSR 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K+  EP+  EI+K   +P   +   L   + P+SL  P+  +  DT ++ D I DK    
Sbjct: 135 KLVHEPSLAEISKDCGIPENDILYALDAIQTPLSLFDPVYTDGGDTLYVMDQISDKKNKE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                                  R  +++++RF  G     T  EV ++  +++ ++ ++
Sbjct: 195 EAWVKNLVLDDALKLL-----DDRARQIIKLRFFEG----KTQIEVAEEINISQAQVSRL 245

Query: 660 EAKAIRKL 667
           E  A++ +
Sbjct: 246 EKNALKNM 253


>gi|229113622|ref|ZP_04243069.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|228669818|gb|EEL25214.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|324323938|gb|ADY24981.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 323

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 78/263 (29%), Positives = 130/263 (49%), Gaps = 9/263 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--F 470
           I+ I     +S  E  H+    + GE      +  +   N  LV+SVA+ Y N+     F
Sbjct: 40  IRGIGNYKVLSKEESLHLFKRYKHGE---KDLRDYLFHVNEGLVLSVARNYKNKHPDIEF 96

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDKI 529
            DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I  +     +IP H+    
Sbjct: 97  DDLVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFN 156

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSH 587
            K V    +   +  R P+ EE+ K+L +  E V   KV       ++L+    +ED   
Sbjct: 157 LKYVELEDKYLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGI 216

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVG 646
              F +D++A+   +  I  +L      +    L P+++ VL + FG+     +  +E+ 
Sbjct: 217 SNPFFDDRSAIPSTNEMIIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEIA 276

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
           K   +T ER+ QI+ +AI+KLK 
Sbjct: 277 KALMITTERVSQIKDEAIKKLKK 299


>gi|94312634|ref|YP_585843.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
 gi|93356486|gb|ABF10574.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
          Length = 238

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + + ++V+++  LV  +A +   +    +Q  DLIQ G IGL+ AA++++   
Sbjct: 1   MYTIQGKLEQADVVKSHAPLVRRIALQLAAKLPASVQIDDLIQAGMIGLLDAAKRYEDNH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +            +R    K+ RT R++  K+ R P   E+
Sbjct: 61  GARFETYASQRIRGAMLDEVRANDW---QSRSLRQFTRKIERTQRQLEQKLGRSPIDSEV 117

Query: 553 AKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK+L M +E  +++L      + +  E      +   L   +   +  +PL   +++ +R
Sbjct: 118 AKELEMGLEEYQELLNEVHGCQLLHYEDFERSGEEDFLDRHLGVTDEANPLTVLMESGMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +   R +  L  RE+ VL + +    + +  L E+G    VT  R+ QI ++AI +L++ 
Sbjct: 178 DALIRAIEKLPEREKLVLSLCY----DQELNLREIGAVLEVTESRVCQIRSQAITRLRNQ 233

Query: 671 SR 672
            R
Sbjct: 234 LR 235


>gi|269961637|ref|ZP_06175999.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
 gi|269833678|gb|EEZ87775.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
          Length = 244

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 101/244 (41%), Gaps = 15/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKAITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++ +    +   + R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDIRKGDW---VPRSVHKNNREINQAIAELEGVLNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           P+  E+A  L M ++     L        + +E     +D     D  +D N   P    
Sbjct: 118 PSDSEVAAHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSN---PFKGV 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              + ++     +  L  RE  VL + +    + +  L+E+G    V+  R+ QI ++++
Sbjct: 175 ADESFKKALVESIKQLPEREALVLSLYY----DEELNLKEIGDVLGVSESRVSQILSQSM 230

Query: 665 RKLK 668
           ++L+
Sbjct: 231 QRLR 234


>gi|253573548|ref|ZP_04850891.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251847076|gb|EES75081.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 262

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 116/246 (47%), Gaps = 12/246 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E     AKK+++E  L +V  V+ +      + +   DL   G +GL+ A EKFD+ 
Sbjct: 17  RWKEHGDLEAKKQLIEKYLPIVDYVSGRLAVGLPKNVSKDDLASNGVMGLIDAVEKFDYK 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F TYA W V+ AI   +        +P  +R+K  K+    + +  +  R  T  E
Sbjct: 77  RGLQFETYASWRVRGAILDGLRQGDW---VPRSVREKAKKIEEGYQHLEQQYLRSVTDAE 133

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           ++  L +  +  + +L+        SLE PI +E++      + D+ A +P     +  L
Sbjct: 134 MSSYLNVSEKEFQSMLQEVAVMTLCSLEDPIREEESETRLTLLVDEKAKNPDYKVREFYL 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+  + +  LT +E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+ 
Sbjct: 194 RESLAKGIEKLTEKERTVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLRG 249

Query: 670 PSRSKK 675
               ++
Sbjct: 250 SLEKQR 255


>gi|251789202|ref|YP_003003923.1| flagellar biosynthesis sigma factor [Dickeya zeae Ech1591]
 gi|247537823|gb|ACT06444.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya zeae Ech1591]
          Length = 240

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +  ++    + R P+ +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAQAMQQAEQSLGRAPSEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL+  +  +LR+ 
Sbjct: 122 QTLNISLEEYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLNQLMDVSLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIENLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|291196362|emb|CBG22653.1| DNA-directed RNA polymerase subunit D [Pseudomonas palleroniana]
          Length = 237

 Score =  112 bits (280), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 98/284 (34%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++   + +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYNRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDAKVAKADDDSDDDEAESSDDEEEAESGPDPIIAAQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +++ +       L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRTNKQAIAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKAKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEI 237


>gi|330445383|ref|ZP_08309035.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328489574|dbj|GAA03532.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 240

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 102/234 (43%), Gaps = 15/234 (6%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +   + +  +E    LV  +A     R        DLIQ G IGL++A + +D   G  F
Sbjct: 9   QYQQSPQAFIERYSSLVKRIAHHLMVRLPPSVLVEDLIQSGMIGLLEAQQNYDPTKGASF 68

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            T+A   ++ A+   I        +P  +     K+      + N++ R+P  +EIA+ L
Sbjct: 69  ETFAGIRIRGAMLDDIRRGDW---VPRSVYKNSRKISEAISHLENELGRDPNDQEIAQYL 125

Query: 557 AMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
            MP+E   + L        + +      ED+    + IE+    +P       + R +  
Sbjct: 126 DMPLEQYHQALNDVNCGRLVGISDLGVAEDSVANEESIEEN---APFQDVADDSFRASLA 182

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +L  RE  VL + +    + +  L+E+G    V+  RI QI ++A+++L+
Sbjct: 183 EAIKTLPEREALVLSLYY----DEELNLKEIGAVIGVSESRICQIHSQAMQRLR 232


>gi|269795656|ref|YP_003315111.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269097841|gb|ACZ22277.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 345

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 103/250 (41%), Gaps = 18/250 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDW 490
               C  +  ++ ++     LV SVA +     L       DL+  G  GL+ A EKF+ 
Sbjct: 102 EYKACADAPTRERLILHYAPLVTSVASR-VGMKLPSTVEHADLVSYGMFGLIDAIEKFEL 160

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KF TYA   ++ AI   +        +P  +R K   V R    +  ++ R PT  
Sbjct: 161 DREIKFETYATSRIRGAILDELRANDW---VPRSVRSKARAVDRAHAELEARLHRAPTDP 217

Query: 551 EIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
           EIA+ + + +  +R  + L  T   ++L+   G  D        D      +  P  +  
Sbjct: 218 EIAEHMEIALSELRSIRHLVSTVNLVALDEVFGAGDQVEPVGHLDTGHGARSTDPARTFE 277

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               +   ++ +  L  RE+ +L + +  G     TL E+G    VT  RI Q+   A+ 
Sbjct: 278 SKETKFLLSQAMDQLGEREKIMLVLYYYEG----MTLAEIGAVLGVTESRISQMHTAAMG 333

Query: 666 KLK-HPSRSK 674
           +L+   SRS+
Sbjct: 334 RLREKLSRSE 343


>gi|238752744|ref|ZP_04614214.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
 gi|238709075|gb|EEQ01323.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
          Length = 240

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQKVEQRLGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QNLEIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|188533568|ref|YP_001907365.1| flagellar biosynthesis sigma factor [Erwinia tasmaniensis Et1/99]
 gi|188028610|emb|CAO96472.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           tasmaniensis Et1/99]
          Length = 240

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                 + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTANGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V     R+   + R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAGAMHRVEQALGRSASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRET 612
            +L + +E  R++L  T            E+     + + E     +PL   ++ +LR+ 
Sbjct: 122 AQLDVSLEEYRQILLDTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRDR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++A+++L+
Sbjct: 182 VIEAIEALPDREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAVKRLR 233


>gi|294673921|ref|YP_003574537.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294472533|gb|ADE81922.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 250

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 125/267 (46%), Gaps = 41/267 (15%)

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            +   +  I  E  ++  E R +   + K       A  +++EANL+ V+SVA++Y  +G
Sbjct: 21  ALNRYLDEIGREQLLTNEEERELAERIAK---GDERALSKLIEANLKFVVSVARQYKGKG 77

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DL+ EGN+GLMKAA KFD   G +F  +A  +++Q+I ++I  Q    ++P  ++ 
Sbjct: 78  VDMEDLVSEGNLGLMKAAAKFDASKGVRFVNFAFVYIRQSIEKAIDQQGGLYQVPKDVKQ 137

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                                  E+A++ A              + +S++ P+G      
Sbjct: 138 -----------------------EVARQQA--------------QAVSVDAPLGHRTNMS 160

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L   + +K+A    +      + +     L +L  RE RV+   +GI    + T+ E+ +
Sbjct: 161 LLSVLVNKDAPLADERVHSEAIEDAIEFALGTLDARERRVINAFYGINQEHE-TMAEIAE 219

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
              V RER+RQI  KA+RKL+   R+K
Sbjct: 220 DMDVKRERVRQIREKAVRKLRKAYRNK 246



 Score = 41.7 bits (96), Expect = 0.41,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
           YL E+G  +LL+ E E  +A+RI  G    ++ L E+ L F   +  + +
Sbjct: 25  YLDEIGREQLLTNEEERELAERIAKGDERALSKLIEANLKFVVSVARQYK 74


>gi|20807766|ref|NP_622937.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|20516321|gb|AAM24541.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
          Length = 240

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 119/244 (48%), Gaps = 12/244 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
               + +++  +     + ++++  N  L+ S+ KK+ NRG +  DL Q G IG +KA +
Sbjct: 3   EEENLELIKLAKNNDKASLEKLILENSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAVQ 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R + D    I++   +++   K       +SN++ RE
Sbjct: 63  KFDESYNVKFSTYAVPIIMGEIKRFLRD-DGLIKVSRSLKELSSKAFYMKEVLSNELNRE 121

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           PT  EIA++L +  E +    +      SL ++   +E+   L + + DK        ++
Sbjct: 122 PTINEIAERLNVTPEEIAMAFESAATAESLYDSISHEEEDRQLIEMVGDKE------DSV 175

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               + T   ++  L PRE++V+ +R+      D T  EV     +++ ++ +IE K + 
Sbjct: 176 DLEEKLTLHMIIDKLKPREKQVIFLRYF----KDMTQTEVANILGISQVQVSRIEKKVLE 231

Query: 666 KLKH 669
           K++ 
Sbjct: 232 KIRK 235


>gi|309778067|ref|ZP_07673006.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308914161|gb|EFP59962.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 259

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 121/250 (48%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E + +   +++       AK+ ++  NL+LV+S+ ++++NR     DL Q G IGL
Sbjct: 19  LTNAEMKELFVQLQQ---GDEQAKETLINGNLKLVLSIVQRFSNRCENMDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ + FD     +FSTYA+  +   I R + D    IR+  H++D  ++  +      +
Sbjct: 76  VKSIDNFDLKHEVRFSTYAVPMIMGEIKRYLRDNQ-VIRVSRHLKDLAYRAFKLKEEYVH 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
           K ++EPT   +A++L +  + +   L  T+  +S+  P+ + D     L D I+D     
Sbjct: 135 KNQKEPTIAWLAEQLEVKEKDIVDALDSTQSVLSIFEPVYNSDGDELFLLDQIKDDKD-- 192

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                   N      R L  L  +E  +++ R+      D T  E+  +  +++ ++ ++
Sbjct: 193 ---EIEHLNNIMALKRSLKRLKGKELDIIQKRY----YQDMTQTEIAGELGISQAQVSRL 245

Query: 660 EAKAIRKLKH 669
           E  AI  LK 
Sbjct: 246 EKNAIAVLKK 255


>gi|295399836|ref|ZP_06809817.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111652|ref|YP_003989968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
 gi|294978239|gb|EFG53836.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216753|gb|ADP75357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
          Length = 254

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 107/250 (42%), Gaps = 15/250 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLM 482
           E R      R        A  ++V+  + LV    ++      + +   +LI  G +GL 
Sbjct: 8   EERKYWD--RWIYDRDPQAGNKLVQTYMPLVHYHVQRIAASLPKNISKQELISLGLVGLY 65

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A EKFD     KF TYA + ++ AI   +  +     +P  +R+K  K+  T  ++  +
Sbjct: 66  DALEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDW---LPRSIREKAKKIEETIEKLEQR 122

Query: 543 IKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDF-IEDKNAVS 599
             R  T +E+A +L +    V            +S +    + D        I D+  +S
Sbjct: 123 YMRSVTAKEVADELGITEAEVYTVVNEHFFANVLSFQHVATENDEEENALLAIRDEKTLS 182

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P +  ++  L E    V+  L+ +E+ V+ + +      + T  E+G+   ++  RI Q+
Sbjct: 183 PEEEVLKQELYEKLAEVIQQLSEKEQLVISLFY----KEELTFTEIGEILGLSTSRISQL 238

Query: 660 EAKAIRKLKH 669
            +KAI KL+ 
Sbjct: 239 HSKAIFKLRK 248


>gi|225619299|ref|YP_002720525.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
 gi|225214118|gb|ACN82852.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
          Length = 275

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 114/246 (46%), Gaps = 17/246 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT-----NRGLQFLDLIQEGNIGLMKAAEK 487
            +   +  +   ++ ++     LV  VA K +     ++ ++F DL+  G+ GLM A +K
Sbjct: 26  WLEFKKTLSPYIREALIIKYSPLVKYVASKISVNMGSHKHIEFQDLVGFGSFGLMDAIDK 85

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           ++     KF TYA+  ++ AI   +        +P  +R  + ++ +    +  ++ R  
Sbjct: 86  YNPNRDIKFKTYAVTRIRGAIYDELRKLD---YLPRSIRKDVKEIEKAREILEARLSRNI 142

Query: 548 TPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLD 602
            P+EIA  L +P+    + +   I   P SL       D S    + D ++  +  +P  
Sbjct: 143 KPQEIADMLGIPISKYNETMKRYIEASPTSLSDVWYVGDDSDEISVIDTLKSNDKTNPEY 202

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A + +++      L  L  +E++VL + +      D TL+E+GK   V+  RI Q+  K
Sbjct: 203 LAEREDVKNKIIAALKKLPEKEQQVLILYY----YDDLTLKEIGKVLEVSESRISQLHTK 258

Query: 663 AIRKLK 668
           AI++L+
Sbjct: 259 AIQQLR 264


>gi|154503257|ref|ZP_02040317.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
 gi|153796251|gb|EDN78671.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
          Length = 238

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 133/246 (54%), Gaps = 12/246 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H ++++ K       A++++VE N+ L+  V K++  RG++  DL Q G+IGL+KA +KF
Sbjct: 3   HTIALIEKSHNGDKEAREQLVEENIGLIWCVVKRFYGRGIEAEDLFQIGSIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +++ +T  +M++ + REPT
Sbjct: 63  DLSYDVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELSYRIFQTREKMTDGLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            EE+++++ +  E + + ++ + E  SL  PI  ++ S   L D +E+K          +
Sbjct: 122 LEELSQEMGVEKEELVQAMEASGEVESLYRPIHQKEGSEISLLDKLEEKE-----HREEK 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R    ++L  L  +E  ++ +R+      + T   VGK+  +++ ++ ++E K I+ 
Sbjct: 177 ILDRMLLGQLLEKLDGQERTLIYLRYFA----EKTQSAVGKEMGISQVQVSRMEKKIIQN 232

Query: 667 LKHPSR 672
           L+  + 
Sbjct: 233 LREMTH 238


>gi|291196332|emb|CBG22638.1| DNA-directed RNA polymerase subunit D [Pseudomonas mandelii]
          Length = 238

 Score =  112 bits (279), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 91/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D E A   + D+      P             D+ +
Sbjct: 50  GIAPPAAEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +     +  L  +AE++                                 
Sbjct: 110 ITRKALKKHGRGNKLAIAELVLLAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEI 238


>gi|319944142|ref|ZP_08018420.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
 gi|319742636|gb|EFV95045.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
          Length = 241

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 110/238 (46%), Gaps = 12/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                 ++ +  ++E   ++V  VA +   R    ++  DLIQ G IGL+ A  +FD  +
Sbjct: 4   MYTPRGTLDRDSVIERYGKMVRRVAVQMAARLPSSIELDDLIQAGLIGLVDAVSRFDAAM 63

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+AM  V+ A+   + +       P  +R     + +    +  ++ R     EI
Sbjct: 64  GVQFDTFAMQRVRGAMLDELRNADWM---PRSVRKSQRSIEQAIHAVEQRLGRPAQEREI 120

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L +P+E  +++L   K    +  E    ++D     + +   +A +P      A  R
Sbjct: 121 ADELQVPLEEYQRLLSSAKGSQLLYFEDSASEDDDESRIEQMLPDDAPTPDRRLEDARFR 180

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+    +  L  RE+ ++ + +      + TL+E+G+   VT  R+ Q+ ++A+ +L+
Sbjct: 181 ESLVAAIDGLPEREKLLMNLYYV----EELTLKEIGEVLGVTESRVSQLHSQAVARLR 234


>gi|238788344|ref|ZP_04632138.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
 gi|238723590|gb|EEQ15236.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
          Length = 240

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQKVEQRLGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|291196294|emb|CBG22618.1| DNA-directed RNA polymerase subunit D [Pseudomonas tremae]
          Length = 238

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 92/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + +    + T+ D E +A  S D+      P             D+ +
Sbjct: 50  GIAPPAEVPPPVDSKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +     +  +  +AE++                                 
Sbjct: 110 ITRKALKKFGRDDKHAIAEMVALAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I + + ++ ++  ETG+ I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALGEETGLKIAEI 238


>gi|124268265|ref|YP_001022269.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
 gi|124261040|gb|ABM96034.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
          Length = 237

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 99/244 (40%), Gaps = 12/244 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                  +    M++    LV  +A +   +    ++  DLIQ G IGL  A  +FD   
Sbjct: 1   MYTATGRLETNAMIKQYSPLVRRLAHQMIAKLPANVEIDDLIQVGLIGLTDAMSRFDSAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   +       R     R +  ++     ++  ++ R P   EI
Sbjct: 61  GVQFETFATQRIRGAMLDELRGSDWMSRGN---RKQQREIEVAVHKLQQQLGRAPAESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK++ + +   +++L      + + LE   GD+  +   D        +P+       +R
Sbjct: 118 AKQMGLSLADYQELLGKVRGTQLVYLEDMSGDDGDNDFLDRHVADENENPVALLQDHRMR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 + +L  RE+       G+    D  L+E+     VT  R+ Q+ +++I +L+  
Sbjct: 178 LALIEAIKTLPEREQ----FVMGMYYEQDMNLKEIAAVLGVTESRVCQLHSQSIARLRAK 233

Query: 671 SRSK 674
            R  
Sbjct: 234 LRDH 237


>gi|238758082|ref|ZP_04619262.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
 gi|238703620|gb|EEP96157.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
          Length = 240

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVATAMQKVEQRVGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QTLDIELSEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIEALPDREKMVLTLYY----QEELNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|91776300|ref|YP_546056.1| flagellar biosynthesis sigma factor [Methylobacillus flagellatus
           KT]
 gi|91710287|gb|ABE50215.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Methylobacillus
           flagellatus KT]
          Length = 244

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 109/235 (46%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+++ +  LV  +A +   +    +   DLIQ G +GL+ A+ +++   G +F TYA 
Sbjct: 11  KEELLKQHASLVKKIAYQLKAKLPASVDIDDLIQAGMMGLLDASNRYEDNHGAQFETYAA 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +        +P  +R  +  V      +  K+ R PT  E+A++L + ++
Sbjct: 71  QRIRGSMIDELRRADW---LPRSVRKNMRDVESAVHLLEQKLGRPPTEGELARELNLSMD 127

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             + +L      + I  E     +   H  D  +  ++  PL + + ++ RE     + +
Sbjct: 128 DFQGMLDDCSGHQLIYYEDFSEQDSGDHFLDRYQSDDSGDPLKALLSSDFREALIEAIEA 187

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  RE+    +  G+    +  L+++G    V+  R+ Q+  +A+ +L+   + K
Sbjct: 188 LPEREK----ILMGLYYEQEMNLKDIGAIMSVSESRVCQLHTQAVARLRAKLKEK 238


>gi|167037535|ref|YP_001665113.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256752057|ref|ZP_05492925.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|320115950|ref|YP_004186109.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166856369|gb|ABY94777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256749067|gb|EEU62103.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|319929041|gb|ADV79726.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 246

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 115/241 (47%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++R  +     + ++++  N  L+ S+ KK++NRG +  DL Q G IG +KA +KF
Sbjct: 11  ENLELIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVKAIQKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K STYA+  +   I R + D    I++   +++   K       +SN++ REPT
Sbjct: 71  DESYNVKLSTYAVPIIMGEIKRFLRD-DGLIKVSRSLKELSTKAFYVKEILSNELNREPT 129

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EIA++L +  E +    +      SL      ++   L         VS  +  +  +
Sbjct: 130 INEIAERLNVSPEEIAMAFESAATAESLYDNATHDEDDKLL-----IEMVSEEEKEVDID 184

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     V+  L PRE++++ +R+      D T  EV     +++ ++ ++E K ++KL+
Sbjct: 185 DKLALQMVINKLKPREKQIIFLRYF----KDMTQMEVANILGISQVQVSRLEKKVLQKLR 240

Query: 669 H 669
            
Sbjct: 241 K 241


>gi|226939710|ref|YP_002794783.1| FliA1 [Laribacter hongkongensis HLHK9]
 gi|226714636|gb|ACO73774.1| FliA1 [Laribacter hongkongensis HLHK9]
          Length = 247

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 112/251 (44%), Gaps = 15/251 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +S +R  +  A+      +  +L LV  +A    +R    ++  DL+Q G IGL++AA++
Sbjct: 1   MSKLRAYQSAATTNSSVDITEHLTLVRKLASMMISRLPASVELDDLVQVGMIGLIEAAQQ 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G  F T+A   ++ A+   +        +P   R    ++     ++   +   P
Sbjct: 61  FDPAQGVLFETFASQRIRGAMLDELRRLDW---LPRQARRNAKQIEEAMAQLEQSLGHPP 117

Query: 548 TPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLD 602
              EIA +L + V+  + +L      + +  E    D+D      + + + D+  V+P +
Sbjct: 118 GEGEIAARLGLSVDEYQTMLFECKGHQLVYFEDFGHDDDEGSSTRMVEQVADQGMVNPFE 177

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              ++  R      +  L  R++ V+ + +      +  L+E+G    VT  R+ Q+ ++
Sbjct: 178 ILGESRFRSHLVAAIKELPERDQLVMSLYY----EQELNLKEIGAVLNVTESRVCQLHSQ 233

Query: 663 AIRKLKHPSRS 673
           A+ +L+   ++
Sbjct: 234 AVARLRTKLKA 244


>gi|315001918|emb|CBI75445.1| RNA polymerase sigma factor [Aeromonas sobria]
          Length = 242

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/285 (17%), Positives = 92/285 (32%), Gaps = 44/285 (15%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P             +         E
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNETE-----DVAPTATHIGSELSE 53

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            +  D  E E + E     + DD       PE A      L    + +  ++        
Sbjct: 54  DDLADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREKFGELRAQYEVTRLSI-------- 105

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                                      QK+ ++    +    +L  +     L   + D 
Sbjct: 106 ---------------------------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDR 138

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV  + ++ +R+   E  +L+L  +   + +  F+      E D  W  Y K   +  W 
Sbjct: 139 LVNNMREMMERVRVQERIILKLCVEQAKMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WS 197

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +    D +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMADDVLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|209408350|emb|CAP19916.2| DNA-directed RNA polymerase subunit D [Pseudomonas balearica]
          Length = 241

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 48/283 (16%), Positives = 93/283 (32%), Gaps = 44/283 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++   D +      L +I  L   I P+  G       
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDGILADYDRVVSEGGRLSDI--LSGYIDPDDDGAAAPQEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                +    +   ++      + + +  +  S ++       PE A      + E    
Sbjct: 59  EPVAPQVASKAAADDK-----DDDEEDEESSDSDEEEGDGGPDPEVARIRFGAVAEQLAK 113

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + S +     E L  L
Sbjct: 114 AQKAL-----------------------------------KKFGRGSQQATDELEALAIL 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++ D   RI   E  +++L      + R  FL      E +  W
Sbjct: 139 FMPIKLVPKQYDALVERVRDALARIRAQERAIMQLCVRDARMPRADFLREFPNNETNLGW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
              A    + ++   +A   D I   + ++  +  ETG+S+++
Sbjct: 199 AE-AIASGKSKYAEAIAARKDDIRACQQKLVDLEQETGLSVAD 240


>gi|164686436|ref|ZP_02210464.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
 gi|164604447|gb|EDQ97912.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
          Length = 256

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 117/259 (45%), Gaps = 9/259 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K  S  T     E + + + +   +      +  ++E NL LV  +AKKY N+G++F D
Sbjct: 1   MKHTSSITNYLDMETKELFN-IYSNDKSNKEVRDILIERNLYLVSILAKKYINKGVEFED 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G++ L+ A E++D   GY+FS++A   +   I +   D+  T+R+P  +++   KV
Sbjct: 60  LYQVGSLALIYAIERYDISKGYEFSSFATPTIIGEIKKYFRDKVWTMRVPRRVQELNKKV 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAM--PVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
                 +  + K++P   EIA+ +                 +P+SL++P+  +       
Sbjct: 120 NEAKLLLEQQNKKKPKVNEIAEYIGCREEEVLEALEASYGYQPVSLDSPVNSDSEEAEIS 179

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I      S  ++      ++   +  + L   E  +   RF      + T   + K+  
Sbjct: 180 LI--DKIGSQENNFSDIEYKDFIEKFTSKLNELERNIFEGRFF----KEKTQSALAKELD 233

Query: 651 VTRERIRQIEAKAIRKLKH 669
           +++  I +IE K ++KL+ 
Sbjct: 234 ISQMTISRIERKVVQKLRK 252


>gi|256379404|ref|YP_003103064.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923707|gb|ACU39218.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 243

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 101/244 (41%), Gaps = 19/244 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +     + E    + + ++V   L +   +A ++  RG    DL Q   +GL+ A +
Sbjct: 11  FRELAEAQSRVERRQEL-RDQLVTEYLPVAWHIADRFAERGESVEDLRQVAAVGLIHAVD 69

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  F  +A+  +   + R + DQ   +R+P  +++    +      ++    R 
Sbjct: 70  RFDVQRGIDFLAFAVPTITGEVRRHLRDQGWAVRVPRRLKELCLAIDAARVELARASGRT 129

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PTP E+A+ L + +  V + L        +SL+            +   D        + 
Sbjct: 130 PTPSEVARHLNLSLAEVYEGLHATSANHMVSLD------------EVDSDHRLGVDDPAL 177

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               L+     +L  L  RE R++ +RF        T  ++     V++  + ++ ++++
Sbjct: 178 EVVELQHALDPMLRGLPKRERRIVLLRFFRN----MTQSQIADSVGVSQMHVSRLLSRSL 233

Query: 665 RKLK 668
            +L+
Sbjct: 234 ARLR 237


>gi|323703189|ref|ZP_08114842.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531848|gb|EGB21734.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 251

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 110/244 (45%), Gaps = 14/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCL 492
                   A+++++   L LV  +A +   +   F    DL   G IGLM+A +KFD  +
Sbjct: 10  YITSRDERARQQLILHYLPLVKHLAGRLAVKLPSFIQREDLEGYGVIGLMEALDKFDHTM 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F  YA   ++ AI   +  Q+    +P     K+  + +T  R+  ++      E +
Sbjct: 70  GNSFDAYAYHRIRGAILDQVRRQNW---LPRTAWQKLQHLKQTRERLERELGGAVPDEIL 126

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQAN 608
           A+++ + V+ +  +         +SL+  +   D S +   D +ED  +  PL    +  
Sbjct: 127 AREMGISVDELNHLASSAGKMYLMSLDEEVPGSDGSVVRKLDLVEDTGSPDPLSIVEEKE 186

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+   R +  L  R++ +L + +  G     TL+E+G+   V+  R+ Q+  + +RKL+
Sbjct: 187 NRKLLARAIEKLGQRDQLILSLYYTEG----LTLKEIGQVLEVSESRVCQLHGQVMRKLR 242

Query: 669 HPSR 672
              +
Sbjct: 243 KTLQ 246


>gi|291196328|emb|CBG22636.1| DNA-directed RNA polymerase subunit D [Pseudomonas lutea]
          Length = 235

 Score =  112 bits (279), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 46/284 (16%), Positives = 99/284 (34%), Gaps = 50/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T + ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + + + V+  + D E +A    +  +  D                   
Sbjct: 50  GIAPPAEVPPPVDPKAEKVEGADDDEEDSADDEDEVETGPDPV----------------I 93

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+    + AL                     K  + S +       L +L
Sbjct: 94  AAQRFGAVSDQM-AIAIKALK--------------------KHGRGSKQANAELLALAEL 132

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 133 FMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDQSW 192

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I + + ++ ++  ETG++I E 
Sbjct: 193 TD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLTILEI 235


>gi|292696829|dbj|BAI99587.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696835|dbj|BAI99590.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 253

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 103/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E +D+  T   I S            +   +  E+ + + D+ +  
Sbjct: 49  --------------ETEDIAPTATHIGSELGEDDLADEDEEDEEDEDEDGDSSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ QK+ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|238798562|ref|ZP_04642039.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238717582|gb|EEQ09421.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 240

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVIDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQQVEQRVGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           K L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 KILDIDLVEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|297162318|gb|ADI12030.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 261

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 115/253 (45%), Gaps = 14/253 (5%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T  +  +F  +  +    E +A   ++ ++ A L +   +A ++ N+G    DL Q  ++
Sbjct: 14  TPDTDGDFARLSRLPSGPERDAL--REAIICAWLPVAKRLALRFRNKGENMEDLTQVASL 71

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            L+KA +++D  LG+ F +YA+  +   + R   D   T+ +P ++++   +       +
Sbjct: 72  ALVKAVDRYDPDLGHAFPSYAIPVITGELKRHFRDYLWTLHVPRNIQEVRSRTRSARDAL 131

Query: 540 SNKI-KREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKN 596
             ++  R PT  EI+ +  MP E V   L+   +  P+SL   +   +   L + +   +
Sbjct: 132 EQELGGRTPTITEISTRTGMPKEDVMAGLEASASCTPLSLNAAVQGAEERLLAETVGADD 191

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A        +   RE    ++  L+ ++  VL +RF +G     +  ++G+    ++  I
Sbjct: 192 AA-----IERVVNREALRALITHLSEQDRYVLYLRFFVG----LSQSQIGEILGFSQMHI 242

Query: 657 RQIEAKAIRKLKH 669
            +  ++   +L+ 
Sbjct: 243 SRRLSRLYSELRQ 255


>gi|292696969|dbj|BAI99657.1| RNA polymerase sigma-70 factor [Aeromonas sp. TSC1]
          Length = 253

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 102/292 (34%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +   + + + D+ +  
Sbjct: 49  --------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + +LR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      V  + D +L+   +++ I  ETG+SI + + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLVEMDED-VLRAIGKLQQIEEETGLSIEQIKDINRRM 248


>gi|6010722|gb|AAF01227.1|AF184096_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 228

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 69/174 (39%), Positives = 116/174 (66%), Gaps = 3/174 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 225



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|300814743|ref|ZP_07094991.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|300511130|gb|EFK38382.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 258

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 53/265 (20%), Positives = 124/265 (46%), Gaps = 15/265 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +    ++  ++  E + +   +   + +    +  ++E  L +   ++KKY  +G+ + D
Sbjct: 1   MNIKELDRKLTKEEKKELF--LEYYKTKDQDLRTILIEEYLYIAEILSKKYIGKGIDYDD 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           + Q  +IGL+ + ++FD   GY+FS++A   +   I +   D+  TIR+P  +++   K+
Sbjct: 59  IYQVASIGLIYSVDRFDPTKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELSKKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDT--SHL 588
           +    ++S + +R PT E+IA+ L    E + + ++ +    P SL+      D     L
Sbjct: 119 MIAKNKLSQEYQRTPTVEDIAEFLNASPEEIIESMEASKVYTPQSLDIVYDSGDDKKMSL 178

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I +           + +L++   + + +L   E+ +L  R+        T   + K+
Sbjct: 179 QDLIGEDE-----KYFDKIDLKDFLLKSMKNLNEVEKTILIDRYF----NKKTQIVIAKK 229

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             +++  + +IE K + K++   + 
Sbjct: 230 LNISQMTVSRIEKKVLEKMRKEIKK 254


>gi|291525265|emb|CBK90852.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale DSM
           17629]
 gi|291529276|emb|CBK94862.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale
           M104/1]
          Length = 259

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 121/248 (48%), Gaps = 15/248 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   +   ++K       A+++ +  NLRLV+SV ++++N      DL Q G IGL
Sbjct: 19  LKDDEKEELFEKIKK---GDKAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK+ + FD  +G KFSTYA+  +   + R + D S   RIP  +RD  ++ +++  ++S 
Sbjct: 76  MKSIDNFDPTIGVKFSTYAVPMIIGEVRRYLRDNS-AYRIPRSLRDTAYQAIKSKEKLSR 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           K+  +P+  EI+K   +P   +   L   + P+SL  P+  +  DT ++ D I DK    
Sbjct: 135 KLVHDPSLAEISKDCGIPENDILYALDAIQTPLSLFDPVYTDGGDTLYVMDQISDKKNKE 194

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                                  R  +++++RF  G     T  EV ++  +++ ++ ++
Sbjct: 195 EAWVKNLVLDDALKLL-----DDRARQIIKLRFFEG----KTQIEVAEEINISQAQVSRL 245

Query: 660 EAKAIRKL 667
           E  A++ +
Sbjct: 246 EKNALKNM 253


>gi|291196358|emb|CBG22651.1| DNA-directed RNA polymerase subunit D [Pseudomonas otitidis]
          Length = 239

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 97/284 (34%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P    +++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGAVDSILAEYQRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +  +  + K     +  + D E     S D   + D  P            D ++
Sbjct: 50  GSLPAEEVEPVELKSDSAAKAKDEDEEDEESESDDTEEEGDGGP------------DPEE 97

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +    +A+ DQ                     L+      +K  + S +     + L +L
Sbjct: 98  ALRRFTAVSDQ---------------------LEKARKALKKHGRDSKQATEELQALAEL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++     R+   E  +++L      + R  FL    G E+D  W
Sbjct: 137 FMPIKLVPKQFDALVERVRGALDRVRGQERAIMQLCVRDARMPRADFLRLFPGNEVDLTW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +   +D I + + ++  +  E  + ++E 
Sbjct: 197 AEDIAK-GKAKYAEAIGKLLDDIKRNQQKLVDLEKEVDLKVAEI 239


>gi|332654157|ref|ZP_08419901.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
 gi|332517243|gb|EGJ46848.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 103/238 (43%), Gaps = 12/238 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++      + A ++++E N  L+ SV ++Y  RG++  DL Q G +G +KA   FD  
Sbjct: 9   ELLQAAREGDNRACEQVLEENNGLIWSVVRRYYGRGVEPDDLYQLGCLGFLKAVRGFDPA 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +FSTYA+  +   I R + D    +++   ++++   +     ++ + + REP   E
Sbjct: 69  FGTQFSTYAVPKIAGEIRRFLRD-DGAVKVSRGLKEQGALIRGVRSQLWSTLGREPALSE 127

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+   +  E +          +SL+     E    L   +        L   I      
Sbjct: 128 LAQATGLTPEEIAAAETAADPVVSLQAE-TGEGGLTLEGVLSAGGMEEGLVERI------ 180

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                L  L  RE  VL +R+  G     T     +   V++ +I ++E +A+ +L+ 
Sbjct: 181 ALRGALEQLPEREREVLLLRYYKG----LTQTNTARVLGVSQVQISRLERRAVDRLRQ 234


>gi|242371561|ref|ZP_04817135.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
 gi|242350713|gb|EES42314.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
          Length = 256

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 122/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SINEIAERLEVTDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSDRERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  ++
Sbjct: 249 KLQEAAK 255


>gi|239934528|emb|CAR94578.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 243

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 49/303 (16%), Positives = 94/303 (31%), Gaps = 62/303 (20%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           ++   G I IAKRIE G   +  +L   P T   L+   + +  G + L ++I       
Sbjct: 1   IVDARGXIRIAKRIEKGLNQVRGALVMFPPTIDLLLDLYEPVAAGESRLVDVI------- 53

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                GF    +    QK +  +                S     ++        PE+A+
Sbjct: 54  ----AGFIDPNQTDEVQKPKTKT--------------GNSDDDDDEEKEKDTGPDPEDAK 95

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                                            +I  +   +  L +             
Sbjct: 96  -----------------------------KRFAKIKRLRNRVIKLIE------DHGTGDP 120

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFL 371
           K    ++ L   V  L L     D L+ QL      I   E +++    +   + R  FL
Sbjct: 121 KTLKARKSLAAEVLELKLTPKVFDKLIGQLRATVSTIRRQERQIMVYCVREARMPRKDFL 180

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
                 E +  W+       + +  + ++   + IL+ + ++  I     +SI+E + I 
Sbjct: 181 ASFPANETNLQWIDKHI-RAKRKHSSVLSKLKEDILRSQRKLIGIEELCHLSIAEIKEIN 239

Query: 432 SMV 434
             +
Sbjct: 240 RQM 242


>gi|254250894|ref|ZP_04944212.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
 gi|124893503|gb|EAY67383.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
          Length = 369

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/209 (23%), Positives = 93/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 162 VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 218

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 219 TSREVEHAVHQVEQQLGRAASEAEIAQHLNMPLDEYQAMLQDLHGSQLIYYEDFDRAADD 278

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LR+     +  L  RE+ ++ + +  G      L E+
Sbjct: 279 EPFLDRFRVDHA-DPLSALLDEHLRDALVEAIERLPEREKLLMSLYYERG----LNLREI 333

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 334 GAVLEVSESRVCQLHSQAVARLRARLREQ 362


>gi|292696849|dbj|BAI99597.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 29]
          Length = 253

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EVDDVAPTATHIGSELSEDDLADEDEDEDQDEDEDGDNSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|292696827|dbj|BAI99586.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696841|dbj|BAI99593.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 34]
 gi|292696847|dbj|BAI99596.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 141]
 gi|292696857|dbj|BAI99601.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 62]
 gi|292696893|dbj|BAI99619.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696901|dbj|BAI99623.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292696935|dbj|BAI99640.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO548]
 gi|292696937|dbj|BAI99641.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO527]
 gi|292696943|dbj|BAI99644.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO1682]
 gi|292696957|dbj|BAI99651.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO1866]
 gi|292696967|dbj|BAI99656.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696973|dbj|BAI99659.1| RNA polymerase sigma-70 factor [Aeromonas sp. TSC4]
 gi|292696983|dbj|BAI99664.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC4]
 gi|292696991|dbj|BAI99668.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696997|dbj|BAI99671.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC7]
 gi|292698262|dbj|BAI99675.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC11]
 gi|292698276|dbj|BAI99682.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292698278|dbj|BAI99683.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292698282|dbj|BAI99685.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292698302|dbj|BAI99695.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292698308|dbj|BAI99698.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292698326|dbj|BAI99707.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698330|dbj|BAI99709.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698332|dbj|BAI99710.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698348|dbj|BAI99718.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698362|dbj|BAI99725.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|161898899|gb|ABX80439.1| SigB [Listeria monocytogenes]
          Length = 229

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           R    +VL  L  RE+++L+  F      + + +E G+   +++  + +I+ 
Sbjct: 182 RMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMHVSRIQR 229


>gi|160880817|ref|YP_001559785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
 gi|160429483|gb|ABX43046.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
          Length = 254

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 103/228 (45%), Gaps = 10/228 (4%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA +   Y    +++ DL+  G  GL+ A +KFD   G KF TYA 
Sbjct: 22  REKIIIEYANLVKIVAGRLSIYLGYNVEYDDLVGYGTFGLIDAIDKFDCEKGAKFETYAS 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I        IP  +R K  ++    +++     R+ T EE+AK+L +  E
Sbjct: 82  LRIRGAILDQIRKMDW---IPRTLRQKQKRLDAAYQKLETMYGRQATDEEVAKELEITTE 138

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +      TK    +      E      + I  ++   P     +  L+    + L  LT
Sbjct: 139 ELETWQNQTKISNLVSLDEYMEQGEVKVESIASEDYAQPEKVMEKQELKAMLVKALEYLT 198

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +E++V+ + +      D TL+E+     V+  RI Q+  KA++K++ 
Sbjct: 199 EKEKKVIVLYY----YEDLTLKEISAVLEVSESRISQLHTKALQKMRQ 242


>gi|292698304|dbj|BAI99696.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 253

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 97/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F       E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFFAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|127512314|ref|YP_001093511.1| flagellar biosynthesis sigma factor [Shewanella loihica PV-4]
 gi|126637609|gb|ABO23252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           loihica PV-4]
          Length = 239

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KASIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASAKFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     ++ +    +  ++ R+    EIA +L M ++
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRIAQVIDELEQELGRDAKDNEIADRLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +  ED +     +S  +    E     +  
Sbjct: 130 EYHHIL----NDVSVGKVVGIEDLGVSVDVVRQEDDHQDDAFESLAETQFHEALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYY----DEALNLKEIGAVLDVSESRVSQIHSQAMLRLK 230


>gi|126435251|ref|YP_001070942.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           JLS]
 gi|126235051|gb|ABN98451.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 284

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 47/227 (20%), Positives = 102/227 (44%), Gaps = 10/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++ A + +   +A ++  RG    D+IQ   IGL+K  +++D   G+ F  +A+  +
Sbjct: 46  RRHIITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVDRYDPDKGH-FLAFAVPTI 104

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I R   D + T+R+P  +++   ++      +S ++ R PT  E+A++L +  E + 
Sbjct: 105 RGEIRRHFRDNTWTVRVPRKVQETQLRMRDAVNTLSQRLNRTPTGVELAEELDVGSEELG 164

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     P+SL+ P+        GD +               +L       ++ L P
Sbjct: 165 DCQAATTAYRPVSLDAPLLTAQND--GDTVGSMQGGDDPGYGRVEDLI-LLQEAISDLDP 221

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R   ++ M F        T  EV ++  V++ +I ++   A+ +++ 
Sbjct: 222 RRRAIVGMIFF----DCLTQREVARRLHVSQVQISRLLNDALARIRQ 264


>gi|327441027|dbj|BAK17392.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 106/249 (42%), Gaps = 12/249 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFD 489
            VR  +     A   +++    LV    ++      + +   DL+  G +GL  A  KFD
Sbjct: 13  WVRWTKNRDPEAGDLLIKKFKPLVSYHVQRIAVGLPKNISRDDLMSLGMMGLFDALNKFD 72

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF TYA + V+ AI   +  +     +P   R+K  K+      +  K+ R  T 
Sbjct: 73  INRDLKFDTYASFRVRGAILDGLRKEDW---LPRSAREKAKKLESQIESLEQKLMRHATA 129

Query: 550 EEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           EE+A  + +PVE V +          +S+   +  E++      I D N  +P   ++  
Sbjct: 130 EEVAAHMNLPVEEVYQTFQEHFFSNVLSINEQLDQEESEGKSFVIRDDNTKTPEQHSVHV 189

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L       +  L  +E+ V+ + +      + TL E+G+   ++  RI QI +KA+ KL
Sbjct: 190 ELLGDLAENIKKLNEKEQLVISLFYS----EELTLTEIGEILDLSTSRISQIHSKALFKL 245

Query: 668 KHPSRSKKL 676
           +    S+ +
Sbjct: 246 RKLLSSEMI 254


>gi|239623681|ref|ZP_04666712.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521712|gb|EEQ61578.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 239

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++         A+ ++V  N+ L+ S+ ++++ RG +  DL Q G+IGL+KA +KF
Sbjct: 3   ETMKLINMAHEGDKAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++   KV      M+  + REPT
Sbjct: 63  DTGFEVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSIKELGFKVRAAREEMTYSLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLE--TPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            EEIA +L    E V   ++   E  SL   T  GD++T  L D +E++N     +   +
Sbjct: 122 IEEIAARLDTSREEVAASMEAGAEVESLYRPTGNGDDNTMFLMDRLEEEN-----NDHEE 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     ++  L   +  ++  R+           ++ K+  +++ ++ ++E + +++
Sbjct: 177 LLNRMVLKELMEDLGEEQREIIVRRYFYNQTQ----TQIAKELGISQVQVSRLEKRILKE 232

Query: 667 LK 668
           ++
Sbjct: 233 MR 234


>gi|206603135|gb|EDZ39615.1| Putative RNA polymerase sigma 28 subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 251

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 101/229 (44%), Gaps = 14/229 (6%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           ++     V   A +Y++R    L   DLI  G  GL+ AA +FD   G KF T A   ++
Sbjct: 10  LKEFAVTVKFFALRYSHRLPPELDIDDLISAGMGGLLDAARRFDPARGIKFKTLAEHRIR 69

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   I         P  +R+K+  V +    +  + KREPT +EIA ++ M  E   +
Sbjct: 70  GAMLDEIRAADWM---PRSVREKLTHVQQVKTELIARYKREPTRQEIAARMEMTEEEFDR 126

Query: 566 VLKIT--KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +         +SLE  +  ED     L D +       PL S +Q  + E   + L  L 
Sbjct: 127 LSVDIEPHHLVSLEDLMDPEDGDSPSLLDRLSAPQEGDPLASLLQNEVSEKLCQALDRLP 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            ++  VL + +      + T++EV +   V+  R+ QI  +A+  LK  
Sbjct: 187 EKQRLVLSLYY----YEELTMKEVARVVGVSESRVSQIHGQALAALKQS 231


>gi|145224387|ref|YP_001135065.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216873|gb|ABP46277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 301

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 112/246 (45%), Gaps = 11/246 (4%)

Query: 427 FRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
            + + SM       E    ++ ++   L L   +A ++  RG    DLIQ   IGL+K+ 
Sbjct: 55  EKQLSSMAACGDRAERRRRRQHIITECLPLADHIACRFAGRGEPSDDLIQVARIGLVKSV 114

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +++    G +F  +A+  ++  + R   D + ++R+P  ++D   ++   A  +S ++KR
Sbjct: 115 DRYVPDKG-RFMAFAVPTIRGEVRRHFRDSTWSMRVPRKIQDTQLRMRHAAEELSQRLKR 173

Query: 546 EPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EIA++L +    V +         P+SL+ P   +         E + A  P   
Sbjct: 174 APTDREIARELGVDDGEVSRCHSAHWAYRPVSLDAP-RGDAEQECAGIGELRGADDPGFD 232

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +++  +    + V+A L PR   +L MRF        T  E+  +  V++ ++ ++    
Sbjct: 233 SVEDLI--VLSGVIAELDPRRRAILGMRF----YDCLTQREIALRLNVSQVQVSRLLDST 286

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 287 LARLRQ 292


>gi|319940794|ref|ZP_08015133.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319805676|gb|EFW02457.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 281

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 68/266 (25%), Positives = 120/266 (45%), Gaps = 13/266 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +++      ++  E + +   +R  +     A +++V ++LRLVIS+A+ +   GL + D
Sbjct: 8   LRAAERAPMLTAEEEKTLALKLR--DQNDLEAAQKLVLSHLRLVISIARGFLGYGLPYAD 65

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHK 531
           LIQEGNIGLMKA  ++D   G +  T+A+ W++  I   I      +++     + K+  
Sbjct: 66  LIQEGNIGLMKAIRRYDPDRGARLMTFAVHWIRSEIQEYIIRNWRIVKLATTKNQRKLFF 125

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGV---RKVLKITKEPISLETPIGDEDTSHL 588
            +R  +  S         + IA  L +  + V    + +   +  I       D+D    
Sbjct: 126 NLRQLKEDSQAALTNQEAQRIALTLDVKPKEVLDMEERMYGQETSIDGPADSDDDDRFSP 185

Query: 589 GDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF----GIGMNTDHT 641
            D++    D+          Q    E     LA+L PR  RV+  R+      G     T
Sbjct: 186 SDWLTRTSDQPEAILEAEDRQHLEGEGLQTALAALDPRSRRVIEARYLTVDADGTAKPVT 245

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+ +  +  V+ ER+RQIE  AI+K+
Sbjct: 246 LQALAHELGVSAERVRQIEKLAIKKM 271


>gi|86609923|ref|YP_478685.1| RNA polymerase sigma factor SigF [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558465|gb|ABD03422.1| RNA polymerase sigma factor, group 3 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 293

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 111/244 (45%), Gaps = 12/244 (4%)

Query: 429 HIVSMVR-KGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAE 486
               ++R   +      +  +VE NL LV   A  + N+    + DL+Q G +GL++A E
Sbjct: 48  RTAELLRLYHQNRDPALRNRLVEMNLGLVRKEAHHWRNQCNEGYDDLVQVGCLGLIQAIE 107

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G  FS++A+ +++  I   + D+S T+RIP        +  +   R+  ++ R 
Sbjct: 108 RFDISRGLAFSSFALPYIRGEIQHYLRDKSPTMRIPRRWTTLQRQAKKVIARLRQELGRS 167

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS-HLGDFIEDKNAVSPLDS 603
           P+  E+ + L +  +  R++    +    +SL+ PI  E+ S  LG+ + D+   S   +
Sbjct: 168 PSEAEVREALQLTEQEWRELELAQQNSLLLSLDAPIQTEEDSVALGEVVPDQRYRSFQLA 227

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      LA L  R  ++L   F      D T +E  ++  ++   + +   K 
Sbjct: 228 EED---RIRLQHALAQLEERTRKILEFVFF----YDLTQKETAERLGISAVTVSRQVKKG 280

Query: 664 IRKL 667
           + +L
Sbjct: 281 LERL 284


>gi|291196376|emb|CBG22660.1| DNA-directed RNA polymerase subunit D [Pseudomonas poae]
          Length = 238

 Score =  111 bits (278), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 42/284 (14%), Positives = 94/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGI------- 51

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       + +     +   D ++ A    +D  +    P  A      + +  + 
Sbjct: 52  -APPAAEVPPPVDPKAPKADDETEDDDAEASSDDEDEVESGPDPVIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +S+ +       L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRSNKQAIAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 238


>gi|220934511|ref|YP_002513410.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219995821|gb|ACL72423.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 241

 Score =  111 bits (278), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 103/227 (45%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +V+A++ LV  +A     R    +Q  DLIQ G +GL++AA+++D   G  F TYA 
Sbjct: 9   RNRLVDAHVPLVKRIAYHLLGRLPSSVQVDDLIQAGVVGLLEAAQQYDATQGASFETYAG 68

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +         P  +     +V    R + N++ RE  P E+A +L + ++
Sbjct: 69  IRIRGAMLDEVRRSDW---TPRSVHRNARRVSEAMRLVENRLGREAQPAEVAAELGVSLD 125

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             + ++        L      E  S   D +   +  SP ++      R    R + +L 
Sbjct: 126 EYQHMVSDAASCKVLSFEDIFEPDSEGEDLLP-GDEPSPFEALQSDGFRAALAREVGALP 184

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  V+ + +    + +  L E+G+   V+  R+ Q+  +A+ +L+
Sbjct: 185 ERERLVMSLYY----DDELNLREIGEVLGVSESRVCQLHGQALVRLR 227


>gi|291326349|ref|ZP_06124166.2| motility sigma factor FliA [Providencia rettgeri DSM 1131]
 gi|291314661|gb|EFE55114.1| motility sigma factor FliA [Providencia rettgeri DSM 1131]
          Length = 241

 Score =  111 bits (278), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 104/241 (43%), Gaps = 13/241 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  I K  + E    L+   A K   R    +   DLIQ G IGL+ A E+FD   G
Sbjct: 9   YTAEGVINKNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDVTQG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +     +P  +R +  ++ +    +   + R  T  EIA
Sbjct: 69  ASFATYAVQRIRGSMLDELRSRDW---VPRSVRRQAREMTKAIGALEQSLGRSATEPEIA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K L + +   R+ L  T      S +        S      ED    +PL   + ++LR+
Sbjct: 126 KALDIDLAEYRQALLDTNNSQLFSYDEWHEIHGESCEPQMDEDDGG-NPLSLLLDSSLRD 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+   
Sbjct: 185 QIAAAIEQLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRGRL 240

Query: 672 R 672
           R
Sbjct: 241 R 241


>gi|300694351|ref|YP_003750324.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum PSI07]
 gi|299076388|emb|CBJ35704.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum PSI07]
          Length = 245

 Score =  111 bits (278), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 104/245 (42%), Gaps = 11/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +          K + + A   LV  +A +   +    ++  DLIQ G +GL+ A  +++ 
Sbjct: 1   MDMYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEE 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  
Sbjct: 61  TQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTET 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA  L M +   ++ L   +    L       ED     +    +N  +PLD  +  +L
Sbjct: 118 EIAAALDMSLADYQRQLVELQGSQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDL 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+    +  L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++ 
Sbjct: 178 RESVVAAIEGLPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRA 233

Query: 670 PSRSK 674
             R +
Sbjct: 234 RLRER 238


>gi|292696917|dbj|BAI99631.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 253

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 98/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQVGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|296125231|ref|YP_003632483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
 gi|296017047|gb|ADG70284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
          Length = 272

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 60/265 (22%), Positives = 118/265 (44%), Gaps = 19/265 (7%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT-----NRGL 468
           K       I+    +      +    ++   ++ ++     LV  VA K +     ++ +
Sbjct: 6   KEKGKIPNITNDNEQEYWQEFK--NTQSPYIREALIIKYSPLVKYVASKISVNMGSHKHI 63

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +F DL+  G+ GLM A +K++     KF TYA+  ++ AI   +        +P  +R  
Sbjct: 64  EFQDLVGFGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDELRKLD---YLPRSIRKD 120

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS 586
           + ++ +    +  ++ R   P+EIA  L +P+    + +   I   P SL       D S
Sbjct: 121 VKEIEKAREILEARLSRNIKPQEIADMLGIPISKYNETMKRYIEASPTSLSDVWYVGDDS 180

Query: 587 ---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               + D ++  +  +P   A + +++      L  L  +E++VL + +      D TL+
Sbjct: 181 DEISVIDTLKSNDKTNPEYLAEREDVKNKIVAALKKLPEKEKQVLILYY----YDDLTLK 236

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+GK   V+  RI Q+  KAI++L+
Sbjct: 237 EIGKVLEVSESRISQLHTKAIQQLR 261


>gi|83749399|ref|ZP_00946393.1| RNA polymerase sigma-f factor for flagellar operon (fliA)
           [Ralstonia solanacearum UW551]
 gi|83723926|gb|EAP71110.1| RNA polymerase sigma-f factor for flagellar operon (fliA)
           [Ralstonia solanacearum UW551]
          Length = 253

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 106/245 (43%), Gaps = 11/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +          K + + A   LV  +A +   +    ++  DLIQ G +GL+ A  +++ 
Sbjct: 9   MDMYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEE 68

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  
Sbjct: 69  TQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTET 125

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA  L M +   +K+L   +    L       ED     +    +N  +PLD  +  +L
Sbjct: 126 EIAAALEMSLADYQKLLVELQGSQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDL 185

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+    + +L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++ 
Sbjct: 186 RESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRA 241

Query: 670 PSRSK 674
             R +
Sbjct: 242 RLRER 246


>gi|238764885|ref|ZP_04625825.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
 gi|238696904|gb|EEP89681.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
          Length = 240

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQKVEQRLGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|161898843|gb|ABX80411.1| SigB [Listeria monocytogenes]
          Length = 228

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D 
Sbjct: 1   IWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDA 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   
Sbjct: 61  TFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQIS 120

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           +IA  + +  E V + +++ K   +L      E  S               D   + N R
Sbjct: 121 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQR 180

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
               +VL  L  RE+++L+  F        + +E G+   +++  + +I+ +
Sbjct: 181 MLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDISQMHVSRIQRQ 228


>gi|220931546|ref|YP_002508454.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
 gi|219992856|gb|ACL69459.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
          Length = 257

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 67/256 (26%), Positives = 120/256 (46%), Gaps = 9/256 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I ++     +S  E RH    ++K +     A  ++VE NLRLV+ V  ++ + G    D
Sbjct: 5   IINLPKVRLLSEEETRHY---IKKAQNNDQKALDKLVEHNLRLVLKVINRFKSSGYDPQD 61

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G IGL+KA + FD   G KFSTYA+  +   I R        I++   ++   + V
Sbjct: 62  LFQIGVIGLIKAIKNFDLDRGVKFSTYAVSRIIGEI-RLHIRDDGIIKVSRSLKKIANDV 120

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +    +  K    P+  E++KK     E + + L+  K P S+   + ++D S L   +
Sbjct: 121 RKKEEELKKKNNCSPSILELSKKTGYSKEEIVQALEANKAPTSIYETVYEDDGSELY-VV 179

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++    S  +  I    +     +L  L  R  +++ +R+      D T +EV  +  V+
Sbjct: 180 DNLANESKDEEKIPDFNKILLVDLLKKLDERSRKIIYLRYF----EDKTQQEVADEIGVS 235

Query: 653 RERIRQIEAKAIRKLK 668
           + +I ++E K + KL+
Sbjct: 236 QVQISRLEKKILHKLR 251


>gi|294634080|ref|ZP_06712635.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829894|gb|EFF88248.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 311

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 112/253 (44%), Gaps = 16/253 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +    E ++  A+ E+V A L +   +A ++ +RG    DL Q   +GL+KA +
Sbjct: 58  FRRLADLPDGPERDS--ARDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAID 115

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-R 545
           +FD   G  F +YA+  +   + R   D+   +R+P  +++  +KV    R ++      
Sbjct: 116 RFDPDRG-AFESYAVPTITGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELTQNPGSP 174

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLD 602
           EP+   +A    +  + V   ++   +   +SL+  +    D   L D +    A     
Sbjct: 175 EPSVAAVAAHTGLTEDEVNTGMEALDSFSTLSLDAEMSTGADGYSLADTL---GAADSSY 231

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +    RE+    L  L  RE  +L MRF      D T   +  +  +++  + ++ ++
Sbjct: 232 DVVVD--RESAKEGLRRLPERERAILYMRFF----EDMTQSRIADRLGISQMHVSRLISR 285

Query: 663 AIRKLKHPSRSKK 675
           +  +++    +++
Sbjct: 286 SCARVRDEVLAER 298


>gi|67921068|ref|ZP_00514587.1| Sigma-70 region 3:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
 gi|67857185|gb|EAM52425.1| Sigma-70 region 3:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
          Length = 179

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 61/176 (34%), Positives = 107/176 (60%), Gaps = 1/176 (0%)

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           + TR+IA QS  IR+PVH+ +K++K+ +  R++S    R  + EEI ++L M    VR+V
Sbjct: 3   SCTRAIATQSRIIRLPVHVTEKLNKIKQVQRKISQSKNRNASLEEIGQELGMTAAQVREV 62

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L      +SLE  +G E  + L D +E ++ +SP ++    +LR     +L  LT RE++
Sbjct: 63  LMKIPRSVSLEVKVGKEKDTELVDLLESED-ISPEENLAVESLRRDIGVLLKDLTEREQQ 121

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           V+++R+G      ++L  +G+   ++RER+RQIEAK ++KL+ P R  ++R + + 
Sbjct: 122 VIKLRYGFEDGVAYSLAGIGRVLELSRERVRQIEAKTLQKLRQPRRRNQIRDYFES 177


>gi|299143454|ref|ZP_07036534.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298517939|gb|EFI41678.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 260

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 55/257 (21%), Positives = 123/257 (47%), Gaps = 16/257 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  SE + +    +    +    +  ++E +L +   ++KKY+ RG+ + D+ Q  +IGL
Sbjct: 13  LDKSERKELFEAYK--LNKDPEIRDILIEEHLYIAEILSKKYSGRGIDYDDIFQVASIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A +++D+  GY+FS++A   +   I +   D+  TIR+P  +++   K+     +++ 
Sbjct: 71  IYAIDRYDFEKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELSKKINNAKTQLTQ 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLE---TPIGDEDTSHLGDFIEDKN 596
           +++R PT E+IA  L    E V + ++ +    P SL+      GD+   +L D +    
Sbjct: 131 ELQRIPTVEDIADYLETTPEEVIEAMEASKVYTPQSLDVTYDTNGDDKELNLADLVG--- 187

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +++   R ++ L   E  +L  R+        T   + ++  +++  I
Sbjct: 188 --ENEKYFEKIEMKDFLERAMSELNDMERTILIERYF----EKKTQVAIAEKLDISQMTI 241

Query: 657 RQIEAKAIRKLKHPSRS 673
            +IE K ++K++   + 
Sbjct: 242 SRIEKKVLKKMREEIKK 258


>gi|239927803|ref|ZP_04684756.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 220

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 51/219 (23%), Positives = 100/219 (45%), Gaps = 13/219 (5%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           +   +A ++ +RG  F DL Q   +GL+KA +++D  LG  F +YA+  +   I R   D
Sbjct: 1   MADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTITGEIKRHFRD 60

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRM-SNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TK 571
              T+ +P  +++  ++V   ++ +  +   R PT  EIA+   +  E VR       + 
Sbjct: 61  HMWTLHVPRRVQELRNRVRSASQDLSLSGSGRPPTVAEIAEHADLSEEDVRTGQGALDSF 120

Query: 572 EPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             +SL+  +   +D   LGD +   +             RE     LA+L  RE+ +L M
Sbjct: 121 TALSLDAELTSGDDGYSLGDTLGAPDPALDTVVD-----REAVRERLAALPEREQAILYM 175

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RF      D T   +  +  +++  + ++ ++   +++ 
Sbjct: 176 RFF----GDMTQSSIAAELGISQMHVSRLISRCCGRIRE 210


>gi|223043961|ref|ZP_03614002.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|314934140|ref|ZP_07841501.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
 gi|222442676|gb|EEE48780.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|313653045|gb|EFS16806.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
          Length = 256

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 122/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKISDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE ++++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSDRERQIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  ++
Sbjct: 249 KLQEAAK 255


>gi|331269335|ref|YP_004395827.1| RNA polymerase sigma 28 subunit FliA/WhiG [Clostridium botulinum
           BKT015925]
 gi|329125885|gb|AEB75830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium botulinum
           BKT015925]
          Length = 242

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 109/231 (47%), Gaps = 13/231 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +V+  + LV  +A +     ++ ++F DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 10  REHIVKKYIPLVKYIASRVIIGKSKYIEFEDLLGYGMIGLMDALNKFDESKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I   S    I     DK+++       +  K   EP  ++IA++L M V 
Sbjct: 70  IRIRGSMIDEIRKNS---PISKGAMDKLNRYNNAIETLQKKNLTEPNIKDIAQELQMTVN 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  ++D   L   IED+ + +P          E   + L 
Sbjct: 127 EVGEIENFINYISIVSLEDLIFSEDDDISLMGTIEDEKSPNPEKDFEDQERLEYLAKALD 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  +++ VL + +  G     TL+E+G    V+  R+ Q+ ++AI  L+ 
Sbjct: 187 MLNDKDKTVLSLYYYEG----MTLKEIGSVLGVSESRVCQLHSRAIVHLRK 233


>gi|292696843|dbj|BAI99594.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 34-2]
 gi|292696859|dbj|BAI99602.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 21]
 gi|292696903|dbj|BAI99624.1| RNA polymerase sigma-70 factor [Aeromonas punctata]
 gi|292696955|dbj|BAI99650.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO1761]
          Length = 253

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/292 (16%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  +   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EVDDVAPSATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|213583576|ref|ZP_03365402.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
          Length = 201

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/202 (24%), Positives = 100/202 (49%), Gaps = 8/202 (3%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DL+Q G IGL+ A +++D   G  F+TYA+  ++ A+   +  +     +P  +R 
Sbjct: 1   MELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRR 57

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              +V +   ++  ++ R  T  E+A++L +PV   R++L  T            E+   
Sbjct: 58  NAREVAQAMGQLEQELGRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHGD 117

Query: 588 LGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             + + E+    +PL   ++ +LR+     + SL  RE+ VL + +      +  L+E+G
Sbjct: 118 SIELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYY----QEELNLKEIG 173

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V   R+ Q+ ++AI++L+
Sbjct: 174 AVLEVGESRVSQLHSQAIKRLR 195


>gi|331696243|ref|YP_004332482.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950932|gb|AEA24629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 273

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 118/247 (47%), Gaps = 15/247 (6%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKA 484
           + R + ++ R      ++ + E++ A L +   +  +Y T+R     D+ Q  +  +++A
Sbjct: 30  QLRRLSTLPRDDPEHDAL-RTELILAFLPVAERLVGRYATSRPWSRDDIAQAASEAVVRA 88

Query: 485 AEKFDWCLGY-KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            + +D          Y +  V+ AI R   DQS ++R+P  ++D    + +    +S ++
Sbjct: 89  VDHWDPDRARGDVLGYLVPCVRGAILRWFRDQSWSLRVPRRVKDLSVAIRQAVGPLSQEL 148

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            R P P E+A++L + V+ + + L      +  +L+ P   +D S  G+ I D +     
Sbjct: 149 GRAPRPSELARRLDVDVDEIVEALYAEDNHQAATLDAPA-GDDDSSPGERIGDVDPRLGR 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +     ET   +LA L+ RE R++ +RF  G     T  ++G++  V++  + ++ A
Sbjct: 208 VEDV-----ETLRPLLAGLSERERRIVVLRFFCG----RTQSQIGEEIGVSQMHVSRLLA 258

Query: 662 KAIRKLK 668
             + KL+
Sbjct: 259 GTLAKLR 265


>gi|291196386|emb|CBG22665.1| DNA-directed RNA polymerase subunit D [Pseudomonas resinovorans]
          Length = 239

 Score =  111 bits (277), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 95/284 (33%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P     ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGAVDGILAEYQRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +  +  + K      + + + E     S D   + D  P            D ++
Sbjct: 50  GTVPAEEVEPVELKSDTAAAKDKDEDEEEEGESDDAEEEGDGGP------------DPEE 97

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +    +A+ DQL                            +K  +SS +       L +L
Sbjct: 98  ALRRFTAVSDQLDKA---------------------KKALKKHGRSSKQAIEELLALAEL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++     R+   E  +++L      + R  FL    G E+D  W
Sbjct: 137 FMPIKLVPKQFDALVEKVRSALDRVRAQERTIMQLCVRDARMPRADFLRLFPGNEVDLDW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +   V  I + + ++  +  E  ++++E 
Sbjct: 197 ADGLAK-GKAKYAEAIGKLVGDIKRNQQKLVDLEQEVELTVNEI 239


>gi|292696975|dbj|BAI99660.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
          Length = 253

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 98/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHDDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|284044899|ref|YP_003395239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949120|gb|ADB51864.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 273

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 104/232 (44%), Gaps = 11/232 (4%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R ++   R        A++E++   L L   +A +Y +      DL+Q  ++GL+KA ++
Sbjct: 33  RRLLE--RYHLRGDERAREELITRFLPLARQLALRYYHGREPLDDLVQVASVGLVKAVDR 90

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+      F++YA+  +   + R   D    + +P  ++++   V RTA R+       P
Sbjct: 91  FEVRRTTAFASYAVPVMLGELRRYFRDNGWALHVPRGLQERALAVDRTADRLQVAQGAAP 150

Query: 548 TPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           TP +IA++L + VE V + +   +  + +SL+ P    D     D + D           
Sbjct: 151 TPAQIAEQLKLTVEEVVEAMAAARATDTVSLDAPRPSADGER--DALVDSLGAD-DSRLE 207

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
               RE     L +L  RE  +LR+RF      D T  E+  +  V++ +I 
Sbjct: 208 LVEYREAIAGALDALPVREREILRLRF----EEDRTQSEIAARLGVSQMQIS 255


>gi|223717679|emb|CAX46419.1| RNA polymerase sigma factor [Vibrio natriegens]
          Length = 255

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 51/294 (17%), Positives = 103/294 (35%), Gaps = 40/294 (13%)

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            + +S+ E P T   ++   D++      L ++I     + P+++      T  H   + 
Sbjct: 1   QVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPDAED-TAAPTATHIGSEL 57

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            +S  E E D   + + + E     S+D    V   PE A                    
Sbjct: 58  SESQLEDEDDTDVDDDDEDEDGDDDSEDTEEDVGIDPELA-------------------- 97

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                    +   +++   Y+ L+      +   +    S K  V  E ++ +     L 
Sbjct: 98  ---------LEKFNQLRSTYQNLQ------LAINEYGYESPKATVANEMMLDVFKEFRLT 142

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDF 390
             + D LV +L     R+   E  +++    YG + +  F+    G E    W+      
Sbjct: 143 PKQFDHLVNELRTSMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSDAWLDEILA- 201

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
            +  +   +    + I +   ++K I  ET +S+   + I   +  GE +A  A
Sbjct: 202 SDKPYAEKIKRNEEEIRRSITKLKMIEEETSLSVQNVKDISRRMSIGEAKARRA 255


>gi|223717677|emb|CAX46418.1| RNA polymerase sigma factor [Vibrio natriegens]
          Length = 255

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 51/294 (17%), Positives = 103/294 (35%), Gaps = 40/294 (13%)

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
            + +S+ E P T   ++   D++      L ++I     + P+++      T  H   + 
Sbjct: 1   QVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLI--SGFVDPDAED-TAAPTATHIGSEL 57

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            +S  E E D   + + + E     S+D    V   PE A                    
Sbjct: 58  SESQLEDEDDTDVDEDDEDEDGDDDSEDTEEDVGIDPELA-------------------- 97

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLN 331
                    +   +++   Y+ L+      +   +    S K  V  E ++ +     L 
Sbjct: 98  ---------LEKFNQLRSTYQNLQ------LAINEYGYESPKATVANEMMLDVFKEFRLT 142

Query: 332 QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDF 390
             + D LV +L     R+   E  +++    YG + +  F+    G E    W+      
Sbjct: 143 PKQFDHLVNELRTSMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSDAWLDEILA- 201

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
            +  +   +    + I +   ++K I  ET +S+   + I   +  GE +A  A
Sbjct: 202 SDKPYAEKIKRNEEEIRRSITKLKMIEEETSLSVQNVKDISRRMSIGEAKARRA 255


>gi|3249727|gb|AAC26666.1| RNA polymerase sigma-like factor [Pseudonocardia autotrophica]
          Length = 152

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 70/152 (46%), Positives = 100/152 (65%)

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA WW++QAITR++ADQ+ TIRIPVHM + I+K+ R  R +   + REPTPEE+AK++ +
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDI 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             E V +  +  +EPISL+  IGDE  S LGDFIED  A SP D+     L++     L 
Sbjct: 61  TPEKVLETQQYAREPISLDQTIGDEGDSQLGDFIEDSEAASPSDAVSFTLLQDQLQSTLG 120

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +L+ RE  V+R+RFG+      TL+E+G+ + 
Sbjct: 121 TLSEREAGVVRLRFGLTDGRPRTLDEIGQVYG 152


>gi|300697965|ref|YP_003748626.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CFBP2957]
 gi|299074689|emb|CBJ54246.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CFBP2957]
          Length = 245

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 106/245 (43%), Gaps = 11/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +          K + + A   LV  +A +   +    ++  DLIQ G +GL+ A  +++ 
Sbjct: 1   MDMYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEE 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  
Sbjct: 61  TQGVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTET 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EIA  L M +   +K+L   +    L       ED     +    +N  +PLD  +  +L
Sbjct: 118 EIAASLEMSLAEYQKLLVELQGSQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDL 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+    + +L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++ 
Sbjct: 178 RESVVAAIEALPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRA 233

Query: 670 PSRSK 674
             R +
Sbjct: 234 RLRER 238


>gi|312135825|ref|YP_004003163.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775876|gb|ADQ05363.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 246

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 121/253 (47%), Gaps = 22/253 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K++++   + LV  VA +   Y    +++ DL+  G+IGL+ A EKFD  
Sbjct: 9   KFIKTKDQKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   ++ AI   +  Q     +P  +R K  ++ +    +  +  R PT  E
Sbjct: 69  KGVKFETYAYTRIRGAIIDCVRSQDF---LPRSIRQKAKEIEKAYIEIERE-GRTPTDYE 124

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK+L + +  ++K+     +   +SLE+ +     S +G     ++ VS  +  I+   
Sbjct: 125 VAKRLGISISELQKLQEKISSGMIVSLESFLEQSYESKIGGL---EDFVSQPEHFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+    + + +L   E  V+ + +      + +++E+ K   ++  R+ Q+  +A+ KL+
Sbjct: 182 LKNVLRQQIDNLMENERMVIMLYY----YEELSIKEIAKILGISESRVSQLHTRALLKLR 237

Query: 669 HPSRSKKLRSFLD 681
                  L+ +L+
Sbjct: 238 SA-----LQKYLE 245


>gi|284032127|ref|YP_003382058.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Kribbella
           flavida DSM 17836]
 gi|283811420|gb|ADB33259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Kribbella
           flavida DSM 17836]
          Length = 269

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 105/234 (44%), Gaps = 15/234 (6%)

Query: 432 SMVRKGECEASIAKKEMVEA----NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            ++R    E    + E++E      + +  ++A +Y  RG+   DL+Q  ++GL+KAA  
Sbjct: 31  RLLRLAAEETGARRTELIEQAVVEGVPMARTLAARYHRRGVDSDDLLQVASVGLVKAAHG 90

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +       F +YA+  ++  + R   DQ+  +R P  ++D    +      +++ ++  P
Sbjct: 91  YRPGPDTDFRSYAIPTIRGELRRHFRDQAWMVRPPRRIQDLQTAINAAEADLASTLQHWP 150

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           T E++A  + +PVE +    +      P SL+  +       LG  I DK     L   I
Sbjct: 151 TTEDLAAAIGVPVEDIVDAQRAQGCFRPASLDAKLTGAPALSLGTVIADKTNTYELVDHI 210

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                ET   V+  L  R+  +L  RF        T  E+G++  V++ ++ ++
Sbjct: 211 -----ETLRPVVEDLPARDRLILHRRFVDH----RTQAEIGEEIGVSQMQVSRL 255


>gi|89094438|ref|ZP_01167378.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
 gi|89081330|gb|EAR60562.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
          Length = 236

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 98/227 (43%), Gaps = 14/227 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E++E    LV  +A     R        DLIQ G IGL++AA K+D   G  F TYA   
Sbjct: 12  ELIEQYAPLVKRIAHHLLARLPSTVLLDDLIQAGMIGLLEAASKYDASKGASFETYAGIR 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ +I   +         P  +     +V    +++  +  R+ +  E+AK+L + V+  
Sbjct: 72  IRGSIIDEVRRGDW---TPRSVHRNSRRVTEAIQQIEARTGRDASDSEVAKELGISVDEY 128

Query: 564 RKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             +LK + +    S E  +  E       F  D    +      +    +  +  + +L 
Sbjct: 129 HNLLKDSLDSRLFSFEEMLNPEHEGPGESFANDDPGPN--KHIEREAFLKALSEAINNLP 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE+ VL     +  + +  L+E+G+   V+  R+ QI ++A  +L+
Sbjct: 187 EREKLVL----ALYYDEELNLKEIGQVLGVSESRVSQIHSQAALRLR 229


>gi|125975381|ref|YP_001039291.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|281419342|ref|ZP_06250357.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|125715606|gb|ABN54098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Clostridium
           thermocellum ATCC 27405]
 gi|281406962|gb|EFB37225.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|316939496|gb|ADU73530.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 252

 Score =  111 bits (277), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 106/227 (46%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V   L L   +AKK+ NRG+ + D+ Q  +I L+KA E+FD   G KF ++A   +
Sbjct: 31  RNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVASIALIKAVERFDPDKGVKFISFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   IRIP  + +   K+      ++ ++KR P  +E+A+ L +  E V 
Sbjct: 91  IGEIKRYFRDKGSVIRIPRRIYEVYQKINHARESLTQELKRPPRIDELARHLNISEESVV 150

Query: 565 KVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +++         S    +   D   L + I D+++        +   R+   + L   + 
Sbjct: 151 EIIESYNAYNIQSFSQNVYANDELELHEVIGDQDST-----FERIENRDFLEKSLDKFSD 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E+  + MR+        T +++ ++  V++  I ++E K + K + 
Sbjct: 206 VEKEFISMRYFDN----KTQKDIAQKMGVSQMYISRLERKVLEKFRR 248


>gi|123442749|ref|YP_001006726.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332161358|ref|YP_004297935.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122089710|emb|CAL12562.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318605283|emb|CBY26781.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665588|gb|ADZ42232.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859514|emb|CBX69857.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 240

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQKVEQRLGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QNLDIDLTEYRQILLDTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|292696845|dbj|BAI99595.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 23]
 gi|292696861|dbj|BAI99603.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696889|dbj|BAI99617.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696895|dbj|BAI99620.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696897|dbj|BAI99621.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292696899|dbj|BAI99622.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696905|dbj|BAI99625.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696909|dbj|BAI99627.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696913|dbj|BAI99629.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696915|dbj|BAI99630.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696919|dbj|BAI99632.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696923|dbj|BAI99634.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|292696941|dbj|BAI99643.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO559]
 gi|292696953|dbj|BAI99649.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO044]
 gi|292696971|dbj|BAI99658.1| RNA polymerase sigma-70 factor [Aeromonas veronii bv. sobria]
 gi|292696987|dbj|BAI99666.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292696995|dbj|BAI99670.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC6]
 gi|292697001|dbj|BAI99673.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC9]
 gi|292697370|dbj|BAI99674.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC10]
 gi|292698264|dbj|BAI99676.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC12]
 gi|292698268|dbj|BAI99678.1| RNA polymerase sigma-70 factor [Aeromonas sp. KC14]
 gi|292698286|dbj|BAI99687.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292698306|dbj|BAI99697.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698312|dbj|BAI99700.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|292698334|dbj|BAI99711.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698336|dbj|BAI99712.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698340|dbj|BAI99714.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698344|dbj|BAI99716.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698346|dbj|BAI99717.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698356|dbj|BAI99722.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|292698358|dbj|BAI99723.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 51/291 (17%), Positives = 98/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + + I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|187935068|ref|YP_001885063.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723221|gb|ACD24442.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 242

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 115/244 (47%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               + +  K+++V+  + LV  +A +     N+ +++ DL+  G IGLM A  KF+   
Sbjct: 1   MCNLQDNDVKEQIVKEYIPLVKYIASRIMIGKNKYMEYEDLVSYGIIGLMDAISKFNPEK 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G KFS+YA   +K AI   I        I     DK+++       + NK+ REP   EI
Sbjct: 61  GMKFSSYASIRIKGAIIDQIRK---NRPITKGAMDKLNRYNGAIEALQNKLLREPNILEI 117

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANL 609
           AK L + +E V ++         +SLE  I  +D   +L   IEDKN+ SP     +   
Sbjct: 118 AKYLELSLEEVSQIENYINHISMVSLENIIFSDDEEVNLLGIIEDKNSPSPEGELEEKEK 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E  +  +  L  +E+ +L + +        TL+E+G    V+  R+ Q+ A++I  L+ 
Sbjct: 178 LEVLSDAIKLLKEKEQLILNLYY----YEKLTLKEIGAILSVSESRVCQLHARSISNLRE 233

Query: 670 PSRS 673
             + 
Sbjct: 234 AMKK 237


>gi|121533733|ref|ZP_01665560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121307724|gb|EAX48639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 252

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 102/227 (44%), Gaps = 16/227 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++E  L LV  VA +      + +   DLI  G  GL+ A E+FD     KF TYA+
Sbjct: 28  REKLIEKYLPLVKMVAGRVAIGLPQHIDKEDLISYGFFGLLDAIERFDPSRNIKFETYAV 87

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ +I  +I  Q     +P  +R K   + RT   + N + R  T  EIA+ +   VE
Sbjct: 88  ARIRGSIFDAIRVQDW---LPASLRQKGRLLERTVAELENSLGRSATDAEIAQAMNFTVE 144

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + +++        L           + +   ++ + +      Q  +++T  + +  L 
Sbjct: 145 QLHQLINQ------LNASTLIPLEEFVQNETVNQASPNLAQEIEQEEVKKTLAKAIDRLP 198

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +E  V+ + +  G     TL+E+     ++  RI Q+  KAI +L+
Sbjct: 199 EKERLVISLYYYEG----LTLKEISLILKLSEARISQLHTKAIFRLR 241


>gi|238794024|ref|ZP_04637642.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
 gi|238726656|gb|EEQ18192.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
          Length = 240

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQKVEQRVGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QILDIDLAEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|307328384|ref|ZP_07607560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885957|gb|EFN16967.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 261

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 111/246 (45%), Gaps = 14/246 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F  +  +    E +A   ++ ++ A L +   +A ++ N+G    DL Q  ++ L+KA +
Sbjct: 21  FLRLSRLPSGPERDAL--RETIICAWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVD 78

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KR 545
           +++  LG+ F +YA+  +   + R   D   T+ IP ++++   +       +  ++  R
Sbjct: 79  RYNPDLGHAFPSYAIPVITGELKRHFRDYLWTLHIPRNIQEVRSRTRSARDALEQELGGR 138

Query: 546 EPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EI  +  MP E V   L+   +  P+SL   +   +   L + +   +A      
Sbjct: 139 TPTIHEICLRTGMPQEDVMAGLEASASCTPLSLNAAVQGAEERLLAETVGADDAA----- 193

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   RE    ++A L+ ++  VL +RF  G     +  ++G+    ++  I +  ++ 
Sbjct: 194 IERVVNREALRVLIAELSEQDRYVLYLRFFAG----LSQSQIGEILGFSQMHISRRLSRL 249

Query: 664 IRKLKH 669
             +L+ 
Sbjct: 250 YSELRQ 255


>gi|300856558|ref|YP_003781542.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
 gi|300436673|gb|ADK16440.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
          Length = 251

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 117/239 (48%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++  +     A  ++VE NL LV S++KK+ NRG ++ D+ Q G +GLMKA   F+ 
Sbjct: 17  LELIKYAKKGDKDALNKLVELNLPLVASISKKFLNRGYEYEDIFQIGCMGLMKAVNNFNE 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++   K+      ++ K+ REPT +
Sbjct: 77  EYNVKFSTYAVPMILGEIKRFLRD-DGMIKVSRSVKNTAKKIHYDREALTKKLNREPTIQ 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+   + VE +    +       L   I  +D S +   + DK + +P +     + +
Sbjct: 136 ELAEYSGVEVEELIFATESASSLQYLYDTIHQDDGSPV--LLIDKISENPKEDVEMVD-K 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L +L  +  +++ +R+      D T  +V K   + + ++ +IE K ++ ++ 
Sbjct: 193 IALKEALNNLDVKSRQIIMLRYF----KDKTQVQVAKMLGINQVQVSRIEKKVLKTMRE 247


>gi|42780162|ref|NP_977409.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 10987]
 gi|42736080|gb|AAS40017.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10987]
          Length = 257

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 120/261 (45%), Gaps = 10/261 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++  S  T ++  +   +++  ++ +C+   A++ +VE    LV S+A +Y+  G    D
Sbjct: 1   MEIQSQPTTLTKEDVMKLIAEFQQNQCD--EAQERLVEHYKNLVYSIAYRYSKGGPMHED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+
Sbjct: 59  IIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
                 ++++++R P   EIA  L +  E V +++         SL+  + +        
Sbjct: 119 KLAIEELTDQLQRSPKIIEIADHLELSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            IE  +         +   R     +   L   E+ V+   F      +   ++ G++  
Sbjct: 179 RIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLG 232

Query: 651 VTRERIRQIEAKAIRKLKHPS 671
           +++  + +I+ +AI KLK  +
Sbjct: 233 ISQMHVSRIKRQAISKLKQAA 253


>gi|124300781|dbj|BAF45888.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 226

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 38/273 (13%), Positives = 76/273 (27%), Gaps = 48/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +      L ++I            GF     
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLI-----------TGFVDPNA 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                        +   +  + + D +                PE A             
Sbjct: 50  EEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKF--------- 100

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +LR + +   D I                     +S    +    KL ++
Sbjct: 101 ---------AELRAQYIVTRDTIKAK-----------------GRSHAAAQEEILKLSEV 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E    W
Sbjct: 135 FKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
            + A    +  W   +    + + +   +++ I
Sbjct: 195 FNAAIAMNKP-WSEKLHDVSEEVHRALQKLQQI 226


>gi|302549077|ref|ZP_07301419.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466695|gb|EFL29788.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 287

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 101/230 (43%), Gaps = 12/230 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
              + E+V   L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+
Sbjct: 47  EAVRDELVALWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAVDRFDPSRG-AFESYAV 105

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPV 560
             +   + R   D+   +R+P  +++  +KV    R ++      EP+   +A    +  
Sbjct: 106 PTITGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELTQNPGSPEPSVPALAAHTGLTE 165

Query: 561 EGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           E V   L+   +   +SL+  +  +D  +    + D    S     +  + RE+    L 
Sbjct: 166 EEVNAGLEALDSFSTLSLDAELSADDDGY---SLADTLGASDTSYDVVVD-RESAKEGLR 221

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  RE  +L MRF      D T   +  Q  +++  + ++  ++  +++
Sbjct: 222 RLPERERAILYMRFF----EDMTQSRIADQLGISQMHVSRLITRSCARVR 267


>gi|292698364|dbj|BAI99726.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 104/292 (35%), Gaps = 46/292 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGIIQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E DDV  T   I S            D   +  E+ + + D+ +  
Sbjct: 49  --------------EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGG 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVK 323
               ++                  E + ELR+  +   ++ Q++ ++    +    +L  
Sbjct: 95  PDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLAD 137

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPH 382
           +     L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  
Sbjct: 138 VFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETA 197

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           W  Y K   +      +  + + +L+   +++ I  ETG+SI++ + I   +
Sbjct: 198 WFEYQKQAGKAWSPRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|187934214|ref|YP_001885077.1| sporulation sigma factor SigF [Clostridium botulinum B str. Eklund
           17B]
 gi|187722367|gb|ACD23588.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 251

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 112/240 (46%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++   +   + A   ++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD  
Sbjct: 18  QLLPLAKDGDNEAMNRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLS 77

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++  +++    ++  T   ++ K+ R PT EE
Sbjct: 78  YNVKFSTYAVPMIIGEIKRFLRD-DGMIKVSRNVKSLAKRIHFTKEELTKKLNRSPTIEE 136

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANL 609
           +A+   +  E +   ++       L   I  +D +   L D + +K              
Sbjct: 137 LAEYSGVDKEEIIFAIESATSLQYLYDTIHQDDGAPVLLIDKLSEKGEDDIGMIN----- 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L SL  +  +++ +R+      D T  +V K   +++ ++ +IE K + +++ 
Sbjct: 192 KIALKEALRSLDEKARQIIVLRYF----KDKTQVQVAKLLGISQVQVSRIEKKVLLRMRE 247


>gi|57996880|emb|CAI45888.1| negative response regulator [Escherichia coli]
          Length = 158

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 67/157 (42%), Positives = 111/157 (70%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I 
Sbjct: 2   RLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +  
Sbjct: 62  NQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 121

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            S++TP+G +    L D + D+    P D+    +++
Sbjct: 122 TSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMK 158


>gi|313901043|ref|ZP_07834531.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
 gi|312954001|gb|EFR35681.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
          Length = 259

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 122/250 (48%), Gaps = 15/250 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E + +   +++       AK+ ++  NL+LV+S+ ++++NR     DL Q G IGL
Sbjct: 19  LTNAEMKELFVKLQQ---GDESAKETLINGNLKLVLSIVQRFSNRCENMDDLFQVGCIGL 75

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K+ + FD     +FSTYA+  +   I R + D    IR+  H++D  ++  +      +
Sbjct: 76  VKSIDNFDLKHEVRFSTYAVPMIMGEIKRYLRDNQ-VIRVSRHLKDLAYRAFKLKEEYVH 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
           K ++EP+   +A++L +  + +   L  T+  +S+  P+ + D     L D I+D     
Sbjct: 135 KHQKEPSVSWLAQQLEVKEKDIVDALDSTQSVLSIFEPVYNSDGDELFLLDQIKDDKD-- 192

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 + N      R L  L  +E  +++ R+      D T  E+  +  +++ ++ ++
Sbjct: 193 ---EIERLNNLMALKRSLTRLKGKELDIIQKRY----YQDMTQTEIAGELGISQAQVSRL 245

Query: 660 EAKAIRKLKH 669
           E  AI  LK 
Sbjct: 246 EKNAIAVLKK 255


>gi|15834951|ref|NP_296710.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270285123|ref|ZP_06194517.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270289144|ref|ZP_06195446.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Weiss]
 gi|301336518|ref|ZP_07224720.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum
           MopnTet14]
 gi|7190373|gb|AAF39194.1| RNA polymerase sigma factor, sigma-70 family [Chlamydia muridarum
           Nigg]
          Length = 253

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 55/241 (22%), Positives = 107/241 (44%), Gaps = 15/241 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +    +  ++EA L LV +VA +  +     ++  DL   G  GL++A E+FD   
Sbjct: 13  YWSTKEIHHRDFLIEAYLPLVKNVAHRLASGMPSHVKIEDLYASGVEGLVRAVERFDPEK 72

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F +YA++ +K AI   +  Q     +P  +  + +++      +   + +EPT  ++
Sbjct: 73  SKRFESYALFIIKAAIIDDLRKQDW---VPRSVYQRANRLADAMDALRQTLGKEPTDGDL 129

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQA 607
            + L +  + +      ++    +SL      +D      L + I D+ A +  D   + 
Sbjct: 130 CEYLNISQQELSHWFSSSRPALVLSLNDDFSCQDEDEGLALEERIADERAENGYDVIRKK 189

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 T  L SL  +E +V+     +    D  L+E+GK   V+  R+ QI +KA+ KL
Sbjct: 190 EAISILTEALLSLDEKERQVM----ALYYYDDLVLKEIGKILGVSESRVSQIHSKALLKL 245

Query: 668 K 668
           +
Sbjct: 246 R 246


>gi|229915244|gb|ACQ90684.1| DNA-directed RNA polymerase subunit D [Marinobacterium sp. KW44]
          Length = 262

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 48/306 (15%), Positives = 105/306 (34%), Gaps = 47/306 (15%)

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            I IAKRIE G   +M +L   P +   ++   +++      L +I      I P++   
Sbjct: 3   RIDIAKRIEEGIREVMMALSRFPGSVDIILDAYNQVLQEEGRLSDI--FSGYIDPDADV- 59

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                                 D+        +       +D  + +   ++  N+E+  
Sbjct: 60  --------------------PEDETDAPVELDDDDQDERDEDEDEDEDNKDSDSNEEKER 99

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
             D +++      +++ L                      D       +  S  + +   
Sbjct: 100 GPDPEEARQRFGLIQECL----------------------DKYHQAVANNGSVDEIEFAA 137

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGR 377
             L      + L+    DLLVE++ D    I   E  ++R+  Q   + R VF++   G 
Sbjct: 138 MALANAFAPIKLSPRFYDLLVERVRDCIDGIRKQERTIMRICTQRAKMPRPVFIKSFPGN 197

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E+   W+    +  +  +   +   +  + + +  +  I   TG++++E + +   +  G
Sbjct: 198 EVSQEWLDTLAN-SDKPYAAAIGRSMPDLQRAQRRLLQIEENTGLTLAEVKEVNRNLSIG 256

Query: 438 ECEASI 443
           E  A  
Sbjct: 257 EARARR 262


>gi|308068681|ref|YP_003870286.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
 gi|305857960|gb|ADM69748.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
          Length = 262

 Score =  111 bits (276), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  E     AKK+++E  L +V  V+ +      + +   DL   G +GL+ A EKFD+ 
Sbjct: 17  QWKEHGDKEAKKQLIEKYLHIVEYVSGRLAVGLPKNVSKDDLASNGVMGLIDALEKFDYE 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F TYA W V+ AI   +        +P  +R+K  K+    + +  +  R  + EE
Sbjct: 77  RGLQFETYASWRVRGAILDGLRQGDW---VPRSVREKAKKIEDAYQHLEQRYLRTVSDEE 133

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           ++  L +  +  + +++       +SLE PI +E++      + D+ A +P     +  L
Sbjct: 134 MSHYLDVSEKEFQNMIQEVAVMSIVSLEDPIREEESETRLSLLVDEKAKNPDHKVNEFTL 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + +  LT +E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+ 
Sbjct: 194 RDALAQGIDKLTEKERIVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLRA 249

Query: 670 PSRSKK 675
               ++
Sbjct: 250 TLDKQR 255


>gi|229051333|ref|ZP_04194847.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
 gi|229125362|ref|ZP_04254451.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228658091|gb|EEL13842.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228722026|gb|EEL73457.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
          Length = 325

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 124/249 (49%), Gaps = 6/249 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKF 488
           + + ++ +      +  +   N  LV+S+A+ Y N+     F DL+QEGN G+++A E F
Sbjct: 57  LHLFKRYKHGEKDLRDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGNEGMLRAMEDF 116

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +  LGY FSTYA WW+++++   I  +     +IP H+     K V    +   +  R P
Sbjct: 117 NPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLKYVELEDKYLQRYNRTP 176

Query: 548 TPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + EE+ K+L +  E V   KV       ++L+    +ED      F +DK+A+   +  I
Sbjct: 177 SVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTPFFDDKSAIPSTNEMI 236

Query: 606 QANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             +L      +    L P+++ VL + FG+     +  +E+ K   +T ER+ QI+ +AI
Sbjct: 237 IEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKDEAI 296

Query: 665 RKLKHPSRS 673
           +KLK     
Sbjct: 297 KKLKKCQHK 305


>gi|207724998|ref|YP_002255395.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum MolK2]
 gi|207738855|ref|YP_002257248.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum IPO1609]
 gi|206590225|emb|CAQ37186.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum MolK2]
 gi|206592225|emb|CAQ59131.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum IPO1609]
          Length = 243

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 55/243 (22%), Positives = 105/243 (43%), Gaps = 11/243 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                    K + + A   LV  +A +   +    ++  DLIQ G +GL+ A  +++   
Sbjct: 1   MYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F  YA   ++ AI   +        +P  +R     + +  +++  +  R PT  EI
Sbjct: 61  GVQFEFYAAQRIRGAILDELRGSDW---LPRGLRRNARTIEQAIQKLQQQKGRAPTETEI 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A  L M +   +K+L   +    L       ED     +    +N  +PLD  +  +LRE
Sbjct: 118 AAALEMSLADYQKLLVELQGSQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDLRE 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           +    + +L  RE+ ++ + +      D  L E+G    V+  R+ QI ++AI +++   
Sbjct: 178 SVVAAIEALPEREKLMMSLYY----EQDLNLREIGAVMGVSESRVCQIHSQAIARIRARL 233

Query: 672 RSK 674
           R +
Sbjct: 234 RER 236


>gi|108799609|ref|YP_639806.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119868720|ref|YP_938672.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           KMS]
 gi|108770028|gb|ABG08750.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694809|gb|ABL91882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
          Length = 284

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 47/227 (20%), Positives = 101/227 (44%), Gaps = 10/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++ ++ A + +   +A ++  RG    D+IQ   IGL+K  +++D   G+ F  +A+  +
Sbjct: 46  RRHIITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVDRYDPDKGH-FLAFAVPTI 104

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I R   D + T+R+P  +++   ++      +S ++ R PT  E+A +L +  E + 
Sbjct: 105 RGEIRRHFRDNTWTVRVPRKVQETQLRMRDAVNTLSQRLNRTPTGVELADELDVGSEELG 164

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                     P+SL+ P+        GD +               +L       ++ L P
Sbjct: 165 DCQAATTAYRPVSLDAPLLTAQND--GDTVGSMQGGDDPGYGRVEDLI-LLQEAISDLDP 221

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R   ++ M F        T  EV ++  V++ +I ++   A+ +++ 
Sbjct: 222 RRRAIVGMIFF----DCLTQREVARRLHVSQVQISRLLNDALARIRQ 264


>gi|302540326|ref|ZP_07292668.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302457944|gb|EFL21037.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 263

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 112/244 (45%), Gaps = 13/244 (5%)

Query: 430 IVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            + M R        A ++ ++   L +   +A ++ N+G    DL Q  ++ L+KA +++
Sbjct: 23  FLRMSRLPSGPERDALREAIICEWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVDRY 82

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI-KREP 547
           +  LG+ F +YA+  +   + R   D   T+ IP ++++   +       +  ++  R P
Sbjct: 83  NPDLGHAFPSYAIPVITGELKRHFRDYLWTLHIPRNIQEVRSRTRSARDALEQELGGRTP 142

Query: 548 TPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           T  EI+ +  MP E VR  L+   +  P+SL   +   +   L + +   +A        
Sbjct: 143 TVGEISTRTGMPQEDVRAGLEASASCTPLSLNAAVQGAEERLLAETVGADDAA-----IE 197

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   RE+   ++A+L+ ++  VL +RF  G     +  ++G+    ++  I +  ++   
Sbjct: 198 RVVNRESLRVLIANLSEQDRYVLYLRFFAG----LSQSQIGEILGFSQMHISRRLSRLYS 253

Query: 666 KLKH 669
           +L+ 
Sbjct: 254 ELRQ 257


>gi|255523683|ref|ZP_05390649.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296186687|ref|ZP_06855089.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
 gi|255512552|gb|EET88826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296048724|gb|EFG88156.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
          Length = 241

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 117/238 (49%), Gaps = 13/238 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + +++ DL+  G +GLM A  KFD   G KFSTY+ 
Sbjct: 10  KEELVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMLGLMDAIGKFDNTRGMKFSTYSS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K A+   I   S    I     DK+++      R+   + REP+ +EIA +L + ++
Sbjct: 70  IRIKGAMIDEIRKNS---PISKGAMDKLNRYNAAVERLQKTLGREPSDKEIANELNITLK 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++         +SLE  I  ++D   L   I+D  + SP  S  +    E   + L 
Sbjct: 127 EMIEIENYINYISIVSLEDLIFSEDDDIPLIGTIQDNKSPSPEKSLEEKEELEYLAKALD 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            L  +++ VL + +  G     TL+E+GK   V+  R+ Q+ ++AI  L++  +  K 
Sbjct: 187 LLNEKDKTVLSLYYYEG----LTLKEIGKVLSVSESRVCQLHSRAIVHLRNAMQKLKY 240


>gi|124300730|dbj|BAF45873.1| RNA polymerase sigma-subunit [Erwinia pyrifoliae]
 gi|124300773|dbj|BAF45884.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 224

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 39/273 (14%), Positives = 77/273 (28%), Gaps = 50/273 (18%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I        E          
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHV 60

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      E   ++++ +   ++  D  S               PE A     +L    + 
Sbjct: 61  GSELSAEEREDEDEDEESDDDSSDDDNSID-------------PELAREKFGDLRIQYET 107

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 108 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 132

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 133 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 192

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   +++ I
Sbjct: 193 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLQQI 224


>gi|292696963|dbj|BAI99654.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 253

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 98/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKTWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|315179524|gb|ADT86438.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           NCTC 11218]
          Length = 244

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 53/226 (23%), Positives = 97/226 (42%), Gaps = 15/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            ++    LV  +A     R        DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 19  FLDKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +  ++ R+PT  E+AK L M ++   
Sbjct: 79  RGAMLDDIRRGDW---VPRSVHKHNREIGQAIAVLEGELNRDPTDSEVAKHLGMSLDQYH 135

Query: 565 KVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            VL        + +E     +D     D   D    SP       + R+     + SL  
Sbjct: 136 SVLTDINCSRIVGIEDLGVTDDAISPVD---DDEDNSPFKGVADESFRKALVESIKSLPE 192

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  VL + +    + +  L+E+G+   V+  R+ QI ++A+++L+
Sbjct: 193 REALVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQAMQRLR 234


>gi|229100411|ref|ZP_04231282.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
 gi|229107324|ref|ZP_04237193.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228676119|gb|EEL31095.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228683031|gb|EEL37038.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
          Length = 323

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 132/264 (50%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-- 469
           EIK I     +S  E    + + ++ +      +  +   N+ LV+S+A+KY N+     
Sbjct: 39  EIKEIGNYKVLSKQES---LKLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I  +     +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS 586
             K V    +      R PT EE+ K+L +  E V +     K    ++L+    +ED  
Sbjct: 156 NLKYVELEDKYLQMYNRTPTVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
               F +D +A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 MSKPFYDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K   +T ER+ QI+ +AI+KLK 
Sbjct: 276 AKALMITTERVSQIKEEAIKKLKK 299


>gi|149188340|ref|ZP_01866634.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837929|gb|EDL54872.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 285

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 120/276 (43%), Gaps = 10/276 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
            A   ++   +   ++ ++  + +   E R + + +     E  I+K  +V  +LR V+ 
Sbjct: 6   AAISFNNSQNLSYYMQYVNSHSILKECEERQLANDLYYNNNEDVISK--LVLPHLRYVVY 63

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK +   GL  +D+IQ GNIGL+KA +KF+  LG++  ++A+ W+K  IT  I      
Sbjct: 64  IAKGFAGYGLPLVDMIQSGNIGLLKAVKKFNPELGFRLVSFAVHWIKSEITDFIIKNWSI 123

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           ++I      +         + S +   E   E +A KL +  + V  +        S   
Sbjct: 124 VKIATTKSQRKLFFNLKKYKQSQEWMSESEAENLASKLKVSKKDVLSMDGRLSARDSYID 183

Query: 579 PIGDEDTSHLGDFIED------KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           P   ED   +    E         A+         ++ +     LA L  R   ++  R+
Sbjct: 184 PKIGEDEDQVISTGEVFAEPQLDVAIEYETQDWDRHINDELNAGLAKLDARSRDIIVSRW 243

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  +   TL E+ ++  V+ ER+RQIE   + KLK
Sbjct: 244 LL--SEKVTLNELAERHRVSAERVRQIELMTLEKLK 277


>gi|310641572|ref|YP_003946330.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309246522|gb|ADO56089.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 262

 Score =  111 bits (276), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  E     AKK+++E  L +V  V+ +      + +   DL   G +GL+ A EKFD+ 
Sbjct: 17  QWKEYGDKEAKKQLIEKYLHIVEYVSGRLAVGLPKNVSKDDLASNGVMGLIDALEKFDYE 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +F TYA W V+ AI   +        +P  +R+K  K+    + +  +  R  + EE
Sbjct: 77  RGLQFETYASWRVRGAILDGLRQGDW---VPRSVREKAKKIEDAYQHLEQRYLRTVSDEE 133

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           ++  L +  +  + +++       +SLE PI +E++      + D+ A +P     +  L
Sbjct: 134 MSHYLDVSEKEFQSMIQEVAVMSIVSLEDPIREEESETRLSLLVDEKAKNPDHKVNEFTL 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + +  LT +E  V+ + +      D +L E+ +   ++  RI Q+ +KAI +L+ 
Sbjct: 194 RDALAQGIDKLTEKERIVVSLLY----YEDLSLSEIAEVMSLSPSRISQLHSKAILRLRA 249

Query: 670 PSRSKK 675
               ++
Sbjct: 250 TLDKQR 255


>gi|302874610|ref|YP_003843243.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|307690779|ref|ZP_07633225.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|302577467|gb|ADL51479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
          Length = 241

 Score =  110 bits (275), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 111/237 (46%), Gaps = 13/237 (5%)

Query: 447 EMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E++   + LV  +A +     ++ ++F DL+  G +GLM A  KFD   G KFS+YA   
Sbjct: 12  EIITKYIPLVKYIASRVIIGKSKHIEFDDLVSNGILGLMDALNKFDESKGMKFSSYASIR 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K A+   +        IP    DK+++       + N + REPT +EIA ++A+ +  V
Sbjct: 72  IKGAMIDELR---RNSPIPKGAMDKLNRYNSAIDSLRNTLLREPTVDEIACEMAIDIADV 128

Query: 564 RKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            ++         +SLE  I  ++D   L   I+D  + SP          E   + +  L
Sbjct: 129 IEIENHINYLSVVSLEELIYSEDDDMPLIGTIKDNKSPSPEKDLEDKEKMEYLAKAIELL 188

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             +++ VL + +  G     TL+E+GK   V+  R+ Q+  +AI  L+      K +
Sbjct: 189 NEKDKLVLNLYYYEG----LTLKEIGKILEVSESRVCQLHTRAIAHLRKNLSKLKYK 241


>gi|146295518|ref|YP_001179289.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409094|gb|ABP66098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 257

 Score =  110 bits (275), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 13/239 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + ++E   +    RK +      + E+V  +L +   VAKK+ NRG+++ DL Q   + L
Sbjct: 10  LDVAEIDKLFEEYRKTKDINL--RNELVNRHLYIAEIVAKKFINRGIEYDDLYQVACMAL 67

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A E+F+   GYKF+++A   +   I R   D++  IR+P  + +   K+      +S 
Sbjct: 68  INAVERFEPNKGYKFTSFATPTIMGEIKRYFRDRASLIRLPRRIYETSAKIKLATEILSA 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVS 599
           K+K+ P  EEIA+ + +  E V +V++ +    P SL+  + +++   LGD +   +   
Sbjct: 128 KLKQPPKIEEIAQYIGITPEEVLEVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDE-- 185

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              + +Q    ET  + +  L+P E   ++ RF      + T  E+  +  V++  I +
Sbjct: 186 ---NLVQIENTETVKKAIDKLSPLEREFVQKRFF----EEKTQREIADEMKVSQMYISR 237


>gi|146296307|ref|YP_001180078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409883|gb|ABP66887.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 245

 Score =  110 bits (275), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 114/240 (47%), Gaps = 17/240 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +    K+++    + LV  +A +   Y    +++ DL+  G++GL+ A EK+D  
Sbjct: 9   KYSKTKDPKIKEQLTLRYMPLVKLIAGRMAMYFGGNVEYDDLVSYGSLGLLDAIEKYDSQ 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   ++ AI   +  Q     +P  +R K  +V +    +  +  + PT EE
Sbjct: 69  KGVKFETYAYTRIRGAIIDCVRSQDW---VPRSIRQKAKEVEKAYIEIEKE-GKIPTDEE 124

Query: 552 IAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-AN 608
           +AK+  + +   +  K    +   +SLE  +       +G     ++ VS  +  I+   
Sbjct: 125 VAKRTGLTLSEFQKLKEKISSGMILSLEGFLEQNYEIKIGGL---EDFVSHPEVFIENEE 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E   + + +L+  E+ V+ + +      + +++E+ K   V+  R+ Q+  +A+ KL+
Sbjct: 182 LKEVLRQEIENLSENEKMVILLYYF----EELSIKEIAKILGVSESRVSQLHTRALLKLR 237


>gi|282881777|ref|ZP_06290435.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
 gi|281298387|gb|EFA90825.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
          Length = 261

 Score =  110 bits (275), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 123/261 (47%), Gaps = 15/261 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
            ++  ++  E + +   +   + +    +  ++E  L +   ++KKY  +G+ + D+ Q 
Sbjct: 8   ELDRKLTKEEKKELF--LEYYKTKDQDLRTILIEEYLYIAEILSKKYIGKGIDYDDIYQV 65

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
            +IGL+ + ++FD   GY+FS++A   +   I +   D+  TIR+P  +++   K++   
Sbjct: 66  ASIGLIYSVDRFDPTKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELSKKIMIAK 125

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDT--SHLGDFI 592
            ++S + +R PT E+IA+ L    E + + ++ +    P SL+      D     L D I
Sbjct: 126 NKLSQEYQRTPTVEDIAEFLNASPEEIIESMEASKVYTPQSLDIVYDSGDDKKMSLQDLI 185

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +           + +L++   + + +L   E+ +L  R+        T   + K+  ++
Sbjct: 186 GEDE-----KYFDKIDLKDFLLKSMKNLNEIEKTILIDRYF----NKKTQIVIAKKLNIS 236

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
           +  + +IE K + K++   + 
Sbjct: 237 QMTVSRIEKKVLEKMRKEIKK 257


>gi|239934520|emb|CAR94574.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 260

 Score =  110 bits (275), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 60/303 (19%), Positives = 117/303 (38%), Gaps = 48/303 (15%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G    MAS+   P + + L+   + +      L +I+       
Sbjct: 3   LLTREGEIVIAKRIEEGIRESMASISVFPGSVEHLLSEYELVKKEERRLADIL------- 55

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                G+ +  E      +  ++ E   ++  + E D     K   +D       P  A+
Sbjct: 56  ----TGYLNPMEHVPSASQVAAAAESAAENKTKAEKDKADKDKKDDEDEKDNGPDPVEAK 111

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
               +L    +     L+A+E                                K  + S 
Sbjct: 112 KRFDSLRRAHN---KVLAAIE--------------------------------KHGRYSE 136

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
           + +       ++     L   ++D L + + D   +I   E  ++R+     G+KR +FL
Sbjct: 137 QAQKQLHTRAEVFKYFKLTPRQLDPLAKNVRDAISQIRRQERLIMRICVREVGMKRKLFL 196

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
           +  Q +E + +W+  A+     +  + +      I + +N++ S++  TG+ IS+ + I 
Sbjct: 197 KEFQSQESESNWID-AQIKKHKDLADKLQIAKPEIERAQNKLASMAEATGLQISDIKEIN 255

Query: 432 SMV 434
             +
Sbjct: 256 RRM 258


>gi|304439070|ref|ZP_07398989.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372429|gb|EFM26016.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 260

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 115/251 (45%), Gaps = 14/251 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
              +      +++++E NL +   +AKKY  RG+ + D+ Q  +IGL+ A +++D   G+
Sbjct: 19  EYNKTRDPELREKLIEDNLYIAEILAKKYYGRGIDYDDIYQVASIGLIYAVDRYDPSKGF 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FS++A   +   I +   D+  TIR+P  +++   K+      ++  +++ PT  +IA+
Sbjct: 79  EFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELSKKINNARVYLAQNLQKAPTVSDIAE 138

Query: 555 KLAMPVEGVRKVLKIT--KEPISLE---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            L    E V + ++ +   +P SL+       D+   +L D I             +  +
Sbjct: 139 YLNTTEEEVLEAIEASRVYQPQSLDISYESQSDDKEVNLADIIGQDEE-----YFEKIEM 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +    +  +L   E+ +L  R+        T   + +Q  +++  + +IE K + +LK 
Sbjct: 194 NDLMESLFKNLNEVEKTILVERYF----NRKTQVAIAEQLNISQMTVSRIEKKVLERLKK 249

Query: 670 PSRSKKLRSFL 680
               K +   L
Sbjct: 250 DVEGKTMGEVL 260


>gi|253688938|ref|YP_003018128.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251755516|gb|ACT13592.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 240

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R    +V +  ++   ++ R PT +E+A
Sbjct: 65  TAFTTYAVQRIRGSMLDELRSRDW---APRSVRRNAREVAQAMQQAEQQLGRTPTEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL   ++ NLR  
Sbjct: 122 QALNITLEDYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRHR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIESLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|292698318|dbj|BAI99703.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 253

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 98/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITCLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D I +   +++ I  ETG+SI++ + I   +
Sbjct: 199 FEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRM 248


>gi|218887101|ref|YP_002436422.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218758055|gb|ACL08954.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 265

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 99/234 (42%), Gaps = 13/234 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +V      V  +A +      R ++  +LI  G +GLM+A  KF   LG +F TYA 
Sbjct: 36  QERIVRHYAPKVRFLALRLKAKLPRNVELNELISAGTLGLMEALGKFRPQLGIRFETYAE 95

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +         P  +R ++ ++    +R+ ++  R PT  E+     +  +
Sbjct: 96  SRIRGAMLDELRRLDW---FPRSLRQRVRQLDEAIQRIEHEKGRHPTEAELQDATGLDQK 152

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR  L+  +  + L      +    L      +    P  +     L E    ++  LT
Sbjct: 153 DVRLGLEALQNQLCLSLDAIQD---SLAPDTGVQGEGEPFQTTATQELIERVAGLIDELT 209

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           PRE+ VL + +      +  + E  +   +T  R+ Q+ ++A+ +L+   R+  
Sbjct: 210 PREKLVLSLYYS----DELNMRETAEVMGITEGRVSQLHSQALNRLRKEFRNHY 259


>gi|167766746|ref|ZP_02438799.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
 gi|167711500|gb|EDS22079.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
          Length = 232

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 120/234 (51%), Gaps = 8/234 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R  +     A+++++  N+ L+ SV +++TNRG +  DL Q G+IGLMKA +KFD  
Sbjct: 6   ELLRLTKEGNEAAREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLS 65

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++   +++ ++K+++   +   + +RE T EE
Sbjct: 66  YDVKFSTYAVPMITGEIRRFLRD-DGMIKVSRSLKENVYKIMKAREKFCQQYQREATIEE 124

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           I++   +  E +   L+ + E  S+      +D S +    +     +  +  +   L  
Sbjct: 125 ISEITKITREEIVTSLEASNEVESIHQSAYQKDGSEISLLDKLSKGENESEKVVDHVL-- 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                +  L  +E++++  R+  G     T +E+ K F +++ ++ +I+ K ++
Sbjct: 183 -LKEAMKHLEQKEQQMIYYRYFEG----KTQQEIAKIFHISQVQVSRIQKKILK 231


>gi|85859187|ref|YP_461389.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
 gi|85722278|gb|ABC77221.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
          Length = 261

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 54/248 (21%), Positives = 104/248 (41%), Gaps = 14/248 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAEKFDWC 491
                    ++ ++   L  V +V  +  ++         DLI  G IGLM A EK+D  
Sbjct: 21  WVMNADKKDREALILKYLPFVKAVVGRMASKIPIDAGDKEDLIHVGIIGLMSAIEKYDTR 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +F TYA   ++ A+   +  +     +P  +R + +++ +    +   ++R P   E
Sbjct: 81  RNVRFETYAGIRIRGAVLDELRARDW---VPRAVRSRDNEITKAISSLQKILRRAPDDHE 137

Query: 552 IAKKLAMPVEGVRKVLKITKE---PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           I++ L + +E   K+L  ++      S + P    D     D I      S LD      
Sbjct: 138 ISEYLGLSIEEYFKLLDDSRCISLISSEDLPGDYLDRYSCSDVIRAVEQGSALDLITDHE 197

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    + +  L  +E  VL + +      + T++E+GK   +T  R+ Q+ ++AI +L+
Sbjct: 198 FRMQLKKAMELLPDKERLVLTLYY----YEELTMKEIGKVLDLTESRVCQLHSQAIFRLR 253

Query: 669 HPSRSKKL 676
              +   L
Sbjct: 254 AAVKKINL 261


>gi|264676583|ref|YP_003276489.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
 gi|262207095|gb|ACY31193.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
          Length = 239

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 102/247 (41%), Gaps = 16/247 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  ++ LV  +A     +    ++  DLIQ G IGL +A  +F+   
Sbjct: 1   MYTAKGQLDRDALIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R    ++ +   R+  ++ R P   EI
Sbjct: 61  GVQFDTFASQRIRGAMLDELREGDWM---SRSSRKSQKEIEQALNRLEQRLGRPPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQA 607
           A +L M ++  + +L      + + LE   G +      +L   + D  A        Q 
Sbjct: 118 AAELGMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVADSGADPFALLRDQ- 176

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +R      + +L  RE+       G+    D  L+E+     VT  R+ Q+ ++AI +L
Sbjct: 177 RMRSALVEAIKTLPEREQ----YVMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQAIARL 232

Query: 668 KHPSRSK 674
           +   RS 
Sbjct: 233 RTKMRSH 239


>gi|239637364|ref|ZP_04678346.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
 gi|239596964|gb|EEQ79479.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
          Length = 256

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 122/247 (49%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +  + S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQEDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAARLEVTDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE+ +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSDREKEIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  ++
Sbjct: 249 KLQEAAK 255


>gi|229118995|ref|ZP_04248338.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
 gi|228664438|gb|EEL19936.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
          Length = 294

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 132/264 (50%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-- 469
           EIK I     +S  E    + + ++ +      +  +   N+ LV+S+A+KY N+     
Sbjct: 10  EIKEIGNYKVLSKQES---LKLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIE 66

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA WW+++++   I  +     +IP ++   
Sbjct: 67  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQF 126

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS 586
             K V    +      R PT EE+ K+L +  E V +     K    ++L+    +ED  
Sbjct: 127 NLKYVELEDKYLQMYNRTPTVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINEDIG 186

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
               F +D +A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 187 MSKPFYDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 246

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K   +T ER+ QI+ +AI+KLK 
Sbjct: 247 AKALMITTERVSQIKEEAIKKLKK 270


>gi|291196400|emb|CBG22672.1| DNA-directed RNA polymerase subunit D [Pseudomonas umsongensis]
          Length = 237

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 97/284 (34%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDTKTAKADDDSDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +     A++   R   +   + +A                                L  L
Sbjct: 110 TRK---ALKKHGRHNKLAIAELLA--------------------------------LSDL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEI 237


>gi|73539441|ref|YP_299808.1| sigma-70 region 4 [Ralstonia eutropha JMP134]
 gi|72122778|gb|AAZ64964.1| Sigma-70 region 4 [Ralstonia eutropha JMP134]
          Length = 238

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 53/207 (25%), Positives = 96/207 (46%), Gaps = 9/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL+ AA++++   G +F TYA   ++ A+   +            +R 
Sbjct: 36  VQIDDLIQAGMIGLLDAAKRYEDTHGARFETYASQRIRGAMLDEVRANDW---QSRSLRQ 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDT 585
              ++ RT R +  K+ R P   E+A++L MP++  + +L      + +  E      + 
Sbjct: 93  FTRRIERTQRGLEQKLGRAPLDSEVAQELEMPLDEYQTLLNEVYGCQLLHYEDFERSGEE 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L   +      +PL   ++  +R    R +  L  RE+ VL + +    + +  L E+
Sbjct: 153 DFLDRHLGGSEDGNPLTQLMENGMRAALIRAIERLPEREKLVLSLCY----DQELNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    VT  R+ QI  +AI +L++  R
Sbjct: 209 GAVLDVTESRVCQIRGQAITRLRNQLR 235


>gi|28211312|ref|NP_782256.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
 gi|28203752|gb|AAO36193.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
          Length = 242

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 116/239 (48%), Gaps = 15/239 (6%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+ +V+  + LV  +A +      + + + DL+  G +GLM A +KFD   G KFSTYA 
Sbjct: 10  KEGLVKKYIPLVKYIASRVIIGKTKYIDYDDLVGYGMLGLMDAMQKFDPSKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +        I     DK+++      ++  K  +EP  EE+AK+L M ++
Sbjct: 70  IRIRGSMIDELR---RISPISKSAMDKLNRYNEAVEKLQMKNFKEPKLEEVAKELDMSLK 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  DE+   L   + DKN+ SP     +  L E   + + 
Sbjct: 127 EVAQIENYINYISIVSLEDFIFSDEEDMSLMATVVDKNSPSPEKILEEKELIEYLEKAIN 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            L  R+  VL + +        TL+E+GK   V+  R+ Q+ ++AI  L+  S  KKL+
Sbjct: 187 KLKERDRIVLSLYY----YERLTLKEIGKVLDVSESRVCQLHSRAIVHLR--SELKKLK 239


>gi|148244663|ref|YP_001219357.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326490|dbj|BAF61633.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 277

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 122/253 (48%), Gaps = 11/253 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +   V+  E     A +++V +++R V  +A  Y   GL+  DL+QEG IGL
Sbjct: 25  LSSEEEHELA--VQLYENHNLSAARKLVLSHMRFVAFIAHSYKGYGLEQADLVQEGTIGL 82

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRM 539
           MKA ++F+     + +++A++W++  I   I      +++      R    K+ +    +
Sbjct: 83  MKAVKRFNPHRNVRLASFAVYWIRAEIHEFIFKNWKIVKVATTKAQRKLFFKLKQAKAHI 142

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
            N +  E   ++IAK L +  + V ++    +          +ED+     ++ ++N  +
Sbjct: 143 YNSLNEEQ-ADKIAKDLGVRRKDVLEMESRLQFSDVTFEVFDEEDSHAPEQYLTNENIQT 201

Query: 600 PLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           P    +  +     ++   + L+SL  R   +L+ R+        TL  +  ++ +++ER
Sbjct: 202 PEQLLLTDDSKKTQQQRLYKALSSLDERSLDILQSRYL--KEEKTTLYTLADKYSISKER 259

Query: 656 IRQIEAKAIRKLK 668
           +RQ+E KA++KLK
Sbjct: 260 VRQLETKAMQKLK 272


>gi|86146119|ref|ZP_01064445.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218708840|ref|YP_002416461.1| flagellar biosynthesis sigma factor [Vibrio splendidus LGP32]
 gi|85836066|gb|EAQ54198.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218321859|emb|CAV17839.1| RNA polymerase sigma factor for flagellar operon [Vibrio splendidus
           LGP32]
          Length = 244

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 100/245 (40%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAE 486
           +   +   +     +++   E    LV  +A     R        DLIQ G IGL++A +
Sbjct: 1   MNKALTYDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++      +   + R+
Sbjct: 61  NYDGTKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKNNREISSAIAELEGTLNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDS 603
           P+  E+AK + + ++            I+    +G ED     D I   ED    +P   
Sbjct: 118 PSDAEVAKHMGLSLDQY----HSALTDINCSKLVGIEDLGVSDDVISPNEDSQDNTPFQG 173

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               + R+     +  L  RE  VL + +    + +  L+E+G+   V+  R+ QI +++
Sbjct: 174 VADESFRQALIDSIKQLPEREGLVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQS 229

Query: 664 IRKLK 668
           +++L+
Sbjct: 230 MQRLR 234


>gi|326332680|ref|ZP_08198943.1| hypothetical protein NBCG_04120 [Nocardioidaceae bacterium Broad-1]
 gi|325949508|gb|EGD41585.1| hypothetical protein NBCG_04120 [Nocardioidaceae bacterium Broad-1]
          Length = 264

 Score =  110 bits (275), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 58/258 (22%), Positives = 110/258 (42%), Gaps = 16/258 (6%)

Query: 418 VETGISISEFRHI-VSMVRKGECEASIAKKEMVEA----NLRLVISVAKKYTNRGLQFLD 472
            ET +  +E + +   ++          +  ++E     N  +  S+A +YT RG+   D
Sbjct: 6   FETDLPRAERQRLTSELLAAAHEAEGEEQDRLIEEVILLNAAVARSIAHRYTGRGIPRAD 65

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q   I L++AA+ F       F TYA+  ++  + R   D   T+R P  +++    +
Sbjct: 66  LEQVAYIALVRAAKSFHPDRADDFLTYAVPTIRGEVKRWFRDHGWTVRPPRPIQELQSTL 125

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGD 590
           +R      N         E+A+   +P + VR+ L       P SL+ P+   D+   G+
Sbjct: 126 LRIGSERGN-----LPTSELAEIAEVPEQKVREALDARGCFTPSSLDAPLRSGDSQSSGE 180

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
                              R    + + +L PR++ V+R+RF      D +  E+G+   
Sbjct: 181 ATIGDMLPGVDGGLSDCETRLALEQAIHALCPRDQLVVRLRFL----EDRSQAEIGEAIG 236

Query: 651 VTRERIRQIEAKAIRKLK 668
           VT+ ++ +I  + I +L+
Sbjct: 237 VTQTQVSRILTRIIDELR 254


>gi|302392455|ref|YP_003828275.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
 gi|302204532|gb|ADL13210.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
          Length = 253

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 65/255 (25%), Positives = 136/255 (53%), Gaps = 11/255 (4%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           +I  +  +S +E + ++   +        AK ++V  N++LV+ VA ++ N+   + +L 
Sbjct: 7   NIPQKELLSEAETKELLKKAQ---AGDQKAKDKLVNHNVKLVLKVAHRFANKNYDYEELF 63

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G+IGL+KA E+FD     KFSTYA+  +   I R + D    +++   ++ + H++  
Sbjct: 64  QIGSIGLLKAIERFDLERDVKFSTYAVPLIIGEIKRFLRDDD-AVKVSRSLKRRAHRINE 122

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
               ++ ++ REPT +EIA+++ +  E +   L+  +EP S+ +P+ + + + +   + D
Sbjct: 123 VKESLTAELNREPTIQEIAEEMEVDKEEIVNALEAVREPTSIYSPVYENEGNSIE--LVD 180

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           + A S  +   + + R     V+  L  RE  +L++RF      + T +EV  +  V++ 
Sbjct: 181 QLAASSENQEQEID-RLALREVIDELKTRERLILKLRFF----DEKTQQEVADRIGVSQV 235

Query: 655 RIRQIEAKAIRKLKH 669
           ++ ++E K I K++ 
Sbjct: 236 QVSRLERKIIDKVRE 250


>gi|258514023|ref|YP_003190245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777728|gb|ACV61622.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 249

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 54/244 (22%), Positives = 104/244 (42%), Gaps = 14/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                   A+++++   L LV  ++ +   R   G+ + DL   G +GL+++ EKF+   
Sbjct: 10  YISNRDKKAREKLILMYLPLVKHLSGRLAVRLPIGISYEDLEGYGVVGLIESIEKFNPAK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F T+A   ++ AI   +        +P  +  K   V     R+        T E++
Sbjct: 70  GVSFETFAYRRIRGAIIDEVRKLYW---VPRTLWQKFQAVNAERERLRRINGDNVTDEQV 126

Query: 553 AKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN 608
           A  L + +  + K      +    SL+  +   D     LG+ I D N+  PLD   + +
Sbjct: 127 AASLNISIAELHKTSNCYNQLNMNSLDEVLTSSDGDSVRLGNLIPDPNSPDPLDVVEEQD 186

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R      + SL  ++  V+     +      TL+E+G+   V+  R+ Q+ A+A+ +L+
Sbjct: 187 GRRILAEAVNSLNEKDRLVM----ALYYQERLTLKEIGQVLEVSESRVCQLHARAMSRLR 242

Query: 669 HPSR 672
              +
Sbjct: 243 QKIK 246


>gi|291196326|emb|CBG22635.1| DNA-directed RNA polymerase subunit D [Pseudomonas lundensis]
          Length = 238

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 48/284 (16%), Positives = 98/284 (34%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    E + + E     + D+      P             D   
Sbjct: 50  GITPPAAEVPPPVDPKTAKAEGDDEEEEKDDATDDEEEVESGP-------------DPII 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  + S +       L +L
Sbjct: 97  AAQRFGAVSDQM------------EITRKALK---------KHGRDSKQAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL    G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRLFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +A     I++ + ++ ++  ETG+ I+E 
Sbjct: 196 SD-ALAKGKSKYAEAIARLQPDIIRCQQKLSALEAETGLKIAEI 238


>gi|331269204|ref|YP_004395696.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329125754|gb|AEB75699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 252

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 118/239 (49%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++++ +     A  ++V+ NL LV +++KK+ NRG ++ D+ Q G++GL+KA   FD 
Sbjct: 18  LELIKQAKLGDKKAVDQLVQKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 77

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R I D    I++   ++    K+     +++ ++ REP+ E
Sbjct: 78  SYNVQFSTYAVPMIMGEIKRFIRD-DGLIKVSRSVKYTAKKLHYDKEKLTKQLNREPSIE 136

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K   +  E +    +   EP  L   I  +D S +  ++ DK  V       + + +
Sbjct: 137 ELSKFSGISKEEIIFSSEAINEPKYLYDTIHQDDGSPI--YLIDKVVVDDKGEIDELD-K 193

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L+ L  R  +++ +R+   +        V K   +++ ++ +IE K ++ +K 
Sbjct: 194 IALKEALSKLDQRSRQIIILRYFKDITQVK----VAKMLGISQVQVSRIEKKVLKSMKE 248


>gi|326204596|ref|ZP_08194452.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
 gi|325985163|gb|EGD46003.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
          Length = 254

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 107/247 (43%), Gaps = 11/247 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  E + + AK++++     L+  VA +   Y    ++F DL+  G  GL+ A EK+D  
Sbjct: 12  QYIENKEAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEKYDLA 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   ++ +I  SI D      +P  +R K  ++ +    + N+     T +E
Sbjct: 72  KGVKFETYASLRIRGSIIDSIRDMDW---VPRSLRQKNKELEKVYAEIENEKGHTATDKE 128

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-DFIEDKNAVSPLDSAIQANLR 610
           +A+K+ + ++   K+L        +      E     G +   +     P  S     ++
Sbjct: 129 VAEKMGLGMDDFYKLLNDVNVSSMMSLDEFMEQNYERGLEIFSESTEDKPEASLEFNEMK 188

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     +  L  +E+ V+   +      + TL+E+     VT  RI Q+  KA+ ++K  
Sbjct: 189 QLLADSIDKLPEKEKAVITFYYF----EELTLKEISAIMSVTESRISQLHTKALLRMKGK 244

Query: 671 SRSKKLR 677
               ++ 
Sbjct: 245 LFRHRIM 251


>gi|302556940|ref|ZP_07309282.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474558|gb|EFL37651.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 285

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 103/227 (45%), Gaps = 12/227 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 48  RDELVTAWLPMAHRIAGRFRDRGEAVEDLRQVAALGLVKAIDRFDPSRG-AFESYAVPTI 106

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              + R   D+   +R+P  +++  +KV    R ++      EP+   IA    +  + V
Sbjct: 107 TGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELTQSPGSPEPSVAAIAAHTGLTEDEV 166

Query: 564 RKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              ++   +   +SL+  +  +D  +    + D    S     +  + RE+    L  L 
Sbjct: 167 GAGMEALESFSTLSLDAELSSDDDGY---SLADTLGASDSSYDVVVD-RESAKEGLRRLP 222

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  +L MRF      D T   +  Q  +++  + ++ +++  +++
Sbjct: 223 ERERAILYMRFF----EDMTQSRIADQLGISQMHVSRLISRSCARVR 265


>gi|238756654|ref|ZP_04617944.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
 gi|238705123|gb|EEP97550.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
          Length = 240

 Score =  110 bits (275), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V +  R++  K+ R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVAQAMRQVEQKVGRPASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+     + + D  +  +PL   ++ NLR+ 
Sbjct: 122 QILDISLVEYRQILLDTNNSQLFSYDEWREEHGESVEPVLDGLDDANPLQQLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|88809561|ref|ZP_01125068.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786311|gb|EAR17471.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 211

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 53/146 (36%), Positives = 90/146 (61%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 ++       AK +M+ ANLRLV+++AK+Y  +GL  LDLIQEG +GL +A EK+
Sbjct: 51  EYSEDEKRIIKRGEKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKY 110

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G++FSTYA WW++Q + R+++ QS TIRIPV++ +K+ K+  +  R+  +    P+
Sbjct: 111 DPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEKLTKLRASKARLMQRNGLSPS 170

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPI 574
            E+++  + +P+  V  +L      +
Sbjct: 171 TEQLSDDMNLPISEVEDLLGCELRSV 196


>gi|172057862|ref|YP_001814322.1| RNA polymerase sigma factor SigD [Exiguobacterium sibiricum 255-15]
 gi|171990383|gb|ACB61305.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium
           sibiricum 255-15]
          Length = 257

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 106/250 (42%), Gaps = 13/250 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +            +++    LV    ++ +    + +   +L   G +GL  A +KFD  
Sbjct: 11  QWLSTRDIAVADRLLQNYEPLVHYHVQRLSATLPKSVDRDELKSLGMMGLYDALQKFDQN 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +        +P  +R+K  +V      +   ++R PT +E
Sbjct: 71  HNNKFDTYAAFRIRGAILDGLRKIDW---LPRSLREKSKRVEAAVEILEQSLQRTPTIDE 127

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDF-IEDKNAVSPLDSAIQAN 608
           ++  + M  E V+  L  +     +S++  +  +D          D +  +P D+ +   
Sbjct: 128 VSSIVDMSPEEVKTALAESYFANILSIDEAVTLQDEGKAMAVSYLDPDTATPEDTLLMRE 187

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L       +  L+ +E+ V+ + +      + TL E+G+   ++  RI QI +KA+RKLK
Sbjct: 188 LISKLAEEVEQLSEKEQYVVSLFYF----EELTLTEIGEVLGLSTSRISQIHSKALRKLK 243

Query: 669 HPSRSKKLRS 678
               S  L  
Sbjct: 244 QALGSAYLSD 253


>gi|221635447|ref|YP_002523323.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
 gi|221157679|gb|ACM06797.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
          Length = 262

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 113/260 (43%), Gaps = 11/260 (4%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQE 476
             I   +   +   +R+ E      + ++VE    LV  V  +        ++  DLI  
Sbjct: 1   MAIPARQEGRLRQRLRRIEARD-DTRAQLVEQYAPLVKYVVDRLRLSLPPSVERDDLIGY 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL++A ++FD   G KF TYA   ++ AI  ++        +P   R +  ++ +  
Sbjct: 60  GTIGLLEALDRFDDTRGVKFETYAAMRIRGAILDALRTLD---IVPRSARSRARQIEQAT 116

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           R    +  R P+  E+A  L M    +++ +              D DT  L + + D N
Sbjct: 117 REFFAEYGRMPSENELADHLGMTTTELQQAISDAACLFLPLQASEDPDTLTLEEQLADPN 176

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A+ P + A + +L++     LA+L+ R+  ++ + +      D T+ E+ +   ++  R+
Sbjct: 177 ALEPGEVAAEEDLKQRIAAALATLSERDRLIVSLYY----YEDLTMREISQLLGISESRV 232

Query: 657 RQIEAKAIRKLKHPSRSKKL 676
            QI  +   +L+   R + +
Sbjct: 233 SQILNRVRLQLRALLRERGV 252


>gi|167949416|ref|ZP_02536490.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 134

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 80/113 (70%), Positives = 96/113 (84%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +  GE +A  AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  G
Sbjct: 1   MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 60

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           YKFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M  ++ RE
Sbjct: 61  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGRE 113


>gi|114566161|ref|YP_753315.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114337096|gb|ABI67944.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 243

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 110/237 (46%), Gaps = 9/237 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +++R  +     AK ++ EAN+ L+  V +++ N      DL Q G +GL+KA E+FD+ 
Sbjct: 12  ALLRLAQGGDQEAKAQLYEANVGLIYLVLERFKNTSYDQEDLFQVGAMGLLKAIERFDFS 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +FSTYA+  +   I + + D    +++   +++   +V     ++   + REP   E
Sbjct: 72  FDVRFSTYAVPMIIGEIKKFLRD-DGMVKVQRGIKELYARVRWAQDKLRGDLGREPGVNE 130

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA  L M  E +   ++  + P  +   +  E+   L   + DK      + AI   L  
Sbjct: 131 IASLLEMEKEDIVVAMEACQAPAYIHDVVPSEEKEQLS--LLDKLVHEEGNVAILEKL-- 186

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                LA L  RE  V+  RF      D T   + +   V++ +I +IE  AI KL+
Sbjct: 187 ALREALAKLDERERVVIIRRFF----QDETQTVIAEDLGVSQVQISRIEKSAILKLR 239


>gi|257095368|ref|YP_003169009.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
 gi|257047892|gb|ACV37080.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 248

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 103/238 (43%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                  + + ++V+  + LV  +A     R    +Q  DLIQ G +GL+ A  +F+  +
Sbjct: 1   MYNAAGQLNRDQLVQHFVPLVKRIACHLMARLPASVQVDDLIQNGMLGLLDAISRFEATM 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F  YA   V+ A+   + +      +P  +R    ++     R+  +  R PT +E+
Sbjct: 61  GAQFEAYAAQRVRGAMLDGLRENDW---LPRSLRSDCRRIEVAIARLEQEHGRAPTEKEL 117

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L M +   +K+L+     + + LE  + +     L   + D +A  P     +   R
Sbjct: 118 ADSLGMALADYQKMLQDARGHQLVYLEDMVAERGEDFLERHLVDADA-DPSKLLEEETFR 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +  L  RE  ++     +    D  + E+G+   VT  R+ Q+ ++ + +L+
Sbjct: 177 RLLVQAIDGLPERERLLM----ALYYEQDLNMREIGEVMGVTESRVCQLHSQVVLRLR 230


>gi|261821180|ref|YP_003259286.1| flagellar biosynthesis sigma factor [Pectobacterium wasabiae
           WPP163]
 gi|261605193|gb|ACX87679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           wasabiae WPP163]
          Length = 240

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E ++ K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGTMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R    +V +  ++   ++ R PT +E+A
Sbjct: 65  TAFTTYAVQRIRGSMLDELRSRDW---APRSVRRNAREVAQAMQQAEQQLGRTPTEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           + L + +E  R++L  T            E+     +  +E     +PL   ++ NLR  
Sbjct: 122 QTLNITLEDYRQILLDTNNTQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRHR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VMDAIESLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|21225590|ref|NP_631369.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|8347047|emb|CAB93752.1| probable RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 299

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 104/235 (44%), Gaps = 14/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 53  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVPTI 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              + R   D+   +R+P  +++  +KV    R ++      EP+   +A    +  + V
Sbjct: 112 TGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELAQSPGSPEPSVAALAAHTGLSEDEV 171

Query: 564 RKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              ++   +   +SL+  +   +D   L D +    A       +    RE+    L  L
Sbjct: 172 GAGMEALESFSTLSLDAELSAGDDGYSLADTL---GAADTSYDTVID--RESAKEGLRRL 226

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
             RE  +L MRF      D T   +     +++  + ++ +++  +++  +  ++
Sbjct: 227 PERERAILYMRFF----EDMTQSRIADCLGISQMHVSRLISRSCARVRDEAMGQR 277


>gi|303242484|ref|ZP_07328964.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302589952|gb|EFL59720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 252

 Score =  110 bits (274), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 108/227 (47%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L L   ++KK+ NRG+ + D+ Q  +I L+KA E+FD   G KF+++A   +
Sbjct: 31  RNEIVSKYLYLAEIISKKFVNRGIDYEDIYQVASIALIKAVERFDPDKGVKFASFATPTL 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IRIP  + +   KV      ++ ++ R P  +EIAK L +  E V 
Sbjct: 91  IGEIKRFFRDKASVIRIPRRIYEVYQKVSHARESLTQELSRPPRIDEIAKYLNISEETVM 150

Query: 565 KVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +++         S +  +  +D   L + I +++A        +   R+   + L     
Sbjct: 151 EIIESNNAHNLQSFDQNVYTDDDLELHETIGEEDAT-----FEKIENRDFLKKSLDKFND 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E+  + MR+        T +E+ ++  V++  + ++E K + + + 
Sbjct: 206 AEKEFIDMRYFNN----RTQKEIAERLGVSQMYVSRLEKKVLDRFRR 248


>gi|330684827|gb|EGG96520.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU121]
          Length = 256

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 120/247 (48%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +  + S A+ ++V    +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQEDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V +   +  +   +S++  I  +        ++            
Sbjct: 135 SISEIAARLEVTDEEVLEAIEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE+ +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSDREKEIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  ++
Sbjct: 249 KLQEAAK 255


>gi|291196306|emb|CBG22625.1| DNA-directed RNA polymerase subunit D [Pseudomonas graminis]
          Length = 236

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 97/284 (34%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + + + V+  + + E A+   +D+      P                 
Sbjct: 50  GIAPPAEVPPPVDPKAEKVEGADDEEEDASDDEEDEVESGPDPV---------------I 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+   V                        +K  + S +       L +L
Sbjct: 95  AAQRFGAVSDQMAIAVKAL---------------------KKHGRGSKQANAELLALAEL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 134 FMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDQSW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +      I + + ++ ++  ETG++I E 
Sbjct: 194 TDGLAK-GKSKYAEAIGRLQADIQRCQQKLTALEEETGLTILEI 236


>gi|291549326|emb|CBL25588.1| RNA polymerase sigma-F factor [Ruminococcus torques L2-14]
          Length = 239

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 132/247 (53%), Gaps = 12/247 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++++RK       A++E+VE N+ L+  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   DTIALIRKSHDGDKKAREELVEKNIGLIWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+    +FSTYA+  +   I R + D    I++   +R+  +K ++   +M+  + REPT
Sbjct: 63  DFSYEVQFSTYAVPMISGEIRRFLRD-DGMIKVSRSLRELSYKSLQAREKMTRILGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            +E++++L +  E + + ++ + E  S+  PI  ++ S   L D +E+K+         +
Sbjct: 122 LKELSEELQIDCEEIVQAMESSVEVESIYKPIHQKEGSEILLMDKLEEKD-----RQEEK 176

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R     VL +L  +E  ++ +R+  G     T  E+GK+  +++ ++ + E K + +
Sbjct: 177 VLDRIVLKEVLETLEAKERTIIYLRYFAG----KTQAEIGKKMGMSQVQVSRTEKKVLER 232

Query: 667 LKHPSRS 673
           ++   + 
Sbjct: 233 MRKEMKR 239


>gi|320354339|ref|YP_004195678.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
 gi|320122841|gb|ADW18387.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
          Length = 244

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 109/230 (47%), Gaps = 13/230 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + +++  N+ LV  V ++ T +   F+   D+I    +GL+ AA KFD   G KF T+A 
Sbjct: 11  RSQLIRENMPLVELVVQRMTPQVPSFMTKEDMISAAMVGLVDAANKFDPTKGVKFKTFAE 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + V+ AI   +            MRDK + + +T  R+  ++ R P  EE+A+++A+ ++
Sbjct: 71  YRVRGAIFDEMRKLDWF---SRSMRDKQNTLTQTMLRLERQLGRSPEEEEMAREMALSID 127

Query: 562 GVRKVLKITKE--PISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             R +L        +SL   +   ED     D +ED     P D   +  +      +L 
Sbjct: 128 EYRDLLAEVSHLGCVSLHETLDHTEDGRSFLDSLEDIGGPVPDDLLEKEEMTRVMAEILE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L+ +E  V+     +    + T +E+ +   V+  R+ Q+ ++A+ KL+
Sbjct: 188 ELSEKERLVI----ALYYYEELTQKEIAEVLSVSEGRVSQLHSQALLKLR 233


>gi|256783387|ref|ZP_05521818.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767263|ref|ZP_06526641.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289697462|gb|EFD64891.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 287

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 104/235 (44%), Gaps = 14/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 53  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVPTI 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              + R   D+   +R+P  +++  +KV    R ++      EP+   +A    +  + V
Sbjct: 112 TGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELAQSPGSPEPSVAALAAHTGLSEDEV 171

Query: 564 RKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              ++   +   +SL+  +   +D   L D +    A       +    RE+    L  L
Sbjct: 172 GAGMEALESFSTLSLDAELSAGDDGYSLADTL---GAADTSYDTVID--RESAKEGLRRL 226

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
             RE  +L MRF      D T   +     +++  + ++ +++  +++  +  ++
Sbjct: 227 PERERAILYMRFF----EDMTQSRIADCLGISQMHVSRLISRSCARVRDEAMGQR 277


>gi|317492397|ref|ZP_07950826.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
 gi|316919736|gb|EFV41066.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
          Length = 240

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  I K  + +    LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTADGVIDKNSLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V    +R   ++ R PT  EIA
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVSAAMQRAEQRLHRAPTETEIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRET 612
           ++L MP+   +++L  T            E+     +   +     +PL   ++ +LR+ 
Sbjct: 122 QELDMPLVEYQQILLDTNTSHLFSYDEWREEHGDSAEPVFQQHEDANPLKQLLEGDLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIAAIEALPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|297196315|ref|ZP_06913713.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722893|gb|EDY66801.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 272

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 110/257 (42%), Gaps = 17/257 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR +  +      E    ++E+V A L +   +A ++ NRG    DL Q   +GL+KA +
Sbjct: 21  FRRLAEL--DDGPERQEVRQEIVSAWLPMAERIAGRFRNRGESIEDLQQVAALGLVKAVD 78

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-IKR 545
           ++D   G  F ++A+  V   + R   D    + +P  ++D  ++V    + +      R
Sbjct: 79  RYDPSRG-AFESFAVPTVVGEVKRHFRDHMWALHVPRRVQDLRNRVRFARQDLVQTVSGR 137

Query: 546 EPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGD-EDTSHLGDFIEDKNAVSPLD 602
            PT  EIA++  +  E   V      +   +SL+  +   +D   L D +   +    + 
Sbjct: 138 APTVAEIAERAGVSEEDALVGLEALESFTALSLDAELPGADDGYSLSDTLGSADPAIDVL 197

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  RE     L  L  RE+ +L MRF      D T   + +   +++  + ++ ++
Sbjct: 198 VD-----REAVKPGLRKLPEREQNILYMRFF----RDMTQSSIAQTLGISQMHVSRLISR 248

Query: 663 AIRKLKHP-SRSKKLRS 678
              +L++   R + LR 
Sbjct: 249 CCDQLRNEVMRDEALRE 265


>gi|119775415|ref|YP_928155.1| flagellar biosynthesis sigma factor [Shewanella amazonensis SB2B]
 gi|119767915|gb|ABM00486.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella amazonensis
           SB2B]
          Length = 239

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G IGL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHMLARLPASVQLDDLLQAGMIGLLEASAKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     +V +    +  ++ R+    EIA++L M +E
Sbjct: 73  IRIRGAMLDEIRKGDW---VPRSVHRNQRRVAQVIDELEQELGRDARDTEIAERLDMSME 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +  + +      D   Q+  ++     +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSHDVLVPDGEQTNDIYDDLAQSQFQQALADAIRQ 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILDVSESRVCQIHSQAMLRLK 230


>gi|315444719|ref|YP_004077598.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263022|gb|ADT99763.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 275

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 112/246 (45%), Gaps = 11/246 (4%)

Query: 427 FRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
            + + SM       E    ++ ++   L L   +A ++  RG    DLIQ   IGL+K+ 
Sbjct: 29  EKQLSSMAACGDRAERRRRRQHIITECLPLADHIACRFAGRGEPSDDLIQVARIGLVKSV 88

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +++    G +F  +A+  ++  + R   D + ++R+P  ++D   ++   A  +S ++KR
Sbjct: 89  DRYVPDKG-RFMAFAVPTIRGEVRRHFRDSTWSMRVPRKIQDTQLRMRHAAEELSQRLKR 147

Query: 546 EPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            PT  EIA++L +    V +         P+SL+ P   +         E + A  P   
Sbjct: 148 APTDREIARELGVDDGEVSRCHSAHWAYRPVSLDAP-RGDAEQECAGIGELRGADDPGFD 206

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +++  +    + V+A L PR   +L MRF        T  E+  +  V++ ++ ++    
Sbjct: 207 SVEDLI--VLSGVIAELDPRRRAILGMRF----YDCLTQREIALRLNVSQVQVSRLLDST 260

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 261 LARLRQ 266


>gi|291196348|emb|CBG22646.1| DNA-directed RNA polymerase subunit D [Pseudomonas moraviensis]
          Length = 237

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 95/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDPKAVKADDDTDDDEADSSDDEEEAESGPDPVIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRHNKAAVAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEI 237


>gi|51596050|ref|YP_070241.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|153949581|ref|YP_001401249.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|170024605|ref|YP_001721110.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           YPIII]
 gi|186895155|ref|YP_001872267.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|51589332|emb|CAH20954.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
 gi|152961076|gb|ABS48537.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 31758]
 gi|169751139|gb|ACA68657.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis YPIII]
 gi|186698181|gb|ACC88810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 240

 Score =  110 bits (274), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQQVEQRVGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QVLDIGLVEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLKHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIEAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|229076790|ref|ZP_04209702.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
 gi|228706352|gb|EEL58613.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
          Length = 252

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 116/228 (50%), Gaps = 6/228 (2%)

Query: 448 MVEANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           M   N+ LV+S+A+KY  +   ++F DL+QEGN G+++A E FD  LGY FSTYA  W+K
Sbjct: 1   MFHVNIGLVLSIARKYKKKHPEIEFDDLVQEGNEGMLRAIEDFDPDLGYCFSTYAYCWIK 60

Query: 506 QAITRSIADQSC-TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +++   I  +     +IP ++     K V    +      R PT EE+ K+L +  E V 
Sbjct: 61  KSMLGFICKKKSGPFKIPNYVNQFNVKYVEIEDKYLQMHNRIPTVEEVVKELDVTREKVV 120

Query: 565 KVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LT 621
           +          ++L+    +ED   L  F  D +A+   +  I  +L      +    L 
Sbjct: 121 RHNVYYNRVTTMTLDIDTINEDIGILNSFCNDNSAIPSTNEMIMEDLNYEIWIIFDEVLN 180

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           P+++ VL + FG+     H  +E+ K   +T ER+ Q++ +AI +LK 
Sbjct: 181 PKQKMVLNLCFGLLDGEIHLHKEIAKALMITTERVSQLKDEAINRLKK 228


>gi|84388128|ref|ZP_00991024.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
 gi|84377195|gb|EAP94065.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
          Length = 244

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 100/245 (40%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAE 486
           +   +   +     +++   E    LV  +A     R        DLIQ G IGL++A +
Sbjct: 1   MNKALTYDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++      +   + R+
Sbjct: 61  NYDGTKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKNNREISSAIAELEGALNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDS 603
           P+  E+AK + + ++            I+    +G ED     D I   ED    +P   
Sbjct: 118 PSDAEVAKHMGLSLDQY----HNALTDINCSRLVGIEDLGVSDDVISPNEDSQDNTPFQG 173

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               + R+     +  L  RE  VL + +    + +  L+E+G+   V+  R+ QI +++
Sbjct: 174 VADESFRQALIDSIKQLPEREGLVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQS 229

Query: 664 IRKLK 668
           +++L+
Sbjct: 230 MQRLR 234


>gi|168334573|ref|ZP_02692729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 247

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 21/249 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + ++   K++++E    LV  VA +   Y N  L+  DL+  G IGL+ A +K+D+ 
Sbjct: 10  KYKKTKSRELKEQLIEHYAPLVKIVAGRLGIYLNSYLELDDLLGFGVIGLIDAIDKYDYD 69

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA   ++ AI   I        +P  +R K  + +R   R+  KI   PT  +
Sbjct: 70  KKIKFETYASLRIRGAIIDEIRKLDW---VPRSIRQKQKEYIRAYERVEAKIGHSPTDTD 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF-IEDKNAVSPLDSAIQANLR 610
           + K+L +      K++  T       + +   D S L +F IED    +P          
Sbjct: 127 VRKELNINESEYNKLVHDTNI-----STLVSIDESELYEFNIEDITTKNPYQELENKEAL 181

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     + +LT RE+ ++++ +      + TL+E+     ++  R+ QI +K + KL++ 
Sbjct: 182 EILEHEILALTEREQLLIKLYY----YEELTLKEISLILEISESRVSQIHSKLMVKLRN- 236

Query: 671 SRSKKLRSF 679
               KL+ +
Sbjct: 237 ----KLKKY 241


>gi|292696855|dbj|BAI99600.1| RNA polymerase sigma-70 factor [Aeromonas sp. No. 14-2]
          Length = 252

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 50/291 (17%), Positives = 95/291 (32%), Gaps = 45/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E +D+  T   I S            +   E+ + D  + D D   
Sbjct: 49  --------------EAEDMAPTATHIGSELGEDDLADEDEEDEDEDEDGDSSDDDGDGGP 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +LR +       I                 QK+ ++    +     L  +
Sbjct: 95  DPEVAREKFAELRAQYEVTRLSI-----------------QKNGRAHNDTQAAIALLADV 137

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 138 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 197

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D + +   +++ I  ETG+SI++ + I   +
Sbjct: 198 FEYQKQAGKAWSPRLVEMDED-VQRAIGKLQQIEEETGLSIAQIKDINRRM 247


>gi|289578405|ref|YP_003477032.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544681|ref|YP_003676983.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528118|gb|ADD02470.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842456|gb|ADH60972.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 99/230 (43%), Gaps = 15/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++   + LV  + KK     +   ++ DLI +G +GL+ A EK+    G KF TYA 
Sbjct: 21  RNEIIIKYMPLVKHIVKKLIISDVTQSEYEDLINQGVLGLIDAIEKYQPSKGVKFETYAT 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +  +      P  ++ K  K+  T   +  K  REPT EEI +   +   
Sbjct: 81  LRIRGEIIDYLRKKDWM---PRSLKKKYKKIEETVETLQQKYNREPTVEEITEACGLNET 137

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V K L         SLE  I +    H    I D    +P +  +   L+      + +
Sbjct: 138 DVLKTLSYINVSNINSLEEAIENNFKLH---AISDVELKNPEEEVLYKELKRKLANAIKN 194

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  +E  V+ + +      D   +++ K   +T  RI QI  KAI++++ 
Sbjct: 195 LPDKERLVITLYY----YEDLNYKDISKILNLTESRISQIHTKAIKRIRE 240


>gi|113969642|ref|YP_733435.1| flagellar biosynthesis sigma factor [Shewanella sp. MR-4]
 gi|114046872|ref|YP_737422.1| flagellar biosynthesis sigma factor [Shewanella sp. MR-7]
 gi|113884326|gb|ABI38378.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888314|gb|ABI42365.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
          Length = 237

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 99/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     +V +    +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDW---VPRSVHRNNRRVAQAIDELEQVLGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +   D  +    ++  +          +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDILTPSDNVSDGTFEALAETQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|310772144|emb|CBX46976.1| RNA polymerase subunit D, sigma factor [Pseudomonas
           cuatrocienegasensis]
          Length = 254

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 49/300 (16%), Positives = 102/300 (34%), Gaps = 48/300 (16%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T  +++     +      L E+             G+    +G    +     
Sbjct: 1   AIAHFPGTVDSILGEYTRVTTEGGRLVEVF-----------SGYIDPDDGIVPAEAAAPV 49

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
             K+ D   + + + +      +++       PE A      + +  + +   L      
Sbjct: 50  PAKDGDAADDKDDEEDGDDSDDEEEEGDGGPDPEEALRRFTAIGDALELAKKAL------ 103

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  + S +       L +L   + L   + 
Sbjct: 104 -----------------------------KKHGRGSKQATEALVGLAELFMPIKLVPKQY 134

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           D LV ++    +R+   E  +++L      + R  FL    G E DP W        +G+
Sbjct: 135 DALVVRVRGALERLRAQERAIMQLCVRDARMPRADFLRLFPGNETDPTWAEGLAK-GKGK 193

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           +   +      I + + ++ ++  E  ++++E + I   +  GE +A  AK EMVEANLR
Sbjct: 194 YAEAIGNLQADIQRCQQKLTALEAECDLTLAEIKDINRRMSIGEAKARRAKNEMVEANLR 253


>gi|291196336|emb|CBG22640.1| DNA-directed RNA polymerase subunit D [Pseudomonas meliae]
          Length = 238

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 92/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + +    + T+ D E +A  S D+      P             D+ +
Sbjct: 50  GIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +     +  +  +AE++                                 
Sbjct: 110 ITCKALKKFGRDDKHAIAEMVALAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I + + ++ ++  ETG+ I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEI 238


>gi|291196340|emb|CBG22642.1| DNA-directed RNA polymerase subunit D [Pseudomonas migulae]
          Length = 237

 Score =  110 bits (274), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 94/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDPKAVKADDDTDDDDAEATDDEEEAESGPDPIIAAQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRGNKLAIAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 TD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|149183910|ref|ZP_01862298.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
 gi|148848374|gb|EDL62636.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
          Length = 227

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 64/220 (29%), Positives = 112/220 (50%), Gaps = 9/220 (4%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 14  RNKVEICGVDTSKLPVLKNEEMRKLFREMQAGDISAREKLVNGNLRLVLSVIQRFNNRGE 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     +FSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 74  YVDDLFQVGCIGLMKSIDNFDLGQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 132

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTS 586
            +K ++   ++  +  +EPT EEIAK L +P E +   +   ++P+SL  PI ++  D  
Sbjct: 133 AYKALQVREKLMGETSKEPTAEEIAKVLDVPHEDIVFAMDAIQDPVSLFEPIYNDGGDPI 192

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            + D + D+           A         +  L  RE+ 
Sbjct: 193 FVMDQLSDERNRDHTWIEEIA-----LQEGMRRLNDREKM 227


>gi|292698300|dbj|BAI99694.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 253

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 97/291 (33%), Gaps = 44/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II            GF    E
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                                     E  A  +    S++       E++E   DEDED 
Sbjct: 50  -------------------------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDG 84

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            +                   E+   Y          ++ QK+ ++    +    +L  +
Sbjct: 85  DSSDDDGDGGPDPEVAREKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADV 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 139 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D I +   +++ I  ETG+SI++   I   +
Sbjct: 199 FEYQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSIAQILDINRRM 248


>gi|253682632|ref|ZP_04863429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
 gi|253562344|gb|EES91796.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
          Length = 242

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 109/231 (47%), Gaps = 13/231 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +V+  + LV  +A +     ++ ++F DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 10  REHIVKKYIPLVKYIASRVIIGKSKYIEFEDLLGYGMIGLMDALNKFDESKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I   S    I     DK++K       +  +   EP  ++IA++L M V 
Sbjct: 70  IRIRGSMIDEIRKNS---PISKGAMDKLNKYNSAIETLQKRNLTEPNIKDIAEELEMTVN 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  ++D   L   IED+ + +P          E   + L 
Sbjct: 127 EVGEIENFINYISVVSLEDLIFSEDDDISLMGTIEDEKSPNPEKDFEDQERLEYLAKALD 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  +++ VL + +  G     TL+E+G    V+  R+ Q+ ++AI  L+ 
Sbjct: 187 MLNDKDKTVLSLYYYEG----MTLKEIGIVLGVSESRVCQLHSRAIVHLRK 233


>gi|227485765|ref|ZP_03916081.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
 gi|227236320|gb|EEI86335.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
          Length = 258

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 109/232 (46%), Gaps = 8/232 (3%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            +      + E++E +L +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY F
Sbjct: 22  HKTRDKKLRDELIEEHLYIVDILSNKYVGKGIEKDDLYQVASLGLINAVDRYDPSKGYAF 81

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           S++A   +   I R   D+   I++P  +++   K+    + +  +++R PT  +IA  L
Sbjct: 82  SSFATPTIMGEIKRYFRDKGWVIKVPRRIQNLYKKINVAKKVLPQELQRVPTIADIADYL 141

Query: 557 AMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
               E + + ++ +    P SL+     +   +  D  E          +++  L++   
Sbjct: 142 GEDEETILETMEASKVYTPQSLDMKYSVQKGENAIDLAEIIGEEDKNFDSVE--LKDLIE 199

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           +    LT  E+ +L +R+  G     T  ++ +   +++  + +IE K + K
Sbjct: 200 KSKERLTDLEKEILELRYYEG----RTQVDIAESLDISQMTVSRIEKKILNK 247


>gi|167755749|ref|ZP_02427876.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
 gi|167704688|gb|EDS19267.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
          Length = 258

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 13/247 (5%)

Query: 429 HIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
               ++ + +   + A K  +V  N +LV+S+A+++  R     DL Q G IGL+KA E 
Sbjct: 22  ETYKLIDEYQATKNEAIKDRLVNDNTKLVLSMARRFYGREDSMDDLFQVGMIGLIKAIEN 81

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+   G KFSTYA+  +   + R + D    I+I   +RD  +KV++       K+ REP
Sbjct: 82  FNTSFGLKFSTYAVPLIIGEMKRYLRDNH-QIKISRSIRDLAYKVLKVKDSYITKLNREP 140

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAI 605
           T  E+A +L +    V + L  T    SL+  + ++D ++L   D I D   V       
Sbjct: 141 TINELANELEVEPSAVIEALLSTNSVSSLQEEVKNDDGNNLKMIDSITDDKTV-----VS 195

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + N        L SL  +E RV++ R+  G     +  E+ K+  +++ ++ +IE KA+ 
Sbjct: 196 RTNETIDLYDALKSLNQKEHRVIKQRYFEG----LSQSEIAKELFISQAQVSRIERKALD 251

Query: 666 KLKHPSR 672
            L +  +
Sbjct: 252 NLHNYLK 258


>gi|146293655|ref|YP_001184079.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|145565345|gb|ABP76280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
 gi|319427054|gb|ADV55128.1| RNA polymerase sigma-28 factor for flagellar operon, FliA
           [Shewanella putrefaciens 200]
          Length = 237

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     +V +    +  ++ R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDW---VPRSVHRNNRRVAQAIDELEQELGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D   + D++     ++  +          +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDILTLSDRSDDGSFEALAETQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|321117376|dbj|BAJ72165.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
 gi|321117388|dbj|BAJ72171.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 43/273 (15%), Positives = 84/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI--IGFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++ ++ E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEEREDDEXEDEESDDDSSDDDNSID--PELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLQQI 225


>gi|251772425|gb|EES52992.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptospirillum
           ferrodiazotrophum]
          Length = 250

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 103/237 (43%), Gaps = 14/237 (5%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            +M++     +   A +Y +R    L   DLI  G   L+++A +FD   G KF T A  
Sbjct: 7   DQMIKEFAGTIKYHAMRYAHRLPPELGVEDLISVGLHSLVESARRFDPSRGLKFKTMAEH 66

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ A+   I        +P  +R+K   V      +  ++ R P   E+A +L + +E 
Sbjct: 67  RIRGAMLDEIRSMDW---VPRSVREKQADVQMARESLERELGRHPEDAELAARLGLSLED 123

Query: 563 VRKVLKIT--KEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  +L        +SL+   G ++     LGD +       PL   +Q    +     L 
Sbjct: 124 LETLLWEIDPHPVLSLDEVFGPDESEGESLGDHLPGPKGEDPLSRLLQGEALDALAGALD 183

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +L  ++  VL + +      + T++EV +   V+  R+ QI ++A+R ++     ++
Sbjct: 184 ALPEKQRLVLTLYY----YEELTMKEVAQVLDVSESRVSQIHSQALRGIRALLEERR 236


>gi|300871802|ref|YP_003786675.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
 gi|300689503|gb|ADK32174.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
          Length = 270

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 112/246 (45%), Gaps = 17/246 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT-----NRGLQFLDLIQEGNIGLMKAAEK 487
            +   +  +   K+ +V     LV  VA +        R ++F DL+  G +GL+ A EK
Sbjct: 21  WIEYKKTLSPHIKEALVIKYSNLVKYVANQINFNMKATRDIEFDDLVGYGALGLIDAIEK 80

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D     KF TYA   +K +I   +       ++P  +R +I  +      + +K+ R  
Sbjct: 81  YDPNKEVKFKTYATTRIKGSIYDELRKID---KLPRSIRREIKDIEIAREFLESKLGRNV 137

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS---HLGDFIEDKNAVSPLD 602
             +EIA  + +P+  + + ++ + E    SL       D S    + D ++  +  +P  
Sbjct: 138 NSQEIADTMGIPLSKINETMRYSIEASTTSLSEVWYHGDDSDEISIMDTLKASDKNNPEY 197

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A + ++++     L  L  +E  VL + +      D TL+E+GK   V+  R+ Q+  K
Sbjct: 198 LAERKDVQKKIVEALDKLPEKERSVLILYY----YEDLTLKEIGKVLDVSESRVSQLHTK 253

Query: 663 AIRKLK 668
           A+++L+
Sbjct: 254 AVQQLR 259


>gi|239934530|emb|CAR94579.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 233

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/298 (16%), Positives = 98/298 (32%), Gaps = 66/298 (22%)

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
           +ELL+    I IAKRIE G   +  ++   P++   ++   D    G   L +I  +   
Sbjct: 1   VELLTARX-IEIAKRIEDGLNRVRRAMARFPISINWMLASYDNTVAGEGRLADI--MTGF 57

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           I P +                                           DD  +VD+ P+ 
Sbjct: 58  IDPNADDTPIPP----------------------------GGVNNNKDDDEEEVDTGPDP 89

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            E                           V    +++  ++ ++ +  +        EK+
Sbjct: 90  VE---------------------------VKKRFNKLKRLHNKIITAFEA------GEKA 116

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDV 369
             K +  +++LV+    +       D +V  +    + I  +E +++R      G+ R  
Sbjct: 117 DPKTEKARDQLVEEFMQIKFAPKCQDSMVALVQHSIQEIRTHERQIMRYCVAQAGMPRKD 176

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           F+      E +  W+                 + D IL+ + ++  I   +G+SI+E 
Sbjct: 177 FISSFPANETNLEWIDKHIRAKRKHSSILSKLKTD-ILRAQRKLVEIEFSSGLSINEI 233


>gi|37525878|ref|NP_929222.1| flagellar biosynthesis sigma factor [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36785307|emb|CAE14248.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 240

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 111/237 (46%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E+FD   G
Sbjct: 5   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPACVELDDLLQAGGIGLLNAVERFDSLQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    R++   + R  + +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVTHIIRKLEQDLGRPASEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K+L + +   R++L  T      S +        S     IE+ +  +PL   +++++R+
Sbjct: 122 KELKIDLVEYRQILLDTNNSQLFSYDEWHEMHGES-CEPVIEEGHETNPLQQLLESDVRQ 180

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + SL  RE+ VL + +      +  L+E+G    V   RI Q+ ++AI++L+
Sbjct: 181 RVIEAIDSLPEREKMVLTLYY----QEELNLKEIGAVLEVGESRISQLHSQAIKRLR 233


>gi|291196320|emb|CBG22632.1| DNA-directed RNA polymerase subunit D [Pseudomonas koreensis]
          Length = 237

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 95/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDPKAVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRHNKAAIAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEI 237


>gi|291196272|emb|CBG22607.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. aurantiaca]
 gi|291196274|emb|CBG22608.1| DNA-directed RNA polymerase subunit D [Pseudomonas chlororaphis
           subsp. aureofaciens]
          Length = 237

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 95/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T + ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPVDAKAAKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +   +       L +L
Sbjct: 110 TRKAL-----------------------------------KKHGREHKQALAEMLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|291613029|ref|YP_003523186.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
 gi|291583141|gb|ADE10799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
          Length = 247

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 105/248 (42%), Gaps = 11/248 (4%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEK 487
           + M           K+E ++    LV  +A          ++  DLIQ G +GL+ AA +
Sbjct: 7   LKMKAMYTPNGLSDKEECLKEYAPLVKRIAHHMMLKLPGSVEVDDLIQAGMMGLLDAASR 66

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G +F TYA   ++ A+   +        +P  +R  + ++     R+  ++ + P
Sbjct: 67  YDELRGAQFETYAAQRIRGAMLDELRGADW---LPRSLRRDMRRIETAVSRLQQQMGKTP 123

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              EIA++L + +   +++L+  +    L       E+     +  E     +PL+    
Sbjct: 124 NETEIARELGVSLHEYQQMLQEGRGAQLLYYEDFHGEEGEDFFERFEFSGDSNPLELLQD 183

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              RE     +  L  RE +++ M +      D  L E+G+   V+  R+ Q+ ++A+ +
Sbjct: 184 ERFREALIHAIERLPERERQMMGMHY----EQDMNLREIGEVMGVSESRVCQLHSQAVAR 239

Query: 667 LKHPSRSK 674
           L+   +  
Sbjct: 240 LRASMKGH 247


>gi|114776576|ref|ZP_01451621.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114553406|gb|EAU55804.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 281

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 51/266 (19%), Positives = 123/266 (46%), Gaps = 5/266 (1%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           + ++  +    + +     +   E   +    ++    AS+  ++++ ANL +V ++A++
Sbjct: 7   LKALTSLDRFYQELRRIPKLDREEEDALARKWQRDHDLASV--QQLINANLHVVAAIARE 64

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y + GL   DLIQEG +GLM+A ++FD   G++  TYA +W++ +I   I      +++ 
Sbjct: 65  YRHFGLPEEDLIQEGTLGLMQAVKRFDPDRGFRLKTYAAYWIRASIHDFILRSWSIVKMG 124

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV-LKITKEPISLETPIG 581
            +   +           +         E +A +  +  E  +++     +   S+++   
Sbjct: 125 TNKLQRRIFAGLQKAECAIAALEGRGLEGVASQYGVSGESYQQIAASFLRRDYSIDSDAT 184

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           ++          D    + +    Q+       + + +L+ R+  ++R R+ +      T
Sbjct: 185 EDGNIIELPAPGDTPEQALVAKDWQSFTTMQLKQAMEALSERDRNIIRQRYLVEP--PST 242

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+E+ +   ++ ER+RQ+EA+A++K+
Sbjct: 243 LKELSEDLGISIERVRQLEARAMKKI 268


>gi|296506459|ref|YP_003667693.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
 gi|296327046|gb|ADH09973.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
          Length = 323

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 124/249 (49%), Gaps = 6/249 (2%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKF 488
           + + ++ +      +  +   N  LV+S+A+ Y N+     F DL+QEGN G+++A E F
Sbjct: 55  LHLFKRYKHGEKDLRDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGNEGMLRAMEDF 114

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +  LGY FSTYA WW+++++   I  +     +IP H+     K V    +   +  R P
Sbjct: 115 NPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLKYVELEDKYLQRYNRTP 174

Query: 548 TPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + EE+ K+L +  E V   KV       ++L+    +ED      F +D++A+   +  I
Sbjct: 175 SVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTPFFDDRSAIPSTNEMI 234

Query: 606 QANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             +L      +    L P+++ VL + FG+     +  +E+ K   +T ER+ QI+ +AI
Sbjct: 235 IEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKDEAI 294

Query: 665 RKLKHPSRS 673
           +KLK     
Sbjct: 295 KKLKKCQHK 303


>gi|124300728|dbj|BAF45872.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 224

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 39/273 (14%), Positives = 77/273 (28%), Gaps = 50/273 (18%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I        E          
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHV 60

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      E   ++++ +   ++  D  S               PE A     +L    + 
Sbjct: 61  GSELSAEEREDEDEDEESDDDSSDDDNSID-------------PELAREKFGDLRIQYET 107

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 108 TRTMIKAK-----------------------------------SRSHADAIAEIQNLSDV 132

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 133 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 192

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   +++ I
Sbjct: 193 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLQQI 224


>gi|302670750|ref|YP_003830710.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
 gi|302395223|gb|ADL34128.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
          Length = 257

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 106/251 (42%), Gaps = 17/251 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
                +++  +++++     LV  VA +   Y    +++ DL+  G  GL+ A +KFD  
Sbjct: 12  EYHNTKSAEVREKLILEYAPLVKLVAGRLSMYLGFNVEYDDLVGYGIFGLIDAIDKFDLM 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA   ++ AI   I        IP  +R +  K+    R +        T  E
Sbjct: 72  KDVKFETYASLRIRGAILDQIRKMDW---IPRTIRQRQKKIEAAIREIERDGGHVATDAE 128

Query: 552 IAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           IA K+ +  +         K    +SL   +                 V P ++  +  L
Sbjct: 129 IAAKMQISEDEYANWQNQMKVTGVVSLNEFMDQGADIPEDSNNRSSGFVKPEEAIEKEEL 188

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L SLT +E++V+     +    + TL+E+ +   V+  R+ Q+  KA++K++ 
Sbjct: 189 KKMLAQSLESLTDKEKKVI----LLYYYEELTLKEISQVLEVSESRVSQLHTKALQKMR- 243

Query: 670 PSRSKKLRSFL 680
               +KL  +L
Sbjct: 244 ----EKLGDYL 250


>gi|291196384|emb|CBG22664.1| DNA-directed RNA polymerase subunit D [Pseudomonas reinekei]
          Length = 237

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 96/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDPKAVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +++         L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRNNKAAIAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 TD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|148976430|ref|ZP_01813136.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
 gi|145964253|gb|EDK29509.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
          Length = 244

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 101/245 (41%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAE 486
           +   +   +     +++   E    LV  +A     R        DLIQ G IGL++A +
Sbjct: 1   MNKALTYDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQ 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++      + + + R+
Sbjct: 61  NYDGTKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKNNREISSAIAELESTLNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDS 603
           P+  E+AK + + +E            I+    +G ED     D I   ED    +P   
Sbjct: 118 PSDAEVAKHMGLSLEQY----HSALTDINCSRLVGIEDLGVSDDVISPNEDSQDNAPFQG 173

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               + R+     +  L  RE  VL + +    + +  L+E+G+   V+  R+ QI +++
Sbjct: 174 VADESFRQALIDSIKQLPEREGLVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQS 229

Query: 664 IRKLK 668
           +++L+
Sbjct: 230 MQRLR 234


>gi|325002338|ref|ZP_08123450.1| RpoD family RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 425

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 118/234 (50%), Gaps = 22/234 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R        A +  V ANLRLV+S+A  Y   GL  LDL+QEG +GL++A +KFD   G
Sbjct: 198 LRLLIAAGEGAYERFVTANLRLVLSIASGYGAPGLDALDLVQEGTLGLIRAVQKFDIAQG 257

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA WW++QAITR+IADQS TIR PVH+ ++++   R A                 
Sbjct: 258 TKFSTYATWWIRQAITRAIADQSRTIRYPVHLVERLNAFSRRAL---------------- 301

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                    +   L  T    S    +G+E    + D   D  A       +     E  
Sbjct: 302 PDDDSATAELVATLPTTVPFESARDVLGEEVLQDVADRYLDPPAPDLRGFTV-----EDV 356

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              L+ L+ RE  ++  RFG  +    TL+ +G +  VTRERIRQI++KA+ +L
Sbjct: 357 AAALSILSERERTIVDRRFGF-VGDAATLDVIGGELGVTRERIRQIQSKALGRL 409


>gi|221069309|ref|ZP_03545414.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
 gi|220714332|gb|EED69700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
          Length = 239

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 102/247 (41%), Gaps = 16/247 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  ++ LV  +A     +    ++  DLIQ G IGL +A  +F+   
Sbjct: 1   MYTAKGQLDRDALIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R    ++ +   R+  ++ R P   EI
Sbjct: 61  GVQFDTFASQRIRGAMLDELREGDWM---SRSSRKSQKEIEQALNRLEQRLGRPPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQA 607
           A +L M ++  + +L      + + LE   G +      +L   + D  A        Q 
Sbjct: 118 AAELGMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVADSGADPFALLRDQ- 176

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +R      + +L  RE+       G+    D  L+E+     VT  R+ Q+ ++AI +L
Sbjct: 177 RMRSALVEAIKALPEREQ----YVMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQAIARL 232

Query: 668 KHPSRSK 674
           +   RS 
Sbjct: 233 RTKMRSH 239


>gi|167037640|ref|YP_001665218.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167040301|ref|YP_001663286.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|256750769|ref|ZP_05491654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914385|ref|ZP_07131701.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724379|ref|YP_003904130.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320116055|ref|YP_004186214.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|166854541|gb|ABY92950.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|166856474|gb|ABY94882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256750352|gb|EEU63371.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889320|gb|EFK84466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581440|gb|ADN54839.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319929146|gb|ADV79831.1| RNA polymerase sigma factor, FliA/WhiG family [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 246

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 99/230 (43%), Gaps = 15/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++   + LV  + KK     +   ++ DLI +G IGL+ A EK+    G KF TYA 
Sbjct: 21  RNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAIEKYQPSKGVKFETYAT 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +  +      P  ++ K  K+  T   +  K  REPT EEI +   +   
Sbjct: 81  LRIRGEIIDYLRKKDWM---PRSLKKKYRKIEETVETLQQKYNREPTVEEITEACGLNET 137

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V K L         SLE  I +    H    I D    +P +  +   L+      + +
Sbjct: 138 DVLKTLSYINVSNINSLEEAIENNFKLH---AISDVELKNPEEEVLYKELKRKLANAIEN 194

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  +E  V+ + +      D   +++ K   +T  RI QI  KAI++++ 
Sbjct: 195 LPDKERLVITLYY----YEDLNYKDISKILNLTESRISQIHTKAIKRIRE 240


>gi|313624456|gb|EFR94462.1| RNA polymerase sigma-B factor [Listeria innocua FSL J1-023]
          Length = 215

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 47/218 (21%), Positives = 103/218 (47%), Gaps = 4/218 (1%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A+KY+       DL+Q GNIGL+ A  ++D   G  F  +A+  +   I R + D++ ++
Sbjct: 2   ARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
            +P  +++   K+      ++ +++  P   +IA  + +  E V + +++ K   +L   
Sbjct: 62  HVPRRIKELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVD 121

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
              E  S               D   + N R    +VL  L  RE+++L+  F      +
Sbjct: 122 HSIEADSDGSTITLLDVVGGTDDGFERVNQRMLLEKVLPVLDEREQKILQYTF----IEN 177

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            + +E G+   +++  + +I+ +AI+KL+   +++++ 
Sbjct: 178 RSQKETGELLDISQMHVSRIQRQAIKKLREALQNEEVE 215


>gi|290879074|emb|CBK39761.1| sigma factor of RNA polymerase [Pseudomonas sp. a398]
          Length = 240

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 38/282 (13%), Positives = 93/282 (32%), Gaps = 48/282 (17%)

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           M+++   P T   ++     +      L +++            G+    +G +    E 
Sbjct: 1   MSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEV 49

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                 +    +   D + A     ++ ++    P  A      + +  + +   L    
Sbjct: 50  PPPVDPKAAKADDAEDDDEAESSDDEEEAESGPDPVIAAQRFGAVSDQMEITRKAL---- 105

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                          +K  +S+         L +L   + L   
Sbjct: 106 -------------------------------KKHGRSNKAAIAELLALAELFMPIKLVPK 134

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A    +
Sbjct: 135 QFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD-ALAKGK 193

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            ++   +      I++ + ++ ++  ETG++I+E + I   +
Sbjct: 194 SKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKDINRRM 235


>gi|1706832|sp|P52621|FLIA_YEREN RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|790557|gb|AAC43394.1| FliA [Yersinia enterocolitica (type O:9)]
          Length = 230

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 106/228 (46%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDRLQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A+ L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---APRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNLDIDLT 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+    +   +E     +PL   ++ NLR+     + +L
Sbjct: 120 EYRQILLDTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQRVIEAIEAL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|117919807|ref|YP_868999.1| flagellar biosynthesis sigma factor [Shewanella sp. ANA-3]
 gi|117612139|gb|ABK47593.1| RNA polymerase, sigma 28 subunit [Shewanella sp. ANA-3]
          Length = 237

 Score =  109 bits (273), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 99/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     +V +    +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDW---VPRSVHRNNRRVAQAIDELEQVLGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +   D  +    ++  +          +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDILTSSDNVSDGTYEALAETQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|291538524|emb|CBL11635.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis XB6B4]
          Length = 254

 Score =  109 bits (272), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 106/240 (44%), Gaps = 13/240 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              +  ++  +++++     LV  VA +   Y    +++ DL+  G  GL+ A +KFD  
Sbjct: 12  EYQKNPSAELREKIIIEYAPLVRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDRG 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA   ++ +I   I        IP  +R K  K+    +++  K  R  + EE
Sbjct: 72  KDVKFETYASLRIRGSILDQIRKMDW---IPRTVRQKRKKIEEAIKQIETKTGRNASDEE 128

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           IA++L +  E +            ISL   +       + D   + + + P +S  +  L
Sbjct: 129 IAQELGIGEEELNDWQTQLNVTNVISLNEFVEQ-GGEPVMDAKNNSHFIQPEESVQEEEL 187

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++     L  LT +E++V+     +    D TL+E+     V+  R+ Q+  KA+ K++ 
Sbjct: 188 KKVLMESLELLTEKEKKVI----LLYYYEDMTLKEISSILEVSESRVSQLHTKALLKMRK 243


>gi|299531273|ref|ZP_07044683.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
 gi|298720680|gb|EFI61627.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
          Length = 239

 Score =  109 bits (272), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 102/247 (41%), Gaps = 16/247 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  ++ LV  +A     +    ++  DLIQ G IGL +A  +F+   
Sbjct: 1   MYTAKGQLDRDALIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R    ++ +   R+  ++ R P   EI
Sbjct: 61  GVQFDTFASQRIRGAMLDELREGDWM---SRSSRKSQKEIEQALNRLEQRLGRPPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQA 607
           A +L M ++  + +L      + + LE   G +      +L   + D  A  P       
Sbjct: 118 AAELGMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVADSGA-DPFALLRDH 176

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +R      + +L  RE+       G+    D  L+E+     VT  R+ Q+ ++AI +L
Sbjct: 177 RMRSALVEAIKALPEREQ----YVMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQAIARL 232

Query: 668 KHPSRSK 674
           +   RS 
Sbjct: 233 RTKMRSH 239


>gi|297616717|ref|YP_003701876.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144554|gb|ADI01311.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 248

 Score =  109 bits (272), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 112/240 (46%), Gaps = 8/240 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            + ++++  +     A++ + ++NL LV    +++ N    F DL Q G IGL+KA  +F
Sbjct: 11  RMEALLKAAQAGDRDAEEAVFQSNLGLVYMALERFKNTPYDFEDLFQIGAIGLLKAIARF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  G KFSTYA+  +   + R + D    +++   +++  ++V      +  +  +EPT
Sbjct: 71  DFGYGVKFSTYAVPMIIGELKRYLRD-DGILKVQRSIKEIYYRVKSAQDDLRREFGKEPT 129

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EIA++L + +  V   ++  + P  +   +  ++       I   + VS  +      
Sbjct: 130 IGEIAERLGLELNDVVMAVEACQPPTYIYNLLPGDEKEQPLPLI---SKVSDREGTEDLL 186

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +  L PRE  V+  RF          E+      +++ ++ ++E +A++KL+
Sbjct: 187 EKVALKEAVMRLDPREREVIVRRFFKDETQSAIAED----LGISQVQVSRLEKRALKKLR 242


>gi|240145473|ref|ZP_04744074.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|257202447|gb|EEV00732.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|291536032|emb|CBL09144.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis M50/1]
          Length = 254

 Score =  109 bits (272), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 106/242 (43%), Gaps = 13/242 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
              +  ++  +++++     LV  VA +   Y    +++ DL+  G  GL+ A +KFD  
Sbjct: 12  EYQKNPSAELREKIIIEYAPLVRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDRG 71

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA   ++ +I   I        IP  +R K  K+    +++  K  R  + EE
Sbjct: 72  KDVKFETYASLRIRGSILDQIRKMDW---IPRTVRQKRKKIEEAIKQIETKTGRNASDEE 128

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           IA++L +  E +            ISL   +       + D   + + + P +S  +  L
Sbjct: 129 IAQELGIGEEELNDWQTQLNVTNVISLNEFVEQ-GGEPVMDAKNNSHFIQPEESVQEEEL 187

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++     L  LT +E++V+     +    D TL+E+     V+  R+ Q+  KA+ K++ 
Sbjct: 188 KKVLMESLELLTEKEKKVI----LLYYYEDLTLKEISSILEVSESRVSQLHTKALLKMRK 243

Query: 670 PS 671
             
Sbjct: 244 KM 245


>gi|294638491|ref|ZP_06716692.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|291088426|gb|EFE20987.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
          Length = 205

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 89/244 (36%), Gaps = 43/244 (17%)

Query: 111 DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
           +S    T DPVRMY+REMG++ELL+REGEI IAKRIE G   +  S+ E P     L+  
Sbjct: 4   ESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQ 63

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
            D +  G   L ++I   A I P ++          S         ++  +D ++ + D 
Sbjct: 64  YDRVEAGEARLSDLIT--AFIDPNAE------EVAESEDVNLGKEDDEVANDAEDEDEDE 115

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           +       D        PE A      L E  + +  T+ A     +   +  L      
Sbjct: 116 DEDGDNDSDSDDDNSIDPELARQKFTELREQYEKTRQTIKAKGRNHKDTELEIL------ 169

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
                                         L ++     L   + D LV  + ++  R+ 
Sbjct: 170 -----------------------------LLSEIFKQFRLVPKQFDYLVNNMREMMDRVR 200

Query: 351 HNEG 354
             E 
Sbjct: 201 TQER 204


>gi|319764532|ref|YP_004128469.1| RNA polymerase sigma factor, flia/whig family [Alicycliphilus
           denitrificans BC]
 gi|330826748|ref|YP_004390051.1| RNA polymerase sigma 28 subunit FliA/WhiG [Alicycliphilus
           denitrificans K601]
 gi|317119093|gb|ADV01582.1| RNA polymerase sigma factor, FliA/WhiG family [Alicycliphilus
           denitrificans BC]
 gi|329312120|gb|AEB86535.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alicycliphilus
           denitrificans K601]
          Length = 238

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 98/246 (39%), Gaps = 15/246 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  +   +L LV  +A     +    ++  DL+Q G IGL  A  +++   
Sbjct: 1   MYTAKGQLDRDALFHQHLPLVRRIAHHMIAKLPPNVELDDLVQVGMIGLTDALSRYEAAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + D           R    ++ +   R+  ++ R P   EI
Sbjct: 61  GVQFETFASQRIRGAMLDELRDGDWM---SRGARKSQKEIEQALHRVEQRLGRSPMESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           A +L M +   + +L      + + LE      + +   L   + D+ A        Q  
Sbjct: 118 AAELGMDLADYQALLGKVRGTQLVYLEDMGGGEEGEEGFLDRHVADEGADPMAVLRDQ-R 176

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR +    +  L  RE+       G+    D  L+E+     VT  R+ Q+ ++AI +L+
Sbjct: 177 LRTSLVAAIKQLPEREQ----HIMGMYYEHDMNLKEIAAVLGVTESRVCQLHSQAIARLR 232

Query: 669 HPSRSK 674
              R  
Sbjct: 233 TKMRGH 238


>gi|225174854|ref|ZP_03728851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169494|gb|EEG78291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 219

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 93/224 (41%), Gaps = 15/224 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
             E  E +L LV S+ K+Y     +  DL Q G IGL+KA +KFD   G  F+TYA+  +
Sbjct: 4   MAETFEKHLPLVHSLVKRYQGEYAESDDLFQVGCIGLLKALKKFDPARGNAFATYAVPVI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I   +  Q    +    +  +  ++ R    +   + R+PT  E+A    +  E + 
Sbjct: 64  AGEIKMYLRGQGAM-KFSRSLVTQAGRIKRVQNELEQALGRQPTLGELAAASGLGREELL 122

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             L   + P+SL+  +  E         E    V           R      L  L  RE
Sbjct: 123 MALDAVRSPVSLDAAVPGETAELAVTQAETDEVVD----------RVALREALTDLPERE 172

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R++  RF        + +EV +   +++  + ++E K + +LK
Sbjct: 173 RRIVLYRFFRH----KSQQEVAEILGISQMHVSRLEKKVLARLK 212


>gi|154499842|ref|ZP_02037880.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
 gi|150271440|gb|EDM98697.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
          Length = 235

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 108/241 (44%), Gaps = 13/241 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             +S++       + A   M+E N  L+ S+ ++Y  RG+   DL Q G +G +KA   F
Sbjct: 4   DTLSLLEAARQGDNDACARMMEENSGLIWSIVRRYYGRGVDPEDLYQLGCMGFLKAVRGF 63

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G +FSTYA+  +   I R + D    +++   ++++   +     R+   + REPT
Sbjct: 64  DPAFGCQFSTYAVPKIAGEIRRFLRD-DGAVKVSRGLKERAGSIRTARDRLQADLGREPT 122

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A++  +  E +    +      SL   +   D   L   +  +     +       
Sbjct: 123 LSELAEETGLEPEEIAAAEEANAPVASL--QMETGDGFTLESVLGTEGMEEGIVE----- 175

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE     ++SL  RE +V+ +R+  G+  D T     +   V++ +I ++E KA+  L+
Sbjct: 176 -REALRSAVSSLPDRERQVIVLRYFRGLTQDRT----ARIMGVSQVQISRVEKKAMEYLR 230

Query: 669 H 669
            
Sbjct: 231 R 231


>gi|325860122|ref|ZP_08173248.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|325482407|gb|EGC85414.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
          Length = 228

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 119/262 (45%), Gaps = 39/262 (14%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I+ I+    +S  E R +   ++      + A +++ +ANL+ V+S+A +Y NRGL  
Sbjct: 6   KYIEEIAGGQPLSDVEERTLAERIK---VGDAHALEKLTKANLKYVVSLAHQYRNRGLGE 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA++FD   G +F  +A  ++++A+  +I +Q+   R+P +      
Sbjct: 63  DDLISEGNIGMMHAAQRFDGTRGVRFVVFAAPYIRKAMEEAIKEQAVLYRLPRN------ 116

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
                          E    E  +  A+ ++                 P+G  +   L +
Sbjct: 117 ---------------EKNRSEQKRSHAISIDQPV--------------PVGSSNNFTLQN 147

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E+ NA    +   Q  L     + L  L  RE +V+   +G+     +T+ E  +   
Sbjct: 148 VLENDNAPHADEQLNQEILSAEIQKGLGVLNERERQVITCLYGLSGIH-YTMAEAAEHMG 206

Query: 651 VTRERIRQIEAKAIRKLKHPSR 672
           + RER+RQI   A+RKL    +
Sbjct: 207 LKRERVRQIRDGALRKLHKRMK 228


>gi|291196314|emb|CBG22629.1| DNA-directed RNA polymerase subunit D [Pseudomonas jessenii]
          Length = 237

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 96/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D E       ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDAKAVKADDDSDDEEGEASDDEEEAESGPDPIIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +++         L +L
Sbjct: 110 TRKAL-----------------------------------KKHGRNNKAAIAELLALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    +G++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKGKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|291196388|emb|CBG22666.1| DNA-directed RNA polymerase subunit D [Pseudomonas rhizosphaerae]
          Length = 236

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 98/284 (34%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T + ++   D +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVEHILSEYDRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         EK  +     + + E +    +++      P       ++      D 
Sbjct: 50  GIAPPAEVPPPVEKPAEKADAKDDEEEESDSDDEEETESGPDPV----VAQQRFGAVSDQ 105

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            A TL A++                                K  + S +       L +L
Sbjct: 106 LAVTLKALK--------------------------------KHGRHSKQGIAEMLLLAEL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 134 FMPIKLVPKQFEGLVERVRGALERLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDQTW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I + + ++ ++  ETG++I+E 
Sbjct: 194 SD-ALANGKAKYAEAIGRLQADIQRCQQKLSTLEAETGLTIAEI 236


>gi|269103161|ref|ZP_06155858.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163059|gb|EEZ41555.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 240

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 99/231 (42%), Gaps = 15/231 (6%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +  +  LV  +A     R        DLIQ G IGL++A + +D   G  F T+A   +
Sbjct: 17  FIARHSSLVKRIAHHLMARLPPNILIEDLIQAGMIGLLEAQQNYDPTKGASFETFAGIRI 76

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++     ++ +++ R+P   E+A+ L M +E   
Sbjct: 77  RGAMLDDIRRGDW---VPRSVYKNSRRISEAMAQLEHELGRDPNDHEVAEHLEMSLEQYH 133

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + L        + ++     ED     + +E+     P    +  + R+     + +L  
Sbjct: 134 QALNDVNCGRLVGIDDLGISEDAVANDELLEEN---LPFQGVVDDSFRQALAEAIKTLPE 190

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           RE  VL + +    + +  L+E+G    V+  RI QI  +A+++LK   ++
Sbjct: 191 REALVLSLYY----DEELNLKEIGAVIGVSESRICQIHTQAMQRLKAKLKA 237


>gi|182418456|ref|ZP_02949750.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237666966|ref|ZP_04526951.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377838|gb|EDT75382.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237658165|gb|EEP55720.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 252

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 117/238 (49%), Gaps = 7/238 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++   +   + A  +++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD  
Sbjct: 18  ELLSLAKKGDNDAMNKLIEINLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLN 77

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++  +++    K+     +++NK+KR PT EE
Sbjct: 78  YNVKFSTYAVPMIMGEIKRFLRD-DGMIKVSRNVKSLARKIHYYREQLTNKLKRSPTIEE 136

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+   +  E +   ++       L   I  +D + +   + DK +    +  +    + 
Sbjct: 137 LAEYAGVEKEEIVFAIESANSLQYLYDTIHQDDGAPVM--LIDKLSEKKGEDDVNLIEKI 194

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                L SL  +  +++ +R+      D T  +V K   +++ ++ +IE K + ++K 
Sbjct: 195 ALKEALRSLDEKARQIIMLRYF----KDKTQIQVAKMLGISQVQVSRIEKKVLLQMKK 248


>gi|297746571|emb|CAZ61003.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 242

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 47/285 (16%), Positives = 92/285 (32%), Gaps = 44/285 (15%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P             +         E
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSE 53

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            +  D  E E + E     + DD       PE A      L    + +  ++        
Sbjct: 54  DDLADEDEDEDEDEDEDGDNSDDEGDGGPDPEVAREKFGELRAQYEVTRLSI-------- 105

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                                      QK+ ++    +    +L  +     L   + D 
Sbjct: 106 ---------------------------QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDR 138

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +    
Sbjct: 139 LVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSP 198

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 199 RLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|292696945|dbj|BAI99645.1| RNA polymerase sigma-70 factor [Aeromonas sp. KYO28]
          Length = 252

 Score =  109 bits (272), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 50/291 (17%), Positives = 95/291 (32%), Gaps = 45/291 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   + +S+ E P     L+   D+       L +II     I P           
Sbjct: 1   RIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN---------- 48

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                         E +D+  T   I S            +   E+ + D  + D D   
Sbjct: 49  --------------EAEDMAPTATHIGSELGEDDLADEDEEDEDEDEDGDSSDDDGDGGP 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +LR +       I                 QK+ ++    +     L  +
Sbjct: 95  DPEVAREKFAELRAQYEVTRLSI-----------------QKNGRAHDDTQAAIALLADV 137

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  + ++ +R+   E  +++L  +   + +  F+      E +  W
Sbjct: 138 FRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAW 197

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
             Y K   +      V  + D + +   +++ I  ETG+SI++ + I   +
Sbjct: 198 FEYQKQAGKAWSPRLVEMDED-VQRAIGKLQQIEEETGLSIAQIKDINRRM 247


>gi|310777993|ref|YP_003966326.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
 gi|309747316|gb|ADO81978.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
          Length = 329

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 70/260 (26%), Positives = 138/260 (53%), Gaps = 9/260 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +      IS+ T I   + + IV   +        A++ +V +NL+LV  +A KY+  G+
Sbjct: 71  LEQYFHDISLYTPIPKEKEKDIVKKAQ---DGDEEAREMLVTSNLKLVAKIAMKYSKSGV 127

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            ++DLIQ+G IGL+ A +K+D   G+ F++Y++WW+K+ I  SIA++   I+IP ++   
Sbjct: 128 NYIDLIQDGTIGLIAAIDKYDLSKGHSFTSYSVWWIKREIINSIANRINAIKIPSYVYLM 187

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             K+         +  ++P+ +EI++ L + +E V K+ + ++  +       + D   L
Sbjct: 188 NKKIRIFEDDFMERNNKKPSYQEISEALNLSLEEVEKMKEASEIGVGGFADGNEPD---L 244

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GDF         L+   +   R   + ++  ++P E++V+ M +G+  N     +E+ K 
Sbjct: 245 GDFNTVDQIDKELNLLEE---RSKISNLMRKISPEEQKVVEMYYGLDDNKRLGFKEISKI 301

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             V+ E+++ ++ +AI KLK
Sbjct: 302 MGVSVEKVKFLKERAILKLK 321


>gi|227112555|ref|ZP_03826211.1| flagellar biosynthesis sigma factor [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
 gi|227329198|ref|ZP_03833222.1| flagellar biosynthesis sigma factor [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 230

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 107/228 (46%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +  +      P  +R    +V +  ++   ++ R PT +E+A+ L + +E
Sbjct: 63  QRIRGSMLDELRSRDW---APRSVRRNAREVAQAMQQAEQQLGRTPTEQEVAQTLNITLE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+     +  +E     +PL   ++ NLR      + SL
Sbjct: 120 DYRQILLDTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRHRVMDAIESL 179

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 180 PEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|124300726|dbj|BAF45871.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 225

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 42/273 (15%), Positives = 83/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--GFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++  + E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEERDDDEDEDEESDDDSSDDDNSID--PELAREKFSDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    + + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSEDVNRGLQKLQQI 225


>gi|229918653|ref|YP_002887299.1| RNA polymerase sigma factor SigD [Exiguobacterium sp. AT1b]
 gi|229470082|gb|ACQ71854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium sp.
           AT1b]
          Length = 256

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 106/250 (42%), Gaps = 13/250 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R           E++     L+    ++      + ++  +L   G +GL  A  K+D  
Sbjct: 11  RWNMDRDMDTANELLAHYEFLIHYHVQRMIVTLPKSVERDELKSLGYMGLYDALMKYDPE 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +        +P  +R+K+ K+   A ++   + R PT  E
Sbjct: 71  HNNKFDTYAAFRIRGAIIDGLRKVDW---LPRSVREKVKKIDHVAEQLEQSLHRAPTKSE 127

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQAN 608
           +A    +P+  + + +        +S++  +  ++   +      D ++  P D+ +Q  
Sbjct: 128 LASACDLPISEIERTMAEGYFANMLSIDEAVTLQEEGKVMSVTYFDPDSEKPEDTLLQRE 187

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +     +  L+ +E  V+ + +      + TL E+G+   ++  RI QI +KA++ LK
Sbjct: 188 LIDVLAAEVDHLSEKERLVVSLFYF----DELTLTEIGEVLELSTSRISQIHSKALKTLK 243

Query: 669 HPSRSKKLRS 678
           H      L  
Sbjct: 244 HALGRSYLEE 253


>gi|120613052|ref|YP_972730.1| FliA/WhiG family RNA polymerase sigma factor [Acidovorax citrulli
           AAC00-1]
 gi|120591516|gb|ABM34956.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidovorax
           citrulli AAC00-1]
          Length = 238

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 103/245 (42%), Gaps = 13/245 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  +  LV  +A     +    ++  DLIQ G IGL +A  +++   
Sbjct: 1   MYTAKGQLNRDALIRQHAPLVRRIAHHMIAKLPPNVELDDLIQVGMIGLNEALSRYEVTQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R    ++     R+  K+ R P   EI
Sbjct: 61  GVQFETFASQRIRGAMLDELREGDWM---SRSSRKSQKEIEHAVTRLEQKLGRSPHESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A +L + +   + +L      + + LE     D+D     D     +A  P+       L
Sbjct: 118 ATELELSLAEYQSLLSKVRGTQLVYLEDMTRGDDDDDGFLDRHVADSAADPMAMLRDQRL 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R +    + +L  RE++++    G+    D  L+E+     VT  RI Q+ +++I +L+ 
Sbjct: 178 RASLVAAIKALPEREQQIM----GMYYEHDMNLKEIAAVLGVTESRICQLHSQSIARLRA 233

Query: 670 PSRSK 674
             RS 
Sbjct: 234 KMRSH 238


>gi|210624023|ref|ZP_03294140.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
 gi|210153230|gb|EEA84236.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
          Length = 255

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 122/259 (47%), Gaps = 11/259 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +KS++        + + +  +    + +    +  ++E +L L   +AKKY N+G+ + D
Sbjct: 1   MKSVAGAANYLDMDTKELFRL--YSDNKDIDIRNILIERHLYLARILAKKYINKGVDYED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           + Q  ++ L+ A +++D   G++FS++A   +   I +   D+  T+R+P  +++   K+
Sbjct: 59  IYQVASLALIYAIDRYDISKGFEFSSFATPTIIGEIKKYFRDKVWTMRVPRRIQELSKKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGD 590
                 +  + KR P+ ++IA+ +    E V + ++   + +P+SL+   GD+    L  
Sbjct: 119 SNAKIAIEQEKKRHPSVKDIAEYIGCREEDVLEAMEASYSYQPVSLDASSGDDSEDDL-- 176

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            + D+  V           ++   R + +L   E ++L  RF        T   +  +  
Sbjct: 177 TLSDRVGVE-EKDFGNIEQKDFLNRFMQTLNELEVKILEDRFFHN----KTQSVIATELN 231

Query: 651 VTRERIRQIEAKAIRKLKH 669
           +++  + ++E K + KL+ 
Sbjct: 232 ISQMTVSRLEKKVVEKLRK 250


>gi|126175111|ref|YP_001051260.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|153001435|ref|YP_001367116.1| flagellar biosynthesis sigma factor [Shewanella baltica OS185]
 gi|160876160|ref|YP_001555476.1| flagellar biosynthesis sigma factor [Shewanella baltica OS195]
 gi|217972633|ref|YP_002357384.1| flagellar biosynthesis sigma factor [Shewanella baltica OS223]
 gi|304409942|ref|ZP_07391561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|307302345|ref|ZP_07582103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|125998316|gb|ABN62391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|151366053|gb|ABS09053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS185]
 gi|160861682|gb|ABX50216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS195]
 gi|217497768|gb|ACK45961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS223]
 gi|304351351|gb|EFM15750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|306914383|gb|EFN44804.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|315268356|gb|ADT95209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS678]
          Length = 237

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 99/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     KV      +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDW---VPRSVHRNNRKVAHAIDELEQALGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +   D++     ++  +          +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDILTVSDRSDDDSFEALAENQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|226313041|ref|YP_002772935.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
 gi|226095989|dbj|BAH44431.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 117/248 (47%), Gaps = 14/248 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKA 484
           +     V   +  +  A+ +++   L LV  VA +        +   DLI  G  GL+ A
Sbjct: 11  KEFDKWVMWKQEGSREAEVDLITRFLPLVDKVANRLAINLPANVDKDDLISYGRFGLLDA 70

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             KFD   G +F TYAMW ++ A+   + +      IP  +RDK  K+      +  ++ 
Sbjct: 71  LAKFDHTRGLQFETYAMWRIRGAMIDGLRENDW---IPRTVRDKAKKIEEAYTTLEQQML 127

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDT--SHLGDFIEDKNAVSP 600
           R PT +E++  L +  + +++V   T     +S++  +GDED   +    +I D+    P
Sbjct: 128 RMPTDQEVSDYLGISKKELQQVFLETSLASMVSIDEAVGDEDEQKTARHSYIIDELTPRP 187

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            + A  ++L+E    V+  L  +E  V+ + +      + TL E+ +   ++  RI Q+ 
Sbjct: 188 DNVAEVSSLKEVLVTVIDKLPEKERLVISLFYF----EEMTLSEIAEIMSLSPSRISQLH 243

Query: 661 AKAIRKLK 668
           +KA+ +L+
Sbjct: 244 SKALFRLR 251


>gi|188589224|ref|YP_001920224.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778902|ref|ZP_04821822.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499505|gb|ACD52641.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083217|gb|EES49107.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 242

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 113/235 (48%), Gaps = 13/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+++V+  + LV  +A +     N+ +++ DL+  G IGLM A  KF+   G KFS+YA 
Sbjct: 10  KEQIVKEYIPLVKYIASRIMIGKNKYMEYEDLVSYGIIGLMDAISKFNPDKGMKFSSYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K AI   I        I     DK+++       + NK+ REP   EIA+ L + ++
Sbjct: 70  IRIKGAIIDQIRK---NRPITKGAMDKLNRYNSAIESLQNKLLREPNILEIAQYLELSLQ 126

Query: 562 GVRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  +D   +L   IEDKN+ SP     +    E  +  + 
Sbjct: 127 EVSQIENYINHISMVSLENIIFSDDEEVNLLGIIEDKNSPSPEGELEEKEQLEVLSDAIK 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            L  +E+ +L + +        TL+E+G    V+  R+ Q+ A++I  L+   + 
Sbjct: 187 LLKEKEQLILNLYY----YEKLTLKEIGSILSVSESRVCQLHARSISNLREAMKK 237


>gi|153803716|ref|ZP_01958302.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
 gi|124120749|gb|EAY39492.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
          Length = 242

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 101/227 (44%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R        DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 19  FLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +  ++ R+PT  E+AK L M +E   
Sbjct: 79  RGAMLDDIRRGDW---VPRSVHKHNREISQAIAVLEGELNRDPTDAEVAKFLNMSLEQYH 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VL      I+    +G ED     D I   E+    SP     + + R+     + SL 
Sbjct: 136 SVLM----DINCSRIVGIEDLGVSDDAISPFEEGEDNSPFHGVAEESFRKALVESIKSLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G+   V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQSMQRLR 234


>gi|321117380|dbj|BAJ72167.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 38/273 (13%), Positives = 73/273 (26%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I            GF     
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI-----------IGFVDPNA 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                    +    E    +  + + E                PE A     +L    + 
Sbjct: 50  EEDI-APTATHVGSELSAEEREDDEYEDEESDDDSSDDDNSIDPELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLQQI 225


>gi|330721193|gb|EGG99303.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC2047]
          Length = 246

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 51/242 (21%), Positives = 105/242 (43%), Gaps = 15/242 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
            +    + +       +VE +  LV  +A     R    +Q  DL+Q G +GL++AA+KF
Sbjct: 6   KLAMYSDDQQQHRTTLLVEQHAPLVKRIAHHLMARLPSTVQLNDLVQSGMVGLLEAAQKF 65

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G  F T+A   V+ A+   +         P  +     +V    + +  +  R+ +
Sbjct: 66  DASKGASFETFAGIRVRGAMLDDVRKDDW---APRSVHRNARRVSEAIKAVEGRTGRDAS 122

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            +E+A ++ +P+E     L+ +      S +     +D+S L   +      +P ++  +
Sbjct: 123 DQEVAAEMGIPLEDYYAYLQDSAGTRLFSYDEVTEQDDSSIL---LAASATPTPHENVQR 179

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              ++   + + +L  RE  VL     +    +  L+E+G    V+  R+ QI ++A  +
Sbjct: 180 QAFKDNLAQAIEALPERERMVL----ALYYQEELNLKEIGSVLGVSESRVSQIHSQAALR 235

Query: 667 LK 668
           L+
Sbjct: 236 LR 237


>gi|291196264|emb|CBG22603.1| DNA-directed RNA polymerase subunit D [Pseudomonas alcaliphila]
          Length = 237

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 95/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L E++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +       KE    +E++ + E  +   +++       PE A      + E +D 
Sbjct: 50  GSVPDEAAAPVPVKEGAAAEESDDEEEDESGDDEEEEGDGGPDPEEAARRFNAVAEQQD- 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                         KV+ AL                     K  + S +       L +L
Sbjct: 109 --------------KVLKALK--------------------KHGRGSKQAIEELATLAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV Q+     R+   E  +++L      + R  FL    G E+D  W
Sbjct: 135 FMPIKLVPKQYDALVTQVRGALDRLRAQERAIMQLCVRDARMPRADFLRLFPGNEIDMDW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            +      + ++   +      I + + ++  +  E  +S++E 
Sbjct: 195 AADLAK-GKAKYAEALGNLQADIQRCQQKLADLEAECSLSLAEI 237


>gi|291196276|emb|CBG22609.1| DNA-directed RNA polymerase subunit D [Pseudomonas avellanae]
          Length = 238

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 91/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + +    +  + D E +A  S ++      P             D+ +
Sbjct: 50  GIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +     +  L  +AE++                                 
Sbjct: 110 ITRKALKKFGRDDKHAIAELVALAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   +G++   +      I + + ++ ++  ETG+ I+E 
Sbjct: 196 TDGLAK-GKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEI 238


>gi|227355968|ref|ZP_03840360.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
 gi|227163956|gb|EEI48858.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
          Length = 244

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 109/237 (45%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + E  + LV   A +   +    ++  DL+Q G IGL+ A E++D   G
Sbjct: 9   YTAEGVMDKNSLWERYVPLVRHEALRLQVKLPASVELDDLLQAGGIGLLNAVERYDSMQG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R    +V ++  ++   + R P+ +E+A
Sbjct: 69  AAFTTYAVQRIRGSMLDELRSRDW---APRSVRRNAREVTQSIHQLEQDLGRPPSEQEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             L + +   R++L  T      S +        S      ED +  +PL   +++++R+
Sbjct: 126 DHLQIELAEYRQILLDTNNSQLFSYDEWHEIYGESCEPSQDEDHDD-NPLQMLLESDIRQ 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 185 RVIDAIELLPEREKMVLTLYYQ----EELNLKEIGAVLNVGESRVSQLHSQAIKRLR 237


>gi|218778853|ref|YP_002430171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760237|gb|ACL02703.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
          Length = 252

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 122/257 (47%), Gaps = 19/257 (7%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
            + V + + +    + E++     L    A +   R    +   DLI  G +GL+ A +K
Sbjct: 4   AAHVPREKSKERAKRDELITKYAYLAKLCAHRLAMRLPPSVNVDDLISAGIMGLLDALDK 63

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G KF TYA + ++ A+   +        +P  +R K+ ++ +   R+  +  R  
Sbjct: 64  YDEGRGVKFRTYAEFRIRGAMLDELRAMDW---VPRSVRKKVQEIEQAVNRVEKRESRPA 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLG-----DFIEDKNAVSP 600
             EEIA +L + ++  + +L        +SL+ P+   D +  G     D +ED    +P
Sbjct: 121 DAEEIANELGVDMDTYQNMLSKAGGIELVSLDEPLWSNDNTKDGRRTHVDLLEDN--ANP 178

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               + +  ++   + ++SLTP+E+++L + +      + TL+EVG+   +T  RI QI 
Sbjct: 179 DRDLMDSEFKKILAQSISSLTPKEQQILSLYY----QDELTLKEVGEVMGLTESRICQIH 234

Query: 661 AKAIRKLKHPSRSKKLR 677
            + + KL+   ++++ R
Sbjct: 235 TQCMIKLRSKLKTQEAR 251


>gi|291196390|emb|CBG22667.1| DNA-directed RNA polymerase subunit D [Pseudomonas rhodesiae]
          Length = 238

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 97/284 (34%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + +   DD  E   D E   +   D                         
Sbjct: 59  PPPVDAKAAKADDDSDDDDAEASSDDEEEVESGPDPI----------------------I 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  +++ +       L +L
Sbjct: 97  AAQRFGAVSDQM------------EITRKALK---------KHGRANKQAIAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLSALEAETGLTIAEI 238


>gi|321117382|dbj|BAJ72168.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
 gi|321117384|dbj|BAJ72169.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/273 (15%), Positives = 83/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI--IGFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++ ++ E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEEREDDEXEDEESDDDSSDDDNSID--PELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   ++  I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLXQI 225


>gi|56964009|ref|YP_175740.1| RNA polymerase sigma factor SigD [Bacillus clausii KSM-K16]
 gi|56910252|dbj|BAD64779.1| DNA-directed RNA polymerase sigma-28 factor sigma-D [Bacillus
           clausii KSM-K16]
          Length = 254

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 115/248 (46%), Gaps = 15/248 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  +  + +A + ++E  + LV    ++ +N     +   +L      GL+ A  KFD  
Sbjct: 10  QWDDEHSEVAAEALIEHYMPLVAYHVQRISNGLPSSISKDELKSHALSGLLDAIAKFDSK 69

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +  +     +P  +RDK+ K+ +   ++  +  R   P E
Sbjct: 70  RALKFDTYASFRIRGAIIDGLRKEDR---LPRTIRDKVKKLEQITEQLEQEKGRSVLPGE 126

Query: 552 IAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDT---SHLGDFIEDKNAVSPLDSAIQ 606
           +A  + +P + +   K  +     +SL+  +   D    S +    ED+ A+ P D  ++
Sbjct: 127 VAAAMGLPEKEIEALKREQFASHTLSLDDVMHMNDHLDPSAVAYQFEDEQAIMPDDKLVE 186

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            + R+    ++  L   E+ V+++ +      + +L E+G+   ++  RI QI A+AI K
Sbjct: 187 EDTRKELAEMIKELGRNEQLVIQLSY----YEELSLTEIGRILNLSTSRISQIHARAIAK 242

Query: 667 LKHPSRSK 674
           L+   + K
Sbjct: 243 LRKGLQKK 250


>gi|37680648|ref|NP_935257.1| flagellar biosynthesis sigma factor [Vibrio vulnificus YJ016]
 gi|37199396|dbj|BAC95228.1| polar Flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           vulnificus YJ016]
          Length = 245

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 97/227 (42%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 20  FIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDASKGASFETYAGIRI 79

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +   + R+PT  E+AK + + +E   
Sbjct: 80  RGAMLDDIRRGDW---VPRSVHKSNREISQAIAELEGLLNRDPTDAEVAKHMGLSLEQY- 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                    I+    IG ED     D I   ED    +P         R+     +  L 
Sbjct: 136 ---HGALTDINCSRLIGIEDLGVSDDVITSVEDSENNTPFKGVADEYFRKALVESIKQLP 192

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G+   V+  R+ QI ++++++L+
Sbjct: 193 EREALVLSLYY----DEELNLKEIGEILSVSESRVSQILSQSMQRLR 235


>gi|162418642|ref|YP_001606497.1| flagellar biosynthesis sigma factor [Yersinia pestis Angola]
 gi|162351457|gb|ABX85405.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Angola]
          Length = 240

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G I L+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIDLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++    T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQQVEQRVGSPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QVLDIGLVEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLKHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|256005472|ref|ZP_05430434.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255990527|gb|EEU00647.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
          Length = 252

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 106/227 (46%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + ++V   L L   +AKK+ NRG+ + D+ Q  +I L+KA E+FD   G KF ++A   +
Sbjct: 31  RNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVVSIALIKAVERFDPDKGVKFISFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D+   IRIP  + +   K+      ++ ++KR P  +E+A+ L +  E V 
Sbjct: 91  IGEIKRYFRDKGSVIRIPRRIYEVYQKINHARESLTQELKRPPRIDELARHLNISEESVV 150

Query: 565 KVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +++         S    +   D   L + I D+++        +   R+   + L   + 
Sbjct: 151 EIIESYNAYNIQSFSQNVYANDELELHEVIGDQDST-----FERIENRDFLEKSLDKFSD 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E+  + MR+        T +++ ++  V++  I ++E K + K + 
Sbjct: 206 VEKEFISMRYFDN----KTQKDIAQKMGVSQMYISRLERKVLEKFRR 248


>gi|225181587|ref|ZP_03735028.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
 gi|225167695|gb|EEG76505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
          Length = 239

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 114/249 (45%), Gaps = 23/249 (9%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKK-------YTNRGLQFLDLIQEGNIGLMKAA 485
            V+  E +    ++ +VE  L LV   A +       + NR     DL+Q G +GL++A 
Sbjct: 7   WVKYQETKEEGLQETLVEKYLPLVRLHAGRLALGLPAHVNR----DDLLQAGMLGLLEAL 62

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++FD   G KF ++A   ++ A+   +        +P  +  ++ ++ R  + ++ ++ R
Sbjct: 63  QRFDPTRGVKFESFAALRIRGAMLDELR---RLCWVPRSVVREMREMDRAVQELATQLGR 119

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP  EEIA+K+ + +  +RK+  +      L       + + L     D   V  LD  I
Sbjct: 120 EPAEEEIAEKMGITIPQLRKITGMINSSSLLSL-----EDTLLAVPAVDGPEVEALDRLI 174

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
            A  R+     +  L  R +++L     +    D TL+EVG    VT  R+ Q+ A+ I 
Sbjct: 175 AAEDRQRLAEAIGQLPERHQQLL----ALYYQEDLTLKEVGLVLGVTESRVCQLHARIIA 230

Query: 666 KLKHPSRSK 674
           +L+   + +
Sbjct: 231 RLRTALQDE 239


>gi|223635923|emb|CAQ03763.1| RNA polymerase sigma factor [Enterovibrio norvegicus]
          Length = 246

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 46/297 (15%), Positives = 90/297 (30%), Gaps = 52/297 (17%)

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +  S+ E P +   L+   D++      L +II            GF   ++  
Sbjct: 1   EDGINQVQVSVAEFPGSISYLLDQFDKVEAEELRLTDII-----------SGFVDPSQDD 49

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
                     E      QE   D +       ++       PE A      L    ++  
Sbjct: 50  IAPTATHIGSELS----QEELDDEDKNDDDDDEEEEDTGIDPELAREKFNELRVSYENMQ 105

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             +                                   QK+ +          +L +   
Sbjct: 106 AAI-----------------------------------QKNGRFHADTAGSVAELSETFK 130

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVS 385
              L   + D LV Q+ +   R+   E  ++RL      + +  F++   G E    W+ 
Sbjct: 131 QFRLIPKQFDRLVTQMRNTMDRVRTQERLVMRLCVDQAKMPKKTFVQLFAGNESSDSWLD 190

Query: 386 YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
            A    +  +   +    + + +   ++K I  ETG+++   + I   +  GE +A 
Sbjct: 191 KALS-SDKPFAERMKQYEEDLRRCVQKLKIIEDETGLNVERIKDISRRMSIGEAKAR 246


>gi|310826431|ref|YP_003958788.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
 gi|308738165|gb|ADO35825.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
          Length = 250

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 107/258 (41%), Gaps = 16/258 (6%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     ++  E + +   +   +      +  ++E  L +   + KKY  R     D+ Q
Sbjct: 1   MEYPNQMTKQESKKLF--IEYKKTGDKEIRDRLIENFLYIPKLLVKKYAYRSNDVEDIYQ 58

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
              +GLM A E++D   G++F T+A   +   I +   D+   IR+P  +++   ++ R 
Sbjct: 59  VACLGLMYAVERYDPDRGFEFDTFASPTIIGEIKKYYRDKQWIIRVPRRIQELNREINRA 118

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDE---DTSHLGD 590
              + +K+ + PT  EIA  L +  E V + +       P SL T          + L D
Sbjct: 119 KTTLEHKLMKTPTISEIADYLEVTEEAVIEAMEGNNVFYPKSLSTEFESNADGQEATLLD 178

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I +++              E   + L SL P E  ++  R+  G     T +EV     
Sbjct: 179 LIGEEDE-----RIENIGNVEDLRQRLESLNPVERMIIEERYYNG----KTQKEVAAIIG 229

Query: 651 VTRERIRQIEAKAIRKLK 668
            ++  + ++E K + KL+
Sbjct: 230 KSQMTVSRLEKKVMEKLR 247


>gi|300113620|ref|YP_003760195.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Nitrosococcus
           watsonii C-113]
 gi|299539557|gb|ADJ27874.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Nitrosococcus watsonii C-113]
          Length = 241

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 95/228 (41%), Gaps = 17/228 (7%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E+V     LV  +A     R    +Q  DLIQ G IGL++A   ++   G  F TYA  
Sbjct: 18  DELVTQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAVRNYNASQGASFETYAGI 77

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   I         P  +  K  +V    R + N+  R+    E+ ++L +P+  
Sbjct: 78  RIRGAILDEIRRNDW---APRSVHRKARQVAEVMREVENREGRDARDYEVVEELGLPLNE 134

Query: 563 VRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             ++L+        SL+     E+   L   ++      P +     N R      +  L
Sbjct: 135 YHRLLQDAGGYRVFSLDEFNEGEEAEPLSAPLK-----GPYEGLQDQNFRGALVEAIEGL 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  V+ + +      D  L E+G+   V+  R+ QI ++A+ +L+
Sbjct: 190 PERERLVMSLYYV----EDLNLREIGEVLGVSESRVSQIHSQAVLRLR 233


>gi|153955768|ref|YP_001396533.1| sporulation sigma factor SigF [Clostridium kluyveri DSM 555]
 gi|146348626|gb|EDK35162.1| RNA polymerase sigma-F factor [Clostridium kluyveri DSM 555]
          Length = 251

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 116/239 (48%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++        A  ++VE NL LV +++KK+ NRG ++ D+ Q G +GLMKA   FD 
Sbjct: 17  LKLIKCAREGDKEALNKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVNNFDE 76

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++   K+      ++ K+ REPT E
Sbjct: 77  TYNVKFSTYAVPMILGEIKRFLRD-DGMIKVSRSIKNTAKKLHYDREALTKKLNREPTIE 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+   +  E +    + T     L   I  +D S +   + DK + +P +     + R
Sbjct: 136 ELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPV--LLIDKISENPKEDVEVID-R 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L +L  +  +++ +R+      D T  +V K   + + ++ +IE K ++ ++ 
Sbjct: 193 IALKEALRNLDVKSRQIIMLRYF----KDKTQVQVAKMLGINQVQVSRIEKKVLKTMRE 247


>gi|308273000|emb|CBX29604.1| hypothetical protein N47_J05850 [uncultured Desulfobacterium sp.]
          Length = 326

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 129/265 (48%), Gaps = 12/265 (4%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GL 468
           ++ ++ IS    +S  E   +   +   + +   +  +++ +NLRLV+ +A  + +    
Sbjct: 47  QSYLREISQYRLLSREEEIELA--INVKDKDDKESASKLITSNLRLVVKIAFNFQHYLAN 104

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGL+ A +K+D   G KFS YA +W++  I + I +    ++I      R
Sbjct: 105 NVPDLIQEGNIGLIHAVKKYDPYKGVKFSYYAAFWIRAYIFKFIMNNWDMLKIGTTQKQR 164

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDT 585
                + +  R+++ +    P P+ +A++L +    + +++      P+SL  P+ ++  
Sbjct: 165 KLFFNLNKERRQITAE-GLNPEPKLLAERLGVQENDIVQMIPRLDYSPLSLNQPLSEDSK 223

Query: 586 SHLGDFIEDKNAVSPLDSAI---QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
             L + ++DKNA +    ++   + NL     +    L   +  +      I      +L
Sbjct: 224 ECLEERVQDKNASTIDQLSVLESKTNLERELKKFRKLLKGIKADIFD--MRIMAENPVSL 281

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           + +G ++ ++RER+RQI+   I K+
Sbjct: 282 QSIGDRYQISRERVRQIQEMIINKI 306



 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 1/85 (1%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +   + + +  ++ +S +            + +  + YLRE+    LLSRE EI +A  +
Sbjct: 12  KEDVEDIAINETSGSSDILFCIVSKRYSPDSSNLFQSYLREISQYRLLSREEEIELAINV 71

Query: 147 -EAGRAMMMASLCESPLTFQALIIW 170
            +       + L  S L     I +
Sbjct: 72  KDKDDKESASKLITSNLRLVVKIAF 96


>gi|91792701|ref|YP_562352.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91714703|gb|ABE54629.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 239

 Score =  109 bits (271), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  ++E    LV  +A     R    +Q  DL+Q G +GL++AA KFD   G KF T+A 
Sbjct: 13  KSSVIEQYAPLVKKIAHHMLARLPASVQLDDLLQAGMMGLLEAASKFDGTKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     +V +    +     R+    EIA+KL M ++
Sbjct: 73  IRIRGAMIDEIRRGDW---VPRSVHRNQRRVAQVIDELEQHFGRDARDTEIAEKLDMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D I  E+ +     D  ++   +      + +
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDVIITEETSMDESFDELVETQFQSALVEAIKT 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|169837518|ref|ZP_02870706.1| RNA polymerase sigma factor rpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 149

 Score =  108 bits (270), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 78/152 (51%), Positives = 107/152 (70%), Gaps = 3/152 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             ++ I     +S  E       V         AK++++E+NLRLV+S+AKK+TNRGL+ 
Sbjct: 1   MYLREIGQIPLLSYEEEIDYAQRV---LNGEEEAKQKLIESNLRLVVSIAKKHTNRGLKM 57

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
           LDLIQEGN+GLMKA EKF++  G+KFSTYA WW++QAITR+IADQ  TIRIPVHM + I+
Sbjct: 58  LDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETIN 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           K+ + +R +  +  +EPT EE+AKKL +PVE 
Sbjct: 118 KIKKESRIILQETGKEPTAEELAKKLELPVER 149



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/93 (33%), Positives = 37/93 (39%), Gaps = 9/93 (9%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYLRE+G I LLS E EI  A+R+  G       L ES L     I  +   N G  +L 
Sbjct: 1   MYLREIGQIPLLSYEEEIDYAQRVLNGEEEAKQKLIESNLRLVVSIAKK-HTNRGLKMLD 59

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            I         E   G     E   Y+K    S
Sbjct: 60  LI--------QEGNMGLMKAVEKFEYEKGFKFS 84


>gi|307323818|ref|ZP_07603027.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306890267|gb|EFN21244.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 268

 Score =  108 bits (270), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 107/245 (43%), Gaps = 15/245 (6%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           FR I  +    E EA   ++E+V A + +   +A +Y NRG    DL Q   +GL+KA +
Sbjct: 26  FRRIAELPDGSEKEAL--REEVVRAWMPMAERIASQYRNRGETHEDLRQVAMVGLVKAVK 83

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-IKR 545
           +++   G  F +YA+  V   + R   D    + +P  +++  ++V    + ++     R
Sbjct: 84  RYEPDRGSAFESYAVPTVVGEVKRHFRDHMWGLHVPRRVQELRNRVRTAVQELTRSPDDR 143

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLD 602
            P+  +IA+   M  E V   ++   +   +SL+  +   D  + L D +      S   
Sbjct: 144 SPSVRDIARHTGMAEEDVLLGMEALESFRTLSLDAALRGADDGYALVDTLG-----STES 198

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           S  +   RE+    L  L  RE  +L +RF            +  +  +++  + ++ ++
Sbjct: 199 SYERVVQRESLKPCLRRLPEREREILYLRFFCDETQSR----IADRLGISQMHVSRLISR 254

Query: 663 AIRKL 667
              +L
Sbjct: 255 TCARL 259


>gi|89098615|ref|ZP_01171497.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
 gi|89086577|gb|EAR65696.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
          Length = 253

 Score =  108 bits (270), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 109/244 (44%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             +   + A   +V+  + LV    ++ +    + +   +L   G +GL  A EKFD   
Sbjct: 15  WQQSRDAEAGNSLVKRYMPLVSYHVQRISAGLPKNVSRDELRSLGLMGLYDALEKFDPTR 74

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA + ++ +I   +  +     +P   R+K  K+   A R+   + R+ T  EI
Sbjct: 75  DLKFDTYASFRIRGSIIDGLRKEDW---LPRSTREKAKKIEAAAERLEQHLMRKATAAEI 131

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANL 609
            K++ +  + V+ V+        +S++    D+D      +I +D  AV P +   +  L
Sbjct: 132 GKEVDLHEDEVQTVMSEHFFANVLSMDEQPQDQDEKDGATYILKDHRAVVPEEKVAKDEL 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                  ++ L  +E+ V+ + +      + TL E+G+   ++  RI QI  KAI  L+H
Sbjct: 192 LSEMADAVSCLNEKEQLVISLFY----KEELTLTEIGQVMGLSTSRISQIHTKAIFSLRH 247

Query: 670 PSRS 673
             + 
Sbjct: 248 TLQK 251


>gi|189426332|ref|YP_001953509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter lovleyi SZ]
 gi|189422591|gb|ACD96989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter lovleyi SZ]
          Length = 250

 Score =  108 bits (270), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 108/258 (41%), Gaps = 19/258 (7%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
            + +   +    +   ++ M+ ++L LV  +  ++T +    +   DL     IGL+ AA
Sbjct: 3   RLRAYEEQVGERSHQLRETMITSHLPLVRYLVNRFTAQLPSHIDPQDLASAAVIGLIHAA 62

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +++D   G +F T+A   ++ AI   +        +   MRDK   V R   R  +++ R
Sbjct: 63  DRYDPGRGVQFKTFAEQHIRGAILDELRACD---PLSRTMRDKCKMVEREMHRQEHQLGR 119

Query: 546 EPTPEEIAKKLAMPVEGV----RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            PT  E+A+ L + ++       ++ + +   I       +     L D + D     P 
Sbjct: 120 NPTGREMAEALQISLDDYYGLLDEIHEFSFISIDDSWDDDEGHPLSLADILGDDENKGPQ 179

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +     +     + SL  +E   + + +      +  L+E+G    +T  RI QI +
Sbjct: 180 CQVMAGQAAQALGSAIESLPEKERLAVTLYY----YEELNLKEIGAVLGLTESRICQILS 235

Query: 662 KAIRKLKHPSRSKKLRSF 679
           +A+ +LK      KL+ F
Sbjct: 236 QAMIRLK-----GKLKPF 248


>gi|118581847|ref|YP_903097.1| FliA/WhiG family RNA polymerase sigma factor [Pelobacter
           propionicus DSM 2379]
 gi|118504557|gb|ABL01040.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pelobacter
           propionicus DSM 2379]
          Length = 250

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 113/245 (46%), Gaps = 14/245 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  A + ++E++  ++ +   +  + + +    L   DL+    IGL+ AA++FD   G 
Sbjct: 12  DETAPLTREELIVKHMPMARYLVARISPQLPPHLDQQDLMSAAMIGLIHAADRFDPNRGV 71

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F T+A   ++  I   +        +   MRDK  ++ R    + +++ R PT EE+A+
Sbjct: 72  LFKTFAEQHIRGTIIDELRSYD---VLSRTMRDKYKRLSRQLVSLEHQLGRNPTSEEVAE 128

Query: 555 KLAMPVEGVRKVLK----ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + +E   ++L      +   I       + ++  LGD + +  A SP    +   L 
Sbjct: 129 SLGIGLEEYYELLDDVHAYSFISIDDSWDDDEGNSLCLGDVLCESEAKSPQQQVMTMQLA 188

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E   + + +L  ++  V+ + +      D  L+E+G+   +T  RI QI ++A+ +L+  
Sbjct: 189 EELGKAIDALPEKDRLVVTLYY----KEDLRLKEIGEAMGLTESRISQILSQAMVRLRSK 244

Query: 671 SRSKK 675
            +  K
Sbjct: 245 LKLHK 249


>gi|292493580|ref|YP_003529019.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus
           halophilus Nc4]
 gi|291582175|gb|ADE16632.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus
           halophilus Nc4]
          Length = 241

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 102/241 (42%), Gaps = 22/241 (9%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E+V     LV  +A     R    +Q  DLIQ G IGL++AA  ++   G  F TYA  
Sbjct: 18  DELVIQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAARNYNASQGASFETYAGI 77

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   I         P  +  K  +V    R + N+  R+    E+AK+L + +  
Sbjct: 78  RIRGAILDEIRRNDW---APRSVHRKARQVAEVMREIENREGRDARDHEVAKELGLSLND 134

Query: 563 VRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             ++L+        SL+     E+T  L   ++      P D     + R      +  L
Sbjct: 135 YHRLLQDAGGYRVFSLDEFNEGEETEPLTTPLQ-----GPFDGLQDQSFRSALVGAIDGL 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             RE  V+ + +      D  L E+G+   V+  R+ QI ++A+ +L+      +L  +L
Sbjct: 190 PERERLVMSLYYV----EDLNLREIGEVLGVSESRVSQIHSQAVLRLR-----ARLSEWL 240

Query: 681 D 681
           D
Sbjct: 241 D 241


>gi|124300775|dbj|BAF45885.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 224

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 39/273 (14%), Positives = 76/273 (27%), Gaps = 50/273 (18%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I        E          
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHV 60

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      E   ++++ +   ++  D  S               PE A     +L    + 
Sbjct: 61  GSELSAEEREDEDEDEESDDDSSDDDNSID-------------PELAREKFGDLRIQYET 107

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 108 TRTMIKAK-----------------------------------SRSHADAIAEIQNLSDV 132

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 133 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 192

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   ++  I
Sbjct: 193 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLXQI 224


>gi|260439092|ref|ZP_05792908.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
 gi|292808404|gb|EFF67609.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
          Length = 241

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 8/245 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H   ++         A+  +V  N+ LV S+AK++ NRG +  D++  G IGL+KA +KF
Sbjct: 3   HTKELIALAHEGNKEARDMLVMHNMGLVYSIAKRFANRGYEMDDIVSIGTIGLIKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D  +    STYA+  +   I R I D    I+I   +++   K+ +    +S K+KRE T
Sbjct: 63  DLNMDVMLSTYAVPMISGEIKRFIRD-DGIIKISRSIKENGWKINQAKDYLSQKLKREVT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS-PLDSAIQA 607
            EEI+K+  +  E +   ++ +K+  S+   I   D + +  ++ DK A S       + 
Sbjct: 122 IEEISKETGICTEDIVVAMEASKDVESIYQTIYQSDGNQI--YVVDKLAASAKESDHDKI 179

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                    +  L   E+ ++ MR+      + T  EV K   +++ ++ ++E K + ++
Sbjct: 180 MNHVMLEETMNILEKDEKTIIEMRYF----QEKTQSEVAKILGISQVQVSRMEKKILLRM 235

Query: 668 KHPSR 672
           +    
Sbjct: 236 RKNME 240


>gi|27365297|ref|NP_760825.1| flagellar biosynthesis sigma factor [Vibrio vulnificus CMCP6]
 gi|320155681|ref|YP_004188060.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
 gi|27361444|gb|AAO10352.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           CMCP6]
 gi|319930993|gb|ADV85857.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
          Length = 244

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 97/227 (42%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 19  FIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDASKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +   + R+PT  E+AK + + +E   
Sbjct: 79  RGAMLDDIRRGDW---VPRSVHKSNREISQAIAELEGLLNRDPTDAEVAKHMGLSLEQY- 134

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
                    I+    IG ED     D I   ED    +P         R+     +  L 
Sbjct: 135 ---HGALTDINCSRLIGIEDLGVSDDVITSVEDSENNTPFKGVADEYFRKALVESIKQLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G+   V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGEILSVSESRVSQILSQSMQRLR 234


>gi|294856621|gb|ADF45248.1| RNA polymerase sigma S factor [Escherichia sp. B827]
 gi|294856623|gb|ADF45249.1| RNA polymerase sigma S factor [Escherichia sp. E1492]
 gi|294856625|gb|ADF45250.1| RNA polymerase sigma S factor [Escherichia sp. E807]
 gi|294856627|gb|ADF45251.1| RNA polymerase sigma S factor [Escherichia sp. H442]
 gi|294856629|gb|ADF45252.1| RNA polymerase sigma S factor [Escherichia sp. M863]
 gi|294856631|gb|ADF45253.1| RNA polymerase sigma S factor [Escherichia sp. TW10509]
 gi|294856633|gb|ADF45254.1| RNA polymerase sigma S factor [Escherichia sp. TW11930]
 gi|294856635|gb|ADF45255.1| RNA polymerase sigma S factor [Escherichia sp. TW11966]
 gi|294856639|gb|ADF45257.1| RNA polymerase sigma S factor [Escherichia sp. TW09231]
 gi|294856641|gb|ADF45258.1| RNA polymerase sigma S factor [Escherichia sp. TW09276]
 gi|294856643|gb|ADF45259.1| RNA polymerase sigma S factor [Escherichia sp. TW09254]
 gi|294856645|gb|ADF45260.1| RNA polymerase sigma S factor [Escherichia sp. TW09266]
 gi|294856647|gb|ADF45261.1| RNA polymerase sigma S factor [Escherichia sp. TA04]
 gi|294856649|gb|ADF45262.1| RNA polymerase sigma S factor [Escherichia sp. B685]
 gi|294856651|gb|ADF45263.1| RNA polymerase sigma S factor [Escherichia sp. TW14182]
 gi|294856653|gb|ADF45264.1| RNA polymerase sigma S factor [Escherichia albertii TW11588]
 gi|294856655|gb|ADF45265.1| RNA polymerase sigma S factor [Escherichia sp. H605]
 gi|294856657|gb|ADF45266.1| RNA polymerase sigma S factor [Escherichia sp. B49]
 gi|294856659|gb|ADF45267.1| RNA polymerase sigma S factor [Escherichia sp. TW09308]
 gi|294856661|gb|ADF45268.1| RNA polymerase sigma S factor [Escherichia sp. B1225]
 gi|294856663|gb|ADF45269.1| RNA polymerase sigma S factor [Escherichia sp. B646]
 gi|294856665|gb|ADF45270.1| RNA polymerase sigma S factor [Escherichia sp. E1118]
 gi|294856667|gb|ADF45271.1| RNA polymerase sigma S factor [Escherichia sp. E1195]
 gi|294856669|gb|ADF45272.1| RNA polymerase sigma S factor [Escherichia sp. E1196]
 gi|294856671|gb|ADF45273.1| RNA polymerase sigma S factor [Escherichia sp. E471]
 gi|294856673|gb|ADF45274.1| RNA polymerase sigma S factor [Escherichia sp. E472]
 gi|294856675|gb|ADF45275.1| RNA polymerase sigma S factor [Escherichia sp. E620]
 gi|294856677|gb|ADF45276.1| RNA polymerase sigma S factor [Escherichia sp. M1108]
 gi|294856679|gb|ADF45277.1| RNA polymerase sigma S factor [Escherichia sp. TA290]
 gi|294856681|gb|ADF45278.1| RNA polymerase sigma S factor [Escherichia sp. TW14263]
 gi|294856683|gb|ADF45279.1| RNA polymerase sigma S factor [Escherichia sp. TW14264]
 gi|294856685|gb|ADF45280.1| RNA polymerase sigma S factor [Escherichia sp. TW14265]
 gi|294856687|gb|ADF45281.1| RNA polymerase sigma S factor [Escherichia sp. TW14266]
 gi|294856689|gb|ADF45282.1| RNA polymerase sigma S factor [Escherichia sp. TW14267]
 gi|294856691|gb|ADF45283.1| RNA polymerase sigma S factor [Escherichia sp. RL325/96]
 gi|294856693|gb|ADF45284.1| RNA polymerase sigma S factor [Escherichia sp. Z205]
 gi|294856695|gb|ADF45285.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856697|gb|ADF45286.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856699|gb|ADF45287.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856701|gb|ADF45288.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856703|gb|ADF45289.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856705|gb|ADF45290.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856707|gb|ADF45291.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856709|gb|ADF45292.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856711|gb|ADF45293.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856713|gb|ADF45294.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856715|gb|ADF45295.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856717|gb|ADF45296.1| RNA polymerase sigma S factor [Escherichia fergusonii]
          Length = 157

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 64/156 (41%), Positives = 109/156 (69%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 2   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 62  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 121

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +G +    L D + D+    P D+    +++++  +
Sbjct: 122 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVK 157


>gi|52629120|gb|AAU27861.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 262

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 108/245 (44%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           IV  +          ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA 
Sbjct: 24  IVDALAAYSKVNQQTQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAAR 83

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++  +   +        +P  +      +    R + +K+ RE
Sbjct: 84  HYDSSKGASFETYAGIRIRGHMLDEVRRNDW---VPRSVYRNSRMISDAVRILEHKLGRE 140

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDS 603
               EIA++L + ++    +L+ +          G +D     D + D     +  P  +
Sbjct: 141 AKDNEIAEELGVSLDDYHDMLQDSIS----SHLYGFDDLGVTDDVLFDHEGNGSTEPHRN 196

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +++++    T+V+ SL  +E  VL + +      D  L+E+G+   V+  RI QI ++A
Sbjct: 197 VMRSDMMNRLTQVIDSLPRKERLVLSLYY----EQDLNLKEIGEILEVSESRISQILSQA 252

Query: 664 IRKLK 668
             +++
Sbjct: 253 THRIR 257


>gi|302387774|ref|YP_003823596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302198402|gb|ADL05973.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 106/242 (43%), Gaps = 13/242 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFD 489
           +++    +    K E+V   + +V S++ +  +  L F    D++ EG + +M   EKFD
Sbjct: 14  LIKYKRTKDIHIKHELVMRYMYMVRSISIQMRDVYLSFAQVEDIVNEGVLTIMSGIEKFD 73

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             +  KF TY    ++  I      Q     IP  +R    ++      + N++ R P+P
Sbjct: 74  PEMNVKFETYISKRIRGMIIDMARKQDW---IPRSVRKNAKELDNAVMELCNRLGRFPSP 130

Query: 550 EEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQ 606
            E A+ + + +E  ++ L  T     +SL+  +    D               P D  +Q
Sbjct: 131 RETAEYMNISLEKYQEALGKTNVYSVLSLDMVLEAGNDNKKTVQLPAVNENEQPEDHYLQ 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              ++   + + +L   E++V+ + +      +  ++E+ +   V+  RI QI + AI+K
Sbjct: 191 EEFKQILVQAINNLKENEQKVISLYY----MDELNMKEIAQVMNVSEPRISQIHSNAIQK 246

Query: 667 LK 668
           LK
Sbjct: 247 LK 248


>gi|239934558|emb|CAR94593.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 208

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 97/252 (38%), Gaps = 45/252 (17%)

Query: 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND 176
           T DPVRMY+ EMG++ELL+REGEI IA+RIE G   +  +L   P T+  ++   + +  
Sbjct: 1   TTDPVRMYMSEMGTVELLTREGEIRIAERIEEGLDAVRTALSMYPPTYSLMLSQYEGVAT 60

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
            T  L +II            GF             +    +   +++    +     + 
Sbjct: 61  QTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAAAEIENEAEEEAEEGEG 109

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
           + ++   +++ P+  E   R                            D +++ + +++ 
Sbjct: 110 ASEEEETLETGPDPEEAARR---------------------------FDSLSKTFVQVQK 142

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
                    +      K   L++KL      L L+    D+L+ Q+      I + E ++
Sbjct: 143 ------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLITQIRRSLTDIRNVERQV 196

Query: 357 LRLAQS-YGIKR 367
           + L     G+ R
Sbjct: 197 MLLCVRDSGMPR 208


>gi|23099037|ref|NP_692503.1| RNA polymerase sigma factor SigD [Oceanobacillus iheyensis HTE831]
 gi|22777265|dbj|BAC13538.1| RNA polymerase sigma-D factor [Oceanobacillus iheyensis HTE831]
          Length = 258

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 102/247 (41%), Gaps = 15/247 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +    +   A  +++   + LV    ++  +     +   D+   G +GL  A +KFD  
Sbjct: 15  KWKNHQDGEAANQLINNYMYLVNYHTERIASHLPNNVVKDDIRSFGILGLYDALKKFDPS 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + +K +I   +  +     +P  +R+K  KV +         +RE    E
Sbjct: 75  RDLKFDTYASFRIKGSIMDGLRKEDW---LPRSIREKTKKVEQAMEEYEQSYQREANSSE 131

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT---SHLGDFIEDKNAVSPLDSAIQ 606
           IA    M  E V   +K       +S+E             +G  I D+ A+ P +  + 
Sbjct: 132 IANLTGMTTEEVETTMKDALFSNILSIEEKPKGNSDQLKEGIGYSISDERAILPENHIVN 191

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+E   + +  L  +E+ V+ + +    N + T  E+G+   +T  RI QI  ++I K
Sbjct: 192 EELKEELIQGIKLLNEKEQLVVSLFY----NEELTFTEIGQVVGLTTSRISQIHKRSIFK 247

Query: 667 LKHPSRS 673
           LK     
Sbjct: 248 LKKTLEK 254


>gi|22126347|ref|NP_669770.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM 10]
 gi|45441369|ref|NP_992908.1| flagellar biosynthesis sigma factor [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807215|ref|YP_651131.1| flagellar biosynthesis sigma factor [Yersinia pestis Antiqua]
 gi|108812441|ref|YP_648208.1| flagellar biosynthesis sigma factor [Yersinia pestis Nepal516]
 gi|145598571|ref|YP_001162647.1| flagellar biosynthesis sigma factor [Yersinia pestis Pestoides F]
 gi|149366211|ref|ZP_01888246.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CA88-4125]
 gi|165925981|ref|ZP_02221813.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165938720|ref|ZP_02227275.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010831|ref|ZP_02231729.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166210907|ref|ZP_02236942.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167401029|ref|ZP_02306532.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167420291|ref|ZP_02312044.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167425870|ref|ZP_02317623.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470709|ref|ZP_02335413.1| flagellar biosynthesis sigma factor [Yersinia pestis FV-1]
 gi|218928962|ref|YP_002346837.1| flagellar biosynthesis sigma factor [Yersinia pestis CO92]
 gi|229896290|ref|ZP_04511460.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Pestoides A]
 gi|229897227|ref|ZP_04512383.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229897954|ref|ZP_04513105.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229902815|ref|ZP_04517932.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Nepal516]
 gi|270486604|ref|ZP_06203678.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM D27]
 gi|294503994|ref|YP_003568056.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|21959330|gb|AAM86021.1|AE013850_3 alternative sigma factor 28 [Yersinia pestis KIM 10]
 gi|45436229|gb|AAS61785.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108776089|gb|ABG18608.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Nepal516]
 gi|108779128|gb|ABG13186.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Antiqua]
 gi|115347573|emb|CAL20483.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CO92]
 gi|145210267|gb|ABP39674.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides F]
 gi|149292624|gb|EDM42698.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CA88-4125]
 gi|165913334|gb|EDR31956.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165922185|gb|EDR39362.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165990175|gb|EDR42476.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166208087|gb|EDR52567.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166961986|gb|EDR58007.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167049418|gb|EDR60826.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167055269|gb|EDR65066.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229680262|gb|EEO76361.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Nepal516]
 gi|229688995|gb|EEO81060.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229693564|gb|EEO83613.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229701213|gb|EEO89242.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Pestoides A]
 gi|262361821|gb|ACY58542.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D106004]
 gi|262366043|gb|ACY62600.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D182038]
 gi|270335108|gb|EFA45885.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM D27]
 gi|294354453|gb|ADE64794.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|320015417|gb|ADV98988.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 240

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 107/236 (45%), Gaps = 11/236 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G I L+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIDLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +      P  +R    +V    +++  ++ R  T +E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---APRSVRRNAREVASAMQQVEQRVGRPATEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANLRET 612
           + L + +   R++L  T            E+    +   +E     +PL   ++ NLR+ 
Sbjct: 122 QVLDIGLVEYRQILLDTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLKHLLEGNLRQR 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 182 VIDAIEALPEREKMVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|302392368|ref|YP_003828188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
 gi|302204445|gb|ADL13123.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
          Length = 260

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 114/250 (45%), Gaps = 14/250 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFD 489
            +   E     AK+E++   + LV  VA +          F DL   G IGL+ A E+FD
Sbjct: 13  WIEFKEHNNQQAKEELMLRFMPLVKYVANRVAINLPDKFEFEDLQNYGIIGLIDAIERFD 72

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G KFSTYA+  ++ +I   +        +P  +R K  +V      ++NK+ R PT 
Sbjct: 73  HRRGMKFSTYAISRIRGSIIDQLRRLDW---VPTTIRRKAKQVAEINSELANKLGRLPTD 129

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPI--SLETPIG--DEDTSHLGDFIEDKNAVSPLDSAI 605
           EEI ++L +  +   +++     P   SL++ I     D   L + I D++A  P  +  
Sbjct: 130 EEIRQELDLDSDEYSQLMSEINIPQETSLDSFINSRQADGVTLIEVIADEDAARPEQTFR 189

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              ++      +  L P+E +V+ + +  G      L E+G+   VT  RI Q+  KAI 
Sbjct: 190 YEEIKRILGEAIEKLKPQERKVVTLYYYEG----LNLTEIGEVLEVTTARISQLHTKAIY 245

Query: 666 KLKHPSRSKK 675
           +L+     KK
Sbjct: 246 RLRGYLSRKK 255


>gi|291196312|emb|CBG22628.1| DNA-directed RNA polymerase subunit D [Pseudomonas indica]
          Length = 239

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 96/284 (33%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T  +++   + +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMSAIAHFPGTVGSILSEYERVTQEGGRLSDV--LSGYIDPDDGT------- 51

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             + +   +          +  + + ES  + S +D       PE A      + E  + 
Sbjct: 52  LPAEEVPVELKSSTAAAAEEPEDDEEESGEESSDEDEGDGGPDPEVARQRFGAVAEQLEK 111

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + S +     + L  L
Sbjct: 112 ANKAL-----------------------------------KKHGRGSKQANEELQALADL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 FMPIKLVPKQFDALVERVRSALERVRAQERAIMQLCVRDARMPRADFLRQFPGNEVDLDW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +A   D I + + ++  +  E  ++I+E 
Sbjct: 197 ADSLAK-GKSKYAEAIAALQDDIKRNQQKLIDLQNEVELNIAEI 239


>gi|307152337|ref|YP_003887721.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306982565|gb|ADN14446.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 257

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 103/240 (42%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           ++      +   + ++VE N  LV  VA + + +    + DL Q G +GL++A E+F+  
Sbjct: 16  LIAYSRNPSLKLRNQLVELNAGLVRQVAHRISRQCCEPYEDLEQVGYLGLIRAIERFNPQ 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +V+  I   + D+   +RIP   +D   K  +  ++++  + R+P   E
Sbjct: 76  QGCAFSSFAIPYVRGEILHYLRDRGSVMRIPRRWQDLYTKGKKLRKQLAQTLGRQPKESE 135

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQA 607
           IA+ L +  +   +       +  +SL+  I    +     GD + D  +          
Sbjct: 136 IAQALGVSYQEWNECQLALQNRLLVSLDATINQVHDGVITFGDTLPDPKSQGQQRMQED- 194

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    R ++ L  + +  +   F      D   +E  KQ  ++   + +   K + +L
Sbjct: 195 --RLQLQRAMSQLEDKTKAAIECVFLW----DLPRKEAAKQIGISPMTVTRHLQKGLEQL 248


>gi|77918763|ref|YP_356578.1| flagellar biosynthesis protein, alternative sigma factor 28
           [Pelobacter carbinolicus DSM 2380]
 gi|77544846|gb|ABA88408.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pelobacter
           carbinolicus DSM 2380]
          Length = 255

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 52/237 (21%), Positives = 112/237 (47%), Gaps = 13/237 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL---DLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +++++L +V  +A++  ++   F+   D+     +GL+ AA +F   +G  F T+A 
Sbjct: 15  KDRLIKSHLHMVSFLAERMVSQVPAFMTREDISSAAMVGLVDAANRFKPSMGVLFKTFAE 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +            +R K  ++ +T   +  ++ R P   E+A +L M +E
Sbjct: 75  KRMRGAVLDEVRRMDWF---SRSLRQKQSRIAKTMEALEKRLGRPPEEHEMAAELEMDLE 131

Query: 562 GVRKVLKITKE--PISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             R+ L        +SL   I D  D   + D IED+N+ S ++    + L +   R + 
Sbjct: 132 SYRQALGEVSYLGCVSLHETIEDTPDGPTMLDNIEDQNSPSAVEMLENSELTQELARQID 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            LT +E  V+ + +      + + +E+ +   ++  R+ Q+ ++A+ KLK   +  +
Sbjct: 192 RLTDKERLVVSLYY----YEELSQKEIAEVLELSEGRVSQLHSQALIKLKTSIKRSQ 244


>gi|321117392|dbj|BAJ72173.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 42/273 (15%), Positives = 82/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI--IGFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++ ++ E +   +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEEREDDEXEDXESDDDSSDDDNSID--PELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L     D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKXFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLQQI 225


>gi|321117390|dbj|BAJ72172.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 43/273 (15%), Positives = 83/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI--IGFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++ ++ E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEEREDDEXEDEESDDDSSDDDNSID--PELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L     D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKXFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLQQI 225


>gi|325270141|ref|ZP_08136748.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
 gi|324987442|gb|EGC19418.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
          Length = 228

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 119/257 (46%), Gaps = 39/257 (15%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             ++ I+    +S  E R +   ++      + A +++ +ANL+ V+S+A +Y NRGL  
Sbjct: 6   KYMEEIAGGQPLSDREERTLAGRIK---VGDAQALEKLTKANLKYVVSLAHQYRNRGLGE 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA++FD   G +F  +A  ++++A+  +I +Q+   R+P +      
Sbjct: 63  DDLISEGNIGMMHAAQRFDGSRGVRFVVFAAPYIRKAMEEAIKEQAALYRLPRN------ 116

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
                          E    E  +  A+ ++                 P+G  +   L +
Sbjct: 117 ---------------EKNRSEQKRSHAISIDQPV--------------PVGSSNNFTLQN 147

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E+ NA    +   Q  L     + L  L  RE +V+   +G+     +T+ E  +   
Sbjct: 148 VLENDNAPHADEQLNQEILSSEIQKGLGVLNERERQVIACLYGLSGVH-YTMAEAAEHMG 206

Query: 651 VTRERIRQIEAKAIRKL 667
           + RER+RQI  KA+RKL
Sbjct: 207 LKRERVRQIRDKALRKL 223


>gi|24374722|ref|NP_718765.1| flagellar biosynthesis sigma factor [Shewanella oneidensis MR-1]
 gi|24349382|gb|AAN56209.1|AE015759_1 RNA polymerase sigma-27 factor [Shewanella oneidensis MR-1]
          Length = 237

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 98/229 (42%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     ++ +    +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDW---VPRSVHRNNRRIAQAIDELEQVLGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +   D  +    +   +          +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSEDILTTSDNVSDGTFEVLAETQFHSALVEAIKI 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|70725968|ref|YP_252882.1| RNA polymerase sigma factor SigB [Staphylococcus haemolyticus
           JCSC1435]
 gi|68446692|dbj|BAE04276.1| sigma factor B [Staphylococcus haemolyticus JCSC1435]
          Length = 256

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 117/247 (47%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECEA-SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +  A + A+  +V    +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQDNANTEAQDRLVNHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SIAEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQKDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  ++
Sbjct: 249 KLQQAAK 255


>gi|212634384|ref|YP_002310909.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212555868|gb|ACJ28322.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 239

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+    EIA++L M ++
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRVAQVIDELEQELGRDARDPEIAERLEMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +  ED +     +S  +          +  
Sbjct: 130 EYYSIL----NDVSVGKVVGIEDLGVAVDVVNHEDNHDDVAYESLAEVEFHSALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|169334044|ref|ZP_02861237.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258761|gb|EDS72727.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
          Length = 253

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 125/264 (47%), Gaps = 16/264 (6%)

Query: 409 IRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           +  +++   V T  +     + I  M+ + +      K E +  NLRLV+SV ++++NR 
Sbjct: 1   MIRKVEICGVNTATLPNLNNKEIEDMLIRIKNGEEDLKNEFIRCNLRLVLSVVQRFSNRN 60

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
               DL Q G IGL+KA + FD   G KFSTYA+  +   + R + D   TIR+   ++D
Sbjct: 61  ENMDDLFQVGCIGLIKAIDNFDVKFGVKFSTYAVPMIIGEVRRYLRDNG-TIRVSRSLKD 119

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DT 585
             +K ++            PT  EIAKKL +  + +   L    EP SL   + ++  D+
Sbjct: 120 MAYKALKYKEAHK---DTNPTNREIAKKLGVKEKDLNFALDSIVEPCSLYDQMYNDNGDS 176

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D + D+       +      + +    +  L  RE+ ++  R+ +G     T  EV
Sbjct: 177 ISLIDQVGDEKNREENWTE-----KLSLKEAVEKLKGREKEIILKRYYLG----RTQIEV 227

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
             +  +++ ++ ++E   +RK+K+
Sbjct: 228 ANEIGISQAQVSRLEKSGLRKIKN 251


>gi|253682486|ref|ZP_04863283.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
 gi|253562198|gb|EES91650.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
          Length = 252

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 58/239 (24%), Positives = 118/239 (49%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++++ +     A  E+V+ NL LV S++KK+ NRG ++ D+ Q G++GL+KA   FD 
Sbjct: 18  LELIKQAKLGDKKAVDELVQKNLPLVSSISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 77

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +FSTYA+  +   I R I D    I++   ++    K+     +++ ++ REP+ E
Sbjct: 78  SYDVQFSTYAVPMIMGEIKRFIRD-DGLIKVSRSVKYTAKKLHYDKEKLTKELNREPSLE 136

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++K   +  E +    +   EP  L   I  +D S +  ++ DK  +       + + +
Sbjct: 137 ELSKFSGISKEDIIFSSEAINEPKYLYDTIHQDDGSPI--YLIDKVVLDDKGEIDELD-K 193

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L+ L  R  +++ +R+   +        V K   +++ ++ +IE K ++ +K 
Sbjct: 194 IALKEALSKLDQRSRQIIILRYFKDITQVK----VAKMLGISQVQVSRIEKKVLKSMKE 248


>gi|120598267|ref|YP_962841.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|120558360|gb|ABM24287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
          Length = 237

 Score =  108 bits (270), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +     +V +    +  ++ R+    EIA+KL M ++
Sbjct: 73  IRIRGAMLDEIRRGDW---VPRSVHRNNRRVAQAIDELEKELGRDARDTEIAEKLDMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D   + D++     ++  +          +  
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDILTLSDRSDDGSFEALAETQFHSALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|254491912|ref|ZP_05105091.1| RNA polymerase sigma factor, FliA/WhiG family [Methylophaga
           thiooxidans DMS010]
 gi|224463390|gb|EEF79660.1| RNA polymerase sigma factor, FliA/WhiG family [Methylophaga
           thiooxydans DMS010]
          Length = 234

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 100/233 (42%), Gaps = 11/233 (4%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +K E+VE N  LV  +A     R    +   DLIQ G IGL+ A+ +FD   G  F TY
Sbjct: 6   QSKSELVEQNAALVKRIAYHLIARLPASVDVEDLIQAGMIGLLDASHQFDSSQGASFETY 65

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++ A+   I         P  +  K  ++  T + +  +  R  +  E+A+ + + 
Sbjct: 66  AGIRIRGAMLDEIRRNDW---APRSVHRKAREISSTMQVIEQQKGRNASDAEVAQAMGLD 122

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +    + L+ +            ++       I    A  P +   Q + ++   R + S
Sbjct: 123 ISEYHQQLQDSTGHQLFSLDEFSDNDEVHARPISSGPAA-PEEEVQQDDFQQAMVRAIDS 181

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           L  RE  ++ + +    N +  L+E+G+   V+  R+ QI ++ + +L+   R
Sbjct: 182 LPERERLLMSLYY----NDELNLKEIGEVLGVSESRVSQIHSQTVIRLRSKLR 230


>gi|219856135|ref|YP_002473257.1| hypothetical protein CKR_2792 [Clostridium kluyveri NBRC 12016]
 gi|219569859|dbj|BAH07843.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 254

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 116/239 (48%), Gaps = 8/239 (3%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +++        A  ++VE NL LV +++KK+ NRG ++ D+ Q G +GLMKA   FD 
Sbjct: 20  LKLIKCAREGDKEALNKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVNNFDE 79

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  +   I R + D    I++   +++   K+      ++ K+ REPT E
Sbjct: 80  TYNVKFSTYAVPMILGEIKRFLRD-DGMIKVSRSIKNTAKKLHYDREALTKKLNREPTIE 138

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+   +  E +    + T     L   I  +D S +   + DK + +P +     + R
Sbjct: 139 ELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPV--LLIDKISENPKEDVEVID-R 195

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L +L  +  +++ +R+      D T  +V K   + + ++ +IE K ++ ++ 
Sbjct: 196 IALKEALRNLDVKSRQIIMLRYF----KDKTQVQVAKMLGINQVQVSRIEKKVLKTMRE 250


>gi|126348076|emb|CAJ89797.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 289

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 105/235 (44%), Gaps = 14/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++FD   G  F +YA+  +
Sbjct: 53  RDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVPTI 111

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              + R   D+   +R+P  +++  +KV    R ++      EP+   +A    +  + V
Sbjct: 112 TGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELTQNPGSPEPSVAALAAHTGLTEDEV 171

Query: 564 RKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              ++   +   +SL+  +   +D   L D +    A       +    RE+    L  L
Sbjct: 172 SAGMEALESFSTLSLDAELSAGDDGYSLADTL---GAADGSYDTVID--RESAKEGLRRL 226

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
             RE  +L MRF      D T   +  +  +++  + ++ +++  +++  +  ++
Sbjct: 227 PERERAILYMRFF----EDMTQSRIADRLGISQMHVSRLISRSCARVRDEALGER 277


>gi|294856637|gb|ADF45256.1| RNA polymerase sigma S factor [Escherichia sp. B1147]
          Length = 157

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 64/156 (41%), Positives = 109/156 (69%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
           A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TI
Sbjct: 2   ARRYGNRGLALLDLIKEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 61

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
           R+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++TP
Sbjct: 62  RLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 121

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +G +    L D + D+    P D+    +++++  +
Sbjct: 122 LGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVK 157


>gi|327314688|ref|YP_004330125.1| sigma-70, region 4 [Prevotella denticola F0289]
 gi|326944846|gb|AEA20731.1| sigma-70, region 4 [Prevotella denticola F0289]
          Length = 228

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 119/262 (45%), Gaps = 39/262 (14%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I+ I+    +S  E R +   ++      + A +++ +ANL+ V+S+A +Y NRGL  
Sbjct: 6   KYIEEIAGGQPLSDVEERTLAERIK---VGDAHALEKLTKANLKYVVSLAHQYRNRGLGE 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA++FD   G +F  +A  ++++A+  +I +Q+   R+P +      
Sbjct: 63  DDLISEGNIGMMHAAQRFDGARGVRFVVFAAPYIRKAMEEAIKEQAALYRLPRN------ 116

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
                          E    E  +  A+ ++                 P+G  +   L +
Sbjct: 117 ---------------EKNRSEQKRSHAISIDQPV--------------PVGSSNNFTLQN 147

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +E+ NA    +   Q  L     + L  L  RE +V+   +G+     +T+ E  +   
Sbjct: 148 VLENDNAPHADEQLNQEILSAEIQKGLGVLNERERQVITCLYGLSGIH-YTMAEAAEHMG 206

Query: 651 VTRERIRQIEAKAIRKLKHPSR 672
           + RER+RQI   A+RKL    +
Sbjct: 207 LKRERVRQIRDGALRKLHKRMK 228


>gi|291196396|emb|CBG22670.1| DNA-directed RNA polymerase subunit D [Pseudomonas thermotolerans]
          Length = 239

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 96/284 (33%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L E++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDTILSEYQRVTTEGGRLAEVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             +        + K        + D +  A+ S DD ++ D  P            D ++
Sbjct: 50  DIAEPSEAPVPELKNGSAAVADDDDEDEDAEASDDDEAEGDGGP------------DPEE 97

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A   SA+ +Q                     L+      +K  + S +     + L  L
Sbjct: 98  AARRFSAVAEQ---------------------LEKTHKALEKYGRGSKQGIAELQALADL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV  + D   R+   E  +++L      + R  FL    G E++  W
Sbjct: 137 FMPIKLVPKQYDALVAVVRDALDRVRAQERAIMQLCVRDARMPRADFLRLFPGNEVNLDW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +      I + +  +  +  ET ++I+E 
Sbjct: 197 APEIAK-SKAKYAEAIGNLQADIQRCQQMLAELQDETKLTIAEI 239


>gi|284045933|ref|YP_003396273.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950154|gb|ADB52898.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 263

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 58/245 (23%), Positives = 111/245 (45%), Gaps = 13/245 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +  +       A++ ++  +L L  ++A++Y        DL+Q  ++GL+KA ++FD  
Sbjct: 28  MLATRARNGDGRAREALIAEHLPLARALARRYRRGSESLDDLVQVASVGLIKAVDRFDPD 87

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+ FST+A   +   + R   D    + +    ++   KV   A  +  +     TP +
Sbjct: 88  RGHSFSTFAQPTIVGELLRHFRDTGWGVHVARGTQELALKVRSAAEAIETETGAVATPRQ 147

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQA 607
           IA++    +E V + L     +  +SL TP G +D   + + D + D       +    A
Sbjct: 148 IAERTGAELEAVVEALGALANRTALSLATPAGHDDEGDATIADTLGD-----VEEGYRAA 202

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R      L  L  RE+R++RMRF      D T  E+  +  V++ +I ++  +++ KL
Sbjct: 203 EARALLGPALRHLPEREQRIIRMRFV----DDLTQSEIATEIGVSQMQISRLLRQSLDKL 258

Query: 668 KHPSR 672
              +R
Sbjct: 259 HELTR 263


>gi|153852719|ref|ZP_01994156.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
 gi|149754361|gb|EDM64292.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
          Length = 237

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 117/241 (48%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           H +++++K       A+ ++VE N  LV  + +++T RG +  DL Q G IGL+KA +KF
Sbjct: 3   HTIALIQKSHEGDEEARAQIVEENTGLVWCIVRRFTGRGTELEDLFQIGTIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K  +    +  K+ REP+
Sbjct: 63  DLSYEVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELSYKGYQAQEVLGRKLGREPS 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E+A+ L +  E +   +    +  SL  P+  ++       I     V   D A +  
Sbjct: 122 VTELAEYLDVSPEELTMAMDACTDVESLHRPVYKKEGQE----ISLMEKVGKEDGAEERV 177

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L     + L +   +EER L     +    + T  ++GK+  +++ ++ ++E K ++ L+
Sbjct: 178 LDHLLLKELLTSLDKEERKL---IYLRYFAEKTQTQIGKEMGISQVQVSRMEKKILKNLR 234

Query: 669 H 669
            
Sbjct: 235 E 235


>gi|227500978|ref|ZP_03931027.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
 gi|227216751|gb|EEI82149.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
          Length = 256

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  + +    + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A E++D   G+
Sbjct: 19  QYYKTKDKKLRDELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIERYDPSKGF 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FS++A   +   + R   D+   IR+P  +++   K+    + +  +++R PT  +IA 
Sbjct: 79  AFSSFATPTIMGELKRYFRDKGWVIRVPRRIQNLYKKINTAKKILPQELQRTPTVADIAD 138

Query: 555 KLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L    E + + ++ +    P SL+     +   +  D  +          +I+  L++ 
Sbjct: 139 YLGEDEETILETMEASKVYTPQSLDMKYQVQKGENAVDLSDMIGEEDKNFDSIE--LKDL 196

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             + +  L   E+ +L +R+  G     T  ++     +++  + +IE K ++K
Sbjct: 197 IDKSMERLNDLEKEILELRYYEG----RTQVDIANSLDISQMTVSRIEKKILQK 246


>gi|118443948|ref|YP_877996.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
 gi|118134404|gb|ABK61448.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
          Length = 242

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 112/231 (48%), Gaps = 13/231 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + ++F DL+  G +GLM A  KFD   G KFSTYA 
Sbjct: 10  KEEIVKKYIPLVKYIASRVIIGKTKYIEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I   S    I     DK++K       +  +   EP  ++IAK+L M V+
Sbjct: 70  IRIRGSMIDEIRKNS---PISKGAMDKLNKYNSAIESLQKRNLAEPNIKDIAKELDMTVK 126

Query: 562 GVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  ++D   L   IED N+ +P +        E  ++ L 
Sbjct: 127 QVGEIENFINYISIVSLEDLIFSEDDDISLMGTIEDINSPNPEEEYENDEKLEYLSKGLD 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  ++  VL + +      + TL+E+GK   V+  R+ Q+ ++AI  L+ 
Sbjct: 187 MLNEKDRTVLSLYY----YEEMTLKEIGKILGVSESRVCQLHSRAIVHLRK 233


>gi|308273536|emb|CBX30138.1| RNA polymerase sigma factor whiG [uncultured Desulfobacterium sp.]
          Length = 255

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 109/240 (45%), Gaps = 19/240 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++     LV  ++ +  NR    +   DL   G IGL  A E FD   G KF TYA + +
Sbjct: 30  LILKYAPLVKYISDRLANRMPSHISRDDLNSAGIIGLFDAIENFDSSRGIKFETYASYRI 89

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + AI   +        IP  +R  I KV         K+ R P   EIA++L + +E   
Sbjct: 90  RGAILDEMRKLDW---IPRSVRKDIQKVETAVTAAQTKLGRTPEDHEIAEELGVNLEDFY 146

Query: 565 KVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           K++  T     +SL+ P      + +     + +  SPLD   ++ + +     LA+L  
Sbjct: 147 KIIDRTHNVNLLSLDEPALGTSVTTVNRL--ESDNPSPLDKVKKSEIEKVIASALANLPE 204

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           + + V+ + +      + TL+E+ +   +T  RI QI +KAI  L+      KL+++ +G
Sbjct: 205 KVQMVISLYY----YDEMTLKEIAEIMGLTESRISQIHSKAIIILR-----SKLKAYFEG 255


>gi|290879082|emb|CBK39765.1| sigma factor of RNA polymerase [Pseudomonas jessenii]
          Length = 238

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 38/282 (13%), Positives = 94/282 (33%), Gaps = 48/282 (17%)

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           M+++   P T   ++     +      L +++            G+    +G +    E 
Sbjct: 1   MSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEV 49

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                 +    + + D E       ++ ++    P  A      + +  + +   L    
Sbjct: 50  PPPIDAKAVKADDDSDDEEGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKAL---- 105

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                          +K  +++         L +L   + L   
Sbjct: 106 -------------------------------KKHGRNNKAAIAELLALAELFMPIKLVPK 134

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A    +
Sbjct: 135 QFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD-ALAKGK 193

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G++   +      I++ + ++ ++  ETG++I+E + I   +
Sbjct: 194 GKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRM 235


>gi|323705419|ref|ZP_08116994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535321|gb|EGB25097.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 246

 Score =  108 bits (269), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 109/240 (45%), Gaps = 15/240 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +   +K++++   + LV  + K+     L      DLI +G IGL+ A  K+D  
Sbjct: 11  KYEKQKDGSSKEDIIIKYMPLVKHIVKRICLSELSKEDTDDLISQGMIGLIDAVNKYDVS 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K  I   +  +     IP  ++ +   + +T  ++  + KREPT EE
Sbjct: 71  KGVKFETYASIRIKGEIIDYLRKKDW---IPRSLKKRYKSIEKTIEQLEQEYKREPTIEE 127

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           I +   +    V K L         SL+  I +         I D    +P +  +  +L
Sbjct: 128 IMEATKLSKNDVLKTLSYMNAGYISSLDEVIENNLKIT---SITDNEVTNPENEVMMFDL 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++  ++ + +L  +E  ++ + +      D   +E+ K   +T  RI QI +KAI+KLK 
Sbjct: 185 KQNISKAIDTLQEKERLIISLYY----YEDLNYKEISKIMGLTESRISQIHSKAIKKLKE 240


>gi|306821834|ref|ZP_07455426.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550141|gb|EFM38140.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 268

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 107/236 (45%), Gaps = 4/236 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +   E      + E+++ NL +   ++KKY N+G+++ D+ Q  ++GL+ A E++D   G
Sbjct: 31  LMYSEKRDIAIRNELIQRNLYIAEILSKKYINKGIEYEDIYQVASLGLIYAIERYDITKG 90

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FS++A   +   I +   D+  +IR+P  +++   +V      +  +  + P   +IA
Sbjct: 91  FEFSSFATPTIIGEIKKYFRDKGWSIRVPRRIQELSKRVNTVKNELQQETHKTPRISDIA 150

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +KL +  E V + +        +   +  ++     D    +       S  +    +  
Sbjct: 151 EKLGITQEEVLETMDAAGAYAPISLDVKYDNEGEDKDVALHELIGKDDKSFAEIEDGDFL 210

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             V+ SL+  E++++  R+          +E      +++  + ++E K + KLK 
Sbjct: 211 RNVMESLSEVEKKIIMDRYFDNKTQMTVAKE----LDISQMTVSRMEKKILTKLKK 262


>gi|302343749|ref|YP_003808278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
 gi|301640362|gb|ADK85684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
          Length = 260

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 59/246 (23%), Positives = 111/246 (45%), Gaps = 20/246 (8%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           +  ++ ++     ++  VA +   R    +   DLI  G +GL+ A +KFD     KF T
Sbjct: 23  AAERERLILEYAPMIRYVAGRIAMRLPAHVSMEDLIGAGVLGLIDAVDKFDPEKNVKFKT 82

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA + V+ AI   +        +P  +R K   +     R+ N++ R    EEIA++L +
Sbjct: 83  YAEFRVRGAILDELRAMDW---VPRSVRKKSSDLEDAIGRLQNRLGRPAEDEEIAQELGI 139

Query: 559 PVEGVRKVLKITKEP--ISLET---PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            ++ + ++L        +SL+    P+G+ D+  + + +  +    PL       LR   
Sbjct: 140 GLDDLHRLLDEVSGVNLLSLDDADSPLGNLDSEQVMEAMGREGLEDPLVMLGLVELRRVI 199

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +  L  +E+ V+ + +      + T+ E+G+    T  RI Q+  KAI +L+     
Sbjct: 200 ASAIEGLPEKEKLVVSLYY----YDELTMREIGEVLGYTESRISQMHTKAILRLR----- 250

Query: 674 KKLRSF 679
            +LR F
Sbjct: 251 ARLRDF 256


>gi|330444437|ref|YP_004377423.1| RNA polymerase sigma factor [Chlamydophila pecorum E58]
 gi|328807547|gb|AEB41720.1| RNA polymerase sigma factor [Chlamydophila pecorum E58]
          Length = 256

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 103/242 (42%), Gaps = 17/242 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCL 492
             E +    +  ++E+ L LV S   +            DL   G  GL++A E+++   
Sbjct: 16  YWETQDIQYRDSLIESYLHLVKSAVHRLIVGMPPHIKTQDLYASGVEGLVRAVERYNPER 75

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F  +A++ +K AI   +  Q     +P  +  K +K+      +   + +EPT  E+
Sbjct: 76  S-RFEGFAIFLIKAAIIDDLRKQDW---VPRSVYQKANKLTEAMDTLRQSLGKEPTDLEL 131

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPI----GDEDTSHLGDFIEDKNAVSPLDSAIQ 606
            + L + +  + +    ++    ISL T       + +   L + I D+ A +  D   +
Sbjct: 132 CEYLNISLHELSQWFASSRPALIISLNTDWPSHSCEGEGIALEERIPDERAETGYDVVDK 191

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                     +  L  +E +V+ + +  G      L+E+GK   V+  R+ QI +KA+ K
Sbjct: 192 KEFCSFLALAIQGLEEKERQVMALYYYEG----LVLKEIGKILGVSESRVSQIHSKALIK 247

Query: 667 LK 668
           L+
Sbjct: 248 LR 249


>gi|124300724|dbj|BAF45870.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 225

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 42/273 (15%), Positives = 82/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--GFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++  + E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEERDDDEDEDEESDDDSSDDDNSID--PELAREKFNDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E    W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETSETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    + + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSEDVNRGLQKLQQI 225


>gi|124300769|dbj|BAF45882.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 225

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 42/273 (15%), Positives = 82/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGXNQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIT--GFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++  + E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEERDDDEDEDEESDDDSSDDDNSID--PELAREKFNDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E    W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETSETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    + + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSEDVNRGLQKLQQI 225


>gi|323499559|ref|ZP_08104529.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
 gi|323315432|gb|EGA68473.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
          Length = 244

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 104/245 (42%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKALTYDQYANQNSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++ +    +  ++ R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKHNREISQAISVLEGELNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDS 603
           PT  E+A+ L M +             I+    +G ED     D I   +D  A +P   
Sbjct: 118 PTDAEVAQHLGMSLAQY----HSALADINCSRLVGIEDLGVSEDVISPEDDDEANTPFQG 173

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R+     + +L  RE  VL + +    + +  L+E+G    V+  R+ QI +++
Sbjct: 174 VADEYFRKALVDSIKALPEREALVLSLYY----DEELNLKEIGDVIGVSESRVSQILSQS 229

Query: 664 IRKLK 668
           +++L+
Sbjct: 230 MQRLR 234


>gi|291196342|emb|CBG22643.1| DNA-directed RNA polymerase subunit D [Pseudomonas mohnii]
          Length = 237

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 93/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDPKAVKADDDSDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L  L
Sbjct: 110 TRKAL-----------------------------------KKHGRHNKAAIAELLALADL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|255021389|ref|ZP_05293437.1| RNA polymerase sigma factor for flagellar operon [Acidithiobacillus
           caldus ATCC 51756]
 gi|254969252|gb|EET26766.1| RNA polymerase sigma factor for flagellar operon [Acidithiobacillus
           caldus ATCC 51756]
          Length = 241

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 108/248 (43%), Gaps = 12/248 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF- 488
           M+ +   +    +  +V   + LV  +A++   R    +   DLIQ G IGL+   E++ 
Sbjct: 1   MIAQRAWDQDPQRSALVARYVPLVQRIAQRLRARLPANVDLGDLIQAGLIGLLDVLEQYP 60

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +      F  YA   ++ ++   + +Q     +P   R K  +V R   ++  ++ R P+
Sbjct: 61  EPDDSDAFLRYATLRIRGSMIDELREQDW---LPRRARAKEQQVSRAMAQLEQQLGRPPS 117

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            +E+AK L   ++  +K +  +   +     +  ++ S +G ++ D++A           
Sbjct: 118 DQEVAKHLGWDLDDYQKAIADSGGQLVYLEDLAADNDSFVGQYLRDRHADISEVLGSLEF 177

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R      +  L  RE  VL + +      + TL E+G+   VT  R+ QI  +A+ +L+
Sbjct: 178 DRH-LQEAITRLPERERLVLSLYYR----EELTLREIGEVLEVTESRVSQIVRQAVLRLR 232

Query: 669 HPSRSKKL 676
              +   L
Sbjct: 233 ASLQLGSL 240


>gi|15895573|ref|NP_348922.1| sporulation sigma factor SigF [Clostridium acetobutylicum ATCC 824]
 gi|15025312|gb|AAK80262.1|AE007731_7 Sporulation-specific sigma factor F [Clostridium acetobutylicum
           ATCC 824]
 gi|325509722|gb|ADZ21358.1| sporulation sigma factor SigF [Clostridium acetobutylicum EA 2018]
          Length = 252

 Score =  108 bits (269), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 113/240 (47%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++        A  +++E NL LV ++++K+ NRG ++ D+ Q G +GL+KA   F+  
Sbjct: 19  KLIKSVHEGNKEALNKIIENNLPLVSAISRKFLNRGYEYDDIFQIGCMGLVKAVNNFNSD 78

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++   ++    ++     ++  ++ REPT +E
Sbjct: 79  YKVKFSTYAVPMIMGEIKRFLRD-DGIIKVSRSVKSTARQLHYDREKLVKELNREPTIDE 137

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANL 609
           ++K   +  E +    + T     L   +  +D S   L D + D  +            
Sbjct: 138 LSKFSGIDKEEIIMATESTTSMQYLYDVVHQDDGSPVLLIDKLSDPYSEDSDVID----- 192

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +    +++ SL  + ++++ +R+      D T  +V     +++ ++ +IE + ++ ++ 
Sbjct: 193 KIVLKQIIKSLDNKSKQIIMLRYF----KDKTQTQVANMLGISQVQVSRIEKRILKAIRE 248


>gi|124300777|dbj|BAF45886.1| RNA polymerase sigma-subunit [Pectobacterium carotovorum subsp.
           carotovorum]
          Length = 222

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 39/273 (14%), Positives = 83/273 (30%), Gaps = 52/273 (19%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G + L ++I            GF     
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLI-----------TGFVDPNA 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                     +      ++   E D +   +  +++       PE A      L E  + 
Sbjct: 50  EEDI----APTATHVGSELSTEEMDDDDEEEDDEEEEDDNSIDPELAREKFTELREQYET 105

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A     R   + A + +                                 L ++
Sbjct: 106 TRQVIKA---HGRSHALAAQEILN--------------------------------LSEV 130

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L  +   + +  F+    G E +  W
Sbjct: 131 FKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVTMFTGNETNNTW 190

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
            + A    +  W   +    + + +   +++ I
Sbjct: 191 FAAAVAMGKP-WSEKLNDVEEDVTRSLQKLQQI 222


>gi|304406109|ref|ZP_07387766.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304344693|gb|EFM10530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 257

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 120/241 (49%), Gaps = 13/241 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +   +     ++E +  +V   A K   NR   F DL+Q G + L+K   ++D  +
Sbjct: 17  ADYQQSPDNDKATILIERHAPMVRMAAGKIARNRPDLFEDLVQVGQMSLLKLFHQYDPSV 76

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F  YAM  +   +   + D+S  I++P  +++K   V +    ++ K++R P  EEI
Sbjct: 77  GVQFEPYAMKSIIGHMKNYLRDKSWYIQVPRRIKEKGIAVQQAIDELTVKLERSPRVEEI 136

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANL 609
           A+++ + VE   ++L  +     +SL+TPI +E+ T+ LG+ I      SPLD     + 
Sbjct: 137 AERMELTVEETVEILGGRDLYHYVSLDTPISEEESTTTLGELIG-----SPLDDFGLIDK 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      +A+L P E +VL++ F  G         + +Q  V++  I +I+ +AI KLK 
Sbjct: 192 KLDIEAAMAALKPEERQVLKLVFEDG----EPQRVIAEQLGVSQMSISRIQRRAIEKLKR 247

Query: 670 P 670
            
Sbjct: 248 S 248


>gi|330862243|emb|CBX72404.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 113

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 78/107 (72%), Positives = 85/107 (79%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S   PIGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI
Sbjct: 6   SQWNPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGI 65

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 66  DMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 112


>gi|146282908|ref|YP_001173061.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri A1501]
 gi|145571113|gb|ABP80219.1| flagellar biosynthesis sigma factor FliA [Pseudomonas stutzeri
           A1501]
          Length = 241

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 101/242 (41%), Gaps = 17/242 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +   + +A  A+  +++    LV  +A     R    +Q  DLIQ G IGL++AA+K+D 
Sbjct: 1   MYYSKAQAKDAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDA 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++  +   +         P  +      V    R +  K  R+    
Sbjct: 61  GKGASFETYAGIRIRGTMLDEVRKGDW---APRSVHRNSRMVSEAIRAIEAKTGRDAKDH 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQ 606
           E+A +L + ++    +L  T      S +  +        GD  ED  +    P      
Sbjct: 118 EVAAELKLSLDEYYGILGDTLGSRLFSFDDLLQ---EGEHGDLQEDAGSTHPEPFRDLED 174

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              ++     +A+L  RE+ VL + +    + +  L+E+G+   V+  R+ Q+ ++   +
Sbjct: 175 ERFQQALADAIANLPEREKLVLSLYY----DEELNLKEIGQVLGVSESRVSQLHSQCAAR 230

Query: 667 LK 668
           L+
Sbjct: 231 LR 232


>gi|291196308|emb|CBG22626.1| DNA-directed RNA polymerase subunit D [Pseudomonas grimontii]
 gi|291196364|emb|CBG22654.1| DNA-directed RNA polymerase subunit D [Pseudomonas panacis]
          Length = 238

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 93/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + +   DD  E   D         +D  +    P  A      + +  + 
Sbjct: 59  PPPVDAKAAKADDDTEDDDAEASTD--------DEDEVESGPDPIIAAQRFGAVSDQMEI 110

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +S+         L +L
Sbjct: 111 TRKAL-----------------------------------KKHGRSNKLAIAELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGHEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 SD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 238


>gi|225026792|ref|ZP_03715984.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
 gi|224955911|gb|EEG37120.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
          Length = 245

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 113/250 (45%), Gaps = 12/250 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
                 ++++ +     A+  +VE N  L+ SV K++  RG    DL Q G+IGL+K  E
Sbjct: 1   MERTCELIKQAKEGNKEAQSILVEENSGLIWSVVKRFQGRGYDKEDLFQIGSIGLLKCIE 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD     KFSTYA+  +   I R + D    +++   +++  +K+ R          RE
Sbjct: 61  NFDLERNVKFSTYAVPLIMGEIKRFLRD-DGIVKVSRSLKEASYKIKREKEHYQKLYNRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSA 604
           PT +EIA  L M    +   ++  +E  SL   I     D  HL D +E        D  
Sbjct: 120 PTLKEIAVTLDMDESDILMAMESGQEVCSLHQVIYQSEGDEIHLEDKLE-----QQADLI 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            Q         +L  L  +E +++ MR+      + T   + K+  +++ ++ ++E K +
Sbjct: 175 EQTVDNIYVQELLKKLNEQERQIIHMRYF----QNQTQAAIAKKIGISQVQVSRMEKKIL 230

Query: 665 RKLKHPSRSK 674
            KL+  + +K
Sbjct: 231 NKLRKNANTK 240


>gi|168186139|ref|ZP_02620774.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
 gi|169295860|gb|EDS77993.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
          Length = 242

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + ++F DL+  G +GLM A  KFD   G KFSTYA 
Sbjct: 10  KEEIVKKYIPLVKYIASRVIIGKTKYIEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I   S    I     DK++K       +  K   EP  ++IA++L M V 
Sbjct: 70  IRIRGSMIDEIRKNS---PISKGAMDKLNKYNAAIENLQRKNLSEPNIKDIAQELDMTVS 126

Query: 562 GVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  D+D   L   IED N+  P +   +    E  ++ L 
Sbjct: 127 QVGEIENFINYISIVSLEDLIFSDDDDISLIGTIEDINSPDPEEEFERDEKLEYLSKGLD 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  ++  VL + +      + TL+E+GK   V+  R+ Q+ ++AI  L+ 
Sbjct: 187 MLNDKDRTVLSLYY----YEEMTLKEIGKVLGVSESRVCQLHSRAIVHLRK 233


>gi|325264312|ref|ZP_08131043.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030383|gb|EGB91667.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 288

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 115/260 (44%), Gaps = 13/260 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEK 487
            + + ++ G  EA     ++ + N   +  + +++  +G  +  DL+QEG I L +A   
Sbjct: 5   QLAARIQAGIDEAE-NMLQLWQQNEPFIRMMGRRFAGQGKAELDDLMQEGYIALCEAVRH 63

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD      F  YA +W+KQ + R I +   T+RIP H RD + +  +           +P
Sbjct: 64  FDSEQAVPFINYAAFWIKQGMKRYIENCCGTVRIPTHARDWVRRYGKIVAEYCKYYGSDP 123

Query: 548 TPEEIAKKLAMPVEG---VRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDS 603
             + +   L +  E    VRK   + K   SL  P+G ED   ++ +FI  +  +     
Sbjct: 124 EDDVLCALLNISREKLQAVRKSEHMGKIC-SLNEPLGQEDGDLNMEEFIASEEDLEGETV 182

Query: 604 A--IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                 N++E     +  L  ++  V+R RF        TL E G+   +T++ +   + 
Sbjct: 183 RRLDYQNMKEMLWEAVEGLEEKQAEVIRCRFLDH----KTLRETGELIGITKDAVVHQQN 238

Query: 662 KAIRKLKHPSRSKKLRSFLD 681
            A+R L  P R +K R + +
Sbjct: 239 NALRLLGQPGRCRKYRGYYE 258


>gi|310657328|ref|YP_003935049.1| RNA polymerase sigma-37 factor (sigma-b) [Clostridium sticklandii
           DSM 519]
 gi|308824106|emb|CBH20144.1| RNA polymerase sigma-37 factor (sigma-B) [Clostridium sticklandii]
          Length = 273

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 110/227 (48%), Gaps = 8/227 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V+ +L +   ++KK+ N+G+++ D+ Q  ++GL+ A E+FD   G++FS++A   +
Sbjct: 46  RNELVKRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIFAIERFDVSKGFEFSSFATPTI 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  +IR+P  +++   KV      +  ++ R P  E+IAK L    E V 
Sbjct: 106 IGEIKKYFRDKGWSIRVPRRIQELSKKVNTAKSYLQQELHRVPKIEDIAKYLDCTEEEVL 165

Query: 565 KVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + ++ +   +P SL+    +E        ++         + I+   ++     L+ L  
Sbjct: 166 EAIEASHVYKPKSLDLSYDNEGDDKDILLLDLVGDEDKSFNMIEN--KDFIENALSKLNE 223

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E ++++ RF       H    V     V++  + ++E K + KLK 
Sbjct: 224 IETKIIKDRFFKNKTQMH----VANDLGVSQMTVSRMEKKILAKLKK 266


>gi|169829726|ref|YP_001699884.1| RNA polymerase sigma-B factor [Lysinibacillus sphaericus C3-41]
 gi|168994214|gb|ACA41754.1| RNA polymerase sigma-B factor (Sigma-37) (General stress protein
           84) (GSP84) [Lysinibacillus sphaericus C3-41]
          Length = 261

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 118/240 (49%), Gaps = 14/240 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
               E   A+  +V     LV S+A+KY+N    + D++Q G +GL+ A  +FD  +G  
Sbjct: 22  YQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRS 81

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A+  +   I R + D++  + +P  +++   ++  T   ++ +++R P+ +EIA++
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKEIGPRIKTTVEALTIELQRSPSIQEIAER 141

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR 610
           L +  E V + +++++   +L      E  S      L D +  ++           + R
Sbjct: 142 LEVAEEEVLEAMEMSRSYQALSMDHSIESDSDGSTVTLFDILGREDD-----GYEMTDKR 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +  +  L  RE++++++ +        + +E G+Q  +++  + +I+ KAI+KL+  
Sbjct: 197 MIVSEAMVVLNEREKQIIQLTYL----EQLSQKEAGEQLGISQMHVSRIQRKAIKKLQEA 252


>gi|114777586|ref|ZP_01452567.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
 gi|114552057|gb|EAU54574.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
          Length = 243

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 96/231 (41%), Gaps = 15/231 (6%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E++E  L LV   A +   R    ++F DLI  G +GL+  A++FD     +F T+  +
Sbjct: 14  DELLEEYLPLVRYHADQLMRRTPDSIEFDDLINAGVLGLLDGAQRFDHSRDVQFKTFVSY 73

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+ A+   +         P  +RD   ++    +++     R     EIAK L + ++ 
Sbjct: 74  RVRGAMIDYLRAFDWM---PRGLRDHAKEMQTAFQQLEQVYGRPAEETEIAKHLNISLDE 130

Query: 563 VRKVLK--ITKEPISLET---PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            R  L    +   I  +        +D   + + +    A +P          +     +
Sbjct: 131 YRTRLTNVRSMSIIHFDDLPVNNDFDDEISILETLAGDPADTPEAQNSLMQFVQQLADGI 190

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + L  RE+ ++ + +      + T++E+     +T  R+ Q+ ++ + +L+
Sbjct: 191 SRLPAREQVLVTLYY----YEELTMKEIALILGLTESRVSQLHSQMVVRLR 237


>gi|126651479|ref|ZP_01723683.1| sigma factor B [Bacillus sp. B14905]
 gi|126591732|gb|EAZ85828.1| sigma factor B [Bacillus sp. B14905]
          Length = 261

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 118/240 (49%), Gaps = 14/240 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
               E   A+  +V     LV S+A+KY+N    + D++Q G +GL+ A  +FD  +G  
Sbjct: 22  YQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRS 81

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A+  +   I R + D++  + +P  +++   ++  T   ++ +++R P+ +EIA++
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKEIGPRIKSTVEALTIELQRSPSIQEIAER 141

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR 610
           L +  E V + +++++   +L      E  S      L D +  ++           + R
Sbjct: 142 LEVAEEEVLEAMEMSRSYQALSMDHSIESDSDGSTVTLFDILGREDD-----GYEMTDKR 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              +  +  L  RE++++++ +        + +E G+Q  +++  + +I+ KAI+KL+  
Sbjct: 197 MIVSEAMVVLNEREKQIIQLTYL----EQLSQKEAGEQLGISQMHVSRIQRKAIKKLQEA 252


>gi|254974392|ref|ZP_05270864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-66c26]
 gi|255091783|ref|ZP_05321261.1| RNA polymerase sigma-F factor [Clostridium difficile CIP 107932]
 gi|255099887|ref|ZP_05328864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-63q42]
 gi|255305776|ref|ZP_05349948.1| RNA polymerase sigma-F factor [Clostridium difficile ATCC 43255]
 gi|255313518|ref|ZP_05355101.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-76w55]
 gi|255516203|ref|ZP_05383879.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-97b34]
 gi|255649300|ref|ZP_05396202.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-37x79]
 gi|255654820|ref|ZP_05400229.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-23m63]
 gi|260682470|ref|YP_003213755.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260686069|ref|YP_003217202.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296449564|ref|ZP_06891341.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296878113|ref|ZP_06902128.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
 gi|306519396|ref|ZP_07405743.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-32g58]
 gi|260208633|emb|CBA61376.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260212085|emb|CBE02685.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296261628|gb|EFH08446.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296430866|gb|EFH16698.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
          Length = 254

 Score =  108 bits (268), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 117/241 (48%), Gaps = 7/241 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++ K +     AK+ ++ +NL LV SV  ++ N G    DL Q G+IGL+K+  KF
Sbjct: 18  ETLELIEKVQNGDEEAKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSIGLIKSIYKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   ++    K    +  ++ K+ REP+
Sbjct: 78  DPKFNVKFSTYAVPMILGEIKRYLRD-DGMIKVSRSLKQIAVKAKMESEALTKKLGREPS 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+AK + +  E +   ++       L+  I +E+ S +   + DK ++       +  
Sbjct: 137 IEELAKAIDVEKEDLVMAMEANFNVEYLQGVIHEEEGSPI--CLIDKISMKGESEEEKVV 194

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +L  L  RE +++ +R+      D T  E+G+   +++ ++ +IE K + KLK
Sbjct: 195 DNILLKDILGRLDKRERQIIVLRYF----EDMTQSEIGEMLNISQVQVSRIEKKVLSKLK 250

Query: 669 H 669
            
Sbjct: 251 E 251


>gi|295798118|emb|CAX68947.1| RNA polymerase sigma factor 70 [uncultured bacterium]
          Length = 259

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 108/248 (43%), Gaps = 15/248 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  +    + ++E+V   + LV  VA +        ++F DL+  G +GL  A EK+D  
Sbjct: 11  KYKQRRTKLLREEIVRKYMYLVKYVAGRVAIGLPSNVEFNDLVSYGLLGLFDAIEKYDVM 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA+  ++ AI   +         P  +R +  ++ + +R + ++  R  T +E
Sbjct: 71  QGNKFETYAVSRIRGAIMDELRKLDW---APRLLRKRAREIEKKSRELEDQFGRMATDDE 127

Query: 552 IAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDT---SHLGDFIEDKNAVSPLDSAIQ 606
           +A+ L M VE +        +   +SL+    ++D          +ED    +  +   Q
Sbjct: 128 LAQSLGMSVEDLNGIYSELNSTTFLSLDEVWQNDDGNKPISRLQTVEDSLITNQFNYVNQ 187

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +++     +  L  +E+ V+ + +        TL E+G    V+  R+ QI  K + +
Sbjct: 188 NEVKQLLAESIDLLPEKEKLVVVLYYYEN----LTLREIGDVLNVSESRVCQIHTKVVSR 243

Query: 667 LKHPSRSK 674
           L+     K
Sbjct: 244 LRSHLMKK 251


>gi|15642066|ref|NP_231698.1| flagellar biosynthesis sigma factor [Vibrio cholerae O1 biovar El
           Tor str. N16961]
 gi|121586929|ref|ZP_01676709.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121727398|ref|ZP_01680537.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|147674794|ref|YP_001217593.1| flagellar biosynthesis sigma factor [Vibrio cholerae O395]
 gi|153213706|ref|ZP_01948958.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|153821715|ref|ZP_01974382.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|153826072|ref|ZP_01978739.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|153828895|ref|ZP_01981562.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|227082193|ref|YP_002810744.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|229507844|ref|ZP_04397349.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229511920|ref|ZP_04401399.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229513722|ref|ZP_04403184.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229519056|ref|ZP_04408499.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229522025|ref|ZP_04411442.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229524074|ref|ZP_04413479.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229528916|ref|ZP_04418306.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229607389|ref|YP_002878037.1| flagellar biosynthesis sigma factor [Vibrio cholerae MJ-1236]
 gi|254226075|ref|ZP_04919673.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|254286814|ref|ZP_04961767.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|254849153|ref|ZP_05238503.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297579572|ref|ZP_06941500.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|298497906|ref|ZP_07007713.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|9656612|gb|AAF95212.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O1 biovar El Tor str. N16961]
 gi|121548865|gb|EAX58908.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121630290|gb|EAX62688.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|124115767|gb|EAY34587.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|125621387|gb|EAZ49723.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|126520813|gb|EAZ78036.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|146316677|gb|ABQ21216.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|148875601|gb|EDL73736.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|149740189|gb|EDM54342.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|150423105|gb|EDN15053.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|227010081|gb|ACP06293.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|227013963|gb|ACP10173.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|229332690|gb|EEN98176.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229337655|gb|EEO02672.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229340950|gb|EEO05955.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229343745|gb|EEO08720.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229348903|gb|EEO13860.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229351885|gb|EEO16826.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229355349|gb|EEO20270.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229370044|gb|ACQ60467.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MJ-1236]
 gi|254844858|gb|EET23272.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297537166|gb|EFH75999.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|297542239|gb|EFH78289.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|327484600|gb|AEA79007.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 101/227 (44%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R        DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 19  FLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +  ++ R+PT  E+AK L M +E   
Sbjct: 79  RGAMLDDIRRGDW---VPRSVHKHNREISQAIAVLEGELNRDPTDAEVAKFLNMSLEQYH 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VL      I+    +G ED     D I   E+    SP     + + R+     + SL 
Sbjct: 136 SVLM----DINCSRIVGIEDLGVSDDAISPFEEGEDNSPFHGVAEESFRKALVESIKSLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G+   V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQSMQRLR 234


>gi|321117386|dbj|BAJ72170.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 43/273 (15%), Positives = 82/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI--IGFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++ ++ E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEEREDDEXEDEESDDDSSDDDNSID--PELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L     D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKXFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   ++  I
Sbjct: 194 FKAALAMNKP-WSEXLNDVSDDVNRGLQKLXQI 225


>gi|302548084|ref|ZP_07300426.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302465702|gb|EFL28795.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 264

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 110/249 (44%), Gaps = 15/249 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + +EFR I ++    E EA   ++++V A + +   +A+++ NRG    DL Q   +GL+
Sbjct: 18  TSAEFRRIATLPEGPEREAL--RQDVVRAWMPMAERLARQFRNRGESAEDLRQVAMLGLV 75

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++++   G  F+++A+  V   I R   D    + +P  +++  ++V   A+ ++  
Sbjct: 76  KAVKRYEPDRGSAFASFAVPTVVGEIKRHFRDHMWGVHVPRRVQELRNRVRAAAQELTRT 135

Query: 543 -IKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAV 598
              R P+   I +   M  E V        +   +SL+  +   ED   L D +      
Sbjct: 136 PDDRSPSVSAIVEHTGMSEEDVLLGMEAMESFSALSLDAELPGAEDGYSLADTLG----- 190

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P  S  +   RE     L +L  RE  +L +RF          E    Q  +++  + +
Sbjct: 191 APEPSYDRVIQREALKPRLRALPERERHILYLRFFREETQGRIAE----QLGISQMHVSR 246

Query: 659 IEAKAIRKL 667
           +  +   +L
Sbjct: 247 LINRTCARL 255


>gi|157961206|ref|YP_001501240.1| flagellar biosynthesis sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846206|gb|ABV86705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella pealeana
           ATCC 700345]
          Length = 239

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 100/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+  FD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSNFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+    EIA++L + +E
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRVAQVIDELEQELGRDARDGEIAERLEVSLE 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D I  ED +     +S  +          +  
Sbjct: 130 EYHAIL----NDVSVGKVVGIEDLGVAADGINPEDGHEDDAYESLAEVEFHSALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|291196392|emb|CBG22668.1| DNA-directed RNA polymerase subunit D [Pseudomonas salomonii]
          Length = 238

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 48/284 (16%), Positives = 96/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEV 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                 +   + +   DD  E   D E   +   D                         
Sbjct: 59  PPPVDAKAAKADDDTEDDDAEASSDDEDEVESGPDPI----------------------I 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ DQ+            E+ R+            K  +S+         L +L
Sbjct: 97  AAQRFGAVSDQM------------EITRKALK---------KHGRSNKLAIAELVALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 136 FMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 TD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 238


>gi|326389454|ref|ZP_08211021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325994459|gb|EGD52884.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 98/230 (42%), Gaps = 15/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++   + LV  + KK     +   ++ DLI +G IGL+ A EK+    G KF TYA 
Sbjct: 21  RNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAIEKYQPSKGVKFETYAT 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +  +      P  ++ K  K+  T   +  K  REPT EEI +   +   
Sbjct: 81  LRIRGEIIDYLRRKDWM---PRSLKKKYKKIEETVETLQQKYNREPTVEEITEACGLNEI 137

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V K L         SLE  I +    H    +E KN        +   L+      + S
Sbjct: 138 DVLKTLSYINVSNVNSLEEAIENNFKLHAISNVELKNPEE---EVLYKELKRKLASAIES 194

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  +E  V+ + +      D   +++ K   +T  RI QI  KAI++++ 
Sbjct: 195 LPDKERLVITLYY----YEDLNYKDISKILNLTESRISQIHTKAIKRIRE 240


>gi|291196288|emb|CBG22615.1| DNA-directed RNA polymerase subunit D [Pseudomonas congelans]
          Length = 238

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 38/284 (13%), Positives = 91/284 (32%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + +    +  + + E +A  S ++      P             D+ +
Sbjct: 50  GIAPPAEVPPPVDPKAVKAEGADDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQME 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                     +     +  +  +AE++                                 
Sbjct: 110 ITRKALKKFGRDDKHAIAEMVALAELF--------------------------------- 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 137 -MPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I + + ++ ++  ETG+ I+E 
Sbjct: 196 TD-ALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEI 238


>gi|239929464|ref|ZP_04686417.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
          Length = 245

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 51/214 (23%), Positives = 104/214 (48%), Gaps = 10/214 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAA 485
           F   ++++ +G  E   A+  ++E N+ LV   A ++ +RG  +  D++Q G IGL+KA 
Sbjct: 34  FFRQLAVLEEGTPEYQYARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAI 93

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           ++F+     +F+++A+ ++   + R   D S ++ +P  +++   ++ R    +  ++ R
Sbjct: 94  DRFELSREVEFTSFAIPYIVGEMKRFFRDTSWSVHVPRRLQEARVQLARATEELRTRLGR 153

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
            PT  E+A+ +++  E V +           SL+  I    +  S L DFI  ++A   L
Sbjct: 154 TPTTRELAQLMSLTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFIGSEDAALEL 213

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
                A        ++A L  RE +++  RF   
Sbjct: 214 VEDFHA-----LAPMIAELDERERKIIHWRFVEE 242


>gi|254519401|ref|ZP_05131457.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
 gi|226913150|gb|EEH98351.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
          Length = 241

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 115/232 (49%), Gaps = 13/232 (5%)

Query: 443 IAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           I K+++VE  + LV  +A +      + +++ DL+  G +GL+ A  ++D   G KFS+Y
Sbjct: 8   IHKEQIVEKYIPLVKYLASRVMLGKTKYIEYEDLVSYGIVGLLDAINRYDSTKGMKFSSY 67

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   +K A+   I        I     DK+ K      ++ N+  REP+ +EIA +L + 
Sbjct: 68  ATLRIKGAMIDEIRKC---RPISKGAMDKLAKYNECVEKLQNRYMREPSLQEIALELNIS 124

Query: 560 VEGV--RKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            E V   +        ISLE+ I  +D    + + +EDKN++SP +S       E     
Sbjct: 125 EEEVSQVENYINYMSIISLESIIYSDDDDVTIMETLEDKNSISPEESLEDKEKLEILAEA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L  +++ +L + +        TL+E+G+   V+  R+ Q+ ++AIR L+
Sbjct: 185 IEKLKDKDKLILNLYY----YEKLTLKEIGQILEVSESRVCQLHSRAIRNLR 232


>gi|329937662|ref|ZP_08287181.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329303061|gb|EGG46949.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 327

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 115/250 (46%), Gaps = 14/250 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + S+F  + ++    E EA   + E+V A L +   +A ++ +RG    DL Q   +GL+
Sbjct: 70  TASDFARLAALEDGPEREAL--RDELVTAWLPMAHRIAGRFRDRGESLEDLRQVAALGLV 127

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +++D   G  F +YA+  +   I R   D+   +R+P  +++  +KV    R +   
Sbjct: 128 KAIDRYDCERG-AFESYAVPTITGEIKRHFRDRMWALRVPRRVQELRNKVRVARRELMQS 186

Query: 543 IK-REPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
               EP+  ++A+   +  E V   ++   +   +SL+  +  +D ++    + D   V+
Sbjct: 187 PGSPEPSAADVARHTGLTEEEVGTGMEALESFSTLSLDAAMSADDDAY---SLADTLGVA 243

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                +  + RE     L  L  RE  +L MRF      D T   +  +  +++  + ++
Sbjct: 244 EASYDVVVD-REAAKEGLRRLPERERAILYMRFF----QDMTQNRIADRLGISQMHVSRL 298

Query: 660 EAKAIRKLKH 669
            +++  +++ 
Sbjct: 299 ISRSCARVRE 308


>gi|148381038|ref|YP_001255579.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933259|ref|YP_001385409.1| sporulation sigma factor SigF [Clostridium botulinum A str. ATCC
           19397]
 gi|153935896|ref|YP_001388816.1| sporulation sigma factor SigF [Clostridium botulinum A str. Hall]
 gi|153939970|ref|YP_001392365.1| sporulation sigma factor SigF [Clostridium botulinum F str.
           Langeland]
 gi|170754271|ref|YP_001782722.1| sporulation sigma factor SigF [Clostridium botulinum B1 str. Okra]
 gi|226950516|ref|YP_002805607.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|148290522|emb|CAL84650.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929303|gb|ABS34803.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152931810|gb|ABS37309.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. Hall]
 gi|152935866|gb|ABS41364.1| RNA polymerase sigma-F factor [Clostridium botulinum F str.
           Langeland]
 gi|169119483|gb|ACA43319.1| RNA polymerase sigma-F factor [Clostridium botulinum B1 str. Okra]
 gi|226844449|gb|ACO87115.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|295320356|gb|ADG00734.1| RNA polymerase sigma-F factor [Clostridium botulinum F str. 230613]
 gi|322807388|emb|CBZ04962.1| RNA polymerase sporulation specific sigma factor SigF [Clostridium
           botulinum H04402 065]
          Length = 251

 Score =  108 bits (268), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 119/243 (48%), Gaps = 8/243 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   + ++ K       A  ++VE NL LV +++KK+ NRG ++ D+ Q G IGL+KA  
Sbjct: 13  FEDNMELMEKARSGNKEALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAIN 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F+     KFSTYA+  +   I R + D    I++   ++    K+     ++  ++ RE
Sbjct: 73  NFETKYNVKFSTYAVPMIMGEIKRFLRD-DGIIKVSRSIKTAAKKLHYDKEKLCKELNRE 131

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE+++     V+ +    + +  P  L   I  +D + +   I+  +  +  D+ I 
Sbjct: 132 PTIEELSQFSGYTVDEILMATESSSSPQYLYDVIHQDDGAPVL-LIDKISENTEEDNKIV 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N+       L +L  +  +++ +R+      D T  EV KQ  +++ ++ +IE K ++ 
Sbjct: 191 DNI--ALKEALKNLDIKSRQIIILRYF----KDKTQIEVAKQLGISQVQVSRIEKKVLKL 244

Query: 667 LKH 669
           +K 
Sbjct: 245 MKE 247


>gi|321117378|dbj|BAJ72166.1| RNA polymerase sigma-subunit [Erwinia sp. 'uzenensis']
          Length = 225

 Score =  107 bits (267), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 43/273 (15%), Positives = 82/273 (30%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I     + P +        E
Sbjct: 1   RIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLI--IGFVDPNA--------E 50

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                       E   ++ ++ E + E +   S DD + +D  PE A     +L    + 
Sbjct: 51  EDIAPTATHVGSELSAEEREDDEXEDEESDDDSSDDDNSID--PELAREKFGDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L     D LV  +  +  R+   E  +++L      + +  F+    G E +  W
Sbjct: 134 FKQFRLVPKXFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETNETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    D + +   ++  I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSDDVNRGLQKLXQI 225


>gi|197285477|ref|YP_002151349.1| flagellar biosynthesis sigma factor [Proteus mirabilis HI4320]
 gi|6959882|gb|AAF33246.1|AF221596_2 FliA [Proteus mirabilis]
 gi|194682964|emb|CAR43378.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           HI4320]
          Length = 240

 Score =  107 bits (267), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 109/237 (45%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + E  + LV   A +   +    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKNSLWERYVPLVRHEALRLQVKLPASVELDDLLQAGGIGLLNAVERYDSMQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R    +V ++  ++   + R P+ +E+A
Sbjct: 65  AAFTTYAVQRIRGSMLDELRSRDW---APRSVRRNAREVTQSIHQLEQDLGRPPSEQEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             L + +   R++L  T      S +        S      ED +  +PL   +++++R+
Sbjct: 122 DHLQIELAEYRQILLDTNNSQLFSYDEWHEIYGESCEPSQDEDHDD-NPLQMLLESDIRQ 180

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 181 RVIDAIELLPEREKMVLTLYYQ----EELNLKEIGAVLNVGESRVSQLHSQAIKRLR 233


>gi|192362157|ref|YP_001982606.1| FliA [Cellvibrio japonicus Ueda107]
 gi|190688322|gb|ACE86000.1| FliA [Cellvibrio japonicus Ueda107]
          Length = 247

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 99/228 (43%), Gaps = 13/228 (5%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           VE    LV  +A     R    +Q  DLIQ G IGL++A++K+D   G  F TYA   ++
Sbjct: 22  VEDYAPLVKRIAYHMMLRMPASVQVEDLIQAGMIGLIEASQKYDASRGASFETYAGIRIR 81

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            AI   +         P  +     ++ +    +  +  R+ +  EIA +L + ++   +
Sbjct: 82  GAIVDEMRRGDW---APRSVHRNGRRISQAMAAVEARTGRDASDTEIAAELDVGLDEYYQ 138

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLASLTPR 623
           +L+ +             +     D   D ++V  SPL+S  +  L+      +A L  R
Sbjct: 139 MLQDSSGSRLFSYEETFGEEDSNIDG-SDHSSVFASPLESIQRDGLKRALADAIALLPER 197

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           E  VL     +  + +  L+E+G    V+  RI QI ++A  +L+   
Sbjct: 198 ERLVL----ALYYDEELNLKEIGLVLGVSESRISQIHSQAAARLRQKM 241


>gi|116748823|ref|YP_845510.1| FliA/WhiG family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697887|gb|ABK17075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 279

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 103/229 (44%), Gaps = 14/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+ ++  +  LV  +A +  +R    +   DLI  G IGL+ A +K+D   G  F  YA 
Sbjct: 32  KELVILKHSDLVKHMALRLFSRLPDHVSIDDLISAGVIGLIDAVDKYDSGQGIPFKFYAK 91

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +R K + + RT   +  K+ R P+ E++A +L + +E
Sbjct: 92  IRIRGAMLDEIRAMDW---VPRSLRQKGNVLERTFSALEQKLGRCPSDEQVAGELNIGIE 148

Query: 562 GVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              ++L   K    L   I +   +    G    D   +     A +  ++      + +
Sbjct: 149 DYHRLLDEIKGISFLPENINEALLENGESGSLASDSEEL--FQHAYRQEIQRHLADAIRT 206

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LT +E+ VL + +      + T++EVG     T  RI QI  KAI KL+
Sbjct: 207 LTEKEQLVLSLYY----YDELTMKEVGTALGYTESRISQIHTKAIIKLR 251


>gi|239907027|ref|YP_002953768.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
 gi|239796893|dbj|BAH75882.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
          Length = 264

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 105/243 (43%), Gaps = 13/243 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + +   +  ++E+V      +  VA +   +    ++  +LI  G +GL++A  +F   L
Sbjct: 27  RWDDFDARDRQEIVRHYSPKIKIVASRLRAKLPPSVELNELISAGAMGLLEALGRFRPEL 86

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G KF TYA   +K A+   +             R ++  +   +RR+ N      + E++
Sbjct: 87  GIKFETYAESRIKGAMLDDLRRMDW---FSRGQRQRVRTLEEASRRIENDSGGPASLEQL 143

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+   +    V   L+  +  + L      E+ S      +++    P  SA    L + 
Sbjct: 144 AEATGLTEREVSMGLEALQNQLCLSLDAITENISSYQ---KNQLENEPYKSAEFKELVDK 200

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              ++  LTPRE+ VL + +G     +  + E  +   +T  R+ Q+ ++A+ +L+   +
Sbjct: 201 LASLIDDLTPREKLVLSLYYG----EELNMRETSEVMGITEGRVSQLHSQALARLRQKFK 256

Query: 673 SKK 675
           S+ 
Sbjct: 257 SQY 259


>gi|114562377|ref|YP_749890.1| flagellar biosynthesis sigma factor [Shewanella frigidimarina NCIMB
           400]
 gi|114333670|gb|ABI71052.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 239

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHMLARLPASVQLDDLLQAGMMGLLEASSKFDNSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I        +P  +      V      +   + R+    EIA+KL M ++
Sbjct: 73  IRIRGAMIDEIRRGDW---VPRSVHRNNRLVAHAIDELGQLLGRDANDTEIAEKLDMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D +  ++++     DS  +   +      + +
Sbjct: 130 EYHHIL----NDVSVGKIIGIEDLGVSQDVLITDNESPDETFDSLAEIQFQSALVEAIKT 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|326385162|ref|ZP_08206830.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196127|gb|EGD53333.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 250

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 103/226 (45%), Gaps = 11/226 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E + A L L   +A++Y  RG  F DL Q   +GL+ A ++FD   G  F ++A+  +
Sbjct: 30  RDEAIVACLPLARHIAQRYRERGEPFDDLEQVARLGLVHAVDRFDPTQGNDFLSFAVPTI 89

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D++ +IR+P    +   ++     ++     R P  +EIA  L    + + 
Sbjct: 90  IGEVRRHFRDRTASIRLPRSAIELRGRIREAEEQLEQTHGRTPDDDEIAAFLGESPDAIV 149

Query: 565 KVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +     I +  +SL+   GD++ + L + +    A  P  + ++  L       +  L  
Sbjct: 150 RARAADIAQSAVSLDAGAGDDERALLLELL---GADDPGYARVERCL--ALRPAVLRLPE 204

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+  ++ MRF        T  ++  +  +++  + ++ A ++ +L+
Sbjct: 205 RDRTIIGMRF----YEQRTQSDIACRMGISQMHVSRLLAASLGQLR 246


>gi|220911344|ref|YP_002486653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219858222|gb|ACL38564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 310

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 49/224 (21%), Positives = 102/224 (45%), Gaps = 11/224 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V   L L  ++A ++  RG +  DL Q   +GL+KAA  FD   G  F  YA   +   
Sbjct: 47  LVLGYLDLAEALAARFEARGRERADLNQVAYLGLVKAARGFDRSKGESFPAYAAPTITGE 106

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R + D++  +R P +++D   ++ R    ++  + R P+ EE+A +L      V++ +
Sbjct: 107 LKRYLRDRTWVVRPPRNIQDLRTRLFRAEPELTQALGRSPSVEELAGELETDPAAVQEAM 166

Query: 568 KIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +    P SL+    + D   +GD +   +         +          +  L P + 
Sbjct: 167 SASSSMHPDSLDAVNPNSDAPSIGDMLACPDTP-----LERLEELACLRDAMHDLAPADR 221

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +L  R+      + T  ++GK+  +++ ++ +  A+ + +L+H
Sbjct: 222 ELLYRRYFC----EETQVQLGKRLGMSQMQVSRRLARVLVELQH 261


>gi|149188355|ref|ZP_01866649.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837944|gb|EDL54887.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 290

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 119/279 (42%), Gaps = 15/279 (5%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             +S   + + + SIS    +S  + R + + V    C  S+   E++  +LR V  +AK
Sbjct: 9   NAESKDSLSHYLGSISKYPLLSEEKERTLANKVVTENCSQSL--NELILPHLRYVAYIAK 66

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
            +   G+  LD+IQ GN+GL+KA +KF+   G +  ++A+ W+K  I   I      +++
Sbjct: 67  NFVGYGMSTLDIIQAGNVGLIKAIKKFNPARGIRLVSFAIHWIKSEINEYIIKNWSMVKV 126

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPI 580
                 +         +  +    E   ++IAK L + V  V     +++ +   LE+  
Sbjct: 127 ATTKEQRKLFFNLRKHKNDSGWVSEEQAKDIAKNLKVRVRDVFVMDGRLSNKDKQLESHN 186

Query: 581 GDEDTSHLGDFIE--------DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
              D      + E        D  A +  +     +L       +  L  R + ++  R+
Sbjct: 187 Y--DEEFHCPYTEDNYFREHRDDFADNHEEENWSNHLSSELKIAIQKLDERSKDIIFHRW 244

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               N   TL E+  +  ++ ERIRQIE   + KLK+  
Sbjct: 245 L--TNEKATLSELADKHQLSAERIRQIEVATLAKLKNLM 281


>gi|46581631|ref|YP_012439.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120601210|ref|YP_965610.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           vulgaris DP4]
 gi|46451054|gb|AAS97699.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120561439|gb|ABM27183.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           vulgaris DP4]
 gi|311235273|gb|ADP88127.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio vulgaris RCH1]
          Length = 265

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 104/242 (42%), Gaps = 13/242 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               A   K+ +V      +  +A +      R ++  +LI  G +GLM+A  KF   LG
Sbjct: 28  WPDFAPAEKEAIVRHYAPKIRFLALRLKAKLPRNVELGELISAGTLGLMEALGKFKPQLG 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F TYA   ++ A+   +         P  +R ++ ++    +R+ ++  R  T E++ 
Sbjct: 88  IRFETYAESRIRGAMLDELRRLDWF---PRSLRQRVRQLDEAMQRIEHETGRRATEEDLQ 144

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K   +  + VR  L+  +  + L      +  +  G    D     P+ +A    L E  
Sbjct: 145 KATGLDEKDVRLGLEALQNQLCLSLEAMQDSLAGEGGPQSD---ADPMQTAATQELIERV 201

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             ++  LTPRE+ VL + +      +  + E  +   +T  R+ Q+ ++A+ +L+   R+
Sbjct: 202 ASLIDELTPREKLVLSLYYS----DELNMRETAEVMGITEGRVSQLHSQALGRLRREFRN 257

Query: 674 KK 675
             
Sbjct: 258 HY 259


>gi|168179581|ref|ZP_02614245.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|168181777|ref|ZP_02616441.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|170761116|ref|YP_001788407.1| sporulation sigma factor SigF [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237796543|ref|YP_002864095.1| sporulation sigma factor SigF [Clostridium botulinum Ba4 str. 657]
 gi|169408105|gb|ACA56516.1| RNA polymerase sigma-F factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182669805|gb|EDT81781.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|182675139|gb|EDT87100.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|229260985|gb|ACQ52018.1| RNA polymerase sigma-F factor [Clostridium botulinum Ba4 str. 657]
          Length = 251

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 119/243 (48%), Gaps = 8/243 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   + ++ K       A  ++VE NL LV +++KK+ NRG ++ D+ Q G IGL+KA  
Sbjct: 13  FEDNMELMEKARSGNKEALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAIN 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F+     KFSTYA+  +   I R + D    I++   ++    K+     ++  ++ RE
Sbjct: 73  NFETKYNVKFSTYAVPMIMGEIKRFLRD-DGIIKVSRSIKTAAKKLHYDKEKLCKELNRE 131

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE+++     V+ +    + +  P  L   I  +D + +   I+  +  +  D+ I 
Sbjct: 132 PTIEELSQFSGYTVDEILMATESSSSPQYLYDVIHQDDGAPVL-LIDKISENTEEDNKII 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N+       L +L  +  +++ +R+      D T  EV KQ  +++ ++ +IE K ++ 
Sbjct: 191 DNI--ALKEALKNLDIKSRQIIILRYF----KDKTQIEVAKQLGISQVQVSRIEKKVLKL 244

Query: 667 LKH 669
           +K 
Sbjct: 245 MKE 247


>gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana]
          Length = 498

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 124/229 (54%), Gaps = 9/229 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + ++    E  +A++++  +N+RLV+S+A++Y N G +  DL+Q G IGL++  EKFD  
Sbjct: 247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 306

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++ STY  WW++Q ++R++ D S T+R+P H+ +++  +     R+  +    P+ + 
Sbjct: 307 KGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRL-QEKGITPSIDR 365

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD----FIEDKN-AVSPLDSAIQ 606
           IA+ L M  + VR   +   +  SL+           G+    +I D     +P      
Sbjct: 366 IAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDD 425

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             L+E  ++++ A+L  RE+ ++R+ +G+      T E++ K+  + RE
Sbjct: 426 LALKEEVSKLISATLGEREKEIIRLYYGLDK-ECLTWEDISKRI-IERE 472


>gi|291545019|emb|CBL18128.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 220

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 103/220 (46%), Gaps = 14/220 (6%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E NL LV   A ++  RG+++ DL   G IGLMKA   FD   G +FSTYA+  +   I 
Sbjct: 11  EENLGLVHLCANRFRGRGVEYDDLYSAGCIGLMKAVNAFDTERGVRFSTYAVPVILGEIK 70

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R   D   T+++   M++   +VVR    +  +  +EPT +++A+++ +    + + L +
Sbjct: 71  RLFRDGG-TVKVSRSMKELSMRVVRLRDELRMQSGKEPTVQQLAREMGVEEAEIVQALCV 129

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +  P+SL       D    G+   D     P              +++ +L+ R+  +L 
Sbjct: 130 SVPPVSL------TDPGESGEGQLDIPVPPPDTEIGDVL---ALRQIMQTLSERDRMLLT 180

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           MR+      + T  +  +   +T+ ++ + E K +  ++ 
Sbjct: 181 MRY----YQNKTQSQTAQALGMTQVQVSRREKKLLLTMRE 216


>gi|119715356|ref|YP_922321.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119536017|gb|ABL80634.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 244

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 105/243 (43%), Gaps = 28/243 (11%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ----FLDLIQEGNIGLMKAAEKFDW 490
           R  +     A+  +V     LV  VA +    GL       DL+ +G IGL+ A +KFD 
Sbjct: 15  RFKQDGDREARDRLVVHYSPLVKFVAGR-VRSGLPPAVEHADLVSDGVIGLLDALDKFDP 73

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +F TYA+  ++ A+   +        +P  +R+KI  +      +  ++ R P   
Sbjct: 74  ERGLQFQTYAVSRIRGAMVDGLRAADW---VPRSVREKIRDINTAQTELERRLGRAPKDA 130

Query: 551 EIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQ 606
           E+A +L + V  +RK+   T     +S ET + +EDT      +   D +      +A++
Sbjct: 131 EVADRLGISVGDLRKIYSQTAHTSVVSFETVLDEEDTPRATTDLPGADDDIPPGFLAAVR 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
                        L  R++ V+ + +        TL E+G+   V+  R+ Q+ ++A   
Sbjct: 191 E------------LPERDQVVVALYYW----ERLTLAEIGQVLGVSESRVSQLHSRATLA 234

Query: 667 LKH 669
           L+ 
Sbjct: 235 LRR 237


>gi|67922879|ref|ZP_00516377.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
 gi|67855303|gb|EAM50564.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
          Length = 260

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 105/228 (46%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE NL LV  VA + +N+    + DL Q G +G ++A E+F+   G  FS++ + +
Sbjct: 31  RNQLVECNLGLVRQVAHRISNQCSEPYEDLEQIGYLGFIRAIERFNPQQGCAFSSFDIPY 90

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+   +RIP   ++  +K  +  ++++  +KR P   EIA+ L +P+E  
Sbjct: 91  IRGEMLHYLRDKGSVMRIPRRWQELHNKGKKIRKQLTASLKRSPFDWEIAEALMIPLEEW 150

Query: 564 RKVLKI--TKEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +       +  +SL+  I       L  GD + D++  +          R    R L  
Sbjct: 151 NECQLALQNRLLVSLDATISHNMDCSLSFGDTLPDQHYQAKQRLEED---RLQLQRALGQ 207

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  + +  +   F      +   +E  KQ  ++   + +   K I++L
Sbjct: 208 LEDKTKAAIECVFL----NELPRKEAAKQIGISPMTVTRHLKKGIQQL 251


>gi|319937136|ref|ZP_08011543.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807502|gb|EFW04095.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 259

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 64/256 (25%), Positives = 116/256 (45%), Gaps = 10/256 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           I     +S  E  +++   +  +      K+++V +NL+LV+S+ +KY  R     DL Q
Sbjct: 13  IQEYEKLSHQETMNLLD--QYHQTNDENIKEKLVLSNLKLVLSLVQKYHQRVSNLDDLFQ 70

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA + FD  L  +FSTYA+  +   I R I D S  +RIP  MRD  +K +  
Sbjct: 71  VGVIGLIKAIDHFDTSLDVRFSTYAVPLIIGEIKRYIRDNS-PMRIPRSMRDLAYKALLA 129

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
                 K  +E + +E++K L +    + + L  T    SL   + ++    +     + 
Sbjct: 130 NEEYMKKHHKEASTKELSKILDVDEFLLVEALSSTNSVTSLSQEVQNDGNGQID---LES 186

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                 +              +  L  +E +++  R+  G    HT  E+ K+  +++ +
Sbjct: 187 QIPDRKNQMEDMQNSIDLYEAMNHLDEKELQIINERYFKG----HTQSEIAKELFISQAQ 242

Query: 656 IRQIEAKAIRKLKHPS 671
           + +IE +A+  LK   
Sbjct: 243 VSRIEKQALSHLKKYM 258


>gi|294339807|emb|CAZ88170.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Thiomonas sp. 3As]
          Length = 250

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 106/245 (43%), Gaps = 10/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ G   A   ++E +  +L +V  +A +   +    + F DL Q G IGL  A ++ + 
Sbjct: 1   MKPGLYPAPETREERLSKHLPMVRRIAGQMAAQLPASVDFSDLEQAGMIGLWDALDRGEM 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +F+TYA   ++ AI   +        +P   R K  ++ R  + ++ ++ R P   
Sbjct: 61  QSPAQFATYAAIRIRGAIYDELRKLDW---LPRRSRAKERQIERAEQLLTQRLGRHPEDG 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  L   +      L  T   +     +  +D     D   D+ ++ P +    A L 
Sbjct: 118 ELAAHLGWELAEYYDALAETSMQLVYLEDLTHDDGGDYADRKADEASLLPEELLQDAQLE 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +A L  RE+ VL + +      D  L+++G+   V+  R+ Q+  +A+ +L+  
Sbjct: 178 RDLQAAIADLPEREKLVLSLYY----QEDLQLKDIGRVLEVSESRVSQLMKQAVMRLRAR 233

Query: 671 SRSKK 675
            ++ +
Sbjct: 234 LQAHQ 238


>gi|296121398|ref|YP_003629176.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
 gi|296013738|gb|ADG66977.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
          Length = 259

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 108/260 (41%), Gaps = 18/260 (6%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIG 480
           + E    V    K +  +   +  ++E  L LV   A++  ++   G+   DLI  G  G
Sbjct: 5   VIEDIQAVWNAYKQDQSSKALRNRLMENYLPLVRYNAERVWSKLPDGVDINDLISAGVFG 64

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           LM A E FD   G KF TY +  ++ A+   +        +P  +R K  K+    ++  
Sbjct: 65  LMDAIEAFDMERGVKFETYCVPRIRGAMLDELRTMDW---VPRLVRSKASKLESARKQAE 121

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDED---TSHLGDFIEDK 595
            ++ R P   E+A K+ +P++   K+         +SL     + D        D IED 
Sbjct: 122 AELGRPPADNEVAAKMGVPLDEYEKLKSEASAVNLVSLNKKWYETDSYKDVREIDIIEDT 181

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               P  S  + +L +  T+ L        R  R+   +    + T++E+G    ++  R
Sbjct: 182 KGEDPTLSIQKRDLMKLVTKGLN-------RNERLIIILYYYEELTMKEIGSTLGLSESR 234

Query: 656 IRQIEAKAIRKLKHPSRSKK 675
           + Q+ +  + +LK     ++
Sbjct: 235 VSQMHSSIVNRLKEQLGRRR 254


>gi|290879080|emb|CBK39764.1| sigma factor of RNA polymerase [Pseudomonas moorei]
          Length = 238

 Score =  107 bits (267), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 37/282 (13%), Positives = 92/282 (32%), Gaps = 48/282 (17%)

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           M+++   P T   ++     +      L +++            G+    +G +    E 
Sbjct: 1   MSAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAAEV 49

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                 +    + + D + A     ++ ++    P  A      + +  + +   L    
Sbjct: 50  PPPIDPKAVKADDDSDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKAL---- 105

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                          +K  + +         L  L   + L   
Sbjct: 106 -------------------------------KKHGRHNKAAIAELLALADLFMPIKLVPK 134

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A    +
Sbjct: 135 QFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD-ALAKGK 193

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
            ++   +      I++ + ++ ++  ETG++I+E + I   +
Sbjct: 194 SKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRM 235


>gi|226326542|ref|ZP_03802060.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
 gi|225205141|gb|EEG87495.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
          Length = 244

 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 107/237 (45%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + E  + LV   A +   +    ++  DL+Q G IGL+ A E++D   G
Sbjct: 9   YTAEGVMDKNSLWERYVPLVRHEALRLQVKLPASVELDDLLQAGGIGLLNAVERYDSMQG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ ++   +  +      P  +R    +V  +  ++   + R P  +E+A
Sbjct: 69  AAFTTYAVQRIRGSMLDELRSRDW---APRSVRRNAREVTHSIHQLEQDLGRPPLEQEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
             L + +   R++L  T      S +        S      ED +  +PL   +++++R+
Sbjct: 126 DHLQIELAEYRQILLDTNNSQLFSYDEWHEIYGESCEPSQDEDHDD-NPLQMLLESDIRQ 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 185 RVIDAIELLPEREKMVLTLYYQ----EELNLKEIGAVLNVGESRVSQLHSQAIKRLR 237


>gi|126698352|ref|YP_001087249.1| RNA polymerase sigma-F factor [Clostridium difficile 630]
 gi|115249789|emb|CAJ67606.1| RNA polymerase sigma-F factor [Clostridium difficile]
          Length = 254

 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 117/241 (48%), Gaps = 7/241 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++ K +     AK+ ++ +NL LV SV  ++ N G    DL Q G+IGL+K+  KF
Sbjct: 18  ETLELIEKVQNGDEEAKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSIGLIKSIYKF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   ++    K    +  ++ K+ REP+
Sbjct: 78  DPKFNVKFSTYAVPMILGEIKRYLRD-DGMIKVSRSLKQIAIKAKMESEALTKKLGREPS 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+AK + +  E +   ++       L+  I +E+ S +   + DK ++       +  
Sbjct: 137 IEELAKAIDVEKEDLVMAMEANFNVEYLQGVIHEEEGSPI--CLIDKISMKGESEEEKVV 194

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                  +L  L  RE +++ +R+      D T  E+G+   +++ ++ +IE K + KLK
Sbjct: 195 DNILLKDILGRLDKRERQIIVLRYF----EDMTQSEIGEMLNISQVQVSRIEKKVLSKLK 250

Query: 669 H 669
            
Sbjct: 251 E 251


>gi|299538306|ref|ZP_07051591.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
 gi|298726508|gb|EFI67098.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
          Length = 261

 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 117/240 (48%), Gaps = 14/240 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
               E   A+  +V     LV S+A+KY+N    + D++Q G +GL+ A  +FD  +G  
Sbjct: 22  YQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRS 81

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A+  +   I R + D++  + +P  +++   ++  T   ++ +++R P+ ++IA++
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKELGPRIKSTVEALTIELQRSPSIKDIAER 141

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQANLR 610
           L +  E V + +++++   +L      E  S      L D +  ++           N R
Sbjct: 142 LEVAEEEVLEAMEMSRSYQALSMDHSIESDSDGSTVTLFDILGREDD-----GYEMTNQR 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 L  L  RE++++++ +        + +E G++  +++  + +I+ KAI+KL+  
Sbjct: 197 MIVQDALVVLNEREKQIIQLTYL----EQLSQKEAGERLGISQMHVSRIQRKAIKKLQEA 252


>gi|288802544|ref|ZP_06407983.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288335072|gb|EFC73508.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 257

 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 119/264 (45%), Gaps = 43/264 (16%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I+ I+ E  +S  E + +   ++      + A +++ +ANL+ V+S+A +Y NRGL  
Sbjct: 35  KYIEDIANEQLLSDKEEQDLAEKIK---VGDARALEKLTKANLKFVVSLAHQYHNRGLGE 91

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I                  
Sbjct: 92  DDLISEGNIGMMYAAQKFDGSKGVRFVVFAAPYIRKAMEEAI------------------ 133

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHL 588
                              +E A    +P     +  +     IS++ P+     +   L
Sbjct: 134 -------------------KEQATLYKLPKNETSRFEQKRSHAISIDQPVPVGSNNNFTL 174

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              +E++NA    +   Q  L     + L  L  RE+RV+   +G+     +T+ E+ + 
Sbjct: 175 QHILENENAKHADEHLNQEILSNEIQKGLDVLDEREKRVITYIYGL-TGAHYTMAEIAED 233

Query: 649 FCVTRERIRQIEAKAIRKLKHPSR 672
             + RER+RQI  KA+RKL    +
Sbjct: 234 MGLKRERVRQIRDKALRKLHKKMK 257


>gi|324999864|ref|ZP_08120976.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 271

 Score =  107 bits (267), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 112/248 (45%), Gaps = 14/248 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            + R +  M         + +  ++ A L L  +++++Y        D+ Q   +GL+KA
Sbjct: 31  PDLRRLAGMDPADPARGPL-RDRVICAFLPLARNLSRRYVTGVHSADDVEQAATLGLIKA 89

Query: 485 AEKFDWCLGYKFS-TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            +++D  +       Y +  V+  + R + D S  +R+P  ++++   + R A  ++ ++
Sbjct: 90  VDRYDPDVATGGPLGYLVPCVRGELMRYLRDHSWALRVPRDLKERSVGLNRAAVTLTQRL 149

Query: 544 KREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            R P P E+A +L +    V + L    +   +SL+ P G +  + LG+ + + +     
Sbjct: 150 GRAPRPSELASELDVDTSEVVEALGAMESYNAVSLDEP-GPDGETTLGERLGEDDGA-LE 207

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            + ++  LRE        L  RE R+L +RF        T  E+ +   V++  + ++  
Sbjct: 208 GAPVRTELRERIGE----LPERERRILLLRFYGN----RTQSEIAEDIGVSQMHVSRLLT 259

Query: 662 KAIRKLKH 669
           + +  L+H
Sbjct: 260 RTVATLRH 267


>gi|288553039|ref|YP_003424974.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
 gi|288544199|gb|ADC48082.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 257

 Score =  107 bits (266), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 109/244 (44%), Gaps = 18/244 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +        A  E++   + +V    ++ +    + +   DL   G +GL  A EKF+  
Sbjct: 15  KWLTSRDLDACDELIRLYMPIVNYHVQRISVGLPKNVSKDDLTSHGMLGLYDALEKFNPN 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + V+ AI   +  +     +P  MR+KI +V    +++  +  R  + +E
Sbjct: 75  RDLKFDTYASFRVRGAIIDGLRKEDW---LPRSMREKIKRVEACIQQLEQEFGRNVSAKE 131

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS------HLGDFIEDKNAVSPLDS 603
           +  KL MP E V +++        +S++    D D S           + DK   +P +S
Sbjct: 132 VGVKLDMPEEEVYQIMNEHYLSNLLSIDERTNDSDRSDSNNSASYSATLIDKQTKTPEES 191

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +   ++E   + +  L+  E+ V+ + +      + TL E+G    ++  RI QI +KA
Sbjct: 192 LMFEAVKEELIKGINRLSENEKLVISLFYF----DELTLTEIGHILNLSTSRISQIHSKA 247

Query: 664 IRKL 667
           + ++
Sbjct: 248 LFRM 251


>gi|15618277|ref|NP_224562.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           CWL029]
 gi|15835895|ref|NP_300419.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           J138]
 gi|16752677|ref|NP_444944.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           AR39]
 gi|33241705|ref|NP_876646.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           TW-183]
 gi|4376638|gb|AAD18506.1| Sigma-28/WhiG Family [Chlamydophila pneumoniae CWL029]
 gi|7189319|gb|AAF38240.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
 gi|8978734|dbj|BAA98570.1| sigma-28/WhiG family [Chlamydophila pneumoniae J138]
 gi|33236214|gb|AAP98303.1| transcription initiation factor sigmaD protein [Chlamydophila
           pneumoniae TW-183]
 gi|269303237|gb|ACZ33337.1| RNA polymerase sigma factor, FliA [Chlamydophila pneumoniae LPCoLN]
          Length = 257

 Score =  107 bits (266), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 98/234 (41%), Gaps = 18/234 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +  ++E  L LV SV  +    G+       DL   G  GL++A E+++     +F  YA
Sbjct: 25  RDSLIEFYLPLVKSVVHR-LISGMPSHVKTEDLYASGVEGLVRAVERYNPERSRRFEGYA 83

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++ +K AI   +  Q     +P  +  K +K+      +   + +EPT  E+ + L +  
Sbjct: 84  VFLIKAAIIDDLRKQDW---VPRSVHQKANKLSGAMDSLRQSLGKEPTDLELCEYLNISQ 140

Query: 561 EGVRKVLKITKEP--ISLETPIGDEDT----SHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           + +       +    +SL      +        L + I D+ A +  D   +        
Sbjct: 141 QELSGWFVSARPALIVSLNEEWPSQSDEGAGMALEERIPDERAETGYDVVDKQEFSLCLA 200

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  +E +V+     +    +  L+E+GK   V+  R+ QI +KA+ KL+
Sbjct: 201 NAIQELEEKERKVM----ALYYYEELVLKEIGKVLGVSESRVSQIHSKALLKLR 250


>gi|89902470|ref|YP_524941.1| sigma 28 (flagella/sporulation) [Rhodoferax ferrireducens T118]
 gi|89347207|gb|ABD71410.1| sigma 28 (Flagella/Sporulation) [Rhodoferax ferrireducens T118]
          Length = 238

 Score =  107 bits (266), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 101/245 (41%), Gaps = 13/245 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  M+     LV  +A     +    ++  DLIQ G IGL +A  +++   
Sbjct: 1   MYTAKGQLDRNAMIRQYQPLVRRLAHHMMAKLPANVEVDDLIQVGLIGLSEALTRYEAAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   +             R     + +  RR+ +K+ R P   EI
Sbjct: 61  GVQFETFATQRIRGAMLDELRGNDWM---SRGSRKSQKDIEQALRRLEHKLGRTPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A  L + +   + +L      + + LE     +++     D     +   P++      L
Sbjct: 118 AADLGLSLVDYQTLLGKVRGTQLVYLEDMARGNDEEDSFLDRHVGDSDADPMNVLRDQRL 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     + +L  RE+ ++ M +      D  L+E+     VT  RI Q+ +++I +L+ 
Sbjct: 178 RQALVAAIKNLPEREQFIMSMYY----EQDMNLKEIAAVLDVTESRICQLHSQSIARLRA 233

Query: 670 PSRSK 674
             R+ 
Sbjct: 234 KMRAH 238


>gi|317153074|ref|YP_004121122.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316943325|gb|ADU62376.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 261

 Score =  107 bits (266), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 109/252 (43%), Gaps = 14/252 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMK 483
           +R + +  +  +  +S  ++++       +  +A +      + ++  +LI  G++GL+ 
Sbjct: 18  WRELENGAKNWDDFSSRDREDIARFYAPKIRILALRLKAKLPQSVELNELISAGSLGLLD 77

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  K++   G KF TY+   +K A+   +            +R K+  +    R++ ++ 
Sbjct: 78  ALGKYNAQRGIKFDTYSENRIKGAMLDELRRMDWF---SRGLRQKVKALEDAQRQVEHET 134

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
               T E++     M  + VR+ L+     + L      E+        ED+    P  S
Sbjct: 135 GGPATTEQLQALTGMSEKDVRQGLEALHNQMCLSLDSFHENVIGRKAMTEDE----PFQS 190

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                + +    ++  LTPRE+ V+ + +G     +  ++E  +   +T  R+ Q+ ++A
Sbjct: 191 TAFQEIVDKVASLIEELTPREKLVISLYYG----EELNMKETAEVMDITEGRVSQLHSQA 246

Query: 664 IRKLKHPSRSKK 675
           + KL+   R++ 
Sbjct: 247 LTKLRKTFRARY 258


>gi|296135638|ref|YP_003642880.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thiomonas
           intermedia K12]
 gi|295795760|gb|ADG30550.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thiomonas
           intermedia K12]
          Length = 250

 Score =  107 bits (266), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 106/245 (43%), Gaps = 10/245 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++ G   A   ++E +  +L +V  +A +   +    + F DL Q G IGL  A ++ + 
Sbjct: 1   MKPGLYPAPETREERLSKHLPMVRRIAGQMAAQLPASVDFSDLEQAGMIGLWDALDRGEM 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +F+TYA   ++ AI   +        +P   R K  ++ R  + ++ ++ R P   
Sbjct: 61  QSPAQFATYAAIRIRGAIYDELRKLDW---LPRRSRAKERQIERAEQLLTQRLGRHPEDG 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  L   +      L  T   +     +  +D     D   D+ ++ P +    A L 
Sbjct: 118 ELAAHLGWELAEYYDALAETSMQLVYLEDLTHDDGGDYADRKADEASLLPEELLQDAQLE 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +A L  RE+ VL + +      D  L+++G+   V+  R+ Q+  +A+ +L+  
Sbjct: 178 RDLQAAIADLPEREKLVLSLYY----QEDLQLKDIGRVLEVSESRVSQLMKQAVMRLRAR 233

Query: 671 SRSKK 675
            ++ +
Sbjct: 234 LQAHQ 238


>gi|254478671|ref|ZP_05092042.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035358|gb|EEB76061.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 215

 Score =  107 bits (266), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 62/221 (28%), Positives = 109/221 (49%), Gaps = 12/221 (5%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
             N  L+ S+ KK+ NRG +  DL Q G IG +KA +KFD     KFSTYA+  +   I 
Sbjct: 1   MENSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAVQKFDESYNVKFSTYAVPIIMGEIK 60

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R + D    I++   +++   K       +SN++ REPT  EIA++L +  E +    + 
Sbjct: 61  RFLRD-DGLIKVSRSLKELSSKAFYMKEVLSNELNREPTINEIAERLNVTPEEIAMAFES 119

Query: 570 TKEPISL-ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
                SL ++   +E+   L + + DK        ++    + T   ++  L PRE++V+
Sbjct: 120 AATAESLYDSISHEEEDRQLIEMVGDKE------DSVDLEEKLTLHMIIDKLKPREKQVI 173

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +R+      D T  EV     +++ ++ +IE K + K++ 
Sbjct: 174 FLRYF----KDMTQTEVANILGISQVQVSRIEKKVLEKIRK 210


>gi|119897398|ref|YP_932611.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
 gi|119669811|emb|CAL93724.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 256

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 110/238 (46%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + E ++ K  +V A   LV  +A +   +    ++  DLIQ G +GL+ A  +++  L
Sbjct: 1   MYDAEGNLDKDHLVVAYAPLVKRIAFQLMAKLPASVEVEDLIQNGMMGLLDAIGRYEEGL 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA+  V+ A+   + +      +P  +R  + ++      +  +  R P+  E+
Sbjct: 61  GAQFETYAVQRVRGAMLDGLRENDW---LPRSLRRDMRRIESAIHVLEQQHGRPPSETEL 117

Query: 553 AKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ L +P+   +++L+     + +  E     E    L   +    + +P +    A++R
Sbjct: 118 AESLGVPLPEYQRMLQDARGHQLVYFEDFTDGEGEDFLDRHLGAHES-NPAELLEDADMR 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               R +  L  RE+ V+     +    +  L E+G+   VT  R+ Q+ ++A+ +L+
Sbjct: 177 ANLIRAIDDLPEREKLVM----ALYYEEELNLREIGEVLGVTESRVCQLHSQAVARLR 230


>gi|124300771|dbj|BAF45883.1| RNA polymerase sigma-subunit [Erwinia amylovora]
          Length = 225

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 38/273 (13%), Positives = 69/273 (25%), Gaps = 49/273 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +  S+ E P     L+   D +  G   L ++I        E          
Sbjct: 1   RIEDGXNQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATHV 60

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G      E    E E                            PE A     +L    + 
Sbjct: 61  GSELSAEERDDDEDED------------EESDDDSSDDDNSJDPELAREKFNDLRIQYET 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   + A                                     +S        + L  +
Sbjct: 109 TRTVIKAK-----------------------------------SRSHADAIAEIQNLSDV 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
                L   + D LV  +  +  R+   E  +++L      + +  F+    G E    W
Sbjct: 134 FKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNFITLFTGNETSETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
              A    +  W   +    + + +   +++ I
Sbjct: 194 FKAALAMNKP-WSEKLNDVSEDVNRGLQKLQQI 225


>gi|297584063|ref|YP_003699843.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
 gi|297142520|gb|ADH99277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
          Length = 253

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 107/240 (44%), Gaps = 13/240 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             E     A   ++EA L LV     +   +  + +   DL   G +GL  A EKFD   
Sbjct: 17  WEEKRDRSAGDRLIEAFLPLVDYHVHRIGVHLPKNVSSDDLRSHGLMGLFDALEKFDRKR 76

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA + ++ AI   +  +     +P  +RDK  K+ +    +  ++ R  +P+EI
Sbjct: 77  ELKFDTYASFRIRGAIIDGLRQEDW---LPRTLRDKAKKIEQVTESLEQQLGRNVSPKEI 133

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGD-EDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A +  +    V K          +S++ P  + + T      I D+  ++P +S  +   
Sbjct: 134 ADEAGLTEADVIKTSNENFFSHLLSIDEPTQEGDQTETYASSIADQQTLTPAESLSKQAD 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +     + +L  +E+ V+ + +      + TL E+G+   ++  RI QI +KA+ KL+ 
Sbjct: 194 YDELADAIQNLNEKEQLVISLFY----YEELTLTEIGEALSLSTSRISQIHSKAVYKLQQ 249


>gi|330828816|ref|YP_004391768.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803952|gb|AEB49151.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 225

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 97/235 (41%), Gaps = 17/235 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA   +
Sbjct: 2   LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIRI 61

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +      +      +     R+    E+A ++ + +    
Sbjct: 62  RGAMLDEIRRGDW---VPRSVHRNSRAIAEAIENVEQTHGRDARDTEVAAEMGVSIADYH 118

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +L+     +S    IG ED     D I   +D  + S  D       +   +  +  L 
Sbjct: 119 AMLQ----DVSCGKIIGIEDLGVSEDVIGHPDDAPSGSGFDELAAERFQIQLSEQIGRLP 174

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ +L+   R   L
Sbjct: 175 EREALVLSLYY----DEELNLREIGEVLNVSESRVSQIHSQAMHRLRARLRDWHL 225


>gi|289550312|ref|YP_003471216.1| RNA polymerase sigma factor SigB [Staphylococcus lugdunensis
           HKU09-01]
 gi|315660227|ref|ZP_07913082.1| RNA polymerase sigma-B factor [Staphylococcus lugdunensis M23590]
 gi|289179844|gb|ADC87089.1| RNA polymerase sigma factor SigB [Staphylococcus lugdunensis
           HKU09-01]
 gi|315494654|gb|EFU82994.1| RNA polymerase sigma-B factor [Staphylococcus lugdunensis M23590]
          Length = 256

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 120/247 (48%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ + + ++ A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQEDKSTEAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDISFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SITEIANRLEVTEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    R+L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILERILPILSEREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  ++
Sbjct: 249 KLQQAAK 255


>gi|271964601|ref|YP_003338797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270507776|gb|ACZ86054.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 258

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 64/253 (25%), Positives = 117/253 (46%), Gaps = 12/253 (4%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           T ++  E    + +    E  A   ++ +VE +  L + +A++Y  RG    DL+Q   +
Sbjct: 9   TDMTAEELLAEMVLPEISEYRAERLRERIVEMHRPLAMEIARRYRYRGEPLEDLLQAAYV 68

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GLMKA   FD  LG+ F  YA+  +   + R   D++  IR+P   +++  ++ R    +
Sbjct: 69  GLMKAINGFDPTLGHAFRGYAVVTMTGEVKRHFRDRTWAIRVPRVYQERRAELNRLVADL 128

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET---PIGDEDTSHLGDFIEDKN 596
           S  + R PT  E+A K+ +  E V   L  +    +L        D+D + LGD I D++
Sbjct: 129 SQDLGRAPTVAELAVKMRISEEDVLLTLDASAAYSALSLDAPLGADDDAAALGDIIPDED 188

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
               +        RE    ++  L  RE+ +L +RF        T  E+  +F +++  +
Sbjct: 189 DALGVLVD-----REAVKPLIDKLPTREKNILLLRFFGN----MTQAEIAAEFGISQMHV 239

Query: 657 RQIEAKAIRKLKH 669
            +I  K + +L+ 
Sbjct: 240 SRILRKVLDQLRE 252


>gi|225850934|ref|YP_002731168.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
 gi|225645790|gb|ACO03976.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
          Length = 241

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 97/200 (48%), Gaps = 10/200 (5%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G +GL+ A  K+D   G K STYA   ++  I  S+        +P ++R K   
Sbjct: 39  DLINTGVLGLIDAINKYDPSKGVKLSTYAEIRIRGQIIDSLRKLDW---VPRNVRQKARH 95

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHL- 588
           +      +  K+ RE TPEEIA+ L M VE   K  +       IS++T +G ++ ++  
Sbjct: 96  IEAAILEVEQKLGREATPEEIAEYLGMDVEEYMKYAEKISNSGLISIDTTVGSDEDANTK 155

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              I   N  +P     +  L++  + +++ L  RE  V+ + +      + +++E+G+ 
Sbjct: 156 LWQIISINDDTPDKYVEEEELKKIISDIISKLNERERLVITLYY----YEELSMKEIGEV 211

Query: 649 FCVTRERIRQIEAKAIRKLK 668
             +T  RI QI  K + K+K
Sbjct: 212 LGLTESRISQIHTKTMMKIK 231


>gi|327481248|gb|AEA84558.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 99/240 (41%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +   + +A  A+  +++    LV  +A     R    +Q  DLIQ G IGL++AA+K+D 
Sbjct: 1   MYYSKAQAKDAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDA 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++  +   +         P  +      V    R +  K  R+    
Sbjct: 61  GKGASFETYAGIRIRGTMLDEVRKGDW---APRSVHRNSRMVSEAIRAIEAKTGRDAKDH 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + + +   L +         P        
Sbjct: 118 EVAAELKLSLDEYYAILGDTLGSRLFSFDDLLQEGEHGELQE-DASSTHPEPFRDLEDER 176

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++     + +L  RE+ VL + +    + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 177 FQQALADAIGNLPEREKLVLSLYY----DEELNLKEIGQVLGVSESRVSQLHSQCAARLR 232


>gi|168700558|ref|ZP_02732835.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 260

 Score =  107 bits (266), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 107/239 (44%), Gaps = 18/239 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE  L LV   A++  +R   G++  DLI  G  GL+ A + FD   G KF TY +
Sbjct: 26  RNRLVERYLSLVKYNAERIWSRLPDGVELDDLISAGVFGLLDAIDAFDLTRGVKFETYCV 85

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  K+    +++   + R P PEE+++KL +P+E
Sbjct: 86  PRIRGAMLDELRTMDW---VPRLVRSKASKMEAARKQLEAALGRPPKPEELSEKLGIPLE 142

Query: 562 GVRKVLKITKEP--ISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +   +        +SL     + D        D +EDK A SP       +L +  TR 
Sbjct: 143 QLESYVGDATAVNLVSLNKKWYETDSYKDVREIDILEDKKAESPTGRLQNRDLMKLVTRG 202

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L        R  R+   +    + T++E+G    ++  R+ Q+ +  + +L+     +K
Sbjct: 203 LN-------RNERLIVILYYYEEMTMKEIGATLNLSESRVSQMHSSIVARLQSHLAKRK 254


>gi|325846834|ref|ZP_08169712.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481206|gb|EGC84249.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 256

 Score =  107 bits (266), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +      + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY
Sbjct: 20  QFYKTRDKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGY 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FS++A   +   + R   D+   IR+P  +++   K+    + +  +++R PT ++IA 
Sbjct: 80  EFSSFATPTIMGELKRYFRDKGWVIRVPRRIQNLYKKINVAKKILPQELQRTPTIKDIAA 139

Query: 555 KLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L    E + + ++ +    P SL+     +   +  D            +     L++ 
Sbjct: 140 YLGEDEETILETMEASKVYTPQSLDMKYQVQKGENSVDL--SDMIGEDDKNFDSIELKDL 197

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +    L   E+++L +R+  G     T  ++ K+  +++  + +IE K ++K
Sbjct: 198 IEKSTERLNDLEKQILELRYYEG----RTQVDIAKKLSISQMTVSRIEKKILQK 247


>gi|3451022|gb|AAC32644.1| RNA polymerase sigma factor [Escherichia coli RS218]
          Length = 220

 Score =  107 bits (266), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 66/165 (40%), Positives = 110/165 (66%), Gaps = 3/165 (1%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 171

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
             +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ 
Sbjct: 172 VKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN 216



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|291196402|emb|CBG22673.1| DNA-directed RNA polymerase subunit D [Pseudomonas vancouverensis]
          Length = 237

 Score =  107 bits (266), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 39/284 (13%), Positives = 91/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    +   D E       ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDAKTVKADDADDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L  L
Sbjct: 110 TRKAL-----------------------------------KKHGRHNKAAVAELLALADL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEIDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 SEGLAK-GKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEI 237


>gi|302547278|ref|ZP_07299620.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302464896|gb|EFL27989.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 264

 Score =  107 bits (266), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 110/249 (44%), Gaps = 15/249 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           + +EFR I ++    E EA   ++++V A + +   +A+++ NRG    DL Q   +GL+
Sbjct: 18  TSAEFRRIATLPEGAEKEAL--RQDVVRAWMPMAERLARQFRNRGESAEDLRQVAMLGLV 75

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA ++++   G  F+++A+  V   I R   D    + +P  +++  ++V   A+ ++  
Sbjct: 76  KAVKRYEPDRGSAFASFAVPTVVGEIKRHFRDHMWGVHVPRRVQELRNRVRAAAQELTRT 135

Query: 543 I-KREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIG-DEDTSHLGDFIEDKNAV 598
              R P+   I +   M  E V        +   +SL+  +   ED   L D +      
Sbjct: 136 PDDRSPSVSAIVEHTGMSEEDVLLGMEAMESFSALSLDAELPGAEDGYSLADTLG----- 190

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P  S  +   RE     L +L  RE  +L +RF          E    Q  +++  + +
Sbjct: 191 APEPSYDRVIQREALKPRLRALPERERHILYLRFFREETQGRIAE----QLGISQMHVSR 246

Query: 659 IEAKAIRKL 667
           +  +   +L
Sbjct: 247 LINRTCARL 255


>gi|302346408|ref|YP_003814706.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302150820|gb|ADK97081.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 228

 Score =  106 bits (265), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 118/264 (44%), Gaps = 43/264 (16%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I+ I+ E  +S  E + +   ++      + A +++ +ANL+ V+S+A +Y NRGL  
Sbjct: 6   KYIEDIANEQLLSDKEEQELAEKIK---VGDARALEKLTKANLKFVVSLAHQYRNRGLGE 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA+KFD   G +F  +A  ++++A                       
Sbjct: 63  DDLISEGNIGMMYAAQKFDGSKGVRFVIFAAPYIRKA----------------------- 99

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHL 588
                          E T +E A    +P     +  +     IS++ P+     +   L
Sbjct: 100 --------------MEETIKEQATLYKLPKNETSRFEQKRSHAISIDQPVPVGSNNNFTL 145

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              +E++NA    +   Q  L     + L  L  RE+RV+   +G+     +T+ E+ + 
Sbjct: 146 QHILENENAKHADEHLNQEILSNEIQKGLDVLDEREKRVITYIYGL-TGAHYTMAEIAED 204

Query: 649 FCVTRERIRQIEAKAIRKLKHPSR 672
             + RER+RQI  KA+RKL    +
Sbjct: 205 MGLKRERVRQIRDKALRKLHKKMK 228


>gi|307264896|ref|ZP_07546458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306920154|gb|EFN50366.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 246

 Score =  106 bits (265), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 98/230 (42%), Gaps = 15/230 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++   + LV  + KK     +   ++ DLI +G IGL+ A EK+    G KF TYA 
Sbjct: 21  RNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAIEKYQPSKGVKFETYAT 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +  +      P  ++ K  K+  T   +  K  REPT EEI +   +   
Sbjct: 81  LRIRGEIIDYLRRKDWM---PRSLKKKYKKIEETVETLQQKYNREPTVEEITEACGLNET 137

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V K L         SLE  I +    H    +E KN        +   L+      + S
Sbjct: 138 DVLKTLSYINVSNINSLEEAIENNLKLHAISNVELKNPEE---EVLYKELKRKLASAIES 194

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  +E  V+ + +      D   +++ K   +T  RI QI  KAI++++ 
Sbjct: 195 LPDKERLVITLYY----YEDLNYKDISKILNLTESRISQIHTKAIKRIRE 240


>gi|254700317|ref|ZP_05162145.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261750811|ref|ZP_05994520.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261740564|gb|EEY28490.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
          Length = 262

 Score =  106 bits (265), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 106/251 (42%), Gaps = 14/251 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   ++ I     +   E   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LTRYLEEIRRFPMLEPQEEYMLAK--RYHEHADPKAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              ++I EGN+GLM+A ++F+   G++ +TYAMWW+K +I   I      +++      K
Sbjct: 74  PIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 529 I-----HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                  K+    + + +        ++IA KL +  + V  + +      SL  P+   
Sbjct: 134 RLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNAPLRAS 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++    D++ D +         Q  L   R    + + +L  RE R+   R       
Sbjct: 194 EGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRLAE--E 251

Query: 639 DHTLEEVGKQF 649
             TLE++  +F
Sbjct: 252 PMTLEDLSGEF 262


>gi|187778269|ref|ZP_02994742.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
 gi|187771894|gb|EDU35696.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
          Length = 251

 Score =  106 bits (265), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 119/243 (48%), Gaps = 8/243 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           F   + ++ +       A  ++VE NL LV +++KK+ NRG ++ D+ Q G IGL+KA  
Sbjct: 13  FEDNMELMEEARSGNKQALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAIN 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F+     KFSTYA+  +   I R + D    I++   ++    K+     ++  ++ RE
Sbjct: 73  NFETKYNVKFSTYAVPMIMGEIKRFLRD-DGIIKVSRSIKTAAKKLHYDKEKLCKELNRE 131

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE+++     V+ +    + +  P  L   I  +D + +   I+  +  +  D+ I 
Sbjct: 132 PTIEELSQFSGYTVDEILMATESSSSPQYLYDVIHQDDGAPVL-LIDKISENTEEDNKII 190

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            N+       L +L  +  +++ +R+      D T  EV KQ  +++ ++ +IE K ++ 
Sbjct: 191 DNI--ALKEALKNLDIKSRQIIILRYF----KDKTQIEVAKQLGISQVQVSRIEKKVLKL 244

Query: 667 LKH 669
           +K 
Sbjct: 245 MKE 247


>gi|158341383|ref|YP_001522549.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311624|gb|ABW33234.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 110/239 (46%), Gaps = 15/239 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + + +     A+   +  N RLV   AK+Y    + + DL+  G +GL  A +KFD   
Sbjct: 25  QIERAQAGDRRAEDRFIRKNQRLVFKEAKRYRG-LVDWDDLVNAGTLGLSIAIQKFDLSR 83

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA+  ++  I + I +      +   +   + K+    + +  +++R+PT +E+
Sbjct: 84  GFQFSTYAVKPIRTEIRQLICE---QRGLSREITKHLKKIDEAEQDLELELERKPTLDEL 140

Query: 553 AKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++       +       +  +  SL    G E      DF+ED   +   D A   N++
Sbjct: 141 AERTGYSHRVITNAWNKARVVDTSSLNVLTGTEQGIECLDFVEDFEQLDSWDFAESINMK 200

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     +A L  RE  ++R R        H+  E+G    ++ ERIRQ+  KA+  LKH
Sbjct: 201 DY----IAQLPDRESFIVRARR-----DGHSYREIGTMLKLSGERIRQLYQKALEYLKH 250


>gi|258621167|ref|ZP_05716201.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
 gi|258626709|ref|ZP_05721533.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258581005|gb|EEW05930.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258586555|gb|EEW11270.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
          Length = 244

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 101/227 (44%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R        DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 19  FLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +  ++ R+PT  E+AK L M +E   
Sbjct: 79  RGAMLDDIRRGDW---VPRSVHKHNREISQAIAVLEGELNRDPTDAEVAKFLEMSLEQYH 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VL      I+    +G ED     D I   E+    SP     + + R+     + SL 
Sbjct: 136 SVLM----DINCSRIVGIEDLGVSDDAISPFEEGEDNSPFHGVAEESFRKALVESIKSLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G+   V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQSMQRLR 234


>gi|209408322|emb|CAP19904.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 239

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 46/284 (16%), Positives = 100/284 (35%), Gaps = 46/284 (16%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +M+++   P T  +++   + +      L +I  L   I P+  G      
Sbjct: 1   KRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA---- 54

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
              + Q+ E  + +       + + D E     S+++       PE A      + E  +
Sbjct: 55  ---APQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLE 111

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +   L                                   +K  ++S +     E L  
Sbjct: 112 KANKAL-----------------------------------KKHGRASQQAVEELEALAI 136

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           L   + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  
Sbjct: 137 LFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLD 196

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           W        +G++   +    + I++ + ++  +  E  ++I++
Sbjct: 197 WAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLAIAD 239


>gi|18311030|ref|NP_562964.1| sporulation sigma factor SigF [Clostridium perfringens str. 13]
 gi|110799417|ref|YP_696728.1| sporulation sigma factor SigF [Clostridium perfringens ATCC 13124]
 gi|110803821|ref|YP_699329.1| sporulation sigma factor SigF [Clostridium perfringens SM101]
 gi|168205856|ref|ZP_02631861.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|168208750|ref|ZP_02634375.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168212915|ref|ZP_02638540.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|168215675|ref|ZP_02641300.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
 gi|182623955|ref|ZP_02951743.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145712|dbj|BAB81754.1| RNA polymerase sigma-F factor [Clostridium perfringens str. 13]
 gi|110674064|gb|ABG83051.1| RNA polymerase sigma-F factor [Clostridium perfringens ATCC 13124]
 gi|110684322|gb|ABG87692.1| RNA polymerase sigma-F factor [Clostridium perfringens SM101]
 gi|170662589|gb|EDT15272.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|170712973|gb|EDT25155.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170715517|gb|EDT27699.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|177910848|gb|EDT73202.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|182382022|gb|EDT79501.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
          Length = 251

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 112/239 (46%), Gaps = 13/239 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++   +     A  +++E N  LV S+ K++TNRG  + D+ Q G++GL+KA   F+   
Sbjct: 19  LIVMAKEGNKEAMNKLIEVNTPLVSSICKRFTNRGYDYEDIFQIGSMGLVKAINNFNDSF 78

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KFSTYA+  +   I R + D    I++    +    K+      +  K+ R+PT +E+
Sbjct: 79  NVKFSTYAVPMIIGEIKRFLRD-DGIIKVSRSTKTLAKKLHYNKEELIKKLNRDPTVDEL 137

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLR 610
           A+   +  E V   L+       L   I  ++ +   L D + +K     + + I     
Sbjct: 138 AEYSGVDKEEVIVALESASSMQYLYDTIHHDEGTPVLLIDKLSEKGEDDDMVNKI----- 192

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 ++SL  + ++++ +R+      D T  +V K   +++ ++ +IE K ++ +K 
Sbjct: 193 -ALREAISSLDSKGKQIIMLRYF----KDKTQIQVAKMLGISQVQVSRIEKKVLKIMKE 246


>gi|322381761|ref|ZP_08055715.1| sporulation sigma factor SigF-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154149|gb|EFX46471.1| sporulation sigma factor SigF-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 200

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 54/208 (25%), Positives = 100/208 (48%), Gaps = 14/208 (6%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            NRG +  DL Q G IGL+K+ +KF+     KFSTYA+  +   I R + D   T+++  
Sbjct: 1   MNRGYEADDLFQIGCIGLLKSVDKFNLSYEVKFSTYAVPMIIGEIQRFLRD-DGTLKVSR 59

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
            +++  +KV +T   +S  ++R PT +E+A  L +  E V    +  K   S+   +   
Sbjct: 60  SLKELANKVRKTKDELSKNLERLPTLKEVANALGITPEEVVFAQEANKPLSSIHETVFEN 119

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           D D   L D I D +     D       +      +  L+ RE  ++ +R+      D T
Sbjct: 120 DWDPITLMDQIADDSQEKWFD-------KLALNEAIEGLSERERLIVYLRYF----KDQT 168

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             EV  +  +++ ++ ++E K ++ +++
Sbjct: 169 QSEVANRLGISQVQVSRLEKKILQSIRN 196


>gi|20807860|ref|NP_623031.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478885|ref|ZP_05092249.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
 gi|20516424|gb|AAM24635.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|214035198|gb|EEB75908.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
          Length = 246

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 106/239 (44%), Gaps = 15/239 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCL 492
               +   A+ E++   L LV  + KK     +   ++ DLI +G +GL+ A EK+    
Sbjct: 12  YNLQKDPDARNEIIVKYLPLVKHIVKKLVISDIAQSEYEDLIHQGILGLIDAIEKYQPDK 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G KF TYA   ++  I   +  +      P  ++ K  K+  T  ++  +  REPT EEI
Sbjct: 72  GVKFETYATLRIRGEIIDYLRKRDWM---PRSLKKKYKKIEETVEKLQQRYNREPTVEEI 128

Query: 553 AKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            +   +  E V K L         SLE  I +    H    I + +  +P +  +   L+
Sbjct: 129 TEACGLEEEDVLKTLSYINVSNINSLEEAIENNLKIH---SISEIDLKNPEEELLYKELK 185

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     +  L+ +E  V+ + +      D   +++ K   +T  RI QI +KAI+K++ 
Sbjct: 186 KKLAHAIEKLSEKERLVITLYY----YEDLNYKDISKILNLTESRISQIHSKAIKKIRE 240


>gi|197303735|ref|ZP_03168772.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
 gi|197297255|gb|EDY31818.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
          Length = 265

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 106/266 (39%), Gaps = 58/266 (21%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I  +   +   +    ++  E ++     +K       AK  ++E NLRLV  + +KY N
Sbjct: 51  ISNVLRGVSLKTFPNPLTPDEEKYYF---QKYTEGDLEAKHILIERNLRLVAHIVRKYQN 107

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G +  DLI  G IGL+KA   FD   G + + YA   V+  I                 
Sbjct: 108 LGEEMEDLISIGTIGLIKAVISFDPEKGNRLAAYASRCVENEILMY-------------- 153

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
                  +R  ++   +                               ISL  PIG +  
Sbjct: 154 -------LRARKKGGKE-------------------------------ISLYEPIGTDRD 175

Query: 586 SH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            +   L D IE  +   P    ++ N+++   +V + L+PRE  VL+MR+G+    ++T 
Sbjct: 176 GNEIRLYDIIETTDTDVPEKLYLKENIQKLYEKVESELSPRERLVLKMRYGLYNGEEYTQ 235

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            E+     ++R  + +IE  A+ KL+
Sbjct: 236 REIASLLGISRSYVSRIEKSAVEKLR 261


>gi|149201624|ref|ZP_01878598.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
 gi|149144672|gb|EDM32701.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
          Length = 242

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 103/233 (44%), Gaps = 18/233 (7%)

Query: 447 EMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +VE ++ LV  +A  +     R ++  DL+Q G +GL+ A++++  C G  F+ YA   
Sbjct: 16  RLVEQHMPLVQRLAWHFHGRVGRFIEIDDLLQAGYLGLIDASQRYSVCDGVSFAAYATIR 75

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ +I   +   S   R  + MR    K+  T R++S K+ REP   E+A+ L +  E  
Sbjct: 76  IRGSIIDHLRRNSNLCRNSITMRQ---KIEATRRKLSQKLGREPEVPELAQSLELSTEEF 132

Query: 564 RKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +       T +  SL+    D         +   +  +P D      L+      L  L 
Sbjct: 133 QDWENRFQTNQLQSLDEVYTDHS------LLFSDHGSTPEDEVEHIQLKALLQSALQDLP 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            R   VL++ +      +  + E+     VT  R+ QI+  AI +L+   +++
Sbjct: 187 ERSALVLQLYYV----EELNVYEIAAILDVTTGRVSQIKKAAIGQLRDLMQAR 235


>gi|225871941|ref|YP_002753395.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
 gi|225792596|gb|ACO32686.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
          Length = 336

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 104/229 (45%), Gaps = 12/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++ +  +L  V  +A++   R    ++  DL+  G +GL+ A  KFD     +F +YA 
Sbjct: 77  QEQQLMEHLPTVRYLARRIHERLPHHVELDDLVSAGVVGLLDAMRKFDPAKKVQFRSYAQ 136

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + ++ AI  S+         P  +R K   V    R ++ ++ R P   E+A ++ +P+ 
Sbjct: 137 FRIRGAILDSLRMLDW---SPRELRRKGRAVEEAIRAVTARLGRAPQESEVAGEMGLPLH 193

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +++L   K  E  +L     ++       F+ +     PL   ++  +RE     + +
Sbjct: 194 EYQQLLGELKGLEIGTLHVERSEDSGEEELAFLPNDPEDDPLFRCLKGEMRERLMAAIDA 253

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  V+ + +      + T++E+G    V   R+ Q+ + A+  L+
Sbjct: 254 LPERERLVMTLYY----YEEMTMKEIGLTLGVVESRVSQMHSSAVLHLR 298


>gi|212697380|ref|ZP_03305508.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675572|gb|EEB35179.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 256

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +      + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY
Sbjct: 20  QFYKTRDKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGY 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FS++A   +   + R   D+   IR+P  +++   K+    + +  +++R PT ++IA 
Sbjct: 80  EFSSFATPTIMGELKRYFRDKGWVIRVPRRIQNLYKKINVAKKILPQELQRTPTIKDIAA 139

Query: 555 KLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L    E + + ++ +    P SL+     +   +  D            +     L++ 
Sbjct: 140 YLGEDEETILETMEASKVYTPQSLDMKYQVQKGENSVDL--SDMIGEDDKNFDSIELKDL 197

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +    L   E+++L +R+  G     T  ++ ++  +++  + +IE K ++K
Sbjct: 198 IEKSTERLNDLEKQILELRYYEG----RTQVDIAQKLSISQMTVSRIEKKILQK 247


>gi|169831890|ref|YP_001717872.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638734|gb|ACA60240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score =  106 bits (265), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 103/248 (41%), Gaps = 16/248 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAA 485
            I    R         +++++  +L LV  +A +   R   F    DL   G  GL++A 
Sbjct: 4   EIWRRYRDTRNSGL--REQLIVEHLPLVRLIAGRLAVRPPSFIAQEDLEGWGIFGLIEAV 61

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK+D   G  F T+A   ++ AI   +  QS   R   H   K+ ++     R+  +   
Sbjct: 62  EKYDPNHGTDFRTFAYHRIRGAILDEVRRQSWLPRSLWH---KLQEINEARARLERETGA 118

Query: 546 EPTPEEIAKKLAMPVEGVRK--VLKITKEPISLET--PIGDEDTSHLGDFIEDKNAVSPL 601
             T  E+A  L M      +      +   +SL+      + +    G  IED  +  PL
Sbjct: 119 SVTDAEVAASLGMTDLEFHRLANHFRSVSVMSLDDVRTTRNGEAVPWGSLIEDTGSPDPL 178

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  ++    +T    +  L  ++  VL + +  G     TL+E+G+   VT  R  Q+ A
Sbjct: 179 EQVLEEEDHQTLVAAITQLEEKDRLVLALYYQEG----LTLKELGRVLEVTESRACQLHA 234

Query: 662 KAIRKLKH 669
           +AI +L+ 
Sbjct: 235 RAIARLRE 242


>gi|291196360|emb|CBG22652.1| DNA-directed RNA polymerase subunit D [Pseudomonas pachastrellae]
          Length = 241

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 94/284 (33%), Gaps = 44/284 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +MA++   P T   ++     + +    L +I      I P+       G  
Sbjct: 1   RIEEGIREVMAAISMFPGTVDDILADYARVVEEGGRLSDI--FSGYIDPDD-----DGMS 53

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +   +  + ++    + E + +S      D+       PE A      ++E    
Sbjct: 54  GTDNAEIPAAKAKDQKKSEDDDEDEDDSDDDSDDDNEGDGGPDPEVARLRFGAIEE---- 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                                           LQ      +K  +S+ K    +E L  L
Sbjct: 110 -------------------------------QLQKLQKALKKHPRSNPKVVAEQEALATL 138

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LV ++     +I   E  +++L      + R  FL    G E++  W
Sbjct: 139 FMPIKLIPKQYEALVTRVRGAQDQIRQQERAIMQLCVRDARMPRADFLRSFPGNEINEGW 198

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           V       +  +   +      IL+ + ++  +   + ++ISE 
Sbjct: 199 VDELLA-DKPRYSEGLEALKGDILRAQKKLAELEETSRLTISEI 241


>gi|284029882|ref|YP_003379813.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Kribbella
           flavida DSM 17836]
 gi|283809175|gb|ADB31014.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Kribbella
           flavida DSM 17836]
          Length = 272

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 101/224 (45%), Gaps = 10/224 (4%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E+VE N+ +   +A+++  RG +  DL Q   +GL+KAA  +       F  +A+  ++ 
Sbjct: 47  EVVELNIEMARGIARRFRGRGAEADDLEQVAYLGLVKAAHHYRLDADTPFIGFAIPTIRG 106

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            + R   D + T+RIP  +++    +      +   + REPTP EIA  L + +  V + 
Sbjct: 107 EVKRYFRDCAWTVRIPRRLQEMQGTIAAKLPYLEQLLNREPTPAEIADHLGVELSEVEQA 166

Query: 567 LKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           L        +SL+ P   +    L     D  A     +  Q    +    VLA L  RE
Sbjct: 167 LAAKGCFNVLSLDRPAEADADLTLA----DVVADDDDATIDQLEAVDMLQPVLADLGERE 222

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+L++RF  G        E+G    V++ ++ ++  + +  L+
Sbjct: 223 RRILQLRFVEGWTQS----EIGADIGVSQMQVSRVLRRILDDLR 262


>gi|149188102|ref|ZP_01866397.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
 gi|148838090|gb|EDL55032.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
          Length = 243

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 100/244 (40%), Gaps = 16/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAE 486
           +   +   +      ++  +E    LV  +A     R        DLIQ G IGL++A +
Sbjct: 1   MNKALTYDQHANLSGQQAFLEKYSVLVKRIAHHLIGRLPPNVLVEDLIQAGMIGLIEAQK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +      + +    +  ++ R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKHSRDISQAISVLEVELNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSA 604
           PT  E+A  L + +    K L      I+    +G ED     D   + D+   +P    
Sbjct: 118 PTDSEVANYLGLSLAQYHKAL----TDINCSKLVGIEDLGVSEDSVSVSDEEDNTPFQGV 173

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                RE     + SL  RE   L + +    + +  L+E+G+   V+  R+ QI ++++
Sbjct: 174 ADDAFREALIESIKSLPEREALTLSLYY----DEELNLKEIGEVLGVSESRVSQILSQSM 229

Query: 665 RKLK 668
           ++L+
Sbjct: 230 QRLR 233


>gi|91200244|emb|CAJ73289.1| strongly similar to RNA polymerase sigma factor for flagellar
           operon [Candidatus Kuenenia stuttgartiensis]
          Length = 259

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 105/237 (44%), Gaps = 15/237 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++++V  NL LV  V  K+      F    DLI+ G IGL++A+E+FD C+  KF T+A+
Sbjct: 26  REKLVTENLSLVKYVVNKFIIYLPSFVDKEDLIEYGVIGLLEASERFDPCMDTKFGTFAV 85

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +  Q     +P  +R+K+         +  K+ R P PEEIA +L +   
Sbjct: 86  SRIRGAILDHLRAQDW---LPRSVREKVSLAREAYATLEQKLNRHPLPEEIAAELKIDTA 142

Query: 562 GVRKVLKITK--EPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              K+L        +SLE      +  +   +G    D     PL +      +E     
Sbjct: 143 EWEKLLVEINFGMFLSLEEMNAKSEDGNKEAVGMLFADSKIGDPLSNIETEEEKELLVAA 202

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +  L  RE+ V+ + +      D  L E+ +   ++  R+ QI  + +  L+   R 
Sbjct: 203 IKELPAREKLVITLYY----YEDLMLREISQMLDISESRVSQIHHQGLFMLRSKVRK 255


>gi|83719422|ref|YP_443660.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           E264]
 gi|167582695|ref|ZP_02375569.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           TXDOH]
 gi|167620811|ref|ZP_02389442.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           Bt4]
 gi|83653247|gb|ABC37310.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 243

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 47/209 (22%), Positives = 90/209 (43%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R     EIA  L MP++  + +L+       +  E      D 
Sbjct: 93  TSREVEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSMLQDLHGSQLVYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYRADHS-DPLSALLDEHLRSALVDAIEHLPEREKLLMSLYYERG----LNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 208 GAVLEVSESRVCQLHSQAVARLRAKLREQ 236


>gi|115350241|ref|YP_772080.1| flagellar biosynthesis sigma factor [Burkholderia ambifaria AMMD]
 gi|115280229|gb|ABI85746.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           ambifaria AMMD]
          Length = 243

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 93/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYRVDHA-DPLSALLDDHLREALVDAIDRLPEREKLLMSLYYERG----LNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 208 GAVLEVSESRVCQLHSQAVARLRARLREQ 236


>gi|56752504|ref|YP_173205.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|81300319|ref|YP_400527.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|56687463|dbj|BAD80685.1| group3 RNA polymerase sigma factor SigF1 [Synechococcus elongatus
           PCC 6301]
 gi|81169200|gb|ABB57540.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 259

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 57/246 (23%), Positives = 114/246 (46%), Gaps = 12/246 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           + +  +      +  +VE NL LV   A ++  R    F +L+Q G++GL+ A ++F+  
Sbjct: 17  LRQYQQTRDHRIRNRLVELNLGLVRQEAYRWVQRCPESFEELVQIGSLGLIAAIDRFELE 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D+S T+R+P    +   ++     ++  ++ R PT EE
Sbjct: 77  RGKAFSSFAVPYIRGEIQHYLRDRSGTVRVPRRWAELHQQIDPLRHKLQRELGRSPTEEE 136

Query: 552 IAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQA 607
           + + L +  E  ++V  +   +  +SL+ P+  ++   + LGD I D    S   +    
Sbjct: 137 LRQGLGLDAEEWQEVRLIGRNRTTLSLDQPLYADEEQVTSLGDSIADPKYRSFQLAEED- 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    + +  L  R   +L   F      D T  EV ++  ++   + +   K ++ L
Sbjct: 196 --RIRLQQAMQLLEQRTREILEFVFF----YDLTQREVAEKLGLSAVTVSRQVKKGLKHL 249

Query: 668 KHPSRS 673
           K   RS
Sbjct: 250 KSILRS 255


>gi|295706259|ref|YP_003599334.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
 gi|294803918|gb|ADF40984.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
          Length = 253

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 105/251 (41%), Gaps = 12/251 (4%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNI 479
           SI E           E   S A   +V+  + LV    ++ +    + +   +L   G I
Sbjct: 3   SIQEVEEHKIWQEWRETRDSHAGNMLVKKYMPLVNYHVQRISVGLPKNIHKEELRSLGLI 62

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL  A EKFD+    KF TYA + ++ AI   +  +     +    R+K  ++ +    +
Sbjct: 63  GLYDALEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDW---LSRSAREKTKRIEQATEAL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNA 597
             +  R   P E+AK++ M    V   +        +S+E    + +       I+D+  
Sbjct: 120 EQRYLRRVAPSEVAKEVGMTEADVVHTMNEGFLANVLSMEEQPKEYEDGEQKYTIKDEKT 179

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +SP +  I     +    V+  L  +E+ V+ + +      + T  E+ +   ++  RI 
Sbjct: 180 LSPEEELINDERYQELAEVIEQLNEKEQLVVSLFY----KEELTFTEIAQLLGLSTSRIS 235

Query: 658 QIEAKAIRKLK 668
           QI +KA+ K++
Sbjct: 236 QIHSKALFKMR 246


>gi|260886663|ref|ZP_05897926.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|330839507|ref|YP_004414087.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
 gi|260863515|gb|EEX78015.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|329747271|gb|AEC00628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
          Length = 252

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 109/248 (43%), Gaps = 22/248 (8%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLM 482
           E + + ++ R  E  A   + ++VE  L LV  +A +        +   DL+  G  GL+
Sbjct: 10  EIQDLWALYR--ETRAPEVRDKIVEKYLPLVNIIAGRVVVGLPAHVDRDDLVSSGFFGLL 67

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            A E++D   G KF TY    ++ A+   +        IPV  R KI +  +    +  +
Sbjct: 68  DAIERYDVERGNKFETYGGVRIRGAMLDYLRTMDW---IPVSKRQKIRRYEQAVTTLEGR 124

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSP 600
           + R  T +E+A +L +  + +  ++  T     I LE  +  E  S           + P
Sbjct: 125 LGRSATDDELAAELKISKKELHDLVSQTNIATVIPLEEYVRTESPSS--------QTIDP 176

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
            ++A +  LR+T    +  L  +E  V+ + +      + TL+E+     ++  RI Q+ 
Sbjct: 177 EENAEKNELRDTLAEAIDQLPEKERTVVSLYY----YEELTLKEISLILHLSEARISQLH 232

Query: 661 AKAIRKLK 668
            KA+ +L+
Sbjct: 233 TKAVFRLR 240


>gi|206558549|ref|YP_002229309.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           J2315]
 gi|198034586|emb|CAR50452.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia cenocepacia J2315]
          Length = 243

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYRVDHA-DPLSALLDEHLREALVEAIERLPEREKLLMSLYYERG----LNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 208 GAVLEVSESRVCQLHSQAVARLRARLREQ 236


>gi|291196284|emb|CBG22613.1| DNA-directed RNA polymerase subunit D [Pseudomonas cannabina]
          Length = 237

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 39/284 (13%), Positives = 94/284 (33%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +         + +    +  + + E+A     ++  +    P  A+     + +  + 
Sbjct: 50  GIAPPAEVPPPVDPKAAKAEGDDEEEETAEATDDEEEVESGPDPVIAQQRFGAVSDQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +           L +L
Sbjct: 110 TRKAL-----------------------------------KKFGRDDKHAIAEMVALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +A     I + + ++ ++  +TG+ I+E 
Sbjct: 195 TD-ALAKGKSKYAEAIARLQPDIQRCQQKLSALEEDTGLKIAEI 237


>gi|153953795|ref|YP_001394560.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219854411|ref|YP_002471533.1| hypothetical protein CKR_1068 [Clostridium kluyveri NBRC 12016]
 gi|146346676|gb|EDK33212.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219568135|dbj|BAH06119.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 241

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 109/233 (46%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  L LV  +A +      + +++ DL+  G +GLM A  KFD   G KFSTYA 
Sbjct: 10  KEELVKKYLPLVKYIASRVIIGKTKYIEYEDLVSYGTLGLMDAINKFDKDRGMKFSTYAS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK+++       +  ++ REP   EIA KL + ++
Sbjct: 70  IRIKGSMIDELR---RNSPISKGAMDKLNRYNAAVEYLQGELGREPNSVEIASKLGISLK 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            + ++         +SLE  +  DED   +   IED  + SP  +  +    +   + L 
Sbjct: 127 EMMEIENYINYISMVSLEDLVFSDEDNIPIMGTIEDTKSPSPERNLEEKEKLKYLAKALE 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  VL + +      + TL+E+G    V+  R+ Q+ ++AI  L+   
Sbjct: 187 LLNEKDNLVLTLYY----YEELTLKEIGHILNVSESRVCQLHSRAIVHLRKAM 235


>gi|116625262|ref|YP_827418.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116228424|gb|ABJ87133.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 255

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 103/247 (41%), Gaps = 10/247 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK-YTN--RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R     +   + ++V  +L LV ++A + + N    +   DLI  G +GL  A  K+D  
Sbjct: 9   RSQSEVSLQQRDQIVLDHLPLVKAIAIRVHENLPVHVDLDDLIHAGVMGLFDAVTKYDGD 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F +YA   +K AI  S+            +R +  +V    R +  K+ R P   E
Sbjct: 69  KNVAFHSYAKHRIKGAILDSLRQLDW---ASRDLRRRQKQVESVTRDLGVKLGRSPHDSE 125

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA+++ + +   R++    +    +      +           K  + P     Q  L  
Sbjct: 126 IAEQMGVGLARWRQMQIEMRTVGLVSATPNPDQDRERAQEFPAKPNLQPDRMCEQRQLES 185

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           T  R + +L  R ++V+ + +      D T++E+G+   V   R+ QI   A++K+    
Sbjct: 186 TLARAIGTLPLRYQKVVFLYY----TNDLTMKEIGEVLGVNESRVSQIHKIALKKMAGVL 241

Query: 672 RSKKLRS 678
            S+ +RS
Sbjct: 242 ESEGIRS 248


>gi|291196330|emb|CBG22637.1| DNA-directed RNA polymerase subunit D [Pseudomonas luteola]
          Length = 238

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 96/284 (33%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P + + ++   D +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGSVEYILSEYDRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G   +   D     +  D    + D E  ++    +      P             D ++
Sbjct: 50  GTLPESESDDIPVPKAKDAAAAQSDDEEESESDDSEEETESGP-------------DPEE 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +    +A+ +Q                     L+      QK  +SS +       L  L
Sbjct: 97  ARQRFAAVAEQ---------------------LEKTQKALQKHGRSSDQAIEELVALATL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + ++LV ++ +   R+   E  +++L      + R  FL      E +  W
Sbjct: 136 FMPIKLVPKQYEILVGRVRESLDRVRAQERAIMQLCVRDARMPRADFLRSFPSNETNLEW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           V       + ++   +      I + + ++ ++  E  ++++E 
Sbjct: 196 VDKVLKN-KPKYAEAIERLRPDIQRNQEKLIALQKELDLTVAEI 238


>gi|258404724|ref|YP_003197466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfohalobium
           retbaense DSM 5692]
 gi|257796951|gb|ACV67888.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfohalobium
           retbaense DSM 5692]
          Length = 241

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 108/242 (44%), Gaps = 13/242 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFD 489
           M+         A+ +++  ++ +V    ++   +   F    ++      GL+ AA +FD
Sbjct: 1   MLWTYTQNGEDARTQLIREHMNMVSYWVERMVTQVPAFMSRDEIRSAAMEGLINAANRFD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F T+A   ++ AI   +            MRDK  ++  T R +   ++R P  
Sbjct: 61  PNQGVLFKTFAEHRIRGAIFDEVRRLDWF---SRSMRDKHQRLAETIRELEISLERAPNE 117

Query: 550 EEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQ 606
            E+A  + M + G  ++L        +SL+  + D DT     D +ED + + P ++  Q
Sbjct: 118 NEVAAAMDMDLTGYHRMLGEVSHLGCMSLQEVLSDSDTGQSFLDVLEDTDGMPPEEAVEQ 177

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A L      +L  L+ +E++V+ + +  G     + +E+     +T  RI Q+ ++A+ K
Sbjct: 178 AELTREVAGMLHELSEKEQQVIALLYHEG----LSQKEIADVLSLTEGRISQLHSQALAK 233

Query: 667 LK 668
           L+
Sbjct: 234 LR 235


>gi|117619369|ref|YP_855921.1| flagellar biosynthesis sigma factor [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560776|gb|ABK37724.1| RNA polymerase sigma factor for flagellar operon [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 239

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 52/231 (22%), Positives = 95/231 (41%), Gaps = 17/231 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA   +
Sbjct: 16  LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIRI 75

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   I        +P  +      +      +     R+    E+A ++ + +    
Sbjct: 76  RGSMLDEIRRGDW---VPRSVHRNSRTIAEAIENVEQAHGRDARDSEVAAQMGVSLGEYH 132

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +L+     +S    IG ED     D I   +D+   +  D       +      +  L 
Sbjct: 133 TMLQ----DVSCGKIIGIEDLGVSEDVIGHPDDEPGSNGFDELAAERFQGALAEHIGRLP 188

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ +L+   R
Sbjct: 189 EREALVLSLYY----DEELNLREIGEVLNVSESRVSQIHSQAMHRLRARLR 235


>gi|167587836|ref|ZP_02380224.1| flagellar biosynthesis sigma factor [Burkholderia ubonensis Bu]
          Length = 244

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 52/209 (24%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 94  TSREVEHAVHQVEQHLGRAASEAEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL S +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 154 EPFLDRYRVDHA-DPLSSLLDEHLREALIEAIERLPEREKLLMSLYYERG----LNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 209 GAVLEVSESRVCQLHSQAVARLRARLREQ 237


>gi|58699689|ref|ZP_00374359.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58533795|gb|EAL58124.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 256

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 69/192 (35%), Positives = 110/192 (57%), Gaps = 13/192 (6%)

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF------ 370
           +  ++  +   + L+ + +  + ++LY I++ I   E  L+  A+ Y I R+ F      
Sbjct: 1   MYNQIWSIALQIKLSDAAVARITQELYKINRSITLEEANLIAEARKYDIDRESFYKVYDD 60

Query: 371 -LERHQGRELDPHWVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISIS 425
            L +H+ +++    ++  +    GE KN    F+    + I    N IK        ++ 
Sbjct: 61  VLLKHELKKISLLKINENQSSFTGELKNKFLRFIDDNSEHIASTLNGIKQH--IQEDNVQ 118

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EF+ ++  ++K E E S AK+EM++ANLRLV+S+AKKY+ RGL  LDLIQEGNIGLMKA 
Sbjct: 119 EFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAV 178

Query: 486 EKFDWCLGYKFS 497
           +KFD+  GYKFS
Sbjct: 179 DKFDYKRGYKFS 190


>gi|254455073|ref|ZP_05068509.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
 gi|198263775|gb|EDY88046.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
          Length = 249

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 60/204 (29%), Positives = 102/204 (50%), Gaps = 11/204 (5%)

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM--RDKIHK 531
           +Q  NIGL+KAA++FD   G++FSTYA WW++  I          +++P     R   + 
Sbjct: 1   MQHANIGLLKAADRFDPDKGFRFSTYAAWWIRAEIQDYKLQGWSLVKLPNSAFGRKLFYN 60

Query: 532 VVRTARRM--SNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTS-H 587
           + R   R+    ++  E   + IA  L +  E V     ++     SL  P+ D+  +  
Sbjct: 61  LKRVETRLVAEGEVPPEHLVDRIATDLGVTPEQVVLMQQRLAAPDGSLNRPVSDDGGTAQ 120

Query: 588 LGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           L D +ED +A    + + + + R    T +  L  L+ RE+ ++   +    +T  TL E
Sbjct: 121 LQDLLEDPDADVEKEVSARLDSRAFWTTLSFHLNRLSKREQEIIIEIYV--SDTPKTLYE 178

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +G+QF V+ ERIRQI   A+ +L+
Sbjct: 179 LGEQFSVSHERIRQIREAALTRLR 202


>gi|242089059|ref|XP_002440362.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
 gi|241945647|gb|EES18792.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
          Length = 529

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 75/271 (27%), Positives = 129/271 (47%), Gaps = 9/271 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    + ++K   E+ S       +  +   ++S ++ G C     ++ ++     LV  
Sbjct: 247 LEKIREKMVKEGQEV-SYHRWAEAAGMDEAELMSRLQTGYC----CRERLLVTTEWLVRC 301

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ YT  G    DL+Q G +G++  AEKFD   G +FSTY  +W+++ +   +A+ S  
Sbjct: 302 IARSYTGMGTALDDLLQAGKMGVLDGAEKFDTRKGCRFSTYVKYWIRKGMLALLAENSGV 361

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
             +P  M   + KV    R +     R P+  E+A  + + V  VR   K ++ P+SL +
Sbjct: 362 TLLPARMESIMRKVKEARRGIRYSEGRNPSDSEVAAAVGVSVANVRLARKCSRRPVSLYS 421

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAI----QANLRETTTRVLASLTPREERVLRMRFGI 634
            IG    +   + I D+ A +          +  LRE    VL  L  RE  VLR+R G+
Sbjct: 422 EIGIGQHAKFAEVIPDEAAAAAEAPDEAALFRGQLRERLLLVLGRLPAREGHVLRLRHGL 481

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                 +LEE+G  + V++E IR+IE  A+ 
Sbjct: 482 EDGRCRSLEEIGGMYRVSKEWIRKIEKSAMA 512


>gi|291196346|emb|CBG22645.1| DNA-directed RNA polymerase subunit D [Pseudomonas moorei]
          Length = 237

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 93/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +    E       +    + + D + A     ++ ++    P  A      + +  + 
Sbjct: 50  GIAPPAAEVPPPIDPKAVKADDDSDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEI 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + +         L  L
Sbjct: 110 TRKAL-----------------------------------KKHGRHNKAAIAELLALADL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LVE++     R+   E  +++L      + R  FL +  G E+D  W
Sbjct: 135 FMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              A    + ++   +      I++ + ++ ++  ETG+ I+E 
Sbjct: 195 SD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLRIAEI 237


>gi|56460225|ref|YP_155506.1| flagellar biosynthesis sigma factor [Idiomarina loihiensis L2TR]
 gi|56179235|gb|AAV81957.1| DNA-directed RNA polymerase specialized sigma 28 subunit
           [Idiomarina loihiensis L2TR]
          Length = 241

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 106/243 (43%), Gaps = 18/243 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
               +  +  ++E +  LV  +A     R    +Q  DLIQ G IGL++AA  FD   G 
Sbjct: 7   YAATADNRNAIIEQHTGLVKRIAHHMMARLPASVQVDDLIQAGMIGLLEAARNFDNSKGA 66

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F T+A   ++ A+   I         P  +     +V+   R++ N+  R+    E+A 
Sbjct: 67  SFETFAGIRIRGAMLDEIRRGDW---APRSVHRNHRRVLEAIRQVENETGRDAKDTEVAA 123

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK----NAVSPLDSAIQANLR 610
           KL M ++    +L      +S    +G ED     D I  +    +A  P      A   
Sbjct: 124 KLNMGMDEYHHIL----RDVSTGRIVGIEDLGVSEDAIMPEQVTGSAYEPQKDVENAAFH 179

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     ++SL  RE  VL + +    + +  L+E+G+   V+  R+ QI ++A+ +LK  
Sbjct: 180 KALVSTISSLPEREALVLSLYY----DEELNLKEIGEVLSVSESRVSQIHSQAMLRLKSR 235

Query: 671 SRS 673
            ++
Sbjct: 236 MQN 238


>gi|107024379|ref|YP_622706.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia AU
           1054]
 gi|116688295|ref|YP_833918.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           HI2424]
 gi|170731608|ref|YP_001763555.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|105894568|gb|ABF77733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia AU 1054]
 gi|116646384|gb|ABK07025.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia HI2424]
 gi|169814850|gb|ACA89433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 243

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYRVDHA-DPLSALLDDHLREALVEAIERLPEREKLLMSLYYERG----LNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 208 GAVLEVSESRVCQLHSQAVARLRARLREQ 236


>gi|325479184|gb|EGC82281.1| sigma-70, region 4 [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 343

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 79/262 (30%), Positives = 127/262 (48%), Gaps = 10/262 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQ 475
              +S      IV   + G   A  A   +VE N  LV S A  +       L   DL+Q
Sbjct: 85  MMKLSDLTNEQIVEQFQIGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQ 141

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ + 
Sbjct: 142 SGMLGMIRAAEKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQI 201

Query: 536 ARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
            +        E     E         + +  + +      SL   +  ED++   L D +
Sbjct: 202 LKANPEASDEELYRILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMV 261

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D++        ++ ++     + L  LT RE++++  R+G+      TLEE+GK + ++
Sbjct: 262 GDESTP-VDMLILEKDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTLEEIGKIYDLS 320

Query: 653 RERIRQIEAKAIRKLKHPSRSK 674
           RERIRQIE +A+ KLK  S  +
Sbjct: 321 RERIRQIENQALGKLKEFSERE 342


>gi|289523542|ref|ZP_06440396.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503234|gb|EFD24398.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 251

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 58/239 (24%), Positives = 103/239 (43%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  +  +   K+E+V   L LV  V  + +     GL   DL+  G +GL+ A +++D  
Sbjct: 16  KYVDTRSEAIKEEIVGLFLPLVRYVVGRMSIVIPPGLSQDDLLSFGAMGLLDAIDRYDPS 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F+T+A   ++ AI   +        +    RDKI ++ +    M N+   +   E 
Sbjct: 76  RGVSFNTFAFSRIRGAILDELRRYDW---LSRGARDKIQRLEKAIAEM-NEQGLKANDEM 131

Query: 552 IAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           + +KL M  + +R    L      +SL+  I  ++       +    + +P +       
Sbjct: 132 LMEKLQMDEKELRWLYELMSRSYVVSLDEVISLDEGDVERSALVPDTSPNPEEYMEAMED 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +T    L  L  RE+ VL + +  G     T +E+G+   VT  R+ QI  KA+  LK
Sbjct: 192 CDTLKGALEKLEEREQLVLSLYYYEG----LTFKEIGEVLGVTESRVSQIHGKALAMLK 246


>gi|171320641|ref|ZP_02909660.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MEX-5]
 gi|172059263|ref|YP_001806915.1| flagellar biosynthesis sigma factor [Burkholderia ambifaria MC40-6]
 gi|171094127|gb|EDT39215.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MEX-5]
 gi|171991780|gb|ACB62699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MC40-6]
          Length = 244

 Score =  106 bits (264), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 93/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 94  TSREVEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 154 EPFLDRYRVDHA-DPLSALLDDHLREALVDAIDRLPEREKLLMSLYYERG----LNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 209 GAVLEVSESRVCQLHSQAVARLRARLREQ 237


>gi|167838290|ref|ZP_02465149.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           MSMB43]
          Length = 244

 Score =  106 bits (264), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 103/244 (42%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I++ E++     LV  +  +   +    +   DLIQ G IGL+ AA ++    
Sbjct: 2   MYNAQGKISQDEVLTQYAPLVRRLGLQLVAKMPASVDLDDLIQAGMIGLLDAASRYKEDQ 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P  +R    +V     ++  ++ R     EI
Sbjct: 62  GAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSREVEHAVHQVEQRLGRSANETEI 118

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L MP++  + +L+       +  E      D     D     ++  PL + +  +LR
Sbjct: 119 AAHLQMPLDEYQSMLQDLHGSQLVYYEDFDRSADDEPFLDRYRADHS-DPLSALLDEHLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     +  L  RE+ ++ + +  G      L E+G    V+  R+ Q+ ++A+ +L+  
Sbjct: 178 DALVDAIEHLPEREKLLMSLYYERG----LNLREIGAVLEVSESRVCQLHSQAVARLRAK 233

Query: 671 SRSK 674
            R +
Sbjct: 234 LREQ 237


>gi|157376181|ref|YP_001474781.1| flagellar biosynthesis sigma factor [Shewanella sediminis HAW-EB3]
 gi|157318555|gb|ABV37653.1| Phosphatidylserine decarboxylase [Shewanella sediminis HAW-EB3]
          Length = 239

 Score =  106 bits (264), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 100/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KASIVEQYAPLVKKIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+    EIA++L M ++
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRVAQVIDELGQELGRDAVDSEIAQRLDMSLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +  E+       +S       +     +  
Sbjct: 130 EYHHIL----NDVSVGKVVGIEDLGVSVDVVSHEEVQQDDIFESIADVEFHKALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|172058807|ref|YP_001815267.1| RNA polymerase sigma factor SigB [Exiguobacterium sibiricum 255-15]
 gi|171991328|gb|ACB62250.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Exiguobacterium
           sibiricum 255-15]
          Length = 265

 Score =  106 bits (264), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 118/262 (45%), Gaps = 5/262 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           + + S +   S  E   ++ + ++ + +       ++     LV ++A+K++       D
Sbjct: 1   MPAKSQQRHHSDDEVLRLIDLYQQDD-QDEEVHAALLARYSDLVEALARKFSRGRPIHDD 59

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L+Q G IGL+ A  +FD   G  F ++A+  +   I R I D++ ++ +P  +++   K+
Sbjct: 60  LVQVGMIGLLAALRRFDKEFGRSFESFAVPTIIGEIKRFIRDKTWSVHVPRRIKELGPKI 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +    ++ +++R P  +EIA +L +  E V + L++ K   +L      E         
Sbjct: 120 KKAVEELTTELQRSPRIDEIAARLEVSEEEVLETLEMGKSYQALSVDSSIEADQEGSTVT 179

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                 +  +     + +    +  A LT RE  +L   +        + +E G+   ++
Sbjct: 180 LLDLVGNQENGYDSVDQKLILEKAFAVLTDRERSILECAYYRN----MSQKETGELLGIS 235

Query: 653 RERIRQIEAKAIRKLKHPSRSK 674
           +  + +++ +A++KL+   + +
Sbjct: 236 QMHVSRLQRRALQKLREAIKVE 257


>gi|239934534|emb|CAR94581.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 250

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 103/283 (36%), Gaps = 37/283 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI+IAKRIE G   ++ S+   P   + ++    +  +G   L +I  L   + PE
Sbjct: 4   TREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLKEYKDYQEGERRLADI--LSGYLDPE 61

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
           S        E    ++ ED +  K   +V+  + + E     S DD      P       
Sbjct: 62  SDEEIPEVIEDAVLEEDEDETASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAK- 120

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
                                          E+  V++E +S+ +      K  + S + 
Sbjct: 121 ---------------------------VRFTELETVWQETKSVIE------KHGRDSAEA 147

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLER 373
           K   E L  +           D++ E +    ++I  +E E++R A   G + R  F   
Sbjct: 148 KAALEALASVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDRTQFRTS 207

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
             G+E +P W+         + K  +      +L  + +I  I
Sbjct: 208 FPGQESNPGWLDEQMAKASPDIKGHLEKVRPDVLAFQQKIADI 250


>gi|52080250|ref|YP_079041.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|52785627|ref|YP_091456.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|319645970|ref|ZP_08000200.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52003461|gb|AAU23403.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus licheniformis
           ATCC 14580]
 gi|52348129|gb|AAU40763.1| SigD [Bacillus licheniformis ATCC 14580]
 gi|317391720|gb|EFV72517.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 254

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 100/233 (42%), Gaps = 13/233 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R  E +   A  +++   + LV     +      + +   DL+  G +GL  A EKFD  
Sbjct: 14  RWKEWKDPQAGDDLIRRYMPLVTYHVGRIAVGLPKSVHKDDLVSLGMLGLYDALEKFDPG 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + ++ AI   +  +     +P   R+K  KV     ++  +  R  +P E
Sbjct: 74  RDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKTKKVEAAIEKLEQRYLRNVSPSE 130

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           IA +L M  + V   +        +S++  +   ED  ++   I D    +P +  ++  
Sbjct: 131 IAAELGMSEQDVVTTINEGFFANLLSIDEKLHDHEDGENVQVMIRDDKTSTPEEKMLKDE 190

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           L       +  L+ +E+ V+ + +      + TL E+G+   ++  RI QI +
Sbjct: 191 LISQLAEKINELSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHS 239


>gi|258592481|emb|CBE68790.1| RNA polymerase sigma factor whiG (modular protein) [NC10 bacterium
           'Dutch sediment']
          Length = 459

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 106/232 (45%), Gaps = 15/232 (6%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  ++ AN+ LV  VA + +      ++  DL   G +GL+ A E +D     +F+TYA 
Sbjct: 20  RDRLITANISLVRQVAGRLSLQLPSCVELDDLESAGAVGLVSAVEHYDPDQPSEFATYAQ 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + ++ AI   +  Q      P  +R K  ++ +T  R+   + REP+ +E+A  L M  E
Sbjct: 80  YRIRGAILDDLRAQDF---APRSLRAKAREIQQTLVRLEVDLGREPSDDEVAAALGMDRE 136

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              + L        +SL+ P  + D +    L   + D+    P   A +         +
Sbjct: 137 TYWRTLGEIRGMVLVSLDEPGVEADGTESDRLIWELPDRAGRDPSTEAARRERVRLLGGI 196

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +L  +E  VL + +      + T++E+G+   V+  R+ QI   AI +++
Sbjct: 197 IEALPAQERLVLTLYYF----EELTMKEIGRVLEVSESRVSQIHTSAILRMR 244


>gi|59712441|ref|YP_205217.1| flagellar biosynthesis sigma factor [Vibrio fischeri ES114]
 gi|59480542|gb|AAW86329.1| RNA polymerase, sigma-28 (sigma-F, FliA) factor [Vibrio fischeri
           ES114]
          Length = 243

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 98/227 (43%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +   DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 19  FLERYSDLVKRIAHHLMARLPASVLVDDLIQAGMIGLLEAQQNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   I        +P  +      +    R +  K+ R+PT +EIA  L +P++   
Sbjct: 79  RGSMLDEIRRGDW---VPRSVHKNSRMINSAIRELEAKLSRDPTDKEIADYLELPLDQYY 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLT 621
           ++L      ++    +G ED     D I  +       P       + R      + +L 
Sbjct: 136 QIL----NDVNCGKLVGMEDLGVSDDVIATEEQADDNLPFQGVADEHFRVALVEAIKTLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G    V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGAVIGVSESRVSQIHSQSMQRLR 234


>gi|294500913|ref|YP_003564613.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
 gi|294350850|gb|ADE71179.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
          Length = 253

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 105/251 (41%), Gaps = 12/251 (4%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNI 479
           SI E           E   S A   +V+  + LV    ++ +    + +   +L   G I
Sbjct: 3   SIQEVEEHKIWQEWIETRDSHAGNMLVKKYMPLVNYHVQRISVGLPKNIHKEELRSLGLI 62

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL  A EKFD+    KF TYA + ++ AI   +  +     +    R+K  ++ +    +
Sbjct: 63  GLYDALEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDW---LSRSAREKTKRIEQATEAL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNA 597
             +  R   P E+AK++ M    V   +        +S+E    + +       I+D+  
Sbjct: 120 EQRYLRRVAPSEVAKEVGMTEADVVHTMNEGFLANVLSMEEQPKEYEDGEQKYTIKDEKT 179

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +SP +  I     +    V+  L  +E+ V+ + +      + T  E+ +   ++  RI 
Sbjct: 180 LSPEEELINDERYQELAEVIEQLNEKEQLVVSLFY----KEELTFTEIAQLLGLSTSRIS 235

Query: 658 QIEAKAIRKLK 668
           QI +KA+ K++
Sbjct: 236 QIHSKALFKMR 246


>gi|197335206|ref|YP_002156660.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio fischeri MJ11]
 gi|197316696|gb|ACH66143.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio fischeri MJ11]
          Length = 243

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 98/227 (43%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +   DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 19  FLERYSDLVKRIAHHLMARLPASVLVDDLIQAGMIGLLEAQQNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   I        +P  +      +    R +  K+ R+PT +EIA  L +P++   
Sbjct: 79  RGSMLDEIRRGDW---VPRSVHKNSRMINSAIRELEAKLSRDPTDKEIADYLELPLDQYY 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLT 621
           ++L      ++    +G ED     D I  +       P       + R      + +L 
Sbjct: 136 QIL----NDVNCGKLVGMEDLGVSDDVIATEEQADDNIPFQGVADEHFRVALVEAIKTLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G    V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGAVIGVSESRVSQIHSQSMQRLR 234


>gi|228931462|ref|ZP_04094387.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229188107|ref|ZP_04315191.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228595348|gb|EEK53084.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228828268|gb|EEM73978.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 323

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 73/264 (27%), Positives = 130/264 (49%), Gaps = 9/264 (3%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-- 469
           EIK I     +S  E    +++ ++ +      +  +   N+ LV+S+A+KY N+     
Sbjct: 39  EIKEIGNYQVLSKQES---LNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIE 95

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC-TIRIPVHMRDK 528
           F DL+QEGN G+++A E F+  LGY FSTYA  W+++ +   I  +     +IP ++   
Sbjct: 96  FDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFCWIQKRMLGIICKKRSGPFKIPNYVNQF 155

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS 586
             K V    +      R P+ EE+ K L +  E V +     K    ++L+    +ED  
Sbjct: 156 NLKYVELEDKYLQMYNRPPSVEEVVKDLDVTSEIVIRHNVYYKRATTMTLDIDTINEDIG 215

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEV 645
                 +DK+A+  ++  +  +L      +    L P+++ VL + FG+     +  +E+
Sbjct: 216 ISNSSHDDKSAIPSINEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYLHKEI 275

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
            K   +T ER+ QI+ +AI+KLK 
Sbjct: 276 AKALMITTERVSQIKEEAIKKLKK 299


>gi|78064851|ref|YP_367620.1| flagellar biosynthesis sigma factor [Burkholderia sp. 383]
 gi|77965596|gb|ABB06976.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia sp.
           383]
          Length = 244

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 94  TSREVEHAVHQVEQNLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 154 EPFLDRYRVDHA-DPLSALLDEHLREALVEAIERLPEREKLLMSLYYERG----LNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 209 GAVLEVSESRVCQLHSQAVARLRARLREQ 237


>gi|134294347|ref|YP_001118082.1| flagellar biosynthesis sigma factor [Burkholderia vietnamiensis G4]
 gi|134137504|gb|ABO53247.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           vietnamiensis G4]
          Length = 244

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/209 (23%), Positives = 93/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  +++L+       I  E      D 
Sbjct: 94  TSREVEHAVHQVEQQLGRSASEAEIAQHLKMPLDEYQEMLQDLHGSQLIYYEDFDRAADD 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 154 EPFLDRYRVDHA-DPLSALLDDHLRGALVDAIDRLPEREKLLMSLYYERG----LNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 209 GAVLEVSESRVCQLHSQAVARLRARLREQ 237


>gi|238924140|ref|YP_002937656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|238875815|gb|ACR75522.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|291524873|emb|CBK90460.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale DSM 17629]
 gi|291529014|emb|CBK94600.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale M104/1]
          Length = 255

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 101/230 (43%), Gaps = 13/230 (5%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++    +LV  VA +   Y    +++ DL+  G  GL+ A +KF+     KF TYA 
Sbjct: 22  REQLIIEYAQLVRLVAGRLSMYLGHNVEYDDLVSYGIFGLIDAIDKFNLEKNVKFETYAS 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   I        IP  +R +  K+    + +  +  +     ++AK+L++  +
Sbjct: 82  LRIRGAILDQIRKMDW---IPRTVRQRQRKIDEAIKNIELRTGKTANDADLAKELSISED 138

Query: 562 GVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +            +SL+    +     + D   + +   P +   Q  L+    + L +
Sbjct: 139 ELCSWQSQLKVTNVVSLDEF-DESGPEPVMDAAHNSHYAQPEEIVTQEELKTMLVKSLDN 197

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LT +E RV+ + +      D TL+E+     V+  R+ Q+  K + K++ 
Sbjct: 198 LTEKERRVIELYY----YEDLTLKEISNILEVSESRVSQLHTKGLIKMRK 243


>gi|158341591|ref|YP_001522756.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311832|gb|ABW33441.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 111/239 (46%), Gaps = 15/239 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            + + +     A+   +  N RLV + AK+Y    + + DL+  G +GL  A +KFD   
Sbjct: 25  QIERAQAGDRRAEDRFIRKNQRLVFNEAKRYRG-LVDWDDLVNAGTLGLSIAIQKFDLSR 83

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G++FSTYA+  ++  I + I +      +   +   + K+    + +  +++R+PT +E+
Sbjct: 84  GFQFSTYAVKPIRTEIRQLICE---QRGLSREITKHLKKIDEAEQDLKLELERKPTLDEL 140

Query: 553 AKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++       +       +  +  SL    G E      DF+ED   +   D A   N++
Sbjct: 141 AERTGYSHRVITNAWSKARVVDTSSLNVLTGTEQGIECLDFVEDLEQLDSWDFAESINMK 200

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     +A L  RE  ++R R        H+  E+G    ++ ERIRQ+  KA+  LKH
Sbjct: 201 DY----IAQLPDRESFIVRARR-----DGHSYREIGTMLKLSGERIRQLYQKALEYLKH 250


>gi|288554854|ref|YP_003426789.1| RNA polymerase sigma factor SigB [Bacillus pseudofirmus OF4]
 gi|288546014|gb|ADC49897.1| RNA polymerase sigma factor SigB [Bacillus pseudofirmus OF4]
          Length = 261

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 113/247 (45%), Gaps = 5/247 (2%)

Query: 429 HIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            +   +R  +       + ++V+    LV S+A+K++       DL Q G +GL+ A  +
Sbjct: 14  EVYEWIRLYQETGEEEVQVKLVKHYEALVRSLARKFSKGREYDEDLYQVGMVGLLAALTR 73

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G  F ++A+  +   I R I D++ ++ +P  +++   K+ +    ++ ++ R P
Sbjct: 74  FDSEFGRSFESFAVPTIVGEIKRFIRDKTWSVHVPRRIKELGPKIKKAVESLTVELNRSP 133

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              EIA  L +  E V + ++++K   +L      E     G+        +      + 
Sbjct: 134 LVHEIAAYLEVSEEEVLETMEMSKSYQALSVDRSLEADQEGGEVTLLDLVGNEDSGFEKT 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + +    +    L  RE+++L + +        + +E G++  +++  + +++ +A++KL
Sbjct: 194 DQKMLLQKAFQVLNEREKQILMLTYYDN----LSQKETGEKLGISQMHVSRLQRRALQKL 249

Query: 668 KHPSRSK 674
           +   + +
Sbjct: 250 RDSIKVE 256


>gi|145298363|ref|YP_001141204.1| flagellar biosynthesis sigma factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142851135|gb|ABO89456.1| RNA polymerase sigma-27 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 239

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 94/231 (40%), Gaps = 17/231 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA   +
Sbjct: 16  LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIRI 75

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   I        +P  +      +      +     R+    E+A ++ + +    
Sbjct: 76  RGSMLDEIRRGDW---VPRSVHRNSRAIAEAIENVEQAHGRDARDTEVAVQMGVSLGEYH 132

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +L+     +S    IG ED     D I   +D    S  D       +      +  L 
Sbjct: 133 TMLQ----DVSCGKIIGIEDLGVSEDVIGHPDDAGGNSGFDELAAERFQGALAEHIGRLP 188

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ +L+   R
Sbjct: 189 EREALVLSLYY----DEELNLREIGEVLNVSESRVSQIHSQAMHRLRARLR 235


>gi|218289600|ref|ZP_03493820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240250|gb|EED07433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 222

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 52/220 (23%), Positives = 95/220 (43%), Gaps = 13/220 (5%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             +     +S  E R ++          + A++ ++  N RLV +V +++  RG +  DL
Sbjct: 11  HHVDEYEKLSDEEVRELLER---SHNGDAEARERLIVHNQRLVWAVVQRFLGRGYEAEDL 67

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q G IGLMKA +KFD     KFSTYA+  +   I R + D   T+++   +++   ++ 
Sbjct: 68  FQIGCIGLMKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DSTVKVSRSLKETAKQIR 126

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDF 591
               R++ ++ R+P   EIA+ + M    +    +  + P S+   + + D    +L D 
Sbjct: 127 HVRDRLAKELGRQPHITEIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYLMDQ 186

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           I D+      D             ++  L  RE       
Sbjct: 187 IADEETEGKFDKVE-------LHEIIGRLPERERSSFTCD 219


>gi|126659593|ref|ZP_01730724.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619136|gb|EAZ89874.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 245

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 110/240 (45%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           ++      +   +  +VE NL LV  VA + + +    + DL Q G +GL++A E+FD  
Sbjct: 4   LIAYARNPSLELRNRLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFDPQ 63

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  +   + D+   +RIP   ++  +K  +  ++++  +KR PT +E
Sbjct: 64  QGCAFSSFAIPYIRGEMLHYLRDKGSVMRIPRRWQELHNKAKKIRKQLTVSLKRPPTDQE 123

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
           IA  L +P++   +       +  +SL+  I    + +   GD + D++  +        
Sbjct: 124 IANALEVPLKEWNECQLALQNRLLVSLDATISQNVDCSISFGDTLPDQDYQAKQKLEED- 182

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    R L  L  + +  +   F      +   +E  KQ  ++   + +   K I++L
Sbjct: 183 --RLQLQRALGQLEEKTKAAIECVFL----NELPRKEAAKQIGISPMTVTRHLKKGIQQL 236


>gi|119476300|ref|ZP_01616651.1| RNA polymerase sigma factor for flagellar operon [marine gamma
           proteobacterium HTCC2143]
 gi|119450164|gb|EAW31399.1| RNA polymerase sigma factor for flagellar operon [marine gamma
           proteobacterium HTCC2143]
          Length = 240

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 96/227 (42%), Gaps = 11/227 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             EMVE    LV  +A     R    +Q  DL+Q G IGL++AA  +D   G  F TYA 
Sbjct: 10  MDEMVERYAPLVKRIAHHLMARMPSSVQVEDLVQAGLIGLLEAARNYDASKGASFETYAG 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   +         P  +     +V    + + +++ R+ T +E+A +L++ ++
Sbjct: 70  IRIRGSMIDDVRRGDW---APRSIHRNSRRVSEALKIVESRLGRDATDQEVAAELSVSLD 126

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              ++L+ +                   + +    A         A LR+     + +L 
Sbjct: 127 DYYRMLQDSASSKLFSFDEITSGEDKPEEQLPSSTASPFDGIQANA-LRQGLADAIGTLP 185

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL     +  + +  L+E+G    V+  R+ QI ++A  +L+
Sbjct: 186 ERERLVL----ALYYDEELNLKEIGLILGVSESRVSQIHSQAATRLR 228


>gi|74055051|gb|AAZ95856.1| FliA [Aeromonas hydrophila]
          Length = 239

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 95/231 (41%), Gaps = 17/231 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  +A+    R    +   DLIQ G IGL++A+  FD   G  F TYA   +
Sbjct: 16  LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIRI 75

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   I        +P  +      +      +     R+    E+A ++ + +    
Sbjct: 76  RGSMLDEIRRGDW---VPRSVHRNSRSIAEAIENVEQAHGRDARDTEVAAQMGVSLGEYH 132

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +L+     +S    IG ED     D I   +D  + S  D       +      +  L 
Sbjct: 133 TMLQ----DVSCGKIIGIEDLGVSEDVIGHPDDAASNSGFDELAAERFQGALAEHIGRLP 188

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ +L+   R
Sbjct: 189 EREALVLSLYY----DEELNLREIGEVLNVSESRVSQIHSQAMHRLRARLR 235


>gi|213610106|ref|ZP_03369932.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 103

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 76/102 (74%), Positives = 83/102 (81%)

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           IGD++ SHLGDFIED     PLDSA   +LR  T  VLA LT RE +VLRMRFGI MNTD
Sbjct: 1   IGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTD 60

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           HTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFLD
Sbjct: 61  HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 102


>gi|49082218|gb|AAT50509.1| PA1455 [synthetic construct]
          Length = 248

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 100/238 (42%), Gaps = 14/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +A  +++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K+D   
Sbjct: 10  YSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E+
Sbjct: 70  GASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVTDAIRAIEARTGRDAKDHEV 126

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + +E    +L  T+     S +  + D +     D     N    +   +    +
Sbjct: 127 AAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTSLSHNEP--IHGLLDERFQ 184

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 AALADAIAKLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 238


>gi|32475302|ref|NP_868296.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|32445843|emb|CAD78574.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|327540927|gb|EGF27485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodopirellula baltica
           WH47]
          Length = 272

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 102/241 (42%), Gaps = 18/241 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + ++VE  ++LV    ++   R   G++  DLI  G  GLM A + +D   G KF T+ +
Sbjct: 39  RNQLVERYMQLVRYNGERIWQRLPDGVELDDLISAGMFGLMDAIDAYDTERGVKFETFCV 98

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  K+    + +  +  R PT +E++  + + V+
Sbjct: 99  PRIRGAMLDELRKMDW---VPRLVRSKASKLATATKTLEARFGRAPTVQELSAHMEIDVK 155

Query: 562 GVRKVLKITK--EPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            V K+         +SL     + D        D +EDK    P     + +L    T+ 
Sbjct: 156 EVEKMQSEANAVGVVSLNKKWYETDSYKDVREIDILEDKKGEDPTRRVQKNDLMRLVTKG 215

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L        R  R+   +    + T++E+G    ++  R+ Q+    + +L+     ++L
Sbjct: 216 LN-------RNERLIIILYYYEELTMKEIGATLDLSESRVSQMHTAIVNRLQQQLGVRRL 268

Query: 677 R 677
            
Sbjct: 269 E 269


>gi|223986127|ref|ZP_03636150.1| hypothetical protein HOLDEFILI_03458 [Holdemania filiformis DSM
           12042]
 gi|223961932|gb|EEF66421.1| hypothetical protein HOLDEFILI_03458 [Holdemania filiformis DSM
           12042]
          Length = 241

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 119/247 (48%), Gaps = 15/247 (6%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           +++ +    ++ + +     A+++ V  N+ LV S+  ++        DL Q G +GLMK
Sbjct: 1   MNDQQEFFDLLHQAQQGDEQAREQCVLRNVGLVWSIVNRFK-THSSAQDLFQIGCLGLMK 59

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A   FD      FSTYA+  +   I R   D+   ++I   ++++  +V ++  R++ K+
Sbjct: 60  AINNFDTSYNVMFSTYAVPIILGEIKRYFRDEG-QMKISRSLKERYLQVQKSRERLAQKL 118

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPL 601
           +REPT  EI + L +    V   ++  +   S++     +D S   L D +ED++     
Sbjct: 119 QREPTYREIGEDLGVEENDVMLAMEANQFLASMDEAFYQKDGSTIKLEDKVEDRHGEDVP 178

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  ++    + +  L  RE+ ++ +R+ +  N     E + K+  +++ ++ ++E 
Sbjct: 179 -------MKLALKKEIGHLEQREQYLIYLRYELEYNQ----EAIAKKMGISQVQVSRLEK 227

Query: 662 KAIRKLK 668
           K + KLK
Sbjct: 228 KILNKLK 234


>gi|153938360|ref|YP_001391942.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|152934256|gb|ABS39754.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|295319962|gb|ADG00340.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. 230613]
          Length = 242

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 111/236 (47%), Gaps = 13/236 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           S  K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFST
Sbjct: 8   SYVKEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFST 67

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   +K ++   +        I     DK+++      ++  K+ +EP   +IA +L +
Sbjct: 68  YASIRIKGSMIDELR---RNSPISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIAGELNI 124

Query: 559 PVEGVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            ++ V ++         ISLE  I   ED   L   I+D+ + SP     +    +   +
Sbjct: 125 SLKEVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAK 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            +  L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK   
Sbjct: 185 AIELLNEKDRLVVTLYY----YEELTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236


>gi|297746573|emb|CAZ61004.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 242

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/285 (16%), Positives = 91/285 (31%), Gaps = 44/285 (15%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P             +         E
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSE 53

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            +  D  E E + E       +D       PE A      L    + +  ++        
Sbjct: 54  DDLADEDEEEDEDEDGDGDDAEDEGDGGPDPEVAREKFGELRAQYEVTRLSI-------- 105

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                                      QK+ ++    +    +L  +     L   + D 
Sbjct: 106 ---------------------------QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDR 138

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +    
Sbjct: 139 LVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSP 198

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +  + D +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 199 RLLEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|325527508|gb|EGD04836.1| flagellar biosynthesis sigma factor [Burkholderia sp. TJI49]
          Length = 243

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/209 (23%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVEHAVHQVEQQLGRAASEAEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYRVDHA-DPLSALLDDHLRGALVEAIERLPEREKLLMSLYYERG----LNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 208 GAVLEVSESRVCQLHSQAVARLRARLREQ 236


>gi|291558216|emb|CBL35333.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum V10Sc8a]
          Length = 251

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 59/267 (22%), Positives = 120/267 (44%), Gaps = 22/267 (8%)

Query: 422 ISISEFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEG 477
           +++     +  ++ K      +  + E+V   + LV  +A    N      +  D+I EG
Sbjct: 1   MAVQSKERLNELLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYAESDDIINEG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            I LM A + FD     KF TYA   +K A+   +        +P  +R    ++     
Sbjct: 61  VIALMAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRKLDR---VPRTLRKLSKQLDDNFA 117

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDK 595
           R+++++ R PT EE+A+ + M    + K++  T     +S E  + ++   +L + I   
Sbjct: 118 RLNSELCRTPTDEELAESMNMTTAQLSKLMANTAGMITLSFEELLYED---NLDESIS-A 173

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           ++ +      +   ++     +A+L  +E++V+ M +           E+ K   +T+ R
Sbjct: 174 SSETADAKMYEREKKQVIANAVATLPEKEKQVVTMYY----YERLKYSEIAKVMSITQSR 229

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           + QI +KA+  LK+     KL S+++G
Sbjct: 230 VCQIHSKAMLTLKN-----KLESYING 251


>gi|288573001|ref|ZP_06391358.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288568742|gb|EFC90299.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 248

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 106/243 (43%), Gaps = 15/243 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
             + +        K E+V   + LV  V  + T     GL + DLI  G +GL+ A ++F
Sbjct: 8   EALWQRYRSNPSEKDEIVSRYIPLVKYVVARMTVTPPPGLDYEDLISFGLMGLLDAIDRF 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +   G+ F T+A+  ++ A+   +       R     R+K+ ++ R   R+  +    P 
Sbjct: 68  EIERGFSFQTFAVPRIRGAVLDELRKCDWFSRTG---REKLQRLERATERLMIQ-GITPD 123

Query: 549 PEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAI 605
            E + +++ +  +  R++L +      +SL+  +  ++     GD +    A +      
Sbjct: 124 DESLKREMDVDDKTYREMLSLASRGYVVSLDEVMSLDEGDVQKGDLLSYTGASAQEFLEN 183

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R+     L  L+ RE  VL M +      + TL+E+G    VT  R+ QI  KAI 
Sbjct: 184 REE-RDLVVGALNRLSERERLVLSMYYL----EEMTLKEIGLVLGVTESRVSQIHGKAIV 238

Query: 666 KLK 668
            LK
Sbjct: 239 SLK 241


>gi|152965591|ref|YP_001361375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
 gi|151360108|gb|ABS03111.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 286

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 95/241 (39%), Gaps = 11/241 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               ++  +  +VE NL LV  +  ++  R    +   DL   G + L +A+  +D   G
Sbjct: 1   MVELSAAERHALVEKNLPLVGYITSEFIGRLPSHVSRDDLTSAGLMALFQASRGYDPNTG 60

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+ YA   ++ AI   +            +R +  ++ RT  +++ ++ R PT  E+A
Sbjct: 61  VPFNRYANTRIRGAILDDLRGADW---ASRGVRSRQRQLSRTEDQLTTELGRTPTSAELA 117

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             L +  + +       +  + L       +   + D +   +A  P    +        
Sbjct: 118 ASLGVSEKELASTRDEAQRSMVLSMQGFTAEGGSIDDHLP-THAPGPEQELLHRERLGYL 176

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              +A L  R + V+   F      +  + E+ ++  V+  RI Q+ A+A+  L+    +
Sbjct: 177 RSAIAVLPERLKHVIEGYF----IQERPMAELAEELEVSESRISQMRAEALALLRDGMNT 232

Query: 674 K 674
            
Sbjct: 233 H 233


>gi|15927639|ref|NP_375172.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus N315]
 gi|148268516|ref|YP_001247459.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394579|ref|YP_001317254.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JH1]
 gi|253315694|ref|ZP_04838907.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|257794514|ref|ZP_05643493.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9781]
 gi|258411256|ref|ZP_05681534.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9763]
 gi|258419772|ref|ZP_05682738.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9719]
 gi|258438079|ref|ZP_05689458.1| sigma factor B [Staphylococcus aureus A9299]
 gi|258441327|ref|ZP_05690812.1| sigma factor B [Staphylococcus aureus A8115]
 gi|258446979|ref|ZP_05695131.1| sigma factor B [Staphylococcus aureus A6300]
 gi|258449788|ref|ZP_05697888.1| sigma factor B [Staphylococcus aureus A6224]
 gi|258453474|ref|ZP_05701453.1| sigma factor B [Staphylococcus aureus A5937]
 gi|269203699|ref|YP_003282968.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282895212|ref|ZP_06303428.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8117]
 gi|295407610|ref|ZP_06817401.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8819]
 gi|296275695|ref|ZP_06858202.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297246607|ref|ZP_06930438.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8796]
 gi|13701859|dbj|BAB43151.1| sigma factor B [Staphylococcus aureus subsp. aureus N315]
 gi|147741585|gb|ABQ49883.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149947031|gb|ABR52967.1| RNA polymerase sigma-B type [Staphylococcus aureus subsp. aureus
           JH1]
 gi|257788486|gb|EEV26826.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9781]
 gi|257840011|gb|EEV64477.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9763]
 gi|257844254|gb|EEV68637.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9719]
 gi|257848496|gb|EEV72486.1| sigma factor B [Staphylococcus aureus A9299]
 gi|257852371|gb|EEV76296.1| sigma factor B [Staphylococcus aureus A8115]
 gi|257854212|gb|EEV77163.1| sigma factor B [Staphylococcus aureus A6300]
 gi|257856962|gb|EEV79863.1| sigma factor B [Staphylococcus aureus A6224]
 gi|257864346|gb|EEV87095.1| sigma factor B [Staphylococcus aureus A5937]
 gi|262075989|gb|ACY11962.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282762402|gb|EFC02546.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8117]
 gi|285817729|gb|ADC38216.1| RNA polymerase sigma factor SigB [Staphylococcus aureus 04-02981]
 gi|294967508|gb|EFG43546.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8819]
 gi|297176507|gb|EFH35773.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8796]
 gi|312830416|emb|CBX35258.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315128403|gb|EFT84412.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|329727790|gb|EGG64242.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21172]
          Length = 256

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 116/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|307243397|ref|ZP_07525554.1| putative RNA polymerase sigma-B factor [Peptostreptococcus stomatis
           DSM 17678]
 gi|306493207|gb|EFM65203.1| putative RNA polymerase sigma-B factor [Peptostreptococcus stomatis
           DSM 17678]
          Length = 257

 Score =  106 bits (263), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 109/243 (44%), Gaps = 12/243 (4%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + + E   I S     +   +  +  ++E +L L   +++KY N+G+ + DL Q  
Sbjct: 8   KYEEMDVKELFKIFS----DDKTNAAVRNILIEKHLYLAKILSRKYMNKGVDYEDLYQVA 63

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           ++ L+ A +++D   G++FS++A   +   I +   D+  T+R+P  +++   K+     
Sbjct: 64  SLALIYAIDRYDISKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQELSKKISNAKV 123

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDK 595
            +  +++R PTP EIA  L +  E V + ++ +   +P+SL+TP  D+         +  
Sbjct: 124 YLEQELRRSPTPSEIAGYLDITEEEVLEAMEASYGYQPVSLDTPSNDDSEDKDMTLGDRV 183

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                    I+    +     + +L   E +++R RF          EE      +++  
Sbjct: 184 GTEEKNFRHIEEM--DFINHFMKTLNELEVQIIRGRFFDNKTQSVIAEE----LGISQMT 237

Query: 656 IRQ 658
           + +
Sbjct: 238 VSR 240


>gi|227501074|ref|ZP_03931123.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227216847|gb|EEI82245.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 344

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 79/262 (30%), Positives = 127/262 (48%), Gaps = 10/262 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQ 475
              +S      IV   + G   A  A   +VE N  LV S A  +       L   DL+Q
Sbjct: 86  MMKLSDLTNEQIVEQFQIGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQ 142

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ + 
Sbjct: 143 SGMLGMIRAAEKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQI 202

Query: 536 ARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
            +        E     E         + +  + +      SL   +  ED++   L D +
Sbjct: 203 LKANPEASDEELYRILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMV 262

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D++        ++ ++     + L  LT RE++++  R+G+      TLEE+GK + ++
Sbjct: 263 GDESTP-VDMLILEKDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTLEEIGKIYDLS 321

Query: 653 RERIRQIEAKAIRKLKHPSRSK 674
           RERIRQIE +A+ KLK  S  +
Sbjct: 322 RERIRQIENQALGKLKEFSERE 343


>gi|94500298|ref|ZP_01306831.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
 gi|94427597|gb|EAT12574.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
          Length = 245

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 95/226 (42%), Gaps = 10/226 (4%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
             +VE    LV  +A     R    +Q  DLIQ G IGL++AA+K++   G  F TYA  
Sbjct: 17  NTLVEEYASLVKRIAHHLKGRLPDSVQVDDLIQSGMIGLIEAAQKYEPSKGASFETYAGI 76

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ ++   I         P  +     ++    R + ++  R+   +E+AK L M +E 
Sbjct: 77  RIRGSMLDEIRKGDW---APRSVHRNSRRISEAIRYVESQTGRDAQDQEVAKALGMELEE 133

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
             + L+              E            +  SPL      + ++   + ++ L  
Sbjct: 134 YHQHLQDGAGSRLFSFEDLLEQRGEQESDFMGHDDESPLQDLQSEHFQQQLAKAISQLPE 193

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ VL     +  + +  L+E+G    V+  R+ QI ++A  +L+
Sbjct: 194 REQLVL----ALYYDEELNLKEIGAVLEVSESRVSQIHSQAAHRLR 235


>gi|302389688|ref|YP_003825509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
 gi|302200316|gb|ADL07886.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
          Length = 245

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 104/253 (41%), Gaps = 22/253 (8%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKA 484
           R     +       S  K+ ++E  + LV  +A +        + + DL+  G IGL++A
Sbjct: 6   RAENLWIEYKNTGDSNLKERLIEEYIPLVKHIAARLAINLPPCVDYDDLVSAGIIGLLQA 65

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E++D   G +F T+A   ++ A+   +   +   +  +   +K   +     +M  ++ 
Sbjct: 66  IERYDVGKGVRFETFAYTRIRGAMLDELRRLNWIPQKTM---EKAKLLQDAYSQMEQELN 122

Query: 545 REPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
                E+IA+KL + +  + +  K       +SLE              +  ++   P+ 
Sbjct: 123 GNVKDEDIARKLNITIAELHQTYKELAATNLVSLEEIFS----------VAVEDNGEPVS 172

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              +  ++      +  L P+E+ V+ + +  G      L+E+     ++  RI Q+  K
Sbjct: 173 HVEKEEIKRILGEAIDRLPPKEKLVIALYYYEG----LNLKEISVVLNLSPARISQLHTK 228

Query: 663 AIRKLKHPSRSKK 675
           AI +L+     K+
Sbjct: 229 AILRLRGSLSRKR 241


>gi|227485585|ref|ZP_03915901.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227236451|gb|EEI86466.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 340

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 78/261 (29%), Positives = 126/261 (48%), Gaps = 10/261 (3%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQ 475
              +S      IV   + G   A  A   +VE N  LV S A  +       L   DL+Q
Sbjct: 82  MMKLSDLNNEEIVEQFQLGNQNALAA---LVEKNQGLVRSRASYFFRSHGNDLDLEDLVQ 138

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +  TIRIP     K++K+ + 
Sbjct: 139 SGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQI 198

Query: 536 ARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFI 592
            +        E     E         + +  + +      SL   +  ED++   L D +
Sbjct: 199 LKANPEASDEEIYRILENEGINKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMV 258

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D++        ++ ++     + L  LT RE++++  R+G+      TLE++G  + ++
Sbjct: 259 GDESTP-VDMLILEKDMENFLMQALDQLTDREKQIIIYRYGLDNEKPKTLEQIGAIYDLS 317

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
           RERIRQIE +A+ KLK  S S
Sbjct: 318 RERIRQIENQALGKLKDYSDS 338


>gi|282929291|ref|ZP_06336862.1| RNA polymerase sigma-B factor [Staphylococcus aureus A10102]
 gi|282589101|gb|EFB94200.1| RNA polymerase sigma-B factor [Staphylococcus aureus A10102]
          Length = 256

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 115/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ +  +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSAHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|254239804|ref|ZP_04933126.1| sigma factor FliA [Pseudomonas aeruginosa 2192]
 gi|126193182|gb|EAZ57245.1| sigma factor FliA [Pseudomonas aeruginosa 2192]
          Length = 247

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 100/238 (42%), Gaps = 14/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +A  +++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K+D   
Sbjct: 10  YSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E+
Sbjct: 70  GASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVTDAIRTIEARTGRDAKDHEV 126

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + +E    +L  T+     S +  + D +     D     N    +   +    +
Sbjct: 127 AAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTSLSHNEP--IHGLLDERFQ 184

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 AALADAIAKLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 238


>gi|186477706|ref|YP_001859176.1| flagellar biosynthesis sigma factor [Burkholderia phymatum STM815]
 gi|184194165|gb|ACC72130.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia phymatum
           STM815]
          Length = 244

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/209 (22%), Positives = 91/209 (43%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVESAVHQVEQSLGRSASETEIAEHLKMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDESLRGALVEAIDRLPEREKLLMSLYYERG----LNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRTRLREQ 236


>gi|307731372|ref|YP_003908596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1003]
 gi|307585907|gb|ADN59305.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1003]
          Length = 244

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/207 (23%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDESLRSALVDAIDRLPEREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRTRLR 234


>gi|323527722|ref|YP_004229875.1| RNA polymerase sigma-28 subunit FliA/WhiG [Burkholderia sp.
           CCGE1001]
 gi|323384724|gb|ADX56815.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           CCGE1001]
          Length = 244

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/207 (23%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDESLRSALVEAIDRLPEREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRTRLR 234


>gi|170760209|ref|YP_001787962.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
 gi|169407198|gb|ACA55609.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
          Length = 242

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK+++      ++  K+ +EP   +IA +L + ++
Sbjct: 71  IRIKGSMIDELR---RNSPISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNISLK 127

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + + 
Sbjct: 128 EVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAIE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK   
Sbjct: 188 LLNEKDRLVVTLYY----YEELTLKEIGKILNVSESRVCQLHSRAIVHLKKAM 236


>gi|256545958|ref|ZP_05473313.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
 gi|256398380|gb|EEU12002.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
          Length = 256

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +      + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A +++D   GY
Sbjct: 20  QFYKTRDKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGY 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FS++A   +   + R   D+   IR+P  +++   K+    + +  +++R PT ++IA 
Sbjct: 80  EFSSFATPTIMGELKRYFRDKGWVIRVPRRIQNLYKKINVAKKILPQELQRTPTIKDIAA 139

Query: 555 KLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L    E + + ++ +    P SL+     +   +  D            +     L++ 
Sbjct: 140 YLGEDEETILETIEASKVYSPQSLDMKYQVQKGENSVDL--SDMIGEDDKNFDSVELKDL 197

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +    L   E+++L +R+  G     T  ++  +  +++  + +IE K ++K
Sbjct: 198 IDKSTERLNDLEKQILELRYYEG----RTQVDIANKLSISQMTVSRIEKKILQK 247


>gi|220903606|ref|YP_002478918.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219867905|gb|ACL48240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 260

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 102/236 (43%), Gaps = 14/236 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            E  +   ++ +V      +  +A +      R ++  +LI  G +GLM+A  KF   LG
Sbjct: 24  WENFSPAEQEAVVRHYAPKIRFLALRLKAKLPRSVELGELISSGTLGLMEALGKFRPQLG 83

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F TYA   ++ A+   +         P  +R ++  +    R++ ++  R+ T EE+ 
Sbjct: 84  IRFETYAESRIRGAMLDELRRLDWF---PRSLRQRVRTLDEAIRKVEHEHGRQATEEELQ 140

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               +P+  VR+ L+  +  + L      +  S  GD    +    P        L E  
Sbjct: 141 AITGLPLRDVRQGLEALQNQLWLSLDAIQDTIS--GD--AQEPGGEPYRKTAFRELVERV 196

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++  LTPRE+ VL + +      +  + E  +   +T  R+ Q+ ++A+ +L+ 
Sbjct: 197 APLIDRLTPREKLVLSLYY----TDELNMRETAEVMGITEGRVSQLHSQALSRLRK 248


>gi|254422308|ref|ZP_05036026.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196189797|gb|EDX84761.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 259

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 117/249 (46%), Gaps = 14/249 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEK 487
            ++S+ +K        +  +V+ N+ LV   A ++    G  F DL+Q G++GL+ A E+
Sbjct: 15  ELLSLYQKDRSL--QLRNRLVQLNIGLVRQEAYRWLGYSGETFDDLMQIGSLGLINAIER 72

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY FS++A+ +++  I   + D+   +RIP   +   ++  +  R + N++ R+P
Sbjct: 73  FDLEKGYAFSSFAIPYIRGEIQHYLRDKGTVVRIPRKWQALQNQAAQAIRHLQNELNRKP 132

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDS 603
              E+A +L + VE  +  K+    +  +SL+ PI ++    S LG+ + D    S   +
Sbjct: 133 NDYEVAARLNVTVEEWQQVKLASSNRHLLSLDAPIREDRNGASSLGELLPDARYRSFQLA 192

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R    + L  L  R   VL   F      D T +E  K+  ++   + +   K 
Sbjct: 193 QED---RIRLQQALEQLEKRTREVLEFVFL----QDLTQKETAKKLGISSVTVSRRVRKG 245

Query: 664 IRKLKHPSR 672
           ++ L+   R
Sbjct: 246 LQHLQAIMR 254


>gi|53720901|ref|YP_109887.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           K96243]
 gi|76811948|ref|YP_331475.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           1710b]
 gi|52211315|emb|CAH37304.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia pseudomallei K96243]
 gi|76581401|gb|ABA50876.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 1710b]
          Length = 243

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 102/244 (41%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I++ E++     LV  +  +   +    +   DLIQ G IGL+ AA ++    
Sbjct: 1   MYNAQGKISQDEVLTQYAPLVRRLGLQLVAKMPASVDLDDLIQAGMIGLLDAASRYKEDQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P  +R    +V     ++  ++ R     EI
Sbjct: 61  GAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSREVEHAVHQVEQRLGRSANETEI 117

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L MP++  + +L+       +  E      D     D     ++  PL + +  +LR
Sbjct: 118 AAHLQMPLDEYQSMLQDLHGSQLVYYEDFDRSADDEPFLDRYRADHS-DPLSALLDEHLR 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +  L  RE+ ++ + +  G      L E+G    V+  R+ Q+ ++A+ +L+  
Sbjct: 177 SALVDAIERLPEREKLLMSLYYERG----LNLREIGAVLEVSESRVCQLHSQAVARLRAK 232

Query: 671 SRSK 674
            R +
Sbjct: 233 LREQ 236


>gi|15596652|ref|NP_250146.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PAO1]
 gi|116049400|ref|YP_791797.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218892672|ref|YP_002441541.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa LESB58]
 gi|254234554|ref|ZP_04927877.1| sigma factor FliA [Pseudomonas aeruginosa C3719]
 gi|296390178|ref|ZP_06879653.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PAb1]
 gi|120310|sp|P29248|FLIA_PSEAE RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-28; AltName: Full=Sigma-F factor
 gi|9947407|gb|AAG04844.1|AE004575_3 sigma factor FliA [Pseudomonas aeruginosa PAO1]
 gi|45322|emb|CAA43548.1| sigma-28 class sigma factor [Pseudomonas aeruginosa]
 gi|115584621|gb|ABJ10636.1| motility sigma factor FliA [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126166485|gb|EAZ51996.1| sigma factor FliA [Pseudomonas aeruginosa C3719]
 gi|218772900|emb|CAW28712.1| sigma factor FliA [Pseudomonas aeruginosa LESB58]
          Length = 247

 Score =  105 bits (262), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 100/238 (42%), Gaps = 14/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +A  +++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K+D   
Sbjct: 10  YSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E+
Sbjct: 70  GASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVTDAIRAIEARTGRDAKDHEV 126

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + +E    +L  T+     S +  + D +     D     N    +   +    +
Sbjct: 127 AAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTSLSHNEP--IHGLLDERFQ 184

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 AALADAIAKLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 238


>gi|213958528|gb|ACJ54685.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 19-20cm4R]
          Length = 233

 Score =  105 bits (262), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 37/278 (13%), Positives = 87/278 (31%), Gaps = 47/278 (16%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            E       +    + + D E A   + D+      P             D+ +      
Sbjct: 51  AEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 111 KKHGRGNKLAIAELVLLAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
              + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A  
Sbjct: 137 VPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALA 195

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 196 KGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEI 233


>gi|322806971|emb|CBZ04541.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           botulinum H04402 065]
          Length = 242

 Score =  105 bits (262), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK+++      ++  K+ +EP   +IA +L + ++
Sbjct: 71  IRIKGSMIDELR---RNSPISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNISLK 127

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + + 
Sbjct: 128 EVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAIE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK   
Sbjct: 188 LLNEKDRLVVTLYY----YEELTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236


>gi|108804234|ref|YP_644171.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765477|gb|ABG04359.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 264

 Score =  105 bits (262), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 105/240 (43%), Gaps = 19/240 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +R+ E      +  +V     LV  VA +   R   G++  DL+  G +GL+KA E FD 
Sbjct: 33  LRRAERRVGQLRDRLVVNYSPLVKYVAGRMAARIPGGVEQEDLVSWGVVGLLKAVETFDP 92

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G KF TYA+  ++ AI   +       R       +     R A  ++  ++R PT  
Sbjct: 93  ARGAKFETYAISKIRWAILDELRKADPLPRRVRRRVRETQ---RAASALTQTLRRAPTEA 149

Query: 551 EIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIA+++ + +   R+ L+        SLE  +           + D  A +       A 
Sbjct: 150 EIAREVGVGLAEHRETLERYHRARTWSLEELLSGMGEGGRELSVSDPTAET-------AE 202

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LRE     L SL+ RE  V+   +  G     TL E+G+   +T  RI QI  +A+++L+
Sbjct: 203 LRERLAEALESLSERERVVITFYYYQG----LTLREIGRALNLTEGRISQILRRALQRLR 258


>gi|213958526|gb|ACJ54684.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 19-20cm3R]
          Length = 232

 Score =  105 bits (262), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 37/278 (13%), Positives = 87/278 (31%), Gaps = 47/278 (16%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 1   REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPA 49

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            E       +    + + D E A   + D+      P             D+ +      
Sbjct: 50  AEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKAL 109

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 110 KKHGRGNKLAIAELVLLAELF----------------------------------MPIKL 135

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
              + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A  
Sbjct: 136 VPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALA 194

Query: 390 FPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
             + ++   +      I++ + ++ ++  ETG++I+E 
Sbjct: 195 KGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEI 232


>gi|49484290|ref|YP_041514.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|82751667|ref|YP_417408.1| RNA polymerase sigma factor SigB [Staphylococcus aureus RF122]
 gi|257426202|ref|ZP_05602617.1| SigB protein [Staphylococcus aureus subsp. aureus 55/2053]
 gi|257428861|ref|ZP_05605255.1| SigB protein [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257431471|ref|ZP_05607844.1| SigB protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257434181|ref|ZP_05610531.1| SigB protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257437094|ref|ZP_05613134.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M876]
 gi|258422934|ref|ZP_05685834.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9635]
 gi|282904730|ref|ZP_06312604.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C160]
 gi|282906409|ref|ZP_06314260.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282909377|ref|ZP_06317192.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911631|ref|ZP_06319430.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914909|ref|ZP_06322689.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M899]
 gi|282917412|ref|ZP_06325165.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           D139]
 gi|282920240|ref|ZP_06327964.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C427]
 gi|282925452|ref|ZP_06333106.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C101]
 gi|283771232|ref|ZP_06344121.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           H19]
 gi|283958843|ref|ZP_06376288.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|293508983|ref|ZP_06667770.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510895|ref|ZP_06669594.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M809]
 gi|293547495|ref|ZP_06672170.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M1015]
 gi|295428651|ref|ZP_06821277.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589872|ref|ZP_06948512.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MN8]
 gi|49242419|emb|CAG41133.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|61889366|emb|CAI72514.1| SigB protein [Staphylococcus aureus]
 gi|82657198|emb|CAI81638.1| RNA polymerase sigma factor B [Staphylococcus aureus RF122]
 gi|257270907|gb|EEV03080.1| SigB protein [Staphylococcus aureus subsp. aureus 55/2053]
 gi|257274203|gb|EEV05720.1| SigB protein [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257277712|gb|EEV08382.1| SigB protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257280820|gb|EEV10965.1| SigB protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257283487|gb|EEV13614.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M876]
 gi|257846958|gb|EEV70972.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9635]
 gi|282312853|gb|EFB43254.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C101]
 gi|282316100|gb|EFB46481.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C427]
 gi|282318614|gb|EFB48971.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           D139]
 gi|282321112|gb|EFB51443.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M899]
 gi|282324396|gb|EFB54709.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326647|gb|EFB56945.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282330359|gb|EFB59877.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282594763|gb|EFB99740.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C160]
 gi|283459437|gb|EFC06530.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           H19]
 gi|283471280|emb|CAQ50491.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ST398]
 gi|283789561|gb|EFC28384.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|290919615|gb|EFD96688.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291094687|gb|EFE24959.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466180|gb|EFF08707.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127321|gb|EFG56961.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297577000|gb|EFH95714.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MN8]
 gi|298695339|gb|ADI98561.1| RNA polymerase sigma factor B [Staphylococcus aureus subsp. aureus
           ED133]
 gi|302333711|gb|ADL23904.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|312437522|gb|ADQ76593.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|315193223|gb|EFU23621.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|323439220|gb|EGA96947.1| RNA polymerase sigma factor SigB [Staphylococcus aureus O11]
 gi|323442402|gb|EGB00031.1| RNA polymerase sigma factor SigB [Staphylococcus aureus O46]
 gi|329729290|gb|EGG65698.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21193]
          Length = 256

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 116/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|258655075|ref|YP_003204231.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258558300|gb|ACV81242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 308

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 54/255 (21%), Positives = 102/255 (40%), Gaps = 15/255 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKE--MVEANLRLVISVAKKYTNRGLQFLDLI 474
           +  TG      R ++           + + +  +V   + +  S+A +Y+ RG++  DL 
Sbjct: 59  AAPTGDRARRVRELLEYTAGCTDPDELRRCQQQVVTEYIPVARSLAARYSGRGVERSDLE 118

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q   +GL+KA +++       F  +A+  +   I R   D S  +R P  +++    +  
Sbjct: 119 QLAYMGLIKAVQRWRPGRSDDFLQFAVPTIVGEIKRYFRDHSWLVRPPRRIQELRAAISE 178

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFI 592
             +   ++  R P+  E+AK     V  + +         P SL+   G      L    
Sbjct: 179 AEQSQRHQDGRAPSDAELAKATGATVTDIDEARAAAACCRPRSLDEEQGPGLALALSWGE 238

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED           +   R T  R+L +LT RE  V+ MRF  G +       +G++  V+
Sbjct: 239 ED-------AELRRVEDRATVERLLDALTDRERDVVHMRFDNGWSQSR----IGREIGVS 287

Query: 653 RERIRQIEAKAIRKL 667
           + ++ +       KL
Sbjct: 288 QMQVSRWLRSITEKL 302


>gi|71281710|ref|YP_268261.1| flagellar biosynthesis sigma factor [Colwellia psychrerythraea 34H]
 gi|71147450|gb|AAZ27923.1| motility sigma factor FliA [Colwellia psychrerythraea 34H]
          Length = 239

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 109/246 (44%), Gaps = 15/246 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
           MV+       I K  ++E    LV  +A     R    +Q  DLIQ G IGL +AA  FD
Sbjct: 1   MVKVNSYNNQIDKAALLEQQTVLVKRIAYHLLARLPASVQVDDLIQSGMIGLFEAANNFD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F T+A   ++ A+   I         P  +      +    +++  ++ R+ + 
Sbjct: 61  NTKGASFETFAGIRIRGAMLDEIRRGDW---TPRSVHKNSRMISEAIKQLEAQLGRDVSD 117

Query: 550 EEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            E+A+KL + ++   ++L    T + + ++    +ED     D   D     P  S  + 
Sbjct: 118 VEVAEKLDISLKDYHQILSEVSTGKILGIDDLGVNEDAIKPSD---DYIGDDPYQSIERI 174

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             ++  T+ + SL  RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ +L
Sbjct: 175 AFKKGLTQCIKSLPEREALVLSLYY----DEELNLREIGQVLDVSESRVSQIHSQAMHRL 230

Query: 668 KHPSRS 673
           K   +S
Sbjct: 231 KARMQS 236


>gi|205373400|ref|ZP_03226204.1| RNA polymerase sigma factor SigD [Bacillus coahuilensis m4-4]
          Length = 257

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 57/246 (23%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAA 485
            +V      E     A   +V+  + LV    ++ ++   + +   DL   G +GL+ A 
Sbjct: 9   ELVLWKSWIENRNEEAGDLLVKKYMHLVSFHVQRISSTLPKNISKDDLKSLGMMGLLDAL 68

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +KFD     KF TYA + ++ +I   +  +     +P + RDK  K+ +T  R+   + R
Sbjct: 69  QKFDIERDLKFDTYASFRIRGSIIDGLRKEDW---LPRNTRDKAKKIEKTISRLEQTLMR 125

Query: 546 EPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +  PE++AK+L M  + V +++        +S++    +E+       ++D+ + SP + 
Sbjct: 126 KIVPEDVAKELDMSADEVIQIMNEHFFANVLSMDEMTREEEKDSPKFQMQDEKSRSPEEE 185

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +++       + +  L  +E+ VL + +      + TL E+G+   ++  RI QI +KA
Sbjct: 186 LVKSEQIRDLEQHIRGLNEKEQLVLSLFY----QEELTLTEIGEVLQLSTSRISQIHSKA 241

Query: 664 IRKLKH 669
           + KL+ 
Sbjct: 242 LFKLRK 247


>gi|91785643|ref|YP_560849.1| flagellar biosynthesis sigma factor [Burkholderia xenovorans LB400]
 gi|296157465|ref|ZP_06840300.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           Ch1-1]
 gi|91689597|gb|ABE32797.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           xenovorans LB400]
 gi|295892237|gb|EFG72020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           Ch1-1]
          Length = 244

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 48/207 (23%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDDSLRSALVEAIDRLPEREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRTRLR 234


>gi|53724308|ref|YP_104354.1| flagellar biosynthesis sigma factor [Burkholderia mallei ATCC
           23344]
 gi|67639807|ref|ZP_00438640.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Burkholderia mallei GB8
           horse 4]
 gi|121601051|ref|YP_994697.1| flagellar biosynthesis sigma factor [Burkholderia mallei SAVP1]
 gi|124385599|ref|YP_001027679.1| flagellar biosynthesis sigma factor [Burkholderia mallei NCTC
           10229]
 gi|126442044|ref|YP_001060834.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 668]
 gi|126450811|ref|YP_001082651.1| flagellar biosynthesis sigma factor [Burkholderia mallei NCTC
           10247]
 gi|126454531|ref|YP_001068141.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           1106a]
 gi|134281398|ref|ZP_01768106.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 305]
 gi|167002947|ref|ZP_02268737.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei PRL-20]
 gi|167721669|ref|ZP_02404905.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           DM98]
 gi|167740651|ref|ZP_02413425.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 14]
 gi|167817858|ref|ZP_02449538.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 91]
 gi|167826237|ref|ZP_02457708.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 9]
 gi|167847745|ref|ZP_02473253.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           B7210]
 gi|167896335|ref|ZP_02483737.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           7894]
 gi|167904709|ref|ZP_02491914.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei NCTC
           13177]
 gi|167912987|ref|ZP_02500078.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 112]
 gi|167920926|ref|ZP_02508017.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           BCC215]
 gi|217423992|ref|ZP_03455492.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 576]
 gi|226193247|ref|ZP_03788857.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pakistan 9]
 gi|237814231|ref|YP_002898682.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Burkholderia pseudomallei MSHR346]
 gi|242316800|ref|ZP_04815816.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106b]
 gi|254174808|ref|ZP_04881469.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei ATCC 10399]
 gi|254183872|ref|ZP_04890463.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|254186350|ref|ZP_04892867.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254194761|ref|ZP_04901192.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei S13]
 gi|254201430|ref|ZP_04907794.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei FMH]
 gi|254206772|ref|ZP_04913123.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei JHU]
 gi|254261523|ref|ZP_04952577.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1710a]
 gi|254298806|ref|ZP_04966257.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|254357205|ref|ZP_04973479.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei 2002721280]
 gi|52427731|gb|AAU48324.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           mallei ATCC 23344]
 gi|121229861|gb|ABM52379.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei SAVP1]
 gi|124293619|gb|ABN02888.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           mallei NCTC 10229]
 gi|126221537|gb|ABN85043.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 668]
 gi|126228173|gb|ABN91713.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106a]
 gi|126243681|gb|ABO06774.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei NCTC 10247]
 gi|134247065|gb|EBA47151.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 305]
 gi|147747324|gb|EDK54400.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei FMH]
 gi|147752314|gb|EDK59380.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei JHU]
 gi|148026269|gb|EDK84354.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei 2002721280]
 gi|157808491|gb|EDO85661.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|157934035|gb|EDO89705.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160695853|gb|EDP85823.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei ATCC 10399]
 gi|169651511|gb|EDS84204.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei S13]
 gi|184214404|gb|EDU11447.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|217393055|gb|EEC33077.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 576]
 gi|225934847|gb|EEH30824.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pakistan 9]
 gi|237506113|gb|ACQ98431.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Burkholderia pseudomallei MSHR346]
 gi|238520417|gb|EEP83877.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Burkholderia mallei GB8
           horse 4]
 gi|242140039|gb|EES26441.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106b]
 gi|243061438|gb|EES43624.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei PRL-20]
 gi|254220212|gb|EET09596.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1710a]
          Length = 244

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 102/244 (41%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I++ E++     LV  +  +   +    +   DLIQ G IGL+ AA ++    
Sbjct: 2   MYNAQGKISQDEVLTQYAPLVRRLGLQLVAKMPASVDLDDLIQAGMIGLLDAASRYKEDQ 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P  +R    +V     ++  ++ R     EI
Sbjct: 62  GAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSREVEHAVHQVEQRLGRSANETEI 118

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L MP++  + +L+       +  E      D     D     ++  PL + +  +LR
Sbjct: 119 AAHLQMPLDEYQSMLQDLHGSQLVYYEDFDRSADDEPFLDRYRADHS-DPLSALLDEHLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +  L  RE+ ++ + +  G      L E+G    V+  R+ Q+ ++A+ +L+  
Sbjct: 178 SALVDAIERLPEREKLLMSLYYERG----LNLREIGAVLEVSESRVCQLHSQAVARLRAK 233

Query: 671 SRSK 674
            R +
Sbjct: 234 LREQ 237


>gi|313901762|ref|ZP_07835188.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467968|gb|EFR63456.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
          Length = 244

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 88/232 (37%), Gaps = 55/232 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   +
Sbjct: 63  RHTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYASKCI 122

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +   S                                                
Sbjct: 123 ENEILMHLRRTSR----------------------------------------------- 135

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                T+  +SL+ P+  +   +   L D I   +             R    R LA LT
Sbjct: 136 -----TRYEVSLDEPLNVDWEGNELLLSDVIPATDGDVIYRDLEAKVDRHLLHRALARLT 190

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           PRE  ++ +RFG+    + T ++V     +++  I ++E + I +L+   R 
Sbjct: 191 PRERLIMELRFGLVDGIERTQKQVADHLGISQSYISRLEKRIINRLRREIRK 242


>gi|21283717|ref|NP_646805.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49486858|ref|YP_044079.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|297210116|ref|ZP_06926509.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC 51811]
 gi|300910479|ref|ZP_07127931.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|21205159|dbj|BAB95853.1| sigma factor B [Staphylococcus aureus subsp. aureus MW2]
 gi|49245301|emb|CAG43776.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|296885316|gb|EFH24256.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC 51811]
 gi|300888321|gb|EFK83512.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH70]
          Length = 256

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 116/247 (46%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  + 
Sbjct: 249 KLQEAAH 255


>gi|331006368|ref|ZP_08329678.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330419828|gb|EGG94184.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 251

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 100/234 (42%), Gaps = 15/234 (6%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           VE    LV  +A+    +    +Q  DLIQ G IGL++AA+K+D   G  F TYA   ++
Sbjct: 27  VEDYADLVKRIAQHMVAKMPASVQVDDLIQSGMIGLLEAAKKYDGSRGASFETYAGIRIR 86

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            AI   I        +P  +      +  T  ++   + R+    EIA+ + + ++    
Sbjct: 87  GAIVDEIRKGDW---VPRSVHRNSRLISNTIHQLEASLGRDAKDSEIAEAMGVDIDEYYA 143

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + +              E    +    ++   V P D A    L+ +    +  L  RE+
Sbjct: 144 MSRDASSSRLFSIDESFESDESVISNEKNSPFVDPHDGAQHQALKSSLVTAIDKLPEREK 203

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            VL + +    + +  L+E+G+   VT  R+ QI ++A  +LK      KL+ +
Sbjct: 204 LVLSLYY----DEELNLKEIGQILGVTESRVSQIHSQAALRLK-----SKLKDW 248


>gi|224009562|ref|XP_002293739.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220970411|gb|EED88748.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 316

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 76/282 (26%), Positives = 140/282 (49%), Gaps = 25/282 (8%)

Query: 414 KSISVETGIS-ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN----RGL 468
           +  +   G+S  +E R +VS  R        AK+E+V +N+ LV +V K Y+     RG+
Sbjct: 41  RQWATLAGLSSPNELRKVVSEYR-------SAKQELVASNMGLVHAVVKNYSRKAYYRGI 93

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              +L+QEG++GL++AAE FD   G +FSTYA  W+K  ++ S       + +P   R  
Sbjct: 94  TIDELVQEGSLGLIRAAELFDPAKGLRFSTYATIWIKGVLSNSRV--DEMVLVPQRERQI 151

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAM---PVEGVRKVLKITKEPISLE------TP 579
            +K+   ++ + ++  R  T + IAKKL +    VE   + +      +SL+      T 
Sbjct: 152 WNKIREVSKDVDDEDGRLST-DMIAKKLGLDKSSVEQNIQRMSSVNNMLSLDYQYASTTR 210

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNT 638
            G+ D S   + +    + S  D A +A  +      L  +L  RE +++R+ +G+    
Sbjct: 211 SGETDGSKPFEALMADKSGSDADLAERAQFKADLVAGLVRNLNEREIQLIRLMYGMHDGH 270

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++++++  K   + RE  R +    ++KL+  S  + L+ +L
Sbjct: 271 EYSVKDSAKIMGINRETARLLHHACLKKLREASNMESLQEYL 312


>gi|148380599|ref|YP_001255140.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 3502]
 gi|153931945|ref|YP_001384886.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|153937160|ref|YP_001388355.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|168182725|ref|ZP_02617389.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|170754752|ref|YP_001782258.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|226950054|ref|YP_002805145.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|237796081|ref|YP_002863633.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
 gi|148290083|emb|CAL84202.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152927989|gb|ABS33489.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|152933074|gb|ABS38573.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|169119964|gb|ACA43800.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|182674219|gb|EDT86180.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|226840945|gb|ACO83611.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|229261699|gb|ACQ52732.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
          Length = 242

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK+++      ++  K+ +EP   +IA +L + ++
Sbjct: 71  IRIKGSMIDELR---RNSPISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNISLK 127

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + + 
Sbjct: 128 EVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAIE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK   
Sbjct: 188 LLNEKDRLVVTLYY----YEELTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236


>gi|293400808|ref|ZP_06644953.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305834|gb|EFE47078.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 241

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 110/226 (48%), Gaps = 10/226 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++++ +     AK   VE N  LV S+ ++++ + +   DL Q G +GLMKA   FD  
Sbjct: 9   ELIQRIKDGDEEAKSIFVEKNSPLVYSIVRRFSRQRIAMDDLFQIGCVGLMKALNNFDTS 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R   D    +RI   +++   ++ +    +  K+ REPT +E
Sbjct: 69  YQVKFSTYAVPIIMGEIKRFFRD-DGNMRISRSLKEGYLQMSKKKEELLQKLNREPTYQE 127

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA  L+M V  V    +  +   SL+  I + D S +   +EDK +    +  +   ++ 
Sbjct: 128 IADALSMDVADVILAFEANQFVYSLDETIYENDGSPI--LLEDKVSNRKEEDVV---MKV 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +    +A L  RE+ +L  R+ +G       EE+ K+  +++ ++ 
Sbjct: 183 SLQNEIAHLEQREQLLLHYRYDLG----MKQEEIAKKLQISQVQVS 224


>gi|209695722|ref|YP_002263652.1| flagellar biosynthesis sigma factor [Aliivibrio salmonicida
           LFI1238]
 gi|208009675|emb|CAQ79974.1| RNA polymerase sigma factor for flagellar regulon FliA [Aliivibrio
           salmonicida LFI1238]
          Length = 243

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 100/227 (44%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R    +   DLIQ G IGL++A + +D   G  F TYA   +
Sbjct: 19  FLERYSELVKRIAHHLMARLPASVLVDDLIQSGMIGLLEAQQNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   I        +P  +      V    + +  K+ REPT +EIA+ L +P++   
Sbjct: 79  RGSMLDEIRRGDW---VPRSVHKNSRMVNAAIKALEAKLSREPTDKEIAEHLELPLDQYY 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDSAIQANLRETTTRVLASLT 621
           ++L      ++    +G ED     D I  +       P    +  + R      + +L 
Sbjct: 136 QIL----NDVNCGKLVGMEDLGVSEDVITTEEHADDNIPFQGVVDEHFRVALVEAIKTLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G    V+  R+ QI ++++++L+
Sbjct: 192 EREALVLSLYY----DEELNLKEIGAVIGVSESRVSQIHSQSMQRLR 234


>gi|37781598|gb|AAP42804.1| SigB [Staphylococcus aureus]
          Length = 256

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 117/248 (47%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD  L  KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSLERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|325678908|ref|ZP_08158506.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
 gi|324109412|gb|EGC03630.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
          Length = 217

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 110/228 (48%), Gaps = 20/228 (8%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  + E NL LV   A ++  RG+++ DL   G IGL+KA++ FD   G KFSTYA+  
Sbjct: 3   AESHLPEDNLGLVHLCANRFRGRGIEYDDLYGAGCIGLLKASKAFDSGRGVKFSTYAVPV 62

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +   I R   D   T+++   +++   ++   A+  ++K  REPT EE+AK +  PVE V
Sbjct: 63  ILGEIKRLFRDGG-TVKVSRSLKELSLRLTGEAQVFAHKNGREPTVEELAKIVGTPVEDV 121

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDF---IEDKNAVSPLDSAIQANLRETTTRVLASL 620
            + L   +  ISL   +GD++     D      D++             R    +VL  L
Sbjct: 122 IEALNAAQPVISL--TVGDDENETQADLPAPAPDEDITD----------RLALRQVLTEL 169

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +++ +R+  GM              +T+ ++ + E K +  ++
Sbjct: 170 DDKDRQLIELRYFQGMTQSAA----AAVLGMTQVQVSRKEKKLLLYMR 213


>gi|332533108|ref|ZP_08408977.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332037390|gb|EGI73844.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 236

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 10/224 (4%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 12  IVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAGIRI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +         P  +  K  +V      + + + REPT  E+A+KL + +    
Sbjct: 72  RGAMLDEMRRGDW---APRSVHRKNRQVAEAITELESSLNREPTDIEVAEKLEISLNEYH 128

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +L        L       D   +    +D     P ++       E+    + SL  R+
Sbjct: 129 HILNDANTSKILGIEDLGVDEDVITPVGQDLAQDKPFNNVKNDRFNESLLSAIKSLPERD 188

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL + +    N +  L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 189 AMVLSLYY----NDEMNLKEIGHILDVSESRVSQIHGQAMIKLK 228


>gi|167623396|ref|YP_001673690.1| flagellar biosynthesis sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353418|gb|ABZ76031.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella
           halifaxensis HAW-EB4]
          Length = 239

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+  FD   G KF T+A 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSNFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+    EIA++L MP++
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRVAQVIDELEQELGRDARDGEIAERLEMPLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     + +  +D +     +S  +          +  
Sbjct: 130 EYYSIL----NDVSVGKVVGIEDLGVAVEGLNQDDGHEDDAYESLAEVEFHSALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDALVLSLYY----DEALNLKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|161523359|ref|YP_001578371.1| flagellar biosynthesis sigma factor [Burkholderia multivorans ATCC
           17616]
 gi|189351868|ref|YP_001947496.1| flagellar biosynthesis sigma factor [Burkholderia multivorans ATCC
           17616]
 gi|221202383|ref|ZP_03575416.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2M]
 gi|221208978|ref|ZP_03581974.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2]
 gi|221214209|ref|ZP_03587181.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD1]
 gi|160340788|gb|ABX13874.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           multivorans ATCC 17616]
 gi|189335890|dbj|BAG44960.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans ATCC 17616]
 gi|221165864|gb|EED98338.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD1]
 gi|221171100|gb|EEE03551.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2]
 gi|221177797|gb|EEE10211.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2M]
          Length = 244

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 50/209 (23%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 94  TSREVELAVHQVEQRLGRAASEAEIAQHLNMPLDEYQAMLQDLHGSQLIYYEDFDRAADD 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     +A  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 154 EPFLDRYRVDHA-DPLSALLDEHLRGALVEAIERLPEREKLLMSLYYERG----LNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 209 GAVLEVSESRVCQLHSQAVARLRARLREQ 237


>gi|218439022|ref|YP_002377351.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218171750|gb|ACK70483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 257

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 104/240 (43%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           ++          + ++VE N  LV  VA + + +    + DL Q G +GL++A E+F+  
Sbjct: 16  LIAYSRNPTLKLRNQLVELNAGLVRQVAHRISRQCCEPYEDLEQVGYLGLIRAIERFNPQ 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D+   +RIP   +D   K  +  + ++  + R+P   E
Sbjct: 76  QGSAFSSFAIPYIRGEILHYLRDRGSVMRIPRRWQDLYTKGKKLRKELAQTLGRQPRESE 135

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQA 607
           IA+ L +  +   +       +  +SL+  +    +     GD + D    S     IQ 
Sbjct: 136 IAQALGISSQEWNECQLALQNRLLVSLDATVNQAHDGMISFGDTLPDPK--SQGQQKIQE 193

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R    + ++ L  + +  +   F      D   +E  K+  ++   + +   K + +L
Sbjct: 194 D-RLQLQKAMSQLEDKTKAAIECVFLW----DLPRKEAAKRIGISPMTVTRHLQKGLDQL 248


>gi|297746539|emb|CAZ60987.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|297746541|emb|CAZ60988.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 242

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/285 (16%), Positives = 93/285 (32%), Gaps = 44/285 (15%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P             +         E
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELGE 53

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            +  D  E E + E     S DD       PE A     +L    + +  ++        
Sbjct: 54  DDLADEDEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEVTRLSI-------- 105

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                                      QK+ ++    +    +L  +     L   + D 
Sbjct: 106 ---------------------------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDR 138

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +    
Sbjct: 139 LVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSP 198

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
             +  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 199 RLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|260893856|ref|YP_003239953.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
 gi|260865997|gb|ACX53103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
          Length = 252

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 95/230 (41%), Gaps = 12/230 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V   L LV  +  +   R    +   D+   G +GL+ A E++D   G +F +YA 
Sbjct: 19  KEELVRRYLPLVKYLVGRLAVRLPPWVSLEDIEGAGILGLLAAMERYDPSQGVEFESYAR 78

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + +  A+   +   +           ++  V++   R   +    P  E++A++L     
Sbjct: 79  YRIWGAMLDEVRRWARF---SRRTWQQMQAVLKVQERWEREKGCRPKVEDVAQELGWEPA 135

Query: 562 GVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V +           SLE     E  S   +F+ D     PL+  ++          +  
Sbjct: 136 QVDRLGRYFAAFNSFSLEEVRSAEGRSPWEEFLADPKGQDPLEELLEKEDLGRLAEAIGR 195

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  R + +L + +  G     TL E+G+   ++  R+ Q+ ++A+ KL+ 
Sbjct: 196 LEERLQLILALYYQEG----LTLREIGEVLGISESRVCQLHSRALTKLRE 241


>gi|15925054|ref|NP_372588.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|156980380|ref|YP_001442639.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|255006853|ref|ZP_05145454.2| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|14247837|dbj|BAB58226.1| sigma factor B [Staphylococcus aureus subsp. aureus Mu50]
 gi|156722515|dbj|BAF78932.1| sigma factor B [Staphylococcus aureus subsp. aureus Mu3]
          Length = 256

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 115/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +   +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVARRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|302874980|ref|YP_003843613.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
 gi|307690403|ref|ZP_07632849.1| sporulation sigma factor SigF [Clostridium cellulovorans 743B]
 gi|302577837|gb|ADL51849.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
          Length = 265

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 116/258 (44%), Gaps = 12/258 (4%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +++ S +   SI+++   V +++  +   + A  ++++ N+ LV +++KK+ NRG ++ D
Sbjct: 13  LENESSKQNNSINDYTDNVELIKLAQGGDNEALNDLIKKNMPLVAAISKKFLNRGYEYDD 72

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           + Q G +GL+KA   F+     KFSTYA+  +   I R + D    I+I   ++    K+
Sbjct: 73  IFQIGCMGLIKAVNNFNTDFNVKFSTYAVPMIMGEIKRFLRD-DGIIKISRSIKATAKKL 131

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGD 590
                 ++N + REPT EE++K   +  + +    + +     L   I  +D S   L D
Sbjct: 132 HYDRENLTNILNREPTIEELSKYSGISKDDIIMATESSGSLQYLYDVIHQDDGSPVLLID 191

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I +            A           S         R    +    D T  +V K   
Sbjct: 192 KISETGEDDKDMIDKLALKDALLKLDTKS---------RQIILLRYFKDKTQIQVAKMLG 242

Query: 651 VTRERIRQIEAKAIRKLK 668
           +++ ++ +IE K ++ +K
Sbjct: 243 ISQVQVSRIEKKVLKLMK 260


>gi|238025872|ref|YP_002910103.1| flagellar biosynthesis sigma factor [Burkholderia glumae BGR1]
 gi|124695885|gb|ABN14279.1| FliA [Burkholderia glumae BGR1]
 gi|237875066|gb|ACR27399.1| FliA [Burkholderia glumae BGR1]
          Length = 241

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/209 (22%), Positives = 91/209 (43%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 34  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 90

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V +   ++  ++ R     E+A  L MP++  + +L+       I  E      D 
Sbjct: 91  TSREVEQAIHQVEQRLGRSANESEVATHLEMPLDDYQAMLQDLHGSQLIYYEDFDRSADD 150

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 151 EPFLDRYRVDHS-DPLSALLDEHLRAALVEAIDRLPEREKLLMSLYYERG----LNLREI 205

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 206 GAVLEVSESRVCQLHSQAVARLRARLREQ 234


>gi|320102910|ref|YP_004178501.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Isosphaera pallida
           ATCC 43644]
 gi|319750192|gb|ADV61952.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Isosphaera
           pallida ATCC 43644]
          Length = 273

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 98/232 (42%), Gaps = 18/232 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE  L LV   A++   R   G+   DLI  G  GLM A + FD   G KF TY +
Sbjct: 40  RNRLVERYLPLVKYNAERIWQRLPDGVDLDDLISAGTFGLMDAIDAFDLSRGVKFETYCV 99

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  ++    + +     R PT  EIA++L +  E
Sbjct: 100 PRIRGAMLDELRTMDW---VPRLVRSKHSRMEEARKALEAIHGRPPTDAEIAERLGVTPE 156

Query: 562 GVRKVLKITKEP--ISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
              K+   +     +SL     + D        D +EDK    P     + +L    TR 
Sbjct: 157 EFEKMALESNAVGLVSLNKKWYETDSYKDVREIDILEDKKGEDPTRRLQRKDLMRMVTRG 216

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L        R  R+   +    + T++E+G    ++  R+ Q+ +  I++L+
Sbjct: 217 LN-------RNERLIIILYYYEELTMKEIGATLDLSESRVSQMHSSIIQRLQ 261


>gi|253731099|ref|ZP_04865264.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733102|ref|ZP_04867267.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|253725174|gb|EES93903.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728935|gb|EES97664.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus TCH130]
          Length = 256

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 116/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|257065529|ref|YP_003151785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256797409|gb|ACV28064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 255

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 108/234 (46%), Gaps = 8/234 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
              +      + E+++ ++ +V  ++ KY  +G++  DL Q  ++GL+ A E++D   GY
Sbjct: 19  EYYQTRDLKLRDELIKEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAVERYDPTKGY 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FS++A   +   + R   D+   IR+P  +++   K+    + +  +++R PT  +IA 
Sbjct: 79  AFSSFATPTIMGELKRYFRDKGWVIRVPRRIQNLYKKINTAKKILPQELQRTPTIADIAD 138

Query: 555 KLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L    E + + ++ +    P SL+     +   +  D  +          +I+  L++ 
Sbjct: 139 YLGEDEETILETMEASKVYTPQSLDMKYQVQKGENAIDLSDMIGEEDKNFDSIE--LKDL 196

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +    L   E+ +L +R+  G     T  ++     +++  + +IE K ++K
Sbjct: 197 IDKSKERLNDLEKEILELRYYEG----RTQVDIANTLDISQMTVSRIEKKILQK 246


>gi|168180934|ref|ZP_02615598.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
 gi|182668292|gb|EDT80271.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
          Length = 242

 Score =  105 bits (261), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK+++      ++  K+ +EP   +IA +L + ++
Sbjct: 71  IRIKGSMIDELR---RNSPISKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADELNVSLK 127

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         ISLE  I   ED   L   I+D+ + SP     +    +   + + 
Sbjct: 128 EVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDEKSPSPEKHVEENEQLDYLAKAIE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK   
Sbjct: 188 LLNEKDRLVVTLYY----YEELTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236


>gi|37781593|gb|AAP42800.1| SigB [Staphylococcus aureus]
          Length = 256

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 115/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKEGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G +  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGGRIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|298490935|ref|YP_003721112.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298232853|gb|ADI63989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 265

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 117/251 (46%), Gaps = 14/251 (5%)

Query: 425 SEFRHIVSMV--RKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGL 481
           +E +H +S +     +C +   + ++V+ N  LV   A  + N+    + DLIQ G +GL
Sbjct: 14  NELKHEISQLLREYQQCPSERLRNQLVKVNFGLVRKEAHYWINQCQESYDDLIQVGCLGL 73

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKF+   G  FS+YA+ +++  I   + D+  T+RIP        + +  +R +  
Sbjct: 74  IRAIEKFELSKGNAFSSYAIPYIRGEIQHYLRDKGVTMRIPRRWLALQQQAIGLSRSLRE 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNA 597
           K  R+PT  E+A  LA+ +    ++    + + P+SL+ PI D  E  S LG+ + D + 
Sbjct: 134 KYNRQPTDAELAAVLAISLSEWEEIKLAWMNRSPLSLDVPIKDGEEGASCLGELVPDPHY 193

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S   +           + L  L  R   VL   F      D T ++V +   ++   + 
Sbjct: 194 RSFQLAQEDQI---RLQQALVQLENRTREVLECVFL----QDLTQKQVAEHLGISVVTVS 246

Query: 658 QIEAKAIRKLK 668
           +   K +  LK
Sbjct: 247 RRVKKGLDLLK 257


>gi|85058037|ref|YP_453739.1| flagellar biosynthesis sigma factor [Sodalis glossinidius str.
           'morsitans']
 gi|84778557|dbj|BAE73334.1| RNA polymerase sigma factor for flagellar operon FliA [Sodalis
           glossinidius str. 'morsitans']
          Length = 241

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 102/238 (42%), Gaps = 14/238 (5%)

Query: 437 GECEASIAKKE-MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
              +  +A    + +    ++   A +   R    ++  DLIQ G IGL+ A + FD   
Sbjct: 5   YNHQGRLADDRGLWQQYAPIIRHEALRLQVRLPASVELEDLIQAGMIGLLAAIDSFDAAQ 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+TYA   ++  +   + ++     +P  +R    ++    +R+  ++    + ++I
Sbjct: 65  GASFTTYARSRIRWGMLDELRERDW---VPRSVRRNAREIAAAIQRLEQRLGANTSEQQI 121

Query: 553 AKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + +   + +L  T      SL+  +  E     G  +       P    +   LR
Sbjct: 122 ADELGVSLTAYQTMLHETNCSQLFSLDELMAQEAQGT-GPALPADAGQDPFQLLMAGGLR 180

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +     +  L  RE+ +L + +    + +  L+E+G+   V   R+ Q+ + AI++L+
Sbjct: 181 KQVKDEIGRLPEREQLLLNLYY----HQELNLKEIGEVLGVGESRVSQLHSLAIKRLR 234


>gi|254673642|emb|CBA09200.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha275]
          Length = 268

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 115/250 (46%), Gaps = 11/250 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I +++    +S  E   +             A K+++ ++LR+V+S+A+ Y   GL
Sbjct: 17  LEQYIHTVNSIPMLSQEEETRLAER---RIKGDLNAAKQLILSHLRVVVSIARGYDGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RD 527
              DLIQEGNIGLMKA ++++   G +  ++A+ W+K  I   I      +R+     + 
Sbjct: 74  NQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQR 133

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS 586
           K+   +R+ R+  N +      ++IA  L + +  V     ++T   I++     D++ S
Sbjct: 134 KLFFNLRSMRKNLNALSP-KEAQDIADDLGVKLSEVLEMEQRMTGHDIAIMADNSDDEDS 192

Query: 587 H-LGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
               D++ D ++      + QA+     E     LA L  R  R++  R+        TL
Sbjct: 193 FAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVESRWLQDDGG-LTL 251

Query: 643 EEVGKQFCVT 652
            ++  ++ V+
Sbjct: 252 HQLAAEYGVS 261


>gi|61889360|emb|CAI72509.1| SigB protein [Staphylococcus aureus]
          Length = 256

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 116/248 (46%), Gaps = 9/248 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSNREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSRS 673
           KL+  +  
Sbjct: 249 KLQEAAHK 256


>gi|57650736|ref|YP_186870.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus COL]
 gi|87160164|ref|YP_494668.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195964|ref|YP_500776.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|151222182|ref|YP_001333004.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|161510276|ref|YP_001575935.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221141586|ref|ZP_03566079.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|258453225|ref|ZP_05701216.1| RNA polymerase sigma-B factor [Staphylococcus aureus A5948]
 gi|262049235|ref|ZP_06022110.1| sigma factor B [Staphylococcus aureus D30]
 gi|262052481|ref|ZP_06024679.1| sigma factor B [Staphylococcus aureus 930918-3]
 gi|282923053|ref|ZP_06330738.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9765]
 gi|284025100|ref|ZP_06379498.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus 132]
 gi|294850549|ref|ZP_06791276.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9754]
 gi|304379245|ref|ZP_07361984.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|1729797|emb|CAA71068.1| sigma-B [Staphylococcus aureus subsp. aureus COL]
 gi|1934991|emb|CAA68932.1| sigma factor B [Staphylococcus aureus]
 gi|37781588|gb|AAP42796.1| SigB [Staphylococcus aureus]
 gi|57284922|gb|AAW37016.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           COL]
 gi|87126138|gb|ABD20652.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87203522|gb|ABD31332.1| sigma factor B, putative [Staphylococcus aureus subsp. aureus NCTC
           8325]
 gi|150374982|dbj|BAF68242.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160369085|gb|ABX30056.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|257859171|gb|EEV82028.1| RNA polymerase sigma-B factor [Staphylococcus aureus A5948]
 gi|259159602|gb|EEW44648.1| sigma factor B [Staphylococcus aureus 930918-3]
 gi|259162600|gb|EEW47167.1| sigma factor B [Staphylococcus aureus D30]
 gi|269941665|emb|CBI50072.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282593244|gb|EFB98241.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9765]
 gi|294822569|gb|EFG39011.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9754]
 gi|302751946|gb|ADL66123.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304342104|gb|EFM08004.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|315197004|gb|EFU27346.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140765|gb|EFW32617.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320143740|gb|EFW35517.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329314750|gb|AEB89163.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           T0131]
 gi|329724065|gb|EGG60589.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21189]
          Length = 256

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 116/247 (46%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  + 
Sbjct: 249 KLQEAAH 255


>gi|326796449|ref|YP_004314269.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas
           mediterranea MMB-1]
 gi|326547213|gb|ADZ92433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas
           mediterranea MMB-1]
          Length = 228

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 49/226 (21%), Positives = 98/226 (43%), Gaps = 14/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++    LV  +A     R    +   DL Q G IGL++A ++F+   G  F TYA   +
Sbjct: 4   IIQQYGYLVKKIAYHLLARLPNHVDVDDLTQAGMIGLIEAYKRFESTKGASFETYAGIRI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + AI   +         P  +R     V    + +  K+ R+ T  E+++ + + V+   
Sbjct: 64  RGAIMDEMRKSDW---APRSVRRNGRAVTEAIKELEGKLGRDVTDNEVSEHMGISVDEYH 120

Query: 565 KVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           ++++ +      S E  +  E  S+  +   D +     D   +   ++     +  L  
Sbjct: 121 EIMRSSMSTQLFSYEEMLESEHGSNEINIESDDSQP--YDVVEEGGFQKQLAVEIDKLPE 178

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ VL + +    N +  L+E+G    V+  R+ QI ++A  +L+
Sbjct: 179 REKLVLSLYY----NEELNLKEIGAVLGVSESRVSQIHSQAAMRLR 220


>gi|112981044|gb|ABI29246.1| DNA-dependent RNA polymerase sigma factor D subunit [Brachymonas
           denitrificans]
          Length = 270

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 62/329 (18%), Positives = 122/329 (37%), Gaps = 60/329 (18%)

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +REMG++ELL+REGEI IAKRIE                                     
Sbjct: 1   MREMGTVELLTREGEIEIAKRIE------------------------------------- 23

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                       GG     E  S             D+++E +  I +      D     
Sbjct: 24  ------------GGMMDMMEAISGSPATIDEILAMADEIREDKVVITTVVDGFTDADEND 71

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           D     AE DE  +D+D+D    + + M + ++ + +   D+I   +  + +  +     
Sbjct: 72  DYV---AEEDEDEVDDDDDGGTKSQTKMMEMVKNEALRRFDDIRASFESMLAAYE----- 123

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL-AQSY 363
            KD   S      ++K+   + ++      I+ L + + +  + +  N+  L ++     
Sbjct: 124 -KDGYGSPAYVQAQKKISSRLMTIRFTAKTIEKLCDTVREQVEEVRKNQRLLRQIIVDKC 182

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            + ++ F+       L+  WV       +  W   +   +  + +++  +  +     + 
Sbjct: 183 HMPQEKFVAEFTDNLLNLQWVEQQAAAGKP-WSTTLGRNIPPVQELQQRLIDLQKRVVVP 241

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           + E ++I   +  GE  +  AKKEM+EAN
Sbjct: 242 LEELKNINKRMIDGERFSRNAKKEMIEAN 270


>gi|298528406|ref|ZP_07015810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298512058|gb|EFI35960.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 261

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 52/235 (22%), Positives = 103/235 (43%), Gaps = 14/235 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  ++  K E+V A  + +   A +  ++    +   DLI  G++GL++A   FD   G
Sbjct: 28  FDQLSAADKNEIVRAYGQKIRITAARLKHKLPAHVDVNDLISAGSLGLIEALGNFDPTQG 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K  T+A   +K A+   +            +R K+ K+ ++ R         P+  E+ 
Sbjct: 88  IKLETFADNRIKGAMLDELRRMDWF---SRGLRKKVKKLEQSMREFEQNTGHSPSHSELK 144

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +      E V + L   +  I L      E+ S  G    D+  +S +      +L +  
Sbjct: 145 EITGYSREEVEEGLLALQNQICLSLEAIQENFSATGTQDSDEPQLSVVFH----DLVDKV 200

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++  L+ +E+ VL + +      + T++EV +   VT  R+ Q+ ++AI+K+K
Sbjct: 201 AAIIEKLSNKEQLVLSLYY----TEELTMKEVAQVLDVTEGRVSQLHSQAIKKVK 251


>gi|170694383|ref|ZP_02885537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia graminis
           C4D1M]
 gi|170140806|gb|EDT08980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia graminis
           C4D1M]
          Length = 244

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/207 (22%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  E+A+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHKVEQNLGRSASETEVAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDDSLRSALVEAIDRLPEREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRTRLR 234


>gi|116668918|ref|YP_829851.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116609027|gb|ABK01751.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
          Length = 275

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 111/230 (48%), Gaps = 13/230 (5%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             +V   L L  ++A ++  RG    DL Q   +GL+KAA  FD   G  F  YA   + 
Sbjct: 29  NHLVLDYLDLAEALAARFQARGRDRADLNQVAYLGLVKAARGFDEARGASFPAYAAPTIT 88

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             + R + D+   +R P H++D   +++R    ++  + R P+  E+A++LA+  E V +
Sbjct: 89  GELKRYLRDRCWMVRPPRHVQDLRSELLRAEPALAQSLGRPPSAAELARELAVSPEAVNE 148

Query: 566 --VLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTP 622
                 +  P SL+    + DT+ L + +   ++ ++ L+  I         + +  LT 
Sbjct: 149 ATAAAASLHPDSLDAVDANTDTAPLAETLSSGEDPLARLEELI------CLNQAIHELTA 202

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            ++ +L  R+      + +  E+G++F V++ ++ +  ++ + +L+   +
Sbjct: 203 EDQELLYRRYFC----EESQAELGRRFGVSQMQVSRRLSRVLVQLQRLLQ 248


>gi|187778769|ref|ZP_02995242.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
 gi|187772394|gb|EDU36196.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
          Length = 242

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 13/233 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+E+V+  + LV  +A +      + +++ DL+  G IGLM A  KFD   G KFSTYA 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K ++   +        I     DK+++      R+  K+ +EP   +IA +L + ++
Sbjct: 71  IRIKGSMIDELR---RNSPISKGAMDKLNRYNEAIERLQKKLNKEPNLIQIADELNISLK 127

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         ISLE  I   ED   L   I+D  + SP     +    +   + + 
Sbjct: 128 EVSEIENYINYISVISLEDLIFSSEDEVPLIGTIKDDKSPSPEKHVEENEQLDYLAKAIE 187

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  ++  V+ + +      + TL+E+GK   V+  R+ Q+ ++AI  LK   
Sbjct: 188 LLNEKDRLVVTLYY----YEELTLKEIGKILSVSESRVCQLHSRAIIHLKKAM 236


>gi|312134334|ref|YP_004001672.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774385|gb|ADQ03872.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 256

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 61/216 (28%), Positives = 110/216 (50%), Gaps = 11/216 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   +AKK+ NRG+ + DL Q   + L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNRHLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++   +  P SL+  + +++   LGD +   +      S +Q    E   + +  L+P
Sbjct: 151 EVMEASNSYLPQSLDQTMYEDEEMTLGDVLGKSDE-----SILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            E   L+ RF      + T +E+ ++  V++  I +
Sbjct: 206 FEREFLQKRFF----EEKTQKEIAEEMNVSQMYISR 237


>gi|170701719|ref|ZP_02892658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           IOP40-10]
 gi|170133382|gb|EDT01771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           IOP40-10]
          Length = 244

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 92/209 (44%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGLM AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 37  VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 93

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++  ++ R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 94  TSREVEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGMLQDLHGSQLIYYEDFDRAADD 153

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D      A  PL + +  +LRE     +  L  RE+ ++ + +  G      L E+
Sbjct: 154 EPFLDRYRVDLA-DPLSALLDDHLREALVDAIDRLPEREKLLMSLYYERG----LNLREI 208

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 209 GAVLEVSESRVCQLHSQAVARLRARLREQ 237


>gi|187925770|ref|YP_001897412.1| flagellar biosynthesis sigma factor [Burkholderia phytofirmans
           PsJN]
 gi|187716964|gb|ACD18188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           phytofirmans PsJN]
          Length = 244

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 48/207 (23%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDDSLRSALVEAIDRLPDREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRTRLR 234


>gi|289422547|ref|ZP_06424390.1| RNA polymerase sigma-B factor [Peptostreptococcus anaerobius 653-L]
 gi|289157119|gb|EFD05741.1| RNA polymerase sigma-B factor [Peptostreptococcus anaerobius 653-L]
          Length = 257

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 113/227 (49%), Gaps = 8/227 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E +L L   +++KY N+G+ + D+ Q  ++ L+ A +++D   G++FS++A   +
Sbjct: 31  RNILIEKHLYLAKILSRKYMNKGVDYEDIFQVASLALIFAIDRYDVSKGFEFSSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  T+R+P  +++   K+  T   +  ++KR P P EIA+ L + +E V 
Sbjct: 91  VGEIKKYFRDKVWTLRVPRRIQELSKKISNTKTLLEQELKRSPKPIEIAEYLEVDLEDVL 150

Query: 565 KVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + ++ +   +P+SL+TP  +++     D            +  Q    +   + + +L  
Sbjct: 151 EAMEASYGYQPMSLDTPSNEDNEDK--DITLGDKIGFEEKNFSQIEDMDFLDKFMETLNE 208

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E  +++ RF        T   +  +  +++  + ++E K + KLK 
Sbjct: 209 LEVSIVKGRFFEN----KTQSVIAGELGISQMTVSRLEKKIVEKLKK 251


>gi|254412979|ref|ZP_05026751.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196180143|gb|EDX75135.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 119/252 (47%), Gaps = 14/252 (5%)

Query: 425 SEFRHIVSMVRKGECEASIA--KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGL 481
            E +H    + +   ++  A  + ++V  N+ LV   A  + N+    + DL+Q G +GL
Sbjct: 9   QELKHESLRLLRDYQQSKSAETRNQLVYLNIGLVRREAHYWVNQCTESYEDLLQVGCLGL 68

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E+F    G  FS++A+ +++  I   + D+   IRIP        + +   R++  
Sbjct: 69  IRAIERFAPSKGNAFSSFAIPYIRGEIQHYLRDRGGCIRIPRRWLALQQQSIAIIRQLRA 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNA 597
           ++ R+PT  E+A+ L +P+   +++      +EP+SL+TP+GDE+   + LGD + D   
Sbjct: 129 QLNRQPTDAEVAEALEIPLAEWQEIKLAHQNREPLSLDTPVGDEEDGTTSLGDIVPDPQY 188

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S   +           + L  L  R   VL   F      D T +EV +   ++   + 
Sbjct: 189 RSFQLAQEDQI---RLQQALVHLEQRTREVLEFVFLH----DLTQKEVAELLNISVVTVS 241

Query: 658 QIEAKAIRKLKH 669
           +   K +  +K+
Sbjct: 242 RRMKKGLNAMKN 253


>gi|270157125|ref|ZP_06185782.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|289164470|ref|YP_003454608.1| sigma factor 28 [Legionella longbeachae NSW150]
 gi|269989150|gb|EEZ95404.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|288857643|emb|CBJ11483.1| sigma factor 28 [Legionella longbeachae NSW150]
          Length = 238

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 51/233 (21%), Positives = 102/233 (43%), Gaps = 17/233 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +A     R   G+Q  DLIQ G +GL++AA  +D   G  F T
Sbjct: 12  QQIQETLVKNHALLVKRIAHHLLGRLPQGIQLDDLIQAGMLGLLEAARHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    + + +++ RE    EIA +L +
Sbjct: 72  YAGIRIRGYMLDEVRRNDW---VPRSVHRNSRLISEAVKYVEHRLGREAKDSEIAAELGV 128

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTR 615
            +    ++L+ +          G +D     D ++  N   +  P  +   ++L    + 
Sbjct: 129 SLAEYHEMLQDSVS----SHLYGFDDLGVTDDALQTDNQSASTEPHVNVFHSDLMRRLSE 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+  L  +E  VL + +      D  L+E+G+   V+  R+ QI ++A  ++K
Sbjct: 185 VIRGLPHKERMVLSLYY----EHDLNLKEIGEVIGVSESRVSQILSQATHRIK 233


>gi|161898839|gb|ABX80409.1| SigB [Listeria monocytogenes]
          Length = 222

 Score =  104 bits (260), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 99/226 (43%), Gaps = 4/226 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 1   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+    + ++ +++  P  
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVKELTRELQSSPQI 120

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 121 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           R    +VL  L  RE+++L+  F      + + +E G+   +++  
Sbjct: 181 RMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDISQMH 222


>gi|167745425|ref|ZP_02417552.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|317473026|ref|ZP_07932327.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655146|gb|EDR99275.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|316899509|gb|EFV21522.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
          Length = 241

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 122/248 (49%), Gaps = 15/248 (6%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           + E R ++ + +        A++++V  N+ L+ SV K++T RG +  DL Q G+IGL+K
Sbjct: 1   MDETRELLKLTK---EGDQDAREKIVLDNMGLIWSVVKRFTGRGHEPEDLFQIGSIGLLK 57

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +KFD     KFSTYA+  +   I R + D    I++   +++  ++V +     + K 
Sbjct: 58  AVDKFDLSYDVKFSTYAVPMITGEIKRFLRD-DGMIKVSRSLKEIAYQVRQAGEAFAMKY 116

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPL 601
            RE T +E++++  +  + +   L+  K+  S+  P    D S   L D +  +   S  
Sbjct: 117 NREATIDELSRETKIARDEIVVALEANKDVESIYQPSYQSDDSQVLLVDKLPGEENESDT 176

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                         ++ +L+  E  ++ MR+  G     T +E+ K+  +++ ++ ++E 
Sbjct: 177 VIN-----HVMLEELMDTLSGDERELITMRYFHG----KTQQEIAKKLSISQVQVSRMEK 227

Query: 662 KAIRKLKH 669
           K + +++ 
Sbjct: 228 KILLRMRK 235


>gi|144971|gb|AAA23295.1| ORF1 [Corynebacterium diphtheriae]
 gi|144975|gb|AAA23298.1| open reading frame [Corynebacterium diphtheriae PW8]
          Length = 143

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 48/141 (34%), Positives = 90/141 (63%)

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           M  ++ RE T EE+A++  +    +  +L+ +++P+SL+ P+G ++ + LGDFIED  A 
Sbjct: 1   MYQQLGREATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEAT 60

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               + + +        VL +L  RE+ V+R+R+G+      TL+++G+QF ++RER+RQ
Sbjct: 61  DAESAVVASLRHSDIRTVLDTLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQ 120

Query: 659 IEAKAIRKLKHPSRSKKLRSF 679
           IE + + KL+  +R++KLR++
Sbjct: 121 IEREVMSKLRDGARAEKLRAY 141


>gi|294140220|ref|YP_003556198.1| RNA polymerase sigma-27 factor [Shewanella violacea DSS12]
 gi|293326689|dbj|BAJ01420.1| RNA polymerase sigma-27 factor [Shewanella violacea DSS12]
          Length = 239

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 100/229 (43%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KALIVEQYAPLVKKIAHHLLARLPASVQIDDLLQAGMMGLLEASSKFDGNKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+    EIA++L M + 
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRVAQVIDELEQELGRDAKDAEIAQRLDMTLN 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL--DSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D I   N V+    +S  +          +  
Sbjct: 130 EYHHIL----NDVSVGKVIGIEDLGVSVDVISHDNGVNDDTFESIAEGEFHLALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|206901861|ref|YP_002251028.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
 gi|206740964|gb|ACI20022.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
          Length = 413

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 63/154 (40%), Positives = 101/154 (65%), Gaps = 1/154 (0%)

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              K  +   +     K +     + +++    E VR++  + +EP+SLE P+G+++ + 
Sbjct: 260 LKAKNNKVPTKEEINEKAKELKHVLEEEIRQQTEKVREISMMGQEPLSLEMPVGEDEDNR 319

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L DF+E+K+ +SP D A+Q +L++    +L  L+ RE  +L++RFG+  N   TLEEVGK
Sbjct: 320 LADFVENKD-LSPADIAVQKSLKKDIEELLNELSEREREILKLRFGLEDNQPRTLEEVGK 378

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            F VTRERIRQIEAKA+R+L+HPSRSKK++ +L+
Sbjct: 379 LFNVTRERIRQIEAKALRRLRHPSRSKKIKDYLE 412



 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 76/146 (52%), Positives = 104/146 (71%), Gaps = 3/146 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++  +K I     ++  E   +   V +       AKK+++EANLRLV+SVAK+Y  RGL
Sbjct: 72  VKMYLKEIGKIPLLTPEEEIELAKRVEQ---GDEEAKKKLIEANLRLVVSVAKRYIGRGL 128

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            FLDLIQEGN+GL+KA EKFDW  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + 
Sbjct: 129 SFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 188

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAK 554
           ++K+ +  R ++  + R+PT E+IAK
Sbjct: 189 MNKIHKITRLLTQNLGRKPTEEDIAK 214



 Score = 67.9 bits (164), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 1/103 (0%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +  +   SED               ++ +   D   DDPV+MYL+E+G I LL+ E EI 
Sbjct: 33  EDHELVDSEDLYVDIKEDKIPENIEEEVEIPEDIELDDPVKMYLKEIGKIPLLTPEEEIE 92

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +AKR+E G       L E+ L     +  R  +  G + L  I
Sbjct: 93  LAKRVEQGDEEAKKKLIEANLRLVVSVAKRY-IGRGLSFLDLI 134


>gi|225848018|ref|YP_002728181.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225644246|gb|ACN99296.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 240

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 53/206 (25%), Positives = 91/206 (44%), Gaps = 11/206 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G +GL  A EK+D   G K STYA   ++  I   +        +P  +R 
Sbjct: 35  VDEEDLIQVGVLGLYDALEKYDPSKGIKLSTYAEIRIRGYIIDHLRQLDW---VPRSVRS 91

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDT 585
           KI  +     ++  ++ R+   EEIA  L M VE      +    K  ISL++ +  +D 
Sbjct: 92  KIKNLENKIAQLEAQLGRQAKTEEIANYLGMTVEEYMTYAEVLANKVLISLDSDVSKDDD 151

Query: 586 SHL-GDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLE 643
             L    +   N  +P     +  L+E  +  +L  L  RE  ++ + +      +  ++
Sbjct: 152 ESLHLWEVISSNDDTPDKVVEEKQLKEILSDIILNHLDERERLLISLYY----YEELNMK 207

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+     +T  R+ Q+  K + KLK+
Sbjct: 208 EIADILGITESRVSQLHTKIMLKLKN 233


>gi|121607918|ref|YP_995725.1| FliA/WhiG family RNA polymerase sigma factor [Verminephrobacter
           eiseniae EF01-2]
 gi|121552558|gb|ABM56707.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Verminephrobacter eiseniae EF01-2]
          Length = 241

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 102/248 (41%), Gaps = 16/248 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + +  ++  ++ LV  +A     +    ++  DLIQ G +GL  A  ++    
Sbjct: 1   MYTAKGQLDRDALLRQHVPLVRKIAHHMIAKLPANVELDDLIQVGMMGLADALSRYQVAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   + +           R    ++ +   R+  ++ R P   EI
Sbjct: 61  GVQFETFASQRIRGAMLDQLREGDWM---SRSARKSQKEIEQAVHRLEQRLGRSPLESEI 117

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGD-FIED---KNAVSPLDSAIQ 606
           A ++ + +   + +L      + + LE      D     D F+E     +A  P++    
Sbjct: 118 ASEMGLHLASYQSLLGKVRGTQLVYLEDMGQGRDEREAEDGFLERHIVDSAADPVELLRD 177

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L+ +    + SL  RE+       G+    D  L+E+     +T  R+ Q+ +++I +
Sbjct: 178 QRLKTSLVAAIQSLPEREQ----HIMGMYYEHDMNLKEIAAVLGITESRVCQLHSQSIVR 233

Query: 667 LKHPSRSK 674
           L+   R+ 
Sbjct: 234 LRAKMRAH 241


>gi|283781321|ref|YP_003372076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
 gi|283439774|gb|ADB18216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
          Length = 261

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 57/248 (22%), Positives = 103/248 (41%), Gaps = 18/248 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           K +      +  +VE  L LV    ++   R   G++  DLI  G  GLM A + FD   
Sbjct: 19  KHDPNQKELRNLLVEHYLPLVKYNGERIWARLPEGVELDDLISAGIFGLMDAIDAFDMTR 78

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G KF TY +  ++ A+   +        +P  +R K  K+    + +  ++ R PT  E+
Sbjct: 79  GVKFETYCVPRIRGAMLDELRTMDW---VPRLVRSKASKLGEATKTLEARLGRHPTTVEL 135

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQA 607
           A ++ M V  V K++        ISL     + D        D +EDK    P     + 
Sbjct: 136 AAQMEMSVPEVEKMVSEASAVGLISLNKKWYETDSYKDVREIDILEDKKGEDPTRRIQKN 195

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +L    T+ L        R  R+   +    + T++E+G    ++  R+ Q+ +  + +L
Sbjct: 196 DLMRLVTKGLN-------RNERLIIILYYYEELTMKEIGATLDLSESRVSQMHSSIVSRL 248

Query: 668 KHPSRSKK 675
           +     ++
Sbjct: 249 QSQLGRRR 256


>gi|332799203|ref|YP_004460702.1| RNA polymerase sigma-28 subunit FliA/WhiG [Tepidanaerobacter sp.
           Re1]
 gi|332696938|gb|AEE91395.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Tepidanaerobacter sp.
           Re1]
          Length = 246

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 57/249 (22%), Positives = 104/249 (41%), Gaps = 22/249 (8%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD 489
            +     +    K ++VE  + L+  +  +        L++ DLI  G  GLM+A E++D
Sbjct: 10  WMNYNNTKDKYVKGQLVEKYVPLIKHIVNRMNINLPPYLEYEDLISYGVFGLMQAIERYD 69

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G KF TYA   +K +I   +        IP  +R KI  +      M   +      
Sbjct: 70  TKKGIKFETYAYTRIKGSIIDELRKTD---MIPQDIRKKIKMLQNAFSEMEQILGHSAND 126

Query: 550 EEIAKKLAMPVE---GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           ++I+  L +  +    + K +      +S +  I  ED          + +  P   A +
Sbjct: 127 DDISNYLGISKKDLYKIYKEISAAYGVLSFDELIEYEDVG--------QASGQPDIQAEK 178

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             ++E     +  L P+E+ V+ + +  G       +E+ +   +++ RI QI  KAI +
Sbjct: 179 EEVKEILGNAINQLPPQEKLVITLYYYEG----LNFKEIAEVLELSQGRISQIHTKAILR 234

Query: 667 LK-HPSRSK 674
           L+ H SR K
Sbjct: 235 LRGHLSRKK 243


>gi|107100889|ref|ZP_01364807.1| hypothetical protein PaerPA_01001919 [Pseudomonas aeruginosa PACS2]
 gi|152986686|ref|YP_001349226.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PA7]
 gi|313106454|ref|ZP_07792685.1| motility sigma factor FliA [Pseudomonas aeruginosa 39016]
 gi|150961844|gb|ABR83869.1| sigma factor FliA [Pseudomonas aeruginosa PA7]
 gi|310879187|gb|EFQ37781.1| motility sigma factor FliA [Pseudomonas aeruginosa 39016]
          Length = 239

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 100/238 (42%), Gaps = 14/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +A  +++++++    LV  +A     R    +Q  DL+Q G IGL++AA+K+D   
Sbjct: 2   YSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGK 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E+
Sbjct: 62  GASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVTDAIRAIEARTGRDAKDHEV 118

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + +E    +L  T+     S +  + D +     D     N    +   +    +
Sbjct: 119 AAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTSLSHNEP--IHGLLDERFQ 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 177 AALADAIAKLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 230


>gi|158333719|ref|YP_001514891.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158303960|gb|ABW25577.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 264

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 118/249 (47%), Gaps = 14/249 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKA 484
           E   ++   ++  C  +  +  +V+ NL LV   A ++       F DL+Q G++GL++A
Sbjct: 12  ESLELLQQYQQSSC--TELRNRLVQMNLGLVRREAHRWVGHSTESFDDLMQVGSLGLIRA 69

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E+FD   G+ FS++A+ +++  I   + D+S  +RIP    +   + +   R M ++++
Sbjct: 70  IERFDPFKGHAFSSFAVPYIRGEIQHYLRDKSPQVRIPRKWHELQRQAINVTREMRDELQ 129

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGD--EDTSHLGDFIEDKNAVSP 600
           R+PT  E+A  L +  +  ++V   +     +SL+ P+ +  +++  LG+ + D++  S 
Sbjct: 130 RQPTDVEVAAALDICQKEWQEVKLASCNRSVLSLDAPVHNSEQESMSLGELLPDRHYHSF 189

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +           + L+ L  R   VL   F      D T +E  +   ++   + +  
Sbjct: 190 QLAQEDQI---RLRQALSKLEKRTSDVLEFVFFH----DLTQKETAEVLGISAVTVSRQV 242

Query: 661 AKAIRKLKH 669
            K +  L+ 
Sbjct: 243 KKGLVALRQ 251


>gi|4103484|gb|AAD01787.1| sigma-D factor [Myxococcus xanthus]
          Length = 297

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 109/256 (42%), Gaps = 48/256 (18%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++++     ++  +   +    RK       A++    +NL  V++VAKK+ NRG 
Sbjct: 12  LSHYLRNLGGHQQLTREQEYELARRARK---GDESARQTTASSNLAFVVAVAKKFANRGA 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLIQEGN+GLMKA E FD     +F+TYA+WW++  ITR + D    +R        
Sbjct: 69  RLDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGG------ 122

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
                                               +  + +    SL+  I ++  +  
Sbjct: 123 ------------------------------------EAERGSMVDFSLDATIDEDGETTF 146

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF--GIGMNTDHTLEEVG 646
            D +ED N+ SP    +           LA +  R   +        +  +   TLEE+G
Sbjct: 147 LDRLED-NSPSPQQVFLAHEQDTEIQEALAKVRKRIGDLGWDILTERLTQDKPLTLEELG 205

Query: 647 KQFCVTRERIRQIEAK 662
           +++ V+RE +RQ+E K
Sbjct: 206 QRWGVSREPVRQVELK 221



 Score = 45.6 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 60/180 (33%), Gaps = 19/180 (10%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLR +G  + L+RE E  +A+R   G      +   S L F  ++    +  +    L +
Sbjct: 15  YLRNLGGHQQLTREQEYELARRARKGDESARQTTASSNLAF--VVAVAKKFANRGARLDD 72

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK---------ERDDVQETEGDIESAA 234
           +I        E   G     E    +K    +                   ++     A 
Sbjct: 73  LI-------QEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGGEAE 125

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           + S  D S   +  E+ E    +  ED   S   +    +Q    +  AL ++ +   +L
Sbjct: 126 RGSMVDFSLDATIDEDGETTFLDRLEDNSPSPQQVFLAHEQDTE-IQEALAKVRKRIGDL 184


>gi|149927789|ref|ZP_01916040.1| sigma 28 (Flagella/Sporulation) [Limnobacter sp. MED105]
 gi|149823411|gb|EDM82642.1| sigma 28 (Flagella/Sporulation) [Limnobacter sp. MED105]
          Length = 238

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 99/245 (40%), Gaps = 13/245 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               + ++ K + V+  + LV  +A     +    +Q  DLIQ G IGLM A  +F+   
Sbjct: 1   MYTAQGTLDKSKQVDQYIPLVRRLAHHLIAKLPASVQIDDLIQAGLIGLMDAITRFEEGQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +         P  +R    K+     R   K+ R  + +EI
Sbjct: 61  GAQFETYASQRIRGAMLDELRSADWM---PRGVRQAQRKIETATLRAEQKLGRSASEKEI 117

Query: 553 AKKLAMPVEGVRKVLKITKE---PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           A  + + ++  + +L  ++        +     +   +L   I      +PL+       
Sbjct: 118 ADVMGVSLDEYQDMLFDSRGASLVFYDDYADDGDGEGYLDRQIGGDEEANPLEMLGDQRF 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE   + +  L  RE+ ++    G+    +    E+     VT  R+ Q+  +A+ +LK 
Sbjct: 178 RENLIQAIEDLPEREKMLM----GLYYEQELNFREIAAVLGVTESRVCQLHTQAVSRLKA 233

Query: 670 PSRSK 674
             R  
Sbjct: 234 KLREH 238


>gi|167564488|ref|ZP_02357404.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           EO147]
          Length = 244

 Score =  104 bits (259), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 101/244 (41%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I++ E++     LV  +  +   +    +   DLIQ G IGL+ AA ++    
Sbjct: 2   MYNAQGKISQDEVLTQYAPLVRRLGLQLVAKMPASVDLDDLIQAGMIGLLDAASRYKEDQ 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P  +R    +V     ++  ++ R     E+
Sbjct: 62  GAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSREVEHAIHQVEQRLGRSANETEV 118

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L MP+   + +L+       +  E      D     D     +A  PL + +  +LR
Sbjct: 119 AAHLQMPLGEYQSMLQDLHGSQLVYYEDFDRSADDEPFLDRYRADHA-DPLSALLDDHLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +  L  RE+ ++ + +  G      L E+G    V+  R+ Q+ ++A+ +L+  
Sbjct: 178 SALVDAIEHLPEREKLLMSLYYERG----LNLREIGAVLEVSESRVCQLHSQAVARLRAK 233

Query: 671 SRSK 674
            R +
Sbjct: 234 LREQ 237


>gi|304311117|ref|YP_003810715.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
 gi|301796850|emb|CBL45062.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
          Length = 244

 Score =  104 bits (259), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 107/248 (43%), Gaps = 14/248 (5%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           + +       +A  +   +VE +L LV  +A     R    +   DLIQ G IGL+ A +
Sbjct: 3   LANRRPMYTEQAHASLDTLVEQHLPLVRRIAHHMIGRLPSNVIVDDLIQAGVIGLIDALQ 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           K+D   G  F TYA   ++ A+   I         P  +      +    R +  +++R+
Sbjct: 63  KYDTGKGASFETYAGIRIRGAMIDEIRRGEW---APRSVHRNARAIQDAIRNVEARVQRD 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            T  E+A++L +P++    + + +      S+E     E     GD  +  +  +P    
Sbjct: 120 ATDREVAEELGVPLDAYHAMAQDSMATRLFSMEELTAPESIIDRGDLQQAHD--NPASHF 177

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +  +  +    +  L  RE+ VL + +    + +  L+E+G+   V+  R+ QI ++A 
Sbjct: 178 QRDMMLTSMANAIKDLPEREQLVLSLYY----DEELNLKEIGEVLGVSESRVCQIHSQAT 233

Query: 665 RKLKHPSR 672
            +L+   R
Sbjct: 234 HRLRARLR 241


>gi|87311163|ref|ZP_01093286.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
 gi|87286071|gb|EAQ77982.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
          Length = 261

 Score =  104 bits (259), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 102/239 (42%), Gaps = 18/239 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE  L LV    ++   R   G++  DLI  G  GLM A + FD   G KF TY +
Sbjct: 27  RNRLVERYLPLVKYNGERIWARLPEGVELDDLISAGVFGLMDAIDAFDMSRGVKFETYCV 86

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        +P  +R K  K+    +++  K  R+PT  E++  + M V+
Sbjct: 87  PRIRGAMLDELRTMDW---VPRLVRSKASKLNEANKQLEAKFGRQPTEIELSAHMGMSVK 143

Query: 562 GVRKVLKITKEP--ISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + K++        ISL     + D        D +ED     P     + +L    T+ 
Sbjct: 144 ELEKMISDANAVGLISLNKKWYETDSYKDVREIDILEDIKGEDPTRRIQKNDLMRLVTKG 203

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L        R  R+   +    + T++E+G    ++  R+ Q+ +  +++L+     ++
Sbjct: 204 LN-------RNERLIIILYYYEELTMKEIGATLDLSESRVSQMHSSIVQRLQSQLGRRR 255


>gi|325478815|gb|EGC81925.1| putative RNA polymerase sigma-F factor [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 255

 Score =  104 bits (259), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 108/234 (46%), Gaps = 8/234 (3%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
              +      + E++E ++ +V  ++ KY  +G++  DL Q  ++GL+ A ++FD   GY
Sbjct: 19  EYYKTRDKKLRDELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRFDPTKGY 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FS++A   +   + R   D+   IR+P  +++   K+    + +  +++R PT  +IA 
Sbjct: 79  AFSSFATPTIMGELKRYFRDKGWVIRVPRRIQNLYKKINTAKKILPQELQRTPTVADIAD 138

Query: 555 KLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L    E + + ++ +    P SL+     +   +  D  E          +I+  L++ 
Sbjct: 139 YLGEDEETILETMEASKVYAPQSLDMKYQVQKGENAIDLSEMIGEEDKNFDSIE--LKDL 196

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +    L   E+ +L +R+  G     T  ++     +++  + +IE K I+K
Sbjct: 197 IDKSKERLNDLEKEILELRYYEG----RTQVDIANTLDISQMTVSRIEKKIIQK 246


>gi|304316881|ref|YP_003852026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778383|gb|ADL68942.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 246

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 105/240 (43%), Gaps = 15/240 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +  + +   +K++++   + LV  + K+            DLI +G IGL+ A  K+D  
Sbjct: 11  KYEKLKDGSSKEDIIIKYMPLVKHIVKRICLSEISKEDVDDLISQGMIGLIDAVNKYDIS 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KF TYA   +K  I   +  +     IP  ++ +   + +T  R+  + KREPT EE
Sbjct: 71  KGVKFETYASIRIKGEIIDYLRKKDW---IPRSLKKRYKSIEKTIERLEQEYKREPTIEE 127

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           I     +    V K L         SL+  I +         I +    +P +  +  +L
Sbjct: 128 IMDATKLSKNDVLKTLSYMNAGYISSLDEVIENNLKIS---SITESEITNPENEVLMYDL 184

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + +  L  +E  ++ + +      D   +E+ K   +T  RI QI +KAI+KLK 
Sbjct: 185 KQNIAKAIDMLQEKERLIISLYY----YEDLNYKEISKIMGLTESRISQIHSKAIKKLKE 240


>gi|167571638|ref|ZP_02364512.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           C6786]
          Length = 244

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 101/244 (41%), Gaps = 13/244 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I++ E++     LV  +  +   +    +   DLIQ G IGL+ AA ++    
Sbjct: 2   MYNAQGKISQDEVLTQYAPLVRRLGLQLVAKMPASVDLDDLIQAGMIGLLDAASRYKEDQ 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P  +R    +V     ++  ++ R     E+
Sbjct: 62  GAQFETYATQRIRGAMLDELRSNDW---LPRSLRKTSREVEHAVHQVEQRLGRSANETEV 118

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A  L MP+   + +L+       +  E      D     D     +A  PL + +  +LR
Sbjct: 119 AAHLQMPLGEYQSMLQDLHGSQLVYYEDFDRSADDEPFLDRYRADHA-DPLSALLDDHLR 177

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +  L  RE+ ++ + +  G      L E+G    V+  R+ Q+ ++A+ +L+  
Sbjct: 178 SALVDAIEHLPEREKLLMSLYYERG----LNLREIGAVLEVSESRVCQLHSQAVARLRAK 233

Query: 671 SRSK 674
            R +
Sbjct: 234 LREQ 237


>gi|218245540|ref|YP_002370911.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|257058577|ref|YP_003136465.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|218166018|gb|ACK64755.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
 gi|256588743|gb|ACU99629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 255

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 106/240 (44%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           ++      +   + ++VE +  LV  VA + +N+    + DL Q G +GL+ A E+F+  
Sbjct: 14  LITYSRNPSLALRNQLVELHTGLVRQVAHRISNQCTEPYEDLEQIGYLGLINAIERFNPH 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  +   + D+   +RIP   ++  +K  +  ++++  + R P  +E
Sbjct: 74  QGCAFSSFAIPYIRGEMLHYLRDKGSVMRIPRRWQELYNKGKKVRKQLTTSLGRTPKDQE 133

Query: 552 IAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQA 607
           +A  L + +E   +       +  +SL++ I     S    G+ + D           Q 
Sbjct: 134 LADALQVSLEEWHECELALQNRMLVSLDSTINQNTDSTVSFGETLPDHR---YQAKQSQE 190

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    R ++ L  + +  +   F      +   +E  K+  ++   + +   K I++L
Sbjct: 191 EDRLQLQRAMSQLEDKTKEAIECVF----IKELPRKEAAKRIGMSPMTVTRHLHKGIKQL 246


>gi|37781579|gb|AAP42789.1| SigB [Staphylococcus aureus]
          Length = 256

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 116/247 (46%), Gaps = 9/247 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA +L +  E V     +  +   +S++  I  +        ++            
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKEGSTVTLLDIMGQQDDHYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R    ++L  L+ RE  +++  F  G     + +E G++  +++  + +++  AI+
Sbjct: 195 EK--RMILEKILPILSDREREIIQCTFIEG----LSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 666 KLKHPSR 672
           KL+  + 
Sbjct: 249 KLQEAAH 255


>gi|82702442|ref|YP_412008.1| sigma 28 (flagella/sporulation) [Nitrosospira multiformis ATCC
           25196]
 gi|82410507|gb|ABB74616.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosospira
           multiformis ATCC 25196]
          Length = 242

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 103/237 (43%), Gaps = 11/237 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                 +I K++ +     LV  +A     R    ++  DL+Q G IGLM+A  +++   
Sbjct: 1   MYTSVGTIDKQQHIVEFTPLVKRIANHMMARLPVSVEADDLVQVGMIGLMEALNRYEEMP 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P   R  + ++      + +++ R P+  +I
Sbjct: 61  GAQFETYAQQRIRGAMLDELRQLDW---LPRGARRVMRQIESAINVLQHRLGRSPSERQI 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           A++L + +E  +++L   K    +      D++     +     N   PL + +  +LR 
Sbjct: 118 AEELGVSIESYQQMLFEAKGTQLIHYEDFSDDEDDDFLERNCADNTADPLAALLDGDLRR 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE+       G+    +   +E+G    V+  RI Q+ ++AI +L+
Sbjct: 178 ILINAIEILPEREK----TLMGLYYEQELNFKEIGAVLGVSESRICQMHSQAIARLR 230


>gi|317121712|ref|YP_004101715.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
 gi|315591692|gb|ADU50988.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
          Length = 245

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 89/232 (38%), Gaps = 55/232 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   +
Sbjct: 64  RHTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYASKCI 123

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +   S                                                
Sbjct: 124 ENEILMHLRRTSR----------------------------------------------- 136

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                T+  +SL+ P+  +   +   L D I   +             R    R LA L+
Sbjct: 137 -----TRYEVSLDEPLNVDWEGNELLLSDVIPATDGDVIYRDLEAKVDRHLLYRALARLS 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           PRE  ++ +RFG+    + T ++V  +  +++  I ++E + I +L+   R 
Sbjct: 192 PRERLIMELRFGLVDGIERTQKQVADRLGISQSYISRLEKRIINRLRREIRK 243


>gi|268316324|ref|YP_003290043.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodothermus marinus
           DSM 4252]
 gi|262333858|gb|ACY47655.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodothermus marinus
           DSM 4252]
          Length = 253

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 114/251 (45%), Gaps = 13/251 (5%)

Query: 429 HIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKA 484
            +  +V +   + S A ++ +V A + LV S+  + +          DL   G +GL++A
Sbjct: 4   DLQRLVEQYVADPSSANREAVVLAAVPLVRSMVGRLSVPDHPLVTREDLENVGLMGLLQA 63

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + +D   G  F +YA   ++ A+   +        +P   R K+ ++ +    +   + 
Sbjct: 64  LDSYDPERGTPFVSYAYGRIRGALVDYLRSID---ALPRERRRKLAELQQAIETLRQTLG 120

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
            EP  +++A  L + ++    +L   +    +SL+  +G++    + + I +++A   L+
Sbjct: 121 GEPEDQDVADYLGISLQEYYTLLTDAQRRFALSLQETVGEDGDQSVLETIPNEDAEKQLE 180

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              +A+L E  T+++  L  RE+ +L     +    + TL E+ +   +T  RI QI  K
Sbjct: 181 DIDRASLIEYVTKLIQRLPEREQNIL----ALYYYENLTLREIAQLLGLTEARISQILGK 236

Query: 663 AIRKLKHPSRS 673
            +  L+   + 
Sbjct: 237 TLLTLRTELQR 247


>gi|88798984|ref|ZP_01114565.1| flagellar biosynthesis sigma factor FliA [Reinekea sp. MED297]
 gi|88778211|gb|EAR09405.1| flagellar biosynthesis sigma factor FliA [Reinekea sp. MED297]
          Length = 238

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 99/231 (42%), Gaps = 12/231 (5%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++E    LV  +A     R    +   DLIQ G IGL +AA  +D   G  F TYA   
Sbjct: 12  QLIEDYGVLVKRIAHHLLARLPDSVHVEDLIQSGMIGLFEAAANYDQSKGASFETYAGIR 71

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ ++   I        IP  +     ++      +  +  R+    E+A++L + ++  
Sbjct: 72  IRGSMLDEIRKGDW---IPRSVHRNSRRISDAIHTVEMREGRDAQDHEVAQELGVSLDEY 128

Query: 564 RKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             ++K T+     S E  + +  + H  +  +    ++P      + + +     + +L 
Sbjct: 129 YTLMKDTQGSRLFSFEELVDNSPSDHHENRPDASEGMAPHSGHQSSQMNDQLVEAIKALP 188

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            RE+ VL + +      +  L+E+G    V+  R+ QI ++A  +L+   R
Sbjct: 189 EREQIVLSLYY----EEELNLKEIGAVLGVSESRVSQIHSQATLRLRSKMR 235


>gi|210621718|ref|ZP_03292767.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
 gi|210154600|gb|EEA85606.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
          Length = 252

 Score =  104 bits (258), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 113/241 (46%), Gaps = 10/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I+S++   +     +K ++++ N+ LV     K++   L   DL Q G IGL+KA E+F
Sbjct: 18  EILSLISLAQKGDLKSKNKLIKLNIGLVKKAVSKFSFSSLDNDDLYQLGCIGLVKAIERF 77

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D  LG  FS+YA+  ++  I R + D    I+I   ++    K  +   +   K  +E +
Sbjct: 78  DPNLGNMFSSYAVPLIEGEIKRFLRD-DGIIKISRELKTIGWKAKKYKTQYFKKTGKEAS 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            + ++K+L +P+E ++  L      +S        ++      ++  N +   DS     
Sbjct: 137 LQALSKELNIPIEKIQSALIA----LSPVEYFNIYESDSEYTQLDLSNNIIMEDSIPYTE 192

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E    ++  L   E++V+++R+        T    G+   +++ ++ +IE KA+  LK
Sbjct: 193 LIE-LNEIIDELPDLEKKVMKLRYFEDFTQAKT----GEILGISQVQVSRIERKALMLLK 247

Query: 669 H 669
            
Sbjct: 248 K 248


>gi|209408338|emb|CAP19912.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 241

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 45/285 (15%), Positives = 97/285 (34%), Gaps = 46/285 (16%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +M+++   P T  +++   + +      L +I  L   I P+  G      
Sbjct: 1   KRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA---- 54

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                Q+ E  + +       + + D E     S+++       PE A      + E  +
Sbjct: 55  ---GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLE 111

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +                                       +K  ++S +     E L  
Sbjct: 112 KAKKA-----------------------------------LKKHGRASQQAVEELEALAI 136

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           L   + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  
Sbjct: 137 LFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLD 196

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           W        +G++   +    + I++ + ++  +  E  + I++ 
Sbjct: 197 WAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADI 240


>gi|295678067|ref|YP_003606591.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1002]
 gi|295437910|gb|ADG17080.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1002]
          Length = 244

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 47/207 (22%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     ++   + R  +  E+A+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHKVEQNLGRSASEAEVAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDDSLRSALIEAIDRLPEREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRARLR 234


>gi|254432127|ref|ZP_05045830.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
 gi|197626580|gb|EDY39139.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
          Length = 335

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 127/278 (45%), Gaps = 29/278 (10%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECE----------ASIAKKEMVEANLRLVIS 458
           + + ++ I+    ++ +E  H+   V++               + A+  MV ANLRLV+ 
Sbjct: 59  LSDYLRLIARVPLLTPAEELHLAGTVQEWLQHPDPPLSLRRRGTRARNRMVTANLRLVVM 118

Query: 459 VAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           V ++Y  R     L+ LDL Q GNIGLM+A E FD   GY+ STYA  W+ QA+ R +  
Sbjct: 119 VCRRYRGRIGNLQLEMLDLYQAGNIGLMRAVELFDPSRGYRLSTYAFSWIHQAVQRCMTA 178

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KE 572
               IRIP  +R+  ++    A+ +    ++  +   IA  L    + ++  L +     
Sbjct: 179 TGNGIRIPTALRNIAYR----AQLLEACAEQPLSIGAIAALLGEKEQRLQTALTVVRQCS 234

Query: 573 PISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             SL+ P     + + L + I D+    P D              L +L  R+ +VL++R
Sbjct: 235 TTSLDKPSASMGEDTTLIEVIPDRRGNVPHDDY------RWLHEHLDALDLRDRQVLQLR 288

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +G       +  +  +   V++  ++ +E + ++ L+ 
Sbjct: 289 YGDD--ESRSCSKTARVLGVSKSCVQSVERRTLKNLRR 324


>gi|319649539|ref|ZP_08003695.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398701|gb|EFV79383.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 251

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 106/241 (43%), Gaps = 11/241 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFD 489
             +  +   + A   +V+  L LV    ++ +    + +   D+   G +GL  A EKFD
Sbjct: 12  WAKWVDSRDAQAGNFLVKKYLPLVSYHVQRISATLPKNVSRDDIRSLGLMGLYDALEKFD 71

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF TYA + ++ AI   +  +     +P   RDK  K+     ++  ++ R  T 
Sbjct: 72  PARDLKFDTYASFRIRGAILDGLRKEDW---LPRSTRDKAKKIDAAIEKLEQRLMRNATV 128

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF-IEDKNAVSPLDSAIQAN 608
            EIA++  M  + V  V+        L      +     G + I+D+ A+ P +  ++  
Sbjct: 129 HEIAEEAEMQEDEVYSVMNEHFYANILSIDEQPDADEKDGSYSIKDEKAIIPEEKVLKNE 188

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E     +  L  +E+ VL + +      + TL E+G+   ++  RI QI +K+I KL+
Sbjct: 189 LLEEMAEKILQLNEKEQMVLSLFY----KEELTLTEIGEVMGLSTSRISQIHSKSIFKLR 244

Query: 669 H 669
            
Sbjct: 245 Q 245


>gi|254506869|ref|ZP_05119008.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
 gi|219550154|gb|EED27140.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
          Length = 220

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 53/219 (24%), Positives = 96/219 (43%), Gaps = 17/219 (7%)

Query: 456 VISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           V  +A     R    +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I
Sbjct: 3   VKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDDI 62

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                   +P  +     ++ +    +  ++ R+PT  E+A+ L + +      L     
Sbjct: 63  RRGDW---VPRSVHKHSREISQAISVLEGELNRDPTDAEVAQHLGLSLTQYHTAL----T 115

Query: 573 PISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            I+    +G ED     D I    D+ A +P         R+     + SL  RE  VL 
Sbjct: 116 DINCSRLVGIEDLGVSEDVITPDGDEEANTPFQGVADEYFRKALIDSIKSLPEREALVLS 175

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +    + +  L+E+G    V+  R+ QI ++++++L+
Sbjct: 176 LYY----DEELNLKEIGDVIGVSESRVSQILSQSMQRLR 210


>gi|330815163|ref|YP_004358868.1| FliA [Burkholderia gladioli BSR3]
 gi|327367556|gb|AEA58912.1| FliA [Burkholderia gladioli BSR3]
          Length = 254

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 90/209 (43%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 47  VDLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDW---LPRSLRK 103

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V +   R+  ++ R     EIA  L MP+   + +L+       I  E      D 
Sbjct: 104 TSREVEQAVHRVEQQLGRSANESEIASHLEMPLPDYQAMLQDLHGSQLIYYEDFDRSADD 163

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 164 EPFLDRYRVDHS-DPLSALLDDHLRAALVEAIERLPEREKLLMSLYYERG----LNLREI 218

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    V+  R+ Q+ ++A+ +L+   R +
Sbjct: 219 GAVLEVSESRVCQLHSQAVARLRARLREQ 247


>gi|239934408|emb|CAR92334.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 245

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 44/287 (15%), Positives = 93/287 (32%), Gaps = 47/287 (16%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++   D +      L ++  L   I P+               K   + +E + D+
Sbjct: 1   TVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDDE 58

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   GD E  A+   D                         +A    A+ DQ       
Sbjct: 59  EESESGDDEEEAESGPDPVV----------------------AAQRFGAVSDQ------- 89

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                         LQ  +   +K+ ++  +     + L  L   + L   + ++LVE++
Sbjct: 90  --------------LQVTSKVLKKNGRNHKESIEALQALANLFMPIKLVPKQFEVLVERV 135

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL      E +  W           W   +  
Sbjct: 136 RDALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETNQTWSGDLAKRNTK-WAAALGE 194

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +  +I+  + ++  +  ETG++++E + I       +   +  +  M
Sbjct: 195 KNAAIVACQQKLIDLETETGLTVAEIKEINRRANSADIHHTGGRSSM 241


>gi|256546106|ref|ZP_05473459.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
 gi|256398223|gb|EEU11847.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
          Length = 333

 Score =  104 bits (258), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 120/244 (49%), Gaps = 7/244 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDW 490
           V + +     A   +V+ N  LV S A  +       L+  DL+Q G +G+++AAEKFD 
Sbjct: 88  VEQFQEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELEDLVQSGMLGMIRAAEKFDL 147

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQS---CTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
            LGYKF+TYA  W+ +AI ++I  +              +K+ ++++     S +   + 
Sbjct: 148 TLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLKLNKLKQILKANPEASEEELYKI 207

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             +E   K       +    ++    +++     D     L D + D +++   D  ++ 
Sbjct: 208 LKQEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGD-DSIPVDDQILKK 266

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++ +   + L  L+ RE++++  R+G+      TLEE+G  + ++RERIRQIE +A+ KL
Sbjct: 267 DMEDFLMKALDQLSDREKQIIIYRYGLDNEKPKTLEEIGTIYNLSRERIRQIENQALGKL 326

Query: 668 KHPS 671
           K  S
Sbjct: 327 KQYS 330


>gi|29840191|ref|NP_829297.1| RNA polymerase sigma factor sigma-28 [Chlamydophila caviae GPIC]
 gi|29834539|gb|AAP05175.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 257

 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 96/234 (41%), Gaps = 18/234 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +  +++  L LV  V  +    G+       DL   G  GL++A E+FD     +F  YA
Sbjct: 25  RDTLIDFYLHLVKCVVHR-LISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYA 83

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++ +K AI   +  Q     +P  +  K +K+      +   + REPT  ++ +   +  
Sbjct: 84  LFLIKAAIIDDLRKQDW---VPRSVHQKANKLSEAMDTLRQSLGREPTDGDLCEYFQISQ 140

Query: 561 EGVRKVLKITKEP--ISLETP----IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           + +       +    ISL          E    L + I D+ A +  D   +        
Sbjct: 141 QELSGWFISARPALIISLNEERPSLSDGESGVALEERIPDERAETGYDIVDKKEFSSFLA 200

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  +E +V+     +    +  L+E+GK   V+  R+ QI +KA+ KL+
Sbjct: 201 NAIEGLEEKERKVM----ALYYYEELVLKEIGKILGVSESRVSQIHSKALIKLR 250


>gi|239628979|ref|ZP_04672010.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47_FAA]
 gi|239519125|gb|EEQ58991.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47FAA]
          Length = 244

 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 100/244 (40%), Gaps = 18/244 (7%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + ++V   L +V S A +        L+  DL  +G + LM+  +++D   G +F TYA 
Sbjct: 13  RNKLVLHYLPIVRSAAVQLRTMAGSLLEQEDLTDQGVLALMECLDRYDPGKGARFETYAF 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+ A+   I  Q        + +    KV      +S++   EP  +++A  L MPVE
Sbjct: 73  VRVRGAMIDYIRSQDWVPHRARNFQK---KVDEAFSILSHEKMGEPDVKDVAGYLDMPVE 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V   +K       L      +D + +   G+         P +S     + E  T  + 
Sbjct: 130 KVENHIKYMNHASVLSFEAALQDMTAIFAKGELEAGDMDGKPEESLFYREMMEMLTAAID 189

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L  +E  V+ + +      +    E+ +   + + R+ QI  KAIRKLK       L  
Sbjct: 190 GLGEKERLVITLYY----YEELKYSEIAEVMGIGQSRVCQIHTKAIRKLKSS-----LED 240

Query: 679 FLDG 682
           ++ G
Sbjct: 241 YMRG 244


>gi|260776433|ref|ZP_05885328.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607656|gb|EEX33921.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 244

 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 106/245 (43%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKALTYDQYANQDSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     ++ +   ++  ++ R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKNSREISQAIAQLEGELNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS---PLDS 603
           PT  E+AK+L M +E            I+    IG +D     D I  ++A     P   
Sbjct: 118 PTDAEVAKRLEMSLEQY----HSALTDINSSRLIGIDDLGVSEDAISHEDADEENIPFQG 173

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      + SL  RE  VL + +    + +  L+E+G+   V+  R+ QI +++
Sbjct: 174 VADEYFRTALVESIKSLPEREALVLSLYY----DEELNLKEIGEVIGVSESRVSQILSQS 229

Query: 664 IRKLK 668
           +++L+
Sbjct: 230 MQRLR 234


>gi|284042121|ref|YP_003392461.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
 gi|283946342|gb|ADB49086.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
          Length = 300

 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 112/233 (48%), Gaps = 6/233 (2%)

Query: 444 AKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           A+ E+V+  + L+ SVA+ Y     +   +L+Q G +GL+ A E+FD      F TYA W
Sbjct: 67  ARDELVDVFMPLIGSVARLYRGVTSVHRAELMQAGVVGLLTALERFDPSRRAPFWTYASW 126

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WV+QA+ + +A+ +  + +      ++ ++    R  +      P+   +A    +  E 
Sbjct: 127 WVRQAMQQVVAELARPVVMSDRGLRELARMRAARRDFTRLHDAGPSSVRLAAATGLTRER 186

Query: 563 VRKVLKITKEPISLETPIGDEDTSHL----GDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  +L +   P +LE+     D   L    G  +ED  A    D  +     +   R++ 
Sbjct: 187 IETLLALELVPETLESEPAWSDEDDLARRSGHPLEDPGAEEAFDRVLDRVECDRLLRLIG 246

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            L  RE  +L  RFG+    + TL EV +   ++ ER+RQ+E +A+ +L+  +
Sbjct: 247 DLRQRERVILHARFGLD-GQERTLREVARMVGLSAERVRQLEHEALDELRAAA 298


>gi|304570578|ref|YP_386879.2| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
          Length = 265

 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 100/228 (43%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++++V      +  +A +   +    ++  +LI  G +GLM+A  KF   LG KF TYA 
Sbjct: 36  QEQVVRHYAPKIKFLALRLKGKLPKSVELNELISAGTLGLMEAFGKFQPKLGIKFDTYAE 95

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +         P  +R ++  +  T  R+ ++  R P+ EE+ K   +  +
Sbjct: 96  NRIRGAMLDELRRLDW---FPRSLRQRVRLLEDTINRLEHEKGRRPSEEELQKATGLEEK 152

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R  L+  +  + +      E  +  G    D     P  S     L E    ++  LT
Sbjct: 153 DLRSGLEALQNHLCISLDAIQETFAADG---RDHLEGEPFHSTATQELIERIASLIDQLT 209

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           PRE+ VL + +      +  + E  +   VT  R+ Q+ ++A+ +L+ 
Sbjct: 210 PREKLVLSLYYS----DELNMRETAEVMGVTEGRVSQLHSQALNRLRK 253


>gi|260592476|ref|ZP_05857934.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
 gi|260535522|gb|EEX18139.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
          Length = 228

 Score =  103 bits (257), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 66/264 (25%), Positives = 120/264 (45%), Gaps = 43/264 (16%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I+ I  E  +S  E + + + ++      + A +++ +ANL+ V+S+A  Y N+GL  
Sbjct: 6   KYIEEIVQEQLLSSEEEQTLAAKIK---LGDAKALEKLTKANLKFVVSLAHHYKNQGLGE 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL+ EGNIG+M AA+KFD   G +F +YA  ++++A+  +I                  
Sbjct: 63  DDLVSEGNIGMMHAAQKFDGTKGIRFVSYAAPYIRKAMEEAI------------------ 104

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHL 588
                              +E      +P +   K  +     IS++ PI     +   L
Sbjct: 105 -------------------KEQTALYKLPKDEKSKFERKRTHAISIDQPIPVGSSNNFTL 145

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              +E+++A    +   +  L     + L  L  RE+R++   +G+   T +T+ E+ + 
Sbjct: 146 QHVLENEDAPQADEHLNKELLNFEIQKGLNELNEREKRIIIAIYGLN-GTHYTMAEIAEN 204

Query: 649 FCVTRERIRQIEAKAIRKLKHPSR 672
             + RER+RQI  KA+RKL    +
Sbjct: 205 MGLKRERVRQIRNKALRKLHKKMK 228


>gi|163867068|gb|ABY47630.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867070|gb|ABY47631.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
          Length = 249

 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 39/283 (13%), Positives = 98/283 (34%), Gaps = 36/283 (12%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++   + + +    + E++D           G    
Sbjct: 1   AKRIEEGLKHMVQAISACPTTIADILGMAERVANDEIRVDELVD-----------GLLDA 49

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +     + + +   D  +E E + + A     ++     +                
Sbjct: 50  EAAEAAANEAELASQDSDDIDEEEEEEEDDAEDDEDEEDGDEGA---------------- 93

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
              A   +A  + L+   +    +I+  +  +R   +      K+   S      +E + 
Sbjct: 94  -RQASANAAQLEALKRAALEKFGKISTEFSAMRDAYE------KEGYQSPAYLHAQEAIQ 146

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELDP 381
           + + S+      ++ L + L    + +   E +LL  +    G+ R  F++R  G E + 
Sbjct: 147 QELTSIRFTARTVERLCDTLRAQVEEVRSVERQLLATVVDRCGMSRAEFIQRFPGNETNL 206

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            W + A       +   +   + +I + + ++  +     + +
Sbjct: 207 EW-AQAIVDERHPYSAVLERNIPAIREQQQKLIDLQARVVLPL 248


>gi|89895713|ref|YP_519200.1| hypothetical protein DSY2967 [Desulfitobacterium hafniense Y51]
 gi|89335161|dbj|BAE84756.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 94/239 (39%), Gaps = 15/239 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E +E  L LV  ++ +      + +   DLI  G  GL+ A E+FD   G KF TYA 
Sbjct: 14  RVEQIEKYLPLVKRISGRLLISLPQHVDEDDLIGYGVFGLLDALERFDPVRGVKFETYAT 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +             R KI ++      +  +  R  + EE+A  L M   
Sbjct: 74  LRIRGAIIDGLRTMDWVPH---SARQKIKRIQDAFAEVEARHGRPASNEEVAVLLQMEPR 130

Query: 562 GVRKVLKITKE--PISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   L   +     SL+     E+         + D  A            ++     +
Sbjct: 131 DLEAALHQGQMLTLTSLDEVAVGEEGEAYTPRTQLADPIAQEAFQEVELDEQKKILADAI 190

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
             L  +E+ V+     +    D TL+E+     ++  RI Q+ ++AI +L+   SR KK
Sbjct: 191 EKLPEKEKLVV----ALYYQEDLTLKEIAVIMKLSESRISQLHSQAILRLRGRLSRQKK 245


>gi|77359758|ref|YP_339333.1| flagellar biosynthesis sigma factor [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874669|emb|CAI85890.1| Polar Flagellar-specific RNA polymerase sigma factor FliA (sigma F)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 236

 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 59/224 (26%), Positives = 98/224 (43%), Gaps = 10/224 (4%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 12  IVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAGIRI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +         P  +  K  +V+     + + + REPT  E+A+KL + +E   
Sbjct: 72  RGAMLDEMRRGDW---APRSVHRKSRQVIEAISALESSLNREPTDSEVAQKLEITLEQYH 128

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +L        L       D   +     D     P ++       E+    + SL  R+
Sbjct: 129 HILTDVNSSKILGIEDLGIDEDVITPVGHDLALDKPFNNVKNERFNESLLSAIKSLPERD 188

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL + +    N +  L+E+G+   V+  R+ QI  +A+ KLK
Sbjct: 189 AMVLSLYY----NDEMNLKEIGQILDVSESRVSQIHGQAMIKLK 228


>gi|163867072|gb|ABY47632.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
          Length = 249

 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 40/283 (14%), Positives = 98/283 (34%), Gaps = 36/283 (12%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++   + + +    + E++D           G    
Sbjct: 1   AKRIEEGLKHMVQAISACPTTIADILGMAERVANDEIRVDELVD-----------GLLDA 49

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +     + + +   D  +E E + + A     ++     +                
Sbjct: 50  EAAEAAANEAELASQDSDDIDEEEEEEEDDAEDDEDEEDGDEGA---------------- 93

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
              A   SA  + L+   +    +I+  +  +R   +      K+   S      +E + 
Sbjct: 94  -RQASANSAQLEALKRAALEKFGKISTEFSAMRDAYE------KEGYQSPAYLHAQEAIQ 146

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELDP 381
           + + S+      ++ L + L    + +   E +LL  +    G+ R  F++R  G E + 
Sbjct: 147 QELTSIRFTARTVERLCDTLRAQVEEVRSVERQLLATVVDRCGMSRAEFIQRFPGNETNL 206

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            W + A       +   +   + +I + + ++  +     + +
Sbjct: 207 EW-AQAIVDERHPYSAVLERNIPAIREQQQKLIDLQARVVLPL 248


>gi|161089504|gb|ABX57700.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867058|gb|ABY47625.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867060|gb|ABY47626.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867062|gb|ABY47627.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867064|gb|ABY47628.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867066|gb|ABY47629.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867074|gb|ABY47633.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867076|gb|ABY47634.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
 gi|163867080|gb|ABY47636.1| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
          Length = 249

 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 40/283 (14%), Positives = 98/283 (34%), Gaps = 36/283 (12%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++   + + +    + E++D           G    
Sbjct: 1   AKRIEEGLKHMVQAISACPTTIADILGMAERVANDEIRVDELVD-----------GLLDA 49

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +     + + +   D  +E E + + A     ++     +                
Sbjct: 50  EAAEAAANEAELASQDSDDMDEEEEEEEDDAEDDEDEEDGDEGA---------------- 93

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
              A   SA  + L+   +    +I+  +  +R   +      K+   S      +E + 
Sbjct: 94  -RQASANSAQLEALKRAALEKFGKISTEFSAMRDAYE------KEGYQSPAYLHAQEAIQ 146

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELDP 381
           + + S+      ++ L + L    + +   E +LL  +    G+ R  F++R  G E + 
Sbjct: 147 QELTSIRFTARTVERLCDTLRAQVEEVRSVERQLLATVVDRCGMSRAEFIQRFPGNETNL 206

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            W + A       +   +   + +I + + ++  +     + +
Sbjct: 207 EW-AQAIVDERHPYSAVLERNIPAIREQQQKLIDLQARVVLPL 248


>gi|188011951|gb|ACD45272.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 222

 Score =  103 bits (257), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 97/226 (42%), Gaps = 4/226 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 1   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S                   +
Sbjct: 121 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDYGFER 180

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            N R    +VL  L  RE+++L+  F      + + +E G+   ++
Sbjct: 181 VNQRMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDIS 222


>gi|186684907|ref|YP_001868103.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186467359|gb|ACC83160.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 269

 Score =  103 bits (257), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 117/270 (43%), Gaps = 14/270 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMV--RKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           I N +           +E +H +  +     +  +   + ++V+ N  LV   A  +TN+
Sbjct: 2   IVNLLNRHGAMPTTVTNELKHEIWQLLREYQQSRSENVRNKLVKLNFGLVRKEAHYWTNQ 61

Query: 467 -GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
               + DL+Q G +GL++A EKF+   G+ FS+YA+ +++  I   + D+  T+RIP   
Sbjct: 62  CHETYDDLLQVGCLGLIRAIEKFELSKGHAFSSYALPYIRGEIQHYLRDKGVTVRIPRKW 121

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDE 583
                + +  +R    K  R+PT  E+A  L +     +++    I + P+SL+ PI D 
Sbjct: 122 LALQQQAIGVSRSWREKHNRQPTDTELAAALEISPNEWQEIKLAWINRAPLSLDVPIQDG 181

Query: 584 DTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +     LG+ + D +  S   +           + L  L  R   VL   F      D T
Sbjct: 182 EEGSTCLGELVPDPHYRSFQLAQEDQL---RLQQALVQLEQRTRDVLECVFL----QDLT 234

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            ++V +   ++   + +   K +  +K   
Sbjct: 235 QKQVAEHLGISVVTVSRRVKKGLDLMKQLM 264


>gi|291196316|emb|CBG22630.1| DNA-directed RNA polymerase subunit D [Pseudomonas jinjuensis]
          Length = 237

 Score =  103 bits (257), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 34/284 (11%), Positives = 92/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++ + P    +++   + +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAQFPGAVDSILDEYNRIVAEGGRLSDVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +  +   +    + ++ + + E       +D       PE A      + E  + 
Sbjct: 50  GSVPAEEVELDLKDNAAESKDKDDEEEEEESDDSEDEGDGGPDPEEAARRFGAVSEQLEK 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +                                       +K  + S +       L +L
Sbjct: 110 AKKA-----------------------------------LKKHGRGSKQASEELVALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++ D   ++   E  +++L      + R  FL +  G E +  W
Sbjct: 135 FMPIKLVPKQFDALVARVRDALDQVRRQERAIMQLCVRDARMPRADFLRQFPGNETNESW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           V       + ++   +      + + + ++ ++  +  + ++E 
Sbjct: 195 VDSVLKN-KPKYAEALERVKADVQRNQQKMAALESDVDLKVAEI 237


>gi|254519896|ref|ZP_05131952.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
 gi|226913645|gb|EEH98846.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
          Length = 251

 Score =  103 bits (257), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 115/248 (46%), Gaps = 12/248 (4%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           +     ++   +     A  +++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA  
Sbjct: 13  YEENSQLIPLAKAGNQDAMNKVIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAIN 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD     KFSTYA+  +   I R I D    I++  +++    K+     +++ K+ RE
Sbjct: 73  NFDDKFNVKFSTYAVPMIIGEIKRFIRD-DGIIKVSRNVKSLARKLHFDKEQLTKKLDRE 131

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSA 604
           PT EE+++   +  E +   ++ +     L   I  +D +   L D + +K         
Sbjct: 132 PTIEELSQFSGVDKEEILFAIESSASMQYLYDTIHQDDGAPVLLIDKLSEKGEDDSDMIN 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                R      L SL  +  +++ +R+      D T  +V K   +++ ++ +IE K +
Sbjct: 192 -----RIALKEALRSLDSKARQIIMLRYF----KDKTQVQVAKMLGISQVQVSRIEKKVL 242

Query: 665 RKLKHPSR 672
             +K   +
Sbjct: 243 VLMKQKLQ 250


>gi|218249036|ref|YP_002374407.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|218169514|gb|ACK68251.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
          Length = 258

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 112/235 (47%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + N     + DL+Q G++GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRKEAYHWVNHCSESYEDLLQVGSLGLIRAIERFNSEKGHAFSSFALPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   +V    +    +  R+PT  EIA+ L +P++  
Sbjct: 89  IRGEIQHYLRDKGYTVRIPRRWLEIGQQVKSIKQDFRERFNRQPTDSEIAQILEIPLKEW 148

Query: 564 RKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+  +G++    + L D + D N  S   S           + LA 
Sbjct: 149 QEIQLAFQNREPLSLDLKVGNDSDGQTSLADLVPDPNYRSFQLSQEDQI---RLQQGLAQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  R  R+L   F      D T  E  +Q  ++   + +   K +  LK    ++
Sbjct: 206 LEERTRRILEFVFL----QDLTQRETAEQLGISVVTVSRRVKKGLEILKQTMTAE 256


>gi|124300779|dbj|BAF45887.1| RNA polymerase sigma-subunit [Erwinia mallotivora]
          Length = 224

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 37/272 (13%), Positives = 72/272 (26%), Gaps = 49/272 (18%)

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +  S+ E P     L+   D +  G   L ++I            GF      
Sbjct: 1   IEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEARLSDMI-----------TGFVDPN-A 48

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
                   +    E  + +  + D E       +        PE A     +L    + +
Sbjct: 49  EEEMAPTATHVGSELSEEERDDDDDEDEDSDDDNSDDDNSIDPELAREKFNDLRVQYEKT 108

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
              + A                                     +S        + L  + 
Sbjct: 109 RTVIKAK-----------------------------------GRSHADAVSEIQNLSDVF 133

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
               L   + D LV  +  +  R+   E  +++L      + +  F+    G E    W 
Sbjct: 134 KQFRLVPKQFDYLVNNMRTMMDRVRTQERIIMKLCVEICKMPKKNFITLFTGNETSETWF 193

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
             A    +  W   +    + + +   ++  I
Sbjct: 194 KAALAMNKP-WSEKLKEVTEDVQRSLMKLLQI 224


>gi|26991031|ref|NP_746456.1| flagellar biosynthesis sigma factor [Pseudomonas putida KT2440]
 gi|148546765|ref|YP_001266867.1| flagellar biosynthesis sigma factor [Pseudomonas putida F1]
 gi|24986061|gb|AAN69920.1|AE016630_11 flagellar biosynthesis sigma factor FliA [Pseudomonas putida
           KT2440]
 gi|148510823|gb|ABQ77683.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida F1]
 gi|313497816|gb|ADR59182.1| FliA [Pseudomonas putida BIRD-1]
          Length = 246

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 97/239 (40%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ A K+D  
Sbjct: 7   KMYSRAAKDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAMRAVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANL 609
           +A +L + ++    +L  T            +D  H G   ED     V P     +   
Sbjct: 124 VAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASGQVEPARGLEEERF 182

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   T  +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 183 QAALTEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|323493327|ref|ZP_08098450.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
 gi|323312413|gb|EGA65554.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
          Length = 244

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 53/245 (21%), Positives = 109/245 (44%), Gaps = 17/245 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     +++  +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKALTYEQYANQNSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     +V +    +  ++ R+
Sbjct: 61  NYDGSKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKHNREVSQAISELEGQLNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSA 604
           P+  E+A+ + + +E    +L      I+    +G ED     D I  +D++  +     
Sbjct: 118 PSDAEVAQHMGISLEQYHTIL----TDINCSRLVGIEDLGVSEDVISPDDRDEENLPFQG 173

Query: 605 I-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           +     R+     + SL  RE  VL + +    + +  L+E+G+   V+  R+ QI +++
Sbjct: 174 VADEYFRKALIDSIKSLPEREALVLSLYY----DEELNLKEIGEVIGVSESRVSQILSQS 229

Query: 664 IRKLK 668
           +++L+
Sbjct: 230 MQRLR 234


>gi|257062124|ref|YP_003140012.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|256592290|gb|ACV03177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 258

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 112/235 (47%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + N     + DL+Q G++GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRKEAYHWVNHCSESYEDLLQVGSLGLIRAIERFNSEKGHAFSSFALPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   +V    +    +  R+PT  EIA+ L +P++  
Sbjct: 89  IRGEIQHYLRDKGYTVRIPRRWLEIGQQVKSIKQDFRERFNRQPTDSEIAQILEIPLKEW 148

Query: 564 RKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+  +G++    + L D + D N  S   S           + LA 
Sbjct: 149 QEIQLAFQNREPLSLDLKVGNDSDGQTSLADLVPDPNYRSFQLSQEDQI---RLQQGLAQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  R  R+L   F      D T  E  +Q  ++   + +   K +  LK    ++
Sbjct: 206 LEERTRRILEFVFL----QDLTQRETAEQLGISVVTVSRRVKKGLEILKQTMTAE 256


>gi|167750707|ref|ZP_02422834.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
 gi|167656386|gb|EDS00516.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
          Length = 251

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 59/267 (22%), Positives = 119/267 (44%), Gaps = 22/267 (8%)

Query: 422 ISISEFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEG 477
           +++     +  ++ K      +  + E+V   + LV  +A    N      +  D+I EG
Sbjct: 1   MAVQSKERLNELLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYAESDDIINEG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            I LM A + FD     KF TYA   +K A+   +        +P  +R    ++     
Sbjct: 61  VIALMAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRKLDR---VPRTLRKLSKQLDDNFA 117

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDK 595
           R+++++ R PT EE+A+ + M    + K++  T     +S E  + ++   +L + I   
Sbjct: 118 RLNSELCRTPTDEELAESMNMTTAQLSKLMANTAGMITLSFEELLYED---NLDENIS-A 173

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           ++ +      +   ++     +A+L  +E++V+ M +           E+ K   +T+ R
Sbjct: 174 SSETADAKMYEREKKQVIADAVATLPEKEKQVVTMYY----YERLKYSEIAKVMSITQSR 229

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           + QI +KA+  LK+     KL S++ G
Sbjct: 230 VCQIHSKAMLTLKN-----KLESYIKG 251


>gi|209522287|ref|ZP_03270915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp. H160]
 gi|209497281|gb|EDZ97508.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp. H160]
          Length = 244

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/207 (23%), Positives = 90/207 (43%), Gaps = 10/207 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQ G IGL+ AA ++    G +F TYA   ++ A+   +        +P  +R 
Sbjct: 36  VDLDDLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDW---LPRSLRR 92

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V     R+   + R  +  EIA+ L MP++  + +L+       I  E      D 
Sbjct: 93  TSREVETAVHRVEQNLGRSASEAEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDRSADD 152

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               D     ++  PL + +  +LR      +  L  RE+ ++ + +  G      L E+
Sbjct: 153 EPFLDRYCVDHS-DPLSALLDDSLRSAVVDAIDRLPEREKLLMSLYYERG----MNLREI 207

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSR 672
           G    V+  R+ Q+ ++A+ +L+   R
Sbjct: 208 GAVMEVSESRVCQLHSQAVARLRARLR 234


>gi|297569692|ref|YP_003691036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
 gi|296925607|gb|ADH86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
          Length = 262

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 54/259 (20%), Positives = 107/259 (41%), Gaps = 21/259 (8%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
           +   + E      ++E++     L+  +A +  +R    +   DLI  G +GL+ A  KF
Sbjct: 17  AYFDRREQLDPAKREELILNYTPLIKYIASRLASRLPPQVAVDDLISCGIVGLIDAINKF 76

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +F TYA + +K A+   +        +P  +R K+ ++ +    +  K+ R  T
Sbjct: 77  DPAKNVQFKTYAEFRIKGAMLDELRALDW---VPRSIRRKVTELEQVCSELEVKLGRPAT 133

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDS 603
            EE A  L + +E   ++L  TK    L+          E   +L +     +       
Sbjct: 134 DEETATALGIGLEEYHRLLDETKSVSFLDIEYLRRQAPAEVEGNLAEVFASDDKDPFAAL 193

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +    +    + +  L  +E+  +     +  + + T+ E+G+    T  RI Q+ +KA
Sbjct: 194 NL-GETKALLAKAINELPEKEKLTV----ALYYHEELTMREIGEVLGYTESRISQMHSKA 248

Query: 664 IRKLKHPSRSKKLRSFLDG 682
           + +L+      KL+  LD 
Sbjct: 249 MLRLR-----GKLKKSLDA 262


>gi|326682092|emb|CBL30937.1| RNA polymerase sigma factor [Aeromonas veronii]
          Length = 244

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/287 (17%), Positives = 93/287 (32%), Gaps = 44/287 (15%)

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           E P     L+   D+       L +II     I P    G+       +         E 
Sbjct: 1   EYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNESEGW-----APTATHIGSELGED 53

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
           +  D  E + + E       DD       PE A      L    + +  ++         
Sbjct: 54  DLADEDEEDEEDEDEDGDRSDDDGDGGPDPEVAREKFGELRAQYEVTRLSI--------- 104

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
                                     QK+ ++    +    +L  +     L   + D L
Sbjct: 105 --------------------------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRL 138

Query: 339 VEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +     
Sbjct: 139 VNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPR 198

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
            V  + D I +   +++ I  ETG+SI++ + I   +  GE +A  A
Sbjct: 199 LVEMDED-IQRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRA 244


>gi|209408320|emb|CAP19903.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 240

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/285 (15%), Positives = 97/285 (34%), Gaps = 46/285 (16%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +M+++   P T  +++   + +      L +I  L   I P+  G      
Sbjct: 1   KRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA---- 54

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                Q+ E  + +       + + D E     S+++       PE A      + E  +
Sbjct: 55  ---GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLE 111

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +                                       +K  ++S +     E L  
Sbjct: 112 KAKKA-----------------------------------LKKHGRASQQAVEELEALAI 136

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           L   + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  
Sbjct: 137 LFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLD 196

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           W        +G++   +    + I++ + ++  +  E  + I++ 
Sbjct: 197 WAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADI 240


>gi|312128428|ref|YP_003993302.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778447|gb|ADQ07933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 256

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 111/226 (49%), Gaps = 11/226 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                +A   + E+V  +L +   +AKK+  RG+ + DL Q   I L+ A E+F+   GY
Sbjct: 21  EYQRTKAIELRNELVNKHLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPNKGY 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KF+++A   +   I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+
Sbjct: 81  KFTSFATPTIMGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAR 140

Query: 555 KLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L M  E V +V++ +    P SL+  + +++   LGD +   +      + +Q    E 
Sbjct: 141 HLNMSTEEVLEVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDE-----NILQVENVEA 195

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             + +  L+P E   ++ RF      + T +E+ ++  V++  I +
Sbjct: 196 VKKAIERLSPFEREFVQKRFF----EEKTQKEIAEEMNVSQMYISR 237


>gi|225375354|ref|ZP_03752575.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
 gi|225212843|gb|EEG95197.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
          Length = 256

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 106/241 (43%), Gaps = 18/241 (7%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA +   Y    +++ DL+  G  GL+ A +KFD     KF TYA 
Sbjct: 22  REKLIIEYSPLVKLVAGRLSMYLGYNVEYDDLVSYGIFGLIDAIDKFDLGKEVKFETYAS 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   I        IP  +R K  K+    +++  +  +  + EEIA++L +  +
Sbjct: 82  LRIRGTILDQIRKMDW---IPRTVRQKQKKIDEAIKQVEMRTGKNASDEEIAQELGLSED 138

Query: 562 GVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +            +SL   +       + D   + + + P D   +  L++     L  
Sbjct: 139 ELTTWQSQLKVTNIVSLNEYLEQ-GAEPVMDARRNSHFIQPEDKVEEEELKQKLEESLEV 197

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           LT +E +V+     +    D TL+E+     V+  RI Q+  KA+ K++     KKL ++
Sbjct: 198 LTEKERKVI----LLYYYEDLTLKEISSILEVSESRISQLHTKALLKMR-----KKLGNY 248

Query: 680 L 680
           L
Sbjct: 249 L 249


>gi|291196278|emb|CBG22610.1| DNA-directed RNA polymerase subunit D [Pseudomonas azotifigens]
          Length = 239

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 96/284 (33%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T  +++   + +      L +I  L   I P+  G       
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA----- 53

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
               Q+ E  + +       + + D E     S+++       PE A      + E  + 
Sbjct: 54  --GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEK 111

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +                                       +K  ++S +     E L  L
Sbjct: 112 AKKA-----------------------------------LKKHGRASQQAVEELEALAIL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  W
Sbjct: 137 FMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   +G++   +    + I++ + ++  +  E  + I++ 
Sbjct: 197 AEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADI 239


>gi|326682098|emb|CBL30940.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 244

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/288 (17%), Positives = 100/288 (34%), Gaps = 46/288 (15%)

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           E P     L+   D+       L +II     I P                         
Sbjct: 1   EYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ 34

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
           E DDV  T   I S            D   +   + + + D+ +      ++        
Sbjct: 35  ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA-------- 86

Query: 279 KVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                     E + +LR+  +   ++ Q++ ++    +    +L  +     L   + D 
Sbjct: 87  ---------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFDR 137

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +    
Sbjct: 138 LVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSP 197

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             V  + D +L+   +++ I  ETG+SI++ + I   +  GE +A  A
Sbjct: 198 RLVEMDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRA 244


>gi|187478163|ref|YP_786187.1| RNA polymerase sigma factor for flagellar operon [Bordetella avium
           197N]
 gi|115422749|emb|CAJ49277.1| RNA polymerase sigma factor for flagellar operon [Bordetella avium
           197N]
          Length = 244

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 56/222 (25%), Positives = 101/222 (45%), Gaps = 12/222 (5%)

Query: 451 ANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
               LV  +A +   R    +Q  DLIQ G IGL+ A  ++      +F TYA   ++ A
Sbjct: 10  QYSPLVRKLALQLLARLPASVQLDDLIQAGMIGLLDAVRRYQKNPDAQFETYATARIRGA 69

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +   +  Q     +P  +R K  ++    +R    + R PT  EIA++L +P++  + +L
Sbjct: 70  MLDELRSQDW---LPRSVRSKSRRIETAIQRQEQVLMRPPTEIEIAQELGLPLDEYQAML 126

Query: 568 KITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
              +    L    I  E      +   D    +PL++ + A+LR +  + +  L  RE+ 
Sbjct: 127 SDAQGIQILHYENIDAEGDGDWHEGAGDGGG-NPLNALLAADLRASLIQAIERLPEREQL 185

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L + +  G      L+E+G    VT  R+ Q+  +A  +L+
Sbjct: 186 LLSLYYEQG----LNLKEIGAVLNVTEARVCQLRTQATARLR 223


>gi|10834759|gb|AAG23813.1|AF274004_5 SigB [Staphylococcus epidermidis]
          Length = 246

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 111/232 (47%), Gaps = 9/232 (3%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    S A+ ++V+   +L+ S+A +Y+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++N+++R P
Sbjct: 75  FDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           +  EIA++L +  E V + +++  +   +S++  I  +        ++            
Sbjct: 135 SISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDNYDLT 194

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +   R     +L  L+ RE ++++  F  G     + +E G++  +++  + 
Sbjct: 195 EK--RMILECILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMHVS 240


>gi|325520258|gb|EGC99421.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 167

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 66/167 (39%), Positives = 100/167 (59%), Gaps = 1/167 (0%)

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           + TIR+PVH+ D+  +V R A R   +  R+PTP E+A +  +    +R VL +  EP+S
Sbjct: 2   ARTIRVPVHVGDQQQRVRRHALRFHQRTGRQPTPAELAAETGLDETRLRAVLALPAEPVS 61

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L+TP+ D DT  L D IED+++ SP +      +RE  T +L S+TP E  VLR RFG+G
Sbjct: 62  LDTPLPDADTG-LVDLIEDQSSASPFERLADTRMRECVTSLLRSVTPAEADVLRRRFGLG 120

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
                T + + K   ++RER+RQIE +A+  L+  + ++   SFLD 
Sbjct: 121 GTEPDTYDAIAKDAGMSRERVRQIEKRALAALRTIAEAEDAHSFLDA 167


>gi|311695193|gb|ADP98066.1| flagellar biosynthesis sigma factor FliA [marine bacterium HP15]
          Length = 247

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 104/242 (42%), Gaps = 12/242 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +      ++    +++E +  LV  +A     R    +Q  DL+Q G IGL++AA+
Sbjct: 3   LAKNLGIYNQSSAQKPAQLIEQHAPLVKKIALHLMARLPASVQLEDLMQAGMIGLLEAAQ 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G  F TYA   ++ A+   I        +P  +     ++ +  + + +++ RE
Sbjct: 63  RYSSTKGATFETYAGIRIRGAMVDEIRKGDW---VPRSVHRNARRISQAIKAVEDRLGRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
              +E+A++L M +      L  +           +E      +  E ++  +PL+    
Sbjct: 120 AHDQEVAEELGMGLPEYHSYLSDSNSGRLFSLDELNESGELPIEQTETQD--NPLEGLSS 177

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R +    +  L  RE+ VL + +      +  L+E+G    V+  R+ QI ++A  +
Sbjct: 178 DAFRRSLAEAIEDLPEREKLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAALR 233

Query: 667 LK 668
           L+
Sbjct: 234 LR 235


>gi|33592168|ref|NP_879812.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis Tohama I]
 gi|33601519|ref|NP_889079.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           bronchiseptica RB50]
 gi|33571813|emb|CAE41322.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis Tohama I]
 gi|33575955|emb|CAE33034.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           bronchiseptica RB50]
 gi|332381584|gb|AEE66431.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis CS]
          Length = 245

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 53/222 (23%), Positives = 98/222 (44%), Gaps = 11/222 (4%)

Query: 451 ANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
               LV  +A +   R    +Q  DL+Q G IGL+ A  ++      +F TYA   ++ A
Sbjct: 10  QYAPLVRKLALQLLARLPSSVQLDDLVQAGMIGLLDAVRRYQESPDAQFETYATARIRGA 69

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +   +  Q     +P  +R K  ++    +R   ++ R P+  EIA++L +P+   + +L
Sbjct: 70  MLDELRSQDW---LPRSVRSKSRRIETAIQRKEQELMRAPSEGEIAEELGVPLAEYQGML 126

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLASLTPREER 626
              +    L     + D      + E       PLD+ +  +LR      +  L  RE+ 
Sbjct: 127 ADAQGVQILHYEDFNTDGDSDSPWAESSAEHADPLDALLAGDLRRALIDAIDGLPEREKL 186

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +L + +  G      L+E+G    VT  R+ Q+ A+A  +++
Sbjct: 187 LLSLCYEQG----LNLKEIGAVLNVTEARVCQLRAQATARIR 224


>gi|89898386|ref|YP_515496.1| RNA polymerase sigma factor sigma-28 [Chlamydophila felis Fe/C-56]
 gi|89331758|dbj|BAE81351.1| DNA-directed RNA polymerase sigma 28 [Chlamydophila felis Fe/C-56]
          Length = 257

 Score =  103 bits (256), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 96/234 (41%), Gaps = 18/234 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           +  +++  L LV  V  +    G+       DL   G  GL++A E+F+     +F  YA
Sbjct: 25  RDTLIDLYLHLVKCVVHR-LISGMPSHIKTEDLYASGVEGLVRAVERFNPEKSRRFEGYA 83

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           ++ +K AI   +  Q     +P  +  K +K+      +   + REPT  ++ +   +  
Sbjct: 84  LFLIKAAIIDDLRKQDW---VPRSVHQKANKLSDAMDTLRQSLGREPTDGDLCEYFQISQ 140

Query: 561 EGVRKVLKITKEP--ISLETP----IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           + +       +    ISL          E    L + I D+ A +  D   +        
Sbjct: 141 QELSGWFVSARPALIISLNEERPLLSDGESGVALEERIPDERAETGYDIVDRKEFSSFLA 200

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L  +E +V+     +    +  L+E+GK   V+  R+ QI +KA+ KL+
Sbjct: 201 NAIEGLEEKERKVM----ALYYYEELVLKEIGKILGVSESRVSQIHSKALIKLR 250


>gi|320101986|ref|YP_004177577.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319749268|gb|ADV61028.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 565

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 94/460 (20%), Positives = 166/460 (36%), Gaps = 98/460 (21%)

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           PE  E+  R      ++    L  +E   R  V  A++   E  R      D      +D
Sbjct: 169 PEEREDIIRRARRLAEEDRVGLGLIEIARRIAV--AMERSTETIRTTLRDYD------RD 220

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI-- 365
                        L      +  NQ R+ + VE L    +R   +   ++   ++  +  
Sbjct: 221 HPDRPIFPEWSAPLEDETKQMIFNQHRLGVAVEVLAKQHRRTRSSIYRIINEVRAQRLLA 280

Query: 366 KRDVFL--ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
            +  F+  E       DP   +                +  +   +   + S+     +S
Sbjct: 281 TKLEFIDNEEFPAIAADPVRKAEVLGPMPMPEDGKTPRKAKAPKGLPPYLASLYEVPLLS 340

Query: 424 ISEFRHIVSMVRKGECEAS---------------------------IAKKEMVEANLRLV 456
             +  H+   +   +  A                              K +++ ANLRLV
Sbjct: 341 REQETHLFRKMNFLKYLAQKLRDQVDPARARAGDLDQIEALQEEALAVKNQIISANLRLV 400

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +S+AK++      F DL+ +GN+ L++A EKFD+  G KFSTYA W + +   R+     
Sbjct: 401 VSIAKRHVGPSNNFFDLVSDGNMSLIRAVEKFDFARGNKFSTYASWAIMKNFART----- 455

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                                                    +P E  R+   +T      
Sbjct: 456 -----------------------------------------IPEENYRRDRFVTGHEEMF 474

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           E                D  +      + Q  +RE    +L+ L PRE++++  RFGI  
Sbjct: 475 EAA-------------ADNRSDEHEQESNQRRMREGVNGMLSKLEPREQKIIVSRFGING 521

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             + TLE++GK+  +T+ER+RQIEA+A +KL+  ++ +K+
Sbjct: 522 AKEMTLEQLGKELGITKERVRQIEARAQQKLRKIAQEEKI 561


>gi|325273563|ref|ZP_08139791.1| flagellar biosynthesis sigma factor [Pseudomonas sp. TJI-51]
 gi|324101302|gb|EGB98920.1| flagellar biosynthesis sigma factor [Pseudomonas sp. TJI-51]
          Length = 246

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 97/239 (40%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ A K+D  
Sbjct: 7   KMYSRAAKDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAMRAVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANL 609
           +A +L + ++    +L  T            +D  H G   ED     V P     +   
Sbjct: 124 VAAELQLSLDDYYAILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASGQVEPARGLEEERF 182

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   T  +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 183 QLALTEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|312623242|ref|YP_004024855.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203709|gb|ADQ47036.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 256

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 59/216 (27%), Positives = 108/216 (50%), Gaps = 11/216 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L +   +AKK+  RG+ + DL Q   I L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNRYLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +      + +Q    E   + +  L+P
Sbjct: 151 EVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDE-----NILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            E   ++ RF      + T +E+ ++  V++  I +
Sbjct: 206 FEREFVQKRFF----EEKTQKEIAEEMNVSQMYISR 237


>gi|146307827|ref|YP_001188292.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina ymp]
 gi|145576028|gb|ABP85560.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           mendocina ymp]
          Length = 248

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +A  ++ +++E    LV  +A     R    +Q  DLIQ G IGL++A+ K+D   
Sbjct: 10  YNKAQAQDSQHQLIERYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEASRKYDSGK 69

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F T+A   ++ A+   +         P  +      V    R +  +  R+    E+
Sbjct: 70  GASFETFAGIRIRGAMLDEVRKGDW---APRSVHRNSRMVSDAIRVVEARTGRDAKDHEV 126

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQAN 608
           A +L + +E    +L  T      S +  +        G   ED     + P        
Sbjct: 127 AAELQLSLEDYYGILGDTLGSRLFSFDDLLQ---DGEHGGLHEDAGHTHLEPSRDLEDER 183

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 184 FQAALADAIAGLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 239


>gi|72161291|ref|YP_288948.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
 gi|71915023|gb|AAZ54925.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
          Length = 307

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 55/249 (22%), Positives = 104/249 (41%), Gaps = 14/249 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E    +  VR           ++ E +  +   +A++Y NRG    DL Q   +GL  A
Sbjct: 63  RELLAELDRVRDDPKARERIYLKLTELHAPVARRIARQYRNRGEPEEDLRQVAMVGLYNA 122

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              FD   G +F +YA+  +   + R   D++  IR+P   ++K  ++ R     + +  
Sbjct: 123 IRNFDPAYGKEFISYALPMMTGEVKRHFRDRTWAIRVPRKYQEKRAELNRVTAEFTQRHG 182

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS-HLGDFIED-KNAVSP 600
           R PT  E+A+ L M  E   +++        +SL+ P G +D    LGD +    +A+  
Sbjct: 183 RSPTVRELAELLEMDEEQTLELIDAARAYSTLSLDVPFGPDDDGATLGDTLGGLDDALER 242

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +                   +PR+ R+L +RF      D T  ++ +   +++  + +  
Sbjct: 243 VVDHAALRPALAAL------SPRDRRILLLRFA----GDKTQAQIAEIVGLSQMHVSRRL 292

Query: 661 AKAIRKLKH 669
           A  +  L+ 
Sbjct: 293 AAILTTLRR 301


>gi|302878264|ref|YP_003846828.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
 gi|302581053|gb|ADL55064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
          Length = 236

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 104/237 (43%), Gaps = 11/237 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
                    K + +     LV  +A +  +     +Q  D+IQ G +GL+ AA ++D   
Sbjct: 1   MYNASGLQDKNQCLRDYAPLVKRIAHQMMSKLPYSVQIDDIIQAGMMGLLDAATRYDEIH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +        +P  +R  + ++ +   R+  K+ R P   EI
Sbjct: 61  GAQFETYATQRIRGAMLDELRSADW---LPRSLRRDMRRIEQGVSRLQQKLGRAPNETEI 117

Query: 553 AKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           AK+L + +   +++L+ ++   +       DED     +  E  N   PL        + 
Sbjct: 118 AKELEVSLVEYQQMLQESRGAQLIYYEDFQDEDHEDFFERFEFANDTDPLALLQDDRFKS 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              R +  L  RE  ++ + +      +  L EVG+ F V+  RI Q+ ++A+ +L+
Sbjct: 178 ELARAIDVLPERERLLMALIY----EQELNLREVGEVFGVSESRISQLHSQAVLRLR 230


>gi|160933635|ref|ZP_02081023.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
 gi|156867512|gb|EDO60884.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
          Length = 217

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 57/224 (25%), Positives = 112/224 (50%), Gaps = 14/224 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +E+N+ LV + AK++  RG+++ DL+Q G +GL+KA + FD   G +FSTYA+  +
Sbjct: 4   REQAIESNMGLVHACAKRFRGRGIEYDDLVQAGCLGLVKAVDHFDEGRGLQFSTYAVPVI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              + R   D    I++   +++   K  R     S +  R+PT  E+A++L +      
Sbjct: 64  LGEMRRLFRDGG-AIKVGRALKELSLKAARACNEFSLREGRQPTISELAEQLGVEPAEAS 122

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L  +++P+SL       D  + G  I+          +    L++    V+  L PR+
Sbjct: 123 QALGASQQPLSLSA-----DEENGGGQIDVPTEAPEEKISELIALKQ----VVGELDPRD 173

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ MRF        T  +  +   +T+ ++ + E K +++LK
Sbjct: 174 RSLIVMRFF----KSRTQTQTAEVLGMTQVQVSRREKKILQELK 213


>gi|291532045|emb|CBK97630.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 251

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 119/267 (44%), Gaps = 22/267 (8%)

Query: 422 ISISEFRHIVSMVRKGECEASI-AKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEG 477
           +++     +  ++ K      +  + E+V   + LV  +A    N      +  D+I EG
Sbjct: 1   MAVQSKERLNELLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYAESDDIINEG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            I LM A + FD     KF TYA   +K A+   +        +P  +R    ++     
Sbjct: 61  VIALMAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRKLDR---VPRTLRKLSKQLDDNFA 117

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDK 595
           R+++++ R PT EE+A+ + M    + K++  T     +S E  + ++   +L + I   
Sbjct: 118 RLNSELCRTPTDEELAESMNMTTAQLSKLMANTAGMITLSFEELLYED---NLDENIS-A 173

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           ++ +      +   ++     +A+L  +E++V+ M +           E+ K   +T+ R
Sbjct: 174 SSETADAKMYEREKKQVIADAVATLPEKEKQVVTMYY----YERLKYSEIAKVMSITQSR 229

Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           + QI +KA+  LK+     KL S+++ 
Sbjct: 230 VCQIHSKAMLTLKN-----KLESYINS 251


>gi|291196372|emb|CBG22658.1| DNA-directed RNA polymerase subunit D [Pseudomonas pertucinogena]
          Length = 244

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/283 (15%), Positives = 93/283 (32%), Gaps = 41/283 (14%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +MA++   P T   ++     + +    L +I      I P+  G       
Sbjct: 1   RIEEGIREVMAAISMFPGTVDGILTEYQRIAEEGGRLTDI--FNGYIDPDDDGLSGTDNA 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                  +   ++K      + + + E   +   ++ +     PE A      + E  + 
Sbjct: 59  VVPAAAAKPKDEKK----ASDDDEEEEEDTEDDTEEETDGGPDPEIARQRFGAVQEQLEK 114

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               L A                                  K ++S        E L +L
Sbjct: 115 VRKVLKAK---------------------------------KGDRSHPDVVAEMETLAQL 141

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++  +   I   E  +++L      + R  FL    G E +  W
Sbjct: 142 FMPIKLVPKQYDALVARVRGVQDDIRARERAIMQLCVRDARMPRADFLRSFPGNETNEKW 201

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           +       +  + + +A     IL+ + ++ ++  +  ++I++
Sbjct: 202 IDEVLA-KKPAYADALAALQPDILRQQQQLIALEQDAQLTIAQ 243


>gi|150015700|ref|YP_001307954.1| sporulation sigma factor SigF [Clostridium beijerinckii NCIMB 8052]
 gi|149902165|gb|ABR32998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 251

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 114/240 (47%), Gaps = 12/240 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++       + A   ++E NL LV S++KK+ NRG  + D+ Q G+IGL+KA   FD  
Sbjct: 18  KLLALARSGDTDAMNTLIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLN 77

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R + D    I++  +++    K+      ++ K+KR PT EE
Sbjct: 78  YNVKFSTYAVPMIIGEIKRFLRD-DGMIKVSRNVKSLARKIHFQKEILTKKLKRSPTIEE 136

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANL 609
           +A    +  E +   ++ +     L   I  +D +   L D + +K+A            
Sbjct: 137 LADYANVDKEEILFAIESSNSLQYLYDTIHQDDGAPVLLIDKLSEKSADD-----ENLIE 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L SL  + ++++ +R+      D T  +V K   +++ ++ +IE K + +++ 
Sbjct: 192 KIALKEALNSLDNKAKQIIMLRYF----KDKTQVQVAKMLGISQVQVSRIEKKVLAEMRK 247


>gi|163958191|gb|ABY47635.2| DNA-directed RNA polymerase subunit D [Burkholderia andropogonis]
          Length = 249

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 40/283 (14%), Positives = 98/283 (34%), Gaps = 36/283 (12%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   M+ ++   P T   ++   + + +    + E++D           G    
Sbjct: 1   AKRIEEGLKHMVQAISACPTTIADILGMAERVANDEIRVDELVD-----------GLLDA 49

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +     + + E   D  +E E + + A     ++     +                
Sbjct: 50  EAAEAAANEAELASEDSDDMDEEEEEEEDDAEDDEDEEDGDEGA---------------- 93

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
              A   +A  + L+   +    +I+  +  +R   +      K+   S      +E + 
Sbjct: 94  -RQASANAAQLEALKRAALEKFGKISTEFSAMRDAYE------KEGYQSPAYLHAQEAIQ 146

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-RLAQSYGIKRDVFLERHQGRELDP 381
           + + S+      ++ L + L    + +   E +LL  +    G+ R  F++R  G E + 
Sbjct: 147 QELTSIRFTARTVERLCDTLRAQVEEVRSVERQLLATVVDRCGMSRAEFIQRFPGNETNL 206

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
            W + A       +   +   + +I + + ++  +     + +
Sbjct: 207 EW-AQAIVDERHPYSAVLERNIPAIREQQQKLIDLQARVVLPL 248


>gi|78217835|gb|ABB37184.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 227

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 52/225 (23%), Positives = 97/225 (43%), Gaps = 13/225 (5%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           MV      +  +A +   +    ++  +LI  G +GLM+A  KF   LG KF TYA   +
Sbjct: 1   MVRHYAPKIKFLALRLKGKLPKSVELNELISAGTLGLMEAFGKFQPKLGIKFDTYAENRI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +         P  +R ++  +  T  R+ ++  R P+ EE+ K   +  + +R
Sbjct: 61  RGAMLDELRRLDW---FPRSLRQRVRLLEDTINRLEHEKGRRPSEEELQKATGLEEKDLR 117

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             L+  +  + +      E  +  G    D     P  S     L E    ++  LTPRE
Sbjct: 118 SGLEALQNHLCISLDAIQETFAADG---RDHLEGEPFHSTATQELIERIASLIDQLTPRE 174

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + VL + +      +  + E  +   VT  R+ Q+ ++A+ +L+ 
Sbjct: 175 KLVLSLYYS----DELNMRETAEVMGVTEGRVSQLHSQALNRLRK 215


>gi|302871075|ref|YP_003839711.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302573934|gb|ADL41725.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 256

 Score =  102 bits (255), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 112/226 (49%), Gaps = 11/226 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                +A   + E+V   L +   +AKK+ NRG+ + DL Q   + L+ A E+F+   GY
Sbjct: 21  EYQRTKAIELRNELVNKYLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPNKGY 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KF+++A   +   I R   D++  IR+P  + +   K+      +S+K+KR P  EEIA+
Sbjct: 81  KFTSFATPTIMGEIKRYFRDRASIIRLPRRLYETSAKIKLVTEMLSSKLKRPPKVEEIAQ 140

Query: 555 KLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L M  E V +V++   +  P SL+  + +++   LGD +   +      + +Q    E 
Sbjct: 141 HLNMSTEEVLEVMEASNSYLPQSLDQTMYEDEEMTLGDVLGKSDE-----NILQIENVEA 195

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
             + +  L+P E   ++ RF      + T +E+ ++  V++  I +
Sbjct: 196 VKKAIERLSPFEREFVQKRFF----EEKTQKEIAEEMNVSQMYISR 237


>gi|188011759|gb|ACD45176.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011761|gb|ACD45177.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011765|gb|ACD45179.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011767|gb|ACD45180.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011769|gb|ACD45181.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011771|gb|ACD45182.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011773|gb|ACD45183.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011775|gb|ACD45184.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011777|gb|ACD45185.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011779|gb|ACD45186.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011781|gb|ACD45187.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011783|gb|ACD45188.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011785|gb|ACD45189.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011787|gb|ACD45190.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011789|gb|ACD45191.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011791|gb|ACD45192.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011793|gb|ACD45193.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011795|gb|ACD45194.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011797|gb|ACD45195.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011799|gb|ACD45196.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011801|gb|ACD45197.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011803|gb|ACD45198.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011805|gb|ACD45199.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011807|gb|ACD45200.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011809|gb|ACD45201.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011811|gb|ACD45202.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011813|gb|ACD45203.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011815|gb|ACD45204.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011817|gb|ACD45205.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011819|gb|ACD45206.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011821|gb|ACD45207.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011823|gb|ACD45208.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011825|gb|ACD45209.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011827|gb|ACD45210.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011829|gb|ACD45211.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011831|gb|ACD45212.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011833|gb|ACD45213.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011835|gb|ACD45214.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011837|gb|ACD45215.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011839|gb|ACD45216.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011841|gb|ACD45217.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011843|gb|ACD45218.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011845|gb|ACD45219.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011847|gb|ACD45220.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011849|gb|ACD45221.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011851|gb|ACD45222.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011853|gb|ACD45223.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011855|gb|ACD45224.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011857|gb|ACD45225.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011859|gb|ACD45226.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011861|gb|ACD45227.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011863|gb|ACD45228.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011867|gb|ACD45230.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011869|gb|ACD45231.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011875|gb|ACD45234.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011877|gb|ACD45235.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011879|gb|ACD45236.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011881|gb|ACD45237.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011883|gb|ACD45238.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011885|gb|ACD45239.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011887|gb|ACD45240.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011889|gb|ACD45241.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011891|gb|ACD45242.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011893|gb|ACD45243.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011895|gb|ACD45244.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011899|gb|ACD45246.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011903|gb|ACD45248.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011905|gb|ACD45249.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011907|gb|ACD45250.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011909|gb|ACD45251.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011911|gb|ACD45252.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011913|gb|ACD45253.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011917|gb|ACD45255.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011919|gb|ACD45256.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011921|gb|ACD45257.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011923|gb|ACD45258.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011925|gb|ACD45259.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011927|gb|ACD45260.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011929|gb|ACD45261.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011931|gb|ACD45262.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011933|gb|ACD45263.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011935|gb|ACD45264.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011937|gb|ACD45265.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011939|gb|ACD45266.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011941|gb|ACD45267.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011943|gb|ACD45268.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|281324217|gb|ADA60650.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324221|gb|ADA60652.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324239|gb|ADA60661.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324273|gb|ADA60678.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 97/226 (42%), Gaps = 4/226 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 1   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 121 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 180

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            N R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 181 VNQRMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 222


>gi|299472406|emb|CBN77594.1| RpoD family RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 242

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 53/208 (25%), Positives = 99/208 (47%), Gaps = 7/208 (3%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L  +DLIQEG I L  AAE++D   G +F TYA W ++ A  R+ A Q+ TI IP ++  
Sbjct: 11  LSSMDLIQEGAIALHLAAERYDPQRGVRFFTYADWSLRAAFERAEASQATTIAIPRYVYV 70

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +  ++      +  +     T +++A  L +    + K+L+  K+  S+   +       
Sbjct: 71  QKRRLK----AILGQHCGPQTSQDLATSLGISERQLAKLLRRAKDCQSMN-RVLVSSGVA 125

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LG+ I    A S  D   + +   +   +L +L P+EE V+  R+G+      +   V  
Sbjct: 126 LGEMIP--GAQSCEDILRRLDAEASLVGLLGTLKPQEEEVIVHRYGLFGRRRKSTPAVAA 183

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKK 675
              V+R+ + ++   A+ K++    + +
Sbjct: 184 VMGVSRQYVGRVHRSALEKMRASFEADQ 211


>gi|254497491|ref|ZP_05110284.1| flagellar biosynthesis sigma factor FliA [Legionella drancourtii
           LLAP12]
 gi|254353306|gb|EET12048.1| flagellar biosynthesis sigma factor FliA [Legionella drancourtii
           LLAP12]
          Length = 238

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 102/231 (44%), Gaps = 13/231 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++A   +D   G  F T
Sbjct: 12  QQIQETLVKNHALLVKRIAHHLLGRLPQSVQLDDLIQAGMLGLLEATRHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    + + +++ RE    EIA ++ +
Sbjct: 72  YAGIRIRGYMLDEVRRNDW---VPRSVYRNSRMISEAVKHVEHRLGREAKDFEIAAEIGI 128

Query: 559 PVEGVRKVLKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +    ++L+      +     +G  D +  G+  E +++  P  +   ++L      V+
Sbjct: 129 SLTEYHEMLQDSASSHLYGFEDLGVTDDALHGE--EGQSSTEPHANVFHSDLMNRLAEVI 186

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L  +E+ VL + +      D  L+E+G+   V+  R+ QI ++A  ++K
Sbjct: 187 KGLPHKEQMVLSLYY----EHDLNLKEIGEVLGVSESRVSQILSQATHRIK 233


>gi|220909315|ref|YP_002484626.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219865926|gb|ACL46265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 262

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 120/243 (49%), Gaps = 15/243 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWC 491
           +    +  A   +  +V+ NL LV   A ++ +   + + DL+Q G++GL++A E+FD  
Sbjct: 21  LQAYQKNPAPSLRNRLVQMNLGLVRKEAHRWLSYSTETYEDLVQVGSLGLIRAIERFDIT 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G+ FS++AM +++  I   + D+S  +RIP   +    +    A+ +  ++ R PT +E
Sbjct: 81  KGHAFSSFAMPYIRGEIQHYLRDKSPQVRIPRRWQVLQKQASLVAQELREQLHRVPTDDE 140

Query: 552 IAKKLAMPVEGVR--KVLKITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQA 607
           +A  L + ++  +  K+    + P+SL+ P+G++D  ++ LG+ + D+   S   +    
Sbjct: 141 MALALGIGLQEWQQVKLSSYNRSPLSLDAPVGEDDFGSTCLGEMVPDQRYRSFQLAQED- 199

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK---AI 664
             R    + L +L  R   +L   F      D T +E  +   ++   + +   K   A+
Sbjct: 200 --RLRLQQALQTLESRTCEILEFVFLH----DLTQKETAELLGISAVTVSRQVKKGLIAL 253

Query: 665 RKL 667
           RKL
Sbjct: 254 RKL 256


>gi|188011585|gb|ACD45089.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011587|gb|ACD45090.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011589|gb|ACD45091.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011591|gb|ACD45092.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011593|gb|ACD45093.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011595|gb|ACD45094.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011597|gb|ACD45095.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011599|gb|ACD45096.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011601|gb|ACD45097.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011603|gb|ACD45098.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011605|gb|ACD45099.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011607|gb|ACD45100.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011609|gb|ACD45101.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011611|gb|ACD45102.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011613|gb|ACD45103.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011615|gb|ACD45104.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011617|gb|ACD45105.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011619|gb|ACD45106.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011621|gb|ACD45107.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011623|gb|ACD45108.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011625|gb|ACD45109.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011627|gb|ACD45110.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011629|gb|ACD45111.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011631|gb|ACD45112.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011633|gb|ACD45113.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011635|gb|ACD45114.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011637|gb|ACD45115.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011639|gb|ACD45116.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011641|gb|ACD45117.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011643|gb|ACD45118.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011645|gb|ACD45119.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011647|gb|ACD45120.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011649|gb|ACD45121.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011651|gb|ACD45122.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011653|gb|ACD45123.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011655|gb|ACD45124.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011657|gb|ACD45125.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011659|gb|ACD45126.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011661|gb|ACD45127.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011663|gb|ACD45128.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011665|gb|ACD45129.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011667|gb|ACD45130.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011669|gb|ACD45131.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011671|gb|ACD45132.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011673|gb|ACD45133.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011675|gb|ACD45134.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011677|gb|ACD45135.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011679|gb|ACD45136.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011681|gb|ACD45137.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011683|gb|ACD45138.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011685|gb|ACD45139.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011687|gb|ACD45140.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011689|gb|ACD45141.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011691|gb|ACD45142.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011693|gb|ACD45143.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011695|gb|ACD45144.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011697|gb|ACD45145.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011699|gb|ACD45146.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011701|gb|ACD45147.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011703|gb|ACD45148.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011705|gb|ACD45149.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011707|gb|ACD45150.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011709|gb|ACD45151.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011711|gb|ACD45152.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011713|gb|ACD45153.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011715|gb|ACD45154.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011717|gb|ACD45155.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011719|gb|ACD45156.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011721|gb|ACD45157.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011723|gb|ACD45158.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011725|gb|ACD45159.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011727|gb|ACD45160.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011729|gb|ACD45161.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011731|gb|ACD45162.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011733|gb|ACD45163.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011735|gb|ACD45164.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011737|gb|ACD45165.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011739|gb|ACD45166.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011741|gb|ACD45167.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011743|gb|ACD45168.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011745|gb|ACD45169.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011747|gb|ACD45170.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011749|gb|ACD45171.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011751|gb|ACD45172.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011753|gb|ACD45173.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011755|gb|ACD45174.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011757|gb|ACD45175.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011763|gb|ACD45178.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011865|gb|ACD45229.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011871|gb|ACD45232.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011873|gb|ACD45233.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011945|gb|ACD45269.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011947|gb|ACD45270.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011949|gb|ACD45271.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|211906951|gb|ACJ11994.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906953|gb|ACJ11995.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906955|gb|ACJ11996.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906957|gb|ACJ11997.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906959|gb|ACJ11998.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906961|gb|ACJ11999.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906963|gb|ACJ12000.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|281324219|gb|ADA60651.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324223|gb|ADA60653.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324225|gb|ADA60654.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324227|gb|ADA60655.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324229|gb|ADA60656.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324231|gb|ADA60657.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324233|gb|ADA60658.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324235|gb|ADA60659.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324237|gb|ADA60660.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324241|gb|ADA60662.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324243|gb|ADA60663.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324245|gb|ADA60664.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324247|gb|ADA60665.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324249|gb|ADA60666.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324251|gb|ADA60667.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324253|gb|ADA60668.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324255|gb|ADA60669.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324257|gb|ADA60670.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324259|gb|ADA60671.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324261|gb|ADA60672.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324263|gb|ADA60673.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324265|gb|ADA60674.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324267|gb|ADA60675.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324269|gb|ADA60676.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324271|gb|ADA60677.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324275|gb|ADA60679.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324277|gb|ADA60680.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324279|gb|ADA60681.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324281|gb|ADA60682.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324283|gb|ADA60683.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 97/226 (42%), Gaps = 4/226 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 1   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 121 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 180

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            N R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 181 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDIS 222


>gi|163750532|ref|ZP_02157770.1| flagellar biosynthesis sigma factor FliA [Shewanella benthica KT99]
 gi|161329687|gb|EDQ00676.1| flagellar biosynthesis sigma factor FliA [Shewanella benthica KT99]
          Length = 246

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 106/243 (43%), Gaps = 20/243 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+ KFD   G KF T+A 
Sbjct: 13  KALIVEQYASLVKKIAHHLLARLPASVQLDDLLQAGMMGLLEASAKFDANKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+   +EIA++L M ++
Sbjct: 73  IRIRGSMLDDIRRGDW---VPRSVHRNQRRVAQVIDELEQELGRDAKDDEIAQRLEMTLD 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQANLRETTTRVLAS 619
               +L      +S+   IG ED     D I   + V     +S  +          +  
Sbjct: 130 EYHHILNN----VSVGKIIGIEDLGVSVDVISHDDGVKDDTYESIAEDKFHAALVAAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI----RKLKHPSRSKK 675
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+     KLKH +++  
Sbjct: 186 LPERDGLVLSLYY----DEALNLKEIGAILEVSESRVSQILSQAMLRLKAKLKHWTKNND 241

Query: 676 LRS 678
             S
Sbjct: 242 YMS 244


>gi|209408336|emb|CAP19911.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 239

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 97/284 (34%), Gaps = 46/284 (16%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
           KRIE G   +M+++   P T  +++   + +      L +I  L   I P+  G      
Sbjct: 1   KRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA---- 54

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                Q+ E  + +       + + D E     S+++       PE A      + E  +
Sbjct: 55  ---GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLE 111

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            +                                       +K  ++S +     E L  
Sbjct: 112 KAKKA-----------------------------------LKKHGRASQQAVEELEALAI 136

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           L   + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  
Sbjct: 137 LFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLD 196

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           W        +G++   +    + I++ + ++  +  E  + I++
Sbjct: 197 WAEQLAS-GKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIAD 239


>gi|161723249|ref|YP_095808.2| flagellar biosynthesis sigma factor [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|307610482|emb|CBX00054.1| sigma factor 28 [Legionella pneumophila 130b]
          Length = 238

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 105/233 (45%), Gaps = 17/233 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F T
Sbjct: 12  QQTQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    R + +K+ RE    EIA++L +
Sbjct: 72  YAGIRIRGHMLDEVRRNDW---VPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGV 128

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTR 615
            ++    +L+ +          G +D     D + D     +  P  + +++++    T+
Sbjct: 129 SLDDYHDMLQDSIS----SHLYGFDDLGVTDDVLFDHEGNGSTEPHRNVMRSDMMNRLTQ 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+ SL  +E  VL + +      D  L+E+G+   V+  RI QI ++A  +++
Sbjct: 185 VIDSLPRKERLVLSLYY----EQDLNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|317133468|ref|YP_004092782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
 gi|315471447|gb|ADU28051.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
          Length = 248

 Score =  102 bits (255), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 109/253 (43%), Gaps = 18/253 (7%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNI 479
           +  E    +  V +    +  A+  +V     LV ++  +    +    +  DL   G I
Sbjct: 4   TTQEESEPLWQVYRETR-SREARNRLVLHYGWLVRAIVHRVMSVSGSYAESDDLTSCGTI 62

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+KA EKFD   G +FST+A + ++  I   +        +P  +R ++ ++      +
Sbjct: 63  GLIKAIEKFDSDKGVQFSTFATYRIRGEILDFVRRSDW---VPRGVRKRVLEMESAESEL 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-NAV 598
           ++ + R P+  E+ ++L +P   + K         S+E          L D   D     
Sbjct: 120 ASSLGRRPSDSELCERLGVPDRVLAKTR------ASMERFNVISFEEMLRDAARDMAGDD 173

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP ++  ++ L E  T+ +  L  R+  V+ + +      D TL E+ +   VT  R+ Q
Sbjct: 174 SPENALQESELLEVLTKAVEDLPERDRLVITLYY----YEDLTLREISEVIGVTESRVSQ 229

Query: 659 IEAKAIRKLKHPS 671
           I ++A+ ++K   
Sbjct: 230 IHSRAVGRMKAAM 242


>gi|325528539|gb|EGD05649.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. TJI49]
          Length = 115

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 34/115 (29%), Positives = 61/115 (53%)

Query: 34  MIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           M+ LA ++GY+T  +L   LPP+  S + ++   A L+++GI V+D         +  + 
Sbjct: 1   MLALAGEQGYLTHADLVDALPPESDSPDALDVVRAALADIGIAVLDEPVASQPFAAAPAA 60

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           D+   A +    L         ++ DP+ +Y+R M ++ LL+RE EI +A+ IE 
Sbjct: 61  DVDRDALDEGRTLLGDLARGASASTDPLALYMRRMHAVPLLTREDEIVLAREIET 115


>gi|325845925|ref|ZP_08169123.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325481831|gb|EGC84863.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 333

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 134/275 (48%), Gaps = 12/275 (4%)

Query: 405 SILKIRNEI--KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +I KI+N +  K  S    +S      IV   ++G   A  A   +V+ N  LV S A  
Sbjct: 60  NIHKIKNSLVAKKRSDIIRLSDLTNEQIVEQFQEGNQNALGA---LVDKNQGLVRSRASY 116

Query: 463 YTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS--- 516
           +       L+  DL+Q G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +    
Sbjct: 117 FYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTI 176

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                     +K+ ++++     S +   +   +E   K       +    ++    +++
Sbjct: 177 RIPAGKYLKLNKLKQILKANPEASEEELYKILKQEGIDKKQADDLFLINRNQVNSTSLNI 236

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                D     L D + D +++   D  ++ ++ +   + L  L+ RE++++  R+G+  
Sbjct: 237 NLDSEDSTGDELMDMVGD-DSIPVDDQILKKDMEDFLMKALDQLSDREKQIIIYRYGLDN 295

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               TLEE+G  + ++RERIRQIE +A+ KLK  S
Sbjct: 296 EKPKTLEEIGTIYSLSRERIRQIENQALGKLKQYS 330


>gi|312140062|ref|YP_004007398.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311889401|emb|CBH48717.1| sigma-70 factor [Rhodococcus equi 103S]
          Length = 289

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 51/260 (19%), Positives = 103/260 (39%), Gaps = 12/260 (4%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           ++   +    I E R   +       E       +  A L +   VA +Y NRG+   +L
Sbjct: 33  EACDEQVRRCIEELRDHCASGETDPEELHRCVDRLCVAALPMAYRVAGRYRNRGVPTAEL 92

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q   + L+ AA +FD   G  F  YA+  V+  I +   D + +  +P  +++    V 
Sbjct: 93  RQVAALALVGAARRFDPSRGTDFIPYAVTSVRGEIRKYFRDFTWSTHVPRRLQESHLAVR 152

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDF 591
                +S ++ R    +E+A  L MPVE   +  ++       SL+    D     L   
Sbjct: 153 NRMESLSTELGRTVRLDEVAHSLGMPVEEAEEAERVGELYSCESLDATPVDGSVPRL--- 209

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
                         +   R    R++A+L  R+  +L +R+        +  E+ +Q  +
Sbjct: 210 ---HTTGDVDADLSRVEHRHLLRRLMATLDERQRTLLWLRYFH----QMSQSEIAEQVGL 262

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           ++  + ++  +++  L+  +
Sbjct: 263 SQMHVSRLLRQSLEHLRRQA 282


>gi|188011897|gb|ACD45245.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011901|gb|ACD45247.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717586|gb|ADN88846.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717610|gb|ADN88858.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717630|gb|ADN88868.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717636|gb|ADN88871.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
 gi|307717638|gb|ADN88872.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
 gi|307717646|gb|ADN88876.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 97/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F      + + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDIS 220


>gi|307717588|gb|ADN88847.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717632|gb|ADN88869.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 97/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V    +LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 220


>gi|261855330|ref|YP_003262613.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothiobacillus
           neapolitanus c2]
 gi|261835799|gb|ACX95566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothiobacillus
           neapolitanus c2]
          Length = 239

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/227 (21%), Positives = 93/227 (40%), Gaps = 12/227 (5%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           V  +  LV  +A    NR    +Q  DLIQ G IGL++A+  +D   G  F TYA   ++
Sbjct: 19  VAEHAGLVKRIAFHLMNRLPDHIQAEDLIQAGMIGLLEASNHYDAAQGASFETYAGIRIR 78

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   +         P  +  +  ++ +    +  +   E    ++   L + ++   +
Sbjct: 79  GAMLDEVRRNDW---APRSVHRRHREISQAVHEIETRTGCEAKDADVCALLGISLDDYYE 135

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            L  + +        G ED +   D  + ++      S  +    E     +++L  RE 
Sbjct: 136 ALNDSVQVRLAPLDAGGEDHNETIDVADHRDQPDQYLSHER--FHEDLAEHISALPERER 193

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            V+ + +      +   +E+G    V+  R+ QI+ KAI +LK   +
Sbjct: 194 LVMSLYYV----DELNQKEIGAVLGVSESRVCQIQNKAILRLKSSLK 236


>gi|167034905|ref|YP_001670136.1| flagellar biosynthesis sigma factor [Pseudomonas putida GB-1]
 gi|166861393|gb|ABY99800.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida
           GB-1]
          Length = 246

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 96/239 (40%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ A K+D  
Sbjct: 7   KMYSRAAKDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAMRAVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANL 609
           +A +L + ++    +L  T            +D  H G   ED     V P         
Sbjct: 124 VAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASGQVEPARGLEDERF 182

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   T  +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 183 QVALTEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|307109682|gb|EFN57919.1| hypothetical protein CHLNCDRAFT_141989 [Chlorella variabilis]
          Length = 509

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 109/253 (43%), Gaps = 9/253 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E   +  +          A   +  AN  LV  +A K+  RGL   DL+ EG + L
Sbjct: 50  LTAAEEAQLAELA---VGGDHRAAAMLAHANRPLVTWLAAKFAGRGLAKEDLVAEGMLAL 106

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            +AA  F      +F T+A   +  A++R+I  QS  IRIP      +  V +    +S 
Sbjct: 107 ERAAGSFHPDREARFGTFAAAAISNALSRAIRRQSRVIRIPETHYRDMAVVRQAMAELSA 166

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED---KNAV 598
           ++ R P  EEIA+   +    V+  L + +   + +   G  + +   D ++D   +   
Sbjct: 167 ELGRPPRCEEIAQSCVLT---VKHTLHLLRAMGTQQQQGGGSEAAEEYDVVDDSLEEEEC 223

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           S      Q  LR+  +  LA L  ++  ++ +R G+      + +E+G++   T   +  
Sbjct: 224 SFAQEERQGMLRQELSSRLAQLDSKQALIVSLRHGLHDGRAWSCKEIGERLDCTAAWVAA 283

Query: 659 IEAKAIRKLKHPS 671
               A  KL+  +
Sbjct: 284 QYKMAAHKLQRQA 296


>gi|188011915|gb|ACD45254.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 221

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/225 (21%), Positives = 98/225 (43%), Gaps = 4/225 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  +
Sbjct: 1   KVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P
Sbjct: 61  YDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSP 120

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              +IA  + +  E V + +++ K   +L      E  S               D   + 
Sbjct: 121 QISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERV 180

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           N R    +VL  L  RE+++L+  F      + + +E G+   ++
Sbjct: 181 NQRMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDIS 221


>gi|143615|gb|AAA22791.1| sporulation protein [Bacillus subtilis]
          Length = 195

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 50/177 (28%), Positives = 90/177 (50%), Gaps = 4/177 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           E+K       +   E + +   +++ +     A+  ++E N+RLV SV +++ NRG +  
Sbjct: 4   EVKKNGKNAQLKDHEVKEL---IKQSQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPD 60

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL Q G IGL+K+ +KFD     +FSTYA+  +   I R I D   T+++   +++  +K
Sbjct: 61  DLFQIGCIGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRD-DGTVKVSRSLKELGNK 119

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
           + R    +S  + R PT +EIA  L +  E V    +  + P S+   + + D   +
Sbjct: 120 IRRAKDELSKTLGRVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPI 176


>gi|219670137|ref|YP_002460572.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
 gi|219540397|gb|ACL22136.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
          Length = 248

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 94/239 (39%), Gaps = 15/239 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E +E  L LV  ++ +      + +   DLI  G  GL+ A E+FD   G KF TYA 
Sbjct: 14  RVEQIEKYLPLVKRISGRLLISLPQHVDEDDLIGYGVFGLLDALERFDPVRGVKFETYAT 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +             R KI ++      +  +  R  + EE+A  L M   
Sbjct: 74  LRIRGAIIDGLRTMDWVPH---SARQKIKRIQDAFAEVEARHGRPASNEEVAVLLEMEPR 130

Query: 562 GVRKVLKITKE--PISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +   L   +     SL+     E+         + D  A            ++     +
Sbjct: 131 DLEAALHQGQMLTLTSLDEVAVGEEGEAYTPRTQLTDPIAQEAFQEVELDEQKKILADAI 190

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-HPSRSKK 675
             L  +E+ V+     +    D TL+E+     ++  RI Q+ ++AI +L+   SR KK
Sbjct: 191 EKLPEKEKLVV----ALYYQEDLTLKEIAVIMKLSESRISQLHSQAILRLRGRLSRQKK 245


>gi|239817113|ref|YP_002946023.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Variovorax paradoxus
           S110]
 gi|239803690|gb|ACS20757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Variovorax paradoxus
           S110]
          Length = 243

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 108/243 (44%), Gaps = 17/243 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               + +  K  +++ +  +V  +A +   +    ++  DLIQ G IGL+ A+ ++    
Sbjct: 1   MYTAQGTFEKSHLLKQHQPMVRRMALQMLAKLPASVELDDLIQAGMIGLLDASTRYQDNR 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F T+A   ++ A+   +            +R    KV +  + + +++ R  +  EI
Sbjct: 61  GAQFETFASQRIRGAMLDELRASDW---GSRGLRQSARKVEQAIQALEHRLGRSASEGEI 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK-------NAVSPLDSAI 605
           A++L M ++  + +L+  +    L      +D      ++E +           PL   +
Sbjct: 118 ARELKMELDDYQSLLQDIQGCQLLYVEDFAQDGEAENPWLERQAQADARLGGDDPLAQLL 177

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +A  R      +A+L  R++ +L + +      +  L E+G    VT+ R+ Q+ ++AI 
Sbjct: 178 EAGFRHELVDAIAALPERDQLLLNLYY----EEELNLREIGAILEVTQSRVCQLHSQAIS 233

Query: 666 KLK 668
           +L+
Sbjct: 234 RLR 236


>gi|330502783|ref|YP_004379652.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina NK-01]
 gi|328917069|gb|AEB57900.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina NK-01]
          Length = 240

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +A  ++ +++E    LV  +A     R    +Q  DLIQ G IGL++A+ K+D   
Sbjct: 2   YNKAQAQDSQHQLIERYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEASRKYDSGK 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F T+A   ++ ++   +         P  +      V    R +  +  R+    E+
Sbjct: 62  GASFETFAGIRIRGSMLDEVRKGDW---APRSVHRNSRMVSDAIRTVEARTGRDAKDHEV 118

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQAN 608
           A +L + +E    +L  T      S +  +        G   ED     + P        
Sbjct: 119 AAELQLSLEDYYGILGDTLGSRLFSFDDLLQ---DGEHGGLHEDAGHTHLEPSRDLEDER 175

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 176 FQAALADAIAGLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 231


>gi|158340672|ref|YP_001521840.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158310913|gb|ABW32526.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 440

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 113/241 (46%), Gaps = 15/241 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
               ++ K +     A++ ++ +NL  + S   +++ +G+   +LI EG  GL +A +++
Sbjct: 27  REAELIIKAQNGDYEARQTVIYSNLAWICSRGGQFSRKGIDDGELINEGYWGLNRAIDQW 86

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G    TY+   + +  + +I  ++  IR+P    +++ K+ +    +      + T
Sbjct: 87  DPTKGANLRTYSERKIYKFQSEAIRQKN-HIRLPKSTYEQLSKLKKATESL----GEDAT 141

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             ++A++  +  + +RK+ +I+ +P+SL +  G+ +   L D   D +  S   +     
Sbjct: 142 VAQLAEETEIKEKRIRKLQEIS-QPVSLNSVTGERENLELLDQQADDSLGSLDPA----- 195

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L      ++  L PR+  +L +        + + +++     +  +++R++  KA+  L+
Sbjct: 196 LSSELLDLVDKLHPRQREILHLYHW----EELSFQKISDYLGLPAKQVRKLYKKALDLLR 251

Query: 669 H 669
            
Sbjct: 252 K 252


>gi|85679193|gb|ABC72013.1| SigB [Listeria monocytogenes]
 gi|85679197|gb|ABC72015.1| SigB [Listeria monocytogenes]
 gi|85679199|gb|ABC72016.1| SigB [Listeria monocytogenes]
 gi|85679201|gb|ABC72017.1| SigB [Listeria monocytogenes]
 gi|85679203|gb|ABC72018.1| SigB [Listeria monocytogenes]
 gi|85679207|gb|ABC72020.1| SigB [Listeria monocytogenes]
 gi|85679209|gb|ABC72021.1| SigB [Listeria monocytogenes]
 gi|85679215|gb|ABC72024.1| SigB [Listeria monocytogenes]
 gi|307717584|gb|ADN88845.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717618|gb|ADN88862.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717628|gb|ADN88867.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 97/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F      + + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQFTF----IENRSQKETGELLDIS 220


>gi|312962254|ref|ZP_07776746.1| RNA polymerase sigma factor for flagellar operon FliA [Pseudomonas
           fluorescens WH6]
 gi|311283591|gb|EFQ62180.1| RNA polymerase sigma factor for flagellar operon FliA [Pseudomonas
           fluorescens WH6]
          Length = 246

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  A  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G
Sbjct: 9   YKKSARDSQGELIERYAPLVKRIAYHLLGRLPASVQVEDLIQAGMIGLLEVSTKYDASKG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ A+   +         P  +      V    R +  K  R+    E+A
Sbjct: 69  ASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDHEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET- 612
            +L + ++    +L  T            +D  H G   ED  +     S    + R   
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASAHMEPSRDLEDQRFQG 184

Query: 613 -TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 ALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|226944861|ref|YP_002799934.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
 gi|226719788|gb|ACO78959.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
          Length = 231

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 104/237 (43%), Gaps = 13/237 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I +++++E  L LV   A     R    ++  DLIQ G IGL+ A  ++D   
Sbjct: 1   MYTAQGKIRQRDLLEEYLPLVRRQALNLQTRLPASVELDDLIQAGTIGLLDALSRYDAAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+T+A   V+ A+   +  +     +P  +R     +  T R++  ++ R     EI
Sbjct: 61  GASFATFASQRVRGAMLDELRSRDW---VPRSVRRNARALEDTLRQLEQRLGRPAEEREI 117

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + + +   R++L  +     +      ED     D +   +  SP     +    E 
Sbjct: 118 ATSMGLDLAEYRQLLLDSNGSQLVAIDDLGEDE---VDAMSVGHYASPFVELAEGRDLER 174

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + + +L  RE+ VL    G+    D  L+E+G    V+  R+ Q+ ++A+ +L++
Sbjct: 175 LVKAIEALPEREKLVL----GLYYQEDLNLKEIGAVLGVSESRVCQLHSQAVARLRN 227


>gi|283850718|ref|ZP_06368005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
 gi|283573961|gb|EFC21934.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
          Length = 264

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 108/250 (43%), Gaps = 13/250 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAA 485
            + S   + +   +  ++E+V      +  VA +      + ++  +L+  G +GL++A 
Sbjct: 20  RLESGATQWKDFDARDRQEIVRHYSPKIKIVASRLKAKLPQSVEMGELLSAGAMGLIEAL 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            +F   LG KF TYA   +K ++   +       R   H       +   +RR+ N   +
Sbjct: 80  GRFRPELGIKFETYAESRIKGSMLDDLRRMDWFSRGQRHRVRT---LEEASRRIENDSGK 136

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             T E++A+   +    V + L+  +  + L      E+ S      +++    P  SA 
Sbjct: 137 AATVEQLAEATGLTEREVTQGLEALQNQLCLSLDAITENISSYQ---KNQLENEPYKSAE 193

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L +    ++  LTPRE+ VL + +G     +  + E  +   +T  R+ Q+ ++A+ 
Sbjct: 194 FKELVDKLASLIDDLTPREKLVLSLYYG----EELNMRETSEVMGITEGRVSQLHSQALA 249

Query: 666 KLKHPSRSKK 675
           +L+   +++ 
Sbjct: 250 RLRQKFKAQY 259


>gi|148645064|gb|ABR01057.1| RpoD [uncultured Geobacter sp.]
          Length = 102

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 72/101 (71%), Positives = 91/101 (90%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+S+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA WW++QAITR+IA
Sbjct: 2   RLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIA 61

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           DQ+ TIRIPVHM + I+K++RT+R++  +I REP+PEEIA+
Sbjct: 62  DQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAE 102


>gi|310659013|ref|YP_003936734.1| RNA polymerase sigma-28 factor (sigma-d) [Clostridium sticklandii
           DSM 519]
 gi|308825791|emb|CBH21829.1| RNA polymerase sigma-28 factor (sigma-D) [Clostridium sticklandii]
          Length = 247

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 55/225 (24%), Positives = 105/225 (46%), Gaps = 13/225 (5%)

Query: 452 NLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            + LV  +A K   Y    +++ DL+  G IGL+ A +K+D     KF TYA   ++ +I
Sbjct: 31  YINLVKIIAGKLYNYYASNIEYDDLMSYGVIGLIDAIDKYDPTKNIKFETYASIRIRGSI 90

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
              I +      IP  +R K   +      + +K  RE + +EIAK L    + V  +++
Sbjct: 91  IDQIRNLDW---IPRSIRQKSKILKDANEALESKYGREASYQEIAKYLGKSEQEVLTLIE 147

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASLTPREERV 627
            T     L       ++  +   ++D++   SP D  +  +  +   R ++ L  RE+ +
Sbjct: 148 ETSVYNVLSIEDDFNESFKIQ--LKDESLESSPEDLTVYNDTVKELERTISELNEREQLI 205

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           + + +  G     T +E+G+   ++  R+ QI +KAI K++   +
Sbjct: 206 INLYYYEG----LTYKEIGEILNISESRVSQIHSKAISKMRKQFQ 246


>gi|255085668|ref|XP_002505265.1| predicted protein [Micromonas sp. RCC299]
 gi|226520534|gb|ACO66523.1| predicted protein [Micromonas sp. RCC299]
          Length = 477

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 80/308 (25%), Positives = 128/308 (41%), Gaps = 58/308 (18%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN------RGL-QFLDLIQEGNIGLMKA 484
           + +++       A++ +V  N+ L  +VA           RGL    DL+QEG  GL  A
Sbjct: 73  AQLKERVDAGQEARRVLVTRNVGLARTVAADIHAKLNDADRGLLSVSDLMQEGCAGLATA 132

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           A+KFD   GY+FSTYA +W+K+A+   + +   TIR+P+H+ + I K+ +  R +     
Sbjct: 133 ADKFDPQRGYRFSTYAFFWIKKAVIDCVGNSGRTIRLPIHVNENIQKMKKATRELKEIKV 192

Query: 545 REPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT------------------ 585
           R+PT +E+A +L   V  +R++     + P+S++     +                    
Sbjct: 193 RDPTEDELADRLGWSVVKLRQMKVWAFRTPVSMDATTAKKGDPWEDADDAVAEAASLNAA 252

Query: 586 SHLGDFIEDKNAVSP--LDSAIQANLRETTTRVLASLTPREERVLRMRFGI--------- 634
               DF    NA S           LR     V ++L PRE  +LR RFG+         
Sbjct: 253 MQSSDFGTGLNAPSDTAEADVDADLLRMALEEVFSTLLPREAFILRHRFGLAAASTAMEG 312

Query: 635 ---------------------GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                                G       + +G    V+ E +R  E +A+ KLK P R 
Sbjct: 313 GDWLKASRAEVLSALRDDEGMGTRGGANFKTLGNLLGVSSESVRTYERRALAKLKQPDRI 372

Query: 674 KKLRSFLD 681
             L   L+
Sbjct: 373 ALLLPHLN 380


>gi|212695902|ref|ZP_03304030.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212677025|gb|EEB36632.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 333

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 134/275 (48%), Gaps = 12/275 (4%)

Query: 405 SILKIRNEI--KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +I KI+N +  K  S    +S      IV   ++G   A  A   +V+ N  LV S A  
Sbjct: 60  NIHKIKNSLVAKKRSDIIRLSDLTNEQIVEQFQEGNQNALGA---LVDKNQGLVRSRASY 116

Query: 463 YTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS--- 516
           +       L+  DL+Q G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  +    
Sbjct: 117 FYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTI 176

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                     +K+ ++++     S +   +   +E   K       +    ++    +++
Sbjct: 177 RIPAGKYLKLNKLKQILKANPEASEEELYKILKQEGIDKKQADDLFLINRNQVNSTSLNI 236

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                D     L D + D +++   D  ++ ++ +   + L  L+ RE++++  R+G+  
Sbjct: 237 NLDSEDSTGDELMDMVGD-DSIPVDDQILKKDMEDFLMKALDQLSDREKQIIIYRYGLDN 295

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
               TLEE+G  + ++RERIRQIE +A+ KLK  S
Sbjct: 296 EKPKTLEEIGTIYSLSRERIRQIENQALGKLKQYS 330


>gi|291196318|emb|CBG22631.1| DNA-directed RNA polymerase subunit D [Pseudomonas knackmussii]
          Length = 237

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 103/284 (36%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P    +++     +      L +I  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAQFPGAVDSILDDYKRVVTEGGRLSDI--LSGYIDPDDGSVP----- 53

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                              +E E D++ ++  +K++  + +    ++E +E +   D ++
Sbjct: 54  ------------------AEEVELDLKDSSAAAKEEEDEEEESESDSEEEEGDGGPDPEE 95

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A     + DQL            E +++            K  + + +       L +L
Sbjct: 96  AARRFGLVADQL------------EKFKKALK---------KHGRGTKQVDEELLALSEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++ D   R+   E  +++L      + R  FL    G E D  W
Sbjct: 135 FMPIKLVPKQFDALVARVRDALDRVRQQERAIMQLCVRDARMPRADFLRLFPGNETDEGW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           V       + ++   +      +++ + ++ ++  E  + ++E 
Sbjct: 195 VDAVLK-GKPKYAEALERLKADVVRNQQKMSALESEVELKVNEI 237


>gi|15895412|ref|NP_348761.1| sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|15025135|gb|AAK80101.1|AE007715_6 Sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|325509558|gb|ADZ21194.1| Sigma factor of SigD/WhiG family [Clostridium acetobutylicum EA
           2018]
          Length = 241

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 113/239 (47%), Gaps = 13/239 (5%)

Query: 445 KKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +++  + LV  +A +     ++ +++ DL+  G IGLM A +KFD   G KFSTY+ 
Sbjct: 10  REALIKKYIPLVKYIASRVIIGKSKYIEYEDLVGYGMIGLMDALKKFDQSKGMKFSTYSS 69

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K A+   +   S    I     DK+++      R+  ++ REPT  EIA  L +  +
Sbjct: 70  IRIKGAMIDELRKNS---PISKGAMDKLNRYNLVVERLEKELSREPTELEIASGLGVGRK 126

Query: 562 GVRKVLKITKE--PISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            V ++         +SLE  I  ++D   L   IED+ + SP  +  +    E   + + 
Sbjct: 127 EVGEIEGYINYISVVSLEDLIFSEDDDMPLIGTIEDEKSPSPEKALEEKEEIEYLAKGIE 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            L  ++  VL + +  G     TL+++G    V+  R+ Q+  +AI  L+   +  K  
Sbjct: 187 LLNEKDRMVLSLYYYEG----LTLKKIGNILNVSESRVCQLHTRAIMHLRKSLKKLKYE 241


>gi|291196266|emb|CBG22604.1| DNA-directed RNA polymerase subunit D [Pseudomonas anguilliseptica]
          Length = 236

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 99/284 (34%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T  +++   + +      L E++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVNSILAEYNRVTTNGGRLVEVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +       K+ D  +ET+ D   A+   +++      P                 
Sbjct: 50  GIVPAEAAAPVPVKDGDAAEETDDDDAEASDDEEEEGDGGPDPE---------------- 93

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                         + +     I +      +L+      +K  ++S +     +++ +L
Sbjct: 94  --------------EALRRFTAIGD------ALELAKKALKKHGRNSKQGTAALKEMAEL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++    +R+   E  +++L      + R  FL    G E+D  W
Sbjct: 134 FMPIKLVPKQYDALVVRVRSSLERLRAQERAIMQLCVRDARMPRADFLRLFPGNEIDAEW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            S      + ++   +      I + + ++ ++  E  ++++E 
Sbjct: 194 -SAGLAKGKAKYAEAIGNLQGDIQRCQQKLSALEAECELTLAEI 236


>gi|146277655|ref|YP_001167814.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
 gi|145555896|gb|ABP70509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 239

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 103/236 (43%), Gaps = 14/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E +   + +V A++ LV  +A        R ++  DLIQ G +GL+ A+ +++   
Sbjct: 5   RGYAEQAQTPERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQIGYMGLVDASRRYEPRD 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+ YA   ++ +I   +   S   R  + M+    KV    +R+ +++ R P   E+
Sbjct: 65  GVTFAAYAAIRIRGSIMDFLRSNSALCRTTILMQQ---KVKAAVQRLESRLMRAPETPEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L MPV   +  L       +       +D S L       +  S  D      +R  
Sbjct: 122 AAELGMPVGEYQDWLAQFAGSQTASLDEVYDDQSSLFQ----GSEPSAEDRLQATQMRGL 177

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  +  RE  +L++ F      +  + EV +   VT  R+ QI+  AI +L+
Sbjct: 178 LRQALGKMPEREALLLQLIFV----EEMNVYEVAEILGVTTGRVSQIKKAAIERLR 229


>gi|307717644|gb|ADN88875.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 96/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSMEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 220


>gi|222528460|ref|YP_002572342.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455307|gb|ACM59569.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 256

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/216 (27%), Positives = 108/216 (50%), Gaps = 11/216 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V   L +   +AKK+  RG+ + DL Q   I L+ A E+F+   GYKF+++A   +
Sbjct: 31  RNELVNKYLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPNKGYKFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEVLSTKLKRPPKVEEIAQHLNMSAEEVL 150

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++ +    P SL+  + +++   LGD +   +      + +Q    E   + +  L+P
Sbjct: 151 EVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDE-----NILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            E   ++ RF      + T +E+ ++  V++  I +
Sbjct: 206 FEREFVQKRFF----EEKTQKEIAEEMNVSQMYISR 237


>gi|257650082|emb|CAX37103.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|257650084|emb|CAX45874.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|257650086|emb|CAX45875.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|257650088|emb|CAX45876.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|288856429|emb|CAX45877.1| RNA polymerase sigma-70 factor [Aeromonas sp. AH-3]
          Length = 244

 Score =  102 bits (254), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 51/288 (17%), Positives = 100/288 (34%), Gaps = 46/288 (15%)

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           E P     L+   D+       L +II     I P                         
Sbjct: 1   EYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ 34

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
           E DDV  T   I S            D   +  ++ E + D+ +      ++        
Sbjct: 35  EADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGESSDDDGDGGPDPEVA-------- 86

Query: 279 KVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                     E + ELR+  +   ++ QK+ ++    +     L  +     L   + D 
Sbjct: 87  ---------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFDR 137

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +  W 
Sbjct: 138 LVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WS 196

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             +    + +L+   +++ I  ETG+SI++ + I   +  GE +A  A
Sbjct: 197 PRLVDMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRA 244


>gi|307717606|gb|ADN88856.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 97/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA+ + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIAEFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 220


>gi|104782801|ref|YP_609299.1| flagellar biosynthesis sigma factor [Pseudomonas entomophila L48]
 gi|95111788|emb|CAK16512.1| sigma factor FliA [Pseudomonas entomophila L48]
          Length = 246

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 95/239 (39%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     A  A+ E+VE    LV  +A     R    +Q  DLIQ G IGL++ A K+D  
Sbjct: 7   KMYSKAAKDAQYELVERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRSVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANL 609
           +A +L + ++    +L  T            +D  H G   ED     + P         
Sbjct: 124 VAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASGQLEPSRDLEDERF 182

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 183 QSALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|254411015|ref|ZP_05024793.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196182370|gb|EDX77356.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 111/240 (46%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           ++   +  +   + ++V  N  LV  +A + + +    + DL+Q G +GL++A E+F   
Sbjct: 14  LMAYSQNPSIELRNQLVRLNSGLVKKIAYRVSQQCSEPYDDLVQLGYLGLIRAIERFKPD 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY FS++A+ +++  +   + D+   ++IP   ++   +  R ++R++  + R P   E
Sbjct: 74  QGYAFSSFAVPFIRGEMLHFLRDKGNIVKIPRRWQELQQEGQRVSKRLTATLGRPPKEAE 133

Query: 552 IAKKLAMPVEGVRKVLKITKE--PISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
           IA+ L + ++  ++    +K   P+SL+  +G   +    LGD + D  +        + 
Sbjct: 134 IAQALNISMQEWQESKLASKNRLPLSLDLTVGHNVDHPVTLGDMLPD--SYDQTLQHWEE 191

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R+     +A L  + +  +   F      D   +E  K   V+   + +   + I +L
Sbjct: 192 D-RQQLQGAIAQLETKTQAAIEFVFF----RDLPRKEAAKHIGVSPMTVTRHLQRGINEL 246


>gi|113477360|ref|YP_723421.1| RNA polymerase sigma factor SigF [Trichodesmium erythraeum IMS101]
 gi|110168408|gb|ABG52948.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 254

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 113/245 (46%), Gaps = 12/245 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           + +  +  +   + ++V+ N+ LV   A  + N+    + DL+Q G IGL+ A E+FD  
Sbjct: 17  LQQYQQFPSYELRNKLVQLNVGLVRKEAYHWLNKCSETYDDLLQVGYIGLILAIERFDVS 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               FS++A  +++  I   + D+S ++RIP +      +  +  + +  K +R+PT +E
Sbjct: 77  KARAFSSFATPYIRGEIKHYLRDKSPSVRIPRNWLAIDRQATKVIQDLRMKFQRKPTDQE 136

Query: 552 IAKKLAMPVEGVRKVLKITKE--PISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQA 607
           +A  L + ++   K+    +   P+SL+ P+ D+   ++ LG+ + D    S   +    
Sbjct: 137 VASALGISLDQWHKIQMACRNLAPLSLDAPVQDQAYGSTSLGELVPDSQYRSFQLAQEDQ 196

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  + L+ L     +VL   F      D T +E  ++  ++   + +     ++ L
Sbjct: 197 I---RLQQALSKLEESTRKVLEFVFLC----DLTQKETAERMGISAVTVSRRVKNGLKCL 249

Query: 668 KHPSR 672
           +   +
Sbjct: 250 QKIMQ 254


>gi|307717612|gb|ADN88859.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 95/223 (42%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIAYFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+ +L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQMILQYTFIEN----RSQKETGELLDIS 220


>gi|317055657|ref|YP_004104124.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447926|gb|ADU21490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 218

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 58/219 (26%), Positives = 105/219 (47%), Gaps = 14/219 (6%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E NL LV   A ++  RG+++ DL   G +GL+KA+  FD   G KFSTYA+  +   I 
Sbjct: 10  EDNLGLVHLCANRFRGRGIEYDDLYGAGCMGLVKASRAFDASRGVKFSTYAVPVILGEIK 69

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R   D   T+++   +++   K+ R ++  ++K  REPT  E++       + V + L  
Sbjct: 70  RLFRDGG-TVKVSRSLKELSLKITRASQTFAHKNGREPTVSELSDITGADPDDVIEALNA 128

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           ++  +SL   IGDED     D   +       D       R    +VL+ L+  + +++ 
Sbjct: 129 SQPTVSL--TIGDEDGESQTDLPTEPPDEDITD-------RLALRQVLSELSADDRKLID 179

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R+  GM      E    +  +T+ ++ + E K +  ++
Sbjct: 180 LRYFKGMTQTAAAE----KLGMTQVQVSRREKKLLTYMR 214


>gi|54297695|ref|YP_124064.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Paris]
 gi|53751480|emb|CAH12898.1| sigma factor 28 [Legionella pneumophila str. Paris]
          Length = 238

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 104/233 (44%), Gaps = 17/233 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F T
Sbjct: 12  QQTQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    R + +K  RE    EIA++L +
Sbjct: 72  YAGIRIRGHMLDEVRRNDW---VPRSVYRNSRMISDAVRILEHKFGREAKDNEIAEELGV 128

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTR 615
            ++    +L+ +          G +D     D + D     +  P  + +++++    T+
Sbjct: 129 SLDDYHDMLQDSIS----SHLYGFDDLGVTDDVLFDHEGNGSTEPHRNVMRSDMMNRLTQ 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+ SL  +E  VL + +      D  L+E+G+   V+  RI QI ++A  +++
Sbjct: 185 VIDSLPRKERLVLSLYY----EQDLNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|330959578|gb|EGH59838.1| putative RNA polymerase sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 532

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 90/429 (20%), Positives = 165/429 (38%), Gaps = 23/429 (5%)

Query: 257 NLDEDEDDSAHTLSAMEDQ-LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
             D  E ++     A+ DQ     V   L+ I  +  ELR      ++G     S+    
Sbjct: 111 EGDYSEKEAHKAAKAIADQKFASLVRRKLNTIRTLISELRGYAAEGMDGTLF--STAVRD 168

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
            L+ KL ++V    +     D       ++S R       +    +   IK +  +    
Sbjct: 169 ELRLKLAEIVPYDYILNRAADQFRVNCKELSGRTRDLIKFICDEVRISKIKVEGII---S 225

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDS----ILKIRNEIKSISVETGISISEFRHIV 431
           G    P  +         E K F    +      I   +  I   +        E     
Sbjct: 226 GNWTSPKLIPALLISGGYELKLFPPAAMKKLRLGITGRQQAILEAASAGEAPAIEILSAW 285

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S+  + + +          AN+RLV     ++  R           N+GL +A  +F   
Sbjct: 286 SVFNRVDRDIEKCADIFTNANVRLVEQQIGRF--RFADKEIARSAANMGLTRAVYRFAPE 343

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           +G++FST A+ W+  +I+R +ADQ           + +HK  R    M  +     + + 
Sbjct: 344 MGFRFSTIALTWINVSISRDLADQESIRLP-----EGMHKHRRMIANML-RDHPNVSIKT 397

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQAN 608
           +A+   +  + VR ++       S++T     D+S    L + + D N    +      +
Sbjct: 398 LAEATKLEQDVVRDLVHFAGGQRSIDTAFQGTDSSEADGLHELLADTN-NDFISEIEDDS 456

Query: 609 LRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +R+     L   LT RE  VL  RFG+G   + TL E+  +  +++ER+RQ+E +A+ K+
Sbjct: 457 MRQFVESALGDVLTQREIFVLVNRFGMGDAREKTLAELSIEMKLSKERVRQLEIQALGKI 516

Query: 668 KHPSRSKKL 676
           +    ++ L
Sbjct: 517 RDSEFAETL 525


>gi|323341369|ref|ZP_08081613.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
 gi|323091246|gb|EFZ33874.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
          Length = 250

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 54/248 (21%), Positives = 107/248 (43%), Gaps = 13/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKA 484
            + I     +      + +++ +   L LV  VA + +  N   ++ DL   G IGL+ A
Sbjct: 1   MQRINQRKGQCRFMYEVDREQEILKYLPLVERVANRISIKNTEYEYDDLYNIGVIGLIDA 60

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD      F  YA   ++ AI   +       +I  +    ++   +  + +  ++K
Sbjct: 61  MQKFDSSKKVPFENYAAIRIRGAIIDEVR---RHSKISRYKMGNVNSFYQAKQELEQEMK 117

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLG--DFIEDKNAVSP 600
           RE T +EI KK+ +    +  +    +    +SLE+ +   +   +   D + D  A S 
Sbjct: 118 REVTDKEIMKKMGITSSQLGDIYDSIQYLSSVSLESTLYSNNDETVMVQDTLRDSKAPSG 177

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               ++   ++     +  L+ RE+ VL + +      D TL+E+     V+  R+ QI 
Sbjct: 178 EKELMKQERKKELIEAIKRLSEREQLVLSLYY----EEDATLKEIAAILDVSIARVSQIH 233

Query: 661 AKAIRKLK 668
            +AI K++
Sbjct: 234 GRAIAKIR 241


>gi|209524790|ref|ZP_03273336.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Arthrospira
           maxima CS-328]
 gi|209494669|gb|EDZ94978.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Arthrospira
           maxima CS-328]
          Length = 255

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 112/248 (45%), Gaps = 14/248 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKA 484
           E   ++         ++  + ++V+ N+ LV      + N+    + DL+Q G IGL++A
Sbjct: 12  ESLELLR--EYQHSPSNSVRNQLVQINIGLVRKEVHHWLNQCTESYDDLLQVGCIGLIRA 69

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E+FD   G+ FS++A+ +++  I   + D+S ++R+P      + K     + +  K+ 
Sbjct: 70  IERFDMSKGHAFSSFAIPYIRGEIQHYLRDKSPSVRVPRQWLTLLRKATPCIQDLQVKLG 129

Query: 545 REPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP 600
           R+PT  EIA  L + VE     K+    +  +SL+ PI DE+   + LGD + D    S 
Sbjct: 130 RKPTDAEIASALEISVEEWNQVKLASQNRSLLSLDAPIQDEEEGSTSLGDLVPDTRYRSF 189

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +           + L  L     +VL   F      D T +E  ++  ++   + +  
Sbjct: 190 QLAQEDQI---RLQQALGHLEDGTRKVLEFVFL----YDLTQKETAEKLGISAVTVSRRV 242

Query: 661 AKAIRKLK 668
            + +  LK
Sbjct: 243 KRGLSLLK 250


>gi|220932500|ref|YP_002509408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
 gi|219993810|gb|ACL70413.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
          Length = 254

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 108/240 (45%), Gaps = 16/240 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A+KE++   L LV    ++       F    DL   G IGL+ A EK+D+ LG KF+T
Sbjct: 23  QEARKELILNYLPLVKYQVERVKMIIPDFIEEDDLESYGIIGLIDAIEKYDYRLGIKFNT 82

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++ +I   +            +R +  ++ + A +++ ++ R+PT  E+A K  +
Sbjct: 83  YASRRIRGSIIDHLRKLDWLPH---SLRREGKELQKVADKLAKELGRKPTVAELANKTNI 139

Query: 559 PVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
             E V K+     + + +SL         S + +FI+  + + P     +    +   R 
Sbjct: 140 SREKVTKIYSKLNSAKWVSLYED---WGESTVFNFIK-GDCLPPDRILDKKERIKLLARA 195

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  L+  E  V+ + +      + T +E+ +   ++  RI QI  +A+ +L+     +K 
Sbjct: 196 IDRLSESERTVISLYY----YEELTQKEIAEVMGLSPARISQIHKRAVYRLRGYLARRKY 251


>gi|323698081|ref|ZP_08109993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           ND132]
 gi|323458013|gb|EGB13878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans ND132]
          Length = 261

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 108/250 (43%), Gaps = 14/250 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAA 485
            +   VR  +  +   ++ +V      +  +A +      + ++  +LI  G++GL+ A 
Sbjct: 20  ELEQGVRHWDDFSPRDRENIVRYYAPKIRILALRLKAKLPQSVELNELISAGSLGLLDAL 79

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            KF+  LG KF TY+   +K A+   +            +R K+  +  + R++ ++   
Sbjct: 80  GKFNPELGIKFDTYSENRIKGAMLDELRRMDWF---SRGLRQKVKVLEDSMRQIEHETGS 136

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             T E++     M    V++ L+     + L      E+        +++    P  SA 
Sbjct: 137 PATTEQLCAHTGMSDREVQQGLEALNNQVCLSLDSFQENLVGQKKMTDNE----PFQSAA 192

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              + +    ++  LTPRE+ V+ + +G     +  ++E  +   +T  R+ Q+ ++A+ 
Sbjct: 193 FQEIVDKVANLIEELTPREKLVISLYYG----EELNMKETAEVMDITEGRVSQLHSQALN 248

Query: 666 KLKHPSRSKK 675
           KL+   R++ 
Sbjct: 249 KLRKTFRARY 258


>gi|307717590|gb|ADN88848.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717592|gb|ADN88849.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717624|gb|ADN88865.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717626|gb|ADN88866.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 96/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+ +L+  F      + + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQMILQYTF----IENRSQKETGELLDIS 220


>gi|75908065|ref|YP_322361.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75701790|gb|ABA21466.1| Sigma 32 (RpoH) [Anabaena variabilis ATCC 29413]
          Length = 258

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 120/254 (47%), Gaps = 14/254 (5%)

Query: 425 SEFR-HIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGL 481
           +E +  I  ++R+ +   +   + ++V+ NL LV   A  + N+    + DL+Q G +GL
Sbjct: 7   NELKYEIWQLLREYQQSRSETVRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQVGCLGL 66

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E+F+   G+ FS++A+ +++  I   + D+  T+RIP        + +  +R +  
Sbjct: 67  IRAIERFEIAKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIPRRYLAIQQRAIGVSRSLRE 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNA 597
           +  R+PT  E+A  L +  +  +++    + + P+SL+ P+ D  E  + LG+ + D + 
Sbjct: 127 QYNRQPTDSELATALDISPDEWQEIKLAWVNRAPLSLDVPVQDGEEGATSLGELVPDHHY 186

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S   +           + L  L  R   VL   F      D T ++V +   ++   + 
Sbjct: 187 RSFQLAQEDQI---RLQQALFQLEQRTREVLECVFL----QDLTQKQVAEHLGISVVTVS 239

Query: 658 QIEAKAIRKLKHPS 671
           +   K +  LKH  
Sbjct: 240 RRVKKGLDLLKHLM 253


>gi|114320145|ref|YP_741828.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226539|gb|ABI56338.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 242

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 96/242 (39%), Gaps = 16/242 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                A+    +++  +  LV  +A     R    +Q  DLIQ G +GL++AA +FD   
Sbjct: 6   MYAEVAAQHDNDLLVQHASLVKRIAHHLAGRLPPSVQLDDLIQAGMVGLLEAARQFDPGQ 65

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   I         P  +  K   V    R + ++  R+    E+
Sbjct: 66  GASFQTYAGIRIRGAMLDEIRRLDW---TPRSVHRKGRSVAEAIRAVEHRTGRDARDHEV 122

Query: 553 AKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++L + ++   ++L+   T    S++         H        +   P         +
Sbjct: 123 AQELGITLDEYHQILQDVSTSRIFSIDQEDPATGEPHQLP----GDHPEPFAEITDEGFQ 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 +  L  RE+ ++     +  + +  L E+G+   VT  R+ QI  + + KL+  
Sbjct: 179 RALAEAIRRLPEREQLIM----ALYYDEELNLREIGEVLNVTESRVSQIHGRIVVKLREA 234

Query: 671 SR 672
            +
Sbjct: 235 LK 236


>gi|312794377|ref|YP_004027300.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312876651|ref|ZP_07736632.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796604|gb|EFR12952.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|312181517|gb|ADQ41687.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 256

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/216 (27%), Positives = 110/216 (50%), Gaps = 11/216 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V  +L +   +AKK+ NRG+ + DL Q   I L+ A E+F+   GY+F+++A   +
Sbjct: 31  RNELVNKHLYIAEIIAKKFVNRGIDYEDLYQVACIALINAVERFEPNKGYRFTSFATPTI 90

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D++  IR+P  + +   K+      +S K+KR P  EEIA+ L M  E V 
Sbjct: 91  MGEIKRYFRDRASIIRLPRRIYETSAKIKLATEILSTKLKRPPKVEEIAQHLNMSTEEVL 150

Query: 565 KVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +V++   +  P SL+  + +++   LGD +   +      + +Q    E   + +  L+P
Sbjct: 151 EVMEASSSYLPQSLDQTMYEDEEMTLGDVLGKSDE-----NILQVENVEAVKKAIERLSP 205

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            E   ++ RF      + T +E+ ++  V++  I +
Sbjct: 206 FEREFVQKRFF----EEKTQKEIAEEMNVSQMYISR 237


>gi|315001910|emb|CBI75441.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 242

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 47/286 (16%), Positives = 99/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +   + + + D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + +LR+  +   ++ Q++ ++    +    +L  +     L   + D
Sbjct: 88  ----------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|291196370|emb|CBG22657.1| DNA-directed RNA polymerase subunit D [Pseudomonas peli]
          Length = 236

 Score =  102 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 99/284 (34%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T  +++     +      L E++            G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDSILAEYTRVTTDGGRLVEVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +       K+ D  +ET+ D   A+   +++      P                 
Sbjct: 50  GIVPAEAAAPVPVKDGDAAEETDDDDAEASDDEEEEGDGGPDPE---------------- 93

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                         + +     I +      +L+      +K  ++S +     +++ +L
Sbjct: 94  --------------EALRRFTAIGD------ALELAKKALKKHGRNSKQGTAALKEMAEL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++    +R+   E  +++L      + R  FL+   G E+D  W
Sbjct: 134 FMPIKLVPKQYDALVVRVRSSLERLRAQERAIMQLCVRDARMPRADFLKLFPGNEIDAEW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            S      + ++   +      I + + ++ ++  E  ++++E 
Sbjct: 194 -SVGLAKGKAKYAEAIGNVQADIQRCQQKLTALEAECELTLAEI 236


>gi|32490948|ref|NP_871202.1| flagellar biosynthesis sigma factor [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166154|dbj|BAC24345.1| fliA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 246

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 102/226 (45%), Gaps = 12/226 (5%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + +    ++   A +   +    ++  DLIQ G IG + A + FD   G  F TYA   V
Sbjct: 21  LWKKYTPMIRREALRLQVKLPGSVELDDLIQAGMIGFLSAIDNFDINQGASFPTYARSRV 80

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + ++   + ++     +P  +R     +    +R+  ++    + ++IAK+L + +   +
Sbjct: 81  RWSMLDELRERDW---VPRSVRRNARDIASAIQRLEQRLGSSASEKQIAKELKISLCEYQ 137

Query: 565 KVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           K+L+ T      SL+     E     G  I   ++  P    +  +L++   + +  L  
Sbjct: 138 KMLQETNCGQIFSLDELNNQEIIGSFGMNIPIDHSKDPCQLLLINSLKKKIIKEIQKLPK 197

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE+ +L + +      +  L+E+G+   V   R+ Q+ + AI++L+
Sbjct: 198 REKILLNLYYQ----QELNLKEIGEVLGVGESRVSQLHSLAIKRLR 239


>gi|332708995|ref|ZP_08428965.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
 gi|332352184|gb|EGJ31754.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
          Length = 258

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 116/248 (46%), Gaps = 15/248 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           + +  +      + ++V  NL LV   A  +  +    + DL+Q G IGL+ A E+FD  
Sbjct: 17  LQKYQQYPDPELRNQLVALNLGLVRREAHHWVKQCNESYEDLLQVGCIGLIVAIERFDST 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D+  +IRIP        K V   + +   + R+PT EE
Sbjct: 77  KGIAFSSFAIPYIRGEIQHYLRDRGYSIRIPRRWLALRQKSVEITQNLRATLNRQPTEEE 136

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           IA  L + +E  +++      +EP+SL+TP+   ++  + LG+ + D    S   +    
Sbjct: 137 IAAALNISLEEWQEITLAHQNREPLSLDTPVGDSEDRNTSLGELVPDPRYRSFQLAQEDQ 196

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK---AI 664
                  + LA L  R   VL   F      D T +EV ++  ++   + +   K   A+
Sbjct: 197 I---RIQQALAHLEKRTREVLEFVFLH----DLTQKEVAQRLDISVVTVSRRVKKGLEAL 249

Query: 665 RKLKHPSR 672
           +KL  P++
Sbjct: 250 QKLMTPTQ 257


>gi|300864899|ref|ZP_07109744.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
 gi|300337103|emb|CBN54894.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
          Length = 292

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 113/242 (46%), Gaps = 12/242 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           +    +  ++  + E+V+ N+ LV      + ++    + DL+Q G+IGL++A E+FD  
Sbjct: 54  LREYQQAPSNEVRNELVKLNIGLVRKEVHHWLHQCTESYDDLLQVGSIGLIRAIERFDMS 113

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D+S ++R+P H      +     + +  ++ R PT  E
Sbjct: 114 KGNAFSSFAIPYIRGEIQHYLRDKSPSVRVPRHWLTLERQSSSIVKDLQVRLNRHPTDIE 173

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQA 607
           +A  L + V   +++      + P+SL+ P+ DE+   + LG+ + D    S   +    
Sbjct: 174 VATALNISVGEWQEIKLACRNRSPLSLDAPLQDEEEGATCLGELVPDNRYRSFQLAQED- 232

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R    + LA L  R   +L   F      D T +E  ++  ++   + +   K +  L
Sbjct: 233 --RIRLQQALAKLEERTREILEFVFL----YDLTQKETAERLGISAVTVSRRVKKGLDSL 286

Query: 668 KH 669
           K 
Sbjct: 287 KE 288


>gi|87119467|ref|ZP_01075364.1| flagellar biosynthesis sigma factor FliA [Marinomonas sp. MED121]
 gi|86164943|gb|EAQ66211.1| flagellar biosynthesis sigma factor FliA [Marinomonas sp. MED121]
          Length = 244

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 50/228 (21%), Positives = 102/228 (44%), Gaps = 15/228 (6%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++++    LV  +A     R    ++  DLIQ G +GL++A ++F+   G  F TYA  
Sbjct: 19  DQIIDEYGFLVKKIAYHLLARLPSSVELDDLIQAGMMGLIEAFKRFESTKGASFETYAGI 78

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ +I   +         P  +R     +    + +  K+ RE +  EI++ + + +  
Sbjct: 79  RIRGSIMDEVRKSDW---APRSVRRNGRAIASAIKELEAKLGREASDLEISQAMDISLNE 135

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLASL 620
             ++L+ +   +S +    +E     G  IE  +       +   +L  +    + + SL
Sbjct: 136 YHEMLQSS---MSTQLFSFEELLDSEGLNIETDSEEDSAPYSFVEDLGFQTQLAQEIDSL 192

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +    N +  L+E+G    V+  R+ QI ++A  +LK
Sbjct: 193 PEREKLVLSLYY----NDELNLKEIGSVLGVSESRVSQIHSQAAMRLK 236


>gi|297746525|emb|CAZ60980.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 238

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/279 (17%), Positives = 94/279 (33%), Gaps = 46/279 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +  E+ E + D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGESSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              V  + + +L+   +++ I  ETG+SI + + I   +
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIGQIKDINRRM 235


>gi|77463598|ref|YP_353102.1| sigma factor FliA (sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126462430|ref|YP_001043544.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332558454|ref|ZP_08412776.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
 gi|77388016|gb|ABA79201.1| sigma factor FliA (Sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126104094|gb|ABN76772.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332276166|gb|EGJ21481.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
          Length = 239

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 106/236 (44%), Gaps = 14/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E +   + +V A++ LV  +A        R ++  DLIQ G +GL+ A+ +++   
Sbjct: 5   RGYAEQTQTPERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPRE 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+ YA   ++ +I   +   S   R  + M+    KV    +R+  ++ R P   E+
Sbjct: 65  GVSFAAYAAIRIRGSIMDFLRSNSALCRTTILMQQ---KVKAAVQRLEGRLMRAPETPEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L+MPV   +  L       +       +D S L +     +  S  D    + +R  
Sbjct: 122 AAELSMPVGEYQDWLAQFAGSQTASLDEVYDDQSALFE----GHDPSAEDRLQASQMRGL 177

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  +  RE  +L++ F      +  + EVG+   VT  R+ QI+  AI +L+
Sbjct: 178 LRQALGRMPEREALLLQLIFV----EELNVYEVGEILGVTTGRVSQIKKAAIERLR 229


>gi|284050443|ref|ZP_06380653.1| RNA polymerase sigma factor SigF [Arthrospira platensis str.
           Paraca]
 gi|291567732|dbj|BAI90004.1| group 3 RNA polymerase sigma factor SigF [Arthrospira platensis
           NIES-39]
          Length = 261

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 112/248 (45%), Gaps = 14/248 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKA 484
           E   ++         ++  + ++V+ N+ LV      + N+    + DL+Q G IGL++A
Sbjct: 12  ESLELLR--EYQHSPSNSIRNQLVQINIGLVRKEVHHWLNQCTESYDDLLQVGCIGLIRA 69

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E+FD   G+ FS++A+ +++  I   + D+S ++R+P      + K     + +  K+ 
Sbjct: 70  IERFDMSKGHAFSSFAIPYIRGEIQHYLRDKSPSVRVPRQWLTLLRKATPCIQELQVKLG 129

Query: 545 REPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSP 600
           R+PT  EIA  L + VE     K+    +  +SL+ PI DE+   + LGD + D    S 
Sbjct: 130 RKPTDVEIASALEISVEEWNQVKLASQNRSLLSLDAPIQDEEEGSTSLGDLVPDTRYRSF 189

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             +           + L  L     +VL   F      D T +E  ++  ++   + +  
Sbjct: 190 QLAQEDQI---RLQQALGHLEDGTRKVLEFVFL----YDLTQKETAEKLGISAVTVSRRV 242

Query: 661 AKAIRKLK 668
            + +  LK
Sbjct: 243 KRGLSLLK 250


>gi|77457790|ref|YP_347295.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens Pf0-1]
 gi|77381793|gb|ABA73306.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           fluorescens Pf0-1]
          Length = 246

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +   +  A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   MNFYKKSARDAQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDA 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  SKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRSIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQAN 608
           E+A +L + ++    +L  T            +D  H G   ED  +  + P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASAHLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|211906943|gb|ACJ11990.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906945|gb|ACJ11991.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906947|gb|ACJ11992.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906949|gb|ACJ11993.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
          Length = 222

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 97/226 (42%), Gaps = 4/226 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 1   EKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 120

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           P   +IA  + +  E V + +++ K   +L      E  S               D   +
Sbjct: 121 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFER 180

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            N R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 181 VNQRMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDIS 222


>gi|330808235|ref|YP_004352697.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327376343|gb|AEA67693.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 247

 Score =  102 bits (253), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 95/237 (40%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G
Sbjct: 10  YKKSARDAQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSNKYDASKG 69

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ A+   +         P  +      V    R +  K  R+    E+A
Sbjct: 70  ASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDHEVA 126

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA--IQANLRE 611
            +L + ++    +L  T            +D  H G   ED  +     S        + 
Sbjct: 127 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDNASAHMEPSRDLEDERFQS 185

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 186 ALAEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 238


>gi|288942618|ref|YP_003444858.1| RNA polymerase sigma-28 subunit FliA/WhiG [Allochromatium vinosum
           DSM 180]
 gi|288897990|gb|ADC63826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Allochromatium vinosum
           DSM 180]
          Length = 248

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 96/240 (40%), Gaps = 11/240 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
           +  R G   A      +V  ++ LV  +A     R    +Q  DLIQ G +GL++AA +F
Sbjct: 4   ARSRMGYASAGDEAARLVSEHVDLVRRIAHHLVARLPASVQVEDLIQSGMVGLIEAARQF 63

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
               G  F+TYA   V+ A+   +         P  +     ++     ++ ++  R  +
Sbjct: 64  QTGQGATFATYAGIRVRGAMIDELRRADW---TPRSVHRNSRRIAEAIHQVESREGRAAS 120

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             EIA+ L + ++    +L+ T     L       + +    F+             +  
Sbjct: 121 DREIAETLGVTLDDYHGMLQDTASCQILGLEDLFGEDADSDRFLPGAGTAPTEQL-EREQ 179

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +     LA L  RE  VL     +  + +  L E+G    VT  R+ QI ++A+ +L+
Sbjct: 180 FAQALAEALADLPERERLVL----ALYYDEELNLREIGAVLDVTESRVSQIRSQALHRLR 235


>gi|121997280|ref|YP_001002067.1| FliA/WhiG family RNA polymerase sigma factor [Halorhodospira
           halophila SL1]
 gi|121588685|gb|ABM61265.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Halorhodospira
           halophila SL1]
          Length = 247

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 52/237 (21%), Positives = 93/237 (39%), Gaps = 12/237 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                A    +++V  +  LV  +A    +R    +Q  DLIQ G IGL++AA ++D   
Sbjct: 6   MYTAVAQQGDEDLVTRHASLVKRIAHHLASRLPPSVQLEDLIQAGMIGLLEAARQYDSSQ 65

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   +         P  +  K  +V    R + ++  R+    E+
Sbjct: 66  GASFQTYAGIRIRGAMLDEMRRLDW---TPRSVHRKGREVAEAIRTIEHQTGRDARDHEV 122

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ L + V     +L+           I  ED           +   PL        +  
Sbjct: 123 AEALGISVAEYHNILQDVSSAKVFS--IDQEDPGTGEPHEPAGHEPGPLAMLQDEAFQGE 180

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +  L  RE  V+     +  + +  L E+G+   V+  R+ QI  + + KL++
Sbjct: 181 LAEAIRELPERERLVM----ALYYDEELNLREIGEVLGVSESRVSQIHGRIMLKLRN 233


>gi|307717596|gb|ADN88851.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717598|gb|ADN88852.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717600|gb|ADN88853.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717602|gb|ADN88854.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 96/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 220


>gi|170078529|ref|YP_001735167.1| RNA polymerase sigma factor SigF [Synechococcus sp. PCC 7002]
 gi|5359699|gb|AAD42767.1|AF121848_2 SigF [Synechococcus sp. PCC 7002]
 gi|169886198|gb|ACA99911.1| SigF [Synechococcus sp. PCC 7002]
          Length = 259

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 105/242 (43%), Gaps = 12/242 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           +    + +    + ++V  N+ LV   A  ++ +    F DL+Q G++GL++A E+F   
Sbjct: 20  LQEYRQSQDVKIRNQIVSLNIGLVRKEAHHWSRQCSENFDDLMQVGSLGLLRAIERFTLE 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A  +++  I   + D+S T+RIP  M     +  R       +  R+P+  E
Sbjct: 80  RGNAFSSFANPYIRGEIQHYLRDKSSTVRIPRRMLQLRQQSNRFIHTFRQEHNRQPSAIE 139

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQA 607
           IA+ L + V   + +      ++P+SL+  +  +  + + LGD + D    S   +    
Sbjct: 140 IAEHLNISVTEWQSINLAYQNRDPVSLDVSVKADQGENTSLGDLVPDPGYKSFQLAIEDQ 199

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  + LA L     +VL   F      D T +E      V+   + +   K I  L
Sbjct: 200 I---RIQQGLAQLEEHTRKVLEFVFLH----DLTQKEAADLLGVSVITVSRRIKKGINSL 252

Query: 668 KH 669
           K 
Sbjct: 253 KK 254


>gi|307717634|gb|ADN88870.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 97/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVNYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F      + + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTF----IENRSQKETGELLDIS 220


>gi|303326430|ref|ZP_07356873.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
 gi|302864346|gb|EFL87277.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
          Length = 260

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 105/239 (43%), Gaps = 20/239 (8%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            E  +S  ++E+V      +  +A +  +   R ++  ++I  G +GLM+A  KF   LG
Sbjct: 24  WEDFSSAEQEEVVRHYAPKIRFLALRLKSKLPRSVELGEMISSGTLGLMEALGKFRPQLG 83

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F TYA   ++ A+   +         P  +R ++  +    R++ ++  R+ T EE+ 
Sbjct: 84  IRFETYAENRIRGAMLDELRRLDW---FPRSLRQRVRVLDEAMRKVEHEQGRQATEEELQ 140

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               + +  VR+ L+  +  + L           + D +      S  +      LRE  
Sbjct: 141 DITGLELRDVRQGLEALQNQLWLSL-------DAIQDTLAGDGPESGGEPYSNTALRELV 193

Query: 614 TRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RV   +  LTPRE+ VL + +      +  + E  +   +T  R+ Q+ ++A+ +L+ 
Sbjct: 194 ERVAPLIERLTPREKLVLSLYY----TDELNMRETAEIMGITEGRVSQLHSQALGRLRK 248


>gi|85679195|gb|ABC72014.1| SigB [Listeria monocytogenes]
 gi|85679205|gb|ABC72019.1| SigB [Listeria monocytogenes]
 gi|85679211|gb|ABC72022.1| SigB [Listeria monocytogenes]
 gi|85679213|gb|ABC72023.1| SigB [Listeria monocytogenes]
 gi|307717608|gb|ADN88857.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717616|gb|ADN88861.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 96/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQFTFIEN----RSQKETGELLDIS 220


>gi|94264039|ref|ZP_01287839.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|94266375|ref|ZP_01290074.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93453027|gb|EAT03515.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93455550|gb|EAT05737.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 256

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 53/252 (21%), Positives = 110/252 (43%), Gaps = 16/252 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
            +   + E      + E++     L+  +A +  +R    +   DLI  G +GL+ A  K
Sbjct: 10  NAYFSRNEQFDPARRDELILTYTPLIKYIASRLASRLPPQVAVDDLISCGIVGLIDAINK 69

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     +F TYA + +K A+   +        +P  +R KI ++ + +  + +K+ R P
Sbjct: 70  FDPAKNVQFKTYAEFRIKGAMLDELRALDW---VPRSVRRKITELEKISGELESKLGRPP 126

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLE-----TPIGDEDTSHLGDFIEDKNAVSPLD 602
             EE A  L + +    ++L  TK    L+     + + DE    +G+    ++   P  
Sbjct: 127 DDEETAAALGIELADFHRLLDETKSVTFLDIDYLRSKVPDEIEGDVGEIFA-RDDKDPFT 185

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +      R    + +  L  +E+  +     +  + + T++E+G+    T  RI Q+ +K
Sbjct: 186 ALNLGETRNLLAKAIGELPEKEKLTV----ALYYHEELTMKEIGEVLGYTESRISQMHSK 241

Query: 663 AIRKLKHPSRSK 674
           A+ +L+   + +
Sbjct: 242 AMLRLRAKLKKQ 253


>gi|150387863|ref|YP_001317912.1| RinA family phage transcriptional regulator [Alkaliphilus
           metalliredigens QYMF]
 gi|149947725|gb|ABR46253.1| phage transcriptional regulator, RinA family [Alkaliphilus
           metalliredigens QYMF]
          Length = 266

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 114/241 (47%), Gaps = 14/241 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +   E +    + E+V   L +   ++KK+ N+G+ + D+ Q  ++GL+ A E+FD   G
Sbjct: 28  IEYQENKKVEVRNELVNRYLYIAEILSKKFLNKGIDYEDIYQVASLGLIYAIERFDLSRG 87

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FS++A   +   I +   D+  +IR+P  +++   KV      +   ++R P  ++IA
Sbjct: 88  FEFSSFATPTIIGEIKKHFRDKGWSIRVPRRIQELSKKVNTAKMTLHQNLQRTPMIKDIA 147

Query: 554 KKLAMPVEGVRKVLKIT--KEPISLETPIGDED---TSHLGDFIEDKNAVSPLDSAIQAN 608
           + L    E V + ++ +    P SL+    ++       L D I +K+      +  +  
Sbjct: 148 EYLNCTQEEVMEAMEASQVYTPKSLDLTYDNDGEDKDIQLIDLIGEKD-----KNFDEIE 202

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R+   + + +L   E++VL  RF        T   V ++  V++  + ++E + I K +
Sbjct: 203 NRDFLKKAMRNLNEVEKKVLEDRFF----NSKTQMNVAEELNVSQMTVSRMEKRIIEKFR 258

Query: 669 H 669
            
Sbjct: 259 K 259


>gi|269792915|ref|YP_003317819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100550|gb|ACZ19537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 245

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 99/229 (43%), Gaps = 13/229 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +V+  + LV  VA +       GL + D++  G +GL+ A ++FD   G+ F T+A+
Sbjct: 21  RERIVKRYIPLVKYVAGRMAVTPPPGLDYDDILSFGVMGLLDAMDRFDPSRGFCFQTFAV 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +       R       +    +  A   +         E + ++L M  +
Sbjct: 81  PRIRGAILDELRRYDWISRTGRDKLQR----LERAMEEAAAEGTLLDDEALMERLGMNEK 136

Query: 562 GVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             R++L+I      +SL+  +G ED     D + +  + SP +   +        R L  
Sbjct: 137 SYRELLEIASRSYVVSLDEVLGLEDGEVKRDGLLEDPSPSPQEEVERREELALVRRALEE 196

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  RE  +L + +  G     TL+EVG    VT  R  Q+  +AI  L+
Sbjct: 197 LPERERLLLSLYYQEG----LTLKEVGAVLGVTESRASQLHGRAIAMLR 241


>gi|51246530|ref|YP_066414.1| RNA polymerase sigma factor (FliA) [Desulfotalea psychrophila
           LSv54]
 gi|50877567|emb|CAG37407.1| related to RNA polymerase sigma factor (FliA) [Desulfotalea
           psychrophila LSv54]
          Length = 245

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 105/236 (44%), Gaps = 14/236 (5%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++V+ +L LV  +  +  ++   F    D+   G  GL  A++KFD      F T+A +
Sbjct: 15  NQLVDDHLYLVDILVSRMVSQVPSFMSRDDMRSAGMFGLFDASKKFDASKNILFKTFAEY 74

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   +            +RDK +K+ R    +  K+ R+P   EIA+ L M ++ 
Sbjct: 75  RIRGAIFDEMRKLDWF---SRSLRDKHNKIGRAILALELKLGRDPEEFEIAQSLNMNLDA 131

Query: 563 VRKVLKITKE--PISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAI-QANLRETTTRVLA 618
              +L        +SL   + +        D + DK   +   + I Q  L      +L 
Sbjct: 132 YHNLLGQVSHLGCVSLNEVLDNSQEGRSFLDSLVDKRKNNTPTAFIEQQELNIKIAEILD 191

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            L+ +E+ V+ + +      + + +E+ +   V+  RI Q+ ++++ KLK   +++
Sbjct: 192 QLSEKEKLVISLYY----YEELSQKEIAEVIGVSEGRISQLHSQSLIKLKLKMQNQ 243


>gi|307717642|gb|ADN88874.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 96/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 220


>gi|293604981|ref|ZP_06687378.1| DNA-directed RNA polymerase sigma subunit FliA [Achromobacter
           piechaudii ATCC 43553]
 gi|292816809|gb|EFF75893.1| DNA-directed RNA polymerase sigma subunit FliA [Achromobacter
           piechaudii ATCC 43553]
          Length = 251

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 105/237 (44%), Gaps = 18/237 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A   +VE    LV  +A +   R    ++  DLIQ G IGL+ A  ++      +F T
Sbjct: 2   PHADDSLVE-YAPLVRKLALQLLARLPASVELDDLIQAGMIGLLDAVRRYQETADAQFET 60

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++ A+   +  Q     +P  +R K  K+ +  +++  ++ R PT  EIA +L M
Sbjct: 61  YATTRIRGAMLDELRGQDW---LPRSVRTKARKIEQAIQQLEQRLMRAPTEAEIAAQLEM 117

Query: 559 PVEGVRKVLKITKEPISL---ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL----RE 611
           P+   + +L   +    +   +     +  S   D+    N  S   + + A L    R+
Sbjct: 118 PIGEYQSLLHDAQGVQIVHYEDFTTEPDSASGQSDWTATLNHGSAGGNPLDALLAGDFRQ 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + +L  RE+ +L + +  G      L+E+G    VT  R+ Q+ ++A  +++
Sbjct: 178 ALVHAIDALPDREKLLLSLCYEQG----LNLKEIGAIMNVTEARVCQLRSQATARIR 230


>gi|225164039|ref|ZP_03726324.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
 gi|224801345|gb|EEG19656.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
          Length = 274

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 97/241 (40%), Gaps = 20/241 (8%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               ++ ++E  L LV +V  +        ++  DL   G  GL+ A +++D   G  F+
Sbjct: 32  DRDDEQTLIERYLPLVRNVVDRIKMNLPAHVEVEDLYSVGVTGLLAAIQRYDPEQGNTFA 91

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA   ++ A+   +         P   R K  K+      +  +  R  T  E+++ L 
Sbjct: 92  GYATLRIRGAVLDELRRLDWC---PRRARAKARKIKDAIGELEQRHGRAVTDAEVSEHLG 148

Query: 558 MPVEGVRKVLKITKEP--ISLETPIGDEDTS--------HLGDFIEDKNAVSPLDSAIQA 607
           + +      L+ ++    ++++ P   +D           L + I DKN     +   + 
Sbjct: 149 ISLHDYAHWLEESRPVTFVAIDQPASGDDGGSSGGGSGVSLHEVIADKNDTPVRERMEKE 208

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            + +   + +  L   ++R+L M +         L E+   F +T  RI QI ++A+  L
Sbjct: 209 EVWQLIAQRITELPDIQKRILAMYYFEN----MRLAEIAAVFRLTESRICQIHSQAVLTL 264

Query: 668 K 668
           +
Sbjct: 265 R 265


>gi|2853597|gb|AAC08061.1| FliA [Pseudomonas putida]
          Length = 246

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 97/239 (40%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D  
Sbjct: 7   KMYSRAAKDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVSSKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAMRAVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQANL 609
           +A +L + ++    +L  T            +D  H G   ED  +  V P         
Sbjct: 124 VAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASGHVEPARGLEDERF 182

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   T  +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 183 QAALTEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|904172|gb|AAB38522.1| flagellin sigma factor [Yersinia enterocolitica (type O:8)]
          Length = 229

 Score =  101 bits (252), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 103/228 (45%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +   +   +  +      P  +R    +V    +++  ++    T +E+A+ L + + 
Sbjct: 63  QRI-APMLDELRQRDW---APRRLRRNAREVASAMQKVEQRLGAPATEQEVAQNLDIDLT 118

Query: 562 GVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             R++L  T            E+    +   +E     +PL   ++ NLR+     + +L
Sbjct: 119 EYRQILLDTNNSQLFSYDEWREEHGRTVEPMLEGHEDANPLQHLLEGNLRQRVIEAIEAL 178

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 179 PEREKMVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 222


>gi|257067128|ref|YP_003153384.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
 gi|256799008|gb|ACV29663.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
          Length = 343

 Score =  101 bits (252), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 86/343 (25%), Positives = 150/343 (43%), Gaps = 11/343 (3%)

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           +++  I+ +      +L     S  +  +  +   +G  L         D    E  +  
Sbjct: 3   DKMDKINLKDKKTLEKLQEYLNSEDLTEEEIISILEG--LTEEEKDEIMDIISDEVDDDD 60

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIV--SMVRKGECEASIAKKEMVEANLRLVI 457
             +     K      SI   +   + E   +    +V + +     A   +VE N  LV 
Sbjct: 61  EDDDFEERKTNVSKASIMPISRRDMIELSDLTNEQIVEQFQIGNQNALAALVEKNQGLVR 120

Query: 458 SVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           S A  +       L   DL+Q G +G+++AAEKFD  LGYKF+TYA  W+ +AI ++I  
Sbjct: 121 SRASYFFRSHGNDLDLEDLVQSGMLGMIRAAEKFDLSLGYKFTTYAYKWIDKAIRKAINK 180

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE-PTPEEIAKKLAMPVEGVRKVLKITKEP 573
           +  TIRIP     K++K+ +  +        E     E         + +  + +     
Sbjct: 181 EGHTIRIPAGKYLKLNKLKQILKANPEASDEELYRILEKEGIDKKQADDLFLINRNQVNS 240

Query: 574 ISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            SL   +  ED++   L D + D++        ++ ++     + L  LT RE++++  R
Sbjct: 241 TSLNINLDSEDSTGDELMDMVGDESTP-VDMLILEKDMENFLLKALDQLTDREKQIIIFR 299

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +G+      TLEE+GK + ++RERIRQIE +A+ KLK  S  +
Sbjct: 300 YGLDNEKPKTLEEIGKIYDLSRERIRQIENQALGKLKEFSERE 342


>gi|88858091|ref|ZP_01132733.1| flagellar biosynthesis sigma factor FliA [Pseudoalteromonas
           tunicata D2]
 gi|88819708|gb|EAR29521.1| flagellar biosynthesis sigma factor FliA [Pseudoalteromonas
           tunicata D2]
          Length = 227

 Score =  101 bits (252), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 100/226 (44%), Gaps = 14/226 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++E ++ LV  +A     R    +Q  DL Q G IGL++AA+ FD   G  F TYA   +
Sbjct: 4   LIERHVSLVKRIAYHLLARLPASVQLDDLTQSGMIGLIEAAKNFDGTKGASFETYAGIRI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +      V +    +  ++ RE    E+A+KL + +    
Sbjct: 64  RGAMLDEIRKGDW---VPRSVHKNARMVAQATAELEAELGREVKDVEVAEKLDITLNEYH 120

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            +L    +   I +E    DED  H  D +   ++        + NL  +    + SL  
Sbjct: 121 DILNDVNSGRIIGIEDLGVDEDVLHSDDQVHAFDSPFNHTQTEKFNL--SLVEAIKSLPE 178

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+  VL + +    N +  L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 179 RDALVLSLYY----NDEMNLKEIGLILEVSESRVSQIHGQAMVKLK 220


>gi|303326435|ref|ZP_07356878.1| flagellar biosynthesis protein FlhG [Desulfovibrio sp. 3_1_syn3]
 gi|302864351|gb|EFL87282.1| flagellar biosynthesis protein FlhG [Desulfovibrio sp. 3_1_syn3]
          Length = 555

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 100/240 (41%), Gaps = 24/240 (10%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            E  +   ++ +       +  +A +   R    ++  +L+  G +GL++A   F    G
Sbjct: 316 WEDFSPAEREVVARHYAPRIRPLALRLKARLPFHVELDELLGAGALGLVEALCNFRPERG 375

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  YA   ++ A+   +  Q     +P  +R  + ++    R +     R+ T EE+ 
Sbjct: 376 VCFERYAENRIRGAMLDELRRQDW---LPRSLRRAMRRLDEARRMVERGRGRQATEEELL 432

Query: 554 KKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDK---NAVSPLDSAIQAN 608
               +    +R  ++    ++  SL+          + D +       A  P  +A+   
Sbjct: 433 SMTGLEPRTLRYAMEALEARQFFSLDA---------IQDSLAADGPGGADEPCHTAVMRE 483

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L E   R+LA LTPRE+ VL + +  G     T+ E  +   +T  R+ Q+ A+A+ +L+
Sbjct: 484 LAEHMERLLARLTPREKMVLSLYYTDG----LTMREAAEVMSITECRVSQLHAQALARLR 539


>gi|254517024|ref|ZP_05129082.1| flagellar biosynthesis sigma factor FliA [gamma proteobacterium
           NOR5-3]
 gi|219674529|gb|EED30897.1| flagellar biosynthesis sigma factor FliA [gamma proteobacterium
           NOR5-3]
          Length = 243

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 102/228 (44%), Gaps = 24/228 (10%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V   L LV  +  +   +    ++  DL+Q G IGL++A E +D   G  FSTYA   +
Sbjct: 25  LVREYLPLVKKIGLRLAAKLPAEIELDDLMQVGLIGLLRARESYDAAQGASFSTYAGIRI 84

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           K A+   I        +P  ++ ++ +V     R   ++ R     EIA +L MP++  +
Sbjct: 85  KGAMLDEIRSHDW---LPRSVQSQLRQVSEAIDRADARLGRPANDAEIAGELDMPLDEYQ 141

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV----SPLDSAIQANLRETTTRVLASL 620
           +          L   +     +H+ D +E + AV    +PLD   +   RE     +  L
Sbjct: 142 Q----------LSGQLACARMTHIEDSVEAETAVLNTHTPLDEVGEEGFREALAESVTQL 191

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +E  ++ + +  G      L+E+G    V+  R+ Q+  +A+ +L+
Sbjct: 192 PEKERLMMSLYYSEG----LNLKEIGAVLGVSESRVSQLHGQALARLR 235


>gi|331092383|ref|ZP_08341209.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401407|gb|EGG80993.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 237

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 114/243 (46%), Gaps = 8/243 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             H ++++++       A+ ++VE N+ LV  V K++  RG +  DL Q G+IGL+KA +
Sbjct: 1   MEHTIALIKRSHKGDEKARTQLVEENVGLVWCVVKRFYGRGTEPEDLFQIGSIGLLKAID 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD     KFSTYA+  +   I R + D    I++   +++  +K       M  ++ RE
Sbjct: 61  KFDLSYDVKFSTYAVPMISGEIKRFLRD-DGMIKVSRSLKELAYKAYLAKEEMKERLNRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT EE+A+KL +  E +   L+   E  SL  PI  +D + +   ++        +  I 
Sbjct: 120 PTVEELAEKLEVEKEELALALESGGEVESLHKPIYQKDGNEIQ-LMDKLEEKEEQEEKIL 178

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            ++             R+         +    + T  E+GK   +++ ++ ++E K +  
Sbjct: 179 NHMLLQQLLEQLKKEERQ------LIYMRYFANKTQSEIGKTMGISQVQVSRLEKKILGY 232

Query: 667 LKH 669
           L+ 
Sbjct: 233 LRE 235


>gi|17231345|ref|NP_487893.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17132987|dbj|BAB75552.1| group 3 sigma 37-type sigma factor [Nostoc sp. PCC 7120]
          Length = 258

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 120/254 (47%), Gaps = 14/254 (5%)

Query: 425 SEFR-HIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGL 481
           +E +  I  ++R+ +   +   + ++V+ NL LV   A  + N+    + DL+Q G +GL
Sbjct: 7   NELKYEIWQLLREYQQSRSETVRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQVGCLGL 66

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A E+F+   G+ FS++A+ +++  I   + D+  T+RIP        + +  +R +  
Sbjct: 67  IRAIERFEIAKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIPRRYLAIQQRAIGVSRSLRE 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNA 597
           +  R+PT  E+A  L +  +  +++    + + P+SL+ P+ D  E  + LG+ + D + 
Sbjct: 127 QYNRQPTDSELATALEISPDEWQEIKLAWVNRAPLSLDVPVQDGEEGATSLGELVPDHHY 186

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S   +           + L  L  R   VL   F      D T ++V +   ++   + 
Sbjct: 187 RSFQLAQEDQI---RLQQALFQLEQRTREVLECVFL----QDLTQKQVAEHLGISVVTVS 239

Query: 658 QIEAKAIRKLKHPS 671
           +   K +  LKH  
Sbjct: 240 RRVKKGLDLLKHLM 253


>gi|297746527|emb|CAZ60981.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 242

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 51/286 (17%), Positives = 99/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +  E+ E + D+ +      ++       
Sbjct: 36  -ESDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGESSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|315001596|emb|CBI75433.1| RNA polymerase sigma factor [Aeromonas bestiarum]
          Length = 242

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 50/286 (17%), Positives = 98/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +   + E + D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDXDGESSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|297746535|emb|CAZ60985.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 242

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 49/286 (17%), Positives = 97/286 (33%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +   + +   D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDGDGDDADDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|297746529|emb|CAZ60982.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|297746531|emb|CAZ60983.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|315001594|emb|CBI75432.1| RNA polymerase sigma factor [Aeromonas bestiarum]
 gi|315001598|emb|CBI75434.1| RNA polymerase sigma factor [Aeromonas bestiarum]
 gi|315001600|emb|CBI75435.1| RNA polymerase sigma factor [Aeromonas bestiarum]
          Length = 242

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 51/286 (17%), Positives = 99/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +  E+ E + D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGESSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|146344354|ref|YP_001202210.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
 gi|146188166|emb|CAM96497.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
          Length = 533

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 78/420 (18%), Positives = 162/420 (38%), Gaps = 22/420 (5%)

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQ----DNAVNGQKDEKSSVKCKVLKEKLVKLV 325
           SA E     K +      + V R+L +++    +      +    ++    ++++L   +
Sbjct: 116 SAKEAHKNAKAIADQKFASLVRRKLNTIRTLISELRGYAAEGMDGTLFSAAVRDELRLKL 175

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWV 384
             +      ++   +Q     K +     +L++ +     I +        G    P  +
Sbjct: 176 AEIVPYDYILNRAADQFRVNCKELSARTRDLIKFICDEVRISKIKVEGIISGNWTSPKLI 235

Query: 385 SYAKDFPEGEWKNFVACEVDS----ILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
                    E K F    +      I   +  I   +        +     S+  + + +
Sbjct: 236 PALLISGGYELKLFPPAAMKKLRLGITSRQQAILDAASTGEAPAIDILSAWSVFNRVDRD 295

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
                     AN+RLV     ++  R           N+GL +A  +F   +G++FST A
Sbjct: 296 IEKCADIFTNANVRLVEQQIGRF--RFADKEIARSAANMGLTRAVYRFAPEMGFRFSTIA 353

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           + W+  +I+R +ADQ           + +HK  R    M  + +   +   +A+   +  
Sbjct: 354 LTWINVSISRDLADQESIRLP-----EGMHKHRRMISNML-RDQPNVSINSLAEATKLEQ 407

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           + VR ++       S++T     D+S    L + + D N    +      ++R+     L
Sbjct: 408 DVVRDLVHFAGGQRSIDTAFQGTDSSDADGLHELLADTN-NDFMSEIEDDSMRQFVESAL 466

Query: 618 -ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              LT RE  V+  RFG+G   + TL E+  +  +++ER+RQ+E +A+ K++    ++ L
Sbjct: 467 GDVLTQREIFVIVNRFGMGDAREKTLAELSVEMNLSKERVRQLEIQALSKIRDSEFAETL 526


>gi|154484618|ref|ZP_02027066.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
 gi|149734466|gb|EDM50383.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
          Length = 237

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 119/242 (49%), Gaps = 11/242 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++++ +      +A+ +++  N  L+ S+ +++ NRG +  DL Q G IG++KA ++F
Sbjct: 2   DTLTLINRAHQGDKLARDKILIENTGLIWSIVRRFLNRGHEGEDLFQIGCIGMLKAIDRF 61

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D      FSTYA+  +   I R I D    ++I   +++   K++       N+ K+EPT
Sbjct: 62  DTEFDVAFSTYAVPMIAGEIRRFIRD-DGIVKISRKIKENQMKIMHQREIYINEKKQEPT 120

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQA 607
            EE+ K   +  E +   +  ++   S++  +  +D+++ L D  ED   +         
Sbjct: 121 IEELEKVCDLTKEEIVMAMDASRNVESIDKEMYSKDSAYTLMDLAEDDTNIEETVLN--- 177

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +    +++  L  +E +++ +R+        T  +V K+  +T+ ++ ++E K +  +
Sbjct: 178 --KIMVQQLMDMLESKERKIINLRYFKN----KTQSQVAKEMGMTQVQVSRLEKKILNSM 231

Query: 668 KH 669
           ++
Sbjct: 232 RN 233


>gi|312879616|ref|ZP_07739416.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
 gi|310782907|gb|EFQ23305.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
          Length = 247

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 62/221 (28%), Positives = 100/221 (45%), Gaps = 13/221 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+ +V   L LV  VA +       GL F DL+  G +GL+ A E+FD   G+ F T+A+
Sbjct: 21  KERLVRRYLPLVRYVAGRMAVSPPPGLDFEDLLSFGAMGLLDAIERFDLDRGFCFQTFAV 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +        I    R+K+ K+ RT  R +      P  E +   L M  +
Sbjct: 81  PRIRGAILDELRRYDW---ISRTGREKLQKLERTVERFARTQGN-PDDETLMDALGMNEK 136

Query: 562 GVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +++L+I      +SL+  +  ED     + I + +A SPLD   Q    +     L+ 
Sbjct: 137 AYKELLEIASRSYVVSLDEVLALEDGDVQREGILEDDAPSPLDRMEQKEEVDRVLAGLSE 196

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           L  RE  ++ + +  G     TL+E+G    VT  R  Q+ 
Sbjct: 197 LPERERLLISLYYYEG----LTLKEIGGVLGVTESRASQLH 233


>gi|315001602|emb|CBI75436.1| RNA polymerase sigma factor [Aeromonas piscicola]
 gi|315001604|emb|CBI75437.1| RNA polymerase sigma factor [Aeromonas piscicola]
 gi|315001606|emb|CBI75438.1| RNA polymerase sigma factor [Aeromonas piscicola]
 gi|315001608|emb|CBI75439.1| RNA polymerase sigma factor [Aeromonas piscicola]
 gi|315001908|emb|CBI75440.1| RNA polymerase sigma factor [Aeromonas piscicola]
          Length = 242

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 50/286 (17%), Positives = 99/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +  ++ E + D+ +      ++       
Sbjct: 36  -EADDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGESSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +  W
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-W 196

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              +    + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 197 SPRLVDMDEEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|307564926|ref|ZP_07627446.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
 gi|307346366|gb|EFN91683.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
          Length = 228

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 70/264 (26%), Positives = 112/264 (42%), Gaps = 43/264 (16%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             I  I  E  +S  E   + + ++      + A +++ +ANL  V+S+A +Y  +GL  
Sbjct: 6   KYIGDIIGENLLSDEEEVQLSNRIK---IGDAKALEKLTKANLTFVVSIAHQYKEQGLDE 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA+KFD   G +F  +A  ++++AI                      
Sbjct: 63  DDLISEGNIGMMYAAQKFDGSKGIRFVKFAAPYIRKAI---------------------- 100

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD--EDTSHL 588
                          E + +E      +P +  +   K   +P+SL+ PI     +   L
Sbjct: 101 ---------------EKSIKEQTTLYKVPKKENKLFEKKRAKPVSLDQPIPVGSNNKLTL 145

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + I + N     DS     L     + +  L  RE+ V+   +GI   T  T+ EV   
Sbjct: 146 QNLIPNNNNKDTDDSVNSNILNTILMQSINCLNEREKAVITQLYGIN-GTSLTMAEVATS 204

Query: 649 FCVTRERIRQIEAKAIRKLKHPSR 672
             + RER+RQI   A+RKL    R
Sbjct: 205 LGLKRERVRQIRNTALRKLYRKMR 228


>gi|90021809|ref|YP_527636.1| flagellar protein FliS [Saccharophagus degradans 2-40]
 gi|89951409|gb|ABD81424.1| RNA polymerase sigma factor, FliA/WhiG [Saccharophagus degradans
           2-40]
          Length = 250

 Score =  101 bits (251), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 96/235 (40%), Gaps = 13/235 (5%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           VE    LV  +A     R    +Q  DLIQ G +GL++AA+K+D   G  F TY+   ++
Sbjct: 24  VEDYAYLVKRIAHHMMARMPSCVQIEDLIQAGMLGLLEAAQKYDASKGASFETYSGIRIR 83

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            AI   +         P  +     +V      +  +  R+    EIA+++ + ++    
Sbjct: 84  GAIVDEMRRGDW---APRSVHRNSRRVAEAIATVEARHGRDARDHEIAEEMGLSLDEYYA 140

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN-LRETTTRVLASLTPRE 624
           + + +            E+     D  E  + +      +  N L       +  L  RE
Sbjct: 141 MARDSASTRLFSYEETYENDESRFDEYEPSDGLRGPSEQVHRNALYTDLVAAIGKLPERE 200

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             VL + +      +  L+E+G    V+  R+ QI ++A  +LK  SR +  +S+
Sbjct: 201 RLVLSLYY----EQEMNLKEIGLVLGVSESRVSQIHSQAALRLK--SRMQDWQSY 249


>gi|311105912|ref|YP_003978765.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans A8]
 gi|310760601|gb|ADP16050.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans A8]
          Length = 259

 Score =  101 bits (251), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 111/237 (46%), Gaps = 18/237 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A   +VE    LV  +A +   R    ++  DLIQ G IGL+ A  ++      +F T
Sbjct: 10  PHADDSLVE-YAPLVRKLALQLLARLPASVELDDLIQAGMIGLLDAVRRYQETADAQFET 68

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++ A+   +  Q     +P  +R K  K+ +  +++  ++ R P+  EIA++L M
Sbjct: 69  YATTRIRGAMLDELRGQDW---LPRSVRAKARKIEQAIQQLEQRLMRAPSEAEIAQQLDM 125

Query: 559 PVEGVRKVLKITK--EPISLETPIGDEDTSH-LGDFIEDKN----AVSPLDSAIQANLRE 611
           P+   + +L   +  + +  E    + D++    D+    N      +PLDS +  + R+
Sbjct: 126 PLGDYQSLLHDAQGVQIVHYEDFATEPDSASGQSDWAATLNHGAAGGNPLDSLLAGDFRQ 185

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + SL  RE+ +L + +  G      L+E+G    VT  R+ Q+ ++A  +++
Sbjct: 186 ALVHAIDSLPEREKLLLSLCYEQG----LNLKEIGAILNVTEARVCQLRSQATARIR 238


>gi|291196352|emb|CBG22648.1| DNA-directed RNA polymerase subunit D [Pseudomonas nitroreducens]
          Length = 239

 Score =  101 bits (251), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 98/284 (34%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++ + P     ++   + +      L ++  L   I P+          
Sbjct: 1   RIEEGIREVMSAIAQFPGAVDGILEEYNRIVAEGGRLSDV--LSGYIDPDDGTLPAEEV- 57

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                               E  G  + A    KD   + +    ++E +E +   D ++
Sbjct: 58  --------------------EPVGLKDDAEAKDKDKDEEDEESDGDSEEEEGDGGPDPEE 97

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ +QL                            +K  + S +       L +L
Sbjct: 98  AARRFGAVSEQLEKA---------------------KKALKKHGRGSKQATEELVALAEL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D+LV ++ D    +   E  +++L      + R  FL +  G E D  W
Sbjct: 137 FMPIKLVPKQFDVLVAKVRDALDSVRRQERAIMQLCVRDARMPRADFLRQFPGHETDTAW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           V       + ++   +    D IL+ + ++  +   + ++++E 
Sbjct: 197 VDSILK-GKPKYAEAIERLRDDILRNQQKLVDLETSSQLTVAEI 239


>gi|256831228|ref|YP_003159956.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
 gi|256580404|gb|ACU91540.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
          Length = 267

 Score =  101 bits (251), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 43/203 (21%), Positives = 83/203 (40%), Gaps = 10/203 (4%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            ++  DLI  G +GLM+A  KF   L  +F T+A   ++ A+   +            +R
Sbjct: 65  HIELSDLISAGTLGLMEALGKFQPELNIRFETFADSRIRGAMLDELRRMDWY---SRGLR 121

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            +I K+ +  R    +    PT  E+ +      + +   L+     I L      +  +
Sbjct: 122 QRIKKLEQVIRGFEQENGHAPTRSELLELTGQDRQELEATLEAVNSQIILSLDAIQDQWN 181

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             GD     N   P  +    ++ +    ++  L  RE+ VL + +      +  ++EV 
Sbjct: 182 QPGD---GGNHREPFAAVAFHDIIDKLGHLIDRLNEREKLVLSLYY----TEEFNMKEVA 234

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +T  R+ Q+ ++A+ KLK 
Sbjct: 235 LALDITEGRVSQLHSQALGKLKK 257


>gi|161898885|gb|ABX80432.1| SigB [Listeria monocytogenes]
          Length = 217

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 48/219 (21%), Positives = 94/219 (42%), Gaps = 4/219 (1%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 3   AAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 63  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 122

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 123 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 182

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 183 EKVLPVLDEREQKILQFTFIEN----RSQKETGELLDIS 217


>gi|261366790|ref|ZP_05979673.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
 gi|282571621|gb|EFB77156.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
          Length = 232

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 13/232 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E +E NL LV + A ++  RG+++ +L   G +GL+KA + FD   G  FSTYA+  +
Sbjct: 11  RAEFIEKNLGLVHACAGRFKGRGIEYEELYAAGCLGLVKACDGFDTSRGVCFSTYAVPVI 70

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D   T+++   +++   K+     R   K  +EP   ++A+ L    E + 
Sbjct: 71  LGEIKKLFRDGG-TVKVSRSLKELSLKINAERERCLKKTGQEPGVTQLAEILQTTPEQIA 129

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             ++ +   ISL TP  +ED     D   D    S  D       R     V+  L+P +
Sbjct: 130 LAIRASLPAISL-TPTDEEDGQREWDVPVDSPEESLSD-------RIGLAEVMEKLSPTD 181

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            +++R+RF  G     T  E  +    T+ +I + E K ++ ++     + L
Sbjct: 182 RQMIRLRFFGG----RTQSETARVLGTTQVQISRRERKVLKWMRAELLGESL 229


>gi|315001912|emb|CBI75442.1| RNA polymerase sigma factor [Aeromonas caviae]
          Length = 242

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 48/286 (16%), Positives = 100/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +  E+ + + D+ +      ++       
Sbjct: 36  -EVDDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              +  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|221639440|ref|YP_002525702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
 gi|221160221|gb|ACM01201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
          Length = 239

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 106/236 (44%), Gaps = 14/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +G  E +   + +V A++ LV  +A        R ++  DLIQ G +GL+ A+ +++   
Sbjct: 5   RGYAEQTQTPERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPRE 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F+ YA   ++ +I   +   S   R  + M+    KV    +R+  ++ R P   E+
Sbjct: 65  GVTFAAYAAIRIRGSIMDFLRSNSALCRTTILMQQ---KVKAAVQRLEGRLMRAPETPEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A +L+MPV   +  L       +       +D S L +     +  S  D    + +R  
Sbjct: 122 AAELSMPVGEYQDWLAQFAGSQTASLDEVYDDQSALFE----GHDPSAEDRLQASQMRGL 177

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  +  RE  +L++ F      +  + EVG+   VT  R+ QI+  AI +L+
Sbjct: 178 LRQALGRMPEREALLLQLIFV----EELNVYEVGEILGVTTGRVSQIKKAAIERLR 229


>gi|317403792|gb|EFV84272.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans C54]
          Length = 253

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 113/249 (45%), Gaps = 20/249 (8%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A   +VE    LV  +A +   R    ++  DLIQ G IGL+ A  ++      +F T
Sbjct: 2   PHADDSLVE-YAPLVRKLALQLLARLPASVELDDLIQAGMIGLLDAVRRYQETADAQFET 60

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++ A+   +  Q     +P  +R K  K+ +  + +  ++ R PT  EIA+++ +
Sbjct: 61  YATTRIRGAMLDELRGQDW---LPRSVRAKARKIEQAIQSLEQRLMRAPTEAEIAQQMEI 117

Query: 559 PVEGVRKVLKITK--EPISLETPIGDEDTSH---LGDFIEDKN----AVSPLDSAIQANL 609
           P+   + +L   +  + +  E    + DT       D+    N    + +PLDS +  + 
Sbjct: 118 PLNEYQTLLHDAQGVQIVHYEDFATEPDTGSGSGQSDWTATLNHGAASGNPLDSLLAGDF 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     + SL  RE+ +L + +  G      L+E+G    VT  R+ Q+ ++A  +++ 
Sbjct: 178 RQALIHAIDSLPDREKLLLSLCYEQG----LNLKEIGAIMNVTEARVCQLRSQATARIRA 233

Query: 670 PSRSKKLRS 678
             R +  + 
Sbjct: 234 KLREQAWQD 242


>gi|329942781|ref|ZP_08291560.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Chlamydophila psittaci Cal10]
 gi|332287373|ref|YP_004422274.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313847955|emb|CBY16951.1| putative RNA polymerase sigma factor [Chlamydophila psittaci RD1]
 gi|325507072|gb|ADZ18710.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328815041|gb|EGF85030.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Chlamydophila psittaci Cal10]
 gi|328914621|gb|AEB55454.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           psittaci 6BC]
          Length = 257

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 99/243 (40%), Gaps = 18/243 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWC 491
             + +    +  +++  L LV  VA +    G+       DL   G  GL++A E+F+  
Sbjct: 16  YWQTQEIKYRDTLIDFYLHLVKCVAHR-LISGMPSHVKTEDLYASGVEGLVRAVERFNPE 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +F  YA++ +K AI   +  Q     +P  +  K +K+      +   + REPT  +
Sbjct: 75  KSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANKLADAMDALRLSLGREPTDGD 131

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETP----IGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + +   +  + +       +    ISL          E    L + I D+ A +  D   
Sbjct: 132 LCEYFQISQQELSGWFASARPALIISLNEERPSLSDGESGVALEERIADERAETGYDIVD 191

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +          +  L  +E +V+     +    +  L+E+GK   V+  R+ QI +KA+ 
Sbjct: 192 KKEFSSFLASAIEGLEEKERKVM----ALYYYEELVLKEIGKILGVSESRVSQIHSKALI 247

Query: 666 KLK 668
           KL+
Sbjct: 248 KLR 250


>gi|332284050|ref|YP_004415961.1| RNA polymerase sigma factor for flagellar operon [Pusillimonas sp.
           T7-7]
 gi|330428003|gb|AEC19337.1| RNA polymerase sigma factor for flagellar operon [Pusillimonas sp.
           T7-7]
          Length = 255

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 111/236 (47%), Gaps = 20/236 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++V     LV  +A +   +    ++  DL+Q G +GL+ A  ++      +F TYA+ 
Sbjct: 6   DQLVGQYAPLVRRLALQLVAKLPASVEVDDLMQAGMMGLLDAIRRYQQTADAQFETYAVT 65

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ A+   +  Q     +P  +R K   + +    +++++ R P   EIA+++ +P+  
Sbjct: 66  RIRGAMLDELRSQDW---LPRSVRSKTRNIEQAIHTLTHRLLRAPAESEIAEEMGVPLPE 122

Query: 563 VRKVLKITKEPISLE----TPIGDEDTSHLGDFIEDKNAV------SPLDSAIQANLRET 612
            +++L+  +    L        G++  S L    ED++A       +PL+  +   LR  
Sbjct: 123 YQQLLEEARGVQILHYEDLAGQGEDAGSSLDRSSEDESATQAAHWSNPLNQLVSKGLRRA 182

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +L  RE+ +L ++F      D   +E+G    +T  R+ Q+ ++A+ +++
Sbjct: 183 LVEAIKALPEREQLLLSLQF----EQDLNQKEIGLVMGITEGRVSQLRSQAVARIR 234


>gi|297746537|emb|CAZ60986.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 242

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 49/286 (17%), Positives = 97/286 (33%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +   + +   D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDGDGDDADDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNTMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|327399094|ref|YP_004339963.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hippea maritima DSM
           10411]
 gi|327181723|gb|AEA33904.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hippea maritima DSM
           10411]
          Length = 238

 Score =  101 bits (250), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 112/237 (47%), Gaps = 14/237 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG-YKFSTYA 500
           K+E++++   +V  + KK   R   G    D +Q G +GL+KA E +D      +F +YA
Sbjct: 4   KEEIIQSYYPIVRRIVKKTVVRMPEGYDEEDFVQIGMMGLLKAIENWDENKSLSEFKSYA 63

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +        +  + RDK+ K+    R++ ++    PT +EIA++  M +
Sbjct: 64  NTKIRGYILDKLRSID---PVSRYARDKLKKINMAYRQLMSEGNFNPTDDEIAERADMSI 120

Query: 561 EGVRKVLK--ITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           +   ++L        +S++  +  +D    L + IE+K++ SPL    +  L++     L
Sbjct: 121 DEFNELLYKQSNSTMLSIDEAVSSDDGDMVLLEVIENKSSKSPLAILEEEELKDIVKEAL 180

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +L   E  VL + +    N    ++E+      T  RI QI+ KA+ K++    +K
Sbjct: 181 KALNETEITVLSLYYYEDFN----MKEIASLIGKTESRISQIKTKALLKIRAYVENK 233


>gi|325523156|gb|EGD01548.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 206

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 54/131 (41%), Positives = 84/131 (64%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++    +       + + + + E     A+ ++V++NLRLV+S+AK+Y +RGL   DL
Sbjct: 74  RMLARSPDLPPDTIAALDARIERIERATRPARTKLVKSNLRLVVSIAKRYPDRGLPLPDL 133

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           IQEGNIGL+KA E++D   G+KFSTYA WW++QAIT ++AD   TIR+P H  D ++K+ 
Sbjct: 134 IQEGNIGLLKAVERYDHRRGFKFSTYATWWIRQAITHALADLGRTIRVPAHTVDAVNKLA 193

Query: 534 RTARRMSNKIK 544
           R AR    +  
Sbjct: 194 RIARDHVQRAG 204


>gi|331696172|ref|YP_004332411.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950861|gb|AEA24558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 270

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 108/250 (43%), Gaps = 14/250 (5%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKA 484
           E  H ++ +   +      + +++   L +   +A ++ +       DL Q  +  +++A
Sbjct: 24  ERLHRLARLPADDPARDALRDDLILTFLPVAERIAGRHASATPWSREDLRQAASEAVVRA 83

Query: 485 AEKFDWCL-GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            +++D       F  Y +  V+  + R   DQS ++R+P  +++    +      M+ ++
Sbjct: 84  VDRWDPERAQGDFLGYLVPCVRGEVLRWFRDQSWSVRVPRRLKELSVAIRSAHGPMAQRL 143

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
              P P E+A++L + +E V + L         +L+ P   ++       +  +      
Sbjct: 144 GSAPRPSELARELGVDIEEVLEALHAEENHRAATLDAPAPGDER------LPGEQLGEID 197

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                    ET   ++A+L  RE R+L +RF  G     T  ++G++  V++  + ++ +
Sbjct: 198 RQLELVEDAETLRPLIAALPERERRILLLRFYGG----RTQSQIGEELGVSQMHVSRLLS 253

Query: 662 KAIRKLKHPS 671
           + + +L+   
Sbjct: 254 RTLARLRAAM 263


>gi|148359326|ref|YP_001250533.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|296107373|ref|YP_003619073.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148281099|gb|ABQ55187.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|295649274|gb|ADG25121.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 238

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 104/233 (44%), Gaps = 17/233 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F T
Sbjct: 12  QQTQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    R + +K+ RE    EIA++L +
Sbjct: 72  YAGIRIRGHMLDEVRRNDW---VPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGV 128

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTR 615
            +     +L+ +          G +D     D + D     +  P  + +++++    T+
Sbjct: 129 SLNDYHDMLQDSIS----SHLYGFDDLGVTDDILFDDEGNGSTEPHRNVMRSDMMNRLTQ 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+ SL  +E  VL + +      D  L+E+G+   V+  RI QI ++A  +++
Sbjct: 185 VIDSLPRKERLVLSLYY----EQDLNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|126664990|ref|ZP_01735973.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
 gi|126630360|gb|EBA00975.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
          Length = 246

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 97/242 (40%), Gaps = 12/242 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +   +     ++E +  LV  +A     R    +Q  DL+Q G IGL++A++
Sbjct: 3   LAKDLGVYQRSGASDASWLIEEHAPLVKKIALHLLARLPSSVQLEDLMQAGMIGLLEASQ 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G  F TYA   ++ A+   I        +P  +     ++    + +  +  RE
Sbjct: 63  RYTTGKGATFETYAGIRIRGAMVDEIRKGDW---VPRSVHRNSRRISSAIKAVEGREGRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
               E+A +L M +      L  +           ++      +  E  +  +PL    +
Sbjct: 120 SHDVEVAAELDMTLSEYHSCLADSNSGRLFSLDELNDSGELPIEQSETDD--NPLHGVSE 177

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R +    + +L  RE+ VL + +      +  L E+G    V+  R+ QI ++A  +
Sbjct: 178 FAFRNSLAAAIETLPEREKLVLSLYY----QEELNLREIGAVLDVSESRVSQIHSQAALR 233

Query: 667 LK 668
           L+
Sbjct: 234 LR 235


>gi|262276378|ref|ZP_06054187.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
 gi|262220186|gb|EEY71502.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
          Length = 224

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 52/227 (22%), Positives = 96/227 (42%), Gaps = 17/227 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           M E    LV  +A     R    +Q  DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 1   MFEQYATLVKRIAHHLVARLPPNVQVEDLIQAGMVGLLEAQQNYDASKGASFETYAGIRI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++     ++  ++ R+P  +EIAK+L M +E   
Sbjct: 61  RGAMLDDIRKGDW---VPRSVHKNNRQISEVIAQLEGELGRDPKDKEIAKRLGMSLEQY- 116

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ---ANLRETTTRVLASLT 621
                 +  I+    IG  D     D    ++         +    + +      +  L 
Sbjct: 117 ---HQAQNDINAGRLIGIVDLGVSEDAFVTESHRDENLPFEEVAGDSFKSHLANAIRGLP 173

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G    V+  R+ QI+ +A+++L+
Sbjct: 174 EREALVLSLYY----DEELNLKEIGAIIGVSESRVCQIQNQAMQRLR 216


>gi|160939653|ref|ZP_02087001.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437444|gb|EDP15208.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 55/256 (21%), Positives = 103/256 (40%), Gaps = 18/256 (7%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFD 489
           +    +  +   +  ++   L +V S A +        L+  +LI +G + L++  E++D
Sbjct: 15  LEEYRKNGSQELRNRLIMHYLPIVRSAAVQLRSMAGSLLEQEELIDQGVLALIECLERYD 74

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +F T+A   V+ A+   I  Q        + +    KV      +S+K  REP  
Sbjct: 75  PDRGARFETFAFMRVRGAMIDYIRSQDWVPHRARNFQK---KVEEACSILSHKQMREPDV 131

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL---GDFIEDKNAVSPLDSAIQ 606
            E+A  L +PVE V   +K       L      +D + +   G+         P ++   
Sbjct: 132 NEVADYLDLPVEKVENHIKYMNHANLLSFESVLQDMTAIVAKGELESGDIEGKPEENLFY 191

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L  T T  +  L  +E  V+ + +      +    E+ +   + + R+ QI  +AI+K
Sbjct: 192 KELMGTLTSAIDGLGEKERLVITLYY----YEELKYSEIAQVMGIGQSRVCQIHTRAIQK 247

Query: 667 LKHPSRSKKLRSFLDG 682
           LK       L  ++ G
Sbjct: 248 LKAS-----LEDYMRG 258


>gi|116626504|ref|YP_828660.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116229666|gb|ABJ88375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 251

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 97/235 (41%), Gaps = 13/235 (5%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                 ++ ++  +L  V  +A++   R    +   DL+  G +GL+ A + FD     K
Sbjct: 9   EMREDERERLILEHLPQVRLIARRIQERLPESISLDDLVSTGVLGLISAIDNFDASHNVK 68

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
             TYA + ++ AI  S+         P   R K  ++         ++   P  EEIA +
Sbjct: 69  LKTYAEYKIRGAILDSLRGLDW---APRQKRRKSKQIEAAIAVAEQRLHASPGEEEIAGE 125

Query: 556 LAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L + V+   + L         SLE   G+E    L  +I D +   P     ++ L    
Sbjct: 126 LGITVDEYHEWLVEIRGLNVASLE-YAGNEQGRDLLHYIPDGSDNLPSTLLERSELERLL 184

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  +   E  VL + F    + + TL E+ +   +   RI Q++++AI +L+
Sbjct: 185 ASSIDGIPAIERTVLSLYF----HEELTLREIAQVVNLHESRISQLKSQAILRLR 235


>gi|317497563|ref|ZP_07955881.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895122|gb|EFV17286.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 215

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 57/199 (28%), Positives = 101/199 (50%), Gaps = 4/199 (2%)

Query: 400 ACEVDSILKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
             +++ ++  R +++   V T  + +        +  + E    +A++  ++ NLRLV+S
Sbjct: 6   ESQMEELIMARKKVEICGVNTSSLPLLSEEEKEDLFERIEQGDLLAREHYIKGNLRLVLS 65

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           + ++++       DL Q G IGLMKA + FD  L  KFSTYA+  +   + R + D    
Sbjct: 66  IIQRFSGSSENADDLFQVGCIGLMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM 125

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
            R+   +RD  +K +     ++ K+  EPT + IAK++ M  E V   L     P+SL  
Sbjct: 126 -RVSRSLRDTAYKAINAREVLTKKLNHEPTIDVIAKEIDMKKEDVLFALDAIATPLSLYE 184

Query: 579 PIGDE--DTSHLGDFIEDK 595
           P+  +  DT +L D ++DK
Sbjct: 185 PVYQDGGDTLYLMDQVKDK 203


>gi|222431375|gb|ACM50640.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 36/270 (13%), Positives = 87/270 (32%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPVDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D E       ++ ++    P  A      + +  + +   L           
Sbjct: 50  AVKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++         L  L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKATIAELLALAGLFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    +G++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD-ALAKGKGKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
                 I++ + ++ ++  ETG++I+E + 
Sbjct: 194 GRLQPDIIRCQQKLTALQTETGLTIAEIKD 223


>gi|62185044|ref|YP_219829.1| RNA polymerase sigma factor sigma-28 [Chlamydophila abortus S26/3]
 gi|62148111|emb|CAH63868.1| putative RNA polymerase sigma factor [Chlamydophila abortus S26/3]
          Length = 257

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 53/243 (21%), Positives = 100/243 (41%), Gaps = 18/243 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAEKFDWC 491
             + +    +  +++  L LV  VA +    G+       DL   G  GL++A E+F+  
Sbjct: 16  YWQTQEIEYRDTLIDFYLHLVKCVAHR-LISGMPSHVKTEDLYASGVEGLVRAVERFNPE 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              +F  YA++ +K AI   +  Q     +P  +  K +K+      +   + REPT  +
Sbjct: 75  KSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANKLADAMDALRLSLGREPTDGD 131

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETP----IGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + +   +  + +       +    ISL          E    L + I D+ A +  D   
Sbjct: 132 LCEYFQISQQELSGWFASARPALIISLNEERPSLSDGESGVALEERIADERAETGYDIVD 191

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +          + SL  +E +V+     +    +  L+E+GK   V+  R+ QI +KA+ 
Sbjct: 192 KKEFSSFLASAIESLEEKERKVM----ALYYYEELVLKEIGKILGVSESRVSQIHSKALI 247

Query: 666 KLK 668
           KL+
Sbjct: 248 KLR 250


>gi|120554892|ref|YP_959243.1| FliA/WhiG family RNA polymerase sigma factor [Marinobacter
           aquaeolei VT8]
 gi|120324741|gb|ABM19056.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Marinobacter
           aquaeolei VT8]
          Length = 247

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 101/242 (41%), Gaps = 12/242 (4%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +       + +   ++E +  LV  +A     R    +Q  DL+Q G IGL++AA+
Sbjct: 3   LAKNLGIYHQAGARSPSALIEEHAPLVKKIALHLMARLPPSVQLEDLMQAGMIGLLEAAQ 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    G  F TYA   ++ A+   I        +P  +     ++    +++ ++  RE
Sbjct: 63  RYSSGKGATFETYAGIRIRGAMVDEIRKGDW---VPRSVHRNARRIASAIKQVEDRTGRE 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
               E+A++L + ++     L              +E      +  E + + +PLD    
Sbjct: 120 AQDAEVAEELGIGLDEYHASLADANSGRIFSLDELNESGELPIE--EAEASDNPLDGIAS 177

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              + +    +  L  RE+ VL + +      +  L+E+G    V+  R+ QI ++A  +
Sbjct: 178 GAFQRSLADAIEQLPEREKLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAALR 233

Query: 667 LK 668
           L+
Sbjct: 234 LR 235


>gi|320325134|gb|EFW81203.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. B076]
          Length = 246

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKASRNSQYELIERYAPLVKRIAYHLLARLPASVQVQDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|170725990|ref|YP_001760016.1| flagellar biosynthesis sigma factor [Shewanella woodyi ATCC 51908]
 gi|169811337|gb|ACA85921.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella woodyi ATCC
           51908]
          Length = 242

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 97/229 (42%), Gaps = 16/229 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +VE    LV  +A     R    +Q  DL+Q G +GL++A+  FD   G KF T+A 
Sbjct: 13  KASIVEQYAPLVKKIAHHLLARLPASVQIDDLLQAGMMGLLEASTNFDGSKGAKFETFAG 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I        +P  +     +V +    +  ++ R+    EIA++L + + 
Sbjct: 73  IRIRGSMLDEIRRGDW---VPRSVHRNQRRVAQVIDELEQELGRDAKDTEIAQRLDISLN 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
               +L      +S+   +G ED     D +   ++      +S             +  
Sbjct: 130 EYHHIL----NDVSVGKVVGIEDLGVSLDVVGQAEERKDDTFESIADVEFHTALVEAIKL 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  R+  VL + +    +    L+E+G    V+  R+ QI ++A+ +LK
Sbjct: 186 LPERDGLVLSLYY----DEALNLKEIGSILEVSESRVSQILSQAMLRLK 230


>gi|239934424|emb|CAR92342.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 244

 Score =  101 bits (250), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 45/287 (15%), Positives = 92/287 (32%), Gaps = 47/287 (16%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++   D +      L ++  L   I P+               K   + +E + D+
Sbjct: 1   TVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDDE 58

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   GD E  A+   D                         +A    A+ DQ       
Sbjct: 59  EESESGDDEEEAESGPDPVV----------------------AAQRFGAVSDQ------- 89

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                         LQ  +   +K+ ++  +     + L  L   + L   +  +LVE++
Sbjct: 90  --------------LQVTSKVLKKNGRNHKESIEALQALADLFMPIKLVPKQFGVLVERV 135

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL      E D  W           W   +  
Sbjct: 136 RDALSRLRQQERAVMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGE 194

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           +  +I+  + ++  +  ETG++++E + I       +   +  +  M
Sbjct: 195 KNAAIVACQQKLIDLETETGLTVAEIKEINRRANSADIHHTGGRSSM 241


>gi|85712287|ref|ZP_01043338.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
 gi|85693914|gb|EAQ31861.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
          Length = 241

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 104/240 (43%), Gaps = 18/240 (7%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
            +  ++ ++E +  LV  +A     R    +Q  DLIQ G IGL++AA  FD   G  F 
Sbjct: 10  HADNRQAIIEQHTGLVKRIAHHMMARLPASVQVDDLIQSGMIGLLEAARNFDNSKGASFE 69

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           T+A   ++ A+   I         P  +     +V+   R++ N+  R+    E+A+KL 
Sbjct: 70  TFAGIRIRGAMLDEIRRGDW---APRSVHRNHRRVLEAIRQVENETGRDAKDVEVAEKLE 126

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV----SPLDSAIQANLRETT 613
           MP+E    +L      ++    IG ED     D I  +        P             
Sbjct: 127 MPLEEYHAIL----RDVNSGRIIGIEDLGVSEDAIMPEQVTGANYEPQKDVENDAFHRAL 182

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
              ++ L  RE  VL + +    + +  L+E+G+   V+  R+ QI ++A+ +LK   +S
Sbjct: 183 VETISGLPEREALVLSLYY----DEELNLKEIGEVLSVSESRVSQIHSQAMMRLKTRMQS 238


>gi|307717594|gb|ADN88850.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717604|gb|ADN88855.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717614|gb|ADN88860.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717620|gb|ADN88863.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717622|gb|ADN88864.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 96/223 (43%), Gaps = 4/223 (1%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           R    +VL  L  RE+++L+  F        + +E G+   ++
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIEN----RSQKETGELLDIS 220


>gi|297746559|emb|CAZ60997.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 242

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 47/286 (16%), Positives = 98/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +   + + + D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + +LR+  +   ++ Q++ ++    +    +L  +     L   + D
Sbjct: 88  ----------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            LV  + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I      GE +A
Sbjct: 198 PRLVEMD-EDVLRAIGKLQQIEEETGLSIAQIKDINRRXSIGEAKA 242


>gi|213967540|ref|ZP_03395688.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato T1]
 gi|301382877|ref|ZP_07231295.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato Max13]
 gi|302062797|ref|ZP_07254338.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato K40]
 gi|302131296|ref|ZP_07257286.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato NCPPB 1108]
 gi|213927841|gb|EEB61388.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato T1]
          Length = 246

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKTSRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSEAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|239934526|emb|CAR94577.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 250

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 58/296 (19%), Positives = 113/296 (38%), Gaps = 48/296 (16%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           LL+REGEI IAKRIE G    MAS+   P + + L+   + +      L +I+       
Sbjct: 2   LLTREGEIVIAKRIEEGIRESMASISVFPGSVEHLLSEYELVKKEERRLADIL------- 54

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                G+ +  E      +  ++ E   ++  + E D     K   +D       P  A+
Sbjct: 55  ----TGYLNPMEHVPSASQVAAAAEPAAENKTKAEKDKADKDKKDDEDEKDNGPDPVEAK 110

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
               +L    +     L+A+E                                K  + S 
Sbjct: 111 KRFDSLRRAHN---KVLAAIE--------------------------------KHGRYSE 135

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
           + +       ++     L   ++D L + + D   +I   E  ++R+      +KR +FL
Sbjct: 136 QAQKQLHTRAEVFKYFKLTPRQLDPLAKNVRDAISQIRRQERLIMRICVREVDMKRKLFL 195

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +  Q +E + +W+  A+     +  + +      I + +N++ S++  TG+ IS+ 
Sbjct: 196 KEFQSQESESNWID-AQIKKHKDLADKLQIAKPEIERAQNKLASMAEATGLQISDI 250


>gi|307153354|ref|YP_003888738.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306983582|gb|ADN15463.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 258

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 111/232 (47%), Gaps = 12/232 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++    + DL+Q G +GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRREAYHWVSQCNENYEDLLQVGCLGLIRAIERFETGKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  ++RIP    D   + +   R    ++ R+P+ EEIA+ L +  +  
Sbjct: 89  IRGEIQHYLRDKGYSVRIPRRWLDLGRQAMTIRRDFQTRLNRQPSDEEIAEILEISAKEW 148

Query: 564 RKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+  I  +D   + LGD + D    S     +  + R    + LA 
Sbjct: 149 QEIKLAFQNREPLSLDVSINHDDDGQTSLGDLVPDPKYRSF---QLSEDDRIRLQQALAQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           L  R  RVL   F      D T  E  +Q  ++   + +   K +  LK   
Sbjct: 206 LEERTRRVLEFVFL----YDLTQRETAEQLGISVVTVSRRVKKGLDLLKETM 253


>gi|54294669|ref|YP_127084.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Lens]
 gi|53754501|emb|CAH15985.1| sigma factor 28 [Legionella pneumophila str. Lens]
          Length = 238

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 103/233 (44%), Gaps = 17/233 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +A     R    +Q  DLIQ G +GL++AA  +D   G  F T
Sbjct: 12  QQTQEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    R + +K  RE    EIA++L +
Sbjct: 72  YAGIRIRGHMLDEVRRNDW---VPRSVYRNSRMISDAVRILEHKFGREAKDNEIAEELGV 128

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTR 615
            +     +L+ +          G +D     D + D     +  P  + +++++    T+
Sbjct: 129 SLNDYHDMLQDSIS----SHLYGFDDLGVTDDVLFDDEGNGSTEPHRNVMRSDMMNRLTQ 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+ SL  +E  VL + +      D  L+E+G+   V+  RI QI ++A  +++
Sbjct: 185 VIDSLPRKERLVLSLYY----EQDLNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|307717640|gb|ADN88873.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 47/212 (22%), Positives = 91/212 (42%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
            + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P  
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQI 121

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            +IA  + +  E V + +++ K   +L      E  S               D   + N 
Sbjct: 122 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQ 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           R    +VL  L  RE+++L+  F    +   T
Sbjct: 182 RMLLEKVLPVLDEREQKILQYTFIENRSQKET 213


>gi|297531625|ref|YP_003672900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297254877|gb|ADI28323.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 256

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 113/239 (47%), Gaps = 14/239 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
             + +   A   ++     L+ + AKK       F  DL Q G +  ++  + +D   G 
Sbjct: 20  YQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLSFLRLLDHYDPKQGT 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F +YAM  +   +   + D++  I++P  +++K  KV +    ++ K++R PT +EIA 
Sbjct: 80  SFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKGSKVQQAIDELTVKLERSPTLDEIAG 139

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + VE   ++L  +   + +SL+ P+ D  +D + +GDF+ D+      +       R
Sbjct: 140 HLGLSVEETIEILAGRDHYQAVSLDAPVQDGEKDATTIGDFVADE-----ANEIESLIER 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + +  L+ +E+ V+   F  G     T   + ++  V++  I +I+ +AI KLK 
Sbjct: 195 MDLEQAIGKLSEQEQIVIDAIFRRG----ETQRALAERLGVSQMTISRIQKRAIAKLKR 249


>gi|282858710|ref|ZP_06267864.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588514|gb|EFB93665.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 228

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 117/260 (45%), Gaps = 43/260 (16%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +  I++I  ET ++  E R +   ++      + A +++ +ANL  V+S+A +Y  +GL 
Sbjct: 5   KKYIENIIGETILTNEEERQLADRIK---VGDAKALEKLTKANLTFVVSIAHQYKEQGLD 61

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I +Q+   ++P + +++ 
Sbjct: 62  ENDLISEGNIGMMYAAQKFDGTKGVRFVNFAASYIRKAMEDAIKEQTALYKVPKNEKNRF 121

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSH 587
            +  R                                       ISL+ P+     +   
Sbjct: 122 EQ-KRAK------------------------------------AISLDQPVPVGSNNNFT 144

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L + I + +  +  D      L     + +  L  RE  V+   +G+      T+ EV +
Sbjct: 145 LQNVIVNGDTANTDDDVTTNMLNTALKQSMKFLNERETAVITQLYGLDGVH-FTMAEVAE 203

Query: 648 QFCVTRERIRQIEAKAIRKL 667
              + RERIRQI   A+RKL
Sbjct: 204 TLGLKRERIRQIRNTALRKL 223


>gi|188997568|ref|YP_001931819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932635|gb|ACD67265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 242

 Score =  100 bits (249), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 55/206 (26%), Positives = 95/206 (46%), Gaps = 11/206 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DL Q G +GL  A EKFD   G KFSTYA   V+  I   +        IP ++R+
Sbjct: 35  VDEEDLFQVGVLGLYDALEKFDPAKGVKFSTYAEIRVRGYILDHLRQLDW---IPRNIRN 91

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG--VRKVLKITKEPISLETPIGDEDT 585
           K+  +      +  K+ RE  PEEIA+ L M +E   +     + K  ISL++ +  +D 
Sbjct: 92  KVKNLENKIVELETKLGREAKPEEIAEYLGMSLEEYMIYAEKAVNKILISLDSDVSKDDD 151

Query: 586 SHL-GDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLE 643
             L    +   N  +P     +  L+E  +  ++  L  RE+ ++ + +      D  ++
Sbjct: 152 ESLHLWEVISTNDDTPEKYVEEKQLKEILSDIIMNKLDEREKLIVTLYY----YEDLNMK 207

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+ +    T  R+ Q+  K + K++ 
Sbjct: 208 EIAEILGCTESRVSQLHTKIMLKIRK 233


>gi|325107978|ref|YP_004269046.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
 gi|324968246|gb|ADY59024.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
          Length = 259

 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 57/266 (21%), Positives = 110/266 (41%), Gaps = 19/266 (7%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
           + T +S  E   I    +K +      +  ++E  L LV   A++   +   G+   DL+
Sbjct: 1   MATKLSPEEVLEIWEAYKKDQTN-QHLRNRLIERYLPLVRYNAERVWAKLPDGVDLNDLM 59

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G  GLM A + FD   G KF TY +  ++ A+   +        +P  +R K  K+  
Sbjct: 60  SAGVFGLMDAIDAFDMERGVKFETYCVPRIRGAMLDELRTMDW---VPRLVRSKASKLAA 116

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDED---TSHLG 589
            ++ +  +  R PT  E+A K+ + +E     K        +SL     + D        
Sbjct: 117 ASKAVEAETGRPPTDVEVAAKMELSLEEFEKLKSEAAAVGLVSLNKKWYETDSYKDVREV 176

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +ED     P +   + ++ +  T+ L        R  R+   +    + T++E+G   
Sbjct: 177 DILEDGKGEDPTNGIQKRDIMKLVTKGLN-------RNERLIMILYYYEELTMKEIGMTL 229

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKK 675
            ++  R+ Q+ +  + +LK   R ++
Sbjct: 230 GLSESRVSQMHSSIVNRLKDQLRKRR 255


>gi|321309572|ref|YP_004191901.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801416|emb|CBY92062.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 461

 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 71/244 (29%), Positives = 131/244 (53%), Gaps = 6/244 (2%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     +++ E   +  ++       S A K++  +NLRLV SVAKKY N G    DL+Q
Sbjct: 148 LKFTRKLTLEEETALSKLME-NPKTRSFAIKQLTISNLRLVQSVAKKYLNYGFPMEDLVQ 206

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EG  GLMKA +KF++ LG KFSTYA WW++QAI RSIA++   IR+PVH+++ I +  + 
Sbjct: 207 EGFFGLMKAVQKFNYNLGNKFSTYATWWIRQAIVRSIAEKYRVIRVPVHLQEIIKRFNKV 266

Query: 536 ARRMSNKIKREPTPEEIAKKL----AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +  +  +       + + +         +E +  + +++K+ +SL+  +  E+   L   
Sbjct: 267 SMTLMAEKGEPSLQDILVEMQKYYPNFDLEKITNIKQLSKDLLSLDGVLDSEEFFPLSGA 326

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           I D++ +   + + +A   E    +L + L P E  ++++R+G      H++ E+ ++  
Sbjct: 327 IRDEDMMDAEELSFKAYRVEMLNDMLENELKPDEISLVKLRYGFLEYGKHSVREIVEEKL 386

Query: 651 VTRE 654
           +  E
Sbjct: 387 LDPE 390


>gi|289678962|ref|ZP_06499852.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae FF5]
          Length = 239

 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKTSRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRSIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|229101713|ref|ZP_04232430.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
 gi|228681661|gb|EEL35821.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
          Length = 203

 Score =  100 bits (249), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         Q   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEQTERRLVLNDIFNVLNETEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAINKLKQAA 199


>gi|313901053|ref|ZP_07834541.1| RNA polymerase sigma-F factor [Clostridium sp. HGF2]
 gi|312954011|gb|EFR35691.1| RNA polymerase sigma-F factor [Clostridium sp. HGF2]
          Length = 241

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 106/227 (46%), Gaps = 10/227 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ +       AK   V+ N  LV S+ ++++ + +   DL Q G +GLMKA   FD  
Sbjct: 9   ELIERIRLGDEEAKSCFVQQNSALVYSIIRRFSRQRISNEDLFQIGCVGLMKALNNFDTS 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R   D    IRI   +++   ++V+    +  K+  EPT +E
Sbjct: 69  YEVKFSTYAVPIIMGEIKRFFRDDGS-IRISRSLKEGYLQMVKAKEVLLQKLNHEPTYQE 127

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA  + + V  V    +  +   SL+  I + D S +   +EDK +    +  +   ++ 
Sbjct: 128 IADAMELDVADVILAFEANQFIYSLDETIYENDGSPI--LLEDKVSNKKEEDVV---MKV 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +    +  L  RE+ +L  R+ +        EE+ ++  +++ ++ +
Sbjct: 183 SLRDEIQKLDQREQLLLHYRYDL----SMKQEEIARKLNISQVQVSR 225


>gi|258511987|ref|YP_003185421.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478713|gb|ACV59032.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 239

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 63/278 (22%), Positives = 104/278 (37%), Gaps = 53/278 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A     +    + +K  +    +S  E       +R      + A+  ++E NLRLV 
Sbjct: 7   LLALVFKDVSLFVSYVKQGAFPHPLSPEEEE---RAIRDYLAGDADARNRLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            +AKKY + G +  DLI  G IGL+KA E +    G K +TYA   ++  I   +     
Sbjct: 64  HLAKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATYAARCIENEILMYLR---- 119

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                 H RD                        ++  +    +G               
Sbjct: 120 --SSKKHRRDAF----------------------LSDPVGTDKDG--------------- 140

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                 +   L D +   +    +D+   +  ++     L  L PRE  VL  RFG+   
Sbjct: 141 ------NEMTLADLLG-SDPDDVIDAVDMSWEKQKMFECLPLLAPREREVLCKRFGLPDG 193

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            + T  E+ K+  ++R  + +IE KAI KL    R +K
Sbjct: 194 EERTQREIAKELGISRSYVSRIEQKAIVKLYENMRQRK 231


>gi|317501595|ref|ZP_07959789.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897012|gb|EFV19089.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 239

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 120/241 (49%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   DTIALIRKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K V+   R+ + + REPT
Sbjct: 63  DLTYNVKFSTYAVPLISGEIKRFLRD-DGMIKVSRSLKEIAYKSVQARERLISSLGREPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+++++ +  E + + ++   E  S+  P+  ++ S +         +  L+   +  
Sbjct: 122 IEELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEI-------RLLDKLEEKEKRE 174

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     VL  L    +   +    +    D T  +VGK   +++ ++ + E + I KL+
Sbjct: 175 DKILDLIVLKELLETLDEEEKQLIFLRYFADRTQSDVGKIMGISQVQVSRSEKRIIEKLR 234

Query: 669 H 669
            
Sbjct: 235 K 235


>gi|227873530|ref|ZP_03991775.1| possible DNA-directed RNA polymerase sigma subunit D [Oribacterium
           sinus F0268]
 gi|227840620|gb|EEJ51005.1| possible DNA-directed RNA polymerase sigma subunit D [Oribacterium
           sinus F0268]
          Length = 259

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 103/234 (44%), Gaps = 11/234 (4%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              K+E+    + +V S+A +       F    D++ EG I +M+A E++D     KF T
Sbjct: 27  QEVKQELTMRYVYIVRSIAYQMREMYHDFMQTDDIVNEGVIEIMRAIERYDESKDNKFET 86

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +    ++  +   +        +P +       +      ++N++ R PT EE+A  L M
Sbjct: 87  FISRRIRGMVIDMMRKNDW---LPRNFHKDSRSIETATVELNNRLGRAPTDEELADYLNM 143

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V+ ++K+ +++     L   +  ++    L     + ++  P  S +Q       T  +
Sbjct: 144 NVKKLQKIQRMSNMVNVLSLDMTYDEGNETLLQIPSEDHSTQPEFSFMQKENVRALTEAI 203

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            SL  +E+ V+ + +      +  + ++ +   V++ R+ Q+ + AIRKL+   
Sbjct: 204 ESLQEKEKLVISLYYV----EELNMNQIAEVMEVSQPRVSQLHSIAIRKLRKYM 253


>gi|323490161|ref|ZP_08095381.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
 gi|323396209|gb|EGA89035.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
          Length = 252

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 100/243 (41%), Gaps = 15/243 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAA 485
            +V      +     A + +VE  L LV  V +++     + ++  D+      GL+ A 
Sbjct: 10  ELVCWSDWQQHRDPDAGEYLVEQYLPLVDYVIQRFMISLPKTVEKDDVRSYAYEGLLDAL 69

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            KF+     KF TYA W +K AI   +        +P  +RDK+ K+ +    +  +   
Sbjct: 70  SKFNIERDLKFETYASWRIKGAIIDGLRQSDW---LPRSVRDKVKKIEKAFLLLEQQSGV 126

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSA 604
             + EE++  L +        L  T    +L T I  +D        + + +  SP    
Sbjct: 127 SVSDEEVSSYLGITKAE----LNKTVSEAALSTMISMDDDNFEEQGKLVNYHVDSPERHL 182

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +   +E+  R +  L  +E+  + + +      +  L E+ +   V+  R+ Q+ +KA+
Sbjct: 183 SEQMRKESLVRAIERLPEKEKITVSLCYF----EEMKLTEIAEILNVSVSRVSQLHSKAM 238

Query: 665 RKL 667
            +L
Sbjct: 239 LRL 241


>gi|313672893|ref|YP_004051004.1| RNA polymerase, sigma 28 subunit, sigd/flia/whig [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939649|gb|ADR18841.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 242

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 118/247 (47%), Gaps = 13/247 (5%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +S+         I ++E+V+  L  +     + +NR    +   +L     +GL+++ +K
Sbjct: 1   MSLALYQGSLDRIEQEEIVKEFLPKIKVWVLRVSNRLPANVDNDELYSAACMGLVESLQK 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD      F +YA   +K AI  ++        +P ++R K+ +     + ++ K+ R+P
Sbjct: 61  FDKGRSVDFYSYAERRIKGAILDALRQMDF---LPRNVRTKLKQFEEKLQELTVKLGRKP 117

Query: 548 TPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             +EI +   +  E V   L +  T +  SL+T + ++    L D I+      P DSAI
Sbjct: 118 NTDEIVEYTNLSQEDVFNFLNLIETGQLTSLDTSLDEDGDISLLDTIKSF-VEGPEDSAI 176

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L      ++ SL  +E+ V+ + +      + T++E+G+   ++  R+ QI ++A++
Sbjct: 177 KEQLISKLGEIIDSLPDKEKLVITLYY----YEELTMKEIGEVLKISESRVSQIHSEAVK 232

Query: 666 KLKHPSR 672
           KLK   +
Sbjct: 233 KLKRKLK 239


>gi|209408328|emb|CAP19907.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 207

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 76/244 (31%), Gaps = 45/244 (18%)

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T  +++   + +      L +I  L   I P+  G        
Sbjct: 1   IEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA------ 52

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
              Q+ E  + +       + + D E     S+ +       PE A      + E  + +
Sbjct: 53  -GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEKEEGDGGPDPEVARMRFGAVAEQLEKA 111

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                                  +K  ++S +     E L  L 
Sbjct: 112 KKA-----------------------------------LKKHGRASQQAVEELEALAILF 136

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWV 384
             + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  W 
Sbjct: 137 MPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWA 196

Query: 385 SYAK 388
               
Sbjct: 197 EQLA 200


>gi|28869183|ref|NP_791802.1| motility sigma factor FliA [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|66046666|ref|YP_236507.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae B728a]
 gi|237799256|ref|ZP_04587717.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           oryzae str. 1_6]
 gi|28852423|gb|AAO55497.1| motility sigma factor FliA [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|63257373|gb|AAY38469.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas
           syringae pv. syringae B728a]
 gi|330964675|gb|EGH64935.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           actinidiae str. M302091]
 gi|330972456|gb|EGH72522.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aceris str. M302273PT]
 gi|331016985|gb|EGH97041.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
 gi|331022111|gb|EGI02168.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           oryzae str. 1_6]
          Length = 246

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKTSRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|160895319|ref|ZP_02076090.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
 gi|156863012|gb|EDO56443.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
          Length = 225

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 110/228 (48%), Gaps = 20/228 (8%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ + +     AK++++E NL LV SVA+++T RG    DL Q G IGL+K  +KF +
Sbjct: 5   LDLLLQAKNGDDHAKEKLIEQNLGLVWSVARRFTGRGYDIEDLFQIGCIGLIKCIDKFSF 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               KFSTYA+  ++  I R + D    I++   +++   KV +  +++  +   EP   
Sbjct: 65  EYDVKFSTYAVPLIQGEIRRFLRDSG-AIKVSRSLKEMNMKVEQYRQKIKKEKGYEPEIT 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA  L+     +   ++ + E  SL+TP     T      I D                
Sbjct: 124 EIAAALSFDAGDIVMAMEASMEIESLDTPGVLSKTEEYSQDIVD---------------H 168

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            T +++L  L P E+ ++R+R+      D T  E GK   +++ ++ +
Sbjct: 169 ITLSQLLDRLDPDEQMLIRLRYF----EDRTQTETGKALGLSQVQVSR 212


>gi|119470003|ref|ZP_01612808.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
 gi|119446713|gb|EAW27986.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
          Length = 240

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 59/224 (26%), Positives = 95/224 (42%), Gaps = 10/224 (4%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 16  IVEKHASLVKKVACHLIARLPASVQLDDLIQSGMIGLIEASKSFDATKGASFETFAGIRI 75

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +         P  +  K   V  T   +   + REPT  E+A+KL + +    
Sbjct: 76  RGAMLDEMRRGDW---APRSVHRKSRLVAETIAFLEKSLNREPTDIEVAEKLEISLNEYH 132

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +L        L       D   +    +D     P ++       E+    + SL  R+
Sbjct: 133 HILNDVNASKVLGIEDLGVDEDAISPVGQDLALDKPFNNVKNERFNESLLGAIKSLPERD 192

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL + +    N +  L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 193 AMVLSLYY----NDEMNLKEIGHILDVSESRVSQIHGQAMIKLK 232


>gi|312882106|ref|ZP_07741856.1| flagellar biosynthesis sigma factor [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309370242|gb|EFP97744.1| flagellar biosynthesis sigma factor [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 244

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 105/244 (43%), Gaps = 15/244 (6%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAE 486
           +   +   +     ++++ +E    LV  +A     R    +Q  DLIQ G IGL++A +
Sbjct: 1   MNKALTYEQYTKQDSQRDFLEKYSVLVRRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D   G  F TYA   ++ A+   I        +P  +     +V +    +   + R+
Sbjct: 61  NYDGNKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKHNREVSQAIATLEGILNRD 117

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           PT  E+AKKL + ++    +L        I +E     EDT  +G          P    
Sbjct: 118 PTDAEVAKKLGLELDQYHNILTDINCSRLIGIEDLGVSEDTITMGGC---DEENLPFQGV 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                R+     + SL  RE  VL + +    + +  L+E+G+   V+  R+ QI ++++
Sbjct: 175 SDEFFRKALVDSIKSLPERESLVLSLYY----DEELNLKEIGEVIGVSESRVSQILSQSM 230

Query: 665 RKLK 668
           ++L+
Sbjct: 231 QRLR 234


>gi|330899448|gb|EGH30867.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           japonica str. M301072PT]
 gi|330940686|gb|EGH43699.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv. pisi
           str. 1704B]
 gi|330976015|gb|EGH76081.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aptata str. DSM 50252]
          Length = 246

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKTSRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRSIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|330876038|gb|EGH10187.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 246

 Score =  100 bits (248), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKTSRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|330961240|gb|EGH61500.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 246

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKSSRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|323702739|ref|ZP_08114399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532256|gb|EGB22135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 232

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 100/249 (40%), Gaps = 59/249 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + ++S +++      +A+  +VE NLRLV ++A K+ +RG+   DL Q G IGL
Sbjct: 33  LSAEEEQELLSRLQQ---GDQLARSVLVERNLRLVATIANKHKDRGIDKQDLFQVGVIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     KF+TYA   ++  +   +                             
Sbjct: 90  IKAVNTFNPARTNKFATYAGVCIENEMRMMLRKN-------------------------- 123

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAV 598
                              +  R         +SL  P+  +       L D +   +  
Sbjct: 124 ------------------KDEYR--------CLSLSEPLDYDKEGNPLELQDTLMADDVP 157

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +  +     E     +  LTPRE  V+ +RFG+    + T  EVGKQ  ++R  I +
Sbjct: 158 -VDEQVVHNLETERLGAAMQKLTPRERVVINLRFGLNGGRELTQREVGKQLNISRSFISR 216

Query: 659 IEAKAIRKL 667
           IE+K+I KL
Sbjct: 217 IESKSISKL 225


>gi|149376625|ref|ZP_01894385.1| flagellar biosynthesis sigma factor FliA [Marinobacter algicola
           DG893]
 gi|149359143|gb|EDM47607.1| flagellar biosynthesis sigma factor FliA [Marinobacter algicola
           DG893]
          Length = 207

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 46/201 (22%), Positives = 91/201 (45%), Gaps = 9/201 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DL+Q G IGL++AA+++    G  F TYA   ++ A+   I        +P  +  
Sbjct: 8   VQLDDLMQAGMIGLLEAAQRYSSDKGATFETYAGIRIRGAMVDEIRKGDW---VPRSVHR 64

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
              ++ +  + + +++ RE    E+A++L + ++     L              +E    
Sbjct: 65  NSRRIAKAIKAVEDRLGREAQDSEVAEELGLDLDEYYSSLSDANSGRLFSLDELNESGEL 124

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             +  ED +  +PLD     N R++    +  L  RE+ VL + +      +  L+E+G 
Sbjct: 125 PIEETEDSD--NPLDGLASDNFRKSLATAIGDLPEREKLVLSLYY----QEELNLKEIGA 178

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              V+  R+ QI ++A  +L+
Sbjct: 179 VLGVSESRVSQIHSQAALRLR 199


>gi|167462462|ref|ZP_02327551.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B)
           [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322381881|ref|ZP_08055835.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154269|gb|EFX46591.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 260

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 113/245 (46%), Gaps = 13/245 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +   + E++     ++      V   A K   NR   + DL Q G + L+K  ++FD   
Sbjct: 18  LEYQDSESNEIATTLLLQFESTVRMAAGKMSRNRPDLYEDLYQVGQMSLLKLFKQFDPSH 77

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F  Y M  +   +   + D+S  I++P  +++K  ++ +    ++ K++R P  +EI
Sbjct: 78  GVQFEAYMMKSIIGHMKNYLRDKSWYIQVPRRIKEKGFQIQQAIDSLTMKLERSPNVDEI 137

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANL 609
           A +L +  E   ++L  +     +SL+ P+  E+  S +GD +         D  +  + 
Sbjct: 138 ANELGLSTEETIEILAGRECYHYVSLDMPLSTEENGSTIGDVLG-----IQEDEYLHVDN 192

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R      +  L P E++ L + +  G    ++   + ++  +++  + +++ +A+ KL+ 
Sbjct: 193 RLDLQEAMEHLKPEEKKALILAYIDG----YSQRTIAQELDISQMSVSRMQRRALSKLRE 248

Query: 670 PSRSK 674
             + K
Sbjct: 249 YFKVK 253


>gi|313895821|ref|ZP_07829375.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320529404|ref|ZP_08030492.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
 gi|312975246|gb|EFR40707.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320138370|gb|EFW30264.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
          Length = 246

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 101/229 (44%), Gaps = 20/229 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  + E  L LV  VA +      + +   DL+  G  GL+ A E+++   G KF TYA 
Sbjct: 23  RNRIAEYYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLLDAIERYELTRGNKFETYAG 82

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+ A+   +  +     IPV +R  I K  +    +  K+ R  T EE+A +L +  E
Sbjct: 83  VRVRGAMLDHLRSKDW---IPVSVRQNIKKYEKAVASLEGKLGRTATDEELAAELGLTRE 139

Query: 562 GVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           G+R  +        I LE  +  +    L D         P++ A    ++ET    + +
Sbjct: 140 GLRHLESQVSAATVIPLEEYLRTDSPVSLED--------GPVEHAEWTEVKETLAAAIEN 191

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E  V+     +    + TL+E+     ++  RI Q+  KAI +++
Sbjct: 192 LPEKERTVV----ALYYYDEMTLKEIAAILHLSEARISQLHTKAIFRMR 236


>gi|58699726|ref|ZP_00374383.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533758|gb|EAL58100.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 216

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 53/200 (26%), Positives = 93/200 (46%), Gaps = 11/200 (5%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           VDS   +   I  +     +S  E   +       + +   +  +++ ++L LV+ +A K
Sbjct: 6   VDSRTNLMQYIARVQKFPMLSQEEEVRLAK--NWNQYKDVSSAHKLITSHLNLVVKIAMK 63

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N GL  +DL+ EGN+GLM A +KF+  LG++FSTYA+WW++ +I   I      ++I 
Sbjct: 64  FKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIG 123

Query: 523 VH--MRDKIHKVVRTARRMSNKIKREPTPEE----IAKKLAMPVEGV-RKVLKITKEPIS 575
                R     + +  +R+     RE    E    I+ +L++    V +   ++  +  S
Sbjct: 124 TTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQS 183

Query: 576 LETPIGDEDTS--HLGDFIE 593
           L   I   D S   L D I 
Sbjct: 184 LNDCIKIGDDSKRELQDMIP 203


>gi|182412226|ref|YP_001817292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
 gi|177839440|gb|ACB73692.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
          Length = 262

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 106/247 (42%), Gaps = 14/247 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
             V    +G   +++ +K+++E +L LV +V  +        +   DL   G  GL+ A 
Sbjct: 14  KTVWRAYQGVSPSNVDEKDLIERHLYLVRNVVDRIKLNLPTHIDADDLYSVGVTGLIAAV 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            KFD   G  F++YA   ++ A+   +         P   R +  K+  T   +  K+ R
Sbjct: 74  RKFDPEQGCTFASYAAMRIRGAVLDELRRMDWC---PRRARARSRKLKETIIEVEQKLGR 130

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE----DTSHLGDFIEDKNAVSPL 601
             + EEI   L +  +   K ++  +    L     +E    + + L + ++D+  V+  
Sbjct: 131 AASDEEICSALGLTQKDYAKWVEDARPVTFLAIDHRNENEDGEGASLHELLKDETDVTGR 190

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++  +  L E  T+ ++ L    +++L M +         L E+   F +T  RI QI A
Sbjct: 191 ENLEKRELLELLTQRISELPDIPKKILAMYYFEN----MRLAEIAAVFNLTESRICQIHA 246

Query: 662 KAIRKLK 668
           + I  L+
Sbjct: 247 QTILGLR 253


>gi|229544420|ref|ZP_04433478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
 gi|229324905|gb|EEN90582.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
          Length = 257

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 102/248 (41%), Gaps = 14/248 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             +     A   +V+  + LV    ++      R +   DL   G  GL+ +  KFD   
Sbjct: 17  WLKSRDPEAGNALVKRYMPLVSFHVQRIAAGLPRNVSKEDLKSLGMFGLLDSLNKFDPSR 76

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F TYA + ++ AI   +  +     +    R+K  K+      +  K  R  +P+E+
Sbjct: 77  ELRFDTYASFRIRGAILDGLRKEDW---LSRGTREKAKKIESAIESLEQKYLRTVSPKEV 133

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGD--FIEDKNAVSPLDSAIQAN 608
           A +L M    V   +  +     +S+E    D D           D+NA  P     +  
Sbjct: 134 ALELGMEETEVCTTMNEQFFANVLSIEETGTDNDEPEAASRFVSGDRNAGQPESELEKKE 193

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +     + +L+ +E+ VL + +      + TL E+G+   ++  RI QI +KAI KL+
Sbjct: 194 TVKELAEAIRALSEKEQLVLSLFYQ----EECTLTEIGEVMGLSTSRISQIHSKAIYKLR 249

Query: 669 HPSRSKKL 676
           +    + L
Sbjct: 250 NILEKRLL 257


>gi|172037479|ref|YP_001803980.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171698933|gb|ACB51914.1| group 3 sigma-70 RNA polymerase sigma factor F [Cyanothece sp. ATCC
           51142]
          Length = 269

 Score =  100 bits (248), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 107/235 (45%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++    + DL+Q G++GL++A E+F    G  FS++A+ +
Sbjct: 40  RNQILELNFGLVRKEAHHWVHQCPESYEDLVQVGSLGLIRAIERFSIDKGNAFSSFAIPY 99

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   + +   +    K  R+PT  EIA+ L + ++  
Sbjct: 100 IRGEIQHYLRDKKYTVRIPRRWLELGRQSMNVRQEFREKFNRQPTDSEIAQVLEISLKEW 159

Query: 564 RKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+  + ++    + LGD + D N  S   +           + L  
Sbjct: 160 QEIKLAFQNREPVSLDVKVSNDGEGQTSLGDLVPDANYRSFQLAQEDQI---RLQQALEQ 216

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  R   +L   F      D T  E  +Q  ++   + +   K +  LK     +
Sbjct: 217 LEERTRHILEFVFL----KDLTQRETAEQLGISVVTVSRRVKKGLEVLKKNMNKE 267


>gi|158340157|ref|YP_001521327.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
 gi|158310398|gb|ABW32013.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
          Length = 421

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 104/235 (44%), Gaps = 19/235 (8%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKF 496
           +      +   +  N RLV   A +Y  RGL  + DL+  GN GL +A EKFD   G KF
Sbjct: 30  QAGDRRTEDRFIRKNQRLVFKEANRY--RGLDDWNDLVTAGNWGLARAIEKFDVSKGCKF 87

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           S+YA+  ++  I + + D      +   +   +  + + ++++  +++R+PT EE++++ 
Sbjct: 88  SSYAVKVIRTEIQQFLND---QRGLSKEIAKHLKDIKQASQKLEWELERQPTLEELSERT 144

Query: 557 AMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
                 +   L   +  E  SL  P+G+   +   D +E  + +      I         
Sbjct: 145 GYSQRIITSTLDRARVVETSSLNIPVGENLKAEQIDLVEGDDDLWDYAENIDE------K 198

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +A L  R                H+   +G+ F ++ ERIRQ+  +A+  LKH
Sbjct: 199 EYIAQLPER-----YNVIVRARRDGHSYRAIGRMFGLSGERIRQLFKEALAYLKH 248


>gi|319787083|ref|YP_004146558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317465595|gb|ADV27327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 248

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 96/236 (40%), Gaps = 11/236 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
              +    +  A     +   R+   +A +     ++  DLIQ G IGL++A+  +D   
Sbjct: 8   RAVQQRASSDDAVVRHADLVRRIAHHLAARLPAS-VEVDDLIQAGMIGLIEASRSYDPEQ 66

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R +     R   P+E+
Sbjct: 67  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVREIEQATGRAAAPQEV 123

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A KL MP+    ++L+       L      ED    GD   + N+ +P     + +    
Sbjct: 124 AAKLDMPLPEYLRLLEDASRGQVLSLDSHVEDH---GDVQVNSNSPTPQQVLERGDFGRE 180

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               ++ L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 181 LATAISGLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVLRLR 232


>gi|307824496|ref|ZP_07654721.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
 gi|307734480|gb|EFO05332.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
          Length = 237

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 94/226 (41%), Gaps = 11/226 (4%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E V  +  LV  +A     R    +Q  DLIQ G +GL++A + +D   G  F TYA  
Sbjct: 11  DERVMQHAPLVKRIAYHLLGRLPDSVQVDDLIQAGMLGLLEAIKNYDASQGASFDTYAGI 70

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ ++   +         P  +  K   V    R + NK  RE    ++AK L + ++ 
Sbjct: 71  RIRGSMLDEVRRSDW---TPRSVHKKSRMVSDAIRTIENKTGREARDVDVAKYLGIAIDE 127

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
              +L+ +            +D  H  D     +   P+D   +   ++     +  L  
Sbjct: 128 YNHILQDSSSCRVFSVEELAQDGDHYMDETL-SHEEGPVDGLSREGFQQALANAIMGLPE 186

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  V+ + +    + +  L E+G+   ++  R+ QI  +A+ +L+
Sbjct: 187 RERLVISLYY----DEEFNLREIGEVLNISESRVSQICTQAVLRLR 228


>gi|213027483|ref|ZP_03341930.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 253

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 51/239 (21%), Positives = 106/239 (44%), Gaps = 13/239 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDED 584
                + +T +R+    + E   E +A++L +  + VR++      ++     +   + D
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNT 638
           +  +   +  ++  S     I+ +  E       T  +  L  R + ++R R+    N 
Sbjct: 192 SQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNK 250


>gi|289208354|ref|YP_003460420.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
 gi|288943985|gb|ADC71684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
          Length = 253

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 95/224 (42%), Gaps = 13/224 (5%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E +E   R+   +  +  +  +Q  DLIQ G IGL++AA +F+   G  F+TYA   ++ 
Sbjct: 25  EHIELVHRIAHHLMARLPSS-VQVDDLIQAGMIGLLEAARQFEGGQGATFATYAGIRIRG 83

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           A+   +         P  +     K+    + +  +  R     E+A++L +P++    +
Sbjct: 84  AMIDELRRSDW---TPRSVHRNSRKIAEAIQTVEAREGRAARGVEVAEELEVPIDEYYSM 140

Query: 567 L--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           L         +L+   G +      D + +    SP  +      RE     L  L  RE
Sbjct: 141 LQDHAGAHLFALDDLGGTDGD---ADRVIEGQEASPSRTIEAGEFREELAAALGDLPERE 197

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL + +      +  L E+G    VT  R+ QI ++A+ +L+
Sbjct: 198 RLVLSLYY----IEELNLREIGAVLGVTESRVSQIRSQAVIRLR 237


>gi|257484896|ref|ZP_05638937.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289629013|ref|ZP_06461967.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289647088|ref|ZP_06478431.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|298487813|ref|ZP_07005854.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|302185382|ref|ZP_07262055.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae 642]
 gi|298157905|gb|EFH98984.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320329393|gb|EFW85386.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. race 4]
 gi|330866465|gb|EGH01174.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330880595|gb|EGH14744.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. race 4]
 gi|330889039|gb|EGH21700.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv. mori
           str. 301020]
 gi|330953768|gb|EGH54028.1| flagellar biosynthesis sigma factor [Pseudomonas syringae Cit 7]
 gi|330986509|gb|EGH84612.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 246

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKASRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E+A +L + ++    +L  T      S +  + D D   L +      ++ P        
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDER 181

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 FQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|325844829|ref|ZP_08168281.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
 gi|325489016|gb|EGC91404.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
          Length = 229

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 66/274 (24%), Positives = 114/274 (41%), Gaps = 59/274 (21%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+     +++ +   I + +    +S  E  H ++++         A+++++E NLRLV
Sbjct: 5   QFIVSLFSNLIPLMGSISNQAFPNPLSPEEEEHYLTLM---ANGDKNAREKLIEHNLRLV 61

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
             + KKY N+     DLI  G IGL+KA + F    G K +TYA   +   I        
Sbjct: 62  AHIVKKYQNQTDDKEDLISIGTIGLIKAIDSFSPDKGTKLATYAARCIDNEILM------ 115

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                          + R+ ++M N                                +SL
Sbjct: 116 ---------------LFRSTKKMRN-------------------------------DVSL 129

Query: 577 ETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
             PIG +   +   L D ++D+N     D  IQ    E   + L SLT RE  ++  RFG
Sbjct: 130 YDPIGYDKEGNEICLIDVVKDEN-KDLNDIIIQQLAFEKIEKNLKSLTQRERDIIVRRFG 188

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  + + T +E+ K + ++R  + +IE +A+ KL
Sbjct: 189 LENHEEETQQEIAKSYGISRSYVSRIEKRALMKL 222


>gi|239934540|emb|CAR94584.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 241

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 56/274 (20%), Positives = 99/274 (36%), Gaps = 37/274 (13%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI+IAKRIE G   ++ S+   P   + ++    +  +G   L +I  L   + PE
Sbjct: 4   TREGEISIAKRIEEGIRDVLHSIAYWPNAVEVVLKEYKDYQEGERRLADI--LSGYLDPE 61

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
           S        E    ++ ED +  K   +V+  + + E     S DD      P       
Sbjct: 62  SDEEIPEVIEDAVLEEDEDETASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAK- 120

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
                                          E+  V++E +S+ +      K  + S + 
Sbjct: 121 ---------------------------VRFTELETVWQETKSVIE------KHGRDSAEA 147

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLER 373
           K   E L  +           D++ E +    ++I  +E E++R A   G + R  F   
Sbjct: 148 KAALEALASVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDRTQFRTS 207

Query: 374 HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
             G+E +P W+         + K  +      +L
Sbjct: 208 FPGQESNPGWLDEQMAKASPDIKGHLEKVRPDVL 241


>gi|238782801|ref|ZP_04626830.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238716224|gb|EEQ08207.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 241

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 106/239 (44%), Gaps = 17/239 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              +  I K ++      LV   A +   R    ++  DLIQ G IGL+ A + FD   G
Sbjct: 5   YNHDGVIQKDQLWPKYGFLVRHEALRLQARLPASVELDDLIQAGAIGLLTAIDHFDPKKG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
              STY    V+ A+   + ++     +P  +R    ++    +R+  +     T  ++A
Sbjct: 65  IGLSTYITQRVRWAMIDELRERDW---VPRRVRSNAREIAVIIQRIEQESGHVATEADVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA----VSPLDSAIQANL 609
             + + +   +K+L  T    S +    DE    L D  E  +     ++PL   ++ NL
Sbjct: 122 NSMGVTLPEYQKMLADTN---SSQLYSLDELQEELADGFEQSDTQHEMLNPLHEIMKGNL 178

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  +R + +L  RE+ +L + +      +  ++E+     VT  R+ Q+ ++AI++L+
Sbjct: 179 TKQISREIKALPEREQLLLNLYY----QQELNMKEISVLLNVTETRVSQLHSQAIKRLR 233


>gi|218288661|ref|ZP_03492938.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218241318|gb|EED08493.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 239

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 63/279 (22%), Positives = 103/279 (36%), Gaps = 53/279 (18%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
             +A     +    + +K  +    +S  E       +R        A+  ++E NLRLV
Sbjct: 6   MLLALVFKDVSLFVSYVKQGAFPHPLSPDEEE---RAIRDYLAGDGDARNRLIEHNLRLV 62

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
             +AKKY + G +  DLI  G IGL+KA E +    G K +TYA   ++  I   +    
Sbjct: 63  AHLAKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATYAARCIENEILMYLR--- 119

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                  H RD                        ++  +    +G              
Sbjct: 120 ---SSKKHRRDAF----------------------LSDPVGTDKDG-------------- 140

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                  +   L D +   +    +D+   +  ++     L  L PRE  VL  RFG+  
Sbjct: 141 -------NEMTLADLLG-SDPDDVIDAVDMSWEKQKMFECLPLLAPREREVLCKRFGLPD 192

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
             + T  E+ K+  ++R  + +IE KAI KL    R +K
Sbjct: 193 GEERTQREIAKELGISRSYVSRIEQKAIVKLYENMRQRK 231


>gi|309775720|ref|ZP_07670717.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916525|gb|EFP62268.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 241

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 56/227 (24%), Positives = 107/227 (47%), Gaps = 10/227 (4%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ +       AK   V+ N  LV S+ ++++ + +   DL Q G +GLMKA   FD  
Sbjct: 9   ELIERIRLGDEEAKSCFVQQNSALVYSIIRRFSRQRISNEDLFQIGCVGLMKALNNFDTS 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KFSTYA+  +   I R   D    IRI   +++   ++V+T   +  K+  EPT +E
Sbjct: 69  YEVKFSTYAVPIIMGEIKRFFRDDGS-IRISRSLKEGYLQMVKTKEMLLQKLNHEPTYQE 127

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           IA  + + V  V    +  +   SL+  I + D S +   +EDK +    +  +   ++ 
Sbjct: 128 IADAMELDVADVILAFEANQFIYSLDETIYENDGSPI--LLEDKVSNKKEEDVV---MKV 182

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +    +  L  RE+ +L  R+ +        E++ K+  +++ ++ +
Sbjct: 183 SLRDEIQKLDQREQLLLHYRYDL----SMKQEDIAKKLNISQVQVSR 225


>gi|253580726|ref|ZP_04857990.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848097|gb|EES76063.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 209

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 103/257 (40%), Gaps = 58/257 (22%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             + +  +SIS+ ++ +   +K +   S AK  ++E NLRLV  V KKY   G    DLI
Sbjct: 1   MKAFQKPLSISQEKYYL---QKYQEGDSQAKNILIEHNLRLVAHVVKKYQGTGEDTDDLI 57

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+KA   F+     + STYA   ++  +                         R
Sbjct: 58  SIGTIGLIKAVTTFNPQKASRLSTYAARCIENELLMYF---------------------R 96

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDF 591
             ++ S +                               +SL  PIG +   +  +L D 
Sbjct: 97  AKKKHSKE-------------------------------VSLYEPIGTDKEGNEINLLDV 125

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE        D  I+ N       +   L+ +E +V+  R+G+    + T  E+ ++ C+
Sbjct: 126 IESAPVDIVEDCYIRENTDYLLRSLKKVLSDKEYQVICCRYGLFGMEEETQREIARKLCI 185

Query: 652 TRERIRQIEAKAIRKLK 668
           +R  + +IE  A++KL+
Sbjct: 186 SRSYVSRIEKTALQKLR 202


>gi|7677125|gb|AAF67044.1|AF183382_4 motility sigma factor FliA [Pseudomonas putida]
          Length = 245

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 94/239 (39%), Gaps = 14/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     A  A+ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D  
Sbjct: 7   KMYSRAAKDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVSSKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAMRAVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +A +L + ++    +L  T      S +  +         D       V P         
Sbjct: 124 VAAELQLSLDDYYGILNDTLGSRLFSFDDLLQTRARRLHEDGASGH--VEPARGLEDERF 181

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   T  +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 182 QAALTEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 236


>gi|255994576|ref|ZP_05427711.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
 gi|255993289|gb|EEU03378.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
          Length = 249

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/215 (22%), Positives = 106/215 (49%), Gaps = 5/215 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  +VE  L +V  + +KY N+G+++ DL Q G + L+ A E+FD   G++FS++A   +
Sbjct: 19  RNAIVEDYLYIVDILVRKYLNKGVEYDDLYQVGAMALIMAVERFDASRGFEFSSFATPTI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+   +++P  +++    +      +  K++R+PT +EIA++  M  E V 
Sbjct: 79  LGEIKKYFRDKEWKLKVPRSVKEANAAIQSARESLFAKLQRDPTVKEIAEEKNMKEEEVA 138

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRVLASLTPR 623
           K++  +    +L   +  +D+         +  ++   S I++    E    +L+ L+ +
Sbjct: 139 KLIDSSMAYNTLSLDVTFDDSGSDSGVSRYEKYMAVEGSGIESLEYEEMIESILSVLSEK 198

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              + + RF  G     T  E+ ++  V++  I +
Sbjct: 199 NRYIFKKRFLEG----KTQSEIAEKLGVSQMTISR 229


>gi|242280062|ref|YP_002992191.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
 gi|242122956|gb|ACS80652.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
          Length = 263

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 101/231 (43%), Gaps = 13/231 (5%)

Query: 448 MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V      +  +A +      + ++  +LI  G++GL+++  KF   L  KF TYA   +
Sbjct: 39  IVRHYSPKIRIIALRMKAKLPQNVELGELISAGSLGLVESLGKFRPELKIKFETYAENRI 98

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           K A+   +            +R K+  +    R + ++   +PT  ++ +      + V+
Sbjct: 99  KGAMLDELRRMDW---FSRGLRQKVKTIENCIREIEHETGEKPTSAQLEEATGFSAKEVQ 155

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L+  +  + +     +++     D   D     P  SA+     +    ++ +LTPRE
Sbjct: 156 QGLEALQNQLCVNLDAFNDNIPSNKDSQLDDE---PFQSAVFQETVDKVADLIDNLTPRE 212

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           + VL + +G     +  ++E  +   +T  R+ Q+ ++A++KL+     K 
Sbjct: 213 KLVLSLYYG----EELNMKETSEVMEITEGRVSQLHSQALKKLRKMFHDKY 259


>gi|163816725|ref|ZP_02208088.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
 gi|158447982|gb|EDP24977.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
          Length = 224

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 114/240 (47%), Gaps = 20/240 (8%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++R  +     A+  ++  N+ LV+SVAK+Y  RG +  DLIQ G IGL+KA ++FD 
Sbjct: 5   LQLLRLAKEGDITARDRLITENMGLVVSVAKRYIGRGQELEDLIQIGLIGLIKAVDRFDL 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                FSTY++  ++  I R + D    +R+  +++   ++  +  +       REPT +
Sbjct: 65  EYDVMFSTYSVPLIQGEIRRFLRD-DGLVRVSRNLKTIHYRAEKYRQEYQRTNGREPTVD 123

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI  K+    E +   ++   +  ++E                     +      +   +
Sbjct: 124 EICAKIGSDPEELVMAMESAVDISNIEEM---------------GELQTSRREEERVVEK 168

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               ++L +L  RE++++ +R+      + T  E+G+   +++ ++ ++E K +R+LK  
Sbjct: 169 LYVKQLLDTLPEREKKLITLRYF----GEKTQGEIGRILGMSQVQVSRLEKKILRELKRA 224


>gi|331088539|ref|ZP_08337452.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330407801|gb|EGG87295.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 239

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 120/241 (49%), Gaps = 8/241 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   DTIALIRKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K V+   R+ + + R+PT
Sbjct: 63  DLTYNVKFSTYAVPLISGEIKRFLRD-DGMIKVSRSLKEIAYKSVQARERLISSLGRDPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+++++ +  E + + ++   E  S+  P+  ++ S +         +  L+   +  
Sbjct: 122 IEELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEI-------RLLDKLEEKEKRE 174

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     VL  L    +   +    +    D T  +VGK   +++ ++ + E + I KL+
Sbjct: 175 DKILDLIVLKELLETLDEEEKQLIFLRYFADRTQSDVGKIMGISQVQVSRSEKRIIEKLR 234

Query: 669 H 669
            
Sbjct: 235 K 235


>gi|170722830|ref|YP_001750518.1| flagellar biosynthesis sigma factor [Pseudomonas putida W619]
 gi|169760833|gb|ACA74149.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida
           W619]
          Length = 246

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 96/238 (40%), Gaps = 11/238 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +     +  A+ ++VE    LV  +A     R    +Q  DLIQ G IGL++ A K+D  
Sbjct: 7   KMYSKASKDAQYDLVERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDAS 66

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++ A+   +         P  +      V    R +  +  R+    E
Sbjct: 67  KGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAMRAVEARTGRDAKDHE 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLR 610
           +A +L + ++    +L  T            +D  H G   E  +  V P         +
Sbjct: 124 VAAELKLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEGLHEEGASGQVEPSRDLEDERFQ 183

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              T  +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 184 AALTDAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|315649479|ref|ZP_07902564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily protein
           [Paenibacillus vortex V453]
 gi|315274952|gb|EFU38327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily protein
           [Paenibacillus vortex V453]
          Length = 256

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 59/251 (23%), Positives = 117/251 (46%), Gaps = 15/251 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGL 481
           S  E  H++   ++ +   +     +++    +V   A K   NR   + DL Q G + L
Sbjct: 10  SRDEAVHLIQQYQQTK--DNDIATVLIKKYEPMVKMAAGKIARNRPDLYEDLYQVGQMAL 67

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++  +++D  LG  F  YAM  +   +   + D+S  I++P  +++K   V +    +  
Sbjct: 68  IRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELMV 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS-HLGDFIEDKNAV 598
           K++R P   EIA  L + VE   +VL  +     +SL++P+  E+T   LG+ I      
Sbjct: 128 KLERSPDVNEIAAYLDLSVEETVEVLAGRECYHYVSLDSPLSQEETGATLGELIS----- 182

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           S ++       R    + ++ L  +E++VL + F  G     +   + ++  V++  + +
Sbjct: 183 SDVNDFDSVEKRMDLQQAMSQLKEQEQKVLLLAFQEG----QSQRAIAQRLGVSQMSVSR 238

Query: 659 IEAKAIRKLKH 669
           I+ +A  KLK 
Sbjct: 239 IQKRATEKLKQ 249


>gi|317132447|ref|YP_004091761.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470426|gb|ADU27030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 237

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 108/238 (45%), Gaps = 13/238 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++  +     + A+ ++VE NL LV + A+ +  +G+++ DL Q G +GL+KA   FD  
Sbjct: 9   ALFIRAGKGDAAAQTQLVEENLGLVHAAARHFNGKGIEYDDLYQAGCMGLVKAVTGFDIT 68

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G +FSTYA+  +   + R   D    +++   +++   K +R   ++S ++ REPT  E
Sbjct: 69  RGVQFSTYAVPVIMGEMRRLFRD-DGPVKVSRSLKELSLKAMRAREKLSARLCREPTLSE 127

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A +L        + L+    P+SL      ED  +    I   +    L   +      
Sbjct: 128 LAAELETDPAEAAQALEAAAAPLSL--TSSREDEENGQTDIPVDSEEDALVDHL------ 179

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                L SL   +  ++ +R+  G     T  E      +T+ ++ + E K +  L++
Sbjct: 180 ALKDALGSLPADDRLLILLRYFQG----KTQTETASVLHMTQVQVSRREKKILALLRN 233


>gi|46371303|gb|AAS90418.1| stationary phase sigma factor [Azotobacter chroococcum]
          Length = 172

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 53/167 (31%), Positives = 96/167 (57%)

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           I +Q+ TIR+P+H+  +++  +R AR ++ K+  EP+ EEIA  L  PV  V+++L + +
Sbjct: 1   IMNQTGTIRLPIHVVKELNVYLRAARELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNE 60

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              S++  +G +    L D + +     P D     +L ++  + L  LT ++  V+  R
Sbjct: 61  RVTSVDVSLGPDSDRTLLDVLTEDRPSDPCDLLQDDDLSQSIDQWLFDLTDKQREVVVRR 120

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           FG+  +   TLEEVG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 121 FGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 167


>gi|259907643|ref|YP_002647999.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963265|emb|CAX54749.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|283477486|emb|CAY73402.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
          Length = 243

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 103/228 (45%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +      +V   A +   R    ++  DLIQ G++G + A + FD   G   S +  
Sbjct: 13  KTILWGKYNHIVRQEALRLQKRLPASVELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLA 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + ++     +P  +R    +V    +++      E +  +IA ++ + V 
Sbjct: 73  QRIRWALMDELRERDW---VPRRVRKHAREVTAVIQQLEQNKGGEASEADIATEMGVSVG 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
            ++++L  T            E  +   + I++ N A++P+  A+Q NL       ++ +
Sbjct: 130 ELQQMLADTNSSQIYSLDELQEQFADSYETIDEGNEALNPVHQAVQENLVGKIAEHISVI 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+R+L++ +      D  + E+G    +T  R+ Q+ + AI++++
Sbjct: 190 PEREQRILQLYY----QQDLNMREIGAVLSLTETRVSQLHSLAIKRIR 233


>gi|217968787|ref|YP_002354021.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
 gi|217506114|gb|ACK53125.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
          Length = 590

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 65/125 (52%), Positives = 86/125 (68%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
             T ++  + R I + V      A   +  M+++NLRLVIS+AKKYT+ G  FLDLIQEG
Sbjct: 449 CNTLLASPDHRDIGAAVAVALNSALDHRNRMIKSNLRLVISIAKKYTHTGFPFLDLIQEG 508

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
           N+GLMKA EKFD+  G+KFSTYA WW++QAITR IADQ   +R+PVHM + I+KV R  R
Sbjct: 509 NLGLMKAVEKFDYRRGFKFSTYATWWIRQAITRGIADQQRLVRVPVHMVESINKVSRVLR 568

Query: 538 RMSNK 542
            +  +
Sbjct: 569 ELEGR 573



 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 83/230 (36%), Gaps = 10/230 (4%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPP--DEVSSEQMEDTVAMLSNMGINVVDGDD 82
           D      + ++      G+V   ++        +   ++  E    ++ ++G+++   +D
Sbjct: 201 DEDLARLRLLLMQGLSVGFVNRSDIVEACADATESHEADLEERIERLIGDLGLHI---ED 257

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
           +    G ++     S  +        R   +    +DP+++Y+RE+G  + L+RE E  I
Sbjct: 258 VSPSFGLDEHGAAESEDACEDALEYLRDICSGD--NDPLKLYIREVGPHQALTREDEAFI 315

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           A+ +E G +  + ++         +I   D +  G     +   +        +      
Sbjct: 316 ARAMEEGVSQAIRTIASCKAALDQIIDAGDAVCRGEA---DAGSMFDRAAGNPEDEPHES 372

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
             G S   ++D   +   D  ++             D R  V S P + E
Sbjct: 373 AFGLSSTMQDDEQDQASDDAGRQQMQLQPELGAALADLRRLVYSLPASTE 422


>gi|291196382|emb|CBG22663.1| DNA-directed RNA polymerase subunit D [Pseudomonas psychrotolerans]
          Length = 240

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/284 (14%), Positives = 88/284 (30%), Gaps = 45/284 (15%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P T   ++     +      L ++  L   I P+         E
Sbjct: 1   RIEEGIREVMGAIAQFPGTVDYILSEYTRVTTEGGRLSDV--LAGYIDPDDGSLPNESDE 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                K  D+        V + + D E +     ++       PE A      + E  + 
Sbjct: 59  LPVPNKAADA------KAVDDEKDDEEESDGDDAEEEGDGGPDPEEARLRFGAVAEQLEK 112

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  +   +       L  L
Sbjct: 113 TQKVL-----------------------------------KKHGRDDDRAVEEFVALALL 137

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LV ++ +  +R+   E  +++LA     + R  FL    G E +  W
Sbjct: 138 FSPIKLVPKQYEALVTRVRESLERVRGLERAIMQLAVRDARMPRADFLRHFPGNETNTEW 197

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            +      + ++   +      I   + ++  +  +  + +S+ 
Sbjct: 198 TAGLLK-GKPKYAEGLERFQADIQAKQAQLAELERDYELKVSQI 240


>gi|261252375|ref|ZP_05944948.1| RNA polymerase sigma factor for flagellar operon [Vibrio orientalis
           CIP 102891]
 gi|260935766|gb|EEX91755.1| RNA polymerase sigma factor for flagellar operon [Vibrio orientalis
           CIP 102891]
          Length = 203

 Score =   99 bits (247), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/203 (24%), Positives = 94/203 (46%), Gaps = 12/203 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +Q  DLIQ G IGL++A + +D   G  F TYA   ++ A+   I        +P  +  
Sbjct: 1   MQVEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHK 57

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDT 585
              +V +    +  ++ R+PT  E+A+++ + +E    +L        + +E     ED+
Sbjct: 58  HNREVSQVIAILEGELNRDPTDAEVAQRMGISLEQYHVILTDINCSRLVGIEDLGISEDS 117

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
              GD  ED N             R+     + +L  RE  VL + +    + +  L+E+
Sbjct: 118 ISPGDS-EDDNLP--FKGVADEYFRKALVDSIKTLPEREALVLSLYY----DEELNLKEI 170

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
           G+   V+  R+ QI ++++++L+
Sbjct: 171 GEVIGVSESRVSQILSQSMQRLR 193


>gi|167636574|ref|ZP_02394868.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
 gi|167527997|gb|EDR90803.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
          Length = 211

 Score = 99.5 bits (246), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 62/202 (30%), Positives = 104/202 (51%), Gaps = 10/202 (4%)

Query: 410 RNEIKSISVETG----ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           RN+++   V+T     +   E R +   ++ GE     A++++V  NLRLV+SV +++ N
Sbjct: 3   RNKVEICGVDTAKLPVLKNDEMRKLFREMQSGEIS---AREKLVNGNLRLVLSVIQRFNN 59

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RG    DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +
Sbjct: 60  RGEYVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL 118

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  +K ++   ++  +  +EPT  +IAK L +  E +   L   ++P+SL  PI ++  
Sbjct: 119 RDIAYKALQVREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGG 178

Query: 584 DTSHLGDFIEDKNAVSPLDSAI 605
           D   + D + D+          
Sbjct: 179 DPIFVMDQLSDEKQKDEQWVEE 200


>gi|327539462|gb|EGF26077.1| sigma-70 factor [Rhodopirellula baltica WH47]
          Length = 557

 Score = 99.5 bits (246), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 108/248 (43%), Gaps = 60/248 (24%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  ++    EA   K ++V+ANLRLV+S+AK++      F  LI +GN+ L++A EKFD
Sbjct: 362 VMDQIQSLYEEAVKVKNKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAVEKFD 421

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
           +  G KFSTYA W + +   R+I ++            K     R               
Sbjct: 422 YSRGNKFSTYASWAIMKNFARTIPNEF-----------KHRDRFRATP------------ 458

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
                                      +          L  ++E           +Q   
Sbjct: 459 ---------------------------DEMFVAHQDERLDPYLE---------ETVQLQR 482

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    R+L  L  RE++++  RFG+       TL+EVG++  VT+ER+RQ+EA+A+ KL+
Sbjct: 483 QRELARILDRLDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARALSKLR 542

Query: 669 HPSRSKKL 676
             +R  K+
Sbjct: 543 DAARDAKI 550


>gi|221133291|ref|ZP_03559596.1| flagellar biosynthesis sigma factor [Glaciecola sp. HTCC2999]
          Length = 243

 Score = 99.5 bits (246), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 106/237 (44%), Gaps = 15/237 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLG 493
            +C  S++ +E+VE +  LV  +A     R        DLIQ G +GL++AA+ F+   G
Sbjct: 6   NDCNQSLSSEELVEKHTILVKRIAHHLLARLPPNILVDDLIQAGMLGLLEAAKNFNSTKG 65

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F T+A   ++ ++   I         P  +      + +    + N++  +    +IA
Sbjct: 66  ASFETFAGIRIRGSMLDDIRKGDW---TPRSVHKNSRAITQAISSVENEMNSDAKDSDIA 122

Query: 554 KKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           K+L + +    K+L        + +E     ED     DF   K+  +P D  +    ++
Sbjct: 123 KRLGIELPQYHKMLNEVNIGKLVGIEDLGISEDVIATPDF---KSTNTPYDELVHGCFQK 179

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              + + SL  RE  VL + +    + D +L E+G+   V+  R+ QI ++A  KLK
Sbjct: 180 ALAKAIVSLPEREAIVLSLYY----DEDLSLREIGQALNVSESRVSQIHSQAKSKLK 232


>gi|149176711|ref|ZP_01855322.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
 gi|148844352|gb|EDL58704.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
          Length = 258

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 104/264 (39%), Gaps = 18/264 (6%)

Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQE 476
             I  SE    +  V K +      +  ++E  + LV   A++   +   G+   DLI  
Sbjct: 1   MAIKASEEIAEIWKVFKQDQSNQALRNMLIEQYVPLVRYNAERVWAKLPEGVDLNDLISA 60

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G  GLM A   FD   G KF TY +  ++ A+   +        +P  +R K  K+    
Sbjct: 61  GVFGLMDAINAFDLERGVKFETYCVPRIRGAMLDELRTMDW---VPRLVRSKASKLEAAR 117

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDED---TSHLGDF 591
           +    +  R P  EEIA+K+ +  +   K+         +SL     + D        D 
Sbjct: 118 KAAEAEFGRPPADEEIARKMQLSRKEFEKLKNEANAVGLVSLNKKWYETDSYKDVREVDI 177

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +ED     P  S  + +L    T+ L        R  R+   +    + T++E+G    +
Sbjct: 178 LEDAKGEDPTKSIQKRDLMRLVTKGLN-------RNERLIIILYYYEELTMKEIGSTLGL 230

Query: 652 TRERIRQIEAKAIRKLKHPSRSKK 675
           +  R+ Q+ +  + +LK     ++
Sbjct: 231 SESRVSQMHSSIVNRLKEQLGRRR 254


>gi|228906737|ref|ZP_04070609.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
 gi|228964059|ref|ZP_04125186.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228795629|gb|EEM43109.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228852914|gb|EEM97696.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
          Length = 203

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         Q   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEQTERRLVLEDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|297529299|ref|YP_003670574.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297252551|gb|ADI25997.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 245

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 110/270 (40%), Gaps = 59/270 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  +  + + IK+ +    +S  E    ++++ K       A+  ++E NLRLV  + KK
Sbjct: 20  LKELTFLVSYIKNNAFPQPLSAQEEEKYLALMAK---GDEQARNRLIEHNLRLVAHIVKK 76

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G +  DLI  G IGL+KA E +    G K +TYA   ++  I   +          
Sbjct: 77  FENTGEEVEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEILMHLRS-------- 128

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T++ +SL  PIG 
Sbjct: 129 --------------------------------------------LKKTRKDVSLHEPIGQ 144

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D ++ +      +  +   L E   + ++ L  RE+ V+  RFG+G   +
Sbjct: 145 DKEGNEISLLDILKAEGQDIVDEIHLNMEL-EQVKQYISVLDEREKEVIINRFGLGRQRE 203

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 204 KTQREIAKELGISRSYVSRIEKRALMKMFH 233


>gi|228951468|ref|ZP_04113574.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228808175|gb|EEM54688.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 203

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 93/205 (45%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      ++++ +R P  +EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDRFQRSPKIKEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +A  R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEEAERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|261420836|ref|YP_003254518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC61]
 gi|319768505|ref|YP_004134006.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC52]
 gi|261377293|gb|ACX80036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC61]
 gi|317113371|gb|ADU95863.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC52]
          Length = 256

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 113/239 (47%), Gaps = 14/239 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
             + +   A   ++     L+ + AKK       F  DL Q G +  ++  + +D   G 
Sbjct: 20  YQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLSFLRLLDHYDPKQGT 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F +YAM  +   +   + D++  I++P  +++K  KV +    ++ K++R PT +EIA 
Sbjct: 80  SFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKGSKVQQAIDELTVKLERSPTIDEIAG 139

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + VE   ++L  +   + +SL+ P+ D  +D + +G+F+ D+      +       R
Sbjct: 140 HLGLSVEETIEILAGRDHYQAVSLDAPVQDGEKDATTIGEFVADE-----ANEIESLIER 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + +  L+ +E+ V+   F  G     T   + ++  V++  I +I+ +AI KLK 
Sbjct: 195 MDLEQAIGKLSEQEQIVIDAIFRRG----ETQRSLAERLGVSQMTISRIQKRAIAKLKR 249


>gi|229591832|ref|YP_002873951.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens SBW25]
 gi|229363698|emb|CAY51076.1| RNA polymerase sigma factor for flagellar regulon FliA [Pseudomonas
           fluorescens SBW25]
          Length = 246

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  A  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G
Sbjct: 9   YKKSARDSQGELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ A+   +         P  +      V    R +  K  R+    E+A
Sbjct: 69  ASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDHEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET- 612
            +L + ++    +L  T            +D  H G   ED  +     S    + R   
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASAHMEPSRDLEDERFQG 184

Query: 613 -TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 ALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|206890966|ref|YP_002249859.1| RNA polymerase sigma factor for flagellar operon
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206742904|gb|ACI21961.1| RNA polymerase sigma factor for flagellar operon
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 236

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 105/237 (44%), Gaps = 17/237 (7%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            +   K+ +++  L  +   A +Y +     L+  DLI  G  GL++A  K++  L    
Sbjct: 3   YSEDDKESLIKQFLPKIKHYALRYHHIVQSVLELEDLISAGIKGLLEALNKYNPSLNVPL 62

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
             +  + ++ AI   I       +      + + K      +   +  ++PT EE+A  L
Sbjct: 63  VAFIDYRIRGAILDEIRSVDVFSKEFRKKVENVKK----TYKNLKQSGKDPTDEELANYL 118

Query: 557 AMPVEGVRKVLKI--TKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            +  E +++V +     + +SL++ +  E  D  +L + I D+   +  +      L+E 
Sbjct: 119 NITQEELQEVYQSITASDIVSLDSFVVGENGDKLNLLEVISDEK--NIFEDIKFRELKEK 176

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  + +L+  E+ ++ + +      +  ++E+ +   ++  R+ QI  K + KLK+
Sbjct: 177 LTSAIENLSETEKLIISLYY----YEELNMKEIAQVLGISLSRVSQIHGKTLLKLKN 229


>gi|239995147|ref|ZP_04715671.1| flagellar biosynthesis sigma factor [Alteromonas macleodii ATCC
           27126]
          Length = 243

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 105/235 (44%), Gaps = 17/235 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K ++VE +  LV  +A     R    +   DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  KAQLVERHAPLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I         P  +      +     ++ ++  R+    +IA KL + ++
Sbjct: 74  IRIRGAMLDEIRKGDW---TPRSVHRNGRAITEAISQVESETGRDARDSDIADKLNVSLQ 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLA 618
              ++L      ++    +G ED     D I  +    + +PL+  +Q   ++     + 
Sbjct: 131 DYHQMLN----EVNAGKLVGIEDLGVSEDVISTEQNRGSDAPLEDLMQGAFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L  RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ KLK   +S
Sbjct: 187 TLPEREAIVLSLYY----DEELNLREIGEVLDVSESRVSQIHSQAMLKLKSRMKS 237


>gi|291196366|emb|CBG22655.1| DNA-directed RNA polymerase subunit D [Pseudomonas panipatensis]
          Length = 238

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 39/284 (13%), Positives = 100/284 (35%), Gaps = 47/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++ + P     ++   + +      L +++            G+    +
Sbjct: 1   RIEEGIREVMSAIAQFPGAVDGILDEYNRVVSEGGRLSDVL-----------SGYIDADD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +  +               D++  +  +K+   + +    ++E +E +   D ++
Sbjct: 50  GTLPAEEVEPV-------------DLKDDSTDAKEKDDEDEEGDGDSEEEEGDGGPDPEE 96

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A    A+ +QL                            +K  + S +       L +L
Sbjct: 97  AARRFGAVAEQLEKA---------------------KKALKKHGRGSAQASEELLALAEL 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++ D   R+   E  +++L      + R  FL    G E D  W
Sbjct: 136 FMPIKLVPKQFDALVARVRDALDRVRQQERAIMQLCVRDARMPRADFLRLFPGNETDEAW 195

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +       + ++   +      +L+ + ++ ++  E  + +++ 
Sbjct: 196 LDSVLK-GKPKYAEALERVKADVLRNQQKLSALESEVELKVADI 238


>gi|229126412|ref|ZP_04255427.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-Cer4]
 gi|228656992|gb|EEL12815.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-Cer4]
          Length = 203

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPRIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|78485092|ref|YP_391017.1| sigma 28 (flagella/sporulation) [Thiomicrospira crunogena XCL-2]
 gi|78363378|gb|ABB41343.1| sigma 28 (Flagella/Sporulation) [Thiomicrospira crunogena XCL-2]
          Length = 241

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 12/227 (5%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +EA L LV  +A     R    +   DLIQ G IGL+++++KFD   G  F TYA   ++
Sbjct: 21  IEAFLPLVKRIAYHLKGRLPDSVMVDDLIQSGIIGLIESSQKFDATQGASFETYAGIRIR 80

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   I         P  +  K  +V     ++ ++  RE   EEIA+ + + ++    
Sbjct: 81  GAMLDEIRKGDW---TPRSVYRKSREVSEAILKVESEKGREARDEEIAEVMGVSLDEYYH 137

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L+ T     L   I + D   L +        +P+   ++++ +      +  L  +E+
Sbjct: 138 ILQDTNSAQLLS--IDEPDHDELAEDRMVGTIKTPITELVESDFQGALAEQINELPEKEK 195

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            V+     +  + +  L+E+G+   V+  R+ QI ++AI++LK   R
Sbjct: 196 LVM----ALYYDEELNLKEIGEVLEVSESRVSQIHSQAIKRLKSRLR 238


>gi|228943728|ref|ZP_04106130.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976238|ref|ZP_04136717.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977712|ref|ZP_04138098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|229042834|ref|ZP_04190570.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|229143711|ref|ZP_04272133.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228639767|gb|EEK96175.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228726494|gb|EEL77715.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|228782010|gb|EEM30202.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|228783483|gb|EEM31583.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228815947|gb|EEM62170.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 203

 Score = 99.5 bits (246), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|70729057|ref|YP_258793.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens Pf-5]
 gi|68343356|gb|AAY90962.1| motility sigma factor FliA [Pseudomonas fluorescens Pf-5]
          Length = 246

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 96/237 (40%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  A  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G
Sbjct: 9   YKKSARDSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ A+   +         P  +      V    R +  K  R+    E+A
Sbjct: 69  ASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDHEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQANLRE 611
            +L + ++    +L  T            +D  H G   ED  +  + P         + 
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASAHLEPSRDLEDERFQA 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 ALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|332653441|ref|ZP_08419186.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332518587|gb|EGJ48190.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 96/254 (37%), Gaps = 59/254 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            T +S  E   ++  +++       A++ ++E NLRLV+ +A+++ N G+   DLI  G 
Sbjct: 36  PTPLSREEEGELMERLQQ---GDQRARQTLIEHNLRLVVYIARRFENTGINIEDLISIGT 92

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   +      K +TYA   ++  I   +   S                      
Sbjct: 93  IGLIKAVGTYQPARSIKLATYASRCIENEILMYLRKTSSQKTE----------------- 135

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                              +S + P+  +   +   L D +   
Sbjct: 136 -----------------------------------LSFDEPLNTDWDGNELLLSDILGTD 160

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
             +         + R+   + L  L  RE  ++ +RFG+G   + T +EV  +  +++  
Sbjct: 161 GDLVMRPIEADVD-RQLLRQALEKLDERERTIISLRFGLGGGEEQTQKEVADRMGISQSY 219

Query: 656 IRQIEAKAIRKLKH 669
           I ++E + I++LK 
Sbjct: 220 ISRLEKRIIQRLKK 233


>gi|293392779|ref|ZP_06637097.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424638|gb|EFE97849.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 202

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 61/149 (40%), Positives = 100/149 (67%), Gaps = 3/149 (2%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y+N
Sbjct: 57  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVPSRRRMIESNLRLVVKIARRYSN 113

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+
Sbjct: 114 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI 173

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAK 554
             +++  +RTAR +S+K+  EP+ EEIA+
Sbjct: 174 VKELNVYLRTARELSHKLDHEPSAEEIAE 202



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/107 (26%), Positives = 41/107 (38%), Gaps = 1/107 (0%)

Query: 78  VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSRE 137
            D +  E E   E +L    ++ N     +       +   D  ++YL E+G   LL+ E
Sbjct: 17  FDENGTEAESFDEKALAEEEASENDLAEEELLSQGVTQRVLDATQLYLGEIGYSPLLTAE 76

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  EEVYFARRALRGDVPSRRRMIESNLRLVVKIARRYS-NRGLALLDLI 122


>gi|121488773|emb|CAJ18271.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 58/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLXPREADVIRSYFGIGMD 165


>gi|229189193|ref|ZP_04316217.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
 gi|228594237|gb|EEK52032.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
          Length = 203

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 92/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G IGL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMIGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      ++++++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIRLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|229074589|ref|ZP_04207614.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
 gi|229095607|ref|ZP_04226590.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|229114558|ref|ZP_04243973.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228668908|gb|EEL24335.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228687817|gb|EEL41712.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|228708547|gb|EEL60695.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
          Length = 203

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         Q   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEQTERRLVLEDIFNVLNETEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|313905149|ref|ZP_07838518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Eubacterium
           cellulosolvens 6]
 gi|313470052|gb|EFR65385.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Eubacterium
           cellulosolvens 6]
          Length = 258

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 111/250 (44%), Gaps = 13/250 (5%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGL 481
           +E    +      + +  I ++E+    L +V ++A +  +  + F    D+I EG + +
Sbjct: 11  NEELFYLYRNATDDNDRKILRQELTMRYLYIVKAIAYQMRDMYIGFAQPDDIINEGVLEI 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK  +++D     KF T+    ++  +   +         P +       +  T + +S 
Sbjct: 71  MKGIDRYDPDRDNKFDTFISRRIRGMVIDLMRKNDWM---PRNFHRDRRTIEDTVQELSE 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVS 599
           K+ R PT EE A KL + V+ ++KV  +T     +SL+    + D + L    ED + V 
Sbjct: 128 KLGRTPTDEETAHKLGIEVKKLQKVRTMTTMVNVLSLDMTYDENDEAVLQVPTEDIS-VQ 186

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P  + ++          + SL  +E+ ++ + +         + ++     +++ R+ Q+
Sbjct: 187 PERNFMRGETVRILADAINSLQEKEKMIISLYYVDN----LNMSQIASVMDISQPRVSQL 242

Query: 660 EAKAIRKLKH 669
            A+A++KL+ 
Sbjct: 243 HAQAVKKLRK 252


>gi|121488749|emb|CAJ18259.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 59/166 (35%), Positives = 102/166 (61%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  S  + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHSLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|224370767|ref|YP_002604931.1| FliA [Desulfobacterium autotrophicum HRM2]
 gi|223693484|gb|ACN16767.1| FliA [Desulfobacterium autotrophicum HRM2]
          Length = 238

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 19/231 (8%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           M+     LV  +A ++  R    + F +L+  G++GL+ A +KFD        TYA + +
Sbjct: 1   MIVEYAFLVRQIASRFARRLPSSVLFDELVSAGSLGLIDAVDKFDSGKHVSLKTYAQYRI 60

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           K AI   +            MR KI  + R  + + +K K   +  E+AK L +P+E   
Sbjct: 61  KGAILDELRSMD---TYSRSMRKKIQDISRAVKAIEDKKKGPASDNEVAKLLEVPLESYY 117

Query: 565 KVLKITKEP--ISLETPIGDEDTSH-----LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            +L        +SL+  I   D            I+ ++  + L    +  L+    R +
Sbjct: 118 DMLTDIHGAAILSLDAFIRTGDNDTSSMTRFQAGIKGEHTPADLLD--REELKGVLARAV 175

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +LT +E+ V+ + +      + TL+E+G+   +T  RI QI    + KLK
Sbjct: 176 TTLTEKEQLVVSLYY----YEELTLKEIGEVLTLTESRICQIHTAILIKLK 222


>gi|158338094|ref|YP_001519270.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308335|gb|ABW29952.1| RNA polymerase sigma factor, group3 [Acaryochloris marina
           MBIC11017]
          Length = 266

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 110/243 (45%), Gaps = 15/243 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           +V   +  +   +  +V  N+ LV  VA + T++    + DL Q G +GL+ A E+FD  
Sbjct: 15  LVAYRQKPSVQLRNRLVRLNMGLVRKVAHRLTHQCAEPYEDLEQCGFLGLITAIERFDPS 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY FS++A+ +++  I   + D++ T+RIP   +       +  + ++ ++ R+P  +E
Sbjct: 75  QGYAFSSFAVPYIRGEILHFLRDRANTVRIPRRWQQLSRDAAKARQALTMELGRQPNDQE 134

Query: 552 IAKKLAMPVEGVR--KVLKITKEPISLETPI-----GDEDTSHLGDFIEDKNAVSPLDSA 604
           IA  L++ ++  R  K+    + P+SL   +       +    LGD + D ++       
Sbjct: 135 IADALSLSMQEWRSVKLATTNRVPLSLNARVSSGHSQSDSAMTLGDTLMDVHS---QILQ 191

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                R    + L  L  R   ++   F        + +EV K+  V+   + +   K I
Sbjct: 192 ANQEDRIELQQALNQLEDRTRIMIESVFF----QQLSRQEVAKRIGVSSVTVTRNMKKGI 247

Query: 665 RKL 667
            KL
Sbjct: 248 DKL 250


>gi|323705323|ref|ZP_08116898.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535225|gb|EGB25001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 247

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 110/231 (47%), Gaps = 9/231 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++RK +     + +++++ N  L+ S+ KK++ RG +  DL Q G IG +KA  KF
Sbjct: 11  DVNELIRKSKNNDKSSMEKLLKENSGLIWSIVKKFSYRGYEAEDLYQIGCIGFVKAINKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K STYA+  +   I R + D    I++   +++  +K      ++  ++ REPT
Sbjct: 71  DESYNVKLSTYAVPIIIGEIKRFLRD-DGLIKVSRSLKELSNKAYFMKDKLEKELNREPT 129

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            +EIA KL +  E V    + T     L       +  +L   + +K  +   +  I+  
Sbjct: 130 IQEIASKLDVSAEEVAMAFESTATAEYLYDNSQHNEDDNL--LLIEKIGIDEQEYEIEDK 187

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           L      VL +L  RE +++ +R+      D T  EV K   +++ ++ +I
Sbjct: 188 L--ALRMVLKNLNSRERQIIVLRYF----KDMTQTEVSKILGISQVQVSRI 232


>gi|113955141|ref|YP_730472.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882492|gb|ABI47450.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 282

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 135/272 (49%), Gaps = 23/272 (8%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRK---------GECEASIAKKEMVEANLRLVISV 459
           I   +  I     ++ +E   + + VR           +     AK  M++ANLRLV++V
Sbjct: 9   IDQFLDEIGRTPLLTAAEEITLGTSVRMSQSPEATPAQKRAGKRAKDRMIKANLRLVVTV 68

Query: 460 AKKYTNRGL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           ++KY +R L   +F DL+QEG+IGL +A EKFD  LGYKFSTYA WW++Q+I+R+I   S
Sbjct: 69  SRKYLHRQLGQLEFGDLVQEGSIGLNRAVEKFDPELGYKFSTYAYWWIRQSISRAIDQTS 128

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
            TIR+P  M   + K+     ++   +  E   E +  +++       +   + K   SL
Sbjct: 129 ATIRVPTSMNLVLAKLN----QLPQGLNDEQICELL--EVSDTQLKNLRHAFVAKRIASL 182

Query: 577 ETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           +  +G + D S L + + D+ +    D      ++ +           ++ +LR      
Sbjct: 183 DMKLGADRDGSTLTELLCDEQSTLNYDEFQWEAVKRSLGDQAKIALNNDQELLRR----N 238

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  + +L+ +  +  ++RER+RQ   +A + L
Sbjct: 239 VVDEQSLQSIANEIGISRERVRQKVDRAKKHL 270


>gi|310822395|ref|YP_003954753.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309395467|gb|ADO72926.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 245

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 113/279 (40%), Gaps = 63/279 (22%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ +     ++  +   +    RK       A++ +  +NL  V++VAKK+ NRG 
Sbjct: 12  LSHYLRHLGGHHQLTREQEYELARAARK---GDESARQTLATSNLAFVVAVAKKFANRGA 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
           +  DLIQEGN+GLMKA E FD     +F+TYA+WW++  ITR + D    +R     R  
Sbjct: 69  RLDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGGESERG- 127

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
                                                    +    SL+  I +E  +  
Sbjct: 128 -----------------------------------------SMVDFSLDATIDEEGETTF 146

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF-----GIGMNTDHTLE 643
            D +ED               RE    V  +L    +R+  + +      +  +   TLE
Sbjct: 147 MDRLEDGGPSPSDVYLS----REQDQEVHEALVKVRKRIGDLGWDILQERLTQDKPLTLE 202

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           E+G+++ V+RER+RQ+E K             L  +L+ 
Sbjct: 203 ELGQRWGVSRERVRQVELKT---------KSFLERYLEA 232



 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLR +G    L+RE E  +A+    G      +L  S L F  ++    +  +    L +
Sbjct: 15  YLRHLGGHHQLTREQEYELARAARKGDESARQTLATSNLAF--VVAVAKKFANRGARLDD 72

Query: 184 II 185
           +I
Sbjct: 73  LI 74


>gi|332994104|gb|AEF04159.1| flagellar biosynthesis sigma factor [Alteromonas sp. SN2]
          Length = 243

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 104/235 (44%), Gaps = 17/235 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K ++VE +  LV  +A     R    +   DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  KSQLVERHASLVKRIAHHLMARLPASVLVDDLIQSGMIGLLEAARNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I         P  +      +     ++  +  R+    +IA K+ + ++
Sbjct: 74  IRIRGAMLDEIRKGDW---TPRSVHKNGRAITEAISQVEGETGRDARDVDIAAKMNVSMQ 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK---NAVSPLDSAIQANLRETTTRVLA 618
              ++L      ++    +G ED     D I  +    + +PL+  +Q   ++     + 
Sbjct: 131 DYHQMLN----EVNAGKLVGIEDLGVSEDVISTEKNRGSDAPLEDLMQGAFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L  RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ KLK   +S
Sbjct: 187 TLPEREAIVLSLYY----DEELNLREIGEVLDVSESRVSQIHSQAMLKLKSRMKS 237


>gi|293374267|ref|ZP_06620595.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
 gi|292647100|gb|EFF65082.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
          Length = 229

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 66/274 (24%), Positives = 114/274 (41%), Gaps = 59/274 (21%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            F+     +++ +   I + +    +S  E  H ++++         A+++++E NLRLV
Sbjct: 5   QFIVSLFSNLIPLMGSISNQAFPNPLSAEEEEHYLTLM---ANGDKNAREKLIEHNLRLV 61

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
             + KKY N+     DLI  G IGL+KA + F    G K +TYA   +   I        
Sbjct: 62  AHIVKKYQNQTDDKEDLISIGTIGLIKAIDSFSPDKGTKLATYAARCIDNEILM------ 115

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                          + R+ ++M N                                +SL
Sbjct: 116 ---------------LFRSTKKMRN-------------------------------DVSL 129

Query: 577 ETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
             PIG +   +   L D ++D+N     D  IQ    E   + L SLT RE  ++  RFG
Sbjct: 130 YDPIGYDKEGNEICLIDVVKDEN-KDLNDIIIQQLAFEKIEKNLKSLTQRERDIIVRRFG 188

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +  + + T +E+ K + ++R  + +IE +A+ KL
Sbjct: 189 LENHEEETQQEIAKSYGISRSYVSRIEKRALMKL 222


>gi|229068653|ref|ZP_04201951.1| RNA polymerase sigma-B factor [Bacillus cereus F65185]
 gi|229078304|ref|ZP_04210868.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-2]
 gi|229177534|ref|ZP_04304912.1| RNA polymerase sigma-B factor [Bacillus cereus 172560W]
 gi|228605896|gb|EEK63339.1| RNA polymerase sigma-B factor [Bacillus cereus 172560W]
 gi|228704979|gb|EEL57401.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-2]
 gi|228714400|gb|EEL66277.1| RNA polymerase sigma-B factor [Bacillus cereus F65185]
          Length = 203

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      ++++ +R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|261418447|ref|YP_003252129.1| sporulation sigma factor SigK [Geobacillus sp. Y412MC61]
 gi|319767593|ref|YP_004133094.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
 gi|261374904|gb|ACX77647.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC61]
 gi|317112459|gb|ADU94951.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
          Length = 245

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 110/270 (40%), Gaps = 59/270 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  +  + + IK+ +    +S  E    ++++ K       A+  ++E NLRLV  + KK
Sbjct: 20  LKELTFLVSYIKNNAFPQPLSAQEEEKYLALMAK---GDEQARNRLIEHNLRLVAHIVKK 76

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G +  DLI  G IGL+KA E +    G K +TYA   ++  I   +          
Sbjct: 77  FENTGEEVEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEILMHLRS-------- 128

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T++ +SL  PIG 
Sbjct: 129 --------------------------------------------LKKTRKDVSLHEPIGQ 144

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D ++ +      +  +   L E   + ++ L  RE+ V+  RFG+G   +
Sbjct: 145 DKEGNEISLLDILKAEGEDIVDEIHLNMEL-EQVKQYISVLDEREKEVIINRFGLGRQRE 203

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 204 KTQREIAKELGISRSYVSRIEKRALMKMFH 233


>gi|229149313|ref|ZP_04277550.1| RNA polymerase sigma-B factor [Bacillus cereus m1550]
 gi|229154668|ref|ZP_04282783.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 4342]
 gi|228628616|gb|EEK85328.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 4342]
 gi|228634127|gb|EEK90719.1| RNA polymerase sigma-B factor [Bacillus cereus m1550]
          Length = 203

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|254425398|ref|ZP_05039116.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196192887|gb|EDX87851.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 246

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 111/234 (47%), Gaps = 13/234 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++     +   + ++V  N  LV  +A + +++    + DL Q G IGL+++ E+FD   
Sbjct: 1   MQYKVDRSVKLRNQLVRLNAGLVRKIAHRVSHQCAEPYEDLEQIGYIGLIRSIERFDPGQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  FS++A+ +++  +   + D+  T++IP   +D   +  +    +  +  R+P+  E+
Sbjct: 61  GCAFSSFAVPYIRGEMLHFLRDRGTTVKIPRRWQDLQKEGQKRQSELIRRYGRQPSDIEM 120

Query: 553 AKKLAMPVEGVR--KVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQAN 608
           A+ L + V+  R  K+    + P+SL+  +    + +  LGD + D   V    + I   
Sbjct: 121 AEALTVSVQEWRQVKLANKNRMPLSLDATVCHQIDSSITLGDTLPD---VHYQLTQILEE 177

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI-RQIEA 661
            R+   R ++ L  +    +   F  G     + +EV ++  V+   + R+I+ 
Sbjct: 178 DRQQIQRAMSQLEEKTRSAIEFVFFKG----LSRKEVAERIGVSPMTVTRRIQR 227


>gi|303248004|ref|ZP_07334270.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
 gi|302490561|gb|EFL50466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
          Length = 225

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 46/209 (22%), Positives = 95/209 (45%), Gaps = 10/209 (4%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           + ++  +L+  G +GL++A  +F   LG KF TYA   +K A+   +       R   H 
Sbjct: 21  QSVELGELLSAGAMGLLEALGRFRPELGIKFETYAESRIKGAMLDDLRRMDWFSRGQRHR 80

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
                 +   +RR+ +   R P+ E++A+   +    V + L+  +  + L      E+ 
Sbjct: 81  VRT---LEEASRRIESDSGRTPSVEQLAEATGLSEREVTQGLEALQNQLCLSLDAITENI 137

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S      +++    P  SA    L +    ++  LTPRE+ VL + +G     +  + E 
Sbjct: 138 SSYQ---KNQLENEPYKSAEFKELVDKLASLIDDLTPREKLVLSLYYG----EELNMRET 190

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            +   +T  R+ Q+ ++A+ +L+   +++
Sbjct: 191 SEVMGITEGRVSQLHSQALARLRQKFKAQ 219


>gi|222431353|gb|ACM50629.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 37/270 (13%), Positives = 90/270 (33%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D + A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AAKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
           A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 194 ARLQPDIVRCQQKLSALETETGLSIAEIKD 223


>gi|292669753|ref|ZP_06603179.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
 gi|292648550|gb|EFF66522.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
          Length = 251

 Score = 99.1 bits (245), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 103/229 (44%), Gaps = 20/229 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  + E  L LV  VA +      + +   DL+  G  GL+ A E+++   G KF TYA 
Sbjct: 28  RNRIAEHYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLLDAIERYELARGNKFETYAG 87

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+ A+   +  +     IPV +R  I K  +    +  ++ R  T EE+A++L + +E
Sbjct: 88  VRVRGAMLDHLRAKDW---IPVSVRQNIKKYEKAVAHLEGELGRTATDEELAEELDLTIE 144

Query: 562 GVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           G+   +        I LE  +  +  + L D         P++ A    ++ET    +  
Sbjct: 145 GLHHLEGQVSAATVIPLEEYLRTDSPTSLED--------GPVEHAEWTEVKETLAAAIEK 196

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E  V+ + +      + TL+E+     ++  RI Q+  KAI +++
Sbjct: 197 LPEKERTVITLYY----YDEMTLKEIAAILHLSEARISQLHTKAIFRMR 241


>gi|22596849|gb|AAN03367.1|AF481091_4 FliA [Pseudomonas fluorescens]
          Length = 246

 Score = 98.8 bits (244), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 96/237 (40%), Gaps = 13/237 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            +  A  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   G
Sbjct: 9   YKKSARDSQGELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKG 68

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ A+   +         P  +      V    R +  K  R+    E+A
Sbjct: 69  ASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDHEVA 125

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSAIQANLRE 611
            +L + ++    +L  T            +D  H G   ED  +  + P         + 
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGEHEG-LHEDGASAHLEPSRDLEDERFQS 184

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 185 ALAEAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|325674464|ref|ZP_08154152.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
 gi|325554724|gb|EGD24398.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
          Length = 269

 Score = 98.8 bits (244), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 51/260 (19%), Positives = 103/260 (39%), Gaps = 12/260 (4%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           ++   +    I E R   +       E       +  A L +   VA +Y NRG+   +L
Sbjct: 13  EACDEQVRRCIEELRDHCASGETDPEELHRCVDRLCVAALPMAYRVAGRYRNRGVPTAEL 72

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q   + L+ AA +FD   G  F  YA+  V+  I +   D + +  +P  +++    V 
Sbjct: 73  RQVAALALVGAARRFDPSRGTDFIPYAVTSVRGEIRKYFRDFTWSTHVPRRLQESHLAVR 132

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDF 591
                +S ++ R    +E+A  L MPVE   +  ++       SL+    D     L   
Sbjct: 133 NRMESLSTELGRTVRLDEVAHSLGMPVEEAEEAERVGELYSCESLDATPVDGSVPRL--- 189

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
                         +   R    R++A+L  R+  +L +R+        +  E+ +Q  +
Sbjct: 190 ---HTTGDVDADLSRVEHRHLLRRLMATLDERQRTLLWLRYFH----QMSQSEIAEQVGL 242

Query: 652 TRERIRQIEAKAIRKLKHPS 671
           ++  + ++  +++  L+  +
Sbjct: 243 SQMHVSRLLRQSLEHLRRQA 262


>gi|228957370|ref|ZP_04119129.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229028783|ref|ZP_04184888.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228732530|gb|EEL83407.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228802319|gb|EEM49177.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 203

 Score = 98.8 bits (244), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 91/205 (44%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|68164561|gb|AAY87290.1| predicted flagellar-specific RNA polymerase sigma factor FliA
           [uncultured bacterium BAC17H8]
          Length = 240

 Score = 98.8 bits (244), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 103/239 (43%), Gaps = 14/239 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +R    E     +E++ +++ LV  +A     R    ++  DLIQ G  GL+ AA+ +  
Sbjct: 1   MRNQYLEQKPDVEELITSHMELVRQIAWHMHGRLHSSIEIEDLIQIGYFGLVTAAQNYTL 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F++YA   ++ AI   +   S   R  + M+ K +      R + N++ REPT  
Sbjct: 61  REGATFASYAGIRIRGAIVDHLRKSSNLCRTTIEMQKKANV---AGRELRNRLGREPTSA 117

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A+ + +  + +       +  +        ++ S   +  E+    +      +  LR
Sbjct: 118 EMAEHMCISEDEMHNWEHAFQANVHQSLDSVYDEFSIWFESPENTPEENIN----EEELR 173

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 L +L  RE  V+++ +      +  + E+ +   VT  R+ QI+  AI  L+H
Sbjct: 174 NLLKEALRTLPEREALVIQLYYV----EELNVYEIAEVLEVTTGRVSQIKKSAIGSLRH 228


>gi|315127302|ref|YP_004069305.1| flagellar biosynthesis sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315015816|gb|ADT69154.1| flagellar biosynthesis sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 236

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 10/224 (4%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +VE +  LV  VA     R    +Q  DLIQ G IGL++A++ FD   G  F T+A   +
Sbjct: 12  IVEKHASLVKKVACHLIARLPASVQLDDLIQSGMIGLIEASKNFDASKGASFETFAGIRI 71

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +        +P  +  K   V  T   + N + REP   E+A+KL + +    
Sbjct: 72  RGAMIDEMRRGDW---VPRSVHRKSRLVAETIVALENSLNREPKDSEVAEKLEISLNEYH 128

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            +L        L       D   +    +D     P ++       E+    + SL  ++
Sbjct: 129 HILNDVNVSKVLGIEDLGIDDDVITPHGQDLALDKPFNNVKNERFNESLLSAIKSLPEKD 188

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             VL + +    N +  L+E+G    V+  R+ QI  +A+ KLK
Sbjct: 189 AMVLSLYY----NDEMNLKEIGHILDVSESRVSQIHGQAMIKLK 228


>gi|222431343|gb|ACM50624.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431345|gb|ACM50625.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 37/270 (13%), Positives = 90/270 (33%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D + A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
           A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 194 ARLQPDIVRCQQKLSALEAETGLSIAEIKD 223


>gi|163856407|ref|YP_001630705.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii
           DSM 12804]
 gi|163260135|emb|CAP42436.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii]
          Length = 246

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 52/223 (23%), Positives = 103/223 (46%), Gaps = 12/223 (5%)

Query: 451 ANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
               LV  +A +   R    +Q  DLIQ G IGL+ AA ++      +F TYA   ++ A
Sbjct: 10  RYAPLVRKLALQLLARLPASVQLDDLIQAGMIGLLDAARRYQETPDAQFETYATARIRGA 69

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +   +  Q     +P  +R K  ++    +R  +++ R P+  EIA +L +P++  + +L
Sbjct: 70  MLDELRSQDW---LPRSVRSKGKRIEAAIQRKEHELMRPPSESEIADELELPLDEYQAML 126

Query: 568 KITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
              +  + +  +    ++        +   +   PLD+ +  +LR      + +L  RE+
Sbjct: 127 NDARGIQILHYDDIGSNDPDERGWRDVPADSGGDPLDALLTGDLRRALVNAIETLPEREK 186

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            VL + +  G      L+E+G    VT  R+ Q+ ++A  +++
Sbjct: 187 LVLSLCYEQG----LNLKEIGAVLEVTEARVCQLRSQATARIR 225


>gi|304317194|ref|YP_003852339.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778696|gb|ADL69255.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 241

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 105/267 (39%), Gaps = 57/267 (21%)

Query: 407 LKIRNEIKSISVETGISIS-EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           LKIR  I  +     +         + ++ K E   + AK  ++E NLRLV+ +AKK+ N
Sbjct: 22  LKIRESIFYVGGSEALPPPLSTEEEIFLIAKMESGDNAAKSMLIERNLRLVVYIAKKFEN 81

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G+   DLI  G IGL+KA   F+     K +TYA   ++  I   +   S         
Sbjct: 82  TGVGIEDLISIGTIGLIKAINTFNPHKKIKLATYASRCIENEILMYLRRNSK-------- 133

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
                                                       T+  +S + P+  +  
Sbjct: 134 --------------------------------------------TRMEVSFDEPLNIDWD 149

Query: 586 SH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            +   L D +   N +       + + ++     L  L+ RE+R++ +RFG+G   + T 
Sbjct: 150 GNELLLSDILGTDNEIVYKMIEDEVD-KQLLKTALKKLSEREKRIIGLRFGLGGGAEMTQ 208

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +EV     +++  I ++E + +++LK 
Sbjct: 209 KEVADMLGISQSYISRLEKRILKRLKK 235


>gi|239934412|emb|CAR92336.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 225

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 61/155 (39%), Gaps = 2/155 (1%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             LQ  +   +K+ ++  +     + L  L   + L   + ++LVE++ D   R+   E 
Sbjct: 69  DQLQVTSKVLKKNGRNHKESIEALQALADLFMPIKLVPKQFEVLVERVRDALSRLRQQER 128

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L      + R  FL      E D  W           W   +  +  +I+  + ++
Sbjct: 129 AIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKNAAIVACQQKL 187

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             +  ETG++++E + I       +   +  +  M
Sbjct: 188 IDLETETGLTVAEIKEINRRANSADIHHTGGRSSM 222


>gi|121488769|emb|CAJ18269.1| sigma 70-type sigma factor [Chlorobium limicola]
 gi|121488771|emb|CAJ18270.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 58/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|304316787|ref|YP_003851932.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778289|gb|ADL68848.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 247

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 106/231 (45%), Gaps = 9/231 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +  ++RK +    ++ +++++ N  L+ S+ KK++NRG +  DL Q G IG +KA  KF
Sbjct: 11  DVNELIRKSKNNDKLSLEKLLKENSGLIWSIVKKFSNRGYEAEDLYQIGCIGFVKAINKF 70

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K STYA+  +   I R + D    I++   +++  +K       +  ++ REPT
Sbjct: 71  DESYNVKLSTYAVPIILGEIKRFLRD-DGLIKVSRSLKELSNKAYYIKDELEKELNREPT 129

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            +EIA KL +  E +    + T     L       +  ++   IE   +           
Sbjct: 130 IQEIASKLNVSAEEIAMAFESTATAEYLYDNSQHSEDDNML-LIEKIGSEDNEYDIED-- 186

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +     VL  L  RE +++ +R+      D T  EV K   +++ ++ +I
Sbjct: 187 -KLALRMVLKKLDSRERQIIVLRYF----KDMTQTEVSKILGISQVQVSRI 232


>gi|88704270|ref|ZP_01101984.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
 gi|88701321|gb|EAQ98426.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
          Length = 236

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 105/245 (42%), Gaps = 24/245 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +S V       + +   +V   L LV  +  +   +    ++  DL+Q G IGL++A E 
Sbjct: 1   MSRVSAYAEPVASSADALVREFLPLVKKIGLRLAAKLPAEIEVDDLMQVGLIGLLRARES 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D   G  F+TYA   +K A+   I        +P  ++ ++ +V     R   ++    
Sbjct: 61  YDASQGASFATYAGIRIKGAMLDEIRAHDW---LPRSVQTQLRQVSVAIERADARLGHPA 117

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV----SPLDS 603
              +IA +L MP+   ++          L   +     +H+ D  E +NAV    +P D 
Sbjct: 118 QDADIAAELDMPLAEYQQ----------LSGQLACARMTHIEDSAEAENAVLNTVNPFDE 167

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   RE     +A L  +E  ++ + +      D  L+E+G    V+  R+ Q+  +A
Sbjct: 168 VGEEGFREALAESVAQLPEKERLMMSLYYA----EDLNLKEIGAVLGVSESRVSQLHGQA 223

Query: 664 IRKLK 668
           + +L+
Sbjct: 224 LARLR 228


>gi|121488727|emb|CAJ18247.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLXKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  +  + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|188586278|ref|YP_001917823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350965|gb|ACB85235.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 253

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 121/235 (51%), Gaps = 7/235 (2%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +  +     A+K ++E N+ LV SV K++   G++  DL Q G +GL+KA +KFD+    
Sbjct: 21  KWQQKGDREARKIIIEENINLVKSVVKRFVGSGIEEEDLTQLGLMGLIKAIDKFDYRKEV 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +FSTYA+  +   I   + D    I++  ++++  ++     R ++ K++REPT  E+A 
Sbjct: 81  RFSTYAVPLIIGEIKTFLRD-DHPIKVSRNLKELFNRSKEVKRWLTLKLRREPTISEVAD 139

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
           +L +  E +    +  +E ISL+ P+ DE        + D    +  D+ I   L  T  
Sbjct: 140 ELEVSKEELATAEEANQELISLDKPVSDEHNHESEKALIDTIPDNSFDAKIHNEL--TIQ 197

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +L  L  ++ R++ +R+ +    + + +E G    +++ ++ ++E + +  L+ 
Sbjct: 198 ELLKKLDQKKRRLIVLRYFL----EKSQQETGVILGMSQVQVSRMERRILNNLQR 248


>gi|121488745|emb|CAJ18257.1| sigma 70-type sigma factor [Chlorobaculum thiosulfatiphilum]
          Length = 165

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHGLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|222431355|gb|ACM50630.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431357|gb|ACM50631.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431359|gb|ACM50632.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 37/270 (13%), Positives = 90/270 (33%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D + A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AAKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
           A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 194 ARLQPDIVRCQQKLSALEAETGLSIAEIKD 223


>gi|157363480|ref|YP_001470247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
 gi|157314084|gb|ABV33183.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
          Length = 236

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 52/227 (22%), Positives = 102/227 (44%), Gaps = 13/227 (5%)

Query: 447 EMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E+++  L  V  +A    +   + ++  DLIQEG + L+ A  ++D   G    ++ +  
Sbjct: 8   EIIKEMLPSVKRIAMDLLHTLPKNVEVDDLIQEGVLALLSAIRRYDPKKGVSMYSFVVKR 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K A+   +         P ++R  + +V +    + N + + P+ EEIA    +    V
Sbjct: 68  IKGAMYDYLRKIDWM---PRNLRKNVKEVEKAIHELENHLNKHPSIEEIALHTGLSTNEV 124

Query: 564 RKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           ++ L  T     L       E      D I+  +  S  ++A +  + E     + +L+ 
Sbjct: 125 KRALDETVRKQLLRLDEFIYEGLDSFSDIIKADDEPS--ENAFREIILEKVAEAIRTLSK 182

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+ VL +RF      D +L+E+G    V+  R+ QI + ++ K+K 
Sbjct: 183 REQLVLSLRF----EQDLSLKEIGTVIGVSESRVSQILSSSLIKIKR 225


>gi|153814969|ref|ZP_01967637.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
 gi|145847537|gb|EDK24455.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
          Length = 243

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 123/248 (49%), Gaps = 8/248 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++++RK       A++++V+ N+ LV  V K++  RG +  DL Q G+IGL+KA +KF
Sbjct: 3   DTIALIRKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     KFSTYA+  +   I R + D    I++   +++  +K V+   R+ + + R+PT
Sbjct: 63  DLTYNVKFSTYAVPLISGEIKRFLRD-DGMIKVSRSLKEIAYKSVQARERLISSLGRDPT 121

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EE+++++ +  E + + ++   E  S+  P+  ++ S +         +  L+   +  
Sbjct: 122 IEELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEI-------RLLDKLEEKEKRE 174

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +     VL  L    +   +    +    D T  +VGK   +++ ++ + E + I KL+
Sbjct: 175 DKILDLIVLKELLETLDEEEKQLIFLRYFADRTQSDVGKIMGISQVQVSRSEKRIIEKLR 234

Query: 669 HPSRSKKL 676
                K++
Sbjct: 235 KKEEDKRI 242


>gi|222431337|gb|ACM50621.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431339|gb|ACM50622.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431341|gb|ACM50623.1| RNA polymerase sigma factor [Pseudomonas brassicacearum]
          Length = 223

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 37/270 (13%), Positives = 90/270 (33%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D + A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AVKADDDTDDDEAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
           A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 194 ARLQPDIVRCQQKLSALEAETGLSIAEIKD 223


>gi|138897001|ref|YP_001127454.1| sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
 gi|134268514|gb|ABO68709.1| Sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
          Length = 258

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 107/239 (44%), Gaps = 14/239 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
             + +   A   ++     L+ + AKK       F  DL Q G +  ++  E +D   G 
Sbjct: 22  YQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQVGRLSFLRLLEHYDPNQGT 81

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F +YAM  +   +   + D++  I++P  +++   KV +    ++  ++R P  EEIA 
Sbjct: 82  SFESYAMKSLIGYMKNYLRDKAWYIQVPRRVKENGSKVQKAIDELTVTLERSPNIEEIAN 141

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + VE   ++L  +   + IS++ P+ D  +D + +G+F+ D       +       R
Sbjct: 142 HLGLSVEETIEILAGRDHYQAISIDAPVQDGEKDATTIGEFLADDT-----NEVEALIER 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 +  L+ +E  V+   F  G     T   + K+  V++  I +I+ +AI KLK 
Sbjct: 197 LDLQEAIGKLSEQERIVIEAVFRRG----ETQRSLAKRLGVSQMTISRIQKRAIEKLKR 251


>gi|1419613|emb|CAA67397.1| signma factor 28 [Legionella pneumophila str. Corby]
          Length = 238

 Score = 98.8 bits (244), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 52/233 (22%), Positives = 103/233 (44%), Gaps = 17/233 (7%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              ++ +V+ +  LV  +      R    +Q  DLIQ G +GL++AA  +D   G  F T
Sbjct: 12  QQTQEALVKTHATLVKRIRHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFET 71

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  +   +        +P  +      +    R + +K+ RE    EIA++L +
Sbjct: 72  YAGIRIRGHMLDEVRRNDW---VPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGV 128

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTR 615
            +     +L+ +          G +D     D + D     +  P  + +++++    T+
Sbjct: 129 SLNDYHSMLQDSIS----SHLYGFDDLGVTDDILFDDEGNGSTEPHRNVMRSDMMNRLTQ 184

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+ SL  +E  VL + +      D  L+E+G+   V+  RI QI ++A  +++
Sbjct: 185 VIDSLPRKERLVLSLYY----EQDLNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|305675234|ref|YP_003866906.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|161168469|dbj|BAF93933.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto]
 gi|291485028|dbj|BAI86103.1| hypothetical protein BSNT_03833 [Bacillus subtilis subsp. natto
           BEST195]
 gi|305413478|gb|ADM38597.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 242

 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 110/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 8   ALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 65  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 121

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 122 -------------------------------------------------LKKTKKDVSLH 132

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +N        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 133 DPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKQYIDILDDREKEVIVGRFGL 191

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 192 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 226


>gi|261409324|ref|YP_003245565.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Paenibacillus
           sp. Y412MC10]
 gi|329928598|ref|ZP_08282465.1| putative RNA polymerase sigma factor SigB [Paenibacillus sp. HGF5]
 gi|261285787|gb|ACX67758.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. Y412MC10]
 gi|328937714|gb|EGG34123.1| putative RNA polymerase sigma factor SigB [Paenibacillus sp. HGF5]
          Length = 256

 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 59/251 (23%), Positives = 117/251 (46%), Gaps = 15/251 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGL 481
           S  E  H++   ++ +   +     +++    +V   A K   NR   + DL Q G + L
Sbjct: 10  SRDEAVHLIEQYQQTK--DNDIATVLIKKYEPMVKMAAGKIARNRPDLYEDLYQVGQMAL 67

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++  +++D  LG  F  YAM  +   +   + D+S  I++P  +++K   V +    +  
Sbjct: 68  IRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELMV 127

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS-HLGDFIEDKNAV 598
           K++R P   EIA  L + VE   +VL  +     +SL++P+  E+T   LG+ I      
Sbjct: 128 KLERSPDVNEIASYLDLSVEETVEVLAGRECYHYVSLDSPLSQEETGATLGELIS----- 182

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           S ++       R    + ++ L  +E++VL + F  G     +   + ++  V++  + +
Sbjct: 183 SDVNDFDSVEKRMDLQQAMSQLKEQEQKVLLLAFQEGQ----SQRAIAQRLGVSQMSVSR 238

Query: 659 IEAKAIRKLKH 669
           I+ +A  KLK 
Sbjct: 239 IQKRATEKLKQ 249


>gi|222431351|gb|ACM50628.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 38/270 (14%), Positives = 90/270 (33%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D E A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AVKADDDTDDEDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
           A     I++ + ++ ++  ETG+SI+E + 
Sbjct: 194 ARLQPDIIRCQQKLSALEAETGLSIAEIKD 223


>gi|307546921|ref|YP_003899400.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
 gi|307218945|emb|CBV44215.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
          Length = 235

 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 108/242 (44%), Gaps = 15/242 (6%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  I + +++E  L LV   A     R    ++  DLIQ G +GL++A  +FD   
Sbjct: 1   MYTAQGKIEQGDLLEEYLPLVRRQALALQVRLPASIELDDLIQAGTVGLLEALGRFDAAQ 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  FST+A   ++ A+   +  +     +P  +R          RR+   + R P   EI
Sbjct: 61  GASFSTFASQRIRGAMLDELRSRDW---LPRSVRRGARAADEAVRRLEQSLGRPPEEAEI 117

Query: 553 AKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A+ L M ++  R++L  T   + +  E  + +     L D   ++ A +P+   +    R
Sbjct: 118 AEALDMDIDAYRRLLSDTNSGQLLPFEDLMSEGGEGRLRD---NETAETPVSLLVDDERR 174

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
              T  + +L  RE+ ++     +    +  L+E+G    VT  R+ Q+ ++A+ +L+  
Sbjct: 175 RQLTAGIEALPEREKLLM----ALYYQEELNLKEIGAVLGVTESRVCQLHSQAVSRLRGR 230

Query: 671 SR 672
            R
Sbjct: 231 LR 232


>gi|213027409|ref|ZP_03341856.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 185

 Score = 98.4 bits (243), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 42/186 (22%), Positives = 89/186 (47%), Gaps = 8/186 (4%)

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A +++D   G  F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++
Sbjct: 1   AVDRYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQEL 57

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLD 602
            R  T  E+A++L +PV   R++L  T            E+     + + E+    +PL 
Sbjct: 58  GRNATETEVAERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLH 117

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++ +LR+     + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++
Sbjct: 118 QLLEGDLRQRVMDAIESLPEREQLVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQ 173

Query: 663 AIRKLK 668
           AI++L+
Sbjct: 174 AIKRLR 179


>gi|239934426|emb|CAR92343.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 224

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 36/271 (13%), Positives = 88/271 (32%), Gaps = 48/271 (17%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++     +      L +++            G+    +G +    E       +  
Sbjct: 1   TVXYILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAKAV 49

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
             + + D E       ++ ++    P  A      + +  + +   L             
Sbjct: 50  KADDDSDDEDGEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL------------- 96

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                                 +K  +++         L +L   + L   + + LVE++
Sbjct: 97  ----------------------KKHGRNNKATIAELLALAELFMPIKLVPKQFEGLVERV 134

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
                R+   E  +++L      + R  FL +  G E+D  W   A    +G++   +  
Sbjct: 135 RSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWSD-ALAKGKGKYAEAIGR 193

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVS 432
               I++ + ++ ++  ETG++I+E + I  
Sbjct: 194 LQPDIIRCQQKLTALETETGLTIAEIKDINR 224


>gi|196249822|ref|ZP_03148518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196210698|gb|EDY05461.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 256

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 107/239 (44%), Gaps = 14/239 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
             + +   A   ++     L+ + AKK       F  DL Q G +  ++  E +D   G 
Sbjct: 20  YQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQVGRLSFLRLLEHYDPNQGT 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F +YAM  +   +   + D++  I++P  +++   KV +    ++  ++R P  EEIA 
Sbjct: 80  SFESYAMKSLIGYMKNYLRDKAWYIQVPRRVKENGSKVQKAIDELTVTLERSPNIEEIAN 139

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + VE   ++L  +   + IS++ P+ D  +D + +G+F+ D       +       R
Sbjct: 140 HLGLSVEETIEILAGRDHYQAISIDAPVQDGEKDATTIGEFLADDT-----NEVEALIER 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 +  L+ +E  V+   F  G     T   + K+  V++  I +I+ +AI KLK 
Sbjct: 195 LDLQEAIGKLSEQERIVIEAVFRRG----ETQRSLAKRLGVSQMTISRIQKRAIEKLKR 249


>gi|229171759|ref|ZP_04299331.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
 gi|228611656|gb|EEK68906.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
          Length = 203

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 90/205 (43%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D  +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDCSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   FG  +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|109899335|ref|YP_662590.1| flagellar biosynthesis sigma factor [Pseudoalteromonas atlantica
           T6c]
 gi|109701616|gb|ABG41536.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudoalteromonas
           atlantica T6c]
          Length = 242

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 107/240 (44%), Gaps = 17/240 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE +  LV  +A     R    +   DLIQ G IGL++A+  FD   G  F T+A 
Sbjct: 14  RNALVERHAPLVKRIAHHLIARLPASVLVDDLIQAGMIGLLEASRNFDGTKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I         P  +      +     ++  +  R+    +IAKKL + +E
Sbjct: 74  IRIRGSMLDEIRKGDW---TPRSVHKNGRAITDAINKVERETGRDARDVDIAKKLEVSIE 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLA 618
              ++L      ++    IG ED     D +   + K + +P +  +Q + ++     + 
Sbjct: 131 QYHQMLG----EVNAGKIIGMEDLGVSEDVVTTEQTKGSDTPFEDLLQGSFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +L  RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ KLK   ++ ++  
Sbjct: 187 TLPEREAIVLSLYY----DEELNLREIGEVLDVSESRVSQIHSQAMLKLKSKMQTWRIEE 242


>gi|254446671|ref|ZP_05060147.1| RNA polymerase sigma factor, FliA/WhiG family [Verrucomicrobiae
           bacterium DG1235]
 gi|198260979|gb|EDY85287.1| RNA polymerase sigma factor, FliA/WhiG family [Verrucomicrobiae
           bacterium DG1235]
          Length = 269

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 89/233 (38%), Gaps = 17/233 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+ E  + LV S+  +        +   DL   G  GL+ A +K+D      F +YA 
Sbjct: 36  QAELFETYMPLVRSIVARIKINLPPHIDEQDLHSVGITGLIAALKKYDPAQKKSFGSYAA 95

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ +I   +         P + R    K+  T   +  ++ R  T EEI  +L +  +
Sbjct: 96  MRIRGSILDELRRMDWM---PRNARTNFKKLRATIEEVEQRLGRPATEEEIRAELGLNRK 152

Query: 562 GVRKVLKITKEPIS---LETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTR 615
                L     P+S   L+      D      L + I D N V       +  +      
Sbjct: 153 EY-DQLMAETRPVSFLPLDNAAAGGDDGEGADLYEVIPDDNVVPVTSKMEKDEVTRLVAE 211

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L     +VL M +      D  L E+ + F +T  RI QI ++AI  L+
Sbjct: 212 RINQLPETPRKVLAMYYF----QDMRLAEIAEVFGLTESRICQIHSQAIISLR 260


>gi|291165879|gb|EFE27926.1| RNA polymerase sigma-B factor [Filifactor alocis ATCC 35896]
          Length = 273

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 116/242 (47%), Gaps = 14/242 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++   + +    + E+++ NL +   ++KKY N+G+++ D+ Q  ++GL+ A E++D   
Sbjct: 32  LLYNEDKQNRELRNELIQKNLYIAEILSKKYLNKGIEYDDIFQVASLGLILAIERYDVTK 91

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G+KFS++A   +   I +   D+  +IR+P  +++   KV +    + N+    P  ++I
Sbjct: 92  GFKFSSFATPTIIGEIKKYFRDKGWSIRVPRKIQELSKKVTQAREYLQNEKGAIPEVKDI 151

Query: 553 AKKLAMPVEGVRKVLKITKEPI--SLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQA 607
           A+ L +  E V +V++ ++     SL+    +   +    L D + D++      S  + 
Sbjct: 152 AEYLEISEEEVMEVMEASQVYHLKSLDVTYENGGEDKEVSLIDVLGDED-----KSFSEI 206

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R+   ++   L   E  ++  RF          EE      +++  + +IE K + K+
Sbjct: 207 ENRDFFEKMFQKLDDVEREIIIGRFFKQKTQMKIAEE----LNISQMTVSRIEKKVLSKI 262

Query: 668 KH 669
           K 
Sbjct: 263 KK 264


>gi|311069177|ref|YP_003974100.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
 gi|310869694|gb|ADP33169.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
          Length = 242

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 61/275 (22%), Positives = 110/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 8   ALGFVVKELVFLVSYVKNNAFPQPLSGSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 65  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 121

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 122 -------------------------------------------------LKKTKKDVSLH 132

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ ++        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 133 DPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMEL-EKVKKYIDILDDREKEVIVGRFGL 191

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 192 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 226


>gi|158319069|ref|YP_001511576.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158139268|gb|ABW17580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 270

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 110/227 (48%), Gaps = 8/227 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E++  +L +   ++KK+ N+G+++ D+ Q  ++GL+ A E++D   G++FS++A   +
Sbjct: 43  RNELINRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIYAIERYDVTKGFEFSSFATPTI 102

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I +   D+  +IR+P  +++   KV  +   +   ++R PT ++IA+ L    E V 
Sbjct: 103 IGEIKKYFRDKGWSIRVPRRIQELSKKVNVSKNTLQQTLQRTPTVKDIAEYLNCTEEEVI 162

Query: 565 KVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + ++ +    P SL+    ++        ++    +      I+   ++   + +  L  
Sbjct: 163 EAMEASQVYTPKSLDLIYDNDGDDKDIQLLDLIGELDKRFDDIEN--KDFFQKAIDKLNE 220

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E++VL+ RF          EE      V++  + ++E + I K K 
Sbjct: 221 VEKKVLKDRFFNNKTQMKVSEE----LNVSQMTVSRMEKRIIEKFKK 263


>gi|296333262|ref|ZP_06875715.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|296149460|gb|EFG90356.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
          Length = 241

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 110/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 7   ALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +N        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKQYIDILDDREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|310764851|gb|ADP09801.1| RNA polymerase sigma factor for flagellar operon [Erwinia sp.
           Ejp617]
          Length = 243

 Score = 98.4 bits (243), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 103/228 (45%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +      +V   A +   R    ++  DLIQ G++G + A + FD   G   S +  
Sbjct: 13  KTILWGKYNHIVRQEALRLQKRLPASVELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLA 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + ++     +P  +R    +V    +++      E +  +IA ++ + V 
Sbjct: 73  QRIRWALMDELRERDW---VPRRVRKHAREVTAVIQQLEQNKGGEASEADIATEMGVSVG 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
            ++++L  T            E  +   + I+++N A++P+  A+Q NL       ++ +
Sbjct: 130 ELQQMLADTNSSQIYSLDELQEQFADSYETIDEENEALNPVHQAVQENLVGKIAEHISVI 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L++ +      D  + E+G    +T  R+ Q+ + AI++++
Sbjct: 190 PEREQVILQLYY----QQDLNMREIGAVLSLTETRVSQLHSLAIKRIR 233


>gi|332305676|ref|YP_004433527.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173005|gb|AEE22259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 242

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 104/239 (43%), Gaps = 15/239 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +VE +  LV  +A     R    +   DLIQ G IGL++A+  FD   G  F T+A 
Sbjct: 14  RNALVERHAPLVKRIAHHLIARLPASVLVDDLIQAGMIGLLEASRNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ ++   I         P  +      +     ++  +  R+    +IAKKL + +E
Sbjct: 74  IRIRGSMLDEIRKGDW---TPRSVHKNGRAITDAINKVERETGRDARDVDIAKKLEVSIE 130

Query: 562 GVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              ++L      + I +E     ED          K + +P +  +Q + ++     + +
Sbjct: 131 QYHQMLSEVNAGKIIGMEDLGVTEDVVTTEQT---KGSDTPFEDLLQGSFQKALAHAITT 187

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           L  RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ KLK   ++ ++  
Sbjct: 188 LPEREAIVLSLYY----DEELNLREIGEVLDVSESRVSQIHSQAMLKLKSKMQTWRIEE 242


>gi|260893401|ref|YP_003239498.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
 gi|260865542|gb|ACX52648.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
          Length = 242

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 53/252 (21%), Positives = 101/252 (40%), Gaps = 59/252 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E  H++  +          +  +VE NLRLV+ +A+KY + G+   DL+  G+IGL
Sbjct: 40  LDAEEEAHLLKRLE---AGDQSVRNTLVERNLRLVVYIARKYESTGINLEDLVSIGSIGL 96

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +  QS T+R                     
Sbjct: 97  IKAVNTFNPQRKVKLATYASRCIENEILMFLRRQSRTLRQE------------------- 137

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +  +  V
Sbjct: 138 --------------------------------VSFDEPLNTDWDGNELLLSDVLGTEGDV 165

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIR 657
           +      + + R      LASL+ RE  ++ +RFG+G +  + T +EV     +++  I 
Sbjct: 166 TSRHLEEEVD-RRVLKLALASLSGRERVIMELRFGLGADGEEKTQKEVADLLGISQSYIS 224

Query: 658 QIEAKAIRKLKH 669
           ++E + +++L+ 
Sbjct: 225 RLEKRILKRLRR 236


>gi|71736085|ref|YP_275521.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71556638|gb|AAZ35849.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           syringae pv. phaseolicola 1448A]
          Length = 239

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 96/238 (40%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
                +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D   
Sbjct: 1   MYSKASRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTK 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ A+   +         P  +      V    R +  K  R+    E+
Sbjct: 61  GASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDHEV 117

Query: 553 AKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A +L + ++    +L  T      S +  + D D   L +      ++ P         +
Sbjct: 118 AAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDERFQ 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +A+L  RE  VL     +  + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 177 AALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 230


>gi|138896107|ref|YP_001126560.1| sporulation sigma factor SigK [Geobacillus thermodenitrificans
           NG80-2]
 gi|196249000|ref|ZP_03147700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134267620|gb|ABO67815.1| RNA polymerase sigma-K factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211876|gb|EDY06635.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 237

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 110/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
             A  +  +  + + IK+ +    +S  E    + ++ K       A+  ++E NLRLV 
Sbjct: 7   AFAFLLKELTFLVSYIKNNAFPQPLSPKEEEKYLELMAK---GDEQARNRLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G +  DLI  G IGL+KA E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEEVEDLISIGTIGLIKAIESYSPNKGTKLATYAARCIENEILMHLRS--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK T++ +SL 
Sbjct: 121 -------------------------------------------------LKKTRKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +      +  +   L E   + ++ L  RE+ V+  RFG+
Sbjct: 132 EPIGQDKEGNEISLLDILKSEGQDIVDEIQLNMEL-EQVKKYISVLDEREKEVIVNRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           G   + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 GRQREKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|254478789|ref|ZP_05092157.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035301|gb|EEB76007.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 244

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 101/255 (39%), Gaps = 59/255 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 44  LSVEEESYLISKMEK---GDNEAKSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +                             
Sbjct: 101 IKAINTFNPRKKIKLATYASRCIENEILMYLRRN-------------------------- 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       T+  +S + P+  +   +   L D +   N  
Sbjct: 135 --------------------------NKTRLEVSFDEPLNVDWDGNELLLSDILGTDN-E 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +          RE  T  L  L  RE++++R+RFG+   T+ T +EV     +++  I +
Sbjct: 168 TVYKYIEDEVERELLTSALKKLPDREKKIIRLRFGLEGGTEKTQKEVADMLGISQSYISR 227

Query: 659 IEAKAIRKLKHPSRS 673
           +E K +++LK     
Sbjct: 228 LEKKILKRLKKEMNR 242


>gi|258511273|ref|YP_003184707.1| sporulation sigma factor SigE [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257477999|gb|ACV58318.1| RNA polymerase, sigma 28 subunit, SigE [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 249

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 99/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E ++++  +          +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 49  LTKEEEQYLLERL---PSGDPSVRSMLIERNLRLVVYIARKFENTGVNIEDLVSIGTIGL 105

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +               + +K+         
Sbjct: 106 IKAVNTFDPSKKIKLATYASRCIENEILMYLR--------------RNNKLR-------- 143

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +SL+ P+  +   +   L D +   ++ 
Sbjct: 144 ------------------------------AEVSLDEPLNVDWDGNELLLSDVLG-TDSD 172

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +   +      RE     L  L+ RE  ++ +RFG+G   + T ++V     +++  I +
Sbjct: 173 TIYRNLEDEVDRELLYDALDKLSERERTIMELRFGLGTGQEMTQKDVADLLGISQSYISR 232

Query: 659 IEAKAIRKLKH 669
           +E + +++L+ 
Sbjct: 233 LEKRILKRLQR 243


>gi|56421959|ref|YP_149277.1| DNA-directed RNA polymerase sigma-37 factor [Geobacillus
           kaustophilus HTA426]
 gi|56381801|dbj|BAD77709.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B) [Geobacillus
           kaustophilus HTA426]
          Length = 256

 Score = 98.0 bits (242), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 112/239 (46%), Gaps = 14/239 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL-DLIQEGNIGLMKAAEKFDWCLGY 494
             + +   A   ++     L+ + AKK       F  DL Q G +  ++  + +D   G 
Sbjct: 20  YQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLSFLRLLDHYDPSQGA 79

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F +YAM  +   +   + D++  I++P  +++K  KV +    ++ K++R P  +EIA 
Sbjct: 80  SFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKGSKVQQAIDELTVKLERSPNIDEIAA 139

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + VE   ++L  +   + ISL+ P+ D  +D + +G+F+ D+      +       R
Sbjct: 140 HLGLSVEETIEILAGRDHYQAISLDAPVQDGEKDATTIGEFVADE-----ANEIESLIER 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + +  L+ +E+ V+   F  G     T   + ++  V++  I +I+ +AI KLK 
Sbjct: 195 MDLEQAIGKLSEQEQIVIDAVFRRG----ETQRSLAERLGVSQMTISRIQKRAIAKLKR 249


>gi|289578665|ref|YP_003477292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528378|gb|ADD02730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 241

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 98/252 (38%), Gaps = 53/252 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  ++VS + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEETYLVSKMEK---GDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNS------------------------- 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + EE                            +  +    L   I   +  +  
Sbjct: 133 KTKLEVSFEEP-------------------------LNVDWDGNELLLSDILGTDNETVY 167

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   RE  T  L  L  RE++++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 168 KYIEDEVERELLTSALKKLPDREKKIIGLRFGLDGGVEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLKHPSRS 673
           K +++LK     
Sbjct: 228 KILKRLKKEMNR 239


>gi|332140599|ref|YP_004426337.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550621|gb|AEA97339.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 243

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 105/235 (44%), Gaps = 17/235 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K ++VE +  LV  +A     R    +   DLIQ G IGL++AA  FD   G  F T+A 
Sbjct: 14  KSQLVERHASLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFDGSKGASFETFAG 73

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   I         P  +      +     ++ ++  R+    +IA KL + ++
Sbjct: 74  IRIRGAMLDEIRKGDW---TPRSVHRNGRAITEAISQVESETGRDARDSDIADKLNVSLQ 130

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA---VSPLDSAIQANLRETTTRVLA 618
              ++L      ++    +G ED     D I  + +    +PL+  +Q   ++     + 
Sbjct: 131 DYHQMLN----EVNAGKLVGIEDLGVSEDVITTEQSRGSDAPLEDLMQGAFQKALAHAIT 186

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L  RE  VL + +    + +  L E+G+   V+  R+ QI ++A+ KLK   +S
Sbjct: 187 TLPEREAIVLSLYY----DEELNLREIGEVLDVSESRVSQIHSQAMLKLKSRMKS 237


>gi|224992874|gb|ACN76152.1| SigB [Listeria monocytogenes]
 gi|224992886|gb|ACN76158.1| SigB [Listeria monocytogenes]
 gi|224992898|gb|ACN76164.1| SigB [Listeria monocytogenes]
 gi|224992902|gb|ACN76166.1| SigB [Listeria monocytogenes]
          Length = 214

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 90/210 (42%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 2   AAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 62  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 122 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +VL  L  RE+++L+  F    +   T E
Sbjct: 182 EKVLPVLDEREQKILQYTFIENRSQKETGE 211


>gi|297746553|emb|CAZ60994.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 245

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 45/289 (15%), Positives = 92/289 (31%), Gaps = 46/289 (15%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P          +  +       S+ 
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE-------ADDVAPTATHIGSEL 51

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E D   E E + E     S DD       PE A     +L    + +  ++        
Sbjct: 52  GEDDLADEDEDEDEXDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEVTRLSI-------- 103

Query: 278 PKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
                                      Q++ ++    +     L  +     L   +   
Sbjct: 104 ---------------------------QQNGRAHEDTQAAIAHLADVFRQFRLMPKQFHR 136

Query: 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK 396
           L   + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +    
Sbjct: 137 LGNNMPEMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSP 196

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             +  + + +L+   +++ I  ETG+SI++ + I   +  GE +    K
Sbjct: 197 RLLEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKGPPCK 244


>gi|224992858|gb|ACN76144.1| SigB [Listeria monocytogenes]
 gi|224992860|gb|ACN76145.1| SigB [Listeria monocytogenes]
 gi|224992862|gb|ACN76146.1| SigB [Listeria monocytogenes]
 gi|224992864|gb|ACN76147.1| SigB [Listeria monocytogenes]
 gi|224992866|gb|ACN76148.1| SigB [Listeria monocytogenes]
 gi|224992868|gb|ACN76149.1| SigB [Listeria monocytogenes]
 gi|224992870|gb|ACN76150.1| SigB [Listeria monocytogenes]
 gi|224992872|gb|ACN76151.1| SigB [Listeria monocytogenes]
 gi|224992876|gb|ACN76153.1| SigB [Listeria monocytogenes]
 gi|224992878|gb|ACN76154.1| SigB [Listeria monocytogenes]
 gi|224992880|gb|ACN76155.1| SigB [Listeria monocytogenes]
 gi|224992882|gb|ACN76156.1| SigB [Listeria monocytogenes]
 gi|224992884|gb|ACN76157.1| SigB [Listeria monocytogenes]
 gi|224992888|gb|ACN76159.1| SigB [Listeria monocytogenes]
 gi|224992890|gb|ACN76160.1| SigB [Listeria monocytogenes]
 gi|224992892|gb|ACN76161.1| SigB [Listeria monocytogenes]
 gi|224992894|gb|ACN76162.1| SigB [Listeria monocytogenes]
 gi|224992896|gb|ACN76163.1| SigB [Listeria monocytogenes]
 gi|224992900|gb|ACN76165.1| SigB [Listeria monocytogenes]
          Length = 214

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 90/210 (42%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 2   AAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 62  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 122 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +VL  L  RE+++L+  F    +   T E
Sbjct: 182 EKVLPVLDEREQKILQFTFIENRSQKETGE 211


>gi|121488735|emb|CAJ18251.1| sigma 70-type sigma factor [Chlorobium chlorovibrioides]
          Length = 165

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  +  + +L     R L+ L PRE  V+R  FGIGM 
Sbjct: 121 LQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFGIGME 165


>gi|254387242|ref|ZP_05002505.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346050|gb|EDX27016.1| sigma factor [Streptomyces sp. Mg1]
          Length = 272

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 117/252 (46%), Gaps = 23/252 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLV----ISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
           + ++ +G  E   A+  ++E NL LV         +    G+   D++Q G IGL+KA +
Sbjct: 23  LRVLEEGTREYQYARNTLIEMNLSLVQFAARRFRARAFGGGIDMDDIVQVGTIGLIKAID 82

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D     +FST A+ ++   I R   D +  + +P  +++   ++ +    +++ + R 
Sbjct: 83  RYDPEREVEFSTLALPYITGEIKRHFRDTTWAVHVPRRLQELRTELAKAQESLTDVLGRA 142

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPI--SLETPIGDEDTSH--------LGDFIEDKN 596
           PT +EIA+ L +P E + + L         SL+T   + D           L + I D +
Sbjct: 143 PTVKEIAQHLELPEEEIIEGLVAANGYTSGSLDTAGSEGDNQSTSSRGTRPLAEKIGDND 202

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
               L          T   +L  L  R+  +LRMRFG     + T  E+G +  +++ ++
Sbjct: 203 PAMELFEEFH-----TLAPLLEKLDERDLLILRMRFG----EEKTQAEIGAELGISQMQV 253

Query: 657 RQIEAKAIRKLK 668
            +I ++ + +L+
Sbjct: 254 SRILSRTLTRLR 265


>gi|297746533|emb|CAZ60984.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 242

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 50/286 (17%), Positives = 98/286 (34%), Gaps = 46/286 (16%)

Query: 158 CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQE 217
            E P     L+   D+       L +II     I P                        
Sbjct: 1   AEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN----------------------- 35

Query: 218 KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR 277
            E DDV  T   I S            D   +  E+ E + D+ +      ++       
Sbjct: 36  -ETDDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGESSDDDGDGGPDPEVA------- 87

Query: 278 PKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
                      E + ELR+  +   ++ QK+ ++    +     L  +     L   + D
Sbjct: 88  ----------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFD 137

Query: 337 LLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            L   + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +   
Sbjct: 138 RLTTCMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWS 197

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
              V  + + +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 198 PRLVEMD-EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 242


>gi|319651643|ref|ZP_08005770.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396710|gb|EFV77421.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 109/270 (40%), Gaps = 59/270 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  I+ + + +K+ +    +S ++ +  + ++       + A+  ++E NLRLV  + KK
Sbjct: 12  VKEIVFLVSYVKNNAFPQPLSPADEKKYLRLM---AAGDAHARNMLIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +          
Sbjct: 69  FENTGEDSEDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEILMHLRA-------- 120

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK TK+ +SL  PIG 
Sbjct: 121 --------------------------------------------LKKTKKDVSLHDPIGQ 136

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D ++ ++        +   L E     +  L  RE+ V+  RFG+ +  +
Sbjct: 137 DKEGNEISLIDVLKSESEDVINTIQLNMEL-EKVKEYIDVLDDREKEVIVGRFGLDLQKE 195

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|255094683|ref|ZP_05324161.1| RNA polymerase sigma-B factor [Clostridium difficile CIP 107932]
          Length = 252

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 109/246 (44%), Gaps = 6/246 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+++  T     + + + ++  K +      +  ++E +L L   +AKKY N+G+ F D
Sbjct: 1   MKNVANATHYLNMDTKELFNLYNKNKNVD--IRNILIERHLYLARLLAKKYINKGVDFED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           + Q  ++ L+ A +++D   G++FS++A   +   I +   D+  T+R+P  +++   K+
Sbjct: 59  IYQVASLALIYAIDRYDVEKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQELSKKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                ++  + K+ P  ++IA  + +  E V + ++ +     +       D S   D  
Sbjct: 119 SDAKIKLEQENKKHPKVKDIADYIGVSEEDVLEAMEASYGYQPMSLDSSSNDDSEDKDIT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                     +       +   + + +L   E ++ + RF      D T   + K+  ++
Sbjct: 179 LIDKIGKEEGNFGSIEYEDFINKFIETLNELEVKIFKDRFFF----DKTQSSIAKELGIS 234

Query: 653 RERIRQ 658
           +  + +
Sbjct: 235 QMTVSR 240


>gi|239934400|emb|CAR92330.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 236

 Score = 98.0 bits (242), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 60/155 (38%), Gaps = 2/155 (1%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             LQ      +K+ ++  +     + L  L+  + L   + ++LVE++ D   R    E 
Sbjct: 79  EQLQATTKVLKKNGRTHKESVEALQALADLLMPIKLVPKQFEILVERVRDALNRXRQQER 138

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L      + R  FL      E D  W           W   +  +  +I+  + ++
Sbjct: 139 AIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEKDAAIVACQQKL 197

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             +  ETG++++E + I       +   +  +  M
Sbjct: 198 IDLETETGLTVAEIKEINRRANSADIHHTGGRSSM 232


>gi|222431371|gb|ACM50638.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 224

 Score = 97.6 bits (241), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 37/270 (13%), Positives = 88/270 (32%), Gaps = 47/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L ++  L   I P+                      + + 
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGI--------APPAAEVPPPVDPKA 50

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               +   D ++ A    +D  +    P  A      + +  + +     A++   R   
Sbjct: 51  PKADDDTDDDDAEASSDDEDEVESGPDPIIAAQRFGAVSDQMEITRK---ALKKHGRGNK 107

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
           +   + +A                                L +L   + L   + + LVE
Sbjct: 108 LAIAELVA--------------------------------LAELFMPIKLVPKQFEGLVE 135

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++    +R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 136 RVRSALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKAKYAEAI 194

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
                 I++ + ++ ++  ETG++I+E + 
Sbjct: 195 GRLQPDIIRCQQKLTALQTETGLTIAEIKD 224


>gi|306820145|ref|ZP_07453793.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551923|gb|EFM39866.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 247

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 109/242 (45%), Gaps = 15/242 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            K   +    K+E++   + LV  V+ K   Y  + +++ DL+  G IGL+ A +KFD+ 
Sbjct: 15  EKNPDKKRKIKEEIITKYVSLVKIVSGKLFNYYAQKIEYDDLMGYGIIGLIDAIDKFDYS 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA   ++ AI   I  Q     +P  +R K+  +      + NK+ RE T  E
Sbjct: 75  KNIKFETYASIRIRGAIIDEIRSQDW---VPRGIRKKMKTLNTAMEELENKLGREATRHE 131

Query: 552 IAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +++ L + ++ V ++     T   +S+E  + +     + D    K   SP    I  + 
Sbjct: 132 LSEHLGISLKEVDELFDETATFNIVSIEDELSENVKIQIPDT---KVENSPEQQLIYTDT 188

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                + + +L  +E+ ++ + +        T +E+ +   ++  RI QI +  + KL+ 
Sbjct: 189 VNDLAKAIDTLKEKEKIIINLYYYEN----LTYKEISEIIGISESRISQIISACLTKLRK 244

Query: 670 PS 671
             
Sbjct: 245 LM 246


>gi|330946033|gb|EGH47317.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 166

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 46/155 (29%), Positives = 86/155 (55%)

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +G +
Sbjct: 7   HVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGPD 66

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
               L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   TLE
Sbjct: 67  SDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHESSTLE 126

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           +VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 127 DVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 161


>gi|229108567|ref|ZP_04238180.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
 gi|228674898|gb|EEL30129.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
          Length = 203

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 42/205 (20%), Positives = 90/205 (43%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   F   +N     ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFRENLNQ----KDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|149908440|ref|ZP_01897103.1| flagellar biosynthesis sigma factor FliA [Moritella sp. PE36]
 gi|149808603|gb|EDM68538.1| flagellar biosynthesis sigma factor FliA [Moritella sp. PE36]
          Length = 241

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 46/230 (20%), Positives = 94/230 (40%), Gaps = 15/230 (6%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           VE    LV  +A     R    +Q  DLIQ G IGL+ AA  FD   G  F TYA   ++
Sbjct: 18  VEQFGYLVKRIAHHLLLRLPPSVQLDDLIQSGMIGLLDAARNFDGSKGASFETYAGIRIR 77

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            ++   +        +P  +      +     R+  +   +    +IA +L + +     
Sbjct: 78  GSMIDEMRRGDW---VPRSVHKNGRNIAAAIDRIEKQTGTDAKDTDIAGELGVSLADYHS 134

Query: 566 VLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +L    +   +++E      + ++      +  + +P     +   ++     + +L  R
Sbjct: 135 MLMDVNSGHILAVEDLTVSNEDAYSA---YEGKSSTPCAEFSEQRFQQALADCIKTLPER 191

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E  VL + +    + +  L E+G+   V+  R+ QI ++A+ ++K    +
Sbjct: 192 ESLVLSLYY----DEELNLREIGEVLSVSESRVSQIHSQAMHRVKARMHA 237


>gi|121488785|emb|CAJ18277.1| sigma 70-type sigma factor [Pelodictyon clathratiforme]
          Length = 165

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 57/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELATLLEMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V++  FGIGM+
Sbjct: 121 LQNDGHL-PDYGLNRDSLTLEVERSLSVLAPREADVIKSYFGIGMD 165


>gi|325288837|ref|YP_004265018.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964238|gb|ADY55017.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 250

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 48/228 (21%), Positives = 96/228 (42%), Gaps = 56/228 (24%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K  ++E NLRLV+ +++K+ N G+   DL+  G IGL+KA   FD     K +TYA   +
Sbjct: 70  KGTLIERNLRLVVYISRKFENTGISIEDLVSIGTIGLIKAVNTFDPTKKIKLATYASRCI 129

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +               + +K+                                
Sbjct: 130 ENEILMYLR--------------RNNKIR------------------------------- 144

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                    +S + P+  +   +   L D +  +N +       + + R+   + ++SL+
Sbjct: 145 -------SEVSFDEPLNIDWDGNELLLSDVLGTENDIISKPIEEEVD-RQLLAQAMSSLS 196

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++ +RFG+G   + T +EV  +  +++  I ++E K I++L+ 
Sbjct: 197 EREQLIMELRFGMGGKEEKTQKEVADKLGISQSYISRLEKKIIKRLRK 244


>gi|126659553|ref|ZP_01730685.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619192|gb|EAZ89929.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 258

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 107/235 (45%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++    + DL+Q G++GL++A E+F    G+ FS++A+ +
Sbjct: 29  RNKILELNFGLVRKEAHHWVHQCPESYEDLVQVGSLGLIRAIERFSIEKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  T+RIP    +   + +   R    K  R+PT  EIA+ L + ++  
Sbjct: 89  IRGEIQHYLRDKKYTVRIPRRWLELGRQSMNVRREFREKFNRQPTDSEIAQVLEISLKEW 148

Query: 564 RKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+  +  E    + LGD + D N  S   +           + L  
Sbjct: 149 QEIKLAFQNREPVSLDVKVSSEGEGQTSLGDLVPDANYRSFQLAQEDQI---RLQQALEQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  R   +L   F      D T  E  +Q  ++   + +   K +  LK     +
Sbjct: 206 LEERTRNILEFVFL----KDLTQRETAEQLGISVVTVSRRVKKGLEILKQNMHKE 256


>gi|312173282|emb|CBX81537.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 243

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 103/228 (45%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +      +V   A +   R    ++  DLIQ G++G + A + FD   G   S +  
Sbjct: 13  KTILWGKYNHIVRQEALRLQKRLPASVELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLA 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + ++     +P  +R    ++    +++      E +  +IA ++ + V 
Sbjct: 73  QRIRWALMDELRERDW---VPRRVRKHAREMTAVIQQLEQNKGGEASEADIATEMGVSVC 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
            ++++L  T            E  +   + I+++N A++P+  A+Q NL       ++ +
Sbjct: 130 ELQQMLADTNSSQIYSLDELQEQFADSYETIDEENEALNPVHQAVQENLVGKIAEHISVI 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L++ +      D  + E+G    +T  R+ Q+ + AI++++
Sbjct: 190 PEREQVILQLYY----QQDLNMREIGAVLSLTETRVSQLHSLAIKRIR 233


>gi|315001914|emb|CBI75443.1| RNA polymerase sigma factor [Aeromonas eucrenophila]
          Length = 238

 Score = 97.6 bits (241), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 48/281 (17%), Positives = 97/281 (34%), Gaps = 46/281 (16%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
               L+   D+       L +II     I P                         E DD
Sbjct: 2   AITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EADD 35

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
           V  T   I S            D   +   + +   DE +      ++            
Sbjct: 36  VAPTATHIGSELSEDDLADEDEDEDEDEDGDGDDXDDEGDGGPDPEVA------------ 83

Query: 283 ALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
                 E + ELR+  +   ++ QK+ ++  + +    +L  +     L   + D LV  
Sbjct: 84  -----REKFGELRAQYEVTRLSIQKNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLVNN 138

Query: 342 LYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
           + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      + 
Sbjct: 139 MREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLLE 198

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
            + D +L+   +++ I  ETG+SI++ + I   +  GE +A
Sbjct: 199 MDED-VLRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKA 238


>gi|292489124|ref|YP_003532011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292900243|ref|YP_003539612.1| RNA polymerase sigma factor for flagellar operon [Erwinia amylovora
           ATCC 49946]
 gi|291200091|emb|CBJ47217.1| RNA polymerase sigma factor for flagellar operon [Erwinia amylovora
           ATCC 49946]
 gi|291554558|emb|CBA22163.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
          Length = 243

 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 103/228 (45%), Gaps = 11/228 (4%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  +      +V   A +   R    ++  DLIQ G++G + A + FD   G   S +  
Sbjct: 13  KTILWGKYNHIVRQEALRLQKRLPASVELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLA 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   + ++     +P  +R    ++    +++      E +  +IA ++ + V 
Sbjct: 73  QRIRWALMDELRERDW---VPRRVRKHAREMTAVIQQLEQNKGGEASEADIATEMGVSVC 129

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDSAIQANLRETTTRVLASL 620
            ++++L  T            E  +   + I+++N A++P+  A+Q NL       ++ +
Sbjct: 130 ELQQMLADTNSSQIYSLDELQEQFADSYETIDEENEALNPVHQAVQENLVGKIAEHISVI 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L++ +      D  + E+G    +T  R+ Q+ + AI++++
Sbjct: 190 PEREQVILQLYY----QQDLNMREIGAVLSLTETRVSQLHSLAIKRIR 233


>gi|126697577|ref|YP_001086474.1| RNA polymerase sigma-B factor [Clostridium difficile 630]
 gi|254977353|ref|ZP_05273825.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-66c26]
 gi|255102910|ref|ZP_05331887.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-63q42]
 gi|255308730|ref|ZP_05352901.1| RNA polymerase sigma-B factor [Clostridium difficile ATCC 43255]
 gi|255316437|ref|ZP_05358020.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-76w55]
 gi|255519098|ref|ZP_05386774.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-97b34]
 gi|255652280|ref|ZP_05399182.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-37x79]
 gi|260681780|ref|YP_003213065.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260685377|ref|YP_003216510.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296452670|ref|ZP_06894361.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296880077|ref|ZP_06904046.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
 gi|306521994|ref|ZP_07408341.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-32g58]
 gi|115249014|emb|CAJ66825.1| RNA polymerase sigma-B factor (Sigma-37) [Clostridium difficile]
 gi|260207943|emb|CBA60060.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260211393|emb|CBE01463.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296258452|gb|EFH05356.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296428944|gb|EFH14822.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
          Length = 257

 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 109/246 (44%), Gaps = 6/246 (2%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+++  T     + + + ++  K +      +  ++E +L L   +AKKY N+G+ F D
Sbjct: 1   MKNVANATHYLNMDTKELFNLYNKNKNVD--IRNILIERHLYLARLLAKKYINKGVDFED 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           + Q  ++ L+ A +++D   G++FS++A   +   I +   D+  T+R+P  +++   K+
Sbjct: 59  IYQVASLALIYAIDRYDVEKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQELSKKI 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                ++  + K+ P  ++IA  + +  E V + ++ +     +       D S   D  
Sbjct: 119 SDAKIKLEQENKKHPKVKDIADYIGVSEEDVLEAMEASYGYQPMSLDSSSNDDSEDKDIT 178

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                     +       +   + + +L   E ++ + RF      D T   + K+  ++
Sbjct: 179 LIDKIGKEEGNFGSIEYEDFINKFIETLNELEVKIFKDRFFF----DKTQSSIAKELGIS 234

Query: 653 RERIRQ 658
           +  + +
Sbjct: 235 QMTVSR 240


>gi|159029418|emb|CAO90794.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 258

 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 109/249 (43%), Gaps = 13/249 (5%)

Query: 429 HIVSMVRKGECEAS-IAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAE 486
             +++ +K +       + +++  NL LV   A  + N+    + DL+Q G +GL++A +
Sbjct: 12  ETLTLFKKYQKTGENQLRDQIIRLNLGLVRREAHHWVNQCHENYEDLVQVGCMGLIRAIK 71

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G+ FS++A+ +++  I   + D+  T+RIP    D   +     R       R+
Sbjct: 72  RFDSSKGHAFSSFAIPYIRGEIQHYLRDKGYTVRIPRRWLDLGRQAANMRRDFQTIHNRQ 131

Query: 547 PTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLD 602
           P   EI+  L + +E  ++V      +EP+SL+  + +++   + L D + D    S   
Sbjct: 132 PNDTEISLALNISLEEWQEVKLAFQNREPLSLDATVNNDEDNNTCLKDIVPDPGYRSFQL 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  R    + LA L  +   +L   F      D T  E  +Q  ++   + +   K
Sbjct: 192 CQED---RIRLQQALAQLEEKTRYILEFVFL----KDLTQRETAEQLGISIVTVSRRVKK 244

Query: 663 AIRKLKHPS 671
            +  LK   
Sbjct: 245 GLEMLKETM 253


>gi|108762696|ref|YP_629049.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
 gi|108466576|gb|ABF91761.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
          Length = 273

 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 54/226 (23%), Positives = 92/226 (40%), Gaps = 10/226 (4%)

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V  +L+LV  +A KY   GL   +L+ EGN+GLM+AA +F+   G  F+ YA  W++  I
Sbjct: 35  VREHLKLVRRLAWKYRWTGLSMEELVAEGNVGLMEAAGRFE-ERGVPFAAYASQWIRARI 93

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE--IAKKLAMPVEGVRKV 566
              +                + ++ R   R+  +        E  +A+ L    + V   
Sbjct: 94  RAYVGRNWSMAGGRAPWV--VFQLRRERSRLEARWGEGHPEVEKRLAEALGKREDEVALA 151

Query: 567 LKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++     +SL+ P+  +  +   + +    D        +     LR +       L  R
Sbjct: 152 MEALSRDVSLDAPVSPDSEATRLEGLMADADSQEDQVDRAKWARRLRASVDAAWPELDAR 211

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E  ++  R          L  + ++F VT  RIRQIE     KL+H
Sbjct: 212 ERALVEERMLAEDGVSAEL--LARRFGVTAVRIRQIEQGLRVKLRH 255


>gi|222431331|gb|ACM50618.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431333|gb|ACM50619.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431335|gb|ACM50620.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 35/270 (12%), Positives = 89/270 (32%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDPK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D + A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
                 I++ + ++ ++  ETG++I+E + 
Sbjct: 194 GRLQPDIIRCQQKLTALETETGLTIAEIKD 223


>gi|330945998|gb|EGH47306.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 163

 Score = 97.6 bits (241), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 47/158 (29%), Positives = 89/158 (56%)

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+  +++  +R AR ++ K+  EP+PEEIA  L  PV  V+++L + +   S++  +
Sbjct: 1   MPIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL 60

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G +    L D + D     P +     +L ++  + L+ LT ++  V+  RFG+  +   
Sbjct: 61  GPDSDKTLLDTLTDDRPTDPCELLQDDDLSQSIDQWLSELTEKQREVVIRRFGLRGHESS 120

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           TLE+VG +  +TRER+RQI+ + +++L+       L S
Sbjct: 121 TLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSS 158


>gi|47168808|pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168810|pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168812|pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168814|pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47169132|pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
          Length = 239

 Score = 97.2 bits (240), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 102/238 (42%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAK---KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           K      I ++E++   L LV ++A    K+    +   DLI  G IGL+KA +      
Sbjct: 5   KNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTEN 64

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +   Y    +K AI   +            +R+K  ++     ++  K+ REPT EE+
Sbjct: 65  PKRAEAYIKLRIKGAIYDYLRSLDF---GSRQVREKERRIKEVVEKLKEKLGREPTDEEV 121

Query: 553 AKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           AK+L +  E + K L        L    +  +      + I   ++ +  +  I+  L E
Sbjct: 122 AKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIP--SSTNVEEEVIKRELTE 179

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                ++ L  RE+ V+++ F      +   +EV K    +  R+ Q++AKA+ +L+ 
Sbjct: 180 KVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLRE 233


>gi|119511848|ref|ZP_01630948.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119463490|gb|EAW44427.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 258

 Score = 97.2 bits (240), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 118/252 (46%), Gaps = 14/252 (5%)

Query: 425 SEFR-HIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGL 481
           +E +  I  ++R+ E   S   + ++V+ N  LV   A  + N+    + DL+Q G +GL
Sbjct: 7   NELKNEIWQLLREYEQSRSDTIRNKLVKLNFGLVRKEAHYWMNQCRENYDDLVQVGYLGL 66

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A EKF+   G+ FS++A+ +++  I   + D+  T+RIP        + +  +R +  
Sbjct: 67  IRAIEKFEISKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIPRRYLALQQQAIGVSRDLCE 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPI--GDEDTSHLGDFIEDKNA 597
           K  R+PT  E+A  LA+ +   +++    + + P+SL+ P+   +E T+ LG+ + D   
Sbjct: 127 KYNRQPTDSELAAALAISLNEWQEIKLAWVNRSPLSLDVPVLDSEEGTTSLGELVPDPKY 186

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S   +           + L  L      VL   F      D T ++V +   ++   + 
Sbjct: 187 RSFQLAQEDQI---RLQQALFELEKCTREVLECVFF----QDLTQKQVAEHLGISVVTVS 239

Query: 658 QIEAKAIRKLKH 669
           +   K +  LK 
Sbjct: 240 RRVKKGLGLLKK 251


>gi|325001881|ref|ZP_08122993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia sp. P1]
          Length = 258

 Score = 97.2 bits (240), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 105/232 (45%), Gaps = 13/232 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            ++  ++ +VE +  LV  +  K   R    ++  DL+Q G  GL+ A ++FD   G +F
Sbjct: 28  RSADTRRLLVEHHAPLVRGIGAKLATRLPSSIELADLLQSGTFGLIDAVDRFDPARGVRF 87

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
             YA   V+ A+   +  Q     +P  +R +  ++ R    + +K+ R  +  E+A +L
Sbjct: 88  EGYAAQRVRGAMLDELRAQDW---VPRTVRSRSREIERAREAVQSKVGRPASDRELAAEL 144

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            + +  +R+     +  + +     D + +     +   +   P+ +A++          
Sbjct: 145 GIGLRDLRQ---AVRPALLVSADDLDGNAAPGPAALAAADTADPVATAVRRETGAELRAA 201

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +A L  R+  VLR+ +      DHTL E+G    VT  R+ Q+  + + +L+
Sbjct: 202 IAQLGERDRTVLRLYYV----EDHTLAEIGALLGVTESRVCQLHTRMLTRLR 249


>gi|253577386|ref|ZP_04854702.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251843186|gb|EES71218.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 257

 Score = 97.2 bits (240), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 114/239 (47%), Gaps = 13/239 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +  +   +    ++++    +V   A K   NR   + DL Q G + L++  +++D  LG
Sbjct: 20  QYQQTRDNEIATQLIQKYDSMVKMAAGKIARNRPDLYEDLYQVGEMALVRLLQQYDSDLG 79

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  YAM  +   +   + D+S  I++P  +++K   V +    ++ K++R P  +EIA
Sbjct: 80  IPFEPYAMKSMIGHMKNYLRDKSWYIQVPRRIKEKGALVQQAIDELTLKLERSPNVQEIA 139

Query: 554 KKLAMPVEGVRKVL--KITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLR 610
           + L + VE   +VL  +     +SL++P+  ++++  LG+ I      +  D       R
Sbjct: 140 EYLELSVEETVEVLAGRDCYHYVSLDSPLSPDESAVTLGEVIS-----ADADDYDALENR 194

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + L  L  +E++VL M +  G     +   + ++  +++  + +I+ +A  +LK 
Sbjct: 195 MDLQQALGQLKAQEQQVLLMAYQEG----QSQRAIARKLGISQMSVSRIQKRATERLKQ 249


>gi|222431361|gb|ACM50633.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431363|gb|ACM50634.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431365|gb|ACM50635.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431367|gb|ACM50636.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431369|gb|ACM50637.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 97.2 bits (240), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 37/270 (13%), Positives = 89/270 (32%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGITPPAAEVPPPVDTK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + + E A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  TAKADDDSEDEEAEATEDEEEAESGPDPVIAAQRFGAVADQMEVTRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  + + +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRENKQAIAEMLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
           A     I++ + ++ ++ VETG+ I+E + 
Sbjct: 194 ARLQPDIIRCQQKLTALEVETGLKIAEIKD 223


>gi|52081127|ref|YP_079918.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52786504|ref|YP_092333.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52004338|gb|AAU24280.1| RNA polymerase sporulation-specific sigma factor [Bacillus
           licheniformis ATCC 14580]
 gi|52349006|gb|AAU41640.1| SpoIIIC [Bacillus licheniformis ATCC 14580]
          Length = 241

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 111/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   +  ++ + + +K+ +    +S S+ +  + ++ +       A+  ++E NLRLV 
Sbjct: 7   ALGYVIKELVFLVSYVKNNAFPQPLSSSDEKKYLELMAQ---GDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +N        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKKYIDILDGREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|56421070|ref|YP_148388.1| sporulation sigma factor SigK [Geobacillus kaustophilus HTA426]
 gi|56380912|dbj|BAD76820.1| sporulation mother cell-specific RNA polymerase sigma-27 factor
           precursor (sigma K) (stage IV sporulation protein CB)
           [Geobacillus kaustophilus HTA426]
          Length = 237

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 110/270 (40%), Gaps = 59/270 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  +  + + IK+ +    +S  E    ++++ K       A+  ++E NLRLV  + KK
Sbjct: 12  LKELTFLVSYIKNNAFPQPLSAQEEEKYLALMAK---GDEQARNRLIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G +  DLI  G IGL+KA E +    G K +TYA   ++  I   +          
Sbjct: 69  FENTGEEVEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEILMHLRS-------- 120

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T++ +SL  PIG 
Sbjct: 121 --------------------------------------------LKKTRKDVSLHEPIGQ 136

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D ++ +      +  +   L E   + ++ L  RE+ V+  RFG+G   +
Sbjct: 137 DKEGNEISLLDILKAEGEDIADEIHLNMEL-EQVKQYISVLDEREKEVIINRFGLGRQRE 195

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|239934428|emb|CAR92344.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 222

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 39/268 (14%), Positives = 85/268 (31%), Gaps = 47/268 (17%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++   D +      L ++  L   I P+                            
Sbjct: 1   TVDYILGEYDRVTTEGGRLSDV--LSDYIDPDDNIAAP---------------------- 36

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +E       AA   ++   + +      + +E     D   +A    A+ +Q       
Sbjct: 37  TEEVPIPGTKAAAAKEESDDEEEESEGGDDEEEAESGPDPVVAAQRFGAVSEQ------- 89

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                         LQ      +K+ ++  +     + L  L   + L   + ++LVE++
Sbjct: 90  --------------LQATTKVLKKNGRTHKESVEALQALADLFMPIRLVPKQFEVLVERV 135

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL      E D  W           W   +  
Sbjct: 136 RDALNRLRQQERAIMQLCVRDARMPRADFLRVFPSNETDQTWSGDLAKRNTK-WAAALGE 194

Query: 402 EVDSILKIRNEIKSISVETGISISEFRH 429
           +  +I+  + ++  +  ETG++++E + 
Sbjct: 195 KDAAIVACQQKLIDLETETGLTVAEIKE 222


>gi|254785490|ref|YP_003072919.1| RNA polymerase sigma factor for flagellar operon [Teredinibacter
           turnerae T7901]
 gi|237687129|gb|ACR14393.1| RNA polymerase sigma factor for flagellar operon [Teredinibacter
           turnerae T7901]
          Length = 235

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 97/237 (40%), Gaps = 15/237 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLG 493
            E     A    VE  + LV  +A     R        DL+Q G IGL++AA+K+D   G
Sbjct: 3   YEQAQEAAVAIRVEDYVPLVKRIAHHMMARMPSHVLVDDLMQAGMIGLLEAAQKYDAGKG 62

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F TYA   ++ AI   +         P  +     +V      +  ++ R+    EIA
Sbjct: 63  ASFETYAGIRIRGAIVDEMRRGDW---APRSVHRNARRVSEAIGNVEARLGRDARDGEIA 119

Query: 554 KKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           ++L M ++    +L+ +      SLE    + +       +  +    P +      +R+
Sbjct: 120 EELQMSLDEYHDILRDSTSTRLYSLEETFEENENQF---SLGTEGLDEPAEKVQIDAMRK 176

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +  L  RE+ VL + +      +  L+E+G    V+  RI QI ++A  +LK
Sbjct: 177 ALAGAIEGLPEREQLVLSLYY----EQEMNLKEIGLVLGVSESRISQIHSQAALRLK 229


>gi|325662347|ref|ZP_08150956.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471349|gb|EGC74572.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 234

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 59/218 (27%), Positives = 108/218 (49%), Gaps = 10/218 (4%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           +E +   ++  K +     A++  ++ NLRLV+SV K++ +      DL Q G +GLMKA
Sbjct: 21  NEEKE--ALFVKIKEGDEAARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCVGLMKA 78

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + F+  L  KFSTYA+  +   I R + D +  IR+   +RD  +K +        +  
Sbjct: 79  IDNFNTDLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAYKAIYAKEGYMKRHL 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLD 602
           +EPT EEIA+++ +  E +   L   + P+SL  P+ ++  D  ++ D I DK   +  +
Sbjct: 138 KEPTVEEIAEEIGIAKEDIIFALDAIQAPMSLNEPVYNDSGDALYVMDQISDKK--NREE 195

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             ++     +    +  L  RE  ++++RF    +   
Sbjct: 196 YWVEGL---SLEAAMERLNERERFIIQLRFLKERHRWK 230


>gi|224992792|gb|ACN76111.1| SigB [Listeria innocua]
 gi|224992796|gb|ACN76113.1| SigB [Listeria innocua]
 gi|224992810|gb|ACN76120.1| SigB [Listeria innocua]
 gi|224992814|gb|ACN76122.1| SigB [Listeria innocua]
 gi|224992832|gb|ACN76131.1| SigB [Listeria innocua]
 gi|224992834|gb|ACN76132.1| SigB [Listeria innocua]
 gi|224992848|gb|ACN76139.1| SigB [Listeria innocua]
 gi|224992850|gb|ACN76140.1| SigB [Listeria innocua]
 gi|224992856|gb|ACN76143.1| SigB [Listeria innocua]
          Length = 214

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 90/210 (42%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 2   AAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 62  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 122 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +VL  L  RE+++L+  F    +   T E
Sbjct: 182 EKVLPVLDEREQKILQYTFIENRSQKETGE 211


>gi|119503682|ref|ZP_01625765.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2080]
 gi|119460744|gb|EAW41836.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2080]
          Length = 237

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 101/241 (41%), Gaps = 20/241 (8%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
             +   G C  +     +V A+L LV  +A++   R    ++  DLIQ G IGL+KA++ 
Sbjct: 7   AKLSEYGACGGASQGDALVRAHLPLVKRIAQQLLVRLPAHIEMDDLIQVGLIGLLKASDD 66

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
                G +FSTYA   ++ A+   +  +     +P  ++  + +V     R   ++ R  
Sbjct: 67  HQADSGAQFSTYAAIRIRGAMLDELRSRDW---LPRSVQRDLGRVAAAIERAEQRVGRPA 123

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T +EIA +L M ++  ++          L   +       L +        +       +
Sbjct: 124 TDQEIADQLEMDLDSYQQ----------LSGELACARIGQLEELDVPTEVDATTSIVFDS 173

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE     +  L  +E  +L + +  G      L+E+G    V+  R+ QI  +A+ +L
Sbjct: 174 ARREAVVEAIGRLPEKEGLMLSLYYTEG----LNLKEIGMVLNVSESRVSQIHGQAVARL 229

Query: 668 K 668
           +
Sbjct: 230 R 230


>gi|209408332|emb|CAP19909.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 197

 Score = 97.2 bits (240), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 78/241 (32%), Gaps = 45/241 (18%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           AKRIE G   +M+++   P T  +++   + +      L +I  L   I P+  G     
Sbjct: 1   AKRIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA--- 55

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                 Q+ E  + +       + + D E     S+ +       PE A      + E  
Sbjct: 56  ----GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEKEEGDGGPDPEVARMRFGAVAEQL 111

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           + +                                       +K  ++S +     E L 
Sbjct: 112 EKAKKA-----------------------------------LKKHGRASQQAVEELEALA 136

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
            L   + L   + D LVE++ +   +I   E  +++L      + R  FL +    E + 
Sbjct: 137 ILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNL 196

Query: 382 H 382
            
Sbjct: 197 D 197


>gi|332982149|ref|YP_004463590.1| RNA polymerase sigma-29 subunit SigE [Mahella australiensis 50-1
           BON]
 gi|332699827|gb|AEE96768.1| RNA polymerase, sigma 29 subunit, SigE [Mahella australiensis 50-1
           BON]
          Length = 239

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 100/248 (40%), Gaps = 52/248 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + I   +++        K  ++E NLRLV+ +A+++ N G+   DLI  G IGL
Sbjct: 38  LSADEEQDI---MKRLSDGDESVKSILIERNLRLVVYIARRFENTGIPVEDLISIGTIGL 94

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +       +  V + +              
Sbjct: 95  IKAVNTFDPDKKIKLATYASRCIENEILMYLRRNCRFNKTEVSIDEP------------- 141

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + +   +   + + IED+      
Sbjct: 142 -LNTDWDGNEL-----------------------LLSDVLGTEVDLVYNIIEDEVD---- 173

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     L  L+ RE+R++++RFG+    + T +EV     +++  I ++E 
Sbjct: 174 --------KQLLNIALNKLSSREQRIMQLRFGLDDGVEKTQKEVADMLGISQSYISRLEK 225

Query: 662 KAIRKLKH 669
           + I++LK 
Sbjct: 226 RIIKRLKK 233


>gi|121488765|emb|CAJ18267.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 57/166 (34%), Positives = 99/166 (59%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V+R  F IGM+
Sbjct: 121 LQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFXIGMD 165


>gi|20808064|ref|NP_623235.1| sporulation sigma factor SigE [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516645|gb|AAM24839.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 241

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 101/255 (39%), Gaps = 59/255 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEESYLISKMEK---GDNEAKSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +                             
Sbjct: 98  IKAINTFNPRKKIKLATYASRCIENEILMYLRRN-------------------------- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       T+  +S + P+  +   +   L D +   N  
Sbjct: 132 --------------------------NKTRLEVSFDEPLNVDWDGNELLLSDILGTDN-E 164

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +          RE  T  L  L  RE++++R+RFG+   T+ T +EV     +++  I +
Sbjct: 165 TVYKYIEDEVERELLTSALKKLPDREKKIIRLRFGLEGGTEKTQKEVADMLGISQSYISR 224

Query: 659 IEAKAIRKLKHPSRS 673
           +E K +++LK     
Sbjct: 225 LEKKILKRLKKEMNR 239


>gi|167750689|ref|ZP_02422816.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|167656368|gb|EDS00498.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|291558233|emb|CBL35350.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 221

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 52/222 (23%), Positives = 100/222 (45%), Gaps = 13/222 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            +  +  LV S+A ++ NRG+++ +L   G +GL+KA   FD   G KFSTYA+  +   
Sbjct: 9   FITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D   T+++   +++   K+ R    +  K   EP    +A+KL +  E     L
Sbjct: 69  IKQLFRDGG-TVKVSRSLKELSLKICRLRDELI-KNGEEPHISVLAEKLGITPEEASLAL 126

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             +  P+SL +   +E+     D   +           +A  R    ++++ L P + R+
Sbjct: 127 GASLPPVSLSSYDDEENDEGSFDLPVEPEQP-------KALDRMALRQLVSRLEPLDRRL 179

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +R+        T E       +T+ ++ + E K +  L+ 
Sbjct: 180 IILRYSEECTQSRTAE----ILGMTQVQVSRREKKILEGLRK 217


>gi|209408330|emb|CAP19908.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 200

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 77/243 (31%), Gaps = 45/243 (18%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T  +++   + +      L +I  L   I P+  G       
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA----- 53

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
               Q+ E  + +       + + D E     S+ +       PE A      + E  + 
Sbjct: 54  --GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEKEEGDGGPDPEVARMRFGAVAEQLEK 111

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +                                       +K  ++S +     E L  L
Sbjct: 112 AKKA-----------------------------------LKKHGRASQQAVEELEALAIL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LVE++ +   +I   E  +++L      + R  FL +    E +  W
Sbjct: 137 FMPIELVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDW 196

Query: 384 VSY 386
              
Sbjct: 197 AEQ 199


>gi|297616993|ref|YP_003702152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144830|gb|ADI01587.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 241

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 101/244 (41%), Gaps = 56/244 (22%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++++ E   +  K  ++E NLRLV+ +AKK+ N G+   DL+  G IGL+KA   F+   
Sbjct: 49  LLQRLEQGDNGVKSTLIEHNLRLVVYIAKKFENTGINIEDLVSIGTIGLIKAVNTFEPRK 108

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +                  + ++T                 
Sbjct: 109 NIKLATYASRCIENEILMYLR-----------------RNLKTRAE-------------- 137

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +SL+ P+  +   +   L D +   +      +  +   
Sbjct: 138 ---------------------VSLDEPLNVDWDGNELLLSDVLG-TDGDMIYKTIEEEVE 175

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++  ++ +  L PRE+R++++RFG+    + T +EV     +++  I ++E + +++L+ 
Sbjct: 176 KKLLSQAILRLPPREKRIIQLRFGLEDGYEKTQKEVADILGISQSYISRLEKRILKRLRR 235

Query: 670 PSRS 673
             R 
Sbjct: 236 EIRK 239


>gi|297544885|ref|YP_003677187.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842660|gb|ADH61176.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 241

 Score = 97.2 bits (240), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 98/252 (38%), Gaps = 53/252 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  ++VS + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSMEEETYLVSKMEK---GDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNS------------------------- 132

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K K E + EE                            +  +    L   I   +  +  
Sbjct: 133 KTKLEVSFEEP-------------------------LNVDWDGNELLLSDILGTDNETVY 167

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   RE  T  L  L  RE++++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 168 KYIEDEVERELLTSALKKLPDREKKIIGLRFGLDGGVEKTQKEVADMLGISQSYISRLEK 227

Query: 662 KAIRKLKHPSRS 673
           K +++LK     
Sbjct: 228 KILKRLKKEMNR 239


>gi|169827149|ref|YP_001697307.1| RNA polymerase sigma factor SigD [Lysinibacillus sphaericus C3-41]
 gi|168991637|gb|ACA39177.1| RNA polymerase sigma-D factor (Sigma-28) [Lysinibacillus sphaericus
           C3-41]
          Length = 271

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 100/234 (42%), Gaps = 12/234 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R        A   +++  + LV    ++ +    + +   DL   G IGL  A  KFD  
Sbjct: 30  RWIHERDPDAGDLLIKKYISLVSYHVQRISAGLPKSVSRDDLTSLGMIGLFDALNKFDIN 89

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + V+ AI   +  +     +P   R+K  K+     ++  K  R  TPEE
Sbjct: 90  RDLKFDTYASFRVRGAIIDGLRKEDW---LPRSAREKAKKLDAQIEQLEQKYMRHVTPEE 146

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +AK + +PVE V +          +S+      E+       I D    +P  S +++ L
Sbjct: 147 LAKHMEVPVEDVYQTVQEHFFSNVLSINEQQDQEEVDGKSFVIRDDTTKTPEQSVVKSEL 206

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     +  L  +E+ VL + +      + TL E+G+   ++  RI QI +KA
Sbjct: 207 LDDLAENIQKLNEKEQLVLSLFY----TEELTLTEIGEMLELSTSRISQIHSKA 256


>gi|222431347|gb|ACM50626.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431349|gb|ACM50627.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 223

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 35/270 (12%), Positives = 89/270 (32%), Gaps = 48/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L +++            G+    +G +    E       +
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAK 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + + D + A     ++ ++    P  A      + +  + +   L           
Sbjct: 50  AVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL----------- 98

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   +K  +++ +       L +L   + L   + + LVE
Sbjct: 99  ------------------------KKHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVE 134

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 135 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAI 193

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
                 I++ + ++ ++  ETG++I+E + 
Sbjct: 194 GRLQPDIIRCQQKLTALETETGLTIAEIKD 223


>gi|158341138|ref|YP_001522305.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
 gi|158311379|gb|ABW32991.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
          Length = 427

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 106/243 (43%), Gaps = 21/243 (8%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWC 491
           ++ + +     A+   +  N  LV   A K+  RGL  + DL+  GN+GL  A +KFD  
Sbjct: 25  LIIQAQAGDLRARDRFIRQNEGLVFQQAHKF--RGLADWDDLVNAGNLGLAIAIQKFDVA 82

Query: 492 LGYKFSTYAMWWVKQAITR-SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
            GYKFS+YA+  ++  I R     +  +I I +H+++    + + ++ +   + REPT  
Sbjct: 83  KGYKFSSYAVKVIRTEIRRLIHEFKGISIEISLHLKE----IEQASQAIRMDLDREPTIT 138

Query: 551 EIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           E++ +     + +          E  SL  P+ D+      D I   +        +   
Sbjct: 139 ELSDETGYSQQVIFNAWNKANVVETASLNIPLNDDQGCEQLDVIGVDDRTWEFTETLDQ- 197

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                   +A L  RE  ++R +     N     +E+G    ++ ER+RQ+  +A   LK
Sbjct: 198 -----KNYIAQLPDREAFIVRAKRDGFSN-----KEIGTMLSLSGERVRQLLKQARAFLK 247

Query: 669 HPS 671
           H  
Sbjct: 248 HLM 250


>gi|226323675|ref|ZP_03799193.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
 gi|225207859|gb|EEG90213.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
          Length = 205

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 60/203 (29%), Positives = 101/203 (49%), Gaps = 8/203 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +  K +     AK++ ++ NLRLV+SV K+++       DL Q G IGL+KA   F+  
Sbjct: 1   MLFEKIKAGDEEAKEQYIKGNLRLVLSVIKRFSGSSENPDDLFQIGCIGLIKAINNFNPE 60

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           L  KFSTYA+  +   I R I D +  IR+   +RD  +K +          ++EPT +E
Sbjct: 61  LEVKFSTYAVPMIIGEIRRFIRDNNS-IRVSRSLRDTAYKAIYAKENYVKVNQKEPTVQE 119

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANL 609
           IA+++ +  E +   L   + P+SL  P+ ++  D  ++ D I DK              
Sbjct: 120 IAEEIGIAKEEIVYALDAIQMPVSLNEPVYNDNGDAMYVMDQISDKRNKEDRWVE----- 174

Query: 610 RETTTRVLASLTPREERVLRMRF 632
           + +    +  L  RE+ ++R+RF
Sbjct: 175 KLSLQAAMDRLGKREKYIIRLRF 197


>gi|291532029|emb|CBK97614.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           70/3]
          Length = 221

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 52/222 (23%), Positives = 100/222 (45%), Gaps = 13/222 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            +  +  LV S+A ++ NRG+++ +L   G +GL+KA   FD   G KFSTYA+  +   
Sbjct: 9   FITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGE 68

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I +   D   T+++   +++   K+ R    +  K   EP    +A+KL +  E     L
Sbjct: 69  IKQLFRDGG-TVKVSRSLKELSLKICRLRDELI-KNGEEPHISVLAEKLGITPEEASLAL 126

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
             +  P+SL +   +E+     D   +           +A  R    ++++ L P + R+
Sbjct: 127 GASLPPVSLSSYDDEENDEGSFDLPVEPEQP-------KALDRMALRQLVSRLEPIDRRL 179

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +R+        T E       +T+ ++ + E K +  L+ 
Sbjct: 180 IILRYSEECTQSRTAE----ILGMTQVQVSRREKKILEGLRK 217


>gi|295696140|ref|YP_003589378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411742|gb|ADG06234.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 50/220 (22%), Positives = 94/220 (42%), Gaps = 14/220 (6%)

Query: 449 VEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           +   L +V ++A++  +R       DL+  G +GL++AA ++D      F  +A   ++ 
Sbjct: 13  ITLYLPMVENIARRLKSRFKPAAMEDLVSFGMLGLLEAARRYDPGQETPFEVFARLRIRG 72

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
           A+   +  +           +++ KV     R+ +K  +  + EE+ K+L +        
Sbjct: 73  AMIDGVRAEG---PASRRRWERVKKVQEAYERLFSK-GKSGSDEEMCKELGVDRGTFIGW 128

Query: 567 LKIT--KEPISLETPIGDEDTSHL--GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           L+      PISL+  I  ED       D I D   V P  +  +  +R+     + +L  
Sbjct: 129 LEEFERFHPISLDRVIHTEDGESFRIADAIPDPEGVDPAQTVSRQAVRQMLAEAITALPE 188

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           RE+ VL + +  G     +  EV     VT  R+ Q+ +K
Sbjct: 189 REKYVLSLHYIEG----LSFREVAAVLGVTPARVSQLHSK 224


>gi|194017684|ref|ZP_03056294.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
 gi|194010584|gb|EDW20156.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
          Length = 289

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 59/289 (20%), Positives = 113/289 (39%), Gaps = 59/289 (20%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++  +          +   V  ++ + + +K+ +    +S  + +  ++++ +       
Sbjct: 41  LNMVEVKIVAGVFTAMGLMVKELVFLVSYVKNNAFPQPLSGDDEKKYLALMAQ---GDEH 97

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 98  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATYAARC 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                                                   
Sbjct: 158 IENEILMHLRA------------------------------------------------- 168

Query: 564 RKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              LK TK+ +SL  PIG +   +   L D ++ ++        +   L E     +  L
Sbjct: 169 ---LKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMEL-EKVKEYIDIL 224

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 225 DGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 273


>gi|51892359|ref|YP_075050.1| sporulation sigma factor SigE [Symbiobacterium thermophilum IAM
           14863]
 gi|51856048|dbj|BAD40206.1| RNA polymerase sigma factor similar to B. subtilis SigE
           [Symbiobacterium thermophilum IAM 14863]
          Length = 251

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 97/244 (39%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
              +++++        K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA + F
Sbjct: 55  EEAALLQRLTQGDESVKNTLIERNLRLVVYIARKFDNTGIWVEDLVSIGTIGLIKAVKTF 114

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA   ++  I   +   S                                
Sbjct: 115 DPSKRIKLATYASKCIENEILMYLRRASR------------------------------- 143

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                T+  +S + P+  +   +   L D +   + ++      
Sbjct: 144 ---------------------TRSEVSFDEPLNKDWEGNELLLSDVMGTDSDITYRGLEE 182

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + + R    + +A LT RE+R++ +RFG+    + T +EV     +++  I ++E +  +
Sbjct: 183 EVD-RMLLRKAMAKLTGREKRIMELRFGLVDGRERTQKEVADLLGISQSYISRLEKRIFK 241

Query: 666 KLKH 669
           +LK 
Sbjct: 242 RLKK 245


>gi|222431373|gb|ACM50639.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 224

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 43/270 (15%), Positives = 90/270 (33%), Gaps = 47/270 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L ++  L   I P+                +   + +   
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAAEVPPPVDAKAVKADDDSD 58

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DD  E   D E   +   D                         +A    A+ DQ+    
Sbjct: 59  DDDAEASSDDEEEVESGPDPIV----------------------AAQRFGAVSDQM---- 92

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                   E+ R+            K  +S+ +       L +L   + L   + + LVE
Sbjct: 93  --------EITRKALK---------KHGRSNKQAIAELLALAELFMPIKLVPKQFEGLVE 135

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++    +R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +
Sbjct: 136 RVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESWSD-ALAKGKAKYAEAI 194

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
                 I++ + ++ ++  ETG++I+E + 
Sbjct: 195 GRLQPDIIRCQQKLTALETETGLTIAEIKD 224


>gi|54654477|gb|AAV37115.1| RpoD [Vibrio lentus]
          Length = 176

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 64/158 (40%), Gaps = 2/158 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L     R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKATLATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +    + I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNENDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             ET +++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 139 EKETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLR 176


>gi|304399205|ref|ZP_07381072.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
 gi|304353259|gb|EFM17639.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
          Length = 172

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 54/164 (32%), Positives = 104/164 (63%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 1   MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 60

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 61  ITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 120

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 121 GLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQGL 164


>gi|218441823|ref|YP_002380152.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218174551|gb|ACK73284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 258

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 108/235 (45%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  +T +    + DL+Q G +GL++A E+F+   G+ FS++A+ +
Sbjct: 29  RNQILELNFGLVRREAHHWTTQCNENYEDLLQVGCLGLIRAIERFELGKGHAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   + D+  ++RIP    D   + +   R    +  R+PT  EIA  L + ++  
Sbjct: 89  IRGEIQHYLRDKGYSVRIPRRWLDLGRQAMIIRREFQTQFNRQPTDTEIAYGLEVSLKEW 148

Query: 564 RKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +++      +EP+SL+  I  ++   + L D + D    S   S           + L+ 
Sbjct: 149 QEIKLAFQNREPLSLDVSINHDEEGQTSLADLVPDPKYRSFQLSQDDQI---RLQQALSQ 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  R  RVL   F      D T  E  +Q  ++   + +   K +  LK   + +
Sbjct: 206 LEERTRRVLEFVFL----QDLTQREAAEQLGISVVTVSRRVKKGLDFLKETMKKE 256


>gi|261342188|ref|ZP_05970046.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315521|gb|EFC54459.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 172

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 54/164 (32%), Positives = 103/164 (62%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 1   MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 60

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 61  ITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 120

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 121 GLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGL 164


>gi|323706112|ref|ZP_08117681.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534556|gb|EGB24338.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 241

 Score = 96.8 bits (239), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 107/267 (40%), Gaps = 57/267 (21%)

Query: 407 LKIRNEIKSISVETGISIS-EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           LKIR+ I  +     +         + ++ K E   + AK  ++E NLRLV+ +AKK+ N
Sbjct: 22  LKIRDSIFYVGGSEALPPPLSAEEEMFLIAKMESGDNEAKSMLIERNLRLVVYIAKKFEN 81

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G+   DLI  G IGL+K+   F+     K +TYA   ++  I   +   S         
Sbjct: 82  TGVGIEDLISIGTIGLIKSINTFNPRKKIKLATYASRCIENEILMYLRRNSK-------- 133

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
                                                       T+  +S + P+  +  
Sbjct: 134 --------------------------------------------TRMEVSFDEPLNIDWD 149

Query: 586 SH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            +   L D +   N +       + + ++  T  L  L+ RE+R++ +RFG+   T+ T 
Sbjct: 150 GNELLLSDILGTDNELVYKIIEDEVD-KQLLTNALKKLSDREKRIIGLRFGLSGGTEMTQ 208

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +EV     +++  I ++E + +++LK 
Sbjct: 209 KEVADLLGISQSYISRLEKRILKRLKK 235


>gi|317122054|ref|YP_004102057.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
 gi|315592034|gb|ADU51330.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
          Length = 251

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 98/254 (38%), Gaps = 54/254 (21%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E  H +  +R        A+  ++E NLRLV  +AKK+   G    DLI  
Sbjct: 29  SFPQPLTPEEEAHYLERMR---HGDERARDVLIERNLRLVAHIAKKFDETGEDPEDLISI 85

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+K  + +D   G + +TYA   ++  I   +                     R  
Sbjct: 86  GTVGLIKGVDTYDPSKGTRLATYAARCIENEILMHLRATRR---------------NRRE 130

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + N I  +    E+     +P +                            D +ED  
Sbjct: 131 VFLQNPIGVDREGNEVTLMDMLPADD---------------------------DAVEDTV 163

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
               L   I+  +RE        L PRE RVL +RFG+     +T  EV +   ++R  +
Sbjct: 164 GRRLLARRIREAVRE--------LGPRERRVLELRFGLDGQRRYTQREVARVLGISRSYV 215

Query: 657 RQIEAKAIRKL-KH 669
            +IE +A+RKL +H
Sbjct: 216 SRIEKRAVRKLTRH 229


>gi|228899672|ref|ZP_04063925.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
 gi|228859981|gb|EEN04388.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
          Length = 203

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 90/205 (43%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         Q   R     +   L   E+ V+   FG  +N     ++  
Sbjct: 121 SSVARIE--SVGEVEQGYEQTERRLVLEDIFNVLNDMEKSVIHYIFGENLNQ----KDTR 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|313902394|ref|ZP_07835797.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467325|gb|EFR62836.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
          Length = 247

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 98/255 (38%), Gaps = 56/255 (21%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E  H +  +R   C    A++ ++E NLRLV  +AKK+   G    DLI  
Sbjct: 29  SFPQPLSPEEEAHYLERMR---CGDERAREVLIERNLRLVAHIAKKFDETGEDPEDLISI 85

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+K  + +D   G + +TYA   ++  I   +                     R  
Sbjct: 86  GTVGLIKGVDTYDPSKGTRLATYAARCIENEILMHLRATRR---------------NRRE 130

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DK 595
             + N I  +    E+                                   L D +  D+
Sbjct: 131 VFLQNPIGVDREGNEV----------------------------------TLMDMLPADE 156

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +AV       +  L       +  L PRE RVL +RFG+     +T  EV +   ++R  
Sbjct: 157 DAVEETVG--RRLLARRIREAVRELGPRERRVLELRFGLDGRRRYTQREVARVLGISRSY 214

Query: 656 IRQIEAKAIRKL-KH 669
           + +IE +A+RKL +H
Sbjct: 215 VSRIEKRAVRKLTRH 229


>gi|228950124|ref|ZP_04112308.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229120608|ref|ZP_04249853.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228662893|gb|EEL18488.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228809547|gb|EEM55984.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 203

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/205 (20%), Positives = 89/205 (43%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   F      +   ++ G
Sbjct: 121 SSVARIE--SVGEVEKGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|298708236|emb|CBJ48299.1| rpoD [Ectocarpus siliculosus]
          Length = 381

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 142/328 (43%), Gaps = 36/328 (10%)

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV-----SMVRK 436
            W    K+      +  +      I  ++ E++       +++ E+           +  
Sbjct: 49  DWRDLTKEEETALCELIIEN--RRIQDLQVELERKESR-PVTVQEWAVAAGHPSAHQLMA 105

Query: 437 GECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
              E   A++ +   +  LV SVA +Y   +R L   DL QEGN+GL++A EKFD   G 
Sbjct: 106 ALQEGRKAQRTLALCHQGLVRSVAYRYKQVSRNLSLDDLTQEGNVGLLEAVEKFDSTKGT 165

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE-PTPEEIA 553
           +FS+YA++ +K ++ R+IAD+   +R+PVH +D   +++  +  +  +   + PT  ++A
Sbjct: 166 RFSSYAVFRIKASVLRAIADKDRLVRVPVHAQDAAMRILAASHALQLESGGDVPTDAQLA 225

Query: 554 KKLAMPVEGV----RKVLKITKEPI---SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             L MP   V    + +L      +   +L +       S           V       +
Sbjct: 226 VALGMPEASVALYRKSLLPQNIADLDNPALPSSPQGRGGSGAAGGGSLGGRVGGEQWPWE 285

Query: 607 AN--------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTL----------EEVGKQ 648
           A+         R+    + A L+P EER LR+RFG+G                 +E+G+ 
Sbjct: 286 ASQLAQAHVVRRDMMRAMQACLSPTEERALRLRFGLGGAEKEGAVADGGGALTFKEIGRT 345

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             ++ E IR++  ++I KL+    +  L
Sbjct: 346 MELSAEGIRKMVFRSIAKLQASDEANGL 373


>gi|220907105|ref|YP_002482416.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219863716|gb|ACL44055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 263

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 107/249 (42%), Gaps = 15/249 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           ++   +      + ++V  +L LV  VA +   +    + DL+Q G +GL+ A E+FD  
Sbjct: 15  LLTYHQNPTIAVRNQLVRLHLGLVRKVAHRLARQCKEPYEDLVQCGCLGLIAAIERFDPS 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY FS++A+ +++  I   + D++  ++IP   +       +  + ++  + R PT E+
Sbjct: 75  QGYAFSSFAVPYIRGEILHFLRDRAYMLKIPRRWQQLNQDGQKVRQELAKVLDRPPTEEQ 134

Query: 552 IAKKLAMPVEGVR--KVLKITKEPISLETPIGDE-----DTSHLGDFIEDKNAVSPLDSA 604
           +A +L +  E  R  ++    + P+S+ T +            L D + D          
Sbjct: 135 VASQLQVSPEEWRSVRLAMRNRTPLSINTTLSSSAQAAGMALTLADLLVDAQEEVRQSQT 194

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             +       + LA L  R  +++   F   +      +EV  +  V+   + +   K I
Sbjct: 195 EDSL---ELYQALAQLEERTRQMIEEVFLHHLTR----QEVASRKGVSPITVSRHIQKGI 247

Query: 665 RKLKHPSRS 673
            +L +  +S
Sbjct: 248 EQLMNLLQS 256


>gi|121488781|emb|CAJ18275.1| sigma 70-type sigma factor [Chlorobium phaeovibrioides]
          Length = 165

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 55/166 (33%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A +L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANQLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L PRE  V++  FGI  +
Sbjct: 121 LQNDGHL-PDHGLNRDSLTLEVERSLSVLAPREADVIKSYFGIXXD 165


>gi|91981544|gb|ABE68114.1| RNA polymerase subunit D [Pseudomonas sp. PITR2]
          Length = 220

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 58/127 (45%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALETETGLSI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|54654479|gb|AAV37116.1| RpoD [Vibrio cyclitrophicus]
          Length = 176

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 63/158 (39%), Gaps = 2/158 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L     R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKATIATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             ET +++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLR 176


>gi|32474462|ref|NP_867456.1| sigma-70 factor [Rhodopirellula baltica SH 1]
 gi|32445000|emb|CAD75002.1| sigma-70 factor [Rhodopirellula baltica SH 1]
          Length = 557

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 80/423 (18%), Positives = 160/423 (37%), Gaps = 70/423 (16%)

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK-LV 322
           +    ++ +  +    V   L       R+L     +      ++K  +    L    + 
Sbjct: 188 EVIQQIATIMHRSPETVRYTLKNFDAKNRQLAIFPHHRETLSDEDKRVIHQLQLHGATIP 247

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           +L       ++ I  ++ ++  +   +      +         + + +L      E    
Sbjct: 248 QLCKRFKRTRTSIQRILNEVR-MQHLLEMPLEYIYNEDFEDASRENEYLAEMPVSETARK 306

Query: 383 WVSYAKDFPEGEWKN----FVACEVDSILKIRNEIKSISVETGISISEFRH----IVSMV 434
             + ++                 +   + +  N +K  + +   S+++       ++  +
Sbjct: 307 VRAPSELPSYLAALYDVPLLTREQEGHLFRKMNYLKHRANKLRQSLTDADRMDTAVMDQI 366

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +    EA   K ++V+ANLRLV+S+AK++      F  LI +GN+ L++A EKFD+  G 
Sbjct: 367 QSLYEEAVKVKNKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAVEKFDYSRGN 426

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           KFSTY       A    + + + TI      RD+                   TP+E+  
Sbjct: 427 KFSTY-------ASWAIMKNFARTIPNEFKHRDRFRA----------------TPDEMFV 463

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
                                                 +D+     L+  +Q   +    
Sbjct: 464 AH------------------------------------QDERLDPYLEETVQLQRQRELA 487

Query: 615 RVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R+L  L  RE++++  RFG+       TL+EVG++  VT+ER+RQ+EA+A+ KL+  +R 
Sbjct: 488 RILDRLDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARALSKLRDAARD 547

Query: 674 KKL 676
            K+
Sbjct: 548 AKI 550


>gi|1378114|gb|AAB41955.1| whiG [Streptomyces sp.]
          Length = 209

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 54/218 (24%), Positives = 94/218 (43%), Gaps = 24/218 (11%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA + +      ++  D +  G  GL+ A EKFD     KF TYA+
Sbjct: 3   REQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDVDREIKFETYAI 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +        IP  +R K   V R    +  + +R P+  E+A ++ + +E
Sbjct: 63  TRIRGAMIDELRALDW---IPRSVRQKARNVERAYATLEAQFRRTPSEAEVASEMGIALE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSH----------LGDFIEDKNAVSPLDSAIQANLRE 611
                L      +SL   +  E+  H          L D +ED  A +P++ A    LR 
Sbjct: 120 E----LHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTLEDTAADNPVEVAEDRELRR 175

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
              R + +L  RE+ V+ + +  G     TL E+G   
Sbjct: 176 LLARAINTLPDREKTVVTLYYYEG----LTLAEIGNVL 209


>gi|269796407|ref|YP_003315862.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269098592|gb|ACZ23028.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 300

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 89/228 (39%), Gaps = 17/228 (7%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +V  NL LV     +   R    +   DL   G + L++AA  +D   G  F+ YA 
Sbjct: 5   QNRLVTENLPLVGYHVSEMLMRVPSHVSRDDLASAGALALVQAARAYDATTGVPFNRYAA 64

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K A+   +        +    R +  K+   A  ++  + R PT EEIA  L + V 
Sbjct: 65  IRIKGAMVDELRSMDW---VSRGARQRARKLTTVADELTADLGRAPTREEIAHALGVDVS 121

Query: 562 GVRKVLK-ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            V    +      +SLE          L + +  +         +   L       +++L
Sbjct: 122 EVDTAREAAATRVLSLEGY-----DGALAEVLPAREVGPEESVILDERLT-YLHAAVSTL 175

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             R   V+   F      D T+ ++ K   VT+ R+ Q+ A+A+  L+
Sbjct: 176 PERLRTVVEQVFFH----DRTVTDIAKDMGVTQSRVSQLRAEAMVLLR 219


>gi|291196356|emb|CBG22650.1| DNA-directed RNA polymerase subunit D [Pseudomonas oryzihabitans]
          Length = 239

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 35/284 (12%), Positives = 91/284 (32%), Gaps = 46/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++ + P T   ++     +      L +++            G+    +
Sbjct: 1   RIEEGIREVMGAIAQFPGTVDYILSEYTRVTTEGGRLSDVL-----------AGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    + ++     +  D +  + + +   +   D   + D  P+  E            
Sbjct: 50  GSLPNESDELPVPNKAADAKAVDDEKDDEEESDDDAEEEGDGGPDPEEAR---------- 99

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                                 +AE   + + +       +K  +   +       L  L
Sbjct: 100 -----------------LRFGAVAEQLEKTQKV------LKKHGRDDDRAVEEFVALALL 136

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LV ++ +  +R+   E  +++LA     + R  FL    G E +  W
Sbjct: 137 FSPIKLVPKQYEALVTRVRESLERVRGLERAIMQLAVRDARMPRADFLRHFPGNETNTEW 196

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            +      + ++   +      I   + ++  +  +  + +S+ 
Sbjct: 197 TAGLLK-GKPKYAEGLERFQADIQAKQAQLAELERDYELKVSQI 239


>gi|239827809|ref|YP_002950433.1| sporulation sigma factor SigK [Geobacillus sp. WCH70]
 gi|239808102|gb|ACS25167.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. WCH70]
          Length = 236

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 108/270 (40%), Gaps = 59/270 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  ++ + + IK+ +    +S  E    + ++ K       A+  ++E NLRLV  + KK
Sbjct: 12  IKELVFLVSYIKNNAFPQPLSAKEEEKYLQLMAK---GDEQARNILIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +          
Sbjct: 69  FENTGEDAEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEILMHLRS-------- 120

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T++ +SL  PIG 
Sbjct: 121 --------------------------------------------LKKTRKDVSLHEPIGQ 136

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D ++ +      +  +   L E   + +  L  RE+ V+  RFG+ M  +
Sbjct: 137 DKEGNEISLIDVLKSEGNDIIDEIQLNMEL-EQVKKYIDVLDEREKEVIISRFGLDMQQE 195

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|228932399|ref|ZP_04095281.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228984185|ref|ZP_04144367.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229183301|ref|ZP_04310530.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228600171|gb|EEK57762.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228775472|gb|EEM23856.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228827335|gb|EEM73087.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 203

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/205 (20%), Positives = 89/205 (43%), Gaps = 8/205 (3%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              D+IQ G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D 
Sbjct: 1   MHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDL 60

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586
             K+      +++ ++R P   EIA  L +  E V +++         SL+  + +    
Sbjct: 61  GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDG 120

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
                IE  +         +   R     +   L   E+ V+   F      +   ++ G
Sbjct: 121 SSVARIE--SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTG 174

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPS 671
           ++  +++  + +I+ +AI KLK  +
Sbjct: 175 ERLGISQMHVSRIKRQAISKLKQAA 199


>gi|119491111|ref|ZP_01623269.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
 gi|119453656|gb|EAW34816.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
          Length = 304

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 127/300 (42%), Gaps = 17/300 (5%)

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL-KIRNEIKSISVETGISISEFRHIVSM 433
           +G EL     +   +  +  +   +A + D I  ++   I  I+  T     +   +  +
Sbjct: 4   KGVELGDSKANLKANTSKVGY---LAIDCDEIATQLSFNIIMINTLTSPRCLKQSSLELL 60

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCL 492
               +      + ++V+ N+ LV      +  +    + DL Q G IGL++A E+FD   
Sbjct: 61  QEYKQFPCQSIRNQIVQLNMGLVRQEVHHWVKKCPESYDDLFQIGCIGLIQAIERFDLTK 120

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  FS++A+ +++  I   + D+S  IR+P        +  +    +  K+ R+PT  EI
Sbjct: 121 GCAFSSFAVPYIRGEILHYLRDKSLLIRVPRRCSQLKQEAAKLVILLQEKLHRKPTDLEI 180

Query: 553 AKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQAN 608
           A  L + +E     K+       +SL+ P+ DE      LG+ I D N  + +    + +
Sbjct: 181 ANSLGISIEKWNQVKLTVKNSSVLSLDIPLNDEFNEKHCLGELIVDSNPNASMSQEEKID 240

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L       L  L      +L + F        T +EV KQ  ++   + +   +++R LK
Sbjct: 241 L----EMALLKLKAENRDILELVFFKN----LTYKEVAKQMNISVMTVSRRLKQSLRDLK 292


>gi|238796912|ref|ZP_04640416.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238719172|gb|EEQ10984.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 241

 Score = 96.4 bits (238), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 110/248 (44%), Gaps = 19/248 (7%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                 + K E+      LV   A +   R    ++  DLIQ G IGL+ A E FD   G
Sbjct: 5   YTHNGVVKKDELWPKYGFLVRHEALRLQARLPASVELDDLIQAGAIGLLTAIEHFDPKKG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
              S Y    V+ A+   + ++     +P  +R    +V    +R+  +     T  ++A
Sbjct: 65  IAISIYITQKVRWAMIDELRERDW---VPRRVRSNAREVAAVIQRVEQESGTVATEADVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN----AVSPLDSAIQANL 609
             + + +   +++L  T    S +    DE    L D IE  +     ++PL   ++ NL
Sbjct: 122 AAMGVTLREYQQMLADTN---SSQLYSLDELQEELSDSIEQPDIQHEMLNPLHELMKENL 178

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  ++ + +L  R++ +L + +      D  ++EVG    +T  R+ Q+ ++AI++L+ 
Sbjct: 179 TKHISQEIKALPERDQLLLNLYY----QQDLNMKEVGILLEITETRVSQLHSQAIKRLR- 233

Query: 670 PSRSKKLR 677
            +R   LR
Sbjct: 234 -ARLDALR 240


>gi|91981546|gb|ABE68115.1| RNA polymerase subunit D [Pseudomonas sp. PILH1]
 gi|91981550|gb|ABE68117.1| RNA polymerase subunit D [Pseudomonas sp. Q2-87]
          Length = 220

 Score = 96.4 bits (238), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 58/127 (45%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|15606452|ref|NP_213832.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
 gi|2983663|gb|AAC07229.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
          Length = 236

 Score = 96.4 bits (238), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 102/238 (42%), Gaps = 13/238 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAK---KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           K      I ++E++   L LV ++A    K+    +   DLI  G IGL+KA +      
Sbjct: 2   KNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTEN 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +   Y    +K AI   +            +R+K  ++     ++  K+ REPT EE+
Sbjct: 62  PKRAEAYIKLRIKGAIYDYLRSLDF---GSRQVREKERRIKEVVEKLKEKLGREPTDEEV 118

Query: 553 AKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           AK+L +  E + K L        L    +  +      + I   ++ +  +  I+  L E
Sbjct: 119 AKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIP--SSTNVEEEVIKRELTE 176

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                ++ L  RE+ V+++ F      +   +EV K    +  R+ Q++AKA+ +L+ 
Sbjct: 177 KVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLRE 230


>gi|126653717|ref|ZP_01725635.1| sigma factor SigD [Bacillus sp. B14905]
 gi|126589681|gb|EAZ83817.1| sigma factor SigD [Bacillus sp. B14905]
          Length = 256

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 100/234 (42%), Gaps = 12/234 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R        A   +++  + LV    ++ +    + +   DL   G IGL  A  KFD  
Sbjct: 15  RWIHERDPDAGDLLIKKYISLVSYHVQRISAGLPKSVSRDDLTSLGMIGLFDALNKFDIN 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + V+ AI   +  +     +P   R+K  K+     ++  K  R  TPEE
Sbjct: 75  RDLKFDTYASFRVRGAIIDGLRKEDW---LPRSAREKAKKLDAQIEQLEQKYMRHVTPEE 131

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +AK + +PVE V +          +S+      E+       I D    +P  S +++ L
Sbjct: 132 LAKHMEVPVEDVYQTVQEHFFSNVLSINEQQDQEEVDGKSFVIRDDTTKTPEQSVVKSEL 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     +  L  +E+ VL + +      + TL E+G+   ++  RI QI +KA
Sbjct: 192 LDDLAENIQKLNEKEQLVLSLFY----TEELTLTEIGEMLELSTSRISQIHSKA 241


>gi|121488747|emb|CAJ18258.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 58/166 (34%), Positives = 101/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+K A++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKXAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P  S  + +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHSLNRDSLTLEVERSLSVLAPREADVIRSYFGIGMD 165


>gi|26249145|ref|NP_755185.1| hypothetical protein c3306 [Escherichia coli CFT073]
 gi|289829787|ref|ZP_06547302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|26109552|gb|AAN81755.1|AE016765_157 Hypothetical protein c3306 [Escherichia coli CFT073]
 gi|323154962|gb|EFZ41154.1| RNA polymerase sigma factor rpoS [Escherichia coli EPECa14]
          Length = 172

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 54/164 (32%), Positives = 104/164 (63%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ + 
Sbjct: 1   MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 60

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             S++TP+G +    L D + D+    P D+    +++++  + L  L  ++  VL  RF
Sbjct: 61  ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRF 120

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 121 GLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 164


>gi|239934372|emb|CAR92316.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 225

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 38/270 (14%), Positives = 89/270 (32%), Gaps = 46/270 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGYGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +      +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCARDARMPRADFLRQFPNNGTNLDWAEQLAS-GKGKYAETIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVS 432
            + I++ + ++  +  E  ++I++ + I  
Sbjct: 196 KEDIVRCQQKLIELEQECDLAIADIKDINR 225


>gi|229093408|ref|ZP_04224513.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
 gi|228690002|gb|EEL43805.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
          Length = 258

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 22  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 78

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 79  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 122

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 123 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 146

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 147 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 205

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 206 ALGISRSYVSRIEKRALMKMFH 227


>gi|167770197|ref|ZP_02442250.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
 gi|167667519|gb|EDS11649.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
          Length = 257

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 65/269 (24%), Positives = 110/269 (40%), Gaps = 22/269 (8%)

Query: 424 ISEFRHIVS----MVRKGECEASIA-KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQ 475
           + E R I      ++R  +   S   +  +V     +  SVA +  N   +     +++ 
Sbjct: 1   MQEERQIEENPEELMRLYKETGSQELRNRIVMHYSYIAKSVAIEMNNMFHKYATIEEMVN 60

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           +G I L+ + ++FD   G KFSTYA   VK AI   +  Q     +P  +R    +V   
Sbjct: 61  QGVIALIDSVDRFDPDHGVKFSTYAFTKVKGAIIDYVRKQDW---LPRRVRHNAIRVNNA 117

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--E 593
              +  K+ R PT  E+AK+L M      + +                D     + +   
Sbjct: 118 YNDLPMKLGRNPTRSEMAKQLDMSEREFDQCIYEMSGESIFSYESLLADGPQNQNMLWPM 177

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           +   V+P        LRE     + SL  +E  VL + +        T++E+G    V+ 
Sbjct: 178 EGEIVNPEGCVDAKELREQLGMAIDSLNEQERHVLSLYYYEN----LTMKEIGGVLGVSE 233

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +RI QI  K I+KL++     KL  ++ G
Sbjct: 234 QRIGQINRKLIQKLRN-----KLEQYMKG 257


>gi|295696453|ref|YP_003589691.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412055|gb|ADG06547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 93/241 (38%), Gaps = 56/241 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +++ +        +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD  
Sbjct: 49  ALLVRLIEGDESVRSTLIERNLRLVVYIARKFENTGIYIEDLVSIGTIGLIKAVNTFDPQ 108

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              K +TYA   ++  I   +   +                                   
Sbjct: 109 KRIKLATYASRCIENEILMFLRRNN----------------------------------- 133

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQAN 608
                      VR         +S + P+  +   +   L D +  +N     +   Q +
Sbjct: 134 ----------KVRAE-------VSFDEPLNVDWDGNELLLSDVLGTENDTIYRNIEEQID 176

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      L  LT RE +++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 177 -KHLLYDALGKLTERERKIMELRFGLAGGQEMTQKDVADLLGISQSYISRLEKRIIKRLR 235

Query: 669 H 669
            
Sbjct: 236 K 236


>gi|311741871|ref|ZP_07715682.1| DNA-directed RNA polymerase sigma subunit SigF [Aeromicrobium
           marinum DSM 15272]
 gi|311314877|gb|EFQ84783.1| DNA-directed RNA polymerase sigma subunit SigF [Aeromicrobium
           marinum DSM 15272]
          Length = 258

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 114/259 (44%), Gaps = 15/259 (5%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKE--MVEANLRLVISVAKKYTNRGLQFLDLI 474
           S+ + I  SE   ++         A  A+ E  +V ++L    S+A +Y NRGL+  DL 
Sbjct: 3   SITSAIPSSEETSLLLTRAADAEPAERAQLEDDVVRSHLGFANSLASRYRNRGLELDDLR 62

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q  N+ L+KA  +F    G  F+++A   +   + R   D   TIR P  ++     + +
Sbjct: 63  QVANLALVKAVRRFRADRG-DFASFAAVTISGELKRHFRDHGWTIRPPRSIQQLQVDLRK 121

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFI 592
                +++   EPT +E+A +L +P E V +           SL+ P      + L D +
Sbjct: 122 AKEEAAHESSVEPTLDELAARLHVPREAVAEASAANGCFRTTSLDEP-RGASEAPLADRL 180

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
               AV      ++       T     LT  ++ ++++RF  G     T  E+G+   V+
Sbjct: 181 A---AVGDDMEFVEE--WCDFTPAWEGLTDEDKELIKLRFFEG----LTQREIGEAVGVS 231

Query: 653 RERIRQIEAKAIRKLKHPS 671
           + +I +  ++ ++ L+   
Sbjct: 232 QMQISRRLSRVLQSLRTSM 250


>gi|148833413|gb|ABR14576.1| DNA-dependent RNA polymerase sigma factor D subunit [Alcanivorax
           venustensis]
          Length = 260

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/280 (14%), Positives = 95/280 (33%), Gaps = 24/280 (8%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M +L   P   + ++     + D    L ++I            G+    +  +   
Sbjct: 2   REVMHALAFWPGAVEMVLDEYQRITDEERKLTDVI-----------AGYLDPNDDGAAAT 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             +      +   +E E   +   +  + +++K     E  + D+     D D+      
Sbjct: 51  NANKEPRFSQKKREEAEKAAKEKEREKEKEKAKQKDDDEEDDADKNTAGADADEEEEDEG 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLS 329
            ++  L           AE + EL+ L + A    K + +        +E L        
Sbjct: 111 GLDPVLA----------AERFAELKKLYEKAQRSFKRNGRDHASTAKAQEALAAHFTLFK 160

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAK 388
           L     D L+         +   E  ++ LA +  G+ R  F++   G E +  WV    
Sbjct: 161 LVPRIYDQLLVGARTHLDTVRRFERHIMALAIRRAGVPRRDFIKIFPGNETNMDWVDQTL 220

Query: 389 DFPE-GEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              +  ++ + +    + I + + +I ++    G+ +++ 
Sbjct: 221 KSKKSKDYADKLRLVKEDIQRNQRKIMTLEEVIGLPVADI 260


>gi|54654457|gb|AAV37105.1| RpoD [Vibrio gigantis]
 gi|54654481|gb|AAV37117.1| RpoD [Vibrio crassostreae]
          Length = 176

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 64/158 (40%), Gaps = 2/158 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             ET +++   + I   +  GE +A  AKKEMVEANLR
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLR 176


>gi|56752318|ref|YP_173019.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|56687277|dbj|BAD80499.1| group3 RNA polymerase sigma factor SigF2 [Synechococcus elongatus
           PCC 6301]
          Length = 275

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 107/240 (44%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           +V   E  +   + ++V+ NL LV  +A + + +    + DL Q G +GL++A E+F   
Sbjct: 30  LVAYAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQPH 89

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D   +IRIP   ++   +  +    + ++  R PT +E
Sbjct: 90  QGCAFSSFAVPYIRGEILHFLRDSCHSIRIPRRWQELQRQGQQLREVLRHEWGRAPTEQE 149

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
           +A  L + +   +++   +  + P+SL+  +     S   L + + D    S        
Sbjct: 150 LAFALNLSMTEWQEIHLARRNRMPMSLDATLSQAGDSSVTLVETLPD---TSQQWQQAAL 206

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R+     +  L  +    +   +  G+      +E  +QF ++   I +   + ++K+
Sbjct: 207 EERQQLVEAIGQLEEKARTAIESVYLRGLTR----KEAAQQFGISPMTITRRINRGVQKI 262


>gi|332799103|ref|YP_004460602.1| RNA polymerase sigma-28 subunit SigE [Tepidanaerobacter sp. Re1]
 gi|332696838|gb|AEE91295.1| RNA polymerase, sigma 28 subunit, SigE [Tepidanaerobacter sp. Re1]
          Length = 239

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 93/244 (38%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V  ++K +      K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F
Sbjct: 43  EEVFYLKKLQMGDQTVKTVLIERNLRLVVYIARKFENTGICIEDLISIGTIGLIKAINTF 102

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA   ++  I   +                                    
Sbjct: 103 DPNKKIKLATYASKCIENEILMYLRRN--------------------------------- 129

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                T+  +S + P+  +   +   L D +   N +       
Sbjct: 130 -------------------NKTRMEVSFDEPLNIDWDGNELLLSDILGTDNDMIYKYIED 170

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + + RE     +  L+ RE  ++++RFG+    + T +EV     +++  I ++E K I+
Sbjct: 171 EVD-RELLYTAMKRLSQRERCIIKLRFGLNGGVEKTQKEVADLLGISQSYISRLEKKIIK 229

Query: 666 KLKH 669
           +LK 
Sbjct: 230 RLKK 233


>gi|257440909|ref|ZP_05616664.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
 gi|257196689|gb|EEU94973.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
          Length = 222

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 101/229 (44%), Gaps = 14/229 (6%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
             I +   +E NL LV + A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA
Sbjct: 4   DKIRRSAFIEQNLGLVHACAGRFRGRGIEYDDLYGAGCMGLVKATDGFDEGRGVCFSTYA 63

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +   I +   +   T+++   +++   +V             EPT  ++A++L   V
Sbjct: 64  VPVILGEIKKLFREGG-TVKVSRSLKELGLRVNAAREHHRKLCGTEPTLSQLAEELGESV 122

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +   ++  +  +SL      E+     D I  ++    L   I          VL SL
Sbjct: 123 ENITLAIQAAQPALSL--TPEGENNDRQID-IPVESPEEELADKI------GLAEVLESL 173

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +  ++R+RF        T  E  K    T+ +I + E K +RK++ 
Sbjct: 174 PEEDRLLIRLRFYAN----RTQSETAKVLHTTQVQISRRERKILRKMRE 218


>gi|239934394|emb|CAR92327.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 199

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 27/166 (16%), Positives = 64/166 (38%), Gaps = 3/166 (1%)

Query: 285 DEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A  +  +   QD  +   +K  + S +       L +L   + L   + D LV ++ 
Sbjct: 31  EEAARRFTAVAEQQDKVLKALKKHGRGSKQAIEELAALAELFMPIKLVPKQYDALVTRVR 90

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL    G E+D  W +      + ++   +   
Sbjct: 91  DALDRLRTQERAIMQLCVRDARMPRADFLRLFPGNEIDMAWAADLAK-GKAKYAEALGNL 149

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              I + + ++  +  +  ++++E + I       +   +  +  M
Sbjct: 150 QADIQRCQQKLADLEAKCSLTLAEIKDINRRANSADIHHTGGRSSM 195


>gi|224992794|gb|ACN76112.1| SigB [Listeria innocua]
 gi|224992800|gb|ACN76115.1| SigB [Listeria innocua]
 gi|224992802|gb|ACN76116.1| SigB [Listeria innocua]
 gi|224992804|gb|ACN76117.1| SigB [Listeria innocua]
 gi|224992806|gb|ACN76118.1| SigB [Listeria innocua]
 gi|224992808|gb|ACN76119.1| SigB [Listeria innocua]
 gi|224992812|gb|ACN76121.1| SigB [Listeria innocua]
 gi|224992816|gb|ACN76123.1| SigB [Listeria innocua]
 gi|224992818|gb|ACN76124.1| SigB [Listeria innocua]
 gi|224992820|gb|ACN76125.1| SigB [Listeria innocua]
 gi|224992822|gb|ACN76126.1| SigB [Listeria innocua]
 gi|224992824|gb|ACN76127.1| SigB [Listeria innocua]
 gi|224992826|gb|ACN76128.1| SigB [Listeria innocua]
 gi|224992828|gb|ACN76129.1| SigB [Listeria innocua]
 gi|224992830|gb|ACN76130.1| SigB [Listeria innocua]
 gi|224992836|gb|ACN76133.1| SigB [Listeria innocua]
 gi|224992838|gb|ACN76134.1| SigB [Listeria innocua]
 gi|224992840|gb|ACN76135.1| SigB [Listeria innocua]
 gi|224992842|gb|ACN76136.1| SigB [Listeria innocua]
 gi|224992844|gb|ACN76137.1| SigB [Listeria innocua]
 gi|224992846|gb|ACN76138.1| SigB [Listeria innocua]
 gi|224992852|gb|ACN76141.1| SigB [Listeria innocua]
 gi|224992854|gb|ACN76142.1| SigB [Listeria innocua]
          Length = 214

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 90/210 (42%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 2   AAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 62  KSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 122 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +VL  L  RE+++L+  F    +   T E
Sbjct: 182 EKVLPVLDEREQKILQYTFIENRSQKETGE 211


>gi|225569957|ref|ZP_03778982.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
 gi|225161427|gb|EEG74046.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
          Length = 274

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 108/263 (41%), Gaps = 15/263 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-- 470
           ++    +  ++      ++ + RK        K+E+    L +V S+A +  N    F  
Sbjct: 2   VQEEKRKKNLADQTNEELLELYRKTGSL--EVKQEIALRYLYIVKSIAVQMRNVYAGFSQ 59

Query: 471 -LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             D++ EG I LMKA +K++     KF TY    ++  I      Q     IP  +R   
Sbjct: 60  VEDIVNEGVIMLMKAIDKYEADKNAKFETYVSKRIRGMIIDIARKQDW---IPRTVRKSY 116

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSH 587
             +   +    ++  REP  EE+++ L M +E  R ++        +SL+  + +    +
Sbjct: 117 RDIKEASAVFYSEHGREPEAEELSELLHMDIEKFRDIMGKASLFSVLSLDMVLEETKEQY 176

Query: 588 LGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
               I  DK    P    +    R      + SL   E+ V+ + +      +  ++E+ 
Sbjct: 177 RSIQIPSDKKEEQPEAHLMDKEFRHMLADGIRSLKENEQTVISLYY----MEELNMKEIA 232

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               V+  RI QI A AIRKL+ 
Sbjct: 233 GILHVSEPRISQIHAGAIRKLRE 255


>gi|153953966|ref|YP_001394731.1| sporulation sigma factor SigE [Clostridium kluyveri DSM 555]
 gi|219854580|ref|YP_002471702.1| hypothetical protein CKR_1237 [Clostridium kluyveri NBRC 12016]
 gi|146346847|gb|EDK33383.1| SigE2 [Clostridium kluyveri DSM 555]
 gi|219568304|dbj|BAH06288.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 235

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 96/248 (38%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +VS +          +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 35  LSKKEEEDLVSRL---VSGNEKVRATLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                V+       
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSK---------------VKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   D   +  FIED+      
Sbjct: 137 PLNVDWDGNEL-----------------------LLSDILGTDNDVVYSFIEDEVD---- 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     +  L+ RE+ ++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 170 --------KQLLVIAMKKLSDREKEIVNLRFGLNGKKEKTQKEVADLLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           + IR+L+ 
Sbjct: 222 RIIRRLRK 229


>gi|91981580|gb|ABE68132.1| RNA polymerase subunit D [Pseudomonas sp. Q13-87]
          Length = 220

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 58/126 (46%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|315646039|ref|ZP_07899160.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
 gi|315278800|gb|EFU42114.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
          Length = 240

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 99/263 (37%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
            EI  I     +     +     +++K     +  +  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 25  QEIYYIGGSEALPPPLTKEEEEFLLKKLPSGDAATRAMLIERNLRLVVYIARKFENTGIN 84

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+  G IGL+KA   FD     K +TYA   ++  I   +                 
Sbjct: 85  IEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------- 130

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                   T+  +S + P+  +   +  
Sbjct: 131 --------------------------------------NKTRSEVSFDEPLNIDWDGNEL 152

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  +N     +   Q + R+   + L  L+ RE  ++ +RFG+    + T ++V 
Sbjct: 153 LLSDVLGTENDTIYRNIEEQVD-RKLLQKALDKLSDRERMIMELRFGLQDGEEKTQKDVA 211

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 212 DLLGISQSYISRLEKRIIKRLRK 234


>gi|91981536|gb|ABE68110.1| RNA polymerase subunit D [Pseudomonas sp. Q65c-80]
 gi|91981542|gb|ABE68113.1| RNA polymerase subunit D [Pseudomonas sp. CM1'A2]
 gi|91981562|gb|ABE68123.1| RNA polymerase subunit D [Pseudomonas sp. P97.30]
 gi|91981564|gb|ABE68124.1| RNA polymerase subunit D [Pseudomonas sp. K94.31]
 gi|91981584|gb|ABE68134.1| RNA polymerase subunit D [Pseudomonas sp. TM1A3]
          Length = 220

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 58/127 (45%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|322432980|ref|YP_004210229.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidobacterium sp.
           MP5ACTX9]
 gi|321165207|gb|ADW70911.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidobacterium sp.
           MP5ACTX9]
          Length = 278

 Score = 96.1 bits (237), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 106/246 (43%), Gaps = 13/246 (5%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
           H +  +   E      + E++   L  V  +A +   R    ++  DL+  G IGL++A 
Sbjct: 5   HTIYKMIAEEEGGFEERNELILQELPQVHYIASRMMERLPQHVELGDLVHAGVIGLLEAY 64

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
             FD     +F T+A + +K AI  S+            +R K  ++     ++   + R
Sbjct: 65  RTFDNTKNAQFKTFAKFRIKGAILDSLRALDW---GSRGIRRKAREIAEATLKLEGALGR 121

Query: 546 EPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLD 602
            P+ EEI+ +L + +  + ++  ++    +  +      +     D IE    +  +P +
Sbjct: 122 SPSKEEISAELGLTIADLNEIQTQLNGLHLVGQEVTSSFEGETAHDLIESAPSSWDNPFE 181

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
              +A  +    R ++ L+ RE+ +L + +      + T++EV +   +   R+ QI + 
Sbjct: 182 MYAKAESKAHLIRAISELSEREQLILSLYYR----EELTMKEVAEVVGLAVSRVSQIHSA 237

Query: 663 AIRKLK 668
            + KLK
Sbjct: 238 VLAKLK 243


>gi|319644916|ref|ZP_07999149.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392725|gb|EFV73519.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 241

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 111/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   +  ++ + + +K+ +    +S S+ +  + ++ +       A+  ++E NLRLV 
Sbjct: 7   ALGYVIKELVFLVSYVKNNAFPQPLSSSDEKKYLELMAQ---GDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +N        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKKYIDILDGREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|160944585|ref|ZP_02091813.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444367|gb|EDP21371.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|295103334|emb|CBL00878.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 224

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 104/228 (45%), Gaps = 13/228 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
               ++  +  NL LV + A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA
Sbjct: 4   DKTRREAFITQNLGLVHACAGRFRGRGMEYDDLYSAGCVGLIKAYDNFDESRGVCFSTYA 63

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +   I +   D   T+++   +++   +V             EPT +++A++L  P+
Sbjct: 64  VPVILGEIKKLFRDGG-TVKVSRSLKELGMRVQAAREHTMKLCGAEPTLQQLAEQLDEPI 122

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E V   ++  +  +SL    G++    L   +E                R +   V+ +L
Sbjct: 123 ENVALAIQAAQPAMSLTPEGGEDGDRQLDIPVESPEEELAD--------RISLAEVIEAL 174

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++++++R+RF        T  E  K    T+ +I + E K + +L+
Sbjct: 175 PEQDKQLIRLRFYGN----RTQSETAKALHTTQVQISRRERKILIRLR 218


>gi|291196280|emb|CBG22611.1| DNA-directed RNA polymerase subunit D [Pseudomonas borbori]
          Length = 237

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 38/284 (13%), Positives = 86/284 (30%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T  +++     +      L E+  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDSILAEYTRVTTEGGRLVEV--LNGYIDPDDGSVPAEAAA 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
               +    S    ++++ ++   + E                                 
Sbjct: 59  PVPAKDDAASDAGDDKEEDEDDAEEEEEGDGGPD-------------------------- 92

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                         + +     IAE       L        K  + S +     + L +L
Sbjct: 93  ------------PEEALRRFTAIAEQ------LAIAKTTLDKHGRGSKQGIAELKALAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LV  +    +R+   E  +++L      + R  FL    G E+D  W
Sbjct: 135 FMPIKLVPKQYEALVVHVRSALERLRAQERAIMQLCVRDARMPRADFLRLFPGNEVDATW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
                   + ++   +      I + + ++ ++  E  ++++E 
Sbjct: 195 SEQLAK-GKAKYAEAIGGLQGDIQRCQQKLVALQAECDLTLAEI 237


>gi|28203259|gb|AAO35702.1| RNA polymerase sigma-E factor [Clostridium tetani E88]
          Length = 261

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 101/277 (36%), Gaps = 51/277 (18%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEAN 452
           + K F+   +  +      I  I     +     R     +V K        +  ++E N
Sbjct: 29  KLKVFLNKILSKLKIFARNIYYIGGSDVLPPPLTREEEENLVEKLNYGDESIRSILIERN 88

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   ++  I   +
Sbjct: 89  LRLVVYIARKFENTGIGIEDLVSVGTIGLIKAVNTFDPSKKIKLATYASRCIENEILMYL 148

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                                       NKIK E +  E                     
Sbjct: 149 RRN-------------------------NKIKSEISFYEP-------------------- 163

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
                  +  +    L   I   +     D   +   +E     +  L  RE++++ +RF
Sbjct: 164 -----LNVDWDGNELLLSDILGTDTDIVYDYIEEEVDKELLLIAMDKLNNREKQIVNLRF 218

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           G+G  T+ T +EV     +++  I ++E + I++LK 
Sbjct: 219 GLGGKTEKTQKEVADMLGISQSYISRLEKRIIKRLKK 255


>gi|323345486|ref|ZP_08085709.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
 gi|323093600|gb|EFZ36178.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
          Length = 238

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 59/265 (22%), Positives = 122/265 (46%), Gaps = 46/265 (17%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I  E+ ++  E   +   ++        A + + +ANL+ V+ +AK+Y ++G+   
Sbjct: 12  YLDEIGGESLLTSLEEMKLAEKIQ---NGDEAALERLTKANLKFVVFIAKQYQHQGVDME 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL+ EGNIGL+ AA+K+      +F+ +A  +++                    +     
Sbjct: 69  DLVSEGNIGLLYAAKKYTPSKEKRFAPFAAPFIR--------------------KQIEQL 108

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHLG 589
           ++R      +++    T E                   +K+ +S+E PI     ++ +L 
Sbjct: 109 LLRQGADSQSRLSASLTSE-------------------SKKVVSVEAPIPAGSRNSFNLL 149

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
             ++D NA+   +     + +    R++   L  R+++V+ + FGIG    HTL E+G  
Sbjct: 150 HVLKDTNALMADEHINDESFKAELERLMRRVLDQRQQQVISLFFGIGC-EKHTLMEIGDF 208

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRS 673
             + RER+RQI  KA++K++  +++
Sbjct: 209 MNLKRERVRQIRDKALQKIRKIAKT 233



 Score = 40.6 bits (93), Expect = 0.84,   Method: Composition-based stats.
 Identities = 32/174 (18%), Positives = 66/174 (37%), Gaps = 12/174 (6%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN--DGT 178
           +++YL E+G   LL+   E+ +A++I+ G    +  L ++ L F   I  + +    D  
Sbjct: 9   MKLYLDEIGGESLLTSLEEMKLAEKIQNGDEAALERLTKANLKFVVFIAKQYQHQGVDME 68

Query: 179 TLLRE----IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
            L+ E    ++       P  +  F         ++ E     +  D        + S +
Sbjct: 69  DLVSEGNIGLLYAAKKYTPSKEKRFAPFAAPFIRKQIEQLLLRQGADSQSRLSASLTSES 128

Query: 235 KVSKDDRSKVDSPPENAEN------DERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
           K      + + +   N+ N      D   L  DE  +  +  A  ++L  +V+ 
Sbjct: 129 KKVVSVEAPIPAGSRNSFNLLHVLKDTNALMADEHINDESFKAELERLMRRVLD 182


>gi|169334413|ref|ZP_02861606.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259130|gb|EDS73096.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
          Length = 250

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 54/247 (21%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            I  ++   +     + +E+   N  L+ S+ K+Y +  + + DL Q G IGL+KA ++F
Sbjct: 14  EIKELIVNAQNGDKNSLEELTVINTPLINSILKRYLSYSISYDDLFQIGAIGLIKAIKRF 73

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
            +    KFSTYA++ +     R   D+   I++  +++    K          K   EP+
Sbjct: 74  SFEFNTKFSTYAVYVINGEYKRYFRDEG-IIKVGRNLKTIYLKTKTIREDYVKKNGVEPS 132

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
            + +++K+ +  E V   L+  ++P SL   + + + +   L D I+D+N      S  +
Sbjct: 133 IDYLSEKIGVSSEDVLMALEACRQPESLSKELNNNENTPILLMDKIKDEND-----SNEK 187

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +      + +L  R+ +++ +R+        T +EV +   +++ ++ ++E K I  
Sbjct: 188 IVEKLDLKNAIMNLEKRDRQIIVLRYFKN----KTQKEVAEVLGLSQVQVSRLEKKIIEN 243

Query: 667 LKHPSRS 673
           +K    S
Sbjct: 244 MKKTFES 250


>gi|328554314|gb|AEB24806.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens TA208]
          Length = 241

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 59/275 (21%), Positives = 109/275 (39%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S +E +  + ++         A+  ++E NLRLV 
Sbjct: 7   ALGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLM---AEGDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ ++        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMEL-EKVKKYIDILDDREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|291196298|emb|CBG22620.1| DNA-directed RNA polymerase subunit D [Pseudomonas flavescens]
          Length = 236

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 44/284 (15%), Positives = 98/284 (34%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T  +++     +      L E+  L   I P+          
Sbjct: 1   RIEEGIREVMGAVAHFPGTVDSILAEYTRVTTEGGRLVEV--LSGYIDPDDGSVPAEAAA 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                  + + ++ E +D    + + E       ++                        
Sbjct: 59  PVPAAAGDAADKDDEEEDGDSDDEEEEGDGGPDPEE------------------------ 94

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +    +A+ DQL         EIA+   +            K  +SS +     + L +L
Sbjct: 95  ALRRFTAVSDQL---------EIAKKALK------------KHGRSSKQAIQELKALAEL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++ +   R+   E  +++L      + R  FL    G E+D  W
Sbjct: 134 FMPIKLVPKQYDALVVRVREALDRLRGQERAIMQLCVRDARMPRADFLRLFPGNEVDLDW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            +      + ++   +      I + + ++ ++  E+ ++++E 
Sbjct: 194 AASLAK-GKSKYAEAIGNLQADIQRCQQKLIALQTESDLTLAEI 236


>gi|313115504|ref|ZP_07800969.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310622214|gb|EFQ05704.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 223

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 103/229 (44%), Gaps = 14/229 (6%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
               +   +E NL LV + A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA
Sbjct: 4   DKTRRDAFIEQNLGLVHACAGRFRGRGIEYDDLYSAGCMGLVKACDNFDESRGVCFSTYA 63

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +   I +   D   T+++   +++   +V             EPT  ++A++L  P 
Sbjct: 64  VPVILGEIKKLFRDSG-TVKVSRSLKELGMRVQAAREHHMKVCGTEPTLSQLAEELNEPA 122

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +   ++  +  +SL     +E+     D I  ++    L   I      +   VL +L
Sbjct: 123 ENITLAIQAAQPAMSL--TPENEEEDRQMD-IPVESPEEALAERI------SLEEVLHAL 173

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ +++R+RF        T  E  K    T+ +I + E K + +L+ 
Sbjct: 174 PEQDRQLIRLRFYGN----KTQSETAKVLHTTQVQISRRERKILVQLRR 218


>gi|121488757|emb|CAJ18263.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 163

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/164 (33%), Positives = 97/164 (59%), Gaps = 1/164 (0%)

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ + 
Sbjct: 1   EGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKA 60

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
             ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D +++ 
Sbjct: 61  YSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQND 120

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
             + P     + +L     R L+ L PRE  V+R  FGIGM+  
Sbjct: 121 GHL-PDHGLNKDSLTLEVERSLSVLAPREADVIRSYFGIGMDNP 163


>gi|119485331|ref|ZP_01619659.1| sigma factor SigF [Lyngbya sp. PCC 8106]
 gi|119457087|gb|EAW38213.1| sigma factor SigF [Lyngbya sp. PCC 8106]
          Length = 259

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 58/247 (23%), Positives = 116/247 (46%), Gaps = 13/247 (5%)

Query: 429 HIVSMVRKGEC-EASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAE 486
             + ++R  +C  +   + ++V+ N+ LV      + N+    + DL+Q G IGL++A E
Sbjct: 12  ETLELLRDYQCSNSKELRNQLVQLNIGLVRKEVHHWVNQCTENYDDLLQVGCIGLIRAIE 71

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G+ FS++A+ +++  I   + D+S  +R+P H      + ++ A+ +  K+KR+
Sbjct: 72  RFDLSKGHAFSSFAIPYIRGEIQHYLRDKSLPLRVPRHWLTLQRQGMKLAQELQVKLKRQ 131

Query: 547 PTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLD 602
           PT  EIA+ L +        K+    +  +SL+ P+ DE+     LG+ + D    S   
Sbjct: 132 PTDTEIARGLNISETEWSQVKLAGYNRSLLSLDAPVQDENEGTTCLGELVPDNRYRSFQL 191

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           +           + L+ L     +VL   F      D T +E  ++  ++   + +   K
Sbjct: 192 AQEDQI---RLQQGLSKLEEGTRKVLEFVFL----YDLTQKETAERLGISAVTVSRRVKK 244

Query: 663 AIRKLKH 669
            +  L+ 
Sbjct: 245 GLNLLQR 251


>gi|315001920|emb|CBI75446.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 180

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 30/162 (18%), Positives = 72/162 (44%), Gaps = 3/162 (1%)

Query: 285 DEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +   E + +LR+  +   ++ QK+ ++    +    +L  +     L   + D LV  + 
Sbjct: 20  EVAREKFGDLRAQYEVTRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMR 79

Query: 344 DISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      +  +
Sbjct: 80  EMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMD 139

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
            + +L+   +++ I  ETG+SI++ + I   +  GE +A  A
Sbjct: 140 -EEVLRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRA 180


>gi|332272491|gb|AEE38929.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|332272493|gb|AEE38930.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|332272495|gb|AEE38931.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
 gi|332272497|gb|AEE38932.1| RNA polymerase sigma-70 factor [Aeromonas sobria]
          Length = 219

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 79/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P             +         E + 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNETE-----DVAPTATHIGSELSEDDL 53

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D  E E + E     + DD       PE A      L    + +  ++           
Sbjct: 54  ADEDEEEDEDEDEDGDNSDDEGDSGPDPEVAREKFGELRAQYEVTRLSI----------- 102

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   QK+ ++    +    +L  +     L   + D LV 
Sbjct: 103 ------------------------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+L  +   + +  F+      E D  W  Y K   +  W   +
Sbjct: 139 NMREMMERVRVQERIILKLCVEQAKMPKKTFVAAFTNNECDSAWFEYQKQAGKA-WSPRL 197

Query: 400 ACEVDSILKIRNEIKSISVETG 421
               + +L+   +++ I  ETG
Sbjct: 198 VEMAEDVLRAIGKLQQIEEETG 219


>gi|239934336|emb|CAR92298.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 245

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/286 (13%), Positives = 94/286 (32%), Gaps = 46/286 (16%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I++ + ++  +  E  ++I++ + I       +   +  +  M
Sbjct: 196 KEDIVRCQQKLIELEQECDLAIADIKDINRRANSADIHHTGGRSSM 241


>gi|261405673|ref|YP_003241914.1| sporulation sigma factor SigE [Paenibacillus sp. Y412MC10]
 gi|329922715|ref|ZP_08278267.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
 gi|261282136|gb|ACX64107.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. Y412MC10]
 gi|328942057|gb|EGG38340.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
          Length = 240

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 99/263 (37%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
            EI  I     +     +     +++K     +  +  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 25  QEIYYIGGSEALPPPLTKEEEEFLLKKLPTGDAATRAMLIERNLRLVVYIARKFENTGIN 84

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+  G IGL+KA   FD     K +TYA   ++  I   +                 
Sbjct: 85  IEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------- 130

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                   T+  +S + P+  +   +  
Sbjct: 131 --------------------------------------NKTRSEVSFDEPLNIDWDGNEL 152

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  +N     +   Q + R+   + L  L+ RE  ++ +RFG+    + T ++V 
Sbjct: 153 LLSDVLGTENDTIYRNIEEQVD-RKLLQKALDKLSDRERMIMELRFGLQDGEEKTQKDVA 211

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 212 DLLGISQSYISRLEKRIIKRLRK 234


>gi|91981578|gb|ABE68131.1| RNA polymerase subunit D [Pseudomonas sp. Q7-87]
          Length = 219

 Score = 95.7 bits (236), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 58/126 (46%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|163941644|ref|YP_001646528.1| sporulation sigma factor SigE [Bacillus weihenstephanensis KBAB4]
 gi|229013089|ref|ZP_04170254.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|163863841|gb|ABY44900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228748343|gb|EEL98203.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|322510149|gb|ADX05463.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 96/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +   + ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEAVLLNKLPNGDQAARSMLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|332976341|gb|EGK13197.1| DNA-directed RNA polymerase sigma subunit SigE [Desmospora sp.
           8437]
          Length = 240

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 98/250 (39%), Gaps = 57/250 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E  H++  +       +  +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 40  LTREEEEHLLIRL---PSGDAAVRAMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGL 96

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +               + +K+         
Sbjct: 97  IKAVNTFDPSKKIKLATYASRCIENEILMFLR--------------RNNKIR-------- 134

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
                                           +S + P+  +   +  L   +   +  +
Sbjct: 135 ------------------------------SEVSFDEPLNMDWDGNELLLSDVMGTDNDT 164

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              +  +   R+     L+ L+ RE +++ +RFG+    + T ++V     +++  I ++
Sbjct: 165 IYRNIEEQVDRKILRTALSRLSERERKIMELRFGLNGGEEKTQKDVADLLGISQSYISRL 224

Query: 660 EAKAIRKLKH 669
           E + I++L+ 
Sbjct: 225 EKRIIKRLRK 234


>gi|304404017|ref|ZP_07385679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304346995|gb|EFM12827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 240

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 91/232 (39%), Gaps = 56/232 (24%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            +  +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA
Sbjct: 56  DTAIRAMLIERNLRLVVYIARKFENTGIHIEDLVSIGAIGLIKAVNTFDPEKKIKLATYA 115

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +   S                                            
Sbjct: 116 SRCIENEILMYLRRNSK------------------------------------------- 132

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
                    T+  +S + P+  +   +   L D +  +N     +   Q + R+   + L
Sbjct: 133 ---------TRTEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVD-RKLLHKAL 182

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             LT RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 183 DKLTERERIIMELRFGLADGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 234


>gi|91981582|gb|ABE68133.1| RNA polymerase subunit D [Pseudomonas sp. Q128-87]
 gi|91981586|gb|ABE68135.1| RNA polymerase subunit D [Pseudomonas sp. C*1A1]
 gi|91981588|gb|ABE68136.1| RNA polymerase subunit D [Pseudomonas sp. TM1B2]
 gi|91981598|gb|ABE68141.1| RNA polymerase subunit D [Pseudomonas sp. P96.25]
          Length = 220

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 58/126 (46%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|308070731|ref|YP_003872336.1| DNA-directed RNA polymerase specialized sigma subunit
           [Paenibacillus polymyxa E681]
 gi|305860010|gb|ADM71798.1| DNA-directed RNA polymerase specialized sigma subunit
           [Paenibacillus polymyxa E681]
          Length = 257

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 110/240 (45%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               + + +     ++     +V   A K   NR   + DL Q G + L++  +++D  L
Sbjct: 19  WEYQQTKDNEIATVLIRKYEPMVKMAAGKISRNRPDLYEDLYQTGQMALIRLLQQYDISL 78

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F  YAM  +   +   + D+S  I++P  +++K   V      ++ K++R P  +EI
Sbjct: 79  GIPFEPYAMKSMLGHMKNYLRDKSWYIQVPRRIKEKGALVQHAIDELTVKLERSPNVDEI 138

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANL 609
           A  L + VE   +VL  +     +SL++P+  E++ + LG+ I      S  +       
Sbjct: 139 ATYLDLTVEETIEVLAGRECYHYVSLDSPLSQEESAATLGELIS-----SDANDYDTVEK 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    + L+ L  +E++VL + F  G     +   + +   V++  + +I+ +A  KLK 
Sbjct: 194 RMDLQQALSQLKEQEQKVLLLAFQDG----QSQRAIAQTLGVSQMSVSRIQKRATEKLKQ 249


>gi|291196310|emb|CBG22627.1| DNA-directed RNA polymerase subunit D [Pseudomonas guineae]
          Length = 237

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/284 (14%), Positives = 97/284 (34%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T  +++     +      L E+ +           G+    +
Sbjct: 1   RIEEGIREVMGAIAHFPGTVDSILAEYTRVTTDGGRLVEVFN-----------GYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +      +    +  D  +   D +S     +++       PE A      + E  + 
Sbjct: 50  GIAAPAEAAAPVPAKDGDADKDSDDDDSDDSDEEEEEGDGGPDPEEALRRFTAIGEALE- 108

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +A  +     +   + + AL E+AE++                                 
Sbjct: 109 AAKKVLKKHGRSSKQGIAALKEMAELF--------------------------------- 135

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LV ++    +R+   E  +++L      + R  FL+   G E+D  W
Sbjct: 136 -MPIKLIPKQYEALVVRVRSSLERLRAQERAIMQLCVRDARMPRADFLKLFPGNEIDAEW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            S      + ++   +      I + + ++ ++  E  ++++E 
Sbjct: 195 -SVGLAKGKAKYAEAIGNLQGDIQRCQQKLSALEAECELTLAEI 237


>gi|239934416|emb|CAR92338.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 220

 Score = 95.7 bits (236), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 87/266 (32%), Gaps = 47/266 (17%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++   D +      L ++  L   I P+               K   + +E + D+
Sbjct: 1   TVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDDE 58

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   GD E  A+   D                         +A    A+ DQ       
Sbjct: 59  EESESGDDEEEAESGPDPVV----------------------AAQRFGAVSDQ------- 89

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                         LQ  +   +K+ ++  +     + L  L   + L   + ++LVE++
Sbjct: 90  --------------LQVTSKVLKKNGRNHKESIEALQALADLFMPIKLVPKQFEVLVERV 135

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL      E D  W           W   +  
Sbjct: 136 RDALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGE 194

Query: 402 EVDSILKIRNEIKSISVETGISISEF 427
           +  +I+  + ++  +  ETG++++E 
Sbjct: 195 KNAAIVACQQKLIDLETETGLTVAEI 220


>gi|194365639|ref|YP_002028249.1| RNA polymerase sigma-28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
 gi|194348443|gb|ACF51566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
          Length = 247

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 99/249 (39%), Gaps = 17/249 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
             +       A  E++  +  LV  +A     R    ++  DLIQ G +GL++A+  +D 
Sbjct: 4   AAQYREVQRSAANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYDA 63

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ ++   I        +P  +  +      T RR+     R  +  
Sbjct: 64  DQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAATIRRLEQSSGRAASAT 120

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  + MP+    ++++       L      ED   L      +   +P     +    
Sbjct: 121 EVAAAMEMPLPEYLRLMEDAARGQVLSLESRIEDQGELDTVT--QGGPTPQQVLERGEFG 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+  
Sbjct: 179 RELGKAIGHLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVLRLR-- 232

Query: 671 SRSKKLRSF 679
               +L++F
Sbjct: 233 ---GRLKNF 238


>gi|121488532|emb|CAJ18256.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 57/166 (34%), Positives = 100/166 (60%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI EGN+GL+KAA++FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +++   + P     + +L     R L+ L P E  V+R  FGIGM+
Sbjct: 121 LQNDGHM-PDHGLNRDSLTLEVERSLSVLAPGEADVIRSXFGIGMD 165


>gi|88813218|ref|ZP_01128458.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
 gi|88789540|gb|EAR20667.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
          Length = 240

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 50/225 (22%), Positives = 96/225 (42%), Gaps = 14/225 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V  +  LV  +A     R    +   DLIQ G IGL++AA ++D   G  F TYA   +
Sbjct: 19  LVVRHAPLVKRIAHHLAGRLPASVLVDDLIQAGMIGLLEAARQYDATQGASFQTYAAIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I         P  +  K  +V      + ++  RE    E+ ++L + +    
Sbjct: 79  RGAMLDEIRRLDW---TPRSVHRKAREVASAVAEIEHRTGREAKDWEVVQQLGLDLNDYH 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           ++L+             D+    LG+  E   +  + ++   Q + +      +  L  R
Sbjct: 136 QILQDAATARIFS---IDDQDPELGEPHEIAGHEPTAMEILEQQDFQAALIAAIRELPER 192

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+ V+++ +    N +  L+E+G+   V+  R+ QI  +   KL+
Sbjct: 193 EQLVMQLYY----NEELNLKEIGQVLGVSESRVSQIHGRIALKLR 233


>gi|291562040|emb|CBL40856.1| RNA polymerase sigma factor, sigma-70 family [butyrate-producing
           bacterium SS3/4]
          Length = 265

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 111/253 (43%), Gaps = 14/253 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMK 483
            + + ++ +K +      KKE+    L +  + A K     +  +Q  D + EG + ++K
Sbjct: 9   EKELFALYKKTK--DPEIKKEITMQYLYIARTTATKLYDLYSTTMQMEDAVNEGVVAIIK 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
             + +D     KFSTY    V+ A+   +  Q    R           +      M  ++
Sbjct: 67  GIDMYDPDKNIKFSTYITTRVRGAMLDYVRKQEWMPRGFYKQLGI---IESACEDMKREL 123

Query: 544 KREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            R PT +E+AK L +  +  +++  +K  +   SL+  + +++TS+      +   V P 
Sbjct: 124 GRTPTVDELAKHLGIEKKRCQRIISMKNRRNIQSLDFLLENQNTSNGLQITNNDTQVQPE 183

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ +           +A L  +E++ L + +  G      +E+VG+   V++ R  QI  
Sbjct: 184 EACLWEEDMRVLAEGIAQLNEKEQKTLALHYMEG----LKMEQVGRVIGVSQPRASQIHT 239

Query: 662 KAIRKLKHPSRSK 674
            A+RKL+H   +K
Sbjct: 240 IALRKLRHFIETK 252


>gi|160943881|ref|ZP_02091111.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444557|gb|EDP21561.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104730|emb|CBL02274.1| RNA polymerase, sigma 29 subunit, SigE [Faecalibacterium
           prausnitzii SL3/3]
          Length = 234

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 99/261 (37%), Gaps = 59/261 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S+   ++  + + ++  +       + A++E++  NLRLV+ +AKKY N G+   DL+  
Sbjct: 30  SLPPPLTPEQEKALLDRM---AAGDAAAREELITHNLRLVVYLAKKYENSGVPAEDLVSI 86

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F      K +TYA   +   I   +   S   +                
Sbjct: 87  GTIGLIKAVNTFTPARSIKLATYASRCIGNEILMYLRKSSNRRQEA-------------- 132

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
                                                 S++ P+  +   +   L D + 
Sbjct: 133 --------------------------------------SIDEPLNVDGDGNELLLSDILG 154

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +A +      Q   R      +A+L+ RE +++ +RFG+    + T +E      +++
Sbjct: 155 -SDANAVSQQLEQDAERAVLRSAVAALSARERQIMELRFGLTDGVERTQKEAADALGISQ 213

Query: 654 ERIRQIEAKAIRKLKHPSRSK 674
             I ++E + IR LK    S+
Sbjct: 214 SYISRLEKRIIRTLKARLESE 234


>gi|332669182|ref|YP_004452190.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Cellulomonas
           fimi ATCC 484]
 gi|332338220|gb|AEE44803.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cellulomonas
           fimi ATCC 484]
          Length = 296

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 98/232 (42%), Gaps = 17/232 (7%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E+V  +L LV     +  +R        +L   G++ L+ AA+ +D   G  F+ YA  
Sbjct: 9   DELVLTHLPLVGYAVSEMLHRVPPTVSRDELASAGSLALVLAAQAYDPTTGVPFARYASL 68

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ A+   +             R ++ ++  T  R++  ++R+PT +E+A+ + + V  
Sbjct: 69  RIRGALVDELRSMDW---ASRGARQRVRELAATTERLTAVLRRKPTRDELAEAMGVDVRA 125

Query: 563 VRKVLKIT-KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           V    +   +  +S++          + D + D    +P +S +           + +L 
Sbjct: 126 VDDAARDAERRVLSMDAT-----EGTVADLVVDAE-PTPEESLLNDERHRWLRAAVETLP 179

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
            R   V+   F +    D ++ E+  +  VT+ RI Q+  +A+  L+    +
Sbjct: 180 DRLRTVVVGLFLL----DRSVAELAAELGVTQSRISQLRTEALGLLRDGMNA 227


>gi|268612026|ref|ZP_06145753.1| anti-sigma F factor [Ruminococcus flavefaciens FD-1]
          Length = 219

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 51/220 (23%), Positives = 98/220 (44%), Gaps = 15/220 (6%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           E NL LV   A ++ NRG+++ +L   G +GL+KA + FD   G +FSTYA+  +   I 
Sbjct: 11  EENLGLVHLCANRFRNRGIEYEELYSAGCVGLLKAVKAFDPDRGAQFSTYAVPVILGEIR 70

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           R   D    IR+   +++   ++ +       +  REPT  E+A         V + L +
Sbjct: 71  RLFRDGG-AIRVSRSLKELSMRIQKMCTDFRQREMREPTISELAVISGESEADVSEALCV 129

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           ++  +SL     DE    +     D+  V  L             ++++ L  R+  +L 
Sbjct: 130 SQPMLSLTAGDDDEGQIDIPTDAPDEAIVDVL----------ALRQIMSGLDSRDRALLE 179

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +R+        T  +  +   +T+ ++ + E K + +++ 
Sbjct: 180 LRYF----RCLTQTKTAQALGMTQVQVSRREKKLLAEMRK 215


>gi|254523268|ref|ZP_05135323.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
 gi|219720859|gb|EED39384.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
          Length = 247

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 95/238 (39%), Gaps = 12/238 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
             +       A  E++  +  LV  +A     R    ++  DLIQ G +GL++A+  +D 
Sbjct: 4   AAQYREVQRSAANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYDA 63

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TY    ++ ++   I        +P  +  +      T RR+     R  +  
Sbjct: 64  DQGASFETYTSIRIRGSMIDEIRRGDW---VPRSVHRRARDAAATIRRLEQSSGRAASAT 120

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  + MP+    ++++       L      ED   L D +  +   +P     +    
Sbjct: 121 EVAAAMEMPLPEYLRLMEDAARGQVLSLESRIEDQGEL-DTVA-QGGPTPQQVLERGEFG 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 179 RELGKAIGHLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVLRLR 232


>gi|206895926|ref|YP_002247112.1| RNA polymerase sigma-37 factor [Coprothermobacter proteolyticus DSM
           5265]
 gi|206738543|gb|ACI17621.1| RNA polymerase sigma-37 factor [Coprothermobacter proteolyticus DSM
           5265]
          Length = 243

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 98/240 (40%), Gaps = 14/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R  E      +  +      L  SV  ++    +   DL QE    L+ A ++F+   
Sbjct: 13  LERYAETRDPRIRDTLFLMYKPLADSVVNRFAPYQIDKDDLRQEAYRALVDAIDRFNPSY 72

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F T+A+  +   + R + D    I +P  M D  + + +    ++ K+  EPT +EI
Sbjct: 73  GNLFETFAIPTIVGNLKRYLRDYGWAISVPRSMVDMAYSIQKKLPEIAEKLGHEPTIKEI 132

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           A++L +  E V +VL     K   S+++ I DE  +   + +        L S       
Sbjct: 133 AEELELDEEQVSEVLAIMAVKNTSSIDSKITDESDTTGEELL-------GLLSDRDLEDE 185

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                 ++ L   E  ++  R         +  E+ K   +++ ++ + E KAI KLK  
Sbjct: 186 ALLEIAVSELPEPERFIIEKRL-----EGLSQSEIAKLLNISQAQVSRFERKAITKLKEA 240


>gi|54654469|gb|AAV37111.1| RpoD [Vibrio tasmaniensis]
          Length = 175

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 34/156 (21%), Positives = 61/156 (39%), Gaps = 2/156 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L     R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKATLATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDII 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             ET +++   + I   +  GE +A  AKKEMVEAN
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEAN 174


>gi|1588993|prf||2209422A fliA gene
          Length = 237

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 51/239 (21%), Positives = 104/239 (43%), Gaps = 13/239 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           +        + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D 
Sbjct: 1   MSDLYTAERMDKNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDA 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F+TYA+  +   +   +  +      P  +R    +V    +++  ++    T +
Sbjct: 61  LQGTAFTTYAVQRI-APMLDELRQRDW---APRRIRRNAREVASAMQKVEQRLGAPATEQ 116

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANL 609
           E+A+ L + +   R++L  T            E+    +   +E     +PL   ++ NL
Sbjct: 117 EVAQNLDIDLTEYRQILLDTNNSQLFSYDEWREEHGRTVEPMLEGHEDANPLQHLLEGNL 176

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+       +L  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 177 RQRVIEA-EALPEREKMVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 230


>gi|89100825|ref|ZP_01173677.1| SpoIIIC [Bacillus sp. NRRL B-14911]
 gi|89084471|gb|EAR63620.1| SpoIIIC [Bacillus sp. NRRL B-14911]
          Length = 240

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 61/277 (22%), Positives = 110/277 (39%), Gaps = 59/277 (21%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              +   V  I+ + + +K+ +    +S ++ R  + ++       + A+  ++E NLRL
Sbjct: 5   ATALGYLVKEIVFLVSYVKNNAFPQPLSAADERKYLRLM---AEGDAHARNMLIEHNLRL 61

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +   
Sbjct: 62  VAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEILMHLRA- 120

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
                                                              LK TK+ +S
Sbjct: 121 ---------------------------------------------------LKKTKKDVS 129

Query: 576 LETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           L  PIG +   +   L D ++ ++        +   L E     +  L  RE+ V+  RF
Sbjct: 130 LHDPIGQDKEGNEISLIDVLKSESEDVINTIQLNMEL-EKVKEYIDVLDDREKEVIIGRF 188

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           G+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 189 GLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|310643955|ref|YP_003948713.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248905|gb|ADO58472.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 257

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 110/240 (45%), Gaps = 13/240 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
               + + +     ++     +V   A K   NR   + DL Q G + L++  +++D  L
Sbjct: 19  WEYQQTKDNEIATVLIRKYEPMVKMAAGKISRNRPDLYEDLYQTGQMALIRLLQQYDISL 78

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F  YAM  +   +   + D+S  I++P  +++K   V      ++ K++R P   EI
Sbjct: 79  GIPFEPYAMKSMLGHMKNYLRDKSWYIQVPRRIKEKGALVQHAIDELTVKLERSPNVNEI 138

Query: 553 AKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANL 609
           A+ L + VE   +VL  +     +SL++P+  E++ + LG+ I      S  +       
Sbjct: 139 AEYLDLTVEETIEVLAGRECYHYVSLDSPLSQEESAATLGELIS-----SDANDFDTVEK 193

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    + L+ L  +E++VL + F  G     +   + +   V++  + +I+ +A  KLK 
Sbjct: 194 RMDLQQALSQLKEQEQKVLLLAFQDG----QSQRAIAQTLGVSQMSVSRIQKRATEKLKQ 249


>gi|167037236|ref|YP_001664814.1| sporulation sigma factor SigE [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|307266545|ref|ZP_07548078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307267688|ref|ZP_07549142.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|320115655|ref|YP_004185814.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326392136|ref|ZP_08213613.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166856070|gb|ABY94478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|306917290|gb|EFN47610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306918464|gb|EFN48705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|319928746|gb|ADV79431.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325991823|gb|EGD50338.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 241

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 100/255 (39%), Gaps = 59/255 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEEIYLISKMEK---GDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSK------------------------ 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       TK  +S + P+  +   +   L D +   N  
Sbjct: 134 ----------------------------TKLEVSFDEPLNVDWDGNELLLSDILGTDN-E 164

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +          +E  T  L  L  RE++++ +RFG+    + T +EV     +++  I +
Sbjct: 165 TVYKYIEDEVEKELLTSALKKLPDREKKIIGLRFGLEGGVEKTQKEVADMLGISQSYISR 224

Query: 659 IEAKAIRKLKHPSRS 673
           +E K +++LK     
Sbjct: 225 LEKKILKRLKKEMNR 239


>gi|91981558|gb|ABE68121.1| RNA polymerase subunit D [Pseudomonas sp. K94.37]
          Length = 220

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|91981596|gb|ABE68140.1| RNA polymerase subunit D [Pseudomonas sp. K93.3]
          Length = 219

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 58/126 (46%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|326384337|ref|ZP_08206018.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196935|gb|EGD54128.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 215

 Score = 95.3 bits (235), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 48/220 (21%), Positives = 91/220 (41%), Gaps = 12/220 (5%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
            A L L   +A++Y  RG  F DL Q   +GL+ A ++FD   G  F ++A+  V   + 
Sbjct: 1   MACLPLAKHIAQRYRERGEAFDDLEQVARLGLVHAVDRFDPTQGTDFLSFAIPTVMGEVK 60

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV--EGVRKVL 567
           R   D S +IR+P    +   ++     +   K  R P   E+AK L          +  
Sbjct: 61  RHFRDHSASIRMPRSAGELRSRIRLAEEQFEQKHGRSPDDTEVAKILGETPTAVSRARAA 120

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            I +  +SL+   G +D   L D +   +           +        +  L  R+ ++
Sbjct: 121 AIAQASVSLD-GSGSDDERALLDVLGSDD-----PGYAHVDRALALRPAVRRLPERDRKI 174

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L MRF        T  ++ ++  +++  + ++   ++ +L
Sbjct: 175 LGMRFF----EQRTQSDIARRMGISQMHVSRLLTASLGQL 210


>gi|291196334|emb|CBG22639.1| DNA-directed RNA polymerase subunit D [Pseudomonas marincola]
          Length = 236

 Score = 95.3 bits (235), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 42/284 (14%), Positives = 89/284 (31%), Gaps = 49/284 (17%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T ++++   + +      L E+  L   I P+          
Sbjct: 1   RIEEGIREVMGAIAHFPGTVESILAEYNRVTTEGGRLVEV--LNGYIDPDDGIAPAAEAP 58

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
                K   +  + + DD  ++E + E                                 
Sbjct: 59  APIPAKEGAADDDNDDDDADDSEDEEEGDGGPDP-------------------------- 92

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
                         + +     I E       L       +K  + S +     ++L  L
Sbjct: 93  -------------EEALRRFTAIGEQ------LDIAKQALKKHGRGSKQANAELKELATL 133

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + + LV +L     R+   E  ++++      + R  FL    G E+D  W
Sbjct: 134 FMPIKLVPKQYEALVVRLRGALDRLRGQERAIMQICVRDARMPRTDFLRLFPGNEIDETW 193

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            +          +     E D I + + ++ ++  E  ++++E 
Sbjct: 194 AAGLAKGKAKYAEAIGEREAD-IQRCQQKLIALQEECELTLAEI 236


>gi|167040624|ref|YP_001663609.1| sporulation sigma factor SigE [Thermoanaerobacter sp. X514]
 gi|300914665|ref|ZP_07131981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724101|ref|YP_003903852.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|166854864|gb|ABY93273.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889600|gb|EFK84746.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581162|gb|ADN54561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
          Length = 241

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 100/255 (39%), Gaps = 59/255 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEEMYLISKMEK---GDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSK------------------------ 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       TK  +S + P+  +   +   L D +   N  
Sbjct: 134 ----------------------------TKLEVSFDEPLNVDWDGNELLLSDILGTDN-E 164

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +          +E  T  L  L  RE++++ +RFG+    + T +EV     +++  I +
Sbjct: 165 TVYKYIEDEVEKELLTSALKKLPDREKKIIGLRFGLEGGVEKTQKEVADMLGISQSYISR 224

Query: 659 IEAKAIRKLKHPSRS 673
           +E K +++LK     
Sbjct: 225 LEKKILKRLKKEMNR 239


>gi|157693076|ref|YP_001487538.1| sporulation sigma factor SigK [Bacillus pumilus SAFR-032]
 gi|157681834|gb|ABV62978.1| DNA-directed RNA polymerase sigma subunit SigK carboxy-terminus
           [Bacillus pumilus SAFR-032]
          Length = 289

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 63/296 (21%), Positives = 118/296 (39%), Gaps = 60/296 (20%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           ++  +          +   V  ++ + + +K+ +    +S  + +  ++++ +       
Sbjct: 41  LNMVEVKIVAGVFTAMGLMVKELVFLVSYVKNNAFPQPLSGDDEKKYLALMAQ---GDEH 97

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   
Sbjct: 98  ARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATYAARC 157

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +                                                   
Sbjct: 158 IENEILMHLRA------------------------------------------------- 168

Query: 564 RKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              LK TK+ +SL  PIG +   +   L D ++ +N        +   L E     +  L
Sbjct: 169 ---LKKTKKDVSLHDPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKEYIDIL 224

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP-SRSKK 675
             RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H  SR++K
Sbjct: 225 DGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFHEFSRAEK 280


>gi|295102468|emb|CBL00013.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 224

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 103/228 (45%), Gaps = 13/228 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
               +   +E NL LV S A ++  RG+++ DL   G +GL+KA + FD   G  FSTYA
Sbjct: 4   DKTRRSAFIEQNLGLVHSCAGRFRGRGIEYDDLYSAGCMGLVKAYDGFDESRGVCFSTYA 63

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +   I +   D   T+++   +++   ++       S     EPT  ++A++L   V
Sbjct: 64  VPVILGEIKKLFRDGG-TVKVSRSLKELSLRINAAREHHSKLCGAEPTLSQLAEELGESV 122

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           E +   ++  +  +SL TP   E+     D I  ++    L   I          VL SL
Sbjct: 123 ENITLAIQAAQPAVSL-TPENREEGDRQMD-IPVESPEEELADKI------GLAEVLKSL 174

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  ++++RF  G     T  +  K    T+ +I + E K ++ ++
Sbjct: 175 PEEDRLIIQLRFYGG----KTQSDTAKLLHTTQVQISRRERKILKVMR 218


>gi|78044674|ref|YP_359860.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996789|gb|ABB15688.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 254

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 106/230 (46%), Gaps = 12/230 (5%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++E  L LV  V+   +      L   D+   G IGL++A E +D   G KF +YA 
Sbjct: 24  RNELLEYYLPLVRKVSAAMSLKLPTHLSREDIEGYGIIGLIEAVETYDQNRGVKFESYAS 83

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +  Q     +P  + DKI KV  +   + N +  E   E++A++L + V 
Sbjct: 84  LKIRAAIIDELRKQ---NFLPRSVWDKIKKVTTSEEMLLNALGEEVPVEKVAEQLGVSVS 140

Query: 562 GV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V   K L   K  +SL+  I  E +      + D    SP +  ++    E     L  
Sbjct: 141 DVLKIKTLIALKNHLSLDEIIDPEGSVDRFAGLADDEKYSPENKFLKRVEIEELREALKR 200

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L+ RE  +L++ +      + +L+E+     ++  R+ QI +KA+ KL+ 
Sbjct: 201 LSDRERLILQLFYV----EELSLKEIAAVLDISTSRVSQIASKALGKLRK 246


>gi|154686834|ref|YP_001421995.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens FZB42]
 gi|154352685|gb|ABS74764.1| SpoIIIC [Bacillus amyloliquefaciens FZB42]
          Length = 240

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 59/275 (21%), Positives = 109/275 (39%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S +E +  + ++         A+  ++E NLRLV 
Sbjct: 7   ALGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLM---AEGDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ ++        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMEL-EKVKKYIDILDDREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|190574220|ref|YP_001972065.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
 gi|190012142|emb|CAQ45765.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
          Length = 247

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 96/238 (40%), Gaps = 12/238 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
             +       A  E++  +  LV  +A     R    ++  DLIQ G +GL++A+  +D 
Sbjct: 4   AAQYREVQRSAANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYDA 63

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ ++   I        +P  +  +      T RR+     R  +  
Sbjct: 64  DQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAATIRRLEQSSGRAASAT 120

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  + MP+    ++++       L      ED   L D +  +   +P     +    
Sbjct: 121 EVAAAMEMPLPEYLRLMEDAARGQVLSLESRIEDQGEL-DTVA-QGGPTPQQVLERGEFG 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 179 RELGKAIGHLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVLRLR 232


>gi|121488787|emb|CAJ18278.1| sigma 70-type sigma factor [Prosthecochloris aestuarii]
          Length = 165

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 57/166 (34%), Positives = 98/166 (59%), Gaps = 1/166 (0%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DL  EGN+GL+KAA++FD   G+KF +YA+WW++Q+  +++A+QS  +R+P++    ++K
Sbjct: 1   DLXXEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSXLQALAEQSRIVRLPLNRVGTLNK 60

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 61  ISKAYSQLEQEYERDPNTKELANVLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 120

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           ++  +   P  S  + +L     R L+ L PRE  V+R  FGIGM 
Sbjct: 121 LQ-HDGQKPDYSLTKDSLTLEVERSLSVLAPREADVIRSYFGIGME 165


>gi|312110136|ref|YP_003988452.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
 gi|311215237|gb|ADP73841.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
          Length = 236

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 108/270 (40%), Gaps = 59/270 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  ++ + + IK+ +    +S  E    + ++ K       A+  ++E NLRLV  + KK
Sbjct: 12  IKELMFLVSYIKNNAFPQPLSAKEEEKYLQLMAK---GDEQARNILIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +          
Sbjct: 69  FENTGEDVEDLISIGTIGLIKAIESYSSNKGTKLATYAARCIENEILMHLRS-------- 120

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T++ +SL  PIG 
Sbjct: 121 --------------------------------------------LKKTRKDVSLHEPIGQ 136

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D ++ +      +  +   L E   + +  L  RE+ V+  RFG+ M  +
Sbjct: 137 DKEGNEISLIDVLKSEGNDIIDEIQLNMEL-EQVKKYIDVLDEREKEVIINRFGLDMQQE 195

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|91981560|gb|ABE68122.1| RNA polymerase subunit D [Pseudomonas sp. K93.2]
          Length = 220

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|224992798|gb|ACN76114.1| SigB [Listeria innocua]
          Length = 214

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 89/210 (42%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  ++D   G
Sbjct: 2   AAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFG 61

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  +A+  +   I R + D+  ++ +P  +++   K+      ++ +++  P   +IA
Sbjct: 62  KSFEAFAVPTIVGEIKRFLRDKKWSVHVPRRIKELGPKIKNAVEELTRELQSSPQISDIA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
             + +  E V + +++ K   +L      E  S               D   + N R   
Sbjct: 122 DFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLDVVGGTDDGFERVNQRMLL 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLE 643
            +VL  L  RE+++L+  F    +   T E
Sbjct: 182 EKVLPVLDEREQKILQYTFIENRSQKETGE 211


>gi|239934354|emb|CAR92307.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
 gi|239934360|emb|CAR92310.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 244

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 40/286 (13%), Positives = 94/286 (32%), Gaps = 46/286 (16%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I++ + ++  +  E  ++I++ + I       +   +  +  M
Sbjct: 196 KEDIVRCQQKLIELEQECDLAIADIKDINRRANSADIHHTGGRSSM 241


>gi|224002653|ref|XP_002290998.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220972774|gb|EED91105.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 345

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 127/264 (48%), Gaps = 22/264 (8%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAE 486
           +  + +   E   AK ++V +NLR+V  V   Y   GL       DL+Q+G + L++AAE
Sbjct: 72  MEALEQVLEEGIEAKNQLVASNLRMVQRVVNLYIRNGLGSEYNAGDLMQDGTMALIRAAE 131

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           K++   G++FSTYAM+W++ A+ RS   QS  + +P  + +   +V +T  R+  ++ R+
Sbjct: 132 KYEPERGFRFSTYAMYWIRSAVKRSQTMQSRIVNVPQRIHETYKRVTKTEARLRKELGRD 191

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDE--------DTSHLGDFIEDKNA 597
           PT  E++    + V  + +  +  ++   SL+  + +             + D +  K  
Sbjct: 192 PTKVELSAACDITVVQLDRCRRAMQQAAFSLDAEVQNTYKPNNSNSRKDTMYDLVASKVD 251

Query: 598 VSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNT--------DHTLEEVGKQ 648
            +  +   +  ++E     L   L+P E  +L +R+G+              T+ EV K 
Sbjct: 252 ETEYEKTQRLLMKEHLISTLRRYLSPHEVDLLLLRYGLMDERALPKGMSGPLTIAEVSKL 311

Query: 649 FCVTRERIRQIEAKAIRKLKHPSR 672
             +  +++R+I   + ++L+H  +
Sbjct: 312 VGLKPDKVRRIIINSQKQLRHLMK 335


>gi|188585936|ref|YP_001917481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350623|gb|ACB84893.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 239

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 94/248 (37%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + ++  ++         +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LTNEEEKDLLEKLK---AGDKKVRSTLIERNLRLVVYIARKFENTGVNIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                            N
Sbjct: 96  IKAVNTFDPQKKIKLATYASKCIENEILMYLRRN-------------------------N 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K+K E + +E                            I  +    L   +   +     
Sbjct: 131 KLKNEVSIDEP-------------------------LNIDWDGNELLLSDVLGTDIDIIH 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +  Q   +      L  L+ RE+ ++++RFG+G     T +EV     +++  I ++E 
Sbjct: 166 QNIEQKVNKNLLKMALEKLSQREKTIMKLRFGLGRQEGKTQKEVADILGISQSYISRLEK 225

Query: 662 KAIRKLKH 669
           + I +++ 
Sbjct: 226 RIINRMRK 233


>gi|308174363|ref|YP_003921068.1| RNA polymerase sporulation-specific sigma-K factor [Bacillus
           amyloliquefaciens DSM 7]
 gi|307607227|emb|CBI43598.1| RNA polymerase sporulation-specific sigma-K factor precursor
           (Sigma-27) (C-terminal fragment) [Bacillus
           amyloliquefaciens DSM 7]
          Length = 240

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 109/275 (39%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++         A+  ++E NLRLV 
Sbjct: 7   ALGFIVKELVFLVSYVKNNAFPQPLSNSEEKKYLDLM---AEGDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ ++        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMEL-EKVKKYIDILDDREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|169831144|ref|YP_001717126.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169637988|gb|ACA59494.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 256

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 99/262 (37%), Gaps = 59/262 (22%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I + S    +S  E +  V  +         A+  + E NLRLV  + KKY + G 
Sbjct: 41  LLSHITNNSFPQPLSREEEKEYVRRM---LAGDEHARNILTERNLRLVAHIIKKYDSTGE 97

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLI  G IGL+KA   F+   G + +TYA   ++  I   +                
Sbjct: 98  DTDDLISIGTIGLIKAINTFNPHKGARLATYAARCIENEILMHLRT-------------- 143

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DT 585
              V +T                                      +SL+ PIG +   + 
Sbjct: 144 ---VKKTRFE-----------------------------------VSLQDPIGVDKEGNE 165

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D +     V           R    + +  L+ RE++VL +RFG+  +T  T +E+
Sbjct: 166 ITLIDILGTNPEVVEDKVETHFEQRRLLEK-MHKLSRREKKVLALRFGLVDDTRQTQQEI 224

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
            +   ++R  + +IE +A+ KL
Sbjct: 225 AQDLGISRSYVSRIEKRALNKL 246


>gi|160942608|ref|ZP_02089853.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446087|gb|EDP23090.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
          Length = 234

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 53/243 (21%), Positives = 87/243 (35%), Gaps = 52/243 (21%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R   +         + A+++++  NLRLV  + KKY        DL+  G IGLMKA + 
Sbjct: 39  REEAAAFSALHAGDAAAREKLIRHNLRLVAHIVKKYYALPGDQEDLVSIGTIGLMKAVDT 98

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     +FSTYA   ++  I                         R   R   K  +  
Sbjct: 99  FDATRKARFSTYASRCIENEI-------------------------RMQFRRERKSGQTV 133

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           + +E                       SLE     +    L D I+D       DS  + 
Sbjct: 134 SLQE-----------------------SLEAD--GDSALTLADVIQD--GFCMEDSCERQ 166

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  ++L +L  RE ++L +R+G+      T  E      ++R  + ++E  A+  L
Sbjct: 167 EDVRRLRQLLDTLPARERQILLLRYGLAGQPPLTQLETAGLLGISRSYVSRLETHALELL 226

Query: 668 KHP 670
           +  
Sbjct: 227 RQA 229


>gi|294501329|ref|YP_003565029.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|295706676|ref|YP_003599751.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
 gi|294351266|gb|ADE71595.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|294804335|gb|ADF41401.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
          Length = 242

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 110/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +      ++ + + +K+ +    +S +E +  +S++ +       A+  ++E NLRLV 
Sbjct: 7   ALGYFFKELVFLVSYVKNNAFPQPLSAAEEKRYLSLMEQ---GDQEARNLLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKAIESYSQGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ ++        +   L E     +  L  RE+ V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLKSESDDVIDMIQLNMEL-EKIKEYIDILDDREKEVIVGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 DLQDEKTQREIAKELNISRSYVSRIEKRALMKMFH 225


>gi|228992639|ref|ZP_04152565.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
 gi|228998685|ref|ZP_04158272.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|229006188|ref|ZP_04163874.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228755029|gb|EEM04388.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228761153|gb|EEM10112.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|228766971|gb|EEM15608.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
          Length = 239

 Score = 94.9 bits (234), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 97/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +   D     + R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDIITKDLEANVD-RHLLKKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|182418945|ref|ZP_02950202.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237668989|ref|ZP_04528973.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377228|gb|EDT74796.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237657337|gb|EEP54893.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 235

 Score = 94.9 bits (234), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 96/248 (38%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++  +          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKDEEEELLKKL---NNGDEKIRSTLIERNLRLVVYIARKFENTGVYVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                V+       
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSK---------------VKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   +   + + IED+      
Sbjct: 137 PLNIDWDGNEL-----------------------LLSDILGTENDTVYNLIEDEVD---- 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     L SL  RE+ ++R+RFG+    + T +EV     +++  I ++E 
Sbjct: 170 --------KQLLFMALKSLNDREKEIVRLRFGLNGAREKTQKEVADMLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           K I++LK 
Sbjct: 222 KIIKRLKK 229


>gi|87306557|ref|ZP_01088704.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87290736|gb|EAQ82623.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 556

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 107/244 (43%), Gaps = 60/244 (24%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           + +    A   K ++V++NLRLV+S+AK++     +F +L+ +GN+ L++A EKFD+  G
Sbjct: 366 IERLYEAAVEVKNQIVQSNLRLVVSIAKRHLGAADEFFELVSDGNMSLIRAVEKFDYSRG 425

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTY  W +       + + + TI +    RD+                         
Sbjct: 426 NKFSTYCSWAI-------MKNFARTIPVEFKHRDRFR----------------------- 455

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                                SL+                D  +      A+Q       
Sbjct: 456 --------------------TSLDELFQGR---------VDNRSDQYEQEAMQQQRERQI 486

Query: 614 TRVLASLTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            R+L  L  RE++++  R+G+   +   TL+EVG +  VT+ERIRQIEA+A+ KL+  ++
Sbjct: 487 QRILNRLDEREQKIIIRRYGLDHDHEPQTLKEVGAELGVTKERIRQIEARALNKLRVAAQ 546

Query: 673 SKKL 676
             KL
Sbjct: 547 EAKL 550


>gi|270210814|gb|ACZ63224.1| RNA polymerase sigma 70 factor [Aeromonas rivuli]
          Length = 219

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 80/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P             +         E + 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSEDDL 53

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D  E E + E     S DD +     PE A      L    + +  ++           
Sbjct: 54  ADEDEDEDEDEDEDGDSSDDEADTGPDPEVAREKFGELRAQYEVTRLSI----------- 102

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   Q + ++    +    +L  +     L   + D LV 
Sbjct: 103 ------------------------QNNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+L  +   + +  F+      E D  W  Y K   +      V
Sbjct: 139 NMREMMERVRIQERIILKLCVEQAKMPKKTFVAAFTNNECDTAWFEYQKQAGKAWSPRLV 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + +L+   +++ I VETG
Sbjct: 199 EMD-EDVLRAIGKLQQIEVETG 219


>gi|323701301|ref|ZP_08112976.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533903|gb|EGB23767.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 243

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 104/251 (41%), Gaps = 57/251 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   ++  + +G+ + SI K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 41  LTSDEENDLIGRLGEGDIDGSI-KSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                             
Sbjct: 100 IKAVNTFDPNKKIKLATYASRCIENEILMYLRRN-------------------------- 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       T+  +S + P+  +   +   L D +  +N +
Sbjct: 134 --------------------------NKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDI 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +   + + ++   + L  L+ RE R++ +RFG+   T+ T +EV     +++  I +
Sbjct: 168 IYKNIEEEVD-KKLLHQALLKLSGRERRIMELRFGLNNGTEKTQKEVADMLGISQSYISR 226

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 227 LEKRIIKRLKK 237


>gi|332653851|ref|ZP_08419595.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332516937|gb|EGJ46542.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 231

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 86/255 (33%), Gaps = 53/255 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +   E R  +            A+  +VE NLRLV  + KKY  +     DLI  
Sbjct: 25  SFPRPLKAEEERKYLER---CAQGDLEARNILVEHNLRLVAHIVKKYYAQTGDQDDLISI 81

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K    F      + +TYA   ++  I                         R  
Sbjct: 82  GTIGLIKGISTFKADKNVRLATYASRCIENEILMHF---------------------RAQ 120

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
           +++  ++    T E                       +SL   I  +D       +ED +
Sbjct: 121 KKLQGEVSLSDTMENGGD----------------GNSLSLMDVIAVDDN-----MLEDLD 159

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                        R     V   L PRE  ++ +R+G+      T  EV  +  ++R  +
Sbjct: 160 TRDAC--------RRVRQCVGECLNPRERAIITLRYGLDDQPPRTQREVAARCGISRSYV 211

Query: 657 RQIEAKAIRKLKHPS 671
            +IE +A+ KL+   
Sbjct: 212 SRIEKRALAKLEQAM 226


>gi|119511138|ref|ZP_01630256.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119464233|gb|EAW45152.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 261

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 107/240 (44%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +    +  +   + ++V+ +  LV  +A K++++    + DL Q G  GL++A E+FD  
Sbjct: 16  LHSYHQNPSIKLRNQLVQLHTGLVRKIAHKFSHQCHEPYEDLEQIGYFGLIRAIERFDPS 75

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY FS++A+ +++  +   + D+S  ++IP   ++  +   +  + ++  + R P   E
Sbjct: 76  QGYAFSSFAVPYIRGEMLHFLRDRSSLLKIPRRWQELYNDGQKVRKELAVSLGRSPRDAE 135

Query: 552 IAKKLAMPVEGVRKVLKITK--EPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           IA+KL + V   ++     +   P+SL+       +    LG+ +    +++      Q 
Sbjct: 136 IAQKLQVSVHEWQETKLAAQNRMPLSLDATAAHYVDCQITLGEALPCPRSIA---LQQQD 192

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R+     +  L  +    + M F      + + ++  K    +   + +   K I+ L
Sbjct: 193 EERQQLQGAINMLEDKPRMAVEMVFL----KELSRKDAAKNIGTSPMTVTRYLQKGIQDL 248


>gi|238927435|ref|ZP_04659195.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
 gi|238884717|gb|EEQ48355.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
          Length = 252

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 115/249 (46%), Gaps = 21/249 (8%)

Query: 426 EFRHIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGL 481
           E  +I ++ ++ E E ++A +  + E  L LV  VA +      + +   DL+  G  GL
Sbjct: 9   EEENIEALWQEYEREKTVAVRNRIAEYYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGL 68

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + A E+++   G KF TYA   V+ A+   +  +     +PV +R  I K  +T  ++  
Sbjct: 69  LDAIERYELARGNKFETYAGVRVRGAMLDHLRAKDW---VPVSVRQNIKKYEKTVAQLEG 125

Query: 542 KIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
           ++ R  T +E+A++L + +E +   +        I LE  +  +  + L D         
Sbjct: 126 ELGRAATDKELAEELNLSIEELHHLESQVSAATVIPLEEYLRADTQASLED--------G 177

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P++ A    ++ET    +  L  +E  V+     +    + TL+E+     ++  RI Q+
Sbjct: 178 PVEHAEWTEVKETLAAAIEKLPEKERTVI----ALYYYDEMTLKEIAAILHLSEARISQL 233

Query: 660 EAKAIRKLK 668
             KAI +++
Sbjct: 234 HTKAIFRMR 242


>gi|134298554|ref|YP_001112050.1| sporulation sigma factor SigE [Desulfotomaculum reducens MI-1]
 gi|134051254|gb|ABO49225.1| RNA polymerase, sigma 29 subunit, SigE [Desulfotomaculum reducens
           MI-1]
          Length = 241

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 99/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +SI E   ++  +          K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 41  LSIDEEIDLIERL---GDGDLKVKNVLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                             
Sbjct: 98  IKAVNTFDPHKKIKLATYASRCIENEILMHLRRN-------------------------- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       T+  +S + P+  +   +   L D +  +N +
Sbjct: 132 --------------------------NKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDI 165

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +   + + ++   + L  L+ RE R++ +RFG+   ++ T +EV     +++  I +
Sbjct: 166 IYKNIEEEVD-KKLLHQALLKLSGRERRIMELRFGLNNGSEKTQKEVADMLGISQSYISR 224

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 225 LEKRIIKRLKK 235


>gi|254479124|ref|ZP_05092475.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214034938|gb|EEB75661.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 234

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 104/270 (38%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            V   V  IL +     + S  + +S  E R  +   R+       A+  ++E NLRLV 
Sbjct: 11  LVGTIVKEILNLGYLTNTNSFPSPLSPEEERKYLEAYRR---GDEEARNILIERNLRLVA 67

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA + +D+  G   +TYA   ++  I  S      
Sbjct: 68  HVVKKYSGTGRDLDDLISIGTIGLIKAIDTYDFEKGTHLATYAAKCIENEILMS------ 121

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                          +R  ++M  ++        +   + +  EG               
Sbjct: 122 ---------------IRAEKKMKGEVF-------LQDPIGVDKEG--------------- 144

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                 +   L D +             +  +++  +++ + L  RE  ++ MR+G+   
Sbjct: 145 ------NEISLMDVLGTDEDEVSEQVEKKIQIKKLYSKLNSVLKNRERMIIEMRYGLYNG 198

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T  E+ K   ++R  + +IE KA+ KL
Sbjct: 199 RVRTQREIAKMLGISRSYVSRIEKKALNKL 228


>gi|251797867|ref|YP_003012598.1| sporulation sigma factor SigE [Paenibacillus sp. JDR-2]
 gi|247545493|gb|ACT02512.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. JDR-2]
          Length = 240

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 52/263 (19%), Positives = 99/263 (37%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
            EI  I     +     R     ++ K     +  +  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 25  EEIYYIGGSEALPPPLTREEEEYLLDKLPSGDTAIRAMLIERNLRLVVYIARKFENTGIH 84

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+  G IGL+KA   FD     K +TYA   ++  I   +   S             
Sbjct: 85  IEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSK------------ 132

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                   T+  +S + P+  +   +  
Sbjct: 133 ----------------------------------------TRTEVSFDEPLNIDWDGNEL 152

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  +N     +   Q + R+   + L  L+ RE  ++ +RFG+    + T ++V 
Sbjct: 153 LLSDVLGTENDTIYRNIEEQVD-RKLLHKALDKLSERERIIMELRFGLADGEEKTQKDVA 211

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 212 DLLGISQSYISRLEKRIIKRLRK 234


>gi|148833411|gb|ABR14575.1| DNA-dependent RNA polymerase sigma factor D subunit [Alcanivorax
           dieselolei]
          Length = 242

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 40/280 (14%), Positives = 94/280 (33%), Gaps = 42/280 (15%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M +L   P   + ++   D +      L ++I     + P+  G             
Sbjct: 2   REVMHALAFWPGAVEMVLDEYDRILSEERKLTDVI--AGYLDPDDDGAAATNANKEPRFN 59

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
           ++  ++  E+D  ++ + D +S +    ++      P   AE                  
Sbjct: 60  QKKQAEAAEKDKDKDDDDDDKSDSDDDSEEDEGGLDPVLAAER----------------- 102

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLS 329
                               + EL+ L + A    K + +         E L        
Sbjct: 103 --------------------FGELKKLHEKAERALKRNGRDHASSAKALEALAGHFTLFK 142

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV-SYA 387
           L     D L++        +   E +++ LA +  G+ R  F+++  G E +  WV ++A
Sbjct: 143 LVPRIYDQLLQGARTHLDIVRKFERQIMALAIRRAGVPRKDFVQQFPGNETNLEWVAAHA 202

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           K     ++   +    + I + + +I ++    G+ +++ 
Sbjct: 203 KTKRAKDYSERLLAVAEDIQRNQRKIITVEEVIGLPVADI 242


>gi|91981540|gb|ABE68112.1| RNA polymerase subunit D [Pseudomonas sp. Q37-87]
          Length = 220

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 26/127 (20%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +S+ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRSNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 155 MPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|239934398|emb|CAR92329.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 245

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 25/155 (16%), Positives = 59/155 (38%), Gaps = 2/155 (1%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             LQ  +   +K+ ++        + L  L   + L   + ++LVE++ D   R+   E 
Sbjct: 88  DQLQVTSKVPKKNGRNHKGSIEALQALANLFMPIKLVPKQFEVLVERVRDALSRLRQQER 147

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
            +++L      + R  FL      E +              W   +  +  +I+  + ++
Sbjct: 148 AIMQLCVRDARMPRADFLRMFPSNETNQTXSGDLAKRNTK-WAAALGEKNAAIVACQQKL 206

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             +  ETG++++E + I       +   +  +  M
Sbjct: 207 IDLETETGLTVAEIKEINRRANSADIHHTGGRSSM 241


>gi|91981538|gb|ABE68111.1| RNA polymerase subunit D [Pseudomonas sp. F113]
          Length = 220

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 155 MPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|258514353|ref|YP_003190575.1| sporulation sigma factor SigE [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778058|gb|ACV61952.1| RNA polymerase, sigma 28 subunit, SigE [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 241

 Score = 94.5 bits (233), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 94/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ + E      +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 49  LINRLETGDGAVRGVLIERNLRLVVYIARKFENTGISIEDLVSIGTIGLIKAVNTFDPAK 108

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +                                        
Sbjct: 109 KIKLATYASRCIENEILMYLRRN------------------------------------- 131

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                            T+  +S + P+  +   +   L D +  +N V       + + 
Sbjct: 132 ---------------NKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDVIYKYIEEEVD- 175

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     L  L+ RE R++ +RFG+   ++ T +EV     +++  I ++E + I++LK 
Sbjct: 176 RKLLHLALQKLSGRERRIMELRFGLNNGSEKTQKEVADMLGISQSYISRLEKRIIKRLKR 235


>gi|291196270|emb|CBG22606.1| DNA-directed RNA polymerase subunit D [Pseudomonas argentinensis]
          Length = 237

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 39/284 (13%), Positives = 93/284 (32%), Gaps = 48/284 (16%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M ++   P T  +++     +      L E++            G+    +
Sbjct: 1   RIEEGIREVMGAVAHFPGTVDSILAEYTRVTTEGGRLVEVL-----------SGYIDPDD 49

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G    +          D  ++ + + E      +++       PE A      + +  + 
Sbjct: 50  GSVPAEAAAPVPASSDDKAEDKDDEEEDGDSDDEEEEGDGGPDPEEALRRFTAVADQLEA 109

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +   L                                   +K  + S +      +L +L
Sbjct: 110 AKKAL-----------------------------------KKHGRDSKQAIEELRQLAEL 134

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
              + L   + D LV ++ D   R+   E  +++L      + R  FL    G E+D  W
Sbjct: 135 FMPIKLVPKQYDALVVRVRDALDRLRGQERAIMQLCVRDARMPRADFLRLFPGNEVDLGW 194

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            +      + ++   +      I + + ++ ++  E+ ++++E 
Sbjct: 195 AASLAK-GKAKYAEAIGNLEADIQRCQQKLIALQEESDLTLAEI 237


>gi|93007303|gb|ABE97152.1| Sigma-70 [Pasteuria ramosa]
          Length = 241

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 49/228 (21%), Positives = 90/228 (39%), Gaps = 56/228 (24%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   +
Sbjct: 61  RACLIERNLRLVVYIARKFENTGIHIEDLVSTGTIGLIKAVNTFDPEKKIKLATYASRCI 120

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +               + +K+                                
Sbjct: 121 ENEILMFLR--------------RNNKIR------------------------------- 135

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                    IS + P+  +   +   L D +  +N  +          +E     L+ L+
Sbjct: 136 -------SEISFDEPLNIDWDGNELLLSDVLGTEND-TIYRDIEDEVDKEILRTALSMLS 187

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE R++ +RFG+G   + T ++V     +++  I ++E K I +L+ 
Sbjct: 188 DRERRIVILRFGLGGGEEKTQKDVADLLGISQSYISRLEKKVIGRLRK 235


>gi|150016004|ref|YP_001308258.1| sporulation sigma factor SigE [Clostridium beijerinckii NCIMB 8052]
 gi|149902469|gb|ABR33302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 235

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 97/248 (39%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +V+ +          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKDEEEDLVNKL---NGGDENIRSTLIERNLRLVVYIARKFENTGVYVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                ++       
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSK---------------IKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   +   + + IED+      
Sbjct: 137 PLNIDWDGNEL-----------------------LLSDILGTENDTVYNLIEDEVD---- 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     L SL  RE+ ++R+RFG+    + T +EV     +++  I ++E 
Sbjct: 170 --------KQLLVMALKSLNDREKEIVRLRFGLNGTREKTQKEVADMLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           K I++LK 
Sbjct: 222 KIIKRLKK 229


>gi|229137791|ref|ZP_04266393.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST26]
 gi|228645648|gb|EEL01880.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST26]
          Length = 196

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 40/197 (20%), Positives = 88/197 (44%), Gaps = 8/197 (4%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+    
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAI 61

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIED 594
             ++++++R P   EIA  L +  E V +++         SL+  + +         IE 
Sbjct: 62  EELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIE- 120

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +         +   R     +   L   E+ V+   FG  +N     ++ G++  +++ 
Sbjct: 121 -SVGEVEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGENLNQ----KDTGERLGISQM 175

Query: 655 RIRQIEAKAIRKLKHPS 671
            + +I+ +AI KLK  +
Sbjct: 176 HVSRIKRQAISKLKQAA 192


>gi|15894966|ref|NP_348315.1| sporulation sigma factor SigK [Clostridium acetobutylicum ATCC 824]
 gi|15024653|gb|AAK79655.1|AE007679_1 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|528974|gb|AAB94775.1| SigK [Clostridium acetobutylicum]
 gi|325509103|gb|ADZ20739.1| sporulation sigma factor SigK [Clostridium acetobutylicum EA 2018]
          Length = 234

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 104/251 (41%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S SE ++ +  ++       +AK  ++E NLRLV  + KKY+  G +  DLI  
Sbjct: 26  SFPQPLSESEEKYYLKKLK---EGDPLAKNILIERNLRLVAHIVKKYSYSGKEVDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA + ++   G + +TYA   ++  I   I                 +K  +  
Sbjct: 83  GTIGLIKAIDSYNVSKGTRLATYAARCIENEILMLIR---------------NNKKSKNE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                      SL   +  +D S + + +E++ 
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------SLIDILSSDDDS-VIEIVENRI 164

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
            +  L   I              L  RE+ +++MR+G+G        E+ +   ++R  +
Sbjct: 165 QIGKLYVEIN-----------RVLKGREKAIIKMRYGLGDGKPRNQREIAQILGISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE +A++KL
Sbjct: 214 SRIEKRALKKL 224


>gi|161486847|ref|NP_781765.2| sporulation sigma factor SigE [Clostridium tetani E88]
          Length = 235

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 101/277 (36%), Gaps = 51/277 (18%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEAN 452
           + K F+   +  +      I  I     +     R     +V K        +  ++E N
Sbjct: 3   KLKVFLNKILSKLKIFARNIYYIGGSDVLPPPLTREEEENLVEKLNYGDESIRSILIERN 62

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   ++  I   +
Sbjct: 63  LRLVVYIARKFENTGIGIEDLVSVGTIGLIKAVNTFDPSKKIKLATYASRCIENEILMYL 122

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                                       NKIK E +  E                     
Sbjct: 123 RRN-------------------------NKIKSEISFYEP-------------------- 137

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
                  +  +    L   I   +     D   +   +E     +  L  RE++++ +RF
Sbjct: 138 -----LNVDWDGNELLLSDILGTDTDIVYDYIEEEVDKELLLIAMDKLNNREKQIVNLRF 192

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           G+G  T+ T +EV     +++  I ++E + I++LK 
Sbjct: 193 GLGGKTEKTQKEVADMLGISQSYISRLEKRIIKRLKK 229


>gi|332272385|gb|AEE38876.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|332272387|gb|AEE38877.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|332272389|gb|AEE38878.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|332272391|gb|AEE38879.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
 gi|332272393|gb|AEE38880.1| RNA polymerase sigma-70 factor [Aeromonas molluscorum]
          Length = 219

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 80/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P             +         E + 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSEDDL 53

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D  E E + +     S DD +     PE A      L    + +  ++           
Sbjct: 54  ADEDEEEDEEDDDDGDSSDDEADTGPDPEVAREKFGELRAQYEVTRLSI----------- 102

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   Q + ++    +    +L  +     L   + D LV 
Sbjct: 103 ------------------------QNNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+L  +   + +  F+      E D  W  Y K   +      V
Sbjct: 139 NMREMMERVRIQERIILKLCVEQAKMPKKTFVAAFTNNECDTAWFEYQKQAGKAWSPRLV 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + +L+   +++ I VETG
Sbjct: 199 EMD-EDVLRAIGKLQQIEVETG 219


>gi|158337871|ref|YP_001519047.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308112|gb|ABW29729.1| RNA polymerase sigma factor, group 3 [Acaryochloris marina
           MBIC11017]
          Length = 265

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 107/245 (43%), Gaps = 16/245 (6%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDW 490
            +V   +  +   +  +V  N+ LV  VA +  ++    + DL Q G +GL+ A E+FD 
Sbjct: 14  MLVAYRQKPSVQLRNRLVRLNMGLVRKVAHRLAHQCAEPYEDLEQCGFLGLITAIERFDP 73

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             GY FS++A+ +++  I   + D++ T+RIP   +       +  + ++ ++ R P+ +
Sbjct: 74  TQGYAFSSFAVPYIRGEILHFLRDRANTVRIPRRWQQLSRDGAKVRQALTMELGRHPSDQ 133

Query: 551 EIAKKLAMPVEGVR--KVLKITKEPISLETPI------GDEDTSHLGDFIEDKNAVSPLD 602
           EIA +L + ++  R  K+    + P+SL   +        +    LGD + D        
Sbjct: 134 EIADELDLSMQEWRAVKLAASNRVPLSLNARVSSGHHQQSDSMMTLGDTLMD---ARCQI 190

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
                  R    + L  L  R   ++   F        + +EV ++  V+   + +   K
Sbjct: 191 MQTNQEDRLELQQALDQLEDRTREMIESVFVH----QLSRQEVAQRIGVSPVTVTRRIKK 246

Query: 663 AIRKL 667
            I +L
Sbjct: 247 GIDEL 251


>gi|16332163|ref|NP_442891.1| RNA polymerase sigma factor SigF [Synechocystis sp. PCC 6803]
 gi|1653792|dbj|BAA18703.1| RNA polymerase sigma-37 [Synechocystis sp. PCC 6803]
          Length = 258

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 104/235 (44%), Gaps = 12/235 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +  ++E NL LV   A  +T +    F DL Q G +GL++A E+FD   G  FS++A+ +
Sbjct: 29  RNRIMEVNLGLVRKEAHHWTAQCNESFEDLSQVGCLGLIRAIERFDVSKGNAFSSFAIPY 88

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  I   + D+S  +RIP    D   + +   +    K  R  T EEIA+ LA+P+   
Sbjct: 89  VRGEIQHFLRDKSNCVRIPRRWLDLGRQAIAVQQEFRLKYDRAATDEEIAQILAVPLADW 148

Query: 564 RKVLKI--TKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++       +E +SL+T +  +D    +LGD +      S   S           + LA 
Sbjct: 149 QETKLALQNRELVSLDTKVNGDDEGQVNLGDCLAHHEFRSFQLSQEDQI---RLQQALAG 205

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           L  R  R++   F          +E  +   V+   + +   + I  LK    ++
Sbjct: 206 LEERTRRIVEFVFLHDFTH----KEAAEMMGVSVITVSRRIKQGIGALKKALNTE 256


>gi|311029937|ref|ZP_07708027.1| sporulation sigma factor SigE [Bacillus sp. m3-13]
          Length = 239

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  H++    K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LSKEEEAHLL---IKLPNGDQAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   +                         
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNN------------------------- 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                VR         +S + P+  +   +   L D +  +  +
Sbjct: 131 --------------------KVR-------SEVSFDEPLNIDWDGNELLLSDVLGTEEDI 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              D     + R+   + L  L  RE++++ +RFG+    + T ++V     +++  I +
Sbjct: 164 ITKDLEANVD-RKLLLKALEQLNDREKQIMELRFGLIGGEEKTQKDVADMLGISQSYISR 222

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 223 LEKRIIKRLRK 233


>gi|281420137|ref|ZP_06251136.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
 gi|281405937|gb|EFB36617.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
          Length = 205

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 58/235 (24%), Positives = 106/235 (45%), Gaps = 38/235 (16%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            ++V  NL  V SVA +Y  +G++F DL+ EG + ++ AA KF    G  F  YA  +V 
Sbjct: 7   NKIVSENLNYVKSVANQYKGKGVEFDDLVSEGTLAMLMAARKFQADRGTDFVAYAGPFVH 66

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           +AI+++I              DK   + R                       +P +  + 
Sbjct: 67  KAISQAI--------------DKQSGLYR-----------------------LPKDQKKF 89

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +   + +S++ P+   +   L D + D +     D+     +++     +A L PRE+
Sbjct: 90  APRNADKAVSVDAPLSANNPYTLLDILNDPDVKIADDTLNIEMMKKKMAESIADLLPREK 149

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            ++   +GIG+  + T+ E+ +   + RER+RQI    IR+L    R + LR++ 
Sbjct: 150 EIITKFYGIGVPKE-TMAEIAEDMGLKRERVRQIRNLTIRRLNRSIRHQALRNYF 203


>gi|147678181|ref|YP_001212396.1| sporulation sigma factor SigE [Pelotomaculum thermopropionicum SI]
 gi|146274278|dbj|BAF60027.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 92/240 (38%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ + E      +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 51  LISRLESGDGAVRSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPAK 110

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +                                        
Sbjct: 111 KIKLATYASRCIENEILMYL---------------------------------------- 130

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                       +     +  +S + P+  +   +   L D +  +N +           
Sbjct: 131 ------------RRSVKNRAEVSFDEPLNIDWDGNELLLSDVLGTENDI-IYKFIEDEIE 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++     L  L+ RE R++ +RFG+   T+ T +EV     +++  I ++E + I++LK 
Sbjct: 178 KKLLHLALQKLSGRERRIMELRFGLNNGTEKTQKEVADLLGISQSYISRLEKRIIKRLKK 237


>gi|229061510|ref|ZP_04198854.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
 gi|229134714|ref|ZP_04263523.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|229168645|ref|ZP_04296367.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228614801|gb|EEK71904.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228648760|gb|EEL04786.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|228717744|gb|EEL69394.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
          Length = 232

 Score = 94.5 bits (233), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 96/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +   + ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 17  DEIYYIGGSEALPPPLTKEEEAVLLNKLPNGDQAARSMLIERNLRLVVYIARKFENTGIN 76

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 77  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 123 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 144

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 145 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 203

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 204 DMLGISQSYISRLEKRIIKRLRK 226


>gi|270160509|gb|ACZ63220.1| RNA polymerase sigma 70 factor [Aeromonas rivuli]
          Length = 219

 Score = 94.1 bits (232), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 80/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P             +         E + 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSEDDL 53

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D  E E + E     S DD +     PE A      L    + +  ++           
Sbjct: 54  ADEDEDEDEDEDEDGDSSDDEADTGPDPEVAREKFGELRAQYEVTRLSI----------- 102

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   Q + ++    +    +L  +     L   + D LV 
Sbjct: 103 ------------------------QNNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+L  +   + +  F+      E D  W  Y K   +      +
Sbjct: 139 NMREMMERVRIQERIILKLCVEQAKMPKKTFVAAFTNNECDTAWFEYQKQAGKAWSPRLL 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + D +L+   +++ I VETG
Sbjct: 199 EMDED-VLRAIGKLQQIEVETG 219


>gi|163784595|ref|ZP_02179438.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880134|gb|EDP73795.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 154

 Score = 94.1 bits (232), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 53/144 (36%), Positives = 84/144 (58%), Gaps = 3/144 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K I+    IS  E +++   ++        A  ++V+ANLR VI+VAK Y   G+ F 
Sbjct: 13  YLKQIADIPLISPEEEKNLAKKIK---EGDKQALDKLVKANLRFVINVAKNYIGYGVPFQ 69

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  GNIGL++AA++FD   G +F +YA+WW+KQ+I ++I  Q   IRIP    +   +
Sbjct: 70  ELISAGNIGLIEAAKRFDPDRGVRFISYAIWWIKQSIFQTIQQQKDLIRIPHRTSNMAVR 129

Query: 532 VVRTARRMSNKIKREPTPEEIAKK 555
           + +    +  K+ REPT +EI  K
Sbjct: 130 IDKVYLELKEKLGREPTYKEIKSK 153



 Score = 44.4 bits (103), Expect = 0.071,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
           V  YL+++  I L+S E E  +AK+I+ G    +  L ++ L F
Sbjct: 10  VTYYLKQIADIPLISPEEEKNLAKKIKEGDKQALDKLVKANLRF 53


>gi|304438454|ref|ZP_07398394.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368537|gb|EFM22222.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 256

 Score = 94.1 bits (232), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 100/229 (43%), Gaps = 20/229 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  + E  L LV  VA +      + +   DL+  G  GL+ A E+++   G KF TYA 
Sbjct: 33  RNRIAEYYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLLDAIERYELTRGNKFETYAG 92

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V+ AI   +  +     IPV +R  I +  +    +   + R  T +E+A+++ + +E
Sbjct: 93  VRVRGAILDHLRAKDW---IPVSVRQNIKRYEKAVAHLEGTLGRTATDQELAEEMDLSIE 149

Query: 562 GVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            +   +        I LE  +  +  + L D         P++ A    ++ET    +  
Sbjct: 150 ELHRLESQVSAATVIPLEEYLRTDAQASLED--------GPVEHAEWTEIKETLAAAIEK 201

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  +E  V+     +    + TL+E+     ++  RI Q+  KAI +++
Sbjct: 202 LPEKERTVV----ALYYYDEMTLKEIAAVLHLSEARISQLHTKAIFRMR 246


>gi|298345983|ref|YP_003718670.1| putative DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           curtisii ATCC 43063]
 gi|304390259|ref|ZP_07372213.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315657524|ref|ZP_07910406.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|298236044|gb|ADI67176.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           curtisii ATCC 43063]
 gi|304326741|gb|EFL93985.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315491996|gb|EFU81605.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 433

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 100/238 (42%), Gaps = 14/238 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             + + E++E NL LV     +   R   F    DL   G++ L++AA  +D   G  F 
Sbjct: 6   GEVNRNELIENNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAANSYDSATGVPFH 65

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA++ ++ A+   +             R +  ++      ++    R PT EE+A  L 
Sbjct: 66  RYAIYRIRGAMLDELRSMDW---ATRGARQRTKQLEEMTSTLTAAAGRAPTKEELASALG 122

Query: 558 MPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + VE V        +  +S++ P+G ED   L   + D++  SP D+ +           
Sbjct: 123 VDVESVESAQQDAARRVVSMDAPVGSEDERSLE--LPDES-PSPEDTLLDDERLVYLHAS 179

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + +L  R   V+   F      +  +++V  +  VT+ R+ Q+ ++A+  ++      
Sbjct: 180 VRALPQRLRYVVEQVFF----EERPIQDVADELGVTQSRVSQLRSEALTLMREGMNRH 233


>gi|332272311|gb|AEE38839.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|332272313|gb|AEE38840.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|332272315|gb|AEE38841.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|332272317|gb|AEE38842.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|332272319|gb|AEE38843.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
 gi|332272321|gb|AEE38844.1| RNA polymerase sigma-70 factor [Aeromonas encheleia]
          Length = 219

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 79/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P             +         E + 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSEDDL 53

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D  E E + E     + DD       PE A      L    + +  ++           
Sbjct: 54  ADEDEDEDEDEDEDGDNSDDEGDGGPDPEVAREKFGELRAQYEVTRLSI----------- 102

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   QK+ ++    +    +L  +     L   + D LV 
Sbjct: 103 ------------------------QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 139 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLV 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + +L+   +++ I  ETG
Sbjct: 199 EMD-EDVLRAIGKLQQIEEETG 219


>gi|239934352|emb|CAR92306.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 246

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 40/286 (13%), Positives = 92/286 (32%), Gaps = 46/286 (16%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE+  
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERAR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRANFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I++ + ++  +  E  + I++ + I       +   +  +  M
Sbjct: 196 KEDIVRCQQKLIELEQECDLVIADIKDINRRANSADIHHTGGRSSM 241


>gi|253576138|ref|ZP_04853470.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844481|gb|EES72497.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 240

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 52/263 (19%), Positives = 98/263 (37%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
            EI  I     +     R     ++++     S  +  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 25  EEIYYIGGSEALPPPLTREEEEYLLQRLPSGDSAIRAMLIERNLRLVVYIARKFENTGIN 84

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+  G IGL+KA   FD     K +TYA   ++  I   +   S             
Sbjct: 85  IEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKIRTE-------- 136

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                       +S + P+  +   +  
Sbjct: 137 --------------------------------------------VSFDEPLNIDWDGNEL 152

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  +N     +   Q + R+   + L  LT RE  ++ +RFG+    + T ++V 
Sbjct: 153 LLSDVLGTENDTIYRNIEEQVD-RKLLHKALDKLTERERMIMELRFGLVDGDEKTQKDVA 211

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 212 DLLGISQSYISRLEKRIIKRLRK 234


>gi|20807708|ref|NP_622879.1| sporulation sigma factor SigK [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516259|gb|AAM24483.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 231

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 104/270 (38%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            V   V  IL +     + S  + +S  E R  +   R+       A+  ++E NLRLV 
Sbjct: 8   LVGTIVKEILNLGYLTNTNSFPSPLSPEEERKYLEAYRR---GDEEARNILIERNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA + +D+  G   +TYA   ++  I  S      
Sbjct: 65  HVVKKYSGTGRDLDDLISIGTIGLIKAIDTYDFEKGTHLATYAAKCIENEILMS------ 118

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                          +R  ++M  ++        +   + +  EG               
Sbjct: 119 ---------------IRAEKKMKGEVF-------LQDPIGVDKEG--------------- 141

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                 +   L D +             +  +++  +++ + L  RE  ++ MR+G+   
Sbjct: 142 ------NEISLMDVLGTDEDEVSEQVEKKIQIKKLYSKLNSVLKNRERMIIEMRYGLYNG 195

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T  E+ K   ++R  + +IE KA+ KL
Sbjct: 196 RVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|322384113|ref|ZP_08057831.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151193|gb|EFX44502.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 233

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 52/263 (19%), Positives = 97/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
            EI  I     +     R     ++ K     +  +  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 18  QEIYYIGGSEALPPPLTREEEEYLLGKLPSGDAAIRAMLIERNLRLVVYIARKFENTGIN 77

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+  G IGL+KA   FD     K +TYA   ++  I   +   S             
Sbjct: 78  IEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKIRTE-------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                       +S + P+  +   +  
Sbjct: 130 --------------------------------------------VSFDEPLNIDWDGNEL 145

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  +N     +   Q + R+   + L  LT RE  ++ +RFG+    + T ++V 
Sbjct: 146 LLSDVLGTENDTIYRNIEEQVD-RKLLHKALDKLTERERVIMELRFGLQDGEEKTQKDVA 204

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 205 DLLGISQSYISRLEKRIIKRLRK 227


>gi|206900763|ref|YP_002250593.1| SigF [Dictyoglomus thermophilum H-6-12]
 gi|206739866|gb|ACI18924.1| SigF [Dictyoglomus thermophilum H-6-12]
          Length = 235

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 104/239 (43%), Gaps = 16/239 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            ++  E       +E++E    L+   A K+T+ G    DL+Q G +G +KA E +D   
Sbjct: 9   WLKYRETGDKKVLEELLEVFDDLIYYWASKFTSYGEPLEDLVQIGYLGFLKAVENYDPEK 68

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G   STY   +V   I   + D+   I+IP  ++  I+K+    + +  K  R P+ EEI
Sbjct: 69  G-DLSTYISHYVLGEIRHHLRDKIDKIKIPRSVKGLINKMDNFIKEVWEKENRSPSCEEI 127

Query: 553 AKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           AK L + VE V ++ KI      +SLE    + D            A       +    +
Sbjct: 128 AKHLNITVESVEELFKIKEAMMTVSLEDLEIEMDRIR---------AEKLESFKLPIEDK 178

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + LA L   + +V+   F      D T  EV K   +++ ++ +I   A+ KLK 
Sbjct: 179 IALEQALAKLPDIQRKVIEYIF----YQDLTQTEVAKILKISQSQVSRILRSALEKLKE 233


>gi|91981548|gb|ABE68116.1| RNA polymerase subunit D [Pseudomonas sp. P12]
          Length = 220

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 155 MPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|315654569|ref|ZP_07907475.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           ATCC 51333]
 gi|315491033|gb|EFU80652.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           ATCC 51333]
          Length = 433

 Score = 94.1 bits (232), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 100/238 (42%), Gaps = 14/238 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFS 497
             + + E++E NL LV     +   R   F    DL   G++ L++AA  +D   G  F 
Sbjct: 6   GEVNRNELIENNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAANSYDSATGVPFH 65

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA++ ++ A+   +             R +  ++      ++    R PT EE+A  L 
Sbjct: 66  RYAIYRIRGAMLDELRSMDW---ATRGARQRTKQLEEMTSTLTAAAGRAPTKEELASALG 122

Query: 558 MPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
           + VE V        +  +S++ P+G ED   L   + D++  SP D+ +           
Sbjct: 123 VDVESVESAQQDAARRVVSMDAPVGSEDERSLE--LPDES-PSPEDTLLDDERLVYLRAS 179

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + +L  R   V+   F      +  +++V  +  VT+ R+ Q+ ++A+  ++      
Sbjct: 180 VRALPQRLRYVVEQVFF----EERPIQDVADELGVTQSRVSQLRSEALTLMREGMNRH 233


>gi|295097196|emb|CBK86286.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 259

 Score = 94.1 bits (232), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 53/245 (21%), Positives = 108/245 (44%), Gaps = 13/245 (5%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E    K  +      +V   A +   R    ++  DLIQ G++G + A + FD   G
Sbjct: 22  YTAEGLENKTALWSKYHFIVRQEALRLHKRLPANVELDDLIQAGSMGFLSAIDSFDPKKG 81

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
              + +    VK A+   + +     R       +I  +++   ++  +   E T  +IA
Sbjct: 82  VALNAWISQRVKWALMDELRESDWVPRRVRSHSREIVSLIQ---QIEQEKGGEATEADIA 138

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           +++ + ++  +++L               E+ S   +  + +NA ++PL+ AIQ NL   
Sbjct: 139 ERMGVSLKEFQQMLADNNSSQMYSIDELQENYSDSWESNDGENAQLNPLNEAIQENLIAN 198

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               +  +  RE+++L+  +      D  ++E+G    VT  R+ Q+ + AI++L+  SR
Sbjct: 199 IAEHIRMIPRREQQILQFYYQ----QDLNMKEIGLILGVTETRVSQLHSLAIKRLR--SR 252

Query: 673 SKKLR 677
             +LR
Sbjct: 253 MDRLR 257


>gi|167641125|ref|ZP_02399380.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
 gi|167510905|gb|EDR86296.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
          Length = 239

 Score = 94.1 bits (232), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|91981552|gb|ABE68118.1| RNA polymerase subunit D [Pseudomonas protegens]
 gi|91981554|gb|ABE68119.1| RNA polymerase subunit D [Pseudomonas protegens]
 gi|91981576|gb|ABE68130.1| RNA polymerase subunit D [Pseudomonas sp. S8-62]
          Length = 220

 Score = 93.7 bits (231), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + + +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRENKQAIAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++ VETG+ I
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|91981566|gb|ABE68125.1| RNA polymerase subunit D [Pseudomonas sp. P97.38]
 gi|91981590|gb|ABE68137.1| RNA polymerase subunit D [Pseudomonas sp. P97.6]
          Length = 220

 Score = 93.7 bits (231), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 57/127 (44%), Gaps = 2/127 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKAAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALETETGLSI 213

Query: 425 SEFRHIV 431
           +E + I 
Sbjct: 214 AEIKDIN 220


>gi|225019367|ref|ZP_03708559.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
 gi|224947998|gb|EEG29207.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
          Length = 221

 Score = 93.7 bits (231), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 60/225 (26%), Positives = 105/225 (46%), Gaps = 14/225 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +   V+ NL LV S A ++T +G+++ DL   G +GL+KA + FD   G KFSTYA+  +
Sbjct: 8   RDSFVKQNLGLVHSCAHRFTGKGIEYDDLFSAGCMGLVKATDAFDEDRGVKFSTYAVPVI 67

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D    +++   +++   +  +   R   K  REPT  E+A  L +  E   
Sbjct: 68  LGEIRRLFRDGGS-VKVSRSLKELSMRATKERERFMLKTGREPTVSELADLLEVTPEQAI 126

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           + L+++  P+SL T   DE+     D   D       DS        +   V+ SL   +
Sbjct: 127 EALEVSVPPMSLTT--DDEEGGGQLDIRVDSPDEQLTDSI-------SIKEVVNSLDEPD 177

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +++ +R+        T  E  K+  +T+ ++ + E K +  L+ 
Sbjct: 178 RKLILLRYFQY----KTQMETAKELGMTQVQVSRREKKILGFLRE 218


>gi|281371841|gb|ADA63665.1| RNA polymerase [Pseudomonas fluorescens]
          Length = 223

 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 32/192 (16%), Positives = 74/192 (38%), Gaps = 5/192 (2%)

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +  +      ++    ++ DE++++S    +  E    P    AL     V  +L   + 
Sbjct: 36  EEVEPVELKSDSAAKAKDEDEEDEESESDDTEEEGDGGPDPEEALRRFTAVSDQLEKARK 95

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                 K  + S +     + L +L   + L   + D LVE++     R+   E  +++L
Sbjct: 96  ALK---KHGRDSKQATEELQALAELFMPIKLVPKQFDALVERVRGALDRVRGQERAIMQL 152

Query: 360 AQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
                 + R  FL    G E+D  W        + ++   +   +D I + + ++  +  
Sbjct: 153 CVRDARMPRADFLRLFPGNEVDLTWAEDIAK-GKAKYAEAIGKLLDDIKRNQQKLVDLEK 211

Query: 419 ETGISISEFRHI 430
           E  + ++E + +
Sbjct: 212 EVDLKVAEIKDV 223


>gi|91981572|gb|ABE68128.1| RNA polymerase subunit D [Pseudomonas protegens]
          Length = 220

 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 28/126 (22%), Positives = 57/126 (45%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + + +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRENKQAIAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++ VETG+ I
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKI 213

Query: 425 SEFRHI 430
           +E R I
Sbjct: 214 AEIRDI 219


>gi|297616583|ref|YP_003701742.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144420|gb|ADI01177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 235

 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 58/275 (21%), Positives = 109/275 (39%), Gaps = 56/275 (20%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            W   +      +L + + + ++     +S  E R  +   R        AK  ++E NL
Sbjct: 5   GWALAIFSLTKGMLMLFSYLNNLVFPHPLSEEEERIYLEKTR---EGDEEAKHILIEHNL 61

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV  V KK+   G    DLI  G IGL+KA   FD+  G + +TYA   ++  +     
Sbjct: 62  RLVAHVIKKFEGTGEDTEDLISIGTIGLIKAINTFDYARGTRLATYAARCIENEVLMWF- 120

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
                               R +R++  +                               
Sbjct: 121 --------------------RNSRKVKQE------------------------------- 129

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRF 632
           +S+  PIG +   +   F++     + +   ++  L+E    + L +L+ RE +V+ MR+
Sbjct: 130 VSIYEPIGYDKEGNEITFLDILTTDNEIVDVVETRLQEEKIRQKLGALSKRERQVIEMRY 189

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           G+      T  E+ ++  ++R  + +IE +A++KL
Sbjct: 190 GLFSGLKATQREIARKLGISRSYVSRIEKRALKKL 224


>gi|225181965|ref|ZP_03735398.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
 gi|225167327|gb|EEG76145.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
          Length = 234

 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 62/278 (22%), Positives = 105/278 (37%), Gaps = 53/278 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            VA  V  I+ + + + + S    +   E +  ++++ K       A+  ++E NLRLV 
Sbjct: 7   IVAAVVKEIVLLVSYLNNNSFPQPLKPQEEKKYLALMAK---GDEEARSILIERNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KK+ N G    DLI  G +GL+KA + F+   G + +TYA   ++  I   I   + 
Sbjct: 64  HVIKKFENTGEDQEDLISIGTVGLIKAIDSFNNNKGTRLATYAARCIENEILMHIRVITK 123

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                           +    + + I  +    EI                         
Sbjct: 124 ---------------RKAEVLLHDPIGTDKEGNEI------------------------- 143

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                     L D +     +  L+   +  L      V+  L  RE  VL MRFG+ M 
Sbjct: 144 ---------TLLDVLGSDEEL-VLNEVDRKMLEAKLYEVIKKLKLRERTVLAMRFGLPMG 193

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
              T +E+ K   ++R  + +IE K I K+    R ++
Sbjct: 194 RRKTQKEIAKSLGISRSYVSRIEKKVIAKIAEEFRQER 231


>gi|218513990|ref|ZP_03510830.1| RNA polymerase factor sigma-32 [Rhizobium etli 8C-3]
          Length = 217

 Score = 93.7 bits (231), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 51/204 (25%), Positives = 88/204 (43%), Gaps = 9/204 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +  I     +   +   +    R  E     A  ++V ++LRLV  +A  Y   GL
Sbjct: 16  LNRYLDEIRKFPMLEPQQEYMLAK--RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMR 526
              +++ EGN+GLM+A +KFD   G++ +TYAMWW+K +I   I      +++    + +
Sbjct: 74  PIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQK 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG-- 581
                + R   R+      +  PE   EIA KL +  E V  + +      SL  PI   
Sbjct: 134 RLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAA 193

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAI 605
           + D+    D++ D +         
Sbjct: 194 EGDSGQWQDWLVDDHDSQEDVLIE 217


>gi|256833253|ref|YP_003161980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686784|gb|ACV09677.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 348

 Score = 93.7 bits (231), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 104/263 (39%), Gaps = 18/263 (6%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLD 472
            +   G+ + E     S +++     +  ++ +V  NL LV         R    +   +
Sbjct: 30  CAPRVGVKVLEMCPQASRLKRMSTM-TDTQERLVTENLHLVGYHVNDMLVRLPSHVTRDE 88

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L   G   L++AA  FD   G  F+ +A   +K A+   +        +   +R KI  +
Sbjct: 89  LSSAGQFALVQAARNFDPSSGVPFARFAAIRIKGALVDELRSMDW---VSRGVRKKIRDL 145

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGDF 591
            + +  ++  + R PT +E+A  L +P+  +     +   + +S E          L + 
Sbjct: 146 NQVSDTLTATLGRTPTRQELATALGVPLSDIDDARDQAATKVLSFEGY-----DGALAEV 200

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +     V P  + I +         +++L  R   ++   F      + ++ E+ +   V
Sbjct: 201 LP-TREVGPEAALIASEQIVYLKSAVSALPERLRAIVEQIFF----EEKSVTEIAESLGV 255

Query: 652 TRERIRQIEAKAIRKLKHPSRSK 674
           T+ R+ Q+ A+A+  L+    + 
Sbjct: 256 TQSRVSQLRAEAMVLLRDGMNAH 278


>gi|302874723|ref|YP_003843356.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
 gi|307690664|ref|ZP_07633110.1| sporulation sigma factor SigE [Clostridium cellulovorans 743B]
 gi|302577580|gb|ADL51592.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
          Length = 235

 Score = 93.7 bits (231), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 95/248 (38%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +V  +  G+      +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LTKEEEEELVGKLSTGK---EAVRSVLIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +   S                V+       
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSK---------------VKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                                   L D +  +N  +  
Sbjct: 137 PLNIDWDGNEL----------------------------------LLSDILGSEND-NIY 161

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +       R+  +  L  L  RE++++ +R+G+    + T +EV     +++  I ++E 
Sbjct: 162 NLLEDEVDRQLLSIALRKLNEREKQIVELRYGLNGCNEKTQKEVADMLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           + IR+LK 
Sbjct: 222 RIIRRLKK 229


>gi|54654473|gb|AAV37113.1| RpoD [Vibrio chagasii]
          Length = 173

 Score = 93.7 bits (231), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 33/155 (21%), Positives = 62/155 (40%), Gaps = 2/155 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +    + I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRHENDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             ET +++   + I   +  GE +A  AKKEMVEA
Sbjct: 139 EKETSLTVQSIKDISRRMSIGEAKARRAKKEMVEA 173


>gi|78044685|ref|YP_360875.1| sporulation sigma factor SigE [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996800|gb|ABB15699.1| RNA polymerase sigma-E factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 237

 Score = 93.7 bits (231), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 95/251 (37%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +++++       + AK  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 37  LSSEEENTLLTLL---VQGDAAAKSTLIERNLRLVVYIARKFENTGVNIEDLVSIGTIGL 93

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSKIRLE-------------------- 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +  +  +
Sbjct: 134 --------------------------------VSFDEPLNVDWDGNELLLSDVLGTEGDI 161

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                      ++     L+ L  RE +++ +RFG+    + T +EV     +++  I +
Sbjct: 162 -IYKVMEDEVEKKLLKVALSKLNQRERKIMELRFGLTDGYERTQKEVADLLGISQSYISR 220

Query: 659 IEAKAIRKLKH 669
           +E K +++LK 
Sbjct: 221 LEKKILKRLKK 231


>gi|301055395|ref|YP_003793606.1| sporulation sigma factor SigE [Bacillus anthracis CI]
 gi|300377564|gb|ADK06468.1| sporulation sigma factor SigE [Bacillus cereus biovar anthracis
           str. CI]
          Length = 238

 Score = 93.7 bits (231), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 23  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 82

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 83  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 128

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 129 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 150

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 151 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 209

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 210 DMLGISQSYISRLEKRIIKRLRK 232


>gi|291278833|ref|YP_003495668.1| RNA polymerase sigma factor for flagellar operon FliA
           [Deferribacter desulfuricans SSM1]
 gi|290753535|dbj|BAI79912.1| RNA polymerase sigma factor for flagellar operon FliA
           [Deferribacter desulfuricans SSM1]
          Length = 243

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 52/209 (24%), Positives = 104/209 (49%), Gaps = 10/209 (4%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   ++      G ++A +++D      F  YA   VK AI   +        +  ++R 
Sbjct: 42  VDMDEIYSAACFGFVEALKRYDKSRNIDFKYYAEKRVKGAILDVLRKMD---ILSRNVRT 98

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDT 585
           KI  +     R+S+K+ R+P P EIAK+  + ++ V K+L++    + +SL+   G++D+
Sbjct: 99  KIKDLEDKIARLSSKLGRKPHPSEIAKEYNLDIDEVNKLLELLENSDQVSLDITFGEDDS 158

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S L +FI+  + ++P +S  +  L E   + +  L  +E  V+ + +      D T++E+
Sbjct: 159 SSLINFIK-SDILTPEESIEKKELIEVLGKEIEKLNEKERLVITLYY----YEDLTMKEI 213

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           G    ++  R+ Q+   A++KLK     K
Sbjct: 214 GSVLGISESRVSQLHNSAVKKLKKRMEWK 242


>gi|282953999|emb|CBI75477.1| RNA polymerase beta subunit [Pseudomonas arsenicoxydans]
          Length = 208

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 29/144 (20%), Positives = 62/144 (43%), Gaps = 6/144 (4%)

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEK----LVKLVGSLSLNQSRIDLLVEQLYDISK 347
           +   ++ D     +K  K   +   L       L +L   + L   + + LVE++     
Sbjct: 66  QRFGAVSDQMEITRKALKKHGRGNKLAIAELVLLAELFMPIKLVPKQFEGLVERVRSALD 125

Query: 348 RIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +      I
Sbjct: 126 RLRQQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAIGRLQPDI 184

Query: 407 LKIRNEIKSISVETGISISEFRHI 430
           ++ + ++K++  ETG++I+E + I
Sbjct: 185 IRCQQKLKALETETGLTIAEIKDI 208


>gi|118479504|ref|YP_896655.1| sporulation sigma factor SigK [Bacillus thuringiensis str. Al
           Hakam]
 gi|118418729|gb|ABK87148.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Bacillus
           thuringiensis str. Al Hakam]
          Length = 271

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 53  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 109

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 110 EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 153

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 154 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 178 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 236

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 237 ALGISRSYVSRIEKRALMKMFH 258


>gi|212639647|ref|YP_002316167.1| sporulation sigma factor SigE [Anoxybacillus flavithermus WK1]
 gi|212561127|gb|ACJ34182.1| DNA-directed RNA polymerase specialized sigma subunit sigE
           [Anoxybacillus flavithermus WK1]
          Length = 239

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 102/263 (38%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     +++K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEMLLKKLPSGDETARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +   +             
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNN------------- 130

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                            VR         +S + P+  +   +  
Sbjct: 131 --------------------------------KVR-------SEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  ++ V   D     + R    R L  L+ RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTEDDVITKDLEANID-RNLLFRALDQLSDREKQIMELRFGLSGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DLLGISQSYISRLEKRIIKRLRK 233


>gi|91981568|gb|ABE68126.1| RNA polymerase subunit D [Pseudomonas protegens]
 gi|91981574|gb|ABE68129.1| RNA polymerase subunit D [Pseudomonas sp. K94.41]
          Length = 220

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 57/126 (45%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + + +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRENKQAIAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++ VETG+ I
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|220931758|ref|YP_002508666.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
 gi|219993068|gb|ACL69671.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
          Length = 245

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 97/254 (38%), Gaps = 51/254 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S ET     E      ++++     +  ++ +++ NLRLV+ +A+K++N G+   DL+  
Sbjct: 36  SSETLPPPLEEDEEDYLLKRLSEGDNSVRQLLIKHNLRLVVYIARKFSNTGIDIEDLVSI 95

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA + FD     K +TYA   ++  I   +   S                 +  
Sbjct: 96  GTIGLIKAVKTFDVNKNIKLATYASRCIENEILMYLRKNSR---------------KKAE 140

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
               + +  +    E+     M  E                           GD I    
Sbjct: 141 ISFDDPLNIDWDGNELKLSDVMGTE---------------------------GDII---- 169

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG-IGMNTDHTLEEVGKQFCVTRER 655
                 +       E     + +L+ RE+++L +RFG +      T ++V     +++  
Sbjct: 170 ----YRNIESEIDWELLKDAMKTLSDREKKILILRFGLLNSGETKTQKDVADLLGISQSY 225

Query: 656 IRQIEAKAIRKLKH 669
           I ++E + IRKLK 
Sbjct: 226 ISRLEKRIIRKLKR 239


>gi|54654463|gb|AAV37108.1| RpoD [Vibrio crassostreae]
          Length = 175

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 33/156 (21%), Positives = 61/156 (39%), Gaps = 2/156 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
             ET +++   + I   +  GE +A   KKEMVEAN
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRGKKEMVEAN 174


>gi|54654467|gb|AAV37110.1| RpoD [Vibrio pomeroyi]
          Length = 173

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 33/155 (21%), Positives = 62/155 (40%), Gaps = 2/155 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +    + I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNENDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             ET +++   + I   +  GE +A  AKKEMVEA
Sbjct: 139 EKETSLTVQSIKDISRRMSIGEAKARRAKKEMVEA 173


>gi|218677311|ref|ZP_03525208.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 171

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 45/169 (26%), Positives = 84/169 (49%), Gaps = 8/169 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +   +R  + +   A+ ++  A++RLVIS+A K+ N GL   DL+QEG +GL
Sbjct: 5   LARQEEHDLA--IRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 62

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           ++AA +F+     +FSTYA WW++ +I   I      +R       K     + R   ++
Sbjct: 63  LEAAARFEPDRDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 122

Query: 540 SN---KIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED 584
           +    ++  +   +EIA  L + +  V+    +++    SL+ P    D
Sbjct: 123 AKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGD 171


>gi|328912710|gb|AEB64306.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 242

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 58/275 (21%), Positives = 108/275 (39%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S +E +  + ++         A+  ++E NLRLV 
Sbjct: 8   ALGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLM---AEGDEHARNMLIEHNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I   +     
Sbjct: 65  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA--- 121

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 122 -------------------------------------------------LKKTKKDVSLH 132

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +     D ++ ++        +   L E   + +  L  RE+ V+  RFG+
Sbjct: 133 DPIGQDKEGNEISRIDVLKSESEDVIDTIQLNMEL-EKVKKYIDILDDREKEVIVGRFGL 191

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 192 DLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 226


>gi|2224777|emb|CAA80617.1| putative pro-sigma factor E [Clostridium acetobutylicum ATCC 824]
          Length = 235

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 94/252 (37%), Gaps = 61/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +V+ +          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKDEEDDLVNKL---VNGDESIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TY    ++  I   +   S                         
Sbjct: 92  IKAVNTFDPTKKIKLATYGSRCIENEILMYLRRNSKVKAE-------------------- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +   N  
Sbjct: 132 --------------------------------ISFYEPLNIDWDGNKPLLSDILGTDN-- 157

Query: 599 SPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             + + I+  + ++     L  L  RE+R++ +R+G+    + T +EV     +++  I 
Sbjct: 158 DCVYNLIEGEVDKQLLLFALKKLNEREKRIVELRYGLTGVGEKTQKEVADMLGISQSYIS 217

Query: 658 QIEAKAIRKLKH 669
           ++E + I++LK 
Sbjct: 218 RLEKRIIKRLKK 229


>gi|15613848|ref|NP_242151.1| sporulation sigma factor SigK [Bacillus halodurans C-125]
 gi|10173901|dbj|BAB05004.1| RNA polymerase sigma factor (sigma K) precursor [Bacillus
           halodurans C-125]
          Length = 235

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 106/269 (39%), Gaps = 59/269 (21%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             +L   + +K+ +    +S  E RH +  +         A+  ++E NLRLV  + KK+
Sbjct: 13  KEVLVFVSYVKNNAFPQPLSKEEERHYLKRM---AEGDEEARNRLIEHNLRLVAHIVKKF 69

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N      DLI  G IGL+KA E F    G K +TYA   ++  I   +           
Sbjct: 70  ENTREHTEDLISIGTIGLIKAIESFSEGKGTKLATYAARCIENEILMHLRA--------- 120

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                                               ++ V+K        +SL  PIG +
Sbjct: 121 ------------------------------------LKKVKK-------DVSLHDPIGTD 137

Query: 584 ---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
              +   L D ++ +++    DS      ++     +  L  RE+ V+  RFG+ +  + 
Sbjct: 138 KEGNEITLIDVLQ-EDSEDIADSIQLKMEKKQIYEYIHVLDDREKEVIVGRFGLDLEEER 196

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKLFH 225


>gi|213958510|gb|ACJ54676.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 3-3.5cm4R]
          Length = 140

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 25/130 (19%), Positives = 57/130 (43%), Gaps = 2/130 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 8   KHGRNNKAAIAELLLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 67

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 68  MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTI 126

Query: 425 SEFRHIVSMV 434
           +E + I   +
Sbjct: 127 AEIKDINRRM 136


>gi|323099955|gb|ADX23555.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|162708412|gb|ABY19604.1| sigma 70 factor [Pseudomonas syringae pv. apii]
 gi|162708414|gb|ABY19605.1| sigma 70 factor [Pseudomonas syringae pv. tomato str. JL1065]
 gi|162708416|gb|ABY19606.1| sigma 70 factor [Pseudomonas syringae pv. tomato]
 gi|162708418|gb|ABY19607.1| sigma 70 factor [Pseudomonas syringae pv. antirrhini str. 126]
 gi|162708420|gb|ABY19608.1| sigma 70 factor [Pseudomonas syringae pv. maculicola str. M6]
 gi|162708422|gb|ABY19609.1| sigma 70 factor [Pseudomonas syringae pv. maculicola str. M3]
 gi|162708424|gb|ABY19610.1| sigma 70 factor [Pseudomonas syringae pv. tomato]
 gi|162708426|gb|ABY19611.1| sigma 70 factor [Pseudomonas syringae pv. tomato]
          Length = 214

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 35/204 (17%), Positives = 77/204 (37%), Gaps = 5/204 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 9   DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVS 68

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 69  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 125

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +++L      + R  FL +  G E+D  W        +G++   +      I + +
Sbjct: 126 QERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAK-GKGKYAEAIGRLQPDIQRCQ 184

Query: 411 NEIKSISVETGISISEFRHIVSMV 434
            ++ ++  ETG+ I+E + I   +
Sbjct: 185 QKLSALEEETGLKIAEIKDINRRM 208


>gi|302391216|ref|YP_003827036.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
 gi|302203293|gb|ADL11971.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
          Length = 235

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 57/266 (21%), Positives = 103/266 (38%), Gaps = 54/266 (20%)

Query: 403 VDSILKIRNEIKSIS-VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            D IL + + I + +     +   E +  ++           AK+ ++E N+RLV  + K
Sbjct: 14  ADGILVLISYIANNNIFPQPLDDEEEKKYLTR---YLEGDEEAKEVLIEHNMRLVAHIVK 70

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           KY N  +   DLI  G+IGL+KA E +D     K +TYA   ++  I         T R 
Sbjct: 71  KYNNSNVDKEDLISIGSIGLIKAIETYDPSKKVKLATYASRCIENEILMHFRQNKKTNRE 130

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
                                                             +P+S +    
Sbjct: 131 VK----------------------------------------------LHDPLSSD---K 141

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           + +   L D  E  +  + L+    A   E     +  L+ RE++V++MR+G+    + T
Sbjct: 142 EGNEMTLMDVYE-TDEEAVLEKVEMALAEERLYDKIEGLSEREQKVVKMRYGLNNVEELT 200

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
             E+  +  ++R  + +IE +A++KL
Sbjct: 201 QREIANKLGISRSYVSRIEKRALQKL 226


>gi|91981594|gb|ABE68139.1| RNA polymerase subunit D [Pseudomonas sp. P97.26]
          Length = 220

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 57/126 (45%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLSALEAETGLSI 213

Query: 425 SEFRHI 430
           +E   +
Sbjct: 214 AEINDL 219


>gi|239934410|emb|CAR92335.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 224

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 29/218 (13%), Positives = 76/218 (34%), Gaps = 8/218 (3%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                     +    P ++ +  E   D+ E                + +     I +  
Sbjct: 11  DPDDGIVPAEAAAPVPVKDGDAAEETDDDAEASDDEEEEGDGGPDPEEALRRFTAIGD-- 68

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
               +L+      +K  ++S +     +++ +L   + L   + D LV ++    +R+  
Sbjct: 69  ----ALELAKKALKKHGRNSKQGTAALKEMAELFMPIKLVPKQYDALVVRVRSSLERLRA 124

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +++L      + R  FL    G E+D  W S      + ++   +      I + +
Sbjct: 125 QERAIMQLCVRDARMPRADFLRLFPGNEIDVEW-SAGLAKGKAKYAEAIGNLQGDIQRCQ 183

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            ++ ++  E  ++++E + I       +   +  +  M
Sbjct: 184 QKLSALEAECELTLAEIKDINRRANSADIHHTGGRSSM 221


>gi|30021993|ref|NP_833624.1| sporulation sigma factor SigE [Bacillus cereus ATCC 14579]
 gi|30263906|ref|NP_846283.1| sporulation sigma factor SigE [Bacillus anthracis str. Ames]
 gi|42782997|ref|NP_980244.1| sporulation sigma factor SigE [Bacillus cereus ATCC 10987]
 gi|47529336|ref|YP_020685.1| sporulation sigma factor SigE [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49186754|ref|YP_030006.1| sporulation sigma factor SigE [Bacillus anthracis str. Sterne]
 gi|49478442|ref|YP_037966.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141583|ref|YP_085245.1| sporulation sigma factor SigE [Bacillus cereus E33L]
 gi|162382776|ref|YP_896275.2| sporulation sigma factor SigE [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872323|ref|ZP_02216960.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|167636583|ref|ZP_02394877.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170688850|ref|ZP_02880053.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|170708793|ref|ZP_02899229.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|177654897|ref|ZP_02936614.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190566146|ref|ZP_03019065.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035954|ref|ZP_03103356.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196038626|ref|ZP_03105934.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|196045866|ref|ZP_03113095.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|206971306|ref|ZP_03232257.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206976716|ref|ZP_03237620.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217961326|ref|YP_002339894.1| sporulation sigma factor SigE [Bacillus cereus AH187]
 gi|218234749|ref|YP_002368704.1| sporulation sigma factor SigE [Bacillus cereus B4264]
 gi|218899058|ref|YP_002447469.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|218905035|ref|YP_002452869.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|222097350|ref|YP_002531407.1| sporulation sigma factor sige [Bacillus cereus Q1]
 gi|225865886|ref|YP_002751264.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227813186|ref|YP_002813195.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228902410|ref|ZP_04066564.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|228909730|ref|ZP_04073553.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228916542|ref|ZP_04080108.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922657|ref|ZP_04085957.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228928953|ref|ZP_04091985.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935220|ref|ZP_04098046.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228940993|ref|ZP_04103551.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947624|ref|ZP_04109914.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954181|ref|ZP_04116209.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960122|ref|ZP_04121786.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966858|ref|ZP_04127902.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228973924|ref|ZP_04134499.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980513|ref|ZP_04140823.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228987049|ref|ZP_04147174.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229047589|ref|ZP_04193179.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|229071404|ref|ZP_04204626.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|229081157|ref|ZP_04213667.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|229092951|ref|ZP_04224084.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|229111374|ref|ZP_04240927.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|229123418|ref|ZP_04252622.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|229129182|ref|ZP_04258155.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|229140553|ref|ZP_04269108.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|229146476|ref|ZP_04274847.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|229152102|ref|ZP_04280297.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|229180180|ref|ZP_04307524.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|229186145|ref|ZP_04313314.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|229192074|ref|ZP_04319043.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|229198016|ref|ZP_04324730.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|229601447|ref|YP_002868140.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|254683386|ref|ZP_05147246.1| sporulation sigma factor SigE [Bacillus anthracis str. CNEVA-9066]
 gi|254721438|ref|ZP_05183227.1| sporulation sigma factor SigE [Bacillus anthracis str. A1055]
 gi|254735943|ref|ZP_05193649.1| sporulation sigma factor SigE [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739808|ref|ZP_05197501.1| sporulation sigma factor SigE [Bacillus anthracis str. Kruger B]
 gi|254750998|ref|ZP_05203037.1| sporulation sigma factor SigE [Bacillus anthracis str. Vollum]
 gi|254757944|ref|ZP_05209971.1| sporulation sigma factor SigE [Bacillus anthracis str. Australia
           94]
 gi|296504398|ref|YP_003666098.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|49065841|sp|P62177|RP35_BACAN RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065842|sp|P62178|RP35_BACCR RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065843|sp|P62179|RP35_BACTK RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|40335|emb|CAA40026.1| sigma factor 35 [Bacillus thuringiensis serovar kurstaki]
 gi|19918914|gb|AAL99378.1| sigma factor 35 [Bacillus thuringiensis serovar israelensis]
 gi|29897549|gb|AAP10825.1| RNA polymerase sigma-E factor [Bacillus cereus ATCC 14579]
 gi|30258550|gb|AAP27769.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Ames]
 gi|42738924|gb|AAS42852.1| RNA polymerase sigma-29 factor [Bacillus cereus ATCC 10987]
 gi|47504484|gb|AAT33160.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49180681|gb|AAT56057.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Sterne]
 gi|49329998|gb|AAT60644.1| RNA polymerase sporulation-specific sigma E factor [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51975052|gb|AAU16602.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           E33L]
 gi|164711999|gb|EDR17539.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|165973128|gb|ABY76243.1| sigma factor [Bacillus thuringiensis]
 gi|167528006|gb|EDR90812.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170126278|gb|EDS95169.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|170667205|gb|EDT17965.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|172080408|gb|EDT65495.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190563065|gb|EDV17031.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991603|gb|EDX55569.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196023306|gb|EDX61984.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|196030349|gb|EDX68948.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|206734078|gb|EDZ51249.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206745026|gb|EDZ56429.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217065302|gb|ACJ79552.1| RNA polymerase sigma-29 factor [Bacillus cereus AH187]
 gi|218162706|gb|ACK62698.1| RNA polymerase sigma-29 factor [Bacillus cereus B4264]
 gi|218537297|gb|ACK89695.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|218544009|gb|ACK96403.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|221241408|gb|ACM14118.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           Q1]
 gi|225791008|gb|ACO31225.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227003693|gb|ACP13436.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228585495|gb|EEK43599.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|228591400|gb|EEK49250.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|228597321|gb|EEK54972.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|228603389|gb|EEK60866.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|228631451|gb|EEK88085.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|228637109|gb|EEK93568.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|228643114|gb|EEK99390.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|228654419|gb|EEL10284.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|228660194|gb|EEL15830.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|228672150|gb|EEL27441.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|228690455|gb|EEL44239.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|228702201|gb|EEL54677.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|228711695|gb|EEL63648.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|228723836|gb|EEL75191.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|228772643|gb|EEM21084.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228779333|gb|EEM27590.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228785790|gb|EEM33794.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792957|gb|EEM40515.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228799638|gb|EEM46591.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805501|gb|EEM52092.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228812144|gb|EEM58475.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818672|gb|EEM64739.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824385|gb|EEM70191.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830760|gb|EEM76365.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228837086|gb|EEM82427.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228843121|gb|EEM88203.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228850019|gb|EEM94850.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228857154|gb|EEN01660.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|229265855|gb|ACQ47492.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|296325450|gb|ADH08378.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|308154178|gb|ADA55132.3| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|308154180|gb|ADA55133.2| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|324327803|gb|ADY23063.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941674|gb|AEA17570.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 239

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|118418349|gb|ABK86768.1| RNA polymerase, sigma 29 subunit, SigE [Bacillus thuringiensis str.
           Al Hakam]
          Length = 248

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 33  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 92

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 93  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 138

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 139 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 160

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 161 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 219

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 220 DMLGISQSYISRLEKRIIKRLRK 242


>gi|54654465|gb|AAV37109.1| RpoD [Vibrio kanaloae]
 gi|54654471|gb|AAV37112.1| RpoD [Vibrio splendidus]
          Length = 173

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 33/155 (21%), Positives = 60/155 (38%), Gaps = 2/155 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L     R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKATLATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDII 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             ET +++   + I   +  GE +A  AKKEMVEA
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEA 173


>gi|42783467|ref|NP_980714.1| sporulation sigma factor SigK [Bacillus cereus ATCC 10987]
 gi|42739396|gb|AAS43322.1| RNA polymerase sigma-27 factor [Bacillus cereus ATCC 10987]
          Length = 265

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 47  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 103

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 104 EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 147

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 148 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 171

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 172 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 230

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 231 ALGISRSYVSRIEKRALMKMFH 252


>gi|125973527|ref|YP_001037437.1| sporulation sigma factor SigK [Clostridium thermocellum ATCC 27405]
 gi|256003345|ref|ZP_05428336.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281417730|ref|ZP_06248750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713752|gb|ABN52244.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Clostridium
           thermocellum ATCC 27405]
 gi|255992635|gb|EEU02726.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281409132|gb|EFB39390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940233|gb|ADU74267.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 1313]
          Length = 236

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 107/264 (40%), Gaps = 58/264 (21%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E +H + +++K       A+  ++E NLRLV  + KKY++      DLI  
Sbjct: 28  SFPQPLSPEEEQHYLDLLKK---GDEEARNILIERNLRLVAHIVKKYSSTINDSDDLISI 84

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+   G + +TYA   ++  I   I                        
Sbjct: 85  GTIGLIKAISTFNHEKGTRLATYAARCIENEILMHIRSN--------------------- 123

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
                                          K T+  +SL+ PIG +   +   L D I 
Sbjct: 124 -------------------------------KKTQSEVSLQDPIGVDRDGNEIALIDVIG 152

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           +++     +  ++  ++    ++   L  RE+ VL +R+G+   T  T  E+ K   ++R
Sbjct: 153 NESESVVEEVELKMQVKRLYNKMKDVLKAREKMVLELRYGLLNGTGKTQREIAKMLGISR 212

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLR 677
             + +IE KAI+KL    +S+  +
Sbjct: 213 SYVSRIEKKAIKKLGKELKSESFK 236


>gi|229543758|ref|ZP_04432818.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
 gi|229328178|gb|EEN93853.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
          Length = 241

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 110/275 (40%), Gaps = 59/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            V+  +  ++ + + +K+ +    +S SE R  +  +       + A+  ++E NLRLV 
Sbjct: 7   AVSYMMKELVFLVSYVKNNAFPQPLSASEERKYLKRM---AEGDADARNILIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +     
Sbjct: 64  HIVKKFENTGEDTEDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEILMHLRA--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK TK+ +SL 
Sbjct: 121 -------------------------------------------------LKKTKKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D ++ +         +   L E   +    L  RE++V+  RFG+
Sbjct: 132 DPIGQDKEGNEISLIDVLQSEAEDVFDTIQLNMEL-EKVKQFFDILDEREKQVIIGRFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 191 NLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|75761264|ref|ZP_00741246.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74491246|gb|EAO54480.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 271

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 53  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 109

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 110 EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 153

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 154 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 178 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 236

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 237 ALGISRSYVSRIEKRALMKMFH 258


>gi|332707787|ref|ZP_08427814.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
 gi|332353490|gb|EGJ33003.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
          Length = 260

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 106/247 (42%), Gaps = 12/247 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++      +   + ++V  N  LV  +A          + DL Q G IGL++A E+FD  
Sbjct: 14  LIAYYRNPSIQLRNQIVRLNAGLVRKIAHIVSQKCAEPYEDLEQMGYIGLIRAIERFDPH 73

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS+ A+ +++  +   + D+   ++IP   ++      R +++++  + R P  EE
Sbjct: 74  QGCAFSSLAVPYIRGEMLHFLRDRGSLVKIPRRWQELQQAGKRVSKKLATNLGRFPRDEE 133

Query: 552 IAKKLAMPVEGVRKVLKITKE--PISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
           IAK L + ++  ++     +   P+SL+  +    +    LG+ + D    +        
Sbjct: 134 IAKALDVSLQEWQESKLAVQNRLPLSLDATVSQKVDQPMTLGETLPDYYEENLHYWEED- 192

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R+     L+ L  + +  +   F      +   +E  K+  V+   + +   + I++L
Sbjct: 193 --RQQLQGALSQLEDKTQAAIEFVFL----RELPRKEAAKRIGVSPMTVTRHVKRGIQEL 246

Query: 668 KHPSRSK 674
               +S+
Sbjct: 247 VTLMKSQ 253


>gi|237757202|ref|ZP_04585618.1| RNA polymerase sigma-D factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690638|gb|EEP59830.1| RNA polymerase sigma-D factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 242

 Score = 93.4 bits (230), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 52/207 (25%), Positives = 92/207 (44%), Gaps = 13/207 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DL Q G +GL  A EKFD   G KFSTYA   V+  I   +        +P ++R+
Sbjct: 35  VDEEDLFQVGVLGLYDALEKFDPSKGVKFSTYAEIRVRGYILDHLRQLDW---VPRNIRN 91

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV----RKVLKITKEPISLETPIGDE 583
           K+  +      +  K+ RE   EEIA+ L M +E       K +      I  +    D+
Sbjct: 92  KVKNLENKIVELETKLGREAKLEEIAEYLGMSLEEYMIYAEKAVNKILISIDSDISKDDD 151

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTL 642
           ++ HL + I   +  +P     +  L+E  +  ++  L  RE  ++ + +      D  +
Sbjct: 152 ESLHLWEVISTDDD-TPEKYVEEKQLKEILSDIIMNKLDERERLIVTLYY----YEDLNM 206

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E+ +    T  R+ Q+  K + K++ 
Sbjct: 207 KEIAEILGYTESRVSQLHTKIMLKIRK 233


>gi|54654461|gb|AAV37107.1| RpoD [Vibrio gigantis]
          Length = 173

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 33/155 (21%), Positives = 61/155 (39%), Gaps = 2/155 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             ET +++   + I   +  GE +A  AKKEMVEA
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEA 173


>gi|153005080|ref|YP_001379405.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028653|gb|ABS26421.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 241

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 63/265 (23%), Positives = 116/265 (43%), Gaps = 51/265 (19%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
                  ++   +K++     +S  E   +    RK       AK+++V  NL  V+++A
Sbjct: 8   KSSREFEELAPYLKAVRDFPPLSRDEEHALALRARK---GDVRAKQKLVRHNLAFVVAIA 64

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           +K     ++  DLIQEGN+GLM+A EKFD   G +FSTYA+WW++  I + + +   T+R
Sbjct: 65  RKQRRGTVRLDDLIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVR 124

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
                                                       +   + +  +SL++ I
Sbjct: 125 P-------------------------------------------QSGTVAQPDLSLDSAI 141

Query: 581 GDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            +E  +   + IED       + L +   +++R+   +V   +      ++     +  +
Sbjct: 142 DEEGDATHLERIEDDGPGPEDTYLQAEGDSDVRDALGKVRKRIGELGWDIV--HNRLEQD 199

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAK 662
              TLEE+GK++ V+RER+RQ+E K
Sbjct: 200 QPRTLEEIGKRWGVSRERVRQVELK 224



 Score = 46.0 bits (107), Expect = 0.020,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 53/171 (30%), Gaps = 2/171 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+ +     LSR+ E A+A R   G       L    L F   I  +     GT  L +
Sbjct: 19  YLKAVRDFPPLSRDEEHALALRARKGDVRAKQKLVRHNLAFVVAIARKQR--RGTVRLDD 76

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I         +   F                +      ++E    +   +         
Sbjct: 77  LIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVRPQSGTVAQPDLS 136

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +DS  +   +       ++D      + ++ +    V  AL ++ +   EL
Sbjct: 137 LDSAIDEEGDATHLERIEDDGPGPEDTYLQAEGDSDVRDALGKVRKRIGEL 187


>gi|153803628|ref|ZP_01958214.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
 gi|124120837|gb|EAY39580.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
          Length = 193

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 47/194 (24%), Positives = 89/194 (45%), Gaps = 14/194 (7%)

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL++A + +D   G  F TYA   ++ A+   I        +P  +     ++ +   
Sbjct: 1   MVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDW---VPRSVHKHNREISQAIA 57

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI---ED 594
            +  ++ R+PT  E+AK L M +E    VL      I+    +G ED     D I   E+
Sbjct: 58  VLEGELNRDPTDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVSDDAISPFEE 113

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
               SP     + + R+     + SL  RE  VL + +    + +  L+E+G+   V+  
Sbjct: 114 GEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYY----DEELNLKEIGEVLGVSES 169

Query: 655 RIRQIEAKAIRKLK 668
           R+ QI ++++++L+
Sbjct: 170 RVSQILSQSMQRLR 183


>gi|152976265|ref|YP_001375782.1| sporulation sigma factor SigE [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025017|gb|ABS22787.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 239

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 97/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +   D     + R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDIITKDLEANVD-RYLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|294998208|gb|ADF57908.1| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
 gi|308154182|gb|ADF57907.2| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
          Length = 271

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 53  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 109

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 110 EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 153

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 154 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 177

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 178 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 236

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 237 ALGISRSYVSRIEKRALMKMFH 258


>gi|81300593|ref|YP_400801.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|81169474|gb|ABB57814.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 260

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 107/240 (44%), Gaps = 12/240 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWC 491
           +V   E  +   + ++V+ NL LV  +A + + +    + DL Q G +GL++A E+F   
Sbjct: 15  LVAYAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQPH 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  FS++A+ +++  I   + D   +IRIP   ++   +  +    + ++  R PT +E
Sbjct: 75  QGCAFSSFAVPYIRGEILHFLRDSCHSIRIPRRWQELQRQGQQLREVLRHEWGRAPTEQE 134

Query: 552 IAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
           +A  L + +   +++   +  + P+SL+  +     S   L + + D    S        
Sbjct: 135 LAFALNLSMTEWQEIHLARRNRMPMSLDATLSQAGDSSVTLVETLPD---TSQQWQQAAL 191

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             R+     +  L  +    +   +  G+      +E  +QF ++   I +   + ++K+
Sbjct: 192 EERQQLVEAIGQLEEKARTAIESVYLRGLTR----KEAAQQFGISPMTITRRINRGVQKI 247


>gi|160895354|ref|ZP_02076125.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
 gi|156863047|gb|EDO56478.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
          Length = 226

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 57/271 (21%), Positives = 99/271 (36%), Gaps = 59/271 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  I     EI   + +  +S  E  + + +    +     A+K ++E N+RLV  +AKK
Sbjct: 9   IKYIQIAGAEIDVQTFKKPLSPKEEAYFLKL---CKEGDPRARKTLIEYNMRLVAHIAKK 65

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           Y        DLI  G IGL+KA + +D   G +  TYA   ++  +   +       +  
Sbjct: 66  YNGSHEN-DDLISAGTIGLIKAIDTYDSKKGKRLVTYASRCIENELLMLLR------QNR 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
            H R+                                              +SL  PIG 
Sbjct: 119 KHARE----------------------------------------------VSLFEPIGT 132

Query: 583 E---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +   +   L D I               NL++    +L  LT +E  +L  R+G+     
Sbjct: 133 DKEGNEISLMDIISPDTPSILDSMVHDYNLKQLPDCMLHHLTKQEMVLLSRRYGLSGEAP 192

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            T +E+     ++R  + +IE +A+ KL+  
Sbjct: 193 CTQKEIASAMGISRSYVSRIEKRALLKLRKA 223


>gi|138894662|ref|YP_001125115.1| sporulation sigma factor SigE [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247723|ref|ZP_03146425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134266175|gb|ABO66370.1| RNA polymerase sigma-E factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196212507|gb|EDY07264.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 239

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 91/232 (39%), Gaps = 56/232 (24%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA
Sbjct: 55  DKTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 114

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +   +                                            
Sbjct: 115 SRCIENEILMYLRRNN-------------------------------------------- 130

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             VR         +S + P+  +   +   L D +  ++ V   D     + R      L
Sbjct: 131 -KVRAE-------VSFDEPLNIDWDGNELLLSDVLGTEDDVITKDLEADVD-RRLLLNAL 181

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             L+ RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 182 RQLSDREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 233


>gi|239934402|emb|CAR92331.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 242

 Score = 93.0 bits (229), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 31/227 (13%), Positives = 78/227 (34%), Gaps = 8/227 (3%)

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   G I+       D+ +      E A  +E + +E+++               +   
Sbjct: 20  AEVLSGYIDPDDGSVPDEAAAPVPVKEGAAAEESDDEEEDESDDEEEEGDGGPDPEEAAR 79

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               +AE   ++          +K  + S +       L +L   + L   + D LV ++
Sbjct: 80  RFTAVAEQQDKVLK------ALKKHGRGSKQAIEELAALAELFMPIKLVPKQYDALVTRV 133

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R   L    G E+D  W +      + ++   +  
Sbjct: 134 RDALDRLRMQERAIMQLCVRDARMPRADSLRLFPGNEIDMAWAADLAK-GKAKYAEALGN 192

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
               I + + ++  +  +  ++++E + I       +   +  +  M
Sbjct: 193 LQADIQRCQQKLADLEAKCSLTLAEIKDINRRANSADIHHTGGRSSM 239


>gi|239934340|emb|CAR92300.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 245

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/286 (13%), Positives = 92/286 (32%), Gaps = 46/286 (16%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL        +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRXFPNNGTNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I++ + ++  +  E  ++I++ + I       +   +  +  M
Sbjct: 196 KEDIVRCQQKLIELEQECDLAIADIKDINRRANSADIHHTGGRSSM 241


>gi|148380498|ref|YP_001255039.1| sporulation sigma factor SigK [Clostridium botulinum A str. ATCC
           3502]
 gi|170759231|ref|YP_001787857.1| sporulation sigma factor SigK [Clostridium botulinum A3 str. Loch
           Maree]
 gi|226949896|ref|YP_002804987.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|237795980|ref|YP_002863532.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
 gi|148289982|emb|CAL84095.1| RNA polymerase sigma-28 factor [Clostridium botulinum A str. ATCC
           3502]
 gi|169406220|gb|ACA54631.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A3
           str. Loch Maree]
 gi|226844119|gb|ACO86785.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|229261319|gb|ACQ52352.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
          Length = 234

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E ++ +  ++K     ++AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPKPLSDEEEKYYLDRLKK---GDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I                 +K  +  
Sbjct: 83  GTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIR---------------NNKKTKGE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDILSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  + +  +++   ++   L  RE++V++MR+G+      T  E+     ++R  +
Sbjct: 154 DSIIEIVSTKIEVKKLYGKIDTCLRGREKKVIQMRYGLKDGRPRTQREIAGILNISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 214 SRIEKKALKKL 224


>gi|15894972|ref|NP_348321.1| sporulation sigma factor SigE [Clostridium acetobutylicum ATCC 824]
 gi|585930|sp|P33657|RPSE_CLOAB RecName: Full=RNA polymerase sigma-E factor
 gi|15024659|gb|AAK79661.1|AE007679_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|460971|gb|AAC43309.1| putative sigma factor E [Clostridium acetobutylicum ATCC 824]
 gi|325509109|gb|ADZ20745.1| sporulation sigma factor SigE [Clostridium acetobutylicum EA 2018]
          Length = 235

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 94/252 (37%), Gaps = 61/252 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +V+ +          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKDEEDDLVNKL---VNGDESIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TY    ++  I   +   S                         
Sbjct: 92  IKAVNTFDPTKKIKLATYGSRCIENEILMYLRRNSKVKAE-------------------- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +   N  
Sbjct: 132 --------------------------------ISFYEPLNIDWDGNKLLLSDILGTDN-- 157

Query: 599 SPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             + + I+  + ++     L  L  RE+R++ +R+G+    + T +EV     +++  I 
Sbjct: 158 DCVYNLIEGEVDKQLLLFALKKLNEREKRIVELRYGLTGVGEKTQKEVADMLGISQSYIS 217

Query: 658 QIEAKAIRKLKH 669
           ++E + I++LK 
Sbjct: 218 RLEKRIIKRLKK 229


>gi|153953960|ref|YP_001394725.1| sporulation sigma factor SigK [Clostridium kluyveri DSM 555]
 gi|219854574|ref|YP_002471696.1| hypothetical protein CKR_1231 [Clostridium kluyveri NBRC 12016]
 gi|146346841|gb|EDK33377.1| SigE1 [Clostridium kluyveri DSM 555]
 gi|219568298|dbj|BAH06282.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 233

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 100/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E R+ +  ++       +AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPQPLNDEEERYYLRKLK---EGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD C G + +TYA   ++  I   I +               +K ++  
Sbjct: 83  GTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRN---------------NKKIKNE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDVLSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +++  +++   L+ RE+ V+ MR+G+      T  E+ K   ++R  +
Sbjct: 154 DSIIEIVEQKIQVKKLYSKINTCLSQREKSVVEMRYGLLEGKPKTQREIAKILGISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 214 SRIEKKALKKL 224


>gi|52080135|ref|YP_078926.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|52785509|ref|YP_091338.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|319646087|ref|ZP_08000317.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
 gi|52003346|gb|AAU23288.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus licheniformis ATCC 14580]
 gi|52348011|gb|AAU40645.1| SigE [Bacillus licheniformis ATCC 14580]
 gi|317391837|gb|EFV72634.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
          Length = 239

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 96/240 (40%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLHKLPDGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +  +N +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTENDIITKDIEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 KKLLKKALEQLNDREKQIMELRFGLVGGEEKTQKDVADMLGISQSYISRLEKRIIKRLRK 233


>gi|154498128|ref|ZP_02036506.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
 gi|150273118|gb|EDN00275.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
          Length = 240

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 95/251 (37%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +++ +   +      K +++E NLRLV+ +A+++ N G+   DLI  G IGL
Sbjct: 40  LSKGEEAELIARL---DEGEETVKSQLIERNLRLVVYIARRFENTGVGIEDLISIGTIGL 96

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   +      K +TYA   ++  I   +   SC                        
Sbjct: 97  IKAINTYKPAKNIKLATYASRCIENEILMHLRKTSCLKSE-------------------- 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +  +N V
Sbjct: 137 --------------------------------VSFDEPLNTDWDGNELLLSDILGTENDV 164

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                    + R+     +  L  RE++++ MRFG+    + T +EV     +++  I +
Sbjct: 165 VMKPIEDDVD-RQLLLEAMEKLDGREKQIITMRFGLDGRPERTQKEVADLLGISQSYISR 223

Query: 659 IEAKAIRKLKH 669
           +E + I +LK 
Sbjct: 224 LEKRIISRLKK 234


>gi|158320420|ref|YP_001512927.1| sporulation sigma factor SigE [Alkaliphilus oremlandii OhILAs]
 gi|158140619|gb|ABW18931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 244

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 95/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K + + S  +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 52  LISKLKSDESTVRTILIERNLRLVVYIARKFENTGIGIEDLISIGTIGLIKAVNTFNPEK 111

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                                    
Sbjct: 112 NIKLATYASRCIENEILMYLRRNSK----------------------------------- 136

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                             K  +S + P+  +   +   L D +  +N V       + + 
Sbjct: 137 -----------------VKMEVSFDEPLNIDWDGNELLLSDILGTENDVIHKFLEEEVD- 178

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     L  L+ RE++++ +RFG+    + T +EV     +++  I ++E + I +L+ 
Sbjct: 179 RDLLKIALEKLSKREKKIMELRFGLNTGQEKTQKEVADILGISQSYISRLEKRIITRLQK 238


>gi|239626528|ref|ZP_04669559.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516674|gb|EEQ56540.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 209

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 98/250 (39%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +  +      +     A+  ++E N+RLV  V KKY        DL+  G IGL
Sbjct: 8   LSAGEEKEYLER---CKEGDQSARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+   G + +TYA   V+  I                       ++R +++ S 
Sbjct: 65  IKAVNTFNADKGSRLATYAARCVENEILM---------------------LLRASKKFSK 103

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               +SL  PIG +       L D IE  N  
Sbjct: 104 E-------------------------------VSLFEPIGVDKDGETVSLVDVIEMDNKE 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +     ++ +++E      + LT  E+ VL MR+G+    +HT  E+     ++R  + +
Sbjct: 133 TLDTMILKQDVKELYEAFESCLTETEKTVLGMRYGLYRGKEHTQREIAGNLGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE KAI K++
Sbjct: 193 IEKKAIEKIR 202


>gi|222097784|ref|YP_002531841.1| sporulation sigma factor sigk [Bacillus cereus Q1]
 gi|221241842|gb|ACM14552.1| RNA polymerase sigma-27 factor [Bacillus cereus Q1]
          Length = 263

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 45  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 101

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 102 EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 145

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 146 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 169

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 170 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 228

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 229 ALGISRSYVSRIEKRALMKMFH 250


>gi|217077805|ref|YP_002335523.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
 gi|217037660|gb|ACJ76182.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
          Length = 226

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 97/228 (42%), Gaps = 13/228 (5%)

Query: 445 KKEMVEANLRLVISVAK---KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+ +V   L  +  +A    +     ++  DLIQEG +  ++A EKFD   G K  +Y +
Sbjct: 4   KEALVSEYLPYIKKIAYDLKRNLPHNVEVDDLIQEGLVAFIQAIEKFDPKKGAKLRSYLL 63

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             VK A+   +       +   H      K+V  A         +   E+IAK   +P+E
Sbjct: 64  TRVKGAMYDYLRKIDWMPKNLRH----DIKLVEDAIVNMESDTNDIDFEKIAKITNLPIE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V++          L       D S L D I      +P   AI   L+E     +  L 
Sbjct: 120 NVKRAYNELTRKQLLMLDSYISDDSELIDKIASDE--NPYSYAINELLKEQLIEAIKKLD 177

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +E+ +L +RF      + +L+E+GK   VT  R+ Q+ AK + KLK 
Sbjct: 178 DKEQLLLSLRF----EHELSLKEIGKVLNVTESRVSQLLAKTLAKLKK 221


>gi|149183156|ref|ZP_01861605.1| SpoIIIC [Bacillus sp. SG-1]
 gi|148849139|gb|EDL63340.1| SpoIIIC [Bacillus sp. SG-1]
          Length = 238

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 63/276 (22%), Positives = 110/276 (39%), Gaps = 57/276 (20%)

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              +   +  ++ + + +K+ +    +S  E +  +   RK       A+  ++E NLRL
Sbjct: 5   ATAIGYFLKELVFLVSYVKNNAFPQPLSSQEEKKYL---RKMANGDEDARNILIEHNLRL 61

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V  + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +   
Sbjct: 62  VAHIVKKFENTGEDPEDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEILMHLRA- 120

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
                                                              LK TK+ +S
Sbjct: 121 ---------------------------------------------------LKKTKKDVS 129

Query: 576 LETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFG 633
           L  PIG +   +    I+  K+    +   IQ ++  E   + +  L  RE+ V+  RFG
Sbjct: 130 LHDPIGQDKEGNEISLIDILKSDADDVIETIQLSMELEKVRKYICVLDDREKEVIIGRFG 189

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + M  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 190 LDMKEEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|229019107|ref|ZP_04175942.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
 gi|229025351|ref|ZP_04181769.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228735936|gb|EEL86513.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228742207|gb|EEL92372.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
          Length = 232

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 17  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 76

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 77  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 122

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 123 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 144

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 145 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 203

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 204 DMLGISQSYISRLEKRIIKRLRK 226


>gi|166368033|ref|YP_001660306.1| RNA polymerase sigma factor SigF [Microcystis aeruginosa NIES-843]
 gi|166090406|dbj|BAG05114.1| group 3 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 258

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 110/245 (44%), Gaps = 12/245 (4%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +  +   +  + +++E NL LV   A  + N+    + DL+Q G++GL++A E+FD   G
Sbjct: 19  KYQKTADNKLRDQIMELNLGLVRREAHHWVNQCHENYEDLVQVGSMGLIRAIERFDSSKG 78

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           + FS++A+ +++  I   + D+S T+RIP    D   +     R       R+P   EI+
Sbjct: 79  HAFSSFAIPYIRGEIQHHLRDKSYTVRIPRRWLDLGRQATNVRRDFQTIHNRQPNDTEIS 138

Query: 554 KKLAMPVEGVRKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANL 609
           + L +  E  ++V      +EP+SL+  + +++   + L D + D    S          
Sbjct: 139 RALNISSEEWQEVKLAFQNREPLSLDVTVNNDEDNNTCLKDLVPDPRYRSFQLCQED--- 195

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R    + LA L  +   ++   F      D T  E  +Q  ++   + +   K +  +K 
Sbjct: 196 RIRLQQALAQLEEKTRHIIEFVFL----KDLTQRETAEQLGISVVTVSRRVKKGLEMIKE 251

Query: 670 PSRSK 674
               +
Sbjct: 252 TMVKE 256


>gi|116074935|ref|ZP_01472196.1| putative type III sigma factor [Synechococcus sp. RS9916]
 gi|116068157|gb|EAU73910.1| putative type III sigma factor [Synechococcus sp. RS9916]
          Length = 248

 Score = 93.0 bits (229), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 94/234 (40%), Gaps = 9/234 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +   V  +  L      +   RG  +  DL+QE  +GL++ +E+F+   G +FS+YAM  
Sbjct: 6   RNAQVLRHCGLAHLATHRQLGRGCGEHDDLLQEAYLGLIQGSERFEASRGNRFSSYAMRL 65

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
               I     D+   +RIP  +     + +R   + ++  +   +  ++A  L + +E  
Sbjct: 66  ATGRIQHFRRDRVRCLRIPWRLDALHTQAIRLQEQRAHAQRPPFSDHQLASTLGVSLERW 125

Query: 564 RKVL--KITKEPISLETPIGDED--TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           R+ L        ISL+ P   +   +   GD    +       S      RE     L  
Sbjct: 126 RQALIGHQQHHLISLDQPRSRDRYPSDADGDIPLIQELSDMTVSCDDDQQREWLQEQLEQ 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           L  R    +   +  G     + +++ K+   +   IR+I   ++ KL+  + +
Sbjct: 186 LPQRARSCIERHYLAGT----SAKDIAKEDGCSCSEIRRILRSSLEKLRQLANT 235


>gi|325262838|ref|ZP_08129574.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
 gi|324031932|gb|EGB93211.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
          Length = 212

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 64/256 (25%), Positives = 103/256 (40%), Gaps = 58/256 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ SE ++    ++K       AK  ++E NLRLV  V KKY        DLI  
Sbjct: 10  SFPNPLTPSEEKYY---MQKYTEGDLQAKHVLIERNLRLVAHVIKKYQYLDEDPEDLISI 66

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+   G + + YA   V+  I                        +R  
Sbjct: 67  GTIGLIKAVVTFNPDKGNRLAAYASKCVENEILMY---------------------LRAK 105

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
           ++ S +                               ISL  PIG +   +   L D IE
Sbjct: 106 KKTSKE-------------------------------ISLYEPIGTDREGNEIKLYDIIE 134

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
              A  P    ++ N+++   +V   L+ RE  VL+MR+G+    ++T  E+ +Q  ++R
Sbjct: 135 TDEADVPEKIHLKENIQKLYDKVENELSQRERLVLKMRYGLYNGEEYTQREIARQLGISR 194

Query: 654 ERIRQIEAKAIRKLKH 669
             + +IE  A+ KL+ 
Sbjct: 195 SYVSRIEKSAVEKLRE 210


>gi|167628365|ref|YP_001678864.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591105|gb|ABZ82853.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 233

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 61/274 (22%), Positives = 104/274 (37%), Gaps = 61/274 (22%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   +  I  + + I + +    +S +E  + ++ ++        A+ +++E NLRLV 
Sbjct: 9   LIVPFIKGITALLSYISNNAFPQPLSDTEEAYCLARLK---EGDEQARNKLIEHNLRLVA 65

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+   G    DLI  G IGL+KA   FD   G K +TYA   ++  I         
Sbjct: 66  HLVKKFDGTGENNDDLISIGTIGLIKAINTFDASKGTKLATYAARCIENEILMH------ 119

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                          +R  ++M  +                               +SL 
Sbjct: 120 ---------------LRAMKKMRGE-------------------------------VSLY 133

Query: 578 TPIGDE---DTSHLGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            PIG +   +   L D +  D  AVS +        R  +     S   RE  V+ +R+G
Sbjct: 134 DPIGVDKEGNEITLIDILGTDPEAVSDIVENALEQARLLSKLKKLS--KRERYVIELRYG 191

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +      T  E+ K   ++R  + +IE +AI KL
Sbjct: 192 LLSGCRQTQREIAKNLGISRSYVSRIEKRAIMKL 225


>gi|145297471|ref|YP_001140312.1| LafS [Aeromonas salmonicida subsp. salmonicida A449]
 gi|22758825|gb|AAN04223.1| LafS [Aeromonas salmonicida]
 gi|142850243|gb|ABO88564.1| LafS [Aeromonas salmonicida subsp. salmonicida A449]
          Length = 235

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 104/242 (42%), Gaps = 21/242 (8%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           +  +       +   + ++   L LV   A    ++        D+ Q G +GL++A  +
Sbjct: 5   IHRLSLPIRPLARVSRAILTRYLPLVKRAASHLRSQVSACFDQEDMEQVGMMGLLEAWRR 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D     +F +YA   ++ A+   +         P  +R ++H   +  R + N++ R P
Sbjct: 65  YDSEPDPQFESYAFKRIRGAMLDELRRLDW---RPRQLRQQVHSHNQAQRELYNRLGRAP 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T +E+A  L   VE VR++   +            E    L +++E+    +P   +   
Sbjct: 122 TEQELAVSLNCTVEEVRQLAYAS----------QAEALQSLEEWLEN-GGKAPATESDDV 170

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++  T ++VL SL  RE+ +L + +      +  ++E+     +T  R+ Q+  + + +L
Sbjct: 171 DMAMTISKVLTSLDKREQLLLSLYY----QQELNMKEIALVLGLTESRVCQLHKQCVLQL 226

Query: 668 KH 669
           K 
Sbjct: 227 KQ 228


>gi|213028661|ref|ZP_03343108.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 88

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 59/75 (78%), Positives = 64/75 (85%)

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR  T  VLA LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 13  ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 72

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 73  LRHPSRSEVLRSFLD 87


>gi|299534757|ref|ZP_07048087.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
 gi|298729845|gb|EFI70390.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
          Length = 256

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 99/234 (42%), Gaps = 12/234 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWC 491
           R        A   +++  + LV    ++      + +   DL   G +GL  A  KFD  
Sbjct: 15  RWIHERDPDAGDLLIKKYISLVSYHVQRIGAGLPKSVSRDDLTSLGMVGLFDALNKFDIN 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              KF TYA + V+ AI   +  +     +P   R+K  K+     ++  K  R  TPEE
Sbjct: 75  RDLKFDTYASFRVRGAIIDGLRKEDW---LPRSAREKAKKLDAQIEQLEQKYMRHVTPEE 131

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +A+ + + VE V +          +S+      E+T      I D    +P  + I++ L
Sbjct: 132 LAEHMEVSVEDVYQTVQEHFFSNVLSINEQQDQEETDGKTFVIRDDTTKTPEQAIIKSEL 191

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +     +  L  +E+ VL + +      + TL E+G+   ++  RI QI +KA
Sbjct: 192 LDDLAENIQKLNEKEQLVLSLFY----TEELTLTEIGEMLELSTSRISQIHSKA 241


>gi|294084434|ref|YP_003551192.1| RNA polymerase sigma 28 subunit FliA/WhiG [Candidatus
           Puniceispirillum marinum IMCC1322]
 gi|292664007|gb|ADE39108.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Puniceispirillum marinum IMCC1322]
          Length = 241

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/224 (22%), Positives = 99/224 (44%), Gaps = 14/224 (6%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++  ++ LV  +A     R     +  DL+Q G  GL+ AA+ +    G  FS+YA   +
Sbjct: 15  LIRDHMELVRQIAWHIHGRVHASAEIEDLVQIGYYGLVMAAQNYTVQEGATFSSYASIRI 74

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + +I   +   S   R  + M+ K  +       +  K+ R+P+ +E+A  L +  E +R
Sbjct: 75  RGSIVDHLRKNSNLCRTTIQMQKKARQSEEI---LRQKLGRDPSIDEVASDLDIAPEEMR 131

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +  +  +  +        ++ S    F+ ++N      S     LR+     L +L  RE
Sbjct: 132 EWEQAFQANVHQSLDNVYDEFSIW--FVSNENTPEDNIS--DNELRDVLKDALTTLPERE 187

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             V+++ +      +  + E+ +   VT  R+ QI+  AI +L+
Sbjct: 188 ALVIQLYYV----EELNVYEIAEILDVTTGRVSQIKKAAIARLR 227


>gi|160939772|ref|ZP_02087119.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437206|gb|EDP14971.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
          Length = 209

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 99/250 (39%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +  +      +     A+  ++E N+RLV  V KKY        DL+  G IGL
Sbjct: 8   LSAGEEKEYLER---CKEGDQSARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+   G + +TYA   V+  I                       ++R +R+ S 
Sbjct: 65  IKAVNTFNVDKGSRLATYAARCVENEILM---------------------LLRASRKYSK 103

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               +SL  PIG +       L D IE  N  
Sbjct: 104 E-------------------------------VSLFEPIGVDKDGETVSLVDVIEMDNKE 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +     ++ +++E      + LT  E+ VL MR+G+    +HT  E+  +  ++R  + +
Sbjct: 133 TLDTMILKQDVKELYEAFESCLTETEKTVLGMRYGLYRGKEHTQREIAGKLGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE KAI K++
Sbjct: 193 IEKKAIEKIR 202


>gi|91981592|gb|ABE68138.1| RNA polymerase subunit D [Pseudomonas sp. Q12-87]
          Length = 219

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 57/126 (45%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ET +SI
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETRLSI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|90406802|ref|ZP_01214994.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
 gi|90312039|gb|EAS40132.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
          Length = 235

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 94/230 (40%), Gaps = 11/230 (4%)

Query: 447 EMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E++E +  LV  +A     R    +   DL+Q G IGL++AA  FD   G  F T++   
Sbjct: 13  ELIEKHTGLVQKIAYHLMARLPASVLVDDLLQSGMIGLLEAARNFDGSKGASFETFSGIR 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ A+   +        +P  +     ++      +  +   +    EIA +L + +   
Sbjct: 73  IRGAMLDEMRRGDW---VPRSVHKNSREISNAISAVEKRNAGDAKESEIASQLGVTLAKY 129

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +++L+       +         +     + +       +   ++   E    ++  L  R
Sbjct: 130 QQMLRDVNCAKLVNYEDLGGAEATFSSSV-NSEVDPTFNCVSESEYSEQLLLMIKQLPER 188

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           E  VL + +    + +  L+E+G    +   R+ QI ++A+ +LK  +++
Sbjct: 189 EALVLSLYY----DEELNLKEIGLVLELGESRVSQILSQALHRLKAKAQT 234


>gi|15615119|ref|NP_243422.1| sporulation sigma factor SigE [Bacillus halodurans C-125]
 gi|10175176|dbj|BAB06275.1| RNA polymerase sporulation mother cell-specific (early) sigma-29
           factor [Bacillus halodurans C-125]
          Length = 237

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 100/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  H++  +          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 37  LSKEEEAHLLKKL---PSGDKAVRSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +               + +K+         
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMYLR--------------RNNKIR-------- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +   + +
Sbjct: 132 ------------------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDI 161

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + R+   + L +LT RE++++ +RFG+    + T ++V     +++  I +
Sbjct: 162 ITRGIEEKVD-RKLLMKALHTLTDREKQIMELRFGLAGGEEKTQKDVADLLGISQSYISR 220

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 221 LEKRIIKRLQK 231


>gi|291550014|emb|CBL26276.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus torques L2-14]
          Length = 264

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 58/265 (21%), Positives = 97/265 (36%), Gaps = 58/265 (21%)

Query: 410 RNEIKSISVETGISISEFRHIVSMVRKG--ECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + EI  I     +           V +         A+K ++E NLRLV+ +AKK+ N G
Sbjct: 45  QQEIHYIGGSEVLPPPLENEKEREVVRWLGTDRDEKARKILIEHNLRLVVYIAKKFDNTG 104

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLI  G IGL+KA   F+     K +TYA   ++  I   +   S           
Sbjct: 105 VGVEDLISIGTIGLIKAINTFNPSKKIKLATYASRCIENEILMYLRRNSK---------- 154

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                                                     TK  +S++ P+  +   +
Sbjct: 155 ------------------------------------------TKMEVSIDEPLNVDWDGN 172

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLE 643
             L   I      +          R+   R L  L+ RE+ ++RMRFG+      + T +
Sbjct: 173 ELLLSDILGTEEDTIYRDLEDEAERKILFRALNKLSGREKLIVRMRFGLDHPEGKEMTQK 232

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           EV  Q  +++  I ++E K + +L+
Sbjct: 233 EVADQLGISQSYISRLEKKIMHRLR 257


>gi|254437394|ref|ZP_05050888.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198252840|gb|EDY77154.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 207

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/201 (24%), Positives = 90/201 (44%), Gaps = 11/201 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DL+Q G IGL++AA+++    G  F +YA+  ++ AI   +   +    +      
Sbjct: 5   VEIEDLLQVGLIGLIEAAQRYTRQEGVSFESYAVLRIRGAIYDYLRKNT---NLGRKAIL 61

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               V      +S K+ REPT  E+A+ L+M ++ + K  +      S    + DE   H
Sbjct: 62  TSKAVKAALASLSQKLGREPTQPELAEALSMSLQELSKWAQNVNS--SYHNSLQDEYDEH 119

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
              F    N  +      +  L++     L SL  RE  VL++ +      +  L E+  
Sbjct: 120 SLWF--SSNEPTTEHLVDRGRLKDALLAALVSLPKREALVLQLYYV----EELNLYEIAA 173

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              VT  R+ Q+++ A +K++
Sbjct: 174 VLEVTPGRVSQLKSAAFKKMQ 194


>gi|299472548|emb|CBN77333.1| RNA polymerase sigma factor SigD [Ectocarpus siliculosus]
          Length = 825

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 73/278 (26%), Positives = 123/278 (44%), Gaps = 28/278 (10%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL----DLIQEGNIGLMKAAE 486
           V  +R+   E   AK+E+V  NL LV  + K Y            DL Q+  +GL++A E
Sbjct: 97  VESLRQALDEGEKAKQELVLDNLNLVDIIVKNYVGTFAYGRFTEKDLTQDATVGLIRAVE 156

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KFD   G+ F+TY  WWV++ +   + + +  +RIP     +I KV R    +  ++ R 
Sbjct: 157 KFDPEKGFFFATYGRWWVRKYLHEGVQNHNRMVRIPNSAAYRIAKVKRVRDELEGELGRA 216

Query: 547 PTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT-------SHLGD-FIEDKNA 597
           PT  EIA +  + V+ V   L + +     L+  +G           SH G+ F+   + 
Sbjct: 217 PTKPEIALETDLTVQQVEACLEQDSFRIERLDGYMGHGFGMADTVFASHFGEGFLYGSDM 276

Query: 598 VSPLDSA----------IQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVG 646
           ++               IQ++LR   +      L   E   L +R+G+     +++E+  
Sbjct: 277 LTHPGETPAPTVEGEKVIQSSLRGDLSSAFVRLLDATERECLVLRYGLHDGVTNSIEQTA 336

Query: 647 KQFCVT-RERIRQIEAKAIRKLKH---PSRSKKLRSFL 680
                   + +R I  +A+ KL+    P   KKL S+L
Sbjct: 337 AIMDFCDPDDVRIITTQAMAKLRDGCLPEERKKLMSYL 374


>gi|222431377|gb|ACM50641.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431379|gb|ACM50642.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431381|gb|ACM50643.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431383|gb|ACM50644.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431385|gb|ACM50645.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431387|gb|ACM50646.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431389|gb|ACM50647.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431391|gb|ACM50648.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431393|gb|ACM50649.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|222431395|gb|ACM50650.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 222

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/270 (14%), Positives = 91/270 (33%), Gaps = 49/270 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T   ++     +      L ++  L   I P+               K   +  + + 
Sbjct: 1   PGTVDHILSEYTRVTTEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVEAKVAKADDDTDD 58

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D+ + ++ + E+ +                          D   +A    A+ DQ+    
Sbjct: 59  DEAESSDDEEEAESGP------------------------DPVIAAQRFGAVADQM---- 90

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                   E+ R+            K  +++         L +L   + L   + + LVE
Sbjct: 91  --------EITRKALK---------KHGRNNKAAIAELLALAELFMPIKLVPKQFEGLVE 133

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++     R+   E  +++L      + R  FL +    E+D  W   A    + ++   +
Sbjct: 134 RVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPSNEVDESWSD-ALAKGKSKYAEAI 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
                 I++ + ++ ++  ETG++I+E + 
Sbjct: 193 GRVQPDIIRCQQKLIALETETGLTIAEIKD 222


>gi|213421295|ref|ZP_03354361.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 191

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 88/180 (48%), Gaps = 7/180 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDT 585
                + +T +R+    + E   E +A++L +  + VR++  ++  + ++ +    DE  
Sbjct: 134 KLFFNLRKTKQRLGWFNQDE--VEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESD 191


>gi|295091014|emb|CBK77121.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 292

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 54/244 (22%), Positives = 101/244 (41%), Gaps = 13/244 (5%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
             +E+       +  +A KY +      DL QEG + L  A   +    G  F  YA +W
Sbjct: 19  CMEELYSQVKAFIHMLACKYRSAS-DVEDLEQEGFLALYDAVRGYQPDKG-AFLAYAAYW 76

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I R I      + IP   + +  ++ +       +  + P        L + +E  
Sbjct: 77  IEARIRRFIQK-DSCLHIPAGRQGQAKELQQFQEAYEKEYGQTPPDAVSCCFLGLTLEEY 135

Query: 564 --RKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNA--VSPLDSAIQANLRETTTRVL 617
             RK   +T   +SL+ PI D++     LGD +    +     +       L+     ++
Sbjct: 136 QERKKTALTGRCLSLDAPITDQEGEGLTLGDTVAASGSLEEDIIGQIDCQELKRLLWGMV 195

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            SL   +  ++R R+  G     ++ E+  +   + E +R  +AKAIR L++P    +LR
Sbjct: 196 NSLPGMQPAIIRARYQEG----KSIREIAAEQGNSPEEVRGQQAKAIRTLRNPKNLNRLR 251

Query: 678 SFLD 681
            +L+
Sbjct: 252 CYLE 255


>gi|54654475|gb|AAV37114.1| RpoD [Vibrio cyclitrophicus]
          Length = 171

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 31/153 (20%), Positives = 58/153 (37%), Gaps = 2/153 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L     R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKATIATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             ET +++   + I   +  GE +A  AKKEMV
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKEMV 171


>gi|330936784|gb|EGH40944.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 176

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/135 (35%), Positives = 76/135 (56%), Gaps = 3/135 (2%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
                  ++       ++   +  +  I     +S  E  H   +    +      +K M
Sbjct: 44  KHSTSLKQHKYIDYTRALDATQLYLNEIGFSPLLSPEEEVHFARL---SQSGDPAGRKRM 100

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E+NLRLV+ +A++Y NRGL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I
Sbjct: 101 IESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 160

Query: 509 TRSIADQSCTIRIPV 523
            R+I +Q+ TIR+  
Sbjct: 161 ERAIMNQTRTIRLRF 175



 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 50/131 (38%), Gaps = 12/131 (9%)

Query: 54  PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
           P  ++  E +      L   GI + +  + +          +       S  L++ K   
Sbjct: 8   PEFDIDDEVL------LMEAGIVLKEASNEKQPAAVSGRTKVKH-----STSLKQHKYID 56

Query: 114 DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
                D  ++YL E+G   LLS E E+  A+  ++G       + ES L     I  R  
Sbjct: 57  YTRALDATQLYLNEIGFSPLLSPEEEVHFARLSQSGDPAGRKRMIESNLRLVVKIARRY- 115

Query: 174 LNDGTTLLREI 184
           +N G +LL  I
Sbjct: 116 VNRGLSLLDLI 126


>gi|325677679|ref|ZP_08157331.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
 gi|324110647|gb|EGC04811.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
          Length = 231

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 95/253 (37%), Gaps = 63/253 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  SE R     + +       A+  ++  NLRLV  + KKY        DLI  G IGL
Sbjct: 34  LGASEERDCFEKMAQ---GDKSARDRLISHNLRLVAHIIKKYYAAASDQDDLISIGTIGL 90

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD+  G +F+TY    V+  I                                 
Sbjct: 91  IKAVQTFDYTKGTRFATYGSRCVENEILMHFRA--------------------------- 123

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                    LK +   +S+E P   +   +   L D + D   V
Sbjct: 124 -------------------------LKKSASDVSIEEPAQSDKDGNSLCLMDLLTDGEDV 158

Query: 599 SPLDSAIQANLR-ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           +     I+  +R E    +L   L  RE  V+ MR+G+   +  T  EV ++ C++R  +
Sbjct: 159 A---DRIELLMRAEQLYGILGDCLDDREREVVVMRYGLYGGSALTQREVSEKLCISRSYV 215

Query: 657 RQIEAKAIRKLKH 669
            +IE +A+ KL+ 
Sbjct: 216 SRIEKRALEKLRE 228


>gi|261419324|ref|YP_003253006.1| sporulation sigma factor SigE [Geobacillus sp. Y412MC61]
 gi|297530706|ref|YP_003671981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766140|ref|YP_004131641.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
 gi|261375781|gb|ACX78524.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC61]
 gi|297253958|gb|ADI27404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111006|gb|ADU93498.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
          Length = 239

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +++ +         A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LTKEEEEQLIARL---AAGDDTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   +                         
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNN------------------------- 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                VR         +S + P+  +   +   L D +  ++ V
Sbjct: 131 --------------------KVRAE-------VSFDEPLNIDWDGNELLLSDVLGTEDDV 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              D     + R      L  L+ RE++++ +RFG+    + T ++V     +++  I +
Sbjct: 164 ITKDLEADVD-RRLLLNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISR 222

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 223 LEKRIIKRLRK 233


>gi|239934582|emb|CAR94605.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 220

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 44/175 (25%), Positives = 74/175 (42%), Gaps = 3/175 (1%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A  +  L         G  ++     K   L++KL      L L+    D+L+ Q+ 
Sbjct: 46  EEAARRFDSLSKTFVQVQKGMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLITQIR 105

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
                I + E +++ L     G+ R  F+      E +  W+            + +A  
Sbjct: 106 RSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAH-LAKL 164

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            + I   + ++  +   T +SI+  + I   +  GE +A  AKKEMVEANLRLVI
Sbjct: 165 REEIEAQQKKLMGVEELTHLSIAGIKEINREIAVGEAKARRAKKEMVEANLRLVI 219


>gi|239934364|emb|CAR92312.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 225

 Score = 92.6 bits (228), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/270 (14%), Positives = 89/270 (32%), Gaps = 46/270 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +  G   L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTGGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKA--------------- 96

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 97  --------------------LKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVS 432
            ++I++ + ++  +  E  + I++ + I  
Sbjct: 196 KENIVRCQQKLIELGQECDLVIADIKDINR 225


>gi|255525679|ref|ZP_05392612.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296185437|ref|ZP_06853847.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
 gi|255510665|gb|EET86972.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296050271|gb|EFG89695.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
          Length = 235

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 54/248 (21%), Positives = 97/248 (39%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +VS +  GE      +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 35  LSKKEEDDLVSKLDGGE---EKVRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +   S                V+       
Sbjct: 92  IKAVNTFDPSKKIKLATYASRCIENEILMYLRRNSK---------------VKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   D   + + IED+      
Sbjct: 137 PLNIDWDGNEL-----------------------LLSDILGTDNDVVYNLIEDEVD---- 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     +  L  RE+ ++ +RFG+    + T +EV     +++  I ++E 
Sbjct: 170 --------KQLLMVAMKKLNDREKEIVNLRFGLNGQGEKTQKEVADMLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           + I++LK 
Sbjct: 222 RIIKRLKK 229


>gi|168182610|ref|ZP_02617274.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|170759960|ref|YP_001787849.1| sporulation sigma factor SigE [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237795972|ref|YP_002863524.1| sporulation sigma factor SigE [Clostridium botulinum Ba4 str. 657]
 gi|169406949|gb|ACA55360.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182674165|gb|EDT86126.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|229261167|gb|ACQ52200.1| RNA polymerase sigma-E factor [Clostridium botulinum Ba4 str. 657]
          Length = 235

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 93/248 (37%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  + V  +          +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 35  LSKEEEEYFVQRL---INGDEKVRSVLIERNLRLVVYIARKFENTGICIEDLVSVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I   +   S                V+       
Sbjct: 92  IKAVNTFKPDKKIKLATYASRCIENEILMYLRRNSK---------------VKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   D   + + IED+      
Sbjct: 137 PLNIDWDGNEL-----------------------LLSDILGTDNDEVYNLIEDEVD---- 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     +  L  RE+ ++R+RFG+    + T +EV     +++  I ++E 
Sbjct: 170 --------KQLLLLAMKKLNEREKEIVRLRFGLNGKREKTQKEVADMLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           + I+ LK 
Sbjct: 222 RIIKTLKK 229


>gi|308803162|ref|XP_003078894.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
 gi|116057347|emb|CAL51774.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
          Length = 485

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 75/266 (28%), Positives = 124/266 (46%), Gaps = 16/266 (6%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKK-------YTNRGLQFLDLIQEGNIGLMKAA 485
            +R    +  IA++++V AN+ L   VA            R +   D+I EG  GL++A+
Sbjct: 169 KMRAVMRQGKIARQKLVSANIELAAKVATDVFHTFSPMERRSISRQDMIHEGVTGLVRAS 228

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EKFD  LG  FSTYA  W KQA+TR + +   TIR+P  +  +  +    ++RM  ++ R
Sbjct: 229 EKFDPALGCAFSTYAYNWTKQAVTRGVLNNGRTIRVPEQVLYERREAHELSKRMEIELGR 288

Query: 546 EPTPEEIAKK-LAMPVEGVRKVLKIT-KEPISLETPIGDEDTSHLGDF-------IEDKN 596
            PT  EIA +     V+ ++ ++ I  + P+SL+     ++     +         E  +
Sbjct: 289 RPTLHEIAARSQKFSVDKLQLLVGIAKQHPLSLDILGVGDEERDGDETGLSGTWENEMGS 348

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                 +     LR+   + L  L+  E  VL+ RFG+      T  E+G +   + E +
Sbjct: 349 TDEITRTIELEFLRDDIKKTLNELSSDEAYVLKHRFGLVGGEFMTNAEIGSRIGKSAEGV 408

Query: 657 RQIEAKAIRKLKHPSRSKKLRSFLDG 682
           R IE +A+ +LK       L   L G
Sbjct: 409 RYIEKRALERLKSTPDFSDLAQHLKG 434


>gi|226225717|ref|YP_002759823.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
 gi|226088908|dbj|BAH37353.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
          Length = 251

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 103/255 (40%), Gaps = 16/255 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
             + +  +     A+  ++E +L LV  VA++ +        F +L+  G IGLM A E 
Sbjct: 3   NKLWQSYQAGNPSARDRLLEEHLGLVHHVARQVSRTLAVRADFDELVSAGTIGLMTALEG 62

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G  FST+A   ++ AI   +  Q     +P  +R K  ++            R P
Sbjct: 63  FDASRGLAFSTFAAPRIRGAILDELRKQD---HVPRSIRRKTREITAAREAFQRASGRAP 119

Query: 548 TPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHL--GDFIEDKNAVSPLDS 603
              E+A++L + +E + +     +    I L+   G+ + +     + +         DS
Sbjct: 120 EDRELAEQLNVDLETLWRWQADVEGAHHIPLDRAPGERENTTPVPAEVLTSGEESGVEDS 179

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                        +  L  +E  VL + +      +  L E+ K   +T  R+ QI +KA
Sbjct: 180 LTHEQEVSHLKDAILRLKEQERIVLSLYYF----EELKLHEIAKVLELTESRVSQIRSKA 235

Query: 664 IRKLKHPSRSKKLRS 678
           + KL+     K LR 
Sbjct: 236 LSKLR--VELKPLRD 248


>gi|228913674|ref|ZP_04077301.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229090035|ref|ZP_04221286.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228693265|gb|EEL46975.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228845962|gb|EEM90986.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 196

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/197 (19%), Positives = 85/197 (43%), Gaps = 8/197 (4%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+    
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAI 61

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIED 594
             +++ ++R P   EIA  L +  E V +++         SL+  + +         IE 
Sbjct: 62  EELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIE- 120

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +         Q   R     +   L   E+ V+   F      +   ++ G++  +++ 
Sbjct: 121 -SVGEVEQGYEQTERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLGISQM 175

Query: 655 RIRQIEAKAIRKLKHPS 671
            + +I+ +AI KLK  +
Sbjct: 176 HVSRIKRQAISKLKQAA 192


>gi|154504525|ref|ZP_02041263.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
 gi|153795007|gb|EDN77427.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
          Length = 208

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 102/257 (39%), Gaps = 58/257 (22%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             S    ++ SE +     ++K       AK  ++E NLRLV  V KKY        DLI
Sbjct: 1   MKSFPNPLTPSEEKEY---IQKYTEGDLQAKHILIERNLRLVAHVIKKYQYVDEDPEDLI 57

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+KA   F+   G + + YA   V+  I                        +R
Sbjct: 58  SIGTIGLIKAIVTFNPSKGNRLAAYASKCVENEILMH---------------------LR 96

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDF 591
             ++ S +                               ISL  PIG +   +   L D 
Sbjct: 97  ARKKTSKE-------------------------------ISLYEPIGTDREGNEIKLYDI 125

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE      P    ++ N+++   +V   L+ RE+ VL+MR+G+    ++T  EV KQ  +
Sbjct: 126 IETDEDDIPERVCLKENIQKLYEKVENELSQREKLVLKMRYGLYGGEEYTQREVAKQLGI 185

Query: 652 TRERIRQIEAKAIRKLK 668
           +R  + +IE  A+ KL+
Sbjct: 186 SRSYVSRIEKSAVEKLR 202


>gi|239934370|emb|CAR92315.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 225

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 34/270 (12%), Positives = 85/270 (31%), Gaps = 46/270 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTDGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKAA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D +     ++++        E A      + E  + +   L              
Sbjct: 52  GDEKDDEDEDDSDTEEEEGDGGPDSEVARLRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E    L   + L   + + LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEAPAILFMPIKLVPKQYEALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 SALSQIHAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVS 432
            + I + + ++  +  E  ++I++ + I  
Sbjct: 196 KEDIQRCQQKLIELEQECDLAIADIKDINR 225


>gi|229541193|ref|ZP_04430253.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
 gi|229325613|gb|EEN91288.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
          Length = 239

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 102/263 (38%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     +++K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGNEALPPPLSKEEEEMLLKKLPAGDKAARSILIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +               + 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLR--------------RN 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
           +K+                                         +S + P+  +   +  
Sbjct: 130 NKLR--------------------------------------SEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +   D     + ++     L  L+ RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDIITRDLEANVD-KKLLYSALHRLSDREKQIMELRFGLKGQEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|239826532|ref|YP_002949156.1| sporulation sigma factor SigE [Geobacillus sp. WCH70]
 gi|239806825|gb|ACS23890.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. WCH70]
          Length = 239

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 95/241 (39%), Gaps = 56/241 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+  
Sbjct: 46  MLIKKLSSGDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPE 105

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              K +TYA   ++  I   +   +                                   
Sbjct: 106 KKIKLATYASRCIENEILMYLRRNN----------------------------------- 130

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQAN 608
                      VR         +S + P+  +   +   L D +  ++ V   D     +
Sbjct: 131 ----------KVRAE-------VSFDEPLNIDWDGNELLLSDVLGTEDDVITKDLEADVD 173

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R      L  L+ RE++++ +RFG+    + T ++V     +++  I ++E + I++L+
Sbjct: 174 -RRLLFNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 232

Query: 669 H 669
            
Sbjct: 233 K 233


>gi|317128262|ref|YP_004094544.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473210|gb|ADU29813.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 106/265 (40%), Gaps = 57/265 (21%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +K+ +    ++  E R     +R+       A+  ++E NLRLV  + KK+ N   +  D
Sbjct: 22  VKNNAFPQPLNAKEEREY---IRRMNEGDDEARNLLIEHNLRLVAHIVKKFENTREENED 78

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA E +    G K +TYA   ++  I   +                    
Sbjct: 79  LISIGTIGLIKAIESYSPGKGTKLATYAARCIENEILMHLRA------------------ 120

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                                      ++ VRK        +SL  PIG +   +    I
Sbjct: 121 ---------------------------LKKVRK-------DVSLHDPIGQDKEGNEISLI 146

Query: 593 EDKNAVSPLD-SAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +   A +      IQ N+ ++   + +  L  RE+ V+  RFG+ MN + T  E+ K+  
Sbjct: 147 DVLQAETEDVVETIQLNMEKKQIYQYIHVLDEREKEVVVGRFGLDMNKERTQREIAKELG 206

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKK 675
           ++R  + +IE +A+ KL H     +
Sbjct: 207 ISRSYVSRIEKRALMKLFHEFYKHQ 231


>gi|254459646|ref|ZP_05073062.1| flagellar-specific RNA polymerase sigma factor [Rhodobacterales
           bacterium HTCC2083]
 gi|206676235|gb|EDZ40722.1| flagellar-specific RNA polymerase sigma factor [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 219

 Score = 92.2 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 52/231 (22%), Positives = 97/231 (41%), Gaps = 16/231 (6%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
            +R V           ++F DL+Q G +GL++AA+++    G  F +YA+  V+ AI   
Sbjct: 1   MVRKVAHHVHSRVRSIVEFDDLLQIGLMGLIEAAQRYTRQEGISFESYAVIRVRGAINDF 60

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           +   S   R  + +     +V     ++ + + R P   E+AK + + ++      +   
Sbjct: 61  LRKNSALSRKSMKI---NKEVNEARNKLVHDLGRAPEGHEVAKAVGLSLDEFTAWEQTLN 117

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              S    I DE   H   F      +       +A L+E     L +L  RE  VL++ 
Sbjct: 118 S--SYHNSIQDEYDEHSMWFATADAPIEQELD--RARLKEALLYALKTLPEREALVLQLY 173

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +      +  L E+     VT  R+ QI++ A +K++       L+ ++D 
Sbjct: 174 YV----EELNLFEIAAVLDVTSGRVSQIKSSAFKKMQ-----PLLKDYIDN 215


>gi|187778862|ref|ZP_02995335.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
 gi|187772487|gb|EDU36289.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
          Length = 234

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E ++ +  ++K     ++AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPKPLSDEEEKYYLDRLKK---GDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I                 +K  +  
Sbjct: 83  GTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIR---------------NNKKTKGE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDILSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  + +  +++   ++   L  RE++V++MR+G+      T  E+     ++R  +
Sbjct: 154 DSIIEIVSTKIEVKKLYGKIETCLRGREKKVIQMRYGLKDGRPRTQREIAGILNISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 214 SRIEKKALKKL 224


>gi|300854418|ref|YP_003779402.1| RNA polymerase sigma-E factor [Clostridium ljungdahlii DSM 13528]
 gi|300434533|gb|ADK14300.1| RNA polymerase sigma-E factor precursor [Clostridium ljungdahlii
           DSM 13528]
          Length = 241

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 97/248 (39%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +V  +          +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 41  LSKKEEEDLVLKL---VSGDEKVRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S T               +       
Sbjct: 98  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSKT---------------KAEISFYE 142

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   D   + +FIED+      
Sbjct: 143 PLNIDWDGNEL-----------------------LLSDILGTDNDVVYNFIEDEVD---- 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     +  L+ RE+ ++ +RFG+   ++ T +EV     +++  I ++E 
Sbjct: 176 --------KQLLMLAMKKLSDREKEIVNLRFGLNGKSEKTQKEVADLLGISQSYISRLEK 227

Query: 662 KAIRKLKH 669
           + I++L+ 
Sbjct: 228 RIIKRLRK 235


>gi|291543210|emb|CBL16319.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. 18P13]
          Length = 232

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 55/249 (22%), Positives = 98/249 (39%), Gaps = 56/249 (22%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            +S+     +  R G  +A  A++ ++  NLRLV+ +AKK+ + G+   DLI  G IGL+
Sbjct: 31  PLSKEAEAEAFARLGTGDAESARQTLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIGLI 90

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA   F      K +TYA   ++  I   +   S                          
Sbjct: 91  KAVNTFCPEKNIKLATYASRCIENEILMFLRKTSQYRSE--------------------- 129

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVS 599
                                          IS++ P+  +   +   L D +     + 
Sbjct: 130 -------------------------------ISIDEPLNIDWDGNELLLSDVLGTDEDIV 158

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 +A  +    + +  L PRE+R+++MRFG+    + T +EV  +  +++  I ++
Sbjct: 159 NRGIEAEAE-KSVLRQAVDGLEPREKRIMQMRFGLLGGREKTQKEVADEIGISQSYISRL 217

Query: 660 EAKAIRKLK 668
           E K IR+LK
Sbjct: 218 EKKIIRRLK 226


>gi|86157781|ref|YP_464566.1| sigma 28 (flagella/sporulation) [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774292|gb|ABC81129.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 232

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 102/240 (42%), Gaps = 22/240 (9%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
           + V +    A    + ++  +  L+   A++   R    ++  DL   G +GL++AA ++
Sbjct: 6   AAVARYGPPAPEPDEALLRRHATLLDRCARRLAARTGHAVEPGDLWSAGAMGLLEAARRY 65

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     +F T+A   V+ A+   +        +P  +R    +V+    R+   + REP 
Sbjct: 66  DASQDVRFETFAEHRVRGAMLDELR---RMDHLPRRLRADADRVLAARARLEQALGREPD 122

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           P EIA+   +P E V ++L +   P+        ED       +    A+        A 
Sbjct: 123 PVEIAEAAGLPAEQVGELLLLASPPV------PVEDDVAPAPAVPADEALGA------AE 170

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R    R +A+L  R    L++   +  +   T  E+ K   V+  R+ Q+ ++A ++L+
Sbjct: 171 RRGALARAVAALPER----LQVLLALYYDEALTYREIAKVLGVSEPRVCQLHSEAAKRLR 226


>gi|239934390|emb|CAR92325.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 223

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/268 (14%), Positives = 90/268 (33%), Gaps = 46/268 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + + +    L +I  L   I P+  G         + Q+ E  + +     V
Sbjct: 1   VDSILADYERVTNEGGRLSDI--LSGYIDPDDDG-------TAAPQEVEPQTPQSTSKPV 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D +     S+++       PE A      + E  + +   L              
Sbjct: 52  DDDKDDEDEEESESEEEEGDGGPDPEVARLRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   +I   E  +++L      + R  FL +    E +  W        + ++   +   
Sbjct: 137 DALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAA-GKSKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHI 430
            + I + + ++  +  +  ++I++ + I
Sbjct: 196 KEDIQRCQQKLIELEQQCELAIADIKDI 223


>gi|319649653|ref|ZP_08003809.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398815|gb|EFV79497.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 98/241 (40%), Gaps = 56/241 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+  
Sbjct: 46  MLLIKLPKGDKAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPE 105

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
              K +TYA   ++  I   +               + +K+                   
Sbjct: 106 KKIKLATYASRCIENEILMYLR--------------RNNKIR------------------ 133

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQAN 608
                                 +S + P+  +   +   L D +  ++ +   D     +
Sbjct: 134 --------------------SEVSFDEPLNIDWDGNELLLSDVLGTEDDIITKDLEANVD 173

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++   + L  L+ RE++++ +RFG+G   + T ++V     +++  I ++E + I++LK
Sbjct: 174 -KKLLLKALHQLSDREKQIMELRFGLGSGEEKTQKDVADMLGISQSYISRLEKRIIKRLK 232

Query: 669 H 669
            
Sbjct: 233 K 233


>gi|226939286|ref|YP_002794357.1| RpoS [Laribacter hongkongensis HLHK9]
 gi|226714210|gb|ACO73348.1| RpoS [Laribacter hongkongensis HLHK9]
          Length = 170

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/164 (29%), Positives = 87/164 (53%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +QS TIR+PVH+  +++  +R +R + ++I R+PT +EIA  +  P E VR+V+ + + 
Sbjct: 1   MNQSRTIRLPVHVIKELNVYLRASRHLESQIGRDPTIDEIAHLVGKPPEEVRRVMSLNER 60

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             SL+ P+  +    +G+ I D+    P        +       L  LT ++  V+  R+
Sbjct: 61  MASLDAPLDIDPMLTIGESIPDEQQEEPDIKLHGMQVNRYVQTWLKQLTDKQRLVIERRY 120

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           G+      TLEE+     +TRER+RQI+ + +  L+   R K +
Sbjct: 121 GLNGYEICTLEELADSLSLTRERVRQIQIEGLESLRRILRRKGI 164


>gi|91981556|gb|ABE68120.1| RNA polymerase subunit D [Pseudomonas sp. F96.27]
          Length = 220

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 37/267 (13%), Positives = 89/267 (33%), Gaps = 48/267 (17%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
            ++   + +      L +++            G+    +G +    E       +    +
Sbjct: 1   HILSEYNRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPPPIDAKAAKAD 49

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D E A     ++ ++    P  A      + +  + +   L                
Sbjct: 50  DDNDDEDAEAGDDEEEAESGPDPIIAAQRFGAVADQMEITRKAL---------------- 93

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  +++         L +L   + L   + + LVE++   
Sbjct: 94  -------------------KKHGRNNKAAIAELLALAELFMPIKLVPKQFEGLVERVRSA 134

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +A    
Sbjct: 135 LDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQP 193

Query: 405 SILKIRNEIKSISVETGISISEFRHIV 431
            I++ + ++ ++  ETG+SI+E + I 
Sbjct: 194 DIVRCQQKLSALETETGLSIAEIKDIN 220


>gi|148380490|ref|YP_001255031.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153932419|ref|YP_001384713.1| sporulation sigma factor SigE [Clostridium botulinum A str. ATCC
           19397]
 gi|153937804|ref|YP_001388234.1| sporulation sigma factor SigE [Clostridium botulinum A str. Hall]
 gi|153940530|ref|YP_001391830.1| sporulation sigma factor SigE [Clostridium botulinum F str.
           Langeland]
 gi|168180581|ref|ZP_02615245.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|170756639|ref|YP_001782077.1| sporulation sigma factor SigE [Clostridium botulinum B1 str. Okra]
 gi|187778871|ref|ZP_02995344.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226949888|ref|YP_002804979.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|148289974|emb|CAL84087.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152928463|gb|ABS33963.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152933718|gb|ABS39217.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. Hall]
 gi|152936426|gb|ABS41924.1| RNA polymerase sigma-E factor [Clostridium botulinum F str.
           Langeland]
 gi|169121851|gb|ACA45687.1| RNA polymerase sigma-E factor [Clostridium botulinum B1 str. Okra]
 gi|182668430|gb|EDT80409.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|187772496|gb|EDU36298.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226843077|gb|ACO85743.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|295319856|gb|ADG00234.1| RNA polymerase sigma-E factor [Clostridium botulinum F str. 230613]
 gi|322806803|emb|CBZ04372.1| RNA polymerase sporulation specific sigma factor SigE [Clostridium
           botulinum H04402 065]
          Length = 235

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 93/248 (37%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  + V  +          +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 35  LSKEEEEYFVQRL---INGDEKVRSVLIERNLRLVVYIARKFENTGICIEDLVSVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I   +   S                V+       
Sbjct: 92  IKAVNTFKPDKKIKLATYASRCIENEILMYLRRNSK---------------VKAEISFYE 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +  +    E+                       L + I   D   + + IED+      
Sbjct: 137 PLNIDWDGNEL-----------------------LLSDILGTDNDEVYNLIEDEVD---- 169

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   ++     +  L  RE+ ++R+RFG+    + T +EV     +++  I ++E 
Sbjct: 170 --------KQLLLLAMKKLNEREKEIVRLRFGLNGKREKTQKEVADMLGISQSYISRLEK 221

Query: 662 KAIRKLKH 669
           + I+ LK 
Sbjct: 222 RIIKTLKK 229


>gi|229031536|ref|ZP_04187536.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
 gi|229075661|ref|ZP_04208643.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|229098375|ref|ZP_04229320.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|229104467|ref|ZP_04235134.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|229117401|ref|ZP_04246777.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|229162840|ref|ZP_04290797.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|229174571|ref|ZP_04302101.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228608876|gb|EEK66168.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228620722|gb|EEK77591.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|228666011|gb|EEL21477.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|228678909|gb|EEL33119.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|228684992|gb|EEL38925.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|228707437|gb|EEL59628.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|228729825|gb|EEL80805.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
          Length = 239

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 152 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGEEEKTQKDVA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 211 DMLGISQSYISRLEKRIIKRLRK 233


>gi|150390631|ref|YP_001320680.1| sporulation sigma factor SigE [Alkaliphilus metalliredigens QYMF]
 gi|149950493|gb|ABR49021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 244

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E R +++ ++  E   S  +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 44  LSHDEERFLINKLKNDE---STVRTILIERNLRLVVYIARKFENTGIGVEDLISIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 101 IKAVNTFNPDKNIKLATYASRCIENEILMYLRRNSK------------------------ 136

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                        K  +S + P+  +   +   L D +   N +
Sbjct: 137 ----------------------------VKMEVSFDEPLNIDWDGNELLLSDILGTDNDI 168

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + +E     L  L+ RE +++ +RFG+    + T +EV     +++  I +
Sbjct: 169 IYKFLEEEVD-KELLKFALKKLSKRERKIMELRFGLQTGKERTQKEVADLLGISQSYISR 227

Query: 659 IEAKAIRKLKH 669
           +E + I +LK 
Sbjct: 228 LEKRIIIRLKK 238


>gi|290879078|emb|CBK39763.1| sigma factor of RNA polymerase [Pseudomonas reinekei]
          Length = 234

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 31/261 (11%), Positives = 81/261 (31%), Gaps = 48/261 (18%)

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           M+++   P T   ++     +      L +++            G+    +G +    E 
Sbjct: 1   MSAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAAEV 49

Query: 214 SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME 273
                 +    + + D + A     ++ ++    P  A      + +  + +   L    
Sbjct: 50  PPPIDPKAVKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKAL---- 105

Query: 274 DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
                                          +K  +++         L +L   + L   
Sbjct: 106 -------------------------------KKHGRNNKAAIAELLALAELFMPIKLVPK 134

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
           + + LVE++     R+   E  +++L      + R  FL +  G E+D  W   A    +
Sbjct: 135 QFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGK 193

Query: 393 GEWKNFVACEVDSILKIRNEI 413
            ++   +      I++ + ++
Sbjct: 194 SKYAEAIGRLQPDIIRCQQKL 214


>gi|89099620|ref|ZP_01172495.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
 gi|89085773|gb|EAR64899.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
          Length = 239

 Score = 92.2 bits (227), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 97/240 (40%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLIKLPKGDKAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +  +  +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTEEDIITKDLEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  LT RE++++ +RFG+G   + T ++V     +++  I ++E + I++LK 
Sbjct: 174 KKLLLKALHQLTDREKQIMELRFGLGSGEEKTQKDVADMLGISQSYISRLEKRIIKRLKK 233


>gi|229086469|ref|ZP_04218641.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
 gi|228696786|gb|EEL49599.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
          Length = 239

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 50/264 (18%), Positives = 99/264 (37%), Gaps = 59/264 (22%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 24  DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 83

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 84  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 129

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 130 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 151

Query: 588 -LGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
            L D +  D++ ++    A     R    + L  L  RE++++ +RFG+    + T ++V
Sbjct: 152 LLSDVLGTDEDIITKDLEATVD--RHLLMKALHQLNDREKQIMELRFGLAGEEEKTQKDV 209

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
                +++  I ++E + I++L+ 
Sbjct: 210 ADMLGISQSYISRLEKRIIKRLRK 233


>gi|56419662|ref|YP_146980.1| sporulation sigma factor SigE [Geobacillus kaustophilus HTA426]
 gi|56379504|dbj|BAD75412.1| DNA-directed RNA polymerase sigma-29 factor precursor (sigma-E)
           (stage II sporulation protein GB) [Geobacillus
           kaustophilus HTA426]
          Length = 239

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 97/251 (38%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   +++ +         A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LTKEEEEQLIARL---AAGDDTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   +                         
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNN------------------------- 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                VR         +S + P+  +   +   L D +   + V
Sbjct: 131 --------------------KVRAE-------VSFDEPLNIDWDGNELLLSDVLGTDDDV 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              D     + R      L  L+ RE++++ +RFG+    + T ++V     +++  I +
Sbjct: 164 ITKDLEADVD-RRLLLNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISR 222

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 223 LEKRIIKRLRK 233


>gi|285018163|ref|YP_003375874.1| RNA polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Xanthomonas albilineans GPE PC73]
 gi|283473381|emb|CBA15886.1| probable rna polymerase sigma factor for flagellar operon (sigma-f
           factor) protein [Xanthomonas albilineans]
          Length = 249

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 96/234 (41%), Gaps = 17/234 (7%)

Query: 449 VEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   G  F TYA   ++
Sbjct: 19  IAQHSDLVRRIAHHLAARLPASVEIDDLIQAGMIGLIEASRSYDADQGASFETYASIRIR 78

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            ++   I        +P  +  +        R++     R     E+A  + MP+    +
Sbjct: 79  GSMIDEIRRGDW---VPRSVHRRARDAASAIRKIEQNTGRAAAANEVAAAMEMPLPEYMR 135

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++       L      ED   L D I  K   +P     ++       + +A L  RE+
Sbjct: 136 LMEDAARGQVLSLESRIEDHGEL-DTIA-KGGPNPQQMLERSEFGRELGKAIAQLPEREQ 193

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            VL + +      +  L+E+G    V+  R+ QI  +A  +L+      +L++F
Sbjct: 194 LVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQATVRLR-----GRLKAF 238


>gi|152964789|ref|YP_001360573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151359306|gb|ABS02309.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 267

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 54/212 (25%), Positives = 94/212 (44%), Gaps = 20/212 (9%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L L  SVA  Y NRG  + DL+Q   +GL+KAA++FD   G++F+ YA   +   
Sbjct: 18  LVLEHLPLARSVAAHYRNRGEPYDDLVQVAYLGLVKAAQRFDPDTGHRFAAYAAPTITGE 77

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R   D    +R P  +++   +++            +   E +A++L   V  VR   
Sbjct: 78  VRRHFRDHGWNVRPPRRLQELRARLL--------AEDADTPEEVLAQRLDATVAEVRAAR 129

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +       +SL+   G ED   L + + D    +            T  R+ A L  RE 
Sbjct: 130 QASNAYSAVSLDAAHGPEDV-PLCELLADDADDTAAVDDAL-----TLRRITAGLDERER 183

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           R+L +RF      + T  E+  +  V++ ++ 
Sbjct: 184 RILHLRF----YREATQSEIAAEIGVSQMQVS 211


>gi|18310744|ref|NP_562678.1| sporulation sigma factor SigE [Clostridium perfringens str. 13]
 gi|110798939|ref|YP_696448.1| sporulation sigma factor SigE [Clostridium perfringens ATCC 13124]
 gi|110801836|ref|YP_699048.1| sporulation sigma factor SigE [Clostridium perfringens SM101]
 gi|168207289|ref|ZP_02633294.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210605|ref|ZP_02636230.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168217049|ref|ZP_02642674.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
 gi|169342673|ref|ZP_02863714.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625822|ref|ZP_02953588.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145425|dbj|BAB81468.1| probable transcription initiation factor sigma E [Clostridium
           perfringens str. 13]
 gi|110673586|gb|ABG82573.1| RNA polymerase sigma-E factor [Clostridium perfringens ATCC 13124]
 gi|110682337|gb|ABG85707.1| RNA polymerase sigma-E factor [Clostridium perfringens SM101]
 gi|169299179|gb|EDS81249.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661363|gb|EDT14046.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711254|gb|EDT23436.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|177908856|gb|EDT71348.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380960|gb|EDT78439.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
          Length = 235

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 97/251 (38%), Gaps = 53/251 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +S  E   +V+ +          +  ++E NLRLV+ +A+K+ N G+   DLI  G 
Sbjct: 32  PAPLSKEEEEELVNKL---GENDEAIRSILIERNLRLVVYIARKFENTGVGVEDLISVGT 88

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F+     K +TYA   ++  I   +   S                V+    
Sbjct: 89  IGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSK---------------VKAEIS 133

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
               +  +    E+                       L + I   D   + + IED+   
Sbjct: 134 FYEPLNIDWDGNEL-----------------------LLSDILGTDDDIVYNLIEDEVD- 169

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                      +E     + +L+ RE+ ++ +RFG+    + T +EV     +++  I +
Sbjct: 170 -----------KELLFTAMKNLSNREKEIVELRFGLCGYKEKTQKEVADMLGISQSYISR 218

Query: 659 IEAKAIRKLKH 669
           +E K I++LK 
Sbjct: 219 LEKKIIKRLKK 229


>gi|326773494|ref|ZP_08232777.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636724|gb|EGE37627.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 164

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 56/96 (58%), Positives = 75/96 (78%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 69  KLRRELHWVAQDGQRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 128

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           D+  G+KFSTYA WW++QAITR++ADQ+ TIRIPVH
Sbjct: 129 DYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVH 164



 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/45 (44%), Positives = 29/45 (64%), Gaps = 1/45 (2%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
            +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L E
Sbjct: 18  GATADPVKDYLKQIGKVALLNAEQEVELAKRIEAGLY-AEHRLAE 61


>gi|187932801|ref|YP_001885388.1| sporulation sigma factor SigE [Clostridium botulinum B str. Eklund
           17B]
 gi|187720954|gb|ACD22175.1| RNA polymerase sigma-E factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 235

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 91/237 (38%), Gaps = 50/237 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 43  LVNNLMHGDESIRSTLIERNLRLVVYIARKFENTGVHVEDLISVGTIGLIKAVNTFNPEK 102

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                ++        +  +    E+
Sbjct: 103 KIKLATYASRCIENEILMYLRRNSK---------------IKAEISFYEPLNIDWDGNEL 147

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                                  L + I   +   + + IED+              ++ 
Sbjct: 148 -----------------------LLSDILGTENDEVYNLIEDEVD------------KQL 172

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L  L  RE+ ++R+RFG+    + T +EV     +++  I ++E K IR+LK 
Sbjct: 173 LLMALRILNDREKEIVRLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIIRRLKK 229


>gi|154249080|ref|YP_001409905.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
 gi|154153016|gb|ABS60248.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
          Length = 233

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 58/210 (27%), Positives = 98/210 (46%), Gaps = 8/210 (3%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
             ++  DLIQEG I L++AAEK+D   G  F T+A   VK A+   +        +P ++
Sbjct: 28  YNVEIDDLIQEGVIALLQAAEKYDPRYGATFKTFAYTRVKGAMIDYLRKLD---YLPKNV 84

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDED 584
           R  I K  R       + KR PT +E+++ L + VE V ++ +      SL       E 
Sbjct: 85  RQDIKKFDRELLNFYEQNKRLPTYDEMSEILGIDVEEVEEIYRELALKQSLNLDQYLFES 144

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             +    I+ K+  +  ++A ++ L E     +  L  +E+ +L MRF      + +L+E
Sbjct: 145 DENSYGSIDIKSEENVKENAWKSILHEQLVEAINKLDEKEKIILSMRF----EHELSLKE 200

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + +   VT  R+ QI    + KL+   R  
Sbjct: 201 IAEVLGVTESRVSQILGVILSKLRKMLRGD 230


>gi|302389525|ref|YP_003825346.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
 gi|302200153|gb|ADL07723.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
          Length = 239

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 90/243 (37%), Gaps = 54/243 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
               ++ K +   +  +  ++E NLRLV+ +A+K+ N G    DLI  G IGL+KA   F
Sbjct: 43  EEAMLLDKLQMGDNGVRNVLIERNLRLVVYIARKFENTGAGIEDLISIGTIGLIKAINTF 102

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA   ++  I   +   +                                
Sbjct: 103 DPHKKIKLATYASRCIENEILMYLRRNNR------------------------------- 131

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
                                 +  +S + P+  +   +  L   I   ++        +
Sbjct: 132 ---------------------NRAEVSFDEPLNIDWDGNELLLSDILGTDSDMIYKCIEE 170

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +E     +  L+ RE  ++ +RFG+    + T +EV +   +++  I ++E + I++
Sbjct: 171 EVEKELLDTAMKRLSKRERCIMELRFGLNDGKEKTQKEVAELLGISQSYISRLEKRIIKR 230

Query: 667 LKH 669
           L+ 
Sbjct: 231 LRK 233


>gi|149183912|ref|ZP_01862300.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
 gi|148848376|gb|EDL62638.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
          Length = 239

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 94/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLKKLPNGDKTARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +  +  +           
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTEEDI-ITKDLEATVD 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     L  L+ RE++++ +RFG+    + T ++V     +++  I ++E + I++LK 
Sbjct: 174 RKLLFNALTELSDREKQIMELRFGLMGGEEKTQKDVADMLGISQSYISRLEKRIIKRLKK 233


>gi|291542064|emb|CBL15174.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 219

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 98/224 (43%), Gaps = 13/224 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K ++ + N+ LV +  K+++ +G+++ +L   G +GL KA   FD     +FSTYA   +
Sbjct: 4   KNKLADKNMGLVHACCKRFSGKGIEYEELFASGCLGLAKAINNFDESRNLQFSTYAFPVI 63

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
              I R   D    IR+   +++    + R       K  RE T  E+A++L    E + 
Sbjct: 64  MGEIKRLFRDGG-AIRVSRTLKELSLAISRLNNESKLKNGRELTVSELAERLDTSEEKII 122

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
             L  T+ P+SL      E    L         V   D   + + R +    + SL   +
Sbjct: 123 DALNSTRVPLSLTAEYDSEGNPQL--------DVPTDDIQDEISERLSLEEAVKSLCETD 174

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +++++R+        T  +  K   +T+ +I + E K +  ++
Sbjct: 175 RKIIQLRY----YRSKTQTQTAKILSMTQVQISRREKKILTAIR 214


>gi|33322911|gb|AAQ07192.1|AF496500_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 141

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 54/142 (38%), Positives = 86/142 (60%), Gaps = 5/142 (3%)

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                PEE+A ++  P++  ++++ + K     SL+ P+G+E  S LGD +ED  A +P 
Sbjct: 1   GPGCQPEELAAEMNEPLQKXQEIITVAKNQETDSLDKPVGEEGDSQLGDLLEDNKATNPE 60

Query: 602 DSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
           +      L++  + ++   LT RE +VL++RFG+  +  HTLEEVG+   VTRER+RQIE
Sbjct: 61  EYTAFEMLKDQLSSMMGEFLTDREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQIE 120

Query: 661 AKAIRKLKHPSRSKKLRSFLDG 682
           AKA++KLKH   S  L+ +   
Sbjct: 121 AKAVKKLKH--HSDLLQDYFSA 140


>gi|153938998|ref|YP_001391838.1| sporulation sigma factor SigK [Clostridium botulinum F str.
           Langeland]
 gi|168180573|ref|ZP_02615237.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|152934894|gb|ABS40392.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           Langeland]
 gi|182668432|gb|EDT80411.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|295319864|gb|ADG00242.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           230613]
          Length = 234

 Score = 91.8 bits (226), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E ++ +  ++K     ++AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPKPLSDEEEKYYLDRLKK---GDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I                 +K  +  
Sbjct: 83  GTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIR---------------NNKKTKGE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDILSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  + +  +++   ++   L  RE++V++MR+G+      T  E+     ++R  +
Sbjct: 154 DSIIEIVSTKIEVKKLYGKIDTCLRGREKKVIQMRYGLKDGRPRTQREIAGILDISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 214 SRIEKKALKKL 224


>gi|239934366|emb|CAR92313.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
 gi|239934374|emb|CAR92317.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 225

 Score = 91.8 bits (226), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 30/213 (14%), Positives = 76/213 (35%), Gaps = 8/213 (3%)

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D +       +  A   ++   +          D+++ +E++D  +              
Sbjct: 20  DILSGYIDPDDDGAAAPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVA 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 +AE   +           +K  ++S +     E L  L   + L   + D LVE
Sbjct: 80  RVRFGAVAEQLEKANK------ALKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVE 133

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++ +   +I   E  +++L      + R  FL +    E +  W        +G++   +
Sbjct: 134 RVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAI 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               + I++ + ++  +  E  ++I++ + I  
Sbjct: 193 GNRKEDIVRCQQKLIELEQECDLAIADIKDINR 225


>gi|221309406|ref|ZP_03591253.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313731|ref|ZP_03595536.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318655|ref|ZP_03599949.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322928|ref|ZP_03604222.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767354|ref|NP_389415.2| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296331108|ref|ZP_06873582.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674263|ref|YP_003865935.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315297|ref|YP_004207584.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|133472|sp|P06222|RPSE_BACSU RecName: Full=RNA polymerase sigma-E factor; AltName: Full=P31;
           AltName: Full=Sigma-29; AltName: Full=Stage II
           sporulation protein GB; Flags: Precursor
 gi|40169|emb|CAA25620.1| unnamed protein product [Bacillus subtilis]
 gi|225184981|emb|CAB13406.2| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484083|dbj|BAI85158.1| sporulation sigma factor SigE [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151752|gb|EFG92627.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412507|gb|ADM37626.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021571|gb|ADV96557.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|224259|prf||1012299A spoIIG gene
          Length = 239

 Score = 91.8 bits (226), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 95/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLMKLPNGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +   + +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDIITKDIEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 KKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLRK 233


>gi|225418674|ref|ZP_03761863.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
 gi|225041795|gb|EEG52041.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
          Length = 216

 Score = 91.8 bits (226), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 104/263 (39%), Gaps = 58/263 (22%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   +   +    +S  E +  +           +A+  ++E N+RLV  V KKY +   
Sbjct: 1   MLRRLSLKTFPKPLSAREEKEYLER---CNEGDQLARDVLIERNMRLVAHVVKKYQSPDY 57

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+  G IGL+KA   F    G + +TYA   V+  I                    
Sbjct: 58  DIEDLLSVGTIGLIKAVNTFKVDKGSRLATYAAKCVENEILM------------------ 99

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH- 587
              + R ++++S +                               +SL  PIG +     
Sbjct: 100 ---LFRASKKLSKE-------------------------------VSLFEPIGVDKDGEA 125

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D IE +N  +     ++ +++E      + L+  E+ V+RMR+G+    +HT  E+
Sbjct: 126 VSLVDIIEMENKETIDTMILKQDVKELYEAFDSCLSDTEKTVIRMRYGLFRGKEHTQREI 185

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
             Q  ++R  + +IE KA+ KLK
Sbjct: 186 AAQLGISRSYVSRIEKKALEKLK 208


>gi|167757711|ref|ZP_02429838.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
 gi|167664593|gb|EDS08723.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
          Length = 208

 Score = 91.8 bits (226), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 104/256 (40%), Gaps = 58/256 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ +E R+    ++K       AK  ++E NLRLV  + KKY +      DL+  
Sbjct: 6   SFPQPLTAAEERYY---MQKYTEGDLEAKHILIERNLRLVAHIVKKYQSFEEDTEDLLSI 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+     +  TYA   ++  I                        +R  
Sbjct: 63  GTIGLIKAVVTFNPDKCVRLGTYAARCIENEILMH---------------------LRAK 101

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
           ++ S +                               ISL  PIG +   +   L D IE
Sbjct: 102 KKSSRE-------------------------------ISLYEPIGTDREGNEIQLFDIIE 130

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +   +     ++ ++R    RV + L+PRE  VL+MR+G+    ++T  E+ KQ  ++R
Sbjct: 131 TEEDDAHKKVELRDDIRMLYYRVESELSPRERLVLKMRYGLYNEEEYTQREIAKQLGISR 190

Query: 654 ERIRQIEAKAIRKLKH 669
             + +IE  AI KL+ 
Sbjct: 191 SYVSRIEKSAIEKLRE 206


>gi|261405539|ref|YP_003241780.1| sporulation sigma factor SigK [Paenibacillus sp. Y412MC10]
 gi|315645904|ref|ZP_07899025.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|329925929|ref|ZP_08280639.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
 gi|261282002|gb|ACX63973.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. Y412MC10]
 gi|315278665|gb|EFU41979.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|328939580|gb|EGG35929.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
          Length = 233

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 60/281 (21%), Positives = 108/281 (38%), Gaps = 58/281 (20%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +  +  + + +K+ +    ++  E       +++       ++ +++E NLRLV 
Sbjct: 7   AIALFIKELTLLVSYVKNNAFPQPLTEEEE---AKHLQRMAEGDPQSRNKLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +     
Sbjct: 64  HIVKKFDNTGEDLEDLISIGTIGLIKAIESFRPNKGTKLATFAARCIENEILMHLRS--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK T++ +SL 
Sbjct: 121 -------------------------------------------------LKKTRKDVSLH 131

Query: 578 TPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            PIG +   +    I+     A   +D+      +    R L  L  RE+ V+  RFG+ 
Sbjct: 132 DPIGTDKEGNEITLIDILGTEADDIVDAVQLKIEKSKIYRNLDILDDREKEVVIGRFGLE 191

Query: 636 MN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
               + T  E+ K+  ++R  + +IE +A+ KL H    +K
Sbjct: 192 AGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKQK 232


>gi|331269712|ref|YP_004396204.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126262|gb|AEB76207.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 249

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  ++V+ +R         +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 49  LSKEEEENLVAKIR---AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 105

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                  +  +       
Sbjct: 106 IKAVNTFDPEKKIKLATYASRCIENEILMYLR-----------------RNNKVKAE--- 145

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +  +N +
Sbjct: 146 --------------------------------ISFYEPLNTDWDGNKLLLSDILGTENDM 173

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + ++     +  L+ RE+ ++++RFG+    + T ++V     +++  I +
Sbjct: 174 VYNLIEDEVD-KQLLFIAMRKLSEREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISR 232

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 233 LEKRIIKRLKK 243


>gi|326791235|ref|YP_004309056.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
 gi|326541999|gb|ADZ83858.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
          Length = 220

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 93/253 (36%), Gaps = 52/253 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +H +      +     AK  ++E NLRLV  + KKY N      DLI  G IGL
Sbjct: 20  LSAEEEKHYLE---CYQDGDEAAKNILIERNLRLVAHIVKKYNNINNDVDDLISIGTIGL 76

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K    FD     + +TYA   ++  I  SI                  +  R    +  
Sbjct: 77  IKGISSFDPNKCTRLATYAARCIENEILMSIRAG---------------RKQRYETSLHA 121

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            I  +    EI                                   L D +  +N     
Sbjct: 122 PIGMDQEGNEI----------------------------------SLLDILCTENDTIFD 147

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              +   +R+    +   L PRE+ +L +R+G+    + T  E+ +Q  ++R  + +IE 
Sbjct: 148 QVDLDIEVRKLYQHIRILLKPREKEILLLRYGLNNQEEKTQREIAEQMGISRSYVSRIEK 207

Query: 662 KAIRKLKHPSRSK 674
           KA++KL    + K
Sbjct: 208 KALKKLCKELQKK 220


>gi|303237309|ref|ZP_07323879.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
 gi|302482696|gb|EFL45721.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
          Length = 235

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 114/251 (45%), Gaps = 42/251 (16%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             IK I+ E  +S  E + +   ++      + A +++ ++NL+ V+S+A +Y NRGL  
Sbjct: 8   KYIKDIANEQLLSDKEEQELAKQIK---IGDAKALEKLTKSNLKFVVSIAHQYKNRGLGE 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI EGNIG+M AA+KFD   G +F  +A  ++++A+  +I                  
Sbjct: 65  DDLISEGNIGMMYAAQKFDGTKGTRFVKFAAPYIRKAMEEAI------------------ 106

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHL 588
                               E  +   +  +  +K  K T   +S++ PI      T  L
Sbjct: 107 -------------------NEQLETFKVQNKDEKKPRKRTAHRVSIDQPIPAGSNGTFTL 147

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
              +E+ N+    ++  +  +RE   + ++ L  R+ +V+ + + I     +T++E    
Sbjct: 148 QTILENANSQHADENLTKQIVREEIKKAMSVLDARQRKVISLLYAIKDEEAYTMQETADI 207

Query: 649 FCVTRERIRQI 659
             + RER+RQI
Sbjct: 208 MDIKRERVRQI 218


>gi|317502438|ref|ZP_07960602.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331090300|ref|ZP_08339184.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316896176|gb|EFV18283.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330401435|gb|EGG81020.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 206

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 99/259 (38%), Gaps = 58/259 (22%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             S    ++ SE ++    +RK       AK  ++E NLRLV  V KKY N      DLI
Sbjct: 1   MKSFPNPLTPSEEKYY---IRKYTEGDLEAKHILIERNLRLVAHVIKKYQNSEEDPEDLI 57

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+KA   F+   G + + YA   ++  I   +  +                   
Sbjct: 58  SIGTIGLIKAVVTFNPDKGNRLAAYASRCIENEILMYLRSK------------------- 98

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDF 591
                                            K   + ISL  PIG +   +   L D 
Sbjct: 99  ---------------------------------KKAAKEISLYEPIGTDREGNEIKLYDI 125

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE           ++ N++    +V   L+ RE  +L+MR+G+    ++T  E+ +Q  +
Sbjct: 126 IETDEEEVAEKIHLKENIQTLYEKVEKELSQRERIILKMRYGLYNGEEYTQREIARQLGI 185

Query: 652 TRERIRQIEAKAIRKLKHP 670
           +R  + +IE  A+ KL+  
Sbjct: 186 SRSYVSRIEKGAVEKLRKS 204


>gi|56963382|ref|YP_175113.1| sporulation sigma factor SigK [Bacillus clausii KSM-K16]
 gi|56909625|dbj|BAD64152.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus
           clausii KSM-K16]
          Length = 235

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 102/262 (38%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + +  ++ +       + A+  ++E NLRLV  + KK+ N     
Sbjct: 20  SYVKNNAFPQPLSKEDEKKYLARM---AEGDASARNMLIEHNLRLVAHIVKKFENTREDV 76

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 77  EDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEILMHLRA---------------- 120

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                        ++ V+K        +SL  PIG +   +   
Sbjct: 121 -----------------------------LKKVKK-------DVSLHDPIGTDKEGNEIT 144

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++D           +   ++     +  L  RE+ V+  RFG+ M  + T  E+ K
Sbjct: 145 LIDILKDDGEDIVDVLQTEME-KKQIYEYIHVLDEREKEVIIGRFGLNMEEERTQREIAK 203

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
           +  ++R  + +IE +A+ KL H
Sbjct: 204 ELNISRSYVSRIEKRALMKLFH 225


>gi|169831583|ref|YP_001717565.1| sporulation sigma factor SigE [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638427|gb|ACA59933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 241

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 93/240 (38%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ + E      +  ++E NLRLV+ +A+K+ + G+   D++  G IGL+KA   FD   
Sbjct: 49  LISRLEAGDHGVRSTLIERNLRLVVYIARKFESTGVGIEDMVSIGTIGLIKAVNTFDPRK 108

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                                    
Sbjct: 109 RIKLATYASRCIENEILMYLRRNS------------------------------------ 132

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                     VR         IS E P+  +   +   L D +   + +   D  ++ + 
Sbjct: 133 ---------KVR-------GEISFEEPLNIDWDGNELLLSDVLGTDSDIIYKDLEMEVDH 176

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L  L+ RE +++ +RFG+    + T +EV     +++  I ++E + I +LK 
Sbjct: 177 K-LLRLALQKLSQRERKIMELRFGLNNGEEKTQKEVADLLGISQSYISRLEKRIINRLKK 235


>gi|295695806|ref|YP_003589044.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411408|gb|ADG05900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 238

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 104/276 (37%), Gaps = 59/276 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V  I    + IK+ +    +S  E    +  +         A+  ++E NLRLV  + KK
Sbjct: 12  VREIALFVSYIKNSAFPHPLSEEEEEQYLKQM---AEGDERARNLLIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G    DLI  G IGL+KA E F    G K +TYA   ++  I   +          
Sbjct: 69  FENTGEDTEDLISIGTIGLIKAIESFQPHKGTKLATYAARCIENEILMHLRA-------- 120

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T++ +SL  PIG 
Sbjct: 121 --------------------------------------------LKKTRKDVSLHDPIGT 136

Query: 583 EDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +       L D +   +A   +D       +      L  L  RE+ V+R RFG+    +
Sbjct: 137 DKEGNEVTLLDILS-SDADDVVDIVEMKLEKHQIYEKLQELDEREQEVIRGRFGLQNGEE 195

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            T  E+ ++  ++R  + +IE +A+ KL H  R ++
Sbjct: 196 KTQREIAEELGISRSYVSRIEKRALMKLLHDLRPRR 231


>gi|188587739|ref|YP_001920535.1| sporulation sigma factor SigE [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251779018|ref|ZP_04821938.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498020|gb|ACD51156.1| RNA polymerase sigma-E factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083333|gb|EES49223.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 235

 Score = 91.4 bits (225), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 91/237 (38%), Gaps = 50/237 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V          +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 43  LVNNLMHGDESIRSTLIERNLRLVVYIARKFENTGVHVEDLISVGTIGLIKAVNTFNPEK 102

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                ++        +  +    E+
Sbjct: 103 KIKLATYASRCIENEILMYLRRNSK---------------IKAEISFYEPLNIDWDGNEL 147

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                                  L + I   +   + + IED+              ++ 
Sbjct: 148 -----------------------LLSDILGTENDEVYNLIEDEVD------------KQL 172

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L  L  RE+ ++R+RFG+    + T +EV     +++  I ++E K IR+LK 
Sbjct: 173 LLMALRILNDREKEIVRLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIIRRLKK 229


>gi|84514822|ref|ZP_01002185.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
 gi|84510981|gb|EAQ07435.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
          Length = 239

 Score = 91.4 bits (225), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 108/250 (43%), Gaps = 19/250 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCL 492
           +    A +  +++V  +  LV  V+    +R    ++F DL+Q G IGL++AA+++    
Sbjct: 2   QEYPSAKLNVEKLVREHEALVRRVSHHIHSRVRSIVEFDDLLQVGLIGLIEAAQRYTRRE 61

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F  YA+  V+ AI   +   S    +          V      +S K+ R PT  E+
Sbjct: 62  GVSFENYAVLRVRGAIYDYLRKNS---NLGRKTIATTKVVKFAQAELSQKLGRAPTRVEL 118

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A+ ++M +  +    +      S +  + DE   +   F  ++     L    +  L++ 
Sbjct: 119 AEAVSMTIGELNAWEQSLNS--SYQNSLQDEYDEYSMWFSAEEPPAEQLLD--RGRLKDA 174

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               L SL  RE  VL++ +      +  + E+     VT  R+ Q+++ A +K++    
Sbjct: 175 LLIALKSLPQREALVLQLYYV----EELNIYEIAAILEVTPGRVSQLKSMAFKKMQ---- 226

Query: 673 SKKLRSFLDG 682
              LR F +G
Sbjct: 227 -PLLRDFAEG 235


>gi|219669565|ref|YP_002460000.1| sporulation sigma factor SigK [Desulfitobacterium hafniense DCB-2]
 gi|219539825|gb|ACL21564.1| RNA polymerase, sigma 28 subunit, SigK [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score = 91.4 bits (225), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 61/271 (22%), Positives = 105/271 (38%), Gaps = 65/271 (23%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR---------KGECEASIAKKEMVEANLRLVISV 459
           + + I + +    ++  +  H + ++R         K   +A  A+ ++VE NLRLV  +
Sbjct: 21  LVSYINNNAFPHPLNEQDEAHYLKVLRASKSPEATPKDLTKAEYARNKLVEHNLRLVAHL 80

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            KK+   G    DLI  G IGL+K  + FD   G K +TYA   ++  I   +       
Sbjct: 81  VKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLATYAARCIENEILMHLRS----- 135

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
                                                          LK ++  +S+  P
Sbjct: 136 -----------------------------------------------LKKSRGEVSIYDP 148

Query: 580 IGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           IG +   +   L D +  +          +   R    +V  +LT RE  VL++R+G+  
Sbjct: 149 IGVDKEGNEISLMDVLASEGEAISDRIENEFEQRVLLDKV-KNLTRRERLVLQLRYGLMN 207

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +   T  E+ K   ++R  + +IE KAI+KL
Sbjct: 208 SPRRTQREIAKALGISRSYVSRIEKKAIQKL 238


>gi|239934508|emb|CAR94568.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 237

 Score = 91.4 bits (225), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 44/299 (14%), Positives = 92/299 (30%), Gaps = 66/299 (22%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EIA+AKRIEAG   +  ++  SP   +  I + D +  G   L +++            
Sbjct: 2   DEIALAKRIEAGNRQVAKAVSLSPGAMRQFIEFADRIEAGDMKLTDMV------------ 49

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                                E + + +           +  D  +  S P+        
Sbjct: 50  -----------------VDFMELNALDDETVATPGEPGQNAADAEEGPSGPD-------- 84

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCKV 316
                                      DE  E ++++R +     N Q K+   S     
Sbjct: 85  --------------------------FDEAIERFKKVRKIWKLLENAQAKNGVDSKLALK 118

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQ 375
            +  +   +  +    +R + +   L +    +   E  + +   +Y  + R  F E   
Sbjct: 119 HRXAMSDEMLQIKYVPARFEEITATLRNSMDEVRFCERSIAKYCVTYAKVPRKRFREHFS 178

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           G E    W         GE K     E ++I +++ ++  +     + + E + +   +
Sbjct: 179 GNETSSDWFKNLVKASAGEAKKLKDFE-ETIEELQAQLNKVQQNAALDLKELKDLSRKL 236


>gi|330980004|gb|EGH78270.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 214

 Score = 91.4 bits (225), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 42/192 (21%), Positives = 95/192 (49%), Gaps = 8/192 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++  + R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESL--YYEQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HL---GDFIEDK 595
                 +++ED 
Sbjct: 194 AFQSPANYLEDH 205


>gi|294501014|ref|YP_003564714.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|295706363|ref|YP_003599438.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
 gi|294350951|gb|ADE71280.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|294804022|gb|ADF41088.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
          Length = 239

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 96/240 (40%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLKKLPSGDEAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +  +  +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVMGTEEDIITKDLEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 RKLLLKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGISQSYISRLEKRIIKRLRK 233


>gi|91981570|gb|ABE68127.1| RNA polymerase subunit D [Pseudomonas protegens]
          Length = 220

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 56/126 (44%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + + +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 95  KHGRENKQAIAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++ VET + I
Sbjct: 155 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETSLKI 213

Query: 425 SEFRHI 430
           +E + I
Sbjct: 214 AEIKDI 219


>gi|89895149|ref|YP_518636.1| sporulation sigma factor SigK [Desulfitobacterium hafniense Y51]
 gi|89334597|dbj|BAE84192.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 61/271 (22%), Positives = 105/271 (38%), Gaps = 65/271 (23%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR---------KGECEASIAKKEMVEANLRLVISV 459
           + + I + +    ++  +  H + ++R         K   +A  A+ ++VE NLRLV  +
Sbjct: 20  LVSYINNNAFPHPLNEQDEAHYLKVLRASKSPEATPKDLTKAEYARNKLVEHNLRLVAHL 79

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            KK+   G    DLI  G IGL+K  + FD   G K +TYA   ++  I   +       
Sbjct: 80  VKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLATYAARCIENEILMHLRS----- 134

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
                                                          LK ++  +S+  P
Sbjct: 135 -----------------------------------------------LKKSRGEVSIYDP 147

Query: 580 IGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           IG +   +   L D +  +          +   R    +V  +LT RE  VL++R+G+  
Sbjct: 148 IGVDKEGNEISLMDVLASEGEAISDRIENEFEQRVLLDKV-KNLTRRERLVLQLRYGLMN 206

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +   T  E+ K   ++R  + +IE KAI+KL
Sbjct: 207 SPRRTQREIAKALGISRSYVSRIEKKAIQKL 237


>gi|157692207|ref|YP_001486669.1| sporulation sigma factor SigE [Bacillus pumilus SAFR-032]
 gi|157680965|gb|ABV62109.1| DNA-directed RNA polymerase sigma subunit SigE [Bacillus pumilus
           SAFR-032]
          Length = 239

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 99/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + ++    K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LSKDEEQELL---VKLPKGDQTARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +               + +K+         
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLR--------------RNNKIR-------- 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +   + +
Sbjct: 134 ------------------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDI 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              D     + ++   + L  L  RE++++ +RFG+    + T ++V     +++  I +
Sbjct: 164 ITRDIEANVD-KKLLKKALEQLNDREKQIMELRFGLVGGEEKTQKDVADMLGISQSYISR 222

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 223 LEKRIIKRLQK 233


>gi|75764483|ref|ZP_00743968.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488030|gb|EAO51761.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 224

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 9   DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 68

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 69  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 114

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 115 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 136

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 137 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 195

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 196 DMLGISQSYISRLEKRIIKRLRK 218


>gi|83816261|ref|YP_446679.1| RNA polymerase sigma-28 factor [Salinibacter ruber DSM 13855]
 gi|294508614|ref|YP_003572673.1| RNA polymerase sigma factor for flagellar operon [Salinibacter
           ruber M8]
 gi|83757655|gb|ABC45768.1| RNA polymerase sigma-28 factor [Salinibacter ruber DSM 13855]
 gi|294344943|emb|CBH25721.1| RNA polymerase sigma factor for flagellar operon [Salinibacter
           ruber M8]
          Length = 248

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 43/201 (21%), Positives = 87/201 (43%), Gaps = 9/201 (4%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL   G +GL++A + +D     +F+T+A   ++  I   +        +    R K
Sbjct: 48  AHEDLESVGIVGLLEALDNYDPEQA-QFATHAYRRIRGNIIDYLRSID---VLSREKRKK 103

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH- 587
           +  V      +   +  EP+ E++A  + M VE    +L+  +   SL      ED  H 
Sbjct: 104 MGAVQEALSSLRQMLGEEPSDEDVADYMGMAVEEYHDLLRDAQCRFSLSLSRPSEDDDHT 163

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D +   +     +   +A+ ++    ++ +L  R++ +L    G+    D TL+E+G+
Sbjct: 164 MLDVLPSDDGTEGFEQFEKASTQKHLEDLIQTLPERQQTIL----GLYYTEDLTLQEIGE 219

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
              ++  RI Q+  K    L+
Sbjct: 220 VLDLSAARISQLLGKIQLTLQ 240


>gi|89335089|dbj|BAE84684.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 238

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 48/228 (21%), Positives = 91/228 (39%), Gaps = 56/228 (24%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   +
Sbjct: 58  RDVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYASRCI 117

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +                                                    
Sbjct: 118 ENEILMHLRRN------------------------------------------------- 128

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                T+  +S + P+  +   +   L D +  +N +       + + R+     +A LT
Sbjct: 129 ---NKTRTEVSFDEPLNIDWDGNELLLSDVLGTENDIISRPLEEKVD-RQLLHLAMARLT 184

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++ +RFG+    + T +EV  +  +++  I ++E + IR+L+ 
Sbjct: 185 DREKLIMELRFGLDNGEEKTQKEVADRLGISQSYISRLEKRIIRRLRK 232


>gi|239934388|emb|CAR92324.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 225

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 39/270 (14%), Positives = 90/270 (33%), Gaps = 46/270 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPRQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVS 432
            + I++ + ++  +  E  ++I++ + I  
Sbjct: 196 KEDIVRCQQKLIELEQECDLAIADIKDINR 225


>gi|219129831|ref|XP_002185083.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403578|gb|EEC43530.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 435

 Score = 91.1 bits (224), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 70/290 (24%), Positives = 120/290 (41%), Gaps = 61/290 (21%)

Query: 443 IAKKEMVEANLRLVISVAKKYTN--------RGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +++ MV  N+ LV   A             + L   DLIQEG IGL +A ++++  +G 
Sbjct: 147 ASRETMVTRNMGLVHFCANDIVGTQARPSRLQTLSREDLIQEGAIGLARAVDRWNPEIGG 206

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM--------------- 539
           KFSTYA++WV+ AI R IA++   +R+P H+   + K+ R AR++               
Sbjct: 207 KFSTYAVYWVRAAILRCIAERDDLVRVPEHVSAAVRKISRAARQLGIDIDGNDLISSVYS 266

Query: 540 -SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE----PISLETPIG--DEDTSHLGDFI 592
                K     + +A++  +    V + +K+        +S E  +    +  + L   +
Sbjct: 267 KDASWKEAQAAKALAEEAGLTPRQVSEAIKVKARRRGGMLSFEAWMQQGQDFATDLTPVV 326

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI------------------ 634
            D N   PL S     L+ T ++    L P+E   L  R+G+                  
Sbjct: 327 ADDN---PLASLETEQLKSTLSKF---LRPKEMEALSWRYGLQRDYVAEAEEELFGRSPR 380

Query: 635 -------GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
                        +  EVGK+  V+ E  R++  KA+ KL+  +    L 
Sbjct: 381 APITVKGRWGEAMSFTEVGKKMKVSAEYGRRLCHKALNKLRVAAEEGMLE 430


>gi|91794980|ref|YP_564631.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91716982|gb|ABE56908.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 236

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 105/238 (44%), Gaps = 19/238 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V +      +++ +++   L LV     +   +    L   D+ Q G + L++++ ++  
Sbjct: 12  VSEEPALQRLSEDQLIVQYLPLVKRAVLQLRSHCGAMLSLEDMEQIGMMALIESSRRYPG 71

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F ++A   ++ AI   +  Q    R    +R + H +    R +S  + REPT  
Sbjct: 72  EFDNGFISFAGQRIRGAILDELRRQDWRPRP---VRQQAHILNDKVRELSRTLGREPTDT 128

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  L +  E  R+ L  T+     E+    ++   +G+   DK+     +   +  L+
Sbjct: 129 EVATGLGLSPEAYRESLYATQA----ESMKSLDEMLTIGEQPADKH-----NEVERFMLK 179

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +T  + +  L  RE+ +L + +    + +  L+E+     +T  RI Q+  +A+ KL+
Sbjct: 180 KTLIKAMTKLNEREQLILSLYY----HHELNLKEIALTLGLTETRICQLHKQAVAKLQ 233


>gi|310643126|ref|YP_003947884.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248076|gb|ADO57643.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 233

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 59/282 (20%), Positives = 108/282 (38%), Gaps = 60/282 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +  +  + + +K+ +    ++  E    + +  +G   +   +  ++E NLRLV 
Sbjct: 7   AIALFIKELTLLVSYVKNNAFPQPLTEKEEARHLKLFAEGNAHS---RNTLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +     
Sbjct: 64  HIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEILMHLRS--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK T++ +SL 
Sbjct: 121 -------------------------------------------------LKKTRKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D +  +         ++   +    R L  L  RE+ V+  RFG+
Sbjct: 132 DPIGTDKEGNEITLIDILGSEADDIVDKVQLKIE-KSKIYRNLDILDEREKEVVIGRFGL 190

Query: 635 GMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
                + T  E+ ++  ++R  + +IE +A+ KL H    +K
Sbjct: 191 EAGGEERTQREIARELGISRSYVSRIEKRALMKLYHEFYKQK 232


>gi|308070013|ref|YP_003871618.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859292|gb|ADM71080.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 233

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 62/284 (21%), Positives = 111/284 (39%), Gaps = 64/284 (22%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +  +  + + +K+ +    ++  E    + +  +G   +   +  ++E NLRLV 
Sbjct: 7   AIALFIKELTLLVSYVKNNAFPQPLTEKEEARHLKLFAEGNAHS---RNTLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +     
Sbjct: 64  HIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEILMHLRS--- 120

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK T++ +SL 
Sbjct: 121 -------------------------------------------------LKKTRKDVSLH 131

Query: 578 TPIGDE---DTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            PIG +   +   L D +  E  + V  +   I+   +    R L  L  RE+ V+  RF
Sbjct: 132 DPIGTDKEGNEITLIDILGTEADDIVDKVQLKIE---KSKIYRNLDILDEREKEVVIGRF 188

Query: 633 GIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           G+     + T  E+ ++  ++R  + +IE +A+ KL H    +K
Sbjct: 189 GLEAGGEERTQREIARELGISRSYVSRIEKRALMKLYHEFYKQK 232


>gi|194014382|ref|ZP_03052999.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
 gi|194013408|gb|EDW22973.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
          Length = 239

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 99/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + ++    K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LSKDEEQELL---VKLPKGDQTARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +               + +K+         
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLR--------------RNNKIR-------- 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +   + +
Sbjct: 134 ------------------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDI 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              D     + ++   + L  L  RE++++ +RFG+    + T ++V     +++  I +
Sbjct: 164 ITRDIEANVD-KKLLKKALEQLNDREKQIMELRFGLIGGEEKTQKDVADMLGISQSYISR 222

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 223 LEKRIIKRLQK 233


>gi|253682372|ref|ZP_04863169.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
 gi|253562084|gb|EES91536.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  ++V+ +R         +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKEEEENLVAKIR---AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                  +  +       
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLR-----------------RNNKVKAE--- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +  +N +
Sbjct: 132 --------------------------------ISFYEPLNTDWDGNKLLLSDILGTENDM 159

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + ++     +  L+ RE+ ++++RFG+    + T ++V     +++  I +
Sbjct: 160 VYNLIEDEVD-KQLLFIAMRKLSEREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISR 218

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 219 LEKRIIKRLKK 229


>gi|55274881|gb|AAV49243.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 184

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 50/145 (34%), Positives = 92/145 (63%)

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q I R+I +Q+ TIR+P+H+  +++  +RTAR +S+K+  EP+ EEIA
Sbjct: 38  FRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIA 97

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L  PV+ V ++L++ +   S++TP+G +    L D + D+    P D+    +++++ 
Sbjct: 98  EQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSI 157

Query: 614 TRVLASLTPREERVLRMRFGIGMNT 638
            + L  L  ++  VL  RFG+    
Sbjct: 158 VKWLFELNAKQREVLARRFGLLGYE 182


>gi|311031586|ref|ZP_07709676.1| sporulation sigma factor SigK [Bacillus sp. m3-13]
          Length = 237

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 61/274 (22%), Positives = 108/274 (39%), Gaps = 59/274 (21%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           V   +  ++ + + +K+ +    +S  +    + ++ +G      A+  ++E NLRLV  
Sbjct: 8   VGYLIKELVFLVSYVKNNAFPQPLSSGDEAKYLKLMAEGN---EEARNLLIEHNLRLVAH 64

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           + KK+ N G    DLI  G IGL+KA E F    G K +TYA   ++  I   +      
Sbjct: 65  IVKKFENTGEDSEDLISIGTIGLIKAIESFHSGKGTKLATYAARCIENEILMHLRA---- 120

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
                                                           LK TK+ +SL  
Sbjct: 121 ------------------------------------------------LKKTKKDVSLHD 132

Query: 579 PIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           PIG +   +   L D ++ ++        +   L E     +  L  RE  V+  RFG+ 
Sbjct: 133 PIGQDKEGNEISLIDVLKSESEDVIDTIQLNMEL-EKIKVYIDVLDEREREVIVGRFGLD 191

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 192 LKDEKTQREIAKELGISRSYVSRIEKRALMKMFH 225


>gi|229157483|ref|ZP_04285560.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
 gi|228625933|gb|EEK82683.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
          Length = 223

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 95/263 (36%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K       A+  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 8   DEIYYIGGSEALPPPLTKEEEEVLLNKLPKGDQAARSLLIERNLRLVVYIARKFENTGIN 67

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 68  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------- 113

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                    +  +S + P+  +   +  
Sbjct: 114 --------------------------------------NKNRSEVSFDEPLNIDWDGNEL 135

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +   + +           R    + L  L  RE++++ +RFG+    + T ++V 
Sbjct: 136 LLSDVLGTDDDI-ITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 194

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 195 DMLGISQSYISRLEKRIIKRLRK 217


>gi|154685948|ref|YP_001421109.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens FZB42]
 gi|154351799|gb|ABS73878.1| SigE [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 95/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLLKLPSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +   + +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDIITKDIEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 KKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLRK 233


>gi|168214239|ref|ZP_02639864.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
 gi|170714290|gb|EDT26472.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
          Length = 235

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 97/251 (38%), Gaps = 53/251 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +S  E   +V+ +          +  ++E NLRLV+ +A+K+ N G+   DLI  G 
Sbjct: 32  PAPLSKEEEEELVNKL---GENDEAIRSILIERNLRLVVYIARKFENTGVGVEDLISVGT 88

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F+     K +TYA   ++  I   +   S                V+    
Sbjct: 89  IGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSK---------------VKAEIS 133

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
               +  +    E+                       L + I   D   + + IED+   
Sbjct: 134 FYEPLNIDWDGNEL-----------------------LLSDILGTDDDIVYNMIEDEVD- 169

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                      +E     + +L+ RE+ ++ +RFG+    + T +EV     +++  I +
Sbjct: 170 -----------KELLFTAMKNLSNREKEIVELRFGLCGYKEKTQKEVADMLGISQSYISR 218

Query: 659 IEAKAIRKLKH 669
           +E K I++LK 
Sbjct: 219 LEKKIIKRLKK 229


>gi|326773500|ref|ZP_08232783.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636730|gb|EGE37633.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 311

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 47/85 (55%), Positives = 65/85 (76%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 209 KLRRELHWVAQDGQRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 268

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIA 513
           D+  G+KFSTYA WW++QAITR++A
Sbjct: 269 DYTKGFKFSTYATWWIRQAITRAMA 293



 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 89  SEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           S+D     + + +       ++     +T DPV+ YL+++G + LL+ E E+ +AKRIEA
Sbjct: 132 SQDKDGSFTVSDSDEGDEPAQRVVTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEA 191

Query: 149 GRAMMMASLCE 159
           G       L E
Sbjct: 192 GLY-AEHRLAE 201


>gi|288555607|ref|YP_003427542.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
 gi|288546767|gb|ADC50650.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
          Length = 235

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 108/279 (38%), Gaps = 57/279 (20%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                 ++  V  ++   + +K+ +    +   + R  + +++      + A+  ++E N
Sbjct: 2   SGMLAALSYFVKEVIVFVSYVKNNAFPQPLKKDDERKYLKLMQ---EGDAEARNLLIEHN 58

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV  + KK+ N      DLI  G IGL+KA E +    G K +TYA   ++  I   +
Sbjct: 59  LRLVAHIVKKFENTREDTEDLISIGTIGLIKAIESYSDGKGTKLATYAARCIENEILMHL 118

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                                                          ++ V+K       
Sbjct: 119 RA---------------------------------------------LKKVKK------- 126

Query: 573 PISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +SL  PIG +   +    I+   ++A   +D       ++     +  L  RE+ V+  
Sbjct: 127 DVSLHDPIGTDKEGNEISLIDVLQEDADDIVDVIQTKMEKKQIYEYIHVLDEREKEVIVG 186

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RFG+ M  + T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 187 RFGLDMEDELTQREIAKKLGISRSYVSRIEKRALMKLFH 225


>gi|328958265|ref|YP_004375651.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
 gi|328674589|gb|AEB30635.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
          Length = 238

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 106/243 (43%), Gaps = 13/243 (5%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                 +++ +   L LV  +  +           DL   G IGLM A EKFD      F
Sbjct: 1   MYYENDREKEIIKYLPLVEKIVNRIDVKRSEYDRDDLYNIGVIGLMDALEKFDKSKKVPF 60

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
             YA   +K +I   I   +    +      K+++  R   ++   + R PT +EI ++L
Sbjct: 61  EGYAYIRIKGSIIDEIRKTA---PVSRTRMGKLNEYYRAKEKLEATLMRTPTEKEICEEL 117

Query: 557 AMPVEGVRKVLKITKE--PISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRET 612
            +  + + K+ +       ISLE  +  +D     L DF+EDK+     D+ +    ++ 
Sbjct: 118 KIDEKALTKIHETVHNLASISLEKVMFSDDGNSIELIDFLEDKHETGSEDTLLDKERQQL 177

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            T+ ++ L  RE+ +L + +      + +L+E+   F ++  R+ QI  K I KLK   R
Sbjct: 178 LTKNVSKLDKREQTILNLYYV----EELSLKEIAYIFDISVPRVSQIHGKMILKLKELMR 233

Query: 673 SKK 675
            + 
Sbjct: 234 REY 236


>gi|326204637|ref|ZP_08194493.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
 gi|325985204|gb|EGD46044.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
          Length = 243

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ E  ++++ + + +      K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 43  LTLDEETYLLNKLEQSDYGV---KSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   +                         
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEILMYLRRNNRVKAE-------------------- 139

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS++ P+  +   +   L D +   N +
Sbjct: 140 --------------------------------ISIDEPLNIDWDGNELLLSDILGTDNDM 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               S      +E     +  L+ RE++++ +RFG+    + T +EV     +++  I +
Sbjct: 168 -IHRSIEDEVDKELLAAAMKKLSVREKKIMELRFGLSNGVEKTQKEVADMLGISQSYISR 226

Query: 659 IEAKAIRKLKH 669
           +E + I +LK 
Sbjct: 227 LEKRIISRLKK 237


>gi|125972968|ref|YP_001036878.1| sporulation sigma factor SigE [Clostridium thermocellum ATCC 27405]
 gi|256004765|ref|ZP_05429740.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281417179|ref|ZP_06248199.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|125713193|gb|ABN51685.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium thermocellum
           ATCC 27405]
 gi|255991215|gb|EEU01322.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281408581|gb|EFB38839.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|316940796|gb|ADU74830.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 1313]
          Length = 244

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 98/252 (38%), Gaps = 60/252 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E  +++S + K +      K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 43  LTNDEENYLLSKLEKRDFGV---KSILIERNLRLVVYIARKFENTGVGVEDLVSIGTIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +   +                         
Sbjct: 100 IKAINTFDPNKNIKLATYASRCIENEILMYLRRNNRMKTE-------------------- 139

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS++ P+  +   +   L D +  +N +
Sbjct: 140 --------------------------------ISIDEPLNVDWDGNELLLSDILGTENDL 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIR 657
               S      +E     +  L+ RE++++ +RFG+     + T +EV     +++  I 
Sbjct: 168 -IHRSIEDEIDKELLAMAMKKLSVREKKIMELRFGLTNGGVEKTQKEVADMLGISQSYIS 226

Query: 658 QIEAKAIRKLKH 669
           ++E K I +L+ 
Sbjct: 227 RLEKKIISRLRK 238


>gi|311068053|ref|YP_003972976.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
 gi|310868570|gb|ADP32045.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
          Length = 239

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 95/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLLKLPSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +   + +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDIITKDIEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 KKLLKKALEQLNDREKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLRK 233


>gi|238753169|ref|ZP_04614612.1| Lateral flagellar motor protein A (MotA-like) [Yersinia rohdei ATCC
           43380]
 gi|238708608|gb|EEQ00883.1| Lateral flagellar motor protein A (MotA-like) [Yersinia rohdei ATCC
           43380]
          Length = 525

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 46/208 (22%), Positives = 93/208 (44%), Gaps = 21/208 (10%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
            N  +   D+ Q   +GL++A  ++      +F+ YA+  ++ A+   + +       P 
Sbjct: 39  VNSVIDREDMQQIALMGLLEALRRYGHP-DVQFAAYAVHRIRGAVLDQLREHDW---RPR 94

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
            +R K HK+    R +  K+  EP+ EEI  +L +  E  ++ L        LE+    E
Sbjct: 95  RLRQKTHKINEAIRAIMRKLGHEPSFEEITAELKLTAEEYQEYLL-------LESASAME 147

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
               L D +  +     L S    +   + +   + +ASL  RE+ +L + +      + 
Sbjct: 148 ---SLDDILSLETPTDALQSRNLEDSIIVEDNLNQAIASLEEREQMILHLYYQ----KEM 200

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +++E+ +   +T  RI Q+  K ++K+K
Sbjct: 201 SMKEIAEVLDLTEARICQLNKKIVQKIK 228


>gi|118197179|dbj|BAF37059.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197183|dbj|BAF37061.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197185|dbj|BAF37062.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197187|dbj|BAF37063.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197189|dbj|BAF37064.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197191|dbj|BAF37065.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197193|dbj|BAF37066.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197195|dbj|BAF37067.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197197|dbj|BAF37068.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
 gi|118197199|dbj|BAF37069.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
          Length = 233

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 47/282 (16%), Positives = 94/282 (33%), Gaps = 50/282 (17%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL  + L+   ++  +G   L EI+            GF    E   
Sbjct: 1   EGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLIEEEP 49

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                            +  GD +  A V   +     + P+ AE               
Sbjct: 50  APVVVAEDDSA----AADAAGDEDEDADVDASEEDAGPTGPDPAE--------------- 90

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                       V   ++ ++  Y + +          K+         L+  + ++  +
Sbjct: 91  ------------VARRMEVLSAEYAKFKKAY------AKNGAEHKLVAKLRNDIAEVFVT 132

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
           L L     D LV +L D   ++  +E  +L LA     + R  F+   +G + +  WV  
Sbjct: 133 LKLPLPLTDALVRKLRDAMAQVKEHERRVLHLATHVARMPRKDFIRSWEGNQTNVVWVDD 192

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           A    + +W + +    D I+  +     +   T +S++E +
Sbjct: 193 ALKR-KQKWSSALRDVKDQIIAEQEATVGVEQSTYLSLTELK 233


>gi|167769451|ref|ZP_02441504.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
 gi|167668419|gb|EDS12549.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
          Length = 234

 Score = 91.1 bits (224), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 61/257 (23%), Positives = 99/257 (38%), Gaps = 63/257 (24%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E R  +  + +       AK  ++E NLRLV  + KKY +      DLI  
Sbjct: 23  SFPRPLSAKEERECLEGIAR---GDEEAKTRLIEHNLRLVAHIIKKYYSAFKDQDDLISI 79

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F    G +F+TYA   ++  +     ++                     
Sbjct: 80  GTIGLIKAVSTFKPEKGTRFATYASRCIENEVLMHFRNK--------------------- 118

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI- 592
                                          K + + + +  PI  +       L D + 
Sbjct: 119 -------------------------------KKSAQDVYISDPIDTDKDGNSLTLQDIMA 147

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           ED N V  +D  I++   E   R +  +L  RE +++ MR+G+G     T  EV K+  +
Sbjct: 148 EDDNIVDCIDLRIKS---EQLYRFIEGALDERERQIIIMRYGLGGTRSLTQREVAKKLDI 204

Query: 652 TRERIRQIEAKAIRKLK 668
           +R  + +IE KAI  L+
Sbjct: 205 SRSYVSRIEKKAISILR 221


>gi|308173494|ref|YP_003920199.1| RNA polymerase sporulation-specific sigma-29 factor sigma-E
           [Bacillus amyloliquefaciens DSM 7]
 gi|307606358|emb|CBI42729.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553576|gb|AEB24068.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens TA208]
 gi|328911631|gb|AEB63227.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens LL3]
          Length = 239

 Score = 91.1 bits (224), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 95/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLLKLPSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +   + +   D     + 
Sbjct: 134 -------------------SEVSFDEPLNIDWDGNELLLSDVLGTDDDIITKDIEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 KKLLKKALEQLNDREKQIMELRFGLIGEEEKTQKDVADMMGISQSYISRLEKRIIKRLRK 233


>gi|310642979|ref|YP_003947737.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247929|gb|ADO57496.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 246

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 94/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K     +  +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 54  LLGKLSSGDAAVRSMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEK 113

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                                    
Sbjct: 114 KIKLATYASRCIENEILMYLRRNSK----------------------------------- 138

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                            T+  +S + P+  +   +   L D +  +N     +   Q + 
Sbjct: 139 -----------------TRTEVSFDEPLNIDWDGNELLLSDVMGTENDTIYRNIEEQVD- 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + L  LT RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 181 RKLLHKALDKLTDRERLIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 240


>gi|260361298|ref|ZP_05774403.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
 gi|308111826|gb|EFO49366.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
          Length = 158

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 70/140 (50%), Gaps = 4/140 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +      ++I      R
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQR 133

Query: 527 DKIHKVVRTARRMSNKIKRE 546
                + ++ +R+      E
Sbjct: 134 KLFFNLRKSKKRLGWFNNGE 153


>gi|108804004|ref|YP_643941.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765247|gb|ABG04129.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 257

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 102/228 (44%), Gaps = 14/228 (6%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
              A + +  ++  L+ S+A++Y    G  + DL+Q G +GLMKA   +D   G  FS+Y
Sbjct: 27  DRRALERLFASHGALLKSIARRYAGSSGEPYEDLLQAGYVGLMKAVNGYDPSSGAAFSSY 86

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++  I R     S  +R P        +V      ++ ++ R P PEE+A++  + 
Sbjct: 87  AYSMMEGEI-RHHLRDSGLVRRPRWASGLYARVSEATAHLTRELGRPPLPEEVAREANIT 145

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            EG+R+++K     + L T +   D       I   +  S          R      L S
Sbjct: 146 PEGIRELMK-----VYLATSVSSLDEEPDLGAIRSLHYESFSLPVED---RIWLEEALES 197

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L+  + + + + F      D +  E+G++  + + ++ ++ A A++ L
Sbjct: 198 LSELQRKAVYLFF----YKDLSQTEIGRRLGLPQRKVSRLVASAVKSL 241


>gi|4378867|gb|AAD19735.1| sigma-F factor [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 244

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 94/229 (41%), Gaps = 19/229 (8%)

Query: 448 MVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +L+LV  +A     R    ++  DLIQ G + L++AA  F+   G+ F+TYA   +
Sbjct: 25  LIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASMRI 83

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +   +           +   + +    +S  + R P   EIA+KL M     R
Sbjct: 84  RGAMIDYMRQHA---ATARSSIARQKTLNKAREELSATLGRRPEDAEIAEKLNMSPSEYR 140

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +     I     SL+    D  +      I   +         +  L+      + +L  
Sbjct: 141 EWADGAINIRQESLDDVYSDHSS------IFTDDNADQASEMEREALQSALAEQIKTLPE 194

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RE  VL++ +      +  L+E+G+   +   RI QI+  A+  L+   
Sbjct: 195 REALVLQLYYV----EELNLKEIGEVLDLGTARISQIKKSAVDHLRQKM 239


>gi|168182618|ref|ZP_02617282.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
 gi|182674200|gb|EDT86161.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
          Length = 234

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E ++ +  ++K     ++AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPKPLSDEEEKYYLDRLKK---GDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I                 +K  +  
Sbjct: 83  GTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIR---------------NNKKTKGE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDILSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  + +  +++   ++   L  RE++V++MR+G+      T  E+     ++R  +
Sbjct: 154 DSIIEIVSTKIEVKKLYGKIDTCLRGREKKVIQMRYGLKDGRHRTQREIAGILNISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 214 SRIEKKALKKL 224


>gi|239934380|emb|CAR92320.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 222

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 37/267 (13%), Positives = 89/267 (33%), Gaps = 46/267 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + + +    L +I  L   I P+  G         + Q+ E  + +     V
Sbjct: 1   VDSILADYERVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPQTPQSTSKPV 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D +     S+++       PE A      + E  + +   L              
Sbjct: 52  DDDKDDEDEEESESEEEEGDGGPDPEVARLRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   +I   E  +++L      + R  FL +    E +  W        + ++   +   
Sbjct: 137 DALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAA-GKSKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRH 429
            + I + + ++  +  +  ++I++ + 
Sbjct: 196 KEDIQRCQQKLIELEQQCELAIADIKD 222


>gi|161353798|ref|YP_519128.2| sporulation sigma factor SigE [Desulfitobacterium hafniense Y51]
 gi|219670065|ref|YP_002460500.1| sporulation sigma factor SigE [Desulfitobacterium hafniense DCB-2]
 gi|219540325|gb|ACL22064.1| RNA polymerase, sigma 28 subunit, SigE [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 48/228 (21%), Positives = 91/228 (39%), Gaps = 56/228 (24%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   +
Sbjct: 69  RDVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYASRCI 128

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +                                                    
Sbjct: 129 ENEILMHLRRN------------------------------------------------- 139

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                T+  +S + P+  +   +   L D +  +N +       + + R+     +A LT
Sbjct: 140 ---NKTRTEVSFDEPLNIDWDGNELLLSDVLGTENDIISRPLEEKVD-RQLLHLAMARLT 195

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++ +RFG+    + T +EV  +  +++  I ++E + IR+L+ 
Sbjct: 196 DREKLIMELRFGLDNGEEKTQKEVADRLGISQSYISRLEKRIIRRLRK 243


>gi|317132580|ref|YP_004091894.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
 gi|315470559|gb|ADU27163.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
          Length = 242

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 94/242 (38%), Gaps = 56/242 (23%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            + +R  E     AK  ++E NLRLV+ +AKK+ N G+   DL+  G IGL+KA   F  
Sbjct: 48  AACLRGLEAGEKDAKNRLIEHNLRLVVYIAKKFENTGVGVEDLVSIGTIGLIKAVNTFCP 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G K +TYA   ++  I                       + +T  +            
Sbjct: 108 SRGIKLATYASRCIENEILMF--------------------LRKTQNQ------------ 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQA 607
                               K  +S++ P+  +   +   L D +   + V    +  + 
Sbjct: 136 --------------------KNEVSIDEPLHVDWDGNELLLSDVLGTDSDV-VHHNIEKD 174

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +      ++ L+ RE  ++ MRFG+      T +EV     +++  I ++E + I++L
Sbjct: 175 VDKSLLAAAISHLSKRERVIMEMRFGLRGGPGRTQKEVADSLGISQSYISRLEKRIIQRL 234

Query: 668 KH 669
           K 
Sbjct: 235 KK 236


>gi|23099454|ref|NP_692920.1| sporulation sigma factor SigK [Oceanobacillus iheyensis HTE831]
 gi|22777683|dbj|BAC13955.1| RNA polymerase sigma 28 (sigam K) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 234

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 56/267 (20%), Positives = 103/267 (38%), Gaps = 59/267 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ S    +   +    + +++       +A+ +++E NLRLV  + KK+ N G   
Sbjct: 20  SYVKNHSFPQPLPPDKESKYLQLMQ---EGDEVARNKLIEHNLRLVAHIVKKFENTGEDM 76

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+K  E F    G K +TYA   ++  I   +                  
Sbjct: 77  EDLISIGTIGLIKGVESFSTDKGTKLATYAARCIENEILMHLRA---------------- 120

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                        ++ V+K        +SL  PIG +   +   
Sbjct: 121 -----------------------------LKKVKK-------DVSLHDPIGQDKEGNEIS 144

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D +E +N        +   + +   +  + L  RE  V+  R+G+    + T  E+ K
Sbjct: 145 LIDILEAENENVIEYIQLNMEISK-MQKYFSVLDKREREVIVYRYGLNDREEMTQREIAK 203

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +  ++R  + +IE +A+ K+ H    K
Sbjct: 204 KLNISRSYVSRIEKRALMKVFHEYYRK 230


>gi|332272281|gb|AEE38824.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
 gi|332272283|gb|AEE38825.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
 gi|332272285|gb|AEE38826.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
 gi|332272287|gb|AEE38827.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
 gi|332272289|gb|AEE38828.1| RNA polymerase sigma-70 factor [Aeromonas tecta]
          Length = 219

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 78/262 (29%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P             +         E + 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-----ADDVAPTATHIGSELSEDDL 53

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D  E E + E       +D       PE A      L    + +  ++           
Sbjct: 54  ADEDEEEDEDEDGDGDDAEDEGDGGPDPEVAREKFGELRAQYEVTRLSI----------- 102

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   QK+ ++    +    +L  +     L   + D LV 
Sbjct: 103 ------------------------QKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      +
Sbjct: 139 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLL 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + +L+   +++ I  ETG
Sbjct: 199 EMD-EDVLRAIGKLQQIEEETG 219


>gi|152976769|ref|YP_001376286.1| sporulation sigma factor SigK [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025521|gb|ABS23291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 237

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + +  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 19  SYVKNNAFPQPLSPDDEKKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 76  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 119

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 120 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 143

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 144 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 202

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 203 ALGISRSYVSRIEKRALMKMFH 224


>gi|78045111|ref|YP_359473.1| sporulation sigma factor SigK [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77997226|gb|ABB16125.1| RNA polymerase sigma-K factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 234

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 63/283 (22%), Positives = 108/283 (38%), Gaps = 59/283 (20%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V+ +L +   +   +    +S  E  + +  +         A+  + E NLRLV 
Sbjct: 7   LITLVVEGLLFLLGYLAGSAFPQPLSEEEEAYYIDRL---LQGDREARDVLAERNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+   G    DLI  G IGL+KA + F    G K +TYA   V+  I         
Sbjct: 64  HIVKKFEGTGEATEDLISIGTIGLIKAIDTFRPDKGTKLATYAAKCVENEILMH------ 117

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                          +R  ++   +                               +SL 
Sbjct: 118 ---------------LRATKKNRGE-------------------------------VSLY 131

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D +  +  +  L+  ++    ET  + L  LTPRE +V+  RFG+
Sbjct: 132 DPIGFDKEGNEITLLDILGTRGDI-VLEQVVRMLDAETIEKNLKKLTPRERKVIEERFGL 190

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
                 T  E+ K+  ++R  + +IE +AI KL +     K++
Sbjct: 191 SQTPRKTQREIAKKMGISRSYVSRIEKRAILKLLNCFPENKVK 233


>gi|148833417|gb|ABR14578.1| DNA-dependent RNA polymerase sigma factor D subunit [Alcanivorax
           borkumensis SK2]
          Length = 245

 Score = 90.7 bits (223), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 37/280 (13%), Positives = 86/280 (30%), Gaps = 39/280 (13%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             ++ +L   P     +I     + +    L +II     + P   G             
Sbjct: 2   REVLHALAFWPGAVDMVIEEYARVENEERKLTDII--AGYLDPNDDGAAATNANRDPAFA 59

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
            +     +E+   +E   +  S  K S D+  + +   +                     
Sbjct: 60  EKAKKAAEEKAKAKEKAKEEGSDDKDSDDEDEEDEGGLDPVLA----------------- 102

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLS 329
                            AE +  L+ LQ+ A    K + +         E L +      
Sbjct: 103 -----------------AERFETLKKLQEKAERSLKRNGRDHASTAKALEALAEHFTLFK 145

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           L     D ++    D    +   E +++      G + R  F++   G E +  W+    
Sbjct: 146 LVPRIFDSMLVGARDNLDLVRKFERQIMSATIRRGGMDRKDFIKAFPGNETNMEWIDSQL 205

Query: 389 DFPEGEW-KNFVACEVDSILKIRNEIKSISVETGISISEF 427
              +G+   + ++   + + + + +I +I    G+ +++ 
Sbjct: 206 KTKKGKAIADKLSVVKEDVQRAQRKISTIEDIIGLPVADI 245


>gi|121488737|emb|CAJ18252.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 53/165 (32%), Positives = 94/165 (56%), Gaps = 1/165 (0%)

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L  EGN+GL KA  +FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+
Sbjct: 2   LXNEGNLGLXKAXXRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKI 61

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D +
Sbjct: 62  SKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVL 121

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
           ++   + P  +  + +L     R L+ L PRE  V+R  F I M 
Sbjct: 122 QNDGHM-PDHTLNRDSLTLEVERSLSVLAPREADVIRSYFXIXME 165


>gi|239934358|emb|CAR92309.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 244

 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 39/286 (13%), Positives = 91/286 (31%), Gaps = 46/286 (16%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKK---------------- 95

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 96  -------------------ALKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I++ + ++  +  E  + I++ + I       +   +  +  M
Sbjct: 196 KEDIVRCQQKLIELEQECDLVIADIKDINRRANSADIHHTGGRSSM 241


>gi|77165620|ref|YP_344145.1| Sigma28 (flagella) [Nitrosococcus oceani ATCC 19707]
 gi|76883934|gb|ABA58615.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosococcus
           oceani ATCC 19707]
          Length = 234

 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 95/228 (41%), Gaps = 24/228 (10%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E+V     LV  +A     R    +Q  DLIQ G IGL++AA  ++   G  F TYA  
Sbjct: 18  DELVAQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAARNYNASQGASFETYAGI 77

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   I         P  +  K  +V    R + N+  R+    E+A++L +P+  
Sbjct: 78  RIRGAILDEIRRNDW---APRSVHRKARQVAEVMREVENREGRDARDHEVAEELGLPLNE 134

Query: 563 VRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             ++L+        SL+     E++  L   ++      P +     N R      +  L
Sbjct: 135 YHRLLQDAGGYRVFSLDEFNEGEESEPLSASLK-----GPYEGLQDQNFRGALVEAIEGL 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE  V+ + +      D  L E+G+   V+       E++A+ +L+
Sbjct: 190 PERERLVMSLYYV----EDLNLREIGEVLGVS-------ESRAVLRLR 226


>gi|54654459|gb|AAV37106.1| RpoD [Vibrio gigantis]
          Length = 171

 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 58/153 (37%), Gaps = 2/153 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 20  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 79

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 80  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 138

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
             ET +++   + I   +  GE +A  AKKE V
Sbjct: 139 ERETSLTVQSIKDISRRMSIGEAKARRAKKETV 171


>gi|168186813|ref|ZP_02621448.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
 gi|169295137|gb|EDS77270.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 97/251 (38%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +V+ +R         +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKEEEESLVAKIR---AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                  +  +       
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLR-----------------RNNKVKAE--- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +  +N +
Sbjct: 132 --------------------------------ISFYEPLNTDWDGNKLLLSDILGTENDM 159

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + ++     +  L+ RE+ ++++RFG+    + T ++V     +++  I +
Sbjct: 160 VYNLIEDEVD-KQLLFIAMRKLSDREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISR 218

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 219 LEKRIIKRLKK 229


>gi|13446369|gb|AAK20925.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 237

 Score = 90.7 bits (223), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 47/225 (20%), Positives = 99/225 (44%), Gaps = 21/225 (9%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++   L LV   A    ++        D+ Q G +GL++A  ++D     +F  YA   +
Sbjct: 24  ILTRYLPLVKRAASHLRSQVSACFDQEDMEQVGMMGLLEAWRRYDSEPDPQFERYAFKRI 83

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +      +     +R ++H   +  R + N++ R PT +E+A  L   VE VR
Sbjct: 84  RGAMLDELRRLDWRLP---TLRQQVHSHNQAQRELYNRLGRSPTEQELAVSLNCTVEEVR 140

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           ++   +            E    L +++E+    +P   +   ++  T ++VL SL  RE
Sbjct: 141 QLAYAS----------QAEALQSLEEWLEN-GGKAPATESDDVDMAMTISKVLTSLDKRE 189

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +L + +      +  ++E+     +T  R+ Q+  + + +LK 
Sbjct: 190 QLLLSLYY----QQELNMKEIALVLGLTESRVCQLHKQCVLQLKQ 230


>gi|54654455|gb|AAV37104.1| RpoD [Vibrio gigantis]
          Length = 164

 Score = 90.7 bits (223), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 32/155 (20%), Positives = 60/155 (38%), Gaps = 2/155 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 11  QNRQLAINEYGHESPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIM 70

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 71  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMI 129

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
             ET +++   + I   +  GE +A  AKKE VEA
Sbjct: 130 ERETSLTVQSIKDISRRMSIGEAKARRAKKETVEA 164


>gi|239934350|emb|CAR92305.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 245

 Score = 90.7 bits (223), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 40/286 (13%), Positives = 91/286 (31%), Gaps = 45/286 (15%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   + + +    L +I  L   I P+  G         + Q+ E  + +     V
Sbjct: 1   VDGILADYERVTNEGGRLSDI--LSGYIDPDDDGA------AGAPQEVEPVAPQVAAKPV 52

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 53  ADDKDDDEEEESDSEEEEGDGGPDPEVARARFGAVAEQLEKAKK---------------- 96

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S       E L  L   + L   + D LVE++ 
Sbjct: 97  -------------------ALKKHGRASQHAIDELEALAILFMPIKLVPXQYDALVERVR 137

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   +I   E  +++L      + R  FL +    E +  W        + ++   +   
Sbjct: 138 DALNQIRAQERAVMQLCVRDARMPRADFLRQFPSNETNLAWAEELAA-GKSKYAEAIGAR 196

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
            + I + + ++  +  E  ++I++ + I       +   +  +  M
Sbjct: 197 KEDIQRCQQKLIELEQECELAIADIKDINRRANSADIHHTGGRSSM 242


>gi|282952605|emb|CBI75475.1| RNA polymerase beta subunit [Pseudomonas tolaasii]
          Length = 209

 Score = 90.7 bits (223), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 25/126 (19%), Positives = 58/126 (46%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++    +R+   E  +++L      
Sbjct: 85  KHGRTNKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 144

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 145 MPRADFLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTI 203

Query: 425 SEFRHI 430
           +E + I
Sbjct: 204 AEIKDI 209


>gi|148833409|gb|ABR14574.1| DNA-dependent RNA polymerase sigma factor D subunit [Alcanivorax
           indicus]
          Length = 240

 Score = 90.7 bits (223), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 43/280 (15%), Positives = 94/280 (33%), Gaps = 44/280 (15%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             ++ ++   P +   ++   D +      L +II     + P   G       G     
Sbjct: 2   REVLHAMAFWPGSVDLVVGEFDMIALEERRLSDII--AGYLDPNDDGAAATAGNGEPTFA 59

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
               ++ ++ +   + + D    +   +DD S                            
Sbjct: 60  ERAKAKAEKAEAENDDDSDDSDDSDDDEDDGSLDP------------------------- 94

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLS 329
                    V+      AE + +LR+L D      +K+ +         E + +      
Sbjct: 95  ---------VLA-----AERFNQLRALLDKTQKALKKNGRDHSSSGKALEAMAEHFTLFK 140

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           L     D L+  + D    +   E E++ LA   G + R  F++   G E +  W+    
Sbjct: 141 LVPRVYDELLRNVRDTLDVVRKYEKEIMMLAIKRGRMPRADFIKSFPGNESNLKWIDNQL 200

Query: 389 DFPEG-EWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              +G E  + +    D IL+++ +I+ +  + G+ I++ 
Sbjct: 201 RTKKGKEIADQLNVVKDDILRVQRKIQQVEEKVGLPIADI 240


>gi|330874700|gb|EGH08849.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 202

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 40/183 (21%), Positives = 89/183 (48%), Gaps = 5/183 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   + +++    ++    R +   +     +   A ++MV A+LR V+ +A+ Y+  GL
Sbjct: 17  LEAYVHTVNSIPLLTPERERELAESL--YYEQDLDAARQMVLAHLRFVVHIARSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGN+GLMKA ++F+  +G +  ++A+ W+K  I   I      +++     + 
Sbjct: 75  AQADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQR 134

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS 586
           K+   +R+ ++    +  +     +A+ L +    VR++  ++T   ++ +     +D S
Sbjct: 135 KLFFNLRSQKKRLAWLNNDEVHR-VAESLGVEPREVREMESRLTGHDMAFDPAAEADDDS 193

Query: 587 HLG 589
              
Sbjct: 194 AFQ 196


>gi|218289913|ref|ZP_03494103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240053|gb|EED07239.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 46/225 (20%), Positives = 90/225 (40%), Gaps = 56/225 (24%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   ++  
Sbjct: 2   LIERNLRLVVYIARKFENTGVNIEDLVSIGTIGLIKAVNTFDPSKKIKLATYASRCIENE 61

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I   +               + +K+                                   
Sbjct: 62  ILMYLR--------------RNNKLR---------------------------------- 73

Query: 568 KITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
                 +SL+ P+  +   +   L D +   ++ +   +      RE     L  L+ RE
Sbjct: 74  ----AEVSLDEPLNVDWDGNELLLSDVLG-TDSDTIYRNLEDEVDRELLYDALDKLSERE 128

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ +RFG+G   + T ++V     +++  I ++E + +++L+ 
Sbjct: 129 RTIMELRFGLGTGQEMTQKDVADLLGISQSYISRLEKRILKRLQR 173


>gi|318040135|ref|ZP_07972091.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 112/284 (39%), Gaps = 28/284 (9%)

Query: 420 TGISISEFRHIVSMVRKGE-----------CEASIAKKEMVEANLRLVISVAKKYTNRGL 468
              ++ E    +   ++               A  A++++V  NL LV     ++     
Sbjct: 26  CERTVMELSRRIQRWQQHPDGPSHAPKPVRRSALRAREQLVRHNLGLVAHTWGRHRCSLP 85

Query: 469 QFLD----LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              D     +QE  + L++AAEKFD   GY+FSTYA +WV++  T         IR P  
Sbjct: 86  AHDDTTADALQEAALNLVRAAEKFDPAKGYRFSTYATFWVRRGFTEFEQRAKRAIRFPAE 145

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKK-----LAMPVEGVRKV--LKITKEPISLE 577
               + K +R +++       EP  E +A +      AM  E + +           SL+
Sbjct: 146 KAAVVLKALRLSQQHQATTGDEPALEWLAAQLKFDGKAMSAEQLAEFIRQWDATRTGSLD 205

Query: 578 TPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
               + D        D    + A     +        +  ++++ L  +E R++R R+  
Sbjct: 206 GAEEEGDEKGGCSRLDLASLQQAAEQQLTQEPDPQHASLPQLMSCLDEQEHRLIRNRYLR 265

Query: 635 GMNTDHTLEEVGKQF-CVTRERIRQIEAKAIRKLKHPSRSKKLR 677
                 +  ++ +    + RE++ Q+EA A+ KL+  +    L+
Sbjct: 266 RP--PLSPCQLRRSMGGMQREQLEQLEATALDKLRQAATGHNLK 307


>gi|220929479|ref|YP_002506388.1| sporulation sigma factor SigE [Clostridium cellulolyticum H10]
 gi|219999807|gb|ACL76408.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulolyticum
           H10]
          Length = 243

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 99/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ E  ++++ + + +      K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 43  LTLDEETYLLNKLEQSDYGV---KSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   +                         
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEILMYLRRNNRVKAE-------------------- 139

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS++ P+  +   +   L D +  +N +
Sbjct: 140 --------------------------------ISIDEPLNIDWDGNELLLSDILGTENDM 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               S      +E     +  L+ RE++++ +RFG+    + T +EV     +++  I +
Sbjct: 168 -IHRSIEDEVDKELLATAMKKLSVREKKIMELRFGLSNGVEKTQKEVADMLGISQSYISR 226

Query: 659 IEAKAIRKLKH 669
           +E + I +LK 
Sbjct: 227 LEKRIISRLKK 237


>gi|213419681|ref|ZP_03352747.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 174

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 83/174 (47%), Gaps = 8/174 (4%)

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++
Sbjct: 2   FTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVAER 58

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI-EDKNAVSPLDSAIQANLRETTT 614
           L +PV   R++L  T            E+     + + E+    +PL   ++ +LR+   
Sbjct: 59  LGIPVAEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVM 118

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + SL  RE+ VL + +      +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 119 DAIESLPEREQLVLTLYYQ----EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 168


>gi|30022417|ref|NP_834048.1| sporulation sigma factor SigK [Bacillus cereus ATCC 14579]
 gi|228902866|ref|ZP_04067008.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
 gi|228910177|ref|ZP_04073996.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228916971|ref|ZP_04080532.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228929384|ref|ZP_04092407.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935660|ref|ZP_04098474.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941506|ref|ZP_04104056.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954625|ref|ZP_04116649.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960610|ref|ZP_04122256.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228974436|ref|ZP_04135004.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981030|ref|ZP_04141332.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|229025805|ref|ZP_04182204.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|229031990|ref|ZP_04187975.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|229048046|ref|ZP_04193621.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|229062038|ref|ZP_04199363.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|229071846|ref|ZP_04205059.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|229076014|ref|ZP_04208987.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|229098811|ref|ZP_04229749.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|229104971|ref|ZP_04235627.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|229111812|ref|ZP_04241358.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|229117837|ref|ZP_04247201.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|229123878|ref|ZP_04253071.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|229129620|ref|ZP_04258588.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|229141077|ref|ZP_04269619.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|229157954|ref|ZP_04286026.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|229163288|ref|ZP_04291242.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|229169087|ref|ZP_04296802.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|229175013|ref|ZP_04302532.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|229180616|ref|ZP_04307957.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|229192552|ref|ZP_04319513.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|229198467|ref|ZP_04325171.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|29897975|gb|AAP11249.1| RNA polymerase sigma-K factor [Bacillus cereus ATCC 14579]
 gi|228584970|gb|EEK43084.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|228590859|gb|EEK48717.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|228602859|gb|EEK60339.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|228608474|gb|EEK65777.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|228614315|gb|EEK71425.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|228620195|gb|EEK77067.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|228625514|gb|EEK82269.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|228642355|gb|EEK98644.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|228653737|gb|EEL09607.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|228659592|gb|EEL15239.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|228665634|gb|EEL21112.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|228671568|gb|EEL26866.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|228678465|gb|EEL32686.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|228684655|gb|EEL38595.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|228707126|gb|EEL59326.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|228711276|gb|EEL63238.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|228717190|gb|EEL68865.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|228723290|gb|EEL74660.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|228729345|gb|EEL80337.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|228735513|gb|EEL86109.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|228778690|gb|EEM26955.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|228785272|gb|EEM33283.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228799038|gb|EEM46009.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805071|gb|EEM51666.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818156|gb|EEM64231.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824020|gb|EEM69838.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830290|gb|EEM75904.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842692|gb|EEM87779.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849460|gb|EEM94295.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228856740|gb|EEN01258.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
          Length = 240

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 22  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 78

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 79  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 122

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 123 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 146

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 147 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 205

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 206 ALGISRSYVSRIEKRALMKMFH 227


>gi|295399723|ref|ZP_06809704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111758|ref|YP_003990074.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
 gi|294978126|gb|EFG53723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216859|gb|ADP75463.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
          Length = 239

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 52/277 (18%), Positives = 104/277 (37%), Gaps = 57/277 (20%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRL 455
            F+   +  +    +E+  I     +     +     ++ K       A+  ++E NLRL
Sbjct: 10  YFLYKLLKKLGIKMDELYYIGGSEALPPPLTKEEEEMLIGKLSDGDETARSLLIERNLRL 69

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V+ +A+K+ N G+   DLI  G IGL+KA   F+     K +TYA   ++  I   +   
Sbjct: 70  VVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMHLRRN 129

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +                                              VR         +S
Sbjct: 130 N---------------------------------------------KVRAE-------VS 137

Query: 576 LETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            + P+  +   +   L D +  ++ V   D     + R      L  L+ RE++++ +RF
Sbjct: 138 FDEPLNIDWDGNELLLSDVLGTEDDVITKDLEADVD-RNLLFNALRQLSDREKQIMELRF 196

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           G+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 197 GLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 233


>gi|282952590|emb|CBI75472.1| RNA polymerase beta subunit [Pseudomonas lini]
 gi|282952592|emb|CBI75473.1| RNA polymerase beta subunit [Pseudomonas marginalis]
 gi|282952594|emb|CBI75474.1| RNA polymerase beta subunit [Pseudomonas migulae]
 gi|282953997|emb|CBI75476.1| RNA polymerase beta subunit [Pseudomonas veronii]
          Length = 209

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 28/144 (19%), Positives = 62/144 (43%), Gaps = 6/144 (4%)

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEK----LVKLVGSLSLNQSRIDLLVEQLYDISK 347
           +   ++ D     +K  K   +   L       L +L   + L   + + LVE++    +
Sbjct: 67  QRFGAVSDQMEITRKALKKHGRSNKLAIAELVALAELFMPIKLVPKQFEGLVERVRSALE 126

Query: 348 RIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           R+   E  +++L      + R  FL +  G E+D  W   A    + ++   +      I
Sbjct: 127 RLRAQERAIMQLCVRDARMPRTDFLRQFPGNEVDESWTD-ALAKGKAKYAEAIGRLQPDI 185

Query: 407 LKIRNEIKSISVETGISISEFRHI 430
           ++ + ++ ++  ETG++I+E + I
Sbjct: 186 IRCQQKLTALQTETGLTIAEIKDI 209


>gi|225017509|ref|ZP_03706701.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
 gi|224949748|gb|EEG30957.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
          Length = 231

 Score = 90.3 bits (222), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 101/249 (40%), Gaps = 57/249 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ + +    ++++     S A+  ++E NLRLV  +AKKY +   +  DLI  G IGL
Sbjct: 30  LTLKQEKESFELMKQ---GDSAARDRLIEHNLRLVAHIAKKYYSVTNEQDDLISIGTIGL 86

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD+  G +F+TYA   ++  I     +                           
Sbjct: 87  IKAVGTFDYTKGTRFATYASRCIENEILMHFRN--------------------------- 119

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                                V+K    T   + +   I  +   +    I+     + +
Sbjct: 120 ---------------------VKK----TAGDVYINDTIDTDKDGNSISLIDVIADETNI 154

Query: 602 DSAIQANLR-ETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              I   L+ E   + + + LT RE+ ++ +R+G+  +   T  EV  +  ++R  + +I
Sbjct: 155 VDTIDLKLKSEQLHKSIKNLLTEREQMIVILRYGLNGHRPMTQREVADRLKISRSYVSRI 214

Query: 660 EAKAIRKLK 668
           E K++ +LK
Sbjct: 215 EKKSLEQLK 223


>gi|330447923|ref|ZP_08311571.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492114|dbj|GAA06068.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 242

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/218 (21%), Positives = 93/218 (42%), Gaps = 18/218 (8%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           + V++  + +T+    + D+ Q G IGL++AA ++      +F  +A+  ++ AI   + 
Sbjct: 37  KRVVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGDVDDPQFPAFAVCRIRGAILDELR 96

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-- 571
                       R + H++    R +  ++ R+PT  EI   L +      + L+ +   
Sbjct: 97  RLDW---RSRQTRQQAHELNDATRDLMKQLGRQPTEAEITHALGIDNNDYHQRLQASMAS 153

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           E  SL+          L +  ++        S    +LR + T  L  LT RE+ +L + 
Sbjct: 154 EMQSLD---------QLLEAGKELETPFTDTSIEHEHLRRSLTYALTQLTKREQLLLTLF 204

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      +  L E+     +T  RI Q+  +A++ L H
Sbjct: 205 YQH----ELNLHEIALVLNLTPPRICQLHKQALKSLNH 238


>gi|291288738|ref|YP_003505554.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290885898|gb|ADD69598.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 245

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/224 (20%), Positives = 105/224 (46%), Gaps = 13/224 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K +++   +  + S   + +      +   DL     +GL+++ E+FD      F T+  
Sbjct: 18  KDKIILEFMPRIKSWVLRISTTLPDTVDVDDLYSSACLGLIESLERFDKDRNVNFYTFGE 77

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +K AI  ++ +      +P ++R ++ ++ R           +PT EEI +      +
Sbjct: 78  RRIKGAILDTLRNLD---YLPRNVRTRLKQLERHIGNHYRTAGEKPTVEEIIENSDFSEQ 134

Query: 562 GVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            V ++L++ +    +SL+  +G E  + L DFI+    ++P D A++  L +T    + +
Sbjct: 135 EVYRLLELMENDKILSLDESVGPEGDTSLVDFIK-STGLTPEDEALKTRLVDTLGEEIEN 193

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           L+ +E+ V+ + +      + T++E+     +T  R+ QI + A
Sbjct: 194 LSEKEKYVVSLYY----YEELTMKEIAMVLGITESRVSQIHSAA 233


>gi|118134194|gb|ABK61238.1| RNA polymerase sigma-E factor [Clostridium novyi NT]
          Length = 230

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  ++V+ +R         +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 30  LSKEEEENLVNKIR---AGDDSVRTILIERNLRLVVYIARKFENSGILVEDLISVGTIGL 86

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                  +  +       
Sbjct: 87  IKAVNTFDPEKKIKLATYASRCIENEILMYLR-----------------RNNKVKAE--- 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +  +N +
Sbjct: 127 --------------------------------ISFYEPLNTDWDGNKLLLSDILGTENDM 154

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + ++     +  L+ RE+ ++++RFG+    + T ++V     +++  I +
Sbjct: 155 VYNLIEDEVD-KQLLFIAMRKLSDREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISR 213

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 214 LEKRIIKRLKK 224


>gi|31747734|gb|AAO38358.1| Lfe160p1 [Leptospirillum ferrooxidans]
          Length = 218

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 14/217 (6%)

Query: 461 KKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            +Y +R    +   DL+  G  GL+ AA++FD   G KF T A   ++ A+   I     
Sbjct: 1   MRYAHRLPPEIDVDDLVSVGMTGLIDAAKRFDPSRGIKFKTMAEHRIRGAMLDEIRSADW 60

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPIS 575
              +P  +R+K   V      +   + REP   E+AK L+M ++     +         S
Sbjct: 61  ---VPRSVREKASSVHAVREGLRAALLREPDDMEMAKALSMSLDEYLTLENEIEPHHLYS 117

Query: 576 LETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +E     E+   S + D +       PL   +++       + L SL  ++  VL + + 
Sbjct: 118 IEDLFEMEEGAGSSILDRMVVPGEADPLSEFLKSEEASLLEKALDSLPEKQRLVLSLYY- 176

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                + +++EV     V+  R+ QI   AI+ LK  
Sbjct: 177 ---YEELSMKEVAAVLEVSESRVSQIHTLAIKNLKKA 210


>gi|209408324|emb|CAP19905.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 203

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 37/241 (15%), Positives = 76/241 (31%), Gaps = 45/241 (18%)

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
           +++   P T  +++   + + +    L +I  L   I P+  G         + Q+ E  
Sbjct: 1   SAIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPQ 51

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
           + +     V + + D +     S+++       PE A      + E  + +   L     
Sbjct: 52  TPQSTSKPVDDDKDDEDEEESESEEEEGDGGPDPEVARLRFGAVAEQLEKANKAL----- 106

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
                                         +K  ++S +     E L  L   + L   +
Sbjct: 107 ------------------------------KKHGRASQQATEELEALAILFMPIKLVPKQ 136

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            D LVE++ D   +I   E  +++L      + R  FL +    E +  W          
Sbjct: 137 YDALVERVRDALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAAGKSK 196

Query: 394 E 394
            
Sbjct: 197 Y 197


>gi|117929239|ref|YP_873790.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649702|gb|ABK53804.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 297

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 87/229 (37%), Gaps = 18/229 (7%)

Query: 446 KEMVEANLRLV----ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
            ++V+ +L LV       A K     +   DL   G + L +AA  +D   G  F+ +A 
Sbjct: 22  DQLVKDHLPLVGYLVAETASKLPG-HVNRDDLTSAGMMALAQAARTYDPSRGVPFARFAT 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +            +R K  +       ++  + R PT  E+A+ L + V+
Sbjct: 81  VRIRGAIIDELRSHDW---ASRSVRVKARQRAAAEEELAAVLGRLPTQAELAEHLGVSVD 137

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRVLAS 619
            +          + L       D   L   +   D      L +  + N        +A+
Sbjct: 138 ELASTEGDVHRAVVLSLQGFA-DAGTLEGMLPHQDPGPEDVLLNRERVNY---LLDAVAA 193

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L PR   V+   F      +  + E+ ++  VT  RI Q+ A+A+  L+
Sbjct: 194 LPPRLRTVVEGYFF----QERPMAELAEELGVTESRISQMRAEALSLLR 238


>gi|319919245|gb|ADV78240.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
 gi|319919253|gb|ADV78244.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
          Length = 212

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 70/249 (28%), Gaps = 46/249 (18%)

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           E G   +M ++   P T   ++     +      L +++            G+    +G 
Sbjct: 1   EEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGI 49

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +         + +    +  + D E +A  S ++      P             D+ +  
Sbjct: 50  APPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEIT 109

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
                   +     +  L  +AE++                                   
Sbjct: 110 RKALKKFGRDDKHAIAELVALAELF----------------------------------M 135

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
            + L   + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W  
Sbjct: 136 PIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTD 195

Query: 386 YAKDFPEGE 394
                    
Sbjct: 196 GLAKGKGKY 204


>gi|46204236|ref|ZP_00050286.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 182

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/173 (28%), Positives = 84/173 (48%), Gaps = 8/173 (4%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R +   V   E     A   ++ A++RLVI++A ++ + GL   DL+QEG++GL
Sbjct: 6   LARDEERGLA--VAWKEERDERALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 63

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM 539
           M+AA +F+     +FSTYA WW++ +I   I      +R       K     + R   R+
Sbjct: 64  MEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 123

Query: 540 SNKIKREPTPE---EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHL 588
               + +   E    IA  + +  E V     +++   +SL  P+G+E  S L
Sbjct: 124 MQSTEEQVGSEIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEERRSFL 176


>gi|165973130|gb|ABY76244.1| sigma-K factor [Bacillus thuringiensis]
          Length = 237

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 76  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 119

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 120 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 143

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 144 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 202

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 203 ALGISRSYVSRIEKRALMKMFH 224


>gi|89072296|ref|ZP_01158875.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium sp. SKA34]
 gi|89051828|gb|EAR57280.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium sp. SKA34]
          Length = 242

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 102/238 (42%), Gaps = 20/238 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +    E  + +  +V   ++ V++  + +T+    + D+ Q G IGL++AA ++      
Sbjct: 20  QHHIDEDLLIRNHLVL--VKRVVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGNVEDP 77

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F  +A+  ++ AI   +           H R + H++    R +  ++ R+PT  EI  
Sbjct: 78  QFPAFAVCRIRGAILDELRRLDW---RSRHTRQQAHELNDITRDLMKQLGRQPTEAEITS 134

Query: 555 KLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L +  E  +  L   +  E  SL+          L +  ++ +A    +     ++R T
Sbjct: 135 ALGIDSENYQLRLQACMASEMQSLD---------QLLEAGKELDAPLEYNGVEHEHMRRT 185

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               L  L+ RE+ +L + +      +  L E+     +T  RI Q+  +A++ L H 
Sbjct: 186 LEYALTQLSRREQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKSLNHS 239


>gi|332272451|gb|AEE38909.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|332272453|gb|AEE38910.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|332272455|gb|AEE38911.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|332272457|gb|AEE38912.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 217

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 82/262 (31%), Gaps = 46/262 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P          +  +       S+  E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPNE-------ADDVAPTATHIGSELGED 51

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D   E E + E     S DD       PE A     +L    + +  ++           
Sbjct: 52  DLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEVTRLSI----------- 100

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   QK+ ++    +    +L  +     L   + D LV 
Sbjct: 101 ------------------------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVN 136

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      +
Sbjct: 137 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLL 196

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + +L+   +++ I  ETG
Sbjct: 197 EMD-EEVLRSIGKLQQIEEETG 217


>gi|162139704|ref|YP_878335.2| sporulation sigma factor SigE [Clostridium novyi NT]
          Length = 235

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 98/251 (39%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  ++V+ +R         +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 35  LSKEEEENLVNKIR---AGDDSVRTILIERNLRLVVYIARKFENSGILVEDLISVGTIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                  +  +       
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLR-----------------RNNKVKAE--- 131

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS   P+  +   +   L D +  +N +
Sbjct: 132 --------------------------------ISFYEPLNTDWDGNKLLLSDILGTENDM 159

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + + ++     +  L+ RE+ ++++RFG+    + T ++V     +++  I +
Sbjct: 160 VYNLIEDEVD-KQLLFIAMRKLSDREKEIIKLRFGLTGKGEKTQKQVADLLGISQSYISR 218

Query: 659 IEAKAIRKLKH 669
           +E + I++LK 
Sbjct: 219 LEKRIIKRLKK 229


>gi|332187909|ref|ZP_08389642.1| RNA polymerase sigma factor, FliA/WhiG family protein [Sphingomonas
           sp. S17]
 gi|332012070|gb|EGI54142.1| RNA polymerase sigma factor, FliA/WhiG family protein [Sphingomonas
           sp. S17]
          Length = 265

 Score = 90.3 bits (222), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 96/233 (41%), Gaps = 19/233 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++  +L LV  +A              DL+Q G + L++AA  F+   G +F  Y    +
Sbjct: 47  IIRQHLPLVRRIAWHVHGSMSSLIEVEDLVQVGLVALVEAAASFE-ERGVEFGHYLKARL 105

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +               +  +       +S    + PT E +A+KL +  E +R
Sbjct: 106 RGAMIDELR---RQATTTRGAMRRRRQYHEAVTALSQVAGQVPTDEAVAEKLGVTTEKLR 162

Query: 565 KVLKITKEPISLE--TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                T E + +E    +  +D     D     +     +   +++LR+     +ASL  
Sbjct: 163 TD-YKTAEAVRMEPIDDVYADDLPWFAD-----DTPDAFEQLAESDLRDALIAAIASLPE 216

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           RE  V+++ +      +  LEE+G+   V   R+ QI++ A  +LK    +++
Sbjct: 217 REAMVIQLYYV----EELNLEEIGQVLGVGAARVCQIKSAAHARLKKALSAQR 265


>gi|119963836|ref|YP_945938.1| RNA polymerase sigma (70) factor [Arthrobacter aurescens TC1]
 gi|119950695|gb|ABM09606.1| putative RNA polymerase sigma (70) factor [Arthrobacter aurescens
           TC1]
          Length = 258

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/223 (21%), Positives = 97/223 (43%), Gaps = 12/223 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L L  S+A +Y+       D+ Q   +GL+KA+  +D   G  F  YA   +   
Sbjct: 30  LVLDHLNLAKSIAARYSAHTHDLDDVRQVAYMGLIKASRGYDEAKGVSFPAYAAPTIAGE 89

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R + D    +R P  ++D   +V+     M+  ++R P+PEE+A+ L +    VR+ L
Sbjct: 90  VKRYLRDHCWVVRPPRTIQDVRRQVLARTEEMTQTLQRTPSPEEVAEDLNLEPCQVREAL 149

Query: 568 KI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
               +K P SL+ P  D      G      +A       ++  L       +  L+  + 
Sbjct: 150 MAGTSKRPDSLDAPASDGRDGLQGSL----SAFGCPTDRLEDVL--ALRNAIRGLSAEDR 203

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R+      + T   + +   +++ ++ +  +K +  L+
Sbjct: 204 HLLYRRY----YREETQSTIAEALGMSQMQVSRKLSKILVSLQ 242


>gi|65321710|ref|ZP_00394669.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|228923092|ref|ZP_04086384.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228948053|ref|ZP_04110338.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987592|ref|ZP_04147708.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229013560|ref|ZP_04170693.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|229019564|ref|ZP_04176380.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|229081603|ref|ZP_04214099.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|229135165|ref|ZP_04263965.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|229146910|ref|ZP_04275274.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|229152543|ref|ZP_04280733.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|229186579|ref|ZP_04313740.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228596838|gb|EEK54497.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228630909|gb|EEK87548.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|228636509|gb|EEK92975.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|228648293|gb|EEL04328.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|228701709|gb|EEL54199.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|228741730|gb|EEL91914.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|228747720|gb|EEL97590.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|228772133|gb|EEM20583.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228811639|gb|EEM57975.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228836590|gb|EEM81939.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 243

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 25  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 81

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 82  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 125

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 126 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 149

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 150 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 208

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 209 ALGISRSYVSRIEKRALMKMFH 230


>gi|254449115|ref|ZP_05062567.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
 gi|198261307|gb|EDY85600.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
          Length = 227

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/190 (23%), Positives = 92/190 (48%), Gaps = 8/190 (4%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           VA   D++     ++ SI V   +   E + +   + +       A +++V ++LR V  
Sbjct: 38  VALSNDTLDAYMQQVSSIPV---LGAEEEQELAQRLHR--EGDLDAARQLVFSHLRFVTH 92

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +A+ Y   GL   D+IQEGNIGLMKA ++FD  +G +  ++A+ W++  I   I      
Sbjct: 93  IARGYKGYGLPLADVIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIRAEIHEYILRNWRI 152

Query: 519 IRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISL 576
           +++     + K+   +R+ ++    +  E     +AK L +    V ++  ++    ++ 
Sbjct: 153 VKVATTKAQRKLFFKLRSNKKSLGWLNHEEVKT-VAKDLGVEASDVMEMESRLAGSDMAY 211

Query: 577 ETPIGDEDTS 586
           + P  D+D +
Sbjct: 212 DLPGNDDDDA 221


>gi|326390169|ref|ZP_08211730.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993817|gb|EGD52248.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 231

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 102/270 (37%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  V  IL +     + S    ++  E +  +   R        A+  ++E NLRLV 
Sbjct: 8   ILASIVKEILNLGYLTNTNSFPNPLTPEEEKKYLEAYR---NGDEEARNILIERNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   ++  I  S      
Sbjct: 65  HVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMS------ 118

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                          +R  ++M  +I        +   + +  EG               
Sbjct: 119 ---------------IRAEKKMKGEIF-------LQDPIGVDKEG--------------- 141

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                 +   L D +  +          +  +++  +++ + L  RE  ++ MR+G+   
Sbjct: 142 ------NEISLMDVLGTEEDEISEQVEKKLQIKKLYSKMNSVLKNRERLIIEMRYGLYNG 195

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T  E+ K   ++R  + +IE KA+ KL
Sbjct: 196 KVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|260221743|emb|CBA30612.1| hypothetical protein Csp_C24420 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 264

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 112/241 (46%), Gaps = 15/241 (6%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF-DWCLGYKFSTYAM 501
           +++VE +  +V SVA     R    +   DL+Q+G +GLM+A  ++     G  F  Y  
Sbjct: 13  RKLVEDHQPVVRSVANHVGRRLPPNVDRADLVQDGMLGLMEALLRWTKESSGTHFENYIA 72

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
              + A+   +        +   +R  + +V    +++S+++ R PT  E+AK+L MP+ 
Sbjct: 73  LRAQGAMIDGLRAAD---PVSRQVRKDMRRVEVALQQLSHRLGRPPTEGELAKQLDMPLA 129

Query: 562 GVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +++L+  +  +  SL+   GD    +L   +ED     PL    +A LR+     +  
Sbjct: 130 DYQRLLQDAQGYVLISLQDLTGDSVDQYLKRCLEDN--ADPLALLERAALRQALAESIQL 187

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           L  + + +L + +      +  + E+ K   ++  RI Q+  ++I +L+     + ++  
Sbjct: 188 LPRKSQILLTLYY----EHEMRMHEIAKHLGLSEARISQMHTQSIAQLRASLADRDIKRL 243

Query: 680 L 680
           L
Sbjct: 244 L 244


>gi|289754806|ref|ZP_06514184.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695393|gb|EFD62822.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 84

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 37/73 (50%), Positives = 53/73 (72%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L++    VL +L+ RE  V+R+RFG+      TL+E+G+ + VTRERIRQIE+K + KL+
Sbjct: 12  LQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLR 71

Query: 669 HPSRSKKLRSFLD 681
           HPSRS+ LR +LD
Sbjct: 72  HPSRSQVLRDYLD 84


>gi|297626395|ref|YP_003688158.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922160|emb|CBL56728.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 272

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 59/297 (19%), Positives = 120/297 (40%), Gaps = 29/297 (9%)

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
           +D   ++      +   +  +A  +++ +   + ++      G S  E R +V+      
Sbjct: 1   MDATQIASISPRLDAADERELARLIEAGVFAGHALEQDQSPCGASAEELRQVVA------ 54

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               +A ++  E N+ LV  V  ++         DL+ EG +GL++A  +FD  LG++FS
Sbjct: 55  -HGELAWQKFFEGNISLVRCVVARWVPVTHPDSEDLVHEGCMGLVEAIMRFDHALGWRFS 113

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           T A + V Q +  +           V    ++ ++ R   R S       +  E+A  + 
Sbjct: 114 TLAWYLVSQQVAIAAVGNRSCGSGTVAHARRVARIERARSRASASRGAPVSDREVADLVG 173

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             VE VR+ L   +          + D   L   I D+  V  +               L
Sbjct: 174 RSVEAVRRDLGQARRV--------EADQDILEQTIPDERPVHDVS-------------FL 212

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + L  +E RVL + FGI      TL ++ +   ++   + +++ +A+R+ +    ++
Sbjct: 213 SELADQERRVLELNFGIRNGRAQTLVQIAEHMGMSVSAVSRLKQRALRRGRALVHAE 269


>gi|118197181|dbj|BAF37060.1| DNA-directed RNA polymerase subunit D [Xanthomonas albilineans]
          Length = 232

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/282 (15%), Positives = 92/282 (32%), Gaps = 51/282 (18%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
            G + + A+L   PL  + L+   ++  +G   L EI+            GF    E   
Sbjct: 1   EGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIV-----------VGFNDLVEEEP 49

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
                            + + D ++    S++D       P                   
Sbjct: 50  APVVVAEDDGAA---DADADEDEDADVDASEEDAGPTGPDPVE----------------- 89

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
                       V   ++ ++  Y + +          K+         L+  + ++  +
Sbjct: 90  ------------VARRMEVLSTEYVKFKKAY------AKNGAEHKLVAKLRNDIAEVFVT 131

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSY 386
           L L     D LV +L D   ++  +E  +L LA     + R  F+   +G + +  WV  
Sbjct: 132 LKLPLPLTDALVRKLRDAMAQVKEHERRVLHLATHVARMPRKDFIRSWEGNQTNVAWVDD 191

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
           A    + +W + +    D I+  +     +   T +S++E +
Sbjct: 192 ALKR-KQKWSSALRDVKDQIIAEQEATVEVEQSTYLSLTELK 232


>gi|289751356|ref|ZP_06510734.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
 gi|289691943|gb|EFD59372.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
          Length = 470

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 54/132 (40%), Positives = 76/132 (57%), Gaps = 4/132 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT-RSIAD 514
           V+S+AK+YT RG+ FLDLIQEGN+GL++A EKFD+  GYKFSTYA WW++QAIT R    
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITPRHGRP 362

Query: 515 QSCTIRIPVHMR 526
                    H R
Sbjct: 363 GPHHPHPGAHGR 374



 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M  L E
Sbjct: 246 EVELAKRIEAGLYATQLMTELSE 268


>gi|56966075|pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
          Length = 81

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 58/75 (77%), Positives = 64/75 (85%)

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +LR  T  VLA LT RE +VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 6   ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 65

Query: 667 LKHPSRSKKLRSFLD 681
           L+HPSRS+ LRSFLD
Sbjct: 66  LRHPSRSEVLRSFLD 80


>gi|326789987|ref|YP_004307808.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
 gi|326540751|gb|ADZ82610.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
          Length = 274

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 75/256 (29%), Positives = 121/256 (47%), Gaps = 57/256 (22%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKF 488
            +V+  +C  S A + ++EAN  L+  V+ K+    +  +   DL+QEG IGL+ AAEK+
Sbjct: 5   ELVKLYQCGDSKALERLLEANKGLIYKVSMKFYTERDNAIDQDDLVQEGRIGLIVAAEKY 64

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D      F++YA +W+ Q + R +  +                                 
Sbjct: 65  DINGDVPFASYAYYWIYQKMHRFMYPK--------------------------------- 91

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSAIQ 606
                          R ++K + + +SL TPIG++    LGD + ++     S  DS   
Sbjct: 92  ---------------RNMIKSSLKFVSLNTPIGEDGEMELGDTLGEEQEEFCSVEDSIYH 136

Query: 607 ANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             L E   + +  +LT ++ +VL  RFG   N  HTLEE GK+  VTRER+RQIE  ++R
Sbjct: 137 QELAEELRQAMNDNLTLQQRQVLLFRFGFECN-VHTLEETGKEIGVTRERVRQIEVNSLR 195

Query: 666 KLKHPSRSKKLRSFLD 681
           KL+   R  ++R +L+
Sbjct: 196 KLR-SCRWARMR-YLE 209


>gi|291542453|emb|CBL15563.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Ruminococcus bromii
           L2-63]
          Length = 231

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 87/245 (35%), Gaps = 54/245 (22%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +     + K       A+  +VE NLRLV  + KKY     +  DL+  G IGL+KA  
Sbjct: 31  EKQERECLEKSANGDIAARNMLVEHNLRLVAHIIKKYYGTQSEQDDLVSIGTIGLIKAIN 90

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD     K S+YA   ++  I     +                                
Sbjct: 91  TFDMNKNIKLSSYASRCIENEILMHFRNA------------------------------- 119

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
                                K + + ISL   I  +   +    ++  +    +   + 
Sbjct: 120 ---------------------KKSAQDISLNETIDTDKDGNPLTLLDIMSVDDNIIDNLD 158

Query: 607 ANL--RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             L  ++    +   L  RE++++ +R+G+      T + V K   ++R  + +IE KA+
Sbjct: 159 LKLNSKKLGQFIKEELNEREQKIIVLRYGLDGKEALTQKSVAKMLGISRSYVSRIETKAL 218

Query: 665 RKLKH 669
           ++L+ 
Sbjct: 219 KQLRK 223


>gi|254433106|ref|ZP_05046614.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus oceani
           AFC27]
 gi|207089439|gb|EDZ66710.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus oceani
           AFC27]
          Length = 189

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/193 (23%), Positives = 83/193 (43%), Gaps = 14/193 (7%)

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL++AA  ++   G  F TYA   ++ AI   I         P  +  K  +V    R
Sbjct: 1   MIGLLEAARNYNASQGASFETYAGIRIRGAILDEIRRNDW---APRSVHRKARQVAEVMR 57

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDK 595
            + N+  R+    E+A++L +P+    ++L+        SL+     E++  L   ++  
Sbjct: 58  EVENREGRDARDHEVAEELGLPLNEYHRLLQDAGGYRVFSLDEFNEGEESEPLSASLK-- 115

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               P +     N R      +  L  RE  V+ + +      D  L E+G+   V+  R
Sbjct: 116 ---GPYEGLQDQNFRGALVEAIEGLPERERLVMSLYYV----EDLNLREIGEVLGVSESR 168

Query: 656 IRQIEAKAIRKLK 668
           + QI ++A+ +L+
Sbjct: 169 VSQIHSQAVLRLR 181


>gi|30264411|ref|NP_846788.1| sporulation sigma factor SigK [Bacillus anthracis str. Ames]
 gi|47529862|ref|YP_021211.1| sporulation sigma factor SigK [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187232|ref|YP_030484.1| sporulation sigma factor SigK [Bacillus anthracis str. Sterne]
 gi|49481469|ref|YP_038392.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141167|ref|YP_085663.1| sporulation sigma factor SigK [Bacillus cereus E33L]
 gi|163942095|ref|YP_001646979.1| sporulation sigma factor SigK [Bacillus weihenstephanensis KBAB4]
 gi|165873242|ref|ZP_02217852.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167634588|ref|ZP_02392908.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|167638535|ref|ZP_02396811.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|170687349|ref|ZP_02878566.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|170707389|ref|ZP_02897843.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|177653302|ref|ZP_02935554.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190566875|ref|ZP_03019791.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196034403|ref|ZP_03101812.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196039171|ref|ZP_03106477.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|196044956|ref|ZP_03112190.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|206969450|ref|ZP_03230404.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217961829|ref|YP_002340399.1| sporulation sigma factor SigK [Bacillus cereus AH187]
 gi|218231149|ref|YP_002369149.1| sporulation sigma factor SigK [Bacillus cereus B4264]
 gi|218899507|ref|YP_002447918.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225866320|ref|YP_002751698.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227817116|ref|YP_002817125.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229603939|ref|YP_002868629.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|254684096|ref|ZP_05147956.1| sporulation sigma factor SigK [Bacillus anthracis str. CNEVA-9066]
 gi|254721930|ref|ZP_05183719.1| sporulation sigma factor SigK [Bacillus anthracis str. A1055]
 gi|254736444|ref|ZP_05194150.1| sporulation sigma factor SigK [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741481|ref|ZP_05199168.1| sporulation sigma factor SigK [Bacillus anthracis str. Kruger B]
 gi|254750920|ref|ZP_05202959.1| sporulation sigma factor SigK [Bacillus anthracis str. Vollum]
 gi|254757752|ref|ZP_05209779.1| sporulation sigma factor SigK [Bacillus anthracis str. Australia
           94]
 gi|300118668|ref|ZP_07056396.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|49065844|sp|P62180|RP28_BACCR RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065845|sp|P62181|RP28_BACTK RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065846|sp|P62182|RP28_BACAN RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|580953|emb|CAA40024.1| sigma factor 28 [Bacillus thuringiensis serovar kurstaki]
 gi|19918928|gb|AAL99379.1| sigma factor 28 [Bacillus thuringiensis serovar israelensis]
 gi|30259069|gb|AAP28274.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Ames]
 gi|47505010|gb|AAT33686.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181159|gb|AAT56535.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Sterne]
 gi|49333025|gb|AAT63671.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974636|gb|AAU16186.1| RNA polymerase sigma-28 factor [Bacillus cereus E33L]
 gi|163864292|gb|ABY45351.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|164711001|gb|EDR16568.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167513383|gb|EDR88753.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|167530040|gb|EDR92775.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|170127633|gb|EDS96506.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|170668544|gb|EDT19290.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|172081584|gb|EDT66656.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190561866|gb|EDV15835.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992945|gb|EDX56904.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196024444|gb|EDX63117.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|196029798|gb|EDX68399.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|206735138|gb|EDZ52306.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217066768|gb|ACJ81018.1| RNA polymerase sigma-27 factor [Bacillus cereus AH187]
 gi|218159106|gb|ACK59098.1| RNA polymerase sigma-27 factor [Bacillus cereus B4264]
 gi|218543613|gb|ACK96007.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225788740|gb|ACO28957.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227007199|gb|ACP16942.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229268347|gb|ACQ49984.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|298723917|gb|EFI64631.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|324328243|gb|ADY23503.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326942122|gb|AEA18018.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 237

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 76  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 119

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 120 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 143

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 144 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 202

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 203 ALGISRSYVSRIEKRALMKMFH 224


>gi|325290052|ref|YP_004266233.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965453|gb|ADY56232.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 248

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 110/287 (38%), Gaps = 67/287 (23%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMV---------RKGECEASIAKKEMVEANL 453
           +  I  + + I + +    +S +E    + ++         +  E E   A+ +++E NL
Sbjct: 15  LKGITLLVSYINNNAFPQPLSEAEEAQNLKILAESKGEPANKPTEIEVENARNKLIEHNL 74

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV  + KKY   G    DLI  G IGL+K    F+   G + +TYA   ++  I   + 
Sbjct: 75  RLVAHLVKKYDGTGEDSDDLISIGTIGLIKGINTFNTDKGTRLATYAARCIENEILMYLR 134

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
                                                                LK T+  
Sbjct: 135 T----------------------------------------------------LKKTRGE 142

Query: 574 ISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +S+  PIG +   +  + I+    D +A+S    +     +      L  LT RE  VL+
Sbjct: 143 VSMYDPIGTDKEGNSINLIDILGTDPDAISDQVESEFE--QRIVLEKLKCLTKRERMVLQ 200

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +RFG+  +   T  E+ +   ++R  + +IE KA++KL    +  +L
Sbjct: 201 LRFGLLNSPKKTQREIARMLGISRSYVSRIEKKAVQKLTEEMKEHRL 247


>gi|308069873|ref|YP_003871478.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859152|gb|ADM70940.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 246

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 94/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K     +  +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 54  LLGKLSSGDAAVRSMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEK 113

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                                    
Sbjct: 114 KIKLATYASRCIENEILMYLRRNSK----------------------------------- 138

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                            T+  +S + P+  +   +   L D +  +N     +   Q + 
Sbjct: 139 -----------------TRTEVSFDEPLNIDWDGNELLLSDVMGTENDTIYRNIEEQVD- 180

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + L  LT RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 181 RKLLHKALDKLTDRERLIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 240


>gi|307699957|ref|ZP_07637008.1| RNA polymerase sigma factor, FliA/WhiG family [Mobiluncus mulieris
           FB024-16]
 gi|307614995|gb|EFN94213.1| RNA polymerase sigma factor, FliA/WhiG family [Mobiluncus mulieris
           FB024-16]
          Length = 455

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 14/231 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            + +  ++E NL LV     +   R   F    DL   G++ L++AA+ ++   G  F  
Sbjct: 7   ELDRDALIEKNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAAKSYNPETGVPFHR 66

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA++ ++ A+   +             R +  ++      ++    R PT EE+A  L +
Sbjct: 67  YAVFRIRGAMLDELRAMDW---ATRGSRSRTKQLEEMTAALTAAAGRAPTREELAVALGI 123

Query: 559 PVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V  V    L  ++  +S++    ++D   +   I D + ++P D+ +           +
Sbjct: 124 EVGQVEAAQLDASRRMVSIDVSYSEDDPRSIE--IVD-DGLNPEDTVLTDERLVYLKAAV 180

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R   V+   F      + ++ EV     VT+ R+ Q+  +A+  ++
Sbjct: 181 KALPSRLRYVVEQVFF----EEKSVNEVAASLGVTQSRVSQLRTEALSMIR 227


>gi|295092920|emb|CBK82011.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus sp.
           ART55/1]
          Length = 206

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 95/250 (38%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E +  +++          A+  ++E NLRLV  +++KY +      DL+  G IGL
Sbjct: 8   LTPEEEKKYIAL---CLSGDKAARSILIEYNLRLVAHISRKYNSAVRDPEDLLSIGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + +    G K S YA   ++  +  ++             R+              
Sbjct: 65  IKAIDSYKPDKGCKLSGYAAKCIENELLMTLR------HEKKKARE-------------- 104

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S+  PIG +   +   + D I  +N  
Sbjct: 105 --------------------------------VSIYDPIGTDKEGNEIVILDIIGSENVN 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                    +L    + + + L+ RE  ++ MR+G+   +  T +EV +   ++R  + +
Sbjct: 133 VLDKMIQDDHLCLLPSCISSLLSSREREIICMRYGLDGQSPLTQKEVARMLGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE KA+ KL+
Sbjct: 193 IEKKALGKLR 202


>gi|120597321|ref|YP_961895.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|146294534|ref|YP_001184958.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|120557414|gb|ABM23341.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
 gi|145566224|gb|ABP77159.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
          Length = 238

 Score = 89.9 bits (221), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/217 (22%), Positives = 100/217 (46%), Gaps = 20/217 (9%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           + ++S  + +    L   D+ Q G + L++++ ++   L   F ++A   ++ AI   + 
Sbjct: 35  KRIVSQMRSHCGVMLSLEDMEQIGMMALLESSRRYPGELDNGFISFAGQRIRGAILDELR 94

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
            Q    R    +R + H++    RR+S ++ REP+  E+A  L +  E  R+ L  T+  
Sbjct: 95  RQDWRPRP---VRQQAHELNDVVRRLSREMGREPSDLEVASALGLSAEDYRERLYSTQAE 151

Query: 574 I--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              SL+              +  ++ V   +   Q  L++T  +V++ L  RE+ +L + 
Sbjct: 152 SMKSLDEL-----------LLVGEHPVDRGNDVEQLMLKQTLIKVISKLNEREQLILSLY 200

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +    + +  L+E+     +T  RI Q+   AI +LK
Sbjct: 201 Y----HHELNLKEIAMALGLTETRICQLHKSAISQLK 233


>gi|332272489|gb|AEE38928.1| RNA polymerase sigma-70 factor [Aeromonas cavernicola]
          Length = 219

 Score = 89.5 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 85/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ E   D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGENADDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHADTQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + D+ +R+   E  +++L  +   + +  F+      E +  W  + K   +      
Sbjct: 138 NNMRDMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECEAAWFEHQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +    + +L+   +++ I  ETG
Sbjct: 198 LEVN-EEVLRSIGKLQQIEEETG 219


>gi|320178177|gb|EFW53154.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           ATCC 9905]
 gi|320182764|gb|EFW57648.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           ATCC 9905]
          Length = 196

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/192 (22%), Positives = 86/192 (44%), Gaps = 7/192 (3%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 65  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVA 121

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRET 612
           ++L + +   R++L  T            E+     + + D +   +PL   + +NLR+ 
Sbjct: 122 ERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQR 181

Query: 613 TTRVLASLTPRE 624
               + +L  RE
Sbjct: 182 VMEAIETLPERE 193


>gi|254439671|ref|ZP_05053165.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255117|gb|EDY79431.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 235

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 109/233 (46%), Gaps = 13/233 (5%)

Query: 455 LVISVAKKYTNRGLQF--LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +  ++AK+++  GLQ    DL+Q+ NIGLMKAA++FD   GY+FSTY++WW++  I    
Sbjct: 1   MARTMAKRFSA-GLQAAEPDLVQQANIGLMKAADRFDPERGYRFSTYSVWWIRAEIQSYK 59

Query: 513 ADQSCTIRIPVHM--RDKIHKVVRTARRMSNKIKREPTPEE--IAKKLAMPVEGVRK-VL 567
                 +R P     R+ + K+ R    +SN      T  +  +AK L + ++ +     
Sbjct: 60  LASMSIVRRPNSADFRNAVGKLGRLDEAVSNDPTINRTDADALVAKALGVNLQRLNDLRQ 119

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPRE 624
           +++    SL  P   +D       + D  +    D+  + +   LR     ++ SL  RE
Sbjct: 120 QVSGTDYSLNLPSFGDDGEERMARLVDPASTEDADTMHRLDIKKLRGLLVEIIGSLPDRE 179

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +++        +   TL  +G  F ++ ER+RQ+      +L+     + L 
Sbjct: 180 RKIIMAT--QLQDPPATLTALGIHFGISTERVRQLREMGFERLRTTMTQRDLE 230


>gi|56551522|ref|YP_162361.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ZM4]
 gi|56543096|gb|AAV89250.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ZM4]
          Length = 247

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 94/229 (41%), Gaps = 19/229 (8%)

Query: 448 MVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +L+LV  +A     R    ++  DLIQ G + L++AA  F+   G+ F+TYA   +
Sbjct: 28  LIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASMRI 86

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +   +           +   + +    +S  + R P   EIA+KL M     R
Sbjct: 87  RGAMIDYMRQHA---ATARSSIARQKTLNKAREELSATLGRRPEDAEIAEKLNMSPSEYR 143

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +     I     SL+    D  +      I   +         +  L+      + +L  
Sbjct: 144 EWADGAINIRQESLDDVYSDHSS------IFTDDNADQASEMEREALQSALAEQIKTLPE 197

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           RE  VL++ +      +  L+E+G+   +   RI QI+  A+  L+   
Sbjct: 198 REALVLQLYYV----EELNLKEIGEVLDLGTARISQIKKSAVDHLRQKM 242


>gi|227876732|ref|ZP_03994841.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           mulieris ATCC 35243]
 gi|269976259|ref|ZP_06183255.1| FliA/WhiG family RNA polymerase sigma factor [Mobiluncus mulieris
           28-1]
 gi|227842629|gb|EEJ52829.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           mulieris ATCC 35243]
 gi|269935588|gb|EEZ92126.1| FliA/WhiG family RNA polymerase sigma factor [Mobiluncus mulieris
           28-1]
          Length = 455

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 14/231 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            + +  ++E NL LV     +   R   F    DL   G++ L++AA+ ++   G  F  
Sbjct: 7   ELDRDALIEKNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAAKSYNPETGVPFHR 66

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA++ ++ A+   +             R +  ++      ++    R PT EE+A  L +
Sbjct: 67  YAVFRIRGAMLDELRAMDW---ATRGSRSRTKQLEEMTAALTAAAGRAPTREELAVALGI 123

Query: 559 PVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V  V    L  ++  +S++    ++D   +   I D + ++P D+ +           +
Sbjct: 124 EVGQVEAAQLDASRRMVSIDVSYSEDDPRSIE--IVD-DGLNPEDTVLTDERLVYLKAAV 180

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R   V+   F      + ++ EV     VT+ R+ Q+  +A+  ++
Sbjct: 181 KALPQRLRYVVEQVFF----EEKSVNEVAASLGVTQSRVSQLRTEALSMIR 227


>gi|166031221|ref|ZP_02234050.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
 gi|166029068|gb|EDR47825.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
          Length = 227

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 100/255 (39%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ SE ++ +   +K       AK  ++E NLRLV  + KKY     +  DL+  
Sbjct: 25  SFPLPLTASEEQYYL---QKYIEGDLNAKHILIEHNLRLVAHIVKKYQANVEEAEDLLSI 81

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+     +  TYA   ++  I                        +R  
Sbjct: 82  GTIGLIKAVVTFNPGKNVRLGTYAARCIENEILMH---------------------LRAR 120

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
           ++ S +                               +SL  PIG +   +   L D IE
Sbjct: 121 KKTSRE-------------------------------VSLYEPIGTDREGNEIQLFDVIE 149

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +  +      + ++ +    V + L+ RE  VL+MR+G+    ++T  E+ K   ++R
Sbjct: 150 TDDQEAHRKIEEKDDILKLYQHVESKLSTRERLVLKMRYGLYNEEEYTQREIAKLLGISR 209

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE  AI KL+
Sbjct: 210 SYVSRIEKSAIEKLR 224


>gi|289578255|ref|YP_003476882.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
 gi|289527968|gb|ADD02320.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
          Length = 231

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 100/270 (37%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  V  IL +     + S    ++  E +  +   +        A+  ++E NLRLV 
Sbjct: 8   ILASIVKEILNLGYLTNTNSFPNPLTPEEEKKYLEAYK---NGDEEARNILIERNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   ++  I  S+     
Sbjct: 65  HVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMSV----- 119

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                           R  ++M  ++        +   + +  EG               
Sbjct: 120 ----------------RAEKKMKGEVF-------LQDPIGVDKEG--------------- 141

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                 +   L D +  +          +  +++   ++   L  RE  ++ MR+G+   
Sbjct: 142 ------NEISLMDVLGTEENEISEQVEKKIQIKKLYNKMNNVLKNRERLIIEMRYGLYNG 195

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T  E+ K   ++R  + +IE KA+ KL
Sbjct: 196 KVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|209408342|emb|CAP19914.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 79/238 (33%), Gaps = 44/238 (18%)

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
           RIE G   +M+++   P T   ++   + + +    L +I  L   I P+  G       
Sbjct: 1   RIEEGIREVMSAIAHFPGTVDGILADYERVTNEGGRLSDI--LSGYIDPDDDGA------ 52

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             + Q+ E  + +     V + + D E     S+++       PE A      + E  + 
Sbjct: 53  AGAPQEVEPVAPQVAAKPVADDKDDDEEKESDSEEEEGDGGPDPEVARVRFGAVAEQLEK 112

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
           +                                       +K  ++S +     E L  L
Sbjct: 113 AKKA-----------------------------------LKKHGRASQQAIDELEALAIL 137

Query: 325 VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDP 381
              + L   + D LVE++ D   +I   E  +++L      + R  FL +    E + 
Sbjct: 138 FMPIKLVPKQYDALVERVRDALNQIRAQERAVMQLCVRDARMPRADFLRQFPSNETNL 195


>gi|319937328|ref|ZP_08011735.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807694|gb|EFW04287.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 227

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 54/272 (19%), Positives = 100/272 (36%), Gaps = 67/272 (24%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           IK+ + +  ++  E   ++    K       A+ +++E NLRLV  +AKKY +      D
Sbjct: 18  IKTQAFKKQLTPQEENDLLE---KYFQGDQEARNQLIEHNLRLVAHIAKKYESTKDLQED 74

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+KA + +      K  TYA   ++  I   +                    
Sbjct: 75  LISIGTIGLIKAVDSYKPTKATKLGTYAAKCIENEILMHMRGN----------------- 117

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLG 589
                                              K T   +SL   +G +       L 
Sbjct: 118 -----------------------------------KKTALDVSLNEILGVDKDGGEMTLL 142

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +             +  +++     L  LTPRE+ +L  R+G+  +  +T +E+    
Sbjct: 143 DILPSDQKEIIDQIDTEDQIKKLQEYFLL-LTPREQEILIYRYGLNKHKVYTQKEIASTM 201

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            ++R  + ++E +A+ KL        L+++L+
Sbjct: 202 HISRSYVSRLEKRALIKL--------LKAYLN 225


>gi|239934368|emb|CAR92314.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 220

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 37/265 (13%), Positives = 88/265 (33%), Gaps = 46/265 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + + +    L +I  L   I P+  G         + Q+ E  + +     V
Sbjct: 1   VDSILADYERVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPQTPQSTSKPV 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D +     S+++       PE A      + E  + +   L              
Sbjct: 52  DDDKDDEDEEESESEEEEGDGGPDPEVARLRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   +I   E  +++L      + R  FL +    E +  W        + ++   +   
Sbjct: 137 DALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAA-GKSKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEF 427
            + I + + ++  +  +  ++I++ 
Sbjct: 196 KEDIQRCQQKLIELEQQCELAIADI 220


>gi|228993082|ref|ZP_04153005.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
 gi|228999132|ref|ZP_04158714.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|229006680|ref|ZP_04164314.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228754541|gb|EEM03952.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228760749|gb|EEM09713.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|228766730|gb|EEM15370.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
          Length = 228

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + +  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 10  SYVKNNAFPQPLSSDDEKKYLELMEQ---GDAHARNLLIEHNLRLVAHIVKKFENTGEDS 66

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 67  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 110

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 111 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 134

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 135 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 193

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 194 ALGISRSYVSRIEKRALMKMFH 215


>gi|228962768|ref|ZP_04124034.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228796921|gb|EEM44265.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 225

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 108/230 (46%), Gaps = 9/230 (3%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
              LV S+A +Y+       D +Q G +GL+ A  ++D  L  +F  + +  +   + + 
Sbjct: 3   YTNLVHSLAYRYSKGNASHEDFVQIGMLGLLGAIRRYDTSLKKEFEAFLIPTIMGEMKKY 62

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
           + D++  + +P  ++DK   + +T   +++ ++R P  +EIA  + +  E V ++++  +
Sbjct: 63  LRDKTWDVHVPRRIKDKSSTLKKTIEILTSTLQRSPQIQEIAIHMELSEEEVLELMEAKQ 122

Query: 572 EPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
                SL+  I       +G  +E           +  +   T  ++L  LT +E+ +L 
Sbjct: 123 HYQTTSLDAEIETASEGAIGTKVEFVGVEEEGYGKV--DRYLTLEKLLPLLTKQEKEILY 180

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
             F       +  ++ G    +++  + +I+ +A++KL+  S SK L ++
Sbjct: 181 YTF----IKQYNQKDTGNLVGISQMHVSRIQRRALQKLRKASDSK-LETY 225


>gi|239934376|emb|CAR92318.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 222

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 33/267 (12%), Positives = 84/267 (31%), Gaps = 46/267 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTDGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKAA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D +     ++++        E A      + E  + +   L              
Sbjct: 52  GDEKDDEDEDDSDTEEEEGDGGPDSEVARLRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E    L   + L   + + LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEAPAILFMPIKLVPKQYEALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 SALSQIHAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFRH 429
            + I + + ++  +  E  ++I++ + 
Sbjct: 196 KEDIQRCQQKLIELEQECDLAIADIKD 222


>gi|90577362|ref|ZP_01233173.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio angustum S14]
 gi|90440448|gb|EAS65628.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio angustum S14]
          Length = 242

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 103/237 (43%), Gaps = 20/237 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           +    E  + +  +V   ++ V++  + +T+    + D+ Q G IGL++AA ++      
Sbjct: 20  QNHIDEDLLIRNHLVL--VKRVVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGDVEDP 77

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           +F  +A+  ++ AI   +           H R + H++    R +  ++ R+PT  EI  
Sbjct: 78  QFPAFAICRIRGAILDELRRLDW---RSRHTRQQAHELNDITRDLMKQLGRQPTEAEITS 134

Query: 555 KLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L +  E  +  L+ +   E  SL+          L +  ++ ++    +     ++R T
Sbjct: 135 ALGIDSENYQLRLQASMASEMQSLD---------QLLEAGKELDSPLEYNGVEHEHMRRT 185

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L  L+ RE+ +L + +      +  L E+     +T  RI Q+  +A++ L H
Sbjct: 186 LEYALTQLSKREQLLLTLFYQH----ELNLHEIALVLNLTPPRICQLHKQALKSLNH 238


>gi|219112653|ref|XP_002178078.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410963|gb|EEC50892.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 358

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 72/258 (27%), Positives = 124/258 (48%), Gaps = 20/258 (7%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL----QFLDLIQEGNIGLMKAAE 486
           +  +R+   E   AK ++V +NLR+V SV   Y   GL       D++QEG I L++AAE
Sbjct: 87  MEAIRQTIEEGLEAKNQLVTSNLRMVQSVVNTYIRNGLTAQYNAGDMMQEGIIALIRAAE 146

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           KF+   G+KFSTYAM+WV+ ++ RS   QS  I +P  + +   ++++  R M   + R+
Sbjct: 147 KFEPDRGWKFSTYAMYWVRASVKRSQIYQSRVITVPQRLHENHKRLLKVEREMEADLGRK 206

Query: 547 PTPEEIAKKLAMPVEGV-RKVLKITKEPISLET--------PIGDEDTSHLGDFIEDKNA 597
           P+  E+  ++ +    V R    + +   SL+           GD     L + I  K  
Sbjct: 207 PSRIELGAEIGLSKLQVDRCFAAMEQRCQSLDQKLSNSKRPMSGDTSKDTLMEIIGSKTE 266

Query: 598 VSPLDSAIQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTL------EEVGKQFC 650
            +  DS  +  LRE     L   L P E  +L +R+G        L       E+ +   
Sbjct: 267 GNDFDSLNRIFLREDLIETLHRHLDPAEVELLLLRYGFKEVASSKLGGQPTIAELSRTVG 326

Query: 651 VTRERIRQIEAKAIRKLK 668
           +  +++R++  ++++ LK
Sbjct: 327 LKPDKVRRMINRSLKHLK 344


>gi|17227773|ref|NP_484321.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17135255|dbj|BAB77801.1| RNA polymerase sigma-37 factor [Nostoc sp. PCC 7120]
          Length = 261

 Score = 89.5 bits (220), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 104/237 (43%), Gaps = 12/237 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                +   +  +V+ +  LV  +A K++++    + DL Q G  GL++A E+FD   GY
Sbjct: 19  YHHNPSIKLRNRLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGY 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FS++A+ +++  +   + D+S  ++IP   ++  ++  +  + +S  + R P   EIAK
Sbjct: 79  AFSSFAVPYIRGEMLHFLRDRSTLLKIPRRWQELYNEGQKVRKELSISLGRPPKDAEIAK 138

Query: 555 KLAMPVEGVRKVLKITK--EPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + V+  ++     +   P+SL+       +    LG+ +     ++      +    
Sbjct: 139 YLKVSVQEWQETKLAAQNRMPLSLDATAVHYVDCQITLGEALPCPRTIAQQQQDEERQ-- 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 ++ L  +  + + M F      + + ++  K    +   + +   K I+ L
Sbjct: 197 -QLQGAISMLEEKPRQAVEMVFL----KELSRKDAAKNIGTSPMTVTRYLQKGIQDL 248


>gi|197122905|ref|YP_002134856.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter sp.
           K]
 gi|196172754|gb|ACG73727.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter sp.
           K]
          Length = 232

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 102/241 (42%), Gaps = 22/241 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           ++ + +    A      ++  +  L+   A++   R    ++  DL   G +GL++AA +
Sbjct: 5   LAALARYGPPAPGPDDALLRRHAPLLDRCARRLAARTGHAVEPGDLWSAGAMGLLEAARR 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D     +F T+A   V+ A+   +        +P  +R    +V+    R+   + REP
Sbjct: 65  YDPAHDVRFETFAEHRVRGAMLDELR---RMDHLPRRLRADADRVLAARARLEQSLGREP 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P E+A+   +P E V ++L +   P+        ED       +    A+   +     
Sbjct: 122 DPVEVAEAAELPAEQVGELLLLASPPV------PVEDDLAPAPAVPADEALGAAERRRAL 175

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  R +A+L  R    L++   +  +   T  E+ K   V+  R+ Q+ A+A+++L
Sbjct: 176 ------ARTVAALPER----LQVLLALYYDEALTYREIAKVLGVSEPRVCQLHAEAVKRL 225

Query: 668 K 668
           +
Sbjct: 226 R 226


>gi|158341129|ref|YP_001522296.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158311370|gb|ABW32982.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 476

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 114/257 (44%), Gaps = 18/257 (7%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I +I+    +S  +   +   + K +   + A++ ++ +NL  + S+    + +G++  +
Sbjct: 14  IATIARHPNLSPEQEAEL---ILKAQDGDNDARQTVIYSNLAWICSMGGSLSRKGIEDGE 70

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI EG  GL KA +++    G    T++   + +  + ++  ++  IR+P    +++ K+
Sbjct: 71  LISEGYFGLNKAIDQWSSEKGANIRTFSRDKIYKFQSEAVHQKN-HIRLPKSTYEQLSKL 129

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
            +    +      + T  ++A+   +  + +R  L+   +P+SL +  G  +   L D  
Sbjct: 130 KKATAVL----GEDATVAQLAEGTEIKEKRIR-TLQEISQPVSLNSVTGTRENLELLDQQ 184

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D    S   +     L      ++  L PR+  +L +        + + +++     + 
Sbjct: 185 ADDCQGSLDPA-----LSSELLDLVDKLHPRQREILHLYHW----EELSFQKISDYLGLP 235

Query: 653 RERIRQIEAKAIRKLKH 669
            +++R++  +A+  L+ 
Sbjct: 236 AKKVRKLYKQALDLLRK 252


>gi|317969500|ref|ZP_07970890.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 315

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 60/284 (21%), Positives = 112/284 (39%), Gaps = 28/284 (9%)

Query: 420 TGISISEFRHIVSMVRKGE-----------CEASIAKKEMVEANLRLVISVAKKYTNRGL 468
              ++ E    +   ++               A  A++++V  NL LV     ++     
Sbjct: 31  CERTVMELSRRIQRWQQHPDGPSHAPKPLRRSALRAREQLVRHNLGLVAHTWGRHRCSLP 90

Query: 469 QFLD----LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              D     +QE  + L++AAEKFD   GY+FSTYA +WV++  T         IR P  
Sbjct: 91  AHDDTTADALQEAALNLVRAAEKFDPAKGYRFSTYATFWVRRGFTEFEQRAKRAIRFPAE 150

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKK-----LAMPVEGVRKV--LKITKEPISLE 577
               + K +R +++       EP+ E +A +      AM  E + +           SL+
Sbjct: 151 KAAVVLKALRLSQQQQATTGDEPSLEWLAAQLKFDGKAMNAEQLAEFIRQWDATRTGSLD 210

Query: 578 TPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
               D D        D    + A     +           ++++ L  +E R++R R+  
Sbjct: 211 GAEDDGDEKGGCSRLDLASLQQAAEQQQTQEPDPQHAALPQLMSCLDEQEHRLIRNRYLR 270

Query: 635 GMNTDHTLEEVGKQF-CVTRERIRQIEAKAIRKLKHPSRSKKLR 677
                 +  ++ +    + RE++ Q+EA A+ KL+  +    L+
Sbjct: 271 RP--PLSPCQLRRSMGGMQREQLEQLEATALNKLRQSATEHNLK 312


>gi|269308278|gb|ACZ34185.1| RNA polymerase sigma 70 factor [Aeromonas simiae]
          Length = 222

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 83/262 (31%), Gaps = 41/262 (15%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II          + G      G    + + + ++   
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDIISGFVNPDEADEMGPSATHIGSELGEDDLADEDSSD 60

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + E D +     S DD S     PE A      L    + +  ++           
Sbjct: 61  ----DEEEDEDEDGNDSSDDDSDGGPDPEVAREKFGELRTQYEVTRQSI----------- 105

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   + + ++  + +    KL  +     L   + D LV 
Sbjct: 106 ------------------------RTNGRAHDETQAEIAKLADIFRQFRLMPKQFDRLVN 141

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 142 NMREMMERVRVQERIILKLCVEQAKMPKKTFVSAFTNNECETAWFEYQKQAGKAWSAPLV 201

Query: 400 ACEVDSILKIRNEIKSISVETG 421
           A E + +L+   +++ I  ETG
Sbjct: 202 AME-EEVLRSIGKLQQIEEETG 222


>gi|281421843|ref|ZP_06252842.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281404085|gb|EFB34765.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 136

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/105 (46%), Positives = 70/105 (66%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  I  E  +S  E   +   +RKG  E   AK++++ ANLR V+SVAK+Y +RGL  
Sbjct: 17  RYLMKIGREPLLSHDEELELARKIRKGGSEGERAKEKLIRANLRFVVSVAKRYQHRGLAL 76

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
            DLI EGNIGL+KA E+FD   G+KF  YA+WW++Q+I ++IA+Q
Sbjct: 77  TDLIDEGNIGLIKAVERFDETRGFKFIQYAIWWIRQSILQAIAEQ 121



 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAG---RAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL ++G   LLS + E+ +A++I  G          L  + L F  ++            
Sbjct: 18  YLMKIGREPLLSHDEELELARKIRKGGSEGERAKEKLIRANLRF--VVSVAKRYQHRGLA 75

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHS 207
           L ++ID E  IG       F  T G  
Sbjct: 76  LTDLID-EGNIGLIKAVERFDETRGFK 101


>gi|21231354|ref|NP_637271.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66768593|ref|YP_243355.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|188991595|ref|YP_001903605.1| RNA polymerase sigma factor rpoD (Sigma-70). [Xanthomonas
           campestris pv. campestris str. B100]
 gi|21113015|gb|AAM41195.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573925|gb|AAY49335.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|167733355|emb|CAP51556.1| RNA polymerase sigma factor rpoD (Sigma-70) [Xanthomonas campestris
           pv. campestris]
          Length = 255

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 12  QYRAVQRNNANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSDQ 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R++     R     E+
Sbjct: 72  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAATEV 128

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + MP+    ++++       L      ED   L      K   +P     +      
Sbjct: 129 AAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRE 186

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 LGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 238


>gi|254519267|ref|ZP_05131323.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
 gi|226913016|gb|EEH98217.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
          Length = 235

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 86/231 (37%), Gaps = 50/231 (21%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                 +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     K +T
Sbjct: 49  HGDESIRDILIERNLRLVVYIARKFENTGVCVEDLISVGTIGLIKAVNTFNPEKKIKLAT 108

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +   S                V+        +  +    E+      
Sbjct: 109 YASRCIENEILMYLRRNSK---------------VKAEISFYEPLNIDWDGNEL------ 147

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
                                        L D +  +N +       + + R+     L 
Sbjct: 148 ----------------------------LLSDILGTENDIVYNLIEDEVD-RQLLFLALK 178

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L  RE+ ++++RFG+    + T +EV     +++  I ++E K I +LK 
Sbjct: 179 HLNDREKEIVKLRFGLNGTREKTQKEVADMLGISQSYISRLEKKIINRLKK 229


>gi|167465670|ref|ZP_02330759.1| sporulation sigma factor SigE [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 196

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 92/240 (38%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K     +  +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 4   LLGKLPSGDAAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEK 63

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +   S                                    
Sbjct: 64  KIKLATYASRCIENEILMYLRRNSKIRTE------------------------------- 92

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +  +N     +   Q + 
Sbjct: 93  ---------------------VSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVD- 130

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + L  LT RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 131 RKLLHKALDKLTERERVIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 190


>gi|306817679|ref|ZP_07451421.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus mulieris
           ATCC 35239]
 gi|304649493|gb|EFM46776.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus mulieris
           ATCC 35239]
          Length = 455

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 14/231 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            + +  ++E NL LV     +   R   F    DL   G++ L++AA+ ++   G  F  
Sbjct: 7   ELDRDALIEKNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAAKSYNPETGVPFHR 66

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA++ ++ A+   +             R +  ++      ++    R PT EE+A  L +
Sbjct: 67  YAVFRIRGAMLDELRAMDW---ATRGSRSRTKQLEEMTAALTAAAGRAPTREELAVALGI 123

Query: 559 PVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
            V  V    L  ++  +S++    ++D   +   I D + ++P D+ +           +
Sbjct: 124 EVGQVEAAQLDASRRMVSIDVSYSEDDPRSIE--IVD-DGLNPEDTVLTDERLVYLKAAV 180

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +L  R   V+   F      + ++ EV     VT+ R+ Q+  +A+  ++
Sbjct: 181 RALPQRLRYVVEQVFF----EEKSVNEVAASLGVTQSRVSQLRTEALSMIR 227


>gi|228926137|ref|ZP_04089213.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228833502|gb|EEM79063.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 194

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 84/196 (42%), Gaps = 8/196 (4%)

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+ A  ++D+ +G  F  +A+  +   I + + D++  I +P  ++D   K+     
Sbjct: 1   MLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGKIKLAIE 60

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDK 595
            +++ ++R P   EIA  L +  E V +++         SL+  + +         IE  
Sbjct: 61  ELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIE-- 118

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +         +   R     +   L   E+ V+   F      +   ++ G++  +++  
Sbjct: 119 SVGEVEQGYEETERRLVLKDIFNVLNETEKSVIHYIF----EENLNQKDTGERLGISQMH 174

Query: 656 IRQIEAKAIRKLKHPS 671
           + +I+ +AI KLK  +
Sbjct: 175 VSRIKRQAISKLKQAA 190


>gi|143621|gb|AAA22794.1| sporulation protein [Bacillus subtilis]
          Length = 239

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 93/240 (38%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K       A+  ++E  LRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 47  LLMKLPNGDQAARAILIERILRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +               + +K+                    
Sbjct: 107 KIKLATYASRCIENEILMYLR--------------RNNKIR------------------- 133

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S   P+  +   +   L D +   + +   D     + 
Sbjct: 134 -------------------SEVSFYEPLNIDWDGNELLLSDVLGTDDDIITKDIEANVD- 173

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++   + L  L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 174 KKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLRK 233


>gi|312622918|ref|YP_004024531.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203385|gb|ADQ46712.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 244

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 96/251 (38%), Gaps = 58/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +          KK +VE NLRLV+ +A+++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYKIHYQGK--EELKKILVERNLRLVVYIARRFENTKINLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +             R+   K+         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLR------------RNSNKKLE-------- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +   +  
Sbjct: 141 --------------------------------LSIDEPLNVDWDGNELLLSDVLG-TDTE 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +    +  RE   R +  L  RE+R++ +RFG G   + T +EV     +++  I +
Sbjct: 168 EIYNRIESSVEREALLRAIQKLPSREKRIVELRFGFGDGGEKTQKEVADMLGISQSYISR 227

Query: 659 IEAKAIRKLKH 669
           +E K I +LK 
Sbjct: 228 LEKKIITRLKK 238


>gi|126649719|ref|ZP_01721955.1| sporulation sigma factor SigE [Bacillus sp. B14905]
 gi|126593438|gb|EAZ87383.1| sporulation sigma factor SigE [Bacillus sp. B14905]
          Length = 227

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 92/244 (37%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V+++         A+  ++E NLRLV+ +A+++ N G    DLI  G+IGL+KA E F
Sbjct: 30  EEVTVIASFMKGDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLIKAIETF 89

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +     K +TYA   ++  I   +   S                                
Sbjct: 90  NTDKNIKLATYASRCIENEILMHLRKTSRMKGE--------------------------- 122

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                    +SL+ P+  +   +   L D +  +  +  LD+  
Sbjct: 123 -------------------------VSLDEPLNSDADGNELLLSDILGTEEHI-ILDNVE 156

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R+     +  L  RE  ++  RFG+    + T +EV     +++  I ++E K I+
Sbjct: 157 KKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLGISQSYISRLEKKIIQ 216

Query: 666 KLKH 669
            L+ 
Sbjct: 217 DLRE 220


>gi|56964116|ref|YP_175847.1| sporulation sigma factor SigE [Bacillus clausii KSM-K16]
 gi|56910359|dbj|BAD64886.1| DNA-directed RNA polymerase sigma-29 factor sigma-E [Bacillus
           clausii KSM-K16]
          Length = 237

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 99/263 (37%), Gaps = 57/263 (21%)

Query: 411 NEIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +EI  I     +     +     ++ K        +  ++E NLRLV+ +A+K+ N G+ 
Sbjct: 22  DEIYYIGGSEALPPPLSKEEEAELLGKLPSGDKAVRSVLIERNLRLVVYIARKFENTGIN 81

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLI  G IGL+KA   F+     K +TYA   ++  I   +                 
Sbjct: 82  IEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------- 127

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH-- 587
                                                   T+  +S + P+  +   +  
Sbjct: 128 --------------------------------------NKTRSEVSFDEPLNIDWDGNEL 149

Query: 588 -LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L D +  +  +       + + R    + L +L+ RE++++ +RFG+    + T ++V 
Sbjct: 150 LLSDVLGTEEDIITRGIEERVD-RRLLVKALHTLSEREKQIMELRFGLAGEEEKTQKDVA 208

Query: 647 KQFCVTRERIRQIEAKAIRKLKH 669
               +++  I ++E + I++L+ 
Sbjct: 209 DMLGISQSYISRLEKRIIKRLQK 231


>gi|126176138|ref|YP_001052287.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|304412490|ref|ZP_07394096.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS183]
 gi|307307149|ref|ZP_07586887.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           BA175]
 gi|125999343|gb|ABN63418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|304349132|gb|EFM13544.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS183]
 gi|306910388|gb|EFN40819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           BA175]
          Length = 238

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/228 (21%), Positives = 103/228 (45%), Gaps = 23/228 (10%)

Query: 446 KEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           ++++   L L+  +  +  +     L   D+ Q G + L++++ ++   L   F ++A  
Sbjct: 24  QQIIRQYLPLIKRIVSQMRSHCGVMLSLEDMEQIGMMALLESSRRYPGELDNGFISFAGQ 83

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   +  Q    R    +R + H++    RR+S ++ REP+  E+A  L +  E 
Sbjct: 84  RIRGAILDELRRQDWRPRP---VRQQAHELNDVVRRLSREMGREPSDLEVASALGLSAED 140

Query: 563 VRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
            R+ L  T+     SL+              +  +  V   +   +  L++T  +V++ L
Sbjct: 141 YRERLYSTQAESMKSLDEL-----------LLGGEQPVDRSNDVERLMLKQTLIKVISKL 189

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L + +    + +  L+E+     +T  RI Q+   AI +LK
Sbjct: 190 NEREQLILSLYY----HHELNLKEIAMALGLTETRICQLHKSAISQLK 233


>gi|229086911|ref|ZP_04219070.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
 gi|228696421|gb|EEL49247.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
          Length = 228

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + +  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 10  SYVKNNAFPQPLSSDDEKKYLELMEQ---GDAHARNLLIEHNLRLVAHIVKKFENTGEDA 66

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 67  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 110

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 111 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 134

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 135 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 193

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 194 ALGISRSYVSRIEKRALMKMFH 215


>gi|303239292|ref|ZP_07325820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593078|gb|EFL62798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 236

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 100/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E +H + +++        A+  ++E NLRLV  + KKY        DLI  
Sbjct: 28  SFPQPLSPDEEQHYIKLLK---EGDEEARNILIERNLRLVAHIVKKYNATIGDCDDLISI 84

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+   G + +TYA   ++  I                M+ +  K +++ 
Sbjct: 85  GTIGLIKAIATFNHEKGTRLATYAARCIENEIL---------------MQIRSSKKIQSE 129

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EIA                                  L D I ++ 
Sbjct: 130 VSLQDPIGVDREGNEIA----------------------------------LIDVIGNEA 155

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                +  ++  ++    ++   L  RE+ VL +R+G+   T  T  E+ K   ++R  +
Sbjct: 156 ESVVEEVELKMQVKRLYNKMKVVLKSREKVVLELRYGLLNGTSKTQREIAKMLGISRSYV 215

Query: 657 RQIEAKAIRKL 667
            +IE KAI+KL
Sbjct: 216 SRIEKKAIKKL 226


>gi|167630135|ref|YP_001680634.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
 gi|167592875|gb|ABZ84623.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
          Length = 235

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 57/286 (19%), Positives = 109/286 (38%), Gaps = 60/286 (20%)

Query: 395 WKNFVACEVDSILKIRNEIKSI----SVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
            + F   E+  +L+  N ++ +    S ET            ++ + E      K  ++E
Sbjct: 1   MRLFFETELRKLLERLNLVQEVHYIGSSETLPPPLSNDEEYRLLEQLEQGDLTVKSILIE 60

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
            NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA   ++  I  
Sbjct: 61  RNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPLKKIKLATYASRCIENEILM 120

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
            +                                                         T
Sbjct: 121 YLRRN----------------------------------------------------NKT 128

Query: 571 KEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           +  +S + P+  +   +   L D +  +N +    S  +   R+     ++ LT RE R+
Sbjct: 129 RSEVSFDEPLNIDWDGNELLLSDVLGTENDI-IYKSIEEEVDRKLLQAAMSKLTSRERRI 187

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           + +RFG+  + + T +EV     +++  I ++E + I++L+     
Sbjct: 188 VELRFGLRDSREKTQKEVADMLGISQSYISRLEKRIIKRLRKEMNR 233


>gi|83589703|ref|YP_429712.1| sporulation sigma factor SigE [Moorella thermoacetica ATCC 39073]
 gi|83572617|gb|ABC19169.1| RNA polymerase, sigma 29 subunit, SigE [Moorella thermoacetica ATCC
           39073]
          Length = 243

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 94/251 (37%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++  +       +  KK ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 43  LSSDEESDLLLRLE---DGDAAVKKVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +                             
Sbjct: 100 IKAVNTFDPKKRIKLATYASRCIENEILMYLRRN-------------------------- 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       T+  +S + P+  +   +   L D +   N +
Sbjct: 134 --------------------------NKTRAEVSFDEPLNIDWDGNELLLSDVLGTDNDI 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               S  +    +     +  L+ RE +++  RFG+    + T +EV     +++  I +
Sbjct: 168 -IYKSIEEEVDHKLLQLAMRKLSSRERKIMEFRFGLLDGVEKTQKEVADILGISQSYISR 226

Query: 659 IEAKAIRKLKH 669
           +E + I++L+ 
Sbjct: 227 LEKRIIKRLRK 237


>gi|148833415|gb|ABR14577.1| DNA-dependent RNA polymerase sigma factor D subunit [Alcanivorax
           jadensis]
          Length = 246

 Score = 89.1 bits (219), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/280 (15%), Positives = 91/280 (32%), Gaps = 38/280 (13%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             ++ +L   P     LI     + +    L +II            G+    +  +   
Sbjct: 2   REVLHALAFWPGAVDMLITEYARVENEERKLTDII-----------AGYLDPNDDGAAAT 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
             +          +  E   ++      DD  K DS  ++ + DE  LD           
Sbjct: 51  NANKEPTFAEKAKKAAEAKEKAKENGDDDDADKKDSDDDDDDEDEGGLDP---------- 100

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLS 329
                    V+      AE + EL+ L + A    K + +         E L +      
Sbjct: 101 ---------VLA-----AERFAELKKLHEKAERALKRNGRDHASSAKALEALAEHFTLFK 146

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAK 388
           L     D ++    +    +   E +++  A   G + R  F++   G E +  WV    
Sbjct: 147 LVPRIYDEMLVGARNNLDLVRKFERQIMTSAIRRGGMDRRDFIKLFPGNETNMGWVDQQL 206

Query: 389 DFPEGEW-KNFVACEVDSILKIRNEIKSISVETGISISEF 427
              +G+   + ++   + I + + +I ++    G+ + + 
Sbjct: 207 KTKKGKSIADKLSVVKEDIQRAQRKITTVEEIIGLPVGDI 246


>gi|325917849|ref|ZP_08180027.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535933|gb|EGD07751.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 255

 Score = 89.1 bits (219), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 12  QYRAVQRNNANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSDQ 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R++     R     E+
Sbjct: 72  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAATEV 128

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + MP+    ++++       L      ED   L      K   +P     +      
Sbjct: 129 AAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRE 186

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 LGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 238


>gi|239934566|emb|CAR94597.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 220

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 39/172 (22%), Positives = 76/172 (44%), Gaps = 3/172 (1%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEK-SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A  +  ++ L    V   +++     K + L++K+ +    L L+    D L+ Q+ 
Sbjct: 50  EEAARRFASIQKLHQQVVKSLEEKGLDDPKTQKLRKKVAQEFMELKLSPKMFDALIVQMR 109

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +    + + E  ++ L     G+ R  F+      E +  W+       + +    +A  
Sbjct: 110 EHVSEVRNLEKSVMMLCVRDAGMPRKDFITTFPKNETNIKWLDKHI-RAKRKHSAALARL 168

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
            + I K + +++ +     + I+  + I   V  GE +A  AKKEMVEANLR
Sbjct: 169 REDIEKQQMKLQQLEQRVHMEIAVVKEINREVAVGEAKARRAKKEMVEANLR 220


>gi|318040084|ref|ZP_07972040.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 60/284 (21%), Positives = 111/284 (39%), Gaps = 28/284 (9%)

Query: 420 TGISISEFRHIVSMVRKGE-----------CEASIAKKEMVEANLRLVISVAKKYTNRGL 468
              ++ E    +   ++               A  A++++V  NL LV     ++     
Sbjct: 26  CERTVMELSRRIQRWQQHPDGPSHAPKPVRRSALRAREQLVRHNLGLVAHTWGRHRCSLP 85

Query: 469 QFLD----LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              D     +QE  + L++AAEKFD   GY+FSTYA +WV++  T         IR P  
Sbjct: 86  AHDDTTADALQEAALNLVRAAEKFDPAKGYRFSTYATFWVRRGFTEFEQRAKRAIRFPAE 145

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKK-----LAMPVEGVRKV--LKITKEPISLE 577
               + K +R +++       EP+ E +A +      AM  E + +           SL+
Sbjct: 146 KAAVVLKALRLSQQHQASTGDEPSLEWLAAQLKFDGKAMSAEQLAEFIRQWDATRTGSLD 205

Query: 578 TPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
               D D        D    + A     +           ++++ L  +E R++R R+  
Sbjct: 206 GAEDDGDEKGGCTRLDLASLQQAAEQQQTQEPDPQHAALPQLMSCLDEQEHRLIRNRYLR 265

Query: 635 GMNTDHTLEEVGKQF-CVTRERIRQIEAKAIRKLKHPSRSKKLR 677
                 +  ++ +    +  ER+ Q+EA A+ KL+  +    L+
Sbjct: 266 RP--PLSPCQLRRSMGGMQGERLEQLEATALDKLRQAATEHNLK 307


>gi|86158019|ref|YP_464804.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|197122674|ref|YP_002134625.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|220917457|ref|YP_002492761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|85774530|gb|ABC81367.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|196172523|gb|ACG73496.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|219955311|gb|ACL65695.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 241

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 63/262 (24%), Positives = 115/262 (43%), Gaps = 51/262 (19%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
               ++   +K++     ++  +   +    RKGE     AK+++V  NL  V+++A+K 
Sbjct: 11  KEFDELAPYLKAVRDFPPLTREDEHALAIRARKGEVS---AKQKLVRHNLAFVVAIARKQ 67

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
               ++  DLIQEGN+GLM+A EKFD   G +FSTYA+WW++  I + + +   T+R   
Sbjct: 68  RRGTVRLDDLIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVRP-- 125

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                                                    +   + +  +SL++ I +E
Sbjct: 126 -----------------------------------------QSGTVAQPDLSLDSAIDEE 144

Query: 584 DTSHLGDFIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
             +   + IED       + L       +R+   +V   +      ++     +  +   
Sbjct: 145 GDATHLERIEDDGPGPEDTYLSGEGDREVRDALGKVRKRIGELGWDIV--HNRLEQDQPR 202

Query: 641 TLEEVGKQFCVTRERIRQIEAK 662
           TLEE+GK++ V+RER+RQ+E K
Sbjct: 203 TLEEIGKRWGVSRERVRQVELK 224



 Score = 46.0 bits (107), Expect = 0.023,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 53/171 (30%), Gaps = 2/171 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YL+ +     L+RE E A+A R   G       L    L F   I  +     GT  L +
Sbjct: 19  YLKAVRDFPPLTREDEHALAIRARKGEVSAKQKLVRHNLAFVVAIARKQR--RGTVRLDD 76

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +I         +   F                +      ++E    +   +         
Sbjct: 77  LIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVRPQSGTVAQPDLS 136

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
           +DS  +   +       ++D      + +  +   +V  AL ++ +   EL
Sbjct: 137 LDSAIDEEGDATHLERIEDDGPGPEDTYLSGEGDREVRDALGKVRKRIGEL 187


>gi|213958524|gb|ACJ54683.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. 19-20cm2R]
          Length = 205

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 76/197 (38%), Gaps = 5/197 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
            +        ++V  P +       +  +DE+  A T    E +  P  + A      V 
Sbjct: 13  DSDDGLTPPAAEVPPPVDPKAVKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVS 72

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +  K ++   VL   L +L   + L   + + LVE++     R+  
Sbjct: 73  DQMEITRKALKKHGRGNKLAIAELVL---LAELFMPIKLVPKQFEGLVERVRSALDRLRQ 129

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  ++        + R  FL +  G E+D  W   A    + ++   +      I++ +
Sbjct: 130 QERAIMHFCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQ 188

Query: 411 NEIKSISVETGISISEF 427
            ++ ++  ETG++I+E 
Sbjct: 189 QKLTALQTETGLTIAEI 205


>gi|75909293|ref|YP_323589.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75703018|gb|ABA22694.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anabaena
           variabilis ATCC 29413]
          Length = 261

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 105/237 (44%), Gaps = 12/237 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                +   + ++V+ +  LV  +A K++++    + DL Q G  GL++A E+FD   GY
Sbjct: 19  YHHNPSIKLRNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGY 78

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            FS++A+ +++  +   + D+S  ++IP   ++  ++  +  + +S  + R P   EIAK
Sbjct: 79  AFSSFAVPYIRGEMLHFLRDRSTLLKIPRRWQELYNEGQKIRKELSISLGRPPKDAEIAK 138

Query: 555 KLAMPVEGVRKVLKITK--EPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            L + V+  ++     +   P+SL+       +    LG+ +     ++      +    
Sbjct: 139 HLKVSVQEWQETKLAAQNRMPLSLDATAVHYVDCQITLGEALPCPRTIAQQQQDEERQ-- 196

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 ++ L  +  + + M F      + + ++  K    +   + +   K I+ L
Sbjct: 197 -QLQGAISMLEEKPRQAVEMVFL----KELSRKDAAKNIGTSPMTVTRYLQKGIQDL 248


>gi|121535239|ref|ZP_01667053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306124|gb|EAX47052.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 97/252 (38%), Gaps = 60/252 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   ++S ++K        K   +E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 33  LTSDEEVFLLSRLQK---GDKAVKSIFIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +   S                         
Sbjct: 90  IKAVNTFDPIKRIKLATYASRCIENEILMYLRRNSK------------------------ 125

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       T+  +S + P+  +   +   L D +   N +
Sbjct: 126 ----------------------------TRAEVSFDEPLNIDWDGNELLLSDVLGTDNDI 157

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIR 657
               S  +   +      +  L+ RE R++ +RFG+ G   + T +EV     +++  I 
Sbjct: 158 -IYKSVEEEVDKNLLYAAMNKLSGRERRIMELRFGLNGDGMERTQKEVADMLGISQSYIS 216

Query: 658 QIEAKAIRKLKH 669
           ++E + I++L+ 
Sbjct: 217 RLEKRIIKRLRK 228


>gi|251798285|ref|YP_003013016.1| sporulation sigma factor SigK [Paenibacillus sp. JDR-2]
 gi|247545911|gb|ACT02930.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. JDR-2]
          Length = 232

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 64/284 (22%), Positives = 111/284 (39%), Gaps = 64/284 (22%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +  +  + + +K+ +    +   E    + ++ +G   +   +  ++E NLRLV 
Sbjct: 6   AIALFIKQLSLLVSYVKNNAFPQPLHEEEEMKHLQLMAEGNAHS---RNLLIEHNLRLVA 62

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +     
Sbjct: 63  HIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEILMHLRS--- 119

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK T++ +SL 
Sbjct: 120 -------------------------------------------------LKKTRKDVSLH 130

Query: 578 TPIGDE---DTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            PIG +   +   L D +  E  + V  +   I+   +    R L  L  RE+ V+R RF
Sbjct: 131 DPIGTDKEGNEITLIDILGTEADDVVDRVQLKIE---KSKIYRNLDILDEREQEVIRGRF 187

Query: 633 GIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           G+     + T  E+ K+  ++R  + +IE +A+ KL H     K
Sbjct: 188 GLDHGGDERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAK 231


>gi|206975995|ref|ZP_03236905.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
 gi|206745747|gb|EDZ57144.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
          Length = 237

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 76  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 119

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 120 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 143

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 144 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEETQREIAK 202

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 203 ALGISRSYVSRIEKRALMKMFH 224


>gi|332272447|gb|AEE38907.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
 gi|332272449|gb|AEE38908.1| RNA polymerase sigma-70 factor [Aeromonas salmonicida]
          Length = 217

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 82/262 (31%), Gaps = 46/262 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P          +  +       S+  E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLGLSDII--SGFIDPNE-------ADDVAPTATHIGSELGED 51

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D   E E + E     S DD       PE A     +L    + +  ++           
Sbjct: 52  DLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEVTRLSI----------- 100

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   QK+ ++    +    +L  +     L   + D LV 
Sbjct: 101 ------------------------QKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVN 136

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      +
Sbjct: 137 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLL 196

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + +L+   +++ I  ETG
Sbjct: 197 EMD-EEVLRSIGKLQQIEEETG 217


>gi|78047533|ref|YP_363708.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325928018|ref|ZP_08189235.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
 gi|78035963|emb|CAJ23654.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325541614|gb|EGD13139.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
          Length = 255

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 12  QYRAVQRNNANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQ 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R++     R     E+
Sbjct: 72  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAATEV 128

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + MP+    ++++       L      ED   L      K   +P     +      
Sbjct: 129 AAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRE 186

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 LGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 238


>gi|210608671|ref|ZP_03287948.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
 gi|210152928|gb|EEA83934.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
          Length = 247

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 97/253 (38%), Gaps = 54/253 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +++ E    ++ +  G  +   AKK ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 40  PAPLAVEEEAEAINEL--GSKDDEYAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGT 97

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F+     K +TYA   ++  I   +                          
Sbjct: 98  IGLIKAINTFNPTKNIKLATYASRCIENEILMYLRRN----------------------- 134

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK K E + +E                            +  +    L   I      
Sbjct: 135 --NKTKLEVSIDEP-------------------------LNVDWDGNELLLSDILGTEED 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERI 656
           +          R+   + +  L+ RE  ++RMRFG+G     + T +EV     +++  I
Sbjct: 168 TIYRDLENEAERKLLVKAIGRLSNRERMIVRMRFGLGTLDGEEKTQKEVADLLGISQSYI 227

Query: 657 RQIEAKAIRKLKH 669
            ++E K +++LK 
Sbjct: 228 SRLEKKIMQRLKR 240


>gi|73662123|ref|YP_300904.1| RNA polymerase sigma-B factor [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494638|dbj|BAE17959.1| truncated RNA polymerase sigma-B factor [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 192

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 94/198 (47%), Gaps = 8/198 (4%)

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+ A  +FD     KF  + +  V   I R + D++ ++ +P  +++   ++ +   
Sbjct: 1   MVGLIGAINRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVTD 60

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDK 595
            ++N+++R P+  EIA +L +  E V + +++  +   +S++  I  +        ++  
Sbjct: 61  ELTNELERSPSITEIADRLEVNEEDVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIM 120

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                     +   R    ++L  L+ RE ++++  F  G     + +E G++  +++  
Sbjct: 121 GQQDDNYDLTEK--RMILEKILPILSERERQIIQCTFIEG----LSQKETGERIGLSQMH 174

Query: 656 IRQIEAKAIRKLKHPSRS 673
           + +++  AI+KL+  +  
Sbjct: 175 VSRLQRTAIKKLQEAANK 192


>gi|163782183|ref|ZP_02177182.1| RNA polymerase sigma factor FliA [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882715|gb|EDP76220.1| RNA polymerase sigma factor FliA [Hydrogenivirga sp. 128-5-R1-1]
          Length = 235

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 103/242 (42%), Gaps = 12/242 (4%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
           ++         ++E+V   L LV S+A     +    +   DLI  G IGLMKA EK D 
Sbjct: 1   MKNPYTFEEKEREELVLKYLPLVKSIAFTIKRQIPPTIDVRDLIGHGIIGLMKALEKLDT 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +  +Y    ++ AI   +            +R+K  K+    R ++ K+ REPT E
Sbjct: 61  QKNPE--SYLKIRIRGAIYDYLRSLDF---GSRRIREKERKIREALRELTEKLGREPTDE 115

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EIA+ L   +  ++  L        L       +     + +     V   D  ++ +L 
Sbjct: 116 EIAEYLGEDLGTLQHDLSRISFSYILNLEDIFTEERRSYEEVIGSKRVDVEDEIVKKDLI 175

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           E     + +L  RE+ V+++ F      +  L+E+ +    +  R+ QI+A+AI KLK  
Sbjct: 176 EKLKEAIEALDEREKLVIQLIF----YEELPLKEIAQILNCSISRVSQIKAEAIEKLKKF 231

Query: 671 SR 672
            +
Sbjct: 232 MK 233


>gi|166031185|ref|ZP_02234014.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
 gi|166029032|gb|EDR47789.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
          Length = 246

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 88/233 (37%), Gaps = 52/233 (22%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A+K ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +T
Sbjct: 58  AHDEEARKLLIEHNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPTKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                            NK K E + +E       
Sbjct: 118 YASRCIENEILMYLRRN-------------------------NKTKLEVSIDEP------ 146

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
                                +  +    L   I      +      Q   R+   + L 
Sbjct: 147 -------------------LNVDWDGNELLLSDILGTEEDTIYKDLEQEAERKILIKALN 187

Query: 619 SLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L+ RE  +++MRFGIG     + T +EV     +++  I ++E K + +L+ 
Sbjct: 188 LLSARERSIIQMRFGIGTVDGEEKTQKEVADLLGISQSYISRLEKKIMVRLRK 240


>gi|299472120|emb|CBN77105.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 555

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 143/332 (43%), Gaps = 69/332 (20%)

Query: 394 EWKNFVACEVDSILKIRNEI-------KSISVETGISISEFRHIVSMVRKGECEASIAKK 446
           E    +A  + +  ++  E+       +  +    IS  E  H           ++ A++
Sbjct: 190 EEVKILARYLKTREQLEAELGGREPTREEWAASLNISTEELAH-------QMVASARAQE 242

Query: 447 EMVEANLRLVISVAKKY----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            +V AN+ L++ +A+++      RG    D+IQEG++ +++AAE FD  LGY+FSTYA W
Sbjct: 243 RIVGANVGLIVVMARRHHPATMARGTITSDVIQEGSLAVLRAAETFDPRLGYRFSTYAGW 302

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           WV+  +TR +  Q+  IR+P ++ +       T   +  ++ R PT +EIA+++ +    
Sbjct: 303 WVRDRVTRCVTQQARIIRLPQYVHNFRRTASMTEAALLKELGRRPTYDEIAERMRV---D 359

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDK--------------------------- 595
           V +V ++   P   +    D+        + D+                           
Sbjct: 360 VERVTRLMNCP---DAFSLDDAPPPSARIVRDRIGLSGGGGKGGGGGGSGGGGGGGAAKA 416

Query: 596 ------------------NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                             + V+P   A          ++L+ L+  E  V+++R+G+G  
Sbjct: 417 GGGKAAPGAGYRHERVACSMVNPEQRAEVGLFESKLDKLLSVLSEDERLVVKLRYGLGGA 476

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  T  EV  +   T+ R+R +E +A+ KL+ 
Sbjct: 477 SPTTWGEVAARAGSTKHRVRMVETRALNKLRR 508


>gi|302386724|ref|YP_003822546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197352|gb|ADL04923.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 246

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 101/253 (39%), Gaps = 60/253 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   +   I++++  G  +   AK E++E NLRLV+ +AKK+ N  +   DLI  G IGL
Sbjct: 43  LDNEKEAQIIALL--GSDDDQRAKSELIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +                  +  +T      
Sbjct: 101 IKAINTFNPNKNIKLATYASRCIENEILMYLR-----------------RNNKTKME--- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +  +  V
Sbjct: 141 --------------------------------VSIDEPLNVDWDGNELLLSDILGTEEDV 168

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERI 656
              D   +   R      ++ L+PRE +++ +RFG+      + T +EV     +++  I
Sbjct: 169 IYKDLETEVE-RNLLNTAISRLSPRERKIVELRFGLTDEEGEEMTQKEVADLLGISQSYI 227

Query: 657 RQIEAKAIRKLKH 669
            ++E K +++LK 
Sbjct: 228 SRLEKKIMKRLKK 240


>gi|167461547|ref|ZP_02326636.1| RNA polymerase sigma factor [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 361

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 100/230 (43%), Gaps = 28/230 (12%)

Query: 446 KEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK----FST 498
            EM+ A  ++V SVA+KY      GL + DL+  G IGL++A   +D     +    FST
Sbjct: 13  DEMIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRFNRKVSSFST 72

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   +K +I R +AD+  ++R+P  +++K+  + +       +   + + E IA+K   
Sbjct: 73  YAFNMIKWSIQRFLADKRFSVRVPRSIQNKLTVIWK-------QGWDQESAESIAEKTGW 125

Query: 559 PVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            +  +R  K         SL+  +  + T      ++   A++   S             
Sbjct: 126 KLAEIREVKRHLAGWSVASLDQALSSDKTDEEATMLDVLPAMTDFTSV-------HVQDF 178

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           L +L P E  VL +R       D T +E+      T+  + +I  K   K
Sbjct: 179 LCALKPLERAVLELRL-----QDQTQKEIAMHIGKTQMYVSRILKKIKDK 223


>gi|331090017|ref|ZP_08338907.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
 gi|330402931|gb|EGG82497.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 245

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 91/239 (38%), Gaps = 56/239 (23%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R G   A  AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     
Sbjct: 53  RLGTEYAEDAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKI 112

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K +TYA   ++  I   +   S                                      
Sbjct: 113 KLATYASRCIENEILMYLRRNSK------------------------------------- 135

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRET 612
                          TK  +S++ P+  +   +  L   I      +          R+ 
Sbjct: 136 ---------------TKMEVSIDEPLNVDWDGNELLLSDILGTEEDTIYKDLENEAERKL 180

Query: 613 TTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             R L  L  RE+ ++ MRFG+      + T +EV     +++  I ++E K +++LK 
Sbjct: 181 LIRALNKLNSREKLIVSMRFGLDNPDGKEKTQKEVADLLGISQSYISRLEKKIMQRLKR 239


>gi|302389895|ref|YP_003825716.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
 gi|302200523|gb|ADL08093.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
          Length = 239

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/227 (21%), Positives = 89/227 (39%), Gaps = 49/227 (21%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA   F+   G + +TYA
Sbjct: 52  DEEARNILIERNLRLVAHIVKKFANTGEDMDDLISIGTIGLIKAITTFNKTKGNRLATYA 111

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I  ++                  K ++    + + I  +    EI        
Sbjct: 112 ARCIENEILMNLRTT---------------KKIKAEVSLQDPIGVDKEGNEI-------- 148

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                                      L D +  ++     + + +   ++   ++   L
Sbjct: 149 --------------------------SLMDILGTESDAIIEEISNKFQQKKLYDKIRTVL 182

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE++V+ +R+G+      T  E+ K   ++R  + +IE +AI+KL
Sbjct: 183 KGREKKVIELRYGLLNGKARTQREIAKLLGISRSYVSRIEKRAIKKL 229


>gi|83590422|ref|YP_430431.1| sporulation sigma factor SigK [Moorella thermoacetica ATCC 39073]
 gi|83573336|gb|ABC19888.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Moorella
           thermoacetica ATCC 39073]
          Length = 226

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 102/262 (38%), Gaps = 56/262 (21%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  I  + + I + +    +S  E +  + +          A+  ++E NLRLV  + KK
Sbjct: 14  LKGISLLLSYISNNAFPQPLSEEEEQKYLEL---WLQGDQKARNILIEHNLRLVAHITKK 70

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           + N G    DLI  G +GL+KA   ++   G K +TYA   ++  I   +          
Sbjct: 71  FENTGEDTEDLISIGTVGLIKAINTYNKAKGTKLATYAARCIENEILMHLRT-------- 122

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                                                       LK T+  ISL  PIG 
Sbjct: 123 --------------------------------------------LKKTRGEISLYDPIGV 138

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHT 641
           +   +    I+   +   +   ++++  +    + +++LTPRE +VL MR+G+      T
Sbjct: 139 DREGNEIALIDILGSEQDVAEMVESSYEQQRVRQKISTLTPRERKVLEMRYGLWHGLRRT 198

Query: 642 LEEVGKQFCVTRERIRQIEAKA 663
             ++ ++  ++R  + +IE  A
Sbjct: 199 QRDIARKMGISRSYVSRIEKPA 220


>gi|23098930|ref|NP_692396.1| sporulation sigma factor SigE [Oceanobacillus iheyensis HTE831]
 gi|22777158|dbj|BAC13431.1| stage II sporulation protein GB (RNA polymerase
           sporulation-specific sigma E factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 239

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 92/248 (37%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E + ++  +         A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 39  LSKQEEQELLIRL---PKGDKAARAMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +                            N
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------N 130

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K+K E + +E                            I  +    L   +         
Sbjct: 131 KLKSEVSFDEP-------------------------LNIDWDGNELLLSDVMGTEEDIIT 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +      +      L  L  RE++++ +RFG+    + T ++V     +++  I ++E 
Sbjct: 166 KNLESTVDKTLLKSALEKLNAREKQIMELRFGLIGEEEKTQKDVADMLGISQSYISRLEK 225

Query: 662 KAIRKLKH 669
           K IR+LK 
Sbjct: 226 KIIRRLKK 233


>gi|125973016|ref|YP_001036926.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125713241|gb|ABN51733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Clostridium
           thermocellum ATCC 27405]
          Length = 218

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/209 (22%), Positives = 91/209 (43%), Gaps = 7/209 (3%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKA 484
           + +    +  + +    K++++     +V  +A +   Y    +++ DLI  G  GL+ A
Sbjct: 7   KQLELWKQYADTKNPAIKEQLIIEYSNIVKYIAGRLSIYFGSNVEYDDLIGYGIFGLIDA 66

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            EKFD   G KF TYA   ++ +I  SI +      +P  +R K  ++ +    + N++ 
Sbjct: 67  IEKFDINKGVKFETYASLRIRGSIIDSIRELDW---VPRSLRQKNKELEKVYAEIENELG 123

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG-DFIEDKNAVSPLDS 603
           R  + +E+A KL + V+ + K+L        +      E    +G     +     P   
Sbjct: 124 RSASDKEVADKLGITVDELNKLLNEVNLSSMISLEEFLEQNYEIGVTTAPESRDEKPEGY 183

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRF 632
              A LRE     ++ L  +E+ V+ + +
Sbjct: 184 IEMAELREILADAISKLPEKEKMVITLYY 212


>gi|288553151|ref|YP_003425086.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
 gi|288544311|gb|ADC48194.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
          Length = 237

 Score = 88.7 bits (218), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 94/240 (39%), Gaps = 56/240 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++K        +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+   
Sbjct: 45  LLKKLPTGDKAVRSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 104

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +                                        
Sbjct: 105 KIKLATYASRCIENEILMYLRRN------------------------------------- 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                            T+  +S + P+  +   +   L D +  +  +       + + 
Sbjct: 128 ---------------NKTRSEVSFDEPLNIDWDGNELLLSDVLGTEEDIITRGIEEKVD- 171

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+   + L +L  RE++++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 172 RKLLVKALHTLNEREKQIMELRFGLAGEEEKTQKDVADMLGISQSYISRLEKRIIKRLQK 231


>gi|251780405|ref|ZP_04823325.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243084720|gb|EES50610.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 232

 Score = 88.4 bits (217), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 95/252 (37%), Gaps = 52/252 (20%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
             + ++ SE    +  ++        AK  ++E NLRLV  + KKY+       +LI  G
Sbjct: 27  FPSPLNESEEEEYLKRLK---DGDKTAKGVLIERNLRLVAHIVKKYSFPNKDVDELISIG 83

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+KA + FD   G + +TYA   ++  I                M  + +K  ++  
Sbjct: 84  TVGLIKAIDSFDSGKGTRLATYASRCIENEIL---------------MLFRNNKKQKSEV 128

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            + + I  +    EI                                   L D +   + 
Sbjct: 129 YLQDPIGVDKEGNEIC----------------------------------LIDILSSDSD 154

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                      +++   ++  SLT RE  +L MR+G+      T  E+     ++R  + 
Sbjct: 155 SVLEKVESNLQIKDLYIKIKDSLTKRESTILIMRYGLIDGNRKTQREIAGTLGISRSYVS 214

Query: 658 QIEAKAIRKLKH 669
           +IE KA++KL+ 
Sbjct: 215 RIEKKALKKLRK 226


>gi|21242677|ref|NP_642259.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|294664736|ref|ZP_06730065.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|21108148|gb|AAM36795.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|292605490|gb|EFF48812.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 255

 Score = 88.4 bits (217), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 12  QYRAVQRNNANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQ 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R++     R     E+
Sbjct: 72  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAATEV 128

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + MP+    ++++       L      ED   L      K   +P     +      
Sbjct: 129 AAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRE 186

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 LGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 238


>gi|266624394|ref|ZP_06117329.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288863758|gb|EFC96056.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 216

 Score = 88.4 bits (217), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 98/250 (39%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R     + + +     A+  ++E N+RLV  VAKKY N      DL+  G IGL
Sbjct: 8   LTAREERE---CLDRYQEGDQEARATLIERNMRLVAHVAKKYQNTDYDMEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F    G + +TYA   V+  I                       ++R  ++ S 
Sbjct: 65  IKAVNTFHTDRGSRLATYAAKCVENEILM---------------------LLRANKKYSK 103

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               +SL  PIG +       L D IE +N  
Sbjct: 104 E-------------------------------VSLFEPIGVDKDGETVSLVDVIEMENKE 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +     +  ++RE        L   E++V+ MR+G+    +HT  E+     ++R  + +
Sbjct: 133 ALETIILSQDIRELYDAFDHCLRDTEKKVIGMRYGLYGGKEHTQREIADMLGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE K+I KL+
Sbjct: 193 IEKKSIEKLR 202


>gi|332272459|gb|AEE38913.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|332272461|gb|AEE38914.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|332272463|gb|AEE38915.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|332272465|gb|AEE38916.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
 gi|332272467|gb|AEE38917.1| RNA polymerase sigma-70 factor [Aeromonas popoffii]
          Length = 219

 Score = 88.4 bits (217), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/263 (16%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S    +       D   +  ++ E + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELGEADLADEDEDEDEDEDDDGESSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +     L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             +  + +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMRGMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + D +L+   +++ I  ETG
Sbjct: 198 VEMDED-VLRSIGKLQQIEEETG 219


>gi|332272381|gb|AEE38874.1| RNA polymerase sigma-70 factor [Aeromonas simiae]
 gi|332272383|gb|AEE38875.1| RNA polymerase sigma-70 factor [Aeromonas simiae]
          Length = 222

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 83/262 (31%), Gaps = 41/262 (15%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II          + G      G    + + + ++   
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDIISGFVNPDEADEMGPSATHIGSELGEDDLADEDSSD 60

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
               + E D +     S DD S     PE A      L    + +  ++           
Sbjct: 61  ----DEEEDEDEDGNDSSDDDSDGGPDPEVAREKFAELRTQYEVTRQSI----------- 105

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                                   + + ++  + +    KL  +     L   + D LV 
Sbjct: 106 ------------------------RTNGRAHDETQAEIAKLADIFRQFRLMPKQFDRLVN 141

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 142 NMREMMERVRVQERIILKLCVEQAKMPKKTFVSAFTNNECETAWFEYQKQAGKAWSAPLV 201

Query: 400 ACEVDSILKIRNEIKSISVETG 421
           A E + +L+   +++ I  ETG
Sbjct: 202 AME-EEVLRSIGKLQQIEEETG 222


>gi|212637801|ref|YP_002314326.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212559285|gb|ACJ31739.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 240

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 45/208 (21%), Positives = 95/208 (45%), Gaps = 18/208 (8%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +    L   D+ Q G + L+++A ++       F +YA   ++ AI   +  Q    R  
Sbjct: 43  HCGAVLAIEDMEQIGMMALLESARRYPGEYDNGFISYAGQRIRGAILDELRRQDWRPRP- 101

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +R + H++  T R+++  ++R P+  E+A+ + +  +  RK L       SL   +  
Sbjct: 102 --VRQQAHELNDTVRKLTKMLERAPSDNEVAQAMGLSQDDYRKRLHA-----SLSESMR- 153

Query: 583 EDTSHLGDFIED-KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                L + I D  +     D   Q + +ET  + ++ L  RE+ +L + +      +  
Sbjct: 154 ----SLDELISDGGHFEDKQDVFEQISAKETLFQAISKLNKREQVILSLYYQH----ELN 205

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L+E+     +T  RI Q+  +A+++L++
Sbjct: 206 LKEIAATLGLTETRICQLHKQAVKQLQN 233


>gi|332272291|gb|AEE38829.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC 2469]
 gi|332272293|gb|AEE38830.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC 2472]
          Length = 219

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 85/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            +   +   + +   DE +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEEEDEDEDGDGDDADDEGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EDVLRAIGKLQQIEEETG 219


>gi|188588587|ref|YP_001920530.1| sporulation sigma factor SigK [Clostridium botulinum E3 str. Alaska
           E43]
 gi|188498868|gb|ACD52004.1| RNA polymerase sigma-K factor [Clostridium botulinum E3 str. Alaska
           E43]
          Length = 232

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 95/252 (37%), Gaps = 52/252 (20%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
             + ++ SE    +  ++        AK  ++E NLRLV  + KKY+       +LI  G
Sbjct: 27  FPSPLNESEEEEYLKRLK---DGDKTAKGVLIERNLRLVAHIVKKYSFPNKDVDELISIG 83

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+KA + FD   G + +TYA   ++  I                M  + +K  ++  
Sbjct: 84  TVGLIKAIDSFDSGKGTRLATYASRCIENEIL---------------MLFRNNKKQKSEV 128

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            + + I  +    EI                                   L D +   + 
Sbjct: 129 YLQDPIGVDKEGNEIC----------------------------------LIDILSSDSD 154

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                      +++   ++  SLT RE  +L MR+G+      T  E+     ++R  + 
Sbjct: 155 SVLEKVESNLQIKDLYIKIKDSLTKRESTILIMRYGLIDGNRKTQREIAGALGISRSYVS 214

Query: 658 QIEAKAIRKLKH 669
           +IE KA++KL+ 
Sbjct: 215 RIEKKALKKLRK 226


>gi|304316726|ref|YP_003851871.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778228|gb|ADL68787.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 231

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 54/254 (21%), Positives = 95/254 (37%), Gaps = 58/254 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E +      +        AK  ++E NLRLV  + KKY+N G    DLI  
Sbjct: 27  SFPQPLTAEEEKKYFEAYK---NGDEEAKNILIERNLRLVAHIVKKYSNTGKDVDDLISI 83

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   +D   G   +TYA   ++  I  S+                        
Sbjct: 84  GTIGLIKAISTYDASKGTHLATYAARCIENEILMSLR----------------------- 120

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIE 593
                                   + ++         ISL+ PIG +       L D + 
Sbjct: 121 ----------------------SEKKIK-------SEISLQDPIGIDKEGNAISLIDILG 151

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +         ++  +++  +++ + L  RE  ++ +R+G+      T  E+ K   ++R
Sbjct: 152 TETDEVSDQVELEMQIKKLYSKINSVLKNRERLIIELRYGLVNGGAKTQREIAKMLGISR 211

Query: 654 ERIRQIEAKAIRKL 667
             + +IE KA+ KL
Sbjct: 212 SYVSRIEKKALSKL 225


>gi|153814605|ref|ZP_01967273.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|317501234|ref|ZP_07959439.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|145848099|gb|EDK25017.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|316897410|gb|EFV19476.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 246

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 91/239 (38%), Gaps = 56/239 (23%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R G   A  AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     
Sbjct: 54  RLGTEYAEDAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKI 113

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K +TYA   ++  I   +   S                                      
Sbjct: 114 KLATYASRCIENEILMYLRRNSK------------------------------------- 136

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRET 612
                          TK  +S++ P+  +   +  L   I      +          R+ 
Sbjct: 137 ---------------TKMEVSIDEPLNVDWDGNELLLSDILGTEEDTIYKDLENEAERKL 181

Query: 613 TTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             R L  L  RE+ ++ MRFG+      + T +EV     +++  I ++E K +++LK 
Sbjct: 182 LIRALNKLNSREKLIVSMRFGLDNPDGKEKTQKEVADLLGISQSYISRLEKKIMQRLKR 240


>gi|332272301|gb|AEE38834.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
 gi|332272303|gb|AEE38835.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
 gi|332272305|gb|AEE38836.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
 gi|332272307|gb|AEE38837.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
 gi|332272309|gb|AEE38838.1| RNA polymerase sigma-70 factor [Aeromonas eucrenophila]
          Length = 219

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + +   DE +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEDEDEDEDGDGDDADDEGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++  + +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +  + + +L+   +++ I  ETG
Sbjct: 198 LEMD-EDVLRAIGKLQQIEEETG 219


>gi|332272295|gb|AEE38831.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC 2467]
 gi|332272297|gb|AEE38832.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC 2473]
 gi|332272299|gb|AEE38833.1| RNA polymerase sigma-70 factor [Aeromonas sp. MDC 2468]
          Length = 219

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 41/263 (15%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            +   +   + +   DE +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEEEDEDEDGDGDDADDEGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++  + +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +  + + +L+   +++ I  ETG
Sbjct: 198 LEMD-EDVLRAIGKLQQIEEETG 219


>gi|114566068|ref|YP_753222.1| sporulation sigma factor SigK [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337003|gb|ABI67851.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 244

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 55/274 (20%), Positives = 108/274 (39%), Gaps = 56/274 (20%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           W   +   +   L +   + +      +S  + R  +  +++       A+  ++E NLR
Sbjct: 6   WALAITGILKGSLCLFAYLNNQVFPQPLSEEDERKCLQEMQR---GGEEARNILIEHNLR 62

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV  V KKY + G    DLI  G IGL+KA   +++  G + +TYA   +   +      
Sbjct: 63  LVAHVVKKYESSGEDLEDLISIGTIGLIKAIRTYNFERGVRLATYAARCIDNEVLMH--- 119

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
                             +R++++   +                               +
Sbjct: 120 ------------------LRSSKKQKQE-------------------------------V 130

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFG 633
           SL  PIG +   +    I+     + +   ++A ++E      +  L+ RE +V+ MR+G
Sbjct: 131 SLYDPIGHDKEGNEISLIDILTNDNEIVDLVEAKMQEEKIKEKINLLSRRERQVIEMRYG 190

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +      T  ++ K+  ++R  + +IE KAI+KL
Sbjct: 191 LFNGLKETQRDIAKKLGISRSYVSRIEKKAIKKL 224


>gi|303238907|ref|ZP_07325438.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593540|gb|EFL63257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 244

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 98/252 (38%), Gaps = 60/252 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  ++++ + K +      K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL
Sbjct: 43  LSNDEESYLLNKLEKNDYGV---KTILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   +                         
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEILMYLRRNNRMKTE-------------------- 139

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS++ P+  +   +   L D +  +N +
Sbjct: 140 --------------------------------ISIDEPLNIDWDGNELLLSDILGTENDL 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIR 657
               S      +E     +  L+ RE++++ +RFG+     + T +EV     +++  I 
Sbjct: 168 -IHRSIEDEVDKELLNTAMKKLSMREKKIMELRFGLSNGGMEKTQKEVADMLGISQSYIS 226

Query: 658 QIEAKAIRKLKH 669
           ++E K I +LK 
Sbjct: 227 RLEKKIICRLKK 238


>gi|297544535|ref|YP_003676837.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842310|gb|ADH60826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 231

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 56/270 (20%), Positives = 101/270 (37%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  V  IL +     + S    ++  E +  +   +        A+  ++E NLRLV 
Sbjct: 8   ILASIVKEILNLGYLTNTNSFPNPLTPEEEKKYLEAYK---NGDEEARNILIERNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   ++  I  S      
Sbjct: 65  HVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMS------ 118

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                          +R  ++M  ++        +   + +  EG               
Sbjct: 119 ---------------IRAEKKMKGEVF-------LQDPIGVDKEG--------------- 141

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                 +   L D +  +          +  +++   ++   L  RE+ ++ MR+G+   
Sbjct: 142 ------NEISLMDVLGTEENEISEQVEKKIQIKKLYNKMNNVLKNREKLIIEMRYGLYNG 195

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T  E+ K   ++R  + +IE +A+ KL
Sbjct: 196 KVRTQREIAKMLGISRSYVSRIEKRALNKL 225


>gi|317129289|ref|YP_004095571.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474237|gb|ADU30840.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 97/244 (39%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
               +++K        +  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F
Sbjct: 42  EEAYLLKKLPSGDDSVRSVLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVSTF 101

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA   ++  I   +               + +K+                
Sbjct: 102 DPEKKIKLATYASRCIENEILMYLR--------------RNNKIR--------------- 132

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                    +S + P+  +   +   L D +  +  +       
Sbjct: 133 -----------------------SEVSFDEPLNIDWDGNELLLSDVLGTEEDIITKGIED 169

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + + R+   + L +L  RE++++ +RFG+  + + T ++V     +++  I ++E + I+
Sbjct: 170 KVD-RKLLVKALEALNDREKQIMELRFGLAGDEEKTQKDVADMLGISQSYISRLEKRIIK 228

Query: 666 KLKH 669
           +L+ 
Sbjct: 229 RLQK 232


>gi|317970154|ref|ZP_07971544.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 253

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 54/224 (24%), Positives = 96/224 (42%), Gaps = 8/224 (3%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           + R  +      +  +V ANL LV  VA++ +   G  F DL QEG  GL+KA E+FD  
Sbjct: 11  LSRYLKDPNHAHRNAVVAANLPLVWKVARRESERSGHSFEDLAQEGVRGLIKAVERFDPS 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           LGY  ST A+ W++ A+   + D+        ++ + + +     RR   +         
Sbjct: 71  LGYTLSTAAVPWIRGAMRHYLRDRCRVFSGARNVIELLQRGAALQRRREQQGLSPMNDSS 130

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQAN 608
           +A+ L    +  ++   L+      SL+ P G  D  + L + + D+ A        +  
Sbjct: 131 LARALGCSQQRWQEAQALQTCLRVASLDQPGGGSDPETPLVEQLSDQQAPGQYGWLERCE 190

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           LR    R L +L   + R++  R         T +++G    ++
Sbjct: 191 LRRQLWRGLKTLQASQRRLVLARVL----QQRTWQDLGAMAGIS 230


>gi|220917697|ref|YP_002493001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955551|gb|ACL65935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 232

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 103/241 (42%), Gaps = 22/241 (9%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           ++ + +    A      ++  +  L+   A++   R    ++  DL   G +GL++AA +
Sbjct: 5   LAALARYGPPAPEPDDALLRRHAPLLDRCARRLAARTGHAVEPGDLWSAGAMGLLEAARR 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D     +F T+A   V+ A+   +        +P  +R    +V+    R+   + REP
Sbjct: 65  YDPAHDVRFETFAEHRVRGAMLDELR---RMDHLPRRLRADADRVLAARARLEQSLGREP 121

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
            P E+A+   +P E V ++L +   P+        ED       +    A+   +     
Sbjct: 122 DPVEVAEAAELPAEQVGELLLLASPPV------PVEDDLAPTPALPADEALGAAERRRAL 175

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  R++A+L  R    L++   +  +   T  E+ K   V+  R+ Q+ A+A+++L
Sbjct: 176 ------ARMVAALPER----LQVLLALYYDEALTYREIAKVLGVSEPRVCQLHAEAVKRL 225

Query: 668 K 668
           +
Sbjct: 226 R 226


>gi|241761164|ref|ZP_04759253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|241374783|gb|EER64244.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
          Length = 247

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 97/226 (42%), Gaps = 19/226 (8%)

Query: 448 MVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +L+LV  +A     R    ++  DLIQ G + L++AA  F+   G+ F+TYA   +
Sbjct: 28  LIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASMRI 86

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +   + T R  +  +     + +    +S  + R P   EIA+KL M     R
Sbjct: 87  RGAMIDYMRQHAATARSSIVRQKT---LNKAREELSATLGRRPEEAEIAEKLNMSPSEYR 143

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           +     I     SL+    D  +      I   +         +  L+      + +L  
Sbjct: 144 EWADGAINIRQESLDDVYSDHSS------IFTDDNADQASEMEREALQSALAEQIKTLPE 197

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           RE  VL++ +      +  L+E+G+   +   RI QI+  A+  L+
Sbjct: 198 REALVLQLYYV----EELNLKEIGEVLDLGTARISQIKKSAVDHLR 239


>gi|14346036|gb|AAK59987.1| RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 145

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 49/145 (33%), Positives = 91/145 (62%)

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           ITR +ADQS TIR+PVH+ ++++K+ R  R M   + RE T EE+A++  +    +  +L
Sbjct: 1   ITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQSLGREATNEELAEESGIEENKIEMLL 60

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           + +++P+SL+ P+G ++ + LGDFIED  A     + + +        V+ +L  RE+ V
Sbjct: 61  RQSRDPVSLDMPVGADEEAPLGDFIEDAEATDAETAVVASMRHSDIRDVIGTLEQREQDV 120

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVT 652
           +R+R+G+      TL+++G++F ++
Sbjct: 121 IRLRYGLDDGVPRTLDQIGRKFGLS 145


>gi|240144184|ref|ZP_04742785.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257203788|gb|EEV02073.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|291536439|emb|CBL09551.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           M50/1]
 gi|291538693|emb|CBL11804.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           XB6B4]
          Length = 243

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 90/237 (37%), Gaps = 58/237 (24%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +    +A+K+++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +
Sbjct: 54  DESGQLARKQLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPGKNIKLA 113

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   ++  I   +   S                                         
Sbjct: 114 TYASRCIENEILMYLRRNSK---------------------------------------- 133

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTT 614
                       T+  +S++ P+  +   +   L D +     V   D       R    
Sbjct: 134 ------------TRMEVSIDEPLNVDWDGNELLLSDILGTDEDVIYHDIETDVEHR-LLK 180

Query: 615 RVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +  L+ RE  ++ +RFG+      + T +EV     +++  I ++E K + +LK 
Sbjct: 181 TAIGKLSGRERMIIELRFGLNSIDGEEKTQKEVADMLGISQSYISRLEKKIMGRLKK 237


>gi|166712012|ref|ZP_02243219.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola
           BLS256]
 gi|289666124|ref|ZP_06487705.1| RNA polymerase sigma factor [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 255

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 12  QYRAVQRNNANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQ 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R++     R     E+
Sbjct: 72  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAATEV 128

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + MP+    ++++       L      ED   L      K   +P     +      
Sbjct: 129 AAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRE 186

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 LGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 238


>gi|312128105|ref|YP_003992979.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778124|gb|ADQ07610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 244

 Score = 88.4 bits (217), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 97/251 (38%), Gaps = 58/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +     E    KK ++E NLRLV+ +AK++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYRIHYQGEEGL--KKLLIERNLRLVVYIAKRFENTKINLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +             R+   K+         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLR------------RNSNRKLE-------- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +   +  
Sbjct: 141 --------------------------------LSIDEPLNVDWDGNELLLSDVLG-TDTE 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +    +  +E   + +  L  RE++++ +RFG G   + T +EV     +++  I +
Sbjct: 168 EIYNKIESSVEKEALLQAIQKLPSREKKIVELRFGFGDGGEKTQKEVADMLGISQSYISR 227

Query: 659 IEAKAIRKLKH 669
           +E K I +LK 
Sbjct: 228 LEKKIITRLKK 238


>gi|225028516|ref|ZP_03717708.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
 gi|224954159|gb|EEG35368.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
          Length = 209

 Score = 88.0 bits (216), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 94/255 (36%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S +  +   E R+ + M R        AK++++E NLRLV  + KKY +      DLI  
Sbjct: 3   SFKKPLKAEEERYYLKMYR---DGDEKAKEKLIEHNLRLVAHIVKKYNSPDRDLDDLISI 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   FD   G +  TYA   ++  +                M  +  K++R  
Sbjct: 60  GTIGLIKAVNTFDLNKGGRLVTYAARCIENELLM--------------MIRQEKKILR-- 103

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIE 593
                                                +SL  PIG +       L D I 
Sbjct: 104 ------------------------------------EVSLYEPIGTDQEGNHISLLDIIS 127

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            + A        +  L      V      RE  ++  R+G+  N  HT +EV     ++R
Sbjct: 128 TEEAELIEQYLHKYYLSRLEQEVFLLTDDREREIILKRYGLCGNEPHTQKEVAAMMGISR 187

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE KA+ KL+
Sbjct: 188 SYVSRIEKKALEKLR 202


>gi|266626024|ref|ZP_06118959.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288862073|gb|EFC94371.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 246

 Score = 88.0 bits (216), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 92/236 (38%), Gaps = 58/236 (24%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK E++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F+     K +T
Sbjct: 58  EDDQSAKSELIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPGKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                  +  +T                       
Sbjct: 118 YASRCIENEILMYLR-----------------RNNKTKME-------------------- 140

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTR 615
                          +S++ P+  +   +   L D +     V   D   +   R     
Sbjct: 141 ---------------VSIDEPLNVDWDGNELLLSDILGTDEDVIYKDLETEVE-RNLLNS 184

Query: 616 VLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ++ L+PRE +++ +RFG+      + T +EV     +++  I ++E K +++LK 
Sbjct: 185 AISRLSPRERKIVELRFGLSDEEGEEMTQKEVADLLGISQSYISRLEKKIMKRLKK 240


>gi|296282290|ref|ZP_06860288.1| sigma 28 (flagella/sporulation) [Citromicrobium bathyomarinum
           JL354]
          Length = 240

 Score = 88.0 bits (216), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 103/252 (40%), Gaps = 18/252 (7%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMK 483
            +H  ++        S  +++ V   L LV  +A  Y   G   +   DL+Q G + L +
Sbjct: 1   MKHDQALFAVRHAYGSTVQEK-VTQFLPLVRKLAWYYEGHGSATVDVDDLMQVGMMALTE 59

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AA++ D      F+ YA   V+ A+   +  QS   R       K     +T   +  ++
Sbjct: 60  AAQRHDRPSDDGFAAYAKMRVRGAMVDLLRGQSHRPRSAAAWTRKRDVAEQT---LRTEL 116

Query: 544 KREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
            R P   E+A+ + MP++      L  +    S++    D DT+         N   P  
Sbjct: 117 GRAPNAAEMAQAMEMPLDRYESMRLAASTSATSIDECYSDSDTAF------SDNRPDPEA 170

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
           + + +       + + +L  R + VL++ F      +  L E+     V+  R+ Q++A 
Sbjct: 171 NLLASEDSGVLAQAIGALPERLQLVLKLYF----IEELNLNEIAAVLGVSVPRVHQLKAD 226

Query: 663 AIRKLKHPSRSK 674
           A++K +    S+
Sbjct: 227 ALKKARVAMVSQ 238


>gi|158340150|ref|YP_001521320.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158310391|gb|ABW32006.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 508

 Score = 88.0 bits (216), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 113/277 (40%), Gaps = 20/277 (7%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
           PE       +  +D I +   E KS S  T      F   + +++K       A +++++
Sbjct: 47  PESLKPTTNSRLMDMIGRFTQEPKSDSRLT------FDQELDLIQKVRVGNPRALRQLIK 100

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
                +++ +++Y  R +    L+  G   +  AA+K+D   G++F TY  W ++  I +
Sbjct: 101 EYKGFIVTASQRYD-RSIDRQALVCSGEAAVDIAAKKYDESKGHRFITYFSWVLRTEIQK 159

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
                     I   +   +  V   A  ++N + REP+ EEIA++  + V+ V   L   
Sbjct: 160 ---RYCSEAGISREVSRNVSAVNEAAAFLTNALGREPSVEEIAEQSNLTVQTVLNALMAK 216

Query: 571 KEPISLETPIGDEDTSHLG--DFIEDKNAVSPLD--SAIQANLRETTTRVLASLTPREER 626
               SL      ++ S +     + D +        S  QA++ +        L  +   
Sbjct: 217 NFTQSLSLSGLIDEDSTIQYESALVDHSCDPWAYALSTEQADILQALEES-GRLESKHVD 275

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            +  R        ++ +E+G++  V  ER+RQ   KA
Sbjct: 276 AVTSRI-----EGYSAKEIGERHGVGPERVRQFIKKA 307


>gi|225175485|ref|ZP_03729479.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168814|gb|EEG77614.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
          Length = 243

 Score = 88.0 bits (216), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 93/244 (38%), Gaps = 56/244 (22%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ K +      K  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD   
Sbjct: 51  LLEKLKTGDYAVKAVLIERNLRLVVYIARKFENTGILIDDLVSIGTIGLIKAVNTFDPHK 110

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +                  +  +                  
Sbjct: 111 NIKLATYASKCIENEILMFLR-----------------RNNKVKAE-------------- 139

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANL 609
                                +S + P+  +   +   L D +  +N +       +   
Sbjct: 140 ---------------------VSFDEPLNVDWDGNELLLSDVLGTENDLVIKGIEAEVE- 177

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R+     +  L  RE+R++ +RFG+    + T +EV     +++  I ++E + I++L+ 
Sbjct: 178 RKLLYNAIEKLNRREKRIMELRFGLLGQEEKTQKEVAVMLGISQSYISRLEKRIIKRLQK 237

Query: 670 PSRS 673
             R 
Sbjct: 238 EIRK 241


>gi|197302589|ref|ZP_03167644.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
 gi|197298487|gb|EDY33032.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
          Length = 248

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 99/266 (37%), Gaps = 58/266 (21%)

Query: 410 RNEIKSISVETGISISEFRHIVSMV--RKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + EI  I     +           V  R G  +   AKK ++E NLRLV+ +AKK+ N G
Sbjct: 29  QKEIHYIGGTDVLPPPLENEKEEEVIGRLGTEDDQEAKKLLIEHNLRLVVYIAKKFDNTG 88

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLI  G IGL+KA   F+     K +TYA   ++  I   +   S           
Sbjct: 89  VGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRNSK---------- 138

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                                                     TK  +S++ P+  +   +
Sbjct: 139 ------------------------------------------TKLEVSIDEPLNVDWDGN 156

Query: 588 --LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLE 643
             L   I   +  +          R+   R L  L+ RE+ ++RMRFG+      + T +
Sbjct: 157 ELLLSDILGTDEDTIYKDLENEAERKILFRALNKLSGREKMIVRMRFGLDHPEGKEMTQK 216

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV     +++  I ++E K + +L+ 
Sbjct: 217 EVADLLGISQSYISRLEKKIMTRLRR 242


>gi|327441149|dbj|BAK17514.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 236

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 85/236 (36%), Gaps = 56/236 (23%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  A+  ++E NLRLV+ +A+++ N      DLI  G+IGL+KA E F+     K 
Sbjct: 47  FMNGDLHARDMLIERNLRLVVYIARRFDNTSTPIEDLISIGSIGLIKAIETFNLDKNIKL 106

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +TYA   ++  I   +   S                                        
Sbjct: 107 ATYASRCIENEILMHLRKTSRMKGE----------------------------------- 131

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETT 613
                            +S + P+  +   +   L D +  +  +       +   R+  
Sbjct: 132 -----------------VSFDEPLNADADGNELLLSDILGTEEHI-ITLDVERKIERQHM 173

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +  LTPRE+ ++  RFG+    + T +EV     +++  I ++E K I  L+ 
Sbjct: 174 FNAINQLTPREKYIMECRFGLNGKEEMTQKEVADHLGISQSYISRLEKKIIMDLRE 229


>gi|300854412|ref|YP_003779396.1| putative RNA polymerase sigma-K factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434527|gb|ADK14294.1| predicted RNA polymerase sigma-K factor precursor [Clostridium
           ljungdahlii DSM 13528]
          Length = 233

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 97/251 (38%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E  + +  + +      +AK  +VE NLRLV  + KKY+    +  +LI  
Sbjct: 26  SFPQPLSDEEEEYYLKKLEQ---GDLLAKSILVERNLRLVAHIVKKYSYPSKEVDELISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I                 +K +R  
Sbjct: 83  GTVGLIKAIDSFDMSKGTRLATYAAKCIENEILMLIR---------------NNKKIRNE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLEDPIGVDKEGNEI----------------------------------SLMDVLSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +++  +++   L+ RE+ V+ MR+G+      T  E+ K   ++R  +
Sbjct: 154 GSIIEIVEQKLQVKKLYSKINTCLSEREKSVVEMRYGLLEGKPRTQREIAKLLGISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE KA++KL
Sbjct: 214 SRIEKKALKKL 224


>gi|268610009|ref|ZP_06143736.1| sporulation sigma factor SigK [Ruminococcus flavefaciens FD-1]
          Length = 227

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 92/242 (38%), Gaps = 52/242 (21%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
               +  +  C    A+K+++E NLRLV  + KKYT+   +  +LI  G IGL+KA   F
Sbjct: 30  EEHELFERSSCGDEYARKKLIEHNLRLVAHIVKKYTSSFDEQDELISIGTIGLIKAVSSF 89

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G KF+TYA   ++  I                  D                     
Sbjct: 90  DHTKGSKFATYASRCIENEILMHFR------SAKKSASDLYM------------------ 125

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
                     PVE  +    +T                   D ++D + ++     +  +
Sbjct: 126 --------NEPVETDKDGNALTIM-----------------DLLDDGSDINEQVDLLIRS 160

Query: 609 LRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +   R +   L PRE  ++  R+G+   + HT  E  ++  ++R  + +IE KA+ KL
Sbjct: 161 --KMLYRFIEQCLDPRETDIMIYRYGLYGTSPHTQSETAEKLGISRSYVSRIEKKAVGKL 218

Query: 668 KH 669
           K 
Sbjct: 219 KK 220


>gi|239934430|emb|CAR92345.1| DNA-directed RNA polymerase subunit D [uncultured Alcanivorax sp.]
          Length = 234

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 40/274 (14%), Positives = 91/274 (33%), Gaps = 43/274 (15%)

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
           L   P   + ++   D +      L ++I     + P+  G             ++  ++
Sbjct: 1   LAFWPGAVEMVLDEYDRILSEERKLTDVI--AGYLDPDDDGAAATNANKEPRFNQKKQAE 58

Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
             E+D   + + D   +   S++D   +D                               
Sbjct: 59  AAEKDKDDDDDDDKSDSDDDSEEDEGGLDPVLA--------------------------- 91

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                      AE + EL+ L + A    K + +         E L        L     
Sbjct: 92  -----------AERFGELKKLHEKAERALKRNGRDHASSAKALETLAGHFTLFKLVPRIY 140

Query: 336 DLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV-SYAKDFPEG 393
           D L++        +   E +++ LA +  G+ R  F+++  G E +  WV ++AK     
Sbjct: 141 DQLLQGARTHLDIVRKFERQIMALAIRRAGVPRKDFVQQFPGNETNLEWVAAHAKTKRAK 200

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           ++   +    + I + + +I ++    G+ +++ 
Sbjct: 201 DYSERLLTVAEDIQRNQRKIITVEEVIGLPVADI 234


>gi|255697051|emb|CBA11635.1| RNA polymerase sigma factor [Pseudomonas cichorii]
          Length = 192

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 28/236 (11%), Positives = 67/236 (28%), Gaps = 46/236 (19%)

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
           +++   P T   ++   + +      L +++            G+    +G +       
Sbjct: 1   SAIAHFPGTVDHILSEYERVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPP 49

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
             + +     +++ D E +   S D+      P             D+ +          
Sbjct: 50  PIDAKAAKADDSDDDEEESGDASDDEEEAESGPDPVIAQQRFGAVADQMEITRKALKKFG 109

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           +     +  L  +AE++                                    + L   +
Sbjct: 110 REDKNSIAELVALAELF----------------------------------MPIKLVPKQ 135

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
            + LVE++     R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 136 FEGLVERVRSALDRLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|154503852|ref|ZP_02040912.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
 gi|153795451|gb|EDN77871.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
          Length = 246

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 105/267 (39%), Gaps = 60/267 (22%)

Query: 410 RNEIKSISVETGISIS-EFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRG 467
           + E+  I     +    E      ++R+ G      AKK ++E NLRLV+ +AKK+ N G
Sbjct: 27  QKEVHYIGGSEVLPPPLETERETEVIRRLGSEYDQEAKKMLIEHNLRLVVYIAKKFDNTG 86

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLI  G IGL+KA   F+     K +TYA   ++  I   +   S           
Sbjct: 87  VGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRNSK---------- 136

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                                                     TK  +S++ P+  +   +
Sbjct: 137 ------------------------------------------TKMEVSIDEPLNVDWDGN 154

Query: 588 ---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTL 642
              L D +  +      D   +A  R+   R +  L+ RE+ +++MRFG+      + T 
Sbjct: 155 ELLLSDILGTEEDTIYRDLETEAE-RKLLVRAINQLSSREKLIVKMRFGLDNPDGIEKTQ 213

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +EV     +++  I ++E K +++LK 
Sbjct: 214 KEVADLLGISQSYISRLEKKIMQRLKR 240


>gi|220931430|ref|YP_002508338.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
 gi|219992740|gb|ACL69343.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
          Length = 232

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 98/250 (39%), Gaps = 53/250 (21%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +S  E    +  +R+       A+  ++E NLRLV  + KKY +      DLI  G
Sbjct: 25  FPQPLSPEEEEKYIKRMRQ---GDEEARNILIEHNLRLVAHIVKKYNSVYTDNEDLISIG 81

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL+K    +D     K +TYA   ++  I                        +R+ +
Sbjct: 82  TIGLIKGINTYDETKKTKLATYAARCIENEILMH---------------------LRSVK 120

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           ++SN+         + + +    +G                     +   L D + D   
Sbjct: 121 KLSNETL-------LQESIGSDKDG---------------------NDITLMDVL-DTRE 151

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S ++   ++   E     L  L+PRE++VL +R+G+      T +EV     ++R  + 
Sbjct: 152 DSVINKVEKSIDEEQLYNKLGELSPREKKVLELRYGLLDGKRLTQKEVASILGISRSYVS 211

Query: 658 QIEAKAIRKL 667
           +IE KAI++L
Sbjct: 212 RIEKKAIQEL 221


>gi|331091330|ref|ZP_08340170.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404491|gb|EGG84035.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 206

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 62/257 (24%), Positives = 106/257 (41%), Gaps = 58/257 (22%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             +    ++ SE R+ +   +K       AK  ++E NLRLV  + KKY +      DL+
Sbjct: 1   MKTFPEPLTASEERYYL---QKYTEGDLEAKHILIERNLRLVAHIVKKYQHLDEDPEDLL 57

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+KA   F+   G + +TYA   ++  I   +  +                   
Sbjct: 58  SIGTIGLIKAVSTFNLEKGNRLATYAARCIENEILMMLRGK------------------- 98

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDF 591
                                            K T + +SL  PIG +   +   L D 
Sbjct: 99  ---------------------------------KKTSKEVSLYEPIGTDREGNEIQLFDV 125

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE     +P   A++ +++    +V + L+PRE  VL+MR+G+    ++T  E+ +Q  +
Sbjct: 126 IESDEEDAPSKVALKDDIKMLYEKVSSELSPRERLVLKMRYGLYEGEEYTQREIARQLGI 185

Query: 652 TRERIRQIEAKAIRKLK 668
           +R  + +IE  AI KL+
Sbjct: 186 SRSYVSRIEKSAIEKLR 202


>gi|58582244|ref|YP_201260.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84624137|ref|YP_451509.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188576807|ref|YP_001913736.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188577000|ref|YP_001913929.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|6969595|gb|AAF33832.1|AF226282_6 RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae]
 gi|58426838|gb|AAW75875.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84368077|dbj|BAE69235.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188521259|gb|ACD59204.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188521452|gb|ACD59397.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 251

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 91/238 (38%), Gaps = 12/238 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
             +           +V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D 
Sbjct: 6   AAQYRAVQRNNADNVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ ++   I        +P  +  +        R++     R     
Sbjct: 66  EQGASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAAA 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+A  + MP+    ++++       L      ED   L      K   +P     ++   
Sbjct: 123 EVAAAMEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERSEFG 180

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 181 RELGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 234


>gi|330938480|gb|EGH42083.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 82

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 57/75 (76%), Positives = 65/75 (86%)

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +L+E T  VL+ LT RE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RK
Sbjct: 7   ESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 66

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP+RS+ LRSFLD
Sbjct: 67  LRHPTRSEHLRSFLD 81


>gi|167758775|ref|ZP_02430902.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
 gi|167663515|gb|EDS07645.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
          Length = 247

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 90/230 (39%), Gaps = 52/230 (22%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA 
Sbjct: 62  EEAKKTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPEKNIKLATYAS 121

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +                            NK K E + +E          
Sbjct: 122 RCIENEILMYLRRN-------------------------NKTKMEVSIDEP--------- 147

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                             +  +    L   I   +  +          R+   + ++ L+
Sbjct: 148 ----------------LNVDWDGNELLLSDILGTDEDTIYKDLENEVERKLLVKAISRLS 191

Query: 622 PREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  +++MRFG+G     + T +EV     +++  I ++E K +++LK 
Sbjct: 192 GRERTIIKMRFGLGTPDGEEKTQKEVADMLGISQSYISRLEKKIMQRLKR 241


>gi|149174362|ref|ZP_01852989.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
 gi|148846907|gb|EDL61243.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
          Length = 309

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 106/248 (42%), Gaps = 60/248 (24%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + ++ +    A + + E++  N+RLV S+ KK T  G+ F +L  +G + ++KA +KFD+
Sbjct: 113 LELIEQLLHRAQLVRDEILRRNMRLVASIVKKCTTTGVSFDELFSDGCLTMLKAIDKFDY 172

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G++FSTYA   +     R IA++                                  +
Sbjct: 173 SRGFRFSTYAYHAISNFAYRKIANR---------------------------------KK 199

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E AK   +P E   +     K P+                          + +     L 
Sbjct: 200 ERAKYKQLPPEQSMEETGAVKNPL--------------------------MGTDTWDELS 233

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   + + +L  RE+ +++ RF +G +    T +++  Q  +++ER+RQ+E +A+ KLK 
Sbjct: 234 ELLNQSIDTLDEREQLIVKSRFALGKHRKTLTFQKLADQLGISKERVRQLEQRAVAKLKA 293

Query: 670 PSRSKKLR 677
            ++  +L 
Sbjct: 294 VTQGTRLE 301


>gi|157313256|gb|ABV32521.1| RNA polymerase sigma factor [Xanthomonas campestris]
 gi|157313260|gb|ABV32523.1| RNA polymerase sigma factor [Xanthomonas campestris]
 gi|157313264|gb|ABV32525.1| RNA polymerase sigma factor [Xanthomonas campestris]
 gi|157313266|gb|ABV32526.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 71/172 (41%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + +          K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKAYVKYGAEHKNVA------KAREDMAAIFTTLKLPLPLTDAL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     +++ E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMV 232


>gi|157313254|gb|ABV32520.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 88.0 bits (216), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 71/172 (41%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + +          K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKAYVKYGAEHKNVA------KAREDMAAIFTTLKLPLPLTDAL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     +++ E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMV 232


>gi|332272331|gb|AEE38849.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 219

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 87/263 (33%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDSSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EEVLRSIGKLQQIEEETG 219


>gi|153006912|ref|YP_001381237.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152030485|gb|ABS28253.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 238

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 111/266 (41%), Gaps = 49/266 (18%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
             +  +   +++      ++    R +    R+     + AK E+V  NL LV+ VA+K 
Sbjct: 3   QEMESLAPYLEAARGRKPLTREAERALALRARR---GDARAKDELVRHNLALVVMVARKQ 59

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +   L+  +L+QEG +GL++A EKFD   G +FSTYA+WW++  + + +     ++R   
Sbjct: 60  SRGALRLEELVQEGMLGLLRAIEKFDPNAGTRFSTYAVWWIRAYVWKYLKQARSSVRPRS 119

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
                                                             +SL+T + +E
Sbjct: 120 GAV-------------------------------------------AAADLSLDTAVDEE 136

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM--RFGIGMNTDHT 641
                 D +ED+ A SPL+   +    E     L  +  R   +        +  +   T
Sbjct: 137 GDVSFLDRLEDEGA-SPLERYERVESGERLRASLEKVRKRIGDLGWDIVHTRLQQDPPDT 195

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
           LE++G+++ V+RER+RQ+E +  R L
Sbjct: 196 LEQIGQRWGVSRERVRQVELQTKRFL 221


>gi|327537603|gb|EGF24315.1| RNA polymerase ECF-type sigma factor [Rhodopirellula baltica WH47]
          Length = 340

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 102/242 (42%), Gaps = 60/242 (24%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + ++      A   +  +VEANLRLV S+ KK+ N    F DL+ +G + L++A EK
Sbjct: 145 RHRLELIELFVALADWHRDRIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEK 204

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G++FSTYA   V+                 V ++ +  +                
Sbjct: 205 FDFDRGFRFSTYATQVVR-----------RNSYRTVVLKQQERQ---------------- 237

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
                          V+  L+     +S                  ++   S +      
Sbjct: 238 --------------KVQGGLQDMDIDVS------------------EEERSSAISEKRWH 265

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            LR   + +L  L  RE+ ++R RF +G +   HTL+ +  +  V++ER+RQ+E +A+ K
Sbjct: 266 ELRSRLSVMLGDLDRREKFIIRARFSLGPHRKVHTLQSLADRLGVSKERVRQLERRAMDK 325

Query: 667 LK 668
           L+
Sbjct: 326 LR 327


>gi|297197375|ref|ZP_06914772.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|297146698|gb|EDY58861.2| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 294

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 36/146 (24%), Positives = 70/146 (47%), Gaps = 4/146 (2%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           + E+V A L +   +A ++ +RG    DL Q   +GL+KA ++F+   G  F +YA+  +
Sbjct: 50  RDELVSAWLPMAHRIAGRFRDRGESLEDLRQVAALGLVKAIDRFEPERG-AFESYAVPTI 108

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK-REPTPEEIAKKLAMPVEGV 563
              + R   D+   +R+P  +++  +KV    R ++      EPT  ++A    +  E V
Sbjct: 109 TGEVKRHFRDRMWALRVPRRVQELRNKVRVARRELTQNPGSPEPTTADLAAHTGLTEEEV 168

Query: 564 RKVLKI--TKEPISLETPIGDEDTSH 587
              L+   +   +SL+  +   D  +
Sbjct: 169 TTGLEALESFSTLSLDAELSTGDDGY 194


>gi|319919241|gb|ADV78238.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
 gi|319919247|gb|ADV78241.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
          Length = 210

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 68/245 (27%), Gaps = 46/245 (18%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAELVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
              + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAK 196

Query: 390 FPEGE 394
                
Sbjct: 197 GKGKY 201


>gi|222528793|ref|YP_002572675.1| sporulation sigma factor SigE [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455640|gb|ACM59902.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 244

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 96/251 (38%), Gaps = 58/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +          KK +VE NLRLV+ +A+++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYKIHYQGK--EELKKLLVERNLRLVVYIARRFENTKINLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +             R+   K+         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLR------------RNSNKKLE-------- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +   +  
Sbjct: 141 --------------------------------LSIDEPLNVDWDGNELLLSDVLG-TDTE 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +    +  RE   R +  L  RE++++ +RFG G   + T +EV     +++  I +
Sbjct: 168 EIYNRIESSVEREALLRAIQKLPSREKKIVELRFGFGDGGEKTQKEVADMLGISQSYISR 227

Query: 659 IEAKAIRKLKH 669
           +E K I +LK 
Sbjct: 228 LEKKIITRLKK 238


>gi|213580121|ref|ZP_03361947.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 143

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 34/130 (26%), Positives = 63/130 (48%), Gaps = 4/130 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I++ +    +S  E R +   +         A K ++ ++LR V+ +A+ Y   GL
Sbjct: 16  LESYIRAANAWPMLSADEERALAERL--HYQGDLEAAKTLILSHLRFVVHIARNYAGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MR 526
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      R
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQR 133

Query: 527 DKIHKVVRTA 536
                + +T 
Sbjct: 134 KLFFNLRKTK 143


>gi|312794093|ref|YP_004027016.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181233|gb|ADQ41403.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 244

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 93/248 (37%), Gaps = 52/248 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +     E    KK ++E NLRLV+ +AK++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYRIHYQGEEGL--KKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +   S                         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNS------------------------- 135

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                       KKL M ++                  +  +    L   +   +     
Sbjct: 136 -----------NKKLEMSIDE--------------PLNVDWDGNELLLSEVLGTDTEEIY 170

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +       +E   + +  L  RE++++ +RFG G + + T +EV     +++  I ++E 
Sbjct: 171 NRIENNVEKEALLQAIQKLPSREKKIVELRFGFGDDGEKTQKEVADMLGISQSYISRLEK 230

Query: 662 KAIRKLKH 669
           K I +LK 
Sbjct: 231 KIITRLKK 238


>gi|255280061|ref|ZP_05344616.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255269152|gb|EET62357.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 243

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 61/258 (23%), Positives = 98/258 (37%), Gaps = 58/258 (22%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             S    ++  E       ++K +     AKK ++E NLRLV  VAKKY  +G    +LI
Sbjct: 36  MKSFPKPLTPEEE---AWFLQKYKEGDLEAKKILIERNLRLVAHVAKKYQKQGEDGEELI 92

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G IGL+KA   F+     K +TYA   V+  +                      K+ R
Sbjct: 93  AVGTIGLIKAVSTFNHARTNKLATYAARCVENELLMLFRS--------------RKKISR 138

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDF 591
                                                  +SL  PIG +   +   L D 
Sbjct: 139 --------------------------------------EVSLNEPIGTDKEGNEISLIDV 160

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           IE +N        +  N R     +   LT RE+ +L++R+G+   ++ T  E+  +  +
Sbjct: 161 IEGENIDVIERMELDRNTRTLYRLLENVLTEREKEILKLRYGLYGKSEMTQREIADKMGI 220

Query: 652 TRERIRQIEAKAIRKLKH 669
           +R  + +IE  A+ KL+ 
Sbjct: 221 SRSYVSRIEKSAVAKLRQ 238


>gi|332272395|gb|AEE38881.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
 gi|332272397|gb|AEE38882.1| RNA polymerase sigma-70 factor [Aeromonas bivalvium]
          Length = 219

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 87/263 (33%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDSSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q + ++  + +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQNNGRAHDETQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +L+L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIILKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKSWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EDVLRAIGKLQQIEEETG 219


>gi|157313272|gb|ABV32529.1| RNA polymerase sigma factor [Xanthomonas campestris]
 gi|157313274|gb|ABV32530.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + + +        K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDAL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     +++ E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMV 232


>gi|117573594|gb|ABK40973.1| RNA polymerase subunit D [Pseudomonas sp. K94.38]
          Length = 201

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 22/119 (18%), Positives = 52/119 (43%), Gaps = 2/119 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLT 201


>gi|167037477|ref|YP_001665055.1| sporulation sigma factor SigK [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040139|ref|YP_001663124.1| sporulation sigma factor SigK [Thermoanaerobacter sp. X514]
 gi|256752531|ref|ZP_05493387.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914223|ref|ZP_07131539.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724542|ref|YP_003904293.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115891|ref|YP_004186050.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854379|gb|ABY92788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856311|gb|ABY94719.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256748597|gb|EEU61645.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889158|gb|EFK84304.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581603|gb|ADN55002.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928982|gb|ADV79667.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 231

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 98/270 (36%), Gaps = 52/270 (19%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  V  IL +     + S    ++  E +  +   +        A+  ++E NLRLV 
Sbjct: 8   ILASIVKEILNLGYLTNTNSFPNPLTPEEEKKYLEAYK---NGDEEARNILIERNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            V KKY+  G    DLI  G IGL+KA   FD   G   +TYA   ++  I  SI  +  
Sbjct: 65  HVVKKYSGTGKDIDDLISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMSIRTEKK 124

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                + + I  +    EI                         
Sbjct: 125 MKGEVF---------------LQDPIGVDKEGNEI------------------------- 144

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                     L D +  +          +  +++  +++ + L  RE+ ++ MR+G+   
Sbjct: 145 ---------SLMDVLGTEEDEISEQVEKKLQIKKLYSKMNSVLKNREKLIIEMRYGLYNG 195

Query: 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              T  E+ K   ++R  + +IE KA+ KL
Sbjct: 196 KVRTQREIAKMLGISRSYVSRIEKKALNKL 225


>gi|47569335|ref|ZP_00240019.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228967406|ref|ZP_04128439.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|47554006|gb|EAL12373.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228792294|gb|EEM39863.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 228

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 10  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 66

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA E +    G K +TYA   ++  I   +                  
Sbjct: 67  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV---------------- 110

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSH 587
                                               LK TK+ +SL  PIG +   +   
Sbjct: 111 ------------------------------------LKKTKKDVSLHDPIGQDKEGNEIS 134

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T  E+ K
Sbjct: 135 LIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAK 193

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              ++R  + +IE +A+ K+ H
Sbjct: 194 ALGISRSYVSRIEKRALMKMFH 215


>gi|157313268|gb|ABV32527.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 71/172 (41%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + +          K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKAYVKYGAEHKN------VVKAREDMAAIFTTLKLPLPLTDSL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     +++ E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMV 232


>gi|325567514|ref|ZP_08144181.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158947|gb|EGC71093.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
          Length = 235

 Score = 87.6 bits (215), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 100/235 (42%), Gaps = 14/235 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              + ++  +   L LV  V ++ + +    +  DL   G IGLM A  KFD      F 
Sbjct: 1   MYEVDREAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFE 60

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           +YA   +K AI   +   +   R  +   ++ ++     + +   +KRE T  EI K+L 
Sbjct: 61  SYAAIRIKGAIIDEVRKHAKISRYKMAAVNQFYQ---ARQELEQSLKREATDTEICKQLG 117

Query: 558 MPVEGVRKVLKITKE--PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +    +  + +       +SLE  +    E+   L D + D  A +  D+ +    R   
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTLKDMVRDP-AENVEDTLVAEEKRTAL 176

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  RE+ +L + +      + TL+E+ +   V+  R+ QI  K I KL+
Sbjct: 177 VACIKKLGEREQLILSLYY----TEELTLKEIAEILEVSIPRVSQIHGKTIAKLR 227


>gi|289670573|ref|ZP_06491648.1| RNA polymerase sigma factor [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 255

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 12/236 (5%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 12  QYRAVQRNNANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQ 71

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F TYA   ++ ++   I        +P  +  +        R++     R     E+
Sbjct: 72  GASFETYASIRIRGSMIDEIRRGDW---VPRSVHRRARDAAAAVRKIEQNTGRAAAATEV 128

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A  + MP+    ++++       L      ED   L      K   +P     +      
Sbjct: 129 AAAMEMPLLDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRE 186

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 187 LGKAIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 238


>gi|117573552|gb|ABK40952.1| RNA polymerase subunit D [Pseudomonas sp. C10-186]
 gi|117573554|gb|ABK40953.1| RNA polymerase subunit D [Pseudomonas sp. C10-189]
 gi|117573556|gb|ABK40954.1| RNA polymerase subunit D [Pseudomonas sp. C10-190]
 gi|117573562|gb|ABK40957.1| RNA polymerase subunit D [Pseudomonas sp. C10-205]
          Length = 200

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 52/118 (44%), Gaps = 2/118 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALETETGL 200


>gi|257469127|ref|ZP_05633221.1| RNA polymerase sigma factor RpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 157

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 45/145 (31%), Positives = 77/145 (53%), Gaps = 2/145 (1%)

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           +  D ++KV R            P+ EEIA +L +  + V+ ++   ++P+SL T IG  
Sbjct: 3   YKYDLLNKVNRYVMSRLKDEGNYPSVEEIAAELNIEADKVQDIIMDFQDPMSLSTQIG-- 60

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  +L D +  +   S  +       R+    ++  L  RE+ +L++R+G+     HTLE
Sbjct: 61  DDIYLEDTLAQQEDFSMEEEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIHTLE 120

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           E+G    +TRER+RQIE K ++KL+
Sbjct: 121 EIGNTLNITRERVRQIEKKTLQKLR 145


>gi|332272323|gb|AEE38845.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|332272325|gb|AEE38846.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|332272327|gb|AEE38847.1| RNA polymerase sigma-70 factor [Aeromonas media]
 gi|332272329|gb|AEE38848.1| RNA polymerase sigma-70 factor [Aeromonas media]
          Length = 219

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 87/263 (33%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDSSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +  + + +L+   +++ I  ETG
Sbjct: 198 LEMD-EEVLRSIGKLQQIEEETG 219


>gi|313115572|ref|ZP_07801031.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622087|gb|EFQ05583.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 234

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 99/256 (38%), Gaps = 61/256 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S+   ++  + + ++S +  G+  A     +++  NLRLV+ +AKKY + G+   D+I  
Sbjct: 30  SLPPPLTPEQEKVLLSRMAAGDAAARD---DLITHNLRLVVYLAKKYESSGVPAEDMISI 86

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F      K +TYA   +   I   +   S   +                
Sbjct: 87  GTIGLIKAVNTFTPERSIKLATYASRCIGNEILMYLRKSSNRRQEA-------------- 132

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFI- 592
                                                 S++ P+  +   +   L D + 
Sbjct: 133 --------------------------------------SIDEPLNVDGDGNELLLSDILG 154

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D+N +S      Q   R    R + SL+PRE +++ +RFG+    + T +E      ++
Sbjct: 155 SDENQIS--QRLEQDAERAVLRRAVDSLSPRERQIMELRFGLADGIERTQKEAADALGIS 212

Query: 653 RERIRQIEAKAIRKLK 668
           +  I ++E + I  LK
Sbjct: 213 QSYISRLEKRIIHTLK 228


>gi|114566372|ref|YP_753526.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337307|gb|ABI68155.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 240

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 99/250 (39%), Gaps = 56/250 (22%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  ++++ + +      K  ++E NLRLV+ +AKK+ N G+   DL+  G IGL+KA  
Sbjct: 42  EQEEMALISQLDQGIMSVKATLIEHNLRLVVYIAKKFENTGINIEDLVSIGTIGLIKAVN 101

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F+     K +TYA   ++  I   +             R+  ++V              
Sbjct: 102 TFEPKKNIKLATYASRCIENEILMYLR------------RNIKNRVE------------- 136

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDS 603
                                      ISL+ P+  +   +   L D +  +N +     
Sbjct: 137 ---------------------------ISLDEPLNVDWDGNELLLSDVLGTENDM-IYKQ 168

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 +    + +  L  RE+ ++++RFG+    + T +EV     +++  I ++E + 
Sbjct: 169 IEGEVEKSLLWKAMHKLNNREKTIIQLRFGLADGDEKTQKEVADILGISQSYISRLEKRI 228

Query: 664 IRKLKHPSRS 673
           +++L+   R 
Sbjct: 229 LKRLQREIRK 238


>gi|239934386|emb|CAR92323.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 220

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 29/208 (13%), Positives = 74/208 (35%), Gaps = 8/208 (3%)

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D +       +  A   ++   +          D+++ +E++D  +              
Sbjct: 20  DILSGYIDPDDDGAAAPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVA 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 +AE   +           +K  ++S +     E L  L   + L   + D LVE
Sbjct: 80  RVRFGAVAEQLEKANK------ALKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVE 133

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++ +   +I   E  +++L      + R  FL +    E +  W        +G++   +
Sbjct: 134 RVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAI 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEF 427
               + I++ + ++  +  E  ++I++ 
Sbjct: 193 GNRKEDIVRCQQKLIELEQECDLAIADI 220


>gi|332981685|ref|YP_004463126.1| RNA polymerase sigma-27/28 subunit,RpsK/SigK [Mahella australiensis
           50-1 BON]
 gi|332699363|gb|AEE96304.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Mahella
           australiensis 50-1 BON]
          Length = 236

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 89/251 (35%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E RH + +  +       AK  ++E NLRLV  + KKY N      DLI  
Sbjct: 28  SFPQPLSYEEERHYLELYEQ---GDQQAKNILIEHNLRLVAHIVKKYNNAVKDPEDLISI 84

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K    FD   G + +TYA   ++  I   +                  K  +  
Sbjct: 85  GTIGLIKGITTFDSNKGTRLATYAARCIENEILMYVRAS---------------KKEKKE 129

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             +   I  +    E+                                   L D +    
Sbjct: 130 VFLQEPIGTDKEGNEV----------------------------------TLIDILGTDE 155

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                  + +  + +   ++ + L  RE  +L +R+G+    D T  E+ +   ++R  +
Sbjct: 156 DTITDQVSDKMQIAKLYKKMGSVLKDRERLILELRYGLINGNDKTQREIAQMLGISRSYV 215

Query: 657 RQIEAKAIRKL 667
            +IE KA+ KL
Sbjct: 216 SRIEKKALNKL 226


>gi|307265198|ref|ZP_07546757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306919820|gb|EFN50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 230

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 90/240 (37%), Gaps = 49/240 (20%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R     +         A+  ++E NLRLV  V KKY+  G    DLI  G IGL+KA   
Sbjct: 34  RRGKKYLEAYRNGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAIST 93

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G   +TYA   ++  I  S                     +R  ++M  ++    
Sbjct: 94  FDSSKGTHLATYAARCIENEILMS---------------------IRAEKKMKGEVF--- 129

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
               +   + +  EG                     +   L D +  +          + 
Sbjct: 130 ----LQDPIGVDKEG---------------------NEISLMDVLGTEEDEISEQVEKKL 164

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +++  +++ + L  RE  ++ MR+G+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 165 QIKKLYSKMNSVLKNRERLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRIEKKALNKL 224


>gi|332272345|gb|AEE38856.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 219

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 41/263 (15%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EDVLRAIGKLQQIEEETG 219


>gi|225574871|ref|ZP_03783481.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037945|gb|EEG48191.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
          Length = 230

 Score = 87.6 bits (215), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 62/280 (22%), Positives = 113/280 (40%), Gaps = 60/280 (21%)

Query: 394 EWKNFVACEVDSILKIRNEIKSI-SVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           E   F+   +D  ++I  E+  + + +  +++ E R+ +   +K +     AK  ++E N
Sbjct: 2   EKHEFLVRLID-YIEIPYEVNFLKTFQKPLTVEEERYYL---KKFQEGDLKAKDILIERN 57

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV  V KKY        DLI  G IGL+KA   FD     + STYA   +   +   +
Sbjct: 58  LRLVAHVVKKYQGLEEDLDDLISIGTIGLIKAVSTFDSKKSNRLSTYAARCIDNELLMML 117

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                        R K  +                                         
Sbjct: 118 R-----------ARKKYSR----------------------------------------- 125

Query: 573 PISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
            +SL  PIG +   +  +L D IE        + +++ ++++    +   L+ +E  V+R
Sbjct: 126 DVSLYEPIGTDKEGNEINLLDIIESPPEDVVENYSVKQDIQKAMHLLSTCLSHKEYEVIR 185

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +RFG+    ++T  E+ K+  ++R  + +IE  A+ KL+ 
Sbjct: 186 LRFGLFGEKEYTQREIAKRLNISRSYVSRIEKNALLKLRR 225


>gi|163789630|ref|ZP_02184068.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
 gi|159875162|gb|EDP69228.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
          Length = 238

 Score = 87.2 bits (214), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 100/236 (42%), Gaps = 13/236 (5%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                 +++ +   L LV  +  +           DL   G IGLM A EKFD      F
Sbjct: 1   MYYENDREKEIIKYLPLVEKIVNRIDIKRSEYDRDDLYNIGVIGLMDALEKFDKSKKVPF 60

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
             YA   +K  I   I   +    +      K+++  R   ++  ++ R PT +EI  +L
Sbjct: 61  EGYAYIRIKGTIIDEIRKTA---PVSRTRMGKLNEYYRGKEKLEAELMRTPTEKEICAEL 117

Query: 557 AMPVEGVRKVLKITKE--PISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRET 612
            +  + + K+ +       +SLE  +  +D     L DF+ED +     D+ +    +  
Sbjct: 118 KIDEKSLAKIHETVHNLASVSLEKVMFSDDGNSIELLDFLEDTHETGSEDTLLDKERQHL 177

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            T+ +  L  RE+ +L + +      + +L+E+   F ++  R+ QI  K I KLK
Sbjct: 178 LTKHVGQLDKREQTILNLIYV----EELSLKEIAYIFDISVPRVSQIHGKMILKLK 229


>gi|117573592|gb|ABK40972.1| RNA polymerase subunit D [Pseudomonas sp. K93.52]
 gi|117573600|gb|ABK40976.1| RNA polymerase subunit D [Pseudomonas sp. Q86-87]
          Length = 200

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 52/118 (44%), Gaps = 2/118 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGL 200


>gi|256825196|ref|YP_003149156.1| RNA polymerase sigma factor, sigma-70 family [Kytococcus
           sedentarius DSM 20547]
 gi|256688589|gb|ACV06391.1| RNA polymerase sigma factor, sigma-70 family [Kytococcus
           sedentarius DSM 20547]
          Length = 261

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 94/244 (38%), Gaps = 18/244 (7%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R + +     E        +++  ++     + +++        D  Q   + L+ A ++
Sbjct: 25  RRLTAAHGLPEQHRQQELVDVIADHIPFARRLGRRFAPTPSLVDDCEQVACMALVLAVQR 84

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D       S+YA   +   + R + D +  +R P  +++    V  T   + +   REP
Sbjct: 85  WDPAFDANLSSYAQPTILGELRRFLRDSTWWVRPPRRIQELAALVRSTEEELRHSTGREP 144

Query: 548 TPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           T +EIA+ +    + V +       +   S++  +   +T+ L   ++       +    
Sbjct: 145 TAQEIARAMGASPDEVSEARVAAAGRYVASVDDEVT--ETARLVHPVQSPAVDEWV---- 198

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
                 +    + +L PR+  VL  R+      D T   + +   +++ ++ +   +A+ 
Sbjct: 199 ------SLHPHIQALDPRDRCVLLRRYL----EDETQASIARALGISQAQVSRRLKRALD 248

Query: 666 KLKH 669
            L+ 
Sbjct: 249 TLRE 252


>gi|32471396|ref|NP_864389.1| RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
 gi|32443237|emb|CAD72068.1| probable RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
          Length = 340

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 102/242 (42%), Gaps = 60/242 (24%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           RH + ++      A   +  +VEANLRLV S+ KK+ N    F DL+ +G + L++A EK
Sbjct: 145 RHRLELIELFVALADWHRDRIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEK 204

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD+  G++FSTYA   V+                 V ++ +  +                
Sbjct: 205 FDFDRGFRFSTYATQVVR-----------RNSYRTVVLKQQERQ---------------- 237

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
                          V+  L+     +S                  ++   S +      
Sbjct: 238 --------------KVQGGLQDMDIDVS------------------EEERSSAISEKRWH 265

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            LR   + +L  L  RE+ ++R RF +G +   HTL+ +  +  V++ER+RQ+E +A+ K
Sbjct: 266 ELRSRLSVMLGDLDRREKFIIRARFSLGPHRKVHTLQSLADRLGVSKERVRQLERRAMDK 325

Query: 667 LK 668
           L+
Sbjct: 326 LR 327


>gi|299535876|ref|ZP_07049196.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728628|gb|EFI69183.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 206

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 92/244 (37%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V+++         A+  ++E NLRLV+ +A+++ N G    DLI  G+IGL+KA E F
Sbjct: 9   EEVTVIASFMNGDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLIKAIETF 68

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +     K +TYA   ++  I   +   S                                
Sbjct: 69  NTDKNIKLATYASRCIENEILMHLRKTSRMKGE--------------------------- 101

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                    +SL+ P+  +   +   L D +  +  +  LD+  
Sbjct: 102 -------------------------VSLDEPLNSDADGNELLLSDILGTEEHI-ILDNVE 135

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R+     +  L  RE  ++  RFG+    + T +EV     +++  I ++E K I+
Sbjct: 136 KKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLGISQSYISRLEKKIIQ 195

Query: 666 KLKH 669
            L+ 
Sbjct: 196 DLRE 199


>gi|239623450|ref|ZP_04666481.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521481|gb|EEQ61347.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 246

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 86/236 (36%), Gaps = 58/236 (24%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A+  ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F      K +T
Sbjct: 58  EDDKGARSTLIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFKPDKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                                              
Sbjct: 118 YASRCIENEILMYLRRN------------------------------------------- 134

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTR 615
                      T+  +S++ P+  +   +   L D +     V           +     
Sbjct: 135 ---------NKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDV-IYHDIEDEIEKNLLNN 184

Query: 616 VLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ++ L PRE +++ +R+G+      + T +EV     +++  I ++E K +++LK 
Sbjct: 185 AISRLNPRERKIVELRYGLTNEDGEEMTQKEVADLLGISQSYISRLEKKIMKRLKK 240


>gi|260589594|ref|ZP_05855507.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|260540162|gb|EEX20731.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
          Length = 252

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 97/256 (37%), Gaps = 60/256 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              ++  E   ++  +         A+  ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 46  PAPLTAQEEGEMLDALAGEGK--EEARACLIEHNLRLVVYIAKKFDNTGVGVEDLISIGT 103

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   FD     K +TYA   ++  I   +   S                      
Sbjct: 104 IGLIKAINTFDPVKKIKLATYASRCIENEILMYLRRNSK--------------------- 142

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                          TK  +S++ P+  +   +   L D +   
Sbjct: 143 -------------------------------TKLEVSIDEPLNVDWDGNELLLSDILGTD 171

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTR 653
             V           R+   + +  LT RE+ ++R+RFGI M    + T +EV     +++
Sbjct: 172 EDV-IYKDIENEVERKLLGKAIGKLTKREQTIVRLRFGINMPDGGEKTQKEVADLLGISQ 230

Query: 654 ERIRQIEAKAIRKLKH 669
             I ++E K +++LK 
Sbjct: 231 SYISRLEKKIMKRLKK 246


>gi|319919243|gb|ADV78239.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
 gi|319919251|gb|ADV78243.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
 gi|319919255|gb|ADV78245.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
 gi|319919257|gb|ADV78246.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
          Length = 208

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 68/245 (27%), Gaps = 46/245 (18%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAELVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
              + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAK 196

Query: 390 FPEGE 394
                
Sbjct: 197 GKGKY 201


>gi|134300490|ref|YP_001113986.1| sporulation sigma factor SigK [Desulfotomaculum reducens MI-1]
 gi|134053190|gb|ABO51161.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Desulfotomaculum reducens MI-1]
          Length = 232

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 104/265 (39%), Gaps = 59/265 (22%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           I  + + I S S+   +S  E R ++  +        +AK  ++E NLRLV  +A K  +
Sbjct: 17  IAILVSYISSGSLPDPLSPEEERELLLKM---ATGDKLAKTILIERNLRLVAKIANKLKD 73

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            G+   DL Q G IGL+K  + FD     KFSTYA   ++  +   +  Q          
Sbjct: 74  SGVDKQDLFQVGVIGLIKGVDTFDIKKARKFSTYAGVCIQNEMLMMLRKQKSERNT---- 129

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
                                                           IS+  P+  +  
Sbjct: 130 ------------------------------------------------ISISEPLDFDKD 141

Query: 586 S---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                L D + + N +   +   ++   E   + L +L PRE+ V+++R+G+    + T 
Sbjct: 142 GSPLELQDTLAN-NEIPVDELVEKSLDVERLEKALQTLNPREKIVIKLRYGLEGERELTQ 200

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
            EVGK+  ++R  I +IE+  I KL
Sbjct: 201 REVGKRLDISRSFISRIESSTINKL 225


>gi|306410397|gb|ADM85820.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410399|gb|ADM85821.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410401|gb|ADM85822.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410403|gb|ADM85823.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410405|gb|ADM85824.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|306410407|gb|ADM85825.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CpI1]
 gi|306410409|gb|ADM85826.1| RNA polymerase essential primary sigma 70 factor [Frankia sp.
           Cj1-82]
          Length = 106

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 61/106 (57%), Positives = 89/106 (83%)

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A EKFD+  GYKFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K++R  R+
Sbjct: 1   LGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQ 60

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           +   + REP+PEEIAK++ +  + VR++LK+++EP+SLETPIG+E+
Sbjct: 61  LLQDLGREPSPEEIAKEMDLTPDKVREILKVSQEPVSLETPIGEEE 106


>gi|261886056|ref|ZP_06010095.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 262

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 48/196 (24%), Positives = 87/196 (44%), Gaps = 7/196 (3%)

Query: 41  RGYVTIEELNAFL--PPDEVSSEQMEDTVAMLSNMGINVVDGDD----LEDEEGSEDSLD 94
           +GYVT E+L       P   + +++E    +     I+ V+        E ++  ED L 
Sbjct: 20  KGYVTFEKLVRLFDKAPTVATIKKVETLAELYKIQLISAVEAAKIKNIQEAKKSEEDKLK 79

Query: 95  LASSASNSSVFLQKRKDS-ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
           +  +A      L    D      +D PVRMYLREMG I LL++E E+ I+K+IE G  ++
Sbjct: 80  IIDTALEEEFDLTSENDLLEWSRSDSPVRMYLREMGQISLLTKEEEVEISKKIELGEDII 139

Query: 154 MASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRED 213
           + + C  P     ++ +++ L +    ++E+         E +       E    +  ED
Sbjct: 140 IDAFCSVPYLIDFILDYKEPLINRERRVKELFKSFDEEESEEEEEETTEDEFEYDENEED 199

Query: 214 SSQEKERDDVQETEGD 229
           S+  K++    +   +
Sbjct: 200 SATAKKQPKKLDKRAE 215


>gi|157313258|gb|ABV32522.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 87.2 bits (214), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + +          K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKAYVKYGAEHKNVA------KAREDMAAIFTTLKLPLPLTDAL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     ++++E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLAEIKDISRAMAYGEAKARKAKKEMV 232


>gi|332272369|gb|AEE38868.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 219

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 41/263 (15%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEEDLADEDDDEDEDEDGDGDDSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EDVLRAIGKLQQIEEETG 219


>gi|332272355|gb|AEE38861.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|332272357|gb|AEE38862.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|332272359|gb|AEE38863.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|332272361|gb|AEE38864.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|332272363|gb|AEE38865.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|332272365|gb|AEE38866.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
 gi|332272367|gb|AEE38867.1| RNA polymerase sigma-70 factor [Aeromonas aquariorum]
          Length = 219

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 41/263 (15%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EDVLRAIGKLQQIEEETG 219


>gi|319919259|gb|ADV78247.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
          Length = 207

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 68/245 (27%), Gaps = 46/245 (18%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 1   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 49

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 50  EVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 109

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 110 KKFGRDDKHAIAELVALAELF----------------------------------MPIKL 135

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
              + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 136 VPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAK 195

Query: 390 FPEGE 394
                
Sbjct: 196 GKGKY 200


>gi|225575508|ref|ZP_03784118.1| hypothetical protein RUMHYD_03600 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037258|gb|EEG47504.1| hypothetical protein RUMHYD_03600 [Blautia hydrogenotrophica DSM
           10507]
          Length = 286

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 103/226 (45%), Gaps = 10/226 (4%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           + + N   +  +A  Y  +  +  DL QEG + L +A   +D      F +YA +W+K  
Sbjct: 23  LWQQNEGFIGKLALIYAGQ-AEMEDLKQEGYLALCEAVRGYDVTREVPFLSYASFWLKTR 81

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           + R + DQ+  +R+P ++ D++ +  +T      +   E +  E+   L +  + +RK+ 
Sbjct: 82  MRRYV-DQNKPVRLPSYLGDEVRQYQKTKSDFLKRYGYEASDRELCGLLGVNEKKIRKLK 140

Query: 568 KITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSA--IQANLRETTTRVLASLTPR 623
           +        SL   +   +   L + I  +  +    +A   +  ++E   R +  L  R
Sbjct: 141 RAASMGQIQSLNELLPGTEDFTLEESIASEEDLEEEAAARLDRERMKEELWRSVDELPDR 200

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              V+RMR+      + TL EVG++  V+  R  Q+  +A+R L+ 
Sbjct: 201 LPVVVRMRY----QEETTLNEVGERLGVSLSRAAQMNKQAMRTLRQ 242


>gi|209408334|emb|CAP19910.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 194

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 74/238 (31%), Gaps = 45/238 (18%)

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEG 205
           IE G   +M+++   P T  +++   + +      L +I  L   I P+  G        
Sbjct: 1   IEEGIREVMSAIAHFPGTVDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA------ 52

Query: 206 HSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDS 265
              Q+ E  + +       + + D E     S+ +       PE A      + E  + +
Sbjct: 53  -GPQEVEPETPQTTAKPAADDKDDEEEDDSDSEKEEGDGGPDPEVARMRFGAVAEQLEKA 111

Query: 266 AHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLV 325
                                                  +K  ++S +     E L  L 
Sbjct: 112 KKA-----------------------------------LKKHGRASQQAVEELEALAILF 136

Query: 326 GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
             + L   + D +VE++ +   +I   E  +++L      + R   L +    E +  
Sbjct: 137 MPIKLVPKQYDAVVERVRNALSQIRAQERFIMQLCVRDARMPRADILRQFPNSETNLD 194


>gi|323705266|ref|ZP_08116841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535168|gb|EGB24944.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 231

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 98/254 (38%), Gaps = 58/254 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E R      +        AK  ++E NLRLV  V KKY+N G    DLI  
Sbjct: 27  SFPQPLTAEEERKYFEAFK---NGDEEAKNILIERNLRLVAHVVKKYSNAGKDVDDLISI 83

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   +D   G   +TYA   ++  I  S                     +R  
Sbjct: 84  GTIGLIKAILTYDSSKGTHLATYAARCIENEILMS---------------------LRAE 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIE 593
           +++ ++                               ISL  PIG +   +   L D + 
Sbjct: 123 KKIKSE-------------------------------ISLHDPIGVDKEGNEISLIDILG 151

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +         ++  +++   ++ + L  RE+ ++ +R+G+      T  E+ K   ++R
Sbjct: 152 TETDEVSDQVELRMQVKKLYHKLNSVLKNREKLIIELRYGLINGGAKTQREIAKMLGISR 211

Query: 654 ERIRQIEAKAIRKL 667
             + +IE KA+ KL
Sbjct: 212 SYVSRIEKKALNKL 225


>gi|225568655|ref|ZP_03777680.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
 gi|225162583|gb|EEG75202.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
          Length = 246

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 51/233 (21%), Positives = 89/233 (38%), Gaps = 52/233 (22%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +T
Sbjct: 58  EYDEKAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPEKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                            NK K E + +E       
Sbjct: 118 YASRCIENEILMYLRRN-------------------------NKTKMEVSIDEP------ 146

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
                                +  +    L   I      +          ++   + ++
Sbjct: 147 -------------------LNVDWDGNELLLSDILGTEEDTIYKDLENEVEQKLLLKAIS 187

Query: 619 SLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L+ RE  +++MRFG+G     + T +EV     +++  I ++E K +++L+ 
Sbjct: 188 RLSGRERTIIQMRFGLGTPDGEEKTQKEVADMLGISQSYISRLEKKIMQRLRR 240


>gi|291522682|emb|CBK80975.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus catus GD/7]
          Length = 245

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 60/278 (21%), Positives = 100/278 (35%), Gaps = 55/278 (19%)

Query: 397 NFVACEVDSILKIRNEIKSISVETGISIS---EFRHIVSMVRKGECEASIAKKEMVEANL 453
             V      I K   EI  IS    + +    E       +   E E    +  ++E NL
Sbjct: 10  RMVRGFRSIIYKSNGEIHYISGTDVLPVPLEGEEEKNAIAMLATEAEREHGRNILIEHNL 69

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           RLV+ +A+K+ N G    DLI  G IGL+KA   ++     K +TYA   ++  I   + 
Sbjct: 70  RLVVYIARKFDNTGAGMEDLISIGTIGLIKAINSYNPDKNIKLATYASRCIENEILMYLR 129

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
             S                         K+K E + +E                      
Sbjct: 130 RSS-------------------------KLKMEVSIDEP--------------------- 143

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
                 +  +    L   I   +     +   +        + LA L+PRE+ ++++RFG
Sbjct: 144 ----LNVDWDGNELLLSDILGTDENVIYNKMEEEVNYHLLYKALAKLSPREKTIIQLRFG 199

Query: 634 IG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           I      + T +EV     +++  I ++E K I +LK 
Sbjct: 200 IRTADGEEKTQKEVADFLGISQSYISRLEKKIIGRLKK 237


>gi|332272371|gb|AEE38869.1| RNA polymerase sigma-70 factor [Aeromonas diversa]
 gi|332272373|gb|AEE38870.1| RNA polymerase sigma-70 factor [Aeromonas diversa]
          Length = 221

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 80/262 (30%), Gaps = 42/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II            GF +  E              E 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII-----------SGFVNPDEA------------DEM 37

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                  G       ++ +D S  +   E+ E D  + D D             +LR + 
Sbjct: 38  GPTATHIGSELGEDDLADEDSSDEEEEDEDEEGDGNDDDGDGGPDPEVAREKFAELRAQY 97

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 I                   + ++  + +    +L  +     L   + D LV 
Sbjct: 98  EITRQSIRS-----------------NGRAHEETQAAIAQLADVFRQFRLMPKQFDRLVN 140

Query: 341 QLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+   +   + +  F+      E +  W  Y K   +       
Sbjct: 141 NMREMMERVRVQERLILKMCVEQAKMPKKTFVSAFTNNECETAWFEYQKQAGKAWSAPLA 200

Query: 400 ACEVDSILKIRNEIKSISVETG 421
           A E D +L+   +++ I  ETG
Sbjct: 201 AME-DEVLRSIGKLQQIEEETG 221


>gi|239934538|emb|CAR94583.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 234

 Score = 87.2 bits (214), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 46/293 (15%), Positives = 87/293 (29%), Gaps = 68/293 (23%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESK 196
            EIA+AKRIEAG   +  ++  SP   +  I + D +  G   L + +ID       +  
Sbjct: 7   DEIALAKRIEAGNRQVAKAVSLSPGAMRQFIEFADRIEAGDMKLTDMVIDFMELNALD-- 64

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                                       ET        + + D       P         
Sbjct: 65  ---------------------------DETVATPGEPGQNAADAEEGPSGPD-------- 89

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCK 315
                                       DE  E ++++R +     N Q K+   S    
Sbjct: 90  ---------------------------FDEAIERFKKVRKIWKLLENAQAKNGVDSKLAL 122

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERH 374
             ++ +   +  +    +R + +   L +    +   E  + +   +Y  + R  F E  
Sbjct: 123 KHRQAMSDEMLQIKYVPARFEEITATLRNSMDEVRFCERSIAKYCVTYAKVPRKRFREHF 182

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
            G E    W         GE K     E ++I ++  ++  +     + + E 
Sbjct: 183 SGNETSSDWFKNLVKASAGEAKKLKDFE-ETIEELXAQLNKVQQNAALDLKEL 234


>gi|319919249|gb|ADV78242.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
          Length = 209

 Score = 87.2 bits (214), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 68/245 (27%), Gaps = 46/245 (18%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAELVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
              + + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAK 196

Query: 390 FPEGE 394
                
Sbjct: 197 GKGKY 201


>gi|296061192|emb|CBJ55907.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061194|emb|CBJ55908.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061196|emb|CBJ55909.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061198|emb|CBJ55910.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061200|emb|CBJ55911.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061202|emb|CBJ55912.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061204|emb|CBJ55913.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061208|emb|CBJ55915.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
 gi|296061210|emb|CBJ55916.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
          Length = 199

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 84/243 (34%), Gaps = 45/243 (18%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEIAIAKRIE G + + A+L   PL+ + L+   +   +G   L EI+          
Sbjct: 1   REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E         ++      D    + D +        +     + P+  E   
Sbjct: 51  -VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE--- 106

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                                   V   ++ +A  Y + + +        K+        
Sbjct: 107 ------------------------VATRMENLANEYAKFKKIY------AKNGAEHKLVV 136

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
             +E +  +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   
Sbjct: 137 KAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 196

Query: 375 QGR 377
           +G 
Sbjct: 197 EGN 199


>gi|282952588|emb|CBI75471.1| RNA polymerase beta subunit [Pseudomonas grimontii]
          Length = 211

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 57/126 (45%), Gaps = 2/126 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +S+         L +L   + L   + + LVE++    +R+   E  +++L      
Sbjct: 87  KHGRSNKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 146

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++I
Sbjct: 147 MPRTDFLRQFPGHEVDESWSD-ALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTI 205

Query: 425 SEFRHI 430
           +E + I
Sbjct: 206 AEIKDI 211


>gi|255505283|ref|ZP_05345211.3| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255268593|gb|EET61798.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 249

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 89/231 (38%), Gaps = 58/231 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   
Sbjct: 66  AKSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPGKNIKLATYASRC 125

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +   S                                               
Sbjct: 126 IENEILMYLRRTSK---------------------------------------------- 139

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                 TK  +S + P+  +   +   L D +     V   D   +   +      +  L
Sbjct: 140 ------TKMEVSFDEPLNVDWDGNELLLSDILGTDEDVIYRDMETEVEYK-LLMHAIDKL 192

Query: 621 TPREERVLRMRFGIGMN--TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + RE  ++++RFGIG N   + T +EV     +++  I ++E K I +LK 
Sbjct: 193 SDRERMIIQLRFGIGRNDGEEKTQKEVADMLGISQSYISRLEKKIIGRLKK 243


>gi|332272343|gb|AEE38855.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|332272347|gb|AEE38857.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|332272349|gb|AEE38858.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|332272351|gb|AEE38859.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
 gi|332272353|gb|AEE38860.1| RNA polymerase sigma-70 factor [Aeromonas hydrophila]
          Length = 219

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 40/263 (15%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + +LR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGDLRAQYEVTRLSIQQNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EDVLRAIGKLQQIEEETG 219


>gi|157313252|gb|ABV32519.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 73/172 (42%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + + +        K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDAL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL  +   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     ++++E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLAEIKDISRAMAYGEAKARKAKKEMV 232


>gi|167933077|ref|ZP_02520164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [candidate
           division TM7 single-cell isolate TM7b]
          Length = 103

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 50/99 (50%), Positives = 72/99 (72%)

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+ S LGDFIED++  +P +SA    L+E    +L+SL+ RE+++++MRFG+     HTL
Sbjct: 5   EEDSVLGDFIEDEDTATPEESASSQLLKEQVQGILSSLSDREQKIIKMRFGLENGKSHTL 64

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           EEVG++F VTRERIRQIEAKA+ KL+    +KKL  +L+
Sbjct: 65  EEVGQEFAVTRERIRQIEAKALAKLRKHKDAKKLHEYLN 103


>gi|238916673|ref|YP_002930190.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872033|gb|ACR71743.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 250

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 87/236 (36%), Gaps = 58/236 (24%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   +D     K +T
Sbjct: 62  ASDAEAKHTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINSYDKDKNIKLAT 121

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +   S                                          
Sbjct: 122 YASRCIENEILMYLRRNSKIKAE------------------------------------- 144

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTR 615
                          +S++ P+  +   +   L D I     +   D   +   +    R
Sbjct: 145 ---------------VSIDEPLNVDWDGNELLLSDIIGTDEDIIYRDIETEVECK-MLKR 188

Query: 616 VLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  L  RE  ++ +RFG+      + T +EV     +++  I ++E K +R+L+ 
Sbjct: 189 AINQLPERERIIVDLRFGLSSEDGEEKTQKEVADMLGISQSYISRLEKKIMRQLRK 244


>gi|117573564|gb|ABK40958.1| RNA polymerase subunit D [Pseudomonas sp. C6-16]
 gi|117573570|gb|ABK40961.1| RNA polymerase subunit D [Pseudomonas sp. C6-9]
 gi|117573574|gb|ABK40963.1| RNA polymerase subunit D [Pseudomonas sp. S7-29]
 gi|117573576|gb|ABK40964.1| RNA polymerase subunit D [Pseudomonas sp. S7-42]
 gi|117573578|gb|ABK40965.1| RNA polymerase subunit D [Pseudomonas sp. S7-46]
 gi|117573580|gb|ABK40966.1| RNA polymerase subunit D [Pseudomonas sp. S7-52]
 gi|117573586|gb|ABK40969.1| RNA polymerase subunit D [Pseudomonas sp. S8-151]
 gi|117573588|gb|ABK40970.1| RNA polymerase subunit D [Pseudomonas sp. C6-11]
          Length = 200

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 52/118 (44%), Gaps = 2/118 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGL 200


>gi|302391540|ref|YP_003827360.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
 gi|302203617|gb|ADL12295.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
          Length = 247

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 99/260 (38%), Gaps = 60/260 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  +++S ++         +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL
Sbjct: 44  LSNEEESYLLSKLK---EGDKAVRSVLIERNLRLVVYIARKFENTGIDIEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     K +TYA   ++  I   +   +                         
Sbjct: 101 IKAVNTFDVSKRIKLATYASRCIENEILMYLRRNNKKKSE-------------------- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           IS + P+  +   +   L D +   +  
Sbjct: 141 --------------------------------ISFDEPLNIDWDGNELKLSDVLG-TDMD 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIR 657
                  +   RE   + +  LT RE +++ +RFG+G +  + T +EV     +++  I 
Sbjct: 168 LIYQYIEEDVDRELLLQAMEVLTDRERKIMILRFGLGEDREEMTQKEVADILGISQSYIS 227

Query: 658 QIEAKAIRKLKHPSRSKKLR 677
           ++E + I+KL+      +L 
Sbjct: 228 RLEKRIIKKLQQEISKMQLE 247


>gi|14530750|emb|CAC42416.1| RpoH protein [Ralstonia metallidurans CH34]
          Length = 317

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 43/192 (22%), Positives = 86/192 (44%), Gaps = 4/192 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+++     ++  E   +   +R  +     A + MV ++LRLV+S+A++Y   GL
Sbjct: 58  LDSYIQAVHRIPMLTPEEELSLARDLRDNDSVD--AARRMVMSHLRLVVSIARQYLGYGL 115

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRD 527
              DLIQEGNIGLMKA ++FD      +        +  I   +      +++     + 
Sbjct: 116 PHADLIQEGNIGLMKAVKRFDPEQACAWCRTRCTGSRPEIHEYVLKNWRMVKVATTKAQR 175

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS 586
           K+   +R+ ++ S+    E       +    P E +    +++   ++LE  I D E+  
Sbjct: 176 KLFFNLRSHKQGSHTFTPEQIEAVARELNVKPEEVMEMETRMSGGDMALEGQIEDGEEEF 235

Query: 587 HLGDFIEDKNAV 598
               ++ D +  
Sbjct: 236 APIAYLADNHNE 247


>gi|331083018|ref|ZP_08332137.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330399755|gb|EGG79416.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 241

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 97/256 (37%), Gaps = 60/256 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              ++  E   ++  +         A+  ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 35  PAPLTAQEEGEMLDALAGEGK--EEARACLIEHNLRLVVYIAKKFDNTGVGVEDLISIGT 92

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   FD     K +TYA   ++  I   +   S                      
Sbjct: 93  IGLIKAINTFDPVKKIKLATYASRCIENEILMYLRRNSK--------------------- 131

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                          TK  +S++ P+  +   +   L D +   
Sbjct: 132 -------------------------------TKLEVSIDEPLNVDWDGNELLLSDILGTD 160

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTR 653
             V           R+   + +  LT RE+ ++R+RFGI M    + T +EV     +++
Sbjct: 161 EDV-IYKDIENEVERKLLGKAIGKLTKREQTIVRLRFGINMPDGGEKTQKEVADLLGISQ 219

Query: 654 ERIRQIEAKAIRKLKH 669
             I ++E K +++LK 
Sbjct: 220 SYISRLEKKIMKRLKK 235


>gi|255697047|emb|CBA11633.1| RNA polymerase sigma factor [Pseudomonas tremae]
          Length = 192

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 66/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D       P             D+ +          +
Sbjct: 51  VDSKAVKAEGTDDDKEESADASDDKDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|308205503|gb|ADO18993.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 158

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/161 (30%), Positives = 100/161 (62%), Gaps = 3/161 (1%)

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +P+H+ +K++K+ +  R +S  + R+PT  EIA++L +  E  R+ ++  ++ +SLE  +
Sbjct: 1   MPIHINEKLNKIKKIQRELSQSLGRKPTVVEIAEELKVKPEQAREYIQADRKLVSLEMRV 60

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
           G+E  + L + + D+  +SPL+    + +R+    +LASL P +  VL +RFG+  +   
Sbjct: 61  GNEQETELSELLADEK-ISPLEELNSSLMRQNIKELLASLAPIQREVLTLRFGLENDHQL 119

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           +L ++G++  ++RERIRQ+E KA+  L+   +   ++ +L+
Sbjct: 120 SLTQIGERLNLSRERIRQLEHKALSILRR--QKSDIKEYLN 158


>gi|239827399|ref|YP_002950023.1| RNA polymerase, sigma 70 family subunit [Geobacillus sp. WCH70]
 gi|239807692|gb|ACS24757.1| putative RNA polymerase, sigma 70 family subunit [Geobacillus sp.
           WCH70]
          Length = 831

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 83/428 (19%), Positives = 148/428 (34%), Gaps = 55/428 (12%)

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
           +    +   +Y EL    + A   Q   +   K   +K+     +G+ SL Q   +LL+ 
Sbjct: 411 LEFFLKDDHLYLELGVFDEKAHTEQMKYEDLAKLSEMKK-----LGTKSLMQHLAELLML 465

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
               +   I     ++              L  +   E     V Y +  P+   K ++ 
Sbjct: 466 HPSGLH--IREIVRDIQEDTTYAESSIRNTLSSYPFFEPIKGKVGYWRFNPKLWKKQYME 523

Query: 401 CE--------VDSILKIRNEIKSIS-----VETGISISEFRHIVSMVRKGECEASIAKKE 447
            E          SI  +R + K  +      +  ++  +F+ +                 
Sbjct: 524 LENNIKNNLKSKSIPTLRQQWKIKALASTKTKRRLTNEQFKQLPKETFLSLAWD------ 577

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
                   +   AKK++   +   DL QE    L KA EK++  LG  F  Y    +   
Sbjct: 578 ---YYSFTIYQYAKKFSCETVPMEDLYQEAYFALHKAYEKYNPELGGSFYHYFRRHLFAR 634

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP-----TPEEIAKKLAMPVEG 562
           + R  +D    IRIP H  + + K  +   +     ++       +   + K   +  E 
Sbjct: 635 LQRYKSDNLSLIRIPTHRIETLMKNDQIFEKQLITNEKTNINLLDSDYILFKTNYISFEE 694

Query: 563 VRKVLKITKEP-----ISLETPIGDEDTSHL-------GDFIEDKNAVSPLDSAIQANL- 609
           +  +            I         + + L         +IE+      L S  +    
Sbjct: 695 LYSLYDDNAGDEARARIYCYFNHPFYEDTSLKRQVFIDYSYIEEPEECDWLLSEERYEEE 754

Query: 610 ---RETTTRVLASL-----TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
              R      +  L      PR+ +++  RFG     + TL+E+G+ F V+RERIRQIE 
Sbjct: 755 IENRVLAESAIDYLRNIIKNPRDWKIILYRFGFMTGEEMTLQEIGELFGVSRERIRQIEN 814

Query: 662 KAIRKLKH 669
           KA++ LK 
Sbjct: 815 KALKHLKK 822


>gi|117573550|gb|ABK40951.1| RNA polymerase subunit D [Pseudomonas sp. C10-181]
 gi|117573558|gb|ABK40955.1| RNA polymerase subunit D [Pseudomonas sp. C10-197]
 gi|117573560|gb|ABK40956.1| RNA polymerase subunit D [Pseudomonas sp. C10-204]
 gi|117573582|gb|ABK40967.1| RNA polymerase subunit D [Pseudomonas sp. S8-110]
 gi|117573584|gb|ABK40968.1| RNA polymerase subunit D [Pseudomonas sp. S8-130]
          Length = 201

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 22/119 (18%), Positives = 52/119 (43%), Gaps = 2/119 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           + R  FL +  G E+D  W   A    + ++   +      I++ + ++ ++  ETG++
Sbjct: 144 MPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLT 201


>gi|255697135|emb|CBA11679.1| RNA polymerase sigma factor [Pseudomonas syringae pv. ribicola]
          Length = 192

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAAKAE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    ++D  +    P  A      + +  + +   L  +  +
Sbjct: 60  GTDDDEE--------ESADASDEEDEVESGPDPVIAAQRFGAVSDQMEITRKALKKLGRE 111

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            +  +   +                                    L +L   + L   + 
Sbjct: 112 DKHAIAEMV-----------------------------------ALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++     R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALDRLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|217967265|ref|YP_002352771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
 gi|217336364|gb|ACK42157.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
          Length = 235

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 106/237 (44%), Gaps = 12/237 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            ++  E       +E++     L+   A K+T+ G    DLIQ G +G +KA E +D   
Sbjct: 9   WLKYKETGDKKFLEELLNVFDDLIHYWASKFTSYGEPLEDLIQIGYLGFLKAIENYDP-K 67

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             + STY   +V   I   + D+   I+IP  ++  I+K+    + +  K  R P+ EEI
Sbjct: 68  KGELSTYISHYVLGEIRHHLRDKIDKIKIPRSVKILINKMDNFIKEVWEKENRSPSCEEI 127

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           AK L + VE V ++ KI +  +     +  ED     D I  +   S      +   +  
Sbjct: 128 AKHLNITVESVDELFKIKEAMM----TVSIEDLEIEVDRIRTERLESFKLPIEE---KIA 180

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + ++ L   +++++   F      D T  EV K   +++ ++ ++   A+ KL+ 
Sbjct: 181 LEQAISKLPEIQKKIIEYIF----YQDLTQTEVAKILKISQTQVSRLLKSALEKLRE 233


>gi|240142271|ref|YP_002966781.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
 gi|240012215|gb|ACS43440.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
          Length = 253

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 73/265 (27%), Positives = 112/265 (42%), Gaps = 33/265 (12%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
            ET +S  E   +V   R   C  S+    +V  + R+  SVA++++N      DL QEG
Sbjct: 10  RETLLSPDEESGLVDAYRNDGCRKSL--DRLVRTHARMAFSVARRWSNNEAHMQDLAQEG 67

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IG+M+AA+KF+   G +F+ Y  WW+  +I       S      V + D   +V    R
Sbjct: 68  MIGIMRAADKFNPSFGKRFAQYCRWWILSSI-------SSRASEVVCVVDMPDRVFVAHR 120

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFI-EDK 595
           R            E A    +               +S+  P+G ++    +GD +  D+
Sbjct: 121 R---------KRLEGADAALV---------GAAVTAVSISEPLGGDEGGATVGDMLVSDE 162

Query: 596 NAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            +        + N   R      +  LT RE  +L  R      T  TLE V   F +TR
Sbjct: 163 TSPESAAVQSEMNWYYRTAVQTAMQGLTEREREILSRRRLAE--TPETLEVVADFFDLTR 220

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRS 678
           ERIRQIE  A+ K++   R+   R+
Sbjct: 221 ERIRQIENAAMAKVERNLRAAGFRA 245


>gi|332799375|ref|YP_004460874.1| RNA polymerase sigma-28 subunit SigK [Tepidanaerobacter sp. Re1]
 gi|332697110|gb|AEE91567.1| RNA polymerase, sigma 28 subunit, SigK [Tepidanaerobacter sp. Re1]
          Length = 240

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 94/250 (37%), Gaps = 52/250 (20%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               ++  E +  + +  K       A+  ++E NLRLV  + KK+ + G    DLI  G
Sbjct: 32  FPQPLTPEEEKKYILLYSK---GDEEARNILIEHNLRLVAHIVKKFASTGEDMDDLISIG 88

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGL+KA   F++  G + +TYA   ++  I  ++                  K +++  
Sbjct: 89  TIGLIKAISTFNYSKGSRLATYAARCIENEILMNLRST---------------KKIKSEV 133

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +   I  +    EI                                   L D +  +  
Sbjct: 134 YLQEPIGVDKEGNEI----------------------------------SLIDVLGTEVD 159

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
               +   +    +   ++  SL  +E +V+ +R+G+      T  E+ K   ++R  + 
Sbjct: 160 AVTDEITKKFQNEKLYEKISTSLKSQERKVIELRYGLFNGVTKTQREIAKILGISRSYVS 219

Query: 658 QIEAKAIRKL 667
           +IE +AI+KL
Sbjct: 220 RIEKRAIKKL 229


>gi|226201181|gb|ACO37583.1| RNA polymerase sigma 70 factor [Aeromonas taiwanensis]
          Length = 219

 Score = 86.8 bits (213), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 87/263 (33%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EV 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +  + + IL+   +++ I  ETG
Sbjct: 198 LEMD-EEILRSIGKLQQIEEETG 219


>gi|169350469|ref|ZP_02867407.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
 gi|169292789|gb|EDS74922.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
          Length = 228

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 94/260 (36%), Gaps = 59/260 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + IKS S E  ++  E    +            A+  ++E NLRLV  +AKKY N     
Sbjct: 16  SYIKSKSFEIPLTPKEEAKYLER---FFNGDQEARNVLIERNLRLVAHIAKKYENNKDLQ 72

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA + +      K +TYA   ++  I   +                  
Sbjct: 73  EDLISIGTIGLIKAVDSYKQNHKTKLATYASRCIENEILMHLRAN--------------- 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--- 587
                                                K T   +SL   IG +       
Sbjct: 118 -------------------------------------KKTNLDVSLNETIGIDKDGSEIV 140

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD I  K     +D   + +     T     L PRE+  L M +G+     ++ +E+ K
Sbjct: 141 LGDTIAIK-QDEFIDIIDKKDTLNRLTTYFNILDPREKETLIMHYGLNNTKKYSQKEIAK 199

Query: 648 QFCVTRERIRQIEAKAIRKL 667
           +  ++R  + ++E +A+ KL
Sbjct: 200 KLNISRSYVSRLEKRALIKL 219


>gi|255697137|emb|CBA11680.1| RNA polymerase sigma factor [Pseudomonas syringae pv. sesami]
          Length = 192

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D+      P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDEGWTDALAK 191


>gi|253682196|ref|ZP_04862993.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
 gi|253561908|gb|EES91360.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E R+ +   +K +   ++AK  ++E NLRLV  + KKY+       DLI  
Sbjct: 26  SFPQPLNEDEERYYL---KKFKGGDALAKGILIERNLRLVAHIVKKYSYPNKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I +                K +++ 
Sbjct: 83  GTVGLIKAIDSFDISKGTRLATYAARCIENEILMLIRNT---------------KKIKSE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDVLSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +++   ++   LT RE+ +++MR+G+      T  E+     ++R  +
Sbjct: 154 NSVIEVVENRMQIKKLYDKINECLTEREKIIIKMRYGLNDGKPKTQREIAAFLNISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE +A++K+
Sbjct: 214 SRIEKRALKKM 224


>gi|225375611|ref|ZP_03752832.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
 gi|225212590|gb|EEG94944.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 106/287 (36%), Gaps = 62/287 (21%)

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC--EASIAKKEM 448
           P  E  +F++      L+  +E+  I     +         +   +      A  A+KE+
Sbjct: 6   PRYEKVHFLSGICSLFLRKEDEVHYIGGAEILPPPLEGEREAYCIRMLDGVHAERARKEL 65

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E NLRLV+ +AKK+ N G+   DLI  G IGL+K    F+     K +TYA   ++  I
Sbjct: 66  IEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKGINTFNPDKNIKLATYASRCIENEI 125

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
              +   S                                                    
Sbjct: 126 LMYLRRNSK--------------------------------------------------- 134

Query: 569 ITKEPISLETPIGDEDTSH---LGDFIE-DKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            TK  +S++ P+  +   +   L D +  D++ V           R+     +  L+ RE
Sbjct: 135 -TKLEVSIDEPLNVDWDGNELLLSDILGTDEDVVGKDMETDVE--RKLLKTAIEKLSGRE 191

Query: 625 ERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ +RFG+      + T +EV     +++  I ++E K + +LK 
Sbjct: 192 RMIIELRFGLNTSDGEEKTQKEVADMLGISQSYISRLEKKIMGRLKK 238


>gi|117573566|gb|ABK40959.1| RNA polymerase subunit D [Pseudomonas sp. C6-23]
 gi|117573568|gb|ABK40960.1| RNA polymerase subunit D [Pseudomonas sp. C6-2]
          Length = 200

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 24/118 (20%), Positives = 52/118 (44%), Gaps = 2/118 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + + +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRENKQAIAEMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++ VETG+
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGL 200


>gi|157313262|gb|ABV32524.1| RNA polymerase sigma factor [Xanthomonas campestris]
 gi|157313276|gb|ABV32531.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + +          K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKAYVKYGAEHKN------VVKAREDMAAIFTTLKLPLPLTDSL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL ++   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLREVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +     +     +++ E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMV 232


>gi|121534479|ref|ZP_01666302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306972|gb|EAX47891.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 59/275 (21%), Positives = 101/275 (36%), Gaps = 57/275 (20%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           +    A  +  I  + + I + +    +S  E +  +  ++        AK  ++E NLR
Sbjct: 5   FAVLAASVLKGIALLVSYITNNTFPLPLSEKEEQIYLERLK---AGDEKAKNVLIERNLR 61

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           LV  + KK+ N G    DLI  G IGL+KA   FD     + +TYA   ++  I   +  
Sbjct: 62  LVAHIVKKFDNTGEDVDDLISIGTIGLIKAINTFDQAKKIRLATYAARCIENEILMHLRS 121

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
                                                                      +
Sbjct: 122 TRRIRSE----------------------------------------------------V 129

Query: 575 SLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRF 632
           SL  PIG +   +    I+    A   +  A++     E  ++ +  L+ RE+ VL MRF
Sbjct: 130 SLYDPIGVDKEGNEITLIDVLGTAPDVVAEAVENQCETERLSKEIHRLSKREKWVLEMRF 189

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           G+   +  T  ++ K   ++R  + +IE +AI KL
Sbjct: 190 GMPDGSRKTQRDIAKLLGISRSYVSRIEKRAISKL 224


>gi|332095502|gb|EGJ00518.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 155-74]
          Length = 186

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/184 (22%), Positives = 84/184 (45%), Gaps = 7/184 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLLASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASL 620
             R++L+ T            E+     + + D +   +PL   + +NL +     + +L
Sbjct: 120 DYRQMLRDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLCQRVMEAIETL 179

Query: 621 TPRE 624
             RE
Sbjct: 180 PERE 183


>gi|255697031|emb|CBA11625.1| RNA polymerase sigma factor [Pseudomonas amygdali]
 gi|255697057|emb|CBA11638.1| RNA polymerase sigma factor [Pseudomonas syringae pv. aesculi]
 gi|255697077|emb|CBA11648.1| RNA polymerase sigma factor [Pseudomonas syringae pv. castaneae]
 gi|255697079|emb|CBA11649.1| RNA polymerase sigma factor [Pseudomonas syringae pv. ciccaronei]
 gi|255697083|emb|CBA11651.1| RNA polymerase sigma factor [Pseudomonas syringae pv.
           cunninghamiae]
 gi|255697085|emb|CBA11652.1| RNA polymerase sigma factor [Pseudomonas syringae pv. cerasicola]
 gi|255697087|emb|CBA11653.1| RNA polymerase sigma factor [Pseudomonas syringae pv. daphniphylli]
 gi|255697089|emb|CBA11654.1| RNA polymerase sigma factor [Pseudomonas syringae pv.
           dendropanacis]
 gi|255697109|emb|CBA11665.1| RNA polymerase sigma factor [Pseudomonas syringae pv. mellea]
 gi|255697111|emb|CBA11666.1| RNA polymerase sigma factor [Pseudomonas syringae pv. mori]
 gi|255697115|emb|CBA11668.1| RNA polymerase sigma factor [Pseudomonas syringae pv. myricae]
 gi|255697133|emb|CBA11678.1| RNA polymerase sigma factor [Pseudomonas syringae pv.
           rhaphiolepidis]
 gi|255697145|emb|CBA11684.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tabaci]
 gi|255697153|emb|CBA11688.1| RNA polymerase sigma factor [Pseudomonas syringae pv. ulmi]
 gi|255697159|emb|CBA11691.1| RNA polymerase sigma factor [Pseudomonas savastanoi pv. fraxini]
 gi|255697163|emb|CBA11693.1| RNA polymerase sigma factor [Pseudomonas syringae pv. phaseolicola]
 gi|255697167|emb|CBA11695.1| RNA polymerase sigma factor [Pseudomonas savastanoi pv. retacarpa]
          Length = 192

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D+      P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|209408326|emb|CAP19906.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 184

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 36/228 (15%), Positives = 72/228 (31%), Gaps = 45/228 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T  +++   + + +    L +I  L   I P+  G         + Q+ E  +
Sbjct: 1   AIAHFPGTVDSILADYERVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPQT 51

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            +     V + + D +     S ++       PE A      + E  + +   L      
Sbjct: 52  PQSTSKPVDDDKDDEDEEESESDEEEGDGGPDPEVARLRFGAVAEQLEKANKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  ++S +     E L  L   + L   + 
Sbjct: 106 -----------------------------KKHGRASQQATEELEALAILFMPIKLVPKQY 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPH 382
           D LVE++ D   +I   E   ++L      + R  FL +    E +  
Sbjct: 137 DALVERVRDALSQIRAQERAXMQLCVRDARMPRADFLRQFPNNETNLD 184


>gi|239934344|emb|CAR92302.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 245

 Score = 86.4 bits (212), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 22/143 (15%), Positives = 54/143 (37%), Gaps = 2/143 (1%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             ++S +     E L      + L   + D LVE++ +   +I   E  +++L      +
Sbjct: 100 HGRASQQAVEELEALAIPFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARM 159

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            R  FL +    E +  W        +G++   +    + I++ +  +  +  E  + I+
Sbjct: 160 PRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNRKEDIVRCQQMLIELEQECDLVIA 218

Query: 426 EFRHIVSMVRKGECEASIAKKEM 448
           + + I       +   +  +  M
Sbjct: 219 DIKDINRRANSADIHHTGGRSSM 241


>gi|239934348|emb|CAR92304.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 204

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 75/249 (30%), Gaps = 46/249 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTDGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKAA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D       ++++       PE A      + E  + +   L              
Sbjct: 52  GDEKDDEGEDDSDTEEEEGDGGPDPEVARLRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + + LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYEALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 SALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRN 411
            + I + + 
Sbjct: 196 KEDIQRCQQ 204


>gi|257876008|ref|ZP_05655661.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
 gi|257810174|gb|EEV38994.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
          Length = 235

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 100/235 (42%), Gaps = 14/235 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              + ++  +   L LV  V ++ + +    +  DL   G IGLM A  KFD      F 
Sbjct: 1   MYEVDREAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFE 60

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           +YA   +K AI   +   +   R  +   ++ ++     + +   +KRE T  EI K+L 
Sbjct: 61  SYAAIRIKGAIIDEVRKHAKISRYKMAAVNQFYQ---ARQELEQSLKREATDTEICKQLG 117

Query: 558 MPVEGVRKVLKITKE--PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +    +  + +       +SLE  +    E+   L D + D  A +  D+ +    R   
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTLKDMVRDP-AENVEDTLVAEEKRTAL 176

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  RE+ +L + +      + TL+E+ +   V+  R+ QI  K I KL+
Sbjct: 177 VACIKKLGEREQLILSLYY----TEELTLKEIAEILEVSIPRVSQIHGKTIAKLR 227


>gi|330948232|gb|EGH48492.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 95

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 67/93 (72%), Positives = 76/93 (81%)

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           PIS+ETPIGD++ SHLGDFIED    SP+D A   +L+E T  VL+ LT RE +VLRMRF
Sbjct: 3   PISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRF 62

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           GI MNTDHTLEEVGKQF VTRERIRQIEAKA+R
Sbjct: 63  GIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 95


>gi|169351192|ref|ZP_02868130.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
 gi|169292254|gb|EDS74387.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
          Length = 231

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 104/260 (40%), Gaps = 60/260 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIG 480
           ++  E +  +  + K     + A+  ++E NLRLV+ VAK+Y TN+     DLI  G IG
Sbjct: 28  LNAFEEKEALEKLAK---GDNDARDLLIEHNLRLVVYVAKRYDTNQNGGIEDLISIGTIG 84

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L+KA   F      K +TYA   ++  I   +               K +K+        
Sbjct: 85  LVKAINTFKTDKNIKLATYASRCIENEILMFLR--------------KNNKLR------- 123

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNA 597
                                            ISL+ P+  +   +   L D I   + 
Sbjct: 124 -------------------------------HEISLDEPLNIDYDGNELLLSDIIGTDSD 152

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +   +   Q++ R         L+ RE+ +L +R+G+    + T ++V K   +++  I 
Sbjct: 153 I-VKNELEQSDQRTMFYEAFKDLSKREKEILMLRYGLMNYDELTQKDVAKMMGISQSYIS 211

Query: 658 QIEAKAIRKLKHPSRSKKLR 677
           ++E K I+KL++     +++
Sbjct: 212 RLEKKIIKKLRNKLNYNEIK 231


>gi|167770714|ref|ZP_02442767.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
 gi|167667309|gb|EDS11439.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
          Length = 243

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 86/245 (35%), Gaps = 52/245 (21%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   IV   RK E     AK+ +   NLRLV+ +AKK+ + G+   DLI  G IGL+KA
Sbjct: 45  REEEQIV--FRKLEEHDEAAKETLTVHNLRLVVYIAKKFESTGICVEDLISIGTIGLIKA 102

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              F      K +TYA   ++  I   +                               K
Sbjct: 103 VNTFCPQKNIKLATYASRCIENEILMHLRKN-------------------------QSHK 137

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            E + +E                            I  +    L   I   +  S     
Sbjct: 138 NEISIDEP-------------------------LNIDWDGNELLLSDILGTDPDSINRPI 172

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                +      +  L  RE  ++++RFG+    + T +EV     +++  I ++E + I
Sbjct: 173 EDEAEKNLLLGAIDRLDGRERMIMQLRFGLLGAEEKTQKEVADIIGISQSYISRLEKRII 232

Query: 665 RKLKH 669
           +KLK 
Sbjct: 233 KKLKK 237


>gi|157373192|ref|YP_001471792.1| flagellar biosynthesis sigma factor [Shewanella sediminis HAW-EB3]
 gi|157315566|gb|ABV34664.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           sediminis HAW-EB3]
          Length = 240

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/207 (21%), Positives = 97/207 (46%), Gaps = 16/207 (7%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +    L   D+ Q G + L++++ ++       F +YA   ++ AI   +  Q    R  
Sbjct: 43  HCGTVLAIEDMEQIGMMALLESSRRYPGEYDNGFISYAGQRIRGAILDELRRQDWRPRP- 101

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +R + H++  T R+++  + REP+  E+A+ + +  E  R+ L  ++     E+    
Sbjct: 102 --VRQQAHELNDTVRKLTRLLGREPSDIEVAEAMGLNREEYRERLYASQS----ESMKSL 155

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           +D   +G    DK  V       Q ++++T  + ++ L+ RE+ +L + +      +  L
Sbjct: 156 DDMLSVGAHFPDKTNV-----IEQFSVQKTLIKAISKLSKREQLILSLYYQH----ELNL 206

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E+     +T  RI Q+  +A++ L+ 
Sbjct: 207 KEIAGTLGLTETRICQLHKQAVKHLQE 233


>gi|255697099|emb|CBA11660.1| RNA polymerase sigma factor [Pseudomonas syringae pv. hibisci]
          Length = 192

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 66/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D       P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDKEESADASDDKDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDEGWTDALAK 191


>gi|34733392|gb|AAP82769.1| sigma 70 [Hydrogenobacter hydrogenophilus]
          Length = 310

 Score = 86.4 bits (212), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 65/223 (29%), Positives = 110/223 (49%), Gaps = 12/223 (5%)

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           E+A+ Y+E  +         +  +          K+ +++  + L  S+ + + ++L ++
Sbjct: 96  ELAKAYKEAIT-WRELYLKYRTPEYKRAYLEKHAKMNRVLKDMKLKYSKFEKVADELLNL 154

Query: 346 SKR----IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            KR    +   E    +L   +    +  ++ +   +        A     G        
Sbjct: 155 YKRYTKKLKEYEIRKQKLESIHP-DVEELIKFYDYNKDLQLKAERA-----GYGFAKFQV 208

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
                L +  E+K +  E G    E   ++ ++++G  + + AK+ MV+ NLRLV+S+A 
Sbjct: 209 LKSEYLSLEKEVKELRKEKGSFPEELDRVMHIIKEGRTKVTKAKQVMVKCNLRLVVSIA- 267

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           KY NRGL FLDLIQEGNIGLMKA +K+D+  GYKFSTYA WW+
Sbjct: 268 KYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWI 310



 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 92/253 (36%), Gaps = 10/253 (3%)

Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
           DPV++YLREMG I LL RE EI  AK+IE GR +M   L  +      ++     + +G 
Sbjct: 1   DPVKLYLREMGRIPLLKREEEIMYAKQIEIGRKIMRRGLLRTSFLIDRVLREWGNVCNGK 60

Query: 179 TLLREIIDLEACIGPESKGGFFHGTEG----HSYQKREDSSQEKERDDVQETEGDIESAA 234
               +++D         +    H            +   + +E         +       
Sbjct: 61  IKATDLMDTMDDSKTVEEHEESHEHLERYFIEKGLELAKAYKEAITWRELYLKYRTPEYK 120

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM--CALDEIAEVYR 292
           +   +  +K++   ++ +      ++  D+  +       +L+   +    L+ I     
Sbjct: 121 RAYLEKHAKMNRVLKDMKLKYSKFEKVADELLNLYKRYTKKLKEYEIRKQKLESIHPDVE 180

Query: 293 ELRSLQDNAVNGQKDEKSS----VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           EL    D   + Q   + +     K +VLK + + L   +   +       E+L  +   
Sbjct: 181 ELIKFYDYNKDLQLKAERAGYGFAKFQVLKSEYLSLEKEVKELRKEKGSFPEELDRVMHI 240

Query: 349 IMHNEGELLRLAQ 361
           I     ++ +  Q
Sbjct: 241 IKEGRTKVTKAKQ 253


>gi|224553534|gb|ACN55005.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/111 (46%), Positives = 84/111 (75%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIGRAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|169827282|ref|YP_001697440.1| RNA polymerase sigma-F factor [Lysinibacillus sphaericus C3-41]
 gi|168991770|gb|ACA39310.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Lysinibacillus sphaericus
           C3-41]
          Length = 195

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 86/189 (45%), Gaps = 14/189 (7%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MK+ +KFD     KFSTYA+  +   I R + D    +++   +R+   K+         
Sbjct: 1   MKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD-DGMVKVSRSIRELNFKIRHATDEFIK 59

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVS 599
           + +  PT +E+A+ L +  E +       ++P SL   + +   D+  L D ++D+ +  
Sbjct: 60  RNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDEKSEQ 119

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P D             VL  L PRE+ ++ +R+           E+  +  +++ ++ ++
Sbjct: 120 PFDYI-------PLKEVLTRLEPREQSIIYLRYFSDCTQ----TEIANRLGISQVQVSRL 168

Query: 660 EAKAIRKLK 668
           E K + +LK
Sbjct: 169 EKKILAQLK 177


>gi|255697161|emb|CBA11692.1| RNA polymerase sigma factor [Pseudomonas syringae pv. glycinea]
          Length = 192

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 66/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D       P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDKEESADASDDKDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|167745312|ref|ZP_02417439.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
 gi|167655033|gb|EDR99162.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
          Length = 243

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 102/275 (37%), Gaps = 54/275 (19%)

Query: 399 VACEVDSILKIRNEIKSISVETGIS-ISEFRHIVSMVRK-GECEASIAKKEMVEANLRLV 456
           V C+  + L    EI  I     +    E +    M+ K G  E   A+ +++E NLRLV
Sbjct: 11  VTCQKRTFLAKGKEIHYIGGAEILPAPLEAKEEEKMIHKLGTAEEPEARAKLIERNLRLV 70

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   ++  I   +    
Sbjct: 71  VYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRN- 129

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                                   NK K E + +E                         
Sbjct: 130 ------------------------NKTKMEVSIDEP------------------------ 141

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
              +  +    L   I   +             R+     +  L+ RE +++ +RFGI  
Sbjct: 142 -LNVDWDGNELLLSDILGTDEDIIYRDLEHEVDRKLLLNAMKILSDRERKIIELRFGINQ 200

Query: 637 --NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + T +EV     +++  I ++E K I++LK 
Sbjct: 201 KDGEEKTQKEVADLMGISQSYISRLEKKIIKRLKR 235


>gi|332272479|gb|AEE38923.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|332272481|gb|AEE38924.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|332272483|gb|AEE38925.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|332272485|gb|AEE38926.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
 gi|332272487|gb|AEE38927.1| RNA polymerase sigma-70 factor [Aeromonas piscicola]
          Length = 219

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  ++ E + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELGEDDLADEDEDEDEDEDDDGESSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +     L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +  W   
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPR 196

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +    + +L+   +++ I  ETG
Sbjct: 197 LVDMDEEVLRSIGKLQQIEEETG 219


>gi|332272477|gb|AEE38922.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 219

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 84/263 (31%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + +   D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELGEDDLADEDEDEDEDEDGDGDDADDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +     L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EEVLRSIGKLQQIEEETG 219


>gi|332272469|gb|AEE38918.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|332272471|gb|AEE38919.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|332272473|gb|AEE38920.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
 gi|332272475|gb|AEE38921.1| RNA polymerase sigma-70 factor [Aeromonas bestiarum]
          Length = 219

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/263 (16%), Positives = 86/263 (32%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ E + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELGEDDLADEDEDEDEDEDEDGESSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +     L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHEDTQAAIALLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           V  + + +L+   +++ I  ETG
Sbjct: 198 VEMD-EEVLRSIGKLQQIEEETG 219


>gi|157826497|ref|YP_001495561.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801801|gb|ABV78524.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 81

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 55/64 (85%), Positives = 61/64 (95%)

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           +LA+LTPREERVLRMRFGIGMNTDHTLEEVG+QF VTRERIRQIE+KA+RKL+HP RSKK
Sbjct: 1   MLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSKK 60

Query: 676 LRSF 679
           L SF
Sbjct: 61  LNSF 64


>gi|325264805|ref|ZP_08131534.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
 gi|324030097|gb|EGB91383.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
          Length = 246

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/235 (22%), Positives = 91/235 (38%), Gaps = 56/235 (23%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +T
Sbjct: 58  EYDQEAKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKKIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +   S                                          
Sbjct: 118 YASRCIENEILMYLRRNSK----------------------------------------- 136

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                      TK  +S++ P+  +   +  L   I   +  +          R+   + 
Sbjct: 137 -----------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDTIYKDLENEAERKLLVKA 185

Query: 617 LASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  L+ RE+ +++MRFG+      + T +EV     +++  I ++E K +++LK 
Sbjct: 186 INKLSSREKMIVKMRFGLDNPEGEEKTQKEVADLLGISQSYISRLEKKIMQRLKR 240


>gi|239934444|emb|CAR92476.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 225

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/273 (16%), Positives = 84/273 (30%), Gaps = 49/273 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D+ +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADAVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               D I + + ++  I  E G+ IS  + I  
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKEINR 225


>gi|291448259|ref|ZP_06587649.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
 gi|291351206|gb|EFE78110.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
          Length = 360

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 57/96 (59%), Positives = 75/96 (78%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 263 KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 322

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           D+  GYKFSTYA WW++QAITR++ADQ+ TIRIPVH
Sbjct: 323 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVH 358



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           + +       ++ +   +T DPV+ YL+++G + LL+ E E+ +AKRIEAG       L 
Sbjct: 197 SDDDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLA 255

Query: 159 ESPLTFQALIIWRDELNDGTTL 180
            +      L    + + +    
Sbjct: 256 NADKLAPKLKRELEIIAEDGRR 277


>gi|255697041|emb|CBA11630.1| RNA polymerase sigma factor [Pseudomonas meliae]
          Length = 192

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 66/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D       P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDKEESADASDDKDEVESGPDPVIAQQRFGAVSDQMEITCKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|169827019|ref|YP_001697177.1| RNA polymerase sigma-35 factor [Lysinibacillus sphaericus C3-41]
 gi|168991507|gb|ACA39047.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 204

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 92/244 (37%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V+++         A+  ++E NLRLV+ +A+++ N G    DLI  G+IGL+KA E F
Sbjct: 7   EEVTVIASFMKGDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLIKAIETF 66

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           +     K +TYA   ++  I   +   S                                
Sbjct: 67  NTDKNIKLATYASRCIENEILMHLRKTSRMKGE--------------------------- 99

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                    +SL+ P+  +   +   L D +  +  +  LD+  
Sbjct: 100 -------------------------VSLDEPLNSDADGNELLLSDILGTEEHI-ILDNVE 133

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   R+     +  L  RE  ++  RFG+    + T +EV     +++  I ++E K I+
Sbjct: 134 KKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLGISQSYISRLEKKIIQ 193

Query: 666 KLKH 669
            L+ 
Sbjct: 194 DLRE 197


>gi|226323679|ref|ZP_03799197.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
 gi|225207863|gb|EEG90217.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
          Length = 247

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 102/253 (40%), Gaps = 60/253 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E  H +S++  G  +    KK ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 43  LSSEEEGHAISLL--GGGQDEEGKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +                  +  +T      
Sbjct: 101 IKAINTFNPEKNIKLATYASRCIENEILMYLR-----------------RNNKTKLE--- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +  +   
Sbjct: 141 --------------------------------VSIDEPLNVDWDGNELLLSDILGTEEDT 168

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERI 656
              D   +A  +    + +  L+ RE  +++MRFG+G     + T +EV     +++  I
Sbjct: 169 IYRDMETEAEHK-LLGKAIGRLSNRERVIVQMRFGLGTPDGEEKTQKEVADLLGISQSYI 227

Query: 657 RQIEAKAIRKLKH 669
            ++E K +++L+ 
Sbjct: 228 SRLEKKIMQRLRR 240


>gi|332272375|gb|AEE38871.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
 gi|332272377|gb|AEE38872.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
 gi|332272379|gb|AEE38873.1| RNA polymerase sigma-70 factor [Aeromonas schubertii]
          Length = 221

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 80/262 (30%), Gaps = 42/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II            GF +  E              E 
Sbjct: 1   PEAITYLLEQYDKFEAEQLRLSDII-----------SGFVNPDEA------------DEM 37

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                  G       ++ +D S  +   E+ E D  + D D             +LR + 
Sbjct: 38  GPTATHIGSELGEDDLADEDSSDEEEEDEDEEGDGNDDDGDGGPDPEVAREKFAELRAQY 97

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 I                   + ++  + +    +L  +     L   + D LV 
Sbjct: 98  EITRQSIRS-----------------NGRAHEETQAAIAQLADVFRQFRLMPKQFDRLVN 140

Query: 341 QLYDISKRIMHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +L+   +   + +  F+      E +  W  Y K   +       
Sbjct: 141 NMREMMERVRVQERLILKMCVEQAKMPKKTFVSAFTNNECETAWFEYQKQAGKAWSAPLA 200

Query: 400 ACEVDSILKIRNEIKSISVETG 421
           A E + +L+   +++ I  ETG
Sbjct: 201 AME-EEVLRSIGKLQQIEEETG 221


>gi|223700510|gb|ACN20374.1| truncated RNA polymerase sigma factor SigB [Listeria monocytogenes]
          Length = 188

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/169 (20%), Positives = 79/169 (46%), Gaps = 2/169 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +  + +    E     A+  +V     LV S+A+KY+       DL+Q GNIGL+ A  
Sbjct: 13  EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++D   G  F  +A+  +   I R + D++ ++ +P  +++   K+      ++ +++  
Sbjct: 73  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKIKNAVEELTRELQSS 132

Query: 547 PTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIE 593
           P   +IA  + +  E V + +++  + + +S++  I  +        ++
Sbjct: 133 PQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEADSDGSTITLLD 181


>gi|332272333|gb|AEE38850.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|332272335|gb|AEE38851.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|332272337|gb|AEE38852.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|332272339|gb|AEE38853.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
 gi|332272341|gb|AEE38854.1| RNA polymerase sigma-70 factor [Aeromonas caviae]
          Length = 219

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/263 (15%), Positives = 87/263 (33%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EV 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +  E+ + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQQNGRAHDDTQNAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +  + + +L+   +++ I  ETG
Sbjct: 198 LEMD-EEVLRSIGKLQQIEEETG 219


>gi|296061190|emb|CBJ55906.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
          Length = 198

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 84/243 (34%), Gaps = 46/243 (18%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEIAIAKRIE G + + A+L   PL+ + L+   +   +G   L EI+          
Sbjct: 1   REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E         ++      D    + D E     + ++ +    P        
Sbjct: 51  -VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDAEDGDDDAAEEEAGPTGPDPVE---- 105

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                                   V   ++ +A  Y + + +        K+        
Sbjct: 106 ------------------------VATRMENLANEYAKFKKIY------AKNGAEHKLVV 135

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
             +E +  +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   
Sbjct: 136 KAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 195

Query: 375 QGR 377
           +G 
Sbjct: 196 EGN 198


>gi|255527843|ref|ZP_05394691.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296185444|ref|ZP_06853854.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
 gi|255508454|gb|EET84846.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296050278|gb|EFG89702.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
          Length = 233

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 93/240 (38%), Gaps = 49/240 (20%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +     ++K +    +AK  +VE NLRLV  + KKY+  G +  DLI  G +GL+KA + 
Sbjct: 34  KEEEYYLKKFKEGDLLAKNILVERNLRLVAHIVKKYSYPGKEVDDLISIGTVGLIKAIDS 93

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G + +TYA   ++  I   I +               +K  +    + + I  + 
Sbjct: 94  FDASKGTRLATYAAKCIENEILMLIRN---------------NKKTKGEIYLQDPIGIDK 138

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              EI                                   L D +             + 
Sbjct: 139 EGNEI----------------------------------SLLDVLSSDEDSIIEIVESKI 164

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +++   ++   L  RE+ V+ MR+G+      T  E+ K   ++R  + +IE +A++KL
Sbjct: 165 QVKKLYDKMNTCLAEREKSVVEMRYGLLEGKPKTQREIAKILGISRSYVSRIEKRALKKL 224


>gi|257866395|ref|ZP_05646048.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257873089|ref|ZP_05652742.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
 gi|257800353|gb|EEV29381.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257807253|gb|EEV36075.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
          Length = 235

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 100/235 (42%), Gaps = 14/235 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              + ++  +   L LV  V ++ + +    +  DL   G IGLM A  KFD      F 
Sbjct: 1   MYEVDREAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFE 60

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           +YA   +K AI   +   +   R  +   ++ ++     + +   +KRE T  EI K+L 
Sbjct: 61  SYAAIRIKGAIIDEVRKHAKISRYKMAAVNQFYQ---ARQELEQSLKREATDTEICKQLG 117

Query: 558 MPVEGVRKVLKITKE--PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +    +  + +       +SLE  +    E+   L D + D  A +  ++ +    R   
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTLKDMVRDP-AENVEETLVAEEKRTAL 176

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  RE+ +L + +      + TL+E+ +   V+  R+ QI  K I KL+
Sbjct: 177 VACIKKLGEREQLILSLYY----TEELTLKEIAEILEVSIPRVSQIHGKTIAKLR 227


>gi|163816759|ref|ZP_02208122.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
 gi|158448016|gb|EDP25011.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
          Length = 207

 Score = 86.0 bits (211), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 97/250 (38%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  + +     + +     + A++ ++E NLRLV  + KKY++      DL+  G IGL
Sbjct: 8   LTPDKEKEY---INRCISGDNEARRVLIEYNLRLVAHIVKKYSSSVRDPEDLLSIGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + +    G K + YA   ++  +              +++R +  K          
Sbjct: 65  IKAIDSYKPEKGCKLAGYAAKCIENEL-------------LMNLRQEKKK---------- 101

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S+  PIG +   +   + D I    + 
Sbjct: 102 -----------------------------SREVSMYEPIGTDKEGNEIVIMDIISTSESC 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  + +L    + +   LTPRE  +++MR+GI      T +E  K   ++R  + +
Sbjct: 133 PLEKLITEDHLNHLPSCMNQILTPREYHIIQMRYGILGEAPLTQKETAKILGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE +A+ KL+
Sbjct: 193 IEKRALSKLR 202


>gi|260220134|emb|CBA27368.1| RNA polymerase sigma-32 factor [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 354

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 46/213 (21%), Positives = 85/213 (39%), Gaps = 24/213 (11%)

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            +D+ +   N +        +++ E +      +        A  ++V ++LRLV+SVA+
Sbjct: 35  NLDAYISAANRLPM------LTLEEEQEFARKFK--NENDLEAAGKLVLSHLRLVVSVAR 86

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y   GL   DLIQEGN+GLMKA ++FD   G +  +YA+ W+K  I   I      +++
Sbjct: 87  QYLGYGLPHGDLIQEGNVGLMKAVKRFDPEQGVRLVSYALHWIKAEIHEYILKNWRMVKV 146

Query: 522 PVH--MRDKIHKVVRTARRMSNK------------IKREPTPEEIAKKLAMPVEGVRKVL 567
                 R     +    +R   +            +  E       +    P E +    
Sbjct: 147 ATTKAQRKLFFNLRSMKQRFKGEDAAADLDTHRDTLNSEQVNTMARELNVKPEEVLEMEA 206

Query: 568 KITKEPISLETPIGDEDTSHLGD--FIEDKNAV 598
           ++    + L+    D+     G   ++ D N  
Sbjct: 207 RLAGGDVLLDPSPSDDGEDAFGPIAYLTDTNHE 239


>gi|239934482|emb|CAR92495.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 225

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/273 (16%), Positives = 83/273 (30%), Gaps = 49/273 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               D I + + ++  I  E G+ IS  + I  
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKEINR 225


>gi|153854689|ref|ZP_01995939.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
 gi|149752793|gb|EDM62724.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
          Length = 246

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 51/233 (21%), Positives = 90/233 (38%), Gaps = 52/233 (22%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   A+K ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +T
Sbjct: 58  EKDENARKILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPDKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                            NK + E + +E       
Sbjct: 118 YASRCIENEILMYLRRN-------------------------NKTRMEVSIDEP------ 146

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
                                +  +    L   I      +          ++   R + 
Sbjct: 147 -------------------LNVDWDGNELLLSDILGTEEDAIYKDLENEAEKKVLIRAIG 187

Query: 619 SLTPREERVLRMRFGIGMN--TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L+ RE+ ++RMRFG+G     + T +EV     +++  I ++E K +++L+ 
Sbjct: 188 RLSGREQMIIRMRFGLGTEDGEEKTQKEVADMLGISQSYISRLEKKIMQRLRR 240


>gi|226201189|gb|ACO37587.1| RNA polymerase sigma 70 factor [Aeromonas sanarellii]
          Length = 219

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 87/263 (33%), Gaps = 46/263 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EV 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DD+  T   I S            D   +  E+ + + D+ +      ++          
Sbjct: 35  DDMAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ QK+ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQKNGRAHDDTQNAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      
Sbjct: 138 NNMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRL 197

Query: 399 VACEVDSILKIRNEIKSISVETG 421
           +  + + IL+   +++ I  ETG
Sbjct: 198 LEMD-EEILRSIGKLQQIEEETG 219


>gi|239934452|emb|CAR92480.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 225

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/273 (16%), Positives = 83/273 (30%), Gaps = 49/273 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETXVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               D I + + ++  I  E G+ IS  + I  
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKEINR 225


>gi|298492777|ref|YP_003722954.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298234695|gb|ADI65831.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 263

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 102/228 (44%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++VE +  LV  +A K+ ++    + DL Q G +GL++A E+F+    Y FS++A+ +
Sbjct: 28  RNQLVEVHKGLVRKMAYKFIHQCNEPYEDLEQIGYLGLIRAIERFNPHQRYAFSSFAIPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D S  ++IP   ++  +   +  ++ +  + R P   +IA KL + ++  
Sbjct: 88  IRGEMLHFLRDHSTLLKIPRRWQELYNAGQKIRKQFTLSLGRPPREIDIATKLNISLQEW 147

Query: 564 RKVLKI--TKEPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++       + P+SL+       +    LGD +     +       Q   R      ++ 
Sbjct: 148 QECKLAVQNRIPLSLDATTANYVDYQITLGDILP---CLRTALLQQQEEERLQLQGAISM 204

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  +   V+     + +  + T ++  K+   +   + +   K ++ L
Sbjct: 205 LDDKRRIVVE----LVLVKELTRKDAAKKIGTSPMTVTRYLHKGVKDL 248


>gi|223984205|ref|ZP_03634353.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
 gi|223963820|gb|EEF68184.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
          Length = 234

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 97/258 (37%), Gaps = 58/258 (22%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           I++ S    ++  E +  +  + K       A+ +++E NLRLV  + KK+  R  Q  D
Sbjct: 20  IRTTSFPQPLTAEEEQDALQRMAK---GDVEARADLIEHNLRLVAHIVKKFDIRREQTED 76

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           LI  G IGL+K  + F    G+K +TY    ++  I   + +                  
Sbjct: 77  LISIGTIGLIKGIDTFKVDKGHKLATYVSRCIENEILMHLRNN----------------- 119

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LG 589
                                              K   +  SL+  IG +       L 
Sbjct: 120 -----------------------------------KHAFQTRSLDDAIGQDKDGSELTLI 144

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I   +   P+D  +    +   T+ +  L  RE  ++  R+G+  + + T  ++ +Q 
Sbjct: 145 DVIPAPDQPDPIDKLMLEENKRKLTQFMGLLDEREHSIIVRRYGLEGHQEMTQRDIARQE 204

Query: 650 CVTRERIRQIEAKAIRKL 667
            ++R  + +IE +A  KL
Sbjct: 205 HISRSYVSRIEKRAFMKL 222


>gi|238924602|ref|YP_002938118.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
 gi|238876277|gb|ACR75984.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
          Length = 244

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 97/253 (38%), Gaps = 59/253 (23%)

Query: 423 SISEFRHIVSMVRKGECEA-SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +  E   ++++V K    +   AKK+++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 39  TDEEKCCLIALVDKNVAMSKEQAKKQLIEHNLRLVVYLAKKFENTGVCVEDLISIGTIGL 98

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +K    F+     K +TYA   ++  I   +   +                         
Sbjct: 99  IKGINTFNPEKKIKLATYASRCIENEILMYLRRNNRVKLE-------------------- 138

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +     V
Sbjct: 139 --------------------------------VSFDEPLNTDWDGNELLLSDILGTDEDV 166

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERI 656
              D   +  +     + + SL  RE +++ +RFG+    N + T +EV     +++  I
Sbjct: 167 IYKDLETEVEI-SLLKKAMLSLNERERQIIELRFGVNRVENKELTQKEVADILGISQSYI 225

Query: 657 RQIEAKAIRKLKH 669
            ++E K + +LK 
Sbjct: 226 SRLEKKIMERLKK 238


>gi|332272443|gb|AEE38905.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|332272445|gb|AEE38906.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
          Length = 219

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 81/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                           
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN-------------------------- 32

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                   D E  A  +    S++       E+++ + DEDED                 
Sbjct: 33  --------DTEDMAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVA 84

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                E+   Y          ++ QK+ ++    +    +L  +     L   + D LV 
Sbjct: 85  REKFAELRAQYEV------TRLSIQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 139 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLV 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + + +   +++ I  ETG
Sbjct: 199 EMD-EEVQRAIGKLQQIEEETG 219


>gi|84502385|ref|ZP_01000521.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
 gi|84389197|gb|EAQ01994.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
          Length = 249

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 118/262 (45%), Gaps = 32/262 (12%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           N I++ +    + I E R+ +   R  +     A   ++ ++ R   S+A ++T+  +  
Sbjct: 4   NSIQAAAKIPLLDIDEERNAIR--RWQDHGDREALTLLLRSHARQAWSMAARWTDNPVHL 61

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL  EG IGL++AA+ FD     +FSTYA WWV   ++ + A              +I 
Sbjct: 62  EDLAAEGVIGLIRAADNFDLGQDVRFSTYAAWWVMNGVSAAAA--------------RIR 107

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
            V+    R   +++     +E    + M ++G+          ++L+ P+  + T  L D
Sbjct: 108 SVIDVPPRAVTEMRSGRLADEDNTVITMAMQGI----------VALDAPV-GDGTHSLLD 156

Query: 591 FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            +   +     +    ++    R    + ++ L  +E  ++R R    +    TLE++  
Sbjct: 157 ALVSSDLTPEETAAAESLHDVQRRLIAKAMSGLNAQEAEIIRRRRLQAV--PETLEDLAD 214

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              +TR+R+RQ+E +A+ +L+ 
Sbjct: 215 AMNMTRDRLRQVERRAMTRLRR 236


>gi|186681796|ref|YP_001864992.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186464248|gb|ACC80049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 261

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 104/228 (45%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + ++V+ +  LV  +A K++++    + DL Q G  GL++A E+FD   GY FS++A+ +
Sbjct: 28  RNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGYAFSSFAVPY 87

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +   + D+S  ++IP   ++  ++  +  + ++  + R+P   EIA +L + V+  
Sbjct: 88  IRGEMLHFLRDRSTLLKIPRRWQELYNEGQKIRKDLAMSLGRQPKDAEIASELRVSVQEW 147

Query: 564 RKVLKITK--EPISLETP--IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           ++     +   P+SL+       +    LG+ +    +        Q   R+     +  
Sbjct: 148 QETKLAAQNRMPLSLDATAVNYVDCQITLGEALPCPRS---HVLLQQEEERQQLQGAINM 204

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  +    + M F      + + ++  K    +   + +   K I+ L
Sbjct: 205 LEEKPRMAVEMVFL----KELSRKDAAKNIGTSPMTVTRYLQKGIQDL 248


>gi|164686361|ref|ZP_02210391.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
 gi|164601963|gb|EDQ95428.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
          Length = 231

 Score = 85.7 bits (210), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 87/238 (36%), Gaps = 57/238 (23%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
                K  ++E NLRLV+ +++K+ N G+   DLI  G IGL+KA   F+     K +TY
Sbjct: 45  YDENVKTILIERNLRLVVYISRKFENTGIDMEDLISIGTIGLIKAVNTFNLDKNIKLATY 104

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++  I   +                  K  +                         
Sbjct: 105 ASRCIENEILMCLR-----------------KNNKKKSE--------------------- 126

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                         +S + P+  +   +   L D +   N         + + +      
Sbjct: 127 --------------VSFDEPLNVDLDGNELLLSDVLGTDNDEIYKIIEEEID-KNLLFMA 171

Query: 617 LASLTPREERVLRMRFGIG-MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           L  L+ RE++++ +RFG+     + T +EV     +++  I ++E K I +LK   + 
Sbjct: 172 LDKLSYREKQIMELRFGLSTKGKEKTQKEVANILGISQSYISRLEKKIIFRLKKEMKK 229


>gi|157313270|gb|ABV32528.1| RNA polymerase sigma factor [Xanthomonas campestris]
          Length = 232

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 73/172 (42%), Gaps = 8/172 (4%)

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           +V   ++ +A  Y + +          K+          +E +  +  +L L     D L
Sbjct: 68  EVATRMENLANEYAKFKKAYVKYGAEHKN------VVKAREDMAAIFTTLKLPLPLTDSL 121

Query: 339 VEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           V QL ++   I  +E ++L LA +   + R  F+   +G + +  WV  A    + +W +
Sbjct: 122 VTQLREVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQTNLEWVEDALKR-KQKWSS 180

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            +    D I+  +         + ++++E + I   +  GE +A  AKKEMV
Sbjct: 181 ALRDVKDQIIAEQQASIDREKSSYLTLAEIKDISRAMAYGEAKARKAKKEMV 232


>gi|291522735|emb|CBK81028.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus catus
           GD/7]
          Length = 206

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 97/239 (40%), Gaps = 55/239 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +R+ +     A+  ++E NLRLV  + KKY N G +  ++I  G +GL+KA   +++  
Sbjct: 16  YLRQYQNGDMHARDILIERNLRLVAHIVKKYMNSGKETDEMISVGIVGLVKAVNTYNFEK 75

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G + +TYA   +   +   +                  K+ R                  
Sbjct: 76  GSRLATYAARCIDNELLMLMRG--------------DRKLSR------------------ 103

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANL 609
                                +SL  PIG +   +   L   +E ++         + +L
Sbjct: 104 --------------------EVSLYDPIGTDKEGNEITLLSILEHEDEDIIDQLDKKQSL 143

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+ +  +   LTPRE  V+  R+G+  + + T  E+ +Q  ++R  + +IE KA+ KL+
Sbjct: 144 RKLSKILSKVLTPREYFVVIRRYGLYGHHETTQRELAEQLNISRSYVSRIEKKALEKLR 202


>gi|160880601|ref|YP_001559569.1| sporulation sigma factor SigE [Clostridium phytofermentans ISDg]
 gi|160429267|gb|ABX42830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 246

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 100/247 (40%), Gaps = 58/247 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R   ++++ G  +   AK  +VE NLRLV+ +AKK+ N G+   DLI  G IGL+KA   
Sbjct: 47  READAIMKLGTPDDVEAKSLLVEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINT 106

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+     K +TYA   ++  I   +   S                               
Sbjct: 107 FNPDKNIKLATYASRCIENEILMYLRRNSK------------------------------ 136

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSA 604
                                 TK  +S++ P+  +   +   L D +  +  V   +  
Sbjct: 137 ----------------------TKLEVSIDEPLNVDWDGNELLLSDILGTEEDVIYKNIE 174

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAK 662
            + + ++   R L+ L  RE+ ++ +RFG+      + T +EV     +++  I ++E K
Sbjct: 175 DEVD-KKLLGRALSKLNDREKIIVSLRFGLNTADGNERTQKEVADMLGISQSYISRLEKK 233

Query: 663 AIRKLKH 669
            I++LK 
Sbjct: 234 IIKRLKK 240


>gi|304407606|ref|ZP_07389258.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343557|gb|EFM09399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 232

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 59/276 (21%), Positives = 106/276 (38%), Gaps = 60/276 (21%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            VA  +  +  + + +K+ +    +   +    + ++ +G   +   +  ++E NLRLV 
Sbjct: 6   AVALFIKQLSLLVSYVKNNAFPQPLHEEDEMKHLQLMAEGNQHS---RNMLIEHNLRLVA 62

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +     
Sbjct: 63  HIVKKFDNTGEDLEDLISIGTIGLIKAIESFQVGKGTKLATFAARCIENEILMHLRS--- 119

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
                                                            LK T++ +SL 
Sbjct: 120 -------------------------------------------------LKKTRKDVSLH 130

Query: 578 TPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
            PIG +   +   L D +  +         ++   +    R L  L  RE+ V+  RFG+
Sbjct: 131 DPIGTDKEGNEITLIDILGSEADDIVEKVQLKIE-KSKIYRNLDILDDREKEVVVGRFGL 189

Query: 635 GMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                + T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 190 EHGGEERTQREIAKELGISRSYVSRIEKRALMKLYH 225


>gi|325662152|ref|ZP_08150770.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471601|gb|EGC74821.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 211

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 101/255 (39%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S  T ++ +E ++    ++K       AK  ++E NLRLV  + KKY        DLI  
Sbjct: 6   SFPTPLTSAEEQYY---MQKYTEGDLEAKHILIEHNLRLVAHIVKKYQRPEEDNEDLISI 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA   F+   G + STYA   ++  I   +                        
Sbjct: 63  GTVGLIKAVITFNPEKGNRLSTYAARCIENEILMMLRS---------------------- 100

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
                                          K +   ISL  PIG +   +   L D +E
Sbjct: 101 ------------------------------RKKSSREISLYEPIGTDREGNEIQLFDVME 130

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
             +        ++ ++R    +V + L+ RE  VL+MR+G+    ++T  E+ K+  ++R
Sbjct: 131 TTDEDIHEKINLKDDVRTLYEKVESELSDRERLVLKMRYGLYNEEEYTQREIAKRLGISR 190

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE  A+ KL+
Sbjct: 191 SYVSRIEKSAVEKLR 205


>gi|226313414|ref|YP_002773308.1| sporulation sigma factor SigE [Brevibacillus brevis NBRC 100599]
 gi|226096362|dbj|BAH44804.1| RNA polymerase sigma-E factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 240

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 91/232 (39%), Gaps = 56/232 (24%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
               +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   FD     K +TYA
Sbjct: 56  DPAVRGMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFDPDKNIKLATYA 115

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +               + +K+                            
Sbjct: 116 SRCIENEILMYLR--------------RNNKIR--------------------------- 134

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
                        +S + P+  +   +   L D +  +N     +   Q + R+   + L
Sbjct: 135 -----------SEVSFDEPLNIDWDGNELLLSDVLGTENDTIYKNIEDQVD-RKLLKKAL 182

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             L+ RE  ++ +RFG+    + T ++V     +++  I ++E + I++L+ 
Sbjct: 183 DKLSDRERIIMELRFGLAGEEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 234


>gi|90415333|ref|ZP_01223267.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2207]
 gi|90332656|gb|EAS47826.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2207]
          Length = 240

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 99/248 (39%), Gaps = 19/248 (7%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
           + + +    A      +V+  + LV  VA     R    ++  +LIQ G IGL++A + F
Sbjct: 4   ARIYEEIQNADQQSTSLVD-YIGLVKRVALHLKGRLPNFMELDELIQVGMIGLIEADKSF 62

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G  F  +A   ++ AI   +   S    +P      I      +  ++ ++ R P+
Sbjct: 63  DSTKGVDFEVFAKNRIRGAILDQVRKMS---YLPRSAIVSIRDHNEASAALTGELGRAPS 119

Query: 549 PEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             E+A  +    +  +K        + +SLE       TS   D +   N+ +P    ++
Sbjct: 120 QAELADFMGKDADTFQKERTHAHRFQTVSLEAQ-----TSESVD-LPTGNSSNPEKELVE 173

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
               +     +  L  R+  ++ + +      +  L+E+G    V+  R+ QI +  ++ 
Sbjct: 174 EQFMDALAASIGELPERDRTIVSLYYV----EEMNLKEIGAVLDVSESRVSQILSACVKT 229

Query: 667 LKHPSRSK 674
           L+    + 
Sbjct: 230 LRVKMHNH 237


>gi|255697035|emb|CBA11627.1| RNA polymerase sigma factor [Pseudomonas caricapapayae]
 gi|255697097|emb|CBA11659.1| RNA polymerase sigma factor [Pseudomonas syringae pv. helianthi]
 gi|255697147|emb|CBA11685.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tagetis]
          Length = 192

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 66/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA     +D  +    P  A+     + +  + +   L      
Sbjct: 60  GADDDEE--------ESADGSDDEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 106 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|160915288|ref|ZP_02077501.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
 gi|158433087|gb|EDP11376.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
          Length = 239

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 90/245 (36%), Gaps = 59/245 (24%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E ++I ++ +        A+ +++E NLRLV  + KKY  +     DLI  G IGL+KA 
Sbjct: 35  ETKYIAALAKGN----QTARDKLIEHNLRLVAHIVKKYDFKKEATEDLISIGTIGLIKAV 90

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + F    G+K +TYA   ++  I   +       +                         
Sbjct: 91  DSFKPEKGHKLTTYASKCIENEILMYLRSSKNYFQN------------------------ 126

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLD 602
                                       +SL  PI  +       L D I      S +D
Sbjct: 127 ----------------------------VSLNEPIATDKDGSEIMLIDAIASPCDTSIID 158

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             + A+      + +  L  RE  ++  RFG+    + T  E+ KQ  ++R  + +IE +
Sbjct: 159 DMLVADNIVKLKQYMHVLDARELEIITKRFGLFGQKEATQREIAKQLHISRSYVSRIEKR 218

Query: 663 AIRKL 667
           A  KL
Sbjct: 219 AFMKL 223


>gi|312876364|ref|ZP_07736349.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796858|gb|EFR13202.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 244

 Score = 85.7 bits (210), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 92/248 (37%), Gaps = 52/248 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +     E    KK ++E NLRLV+ +AK++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYRIHYQGEEGL--KKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +   S                         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNS------------------------- 135

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                       KKL M ++                  +  +    L   +   +     
Sbjct: 136 -----------NKKLEMSIDE--------------PLNVDWDGNELLLSEVLGTDTEEIY 170

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +       +E   + +  L  RE++++ +R G G + + T +EV     +++  I ++E 
Sbjct: 171 NRIENNVEKEALLQAIQKLPSREKKIVELRSGFGDDGEKTQKEVADMLGISQSYISRLEK 230

Query: 662 KAIRKLKH 669
           K I +LK 
Sbjct: 231 KIITRLKK 238


>gi|160935680|ref|ZP_02083055.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441424|gb|EDP19134.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
          Length = 246

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 94/256 (36%), Gaps = 60/256 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +   E   ++S++  G  +   A+  ++E NLRLV+ +AKK+ N  +   DLI  G 
Sbjct: 40  PAPLETEEEGRMISLL--GSEDDKEARAALIEHNLRLVVYIAKKFDNTSVGVEDLISIGT 97

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F      K +TYA   ++  I   +                          
Sbjct: 98  IGLIKAINTFKPDKNIKLATYASRCIENEILMYLRRN----------------------- 134

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                          T+  +S++ P+  +   +   L D +   
Sbjct: 135 -----------------------------NKTRLEVSIDEPLNVDWDGNELLLSDILGTD 165

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTR 653
             V           +      ++ L PRE +++ +R+G+      + T +EV     +++
Sbjct: 166 EDV-IYHDIEDEIEKSLLNNAISRLNPRERKIVELRYGLTNEDGEEMTQKEVADLLGISQ 224

Query: 654 ERIRQIEAKAIRKLKH 669
             I ++E K +++LK 
Sbjct: 225 SYISRLEKKIMKRLKK 240


>gi|296121384|ref|YP_003629162.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013724|gb|ADG66963.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 376

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 97/240 (40%), Gaps = 59/240 (24%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
             +       ++  A+ ++V+ANLRLV+++A+K      Q  +L+ EG + L+++ E FD
Sbjct: 180 YFAQYNLWLNKSITARNQIVQANLRLVVALARKCCGSIEQLAELVSEGVMPLIRSVELFD 239

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             LG +FSTYA W V+                   M     KV         +   E T 
Sbjct: 240 ISLGNRFSTYATWAVRN-----------------QMHRHFKKV---------QTWNEHTT 273

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
             I + L                                 DF   ++ V       Q   
Sbjct: 274 AYIHEALE-----------------------------QFEDF---RSPVETQPGESQEAC 301

Query: 610 RETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +   T +L +L+ RE  V+  RFG+ G     +L E+  +  +++ER+RQI  KA+ KLK
Sbjct: 302 QRELTSLLETLSDRERAVIAARFGLDGQPRGQSLSEISGRIGLSKERVRQIVLKALDKLK 361


>gi|167755748|ref|ZP_02427875.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|237734714|ref|ZP_04565195.1| sporulation sigma factor sigE [Mollicutes bacterium D7]
 gi|167704687|gb|EDS19266.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|229382042|gb|EEO32133.1| sporulation sigma factor sigE [Coprobacillus sp. D7]
          Length = 231

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 102/262 (38%), Gaps = 64/262 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGN 478
           +   E +  +  +       + A+  ++E NLRLV+ VAK+Y    N G++  DLI  G 
Sbjct: 28  LKGIEEKEALEKL---GAGDNDARDLLIEHNLRLVVYVAKRYDTTQNGGIE--DLISIGT 82

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F      K +TYA   ++  I   +               K +K+      
Sbjct: 83  IGLVKAINTFKPDKNIKLATYASRCIENEILMFLR--------------KNNKLR----- 123

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                              ISL+ P+  +   +   L D I   
Sbjct: 124 ---------------------------------HEISLDEPLNIDYDGNELLLSDIIGTD 150

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           + +   +   Q++ +         L+ RE+ +L  R+G+    + T ++V K   +++  
Sbjct: 151 SDI-VKNELEQSDQKAMFYEAFKDLSKREKEILMFRYGLMNYDELTQKDVAKMMGISQSY 209

Query: 656 IRQIEAKAIRKLKHPSRSKKLR 677
           I ++E K I+KL++     +++
Sbjct: 210 ISRLEKKIIKKLRNKLNYNEIK 231


>gi|332272421|gb|AEE38894.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
          Length = 219

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 80/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II            GF    E                
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE---------------- 33

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                     E  A  +    S++       E++E   DEDED                 
Sbjct: 34  ---------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDGDNSDDDGDGGPDPEVA 84

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                E+   Y          ++ QK+ ++    +    +L  +     L   + D LV 
Sbjct: 85  REKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 139 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLV 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + I +   +++ I  ETG
Sbjct: 199 EMD-EDIQRAIGKLQQIEEETG 219


>gi|332272411|gb|AEE38889.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|332272413|gb|AEE38890.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|332272415|gb|AEE38891.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|332272417|gb|AEE38892.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|332272419|gb|AEE38893.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|332272423|gb|AEE38895.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|332272425|gb|AEE38896.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|332272427|gb|AEE38897.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|332272429|gb|AEE38898.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
 gi|332272431|gb|AEE38899.1| RNA polymerase sigma-70 factor [Aeromonas veronii]
 gi|332272433|gb|AEE38900.1| RNA polymerase sigma-70 factor [Aeromonas allosaccharophila]
          Length = 219

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 81/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II            GF    E                
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII-----------SGFIDPNE---------------- 33

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                     E  A  +    S++       E++E   DEDED  +              
Sbjct: 34  ---------TEDMAPTATHIGSELGEDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVA 84

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                E+   Y          ++ QK+ ++    +    +L  +     L   + D LV 
Sbjct: 85  REKFGELRAQYEV------TRLSIQKNGRAHEDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 139 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLV 198

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + + I +   +++ I  ETG
Sbjct: 199 EMD-EDIQRAIGKLQQIEEETG 219


>gi|168704081|ref|ZP_02736358.1| RNA polymerase sigma factor for flagellar operon [Gemmata
           obscuriglobus UQM 2246]
          Length = 247

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/231 (18%), Positives = 85/231 (36%), Gaps = 18/231 (7%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCL 492
                    + E++ ++L LV  V  +       G+   +L   G +GL++AA KFD   
Sbjct: 13  YQRQAEQQRRDELIVSHLPLVKHVIGRLIGDVPPGVDVENLESAGVLGLVEAAAKFDPAR 72

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             +F T+A   ++ AI   +        +P H+  ++  V R  R + +      T E I
Sbjct: 73  NAQFKTFAYLRIRGAIVDEMR---RNSPLPQHVHARLALVRRACRTLPH----PITVEAI 125

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A    +  + V   L   +        +  E  S             P     +    + 
Sbjct: 126 AAATGLSEDEVTDTLSAERMA----KTMSWEQASESTGLEPAGGGEEPGAEMERWESVQQ 181

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               +  L P+E   + + +      D  L+E+ +   ++  R+ ++ +KA
Sbjct: 182 LGDAIQELEPKERIAVTLYY----KEDLRLKEIAEVMKLSVSRVSRLLSKA 228


>gi|323484320|ref|ZP_08089687.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694680|ref|ZP_08108842.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402314|gb|EGA94645.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501272|gb|EGB17172.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 209

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 95/250 (38%), Gaps = 58/250 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ SE R  +   ++ +     AK  ++E NLRLV  V KKY     +  DL+  G IGL
Sbjct: 8   LTASEEREYL---KRCKEGDEEAKAVLIERNLRLVAHVIKKYQYTDYEMEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F    G + +TYA   V+  I                       + R  ++ S 
Sbjct: 65  IKAVNTFKMDRGSRLATYAAKCVENEILM---------------------LFRAGKKHSK 103

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +SL  PIG +       L D IE  +  
Sbjct: 104 -------------------------------DVSLYDPIGVDKDGETVNLIDVIEADDKA 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +     ++ ++ E        L   E+ VL MR+G+    + T  E+  +  ++R  + +
Sbjct: 133 ALETIILEQDVSELYDAYRKCLKNTEQEVLSMRYGLFGEQERTQREIAGKMGISRSYVSR 192

Query: 659 IEAKAIRKLK 668
           IE KA+ KL+
Sbjct: 193 IEKKALEKLR 202


>gi|167626171|ref|YP_001676465.1| flagellar biosynthesis sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167356193|gb|ABZ78806.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella
           halifaxensis HAW-EB4]
          Length = 240

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 45/208 (21%), Positives = 95/208 (45%), Gaps = 18/208 (8%)

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +    L   D+ Q G + L++AA ++       F ++A   ++ AI   +  Q    R  
Sbjct: 43  HCGSVLAIEDMEQIGMMALLEAARRYPGEYDNGFLSFAGQRIRGAILDELRRQDWRPRP- 101

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
             +R + H++  T R+++  ++REP+ +E+A+ + +     R+ L  +            
Sbjct: 102 --VRQQAHELNDTIRKLTRLLEREPSDKEVAEAMGLNEVEYRERLFAS----------QS 149

Query: 583 EDTSHLGDFI-EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
           E    L + I E  N V   D   Q + +E   + ++ L  RE+ +L + +      +  
Sbjct: 150 ESMRSLDELISEGGNFVDNNDMLEQFSAKECLFQAISKLNKREQLILSLYYQH----ELN 205

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L+E+     +T  RI Q+  +A+++L++
Sbjct: 206 LKEIAATLGLTETRICQLHKQAVKQLQN 233


>gi|222832154|gb|EEE70631.1| predicted protein [Populus trichocarpa]
          Length = 299

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/214 (21%), Positives = 82/214 (38%), Gaps = 27/214 (12%)

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           MKA ++FD     +  +YAM W+K  I   I      +++      +  K+    R M  
Sbjct: 1   MKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQR--KLFFNLRSMKQ 58

Query: 542 KIKREPTPEE----------------IAKKLAMPVEGVRKVLKI-TKEPISLETPIGDED 584
            +K +    E                +A+KL +  E V ++        + L+    D+ 
Sbjct: 59  GLKSDAAMAEDGAMLRDTLTSGEIDAVAEKLNVKREEVMEMETRLAGGDVLLDPSPSDDG 118

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTT-----RVLASLTPREERVLRMRFGIGMNTD 639
               G      +      + I++  R+          L SL  R  R++  R+    +  
Sbjct: 119 EQAFGPIAYLADGAHEPTAMIESRQRDHLATDGIAMALDSLDDRSRRIVEERWLKVNDDG 178

Query: 640 ---HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               TL E+   + V+ ERIRQIE  A++K+K  
Sbjct: 179 SGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKA 212


>gi|226329393|ref|ZP_03804911.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
 gi|225202579|gb|EEG84933.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
          Length = 137

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 32/120 (26%), Positives = 60/120 (50%), Gaps = 2/120 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I   I++ +    ++  E + +   +         A + ++ ++LR VI VA+ Y+  GL
Sbjct: 16  IEAYIRAANSYPMLTAEEEKELAERL--HYEGDLDAARTLILSHLRFVIHVARSYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K  I   +      +++      +
Sbjct: 74  PQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKSQR 133


>gi|255697037|emb|CBA11628.1| RNA polymerase sigma factor [Pseudomonas syringae pv.
           coronafaciens]
 gi|255697069|emb|CBA11644.1| RNA polymerase sigma factor [Pseudomonas syringae pv. atropurpurea]
 gi|255697117|emb|CBA11669.1| RNA polymerase sigma factor [Pseudomonas syringae pv. oryzae]
 gi|255697131|emb|CBA11677.1| RNA polymerase sigma factor [Pseudomonas syringae pv. porri]
 gi|255697143|emb|CBA11683.1| RNA polymerase sigma factor [Pseudomonas syringae pv. striafaciens]
 gi|255697157|emb|CBA11690.1| RNA polymerase sigma factor [Pseudomonas syringae pv. zizaniae]
          Length = 191

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 28/235 (11%), Positives = 70/235 (29%), Gaps = 47/235 (20%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + + ESA    ++D  +    P  A+     + +  + +   L  +   
Sbjct: 51  VDPKAAKAEGDDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKLGRD 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            +  +   +                                    L +L   + L   + 
Sbjct: 111 DKHAIAEMV-----------------------------------ALAELFMPIKLVPKQF 135

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 136 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 190


>gi|117573590|gb|ABK40971.1| RNA polymerase subunit D [Pseudomonas sp. F96.26]
 gi|117573596|gb|ABK40974.1| RNA polymerase subunit D [Pseudomonas sp. P97.1]
 gi|117573598|gb|ABK40975.1| RNA polymerase subunit D [Pseudomonas sp. P97.27]
          Length = 200

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 51/118 (43%), Gaps = 2/118 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKAAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALETETGL 200


>gi|117573572|gb|ABK40962.1| RNA polymerase subunit D [Pseudomonas sp. P97.39]
          Length = 200

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 51/118 (43%), Gaps = 2/118 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 84  KHGRNNKAAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 143

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
           + R  FL +  G E+D  W   A    + ++   +A     I++ + ++ ++  ETG+
Sbjct: 144 MPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIARLQPDIVRCQQKLSALETETGL 200


>gi|309388843|gb|ADO76723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Halanaerobium praevalens DSM 2228]
          Length = 251

 Score = 85.3 bits (209), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 104/238 (43%), Gaps = 14/238 (5%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +    +   A++E++  NL LV     +        ++  DL   G IGL++A E F++ 
Sbjct: 10  KYKVDDNQQAREEIILKNLGLVRYAVGRINIMLPEHIEDQDLESYGIIGLIEAIENFNYQ 69

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G KFST+A+  +K  I   +  +        +MR ++ KV    R    K  ++P  +E
Sbjct: 70  RGVKFSTFALPRIKGEIYDYLRSKDWLPD---NMRRELKKVDEQKRSYKAKTGKKPDQKE 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED-KNAVSPLDSAIQANLR 610
           ++K   +    + K+ + ++    +      + T  +     D K AV  L      +  
Sbjct: 127 LSKLTGIKKSRLEKIERHSQLANWISLSHDFDGTELIELVAADFKQAVDRLTEKEAVDF- 185

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + +  L+ +E+ VL + +      + T  E+ +   ++  R+ QI  +AIR+L+
Sbjct: 186 --LAKKIDLLSEKEKLVLSLYY----YEELTQVEIAEIIELSAARVSQIHGRAIRRLR 237


>gi|255697129|emb|CBA11675.1| RNA polymerase sigma factor [Pseudomonas syringae pv. pisi]
          Length = 192

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAAKTE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    ++D  +    P  A+     + +  + +   L      
Sbjct: 60  GADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 106 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|225018358|ref|ZP_03707550.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
 gi|224948875|gb|EEG30084.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
          Length = 245

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 57/248 (22%), Positives = 98/248 (39%), Gaps = 53/248 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R +    +K   +   A+ +++  NLRLV+ +AKK+ + G+   DLI  G IGL
Sbjct: 44  LTKDEERVVF---QKLSEKDPWARDQLIVHNLRLVVYIAKKFESTGIGVEDLISIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I   +                           SN
Sbjct: 101 IKAVNTFSPEKNIKLATYASRCIENEILMHLRK-------------------------SN 135

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            IK E + +E  K                           D +   L D +  +N     
Sbjct: 136 PIKSEISIDEPLK------------------------IDWDGNELLLSDVLGTENDCVNR 171

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
               Q   R+     +  L  RE  +++MRFG+    +HT +EV  +  +++  I ++E 
Sbjct: 172 GIEDQVE-RDLIVSCVNKLGDRERSIMQMRFGMIDGKEHTQKEVADKIGISQSYISRLEK 230

Query: 662 KAIRKLKH 669
           + I++LK 
Sbjct: 231 RIIKRLKK 238


>gi|119715014|ref|YP_921979.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119535675|gb|ABL80292.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 285

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 89/226 (39%), Gaps = 17/226 (7%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           ++  +  LV  + ++  +R    +   DL   G + L++AA+ FD   G  F+ YA   V
Sbjct: 13  LILQHTALVGHIVRETMSRVPAHVDRDDLTSAGLLALVQAAQAFDAERGVPFNRYAATRV 72

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + A+   +       R       +  ++  T  R++  + R  T  E+A    + V+ V 
Sbjct: 73  RGAVVDELRRTDWASRSVRR---RARELDATRSRLATVLGRPATQAEVADTAGLSVDEVT 129

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                    + +SL+      +   +GD +   NA  P  +          T  +A L  
Sbjct: 130 GNDDDIARAQVLSLDAS----EDDGIGDTLV-GNAPDPQGALEHGERLTYLTEAVAELPD 184

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R   V+   F      +  + E+     VT  RI Q+ A+A+  L+
Sbjct: 185 RLRLVVEQYFL----NERPMAEIAATLGVTESRISQLRAEALVLLR 226


>gi|307293798|ref|ZP_07573642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
 gi|306879949|gb|EFN11166.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
          Length = 245

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 96/231 (41%), Gaps = 19/231 (8%)

Query: 447 EMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +    + LV   A     R    ++  DL+Q G + L++AA  F+   G  F++YA   
Sbjct: 26  RLARQYMPLVRKTAWHVHGRVSSAIEIEDLLQIGMVALVEAANGFE-DRGLGFASYAQMR 84

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+ A+   +   +   R  +  R    ++     R+  K+ R P   E++ ++ +     
Sbjct: 85  VRGAMIDHLRRHATMTRSAMAQRK---QLAGIRNRLEQKLGRIPLESEMSAEMGLDPAAY 141

Query: 564 RKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           R+V       +  S++  +  + +    D  E  + V       + +L+    + +  L 
Sbjct: 142 REVADGCEMVQHTSMDE-VYSDQSMWFADVEERADDV-----MERESLKAALAKCIGDLP 195

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            RE  VL++ F      +  LEE+G    +   R+ QI+  A+ KL+   R
Sbjct: 196 QREALVLQLYFV----EELNLEEIGATLDIGAARVCQIKKAALDKLREKLR 242


>gi|296061206|emb|CBJ55914.1| RNA polymerase sigma subunit [Xanthomonas arboricola pv. juglandis]
          Length = 199

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 84/242 (34%), Gaps = 45/242 (18%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           REGEIAIAKRIE G + + A+L   PL+ + L+   +   +G   L EI+          
Sbjct: 1   REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIV---------- 50

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
             GF    E         ++      D    + D +        +     + P+  E   
Sbjct: 51  -VGFNDLIEEADAAAAALAAAGPVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE--- 106

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
                                   V   ++ +A  Y + + +        K+        
Sbjct: 107 ------------------------VATRMENLANEYAKFKKIY------AKNGAEHKLVV 136

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
             +E +  +  +L L     D LV QL  +   I  +E ++L LA +   + R  F+   
Sbjct: 137 KAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 196

Query: 375 QG 376
           +G
Sbjct: 197 EG 198


>gi|255697127|emb|CBA11674.1| RNA polymerase sigma factor [Pseudomonas syringae pv. photiniae]
          Length = 192

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 28/235 (11%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D+      P             ++ +          +
Sbjct: 51  VDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSEQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|239934464|emb|CAR92486.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 218

 Score = 85.3 bits (209), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 25/150 (16%), Positives = 63/150 (42%), Gaps = 3/150 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A+ +  ++   +       +  ++S   +    +L  L   L L   + D LV +  
Sbjct: 70  EEAAKRFNAIQKQNEKTKRAIARYGRNSESTEQHLAELGDLFKXLKLIPKQYDPLVARAR 129

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
              + +  +E  ++ L      + R  F+E   G E +  W +      +  +   +   
Sbjct: 130 AALQEVRRHERAIMMLCIRQAKMPRKEFVESFPGNETNDKW-ALNLSRRKQPYAPAIKNL 188

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVS 432
           +D I++++ ++ S+   +G+SI++ + I  
Sbjct: 189 LDDIIRVQEKLASVEEASGLSITQIKDINR 218


>gi|257871306|ref|ZP_05650959.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
 gi|257805470|gb|EEV34292.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
          Length = 235

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 101/235 (42%), Gaps = 14/235 (5%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR--GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              + ++  +   L LV  V ++ + +    +  DL   G IGLM A  KFD      F 
Sbjct: 1   MYEVDREAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFE 60

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           +YA+  +K AI   +   +   R  +   ++ ++     + +   +KRE T  EI K+L 
Sbjct: 61  SYAVIRIKGAIIDEVRKHAKISRYKMAAVNQFYQ---ARQELEQSLKREATDTEICKQLG 117

Query: 558 MPVEGVRKVLKITKE--PISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           +    +  + +       +SLE  +    E+   + D + D  A +  D+ +    R   
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTIKDMVRDP-AENVEDTLVAEEKRTAL 176

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L  RE+ +L + +      + TL+E+ +   ++  R+ QI  K I KL+
Sbjct: 177 VACIKKLGEREQIILSLYY----TEELTLKEIAEILEISIPRVSQIHGKTIAKLR 227


>gi|160933251|ref|ZP_02080640.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
 gi|156868325|gb|EDO61697.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
          Length = 230

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 101/251 (40%), Gaps = 59/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   ++  VR+GE     A++ ++  NLRLV+ +AKK+ + G    DLI  G IGL
Sbjct: 30  LSREEEDEVMERVRRGEKN---AREPLITHNLRLVVYIAKKFDSNGASVEDLISIGTIGL 86

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I                        +R + ++ N
Sbjct: 87  IKAVNTFCPERNIKLATYASRCIENEILMF---------------------LRKSSQLKN 125

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               IS++ P+  +   +   L D +   N +
Sbjct: 126 E-------------------------------ISIDEPLNVDWDGNELLLSDILGSDNDI 154

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +        + ++ L PRE +++ +RFG+    +HT ++V     +++  I +
Sbjct: 155 -VNRDIEKEVECSLVLQAVSRLAPRERQIMELRFGLCGQKEHTQKQVADVLGISQSYISR 213

Query: 659 IEAKAIRKLKH 669
           +E + I +LK 
Sbjct: 214 LEKRIIERLKK 224


>gi|239934472|emb|CAR92490.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 225

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 44/273 (16%), Positives = 82/273 (30%), Gaps = 49/273 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               D I + +  +  I  E G+ IS  + I  
Sbjct: 193 KQFTDDIRRAQRRLAEIEREHGLDISRIKEINR 225


>gi|149194332|ref|ZP_01871429.1| flagellar biosynthesis sigma factor [Caminibacter mediatlanticus
           TB-2]
 gi|149135507|gb|EDM23986.1| flagellar biosynthesis sigma factor [Caminibacter mediatlanticus
           TB-2]
          Length = 228

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 94/231 (40%), Gaps = 22/231 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +  +    +  V ++A +   R    + F DL+  G   L+K A+++D  +   F  YA 
Sbjct: 15  RDSLAIDYMPAVKAMAARLKERLPSSVDFNDLVSIGYEELVKLAKRYDSSINDNFWGYAQ 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +  A+   +       R     R  I ++ +   R  +    EP  EEIA  L + V 
Sbjct: 75  KRINGAMLDFLRSLDTVSRGD---RKLIKEIDKIIERYMSNHGYEPDDEEIATILDVDVS 131

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V+K  +  +    + + +  ED  +  D               Q  L E    +L  L 
Sbjct: 132 KVKKARQSNE----IYSVMPIEDQLNYFD--------DVSKKVEQDELIEKIEEILNDLG 179

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +E+ ++++ +      + +L+E+ +   VT  R+ QI  K I+KL+   +
Sbjct: 180 EKEQLIIQLYYF----EEMSLKEISEILGVTESRVSQIHKKVIKKLRESLK 226


>gi|153812463|ref|ZP_01965131.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
 gi|149831388|gb|EDM86476.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
          Length = 243

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 94/240 (39%), Gaps = 58/240 (24%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R    +   A+  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F+     
Sbjct: 51  RLKTDQEQEARSLLIEHNLRLVVYIARKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNI 110

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           K +TYA   ++  I   +   S                                      
Sbjct: 111 KLATYASRCIENEILMYLRRNSK------------------------------------- 133

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRE 611
                          T+  +S++ P+  +   +   L D +   + V       +  +  
Sbjct: 134 ---------------TRMEVSIDEPLNVDWDGNELLLSDILGTDDDVISRKLEDEVEIT- 177

Query: 612 TTTRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              + +  L+PRE+ ++R+RFG+      + T +EV     +++  I ++E + +++LK 
Sbjct: 178 LLGKAINKLSPREQTIIRLRFGLNNADGKEKTQKEVADLLGISQSYISRLEKRIMKRLKK 237


>gi|260438830|ref|ZP_05792646.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292808820|gb|EFF68025.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 246

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 52/256 (20%), Positives = 99/256 (38%), Gaps = 60/256 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +  +E   +++ +  G    + AK  ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 40  PAPLEPAEEAEVIADL--GTEYDTKAKTMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGT 97

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   FD     K +TYA   ++  I   +                          
Sbjct: 98  IGLIKAINSFDINKKIKLATYASRCIENEILMYLRRN----------------------- 134

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                          T+  +S++ P+  +   +   L D +   
Sbjct: 135 -----------------------------HKTRMEVSIDEPLNVDWDGNELLLSDILGTD 165

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTR 653
             +   +   +A  ++   + +  L+ RE  ++ +RFG+      + T +EV     +++
Sbjct: 166 EDIIYRNLEDEAE-KKLLLKAVNKLSERERTIIDLRFGLNSPDGKELTQKEVADMLGISQ 224

Query: 654 ERIRQIEAKAIRKLKH 669
             I ++E K I++LK 
Sbjct: 225 SYISRLEKKIIKRLKK 240


>gi|255697045|emb|CBA11632.1| RNA polymerase sigma factor [Pseudomonas syringae]
 gi|255697067|emb|CBA11643.1| RNA polymerase sigma factor [Pseudomonas syringae pv. atrofaciens]
 gi|255697105|emb|CBA11663.1| RNA polymerase sigma factor [Pseudomonas syringae pv. lapsa]
          Length = 192

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAAKAE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    ++D  +    P  A+     + +  + +   L      
Sbjct: 60  GADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 106 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|331269717|ref|YP_004396209.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
 gi|329126267|gb|AEB76212.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
          Length = 226

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 99/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E R+ +   +K +   ++AK  ++E NLRLV  + KKY+       DLI  
Sbjct: 17  SFPQPLNEDEERYYL---KKFKDGDTLAKGILIERNLRLVAHIVKKYSYPNKDIDDLISI 73

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I +                K +++ 
Sbjct: 74  GTVGLIKAIDSFDISKGTRLATYAARCIENEILMLIRNT---------------KKIKSE 118

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 119 VYLQDPIGVDKEGNEI----------------------------------SLMDVLSSDE 144

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +++   ++   LT RE+ +++MR+G+      T  E+     ++R  +
Sbjct: 145 NSVIEVVENRMQVKKLYDKINECLTDREKIIIKMRYGLNDGKPKTQREIAAFLNISRSYV 204

Query: 657 RQIEAKAIRKL 667
            +IE +A++K+
Sbjct: 205 SRIEKRALKKM 215


>gi|325106726|ref|YP_004267794.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324966994|gb|ADY57772.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 332

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 100/255 (39%), Gaps = 63/255 (24%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V+       +A+  +  ++ ANLRLV+SVA+K+    L F +L  +G I LM A EKF
Sbjct: 137 EQVAEAESTLRQANSVRDLLIRANLRLVVSVARKFVTPQLTFDELFSDGVIALMNAVEKF 196

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D+  GY+FSTYA + + +++ R I               + +++                
Sbjct: 197 DYDRGYRFSTYAYYSISRSLYRFI------------KVQRKNRI---------------- 228

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
                                      LE  +  +D    G   E  + V+         
Sbjct: 229 -----------------------HSDVLEQVVEADDDGQSGWNQESWDFVN--------- 256

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHT-LEEVGKQFCVTRERIRQIEAKAIRKL 667
             E    +LA L  RE  ++R R+           + + ++  V  ER+RQ+E +A+ KL
Sbjct: 257 --EELDSMLAQLDQRERWIIRQRYTFDSEGKAPTYKVLAEKLGVCNERVRQLEKRALSKL 314

Query: 668 KHPSRSKKLRSFLDG 682
           ++ S   +    L+ 
Sbjct: 315 RNLSDDGRFSDILEA 329


>gi|253578603|ref|ZP_04855875.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850921|gb|EES78879.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39BFAA]
          Length = 238

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 54/247 (21%), Positives = 98/247 (39%), Gaps = 58/247 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R    + + G  +   AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   
Sbjct: 39  REAFILQKLGTGQEEEAKSVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINT 98

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+     K +TYA   ++  I   +   S                               
Sbjct: 99  FNPVKNIKLATYASRCIENEILMYLRRNSK------------------------------ 128

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSA 604
                                 TK  +S++ P+  +   +   L D +     V      
Sbjct: 129 ----------------------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDVISRRLE 166

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQIEAK 662
            +  +    ++ +  L+PRE+ ++R+RFG+G     + T +EV     +++  I ++E +
Sbjct: 167 DEVEI-SLLSKAIRKLSPREQTIIRLRFGLGKENAAEKTQKEVADLLGISQSYISRLEKR 225

Query: 663 AIRKLKH 669
            +++LK 
Sbjct: 226 IMKRLKK 232


>gi|325662349|ref|ZP_08150958.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331086152|ref|ZP_08335234.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471351|gb|EGC74574.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330406311|gb|EGG85825.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 247

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 61/289 (21%), Positives = 110/289 (38%), Gaps = 60/289 (20%)

Query: 388 KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS-ISEFRHIVSMVRK-GECEASIAK 445
              P+     F++     ++  R EI  I     +    E     +++++        AK
Sbjct: 5   AMLPKQFRMKFLSQFRKIVIGTRREIHYIGGSEVLPAPLEMEEESAVIKELATEYNEKAK 64

Query: 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           K ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   ++
Sbjct: 65  KVLIEHNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRCIE 124

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             I   +                                                     
Sbjct: 125 NEILMYLRRN-------------------------------------------------- 134

Query: 566 VLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
               TK  +S++ P+  +   +   L D +  +      D   +A  +    + +  L+P
Sbjct: 135 --NKTKLEVSIDEPLNVDWDGNELLLSDILGTEEDTIYRDLETEAEQK-MLRKAIEKLSP 191

Query: 623 REERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           RE+ ++ MRFGI      + T +EV     +++  I ++E K +++LK 
Sbjct: 192 REKTIVEMRFGINRSEGEEKTQKEVADLLGISQSYISRLEKKIMQRLKK 240


>gi|168703207|ref|ZP_02735484.1| sigma-70 factor [Gemmata obscuriglobus UQM 2246]
          Length = 566

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 64/279 (22%), Positives = 103/279 (36%), Gaps = 62/279 (22%)

Query: 394 EWKNFVACEVDSILKIRNEIKSISVETGISISEFR---HIVSMVRKGECEASIAKKEMVE 450
           EW      +   + +  N +K    +   +I   R     +    +        +  ++ 
Sbjct: 337 EWPLLTKEQEQHVFRKMNFLKHKLHQLQSAIDPARATVDELRRAEQLRQGVRDTRDVLIN 396

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
            N RLV + AK+    G    DL+ +GN+ LM+A EKFD+  G KFSTYA W + +   R
Sbjct: 397 CNQRLVYAQAKQKLALGENIDDLVSDGNLSLMRAVEKFDYARGNKFSTYATWAIMKNFAR 456

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           S                                              +P     K   +T
Sbjct: 457 S----------------------------------------------IPDAKTHKQRYMT 470

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
                 E            D   D+  V  L    +A       R+L  L  R   V+RM
Sbjct: 471 GHDELFEAK---------ADIRTDEQEVLALADQARA----RVNRLLDHLDARTREVIRM 517

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R G+  + + TLE++G+ F +T+ER+RQI  + ++ L+ 
Sbjct: 518 RTGLDGSEEMTLEQIGQHFGITKERVRQINVRGMKMLRE 556


>gi|195953358|ref|YP_002121648.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195932970|gb|ACG57670.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 245

 Score = 84.9 bits (208), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 103/232 (44%), Gaps = 16/232 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++ +   + LV  +  K +      + + DL+  G IGL+ A +  D     +  +Y  
Sbjct: 17  REKKILEYIPLVKKICGKMSRNLPPSVDYNDLVSNGIIGLINAIDHLDELKNPE--SYIK 74

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             VK AI   +           ++RDK HK+    R   N+ +REPT EEI+  L   +E
Sbjct: 75  IRVKGAIYDYLRSLDF---GSRNIRDKEHKIKEIIRTFQNEYQREPTDEEISSILGESLE 131

Query: 562 GVRKVLKITKEP--ISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             +  L         SLE  +    E+     D     +  +P + A++++L E     +
Sbjct: 132 EYQNSLYKISFSYLQSLEDMVYKITEENESSYDNFVISSIETPEEYAVKSDLAEKLKEAI 191

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             L  RE+ VL++ F         ++EV +   V+  R+ QI+++A+ KL+ 
Sbjct: 192 DKLEEREKLVLQLLFYEEFG----IKEVAEILNVSLSRVSQIKSQALEKLRK 239


>gi|327439575|dbj|BAK15940.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 233

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 95/265 (35%), Gaps = 57/265 (21%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            +  +   +K  +    +S  E   +   + +       A+ E++E N+RLV  V KK+ 
Sbjct: 14  ELPALLGYLKGQTFYKPLSREEEEEV---INRFIKGDESARVELIERNMRLVAHVVKKFH 70

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
                  D I  G IGLMKA   F      + +TYA   ++  I   +  Q         
Sbjct: 71  PSHDLLDDYISIGTIGLMKAVSSFTPEKKTRLATYAARCIENEILMHLRAQ--------- 121

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                                               + V+K        +SL  PIG + 
Sbjct: 122 ------------------------------------KKVQK-------DVSLFEPIGIDK 138

Query: 585 TSHLGDF--IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                    +   +  S ++   +        R L +L PRE  ++  R+G+     HT 
Sbjct: 139 DGQSLQIRDLLQLDEPSTIEKIERQEDFAQLYRYLDTLDPRELEIISYRYGLQNFDPHTQ 198

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           +E+ K+  ++R  + +IE +A+ KL
Sbjct: 199 KEIAKRLNISRSYVSRIEKRALIKL 223


>gi|321116348|emb|CBN73555.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 35/234 (14%), Positives = 72/234 (30%), Gaps = 45/234 (19%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +++   + + +    L +I  L   I P+  G         + Q+ E  + +     V +
Sbjct: 1   SILADYERVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPVAD 51

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D E     ++++       PE A      + E  + +   L                
Sbjct: 52  DKDDDEEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL---------------- 95

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  ++S +     E L  L   + L   + D LVE++ D 
Sbjct: 96  -------------------KKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVRDA 136

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             +I   E  +++L      + R  FL +    E +  W            +  
Sbjct: 137 LNQIRAQERAIMQLCVRDARMPRADFLRQFPSNETNLDWAEQLAAGKSKYAEPI 190


>gi|293376227|ref|ZP_06622470.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325845158|ref|ZP_08168467.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
 gi|292645119|gb|EFF63186.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325488823|gb|EGC91223.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
          Length = 236

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 50/275 (18%), Positives = 96/275 (34%), Gaps = 58/275 (21%)

Query: 398 FVACEVDSILKIRNEIKSISV-ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLV 456
            +        K  N I+        +S  E  ++++  +        A++ ++E NLRLV
Sbjct: 11  LIERLFKRKNKYVNYIRGNETLPEPLSKDEEFNVLTRFQG---GDERARQTLIEHNLRLV 67

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +AKK+ + G+   DLI  G +GL+K  + F      K +TYA   ++  I   +   +
Sbjct: 68  VYIAKKFESSGVNLEDLISIGTLGLIKGVQTFKMDKNIKLATYASRCIENEILMHLRKTN 127

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                                                                    +SL
Sbjct: 128 RIRNE----------------------------------------------------VSL 135

Query: 577 ETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           + P+  +   +  L   I             +   R+     +  L  RE  ++ MRFG+
Sbjct: 136 DEPLNVDWDGNELLLSDILGTEENEVYKDIEEDVERQLVFDAINRLKRREREIMYMRFGL 195

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                 T +EV ++  +++  I ++E K I K++ 
Sbjct: 196 CGEDPLTQKEVAQKLDISQSYISRLEKKIIDKIRK 230


>gi|148554202|ref|YP_001261784.1| RNA polymerase sigma 28 subunit FliA/WhiG [Sphingomonas wittichii
           RW1]
 gi|148499392|gb|ABQ67646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphingomonas wittichii
           RW1]
          Length = 242

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 92/230 (40%), Gaps = 19/230 (8%)

Query: 448 MVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V A+++LV  +A     R    +   DLIQ G I L++AA  ++   G+ FSTYA   V
Sbjct: 24  LVRAHMQLVRKIAWHVHGRVSTAIDVEDLIQIGMIALVEAANGYE-DRGHAFSTYASMRV 82

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +        +      K   ++        K  R P+  E+A+ L +      
Sbjct: 83  RGAMIDHLR---RQAALTRSAMAKRRALLTAKADFEKKHGRSPSESELAQALGLDGAAFH 139

Query: 565 KVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            +L         S++  +  + +    D            +  +  L       ++ L  
Sbjct: 140 ALLDETAATYHESIDE-VYSDQSMWFADV-----EERVDQTIEREELAGALAEHISELPE 193

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           RE  VL++ F      +  LEE+G+   +   R+ QI+  A+ KL+   R
Sbjct: 194 REAMVLQLYFV----EEMNLEEIGQTLGIGAARVCQIKKAALDKLRVSLR 239


>gi|298112129|gb|ADI58449.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
          Length = 190

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 72/235 (30%), Gaps = 46/235 (19%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++     +      L ++  L   I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGI 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K   +    + ++        ESA    ++D  +    P  A      
Sbjct: 59  APPVEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVIAAQRFGA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +  + +   L     + +  +   +                                 
Sbjct: 111 VSDQMEITRKALKKFGREDKHAIAEMV--------------------------------- 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
              L +L   + L   + + LVE++     R+   E  +++L      + R  FL
Sbjct: 138 --ALAELFMPIKLVPKQFEGLVERVRGAFDRLRAQERAIMQLCVRDARMPRADFL 190


>gi|255697029|emb|CBA11624.1| RNA polymerase sigma factor [Pseudomonas avellanae]
 gi|255697061|emb|CBA11640.1| RNA polymerase sigma factor [Pseudomonas syringae pv. antirrhini]
 gi|255697063|emb|CBA11641.1| RNA polymerase sigma factor [Pseudomonas syringae pv. apii]
 gi|255697065|emb|CBA11642.1| RNA polymerase sigma factor [Pseudomonas syringae pv. aptata]
 gi|255697073|emb|CBA11646.1| RNA polymerase sigma factor [Pseudomonas syringae pv. berberidis]
 gi|255697091|emb|CBA11655.1| RNA polymerase sigma factor [Pseudomonas syringae pv. delphinii]
 gi|255697103|emb|CBA11662.1| RNA polymerase sigma factor [Pseudomonas syringae pv. lachrymans]
 gi|255697107|emb|CBA11664.1| RNA polymerase sigma factor [Pseudomonas syringae pv. maculicola]
 gi|255697113|emb|CBA11667.1| RNA polymerase sigma factor [Pseudomonas syringae pv. morsprunorum]
 gi|255697141|emb|CBA11682.1| RNA polymerase sigma factor [Pseudomonas syringae pv. spinaceae]
 gi|255697151|emb|CBA11687.1| RNA polymerase sigma factor [Pseudomonas syringae pv. tomato]
 gi|255697155|emb|CBA11689.1| RNA polymerase sigma factor [Pseudomonas syringae pv. viburni]
          Length = 192

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 28/231 (12%), Positives = 66/231 (28%), Gaps = 46/231 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 51  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W  
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTD 187


>gi|255697101|emb|CBA11661.1| RNA polymerase sigma factor [Pseudomonas syringae pv. japonica]
          Length = 192

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 66/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAAKAE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    + D  +    P  A+     + +  + +   L      
Sbjct: 60  GADDDEE--------ESADASDEKDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 106 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|160902849|ref|YP_001568430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
 gi|160360493|gb|ABX32107.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
          Length = 231

 Score = 84.9 bits (208), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 88/204 (43%), Gaps = 9/204 (4%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
           + ++  DLIQEG IGL+++ ++++   G  F TYA+  +K ++   +       +    +
Sbjct: 31  KNIELEDLIQEGIIGLLQSYKRYNPEKGTSFYTYALKRIKGSMYDYLRRIDWLPKDVRSL 90

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             K   +        N+   + +  E        V+ ++  L   ++ + L+    + + 
Sbjct: 91  VKKYEDL--IYECKDNEYIDDNSVAEKLHIEKNDVDKIKFSLSK-RQILQLDEYFLNNEE 147

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
               + I+++N    L    +  L +  T  +  L  RE+ +L + +  G     T +E+
Sbjct: 148 DTWLEDIQEENDPEILAY--KDMLHDKLTESIEKLEEREKLILSLYYNEG----LTFKEI 201

Query: 646 GKQFCVTRERIRQIEAKAIRKLKH 669
           G    ++  R+ Q+ +  + KLK 
Sbjct: 202 GSVLEISESRVSQLHSVILVKLKK 225


>gi|254255074|ref|ZP_04948391.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
 gi|124899719|gb|EAY71562.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
          Length = 241

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 99/252 (39%), Gaps = 19/252 (7%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            T I+ +E+ ++                      ++ V+     +   G+   DL Q G 
Sbjct: 1   MTSITFTEYENVQRACNGMLPRGEAHWIAEYAPLVKRVVGKLAGHGAAGIDRDDLEQIGI 60

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           +GL++A  ++       F+ YA+  ++ A+   +  Q      P   R   H++    R 
Sbjct: 61  MGLLEALRRY-GEPDDAFANYAVVRIRGAVLDELRRQDW---RPRTARQGAHRLRSCERA 116

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKN 596
           + +K+ REP  ++I   L +      +++      E +SL+  I             D  
Sbjct: 117 LRSKLGREPGKDDICAALGIDGVEYDRIMLDDSANELMSLDELINAHG---------DVP 167

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             +      Q   R    + L  L  RE+RV+++ +      D TL E+G    +T  RI
Sbjct: 168 GEAQAGPEAQVLARRGIEQALLVLDEREQRVIQLYYEF----DLTLPEIGAVLNLTTARI 223

Query: 657 RQIEAKAIRKLK 668
            Q+   A++K++
Sbjct: 224 CQLHRGALKKMR 235


>gi|239934384|emb|CAR92322.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 221

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/266 (13%), Positives = 86/266 (32%), Gaps = 46/266 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKA--------------- 96

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 97  --------------------LKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFR 428
            + I++ + ++  +  E  + I++ +
Sbjct: 196 KEDIVRCQQKLIELEQECDLVIADIK 221


>gi|312134671|ref|YP_004002009.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774722|gb|ADQ04209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 244

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 95/251 (37%), Gaps = 58/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +          KK ++E NLRLV+ +A+++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYRI--HYQGEEELKKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +             R+   K+         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLR------------RNSNKKLE-------- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +   +  
Sbjct: 141 --------------------------------LSIDEPLNVDWDGNELLLSDVLG-TDTE 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +       +E   + +  L  RE++++ +RFG G   + T +EV     +++  I +
Sbjct: 168 EIYNRIESNVEKEALLQAIQKLPSREKKIVELRFGFGDEGEKTQKEVADMLGISQSYISR 227

Query: 659 IEAKAIRKLKH 669
           +E K I +LK 
Sbjct: 228 LEKKIITRLKK 238


>gi|298112131|gb|ADI58450.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
          Length = 190

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 73/235 (31%), Gaps = 46/235 (19%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++     +      L ++  L   I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGI 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K   +    + ++        ESA    ++D  +    P  A      
Sbjct: 59  APPAEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVIAAQRFGA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +  + +   L  +  + +  +   +                                 
Sbjct: 111 VSDQMEITRKALKKLGREDKHAIAEMV--------------------------------- 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
              L +L   + L   + + LVE++     R+   E  +++L      + R  FL
Sbjct: 138 --ALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRADFL 190


>gi|51893096|ref|YP_075787.1| sporulation sigma factor SigK [Symbiobacterium thermophilum IAM
           14863]
 gi|51856785|dbj|BAD40943.1| RNA polymerase sigma factor similar to B. subtilis SigK
           [Symbiobacterium thermophilum IAM 14863]
          Length = 236

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 90/254 (35%), Gaps = 61/254 (24%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               +S  E    +S ++        A+  ++E NLRLV  + KK+ N G    DLI  G
Sbjct: 29  FPQPLSEEEEAKYLSRLQ---NGDEEARAVLIERNLRLVAHIVKKFDNTGEDVDDLISIG 85

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            +GL+KA   F    G + +TYA   ++  I   +                         
Sbjct: 86  TVGLIKAIGTFKPERGTRLATYAARCIENEILMHLRS----------------------- 122

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI-E 593
                                        LK  +  +SL  PIG +       L D +  
Sbjct: 123 -----------------------------LKRVRGEVSLYDPIGVDREGNEITLIDVLGS 153

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           D + V  L        +      L  L  +E +VL +R+GI      T  E+ +   ++R
Sbjct: 154 DPDVVPDLVGKRLDESK--LREKLKKLGGKERQVLELRYGIAGGPRKTQREIARMLGISR 211

Query: 654 ERIRQIEAKAIRKL 667
             + +IE KA+ KL
Sbjct: 212 SYVSRIEKKAVMKL 225


>gi|255697053|emb|CBA11636.1| RNA polymerase sigma factor [Pseudomonas syringae pv. aceris]
 gi|255697119|emb|CBA11670.1| RNA polymerase sigma factor [Pseudomonas syringae pv. papulans]
 gi|255697139|emb|CBA11681.1| RNA polymerase sigma factor [Pseudomonas syringae pv. solidagae]
          Length = 192

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    ++D  +    P  A+     + +  + +   L      
Sbjct: 60  GADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 106 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|224553536|gb|ACN55006.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553538|gb|ACN55007.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553540|gb|ACN55008.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553542|gb|ACN55009.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553546|gb|ACN55011.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553548|gb|ACN55012.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553550|gb|ACN55013.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553552|gb|ACN55014.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553554|gb|ACN55015.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553556|gb|ACN55016.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553558|gb|ACN55017.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553560|gb|ACN55018.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553562|gb|ACN55019.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553564|gb|ACN55020.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553566|gb|ACN55021.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553568|gb|ACN55022.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553570|gb|ACN55023.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553572|gb|ACN55024.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553574|gb|ACN55025.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553576|gb|ACN55026.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553578|gb|ACN55027.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553580|gb|ACN55028.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553582|gb|ACN55029.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553584|gb|ACN55030.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553586|gb|ACN55031.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553588|gb|ACN55032.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553594|gb|ACN55035.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553596|gb|ACN55036.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553598|gb|ACN55037.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553600|gb|ACN55038.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553602|gb|ACN55039.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553604|gb|ACN55040.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553608|gb|ACN55042.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553610|gb|ACN55043.1| RNA polymerase sigma factor [Escherichia coli ETEC H10407]
 gi|224553612|gb|ACN55044.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553614|gb|ACN55045.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553616|gb|ACN55046.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 52/111 (46%), Positives = 84/111 (75%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|149184196|ref|ZP_01862514.1| sigma 28 (Flagella/Sporulation) [Erythrobacter sp. SD-21]
 gi|148831516|gb|EDL49949.1| sigma 28 (Flagella/Sporulation) [Erythrobacter sp. SD-21]
          Length = 241

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 94/227 (41%), Gaps = 17/227 (7%)

Query: 446 KEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E +   L +V  +A  Y       +   DL+Q G I L + A++ +      F+ YA  
Sbjct: 19  NERIGKFLPMVRKLAWYYESSCGSSIDVDDLLQAGMIALTECAQRHERPSEDGFAAYAKM 78

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+ A+   +   S  +R    +R K+         +  +  R+P+ +E+A  L M  E 
Sbjct: 79  RVRGAMIDLLRSNSHHVRGAAALRRKMDA---ATDELRRQFGRDPSGDEVALFLGMTPED 135

Query: 563 VRKVLKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +K         + L+    D D +      E+ +A   L +      +    + +A+L 
Sbjct: 136 YQKARNRVATRMVDLQDCYSDSDPAF---ATEEPDAEEQLVAQAD---KTALAQAIANLP 189

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R + V+++ F      +  L E+     V+  R+ Q++A A+ KLK
Sbjct: 190 ERLQLVIQLHFL----EELNLTEIAAVLEVSVPRVHQLKANALDKLK 232


>gi|219115846|ref|XP_002178718.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409485|gb|EEC49416.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 217

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 57/217 (26%), Positives = 109/217 (50%), Gaps = 17/217 (7%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           R    + ++A+  ++ +N+RLV+S+AKK+  N      + +QEG +GL KAA+++D   G
Sbjct: 1   RSILLDGALARDTLIASNVRLVVSIAKKWAKNAHKAARETVQEGILGLAKAADRYDPERG 60

Query: 494 YKFSTYAMWWVKQAITRSIADQS-CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
            +F+TYA +WV  ++       S   +R+PV   D   K  R  +   ++    P  +++
Sbjct: 61  LRFATYATYWVTNSVRFCFQTASTGCLRVPVGFHDTKTKFKRLVKEYYDEFGDAPGIDDL 120

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--------------LGDFIEDKNAV 598
           A+++ +    +  +L+ T+  +S++ P+     +               L D + D+ A+
Sbjct: 121 AEQMGLTRPRLEVILRSTRPLVSIDAPLRTGAVTQAGKAGNDVSQTNLLLADLLTDEQAL 180

Query: 599 SPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGI 634
            P D    + LR+     +A+ L P E  VLR+R G+
Sbjct: 181 PPEDLVELSFLRQNLENAMATELAPHERDVLRLRLGL 217


>gi|258515964|ref|YP_003192186.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779669|gb|ACV63563.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 234

 Score = 84.5 bits (207), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 98/265 (36%), Gaps = 53/265 (20%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           V+ +L + + I + +    +S  E    + ++         A+  + E NLRLV  + KK
Sbjct: 14  VNGLLLLVSYIANNTFPQPLSEEEEAKYLQLL---FEGDEHARNVLTERNLRLVAHIVKK 70

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +        DLI  G IGL+KA   ++   G K +TYA   ++  I   +          
Sbjct: 71  FDKTVGDTDDLISIGTIGLIKAVNTYNPEKGTKLATYAARCIENEILMHLRFM------- 123

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
                   K VR    + + I  +    EI                              
Sbjct: 124 --------KKVRAEVSLYDPIGVDKEGNEI------------------------------ 145

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                L D +   + V   +    +  ++     +  L+ RE++VL +RFG+      T 
Sbjct: 146 ----TLIDILGTHSEV-VAEIVENSFEQKRLGDKVKLLSRREKKVLELRFGLEGRQRKTQ 200

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
            E+ K   ++R  + +IE +A+ KL
Sbjct: 201 REIAKFLGISRSYVSRIEKRALTKL 225


>gi|332272435|gb|AEE38901.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|332272437|gb|AEE38902.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|332272439|gb|AEE38903.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
 gi|332272441|gb|AEE38904.1| RNA polymerase sigma-70 factor [Aeromonas jandaei]
          Length = 219

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 81/262 (30%), Gaps = 44/262 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                           
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN-------------------------- 32

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
                   D E  A  +    S++       E+++ + DEDED                 
Sbjct: 33  --------DTEDMAPTATHIGSELSEDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVA 84

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                E+   Y          ++ QK+ ++    +    +L  +     L   + D LV 
Sbjct: 85  REKFAELRAQYEV------TRLSIQKNGRAHDDTQAAIAQLADVFRQFRLMPKQFDRLVN 138

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +  W   +
Sbjct: 139 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKA-WSPRL 197

Query: 400 ACEVDSILKIRNEIKSISVETG 421
               + + +   +++ I  ETG
Sbjct: 198 MEMDEEVQRAIGKLQQIEEETG 219


>gi|331090616|ref|ZP_08339467.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401056|gb|EGG80651.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 246

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 94/236 (39%), Gaps = 58/236 (24%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
               +AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +T
Sbjct: 58  ETDDVAKKTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPMKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                                              
Sbjct: 118 YASRCIENEILMYLRRN------------------------------------------- 134

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTR 615
                      T+  +S++ P+  +   +   L D +  +      D   +   R+   +
Sbjct: 135 ---------NKTRLEVSIDEPLNVDWDGNELLLSDILGTEEDTIYRDLETEVE-RKLLMK 184

Query: 616 VLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +  L+ RE+ +++MRFGIG     + T +EV     +++  I ++E K +++LK 
Sbjct: 185 AINRLSSREKTIVQMRFGIGTKDGEEKTQKEVADILGISQSYISRLEKKIMQRLKR 240


>gi|319937135|ref|ZP_08011542.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807501|gb|EFW04094.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 230

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 97/246 (39%), Gaps = 57/246 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAE 486
           +     + K +   + A+  ++E NLRLV+ VAKKY + +     DLI  G IGL+KA  
Sbjct: 32  KEEADALVKLQQGDAQARDLLIEHNLRLVVYVAKKYDSVQNGSIEDLISIGTIGLVKAVN 91

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            F      K +TYA   ++  I                        +R   ++  +    
Sbjct: 92  TFKMDKNIKLATYASRCIENEILMF---------------------LRKNNKLRQE---- 126

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDS 603
                                      ISL+ P+  +   +   L D I     +   D 
Sbjct: 127 ---------------------------ISLDEPLNVDYDGNELLLSDIIGTDKDI-VQDE 158

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               + +E   R L  L  RE+ +L MR+G+  + + T ++V +   +++  I ++E K 
Sbjct: 159 IEHNDQKEKFYRALHHLNEREQEILMMRYGLVGHDELTQKDVAEVLGISQSYISRLEKKI 218

Query: 664 IRKLKH 669
           I+KL++
Sbjct: 219 IKKLRN 224


>gi|261366886|ref|ZP_05979769.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282571000|gb|EFB76535.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 237

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 87/229 (37%), Gaps = 56/229 (24%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A+  ++  NLRLV+ +AKK+        D+I  G IGL+KA   F+     K +TYA   
Sbjct: 56  ARDLLITHNLRLVVYIAKKFETPSAGIEDMISIGTIGLIKAVNTFEPSKNIKLATYASRC 115

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +   S   +                                           
Sbjct: 116 IENEILMYLRKSSNRRQ------------------------------------------- 132

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                      S++ P+  ++  +   L D +   +     +   ++  R      +  L
Sbjct: 133 ---------DASIDEPLNTDNDGNELLLMDVLT-SDQPQVGEELERSAERAALRLAVGRL 182

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            PRE R++ +RFG+   ++HT +EV     +++  I ++E + I++L+ 
Sbjct: 183 APRERRIMELRFGLNHESEHTQKEVADALGISQSYISRLEKRIIKRLRR 231


>gi|255697039|emb|CBA11629.1| RNA polymerase sigma factor [Pseudomonas ficuserectae]
          Length = 192

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 28/235 (11%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S D+      P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + L+E++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLLERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|295109522|emb|CBL23475.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus obeum A2-162]
          Length = 243

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 93/234 (39%), Gaps = 60/234 (25%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A+  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA 
Sbjct: 58  QEARSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNIKLATYAS 117

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++  I   +   S                                             
Sbjct: 118 RCIENEILMYLRRNSK-------------------------------------------- 133

Query: 562 GVRKVLKITKEPISLETPIGDEDTSH---LGDFIE-DKNAVSPLDSAIQANLRETTTRVL 617
                   TK  +S++ P+  +   +   L D +  D++ +S               + +
Sbjct: 134 --------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDVISRRMEDEVEIT--LLAKAI 183

Query: 618 ASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             L+PRE+ ++R+RFG+      + T +EV     +++  I ++E + +++LK 
Sbjct: 184 NKLSPREQTIIRLRFGLNNAEGKEKTQKEVADLLGISQSYISRLEKRIMKRLKK 237


>gi|293400805|ref|ZP_06644950.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305831|gb|EFE47075.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 247

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 91/259 (35%), Gaps = 58/259 (22%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+S S    +   E  H    +     +    + +++E NLRLV  + KKY  +  Q  
Sbjct: 21  YIRSNSFLQPLDKEEEAH---CIAGLSLQDEECRNKLIEHNLRLVAHIVKKYDIKKEQTE 77

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+KA + F    G+K +TYA   ++  I   +       +           
Sbjct: 78  DLISIGTIGLIKAIDSFKPEKGHKLTTYASRCIENEILMYLRSSKNYFQN---------- 127

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---L 588
                                                     +SL  PI  +       L
Sbjct: 128 ------------------------------------------VSLNDPIATDKDGSEITL 145

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I      S ++  +  +      + L  L  RE  ++  RFG+    + T  E+ KQ
Sbjct: 146 IDAISSPQETSIIEDMVVEDNISKLKQFLHVLDSRELEIITKRFGLYGVEEETQREIAKQ 205

Query: 649 FCVTRERIRQIEAKAIRKL 667
             ++R  + +IE +A  KL
Sbjct: 206 LHISRSYVSRIEKRAFMKL 224


>gi|239934414|emb|CAR92337.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 204

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 73/250 (29%), Gaps = 47/250 (18%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++   D +      L ++  L   I P+                            
Sbjct: 1   TVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAP---------------------- 36

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +E       AA   ++   + +      + +E     D   +A    A+ +Q       
Sbjct: 37  TEEVPIPGTKAAAAKEESDDEEEESEGGDDEEEAESGPDPVVAAQRFGAVSEQ------- 89

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                         LQ      +K+ ++  +     + L  L   + L   + ++LVE++
Sbjct: 90  --------------LQATTKVLKKNGRTHKESVEALQALADLFMPIKLVPKQFEVLVERV 135

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL      E D  W           W   +  
Sbjct: 136 RDALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGE 194

Query: 402 EVDSILKIRN 411
           +  +I+  + 
Sbjct: 195 KDAAIVACQQ 204


>gi|167767678|ref|ZP_02439731.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|167710695|gb|EDS21274.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|291560812|emb|CBL39612.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SSC/2]
          Length = 240

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 96/253 (37%), Gaps = 54/253 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +  +E + ++ M+  G      A+  ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 32  PAPLDTAEEQKMIHML--GTVNEETARSMLIERNLRLVVYIAKKFDNTGIGVEDLISIGT 89

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F+     K +TYA   ++  I   +                          
Sbjct: 90  IGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRN----------------------- 126

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK K E + +E                            +  +    L   I   +  
Sbjct: 127 --NKTKMEVSIDEP-------------------------LNVDWDGNELLLSDILGTDED 159

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERI 656
                      ++  TR +  LT RE+ ++ +RFGI      + T +EV     +++  I
Sbjct: 160 IIYKDLEHEVDKKLLTRAMTILTDREKMIIELRFGINQKEGKEKTQKEVADMLGISQSYI 219

Query: 657 RQIEAKAIRKLKH 669
            ++E K I++LK 
Sbjct: 220 SRLEKKIIKRLKR 232


>gi|332294870|ref|YP_004436793.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermodesulfobium
           narugense DSM 14796]
 gi|332177973|gb|AEE13662.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermodesulfobium
           narugense DSM 14796]
          Length = 223

 Score = 84.5 bits (207), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 92/239 (38%), Gaps = 33/239 (13%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
            ++         +  +    L LV  +A K        ++F +L+  G  GL+ + E+F+
Sbjct: 8   WIKYRNNSTQENRNLLALNYLPLVKRIAAKIYTTIQGKVEFEELLNYGIFGLLTSIERFE 67

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                KF T+A   ++ AI   +        +    R K+ K+ R    + + + ++P+ 
Sbjct: 68  ESRNLKFETFATHRIRGAILDGLRQID---PLKRGTRSKVKKIDRAINELKSSLGKDPSD 124

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           +++A  L +  E +        + +S       +      D                   
Sbjct: 125 KDVADYLNITKEELLNW-YAEIDALSTFQSDFSDSEKSYID------------------- 164

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  +  L  RE++V+ + +      D +L+E+ K   ++  R+ QI  KA+ KLK
Sbjct: 165 ---LSMAIEKLEEREKQVIDLYY----YEDLSLDEIAKILNISVSRVSQIHGKALIKLK 216


>gi|296133648|ref|YP_003640895.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032226|gb|ADG82994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 242

 Score = 84.1 bits (206), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 93/244 (38%), Gaps = 56/244 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
               ++ K     +  +  ++E NLRLV+ +A+K+ N G+   DL+  G IGL+KA   F
Sbjct: 46  EENYLISKLATGDAAVRSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTF 105

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D     K +TYA   ++  I   +                                    
Sbjct: 106 DPAKKIKLATYASRCIENEILMYLRRN--------------------------------- 132

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAI 605
                                T+  +S + PI  +   +   L D +  ++ +       
Sbjct: 133 -------------------NKTRAEVSFDEPINIDWDGNELLLSDVMGTESDIIYKFIEE 173

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           + + R+     L  L  RE R++ +RFG+   T+ T +EV     +++  I ++E + ++
Sbjct: 174 EVD-RKLLALALQKLNGRERRIMELRFGLIDGTEKTQKEVADMLGISQSYISRLEKRILK 232

Query: 666 KLKH 669
           +L+ 
Sbjct: 233 RLRK 236


>gi|283797733|ref|ZP_06346886.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291074630|gb|EFE11994.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
          Length = 205

 Score = 84.1 bits (206), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 92/252 (36%), Gaps = 58/252 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R  +   R        AK  ++E NLRLV  V KKY     +  DL+  G IGL
Sbjct: 8   LTAEEEREYLKRCR---EGDEEAKAVLIERNLRLVAHVIKKYQYTDYETEDLLSVGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F    G + +TYA   V+  I                       + R  ++ + 
Sbjct: 65  IKAVNTFKAEKGSRLATYAAKCVENEILM---------------------LFRAGKKRA- 102

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +SL   IG +       L D +E +   
Sbjct: 103 ------------------------------RDVSLYDSIGVDKDGETVSLMDVLEAEETQ 132

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                 ++ ++RE        L   E++V+ MR+G+    +HT  E+     ++R  + +
Sbjct: 133 VLDTIIMEQDVRELYEAYAKCLKDMEKKVVCMRYGLFGTKEHTQREIAAVLGISRSYVSR 192

Query: 659 IEAKAIRKLKHP 670
           IE KAI KL+  
Sbjct: 193 IEKKAIEKLREA 204


>gi|256751991|ref|ZP_05492860.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749101|gb|EEU62136.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 236

 Score = 84.1 bits (206), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 93/240 (38%), Gaps = 59/240 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S+ E  +++S + K     + AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL
Sbjct: 41  LSVEEEMYLISKMEK---GDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F+     K +TYA   ++  I   +   S                         
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSK------------------------ 133

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                       TK  +S E P+  +   +   L D +   N  
Sbjct: 134 ----------------------------TKLEVSFEEPLNVDWDGNELLLSDILGTDN-E 164

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +          +E  T  L  L  RE++++ +RFG+G   + T +EV     +++  I +
Sbjct: 165 TVYKYIEDEVEKELLTSALKKLPDREKKIIGLRFGLGGGVEKTQKEVADMLGISQSYISR 224


>gi|317133668|ref|YP_004092982.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
 gi|315471647|gb|ADU28251.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
          Length = 228

 Score = 84.1 bits (206), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 91/253 (35%), Gaps = 56/253 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ +E R  ++ ++      + A+  ++E NLRLV+ + KKY        DL+  
Sbjct: 25  SFPKPLTAAEERECLARMQ---AGDTKAQDMLIEHNLRLVMHIIKKYYANARDQEDLLSV 81

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K    F    G + +TYA   ++  I                            
Sbjct: 82  GTIGLIKGVITFKPEKGTRLATYAARCIENEILMHFRS---------------------- 119

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                                          K + + + +  PI  +   +    ++  +
Sbjct: 120 ------------------------------QKKSAQDVYISDPIDTDKDGNQLTLMDVVS 149

Query: 597 AVSPLDSAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               +   +   ++ E     +  L PRE  ++ MR+G+      T  EV  +  ++R  
Sbjct: 150 CEDTILDDVDLKMKSEKLRAYIVKLPPRERAIIEMRYGLHGAKPQTQREVAGKLNISRSY 209

Query: 656 IRQIEAKAIRKLK 668
           + +IE +A+ +L+
Sbjct: 210 VSRIEKRALGELR 222


>gi|224553590|gb|ACN55033.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 84.1 bits (206), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 52/111 (46%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G+ FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFCFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|146295966|ref|YP_001179737.1| sporulation sigma factor SigE [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409542|gb|ABP66546.1| RNA polymerase, sigma 29 subunit, SigE [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 246

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 97/251 (38%), Gaps = 58/251 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I++ +          KK +VE NLRLV+ +A+K+ N  +   DL+  G IGL
Sbjct: 45  LTPEEESEILNKI--HYERREELKKVLVERNLRLVVYIARKFENTKINLEDLVSIGTIGL 102

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +             R+   K+         
Sbjct: 103 IKAINTYNPDKNIKLATYASKCIENEILMFLR------------RNSHRKLE-------- 142

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +   ++ 
Sbjct: 143 --------------------------------LSIDEPLNVDWDGNELLLSDVLG-TDSE 169

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               S   +  +E   + +  L  RE+R++ +RFG     + T +EV     +++  I +
Sbjct: 170 GVYSSIESSVEKEALLKAIQKLPKREKRIVELRFGFSDEGEKTQKEVADMLGISQSYISR 229

Query: 659 IEAKAIRKLKH 669
           +E K I +LK 
Sbjct: 230 LEKKIITRLKK 240


>gi|298112119|gb|ADI58444.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
 gi|298112125|gb|ADI58447.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
          Length = 190

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 71/235 (30%), Gaps = 46/235 (19%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++     +      L ++      I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--FSGYIDPDDGI 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K   +    + ++        ESA    ++D  +    P  A      
Sbjct: 59  APPVEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVIAAQRFGA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +  + +   L     + +  +   +                                 
Sbjct: 111 VSDQMEITRKALKKFGREDKHAIAEMV--------------------------------- 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
              L +L   + L   + + LVE++     R+   E  +++L      + R  FL
Sbjct: 138 --ALAELFMPIKLVPKQFEGLVERVRGAFDRLRAQERAIMQLCVRDARMPRADFL 190


>gi|255697055|emb|CBA11637.1| RNA polymerase sigma factor [Pseudomonas syringae pv. actinidiae]
 gi|255697149|emb|CBA11686.1| RNA polymerase sigma factor [Pseudomonas syringae pv. theae]
          Length = 192

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 28/231 (12%), Positives = 66/231 (28%), Gaps = 46/231 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 51  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W  
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTD 187


>gi|291280645|ref|YP_003497479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Deferribacter
           desulfuricans SSM1]
 gi|290755347|dbj|BAI81723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Deferribacter
           desulfuricans SSM1]
          Length = 255

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 47/207 (22%), Positives = 95/207 (45%), Gaps = 12/207 (5%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            +   ++      G ++A  ++D      F  +    VK AI   +        +    R
Sbjct: 50  HIDIDEVYSAACYGFVEALNRYDPSQNIDFKYFVEKRVKGAILDVLRRL---DLLSRTKR 106

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETPIGDED 584
            K+  +    + +S ++ R+PTPEEIA+K  +  E +  +L+++     ISL T +  +D
Sbjct: 107 TKLKDLENKIQTLSKELGRQPTPEEIAEKYGIDTEEIYNLLELSDKTHIISLNTLLDKDD 166

Query: 585 TS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                L DFI+  + ++P +   +  L +   + + +L  +E  V+ + +      + T+
Sbjct: 167 NEGHSLIDFIK-SDLLTPEEQVSKQELIDILQKEIENLKEKERLVITLYY----YEELTM 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E+G+   VT  R+ QI  K + +LK 
Sbjct: 222 KEIGEILGVTEARVCQIHNKVVEQLKE 248


>gi|149191506|ref|ZP_01869755.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148834694|gb|EDL51682.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 125

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 32/106 (30%), Positives = 57/106 (53%), Gaps = 2/106 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL   
Sbjct: 19  YIRSVNSYPMLTADEERELAERLHYDGEI--EAAKGLILSHLRFVVHVARGYSGYGLPMA 76

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   +     
Sbjct: 77  DLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122


>gi|126215794|gb|ABN81017.1| putative sigma factor sigma 70 type group 3 [Rhodococcus opacus]
          Length = 139

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 33/114 (28%), Positives = 61/114 (53%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           EAS+ + E++   L L   +A+++  RG    DL Q   +GL+KA ++FD   G+ F +Y
Sbjct: 25  EASVLRDEVITRCLPLADHIARRFGGRGEAHEDLRQVARLGLVKAVDRFDPDRGFDFVSY 84

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           A+  +   + R   D   ++R+P  M++    + +    +S ++ R P+  EIA
Sbjct: 85  AVPTIMGEVRRYFRDTGWSMRVPRRMQELHALITKAVDDLSQELGRSPSASEIA 138


>gi|298112117|gb|ADI58443.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
 gi|298112127|gb|ADI58448.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
          Length = 190

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 72/235 (30%), Gaps = 46/235 (19%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++     +      L ++      I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--FSGYIDPDDGI 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K   +    + ++        ESA    ++D  +    P  A      
Sbjct: 59  APPAEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVIAAQRFGA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +  + +   L  +  + +  +   +                                 
Sbjct: 111 VSDQMEITRKALKKLGREDKHAIAEMV--------------------------------- 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
              L +L   + L   + + LVE++     R+   E  +++L      + R  FL
Sbjct: 138 --ALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRADFL 190


>gi|291524907|emb|CBK90494.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           DSM 17629]
          Length = 230

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 100/268 (37%), Gaps = 55/268 (20%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I+  +  +    V T +S          ++K       AK E++  N+RLV  V KKY 
Sbjct: 12  NIIYYKQIMTGCYVNTFLSPLSLERETECLKKVAQNDKEAKDELILHNMRLVAHVTKKYA 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
               +  +LI  G IGL+KA   F    G +F+T+A+  ++  I                
Sbjct: 72  VSEDEMEELISIGTIGLIKAVSSFKADYGNRFATFAIRCIENEILMHFRS---------- 121

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                                                      K ++  +S+  PIG + 
Sbjct: 122 ------------------------------------------RKKSRGDVSIFDPIGTDK 139

Query: 585 TS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                HL D IE+  +    D  +  +L+     + + L+ RE  ++  RFG+    + T
Sbjct: 140 EGNQIHLVDVIENGQSDVVSDIEVSESLKILRQNMRSVLSDREYYIITKRFGLDGEKELT 199

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ K   ++R  + +IE   ++KL+ 
Sbjct: 200 QRQIAKTLSISRSYVSRIEKAGLKKLRK 227


>gi|317063374|ref|ZP_07927859.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689050|gb|EFS25885.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 151

 Score = 84.1 bits (206), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 44/139 (31%), Positives = 74/139 (53%), Gaps = 2/139 (1%)

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +KV R            P+ EEIA +L +  + V+ ++   ++P+SL T IG  D  +L 
Sbjct: 3   NKVNRYVMSRLKDEGNYPSVEEIAAELNIEADKVQDIIMDFQDPMSLSTQIG--DDIYLE 60

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D +  +   S  +       R+    ++  L  RE+ +L++R+G+     HTLEE+G   
Sbjct: 61  DTLAQQEDFSMEEEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIHTLEEIGNTL 120

Query: 650 CVTRERIRQIEAKAIRKLK 668
            +TRER+RQIE K ++KL+
Sbjct: 121 NITRERVRQIEKKTLQKLR 139


>gi|298112123|gb|ADI58446.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
          Length = 190

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 73/235 (31%), Gaps = 46/235 (19%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++     +      L ++      I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--FSGYIDPDDGI 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K   +    + ++        ESA    ++D  +    P  A      
Sbjct: 59  APPAEVPPPVDPKAAKAEGTDDDEE--------ESADASDEEDEVESGPDPVVAAQRFGA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +  + +   L  +  + +  +   +                                 
Sbjct: 111 VSDQMEITRKALKKLGREDKHAIAEMV--------------------------------- 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
              L +L   + L   + + LVE++    +R+   E  +++L      + R  FL
Sbjct: 138 --ALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFL 190


>gi|294013075|ref|YP_003546535.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
 gi|292676405|dbj|BAI97923.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
          Length = 245

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 49/229 (21%), Positives = 94/229 (41%), Gaps = 15/229 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
            +    + LV  +A     R    ++  DL+Q G + L++AA  F+   G  F++YA   
Sbjct: 26  RLARQYMPLVRKIAWHVHGRVSSAIEIEDLLQIGMVALVEAANGFE-DRGLGFASYAQMR 84

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+ A+   +   +   R  +  R    ++     R+  ++ R P   E++ ++ +     
Sbjct: 85  VRGAMIDHLRRHATMTRSAMSQRK---QLAAIRNRLEQRLGRAPLEAEMSAEMGLDAAAY 141

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V    +            D S     +ED+      D   + +L+    + +  L  R
Sbjct: 142 REVADGCEMVQHTSMDEVYSDQSMWFADVEDR----ADDIMERESLKGALAQYIGELPQR 197

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           E  VL++ F      +  LEE+G    +   R+ QI+  A+ KL+   R
Sbjct: 198 EALVLQLYFV----EELNLEEIGATLDIGAARVCQIKKAALDKLREKLR 242


>gi|239934378|emb|CAR92319.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 222

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 26/203 (12%), Positives = 72/203 (35%), Gaps = 8/203 (3%)

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
              +  A   ++   +          D+++ +E++D  +                    +
Sbjct: 27  DPDDDGAAAPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAV 86

Query: 288 AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347
           AE   +           +K  ++S +     E    L+  + L   + D LVE++ +   
Sbjct: 87  AEQLEKANK------ALKKHGRASQQAVEELEAPAILLMPIKLVPKQYDALVERVRNALS 140

Query: 348 RIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           +I   E  +++L      + R  FL +      +  W        +G++   +    + I
Sbjct: 141 QIRAQERAIMQLCVRDARMPRADFLRQFPNNGTNLDWAEQLAS-GKGKYAEAIGNRKEDI 199

Query: 407 LKIRNEIKSISVETGISISEFRH 429
           ++ + ++  +  E  ++I++ + 
Sbjct: 200 VRCQQKLIELEQECDLAIADIKD 222


>gi|289805024|ref|ZP_06535653.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 145

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 30/102 (29%), Positives = 54/102 (52%), Gaps = 2/102 (1%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            ++ ++LR V+ +A+ Y   GL   DLIQEGNIGLMKA  +F+  +G +  ++A+ W+K 
Sbjct: 40  RLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKA 99

Query: 507 AITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKRE 546
            I   +      +++      R     + +T +R+    + E
Sbjct: 100 EIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE 141


>gi|269784262|emb|CBH50776.1| RNA polymerase sigma factor [Vibrio sp. Rd 16.13]
          Length = 127

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 48/126 (38%), Gaps = 2/126 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L +   R+   E  ++R    YG + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +      I +   ++  I  ET +++   + I   +  GE 
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDISRRMSIGEA 120

Query: 440 EASIAK 445
           +A  AK
Sbjct: 121 KARRAK 126


>gi|239934382|emb|CAR92321.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 220

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 38/265 (14%), Positives = 87/265 (32%), Gaps = 46/265 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E    L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEAHAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      I R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARIPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEF 427
            + I++ + ++  +  E  ++I++ 
Sbjct: 196 KEDIVRCQQKLIELEQECDLAIADI 220


>gi|239934392|emb|CAR92326.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 224

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 36/266 (13%), Positives = 86/266 (32%), Gaps = 46/266 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPEAPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKA--------------- 96

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++  +     E L  L   + L   + D LVE++ 
Sbjct: 97  --------------------LKKHGRAGQQAVEELEALAILFMPIKLAPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRNEIKSISVETGISISEFR 428
            ++I++ + ++  +  E  + I++ +
Sbjct: 196 KENIVRCQQKLIELEQECDLVIADIK 221


>gi|260589068|ref|ZP_05854981.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|331082498|ref|ZP_08331623.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540488|gb|EEX21057.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|330400476|gb|EGG80106.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 208

 Score = 84.1 bits (206), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 95/239 (39%), Gaps = 55/239 (23%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            +++ +     AK  ++E NLRLV  + KKY     +  DLI  G IGL+KA   FD   
Sbjct: 16  YLQEYKQGNLEAKNILIERNLRLVAHIVKKYQGAPEEMDDLISIGTIGLIKAIHTFDAQK 75

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             + STYA   +   +                       ++R+ ++              
Sbjct: 76  ASRLSTYAARCIDNELLM---------------------LLRSKKK-------------- 100

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANL 609
                            +   +SL  PIG +   +   L D IE +      + +++ ++
Sbjct: 101 -----------------SNREVSLYDPIGTDKEGNEISLLDIIETEPVDVVKNYSLKQDI 143

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 +   LT RE  ++++R+G+    + T  E+ K+  ++R  + +IE  AI KL+
Sbjct: 144 ARLYQLLPKVLTTREREIIKLRYGLYGEQELTQREIAKRLNISRSYVSRIEKNAILKLR 202


>gi|323486720|ref|ZP_08092041.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692141|ref|ZP_08106384.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323400101|gb|EGA92478.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503715|gb|EGB19534.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 246

 Score = 83.7 bits (205), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 95/253 (37%), Gaps = 54/253 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +   E   ++  +  G    + AK +++E NLRLV+ +AKK+ N  +   DLI  G+
Sbjct: 40  PAPLGSKEEAEVLKEL--GTERDAQAKSKLIEHNLRLVVYIAKKFDNTSVGVEDLISIGS 97

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F+     K +TYA   ++  I   +                          
Sbjct: 98  IGLIKAINTFNIDKNIKLATYASRCIENEILMYLRRN----------------------- 134

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK K E + +E                            +  +    L   I   +  
Sbjct: 135 --NKTKMEVSIDEP-------------------------LNVDWDGNELLLSDILGTDED 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERI 656
                      +      ++ L PRE++++ +RFG+G     + T +EV     +++  I
Sbjct: 168 VIYRDLEDEIEKSLLNTAISRLNPREQKIVELRFGLGTENEDEMTQKEVADLLGISQSYI 227

Query: 657 RQIEAKAIRKLKH 669
            ++E K +++LK 
Sbjct: 228 SRLEKKIMKRLKK 240


>gi|225389924|ref|ZP_03759648.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
 gi|225044004|gb|EEG54250.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
          Length = 223

 Score = 83.7 bits (205), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 90/253 (35%), Gaps = 54/253 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +   E   ++ M+     E   A+  ++E NLRLV+ +AKK+ N  +   DLI  G 
Sbjct: 17  PAPLEPEEESRMIGMLS--GEEDQKARAALIEHNLRLVVYIAKKFDNTSVGVEDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F      K +TYA   ++  I   +                          
Sbjct: 75  IGLIKAINTFKPDKNIKLATYASRCIENEILMYLRRN----------------------- 111

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK + E + +E                            +  +    L   I   +  
Sbjct: 112 --NKTRMEVSIDEP-------------------------LNVDWDGNELLLSDILGTDED 144

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI--GMNTDHTLEEVGKQFCVTRERI 656
                      +      ++ L PRE +++ +R+G+      + T +EV     +++  I
Sbjct: 145 VIYHDIEDEIEKNLLNNAISRLNPRERKIVELRYGLTNEDGEEMTQKEVADLLGISQSYI 204

Query: 657 RQIEAKAIRKLKH 669
            ++E K +++L+ 
Sbjct: 205 SRLEKKIMKRLRK 217


>gi|218133504|ref|ZP_03462308.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990879|gb|EEC56885.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
          Length = 238

 Score = 83.7 bits (205), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 83/234 (35%), Gaps = 58/234 (24%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
                  A  A+  ++E NLRLV+ +AK++ N G+   DLI  G IGL+KA   ++    
Sbjct: 53  ADMQGEYAEQARSVLIEHNLRLVVYIAKRFDNTGIGVEDLISIGTIGLIKAIHSYNPDKS 112

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K +TYA   ++  I   +   S                                     
Sbjct: 113 IKLATYASRCIENEILMYLRRNSK------------------------------------ 136

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR 610
                           TK  +S++ P+  +   +   L D +     V           R
Sbjct: 137 ----------------TKAEVSIDEPLNVDWDGNELLLSDILGTDEDV-IYKDIENQAER 179

Query: 611 ETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAK 662
               + +  L+ RE  ++ +R+G+      + T +EV     +++  I ++E K
Sbjct: 180 LMLGKAMEKLSDRERLIVNLRYGLTSPDEREMTQKEVADYLGISQSYISRLEKK 233


>gi|149917001|ref|ZP_01905502.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
 gi|149822279|gb|EDM81670.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
          Length = 411

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 66/254 (25%), Positives = 116/254 (45%), Gaps = 19/254 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           VR         ++ +   +LRLVIS+  +Y  + + F   +  G +GL KA ++F+   G
Sbjct: 151 VRAMLDRILATRRRLFADSLRLVISLVHRYR-KHMDFATGMLRGALGLDKAIDRFEPERG 209

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           ++FSTYA WW++Q ITRS  D +  +R+PVH  ++  +     + + ++    PT EE+ 
Sbjct: 210 WQFSTYATWWIRQNITRSSMDFATALRVPVHAAEQTTRFWMVQQELWSQTGVRPTDEEVL 269

Query: 554 KKLA--MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD-SAIQANLR 610
            +      +E +    +  +        +   D     + I D +  S L+ +     +R
Sbjct: 270 NQANFKFSIERLGDYRRHART-----AHLTRRDQLGAAEAILDSDIPSLLEGNPASGWVR 324

Query: 611 ETTTRVLASLTPRE---------ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                  A +  +E           +   R       ++TL E+G++F +TRERIRQ EA
Sbjct: 325 AAIDHATAQVDDKEHSRPSRGRWHAIFSRRILGDQIQNNTLRELGEEFDITRERIRQNEA 384

Query: 662 KAIRKL-KHPSRSK 674
           K I  L +   R +
Sbjct: 385 KLIDFLARRLFRGQ 398


>gi|150021309|ref|YP_001306663.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
 gi|149793830|gb|ABR31278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
          Length = 226

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 102/228 (44%), Gaps = 12/228 (5%)

Query: 445 KKEMVEANLRLVISVAK---KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K+++++  L  +  +A    K     ++  DLIQEG IGL++A E+++   G K  +Y +
Sbjct: 4   KEKIIQEYLPYIKRIAYDLKKNLPHNIEIDDLIQEGLIGLLQAIERYNPKKGAKLRSYIL 63

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             VK A+   +       +   H      KVV  A        +     EI+K   +P+E
Sbjct: 64  TRVKGAMYDYLRKIDWMPKNLRH----DVKVVEDAISKMENSGKIIDFNEISKITNLPLE 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V++          L       +   + + I   +  +P ++A +  ++E   + +  L 
Sbjct: 120 NVKRAYNEMVRKQFLMLDDYLTEDLEINETISSSD-YTPEETAFKEIIKEELKKAINKLD 178

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +E+ +L +RF      + +L+E+GK   +T  R+ QI +  I KLK 
Sbjct: 179 EKEKIILNLRF----EHELSLKEIGKILNLTESRVSQILSSIILKLKK 222


>gi|238924178|ref|YP_002937694.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|238875853|gb|ACR75560.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|291529048|emb|CBK94634.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           M104/1]
          Length = 230

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 100/268 (37%), Gaps = 55/268 (20%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           +I+  +  +    V T +S          ++K       AK E++  N+RLV  V KKY 
Sbjct: 12  NIIYYKQIMTGCYVNTFLSPLSLERETECLKKVAQNDKEAKDELILHNMRLVAHVTKKYA 71

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
               +  +LI  G IGL+KA   F    G +F+T+A+  ++  I                
Sbjct: 72  VSEDEMEELISIGTIGLIKAVSSFKADYGNRFATFAIRCIENEILMHFRS---------- 121

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                                                      K ++  +S+  PIG + 
Sbjct: 122 ------------------------------------------RKKSRGDVSIFEPIGTDK 139

Query: 585 TS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                HL D IE+  +    D  +  +L+     + + L+ RE  ++  RFG+    + T
Sbjct: 140 EGNQIHLVDVIENGQSDVVSDIEVSESLKILRQNMRSVLSDREYYIITKRFGLDGEKELT 199

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ K   ++R  + +IE   ++KL+ 
Sbjct: 200 QRQIAKTLSISRSYVSRIEKAGLKKLRK 227


>gi|255697093|emb|CBA11656.1| RNA polymerase sigma factor [Pseudomonas syringae pv. dysoxyli]
          Length = 192

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 65/235 (27%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 59

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              +  +        ESA    + D  +    P  A+     + +  + +   L      
Sbjct: 60  GADDDKE--------ESADASDEKDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 105

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 106 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAEFLRQFPGNEVDESWTDALAK 191


>gi|262199287|ref|YP_003270496.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082634|gb|ACY18603.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 244

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 92/245 (37%), Gaps = 20/245 (8%)

Query: 429 HIVSMVRKGECEASI--AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            +    R+ +  A       E+++ ++ L +S+A++   R    +   D+     +GL +
Sbjct: 11  QVQERHRRVDAAARKREHCDELIKEHIELALSMARRMARRLPASVCLDDIESAALLGLTE 70

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           AA ++D      F  +A   ++ AI   +     +  +    R    +V   AR    + 
Sbjct: 71  AARRYDDKRREPFMGFAAKRIRGAILDQLR---RSDMLTRRGRRAARQVAEAARSFEGEH 127

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            R  T  E+A +L +  E        +      +  +   D     D I   +A +    
Sbjct: 128 GRPATDSELADQLGVSDEE-----FHSVYASVRDVTVTGVDD---ADAILPDDAAATFAC 179

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  LR    R L  L  R   VL   +  G     TL E+G+   +T  R+ QI  + 
Sbjct: 180 IERQQLRAALVRALEKLDDRARVVLAAYYQDG----LTLREIGQILGITESRVCQIHTQT 235

Query: 664 IRKLK 668
           +  L+
Sbjct: 236 LALLR 240


>gi|317472443|ref|ZP_07931767.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
 gi|316900087|gb|EFV22077.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
          Length = 238

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 102/275 (37%), Gaps = 54/275 (19%)

Query: 399 VACEVDSILKIRNEIKSISVETGIS-ISEFRHIVSMVRK-GECEASIAKKEMVEANLRLV 456
           V C+  + L    EI  I     +    E +    M+ K G  E   A+ +++E NLRLV
Sbjct: 6   VTCQKRTFLAKGKEIHYIGGAEILPAPLEAKEEEKMIHKLGTAEEPEARAKLIERNLRLV 65

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           + +AKK+ N G+   DLI  G IGL+KA   F+     K +TYA   ++  I   +    
Sbjct: 66  VYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRN- 124

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                                   NK K E + +E                         
Sbjct: 125 ------------------------NKTKMEVSIDEP------------------------ 136

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
              +  +    L   I   +             R+     +  L+ RE +++ +RFGI  
Sbjct: 137 -LNVDWDGNELLLSDILGTDEDIIYRDLEHEVDRKLLLNAMKILSDRERKIIELRFGINQ 195

Query: 637 --NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + T +EV     +++  I ++E K I++LK 
Sbjct: 196 KDGEEKTQKEVADLMGISQSYISRLEKKIIKRLKR 230


>gi|321116354|emb|CBN73558.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/230 (15%), Positives = 71/230 (30%), Gaps = 45/230 (19%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +++   + + +    L +I  L   I P+  G         + Q+ E  + +     V +
Sbjct: 1   SILADYEXVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPVAD 51

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D E     ++++       PE A      + E  + +   L                
Sbjct: 52  DKDDDEEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL---------------- 95

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  ++S +     E L  L   + L   + D LVE++ D 
Sbjct: 96  -------------------KKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVRDA 136

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
             +I   E  +++L      + R  FL +    E +  W           
Sbjct: 137 LNQIRAQERAIMQLCVRDARMPRADFLRQFPSNETNLDWAEQLAAGKSKY 186


>gi|154499126|ref|ZP_02037504.1| hypothetical protein BACCAP_03120 [Bacteroides capillosus ATCC
           29799]
 gi|150271966|gb|EDM99192.1| hypothetical protein BACCAP_03120 [Bacteroides capillosus ATCC
           29799]
          Length = 340

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/102 (42%), Positives = 56/102 (54%), Gaps = 5/102 (4%)

Query: 580 IGDEDTSHLGD-FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
           + ++ +  + D  I D    +  D      L       L+ LT REE VLR+RF  G   
Sbjct: 73  LCEDRSCSITDCTIYDDAISAAEDQIWCEELSGAIESALSQLTTREEEVLRLRFFEG--- 129

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             T  E GK+F VTRERI QIE  A+RKL+HPSRSK L+ F+
Sbjct: 130 -LTGAECGKKFGVTRERIHQIEVTALRKLRHPSRSKFLKPFV 170


>gi|321116228|emb|CBN73495.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V69]
 gi|321116230|emb|CBN73496.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V70]
 gi|321116380|emb|CBN73571.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. VK2]
          Length = 201

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 61/182 (33%), Gaps = 8/182 (4%)

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
                 V  +  + V      A +D  + +ED+D               + +     + E
Sbjct: 27  DPDDGSVPAEAAAPVPVKDGTAADDSDDDEEDDDSGDEEEEGDGGPDPEEALRRFTAVGE 86

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
              +           +K  + S +  V  ++L  L   + L   + D LV ++ D   R+
Sbjct: 87  QLDKANK------ALKKHGRGSKQVTVELQELANLFMPIKLVPKQYDALVARVRDALDRL 140

Query: 350 MHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
              E  +++L      + R  FL    G E+D  W        +G++   +      I +
Sbjct: 141 RAQERAIMQLCVRDARMPRADFLRLFPGNEIDETWAQQLAK-GKGKYAEAIGNLQGDIQR 199

Query: 409 IR 410
            +
Sbjct: 200 CQ 201


>gi|153854402|ref|ZP_01995680.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
 gi|149752928|gb|EDM62859.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
          Length = 230

 Score = 83.7 bits (205), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 97/255 (38%), Gaps = 58/255 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ +E ++ V   +K       AK  ++E NLRLV  + KKY     +  DL+  
Sbjct: 26  SFPQPLTAAEEKYYV---QKYTEGDLEAKHILIERNLRLVAHIVKKYQPPPEEMEDLLSI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGLMKA   FD     + +TYA   ++  +      +                     
Sbjct: 83  GTIGLMKAVVTFDPEKSARLATYAARCIENELLMHFRGK--------------------- 121

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
                                          K + + +SL  PIG +   +   L D IE
Sbjct: 122 -------------------------------KKSSKEVSLYEPIGTDREGNEIQLFDVIE 150

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                       + ++     +V + L+ RE  VL++R+G+    ++T  E+ K   ++R
Sbjct: 151 MGEEDVHHRLEKKEDVIRLYQKVESELSARERIVLKLRYGLYNEEEYTQREIAKMLGISR 210

Query: 654 ERIRQIEAKAIRKLK 668
             + +IE  AI KL+
Sbjct: 211 SYVSRIEKSAIEKLR 225


>gi|298112121|gb|ADI58445.1| DNA-directed RNA polymerase subunit D [Pseudomonas viridiflava]
          Length = 190

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 46/235 (19%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +M ++   P T   ++     +      L ++      I P+   
Sbjct: 1   GEIEIAKRIEEGIREVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--FSGYIDPDDGI 58

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                       K   +    + ++        E+A    ++D  +    P  A      
Sbjct: 59  APPAEVPPPVDPKAAKAEGADDDEE--------ETADASDEEDEVESGPDPVIAAQRFGA 110

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           + +  + +   L  +  + +  +   +                                 
Sbjct: 111 VSDQMEITRKALKKLGREDKHAIAEMV--------------------------------- 137

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFL 371
              L +L   + L   + + LVE++     R+   E  +++L      + R  FL
Sbjct: 138 --ALAELFMPIKLVPKQFEGLVERVRGAFDRLRAQERAIMQLCVRDARMPRADFL 190


>gi|296103602|ref|YP_003613748.1| RNA polymerase sigma factor for flagellar operon FliA [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058061|gb|ADF62799.1| RNA polymerase sigma factor for flagellar operon FliA [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
          Length = 241

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 48/227 (21%), Positives = 102/227 (44%), Gaps = 11/227 (4%)

Query: 451 ANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
               LV   A +   R    ++  DLIQ G+IG + A E FD   G   + +    VK A
Sbjct: 19  KYHYLVRQEALRLHKRLPASVELDDLIQAGSIGFLSAVESFDPKKGVTLTAWISQRVKWA 78

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +   + +      +P  +R    ++V   +++  +   E T  EIA+++ + ++  +++L
Sbjct: 79  LLDELRESDW---VPRRVRTHTREIVALIQQIEQEKGGEATEAEIAERMGVSLQEFQQML 135

Query: 568 KITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                        + +          E+   ++PL+ A++ NL E  T  +  +  RE+ 
Sbjct: 136 ADNNASQMYSVDELQENYADSWETSDEENEQLNPLNDAVRQNLMERITEHIQVIPEREQV 195

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           +L++ +   +N    ++E+G    +T  R+ Q+ + A+++L+    S
Sbjct: 196 LLQLYYLQDLN----MKEIGLILGITETRVSQLHSLAVKRLRSRMES 238


>gi|302874716|ref|YP_003843349.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
 gi|307690671|ref|ZP_07633117.1| sporulation sigma factor SigK [Clostridium cellulovorans 743B]
 gi|302577573|gb|ADL51585.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
          Length = 233

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 97/234 (41%), Gaps = 49/234 (20%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K +    ++K  +VE NLRLV  + KKY+  G    +LI  G +GL+KA + F+   G
Sbjct: 39  LQKLKEGDLLSKSILVERNLRLVAHIVKKYSGVGKDSDELISIGTVGLIKAIDSFNVDKG 98

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            + +TYA   ++  +   I                                 + T  E+ 
Sbjct: 99  TRLATYAARCIENELLMLIR------------------------------NSKKTKGEVY 128

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            +  + V+            ISL   +  E+ S + + +E+   ++ L   I+       
Sbjct: 129 LQDPIGVDK-------EGNEISLMDVLSSEEDS-VIEIVENNMQIAKLYEEIE------- 173

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                 L  RE+ +++MR+G+      T  E+     ++R  + +IE +A++KL
Sbjct: 174 ----KCLKGREKTIIQMRYGLINGKPKTQREIALLLGISRSYVSRIEKRALKKL 223


>gi|269784264|emb|CBH50777.1| RNA polymerase sigma factor [Vibrio sp. Rd2L5]
 gi|269784266|emb|CBH50778.1| RNA polymerase sigma factor [Vibrio sp. Rd 6.8]
          Length = 126

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 48/126 (38%), Gaps = 2/126 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L +   R+   E  ++R    YG + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +      I +   ++  I  ET +++   + I   +  GE 
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDISRRMSIGEA 120

Query: 440 EASIAK 445
           +A  AK
Sbjct: 121 KARRAK 126


>gi|332272399|gb|AEE38883.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
 gi|332272401|gb|AEE38884.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
 gi|332272403|gb|AEE38885.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
 gi|332272405|gb|AEE38886.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
 gi|332272407|gb|AEE38887.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
 gi|332272409|gb|AEE38888.1| RNA polymerase sigma-70 factor [Aeromonas enteropelogenes]
          Length = 218

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 78/262 (29%), Gaps = 45/262 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------EA 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +D+  T   I S            +   E+ + D  + D D             +LR + 
Sbjct: 35  EDMAPTATHIGSELGEDDLADEDEEDEDEDEDGDSSDDDGDGGPDPEVAREKFAELRAQY 94

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 I                 QK+ ++    +     L  +     L   + D LV 
Sbjct: 95  EVTRLSI-----------------QKNGRAHDDTQAAIALLADVFRQFRLMPKQFDRLVN 137

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            + ++ +R+   E  +++L  +   + +  F+      E +  W  Y K   +      V
Sbjct: 138 NMREMMERVRVQERIIMKLCVEQAKMPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLV 197

Query: 400 ACEVDSILKIRNEIKSISVETG 421
             + D + +   +++ I  ETG
Sbjct: 198 EMDED-VQRAIGKLQQIEEETG 218


>gi|239934474|emb|CAR92491.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 228

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/273 (12%), Positives = 87/273 (31%), Gaps = 46/273 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AEIENEVEEEAEEGEGASEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFVQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            + +
Sbjct: 137 QIRRSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAH-L 195

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           A   + I   + ++  +   T +SI+  + I  
Sbjct: 196 AKLREEIEAQQKKLMGVEELTHLSIAGIKEINR 228


>gi|224553592|gb|ACN55034.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 51/111 (45%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEI ++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEITEQLDKPVDDVSRMLRLNERITSVD 111


>gi|159137617|gb|ABW88899.1| HrdB [Streptomyces cacaoi subsp. asoensis]
          Length = 133

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 50/89 (56%), Positives = 68/89 (76%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +   +     +   AK  ++EANLRLV+S+AK+YT RG+ FLDLIQEGN+GL++A EKF
Sbjct: 43  KLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 102

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           D+  GYKFSTYA WW++QAITR++ADQ+ 
Sbjct: 103 DYTKGYKFSTYATWWIRQAITRAMADQAR 131



 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           YL+++G + LL+ E E+ +AKRIEAG       L  +      L    + + +    
Sbjct: 2   YLKQIGKVPLLNAEQEVELAKRIEAGLF-AEDKLANADKLAPKLKRELEIIAEDGRR 57


>gi|255697125|emb|CBA11673.1| RNA polymerase sigma factor [Pseudomonas syringae pv. philadelphi]
          Length = 191

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 27/235 (11%), Positives = 68/235 (28%), Gaps = 47/235 (20%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + + E+A     ++  +    P  A+     + +  + +   L      
Sbjct: 51  VDPKAAKAEGDDDEEETAEATDDEEEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 104

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 105 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 135

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 136 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDALAK 190


>gi|239934498|emb|CAR92503.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 221

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/269 (15%), Positives = 82/269 (30%), Gaps = 49/269 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPE------PLNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFR 428
               D I + + ++  I  E G+ IS  +
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIK 221


>gi|224553606|gb|ACN55041.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 51/111 (45%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FSTYA WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EE A++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|167630813|ref|YP_001681312.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
 gi|167593553|gb|ABZ85301.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
          Length = 252

 Score = 83.3 bits (204), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 104/288 (36%), Gaps = 60/288 (20%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
                F+A  +     +   + S S    +S  E       + +     + A+++++  N
Sbjct: 4   AWVATFLAFLLKGFAALFGGLNSNSFPKPLSAEEEAEY---IARTTGGDAEAREKLITHN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           LRLV  + KKY +   +  DLI  G IGL+KA   F      + STYA   ++  I   +
Sbjct: 61  LRLVAHICKKYYSNDEEIEDLISIGTIGLIKAINTFKAEKQVRLSTYASRCIENEILMHL 120

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            ++    R+                                + + +  +G R        
Sbjct: 121 RNKKRDSRVV----------------------------SFEESVGIDKDGNRMT------ 146

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
                + I   D   + + +E  + +  L + ++             L  +E  +L +R+
Sbjct: 147 ----YSDILGTDGDTVAELVERSSEIEDLQNKVR-----------RRLNKKEREILTLRY 191

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           G+   T  T + V     ++R  + +IE + IRKL        ++ +L
Sbjct: 192 GLSDGTPKTQQTVADLLNISRSYVSRIEGRGIRKL--------MKEYL 231


>gi|283798349|ref|ZP_06347502.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291073934|gb|EFE11298.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|295092808|emb|CBK78915.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium cf.
           saccharolyticum K10]
          Length = 246

 Score = 83.0 bits (203), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 86/233 (36%), Gaps = 52/233 (22%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            +   AK  ++E NLRLV+ +AKK+ N  +   DLI  G IGL+KA   F+     K +T
Sbjct: 58  EKDREAKSRLIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNTGKNIKLAT 117

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   ++  I   +                            NK K E + +E       
Sbjct: 118 YASRCIENEILMYLRRN-------------------------NKTKLEVSIDEP------ 146

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
                                +  +    L   I   +             R      ++
Sbjct: 147 -------------------LNVDWDGNELLLSDILGTDEDVIYRDLEDEIERNLLNTAIS 187

Query: 619 SLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            L PRE++++ +RFG+      + T +EV     +++  I ++E K +++LK 
Sbjct: 188 RLNPREKKIVELRFGLNSENGEEMTQKEVADLLGISQSYISRLEKKIMKRLKK 240


>gi|321116310|emb|CBN73536.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V218]
 gi|321116312|emb|CBN73537.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V219]
 gi|321116314|emb|CBN73538.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V221]
 gi|321116316|emb|CBN73539.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V222]
          Length = 202

 Score = 83.0 bits (203), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 73/248 (29%), Gaps = 47/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L ++  L   I P+   G    TE       +  + ++E    
Sbjct: 1   VDYILGEYDRVTTEGGRLSDV--LSGYIDPDD--GIAAPTEEVPVPGAKAPAAKEES--- 53

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
              + + E       ++ ++    P  A      +++                       
Sbjct: 54  ---DDEEEDGDSSDDEEETESGPDPVVAAQRFGAVND----------------------- 87

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                        LQ      +K+ +   +     + L  L   + L   + ++LVE++ 
Sbjct: 88  ------------QLQATNKVLKKNGRGHKESIAALQALADLFMPIKLVPKQFEVLVERVR 135

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL      E D  W           W   +  +
Sbjct: 136 DALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEK 194

Query: 403 VDSILKIR 410
             +I+  +
Sbjct: 195 DAAIVACQ 202


>gi|109947668|ref|YP_664896.1| flagellar biosynthesis sigma factor [Helicobacter acinonychis str.
           Sheeba]
 gi|109714889|emb|CAJ99897.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter acinonychis str. Sheeba]
          Length = 258

 Score = 83.0 bits (203), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 47/268 (17%), Positives = 105/268 (39%), Gaps = 20/268 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK--- 462
           IL + N +     +T  S    ++   ++   + +    +  +    L  V ++A +   
Sbjct: 2   ILTMENRMPQEIQQTEPSEKSEKNKEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKE 61

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        + 
Sbjct: 62  HLPGSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VVS 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+ E +A+ L   +E +R+    +     +   +  
Sbjct: 119 RSSRKLIKSIDFETTKYLNEHGKEPSDEYLAQALGENIEKIREAKTASD----IYALVPI 174

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 175 DEQFNAIE------QDEITKKIEVEELLEHVQKVLNQMSEREQMLIQLYYF----EELNL 224

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  +AI+K++  
Sbjct: 225 SEIKEILGITESRISQIIKEAIKKVRQS 252


>gi|159795060|pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
           Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
          Length = 68

 Score = 83.0 bits (203), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/67 (82%), Positives = 60/67 (89%)

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VLA LT RE +VLRMRFGI MNTD+TLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 675 KLRSFLD 681
            LRSFLD
Sbjct: 61  VLRSFLD 67


>gi|269784310|emb|CBH50800.1| RNA polymerase sigma factor [Vibrio sp. Cmj 13.4]
          Length = 126

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 47/126 (37%), Gaps = 2/126 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    YG + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +      I +   ++  I  ET +++   + I   +  GE 
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDISRRMSIGEA 120

Query: 440 EASIAK 445
           +A  AK
Sbjct: 121 KARRAK 126


>gi|239934422|emb|CAR92341.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 217

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 26/197 (13%), Positives = 70/197 (35%), Gaps = 8/197 (4%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                     +    P ++ +  E   D+ E                + +     I +  
Sbjct: 28  DPDDGIVPAEAAAPVPVKDGDAAEETDDDAEASDDEEEEGDGGPDPEEALRRFTAIGD-- 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
               +L+      +K  ++S +     +++ +L   + L   + D LV ++    +R+  
Sbjct: 86  ----ALELAKKALKKHGRNSEQGTAALKEMAELFMPIKLVPKQYDALVVRVRSSLERLRA 141

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +++L      + R  FL    G E+D   +S      + ++   +      I + +
Sbjct: 142 QERAIMQLCVRDARMPRADFLRLFPGNEIDVE-LSAGLAKGKAKYAEAIGNLQGDIQRCQ 200

Query: 411 NEIKSISVETGISISEF 427
            ++ ++  E  ++++E 
Sbjct: 201 QKLSALEAECELTLAEI 217


>gi|322384374|ref|ZP_08058069.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150809|gb|EFX44249.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 340

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 54/221 (24%), Positives = 96/221 (43%), Gaps = 28/221 (12%)

Query: 455 LVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK----FSTYAMWWVKQA 507
           +V SVA+KY +    GL + DL+  G IGL++A   +D     +    FSTYA   +K +
Sbjct: 1   MVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFSTYAFNMIKWS 60

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR--K 565
           I R +AD+  ++R+P  +++K+  + +       +   + + E IA+K    +  +R  K
Sbjct: 61  IQRFLADKRFSVRVPRSIQNKLTVIWK-------QGWDQESAESIAEKTGWKLAEIREVK 113

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                    SL+  +  + T      ++   A++   S             L +L P E 
Sbjct: 114 RHLAGWSVASLDQALSSDKTDEEATMLDVLPAMTDFTSV-------HVQDFLCALKPLER 166

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            VL +R       D T +E+      T+  + +I  K   K
Sbjct: 167 AVLELRL-----QDQTQKEIAMHIGKTQMYVSRILKKIKDK 202


>gi|239934478|emb|CAR92493.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 222

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 43/270 (15%), Positives = 82/270 (30%), Gaps = 49/270 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
               D I + + ++  I  E G+ IS  + 
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKE 222


>gi|167574693|ref|ZP_02367567.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           C6786]
          Length = 236

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 96/238 (40%), Gaps = 22/238 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
                  A++ ++ ++E    LV  VA++     N  +   D+ Q G +GL++A  ++  
Sbjct: 12  AAYVGANATVEQRWLIE-YAPLVKRVARQLGSQANGAIALEDMEQIGLMGLLEALRRY-G 69

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F+ YA   V+ AI   +       R   +   +     R   R    + R PT  
Sbjct: 70  SPDEAFAGYAALRVRGAILDELRRHDWRPRAVRNAAHRARDCERALCR---TLGRVPTAG 126

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++  L + ++  R+ +   +        +   D     D++   +         Q  LR
Sbjct: 127 EVSASLGIGIDEYRENVMANRA-----EAMASFDEMLDADWLAHDDNPER-----QVVLR 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + L SL  RE+RV+++ +      D +L E+     +T  R+ QI   A+RK++
Sbjct: 177 RCLEQALTSLDEREQRVIQLYYEF----DLSLREIAAVLELTEARVCQINKAALRKMR 230


>gi|167567742|ref|ZP_02360658.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           EO147]
          Length = 236

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 96/238 (40%), Gaps = 22/238 (9%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
                  A++ ++ ++E    LV  VA++     N  +   D+ Q G +GL++A  ++  
Sbjct: 12  AAYVGANATVEQRWLIE-YAPLVKRVARQLGSQANGVIALEDMEQIGLMGLLEALRRY-G 69

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F+ YA   V+ AI   +       R   +   +     R   R    + R PT  
Sbjct: 70  SPDEAFAGYAALRVRGAILDELRRHDWRPRAVRNAAHRARDCERALCR---TLGRVPTAG 126

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E++  L + ++  R+ +   +        +   D     D++   +         Q  LR
Sbjct: 127 EVSASLGIGIDEYRENVMANRA-----EAMASFDEMLDADWLAHDDNPER-----QVVLR 176

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               + L SL  RE+RV+++ +      D +L E+     +T  R+ QI   A+RK++
Sbjct: 177 RCLEQALTSLDEREQRVIQLYYEF----DLSLREIAAVLELTEARVCQINKAALRKMR 230


>gi|313901033|ref|ZP_07834521.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
 gi|312953991|gb|EFR35671.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
          Length = 242

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 61/274 (22%), Positives = 100/274 (36%), Gaps = 63/274 (22%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+S S +  +   E    +S++         A+ +++E NLRLV  + KKY  +  Q  
Sbjct: 18  YIRSNSFQQPLDKEEEARCISLL---SERDEEARNKLIEHNLRLVAHIVKKYDIKKEQTE 74

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+KA + F    G+K +TYA   ++  I   +       +           
Sbjct: 75  DLISIGTIGLIKAVDSFKPEKGHKLTTYASKCIENEILMYLRSSKNYFQN---------- 124

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---L 588
                                                     +SL  PI  +       L
Sbjct: 125 ------------------------------------------VSLNEPIATDKDGSEITL 142

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I      S +D  I  +      R +  L  RE  ++  RFG+    + T  E+ +Q
Sbjct: 143 IDAISSPEDSSIIDDMIVEDNIARLKRYIHVLDARELEIITKRFGLYGQEEETQREIARQ 202

Query: 649 FCVTRERIRQIEAKAIRKL-----KHPSRSKKLR 677
             ++R  + +IE +A  K+     K   R ++LR
Sbjct: 203 LHISRSYVSRIEKRAFMKIYREFQKEEKRKERLR 236


>gi|239934496|emb|CAR92502.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 224

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 43/270 (15%), Positives = 81/270 (30%), Gaps = 49/270 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDXPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +                L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPDL------LSNLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETXVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
               D I + + ++  I  E G+ IS  + 
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKE 222


>gi|239934490|emb|CAR92499.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 224

 Score = 83.0 bits (203), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/269 (13%), Positives = 87/269 (32%), Gaps = 46/269 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AELETETEEETEEGEANSEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFAQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            + +
Sbjct: 137 QIRQSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAH-L 195

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFR 428
           A   + I   + ++  + V T +SI+  +
Sbjct: 196 AKLREEIESQQKKLMGVEVLTHLSIAGIK 224


>gi|257438786|ref|ZP_05614541.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
 gi|257198754|gb|EEU97038.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
          Length = 188

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 89/236 (37%), Gaps = 56/236 (23%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                + A+ +++  NLRLV+ +AKKY N G+   D+I  G IGL+KA   F      K 
Sbjct: 1   MMAGDAAARDDLITHNLRLVVYLAKKYENSGVPQEDMISIGTIGLIKAVNTFTPARNIKL 60

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +TYA   +   I   +   S   +                                    
Sbjct: 61  ATYASRCIGNEILMYLRKSSNRRQEA---------------------------------- 86

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETT 613
                             S++ P+  +   +   L D +     +  L    QA  R T 
Sbjct: 87  ------------------SIDEPLNTDGDGNELLLSDVLGSDENLVGLQL-EQAAERATL 127

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R +  L PRE +++ +RFG+    +HT +E      +++  I ++E + IR+LK 
Sbjct: 128 RRSVEQLAPRERQIMELRFGLVDGVEHTQKEAADALGISQSYISRLEKRIIRQLKE 183


>gi|239934488|emb|CAR92498.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 223

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/270 (16%), Positives = 83/270 (30%), Gaps = 49/270 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++ S  E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGSDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
               D I + + ++  I  E G+ IS  + 
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKE 222


>gi|164688589|ref|ZP_02212617.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
 gi|164603002|gb|EDQ96467.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
          Length = 234

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 106/256 (41%), Gaps = 57/256 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  ++  E  + +++++        AK+ +V+ N+RLV  ++KKY N G +  DLI  
Sbjct: 6   SFEKPLTPEEEVYYLNLLK--NENNKEAKEVLVQRNMRLVAHISKKYNNSGEELDDLISI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA + F+   G + +TYA   ++  I  +I                        
Sbjct: 64  GTIGLIKAIDTFNVDKGIRLATYASKCIENEILMNIRSN--------------------- 102

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIE 593
                                          K  K  +SL+ PIG +       L D + 
Sbjct: 103 -------------------------------KKNKMQVSLQDPIGVDKEGNAISLIDILG 131

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                      ++  + +   ++   LT RE+ ++++R+G+  +   T  E+ +Q  ++R
Sbjct: 132 TDEDYIVDKVELKMKISKLYEKIEKVLTEREKEIIKLRYGLTPSGYKTQREIAQQLDISR 191

Query: 654 ERIRQIEAKAIRKLKH 669
             + +IE KA++KLK 
Sbjct: 192 SYVSRIEKKALKKLKR 207


>gi|256376481|ref|YP_003100141.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255920784|gb|ACU36295.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 294

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 94/236 (39%), Gaps = 13/236 (5%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           +   +E++  +L LV  + ++   R    ++  +L+  GN+ L+ AA+ FD   G  F+ 
Sbjct: 17  AAEAEELIVKHLPLVGHLVREVLARVPVHVRREELMSAGNLALVAAAKSFDDSRGAPFAA 76

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A+  V+ A+   +  Q         +R K  K+        +K  R PT  EIA  + +
Sbjct: 77  FAVVRVRGALMDELRGQDW---ASRSVRVKARKMNAVQDEFVSKHGRTPTTAEIAGIMEV 133

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
               V  V    +    L           L + +  +    P ++ +           + 
Sbjct: 134 ETREVTAVQDDVQRSALLSLQGFT--GGVLEEVVP-ERQPGPEETLLGRERIGYLHSAID 190

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           +L  R   V+R  F      +  + E+ ++  V   R+ Q+ A+AI  L+    S+
Sbjct: 191 ALPDRLRTVVRGYFF----EERPMAEIAEELGVHESRVSQLRAEAIALLRDGLNSQ 242


>gi|239934480|emb|CAR92494.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 228

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/273 (12%), Positives = 87/273 (31%), Gaps = 46/273 (16%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AEIENEAEEEAEEGEGASEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFVQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            + +
Sbjct: 137 QIRRSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAH-L 195

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
           A   + I   + ++  +   T +SI+  + I  
Sbjct: 196 AKLREEIEAQQKKLMGVEELTHLSIAGIKXINR 228


>gi|221271588|dbj|BAH15082.1| RNA polymerase sigma factor [Enterobacter sp. FPH01022]
          Length = 184

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 20/113 (17%), Positives = 43/113 (38%), Gaps = 2/113 (1%)

Query: 288 AEVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            E + ELR+  +   +  K + +S    +    KL ++     L   + D LV  +  + 
Sbjct: 69  REKFAELRTQYEVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMM 128

Query: 347 KRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            R+   E  +++L  +   + +  F+    G E    W + A    +   +  
Sbjct: 129 DRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKL 181


>gi|221271586|dbj|BAH15081.1| RNA polymerase sigma factor [Enterobacter sp. FPH00672]
          Length = 184

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 20/113 (17%), Positives = 43/113 (38%), Gaps = 2/113 (1%)

Query: 288 AEVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            E + ELR+  +   +  K + +S    +    KL ++     L   + D LV  +  + 
Sbjct: 69  REKFAELRTQYEVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMM 128

Query: 347 KRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            R+   E  +++L  +   + +  F+    G E    W + A    +   +  
Sbjct: 129 DRVRTQERIIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKL 181


>gi|269784304|emb|CBH50797.1| RNA polymerase sigma factor [Vibrio sp. C 2.4]
          Length = 128

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 49/128 (38%), Gaps = 2/128 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    YG + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +      I +   ++  I  ET +++   + I   +  GE 
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDISRRMSIGEA 120

Query: 440 EASIAKKE 447
           +A  AKKE
Sbjct: 121 KARRAKKE 128


>gi|261416067|ref|YP_003249750.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|261372523|gb|ACX75268.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|302327561|gb|ADL26762.1| sigma-70 factor family protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 376

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/259 (21%), Positives = 109/259 (42%), Gaps = 16/259 (6%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT-NRGLQFLDLI 474
           I     I  ++ + +V +  +       A+K  +E NLR+ + +A + +       +D I
Sbjct: 93  IEYVRKIQPADKKEMVRIQYQLFEGHEYARKRAIEGNLRIAVILAYRESVAYNKNIVDCI 152

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
            E  + L+ A   +       F++Y    V   + R+I        IPV++ +   K+ +
Sbjct: 153 GEACLALVSACNSYKPDEHQTFASYISIAVFDYLARTIGVP--FFSIPVNIVNLCRKLYK 210

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
             +   N++ ++     +     +  E    VL        L+  +      ++ D +  
Sbjct: 211 DIK--YNRLGKKDALLYVCSCYGL-EEYWSNVLYDILHVFFLDEDVL----DNVLDNVYS 263

Query: 595 KNAVSPLDSAIQANLRETTTRVL------ASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           ++      + ++ ++     ++L        LT RE  V+  R+G+     H+L E+G  
Sbjct: 264 ESCYENFLTDVENDIERKNVQILINRCLNECLTDREYNVVEHRYGLNGKDSHSLVELGSH 323

Query: 649 FCVTRERIRQIEAKAIRKL 667
             V+RERIRQIE KA+ KL
Sbjct: 324 QVVSRERIRQIEKKALTKL 342


>gi|168186818|ref|ZP_02621453.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
 gi|169295229|gb|EDS77362.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 97/251 (38%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E ++ +   +      ++AK  ++E NLRLV  + KKY+       DLI  
Sbjct: 26  SFPQPLNEKEEKYYLQQFK---EGDALAKGILIERNLRLVAHIVKKYSYPNKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I +                K +++ 
Sbjct: 83  GTVGLIKAIDSFDVDKGTRLATYAARCIENEILMLIRNS---------------KKIKSE 127

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 128 VYLQDPIGVDKEGNEI----------------------------------SLMDVLSSDE 153

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +R+   ++   LT RE+ +++MR+G+      T  E+     ++R  +
Sbjct: 154 DSVIEVVENRMEVRKLYDKIEKCLTEREKIIIKMRYGLVDGKSKTQREIASFLNISRSYV 213

Query: 657 RQIEAKAIRKL 667
            +IE +A++K+
Sbjct: 214 SRIEKRALKKI 224


>gi|225028118|ref|ZP_03717310.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
 gi|224954588|gb|EEG35797.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
          Length = 247

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 92/239 (38%), Gaps = 52/239 (21%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + +     +  AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA + F    
Sbjct: 53  LSQLDTRRSEEAKALLIERNLRLVVYIAKKFENTGIGVEDLISIGTIGLIKAIQTFKLDK 112

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             K +TYA   ++  I   +                            NK K E + +E 
Sbjct: 113 KIKLATYASRCIENEILMYLRRT-------------------------NKTKMEVSIDEP 147

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
                                      +  +    L   I   ++            R+ 
Sbjct: 148 -------------------------LNVDWDGNELLLSDILGTDSDVISKDIEDEIDRKM 182

Query: 613 TTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + + +L+ RE+ ++R+RFGIG     + T +EV     +++  I ++E K I +LK 
Sbjct: 183 LNKAMETLSDREKLIIRLRFGIGGEESEEKTQKEVADLLGISQSYISRLEKKIIHRLKR 241


>gi|321116202|emb|CBN73482.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|321116214|emb|CBN73488.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|321116216|emb|CBN73489.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 202

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 71/248 (28%), Gaps = 47/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L ++  L   I P+            +  +       K     
Sbjct: 1   VDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIA--------APTEEVPIPGAKAAAAK 50

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +E++ + E A     ++ ++    P  A      + +                       
Sbjct: 51  EESDDEEEEAENSDDEEETESGPDPVVAAQRFGAVSD----------------------- 87

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                        LQ      +K  ++  +     + L  L   + L   + ++LVE++ 
Sbjct: 88  ------------QLQATFKVVKKHGRAHKESIAALQALADLFMPIKLVPKQFEVLVERVR 135

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL      E D  W           W   +  +
Sbjct: 136 DALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEK 194

Query: 403 VDSILKIR 410
             +I+  +
Sbjct: 195 DAAIVACQ 202


>gi|225574950|ref|ZP_03783560.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037797|gb|EEG48043.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
          Length = 225

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 100/251 (39%), Gaps = 63/251 (25%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + I  +   G  +   AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA
Sbjct: 26  QEEKVIQKL---GTEQEKEAKALLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKA 82

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              F+     K +TYA   ++  I   +   S                            
Sbjct: 83  INTFNPVKKIKLATYASRCIENEILMYLRRNSK--------------------------- 115

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE-DKNAVSP 600
                                    TK  +S++ P+  +   +   L D +  D++ +S 
Sbjct: 116 -------------------------TKMEVSIDEPLNVDWDGNELLLSDILGTDEDVISR 150

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIG--MNTDHTLEEVGKQFCVTRERIRQ 658
                    R+     ++ L+PRE+ ++ +RFG+      + T +EV     +++  I +
Sbjct: 151 GIEDEVE--RDLLGNAISKLSPREQTIVTLRFGLHSVDGKEKTQKEVADLLGISQSYISR 208

Query: 659 IEAKAIRKLKH 669
           +E + +++LK 
Sbjct: 209 LEKRIMKRLKK 219


>gi|284052567|ref|ZP_06382777.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 232

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 49/96 (51%), Positives = 67/96 (69%), Gaps = 1/96 (1%)

Query: 412 EIKSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           E+K I  E     +E  ++ V  +++ + E   AK  M++ANLRLV+SVAKKY NRGL+ 
Sbjct: 137 ELKQIMAEGKRCWAELANLSVEELKQVQREGIQAKDHMIKANLRLVVSVAKKYQNRGLEL 196

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           LDLIQEG +GL +A EKFD   GY+FSTY+ WW++Q
Sbjct: 197 LDLIQEGTLGLERAVEKFDPTRGYRFSTYSYWWIRQ 232



 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA--MMMASLCESPL 162
            +   +    R T D VR+YL+E+G + LL R+ E++ A++++       +  +  E+  
Sbjct: 39  DVDLSEAHTSRRTTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYVQLVELRDTEAETNG 98

Query: 163 ----TFQALIIWRDELND 176
               T+  L+  RD L  
Sbjct: 99  GVLQTYVNLLKVRDRLCA 116


>gi|255697071|emb|CBA11645.1| RNA polymerase sigma factor [Pseudomonas syringae pv. avii]
 gi|255697123|emb|CBA11672.1| RNA polymerase sigma factor [Pseudomonas syringae pv. persicae]
          Length = 192

 Score = 82.6 bits (202), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 28/231 (12%), Positives = 66/231 (28%), Gaps = 46/231 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 51  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W  
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFLGHEVDESWTD 187


>gi|291548178|emb|CBL21286.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. SR1/5]
          Length = 241

 Score = 82.2 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/256 (21%), Positives = 100/256 (39%), Gaps = 60/256 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +S      ++ M+  G  +    K  ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 35  PAPLSAEREAEVIEML--GTEKEKEGKSVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGT 92

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   FD     K +TYA   ++  I   +   S                      
Sbjct: 93  IGLIKAINTFDPVKNIKLATYASRCIENEILMYLRRNSK--------------------- 131

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDK 595
                                          TK  +S++ P+  +   +   L D +   
Sbjct: 132 -------------------------------TKMEVSIDEPLNVDWDGNELLLSDILGTD 160

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTR 653
           + V       +  +     + ++ LT RE+ ++R+RFGIG     + T +EV     +++
Sbjct: 161 DDVISRRLEDEVEI-ALLGKAISKLTKREQMIIRLRFGIGNREGSEKTQKEVADLLGISQ 219

Query: 654 ERIRQIEAKAIRKLKH 669
             I ++E + +++L+ 
Sbjct: 220 SYISRLEKRIMKRLRK 235


>gi|239934494|emb|CAR92501.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 222

 Score = 82.2 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 43/270 (15%), Positives = 80/270 (29%), Gaps = 49/270 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF    E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFCESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E A                             
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAEQAR---------------------------- 80

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 81  -AHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
               D I + + ++  I  E G+ IS  + 
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDISRIKE 222


>gi|154816043|emb|CAO85715.1| putative RNA polymerase sigma factor rpoD [Clostridium sp.]
          Length = 75

 Score = 82.2 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/75 (54%), Positives = 61/75 (81%), Gaps = 1/75 (1%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L +T + VL++L+PREER++R+R+G+ G     TLEE+G++F +TRERIRQIEA+AIRK
Sbjct: 1   MLGDTLSNVLSTLSPREERIVRLRYGLVGDGESRTLEEIGREFNLTRERIRQIEARAIRK 60

Query: 667 LKHPSRSKKLRSFLD 681
           L+HP+R KKL+ + +
Sbjct: 61  LRHPTRIKKLQGYFE 75


>gi|321116204|emb|CBN73483.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|321116210|emb|CBN73486.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
 gi|321116212|emb|CBN73487.1| DNA-directed RNA polymerase subunit D [Pseudomonas putida]
          Length = 202

 Score = 82.2 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 73/248 (29%), Gaps = 47/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L +++            G+    +  +    E      +    
Sbjct: 1   VDYILGEYDRVTTEGGRLSDVL-----------SGYIDPDDNIAAPTEEVPIPGAKAAAA 49

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +E   D E  A+ S D+      P             D   +A    A+ DQ        
Sbjct: 50  KEESDDEEEEAESSDDEEETESGP-------------DPVVAAQRFGAVSDQ-------- 88

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                        LQ      +K  ++  +     + L  L   + L   + ++LVE++ 
Sbjct: 89  -------------LQATFKVVKKHGRAHKESIAALQALADLFMPIKLVPKQFEVLVERVR 135

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL      E D  W           W   +  +
Sbjct: 136 DALNRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEK 194

Query: 403 VDSILKIR 410
             +I+  +
Sbjct: 195 DAAIVACQ 202


>gi|289524838|emb|CBJ94475.1| RNA polymerase sigma factor [Vibrio sp. Rd 16.2]
 gi|289524840|emb|CBJ94476.1| RNA polymerase sigma factor [Vibrio sp. Vb 11.8]
          Length = 127

 Score = 82.2 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 46/126 (36%), Gaps = 2/126 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    Y  + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYAKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
              W+       +  +   +      I +   ++  I  ET +++   + I   +  GE 
Sbjct: 62  SEAWLDEVLA-SDKPYVEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDISRRMSIGEA 120

Query: 440 EASIAK 445
           +A  AK
Sbjct: 121 KARRAK 126


>gi|239934342|emb|CAR92301.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
 gi|239934346|emb|CAR92303.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 204

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 79/249 (31%), Gaps = 46/249 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRN 411
            + I++ + 
Sbjct: 196 KEDIVRCQQ 204


>gi|302871379|ref|YP_003840015.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574238|gb|ADL42029.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 262

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 94/247 (38%), Gaps = 58/247 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E   I+  +     E    KK ++E NLRLV+ +A+++ N  +   DL+  G IGL
Sbjct: 43  LTPDEEAQILYRIHYQGEEGL--KKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGL 100

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   ++     K +TYA   ++  I   +             R+   K+         
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLR------------RNSNKKLE-------- 140

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S++ P+  +   +   L D +   +  
Sbjct: 141 --------------------------------LSIDEPLNVDWDGNELLLSDVLG-TDTE 167

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +       +E   + +  L  RE++++ +RFG G   + T +EV     +++  I +
Sbjct: 168 EIYNRIESNVEKEALLQAIQKLPSREKKIVELRFGFGDEGEKTQKEVADMLGISQSYISR 227

Query: 659 IEAKAIR 665
           +E + ++
Sbjct: 228 LEKRLLQ 234


>gi|159163074|pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
           Maritima
          Length = 87

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 46/78 (58%), Positives = 58/78 (74%)

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            A++  +RE   +VL +L+PRE  VLRMR+G+      TLEEVG+ F VTRERIRQIE K
Sbjct: 2   EAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK 61

Query: 663 AIRKLKHPSRSKKLRSFL 680
           A+RKL+HPSRSK L+S L
Sbjct: 62  ALRKLRHPSRSKYLKSLL 79


>gi|118442872|ref|YP_878340.1| sporulation sigma factor SigK [Clostridium novyi NT]
 gi|118133328|gb|ABK60372.1| DNA-dependent RNA polymerase sigma subunit [Clostridium novyi NT]
          Length = 225

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 98/251 (39%), Gaps = 52/251 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E ++ +   ++     ++AK  ++E NLRLV  + KKY+       DLI  
Sbjct: 17  SFPQPLNEKEEKYYLQQFKQ---GDALAKGILIERNLRLVAHIVKKYSYPNKDVDDLISI 73

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G +GL+KA + FD   G + +TYA   ++  I   I +                K +++ 
Sbjct: 74  GTVGLIKAIDSFDVDKGTRLATYAARCIENEILMLIRNS---------------KKIKSE 118

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +    
Sbjct: 119 VYLQDPIGVDKEGNEI----------------------------------SLMDILSSDE 144

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    +  +R+   ++   LT RE+ +++MR+G+      T  E+     ++R  +
Sbjct: 145 DSVIEVVENRMEVRKLYDKIEKCLTEREKIIIKMRYGLVDGKSKTQREIASLLNISRSYV 204

Query: 657 RQIEAKAIRKL 667
            +IE +A++K+
Sbjct: 205 SRIEKRALKKI 215


>gi|291542628|emb|CBL15738.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus bromii L2-63]
          Length = 233

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 101/251 (40%), Gaps = 61/251 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E +HI+  + K     S A++ ++  NLRLV+ +AKK+        DLI  G IGL
Sbjct: 33  LTREEEQHIMENIAK---GDSKAREPLIVHNLRLVVYIAKKFETPNASAEDLISIGTIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I                        +R + ++ N
Sbjct: 90  IKAVNTFSPEKNIKLATYASRCIENEILMF---------------------LRKSSQLKN 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFI-EDKNA 597
           +                               +S++ P+  +   +   L D +  D + 
Sbjct: 129 E-------------------------------VSIDEPLNTDWDGNELLLCDVLGSDPDT 157

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           V+          +    + ++ L  RE  ++ +RFG+    +HT ++V  +  +++  I 
Sbjct: 158 VNRNIECELE--KSLVLQAVSKLRDRECLIMELRFGLNGQKEHTQKQVADKLGISQSYIS 215

Query: 658 QIEAKAIRKLK 668
           ++E K IR+LK
Sbjct: 216 RLEKKIIRQLK 226


>gi|317499143|ref|ZP_07957420.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316893556|gb|EFV15761.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 231

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 96/253 (37%), Gaps = 54/253 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +  +E + ++ M+  G      A+  ++E NLRLV+ +AKK+ N G+   DLI  G 
Sbjct: 23  PAPLDTAEEQKMIHML--GTVNEETARSMLIERNLRLVVYIAKKFDNTGIGVEDLISIGT 80

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA   F+     K +TYA   ++  I   +                          
Sbjct: 81  IGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRN----------------------- 117

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK K E + +E                            +  +    L   I   +  
Sbjct: 118 --NKTKMEVSIDEP-------------------------LNVDWDGNELLLSDILGTDED 150

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERI 656
                      ++  TR +  LT RE+ ++ +RFGI      + T +EV     +++  I
Sbjct: 151 IIYKDLEHEVDKKLLTRAMTILTDREKMIIELRFGINQKEGKEKTQKEVADMLGISQSYI 210

Query: 657 RQIEAKAIRKLKH 669
            ++E K I++LK 
Sbjct: 211 SRLEKKIIKRLKR 223


>gi|309775717|ref|ZP_07670714.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916522|gb|EFP62265.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 249

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 93/259 (35%), Gaps = 58/259 (22%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            I+S S +  +   E    +S++         A+ +++E NLRLV  + KKY  +  Q  
Sbjct: 18  YIRSNSFQQPLDKEEEARCISLL---SEHDEEARNKLIEHNLRLVAHIVKKYDIKKEQTE 74

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLI  G IGL+K  + F    G+K +TYA   ++  I   +       +           
Sbjct: 75  DLISIGTIGLIKGVDSFKPEKGHKLTTYASKCIENEILMYLRSSKNYFQN---------- 124

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---L 588
                                                     +SL  PI  +       L
Sbjct: 125 ------------------------------------------VSLNEPIATDKDGSEITL 142

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I      S +D  I  +      R +  L  RE  ++  RFG+    + T  E+ +Q
Sbjct: 143 IDAIASPEDTSIIDDMIVEDNIARLKRFIHVLDARELEIITKRFGLYGQEEETQREIARQ 202

Query: 649 FCVTRERIRQIEAKAIRKL 667
             ++R  + +IE +A  K+
Sbjct: 203 LHISRSYVSRIEKRAFMKI 221


>gi|239934462|emb|CAR92485.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 225

 Score = 82.2 bits (201), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/265 (15%), Positives = 79/265 (29%), Gaps = 49/265 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + + D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAKDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +   +  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDXIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISI 424
               D I + + ++  I  E G+ I
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDI 217


>gi|291525957|emb|CBK91544.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           DSM 17629]
          Length = 224

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 99/228 (43%), Gaps = 15/228 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +V  N+ L+  V K++ NRG+   DL Q G +GL KAA++FD   G+ FSTYA+  +  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    + I   +RD   K+     +       E + E++     M  + +   
Sbjct: 68  EIQRFLRD-DGMVHISRKIRDDARKIAIIREKYRMNENSEISLEKMENISGMSKQDIIIA 126

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPR 623
           ++  K   S+E          + D++++K +    D   + +         +   SL   
Sbjct: 127 MEADKNASSIE-------NESVLDYLDNKMSAEASDKPSETDKVINHIAMQQAFNSLDDS 179

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           E R++ +R+      D T ++V +     +  I ++E   + KL+   
Sbjct: 180 ERRLIMLRY----MQDKTQKQVAEMLGRNQVAISRMEKNTLAKLRRAM 223


>gi|225568718|ref|ZP_03777743.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
 gi|225162217|gb|EEG74836.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
          Length = 189

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 94/239 (39%), Gaps = 55/239 (23%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K       AK  ++E NLRLV  + KKY +      DL+  G IGL+KA   F+    
Sbjct: 1   MQKYTEGDLEAKHVLIERNLRLVAHIVKKYQSLEEDNEDLLSIGTIGLIKAVVTFNPDKC 60

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +  TYA   ++  I   +  +                                      
Sbjct: 61  VRLGTYAARCIENEILMYLRSK-------------------------------------- 82

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR 610
                         K + + +SL  PIG +   +   L D IE     +    A++ ++R
Sbjct: 83  --------------KKSSKEVSLYEPIGTDREGNEIQLFDIIETDEDDAHRKVALKDDIR 128

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               +V   L+ RE  VL+MR+G+    ++T  E+ ++  ++R  + +IE  AI KL+ 
Sbjct: 129 LLYEKVEGELSQRERLVLKMRYGLYNEEEYTQREIARRLGISRSYVSRIEKSAIEKLRE 187


>gi|296132610|ref|YP_003639857.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031188|gb|ADG81956.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 245

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/279 (20%), Positives = 103/279 (36%), Gaps = 53/279 (18%)

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
               G W       ++++L + + I + +    +S  E +  + ++ K       A+  +
Sbjct: 10  FMVSGLWTAIALGALNALLLLVSYISNNTFPQPLSEEEEQKYLELLEK---GDEEARNVL 66

Query: 449 VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           +E NLRLV  + KK+        DLI  G IGL+KA   F+   G + +TYA   ++  I
Sbjct: 67  IERNLRLVAHIVKKFDGALDDNDDLISIGTIGLIKAINTFNRYKGTRLATYAARCIENEI 126

Query: 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568
              +                  K  R    + + I  +    EI                
Sbjct: 127 LMHLRAT---------------KKNRVEVSLYDSIGVDKEGNEI---------------- 155

Query: 569 ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
                              L D +  ++ +           R    +V   L+ RE+ VL
Sbjct: 156 ------------------TLIDVLGTESEIVLDTVESLFEQRRLLEKV-KKLSYREKNVL 196

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++RFG+      T  E+ ++  ++R  + +IE +A+ KL
Sbjct: 197 QLRFGLVNGIRKTQREIARKLGISRSYVSRIEKRALNKL 235


>gi|291334306|gb|ADD93967.1| sigma factor FliA sigma 28 group flagellar [uncultured marine
           bacterium MedDCM-OCT-S09-C247]
          Length = 225

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 102/237 (43%), Gaps = 18/237 (7%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDW 490
           +  G    +  K +++  NL +V  +A  Y  R    ++  DL+Q G +GL++AA  +  
Sbjct: 1   MMHGYNHNTDDKAQLINDNLDIVKKIAFFYVGRVGKVVEVDDLLQLGMVGLIEAAHNYTP 60

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F  YA   VK AI   +   S   R  +  +       R  R++  ++ R+P   
Sbjct: 61  QDDVSFVNYARLRVKGAIVDYLRKSSNLCRGTIRRKQ---DYERAKRKLEKELFRQPETH 117

Query: 551 EIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
           EIAK+L + V  +          +  SLE     E +   GDF+   +  S  +      
Sbjct: 118 EIAKELKVEVSDLLSWQHDFAASQHQSLE-----EASDAYGDFLFATD-KSVEEKIFNGE 171

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           L++     L  L  ++  VL++ +      +  + E+G+   V+  R+ QI++ AI+
Sbjct: 172 LKDILRTKLEDLNEQQLMVLQLYYV----EELNVYEIGEILSVSTGRVSQIKSAAIK 224


>gi|291531057|emb|CBK96642.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum 70/3]
          Length = 239

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 96/261 (36%), Gaps = 58/261 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET             + K   +   A++ ++  NLRLV+ +AKK+ + G+   DLI  
Sbjct: 30  GAETLPPPLSKEEEAKTLAKLNTDFENARETLIVHNLRLVVYIAKKFESTGIGIEDLISI 89

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F      K +TYA   ++  I                       + +T 
Sbjct: 90  GTIGLIKAVNTFSVEKNIKLATYASRCIENEILMY--------------------LRKTN 129

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
            +                                K  +S++ P+  +   +   L D + 
Sbjct: 130 PQ--------------------------------KMEVSIDEPLNVDWDGNELLLSDILG 157

Query: 594 -DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D + VS    +     +      +  L  RE+ ++ +RFG+    + T +EV     ++
Sbjct: 158 TDDDTVSVDIESEAE--KRMLLEAVEKLDEREKLIMELRFGLNNRPEKTQKEVADMIGIS 215

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
           +  I ++E + I++LK    S
Sbjct: 216 QSYISRLEKRIIKRLKKEMES 236


>gi|255697075|emb|CBA11647.1| RNA polymerase sigma factor [Pseudomonas syringae pv.
           broussonetiae]
          Length = 192

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 67/235 (28%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    + T+ D E +A  S DD      P             D+ +          +
Sbjct: 51  VDPKAVKAEGTDDDEEESADASDDDDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGR 110

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  +  +AE++                                    + L   + 
Sbjct: 111 DDKHAIAEMVALAELF----------------------------------MPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 191


>gi|295094809|emb|CBK83900.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus sp. ART55/1]
          Length = 245

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 86/231 (37%), Gaps = 58/231 (25%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           AKK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F      K +TYA   
Sbjct: 62  AKKMLIERNLRLVVYIAKKFDNTGVGIEDLISIGTIGLIKAINTFKNDKNIKLATYASRC 121

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I   +   S                                               
Sbjct: 122 IENEILMFLRRNSKLRTE------------------------------------------ 139

Query: 564 RKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                     +S++ P+  +   +   L D +     V   D   + +        ++ L
Sbjct: 140 ----------VSIDEPLNVDWDGNELLLSDILGTDEDVVYRDLETEVDY-NLLDNAISKL 188

Query: 621 TPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +E  ++ +R+GI      + T +EV     +++  I ++E + I+KL+ 
Sbjct: 189 CEKERTIIELRYGINTIGGVEKTQKEVADLLGISQSYISRLEKRIIKKLRR 239


>gi|167749813|ref|ZP_02421940.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|167657125|gb|EDS01255.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|291557474|emb|CBL34591.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum
           V10Sc8a]
          Length = 239

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 96/261 (36%), Gaps = 58/261 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             ET             + K   +   A++ ++  NLRLV+ +AKK+ + G+   DLI  
Sbjct: 30  GAETLPPPLSKEEEAKTLAKLNTDFENARETLIVHNLRLVVYIAKKFESTGIGIEDLISI 89

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F      K +TYA   ++  I                       + +T 
Sbjct: 90  GTIGLIKAVNTFSVEKNIKLATYASRCIENEILMY--------------------LRKTN 129

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
            +                                K  +S++ P+  +   +   L D + 
Sbjct: 130 PQ--------------------------------KMEVSIDEPLNVDWDGNELLLSDILG 157

Query: 594 -DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D + VS    +     +      +  L  RE+ ++ +RFG+    + T +EV     ++
Sbjct: 158 TDDDTVSVDIESEAE--KRMLLEAVEKLDEREKLIMELRFGLNNRPEKTQKEVADMIGIS 215

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
           +  I ++E + I++LK    S
Sbjct: 216 QSYISRLEKRIIKRLKKEMES 236


>gi|307776476|pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
 gi|307776477|pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
 gi|307776478|pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
          Length = 179

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 51/94 (54%), Positives = 69/94 (73%), Gaps = 4/94 (4%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E +  + + R    E   A++ ++EANLRLV+S+AKKYT RGL FLDLIQEGN GL++
Sbjct: 90  PKELKRYLHIAR----EGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIR 145

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           A EKF++  G+ FSTYA WW++QAI R+IADQ+ 
Sbjct: 146 AVEKFEYKRGFAFSTYATWWIRQAINRAIADQAR 179



 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
            DPVR YL E+G +  L +  E+  A ++E G    +  L E+    Q LI
Sbjct: 1   SDPVRQYLHEIGEVLELDKWAELGAAAKVEEG-MEAIKKLSEATGLDQELI 50


>gi|237732926|ref|ZP_04563407.1| sporulation sigma factor sigK [Mollicutes bacterium D7]
 gi|229383995|gb|EEO34086.1| sporulation sigma factor sigK [Coprobacillus sp. D7]
          Length = 223

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 59/257 (22%), Positives = 95/257 (36%), Gaps = 59/257 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + IKS S E  ++  E    +            A+  ++E NLRLV  +AKKY N     
Sbjct: 16  SYIKSKSFELPLTAKEEERYLEQ---FFNGDKEARNVLIERNLRLVAHIAKKYENNKDMQ 72

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA + +      K +TYA   ++  I   +                  
Sbjct: 73  EDLISIGTIGLIKAVDSYKQNHKTKLATYASRCIENEILMHLRTN--------------- 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--- 587
                                                K T   ISL   IG +       
Sbjct: 118 -------------------------------------KKTNLDISLNETIGIDKDGSEIV 140

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD I  K     +D   + +  +  T   + L PRE+  L MR+G+     +T +++ K
Sbjct: 141 LGDIIAAK-QEEFIDIVDKKDTLDKFTTYFSVLEPREKDTLIMRYGLNNTKKYTQKDIAK 199

Query: 648 QFCVTRERIRQIEAKAI 664
           +  ++R  + ++E +A+
Sbjct: 200 KLNISRSYVSRLEKRAL 216


>gi|258516390|ref|YP_003192612.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
 gi|257780095|gb|ACV63989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
          Length = 239

 Score = 81.8 bits (200), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 94/228 (41%), Gaps = 19/228 (8%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +     ++++ +  RLV   AK Y   G Q  DL+Q G  GL+KA  +FD   G  FSTY
Sbjct: 26  KDEERLRQVMMSGSRLVRHFAKLYA-SGRQTEDLMQSGYEGLLKALGRFDSSRGVLFSTY 84

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   +   I   I  ++     P  + +   ++ R       +  + P+  +IA+ + + 
Sbjct: 85  AAHCIMGEIRHHIRKEASY-ACPAAVAELQARINRFVDDYMKENGQIPSLSQIAEFVNVC 143

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            EGV + ++     +SL+     +  S           +      +    R    + L  
Sbjct: 144 EEGVVQAMRAGF--VSLDEIELHKIQS-----------LKYESFCLPIEDRIVLEQALYK 190

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           LT  ++RV+ + F      D T  E   Q  +++  + +I  K++  L
Sbjct: 191 LTELQQRVIHLLF----YKDMTQTEAASQLGISQRSVSRILRKSLNLL 234


>gi|321116194|emb|CBN73478.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V1]
          Length = 201

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 75/248 (30%), Gaps = 48/248 (19%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L +++            G+    +G +         + +    
Sbjct: 1   VDYILSEYDRVTAEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAPAK 49

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            E+E + E   +  +++ ++    P  A+     + E  + +   L     Q +  V   
Sbjct: 50  AESEDEDEEKEETEEEEETESGPDPVIAQQRFGAVQEQLNATLKVLKKNGRQHKDSVKAM 109

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           L                                   +L +L   + L   + ++LVE++ 
Sbjct: 110 L-----------------------------------ELAELFMPIKLVPKQFEVLVERVR 134

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               R+   E  +++L      + R  FL      E D  W S         W   +  +
Sbjct: 135 GALDRLRRQERAIMQLCVRDARMPRADFLRLFPSNETDQTWSSDLSKRSAK-WAAALGEK 193

Query: 403 VDSILKIR 410
            D+I+  +
Sbjct: 194 NDAIVACQ 201


>gi|239934504|emb|CAR92506.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 224

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 34/269 (12%), Positives = 87/269 (32%), Gaps = 46/269 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AELETETEEETEEGEAASEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      +   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFAQVQK------GMAEKGADDPRVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            + +
Sbjct: 137 QIRQSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAH-L 195

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFR 428
           A   + I   + ++  + V T +SI+  +
Sbjct: 196 AKLREEIESQQKKLMGVEVLTXLSIAGIK 224


>gi|153818374|ref|ZP_01971041.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
 gi|126511064|gb|EAZ73658.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
          Length = 232

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 50/210 (23%), Positives = 87/210 (41%), Gaps = 17/210 (8%)

Query: 448 MVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
            +E    LV  +A     R        DLIQ G +GL++A + +D   G  F TYA   +
Sbjct: 19  FLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSKGASFETYAGIRI 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   I        +P  +     ++ +    +  ++ R+PT  E+AK L M +E   
Sbjct: 79  RGAMLDDIRRGDW---VPRSVHKHNREISQAIAVLEGELNRDPTDAEVAKFLNMSLEQYH 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VL      I+    +G ED     D I   E+    SP     + + R+     + SL 
Sbjct: 136 SVL----MDINCSRIVGIEDLGVSDDAISPFEEGEDNSPFHGVAEESFRKALVESIKSLP 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            RE  VL + +    + +  L+++ +   +
Sbjct: 192 EREALVLSLYY----DEELNLKKLVRYLEL 217


>gi|167756988|ref|ZP_02429115.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
 gi|167703163|gb|EDS17742.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
          Length = 228

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 97/260 (37%), Gaps = 59/260 (22%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + IKS S E  ++  E    +            A+  ++E NLRLV  +AKKY N     
Sbjct: 16  SYIKSKSFELPLTAKEEERYLEQ---FFNGDKEARNVLIERNLRLVAHIAKKYENNKDMQ 72

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DLI  G IGL+KA + +      K +TYA   ++  I   +                  
Sbjct: 73  EDLISIGTIGLIKAVDSYKQNHKTKLATYASRCIENEILMHLRTN--------------- 117

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--- 587
                                                K T   ISL   IG +       
Sbjct: 118 -------------------------------------KKTNLDISLNETIGIDKDGSEIV 140

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           LGD I  K     +D   + +  +  T   + L PRE+  L MR+G+     +T +++ K
Sbjct: 141 LGDIIAAK-QEEFIDIVDKKDTLDKFTTYFSVLEPREKDTLIMRYGLNNTKKYTQKDIAK 199

Query: 648 QFCVTRERIRQIEAKAIRKL 667
           +  ++R  + ++E +A+ KL
Sbjct: 200 KLNISRSYVSRLEKRALIKL 219


>gi|268611133|ref|ZP_06144860.1| sporulation sigma factor SigE [Ruminococcus flavefaciens FD-1]
          Length = 232

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 92/247 (37%), Gaps = 56/247 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
             +T       +    +  K E     A+K ++E NLRLV+ +AKK+ + G+   DL+  
Sbjct: 24  GSDTLPPPLTRQEEAEVFMKLEANDPAARKYLIEHNLRLVVYIAKKFESSGVGIEDLVSI 83

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F      K +TYA   ++  I                        +R +
Sbjct: 84  GTIGLIKAVNTFCPTKNIKLATYASRCIENEILMF---------------------LRKS 122

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE 593
            +  N++                               S++ P+  +   +   L D + 
Sbjct: 123 SQYRNEL-------------------------------SIDEPLNIDYDGNELLLSDVLG 151

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
               +       +A  RE     ++ L+ RE  ++ MRFG+    + T +EV     +++
Sbjct: 152 TDEDIVNKGIETEAE-REILRNAVSELSEREREIMEMRFGLVDGKEKTQKEVADSIGISQ 210

Query: 654 ERIRQIE 660
             I ++E
Sbjct: 211 SYISRLE 217


>gi|209408340|emb|CAP19913.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 185

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/227 (16%), Positives = 70/227 (30%), Gaps = 44/227 (19%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P T   ++   + + +    L +I  L   I P+  G         + Q+ E  + +  
Sbjct: 2   FPGTVDGILADYERVTNEGGRLSDI--LSGYIDPDDDGA------AGAPQEVEPVAPQVA 53

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              V + + D E     S+++       PE A      + E  + +              
Sbjct: 54  AKPVADDKDDDEEEESDSEEEEGDGGPDPEVARARFGAVAEQLEKAKKA----------- 102

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                                    +K  ++S       E L  L   + L   + D LV
Sbjct: 103 ------------------------LKKHGRASQHAIDELEALAILFMPIKLVPKQYDALV 138

Query: 340 EQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVS 385
           E++ D   +I   E  +++L      + R  FL +    E +  W  
Sbjct: 139 ERVRDALNQIRAQERAVMQLCVRDARMPRADFLRQFPSNETNLAWAE 185


>gi|308050008|ref|YP_003913574.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
 gi|307632198|gb|ADN76500.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
          Length = 242

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 90/232 (38%), Gaps = 18/232 (7%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                          ++  +   + +    +   D+ Q G + L+ A  ++       F 
Sbjct: 18  RAHDENHYLRQYLPLVKRAMGQLRSHCGPMMGPEDMEQIGLMALLDALRRYPGEPDNGFI 77

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            +A   ++ AI   +  Q      P  +R + H++  T RR++ ++ R P  +E+A  L+
Sbjct: 78  AFASLRIRGAILDELRRQDW---RPRQLRQQSHELNDTVRRLTRELGRPPHDQEVADALS 134

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-TTTRV 616
           + +E  R+ L  +            E    L + +    ++    +  +   R  T    
Sbjct: 135 LSLEQYRERLYAS----------QAESLQSLDELLGAGASLEQEGNETERFQRHRTLASA 184

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L  L  RE+ VL + +      +  L+E+     +T  RI Q+   A+++LK
Sbjct: 185 LGKLNQREQLVLSLYYQH----ELNLKEIALTLGLTESRICQLHKHAVKQLK 232


>gi|255697095|emb|CBA11657.1| RNA polymerase sigma factor [Pseudomonas syringae pv. eriobotryae]
          Length = 194

 Score = 81.8 bits (200), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 68/235 (28%), Gaps = 44/235 (18%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+       G    +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPD------DGIAPPAEVPPPVDP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
           +  + +   + E +   A+    +D  +    P  A+     + +  + +   L      
Sbjct: 54  KAVKAEGTDDDEEESADASDDEDEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 107

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 108 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 138

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 139 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 193


>gi|239934396|emb|CAR92328.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 193

 Score = 81.4 bits (199), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 69/237 (29%), Gaps = 46/237 (19%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T   ++   D +      L ++  L   I P+               K   + +E + D+
Sbjct: 1   TVDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDDE 58

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   GD E  A+   D                         +A    A+ DQ       
Sbjct: 59  EESESGDDEEEAESGSDPVV----------------------AAQRFGAVSDQ------- 89

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
                         LQ  +   +K+ ++  +     + L  L   + L   + ++LVE++
Sbjct: 90  --------------LQVTSKVLKKNGRNHKESIEALQALANLFMPIKLVPKQFEVLVERV 135

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            D   R+   E  +++L      + R  FL      E +  W               
Sbjct: 136 RDALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETNQTWSGDLAKRNTKWAAAL 192


>gi|331085949|ref|ZP_08335032.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406872|gb|EGG86377.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 192

 Score = 81.4 bits (199), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 93/238 (39%), Gaps = 55/238 (23%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           ++K       AK  ++E NLRLV  + KKY        DLI  G +GL+KA   F+   G
Sbjct: 1   MQKYTEGDLEAKHILIEHNLRLVAHIVKKYQRPEEDNEDLISIGTVGLIKAVITFNPEKG 60

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            + STYA   ++  I   +                                         
Sbjct: 61  NRLSTYAARCIENEILMMLRS--------------------------------------- 81

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLR 610
                         K +   ISL  PIG +   +   L D +E  +        ++ ++R
Sbjct: 82  -------------RKKSSREISLYEPIGTDREGNEIQLFDVMETTDEDIHEKINLKDDVR 128

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +V + L+ RE  VL+MR+G+    ++T  E+ K+  ++R  + +IE  A+ KL+
Sbjct: 129 TLYEKVESELSDRERLVLKMRYGLYNEEEYTQREIAKRLGISRSYVSRIEKSAVEKLR 186


>gi|321116346|emb|CBN73554.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V289]
          Length = 201

 Score = 81.4 bits (199), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 70/248 (28%), Gaps = 48/248 (19%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L +++            G+    +  +    E      +    
Sbjct: 1   VDYILSEYDRVTTEGGRLSDVL-----------SGYIDPDDNIAAPTEEVPVPGAKAAAT 49

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +E   D E + +   +D  +    P  A      + +                       
Sbjct: 50  KEEADDEEXSEESDDEDEVEXGPDPVVAAQRFSAVAD----------------------- 86

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                        LQ      +K  +S+ +     + L  L   + L   + ++LVE++ 
Sbjct: 87  ------------QLQVTNKVLKKSGRSAKESIAALQALADLFMPIKLVPKQFEVLVERVR 134

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL      E D  W           W   +  +
Sbjct: 135 DALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRSTK-WAAALGEK 193

Query: 403 VDSILKIR 410
             +I+  +
Sbjct: 194 DAAIVACQ 201


>gi|224553544|gb|ACN55010.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 81.4 bits (199), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 51/111 (45%), Positives = 83/111 (74%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL  LDLI+EGN+GL++A EKFD   G++FST A WW++Q I R+I +Q+ TIR+P+H+ 
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTSATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
            +++  +RTAR +S+K+  EP+ EEIA++L  PV+ V ++L++ +   S++
Sbjct: 61  KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|255697121|emb|CBA11671.1| RNA polymerase sigma factor [Pseudomonas syringae pv. passiflorae]
          Length = 192

 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 73/235 (31%), Gaps = 46/235 (19%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +    E   
Sbjct: 2   AIAHFPGTVDHILSEYTRVTTEGGRLSDVL-----------SGYIDPDDGIAPPAAEVPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
               +    + + + + A   + D+      P             D   +A    A+ DQ
Sbjct: 51  PVDAKAAKADDDTEDDEAEASTDDEDEVESGP-------------DPIIAAQRFGAVSDQ 97

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
           +            E+ R+            K  +S+         L +L   + L   + 
Sbjct: 98  M------------EITRKALK---------KHGRSNKLAIAELLALAELFMPIKLVPKQF 136

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 137 EGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFPGHEVDESWSDALAK 191


>gi|115378523|ref|ZP_01465679.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
 gi|115364445|gb|EAU63524.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
          Length = 171

 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 40/118 (33%), Positives = 65/118 (55%), Gaps = 3/118 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ +     ++  +   +    RK       A++ +  +NL  V++VAKK+ NRG 
Sbjct: 12  LSHYLRHLGGHHQLTREQEYELARAARK---GDESARQTLATSNLAFVVAVAKKFANRGA 68

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           +  DLIQEGN+GLMKA E FD     +F+TYA+WW++  ITR + D    +R     R
Sbjct: 69  RLDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGGESER 126



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 124 YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
           YLR +G    L+RE E  +A+    G      +L  S L F  ++    +  +    L +
Sbjct: 15  YLRHLGGHHQLTREQEYELARAARKGDESARQTLATSNLAF--VVAVAKKFANRGARLDD 72

Query: 184 II 185
           +I
Sbjct: 73  LI 74


>gi|94495423|ref|ZP_01302003.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
 gi|94424811|gb|EAT09832.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
          Length = 243

 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 97/239 (40%), Gaps = 15/239 (6%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLG 493
                  + + +    + LV  +A     R    ++  DL+Q G + L++AA  F+   G
Sbjct: 13  YGKPGEHSPERLARQYMPLVRKIAWHVHGRVSTAIEVEDLLQIGMVALVEAANSFE-DRG 71

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+ YA   V+ A+   +  Q+   R  +  R    ++     R+  ++ R PT  E++
Sbjct: 72  LGFAAYAQLRVRGAMIDHLRRQATLCRSAMARRK---EIAGVRNRLEQQLGRLPTEAEMS 128

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            ++ +     R+     +            D S     +ED+          + +L++  
Sbjct: 129 SEMGLEPAAYREAADSVEMVQHTSMDEVYSDQSMWFADVEDR----ADQVLERESLKKAM 184

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              ++ L  RE  VL++ F      +  LEE+G+   +   R+ QI+  A+ KL+   R
Sbjct: 185 AACISELPQREAMVLQLYFV----EEMNLEEIGQTLDIGAARVCQIKKAALDKLREKLR 239


>gi|67921071|ref|ZP_00514590.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
 gi|67857188|gb|EAM52428.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
          Length = 250

 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 63/184 (34%), Positives = 93/184 (50%), Gaps = 10/184 (5%)

Query: 334 RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH-QGRELDPHWVSYAKDFP- 391
           R+ LL ++      R +    ELL +        D  +++  Q   +    ++Y    P 
Sbjct: 73  RVPLLTKEEEVSKSRQVQRYVELLEIRNQAAENDDEIMKQFVQVHGIHDQLMAYLGHRPS 132

Query: 392 EGEWKNFVACEVDSILKIRNEIK-SISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
             +W       V  + +I  + K   +V   + ++E   I             AK E+++
Sbjct: 133 WEKWAKASEVSVFELKEILVQGKSQWAVLANMDVAELEEIQK-------SGIKAKDEIIK 185

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ANLRLV+SVAKKY +RGL+ LDLIQEG +GL KA EKFD   GY+FSTYA WW++Q IT 
Sbjct: 186 ANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPVKGYRFSTYAYWWIRQGITS 245

Query: 511 SIAD 514
           +   
Sbjct: 246 AAWR 249



 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 42/85 (49%)

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           +  L +  I  +   D E  E + +  D        ++   +   S +R T D VR+YL+
Sbjct: 10  IDKLDSPEIRPITESDQEVNEIASELGDSLIELELQNINFTETDPSTNRVTTDLVRLYLQ 69

Query: 127 EMGSIELLSREGEIAIAKRIEAGRA 151
           ++G + LL++E E++ +++++    
Sbjct: 70  DIGRVPLLTKEEEVSKSRQVQRYVE 94


>gi|255697033|emb|CBA11626.1| RNA polymerase sigma factor [Pseudomonas cannabina]
 gi|255697059|emb|CBA11639.1| RNA polymerase sigma factor [Pseudomonas syringae pv. alisalensis]
 gi|255697081|emb|CBA11650.1| RNA polymerase sigma factor [Pseudomonas syringae pv.
           coriandricola]
          Length = 191

 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 27/235 (11%), Positives = 68/235 (28%), Gaps = 47/235 (20%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L +++            G+    +G +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 50

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + + E+A     ++  +    P  A+     + +  + +   L      
Sbjct: 51  VDPKAAKAEGDDEEEETAEATDDEEEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 104

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 105 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 135

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 136 EGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDALAK 190


>gi|321116246|emb|CBN73504.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V87]
 gi|321116288|emb|CBN73525.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V194]
 gi|321116290|emb|CBN73526.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V195]
 gi|321116292|emb|CBN73527.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V196]
 gi|321116298|emb|CBN73530.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V199]
 gi|321116300|emb|CBN73531.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V200]
          Length = 202

 Score = 81.4 bits (199), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 75/248 (30%), Gaps = 47/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L ++  L   I P+               K   + +E + D+ 
Sbjct: 1   VDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDDEE 58

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +   GD E  A+   D                         +A    A+ DQ        
Sbjct: 59  ESESGDDEEEAESGPDPVV----------------------AAQRFGAVSDQ-------- 88

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                        LQ  +   +K+ +S  +     + L  L   + L   + ++LVE++ 
Sbjct: 89  -------------LQVTSKVLKKNGRSHKESIEALQALADLFMPIKLVPKQFEVLVERVR 135

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL      E D  W           W   +  +
Sbjct: 136 DALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEK 194

Query: 403 VDSILKIR 410
             +I+  +
Sbjct: 195 NAAIVACQ 202


>gi|321116252|emb|CBN73507.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V111]
          Length = 201

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 61/177 (34%), Gaps = 3/177 (1%)

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           +  DD +  D         E    E+ DD     S  +++         +E A  +  + 
Sbjct: 26  IDPDDGNVPDEAAAPVPVKEGAAAEESDDEEEDDSGDDEEEEGDGGPDPEEAARRFNAVA 85

Query: 296 SLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             QD      +K  + S +       L +L   + L   + D LV Q+ D   R+   E 
Sbjct: 86  EQQDKVQKALKKHGRGSKQAIEELAALAELFMPIKLVPKQYDALVIQVRDALDRLRTQER 145

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            +++L      + R  FL    G E+D  W        + ++   +      I + +
Sbjct: 146 AIMQLCVRDARMPRADFLRLFPGNEVDMDWAGDLAK-GKAKYAEALGNLQADIKRCQ 201


>gi|18310750|ref|NP_562684.1| sporulation sigma factor SigK [Clostridium perfringens str. 13]
 gi|168214245|ref|ZP_02639870.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|169343581|ref|ZP_02864580.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170764185|ref|ZP_02633869.2| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|182420555|ref|ZP_02643878.2| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
 gi|182625679|ref|ZP_02953448.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|18145431|dbj|BAB81474.1| probable transcription initiation factor sigma K [Clostridium
           perfringens str. 13]
 gi|169298141|gb|EDS80231.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170660828|gb|EDT13511.1| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|170714308|gb|EDT26490.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|177909081|gb|EDT71556.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|182379749|gb|EDT77228.1| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
          Length = 233

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 93/249 (37%), Gaps = 55/249 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 31  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 87

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 88  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 132

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 133 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 158

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                     ++E   ++   L+PRE+ +++MR+G+      T  E+     ++R  + +
Sbjct: 159 VLEAVENSLQVKELYKKMSDVLSPREKEIIQMRYGLLDGDIKTQREIAGILGISRSYVSR 218

Query: 659 IEAKAIRKL 667
           IE KA++KL
Sbjct: 219 IEKKALKKL 227


>gi|223984440|ref|ZP_03634576.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
 gi|223963596|gb|EEF67972.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
          Length = 232

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 87/232 (37%), Gaps = 57/232 (24%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A+  ++E NLRLV+ +AK+Y    +   DLI  G IGL+KA   F      K  TYA
Sbjct: 49  DQQARDTLIEHNLRLVVYIAKRYETNPIFMEDLISIGTIGLIKAVNTFKRDKNIKLVTYA 108

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +  +S                                            
Sbjct: 109 SRCIENEILMFLRKKSRRKTE--------------------------------------- 129

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
                        IS + P+  +   +   L D +  +  +       + + R+   + +
Sbjct: 130 -------------ISFDEPLNVDYDGNELLLSDILGTEGDIVAESFYAEEDKRQLL-KAM 175

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + L   E  +L MR+GI  + + T +++  Q  +++  I ++E + I+KL++
Sbjct: 176 SKLKENERMILEMRYGIN-HEELTQKDIADQLGISQSYISRLEKRIIQKLRN 226


>gi|289548919|ref|YP_003473907.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermocrinis albus DSM
           14484]
 gi|289182536|gb|ADC89780.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermocrinis albus DSM
           14484]
          Length = 233

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 43/216 (19%), Positives = 84/216 (38%), Gaps = 10/216 (4%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           + V     ++    +   DLI  G + +M++  + D       STY    VK A+   + 
Sbjct: 22  KSVAKKIHRHLPPSVDINDLIGYGILAVMESLSRIDPTKNP--STYLYMRVKGAMYDYLR 79

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
                      +R++   + R    +  ++ R+PT EEI + L    + + + ++     
Sbjct: 80  SLH---LCSRRVREREKLIRRKMEELRQQLGRDPTDEEIGEALGETPDKIYEDVQRAAFA 136

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
             L       +     + +       P +  ++   R      +  L+ RE+ VL++ F 
Sbjct: 137 QILSLDALFREGRSYEELLA-AAEDGPEEKVLREERRRRLLEAIEKLSYREKLVLQLLF- 194

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                +   + V K   V+  RI QI+ +AI KLK 
Sbjct: 195 ---YEELPAKTVAKLLGVSSARISQIKEQAIEKLKE 227


>gi|239934338|emb|CAR92299.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 204

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 79/249 (31%), Gaps = 46/249 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIRN 411
            + I++ + 
Sbjct: 196 KEDIVRSQQ 204


>gi|291527309|emb|CBK92895.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 224

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 98/228 (42%), Gaps = 15/228 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +V  N+ L+  V K++ NRG+   DL Q G +GL KAA++FD   G+ FSTYA+  +  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    + I   + D   K+     +       E + E++     M  + +   
Sbjct: 68  EIQRFLRD-DGMVHISRKILDDARKIAIIREKYRMNENSEISLEKMENISGMSKQDIIIA 126

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPR 623
           ++  K   S+E          + D++++K +    D   + +         +   SL   
Sbjct: 127 MEADKNASSIE-------NESVLDYLDNKMSAEASDKPSETDKVINHIAMQQAFNSLDDS 179

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           E R++ +R+      D T ++V +     +  I ++E   + KL+   
Sbjct: 180 ERRLIMLRY----MQDKTQKQVAEVLGRNQVAISRMEKNTLAKLRRAM 223


>gi|321116372|emb|CBN73567.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. Vl1]
          Length = 204

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 69/186 (37%), Gaps = 8/186 (4%)

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D +  + V+ DD   V +     E D+   ++D DD +                   
Sbjct: 26  IDPDDDGMSGVNSDDIPAVAAKGAKKEGDDDEEEDDSDDDSDDNEGDGGPDPEVARLRFT 85

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            I E   +L+ +       +K  ++S K    +E L  L   + L   + + LV ++ D 
Sbjct: 86  AIKEQLEKLQKV------LKKHPRNSPKAVAEQEALATLFMPIKLIPKQYEALVNRVRDA 139

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             ++   E  +++L      + R  FL    G E++  WV           +N  A + D
Sbjct: 140 QDQVRKQERAIMQLCVRDARMPRADFLRSFPGNEVNEGWVDALLADSPRYSENLQALKTD 199

Query: 405 SILKIR 410
            I + +
Sbjct: 200 -IQRAQ 204


>gi|163814130|ref|ZP_02205522.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
 gi|158450579|gb|EDP27574.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
          Length = 245

 Score = 81.0 bits (198), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 89/237 (37%), Gaps = 58/237 (24%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           + ++  AKK ++E NLRLV+ +A+K+ N G+   DLI  G IGL+KA   F      K +
Sbjct: 56  QKQSEEAKKMLIERNLRLVVYIARKFDNTGVGIEDLISIGTIGLIKAINTFKNDKNIKLA 115

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   ++  I   +   +                                         
Sbjct: 116 TYASRCIENEILMFLRRNNRLRTE------------------------------------ 139

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTT 614
                           +S++ P+  +   +   L D +     +   D   + +      
Sbjct: 140 ----------------VSIDEPLNVDWDGNELLLSDILGTDEDIVYRDLETEVD-HNLLD 182

Query: 615 RVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++ L  +E  ++ +R+GI      + T +EV     +++  I ++E K I+KL+ 
Sbjct: 183 AAISKLGEKERTIIELRYGINTIGGVEKTQKEVADILGISQSYISRLEKKIIKKLRR 239


>gi|239934470|emb|CAR92489.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 214

 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 54/149 (36%), Gaps = 3/149 (2%)

Query: 286 EIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           E  E +  LR L + A     +   +    +     L +    L L   + + + E + +
Sbjct: 67  EAKERFDTLRQLNNKAKKAINRYGVAHKSTQQHLSALGEHFKFLKLAPRQFEPMAEAVRE 126

Query: 345 ISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
               I   E  ++ L      + R  F+    G E D  W +      E  +   +A   
Sbjct: 127 ALSLIRAEERTVMALCIRQAKMPRTDFIGLFPGHETDESWATGLAKGKEP-YAAAIAVVE 185

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVS 432
             I + +  +  +  +TG++IS+ + I  
Sbjct: 186 PDIQRSQRRLMQLEEKTGLTISQIKDINR 214


>gi|321116198|emb|CBN73480.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V19]
 gi|321116200|emb|CBN73481.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V20]
          Length = 202

 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 75/248 (30%), Gaps = 47/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++   D +      L ++  L   I P+               K   + +E + D+ 
Sbjct: 1   VDYILGEYDRVTTEGGRLSDV--LSGYIDPDDNIAAPTEEVPIPGAKAAAAKEESDDDEE 58

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
           +   GD E  A+   D                         +A    A+ DQ        
Sbjct: 59  ESESGDDEEEAESGPDPVV----------------------AAQRFGAVSDQ-------- 88

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                        LQ  +   +K+ ++  +     + L  L   + L   + ++LVE++ 
Sbjct: 89  -------------LQVTSKVLKKNGRNHKESIEALQALADLFMPIKLVPKQFEVLVERVR 135

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D   R+   E  +++L      + R  FL      E D  W           W   +  +
Sbjct: 136 DALSRLRQQERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTK-WAAALGEK 194

Query: 403 VDSILKIR 410
             +I+  +
Sbjct: 195 NAAIVACQ 202


>gi|121488755|emb|CAJ18262.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 50/163 (30%), Positives = 90/163 (55%), Gaps = 1/163 (0%)

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
            EG  G +KAA++ D   G+KF +YA+WW +Q+  +++A+QS  +R+P++    ++K+ +
Sbjct: 4   NEGXXGXIKAAKRXDETRGFKFISYAVWWXRQSXLQALAEQSRIVRLPLNRVGTLNKISK 63

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D +++
Sbjct: 64  AYXQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQN 123

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
              + P     + +L     R L+ L PRE  V+R  F IGM+
Sbjct: 124 DGHL-PDHGLNKDSLTLEVERSLSVLXPREADVIRSYFXIGMD 165


>gi|239934506|emb|CAR92507.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 219

 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 42/265 (15%), Positives = 80/265 (30%), Gaps = 49/265 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLRSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISI 424
               D I + + ++  I  E G+ I
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDI 217


>gi|325523159|gb|EGD01550.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 126

 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 40/125 (32%), Positives = 68/125 (54%)

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + +P+  V  ++ I +EP+S + P+  +     G+ + D+    P D+A    LR     
Sbjct: 1   MDLPLAKVLDLMAIVREPVSTDVPVSPDGDMTFGEVVPDQATPLPEDAAAATQLRAAMAA 60

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L  RE  VLR+R+GIG     +L ++G+Q  ++ ER+RQIEA A+ +++       
Sbjct: 61  TLGGLPAREATVLRLRYGIGTADGVSLRDIGRQLNLSAERVRQIEASALERIRASGALHG 120

Query: 676 LRSFL 680
           LRSF+
Sbjct: 121 LRSFM 125


>gi|239934476|emb|CAR92492.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 219

 Score = 80.7 bits (197), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 42/265 (15%), Positives = 80/265 (30%), Gaps = 49/265 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHGIRDQIAKLQGSKAPNPEL------LNGLREELLSNVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMGRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISI 424
               D I + + ++  I  E G+ I
Sbjct: 193 KQFTDDIRRAQRKLAEIEREHGLDI 217


>gi|110799358|ref|YP_696454.1| sporulation sigma factor SigK [Clostridium perfringens ATCC 13124]
 gi|110674005|gb|ABG82992.1| RNA polymerase sigma-70 factor family [Clostridium perfringens ATCC
           13124]
          Length = 233

 Score = 80.7 bits (197), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 93/249 (37%), Gaps = 55/249 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 31  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 87

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 88  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 132

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 133 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 158

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                     ++E   ++   L+PRE+ +++MR+G+      T  E+     ++R  + +
Sbjct: 159 VLEAVENSLQVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAAILGISRSYVSR 218

Query: 659 IEAKAIRKL 667
           IE KA++KL
Sbjct: 219 IEKKALKKL 227


>gi|321116336|emb|CBN73549.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V233]
          Length = 201

 Score = 80.7 bits (197), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 60/177 (33%), Gaps = 3/177 (1%)

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           +  DD S  D         E    E+ DD        +++         +E A  +  + 
Sbjct: 26  IDPDDGSVPDEAAAPVPVKEGAAAEESDDEDEEEDGDDEEEEGDGGPDPEEAARRFSAVA 85

Query: 296 SLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             QD      +K  + S +       L +L   + L   + D LV Q+     R+   E 
Sbjct: 86  EQQDKVQKALKKHGRGSKQVTDELAALAELFMPIKLVPKQYDALVIQVRSALDRLRAQER 145

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            +++L      + R  FL    G E+D  W +      + ++   +      I + +
Sbjct: 146 AIMQLCVRDARMPRADFLRLFPGNEVDMDWSADLAK-GKAKYAEALGNLQADIQRCQ 201


>gi|317010689|gb|ADU84436.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           SouthAfrica7]
          Length = 255

 Score = 80.7 bits (197), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 51/268 (19%), Positives = 103/268 (38%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S      +++   K +     A   +    L  V ++A +   
Sbjct: 2   ILMMENRMPKGIQKTEASEKSIEKVLNAYDKQQHHHQNA---LAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+ E +AK L   +E +R+    +     +   +  
Sbjct: 116 RSNRKLIKSIDFEITKYLNEHGKEPSDEYLAKALGENIEKIREAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITKKIEAEELLEHVQKVLNQMSEREQMLIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRQS 249


>gi|321116266|emb|CBN73514.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V125]
          Length = 200

 Score = 80.7 bits (197), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 64/189 (33%), Gaps = 8/189 (4%)

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   G I+       D+ +      E A  +E + +E+++               +   
Sbjct: 19  AEVLSGYIDPDDGSVPDEAAAPVPVKEGAAAEESDDEEEDESDDEEEEGDGGPDPEEAAR 78

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               +AE   ++          +K  + S +       L +L   + L   + D LV ++
Sbjct: 79  RFTAVAEQQDKVLK------ALKKHGRGSKQAIEELAALAELFMPIKLVPKQYDALVTRV 132

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL    G E+D  W +      + ++   +  
Sbjct: 133 RDALDRLRTQERAIMQLCVRDARMPRADFLRLFPGNEIDMAWAADLAK-GKAKYAEALGN 191

Query: 402 EVDSILKIR 410
               I + +
Sbjct: 192 LQADIQRCQ 200


>gi|321116296|emb|CBN73529.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V198]
 gi|321116302|emb|CBN73532.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V202]
          Length = 201

 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 3/177 (1%)

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           +  DD +  D         E    E+ DD     S  +++         +E A  +  + 
Sbjct: 26  IDPDDGNVPDEAAAPVPVKEGAAAEESDDEEEDDSGDDEEEEGDGGPDPEEAARRFNAVA 85

Query: 296 SLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             Q+      +K  + S +       L +L   + L   + D LV Q+ D   R+   E 
Sbjct: 86  EQQEKVQKALKKHGRGSKQAIEELAALAELFMPIKLVPKQYDALVIQVRDALDRLRAQER 145

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            +++L      + R  FL    G E+D  W        + ++   +      I + +
Sbjct: 146 AIMQLCVRDARMPRADFLRLFPGNEVDMDWAGDLAK-GKAKYAEALGNLQSDIKRCQ 201


>gi|239934406|emb|CAR92333.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 202

 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 63/190 (33%), Gaps = 8/190 (4%)

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +   G I+       D+ +      E A  +E + +E+++               +   
Sbjct: 20  AEVLSGYIDPDDGSVPDEAAAPVPVKEGAAAEESDDEEEDESDDEEEEGDGGPDPEEAAR 79

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               +AE    +          +K  + S +       L +L   + L   + D LV ++
Sbjct: 80  RFTAVAEQQDRVLK------ALKKHGRGSKQAIEELAALAELFMPIKLVPKQYDALVTRV 133

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            D   R+   E  +++L      + R  FL    G E+D  W +      + ++   +  
Sbjct: 134 RDALDRLRTQERAIMQLCVRDARMPRADFLRLFPGNEIDMAWAADLAK-GKAKYAEALGN 192

Query: 402 EVDSILKIRN 411
               I + + 
Sbjct: 193 LQADIQRCQQ 202


>gi|126653890|ref|ZP_01725737.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
 gi|126589615|gb|EAZ83754.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
          Length = 235

 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 52/274 (18%), Positives = 95/274 (34%), Gaps = 59/274 (21%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I  +   +K  +     S  E     + + +       A+ +++E N+RLV  V KK+ 
Sbjct: 14  EIPALLGYLKGQTFHKPFSKEEE---AACIERFLGGDEQARLDLIERNMRLVAHVVKKFH 70

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +  Q  D I  G IGLMKA E +      + +TYA   ++  I   +            
Sbjct: 71  PKHEQLDDYISIGTIGLMKAVESYTPDKKTRLATYAARCIENEILMHLR----------- 119

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                                               + V+K        +SL  PIG + 
Sbjct: 120 ----------------------------------TQKKVQK-------DVSLFEPIGTDK 138

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +    I D        +  +   +E        L  L  RE  ++ +R+G+      T
Sbjct: 139 DGNAL-QIRDLLQCDEESATEKIEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDALT 197

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            +E+  +  ++R  + +IE +A+ KL    +  +
Sbjct: 198 QKEIAARLNISRSYVSRIEKRALIKLYQLYKRDQ 231


>gi|32329806|emb|CAD92276.1| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|32440921|emb|CAD92277.2| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|32440923|emb|CAD92272.2| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|32440925|emb|CAD92273.2| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|32440927|emb|CAD92274.2| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|32440929|emb|CAD92275.2| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
          Length = 190

 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 64/182 (35%), Gaps = 5/182 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 13  DPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 72

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 73  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 129

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +++L      + R  FL +  G E+D  W   A    + ++   +      I + +
Sbjct: 130 QERAIMQLCVRDARMPRADFLRQFPGNEVDESWTD-ALAKGKSKYAEAIGRLQPDIQRCQ 188

Query: 411 NE 412
            +
Sbjct: 189 QK 190


>gi|157959887|ref|YP_001499921.1| flagellar biosynthesis sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157844887|gb|ABV85386.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella pealeana
           ATCC 700345]
          Length = 240

 Score = 80.7 bits (197), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 101/242 (41%), Gaps = 21/242 (8%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKF 488
               +      +A+ ++++  L LV     +  +     L   D+ Q G + L+++A ++
Sbjct: 9   QEAAEEVAINRLAESQVMKQYLPLVKRSVSQLRSHCGIALAIEDMEQIGMMALLESARRY 68

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
                  F ++A   ++ AI   +  Q    R    +R + H++    R+++  +KREPT
Sbjct: 69  PGEYDNGFLSFAGQRIRGAILDELRRQDWRPRP---VRQQAHELNDMVRKLTRSLKREPT 125

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA- 607
             E+A+ + +     R+ L  +            E    L + I D          ++  
Sbjct: 126 DLEVAQSMGLSQVEYRERLFAS----------QSESMRSLDELIGDGGHFEDKSDMLEQF 175

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + +ET  + +  L  RE+ +L + +      +  L+E+     +T  RI Q+   A+++L
Sbjct: 176 STKETLFQAILKLNKREQIILSLYYQH----ELNLKEIAATLGLTETRICQLHKHAVKQL 231

Query: 668 KH 669
           + 
Sbjct: 232 QQ 233


>gi|293401517|ref|ZP_06645660.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305155|gb|EFE46401.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 238

 Score = 80.3 bits (196), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 96/255 (37%), Gaps = 57/255 (22%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E    ++ +   E     A+ +++E NLRLV+ +AK+Y    +   DLI  G+IGL+K
Sbjct: 34  PLEKEEELAALIALENGDEEARNKLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIK 93

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A   F      K  TYA   ++  I   +  +S                           
Sbjct: 94  AVNTFKRDKNIKLVTYASRCIENEILMFLRKKSRRKVE---------------------- 131

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSP 600
                                         +S + P+  +   +   L D +   + +  
Sbjct: 132 ------------------------------VSFDEPLNIDYDGNELLLSDILGTDDDI-V 160

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                +   +      +A+L  RE ++L+MR+GI  + + T +++ K+  +++  I ++E
Sbjct: 161 TKEFEKQENKRELLAAMATLKDRERQILQMRYGIE-HEELTQKDIAKRLGISQSYISRLE 219

Query: 661 AKAIRKLKHPSRSKK 675
            + I+KLK   +   
Sbjct: 220 KRIIQKLKVQMKKNH 234


>gi|239934492|emb|CAR92500.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 222

 Score = 80.3 bits (196), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/270 (15%), Positives = 81/270 (30%), Gaps = 49/270 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAXKRH-STRL 192

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRH 429
               D   + + ++  I  E G+ IS  + 
Sbjct: 193 KXFTDDXRRAQRKLAEIEREHGLDISRIKE 222


>gi|254431663|ref|ZP_05045366.1| group3 RNA polymerase sigma factor SigF1 [Cyanobium sp. PCC 7001]
 gi|197626116|gb|EDY38675.1| group3 RNA polymerase sigma factor SigF1 [Cyanobium sp. PCC 7001]
          Length = 257

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 93/238 (39%), Gaps = 9/238 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDW 490
            +    +C A  A+   VE    LV  +A  Y +R      DLIQ G +GL++AAE +  
Sbjct: 8   RLSSHQDCRAIQARNRRVEQYKALVRPIALHYHHRCSEPLDDLIQVGLMGLLRAAELYRP 67

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F  +A   V+ A+   + D +  IR+P  + ++  ++ R          R  T +
Sbjct: 68  STATPFEAFARPHVRGALLHYLRDVALPIRLPRRLDEQRLQLARLRSSWLAAHHRPATEQ 127

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E+ + L +      + L+  ++ + +++     D        E +   +      +A+  
Sbjct: 128 ELRQLLGLDQSHWNR-LQAAEQLVRVQSLDFWLDDGGEPPCAETETGPADPCRGEEAS-- 184

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +LA L     +V+      G +   T         V+   +++   +A+  L+
Sbjct: 185 -APAALLAGLEEPLRQVVERVILAGWSYRRT----ASALNVSPMTVQRRLHRALALLR 237


>gi|88856926|ref|ZP_01131577.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
 gi|88813802|gb|EAR23673.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
          Length = 244

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 97/243 (39%), Gaps = 22/243 (9%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
              ++  +       A  E+  +      S++ K+T RG+   DL  E   GL++AA+ F
Sbjct: 17  REAALAARISNGEMEAVHELAMSGYAWAKSLSHKFTGRGVDLDDLNSEAYFGLVEAAKTF 76

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G +F+ Y+  +V+ AI ++I     ++ IP H  D   ++V    R+S +      
Sbjct: 77  DPTRG-RFAGYSTAFVQGAIWKAIRLSGRSVSIPKHAFD--AELVGNRDRISERYAANAA 133

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
               A     P +              L+ P+  +      D +   +A     + ++  
Sbjct: 134 LASEASAWHFPTQ--------------LDAPLSSDAPGTAADVLI-SDARGVEQTVVEQI 178

Query: 609 LRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  +L+ +   E  VL  RF + G  +      +     + + RI +IE KA+ +L
Sbjct: 179 F---LDGMLSEIPRIEREVLLARFELPGACSAPGQAAISAALNIDQRRISEIEKKALARL 235

Query: 668 KHP 670
           ++ 
Sbjct: 236 RNA 238


>gi|83716542|ref|YP_438382.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
 gi|83650367|gb|ABC34431.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 369

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 96/230 (41%), Gaps = 23/230 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDL---IQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++  +     +V   A++  ++ +  L L    Q G +GL++A  ++       F  YA
Sbjct: 154 AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYGMP-DAAFPCYA 212

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              V+ AI   +         P  +R + H+     R +   + REPT  E++  L +  
Sbjct: 213 ATRVRGAILDELRRHDW---RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSSALGIST 269

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLAS 619
              R+ +                +     D + D +A++  +S  +  +R     + LA 
Sbjct: 270 AEYRERVMANNA-----------EAMASFDSVLDDDALTHEESPERQIVRRRCLEQALAR 318

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+RV+++ +      D +L E+     +T  R+ QI   A++K++ 
Sbjct: 319 LNEREQRVIQLYYEF----DLSLREIASVLELTEARVCQINKAALKKMRE 364


>gi|299535719|ref|ZP_07049040.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728919|gb|EFI69473.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 235

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 52/274 (18%), Positives = 95/274 (34%), Gaps = 59/274 (21%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I  +   +K  +     S  E     + + +       A+ +++E N+RLV  V KK+ 
Sbjct: 14  EIPALLGYLKGQTFHKPFSKEEE---AACIERFLGGDEQARLDLIERNMRLVAHVVKKFH 70

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +  Q  D I  G IGLMKA E +      + +TYA   ++  I   +            
Sbjct: 71  PKHEQLDDYISIGTIGLMKAVESYTPDKKTRLATYAARCIENEILMHLR----------- 119

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                                               + V+K        +SL  PIG + 
Sbjct: 120 ----------------------------------TQKKVQK-------DVSLFEPIGTDK 138

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +    I D        +  +   +E        L  L  RE  ++ +R+G+      T
Sbjct: 139 DGNAL-QIRDLLQCDEESATEKLEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDALT 197

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            +E+  +  ++R  + +IE +A+ KL    +  +
Sbjct: 198 QKEIAARLNISRSYVSRIEKRALIKLYQLYKRDQ 231


>gi|110803132|ref|YP_699053.1| sporulation sigma factor SigK [Clostridium perfringens SM101]
 gi|6715486|gb|AAF26431.1|AF218835_2 RNA polymerase sigma factor SigK [Clostridium perfringens]
 gi|110683633|gb|ABG87003.1| RNA polymerase sigma-70 factor family [Clostridium perfringens
           SM101]
          Length = 233

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 93/249 (37%), Gaps = 55/249 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 31  LNEKEEKIYLDRLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 87

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 88  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 132

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 133 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 158

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                     ++E   ++   L+PRE+ +++MR+G+      T  E+     ++R  + +
Sbjct: 159 VLEAVENSLQVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAAILGISRSYVSR 218

Query: 659 IEAKAIRKL 667
           IE KA++KL
Sbjct: 219 IEKKALKKL 227


>gi|210610056|ref|ZP_03288235.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
 gi|210152667|gb|EEA83673.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
          Length = 208

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 97/256 (37%), Gaps = 58/256 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++ +E ++    ++K       AK  ++E NLRLV  V KKY        DLI  
Sbjct: 6   SFPIPLTAAEEQYY---IQKYIEGDLEAKHILIERNLRLVAHVIKKYQYLDDDPEDLISI 62

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   F+     +  TYA   ++  I   +                        
Sbjct: 63  GTIGLIKAVATFNPSKNNRLGTYAARCIENEILMMLR----------------------- 99

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                                   + V K        ISL  PIG +   +     +   
Sbjct: 100 ----------------------SKKKVSKE-------ISLYEPIGTDREGNEIQLFDIIE 130

Query: 597 AVSPLDSA---IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           A          ++ +++   T+V + L+PRE  VL+MR+G+    ++T  E+  Q  ++R
Sbjct: 131 ADDDDAQTKVALKEDIKMLYTKVESELSPRERLVLKMRYGLYDEEEYTQREIAAQLGISR 190

Query: 654 ERIRQIEAKAIRKLKH 669
             + +IE  AI KL+ 
Sbjct: 191 SYVSRIEKSAIEKLRE 206


>gi|121488741|emb|CAJ18254.1| sigma 70-type sigma factor [Chlorobaculum limnaeum]
          Length = 149

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/150 (31%), Positives = 86/150 (57%), Gaps = 1/150 (0%)

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G+KF +YA+WW++Q+I +++A+QS  +R+P++    ++K+ +   ++  + +R+P
Sbjct: 1   FDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNRVGTLNKISKAYSQLEQEYERDP 60

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             +E+A  L M  + V   LKI    +S++ P    D + L D +++   + P     + 
Sbjct: 61  NTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHM-PDHGLNRD 119

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMN 637
           +L     R L+ L PRE  V+R  FGIGM+
Sbjct: 120 SLTLEVERSLSVLAPREADVIRSYFGIGMD 149


>gi|240145516|ref|ZP_04744117.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257202333|gb|EEV00618.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
          Length = 207

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 92/256 (35%), Gaps = 55/256 (21%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           ++T +S          ++K +  +  A+ E+   N+RLV  VAKKY N      DLI  G
Sbjct: 1   MKTFLSPLTPEQENECLKKLKKGSLEARNELTLHNMRLVAHVAKKYQNSEEDMEDLISIG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            IGLMKA   +    G + +TYA   +   +                         R  +
Sbjct: 61  TIGLMKAIATYKEDYGSRLATYAARCIDNELLMYF---------------------RAKK 99

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIED 594
           ++S +                               +SL  PIG +      HL D +E 
Sbjct: 100 KVSRE-------------------------------VSLYEPIGMDKEGNQIHLLDIVES 128

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +             + +    V   L  RE  ++  R+G+  N   T  E+     ++R 
Sbjct: 129 EEPDVVEMMERTRQIEKLLGLVPKVLQERELYIVVHRYGLFGNKAMTQREIASAVGISRS 188

Query: 655 RIRQIEAKAIRKLKHP 670
            + +IE KA+ KLK  
Sbjct: 189 YVSRIEKKALDKLKKS 204


>gi|260899647|ref|ZP_05908042.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
 gi|308106738|gb|EFO44278.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
          Length = 120

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 32/103 (31%), Positives = 58/103 (56%), Gaps = 2/103 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S++    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEI--EAAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
              DL+QEGNIGLMKA ++F+  +G +  ++A+ W+K  I   
Sbjct: 74  PMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEY 116


>gi|147677483|ref|YP_001211698.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273580|dbj|BAF59329.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/244 (22%), Positives = 101/244 (41%), Gaps = 31/244 (12%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
            +M    +  ++ + +++VEA  RLV      Y   G    DL+Q G  GL+KAA+++D 
Sbjct: 20  AAMAAYLQDGSAESLQKVVEAGTRLVHYFVGLYA-PGHSREDLVQSGFEGLLKAAKRYDP 78

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  FSTYA   +   +   I  ++   R          +V R      N+    PT +
Sbjct: 79  GRGVSFSTYASHCIMGEVRHFIRKEASFSRPGW-AAGLQERVNRFLEEYLNEKGELPTLD 137

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL- 609
           +IA  + +  EG+ +V++                   +G    D+  VS + S    +  
Sbjct: 138 QIAGAVNIRKEGLLQVMR-------------------VGWVAPDEIDVSKIRSQRYESFQ 178

Query: 610 -----RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                R    + +  LT  + RV+ M F        T  E  ++  +T+ ++ ++  K++
Sbjct: 179 LPVEDRIVLRQAVEKLTELQRRVIAMLFFKN----MTQGEAAEELGITQRKVSRVLHKSL 234

Query: 665 RKLK 668
           + L+
Sbjct: 235 KLLR 238


>gi|87201086|ref|YP_498343.1| sigma 28 (flagella/sporulation) [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87136767|gb|ABD27509.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 244

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 88/223 (39%), Gaps = 14/223 (6%)

Query: 449 VEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +   L +V  +A      G   ++  DLIQ G + L + A++ D      F+ YA   V+
Sbjct: 23  IRRFLPMVKRLAWHVHGSGRSGIEIEDLIQAGLVALTECAQRHDGPTEDGFAAYAKLRVR 82

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   +     +  +     ++   +      ++ ++ R P+  E+A+ + +    +  
Sbjct: 83  GAMVDLVR---RSTPLSRSATERRRVLREKTATLATELGRPPSEAELARAVGLTERELAD 139

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +   EP+  E        S+        +     D    A +R      +A L  R  
Sbjct: 140 -QRAADEPLRFEAIDDAYSDSNSAFA---DDRPDSFDMLADAEMRGAVAAAIAGLPER-- 193

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L++   +    +  L E+ +   V+  R+ Q++A+AI KL+
Sbjct: 194 --LQLIIQLYFVEELNLAEIAEVLGVSIPRVHQLKAQAIDKLR 234


>gi|284041500|ref|YP_003391840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283945721|gb|ADB48465.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 270

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 85/250 (34%), Gaps = 16/250 (6%)

Query: 429 HIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKA 484
             +++ R+ +     A +  +V     +V  +  K         +  D I  G   L+ +
Sbjct: 15  DALALWRQYKESGDRAVRDRLVLTFAPMVKYIVYKKVREIPARCEVEDFISCGLEALIHS 74

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            E++D   G     ++   +  A+   +  Q      P  +R     + +          
Sbjct: 75  IERYDPEKGATLEQFSWTRIHGAVLDELRRQDW---APRSLRRWERDINQAREHFIGVHS 131

Query: 545 REPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVS 599
           R P+ EE+A  L      +  R+   +  +  SL T +  +D +    +   + +     
Sbjct: 132 RRPSREELAGALGTTPAELRAREDEIVASDVTSLNTLVLSDDETAIERIDTLVSEDRFAD 191

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           P     +   +         L  RE  V  + +        TL E+G    V+  R+ QI
Sbjct: 192 PEHHTARDQAKMRFREAFERLPRREREVAVLLYVKN----LTLREIGGILGVSESRVCQI 247

Query: 660 EAKAIRKLKH 669
             +  R LK 
Sbjct: 248 HGQLKRMLKE 257


>gi|158339684|ref|YP_001520691.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158309925|gb|ABW31541.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 400

 Score = 80.3 bits (196), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 49/202 (24%), Positives = 81/202 (40%), Gaps = 14/202 (6%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ + +  +     +   E    + ++RK +     +   ++  ++RLV  +AK+Y   
Sbjct: 14  IRLPDYLTQLLHRFPVPNPEEE--LDLIRKAKLGHETSLSWLMIGHVRLVSKLAKQYAWT 71

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
                DLIQEG +G+  A  KFD   G KFSTYA  W++  I R      C    P  +R
Sbjct: 72  LDDAQDLIQEGMLGIRHAVRKFDSTKGCKFSTYARGWIRGYIRRF-----CYKNRPKQLR 126

Query: 527 ---DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
               K   + R  R        +   EEIA+K  + +E +  +L   +     E P   E
Sbjct: 127 LPEKKQVHLDRVYR--LQNQFPDANLEEIAQKANLKLEYIEDLLYWGRSFQ--EIPDWHE 182

Query: 584 DTSHLGDFIEDKNAVSPLDSAI 605
            T +   F  D           
Sbjct: 183 FTINDESFYTDDEEYDEYFDFE 204


>gi|73532520|dbj|BAE19818.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda]
          Length = 168

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/159 (24%), Positives = 75/159 (47%), Gaps = 4/159 (2%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DL+Q G IGL+ A E++D   G  F+TYA+  ++ A+   +  +     +P  +R 
Sbjct: 11  VELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDELRSRDW---VPRSVRR 67

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               V    +R   ++ R P   EIA+++ +P+E  +++L  T            ED   
Sbjct: 68  NARGVSAAMQRAEQRLGRTPGDSEIAQEMGIPLEEYQQILLDTNTSQLFSYDEWREDHGD 127

Query: 588 LGD-FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
             +  +E     +PL   ++++LR      + +L  RE+
Sbjct: 128 SAEPVLEQSEEANPLRQLLESDLRGRVIAAIEALPEREK 166


>gi|306841478|ref|ZP_07474178.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
 gi|306288442|gb|EFM59798.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
          Length = 198

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 84/186 (45%), Gaps = 13/186 (6%)

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE- 550
            +FSTYA WW++ ++   I      +R       K     + R   +++         E 
Sbjct: 1   MRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEI 60

Query: 551 --EIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAI 605
             EI+ +L +    V     +++    SL  P+  E+T  S   DF+ D + +    +  
Sbjct: 61  YREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAES 120

Query: 606 QANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             ++       TR L +L  RE  ++R R         TLE +G++  +++ER+RQIE++
Sbjct: 121 SIDMERRNRWLTRALDTLNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESR 178

Query: 663 AIRKLK 668
           A+ KLK
Sbjct: 179 AMEKLK 184


>gi|154485092|ref|ZP_02027540.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
 gi|149734045|gb|EDM50164.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
          Length = 244

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 92/238 (38%), Gaps = 60/238 (25%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E     AK  ++E NLRLV+ +AKK+ N G+   DLI  G IGL+K    F      K +
Sbjct: 55  ENNDEEAKSMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKGINTFKPDKNIKLA 114

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   ++  I   +                  K  +T                      
Sbjct: 115 TYASRCIENEILMYLR-----------------KNNKTKLE------------------- 138

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIE-DKNAVSPLDSAIQANLRETT 613
                           +S++ P+  +   +   L D +  D++ +S    +     ++  
Sbjct: 139 ----------------VSIDEPLNVDWDGNELLLSDILGTDEDVISKGIESEVE--KKLL 180

Query: 614 TRVLASLTPREERVLRMRFGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            + +  L  RE+ ++ MR+G+      + T +EV     +++  I ++E K I++LK 
Sbjct: 181 YKAIEKLNHREKVIVEMRYGLNNKDGEEMTQKEVADSLGISQSYISRLEKKIIKRLKR 238


>gi|225018077|ref|ZP_03707269.1| hypothetical protein CLOSTMETH_02014 [Clostridium methylpentosum
           DSM 5476]
 gi|224949074|gb|EEG30283.1| hypothetical protein CLOSTMETH_02014 [Clostridium methylpentosum
           DSM 5476]
          Length = 267

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 100/236 (42%), Gaps = 54/236 (22%)

Query: 450 EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
              L+      +++T  G+ + DL+QE    +++A E FD     KF++Y  + +K    
Sbjct: 35  TKCLKWYTRSQERFTRLGVDYDDLVQECYFAMVEAVEAFDPESELKFTSYLNFPIK---- 90

Query: 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
                                ++   +   +++ K +PT                     
Sbjct: 91  --------------------KRLNAISNNRTSRQKNDPTLS------------------- 111

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREE 625
                SL+  +G E    LG+ I DK A  P +   Q +    L+E    VL +LT  ++
Sbjct: 112 ---CTSLDIEVGAEGDCPLGELIPDKTAGIPFEVIEQQDWNRALQEAIETVLDTLTENQQ 168

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            V+R+RF      D +L E+ ++   +RERIRQI+ ++++ +K P   K L+ F D
Sbjct: 169 EVIRLRF----YEDKSLIEISEETGRSRERIRQIQGQSLKAMKKPLPRKILKPFYD 220


>gi|321116368|emb|CBN73565.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. VGXO14]
          Length = 204

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 68/186 (36%), Gaps = 8/186 (4%)

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D +  + V+ DD   V S     ++DE   +ED DD +                   
Sbjct: 26  IDPDDDGMSGVNSDDIPAVASKETKKDDDEDEDEEDSDDDSDDNEGDGGPDPEVARLRFT 85

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            I E   +L+ +       +K  ++S K    +E L  L   + L   + + LV ++ D 
Sbjct: 86  AIKEQLEKLQKV------LKKHPRNSPKAVAEQEALATLFMPIKLIPKQYEALVNRVRDA 139

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             +I   E  +++L      + R  FL    G E++  WV          +   +     
Sbjct: 140 QDQIRKQERAIMQLCVRDARMPRADFLRSFPGNEVNEDWVDSLLADS-PRYSEGLEALKG 198

Query: 405 SILKIR 410
            IL+ +
Sbjct: 199 DILRAQ 204


>gi|293375494|ref|ZP_06621773.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325844950|ref|ZP_08168315.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
 gi|292645894|gb|EFF63925.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325489000|gb|EGC91389.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
          Length = 236

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 107/231 (46%), Gaps = 13/231 (5%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I  ++ K +     A+  +V  ++ LV SV  K+ +  ++  DL Q G +GL+K+  +
Sbjct: 4   KQIHELIAKAQSGDEEARLTLVTNHMDLVWSVVHKFGHIEVEKDDLFQIGCMGLLKSINQ 63

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD       STYA+  +   I   I +QS  I+I   ++  IHK+      ++  ++REP
Sbjct: 64  FDSSYDTTLSTYAIPLIIGEIKAFIREQS-PIKISRSIKSNIHKIQEVKDHLNKVLEREP 122

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
           T +EIA++  +  E +   L       SL+      +   L + I +      L+  I  
Sbjct: 123 TIKEIAQETELSEEQIILALNAPINVTSLDNYER--EDMPLIERIPNHQEGMGLEQKI-- 178

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                  +++++L P E+ ++ +RF +G        EV K+  + +  + +
Sbjct: 179 ----VLKQLVSNLDPIEKLLIYLRFDLGYTQS----EVAKRLEINQVAVSR 221


>gi|321116370|emb|CBN73566.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. Vi1]
          Length = 204

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 68/186 (36%), Gaps = 8/186 (4%)

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D +  + V+ DD   V S     ++DE   +ED DD +                   
Sbjct: 26  IDPDDDGMSGVNSDDIPAVASKETKKDDDEEEDEEDSDDDSDDNEGDGGPDPEVARLRFT 85

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            I E   +L+ +       +K  ++S K    +E L  L   + L   + + LV ++ D 
Sbjct: 86  AIKEQLEKLQKV------LKKHPRNSPKAVAEQEALATLFMPIKLIPKQYEALVNRVRDA 139

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             +I   E  +++L      + R  FL    G E++  WV          +   +     
Sbjct: 140 QDQIRKQERAIMQLCVRDARMPRADFLRSFPGNEVNEGWVDSLLADS-PRYSEGLEALKG 198

Query: 405 SILKIR 410
            IL+ +
Sbjct: 199 DILRAQ 204


>gi|239934522|emb|CAR94575.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 234

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 55/148 (37%), Gaps = 3/148 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           DE+    R +R   + A+           +       +   +  L L     D LV  L 
Sbjct: 88  DEVKARVRVIRRHHNRAIKYLGLHGLKDXRTVKAHADMADQIMELKLAPKXFDALVRNLR 147

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           D+   I   E  +++L     G+ R  FL      E D  W+       + +  + +A  
Sbjct: 148 DVVSIIRSQERLVMQLCVRDAGMPRKDFLSSFPKSETDLAWIDKHI-RAKRKHSSILAKL 206

Query: 403 VDSILKIRNEIKSISVETGISISEFRHI 430
            D + + + ++ ++   T + IS+ + I
Sbjct: 207 KDDVTRAQRKLIAVEEVTQLQISQIKEI 234


>gi|238916719|ref|YP_002930236.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872079|gb|ACR71789.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 223

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 101/250 (40%), Gaps = 50/250 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNI 479
           +S  E + ++  +R      S A+  ++E N+RLV  + KKYT+  R     DLI  G I
Sbjct: 14  LSAQEEKELLIKLR---EGDSAARNALIEKNMRLVAHIVKKYTSTERDYINEDLISVGTI 70

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
           GL+KA + FD     +FSTYA   +   I                               
Sbjct: 71  GLIKAVDSFDIERNVRFSTYAAKCIDNEILM----------------------------- 101

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
              + R+   +E    L  P+   ++        ISL+  IG++      D +ED     
Sbjct: 102 ---LFRQDKKKEREVSLNEPIGKDKEG-----NEISLKDIIGEDSEKKQPDAVED----- 148

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                    ++     +   L PRE  +L+ R+G+    + T  E+  +  ++R  + +I
Sbjct: 149 ---YMFYEQIKCIYGNIEKVLAPREIEILKYRYGLFGAKECTQNELADRLGISRSYVSRI 205

Query: 660 EAKAIRKLKH 669
           E KA+ KL+ 
Sbjct: 206 EKKALGKLRE 215


>gi|260752875|ref|YP_003225768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
 gi|258552238|gb|ACV75184.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
          Length = 195

 Score = 79.9 bits (195), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/204 (22%), Positives = 81/204 (39%), Gaps = 16/204 (7%)

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DLIQ G + L++AA  F+   G+ F+TYA   ++ A+   +   +           + 
Sbjct: 1   MEDLIQIGMVALIEAANAFE-NRGFAFATYASMRIRGAMIDYMRQHA---ATARSSIARQ 56

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTSH 587
             + +    +S  + R P   EIA+KL M     R+     I     SL+    D  +  
Sbjct: 57  KTLNKAREELSATLGRRPEDAEIAEKLNMSPSEYREWADGAINIRQESLDDVYSDHSS-- 114

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
               I   +         +  L+      + +L  RE  VL++ +      +  L+E+G+
Sbjct: 115 ----IFTDDNADQASEMEREALQSALAEQIKTLPEREALVLQLYYV----EELNLKEIGE 166

Query: 648 QFCVTRERIRQIEAKAIRKLKHPS 671
              +   RI QI+  A+  L+   
Sbjct: 167 VLDLGTARISQIKKSAVDHLRQKM 190


>gi|239934510|emb|CAR94569.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 233

 Score = 79.9 bits (195), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/297 (14%), Positives = 87/297 (29%), Gaps = 65/297 (21%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
           GEI IAKRIE G   +  +L   P +   L+    +  +      +II            
Sbjct: 1   GEIKIAKRIEDGLKQVQRALGTYPESINLLLERYQQFQEEQLRFTDII------------ 48

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                                  +  +E +     +     ++        E  +     
Sbjct: 49  -------------------VNFMETTEEIKVAKPPSEDDDDEEVIDTGPDMEEVQRRMLA 89

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
           L +    +   + A       K    +++++ ++ E                     K  
Sbjct: 90  LQKAYAKALKAIDAAGGIQDAKGKAEMEKVSAIFLEF--------------------KYA 129

Query: 318 KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
              +  L   L     RI  L +Q+ D+               +   + R  F++   G 
Sbjct: 130 PAFVAILAVGLRGQVDRIRSLEKQIRDL-------------CVKQCKMPRGTFIQSFPGN 176

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           E D  W+       +  +   +      I  ++  I  ISV + +S+++ + I   +
Sbjct: 177 ETDLTWLDSVTKV-KKPYAKALEERRTEIELLQTRIHQISVSSLLSVTDIKEINRKM 232


>gi|238924921|ref|YP_002938437.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
 gi|238876596|gb|ACR76303.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
          Length = 224

 Score = 79.9 bits (195), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 98/228 (42%), Gaps = 15/228 (6%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
            +V  N+ L+  V K++ NRG+   DL Q G +GL KAA++FD   G+ FSTYA+  +  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
            I R + D    + I   + D   K+     +       E + E++     M  + +   
Sbjct: 68  EIQRFLRD-DGMVHISRKILDDARKIAIIREKYRMNENSEISLEKMEIISGMSKQDIIIA 126

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN---LRETTTRVLASLTPR 623
           ++  K   S+E          + D++++K +    D   + +         +   SL   
Sbjct: 127 MEADKNASSIE-------NESVLDYLDNKMSAEASDKPSETDKVINHIAMQQAFNSLDDS 179

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
           E R++ +R+      D T ++V +     +  I ++E   + KL+   
Sbjct: 180 ERRLIMLRY----MQDKTQKQVAEVLGRNQVAISRMEKNTLEKLRRAM 223


>gi|239934486|emb|CAR92497.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 224

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/269 (13%), Positives = 86/269 (31%), Gaps = 46/269 (17%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AELETETEEETEEGEANSEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFAQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E    W+            + +
Sbjct: 137 QIRQSLTDIRNVEKQVMLLCARDSGMPRKDFISTFPSNETXLSWLDKHIRAKRKHSAH-L 195

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFR 428
           A   + I   + ++  + V T +SI+  +
Sbjct: 196 AXLREEIESQQKKLMGVEVLTHLSIAGIK 224


>gi|327330175|gb|EGE71924.1| RNA polymerase sigma factor [Propionibacterium acnes HL097PA1]
          Length = 270

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 100/240 (41%), Gaps = 25/240 (10%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D   
Sbjct: 50  LRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDVRR 109

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ + I
Sbjct: 110 GARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSDAI 167

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           A ++   V  V K      E          E  + +    +D  +               
Sbjct: 168 AARMGKDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES--------------- 208

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+   +
Sbjct: 209 --GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRHLQ 265


>gi|315453792|ref|YP_004074062.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter felis ATCC 49179]
 gi|315132844|emb|CBY83472.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter felis ATCC 49179]
          Length = 232

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 90/235 (38%), Gaps = 20/235 (8%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            + +   ++  +    L  V ++A +   R    + F DLI  G   L+K A ++D  L 
Sbjct: 7   YDAQIQSSQDALAIQYLPAVRAMAFRLKERLPSCVDFNDLISVGTEELIKLARRYDTSLN 66

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  YA   V  A+   +        +    R  I K+     +  N+  +EP    +A
Sbjct: 67  DSFWGYAKTRVNGAMLDYLRSLD---VVSRASRKLIKKIDHEVSKYYNEHGQEPDDAYLA 123

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           + L   +  +R     +    S    +  ++  +  +        +         L    
Sbjct: 124 EVLGEDISKIRDAKMASDIYAS----VPIDEQFNAIE------QRNINAKLEFEELIAHI 173

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +L +++ RE+ ++++ F      +  L E+ +   VT  RI QI  + I+K++
Sbjct: 174 HAILKTMSEREQLIIQLYFF----EELNLSEIREILGVTESRISQIIKEVIKKIR 224


>gi|119714598|ref|YP_921563.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119535259|gb|ABL79876.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 278

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 77/226 (34%), Gaps = 15/226 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
             + V     LV     +  +  +   DL   G + L++AA  FD   G  F+ YA   +
Sbjct: 10  AVQHVPLVAHLVRETMARVPSY-MDRNDLHSAGLLALVQAARAFDPERGVPFAGYASTRI 68

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + A+   +       R          ++     R++  + + P    +A+ L +  E + 
Sbjct: 69  RGALVDELRSVDWASRSVRRR---AREIEAARARLAATLGQFPDDAAVAEALGITPEEIG 125

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                      + L+          L           P + A+ A   +     +  L  
Sbjct: 126 KADSEVARAVVLPLDAGPNAGFVESLA-----GRDPGPEEEALHAERAQYLAAAIEELPE 180

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R   V+R  F         + E+  +  V+  RI Q+ A+A+  L+
Sbjct: 181 RLRHVVRGYFVA----QRPMAELAAELGVSESRISQLRAEALVLLR 222


>gi|194368262|gb|ACF58023.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/151 (22%), Positives = 66/151 (43%), Gaps = 1/151 (0%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +   D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + 
Sbjct: 1   KDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEEGEKEVLRALLACKVAVEE 60

Query: 167 LIIWRDELNDGTTLLREII-DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           ++   ++L      +R++I D       E                +   S+  + + + +
Sbjct: 61  ILDIGNKLKTAKLRVRDVIKDAPEEAQAEGADEAPEEVGEGDAPAQLAQSELNKIEQICK 120

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                   A+       ++ S  +  E  ++
Sbjct: 121 QIERFRKFAQDCDVLEEELSSKKKLTEVRKK 151


>gi|89276159|gb|ABD66438.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368272|gb|ACF58028.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/133 (26%), Positives = 63/133 (47%), Gaps = 2/133 (1%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +   D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + 
Sbjct: 1   KDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEE 60

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           ++   ++L      +R++I  +         G     E            + E + +++ 
Sbjct: 61  ILDIGNKLKTAKLRVRDVI--KDAPEETQSEGAEEAPEEVGEGDAPAQLAQSELNKIEQI 118

Query: 227 EGDIESAAKVSKD 239
              IE   K ++D
Sbjct: 119 CKQIERFRKFAQD 131


>gi|170737028|ref|YP_001778288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
 gi|169819216|gb|ACA93798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 242

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 106/246 (43%), Gaps = 21/246 (8%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAA 485
              S  R+ +  +   +   +     LV  + +K        ++  DL Q G +GL++A 
Sbjct: 8   EYQSAQRENQTLSPADEARWMTQYAPLVKRIVRKLASQAGGAMEACDLEQLGLMGLLEAL 67

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            ++      +F  +A++ V+ AI   +  Q      P   R   H++  T R +  ++ R
Sbjct: 68  RRY-GEPDDEFEHFALFRVRGAILDELRRQDW---RPRSARQGAHRLRGTERALRRELGR 123

Query: 546 EPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +PT EE+   L +  +   ++      +E +S +  + ++   +  D        S    
Sbjct: 124 DPTKEEVCNALEIGDDEYEQLQLDDCAQEFVSFDALLEEDAERYECD--------SSDGI 175

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +A LR +  + L  L  RE++++++ +      D +  E+G    +TR R+ QI   A
Sbjct: 176 EHRAMLRHSLEQALGVLDAREQQIIQLYYEF----DLSQAEIGAVLGLTRARVCQINKSA 231

Query: 664 IRKLKH 669
           + K+++
Sbjct: 232 LVKMRN 237


>gi|295092257|emb|CBK78364.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 220

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 92/245 (37%), Gaps = 47/245 (19%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVA-KKYTNRGLQ-------FLDLIQEGNIGLMK 483
            +    +   + A+  ++E NL  +  +A ++Y + GL          DL+QEG+IGL+ 
Sbjct: 8   RLCELAQAGDTAARDILLENNLGFIRKIALEQYRSMGLDENDIGIDLDDLVQEGSIGLLN 67

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A   FD   G KF TYA   ++ A+T                      +     +   ++
Sbjct: 68  AIPLFDAGRGMKFLTYAAPAIRNAMTDC--------------------IRAALAQFEQRM 107

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
                              V K      + + L+  + D++     + I D +  +P   
Sbjct: 108 -------------------VDKKNGPGFQRVYLDDILSDDERMLRIEAIADPHTQTPEQI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            IQ          L  LT RE+  L  R+G     +H L      F ++  R +++E +A
Sbjct: 149 YIQKEQLTELYAALDKLTAREQTYLLYRYGFTDGIEHPLIGAALHFHLSESRTKKVEGEA 208

Query: 664 IRKLK 668
           +  L+
Sbjct: 209 MDSLR 213


>gi|321116242|emb|CBN73502.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/224 (14%), Positives = 66/224 (29%), Gaps = 45/224 (20%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +++   + +      L +I  L   I P+  G           Q+ E  + +       +
Sbjct: 1   SILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPAAD 51

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D E     S+ +       PE A      + E  + +                    
Sbjct: 52  DKDDEEEDDSDSEKEEGDGGPDPEVARMRFGAVAEQLEKAKKA----------------- 94

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  ++S +     E L  L   + L   + D LVE++ + 
Sbjct: 95  ------------------LKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNA 136

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAK 388
             +I   E  +++L      + R  FL +    E +  W     
Sbjct: 137 LSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLA 180


>gi|268678937|ref|YP_003303368.1| RNA polymerase sigma factor, FliA/WhiG family [Sulfurospirillum
           deleyianum DSM 6946]
 gi|268616968|gb|ACZ11333.1| RNA polymerase sigma factor, FliA/WhiG family [Sulfurospirillum
           deleyianum DSM 6946]
          Length = 237

 Score = 79.5 bits (194), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 79/228 (34%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V   L  V ++A +   R    +   DLI  G   ++K + ++D      F  Y  
Sbjct: 20  QDELVLQYLPAVRAMAYRLRERLPASVDVNDLISIGTEEMIKLSRRYDKDQNDSFWGYGK 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +       R    +      V +       +   EP    +AK L    E
Sbjct: 80  KRVYGSMLDFLRSLDTMSRANRRLIKL---VDQEITAYLGEHGSEPDDAYLAKVLGEDSE 136

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + +                      L + +   +         +  L E    +L++  
Sbjct: 137 KIAEARNSAMIV----------SVMSLNEQVTILSGEDTAQKVEKDELMEMVQSILSTFN 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++++ +      +  L+E+ +   ++  RI QI  K + KLK 
Sbjct: 187 EREQMIIQLYYF----EELNLKEISEILEISESRISQIHKKLLAKLKE 230


>gi|218680389|ref|ZP_03528286.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 209

 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 51/196 (26%), Positives = 86/196 (43%), Gaps = 12/196 (6%)

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKRE 546
           D   G++ +TYAMWW+K +I   I      +++    + +     + R   R+      +
Sbjct: 1   DAERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGD 60

Query: 547 PTPE---EIAKKLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPL 601
             PE   EIA KL +  E V  + +      SL  PI   + D+    D++ D +     
Sbjct: 61  LKPEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQED 120

Query: 602 DSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
               Q  L   R    + ++ L  RE R+   R         TLE++  +F ++RER+RQ
Sbjct: 121 VLIEQDELDTRRRMLAKAMSVLNERERRIFEARRLAE--DPVTLEDLSTEFDISRERVRQ 178

Query: 659 IEAKAIRKLKHPSRSK 674
           IE +A  K++   R +
Sbjct: 179 IEVRAFEKVQDAVRKE 194


>gi|89276143|gb|ABD66430.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276145|gb|ABD66431.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276147|gb|ABD66432.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276149|gb|ABD66433.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276151|gb|ABD66434.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276155|gb|ABD66436.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276157|gb|ABD66437.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276161|gb|ABD66439.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276163|gb|ABD66440.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276165|gb|ABD66441.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276167|gb|ABD66442.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276169|gb|ABD66443.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276171|gb|ABD66444.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276173|gb|ABD66445.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276175|gb|ABD66446.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276177|gb|ABD66447.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276179|gb|ABD66448.1| sigma factor 70 [Myxococcus xanthus]
 gi|89276181|gb|ABD66449.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368248|gb|ACF58016.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368250|gb|ACF58017.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368252|gb|ACF58018.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368254|gb|ACF58019.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368256|gb|ACF58020.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368258|gb|ACF58021.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368260|gb|ACF58022.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368264|gb|ACF58024.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368268|gb|ACF58026.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368270|gb|ACF58027.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368274|gb|ACF58029.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368276|gb|ACF58030.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368278|gb|ACF58031.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368280|gb|ACF58032.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368282|gb|ACF58033.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/151 (22%), Positives = 66/151 (43%), Gaps = 1/151 (0%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +   D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + 
Sbjct: 1   KDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEE 60

Query: 167 LIIWRDELNDGTTLLREII-DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           ++   ++L      +R++I D       E                +   S+  + + + +
Sbjct: 61  ILDIGNKLKTAKLRVRDVIKDAPEETQSEGAEEAPEEVGEGDAPAQLAQSELNKIEQICK 120

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                   A+       ++ S  +  E  ++
Sbjct: 121 QIERFRKFAQDCDVLEEELSSKKKLTEVRKK 151


>gi|89276153|gb|ABD66435.1| sigma factor 70 [Myxococcus xanthus]
 gi|194368266|gb|ACF58025.1| sigma factor 70 [Myxococcus xanthus]
          Length = 151

 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 59/125 (47%), Gaps = 2/125 (1%)

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +   D     ++DPVR+YLR+MGS+ LL+REGE+ IAKRIE G   ++ +L    +  + 
Sbjct: 1   KDEDDEPGGKSNDPVRLYLRKMGSVSLLTREGEVEIAKRIEDGEKEVLRALLACKVAVEE 60

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           ++   ++L      +R++I  +         G     E            + E + +++ 
Sbjct: 61  ILDIGNKLKTAKLRVRDVI--KDAPEETQSEGAEEAPEEVGEGDAPAQLAQSELNKIEQI 118

Query: 227 EGDIE 231
              IE
Sbjct: 119 CKQIE 123


>gi|126700257|ref|YP_001089154.1| sporulation sigma factor SigE [Clostridium difficile 630]
 gi|254976236|ref|ZP_05272708.1| sporulation sigma factor SigE [Clostridium difficile QCD-66c26]
 gi|255093623|ref|ZP_05323101.1| sporulation sigma factor SigE [Clostridium difficile CIP 107932]
 gi|255101811|ref|ZP_05330788.1| sporulation sigma factor SigE [Clostridium difficile QCD-63q42]
 gi|255307678|ref|ZP_05351849.1| sporulation sigma factor SigE [Clostridium difficile ATCC 43255]
 gi|255518036|ref|ZP_05385712.1| sporulation sigma factor SigE [Clostridium difficile QCD-97b34]
 gi|255651152|ref|ZP_05398054.1| sporulation sigma factor SigE [Clostridium difficile QCD-37x79]
 gi|255656620|ref|ZP_05402029.1| sporulation sigma factor SigE [Clostridium difficile QCD-23m63]
 gi|260684218|ref|YP_003215503.1| sporulation sigma factor SigE [Clostridium difficile CD196]
 gi|260687877|ref|YP_003219011.1| sporulation sigma factor SigE [Clostridium difficile R20291]
 gi|296449924|ref|ZP_06891688.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296878306|ref|ZP_06902314.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|306521002|ref|ZP_07407349.1| sporulation sigma factor SigE [Clostridium difficile QCD-32g58]
 gi|115251694|emb|CAJ69529.1| RNA polymerase sigma-E factor [Clostridium difficile]
 gi|260210381|emb|CBA64762.1| RNA polymerase sigma-E factor [Clostridium difficile CD196]
 gi|260213894|emb|CBE05927.1| RNA polymerase sigma-E factor [Clostridium difficile R20291]
 gi|296261194|gb|EFH08025.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296430604|gb|EFH16443.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 240

 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 92/256 (35%), Gaps = 61/256 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   ++  +          K  ++E NLRLV+ +++K+ N G+   DLI  G IGL
Sbjct: 40  LKPEEEMELLQKL----ETDESVKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I   +   +                         
Sbjct: 96  IKAVNTFKLNKNIKLATYASRCIENEILMYLRKNNKKKTE-------------------- 135

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +  +N  
Sbjct: 136 --------------------------------VSFDEPLNIDLDGNELLLSDVLGTENDE 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIR 657
                  + + R+     L  L+ RE++++ +RFG+     + T +EV     +++  I 
Sbjct: 164 IYKIIEEEID-RDLLVMALDRLSDREKQIMELRFGLIDKGIEKTQKEVAGMLGISQSYIS 222

Query: 658 QIEAKAIRKLKHPSRS 673
           ++E K I +L+   + 
Sbjct: 223 RLEKKIISRLQKEMKK 238


>gi|54307284|ref|YP_128304.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium profundum SS9]
 gi|46911704|emb|CAG18502.1| Hypothetical flagellar-specific transcription initiation factor
           sigma, LafS [Photobacterium profundum SS9]
          Length = 251

 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 431 VSMVRKGECEASIAKKE-MVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAE 486
           +   +K       A+++ +V  +  LV  V +  T +    +   D+ Q G + L+    
Sbjct: 13  LHAYQKSHQLGQKAREQRLVNKHASLVKRVVRHLTAQVTTVMSLEDMEQIGLMALLDVIR 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++           A+  ++ AI   +             R K H++  T R +  ++ R 
Sbjct: 73  RYSDENDASLERLAVQRIRGAILDELRRMDW---RSRRSRQKSHELRDTERALGRQLGRM 129

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT +E+A +L + +  V++    T+           ED                 +S  +
Sbjct: 130 PTDQEVAAELDIELGDVKQRRVDTQAESLTSMDALQEDGEQFFGL------SFQCNSYER 183

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             L++   + LA L+ RE+ +L   +      +  L+E+G  F +T  R+ QI  KA++ 
Sbjct: 184 VALKKAMAQALARLSKREQVMLSFYY----EHEMNLKEIGLVFELTEARVSQIHKKALKS 239

Query: 667 L 667
           L
Sbjct: 240 L 240


>gi|224005495|ref|XP_002291708.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220972227|gb|EED90559.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 541

 Score = 79.1 bits (193), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 92/234 (39%), Gaps = 43/234 (18%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              + +QEG +GL +A +K+D   G +FSTYA  W+                        
Sbjct: 318 SLDEAVQEGMLGLARAVDKYDPERGLRFSTYATHWITSYAA------------------- 358

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD------ 582
                +  +         P  + IAK+L +  + +   ++ T   +S++ P+        
Sbjct: 359 ---YKKIIKDHLQLGTTPPEQKSIAKELGISEQRLTTAIRATGSLVSVDAPVISPGSGSY 415

Query: 583 ------EDTSHLGDFIEDKN----AVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMR 631
                  D S+  + +           P D    + LR+     +A+ LTP E  VLR+R
Sbjct: 416 KGSAAGGDGSNSQELLILDTLRCAEPKPEDQVEISFLRQCLENAMATELTPYERDVLRLR 475

Query: 632 FGIGMNTDHTLEEVGKQFC--VTRERIRQIEAKAIRKLKHPS--RSKKLRSFLD 681
            G+      T+ EV +     VT   +R  E +A +KL+ P+   +  L  +LD
Sbjct: 476 LGLDSGEGKTVREVVEICGGSVTMSDVRSAERRAFKKLRSPTSVHTHNLLEYLD 529


>gi|9368549|emb|CAB98133.1| unnamed protein product [Mycoplasma genitalium]
          Length = 100

 Score = 79.1 bits (193), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/76 (64%), Positives = 61/76 (80%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             A  ++V +NLRLV+S+AKK+  RGL F DLIQEGN+GL+KA  KF+W LG KFSTYA 
Sbjct: 21  KYAINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYAT 80

Query: 502 WWVKQAITRSIADQSC 517
           WW+KQAITR+IADQ+ 
Sbjct: 81  WWIKQAITRAIADQAR 96


>gi|321116378|emb|CBN73570.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. Vm1]
          Length = 204

 Score = 79.1 bits (193), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 69/186 (37%), Gaps = 8/186 (4%)

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D +  + V+ DD   V +     E D+   ++D DD +                   
Sbjct: 26  IDPDDDGMSGVNSDDIPAVAAKGAKKEGDDDEEEDDSDDDSDDNEGDGGPDPEVARLRFT 85

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            I E   +L  +       +K  ++S K    +E L  L   + L   + + LV ++ D 
Sbjct: 86  AIKEQLAKLHKV------LKKHPRNSPKAVAEQEALATLFMPIKLIPKQYEALVNRVRDA 139

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             ++   E  +++L      ++R  FL    G E++  WV           +N  A + D
Sbjct: 140 QDQVRKQERAIMQLCVRDARMRRADFLRSFPGNEVNEGWVDALLADSPRYSENLQALKTD 199

Query: 405 SILKIR 410
            I + +
Sbjct: 200 -IQRAQ 204


>gi|291563982|emb|CBL42798.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SS3/4]
          Length = 246

 Score = 79.1 bits (193), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 57/273 (20%), Positives = 104/273 (38%), Gaps = 64/273 (23%)

Query: 406 ILKIRNEIKSIS----VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           I   R EI  I     +   +S+ E     ++ + G  E   AK E++E NLRLV+ +AK
Sbjct: 23  IRPERGEIHYIGGADILPAPLSLKEETE--ALNKFGTEEEKEAKAELIEHNLRLVVYIAK 80

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           K+ N  +   DLI  G IGL+KA   F+     K +TYA   ++  I   +   S     
Sbjct: 81  KFDNTSVGVEDLISIGTIGLIKAINTFNPTKNIKLATYASRCIENEILMYLRRTSKMKLE 140

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
                                                               +S++ P+ 
Sbjct: 141 ----------------------------------------------------VSIDEPLN 148

Query: 582 DEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI--GM 636
            +   +   L D +  +  V           ++   + ++ L+PRE +++ +R+G+    
Sbjct: 149 VDWDGNELLLSDILGTEEDV-IYKDMEDEVEKDLLKKAVSRLSPRERKIVELRYGLKRRD 207

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + T +EV     +++  I ++E K + +LK 
Sbjct: 208 GAEMTQKEVADLMGISQSYISRLEKKIMMRLKK 240


>gi|226324647|ref|ZP_03800165.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
 gi|225207095|gb|EEG89449.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
          Length = 222

 Score = 79.1 bits (193), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 91/237 (38%), Gaps = 55/237 (23%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +    ++R+     + A+  ++E NLRLV  V KKY +      DL+  G IGL+KA   
Sbjct: 11  KEESELLRRSADSDNEARHILIERNLRLVAHVIKKYQHLEDDTEDLLSIGTIGLIKAVST 70

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           F+     + +TYA   ++  +   +  +                                
Sbjct: 71  FNPDKKARLATYACRCIENELLMMLRTK-------------------------------- 98

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSA 604
                               + +    SL  PIG +   +   L D IE     + +  A
Sbjct: 99  --------------------RKSNRETSLYEPIGTDREGNEIRLYDVIESDEEDACMQLA 138

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           ++ ++     ++ + LT RE+ VL+ R+G+    ++T +EV     ++R  + +IE 
Sbjct: 139 LKNDISLLYEKLESVLTDREQLVLKKRYGLYGEKEYTQKEVAASLGISRSYVSRIEK 195


>gi|326682096|emb|CBL30939.1| RNA polymerase sigma factor [Aeromonas aquariorum]
          Length = 187

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/230 (19%), Positives = 80/230 (34%), Gaps = 44/230 (19%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVPEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            +    +L  +     L   + D LV  + ++ +R+   E  +++L    
Sbjct: 138 TQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 187


>gi|255315371|ref|ZP_05356954.1| sporulation sigma factor SigE [Clostridium difficile QCD-76w55]
          Length = 240

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 92/256 (35%), Gaps = 61/256 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   ++  +          K  ++E NLRLV+ +++K+ N G+   DLI  G IGL
Sbjct: 40  LKPEEEMELLQKL----ETDENVKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGL 95

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I   +   +                         
Sbjct: 96  IKAVNTFKLNKNIKLATYASRCIENEILMYLRKNNKKKTE-------------------- 135

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
                                           +S + P+  +   +   L D +  +N  
Sbjct: 136 --------------------------------VSFDEPLNIDLDGNELLLSDVLGTENDE 163

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIR 657
                  + + R+     L  L+ RE++++ +RFG+     + T +EV     +++  I 
Sbjct: 164 IYKIIEEEID-RDLLVMALDRLSDREKQIMELRFGLIDKGIEKTQKEVAGMLGISQSYIS 222

Query: 658 QIEAKAIRKLKHPSRS 673
           ++E K I +L+   + 
Sbjct: 223 RLEKKIISRLQKEMKK 238


>gi|169829306|ref|YP_001699464.1| RNA polymerase sigma-28 factor [Lysinibacillus sphaericus C3-41]
 gi|168993794|gb|ACA41334.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 228

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 52/274 (18%), Positives = 95/274 (34%), Gaps = 59/274 (21%)

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
            I  +   +K  +     S  E     + + +       A+ +++E N+RLV  V KK+ 
Sbjct: 7   EIPALLGYLKGQTFHKPFSKEEE---AACIERFLGGDEQARLDLIERNMRLVAHVVKKFH 63

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +  Q  D I  G IGLMKA E +      + +TYA   ++  I   +            
Sbjct: 64  PKHEQLDDYISIGTIGLMKAVESYTPDKKTRLATYAARCIENEILMHLR----------- 112

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                                               + V+K        +SL  PIG + 
Sbjct: 113 ----------------------------------TQKKVQK-------DVSLFEPIGTDK 131

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRE---TTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +    I D        +  +   +E        L  L  RE  ++ +R+G+      T
Sbjct: 132 DGNAL-QIRDLLQCDEESATEKIEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDALT 190

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            +E+  +  ++R  + +IE +A+ KL    +  +
Sbjct: 191 QKEIAARLNISRSYVSRIEKRALIKLYQLYKRDQ 224


>gi|326682094|emb|CBL30938.1| RNA polymerase sigma factor [Aeromonas aquariorum]
          Length = 187

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/230 (19%), Positives = 80/230 (34%), Gaps = 44/230 (19%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I P 
Sbjct: 1   TREGEIDIAKRIEDGINQVQSSVPEYPEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN 58

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                                   E DDV  T   I S            D   +   + 
Sbjct: 59  ------------------------ETDDVAPTATHIGSELSEEDLADEDEDEDEDEDGDG 94

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVK 313
           + + D+ +      ++                  E + ELR+  +   ++ Q++ ++   
Sbjct: 95  DDSDDDGDGGPDPEVA-----------------REKFGELRAQYEVTRLSIQQNGRAHED 137

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            +    +L  +     L   + D LV  + ++ +R+   E  +++L    
Sbjct: 138 TQNAXAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQ 187


>gi|126442822|ref|YP_001061239.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 668]
 gi|134280863|ref|ZP_01767573.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 305]
 gi|167725922|ref|ZP_02409158.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           DM98]
 gi|167905082|ref|ZP_02492287.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei NCTC
           13177]
 gi|254182899|ref|ZP_04889492.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|254299694|ref|ZP_04967143.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|125657228|gb|ABN48716.1| RNA polymerase sigma factor [Burkholderia pseudomallei]
 gi|126222313|gb|ABN85818.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 668]
 gi|134247885|gb|EBA47969.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 305]
 gi|157809669|gb|EDO86839.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|184213433|gb|EDU10476.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
          Length = 236

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 96/230 (41%), Gaps = 23/230 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDL---IQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++  +     +V   A++  ++ +  L L    Q G +GL++A  ++       F  YA
Sbjct: 21  AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYGMP-DAAFPCYA 79

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              V+ AI   +         P  +R + H+     R +   + REPT  E++  L +  
Sbjct: 80  ATRVRGAILDELRRHDW---RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSDALGIST 136

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLAS 619
              R+ +                +     D + D +A++  +S  +  +R     + LA 
Sbjct: 137 TEYRERVMANNA-----------EAMASFDSVLDDDALTHEESPEREIVRRRCLEQALAR 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+RV+++ +      D +L E+     +T  R+ QI   A++K++ 
Sbjct: 186 LNEREQRVIQLYYEF----DLSLREIASVLGLTEARVCQINKAALKKMRE 231


>gi|28901410|ref|NP_801065.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio parahaemolyticus RIMD 2210633]
 gi|153835911|ref|ZP_01988578.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|260362964|ref|ZP_05775833.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|260880251|ref|ZP_05892606.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|260895368|ref|ZP_05903864.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) [Vibrio parahaemolyticus Peru-466]
 gi|260901193|ref|ZP_05909588.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|417236|sp|Q03474|LAFS_VIBPA RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-F factor
 gi|677908|gb|AAA62353.1| LafS [Vibrio parahaemolyticus]
 gi|1518952|gb|AAB07356.1| lateral flagellar FliA [Vibrio parahaemolyticus]
 gi|28809957|dbj|BAC62898.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio parahaemolyticus RIMD 2210633]
 gi|149750665|gb|EDM61410.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|308085610|gb|EFO35305.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) [Vibrio parahaemolyticus Peru-466]
 gi|308092554|gb|EFO42249.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|308109363|gb|EFO46903.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|308112404|gb|EFO49944.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|328469344|gb|EGF40290.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio parahaemolyticus 10329]
          Length = 242

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 90/231 (38%), Gaps = 21/231 (9%)

Query: 448 MVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  +V  V  +   +        D+ Q G I L++A  ++       F  +A+  V
Sbjct: 28  LLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDIDDTHFPAFAVCRV 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + AI   +             R + H++    R ++  + R PT  EI K L    +   
Sbjct: 88  RGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRSLGRMPTDSEIIKALGTDEQDYY 144

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R+   +  E  SL+  + +   SH G            D     ++R +    L  L+ 
Sbjct: 145 NRQNAALAGEMQSLDQLMENSTDSHFG---------GQYDGMEHEHIRRSLDSALGRLSK 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++ +L + +      +  L E+     +T  RI Q+  +A+++L     S
Sbjct: 196 RDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNQLMSS 242


>gi|309778066|ref|ZP_07673005.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|313901138|ref|ZP_07834626.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
 gi|308914160|gb|EFP59961.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|312954096|gb|EFR35776.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
          Length = 234

 Score = 78.7 bits (192), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 98/256 (38%), Gaps = 58/256 (22%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            + +   + +++   E     A+  ++E NLRLV+ +AK+Y    +   DLI  G+IGL+
Sbjct: 34  PLDKEEELAALIA-LENGDEEARNTLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLI 92

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA   F      K  TYA   ++  I   +  +S                          
Sbjct: 93  KAVNTFKRDKNIKLVTYASRCIENEILMFLRKKSRRKVE--------------------- 131

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVS 599
                                          +S + P+  +   +   L D +   + V 
Sbjct: 132 -------------------------------VSFDEPLNIDYDGNELLLSDILGTDDDV- 159

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 +   +      +++L  RE ++L+MR+GI  + + T +++ K+  +++  I ++
Sbjct: 160 VTKEFEKKENKRELLEAMSTLKERERQILQMRYGI-QHEELTQKDIAKRLGISQSYISRL 218

Query: 660 EAKAIRKLKHPSRSKK 675
           E + I KLK   ++ +
Sbjct: 219 EKRIIAKLKVQMKNSQ 234


>gi|321116280|emb|CBN73521.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 203

 Score = 78.3 bits (191), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/248 (14%), Positives = 78/248 (31%), Gaps = 46/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKA--------------- 96

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 97  --------------------LKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIR 410
            ++I++ +
Sbjct: 196 KENIVRCQ 203


>gi|119714600|ref|YP_921565.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119535261|gb|ABL79878.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 300

 Score = 78.3 bits (191), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 84/236 (35%), Gaps = 15/236 (6%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R G  EA     E V     +V     +  +  +   DL   G + L+ AA  FD   G 
Sbjct: 22  RPGSAEADRLAVEHVPLVTHVVYETLARVPSY-VDRNDLRSAGLLALVAAARSFDPERGV 80

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            F+ YAM  ++ A+   +       R       +  ++     R++  +   P  E +A 
Sbjct: 81  PFARYAMPRIRGAMVDELRSVDWASRSVRR---RAREIEEARARLAATLGEFPDDEAVAA 137

Query: 555 KLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
            L M ++ V            + L+          L + +  + A     +     +R  
Sbjct: 138 ALGMTLDEVNRVDSEAARGTVLPLDAGAQQG----LAEILPVREAGPEERAVHLERVR-Y 192

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
               +  L  R   V+R  F      +  + E+  +  VT  R+ Q+ A+A+  L+
Sbjct: 193 LADAVEELPERMRLVVRGYFL----EERPMAELAAELGVTESRVSQVRAEALALLR 244


>gi|237751751|ref|ZP_04582231.1| flagellar biosynthesis sigma factor [Helicobacter bilis ATCC 43879]
 gi|229373117|gb|EEO23508.1| flagellar biosynthesis sigma factor [Helicobacter bilis ATCC 43879]
          Length = 240

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 50/228 (21%), Positives = 95/228 (41%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+    L  V ++A +   R    +   DL+  G   L+K A ++D      F  YA 
Sbjct: 23  QDELALQYLPAVKAMAFRLKERLPSSVDMNDLVSIGTEELIKLARRYDSNKNDSFWGYAK 82

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  A+   +        +    R  I  +     R  N+ + EP+ E +AK L   +E
Sbjct: 83  TRVNGAMLDYLRTLD---IVSRSSRKLIKAIEAEVSRYFNEFEEEPSNEYLAKVLNEDIE 139

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + +    +     +   +  ++  +    +ED +    L    Q  L E   +VLA LT
Sbjct: 140 KIHQARLASD----IYAVVPLDEQFN---ALEDGD---ILQYCEQKELMEIIQKVLAKLT 189

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++++ +      + +L E+ +   +T  RI QI  + I+K++ 
Sbjct: 190 EREQLIIQLYYL----EELSLSEISEVLDITESRISQISKEVIKKIRR 233


>gi|239934418|emb|CAR92339.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 201

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 80/250 (32%), Gaps = 50/250 (20%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T  +++   + +      L E++            G+    +G    +       K+ D 
Sbjct: 1   TVDSILAEYNRVTTDGGRLVEVL-----------SGYIDPDDGIVPAEAAAPVPVKDGDA 49

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +ET+ D E++    ++     D                                 + + 
Sbjct: 50  AEETDDDAEASDDEEEEGDGGPDPE-------------------------------EALR 78

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               I +      +L+      +K  ++S +     +++ +L   + L   + D LV ++
Sbjct: 79  RFTAIGD------ALELAKKALKKHGRNSKQGTAALKEMAELFMPIKLVPKQYDALVVRV 132

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
               +R+   E  +++L      + R  FL    G E+D  W S      + ++   +  
Sbjct: 133 RSSLERLRAQERAIMQLCVRDARMPRADFLRLFPGNEVDVEW-SAGLAKGKAKYAEAIGN 191

Query: 402 EVDSILKIRN 411
               I + + 
Sbjct: 192 LQGDIQRCQQ 201


>gi|146295930|ref|YP_001179701.1| sporulation sigma factor SigK [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409506|gb|ABP66510.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 220

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 97/270 (35%), Gaps = 65/270 (24%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL--- 473
           S    +S  E    +  +      A  A+  ++E NLRLV  +AKKYT   L F +L   
Sbjct: 9   SFPHPLSDEEEEMHLKKMW---EGAIEARNILIEKNLRLVAHIAKKYT---LSFPNLTDD 62

Query: 474 -IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
            I  G IGL+KA E +      + STYA   ++  I   +      +             
Sbjct: 63  IISVGTIGLIKAIETYSQEKNTRLSTYAAKCIENEILMYLRQNKKFLS------------ 110

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLG 589
                                                    ISLE PIG +       L 
Sbjct: 111 ----------------------------------------QISLENPIGSDKDGNEITLI 130

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D ++           ++  ++    ++   L  RE+ ++ +R+G+    + T  EV    
Sbjct: 131 DVLQSDQDDIDDQVNVKIQIKNLLRKLDKILKGREKHIIELRYGLKNGKERTQMEVANLL 190

Query: 650 CVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            ++R  + +IE KA++KL +  +     S+
Sbjct: 191 GISRSYVSRIEKKALKKLYNELQKSCKESY 220


>gi|221271590|dbj|BAH15083.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 185

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 1/108 (0%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
             LQ      +K+ ++  +     + L  L   + L   + ++LVE++ D   R+   E 
Sbjct: 78  DQLQATVKVVKKNGRAHKESIEALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQER 137

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            +++L      + R  FL      E D  W                  
Sbjct: 138 AIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTKWAAALGEK 185


>gi|296504831|ref|YP_003666531.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
 gi|296325883|gb|ADH08811.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
          Length = 196

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 94/236 (39%), Gaps = 56/236 (23%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E   + A+  ++E NLRLV  + KK+ N G    DLI  G IGL+KA E +    G K 
Sbjct: 1   MEQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKL 60

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           +TYA   ++  I   +                                            
Sbjct: 61  ATYAARCIENEILMHLRV------------------------------------------ 78

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                     LK TK+ +SL  PIG +   +   L D ++ ++        +   L E  
Sbjct: 79  ----------LKKTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMEL-EKI 127

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +  L  RE+ V+  RFG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 128 KEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 183


>gi|163800115|ref|ZP_02194016.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio sp. AND4]
 gi|159175558|gb|EDP60352.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio sp. AND4]
          Length = 242

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 100/261 (38%), Gaps = 21/261 (8%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            + +    S ++   + +  R  +  A + + ++    ++ V++  + +        D+ 
Sbjct: 1   MLEMNLQESYTQEEEVNTPSRAIDENALLQRHQI---MVKRVVNQLRAHATSHCSIEDMQ 57

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q G I L++A  ++       F  +A+  V+ AI   +             R K H++  
Sbjct: 58  QIGLIALVEAGRRYGEVDDPHFPAFAVCRVRGAILDELRRLDW---RSRKTRQKAHELND 114

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGV--RKVLKITKEPISLETPIGDEDTSHLGDFI 592
             R ++  + R PT  EI K L    +    R+   +  E  SL+  +     SH G   
Sbjct: 115 VTRDLTRALGRMPTDAEIIKALGTDEQDYYNRQNAALAGEMQSLDQLMEAGGESHFG--- 171

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
                    D     ++R +    L  +  R++ +L + +      +  L E+     +T
Sbjct: 172 ------GQYDGMEHEHIRRSLDAALGKMPKRDQLLLTLFYQH----ELNLHEIALVLDLT 221

Query: 653 RERIRQIEAKAIRKLKHPSRS 673
             RI Q+  +A+++L     S
Sbjct: 222 PPRICQLHKQALKQLNQLMSS 242


>gi|46241492|gb|AAS82949.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 182

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 49/133 (36%), Positives = 74/133 (55%), Gaps = 8/133 (6%)

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ---AN 608
           +AK   +PV  V+ +++  +   SL+TPI     + LG  ++D        +  +    +
Sbjct: 28  LAKAAGLPVTRVQMLMETARSAASLDTPI---GGNELGPTVKDSVEDEREAADEEFGSDS 84

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           LR     +L  L  RE RV+R+RFG+    + TLEE+G+   VTRERIRQIEAKA+RKL+
Sbjct: 85  LRNDMEAMLLELPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKALRKLR 144

Query: 669 HPS--RSKKLRSF 679
             +   S KL  +
Sbjct: 145 VKTIDVSGKLMEY 157


>gi|289524828|emb|CBJ94470.1| RNA polymerase sigma factor [Vibrio sp. Cmf 11.16]
          Length = 120

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 18/115 (15%), Positives = 40/115 (34%), Gaps = 2/115 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    Y  + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYAKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
              W+       +  +   +      I +   ++  I  ET +++   + I   +
Sbjct: 62  SEAWLDEVL-TSDKPYVEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDISRRM 115


>gi|314918186|gb|EFS82017.1| sigma-70, region 4 [Propionibacterium acnes HL050PA1]
          Length = 270

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 101/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAARMGQDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 ----GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|289425371|ref|ZP_06427148.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289427143|ref|ZP_06428859.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|295130519|ref|YP_003581182.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|289154349|gb|EFD03037.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289159612|gb|EFD07800.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|291375175|gb|ADD99029.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|313764535|gb|EFS35899.1| sigma-70, region 4 [Propionibacterium acnes HL013PA1]
 gi|313772426|gb|EFS38392.1| sigma-70, region 4 [Propionibacterium acnes HL074PA1]
 gi|313792224|gb|EFS40325.1| sigma-70, region 4 [Propionibacterium acnes HL110PA1]
 gi|313801827|gb|EFS43061.1| sigma-70, region 4 [Propionibacterium acnes HL110PA2]
 gi|313807437|gb|EFS45924.1| sigma-70, region 4 [Propionibacterium acnes HL087PA2]
 gi|313809944|gb|EFS47665.1| sigma-70, region 4 [Propionibacterium acnes HL083PA1]
 gi|313813018|gb|EFS50732.1| sigma-70, region 4 [Propionibacterium acnes HL025PA1]
 gi|313816077|gb|EFS53791.1| sigma-70, region 4 [Propionibacterium acnes HL059PA1]
 gi|313818482|gb|EFS56196.1| sigma-70, region 4 [Propionibacterium acnes HL046PA2]
 gi|313825126|gb|EFS62840.1| sigma-70, region 4 [Propionibacterium acnes HL063PA1]
 gi|313827695|gb|EFS65409.1| sigma-70, region 4 [Propionibacterium acnes HL063PA2]
 gi|313830275|gb|EFS67989.1| sigma-70, region 4 [Propionibacterium acnes HL007PA1]
 gi|313834076|gb|EFS71790.1| sigma-70, region 4 [Propionibacterium acnes HL056PA1]
 gi|313838653|gb|EFS76367.1| sigma-70, region 4 [Propionibacterium acnes HL086PA1]
 gi|314915531|gb|EFS79362.1| sigma-70, region 4 [Propionibacterium acnes HL005PA4]
 gi|314920001|gb|EFS83832.1| sigma-70, region 4 [Propionibacterium acnes HL050PA3]
 gi|314932014|gb|EFS95845.1| sigma-70, region 4 [Propionibacterium acnes HL067PA1]
 gi|314955884|gb|EFT00284.1| sigma-70, region 4 [Propionibacterium acnes HL027PA1]
 gi|314958197|gb|EFT02300.1| sigma-70, region 4 [Propionibacterium acnes HL002PA1]
 gi|314960081|gb|EFT04183.1| sigma-70, region 4 [Propionibacterium acnes HL002PA2]
 gi|314962882|gb|EFT06982.1| sigma-70, region 4 [Propionibacterium acnes HL082PA1]
 gi|314967752|gb|EFT11851.1| sigma-70, region 4 [Propionibacterium acnes HL037PA1]
 gi|314973281|gb|EFT17377.1| sigma-70, region 4 [Propionibacterium acnes HL053PA1]
 gi|314975956|gb|EFT20051.1| sigma-70, region 4 [Propionibacterium acnes HL045PA1]
 gi|314978286|gb|EFT22380.1| sigma-70, region 4 [Propionibacterium acnes HL072PA2]
 gi|314984025|gb|EFT28117.1| sigma-70, region 4 [Propionibacterium acnes HL005PA1]
 gi|314988208|gb|EFT32299.1| sigma-70, region 4 [Propionibacterium acnes HL005PA2]
 gi|314990010|gb|EFT34101.1| sigma-70, region 4 [Propionibacterium acnes HL005PA3]
 gi|315078096|gb|EFT50147.1| sigma-70, region 4 [Propionibacterium acnes HL053PA2]
 gi|315080726|gb|EFT52702.1| sigma-70, region 4 [Propionibacterium acnes HL078PA1]
 gi|315084397|gb|EFT56373.1| sigma-70, region 4 [Propionibacterium acnes HL027PA2]
 gi|315085736|gb|EFT57712.1| sigma-70, region 4 [Propionibacterium acnes HL002PA3]
 gi|315088845|gb|EFT60821.1| sigma-70, region 4 [Propionibacterium acnes HL072PA1]
 gi|315096194|gb|EFT68170.1| sigma-70, region 4 [Propionibacterium acnes HL038PA1]
 gi|315098455|gb|EFT70431.1| sigma-70, region 4 [Propionibacterium acnes HL059PA2]
 gi|327326110|gb|EGE67900.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA2]
 gi|327332019|gb|EGE73756.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA3]
 gi|327443222|gb|EGE89876.1| sigma-70, region 4 [Propionibacterium acnes HL013PA2]
 gi|327446006|gb|EGE92660.1| sigma-70, region 4 [Propionibacterium acnes HL043PA2]
 gi|327448014|gb|EGE94668.1| sigma-70, region 4 [Propionibacterium acnes HL043PA1]
 gi|327450862|gb|EGE97516.1| sigma-70, region 4 [Propionibacterium acnes HL087PA3]
 gi|327453061|gb|EGE99715.1| sigma-70, region 4 [Propionibacterium acnes HL092PA1]
 gi|327453790|gb|EGF00445.1| sigma-70, region 4 [Propionibacterium acnes HL083PA2]
 gi|328753549|gb|EGF67165.1| sigma-70, region 4 [Propionibacterium acnes HL020PA1]
 gi|328754281|gb|EGF67897.1| sigma-70, region 4 [Propionibacterium acnes HL087PA1]
 gi|328754466|gb|EGF68082.1| sigma-70, region 4 [Propionibacterium acnes HL025PA2]
 gi|328760671|gb|EGF74238.1| RNA polymerase sigma factor [Propionibacterium acnes HL099PA1]
          Length = 270

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 101/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAARMGKDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 ----GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|315108409|gb|EFT80385.1| sigma-70, region 4 [Propionibacterium acnes HL030PA2]
          Length = 270

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 101/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRRMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAARMGKDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 ----GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|218458675|ref|ZP_03498766.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 138

 Score = 78.3 bits (191), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 38/120 (31%), Positives = 64/120 (53%), Gaps = 2/120 (1%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F   E+ ++   R  IK       ++  E   + +  R  + +   A+ ++  A++RLVI
Sbjct: 17  FREIEMKNMSADRRMIKIAMAAPYLARQEEHDLAT--RWKDHDDRGARNQIAMAHMRLVI 74

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S+A K+ N GL   DL+QEG +GL++AA +F+     +FSTYA WW++ +I   I     
Sbjct: 75  SMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWS 134


>gi|321116286|emb|CBN73524.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V190]
 gi|321116304|emb|CBN73533.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V203]
 gi|321116366|emb|CBN73564.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. VGXC2]
          Length = 203

 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 2/105 (1%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             + S +       L +L   + L   + D+LV ++ D    +   E  +++L      +
Sbjct: 100 HGRGSKQATEELVALAELFMPIKLVPKQFDVLVAKVRDALDSVRRQERAIMQLCVRDARM 159

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            R  FL +  G E D  WV       + ++   +    D IL+ +
Sbjct: 160 PRADFLRQFPGHETDTAWVDAILK-GKPKYAEAIERLRDDILRNQ 203


>gi|87302171|ref|ZP_01084996.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
 gi|87283096|gb|EAQ75052.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
          Length = 318

 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 89/235 (37%), Gaps = 12/235 (5%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWC 491
           + R         +  +VE NL LV  VA + +    +   DL+Q G +GL++A E FD  
Sbjct: 22  LQRFHSSGDHRLRNRLVELNLPLVRQVAVRQSGSTRVPLDDLVQLGCLGLIRAIEAFDPS 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
                S++A+ +++  +   + D    +R    +R+   +     ++  ++       EE
Sbjct: 82  RHTALSSFAVLYIRGEMQHHLRDHEQPLRCSRQLRELHRRGQALLQQRQHRQLPALGEEE 141

Query: 552 IAKKLAMPVEGVRK--VLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQA 607
           +A  L    +  R+   L       SL+ P  D  E    L + +  +    P  +  + 
Sbjct: 142 LAAALGCSPQRWREALELHQALRLRSLDAPASDGEERGDTLLERLPARELPDPCRADHEG 201

Query: 608 N-------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +        +    R L  L P   +++  R   G +      + G     ++ R
Sbjct: 202 DSLCCEGENQRWLKRRLERLDPSLRQLMLERVLHGASWRRLGVDQGLPARASQRR 256


>gi|321116358|emb|CBN73560.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 203

 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 35/248 (14%), Positives = 77/248 (31%), Gaps = 46/248 (18%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G           Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +                  
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKA--------------- 96

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 97  --------------------LKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
           +   +I   E  +++L      + R  FL +    E +  W        +G++   +   
Sbjct: 137 NALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNR 195

Query: 403 VDSILKIR 410
            + I++ +
Sbjct: 196 KEDIVRCQ 203


>gi|154482592|ref|ZP_02025040.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
 gi|149736617|gb|EDM52503.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
          Length = 192

 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 88/237 (37%), Gaps = 55/237 (23%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
                  AK  ++E NLRLV  V KKY +   +  DLI  G +GL+KA   ++   G + 
Sbjct: 1   MRLGDKKAKDILIERNLRLVAHVVKKYYDENRENQDLISIGIVGLIKAVNTYNPDKGNRL 60

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            TYA   ++  +                       ++R  ++ S                
Sbjct: 61  VTYAAKCIENELLM---------------------MLRAEKKRSK--------------- 84

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETT 613
                            +SL  PIG +       L D +E+    +        N+    
Sbjct: 85  ----------------DVSLNEPIGTDKEGNTISLIDVVENDEMDTLEQIEKAENISLVQ 128

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             V   L  RE+ ++  R+G+      T ++VG++  ++R  + +IE +A+ KLK  
Sbjct: 129 KYVAQILNEREKEIIVWRYGLDGKKPMTQKKVGEKLGISRSYVSRIEKRALEKLKKA 185


>gi|15611460|ref|NP_223111.1| flagellar biosynthesis sigma factor [Helicobacter pylori J99]
 gi|4154925|gb|AAD05973.1| RNA POLYMERASE SIGMA FACTOR (sigma 28) [Helicobacter pylori J99]
          Length = 255

 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 51/268 (19%), Positives = 104/268 (38%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S      +++   K +     A   +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTEASEKSIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+ E +A+ L   +E +R+    +     +   +  
Sbjct: 116 RSSRKLIKSIDIEITKYLNEHGKEPSDEHLAEALGENIEKIREAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +  E               L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIEQDE------ITQKIEAEELLEHIQKVLNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRQS 249


>gi|91223192|ref|ZP_01258458.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 12G01]
 gi|269967118|ref|ZP_06181185.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 40B]
 gi|91192005|gb|EAS78268.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 12G01]
 gi|269828255|gb|EEZ82522.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 40B]
          Length = 242

 Score = 78.0 bits (190), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 43/231 (18%), Positives = 89/231 (38%), Gaps = 21/231 (9%)

Query: 448 MVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  +V  V  +   +        D+ Q G I L++A  ++       F  +A+  V
Sbjct: 28  LLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVCRV 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + AI   +             R + H++    R ++  + R PT  EI + L    +   
Sbjct: 88  RGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRTLGRMPTDAEIIQALGTNEQDYY 144

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R+   +  E  SL+  +     S++G            D     ++R +    L  L  
Sbjct: 145 NRQNAALAGEMQSLDQLMESSGDSYIG---------GQYDGMEHEHIRRSLDSALGKLPK 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++ +L + +      +  L E+     +T  RI Q+  +A+++L     S
Sbjct: 196 RDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNQLMSS 242


>gi|321116338|emb|CBN73550.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V276]
 gi|321116340|emb|CBN73551.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V277]
          Length = 200

 Score = 77.6 bits (189), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 28/189 (14%), Positives = 66/189 (34%), Gaps = 8/189 (4%)

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
           V+   G I+    +   + +      +    +E + DE +                + + 
Sbjct: 19  VEVLNGYIDPDDGIVPAEAAAPVPVKDGDAAEETDDDEADSSDDEEEEGDGGPDPEEALR 78

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               I +      +L+      +K  +SS +     +++ +L   + L   + D LV ++
Sbjct: 79  RFTAIGD------ALELAKKALKKHGRSSKQGIAALKEMAELFMPIKLVPKQYDALVVRV 132

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
               +R+   E  +++L      + R  FL    G E+D  W S      + ++   +  
Sbjct: 133 RSSLERLRAQERAIMQLCVRDARMPRADFLRLFPGNEVDVEW-SAGLAKGKAKYAEAIGN 191

Query: 402 EVDSILKIR 410
               I + +
Sbjct: 192 LQGDIQRCQ 200


>gi|321116244|emb|CBN73503.1| DNA-directed RNA polymerase subunit D [Pseudomonas anguilliseptica]
          Length = 199

 Score = 77.6 bits (189), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 25/180 (13%), Positives = 60/180 (33%), Gaps = 8/180 (4%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                     +    P ++ +  E   D+ E                + +     I +  
Sbjct: 27  DPDDGIVPAEAAAPVPVKDGDAAEETDDDAEASDDEEEEGDGGPDPEEALRRFTAIGD-- 84

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
               +L+      +K  ++S +     +++ +L   + L   + D LV ++    +R+  
Sbjct: 85  ----ALELAKKALKKHGRNSKQGTAALKEMAELFMPIKLVPKQYDALVVRVRSSLERLRA 140

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            E  +++L      + R  FL    G E+D  W S      + ++   +      I + +
Sbjct: 141 QERAIMQLCVRDARMPRADFLRLFPGNEIDVEW-SAGLAKGKAKYAEAIGNLQGDIQRCQ 199


>gi|326386918|ref|ZP_08208532.1| sigma 28 (flagella/sporulation) [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208598|gb|EGD59401.1| sigma 28 (flagella/sporulation) [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 243

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 46/223 (20%), Positives = 85/223 (38%), Gaps = 14/223 (6%)

Query: 449 VEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           +   L +V  +A      G   +   DLIQ G + L + ++K        F+ YA   V+
Sbjct: 22  IRRFLPMVRRLAWHVHGSGRAGIDLEDLIQAGLVALTECSQKHTGQTEDGFAAYAKLRVR 81

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   I     T  +     D+   +      +S  + R+PT  E+A+ + + +     
Sbjct: 82  GAMVDLIR---RTAPMSRSAADRRRTLRDHTESLSCALGRQPTEGELAEAMGLTLAD-LA 137

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            L+   EP+  ET       S +       +             R      +A+L  R  
Sbjct: 138 DLRAAAEPLRFETIDDAYSESSMAFA---DDRPDSFALLADEETRHVVGAAIAALPER-- 192

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             L+M   +    +  L E+     V+  R+ Q++A+A+ KL+
Sbjct: 193 --LQMVIQLYFVEELNLAEIAAVLEVSVPRVHQLKAQALDKLR 233


>gi|327478799|gb|AEA82109.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas stutzeri
           DSM 4166]
          Length = 256

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 96/232 (41%), Gaps = 24/232 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A  A++  +   L LV  + ++ +   N+ L   D+ Q G IGL++   ++      +F 
Sbjct: 21  APGAEQRWLMQYLPLVKRIVRQLSLQANQVLDREDMEQIGMIGLLEGLRRY-GEPDEQFG 79

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            +A   ++ AI   +  Q      P  +R + HKV    R ++ ++   P+ EEI     
Sbjct: 80  RFAALRIRGAILDELRRQDW---RPRQVRQQAHKVRDAIRELTRQLGHTPSDEEIKAFTG 136

Query: 558 MPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-TTT 614
           +  +  +  L    ++   SL+  +              ++     +   +  L+E    
Sbjct: 137 LDEKDYQAFLWADSSEAIESLDELLQSGH----------EHFPDAAELFEERLLKERLLE 186

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + L+ L  RE  VL + +      + +L+E+     V+  R+ Q+  +AI K
Sbjct: 187 QALSRLDERERLVLTLYYQH----ELSLKEIALVLEVSDARVCQLSKQAIGK 234


>gi|255697165|emb|CBA11694.1| RNA polymerase sigma factor [Pseudomonas savastanoi pv. nerii]
          Length = 194

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 68/235 (28%), Gaps = 44/235 (18%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
           ++   P T   ++     +      L ++  L   I P+       G    +        
Sbjct: 2   AIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPD------DGIAPPAEVPPPVDP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
           +  + +   + E +   A+    +D  +    P  A+     + +  + +   L      
Sbjct: 54  KAVKAEGTDDDEEESADASDDEDEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 107

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 108 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 138

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
           + LVE++    +R+   E  +++L      + R  FL +  G E+D  W      
Sbjct: 139 EGLVERVRGALERLRAQERAIMQLCVRDARMLRADFLRQFPGNEVDESWTDALAK 193


>gi|50842442|ref|YP_055669.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|50840044|gb|AAT82711.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|315105463|gb|EFT77439.1| sigma-70, region 4 [Propionibacterium acnes HL030PA1]
          Length = 270

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 101/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAARMGKDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 ----GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|169834796|ref|YP_001715634.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169408903|gb|ACA57313.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 296

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 102/229 (44%), Gaps = 23/229 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E N  L+  VA KY N+ ++  DL Q+G +G +KA +KFD     KFSTYA +W++  
Sbjct: 90  LIEKNQNLIFKVANKYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIEAE 149

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I+                           R++        + +E+        E V+  +
Sbjct: 150 ISSFFNFNVDGSLSISSSYQ--------HRKLKGYENGILSEDEL-------PELVKNHI 194

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++    IS+++ +  ++  +  D++  K  ++  +   +  ++      L+ L+ +E+ +
Sbjct: 195 QLKNNSISVDSIVHGKENENSADYLLGKTDINYNNIESKIVMK----NALSGLSEKEKSI 250

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  R       +   +++ K+F V+ + I+ +   AI KLK   +   L
Sbjct: 251 IISRI----IYEKKYKDIAKEFKVSYQYIQYLYKNAIGKLKRTIKKDIL 295


>gi|239934460|emb|CAR92484.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 185

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 27/150 (18%), Positives = 55/150 (36%), Gaps = 3/150 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A  +  L         G  ++     K   L++KL      L L+    D+L+ Q+ 
Sbjct: 37  EEAARRFDSLSKTFVQVQKGMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLITQIR 96

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
                I + E +++ L     G+ R  F+      E +  W+            + +A  
Sbjct: 97  RSLTDIRNVEKQVMLLCVRDSGMPRKDFISIFPSNETNLSWLDKHIRAKRKHSAH-LAKL 155

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVS 432
            + I   + ++  +   T +SI+  + I  
Sbjct: 156 REEIEAQQKKLMGVEELTHLSIAGIKEINR 185


>gi|168335365|ref|ZP_02693459.1| sporulation sigma factor SigE [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 246

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 54/259 (20%), Positives = 92/259 (35%), Gaps = 54/259 (20%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIA---KKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
              +S  E   ++  + +   +       KK ++E NLRLV+ +AKK+ N      DLI 
Sbjct: 36  PAPLSKEEENELLMQMIEYPDDDEKINEIKKILIERNLRLVVYIAKKFENTNKGMEDLIS 95

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G+IGL+KA   F      K +TYA   ++  I                       + RT
Sbjct: 96  IGSIGLIKAINTFKPDKKIKLATYASRCIENEIL--------------------MDIRRT 135

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
                NK+K E + +E                               +    L   I   
Sbjct: 136 -----NKLKVEVSIDEP-------------------------LNTDWDGNELLLSDILGT 165

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRE 654
           +  S   +      +      L  L+ RE  ++ +R+G      + T +EV     +++ 
Sbjct: 166 DFDSVYRNIEDEVDKALLNTALGQLSTREREIVELRYGFKNEGKEKTQKEVADMLGISQS 225

Query: 655 RIRQIEAKAIRKLKHPSRS 673
            I ++E K I +LK   + 
Sbjct: 226 YISRLEKKIIGRLKKEMKK 244


>gi|229587526|ref|YP_002860564.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
 gi|229260255|gb|ACQ51292.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
          Length = 296

 Score = 77.6 bits (189), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 99/229 (43%), Gaps = 23/229 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           ++E N  L+  VA KY N+ ++  DL Q+G +G +KA +KFD     KFSTYA +W++  
Sbjct: 90  LIEKNENLIFKVANKYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIEAE 149

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I+                           R++        + +E+ K        V+  +
Sbjct: 150 ISSFFNFNVDGSLSISSSYQ--------HRKLKGYENGILSEDELPKL-------VKNHI 194

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           ++    IS+++ +  ++  +  D++  K  ++          +      L+ L+ +E+ +
Sbjct: 195 QLKNNSISVDSIVHGKENENSADYLLGKTDINYN----NIESKIVMENALSGLSDKEKNI 250

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  R       +   +++ K+F V+ + I+ +   AI KL+   +   L
Sbjct: 251 IISRI----IYEKKYKDIAKEFKVSYQYIQYLYNNAIEKLRQTVKKDIL 295


>gi|118474443|ref|YP_892645.1| flagellar biosynthesis sigma factor [Campylobacter fetus subsp.
           fetus 82-40]
 gi|118413669|gb|ABK82089.1| flagellar biosynthesis sigma factor FliA [Campylobacter fetus
           subsp. fetus 82-40]
          Length = 234

 Score = 77.2 bits (188), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 94/249 (37%), Gaps = 22/249 (8%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIG 480
           ++E +     +   + E   ++ E+V + +  + ++A +  +R    ++  DLI  G   
Sbjct: 1   MNELKQ--KQLDAYQKEIKKSQDELVLSYMPALRAMAFRLKSRLPSSIEVNDLISVGATA 58

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           ++K +  +D      F  Y    V  ++   +       R     R  +  +        
Sbjct: 59  MVKLSRTYDKEQNDSFWGYVKQRVYGSMIDYLRGLDFLSRGN---RKLVKDIDNAINEYF 115

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           NK + EP    +AK L      +R+   ++     +      ++ S L       +    
Sbjct: 116 NKFECEPDDAYLAKILGEDEAKIREARNLSD----VSATFPIDEQSQLL------SESDT 165

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                +  L +  T VL     RE+ ++++ +      + +L+E+     +T  RI QI 
Sbjct: 166 ESKIEKDELIQKITDVLNEFGEREQMIIQLYY----YEELSLKEISDILGITESRISQIH 221

Query: 661 AKAIRKLKH 669
            + I K++ 
Sbjct: 222 KRLITKIRE 230


>gi|239934450|emb|CAR92479.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 221

 Score = 77.2 bits (188), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 77/204 (37%), Gaps = 10/204 (4%)

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
           I+ A   ++    +    P   E D    +ED++ +  +         P  +     IA 
Sbjct: 27  IDPAQFEAEPAAMEAVEVPPELEADAEVSEEDDEGATESADTG-----PDPVEVAQRIAA 81

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           +  +   L     + ++   ++   +  ++ LV L          I  L EQL    + I
Sbjct: 82  LQDQYEIL---VTHLREHGPTAESTQTEQQALVHLFLQFKFAPRVIVELGEQLRRTVEDI 138

Query: 350 MHNEGELLR-LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILK 408
             +E +++       G+ R  FL+  Q  E D  W+   +   + +    +A   + I+K
Sbjct: 139 RRHERQIMDFCVNRAGMSRRDFLQVFQEHETDADWIDK-QIRAKRKHSATMARHREDIIK 197

Query: 409 IRNEIKSISVETGISISEFRHIVS 432
           ++ ++  +   T + ++  + I  
Sbjct: 198 LQEQLLQLESATLLPLATIKEINR 221


>gi|254228817|ref|ZP_04922240.1| DNA-directed RNA polymerase specialized sigma subunit [Vibrio sp.
           Ex25]
 gi|262396464|ref|YP_003288317.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
 gi|151938764|gb|EDN57599.1| DNA-directed RNA polymerase specialized sigma subunit [Vibrio sp.
           Ex25]
 gi|262340058|gb|ACY53852.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
          Length = 242

 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 43/231 (18%), Positives = 89/231 (38%), Gaps = 21/231 (9%)

Query: 448 MVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  +V  V  +   +        D+ Q G I L++A  ++       F  +A+  V
Sbjct: 28  LLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVCRV 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + AI   +             R + H++    R ++  + R PT  EI + L    +   
Sbjct: 88  RGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRSLGRMPTDAEIIQALGTNEQDYY 144

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R+   +  E  SL+  +     S++G            D     ++R +    L  L  
Sbjct: 145 NRQNAALAGEMQSLDQLMESSGDSYIG---------GQYDGMEHEHIRRSLDSALGKLPK 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++ +L + +      +  L E+     +T  RI Q+  +A+++L     S
Sbjct: 196 RDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNQLMSS 242


>gi|221271592|dbj|BAH15084.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 185

 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 54/171 (31%), Gaps = 4/171 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                      +V  P   A   +   D+DE++S       E +  P    A      V 
Sbjct: 18  DPDDNIAAPTEEVPIPGTKAAAAKEESDDDEEESESGDDEEEAESGPDPEVARQRFGAVN 77

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            +   LQ      +K+ ++  +     + L  L   + L   + ++LVE++ D   R+  
Sbjct: 78  DQ---LQATNKVLKKNGRAHKESIDALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQ 134

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            E  +++L      + R  FL      E D  W                  
Sbjct: 135 QERAIMQLCVRDARMPRADFLRMFPSNETDQTWSGDLAKRNTKWAAALGEK 185


>gi|318041689|ref|ZP_07973645.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0101]
          Length = 263

 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 50/190 (26%), Positives = 86/190 (45%), Gaps = 5/190 (2%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAE 486
           R+   +    +C  +  +  ++ ANL LV  VA++ + R G  F DL QEG  GL+KA E
Sbjct: 13  RNAALLAAYQQCRTTANRNAVIHANLPLVWRVARQESQRSGHSFDDLTQEGCFGLIKAVE 72

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD   G+  ST A+ W++ AI   + D+S  I    H+ +   +     ++   +    
Sbjct: 73  RFDPGRGHSLSTAAVPWIRGAIRHYLRDRSHPISGSHHLLELHRRGQALQKQRQQQGLAP 132

Query: 547 PTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLD 602
            +   +A  L   +E  +  L  + + +  SLE P  D+D   + L + + D  A     
Sbjct: 133 LSAGALATALGCSLERWQLALARRRSLQLASLEQPHLDDDGDLTPLVEQLRDSRAGDHYA 192

Query: 603 SAIQANLRET 612
             I+   R  
Sbjct: 193 RVIRWEQRRH 202


>gi|291535996|emb|CBL09108.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Roseburia
           intestinalis M50/1]
          Length = 192

 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 86/241 (35%), Gaps = 55/241 (22%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           M  K +  +  A+ E+   N+RLV  VAKKY N      DLI  G IGLMKA   +    
Sbjct: 1   MPEKIKKGSLEARNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGLMKAIATYKEDY 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G + +TYA   +   +                         R  +++S +          
Sbjct: 61  GSRLATYAARCIDNELLMYF---------------------RAKKKVSRE---------- 89

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANL 609
                                +SL  PIG +      HL D +E +             +
Sbjct: 90  ---------------------VSLYEPIGMDKEGNQIHLLDIVESEEPDVVEMMERTRQI 128

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +    V   L  RE  ++  R+G+  N   T  E+     ++R  + +IE KA+ KLK 
Sbjct: 129 EKLLGLVPKVLQERELYIIVHRYGLFGNKAMTQREIASAVGISRSYVSRIEKKALDKLKK 188

Query: 670 P 670
            
Sbjct: 189 S 189


>gi|239934446|emb|CAR92477.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 207

 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/255 (14%), Positives = 75/255 (29%), Gaps = 49/255 (19%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKNFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKIRNEIK 414
               D I + + ++ 
Sbjct: 193 KQFTDDIRRAQRKLA 207


>gi|158340491|ref|YP_001521485.1| RNA polymerase sigma-2 subunit [Acaryochloris marina MBIC11017]
 gi|158310732|gb|ABW32346.1| RNA polymerase sigma-2 subunit domain protein [Acaryochloris marina
           MBIC11017]
          Length = 697

 Score = 77.2 bits (188), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 73/188 (38%), Gaps = 12/188 (6%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            I +    + ++RK +     +   ++  ++RLV  +AK+Y        DLIQEG +G+ 
Sbjct: 28  PIPDPEQELDLIRKAKRGHETSLSWLMIGHVRLVAKLAKQYAWTLDDAQDLIQEGMLGIR 87

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR---DKIHKVVRTARRM 539
            A  KFD   G KFSTYA  W++  I R      C    P  +R    K   + R  R  
Sbjct: 88  HAVGKFDSTKGCKFSTYARGWIRGYIRRF-----CYKNRPKQLRLPEKKQVHLDRVYR-- 140

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
                 +   EEIA+K  + +E +  +L   +     E P   E       F  D     
Sbjct: 141 LQNEFPDANLEEIARKANLKLEYIEDLLYWGRSFQ--EIPDWHEFVIDDASFYTDDEEYD 198

Query: 600 PLDSAIQA 607
                   
Sbjct: 199 EYFDIELE 206


>gi|154173651|ref|YP_001408770.1| flagellar biosynthesis sigma factor [Campylobacter curvus 525.92]
 gi|153792993|gb|EAT99591.2| flagellar biosynthesis sigma factor FliA [Campylobacter curvus
           525.92]
          Length = 234

 Score = 77.2 bits (188), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 96/250 (38%), Gaps = 22/250 (8%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIG 480
           + E +     +   +      + E+V   +  + ++A +   R    +   DLI  G   
Sbjct: 1   MHELKQ--KQLNAYQNTIKKEQDEIVLQYMPALRAMAFRLKERLPSSIDVNDLIGVGVEE 58

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           ++K + K+D      F  Y    +  A+   +        +    R  +  +        
Sbjct: 59  MIKLSRKYDKEQNDSFWGYGKKRIYGAMLDYLRGLD---IMSRTNRKLVKAINSAIDAYF 115

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           N+ + EP  E +AKKL   +E +R+   ++     L           + D +E  +  + 
Sbjct: 116 NEFEEEPDDEYLAKKLGEDIEKIREARGVSSIITVL----------PIDDQMELFSQHNV 165

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
             S  + +L +    +L +   R++ V+++ +      +  L+E+ +   ++  RI QI 
Sbjct: 166 EQSVEKEDLIQKIEAILENFDERDQMVIQLYY----YEELNLKEISEIMQISESRISQIH 221

Query: 661 AKAIRKLKHP 670
            + + +L+  
Sbjct: 222 KRLLDRLRKS 231


>gi|297605001|ref|NP_001056480.2| Os05g0589200 [Oryza sativa Japonica Group]
 gi|255676623|dbj|BAF18394.2| Os05g0589200 [Oryza sativa Japonica Group]
          Length = 464

 Score = 77.2 bits (188), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 55/182 (30%), Positives = 88/182 (48%), Gaps = 5/182 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           +    +++LK  +E+   S      I E     +++R    E    ++ ++     LV  
Sbjct: 279 LEKIRENLLKDGSEVSHASWAKAAGIDE-----ALLRSRLQEGYCCRERLLVTTEWLVKY 333

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           +AK Y   G  F DL+Q G +G++  AEKFD   G KFSTY  +W+++A+   +A+ S  
Sbjct: 334 IAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRKAMLALLAENSGV 393

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           I++P  M   I KV    R +     R P   EIA  + + V  VR   K ++  +SL T
Sbjct: 394 IQLPARMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYT 453

Query: 579 PI 580
            I
Sbjct: 454 EI 455


>gi|317012254|gb|ADU82862.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           Lithuania75]
          Length = 255

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 50/268 (18%), Positives = 104/268 (38%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T IS      +++   K +        ++    L  V ++A +   
Sbjct: 2   ILMMENRMPKGIQKTEISEKNIEKVLNAYDKQQHHHQD---DLAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +R+    +     +   +  
Sbjct: 116 RSNRKLIKSIDAEITKHLNEHGKEPSDAYLAEVLGENIEKIREAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITKKIEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  +AI+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEAIKKVRKS 249


>gi|239934362|emb|CAR92311.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 185

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/226 (15%), Positives = 69/226 (30%), Gaps = 44/226 (19%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   D +      L +I  L   I P+  G            + E ++ +      
Sbjct: 1   VDSILADYDRVTSEGGRLSDI--LSGYIDPDDDGA------AGPQAEVEPATPQAAAKPA 52

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D +     S+++       PE A      + E  D +   L              
Sbjct: 53  GDDKDDEDEDDSDSEEEEGDGGPDPEVARIRFGAVAEQLDVAKKAL-------------- 98

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  + S +     ++L  L+  + L   + D LVE++ 
Sbjct: 99  ---------------------KKHGRGSQQATDALQELAILLMPIKLIPKQYDALVERVR 137

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAK 388
           D   +I   E  ++++      + R  FL +    E D  W     
Sbjct: 138 DSLAQIRAQERAIMQICVRDARMPRADFLRQFPNNETDLDWADKLA 183


>gi|321116256|emb|CBN73509.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V113]
 gi|321116264|emb|CBN73513.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V120]
          Length = 205

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/186 (17%), Positives = 66/186 (35%), Gaps = 8/186 (4%)

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
              D   +   + D  +      + +E+D+   D+ +DDS                    
Sbjct: 27  DPDDDGMSGADNADIPAAKAKDQKKSEDDDEEEDDSDDDSDDDNEGDGGPDPEVARLRFG 86

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            IAE  ++L+         +K  +++ K    +E L  L   + L   + + LV ++   
Sbjct: 87  AIAEQLQKLQK------ALKKHPRNNPKVVAEQEALATLFMPIKLIPKQYEALVTRVRGA 140

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             +I   E  +++L      + R  FL    G E++  WV       +  +   +     
Sbjct: 141 QDQIRQQERAIMQLCVRDARMPRADFLRSFPGNEINEGWVDELLA-DKPRYSEGLEALKG 199

Query: 405 SILKIR 410
            IL+ +
Sbjct: 200 DILRAQ 205


>gi|269784268|emb|CBH50779.1| RNA polymerase sigma factor [Vibrio sp. Rd 8.15]
          Length = 111

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 19/111 (17%), Positives = 41/111 (36%), Gaps = 2/111 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L +   R+   E  ++R    YG + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
              W+       +  +   +      I +   ++  I  ET +++   + I
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDI 111


>gi|257469126|ref|ZP_05633220.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
          Length = 116

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/106 (37%), Positives = 67/106 (63%), Gaps = 3/106 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +   E  +++   +        AK +++ +NLRLV+++AK Y N+GL F+
Sbjct: 10  YLADIRKYKILDKDEELNLLIKAK---AGDEEAKNQLILSNLRLVVNIAKGYINKGLSFI 66

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           DLI EGN+GL+ A EKFD   G++FSTYA+WW+KQ+I++++  +  
Sbjct: 67  DLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGR 112


>gi|325679635|ref|ZP_08159210.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
 gi|324108665|gb|EGC02906.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
          Length = 235

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 94/249 (37%), Gaps = 57/249 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R    +      +   AK+ ++  NLRLV+ +++K+ N G+   DLI  G+IGL
Sbjct: 35  LTKEEERKAFEL---FATDEKKAKELLIVHNLRLVVYISRKFENAGVGLEDLISIGSIGL 91

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   F      K +TYA   ++  I                       + + ++R   
Sbjct: 92  IKAVNTFRPDKNIKLATYASRCIENEILMF--------------------LRKASQR--- 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
                                        +  IS++ P+  +   +  L   I   +  +
Sbjct: 129 -----------------------------RTEISIDEPLNTDHDGNELLLSDILGTDEDT 159

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                     +    R +  L  RE  ++ MRFG+    + T +EV +   +++  I ++
Sbjct: 160 VHKGIESEVEKTLLRREIDKLGERERMIMEMRFGLNGRHEMTQKEVAQTVGISQSYISRL 219

Query: 660 EAKAIRKLK 668
           E K ++ ++
Sbjct: 220 EKKTLKAIR 228


>gi|34557955|ref|NP_907770.1| flagellar biosynthesis sigma factor [Wolinella succinogenes DSM
           1740]
 gi|34483673|emb|CAE10670.1| RNA POLYMERASE SIGMA FACTOR [Wolinella succinogenes]
          Length = 235

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 96/238 (40%), Gaps = 20/238 (8%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC 491
           +        ++ E+  + L  V ++A +   R    +   DL+  G   L+K + +++  
Sbjct: 8   QGYSQHLKYSQDELAVSYLPAVKAMAYRLKERLPSSIDTADLVSIGAEELIKLSRRYNEA 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           L   F  +A   V+ A+   +        +    R  I ++        N+   EP+ E 
Sbjct: 68  LNDSFWGFAKTRVQGAMLDYLRSLD---VVSRGNRKLIKQIDVEISHYMNEHSSEPSDEY 124

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           +A+ L   ++ +R+    +   + +           + D +   +  +      Q  L  
Sbjct: 125 LAEVLGEDIKKIREAKIASDIYVLM----------PIEDQLSALHEEATEGRIEQEELVG 174

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             + +L SL+ RE+ ++++ +      +  L+E+ +   +T  RI QI  + I+K++ 
Sbjct: 175 IISEILESLSEREQLIIQLYYF----EELNLKEISEVLEITESRISQIHKEVIKKIRE 228


>gi|317013857|gb|ADU81293.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           Gambia94/24]
          Length = 255

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/268 (18%), Positives = 102/268 (38%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S      +++   K +     A   +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTEASEKSIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +R+    +     +   +  
Sbjct: 116 RSSRKLIKSIDIEITKYLNEHGKEPSDAYLAEALGENIEKIREAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITQKIEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRQS 249


>gi|313681607|ref|YP_004059345.1| RNA polymerase, sigma 28 subunit, sigd/flia/whig [Sulfuricurvum
           kujiense DSM 16994]
 gi|313154467|gb|ADR33145.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sulfuricurvum
           kujiense DSM 16994]
          Length = 230

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 85/228 (37%), Gaps = 20/228 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++    L  V +++ +   R    + ++DL   G   L+K A ++D      F  YA  
Sbjct: 16  DQLAIQFLPAVKAMSFRLKERLPSSVDYMDLCAIGTEELVKLARRYDESQNDSFWGYAKT 75

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V  A+   +        +    R  I ++             EP+  E++  L +  + 
Sbjct: 76  RVYGAMLDYLRSLD---MVSRSSRRLIKEIDHAIEVYMADHDDEPSDSELSVILGIEEDK 132

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           VR+    +     L           L D +        L+     +L E    VL +   
Sbjct: 133 VREARIASDIYTVL----------PLDDQLGTPEEGGMLERMEHEDLIEAIQEVLMTFEE 182

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           RE+ ++++ +      + TL+E+ +   +T  RI QI    IR++K  
Sbjct: 183 REQIIIQLYYF----EELTLKEISEIVNITESRISQIHKSVIRRIKEA 226


>gi|218669755|gb|ACL00354.1| Bcp26 [Bacillus phage Bcp1]
          Length = 256

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 103/242 (42%), Gaps = 16/242 (6%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
               ++ + +     A + +VE N RLV  V ++  N   ++ DL Q G IGL+ A  KF
Sbjct: 21  ETYELIERSQAGEEEATESLVEHNARLVTYVVRRKNNPYHEYDDLFQLGMIGLITAIAKF 80

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G +FSTYA+ W+   I   + +++  +++P  +   ++K++        K +    
Sbjct: 81  DTSKGLQFSTYAVRWIDAEIGNYLKNRTSILKVPREIGAIVNKILAVKL----KNEEPAI 136

Query: 549 PEEIAKKLAMPVEGVRKVLKITKE-PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             E  K  A  ++ V   L+I     ISL+   G+E    L   +               
Sbjct: 137 IMEKLKLDASQLDNVTIALEIIHNEVISLDKQTGEEKDDSLSSIVGQDVNQDWFSGLAFY 196

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +       ++  L  +E+ VL +++      D +  ++   F     +I ++E  A+ KL
Sbjct: 197 D-------IIRFLDDKEQSVLTLKYVH----DMSSNKIATLFGTYANKISRLEKVALDKL 245

Query: 668 KH 669
           + 
Sbjct: 246 RE 247


>gi|317063372|ref|ZP_07927857.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689048|gb|EFS25883.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 118

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/106 (37%), Positives = 67/106 (63%), Gaps = 3/106 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +  I     +   E  +++   +        AK +++ +NLRLV+++AK Y N+GL F+
Sbjct: 12  YLADIRKYKILDKDEELNLLIKAK---AGDEEAKNQLILSNLRLVVNIAKGYINKGLSFI 68

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           DLI EGN+GL+ A EKFD   G++FSTYA+WW+KQ+I++++  +  
Sbjct: 69  DLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGR 114


>gi|321116248|emb|CBN73505.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V92]
          Length = 205

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 75/248 (30%), Gaps = 44/248 (17%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              ++     + +    L +I      I P+       G  G        +  + ++   
Sbjct: 1   VDGILADYARVVEEGGRLSDI--FSGYIDPDD-----DGMSGTDNADIPAAKAKDQKKSE 53

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + E + +S      D+       PE A                                
Sbjct: 54  DDDEEEDDSDDDSDDDNEGDGGPDPEVAR-----------------------------LR 84

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
              IAE  ++L+         +K  +++ K    +E L  L   + L   + + LV ++ 
Sbjct: 85  FGAIAEQLQKLQK------ALKKHPRNNPKVVAEQEALATLFMPIKLIPKQYEALVTRVR 138

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
               +I   E  +++L      + R  FL    G E++  WV       +  +   +   
Sbjct: 139 GAQDQIRQQERAIMQLCVRDARMPRADFLRSFPGNEINEGWVDELLA-DKPRYSEGLEAL 197

Query: 403 VDSILKIR 410
              IL+ +
Sbjct: 198 KGDILRAQ 205


>gi|322378964|ref|ZP_08053378.1| flagellar biosynthesis sigma factor [Helicobacter suis HS1]
 gi|322379818|ref|ZP_08054115.1| flagellar biosynthesis sigma factor [Helicobacter suis HS5]
 gi|321147786|gb|EFX42389.1| flagellar biosynthesis sigma factor [Helicobacter suis HS5]
 gi|321148640|gb|EFX43126.1| flagellar biosynthesis sigma factor [Helicobacter suis HS1]
          Length = 236

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 91/245 (37%), Gaps = 20/245 (8%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAA 485
            I       +     ++ E+    L  V S+A +   R    + F DL+  G   L+K +
Sbjct: 3   DIHKKSAPYDVHIQNSQNELAIQYLPAVRSMAFRLKERLPSSVDFNDLVSAGTEELIKLS 62

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
            ++D  L   F  YA   V  A+   +        +    R  I  +     +  N   +
Sbjct: 63  RRYDVALNDSFWGYAKTRVNGAMLDYLRSLD---VVSRSSRKLIKNIDHEISKYYNVHGQ 119

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           EP    +A+ L   +  +R     +   +     +  ++  +  +        +      
Sbjct: 120 EPDDAYLAEVLGEDISKIRDAKVASDIYV----HVPIDEQFNAIE------QDTMTKKLE 169

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
              L E T  +L +++ RE+ V+++ F      +  L E+ +   +T  RI QI  + I+
Sbjct: 170 FEELVEATQMILKTMSDREQLVIQLYFF----EELNLSEIREILGITESRISQIIKEVIK 225

Query: 666 KLKHP 670
           K++  
Sbjct: 226 KIRKS 230


>gi|308061767|gb|ADO03655.1| flagellar biosynthesis sigma factor [Helicobacter pylori Cuz20]
          Length = 258

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 104/268 (38%), Gaps = 20/268 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S +  ++I  ++   + +    +  +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTQTSETNEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKE 61

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 62  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 119 RSNRKLIKSIDNEITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPI 174

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 175 DEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 224

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 225 SEIKEILGITESRISQIIKEVIKKVRKS 252


>gi|160914280|ref|ZP_02076501.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
 gi|158433907|gb|EDP12196.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
          Length = 233

 Score = 76.8 bits (187), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 91/248 (36%), Gaps = 57/248 (22%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             E     + +   E     A+  ++E NLRLV+ +AK+Y    +   DLI  G+IGL+K
Sbjct: 32  PLEKEEEQAALIALEHGDEEARNTLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIK 91

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A   F      K  TYA   ++  I   +  +S                           
Sbjct: 92  AVNTFKRNKNIKLVTYASRCIENEILMFLRKKSRRKLE---------------------- 129

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSP 600
                                         +S + P+  +   +   L D +   + V  
Sbjct: 130 ------------------------------VSFDEPLNIDYDGNELLLSDILGTDDDV-V 158

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                +   +    + +  L  RE ++L+MR+GI  + + T +++ K+  +++  I ++E
Sbjct: 159 TKQFEREENKRELLKAMRGLKDRERQILQMRYGIE-HEELTQKDIAKRLGISQSYISRLE 217

Query: 661 AKAIRKLK 668
            + I KLK
Sbjct: 218 KRIIHKLK 225


>gi|207092651|ref|ZP_03240438.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 367

 Score = 76.4 bits (186), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 51/233 (21%), Positives = 100/233 (42%), Gaps = 2/233 (0%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 135 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 194

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
             G  +++ ++C  P     +  ++D L +    ++E+          S        E  
Sbjct: 195 RLGEDIILDAICSVPYLIDFIYAYKDALINRERKVKELFRSFDDDDENSVSDSKKDEENE 254

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             ++ E+  + + R  V   + D +   KV +  ++   +  E  +  E  +DE ED+  
Sbjct: 255 EDEENEEDEENEGRKKVVSEK-DKKRVEKVQESFKALDKAKKEWLKALEAPVDEKEDELV 313

Query: 267 HTLS-AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
             L+ A + Q     +  L+  +++  EL    +  +      +  +K    K
Sbjct: 314 RLLTLAYKRQTLKDRLYDLEPTSKLINELVKTMETTLKSGDGFEKELKRLEYK 366


>gi|313650139|gb|EFS14552.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           2a str. 2457T]
 gi|332757220|gb|EGJ87557.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           2747-71]
 gi|332766654|gb|EGJ96858.1| RNA polymerase sigma factor, sigma-70 family protein [Shigella
           flexneri 2930-71]
          Length = 161

 Score = 76.4 bits (186), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/153 (20%), Positives = 70/153 (45%), Gaps = 5/153 (3%)

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
               +P  +R    +V +   ++  ++ R  T  E+A++L + +   R++L  T      
Sbjct: 7   SRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLF 66

Query: 577 ETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
                 E+     + + D +   +PL   + +NLR+     + +L  RE+ VL + +   
Sbjct: 67  SYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQ-- 124

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L+E+G    V   R+ Q+ ++AI++L+
Sbjct: 125 --EELNLKEIGAVLEVGESRVSQLHSQAIKRLR 155


>gi|269784306|emb|CBH50798.1| RNA polymerase sigma factor [Vibrio sp. C 14.7]
 gi|269784312|emb|CBH50801.1| RNA polymerase sigma factor [Vibrio sp. Vb 11.11]
          Length = 111

 Score = 76.4 bits (186), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 19/111 (17%), Positives = 40/111 (36%), Gaps = 2/111 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    YG + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
              W+       +  +   +      I +   ++  I  ET +++   + I
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDI 111


>gi|239934466|emb|CAR92487.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 216

 Score = 76.4 bits (186), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 24/138 (17%), Positives = 49/138 (35%), Gaps = 3/138 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNGQKDE-KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A  +  L         G  ++     K   L++KL      L L+    D+L+ Q+ 
Sbjct: 80  EEAARRFDSLSKTFXQVQKGMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLITQIR 139

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
                I + E +++ L     G+ R  F+      E +  W+            + +A  
Sbjct: 140 RSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSXH-LAKL 198

Query: 403 VDSILKIRNEIKSISVET 420
            + I   + ++  +   T
Sbjct: 199 REEIEAQQKKLMGVEELT 216


>gi|85710152|ref|ZP_01041217.1| flagellar-specific RNA polymerase sigma factor [Erythrobacter sp.
           NAP1]
 gi|85688862|gb|EAQ28866.1| flagellar-specific RNA polymerase sigma factor [Erythrobacter sp.
           NAP1]
          Length = 242

 Score = 76.4 bits (186), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 86/229 (37%), Gaps = 16/229 (6%)

Query: 449 VEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
           V   L LV   A      G   L+  DL+Q G + L + A++ +      F+ YA   V+
Sbjct: 26  VRRFLPLVRRAAWHIYGSGREGLEIEDLMQAGVVALTECAQRHEGPGEDGFAAYAKIRVR 85

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
            A+   I             R K  ++     R+ N+   EP+   I + L +    + +
Sbjct: 86  GAMFDQIRKLMND---TRTARKKRAQLGEVVERLRNETGEEPSRARICETLGISDAELLE 142

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   +    S+     +  T+   D   D +    L        RE     +  L  R +
Sbjct: 143 IEASSVTVTSIADEYDETSTAFASD---DPDPFQVLAGNED---RERLIAAMVKLPDRLK 196

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            VL++ F      +  L E+     V+  R+ Q+ AKA++ L+    + 
Sbjct: 197 LVLQLFFV----EELNLTEIATVLEVSVPRVHQLRAKALKDLRALMEAD 241


>gi|239934500|emb|CAR92504.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
 gi|239934502|emb|CAR92505.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 209

 Score = 76.4 bits (186), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 52/144 (36%), Gaps = 3/144 (2%)

Query: 286 EIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           E  E +  LR L + A     +   +    +     L +    L L   + + + E + +
Sbjct: 67  EAKERFDTLRQLNNKAKKAINRYGVAHKSTQQHLSALGEHFKFLKLAPRQFEPMAEAVRE 126

Query: 345 ISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
               I   E  ++ L      + R  F+    G E D  W +      E  +   +A   
Sbjct: 127 ALSLIRAEERTVMALCIRQAKMPRTDFIGLFPGHETDESWATGLAKGKEP-YAAAIAVVE 185

Query: 404 DSILKIRNEIKSISVETGISISEF 427
             I + +  +  +  +TG++IS+ 
Sbjct: 186 PDIQRSQRRLMQLEEKTGLTISQI 209


>gi|239934454|emb|CAR92481.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 210

 Score = 76.4 bits (186), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 26/145 (17%), Positives = 52/145 (35%), Gaps = 3/145 (2%)

Query: 286 EIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           E  E +  LR L + A     +   +    +     L +    L L   +   + E + +
Sbjct: 67  EAKERFDTLRQLNNKAKRAINRYGVAHKSTQQHLSALGEHFKFLKLAPRQFKPMAEAVRE 126

Query: 345 ISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
               I   E  ++ L      + R  F+    G E D  W +      E  +   +A   
Sbjct: 127 ALSLIRAEERTVMALCIRQAKMPRTDFIGLFPGHETDESWATGLAKGKEP-YAAAIAVVE 185

Query: 404 DSILKIRNEIKSISVETGISISEFR 428
             I + +  +  +  +TG++IS+ +
Sbjct: 186 PDIQRSQRRLMQLEEKTGLTISQIK 210


>gi|312884823|ref|ZP_07744515.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367475|gb|EFP95035.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 256

 Score = 76.4 bits (186), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/226 (18%), Positives = 84/226 (37%), Gaps = 21/226 (9%)

Query: 447 EMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           E++  +  LV  +  +   + +      D+ Q G IGL++A  ++       F  +A+  
Sbjct: 41  ELLNLHQILVKRIVNQLKVHASSHCSIEDMQQIGLIGLLEAGRRYGDIQDPNFPAFAVCR 100

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   +       R       +++ V R    +   + R+P   EI   L    +  
Sbjct: 101 IRGAILDELRRLDWRSRKTRQAAHELNDVTR---DLMRTLGRQPNDNEIIAALGTDEKDY 157

Query: 564 --RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             R+   +  E  SL+  +      H+             +       R T  + L  L 
Sbjct: 158 IARQNATLAGEMQSLDQLLEHGGEGHI---------DGNYEGMSHEQTRRTLEKALTKLA 208

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE+ ++ + +      +  L E+     +T  RI Q+  KA+ +L
Sbjct: 209 KREQLIMTLFYQH----ELNLHEIALVLNLTPPRICQLHKKALEQL 250


>gi|254779107|ref|YP_003057212.1| flagellar biosynthesis sigma factor [Helicobacter pylori B38]
 gi|254001018|emb|CAX28962.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Helicobacter pylori B38]
          Length = 255

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/268 (17%), Positives = 101/268 (37%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S      +++   K +     A   +    L  V ++A +   
Sbjct: 2   ILMMENRMPKGIQKTETSEKNIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +R+    +     +   +  
Sbjct: 116 RSNRKLIKSIDAEITKHLNEHGKEPSDAYLAQTLGENIEKIREAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITKKIEAEELLEHVKKALNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRKS 249


>gi|103488379|ref|YP_617940.1| RNA polymerase, sigma 28 subunit [Sphingopyxis alaskensis RB2256]
 gi|98978456|gb|ABF54607.1| RNA polymerase, sigma 28 subunit [Sphingopyxis alaskensis RB2256]
          Length = 248

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 96/228 (42%), Gaps = 15/228 (6%)

Query: 448 MVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V     LV  +A +     +R  +  DLIQ G I L++A+  ++   G+ F+TYA   +
Sbjct: 29  LVTEYAPLVRKIAWQVFSRVSRTSELDDLIQTGLIALIEASRHYE-ERGFAFATYASTRI 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           + A+   +        +         ++  T   +  ++ R PT  E+A  L M  E   
Sbjct: 88  RGAMIDQLR---READVGRSAMVAAKRLQATRAALEQQLLRAPTAAEMAVALDMAAEDYF 144

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
            + +      S       ++ + +G F+         D   Q +L     + +  L+ RE
Sbjct: 145 ALERNATHGRSTSL----DELTDIGAFLAADEDALADDRCEQEDLMGALRQCVGRLSERE 200

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           + VL++ F      +  L E+G    V+  RI QI+ +A+ K++   R
Sbjct: 201 QLVLQLYFF----EELNLHEIGLTLDVSAARICQIKREAMIKVERMMR 244


>gi|124265243|ref|YP_001019247.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
 gi|124258018|gb|ABM93012.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
          Length = 265

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 102/250 (40%), Gaps = 23/250 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A+  + E +  +  LV  +AK+   R    ++  +L+Q G IGL +A  +F+   G  F 
Sbjct: 28  AATVRNEQLHQHGALVRRIAKRMRARLPANVEMDELLQAGLIGLNEAITRFEESFGASFD 87

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA   ++ A+  S+        +    R     +    + + +++ R P   E+A +L 
Sbjct: 88  TYASRRIEGAMLDSLRAAD---TLSRDARAHQRAIRAAVQALEHRLLRPPRAMEVASELG 144

Query: 558 MPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIED------KNAVSPLDSAIQANL 609
             +  + + L         + + P+            ED       +   PL +  +   
Sbjct: 145 WSLARLHQRLVEAGAAGQRAGDAPLDGLADEASARGAEDDLHATADDHADPLAALQRRQR 204

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                    +L  RE+ +++M +  G++     ++  +   V+  R+ Q+ A  ++KLK 
Sbjct: 205 TTALNAAFDTLEEREQLMMKMIYERGLDH----QDAAESLGVSPSRVSQMHAVVVQKLK- 259

Query: 670 PSRSKKLRSF 679
               ++L+ +
Sbjct: 260 ----RRLKDW 265


>gi|239934434|emb|CAR92471.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 199

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 29/241 (12%), Positives = 72/241 (29%), Gaps = 45/241 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AELETETEEETEEGEANSEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFAQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            +  
Sbjct: 137 QIRQSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAHLA 196

Query: 400 A 400
            
Sbjct: 197 K 197


>gi|149189848|ref|ZP_01868128.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio shilonii AK1]
 gi|148836334|gb|EDL53291.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio shilonii AK1]
          Length = 242

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/216 (18%), Positives = 85/216 (39%), Gaps = 18/216 (8%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           + V++  + +        D+ Q G IGL++A  ++       F  +A+  ++ +I   + 
Sbjct: 37  KRVVNQLRNHATTHCSIEDMQQIGLIGLLEAGRRYGNIDDPNFPAFAVCRIRGSILDELR 96

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK-- 571
                 R       +++ + R    ++  +KR PT +EI K L          L  +   
Sbjct: 97  RLDWRSRKTRQQAHELNDITR---DLTKALKRMPTEQEIIKALGTDQADYHTRLSASMAG 153

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           E  SL+  I       +          S  +     ++R +    LA L  RE+ ++ + 
Sbjct: 154 EMQSLDQLIEKGLEGQV---------DSAYEGMSHEHIRRSLEVALAKLPKREQLLMTLF 204

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +      +  L E+     +T  RI Q+  +A+++L
Sbjct: 205 YQH----ELNLHEIALVLELTPPRICQLHKQALKQL 236


>gi|167614829|ref|ZP_02383464.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           Bt4]
 gi|257141414|ref|ZP_05589676.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 236

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 96/230 (41%), Gaps = 23/230 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDL---IQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++  +     +V   A++  ++ +  L L    Q G +GL++A  ++       F  YA
Sbjct: 21  AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYGMP-DAAFPCYA 79

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              V+ AI   +         P  +R + H+     R +   + REPT  E++  L +  
Sbjct: 80  ATRVRGAILDELRRHDW---RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSSALGIST 136

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLAS 619
              R+ +                +     D + D +A++  +S  +  +R     + LA 
Sbjct: 137 AEYRERVMANNA-----------EAMASFDSVLDDDALTHEESPERQIVRRRCLEQALAR 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+RV+++ +      D +L E+     +T  R+ QI   A++K++ 
Sbjct: 186 LNEREQRVIQLYYEF----DLSLREIASVLELTEARVCQINKAALKKMRE 231


>gi|323492324|ref|ZP_08097477.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio brasiliensis LMG 20546]
 gi|323313371|gb|EGA66482.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio brasiliensis LMG 20546]
          Length = 223

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 88/227 (38%), Gaps = 21/227 (9%)

Query: 446 KEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            +++  +  LV  +  +   +        D+ Q G IGL++A  ++       F  +A+ 
Sbjct: 7   NKLLAQHQVLVKRIVNQLRAHATSHCSIEDMQQIGLIGLLEAGRRYGNIDDPNFPAFAVC 66

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   +             R + H++    R +  K+ R+P+  EI K L    + 
Sbjct: 67  RIRGAILDELRRLDW---RSRKTRQQAHELNDVTRDLMRKLGRQPSDAEIIKALGTDEQD 123

Query: 563 V--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              R+   +  E  SL+  I     SH+          +  D       R +    L  +
Sbjct: 124 YLARQNASLAGEMQSLDQLIESGVESHI---------DASYDGMAHEQTRRSLQAALDKM 174

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             RE+ +L + +      +  L E+     +T  RI Q+  +A+++L
Sbjct: 175 PQREQLLLTLFYQH----ELNLHEIALVLNLTPPRICQLHKQALKQL 217


>gi|28210822|ref|NP_781766.1| RNA polymerase sigma-G factor [Clostridium tetani E88]
 gi|28203260|gb|AAO35703.1| RNA polymerase sigma-G factor [Clostridium tetani E88]
          Length = 161

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/169 (25%), Positives = 81/169 (47%), Gaps = 12/169 (7%)

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   I R + D +  IR+   +RD  +K ++   ++  K  +EPT  EIAK+L +P E 
Sbjct: 1   MIIGEIRRYLRDNNS-IRVSRSLRDIAYKALQVRDKLIAKNDKEPTVSEIAKELDIPRED 59

Query: 563 VRKVLKITKEPISLETPIGDE--DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           V   L   ++P+SL  PI  +  D+ ++ D I D   +        A         + +L
Sbjct: 60  VVFALDAIQDPLSLFEPIYQDGGDSIYVMDQISDTKNLDDSWIENIA-----IKEAMRNL 114

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             RE+ +L +RF  G     T  EV  +  +++ ++ ++E  A++ ++ 
Sbjct: 115 NKREKLILSLRFFDG----RTQMEVADEIGISQAQVSRLEKTALKHMRK 159


>gi|260767948|ref|ZP_05876882.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           CIP 102972]
 gi|260615978|gb|EEX41163.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           CIP 102972]
 gi|315179652|gb|ADT86566.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio furnissii NCTC 11218]
          Length = 242

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/227 (18%), Positives = 89/227 (39%), Gaps = 21/227 (9%)

Query: 446 KEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
             ++     LV  V+ +   +        D+ Q G IGL++A  ++       F  +A+ 
Sbjct: 26  NRLLSQYQHLVKRVSNQLRVHATTHCSLEDMQQIGLIGLLEAGRRYGNIDDPNFPAFAVC 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ AI   +             R + H++    R ++ K+ R+P+  EI   L    + 
Sbjct: 86  RIRGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRKLGRQPSDREIIAALGTDEQD 142

Query: 563 VRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
               L      E  SL+          L D   ++ A    D     ++R +  + +  L
Sbjct: 143 YYARLNASLAGEMQSLD---------QLIDTGVEQFADGHYDGMTHEHIRRSLEQAVGQL 193

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R++ +L + +      +  L E+     +T  RI Q+  +A+++L
Sbjct: 194 SKRDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQL 236


>gi|315101187|gb|EFT73163.1| sigma-70, region 4 [Propionibacterium acnes HL046PA1]
          Length = 270

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 100/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +  E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGETIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAARMGKDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 ----GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|319788967|ref|YP_004090282.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
 gi|315450834|gb|ADU24396.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 234

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 91/243 (37%), Gaps = 54/243 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 +    +   A++ ++  NLRLV+ ++KK+ + G    DLI  G+IGL+KA   F
Sbjct: 38  EEAKAFQLFATDEKKARELLIVHNLRLVVYISKKFESTGAGIEDLISIGSIGLIKAVNTF 97

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
                 K +TYA   ++  I                       + + ++R          
Sbjct: 98  RPDKNIKLATYASRCIENEILMF--------------------LRKASQR---------- 127

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQ 606
                                 +  IS++ P+  +   +  L   I   +  +       
Sbjct: 128 ----------------------RSEISIDEPLNTDWDGNELLLSDILGTDEDTVHKGIES 165

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    R +  L  RE+ ++ MRFG+   ++ T +EV +   +++  I ++E K ++ 
Sbjct: 166 EVEKTLLRREIDKLGEREKMIMEMRFGLNGKSEMTQKEVAQTVGISQSYISRLEKKTLKA 225

Query: 667 LKH 669
           ++ 
Sbjct: 226 IRE 228


>gi|153831527|ref|ZP_01984194.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|148872037|gb|EDL70854.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
          Length = 242

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 89/231 (38%), Gaps = 21/231 (9%)

Query: 448 MVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  +V  V  +   +        D+ Q G I L++A  ++       F  +A+  V
Sbjct: 28  LLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVCRV 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + AI   +             R + H++    R ++  + R PT  EI K L    +   
Sbjct: 88  RGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRALGRMPTDAEIIKALGTDEQDYY 144

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R+   +  E  SL+  +     SH G            D     ++R +    L  ++ 
Sbjct: 145 NRQNAALAGEMQSLDQLMETGGDSHFG---------GQYDGMEHEHIRRSLDTALGKMSK 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++ +L + +      +  L E+     +T  RI Q+  +A+++L     S
Sbjct: 196 RDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNQLMSS 242


>gi|332675354|gb|AEE72170.1| RNA polymerase sigma factor [Propionibacterium acnes 266]
          Length = 266

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 99/242 (40%), Gaps = 29/242 (11%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAARMGKDVMWVEKRRVECWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                    LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 --------GLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 259

Query: 671 SR 672
            +
Sbjct: 260 LQ 261


>gi|289607021|emb|CBI60914.1| unnamed protein product [Sordaria macrospora]
          Length = 72

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 25/60 (41%), Positives = 47/60 (78%)

Query: 17 DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
          D+ D+ + D ++ S KK++  A++RGY+T+++LN  LP D+++SEQ+ED ++ L++MG+N
Sbjct: 13 DTGDAPLIDLNEGSIKKLVARAKKRGYITVDQLNEMLPQDQMTSEQIEDIMSALNDMGVN 72


>gi|282854097|ref|ZP_06263434.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|282583550|gb|EFB88930.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|314923070|gb|EFS86901.1| sigma-70, region 4 [Propionibacterium acnes HL001PA1]
 gi|314966840|gb|EFT10939.1| sigma-70, region 4 [Propionibacterium acnes HL082PA2]
 gi|314981182|gb|EFT25276.1| sigma-70, region 4 [Propionibacterium acnes HL110PA3]
 gi|315092002|gb|EFT63978.1| sigma-70, region 4 [Propionibacterium acnes HL110PA4]
 gi|315093239|gb|EFT65215.1| sigma-70, region 4 [Propionibacterium acnes HL060PA1]
 gi|315103504|gb|EFT75480.1| sigma-70, region 4 [Propionibacterium acnes HL050PA2]
 gi|327327666|gb|EGE69442.1| RNA polymerase sigma factor [Propionibacterium acnes HL103PA1]
          Length = 270

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 100/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G +GL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTHARQAAVSYRCSVEDLIQAGCVGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ +    P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWHSVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAAQMGKDVMWVEKRRVERWEV----ETSFFEQVAVVQKSCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                ++  LT +E R++ +R G       T+  V  +  ++   +R+IE +A+ +L+  
Sbjct: 209 ----GLIGLLTGQERRIVELRHGFE-GEPMTITAVAHELGLSASNVRRIEQRALGRLRRH 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|321116352|emb|CBN73557.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 76.0 bits (185), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/230 (15%), Positives = 71/230 (30%), Gaps = 45/230 (19%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +++   + + +    L +I  L   I P+  G         + Q+ E  + +     V +
Sbjct: 1   SILADYERVTNEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPQTPQSTSKPVDD 51

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D +     S+++       PE A      + E  + +   L                
Sbjct: 52  DKDDEDEEESESEEEEGDGGPDPEVARLRFGAVAEQLEKANKAL---------------- 95

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  ++S +     E L  L   + L   + D LVE++ D 
Sbjct: 96  -------------------KKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVRDA 136

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
             +I   E  +++L      + R  FL +    E +  W           
Sbjct: 137 LSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAAGKSKY 186


>gi|116334961|ref|YP_802456.1| putative RNA polymerase sigma factor rpoD [Candidatus Carsonella
           ruddii PV]
 gi|116235242|dbj|BAF35090.1| putative RNA polymerase sigma factor rpoD [Candidatus Carsonella
           ruddii PV]
          Length = 320

 Score = 75.6 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 30/81 (37%), Positives = 50/81 (61%)

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +      NL      ++  L  +E+ ++R+RFGIG    +TLEE+G  + +T+ERIRQI
Sbjct: 233 FIREYDNRNLNNLIRLIILELPKKEQIIIRLRFGIGFPKSYTLEEIGLMYYLTKERIRQI 292

Query: 660 EAKAIRKLKHPSRSKKLRSFL 680
           E   + KL+HP+RS+ L+ ++
Sbjct: 293 ELNVLFKLRHPTRSEVLKPYI 313


>gi|315586407|gb|ADU40788.1| DNA-directed RNA polymerase sigma subunit FliA [Helicobacter pylori
           35A]
          Length = 258

 Score = 75.6 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/268 (17%), Positives = 105/268 (39%), Gaps = 20/268 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S +  ++I  ++   + +    +  +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTQTSETSEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKE 61

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 62  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 119 RSNRKLIKSIDIEITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPI 174

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 175 DEQFNAIE------QDEITKKIEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNL 224

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 225 SEIKEILGITESRISQIIKEVIKKVRKS 252


>gi|167576654|ref|ZP_02369528.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           TXDOH]
          Length = 236

 Score = 75.6 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 96/230 (41%), Gaps = 23/230 (10%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDL---IQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           A++  +     +V   A++  ++ +  L L    Q G +GL++A  ++       F  YA
Sbjct: 21  AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYGMP-DAAFPCYA 79

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              V+ AI   +         P  +R + H+     R +   + REPT  E++  L +  
Sbjct: 80  ATRVRGAILDELRRHDW---RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSSALGIST 136

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET-TTRVLAS 619
              R+ +                +     D + D +A++  +S  +  +R     + LA 
Sbjct: 137 AEYRERVMANNA-----------EAMASFDSVLDDDALTHEESPERQIVRRRCLEQALAR 185

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  RE+RV+++ +      D +L E+     +T  R+ QI   A++K++ 
Sbjct: 186 LDEREQRVIQLYYEF----DLSLREIASVLELTEARVCQINKAALKKMRE 231


>gi|261839263|gb|ACX99028.1| flagellar biosynthesis sigma factor [Helicobacter pylori 52]
          Length = 258

 Score = 75.6 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 104/268 (38%), Gaps = 20/268 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S +  ++I  ++   + +    +  +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTQTSETSEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKE 61

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 62  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 119 RSNRKLIKSIDIEITKHLNEHGKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPI 174

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 175 DEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 224

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 225 SEIKEILGITESRISQIIKEVIKKVRKS 252


>gi|315001916|emb|CBI75444.1| RNA polymerase sigma factor [Aeromonas salmonicida]
          Length = 173

 Score = 75.6 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 45/217 (20%), Positives = 72/217 (33%), Gaps = 44/217 (20%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
           ELL+REGEI IAKRIE G   + +S+ E P     L+   D+       L +II     I
Sbjct: 1   ELLTREGEIDIAKRIEDGINQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDII--SGFI 58

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
            P          +  +       S+  E D   E E + E     S DD       PE A
Sbjct: 59  DPNE-------ADDVAPTATHIGSELGEDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVA 111

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
                +L    + +  ++                                   QK+ ++ 
Sbjct: 112 REKFGDLRAQYEVTRLSI-----------------------------------QKNGRAH 136

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
              +    +L  +     L   + D L   + ++ +R
Sbjct: 137 EDTQAAIAQLADVFRQFRLMPKQFDRLGNNMREMMER 173


>gi|119718669|ref|YP_925634.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119539330|gb|ABL83947.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 300

 Score = 75.6 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 37/219 (16%), Positives = 74/219 (33%), Gaps = 15/219 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
             E V     LV     +  +  +   DL   G + L++AA  FD   G  F+ YA   +
Sbjct: 18  AVEHVPLVAHLVRETMARVPSY-MDRNDLHSAGLLALVQAARAFDPERGVPFAGYASTRI 76

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + A+   +       R          ++     R++  + + P    +A+ L +  E + 
Sbjct: 77  RGALVDELRSVDWASRSVRRR---AREIEAARARLAATLGQFPDDAAVAEALGITPEEIG 133

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                      + L+          L           P + A++A   +     +  L  
Sbjct: 134 KADSEVARAVVLPLDAGPNAGFVESLA-----GRDPGPEEEALRAERAQYLAAAVEELPE 188

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           R   V+R  F         + E+  +  V++ RI +++ 
Sbjct: 189 RLRHVVRGYFIA----QRPMAELAAELGVSKSRISRLQT 223


>gi|261837848|gb|ACX97614.1| transcription initiation factor sigma-28 [Helicobacter pylori 51]
          Length = 258

 Score = 75.6 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 105/268 (39%), Gaps = 20/268 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S +  ++I  ++   + +    + ++    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTQTSETSEKNIEKVLNAYDKQQHHHQDDLAIQYLPAVRAMAFRLKE 61

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 62  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 119 RSSRKLIKSIDIEITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPI 174

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 175 DEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 224

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 225 SEIKEILGITESRISQIIKEVIKKVRKS 252


>gi|238762342|ref|ZP_04623313.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Yersinia
           kristensenii ATCC 33638]
 gi|238699327|gb|EEP92073.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Yersinia
           kristensenii ATCC 33638]
          Length = 231

 Score = 75.6 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 109/247 (44%), Gaps = 19/247 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++I E    +++    E +   A   +V+  +R +   A     +     D+ Q   +GL
Sbjct: 1   MAIMETNDNLALTPAEEGKYLQAYLPLVKRIVRQLSFQADSVIGK----EDMQQIALMGL 56

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A  ++    G +F+ YA+  ++ A+   + +       P  +R K HK     R+++ 
Sbjct: 57  LEALRRYGHPDG-QFAAYAVHRIRGAVLDQLREHDW---RPRRLRQKTHKTNEAIRQLAK 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K+  EP+ EEIA  L +  E  ++ L        LE+  G E    +       +A+   
Sbjct: 113 KLGHEPSFEEIATALQLTAEEYQEYLL-------LESASGMESLDEILSLDTPTDALQSR 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +      + +     +ASL  RE+ +L + +      + +++E+ +   +T  RI Q+  
Sbjct: 166 ELEESIIIEDNLNHAIASLEKREQMILHLYYQ----QEMSMKEIAQVLDLTEARICQLNK 221

Query: 662 KAIRKLK 668
           K ++K+K
Sbjct: 222 KLVQKIK 228


>gi|114765238|ref|ZP_01444370.1| RNA polymerase sigma factor protein (sigma-70) [Pelagibaca
           bermudensis HTCC2601]
 gi|114542373|gb|EAU45401.1| RNA polymerase sigma factor protein (sigma-70) [Roseovarius sp.
           HTCC2601]
          Length = 249

 Score = 75.6 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 97/244 (39%), Gaps = 26/244 (10%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +   ++    +     A + ++ ++ R   S A ++T+  +   DL  EG +GL++AA+
Sbjct: 18  EQERAAISGWQDRGDRAALEVLLRSHARQAWSHAARFTDNPVHLEDLAAEGVMGLLRAAD 77

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD     +F+TYA WWV+ A                        V     R+   I   
Sbjct: 78  SFDRAQDVRFATYAAWWVRNA------------------------VSSALSRIKAVIDIP 113

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
                 A+   +  E V  V   T+  ++L+T   ++        +          +++Q
Sbjct: 114 SRTYLDAQMGKLSDEDVFIVQLATRGTLALDTH-QEDAGRDPAQLLVSSEPDPEEHASLQ 172

Query: 607 ANLRETTTRVLASLTPRE-ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  R     +  +L   E E V  +R         TL ++     +T++R+RQ+E +A+ 
Sbjct: 173 SQRRMLLRLIDDALARMEPEEVAVIRRRRLAPEPETLADIAADLGITQDRLRQVERRAMM 232

Query: 666 KLKH 669
           +L+ 
Sbjct: 233 RLRR 236


>gi|4972297|dbj|BAA78111.1| RNA polymerase sigma subunit SigD* [Arabidopsis thaliana]
 gi|16649075|gb|AAL24389.1| sigma-like factor [Arabidopsis thaliana]
 gi|21387209|gb|AAM48008.1| sigma-like factor [Arabidopsis thaliana]
          Length = 267

 Score = 75.6 bits (184), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/79 (49%), Positives = 53/79 (67%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    A++++     RLV+S+A  Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 174 CRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLST 233

Query: 499 YAMWWVKQAITRSIADQSC 517
           Y  WW+KQAI R+IA +S 
Sbjct: 234 YVYWWIKQAILRAIAHKSR 252


>gi|308182585|ref|YP_003926712.1| flagellar biosynthesis sigma factor [Helicobacter pylori PeCan4]
 gi|308063276|gb|ADO05163.1| flagellar biosynthesis sigma factor [Helicobacter pylori Sat464]
 gi|308064770|gb|ADO06662.1| flagellar biosynthesis sigma factor [Helicobacter pylori PeCan4]
 gi|332673262|gb|AEE70079.1| DNA-directed RNA polymerase sigma subunit FliA [Helicobacter pylori
           83]
          Length = 258

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 104/268 (38%), Gaps = 20/268 (7%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S +  ++I  ++   + +    +  +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTQTSETSEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKE 61

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 62  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 118

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 119 RSNRKLIKSIDIEITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPI 174

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 175 DEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 224

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 225 SEIKEILGITESRISQIIKEVIKKVRKS 252


>gi|321116376|emb|CBN73569.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. Vn1]
          Length = 200

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 20/106 (18%), Positives = 43/106 (40%), Gaps = 2/106 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + S +     + L +L   + L   + + LV +L D   R+   E  ++++      
Sbjct: 96  KHGRGSKQANAELKALAELFMPIKLVPKQYEALVVRLRDALARLRGQERAIMQICVRDAR 155

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
           + R  FL +  G E+D  W        + ++   +   V +I + +
Sbjct: 156 MPRADFLRQFPGNEIDESWAENLAK-GKAKYAEAIGTRVANIQRCQ 200


>gi|294673112|ref|YP_003573728.1| sigma factor [Prevotella ruminicola 23]
 gi|294471705|gb|ADE81094.1| putative sigma factor [Prevotella ruminicola 23]
          Length = 238

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 109/262 (41%), Gaps = 48/262 (18%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++   G+   +    V + ++ +   + A+++M+++NL+LV+S+A  Y    +   DLIQ
Sbjct: 18  MARIRGVKALDEEQEVYLAQRIKAGDTKAEEQMIKSNLKLVVSIANSYRPM-MSMEDLIQ 76

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            GNIGL+KA  +F+  LGY+F  YA   +++ I   I + S  +    + +         
Sbjct: 77  NGNIGLIKAVREFNPELGYRFVFYASMMIRKYIIMGIRNDSGIVHSSDYEQ--------- 127

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDFIED 594
                                                  SL+ P  G    +   D +  
Sbjct: 128 ---------------------------------AFISSESLDVPGSGGYKDTSKADMLVG 154

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
              V     ++ A+L+     V   L+P    ++    G+G  T    E +GK+  + + 
Sbjct: 155 DMDVESDLDSLSADLKRAMCSV---LSPCAVDIVCKVMGLGC-TPMYTESIGKELNMPKS 210

Query: 655 RIRQIEAKAIRKLKHPSRSKKL 676
           R+R+I  ++I  L++  R KKL
Sbjct: 211 RVRKIYQESIGILQNNERVKKL 232


>gi|156976180|ref|YP_001447086.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio harveyi ATCC BAA-1116]
 gi|156527774|gb|ABU72859.1| hypothetical protein VIBHAR_04951 [Vibrio harveyi ATCC BAA-1116]
          Length = 242

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 89/231 (38%), Gaps = 21/231 (9%)

Query: 448 MVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  +V  V  +   +        D+ Q G I L++A  ++       F  +A+  V
Sbjct: 28  LLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVCRV 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV- 563
           + AI   +             R + H++    R ++  + R PT  EI K L    +   
Sbjct: 88  RGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRALGRMPTDAEIIKALGTDEQDYY 144

Query: 564 -RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R+   +  E  SL+  +     SH G            D     ++R +    L  ++ 
Sbjct: 145 NRQNAALAGEMQSLDQLMETGGESHFG---------GQYDGMEHEHIRRSLDTALGKMSK 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++ +L + +      +  L E+     +T  RI Q+  +A+++L     S
Sbjct: 196 RDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNQLMSS 242


>gi|321116208|emb|CBN73485.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V29]
          Length = 201

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 19/106 (17%), Positives = 41/106 (38%), Gaps = 2/106 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + +         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 97  KHGRHNKLAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 156

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
           + R  FL +  G E+D  W   A    + ++   +      I++ +
Sbjct: 157 MPRADFLRQFPGNEVDESWSD-ALAKGKSKYAEAIGRLQPDIIRCQ 201


>gi|208434361|ref|YP_002266027.1| alternative transcription initiation factor, sigma-F [Helicobacter
           pylori G27]
 gi|208432290|gb|ACI27161.1| alternative transcription initiation factor, sigma-F [Helicobacter
           pylori G27]
          Length = 247

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 96/247 (38%), Gaps = 20/247 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            ++I  ++   + +    + ++    L  V ++A +   R    + F DL+  G   L+K
Sbjct: 12  EKNIEKVLNAYDKQQHHHQDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIK 71

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            A +++  L   F  YA   V  A+   +        I    R  I  +     +  N+ 
Sbjct: 72  LARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDAEITKHLNEH 128

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EP+   +A+ L   +E +R+    +     +   +  ++  +  +             
Sbjct: 129 GKEPSDAYLAEALGENIEKIREAKTASD----IYALVPIDEQFNAIE------QDEITKK 178

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  RI QI  + 
Sbjct: 179 IEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITESRISQIIKEV 234

Query: 664 IRKLKHP 670
           I+K++  
Sbjct: 235 IKKVRKS 241


>gi|289524830|emb|CBJ94471.1| RNA polymerase sigma factor [Vibrio sp. Cmf 6.5]
 gi|289524832|emb|CBJ94472.1| RNA polymerase sigma factor [Vibrio sp. Cmf 5.9]
 gi|289524834|emb|CBJ94473.1| RNA polymerase sigma factor [Vibrio sp. Rd 14.3]
 gi|289524836|emb|CBJ94474.1| RNA polymerase sigma factor [Vibrio sp. Rd 14.14]
          Length = 111

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 39/111 (35%), Gaps = 2/111 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    Y  + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYAKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
              W+       +  +   +      I +   ++  I  ET +++   + I
Sbjct: 62  SEAWLDEVLA-SDKPYVEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDI 111


>gi|213621148|ref|ZP_03373931.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 150

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/153 (22%), Positives = 69/153 (45%), Gaps = 6/153 (3%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A +++D   G
Sbjct: 1   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQG 60

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F+TYA+  ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A
Sbjct: 61  TAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAMGQLEQELGRNATETEVA 117

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
           ++L +PV   R++L  T            E+  
Sbjct: 118 ERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHG 150


>gi|269784308|emb|CBH50799.1| RNA polymerase sigma factor [Vibrio sp. C 15.19]
          Length = 111

 Score = 75.3 bits (183), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 19/111 (17%), Positives = 42/111 (37%), Gaps = 2/111 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    YG + +++F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKNIFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHI 430
              W+       +  +   +      I +   ++  I  ET +++   + I
Sbjct: 62  SEAWLDEVLA-SDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDI 111


>gi|297379636|gb|ADI34523.1| RNA polymerase sigma factor, FliA/WhiG family [Helicobacter pylori
           v225d]
          Length = 250

 Score = 75.3 bits (183), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 100/256 (39%), Gaps = 20/256 (7%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
            +T  S +  ++I  ++   + +    +  +    L  V ++A +   R    + F DL+
Sbjct: 6   QKTQTSETSEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLV 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G   L+K A +++  L   F  YA   V  A+   +        I    R  I  +  
Sbjct: 66  SIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDI 122

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +  N+  +EP+   +A+ L   +E +++    +     +   +  ++  +  +    
Sbjct: 123 EITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPIDEQFNAIE---- 174

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  
Sbjct: 175 --QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITES 228

Query: 655 RIRQIEAKAIRKLKHP 670
           RI QI  +AI+K++  
Sbjct: 229 RISQIIKEAIKKVRKS 244


>gi|312134632|ref|YP_004001970.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774683|gb|ADQ04170.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 242

 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 93/255 (36%), Gaps = 59/255 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +         A+  ++E NLRLV  +AKKYT        D+I 
Sbjct: 32  SFPQPMSSEEEEMYLNKMW---EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIIS 88

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA E +      K STYA   ++  I   +      +                
Sbjct: 89  VGTIGLIKAIETYSTAKCTKLSTYAAKCIENEILMYLRQNKKFLS--------------- 133

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI 592
                                                 +SLE PIG +       L D +
Sbjct: 134 -------------------------------------QLSLENPIGSDKDGNEITLMDVL 156

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++          ++  ++    ++   L  RE++++ +R+G+    + T  EV     ++
Sbjct: 157 QNNQDDIDEQVDLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVANLLGIS 216

Query: 653 RERIRQIEAKAIRKL 667
           R  + +IE KA++KL
Sbjct: 217 RSYVSRIEKKALQKL 231


>gi|321116254|emb|CBN73508.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116260|emb|CBN73511.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116262|emb|CBN73512.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116322|emb|CBN73542.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116326|emb|CBN73544.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116328|emb|CBN73545.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 26/185 (14%), Positives = 61/185 (32%), Gaps = 8/185 (4%)

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D +       +  A   ++   +          D+++ +E++D  +              
Sbjct: 18  DILSGYIDPDDDGAAAPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVA 77

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 +AE   +           +K  ++S +     E L  L   + L   + D LVE
Sbjct: 78  RVRFGAVAEQLEKANK------ALKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVE 131

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++ +   +I   E  +++L      + R  FL +    E +  W        +G++   +
Sbjct: 132 RVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAI 190

Query: 400 ACEVD 404
               +
Sbjct: 191 GNRKE 195


>gi|302871341|ref|YP_003839977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574200|gb|ADL41991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 242

 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 54/255 (21%), Positives = 93/255 (36%), Gaps = 59/255 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +         A+  +VE NLRLV  +AKKYT        D+I 
Sbjct: 32  SFPQPMSSEEEEMYLNKMW---EGCKEARNILVEKNLRLVAHIAKKYTFSFPNLTDDIIS 88

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA E +      K STYA   ++  I   +      +                
Sbjct: 89  VGTIGLIKAIETYSKDKSTKLSTYAAKCIENEILMYLRQNKKFLS--------------- 133

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI 592
                                                 +SLE PIG +       L D +
Sbjct: 134 -------------------------------------QLSLENPIGSDKDGNEITLMDVL 156

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++          ++  ++    ++   L  RE++++ +R+G+    + T  EV     ++
Sbjct: 157 QNDQDDIDEQVDLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVASLLGIS 216

Query: 653 RERIRQIEAKAIRKL 667
           R  + +IE KA++KL
Sbjct: 217 RSYVSRIEKKALKKL 231


>gi|315638331|ref|ZP_07893511.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter
           upsaliensis JV21]
 gi|315481598|gb|EFU72222.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter
           upsaliensis JV21]
          Length = 231

 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 96/228 (42%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 18  QDELVISYMPALRAMAFRLKERLPSSIDVNDLIGVGIEEMIKLSRRYDKDQNDNFWGFAR 77

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  +  +         + + EP  E +AKKL + VE
Sbjct: 78  KRVNGSMLDYLR---RLDVMSRNNRKILKDIDVILDEYFLENECEPDDEYLAKKLEIDVE 134

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR+V        +L           L + IE  +    L+   +  L E    +L +L 
Sbjct: 135 RVREVRAAHAISYTL----------PLDEQIEMYSEDETLEKIERGELLEHINEILDTLK 184

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   V+  RI QI  K ++KL+ 
Sbjct: 185 ERDQLIIQLYY----YEELSLKEISEILNVSESRISQIHKKLLKKLRE 228


>gi|224373368|ref|YP_002607740.1| flagellar biosynthesis sigma factor [Nautilia profundicola AmH]
 gi|223589587|gb|ACM93323.1| RNA polymerase sigma factor, sigma-F [Nautilia profundicola AmH]
          Length = 229

 Score = 74.9 bits (182), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 47/228 (20%), Positives = 94/228 (41%), Gaps = 22/228 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+    +  V ++A +   R    ++F DL+  G   L+K A ++D      F  YA 
Sbjct: 17  RDELAVDYMPAVKAMAARLKERLPSSVEFNDLVSIGLEELVKLARRYDPKQNDNFWGYAQ 76

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +  ++   +        +    R  I  + +       +   EP  E IA  L + VE
Sbjct: 77  KRIYGSMLDFLRSLD---TVSRSDRKIIKDIEKIVESYQAEHDIEPDDEYIADILGIEVE 133

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR+    ++    +   +  E+  +  D        +      +  L ET  +VL ++T
Sbjct: 134 KVRRAKNASE----IYNVMPIEEQMNFFD--------NVSLKIEEEELIETIKKVLKTMT 181

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +E+ ++++ +      + +L+E+ +   VT  RI QI    I+KL+ 
Sbjct: 182 EKEQLIIQLYYF----EELSLKEISEILGVTESRISQIHKNVIKKLRK 225


>gi|321116272|emb|CBN73517.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V138]
          Length = 199

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 18/117 (15%), Positives = 48/117 (41%), Gaps = 2/117 (1%)

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
            +L+      +K  ++S +     +++ +L   + L   + + LV ++    +R+   E 
Sbjct: 84  EALEAAKKALKKHGRNSKQGIAALKEMAELFMPIKLIPKQYEALVVRVRSSLERLRAQER 143

Query: 355 ELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
            +++L      + R  FL+   G E+D  W +      + ++   +      I + +
Sbjct: 144 AIMQLCVRDARMPRADFLKLFPGNEVDQEWAAGLAK-GKAKYAEAIGNLQGDIQRCQ 199


>gi|321116374|emb|CBN73568.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. Vl2]
          Length = 200

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 2/106 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + S +     + L +L   + L   + + LV +L D   R+   E  ++++      
Sbjct: 96  KHGRGSKQANAELKALAELFMPIKLVPKQYEALVVRLRDALARLRGQERAIMQICVRDAR 155

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
           + R  FL +  G E+D  W        + ++   +   V  I + +
Sbjct: 156 MPRADFLRQFPGNEIDESWAENLAK-GKAKYAEAIGTRVADIQRCQ 200


>gi|304413523|ref|ZP_07394996.1| flagellar biosynthesis sigma factor [Candidatus Regiella
           insecticola LSR1]
 gi|304284366|gb|EFL92759.1| flagellar biosynthesis sigma factor [Candidatus Regiella
           insecticola LSR1]
          Length = 246

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 42/202 (20%), Positives = 89/202 (44%), Gaps = 15/202 (7%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L+  D+ Q   +GL++A  ++      +F+ YA+  ++ AI   + +       P  +R 
Sbjct: 56  LEREDMQQIALMGLLEALRRYGHPDQ-QFAAYAVHRIRGAILDQLREHDW---RPRRLRQ 111

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K HK     R +  ++  EP  +EIA +L++  +  ++ L        LE     E    
Sbjct: 112 KTHKTNEAIRELGKRLGHEPNYDEIAAELSITPQEYQEYLL-------LENAKAMESLDD 164

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L       +A+   +   Q  ++++  + + +L  RE+ +L + +      + +L+E+  
Sbjct: 165 LLSLETHNDALQSRELEEQMIIQDSLRQAIGTLDDREKLILSLYYQ----QELSLKEIAL 220

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              +T  R+ Q+  K   K+K 
Sbjct: 221 VLELTEARVCQLNKKIAEKIKK 242


>gi|229073720|ref|ZP_04206833.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus cereus
           F65185]
 gi|228709429|gb|EEL61490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus cereus
           F65185]
          Length = 236

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 51/207 (24%), Positives = 89/207 (42%), Gaps = 20/207 (9%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           +N GL+  DLIQ G IGL+KA + FD   GYKFST A+  +    TR+I +         
Sbjct: 34  SNTGLEIEDLIQCGMIGLLKARKDFDPAYGYKFSTLAIPKMHGETTRAIINN-------- 85

Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD- 582
                  ++     R+  +   E  PE I++ L + VE V + L+  + P SL       
Sbjct: 86  QKVKVTREIFYLKGRIIREKLAEEKPEVISQLLGVTVEDVEEALRYQQIPSSLHDVTFSS 145

Query: 583 ---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
              +    L   + D+++        + + +      + +L  RE  +  M         
Sbjct: 146 GSGDTDLTLEQMLVDESST---RKTEEIDEKIVMRSFINTLPDRELMIWDMYSNH----- 197

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            + E +G++  VT+ +I +I  +  R+
Sbjct: 198 MSQESIGERVGVTQTQISRILKRINRR 224


>gi|317009060|gb|ADU79640.1| flagellar biosynthesis sigma factor [Helicobacter pylori India7]
          Length = 255

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 102/268 (38%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S +    +++   K +     A   +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQKTQTSETSIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        + 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VVS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 116 RSNRKLIKSIDIEITKHLNEHGKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRKS 249


>gi|224437149|ref|ZP_03658130.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
 gi|313143612|ref|ZP_07805805.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
 gi|313128643|gb|EFR46260.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
          Length = 235

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 92/235 (39%), Gaps = 26/235 (11%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A+ E+    L  V ++A +   R    ++  DL+  G   L+K A ++D  L   F  
Sbjct: 15  KYAQDELALQYLPAVKAMAFRLKERLPSSIEMADLVSIGTEELIKLARRYDSSLNDSFWG 74

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   V  A+   +        +    R  +  +     +  N  + EP+ E +AK L  
Sbjct: 75  YAKTRVNGAMLDYLRSLD---VLSRASRKLVKAIDYEISKYFNDYQEEPSDEYLAKILNE 131

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA---VSPLDSAIQANLRETTTR 615
            V  +++    +             D   L    E  NA    + L+   +  L E    
Sbjct: 132 DVAKIKEARVAS-------------DVYALVPIDEQYNAICGENILEDVQKDELMEIVHN 178

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           VL  L  RE+ ++++ +      +  L+E+ +   +T  RI QI  + I+K++  
Sbjct: 179 VLKKLGKREQMIIQLYYF----EELNLKEISEILEITESRISQITKEVIKKIRQA 229


>gi|218459714|ref|ZP_03499805.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 198

 Score = 74.9 bits (182), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 81/188 (43%), Gaps = 12/188 (6%)

Query: 500 AMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPE---EIAK 554
           AMWW+K +I   I      +++    + +     + R   R+      +  PE   EIA 
Sbjct: 1   AMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIAT 60

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAIQANL--- 609
           KL +  E V  + +      SL  PI   + D+    D++ D +         Q  L   
Sbjct: 61  KLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETR 120

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R   ++ ++ L  RE R+   R         TLE++  +F ++RER+RQIE +A  K++ 
Sbjct: 121 RRMLSKAMSVLNERERRIFEARRLAE--EPVTLEDLSAEFDISRERVRQIEVRAFEKVQD 178

Query: 670 PSRSKKLR 677
             R + L 
Sbjct: 179 AVRKEALE 186


>gi|239934404|emb|CAR92332.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 193

 Score = 74.5 bits (181), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 31/233 (13%), Positives = 72/233 (30%), Gaps = 49/233 (21%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T  +++   + +      L E++            G+    +G            K+ D 
Sbjct: 1   TVDSILAEYNRVTTDGGRLVEVL-----------SGYIDPDDGIVPAGAAAPVPVKDGDA 49

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +ET+ D E++    ++     D                                 + + 
Sbjct: 50  AEETDDDAEASDDEEEEGDGGPDPE-------------------------------EALR 78

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               I +      +L+      +K  ++S +     +++ +L   + L   + D LV ++
Sbjct: 79  RFTAIGD------ALELAKKALKKHGRNSKQGTAALKEMAELFMPIKLVPKQYDALVVRV 132

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
               +R+   E  +++L      + R  FL    G E+D  W +         
Sbjct: 133 RSSLERLRAQERAIMQLCVRDARMPRADFLRLFPGNEIDVEWSAGLAKGKAKY 185


>gi|321116240|emb|CBN73501.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 196

 Score = 74.5 bits (181), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 33/238 (13%), Positives = 69/238 (28%), Gaps = 44/238 (18%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +++   D +      L +I  L   I P+  G           Q+ E            +
Sbjct: 1   SILADYDRVTTEGGRLSDI--LSGYIDPDDDGA------AGPQQEVEPVVPAAAAKPAAD 52

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D E     ++++       PE A      + +  + +   L                
Sbjct: 53  GKDDEEEDDADTEEEEGDGGPDPEVARVRFGAVADQLEVAKKAL---------------- 96

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  ++S +     ++L  L   + L   + D LV ++ D 
Sbjct: 97  -------------------KKHGRASKQAVEALQELAILFMPIKLIPKQYDALVLRVRDA 137

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
             ++   E  +++L      + R  FL +    E D  W            +   A +
Sbjct: 138 LSQVRAQERAIMQLCVRDARMPRADFLRQFPNHETDLDWAEQLAGGKSKYAEAIGARK 195


>gi|154500630|ref|ZP_02038668.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
 gi|150270519|gb|EDM97828.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
          Length = 221

 Score = 74.5 bits (181), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 82/246 (33%), Gaps = 61/246 (24%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +   E R  +            A+  ++E NLRLV  + KKY  +     DLI  
Sbjct: 31  SFPRPLKAEEERMYLER---CAAGDLEARNILIEHNLRLVAHIIKKYYTQTDDQDDLISI 87

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+K    F      + +TYA   ++  I                         R+ 
Sbjct: 88  GTIGLIKGISTFKPDKNVRLATYASRCIENEILMHF---------------------RSR 126

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIE 593
           +++  +                               +SL   +  +       L D I 
Sbjct: 127 KKLQGE-------------------------------VSLSDTLEADGDGSSLSLMDVIS 155

Query: 594 -DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            D + +  LD+  + +  +    V   L  RE  ++ +R+G+G     T  E+  Q  ++
Sbjct: 156 VDDDMLDNLDA--RESCIKVRQCVKDCLNEREAMIIGLRYGLGGQNPLTQREIAAQCGIS 213

Query: 653 RERIRQ 658
           R  + +
Sbjct: 214 RSYVSR 219


>gi|159901988|gb|ABX10718.1| RNA polymerase sigma factor [uncultured planctomycete 13FN]
          Length = 391

 Score = 74.5 bits (181), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 112/244 (45%), Gaps = 61/244 (25%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            ++    K   +A   +  +++ANLRLV+S+A+++    +   +LI +GN+ LMKA ++F
Sbjct: 194 RVMVRTEKDLDDARQVRDHIIQANLRLVVSIARRFVTDFISLDELISDGNLILMKAVDRF 253

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           ++ LG++FSTYA   V++   R+  +                                  
Sbjct: 254 NFSLGFRFSTYATHAVQRDFYRNYKNGRR------------------------------- 282

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
                          R+V++I  +P  L   +   D       I D +AV+ L       
Sbjct: 283 ---------------RRVMEIATDPAVLFGSVVASDDEQ---QINDVHAVAYLK------ 318

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
                  ++ +L+PRE+ +L MR G+  +    TL EVG++  +++ER+RQ++ +AI ++
Sbjct: 319 -----KLLVDALSPREQTILDMRLGLKADDGGKTLREVGEKLSISKERVRQLQTRAIEQV 373

Query: 668 KHPS 671
           +  +
Sbjct: 374 RELA 377


>gi|57241943|ref|ZP_00369883.1| alternative transcription initiation factor, sigma-F (fliA)
           [Campylobacter upsaliensis RM3195]
 gi|57017135|gb|EAL53916.1| alternative transcription initiation factor, sigma-F (fliA)
           [Campylobacter upsaliensis RM3195]
          Length = 231

 Score = 74.5 bits (181), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 94/228 (41%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 18  QDELVISYMPALRAMAFRLKERLPSSIDVNDLISVGIEEMIKLSRRYDKDQNDNFWGFAR 77

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  +  +         + + EP  E +AKKL + VE
Sbjct: 78  KRVNGSMLDYLR---RLDVMSRNNRKILKDIDVILDEYFLENECEPDDEYLAKKLEIDVE 134

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            VR+V        +L             + IE  +    L+   +    E    +L +L 
Sbjct: 135 RVREVRAAHAISYTL----------PFDEQIEMYSEDETLEKIERGEFLEHINEILDTLK 184

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   V+  RI QI  K ++KL+ 
Sbjct: 185 ERDQLIIQLYY----YEELSLKEISEILNVSESRISQIHKKLLKKLRE 228


>gi|295094135|emb|CBK83226.1| RNA polymerase sigma factor, sigma-70 family [Coprococcus sp.
           ART55/1]
          Length = 220

 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 92/245 (37%), Gaps = 47/245 (19%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVA-KKYTNRGLQ-------FLDLIQEGNIGLMK 483
            + R  +   + A+  ++E NL  +  +A ++Y N GL          DL+QEG+IGL+ 
Sbjct: 8   QLCRLAQKGDTAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIGLLN 67

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A   FD   G KF TYA   ++ A+T                      +         ++
Sbjct: 68  AIPLFDAGRGMKFLTYAAPALRNAMTDC--------------------IRAALGLFEQRM 107

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
                              V K      + + L+  + +++     + I D +  +P   
Sbjct: 108 -------------------VDKKDAPGFQRVYLDDVLSEDERMLRIEAIADPHTQTPEQI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            IQ          L  LT RE+  L  R+G     +H L      F ++  R +++E +A
Sbjct: 149 YIQKEQLIELYAALDKLTAREQTYLLYRYGFTDGIEHPLIGAALHFHLSESRTKKVEGEA 208

Query: 664 IRKLK 668
           +  L+
Sbjct: 209 MDSLR 213


>gi|321116320|emb|CBN73541.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 69/240 (28%), Gaps = 46/240 (19%)

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
           +++     +      L +I  L   I P+  G           Q+ E  + +       +
Sbjct: 1   SILADYXRVTTEGGRLSDI--LSGYIDPDDDGAA-------GPQEVEPETPQTTAKPAAD 51

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            + D E     S+ +       PE A        E  + +                    
Sbjct: 52  DKDDEEEDDSDSEXEEGDGGPDPEVAXMRFGAFAEQLEKAKKA----------------- 94

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
                              +K  ++S +     E L  L   + L   + D LVE++ + 
Sbjct: 95  ------------------LKKHGRASQQAVXELEXLXILFMPIKLVPKQYDALVERVRNA 136

Query: 346 SKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
             +I   E  ++ L      + R  FL +    E +  W        +G++   +    +
Sbjct: 137 LSQIRAQERSIMXLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIGNRKE 195


>gi|307637111|gb|ADN79561.1| RNA polymerase sigma factor [Helicobacter pylori 908]
 gi|325995702|gb|ADZ51107.1| RNA polymerase sigma factor of flagellar operon [Helicobacter
           pylori 2018]
 gi|325997298|gb|ADZ49506.1| Flagellar biosynthesis sigma factor [Helicobacter pylori 2017]
          Length = 247

 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 46/256 (17%), Positives = 96/256 (37%), Gaps = 23/256 (8%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
            +T  S      +++   K +     A   +    L  V ++A +   R    + F DL+
Sbjct: 6   QKTEASEKSIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKERLPSSIDFNDLV 62

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G   L+K A +++  L   F  YA   V  A+   +        I    R  I  +  
Sbjct: 63  SIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSSRKLIKSIDI 119

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +  N+   EP+   +A+ L   +E +R+    +     +   +  ++  +  +    
Sbjct: 120 EITKYLNEHGEEPSDAYLAEVLGENIEKIREAKTASD----IYALVPIDEQFNAIE---- 171

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         L E   +VL  ++ RE+ ++++ +      +  L E+ +   +T  
Sbjct: 172 --QDEITQKIEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNLSEIKEILGITES 225

Query: 655 RIRQIEAKAIRKLKHP 670
           RI QI  + I+K++  
Sbjct: 226 RISQIIKEVIKKVRQS 241


>gi|113473821|ref|YP_718084.1| RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
 gi|112821501|dbj|BAF03372.1| Probable RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
          Length = 328

 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 36/92 (39%), Positives = 52/92 (56%)

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D     D  E   A S   S          T  L+ L+ REERV+R+RFG+G + + TL+
Sbjct: 25  DAPERVDMAEAMQATSEPRSIDLIGDIGVLTAALSCLSAREERVIRLRFGLGGHGEWTLQ 84

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++G +F V  +RIRQIE KA+R+L+H  R + 
Sbjct: 85  QIGDEFGVNPQRIRQIEMKALRRLRHQFRKRY 116


>gi|168704991|ref|ZP_02737268.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 169

 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 42/153 (27%), Positives = 71/153 (46%), Gaps = 11/153 (7%)

Query: 456 VISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           V   A++  +R   G++  DLI  G  GL+ A + FD   G KF TY +  ++ A+   +
Sbjct: 4   VKYNAERIWSRLPDGVELDDLISAGVFGLLDAIDAFDLTRGVKFETYCVPRIRGAMLDEL 63

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                   +P  +R K  K+    +++   + R P PEE+++KL +P+E +   +     
Sbjct: 64  RTMDW---VPRLVRSKASKMEAARKQLEAALGRPPKPEELSEKLGIPLEQLESYVGDATA 120

Query: 573 P--ISLETPIGDED---TSHLGDFIEDKNAVSP 600
              +SL     + D        D +EDK A SP
Sbjct: 121 VNLVSLNKKWYETDSYKDVREIDILEDKKAESP 153


>gi|317471864|ref|ZP_07931199.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|316900637|gb|EFV22616.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 207

 Score = 74.5 bits (181), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 95/256 (37%), Gaps = 58/256 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +    +S  E ++ +   R        A+  +VE NLRLV  + KKY N      DLI  
Sbjct: 3   AFLEPLSQEEEQYYLKKSR---LGDMEARNILVEHNLRLVAHIVKKYNNFDRDKDDLISV 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   ++   G++  TYA   ++  +   +  +                     
Sbjct: 60  GTIGLIKAINTYNMEKGHRLVTYASRCIENELLMMLRQE--------------------- 98

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIE 593
                                          + + +  SL  PIG +   +  +L D + 
Sbjct: 99  -------------------------------RKSAKDTSLYEPIGIDKEGNEINLLDVLG 127

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                   +  ++  +R+    V      RE+  L MR+G+      T +EV K+  ++R
Sbjct: 128 ADENDIVDELDLKEKIRDLYKMVDEMEPSREKTTLIMRYGLYGKKPMTQKEVAKELHISR 187

Query: 654 ERIRQIEAKAIRKLKH 669
             + +IE KA+ K+K 
Sbjct: 188 SYVSRIEKKAVEKIKR 203


>gi|327188541|gb|EGE55752.1| RNA polymerase sigma factor RpoD [Rhizobium etli CNPAF512]
          Length = 764

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/93 (34%), Positives = 47/93 (50%)

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
            G+  +D   VS         L  +   +L     R+  V+  RFG+G N   TLEE+G 
Sbjct: 119 FGEKQQDDEHVSADKIPTFETLDASLDWLLGQCNARDRLVIERRFGLGSNARETLEEIGS 178

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            + VTRERIRQIE +A+ +++   R   L  F+
Sbjct: 179 DYGVTRERIRQIEKRALTRMRVRMRHVPLADFV 211


>gi|93007309|gb|ABE97157.1| SigF [Pasteuria ramosa]
          Length = 131

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 37/122 (30%), Positives = 68/122 (55%), Gaps = 4/122 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E R +   +   +   + A+  +V  N+RLV SV +++ NRG +  D+ Q G IGL
Sbjct: 14  LTDTEVREL---IISSQKGDTKARDRLVSHNIRLVWSVVQRFLNRGYESDDIFQIGCIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA +KF+     KFSTYA+  +   I R + D    +++   +++  H+V +T   +S 
Sbjct: 71  LKAVDKFNLEYEVKFSTYAVPMILGEIQRFLRD-DGIVKVSRSLKEMAHRVRKTRDELSK 129

Query: 542 KI 543
           K+
Sbjct: 130 KL 131


>gi|239934484|emb|CAR92496.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 209

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 30/254 (11%), Positives = 78/254 (30%), Gaps = 46/254 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + +    +++ P+  E   R                        
Sbjct: 50  AEIENEAEEEAEEGEGASEGEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      +   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFVQVQK------GMAEKGADDPQVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            + +
Sbjct: 137 QIRRSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAH-L 195

Query: 400 ACEVDSILKIRNEI 413
           A   + I   + ++
Sbjct: 196 AKLREEIEAQQXKL 209


>gi|308184219|ref|YP_003928352.1| flagellar biosynthesis sigma factor [Helicobacter pylori SJM180]
 gi|308060139|gb|ADO02035.1| flagellar biosynthesis sigma factor [Helicobacter pylori SJM180]
          Length = 255

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 97/247 (39%), Gaps = 20/247 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            ++I  ++   + +    + ++    L  V ++A +   R    + F DL+  G   L+K
Sbjct: 20  EKNIEKVLNAYDKQQHHHQDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIK 79

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            A +++  L   F  YA   V  A+   +        I    R  I  +     +  N+ 
Sbjct: 80  LARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDIEITKHLNEH 136

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EP+   +A+ L   +E +R+    +     +   +  ++  +  +             
Sbjct: 137 GKEPSDAYLAEALGENIEKIREAKTASD----IYALVPIDEQFNAIE------QDEITKK 186

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L E   +VL  ++ RE+ ++++ +      +  L E+ +   +T  RI QI  + 
Sbjct: 187 IEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNLSEIKEILGITESRISQIIKEV 242

Query: 664 IRKLKHP 670
           I+K++  
Sbjct: 243 IKKVRQS 249


>gi|269960144|ref|ZP_06174520.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio harveyi 1DA3]
 gi|269835115|gb|EEZ89198.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio harveyi 1DA3]
          Length = 242

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 43/231 (18%), Positives = 89/231 (38%), Gaps = 21/231 (9%)

Query: 448 MVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +++ +  +V  V  +   +        D+ Q G I L++A  ++       F  +A+  V
Sbjct: 28  LLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVCRV 87

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG-- 562
           + AI   +             R + H++    R ++  + R P+  EI K L    +   
Sbjct: 88  RGAILDELRRLDW---RSRKTRQQAHELNDVTRDLTRALGRMPSDAEIIKALGTDEQDFY 144

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
            R+   +  E  SL+  +     SH G            D     ++R +    L  ++ 
Sbjct: 145 NRQNAALAGEMQSLDQLMETGGDSHFG---------GQYDGMEHEHIRRSLDTALGKMSK 195

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           R++ +L + +      +  L E+     +T  RI Q+  +A+++L     S
Sbjct: 196 RDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNQLMSS 242


>gi|239934440|emb|CAR92474.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 200

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 29/241 (12%), Positives = 72/241 (29%), Gaps = 45/241 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPVNPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AEIENEAEEEAEEGEGASEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFVQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            +  
Sbjct: 137 QIRRSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAHLA 196

Query: 400 A 400
            
Sbjct: 197 K 197


>gi|239934432|emb|CAR92346.1| DNA-directed RNA polymerase subunit D [uncultured Alcanivorax sp.]
          Length = 218

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 38/257 (14%), Positives = 81/257 (31%), Gaps = 42/257 (16%)

Query: 157 LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
           L   P   + ++   D +      L ++I     + P+  G             +    +
Sbjct: 1   LAFWPGAVEMVLDEYDRILXEERKLTDVI--AGYLDPDDDGAAATNANKELRFNQRKQXE 58

Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
             E+D  ++ + D +S +    ++      P   AE                        
Sbjct: 59  AAEKDKDKDDDDDDKSDSDDDSEEDEGGLDPVLAAER----------------------- 95

Query: 277 RPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                         + EL+ L + A    K + +         E L        L     
Sbjct: 96  --------------FGELKKLHEKAERALKRNGRDHASSAKALEALAGHFTLFKLVPRIY 141

Query: 336 DLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWV-SYAKDFPEG 393
           D L++        +   E +++ LA +  G+ R  F+++  G E +P WV ++AK     
Sbjct: 142 DQLLQGARTHLDIVRKFEHQIMALAIRRAGVPRKDFVQQFPGNETNPEWVAAHAKTKKAK 201

Query: 394 EWKNFVACEVDSILKIR 410
           ++   +    + I + +
Sbjct: 202 DYSERLMTVAEDIQRNQ 218


>gi|87125785|ref|ZP_01081628.1| putative type III sigma factor [Synechococcus sp. RS9917]
 gi|86166594|gb|EAQ67858.1| putative type III sigma factor [Synechococcus sp. RS9917]
          Length = 262

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 55/249 (22%), Positives = 104/249 (41%), Gaps = 20/249 (8%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEK 487
            I    R+   EA   +   + ++L L   VA + + RG   + DL+QE ++GL+ A E 
Sbjct: 14  RIRREWRRSLPEAIRHRNGEIISHLGLAHHVAGRQSTRGHGDWDDLVQEASLGLIAAVEG 73

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G++ S+YA+      I     D+  TIRIP  +R    + +R   +         
Sbjct: 74  FDSSRGHQLSSYAVSRAHGQILHFRRDRQSTIRIPWRLRSLYGRGMRLQEQQWQAHGAPL 133

Query: 548 TPEEIAKKLAMPVEGVRK--VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
           + E +   L +  E  R+       +E +SL+ P  +   +      ED           
Sbjct: 134 SEEALIAMLEVSRERWRQAVQAHAQEEVLSLDGPGVEPGEAFGEVAAEDPQ--------- 184

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
               R+   + L  L P + R L   +  G+    +L  + ++  V    ++++ A A+ 
Sbjct: 185 ----RQWLHQALPQLQPEQRRWLLAHWVEGV----SLRALARREGVHPAMLKRVLATALE 236

Query: 666 KLKHPSRSK 674
           +L+  ++ +
Sbjct: 237 QLRSLAQVE 245


>gi|307720637|ref|YP_003891777.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sulfurimonas
           autotrophica DSM 16294]
 gi|306978730|gb|ADN08765.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sulfurimonas
           autotrophica DSM 16294]
          Length = 228

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 90/228 (39%), Gaps = 20/228 (8%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            E+    L  V ++A +   R    + F DL   G   L+K A ++D  L   F  YA  
Sbjct: 15  DELAIQYLPAVKAMAFRLKERLPSSVDFSDLCAIGTEELIKLARRYDEKLNDSFWGYAKK 74

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V  A+   +        +    R  +  +    +        EP+ EE+A+ L   VE 
Sbjct: 75  RVYGAMLDYLRSLD---ILSRASRKLVKAIDYAVQEYMLTHDEEPSDEELAQVLDESVEK 131

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
           + +    +    S+ T +   D   +GD        + L    +  L     +VL+S   
Sbjct: 132 IHEARIAS----SIYTVMPLHDQLQVGD------EGAALVQIEKEELITVIKKVLSSYKE 181

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           RE+ ++++ +      + TL+E+     +T  RI QI    I+K+K  
Sbjct: 182 REQMIIQLYYF----EELTLKEISSILDITESRISQIHKSVIQKIKES 225


>gi|150019798|ref|YP_001312052.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium beijerinckii
           NCIMB 8052]
 gi|149906263|gb|ABR37096.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium beijerinckii
           NCIMB 8052]
          Length = 250

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 101/245 (41%), Gaps = 52/245 (21%)

Query: 444 AKKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK--FSTY 499
           A + ++EAN  +V  +A K+   N+ ++F DL+Q G IGL+ AA K++  L  K  F TY
Sbjct: 17  ALESLIEANEGIVKKLANKFNGINKMIEFDDLVQAGIIGLINAANKYNNELENKASFITY 76

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A  ++K+ I   +                                               
Sbjct: 77  AFQYIKREIFSCV-------------------------------------------NGRS 93

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQANLRETTTRV- 616
            + +          +SL+ PI +++   L D IE  D    +  +      LRE      
Sbjct: 94  EKEISNNKLYNSC-VSLDVPIQEDNDIQLKDTIESIDYGFENVEEKIYIKQLREELEDAM 152

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK-K 675
           L + T +E  +L++ +G       T +EV +   ++   I QIE  A+RKL++ +  K K
Sbjct: 153 LDNNTLKEREILQLCYGWNYQKIFTYKEVAETLNISINSIPQIEFNALRKLRNSTWGKEK 212

Query: 676 LRSFL 680
           ++ ++
Sbjct: 213 VKEYM 217


>gi|317177227|dbj|BAJ55016.1| flagellar biosynthesis sigma factor [Helicobacter pylori F16]
          Length = 250

 Score = 74.1 bits (180), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 99/256 (38%), Gaps = 20/256 (7%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
            +T  S +  ++I  ++   + +    +  +    L  V ++A +   R    + F DL+
Sbjct: 6   QKTQTSETSEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLV 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G   L+K A +++  L   F  YA   V  A+   +        I    R  I  +  
Sbjct: 66  SIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDA 122

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +  N+  +EP+   +A+ L   +E +++    +     +   +  ++  +  +    
Sbjct: 123 EITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPIDEQFNAIE---- 174

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  
Sbjct: 175 --QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITES 228

Query: 655 RIRQIEAKAIRKLKHP 670
           RI QI  + I+K++  
Sbjct: 229 RISQIIKEVIKKVRKS 244


>gi|239934356|emb|CAR92308.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 195

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 33/226 (14%), Positives = 68/226 (30%), Gaps = 45/226 (19%)

Query: 164 FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             +++   + +      L +I  L   I P+  G         + Q+ E  + +      
Sbjct: 1   VDSILADYERVTTEGGRLSDI--LSGYIDPDDDGAA-------APQEVEPETPQTTAKPA 51

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            + + D E     S+++       PE A      + E  + +   L              
Sbjct: 52  ADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKAL-------------- 97

Query: 284 LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                                +K  ++S +     E L  L   + L   + D LVE++ 
Sbjct: 98  ---------------------KKHGRASQQAVEELEALAILFMPIKLVPKQYDALVERVR 136

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAK 388
           +   +I   E  +++L      + R  FL +      +  W     
Sbjct: 137 NALSQIRAQERVIMQLCVRDARMPRADFLRQFPNNGTNLDWAEQLA 182


>gi|289524842|emb|CBJ94477.1| RNA polymerase sigma factor [Vibrio sp. C15.18]
          Length = 109

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 17/109 (15%), Positives = 38/109 (34%), Gaps = 2/109 (1%)

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY-GIKRDVFLERHQGREL 379
           +  +     L   + D LV +L     R+   E  ++R    Y  + +  F+    G E 
Sbjct: 2   MQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYAKMPKKSFIALFTGNES 61

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
              W+       +  +   +      I +   ++  I  ET +++   +
Sbjct: 62  SEAWLDEVL-TSDKPYVEKIKRNEHDIRRSIQKLDMIERETSLTVQSIK 109


>gi|68304088|gb|AAY89702.1| FliA [Escherichia coli LW1655F+]
          Length = 157

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 34/156 (21%), Positives = 70/156 (44%), Gaps = 6/156 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G  F+TYA+
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ A+   +  +     +P  +R    +V +   ++  ++ R  T  E+A++L + + 
Sbjct: 63  QRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIA 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
             R++L  T            E+     + + D + 
Sbjct: 120 DYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQ 155


>gi|321116350|emb|CBN73556.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 27/185 (14%), Positives = 62/185 (33%), Gaps = 8/185 (4%)

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D +       +  A   ++   +          D+++ +E++D  +              
Sbjct: 18  DILSGYIDPDDDGAAGPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVA 77

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 +AE       L+      +K  ++S +     E L  L   + L   + D LVE
Sbjct: 78  RMRFGAVAEQ------LEKAKTALKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVE 131

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++ +   +I   E  +++L      + R  FL +    E +  W        +G++   +
Sbjct: 132 RVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAI 190

Query: 400 ACEVD 404
               +
Sbjct: 191 GNRKE 195


>gi|298357290|emb|CBM95512.1| RNA polymerase sigma factor [Vibrio gallaecicus]
          Length = 162

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 20/126 (15%), Positives = 43/126 (34%), Gaps = 2/126 (1%)

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+  +   +    S K  +    +  +     L   + D LV +L +   R+   E  ++
Sbjct: 38  QNRQLAINEYGNDSPKAVLATTMMQDVFKEFRLTPKQFDYLVNELPNSMDRVRTQERLIM 97

Query: 358 RLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416
           R    YG + +  F+    G E    W+       +  +   +      I +   ++  I
Sbjct: 98  RQTVEYGKMPKKSFIALFTGNESSEAWLDEVLA-SDKPYAEKIRRNEHDIRRSIQKLDMI 156

Query: 417 SVETGI 422
             E  +
Sbjct: 157 EREQSL 162


>gi|149908744|ref|ZP_01897405.1| RNA polymerase sigma factor for flagellar operon [Moritella sp.
           PE36]
 gi|149808286|gb|EDM68225.1| RNA polymerase sigma factor for flagellar operon [Moritella sp.
           PE36]
          Length = 238

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 82/199 (41%), Gaps = 16/199 (8%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            + DL+Q G +GL++A  ++     Y F +YA   ++  I   +  Q      P   R +
Sbjct: 48  SYEDLVQIGTMGLLEAIRRYGSEPDYGFESYAFQRIRGEILDELRRQDW---RPRQARQQ 104

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
            H +    R +S  + RE   +E+   L +  E ++ ++  +            E+   L
Sbjct: 105 GHSLNHARRTLSRTLGREANEKELMAFLEIDAEQLQDMIFDS----------VSEEMQSL 154

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            + ++    ++  +S IQ   +    R L       ++  ++   +    +  ++E+   
Sbjct: 155 DELLQAGTDITDENSDIQ---KFDIKRSLKQTLSLLDQRDQLLLTLYYQYELNMKEISLT 211

Query: 649 FCVTRERIRQIEAKAIRKL 667
             +T  R+ Q+   A++KL
Sbjct: 212 LKITESRVCQLHQLALKKL 230


>gi|257437879|ref|ZP_05613634.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
 gi|257199539|gb|EEU97823.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
          Length = 221

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 85/244 (34%), Gaps = 46/244 (18%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKK-YTNRGL-------QFLDLIQEGNIGLMK 483
            +    +   + A   +++ N   +  VA   + +  L          DL Q GN+GL K
Sbjct: 7   RLCALAQKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQAGLNLDTDDLKQAGNMGLWK 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  KFD   G KF TYA   ++ A+   + D                           ++
Sbjct: 67  AVPKFDAARGMKFLTYAAPAIRNAMMDMVRD--------------------AFTAFEQRM 106

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E                      I  + +SL+  +  E+     + I D  A+ P   
Sbjct: 107 VTE------------------DKDGICCQRVSLDDVLPGEEQLRRIEAIADPYAMQPQTI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  LR      L  LT RE+  L  R+G     +H L      F +T+ R ++ E +A
Sbjct: 149 MEEQELRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAQKTEEQA 208

Query: 664 IRKL 667
           +  L
Sbjct: 209 MDNL 212


>gi|313637835|gb|EFS03172.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL S4-171]
          Length = 56

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 38/55 (69%), Positives = 46/55 (83%)

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           VLR+RFG+      TLEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 2   VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 56


>gi|260779335|ref|ZP_05888227.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260605499|gb|EEX31794.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 242

 Score = 74.1 bits (180), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 90/233 (38%), Gaps = 21/233 (9%)

Query: 446 KEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++++ +  LV  +  +   +        D+ Q G IGL++A  ++       F  +A+ 
Sbjct: 26  NKLLKQHQVLVNRIVNQLRAHATPHCSIEDMQQIGLIGLLEAGRRYGNVEDPNFPAFAVC 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            ++ +I   +             R + H++    R +   + R+PT  EI K L    + 
Sbjct: 86  RIRGSILDELRRLDW---RSRKTRQQAHELNDVTRDLMRSLGRQPTDAEIIKALGTDEQD 142

Query: 563 V--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              R+   +  E  SL+  I +   +          + +  D       R +    L  L
Sbjct: 143 YLTRQNAALAGEMQSLDQLIENGIEAQ---------SDAVYDGMSHEQTRRSLEFALNKL 193

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             R++ +L + +      +  L E+     +T  RI Q+  +A+++L H   S
Sbjct: 194 PKRDQLLLTLFYQH----ELNLHEIALVLDLTPPRICQLHKQALKQLNHYLSS 242


>gi|330501119|ref|YP_004377988.1| RNA polymerase sigma 28 subunit FliA/WhiG [Pseudomonas mendocina
           NK-01]
 gi|328915405|gb|AEB56236.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas mendocina
           NK-01]
          Length = 244

 Score = 73.7 bits (179), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 95/231 (41%), Gaps = 22/231 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A  A+++ +   L LV  +  +     N+ L   D+ Q G +GL++   ++      +F 
Sbjct: 22  APGAEQKWLLQYLPLVKRIVSQLALQANQVLDREDMEQIGLMGLLECLRRY-GTPDEQFG 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            +A   ++ AI   +  Q      P  +R + HK+    R+++ ++ R P  EEI +   
Sbjct: 81  RFAALRIRGAILDELRRQDW---RPRQVRQQTHKIRDAIRQLARQLGRAPQEEEILQAAG 137

Query: 558 MPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           +  +  ++ L+        SL+  + +              A        +       T+
Sbjct: 138 INAKEYQEFLQADACEAIESLDELLQNGHEGF---------ACGGSAVEERVLKERLLTQ 188

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L+ L+ RE  VL + +      + +L+E+     ++  R+ Q+  +AI K
Sbjct: 189 ALSQLSERERLVLTLYYQH----ELSLKEIALVLELSDARVCQLSKQAIAK 235


>gi|161546627|ref|NP_860677.2| flagellar biosynthesis sigma factor [Helicobacter hepaticus ATCC
           51449]
          Length = 235

 Score = 73.7 bits (179), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 95/232 (40%), Gaps = 20/232 (8%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
             A+ E+    L  V ++A +   R    ++  DL+  G   L+K A ++D  L   F  
Sbjct: 15  KYAQDELALQYLPAVKAMAFRLKERLPSSIEMADLVSIGTEELIKLARRYDSSLNDSFWG 74

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A   V  A+   +        +    R  +  +     +  N+ + EP+ E +AK L  
Sbjct: 75  FAKTRVNGAMLDYLRSLD---VLSRANRKLVKSIDYEVSKYFNEHQEEPSDEYLAKVLKE 131

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            +  +++    +     +   +  ++  +         A + L+   +  L E    VL 
Sbjct: 132 DIAKIKEARMASD----IYALVPIDEQYNAI------CAENILEDVQKDELMEIIFNVLK 181

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            L  RE+ ++++ +      + +L+E+ +   +T  RI QI  + ++K++  
Sbjct: 182 KLGKREQMIIQLYYF----EELSLKEISEILDITESRISQITKEIVKKIRQA 229


>gi|301312525|ref|ZP_07218422.1| RNA polymerase sigma factor RpoD [Bacteroides sp. 20_3]
 gi|300829491|gb|EFK60164.1| RNA polymerase sigma factor RpoD [Bacteroides sp. 20_3]
          Length = 84

 Score = 73.7 bits (179), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 33/68 (48%)

Query: 31 WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSE 90
           K +I    ++GY+T  E+N  LP D V +EQ+ED + M++ MGI V +     +     
Sbjct: 16 IKLLISKGLEQGYLTYAEVNDHLPDDLVDAEQIEDIIGMINGMGIEVHEVAPDAETLLLA 75

Query: 91 DSLDLASS 98
          D       
Sbjct: 76 DGNTGNRE 83


>gi|315125999|ref|YP_004068002.1| LafS [Pseudoalteromonas sp. SM9913]
 gi|315014513|gb|ADT67851.1| LafS [Pseudoalteromonas sp. SM9913]
          Length = 239

 Score = 73.7 bits (179), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 37/226 (16%), Positives = 88/226 (38%), Gaps = 22/226 (9%)

Query: 447 EMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++     LV   A     +    +   D+ Q G I L+ +  ++   L  KF+ +A   
Sbjct: 24  QLLSQYAFLVNRAAAHMRTQVGVIVDNDDIYQIGIIALLSSIRRYGRDLDEKFAAFAFKR 83

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ A+             P  +R + H++   +R +  K+ R+ T  E+ + L +  + +
Sbjct: 84  IRGAMLDEFRRVDW---RPRQLRQQSHQLRDMSRSLQKKLGRDATDTEMCEALGINHKEL 140

Query: 564 RKVLK--ITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            ++      +   SLE  +       L          +   +  +     T    ++ L 
Sbjct: 141 IQLHYSEQAEAFDSLEALLEANPNLAL----------TCAHTHEKEETAATLKVAMSKLN 190

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE+ +L++ +      +  ++E+     +T  R+ Q+  +A+  L
Sbjct: 191 TREKLLLQLYYMH----EMNMKEIALTLDLTEARVCQLHKQALEAL 232


>gi|317181757|dbj|BAJ59541.1| flagellar biosynthesis sigma factor [Helicobacter pylori F57]
          Length = 250

 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 98/256 (38%), Gaps = 20/256 (7%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
            +T  S +  + I  ++   + +    +  +    L  V ++A +   R    + F DL+
Sbjct: 6   QKTQTSETSEKSIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLV 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G   L+K A +++  L   F  YA   V  A+   +        I    R  I  +  
Sbjct: 66  SIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDA 122

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +  N+  +EP+   +A+ L   +E +++    +     +   +  ++  +  +    
Sbjct: 123 EITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPIDEQFNAIE---- 174

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  
Sbjct: 175 --QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITES 228

Query: 655 RIRQIEAKAIRKLKHP 670
           RI QI  + I+K++  
Sbjct: 229 RISQIIKEVIKKVRKS 244


>gi|239934420|emb|CAR92340.1| DNA-directed RNA polymerase subunit D [uncultured Pseudomonas sp.]
          Length = 192

 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/222 (13%), Positives = 72/222 (32%), Gaps = 49/222 (22%)

Query: 163 TFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
           T  +++   + +      L E++            G+    +G    +       K+ D 
Sbjct: 1   TVDSILAEYNRVTTDGGRLVEVL-----------SGYIDPDDGIVPAEAAAPVPVKDGDA 49

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
            +ET+ D E++    ++     D                                 + + 
Sbjct: 50  AEETDDDAEASDDEEEEGDGGPDPE-------------------------------EALR 78

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
               I +      +L+      +K  ++S +     +++ +L   + L   + D LV ++
Sbjct: 79  RFTAIGD------ALELAKKALKKHGRNSKQGTAALKEMAELFMPIKLVPKQYDALVVRV 132

Query: 343 YDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHW 383
               +R+   E  +++L      + R  FL    G E+D  W
Sbjct: 133 RSSLERLRAQERAIMQLCVRDARMPRADFLRLFPGNEIDVEW 174


>gi|119632740|gb|ABL84377.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus suis]
          Length = 75

 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/75 (61%), Positives = 62/75 (82%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGN+GLMKA +KFD+  G+KFSTYA WW++QAITR+IADQ+ TIRIPVHM + I+K
Sbjct: 1   DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 60

Query: 532 VVRTARRMSNKIKRE 546
           +VR  R +  ++ ++
Sbjct: 61  LVREQRNLLQELGQD 75


>gi|255697043|emb|CBA11631.1| RNA polymerase sigma factor [Pseudomonas savastanoi]
          Length = 169

 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 27/159 (16%), Positives = 55/159 (34%), Gaps = 4/159 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 13  DPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 72

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 73  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 129

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
            E  +++L      + R  FL +  G E+D  W      
Sbjct: 130 QERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 168


>gi|239934442|emb|CAR92475.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 203

 Score = 73.7 bits (179), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 21/135 (15%), Positives = 54/135 (40%), Gaps = 3/135 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A+ +  ++   +       +  ++S   +    +L  L   L L   + D LV +  
Sbjct: 70  EEAAKRFTAIQKQNEKTKRAIARYGRNSESTEQHLAELGDLFKYLKLIPKQYDPLVARAR 129

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
              + +  +E  ++ L      + R  F+E   G E +  W +      +  +   +   
Sbjct: 130 AALQEVRRHERAIMMLCIRQAKMPRKEFVESFPGNETNDKW-ALNLSRRKQPYAPAIKNL 188

Query: 403 VDSILKIRNEIKSIS 417
           +D I++++ ++ S+ 
Sbjct: 189 LDDIIRVQEKLASVE 203


>gi|321116226|emb|CBN73494.1| DNA-directed RNA polymerase subunit D [Pseudomonas anguilliseptica]
          Length = 183

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/163 (14%), Positives = 53/163 (32%), Gaps = 7/163 (4%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                     +    P ++ +  E   D+ E                + +     I +  
Sbjct: 27  DPDDGIVPAEAAAPVPVKDGDAAEETDDDAEASDDEEEEGDGGPDPEEALRRFTAIGD-- 84

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
               +L+      +K  ++S +     +++ +L   + L   + D LV ++    +R+  
Sbjct: 85  ----ALELAKKALKKHGRNSKQGTAALKEMAELFMPIKLVPKQYDALVVRVRSSLERLRA 140

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            E  +++L      + R  FL    G E+D  W +        
Sbjct: 141 QERAIMQLCVRDARMPRADFLRLFPGNEIDVEWSAGLAKGKAK 183


>gi|257063114|ref|YP_003142786.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256790767|gb|ACV21437.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 269

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 36/89 (40%), Positives = 57/89 (64%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
              + + + +   AK+++V A+LRLV  +AK+Y  RG+ F+DL+ EGN+GL++AAE+FD 
Sbjct: 96  ARRLARIQSDGDAAKEQLVGASLRLVARIAKRYIFRGVSFMDLVHEGNMGLIRAAERFDP 155

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTI 519
             G  FS YA WW++ AI+R+        
Sbjct: 156 ASGAAFSVYASWWIRAAISRATGRGRWGC 184



 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 8/66 (12%)

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ--------FCVTRERIRQIEAKA 663
                L+S++ RE   +R RFG+   +  T  E   +          +TRER RQIEAK 
Sbjct: 197 EIETALSSMSERERDYIRFRFGLENGSSRTFGESAPEPGVVCTLPSGITRERARQIEAKF 256

Query: 664 IRKLKH 669
           + KL++
Sbjct: 257 LAKLRN 262



 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 14/70 (20%), Positives = 30/70 (42%)

Query: 84  EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
            +E  +E++    ++ + ++     +  + +   DD  R YL E+    LL  + E  + 
Sbjct: 9   ANEFNTENTRPEHTAEAPTAGAGSLQDMANEYWVDDDTRTYLLEIDRFPLLDSQEEADLV 68

Query: 144 KRIEAGRAMM 153
            +I AG    
Sbjct: 69  AKIRAGAEAA 78


>gi|321116360|emb|CBN73561.1| DNA-directed RNA polymerase subunit D [Pseudomonas borbori]
 gi|321116362|emb|CBN73562.1| DNA-directed RNA polymerase subunit D [Pseudomonas borbori]
          Length = 201

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 44/132 (33%), Gaps = 8/132 (6%)

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
            +     IAE       L        K  + S +     + L +L   + L   + + LV
Sbjct: 77  ALRRFTAIAEQ------LAIAKTTLDKHGRGSKQGIAELKALAELFMPIKLVPKQYEALV 130

Query: 340 EQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
             +    +R+   E  +++L      + R  FL    G E+D  W        + ++   
Sbjct: 131 VHVRSALERLRAQERAIMQLCVRDARMPRADFLRLFPGNEVDATWSEQLAK-GKAKYAEA 189

Query: 399 VACEVDSILKIR 410
           +      I + +
Sbjct: 190 IGGLQVDIQRCQ 201


>gi|223041126|ref|ZP_03611381.1| flagellar biosynthesis sigma factor FliA [Campylobacter rectus
           RM3267]
 gi|222877620|gb|EEF12746.1| flagellar biosynthesis sigma factor FliA [Campylobacter rectus
           RM3267]
          Length = 231

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/230 (19%), Positives = 92/230 (40%), Gaps = 20/230 (8%)

Query: 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           +V A +  + ++A +   R    +   DLI  G   ++K + K+D      F  YA   V
Sbjct: 19  IVLAYMPALRAMAFRLKERLPSHIDVSDLIGAGLEEMVKLSRKYDKEQNDSFWGYAQKRV 78

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
             A+   +        +    R  +  +        NK + EP    IA KL + VE V 
Sbjct: 79  YGAMLDFLR---RLDVVSRSDRTLVKSIETLVDEYFNKFEHEPDDAYIAGKLGIDVEKVS 135

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           +   ++     L           + D +E  +  + L+   + +L E   ++L     R+
Sbjct: 136 EARNVSAVVAVLN----------IDDQMELMSEENTLEQVEKEDLIEKIAQILNEFEERD 185

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + ++++ +      + +L+E+ +   +T  RI QI  + + K++     K
Sbjct: 186 QLIVQLYY----YEELSLKEISEILGITESRISQIHKRLMDKIRKKLEGK 231


>gi|283779412|ref|YP_003370167.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283437865|gb|ADB16307.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 374

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 94/258 (36%), Gaps = 35/258 (13%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN-LRLVISVAKKYTNRGLQFL 471
           +  +   + +S +E R +   +   +  A + ++++   +  R +I   ++   + L   
Sbjct: 136 LARMCETSLLSPTEERDLFRRMNFAKYTADVLRRKINTDHPDRELIVSIERLIAQALADR 195

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           + I   N+ L+ +  K        F       +                           
Sbjct: 196 NRIVRANLRLVVSIAKKFSDARNSFDDLLSEGI-------------------------TS 230

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           ++R   +         +            + VR+ L  + + +  +        + L + 
Sbjct: 231 LLRAVEKFDYDRGFRFSTY--------ATQAVRRTLCRSLQQLMRDRTRFMNAETSLFED 282

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFC 650
             ++     +  A    LR    ++L+ L PRE  ++R RFG+       TL+ +  +F 
Sbjct: 283 TPEEERPGTMSEARFDELRRALAKMLSKLDPRERSIIRCRFGLDRKEQVQTLQSLAGEFG 342

Query: 651 VTRERIRQIEAKAIRKLK 668
           V +ER+RQ+E +AI KL+
Sbjct: 343 VCKERVRQLEMRAISKLR 360


>gi|87124483|ref|ZP_01080332.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168055|gb|EAQ69313.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 213

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 49/213 (23%), Positives = 83/213 (38%), Gaps = 28/213 (13%)

Query: 445 KKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +   VE +LRLV  +A+ Y    G    DL+Q G +GL++AA  +D   G  F  +A   
Sbjct: 8   RNRRVEQHLRLVQPIARHYAQRSGEDRDDLLQVGCLGLIRAAGLYDGAKGVPFEAFARPH 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+ AI   + D    +++P  ++++  ++ R           E   E+    LAM +   
Sbjct: 68  VRGAILHYLRDSRGLVKLPRRLQERAQRLNR----------GEDGTEQRGDALAMALYRN 117

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +          SL+    D +            A        Q   RE   R L  L   
Sbjct: 118 QGRWW------SLDDQGRDVEAMT-------PPADGGWSDLSQRETREQLARQLKRLPVV 164

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           E+R +R     G     +L + G++  V+   +
Sbjct: 165 EQRSVRSVVLEG----LSLRQCGREQGVSAMTV 193


>gi|284050754|ref|ZP_06380964.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 159

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 48/93 (51%), Positives = 65/93 (69%), Gaps = 7/93 (7%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           +  S + G+S SE   I++  R+       AK++M+EANLRLV+S+AKKY  R ++FLDL
Sbjct: 74  EEWSAKAGLSESEMTDIINRGRR-------AKQKMIEANLRLVVSIAKKYQKRNMEFLDL 126

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           IQEG +GL +  EKFD   GYKFSTYA WW++Q
Sbjct: 127 IQEGTLGLERGVEKFDPMRGYKFSTYAYWWIRQ 159



 Score = 42.9 bits (99), Expect = 0.16,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 98  SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           + + ++      ++    ++ D VR YL E+G + LL+RE EI   K+++ 
Sbjct: 2   ATAKTTQTELTSRNPRSGASMDAVRTYLHEIGRVPLLTREEEIIYGKKVQQ 52


>gi|182412871|ref|YP_001817937.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Opitutus terrae
           PB90-1]
 gi|177840085|gb|ACB74337.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Opitutus terrae PB90-1]
          Length = 240

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 47/205 (22%), Positives = 82/205 (40%), Gaps = 14/205 (6%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            +   DL   G + L++A  +FD     +   Y    V+ A+   +        +  H R
Sbjct: 33  HVSREDLASAGKLALVEAMLRFDGP-AEQLRGYCFARVRGALLDELR---RLDPLSRHTR 88

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDED 584
            ++  V R    +  ++ R PT +EI        E +   + L    +  S++      D
Sbjct: 89  SQVTFVRRATAALEKELHRAPTRDEIVTATGYSHETLTQLERLAEAAQACSIDETDAYGD 148

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
             H    IED+ A  P  +A   +   +    LA L      VLR  +      D TL+ 
Sbjct: 149 DLH---VIEDE-AACPARTAESLDAHSSVHVALARLPANHAHVLRRYYL----DDATLDV 200

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           +  +  V++ER+RQ+   A +KL+ 
Sbjct: 201 IAGELGVSKERVRQLREAAEKKLRE 225


>gi|153955577|ref|YP_001396342.1| RNA polymerase sigma factor-related protein [Clostridium kluyveri
           DSM 555]
 gi|146348435|gb|EDK34971.1| RNA polymerase sigma factor-related protein [Clostridium kluyveri
           DSM 555]
          Length = 235

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 91/249 (36%), Gaps = 61/249 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKF 488
            +V+  +     A  +++E N  +V   A ++       +   DL QEG +GLM AA+K+
Sbjct: 5   ELVQLYQAGNKGALDKLIELNKGIVYKFANRFYTEKTNSIDKEDLKQEGFMGLMVAADKY 64

Query: 489 DW--CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +      KFSTYA++W+                                 +M+  IK +
Sbjct: 65  KFNIEKPCKFSTYAVYWI-------------------------------YHKMNRFIKSK 93

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSA 604
            T EE                       SL  P   +      D IE  D    +  D  
Sbjct: 94  NTNEE----------------------TSLNIPNSSDGDIEFMDCIEGVDYGFENVEDKI 131

Query: 605 IQANLRETTTRVLASLTP-REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               L      V+A     +E  +L+ R+G       T  ++G+ + VTR +I  IE  A
Sbjct: 132 YNEQLHRELEEVMARYNTLKEREILKFRYGWDNYKCMTCGQIGEIYNVTRSKINNIEHTA 191

Query: 664 IRKLKHPSR 672
           + K++  S 
Sbjct: 192 LGKIRRSSW 200


>gi|291277483|ref|YP_003517255.1| putative flagellar operon RNA polymerase sigma factor [Helicobacter
           mustelae 12198]
 gi|290964677|emb|CBG40532.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter mustelae 12198]
          Length = 231

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 93/241 (38%), Gaps = 20/241 (8%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKF 488
             +         ++ E+    L  V ++A +   R    +   DLI  G   L+K A K+
Sbjct: 1   MKIDAYNQNLKYSQDELAIQYLPAVRAMAYRMKERLPSSVDVNDLISIGTEELIKLARKY 60

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D  L   F  YA   V  A+   +       R     R  I  + +   R  N+ + EP+
Sbjct: 61  DSKLNDSFWGYAKTRVNGALLDYLRSLDIISRAN---RKLIKSIDQEITRYYNQHQEEPS 117

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
              +A+ L    E +R+    +   + L       +     D +E            +  
Sbjct: 118 DAYLAQVLGEDEEKIREARIASDIYL-LVPIDEQYNAIESDDIVE---------KLEKEE 167

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +   ++L+ L+ RE+ +++M F      +  L E+ +   +T  RI QI  + I+K++
Sbjct: 168 LVQKIKKILSGLSQREQMIMQMYFF----EEMNLNEIKEVLDITESRISQITKEVIKKIR 223

Query: 669 H 669
            
Sbjct: 224 K 224


>gi|295104067|emb|CBL01611.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 220

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 92/245 (37%), Gaps = 47/245 (19%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVA-KKYTNRGLQ-------FLDLIQEGNIGLMK 483
            + R  +   + A+  ++E NL  +  +A ++Y N GL          DL+QEG+IGL+ 
Sbjct: 8   QLCRLAQKGDTAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIGLLN 67

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A   FD   G KF TYA   ++ A+T                      +         ++
Sbjct: 68  AIPLFDAGRGMKFLTYAAPALRNAMTDC--------------------IRAALGLFEQRM 107

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
                              V K      + + L+  + +++     + I D +  +P   
Sbjct: 108 -------------------VDKKDGPGFQRVYLDDVLSEDERMLRIEAIADPHTQTPEQI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            IQ          L +LT RE+  L  R+G     +H L      F ++    +++E +A
Sbjct: 149 YIQKEQLIELYAALDNLTAREQTYLLYRYGFTDGIEHPLIGAALHFHLSESWTKKVEGEA 208

Query: 664 IRKLK 668
           +  L+
Sbjct: 209 MDSLR 213


>gi|188527224|ref|YP_001909911.1| flagellar biosynthesis sigma factor [Helicobacter pylori Shi470]
 gi|188143464|gb|ACD47881.1| flagellar biosynthesis sigma factor [Helicobacter pylori Shi470]
 gi|317179191|dbj|BAJ56979.1| flagellar biosynthesis sigma factor [Helicobacter pylori F30]
          Length = 250

 Score = 73.3 bits (178), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 99/256 (38%), Gaps = 20/256 (7%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLI 474
            +T  S +  ++I  ++   + +    +  +    L  V ++A +   R    + F DL+
Sbjct: 6   QKTQTSETSEKNIEKVLNAYDKQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLV 65

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
             G   L+K A +++  L   F  YA   V  A+   +        I    R  I  +  
Sbjct: 66  SIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDI 122

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +  N+  +EP+   +A+ L   +E +++    +     +   +  ++  +  +    
Sbjct: 123 EITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYALVPIDEQFNAIE---- 174

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
                         L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  
Sbjct: 175 --QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITES 228

Query: 655 RIRQIEAKAIRKLKHP 670
           RI QI  + I+K++  
Sbjct: 229 RISQIIKEVIKKVRKS 244


>gi|221271606|dbj|BAH15091.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271608|dbj|BAH15092.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 72.9 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 2/97 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + +         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRHNKAAIAELLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           + R  FL +  G E+D  W   A    + ++   +A 
Sbjct: 148 MPRADFLRQFPGNEVDESWSD-ALAKGKSKYAEAIAR 183


>gi|210134610|ref|YP_002301049.1| flagellar biosynthesis sigma factor [Helicobacter pylori P12]
 gi|210132578|gb|ACJ07569.1| alternative transcription initiation factor sigma-F [Helicobacter
           pylori P12]
          Length = 255

 Score = 72.9 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 47/268 (17%), Positives = 102/268 (38%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S      +++   K +        ++    L  V ++A +   
Sbjct: 2   ILMMENRMPKGIQKTETSEKNIEKVLNAYDKQQHHHQD---DLAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 116 RSNRKLIKSIDAEITKHLNEHGKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   +VL  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITKKIEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRKS 249


>gi|149175161|ref|ZP_01853784.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148846139|gb|EDL60479.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 349

 Score = 72.9 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 57/249 (22%), Positives = 108/249 (43%), Gaps = 60/249 (24%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           ++  + +   +A   +  +++ANLRLV+S+AK  T+R   F D++ +G++ L++A E FD
Sbjct: 152 LLDRIEQKLKDARRLRNYIIQANLRLVVSIAKNLTDRANLFEDIVSDGHLPLIRAVEIFD 211

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
              G +FSTY  W V+  + R+                K  K  +             T 
Sbjct: 212 VDRGNRFSTYGTWAVRNFLFRTT--------------KKGRKYRK-------------TF 244

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
              A+ LA+ +  +R  ++      S ET   + D                         
Sbjct: 245 LNGAETLALGLSDIRSTMR------SHETYHQNIDD------------------------ 274

Query: 610 RETTTRVLASLTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                +VL +L  RE+ +L+ RFG+   +T     E+ +   V+ ER+RQ+  +++++++
Sbjct: 275 --VLQKVLHTLDEREQVILKRRFGLAQSDTPEKFREIAEDLGVSTERVRQLTIRSLQRMR 332

Query: 669 HPSRSKKLR 677
                +KL 
Sbjct: 333 EAIEEQKLE 341


>gi|251798274|ref|YP_003013005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
 gi|247545900|gb|ACT02919.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
          Length = 184

 Score = 72.9 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 54/225 (24%), Positives = 84/225 (37%), Gaps = 61/225 (27%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +   KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +    
Sbjct: 14  VHNVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEILMHLRS-- 71

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                                                             LK T++ +SL
Sbjct: 72  --------------------------------------------------LKKTRKDVSL 81

Query: 577 ETPIGDE---DTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
             PIG +   +   L D +  E  + V  +   I+   +    R L  L  RE+ V+R R
Sbjct: 82  HDPIGTDKEGNEITLIDILGTEADDVVDRVQLKIE---KSKIYRNLDILDEREQEVIRGR 138

Query: 632 FGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           FG+     + T  E+ K+  ++R  + +IE +A+ KL H     K
Sbjct: 139 FGLDHGGDERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAK 183


>gi|133481|sp|P26768|RPSX_BACTK RecName: Full=Putative RNA polymerase sigma-G factor; AltName:
           Full=ORF3
 gi|580955|emb|CAA40027.1| unnamed protein product [Bacillus thuringiensis serovar kurstaki]
          Length = 125

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 42/123 (34%), Positives = 70/123 (56%), Gaps = 2/123 (1%)

Query: 410 RNEIKSISVET-GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           RN+++   V+T  + + +   +  + R+ +     A++++V  NLRLV+SV +++ NRG 
Sbjct: 3   RNKVEICGVDTAKLPVLKNEEMRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGE 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL Q G IGLMK+ + FD     KFSTYA+  +   I R + D +  IR+   +RD 
Sbjct: 63  YVDDLFQVGCIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDI 121

Query: 529 IHK 531
            +K
Sbjct: 122 AYK 124


>gi|78776905|ref|YP_393220.1| flagellar biosynthesis sigma factor [Sulfurimonas denitrificans DSM
           1251]
 gi|78497445|gb|ABB43985.1| sigma 28 (Flagella/Sporulation) [Sulfurimonas denitrificans DSM
           1251]
          Length = 227

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 91/241 (37%), Gaps = 20/241 (8%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
           M+     +    + E+    L  V ++A +   R    + ++DL   G   L+K A ++D
Sbjct: 1   MISAYTQDLKHKEDELAIQYLPAVKAMAFRLKERLPSSVDYMDLSAIGTEELIKLARRYD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             L   F  YA   V  A+   +        +    R  I  +             EP+ 
Sbjct: 61  ESLNDSFWGYAKKRVYGAMLDYLRSLD---IVSRASRKLIKAIDYAIEEHRAIHDEEPSD 117

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EE+A  +   +E + +    +    S+   +   D   +GD        + L +  +  L
Sbjct: 118 EELALIIGEDIEKIHEARIAS----SIYAVMPLHDQLQVGD------EGASLANIEKEEL 167

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +    VL   + RE+ ++++ +      + +L+E+     +T  RI QI    I K+K 
Sbjct: 168 IDVIKTVLGLYSEREQMIIQLYYF----EELSLKEISDVLGITESRISQIHKSVIHKIKE 223

Query: 670 P 670
            
Sbjct: 224 S 224


>gi|68171972|ref|ZP_00545278.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998602|gb|EAM85349.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
          Length = 205

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/191 (23%), Positives = 80/191 (41%), Gaps = 13/191 (6%)

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRI-PVHMRDKIHKVVRTARRMSNKIKREPT 548
             LG++ STYA+WW+K  I   I      I+I     + K+   +R  ++   K     T
Sbjct: 1   PTLGFRLSTYAIWWIKAFIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLFKYNHNIT 60

Query: 549 PEEI---AKKLAMPVEGV-RKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPL 601
            E+I   A K +   + V +          SL   +   D      L + I+        
Sbjct: 61  KEDIKLIANKCSTSEQEVEQMNRYFLYRDRSLNELVFSNDNQNGVELQEIIKCDTPNQED 120

Query: 602 DSAIQANL---RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +   L   +   ++ L++L  R   +   R  I      TL+++ +++ +++ER+RQ
Sbjct: 121 TYLLNEELNIKKALISQALSTLNERYRDIFIRRRLIE--EPDTLDKLSQEYNISKERVRQ 178

Query: 659 IEAKAIRKLKH 669
           IE  A  K+K+
Sbjct: 179 IEMHAFTKVKN 189


>gi|221271616|dbj|BAH15096.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271624|dbj|BAH15100.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271628|dbj|BAH15102.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271652|dbj|BAH15114.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           + R  FL +  G E+D  W   A    + ++   +A 
Sbjct: 148 MPRADFLRQFPGHEVDESWTD-ALAKGKSKYAEAIAR 183


>gi|219855964|ref|YP_002473086.1| hypothetical protein CKR_2621 [Clostridium kluyveri NBRC 12016]
 gi|219569688|dbj|BAH07672.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 238

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 91/249 (36%), Gaps = 61/249 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKF 488
            +V+  +     A  +++E N  +V   A ++       +   DL QEG +GLM AA+K+
Sbjct: 8   ELVQLYQAGNKGALDKLIELNKGIVYKFANRFYTEKTNSIDKEDLKQEGFMGLMVAADKY 67

Query: 489 DW--CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +      KFSTYA++W+                                 +M+  IK +
Sbjct: 68  KFNIEKPCKFSTYAVYWI-------------------------------YHKMNRFIKSK 96

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSA 604
            T EE                       SL  P   +      D IE  D    +  D  
Sbjct: 97  NTNEE----------------------TSLNIPNSSDGDIEFMDCIEGVDYGFENVEDKI 134

Query: 605 IQANLRETTTRVLASLTP-REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               L      V+A     +E  +L+ R+G       T  ++G+ + VTR +I  IE  A
Sbjct: 135 YNEQLHRELEEVMARYNTLKEREILKFRYGWDNYKCMTCGQIGEIYNVTRSKINNIEHTA 194

Query: 664 IRKLKHPSR 672
           + K++  S 
Sbjct: 195 LGKIRRSSW 203


>gi|228912145|ref|ZP_04075860.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228847482|gb|EEM92421.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 232

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 87/229 (37%), Gaps = 28/229 (12%)

Query: 447 EMVEANLRLVISVAK-KYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++   RLV      +Y  +        GL   DL Q G IGL+KA + FD   G KFS
Sbjct: 5   EFMKKYGRLVHHCVWKRYAKKMKSIEHDTGLDIEDLTQFGMIGLIKARDNFDLEYGCKFS 64

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  +   I R+I D                 V     ++  +   +  PEEIA  L 
Sbjct: 65  TYAVPKIIGEIGRAIRDH--------QKVKVQRSVYSVKGKILRQNLGDEIPEEIASILN 116

Query: 558 MPVEGVRKVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             V  V   L       SL   +      +   L   +EDK A +  D +I    R    
Sbjct: 117 EDVSVVSNALHYQPGTQSLNKVVHQSNGNEELTLESMLEDKKAENVEDVSIN---RMVIQ 173

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              + L+ +E  VL M        + T + +  +   ++ +I +I  K 
Sbjct: 174 SFKSQLSHKEHIVLDMSL-----QNRTQQNIANEVGCSQVQISRILTKI 217


>gi|239934448|emb|CAR92478.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 202

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 72/250 (28%), Gaps = 49/250 (19%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  LQ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLQGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKI 409
               D I + 
Sbjct: 193 KQFTDDIRRA 202


>gi|57168743|ref|ZP_00367874.1| probable RNA polymerase sigma factor for flagellar operon Cj0061c
           [Campylobacter coli RM2228]
 gi|305432515|ref|ZP_07401677.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter coli
           JV20]
 gi|57019790|gb|EAL56473.1| probable RNA polymerase sigma factor for flagellar operon Cj0061c
           [Campylobacter coli RM2228]
 gi|304444554|gb|EFM37205.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter coli
           JV20]
          Length = 230

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 95/228 (41%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + ++V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 17  QDQLVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDSFWGFAR 76

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  A+   +        +  + R  I  +         + + EP  E +AKKL + VE
Sbjct: 77  KRVNGAMLDFLRSLD---VMSRNNRKIIKDIDILIDEYFREHEEEPDDEYLAKKLDLDVE 133

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +++V        +L           + D +E  N    L+   +  L E    VL  L 
Sbjct: 134 KIKEVRTAHAISYTL----------PIDDQLELYNEDDTLEKLEKEQLLEKIHEVLEDLK 183

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   ++  RI QI  K ++KL+ 
Sbjct: 184 ERDQLIIQLYY----YEELSLKEISEILEISESRISQIHKKLLKKLRE 227


>gi|239934436|emb|CAR92472.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 196

 Score = 72.9 bits (177), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 72/240 (30%), Gaps = 45/240 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AELETETEEETEEGEANSEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D +++ + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSKTFAQVQK------GMAEKGADDSKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            +  
Sbjct: 137 QIRQSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSDETNLSWLDKHIRAKRKHSAHLA 196


>gi|225026956|ref|ZP_03716148.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
 gi|224955721|gb|EEG36930.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
          Length = 275

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/163 (28%), Positives = 89/163 (54%), Gaps = 3/163 (1%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K +     +S  + R I    RK       A+  ++EANL   + +AK+Y  RGL   
Sbjct: 109 YLKEMEKANSLSGEQERVIA---RKLVSGDDTARNLLIEANLSRAVEIAKEYEGRGLLLS 165

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           DLIQEGNIGLM A  +F+  +   F  ++   +++ +  ++ + + + R  V M +++++
Sbjct: 166 DLIQEGNIGLMVAVNEFEPDIDKDFHAFSEKMIRKHLEETLEEYNSSTRSAVKMANRVNE 225

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           +   A   + + +RE  P EIA+++ +  E VR+++K++ + I
Sbjct: 226 MNDIATAFAKEYEREAKPSEIAERMGITEEEVRELMKVSLDAI 268



 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 100/261 (38%), Gaps = 21/261 (8%)

Query: 29  DSWKKMIKLARQRG-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87
            + +++ +L    G  +++EE+N++    ++  +Q++       +  I + +     +EE
Sbjct: 29  QAIQELERLGETNGNQLSMEEINSYFSDMKLEEKQLDFICNYFESHHIYITNRVQRFEEE 88

Query: 88  GSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
             ++ +       ++ +                V  YL+EM     LS E E  IA+++ 
Sbjct: 89  IGDEEIPNKEDPMDAEI----------------VAFYLKEMEKANSLSGEQERVIARKLV 132

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
           +G       L E+ L+    +    E      LL ++I         +   F    +   
Sbjct: 133 SGDDTARNLLIEANLSRA--VEIAKEYEGRGLLLSDLIQEGNIGLMVAVNEFEPDIDKDF 190

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
           +   E   ++   + ++E      SA K++  +R    +    A   E   +    + A 
Sbjct: 191 HAFSEKMIRKHLEETLEEYNSSTRSAVKMA--NRVNEMNDIATAFAKEYEREAKPSEIAE 248

Query: 268 TLSAMEDQLRPKVMCALDEIA 288
            +   E+++R  +  +LD IA
Sbjct: 249 RMGITEEEVRELMKVSLDAIA 269


>gi|221271640|dbj|BAH15108.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271642|dbj|BAH15109.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271644|dbj|BAH15110.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271648|dbj|BAH15112.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/218 (12%), Positives = 62/218 (28%), Gaps = 37/218 (16%)

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           +  E     +   G+    +G +    E       +    E   D +       ++ ++ 
Sbjct: 2   VTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPIDAKAAKAEESDDDDDTEASDDEEEAES 61

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
              P  A      + +  + +   L                                   
Sbjct: 62  GPDPVIAAQRFGAVADQMEITRKAL----------------------------------- 86

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-Y 363
           +K  + +         L  L   + L   + + LVE++     R+   E  +++L     
Sbjct: 87  KKHGRHNKAAIAELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDA 146

Query: 364 GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            + R  FL +  G E+D  W   A    + ++   +A 
Sbjct: 147 RMPRADFLRQFPGNEVDESWSD-ALAKGKSKYAEAIAR 183


>gi|15643664|ref|NP_228710.1| RNA polymerase sigma-28 factor, putative [Thermotoga maritima MSB8]
 gi|4981438|gb|AAD35983.1|AE001755_6 RNA polymerase sigma-28 factor, putative [Thermotoga maritima MSB8]
          Length = 220

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 49/202 (24%), Positives = 90/202 (44%), Gaps = 20/202 (9%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DLIQEG +  + + E++D      F+T+ M  VK A+   +         P ++R 
Sbjct: 30  VEVDDLIQEGIVAALSSLERYDPSKA-SFTTFIMKRVKGAMYDYLRKIDWM---PRNLRK 85

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            +  + R       + +  P+ EEIA+K  + ++ V +          L      ED   
Sbjct: 86  NVKMIERVIY----ESEEFPSDEEIARKTGLELKEVVRARNEMMRKQLL-MIDAMEDEIV 140

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L     D+NA        +  L E   + +  L+ +E+ VL +RF  G     +L+E+ +
Sbjct: 141 LKTEGPDENAY-------RELLVEEMKKAIEKLSDKEKLVLSLRFEKG----LSLKEIAR 189

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              V+  R+ QI +K++ K+K 
Sbjct: 190 VLGVSESRVSQIISKSLLKIKK 211


>gi|221271654|dbj|BAH15115.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  +++ +       L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRNNKQAIAELLALAELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           + R  FL +  G E+D  W   A    + ++   +A 
Sbjct: 148 MPRADFLRQFPGHEVDESWSD-ALAKGKSKYAEAIAR 183


>gi|225375310|ref|ZP_03752531.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
 gi|225212799|gb|EEG95153.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
          Length = 196

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 91/242 (37%), Gaps = 55/242 (22%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             ++K +     A+ E++E N+RLV  VAKKY N   +  DLI  G IGL+KA E +   
Sbjct: 6   ECLKKMKNGDLEARNELIERNMRLVAHVAKKYQNPEDEMEDLISIGTIGLIKAVETYKED 65

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G + +TYA   +   +                         R  ++ S +         
Sbjct: 66  YGSRLATYAARCIDNELLMHF---------------------RAKKKTSKE--------- 95

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR- 610
                                 +SL  PIG +   +    ++   +       +    R 
Sbjct: 96  ----------------------VSLYEPIGTDKEGNQIQLLDVVVSEDEDVVELLEQDRK 133

Query: 611 -ETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 ++  +L+ RE  ++  R+G+      T  E+ ++  ++R  + +IE +AI KL+
Sbjct: 134 VRRLNEIIPQTLSGRELFIIINRYGLYGKKTMTQREIARKLGISRSYVSRIEKRAIEKLR 193

Query: 669 HP 670
             
Sbjct: 194 QA 195


>gi|307109683|gb|EFN57920.1| hypothetical protein CHLNCDRAFT_141990 [Chlorella variabilis]
          Length = 357

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 90/231 (38%), Gaps = 32/231 (13%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S +E R +             A   +V+AN  LV  +A+++  +GL   DL+ EG + L 
Sbjct: 124 SAAEQRELARAA---GAGDERAVAALVDANRALVHFLARRFLGKGLAREDLVSEGMLALE 180

Query: 483 KAAEKF--DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM- 539
           +AA ++         F T+A   +   ++R++  QS  +R+PVH    + +V +    + 
Sbjct: 181 RAARRYRPQPGRDASFGTFAAATILNGMSRALHTQSRDVRLPVHHFRDMARVRQATLELA 240

Query: 540 -SNKIKREPTPEEIAKK----LAMPVEGVRKVLKITKEP--------ISLETPIGDEDTS 586
                + + T   +          P+  V                  +SL+         
Sbjct: 241 TEQLRQPDYTLHLLRAMGSQVGQSPLMQVLDQEMAAPMDQDPTQQGGVSLDG-------- 292

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
            L   +ED+ A       I+A LR      LA L P++  V+ +R G+   
Sbjct: 293 -LEVLLEDEVAAEERSQLIEAELR----SCLARLEPQQVSVVELRHGLDGE 338


>gi|217031645|ref|ZP_03437150.1| hypothetical protein HPB128_21g203 [Helicobacter pylori B128]
 gi|216946845|gb|EEC25441.1| hypothetical protein HPB128_21g203 [Helicobacter pylori B128]
          Length = 247

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 95/247 (38%), Gaps = 20/247 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            ++I  ++   + +    +  +    L  V ++A +   R    + F DL+  G   L+K
Sbjct: 12  EKNIEKVLNAYDEQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIK 71

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            A +++  L   F  YA   V  A+   +        I    R  I  +     +  N+ 
Sbjct: 72  LARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDIEITKHLNEH 128

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EP+   +A+ L   +E +++    +     +   +  ++  +  +             
Sbjct: 129 GKEPSDAYLAEALGENIEKIKEAKTASD----IYALVPIDEQFNAIE------QDEITKK 178

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  RI QI  + 
Sbjct: 179 IEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITESRISQIIKEV 234

Query: 664 IRKLKHP 670
           I+K++  
Sbjct: 235 IKKVRKS 241


>gi|332757481|gb|EGJ87816.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-671]
 gi|333017677|gb|EGK36989.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-304]
          Length = 161

 Score = 72.6 bits (176), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/153 (20%), Positives = 69/153 (45%), Gaps = 5/153 (3%)

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
               +P  +R    +V +   ++  ++ R  T  E+A++L + +   R++L  T      
Sbjct: 7   SRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLF 66

Query: 577 ETPIGDEDTSHLGDFIEDKNA-VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
                 E+     + + D +   +PL   + +NLR+     + +L  RE+ VL + +   
Sbjct: 67  SYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYY--- 123

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              +  L+E+G    V   R+ Q+ ++ I++L+
Sbjct: 124 -QEELNLKEIGAVLEVGESRVSQLHSQDIKRLR 155


>gi|312128148|ref|YP_003993022.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778167|gb|ADQ07653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 219

 Score = 72.2 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 93/255 (36%), Gaps = 59/255 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +         A+  ++E NLRLV  +AKKYT        D+I 
Sbjct: 9   SFPQPMSSEEEEMYLNKMW---EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIIS 65

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA E +      K STYA   ++  I   +      +                
Sbjct: 66  VGTIGLIKAIETYSTAKCTKLSTYAAKCIENEILMYLRQNKKFLS--------------- 110

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI 592
                                                 +SLE PIG +       L D +
Sbjct: 111 -------------------------------------QLSLENPIGSDKDGNEITLMDVL 133

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++          ++  ++    ++   L  RE++++ +R+G+    + T  EV     ++
Sbjct: 134 QNDQDDIDEQVDLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVANLLGIS 193

Query: 653 RERIRQIEAKAIRKL 667
           R  + +IE KA++KL
Sbjct: 194 RSYVSRIEKKALQKL 208


>gi|312622956|ref|YP_004024569.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203423|gb|ADQ46750.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 219

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 93/255 (36%), Gaps = 59/255 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +         A+  ++E NLRLV  +AKKYT        D+I 
Sbjct: 9   SFPQPMSPEEEEMYLNKMW---EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIIS 65

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA E +      K STYA   ++  I   +      +                
Sbjct: 66  VGTIGLIKAIETYSSAKCTKLSTYAAKCIENEILMYLRQNKKFLS--------------- 110

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI 592
                                                 +SLE PIG +       L D +
Sbjct: 111 -------------------------------------QLSLENPIGSDKDGNEITLMDVL 133

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++          ++  ++    ++   L  RE++++ +R+G+    + T  EV     ++
Sbjct: 134 QNDQNDIDEQVDLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVANLLGIS 193

Query: 653 RERIRQIEAKAIRKL 667
           R  + +IE KA++KL
Sbjct: 194 RSYVSRIEKKALQKL 208


>gi|312282731|dbj|BAJ34231.1| unnamed protein product [Thellungiella halophila]
          Length = 269

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/79 (49%), Positives = 53/79 (67%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           C    A++++     RLV+S+A  Y  +GL   DLIQEG+IGL++ AE+FD   GYK ST
Sbjct: 176 CRRREAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPERGYKLST 235

Query: 499 YAMWWVKQAITRSIADQSC 517
           Y  WW+KQAI R+IA +S 
Sbjct: 236 YVYWWIKQAILRAIAHKSR 254


>gi|146305232|ref|YP_001185697.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas mendocina
           ymp]
 gi|145573433|gb|ABP82965.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           mendocina ymp]
          Length = 244

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 97/232 (41%), Gaps = 24/232 (10%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           A  A+++ +   L LV  +  +     N+ L   D+ Q G +GL++   ++      +F 
Sbjct: 22  APGAEQKWLLQYLPLVKRIVSQLALQANQVLDREDMEQIGLMGLLECLRRY-GTPDEQFG 80

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            +A   ++ AI   +  Q      P  +R + H++    R+++ ++ R P  EEI     
Sbjct: 81  RFAALRIRGAILDELRRQDW---RPRQVRQQTHRIRDAIRQLARQLGRVPQEEEILAAAG 137

Query: 558 MPVEGVRKVLKITKEPI--SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE-TTT 614
           +  +  ++ L+        SL+  +                 V    +  +  L+E   T
Sbjct: 138 IDAKTYQEFLQADACEAIESLDELLQSGHEGF----------VCGASAVEERVLKERLLT 187

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           + L+ L+ RE  VL + +      + +L+E+     ++  R+ Q+  +AI K
Sbjct: 188 QALSQLSERERLVLTLYYQH----ELSLKEIALVLELSDARVCQLSKQAIAK 235


>gi|332971253|gb|EGK10216.1| hypothetical protein HMPREF9374_2566 [Desmospora sp. 8437]
          Length = 188

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 89/233 (38%), Gaps = 56/233 (24%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC-LGYKFST 498
                ++E+VE + RLV  VA ++    +++ DL+Q G IGL+KA ++++      KFST
Sbjct: 9   MGRDLREELVEQHQRLVYFVANQFRQSKMEWDDLVQIGFIGLIKAVDRYNPGIKKVKFST 68

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A  +++  I   +                                           + +
Sbjct: 69  FAFHYIRGEILHELRALKRHNP----------------------------------AMEV 94

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE V +               G++D   L D +       P +     + R      +A
Sbjct: 95  SVENVVEG-------------GGEDDEIRLMDTL----GTDPDEVETTVSNRVALEESMA 137

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
            LT +E  V+  RFG          E+ + F V  +RIR IE KAIRKL+   
Sbjct: 138 DLTDQEREVISFRFGKQWTQG----EIAELFDVPEKRIRVIEQKAIRKLRRQM 186


>gi|15645646|ref|NP_207822.1| flagellar biosynthesis sigma factor [Helicobacter pylori 26695]
 gi|2314177|gb|AAD08076.1| alternative transcription initiation factor, sigma-F (fliA)
           [Helicobacter pylori 26695]
          Length = 255

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 101/268 (37%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +     +T  S      +++   K +        ++    L  V ++A +   
Sbjct: 2   ILMMENRMPKGIQKTETSEKNIEKVLNAYDKQQHHHQD---DLAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 116 RSSRKLIKSIDIEITKHLNEHGKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +                  L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRKS 249


>gi|307747021|gb|ADN90291.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni M1]
          Length = 238

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 96/228 (42%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 25  QDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNNNFWGFAR 84

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  I  +         + + EP  E +AKKL + VE
Sbjct: 85  KRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEYFLENECEPDDEYLAKKLDLDVE 141

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +++V        +L           + + IE  N  + L+   +  L E    VL  L 
Sbjct: 142 KIKEVRTAHAISYTL----------PIDEQIELYNEDNTLEKIEKEELLEKIHEVLDDLK 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   ++  RI QI  K ++KL+ 
Sbjct: 192 ERDQLIIQLYY----YEELSLKEISEILQISESRISQIHKKLLKKLRE 235


>gi|313810027|gb|EFS47748.1| conserved domain protein [Propionibacterium acnes HL083PA1]
          Length = 52

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/52 (59%), Positives = 40/52 (76%)

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           MRFG+      TL+E+GK + VTRERIRQIE+K + KL+HPSRS+ LR +LD
Sbjct: 1   MRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD 52


>gi|221319748|ref|ZP_03601042.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
          Length = 160

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/111 (28%), Positives = 55/111 (49%), Gaps = 3/111 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 12  ALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 68

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I
Sbjct: 69  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI 119


>gi|225164110|ref|ZP_03726391.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
 gi|224801282|gb|EEG19597.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
          Length = 235

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 76/199 (38%), Gaps = 18/199 (9%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL   G + L+ A  + +         Y    V+ A+   +        +    R++I 
Sbjct: 36  DDLASVGKLALIAALGQRNGE-PDDVRAYCYVRVRGAMLDELR---RLDPLSRRQRNRIS 91

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG- 589
            + R    ++ ++ R PT +EIA    +    +           +++      DT+ +  
Sbjct: 92  FIARARTALTKRLGRLPTLDEIASATQLTKAEL---------TSAIDAATQATDTTEIEW 142

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D I D    SP +     ++R +    L  L   +   LR  +      D TL+ +  + 
Sbjct: 143 DTIPDTQLPSPAEVVELDDIRASLGVALDRLPANQALALRRYYL----EDATLDAIAVEL 198

Query: 650 CVTRERIRQIEAKAIRKLK 668
            V+RER RQ+     +KL+
Sbjct: 199 GVSRERARQVREAGEKKLR 217


>gi|221310502|ref|ZP_03592349.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314826|ref|ZP_03596631.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221324026|ref|ZP_03605320.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321312063|ref|YP_004204350.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|143642|gb|AAA22804.1| spoIVCB peptide precursor [Bacillus subtilis]
 gi|320018337|gb|ADV93323.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 155

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/111 (28%), Positives = 55/111 (49%), Gaps = 3/111 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 7   ALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I
Sbjct: 64  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI 114


>gi|57237071|ref|YP_178083.1| flagellar biosynthesis sigma factor [Campylobacter jejuni RM1221]
 gi|86149716|ref|ZP_01067946.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|86151250|ref|ZP_01069465.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|86154044|ref|ZP_01072245.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|88597726|ref|ZP_01100959.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|121612660|ref|YP_999787.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157414375|ref|YP_001481631.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|167004762|ref|ZP_02270520.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|315123666|ref|YP_004065670.1| flagellar biosynthesis sigma factor FliA [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|57165875|gb|AAW34654.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni RM1221]
 gi|85839984|gb|EAQ57243.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|85841597|gb|EAQ58844.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|85842458|gb|EAQ59672.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87248999|gb|EAQ71961.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|88190030|gb|EAQ94006.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|157385339|gb|ABV51654.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|284925357|gb|ADC27709.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni IA3902]
 gi|315017388|gb|ADT65481.1| flagellar biosynthesis sigma factor FliA [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|315057502|gb|ADT71831.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni S3]
 gi|315927744|gb|EFV07071.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Campylobacter jejuni subsp. jejuni DFVF1099]
          Length = 230

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 96/228 (42%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 17  QDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWGFAR 76

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  I  +         + + EP  E +AKKL + VE
Sbjct: 77  KRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEYFLEHECEPDDEYLAKKLDLDVE 133

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +++V        +L           + + IE  N  + L+   +  L E    VL  L 
Sbjct: 134 KIKEVRTAHAISYTL----------PIDEQIELYNEDNTLEKIEKEELLEKIHEVLDDLK 183

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   ++  RI QI  K ++KL+ 
Sbjct: 184 ERDQLIIQLYY----YEELSLKEISEILQISESRISQIHKKLLKKLRE 227


>gi|299115565|emb|CBN75768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ectocarpus
           siliculosus]
          Length = 244

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/96 (41%), Positives = 60/96 (62%), Gaps = 7/96 (7%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
             +    +++ E    +            AKK MVEAN+R+VIS+A+KY + G+   DLI
Sbjct: 60  EWAESRRMTVVELEESLK-------VGGAAKKTMVEANMRMVISIARKYQHLGVPLTDLI 112

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           QEG++GL++A EKFD   G+K STY+ WW++QAI +
Sbjct: 113 QEGSLGLVRAVEKFDPERGFKLSTYSAWWIQQAIFK 148


>gi|61966525|emb|CAI72582.1| SigB protein [Staphylococcus aureus]
          Length = 186

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 82/168 (48%), Gaps = 3/168 (1%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 15  QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 75  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 134

Query: 548 TPEEIAKKLAMPVEGVR--KVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +  EIA +L +  E V     +  +   +S++  I  +        ++
Sbjct: 135 SISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLD 182


>gi|318041750|ref|ZP_07973706.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 26/229 (11%)

Query: 448 MVEANLRLVISVAKKY-----TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           M++ NLRLV+ +AK Y      +  L+F DL+Q G IGL++A EKFD  LGY FSTYA W
Sbjct: 55  MIKENLRLVVCIAKPYHARIQRSSALEFSDLLQAGTIGLIRAVEKFDPALGYSFSTYASW 114

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           W++QAI R I     +IR+    +    K       +        + +E+A+ L +    
Sbjct: 115 WIRQAIRREIEASESSIRLSARQQQMRLKAHFAPPGL--------SHDELAEYLGVEPRQ 166

Query: 563 VRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           ++++       +  SL+ PI   +       + D  A     S    +L++   R     
Sbjct: 167 LKELQEAWRASQVDSLDRPIEMGNDQL---KLSDSLAAPLNRSLDHQDLQDVAARF---- 219

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI-RQIEAKAIRKLK 668
             R +    +     +    +  EV +   +TR+ + R++E +A ++L+
Sbjct: 220 --RRKAPSEIAVFDRLAQGESQSEVARSMGITRQALNRRLE-RASKRLR 265


>gi|239934456|emb|CAR92482.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 200

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 29/241 (12%), Positives = 71/241 (29%), Gaps = 45/241 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P T+  ++   + +   T  L +II            GF             +    +  
Sbjct: 1   PPTYSLMLSQYEGVATQTVRLADII-----------VGFIDPNAPDEIAAPINPKLAEAA 49

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            +++    +     + + ++   +++ P+  E   R                        
Sbjct: 50  AELETEAEEETEEGEAASEEEETLETGPDPEEAARR------------------------ 85

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               D ++  + +++          +      K   L++KL      L L+    D+L+ 
Sbjct: 86  ---FDSLSMTFAQVQK------GMAEKGADDPKVMKLRKKLADEFMELKLSPKMFDMLIT 136

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           Q+      I + E +++ L     G+ R  F+      E +  W+            +  
Sbjct: 137 QIRRSLTDIRNVEKQVMLLCVRDSGMPRKDFISTFPSNETNLSWLDKHIRAKRKHSAHLA 196

Query: 400 A 400
            
Sbjct: 197 K 197


>gi|160892593|ref|ZP_02073383.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
 gi|156865634|gb|EDO59065.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
          Length = 245

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 79/224 (35%), Gaps = 58/224 (25%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           +    KK ++E NLRLV+ +AKK+ N G+   DLI  G IGL+KA   F      K +TY
Sbjct: 58  DDQEIKKILIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFKCDKNIKLATY 117

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++  I   +   S                                           
Sbjct: 118 ASRCIENEILMYLRRNSK------------------------------------------ 135

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                      +  IS++ P+  +   +   L D +   +  +   +             
Sbjct: 136 ----------LRMEISIDEPLNVDWDGNELLLSDILG-TDEDTVYRNMETEMDHSLLETA 184

Query: 617 LASLTPREERVLRMRFGIGMNT--DHTLEEVGKQFCVTRERIRQ 658
           ++ L+ RE  ++ +R+GI      + T +EV     +++  I +
Sbjct: 185 VSHLSERERTIIELRYGINTINGIERTQKEVADLLGISQSYISR 228


>gi|255322026|ref|ZP_05363176.1| flagellar biosynthesis sigma factor FliA [Campylobacter showae
           RM3277]
 gi|255301130|gb|EET80397.1| flagellar biosynthesis sigma factor FliA [Campylobacter showae
           RM3277]
          Length = 235

 Score = 72.2 bits (175), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 93/233 (39%), Gaps = 20/233 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V A    + ++A +   R    +   DLI  G   ++K + K+D      F  YA 
Sbjct: 20  QDEVVLAYTPALRAMAFRLKERLPAHIDVSDLIGAGLEEMVKLSRKYDKEQNDSFWGYAQ 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  A+   +       R    +      +        NK + EP    IA KL + VE
Sbjct: 80  KRVYGAMLDFLRGLDVVSRSDRTLVK---SIEALVNEYFNKFECEPDDVYIAGKLGIDVE 136

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V +   ++     L           + D +E  +  + L+   + +L E  T++L    
Sbjct: 137 KVSEARNVSAVVAVLN----------IDDQMELMSEENTLERVEKEDLIEKITQILNEFE 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
            R++ ++++ +      + +L+E+ +   +T  RI QI  + + K++     K
Sbjct: 187 ERDQLIVQLYY----YEELSLKEISEILQITESRISQIHKRLMEKIRKKLEGK 235


>gi|317180689|dbj|BAJ58475.1| flagellar biosynthesis sigma factor [Helicobacter pylori F32]
          Length = 247

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 95/247 (38%), Gaps = 20/247 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            ++I  ++   + +    +  +    L  V ++A +   R    + F DL+  G   L+K
Sbjct: 12  EKNIEKVLNAYDEQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIK 71

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            A +++  L   F  YA   V  A+   +        I    R  I  +     +  N+ 
Sbjct: 72  LARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDIEITKHLNEH 128

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EP+   +A+ L   +E +++    +     +   +  ++  +  +             
Sbjct: 129 GKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPIDEQFNAIE------QDEITKK 178

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  RI QI  + 
Sbjct: 179 IEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITESRISQIIKEV 234

Query: 664 IRKLKHP 670
           I+K++  
Sbjct: 235 IKKVRKS 241


>gi|261886377|ref|ZP_06010416.1| flagellar biosynthesis sigma factor [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 234

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 92/248 (37%), Gaps = 22/248 (8%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIG 480
           ++E +     +   + E   ++ E+V + +  + ++A +  +R    ++  DLI  G   
Sbjct: 1   MNELKQ--KQLDAYQKEIKKSQDELVLSYMPALRAMAFRLKSRLPSSIEVNDLISVGATA 58

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           ++K +  +D      F  Y    V  ++   +       R     R  +  +        
Sbjct: 59  MVKLSRTYDKEQSDSFWGYVKQRVYGSMIDYLRGLDFLSRGN---RKLVKDIDSAINEYF 115

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           NK + EP    +AK L      +R+   ++     +      ++ S L       +    
Sbjct: 116 NKFECEPDDAYLAKILGEDEAKIREARNLSD----VSATFPIDEQSQLL------SESDT 165

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                +  L +  T VL     RE+ +++    +    + +L+E+     +T  RI  I 
Sbjct: 166 ESKIEKDELIQKITDVLNEFGEREQMIIQ----LKNYEELSLKEISDILGITESRISHIH 221

Query: 661 AKAIRKLK 668
            + I K++
Sbjct: 222 RRLITKIR 229


>gi|148269170|ref|YP_001243630.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga petrophila
           RKU-1]
 gi|147734714|gb|ABQ46054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga petrophila
           RKU-1]
          Length = 214

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 20/202 (9%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DLIQEG +  + + E++D      F+T+ M  VK A+   +         P ++R 
Sbjct: 24  VEVDDLIQEGIVAALSSLERYDPSKA-SFTTFIMKRVKGAMYDYLRKIDWM---PRNLRK 79

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            +  + R       + +  P+ EEIA+K  + ++ V +          L      ED   
Sbjct: 80  NVKMIERAIY----ESEEFPSDEEIARKTGLELKEVVRARNEMMRKQLL-MIDAMEDEIV 134

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L     D+NA        +  L E   + +  L+ +E+ VL +RF      D +L+E+ K
Sbjct: 135 LKTEGPDENAY-------RELLVEEMKKAIEKLSDKEKLVLSLRF----EKDLSLKEIAK 183

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              V+  R+ QI +K++ K+K 
Sbjct: 184 VLDVSESRVSQIISKSLLKIKK 205


>gi|455127|gb|AAA22315.1| RNA polymerase sigma-K subunit (cisB) [Bacillus subtilis]
 gi|1303780|dbj|BAA12436.1| SpoIVCB [Bacillus subtilis]
          Length = 156

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/111 (28%), Positives = 55/111 (49%), Gaps = 3/111 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +   V  ++ + + +K+ +    +S SE +  + ++ K       A+  ++E NLRLV 
Sbjct: 8   ALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK---GDEHARNMLIEHNLRLVA 64

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            + KK+ N G    DLI  G IGL+K  E +    G K +TYA   ++  I
Sbjct: 65  HIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKVATYAARCIENEI 115


>gi|222823277|ref|YP_002574850.1| flagellar biosynthesis sigma factor, sigma-F [Campylobacter lari
           RM2100]
 gi|222538498|gb|ACM63599.1| flagellar biosynthesis sigma factor, sigma-F [Campylobacter lari
           RM2100]
          Length = 228

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 99/244 (40%), Gaps = 27/244 (11%)

Query: 434 VRKGECEASIAKKE---MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEK 487
           ++     AS  KKE   +V + +  + ++A +   R    +   DLI  G   ++K + +
Sbjct: 1   MQPHNAYASALKKEQDDLVISYMPALRAMAFRLKERLPASIDVNDLISIGVEEMIKLSRR 60

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D      F  +A   V  A+   +        +    R  I  +         + ++EP
Sbjct: 61  YDKEQNDNFWGFARKRVNGAMLDYLRSLD---VMSRSNRKIIKDIDVIVDEYYQENEKEP 117

Query: 548 TPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
             E +A+KL + VE V++          + L+  +   + S++ + IE            
Sbjct: 118 DDEYLAQKLNLEVEKVKEARAAHAISLVMPLDEQLNCFNDSNIIEQIE------------ 165

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L E    VL     RE+ V+++ +      +  L+E+ +   ++  RI QI  + ++
Sbjct: 166 KEELIEKINAVLEEFKEREKLVIQLYY----YEELNLKEIAEILEISESRISQIHKRLLK 221

Query: 666 KLKH 669
           K++ 
Sbjct: 222 KIRE 225


>gi|321116238|emb|CBN73500.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V80]
 gi|321116274|emb|CBN73518.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V141]
 gi|321116276|emb|CBN73519.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V142]
 gi|321116278|emb|CBN73520.1| DNA-directed RNA polymerase subunit D [Pseudomonas sp. V143]
          Length = 199

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 19/106 (17%), Positives = 40/106 (37%), Gaps = 2/106 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + S +     + L  L   + L   + D LV ++ D   R+   E  ++++      
Sbjct: 95  KHGRDSKQGIAELKALAVLFMPIKLVPKQFDALVVRVRDALVRLRAQERAIMQICVRDAR 154

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
           + R  FL    G E+D  W        + ++   +   +  I + +
Sbjct: 155 MPRADFLRLFPGNEIDTTWAEQLAK-GKAKYAEAIGDRLADIQRGQ 199


>gi|298736645|ref|YP_003729171.1| RNA polymerase sigma factor for flagellar operon FliA [Helicobacter
           pylori B8]
 gi|298355835|emb|CBI66707.1| RNA polymerase sigma factor for flagellar operon FliA [Helicobacter
           pylori B8]
          Length = 255

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 100/268 (37%), Gaps = 23/268 (8%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           IL + N +         S      +++   + +     A   +    L  V ++A +   
Sbjct: 2   ILMMENRMPKEIQNIETSEKNIEKVLNAYDEQQHHHQDA---LAIQYLPAVRAMAFRLKE 58

Query: 466 R---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           R    + F DL+  G   L+K A +++  L   F  YA   V  A+   +        I 
Sbjct: 59  RLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VIS 115

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   +  
Sbjct: 116 RSNRKLIKSIDIEITKHLNEHGKEPSDAYLAEALGENIEKIKEAKTASD----IYALVPI 171

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ++  +  +  E               L E   + L  ++ RE+ ++++ +      +  L
Sbjct: 172 DEQFNAIEQDE------ITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNL 221

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            E+ +   +T  RI QI  + I+K++  
Sbjct: 222 SEIKEILGITESRISQIIKEVIKKVRKS 249


>gi|289811768|ref|ZP_06542397.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
          enterica serovar Typhi str. AG3]
          Length = 63

 Score = 71.8 bits (174), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 35/58 (60%)

Query: 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
              K ++   +++GY+T  E+N  LP D V S+Q+ED + M+++MGI V++     D
Sbjct: 6  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDAD 63


>gi|283955444|ref|ZP_06372942.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283793071|gb|EFC31842.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 230

 Score = 71.4 bits (173), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 96/228 (42%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 17  QDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWGFAR 76

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  I  +         + + EP  E +AKKL + VE
Sbjct: 77  KRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEYFLEHECEPDDEYLAKKLDLDVE 133

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +++V        +L           + + IE  N  + L+   +  L E    VL  L 
Sbjct: 134 KIKEVRTAHAISYTL----------PIDEQIELYNEDNTLEKIEKEELLEKIHEVLDDLK 183

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   ++  RI QI  K ++KL+ 
Sbjct: 184 ERDQLIIQLYY----YEELSLKEISEILEISESRISQIHKKLLKKLRE 227


>gi|30263977|ref|NP_846354.1| prophage LambdaBa02, RNA polymerase sigma-F factor, putative
           [Bacillus anthracis str. Ames]
 gi|47529410|ref|YP_020759.1| prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|30258621|gb|AAP27840.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Ames]
 gi|47504558|gb|AAT33234.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. 'Ames Ancestor']
          Length = 299

 Score = 71.4 bits (173), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 97/243 (39%), Gaps = 28/243 (11%)

Query: 448 MVEANLRLVISVAKKY---------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            ++   RLV     KY             L   DLIQ G +GL+ A   F   LG+KF+T
Sbjct: 7   FMKKYSRLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTT 66

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A+  +   I +++ D               ++V     ++S     +   E IAK L +
Sbjct: 67  FAVPRILGYIRKAVRDS--------QKIRITNEVYEIKGKISRMKLHDEEVESIAKLLEV 118

Query: 559 PVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            V  V+   +     ISL+TP+  E   +   L + + DK     LD  I+   +   T 
Sbjct: 119 SVRDVKTAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTLDDVIK---KMIITA 175

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L++L  +E+             + T   +GK+  VT+ +I +I     +K +       
Sbjct: 176 FLSTLCSKEK-----FVWELHAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNKHS 230

Query: 676 LRS 678
           LR 
Sbjct: 231 LRD 233


>gi|261341477|ref|ZP_05969335.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288316273|gb|EFC55211.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 233

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 44/216 (20%), Positives = 90/216 (41%), Gaps = 16/216 (7%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
            R+V  +A + T+  +   D+ Q   +GL+ A  ++      +F  YA   ++ A+   +
Sbjct: 29  HRVVKQLAWQ-TSSVMDREDMEQIALMGLLTALRRYGHP-DEQFGAYAAQRIRGAVLDEL 86

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +       P  +R K HK+    R ++ K+ R P+ E+++  L++  E   + L     
Sbjct: 87  RELDW---RPRRLRQKSHKLNDAIREVTRKLGRTPSFEDLSTHLSITAEEYHEYLL---- 139

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
              L+     E    L         ++      +     T    LASL  RE+ +L + +
Sbjct: 140 ---LDCAKTLESLDELLGGDALNGTLNTCSLEDEMVTSGTLRAALASLDEREQLILSLYY 196

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                 + +L+E+     +T  R+ Q+  K  +K++
Sbjct: 197 QH----EMSLKEIALVLDLTEARVCQLNKKIAQKIQ 228


>gi|255697049|emb|CBA11634.1| RNA polymerase sigma factor [Pseudomonas viridiflava]
          Length = 169

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 26/159 (16%), Positives = 54/159 (33%), Gaps = 4/159 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 13  DPDDGIAPPAEVPPPVDPKAAKAEGTDDDEEESADASDEEDEVESGPDPVIAAQRFGAVS 72

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +++K ++   V    L +L   + L   + + LVE++     R+  
Sbjct: 73  DQMEITRKALKKLGREDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALDRLRA 129

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKD 389
            E  +++L      + R  FL +  G E+D  W      
Sbjct: 130 QERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAK 168


>gi|260896280|ref|ZP_05904776.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio parahaemolyticus Peru-466]
 gi|308088782|gb|EFO38477.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio parahaemolyticus Peru-466]
          Length = 146

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 29/142 (20%), Positives = 59/142 (41%), Gaps = 9/142 (6%)

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS 586
             ++ +    +   + R+PT  E+A  L M ++     L        + +E     +D  
Sbjct: 2   NREINQAVAELEGVLNRDPTDSEVAAHLGMSLDQYHSALTDINCSRLVGIEDLGVSDDVI 61

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              D  +D N   P       + R+     +  L  RE  VL + +    + +  L+E+G
Sbjct: 62  SPADETDDSN---PFKGVADESFRKALVESIKQLPEREALVLSLYY----DEELNLKEIG 114

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               V+  R+ QI ++A+++L+
Sbjct: 115 DVLGVSESRVSQILSQAMQRLR 136


>gi|321116318|emb|CBN73540.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             ++S +     E L  L   + L   + D LVE++ +   +I   E  +++L      +
Sbjct: 98  HGRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARM 157

Query: 366 KRDVFLERHQGRELDPHWVSY 386
            R  FL +    E +  W   
Sbjct: 158 PRADFLRQFPNNETNLDWAEQ 178


>gi|108756900|ref|YP_630657.1| FliA/WhiG family RNA polymerase sigma factor [Myxococcus xanthus DK
           1622]
 gi|108460780|gb|ABF85965.1| RNA polymerase sigma factor, FliA/WhiG/SigD family [Myxococcus
           xanthus DK 1622]
          Length = 278

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 85/225 (37%), Gaps = 17/225 (7%)

Query: 445 KKEMVEANLRLVISVA---KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ ++E     V S+A   +K  N  L+  +L+  G IGL++AAE+FD  +G  F T+A 
Sbjct: 7   RQVILEKYGPYVRSLAATVRKQFNAQLELDELLAYGQIGLLEAAERFDPKVGANFLTFAH 66

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + +K AI   +            +R    +      R +  +      E  A       +
Sbjct: 67  YRIKGAIFDGLRKMG-------VLRGSDARNAYVGERAAAYLGNLSDREAGAGNRGSSFD 119

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                +      +++      E     G       ++       Q  L+      +  L 
Sbjct: 120 DDVNDISDAVTGLAMVFATSIEGADTAGYT---DESLPVDIRMEQEQLKTRVRAAIEKLP 176

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            +E ++L   +  G     TLEE G +   ++    ++ A+AI +
Sbjct: 177 EKERKLLMGYYFQG----RTLEEAGAEIGQSKSWASRLHARAIDR 217


>gi|222528742|ref|YP_002572624.1| sporulation sigma factor SigK [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455589|gb|ACM59851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 219

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 54/255 (21%), Positives = 94/255 (36%), Gaps = 59/255 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +R        A+  ++E NLRLV  +AKKYT        D+I 
Sbjct: 9   SFPQPMSPEEEEMYLNKMR---EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIIS 65

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA E +      K STYA   ++  I   +      +                
Sbjct: 66  VGTIGLIKAIETYSSAKCTKLSTYAAKCIENEILMYLRQNKKFLS--------------- 110

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI 592
                                                 +SLE PIG +       L D +
Sbjct: 111 -------------------------------------QLSLENPIGSDKDGNEITLMDVM 133

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++          ++  ++    ++   L  RE++++ +R+G+    + T  EV     ++
Sbjct: 134 QNDQEDIDEQVDLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVANLLGIS 193

Query: 653 RERIRQIEAKAIRKL 667
           R  + +IE KA++KL
Sbjct: 194 RSYVSRIEKKALQKL 208


>gi|167461107|ref|ZP_02326196.1| SpoIIIC [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322384941|ref|ZP_08058597.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150238|gb|EFX43745.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 181

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 48/217 (22%), Positives = 79/217 (36%), Gaps = 57/217 (26%)

Query: 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +   KK+ N G    DLI  G IGL+KA E F    G K +T+A   ++  I   +    
Sbjct: 11  VHNIKKFDNTGEDLEDLISIGTIGLIKAIESFSPNKGTKLATFAARCIENEILMHLRS-- 68

Query: 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576
                                                             LK T++ +SL
Sbjct: 69  --------------------------------------------------LKKTRKDVSL 78

Query: 577 ETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
             PIG +   +   L D +  +         ++   +    R L  L  RE+ V++ RFG
Sbjct: 79  HDPIGTDKEGNEITLIDILGTEVDEVVDKVQLKIE-KSKIYRNLDILDEREQEVIKGRFG 137

Query: 634 IGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     + T  E+  +  ++R  + +IE +A+ KL H
Sbjct: 138 LEYGGEERTQREIACELGISRSYVSRIEKRALMKLYH 174


>gi|325509467|gb|ADZ21103.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum EA 2018]
          Length = 246

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 105/253 (41%), Gaps = 12/253 (4%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLM 482
            E + +  ++ + +  +  AK  +++++++ +  +A  +   N+ L   DL+QEG I ++
Sbjct: 1   MEDKEVKDLILRAKDGSKDAKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVI 60

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA   +D     KFSTY    +   +   I  +    +IP H   KI K  R A  +  +
Sbjct: 61  KAINSYDLDKNVKFSTYVYSMINFTLISEIKKKYSYFKIPEHQVSKIVKFKRRASELKVE 120

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
                   E   ++ +  E    ++ ++       L+     +      D    ++ V+ 
Sbjct: 121 DTCYKYGCE---RIGLSYEQYADMMHLSKLNNVAYLDEKKYFDGKVSEEDKFAYED-VNY 176

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
                + +L          L+  E+ ++R         D  ++ + K   ++ ++I  I+
Sbjct: 177 KRVEEKIDLNVILKENADKLSQLEKYIIREIL----IKDQKVKNISKITKMSTKKISNIK 232

Query: 661 AKAIRKLKHPSRS 673
             A++K+++  ++
Sbjct: 233 YSALKKIQNSLKN 245


>gi|228943596|ref|ZP_04106021.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976443|ref|ZP_04136903.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981654|ref|ZP_04141950.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228778139|gb|EEM26410.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228783244|gb|EEM31363.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228816045|gb|EEM62245.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 232

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 86/229 (37%), Gaps = 28/229 (12%)

Query: 447 EMVEANLRLVISVAK-KYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++   RLV      +Y  +        GL   DL Q G IGL+KA + FD   G KFS
Sbjct: 5   EFMKKYGRLVHHCVWKRYAKKMKSIEHDTGLDIEDLTQFGMIGLIKARDNFDLEYGCKFS 64

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           TYA+  +   I R+I D                 V     ++  +      PEEIA  L 
Sbjct: 65  TYAVPKIIGEIGRAIRDH--------QKVKVQRSVYSIKGKILRQNLEYEIPEEIASILN 116

Query: 558 MPVEGVRKVLKITKEPISLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
             V  V   L       SL   +      +   L   +EDK A +  D +I    R    
Sbjct: 117 EDVSVVSNALHYQPGTQSLNKVVHQSNGNEELTLESMLEDKKAENVEDVSIN---RMVIQ 173

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              + L+ +E  VL M        + T + +  +   ++ +I +I  K 
Sbjct: 174 AFKSQLSHKEHIVLDMSL-----QNRTQQNIANEVGCSQVQISRILTKI 217


>gi|169334386|ref|ZP_02861579.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259103|gb|EDS73069.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
          Length = 233

 Score = 71.4 bits (173), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 88/250 (35%), Gaps = 56/250 (22%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + ++  +   E   +  K  ++E NLRLV+ +AKK+        DLI  G IGL
Sbjct: 31  LTKEEEQEVLKNLESDETNTT--KTILIERNLRLVVYIAKKFDTSSASVEDLISIGTIGL 88

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + F      K +TYA   ++  I   +                  KV R       
Sbjct: 89  IKAVKTFKVEKNIKLATYASKCIENEILMHLR-----------------KVNRIRGE--- 128

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIEDKNAVS 599
                                           ISL+ P+  +   +  L   I   N   
Sbjct: 129 --------------------------------ISLDEPLNVDYDGNELLLSDILGTNGDP 156

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D   +   +E     +  L   E+ ++  RFG+      T +E+     +++  I ++
Sbjct: 157 VKDKIDKDVNKEIMLLAVDRLKESEKEIINYRFGLNGKEKKTQKELANMLNISQSYISRL 216

Query: 660 EAKAIRKLKH 669
           E + I  LK 
Sbjct: 217 EKRIISNLKK 226


>gi|170287832|ref|YP_001738070.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga sp. RQ2]
 gi|281411468|ref|YP_003345547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermotoga
           naphthophila RKU-10]
 gi|170175335|gb|ACB08387.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga sp. RQ2]
 gi|281372571|gb|ADA66133.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 220

 Score = 71.0 bits (172), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 20/202 (9%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DLIQEG +  + + E++D      F+T+ M  VK A+   +         P ++R 
Sbjct: 30  VEVDDLIQEGIVAALSSLERYDPSKA-SFTTFIMKRVKGAMYDYLRKIDWM---PRNLRK 85

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            +  + R       + +  P+ EEIA+K  + ++ V +          L      ED   
Sbjct: 86  NVKMIERAIY----ESEEFPSDEEIARKTGLELKEVVRARNEMMRKQLL-MIDAMEDEIV 140

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L     D+NA        +  L E   + +  L+ +E+ VL +RF      D +L+E+ K
Sbjct: 141 LKTEGPDENAY-------RELLVEEMKKAIEKLSDKEKLVLSLRF----EKDLSLKEIAK 189

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              V+  R+ QI +K++ K+K 
Sbjct: 190 VLDVSESRVSQIISKSLLKIKK 211


>gi|321116344|emb|CBN73553.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 2/99 (2%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             ++S +     E L  L   + L   + D LVE++ +   +I   E  +++L      +
Sbjct: 98  HGRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARM 157

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            R  FL +    E +  W        +G++   +    +
Sbjct: 158 PRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAIRNPKE 195


>gi|225850277|ref|YP_002730511.1| RNA polymerase sigma factor for flagellar operon [Persephonella
           marina EX-H1]
 gi|225646527|gb|ACO04713.1| RNA polymerase sigma factor for flagellar operon [Persephonella
           marina EX-H1]
          Length = 209

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 97/233 (41%), Gaps = 39/233 (16%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               K+++V  NL LV  VA K  +R     ++F DL+    IGLMKA +++D     KF
Sbjct: 6   DKKNKEQIVLENLSLVKKVASKIYSRLPKGDIEFDDLVNTWIIGLMKAIDRYDKDKA-KF 64

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA   ++  I   +       R       K                            
Sbjct: 65  STYAYIKIRGEILDYLRSLDIVPRTVRDRIKKEKA------------------------- 99

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                     L  +   +S+E  +  +D S  L D +  K   +P +  I+ +L++   +
Sbjct: 100 ---EREEPMPLSTSAVMVSIEKALSTKDESLKLIDTLVSKK-ETPEEEVIKDDLKDRLIK 155

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+  L  +E+RVL+M +      +   + V  +  ++  R+ QI+++A+RKLK
Sbjct: 156 VIDMLNEKEKRVLQMLYF----EELDFKTVASELNISVSRVSQIKSEALRKLK 204


>gi|321116206|emb|CBN73484.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116218|emb|CBN73490.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116220|emb|CBN73491.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116222|emb|CBN73492.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116224|emb|CBN73493.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116234|emb|CBN73498.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116236|emb|CBN73499.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116250|emb|CBN73506.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116258|emb|CBN73510.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116268|emb|CBN73515.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116270|emb|CBN73516.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116282|emb|CBN73522.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116284|emb|CBN73523.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116294|emb|CBN73528.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116306|emb|CBN73534.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116308|emb|CBN73535.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116324|emb|CBN73543.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116330|emb|CBN73546.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116332|emb|CBN73547.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116334|emb|CBN73548.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116342|emb|CBN73552.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116356|emb|CBN73559.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
 gi|321116364|emb|CBN73563.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 195

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/185 (14%), Positives = 61/185 (32%), Gaps = 8/185 (4%)

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           D +       +  A   ++   +          D+++ +E++D  +              
Sbjct: 18  DILSGYIDPDDDGAAGPQEVEPETPQTTAKPAADDKDDEEEDDSDSEEEEGDGGPDPEVA 77

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                 +AE   +           +K  ++S +     E L  L   + L   + D LVE
Sbjct: 78  RMRFGAVAEQLEK------AKKALKKHGRASQQAVEELEALAILFMPIKLVPKQYDALVE 131

Query: 341 QLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           ++ +   +I   E  +++L      + R  FL +    E +  W        +G++   +
Sbjct: 132 RVRNALSQIRAQERAIMQLCVRDARMPRADFLRQFPNNETNLDWAEQLAS-GKGKYAEAI 190

Query: 400 ACEVD 404
               +
Sbjct: 191 GNRKE 195


>gi|186896753|ref|YP_001873865.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|186699779|gb|ACC90408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 231

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 106/247 (42%), Gaps = 19/247 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   EF   +++    E +   A   +V+  +R +   A     +     D+ Q   +GL
Sbjct: 1   MENREFEACLTLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGK----EDMQQIALMGL 56

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK     R+++ 
Sbjct: 57  LEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDW---RPRRLRQKTHKTNEAIRQIAK 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++  EP  EEI+ +L +  +  ++ L        LE     E    +       + +   
Sbjct: 113 RLGHEPNFEEISAELNLTADEYQEYLL-------LENAGAMESLDEILALDAHNDILQSC 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D      + +   + +++L  RE+ +L + +      + +++E+ +   +T  RI Q+  
Sbjct: 166 DLEENIIIEDNLKQAISALDEREQMILHLYYQ----QELSMKEIAQVLDLTEARICQLNK 221

Query: 662 KAIRKLK 668
           K ++K+K
Sbjct: 222 KLVQKIK 228


>gi|108562840|ref|YP_627156.1| flagellar biosynthesis sigma factor [Helicobacter pylori HPAG1]
 gi|107836613|gb|ABF84482.1| alternative transcription initiation factor, sigma-F [Helicobacter
           pylori HPAG1]
          Length = 255

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 96/247 (38%), Gaps = 20/247 (8%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMK 483
            ++I  ++   + +    +  +    L  V ++A +   R    + F DL+  G   L+K
Sbjct: 20  EKNIEKVLNAYDEQQHHHQDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIK 79

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
            A +++  L   F  YA   V  A+   +        I    R  I  +     +  N+ 
Sbjct: 80  LARRYESALNDSFWGYAKTRVNGAMLDYLRSLD---VISRSNRKLIKSIDIEITKHLNEH 136

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            +EP+   +A+ L   +E +++    +     +   +  ++  +  +             
Sbjct: 137 GKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPIDEQFNAIE------QDEITKK 186

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                L E   +VL  ++ RE+ ++++ +      +  L E+ +   +T  RI QI  + 
Sbjct: 187 IEAEELLEHVQKVLNQMSEREQILIQLYYF----EELNLSEIKEILGITESRISQIIKEV 242

Query: 664 IRKLKHP 670
           I+K++  
Sbjct: 243 IKKVRKS 249


>gi|283955505|ref|ZP_06373000.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni 1336]
 gi|283792966|gb|EFC31740.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni 1336]
          Length = 238

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 97/228 (42%), Gaps = 20/228 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 25  QDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWGFAR 84

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  I  +         + + EP  E +AKKL + VE
Sbjct: 85  KRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEYFLENECEPDDEYLAKKLDLDVE 141

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +++V        +L           + + IE  N  + L+   +  L E   +VL  L 
Sbjct: 142 KIKEVRTAHAISYTL----------PIDEQIELYNEDNTLEKIEKEELLEKIHKVLDDLK 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            R++ ++++ +      + +L+E+ +   ++  RI QI  K ++KL+ 
Sbjct: 192 ERDQLIIQLYY----YEELSLKEISEILQISESRISQIHKKLLKKLRE 235


>gi|242309557|ref|ZP_04808712.1| flagellar biosynthesis sigma factor [Helicobacter pullorum MIT
           98-5489]
 gi|239524128|gb|EEQ63994.1| flagellar biosynthesis sigma factor [Helicobacter pullorum MIT
           98-5489]
          Length = 235

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 81/209 (38%), Gaps = 17/209 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++F DL+  G   L+K A K+D  L   F  YA   V  A+   +    C      + R 
Sbjct: 42  VEFADLVSIGTEELIKLARKYDSTLNDSFWGYAKSRVHGAMLDYLRGLDCM---SRYSRT 98

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               + R   +  N+ + EP    +++ L   +E ++     ++    L           
Sbjct: 99  LTKNIDREISKYYNEHQEEPDNAYLSQVLNEDIEKIKDARNASEIYGIL----------P 148

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L + +         +   +  L E   ++L +    E+ V+++ +      +   +E+G+
Sbjct: 149 LDEELSASQDDKTYNKVEKEELIEIIQKILETSPQNEQLVIQLYY----YEELNFKEIGE 204

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              +T  R+ QI    IRK+K     + +
Sbjct: 205 ILEITESRVSQIHKAVIRKIKKYLEERGV 233


>gi|167747049|ref|ZP_02419176.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
 gi|167654009|gb|EDR98138.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
          Length = 200

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 93/253 (36%), Gaps = 58/253 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +    +S  E ++ +   R        A+  +VE NLRLV  + KKY N      DLI  
Sbjct: 3   AFLEPLSQEEEQYYLKKSR---LGDMEARNILVEHNLRLVAHIVKKYNNFDRDKDDLISV 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   ++   G++  TYA   ++  +   +  +                     
Sbjct: 60  GTIGLIKAINTYNLEKGHRLVTYASRCIENELLMMLRQE--------------------- 98

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIE 593
                                          + + +  SL  PIG +   +  +L D + 
Sbjct: 99  -------------------------------RKSAKDTSLYEPIGIDKEGNEINLLDVLG 127

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
                   +  ++  +R+    V      RE+  L MR+G+      T +EV K+  ++R
Sbjct: 128 ADENDIVDELDLKEKIRDLYKMVDEMEPSREKTTLIMRYGLYGKKPMTQKEVAKELHISR 187

Query: 654 ERIRQIEAKAIRK 666
             + +IE K +R+
Sbjct: 188 SYVSRIEKKLLRR 200


>gi|162454470|ref|YP_001616837.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161165052|emb|CAN96357.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 321

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 82/227 (36%), Gaps = 46/227 (20%)

Query: 445 KKEMVEANLRLV---ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E++     LV   +    ++    +Q  DL+  G +GL+ +  K     G  F+ YA 
Sbjct: 132 RPEVLRGYFPLVRKLVRQVSRHLPPNVQRDDLLSAGMLGLVDSLRKNGGSDGETFAGYAK 191

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ AI   +  Q                       +S + +     E  ++     V 
Sbjct: 192 LRIRGAIVDELRAQDW---------------------LSRRAREAVEAEAASRAGGATV- 229

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                       +SL      E+++H+           P+++      R   +  +A L 
Sbjct: 230 -----------FVSLSEVTPTEESAHMS------GEDDPIEAISAQATRRALSFAIARLP 272

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE RV+ M +  G      L+++G +  +   R+ Q+  +A+  L+
Sbjct: 273 ERERRVIGMYYFEG----AKLKDIGAELGIGEPRVSQLHTRALGMLR 315


>gi|295102717|emb|CBL00262.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 86/244 (35%), Gaps = 46/244 (18%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKK-YTNRGL-------QFLDLIQEGNIGLMK 483
            +    +   + A   ++E N   +  VA   + +  L          DL Q GN+GL K
Sbjct: 7   RLCALAQKGDAAALDSLIENNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWK 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  KFD   G KF TYA   ++ A+   + D                           ++
Sbjct: 67  AVSKFDAACGMKFLTYAAPAIRNAMMDMVRD--------------------AFAAFEQRM 106

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E              +GV        + +SL+  +  E+     + I D  A+ P   
Sbjct: 107 VTE------------DKDGV------CYQRVSLDEVLPGEEQLRRIEAIADPYAMQPQSI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   R      L  LT RE+  L  R+G     +H L      F +T+ R ++ E +A
Sbjct: 149 MEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAKKTEEQA 208

Query: 664 IRKL 667
           +  L
Sbjct: 209 MDNL 212


>gi|148926867|ref|ZP_01810545.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8486]
 gi|205356444|ref|ZP_03223208.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8421]
 gi|218561746|ref|YP_002343525.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|112359452|emb|CAL34235.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni NCTC 11168]
 gi|145844444|gb|EDK21552.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8486]
 gi|205345631|gb|EDZ32270.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8421]
 gi|315929165|gb|EFV08390.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Campylobacter jejuni subsp. jejuni 305]
          Length = 238

 Score = 71.0 bits (172), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 100/250 (40%), Gaps = 20/250 (8%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNI 479
           S  +   +    +         + E+V + +  + ++A +   R    +   DLI  G  
Sbjct: 3   SKKDEEMLKEPPKAYAQMLKKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVE 62

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            ++K + ++D      F  +A   V  ++   +        +  + R  I  +       
Sbjct: 63  EMIKLSRRYDKEQNDNFWGFARKRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEY 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             + + EP  E +AKKL + VE +++V        +L           + + IE  N  +
Sbjct: 120 FLEHECEPDDEYLAKKLDLDVEKIKEVRTAHAISYTL----------PIDEQIELYNEDN 169

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L+   +  L E    VL  L  R++ ++++ +      + +L+E+ +   ++  RI QI
Sbjct: 170 TLEKIEKEELLEKIHEVLDDLKERDQLIIQLYY----YEELSLKEISEILQISESRISQI 225

Query: 660 EAKAIRKLKH 669
             K ++KL+ 
Sbjct: 226 HKKLLKKLRE 235


>gi|325679376|ref|ZP_08158961.1| putative RNA polymerase sigma-G factor [Ruminococcus albus 8]
 gi|324108973|gb|EGC03204.1| putative RNA polymerase sigma-G factor [Ruminococcus albus 8]
          Length = 162

 Score = 71.0 bits (172), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 43/168 (25%), Positives = 78/168 (46%), Gaps = 9/168 (5%)

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           M  +   I R + D    IR+   MRD  +K ++       K +REP+ +EIA+      
Sbjct: 1   MPMILGEIKRYMRDF-RPIRVSRSMRDLAYKAMQAKESFIAKHQREPSIDEIAELTGEKR 59

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
             +   L+   +P+S+  P+  E    L    +  ++        + NL+E     L +L
Sbjct: 60  ADIVTALESITDPVSIYEPVYTEGGDALYIVDQICDSNDDKSWLEELNLKE----ALKTL 115

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             RE+ +L +RF  G    HT  EV K+  +++ ++ ++E  A+ K+K
Sbjct: 116 KDREKNILFLRFYKG----HTQMEVAKEIGISQAQVSRLEKNALDKIK 159


>gi|126698826|ref|YP_001087723.1| sporulation sigma factor SigK [Clostridium difficile 630]
 gi|26000675|gb|AAN75197.1| sigma K [Clostridium difficile]
 gi|26000677|gb|AAN75198.1| sigma K [Clostridium difficile]
          Length = 213

 Score = 70.6 bits (171), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 93/243 (38%), Gaps = 51/243 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  ++  E    ++  +        AK  ++E N+RLV  +AKKY N      DLI  
Sbjct: 6   SFEKPLTPEEEIEYLTKFK--IENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA E ++   G + +TYA   ++  I  +I                 +K  +T 
Sbjct: 64  GTIGLIKAIETYNIDKGTRLATYASRCIENEILMNIRS---------------NKKNKTQ 108

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             + + I  +    EI                                   L D +  + 
Sbjct: 109 VSLQDPIGTDKEGNEI----------------------------------SLLDILGTEA 134

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                +  ++  + +   ++   LTPRE  ++++R+G+      T  E+ ++  ++R  +
Sbjct: 135 NYVLDEVELKVQVGKLYEQLNKILTPREREIVQLRYGLTPYGYKTQREIAQKLDISRSYV 194

Query: 657 RQI 659
            +I
Sbjct: 195 SRI 197


>gi|319790426|ref|YP_004152059.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114928|gb|ADU97418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 203

 Score = 70.6 bits (171), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 103/235 (43%), Gaps = 43/235 (18%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             +  +KE+V  +L LV  VA +   R     ++F +L+  G IGL+KA E++D     K
Sbjct: 1   MYTKTRKELVLEHLPLVKKVANRIYRRIPEGAVEFEELVNTGVIGLIKAIERYDENRA-K 59

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   ++  I   +        +P  +R+K+                          
Sbjct: 60  FSTYAYIKIRGEILDYLRKLDF---LPRSVREKVK------------------------- 91

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
               ++ +++ +      IS+E  +  + D   + D +   +   P +  +  + +E  T
Sbjct: 92  -NGDLDDLKEGVASF---ISIEEKLFADSDRFTVKDTLASPDD-GPEERMLLEDAKEKLT 146

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +  L+ +E+ VL++ F      +  L+ +G+   ++  R+ QI++ A++KL+ 
Sbjct: 147 EAIKKLSEKEQLVLQLIFV----EELDLKSIGEILGISVSRVSQIKSSALKKLRK 197


>gi|327485473|gb|AEA79879.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 185

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 40/184 (21%), Positives = 85/184 (46%), Gaps = 13/184 (7%)

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
            ++A+ W+K  I   +      ++I      R     + ++ +R+      E   E +A+
Sbjct: 1   MSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGE--VETVAR 58

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-----FIEDKN---AVSPLDSAIQ 606
           +L +    VR++        +      ++D + +       ++EDK+   A +      +
Sbjct: 59  ELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSDLADNLEAENWE 118

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           A+  +  +  LASL  R + ++R R+ +  +   TL+++ + + V+ ERIRQ+E  A+RK
Sbjct: 119 AHTTQRLSMALASLDERSQHIVRARW-LDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRK 177

Query: 667 LKHP 670
           LK  
Sbjct: 178 LKEA 181


>gi|254729575|ref|YP_003084257.1| RNAP sigma factor [Cyanophage PSS2]
 gi|254211727|gb|ACT65675.1| RNAP sigma factor [Cyanophage PSS2]
 gi|265524923|gb|ACY75815.1| predicted protein [Cyanophage PSS2]
          Length = 284

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 60/203 (29%), Positives = 96/203 (47%), Gaps = 12/203 (5%)

Query: 438 ECEASIAKKEMVEANLRLVISVAK-KYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLG 493
           E +   A + +V+ NLRLV ++ K +Y  R +     L+++QEG IGL  AA +FD   G
Sbjct: 38  ERKGQAALQRIVKGNLRLVAAIWKKRYLKRNIAPAHSLEILQEGAIGLNDAAMRFDPSSG 97

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           Y+FST+A WW+ +++     D    +R    M  K  K V+    M +  K + + EEI 
Sbjct: 98  YRFSTFASWWIIKSMKEYQRDSERLVRFKGDMHWKALKAVK----MLHTEKGQHSTEEIE 153

Query: 554 KKLAMPVEG-VRKVLKITK-EPISLET--PIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           K L MP +  +   +  T+  P SL+    +   D S L +FI D +  +       A+ 
Sbjct: 154 KALKMPAKRAINLAMTFTQLHPKSLDVPNQLSGNDASPLHEFIADPSTTTFDYEIPNADR 213

Query: 610 RETTTRVLASLTPREERVLRMRF 632
                     + PR   ++  RF
Sbjct: 214 IAKYLFDQFDVEPRMRELILNRF 236


>gi|313837242|gb|EFS74956.1| sigma-70, region 4 [Propionibacterium acnes HL037PA2]
 gi|314927738|gb|EFS91569.1| sigma-70, region 4 [Propionibacterium acnes HL044PA1]
 gi|314972014|gb|EFT16112.1| sigma-70, region 4 [Propionibacterium acnes HL037PA3]
 gi|328907208|gb|EGG26974.1| sigma-70, region 4 [Propionibacterium sp. P08]
          Length = 270

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 100/242 (41%), Gaps = 25/242 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +RK   +   A++ +    L +V++ A++          DLIQ G +GL +A E++D 
Sbjct: 48  AELRKISDDGVAARQALWRQMLAIVLTQARQAAVTYRCSVEDLIQSGCVGLGEAIERYDE 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +R P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQRVPSSD 165

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
            IA ++   V  V K      E          E  + +    +D  +             
Sbjct: 166 AIAAQMGKDVMWVEKRRVECWEI----ETSFFEQVAVVQKCCDDPES------------- 208

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                +++ L  +E R++ +R G       T+  V  +  ++    R+IE +A+ +L+  
Sbjct: 209 ----GLISLLMGQERRIVELRHGFE-GEPMTITAVADELGLSASNARRIEHRALARLRRY 263

Query: 671 SR 672
            +
Sbjct: 264 LQ 265


>gi|317131781|ref|YP_004091095.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315469760|gb|ADU26364.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 256

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 91/241 (37%), Gaps = 24/241 (9%)

Query: 429 HIVSMVRKGECEASIAKKE-MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I           S A  E +V A   LV   A  Y   G    D  Q G +GL+KA + 
Sbjct: 14  DINEAYACYTATPSDAALEAVVLAGRPLVYHFAALY-GVGCPLEDTAQTGMLGLVKAIKS 72

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           +D      FST+A   +   I R  A +    R P  +     +  +   R +   +  P
Sbjct: 73  YDGR--VLFSTWASHCIIGEI-RHFARKERVYRRPGCLNRLQEQAEKVLERTAEDGEPPP 129

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
             +++A +L +  EGVR+VL+      S L+              IE  ++       + 
Sbjct: 130 EEDKLADELGIRPEGVREVLRAGLVAFSDLD--------------IEKISSTQMQPFHLP 175

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              R    + +  L   + RV+   F  G     T E+   +  + + ++ ++++  ++ 
Sbjct: 176 LEDRLALAQAMEKLDELQRRVISALFFRG----LTQEQTAAELGLNQRKVSRVKSAGLKS 231

Query: 667 L 667
           L
Sbjct: 232 L 232


>gi|326942736|gb|AEA18632.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 248

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 62/260 (23%), Positives = 98/260 (37%), Gaps = 33/260 (12%)

Query: 408 KIRNEIKSISVETGISISEF-RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           K R+++K+      +S +EF +    +V     +    K + +E              + 
Sbjct: 3   KERDQVKAGVNVREMSDTEFMKKYGRLVHHCVWKRYAKKMKSIEH-------------DT 49

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DL Q G IGL+KA + FD   G KFSTYA+  +   I R+I D            
Sbjct: 50  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAIRDH--------QKV 101

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD---E 583
                V     ++  +      PEEIA  L   V  V   L       SL   +      
Sbjct: 102 KVQRSVYSIKGKILRQNLEYEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVHQSNGN 161

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L   +EDK A +  D +I    R       + L+ +E  VL M        + T +
Sbjct: 162 EELTLESMLEDKKAENVEDVSIN---RMVIQAFKSQLSHKEHIVLDMSL-----QNRTQQ 213

Query: 644 EVGKQFCVTRERIRQIEAKA 663
            +  +   ++ +I +I  K 
Sbjct: 214 NIANEVGCSQVQISRILTKI 233


>gi|224825766|ref|ZP_03698870.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601990|gb|EEG08169.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 230

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 47/215 (21%), Positives = 92/215 (42%), Gaps = 17/215 (7%)

Query: 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           + V        N  ++  D+ Q G + L++A  ++      +F+ YA+  V+ AI   + 
Sbjct: 27  KRVARQLNSQANGVIEREDMEQIGLMALLEALRRY-GEPDARFAGYAVLRVRGAILDELR 85

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
                   P  +R   H++    R ++ ++ REP+  E   +L +  E  R +L      
Sbjct: 86  RLDW---RPRALRQDAHRLRDGLRELTRRLGREPSEAEAVAQLGLSAEDYRALLVAE--- 139

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
                         +   IE  +  +P  S +Q   R T    L++L  RE+RV+++ + 
Sbjct: 140 ---NAEAMASFDELVAAGIEPIDDNTPEASVLQ---RRTLAAALSALDEREQRVIQLYYE 193

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                + +L+E+     +T  R+ QI   A++K+K
Sbjct: 194 F----ELSLKEIAAVLDLTEARVCQINKSALKKMK 224


>gi|330984057|gb|EGH82160.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 227

 Score = 70.6 bits (171), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 37/228 (16%), Positives = 88/228 (38%), Gaps = 14/228 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S  + ++ +ANL++   +   Y    +   D +QE  + L +A   +   +   F+ YA 
Sbjct: 4   SAHQHQLWQANLQVAARLVNDYCYNPVLSQDALQEAQLALWEATFNWQESMEGTFTHYAW 63

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +++ +   +   +         R++           + ++      E ++++  +   
Sbjct: 64  MHMRRKLLTYLTQTASDQPKL-SRRERQVLNELKKHLRAGELISCQLLEALSEETGITRF 122

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            + + L       S+             + IE +                T    +A+L 
Sbjct: 123 RLSQ-LVSYWYQNSITISACSFQAFEELEAIEPEPETDIS----------TLEEGIANLP 171

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ ++        +   TL ++  +F V+ ER+RQ+E+ AI+KL++
Sbjct: 172 EREKLIVLA--RHLQDPRATLADLATKFGVSIERVRQLESSAIKKLRN 217


>gi|187935345|ref|YP_001885383.1| sporulation sigma factor SigK [Clostridium botulinum B str. Eklund
           17B]
 gi|187723498|gb|ACD24719.1| RNA polymerase sigma-K factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 232

 Score = 70.6 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 88/241 (36%), Gaps = 58/241 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ SE    +  ++        AK  ++E NLRLV  + KKY+       +LI  G +GL
Sbjct: 31  LNESEEEEYLKRLK---DGDKTAKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD   G + +TYA   ++  I                       + R  ++  +
Sbjct: 88  IKAIDSFDSGKGTRLATYASRCIENEILM---------------------LFRNNKKQKS 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               + L+ PIG +   +   L D +   N  
Sbjct: 127 E-------------------------------VYLQDPIGVDKEGNEICLIDILSSDNDS 155

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                     +++   ++  SLT RE  +L MR+G+      T  E+     ++R  + +
Sbjct: 156 VLEKVESNLQIKDLYKKIKDSLTKRESTILIMRYGLIDGNRKTQREIAGTLGISRSYVSR 215

Query: 659 I 659
           I
Sbjct: 216 I 216


>gi|160880422|ref|YP_001559390.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160429088|gb|ABX42651.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 207

 Score = 70.6 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 89/236 (37%), Gaps = 49/236 (20%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           +    M+ + +    +A+  ++E NLRLV  + KKY     +  DLI  G IGL+K+ + 
Sbjct: 11  KEENEMLLQCKAGNKVARDTLIERNLRLVAHIVKKYNTPDRETDDLISIGTIGLIKSIDT 70

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   G + +TYA   +   +   +             R+           +   I  + 
Sbjct: 71  FDSTKGIRLATYASRCIDNELLMMLR------SGKKQAREVY---------LYEPIGSDK 115

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
              EI                                  +L D IE  +        IQ 
Sbjct: 116 EGNEI----------------------------------NLLDVIESTDEDIVDIFEIQE 141

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           N++   T +  +L  RE+ ++ MR+G+    + T  E+  +  ++R  + +IE KA
Sbjct: 142 NIKRLYTFLNTALNEREQEIIIMRYGLSGEKEITQREIADKLGISRSYVSRIEKKA 197


>gi|239934438|emb|CAR92473.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 202

 Score = 70.6 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 37/250 (14%), Positives = 72/250 (28%), Gaps = 49/250 (19%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     +    D++  G   L           P    GF+   E  +     D  +E   
Sbjct: 1   PRAMDEVFGLYDQVQAGQLRL-----------PSFVAGFYESDEPVTPP-VADVVEEATP 48

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +   + E D +  +     +  ++    E                             +V
Sbjct: 49  EVDDDAEDDTDDDSDTPAVEEVEIGPDAE-----------------------------QV 79

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               + +  +  ++  L+ +     +          L+E+L+  V  L +   +I+ L  
Sbjct: 80  RAHFEFLHSIRDQIAKLRGSKAPNPEL------LNGLREELLANVLKLRIIPKQIEDLTG 133

Query: 341 QLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            L  +  RI   E  +L L      + R  FL    G E D  W+       +      +
Sbjct: 134 LLRGVMDRIRQQEQVILDLCVNKADMPRKDFLRVFIGHETDVGWLETQVGAKKKH-STRL 192

Query: 400 ACEVDSILKI 409
               D I + 
Sbjct: 193 KQFTDDIRRA 202


>gi|323154963|gb|EFZ41155.1| RNA polymerase sigma factor rpoS domain protein [Escherichia coli
           EPECa14]
          Length = 148

 Score = 70.6 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 38/97 (39%), Positives = 59/97 (60%), Gaps = 3/97 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA W
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 148



 Score = 54.1 bits (128), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|312794136|ref|YP_004027059.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181276|gb|ADQ41446.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 219

 Score = 70.6 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 93/255 (36%), Gaps = 59/255 (23%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +         A+  ++E NLRLV  +AKKYT        D+I 
Sbjct: 9   SFPQPMSSEEEEMYLNKMW---EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIIS 65

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G IGL+KA E +      K STYA   ++  I   +      +                
Sbjct: 66  VGTIGLIKAIETYSKAKSTKLSTYAAKCIENEILMYLRQNKKFLS--------------- 110

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFI 592
                                                 +SLE PIG +       L D +
Sbjct: 111 -------------------------------------QLSLENPIGSDKDGNEITLMDVL 133

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ++          ++  ++    ++   L  RE++++ +R+G+    + T  EV     ++
Sbjct: 134 QNDQDDIDEQVNLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVANLLGIS 193

Query: 653 RERIRQIEAKAIRKL 667
           R  + +IE KA++KL
Sbjct: 194 RSYVSRIEKKALQKL 208


>gi|294673099|ref|YP_003573715.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
 gi|294472548|gb|ADE81937.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
          Length = 240

 Score = 70.6 bits (171), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 87/223 (39%), Gaps = 19/223 (8%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            ++ I     +++ E + +   +       + A+ +++EANLR V++ A       +   
Sbjct: 15  YLEQIENNQPLTMEEEQELGRRI---MAGDTTARNKLIEANLRFVLTCAIDMATPFVPIE 71

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  GN GL  AA +++      F +YA+  +++AI+ +I   +C+++ P  +      
Sbjct: 72  ELIAAGNYGLTIAAARYNPSFDNHFCSYAVHHIRRAISEAIRTWTCSVKTPNLLLGLQAC 131

Query: 532 VVRTARRMSNKIKREPT----------PEEIAKKLAMPVEGVRKVLKITKEP----ISLE 577
           +       ++                   E+ +      EG+R  L     P    + ++
Sbjct: 132 LSLDDCHDTDDDNWSRDLIDRIPAAPLSSEMLRDFEETKEGLRSFLSKWYYPSDVNLMMD 191

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
                 D   + D  +          AI A+LRE    +L  L
Sbjct: 192 LAQMVYDGYSVSDLAKKYGLPIRRMKAIIADLRE--KAILHQL 232


>gi|321116232|emb|CBN73497.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 175

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             ++S +     E L  L   + L   + D LVE++ +   +I   E  +++L      +
Sbjct: 98  HGRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARM 157

Query: 366 KRDVFLERHQGRELDPHW 383
            R  FL +    E +  W
Sbjct: 158 PRADFLRQFPNNETNLDW 175


>gi|160624897|gb|AAT11006.2| sigma 70 factor [Pseudomonas syringae pv. syringae]
          Length = 166

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 55/164 (33%), Gaps = 4/164 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVS 62

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 63  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 119

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
            E  +++L      + R  FL +  G E+D  W           
Sbjct: 120 QERAIMQLCVRDARMPRADFLRQFPGNEVDESWTDALAKGKSKY 163


>gi|89476477|gb|ABD73739.1| SigB [Staphylococcus aureus]
 gi|89476479|gb|ABD73740.1| SigB [Staphylococcus aureus]
 gi|89476485|gb|ABD73743.1| SigB [Staphylococcus aureus]
          Length = 147

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/128 (22%), Positives = 68/128 (53%), Gaps = 1/128 (0%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 4   QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 63

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 64  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 123

Query: 548 TPEEIAKK 555
           +  EIA +
Sbjct: 124 SISEIANR 131


>gi|321116196|emb|CBN73479.1| DNA-directed RNA polymerase subunit D [Pseudomonas stutzeri]
          Length = 176

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGI 365
             ++S +     E L  L   + L   + D LVE++ +   +I   E  +++L      +
Sbjct: 98  HGRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARM 157

Query: 366 KRDVFLERHQGRELDPHWV 384
            R  FL +    E +  W 
Sbjct: 158 PRADFLRQFPNNETNLDWA 176


>gi|154484272|ref|ZP_02026720.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
 gi|149734749|gb|EDM50666.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
          Length = 304

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/187 (24%), Positives = 90/187 (48%), Gaps = 4/187 (2%)

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA 460
              + +  I+  ++ +     +S  E   +   + K     +    ++VEANL LV  +A
Sbjct: 93  ESEEELSFIKMYMEEMEALPNLSKDEEADL---IDKLLAGDTSVSSKIVEANLSLVAKIA 149

Query: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           + +  +G+ F DLIQEGN+GLM A   +       F ++    ++ AI  ++  Q  + R
Sbjct: 150 ESHRGKGVNFGDLIQEGNVGLMLAVSDY-TESVGDFHSFISGRIEDAINNTVNVQINSDR 208

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           I  H+ DK++++    + +S K+ R P  +E+AK + +  +    +LK + + +S+    
Sbjct: 209 IGQHLADKLNRLDEVTKNLSEKLGRVPELDELAKAMNISKDEASILLKTSLDTLSVNEDT 268

Query: 581 GDEDTSH 587
              D S 
Sbjct: 269 QITDGSE 275



 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/132 (15%), Positives = 54/132 (40%), Gaps = 1/132 (0%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
            +VT++++  +         Q +     L+   + V       +   ++D+ + ++  + 
Sbjct: 23  NHVTMDDVKLYFKDLIDDDSQYQFIYDYLALNKVEVEGFTPPANNPLADDAPETSADKTI 82

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP 161
           S          ++      ++MY+ EM ++  LS++ E  +  ++ AG   + + + E+ 
Sbjct: 83  SETVSVSNHVESEEELSF-IKMYMEEMEALPNLSKDEEADLIDKLLAGDTSVSSKIVEAN 141

Query: 162 LTFQALIIWRDE 173
           L+  A I     
Sbjct: 142 LSLVAKIAESHR 153


>gi|320181954|gb|EFW56860.1| RNA polymerase sigma factor RpoH [Shigella boydii ATCC 9905]
          Length = 186

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 86/184 (46%), Gaps = 12/184 (6%)

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVH--MRDKIHKVVRTARRMSNKIKREPTPEE 551
            +  ++A+ W+K  I   +      +++      R     + +T +R+    + E   E 
Sbjct: 1   MRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDE--VEM 58

Query: 552 IAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSH-LGDFIEDKNAVSPLDSAIQANL 609
           +A++L +  + VR++  ++  + ++ +    D+  S  +   +  ++  S     I+ + 
Sbjct: 59  VARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDN 118

Query: 610 RET-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            E       T  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER+RQ+E  A+
Sbjct: 119 WEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAM 177

Query: 665 RKLK 668
           +KL+
Sbjct: 178 KKLR 181


>gi|221271594|dbj|BAH15085.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271596|dbj|BAH15086.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271598|dbj|BAH15087.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271602|dbj|BAH15089.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271604|dbj|BAH15090.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271610|dbj|BAH15093.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271612|dbj|BAH15094.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271614|dbj|BAH15095.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271618|dbj|BAH15097.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271622|dbj|BAH15099.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271626|dbj|BAH15101.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271630|dbj|BAH15103.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271634|dbj|BAH15105.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271636|dbj|BAH15106.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 1/90 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + +         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRHNKAAVAELLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           + R  FL +  G E+D  W           
Sbjct: 148 MPRADFLRQFPGNEVDESWSDALAKGKSKY 177


>gi|77020162|ref|YP_338218.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
 gi|85701416|ref|YP_460001.1| putative RNA polymerase sigma subunit [Bacillus phage WBeta]
 gi|89152515|ref|YP_512346.1| sigma70 factor [Bacillus phage Fah]
 gi|196033415|ref|ZP_03100827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus cereus
           W]
 gi|76445738|gb|ABA42728.1| sigma70 factor [Bacillus phage Fah]
 gi|76564064|gb|ABA46452.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
 gi|83658652|gb|ABC40436.1| putative RNA polymerase sigma subunit [Bacillus phage WBeta]
 gi|83658705|gb|ABC40488.1| putative RNA polymerase sigma subunit [Bacillus phage Gamma isolate
           d'Herelle]
 gi|195993849|gb|EDX57805.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus cereus
           W]
          Length = 248

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 94/245 (38%), Gaps = 28/245 (11%)

Query: 446 KEMVEANLRLVISVAK-KY--------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E +E   RLV      +Y         + GL   DL Q G IGL+KA + FD   G  F
Sbjct: 20  DEFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFGMIGLIKARDNFDLEFGCAF 79

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA+  +   I R+I D                 V     ++ N+   +  PEEIA  L
Sbjct: 80  STYAVPKIIGEIGRAIRDN--------QKIKVQRTVYGVKGKILNQQLADKEPEEIADIL 131

Query: 557 AMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              V  V+  L+      SL   +      +   L   IED       ++ I    R   
Sbjct: 132 DESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTEDIEETTIN---RAVI 188

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
               A+L P+E  VL MR       + T + +  Q   ++ +I +I AK  ++     + 
Sbjct: 189 REFKAALPPKEYIVLDMRL-----QNMTQQNIANQMGYSQVQISRILAKINQRAAQFGKE 243

Query: 674 KKLRS 678
             L+ 
Sbjct: 244 GGLQD 248


>gi|237753387|ref|ZP_04583867.1| flagellar biosynthesis sigma factor [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375654|gb|EEO25745.1| flagellar biosynthesis sigma factor [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 234

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 88/209 (42%), Gaps = 18/209 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           + F DLI  G   L+K A K+D  L   F  YA   V+ A+   +        +  +MR 
Sbjct: 42  VDFSDLISIGTEELIKLARKYDNSLNDSFWGYARPRVQGAMLDYLRSLD---PLSRNMRT 98

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            + ++ +      N+ + EP    ++K L    E +++    ++    L           
Sbjct: 99  LVKRIEKEIAIYYNEHQEEPDNAYLSKLLGENEEKIKEARMASEIYSVL----------P 148

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D + ++   + L+S  +  L     ++L   TP E+ V+++ +      + + +E+ +
Sbjct: 149 IDDQLGEQKEGT-LESIEKEELISVILQILEHATPNEQLVVQLYY----YEELSFKEISQ 203

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              V+  R+ Q+    IR+++     + L
Sbjct: 204 VLEVSEARVSQLHRAVIRRVRQYLEERGL 232


>gi|269792906|ref|YP_003317810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269100541|gb|ACZ19528.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 187

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 82/238 (34%), Gaps = 72/238 (30%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++  +       A++E++ A   +V  +A++  NR   + D++QEG +GL++A + FD  
Sbjct: 15  ALWARLAQGDQEAREELILAYRPMVFWLARRLGNR--AYQDVVQEGMLGLLEAVDNFDPS 72

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G++FSTYA + ++  +                                           
Sbjct: 73  RGHRFSTYAYYRIRGRMINF---------------------------------------- 92

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                   +  V     I  E   LE     ED     D+  D                 
Sbjct: 93  --------LSRVEGSSPIPVEDQVLEELGPWEDGFSRLDWTMD----------------- 127

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                L +L+ RE  V+R         D +  E+ ++  +    I +I  +A+ KL+ 
Sbjct: 128 -LQLALGALSEREADVVRSLVL----EDMSARELAEEKGLDVSYIHKIRRRALAKLRE 180


>gi|254459039|ref|ZP_05072462.1| sigma 28 [Campylobacterales bacterium GD 1]
 gi|207084310|gb|EDZ61599.1| sigma 28 [Campylobacterales bacterium GD 1]
          Length = 227

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 86/241 (35%), Gaps = 20/241 (8%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFD 489
           M+     +    + E+    L  V ++A +   R    + ++DL   G   L+K A ++D
Sbjct: 1   MISAYTQDIKHKEDELAIQYLPAVKAMAFRLKERLPSSIDYMDLSAIGTEELIKLARRYD 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             L   F  YA   V  A+   +        +    R  +  +           + EPT 
Sbjct: 61  EKLNDSFWGYAKKRVYGAMLDYLRSLD---ILSRASRKLVKAIDYAVEEHRLTHEEEPTD 117

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            E+A  L    E V +    +                 L D ++  +  + L    +  L
Sbjct: 118 AELALILGESEEKVHEARIASTIYT----------VMPLHDQLQVGDEGAALALIEKEEL 167

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                +VL+    RE+ +++  +      +  L+E+ +   +T  RI QI    I K+K 
Sbjct: 168 IAVIKKVLSGYNEREQLIIQFYYF----EELNLKEISEILDITESRISQIHKSVIHKIKE 223

Query: 670 P 670
            
Sbjct: 224 S 224


>gi|239934458|emb|CAR92483.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 197

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 50/129 (38%), Gaps = 3/129 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNGQ-KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +E A+ +  ++   +       +  ++S   +    +L  L   L L   + D LV +  
Sbjct: 70  EEAAKRFNAIQKQNEKTKRAIARYGRNSESTEQHLAELGDLFKYLKLIPKQYDPLVARAR 129

Query: 344 DISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACE 402
              + +  +E  ++ L      + R  F+E   G E +  W +      +  +   +   
Sbjct: 130 AALQEVRRHERAIMMLCIRQAKMPRKEFVESFPGNETNDKW-ALNLSRRKQPYAPAIKNL 188

Query: 403 VDSILKIRN 411
           +D I++++ 
Sbjct: 189 LDDIIRVQE 197


>gi|221271600|dbj|BAH15088.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271638|dbj|BAH15107.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271646|dbj|BAH15111.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271650|dbj|BAH15113.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
 gi|221271656|dbj|BAH15116.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 2/97 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + +         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRHNKAAIAELLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           + R  FL +  G E+D  W   A    + ++   +A 
Sbjct: 148 MPRADFLRQFPGNEVDESWSD-ALAKGKSKYAEAIAR 183


>gi|221271632|dbj|BAH15104.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 1/90 (1%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + +         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRYNKAAIAELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
           + R  FL +  G E+D  W           
Sbjct: 148 MPRADFLRQFPGNEVDESWSDALAKGKSKY 177


>gi|220932606|ref|YP_002509514.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
 gi|219993916|gb|ACL70519.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
          Length = 209

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/272 (14%), Positives = 96/272 (35%), Gaps = 64/272 (23%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           I + +K +     +   E + +   ++  +   + A++ ++ +   LV  + ++Y     
Sbjct: 2   INDYLKQLGKIKILEAEEEKEL--WIKYKDYNDTEARQRLITSYQPLVFKIVRQYARDNE 59

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             +DLIQEG +GL+ A + +D   G  FS+YA+++++  +   +                
Sbjct: 60  VVMDLIQEGTLGLIDAIDSYDHKRGKSFSSYALYYIRGRVINYLKKAPACSIPA------ 113

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
             ++         ++  E                                          
Sbjct: 114 --ELRAAGSEFLEQLVTE------------------------------------------ 129

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD +ED           +  + +   + + SL  RE  ++R  +      D   ++V  +
Sbjct: 130 GDDLED--------RVEKNLVMDRIKKAVGSLPSREGYIIREIYL----KDKKPKKVAGE 177

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             ++   + +++ KA+R+L+        R  L
Sbjct: 178 MGISLSYLHRLKKKAVRRLRGKLSWSVYRGLL 209


>gi|152990367|ref|YP_001356089.1| RNA polymerase sigma factor for flagellar operon [Nitratiruptor sp.
           SB155-2]
 gi|151422228|dbj|BAF69732.1| RNA polymerase sigma factor for flagellar operon [Nitratiruptor sp.
           SB155-2]
          Length = 211

 Score = 70.3 bits (170), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 94/229 (41%), Gaps = 38/229 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           K+++V  NL LV  VA K   +      ++F +L+  G IGL KA EK++     +FSTY
Sbjct: 8   KQQIVLDNLALVKKVASKIYFKLPKDANIEFDELVNTGTIGLYKAIEKYNRDKA-QFSTY 66

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A   ++  I   +       R       K  +  +    +SN              + M 
Sbjct: 67  AYIKIRGEILDYLRSLHIVPRTMREKIKKEKEEGQKEIPLSN------------LAIMMS 114

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +E                     E+   L D +   N  SP D AI + + +     L S
Sbjct: 115 MEK---------------ALGESENGPRLMDILI-SNEKSPEDYAISSEIHDKIVEALDS 158

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+  E + L+M +      +   +E+ +   +++ R+ QI++KAI KLK
Sbjct: 159 LSESERKTLQMLYF----EEREPKEISQILGISQSRVSQIKSKAIVKLK 203


>gi|283780334|ref|YP_003371089.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283438787|gb|ADB17229.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 556

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM-NTDHTLEEVGKQFCVT 652
           D  +       +Q   +    ++L  L  RE++++  RFG+   +   TL+EVG +  VT
Sbjct: 468 DNRSDQLGLEHVQQQRQLQVEKILEKLDEREQKIIISRFGLDHSHEPLTLKEVGHELGVT 527

Query: 653 RERIRQIEAKAIRKLKHPS 671
           +ER+RQIEA+A+ KL+  +
Sbjct: 528 KERVRQIEARALNKLREAA 546



 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/101 (35%), Positives = 58/101 (57%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +     EA   K  +V+ANLRLV+S+AK++ N    F  L+ +GN+ L++AAEKFD+  G
Sbjct: 367 IEHLYEEAVAVKNSIVQANLRLVVSIAKRHVNGSEDFFGLVSDGNMSLIRAAEKFDFSRG 426

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
            KFSTYA W + +   R+I ++          +D++    +
Sbjct: 427 NKFSTYASWAIMKNFARTIPEEFKHRDRFRTSQDELFVAKQ 467


>gi|150015999|ref|YP_001308253.1| sporulation sigma factor SigK [Clostridium beijerinckii NCIMB 8052]
 gi|149902464|gb|ABR33297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 232

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 87/239 (36%), Gaps = 55/239 (23%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
             +       ++K +     AK  ++E NLRLV  + KKY+       +LI  G +GL+K
Sbjct: 30  PLDETEEQMYLKKFKEGDKNAKSILIERNLRLVAHIVKKYSFPNKDVDELISIGTVGLIK 89

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A + FD   G + +TYA   ++  I                       + R +++  ++ 
Sbjct: 90  AIDSFDAGKGTRLATYASRCIENEILM---------------------LFRNSKKQKSE- 127

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSP 600
                                         + L+ PIG +   +   L D +  +     
Sbjct: 128 ------------------------------VYLQDPIGVDKEGNEFCLMDILSSEKDSVL 157

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                   +R    +++ SLT RE  ++ MR+G+      T  E+     ++R  + +I
Sbjct: 158 EKVESNLQVRALYKKLIESLTKRESAIIIMRYGLIDGKCKTQREIAVNLGISRSYVSRI 216


>gi|255039934|gb|ACT99724.1| putative sporulation sigma factor [Bacillus phage Wip4]
          Length = 248

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 96/268 (35%), Gaps = 31/268 (11%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K I    G+S  EF      +         AKK     +               L   DL
Sbjct: 9   KEIVDVRGMSDDEFMEKYERLVHHCVWKRYAKKRPAIEHD------------TNLDIEDL 56

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            Q G IGL+KA + F+   G  FSTYA+  +   I R+I D                 V 
Sbjct: 57  TQFGMIGLIKARDNFNPEFGCAFSTYAVPKIIGEIGRAIRDN--------QKVKVQRSVY 108

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGD 590
               ++ N+   +  PEEIA  L  PV  V+  LK      SL   +      +   L  
Sbjct: 109 SVKGKILNQQLSDKGPEEIADILNEPVTLVKMALKYQPSTDSLNKVVYASGSNEDVTLEK 168

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            +ED       ++ I    R       A+L P+E  VL M        + T + +  Q  
Sbjct: 169 MLEDTKVEDIEETTIN---RAVIREFKAALAPKEYIVLDMHL-----QNMTQQNIANQMG 220

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            ++ +I +I AK  ++     +   L+ 
Sbjct: 221 YSQVQISRILAKINQRAAQFGKEGGLQD 248


>gi|295399263|ref|ZP_06809245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978729|gb|EFG54325.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 155

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/111 (28%), Positives = 54/111 (48%), Gaps = 3/111 (2%)

Query: 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
           +  ++ + + IK+ +    +S  E    + ++ K       A+  ++E NLRLV  + KK
Sbjct: 12  IKELMFLVSYIKNNAFPQPLSAKEEEKYLQLMAK---GDEQARNILIEHNLRLVAHIVKK 68

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           + N G    DLI  G IGL+KA E +    G K +TYA   ++  I   + 
Sbjct: 69  FENTGEDVEDLISIGTIGLIKAIESYSSNKGTKLATYAARCIENEILMHLR 119


>gi|89476431|gb|ABD73716.1| SigB [Staphylococcus aureus]
 gi|89476433|gb|ABD73717.1| SigB [Staphylococcus aureus]
 gi|89476435|gb|ABD73718.1| SigB [Staphylococcus aureus]
 gi|89476437|gb|ABD73719.1| SigB [Staphylococcus aureus]
 gi|89476439|gb|ABD73720.1| SigB [Staphylococcus aureus]
 gi|89476441|gb|ABD73721.1| SigB [Staphylococcus aureus]
 gi|89476443|gb|ABD73722.1| SigB [Staphylococcus aureus]
 gi|89476445|gb|ABD73723.1| SigB [Staphylococcus aureus]
 gi|89476447|gb|ABD73724.1| SigB [Staphylococcus aureus]
 gi|89476449|gb|ABD73725.1| SigB [Staphylococcus aureus]
 gi|89476451|gb|ABD73726.1| SigB [Staphylococcus aureus]
 gi|89476453|gb|ABD73727.1| SigB [Staphylococcus aureus]
 gi|89476455|gb|ABD73728.1| SigB [Staphylococcus aureus]
 gi|89476457|gb|ABD73729.1| SigB [Staphylococcus aureus]
 gi|89476459|gb|ABD73730.1| SigB [Staphylococcus aureus]
 gi|89476461|gb|ABD73731.1| SigB [Staphylococcus aureus]
 gi|89476463|gb|ABD73732.1| SigB [Staphylococcus aureus]
 gi|89476465|gb|ABD73733.1| SigB [Staphylococcus aureus]
 gi|89476467|gb|ABD73734.1| SigB [Staphylococcus aureus]
 gi|89476469|gb|ABD73735.1| SigB [Staphylococcus aureus]
 gi|89476471|gb|ABD73736.1| SigB [Staphylococcus aureus]
 gi|89476473|gb|ABD73737.1| SigB [Staphylococcus aureus]
 gi|89476475|gb|ABD73738.1| SigB [Staphylococcus aureus]
 gi|89476481|gb|ABD73741.1| SigB [Staphylococcus aureus]
 gi|89476483|gb|ABD73742.1| SigB [Staphylococcus aureus]
 gi|89476487|gb|ABD73744.1| SigB [Staphylococcus aureus]
          Length = 147

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/128 (22%), Positives = 68/128 (53%), Gaps = 1/128 (0%)

Query: 429 HIVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
            I   +++ +    + A+ ++V+   +L+ S+A KY+       DL+Q G +GL+ A  +
Sbjct: 4   QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINR 63

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD     KF  + +  V   I R + D++ ++ +P  +++   ++ + +  ++ +++R P
Sbjct: 64  FDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSP 123

Query: 548 TPEEIAKK 555
           +  EIA +
Sbjct: 124 SISEIADR 131


>gi|160944734|ref|ZP_02091961.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443918|gb|EDP20922.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 47/200 (23%), Positives = 70/200 (35%), Gaps = 38/200 (19%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DL Q GN+GL KA  KFD   G KF TYA   +  A+   + D             
Sbjct: 51  LDTDDLKQAGNMGLWKAVPKFDAARGMKFLTYAAPAIHNAMMDMVRD------------- 97

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                         ++  E                      I  + +SL+  +  E+   
Sbjct: 98  -------AFTAFEQRMVTE------------------DKDGICYQRVSLDDVLPGEEQLR 132

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             + I D  A+ P     +   R      L  LT RE+  L  R+G     +H L     
Sbjct: 133 RIEAIADPYAMQPQTIMEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAI 192

Query: 648 QFCVTRERIRQIEAKAIRKL 667
            F +T+ R ++ E +A+  L
Sbjct: 193 YFHLTKGRAKKTEEQAMDNL 212


>gi|157165349|ref|YP_001467213.1| flagellar biosynthesis sigma factor [Campylobacter concisus 13826]
 gi|112799934|gb|EAT97278.1| flagellar biosynthesis sigma factor FliA [Campylobacter concisus
           13826]
          Length = 234

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/229 (15%), Positives = 86/229 (37%), Gaps = 20/229 (8%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V   +  + ++A +   R    +   DLI  G   ++K + K+D      F  Y  
Sbjct: 20  QDEIVLKYMPALRAMAFRLKERLPSSIDVNDLISVGVEEMIKLSRKYDKEQNDSFWGYGK 79

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +  ++   +        +    R  +  +        N  + EP+ E +A+KL   +E
Sbjct: 80  KRIYGSMLDYLRALD---VVSRSDRKLVKSINTEIDNYFNTHEEEPSDEYLAEKLNEDIE 136

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +R+   ++     L           + + +E         S  + +L       L    
Sbjct: 137 KIREARGVSGIITIL----------PIDEQMELIGQSDVEKSVEKEDLILKIESALKDFD 186

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            R++ ++++ +      +  L+E+ +   ++  RI QI  + + +++  
Sbjct: 187 ERDQMIVQLYY----YEELNLKEISEIMNISESRISQIHKRLLDRIRRS 231


>gi|293392778|ref|ZP_06637096.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424637|gb|EFE97848.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 119

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/111 (28%), Positives = 64/111 (57%)

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +L++ +   S++TP+G +    L D + D+    P D+    +++++  + L  L  ++ 
Sbjct: 1   MLRLNERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQR 60

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   + + L
Sbjct: 61  EVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQMQGL 111


>gi|160624899|gb|AAT11015.2| sigma 70 factor [Pseudomonas syringae pv. tomato]
          Length = 166

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 55/164 (33%), Gaps = 4/164 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVS 62

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 63  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 119

Query: 352 NEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGE 394
            E  +++L      + R  FL +  G E+D  W           
Sbjct: 120 QERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDGLAKGKGKY 163


>gi|283784102|ref|YP_003363967.1| lateral flagellar sigma factor 28 protein [Citrobacter rodentium
           ICC168]
 gi|282947556|emb|CBG87109.1| lateral flagellar sigma factor 28 protein [Citrobacter rodentium
           ICC168]
          Length = 238

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/202 (21%), Positives = 83/202 (41%), Gaps = 18/202 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   D+ Q   +GL+ A  ++       F+ YA+  ++ AI   +       R+   +R 
Sbjct: 48  IDRQDMEQTALLGLLNAIRRYGMP-DEGFAGYAIHRIRGAILDELRSLDWRPRL---LRQ 103

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTS 586
           K H++    R M  ++ REP  +E+++    P + +  + L+  +   SL+  +  E   
Sbjct: 104 KYHQIKDLIRDMRKQLGREPEWQELSQTGLTPEDYLEFQQLEGAETLASLDELLSGEGHG 163

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
            L                 Q   +E  +  L  L+ +E  VL M +      D  L+E+ 
Sbjct: 164 AL---------PEGRGLEEQFVNQEMLSYALGQLSEKEGLVLSMYYQH----DMNLKEIA 210

Query: 647 KQFCVTRERIRQIEAKAIRKLK 668
               +T  RI Q+  K  +K++
Sbjct: 211 LVLGLTEARICQMNKKITQKIR 232


>gi|331645434|ref|ZP_08346538.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli M605]
 gi|331045596|gb|EGI17722.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli M605]
          Length = 238

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 96/245 (39%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF   + +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAATLVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP  +E+A++     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWQELAEEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFVTQQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|212638647|ref|YP_002315167.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
 gi|212560127|gb|ACJ33182.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
          Length = 129

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/126 (26%), Positives = 58/126 (46%), Gaps = 3/126 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +  ++ + + +K+ +    +   E    +  + K       A+ +++E NLRLV 
Sbjct: 7   ALALFIKELVFLVSYVKNNAFPQPLDAKEEAMYLKQMAK---GDENARNKLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I  +I     
Sbjct: 64  HIVKKFENTGEDPEDLISIGTIGLIKAIESYSTGKGTKLATYAARCIENEIFMTIVCVIK 123

Query: 518 TIRIPV 523
             +  V
Sbjct: 124 CKKNAV 129


>gi|218132856|ref|ZP_03461660.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991729|gb|EEC57733.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
          Length = 205

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 87/241 (36%), Gaps = 52/241 (21%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E +  +   +K       A+ +++E N+RLV  + KKY        DL+  G IGL
Sbjct: 15  LSSEEEKIYL---KKCREGDLEARNKLIEKNMRLVAHIVKKYACADRDTEDLLSVGTIGL 71

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA   FD     + +TYA   +   +   +       R                     
Sbjct: 72  IKAVNTFDMNKSIRLATYAAKCIDNELLMLLRSDRRKSREI------------------- 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                     I + +    EG                     +  +L + I         
Sbjct: 113 ---------SIYEPVGKDKEG---------------------NEINLIEIIGTSEDTVVE 142

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D  ++ ++++  + V   LT RE  ++ MR+G+    + T  E+ ++  ++R  + +IE 
Sbjct: 143 DYELRQDVKKLYSAVEKKLTDREREIIIMRYGLYGTQEITQREIAQKMNISRSYVSRIEK 202

Query: 662 K 662
           K
Sbjct: 203 K 203


>gi|51597620|ref|YP_071811.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|51590902|emb|CAH22558.1| Putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
          Length = 231

 Score = 69.9 bits (169), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 106/247 (42%), Gaps = 19/247 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   EF   +++    E +   A   +V+  +R +   A     +     D+ Q   +GL
Sbjct: 1   MENREFEACLTLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGK----EDMQQIALMGL 56

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK     R+++ 
Sbjct: 57  LEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDW---RPRRLRQKTHKTNEAIRQIAK 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++  EP  EEI+ +L +  +  ++ L        LE     E    +       + +   
Sbjct: 113 RLGHEPNFEEISAELNLTADEYQEYLL-------LENAGAMESLDEILALDAHNDILQSR 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D      + +   + +++L  RE+ +L + +      + +++E+ +   +T  RI Q+  
Sbjct: 166 DLEENIIIEDNLKQAISALDEREQMILHLYYQ----QELSMKEIAQVLDLTEARICQLNK 221

Query: 662 KAIRKLK 668
           K ++K+K
Sbjct: 222 KLVQKIK 228


>gi|295101345|emb|CBK98890.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 69.9 bits (169), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 83/244 (34%), Gaps = 46/244 (18%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKK-YTNRGL-------QFLDLIQEGNIGLMK 483
            +    +   + A   +++ N   +  VA   + +  L          DL Q GN+GL K
Sbjct: 7   RLCALAQKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWK 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  KFD   G KF TYA   ++ A+   + D                           ++
Sbjct: 67  AVPKFDAARGMKFLTYAAPAIRNAMMDMVRD--------------------AFAAFEQRM 106

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E                      I  + +SL+  +  E+     + I D  A+ P   
Sbjct: 107 VTE------------------DKDGICYQRVSLDDVLPGEEQLQRIEAIADPYAMQPQSI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 R      L  LT RE+  L  R+G     +H L      F +T+ R ++ E +A
Sbjct: 149 MEDQESRRELYDGLKRLTQREQTYLLYRYGFTDGKEHPLIGTAIYFHLTKGRAQKTEEQA 208

Query: 664 IRKL 667
           +  L
Sbjct: 209 MDNL 212


>gi|160943408|ref|ZP_02090642.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445268|gb|EDP22271.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 69.9 bits (169), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 47/200 (23%), Positives = 71/200 (35%), Gaps = 38/200 (19%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           L   DL Q GN+GL KA  KFD   G KF TYA   ++ A+   + D             
Sbjct: 51  LDTDDLKQAGNLGLWKAVPKFDAAQGMKFLTYAAPAIRNAMVDMVRD------------- 97

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
                         ++  E                      I  + +SL+  +  E+   
Sbjct: 98  -------AFAAFEQRMVTE------------------DKDGICYQRVSLDDVLPGEEQLR 132

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             + I D  A+ P     +   R      L  LT RE+  L  R+G     +H L     
Sbjct: 133 RIEAIADPYAMQPQSIMEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAI 192

Query: 648 QFCVTRERIRQIEAKAIRKL 667
            F +T+ R ++ E +A+  L
Sbjct: 193 YFHLTKGRAKKTEEQAMDNL 212


>gi|254519270|ref|ZP_05131326.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
 gi|226913019|gb|EEH98220.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
          Length = 231

 Score = 69.9 bits (169), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 87/241 (36%), Gaps = 58/241 (24%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E    + +++        AK  ++E NLRLV  + KKY        +LI  G +GL
Sbjct: 31  LDEEEEEQYLKLLK---NGDKEAKSILIERNLRLVAHIVKKYNFPNKDIDELISIGTVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD   G + +TYA   ++  I                       + R  ++  N
Sbjct: 88  IKAIDSFDASKGTRLATYASRCIENEILM---------------------LFRNNKKQKN 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               + L+ PIG +   +   L D +  +   
Sbjct: 127 E-------------------------------VYLQDPIGVDKEGNEICLIDVLSSEKDS 155

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                     +++   ++  SL+ RE  +++MR+G+      T  E+     ++R  + +
Sbjct: 156 VLEKVESNLQIKQLYNKICVSLSEREGEIVKMRYGLIDGRCRTQREIAALLGISRSYVSR 215

Query: 659 I 659
           I
Sbjct: 216 I 216


>gi|221271620|dbj|BAH15098.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 184

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YG 364
           K  + +         L +L   + L   + + LVE++     R+   E  +++L      
Sbjct: 88  KHGRHNKAAIAELLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDAR 147

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
           + R  FL +  G E+D  W        + ++   +A 
Sbjct: 148 MPRADFLRQFPGNEVDESWSDSLAK-GKSKYAEAIAR 183


>gi|167767366|ref|ZP_02439419.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|317497448|ref|ZP_07955768.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
 gi|167711341|gb|EDS21920.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|316895234|gb|EFV17396.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
          Length = 207

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 98/257 (38%), Gaps = 52/257 (20%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
                +   E RH + + R+G+     A+  +VE NLRLV  + KKY N   +  D+I  
Sbjct: 3   EFLQPLLPEEERHYLILSRQGDMN---ARNLLVEHNLRLVAHIVKKYHNLDREKEDMISI 59

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL+KA   +D   G++  TYA   ++  +   +  +  T +                
Sbjct: 60  GVIGLIKAINTYDISKGHRLVTYAARCIENELLMMLRQEKKTSKNT-------------- 105

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                          + + + +  EG                     +  HL D +  + 
Sbjct: 106 --------------SLYEPIGIDKEG---------------------NEIHLLDILGTQE 130

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                    + N++     +      +E++ L MR+G+      T +EV K+  ++R  +
Sbjct: 131 TDLIKKIEQKENIKRIYEELEKMEMNKEKKTLIMRYGLYGREPMTQKEVAKKLHISRSYV 190

Query: 657 RQIEAKAIRKLKHPSRS 673
            +IE KA+  LK   ++
Sbjct: 191 SRIEKKALMLLKSKIKT 207


>gi|45442811|ref|NP_994350.1| flagellar biosynthesis sigma factor [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108809036|ref|YP_652952.1| flagellar biosynthesis sigma factor [Yersinia pestis Antiqua]
 gi|150260230|ref|ZP_01916958.1| lateral flagellar sigma factor 28 protein [Yersinia pestis
           CA88-4125]
 gi|162420360|ref|YP_001604825.1| flagellar biosynthesis sigma factor [Yersinia pestis Angola]
 gi|165925029|ref|ZP_02220861.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165939031|ref|ZP_02227583.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|166008912|ref|ZP_02229810.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166212025|ref|ZP_02238060.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167398583|ref|ZP_02304107.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167418724|ref|ZP_02310477.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167466317|ref|ZP_02331021.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis FV-1]
 gi|218927931|ref|YP_002345806.1| flagellar biosynthesis sigma factor [Yersinia pestis CO92]
 gi|229837430|ref|ZP_04457593.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides A]
 gi|229840642|ref|ZP_04460801.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229842806|ref|ZP_04462958.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|294502807|ref|YP_003566869.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|45437677|gb|AAS63227.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis biovar Microtus str. 91001]
 gi|108780949|gb|ABG15007.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis Antiqua]
 gi|115346542|emb|CAL19419.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis CO92]
 gi|149289638|gb|EDM39715.1| lateral flagellar sigma factor 28 protein [Yersinia pestis
           CA88-4125]
 gi|162353175|gb|ABX87123.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis Angola]
 gi|165912987|gb|EDR31612.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|165923229|gb|EDR40380.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165992251|gb|EDR44552.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166206771|gb|EDR51251.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|166962718|gb|EDR58739.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167051087|gb|EDR62495.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|229690073|gb|EEO82130.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229697008|gb|EEO87055.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229705553|gb|EEO91563.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides A]
 gi|262360839|gb|ACY57560.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D106004]
 gi|262364784|gb|ACY61341.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D182038]
 gi|294353266|gb|ADE63607.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
          Length = 231

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 107/247 (43%), Gaps = 19/247 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   EF   +++  + E +   A   +V+  +R +   A     +     D+ Q   +GL
Sbjct: 1   MENREFEACLTLTAEEEGKYLNAYLPLVKRIVRQLSFQADSVIGK----EDMQQIALMGL 56

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK     R+++ 
Sbjct: 57  LEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDW---RPRRLRQKTHKTNEAIRQIAK 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++  EP  EEI+ +L +  +  ++ L        LE     E    +       + +   
Sbjct: 113 RLGHEPNFEEISAELNLTADEYQEYLL-------LENAGAMESLDEILALEAHNDILQSR 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D      + +   + +++L  RE+ +L + +      + +++E+ +   +T  RI Q+  
Sbjct: 166 DLEENIIIEDNLKQAISTLDEREQMILHLYYQ----QELSMKEIAQVLDLTEARICQLNK 221

Query: 662 KAIRKLK 668
           K ++K+K
Sbjct: 222 KLVQKIK 228


>gi|225174918|ref|ZP_03728915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169558|gb|EEG78355.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 231

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 50/223 (22%), Positives = 94/223 (42%), Gaps = 24/223 (10%)

Query: 447 EMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
            +VEA   L+   A+ YT   G      +Q G  GLMKA ++++   G  F+TYA   V 
Sbjct: 25  RVVEAGRSLIHHFARLYTGGFGEDA---VQAGMEGLMKAVQRYEVGKGTAFATYAAHCVM 81

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
             I   +  +S   R P  ++D   +V R    +  +    P   EIAK+L +  EGV +
Sbjct: 82  GEIRHYVRKESSYYR-PGSIKDLQFRVARLVDEVLKETGEPPGVSEIAKRLNVKEEGVVQ 140

Query: 566 VLKITKEPISLETPIGDEDTSHLGDFIEDK-NAVSPLDSAIQANLRETTTRVLASLTPRE 624
            ++     +SL+            D   DK  A       +    R    + +  L   +
Sbjct: 141 AMRAGL--VSLD------------DVEVDKIRAEKYETFKLPIEDRLVLEQAIKKLNDLQ 186

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RV+     +    D T  +  ++  +++ ++ ++  K+++++
Sbjct: 187 RRVV----YLLFYKDLTQTQTAEKLGISQRKVSRVLHKSLQEM 225


>gi|313116074|ref|ZP_07801498.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310621671|gb|EFQ05202.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 221

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 82/244 (33%), Gaps = 46/244 (18%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKK-YTNR-------GLQFLDLIQEGNIGLMK 483
            +    +   + A   ++E N   +  VA   + +         L   DL Q GN+G  K
Sbjct: 7   RLCALAQKGDATALDSLIENNKSFIGKVANDLFRSMDLAQSGLNLDTDDLKQAGNLGFWK 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  KFD   G KF TYA   ++ A+   + D                           ++
Sbjct: 67  AVPKFDAARGMKFLTYAAPAIRNAMMDMVRD--------------------AFAAFEQRM 106

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
             E                      I  + +SL   +  E+     + I D  A+ P   
Sbjct: 107 VTE------------------DKDGICYQRVSLNDVLPGEEQLRRIEAIADPYAMQPQSI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   R      L  LT RE+  L  R+G     +H L      F +T+ R ++ E +A
Sbjct: 149 MEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAQKTEEQA 208

Query: 664 IRKL 667
           +  L
Sbjct: 209 MDNL 212


>gi|258624678|ref|ZP_05719613.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM603]
 gi|258583070|gb|EEW07884.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM603]
          Length = 242

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 42/227 (18%), Positives = 89/227 (39%), Gaps = 21/227 (9%)

Query: 446 KEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++++ +  +V  V  +   +        D+ Q G I L++A  ++       F T+A+ 
Sbjct: 26  NQLLQRHKIMVKRVVNQLKVHATAYCSIDDMQQIGLIALIEAGRRYGDISDPNFPTFAVC 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+ AI   +       R       +++ + R    +   + R+PT  E  K L    + 
Sbjct: 86  RVRGAILDELRRLDWRSRKTRQQAHELNDITR---DLIRALGRQPTDAETIKALGTNEQD 142

Query: 563 V--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              R+   +  E  SL+  I +   + L             D     ++R +    L  L
Sbjct: 143 YYARQSAALAGELQSLDQLIENGVENQLS---------GHYDGLKHEHIRRSLETALNKL 193

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R++ +L + +      +  L E+     +T  RI Q+  +A+++L
Sbjct: 194 SKRDQLLLTLFYQH----ELNLNEIALILDLTSPRICQLHKQALKQL 236


>gi|182418995|ref|ZP_02950251.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
 gi|182377278|gb|EDT74846.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
          Length = 232

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 87/241 (36%), Gaps = 56/241 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + + E       ++K +     AK  ++E NLRLV  + KKY+       +LI  G +GL
Sbjct: 29  LPLDEEEE-QMYLKKFKEGDKSAKSILIERNLRLVAHIVKKYSFPNKDVDELISIGTVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD   G + +TYA   ++  I                       + R  ++  +
Sbjct: 88  IKAIDSFDSSKGTRLATYASRCIENEILM---------------------LFRNNKKQKS 126

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
           +                               + L+ PIG +   +   L D +  +   
Sbjct: 127 E-------------------------------VYLQDPIGVDKEGNEFCLMDILSSEKDS 155

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
                     +R    ++  SLT RE  +L MR+G+      T  E+     ++R  + +
Sbjct: 156 VLDKVESNLQVRALYKKLGESLTSRESSILIMRYGLIDGKCKTQREIASNLGISRSYVSR 215

Query: 659 I 659
           I
Sbjct: 216 I 216


>gi|171320713|ref|ZP_02909726.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Burkholderia
           ambifaria MEX-5]
 gi|171094040|gb|EDT39138.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Burkholderia
           ambifaria MEX-5]
          Length = 266

 Score = 69.5 bits (168), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 85/246 (34%), Gaps = 31/246 (12%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKK-YTNRG---LQFLDLIQEGNIGLMKAAEKFDW 490
           R      +  ++ +    L    ++A + Y  R    ++F D +Q  +IGL+++ ++FD 
Sbjct: 29  RWAAERNACNREAVFAHYLPYARAIAARLYAGRHRDDVEFRDFVQLASIGLLESIDRFDP 88

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F T+    V+ AI   +   +   +     R    +V R                
Sbjct: 89  ARGVAFETFCTTRVRGAILTGVEKLTDGQKQISFSR----RVRRERVASLQ--------- 135

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG----DFIEDKNAVSPLDSAIQ 606
                +  P    R  L+      +        D + L     D +   +   P  +   
Sbjct: 136 ---ADIDRPARQGRDALQAIGTLAAGLAIGFMLDGTGLVAQTTDGMPPGDPALPGAAYQG 192

Query: 607 ANLRET---TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
              R+T       +  L  R  ++++  +  G       E++     V++ RI Q+   A
Sbjct: 193 IAWRQTKTRLADAVRHLPERTRKIIQYHYFHG----LAFEQIADILGVSKGRISQLHRAA 248

Query: 664 IRKLKH 669
           + +L+ 
Sbjct: 249 LAELRE 254


>gi|301055830|ref|YP_003794041.1| RNA polymerase sigma-28 factor [Bacillus anthracis CI]
 gi|300377999|gb|ADK06903.1| RNA polymerase sigma-28 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 181

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 50/218 (22%), Positives = 82/218 (37%), Gaps = 56/218 (25%)

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
             +   KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I   +  
Sbjct: 4   FCVHNVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRV 63

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
                                                               LK TK+ +
Sbjct: 64  ----------------------------------------------------LKKTKKDV 71

Query: 575 SLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
           SL  PIG +   +   L D ++ ++        +   L E     +  L  RE+ V+  R
Sbjct: 72  SLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKR 130

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           FG+G++ + T  E+ K   ++R  + +IE +A+ K+ H
Sbjct: 131 FGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKMFH 168


>gi|153947529|ref|YP_001399652.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|152959024|gb|ABS46485.1| flagellar operon sigma factor , sigma-28 [Yersinia
           pseudotuberculosis IP 31758]
          Length = 231

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 106/247 (42%), Gaps = 19/247 (7%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   EF   +++    E +   A   +V+  +R +   A     +     D+ Q   +GL
Sbjct: 1   MEKREFEACLTLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGK----EDMQQIALMGL 56

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           ++A  ++    G +F+ YA+  ++ +I   + +       P  +R K HK     R+++ 
Sbjct: 57  LEALRRYGHPDG-QFAAYAVHRIRGSILDQLREHDW---RPRRLRQKTHKTNEAIRQIAK 112

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           ++  EP  EEI+ +L +  +  ++ L        LE     E    +       + +   
Sbjct: 113 RLGHEPNFEEISAELNLTADEYQEYLL-------LENAGAMESLDEILALDAHNDILQSR 165

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           D      + +   + +++L  RE+ +L + +      + +++E+ +   +T  RI Q+  
Sbjct: 166 DLEENIIIEDNLKQAISALDEREQMILHLYYQ----QELSMKEIAQVLDLTEARICQLNK 221

Query: 662 KAIRKLK 668
           K ++K+K
Sbjct: 222 KLVQKIK 228


>gi|300936144|ref|ZP_07151083.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           21-1]
 gi|300458722|gb|EFK22215.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           21-1]
          Length = 239

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 95/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 10  EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 65

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 66  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 121

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP  +E+A++     + +  + L+  +   SL+  +  E        +  ++      +
Sbjct: 122 HEPEWQELAEEGISHEDYLEYQQLEGAETLASLDELLNGEGPGIP---LAGRDLEDQFVT 178

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 179 ------QQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 228

Query: 664 IRKLK 668
            +K++
Sbjct: 229 AQKIR 233


>gi|324328848|gb|ADY24108.1| FliA/WhiG family RNA polymerase sigma factor [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 248

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 100/260 (38%), Gaps = 33/260 (12%)

Query: 408 KIRNEIKSISVETGISISEF-RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           K R+++K  +    +S +EF +    +V     +    K + +E              + 
Sbjct: 3   KERDQVKVGANVREMSDTEFMKKYERLVHHCVWKRYAKKMKSIEH-------------DT 49

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           GL   DL Q G IGL+KA + F+   G KFSTYA+  +   I R+I D            
Sbjct: 50  GLDIEDLTQFGMIGLIKARDNFNLEYGCKFSTYAVPKILGEIGRAIRDH--------QKV 101

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD---E 583
                V     ++  +   + TPEEIA  L   V  V   L       SL   +      
Sbjct: 102 KVQRNVYSIKGKILRQNLEDETPEEIASILQEDVSVVSNALHYQPGAQSLNKVVHQSNGN 161

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           +   L   +EDK A +  D +I    R       + L+ +E  VL M        + T +
Sbjct: 162 EELTLESMLEDKKAENVEDVSIN---RMVIQAFKSQLSHKEHIVLDMSL-----QNRTQQ 213

Query: 644 EVGKQFCVTRERIRQIEAKA 663
            +  +   ++ ++ +I  K 
Sbjct: 214 NIANEIGCSQVQVSRILTKI 233


>gi|256020244|ref|ZP_05434109.1| flagellar biosynthesis sigma factor [Shigella sp. D9]
 gi|332281406|ref|ZP_08393819.1| lateral flagellar sigma factor 28 protein [Shigella sp. D9]
 gi|332103758|gb|EGJ07104.1| lateral flagellar sigma factor 28 protein [Shigella sp. D9]
          Length = 238

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 94/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRHLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E    L    E ++       
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGILLAGRELEDQFVT--- 177

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 ++   + L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 178 ------QQMLQQALSQLSEKEQLILSMYYKH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|49186821|ref|YP_030073.1| prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus
           anthracis str. Sterne]
 gi|65321304|ref|ZP_00394263.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165872143|ref|ZP_02216782.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0488]
 gi|167641041|ref|ZP_02399298.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0193]
 gi|170688784|ref|ZP_02879988.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0465]
 gi|170705857|ref|ZP_02896320.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0389]
 gi|177654265|ref|ZP_02936194.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0174]
 gi|190565820|ref|ZP_03018739.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis Tsiankovskii-I]
 gi|227813117|ref|YP_002813126.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CDC 684]
 gi|229600567|ref|YP_002868208.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0248]
 gi|254683672|ref|ZP_05147532.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CNEVA-9066]
 gi|254721508|ref|ZP_05183297.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A1055]
 gi|254736016|ref|ZP_05193722.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Western North America USA6153]
 gi|254754314|ref|ZP_05206349.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Vollum]
 gi|254757995|ref|ZP_05210022.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Australia 94]
 gi|49180748|gb|AAT56124.1| prophage LambdaBa02, RNA polymerase sigma-F factor, putative
           [Bacillus anthracis str. Sterne]
 gi|164712090|gb|EDR17628.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0488]
 gi|167511091|gb|EDR86480.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0193]
 gi|170129397|gb|EDS98261.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0389]
 gi|170667300|gb|EDT18059.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0465]
 gi|172080755|gb|EDT65836.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0174]
 gi|190562739|gb|EDV16705.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis Tsiankovskii-I]
 gi|227006745|gb|ACP16488.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CDC 684]
 gi|229264975|gb|ACQ46612.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0248]
          Length = 314

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 97/243 (39%), Gaps = 28/243 (11%)

Query: 448 MVEANLRLVISVAKKY---------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            ++   RLV     KY             L   DLIQ G +GL+ A   F   LG+KF+T
Sbjct: 22  FMKKYSRLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTT 81

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A+  +   I +++ D               ++V     ++S     +   E IAK L +
Sbjct: 82  FAVPRILGYIRKAVRDS--------QKIRITNEVYEIKGKISRMKLHDEEVESIAKLLEV 133

Query: 559 PVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            V  V+   +     ISL+TP+  E   +   L + + DK     LD  I+   +   T 
Sbjct: 134 SVRDVKTAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTLDDVIK---KMIITA 190

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L++L  +E+             + T   +GK+  VT+ +I +I     +K +       
Sbjct: 191 FLSTLCSKEK-----FVWELHAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNKHS 245

Query: 676 LRS 678
           LR 
Sbjct: 246 LRD 248


>gi|189219201|ref|YP_001939842.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186059|gb|ACD83244.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 401

 Score = 69.1 bits (167), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 95/248 (38%), Gaps = 14/248 (5%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAA 485
           F+  + +++  +     A + +   +L +   VA+ Y       + D    G  G++ A 
Sbjct: 128 FKEELPIIQSAKAAEKKALEWLAIHSLPMRQQVARFYLPYLADQWPDAENVGWFGILDAL 187

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           EK+D  +  +F  YA+  VK  +         T+R P  +  +  K+ +   +       
Sbjct: 188 EKWDEQMQIRFFDYAIHHVKNRVRNYANACRTTVRRPNSVYREYRKIEKFLEQGL----- 242

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIGDEDTSHLGDFIEDKNAVSPLDSA 604
             T EEI          + K+L++    ISL  T   +E  +   D +            
Sbjct: 243 --TLEEITALYGYSPYQLEKILQVYSLDISLHFTAFDEESETCFLDLLVYPENPDDSLER 300

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNT---DHTLEEVGKQFCVTRERIRQIEA 661
            +   +     VL+ L     +++   FGI   T         +  +  + R+++ Q+  
Sbjct: 301 EERLRK--LFTVLSHLDEISRKIVFFFFGIEEGTGAKGKPTAWIAHKLKIPRQKVMQMLE 358

Query: 662 KAIRKLKH 669
           +A+++LK 
Sbjct: 359 EALKQLKR 366


>gi|6175924|gb|AAF05338.1|AF182104_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 147

 Score = 69.1 bits (167), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/96 (38%), Positives = 58/96 (60%), Gaps = 3/96 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA 
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 147



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|300817253|ref|ZP_07097471.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           107-1]
 gi|301643537|ref|ZP_07243580.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           146-1]
 gi|307136893|ref|ZP_07496249.1| flagellar biosynthesis sigma factor [Escherichia coli H736]
 gi|331640757|ref|ZP_08341892.1| sigma-70, region 4 subfamily [Escherichia coli H736]
 gi|300530229|gb|EFK51291.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           107-1]
 gi|301078088|gb|EFK92894.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           146-1]
 gi|315616809|gb|EFU97426.1| RNA polymerase sigma factor, FliA/WhiG family protein [Escherichia
           coli 3431]
 gi|323171082|gb|EFZ56731.1| RNA polymerase sigma factor, FliA/WhiG family protein [Escherichia
           coli LT-68]
 gi|331037555|gb|EGI09775.1| sigma-70, region 4 subfamily [Escherichia coli H736]
          Length = 238

 Score = 69.1 bits (167), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 94/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E    L    E ++       
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGILLAGRELEDQFVT--- 177

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
                 ++   + L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 178 ------QQMLQQALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|224005601|ref|XP_002291761.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220972280|gb|EED90612.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 217

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/218 (21%), Positives = 97/218 (44%), Gaps = 12/218 (5%)

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY-----KFSTYAMWWVKQAITRSIADQSCT 518
               + + DL+QEG I L+ A   ++    +      F  YA   ++ ++   +A  S  
Sbjct: 1   RKSSISYPDLVQEGMIALLHAISSYNSYKTHNKNDQSFEKYAQQTIQSSLLHFLAHSSRP 60

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
           IR+P  ++  +      A ++ + + REPT  ++AK++ +    +      T+E    E 
Sbjct: 61  IRLPFSLQTTLQSANEAAAKLRSALGREPTLTQVAKEVNIDAHQLALYPGATEED-DWEI 119

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANL--RETTTRVLASLTPREERVLRMRFGI-- 634
              +   + L D + D   ++   S  Q  L  +E    +  +LT  E  V+++RFG+  
Sbjct: 120 NNPERTVAPLRDILTDTEEINNPLSYTQHYLLTQELDQFLYETLTHDELEVIQLRFGLLD 179

Query: 635 --GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
                   +  ++G++  + +E + +I + A+ KL+  
Sbjct: 180 SKYGGKGWSAGQIGERMNMDKEEVVKIASSALEKLRKA 217


>gi|62550939|emb|CAI79314.1| putative RNA polymerase sigma-32 [Aeromonas caviae]
          Length = 100

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/86 (34%), Positives = 51/86 (59%), Gaps = 2/86 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I++++    +S  E R +   +++       A +++V ++LR V+ VAK Y+  GL
Sbjct: 17  LEGYIQAVNSIPVLSAEEKRELAERLQQDG--DLEAARQLVMSHLRFVVHVAKSYSGYGL 74

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGY 494
              DL+QEGNIGLMKA ++FD  +G 
Sbjct: 75  PQADLVQEGNIGLMKAVKRFDPSVGV 100


>gi|289754805|ref|ZP_06514183.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695392|gb|EFD62821.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 473

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 188 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 247

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M  L E
Sbjct: 248 EVELAKRIEAGLYATQLMTELSE 270



 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 33/104 (31%), Positives = 54/104 (51%), Gaps = 4/104 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 245 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 304

Query: 456 VISVAKKYTNRGLQFLDLI-QEGNIGLMKAAEKFDWCLGYKFST 498
           V+S+AK+YT RG+ FLDLI  +  +GL++A EKF    G +   
Sbjct: 305 VVSLAKRYTGRGMAFLDLIPGKATLGLIRAVEKFRLHQGVQVLH 348


>gi|115377816|ref|ZP_01465004.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|310820297|ref|YP_003952655.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
 gi|115365148|gb|EAU64195.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393369|gb|ADO70828.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
          Length = 260

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 88/232 (37%), Gaps = 21/232 (9%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
           +R + +  +K  N  L+  +L+  G IGL++AA++FD  +G  F T+A + +K AI   +
Sbjct: 1   MRSLAATVRKQFNAQLELDELVSYGQIGLLEAADRFDPKVGANFLTFAHYRIKGAIFDGL 60

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
                       +R    +      R +  +      E+         +     +     
Sbjct: 61  RKMGI-------LRGGDARSAFVGERAAAYLGNLSDREQGGGNRGGSFDDDVNDISNAVA 113

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            +++      E     G       ++          L+      +  L  +E ++L+  +
Sbjct: 114 GLAMVFATSLEGADSAG---YSDESLPADQRLEMEQLKRRVRAAIERLPDKERQLLQGYY 170

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH-------PSRSKKLR 677
             G     TLEE G +   ++    ++ A+AI +LK        P+ S +LR
Sbjct: 171 FQG----RTLEEAGSEIGQSKSWASRLHARAIERLKEFLDEEEAPASSDELR 218


>gi|239934468|emb|CAR92488.1| DNA-directed RNA polymerase subunit D [uncultured gamma
           proteobacterium]
          Length = 214

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 44/135 (32%), Gaps = 3/135 (2%)

Query: 286 EIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           E  E +  LR L + A     +   +    +     L +    L L   + + + E + +
Sbjct: 67  EAKERFDTLRQLNNKAKKAINRYGVAHKSTQQHLSALGEHFKLLKLAPRQFEPMAEAVRE 126

Query: 345 ISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
               I   E  ++ L      + R  F+    G E D  W +      E  +   +A   
Sbjct: 127 ALSLIRAEERTVMALCIRQAKMPRTDFIGLFPGHETDESWATGLAKGKEP-YAAAIAVVE 185

Query: 404 DSILKIRNEIKSISV 418
             I + +  +  +  
Sbjct: 186 PDIQRSQRRLMQLGR 200


>gi|306813287|ref|ZP_07447480.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|305854050|gb|EFM54489.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
          Length = 239

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 95/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 10  EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 65

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 66  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 121

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP  +E+A++     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 122 HEPEWQELAEEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 172

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 173 EDQFVTQQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 228

Query: 664 IRKLK 668
            +K++
Sbjct: 229 AQKIR 233


>gi|296120653|ref|YP_003628431.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296012993|gb|ADG66232.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 558

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVT 652
           D       D  +    RE    +L  L  RE  ++  R+G+       TLE+VG +  VT
Sbjct: 470 DPRTDQFRDEIVNYRQREALMGILGQLELRERDIIMHRYGLETGQQPQTLEQVGHRLGVT 529

Query: 653 RERIRQIEAKAIRKLKHPSRSKKL 676
           +ERIRQIEA+A++KLK  +  ++L
Sbjct: 530 KERIRQIEARALKKLKRIATDERL 553



 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/84 (38%), Positives = 54/84 (64%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            ++  +      ++  K  ++ +NLRLV+S+AKK+++    F ++I +GN+ L+KA EKF
Sbjct: 364 KLMDEIESLLARSTEIKNFLIRSNLRLVVSIAKKHSHPTANFFEMISDGNMSLIKAIEKF 423

Query: 489 DWCLGYKFSTYAMWWVKQAITRSI 512
           D+  G+KFSTYA W + +   RSI
Sbjct: 424 DYTRGFKFSTYASWAIMKNFARSI 447


>gi|207109684|ref|ZP_03243846.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 84

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/79 (45%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT-DHTLEEVGKQFCVTRERIRQIEA 661
             ++ +L+     VL  L  RE+ V+RMRFG+  +  D TLEE+GK+  VTRER+RQIE+
Sbjct: 4   HIMREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIES 63

Query: 662 KAIRKLKHPSRSKKLRSFL 680
            AI+KL+ P   + LR++L
Sbjct: 64  SAIKKLRSPQYGRILRNYL 82


>gi|167464009|ref|ZP_02329098.1| RNA polymerase, sigma 28 subunit [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 175

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/161 (22%), Positives = 78/161 (48%), Gaps = 20/161 (12%)

Query: 446 KEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYK----FST 498
            +++ A  ++V SVA+KY +    GL + DL+  G IGL++A   +D     +    FST
Sbjct: 13  DQIIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFST 72

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           YA   +K +I R +AD+  ++R+P  +++K+  + +       +   + + E IA+K   
Sbjct: 73  YAFNMIKWSIQRFLADKRFSVRVPRSIQNKLTVIWK-------QGWDQESAESIAEKTGW 125

Query: 559 PVEGVRKV------LKITKEPISLETPIGDEDTSHLGDFIE 593
            +  +R+         +     +L +    ++ + + D + 
Sbjct: 126 KLPEIREAQRHIAGWSVASLDQALSSSDKTDEEATMLDVLP 166


>gi|332162882|ref|YP_004299459.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318604274|emb|CBY25772.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325667112|gb|ADZ43756.1| Putative RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330863330|emb|CBX73453.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 228

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/194 (21%), Positives = 88/194 (45%), Gaps = 15/194 (7%)

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q   +GL++A  ++    G +F+ YA+  ++ A+   + +       P  +R K HK   
Sbjct: 47  QIALMGLLEALRRYGHPDG-QFAAYAVHRIRGAVLDQLREHDW---RPRRLRQKTHKTNE 102

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           + R+++ K+  EP+ EEIA +L +  E  ++ L        LE+    E    +      
Sbjct: 103 SIRQLAKKLGHEPSFEEIAAELQLTAEEYQEYLL-------LESAGAMESLDEILSLDTP 155

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +A+   +        +     +ASL  RE+ +L + +      + +++E+ +   +T  
Sbjct: 156 TDALQSRELEESIITEDNLNHAIASLEKREQMILHLYYQ----QEMSMKEIAEVLDLTEA 211

Query: 655 RIRQIEAKAIRKLK 668
           RI Q+    ++K+K
Sbjct: 212 RICQLNKILVQKIK 225


>gi|171058011|ref|YP_001790360.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Leptothrix
           cholodnii SP-6]
 gi|170775456|gb|ACB33595.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Leptothrix cholodnii SP-6]
          Length = 321

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 79/228 (34%), Gaps = 22/228 (9%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWC-------LG 493
           A   ++  N   V   A     R    ++  DLIQ G I + ++A  F W          
Sbjct: 7   ATSALIARNESWVRKQASALVRRLPSNVEKADLIQVGLIAVAQSALGFKWEGDPDSEEAK 66

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             F  YA   VK A+   +        +    R K   +     R   +   +P   E+A
Sbjct: 67  EAFVRYARMRVKGAMLDELRQMD---HLGRAQRRKFKVIQIARERWRARHGSDPGLAELA 123

Query: 554 KKLAMPVEGVRKVLKITKE--PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
               + V+ +  + +        SL+     E+              + +D+AI   +  
Sbjct: 124 GVCGIAVDEISMLDQAALMAQAQSLDDDPDHENREPAHAATPRDEVEARVDTAI---VMR 180

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
              +  A+L  RE +V+    GIG     +  E+     V+  R+ QI
Sbjct: 181 RLEKFFATLPDRERQVIDAYLGIG----MSPVELAGALRVSPSRVSQI 224


>gi|158327335|emb|CAM82841.1| sigma factor FliA [Yersinia enterocolitica W22703]
          Length = 231

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/194 (21%), Positives = 88/194 (45%), Gaps = 15/194 (7%)

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           Q   +GL++A  ++    G +F+ YA+  ++ A+   + +       P  +R K HK   
Sbjct: 50  QIALMGLLEALRRYGHPDG-QFAAYAVHRIRGAVLDQLREHDW---RPRRLRQKTHKTNE 105

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           + R+++ K+  EP+ EEIA +L +  E  ++ L        LE+    E    +      
Sbjct: 106 SIRQLAKKLGHEPSFEEIAAELQLTAEEYQEYLL-------LESAGAMESLDEILSLDTP 158

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            +A+   +        +     +ASL  RE+ +L + +      + +++E+ +   +T  
Sbjct: 159 TDALQSRELEESIITEDNLNHAIASLEKREQMILHLYYQ----QEMSMKEIAEVLDLTEA 214

Query: 655 RIRQIEAKAIRKLK 668
           RI Q+    ++K+K
Sbjct: 215 RICQLNKILVQKIK 228


>gi|261342189|ref|ZP_05970047.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315522|gb|EFC54460.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 147

 Score = 68.7 bits (166), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/96 (38%), Positives = 58/96 (60%), Gaps = 3/96 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           RGL  LDLI+EGN+GL++A EKFD   G++FSTYA 
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 147



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEAFDEKALVEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|283834438|ref|ZP_06354179.1| RNA polymerase sigma factor [Citrobacter youngae ATCC 29220]
 gi|291069985|gb|EFE08094.1| RNA polymerase sigma factor [Citrobacter youngae ATCC 29220]
          Length = 238

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 89/235 (37%), Gaps = 24/235 (10%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K E     A   +V   +R +           +   D+ Q   +GL+ A  ++       
Sbjct: 20  KQESHYLQAYLPLVRKVVRQLAPQCT----CVMDRQDMEQTALMGLLNAIRRY-GQPDEG 74

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F+ YA+  ++ AI   +         P  +R K H++    R    ++  EP+ EE+  +
Sbjct: 75  FAGYAVHRIRGAILDELRSLDW---RPRQLRQKYHQIKDLIRDARTQLGHEPSWEEL-SR 130

Query: 556 LAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           L +  E  ++  ++   +   SL+  +  +              +       Q   +E  
Sbjct: 131 LGLSSEDYQEYQQLEGAETLASLDELLNGDMPIA---------PLEGRGLEEQFVTQEML 181

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +  L+ L+ +E  VL M +      D  L+E+     +T  RI Q+  K   K++
Sbjct: 182 SYALSQLSEKEGLVLSMYYQH----DMNLKEIALVLGLTEARICQMNKKITHKIR 232


>gi|42543555|pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
           Sigma-Region4 Of Thermus Aquaticus Bound To Dna
          Length = 73

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 41/72 (56%), Positives = 52/72 (72%), Gaps = 1/72 (1%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-H 669
           E   + L+ L+ RE  VL++R G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H
Sbjct: 2   EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61

Query: 670 PSRSKKLRSFLD 681
            SR++KLR FL+
Sbjct: 62  ESRTRKLRDFLE 73


>gi|299066547|emb|CBJ37737.1| putative RNA polymerase sigma factor [Ralstonia solanacearum CMR15]
          Length = 272

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 87/235 (37%), Gaps = 25/235 (10%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKK-YTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLG 493
           E   + A+  ++   L    + A   Y  R      F +  Q   +GLM++ E++D   G
Sbjct: 46  EHGDTAARDALIARYLPYAKAQAAMLYARRTHDAFEFEEYHQFAVVGLMESLERYDPQQG 105

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            +F TY    +  ++   +            +  +       A  ++++   E  P+++ 
Sbjct: 106 AQFKTYVTPRIVGSMLNGLE---RLSEQQQQIGLRRRLAAERAASLASEPLSEGNPQKLL 162

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           ++L          L I    +   T +       L D        +         LR   
Sbjct: 163 RELG------EIGLGIALGILLEGTGMVVGQDEGLPD--------NAYSRTELRQLRHQI 208

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++  LT RE  V+R+ +          +EV  +  VT+ R+ Q+  +A+R+L+
Sbjct: 209 WHMVQHLTDRERDVIRLHYQ----QQKPFDEVAAELGVTKGRVSQLHQQALRRLQ 259


>gi|149177082|ref|ZP_01855690.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148844147|gb|EDL58502.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 556

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/85 (31%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG-MNTDHTLEEVGKQFCVT 652
           D+      +  I          +L  L  RE+ +L  R+G+   N   TLE+VG +F VT
Sbjct: 468 DERESQYREELINQKQHAVIMSILDQLDGREKDILIYRYGLNARNEPQTLEQVGDRFGVT 527

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLR 677
           +ERIRQ+E++A++KL+  ++ +++ 
Sbjct: 528 KERIRQLESRALKKLRRITQVERVE 552



 Score = 58.3 bits (139), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 32/82 (39%), Positives = 53/82 (64%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           +  + K   E++  K  ++ +NLRLV+S+AK++   G  F +++ +GN+ L++A EKFD+
Sbjct: 364 MDQIEKLLDESTDVKNFLIRSNLRLVVSIAKRHIRPGGNFFEMVSDGNMSLIRAIEKFDY 423

Query: 491 CLGYKFSTYAMWWVKQAITRSI 512
             G KFSTYA W + +   RSI
Sbjct: 424 TKGNKFSTYASWAIMKNYARSI 445


>gi|148242553|ref|YP_001227710.1| putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
 gi|147850863|emb|CAK28357.1| Putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
          Length = 259

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 37/230 (16%), Positives = 89/230 (38%), Gaps = 14/230 (6%)

Query: 429 HIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAE 486
            ++++ R+      +  +  +VEA+L LV   A ++       + DL Q+G  GL+ A +
Sbjct: 10  ELLALHRRYGQSRCLKLRNRLVEAHLNLVRQQAARFSQASSACYDDLFQQGCFGLLDAVQ 69

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++    GY FSTYA+  ++  +   + D+   IR P  +R  + +  +   +        
Sbjct: 70  RYQPQRGYAFSTYAVTLIRGQMQHYLRDRHHLIRSPWRLRQLLSRWDQLQNQRQQAGLPP 129

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
                 A+ L   VE ++  L++ +  ++L +     +                  +   
Sbjct: 130 LDRRGQARSLGCRVERLQMALQM-RAALNLRSFDAAPEGIAF-------ETADQRPTPEA 181

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
                     + + +P ++ +L        +   +  ++ +Q   +  R+
Sbjct: 182 RLAEAELEEWIEAQSPDDQLLLCGVM----HQGLSQRQLARQLDWSPCRV 227


>gi|289575401|ref|ZP_06455628.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis K85]
 gi|289539832|gb|EFD44410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis K85]
          Length = 470

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M  L E
Sbjct: 246 EVELAKRIEAGLYATQLMTELSE 268



 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 3/83 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGN 478
           V+S+AK+YT RG+ FLDLIQEGN
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGN 325


>gi|224419054|ref|ZP_03657060.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
 gi|253827994|ref|ZP_04870879.1| flagellar biosynthesis sigma factor FliA [Helicobacter canadensis
           MIT 98-5491]
 gi|313142562|ref|ZP_07804755.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
 gi|253511400|gb|EES90059.1| flagellar biosynthesis sigma factor FliA [Helicobacter canadensis
           MIT 98-5491]
 gi|313131593|gb|EFR49210.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
          Length = 235

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 82/209 (39%), Gaps = 17/209 (8%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++F DL+  G   L+K A K+D  L   F  YA   V  A+   +    C      H R 
Sbjct: 42  VEFADLVSIGTEELIKLARKYDQNLNDSFWGYAKSRVYGAMLDYLRGLDCM---SRHTRT 98

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I  + +   +  N+ + EP    ++K L   +E +++    ++    L           
Sbjct: 99  LIKSINKEISKYYNEYQEEPDNAYLSKVLNEDIEKIKEARNASEIYGIL----------P 148

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L + +         +   +  L      +L S +  E+ V+++ +      + + +E+ +
Sbjct: 149 LDEELSAAQEDKTYNKIEKQELIGIIQNILESASKNEQLVIQLYY----YEELSFKEISE 204

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              ++  RI QI    IRK++     + +
Sbjct: 205 ILEISESRISQIHKSVIRKIRAYLEERGI 233


>gi|5360471|dbj|BAA82015.1| principle sigma factor [Pseudomonas syringae pv. syringae]
          Length = 172

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 22/212 (10%), Positives = 58/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G S   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGISPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 51  EVPPPVDPKAAKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  +  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAEMVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|20151058|pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment, Region 4
 gi|20151059|pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
 gi|20151062|pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
          Length = 73

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 42/72 (58%), Positives = 52/72 (72%), Gaps = 1/72 (1%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK-H 669
           E   + L+ L+ RE  VL+MR G+    +HTLEEVG  F VTRERIRQIE KA+RKLK H
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61

Query: 670 PSRSKKLRSFLD 681
            SR++KLR FL+
Sbjct: 62  ESRTRKLRDFLE 73


>gi|260222952|emb|CBA33033.1| hypothetical protein Csp_B17010 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 161

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLED 85
                K +I L + RGY+T  E++  LP   V +E +E  ++ML++MG+ V +     +
Sbjct: 58  RRARLKALITLGKTRGYLTHGEISDHLPDKLVDAETLEVVISMLNDMGVAVYEQTPDAE 116


>gi|258622499|ref|ZP_05717521.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM573]
 gi|258585199|gb|EEW09926.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM573]
          Length = 242

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 90/227 (39%), Gaps = 21/227 (9%)

Query: 446 KEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++++ +  +V  V  +   +        D+ Q G I L+++  ++       F T+A+ 
Sbjct: 26  NQLLQRHKIMVKRVVNQLKVHATAYCSIDDMQQIGLIALIESGRRYGDISDPNFPTFAVC 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+ AI   +       R       +++ + R    +   + R+PT  E  K L +  + 
Sbjct: 86  RVRGAILDELRRLDWRSRKTRQQAHELNDITR---DLIRALGRQPTDAETIKALGINEQD 142

Query: 563 V--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              R+   +  E  SL+  I +   + L             D     ++R +    L  L
Sbjct: 143 YYARQSAALAGELQSLDQLIENGVENQLS---------GHYDGLKHEHIRRSLETALNKL 193

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R++ +L + +      +  L E+     +T  RI Q+  +A+++L
Sbjct: 194 SKRDQLLLTLFYQH----ELNLNEIALILDLTSPRICQLHKQALKQL 236


>gi|302391432|ref|YP_003827252.1| sigma-70 region 4 domain protein [Acetohalobium arabaticum DSM
           5501]
 gi|302203509|gb|ADL12187.1| sigma-70 region 4 domain protein [Acetohalobium arabaticum DSM
           5501]
          Length = 1154

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 52/278 (18%), Positives = 113/278 (40%), Gaps = 16/278 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + NEIK      GI+IS  + + + +++   ++S  K  +++ N +  I ++        
Sbjct: 249 LLNEIKDYLSVVGINIS-VKELQNNIKQLLKKSS--KFNLIDFNEKTAIILSD------- 298

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+ +G + L+    K +    + F  ++       I  +   + C           
Sbjct: 299 YIKDLLNDGPLCLVDLKMKLELEDNWYFCLFSALKKINNIGLNKKRKICLTNNLNARIRF 358

Query: 529 IHK--VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL---ETPIGDE 583
                + +  R  + KI        I  +  + ++ ++K L      +SL   +  + + 
Sbjct: 359 CINSALTKIKRLKNKKIDNLIKNLFINLETPLLLKEIKKYLMFLNIDLSLEEIDELLRNN 418

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE-RVLRMRFGIGMNTDHTL 642
               L D  +                + T  ++L+S       R + +      + D+TL
Sbjct: 419 ADFKLIDVNKWSLDSWDEYPEFNEEFKSTWEQILSSFPEENRERDIDILNKRIFSNDYTL 478

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           E++G++  ++R+R+RQ+E   +RKL H +R K ++ FL
Sbjct: 479 EKLGEEHSISRQRVRQLEESGMRKLVHYTRIKYIKPFL 516


>gi|219685543|ref|ZP_03540360.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
 gi|219672942|gb|EED29964.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
          Length = 631

 Score = 68.3 bits (165), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 59/362 (16%), Positives = 126/362 (34%), Gaps = 44/362 (12%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSED--------- 91
           R  ++  EL+  LP D +  E ++   ++L + GI +V+     D  G+ED         
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDFICSILEDRGIILVNKISELDLVGTEDGNDEEEESE 81

Query: 92  ------------------------------SLDLASSASNSSVFLQKRKDSADRSTDDPV 121
                                           +  S   +      K     D  ++DP+
Sbjct: 82  IESDRNFMILDDGFQSDGEDIDINGKLDDCDEEDISVKDDLGSGYIKSNALKDSHSEDPI 141

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ----ALIIWRDELNDG 177
           ++YL+E+G   LL+   E+ +AK++++G +++   L    L  +     +      +   
Sbjct: 142 KLYLKEIGKEFLLTGNQEVELAKQMDSGESIIENILKNEGLVIENYYNLINTIYSRMERE 201

Query: 178 TTLLRE-IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               RE   D E+     +K            +  +D       +  +  E   +   K 
Sbjct: 202 EFFKREKDKDKESNPDYYNKKKRIASFYKIPLKPIQDRLISYVDNKHRVYELGGDIFEKN 261

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            K +R  +     N    +  L    DD   + + ++D  R + +       E  R+LR 
Sbjct: 262 LKSERLALKELLRNVPLYQDELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRV 321

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           L  +    +K  +     K+ ++ + + +    L Q  ++ +         +I+    E+
Sbjct: 322 LGRDLTIAEKRIEIEKSLKLKEDAIKEQITEAQLAQKELERIEMYYEYPMDKIISMSEEI 381

Query: 357 LR 358
            +
Sbjct: 382 AK 383


>gi|87303692|ref|ZP_01086467.1| group3 RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87281797|gb|EAQ73762.1| group3 RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 267

 Score = 67.9 bits (164), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 91/237 (38%), Gaps = 23/237 (9%)

Query: 449 VEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           V  +L LV  +A  Y++       DL Q G +GL++AAE F    G  F  +A   ++ A
Sbjct: 27  VARHLELVRPIAHHYSSLCREGRDDLTQVGLLGLLRAAELFQSDQGTPFEAFARHHIRGA 86

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE------IAKKLAMPVE 561
           I   + DQ+  IR+P   R+   ++ R  +  +         +E      + + L +   
Sbjct: 87  ILHYLRDQAPVIRLPRRQRELEDRLRRLQQSQAGAAAEGCHRQEALANSSLHQLLGLSEA 146

Query: 562 GVR--KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
             +  + L+     +SL+      +   L     +                E    +LA 
Sbjct: 147 QWQRFEQLRQLGRLVSLD-----GEEEKLA--AAEPEPEDGPGGCEAG---ERIMALLAQ 196

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L  R+  V++     G     +L    ++  V+   + ++ A+A+  L+     + L
Sbjct: 197 LEHRQRTVVKEVVLAGQ----SLRGTARKMQVSPMTVHRLLARALDTLRQRLEGEGL 249


>gi|323191388|gb|EFZ76650.1| RNA polymerase sigma factor, FliA/WhiG family protein [Escherichia
           coli RN587/1]
          Length = 239

 Score = 67.9 bits (164), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 93/245 (37%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 10  EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 65

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 66  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 121

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 122 HEPEWPELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 172

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 173 EDQFVTQQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 228

Query: 664 IRKLK 668
            +K++
Sbjct: 229 AQKIR 233


>gi|218289804|ref|ZP_03494004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240095|gb|EED07280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score = 67.9 bits (164), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 48/221 (21%), Positives = 86/221 (38%), Gaps = 56/221 (25%)

Query: 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519
            KK+   G+   DLI  G +GL+KA + +    G KF+TYA   ++  I   +       
Sbjct: 1   MKKFDTSGIDQDDLISIGTVGLIKAVDTYQPSKGTKFATYAARCIQNEILMQLR------ 54

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
                 + K  K                                          +SL +P
Sbjct: 55  -----AQRKSRK-----------------------------------------DVSLYSP 68

Query: 580 IGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           IG +   +   +GD +  ++  +  + + +  L  T  ++L  L  RE +V+ +RFG+  
Sbjct: 69  IGTDKEGNEITIGDILFSESDSTEDEVSRRMEL-NTMRQLLDVLDERERKVIELRFGLAD 127

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
             + T  EV     ++R  + ++E +A+ K+ H S   K R
Sbjct: 128 GREWTQNEVADSLEISRSYVSRLEKRALLKMFHQSHVAKER 168


>gi|206901181|ref|YP_002249992.1| SigD [Dictyoglomus thermophilum H-6-12]
 gi|206740284|gb|ACI19342.1| SigD [Dictyoglomus thermophilum H-6-12]
          Length = 171

 Score = 67.9 bits (164), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 37/98 (37%), Positives = 56/98 (57%), Gaps = 2/98 (2%)

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                +E+   + D IED    S  ++  Q ++R    R L +L+ RE  +L+ R+G   
Sbjct: 73  YEYFEEENIYAIQDLIEDPR--SIEETIEQIDIRREIERALDALSEREREILKWRYGFKD 130

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
               TLEEVGK F +TRER+RQIE +A+RKL+H  + +
Sbjct: 131 GKPRTLEEVGKLFNITRERVRQIEERALRKLRHILQQR 168


>gi|170682912|ref|YP_001742389.1| flagellar biosynthesis sigma factor [Escherichia coli SMS-3-5]
 gi|170520630|gb|ACB18808.1| lateral flagellar sigma factor 28 protein LafS [Escherichia coli
           SMS-3-5]
          Length = 239

 Score = 67.9 bits (164), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 93/245 (37%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 10  EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 65

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 66  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 121

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 122 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 172

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 173 EDQFVTQQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 228

Query: 664 IRKLK 668
            +K++
Sbjct: 229 AQKIR 233


>gi|260853482|ref|YP_003227373.1| putative RNA polymerase, sigma 28 factor [Escherichia coli O26:H11
           str. 11368]
 gi|307313503|ref|ZP_07593124.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|257752131|dbj|BAI23633.1| predicted RNA polymerase, sigma 28 factor [Escherichia coli O26:H11
           str. 11368]
 gi|306906671|gb|EFN37182.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|315059558|gb|ADT73885.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli W]
 gi|323158087|gb|EFZ44186.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EPECa14]
 gi|323379883|gb|ADX52151.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli KO11]
          Length = 238

 Score = 67.9 bits (164), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 96/247 (38%), Gaps = 26/247 (10%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPL 601
            EP   E+A +     + +  + L+  +   SL+  +  E      +G  +ED       
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGIPLVGRELED------- 173

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
               Q   ++   + L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  
Sbjct: 174 ----QFVTQQMLQQALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNK 225

Query: 662 KAIRKLK 668
           +  +K++
Sbjct: 226 QIAQKIR 232


>gi|147677461|ref|YP_001211676.1| hypothetical protein PTH_1126 [Pelotomaculum thermopropionicum SI]
 gi|146273558|dbj|BAF59307.1| hypothetical protein [Pelotomaculum thermopropionicum SI]
          Length = 127

 Score = 67.6 bits (163), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 32/118 (27%), Positives = 54/118 (45%), Gaps = 3/118 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           G W   V   V+ +L + + I + +    +S  E    + ++         A+  + E N
Sbjct: 4   GLWTLTVVSLVNGLLLLVSYIANNTFPQPLSEEEEAKYLKLL---NMGNEEARNILTERN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           LRLV  + KK+ + G    DLI  G IGL+KA   F+   G + +TYA   ++  +  
Sbjct: 61  LRLVAHIVKKFDSTGEDSDDLISIGTIGLIKAINTFNPGKGTRLATYAAKCIENEMFM 118


>gi|331666562|ref|ZP_08367436.1| sigma-70, region 4 subfamily [Escherichia coli TA271]
 gi|323181563|gb|EFZ66983.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1357]
 gi|331065786|gb|EGI37670.1| sigma-70, region 4 subfamily [Escherichia coli TA271]
          Length = 238

 Score = 67.6 bits (163), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 93/245 (37%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFVTQQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|323976253|gb|EGB71346.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TW10509]
          Length = 238

 Score = 67.6 bits (163), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 94/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++   + L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EEQFITQQMLQQALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|226311507|ref|YP_002771401.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
 gi|226094455|dbj|BAH42897.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 119

 Score = 67.6 bits (163), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 32/114 (28%), Positives = 54/114 (47%), Gaps = 3/114 (2%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            ++     +L     +K+ +    +  +E    + ++ K       A+ +++E NLRLV 
Sbjct: 7   ALSLVFKELLVFVAYVKNNAFPQPLQDTEEEKYLRLMAK---GDPYARNKLIEHNLRLVA 63

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
            + KK+ N G    DLI  G IGL+KA E +    G K +TYA   ++  I  S
Sbjct: 64  HIVKKFENTGEDSEDLISIGTIGLIKAIESYQVDKGTKLATYAARCIENEIVMS 117


>gi|284989565|ref|YP_003408119.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geodermatophilus obscurus DSM 43160]
 gi|284062810|gb|ADB73748.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geodermatophilus obscurus DSM 43160]
          Length = 333

 Score = 67.6 bits (163), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 41/208 (19%), Positives = 81/208 (38%), Gaps = 10/208 (4%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
            +   DL+    + L++ A +FD   G  F+TYA+  ++ A+   +            +R
Sbjct: 74  HVSREDLLSCARVALVEVARRFDPSAGASFATYALARLQGAVLDELRSGDW---ASRSVR 130

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
               +    A  ++ ++ R PT EE+A  L M    +  +       + +          
Sbjct: 131 AAARRTDAAADALAIQLGRPPTREELAASLGMARSDLESLQVDVHRAVMVSIDAETGPDG 190

Query: 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              D + D    SP  + +++         +  L  R + V+   F  G     +L ++ 
Sbjct: 191 ASLD-LPDT-GESPERALLRSERSRYLHEAIRQLPDRLDEVVERNFFGG----ESLTDIA 244

Query: 647 KQFCVTRERIRQIEAKAIRKLKHPSRSK 674
               VT  R+ Q+ A+A+  L H + S+
Sbjct: 245 ADLGVTLSRVSQMRARAL-TLLHAAMSE 271


>gi|262173365|ref|ZP_06041042.1| RNA polymerase sigma factor for flagellar operon [Vibrio mimicus
           MB-451]
 gi|261890723|gb|EEY36710.1| RNA polymerase sigma factor for flagellar operon [Vibrio mimicus
           MB-451]
          Length = 242

 Score = 67.6 bits (163), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 89/227 (39%), Gaps = 21/227 (9%)

Query: 446 KEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
            ++++ +  +V  V  +   +        D+ Q G I L+++  ++       F T+A+ 
Sbjct: 26  NQLLQRHKIMVKRVVNQLKVHATAYCSIDDMQQIGLIALIESGRRYGDISDPNFPTFAVC 85

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+ AI   +       R       +++ + R    +   + R+PT  E  K L    + 
Sbjct: 86  RVRGAILDELRRLDWRSRKTRQQAHELNDITR---DLIRALGRQPTDAETIKALGTNEQD 142

Query: 563 V--RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
              R+   +  E  SL+  I +   + L             D     ++R +    L  L
Sbjct: 143 YYARQSAALAGELQSLDQLIENGVENQLS---------GHYDGLKHEHIRRSLETALNKL 193

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           + R++ +L + +      +  L E+     +T  RI Q+  +A+++L
Sbjct: 194 SKRDQLLLTLFYQH----ELNLNEIALILDLTSPRICQLHKQALKQL 236


>gi|318041416|ref|ZP_07973372.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CB0101]
          Length = 233

 Score = 67.2 bits (162), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 95/237 (40%), Gaps = 16/237 (6%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + +   +    +   V  +L LV  VA  Y      +  DL Q G +GL++AAE++D   
Sbjct: 1   MARRRADPIATRNRQVAEHLFLVRRVANHYAACTAERRDDLQQVGALGLIRAAERYDDRS 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
              F+ +A   ++ A+   + D +  +R+   ++++  ++ R     +   +      + 
Sbjct: 61  AVPFAAFARPHIRGAVLHYLRDVAPLLRLSRRLQERAFQLSRQCGSAAVSQQASHDSRQG 120

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
             +    ++ V+ +     + +  +    +   +   D IED N         Q    ET
Sbjct: 121 ELESLRCLQSVQLLPPWRLQEV--QANSTNCWANPPVDRIEDAN---------QEIESET 169

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               L+ L  R+ +V+      G     TL  V ++  ++   + ++  + + +L+ 
Sbjct: 170 VLAALSQLERRQRQVVEAVVLQG----QTLRTVAERLGISAATVHRVLHQGLAELRR 222


>gi|262385095|gb|ACY64545.1| RNA polymerase sigma-70 factor [Pseudomonas cannabina]
          Length = 165

 Score = 67.2 bits (162), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 22/121 (18%), Positives = 45/121 (37%), Gaps = 4/121 (3%)

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           +  P  + A      V  ++   +       +D+K ++   V    L +L   + L   +
Sbjct: 45  ESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQ 101

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
            + LVE++    +R+   E  +++L      + R  FL +  G E+D  W          
Sbjct: 102 FEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPGHEVDESWTDALAKGKSK 161

Query: 394 E 394
            
Sbjct: 162 Y 162


>gi|229140635|ref|ZP_04269187.1| Prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus cereus
           BDRD-ST26]
 gi|228642831|gb|EEK99110.1| Prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus cereus
           BDRD-ST26]
          Length = 314

 Score = 67.2 bits (162), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 98/243 (40%), Gaps = 28/243 (11%)

Query: 448 MVEANLRLVISVAKKY---------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            ++   RLV     KY             L   DLIQ G +GL+ A   F   LG+KF+T
Sbjct: 22  FMKKYSRLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTT 81

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A+  +   I +++ D               ++V     ++S     +   E IAK L +
Sbjct: 82  FAVPIILGYIRKAVRDS--------QKIRITNEVYEIKGKISRMKLHDEEVESIAKLLEV 133

Query: 559 PVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
            V  V+   +     ISL+TP+  E   +   L + + DK     LD+ I+   +   T 
Sbjct: 134 SVRDVKTAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTLDNVIK---KMIITA 190

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L++L  +E+             + T   +GK+  VT+ +I +I     +K +       
Sbjct: 191 FLSTLCSKEK-----FVWELHAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNKHS 245

Query: 676 LRS 678
           LR 
Sbjct: 246 LRD 248


>gi|327254572|gb|EGE66188.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           STEC_7v]
          Length = 238

 Score = 67.2 bits (162), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 94/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTAQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++   + L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFITQQMLQQALSQLSEKEQLILAMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|218703543|ref|YP_002411062.1| flagellar biosynthesis sigma factor [Escherichia coli UMN026]
 gi|293403374|ref|ZP_06647465.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1412]
 gi|298378986|ref|ZP_06988867.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1302]
 gi|300899471|ref|ZP_07117719.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           198-1]
 gi|218430640|emb|CAR11506.1| putative RNA polymerase sigma factor for flagellar operon
           (FliA/lafS-like) [Escherichia coli UMN026]
 gi|291429227|gb|EFF02247.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1412]
 gi|298280099|gb|EFI21603.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1302]
 gi|300356950|gb|EFJ72820.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           198-1]
          Length = 238

 Score = 67.2 bits (162), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 93/245 (37%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFVTQQMLQYALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|331671820|ref|ZP_08372616.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli TA280]
 gi|331070809|gb|EGI42168.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli TA280]
          Length = 238

 Score = 67.2 bits (162), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 93/245 (37%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   IGL+ A
Sbjct: 9   EEFAAAPILTPQQESHYLQAYLPLVRKVVRHLAPQC----NCIIDRQDMEQTALIGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVQRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFVTQQMLQHALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|170021344|ref|YP_001726298.1| flagellar biosynthesis sigma factor [Escherichia coli ATCC 8739]
 gi|188494786|ref|ZP_03002056.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|169756272|gb|ACA78971.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli ATCC
           8739]
 gi|188489985|gb|EDU65088.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
          Length = 238

 Score = 67.2 bits (162), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 94/245 (38%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNSEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++   + L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFVTQQMLQQALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|153812846|ref|ZP_01965514.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
 gi|149831058|gb|EDM86147.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
          Length = 107

 Score = 67.2 bits (162), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/88 (34%), Positives = 46/88 (52%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             V+++ +       A+  +   N  L+ SVA ++  RG +  DL Q G+IGL+KA +KF
Sbjct: 4   DTVALIGRAHQGDKEARDILFHENTGLIYSVAHRFLGRGAEMEDLFQIGSIGLLKAVDKF 63

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQS 516
           D     KFSTYA+  +   I R + D  
Sbjct: 64  DLSYDVKFSTYAVPMIAGEIKRFLRDDG 91


>gi|145952318|gb|ABP98982.1| sigma factor F [Mycobacterium gilvum]
          Length = 139

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 70/148 (47%), Gaps = 12/148 (8%)

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKE 572
            S ++++P  +++   ++      +S ++ R PT  E+A +L M  + V + L    +  
Sbjct: 1   NSWSVKVPRRLKELHLRLGAATAELSQRLGRAPTATELAAELEMDRDEVIEGLVAGSSYN 60

Query: 573 PISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            +S+++   G+ED   + D + D +      +  Q   RE    +LA+L  RE  VL +R
Sbjct: 61  TLSIDSGRHGNEDAPAIADTLGDVD-----LTLDQIENREALRPLLAALPERERTVLVLR 115

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           F        T  ++ ++  +++  + ++
Sbjct: 116 FF----ESMTQTQIAERVGISQMHVSRL 139


>gi|260866428|ref|YP_003232830.1| putative RNA polymerase, sigma 28 factor [Escherichia coli O111:H-
           str. 11128]
 gi|257762784|dbj|BAI34279.1| predicted RNA polymerase, sigma 28 factor [Escherichia coli O111:H-
           str. 11128]
 gi|323178476|gb|EFZ64054.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1180]
          Length = 213

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/207 (19%), Positives = 85/207 (41%), Gaps = 22/207 (10%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N  +   D+ Q   +GL+ A  ++       F+ YA+  ++ AI   +         P  
Sbjct: 20  NCIIDRQDMEQTALMGLLNAIRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQ 75

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDE 583
           +R K H++    R    K+  EP   E+A +     + +  + L+  +   SL+  +  E
Sbjct: 76  LRQKYHQMKDLIRETRKKLGHEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGE 135

Query: 584 DTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
                 +G  +ED           Q   ++   + L+ L+ +E+ +L M +      +  
Sbjct: 136 GPGIPLVGRELED-----------QFVTQQMLQQALSQLSEKEQLILSMYYQH----EMN 180

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+     +T  RI Q+  +  +K++
Sbjct: 181 LKEIALVLGLTEARICQLNKQIAQKIR 207


>gi|145559057|gb|ABP73390.1| SigF [Mycobacterium aurum]
          Length = 140

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/148 (19%), Positives = 67/148 (45%), Gaps = 11/148 (7%)

Query: 515 QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKE 572
            S ++++P  + +   ++      +S ++ R PTP E+A++L M  + V +      +  
Sbjct: 1   NSWSVKVPRRLEELHLRLGSATAELSQRLGRAPTPTELAEELGMDRDEVVEGPVAGSSYN 60

Query: 573 PISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
            +S+++   G+ED   + D + D +      +  Q   RE    +L SL  RE  V+   
Sbjct: 61  TLSIDSGGSGNEDAPAIADTLGDVD-----LTLDQIENREALRPLLESLPERERTVVV-- 113

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +      T  ++ ++  V++  + ++
Sbjct: 114 -PLRFFESLTQTQIAERIGVSQMHVSRL 140


>gi|325111003|ref|YP_004272071.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324971271|gb|ADY62049.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 555

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/85 (36%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVT 652
           D           Q +       +L  L PRE  ++  RFG+       TLE+VG +F VT
Sbjct: 467 DARDNPFRQELNQQHQHSAIMSILGQLDPRERDIILHRFGLNKGTEPETLEQVGHRFGVT 526

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLR 677
           +ERIRQIE++A+ KLK  +  +KL 
Sbjct: 527 KERIRQIESRALSKLKKIAVEEKLE 551



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/84 (36%), Positives = 53/84 (63%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +++ + +   EA   K  ++ +NLRLV+S+AK++      F +++ +GN+ L++A EKF
Sbjct: 361 RLMTKIEELIREAVAVKNFLIRSNLRLVVSIAKRHFKPQANFFEMVSDGNMSLIRAIEKF 420

Query: 489 DWCLGYKFSTYAMWWVKQAITRSI 512
           D+  G KFSTYA W + +   RSI
Sbjct: 421 DYSQGNKFSTYATWAIMKNYARSI 444


>gi|133722029|gb|ABO37133.1| SigF [Mycobacterium asiaticum]
          Length = 142

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/151 (20%), Positives = 69/151 (45%), Gaps = 13/151 (8%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--T 570
            D S ++++P  +++   ++      +S ++ R PT  E+A +L M    V + L    +
Sbjct: 1   RDNSWSVKVPRRLKELHLRLGTATAELSQRLGRAPTATELAAELGMDRAEVVEGLVAGSS 60

Query: 571 KEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVL 628
              +S+++  G+ED     + D + D +A        +   RE    +L +L  RE  VL
Sbjct: 61  YNTLSIDSGGGNEDDDARAIADTLGDVDA-----GLDRIENREALRPLLEALPERERMVL 115

Query: 629 RMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            +RF        T  ++ ++  +++  + ++
Sbjct: 116 VLRFF----ESMTQTQIAERVGISQMHVSRV 142


>gi|59889798|emb|CAH19154.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Escherichia
           coli]
 gi|284920062|emb|CBG33119.1| lateral flagellar sigma factor 28 protein (FliA-like) [Escherichia
           coli 042]
          Length = 238

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 93/245 (37%), Gaps = 22/245 (8%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            EF     +  + E     A   +V   +R +        N  +   D+ Q   +GL+ A
Sbjct: 9   EEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQC----NCIIDRQDMEQTALMGLLNA 64

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
             ++       F+ YA+  ++ AI   +         P  +R K H++    R    K+ 
Sbjct: 65  IRRYGLP-DEGFAGYAVHRIRGAILDELRALDW---RPRQLRQKYHQMKDLIRETRKKLG 120

Query: 545 REPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
            EP   E+A +     + +  + L+  +   SL+  +  E              ++  + 
Sbjct: 121 HEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI---------PLAGREL 171

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  RI Q+  + 
Sbjct: 172 EDQFVTQQMLQHALSLLSEKEQLILSMYYQH----EMNLKEIALVLGLTEARICQLNKQI 227

Query: 664 IRKLK 668
            +K++
Sbjct: 228 AQKIR 232


>gi|157147079|ref|YP_001454398.1| flagellar biosynthesis sigma factor [Citrobacter koseri ATCC
           BAA-895]
 gi|157084284|gb|ABV13962.1| hypothetical protein CKO_02856 [Citrobacter koseri ATCC BAA-895]
          Length = 231

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/218 (20%), Positives = 97/218 (44%), Gaps = 20/218 (9%)

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512
            ++V  +A + T+  +   D+ Q   +GL+ +  ++      +F+ YA+  V+ A+   +
Sbjct: 27  NKVVKQLAYQ-TSSVIDRDDMEQIALMGLLTSLRRYGHP-DEQFAAYAIQRVRGAVLDEL 84

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KIT 570
                    P  +R K HK+    R ++ ++ R P+ E+I+  L++  E  ++ L     
Sbjct: 85  RLLDW---RPRRLRQKTHKLNDAIREIARQLGRTPSFEDISHHLSITAEEYQEYLLLDCA 141

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           K   SL+  +G++  +          A+       +  +  T    LASL  RE+ +L +
Sbjct: 142 KTLESLDDLLGNDVYA---------GALDSRPLEEEIIVSRTLRNALASLDEREQLILTL 192

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +      + +L+E+     +T  R+ Q+     +K++
Sbjct: 193 YYQH----EMSLKEIALVLNLTEARVCQLNKIIAQKIQ 226


>gi|289444245|ref|ZP_06433989.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
 gi|289417164|gb|EFD14404.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
          Length = 375

 Score = 66.8 bits (161), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 186 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 245

Query: 139 EIAIAKRIEAGR--AMMMASLCE 159
           E+ +AKRIEAG     +M  L E
Sbjct: 246 EVELAKRIEAGLYATQLMTELSE 268



 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 3/89 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 243 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 302

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
           V+S+AK+YT RG+ FLDLIQEGN+GL++ 
Sbjct: 303 VVSLAKRYTGRGMAFLDLIQEGNLGLIRG 331


>gi|238019186|ref|ZP_04599612.1| hypothetical protein VEIDISOL_01050 [Veillonella dispar ATCC 17748]
 gi|237863885|gb|EEP65175.1| hypothetical protein VEIDISOL_01050 [Veillonella dispar ATCC 17748]
          Length = 261

 Score = 66.4 bits (160), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 102/251 (40%), Gaps = 11/251 (4%)

Query: 422 ISISEFRHIVSMVRKGE--CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           ++  E + +     +          K+++V      +IS+A  Y N      DL QEG I
Sbjct: 13  LTKEEEKALFKEYHETPSLRRKKQIKEDLVLNQCGQIISIASIYKN-VDDIEDLFQEGMI 71

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            ++++ E +D+     F+TY    + + I   +     TI +P    +K+ K+ +    +
Sbjct: 72  AVLESFENYDYTHEASFTTYMRRGIFRQICDYLRRN-KTIGLPQAAIEKLKKINKAK-EL 129

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             ++ +  T E I+    +    V ++L               E    + + +EDK A  
Sbjct: 130 LERLNKPITTEAISDITNIKEHNVIEILNTLSVEELDRLCNDGEGEVSILEHVEDKQASK 189

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             D  +      T    ++ L+ RE+ V+ + +        +L ++ ++  +    I   
Sbjct: 190 AFDDVLDDMTEPTID--MSCLSDREKEVIILLYYKN----LSLHQIARRLHLKITLISDA 243

Query: 660 EAKAIRKLKHP 670
           +++A++KL+  
Sbjct: 244 KSRALKKLRKA 254


>gi|295104322|emb|CBL01866.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 221

 Score = 66.4 bits (160), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 82/244 (33%), Gaps = 46/244 (18%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY--------TNRGLQFLDLIQEGNIGLMK 483
            +    +   + A   ++E N   +   A           +   L   DL Q GN+GL K
Sbjct: 7   RLCALAQKGDATALDSLIENNKSFIGKEANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWK 66

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           A  KFD   G KF TYA   +  A+   + D   T    + + DK               
Sbjct: 67  AVPKFDAARGMKFLTYAAPAICNAMMDMVRDAFATFEQRMQIEDKD-------------- 112

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
                                    I  + +SL+  +  E+     + I D  A+ P   
Sbjct: 113 ------------------------GICYQRVSLDDVLPGEEQLRRIEAIADLYAMQPQSI 148

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +   R      L  LT RE+  L  R+G     +H L      F + + R ++ E +A
Sbjct: 149 IEEQESRRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLAKSRAKKTEEQA 208

Query: 664 IRKL 667
           +  L
Sbjct: 209 MDNL 212


>gi|222100647|ref|YP_002535215.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga neapolitana
           DSM 4359]
 gi|221573037|gb|ACM23849.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga neapolitana
           DSM 4359]
          Length = 220

 Score = 66.4 bits (160), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/202 (22%), Positives = 92/202 (45%), Gaps = 20/202 (9%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  DLIQEG +  + A E++D      F+T+ +  VK A+   +         P ++R 
Sbjct: 30  VEVEDLIQEGILAALSAFERYDPSKA-SFTTFVIKRVKGAMYDYLRRIDWM---PRNLRK 85

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            +  V +      ++ +  P+ EE+A+K  + ++ V +          L     DE+ + 
Sbjct: 86  NVKLVEKAI----HESEEFPSDEELARKTGLELKEVIRAKNEMMRRQILMIDAFDEELAL 141

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                       P ++A +  L+E   + +  L+ +E+ VL +RF      + +L+E+ +
Sbjct: 142 --------KTEGPDETAYREILKEKIKKAIEKLSEKEKLVLSLRF----EKELSLKEIAR 189

Query: 648 QFCVTRERIRQIEAKAIRKLKH 669
              V+  R+ QI + A+ K+K 
Sbjct: 190 VLGVSESRVSQIVSLALLKIKR 211


>gi|77020206|ref|YP_338165.1| RNA polymerase sigma factor, putative [Bacillus phage Cherry]
 gi|76563996|gb|ABA46386.1| RNA polymerase sigma factor, putative [Bacillus phage Cherry]
          Length = 248

 Score = 66.4 bits (160), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 93/245 (37%), Gaps = 28/245 (11%)

Query: 446 KEMVEANLRLVISVAK-KY--------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E +E   RLV      +Y         + GL   DL Q   IGL+KA + FD   G  F
Sbjct: 20  DEFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFXMIGLIKARDNFDLEFGCAF 79

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA+  +   I R+I D                 V     ++ N+   +  PEEIA  L
Sbjct: 80  STYAVPKIIGEIGRAIRDN--------QKIKVQRTVYGVKGKILNQQLADKEPEEIADIL 131

Query: 557 AMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              V  V+  L+      SL   +      +   L   IED       ++ I    R   
Sbjct: 132 DESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTEDIEETTIN---RAVI 188

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
               A+L P+E  VL MR       + T + +  Q   ++ +I +I AK  ++     + 
Sbjct: 189 REFKAALPPKEYIVLDMRL-----QNMTQQNIANQMGYSQVQISRILAKINQRAAQFGKE 243

Query: 674 KKLRS 678
             L+ 
Sbjct: 244 GGLQD 248


>gi|50954397|ref|YP_061685.1| RNA polymerase, sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50950879|gb|AAT88580.1| RNA polymerase, sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
          Length = 272

 Score = 66.4 bits (160), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 83/226 (36%), Gaps = 32/226 (14%)

Query: 445 KKEMVEANLRLVISVAKK--YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           +  +V  +L LV  +          L   +L   GN+ L +A   FD   G  F++YA  
Sbjct: 30  RDRLVTDHLPLVGYIVSDLCMKAAHLDRDELASAGNLALPRA---FDPDKGVTFASYART 86

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +  AI+  +  +     +   MR +I         ++  + R PT +E+A  L +  + 
Sbjct: 87  RISGAISDELRSKDW---VSRGMRKRIKAAQSARDDLAKTLGRTPTEDEVASLLGIGKKA 143

Query: 563 VRKVLKI-TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + + +      P+S +            D   D+ A                   + +L 
Sbjct: 144 LAEAMHHQATGPVSFD------------DLAPDEAAEITERDVF-------LRTAVEALP 184

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R   V+   F      +  +++V  +  +T   +   +++A+R L
Sbjct: 185 DRLRLVVTRIF----CEERQVKDVAAELGITHAAVSMTKSEAVRML 226


>gi|329897641|ref|ZP_08272165.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC3088]
 gi|328921090|gb|EGG28499.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC3088]
          Length = 204

 Score = 66.4 bits (160), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 81/205 (39%), Gaps = 12/205 (5%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           ++  +L+Q G IGL++A + FD   G   +++A   ++ AI   +  +S   R       
Sbjct: 11  VELEELVQIGMIGLLEAFKSFDESQGDDLASFATKRIRGAILDEVRRRSPLSRQDNIHAK 70

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
               +         +  R P+  EI+ ++ + +E   +    T         +  E+   
Sbjct: 71  TREAI---IDDHLARTGRRPSAVEISSEMGVTLEDYHRSEMKTHTYQLSSYEVLTENGFE 127

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
                   +A SP +    +         +  L  R++ +L + +      +  L+E+G 
Sbjct: 128 QA-----HDADSPDEEIEHSQTLGILETRIGQLEQRDQLILSLYY----EKELNLKEIGS 178

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSR 672
              ++  R+ Q+ +K + +L+   R
Sbjct: 179 ILNISESRVSQLLSKIVTQLRAEVR 203


>gi|83944156|ref|ZP_00956612.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
 gi|83955144|ref|ZP_00963800.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83840473|gb|EAP79646.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83845023|gb|EAP82904.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
          Length = 223

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 97/247 (39%), Gaps = 51/247 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +++ + R ++        +   A + +V ++ R+V   A+K ++   +  DLI EG +GL
Sbjct: 14  LALEDERVLLK--DWQVSKDKFALESLVLSHARIVFYWARKLSDDQAEREDLISEGILGL 71

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           + AA+ FD     +FSTYA WWVK A   +       +  P  ++  +           +
Sbjct: 72  IHAADLFDLDRDVRFSTYAKWWVKNATMTARNHLRAIVETPAGVQKTVQ----------H 121

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            I  + +   +A +   P E V                                     +
Sbjct: 122 SIDDDDSFALLASEDPNPEEAV-------------------------------------I 144

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             + Q  +R      +  L P +  VLR R         +++++  +  VT  ++RQIE 
Sbjct: 145 AQSSQTLIRARLLEAMERLQPMDREVLRARTL--QQPPESIQDLATRMEVTPAKLRQIER 202

Query: 662 KAIRKLK 668
           +A+ +LK
Sbjct: 203 RAMSRLK 209


>gi|220913709|ref|YP_002489018.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219860587|gb|ACL40929.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 264

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 74/206 (35%), Gaps = 21/206 (10%)

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
             L   DL   G+I L+ +A+ FD  +G  F  +A   +  A    +  Q    R     
Sbjct: 29  SHLSRDDLASVGSIALITSADSFDPAMGVPFGAFARRRIIGAFADEMRSQDWATRSARKR 88

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
             +   V  T   +   + R PT  E+A  L +    V   L      +           
Sbjct: 89  IKETMGVEET---LRGLLGRNPTVPEMAATLGVERSVVEAALADAARTL----------- 134

Query: 586 SHLGDFIEDK---NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           + L D I +       SP  S +     +     + +L  +   V+   +  G     T+
Sbjct: 135 TPLDDVIVETYPAETASPEHSVLADERVKYLRAAVTALPAKMRYVIEEIYLAG----RTV 190

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
           +E+ ++   T   + Q  ++AIR ++
Sbjct: 191 KELAEELGSTHAAVSQQRSEAIRLMR 216


>gi|225849143|ref|YP_002729307.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643617|gb|ACN98667.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 225

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 94/230 (40%), Gaps = 38/230 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           KK +VE NL LV  VA K   R     + F DL Q G IGL+KA E +    G KFSTYA
Sbjct: 7   KKRLVEENLNLVKKVASKIYYRLPDCSIDFDDLFQVGVIGLIKATENYHQDKG-KFSTYA 65

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I                        +R+     +  K   T E+      +P 
Sbjct: 66  YIRIRGEILDF---------------------LRSLEVFPHTEKDYITVEKAEPDDNLP- 103

Query: 561 EGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                    T   +SL+  I  ED S  L D I   +     + A++  + + +  +   
Sbjct: 104 ------YSNTAVILSLDKIISIEDDSISLIDSIVSNSKTPEEEYALKEQIEKISQIIEQY 157

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L   E++V+   F      +   +E+ +   ++  RI QI+AKA+ K++ 
Sbjct: 158 LDENEKKVINYLFF----EEKDPKEIQEIMGISLGRISQIKAKAVEKIRE 203


>gi|291519565|emb|CBK74786.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Butyrivibrio
           fibrisolvens 16/4]
          Length = 194

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/141 (21%), Positives = 58/141 (41%), Gaps = 8/141 (5%)

Query: 445 KKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           +++++     LV  VA +   Y    +++ DL   G  GL+ A +KFD     KF TYA 
Sbjct: 22  REQLILEYAPLVKIVAGRLCMYLGNTVEYEDLCSYGIFGLIDAIDKFDLAKDVKFETYAS 81

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             ++ +I   I        IP  +R +   +    + +  +     + E+IA +L +  +
Sbjct: 82  LRIRGSILDQIRKMDW---IPRTIRQRQRMIDDAIKTVEARTGHSASDEDIAAELNISSD 138

Query: 562 GVRKVLKI--TKEPISLETPI 580
              K          +SL   +
Sbjct: 139 EFLKWQNQLNVTNVVSLNEFV 159


>gi|302385749|ref|YP_003821571.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
 gi|302196377|gb|ADL03948.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
          Length = 203

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/201 (21%), Positives = 97/201 (48%), Gaps = 5/201 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
            +  ++ +      +  E   ++    +G      AKK +VE NLR  +  A++Y  RG+
Sbjct: 6   YQMYLEEMGNIPPCTRDEQERLLKEAAEGR---KEAKKRLVEGNLRTALEYAREYDGRGV 62

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYK--FSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
              DL+QE N+ LM A E+F      +  F ++    +++A+T ++ +Q    +    + 
Sbjct: 63  LITDLVQEANMALMMAVEEFSAMENGRLAFDSFTGRKIREALTAAVEEQQSACQTGEELA 122

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            +++ + + ++ ++ ++ RE T EE+A K+ M VE ++ ++K+  + +S+     D +  
Sbjct: 123 ARVNVLQKVSQALAGELGREATVEELADKMKMSVEEIKGIMKMAMDAMSMNAETMDLEAL 182

Query: 587 HLGDFIEDKNAVSPLDSAIQA 607
              + IE     +  D   + 
Sbjct: 183 AEVEGIEITEDEAAEDYDYEE 203


>gi|326791410|ref|YP_004309231.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
 gi|326542174|gb|ADZ84033.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
          Length = 251

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 91/248 (36%), Gaps = 53/248 (21%)

Query: 425 SEFRHIVSMVRKGECEASIA--KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
            E   I  ++   E E  I   K  ++E NLRLV+ +A+K+ N G+   DLI  G IGL+
Sbjct: 48  EEEILIQKLIEFAEQEEEIKAIKTTLIERNLRLVVYIARKFENTGIYMEDLISIGTIGLI 107

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           K+   F  C   K +TYA   ++  I   +                            NK
Sbjct: 108 KSINTFKPCKKIKLATYASRCIENEILMFLRRT-------------------------NK 142

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           +K E + +E                            +  +    L   I          
Sbjct: 143 LKTEVSIDEP-------------------------LNVDWDGNELLLSDILGTEPDIIYR 177

Query: 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIG-MNTDHTLEEVGKQFCVTRERIRQIEA 661
           +  +   ++   + L  LT RE  ++ +RFG      + T +EV     +++  I ++E 
Sbjct: 178 NIEEEVDKKLLKQALLKLTDREREIVELRFGFTPQGKEKTQKEVADLLGISQSYISRLEK 237

Query: 662 KAIRKLKH 669
           K I +LK 
Sbjct: 238 KIILRLKK 245


>gi|254698074|ref|ZP_05159902.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 118

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 37/120 (30%), Positives = 58/120 (48%), Gaps = 2/120 (1%)

Query: 384 VSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASI 443
           +S +   P       V     +    ++ I+S      +   E R +   +R  E +   
Sbjct: 1   MSSSSTVPANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--IRWKETKDQD 58

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     +FSTYA WW
Sbjct: 59  ALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWW 118


>gi|254698073|ref|ZP_05159901.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 188

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/176 (22%), Positives = 76/176 (43%), Gaps = 13/176 (7%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558
           ++ ++   I      +R       K     + R   +++         E   EI+ +L +
Sbjct: 1   MRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGV 60

Query: 559 PVEGVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRE---T 612
               V     +++    SL  P+  E+T  S   DF+ D + +    +    ++      
Sbjct: 61  STSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRW 120

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            TR L +L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 121 LTRALDTLNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 174


>gi|333024157|ref|ZP_08452221.1| putative RNA polymerase sigma factor WhiG [Streptomyces sp. Tu6071]
 gi|332744009|gb|EGJ74450.1| putative RNA polymerase sigma factor WhiG [Streptomyces sp. Tu6071]
          Length = 123

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 14/115 (12%)

Query: 564 RKVLKITKEPISLETPIGDED----------TSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            + L      +SL   +  E+             + D +ED  A +P++ A    LR+  
Sbjct: 5   VEDLHAVFSQLSLANVVALEELLSVGSEGGGRLSIMDTLEDTGADNPVEVAEGRELRQLL 64

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           +R + SL  RE+ V+ + +  G     TL E+G    VT  R+ QI  K++ +L+
Sbjct: 65  SRAINSLPDREKTVVMLYYYEG----LTLAEIGHVLGVTESRVSQIHTKSVLQLR 115


>gi|260438492|ref|ZP_05792308.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292809081|gb|EFF68286.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 207

 Score = 66.0 bits (159), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 88/248 (35%), Gaps = 52/248 (20%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ SE +  +   +        A   ++  NLRLV  + K Y        + +  G IGL
Sbjct: 8   LTPSEEQEYLKRYK---NGDEEAGNVLILRNLRLVAHIVKHYNFDEKDIEEYLSIGTIGL 64

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           +KA + FD   G + +TYA   +   +  ++                             
Sbjct: 65  IKAIKTFDCSKGNRLATYASKCIDNELLMALRS-------------------------EK 99

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           K  ++ + +E         E     +  T E   L+  I   +   L + IE        
Sbjct: 100 KKNKDISLQETVGIDKEGNEINIIDIIDTGEKDFLDCYILKYNIKKLYEGIE-------- 151

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
                             LT RE+ ++  R+G+  N + T  E+     ++R  + +IE 
Sbjct: 152 ----------------KVLTEREKNIIIKRYGLLRNDEITQRELADGMGISRSYVSRIEK 195

Query: 662 KAIRKLKH 669
           +A+ KLK+
Sbjct: 196 EALNKLKN 203


>gi|239934552|emb|CAR94590.1| DNA-directed RNA polymerase subunit D [uncultured alpha
           proteobacterium]
          Length = 237

 Score = 65.6 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 57/197 (28%), Positives = 83/197 (42%), Gaps = 22/197 (11%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG-----G 198
           KRIEAGR  M+A LCESPLTFQA+IIWRDELN+   LLR+IIDLEA      K       
Sbjct: 8   KRIEAGREAMIAGLCESPLTFQAIIIWRDELNETKILLRDIIDLEATYDGPDKKVDNSIA 67

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                +G +    E ++  +     +  E     A   ++        P   +E+ E   
Sbjct: 68  AVAAEKGETVPPTEGAAPAEGGAPAEGAEPAEGVATTDAEKPAEAASDPQAKSESGETAD 127

Query: 259 -----------------DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                            D+D+ D   +L+AM   +       +       ++LR LQ   
Sbjct: 128 GDTPLKTRPKARATKTRDDDDLDGGISLAAMGSGIETPRSRDVRPHRVELQKLRKLQYQN 187

Query: 302 VNGQKDEKSSVKCKVLK 318
           V     ++S    +V +
Sbjct: 188 VEKALADESLSSAQVKR 204


>gi|56606829|gb|AAW02799.1| sigma factor [Nonomuraea sp. ATCC 39727]
          Length = 92

 Score = 65.6 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 55/90 (61%), Positives = 72/90 (80%)

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
           YKFSTYA WW+KQAITR++ADQ+ TIRIPVHM + I+KV R  RRM N++ REPTPEEIA
Sbjct: 2   YKFSTYATWWIKQAITRAMADQARTIRIPVHMVELINKVARVQRRMQNELGREPTPEEIA 61

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE 583
           ++  + V+ V +V +  +EPISL TP+G+E
Sbjct: 62  QESELEVDRVIEVQRYGREPISLHTPLGEE 91


>gi|332524258|ref|ZP_08400482.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Rubrivivax
           benzoatilyticus JA2]
 gi|332107591|gb|EGJ08815.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Rubrivivax
           benzoatilyticus JA2]
          Length = 304

 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 46/230 (20%), Positives = 80/230 (34%), Gaps = 17/230 (7%)

Query: 448 MVEANLRLVISVAK---KYTNRGLQFLDLIQEGNIGLMKAAEKFDWC-------LGYKFS 497
           +V  N   V   A+   ++    ++  DLIQ G I + +A+  F W            F+
Sbjct: 11  LVARNQSWVRQQAQSLVRHLPANVEKADLIQVGLIAVAQASLSFVWDGDPDTAEAHEAFA 70

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            YA   VK A+   +        +    R KI  +     R  +    E    E+A+   
Sbjct: 71  RYARQRVKGAMIDELRQMD---VLTRAQRRKIKVLQIARERWRSTNGGEAGLAELARLCK 127

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           M +E V  + ++ +      +   D++                      A +        
Sbjct: 128 MDLEEVALLEQLAQASQQRSSSGEDDEPEFTERHHPATEKDEVEARVDTAIVLRHLETFF 187

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           A L  RE RV+    GIG     +  E+     VT  R+ Q+    +R++
Sbjct: 188 AQLPERERRVIDAYLGIG----MSPVELAASLKVTPSRVSQMYHGLLRRM 233


>gi|307690662|ref|ZP_07633108.1| sporulation sigma factor SigG [Clostridium cellulovorans 743B]
          Length = 139

 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 37/146 (25%), Positives = 69/146 (47%), Gaps = 11/146 (7%)

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE-- 583
           RD  ++ ++   ++  +  +EPT  +IAK+L +  E V   L   +EP+SL  PI  +  
Sbjct: 1   RDIAYRALQVRDKLLTENNKEPTVYQIAKELDVAKEEVIFALDAIQEPVSLFEPIYHDGG 60

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D  ++ D I D   +        A         +  L+ RE+ +L MRF  G     T  
Sbjct: 61  DAIYVMDQISDSKNLDESWLENIA-----IKEAMKRLSDREKLILNMRFFDG----RTQM 111

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           EV  +  +++ ++ ++E  A+R ++ 
Sbjct: 112 EVADEIGISQAQVSRLEKNALRHMRK 137


>gi|134298861|ref|YP_001112357.1| sigma-70 region 2 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051561|gb|ABO49532.1| sigma-70 region 2 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 3/116 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           G W   V   V+ ++ + + I + +    +   E    ++++        +A+  + E N
Sbjct: 4   GLWTVTVLSVVNGVMALVSYIANNTFPQPLKEVEEARYLALL---AEGDEMARNILTERN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LRLV  + KK+ + G    DLI  G IGL+KA   F    G + +TYA   ++ AI
Sbjct: 61  LRLVAHIVKKFDSTGEDVDDLISIGTIGLIKAINTFKADKGTRLATYAARCIENAI 116


>gi|32262696|gb|AAP77743.1| RNA polymerase sigma 28 factor [Helicobacter hepaticus ATCC 51449]
          Length = 190

 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 82/201 (40%), Gaps = 17/201 (8%)

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             DL+  G   L+K A ++D  L   F  +A   V  A+   +        +    R  +
Sbjct: 1   MADLVSIGTEELIKLARRYDSSLNDSFWGFAKTRVNGAMLDYLRSLD---VLSRANRKLV 57

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
             +     +  N+ + EP+ E +AK L   +  +++    +     +   +  ++  +  
Sbjct: 58  KSIDYEVSKYFNEHQEEPSDEYLAKVLKEDIAKIKEARMASD----IYALVPIDEQYNAI 113

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                  A + L+   +  L E    VL  L  RE+ ++++ +      + +L+E+ +  
Sbjct: 114 ------CAENILEDVQKDELMEIIFNVLKKLGKREQMIIQLYYF----EELSLKEISEIL 163

Query: 650 CVTRERIRQIEAKAIRKLKHP 670
            +T  RI QI  + ++K++  
Sbjct: 164 DITESRISQITKEIVKKIRQA 184


>gi|298243769|ref|ZP_06967576.1| RNA polymerase sigma factor, sigma-70 family [Ktedonobacter
           racemifer DSM 44963]
 gi|297556823|gb|EFH90687.1| RNA polymerase sigma factor, sigma-70 family [Ktedonobacter
           racemifer DSM 44963]
          Length = 453

 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 58/278 (20%), Positives = 113/278 (40%), Gaps = 57/278 (20%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVR------KGECEASIAKKEMVEANLRLVISVAKK 462
            R  +  IS+   +  ++   +V  ++        + EA    ++++E +LRLVI VA +
Sbjct: 18  YRQYLADISIHPPLVNNQDDRLVQQLKALRNDPTRQDEARAIVQQLIEGSLRLVIFVAAR 77

Query: 463 YTNRG---------LQFLDLIQEGNIGLMKAAEKFDWC--LGYKFSTYAMWWVKQAITRS 511
           +             +  +DLIQ GN+ L++ A ++         FS YA  +++ A+ +S
Sbjct: 78  FYRYYRALDGGRFRVPLMDLIQTGNMALVECAHRYLDREAEHTDFSAYAASYIRFALRKS 137

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
                       ++R  + KV +     + +  R     E++                  
Sbjct: 138 ------------YIRASLFKVPQAEWDEAAEQGRLFQFYEVS------------------ 167

Query: 572 EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              SL+ P  DE T  L D +E    +S           E    +LA +  RE++V+R+R
Sbjct: 168 ---SLDQPFSDESTRSLLDCLETPEPLS-----ENTQACERAETLLARVPEREQQVVRLR 219

Query: 632 FGIGM--NTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +G+       HT +E+  +   + +    IE + ++ L
Sbjct: 220 YGLDPLDQRTHTYQEIADKIGASVQTCLNIEQRVLQAL 257


>gi|262273512|ref|ZP_06051326.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
 gi|262222490|gb|EEY73801.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
          Length = 246

 Score = 65.6 bits (158), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 43/200 (21%), Positives = 78/200 (39%), Gaps = 13/200 (6%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   D+ Q G + L++   ++           A+  ++ A+   +            +R 
Sbjct: 50  MNRDDMEQIGLMALLETIRRYPEEDEGGLKKLAVPRIRGALLDEMRRLDW---RSRQLRQ 106

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           K H++    R ++  + R PT  E+A+ + M V  VR++       +  E        S 
Sbjct: 107 KTHQLCEKEREVAKTLGRAPTDPELAQAMEMSVSDVRQLR------LDYEAERPHSFESM 160

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
             D I         D   +  L       LA+LT RE+ VL   F      + +++E+  
Sbjct: 161 QEDNIAIPGLAVYCDHIEKEKLAVALKAALATLTEREQIVLSFYF----EHEMSMKEIAL 216

Query: 648 QFCVTRERIRQIEAKAIRKL 667
              +T  RI QI+ KA+  L
Sbjct: 217 VLDLTEARICQIQKKALATL 236


>gi|295092950|emb|CBK82041.1| DNA-directed RNA polymerase specialized sigma subunit [Coprococcus
           sp. ART55/1]
          Length = 128

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/113 (28%), Positives = 59/113 (52%), Gaps = 1/113 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++   +     A+ ++V  N+ LV+SVA++Y  RG +  DLIQ G IGL+KA ++FD  
Sbjct: 6   RLLELAKDGDRDARDKLVTDNMGLVVSVARRYVGRGQELEDLIQIGLIGLVKAIDRFDMD 65

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              K STYA+  ++  I R + D    +++  +++   ++  R    +     
Sbjct: 66  YEVKLSTYAVPLIQGEIRRFLRD-DGMVKVSRNLKTIYYRADRYRHEVEKTEG 117


>gi|222833283|gb|EEE71760.1| predicted protein [Populus trichocarpa]
          Length = 152

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/130 (26%), Positives = 65/130 (50%), Gaps = 6/130 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +  + + ++V+++  LV  +A +   +    +Q  DLIQ G IGL+ AA++++   
Sbjct: 1   MYTIQGKLEQADVVKSHAPLVRRIALQLAAKLPASVQIDDLIQAGMIGLLDAAKRYEDNH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA   ++ A+   +            +R    K+ RT R++  K+ R P   E+
Sbjct: 61  GARFETYASQRIRGAMLDEVRANDW---QSRSLRQFTRKIERTQRQLEQKLGRSPIDSEV 117

Query: 553 AKKLAMPVEG 562
           AK+L M +E 
Sbjct: 118 AKELEMGLEE 127


>gi|113954054|ref|YP_730869.1| type III sigma factor [Synechococcus sp. CC9311]
 gi|113881405|gb|ABI46363.1| putative type III sigma factor [Synechococcus sp. CC9311]
          Length = 271

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 46/218 (21%), Positives = 90/218 (41%), Gaps = 17/218 (7%)

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y        DL+QEG +GL+     FD   G++ STY +  V   I     D+   +RI
Sbjct: 44  RYPG---DPDDLVQEGCLGLINGMANFDPQRGFRISTYVLARVNGQILHFRRDRQHALRI 100

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLE-- 577
           P  ++D   + VR   +   +         +A  L +  +  R+ L         SL+  
Sbjct: 101 PWRLKDLHSRGVRLQAQRLQQSLDPLDELGLAASLNVSPQRWREALIAHSFGHVDSLDVA 160

Query: 578 ---TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
                +  E  S L + IED ++V    + ++          + SL P++   L  R+  
Sbjct: 161 PSIQSVDGELRSSLINQIEDPSSV---PALVEEPTLRWLKDAMMSLEPQQCCWLLARYVD 217

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +    +++++  +  V    +RQ   +++ +L+  +R
Sbjct: 218 NI----SIKDLALRDKVDAGLLRQSIRESLSRLRQAAR 251


>gi|257438884|ref|ZP_05614639.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
 gi|257198699|gb|EEU96983.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
          Length = 153

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 33/96 (34%), Positives = 50/96 (52%), Gaps = 3/96 (3%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +++ S    +S  E     + +R        A+++++  NLRLV  VAKKY  +     D
Sbjct: 23  LEAGSFPKPLSAREEIETFAALR---AGDRSAREKIIRHNLRLVAHVAKKYYAQPGDQED 79

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LI  G IGLMKA + FD     +F+TYA   ++ AI
Sbjct: 80  LISIGTIGLMKAVDTFDITRKARFATYASRCIENAI 115


>gi|182625388|ref|ZP_02953161.1| sigma factor [Clostridium perfringens D str. JGS1721]
 gi|177909385|gb|EDT71837.1| sigma factor [Clostridium perfringens D str. JGS1721]
          Length = 232

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 60/252 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +     A  +++E N +L+  VA K+ +     ++F DL+QEG IG + A  K+
Sbjct: 10  ELVVLYQHGDKKALDKLLENNDKLIYKVASKFYSDKTSSIEFDDLLQEGRIGFILACSKY 69

Query: 489 DWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           D       KF TYA +W+ Q I R I                                  
Sbjct: 70  DIEYIKKTKFITYAFYWIYQKIHRFITTH------------------------------- 98

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSA 604
            T EEI                      SL TP+ +E+   L + IE  +       +  
Sbjct: 99  NTNEEI----------------------SLNTPVSEENQDELINSIESHSNEIKDREEEL 136

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             + LR     V+       ER +   +      + +++++   F  +   ++ I+A+AI
Sbjct: 137 YLSELRLELEAVMDKHNTLNEREILKLYYGWDTDELSIDQIADIFETSSSEVKNIKARAI 196

Query: 665 RKLKHPSRSKKL 676
           RKL++    KK+
Sbjct: 197 RKLRNSMWFKKV 208


>gi|325508641|gb|ADZ20277.1| RNA polymerase sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 219

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 52/227 (22%), Positives = 101/227 (44%), Gaps = 23/227 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++VE  + LV S+A+KY NR   L+  D++Q G I ++ A E FD+  G KFSTYA  
Sbjct: 9   RNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFSTYARH 68

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+  +          I +  + R  + ++ +          ++    EI+ +L +  E 
Sbjct: 69  CVEGGMKNYCKKNE-LIHLSEYQRKDLRRIKKLFDE-KQLENKDIDITEISAELGIEKEK 126

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                      I+L   +  +    + D+ E K   S     +   L      ++ +L  
Sbjct: 127 ----------AINLICFLNKDKYIPIDDY-EYKYGKSFEKEIVDNIL---IRSLIENLPK 172

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ++ ++R R       D +  ++GK++ +TR+ ++Q   + I K+K 
Sbjct: 173 NQQNLIRERL-----KDMSFTDIGKKYNITRQAVQQSVKRIINKMKR 214


>gi|207108883|ref|ZP_03243045.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 228

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/94 (29%), Positives = 49/94 (52%)

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
           +  E    L     +   FL+++       +D PVRMYLREMG I+LLS++ EI ++K+I
Sbjct: 135 KTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQI 194

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
             G  +++ ++C  P     +  ++D L +    
Sbjct: 195 RLGEDIILDAICSVPYLIDFIYAYKDALINRERK 228


>gi|218905533|ref|YP_002453367.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218535778|gb|ACK88176.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 149

 Score = 65.2 bits (157), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/103 (29%), Positives = 52/103 (50%), Gaps = 3/103 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K+ +    +S  + R  + ++ +     + A+  ++E NLRLV  + KK+ N G   
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELMEQ---GDAQARNLLIEHNLRLVAHIVKKFENTGEDA 75

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
            DLI  G IGL+KA E +    G K +TYA   ++  I   + 
Sbjct: 76  EDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLR 118


>gi|313113343|ref|ZP_07798935.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310624319|gb|EFQ07682.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 167

 Score = 65.2 bits (157), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/119 (30%), Positives = 53/119 (44%), Gaps = 7/119 (5%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++S S    +S  E     S +R        A+++++  NLRLV  + KKY        D
Sbjct: 28  LESGSFPRPLSAREETEAFSALR---AGDPAAREKLIRHNLRLVAHIVKKYYALPGDQDD 84

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI----TRSIADQSCTIRIPVHMRD 527
           LI  G IGLMKA + FD     +FSTYA   ++ AI       +  +        H+R 
Sbjct: 85  LISIGTIGLMKAVDTFDSDRRARFSTYASRCIENAILSPAHFGMEKRIHLFHAMTHLRQ 143


>gi|310830517|ref|YP_003965618.1| Sporulation sigma factor SigK [Paenibacillus polymyxa SC2]
 gi|309249984|gb|ADO59550.1| Sporulation sigma factor SigK [Paenibacillus polymyxa SC2]
          Length = 248

 Score = 65.2 bits (157), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 45/262 (17%), Positives = 94/262 (35%), Gaps = 48/262 (18%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           ++I   +     E   +V  V+    +A   K +    +  LV  V K + N G+ + +L
Sbjct: 26  ETIEAASAQETKESEEVVEYVKLPLTDAE--KDKHAREDESLVFYVVKMFENSGVDYDEL 83

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
           +    +G  KA   FD     KFSTY++  +K  I   +  +   ++  + M        
Sbjct: 84  VSIAMVGFAKALHAFDKNRLVKFSTYSINCIKNEILFFLRKERNHVKNSISMN------- 136

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
                                   + V+            +SLE  +             
Sbjct: 137 ----------------------CVLSVDK-------NGNSLSLEDTVSTF---------- 157

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           DK+  S  D  + ++  +     L+ L+ +E+ ++  R+G+      T  E+     +++
Sbjct: 158 DKDERSVEDDIVLSDEIKLLRSALSDLSDKEQYIITYRYGLDRGITKTQREIADAIGMSQ 217

Query: 654 ERIRQIEAKAIRKLKHPSRSKK 675
             + +IE   + K+K   + + 
Sbjct: 218 ANVSKIEKNILDKVKKILKDRY 239


>gi|229587513|ref|YP_002860551.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
 gi|229260138|gb|ACQ51175.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
          Length = 271

 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 57/263 (21%), Positives = 101/263 (38%), Gaps = 15/263 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN--- 465
           ++N     S +  ++    R ++   +K   E+   K+E+++    L++    KY     
Sbjct: 2   VQNSEIKRSKKIILADLPERDLIIGSQKNNKESEKYKEELLKRYEGLIVQWTNKYFKILN 61

Query: 466 -RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +G++F DL+ +  +G +KA EKFD   G   STYA   ++  I  SI   +  I++   
Sbjct: 62  VQGMEFDDLLIDAKLGFLKALEKFDINKGNALSTYATHCMRNYILNSIRVNNNMIKLSSR 121

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
             +K  K+ +  +              I  K+      VR  L  T E  S       E 
Sbjct: 122 EVNKRIKLSKKFKANILNKGNYKFNYNIYNKI-FSQHNVR--LIDTHEYQSYLDNSSIEQ 178

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
                +   +K                     L  L   E  ++   FG+      TL E
Sbjct: 179 EISSEEMFMEKEQKRFNT--------RQIISALKILDKTELFIIVHYFGLFNKKKRTLRE 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKL 667
           + K+  +  E  R+I+ KA+ K+
Sbjct: 231 LSKRLNIGYENTRKIKGKALSKI 253


>gi|169834851|ref|YP_001715950.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
 gi|169408958|gb|ACA57368.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
          Length = 271

 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 57/263 (21%), Positives = 101/263 (38%), Gaps = 15/263 (5%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN--- 465
           ++N     S +  ++    R ++   +K   E+   K+E+++    L++    KY     
Sbjct: 2   VQNSEIKRSKKIILADLPERDLIIGSQKNNKESEKYKEELLKRYEGLIVQWTNKYFKILN 61

Query: 466 -RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            +G++F DL+ +  +G +KA EKFD   G   STYA   ++  I  SI   +  I++   
Sbjct: 62  VQGMEFDDLLIDAKLGFLKALEKFDINKGNALSTYATHCMRNYILNSIRVNNNMIKLSSR 121

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
             +K  K+ +  +              I  K+      VR  L  T E  S       E 
Sbjct: 122 EVNKRIKLSKKFKANILNKGNYKFNYNIYNKI-FSQHNVR--LIDTHEYQSYLDNSSIEQ 178

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
                +   +K                     L  L   E  ++   FG+      TL E
Sbjct: 179 EISSEEMFMEKEQKRFNT--------RQIISALKILDKTELFIIVHYFGLFNKKKRTLRE 230

Query: 645 VGKQFCVTRERIRQIEAKAIRKL 667
           + K+  +  E  R+I+ KA+ K+
Sbjct: 231 LSKRLNIGYENTRKIKGKALSKI 253


>gi|15894509|ref|NP_347858.1| RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|15024150|gb|AAK79198.1|AE007635_12 RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
          Length = 227

 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 52/227 (22%), Positives = 101/227 (44%), Gaps = 23/227 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG--LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + ++VE  + LV S+A+KY NR   L+  D++Q G I ++ A E FD+  G KFSTYA  
Sbjct: 17  RNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFSTYARH 76

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            V+  +          I +  + R  + ++ +          ++    EI+ +L +  E 
Sbjct: 77  CVEGGMKNYCKKNE-LIHLSEYQRKDLRRIKKLFDE-KQLENKDIDITEISAELGIEKEK 134

Query: 563 VRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTP 622
                      I+L   +  +    + D+ E K   S     +   L      ++ +L  
Sbjct: 135 ----------AINLICFLNKDKYIPIDDY-EYKYGKSFEKEIVDNIL---IRSLIENLPK 180

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ++ ++R R       D +  ++GK++ +TR+ ++Q   + I K+K 
Sbjct: 181 NQQNLIRERL-----KDMSFTDIGKKYNITRQAVQQSVKRIINKMKR 222


>gi|332975582|gb|EGK12472.1| DNA-directed RNA polymerase sigma subunit SigK [Desmospora sp.
           8437]
          Length = 160

 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/102 (28%), Positives = 46/102 (45%), Gaps = 3/102 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            IK+ +    ++  E    +  +         A+  ++E NLRLV  + KK+ N      
Sbjct: 21  YIKNNAFPQPLNEKEEEKYLKQMAG---GDKEARNILIEHNLRLVAHIVKKFENTSEDNE 77

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           DLI  G IGL+KA E +    G K +TYA   ++  I   + 
Sbjct: 78  DLISIGTIGLIKAIESYQPNKGTKLATYAARCIENEILMHLR 119


>gi|260762514|ref|ZP_05874851.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672940|gb|EEX59761.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 131

 Score = 64.9 bits (156), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/129 (30%), Positives = 62/129 (48%), Gaps = 2/129 (1%)

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           Q  ++ P  +S +   P       V     +    ++ I+S      +   E R +   +
Sbjct: 5   QENQMKPSSMSSSSTVPANRMPMAVRSFPAAAASSQSMIRSAMSAPYLEREEERALA--I 62

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R  E +   A   +  A++RLVIS+A ++    L   DLIQEG +GL++AA +FD     
Sbjct: 63  RWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDV 122

Query: 495 KFSTYAMWW 503
           +FSTYA WW
Sbjct: 123 RFSTYASWW 131


>gi|124023188|ref|YP_001017495.1| hypothetical protein P9303_14841 [Prochlorococcus marinus str. MIT
           9303]
 gi|123963474|gb|ABM78230.1| Hypothetical protein P9303_14841 [Prochlorococcus marinus str. MIT
           9303]
          Length = 237

 Score = 64.9 bits (156), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 78/224 (34%), Gaps = 26/224 (11%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + +E +L+LV  +A  Y  R G    DL Q G +GL++AA+ F       F+ +A   
Sbjct: 8   RNKQIEEHLQLVRPIALHYAFRTGQDKEDLTQVGMLGLIRAAQFFQSSKSVPFAAFAKPH 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   + D    ++IP  + ++   ++R      + +    +  E    +       
Sbjct: 68  IRGAILHYLRDSLGPVKIPRRLEERAQALLR-----DSTLMDSASFIEKLSAVDRTAIES 122

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            K          L+      D     + +                        L  L  +
Sbjct: 123 YKQKGRWYP---LDHQFITADKDQWSELV-------------DKERNRMLMNALEKLDCQ 166

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           E  V+      G     +L        ++   +++   +A+R+L
Sbjct: 167 EFAVVDHVVLRG----ESLRSTASYLGISCMTVQRRVKRALRRL 206


>gi|308205773|gb|ADO19206.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 124

 Score = 64.9 bits (156), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/87 (48%), Positives = 53/87 (60%), Gaps = 7/87 (8%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +S +   + +E   I+           +AK  M+ ANLRLV++VAKKY    L+FLDLI
Sbjct: 23  ELSAQVNKTEAELTQILEQ-------GQLAKHLMITANLRLVVAVAKKYRWSNLEFLDLI 75

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           QEG IGL KA EKF+   GYKFSTYA 
Sbjct: 76  QEGAIGLQKAVEKFEPNRGYKFSTYAK 102


>gi|188586385|ref|YP_001917930.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351072|gb|ACB85342.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 114

 Score = 64.9 bits (156), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 32/110 (29%), Positives = 54/110 (49%), Gaps = 3/110 (2%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
           ++  V  I  + + I S S    +S  + R  +  + +       A++ ++E NLRLV  
Sbjct: 8   ISLIVKEISLLVSYISSNSFPQPLSAEDERKYLKRLEQ---GDDKAREVLIERNLRLVAH 64

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           V KK+ N G    DLI  G IGL+KA   +++  G + +TYA   ++   
Sbjct: 65  VIKKFENSGEDPEDLISIGTIGLIKAINTYNYRKGTRLATYAARCIENES 114


>gi|255599375|ref|XP_002537218.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
 gi|223517098|gb|EEF25164.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
          Length = 124

 Score = 64.9 bits (156), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 24/122 (19%), Positives = 49/122 (40%), Gaps = 7/122 (5%)

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRET 612
           + + +E  + +L        +      +D S   H  D  +      PL + I    RE 
Sbjct: 1   MKISLEEYQSMLADCGGHQLIYYEDFHDDDSGHEHFLDRYQSTETDDPLQNLINGGFREA 60

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
               + +L  RE+    +  G+    +  L+E+G    V+  R+ Q+ ++AI +++   R
Sbjct: 61  VVDSIRALPEREQ----ILMGLYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLR 116

Query: 673 SK 674
             
Sbjct: 117 EH 118


>gi|76564105|gb|ABA46492.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
          Length = 255

 Score = 64.5 bits (155), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 93/245 (37%), Gaps = 28/245 (11%)

Query: 446 KEMVEANLRLVISVAK-KY--------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            E +E   RLV      +Y         + GL   DL Q   IGL+KA + FD   G  F
Sbjct: 27  DEFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFVMIGLIKARDNFDLEFGCAF 86

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           STYA+  +   I R+I D                 V     ++ N+   +  PEEIA  L
Sbjct: 87  STYAVPKIIGEIGRAIRDN--------QKIKVQRTVYGVKGKILNQQLADKEPEEIADIL 138

Query: 557 AMPVEGVRKVLKITKEPISLETPIG---DEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
              V  V+  L+      SL   +      +   L   IED       ++ I    R   
Sbjct: 139 DESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTEDIEETTIN---RAVI 195

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
               A+L P+E  VL MR       + T + +  Q   ++ +I +I AK  ++     + 
Sbjct: 196 REFKAALPPKEYIVLDMRL-----QNMTQQNIANQMGYSQVQISRILAKINQRAAQFGKE 250

Query: 674 KKLRS 678
             L+ 
Sbjct: 251 GGLQD 255


>gi|312879625|ref|ZP_07739425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Aminomonas
           paucivorans DSM 12260]
 gi|310782916|gb|EFQ23314.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Aminomonas
           paucivorans DSM 12260]
          Length = 210

 Score = 64.5 bits (155), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 45/117 (38%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E      +  +       A++ ++ A   LV  +AK++      + DL+QEG + L+ A 
Sbjct: 28  EPEEEERLWSRCCQGDEEARERLILAYRPLVFWLAKRFRVPYGTYPDLVQEGMLALIFAV 87

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           + FD     +F TYA + V+  +   +         P    D   +       +  K
Sbjct: 88  DHFDALRKNRFITYAYYRVRGRMINFLQRVEARAPQPWDEEDLEREAPVAYEDLEWK 144


>gi|239815268|ref|YP_002944178.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Variovorax
           paradoxus S110]
 gi|239801845|gb|ACS18912.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Variovorax
           paradoxus S110]
          Length = 272

 Score = 64.5 bits (155), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 93/243 (38%), Gaps = 16/243 (6%)

Query: 430 IVSMVRKGECE-ASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKA 484
           + ++ R+   E    A+ +++E +L     +A     R     ++F D  Q   +GL++A
Sbjct: 13  LAALWRRWREEGDEGARAQLIEHHLPYARMMAAAAYGRRTHNEVEFADYHQLARLGLIEA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            ++FD   G +F T+A   V+ AI   +   +   +    M    H+ +   +  +++  
Sbjct: 73  VDRFDPAQGAQFKTFAAKRVQGAILNGLPRLTEKNQQISTMMRLRHERLEAIKEAASEDA 132

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEP-------ISLETPIGDEDTSHLGDFIEDKNA 597
              +  E A     P     K+ +   E        + LE     +  +   D       
Sbjct: 133 TSHSENESAPGGPAPSRDTDKLFRYLAEVGIGIALGVLLEETGMVDAEAFDSDAHSPSPE 192

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +S    +    LR     ++  L  R++ V+R  +      + +  E+     +TR R+ 
Sbjct: 193 ISYFRKSEIHQLRNVLRGLVDQLNDRQKTVIRYHYL----QEISFSEIAIAMSLTRGRVS 248

Query: 658 QIE 660
           Q+ 
Sbjct: 249 QLH 251


>gi|317970333|ref|ZP_07971723.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 202

 Score = 64.5 bits (155), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 64/168 (38%), Gaps = 17/168 (10%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC-----------EASIAKKEMVEAN 452
            S+ +     +  +     ++ E    +   ++                  A+ ++V  N
Sbjct: 3   PSVRQWLERSRRHAPLPERTVLELARTIQRWQQHPAGPTQAPRAIQKRGLRARDQLVRHN 62

Query: 453 LRLVISVAKKYTNRGLQ-----FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           L LV    +K  + GL        D +QE  + L++AAEKFD    Y+FSTYA +W+++ 
Sbjct: 63  LALVGFTWRK-QHSGLSPEDAATADALQEAALNLLRAAEKFDPTRSYRFSTYASFWIRRG 121

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           + R        I  P      + K  + +          P+   +A +
Sbjct: 122 LLRFCQRDRRCIAFPREQAALVLKAEQLSEERMRCNGIGPSLSWLAAQ 169


>gi|85859095|ref|YP_461297.1| putative cytoplasmic protein [Syntrophus aciditrophicus SB]
 gi|85722186|gb|ABC77129.1| hypothetical cytosolic protein [Syntrophus aciditrophicus SB]
          Length = 94

 Score = 64.5 bits (155), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 27/57 (47%), Positives = 34/57 (59%)

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           + E  L   +        TLEEVG    VTRERIRQIEAKA++KL+H  R  +L+ F
Sbjct: 28  KNESFLNCTWVACNYGPFTLEEVGDMMGVTRERIRQIEAKALKKLQHKKRRDQLKDF 84


>gi|187935479|ref|YP_001884301.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723632|gb|ACD24853.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 233

 Score = 64.5 bits (155), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 85/250 (34%), Gaps = 60/250 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY---TNRGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +     A  +++E N +LV  +  K+       +   DL QEG +GL+ AA+K+
Sbjct: 5   ELVELYQEGDKQALNKLIENNKKLVFKIVNKFYINATNSIDIEDLEQEGYMGLIMAAKKY 64

Query: 489 D--WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +        FSTY+ +W+ Q                           +    +  K   +
Sbjct: 65  NSNMDYHASFSTYSFYWIYQ---------------------------KINSFIKQKNTND 97

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSA 604
            T                          SL  P+ + +     D IE  D    +  +  
Sbjct: 98  ET--------------------------SLNIPLNEGEEKEKVDLIEYIDNGYENIEEKL 131

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
               LR     ++   T   ER +          + T+  +     ++++R+RQIE   +
Sbjct: 132 YLEQLRSDLENLMEHNTTLRERSILKLHYGWDCRECTMTYIAGMLEISQQRVRQIEKSTL 191

Query: 665 RKLKHPSRSK 674
           RKL+     K
Sbjct: 192 RKLRRTKWIK 201


>gi|224120616|ref|XP_002318375.1| predicted protein [Populus trichocarpa]
 gi|222859048|gb|EEE96595.1| predicted protein [Populus trichocarpa]
          Length = 97

 Score = 64.1 bits (154), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 40/64 (62%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           L SL P+E  V+R R+G+    D TL E+     ++RE +R+ E KA+ KLKHP+R   L
Sbjct: 33  LDSLKPKESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHPTRVDYL 92

Query: 677 RSFL 680
           R ++
Sbjct: 93  RRYV 96


>gi|315931621|gb|EFV10586.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           327]
          Length = 232

 Score = 64.1 bits (154), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 96/246 (39%), Gaps = 20/246 (8%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNI 479
           S  +   +    +         + E+V + +  + ++A +   R    +   DLI  G  
Sbjct: 3   SKKDEEMLKEPPKAYAQMLKKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVE 62

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            ++K + ++D      F  +A   V  ++   +        +  + R  I  +       
Sbjct: 63  EMIKLSRRYDKEQNDNFWGFARKRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEY 119

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
             + + EP  E +AKKL + VE +++V        +L           + + IE  N  +
Sbjct: 120 FLEHECEPDDEYLAKKLDLDVEKIKEVRTAHAISYTL----------PIDEQIELYNEDN 169

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
            L+   +  L E    VL  L  R++ ++++ +      + +L+E+ +   ++  RI QI
Sbjct: 170 TLEKIEKEELLEKIHEVLDDLKERDQLIIQLYY----YEELSLKEISEILQISESRISQI 225

Query: 660 EAKAIR 665
               ++
Sbjct: 226 HKNFLK 231


>gi|148747769|ref|YP_001285848.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Geobacillus virus E2]
 gi|113715711|gb|ABI36860.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Geobacillus virus E2]
          Length = 232

 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 97/232 (41%), Gaps = 36/232 (15%)

Query: 447 EMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           + +E ++RLV  V ++Y        +++ D I  G I L +A +KFD   GY+FSTYA+ 
Sbjct: 16  QAIEKHIRLVHYVVRRYFRSLHEIRIEYDDAISVGVIALARAYQKFDDSHGYRFSTYAVP 75

Query: 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
            +   IT  +   S  I     +++   K       +SN       P + +K+L + V+ 
Sbjct: 76  RIWGEITNCV-KNSSPIHFATRIKNLYLKAKNKQIDLSN-------PTKASKELGVTVDV 127

Query: 563 V--RKVLKITKEPISLETPIGDEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
           V   K    +    SL   + + +    + + DF+  +   S                 L
Sbjct: 128 VMEVKKYVDSFYMTSLSDVVFENEREKKTTIEDFLSTEEDFSSAY----------VRDFL 177

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            +L  R + VL M      +      ++G++  V   R+ QI    +++++H
Sbjct: 178 DTLPNRHKMVLLMVMAGYTH-----VQIGREIGVGSSRVGQI----VKEIRH 220


>gi|124023131|ref|YP_001017438.1| type III sigma factor [Prochlorococcus marinus str. MIT 9303]
 gi|123963417|gb|ABM78173.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9303]
          Length = 269

 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 98/227 (43%), Gaps = 7/227 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V  +L L    A +   RG  +  DLIQE  +GL+ A EKFD   G+K S+YAM  
Sbjct: 39  RNQAVIEHLGLAHLAATRQATRGGEELDDLIQEARLGLIMAMEKFDANRGFKVSSYAMAR 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
               I     D+S  +R+P  +RD   + +R  +   N      T E++A +L +  +  
Sbjct: 99  ANGQILHFRRDRSQIVRVPWRLRDLYTRGMRLQQMQQNDGLNPLTEEQLAAQLNVSSDRW 158

Query: 564 RKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +  +   +   +SL+        +H    +     +           ++   + +  LT
Sbjct: 159 HQAAEAVWQTNLVSLDAKETSTAGNHAEKRVSLLELLKSPKQKEPDLQQQWLKKAIERLT 218

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           P ++ +L   +   +    +L ++ K+  +    +R++    I++L+
Sbjct: 219 PHQQHLLYAHYIDDI----SLRQLAKREKMKENMLRRVLRGLIKQLQ 261


>gi|326566649|gb|EGE16790.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 48

 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/47 (80%), Positives = 43/47 (91%)

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           M +DHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+ LRSFL+ 
Sbjct: 1   MPSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLEN 47


>gi|168213645|ref|ZP_02639270.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|170714810|gb|EDT26992.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
          Length = 227

 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 58/252 (23%), Positives = 96/252 (38%), Gaps = 60/252 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +     A  +++E N +L+  +A K+ +     ++F DL+QEG IGL+ A  K+
Sbjct: 5   ELVVLYQQGDKKALDKLLENNDKLIYKIANKFYSDKTSSIEFDDLLQEGRIGLILACSKY 64

Query: 489 DWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           D       KF TYA +W+ Q I R I   S                              
Sbjct: 65  DIEYIKRTKFITYAFYWIYQKIHRFITKYS------------------------------ 94

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSA 604
                                  T E ISL TP+ +E+T  L + IE  +       +  
Sbjct: 95  -----------------------TNEEISLNTPVSEENTDELINSIESHSDEINDREEKL 131

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             + LR     V+       ER +   +      +  +E++   F  +   I+  +A+AI
Sbjct: 132 YLSELRLELEAVMDKHNTLNEREILKLYYCWDTDELNIEQIADIFETSSSDIKNTKARAI 191

Query: 665 RKLKHPSRSKKL 676
           RKL++    KK+
Sbjct: 192 RKLRNSMWFKKV 203


>gi|46204564|ref|ZP_00049813.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 132

 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 32/120 (26%), Positives = 51/120 (42%), Gaps = 5/120 (4%)

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE---TTT 614
           MP + V  + +      SL  P+ +E      D++ D +       A +   R       
Sbjct: 1   MPEQDVIDMNRRLSGDTSLNAPLREEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALR 60

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
             L  L PRE R+   R         TLE++  +F V+RER+RQIE +A  K++   +  
Sbjct: 61  DALGVLNPRERRIFEARRLAD--DPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 118


>gi|323702293|ref|ZP_08113959.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532783|gb|EGB22656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 121

 Score = 64.1 bits (154), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 3/116 (2%)

Query: 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEAN 452
           G W   V   V+  L + + I + +    ++  E  + +  + K       A+  +VE N
Sbjct: 4   GLWTVTVLSVVNGALALVSYITNNTFPQPLTEEEEAYYLEQLAK---GDESARNVLVERN 60

Query: 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           LRLV  + KK+   G    DLI  G IGL+KA   F    G + +TYA   ++  +
Sbjct: 61  LRLVAHIVKKFDQTGEDVDDLISIGAIGLIKAINTFKTDKGTRLATYAARCIENEM 116


>gi|328474969|gb|EGF45763.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 47

 Score = 63.7 bits (153), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 31/40 (77%), Positives = 37/40 (92%)

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           LEEVG+ F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 8   LEEVGRVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 47


>gi|153932837|ref|YP_001384784.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|170755199|ref|YP_001782157.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
 gi|152928881|gb|ABS34381.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|169120411|gb|ACA44247.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
          Length = 144

 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/99 (33%), Positives = 52/99 (52%), Gaps = 3/99 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E ++ +  ++K     ++AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPKPLSDEEEKYYLDRLKK---GDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G +GL+KA + FD   G + +TYA   ++  I   I + 
Sbjct: 83  GTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNN 121


>gi|167749234|ref|ZP_02421361.1| hypothetical protein EUBSIR_00185 [Eubacterium siraeum DSM 15702]
 gi|167657809|gb|EDS01939.1| hypothetical protein EUBSIR_00185 [Eubacterium siraeum DSM 15702]
          Length = 250

 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 90/257 (35%), Gaps = 58/257 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E R     + K       A+ +++  NLRLV  + KK+     +  DLI  
Sbjct: 40  SFPRQLSAKEERE---CLEKAAQGDLAARDKLINHNLRLVAYIVKKHYPDSKEADDLISI 96

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL++AAE FD+     FSTYA   +   I                            
Sbjct: 97  GIIGLIRAAETFDYRKNISFSTYAGKCINNQIRMYFRKT--------------------- 135

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                    +    EI     M  +                    D +   L D  +D  
Sbjct: 136 ---------KHQQTEIYMNDPMDCDK-------------------DGNAVTLADIFKDGT 167

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-----GMNTDHTLEEVGKQFCV 651
            V+   + +   L +    +   L  RE+ +L  R+G+       +   T  EV  +  +
Sbjct: 168 DVAEEAA-LNIELDKMYRYIDEELDEREKEILTKRYGLSKTSYRTDRIMTQREVADELGI 226

Query: 652 TRERIRQIEAKAIRKLK 668
           +R  I +IE KA+ KL+
Sbjct: 227 SRSYISRIEKKALEKLR 243


>gi|298708238|emb|CBJ48301.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 516

 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 8/132 (6%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVA-----KKYTNRGLQFLDLIQEGNIGLMKAA 485
           V  + +   E   AK+ +VE N+ +VI +       +     + F DL+QEG   L  AA
Sbjct: 201 VEDLPRVLQEGIEAKQTLVERNMPMVIRMVEGQYRWRLRGGQVSFADLLQEGAYALGVAA 260

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           E+FD  +  +F TYA++ V+  +  ++A  +  I +P      + +V R  R ++ ++ R
Sbjct: 261 ERFDPTMPNRFLTYALYTVRDKLDVALARGNSAISVPATA---LKEVHRARRELTGRLGR 317

Query: 546 EPTPEEIAKKLA 557
            P+  E+A   A
Sbjct: 318 TPSEAELANFFA 329



 Score = 41.0 bits (94), Expect = 0.73,   Method: Composition-based stats.
 Identities = 21/110 (19%), Positives = 48/110 (43%), Gaps = 5/110 (4%)

Query: 569 ITKEPISLETPIGDEDTSHLGDFIED--KNAVSPLDSAIQANLRETTTRVLASLTPREER 626
             ++  S++  I   D S +   ++    +       +   ++ E   RV   LTPR+  
Sbjct: 403 AVQKVTSIDRLIRASDGSTMVPLVDTLVGDLEDGQPRSAGGDIAELLPRV---LTPRQAS 459

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           ++RM  G+      T+ E  K+  ++  R + +   +++KL+  + +  L
Sbjct: 460 LVRMACGLSDGKPMTMAECSKELSLSVARTKSLFDSSLQKLRAAAEADDL 509


>gi|149916583|ref|ZP_01905097.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149809510|gb|EDM69370.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 189

 Score = 63.7 bits (153), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 66/179 (36%), Gaps = 13/179 (7%)

Query: 505 KQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRM----SNKIKREPTPEEIAKKLAM 558
           + +I   I      +++      K     + +   ++       ++ E   +        
Sbjct: 1   RASIQEYILRSWSMVKLGTTSAQKKLFFNLRKAKAKIGALEEGDLRPENVKQIAHDLGVT 60

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAV---SPLDSAIQANLRETT 613
             E +    +++    SL   IG +        D++ED++A               RE  
Sbjct: 61  ETEVISMNRRMSGGDASLNAQIGSDGEGSMEWQDWLEDEDADQASDYERRDELEARREML 120

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +  L  RE  +L        +   TLE++  Q+ V+RERIRQIE +A  KL+   R
Sbjct: 121 ALAMDVLNERERDILTQ--RRLSDETVTLEDLSTQYDVSRERIRQIEVRAFEKLQDRMR 177


>gi|304654411|emb|CBL88408.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
          Length = 175

 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 64/216 (29%), Gaps = 45/216 (20%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            PL+ + L+   +   +G   L EI+            GF    E         ++    
Sbjct: 4   FPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPV 52

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             D    + D +        +     + P+  E                           
Sbjct: 53  AVDENAVDEDDDKNGDDDAAEEEAGPTGPDPVE--------------------------- 85

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +        K+          +E +  +  +L L     D LV
Sbjct: 86  VATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALV 139

Query: 340 EQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
            QL  +   I  +E ++L LA +   + R  F+   
Sbjct: 140 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 175


>gi|291231503|ref|XP_002735704.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 3906

 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 110/757 (14%), Positives = 249/757 (32%), Gaps = 100/757 (13%)

Query: 3    IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLA----RQRGYVTIEELNAFLPPDEV 58
            + K  ++ +D+E +      + D  D+  KK+   +    R+R  +   +    L   + 
Sbjct: 2661 MRKGDDKTTDAEKKKEQG--LKDKQDELRKKLRAASSDAERERILLEYAQQMQRLSEKQE 2718

Query: 59   SSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
              +Q       L  +   + D  + + ++     +  A S       +    D +D   D
Sbjct: 2719 QEKQ-----TQLEKLQKQLKDRRNRQKKDLHRKQVSEAKSEGLKDEDVPDMTDPSDAQQD 2773

Query: 119  DPVRMYLREMGSIEL----LSREGEIAIAKRIEAG----------RAMMMASLCESPLT- 163
                   +E   + L    L  E + A A+ +E             A M A +    L  
Sbjct: 2774 -------KEFRLLALQQEKLLAELQKAYAEEMEKAANNEARKSEMDAEMEARMRALNLAN 2826

Query: 164  ---FQALIIWRDELNDGTT--------LLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
                   +   ++ N             ++   D +               EG  Y +  
Sbjct: 2827 KQKVDEALDSLNKKNAQNKDMRKNMKDRMKARKDRKRDKKSLPSNIKPGTEEGKEYLETA 2886

Query: 213  DSSQEKERDDVQETEGDIESAAKVSKDDR----------SKVDSPPENAENDERNLDEDE 262
            ++ ++ +R+  ++    I       +  R             +   E  +    + D++ 
Sbjct: 2887 NTQEDADREREEQALLKIADEVMAEERQRAYWAALNGLMEDSNKTQEERDKIMADYDKNS 2946

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            +   +   A + + + ++M  L     +  EL +  D +V+ + +  S    K +++++ 
Sbjct: 2947 ERIQNKFDAQKQKQQDELMARLAARKRMREELTT--DESVHKELNNASKQVEKQMQKQVE 3004

Query: 323  KLVGSLSLNQSRIDLL----VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR- 377
              V    +       L     ++   I++ I+  +  ++   +    ++++ L+R Q   
Sbjct: 3005 LEVQQKEVENKAQKDLDDEESQETEKINREIVDEKNRIIA-KKDAAFEKEMLLKRKQLSD 3063

Query: 378  -------ELDPHWVSYAKDFPEGEWKN--------FVACEVDSILKIRNEIK-SISVETG 421
                   E     +       + E +         F   +      +R + +  +  E G
Sbjct: 3064 DEYQKLLEKHRQEMERLAAAMDQEKERQKKSLQERFAERKKKMAEHLRKKHQAEMEKELG 3123

Query: 422  ISISE-FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEG 477
                E  + I   +R  E  A  ++ +  + +   VI    +  +      Q   +  E 
Sbjct: 3124 QQHMEREKKIEKEMRGKERPAIDSELQGEDVSAENVIYRVLRQRHIKETVNQNEKMKHER 3183

Query: 478  NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT-A 536
            N  +  A  K +     +     +   +Q +   IA+          + DK   ++R   
Sbjct: 3184 NAAIADARNKMEEARQSE-RDELLEAQRQELMDLIANAG--DMTEEELADKKDDLLRQHK 3240

Query: 537  RRMSNKIKREPTPEEIAKKLAMPVEGVRK-VLKITKEPISLETPIGDEDTSHLG--DFIE 593
             ++    K      E A+K  +P   V++   K+  +   L+           G  D + 
Sbjct: 3241 TQLMEFDKVTGQRVEQAEKDVLPGLDVKQAHEKLALKEKQLQELADAMRDISHGEEDMVR 3300

Query: 594  DKNAVSPLDSAIQANLRETTTRVLASLTPR---EERVLRMRFGIGMNTDHTLEEVGKQFC 650
              +  +   +      RET  + L     +   E++         M     L+ +  +F 
Sbjct: 3301 RYSEEAAKAAEDAKKFRETKMKTLKEQMDQIKAEKKKQDDERRRKMQE--QLKNIEDEFE 3358

Query: 651  VTR----ERI--RQIEAKAIRKLKHPSRSKKLRSFLD 681
              R    +RI  R +E + +R+ +   R K+LRS LD
Sbjct: 3359 KQRLRDEQRIKERDLEREQLRQQQREEREKRLRSDLD 3395


>gi|113954672|ref|YP_730552.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113882023|gb|ABI46981.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 218

 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 91/229 (39%), Gaps = 34/229 (14%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + +E +L+LV  +A  Y  R GL   DL Q G +GL++AAE ++      F  YA   
Sbjct: 8   RNQRIERHLKLVDPIAGHYAKRSGLDRDDLKQVGMLGLLRAAEGYEQGQEKPFEVYARPH 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   + D    +R+P  ++++    ++             +  E  ++ AM  E  
Sbjct: 68  IRGAILHYLRDSVGLVRLPRRLQEQAQNTIK------------NSTAEPQRRQAMSAE-- 113

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLASL 620
                       LE  +         + +++    + +      ++    +   + +  L
Sbjct: 114 ------------LELNVHAYRCRQTWEPLDEGRVAADVPGWQPLLRQERAKRIWKAINRL 161

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            P E+R L      G     +L   G +  V+   +++   +A+ +L+ 
Sbjct: 162 APSEKRALNEVVLEG----ASLRGAGTKLGVSAMTMQRRLKRALAQLRQ 206


>gi|260762513|ref|ZP_05874850.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672939|gb|EEX59760.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 184

 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/172 (23%), Positives = 73/172 (42%), Gaps = 13/172 (7%)

Query: 508 ITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVEG 562
           +   I      +R       K     + R   +++         E   EI+ +L +    
Sbjct: 1   MQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSD 60

Query: 563 VR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLRE---TTTRV 616
           V     +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR 
Sbjct: 61  VEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRA 120

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L +L  RE  ++R R         TLE +G++  +++ER+RQIE++A+ KLK
Sbjct: 121 LDTLNERELHIIRERRLDDDGV--TLEALGEKLGISKERVRQIESRAMEKLK 170


>gi|21104386|dbj|BAB93463.1| putative rpoD gene [Variovorax sp. WFF52]
 gi|21104388|dbj|BAB93464.1| putative rpoD gene [Leptothrix discophora]
 gi|21104390|dbj|BAB93465.1| putative rpoD gene [Sphaerotilus natans]
          Length = 47

 Score = 63.3 bits (152), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/46 (82%), Positives = 42/46 (91%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           VIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++  GYKFSTYA 
Sbjct: 2   VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 47


>gi|312898376|ref|ZP_07757766.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
 gi|310620295|gb|EFQ03865.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
          Length = 205

 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/111 (22%), Positives = 53/111 (47%), Gaps = 2/111 (1%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           ++ +   T +   E + +    +   C  S  +  ++E    LV   A ++        D
Sbjct: 1   MEELQKITLLKPDEEKRLWMAYKDEGCMDS--RGRLIEQYQPLVFREALRWHVGEEHMAD 58

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
           ++QEGN+GL++A E++D+ LG  FS YA+  ++  I   +  +  +  + +
Sbjct: 59  VLQEGNLGLIEAVERYDYKLGVAFSIYAVHRIRGEIVDWLKKEGKSANVSM 109


>gi|317055222|ref|YP_004103689.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447491|gb|ADU21055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 127

 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 3/88 (3%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++ +E R     +       + A+  ++  NLRLV  + KKY        DLI  G IGL
Sbjct: 33  LTAAEERDCFEKM---SEGDAGARDTLIRHNLRLVAHIIKKYYANSSDQDDLISIGTIGL 89

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
           +KA + FD+  G +F+TY    V+ A  
Sbjct: 90  IKAVQTFDYTKGTRFATYGSRCVENATQ 117


>gi|291557292|emb|CBL34409.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium siraeum
           V10Sc8a]
          Length = 250

 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 92/257 (35%), Gaps = 58/257 (22%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E R     + K       A+ +++  NLRLV  + KK+     +  DLI  
Sbjct: 40  SFPRQLSAKEERE---CLEKAAQGDLAARDKLINHNLRLVAYIVKKHYPDSKEADDLISI 96

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
           G IGL++AAE FD+     FSTYA   +   I                            
Sbjct: 97  GIIGLIRAAETFDYRKNISFSTYAGKCINNQIRMYFRK---------------------- 134

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
                    +    E+     M  +                    D +   L D  +D  
Sbjct: 135 --------TKHQQTEVYMNDPMDCDK-------------------DGNAVTLSDIFKDGT 167

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-----GMNTDHTLEEVGKQFCV 651
            V+  ++A+   L +    +   L  RE+ +L  R+G+       +   T  EV  +  +
Sbjct: 168 DVA-EEAALNIELDKMYRYIDEELDEREKEILTKRYGLSKTSYRTDRIMTQREVADELGI 226

Query: 652 TRERIRQIEAKAIRKLK 668
           +R  I +IE KA+ KL+
Sbjct: 227 SRSYISRIEKKALEKLR 243


>gi|326204040|ref|ZP_08193901.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985807|gb|EGD46642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 138

 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +   E ++ V   +     +  A+  ++E NLRLV  + KKY + G    DLI  
Sbjct: 28  SFPQPLKPEEEQYYVEAYK---NGSEDARNILIERNLRLVAHIVKKYGSCGSDSDDLISI 84

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
           G IGL+KA   F+   G + +TYA   ++ AI
Sbjct: 85  GTIGLIKAISTFNMDKGTRLATYAARCIENAI 116


>gi|5360431|dbj|BAA81995.1| principle sigma factor [Pseudomonas syringae pv. phaseolicola]
          Length = 172

 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 23/212 (10%), Positives = 59/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    + T+ D E +A  S D+      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGTDDDEEGSADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  +  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAEMVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|322806877|emb|CBZ04447.1| RNA polymerase sporulation specific sigma factor SigK [Clostridium
           botulinum H04402 065]
          Length = 144

 Score = 62.9 bits (151), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/99 (33%), Positives = 52/99 (52%), Gaps = 3/99 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E ++ +  ++K     ++AK  +VE NLRLV  + KKY+  G    DLI  
Sbjct: 26  SFPKPLSDEEEKYYLDRLKK---GDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISI 82

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G +GL+KA + FD   G + +TYA   ++  I   I + 
Sbjct: 83  GTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNN 121


>gi|163785765|ref|ZP_02180266.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159878964|gb|EDP72967.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 64

 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/63 (34%), Positives = 40/63 (63%)

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            +L  RE  +++ R+G+      TL EVG+   ++RER+RQ+E +A++KL+  +  + L+
Sbjct: 1   KALDEREREIIKHRYGLEGEEPKTLNEVGEMLGISRERVRQLENRALKKLRALAMKRHLK 60

Query: 678 SFL 680
            FL
Sbjct: 61  DFL 63


>gi|33863056|ref|NP_894616.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9313]
 gi|33634973|emb|CAE20959.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9313]
          Length = 269

 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 100/227 (44%), Gaps = 7/227 (3%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + E V  +L L    A +   RG  +  DLIQE  +GL+ A E FD  LG+K S+YAM  
Sbjct: 39  RNEAVVEHLGLAHLAATRQATRGGEELDDLIQEARLGLIMAMENFDANLGFKASSYAMAR 98

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
               I     D+S  +R+P  +RD   + +R  ++  N   +  T E++A +L +  +  
Sbjct: 99  ANGQILHFRRDRSQIVRVPWRLRDLYTRGMRLKQKQQNDGLKPFTEEQLAAQLNVSSDRW 158

Query: 564 RKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +  +   +   +SL+        +H+   +     +            +   + +  LT
Sbjct: 159 HQAAEAIWQTHLVSLDAKESSTGGNHVEKRVPLLERLKSPKQKEPDLQYQWLKKAIQRLT 218

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             ++ +L   +   +    +L ++ K+  +   ++R++    I++L+
Sbjct: 219 SHQQHLLYAHYIDDI----SLRQLAKREKMKENKLRRVLQGLIKQLQ 261


>gi|291544363|emb|CBL17472.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           sp. 18P13]
          Length = 118

 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/93 (31%), Positives = 46/93 (49%), Gaps = 3/93 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           ++    +S  E     + + +     S A+  ++E NLRLV  + KKY        +LI 
Sbjct: 24  MAFPKPLSPKEEADCFARLAQ---GDSQARAMLIEHNLRLVAHMIKKYYANSKDQDELIS 80

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            G +GL+KA   FD   G KF+TYA   +++A 
Sbjct: 81  IGTMGLIKAVNTFDAAKGSKFATYAGRCIEKAT 113


>gi|218669756|gb|ACL00355.1| Bcp25 [Bacillus phage Bcp1]
          Length = 250

 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 108/241 (44%), Gaps = 12/241 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEK 487
             + +V++    +  AK++++     +V ++AK+++  +  +F D+ QEG   L++  +K
Sbjct: 15  ETIELVKEARAGSEEAKEKIILGYKGMVYTLAKRFSRSKQHEFEDMFQEGLTILLEVVDK 74

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
           FD   GY FSTYA  +V   +   +  +   I+I  H+ D I ++ +   +++++ ++E 
Sbjct: 75  FDIDSGYAFSTYAYPFVFGKMNN-VRKRYNPIKISAHITDIISRIRK--YKLTDRSEKEI 131

Query: 548 TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607
             E + K+  +             + +SLE    +++ S     +++  +          
Sbjct: 132 -YEFLNKEYELKWVRAALEYMRRGKVLSLEKTFAEDEESDWAATLKEVVSKDANGDW--- 187

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L       + SLT  E+      F   +  D    ++ ++  V  + + +   KA RK+
Sbjct: 188 ELMMDIKGCVPSLTSYEQ----YAFCEHILKDRMQSDIAEELGVKPQTVSKHVNKACRKI 243

Query: 668 K 668
           K
Sbjct: 244 K 244


>gi|148645062|gb|ABR01056.1| RpoD [uncultured Geobacter sp.]
          Length = 72

 Score = 62.5 bits (150), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/71 (59%), Positives = 58/71 (81%)

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA +KF++  GYKFSTY  WW++QAITR+J DQ+ TIRIPVHM + I+K++RT+R++  +
Sbjct: 1   KAVDKFEYQRGYKFSTYXTWWIRQAITRAJXDQARTIRIPVHMIETINKLIRTSRQLVQE 60

Query: 543 IKREPTPEEIA 553
           I REP PEEIA
Sbjct: 61  IGREPMPEEIA 71


>gi|56964615|ref|YP_176346.1| DNA-directed RNA polymerase sigma factor [Bacillus clausii KSM-K16]
 gi|56910858|dbj|BAD65385.1| DNA-directed RNA polymerase sigma factor [Bacillus clausii KSM-K16]
          Length = 220

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/220 (18%), Positives = 95/220 (43%), Gaps = 29/220 (13%)

Query: 445 KKEMVEANLRLVISVA----KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           + EM+ +N+ LV  +A        +    + DLI  G IGL+ A E ++   G  F+ YA
Sbjct: 7   QNEMILSNMGLVHKIAKDLKWSIRSSWFHYSDLISVGTIGLINAVENYENKKGITFAAYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
           +  +++++ +++  Q   + +P ++ + + ++       S +     + EE+A  L +P 
Sbjct: 67  VPVIRRSMLKALNKQMAGLSVPDYIIELVPRLK------SLENWGNLSVEEVASILGIPT 120

Query: 561 EGVRKVLKITKEP--ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  R +L     P  IS+++ +            ED++      +     +       L 
Sbjct: 121 KKARNLLIAVNRPDLISMDSEVK-----------EDRDYNEVFGARTDYGMI-YVNDFLN 168

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +L  R++ +L  +        ++ +E+   +  + + I Q
Sbjct: 169 TLKERDKEILEAKLA-----GYSQQEIASMYGTSPQAISQ 203


>gi|150390238|ref|YP_001320287.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950100|gb|ABR48628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 149

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/102 (30%), Positives = 46/102 (45%), Gaps = 3/102 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +S  E    +    +       A+  +VE NLRLV  V KKY+N      DLI  
Sbjct: 28  SFPQPLSPEEEAMYLERYEQ---GDEEARNILVERNLRLVAHVVKKYSNVNRDADDLISI 84

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
           G IGL+KA   F+   G + +TYA   +++A+       +  
Sbjct: 85  GTIGLIKAITTFNRGKGTRLATYAARCIEKAMLPKCYMFNRC 126


>gi|5360303|dbj|BAA81931.1| principle sigma factor [Pseudomonas syringae]
 gi|5360319|dbj|BAA81939.1| principle sigma factor [Pseudomonas syringae pv. glycinea]
 gi|5360343|dbj|BAA81951.1| principle sigma factor [Pseudomonas syringae pv. lachrymans]
 gi|5360367|dbj|BAA81963.1| principle sigma factor [Pseudomonas syringae pv. mori]
 gi|5360375|dbj|BAA81967.1| principle sigma factor [Pseudomonas syringae pv. mori]
 gi|5360383|dbj|BAA81971.1| principle sigma factor [Pseudomonas syringae pv. mori]
 gi|5360399|dbj|BAA81979.1| principle sigma factor [Pseudomonas syringae]
 gi|5360407|dbj|BAA81983.1| principle sigma factor [Pseudomonas syringae]
 gi|5360415|dbj|BAA81987.1| principle sigma factor [Pseudomonas syringae]
 gi|5360423|dbj|BAA81991.1| principle sigma factor [Pseudomonas syringae]
 gi|5360487|dbj|BAA82023.1| principle sigma factor [Pseudomonas syringae pv. tabaci]
          Length = 172

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/212 (10%), Positives = 59/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    + T+ D E +A  S D+      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  +  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAEMVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|114566052|ref|YP_753206.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114336987|gb|ABI67835.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 126

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/117 (24%), Positives = 53/117 (45%), Gaps = 3/117 (2%)

Query: 395 WKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
           W   +   +   L +   + +      +S  + R  +  +++       A+  ++E NLR
Sbjct: 6   WALAITGILKGSLCLFAYLNNQVFPQPLSEEDERKCLQEMQR---GGEEARNILIEHNLR 62

Query: 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           LV  V KKY + G    DLI  G IG +KA   +++  G + +TYA   +   ++ S
Sbjct: 63  LVAHVVKKYESSGEDLEDLISIGTIGPIKAIRTYNFERGVRLATYAARCIDNEVSMS 119


>gi|149182533|ref|ZP_01861006.1| sigma factor SigD [Bacillus sp. SG-1]
 gi|148849793|gb|EDL63970.1| sigma factor SigD [Bacillus sp. SG-1]
          Length = 161

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 6/131 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
             + +   A   +V+  L LV    ++ +    + +   DL   G +GL+ A EKFD   
Sbjct: 16  WKKSKDPHAGDMLVKKYLPLVSYHVQRISVGLPKNVSREDLKSLGLMGLLDALEKFDPSR 75

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
             KF TYA + V+ +I   +  +     +P   R++  K+      +  ++ R  TPEEI
Sbjct: 76  DLKFDTYASFRVRGSIIDGLRKEDW---LPRSTRERAKKIEAKIESLEQELLRHVTPEEI 132

Query: 553 AKKLAMPVEGV 563
           A+++ M    V
Sbjct: 133 AQEMQMEEGEV 143


>gi|153812706|ref|ZP_01965374.1| hypothetical protein RUMOBE_03113 [Ruminococcus obeum ATCC 29174]
 gi|149831222|gb|EDM86311.1| hypothetical protein RUMOBE_03113 [Ruminococcus obeum ATCC 29174]
          Length = 114

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/98 (28%), Positives = 51/98 (52%), Gaps = 3/98 (3%)

Query: 574 ISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +SL  PIG +   +   L D IE        + + + ++R   + +   LTP+E +V+  
Sbjct: 13  VSLYEPIGTDKEGNEISLLDIIESPPVDIVEEYSTRQDIRFLFSSMKDILTPKEYQVICC 72

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R+G+  N + T  E+  Q  ++R  + +IE  A++KLK
Sbjct: 73  RYGLFENNEMTQREIADQLHISRSYVSRIEKNALKKLK 110


>gi|34498445|ref|NP_902660.1| flagellar biosynthesis sigma factor [Chromobacterium violaceum ATCC
           12472]
 gi|34104300|gb|AAQ60659.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
          Length = 231

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 92/242 (38%), Gaps = 21/242 (8%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAE 486
                 +    A  A+   V     LV   A++ +          D+ Q G + L+    
Sbjct: 2   YAECYEQPPQAADEARHLAV--YAPLVKRAARQLSSQAGGVFDREDMEQIGLMALLDCLR 59

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           ++      +F+ +AM  ++ AI   +         P  +R + H+V    R +  K++RE
Sbjct: 60  RYGGEPDERFAGFAMLRIRGAILDELRRLDW---RPRSVRQEAHRVRDGLRELRRKLRRE 116

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
           PT  E    L +  +  R  L         E     ++    G  +  +          +
Sbjct: 117 PTEAEALGLLGLDADAYRDALLAENA----EAMASFDELVASGMELAAEGTPE-----AR 167

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +    R L +L  RE++V+++ +      + +L+E+     +T  RI QI   A++K
Sbjct: 168 LERQSELARALTALNEREQQVIQLYYEF----ELSLKEIAAVLELTEARICQINKSALKK 223

Query: 667 LK 668
           ++
Sbjct: 224 MQ 225


>gi|289758831|ref|ZP_06518209.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714395|gb|EFD78407.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 330

 Score = 62.2 bits (149), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 188 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 247

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 248 EVELAKRIEAGL 259



 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 3/82 (3%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASIAKKEMVEANLRL 455
              EV+   +I   + +  + T +S    +   +    +     +   AK  ++EANLRL
Sbjct: 245 AEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRL 304

Query: 456 VISVAKKYTNRGLQFLDLIQEG 477
           V+S+AK+YT RG+ FLDLIQEG
Sbjct: 305 VVSLAKRYTGRGMAFLDLIQEG 326


>gi|195995537|ref|XP_002107637.1| hypothetical protein TRIADDRAFT_51343 [Trichoplax adhaerens]
 gi|190588413|gb|EDV28435.1| hypothetical protein TRIADDRAFT_51343 [Trichoplax adhaerens]
          Length = 7662

 Score = 61.8 bits (148), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 89/675 (13%), Positives = 213/675 (31%), Gaps = 77/675 (11%)

Query: 36   KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDL 95
            +  RQ+G + I++    L  +    E+++   + L      + +   L       +    
Sbjct: 6759 RKNRQKGTIDIDD-EKLLEGNNEEVEKIKQI-SNLQEDADRLYEEAALMQVVAEVEYEGQ 6816

Query: 96   ASSASNSSVFLQKRKDSADRSTDD---PVRMYLREMGSIELLSREGEIAIAKR-IE--AG 149
              +    +  + +     D   DD    V   + E+ +     ++ ++  A   +E    
Sbjct: 6817 TENYEKVAQQVLQDPSFNDVVDDDKALIVEDIMSELAT----KKQQQVDEANGHMELIEA 6872

Query: 150  RAMMMASLCESPLTFQAL-----IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
            +   +    E  LT +A+     +  R  +          +     + P+ K        
Sbjct: 6873 KNESIKKQKECELTAEAVKKQTELSTRAMIELNNVETATAVKKITAVKPDKKVIEIEAEL 6932

Query: 205  GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE-- 262
               + + +   + + R+++ E E   +     + ++  +  +     E+ E      E  
Sbjct: 6933 KEKHLEDQIKLRLEHREEMAEIERQAQEEQNKALEEIVEGMAAKLEEEDVEFQKKAAEAK 6992

Query: 263  -----DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR-SLQDNAVNGQKDEKSSVKCKV 316
                 ++    L   E +L         EIA+   +L   L++     Q+      + ++
Sbjct: 6993 EKLSAEEFQKMLDDHEKELESMQQNQEIEIAKHRDQLNSKLEERRRRKQQQLARKQEIEM 7052

Query: 317  LKEKLVKLVGSLSLN-----QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
             K+ L +   +  LN     +     L E + ++      NE +       + +++    
Sbjct: 7053 QKKLLQQQAEADRLNAEREAKKEDAALAETIKELKNSDNENESKRAENLIYHVMQQRHAK 7112

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS---ISVETGISISEFR 428
            E  Q  E     ++ A    +           D +++ ++E +    ++   GIS  E +
Sbjct: 7113 ETLQHEEQLKKELATALAEAQNNVATKCQDNRDKLVE-QHEHQLAELLAHSDGISPLELK 7171

Query: 429  HIVSMVRKGECE-----ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
                 +   +          A  +M EA  + V+   +            IQ  N  L  
Sbjct: 7172 SRQRALEGKQQTQLAEFDKDAATKMQEA-AKDVMFNLQ------------IQHANARLAL 7218

Query: 484  AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
                          + +M  +             T       +    K+++    M  K+
Sbjct: 7219 ------KTKQLAELSSSMQELAGQRELIAEYTDRTNEATRTAQQDREKIMK---EMEAKL 7269

Query: 544  KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
              E    E  K        + + L+  ++ + LE     +D  +L + I           
Sbjct: 7270 --EKIKAEKRKAQEKQRAELAQQLEALQDELQLE---QSKDEQYLEEQIA-------ERE 7317

Query: 604  AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +    R+    ++ S   +E+     +  +       L E      + ++R R+    A
Sbjct: 7318 KVHEEQRKKKDELMKSKIEKEDLNEDEKQKLIEQHQRDLAE----LEIAQQREREKSRGA 7373

Query: 664  IRKLKHPSRSKKLRS 678
            +++     R KK ++
Sbjct: 7374 LKRKLEERRKKKYQA 7388


>gi|15895322|ref|NP_348671.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|15025038|gb|AAK80011.1|AE007708_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
          Length = 237

 Score = 61.4 bits (147), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 84/209 (40%), Gaps = 8/209 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLM 482
            E + +  ++ + +  +  AK  +++++++ +  +A  +   N+ L   DL+QEG I ++
Sbjct: 3   MEDKEVKDLILRAKDGSKDAKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVI 62

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
           KA   +D     KFSTY    +   +   I  +    +IP H   KI K  R A  +  +
Sbjct: 63  KAINSYDLDKNVKFSTYVYSMINFTLISEIKKKYSYFKIPEHQVSKIVKFKRRASELKVE 122

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
                   E   ++ +  E    ++ ++       L+     +      D    ++ V+ 
Sbjct: 123 DTCYKYGCE---RIGLSYEQYADMMHLSKLNNVAYLDEKKYFDGKVSEEDKFAYED-VNY 178

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLR 629
                + +L          L+  E+ ++R
Sbjct: 179 KRVEEKIDLNVILKENADKLSQLEKYIIR 207


>gi|224533308|ref|ZP_03673902.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
 gi|224513473|gb|EEF83830.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
          Length = 373

 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 53/342 (15%), Positives = 116/342 (33%), Gaps = 44/342 (12%)

Query: 41  RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI------------------------- 75
           R  ++  EL+  LP D +  E ++   ++L + GI                         
Sbjct: 22  RKSLSFSELSNLLPDDILEPEILDCICSVLEDRGIRLVNKISELDLVVSEDGNDEEEEVE 81

Query: 76  -------NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDS-------ADRSTDDPV 121
                   ++D     DEE  +  + L                         D  ++DP+
Sbjct: 82  IESDRNFMILDDGFQSDEEDIDIDVKLDDCDEEDISVKDDLGSGYIKGNVLKDSHSEDPI 141

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII----WRDELNDG 177
           ++YL+E+G   LL+   E+ +AK++++G +++   L    L  +            +   
Sbjct: 142 KLYLKEIGKEFLLTGNQEVELAKQMDSGESIIENILKNEGLVIENYYNLVNTIYSRMERE 201

Query: 178 TTLLRE-IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
               RE   D E+     +K            +  +D       +  +  +   +   K 
Sbjct: 202 EFFKREKDKDKESSPDYYNKKKRIASFYKIPLKPIQDRLISYVDNKHRVYDLGGDIFEKN 261

Query: 237 SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
            K +R  +     +    +  L    DD   + + ++D  R + +       E  R+LR 
Sbjct: 262 LKKERLALKELLRDIPLYQEELRIFSDDYIDSANKIKDLQRQQRIILSRLKIEKIRDLRV 321

Query: 297 LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
           L  +    +K  +     K+ ++ + + +    L Q  ++ +
Sbjct: 322 LGRDLTIAEKKIEIEKSLKLKEDAIKEQITEAQLAQKELERI 363


>gi|307243701|ref|ZP_07525841.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
 gi|306492910|gb|EFM64923.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
          Length = 289

 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 96/260 (36%), Gaps = 16/260 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK------KYTNRGLQFLDLIQ 475
           + I +F+  V ++R        A+ + + + +  +  +         +  RGL   DL Q
Sbjct: 33  LDIEDFKDRVLLMR-SINGDRSARNKFILSKIDYIRKIVTCDNEIKSFKARGLDDDDLFQ 91

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            G +G++ A +KFD+  G K  TY    VK +I  +               + I+K+  +
Sbjct: 92  TGVMGVLCAIDKFDFRPGVKVKTYINNNVKYSIKNTYRKYGSISVSRE--ANSIYKICSS 149

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT---KEPISLETPIGDEDTSHLGDFI 592
              +           +I+++  +P   +   +            +     +      +  
Sbjct: 150 QMDLLEDKIDSRKILKISRETNIPPSRLEYGIMAVKSRNCQYRYDNDGCLDTDLVSMEKY 209

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
             K  ++    A +          ++ L  +E  V++  +      D T +EV +Q   +
Sbjct: 210 SRKVLMNYNQEAKRKFNYWLVMEAISRLEGKENLVIKEIY----INDKTQKEVARQLGCS 265

Query: 653 RERIRQIEAKAIRKLKHPSR 672
              +  I+ +A+ K+++  R
Sbjct: 266 TTSVGNIKRRALEKIRYMMR 285


>gi|215404667|ref|ZP_03416848.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|289746504|ref|ZP_06505882.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687032|gb|EFD54520.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|326904317|gb|EGE51250.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor [Mycobacterium
           tuberculosis W-148]
          Length = 316

 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           D +  E  E  + S D       S    Q RKD+   ++ D VR YL+++G + LL+ E 
Sbjct: 188 DEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEE 247

Query: 139 EIAIAKRIEAGR 150
           E+ +AKRIEAG 
Sbjct: 248 EVELAKRIEAGL 259


>gi|5360335|dbj|BAA81947.1| principle sigma factor [Pseudomonas syringae pv. lachrymans]
 gi|5360351|dbj|BAA81955.1| principle sigma factor [Pseudomonas syringae pv. maculicola]
 gi|5360359|dbj|BAA81959.1| principle sigma factor [Pseudomonas syringae pv. maculicola]
 gi|5360391|dbj|BAA81975.1| principle sigma factor [Pseudomonas syringae]
 gi|5360479|dbj|BAA82019.1| principle sigma factor [Pseudomonas syringae pv. syringae]
 gi|5360511|dbj|BAA82035.1| principle sigma factor [Pseudomonas syringae pv. tomato]
          Length = 172

 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 22/212 (10%), Positives = 58/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAELVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|149920035|ref|ZP_01908509.1| RNA polymerase sigma factor, FliA/WhiG/SigD family protein
           [Plesiocystis pacifica SIR-1]
 gi|149819132|gb|EDM78568.1| RNA polymerase sigma factor, FliA/WhiG/SigD family protein
           [Plesiocystis pacifica SIR-1]
          Length = 229

 Score = 61.4 bits (147), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 96/234 (41%), Gaps = 15/234 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTN--RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           S A+   VEA+ +LV  +A+  +   R L   +L   GN  L+ AA +FD   G  FST+
Sbjct: 6   SDAQAARVEAHTQLVERLARALSRQLRALSVEELESVGNEALVVAAMRFDPSAGASFSTF 65

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
           A + ++ A+  ++  +S         R K   + R     +  + R+   +  AK+    
Sbjct: 66  AHYRIRGAMIDAVRKRSPGR------RRKQRAIQR--LEATQLLMRQAAEDRGAKRAGGG 117

Query: 560 VEGVRKVLKITKEPIS-LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            E + + +   +E +      I   + +H G  +       P    ++A   E     +A
Sbjct: 118 RESLEQRVHAARELVYRAGLAILIAEATHGGLAVAPSEDTDPEQRVLKARQIERLRAAIA 177

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
           +L P    ++   +  G     T  E+ +Q  V+   + +  ++ + +L    R
Sbjct: 178 ALEPESRELIVGLYVHG----KTGRELAEQLGVSAATLSRRHSRLLERLGQALR 227


>gi|284386824|emb|CBJ16588.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386826|emb|CBJ16589.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386836|emb|CBJ16592.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386838|emb|CBJ16593.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386858|emb|CBJ16602.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 54  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 113

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 114 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|152976319|ref|YP_001375836.1| FliA/WhiG family RNA polymerase sigma factor [Bacillus cereus
           subsp. cytotoxis NVH 391-98]
 gi|152025071|gb|ABS22841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 242

 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/230 (17%), Positives = 80/230 (34%), Gaps = 23/230 (10%)

Query: 447 EMVEANLRLVISVAKK-YTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           E ++   + V     K Y +R        GL+F DL+Q G I L+KA E+F   +G+KF 
Sbjct: 14  EFIQKYEKFVFHFIHKKYGHRLQAIKDDTGLEFEDLVQCGMIALIKAREQFKPEMGFKFL 73

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
           T+A+  +   I   I                   V     ++      E + + I++ L 
Sbjct: 74  TFAVPKIIGEIGNEI--------WKTQKLKIERTVYYAKGKILKNKLSEESVDHISETLD 125

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA-NLRETTTRV 616
           +  + V           S++     +D    G+   +K               +      
Sbjct: 126 IDPKLVEAAQDYQPGTFSIDKVFYPDDNGEGGEITLEKQLEDESVDVESTVENKVILHSF 185

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             +L   E     +      +     E +GK+   ++ ++ +I  +  ++
Sbjct: 186 FDTLQHSE-----LVVWDMHSKGTRQENIGKRIGKSQVQVSRILGRINKR 230


>gi|110678161|ref|YP_681168.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
 gi|109454277|gb|ABG30482.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
          Length = 1005

 Score = 61.0 bits (146), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 32/91 (35%), Positives = 49/91 (53%), Gaps = 1/91 (1%)

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           + LG    +    S   S  +  + E     +++L  R++ +L+ R+GI      TLE+V
Sbjct: 436 TELGSIKPEDIKASESASIEELTVTEIIEGCISTLNDRQQDILQRRYGINRGQTETLEQV 495

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              + VTRERIRQIE KA +KL    R+KK+
Sbjct: 496 ASDYDVTRERIRQIEKKAKQKL-ETKRTKKV 525


>gi|5360279|dbj|BAA81919.1| principle sigma factor [Pseudomonas syringae]
 gi|5360495|dbj|BAA82027.1| principle sigma factor [Pseudomonas syringae]
 gi|5360503|dbj|BAA82031.1| principle sigma factor [Pseudomonas syringae]
          Length = 172

 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 22/212 (10%), Positives = 58/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    +  + D E +A  S ++      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  L  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAELVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|5360439|dbj|BAA81999.1| principle sigma factor [Pseudomonas syringae pv. pisi]
          Length = 172

 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 25/212 (11%), Positives = 59/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L ++  L   I P+               K
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPK 59

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
              +    + ++        ESA    ++D  +    P  A+     + +  + +   L 
Sbjct: 60  AAKTEGADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL- 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                                             +K  +           L +L   + L
Sbjct: 111 ----------------------------------KKFGRDDKHAIAEMVALAELFMPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|284386842|emb|CBJ16595.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386862|emb|CBJ16604.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 54  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 113

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 114 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|188997549|ref|YP_001931800.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932616|gb|ACD67246.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 213

 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 96/230 (41%), Gaps = 37/230 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           KK++VE  + LV  VA K   R     ++F DL+Q G +GL+KA E ++   G KFSTYA
Sbjct: 8   KKQIVEEYIGLVKKVASKIFYRLPDCEIEFDDLVQTGIVGLLKALENYNEDKG-KFSTYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +  Q    +             +     ++K+  E           +P+
Sbjct: 67  YIRIRGEILDFLRQQDIMPKTEKD---------KITIEYADKLGDE-----------LPI 106

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS- 619
                        +SL+  I ++        +    + +P +   Q  L E  +  +   
Sbjct: 107 SK-------NAIMLSLDKIISEDGEEFSFIDLFASKSKTPEEEYAQKELLEKISEAIDKY 159

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L   E+++++  +      +   +E+ +   ++  RI Q++++A+ KLK 
Sbjct: 160 LDDIEKKIIQYLYF----EEKDPKEISEIMNISLGRISQLKSRAVEKLKK 205


>gi|167747162|ref|ZP_02419289.1| hypothetical protein ANACAC_01876 [Anaerostipes caccae DSM 14662]
 gi|317473634|ref|ZP_07932923.1| hypothetical protein HMPREF1011_03274 [Anaerostipes sp. 3_2_56FAA]
 gi|167654122|gb|EDR98251.1| hypothetical protein ANACAC_01876 [Anaerostipes caccae DSM 14662]
 gi|316898924|gb|EFV20949.1| hypothetical protein HMPREF1011_03274 [Anaerostipes sp. 3_2_56FAA]
          Length = 249

 Score = 61.0 bits (146), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 38/145 (26%), Positives = 74/145 (51%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V  +     +    + E++E+ L  V   A+ YT  G+   DLIQEGN+GL++A  +   
Sbjct: 96  VRELIVRLADGEDVQNELIESMLADVALDARNYTGHGVLLGDLIQEGNMGLIEAVFELGD 155

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
               +   +     + A+ +++++Q  T  +   M  K +++   AR ++  + RE T  
Sbjct: 156 REPKEAEKFLREAAESAMKKAVSEQMNTDSVGEQMARKANRLDEAARFLAEDLGREATAG 215

Query: 551 EIAKKLAMPVEGVRKVLKITKEPIS 575
           E+A  L M  E V++++K++ + IS
Sbjct: 216 ELADHLKMTEEEVKEIMKMSLDAIS 240


>gi|284386860|emb|CBJ16603.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 54  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 113

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 114 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|5360287|dbj|BAA81923.1| principle sigma factor [Pseudomonas syringae]
 gi|5360327|dbj|BAA81943.1| principle sigma factor [Pseudomonas syringae]
 gi|5360447|dbj|BAA82003.1| principle sigma factor [Pseudomonas syringae pv. pisi]
 gi|5360455|dbj|BAA82007.1| principle sigma factor [Pseudomonas syringae pv. syringae]
 gi|5360463|dbj|BAA82011.1| principle sigma factor [Pseudomonas syringae pv. syringae]
          Length = 172

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/212 (11%), Positives = 59/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L ++  L   I P+               K
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPK 59

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
              +    + ++        ESA    ++D  +    P  A+     + +  + +   L 
Sbjct: 60  AAKAEGADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL- 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                                             +K  +           L +L   + L
Sbjct: 111 ----------------------------------KKFGRDDKHAIAEMVALAELFMPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|283898433|emb|CBJ06258.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|283898435|emb|CBJ06259.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|283898437|emb|CBJ06260.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|283898443|emb|CBJ06263.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|284386830|emb|CBJ16590.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386840|emb|CBJ16594.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386844|emb|CBJ16596.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386852|emb|CBJ16599.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386856|emb|CBJ16601.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 54  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 113

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 114 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|284386832|emb|CBJ16591.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 54  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 113

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 114 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|303242138|ref|ZP_07328628.1| RNA polymerase, sigma 32 subunit, RpoH [Acetivibrio cellulolyticus
           CD2]
 gi|302590325|gb|EFL60083.1| RNA polymerase, sigma 32 subunit, RpoH [Acetivibrio cellulolyticus
           CD2]
          Length = 244

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 96/261 (36%), Gaps = 62/261 (23%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-------FLDLIQEG 477
           +E   +       + +   A  ++ EAN++L+   A +     +        + DLIQE 
Sbjct: 3   NEEIVLAYQTATTDTDKIKAINDLTEANIKLLHYFANRSGGTVISACGDVITYEDLIQES 62

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            I L+ AA+ F    G  F+T+A  ++K              RI  H+ D   KV     
Sbjct: 63  WIALLGAAKSFKPDKGALFTTWASHYIKN-------------RIKRHIGDYTPKVT---- 105

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
                                               IS  TP+  +      D I D  A
Sbjct: 106 -----------------------------------TISTNTPVEPDSDITYEDMIPDSEA 130

Query: 598 VSPLDSAIQA-NLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                + I    LR    +V++  LT +++ +++M +G      +T   +   +  + E 
Sbjct: 131 EKRFWNYIHNKELRFELEQVMSGHLTEQQQEIIKMFYGWNGYE-YTFAHIAGIYSCSSEN 189

Query: 656 IRQIEAKAIRKLKHPSRSKKL 676
           IRQI  KA+R+++     +++
Sbjct: 190 IRQIHNKALRQIRKSEWGQRM 210


>gi|284009587|emb|CBJ16689.1| RNA polymerase sigma factor 70 [Pseudomonas syringae pv. syringae]
 gi|284009589|emb|CBJ16690.1| gyrase subunit B [Pseudomonas syringae pv. syringae]
 gi|284009595|emb|CBJ16693.1| RNA polymerase sigma factor 70 [Pseudomonas syringae pv. syringae]
          Length = 175

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/215 (11%), Positives = 58/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 62

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    ++D  +    P  A+     + +  + +   L      
Sbjct: 63  GADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------ 108

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                                        +K  +           L +L   + L   + 
Sbjct: 109 -----------------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|288572993|ref|ZP_06391350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
 gi|288568734|gb|EFC90291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
          Length = 189

 Score = 60.6 bits (145), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 27/110 (24%), Positives = 55/110 (50%), Gaps = 3/110 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E R + S +         A+++++ A   LV  +AKK+   G  + DLIQEG + L
Sbjct: 6   LAEEEERRLWSSLE---DGDPSAREDLILAYRPLVFWIAKKFNVGGDIYPDLIQEGMMAL 62

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +K  + FD   G++F+TY  + ++  +   +  +     +P+   D+  +
Sbjct: 63  IKGIDSFDPSRGFRFTTYGYYRIRGQMLNYLQRKEAKAPLPMDSFDEELR 112


>gi|99034132|ref|ZP_01314232.1| hypothetical protein Wendoof_01000979 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 148

 Score = 60.6 bits (145), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 34/122 (27%), Positives = 58/122 (47%), Gaps = 7/122 (5%)

Query: 561 EGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDK--NAVSPLDSAIQANLRET-TTR 615
           + ++   ++  +  SL   I   D S   L D I     +      +  +  L+ET    
Sbjct: 24  DVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIPCNLVSQEVTYQNHEEKELKETILNN 83

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            LASL  R   +   R+        TL+E+ K++CV+RERIRQ+  +A+ K+K   +S+ 
Sbjct: 84  ALASLNERARDIFISRYLSENIQ--TLDELSKKYCVSRERIRQLAEQAMAKVKQYIQSES 141

Query: 676 LR 677
           L+
Sbjct: 142 LK 143


>gi|33865766|ref|NP_897325.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33632936|emb|CAE07747.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 225

 Score = 60.6 bits (145), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/225 (18%), Positives = 82/225 (36%), Gaps = 35/225 (15%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + VE +L L   +A+ ++ R GL   DL Q   +GL+KA + +       F  +A   
Sbjct: 25  RNQQVERHLYLAERLARSFSQRTGLDHDDLYQVAVLGLIKATKAYRSETNVPFEAFARVH 84

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
            + AI   + D        V +     ++   A+R+S   + + + EE  + L       
Sbjct: 85  ARGAILHYLRD-------SVALVRLPRRIEEEAQRLSQIHQPKNSREEWVQAL------- 130

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                      S    +   +            + S +   + A  R+      + L   
Sbjct: 131 ---------YRSKNRWLPCPEEQQAQ-------SNSGITMMVNAERRDAIQLAFSQLGDA 174

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E+  ++     G     +L  VG    V+   +++   K +++LK
Sbjct: 175 EKHAVKAVVIDG----RSLRNVGTSLGVSAMTVQRRVKKGLKQLK 215


>gi|160934631|ref|ZP_02082017.1| hypothetical protein CLOLEP_03504 [Clostridium leptum DSM 753]
 gi|156866084|gb|EDO59456.1| hypothetical protein CLOLEP_03504 [Clostridium leptum DSM 753]
          Length = 251

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 50/218 (22%), Positives = 94/218 (43%), Gaps = 14/218 (6%)

Query: 442 SIAKKEMVEANLRLVISVAK-KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           S AKK ++E   + V  + K K+ +    + DL Q G  GL+KA E +D       +TY 
Sbjct: 22  SEAKKAVIEDYSKFVSYIIKEKFYSYRKHWEDLFQCGICGLLKALENYDPHFSKP-TTYF 80

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
            +++ Q I   I+          +   K+  +  +  ++      EP+  E+AK + +  
Sbjct: 81  YYFIVQEINDFISKY--IEGTNRYYSRKVKSLDESILKLKRSGIPEPSARELAKVMNLKE 138

Query: 561 EGVRKVLKITK--EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              R +++I    +PISL+  I           ++D N         +  L+E   + + 
Sbjct: 139 TSARNLIRIKHISQPISLDYLIESN-------LLKD-NQTYVEVLVEKRMLKEILEKAVF 190

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           SL   E++V+  +FG+  +T  T +E+     +    I
Sbjct: 191 SLPKNEKKVIERKFGLFGHTKMTNQEISVDTGIPSNMI 228


>gi|5360241|dbj|BAA81915.1| principle sigma factor [Pseudomonas syringae]
          Length = 172

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/212 (11%), Positives = 59/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L ++  L   I P+               K
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPK 59

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
              +    + ++        ESA    ++D  +    P  A+     + +  + +   L 
Sbjct: 60  AVKAEGADDDEE--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL- 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                                             +K  +           L +L   + L
Sbjct: 111 ----------------------------------KKFGRDDKHAIAEMVALAELFMPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|283898439|emb|CBJ06261.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|284386850|emb|CBJ16598.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386854|emb|CBJ16600.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 53

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 54  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 113

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 114 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|284386828|emb|CBJ17447.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
 gi|284386834|emb|CBJ17448.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 173

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/215 (10%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L +++            G+    +G +        
Sbjct: 3   RIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPP 51

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            + +    +  + D E +A  S ++      P             D+ +          +
Sbjct: 52  VDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGR 111

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
                +  L  +AE++                                    + L   + 
Sbjct: 112 DDKHAIAELVALAELF----------------------------------MPIKLVPKQF 137

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 138 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 172


>gi|238928124|ref|ZP_04659884.1| sigma-70 area 2 domain protein [Selenomonas flueggei ATCC 43531]
 gi|238884084|gb|EEQ47722.1| sigma-70 area 2 domain protein [Selenomonas flueggei ATCC 43531]
          Length = 208

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 81/257 (31%), Gaps = 63/257 (24%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K +S    ++  E + +    +  +   + A++ ++EA   LV      Y +      
Sbjct: 5   YMKKLSAVKKLTPEEEKKLWRAYK--DQGDAAARRRIIEAYQPLVFREVYPYRSLSAAMD 62

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
             +QEG IGL++A E++D   G  FS YA+  V+  I                       
Sbjct: 63  A-VQEGTIGLIEAVERYDPHHGAAFSLYAVHRVRGRIHDF-------------------- 101

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + R  +     ++ E    E AK+  +                                 
Sbjct: 102 LRREGQVDLPCLEAETEAHETAKERLVDE------------------------------- 130

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
                  S  + A +  L       +  L  RE  VL      G         +     V
Sbjct: 131 -----CPSVAEVAERHALVGVLGDAMERLPARERMVLEGVTIGGAG----AGTMADALGV 181

Query: 652 TRERIRQIEAKAIRKLK 668
           T   I +++   IR+++
Sbjct: 182 TPAHIYRLQKNGIRRIR 198


>gi|133722027|gb|ABO37132.1| SigF [Mycobacterium simiae]
          Length = 142

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/147 (20%), Positives = 58/147 (39%), Gaps = 5/147 (3%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            D S ++++P  +++   ++      +S ++ R PT  E+A +L M    V + L     
Sbjct: 1   RDNSWSVKVPRRLKELHLRLGSATADLSQRLGRAPTATELAAELDMDRAEVVEGLVAGSS 60

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
             +L    G          I D        S  +   RE    +L SL  RE  VL +RF
Sbjct: 61  YNTLSIDSGGSGDDDDVRAIADTLG-DVDASIDRIEDREALRPLLGSLPERERTVLVLRF 119

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQI 659
                   T  ++  +  +++  + ++
Sbjct: 120 F----ESMTQTQIADRVGISQMHVSRV 142


>gi|331011084|gb|EGH91140.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 160

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 63/158 (39%), Gaps = 8/158 (5%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDW 490
            +     +  ++ E++E    LV  +A     R    +Q  DLIQ G IGL++ + K+D 
Sbjct: 6   YQMYSKASRNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDS 65

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G  F TYA   ++ A+   +         P  +      V    R +  K  R+    
Sbjct: 66  TKGASFETYAGIRIRGAMLDEVRKGDW---APRSVHRNTRMVSDAIRAIEAKTGRDAKDH 122

Query: 551 EIAKKLAMPVEGVRKVLKITKEP--ISLETPIGDEDTS 586
           E+A +L + ++    +L  T      S +  + D D  
Sbjct: 123 EVAAELQLSLDDYYGILNDTLGSRLFSFDDLLQDGDHE 160


>gi|116074869|ref|ZP_01472130.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116068091|gb|EAU73844.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 203

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/223 (17%), Positives = 82/223 (36%), Gaps = 23/223 (10%)

Query: 455 LVISVAKKYTN-RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           +V  +A  Y         DLIQ G +GL+KAA  +       FS +A   ++ AI   + 
Sbjct: 1   MVTPIALHYARIARQDKDDLIQVGRLGLIKAAGLYQNAFQVPFSAFARPHIRGAILHYLR 60

Query: 514 DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
           D    +R+P  ++++  ++++   + +  ++ + +P ++       VE  R+        
Sbjct: 61  DSVGLVRLPRRVQERAQRLLKQQGQTAQFLQHQVSPSDLQL-----VEDYRQRGGWQPLS 115

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
            S    I   D     +   ++               +   R    L   E+R ++    
Sbjct: 116 ESERQTIPTIDGWTASEIAVEERD-------------QAIRRYWQRLPVMEQRCVQAVVL 162

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            G     +L    +    +   +++    A+  L    R++ L
Sbjct: 163 EGQ----SLRVTAQSLGTSAMTVQRRVKTALSILSRQCRNEGL 201


>gi|330809249|ref|YP_004353711.1| RNA polymerase sigma factor for flagellar regulon FliA [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327377357|gb|AEA68707.1| Putative RNA polymerase sigma factor for flagellar regulon FliA
           [Pseudomonas brassicacearum subsp. brassicacearum
           NFM421]
          Length = 241

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/237 (14%), Positives = 89/237 (37%), Gaps = 35/237 (14%)

Query: 436 KGECEASIAKKEMVEANLRLVISVA----KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   A+  +     + +  +      +Y +   ++ D +   +IGL++A ++F+  
Sbjct: 24  WLDSKTEAARSRLFFFYGQWLRMIVGLLYSRYPHPLAEWGDYVNLASIGLLQAIDRFNPE 83

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
           L  +F +YA  +VK  + + ++      R                     +     +  +
Sbjct: 84  LNTRFQSYAEPYVKGNVLKGLSCYVGDRRRY-----------------YRERLESISGMQ 126

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
              +    +E V  V       + LE+ I D           +    +PL         +
Sbjct: 127 EEGRAESDLEQVANVAIGLAFGLFLESGIVD----------PEPKDNNPLSLYEVERESD 176

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           T    +  L+  E+RV++  +    +   +  E+ +   +++ R+ Q+ A+A++ ++
Sbjct: 177 TLEECVKLLSANEQRVIQGHY----HQHLSFTEISELMGISKSRVSQLHAQALKNIR 229


>gi|255655251|ref|ZP_05400660.1| sporulation sigma factor SigK [Clostridium difficile QCD-23m63]
 gi|296451236|ref|ZP_06892976.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296880412|ref|ZP_06904375.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|296259842|gb|EFH06697.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296428653|gb|EFH14537.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 138

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 2/99 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  ++  E    ++  +        AK  ++E N+RLV  +AKKY N      DLI  
Sbjct: 6   SFEKPLTPEEEIEYLTKFK--IENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G IGL+KA E ++   G + +TYA   ++  I  +I   
Sbjct: 64  GTIGLIKAIETYNIDKGTRLATYASRCIENEILMNIRSN 102


>gi|284386848|emb|CBJ16597.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 175

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/215 (11%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 62

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    + D  +    P  A+     + +  + +   L      
Sbjct: 63  GADDDEE--------ESADSSDEKDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGRD 114

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            +  +   +                                    L +L   + L   + 
Sbjct: 115 DKHAIAELV-----------------------------------ALAELFMPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|153952569|ref|YP_001397326.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           doylei 269.97]
 gi|152940015|gb|ABS44756.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           doylei 269.97]
          Length = 238

 Score = 60.2 bits (144), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/222 (19%), Positives = 91/222 (40%), Gaps = 20/222 (9%)

Query: 445 KKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + E+V + +  + ++A +   R    +   DLI  G   ++K + ++D      F  +A 
Sbjct: 25  QDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWGFAR 84

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             V  ++   +        +  + R  I  +         + + EP  E +AKKL + VE
Sbjct: 85  KRVNGSMLDYLRSLD---VMSRNNRKIIKDIDAIMDEYFLEHECEPDDEYLAKKLDLDVE 141

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            +++V        +L           + + IE  N  + L+   +  L E    VL  L 
Sbjct: 142 KIKEVRTAHAISYTL----------PIDEQIELYNEDNTLEKIEKEELLEKIHEVLYDLK 191

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            R++ ++++ +      + +L+E+ +   ++  RI QI  K 
Sbjct: 192 ERDQLIIQLYY----YEELSLKEISEILQISESRISQIHKKL 229


>gi|304654399|emb|CBL88402.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
          Length = 175

 Score = 59.9 bits (143), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 64/216 (29%), Gaps = 45/216 (20%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            PL+ + L+   +   +G   L EI+            GF    E         ++    
Sbjct: 4   FPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPV 52

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             D    + D +        +     + P+  E                           
Sbjct: 53  AVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE--------------------------- 85

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +        K+          +E +  +  +L L     D LV
Sbjct: 86  VATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALV 139

Query: 340 EQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
            QL  +   I  +E ++L LA +   + R  F+   
Sbjct: 140 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 175


>gi|76664996|emb|CAJ17940.1| DNA-directed RNA polymerase sigma subunit [Candidatus Phytoplasma
           solani]
          Length = 110

 Score = 59.9 bits (143), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/71 (45%), Positives = 50/71 (70%), Gaps = 4/71 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E + +   +++    A +AK  +VE+N RLV+S+AK+Y  RG+ FLDLIQEGN+GL
Sbjct: 44  LTEQEIKDLEFKIQQ----AQLAKDSLVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGL 99

Query: 482 MKAAEKFDWCL 492
           M+A +KFD+  
Sbjct: 100 MRAVDKFDYQK 110


>gi|143644|gb|AAA22805.1| spoIIIC peptide [Bacillus subtilis]
 gi|1303719|dbj|BAA12375.1| SpoIIIC [Bacillus subtilis]
          Length = 138

 Score = 59.9 bits (143), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/108 (27%), Positives = 55/108 (50%), Gaps = 4/108 (3%)

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + LK TK+ +SL  PIG +   +   L D ++ +N        +   L E   + +  L 
Sbjct: 16  RALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKQYIDILD 74

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 75  DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 122


>gi|283898441|emb|CBJ06262.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
          Length = 175

 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/215 (11%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 5   RIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 62

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    + D  +    P  A+     + +  + +   L      
Sbjct: 63  GADDDEE--------ESADSSDEKDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGRD 114

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            +  +   +                                    L +L   + L   + 
Sbjct: 115 DKHAIAELV-----------------------------------ALAELFMPIKLVPKQF 139

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 140 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 174


>gi|330984347|gb|EGH82450.1| putative alternative sigma factor RpoH [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 263

 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 50/275 (18%), Positives = 96/275 (34%), Gaps = 26/275 (9%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           DS   I N+I+        SI E  + + + +   C    A    V A L +V  +A   
Sbjct: 8   DSFFAILNKIQI------PSIQEMDNNIRIFKSTGC--RKAHDACVTALLPMVYGLAVAN 59

Query: 464 TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY---KFSTYAMWWVKQAITRSIADQSCTIR 520
             R  +  D+ Q+G + +M A  KFD         ++   +     ++            
Sbjct: 60  AGR-AEVDDMFQQGALAVMDALRKFDPDDELNILSWTKLYVSRAINSLCVFGTKLIRVPD 118

Query: 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE--GVRKVLKITKE--PISL 576
                        R    + +    E   + +A +L + +E   + + L  +     +S 
Sbjct: 119 TKT----IRLCYRRMGLFLKDGPINEARSKILANELGVSLEDFKIARDLYSSCYEPVLSC 174

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
                        + +E     + +     A++     R++  L P+E  V+R+      
Sbjct: 175 GDEPWQGHDIKTSETLE----EAIIVEDEAAHVTRVVGRLMTVLNPKEAEVIRL--RCLQ 228

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                L  VG+Q   + ER RQ+E  A  K++  +
Sbjct: 229 EEPVQLRLVGEQLGFSTERARQVENIAKDKMRKAA 263


>gi|291544355|emb|CBL17464.1| Sigma-70, region 4 [Ruminococcus sp. 18P13]
          Length = 116

 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 47/107 (43%), Gaps = 4/107 (3%)

Query: 565 KVLKITKEPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +  K T   + ++ PI  +       L D + D + V      +    ++    +   L 
Sbjct: 4   RGQKKTANDVYIDEPIDTDKDGNTLTLMDIVADSSDV-FEQVDLTIRSKQLYRYLDKCLE 62

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           PRE  ++  R+G+  +   T  EV  +  ++R  + +IE +A+ KLK
Sbjct: 63  PRELDIITRRYGLYNHMPQTQREVADRLGISRSYVSRIEKRALSKLK 109


>gi|283898429|emb|CBJ06256.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|283898431|emb|CBJ06257.1| RNA polymerase sigma 70 factor [Pseudomonas syringae pv.
           actinidiae]
 gi|284386846|emb|CBJ17449.1| sigma factor 70 [Pseudomonas syringae pv. actinidiae]
          Length = 173

 Score = 59.9 bits (143), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/215 (11%), Positives = 57/215 (26%), Gaps = 46/215 (21%)

Query: 156 SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
            +   P T   ++     +      L ++  L   I P+               K   + 
Sbjct: 3   RIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAE 60

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
              + ++        ESA    + D  +    P  A+     + +  + +   L      
Sbjct: 61  GADDDEE--------ESADSSDEKDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGRD 112

Query: 276 LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            +  +   +                                    L +L   + L   + 
Sbjct: 113 DKHAIAELV-----------------------------------ALAELFMPIKLVPKQF 137

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQS-YGIKRDV 369
           + LVE++    +R+   E  +++L      + R  
Sbjct: 138 EGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 172


>gi|89068737|ref|ZP_01156123.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
 gi|89045700|gb|EAR51762.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
          Length = 241

 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 96/248 (38%), Gaps = 33/248 (13%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + + + R  +   +        + + ++ ++ R   + A ++T+      DL+ EG I L
Sbjct: 14  LGLDQERQAIE--KWQGEGDRASLELLLRSHARQAYAQATRWTDNPSYIEDLVAEGMIAL 71

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
           M+AAE+FD     +FSTYA WW++ A+  +    S  I +PV    +  +          
Sbjct: 72  MRAAERFDLTREVRFSTYAAWWLRTAMAEAYGRISAVIDVPVKALAEARRAGEA------ 125

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
                     +A++  + ++G  +  +       L  P    +   + D   D  A    
Sbjct: 126 ----------LAQRNVVALDGGARASEEDDMSDRLACPEPTPEDRIIRDSSRDAAARLLH 175

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
            +    +  E T      L+ R                  ++ +  +  ++  R+RQIE 
Sbjct: 176 AALASLSETERTILARRKLSDR---------------PAPVDALAAELSMSPTRLRQIET 220

Query: 662 KAIRKLKH 669
           +A+ +L+ 
Sbjct: 221 RAMGRLRQ 228


>gi|258645545|ref|ZP_05733014.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
 gi|260402901|gb|EEW96448.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
          Length = 205

 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/125 (28%), Positives = 57/125 (45%), Gaps = 2/125 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +   I S+  E  +S  E   +    +        A+++++E    LV   A KY  +  
Sbjct: 2   LSEYISSLPKEGKLSREEEARLWDAYKNEGEL--EARQKLIEHYQLLVFKEATKYPVQET 59

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
             LDLIQEG +GLM+AAEKFD   G  FS YA+  ++  +   +      I +     +K
Sbjct: 60  VLLDLIQEGTVGLMEAAEKFDIEQGVAFSLYAIHRIRGRMLDFLRKGQNDILMGEEQEEK 119

Query: 529 IHKVV 533
           +  + 
Sbjct: 120 LFTLQ 124


>gi|325115811|emb|CBZ51366.1| putative sigma-70, region 3 domain containing protein [Neospora
            caninum Liverpool]
          Length = 1206

 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/200 (15%), Positives = 73/200 (36%), Gaps = 21/200 (10%)

Query: 500  AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
               W++ A+      +    + P     +  +  + +  +  ++ REPT  E+A +L + 
Sbjct: 967  YWLWMRTAMVDWEQQKRQVTQFPWRWWREAARGRKASHGLYAELGREPTEAEVADRLGIS 1026

Query: 560  VEGVRKVLKITKEPISLETPI--------GDEDTSHLGDFIEDKNAVSPLDSAIQANLR- 610
            ++  + +   TK   +LE  +         ++    +GD +  +++    +   +  L  
Sbjct: 1027 LDKWQDISVATKAATALEAELGGPHGSQDPNDRQDTVGDLLASEDSAESDNQMFETELET 1086

Query: 611  ETTTRVLASLTPREERVLRMRFGI------------GMNTDHTLEEVGKQFCVTRERIRQ 658
            +       SL P E R+++                 G   +    +      +  + + +
Sbjct: 1087 QVLDLAAESLQPDEYRMVQALISEPHAFPGRSAASAGWGEEKEAVQAQTLQFMVGDCVDE 1146

Query: 659  IEAKAIRKLKHPSRSKKLRS 678
               KAI+K+K     + L S
Sbjct: 1147 KLKKAIQKMKEAEVKRILES 1166


>gi|158320682|ref|YP_001513189.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158140881|gb|ABW19193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 176

 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/99 (31%), Positives = 45/99 (45%), Gaps = 3/99 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    ++  E    +    +       A+  +VE NLRLV  + KKY+N G    DLI  
Sbjct: 27  SFPQPLTAEEESMYLERYEQ---GDEEARNILVERNLRLVAHIVKKYSNIGRDMDDLISI 83

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G IGL+K    FD   G + +TYA   ++  I  +I   
Sbjct: 84  GTIGLIKGITTFDRSKGTRLATYAARCIENEILMTIRSN 122


>gi|304654401|emb|CBL88403.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654403|emb|CBL88404.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654405|emb|CBL88405.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654407|emb|CBL88406.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654409|emb|CBL88407.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654413|emb|CBL88409.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654415|emb|CBL88410.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
 gi|304654417|emb|CBL88411.1| RNA polymerase sigma factor [Xanthomonas arboricola pv. corylina]
          Length = 175

 Score = 59.5 bits (142), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 64/216 (29%), Gaps = 45/216 (20%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            PL+ + L+   +   +G   L EI+            GF    E         ++    
Sbjct: 4   FPLSTEMLLADYEAHKEGKKRLAEIV-----------VGFNDLIEEADAAAAALAAAGPV 52

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             D    + D +        +     + P+  E                           
Sbjct: 53  AVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVE--------------------------- 85

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V   ++ +A  Y + + +        K+          +E +  +  +L L     D LV
Sbjct: 86  VATRMENLANEYAKFKKIY------AKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALV 139

Query: 340 EQLYDISKRIMHNEGELLRLAQS-YGIKRDVFLERH 374
            QL  +   I  +E ++L LA +   + R  F+   
Sbjct: 140 TQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSW 175


>gi|261368103|ref|ZP_05980986.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282569861|gb|EFB75396.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 118

 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 3/95 (3%)

Query: 574 ISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
           +SL+ P+   E    L D + D       D   +        ++L +L PRE++VL  R+
Sbjct: 13  LSLQEPLEGSEGQLTLADTLPDPAV--MEDDCERRADAARLRKLLETLPPREQQVLTRRY 70

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           G+      T +E+  Q  ++R  I ++E +A++ L
Sbjct: 71  GLDGRPPCTQQEIAGQMGISRSYISRLEKRALQAL 105


>gi|323140910|ref|ZP_08075823.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
 gi|322414648|gb|EFY05454.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
          Length = 211

 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 79/235 (33%), Gaps = 60/235 (25%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
            R+       A + ++ A   LV  +A  +       ++LIQEG +GL++AAE +D+   
Sbjct: 24  WRRDAAGDEAAHQRLMTAYQPLVFKIASSFRLPEADTMELIQEGMVGLLEAAESYDYKRQ 83

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             FS +A + ++             +    H  DK                         
Sbjct: 84  VAFSLFASYRIRG----------SMVDYLRHSTDKGM----------------------- 110

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                                 L           L D +  + A SP +   Q  L E  
Sbjct: 111 ----------------------LYLDSELSKGFTLSDALPSELA-SPSEVTEQHLLCEKV 147

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            + +  L  +E++VL+  +      D   + V     V+   + +++ + +R+++
Sbjct: 148 AQAMDRLPLKEQQVLQGMYL----EDRPAQAVADAIDVSLGHVYRLQKQGVRRIR 198


>gi|295849257|gb|ADG45292.1| sigma 70 factor-like protein [uncultured bacterium]
          Length = 173

 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/90 (30%), Positives = 50/90 (55%), Gaps = 1/90 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           R +  +  +    A+  K +++ ANLRLV+S+A+++    +  ++L+ EG + LM+A + 
Sbjct: 6   RDLAEL-ERHLRRATDTKNQIIRANLRLVVSIARRHLRGSVSLMELVSEGTMTLMRAVDS 64

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           FD   G+KFSTYA   + +   R +     
Sbjct: 65  FDAHRGHKFSTYATLALMKGFARCVPQMLW 94



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 29/50 (58%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
           RE    ++  L  RE  VL   +G+G  T  T E++ ++  +T++RIRQI
Sbjct: 123 REQVGELMRRLDARERDVLLNHYGLGHRTPATYEQLAQRLGLTKQRIRQI 172


>gi|228937937|ref|ZP_04100564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228821728|gb|EEM67729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
          Length = 210

 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 44/207 (21%), Positives = 82/207 (39%), Gaps = 21/207 (10%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I +         H
Sbjct: 8   NTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNS--------H 59

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-- 582
                  + +   +M  +   E   E I K+L + +  V++ L+      SL+  +    
Sbjct: 60  KIKVPRALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMYTSA 119

Query: 583 ---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               +   L D +ED   +       Q            +L   E     +      +  
Sbjct: 120 GGGSEEILLEDMLEDTQVIE---ETEQVENHMVLQSFYQTLEHPE-----LIVWDMHSKH 171

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            T +E+G +    + ++ +I  +  ++
Sbjct: 172 KTQQEIGNRVGRCQVQVSRILKRIQQR 198


>gi|167768028|ref|ZP_02440081.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|317498378|ref|ZP_07956673.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710357|gb|EDS20936.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|291561028|emb|CBL39828.1| Sigma-70 region 3./Sigma-70 region 2 [butyrate-producing bacterium
           SSC/2]
 gi|316894272|gb|EFV16459.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 256

 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 97/209 (46%), Gaps = 4/209 (1%)

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
           + + +       +    V  A+   E E K       +    IR   + +         E
Sbjct: 43  KKLLIASFVEAGIRVLGVDEAQIVAEEEAKEKADISEEEQGAIRFYEEELEQMDLPGEEE 102

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            + ++      + +       ++E+ L  ++ +A+ +T +G+ F DL+QEGNIGL++A  
Sbjct: 103 QKELIHAWLVEKGDGEA----VIESFLPQILEIARTHTGKGVLFGDLVQEGNIGLLEAMA 158

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +       F  +A   V+ +I  +IA Q  +  +   M  K +++   +  +S ++ RE
Sbjct: 159 IYQGKDAEGFLAHAKSAVEDSILDAIAIQRGSDSVGEAMAIKANRLDDASTFLSKELGRE 218

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           P  EE+AK L+M  E V++V+KI+ + +S
Sbjct: 219 PKIEELAKYLSMTEEEVKEVMKISLDALS 247


>gi|222112349|ref|YP_002554613.1| sigma-70 region 4 domain-containing protein [Acidovorax ebreus
           TPSY]
 gi|221731793|gb|ACM34613.1| sigma-70 region 4 domain protein [Acidovorax ebreus TPSY]
          Length = 893

 Score = 59.1 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/116 (25%), Positives = 48/116 (41%), Gaps = 2/116 (1%)

Query: 567 LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
           L    +P +L     +   S + D I+D   +         +L +        L   E  
Sbjct: 296 LHDEVDPKALVDYGPNSKLSAIDDDIQD-GLLKISRHDAALSLIDGIVEAAQCLNENERG 354

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +   R G      HTL+++  Q  V+RER+RQIE K  +K++     + L   LDG
Sbjct: 355 IFAARLGFRC-EPHTLQQISDQIGVSRERVRQIEVKIFKKIRRHLFWESLAERLDG 409


>gi|225155539|ref|ZP_03724029.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
 gi|224803682|gb|EEG21915.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
          Length = 262

 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 65/207 (31%), Gaps = 12/207 (5%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            DL   G + L+ A  +           Y    V+ A+   +        +    RD++ 
Sbjct: 36  DDLASVGKLALIAALGQRQGE-PDDVRAYCYVRVRGAMLDELR---RLDPLSRRQRDRVG 91

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
            + R    ++N++ R PT  EIA    + +  V   +    +                 D
Sbjct: 92  VIARVRTELANRLGRAPTLSEIASATQLTMAEVSSAIDAAAQAADATEIEW--------D 143

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
            I D    SP +     ++R +    L  L P +   LR     G +         +   
Sbjct: 144 SIPDTQLPSPAEVVELDDVRASLGIALDRLPPNQALALRRYLPGGCHARRDRRRTRRLAR 203

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLR 677
                 R    +A  +L+ P     LR
Sbjct: 204 ACASGPRSRRKEAPHRLRRPRPLAILR 230


>gi|325295407|ref|YP_004281921.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065855|gb|ADY73862.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 204

 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 55/243 (22%), Positives = 95/243 (39%), Gaps = 45/243 (18%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
             + ++KE++  NL LV  +A K   R     ++F +L+  G IGL+KA + +D     K
Sbjct: 1   MYTKSRKELIIENLPLVKKIANKIYRRLPENAVEFEELVNTGVIGLIKALDNYDKTKA-K 59

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           FSTYA   ++  I                +R           R+ N    +   EEI   
Sbjct: 60  FSTYAYIKIRGEILDY-------------LRKLDFLSRSARERIKNTEYYQDLKEEIISF 106

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
                             +SLE  I           I   ++ +P +  I    +E    
Sbjct: 107 ------------------VSLEENIFISSDKVKIRDILSSDSKTPEEEVILKEAKERLAN 148

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L+ +E+ +L++ F      +  L+ + +   ++  R+ QI+  AI+KL     SK 
Sbjct: 149 ALKRLSEKEQLILQLIFV----EELDLKSISEIIGISISRVSQIKGAAIKKL-----SKY 199

Query: 676 LRS 678
           L+ 
Sbjct: 200 LKD 202


>gi|228982422|ref|ZP_04142681.1| sporulation sigma factor SigK [Bacillus thuringiensis Bt407]
 gi|228776605|gb|EEM24913.1| sporulation sigma factor SigK [Bacillus thuringiensis Bt407]
          Length = 203

 Score = 59.1 bits (141), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 95/249 (38%), Gaps = 57/249 (22%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +        + K+ +   N RLV  V K + N  +   +L+  G +G  KA   FD    
Sbjct: 5   INHMTHLTEMEKEIIAVENERLVYYVVKMFENSQIDPDELVNAGMVGYAKALNAFDTTRE 64

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KFSTYA+  +K  I   +             ++K H++                     
Sbjct: 65  VKFSTYAINCIKNEILFFLR------------KEKKHRLNN------------------- 93

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDE---DTSHLGDFIEDKN--AVSPLDSAIQAN 608
                               +SL T +  +   +  HL D + +KN    S  D  ++ +
Sbjct: 94  --------------------VSLNTVLSVDKNGNGFHLEDIVAEKNNGEKSLEDRVVEDD 133

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            +      +  L P E+ ++  R+G+  N T+ T +++ +   +++  + +I+   + K+
Sbjct: 134 HKRLIREAIKMLNPEEQYIMTFRYGLDKNGTEKTQKQIAEDINMSQANVSKIQKHCLLKI 193

Query: 668 KHPSRSKKL 676
           K   + +K+
Sbjct: 194 KRLIKEEKV 202


>gi|213027802|ref|ZP_03342249.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
          enterica serovar Typhi str. 404ty]
          Length = 47

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
              K ++   +++GY+T  E+N  LP D V S+Q+ED + M
Sbjct: 6  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQM 47


>gi|168069803|ref|XP_001786584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162660945|gb|EDQ48604.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 406

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/227 (20%), Positives = 88/227 (38%), Gaps = 33/227 (14%)

Query: 445 KKEMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +   +  NLRLV   AK+Y  NRG    D++ EG IGL+ A +++       FST+A  +
Sbjct: 14  RDAFITQNLRLVHMCAKRYAYNRGYD--DVVSEGTIGLILAYDRYS-DATVAFSTFAATY 70

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  I         T+ +P    D   ++             +  PE +A+ L + V+  
Sbjct: 71  IRGYIRNYFRSLRGTVSVPRRTLDNSRRIAEAGLE-------DKAPETVAEALGIAVKHA 123

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              L       S      +E  +      +D                      +    P+
Sbjct: 124 EDALYYLAVTESGSRDYDEEINAKSVHTFDDDTVPD-------------VNAFIERQVPK 170

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            +R+LR+        ++T  E  ++  V+    RQ  ++A+++++ P
Sbjct: 171 NQRLLRLLM-----DEYTQTEAAEKLGVS----RQAASQALKRMRAP 208


>gi|228970817|ref|ZP_04131457.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228977391|ref|ZP_04137786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228782368|gb|EEM30551.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228788942|gb|EEM36881.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
          Length = 234

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 44/207 (21%), Positives = 82/207 (39%), Gaps = 21/207 (10%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I +         H
Sbjct: 32  NTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNS--------H 83

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-- 582
                  + +   +M  +   E   E I K+L + +  V++ L+      SL+  +    
Sbjct: 84  KIKVPRALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMYTSA 143

Query: 583 ---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               +   L D +ED   +       Q            +L   E     +      +  
Sbjct: 144 GGGSEEILLEDMLEDTQVIE---ETEQVENHMVLQSFYQTLEHPE-----LIVWDMHSKH 195

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            T +E+G +    + ++ +I  +  ++
Sbjct: 196 KTQQEIGNRVGRCQVQVSRILKRIQQR 222


>gi|182420443|ref|ZP_02641505.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182382221|gb|EDT79700.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 237

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 93/251 (37%), Gaps = 60/251 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +     A  E++E N +L+  VA K+ +     ++F DL+QEG IG + A  K+
Sbjct: 15  ELVVLYQQGEKKALDELLENNDKLIYKVASKFYSEKTSSIEFDDLLQEGRIGFILACSKY 74

Query: 489 DWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           D       KF TYA +W+ Q I R I                                  
Sbjct: 75  DIEYIKSTKFITYAFYWIYQKIHRFI---------------------------------- 100

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSA 604
                                  T E ISL TP+ +E+   L + IE  +       +  
Sbjct: 101 -------------------TRYNTNEEISLNTPVSEENKDELINSIESNSNEINDREEEL 141

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             ++LR     ++       ER +   +      + ++E++   F  +   ++ I+ KAI
Sbjct: 142 YLSDLRIELESIMDRYNTLNEREILKLYYGWDTEELSIEQIADIFETSSNEVKSIKGKAI 201

Query: 665 RKLKHPSRSKK 675
           RKL++    K 
Sbjct: 202 RKLRNSMWFKM 212


>gi|253681618|ref|ZP_04862415.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum D
           str. 1873]
 gi|253561330|gb|EES90782.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum D
           str. 1873]
          Length = 236

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 89/249 (35%), Gaps = 61/249 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +     A   ++E N  ++  +  ++       +   DL QEG IGL+ AA K+
Sbjct: 5   ELVELYQQGDKQALDSLIEQNKGIIYKLVNRFYVEKTNSIDREDLEQEGTIGLIIAARKY 64

Query: 489 DW--CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           D+      KF TYA+ W+   I R I                                  
Sbjct: 65  DFNNEKKAKFITYAIHWIYSKINRYI---------------------------------- 90

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA--VSPLDSA 604
                                + T +  SL   IG+++ + L D I+D +    +  +  
Sbjct: 91  -------------------NQRNTNDETSLNIHIGEDEENELIDTIKDIDYSYENVEEKI 131

Query: 605 IQANLRETTTRVLASLTP-REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
               LR+    V+       E  +L++R G   N    L ++G+   +   R+R IE +A
Sbjct: 132 YMKELRQEIEEVMKEYNTLEEREILKLRHGWDSNNIMALSDIGELLNINVGRVRTIEDRA 191

Query: 664 IRKLKHPSR 672
            RKL+    
Sbjct: 192 YRKLRRTKW 200


>gi|332652978|ref|ZP_08418723.1| hypothetical protein HMPREF0866_00674 [Ruminococcaceae bacterium
           D16]
 gi|332518124|gb|EGJ47727.1| hypothetical protein HMPREF0866_00674 [Ruminococcaceae bacterium
           D16]
          Length = 291

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/267 (15%), Positives = 95/267 (35%), Gaps = 27/267 (10%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAK---------KYTNRG-------LQFLDLIQ 475
            ++ +       A  ++   N  +V + A          + T  G           +L  
Sbjct: 5   ELLERIANGEEAALTKLCLINTGIVKNRAWSIARQYHCLRQTKYGGLSDYAKETLSELES 64

Query: 476 EGNIGLMKAAEKFDWCLGY-KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
            G + L++      +     +F+TY   ++  A+ R +     T+ +       + K  R
Sbjct: 65  VGKLALVECVRAGGYDAEKGRFTTYVTPFLDGAMRRHLERSMGTLALDRDSMGLVRKAQR 124

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              +   ++       EI   L +P     + +       S+    G +D   + + I  
Sbjct: 125 LYYQEGKELC------EICASLGIPFRTAARAITYPTHFFSVYDLQGPDDDGDIFERIAS 178

Query: 595 KN-AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
              + S  ++ ++    E        L+ +E+ +L   FG+       L+E+  +  +  
Sbjct: 179 TRLSGSAEEAVVRMVTMECLREEFLRLSKKEQDILGRYFGVYGFPKADLQEIAMRNLLKE 238

Query: 654 ERIRQIEAKAIRKLKHPSRSK---KLR 677
             + + + +AI++L+   +S    KLR
Sbjct: 239 SGVERAKDQAIKRLQDQCQSSLAWKLR 265


>gi|291544102|emb|CBL17211.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 235

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 7/109 (6%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL-TPREERVLRMRFG 633
           SL+ P   E  S   + + D  A+       +          +  L +P + RV+ +   
Sbjct: 109 SLDAPADPEGESTFLELLPDPEALPIYTDLEEQEDAAAVHAAVERLKSPVQRRVICLCDF 168

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
            G     + +  G+   V+ ER+RQI   A+R+L+     ++L  +L+ 
Sbjct: 169 SG----MSQKAAGEALGVSGERVRQIRRAALRELRKDPVLQQL--YLEN 211


>gi|261368117|ref|ZP_05981000.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
 gi|282569875|gb|EFB75410.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
          Length = 147

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/111 (33%), Positives = 55/111 (49%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
           F+      +L +   ++S S    +S +  R   + +R G   A+ A+  ++  NLRLV 
Sbjct: 8   FLQAAAGHVLYLMLHLESGSFPRPLSPAREREAFAALRAGGAGAAEARDLLIRHNLRLVA 67

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508
            V KKY        DLI  G IGL+KA + FD     KFS+YA   ++ AI
Sbjct: 68  HVTKKYFAATASQDDLISIGTIGLIKAVDTFDPVRASKFSSYASRCIENAI 118


>gi|251779245|ref|ZP_04822165.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243083560|gb|EES49450.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 234

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 85/250 (34%), Gaps = 58/250 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +       ++++E N +L+  +  K+       +   DL QEG IGLM AAEK+
Sbjct: 5   ELVLLYQQGDKKELEQLIENNKKLIYKIVNKFYVNETNSIDIEDLEQEGMIGLMIAAEKY 64

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
            +             ++     S               +K +                  
Sbjct: 65  KFN------------IENKAKFSTYAIYWIYGRITEFINKRN------------------ 94

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE--DKNAVSPLDSAIQ 606
                                T    SL TPI +E    L D IE  D    +  +    
Sbjct: 95  ---------------------TNYETSLNTPITEEGEKELKDIIEYIDYEFENVEERIYI 133

Query: 607 ANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
             LR     V+   LT RE ++L   +G     + T   +G+ F +T  R+RQI  +A+ 
Sbjct: 134 KELRRELEEVMKEILTLRERQILMFYYG-WHTKECTFNYIGEIFNITSSRVRQIHLRALS 192

Query: 666 KLKHPSRSKK 675
           K++     K 
Sbjct: 193 KIRKSKWGKM 202


>gi|148239620|ref|YP_001225007.1| DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. WH 7803]
 gi|147848159|emb|CAK23710.1| Possible DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. WH 7803]
          Length = 210

 Score = 58.7 bits (140), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 81/225 (36%), Gaps = 46/225 (20%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V  +L+LV  +A+ Y NR G++  DL Q G +GL++AAE F+      F  +A   
Sbjct: 21  RNQRVNDHLQLVSPIARHYANRCGVECDDLNQVGLMGLLRAAENFNADRCIPFHAFARPH 80

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   + D +  +R+P   ++                      EE A+    P+  V
Sbjct: 81  IRGAILHYLRDNASMVRMPRRWQESK------------------ENEEGAQNSGAPLRRV 122

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                                     + + D N      +  Q    +     L+ L   
Sbjct: 123 YCC----------------------AEAVADPNH-ELTVAIEQIERSKLVQTTLSGLGGP 159

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   +      G     +L   GK   V+   +++   + + +L+
Sbjct: 160 ERTAIEEVVLHG----LSLRAAGKASGVSAMTMQRRVKRGLEQLR 200


>gi|317054637|ref|YP_004119704.1| hypothetical protein p3521_p048 [Escherichia coli]
 gi|284433167|gb|ADB84906.1| hypothetical protein [Escherichia coli]
          Length = 528

 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 67/169 (39%), Gaps = 16/169 (9%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R +  +         + D  +   +  R+  N I         AK +A     +
Sbjct: 48  IRGAIKRLLPSEFLEFNDINTVNDLSNYFNKIPRQEHNSIINNLISLSTAKTIAHDKVEI 107

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K       P+ L      +  +   D+I D++ V  L               + SL+ +
Sbjct: 108 QKNSFKQNTPLPL-----CQPNTDFKDYIADEHDVIML-----------IHSAIESLSNK 151

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   SR
Sbjct: 152 RHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKSR 200


>gi|228902053|ref|ZP_04066217.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
 gi|228857479|gb|EEN01975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
          Length = 237

 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 44/207 (21%), Positives = 82/207 (39%), Gaps = 21/207 (10%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I +         H
Sbjct: 35  NTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNS--------H 86

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-- 582
                  + +   +M  +   E   E I K+L + +  V++ L+      SL+  +    
Sbjct: 87  KIKVPRALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMYTSA 146

Query: 583 ---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               +   L D +ED   +       Q            +L   E     +      +  
Sbjct: 147 GGGSEEILLEDMLEDTQVIE---ETEQVENHMVLQSFYQTLEHPE-----LIVWDMHSKH 198

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            T +E+G +    + ++ +I  +  ++
Sbjct: 199 KTQQEIGNRVGRCQVQVSRILKRIQQR 225


>gi|148974250|ref|ZP_01811783.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
 gi|145965947|gb|EDK31195.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
          Length = 235

 Score = 58.7 bits (140), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/210 (15%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
              +Y      F DL Q   + L+    KFD      F       ++  +   +      
Sbjct: 38  YQYRYAVDEGTFEDLKQTAMMTLVIELRKFDHVANDDFRRAVAVRIRGELIDELR---RR 94

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
             +    R  ++++    R++  ++ REPT  E+ + L +     ++ + +         
Sbjct: 95  DYMERDKRQLVNRIKHAERQLLQQLGREPTSNEVCRHLGVEASDYQQAMTLVDVF----- 149

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                      D IE ++ V+ +    +  L     +VL SL   E+R+L + +      
Sbjct: 150 -----------DDIELESVVTAVPETDKEVLFNEVKQVLNSLPAMEQRILYLIYV----K 194

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +E      +   ++ +++ + +  LK
Sbjct: 195 SLSTKETALVLDINEIKVHRLKHRGLDILK 224


>gi|254974785|ref|ZP_05271257.1| sporulation sigma factor SigK [Clostridium difficile QCD-66c26]
 gi|255100257|ref|ZP_05329234.1| sporulation sigma factor SigK [Clostridium difficile QCD-63q42]
 gi|255306197|ref|ZP_05350369.1| sporulation sigma factor SigK [Clostridium difficile ATCC 43255]
 gi|255313912|ref|ZP_05355495.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
 gi|255516591|ref|ZP_05384267.1| sporulation sigma factor SigK [Clostridium difficile QCD-97b34]
 gi|306519807|ref|ZP_07406154.1| sporulation sigma factor SigK [Clostridium difficile QCD-32g58]
          Length = 130

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 2/99 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  ++  E    ++  +        AK  ++E N+RLV  +AKKY N      DLI  
Sbjct: 6   SFEKPLTPEEEIEYLTKFK--IENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G IGL+KA E ++   G + +TYA   ++  I  +I   
Sbjct: 64  GTIGLIKAIETYNIDKGTRLATYASRCIENEILMNIRSN 102


>gi|28210768|ref|NP_781712.1| RNA polymerase sigma factor [Clostridium tetani E88]
 gi|28203206|gb|AAO35649.1| RNA polymerase sigma factor [Clostridium tetani E88]
          Length = 182

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/99 (31%), Positives = 47/99 (47%), Gaps = 3/99 (3%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S    +   E ++ +  + K       AK  ++E NLRLV  + KKY+  G    DLI  
Sbjct: 56  SFPKPLKAEEEKYYLKQLEK---GDISAKGVLIERNLRLVAHIVKKYSFPGKDMDDLISI 112

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G IGL+KA + F    G + +TYA   ++  I   I + 
Sbjct: 113 GTIGLIKAIDSFKIDRGTRLATYAAKCIENEILMLIRNN 151


>gi|300973581|ref|ZP_07172278.1| sigma-70, region 4 [Escherichia coli MS 200-1]
 gi|301030086|ref|ZP_07193035.1| sigma-70, region 4 [Escherichia coli MS 196-1]
 gi|305667846|ref|YP_003864320.1| putative RNA polymerase sigma factor [Escherichia coli]
 gi|309783634|ref|ZP_07678284.1| sigma-70, region 4 family protein [Shigella dysenteriae 1617]
 gi|299877172|gb|EFI85383.1| sigma-70, region 4 [Escherichia coli MS 196-1]
 gi|300309083|gb|EFJ63603.1| sigma-70, region 4 [Escherichia coli MS 200-1]
 gi|304655595|emb|CBM42259.1| putative RNA polymerase sigma factor [Escherichia coli]
 gi|308928530|gb|EFP73987.1| sigma-70, region 4 family protein [Shigella dysenteriae 1617]
 gi|324010801|gb|EGB80020.1| sigma-70, region 4 [Escherichia coli MS 60-1]
          Length = 528

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 67/169 (39%), Gaps = 16/169 (9%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R +  +         + D  +   +  R+  N I         AK +A     +
Sbjct: 48  IRGAIKRLLPSEFLEFNDINTVNDLSNYFNKIPRQEHNSIINNLISLSTAKTIAHDKVEI 107

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K       P+ L      +  +   D+I D++ V  L               + SL+ +
Sbjct: 108 QKNSFKQNTPLPL-----CQPNTDFKDYIADEHDVIML-----------IHSAIESLSNK 151

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   SR
Sbjct: 152 RHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKSR 200


>gi|51038841|gb|AAT94221.1| hypothetical protein [Escherichia coli]
          Length = 528

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 67/169 (39%), Gaps = 16/169 (9%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R +  +         + D  +   +  R+  N I         AK +A     +
Sbjct: 48  IRGAIKRLLPSEFLEFNDINTVNDLSNYFNKIPRQEHNSIINNLISLSTAKTIAHDKVEI 107

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K       P+ L      +  +   D+I D++ V  L               + SL+ +
Sbjct: 108 QKNSFKQNTPLPL-----CQPNTDFKDYIADEHDVIML-----------IHSAIESLSNK 151

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   SR
Sbjct: 152 RHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKSR 200


>gi|292905274|ref|YP_003541145.1| sigma-70 region 2-containing protein [Anabaena variabilis ATCC
           29413]
 gi|75705012|gb|ABA24687.1| Sigma-70 region 2 [Anabaena variabilis ATCC 29413]
          Length = 240

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 57/134 (42%), Gaps = 6/134 (4%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEK 487
            +    R         +  +   + +L   +A +Y         DLIQ   +G++ A E+
Sbjct: 4   ELFREYR--NNPTRQLRDRIFNHHYKLACEIAHQYRICCDEPLEDLIQLAGVGMLTAIER 61

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR---DKIHKVVRTARRMSNKIK 544
           FD      FS++A  ++K  I   + D++ T++IP  ++    +  K+  T  +++  + 
Sbjct: 62  FDPSRSNAFSSFACPYIKGEIRHYLRDKASTVKIPRSLQSLYQRGKKLHGTDEQIAKALG 121

Query: 545 REPTPEEIAKKLAM 558
                 + AK + +
Sbjct: 122 CTQQQWKEAKAIGV 135


>gi|300940820|ref|ZP_07155355.1| sigma-70, region 4 [Escherichia coli MS 21-1]
 gi|300454422|gb|EFK17915.1| sigma-70, region 4 [Escherichia coli MS 21-1]
          Length = 528

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 67/169 (39%), Gaps = 16/169 (9%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R +  +         + D  +   +  R+  N I         AK +A     +
Sbjct: 48  IRGAIKRLLPSEFLEFNDINTVNDLSNYFNKIPRQEHNSIINNLISLSTAKTIAHDKVEI 107

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K       P+ L      +  +   D+I D++ V  L               + SL+ +
Sbjct: 108 QKNSFKQNTPLPL-----CQPNTDFKDYIADEHDVIML-----------IHSAIESLSNK 151

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   SR
Sbjct: 152 RHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKSR 200


>gi|160936421|ref|ZP_02083790.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440704|gb|EDP18442.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
           BAA-613]
          Length = 199

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/159 (22%), Positives = 80/159 (50%), Gaps = 2/159 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     I+  E   +VS++       + A+  +VE  L  V+ + ++Y +  L   DL+Q
Sbjct: 11  LEEMRSITPLERDEMVSVLEGTARGDAGARSRLVEGCLGEVLEMVREYGDSELPLSDLVQ 70

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           E N  LM AA ++D      ++      VK+++  ++ +Q    +I   M  +++ +   
Sbjct: 71  EANTALMLAAIEYDGS--EPWNELMTRRVKESVELALEEQRTENQIEETMAARVNVLQTV 128

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
           ++ ++ ++ RE T EE++ K+ M  + VR ++K+  + +
Sbjct: 129 SQVLAKELGREATLEELSAKMKMSEDEVRDIMKLALDAL 167


>gi|266621294|ref|ZP_06114229.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
           DSM 13479]
 gi|288867054|gb|EFC99352.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
           DSM 13479]
          Length = 188

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 76/171 (44%), Gaps = 1/171 (0%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++         AKK ++E NL   +  AK+Y  +G+   DL+ E N+ L  A  +F   
Sbjct: 17  QLLNDAAAGNEGAKKRLIEGNLEAALKCAKEYDGKGVLLTDLVAEANMALTMAVTEFLTD 76

Query: 492 L-GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
                F  +    +K A+  ++ +Q    +    +  +++ +   ++ ++ ++ RE T E
Sbjct: 77  AGDGDFEGFLAARMKAALDLAVEEQQSAKQTGEELAARVNVLQTVSQMLAKELGREATVE 136

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
           E+A K+ M    V+ ++K+  + +S+     D +     + IE   A    
Sbjct: 137 ELADKMKMTAGEVKDIMKMAMDAMSMNAENADLEDLAEVEGIEITGAEDGE 187


>gi|226201088|ref|YP_002756700.1| hypothetical protein p026VIR_p149 [Escherichia coli]
 gi|219881717|gb|ACL52087.1| hypothetical protein [Escherichia coli]
          Length = 528

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 67/169 (39%), Gaps = 16/169 (9%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R +  +         + D  +   +  R+  N I         AK +A     +
Sbjct: 48  IRGAIKRLLPSEFLEFNDINTVNDLSNYFNKIPRQEHNSIINNLISLSTAKTIAHDKVEI 107

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K       P+ L      +  +   D+I D++ V  L               + SL+ +
Sbjct: 108 QKNSFKQNTPLPL-----CQPNTDFKDYIADEHDVIML-----------IHSAIESLSNK 151

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   SR
Sbjct: 152 RHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKSR 200


>gi|255606356|ref|XP_002538551.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
 gi|223511619|gb|EEF23833.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
          Length = 123

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/122 (21%), Positives = 54/122 (44%), Gaps = 6/122 (4%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
               +    K  ++  ++ LV  +A +   +    ++  DL+Q G +GL+ A  +++   
Sbjct: 1   MYTVKGKADKNSLLTEHMPLVKRLAHQMKAKLPPSVEVDDLVQAGMMGLLDAINRYEENH 60

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G +F TYA+  ++ A+   +         P   R  + KV      +  ++ R P+  E+
Sbjct: 61  GAQFETYAVLRIRGAMLDELRSSDWM---PRSTRANMRKVESAMAALQQQLGRPPSESEV 117

Query: 553 AK 554
           AK
Sbjct: 118 AK 119


>gi|317055256|ref|YP_004103723.1| sigma-70 region 4 domain-containing protein [Ruminococcus albus 7]
 gi|315447525|gb|ADU21089.1| sigma-70 region 4 domain protein [Ruminococcus albus 7]
          Length = 129

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/108 (24%), Positives = 46/108 (42%), Gaps = 4/108 (3%)

Query: 565 KVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + LK T   +S+E P   +       L D I D   V+     +     +    +   L 
Sbjct: 20  RSLKKTANDVSMEEPSHSDKDGSSLSLMDMIADSEDVAERIELLVRA-EQMYIDLDKCLD 78

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE  ++ MR+G+      T  E  K+  ++R  + +IE +A+ KL+ 
Sbjct: 79  DREREIIVMRYGLFGKPALTQREAAKKLGISRSYVSRIEKRALEKLRK 126


>gi|228969112|ref|ZP_04130026.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228790601|gb|EEM38288.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
          Length = 301

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 94/241 (39%), Gaps = 27/241 (11%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQF--------LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           E++  N   + S+   Y                +L+Q   I ++ A   FD+  G KF+T
Sbjct: 15  ELLYENKEFLFSIIAHYKGSIESLKNKFNVDEEELLQHAYIAVITAIRDFDFNKGIKFTT 74

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y    +   + + + + S  +R+     D + ++ +      N++   P  EE+AK L +
Sbjct: 75  YIYRPIIWEVNQLLYNDSRLVRLSRSAVDLLKQMEKV----ENELGYFPKAEELAKLLDV 130

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE +  VL+   E  SL +    E   +   +     +       ++  L+       +
Sbjct: 131 TVERIENVLRFASELTSLNSLESFEPEDYSIGY----ESKVMDKIYVENLLKN------S 180

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+  E +V+ +      N+     ++ K+  V    + +   +   KL +   SK+L  
Sbjct: 181 DLSEFETQVINLIMDGNNNS-----QIAKKLNVYPMTVNRALNRIKNKLDNNFESKRLSK 235

Query: 679 F 679
           +
Sbjct: 236 Y 236


>gi|229073422|ref|ZP_04206558.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228709729|gb|EEL61767.1| RNA polymerase sigma factor [Bacillus cereus F65185]
          Length = 301

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 94/241 (39%), Gaps = 27/241 (11%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQF--------LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           E++  N   + S+   Y                +L+Q   I ++ A   FD+  G KF+T
Sbjct: 15  ELLYENKEFLFSIIAHYKGSIESLKNKFNVDEEELLQHAYIAVITAIRDFDFNKGIKFTT 74

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y    +   I + + + S  +R+     D + ++ +      N++   P  EE+AK L +
Sbjct: 75  YIYRPIIWEINQLLYNDSRLVRLSRSAVDLLKQMEKV----ENELGYFPKAEELAKLLDV 130

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE +  VL+   E  SL +    E   +   +     +       ++  L+       +
Sbjct: 131 TVERIENVLRFASELTSLNSLESFEPEDYSIGY----ESKVMDKIYVENLLKN------S 180

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+  E +V+ +      N+     ++ K+  V    + +   +   KL +   SK+L  
Sbjct: 181 DLSEFETQVINLIMDGNNNS-----QIAKKLNVYPMTVNRALNRIKNKLDNNFESKRLSK 235

Query: 679 F 679
           +
Sbjct: 236 Y 236


>gi|282856209|ref|ZP_06265492.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
 gi|282585968|gb|EFB91253.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
          Length = 196

 Score = 58.3 bits (139), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/96 (28%), Positives = 50/96 (52%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
               S  ++     +          A+++++ A   LV  VAKK+   G +F DL+QEG 
Sbjct: 1   MAEASELQWEKEKKLWLAMSSGDEEAREQLILAYRPLVYWVAKKFRVNGQRFSDLVQEGT 60

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           + L++A +KFD  LG++F+TYA + ++  +   +  
Sbjct: 61  LALIRAVDKFDVSLGHRFTTYACYRIRGQMLNFLQR 96


>gi|210060767|pdb|2K6X|A Chain A, Autoregulation Of A Group 1 Bacterial Sigma Factor
          Involves The Formation Of A Region 1.1- Induced
          Compacted Structure
          Length = 72

 Score = 58.3 bits (139), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMGINVV 78
          +   KK+I L +++GY+T E+++   PPD     +  +E     L   GIN+V
Sbjct: 8  ERRIKKLISLGKKKGYITYEDIDKAFPPDFEGFDTNLIERIHEELEKHGINIV 60


>gi|121534953|ref|ZP_01666772.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
 gi|121306552|gb|EAX47475.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
          Length = 215

 Score = 58.3 bits (139), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 23/110 (20%), Positives = 44/110 (40%), Gaps = 2/110 (1%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             +  +     +  +E   +    +   C     ++ ++E    LV   A ++       
Sbjct: 5   QYLDELKKIRLLEPAEEAALWRGFKVDGCLD--CRRRLIEHYQPLVFKEAMRWRAHEGVV 62

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           +DLIQEG +GL++A E FD   G  FS YA   ++  +   +  +     
Sbjct: 63  MDLIQEGTVGLIEAVENFDPERGVAFSLYAPHRIRGRMLTYLEREGKRKW 112


>gi|73853219|ref|YP_308715.1| hypothetical protein LH0044 [Escherichia coli]
 gi|33414081|gb|AAQ17636.1| hypothetical protein LH0044 [Escherichia coli]
          Length = 320

 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 66/169 (39%), Gaps = 16/169 (9%)

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI R +            + D  +   +  R+  N I         AK +A     +
Sbjct: 48  IRGAIKRLLPSAFLEFNDINTVNDLSNYFNKIPRQEHNSIINNLISLSTAKTIAHDKVEI 107

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           +K       P+ L      +  +   D+I D++ V  L               + SL+ +
Sbjct: 108 QKNSFKQNTPLPL-----CQPNTDFKDYIADEHDVIML-----------IHSAIESLSNK 151

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   SR
Sbjct: 152 RHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKSR 200


>gi|238789522|ref|ZP_04633307.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
 gi|238722472|gb|EEQ14127.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
          Length = 531

 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/90 (28%), Positives = 50/90 (55%), Gaps = 4/90 (4%)

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT-PREERVLRMRFGIGMNTDHTL 642
           D   + DF+ +   +  + S  ++++    +  + SL+  R+  +L MR G+  +  HTL
Sbjct: 134 DEKQITDFVPNTEFLDYVAS--ESDVIMLVSAAVESLSKERDRDILLMRLGMDEH-PHTL 190

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            E+  +  ++RER+RQI+ +A R+L   SR
Sbjct: 191 AEIAIKLGISRERVRQIQERAFRRLAAKSR 220


>gi|326938416|gb|AEA14312.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 243

 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 44/207 (21%), Positives = 82/207 (39%), Gaps = 21/207 (10%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N GL+  DL+Q G IGL+KA   F+  LGY+FSTYA+  +   + + I +         H
Sbjct: 41  NTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNS--------H 92

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-- 582
                  + +   +M  +   E   E I K+L + +  V++ L+      SL+  +    
Sbjct: 93  KIKVPRALYQLRGKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMYTSA 152

Query: 583 ---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
               +   L D +ED   +       Q            +L   E     +      +  
Sbjct: 153 GGGSEEILLEDMLEDTQVIE---ETEQVENHMVLQSFYQTLEHPE-----LIVWDMHSKH 204

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRK 666
            T +E+G +    + ++ +I  +  ++
Sbjct: 205 KTQQEIGNRVGRCQVQVSRILKRIQQR 231


>gi|313682837|ref|YP_004060575.1| sigma-70 region 4 domain protein [Sulfuricurvum kujiense DSM 16994]
 gi|313155697|gb|ADR34375.1| sigma-70 region 4 domain protein [Sulfuricurvum kujiense DSM 16994]
          Length = 83

 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 22/47 (46%), Positives = 33/47 (70%)

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
              D TL E+G+   VTRER+RQIEA AI+KLKHP   + ++++++ 
Sbjct: 37  HGCDFTLSEIGEVLHVTRERVRQIEASAIKKLKHPKMGRVIKAYMES 83


>gi|78184703|ref|YP_377138.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78168997|gb|ABB26094.1| possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 206

 Score = 57.9 bits (138), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/234 (16%), Positives = 86/234 (36%), Gaps = 36/234 (15%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
                   +   ++  L LV  +A++Y+ + G    DL Q G +GL++A+++F    G  
Sbjct: 1   MPKVQQQQRNHRIQKYLSLVHPIARRYSYQSGCYCDDLTQVGYLGLIQASQRFKLTHGNS 60

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
           F  +A   ++ AI   + D    +R+P  + ++  K+     R  N              
Sbjct: 61  FPAFAKPHIRGAILHYLRDHVSLVRLPRGVEERAIKIRGHNERTLN-------------- 106

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHL-GDFIEDKNAVSPLDSAIQANLRETTT 614
                           + + L+    + +   L  D +      S      + N +    
Sbjct: 107 --------------NIDQLILQNYKFNSNWKELNEDCVGGTCNGSDDMEFKEQNRKIEL- 151

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +  L   E+ ++++    G     +L + GK   V+   +++   +A  +L+
Sbjct: 152 -AMKKLAKNEQIIIQLVIFEGN----SLRKAGKIIDVSAMTVQRRLKRARAQLR 200


>gi|88809560|ref|ZP_01125067.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786310|gb|EAR17470.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 131

 Score = 57.9 bits (138), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 36/127 (28%), Positives = 59/127 (46%), Gaps = 7/127 (5%)

Query: 556 LAMPVEGVRKVLKI--TKEPISLETPIG-DEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
           + +P+  V  +L        +SL+  +    D S L D +  +       + I A    +
Sbjct: 1   MNLPISEVEDLLGCELRSVTVSLQGVVKSKSDPSELVDVLPSEEIPPLERAEI-AERTAS 59

Query: 613 TTRVLAS--LTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             ++L    LTP+E  V+ +RFG+ G N   TL EV +Q   +RE  RQ+  +A+RKL+ 
Sbjct: 60  AWKLLDKSNLTPKERTVVMLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLRK 119

Query: 670 PSRSKKL 676
                 L
Sbjct: 120 TGIQHGL 126


>gi|308205502|gb|ADO18992.1| RNA polymerase sigma 70 subunit [Nostoc flagelliforme str.
           Sunitezuoqi]
          Length = 165

 Score = 57.5 bits (137), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/83 (40%), Positives = 48/83 (57%), Gaps = 7/83 (8%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           + ++   G S +E   I+        +   AK++MV ANLRLV+++AKKY NR L+FLDL
Sbjct: 58  RELATSLGQSEAEVESIL-------HQGERAKQKMVTANLRLVVAIAKKYQNRNLEFLDL 110

Query: 474 IQEGNIGLMKAAEKFDWCLGYKF 496
           IQEG +GL +  EK        F
Sbjct: 111 IQEGTLGLYRGVEKLIQTRATNF 133



 Score = 41.7 bits (96), Expect = 0.38,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
             T D V  YL+E+G   LL+ E EI  A+ ++    MM      S L  Q
Sbjct: 3   SPTTDLVHSYLKEIGRYPLLTPEQEITNARLVQQ---MMAIEEQRSNLALQ 50


>gi|167813608|ref|ZP_02445288.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
          Length = 182

 Score = 57.5 bits (137), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/142 (17%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTTASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  M+ +L E+
Sbjct: 129 EIALAAEIEAGREQMLQALAEA 150


>gi|321312139|ref|YP_004204426.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|320018413|gb|ADV93399.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 126

 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/108 (27%), Positives = 55/108 (50%), Gaps = 4/108 (3%)

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + LK TK+ +SL  PIG +   +   L D ++ +N        +   L E   + +  L 
Sbjct: 4   RALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKQYIDILD 62

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 63  DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 110


>gi|239623611|ref|ZP_04666642.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521642|gb|EEQ61508.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 197

 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/193 (19%), Positives = 93/193 (48%), Gaps = 7/193 (3%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +    GI+    +    ++++     + A+  +VE +LR V+++A +Y  R L   D++Q
Sbjct: 10  LEEMGGIAPLTGQEKPELLKETAKGNAGARNRLVEGSLRHVLNLAAEYEGRELPMSDIVQ 69

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           E N  LM AA ++D     ++ +     V++A+  ++ +Q     I   M  +++ +   
Sbjct: 70  EANTALMLAAIEYDGS--EEWDSLLARRVREAVELALEEQKAEAEIEETMAARVNVLQTV 127

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
           ++ ++ ++ RE T +E+A K+ M  + ++ ++K+      L+    + +     D  +D 
Sbjct: 128 SQMLARELGREATLQELAAKMKMTEDEIKDIMKLA-----LDALTVNGEGQAFVDTEDDT 182

Query: 596 NAVSPLDSAIQAN 608
           ++ +P+       
Sbjct: 183 DSSNPIKDGWSME 195


>gi|289523531|ref|ZP_06440385.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503223|gb|EFD24387.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 189

 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 25/111 (22%), Positives = 54/111 (48%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + ++ +     A++E++ +   +V  +AKK+      + DLIQEG + L++A +++D   
Sbjct: 19  LWQRIKFGDEKAREEVIISYRPMVFWLAKKFHVPSDSYQDLIQEGMVALIEAVDRYDAKR 78

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
           G KF TYA + +K  +   +         PV + D +++    +      +
Sbjct: 79  GTKFITYAYYRIKGRMVNFLERSEARAPEPVDIDDHLYESNMASFDDEGWL 129


>gi|262190809|ref|ZP_06049034.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           CT 5369-93]
 gi|262033330|gb|EEY51843.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           CT 5369-93]
          Length = 116

 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 7/107 (6%)

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLT 621
           +        I+    +G ED     D I   E+    SP     + + R+     + SL 
Sbjct: 4   EQYHSVLMDINCSRIVGIEDLGVSDDAISPFEEGEDNSPFHGVAEESFRKALVESIKSLP 63

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            RE  VL + +    + +  L+E+G+   V+  R+ QI ++++++L+
Sbjct: 64  EREALVLSLYY----DEELNLKEIGEVLGVSESRVSQILSQSMQRLR 106


>gi|221310570|ref|ZP_03592417.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314894|ref|ZP_03596699.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319816|ref|ZP_03601110.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221324095|ref|ZP_03605389.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
          Length = 132

 Score = 57.5 bits (137), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/108 (27%), Positives = 55/108 (50%), Gaps = 4/108 (3%)

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + LK TK+ +SL  PIG +   +   L D ++ +N        +   L E   + +  L 
Sbjct: 10  RALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMEL-EKVKQYIDILD 68

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 69  DREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 116


>gi|255658878|ref|ZP_05404287.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
 gi|260848826|gb|EEX68833.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
          Length = 208

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/110 (21%), Positives = 52/110 (47%), Gaps = 3/110 (2%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +++ + +K +     + + E + +       E     A++ ++E+   LV   A  +   
Sbjct: 1   MQLADYLKELRKVKTLDLEEEQAL--WAAFKERGDEGARQRLIESYQPLVFKQAAPFAQL 58

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
                DLIQEG +GL++AAE++D   G  FS +A+  ++  +   +  + 
Sbjct: 59  DCAL-DLIQEGTVGLIEAAERYDHTRGVAFSLFAVHRIRGRMMDFLRREG 107


>gi|188586354|ref|YP_001917899.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|179351041|gb|ACB85311.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 113

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D +   + +      +  + ++   RV+ +L PREE++LR RFG+      T +E
Sbjct: 27  EITLLDILGSDSNMVIDQVTLSID-KDKLRRVIKTLKPREEKILRWRFGLSNEKALTQKE 85

Query: 645 VGKQFCVTRERIRQIEAKAIRKL 667
           V ++  ++R  + +IE + + K+
Sbjct: 86  VAEKLGISRSYVSRIEKRILNKM 108


>gi|290968733|ref|ZP_06560271.1| sigma-70 region 2 [Megasphaera genomosp. type_1 str. 28L]
 gi|290781386|gb|EFD93976.1| sigma-70 region 2 [Megasphaera genomosp. type_1 str. 28L]
          Length = 217

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 46/108 (42%), Gaps = 2/108 (1%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ +   T ++  E + +    ++       A+  ++E    LV     + +    
Sbjct: 2   LTSYLEELKKITLLTREEEQTLWRAYKEQGNM--QARARLIEQYQPLVFKEVMRLSMHSE 59

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
              D IQEG +GL++A E F    G  FS YA+  ++  I   +  + 
Sbjct: 60  WIPDAIQEGTVGLIEAVEHFRIQQGVAFSLYAVHRIRGEILEYLRREG 107


>gi|257451779|ref|ZP_05617078.1| RpoS [Fusobacterium sp. 3_1_5R]
 gi|317058336|ref|ZP_07922821.1| predicted protein [Fusobacterium sp. 3_1_5R]
 gi|313684012|gb|EFS20847.1| predicted protein [Fusobacterium sp. 3_1_5R]
          Length = 201

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 91/246 (36%), Gaps = 59/246 (23%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E +  + ++R  +     A+ E++E N+ L+  + ++Y        D  QEG +    A
Sbjct: 1   METKETLELIRLAKLGNIQARNELIEKNINLIHKINRRYG----SSEDGFQEGVLAFCHA 56

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +KFD     K S+YA  W++Q I R                       R   R+   + 
Sbjct: 57  IDKFDETKKVKLSSYAFHWIRQRIKRYRD--------------------REKYRLPAHVI 96

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
            + T EE   ++                                 DF  +    +  +++
Sbjct: 97  EKMTKEERKIRI----------------------------DFEYQDFNSEDEKTTEEENS 128

Query: 605 IQANLRETTTRVLA-SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
           I   L+ T  + +  +   +E  +L+  +       +  +E+ K+  V R+R+  I  ++
Sbjct: 129 I--CLKTTLEQYIKLACDEKEALILKKIYF----ESYQQQEIAKEMGVCRQRVNAIVKRS 182

Query: 664 IRKLKH 669
           ++KL+ 
Sbjct: 183 LQKLRR 188


>gi|260886518|ref|ZP_05897781.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|330839639|ref|YP_004414219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863661|gb|EEX78161.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|329747403|gb|AEC00760.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 208

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 44/264 (16%), Positives = 87/264 (32%), Gaps = 67/264 (25%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +K+   ++ +     ++  E + +    ++    A  A++ ++E+   LV   A  +   
Sbjct: 1   MKLEEYLQELEKVELLAPEEEQSLWQAFKERGERA--ARQRLIESYQPLVFKTALPWR-M 57

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
               +D+IQEG +GL++AAE FDW  G  FS +A+  ++  +   +  +           
Sbjct: 58  SESIMDIIQEGTVGLIEAAENFDWKRGVAFSLFAVHRIRGRMLNFLQKEGSRDV------ 111

Query: 527 DKIHKVVRTARRMSNKIKREPTP--EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
                  R   R   ++  + TP   E A+   M  E                       
Sbjct: 112 -TCMDAPRADGRAPWELLPDTTPSVAEQAELGFMTRE----------------------- 147

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
                                         R LA L  +E  VL   +            
Sbjct: 148 ----------------------------LHRALARLPQKERVVLESVYLKSETIPK---- 175

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           +     V+   I +++   IR+++
Sbjct: 176 IADVLDVSASHIYRLQKSGIRRVR 199


>gi|75761906|ref|ZP_00741831.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
          israelensis ATCC 35646]
 gi|74490614|gb|EAO53905.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
          israelensis ATCC 35646]
          Length = 109

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 9  RDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVA 68
           D  +  +  +  +  +   +   ++ +L ++RG +T EE+   +   E+ S+QM++   
Sbjct: 2  ADKPARSKQIETEMTLEQVKE---QLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYE 58

Query: 69 MLSNMGINVVDGDDLEDEEGS 89
           L   GI++V  +D E+   +
Sbjct: 59 YLGEQGIDLVGDNDNEEGPNN 79


>gi|313895463|ref|ZP_07829020.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|312976358|gb|EFR41816.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
          Length = 208

 Score = 57.5 bits (137), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 48/106 (45%), Gaps = 3/106 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K +S    +   E R +    +  E     A++ ++EA   LV      Y       
Sbjct: 4   DYVKKLSAVEKLRPDEERALWRAYK--EKGDEGARRRIIEAYQPLVFREVMPYRA-LPAV 60

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +D +QEG IGL++A E++D   G  FS YA+  V+  I   +  + 
Sbjct: 61  MDAVQEGTIGLIEAVERYDPARGVAFSLYAVHRVRGCILDFLRREG 106


>gi|320529893|ref|ZP_08030970.1| sigma-70 region 2 [Selenomonas artemidis F0399]
 gi|320137911|gb|EFW29816.1| sigma-70 region 2 [Selenomonas artemidis F0399]
          Length = 208

 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 48/106 (45%), Gaps = 3/106 (2%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
           + +K +S    +   E R +    +  E     A++ ++EA   LV      Y       
Sbjct: 4   DYVKKLSAVKKLRPDEERALWRAYK--EKGDEGARRRIIEAYQPLVFREVMPYRA-LPAV 60

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
           +D +QEG IGL++A E++D   G  FS YA+  V+  I   +  + 
Sbjct: 61  MDAVQEGTIGLIEAVERYDPARGVAFSLYAVHRVRGCILDFLRREG 106


>gi|207743817|ref|YP_002260209.1| rna polymerase sigma d (sigma-70) factor (partial sequence n
           terminus) protein [Ralstonia solanacearum IPO1609]
 gi|206595217|emb|CAQ62144.1| probable rna polymerase sigma d (sigma-70) factor (partial sequence
           n terminus) protein [Ralstonia solanacearum IPO1609]
          Length = 39

 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/38 (71%), Positives = 34/38 (89%)

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +GK F VTRE IRQ++AKA+RKL+HPSRS KL+SFL+G
Sbjct: 1   MGKHFDVTRESIRQMKAKAVRKLRHPSRSDKLKSFLEG 38


>gi|119947183|ref|YP_944863.1| sigma-28 (sigma F) factor [Psychromonas ingrahamii 37]
 gi|119865787|gb|ABM05264.1| predicted sigma-28 (sigma F) factor [Psychromonas ingrahamii 37]
          Length = 243

 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 77/243 (31%), Gaps = 21/243 (8%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK--YTNRGLQFLDLIQEGNIGLMKAA 485
           +                +  +V   L LV +V KK  Y N      D+ Q G I L+K  
Sbjct: 8   KKYNQTAELTGTRNKQEESFLVNKYLYLVHAVIKKMGYINCISDNDDMKQVGLIALLKMI 67

Query: 486 EKFD-WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            +F       +F       ++ +I   I  +                  +    +   + 
Sbjct: 68  RRFPVMDDEKEFIRLTYIRIRGSILDEIRSRDWRSEESRKNASTFLAQEKA---LMQSLG 124

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
           R P   E+ +   +  +   +        +           S L D +   NA S     
Sbjct: 125 RLPNKSEMLENKVLSEQQYEEARCAINGKV----------FSELSDQLLKDNAQSVDI-C 173

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            + +  +  +  L  LT  E  +L + +      D + +E+         RI +I+ +A 
Sbjct: 174 TEIDNTQCLSVALKQLTEEEVLILHLMY----EKDMSFKEMALATNNNFSRINKIQREAH 229

Query: 665 RKL 667
           RKL
Sbjct: 230 RKL 232


>gi|160933395|ref|ZP_02080783.1| hypothetical protein CLOLEP_02240 [Clostridium leptum DSM 753]
 gi|156867272|gb|EDO60644.1| hypothetical protein CLOLEP_02240 [Clostridium leptum DSM 753]
          Length = 149

 Score = 57.2 bits (136), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 21/102 (20%), Positives = 49/102 (48%), Gaps = 2/102 (1%)

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR-ETTTRVL-ASLTPREERV 627
           + + +S+  PI  +   +    ++  +    +   +   ++ E   + L   LTPRE  +
Sbjct: 38  SAQDVSMNEPIDTDKEGNTLTLMDVMSTEDNIVDNLDIKIKSEQLKKYLVEVLTPRERII 97

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           + +R+G+  +   T  EV ++  ++R  + +IE KA+  L+ 
Sbjct: 98  IELRYGLNGSRPLTQREVAQRLKISRSYVSRIEKKALLTLRK 139


>gi|237668235|ref|ZP_04528219.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237656583|gb|EEP54139.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 146

 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           + + E       ++K +     AK  ++E NLRLV  + KKY+       +LI  G +GL
Sbjct: 29  LPLDEEEE-QMYLKKFKEGDKSAKSILIERNLRLVAHIVKKYSFPNKDVDELISIGTVGL 87

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           +KA + FD   G + +TYA   ++  I     + 
Sbjct: 88  IKAIDSFDSSKGTRLATYASRCIENEILMLFRNN 121


>gi|262273680|ref|ZP_06051493.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
 gi|262222095|gb|EEY73407.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
          Length = 78

 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 40/60 (66%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++    L  L P++  VL  RFG+  +   TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 1   MKKSIVHWLQELNPKQREVLARRFGLLGHEASTLEDVGREIGLTRERVRQIQVEGLRRLR 60


>gi|262196406|ref|YP_003267615.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262079753|gb|ACY15722.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 210

 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 91/241 (37%), Gaps = 39/241 (16%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           ++ +VE N+ L  S+A +        + F DL+     GL++A+ ++D+     F  +A 
Sbjct: 6   RRCLVEQNIGLARSIAGRLQRSMSLQVDFDDLLAHAQAGLIEASLRYDFAAETPFRMFAR 65

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
           + ++ AI   I     + R   + R                   E    E A+++ +PV 
Sbjct: 66  YRIRGAIFDWIRRMGYSRRAGRNAR----------------SPAEGEGAEDAERVRLPVP 109

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
            V                   E++         ++A + L   ++        + L  L 
Sbjct: 110 QVVFQ-------------AAYEESGPQAARAPTESAEAALAQKLRDRF---VAQALTRLP 153

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
            RE++ LR  +      D T    G    ++R +  ++ A+A+  L+    +  +R+F D
Sbjct: 154 AREQQFLRQCY----YEDKTRVAAGASLGLSRYQAFRLHARAVGMLREELAAHGIRAFDD 209

Query: 682 G 682
            
Sbjct: 210 A 210


>gi|228907496|ref|ZP_04071353.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228851988|gb|EEM96785.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 324

 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 93/241 (38%), Gaps = 27/241 (11%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQF--------LDLIQEGNIGLMKAAEKFDWCLGYKFST 498
           E++  N   + S+   Y                +L+Q   I ++ A   FD+  G KF+T
Sbjct: 35  ELLYENKEFLFSIIAHYKGSIESLKNKFNVDEEELLQHAYIAVITAIRDFDFNKGIKFTT 94

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           Y    +   I + + + S  +R+     D + ++ +      N++   P  EE+A  L +
Sbjct: 95  YIYRPIIWEINQLLYNDSRLVRLSRSAVDLLKQMEKV----ENELGYFPKAEELAILLDV 150

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
            VE +  VL+   E  SL +    E   +   +     +       ++  L+       +
Sbjct: 151 TVERIENVLRFASELTSLNSLENFEPEDYSIGY----ESKVMDKIYVENLLKN------S 200

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            L+  E +V+ +      N+     ++ K+  V    + +   +   KL +   SK+L  
Sbjct: 201 DLSEFETQVINLIMDGNNNS-----QIAKKLNVYPMTVNRALNRIKNKLDNNFESKRLSK 255

Query: 679 F 679
           +
Sbjct: 256 Y 256


>gi|26000679|gb|AAN75199.1| sigma K [Clostridium difficile]
 gi|26000681|gb|AAN75200.1| sigma K [Clostridium difficile CD196]
 gi|26000696|gb|AAN75201.1| sigma K [Clostridium difficile]
 gi|26000698|gb|AAN75202.1| sigma K [Clostridium difficile]
 gi|26000700|gb|AAN75203.1| sigma K [Clostridium difficile]
          Length = 108

 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 2/99 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  ++  E    ++  +        AK  ++E N+RLV  +AKKY N      DLI  
Sbjct: 6   SFEKPLTPEEEIEYLTKFK--IENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           G IGL+KA E ++   G + +TYA   ++  I  +I   
Sbjct: 64  GTIGLIKAIETYNIDKGTRLATYASRCIENEILMNIRSN 102


>gi|157962130|ref|YP_001502164.1| sigma-70 region 4 domain-containing protein [Shewanella pealeana
           ATCC 700345]
 gi|157847130|gb|ABV87629.1| sigma-70 region 4 domain protein [Shewanella pealeana ATCC 700345]
          Length = 930

 Score = 57.2 bits (136), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            DF    N     + A    L+E  T+ L+ L  RE+ ++ +R G       TLEEVG +
Sbjct: 370 MDFTAQSNNEFKYNLASNIPLKEHFTQALSLLKDREKEIIELRMGF-HGHILTLEEVGTK 428

Query: 649 FCVTRERIRQIEAKAIRKL 667
           F VTRERIRQI+ K + ++
Sbjct: 429 FGVTRERIRQIQKKHVARI 447


>gi|153815652|ref|ZP_01968320.1| hypothetical protein RUMTOR_01888 [Ruminococcus torques ATCC 27756]
 gi|145847083|gb|EDK24001.1| hypothetical protein RUMTOR_01888 [Ruminococcus torques ATCC 27756]
          Length = 114

 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/104 (26%), Positives = 51/104 (49%), Gaps = 3/104 (2%)

Query: 570 TKEPISLETPIGDEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
             + ISL  PIG +   +   L D IE           ++ N++    +V   L+ RE  
Sbjct: 9   AAKEISLYEPIGTDREGNEIKLYDIIETDEEEVAEKIHLKENIQTLYEKVEKELSQRERI 68

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +L+MR+G+    ++T  E+ +Q  ++R  + +IE  A+ KL+  
Sbjct: 69  ILKMRYGLYNGEEYTQREIARQLGISRSYVSRIEKGAVEKLRKS 112


>gi|270659580|ref|ZP_06222335.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270316998|gb|EFA28670.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 147

 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/146 (22%), Positives = 68/146 (46%), Gaps = 10/146 (6%)

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSH 587
              + +T +R+      E   + +A +L +  E V ++  +++   +  + P  D +T  
Sbjct: 1   FFNLRKTKQRLG--WFNENEVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAETET 58

Query: 588 LGD--FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                ++EDK+   A    +   ++   E     L SL  R + +++ R+        TL
Sbjct: 59  YSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIKARWLDDN--KATL 116

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++  ++ V+ ERIRQ+E  A++KLK
Sbjct: 117 HDLAAKYNVSAERIRQLETNALKKLK 142


>gi|226311518|ref|YP_002771412.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
 gi|226094466|dbj|BAH42908.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 121

 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/108 (26%), Positives = 55/108 (50%), Gaps = 8/108 (7%)

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFI--EDKNAVSPLDSAIQANLRETTTRVLAS 619
           + LK TK+ +SL  PIG +   +   L D +  E    V  +   +++N      + +  
Sbjct: 4   RSLKKTKKDVSLHDPIGTDKEGNEITLIDVLGTETDEVVDAVQLKLESN---KIYQHIHI 60

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L  RE+ V+  RFG+  + + T  E+ ++  ++R  + +IE +A+ KL
Sbjct: 61  LDEREKEVIIGRFGLDQDKEKTQREIARELGISRSYVSRIEKRALMKL 108


>gi|253574829|ref|ZP_04852169.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251845875|gb|EES73883.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 110

 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 3/99 (3%)

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A  +  +  + + +K+ +    ++  E    +  +       S ++  ++E NLRLV 
Sbjct: 15  AIALFIKQLTLLVSYVKNNAFPQPLTEEEETKHLQRM---AEGDSESRNILIEHNLRLVA 71

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
            + KK+ N G    DLI  G IGL+KA E F    G K 
Sbjct: 72  HIVKKFDNTGEDLEDLISIGTIGLIKAIESFRPNKGTKL 110


>gi|167717487|ref|ZP_02400723.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 163

 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 50/142 (35%), Gaps = 9/142 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNA--------FLPPDEVSSEQMEDTVAMLSNMGINVV 78
            +    ++++LA  R      ++              D    + ++   +   + G    
Sbjct: 10  YEQGIDRLLELAGARDDTEYADVADEFASAPSSAFAHDLGEPDSLDHQASD-ESAGAGSF 68

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
                    G  D                        ++ DP+ +++R M ++ LL+   
Sbjct: 69  GDKPTRPAHGDTDVDTDWRDDDAPPSGSNDAAPVDTTASTDPLALFVRRMHAVPLLTHAQ 128

Query: 139 EIAIAKRIEAGRAMMMASLCES 160
           EIA+A  IEAGR  ++ +L E+
Sbjct: 129 EIALAAEIEAGREQVLQALAEA 150


>gi|292670483|ref|ZP_06603909.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
 gi|292647893|gb|EFF65865.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
          Length = 205

 Score = 56.8 bits (135), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 86/254 (33%), Gaps = 63/254 (24%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +S    ++  E   +    +  E     A++ ++EA   LV      Y    +  +D +
Sbjct: 3   KLSAVRKLTPEEEHALWRAYK--EEGDESARRRIIEAYQPLVFREVMPYRTMPV-VMDAV 59

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
           QEG IGL++A E++D   G  FS YA+  V+  I   +  +                   
Sbjct: 60  QEGTIGLIEAVERYDPTRGVAFSLYAVHRVRGRILDFLRREGSVDLP------------- 106

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
                   ++ E   +E AK+                                    + D
Sbjct: 107 -------CLEAETEAQETAKE-----------------------------------LLVD 124

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           + A S  + A    L +    V+  L  RE  VL      G       + + +   VT  
Sbjct: 125 ERA-SVAELAEHHALVDLLGAVMERLPLRERLVLEGVTIGGT----QAQTMAESLGVTPA 179

Query: 655 RIRQIEAKAIRKLK 668
            I +++ + IR+++
Sbjct: 180 HIYRLQQRGIRRVR 193


>gi|163846279|ref|YP_001634323.1| hypothetical protein Caur_0695 [Chloroflexus aurantiacus J-10-fl]
 gi|222524035|ref|YP_002568505.1| tetratricopeptide repeat-containing protein [Chloroflexus sp.
            Y-400-fl]
 gi|163667568|gb|ABY33934.1| Tetratricopeptide TPR_2 repeat protein [Chloroflexus aurantiacus
            J-10-fl]
 gi|222447914|gb|ACM52180.1| Tetratricopeptide TPR_2 repeat protein [Chloroflexus sp. Y-400-fl]
          Length = 1766

 Score = 56.4 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 47/97 (48%)

Query: 17   DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
              D+  + D  D    ++IKL  ++GYV + ++ A +   E  ++++E     L   GI 
Sbjct: 1075 SDDEEPMIDTGDPDLNRLIKLGHRQGYVDLTDIIAVVKDPEQEADRIEQIGWSLYRAGIQ 1134

Query: 77   VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
            + DGD++ D E   +  + A + S+++  L    +  
Sbjct: 1135 IRDGDEIIDMEAELNEEEPAPATSSATADLTPFDEEP 1171


>gi|168206182|ref|ZP_02632187.1| sigma factor [Clostridium perfringens E str. JGS1987]
 gi|170662325|gb|EDT15008.1| sigma factor [Clostridium perfringens E str. JGS1987]
          Length = 227

 Score = 56.4 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 53/250 (21%), Positives = 91/250 (36%), Gaps = 60/250 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKF 488
            +V   +     A  +++E N +L+  +A K+ +     ++F DL+QEG IG + A  K+
Sbjct: 5   ELVVLYQQGDKRALDKLLENNDKLIYKIASKFYSEKINAIEFDDLLQEGRIGFILACNKY 64

Query: 489 DWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           D       KF TYA +W+ Q I R I                                  
Sbjct: 65  DCEYIKKTKFITYAFYWIYQKIHRFITGN------------------------------- 93

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV--SPLDSA 604
            T +EI                      SL TP+ +E+   L + IE          +  
Sbjct: 94  NTNDEI----------------------SLNTPVSEENKDELINGIESNRNEINDREEEL 131

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
             + LR     V+       ER +   +      + ++E++   F  +   I+  +A+AI
Sbjct: 132 YLSELRLELEAVMDKHNTLNEREILKLYYGWDTDELSIEQIADIFETSSSDIKNTKARAI 191

Query: 665 RKLKHPSRSK 674
           RKL+     +
Sbjct: 192 RKLRGSQWFR 201


>gi|256269|gb|AAC60415.1| RpoD2 [Synechococcus]
          Length = 48

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/47 (68%), Positives = 37/47 (78%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           LDLIQEG +GL +  EKFD   GYKFSTYA WW++QAITR+IA QS 
Sbjct: 1   LDLIQEGTLGLERGVEKFDPSKGYKFSTYAYWWIRQAITRAIAQQSR 47


>gi|5360295|dbj|BAA81927.1| principle sigma factor [Pseudomonas syringae]
          Length = 172

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/212 (11%), Positives = 59/212 (27%), Gaps = 45/212 (21%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L +++            G+    +G +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPA 50

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                 + +    + T+ D E +A  S DD      P             D+ +      
Sbjct: 51  EVPPPVDPKAVKAEGTDDDEEESADASDDDDEVESGPDPVIAQQRFGAVSDQMEITRKAL 110

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
               +     +  +  +AE++                                    + L
Sbjct: 111 KKFGRDDKHAIAEMVALAELF----------------------------------MPIKL 136

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 137 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 168


>gi|304438393|ref|ZP_07398334.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368759|gb|EFM22443.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 208

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 3/105 (2%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
            +K +S    ++  E R +    ++    A  A++ ++EA   LV      Y        
Sbjct: 5   YMKKLSAVQKLAPEEERALWRAYKENGDMA--ARRRIIEAYQPLVFREVYPYRALPAAMD 62

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516
             +QEG IGL++A E++D   G  FS YA+  V+  +   +  + 
Sbjct: 63  A-VQEGTIGLIEAVERYDPDYGAAFSLYAVHRVRGRVRDFLRREG 106


>gi|74319489|gb|ABA02889.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319493|gb|ABA02891.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
          Length = 171

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/205 (16%), Positives = 62/205 (30%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P     ++   ++   G   L +I  L   + PE+        E     + ED S  K 
Sbjct: 1   WPNAVDVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEDVEELEEEDESSTKS 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            ++V+  + D E  ++   D        PE A+     L+     +   +          
Sbjct: 59  TNEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIE--------- 109

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                                     K  ++S +     E L  +           D++ 
Sbjct: 110 --------------------------KHGRNSPEANEALESLATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREIMRYAVRRG 168


>gi|21104384|dbj|BAB93462.1| rpoS like gene [Variovorax sp. WFF52]
          Length = 47

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/46 (56%), Positives = 35/46 (76%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           V+++AK Y NRG+ F DLI+EGN+GLM A  KF+   G++FSTYA 
Sbjct: 2   VVNIAKAYLNRGVPFSDLIEEGNLGLMHAITKFEPERGFRFSTYAT 47


>gi|134298777|ref|YP_001112273.1| sigma-70 region 4 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051477|gb|ABO49448.1| sigma-70 region 4 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 6/98 (6%)

Query: 574 ISLETPIGDEDTSHLGDFIE----DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           +SL  PIG +   +    I+    D   V+    +     R      +  LT RE+RVL 
Sbjct: 13  VSLYDPIGVDKEGNEISLIDILGTDPEVVADTVESTFEKNR--LLEKITKLTTREKRVLE 70

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           MRFG+G     T  E+ +   ++R  + +IE +A+ KL
Sbjct: 71  MRFGLGTTARKTQREIARTLGISRSYVSRIEKRALNKL 108


>gi|255092173|ref|ZP_05321651.1| sporulation sigma factor SigK [Clostridium difficile CIP 107932]
 gi|255649691|ref|ZP_05396593.1| sporulation sigma factor SigK [Clostridium difficile QCD-37x79]
          Length = 105

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/97 (31%), Positives = 48/97 (49%), Gaps = 2/97 (2%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           S E  ++  E    ++  +        AK  ++E N+RLV  +AKKY N      DLI  
Sbjct: 6   SFEKPLTPEEEIEYLTKFK--IENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISI 63

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
           G IGL+KA E ++   G + +TYA   ++  I  +I 
Sbjct: 64  GTIGLIKAIETYNIDKGTRLATYASRCIENEILMNIR 100


>gi|313115853|ref|ZP_07801286.1| sporulation sigma factor SigK family protein [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310621830|gb|EFQ05352.1| sporulation sigma factor SigK family protein [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 150

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 49/115 (42%), Gaps = 7/115 (6%)

Query: 560 VEGVRKVLKITKEP---ISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTT 614
              +R   +  ++    +SL+  +  +  S   L D ++D  +    D+    +      
Sbjct: 26  ENEIRMQFRRNRKTGGTVSLQEALESDGDSALTLADVLQD--SFCMEDTCETQDDIRRMR 83

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           ++L  L  RE +++ +R+G+      T  E  K   ++R  + ++E  A+  L+ 
Sbjct: 84  QLLDGLPARERQIILLRYGLSGQPPLTQLETAKLLDISRSYVSRLETHALELLRQ 138


>gi|150389709|ref|YP_001319758.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|150392068|ref|YP_001322117.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949571|gb|ABR48099.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
 gi|149951930|gb|ABR50458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 215

 Score = 56.4 bits (134), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/262 (16%), Positives = 84/262 (32%), Gaps = 51/262 (19%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  ++ +  ++  E + +++  R+        +K ++E NLRLV   A KY N+     D
Sbjct: 2   LHKVNFKEPMTEEESKRLINQFRELNN--EEIRKHLIERNLRLVAYEAYKYKNQ--DSED 57

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +   G IGL+KA + +D     +F TYA   ++  I   I       R      D  +  
Sbjct: 58  IFSVGCIGLIKAIDSYDPSKQTRFDTYANRCIQNEILLYIKRLKKGSRWTFVRLDAKN-- 115

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                                                    +S +      +   L    
Sbjct: 116 -----------------------------------------LSFDDGSSIYNFETLA--- 131

Query: 593 EDKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            D+N         +  + R      L   +  E+   R           T  +V ++  +
Sbjct: 132 SDENLEESFIGREEKLIARSIIKDNLIEESIEEQSTKRQMAIRLRYQGLTQIDVSQRLGI 191

Query: 652 TRERIRQIEAKAIRKLKHPSRS 673
           ++  + +IE +   KL    R 
Sbjct: 192 SQSYVARIEKRYQDKLYQKLRK 213


>gi|14646833|dbj|BAB62001.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 79

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +L ++  + L  LT ++  V+  RFG+  +   TLE+VG +  +TRER+RQI+ + +
Sbjct: 1   QDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGL 60

Query: 665 RKLKHPSRSKKLRS 678
           ++L+       L S
Sbjct: 61  KRLREILEKNGLSS 74


>gi|162449915|ref|YP_001612282.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161160497|emb|CAN91802.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 222

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/220 (14%), Positives = 71/220 (32%), Gaps = 16/220 (7%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
           V     +   R +   DL+  G+  L++     D      F  YA   ++ AI   +  +
Sbjct: 19  VAKRIARRLGRRIPVEDLVALGHPALLEIVRTHDPSRST-FEAYAKRKLRWAIFDGVRRE 77

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
           +                     R ++     P  +E        +      L      ++
Sbjct: 78  TRWRSAAARASALAASARFAEGRGADDDADAPATQEAYAARLGDL------LAGHAAAMA 131

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L       D + + D  +D         A +A L +     +  L  RE  ++   +   
Sbjct: 132 LGLLSSHGDVAAVPDAADDPEE-----RASRAELAQAVRHAVRELPERERTLVERHYF-- 184

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
              D   +++ +   +++    ++ ++AI +L    R+ +
Sbjct: 185 --EDERFDQIAQDLGISKSWASRLHSQAIERLCELLRTAR 222


>gi|152965726|ref|YP_001361510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151360243|gb|ABS03246.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 227

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 67/198 (33%), Gaps = 56/198 (28%)

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534
              N+GL++AA  +D   G + + +    +  AIT     +        H          
Sbjct: 42  SAANLGLLQAARAWDPARG-EVAPHLWHRINGAITDDFRARHGRPGSTRHK--------- 91

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT---SHLGDF 591
                                                  +SL+ P+          LGD 
Sbjct: 92  ----------------------------------AMAAQVSLDMPLVTGGDRVSLTLGDT 117

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           I+D      ++   +A  R   TR +  LT R+ R+L+ RF   ++  H L  +     V
Sbjct: 118 IQDP-----VNHIDRAMDRIDLTRAIDHLTDRDRRLLQWRF---VDELHLLT-IAGYLNV 168

Query: 652 TRERIRQIEAKAIRKLKH 669
           T  R+ Q+E + I +L+ 
Sbjct: 169 TESRVSQMEREVITRLRR 186


>gi|323484667|ref|ZP_08090029.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323694798|ref|ZP_08108953.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
 gi|323402050|gb|EGA94386.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323501114|gb|EGB17021.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
          Length = 192

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/169 (21%), Positives = 87/169 (51%), Gaps = 6/169 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
            +  ++ + +    S  E   ++  +      +  A K +VE  L   + +A++Y +RGL
Sbjct: 28  YQLYLEELKLVPPCSPEEEERLLDEI---LAGSQSAVKRLVEGKLGRAVRMAEEYRDRGL 84

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DL+QE NI L+  A+++    G  F + +   +++ I  ++  Q+   ++   M  +
Sbjct: 85  SMNDLVQEANIALLLTAQEY---KGGDFDSQSEERIRRMIEDALELQNTEYKVEEEMLAR 141

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           ++ +   +  M+ ++ RE T EE+A+++ M  + ++ ++K+T + +S+ 
Sbjct: 142 VNVLKDISAGMAEELGREATVEELAERMKMTEQEIKDIMKLTLDAMSVS 190


>gi|225075400|ref|ZP_03718599.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
 gi|224953218|gb|EEG34427.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
          Length = 113

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 4/96 (4%)

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL---RETTTRVLASLTPREERVLRMRF 632
           +     DED     D++ D +A      + QA+     E     LA L  R  R++  R+
Sbjct: 9   MAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSHRIVESRW 68

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
                   TL E+  ++ V+ ERIRQIEAKA++KL+
Sbjct: 69  LQDDGG-LTLHELAAEYGVSAERIRQIEAKAMQKLR 103


>gi|153933487|ref|YP_001384721.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. ATCC 19397]
 gi|153936370|ref|YP_001388242.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. Hall]
 gi|152929531|gb|ABS35031.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. ATCC 19397]
 gi|152932284|gb|ABS37783.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. Hall]
          Length = 96

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 40/86 (46%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +   L D +           + +  +++   ++   L  RE++V++MR+G+      T
Sbjct: 1   MGNEISLMDILSSDEDSIIEIVSTKIEVKKLYGKIDTCLRGREKKVIQMRYGLKDGRPRT 60

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
             E+     ++R  + +IE KA++KL
Sbjct: 61  QREIAGILNISRSYVSRIEKKALKKL 86


>gi|210611678|ref|ZP_03288975.1| hypothetical protein CLONEX_01165 [Clostridium nexile DSM 1787]
 gi|210151925|gb|EEA82932.1| hypothetical protein CLONEX_01165 [Clostridium nexile DSM 1787]
          Length = 254

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/165 (23%), Positives = 79/165 (47%), Gaps = 3/165 (1%)

Query: 407 LKIRNEIKSISVETG-ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
            + +  +K    + G I  ++     ++  K     ++AK  +VE  L  V+ +AK+  +
Sbjct: 84  EEEQRYLKEYMKDIGGIREADEEEREALFEKVLEGDALAKSRLVEIYLPEVVEIAKQLYH 143

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
             +   DL+QEGN+GL+   +  D     K        ++QAI   I +Q+        M
Sbjct: 144 PEVFLGDLVQEGNVGLILGVDMIDD--LDKAHDVIRREIRQAIQMLIEEQTELKNRDKKM 201

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
            +K++ +  + + ++ ++ R+ T EE+A  + M  E V  +L++T
Sbjct: 202 VEKVNTLDESIQALTEELGRKVTIEELAVYMGMSEEEVEDILRLT 246


>gi|313647806|gb|EFS12252.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2a str. 2457T]
          Length = 76

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 43/68 (63%)

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           ++++  + L  L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+
Sbjct: 1   MKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 60

Query: 669 HPSRSKKL 676
              +++ L
Sbjct: 61  EILQTQGL 68


>gi|5360311|dbj|BAA81935.1| principle sigma factor [Pseudomonas syringae]
          Length = 174

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/212 (11%), Positives = 60/212 (28%), Gaps = 43/212 (20%)

Query: 151 AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
             +M ++   P T   ++     +      L ++  L   I P+       G    +   
Sbjct: 2   REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDV--LSGYIDPD------DGIAPPAEVP 53

Query: 211 REDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLS 270
                +  + +   + E +   A+    +D  +    P  A+     + +  + +   L 
Sbjct: 54  PPVDPKAVKAEGTDDDEEESADASDDEDEDEVESGPDPVIAQQRFGAVSDQMEITRKAL- 112

Query: 271 AMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
                                             +K  +           L +L   + L
Sbjct: 113 ----------------------------------KKFGRDDKHAIAEMVALAELFMPIKL 138

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + + LVE++    +R+   E  +++L   
Sbjct: 139 VPKQFEGLVERVRGALERLRAQERAIMQLCVR 170


>gi|126215764|gb|ABN81002.1| putative RNA polymerase sigma-F factor [Rhodococcus opacus]
          Length = 130

 Score = 56.0 bits (133), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/139 (18%), Positives = 54/139 (38%), Gaps = 12/139 (8%)

Query: 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLE-TP 579
             M++    + +    +S  +   PT  E+A+ L +  E V + L      + +S++ T 
Sbjct: 1   RRMKELHLALSQAVAELSQSLGHAPTVSELAEHLDLEQEEVAQGLLAGNAYQTVSVDNTS 60

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
                   + + + D +A             ET   +L SL  RE  VL +RF       
Sbjct: 61  SDRTGELSMVETLGDYDAA-----MDDVENHETLRPLLQSLPERERTVLMLRFFGN---- 111

Query: 640 HTLEEVGKQFCVTRERIRQ 658
            T  ++  +  +++  + +
Sbjct: 112 MTQTQIADRVGISQMHVSR 130


>gi|74319459|gb|ABA02874.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319461|gb|ABA02875.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319463|gb|ABA02876.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319465|gb|ABA02877.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319467|gb|ABA02878.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319469|gb|ABA02879.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319471|gb|ABA02880.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319473|gb|ABA02881.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319479|gb|ABA02884.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319481|gb|ABA02885.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319491|gb|ABA02890.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319495|gb|ABA02892.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319497|gb|ABA02893.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319501|gb|ABA02895.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319503|gb|ABA02896.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319505|gb|ABA02897.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319509|gb|ABA02899.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319511|gb|ABA02900.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319513|gb|ABA02901.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319517|gb|ABA02903.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319521|gb|ABA02905.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319523|gb|ABA02906.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319525|gb|ABA02907.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319527|gb|ABA02908.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319529|gb|ABA02909.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319531|gb|ABA02910.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319533|gb|ABA02911.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319535|gb|ABA02912.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319537|gb|ABA02913.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319539|gb|ABA02914.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319541|gb|ABA02915.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319543|gb|ABA02916.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319545|gb|ABA02917.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319551|gb|ABA02920.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319553|gb|ABA02921.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
          Length = 171

 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/205 (16%), Positives = 62/205 (30%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P   + ++   ++   G   L +I  L   + PE+        E     + ED S  K 
Sbjct: 1   WPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEDVEELEEEDESSTKS 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +V+  + D E  ++   D        PE A+     L+     +   +          
Sbjct: 59  TKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIE--------- 109

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                                     K  ++S +     E L  +           D++ 
Sbjct: 110 --------------------------KHGRNSPEANEALESLATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREIMRYAVRRG 168


>gi|74319547|gb|ABA02918.1| RNA polymerase sigma factor sigma-70 [Acinetobacter genomosp. 13TU]
 gi|74319549|gb|ABA02919.1| RNA polymerase sigma factor sigma-70 [Acinetobacter genomosp. 13TU]
          Length = 171

 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/205 (16%), Positives = 62/205 (30%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P   + ++   ++   G   L +I  L   + PE+        E     + ED S  K 
Sbjct: 1   WPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEELEEEDESSTKS 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +V+  + D E  ++   D        PE A+     L+     +   +          
Sbjct: 59  TKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIE--------- 109

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                                     K  ++S +     E L  +           D++ 
Sbjct: 110 --------------------------KHGRNSPEANEALESLATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREIMRYAVRRG 168


>gi|150388236|ref|YP_001318285.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149948098|gb|ABR46626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 218

 Score = 55.6 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/262 (16%), Positives = 84/262 (32%), Gaps = 51/262 (19%)

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           +  ++ +  ++  E + +++  R+        +K ++E NLRLV   A KY N+     D
Sbjct: 5   LHKVNFKEPMTEEESKRLINQFRELNN--EEIRKHLIERNLRLVAYEAYKYKNQ--DSED 60

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +   G IGL+KA + +D     +F TYA   ++  I   I       R      D  +  
Sbjct: 61  IFSVGCIGLIKAIDSYDPSKQTRFDTYANRCIQNEILLYIKRLKKGSRWTFVRLDAKN-- 118

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                                                    +S +      +   L    
Sbjct: 119 -----------------------------------------LSFDDGSSIYNFETLA--- 134

Query: 593 EDKNAVSPLDSAIQANL-RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
            D+N         +  + R      L   +  E+   R           T  +V ++  +
Sbjct: 135 SDENLEESFIGREEKLIARSIIKDNLIEESIEEQSTKRQMAIRLRYQGLTQIDVSQRLGI 194

Query: 652 TRERIRQIEAKAIRKLKHPSRS 673
           ++  + +IE +   KL    R 
Sbjct: 195 SQSYVARIEKRYQDKLYQKLRK 216


>gi|169334926|ref|ZP_02862119.1| hypothetical protein ANASTE_01332 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257664|gb|EDS71630.1| hypothetical protein ANASTE_01332 [Anaerofustis stercorihominis DSM
           17244]
          Length = 233

 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 85/234 (36%), Gaps = 49/234 (20%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V+  E     AK+ ++  NLRLV  V+KKY++  +   DLI  G IGL+K    FD+  G
Sbjct: 41  VKFKEENDMHAKEMLINHNLRLVAHVSKKYSSSNITKEDLISIGIIGLIKGINSFDYNKG 100

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            KF+TY    +   I  ++                                      E  
Sbjct: 101 TKFATYGARCIDNEILMALRS------------------------------------ETK 124

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
               + +E            IS +    +     L D +            ++       
Sbjct: 125 TASNVFLEDY----------ISFDEEGNN---ISLLDILATDEDDVNSKVNLKVESEFLY 171

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +   L  RE+ +L +R+G+     +T  E+   + ++R  + +IE KAI K+
Sbjct: 172 KIMDEVLEDREKEILYLRYGLKGKRSYTQREIADMYDISRSYVSRIEKKAIEKI 225


>gi|256532384|gb|ACU81350.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532396|gb|ACU81356.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 58/148 (39%), Gaps = 11/148 (7%)

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---K 542
           F+     +FSTYA WW++ +I   I      +R       K     + R   +++    +
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKLAKGDTQ 60

Query: 543 IKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED--TSHLGDFI--EDKNA 597
           +  +   +EIA  L + +  V+    +++    SL+ P    D  ++   DF+  +D   
Sbjct: 61  LTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPLP 120

Query: 598 VSPLDSAIQANLRE-TTTRVLASLTPRE 624
              + + I    R       L  L  RE
Sbjct: 121 DEQVSNMIDGERRRVWLASALKHLNERE 148


>gi|118363547|ref|XP_001014998.1| hypothetical protein TTHERM_00672210 [Tetrahymena thermophila]
 gi|89296765|gb|EAR94753.1| hypothetical protein TTHERM_00672210 [Tetrahymena thermophila SB210]
          Length = 3482

 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 82/665 (12%), Positives = 211/665 (31%), Gaps = 82/665 (12%)

Query: 6    KRNRDSDSEHEDSDDSLVFDFSD--DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
            K  +++  E++   D  + +  +     KK+I L +++  + ++E N  L   +   ++ 
Sbjct: 2844 KTTKETIEENQMIKDRQLIENKELIQEMKKIIDLNKEQ--LELKE-NKILQLKQTYDKEK 2900

Query: 64   EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
            E  +   +   I     + LE+ +     ++        +      + +      D  ++
Sbjct: 2901 EAILRE-TEHQI----NEKLEEIKAYTLEIEKFRDELVLTKKQLMEEKNRADYFQDQFKI 2955

Query: 124  YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
            Y   MG+ E    + E  I       +      +          +   ++L +    + +
Sbjct: 2956 Y---MGNQEHQKFQQEQIIMNTCLENKRSQQDKI--------HFLNEIEDLKNKNIAVTD 3004

Query: 184  IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
             +D    +           ++       E      ER+  Q     I++     +++R  
Sbjct: 3005 KLDQMIAVNDNLTEVLKEKSQEIQELLIEKDKLLYEREQEQIQLERIQNNLHQLEEEREN 3064

Query: 244  VDSPPENAENDERNLDEDE--------DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                 ++    +  +   E        +D    +   E +   +    L+++ +  +E+ 
Sbjct: 3065 FLKETQDVYELKEKVSHQETNRYKQQIEDLKLQIQQKEFETNEQFQKNLNQLEQSQQEII 3124

Query: 296  SLQDNAVN-----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQ-SRIDLLVEQLYDISKRI 349
             L+D          Q   +  +K +        L+    +N+ ++I+  +  L D   ++
Sbjct: 3125 QLKDQINKLNYQISQIQSEDRLKIQERVHFDSTLLELQKINEDNQIE--IANLKDKLLKL 3182

Query: 350  MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKI 409
             +   +L R       + D+   + +  E +              ++N +A       ++
Sbjct: 3183 ENQRDKLQRQLSEEKEENDL---KFRKSEQN--------------YENQIASLDTKYKRL 3225

Query: 410  RNEIKSISVETGISISE---FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             +E K +S        E   F+  +  +        I   + +E   + +  ++ +    
Sbjct: 3226 LDEFKYLSESYEHKKQELNQFKEELPQIANKIKNEKIELTKSIEEKEKQLDILSIQNKVS 3285

Query: 467  GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
              + LDL  + NI       K +       +            +    ++   +    ++
Sbjct: 3286 NEKILDLESQVNIM----INKNEQIQNTYLALQT---------QYQVLENKYTQQHKKIQ 3332

Query: 527  DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                +   T   ++  +++  T     K   + +E   K L        ++         
Sbjct: 3333 QLEKQNDNTKSHLTISLQQAETQLSQTKMQIIELETKNKRL--------IDDISRANHLK 3384

Query: 587  HLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L  D +ED   +          +RE + + L +   RE+R L  +     N    LE  
Sbjct: 3385 QLMKDQMED---LEINFKKEMDEVREESIKDLNNKFEREKRELNFKIQKLGNQVRQLESD 3441

Query: 646  GKQFC 650
                 
Sbjct: 3442 KDIMK 3446


>gi|256532386|gb|ACU81351.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532388|gb|ACU81352.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532392|gb|ACU81354.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532394|gb|ACU81355.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532398|gb|ACU81357.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532400|gb|ACU81358.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532402|gb|ACU81359.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532404|gb|ACU81360.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532406|gb|ACU81361.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score = 55.6 bits (132), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 58/148 (39%), Gaps = 11/148 (7%)

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---K 542
           F+     +FSTYA WW++ +I   I      +R       K     + R   +++    +
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKLAKGDTQ 60

Query: 543 IKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED--TSHLGDFI--EDKNA 597
           +  +   +EIA  L + +  V+    +++    SL+ P    D  ++   DF+  +D   
Sbjct: 61  LTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPLP 120

Query: 598 VSPLDSAIQANLRE-TTTRVLASLTPRE 624
              + + I    R       L  L  RE
Sbjct: 121 DEQVSNMIDGERRRVWLASALKHLNERE 148


>gi|21104382|dbj|BAB93461.1| unnamed protein product [Roseateles depolymerans]
          Length = 47

 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/46 (56%), Positives = 33/46 (71%)

Query: 456 VISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           V+S+AK Y  RGL   DLI+EGN+GLM A  KF+   G++FSTYA 
Sbjct: 2   VVSIAKNYLGRGLPMSDLIEEGNLGLMHAIGKFEPERGFRFSTYAS 47


>gi|255316500|ref|ZP_05358083.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
          Length = 215

 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/224 (20%), Positives = 79/224 (35%), Gaps = 46/224 (20%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
           K+++  AN +L+  V K+         +L   G +G  KA E FD     KFSTYA+  +
Sbjct: 27  KEKVAYANNKLIHHVIKQLNTNVASHDELYSVGLVGYAKALESFDKKRNVKFSTYAINCI 86

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  I   +               K +   +     +  +  +     +  +  +  + + 
Sbjct: 87  RNEILYFLR--------------KENNHNKNTVSFNKILSSDKDGHNLELEDIISEDEIS 132

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K                        D + DK              RET  + L  L   E
Sbjct: 133 KKR--------------------FEDNLVDKED------------RETILKALEFLKEEE 160

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             V+  RFG+      T  E+GK   +++  I +I+  +I KL+
Sbjct: 161 RIVIIYRFGLNNGIMMTQSEIGKMINMSQANISKIQKSSIDKLR 204


>gi|149191179|ref|ZP_01869437.1| putative RNA polymerase sigma factor for flagellar operon [Vibrio
           shilonii AK1]
 gi|148835017|gb|EDL51996.1| putative RNA polymerase sigma factor for flagellar operon [Vibrio
           shilonii AK1]
          Length = 235

 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/214 (14%), Positives = 75/214 (35%), Gaps = 23/214 (10%)

Query: 459 VAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
              +Y      F DL Q   + L+    KFD      F       ++  +   +      
Sbjct: 38  YQYRYAVDEGTFEDLRQTAMMTLVIELRKFDHVANDDFRRAVAVRIRGELVDELR---RR 94

Query: 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
             +    R  ++++    R++  ++ R+PT  EI   L +     ++ + +         
Sbjct: 95  DYMERDKRQLVNRIKLAERQLVQQLARQPTTNEICHYLGIESNDYQQAMTLVDVF----- 149

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
                      D IE +  V+ +    +  L     +VL +L   E+R+L + +      
Sbjct: 150 -----------DDIELETVVTAVPETDREVLFNEVKQVLNTLPEMEQRILYLVYV----K 194

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
             + +E      +   ++ +++ + +  LK   +
Sbjct: 195 SLSTKETALVLDINEIKVHRLKHRGLDILKSRMK 228


>gi|74319475|gb|ABA02882.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319477|gb|ABA02883.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319483|gb|ABA02886.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319485|gb|ABA02887.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
 gi|74319487|gb|ABA02888.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii]
          Length = 171

 Score = 55.2 bits (131), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/205 (15%), Positives = 62/205 (30%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P   + ++   ++   G   L +I  L   + PE+        E     + ED S  K 
Sbjct: 1   WPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEDVEELEEEDESSTKS 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +V+  + D E  ++   D        PE A+     L+     +   +          
Sbjct: 59  TKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIE--------- 109

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                                     K  +++ +     E L  +           D++ 
Sbjct: 110 --------------------------KHGRNTPEANEALESLATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREIMRYAVRRG 168


>gi|254442345|ref|ZP_05055821.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198256653|gb|EDY80961.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 324

 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/195 (20%), Positives = 80/195 (41%), Gaps = 30/195 (15%)

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            QE  + L++A ++ D      F  YA   +K+ I   I  ++  ++ P+++  K  +  
Sbjct: 138 CQEARLALLEAIDRIDPEQ--PFEAYARQRIKRRIQNYIMKEAVPVKAPINLISKTFR-- 193

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
                            E A +  +    VR        P+ L   +  +      D   
Sbjct: 194 --------SQPDGNLLLEKAIRDGV----VRLDDTHAGGPM-LARELHCD-----SDLAP 235

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVT 652
           D+ AVS       A+        L  LT ++  V+ +RFG+  + T  +L ++ +   ++
Sbjct: 236 DQIAVS-------ADESAKVAEALLQLTDKQREVIELRFGLNDSATPQSLSQIAQHTGIS 288

Query: 653 RERIRQIEAKAIRKL 667
           R+++ Q E +A++KL
Sbjct: 289 RQQVFQREKRALQKL 303


>gi|150390243|ref|YP_001320292.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Alkaliphilus
           metalliredigens QYMF]
 gi|149950105|gb|ABR48633.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alkaliphilus metalliredigens QYMF]
          Length = 117

 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 3/104 (2%)

Query: 574 ISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
           +SL+ PIG +   +   L D +  ++     +  ++  +R+   ++   L  RE+ V+ +
Sbjct: 13  VSLQDPIGVDKEGNEISLLDILGTESDGVVDEVELKIQIRKLYQKMSKVLKSREKMVIEL 72

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           R+GI      T  E+ K   ++R  + +IE +AI KL     S 
Sbjct: 73  RYGIAGCGSKTQREIAKMLGISRSYVSRIEKRAINKLHKAFESN 116


>gi|159900735|ref|YP_001546982.1| TPR repeat-containing protein [Herpetosiphon aurantiacus ATCC 23779]
 gi|159893774|gb|ABX06854.1| Tetratricopeptide TPR_2 repeat protein [Herpetosiphon aurantiacus
            ATCC 23779]
          Length = 1757

 Score = 55.2 bits (131), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 48/296 (16%), Positives = 94/296 (31%), Gaps = 31/296 (10%)

Query: 12   DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
            +   ++  D  +FD        ++ + +Q+GYV + ++       E  +E+++     L 
Sbjct: 823  EQAGQNQSDDPIFD-------ALLGIGQQQGYVDLTDIINQFDDPESQTEEIDRIALALH 875

Query: 72   NMGINVVDGDDL--EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            + GI + DGD++   DEE S D  +   +      F+    D      +        EM 
Sbjct: 876  DNGIQIRDGDEVINMDEEFSGDEAEAYETEEPLENFIAGDFDQPTAEVEP-------EMT 928

Query: 130  SIEL----LSREGEIAIAKRIEAGRAMMMASLCESPLTFQ--ALIIWRDELNDGTTL--L 181
               L    LS E        +  G      +   +P +F    L     E+    T   L
Sbjct: 929  PFSLTDLGLSAEE-----IAMLNGETSEAPTEEPAPFSFDNFELEQPSAEVEPEMTPFSL 983

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE--SAAKVSKD 239
             ++      I   +        E  +    ++   E+   D +              +++
Sbjct: 984  TDLGLSAEEIAMLNGETSEPAAEEPAPFSFDNFELEQPATDAEPEMTPFSLTDLGLSAEE 1043

Query: 240  DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
                     E A  +      D  +     +  E ++ P  +  L   AE    L 
Sbjct: 1044 IAMLNGETSEAAAEEPAPFSFDNFELDQPATDAEPEMTPFSLTDLGLSAEEIAMLN 1099


>gi|266706197|gb|ACY78403.1| sigma factor [Streptomyces chattanoogensis]
          Length = 269

 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 80  GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE 139
           GD  E  EG+E++  + S         Q+   +A  +T DPV+ YL+++G +  L+ E E
Sbjct: 181 GDAPEAAEGAENAGFVLSDEDEDDAPAQQV--AAAGATADPVKDYLKQIGKVPFLNAEQE 238

Query: 140 IAIAKRIEAGR 150
           + +AKRIEAG 
Sbjct: 239 VELAKRIEAGL 249


>gi|331005480|ref|ZP_08328859.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330420756|gb|EGG95043.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 225

 Score = 54.8 bits (130), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 47/208 (22%), Positives = 77/208 (37%), Gaps = 30/208 (14%)

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           ++ N  L+F D    G IGL++A +K+    G  F TYA + +K AI   I   S     
Sbjct: 34  RFDNS-LEFDDYKHYGFIGLLEAKKKYTSDQGASFDTYATYRIKGAILNGIVKNS----- 87

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
              M+   +   R   R+ +    EPT                   ++    + +E    
Sbjct: 88  -EKMQLYAYNSRREKDRLRSLKAPEPTN------------------RMDLFDLFIELTGN 128

Query: 582 DEDTSHLGDFIEDKNAVSPLDS-AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
               S L D  E + +V        Q+ +       +  L   E+ V+   +  G     
Sbjct: 129 LAVASLLDDMSESEISVDECSETYYQSQMSSDLLLGVEHLNGNEKLVVTYHYFGG----L 184

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +EV     VT+ RI Q+   A+ KL+
Sbjct: 185 DFQEVADILEVTKGRISQLHKSALEKLR 212


>gi|170755460|ref|YP_001782085.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum
           B1 str. Okra]
 gi|169120672|gb|ACA44508.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum
           B1 str. Okra]
          Length = 96

 Score = 54.8 bits (130), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 40/86 (46%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +   L D +           + +  +++   ++   L  RE++V++MR+G+      T
Sbjct: 1   MGNEISLMDILSSDEDSIIEIVSTKIEVKKLYGKIDTCLRGREKKVIQMRYGLKDGRPRT 60

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKL 667
             E+     ++R  + +IE KA++KL
Sbjct: 61  QREIAGILDISRSYVSRIEKKALKKL 86


>gi|325114210|emb|CBZ49767.1| hypothetical protein NCLIV_002550 [Neospora caninum Liverpool]
          Length = 5474

 Score = 54.8 bits (130), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 91/684 (13%), Positives = 211/684 (30%), Gaps = 86/684 (12%)

Query: 7    RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKL---ARQRGYVTIEELNAFLPPDEVSSEQM 63
             +  + +        L  +  + + K+++      + RG       N+ LPP    +++ 
Sbjct: 4749 EDSATIAAEAKRLSQLQKNILEFAKKQLVAARNAGKPRGK------NSHLPPLGGWAKEA 4802

Query: 64   EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
            +  +         + D D  E     E  L   S A NS+        +      D +  
Sbjct: 4803 KRLLQ--------IADEDRQEIRADYEKKLKQRSRAENSAASTAPSPTAWGSEDTDKI-- 4852

Query: 124  YLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
                   +         A+  +I   R  +  SL         L    D + D      E
Sbjct: 4853 -------VN--------ALLLKIREKRQEVRNSLF-------FLDDIVDVICDAKLSTSE 4890

Query: 184  IIDLEACIGPESKGGFFHG--------TEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
             + ++A     ++               E  S  +R ++   +ER  +  TE    S  +
Sbjct: 4891 SVQIDALYDRATREVEEEFEREMKQLQEEFESDARRLEAELAEERSRIGRTEEMERSRLE 4950

Query: 236  VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
            V +  +    +  E  E   R+ DE  D       +  +         L    E++    
Sbjct: 4951 VERRLKKATATSDEEIEAVRRDFDERIDRVQREFESEREAQERAFQEKLARRRELFNR-- 5008

Query: 296  SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY-----DISKRIM 350
              Q  A   Q +E    + +  K+ + +   S    ++  + L+++       D  +++ 
Sbjct: 5009 RKQKLAEKAQAEEARVQEDRRRKKTVAERQRS----EATFECLLDEARSHPTSDTIEQLH 5064

Query: 351  HNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR 410
                  L  A +  +     L++   +      V+        + ++    ++D  +   
Sbjct: 5065 KFMAAQLSEAVNATV-----LQQLSEKSSRLTAVAAEMRSKHADERSATEAKLDRQIAAA 5119

Query: 411  NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             ++ S S  +   + E    +  +++ +     A  ++   +   +  +A +   +  + 
Sbjct: 5120 EKMASASDASSPHLLEEIEDLKRMKEEKLRELDATFKLKVDSALQIERLAIE-PVQAERV 5178

Query: 471  LDLIQE------GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR---- 520
              L QE        +    A  +       + +  A   ++    R        +     
Sbjct: 5179 FALQQEHLKNIVKVLSEFVALGEETAVGLTQQAKQAQTRIELERARMKEIAGMKVLDLDK 5238

Query: 521  -IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE-GVRKVLKITKEPISLET 578
             +     +   ++      +  K+K +   EE  ++ A   E   RK  +  ++   L  
Sbjct: 5239 ILKEKEAELKKQMEANIAALREKLKAQQEREEQLQREAHEAEMKKRKEEQRARQLKQLRR 5298

Query: 579  PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
             I            +D  A   +    Q +  E     LA    R+  +L+ +    +N 
Sbjct: 5299 MINCAKA-------DDPEAADDIFKKYQDDA-ERLEAALAKERARQHMILQSQLHQKVNR 5350

Query: 639  DHTLEEVGKQFCVTRERIRQIEAK 662
                     +  ++ ER R  + +
Sbjct: 5351 KELQLRQEGEGQMSEERARLKKTR 5374


>gi|256532390|gb|ACU81353.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score = 54.8 bits (130), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 58/148 (39%), Gaps = 11/148 (7%)

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSN---K 542
           F+     +FSTYA WW++ +I   I      +R       K     + R   +++    +
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKLAKGDTQ 60

Query: 543 IKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDED--TSHLGDFI--EDKNA 597
           +  +   +EIA  L + +  V+    +++    SL+ P    D  ++   DF+  +D   
Sbjct: 61  LTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPLP 120

Query: 598 VSPLDSAIQANLRE-TTTRVLASLTPRE 624
              + + I    R       L  L  RE
Sbjct: 121 DEQVSNMIDGERRRVLLASALKHLNERE 148


>gi|317969864|ref|ZP_07971254.1| DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. CB0205]
          Length = 227

 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 86/221 (38%), Gaps = 21/221 (9%)

Query: 449 VEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           V+ +  LV+  A+ Y  R      DLIQ G +G ++A+ +F          YA  +V+ A
Sbjct: 11  VKRHRGLVLGTARHYAQRCREPIDDLIQAGWVGFLRASARFQPGPDRSLGAYAKPFVRGA 70

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           I R + D S  +R+P  ++D++ ++ +      N+         + ++L      +R + 
Sbjct: 71  ILRHLRDNSRLVRLPRSVQDRLAQLNKIEAATGNQ-----ATVGLGRRLGWSETALRVLQ 125

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           +  +    LE     +     G    D      L        R      LAS+  R  +V
Sbjct: 126 QAEQ----LERLDWLDPERCEGIAAMDDETDPLLP-------RAMAQSWLASIQQRHSQV 174

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           + +    G    ++L        ++   +R+     + +L+
Sbjct: 175 VELVVLEG----YSLRRTAGLLGISSATVRRRLHAGLEELR 211


>gi|95930798|ref|ZP_01313530.1| sigma-70 region 4 [Desulfuromonas acetoxidans DSM 684]
 gi|95133146|gb|EAT14813.1| sigma-70 region 4 [Desulfuromonas acetoxidans DSM 684]
          Length = 251

 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 81/225 (36%), Gaps = 13/225 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQF----LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +++   + V     KY  +G +      DL   G +GL++A   +D   G  +  +A   
Sbjct: 16  LIQRIAQEVFF---KYNLQGFEHSISREDLCHYGVVGLLEARVSYDERSGTPWLAFAALR 72

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           V+  +   +      +           K ++ ARR     + E   + ++  L   ++ V
Sbjct: 73  VRGEMIDHLRKL--PMVRLPQAVQSRVKQLKEARRALQTQQIEVDHQHLSTALDWTLDEV 130

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V  +    ++++  +               +  SP   A+Q  L     R L  L+ +
Sbjct: 131 REVEALLPRRVAVDDGVDQGGDELPSAVTVTSDGPSPETQALQFELAMLINRCLQRLSAQ 190

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
              ++  R   G+               T E IR  + K+  +LK
Sbjct: 191 NRLIVVGRLLEGLKLKEL----AATLGYTAENIRVRQKKSQEQLK 231


>gi|317063373|ref|ZP_07927858.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689049|gb|EFS25884.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 54

 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/50 (50%), Positives = 39/50 (78%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           + F+DLI EGN+GL+ A EKFD   G++FSTYA+WW+KQ+I++++  +  
Sbjct: 1   MSFIDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGR 50


>gi|256271|gb|AAC60416.1| RpoD3 [Synechococcus]
          Length = 48

 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/47 (61%), Positives = 38/47 (80%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           LDLIQEG IG+ +  EKFD   GY+FSTYA WW++QAITR+IA+++ 
Sbjct: 1   LDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKAR 47


>gi|289829788|ref|ZP_06547303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 158

 Score = 54.5 bits (129), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 3/81 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAE 486
           RGL  LDLI+EGN+GL++A+ 
Sbjct: 112 RGLALLDLIEEGNLGLIRASR 132



 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 1/106 (0%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|26249146|ref|NP_755186.1| hypothetical protein c3307 [Escherichia coli CFT073]
 gi|26109553|gb|AAN81756.1|AE016765_158 Putative conserved protein [Escherichia coli CFT073]
          Length = 144

 Score = 54.5 bits (129), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 3/81 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 67  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 123

Query: 466 RGLQFLDLIQEGNIGLMKAAE 486
           RGL  LDLI+EGN+GL++A E
Sbjct: 124 RGLALLDLIEEGNLGLIRAVE 144



 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 27  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 76

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 77  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 132


>gi|78184762|ref|YP_377197.1| putative type III sigma factor [Synechococcus sp. CC9902]
 gi|78169056|gb|ABB26153.1| putative type III sigma factor [Synechococcus sp. CC9902]
          Length = 124

 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 1/109 (0%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLG 493
           R+     +  + + V  +L L   VA +  +RG  +  DL+QE  +GL++  +KFD   G
Sbjct: 12  RRCLPPGTNQRNQKVLQHLGLAHCVAMRQRHRGPEERDDLLQEACLGLIQGLQKFDPSRG 71

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            + S+Y M      +     D+S  +RIP  ++D      R  +  + K
Sbjct: 72  LRPSSYLMSRANGQVLHYRRDRSRMVRIPWRLQDLYVSGQRLQQERTQK 120


>gi|332755592|gb|EGJ85955.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2747-71]
          Length = 133

 Score = 54.1 bits (128), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 3/82 (3%)

Query: 406 ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
           +   +  +  I     ++  E    V   R+       +++ M+E+NLRLV+ +A++Y N
Sbjct: 55  LDATQLYLGEIGYSPLLTAEEE---VYFARRALRGDVASRRRMIESNLRLVVKIARRYGN 111

Query: 466 RGLQFLDLIQEGNIGLMKAAEK 487
           RGL  LDLI+EGN+GL++A EK
Sbjct: 112 RGLALLDLIEEGNLGLIRAVEK 133



 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 45/117 (38%), Gaps = 11/117 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
           +G   LL+ E E+  A+R   G       + ES L     I  R   N G  LL  I
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYG-NRGLALLDLI 120


>gi|303242132|ref|ZP_07328622.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302590319|gb|EFL60077.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 261

 Score = 54.1 bits (128), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 81/244 (33%), Gaps = 57/244 (23%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
             ++     +      ++  N  ++  DL+Q G + L  A + +D   G  F  Y  +++
Sbjct: 22  WDQVRRFIHKQAYLFIQRSGNTKVELDDLVQSGYLALCSAIKNYDPDAGCSFIGYLSFYL 81

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +                                +   +I    +              V 
Sbjct: 82  R-------------------------------HQFRKEIGTRTSR-----------RDVL 99

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV----LASL 620
              +   +PIS +      D  HL D +    A    D  ++    +    +    +  L
Sbjct: 100 LTAESLNKPISED-----NDELHLIDAVPCPEAELAFDDMLEQLEHQRIMNIVFECMQRL 154

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS-- 678
           +PR   +L + +          +E+ +Q  +    +R+I+  A+R+L+      ++++  
Sbjct: 155 SPRHRDILILAYL----KQAKQDEIAEQLGIVYGSVRRIKKDALRELRKKPAIARIQAER 210

Query: 679 FLDG 682
            LDG
Sbjct: 211 ILDG 214


>gi|291563180|emb|CBL41996.1| Sigma-70 region 3 [butyrate-producing bacterium SS3/4]
          Length = 203

 Score = 54.1 bits (128), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/169 (23%), Positives = 81/169 (47%), Gaps = 6/169 (3%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
            R  ++ I+     S +E   ++  +R G      A++ ++E NL+  +   + Y N+G+
Sbjct: 33  YRVYMEEIAAIPPCSEAENAKLLGEIRNGN---KAARERLIEGNLKNALFFVQDYINKGV 89

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
              DLIQE ++ LM  A   D      F       ++  +   I DQ     I   M  +
Sbjct: 90  PMADLIQEASLELMMLA---DEGFEGSFEKLLESRIRVRMEEIINDQKKEADIEEEMLAR 146

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           ++ +   ++ M+ ++ RE    E+A+++ M  + VR+++K+T + +S+ 
Sbjct: 147 VNVLQEVSKSMAEELGREAKLSELAERMKMTEDEVREIMKVTMDALSMS 195


>gi|51245066|ref|YP_064950.1| RNA polymerase sigma factor for flagellar operon [Desulfotalea
           psychrophila LSv54]
 gi|50876103|emb|CAG35943.1| related to RNA polymerase sigma factor for flagellar operon
           [Desulfotalea psychrophila LSv54]
          Length = 242

 Score = 53.7 bits (127), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 82/205 (40%), Gaps = 10/205 (4%)

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526
           G+   DLIQ G IG ++A  + D   G     +    +K      I  Q+          
Sbjct: 29  GISVEDLIQTGIIGYLEAKSRLDKEKGDG-KAFIFMRMKGNQLSLIRRQALVRMPQKTYA 87

Query: 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
                +    R+       E T + +A++L   V+ + ++L       S +    +E++S
Sbjct: 88  KVKELL--AVRKQLEASCVEATDQLLAERLGWTVKEIHQLLASVPRVFSSDDVTDNEESS 145

Query: 587 HLGD--FIEDKNAVSPLDSAIQANLRETTTRVLASL-TPREERVLRMRFGIGMNTDHTLE 643
              +  F+  +N    +    +  + +     LA L  PR+  +L  ++  G+N    ++
Sbjct: 146 DFYESHFLPGQNPQPLISEMEKKEIADLIQGCLARLENPRQRLILVAKYFEGIN----VK 201

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLK 668
           ++  +F  +R  +   E K + +++
Sbjct: 202 KLADRFGCSRYFVESEEQKGLGQMQ 226


>gi|237734716|ref|ZP_04565197.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382044|gb|EEO32135.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 128

 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/133 (26%), Positives = 63/133 (47%), Gaps = 11/133 (8%)

Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL--GDFIEDKNAVS 599
           K+ REPT  E+A +L +    V + L  T    SL+  + ++D ++L   D I D   V 
Sbjct: 5   KLNREPTINELANELEVEPSAVIEALLSTNSVSSLQEEVKNDDGNNLKMIDSITDDKTV- 63

Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
                 + N        L SL  +E RV++ R+  G     +  E+ K+  +++ ++ +I
Sbjct: 64  ----VSRTNETIDLYDALKSLNQKEHRVIKQRYFEG----LSQSEIAKELFISQAQVSRI 115

Query: 660 EAKAIRKLKHPSR 672
           E KA+  L +  +
Sbjct: 116 ERKALDNLHNYLK 128


>gi|226329392|ref|ZP_03804910.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
 gi|225202578|gb|EEG84932.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
          Length = 131

 Score = 53.7 bits (127), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/127 (23%), Positives = 67/127 (52%), Gaps = 8/127 (6%)

Query: 549 PEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSHLGD---FIEDKN---AVSPL 601
            E +A++L +    VR++  +++ + ++ +    D D SH      F+EDK+   A    
Sbjct: 1   MELVARELGVSESDVREMESRMSAQDMAFDMTADDSDDSHPIAPVLFLEDKSSDFADGIE 60

Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
           +     +  +  T  + +L  R + ++R R+ +  +   TL+++  ++ V+ ER+RQ+E 
Sbjct: 61  EDNWDNHAADKLTSAIETLDERSQDIIRARW-LDDDNKSTLQDLATKYGVSAERVRQLEK 119

Query: 662 KAIRKLK 668
            A++KL+
Sbjct: 120 NAMKKLR 126


>gi|147677457|ref|YP_001211672.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
 gi|146273554|dbj|BAF59303.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
          Length = 118

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/106 (28%), Positives = 48/106 (45%), Gaps = 4/106 (3%)

Query: 565 KVLKITKEPISLETPIGDE---DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
           + +K  K  +SL  PIG +   +   L D +     V           +    +V   LT
Sbjct: 4   RFMKKVKVEVSLYDPIGVDKEGNEITLIDILGTHPEVVAEMVENNFEQKRLLEKV-RQLT 62

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            RE++VL +RFG+      T  E+ K   ++R  + +IE KA+ KL
Sbjct: 63  RREKKVLELRFGLEDGARMTQREIAKSLGISRSYVSRIEKKALNKL 108


>gi|256267|gb|AAC60414.1| RpoD1 [Synechococcus]
          Length = 48

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/47 (72%), Positives = 41/47 (87%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
            DLIQEG++GL++AAEKFD   GYKFSTYA WW++QAITR+IADQS 
Sbjct: 1   QDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSR 47


>gi|322806811|emb|CBZ04380.1| RNA polymerase sporulation specific sigma factor SigK [Clostridium
           botulinum H04402 065]
          Length = 89

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 38/79 (48%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +           + +  +++   ++   L  RE++V++MR+G+      T  E+   
Sbjct: 1   MDILSSDEDSIIEIVSTKIEVKKLYGKIDTCLRGREKKVIQMRYGLKDGRPRTQREIAGI 60

Query: 649 FCVTRERIRQIEAKAIRKL 667
             ++R  + +IE KA++KL
Sbjct: 61  LNISRSYVSRIEKKALKKL 79


>gi|310658943|ref|YP_003936664.1| RNA polymerase subunit alpha domain-containing protein [Clostridium
           sticklandii DSM 519]
 gi|308825721|emb|CBH21759.1| RNA polymerase, alpha subunit domain protein [Clostridium
           sticklandii]
          Length = 911

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
             L D ++ K      D    A   E        L  RE         +      TLE+V
Sbjct: 268 DSLNDLLDSKKIDLVFDDKFIAIYDEFHEGAKEHLNERE-----YNVLLQRIQGKTLEDV 322

Query: 646 GKQFCVTRERIRQIEAKAIRKL 667
           G +  VTRERIRQIEAKAI+KL
Sbjct: 323 GLEMNVTRERIRQIEAKAIKKL 344


>gi|312126664|ref|YP_003991538.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311776683|gb|ADQ06169.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 206

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 100/250 (40%), Gaps = 50/250 (20%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +S  E + +V  +++       A +E++ A   L+IS A KY N+   F DL QEG 
Sbjct: 1   MFKLSFDEQKELVCRIKQ---GDKKAAEELICAYEPLIISFAAKY-NKPEIFEDLKQEGY 56

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
             +++AA KF+  LG  F T A++++K+ + R +                     RT R 
Sbjct: 57  CAILQAARKFNVSLGVSFITLAVYYIKRNMDRCVNRD------------------RTIRP 98

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK   E                         + IS++ P+   +       ++D    
Sbjct: 99  PFNKPSTE-----------------------IPQVISMDAPVNTNNYDDEELRVKDTIQS 135

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           S  D   +    ET  +++  L+  E ++L     +     ++ +E+ ++  +T +++  
Sbjct: 136 STADVEEKVMYNETLRKLVELLSNEERKIL-----LLRLKQYSYKEIAEKLGLTEKQVAT 190

Query: 659 IEAKAIRKLK 668
              K   KL+
Sbjct: 191 KAQKIRAKLQ 200


>gi|74319519|gb|ABA02904.1| RNA polymerase sigma factor sigma-70 [Acinetobacter calcoaceticus
           DSM 30006]
          Length = 171

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/205 (14%), Positives = 69/205 (33%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P   + ++   ++   G   L +I  L   + PE+        E  +  + E++   K 
Sbjct: 1   WPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEETELEEEEAPAVKP 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +V+  + + +  ++   D   +    PE A+                           
Sbjct: 59  AKEVKLDDDEEDEESESDDDSEGESGPDPEVAK--------------------------- 91

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                +E+   + + +++ +      K  ++S +     E L  +           D++ 
Sbjct: 92  --VRFNELEAAWTKTKAIIE------KHGRNSPEADDALEALATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREVMRYAVRRG 168


>gi|331027965|ref|YP_004421515.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
 gi|294805578|gb|ADF42417.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
          Length = 261

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 96/270 (35%), Gaps = 27/270 (10%)

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
           D I    N      + T     E    +    +G  E      ++ + NLRLV    + Y
Sbjct: 3   DPITAWLNNAARYELLTAEQTIELGRKIQAAEEGSPERIKLVNKLCQHNLRLVAKFTRAY 62

Query: 464 TNRGL--------QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
              G         + +DL+QEG  GL +AA KFD   GY F+TYA  WV+QA+ +   D+
Sbjct: 63  MKGGTRKLTWGGDETMDLLQEGYFGLRRAANKFDPERGYTFATYANAWVRQALGKYHVDK 122

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
              IR+P     +I            K +   T   +A              +     +S
Sbjct: 123 LSLIRVPESSAREIF-----YYDAHGKPRNSKTSAWVADAAR--------AARAAYGLVS 169

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
            +  +  ++   + D + D+N V      I  +  +     +  +     RV+      G
Sbjct: 170 YDNKL-ADEEHSVIDLLSDENRVHDGKCEISYDRYDQLMEDVG-IDEATRRVIISYCKRG 227

Query: 636 MNTDHTLEEVGKQFCVTRERIR----QIEA 661
                  +    Q    R  IR    QI+A
Sbjct: 228 NLDTAMAKHKVPQTSKARAHIRGAIAQIKA 257


>gi|224771367|dbj|BAH28625.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 80/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLKY---GDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+PRE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196


>gi|224771331|dbj|BAH28607.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771333|dbj|BAH28608.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771337|dbj|BAH28610.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 80/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSSYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+PRE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDVLSPREKEIIQMRYGLLDGDIKTQREIAGIL 196


>gi|294102492|ref|YP_003554350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
 gi|293617472|gb|ADE57626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
          Length = 196

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/92 (27%), Positives = 46/92 (50%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            M+         A++E++ +   LV  +A+K+      + DLIQEG + L+K+ +KF+  
Sbjct: 20  EMLWARCHLDDDAREELIISYRPLVFWLAQKFYVSPSLYPDLIQEGMVALIKSVDKFEPE 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
              KF+TYA + +K  +   +        IP+
Sbjct: 80  RQLKFTTYAFYRIKGQMVNFLQRSEAKAPIPM 111


>gi|256273|gb|AAC60417.1| RpoD4 [Synechococcus]
          Length = 48

 Score = 53.3 bits (126), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/47 (61%), Positives = 39/47 (82%)

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           LDLIQEG++GL +A EKFD  LGYKFSTYA WW++Q++TR+I + + 
Sbjct: 1   LDLIQEGSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAIDNHAR 47


>gi|270650021|ref|ZP_06222215.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
 gi|270317188|gb|EFA28789.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
          Length = 151

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 2/90 (2%)

Query: 285 DEIAEVYRELRSLQDNAVNG-QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           +   E +++LR      +   +K  +S  + +     L ++     L   + DLLV  + 
Sbjct: 61  EVAREKFQQLREQHSKTLAVIEKHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMK 120

Query: 344 DISKRIMHNEGELLR-LAQSYGIKRDVFLE 372
           ++ KR+ + E +L + L    G+ +D F +
Sbjct: 121 EMMKRVRYQERQLQKILVDIAGMPKDDFEK 150


>gi|167515032|gb|ABZ81800.1| RpoD [Aeromonas aquariorum]
          Length = 160

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/203 (14%), Positives = 62/203 (30%), Gaps = 44/203 (21%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     L+   D+       L +II     I P                         E 
Sbjct: 1   PEAITYLLEQYDKYEAEQLRLSDII--SGFIDPN------------------------ET 34

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           DDV  T   I S            D   +   + + + D+ +      ++          
Sbjct: 35  DDVAPTATHIGSELSEEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVA---------- 84

Query: 281 MCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                   E + ELR+  +   ++ Q++ ++    +    +L  +     L   + D LV
Sbjct: 85  -------REKFGELRAQYEVTRLSIQQNGRAHEDTQNAIAQLADVFRQFRLMPKQFDRLV 137

Query: 340 EQLYDISKRIMHNEGELLRLAQS 362
             + ++ +R+   E  +++L   
Sbjct: 138 NNMREMMERVRVQERIIMKLCVE 160


>gi|326675669|ref|XP_694827.4| PREDICTED: apolipoprotein B-100 [Danio rerio]
          Length = 4263

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 66/485 (13%), Positives = 167/485 (34%), Gaps = 41/485 (8%)

Query: 65   DTVAMLSNMGINVVDGDDLED---EEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
              ++++ +  I++ D D   +   E   +  +D A+   + S+ ++   +S   +    V
Sbjct: 2093 QLISLIHDYTISIDDLDAYAERFKEATGKKIIDFATKIRDLSIQIKDGIESGAWANS--V 2150

Query: 122  RMYLREMGSIELLSREGEIAIAKRIEAGRAMM--------MASLCESPLTFQALIIWRDE 173
               L ++G  EL + + +  I K I  G   +        +  L +S  T+   +  + E
Sbjct: 2151 SDILAQIGR-ELKAFDEQYKITKTIIRGIDGIEDVIRQIDLEKLKDSSATWLKQLDAKYE 2209

Query: 174  LN----DGTTLLREII----------DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            +     +  + LR+++          DL   I       +     G    +  +   +  
Sbjct: 2210 IKTKLLEKLSELRKVVETFEINMLLEDLRQYITSIDLTEYVDQLSGQIPYEDIERVLDSA 2269

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            +D +     + E   K+++   +  +       + +  +  ++         ++ +L   
Sbjct: 2270 KDVILNWIEEYEVPEKINRVYLNAQELILRYEIDKKIEVIVEQAIILVKQYRIQ-ELVQA 2328

Query: 280  VMCALDEIAEVY--RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL--NQSRI 335
            V+  L  I   Y   ++  + D+ V+  K          L + +  ++ +       + I
Sbjct: 2329 VVDTLKSIQFEYISDKMMEIMDSIVSLLKRMDFQKIVNDLNDYIQLIIKTFRTFDYNTYI 2388

Query: 336  DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            D +  ++ D+   I     E+  + +     R+ F++  Q       ++   K+    E 
Sbjct: 2389 DEVNRKVRDVVDYINKQINEVYEIPRKIEASRE-FIKEMQA--TVFDYLEKLKNTRIAEV 2445

Query: 396  KNFVACEVDS--ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
               +   +D+     I+ +I+ I  +    IS+   I + +      AS A   M+E  L
Sbjct: 2446 CRNIKDVIDTTAYKDIKLKIQDIIEDVRQRISDM-DIRNEISVYLERASGAYVNMIEYIL 2504

Query: 454  RLVISVAKKYTNRGLQFLDL--IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
                 +  +          L  I +   G+  A +  ++ +      +    +     + 
Sbjct: 2505 TQFTQLIDEMKKMAEDKEILDQISQAVEGVFNALKTAEFDVPAFMLPFTTLEIPAFKIKM 2564

Query: 512  IADQS 516
                 
Sbjct: 2565 ARIHD 2569


>gi|302541651|ref|ZP_07293993.1| RNA polymerase sigma-E factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459269|gb|EFL22362.1| RNA polymerase sigma-E factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 184

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 6/115 (5%)

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
           K+L  P   VR+VL    + +SL   +     + + D  E  +  +  D    A LR   
Sbjct: 51  KRLESPEAYVRQVLYR--QQVSLWRLLRSHRETTVADVAELPDTPAREDGTGAAELRILV 108

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R LA LT R+  +L +R+           EV +    +   +R    +A+ +L+
Sbjct: 109 RRALARLTIRQRAMLVLRYFEDCPE----REVAELLGCSVGTVRSTTHRALARLR 159


>gi|225389367|ref|ZP_03759091.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
           DSM 15981]
 gi|225044546|gb|EEG54792.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
           DSM 15981]
          Length = 384

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/121 (23%), Positives = 55/121 (45%), Gaps = 5/121 (4%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
             ++ +     +S  E   I+            A+K +VE NL+ V+S+AK+Y    L  
Sbjct: 8   MYLEEMGQIAPMSAEEEARILER---TAAGEVQARKRLVEGNLQKVLSIAKEYEGSRLPM 64

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            D++QE N  L  AA ++D     ++       V++A+  ++ +Q   + +  +M  K  
Sbjct: 65  ADIVQEANTALTLAAVEYDG--ATEWEALLDQRVREAVEEAVREQEAELEVEENMAAKGQ 122

Query: 531 K 531
           +
Sbjct: 123 R 123



 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/146 (21%), Positives = 52/146 (35%), Gaps = 6/146 (4%)

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
           MYL EMG I  +S E E  I +R  AG       L E  L  Q ++    E       + 
Sbjct: 8   MYLEEMGQIAPMSAEEEARILERTAAGEVQARKRLVEGNL--QKVLSIAKEYEGSRLPMA 65

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSY----QKREDSSQEKERDDVQETEGDIESAAKVSK 238
           +I+         +   +   TE  +      +       +E++   E E ++ +  + + 
Sbjct: 66  DIVQEANTALTLAAVEYDGATEWEALLDQRVREAVEEAVREQEAELEVEENMAAKGQRAA 125

Query: 239 DDRSKVDSPPENAENDERNLDEDEDD 264
           D             + +    EDEDD
Sbjct: 126 DRFPAFGRGTGPGGDRDGAGREDEDD 151


>gi|219849677|ref|YP_002464110.1| tetratricopeptide repeat-containing protein [Chloroflexus aggregans
            DSM 9485]
 gi|219543936|gb|ACL25674.1| Tetratricopeptide TPR_2 repeat protein [Chloroflexus aggregans DSM
            9485]
          Length = 1838

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/98 (22%), Positives = 43/98 (43%)

Query: 17   DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
              D+  + D  D    ++I+L  ++GYV I ++ A +   E  +E++E     L   GI 
Sbjct: 1198 SDDEEPMIDTGDPVLNRLIQLGHRQGYVDITDIIAVVQDPEREAERIEQIGWSLHRAGIQ 1257

Query: 77   VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
            + DGD++ D E      D ++     +      ++   
Sbjct: 1258 IRDGDEIIDMEAELGEEDTSAMPIADADLTPFAEELPS 1295


>gi|169823613|ref|YP_001691116.1| RNA polymerase sigma factor [Finegoldia magna ATCC 29328]
 gi|167832233|dbj|BAG09148.1| RNA polymerase sigma factor [Finegoldia magna ATCC 29328]
          Length = 288

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 81/242 (33%), Gaps = 28/242 (11%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQF----LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           E++      V S   +   +   F     DL+ EG   + +  + FD     +F+TYA  
Sbjct: 65  ELIPLVYSYVNSYCHRKNYQNFDFSEIRDDLVSEGLTAVYRCFDTFDPSKKIRFTTYASS 124

Query: 503 WVKQAITRSIADQS-CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
            ++  I     D           + + I K  R A++       +      A        
Sbjct: 125 CIQGKIKNYCRDHHLRHFTGTRTLYENIQKDYRKAKQKGIANDFKFDKCNYAT------- 177

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
              K L    +    +  +   +   +    +D   ++ + S           ++L    
Sbjct: 178 --VKSLDELTDAQDKDMYLEFHNDLQIQSLYKDDTNINEVYSENYE-----IFKLLCKGI 230

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL---RS 678
            + E ++ M F    +      ++ ++F V R  + +     ++K+++  R+  L   + 
Sbjct: 231 NKTEYIMTMLFYSNYSKP----QIAEKFNVDRSVVEKCITTTLKKMRN--RAAILGLSKD 284

Query: 679 FL 680
           + 
Sbjct: 285 YF 286


>gi|58699678|ref|ZP_00374352.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533807|gb|EAL58132.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 93

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 601 LDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +  +  L+E      LASL  R   +   R+        TL+E+ K++CV+RERIRQ+
Sbjct: 13  YQNHEEKELKEAILNNALASLNERARDIFISRYLSENIQ--TLDELSKKYCVSRERIRQL 70

Query: 660 EAKAIRKLKHPSRSKKLR 677
             +A+ K+K   +S+ L+
Sbjct: 71  AEQAMAKVKQYIQSESLK 88


>gi|332975577|gb|EGK12467.1| RNA polymerase sigma-K factor [Desmospora sp. 8437]
          Length = 86

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +      L  L  RE+ V+R RFG+    + T  E+ K+  ++R  + +IE +A+ KL H
Sbjct: 19  KSKIYGYLHILDEREQDVIRNRFGLSGGKEKTQREIAKELGISRSYVSRIEKRALIKLFH 78


>gi|74319515|gb|ABA02902.1| RNA polymerase sigma factor sigma-70 [Acinetobacter calcoaceticus]
          Length = 171

 Score = 52.9 bits (125), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 67/205 (32%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P   + ++   ++   G   L +I  L   + PE+        E     + ED S  K 
Sbjct: 1   WPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEELEEEDESSSKS 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +V+  + D E  ++   D        PE A+       E E   A T +A+E      
Sbjct: 59  TKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFT---ELEAAWAKTKAAVE------ 109

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                                     K  ++S + +   E L  +           D++ 
Sbjct: 110 --------------------------KHGRNSPEAEEALEALATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREIMRYAVRRG 168


>gi|296199230|ref|XP_002746996.1| PREDICTED: laminin subunit alpha-2 isoform 2 [Callithrix jacchus]
          Length = 3118

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 64/446 (14%), Positives = 141/446 (31%), Gaps = 35/446 (7%)

Query: 16   EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML--SNM 73
            +D    +  +       +MIK  R++   T +E+      + V++E +   V  L   + 
Sbjct: 1706 QDKTFEINLEGLQKEIDQMIKELRRKNLETQKEIAE---DELVAAEGLLKKVKKLFGESR 1762

Query: 74   GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            G N     DL ++     +    +         + R+ +   + +       + M    L
Sbjct: 1763 GKNEAMEKDLREKLADYKNKVDDAWDLLREATDKIREANHLSAVNQ------KNM--TAL 1814

Query: 134  LSREGEIAIAKR-IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL----REIIDLE 188
              ++  +   KR IE         L E+      +    D + D  T L     E+ D  
Sbjct: 1815 EKKKEAVESGKRQIENTLKEGNDILDEANRLADEINSIIDYVEDIQTKLPPMSEELKDKI 1874

Query: 189  ACIGPESKGG-FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              +  E K                + +      D +     +I   A  + +  S +   
Sbjct: 1875 DDLSQEIKDRKLAEKVSQAESHAAQLNDSSAVLDGILAEAKNISFNATAAFNAYSNIKDN 1934

Query: 248  PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
             + AE   R   +  +++    +     L+     +L +   +  E + L ++    +  
Sbjct: 1935 IDEAEKVAREAKDLANEATKLATGPRGLLKEDAKGSLQKSFRILNEAKKLANDVKENEDH 1994

Query: 308  --------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                    E + V+   L   L   +G LS   +     ++ + D +++      ++L  
Sbjct: 1995 LNGLKARIENADVRNGDLLRALNDTLGKLSAIPNDTAAKLQAVKDKARQANDTAKDVLAQ 2054

Query: 360  AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF--------VACEVDSILKIRN 411
             +      D   + +          + A   P               +  E D ++    
Sbjct: 2055 IKELHQNLDGLKKNYNQLADSVAKTNAAVKDPSKNKIIADADTTVKNLQQEADRLIDKLK 2114

Query: 412  EIKSISVETGISISEFRHIVSMVRKG 437
             IK +      +ISE + +++  RK 
Sbjct: 2115 PIKELEDNLKKNISEIKELINQARKQ 2140



 Score = 42.1 bits (97), Expect = 0.31,   Method: Composition-based stats.
 Identities = 41/312 (13%), Positives = 99/312 (31%), Gaps = 43/312 (13%)

Query: 145  RIEAGRAMMMASLCES--PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
            ++  G   M   L  S  P    A +I   +L +G             +  E        
Sbjct: 1607 KMLYGLENMTEELKHSLSPQRAPARLI---QLAEGNL---------NTLVTEMNELLTRA 1654

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            T+  +  ++     E+     +     ++  A+ ++    K     E     ++  + + 
Sbjct: 1655 TKVTADGEQTGQDAERTNARAKSLGEFVKELARDAEAINEKAIKLNETLGTQDKTFEINL 1714

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAE--------VYRELRSLQDNAVNGQKDEKSSVKC 314
            +     +  M  +LR K +    EIAE        + ++++ L      G+   K+    
Sbjct: 1715 EGLQKEIDQMIKELRRKNLETQKEIAEDELVAAEGLLKKVKKL-----FGESRGKNEAME 1769

Query: 315  KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            K L+EKL          ++++D   + L + + +I               + +       
Sbjct: 1770 KDLREKLADY-------KNKVDDAWDLLREATDKIREAN-------HLSAVNQKNMTALE 1815

Query: 375  QGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVS 432
            + +E         ++  +             D I  I + ++ I  +      E +  + 
Sbjct: 1816 KKKEAVESGKRQIENTLKEGNDILDEANRLADEINSIIDYVEDIQTKLPPMSEELKDKID 1875

Query: 433  MVRKGECEASIA 444
             + +   +  +A
Sbjct: 1876 DLSQEIKDRKLA 1887


>gi|296199228|ref|XP_002746995.1| PREDICTED: laminin subunit alpha-2 isoform 1 [Callithrix jacchus]
          Length = 3122

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 64/446 (14%), Positives = 141/446 (31%), Gaps = 35/446 (7%)

Query: 16   EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML--SNM 73
            +D    +  +       +MIK  R++   T +E+      + V++E +   V  L   + 
Sbjct: 1706 QDKTFEINLEGLQKEIDQMIKELRRKNLETQKEIAE---DELVAAEGLLKKVKKLFGESR 1762

Query: 74   GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
            G N     DL ++     +    +         + R+ +   + +       + M    L
Sbjct: 1763 GKNEAMEKDLREKLADYKNKVDDAWDLLREATDKIREANHLSAVNQ------KNM--TAL 1814

Query: 134  LSREGEIAIAKR-IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL----REIIDLE 188
              ++  +   KR IE         L E+      +    D + D  T L     E+ D  
Sbjct: 1815 EKKKEAVESGKRQIENTLKEGNDILDEANRLADEINSIIDYVEDIQTKLPPMSEELKDKI 1874

Query: 189  ACIGPESKGG-FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              +  E K                + +      D +     +I   A  + +  S +   
Sbjct: 1875 DDLSQEIKDRKLAEKVSQAESHAAQLNDSSAVLDGILAEAKNISFNATAAFNAYSNIKDN 1934

Query: 248  PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
             + AE   R   +  +++    +     L+     +L +   +  E + L ++    +  
Sbjct: 1935 IDEAEKVAREAKDLANEATKLATGPRGLLKEDAKGSLQKSFRILNEAKKLANDVKENEDH 1994

Query: 308  --------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                    E + V+   L   L   +G LS   +     ++ + D +++      ++L  
Sbjct: 1995 LNGLKARIENADVRNGDLLRALNDTLGKLSAIPNDTAAKLQAVKDKARQANDTAKDVLAQ 2054

Query: 360  AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF--------VACEVDSILKIRN 411
             +      D   + +          + A   P               +  E D ++    
Sbjct: 2055 IKELHQNLDGLKKNYNQLADSVAKTNAAVKDPSKNKIIADADTTVKNLQQEADRLIDKLK 2114

Query: 412  EIKSISVETGISISEFRHIVSMVRKG 437
             IK +      +ISE + +++  RK 
Sbjct: 2115 PIKELEDNLKKNISEIKELINQARKQ 2140



 Score = 42.1 bits (97), Expect = 0.31,   Method: Composition-based stats.
 Identities = 41/312 (13%), Positives = 99/312 (31%), Gaps = 43/312 (13%)

Query: 145  RIEAGRAMMMASLCES--PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
            ++  G   M   L  S  P    A +I   +L +G             +  E        
Sbjct: 1607 KMLYGLENMTEELKHSLSPQRAPARLI---QLAEGNL---------NTLVTEMNELLTRA 1654

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            T+  +  ++     E+     +     ++  A+ ++    K     E     ++  + + 
Sbjct: 1655 TKVTADGEQTGQDAERTNARAKSLGEFVKELARDAEAINEKAIKLNETLGTQDKTFEINL 1714

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAE--------VYRELRSLQDNAVNGQKDEKSSVKC 314
            +     +  M  +LR K +    EIAE        + ++++ L      G+   K+    
Sbjct: 1715 EGLQKEIDQMIKELRRKNLETQKEIAEDELVAAEGLLKKVKKL-----FGESRGKNEAME 1769

Query: 315  KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            K L+EKL          ++++D   + L + + +I               + +       
Sbjct: 1770 KDLREKLADY-------KNKVDDAWDLLREATDKIREAN-------HLSAVNQKNMTALE 1815

Query: 375  QGRELDPHWVSYAKDFPEGEWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVS 432
            + +E         ++  +             D I  I + ++ I  +      E +  + 
Sbjct: 1816 KKKEAVESGKRQIENTLKEGNDILDEANRLADEINSIIDYVEDIQTKLPPMSEELKDKID 1875

Query: 433  MVRKGECEASIA 444
             + +   +  +A
Sbjct: 1876 DLSQEIKDRKLA 1887


>gi|170764001|ref|ZP_02637018.2| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170710658|gb|EDT22840.1| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
          Length = 152

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 6/96 (6%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 31  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 87

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
           IGL+KA + FD   G + +TYA   +   I     +
Sbjct: 88  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRN 123


>gi|237749638|ref|ZP_04580118.1| RNA polymerase sigma-K factor [Helicobacter bilis ATCC 43879]
 gi|229374766|gb|EEO25157.1| RNA polymerase sigma-K factor [Helicobacter bilis ATCC 43879]
          Length = 104

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D ++ +N        +   L E   + +  L  RE+ V+  RFG+ +  + T  E
Sbjct: 5   EISLLDVLKAENEDVIDTIQLNMEL-EKVKKYIDILDGREKEVIVGRFGLDLKKEKTQRE 63

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKH 669
           + K+  ++R  + +IE +A+ K+ H
Sbjct: 64  IAKELGISRSYVSRIEKRALMKMFH 88


>gi|283796304|ref|ZP_06345457.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291075701|gb|EFE13065.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|295091614|emb|CBK77721.1| Sigma-70 region 3. [Clostridium cf. saccharolyticum K10]
          Length = 177

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 75/136 (55%), Gaps = 3/136 (2%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
             AKK ++E  L +   ++++Y +RGL   DL+QE N+ L+    +++      F   A 
Sbjct: 43  ERAKKRLIEGCLAMAAELSEEYRDRGLPAGDLVQEANMALLLLVSEYEGGN---FRAQAE 99

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +++A+  ++  Q    +I   M  +++ +   + +M+ ++ RE T EE+A ++ M VE
Sbjct: 100 ERIREALETALDIQDTEQKIEEEMLARVNVLKDISAQMAEELGREATVEELAARMKMTVE 159

Query: 562 GVRKVLKITKEPISLE 577
            ++ ++K+T + +S+ 
Sbjct: 160 EIKDIMKLTLDAMSVS 175


>gi|213584001|ref|ZP_03365827.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 148

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/133 (19%), Positives = 62/133 (46%), Gaps = 8/133 (6%)

Query: 543 IKREPTPEEIAKKLAMPVEGVRKV--LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
              +   E +A++L +  + VR++      ++     +   + D+  +   +  ++  S 
Sbjct: 12  WFNQDEVEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESDSQPMAPVLYLQDKSSN 71

Query: 601 LDSAIQANLRET-----TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
               I+ +  E       T  +  L  R + ++R R+ +  +   TL+E+  ++ V+ ER
Sbjct: 72  FADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAER 130

Query: 656 IRQIEAKAIRKLK 668
           +RQ+E  A++KL+
Sbjct: 131 VRQLEKNAMKKLR 143


>gi|158321550|ref|YP_001514057.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158141749|gb|ABW20061.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           oremlandii OhILAs]
          Length = 190

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 86/244 (35%), Gaps = 63/244 (25%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           EF   V++          AK+ ++     L++S ++KY  +     +L QEG   +++A 
Sbjct: 4   EFDEKVALA---LEGDHSAKEWLIHQLKPLIVSYSRKYGGQVGWDEELYQEGAWQVLEAL 60

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           + FD   G  F  +    +K                  + R K   +             
Sbjct: 61  QDFDRSKGVPFLGFVTVRLKHHYQ--------------NKRRKEKSL------------- 93

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605
                                       ISL+ P+G+E  + L DFI D++ V      +
Sbjct: 94  ----------------------------ISLDEPVGEEQDTTLLDFIVDES-VDIEGDYL 124

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +A         +  L  +E +++   +  G      L+E+ ++  V      +++A ++ 
Sbjct: 125 KAESWIALREAMGRLKEQEHQLIEAYYFNG----RKLKEIAEEAGVHYITAVKLKAHSLE 180

Query: 666 KLKH 669
           KLK 
Sbjct: 181 KLKK 184


>gi|257439708|ref|ZP_05615463.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
 gi|257197848|gb|EEU96132.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
          Length = 118

 Score = 52.5 bits (124), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/104 (17%), Positives = 45/104 (43%), Gaps = 5/104 (4%)

Query: 569 ITKEPISLETPI---GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
                +SL+  +    ++    L D ++D       D+  + +      R++  L  RE 
Sbjct: 8   RNGVVVSLQETLEAGKEDSALTLSDVLQD--GFCMEDACERQDEARRLRRLIEGLPARER 65

Query: 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +++ +R+G+      T  E  +   ++R  + ++E  A+ +L+ 
Sbjct: 66  KLILLRYGLAGQPPLTQLETAQLLQISRSYVSRLETHALNQLRK 109


>gi|224771305|dbj|BAH28594.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771309|dbj|BAH28596.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771311|dbj|BAH28597.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771313|dbj|BAH28598.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771315|dbj|BAH28599.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771317|dbj|BAH28600.1| sporulation sigma factor SigK [Clostridium perfringens CPE str.
           F4969]
 gi|224771323|dbj|BAH28603.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771325|dbj|BAH28604.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771327|dbj|BAH28605.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771329|dbj|BAH28606.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771335|dbj|BAH28609.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771339|dbj|BAH28611.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771341|dbj|BAH28612.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771343|dbj|BAH28613.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771345|dbj|BAH28614.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771347|dbj|BAH28615.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771351|dbj|BAH28617.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771353|dbj|BAH28618.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771355|dbj|BAH28619.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771359|dbj|BAH28621.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771361|dbj|BAH28622.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771365|dbj|BAH28624.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771369|dbj|BAH28626.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771373|dbj|BAH28628.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771375|dbj|BAH28629.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771379|dbj|BAH28631.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771381|dbj|BAH28632.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771383|dbj|BAH28633.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771393|dbj|BAH28638.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771395|dbj|BAH28639.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771397|dbj|BAH28640.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771399|dbj|BAH28641.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771401|dbj|BAH28642.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771403|dbj|BAH28643.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771405|dbj|BAH28644.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 80/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+PRE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDVLSPREKEIIQMRYGLLDGDIKTQREIAGIL 196


>gi|74319499|gb|ABA02894.1| RNA polymerase sigma factor sigma-70 [Acinetobacter calcoaceticus]
 gi|74319507|gb|ABA02898.1| RNA polymerase sigma factor sigma-70 [Acinetobacter calcoaceticus]
          Length = 171

 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/205 (16%), Positives = 67/205 (32%), Gaps = 37/205 (18%)

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
            P   + ++   ++   G   L +I  L   + PE+        E     + ED S  K 
Sbjct: 1   WPNAVEVVLKEYNDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEELEEEDESSSKS 58

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             +V+  + D E  ++   D        PE A+                           
Sbjct: 59  TKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAK--------------------------- 91

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
                 E+   + + +++ +      K  ++S + +   E L  +           D++ 
Sbjct: 92  --VRFTELEAAWAKTKAVVE------KHGRNSPEAEEALEALATVFMMFKFTPRLFDIIS 143

Query: 340 EQLYDISKRIMHNEGELLRLAQSYG 364
           E +    ++I  NE E++R A   G
Sbjct: 144 EMIRGTHEQIRANEREIMRYAVRRG 168


>gi|84687559|ref|ZP_01015435.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664468|gb|EAQ10956.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 562

 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 33/72 (45%)

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
              A      E    +L     R   +L + +G   +   TLE  G+ + +TRER+RQI 
Sbjct: 79  EWHAHDTLESELFALLLEVEDERNAEMLSVFYGFNEDGPKTLEYSGQPYGLTRERVRQIA 138

Query: 661 AKAIRKLKHPSR 672
           A+  +KL+   R
Sbjct: 139 ARTEKKLRELWR 150


>gi|291237949|ref|XP_002738894.1| PREDICTED: espin-like [Saccoglossus kowalevskii]
          Length = 1778

 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 54/372 (14%), Positives = 130/372 (34%), Gaps = 44/372 (11%)

Query: 34   MIKLARQRGYVTIEELNAFLPPDEV-------SSEQMED------TVAMLSNMGINVVDG 80
            + K   + G +T  +++  L  ++        S++++E        VA+  +    V   
Sbjct: 1096 LEKKNTEMGVMTFSDIDKLLAGEKEPTVTQKSSAKEIESQHKQLPLVAVKDDHNSQVKGV 1155

Query: 81   DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI 140
            +  E         +  ++   SS  ++K  DS D   D+ V + + E+   ++L    E+
Sbjct: 1156 ELKEKTALEGKPNEPKTAKKESSNTIEKPDDSIDIGIDEDVSI-VSEVHRNDILVSADEV 1214

Query: 141  AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL-LREIIDLEACIGPESKGGF 199
             +  + E         + E P         ++E N G    L++    EA +  E+    
Sbjct: 1215 TLVGK-EDCSTSKQEGIDEQP---------KEEKNIGNMNGLQD----EAVVTEENGDVE 1260

Query: 200  FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                E +S  K E+   + +     E+        K   DD  ++    EN+  D  ++ 
Sbjct: 1261 MLDVENNSKMKDENQPDDSKNSMKTESMPPQLDKIKNCHDDAQQIKITVENSSVDSPDIA 1320

Query: 260  EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319
                +     SA              +++ +   +   + +      +E  + + K + +
Sbjct: 1321 GVSTEQKVKRSASPLPCEDTREAKKAKLSGLMNHVDDNKASLSKKAIEEIIAAQKKEIYQ 1380

Query: 320  KLVKLVGSLSLNQS--------RIDLLVEQLYDISKRIMHNE-------GELLRLAQSYG 364
             ++K+     ++          +++ L++Q     +R+            E  RL     
Sbjct: 1381 HILKVCEEHRMHDKATITALRRQVNTLLDQNRQWEQRVKQLRTNTQMKVKEQERLQMKAL 1440

Query: 365  IKRDVFLERHQG 376
            + + V  + ++ 
Sbjct: 1441 MPKRVVQKEYRS 1452


>gi|156740060|ref|YP_001430189.1| hypothetical protein Rcas_0032 [Roseiflexus castenholzii DSM 13941]
 gi|156231388|gb|ABU56171.1| TPR repeat-containing protein [Roseiflexus castenholzii DSM 13941]
          Length = 1445

 Score = 52.5 bits (124), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/114 (18%), Positives = 49/114 (42%), Gaps = 9/114 (7%)

Query: 19   DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
            + +      D+   ++I++  +RGYV I ++ A +   E  + ++++   ML    I + 
Sbjct: 1054 ESAPEVSSGDEVVDRLIQIGHERGYVDIADIIAAVKDPEAEAARIDEIGRMLHAARIEIR 1113

Query: 79   DGDDLEDEEGS---------EDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
            DGD++ D +            +    A++A+     ++         +DD + M
Sbjct: 1114 DGDEVIDLDAEYADEEAPLMPEGATPAANAAEEEDLMRPFSLEELGLSDDEIAM 1167


>gi|167628189|ref|YP_001678688.1| hypothetical protein HM1_0052 [Heliobacterium modesticaldum Ice1]
 gi|167590929|gb|ABZ82677.1| hypothetical protein HM1_0052 [Heliobacterium modesticaldum Ice1]
          Length = 238

 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 86/253 (33%), Gaps = 56/253 (22%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY------TNRGLQFLDLIQEGNIGLMKAA 485
            +        + +  ++  A   L+  +  +Y        +G++  DL Q G    + A 
Sbjct: 5   ELAIMAAQGDTESLHKLYFAVAPLIYKITSRYFKYCETNRKGVRPEDLTQCGYFAYLSAL 64

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
           +++      KF++Y  + V +   R                                   
Sbjct: 65  KQYSPERELKFTSYLDFCVARECWR----------------------------------- 89

Query: 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSA 604
                    +L +  +   KVL    E ISLETPI D++    L D I D +A +     
Sbjct: 90  ---------ELGISFQTGGKVLNREVETISLETPISDDEEGLTLEDIISDPDADTYSF-C 139

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              ++R    R +  L+PRE+ V+   F      +   +E G +       +  +   A 
Sbjct: 140 ELNDMRLIVRREIERLSPREQCVIYGIFYNNKTIEGLAQEFGCELGT----VLSVRDTAF 195

Query: 665 RKLKHPSRSKKLR 677
             L+     ++LR
Sbjct: 196 NSLRRSKGIRELR 208


>gi|218134246|ref|ZP_03463050.1| hypothetical protein BACPEC_02138 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991621|gb|EEC57627.1| hypothetical protein BACPEC_02138 [Bacteroides pectinophilus ATCC
           43243]
          Length = 228

 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 71/202 (35%), Gaps = 42/202 (20%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++++     +  +  E+ E     V   A      G    DLIQEG IGL KA + +D  
Sbjct: 17  ALIQMYRDGSRDSIDELFERYKGCVRRKAHAMYIAGGDEEDLIQEGMIGLYKAVQDYDAG 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F+T+A   + + +  ++A                 K  R   ++ N+         
Sbjct: 77  REASFATFASMCINRNMCTAVA-----------------KSNRKKYQLLNES-------- 111

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                                P++++    DE  +HL D +   +A  P +  I     +
Sbjct: 112 ----------------LSLDMPVAVDEEAYDEPQTHLIDVVVASSAQDPENMYIDKERVD 155

Query: 612 TTTRVLAS-LTPREERVLRMRF 632
                + + L+  E++VL +  
Sbjct: 156 VIYEAIRTCLSEYEKQVLDLYI 177


>gi|11466545|ref|NP_044794.1| transcription initiation factor sigma [Reclinomonas americana]
 gi|2258375|gb|AAD11909.1| transcription initiation factor sigma [Reclinomonas americana]
          Length = 532

 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 50/103 (48%), Gaps = 5/103 (4%)

Query: 445 KKEMVEANLRLVISVAKKYT--NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502
           K  ++   +  + +++K+Y       QF DLIQEG  G+  AAEKF    G +F TYA W
Sbjct: 353 KNRIIFNYMPYITTISKQYVKIGYQAQFSDLIQEGISGVSDAAEKFQLGRGVRFLTYAYW 412

Query: 503 WVKQAITRSIADQSCTIRIPVH---MRDKIHKVVRTARRMSNK 542
           W+   + ++   +   +R   H    ++ + K+ +    +  K
Sbjct: 413 WMHNYMMKATIKKKKKLRFNEHETPRKELLLKIEKLQTEIDKK 455


>gi|224771307|dbj|BAH28595.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771319|dbj|BAH28601.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771321|dbj|BAH28602.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 80/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+PRE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196


>gi|313820245|gb|EFS57959.1| sigma-70 region 2 [Propionibacterium acnes HL036PA1]
 gi|313822945|gb|EFS60659.1| sigma-70 region 2 [Propionibacterium acnes HL036PA2]
 gi|314925132|gb|EFS88963.1| sigma-70 region 2 [Propionibacterium acnes HL036PA3]
          Length = 228

 Score = 52.1 bits (123), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/130 (23%), Positives = 62/130 (47%), Gaps = 3/130 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +R+   +   A++ +    L +V++ A++   +      DLIQ G IGL +A E++D 
Sbjct: 48  AELRRISDDGVGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDV 107

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550
             G +FST A  W+++ I   +   S        +  +  +V R    ++ + +  P+ +
Sbjct: 108 RRGARFSTVAWTWIRRRIGEEVVRLS--GARSRSVMREAAEVARIEEELTARWQSVPSSD 165

Query: 551 EIAKKLAMPV 560
            IA ++   V
Sbjct: 166 AIAARMGKDV 175


>gi|47089382|gb|AAT11010.1| sigma 70 factor [Pseudomonas syringae pv. syringae]
          Length = 149

 Score = 51.8 bits (122), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/194 (9%), Positives = 49/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G S         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGISPPAEVPPPVDPKAA 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +  + D E +A  S ++      P             D+ +          +     +
Sbjct: 50  KAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +AE++                                    + L   + + LVE+
Sbjct: 110 AEMVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|153812847|ref|ZP_01965515.1| hypothetical protein RUMOBE_03254 [Ruminococcus obeum ATCC 29174]
 gi|149831059|gb|EDM86148.1| hypothetical protein RUMOBE_03254 [Ruminococcus obeum ATCC 29174]
          Length = 136

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 29/139 (20%), Positives = 58/139 (41%), Gaps = 7/139 (5%)

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
             ++   + REPT  E+A++L M  E +        E  S+  PI   + + L       
Sbjct: 2   REKLEKNLGREPTVTELAEELGMTPEEIAMASDAATEVESIYRPIHQGEGTELQLL---D 58

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                 +   +   +     +L  L   E R++ MR+      D T  EV K+  +++ +
Sbjct: 59  KLPEKENRQERILDKIFLEELLNILGTEERRLICMRYFC----DMTQTEVAKRLGISQVQ 114

Query: 656 IRQIEAKAIRKLKHPSRSK 674
           + ++E + + +LK   + K
Sbjct: 115 VSRMEKRILHRLKKEIQDK 133


>gi|148654935|ref|YP_001275140.1| hypothetical protein RoseRS_0774 [Roseiflexus sp. RS-1]
 gi|148567045|gb|ABQ89190.1| TPR repeat-containing protein [Roseiflexus sp. RS-1]
          Length = 1534

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 45/230 (19%), Positives = 83/230 (36%), Gaps = 20/230 (8%)

Query: 16   EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
            E ++    F+  D++  ++I+L  +RGYV + ++ A +   E  ++++++    L    I
Sbjct: 1153 ELAETFPGFESVDETVDRLIRLGHERGYVDLADIIATVRDPEAEADRIDEIGRKLHAARI 1212

Query: 76   NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR-MYLREMGSIELL 134
             + DGD++ D +   +  +  +     S       D      +D +R   L E+G    L
Sbjct: 1213 QIRDGDEIIDLD--AEYAEEETPLPVESALQPALNDMPSE--EDLMRPFSLEELG----L 1264

Query: 135  SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
            S + EIA+     AG+   +    E P      +            L +  D  A I   
Sbjct: 1265 S-DDEIALLAAAAAGQQENVPPPAEEPSLTPFSL--------EELGLSD--DEIAMISAA 1313

Query: 195  SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                     EG S    E  S   E      +    + A   S     + 
Sbjct: 1314 GSTVETSPVEGPSLSPEEPESSGAEVTQTTRSAATSDVAPPPSATSEVEA 1363


>gi|167945650|ref|ZP_02532724.1| flagellar biosynthesis sigma factor [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 104

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
            +   +      +A L  RE  V+ M +    + +  L E+G+   V+  R+ QI ++A 
Sbjct: 32  QKDAFKNALAEAIAGLPERERLVISMYY----DDELNLREIGQVLGVSESRVCQIHSQAT 87

Query: 665 RKLK 668
            +L+
Sbjct: 88  LRLR 91


>gi|289422613|ref|ZP_06424455.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
 gi|289156964|gb|EFD05587.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
          Length = 289

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 78/237 (32%), Gaps = 13/237 (5%)

Query: 421 GISISEFRHIV--SMVRKGECEASIAKKEMVEANLRLVI------SVAKKYTNRGLQFLD 472
           G  + + R +    +V+  +    +A  +++E   + V            Y  RGL   D
Sbjct: 31  GCDMGDKRELADRKLVKSAKEGDLVALNKVIEKKSKYVKGIIKNDYEIMAYKKRGLDQED 90

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L Q G IGL+ A +KFD+  G KF TY    VK +I     D                  
Sbjct: 91  LFQSGMIGLLNAVKKFDFRDGIKFDTYLAHNVKYSIKNDFRDYGGLSVSREASSIYSKCS 150

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI 592
                   N           ++KL +  E + K +   K   ++ T   D +       +
Sbjct: 151 SSLYEYDGNLSDELLEEL--SEKLYVTKEKISKSILAVKIRNAMYTYTCDGEIEAEEQIL 208

Query: 593 ---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
              + +          +  L       +  L+ +E  +L   +          +E+G
Sbjct: 209 YKYKKQLVEDYESKFEKRMLYREILNQIKKLSDKERYILENLYIKDRTQVSIAQELG 265


>gi|224771371|dbj|BAH28627.1| sporulation sigma factor SigK [Clostridium perfringens NCTC 8239]
 gi|224771377|dbj|BAH28630.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771385|dbj|BAH28634.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771387|dbj|BAH28635.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771389|dbj|BAH28636.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771391|dbj|BAH28637.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771407|dbj|BAH28645.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771409|dbj|BAH28646.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771411|dbj|BAH28647.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 80/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLDRLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+PRE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDILSPREKEIIKMRYGLLDGDIKTQREIAAIL 196


>gi|86148201|ref|ZP_01066499.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|85834048|gb|EAQ52208.1| RNA polymerase sigma factor [Vibrio sp. MED222]
          Length = 83

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + I+S +    ++  E R +   +         A K ++ ++LR V+ VA+ Y+  GL
Sbjct: 16  LDSYIRSANSYPMLTPDEERGLAERLHYKGEID--AAKGLILSHLRFVVHVARGYSGYGL 73

Query: 469 QFLDLIQEGN 478
              DL+QEGN
Sbjct: 74  PMADLVQEGN 83


>gi|301060344|ref|ZP_07201207.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
 gi|300445540|gb|EFK09442.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
          Length = 772

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
           R + + +  F        TLEE+G+ F +TRER+RQI  KAI++ KH +   ++  F
Sbjct: 236 RNQVLTQKMFLFDSERSPTLEEIGQAFGITRERVRQIVKKAIKQFKHTANISQIEKF 292


>gi|283133054|dbj|BAI63821.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci]
          Length = 115

 Score = 51.8 bits (122), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 5/94 (5%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S +  + D D   L +      ++ P         +      +A+L  RE  VL     +
Sbjct: 18  SFDDLLQDGDHEGLHEDGA-SGSLEPSRDLEDERFQAALADAIANLPERERLVL----AL 72

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + +  L+E+G+   V+  R+ Q+ ++   +L+
Sbjct: 73  YYDEELNLKEIGEVLGVSESRVSQLHSQCAARLR 106


>gi|325921797|ref|ZP_08183616.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
 gi|325547729|gb|EGD18764.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
          Length = 135

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 44/113 (38%), Gaps = 6/113 (5%)

Query: 556 LAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
           + MP+    ++++       L      ED   L      K   +P     +        +
Sbjct: 12  MEMPLPDYLRLMEDAARGQVLSLESRIEDHGELDTTA--KGGPNPQQMMERGEFGRELGK 69

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            +  L  RE+ VL + +      +  L+E+G    V+  R+ QI  +A+ +L+
Sbjct: 70  AIGQLPEREQLVLSLYY----EQELNLKEIGAVLGVSESRVCQIHGQAVVRLR 118


>gi|295092949|emb|CBK82040.1| DNA-directed RNA polymerase specialized sigma subunit [Coprococcus
           sp. ART55/1]
          Length = 106

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 21/120 (17%), Positives = 51/120 (42%), Gaps = 19/120 (15%)

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
            EEI + +    E +   +    +   ++    +   +  GD I D              
Sbjct: 1   MEEICEAIGATPEELVMAMDAASDVTCIDDLHAEMCGTEDGDRIVD-------------- 46

Query: 609 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            R   +++L +LTP E +++ +R+      D T  + G+   +++ ++ ++E K + +L+
Sbjct: 47  -RLCVSQLLDTLTPDERKLVVLRYF----QDKTQGQTGQILGMSQVQVSRLEKKILGRLR 101


>gi|88808533|ref|ZP_01124043.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88787521|gb|EAR18678.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 198

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 38/225 (16%), Positives = 80/225 (35%), Gaps = 45/225 (20%)

Query: 445 KKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + + V+ +L+LV  +A+ Y    G+   DL Q G +GL++AAE F+      F  +A   
Sbjct: 8   RNQRVKDHLQLVTPIARHYAQRCGIDADDLRQVGLMGLLRAAENFNTERCTPFKAFARPH 67

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++ AI   + D +  +R P  ++         + +  N+  ++           + +  V
Sbjct: 68  IRGAILHYLRDNASVVRFPRRLQ---------SDKEMNESGKQC--------HGLLLRRV 110

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
                                  + GD          ++   Q          L SL   
Sbjct: 111 -----------------------YCGDETVADTKSETIEEIDQMERSRLIQEALKSLRSP 147

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E   ++     G     +L   G+   V+   +++   + + +L+
Sbjct: 148 ERSAIQEVVLDG----RSLRAAGRVAGVSAMTMQRRVKRGLSRLR 188


>gi|67920929|ref|ZP_00514448.1| Sigma-70 region 2 [Crocosphaera watsonii WH 8501]
 gi|67857046|gb|EAM52286.1| Sigma-70 region 2 [Crocosphaera watsonii WH 8501]
          Length = 110

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 445 KKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           + +++E N  LV   A  + ++    + DL+Q G++GL++A E+F    G+ FS++A+ +
Sbjct: 29  RNKILELNFGLVRREAHHWVHQCPESYEDLVQVGSLGLIRAIERFSIGKGHAFSSFAIPY 88

Query: 504 VKQAITRSIA 513
           ++  I   + 
Sbjct: 89  IRGEIQHYLR 98


>gi|229817514|ref|ZP_04447796.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
 gi|229785303|gb|EEP21417.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
          Length = 621

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 3/58 (5%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +L E+ T +L S   RE         +      TL+E+GK+F +TRER+RQIE KA+R
Sbjct: 134 SLAESLTMLLFSFDERE--YAIATQRLMAEQPSTLDEIGKEFNITRERVRQIE-KALR 188


>gi|163784183|ref|ZP_02179117.1| DNA-directed RNA polymerase specialized sigma subunit
           [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880543|gb|EDP74113.1| DNA-directed RNA polymerase specialized sigma subunit
           [Hydrogenivirga sp. 128-5-R1-1]
          Length = 102

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 4/89 (4%)

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
            DED+      I   N  +P     Q  L++     +A L  RE  V+ + +      + 
Sbjct: 6   NDEDSDTKLWQIIAINDDTPDKYVEQKQLKKILADAIAKLDERERLVITLYY----YEEL 61

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +++E+G+   +T  RI QI  K + KL+ 
Sbjct: 62  SMKEIGEVLGLTESRISQIHTKTMLKLRK 90


>gi|323356683|ref|YP_004223079.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323273054|dbj|BAJ73199.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 538

 Score = 51.4 bits (121), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/52 (46%), Positives = 36/52 (69%), Gaps = 1/52 (1%)

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
           PRE+++LRMR G       TL E+ ++F ++RERIRQIE++A   L H +R+
Sbjct: 177 PREQKILRMRVGFE-GAPRTLAEIAREFDLSRERIRQIESRARNILVHQART 227


>gi|225629823|ref|ZP_03787747.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225591324|gb|EEH12440.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 95

 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 601 LDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
             +  +  L+ET     LASL  R   +   R+        TL+E+ K++CV+RERIRQ+
Sbjct: 15  YQNHEEEELKETILNNALASLNERARDIFISRYLSENIQ--TLDELSKKYCVSRERIRQL 72

Query: 660 EAKAIRKLKHPSRSKKLR 677
             +A+ K+K   +S+ L+
Sbjct: 73  AEQAMAKVKPYIQSESLK 90


>gi|222530382|ref|YP_002574264.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457229|gb|ACM61491.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 210

 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 99/250 (39%), Gaps = 50/250 (20%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +S  E + ++  ++K       A + ++ A   L+IS+A KY N+   F DL QEG 
Sbjct: 5   MFELSFDEQKELIGRIKK---GDKEAAETLIMAYEPLIISLAAKY-NKPDIFEDLKQEGA 60

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           + +++AA+KFD  LG  F T A++++K+ + R                       RT R 
Sbjct: 61  VAILQAAQKFDESLGVSFVTLAIYYIKRNMDRCTNKS------------------RTIRP 102

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
             NK   E                         + IS+E+ I     +   +        
Sbjct: 103 PFNKPNTE-----------------------IPQVISMESVINTNSHADDEELKVKDTVQ 139

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
              +   QA   ET  R++  L+  E ++L     +     ++ +E+ K+  +T +++  
Sbjct: 140 DTANVEEQAMYNETLQRLIKMLSDEERKIL-----LLRLKQYSFKEIAKELGLTEKQVAT 194

Query: 659 IEAKAIRKLK 668
              K   KL+
Sbjct: 195 RAQKIRTKLQ 204


>gi|168212152|ref|ZP_02637777.1| sporulation sigma factor SigK [Clostridium perfringens B str. ATCC
           3626]
 gi|170709952|gb|EDT22134.1| sporulation sigma factor SigK [Clostridium perfringens B str. ATCC
           3626]
          Length = 58

 Score = 51.4 bits (121), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 30/50 (60%)

Query: 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             L+PRE+ +++MR+G+      T  E+     ++R  + +IE KA++KL
Sbjct: 3   DVLSPREKEIIQMRYGLLDGDIKTQREIAGILGISRSYVSRIEKKALKKL 52


>gi|255959709|gb|ACU43606.1| RNA polymerase sigma factor [uncultured Aeromonas sp.]
 gi|255959711|gb|ACU43607.1| RNA polymerase sigma factor [uncultured Aeromonas sp.]
 gi|255959713|gb|ACU43608.1| RNA polymerase sigma factor [uncultured Aeromonas sp.]
 gi|255959715|gb|ACU43609.1| RNA polymerase sigma factor [uncultured Aeromonas sp.]
 gi|255959717|gb|ACU43610.1| RNA polymerase sigma factor [uncultured Aeromonas sp.]
          Length = 67

 Score = 51.0 bits (120), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + +  F+      E +  W  Y K   +      V  + + I +   +++ I  ETG+SI
Sbjct: 1   MPKKTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMD-EDIQRAIGKLQQIEEETGLSI 59

Query: 425 SEFRHIVS 432
           ++ + I  
Sbjct: 60  AQIKDINR 67


>gi|218673042|ref|ZP_03522711.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 88

 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D + D+   + +D       R      L  L  RE +++  R         TLEE+G   
Sbjct: 1   DPLPDEQVSNMIDG---ERRRVWLASALKHLNEREMKIISARRLAEDG--ATLEELGADL 55

Query: 650 CVTRERIRQIEAKAIRKLKHPSRS 673
            +++ER+RQIE++A+ KL+    S
Sbjct: 56  GISKERVRQIESRAMEKLRSALVS 79


>gi|270620051|ref|ZP_06221855.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270317775|gb|EFA29151.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 108

 Score = 51.0 bits (120), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 5/81 (6%)

Query: 591 FIEDKN---AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           ++EDK+   A    +   ++   E     L SL  R + +++ R+        TL ++  
Sbjct: 25  YLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIKARWLDDN--KATLHDLAA 82

Query: 648 QFCVTRERIRQIEAKAIRKLK 668
           ++ V+ ERIRQ+E  A++KLK
Sbjct: 83  KYNVSAERIRQLETNALKKLK 103


>gi|224771357|dbj|BAH28620.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.0 bits (120), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 79/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTSKGIRLATYAAKCIDNEILMFFRNSKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+ RE+ +++MR+G+      T  E+    
Sbjct: 146 VLETVENSLQVKELYKKISDVLSTREKEIIQMRYGLLDGDIKTQREIAGIL 196


>gi|332753464|gb|EGJ83844.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 114

 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/102 (25%), Positives = 39/102 (38%), Gaps = 10/102 (9%)

Query: 68  AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
           A     G+ V D   L +EE S++ L      S  +           +   D  ++YL E
Sbjct: 15  AEFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA----------TQRVLDATQLYLGE 64

Query: 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           +G   LL+ E E+  A+R   G       + ES L     I 
Sbjct: 65  IGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIA 106


>gi|284989337|ref|YP_003407891.1| sigma-70 region 4 domain-containing protein [Geodermatophilus
           obscurus DSM 43160]
 gi|284062582|gb|ADB73520.1| sigma-70 region 4 domain protein [Geodermatophilus obscurus DSM
           43160]
          Length = 896

 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 8/85 (9%)

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           ED  H+  +++        +S ++A L ++  + L +L  R        +G+      TL
Sbjct: 407 EDAEHILHWLKGFTLEEEAESVLRAALGKSADKWLEALGSR--------YGLAGADPQTL 458

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKL 667
           +EVG+   VTRER+RQ+++KA   L
Sbjct: 459 DEVGRTLGVTRERVRQVQSKAQAHL 483


>gi|293375374|ref|ZP_06621655.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325844422|ref|ZP_08168149.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
 gi|292645927|gb|EFF63956.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325489096|gb|EGC91480.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
          Length = 200

 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +V +VR+       A   ++E    L+  +A  Y   G  + D  QEG +  +KA   F
Sbjct: 9   ELVYLVREQN---EEALHIIIEKYSPLIGKIASSYYGIGYDYQDFFQEGRMAFIKAIYSF 65

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           D    Y F +YAM  V+ AIT S      
Sbjct: 66  DENSNYSFYSYAMTCVRNAITTSYRRLKR 94


>gi|260653773|dbj|BAI44426.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
           [Monochamus alternatus]
          Length = 56

 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 32/53 (60%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
                +  +++ ++L LV  +A K+ N GL F+DL+ EGN+GLM   +KF+  
Sbjct: 1   YMDISSAHKLITSHLNLVXKIAMKFKNYGLLFMDLVMEGNMGLMHPVKKFNPD 53


>gi|224023371|ref|ZP_03641737.1| hypothetical protein BACCOPRO_00064 [Bacteroides coprophilus DSM
           18228]
 gi|224016593|gb|EEF74605.1| hypothetical protein BACCOPRO_00064 [Bacteroides coprophilus DSM
           18228]
          Length = 404

 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 22/47 (46%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
           L  RE  +    +G+         E+  +  + +ERIRQ+E K  +K
Sbjct: 28  LKERERMLFISLYGLDETDTRNHTEMAAELGLCKERIRQLEVKVFKK 74


>gi|317127421|ref|YP_004093703.1| LPXTG-motif cell wall anchor domain protein [Bacillus
            cellulosilyticus DSM 2522]
 gi|315472369|gb|ADU28972.1| LPXTG-motif cell wall anchor domain protein [Bacillus
            cellulosilyticus DSM 2522]
          Length = 1287

 Score = 50.6 bits (119), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/192 (13%), Positives = 56/192 (29%), Gaps = 12/192 (6%)

Query: 177  GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                L E+++       E   G     E    +  +    + E  D +  +G+       
Sbjct: 1015 DNIRLVEVVENGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPG 1074

Query: 237  SKDDRSKVDSPPENAENDERNLDEDE---------DDSAHTLSAMEDQLRPKVMCALDEI 287
              +         E  + +  + +  +         D         + +         DE+
Sbjct: 1075 DGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDGEPGDTDEL 1134

Query: 288  AEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL---VGSLSLNQSRIDLLVEQLYD 344
             +   EL  L         D + S +   L+ +L ++   +  L  N + ++  V  L  
Sbjct: 1135 QQRINELMELIAELQARIADLEGSSEIADLENRLSEIEGLLEELKSNFNELEEYVSHLEA 1194

Query: 345  ISKRIMHNEGEL 356
            + K +      L
Sbjct: 1195 LIKDLKDEIAAL 1206


>gi|295399303|ref|ZP_06809285.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geobacillus thermoglucosidasius C56-YS93]
 gi|294978769|gb|EFG54365.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geobacillus thermoglucosidasius C56-YS93]
          Length = 99

 Score = 50.6 bits (119), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
              +   L D ++ +      +  +   L E   + +  L  RE+ V+  RFG+ M  + 
Sbjct: 1   MKGNEISLIDVLKSEGNDIIDEIQLNMEL-EQVKKYIDVLDEREKEVIINRFGLDMQQEK 59

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 60  TQREIAKELGISRSYVSRIEKRALMKMFH 88


>gi|158320673|ref|YP_001513180.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Alkaliphilus
           oremlandii OhILAs]
 gi|158140872|gb|ABW19184.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alkaliphilus oremlandii OhILAs]
          Length = 88

 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/80 (22%), Positives = 41/80 (51%)

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           + D +  +      +  ++  +++  +++ + L  RE  V+ +R+GI      T  E+ +
Sbjct: 1   MIDILGTEADEVLEEVELKMQIKKLYSKMASVLKTRERIVIELRYGICNGGSKTQREIAQ 60

Query: 648 QFCVTRERIRQIEAKAIRKL 667
              ++R  + +IE +AIRKL
Sbjct: 61  MLGISRSYVSRIEKRAIRKL 80


>gi|167470529|ref|ZP_02335233.1| alternative sigma factor RpoH [Yersinia pestis FV-1]
          Length = 127

 Score = 50.6 bits (119), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 9/87 (10%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            + TS   D IE+ N  S           +  +  L  L  R + ++R R+    N   T
Sbjct: 45  QDKTSDFADGIEEDNWDSHAA--------DKLSYALEGLDERSQHIIRARWLDDENKS-T 95

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLK 668
           L+E+  Q+ V+ ER+RQ+E  A++KL+
Sbjct: 96  LQELADQYGVSAERVRQLEKNAMKKLR 122


>gi|317062458|ref|ZP_07926943.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
 gi|313688134|gb|EFS24969.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
          Length = 244

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 95/257 (36%), Gaps = 34/257 (13%)

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
           +K RN  +     T + + E   +             A+ +++   LR +  +  +Y N 
Sbjct: 1   MKTRNMYREYPAITEVEVQELLPLAQ------EGDIEARNKIIVGYLRYITHLNNRYGNG 54

Query: 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV-HM 525
                   Q    G+++    +    G KFSTY  +W+KQ I R+   ++          
Sbjct: 55  SEDCF---QSAIFGVIEGIRNYK-NNGIKFSTYCYFWIKQRINRTRDKENYDGNTSFIER 110

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585
           R K  K+++    +  K        E+ KKL +    +R + + T   ISL+     E  
Sbjct: 111 RKKYEKLIKNDPLLPKK--------EVLKKLQISESTLRGIERSTYAKISLQNKRSWEFL 162

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEE 644
                 +  +  V+          RE   +++    T RE  ++++ +          +E
Sbjct: 163 GTDAGTVAIEQIVN----------REYLEQLIKKYCTKREATIIKLLYFEEYTE----QE 208

Query: 645 VGKQFCVTRERIRQIEA 661
           + K + +T   +  I+ 
Sbjct: 209 LAKIYNITASGVHFIKN 225


>gi|6010734|gb|AAF01233.1|AF184102_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 119

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 36/93 (38%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
           E+  A+R   G       + ES L     I  R
Sbjct: 76  EVYFARRALRGDVASRRRMIESNLRLVVKIARR 108


>gi|224771349|dbj|BAH28616.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 79/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLK---DGDIEAKRVLVERNLRLVAHIVKKYSSSYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+ RE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDVLSTREKEIIQMRYGLLDGDIKTQREIAGIL 196


>gi|224771363|dbj|BAH28623.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 79/231 (34%), Gaps = 55/231 (23%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGN 478
           ++  E +  +  ++        AK+ +VE NLRLV  + KKY++      +  DLI  G 
Sbjct: 18  LNEKEEKIYLERLK---DGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           IGL+KA + FD   G + +TYA   +   I     +   T                    
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKTKGEVF--------------- 119

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + + I  +    EI                                   L D +   +  
Sbjct: 120 LQDPIGVDKEGNEIC----------------------------------LIDILSSDSDS 145

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
                     ++E   ++   L+ RE+ +++MR+G+      T  E+    
Sbjct: 146 VLEAVENSLQVKELYKKMSDVLSHREKEIIQMRYGLLDGDIKTQREIAGIL 196


>gi|255959719|gb|ACU43611.1| RNA polymerase sigma factor [uncultured Aeromonas sp.]
          Length = 67

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
           + +  F+      E +  W    K   +      V  + D I +   +++ I  ETG+SI
Sbjct: 1   MPKKTFVAAFTNNECETAWFECQKQAGKAWSPRLVEMDED-IQRAIGKLQQIEEETGLSI 59

Query: 425 SEFRHIVS 432
           ++ + I  
Sbjct: 60  AQIKDINR 67


>gi|323704017|ref|ZP_08115638.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531020|gb|EGB20938.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 85

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 33/58 (56%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           +      +  L+ RE++VL MRFG+G +   T  E+ +   ++R  + +IE +A+ KL
Sbjct: 18  KNRLLEKVHKLSRREKKVLEMRFGLGTSARKTQREIARALGISRSYVSRIEKRALNKL 75


>gi|124514599|gb|EAY56111.1| putative RNA polymerase sigma-70 factor family [Leptospirillum
           rubarum]
          Length = 99

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           R+L  L  R  +++ +R+GIG     TL+E+G +F +TRER+RQI   ++ KL    R K
Sbjct: 34  RILQDLPDRSRKMVLLRYGIGTGISWTLQEIGLEFGLTRERVRQILRTSLEKLVKRQRRK 93

Query: 675 KLRS 678
           + R 
Sbjct: 94  ESRE 97


>gi|87310296|ref|ZP_01092427.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87287045|gb|EAQ78948.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 287

 Score = 50.2 bits (118), Expect = 0.001,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 94/237 (39%), Gaps = 59/237 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
             + +   +A+  ++++  ANLRLV S+++K +    +F + + E N  L+ A +KFD+ 
Sbjct: 95  REIERLLKDAAETREQIACANLRLVTSISQKLSLSRDEFEEFLAESNAILLNAIDKFDYA 154

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            GY+FSTYA   V                     R+    + +  +R   +   E     
Sbjct: 155 RGYRFSTYATHAV--------------------QRNLFRVIEKRNKRRKLESCEEVALHA 194

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
                A P E                                      P    + +    
Sbjct: 195 ATAPAANPEE--------------------------------------PSGQDVLSAFES 216

Query: 612 TTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
             +R+   L  RE+ ++R RFG+ G+    +L E+G++  +++ER RQ+  ++I KL
Sbjct: 217 IMSRIDQVLDSREQFIVRERFGLDGIGKGKSLREIGEELGISKERTRQLFQRSIEKL 273


>gi|261367813|ref|ZP_05980696.1| putative RNA polymerase sigma-H factor [Subdoligranulum variabile
           DSM 15176]
 gi|282570611|gb|EFB76146.1| putative RNA polymerase sigma-H factor [Subdoligranulum variabile
           DSM 15176]
          Length = 180

 Score = 49.8 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/143 (20%), Positives = 53/143 (37%), Gaps = 13/143 (9%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ + +     A   ++   +  +   A  Y   GL F D +QEG IGL +A   +    
Sbjct: 8   LLVRAQQGDDTALAALIARMMPAIRKGAAVYRAPGLDFEDAVQEGLIGLFQAVRGYRSAA 67

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEI 552
           G  F++YA   +  A   +             +R K   +  +      +   +P PEE+
Sbjct: 68  GTPFASYAATCIHHAQQDAQRAA---------LRKKHAPLNFSVPLPDAENIPQPGPEEL 118

Query: 553 AKKLAMPVEGVRKVLKITKEPIS 575
           A       E     L+  +  +S
Sbjct: 119 AIAG----ERYADTLQRMQTELS 137


>gi|78212878|ref|YP_381657.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78197337|gb|ABB35102.1| possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 85

 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 445 KKEMVEANLRLVISVAKKY-TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           +   +  NL +V  +A+ Y    GL+  DL+Q G +GL+KA  +++   G  F ++A   
Sbjct: 24  RNRQIHDNLHMVRPIARHYAQQTGLESDDLLQVGCLGLIKAYNRYEAKRGAPFPSFAKPH 83

Query: 504 VK 505
           ++
Sbjct: 84  IR 85


>gi|156744109|ref|YP_001434238.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Roseiflexus
           castenholzii DSM 13941]
 gi|156235437|gb|ABU60220.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Roseiflexus castenholzii DSM 13941]
          Length = 220

 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 6/96 (6%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL+ P   +D   L + IED       +   +  +R+     +A+L   E  V+  R   
Sbjct: 124 SLDAP-FGDDGPPLHEVIEDPTPARLAEEHDEEQVRKRLYEAIAALPEIERAVVTHRLSE 182

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
               D     + +   ++   + +I  +AI +L+  
Sbjct: 183 VRGID-----IAQMLGMSPANVSRIYKRAINRLRQA 213


>gi|315652062|ref|ZP_07905063.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
           3986]
 gi|315485709|gb|EFU76090.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
           3986]
          Length = 171

 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/162 (17%), Positives = 73/162 (45%), Gaps = 3/162 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     I   + + I  +          A+  ++E ++   + + K +   G +  DLI 
Sbjct: 11  LEDMKAIKEIDEKEIKELTDALLHGDESARNRLIEGHMMYAVKLIKPFIGCGEEMSDLIS 70

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           E ++ L  A  ++         +     V++ +     ++         + D+I++++  
Sbjct: 71  ESHLALTMAVMEYSHG---DLKSQIKSRVEKRLNEIADEEKSKKDASNKLADRINELMDV 127

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
           +  +++ I +E T EE++++L +P + V ++LKI+   I+LE
Sbjct: 128 SSALASDIGKEATLEELSERLQIPKDEVEELLKISLNAINLE 169


>gi|257468173|ref|ZP_05632269.1| sporulation sigma factor SigG [Fusobacterium ulcerans ATCC 49185]
          Length = 239

 Score = 49.8 bits (117), Expect = 0.002,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 93/249 (37%), Gaps = 31/249 (12%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
                  I+  E + ++ + +        A+ +++   LR +  +  +Y N         
Sbjct: 1   MYREYPAITEVEVQELLPLAQ---EGDIEARNKIIVGYLRYITHLNNRYGNGSEDCF--- 54

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV-HMRDKIHKVV 533
           Q    G+++    +    G KFSTY  +W+KQ I R+   ++          R K  K++
Sbjct: 55  QSAIFGVIEGIRNYK-NNGIKFSTYCYFWIKQRINRTRDKENYDGNTSFIERRKKYEKLI 113

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +    +  K        E+ KKL +    +R + + T   ISL+     E        + 
Sbjct: 114 KNDPLLPKK--------EVLKKLQISESTLRGIERSTYAKISLQNKRSWEFLGTDAGTVA 165

Query: 594 DKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
            +  V+          RE   +++    T RE  ++++ +          +E+ K + +T
Sbjct: 166 IEQIVN----------REYLEQLIKKYCTKREATIIKLLYFEEYTE----QELAKIYNIT 211

Query: 653 RERIRQIEA 661
              +  I+ 
Sbjct: 212 ASGVHFIKN 220


>gi|260437950|ref|ZP_05791766.1| RNA polymerase sigma-H factor [Butyrivibrio crossotus DSM 2876]
 gi|292809701|gb|EFF68906.1| RNA polymerase sigma-H factor [Butyrivibrio crossotus DSM 2876]
          Length = 205

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 4/103 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V K       A   ++E    LV    + Y   G    DL+QEG +GL KA   ++  
Sbjct: 14  ELVAKYHSGDEKAADYLIEKYKNLVRKNVRSYYLAGADNEDLLQEGMLGLFKAIRDYNPD 73

Query: 492 LGYKFSTYAMWW----VKQAITRSIADQSCTIRIPVHMRDKIH 530
               F T+A       ++  ITR    ++  +   V   + I+
Sbjct: 74  RDALFMTFASLCVSRHIRSTITRYNRKKNGPLNCYVSFEETIN 116


>gi|312877884|ref|ZP_07737830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795347|gb|EFR11730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 114

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/100 (30%), Positives = 44/100 (44%), Gaps = 4/100 (4%)

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF-LDLIQ 475
           S    +S  E    ++ +         A+  ++E NLRLV  +AKKYT        D+I 
Sbjct: 9   SFPQPMSSEEEEMYLNKMW---EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIIS 65

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
            G IGL+KA E +      K STYA   ++  I   +   
Sbjct: 66  VGTIGLIKAIETYSKAKSTKLSTYAAKCIENEILMYLRQN 105


>gi|326332685|ref|ZP_08198948.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
 gi|325949513|gb|EGD41590.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
          Length = 176

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V  +L +  S+A +Y+ RG++  DL Q   +GL+KAA ++D   G  F +YA+   K  
Sbjct: 18  LVVRHLPVARSLAARYSGRGIEVEDLRQAARMGLVKAARRYDPEQG-AFLSYAVPMAKGE 76

Query: 508 ITRSIADQSCTIRIP 522
           + R   D +  +R  
Sbjct: 77  MRRCFRDLARCVRAQ 91


>gi|168207186|ref|ZP_02633191.1| RNA polymerase sigma-B factor [Clostridium perfringens E str.
           JGS1987]
 gi|170661420|gb|EDT14103.1| RNA polymerase sigma-B factor [Clostridium perfringens E str.
           JGS1987]
          Length = 184

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 41/207 (19%), Positives = 76/207 (36%), Gaps = 50/207 (24%)

Query: 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
           N  + F +++    +GL+KAA +FD   G+KFSTYAM  ++  I               +
Sbjct: 22  NSSMNFEEVLSAAMLGLVKAANRFDEKKGFKFSTYAMSTMRGQI------------KNDY 69

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET--PIGD 582
             DK   + +                EI +K+++                SL    P+  
Sbjct: 70  YHDKNRFIRK-----------RNGNTEIYEKVSIS---------------SLNDTLPLNL 103

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E    L D +                ++      ++ L   +++V+++ F  G     T 
Sbjct: 104 EKDVELIDTLPSN------FEIDNEIVKLDLKNAISKLPDLQKQVIKIIFFQG----KTQ 153

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
            E  K     + +I +I+ +AI  L+ 
Sbjct: 154 NEAAKLLGTNQVQISRIKNRAIESLRK 180


>gi|237756227|ref|ZP_04584790.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237691619|gb|EEP60664.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 78

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/77 (37%), Positives = 49/77 (63%)

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I+  + E    +L  L  RE+ +++MR+G+      TLEEVG++  ++RER+RQ+E +A
Sbjct: 1   MIEETIHEELESMLDVLDEREKEIIKMRYGLNGEESRTLEEVGEKLGISRERVRQLEQRA 60

Query: 664 IRKLKHPSRSKKLRSFL 680
           ++KLK  +  K L+ FL
Sbjct: 61  LKKLKAVALKKHLKDFL 77


>gi|310829283|ref|YP_003961640.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308741017|gb|ADO38677.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 209

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 81/235 (34%), Gaps = 57/235 (24%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +    +A + +V     L+++   +   +  QF D  Q+G +  M+  +KFD   G  F+
Sbjct: 27  KESGRVAGQMLVMTFKPLILATLSRSGIKDGQFEDAFQDGVVAFMEGLKKFDPGRGTGFN 86

Query: 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
            +   +++Q   +  +                                            
Sbjct: 87  AFIQVYLRQYYKKWQSG------------------------------------------- 103

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN---AVSPLDSAIQANLRETTT 614
                  +     K   +L+ PI   +   L + I DK        ++   ++N ++   
Sbjct: 104 -------QFNHSIKPDKTLDDPIPGREGLTLAEVIPDKEINLEADYIEREEKSNDQKRLA 156

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           R L+ L P    VL   +  G     T  E+ ++  V+ + + Q   +A++KLK 
Sbjct: 157 RGLSRLKPSYRSVLEKHYYEG----RTQTEIAEKEGVSLQAVNQRHDRALKKLKK 207


>gi|159469913|ref|XP_001693104.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158277362|gb|EDP03130.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 525

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 40/201 (19%), Positives = 82/201 (40%), Gaps = 25/201 (12%)

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMV-------RKGECEASIAKKEMVEA 451
           +A      ++++  ++SI             +   +       R      + A+  + + 
Sbjct: 65  LASAAQDFMELQA-LQSIMTSLLRRPPRLAELAEAIHCDEDALRLRLDAGNRARAILAQK 123

Query: 452 NLRLVISVAKKY----------------TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           N RLV++ A K+                 +  L F D +  G  GLM+   KF    GY+
Sbjct: 124 NYRLVVACA-KWACKNGVGGGGAGSGHDGSYELAFEDALTAGMEGLMRGIHKFRPDSGYR 182

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKK 555
            STY  WW++ +I ++++ QS  +++P+ +   +  +V    R++      PT E +A +
Sbjct: 183 LSTYCTWWIRMSIRKTLSRQSTALQLPLSVLQSVEALVSARLRLTKPGASPPTDEAVAAE 242

Query: 556 LAMPVEGVRKVLKITKEPISL 576
           L   +  +R      +   S+
Sbjct: 243 LGWSMTRIRNADAARRFATSI 263


>gi|266623350|ref|ZP_06116285.1| RNA polymerase sigma factor WhiG [Clostridium hathewayi DSM 13479]
 gi|288864870|gb|EFC97168.1| RNA polymerase sigma factor WhiG [Clostridium hathewayi DSM 13479]
          Length = 131

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 6/105 (5%)

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQF---LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + +++   L +V S A +       F    DLI +G + LM+  +++D   G +F TYA 
Sbjct: 27  RNKLIVHFLPIVRSAAAQLRGMAGSFTEEEDLIDQGVLALMECLDRYDASKGAQFETYAF 86

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
             V+ A+   I  Q          +    KV      ++++  RE
Sbjct: 87  IRVRGAMIDYIRSQDWVPHRARSFQK---KVDEAYSMLAHEKMRE 128


>gi|312794234|ref|YP_004027157.1| RNA polymerase, sigma 70 family subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181374|gb|ADQ41544.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 206

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 100/238 (42%), Gaps = 50/238 (21%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
              +S+ E + +V  +++       A +E++ A   L+IS+A KY N+   F DL QEG 
Sbjct: 1   MFKLSLDEQKELVCRIKQ---GDKKAAEELIRAYEPLIISIASKY-NKPDIFEDLKQEGA 56

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           + +++AA+KFD  LG  F T A++++K+   R +                         +
Sbjct: 57  VAILQAAQKFDESLGVSFITLAVYYIKRNTDRCV-------------------------K 91

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
            S  I+      +      + +E V                  D++   + D I+D    
Sbjct: 92  RSQTIRPPFNKFDAIVPQVISMESVINANSYA-----------DDEELKVKDTIQDT--- 137

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
             ++   Q    E   +++  LT  E+++L     +     ++L+E+ ++  +T +++
Sbjct: 138 --INVEEQVVHNEYLKKLVDKLTDEEKKIL-----LLRIKQYSLKEIAEKLGLTEKQV 188


>gi|237745256|ref|ZP_04575737.1| predicted protein [Fusobacterium sp. 7_1]
 gi|229432485|gb|EEO42697.1| predicted protein [Fusobacterium sp. 7_1]
          Length = 200

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 41/245 (16%), Positives = 90/245 (36%), Gaps = 60/245 (24%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E + ++ ++R+ +   + A ++++E  L  +  +  K+ N      D  QEG +G+ +A
Sbjct: 1   MESKEVLELIREAKKGNNEATEKLIERYLNTIRKINHKWGNT----DDGFQEGILGIYQA 56

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
            + +D     KF T+  ++V+  I +                     + +   R+   + 
Sbjct: 57  IKTYDENYNTKFMTHLYFYVEAKIRKY--------------------IDKERYRVPQYVI 96

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
                 E  +     +E                              IED N      + 
Sbjct: 97  ESIKKGEQERVYFSELENFE---------------------------IEDAN-----INN 124

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
                +    +VL   T +E+ V+   F  G    +T EEV ++  ++R+ +  I+ +A 
Sbjct: 125 ENLENKVLIEKVLNYCTDQEKTVINYLFFEG----YTGEEVAQKLGISRQWVHTIKHRAF 180

Query: 665 RKLKH 669
            K+++
Sbjct: 181 EKIRN 185


>gi|78212818|ref|YP_381597.1| DNA-directed RNA polymerase specialized sigma subunit-like
           [Synechococcus sp. CC9605]
 gi|78197277|gb|ABB35042.1| DNA-directed RNA polymerase specialized sigma subunit-like
           [Synechococcus sp. CC9605]
          Length = 183

 Score = 49.5 bits (116), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/139 (20%), Positives = 56/139 (40%), Gaps = 2/139 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAE 486
           RH+    R+        + +    +L L    A++   RG  +F DL+QE  +GL++  +
Sbjct: 15  RHLRHESRRVLPPYIARRNQQALEHLGLAHCAARRQQQRGPEEFDDLLQESRVGLIRGVD 74

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
           +FD     K S+Y +      I     D+S  I++           ++  R      +  
Sbjct: 75  RFDPQRRVKPSSYLLSRATGQILHYRRDRSRMIKVHGGCV-LYAAGMKIQREREQNTQPS 133

Query: 547 PTPEEIAKKLAMPVEGVRK 565
            +  E+A  L++  E   +
Sbjct: 134 LSDLELATALSVLPERWSE 152


>gi|284097320|ref|ZP_06385455.1| hypothetical protein POR_0044 [Candidatus Poribacteria sp. WGA-A3]
 gi|283831170|gb|EFC35145.1| hypothetical protein POR_0044 [Candidatus Poribacteria sp. WGA-A3]
          Length = 119

 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 24/52 (46%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           + E   D  +        +             TDDPVR+YLREMGS+ LLSR
Sbjct: 68  EPESVSDKTEEQEDVLEKNAPEIDLTPGDLSRTDDPVRLYLREMGSVSLLSR 119


>gi|322421804|ref|YP_004201027.1| hypothetical protein GM18_4340 [Geobacter sp. M18]
 gi|320128191|gb|ADW15751.1| hypothetical protein GM18_4340 [Geobacter sp. M18]
          Length = 1030

 Score = 49.1 bits (115), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
            +VLR R  +   +   L E+G+++ VT ERIRQ+E+K +  LK P   + L  +L
Sbjct: 321 RQVLRSRLRLVDGSKCQLRELGRRYGVTGERIRQMESKVMAVLKSPKGLRHL-DYL 375


>gi|108759609|ref|YP_629469.1| putative RNA polymerase sigma-70 factor [Myxococcus xanthus DK
           1622]
 gi|108463489|gb|ABF88674.1| putative RNA polymerase sigma-70 factor [Myxococcus xanthus DK
           1622]
          Length = 353

 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 33/214 (15%), Positives = 72/214 (33%), Gaps = 26/214 (12%)

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYK-FSTYAMWWVKQAITRSIADQSCTIRIP--VH 524
           L   DL Q   + +++A  K+D   G + F   A +  + A  +        + +    H
Sbjct: 161 LSPDDLAQVAAMAMLRAVSKYDATRGRQSFGQVAYFRARAACEQYARLHGTDVHLSDGEH 220

Query: 525 MRDKIHKVVRTARR--MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
            R  +  +    R     +++       + A      V+ +   L+              
Sbjct: 221 KRRTVRSIRSNERNVVRVHRMDIPSHFSDGASADDSWVDELESALREMSCL--------- 271

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
                      D +  +P    + A  R      +  L P +  ++   FGI      ++
Sbjct: 272 -----------DADEETPEAKLLAAERRALVFDAVRRLAPEQRELVSRVFGINR-PAQSV 319

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             V + +   + RI ++ A+A+ +L+     + L
Sbjct: 320 RSVAEAWKAPKSRIDRMLARALAELREALVRQDL 353


>gi|197250155|ref|YP_002147819.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197213858|gb|ACH51255.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 68

 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 21/60 (35%), Positives = 38/60 (63%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           +  L  ++  VL  RFG+      TLE+VG++  +TRER+RQI+ + +R+L+   +++ L
Sbjct: 1   MFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGL 60


>gi|71277215|gb|AAZ29817.1| RpoD [Pseudomonas tremae]
          Length = 151

 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDSKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|331011085|gb|EGH91141.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 83

 Score = 49.1 bits (115), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           ++ P         +      +A+L  RE  VL     +  + +  L+E+G+   V+  R+
Sbjct: 7   SLEPSRDLEDERFQAALADAIANLPERERLVL----ALYYDEELNLKEIGEVLGVSESRV 62

Query: 657 RQIEAKAIRKLK 668
            Q+ ++   +L+
Sbjct: 63  SQLHSQCAARLR 74


>gi|257463359|ref|ZP_05627755.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. D12]
          Length = 155

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 6/121 (4%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++R  +     A+ E++E N+ LV  + + Y        D  QEG +    A +KFD   
Sbjct: 1   LIRLAKLGDIEARNELIEKNINLVHKINRMYG----SSEDGFQEGILAFCHAIDKFDETK 56

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPE 550
             K S+YA  W++Q I R    +   +   V   M  +  K+         K + E T E
Sbjct: 57  NVKLSSYAFHWIRQKIKRYREREKYRLPAHVIEKMSKEERKIRIDFEYRDFKSEDETTIE 116

Query: 551 E 551
           E
Sbjct: 117 E 117


>gi|317132052|ref|YP_004091366.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470031|gb|ADU26635.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 245

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 38/87 (43%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
             +  +       A  ++V + +  + + +      GL+  D++QEG +GL+ A   F  
Sbjct: 58  AELAARACAGDRDAMADLVSSFVPFIRAHSVPVAAAGLEADDMMQEGMLGLLGAVRHFCP 117

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSC 517
             G  F  YA   +K+ +  ++   +C
Sbjct: 118 QNGVPFRAYAHICIKRRMASAVRRATC 144


>gi|167767099|ref|ZP_02439152.1| hypothetical protein CLOSS21_01617 [Clostridium sp. SS2/1]
 gi|167711074|gb|EDS21653.1| hypothetical protein CLOSS21_01617 [Clostridium sp. SS2/1]
          Length = 1305

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 594  DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
            + +++   ++           + L  LT +E++++ + +GI  +    + E+   + ++ 
Sbjct: 1227 EPDSIIYEENWDMICNIADLKKFLNILTKKEQKIICLYYGIECDR-RKIGEIANVYGISG 1285

Query: 654  ERIRQIEAKAIRKLKHPSR 672
            +R+ QI  + + K+K   R
Sbjct: 1286 QRVSQIIKRVLEKIKKYLR 1304


>gi|218905476|ref|YP_002453310.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218536250|gb|ACK88648.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 100

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +   L D ++ ++        +   L E     +  L  RE+ V+  RFG+G++ + T
Sbjct: 1   MGNEISLIDILKSESEDVIDMIQLSMEL-EKIKEYIDILDEREKEVIVKRFGLGLDKEKT 59

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             E+ K   ++R  + +IE +A+ K+ H
Sbjct: 60  QREIAKALGISRSYVSRIEKRALMKMFH 87


>gi|258510244|ref|YP_003183678.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257476970|gb|ACV57289.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 191

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           E     E    L   + D +A +P   A Q++LR    + LA L   + +V+   +  G 
Sbjct: 91  ERRQQHESGEELFPILPD-HAPTPDRVAEQSDLRSRIRQALAKLPEEQRQVVEWMYFQGY 149

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
             +   E  G      + R R     A++KL+   +S
Sbjct: 150 TQNEIAERFGWSLGTVKSRARL----AMQKLRDELQS 182


>gi|284043155|ref|YP_003393495.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947376|gb|ADB50120.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
          Length = 216

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/93 (21%), Positives = 34/93 (36%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++   +     A   +V      V   A  Y   G    DLIQEG +GL KA   +    
Sbjct: 19  LIALAKQGNPDAYDRLVRRYYGFVRLKASSYFLAGGDADDLIQEGLVGLYKAIRDYRTDR 78

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              F  +A   + + I  ++   +     P++ 
Sbjct: 79  ESSFRNFAELCITRQIITAVKTATRNKHTPLNQ 111


>gi|71277209|gb|AAZ29814.1| RpoD [Pseudomonas syringae pv. ciccaronei]
          Length = 151

 Score = 48.7 bits (114), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|242089065|ref|XP_002440365.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
 gi|241945650|gb|EES18795.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
          Length = 182

 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           M+     L   +A+ YT  G     L+Q G IG++  +EKFD   G +FSTY  +W+++ 
Sbjct: 1   MLVTTEWLFSYIARTYTGMGTALDKLLQAGKIGVLDGSEKFDNRKGCRFSTYVKYWIRKG 60

Query: 508 I 508
           +
Sbjct: 61  M 61


>gi|213417805|ref|ZP_03350915.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
          enterica serovar Typhi str. E01-6750]
          Length = 36

 Score = 48.7 bits (114), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 17/31 (54%)

Query: 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEV 58
              K ++   +++GY+T  E+N  LP D V
Sbjct: 6  QSQLKLLVTRGKEQGYLTYAEVNDHLPEDIV 36


>gi|258511073|ref|YP_003184507.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Alicyclobacillus acidocaldarius subsp. acidocaldarius
           DSM 446]
 gi|257477799|gb|ACV58118.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Alicyclobacillus acidocaldarius subsp. acidocaldarius
           DSM 446]
          Length = 176

 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 443 IAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
            A++ +V  N RLV  VA ++ +R    G++F DL+  G +GL KAA  +D     KFS 
Sbjct: 3   AAQEVLVVENQRLVYFVANRFRHRAVAAGIEFDDLVATGMLGLCKAARVYDPSRA-KFSV 61

Query: 499 YAMWWVKQAI 508
            A+  ++  +
Sbjct: 62  LAVRCIENEM 71


>gi|237734715|ref|ZP_04565196.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382043|gb|EEO32134.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 97

 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 429 HIVSMVRKGECEASIA-KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
               ++ + +   + A K  +V  N +LV+S+A+++  R     DL Q G IGL+KA E 
Sbjct: 22  ETYKLIDEYQATKNEAIKDRLVNDNTKLVLSMARRFYGREDSMDDLFQVGMIGLIKAIEN 81

Query: 488 FDWCLGYKFSTYAMW 502
           F+   G KFSTYA+ 
Sbjct: 82  FNTSFGLKFSTYAVP 96


>gi|319644909|ref|ZP_07999142.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|319644913|ref|ZP_07999146.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392718|gb|EFV73512.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392722|gb|EFV73516.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 78

 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 33/59 (55%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   + +  L  RE+ V+  RFG+ +  + T  E+ K+  ++R  + +IE +A+ K+ H
Sbjct: 4   EKVKKYIDILDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFH 62


>gi|71277205|gb|AAZ29812.1| RpoD [Pseudomonas syringae pv. mori]
          Length = 151

 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|221481927|gb|EEE20293.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 1002

 Score = 48.3 bits (113), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 70/199 (35%), Gaps = 20/199 (10%)

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
              W++ A+      +    + P     +  +  + +  +  ++ REPT  E+A +L + 
Sbjct: 764 YWLWMRTAMVDWEQQKRQVTQFPWRWWKEAARGRKASHGLYAELGREPTEAEVADRLGIS 823

Query: 560 VEGVRKVLKITKEPISLET--------PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           ++  R +   TK   SLET           ++    +GD +  + ++       +  L  
Sbjct: 824 LDKWRDISVATKAATSLETELGGPHGSHDPNDRQDTVGDLLVSEESLESESQMFETELET 883

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG--KQFCVTRERIRQI--------- 659
           +        L P E ++++                   K+   TR +  Q          
Sbjct: 884 QVLDLAAECLEPDEFQMIKALISEPHARSEATANSAAWKEDNTTRAQTLQFMVGDCVDEK 943

Query: 660 EAKAIRKLKHPSRSKKLRS 678
             KAI+K+K     + L S
Sbjct: 944 LKKAIQKMKEAEVKRNLES 962


>gi|253581342|ref|ZP_04858568.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836706|gb|EES65240.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 286

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 28/135 (20%), Positives = 60/135 (44%), Gaps = 8/135 (5%)

Query: 378 ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
           E     + +   +   +    +    +    + + ++ +S    IS  E  + +  +   
Sbjct: 29  ENSDKKLEFDSHYTGSKELEDMEEFAEE--TVIDYLEELSNMEVISDEEESNYLKNISDF 86

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +      K++++  NL  V S+A  Y   G+ ++D++QEG +GL+KA + FD      F 
Sbjct: 87  D------KEKIIVKNLNEVASIAFYYVKTGIAYMDIVQEGTVGLIKAVDYFDPDKNGDFK 140

Query: 498 TYAMWWVKQAITRSI 512
            Y+ +W+ + I   I
Sbjct: 141 NYSKYWIVREIVLYI 155


>gi|293400037|ref|ZP_06644183.1| RNA polymerase sigma factor, sigma-70 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291306437|gb|EFE47680.1| RNA polymerase sigma factor, sigma-70 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 262

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 37/265 (13%), Positives = 79/265 (29%), Gaps = 60/265 (22%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKA 484
             + ++ +     + A   + E N +L+  + +K+          F D++QE  I   K 
Sbjct: 2   ECIELIIRYRNGDNTAFDYLFERNKKLIYFITRKHEWMIPYLHYDFDDILQESYIIFTKC 61

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              FD    YKF+TY    +              +    +      +  +    +     
Sbjct: 62  INDFDISSDYKFTTYLGNSI-----------HWGLNKLFNSATNAKRYNKNDDSIIQ--- 107

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
                                        ISLE    D+    L   + D N+ + +   
Sbjct: 108 ----------------------------DISLEQKFNDDQD--LLSVLSDPNSEAEMKLF 137

Query: 605 IQANLRETTTRVLASLT-----------PREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653
           ++    +   +    L             R + +++  +GI        +E+      + 
Sbjct: 138 MEMEFNDQLKKDTRLLLNQVFDVQKDGVQRIKYIIQSNYGIDQ-EVKNAKELSILLNCSY 196

Query: 654 ERIRQIEAKAIRKLKHPSRSKKLRS 678
           + I Q+  K IR +++    K    
Sbjct: 197 QNICQLRNKGIRMIRNSHYGKTYME 221


>gi|71277183|gb|AAZ29801.1| RpoD [Pseudomonas syringae pv. tabaci]
 gi|71277185|gb|AAZ29802.1| RpoD [Pseudomonas syringae pv. aesculi]
 gi|71277189|gb|AAZ29804.1| RpoD [Pseudomonas savastanoi]
 gi|71277199|gb|AAZ29809.1| RpoD [Pseudomonas syringae pv. phaseolicola]
 gi|71277207|gb|AAZ29813.1| RpoD [Pseudomonas savastanoi]
          Length = 151

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|237808347|ref|YP_002892787.1| sigma-70 region 4 domain-containing protein [Tolumonas auensis DSM
           9187]
 gi|237500608|gb|ACQ93201.1| sigma-70 region 4 domain protein [Tolumonas auensis DSM 9187]
          Length = 913

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK-LKHPS 671
           E+ +  +   +  N   TLEE+G  + VTRERIRQ+E+ AI K LK+PS
Sbjct: 404 EKELATIVCRLLSNNKKTLEELGAIYGVTRERIRQLESLAIAKLLKNPS 452


>gi|323183986|gb|EFZ69369.1| sigma-70, region 4 family protein [Escherichia coli 1357]
          Length = 390

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 32/61 (52%)

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                + SL+ +  + + +      ++ H+L ++  +  ++RER+RQ++ +A+  L   S
Sbjct: 2   LIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERALGLLAAKS 61

Query: 672 R 672
           R
Sbjct: 62  R 62


>gi|27383248|ref|NP_774777.1| sigma-70 subunit [Bradyrhizobium japonicum USDA 110]
 gi|27356422|dbj|BAC53402.1| bsr8137 [Bradyrhizobium japonicum USDA 110]
          Length = 65

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 31/53 (58%)

Query: 31 WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
           +  I L R++G+VT E+LN  LP   +  + +E  +  LS+ GIN++D D  
Sbjct: 13 IQAAIGLGRRKGFVTFEQLNQLLPAATIEPKDIEAIMQALSDEGINLIDDDQA 65


>gi|283479514|emb|CAY75430.1| RNA polymerase sigma factor rpoS pseudogene [Erwinia pyrifoliae DSM
           12163]
          Length = 136

 Score = 48.3 bits (113), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 32/86 (37%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L       N           A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEVFDEKALVGNEPGDNDLAEEDLLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTF 164
           E+  A+R   G       + ES L  
Sbjct: 76  EVFFARRALRGDVPSRRRMIESNLRL 101


>gi|320528386|ref|ZP_08029548.1| segregation protein SMC [Solobacterium moorei F0204]
 gi|320131300|gb|EFW23868.1| segregation protein SMC [Solobacterium moorei F0204]
          Length = 981

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 51/302 (16%), Positives = 100/302 (33%), Gaps = 15/302 (4%)

Query: 166 ALIIWRDELNDGTTLLREI-IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
             +   +          +I I+LE  + P  +            Q+ E+        D++
Sbjct: 177 ESLSKLERTKANLDRSNDILIELEKQVSPLKRQARKAEIYREKKQRLEEIEISVLVQDIE 236

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
               DIESA K   D  +K      + + +E  L E     + TL    + L+ ++M   
Sbjct: 237 SIHADIESAKKALFDIETKTTMFSTDIQINETKLSESRRQIS-TLDREINDLQDELMKKF 295

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           +EIA +      L +      +   +  K K L   + +        Q R+D L  ++  
Sbjct: 296 NEIAGLEARRTELDEKRKYIVETGTNEQKAKQLAGLIEEARVEFEDRQKRLDDLNTEIRL 355

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            S+++      ++     Y    D    R +  E   + +      P    +      + 
Sbjct: 356 YSQQLSAAAANIVDKRSEY----DQASNRLRSLENRKNVIDQLMRNPFNNQQG-----IR 406

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464
           SI++ +N +  I    G    +   + S   +    A  A    +          A ++ 
Sbjct: 407 SIMENQNALSGILGVIG----QVLQVESGYEEAVSTALGAAMNHIVTVDEQAARDAIRFL 462

Query: 465 NR 466
           NR
Sbjct: 463 NR 464


>gi|154498065|ref|ZP_02036443.1| hypothetical protein BACCAP_02046 [Bacteroides capillosus ATCC
           29799]
 gi|150273055|gb|EDN00212.1| hypothetical protein BACCAP_02046 [Bacteroides capillosus ATCC
           29799]
          Length = 211

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 30/144 (20%), Positives = 57/144 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++  +      +A++ +V    RLV   A+     G    DLIQEG +GL+ A   +D  
Sbjct: 15  ALCMQAASGDPLAEETLVIRYNRLVRVCARPLFLAGGDSEDLIQEGMVGLLSAIRVYDLS 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
            G  F TYA   ++  +  ++   S     P++            +        +    E
Sbjct: 75  KGASFHTYAETCIRNRLLSAVKAASRDKHTPLNNYISFETPFFDGKTDHYAYGTDQERLE 134

Query: 552 IAKKLAMPVEGVRKVLKITKEPIS 575
             + + +  E +R+ L + K  +S
Sbjct: 135 NPETIMIGREELRERLGVLKGQLS 158


>gi|310826034|ref|YP_003958391.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308737768|gb|ADO35428.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 211

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 46/97 (47%), Gaps = 5/97 (5%)

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L  P G  D   L + I D+ A+      I+   ++   + + +L+ R+ +VL   F   
Sbjct: 116 LSAPAGSSDGLTLEEVIADE-AIDLEGCYIEREDQQRLWQSVHALSARQGKVLYQSF--- 171

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
            +   +L ++ K+  VT + +R++  K ++ LK   +
Sbjct: 172 -HESKSLVQICKEMGVTHKAVRKLRDKGLKNLKKSLK 207


>gi|167771908|ref|ZP_02443961.1| hypothetical protein ANACOL_03281 [Anaerotruncus colihominis DSM
           17241]
 gi|167665706|gb|EDS09836.1| hypothetical protein ANACOL_03281 [Anaerotruncus colihominis DSM
           17241]
          Length = 202

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/92 (20%), Positives = 36/92 (39%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + ++ +     A  +++E    LV   A+ Y    +   D+ QEG I L+KA   +    
Sbjct: 17  LAQRAKNGDDEALADLIERYTPLVCMRARAYARGVMDVDDVYQEGMIALLKAVRNYREDT 76

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
              F T+A   V   +  ++         P+ 
Sbjct: 77  AGSFRTFAAVCVNNKMLSAVTAHMRDKNAPMR 108


>gi|262204446|ref|YP_003275654.1| sigma-70 region 4 domain-containing protein [Gordonia bronchialis
           DSM 43247]
 gi|262087793|gb|ACY23761.1| sigma-70 region 4 domain protein [Gordonia bronchialis DSM 43247]
          Length = 289

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E    V+ SL  R+  +L     I         E+     ++RER+ QIE +   +L+ 
Sbjct: 157 EAVADVIGSLDARDRLILED--RILALRPRRQSELAAMLGISRERVAQIERQLRARLRE 213


>gi|237837087|ref|XP_002367841.1| sigma-70, region 3 domain containing protein [Toxoplasma gondii
           ME49]
 gi|211965505|gb|EEB00701.1| sigma-70, region 3 domain containing protein [Toxoplasma gondii
           ME49]
          Length = 1002

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 69/199 (34%), Gaps = 20/199 (10%)

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
              W++ A+      +    + P     +  +  + +  +  ++ REPT  E+A +L + 
Sbjct: 764 YWLWMRTAMVDWEQQKRQVTQFPWRWWKEAARGRKASHGLYAELGREPTEAEVADRLGIS 823

Query: 560 VEGVRKVLKITKEPISLET--------PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           ++  R +   TK   SLET           ++    +GD +  + ++       +  L  
Sbjct: 824 LDKWRDISVATKAATSLETELGGPHGSHDPNDRQDTVGDLLVSEESLESESQMFETELET 883

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG--KQFCVTRERIRQI--------- 659
           +        L P E ++++                    +   TR +  Q          
Sbjct: 884 QVLDLAAECLEPDEFQMIKALISEPHARSEATANSAAWNEDNTTRAQTLQFMVGDCVDEK 943

Query: 660 EAKAIRKLKHPSRSKKLRS 678
             KAI+K+K     + L S
Sbjct: 944 LKKAIQKMKEAEVKRNLES 962


>gi|153938326|ref|YP_001391685.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           F str. Langeland]
 gi|152934222|gb|ABS39720.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. Langeland]
 gi|295319714|gb|ADG00092.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. 230613]
          Length = 183

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 66/200 (33%), Gaps = 54/200 (27%)

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            + DL QEG +GLMKAA +FD     KFSTYA  +V   I R I                
Sbjct: 27  SYEDLFQEGCLGLMKAANRFDSSRRIKFSTYAYPYVDGQILRMIESDKWYG--------- 77

Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588
                                              RK       P SL+  I   D    
Sbjct: 78  ---------------------------------KNRKERLEGIVPYSLDAAIDGLDNE-- 102

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
             +I+           I+         ++ SL  + + ++ M +        T  E+ ++
Sbjct: 103 IAYIDSIGNYDLNFEKIE------IKTLIDSLPEKLKEIMEMYY----MQSFTQAEIARK 152

Query: 649 FCVTRERIRQIEAKAIRKLK 668
              +R  + +++ +A+  L+
Sbjct: 153 IGCSRSNVTRLKIEALDYLR 172


>gi|71277175|gb|AAZ29797.1| RpoD [Pseudomonas syringae pv. syringae]
 gi|71277177|gb|AAZ29798.1| RpoD [Pseudomonas syringae pv. syringae]
          Length = 151

 Score = 47.9 bits (112), Expect = 0.005,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAAKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|304399206|ref|ZP_07381073.1| sigma-70 region 1.2 [Pantoea sp. aB]
 gi|304353260|gb|EFM17640.1| sigma-70 region 1.2 [Pantoea sp. aB]
          Length = 113

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 37/96 (38%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L    ++ +     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGAEIFDEKALVENEASDSDVAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           E+  A+R   G       + ES L     I     +
Sbjct: 76  EVFFARRALRGDIPSRRRMIESNLRLVVKIARLTAI 111


>gi|332653065|ref|ZP_08418810.1| RNA polymerase sigma-H factor [Ruminococcaceae bacterium D16]
 gi|332518211|gb|EGJ47814.1| RNA polymerase sigma-H factor [Ruminococcaceae bacterium D16]
          Length = 212

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 31/128 (24%), Positives = 48/128 (37%), Gaps = 5/128 (3%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +V    RLV + A+     G    DL QEG +GL+ A   FD      F TYA   V+  
Sbjct: 37  LVRRYGRLVRACARPLFLAGGDSEDLFQEGMLGLLSAIRGFDARRDASFRTYAEVCVRNR 96

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
           +  ++        +P       H V               + EE  + + +  E +R+ L
Sbjct: 97  LYSAVRAAQGDKHLP-----LNHSVSFEPPLFDGPNAYLFSSEESPEDVIIGREELRERL 151

Query: 568 KITKEPIS 575
              K  +S
Sbjct: 152 DALKGQLS 159


>gi|237736225|ref|ZP_04566706.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
 gi|229421778|gb|EEO36825.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
          Length = 232

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/115 (23%), Positives = 49/115 (42%), Gaps = 6/115 (5%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            +  NL LV S+A  Y   G+ +LD++QEG +GL+K  E ++      F  Y  +W+ + 
Sbjct: 40  FIVQNLPLVASIAFNYLREGVAYLDVVQEGTMGLIKGIENYNGEKHGDFENYKKYWIIRE 99

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562
           I   I            ++++     +  R    K+  E    E   ++ +  E 
Sbjct: 100 IVLFI------NNKITDIKNEFKSFFKDKRENFGKVGHEHEEVEDKTEVYLTEED 148


>gi|260768755|ref|ZP_05877689.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           CIP 102972]
 gi|260616785|gb|EEX41970.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           CIP 102972]
 gi|315180458|gb|ADT87372.1| flagellar biosynthesis sigma factor [Vibrio furnissii NCTC 11218]
          Length = 231

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 39/225 (17%), Positives = 82/225 (36%), Gaps = 25/225 (11%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           ++ +E++L L+     KY          DL Q   +  +    KFD  +   F       
Sbjct: 24  QQALESHLYLIQRSLNKYRGVVDPDTLDDLRQIALMAFILELRKFDHVINDDFLKSVTVR 83

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           +K AI   +  +     +    R   +K+  T R+   K  R PT  +I  +L +  E  
Sbjct: 84  LKGAIIDELRARD---YLSREQRSLSNKIKDTERKFMAKYGRSPTQADICSQLNISSEEY 140

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
              +                    + D +E    V+  + + +  +     + L  L P 
Sbjct: 141 MNAII----------------DLTMSDDVELFELVNHAEDSQKEFISLMLEKELKQLAPS 184

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            ++VL   + +G     + +E  +   ++  ++ +I+ K I  ++
Sbjct: 185 IQKVLYFIYVMG----LSTQETAQVLEISEMKVHRIKHKGIEIIR 225


>gi|168335032|ref|ZP_02693146.1| 5'-nucleotidase/2' 3'-cyclic phosphodiesterase and related
            esterases-like protein [Epulopiscium sp. 'N.t. morphotype
            B']
          Length = 3779

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 44/292 (15%), Positives = 85/292 (29%), Gaps = 39/292 (13%)

Query: 47   EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
            +E+     P        ++ V         V D  +   +E  +++        + +  +
Sbjct: 2473 DEVVDAFDP------AADEVVDAFDLATDEVEDEANPATDEVEDEADPATDEVEDEADPI 2526

Query: 107  QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR--IEAGRAMMMASLCESPLTF 164
                  A   T D V               E E   A    I+A          E+    
Sbjct: 2527 ADEVIDAFDPTADEV---------------EDEADPATDEVIDAFDQAADEVEDEADPIA 2571

Query: 165  QALII---------------WRDELNDGTTLL-REIIDLEACIGPESKGGFFHGTEGHSY 208
              +I                  DE+ D    +  E+ID       E +       +    
Sbjct: 2572 DEVIDAFDPTADEVEDEVDPVADEVEDEADPIADEVIDAFDPATDEVEDEANPAVDKVED 2631

Query: 209  QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            +    + + ++  +    E + E+     + +     +  E  +      DE ED++   
Sbjct: 2632 EADPATDEVEDEANPSTDEVEDEADPATDEVEDEADPATDEVEDEANPATDEVEDEANPV 2691

Query: 269  LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               +ED++ P      DE+  V  E+    D A++   D       KV  E 
Sbjct: 2692 TDEVEDEVDPAADEVEDEVDPVADEVVDAFDPAIDEVVDAFDPAADKVEDEA 2743



 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 33/251 (13%), Positives = 72/251 (28%), Gaps = 26/251 (10%)

Query: 54   PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
            P  +   ++ +     + +      D  + E    +++  D A+  ++            
Sbjct: 2646 PSTDEVEDEADPATDEVEDEADPATDEVEDEANPATDEVEDEANPVTDEVEDEVDPAADE 2705

Query: 114  DRSTDDPVRMYLREMGSIELLSREGEI------AIAKRIEAGRAMMMASLCESPLTFQAL 167
                 DPV                 E+      AI + ++A          E+      +
Sbjct: 2706 VEDEVDPV---------------ADEVVDAFDPAIDEVVDAFDPAADKVEDEADPIADEV 2750

Query: 168  IIWRDELNDGT-----TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD 222
            +   D+  D T         E++D       E         +    +    + + ++  D
Sbjct: 2751 VDAFDQAADETDDAFDQAADEVVDAFDQATDEVDEEVDPVADEVEDEVDPSTDEVEDEAD 2810

Query: 223  VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMC 282
                E D        + +     +  E  +  +   DE ED++      +ED+  P    
Sbjct: 2811 PAADETDDAFDPATDEVEDEADPAADEVEDEADPVADEVEDEADPIADEVEDEANPVTDE 2870

Query: 283  ALDEIAEVYRE 293
              DE+     E
Sbjct: 2871 VEDEVGSTTDE 2881



 Score = 41.4 bits (95), Expect = 0.54,   Method: Composition-based stats.
 Identities = 41/276 (14%), Positives = 86/276 (31%), Gaps = 35/276 (12%)

Query: 47   EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
            +E+     P    ++++ED     ++    VVD  D   +E  +++  +A    ++    
Sbjct: 2209 DEVVDAFDPA---TDKVEDEANPATDE---VVDAFDPAVDEVEDEADPIADEVDDAFDPS 2262

Query: 107  QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
                  A     D V                        ++A        +         
Sbjct: 2263 TDEVVDAFDPVADEV------------------------VDAFDQATDEVIDAFDPATDE 2298

Query: 167  LIIWRDELNDG-----TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            +    + + D           E+ D    I  E +  F   T+         + +  +  
Sbjct: 2299 VEDEANPVTDEVEDEANPATDEVEDEADPIADEVEDAFDPATDEVVDAFDPAADEVIDAF 2358

Query: 222  DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
            D    E D E+     +   +   +  E  +  +   DE ED++      +ED+  P   
Sbjct: 2359 DQAADEVDEEADQAADEVVDAFDQAADEVVDAFDPATDEVEDEADPATDEVEDEANPATD 2418

Query: 282  CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
               DE+ +   E+    D A +  +DE   +  +V+
Sbjct: 2419 EVEDEVDQATDEVVDAFDQATDEVEDEADLIADEVI 2454


>gi|71277195|gb|AAZ29807.1| RpoD [Pseudomonas syringae pv. maculicola]
          Length = 151

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEKDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|225181958|ref|ZP_03735391.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiobacter alkaliphilus AHT 1]
 gi|225167320|gb|EEG76138.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiobacter alkaliphilus AHT 1]
          Length = 71

 Score = 47.9 bits (112), Expect = 0.006,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 33/68 (48%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L      V+  L  RE  VL MRFG+ M    T +E+ K   ++R  + +IE K I K+
Sbjct: 1   MLEAKLYEVIKKLKLRERTVLAMRFGLPMGRRKTQKEIAKSLGISRSYVSRIEKKVIAKI 60

Query: 668 KHPSRSKK 675
               R ++
Sbjct: 61  AEEFRQER 68


>gi|54261990|emb|CAD65853.1| Flagellin A [Escherichia coli]
 gi|54261993|emb|CAD65855.1| Flagellin A [Escherichia coli]
 gi|54261996|emb|CAD65857.1| Flagellin A [Escherichia coli]
 gi|54261999|emb|CAD65859.1| Flagellin A [Escherichia coli]
 gi|54262002|emb|CAD65861.1| Flagellin A [Escherichia coli]
 gi|54262005|emb|CAD65863.1| Flagellin A [Escherichia coli]
 gi|54262008|emb|CAD65865.1| Flagellin A [Escherichia coli]
 gi|54262011|emb|CAD65867.1| Flagellin A [Escherichia coli]
          Length = 77

 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 437 GECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLG 493
              E  + K  + +  + LV   A +   R    ++  DL+Q G IGL+ A E++D   G
Sbjct: 5   YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQG 64

Query: 494 YKFSTYAMWWVKQ 506
             F+TYA+  ++ 
Sbjct: 65  TAFTTYAVQRIRG 77


>gi|310828140|ref|YP_003960497.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308739874|gb|ADO37534.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 209

 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 77/239 (32%), Gaps = 56/239 (23%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           ++V++G+     A + ++ A   ++ SV   Y     +  D  QE     ++    F   
Sbjct: 24  ALVKRGQQGDKTAVEALLMAFKPMLWSVVSHYVYNREELEDAYQEACAVFIEGVRDFALD 83

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F T+    +                         + + R   R S  +        
Sbjct: 84  ARIYFQTFMQGRL-----------------------VHYFLKRREGRFSASL-------- 112

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS-HLGDFIEDKNAVSPLDSAIQANLR 610
                                 +SL+ P+   D +  L + I D+ A     + + A  +
Sbjct: 113 -------------------AGTLSLDRPVEGADGAVALAELILDEKA-DVEGACVAAEQQ 152

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +   R    L+P +  VLR ++        TL E+  Q  V+   I Q   +A+  LK 
Sbjct: 153 KALLRAYRKLSPGQREVLRYQYL----EKGTLSELAAQKGVSPAAITQTHKRALAALKR 207


>gi|119490024|ref|ZP_01622648.1| hypothetical protein L8106_20630 [Lyngbya sp. PCC 8106]
 gi|119454176|gb|EAW35328.1| hypothetical protein L8106_20630 [Lyngbya sp. PCC 8106]
          Length = 40

 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/29 (58%), Positives = 25/29 (86%)

Query: 653 RERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           RER+RQIEAKA++KL+ P RS ++R +L+
Sbjct: 5   RERVRQIEAKALQKLRQPKRSNRVRHYLE 33


>gi|71277213|gb|AAZ29816.1| RpoD [Pseudomonas avellanae]
          Length = 151

 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|162451917|ref|YP_001614284.1| hypothetical protein sce3644 [Sorangium cellulosum 'So ce 56']
 gi|161162499|emb|CAN93804.1| hypothetical protein predicted by Glimmer/Critica [Sorangium
           cellulosum 'So ce 56']
          Length = 258

 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 20/41 (48%), Positives = 27/41 (65%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           TLE+VG    +TRERIRQ+E KA+ KL+       LR ++D
Sbjct: 154 TLEDVGAIMNLTRERIRQVEVKALAKLEALKDMMALRDYVD 194


>gi|71277211|gb|AAZ29815.1| RpoD [Pseudomonas syringae pv. theae]
          Length = 151

 Score = 47.5 bits (111), Expect = 0.007,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|118443493|ref|YP_877626.1| sigma-70 region 2 domain-containing protein [Clostridium novyi NT]
 gi|118133949|gb|ABK60993.1| Sigma-70 region 2 domain protein [Clostridium novyi NT]
          Length = 182

 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 58/146 (39%), Gaps = 13/146 (8%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I  +++K + +   A K ++E     ++   +    +G    DLIQ G + ++KA EK+D
Sbjct: 3   IKELIKKSKAKDEEATKILIEKYRPFILRTMQGVYIKGYDREDLIQIGYVSVIKAIEKYD 62

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                 F+ Y    +K                   +R K+ +    +   S +   E T 
Sbjct: 63  LDSKTPFTAYVCNSIKNNYY-------------YKIRGKVKENYDVSYEKSIEEGFEYTN 109

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPIS 575
           EE  +   +    ++++ +  K+  S
Sbjct: 110 EEDIENEVLKNFEIKRLRQALKKLSS 135


>gi|325662599|ref|ZP_08151199.1| hypothetical protein HMPREF0490_01939 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471096|gb|EGC74322.1| hypothetical protein HMPREF0490_01939 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 246

 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 45/222 (20%), Positives = 91/222 (40%), Gaps = 17/222 (7%)

Query: 350 MHNEGELLRLAQSYGIKRDVFLERH--QGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
                E + L   Y + + V ++ +  QG  +       A++    E K ++A  ++ I 
Sbjct: 37  DGLSREQMELVCDYLLSQKVAVKGYVKQGGTVTEKTEEQAEEHYTEEEKRYLARYMEEIK 96

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+ E             E      +        ++A+  ++E  L  V+  AK+  ++ 
Sbjct: 97  TIKAE-------------EAGERQKLFAASIEGDALARGRLIELYLEKVVEAAKEMYHKE 143

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQEGN+ LM A +  +     +     M  V+  +   I +Q+   R    + +
Sbjct: 144 VFLGDLIQEGNVSLMLALD--ELESVEEAHGKIMEEVRAGMQMLIEEQTEVKRRDHTLLE 201

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           K   +    +++  +  R+ T EE++  L MP E +  +L +
Sbjct: 202 KYTDLDDNIKKLKEETGRDVTIEEVSAFLDMPEEEINDILNL 243


>gi|331027981|ref|YP_004421531.1| RNA polymerase sigma factor SigF [Synechococcus phage S-CBS2]
 gi|294805594|gb|ADF42433.1| RNA polymerase sigma factor SigF [Synechococcus phage S-CBS2]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 32/137 (23%), Positives = 61/137 (44%), Gaps = 15/137 (10%)

Query: 445 KKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGY-------KF 496
           ++++   NL L    A +     G+ +  L      GL KAA ++D    +       KF
Sbjct: 14  QQKLAADNLNLARREAWRIQRSTGIDYHTLESVAFEGLCKAAYRYDASRPHPVTGKSMKF 73

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
           S+ A+  ++  +   + D++ ++R+   MR++  K  +   R S       T  EIA  L
Sbjct: 74  SSLAIPTIRGELLHWVRDRTYSMRLSHKMRERWVKGRKLLYRGS-------TDIEIAASL 126

Query: 557 AMPVEGVRKVLKITKEP 573
            + +E  ++V K+   P
Sbjct: 127 GILLEEWQEVRKVCSGP 143


>gi|71277179|gb|AAZ29799.1| RpoD [Pseudomonas syringae pv. syringae]
 gi|71277181|gb|AAZ29800.1| RpoD [Pseudomonas syringae pv. syringae]
          Length = 151

 Score = 47.5 bits (111), Expect = 0.008,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|168185356|ref|ZP_02619991.1| sigma-70 region 2 domain protein [Clostridium botulinum C str.
           Eklund]
 gi|169296292|gb|EDS78425.1| sigma-70 region 2 domain protein [Clostridium botulinum C str.
           Eklund]
          Length = 184

 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 19/80 (23%), Positives = 37/80 (46%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           I  +++K + +   A K ++E     ++   +    +G    DLIQ G + ++KA EK+D
Sbjct: 3   IKELIKKSKAKDEEAIKILIEKYRPFILKTMQGVYIKGYDREDLIQMGYVSIIKAIEKYD 62

Query: 490 WCLGYKFSTYAMWWVKQAIT 509
                 F++Y    +K    
Sbjct: 63  LNSKTPFTSYVCNAIKNNYY 82


>gi|71277193|gb|AAZ29806.1| RpoD [Pseudomonas syringae pv. maculicola]
 gi|71277217|gb|AAZ29818.1| RpoD [Pseudomonas syringae pv. tomato]
          Length = 151

 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|163815060|ref|ZP_02206447.1| hypothetical protein COPEUT_01216 [Coprococcus eutactus ATCC 27759]
 gi|166033464|ref|ZP_02236293.1| hypothetical protein DORFOR_03190 [Dorea formicigenerans ATCC
           27755]
 gi|158449743|gb|EDP26738.1| hypothetical protein COPEUT_01216 [Coprococcus eutactus ATCC 27759]
 gi|166026649|gb|EDR45406.1| hypothetical protein DORFOR_03190 [Dorea formicigenerans ATCC
           27755]
          Length = 217

 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+      L      +   +  DFI D+ A    ++ + A + 
Sbjct: 100 EQYADFYRDRERWRYLQKLDARNSLLSLDGFTDSEGNPLDFIADE-AADIAETVVNAVMV 158

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ +RKL+ 
Sbjct: 159 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILRKLRK 213


>gi|332523817|ref|ZP_08400069.1| sigma-70, region 4 [Streptococcus porcinus str. Jelinkova 176]
 gi|332315081|gb|EGJ28066.1| sigma-70, region 4 [Streptococcus porcinus str. Jelinkova 176]
          Length = 211

 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+      L      +   +  DFI D+ A    ++ + A + 
Sbjct: 94  EQYADFYRDRERWRYLQKLDARNSLLSLDGFTDSEGNPLDFIADE-AADIAETVVNAVMV 152

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ +RKL+ 
Sbjct: 153 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILRKLRK 207


>gi|319757745|gb|ADV69687.1| hypothetical protein SSUJS14_0594 [Streptococcus suis JS14]
          Length = 211

 Score = 47.1 bits (110), Expect = 0.009,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+      L      +   +  DFI D+ A    ++ + A + 
Sbjct: 94  EQYADFYRDRERWRYLQKLDARNSLLSLDGFTDSEGNPLDFIADE-AADIAETVVNAVMV 152

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ +RKL+ 
Sbjct: 153 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILRKLRK 207


>gi|221501380|gb|EEE27159.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 1001

 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 69/199 (34%), Gaps = 20/199 (10%)

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
              W++ A+      +    + P     +  +  + +  +  ++ REPT  E+A +L + 
Sbjct: 763 YWLWMRTAMVDWEQQKRQVTQFPWRWWKEAARGRKASHGLYAELGREPTEAEVADRLGIS 822

Query: 560 VEGVRKVLKITKEPISLET--------PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR- 610
           ++  R +   TK   SLET           ++    +GD +  + ++       +  L  
Sbjct: 823 LDKWRDISVATKAATSLETELGGPHGSHDPNDRQDTVGDLLVSEESLESESQMFETELET 882

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG--KQFCVTRERIRQI--------- 659
           +        L P E ++++                    +   TR +  Q          
Sbjct: 883 QVLDLAAECLEPDEFQMIKALISEPHARSEATANSTAWNEDNTTRAQTLQFMVGDCVDEK 942

Query: 660 EAKAIRKLKHPSRSKKLRS 678
             KAI+K+K     + L S
Sbjct: 943 LKKAIQKMKEAEVKRNLES 961


>gi|71277191|gb|AAZ29805.1| RpoD [Pseudomonas syringae pv. tomato]
          Length = 151

 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 20/196 (10%), Positives = 52/196 (26%), Gaps = 45/196 (22%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
             ++     +      L +++            G+ H  +G +         + +    +
Sbjct: 1   DHILSEYPRVPSEGGRLSDVL-----------SGYIHPDDGIAPPAEVPPPVDPKPVKAE 49

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
             + D E +A    ++      P             D+ + A        +     +  L
Sbjct: 50  GADDDEEESADSCDEEDEVEGGPDPVIAQQRFGAVSDQMEIARKALKKFGRHDKHAIAEL 109

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
             +AE++                                    + L   + + LVE++  
Sbjct: 110 VALAELF----------------------------------MPIKLVPKQFEGLVERVRG 135

Query: 345 ISKRIMHNEGELLRLA 360
             +R+   E  ++ L 
Sbjct: 136 ALQRLRAEERPIMHLC 151


>gi|213422468|ref|ZP_03355534.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 79

 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 9/83 (10%)

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S+  D IED N         +       T  +  L  R + ++R R+ +  +   TL+E+
Sbjct: 1   SNFADGIEDDN--------WEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNKSTLQEL 51

Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
             ++ V+ ER+RQ+E  A++KL+
Sbjct: 52  ADRYGVSAERVRQLEKNAMKKLR 74


>gi|295109457|emb|CBL23410.1| Predicted permease. [Ruminococcus obeum A2-162]
          Length = 1289

 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 36/258 (13%), Positives = 84/258 (32%), Gaps = 4/258 (1%)

Query: 147 EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGH 206
           EAG+  +  +  E     Q L     ++  G T +   I       P+ + G        
Sbjct: 397 EAGKQKIADAKAELDKKQQELTAAIAQVKAGQTTVDTQIAQLNTQIPQLEAGISQLEAAA 456

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
           +       + +  +  V + +  +  A     + + K D+  E A+     L ++  ++ 
Sbjct: 457 AGLNAAQQATDAAQSAVSQAQEAVNVAQAAYDEAKQKADAGDEEAKAQLEVLAQNLGNAQ 516

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L   +  L+     AL    +   +   L++N  +           +  K +L   + 
Sbjct: 517 TALGEADQALKT-AQEALGACQQAAAQKTELENNLADAN---SGLATLQAKKNELAGTLA 572

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +L+ NQ ++D     L    +++   + EL    ++    +       +  E     +  
Sbjct: 573 TLNENQKQLDSGCAALNAEEEKLAPAQKELDANEKTLAASKKQLDASLKKLESSQSQLDA 632

Query: 387 AKDFPEGEWKNFVACEVD 404
            +   +       A E  
Sbjct: 633 NRAKLDSADAQIAANEAK 650


>gi|46371299|gb|AAS90415.1| stationary phase sigma factor [Azomonas macrocytogenes]
          Length = 55

 Score = 47.1 bits (110), Expect = 0.010,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            RFG+  +   TLEEVG++  +TRER+RQI+ +A+++L+       L S
Sbjct: 2   RRFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSS 50


>gi|71277203|gb|AAZ29811.1| RpoD [Pseudomonas syringae pv. garcae]
          Length = 150

 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 19/196 (9%), Positives = 56/196 (28%), Gaps = 46/196 (23%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
             ++     +      L +++            G+    +G +         + +    +
Sbjct: 1   DHILSEYTRVTCEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAAKAE 49

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
             + + ESA    ++D  +    P  A+     + +  + +   L  +    +  +   +
Sbjct: 50  GDDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKLGRDDKHAIAEMV 109

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
                                               L +L   + L   + + LVE++  
Sbjct: 110 -----------------------------------ALAELFMPIKLVPKQFEGLVERVRG 134

Query: 345 ISKRIMHNEGELLRLA 360
             +R+   E  +++L 
Sbjct: 135 ALERLRAQERAIMQLC 150


>gi|266621945|ref|ZP_06114880.1| flagellar biosynthesis sigma factor FliA [Clostridium hathewayi DSM
           13479]
 gi|288866379|gb|EFC98677.1| flagellar biosynthesis sigma factor FliA [Clostridium hathewayi DSM
           13479]
          Length = 103

 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 47/111 (42%), Gaps = 10/111 (9%)

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMR 631
            +S E  + D       D +E  +  +  + ++   +L+ T    + +L  +E  V+ + 
Sbjct: 2   VLSFEAVLQDMTGVIAKDKLEATDIDTKPEESLFYRDLQRTLAEAVEALGDKERLVVSLY 61

Query: 632 FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +      +    E+ +   + + R+ QI  KA++KLK       L  ++ G
Sbjct: 62  Y----YEELKYSEIAEIMGIGQSRVCQIHTKAMKKLKSS-----LEEYVRG 103


>gi|2497599|sp|Q61292|LAMB2_MOUSE RecName: Full=Laminin subunit beta-2; AltName: Full=Laminin-11
            subunit beta; AltName: Full=Laminin-14 subunit beta;
            AltName: Full=Laminin-15 subunit beta; AltName:
            Full=Laminin-3 subunit beta; AltName: Full=Laminin-4
            subunit beta; AltName: Full=Laminin-7 subunit beta;
            AltName: Full=Laminin-9 subunit beta; AltName:
            Full=S-laminin subunit beta; Short=S-LAM beta; Flags:
            Precursor
 gi|1244720|gb|AAC53535.1| laminin beta 2 [Mus musculus]
          Length = 1799

 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 36/311 (11%), Positives = 97/311 (31%), Gaps = 30/311 (9%)

Query: 24   FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
             + ++   +++I+  +            FL  +    + +E     + ++ I        
Sbjct: 1506 VEQANQELRELIQNVK-----------DFLSQEGADPDSIEMVATRVLDISIPASPEQIQ 1554

Query: 84   EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                   + +   +               A++   D  R   R          EGE   A
Sbjct: 1555 RLASEIAERVRSLADVDTILAHTMGDVRRAEQLLQDAHRARSR---------AEGERQKA 1605

Query: 144  KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
            + ++A       +   +    +  ++           ++E +         +        
Sbjct: 1606 ETVQAALEEAQRAQGAAQGAIRGAVVDTQNTEQTLQRVQERMAGAEKSLNSAGERARQLD 1665

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                  K + +         +ET G  +S A+ ++    +            R L E + 
Sbjct: 1666 ALLEALKLKRAGNSLAASTAEETAGSAQSRAREAEKQLREQVGDQY---QTVRALAERKA 1722

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKE 319
            +      A  +QLR     A D +     +L+ LQ+     +++E++    + +   L+ 
Sbjct: 1723 EGVLAAQARAEQLRD---EARDLLQAAQDKLQRLQELEGTYEENERALEGKAAQLDGLEA 1779

Query: 320  KLVKLVGSLSL 330
            ++  ++ +++L
Sbjct: 1780 RMRSVLQAINL 1790


>gi|296226301|ref|XP_002758866.1| PREDICTED: pleckstrin homology-like domain family B member 2
            [Callithrix jacchus]
          Length = 1156

 Score = 47.1 bits (110), Expect = 0.011,   Method: Composition-based stats.
 Identities = 70/508 (13%), Positives = 171/508 (33%), Gaps = 44/508 (8%)

Query: 184  IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
            + DL     P S       +E         + ++   +   +    IE    V  ++  +
Sbjct: 542  LSDLTRTPPPPSSTFPKASSESSYLSILPKTPEDISEEQRSQELAAIEETRIVVLNNLEE 601

Query: 244  VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            +    ++  +       + D     L   +     ++M   + +  + R++  L+ N V 
Sbjct: 602  LKQKIKDINDQMDESSRELDMECALLDGEQQSETTELMKEKEILDHLNRKIAELEKNIVG 661

Query: 304  GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             +  EK  VK    +EKL +L    S  ++++D   E + +  ++ +  + +LL +   +
Sbjct: 662  EKTKEK--VKLDAEREKLERLQELYSEQKTQLDNCPESMREQLQQQLKRDADLLDVESKH 719

Query: 364  GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
                  F +    +      +   K+    +    VA    +I+  + +I ++  +    
Sbjct: 720  ------FEDLEFQQLERESRLDEEKENLTQQLLREVAEYQRNIVSRKEKISALKKQAN-- 771

Query: 424  ISEFRHIVSMVRKGECEASIAKKEMVEANLR---LVISVAKKYT----NRGLQF-LDLIQ 475
                 HIV   ++ +      K  ++    R    + ++ KKY+     +G     + ++
Sbjct: 772  -----HIVQQAQREQDHFVKEKNNLIMMLQREKENLCNLEKKYSSLSGGKGFPINPNTLK 826

Query: 476  EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
            E ++ L ++                    K + +R +       ++    R K     RT
Sbjct: 827  EAHLPLGQSNSCGSV-----LPPSLAAMAKDSESRRMLRGYNHQQMSEGHRQKQEFYNRT 881

Query: 536  ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH--LGDFIE 593
            A   +  +     P+   K                 + +SL++    E +      D I 
Sbjct: 882  ASESNVYLHSFHYPDHSYK-------------DQACDTLSLDSSDSMETSISACSPDNIS 928

Query: 594  DKNAVSPLD-SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
              +  +      ++  L++        L  RE  +   +  +            +    T
Sbjct: 929  SASTSNIARIEEMERLLKQAHAEKTRLLESREREMEAKKRALEEEKRRREILEKRLLEET 988

Query: 653  RERIRQIEAKAIRKLKHPSRSKKLRSFL 680
             +R + IE +   + K  ++++ L  +L
Sbjct: 989  SQRQKLIEKEVKIREKQRAQARPLTRYL 1016


>gi|71277201|gb|AAZ29810.1| RpoD [Pseudomonas syringae pv. persicae]
          Length = 151

 Score = 46.8 bits (109), Expect = 0.011,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 45/129 (34%), Gaps = 3/129 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 26  DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVS 85

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 86  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 142

Query: 352 NEGELLRLA 360
            E  +++L 
Sbjct: 143 QERAIMQLC 151


>gi|71277197|gb|AAZ29808.1| RpoD [Pseudomonas syringae pv. garcae]
          Length = 150

 Score = 46.8 bits (109), Expect = 0.011,   Method: Composition-based stats.
 Identities = 19/196 (9%), Positives = 56/196 (28%), Gaps = 46/196 (23%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
             ++     +      L +++            G+    +G +         + +    +
Sbjct: 1   DHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAAKAE 49

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
             + + ESA    ++D  +    P  A+     + +  + +   L  +    +  +   +
Sbjct: 50  GDDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKLGRDDKHAIAEMV 109

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
                                               L +L   + L   + + LVE++  
Sbjct: 110 -----------------------------------ALAELFMPIKLVPKQFEGLVERVRG 134

Query: 345 ISKRIMHNEGELLRLA 360
             +R+   E  +++L 
Sbjct: 135 ALERLRAQERAIMQLC 150


>gi|301607003|ref|XP_002933101.1| PREDICTED: laminin subunit beta-2-like [Xenopus (Silurana)
            tropicalis]
          Length = 1783

 Score = 46.8 bits (109), Expect = 0.011,   Method: Composition-based stats.
 Identities = 49/361 (13%), Positives = 105/361 (29%), Gaps = 61/361 (16%)

Query: 4    GKKRNRDSDSEHEDSDDS----LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVS 59
              K +R         D +       + S+   +++I+           ++  FL  +   
Sbjct: 1466 KVKADRAKQRAQATLDRANETKARVEQSNKELRELIQ-----------QIKDFLNQEGAD 1514

Query: 60   SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
             + +E   + + ++ I             +   +   +      V      D+    T  
Sbjct: 1515 PDSIEMVASRVLDLTIP-----------ATPKQIQRLAEEIKDRVKTLANVDAILDQTAA 1563

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
             VR              E  +  AKR +     +  +  ES    +  +       +   
Sbjct: 1564 DVR------------KAEQLLHEAKRAKNRAENVKNT-AES---VKRALDDARRAQN--- 1604

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
                           +           +  +   SS E + +D  +  G+++      K 
Sbjct: 1605 -------AAEGAIQSANDDIKDTERKLTAIQTATSSAENQLNDAMDRVGNLDKQIDGLKM 1657

Query: 240  DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE----IAEVYRELR 295
             R+        AE       +  +D+   L          V   +D     I E   +  
Sbjct: 1658 KRANNSLAASRAEESATAALDKANDAKKILEGQLADKYKTVQNVVDRKAKNIKEAKTKAD 1717

Query: 296  SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ---SRIDLLVEQLYDISKRIMHN 352
             LQD A    ++ +   K K L++  V+   +  L Q    R++ L +++ +I   I   
Sbjct: 1718 QLQDEAKKLLENAQD--KLKRLQDLEVEYTKNEKLLQDKAKRLNGLEDKMKEILHAINQQ 1775

Query: 353  E 353
             
Sbjct: 1776 I 1776


>gi|52786517|ref|YP_092346.1| hypothetical protein BLi02782 [Bacillus licheniformis ATCC 14580]
 gi|52349019|gb|AAU41653.1| hypothetical protein BLi02782 [Bacillus licheniformis ATCC 14580]
          Length = 126

 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 41/91 (45%)

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
              L D +           ++QA   + +   L S T  +++ +  RF + +  + T  E
Sbjct: 20  EISLIDALRIGKRRRHRHHSVQAQSLKKSKNSLTSWTAEKKKFIAGRFSLDLKKEKTQRE 79

Query: 645 VGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           + K+  ++R  + +IE +A+ K+ H    +K
Sbjct: 80  IAKELGISRSYVSRIEKRALMKVFHEFYREK 110


>gi|219668837|ref|YP_002459272.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense DCB-2]
 gi|219539097|gb|ACL20836.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
          Length = 206

 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 69/243 (28%), Gaps = 56/243 (23%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I + +         +   +++     +  +A KY     ++ DL+QEG I + KA  
Sbjct: 8   LADIDTQLEAARSGNQDSLNWLIQYYEPEIRKIAYKYFLNRAEYDDLLQEGRIAIYKAIV 67

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D      F  +    +K+ +  S+           H R K   +              
Sbjct: 68  SYDPSSEIPFLHFLRMVIKRKLIDSLRA---------HNRQKHLNLNEAY---------- 108

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
                                       SL   + D+ T     F+   +          
Sbjct: 109 ----------------------------SLNNVLADDKTDSFISFVATHDDPEK-KVIAS 139

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR----ERIRQIEAK 662
              R     ++   +  E +V R  + IG        E+ +   V+       I++I  K
Sbjct: 140 DETRLFLQGLMNGFSELELKVFRYHYLIG----MKQREITQYLGVSSKSLDNTIQRIRRK 195

Query: 663 AIR 665
            I 
Sbjct: 196 VIA 198


>gi|218290353|ref|ZP_03494489.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239589|gb|EED06782.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 191

 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 68/195 (34%), Gaps = 22/195 (11%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            L+ A  +           +   + +   + +             ++D   KV R A   
Sbjct: 9   MLLAAIARGQRD---ALEAFYDRFARLVYSFAYRVTGNVSHAEEIVQDVFVKVWRQAHAY 65

Query: 540 SNKIKREPT-PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
           + ++ +  T    IA++ A+ +    +  +              E    L   + D + +
Sbjct: 66  NPELGKVSTWLLTIARRSAIDLHRRERRQQ-------------HESGEDLFPVLPD-HGL 111

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           +P   A Q++LR    + LA L   + +V+   +  G   +   E  G      + R R 
Sbjct: 112 TPDRVAEQSDLRSRIRQALAKLPEEQRQVVEWMYFQGYTQNEIAERFGWSLGTVKSRARL 171

Query: 659 IEAKAIRKLKHPSRS 673
               A++KL+   +S
Sbjct: 172 ----AMQKLRDELQS 182


>gi|307150553|ref|YP_003885937.1| ECF subfamily RNA polymerase sigma-24 factor [Cyanothece sp. PCC
           7822]
 gi|306980781|gb|ADN12662.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7822]
          Length = 288

 Score = 46.8 bits (109), Expect = 0.012,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 72/212 (33%), Gaps = 13/212 (6%)

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L    ++ +     K         + Y  +W      +    + C   +  +  D    +
Sbjct: 17  LFSLSDLEIGNVLSKSSQFKTVSQNHYQAFWQLWESEQKYFYKLCLRWMGGNSHDAEDVL 76

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD-- 590
            +   +  NK       E+ A K+  P   + +++      I  +         ++ D  
Sbjct: 77  NQVMLKAWNKW------EKSANKIISPKAWLARIIYNFCMDIHRQRQREARGIENIDDLK 130

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           F +D+  VS +       L       L  L       LR  F +    + + +++ KQ  
Sbjct: 131 FADDRALVSEVGIPESNLLNREMQTYLGHLIESLPDKLRHPFILHCYYEKSYQDIAKQLA 190

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           ++ E  R+   KA   LK     K+L+ +L G
Sbjct: 191 LSEENTRKRIQKARSILK-----KQLKKYLAG 217


>gi|291224757|ref|XP_002732368.1| PREDICTED: WD repeat domain 65-like [Saccoglossus kowalevskii]
          Length = 1192

 Score = 46.8 bits (109), Expect = 0.013,   Method: Composition-based stats.
 Identities = 50/309 (16%), Positives = 111/309 (35%), Gaps = 26/309 (8%)

Query: 139  EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            E  IA+ +E     +      +            EL   +  ++E  + +     ESK  
Sbjct: 714  EEEIAELMEKNSKELQDLESANNQKLMLEYEKYQELQAKSQKMQEDYERQLQEMEESKEA 773

Query: 199  FFHGTEGHSYQKRE------DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
                   +   K +      D + ++ R   +E E   +   + +  +   + +  E   
Sbjct: 774  ALEELTEYYEAKLQEKTILLDQANDESRQQQREYEETKKQIEEDADREILDIKNKFERRL 833

Query: 253  NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
             DE+  +         +      L+ ++    +EI ++  E + LQ    + +KD     
Sbjct: 834  RDEKEANLRLKGETGIMKKKFTSLQKEIEDHKEEIKKLNNEQQKLQGVIKSLEKDIYG-- 891

Query: 313  KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
                LK+++ +   ++   + RI       YD+ K+  + E E  +    Y I      +
Sbjct: 892  ----LKKEIQERDETIQDKEKRI-------YDLKKK--NQELEKFKFVLDYKI--KELKK 936

Query: 373  RHQGRELDPHWVSYAKDFPEGEWKNFVACEVD---SILKIRNEIKSISVETGISISEFRH 429
            + + RE D   +       E E + F         +I ++R ++K+   E  +   + R 
Sbjct: 937  QIEPRENDIKAMKEQIQEMESELERFHKQNTQLELNITELRQKLKATEKEMHLERQKVRD 996

Query: 430  IVSMVRKGE 438
              +M+R+ +
Sbjct: 997  SEAMLRRFK 1005



 Score = 44.4 bits (103), Expect = 0.070,   Method: Composition-based stats.
 Identities = 71/494 (14%), Positives = 155/494 (31%), Gaps = 33/494 (6%)

Query: 134  LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL---NDGTTLLREIIDLEAC 190
            L R+ EI  A+ I   ++     L E       L    DEL   N+    L+++   E  
Sbjct: 626  LKRDKEIGYAEEILITKSD----LEEKNSMMSELKTRVDELKMENEYQLRLKDMNYNEKI 681

Query: 191  IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
                 K      +     Q  +    ++E    +E    +E  +K  +D  S  +     
Sbjct: 682  KELTEKFIQEMESLKTKNQVLKTDKDKEEAKHEEEIAELMEKNSKELQDLESANNQKLML 741

Query: 251  AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
                 + L                ++      AL+E+ E Y     LQ+  +   +    
Sbjct: 742  EYEKYQELQAKSQKMQEDYERQLQEMEESKEAALEELTEYYE--AKLQEKTILLDQANDE 799

Query: 311  SVKCKVLKEKLVKLVGSLSLNQSRID-----LLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            S + +   E+           + +I+      +++      +R+   +   LRL    GI
Sbjct: 800  SRQQQREYEE----------TKKQIEEDADREILDIKNKFERRLRDEKEANLRLKGETGI 849

Query: 366  KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI---LKIRNEIKSISVETGI 422
             +  F    +  E     +    +  +       + E D      +I+   ++I  +   
Sbjct: 850  MKKKFTSLQKEIEDHKEEIKKLNNEQQKLQGVIKSLEKDIYGLKKEIQERDETIQDKEKR 909

Query: 423  SISEFRHIVSMVRKGECEASIAKKEM---VEANLRLVISVAKKYTNRGLQFLDLI-QEGN 478
             I + +     + K +       KE+   +E     + ++ ++      +      Q   
Sbjct: 910  -IYDLKKKNQELEKFKFVLDYKIKELKKQIEPRENDIKAMKEQIQEMESELERFHKQNTQ 968

Query: 479  IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
            + L     +       K        V+ +       ++       +++D   K+  + ++
Sbjct: 969  LELNITELRQKLKATEKEMHLERQKVRDSEAMLRRFKTDLHNCIGYIQDP-KKLKDSIKQ 1027

Query: 539  MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
            +  K  ++ TPE  +    +  E  R+   + +   SL   +  +   H  D +      
Sbjct: 1028 LYQKHVQDDTPESASVDADIQREYSRQRKHLEQSVSSLRKKLAKDTEIHRADNVRIMQEN 1087

Query: 599  SPLDSAIQANLRET 612
              L   I    RE 
Sbjct: 1088 VSLIKEINDLRREL 1101


>gi|167834950|ref|ZP_02461833.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 169

 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 29/141 (20%), Positives = 47/141 (33%), Gaps = 22/141 (15%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD--LE 84
            +    ++++LA  RG     ++                  A     G+   D  D    
Sbjct: 10  YEQGIDRLLELAGARGDPEYADVADEFASAPSD--------AHAHTHGLGEPDPLDHHAS 61

Query: 85  DEEGSEDSL------------DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
           DE G   S             D        S             + DP+ +++R M ++ 
Sbjct: 62  DENGGAGSFGDKLTRPAHADADWRDDDDAPSSEPNDAAPDDTVVSTDPLALFVRRMHAVP 121

Query: 133 LLSREGEIAIAKRIEAGRAMM 153
           LL+   EIA+A  IEAGR  +
Sbjct: 122 LLTHAQEIALAAEIEAGREQV 142


>gi|318042873|ref|ZP_07974829.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 95

 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI------GMNTDHTLEEVGKQF 649
           +   P +      LR     +L  L   + RVL+MR+GI        +   +L  +G+  
Sbjct: 5   DGTQPEELVDGECLRSDMRDLLEQLPDLQCRVLKMRYGIPCADVPDPDEPMSLTGIGRIL 64

Query: 650 CVTRERIRQIEAKAIRKLKHPSRS 673
            ++R+R+R +E   +  L+  S +
Sbjct: 65  GMSRDRVRNLERDGLAGLRRLSEN 88


>gi|160933813|ref|ZP_02081201.1| hypothetical protein CLOLEP_02674 [Clostridium leptum DSM 753]
 gi|156867690|gb|EDO61062.1| hypothetical protein CLOLEP_02674 [Clostridium leptum DSM 753]
          Length = 187

 Score = 46.8 bits (109), Expect = 0.014,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 34/93 (36%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V +       A  E++     L+      Y   G+   DL+QE  +GL+ +   F   
Sbjct: 8   ELVARVRQGNQEAFSELISRYYGLLQWKISGYRKLGIDADDLLQEATLGLLDSVMSFQEG 67

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524
            G  F TYA   V   +       +    IP H
Sbjct: 68  KGASFETYATVCVNNRLVTLYRAAARQKNIPFH 100


>gi|1435131|emb|CAA64841.1| halobacterial transducer protein IV [Halobacterium salinarum]
          Length = 810

 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 49/305 (16%), Positives = 98/305 (32%), Gaps = 41/305 (13%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMG-------INVVDGDDL-----EDEEGSEDSLDL 95
           +L   +P D+  +E M    A  + M        I++ +  D      E+ E      + 
Sbjct: 459 DLTRRMPADDTDNEAMAAIAASFNEMLAQWEHTIIDIQEFADAVATASEEAEVGAADAER 518

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI--------------- 140
           AS   + SV          R+  D V     EM   +L +   E+               
Sbjct: 519 ASGQVSESVQEIAGAADEQRNMLDTVS---GEM--TDLSAAIEEVAASADSVAEHSHQTA 573

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IA+  E      +           A +   + L+D    + EI+DL + I  ++     
Sbjct: 574 EIARDGEQTAEDAIERSLSVQEAIDATVQNVEALDDQMAEISEIVDLISDIAEQTN---M 630

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                +    R D S +       E +   E   + + D   ++                
Sbjct: 631 LALNANIEAARADKSGDGFAVVADEVKDLAEETQESAGDIERRITEVQSQTTATVAEARA 690

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKVLKE 319
            E+     + A+E+     V+ A   +++   E  + +Q+ +        S+ +   + E
Sbjct: 691 AEESMDAGIDAVEE-----VVDAFTAVSDHADETDTGVQEISDTTDDQASSTEEAVSMTE 745

Query: 320 KLVKL 324
           ++  L
Sbjct: 746 EVADL 750


>gi|148243883|ref|YP_001220122.1| sigma-70 region 4 domain-containing protein [Acidiphilium cryptum
           JF-5]
 gi|146400446|gb|ABQ28980.1| sigma-70 region 4 domain protein [Acidiphilium cryptum JF-5]
          Length = 894

 Score = 46.4 bits (108), Expect = 0.015,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL-KHPSRSK 674
             ++ ++L MR+G   +   TL+ V     +T+ER+RQIE +A++ L + PSR K
Sbjct: 289 NEKQAQILAMRYGF-FDKPATLDVVSNTVGITKERVRQIEVEAVKHLGREPSRQK 342


>gi|89894412|ref|YP_517899.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense Y51]
 gi|89333860|dbj|BAE83455.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 208

 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 69/243 (28%), Gaps = 56/243 (23%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I + +         +   +++     +  +A KY     ++ DL+QEG I + KA  
Sbjct: 10  LADIDTQLEAARSGNQDSLNWLIQYYEPEIRKIAYKYFLNRAEYDDLLQEGRIAIYKAIV 69

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            +D      F  +    +K+ +  S+           H R K   +              
Sbjct: 70  SYDPSSEIPFLHFLRMVIKRKLIDSLRA---------HNRQKHLNLNEAY---------- 110

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
                                       SL   + D+ T     F+   +          
Sbjct: 111 ----------------------------SLNNVLADDKTDSFISFVATHDDPEK-KVIAS 141

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR----ERIRQIEAK 662
              R     ++   +  E +V R  + IG        E+ +   V+       I++I  K
Sbjct: 142 DETRLFLQGLMNGFSELELKVFRYHYLIG----MKQREITQYLGVSSKSLDNTIQRIRRK 197

Query: 663 AIR 665
            I 
Sbjct: 198 VIA 200


>gi|271969632|ref|YP_003343828.1| hypothetical protein Sros_8441 [Streptosporangium roseum DSM 43021]
 gi|270512807|gb|ACZ91085.1| hypothetical protein Sros_8441 [Streptosporangium roseum DSM 43021]
          Length = 615

 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 15/95 (15%)

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647
           L + + +++      S     L E    V A+L  R+  + R    +  +   TL+++ +
Sbjct: 106 LLEPVTEESVAQVRPSRPDRPLPELIDEVFAALDDRQRAIARD--RLYASQRATLDDLAQ 163

Query: 648 QFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682
           +F VTRERIRQIE             + LR  +D 
Sbjct: 164 RFSVTRERIRQIE-------------RDLRDHVDA 185


>gi|218291390|ref|ZP_03495333.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218238745|gb|EED05961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 187

 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 444 AKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
           A++ +V  N RLV  VA +  +R    G++F DL+  G +GL KAA  +D     KFS  
Sbjct: 15  AQERLVVENQRLVYFVANRLRHRAQEAGVEFEDLVATGMLGLCKAARVYDPSRA-KFSVL 73

Query: 500 AMWWVKQAI 508
           A+  ++  +
Sbjct: 74  AVRCIENEM 82


>gi|47089328|gb|AAT10983.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
          Length = 149

 Score = 46.4 bits (108), Expect = 0.016,   Method: Composition-based stats.
 Identities = 20/194 (10%), Positives = 50/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAV 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             + T+ D E +A  S D+      P             D+ +          +     +
Sbjct: 50  KAEGTDDDEEGSADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +AE++                                    + L   + + LVE+
Sbjct: 110 AEMVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|257470879|ref|ZP_05634969.1| RNA polymerase sigma factor [Fusobacterium ulcerans ATCC 49185]
 gi|317065081|ref|ZP_07929566.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690757|gb|EFS27592.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 284

 Score = 46.4 bits (108), Expect = 0.017,   Method: Composition-based stats.
 Identities = 31/123 (25%), Positives = 59/123 (47%), Gaps = 6/123 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           + + ++ +S    IS  +  + +  +R         K++++  NL  V S+A  Y   G+
Sbjct: 58  VIDYLEELSNMEVISDEDENNYLKDLR------EADKEKVIVKNLNEVASIAFNYVKNGI 111

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK 528
            ++D++QEG +GL+KA + FD      F  Y+ +W+ + I   I ++   IR       K
Sbjct: 112 AYMDVVQEGTVGLIKAVDYFDPDRNGDFKNYSKYWIAREIVLYIENKVADIRNEFKNFFK 171

Query: 529 IHK 531
             K
Sbjct: 172 NKK 174


>gi|170052745|ref|XP_001862361.1| microtubule binding protein D-CLIP-190 [Culex quinquefasciatus]
 gi|167873583|gb|EDS36966.1| microtubule binding protein D-CLIP-190 [Culex quinquefasciatus]
          Length = 1923

 Score = 46.4 bits (108), Expect = 0.017,   Method: Composition-based stats.
 Identities = 59/412 (14%), Positives = 154/412 (37%), Gaps = 13/412 (3%)

Query: 57   EVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRS 116
            E  S+Q+E+  AML    + + +  +    E   +   + ++   +       K      
Sbjct: 663  EPDSDQLEEV-AMLKQRIVFLQEEQERLTTEKDTNHYRIETNGGEAQKQNHSEKPLDPSQ 721

Query: 117  TDDPVRMYLREMGSIELL--SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
             +D  R    +   +E+L  ++E E+  AK        +   L  +    Q      D+L
Sbjct: 722  IEDLRR----KCSELEVLVSTKEEELKAAKEHTNQLTKIEQELLATKEQKQQSDERADQL 777

Query: 175  NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
                T L+  I+       + +    H     +  +   +  E E+  +      +ES  
Sbjct: 778  TVEMTDLKNEINTLLQARQQFEHEVAHLKGKIADLEAALADNEAEKRKLLGKVQTLESEI 837

Query: 235  KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME---DQLRPKVMCALDEIAEVY 291
            + S   R +++   +  ++   +L ++ ++++  L   E   D+ + ++    + + E+ 
Sbjct: 838  EESSKFRDQLEQEVQETKSALESLGQELNENSEKLERFEKQNDEYKQELSEKTETVDELR 897

Query: 292  RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++L   + +A    +D K+ +  +    + ++       +   +  +V QL   ++R+  
Sbjct: 898  QKLEETKKSAERRVQDTKAELSAQEDAREALE--EQFRQSTEELTTMVSQLEQSAQRVNS 955

Query: 352  NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
             E ++  L               + RE     ++  K+  E    +    E++ I  ++ 
Sbjct: 956  LENQISELKLETETAELNRSAAERLREDVEQELNEVKESLEEAKVDCREKEIE-IEDLKR 1014

Query: 412  EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKY 463
            E + +  ET  +  E ++ V  V   +   +    ++ +     + +  ++Y
Sbjct: 1015 ECQRLLQETADAKLELQNDVGEVEVAKQTLAEKLLQLRDYYDGQLKTEKERY 1066


>gi|269925713|ref|YP_003322336.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269789373|gb|ACZ41514.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 785

 Score = 46.4 bits (108), Expect = 0.017,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           +E  +  +  D +I    +E T  +    +PR  RVL  RFG+      TL+E+G +  +
Sbjct: 306 VELSSETTQEDVSITELDKEITKLIQTIKSPRVRRVLEARFGV-SGKILTLQEIGAELKL 364

Query: 652 TRERIRQIEAKAIRKLKH 669
           ++ER+RQ+E + +R ++ 
Sbjct: 365 SKERVRQLEERGLRLIRK 382


>gi|226288372|gb|EEH43884.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb18]
          Length = 1590

 Score = 46.4 bits (108), Expect = 0.017,   Method: Composition-based stats.
 Identities = 60/466 (12%), Positives = 147/466 (31%), Gaps = 25/466 (5%)

Query: 165  QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
            +A I   D    G   LRE ID       +    F    +  +  + E  + EK   +++
Sbjct: 1020 EAAINRLDSKLKGEDDLREEIDSLRDDLRDIGQSFVEAKDKVNELQTEKQALEKTIQNLE 1079

Query: 225  ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
            +   D+          R+   S    AE + ++L  + ++     +A++  L      A 
Sbjct: 1080 KELVDL----------RTNSTSSSAEAEGEHKDLAAEFEELKIKATALQTDLTTTQQLAA 1129

Query: 285  DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
                ++     ++Q      +     S + K  KE+L      L   + R + +  ++ +
Sbjct: 1130 SRFKDLTDLRDTIQKLQPELRTLRAESAELKASKEELKNKTNDLKRLERRHEDVRSEMKN 1189

Query: 345  ISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDPHWVSYAKDFP---EGEWKNF 398
            +  +I   E E+  L Q    +    ++  Q     + D  +    K             
Sbjct: 1190 LRGKIGEQESEIKALNQKVTQETKTRVKAEQALDVAQSDLRYSESKKQEAIETNENTTRL 1249

Query: 399  VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
            ++   + +   R  ++ +  +      +  ++   ++    + + A+  ++ +       
Sbjct: 1250 LSKTQEELRSSRTRLREVEEQVTQLNRDIENLRDEIQLKTAQYASAQS-LMNSMRDQTSE 1308

Query: 459  VAKKY---TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515
            +A +      R     + + + +  L  A    +     +  +         +       
Sbjct: 1309 MAMQVKEARERCESLEEELADAHRLL--AERTREGETMRRLLSDVEMRTDAKVRDFKERL 1366

Query: 516  SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               I       D+ +   R   R   ++K +    E   + A   E  ++ L+   E   
Sbjct: 1367 ETAIEERDRAEDEANLSGRKRAREIEELKSKARDMERELRRA---EQDKRELEAETERSK 1423

Query: 576  LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
             E        + L D + +    +      +  LR +    +  L 
Sbjct: 1424 RELGDVQAAMTELRDALGESENQTLELEKEKIELRRSVEETIQRLE 1469


>gi|302669016|ref|YP_003832841.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302397356|gb|ADL36259.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 378

 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 39/271 (14%), Positives = 96/271 (35%), Gaps = 19/271 (7%)

Query: 423 SISEFRHIVSMVRK--GECEASIAKKEMVEANLRLVISVAKKYTNRGLQF--LDLIQEGN 478
           +  E+  +   +++         A  E VE+   LV+ V  +Y    ++    DLI  G 
Sbjct: 71  TAQEWVRLYYDMKQEDDPELRERALTEFVESLQGLVLFVVNRYYKTYMKDYKDDLIGSGM 130

Query: 479 IGLMKAAEKFDW-----CLGYKFSTYAMWW--VKQAITRSIADQSCTIRIPVHMRDKIHK 531
           IGLM+  +++D        G  F    +    ++ A    +   S  +      +    K
Sbjct: 131 IGLMEGIKRYDPYHNGGNKGEPFVPSTIVTRDIRHACRDYV--NSMILNTKTRYKTIEDK 188

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAM------PVEGVRKVLKITKEPISLETPIGDEDT 585
           + +   R  ++   E    +I   +          +G+   ++     +SL+  + D + 
Sbjct: 189 LRQIIARKRDESGGEDIDIDIDDLVNELGISPKTAQGILANIQTRNNMVSLDEVMQDSNN 248

Query: 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           S     +      +P +  ++        +++      E+R + M          T  E+
Sbjct: 249 STSRHELFASQTKTPEEEYLEKEKTIRINKMMYDNLTDEQREVCMYHYGFYGEKCTNTEI 308

Query: 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
            K   +  +++ +I  ++  +++       +
Sbjct: 309 SKIMGIPVQKVSKIINESELRMRRAMSRSHM 339


>gi|134046323|ref|YP_001097808.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C5]
 gi|132663948|gb|ABO35594.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C5]
          Length = 729

 Score = 46.4 bits (108), Expect = 0.018,   Method: Composition-based stats.
 Identities = 42/358 (11%), Positives = 118/358 (32%), Gaps = 30/358 (8%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D   E++      + +  +  ++IK           +L   +       +++ED +   
Sbjct: 399 ADENTENNTLQKAINTAVANVAQLIK-----------DLREEVDLLTSQVQKVEDELKSA 447

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                 V +  +   E  S+ S  L  ++                + ++ V+    E+G 
Sbjct: 448 EETATQVTEAANQVAEASSDQSAKLQEASDQLENTY-GVAKEVYGAAEETVKA-AEEIG- 504

Query: 131 IELLSREGEIAIAKRIEAGRAMMMA---SLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
                 E      K++E     M +    + E     Q L     ++ND T L+++I + 
Sbjct: 505 ------ENSENGVKKVENAITRMQSITNVIDELGKAIQMLGDDGKKINDVTGLIKDIAEQ 558

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              +   +        +         S  +   ++++++  DI                 
Sbjct: 559 TGLLALNASIEAARAGDAGKGFAVVASEIKALAEEIKKSVEDINHTIDGVNRRIEDTMDL 618

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
               +++        D+    L  ++  +    +    +I ++ +  +S  DN     K+
Sbjct: 619 GLKGKDEVDKGVIAIDEVNDALLRIKGSVNDAAI----KINDIKKGAQSATDNTEGALKN 674

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            +       L E+       ++ +   ++ ++E++  I++ +      + + +  + I
Sbjct: 675 AQD---IAALSEEFTATAEEVTASTEELNSIIEEIRGIAEEVTQVAERVTKKSSQFKI 729


>gi|225573002|ref|ZP_03781757.1| hypothetical protein RUMHYD_01193 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039653|gb|EEG49899.1| hypothetical protein RUMHYD_01193 [Blautia hydrogenotrophica DSM
           10507]
          Length = 245

 Score = 46.0 bits (107), Expect = 0.019,   Method: Composition-based stats.
 Identities = 33/219 (15%), Positives = 87/219 (39%), Gaps = 16/219 (7%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI------------LKIRNEI 413
            R+   +  QG EL+   +   + + + +  +    + +              +  +  +
Sbjct: 26  SREKIQQFFQGEELEESQIDKIEAYLKAQTASSGEIQAEECPAAVQVKMAPLSMDEQRYL 85

Query: 414 KSISVE-TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
           K        ++  E R +  + +      + A+  + +  L  V+ +AK+         D
Sbjct: 86  KDYEESLQWVAPPETRELEKLYQAMSAGKTQAQSRLAQLFLPEVVEIAKRLHTEEGYLGD 145

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQEGN+ LM A  ++          +    ++  I   ++           + +K+ K+
Sbjct: 146 MIQEGNVALMSALNQWRPDGEP--GEWLRRRIESGICGMVSQSERQKFEDDILVEKVRKL 203

Query: 533 VRTARRMSNKI-KREPTPEEIAKKLAMPVEGVRKVLKIT 570
               R ++ +  +++ + EE++  L M ++ +R +L++T
Sbjct: 204 EAAVRELTEENEEKKFSVEELSILLDMDIDEIRDILRLT 242


>gi|146085052|ref|XP_001465158.1| hypothetical protein [Leishmania infantum JPCM5]
          Length = 4824

 Score = 46.0 bits (107), Expect = 0.019,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 85/247 (34%), Gaps = 19/247 (7%)

Query: 60   SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            ++Q+++   +++         D+    E  E   D A+         ++ +  +D   D+
Sbjct: 3983 TDQIDNEDQLMNMKDKEEQQADEQRQGEKDEGEEDTAADVETDFNGQKEHRSESDGEGDE 4042

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
                  +EMG ++  + E E   AK+ +AG A  M                         
Sbjct: 4043 EGEESDKEMGDVDDGT-EQERKKAKK-DAGDADDMNEDAGD--------------AAEEV 4086

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE--RDDVQETEGDIESAAKVS 237
               ++ + +       + G F           ED S E +   DD +    +  S+   S
Sbjct: 4087 PEDDLAEGDEHREDNEETGSFEDKADEIRDADEDRSCEHDVVGDDDKSEMDEDGSSDGDS 4146

Query: 238  KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             +         + +  D++   + +++   +  A E+++         E +E+  E    
Sbjct: 4147 VEHSDTDGEERDESARDDKLPSDADEEPEESDVASEERVDSDA-ATDAERSELGEEEVEQ 4205

Query: 298  QDNAVNG 304
            +DN+ N 
Sbjct: 4206 RDNSENA 4212


>gi|317060933|ref|ZP_07925418.1| predicted protein [Fusobacterium sp. D12]
 gi|313686609|gb|EFS23444.1| predicted protein [Fusobacterium sp. D12]
          Length = 149

 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 31/115 (26%), Positives = 47/115 (40%), Gaps = 6/115 (5%)

Query: 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
                A+ E++E N+ LV  + + Y        D  QEG +    A +KFD     K S+
Sbjct: 1   MGDIEARNELIEKNINLVHKINRMYG----SSEDGFQEGILAFCHAIDKFDETKNVKLSS 56

Query: 499 YAMWWVKQAITRSIADQSCTIRIPV--HMRDKIHKVVRTARRMSNKIKREPTPEE 551
           YA  W++Q I R    +   +   V   M  +  K+         K + E T EE
Sbjct: 57  YAFHWIRQKIKRYREREKYRLPAHVIEKMSKEERKIRIDFEYRDFKSEDETTIEE 111


>gi|321399364|emb|CAM67405.2| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 4825

 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 85/247 (34%), Gaps = 19/247 (7%)

Query: 60   SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            ++Q+++   +++         D+    E  E   D A+         ++ +  +D   D+
Sbjct: 3984 TDQIDNEDQLMNMKDKEEQQADEQRQGEKDEGEEDTAADVETDFNGQKEHRSESDGEGDE 4043

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
                  +EMG ++  + E E   AK+ +AG A  M                         
Sbjct: 4044 EGEESDKEMGDVDDGT-EQERKKAKK-DAGDADDMNEDAGD--------------AAEEV 4087

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE--RDDVQETEGDIESAAKVS 237
               ++ + +       + G F           ED S E +   DD +    +  S+   S
Sbjct: 4088 PEDDLAEGDEHREDNEETGSFEDKADEIRDADEDRSCEHDVVGDDDKSEMDEDGSSDGDS 4147

Query: 238  KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             +         + +  D++   + +++   +  A E+++         E +E+  E    
Sbjct: 4148 VEHSDTDGEERDESARDDKLPSDADEEPEESDVASEERVDSDA-ATDAERSELGEEEVEQ 4206

Query: 298  QDNAVNG 304
            +DN+ N 
Sbjct: 4207 RDNSENA 4213


>gi|119964667|gb|ABM17096.1| putative RNA polymerase sigma factor [Sulfobacillus acidophilus DSM
           10332]
          Length = 177

 Score = 46.0 bits (107), Expect = 0.021,   Method: Composition-based stats.
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
           +   SP+         +     L  L+ RE RVL++ +  G       +E+   + V   
Sbjct: 96  EEFDSPVVDDDGEEDHDWLQDALGQLSDRERRVLQLAYYYGFTQ----KEIAALWGVPVG 151

Query: 655 RIRQIEAKAIRKLKHPS 671
            ++ + ++AI KL+  +
Sbjct: 152 TVKSLASRAIHKLRRQT 168


>gi|332018851|gb|EGI59407.1| Phosphatidylinositol 3-kinase regulatory subunit alpha [Acromyrmex
           echinatior]
          Length = 945

 Score = 46.0 bits (107), Expect = 0.022,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 62/182 (34%), Gaps = 18/182 (9%)

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDD---------SAHTLSAMEDQLRPKVMCALDEIA 288
           +DD     +           LD+D +D           ++ +A E QL+   + A  E  
Sbjct: 644 QDDEIANTTDMAKVRQKYFELDKDINDTIRQYQHCSDLYSKTAYEVQLKRNALEAFTEAI 703

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           +++ E   LQ+      K E    +   L +    L   L   +   + L E L      
Sbjct: 704 KMFEEQIKLQER----CKIEAQPHEISTLTDNSELLKRRLKALEDSKEQLDESLKQQIAY 759

Query: 349 IMHNEGELLRLAQSYGI---KRDVFLERHQGREL--DPHWVSYAKDFPEGEWKNFVACEV 403
               E E+ +L    G+   ++D   +  +  E+  +   V +A    E  W        
Sbjct: 760 YRTLEREMYKLKSEIGVLVRQKDRHSQWLKKNEIKQNKEEVDFAVHSDEKTWLFLKGSRS 819

Query: 404 DS 405
           D+
Sbjct: 820 DA 821


>gi|317498318|ref|ZP_07956616.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894394|gb|EFV16578.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 191

 Score = 46.0 bits (107), Expect = 0.023,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +      DFI D+ A    ++ + A + 
Sbjct: 74  EQYTDFYRDKERWRYLKKLDTKNSLLSLDGFTDSEGKPLDFIADE-AADIAETVVNAVMV 132

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +F +T+  + + +A+ +RKL+ 
Sbjct: 133 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARFGITQSVVNKRKARILRKLRK 187


>gi|47089280|gb|AAT10959.1| sigma 70 factor [Pseudomonas syringae pv. broussonetiae]
 gi|47089284|gb|AAT10961.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089286|gb|AAT10962.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089288|gb|AAT10963.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089290|gb|AAT10964.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089292|gb|AAT10965.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089294|gb|AAT10966.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089296|gb|AAT10967.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089298|gb|AAT10968.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089300|gb|AAT10969.1| sigma 70 factor [Pseudomonas syringae pv. glycinea]
 gi|47089304|gb|AAT10971.1| sigma 70 factor [Pseudomonas syringae pv. lachrymans]
 gi|47089306|gb|AAT10972.1| sigma 70 factor [Pseudomonas syringae pv. lachrymans]
 gi|47089308|gb|AAT10973.1| sigma 70 factor [Pseudomonas syringae pv. lachrymans]
 gi|47089330|gb|AAT10984.1| sigma 70 factor [Pseudomonas syringae pv. mellea]
 gi|47089332|gb|AAT10985.1| sigma 70 factor [Pseudomonas syringae pv. mori]
 gi|47089334|gb|AAT10986.1| sigma 70 factor [Pseudomonas syringae pv. morsprunorum]
 gi|47089336|gb|AAT10987.1| sigma 70 factor [Pseudomonas syringae pv. myricae]
 gi|47089338|gb|AAT10988.1| sigma 70 factor [Pseudomonas syringae pv. myricae]
 gi|47089344|gb|AAT10991.1| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|47089346|gb|AAT10992.1| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|47089348|gb|AAT10993.1| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
 gi|47089366|gb|AAT11002.1| sigma 70 factor [Pseudomonas syringae pv. syringae]
 gi|47089368|gb|AAT11003.1| sigma 70 factor [Pseudomonas savastanoi]
 gi|47089384|gb|AAT11011.1| sigma 70 factor [Pseudomonas syringae pv. tabaci]
          Length = 149

 Score = 46.0 bits (107), Expect = 0.023,   Method: Composition-based stats.
 Identities = 20/194 (10%), Positives = 50/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAV 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             + T+ D E +A  S D+      P             D+ +          +     +
Sbjct: 50  KAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +AE++                                    + L   + + LVE+
Sbjct: 110 AEMVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|254729465|ref|YP_003084147.1| type III RNAP sigma factor [Cyanophage PSS2]
 gi|254211617|gb|ACT65565.1| type III RNAP sigma factor [Cyanophage PSS2]
 gi|265524818|gb|ACY75710.1| predicted protein [Cyanophage PSS2]
          Length = 213

 Score = 46.0 bits (107), Expect = 0.024,   Method: Composition-based stats.
 Identities = 39/145 (26%), Positives = 61/145 (42%), Gaps = 12/145 (8%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKK-YTNRG----LQFLDLIQEGNIGLMKAAEKF 488
           +R      S A++   E NL L    A + +  +     L + DL     IGLMKA  +F
Sbjct: 1   MRPLGFTLSKAQQLKTEENLNLARKEAWRAFKRQSPRSRLPYDDLEAAAFIGLMKACFRF 60

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
           D   G KFSTYA+  ++  I   I D +  +++   MR+   +  R        + +  +
Sbjct: 61  DEEFGCKFSTYAVPKIRGEILHFIRDHTYLLKLTHRMRETWQRGKRL-------LDQGNS 113

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEP 573
             EIAK L + +E           P
Sbjct: 114 DIEIAKALEIELEVWLDTRSACSGP 138


>gi|1654427|gb|AAB17884.1| transducer HtF protein [Halobacterium salinarum]
          Length = 804

 Score = 46.0 bits (107), Expect = 0.024,   Method: Composition-based stats.
 Identities = 50/308 (16%), Positives = 100/308 (32%), Gaps = 38/308 (12%)

Query: 42  GYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG-----INVVDGDDL-----EDEEGSED 91
           G V   +L   +P D+  +E M    A  ++       I++ +  D      E+ E    
Sbjct: 450 GGVADGDLTRRMPADDTDNEAMAAIAASFNDSQWEHTIIDIQEFADAVATASEEAEVGAA 509

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI----------- 140
             + AS   + SV          R+  D V     EM   +L +   E+           
Sbjct: 510 DAERASGQVSESVQEIAGAADEQRNMLDTVS---GEM--TDLSAAIEEVASADSVAEHSH 564

Query: 141 ---AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
               IA+  E      +           A +   + L+D    + EI+DL + I  ++  
Sbjct: 565 QTAEIARDGEQTAEDAIERSLTVQEAIDATVQNVEALDDQMAEISEIVDLISDIAEQTN- 623

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                   +    R D S +       E +   E   + + D   ++             
Sbjct: 624 --MLALNANIEAARADKSGDGFAVVADEVKDFAEETQESAGDIERRITEVQSQTTATVAE 681

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKV 316
               E+     + A+E+     V+ A   +++   E  + +Q+ +        S+ +   
Sbjct: 682 ARAAEESMDAGIDAVEE-----VVDAFTAVSDHSDETDTGVQEISDTTDDQAASTEEAVS 736

Query: 317 LKEKLVKL 324
           + E++  L
Sbjct: 737 MTEEVADL 744


>gi|331002428|ref|ZP_08325946.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330410244|gb|EGG89678.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 172

 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 76/165 (46%), Gaps = 3/165 (1%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
           +     I   +      +++      + AK  ++EA++     + + +   G + +DLI 
Sbjct: 11  LEDMKNIKPLDEAKKDDLLKALCTGDNNAKNRLIEAHMMYATELVQPFMGCGQEVMDLIS 70

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
           E ++ L  A  ++               V++ +   I +Q+        + +++++++  
Sbjct: 71  ESHLALTMAVTEY---KSGDLKAQIRQAVEKRLNEIIDEQNRAKHDSNELTNRLNELMEI 127

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
           +  ++N+  RE T +E++ +L +P + V ++LKI+   I+L+  I
Sbjct: 128 SSALANEYGREATAKELSDRLLIPQDEVEELLKISLNAINLDKNI 172


>gi|325922773|ref|ZP_08184506.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
 gi|325546748|gb|EGD17869.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
          Length = 128

 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 3/88 (3%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +          ++V  +  LV  +A     R    ++  DLIQ G IGL++A+  +D   
Sbjct: 14  QYRAVQRNNANDIVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQ 73

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIR 520
           G  F TYA   ++ ++   I       R
Sbjct: 74  GASFETYASIRIRGSMIDEIRRGDWVPR 101


>gi|205374842|ref|ZP_03227635.1| hypothetical protein Bcoam_17560 [Bacillus coahuilensis m4-4]
          Length = 174

 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 46/115 (40%), Gaps = 7/115 (6%)

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFI--EDKNAVSPLDSAIQANLRETTT 614
           AM  +  R+     +  + L+ PI DE+     ++I  E  +             R+   
Sbjct: 60  AMDYDK-RRRQHENRYSLLLDAPIKDENMETYKEWIVGETPSYYEHSLHLEDVLDRQDVW 118

Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +  LT  ++R L   +      D    E+  +F ++++ + +    A++KL+ 
Sbjct: 119 EAMKLLTKNQKRTLEYAY----IKDMKDTEIASEFGISQQAVSKTRQSALKKLRR 169


>gi|295105020|emb|CBL02564.1| DNA-directed RNA polymerase specialized sigma subunit
           [Faecalibacterium prausnitzii SL3/3]
          Length = 157

 Score = 45.6 bits (106), Expect = 0.025,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNR--------GLQFLDLIQEGNIGLMKAAEKFDWCL 492
              A+  +VE NLR +   A +  +         G++  DL+QEG++GL+     F    
Sbjct: 17  DKWAENALVENNLRFIRKTAYEIWSAQRELNVALGIELNDLVQEGSLGLLGCISSFQPDY 76

Query: 493 GYKFSTYAMWWVKQAITRSIAD 514
           G KF TYA   +  A+   I  
Sbjct: 77  GNKFLTYAAPAIHNAMLDYIRR 98


>gi|15790682|ref|NP_280506.1| Htr5 [Halobacterium sp. NRC-1]
 gi|169236422|ref|YP_001689622.1| transducer protein cosT [Halobacterium salinarum R1]
 gi|12230156|sp|Q9HP84|HTR4_HALSA RecName: Full=Halobacterial transducer protein 4; AltName: Full=HTP
           IV
 gi|10581215|gb|AAG19986.1| Htr5 transducer [Halobacterium sp. NRC-1]
 gi|167727488|emb|CAP14276.1| transducer protein cosT [Halobacterium salinarum R1]
          Length = 810

 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 49/305 (16%), Positives = 98/305 (32%), Gaps = 41/305 (13%)

Query: 48  ELNAFLPPDEVSSEQMEDTVAMLSNMG-------INVVDGDDL-----EDEEGSEDSLDL 95
           +L   +P D+  +E M    A  + M        I++ +  D      E+ E      + 
Sbjct: 459 DLTRRMPADDTDNEAMAAIAASFNEMLAQWEHTIIDIQEFADAVATASEEAEVGAADAER 518

Query: 96  ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEI--------------- 140
           AS   + SV          R+  D V     EM   +L +   E+               
Sbjct: 519 ASGQVSESVQEIAGAADEQRNMLDTVS---GEM--TDLSAAIEEVAASADSVAEHSHQTA 573

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IA+  E      +           A +   + L+D    + EI+DL + I  ++     
Sbjct: 574 EIARDGEQTAEDAIERSLTVQEAIDATVQNVEALDDQMAEISEIVDLISDIAEQTN---M 630

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                +    R D S +       E +   E   + + D   ++                
Sbjct: 631 LALNANIEAARADKSGDGFAVVADEVKDLAEETQESAGDIERRITEVQSQTTATVAEARA 690

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKVLKE 319
            E+     + A+E+     V+ A   +++   E  + +Q+ +        S+ +   + E
Sbjct: 691 AEESMDAGIDAVEE-----VVDAFTAVSDHADETDTGVQEISDTTDDQAASTEEAVSMTE 745

Query: 320 KLVKL 324
           ++  L
Sbjct: 746 EVADL 750


>gi|118092662|ref|XP_421604.2| PREDICTED: similar to KIAA0583 protein [Gallus gallus]
          Length = 1850

 Score = 45.6 bits (106), Expect = 0.026,   Method: Composition-based stats.
 Identities = 44/381 (11%), Positives = 131/381 (34%), Gaps = 36/381 (9%)

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +  K     +  E  +    + +    +  S + ++L    M  L+ + + Y  LR   +
Sbjct: 175 EEMKRLHDEDQKEITDLRSQQQQVMKQNGSSEILNKLYDTAMDKLEGVKKDYDALRKRYN 234

Query: 300 NAVNGQKD-----EKSSVKCKVLKEKLVKLVGS----LSLNQ------SRIDLLVEQLYD 344
             +          E++  + + L++++  L+      +   Q       R + + ++L +
Sbjct: 235 EKIASHNTDLSRLEQAEEENRRLQKQIDMLMKQRDTAIHFQQQYSSSLRRFESVQQELSN 294

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            + +    + E+ RL       + + L+  +  E          +         +  E D
Sbjct: 295 ATAQNKELQREMERLQSEVTRFKTMQLKAAKDSEKYKEERDSVFNE-----YRLIMSERD 349

Query: 405 SILKIRNEIK---SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            ++K  ++++    ++     + S  + + S   +   +   +    +E   + +  + K
Sbjct: 350 QVIKEVDKLQTELELAESKLKNTSSEKRVASEEMEALRQIQDSATLDIERANKEIEMLRK 409

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y     +  + +QE         E       + F        ++   R++ D       
Sbjct: 410 QYEAMSQELKEAVQEA--------EVAKCRRDWAFQERDKIVAERESIRTLCDNLR-RER 460

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG---VRKVLKITKEPISLET 578
              + D    +         K       +E+ +K+   +E     R+++  +    +++T
Sbjct: 461 DRAVSDLAEALRNLDDMRKQKNDAMRELKELKEKMENQLEKEARFRQLMAHSSHDSAIDT 520

Query: 579 PIGDEDTSHLGDFIEDKNAVS 599
               E  + + +F +D++ + 
Sbjct: 521 DS-LEWETEVVEFEKDRDDMD 540


>gi|330983153|gb|EGH81256.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 70

 Score = 45.6 bits (106), Expect = 0.027,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 12  LHQALDVLDERSRDILYQRWLAE--EKATLHDLAQKYNVSAERIRQLEKSAMNKLK 65


>gi|296270991|ref|YP_003653623.1| hypothetical protein Tbis_3033 [Thermobispora bispora DSM 43833]
 gi|296093778|gb|ADG89730.1| hypothetical protein Tbis_3033 [Thermobispora bispora DSM 43833]
          Length = 621

 Score = 45.6 bits (106), Expect = 0.027,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 6/57 (10%)

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTD------HTLEEVGKQFCVTRERIRQIEA 661
           E    + A L  R+  + R R     +         TL+E+ ++F VTRERIRQIE 
Sbjct: 130 EIIDEIFAELDDRQRAIARDRLYADPSQPGEAGQRATLDELAQRFSVTRERIRQIER 186


>gi|312877883|ref|ZP_07737829.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795346|gb|EFR11729.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 90

 Score = 45.6 bits (106), Expect = 0.027,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 39/79 (49%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +++          ++  ++    ++   L  RE++++ +R+G+    + T  EV   
Sbjct: 1   MDVLQNDQDDIDEQVNLKIQIKNLLKKLDKILKGREKKIIELRYGLKNGIERTQMEVANL 60

Query: 649 FCVTRERIRQIEAKAIRKL 667
             ++R  + +IE KA++KL
Sbjct: 61  LGISRSYVSRIEKKALQKL 79


>gi|171741952|ref|ZP_02917759.1| hypothetical protein BIFDEN_01055 [Bifidobacterium dentium ATCC
           27678]
 gi|283456904|ref|YP_003361468.1| RNA polymerase sigma factor [Bifidobacterium dentium Bd1]
 gi|171277566|gb|EDT45227.1| hypothetical protein BIFDEN_01055 [Bifidobacterium dentium ATCC
           27678]
 gi|283103538|gb|ADB10644.1| RNA polymerase sigma factor [Bifidobacterium dentium Bd1]
          Length = 596

 Score = 45.6 bits (106), Expect = 0.027,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +  +  L  RE ++   RF   M    + + +G    +TRERIRQIE  
Sbjct: 115 ALSSAICDLDEREYKIFNERFL--MEEPRSFKAIGGDLGITRERIRQIEKN 163


>gi|322798888|gb|EFZ20399.1| hypothetical protein SINV_07587 [Solenopsis invicta]
          Length = 1523

 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 66/464 (14%), Positives = 156/464 (33%), Gaps = 58/464 (12%)

Query: 16   EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
            +DSD         D  K ++ +A+ +G  +    N  L       EQ+++    L+ +  
Sbjct: 973  KDSDFEKELKNVQDRVKALLSVAK-QGSGSE---NKTL------VEQLDELREQLNTID- 1021

Query: 76   NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
             +    D+   +  + + +  +S + +   L K  +    + D     YL   G+  L S
Sbjct: 1022 KIYQTVDVTTNDVDDITEEGLTSITEAENVLDKIHEQLTEAED-----YLGTEGASALAS 1076

Query: 136  RE-----------------GEIAIAKRIEAGRAMMMASLCES--PLTFQALIIWRDELND 176
             +                  E  +   +    A  +  L E     T +A  + +  ++ 
Sbjct: 1077 AKLRAEQVGQQNQQMTSIAQEARLLAEVNTNEAKKLHMLAEQARNTTLEAYNLAKQTISK 1136

Query: 177  GTTLLREIIDLEACIGP-ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
             + +  EI DLE  +   E +          +  K    SQE     + +      +  +
Sbjct: 1137 YSNITDEIRDLETKLAQLEDRMDEVRNLTAIAATKSSAVSQEALDLLILDLTLPPVNIEQ 1196

Query: 236  VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME--DQLRPKVMCALDEIAEVYRE 293
            + +   S   +  +  E  +  L+++E+        ++  ++L  +        AE+  E
Sbjct: 1197 LRQQIESVSSASLQIKEQAQLLLEKNENFIKEMAEKVKKSEELLDRAQDQEAATAELLAE 1256

Query: 294  LRSLQDNAVNGQKDEKSSVK-CKVLKEKLVKLVGSLSLNQSR-------IDLLVEQLYDI 345
            L    + A    K    ++K  +   +KL +    +   + +       I+ + + +  +
Sbjct: 1257 LDEADETANKAVKRGDQTLKEAQETLKKLGEFDAEVQRERVKAQSALMDIEHIEDLIRYV 1316

Query: 346  SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
            +++    E +L    ++              RE+  +  +YA                  
Sbjct: 1317 NEQARETEKKLNGSEENAK----------SAREIVQNAQNYADKASANANNIRTEANKTK 1366

Query: 406  ILKIR--NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
            I  +R  NE++ + +    + S  +     + K     + A  +
Sbjct: 1367 IEALRLGNEVEKLHLRVDTTDSMIKQYEIQMSKDTNITAEANYK 1410


>gi|166032431|ref|ZP_02235260.1| hypothetical protein DORFOR_02134 [Dorea formicigenerans ATCC
           27755]
 gi|166028154|gb|EDR46911.1| hypothetical protein DORFOR_02134 [Dorea formicigenerans ATCC
           27755]
          Length = 830

 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 67/193 (34%), Gaps = 12/193 (6%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCE-SPLTFQALIIWRDELNDGTTLLR-EIIDL---- 187
           L    E  + +RIE     +  +L E  PL  Q +   R  L D       E+ D     
Sbjct: 630 LGAFDEDELLRRIELHLNELSQALAENQPLVLQLIEKRRRILRDRVLREHPEVFDKLQKH 689

Query: 188 -----EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
                E      +       T   +    ++    +E D  Q+++   +S A    D   
Sbjct: 690 RRKLEERLELQRASVEPQEQTPQPNQTFEKEDVPAQESDAAQDSDAAQDSDAAQDSDAAQ 749

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE-IAEVYRELRSLQDNA 301
             D+  ++    + ++ +D D +  + +A +  +      A D  +A+    ++   +  
Sbjct: 750 DSDTAQDSDAAQDSDVAQDSDAAQDSDAAQDSDVAQDSDAAQDSDVAQDSDNVQKEYELD 809

Query: 302 VNGQKDEKSSVKC 314
            N  + E +  + 
Sbjct: 810 ENTAEQESNLERQ 822


>gi|170593755|ref|XP_001901629.1| Myosin tail family protein [Brugia malayi]
 gi|158590573|gb|EDP29188.1| Myosin tail family protein [Brugia malayi]
          Length = 1985

 Score = 45.6 bits (106), Expect = 0.028,   Method: Composition-based stats.
 Identities = 63/477 (13%), Positives = 161/477 (33%), Gaps = 27/477 (5%)

Query: 151  AMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQK 210
              +   L  +      L+   + L      L   I        E         +     +
Sbjct: 1509 RNLSTELFRAKSAQDELLEQIESLRRENKSLSLEIKDLTDQLTEGGRSVHELQKMVRRLE 1568

Query: 211  REDSSQEKERDDVQETEGDIESAAKVSKDD----RSKVDSPPENAENDERNLDEDEDDSA 266
             E    +K  DD +      E+    ++ +    R++++   +  E +  N  ++   + 
Sbjct: 1569 VEKEELQKALDDAESALEAEEAKVLRAQVEVSQVRAEIEKRIQEKEEEFENTRKNHQRAL 1628

Query: 267  HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK-DEKSSVKCKVLKEKLVKLV 325
             ++ A  +        AL    ++ +++  L+    +  K +  +    K  +E++ +L 
Sbjct: 1629 ESMQATLEAEMKAKQEALRIKKKLEQDINELEVALDHANKANADAQKTIKRYQEQIRELQ 1688

Query: 326  GSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI----KRDVFLERHQGRELDP 381
              +   Q + D L EQL +  KR    + E   LA    +    +R    +  + RE   
Sbjct: 1689 MQIEDEQRQKDDLAEQLSNTQKRAAILQAEKDELANQAEMAERARRAAEQDAIELRETVN 1748

Query: 382  HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
               +                      K+ +E++++ VE     S+ ++   M+++   +A
Sbjct: 1749 DLTNQVNAINNTR------------RKLESELQTVHVELDDVTSQLKNTDEMLKQASADA 1796

Query: 442  SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
            +   +E+ +     V    ++        +  +Q       +AA +     G K      
Sbjct: 1797 ARLAEELRQEQEHSVH--VERMRRALEVQIKEMQVRLDEAEQAALRS----GQKIIAKLE 1850

Query: 502  WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
              +++       +Q  +      ++    ++     +     K      E+  KL + ++
Sbjct: 1851 MRIRELEQELDGEQRRSSDYEKELKKGDRRIKELQFQCEEDRKNNDRLTELVDKLQIKIK 1910

Query: 562  GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
              ++ ++  +E  ++      +  + L D  E  +      + +++  R +T   LA
Sbjct: 1911 IYKRQVEEAEEVAAINLGKYRQLQTQLDDANERADIAENSLAKLRSRNRASTIAPLA 1967


>gi|269121539|ref|YP_003309716.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268615417|gb|ACZ09785.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 309

 Score = 45.6 bits (106), Expect = 0.029,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 95/250 (38%), Gaps = 32/250 (12%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            + + + +       K        + ++V  +L++VI  + +Y   G  FLDL+QE  IG
Sbjct: 72  ELYLDDIKEHNIKQLKIREIDETDRDQLVNKHLKIVIRESLQYVKLGFSFLDLVQEATIG 131

Query: 481 LMKAAEKF-DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV-VRTARR 538
           ++   EK  +     +F      W+K    + I +    I       +  + + ++    
Sbjct: 132 VINGIEKLKNSESDIEF------WLKNFAIKYILEYQKKILKDFKASELAYILYLKVQLE 185

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDFIEDKNA 597
           ++N                + +E + K + I    + +L+      D          +N+
Sbjct: 186 LNN---------------GLSLEEISKQMNIELNYLNALQELFTKMDDMP-------ENS 223

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            S ++       +   + +   L   +ER+L M +G+  +  +  +E+ K   +    I 
Sbjct: 224 YSIVEKVSHLTRKYVLSNIPKKLNYLDERILMMHYGLD-DKFYKTKEISKILNIEESNIN 282

Query: 658 QIEAKAIRKL 667
            +  KA+ KL
Sbjct: 283 VLREKALTKL 292


>gi|322498589|emb|CBZ33661.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 4825

 Score = 45.6 bits (106), Expect = 0.030,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 85/247 (34%), Gaps = 19/247 (7%)

Query: 60   SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            ++Q+++   +++         D+    E  E   D A+         ++ +  +D   D+
Sbjct: 3984 TDQIDNEDQLMNMKDKEEEQADEQRQGEKDEGEEDTAADVETDFNGQKENRSESDGEGDE 4043

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
                  +EMG ++  + E E   AK+ +AG A  M                         
Sbjct: 4044 EGEESDKEMGDVDDGT-EQERKKAKK-DAGDADDMNEDAGD--------------AAEEV 4087

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE--RDDVQETEGDIESAAKVS 237
               ++ + +       + G F           ED S E +   DD +    +  S+   S
Sbjct: 4088 PEDDLAEGDEHREDNEETGGFEDKADEIRDADEDRSCEHDVVGDDDKSEMDEDGSSDGNS 4147

Query: 238  KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             +         + +  D++   + +++   +  A E+++         E +E+  E    
Sbjct: 4148 VEHSDTDGEERDESARDDKLPSDADEEPEESDVASEERVDSDA-ATDAERSELGEEEVEQ 4206

Query: 298  QDNAVNG 304
            +DN+ N 
Sbjct: 4207 RDNSENA 4213


>gi|239934592|emb|CAR94610.1| DNA-directed RNA polymerase subunit D [uncultured Acidobacteria
           bacterium]
          Length = 226

 Score = 45.6 bits (106), Expect = 0.031,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 95/240 (39%), Gaps = 21/240 (8%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP 193
           L+R+GE+ IAKRIE G+  ++ SL  S +  + +I   D+L    ++++++I        
Sbjct: 1   LTRDGEVEIAKRIERGQLAVLKSLSRSTVIVREIISLGDQLMKDPSIIKDLIQFSD---- 56

Query: 194 ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEN 253
                          ++  D   E++ ++   T G+I    K  +  R K+D+  +  + 
Sbjct: 57  ---------------EELTDEKVEQKLEETILTIGEIGKTYKKVQALRVKLDATSKTQKP 101

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
             R        +   LS +   L    +  L  +  + R +  ++       K E+    
Sbjct: 102 QFRRARWKLGRTRVQLSLLIRSLEFSNLEKLRLMDLMKRTVERVRPLQQELTKLER--KA 159

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             V K+    ++  +   + RI+ +  +    +  +      +++   +  I ++  +E 
Sbjct: 160 DHVRKDARKTVLKDIRAVKVRIEAIEAETKSTALELRRTLQSMVQGQITAEIAKNEMVEA 219



 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 44/199 (22%), Positives = 80/199 (40%), Gaps = 34/199 (17%)

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLK 318
           D   T   +E +L   ++  + EI + Y+++++L+       K +K     +  K    +
Sbjct: 56  DEELTDEKVEQKLEETIL-TIGEIGKTYKKVQALRVKLDATSKTQKPQFRRARWKLGRTR 114

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
            +L  L+ SL  +      L++ +    +R+   + EL +L +     R           
Sbjct: 115 VQLSLLIRSLEFSNLEKLRLMDLMKRTVERVRPLQQELTKLERKADHVRKD--------- 165

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
                                   +  I  ++  I++I  ET  +  E R  +  + +G+
Sbjct: 166 -------------------ARKTVLKDIRAVKVRIEAIEAETKSTALELRRTLQSMVQGQ 206

Query: 439 CEASIAKKEMVEANLRLVI 457
             A IAK EMVEANLRLVI
Sbjct: 207 ITAEIAKNEMVEANLRLVI 225


>gi|221482763|gb|EEE21094.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 1373

 Score = 45.6 bits (106), Expect = 0.032,   Method: Composition-based stats.
 Identities = 35/241 (14%), Positives = 78/241 (32%), Gaps = 9/241 (3%)

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
           G  G         S   +   +               D      +  E     E  L E 
Sbjct: 206 GNSGVPTPAAAGRSGSPKTQSLSRAGKRSGMTPFGDFDGAVGPGANDEKTMELEAELKEL 265

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKL 321
                  L+  E Q   +V        E++  ++ L++ +    +      +    +++L
Sbjct: 266 R----GKLAEQERQAADRVRELEKRERELFGRVQELEEQSALQAQVRDGFSELLDAQQQL 321

Query: 322 VKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDP 381
            +L       Q R   LVE+  ++ +++  ++ EL +L Q         L+RH+  E+  
Sbjct: 322 QQLQREHRQLQQREQELVEKESELQRQLEQHQRELQQLHQEVKE-----LQRHRAAEMRT 376

Query: 382 HWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEA 441
           + V  A      E +  V      +  +    + ++    + I        ++++    A
Sbjct: 377 NGVVEASLHEAEEQRAQVQQLERKVRDLEKLHRDVTERDAMRIRALEEENKLLKRTSGAA 436

Query: 442 S 442
           +
Sbjct: 437 A 437


>gi|226949740|ref|YP_002804831.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
 gi|226840763|gb|ACO83429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
          Length = 183

 Score = 45.2 bits (105), Expect = 0.032,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 63/198 (31%), Gaps = 56/198 (28%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +L QEG +GLMKA  +FD   G KFSTYA  +V  AI     D                 
Sbjct: 30  ELFQEGCLGLMKAVNRFDTSRGIKFSTYAYPYVDGAILIMARDDKWYG------------ 77

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
                                           RK       P SL+  I           
Sbjct: 78  ------------------------------KNRKERFEKSAPYSLDAAIKG--------- 98

Query: 592 IEDKNAVSPLDSAIQANLRE-TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +E++     L      N  +     ++  L    + ++ M +  G        E+ K   
Sbjct: 99  LENEMPYINLIGNDDFNFEKIEVKMLVDELPSDLKDIVNMIYIEGFTQ----TEIAKIIG 154

Query: 651 VTRERIRQIEAKAIRKLK 668
            ++  I +++ +A+  L+
Sbjct: 155 CSQISISRLKKEALDYLR 172


>gi|217033290|ref|ZP_03438721.1| hypothetical protein HP9810_9g43 [Helicobacter pylori 98-10]
 gi|216944231|gb|EEC23656.1| hypothetical protein HP9810_9g43 [Helicobacter pylori 98-10]
          Length = 143

 Score = 45.2 bits (105), Expect = 0.034,   Method: Composition-based stats.
 Identities = 23/151 (15%), Positives = 58/151 (38%), Gaps = 14/151 (9%)

Query: 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579
            I    R  I  +     +  N+  +EP+   +A+ L   +E +++    +     +   
Sbjct: 1   MISRSNRKLIKSIDIEITKHLNEHGKEPSDAYLAEVLGENIEKIKEAKTASD----IYAL 56

Query: 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD 639
           +  ++  +  +                  L E   + L  ++ RE+ ++++ +      +
Sbjct: 57  VPIDEQFNAIE------QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EE 106

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
             L E+ +   +T  RI QI  + I+K++  
Sbjct: 107 LNLSEIKEILGITESRISQIIKEVIKKVRKS 137


>gi|148654246|ref|YP_001274451.1| ECF subfamily RNA polymerase sigma-24 factor [Roseiflexus sp. RS-1]
 gi|148566356|gb|ABQ88501.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Roseiflexus sp.
           RS-1]
          Length = 215

 Score = 45.2 bits (105), Expect = 0.034,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 6/96 (6%)

Query: 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFG 633
           +SL+ P   +D   L   IEDK      D+  +  +R      +A L   E +V+ +R  
Sbjct: 118 LSLDAP-TGDDGLPLHRMIEDKTLEQHADAYQEEQIRARLDAAIARLPVIERQVVTLRLD 176

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              + D     + +QF ++   +  I  +A+++LK 
Sbjct: 177 GVASVD-----IARQFGMSPANVTHIHHRAVKRLKQ 207


>gi|291393661|ref|XP_002713463.1| PREDICTED: laminin, beta 2 [Oryctolagus cuniculus]
          Length = 1802

 Score = 45.2 bits (105), Expect = 0.036,   Method: Composition-based stats.
 Identities = 36/311 (11%), Positives = 97/311 (31%), Gaps = 30/311 (9%)

Query: 24   FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
             + ++   +++I+  +            FL  +    + +E     +  + I        
Sbjct: 1509 VEQANQELRELIQSVK-----------DFLSQEGADPDSIEMVATRVLELAIPASPEQIQ 1557

Query: 84   EDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA 143
                   + +   +               A++   D  R   R          EGE   A
Sbjct: 1558 HLAGAIAERVRSLADVDTILARTVGDVRRAEQLLQDAQRARSR---------AEGEKQKA 1608

Query: 144  KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
            + ++A       +   +    +  +    +       ++E +         +        
Sbjct: 1609 ETVQAALEEAQRAQGAAQGAIRGAVADTQDTEQTLRQVQERMAGTEQALSSAGERARQLD 1668

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                  K + +         +ET G   SA   +++    +  P  +     R L E + 
Sbjct: 1669 SLLEALKLKRAGNSLTASTAEETAG---SAQGRAREAEQLLQGPLSDRYQTVRALAERKA 1725

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKE 319
            +      A  +QLR +    L    +   +L+ LQ+     +++E++    + +   L+ 
Sbjct: 1726 EGVLAAQARAEQLRDEARGLLQAAQD---KLQRLQELEGTYEENERALEGKAAQLDGLEA 1782

Query: 320  KLVKLVGSLSL 330
            ++  ++ +++L
Sbjct: 1783 RMRGVLQAINL 1793


>gi|57908870|gb|AAW59363.1| stationary phase sigma factor [Azotobacter salinestris]
          Length = 55

 Score = 45.2 bits (105), Expect = 0.037,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
            RFG+  +   TLEEVG++  +TRER+RQI+ +A++ L+       L S
Sbjct: 2   RRFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKPLREILEKNGLSS 50


>gi|118362282|ref|XP_001014368.1| RNB-like protein [Tetrahymena thermophila]
 gi|89296135|gb|EAR94123.1| RNB-like protein [Tetrahymena thermophila SB210]
          Length = 1273

 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 80/190 (42%), Gaps = 3/190 (1%)

Query: 168  IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
            II    + +   ++R++ +  A    E K       +    Q  +   ++K +D   + +
Sbjct: 902  IIKTYLIFEKRKIVRQLNEYFAICDNEKKQKVQLDQKIQIKQAEKSEEEQKIKDLELQNQ 961

Query: 228  GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE- 286
              IE   ++  DD      P    E+ E++  +DED+    ++    QL+ K +  L + 
Sbjct: 962  EKIEVEEEIQSDDNQMEIIPQIQIEDQEKSFSQDEDEDEDNIN--IAQLKEKKINQLQKQ 1019

Query: 287  IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            I    +E++ +Q    N  K ++ +   +  +++  KL   +   + +ID L +QL ++ 
Sbjct: 1020 IKHKQKEIQKIQKQIPNESKIQELNSNLETYQKQSEKLKEQIKTQEIQIDDLKKQLDELK 1079

Query: 347  KRIMHNEGEL 356
              I      +
Sbjct: 1080 SEIQKINQNI 1089


>gi|116193499|ref|XP_001222562.1| hypothetical protein CHGG_06467 [Chaetomium globosum CBS 148.51]
 gi|88182380|gb|EAQ89848.1| hypothetical protein CHGG_06467 [Chaetomium globosum CBS 148.51]
          Length = 2317

 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 52/435 (11%), Positives = 146/435 (33%), Gaps = 49/435 (11%)

Query: 68   AMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLRE 127
              ++ +   V + +     E ++   ++++  +      +  ++    +T   V M    
Sbjct: 1525 EQVNELQARVAELEQRLRAEETKAEAEVSARRAAEDRAAEAGRELQSVATRIEVEM---- 1580

Query: 128  MGSIELLSR----EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
            +    L  R    E  +  A+     +     +   +      +        +  T LR+
Sbjct: 1581 INKSALNQRIADLEDRVQHAETDAEEQVKGRRA---AEDRLSEVQRLLRIATEEETRLRD 1637

Query: 184  IIDLEACIGPESKG----GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            ++D +      ++          T   + Q     SQ + ++ +   E D   A K ++ 
Sbjct: 1638 LVDEKDEKIKAAEALHSQSAIRLTVLEASQATAHQSQGEAQNRINALEADAREARKEAQH 1697

Query: 240  DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQ 298
             RS+ D         +++L    D++   +  + D L  ++    + I + +R +  S+Q
Sbjct: 1698 WRSETDRIGAIIRRGDKDLAHALDEN-KAMHKLIDTLGTQLQEN-ERIRDTWRTKFISMQ 1755

Query: 299  DNAVNGQK-----DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            D      +     + + + K + L  +   L   L       + +  +L  +        
Sbjct: 1756 DEMAQATREITEENARRTKKEQALLARQEVLDARLQAEARTRERIETELERLEMGERQGM 1815

Query: 354  GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
              +    +  G+  ++  E H+  +    + +  ++  E   +            ++ E+
Sbjct: 1816 RAVSECKRLEGLLAELRTENHKLHQSSLRYQAEFQEARESGAREVQRTR----DAMQAEV 1871

Query: 414  KSISVETGISISEFRHIVSMVR------KGECEASIAKK----------------EMVEA 451
            ++ + +  ++  E    VS +R      K + + + A+                 E+V  
Sbjct: 1872 ENANHQVNVAREELEDQVSRLRSQLDQVKLDADTAKARHDMLLEEAQNSKQTNHDELVRK 1931

Query: 452  NLRLVISVAKKYTNR 466
            +   +  +  +Y  +
Sbjct: 1932 HQNEIEDLQARYERQ 1946


>gi|72393049|ref|XP_847325.1| kinesin [Trypanosoma brucei TREU927]
 gi|62176499|gb|AAX70606.1| kinesin, putative [Trypanosoma brucei]
 gi|70803355|gb|AAZ13259.1| kinesin, putative [Trypanosoma brucei brucei strain 927/4 GUTat10.1]
          Length = 1456

 Score = 45.2 bits (105), Expect = 0.038,   Method: Composition-based stats.
 Identities = 89/610 (14%), Positives = 195/610 (31%), Gaps = 43/610 (7%)

Query: 61   EQMEDTVAMLSNMGINVVDGDDLEDE-EGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            E ++     L     +V D D+   E E S ++L      S +SV  +  +     ++ D
Sbjct: 737  ESLDTLRQQLKESEASVEDRDNRLKEHEESLNTLRQQLKESEASVEDRDNRLKEHETSLD 796

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
             +R  L+E     +  R+  +   K  E     +   L ES  + +      + L +  T
Sbjct: 797  TLRQQLKE-SEASVEDRDNRL---KEHEESLNTLRQQLKESEASVE---DRDNRLKEHET 849

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
             L  +   +      S     +  + H         Q KE +   E   +     + S +
Sbjct: 850  SLDTL-RQQLKESEASVEDRDNRLKEHETSLNTLRQQLKESEASVEDRDNRLKEHEESLN 908

Query: 240  DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
               +     E +  +  N  ++ ++S +TL     +    V    + + E    L +L+ 
Sbjct: 909  TLRQQLKESEASVENRDNRLKEHEESLNTLRQQLKESEASVEDRDNRLKEHEESLNTLRQ 968

Query: 300  NAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                 +   E    + K  +E L  L   L  +++ ++    +L +  + + +   + L+
Sbjct: 969  QLKESEASVEDRDNRLKEHEESLNTLRQQLKESEASVEDRDNRLKEHEESL-NTLRQQLK 1027

Query: 359  LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG---EWKNFVACEVDSILKIRNEIKS 415
             +++    RD  L+ H   E   + +       E    +  N +     S+  +R ++K 
Sbjct: 1028 ESEASVEDRDNRLKEH---ETSLNTLRQQLKESEASVEDRDNRLKEHETSLDTLRQQLKE 1084

Query: 416  ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
                     +  +           E+    ++ ++ +   V     +          L Q
Sbjct: 1085 SEASVEDRDNRLKE--------HEESLDTLRQQLKESEASVEDRDNRLKEHEESLNTLRQ 1136

Query: 476  EGNIGLMKAAEKFDWCLGYKFSTYAMWW---------VKQAITRSIADQSCTIRIPVHMR 526
            +       + E  D  L     +              V+    R    ++    +   ++
Sbjct: 1137 Q-LKESEASVEDRDNRLKEHEESLDTLRQQLKESEASVEDRDNRLKEHETSLDTLRQQLK 1195

Query: 527  DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586
            +    V     R+    +   T  +  K+    VE     LK  +  +        E  +
Sbjct: 1196 ESEASVEDRDNRLKEHEESLNTLRQQLKESEASVEDRDNRLKEHETSLDTLRQQLKESET 1255

Query: 587  HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG 646
             +     D   +       QA+L+E    +   L   EE+        G      ++E+ 
Sbjct: 1256 TVVVLTADLKQLEEEMFIDQADLKERIAFLEVELKRCEEK--------GAYYSALVDEMQ 1307

Query: 647  KQFCVTRERI 656
             +     ER+
Sbjct: 1308 AELHCANERV 1317


>gi|302872420|ref|YP_003841056.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302575279|gb|ADL43070.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 310

 Score = 45.2 bits (105), Expect = 0.039,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 78/230 (33%), Gaps = 58/230 (25%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYT----NRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
               ++ ++ ++  NL+LV  VA K+         +  DLI EG  GL+ AA  +   LG
Sbjct: 7   NQLDNLHRQLLIANNLKLVYHVANKFMPCPKGYMYEVDDLISEGYFGLVVAANNYKPELG 66

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
             FS+YA   ++                         K+ R+  +               
Sbjct: 67  TPFSSYACKVIE------------------------SKIKRSLPKYK------------- 89

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                        L       S  +   +ED+S LG+ I D    S     I+ +  +  
Sbjct: 90  -------------LSSAISLDSPVSKEPEEDSSTLGEIISD--GYSVEKEVIRKDTLDRL 134

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHT--LEEVGKQFCVTRERIRQIEA 661
            R   +LT  E+  +      G N   +  L    ++  + R R  Q EA
Sbjct: 135 QRFFDTLTDEEKERVLYYISTGKNPPASDILFRKARRKIIARMRQEQFEA 184


>gi|326668399|ref|XP_689302.5| PREDICTED: trafficking kinesin-binding protein 2 [Danio rerio]
          Length = 993

 Score = 45.2 bits (105), Expect = 0.039,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 82/236 (34%), Gaps = 13/236 (5%)

Query: 133 LLS-REGEIAIAKRIEAGRAMMMASLCESPLTFQA----LIIWRDELNDGTTLLREIIDL 187
           LLS R+ ++ +A RI          L E   + +      +    +L        E++ +
Sbjct: 113 LLSERDRDLELAARIGQSLLQRNHVLQERNESLEEQLAQALDQVHQLQHELAKKDELLRM 172

Query: 188 EACIGPESKGGFFHGTE-------GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
            A    ES+      T        G +    +  + + +  D++E    + S A   K +
Sbjct: 173 VASASEESETDSSCSTPLRHPVPAGAALALSQLEALQSKLQDLEEENLTLRSEACHLKKE 232

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               +   +   ND      + +    +L+    Q    +M   +EIA++  ++  LQ  
Sbjct: 233 TITYEEKEQQLVNDCVKELRESNSQMVSLTDELSQKNEDLMRHQEEIAQLLSQIVELQHR 292

Query: 301 AVN-GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                 + E+  +  +  KE   +L   L     R    V  L++  + I     +
Sbjct: 293 VKELALEKEELRIHLQASKEAQRQLTNELKELSDRNAECVGMLHESQEEIKDLRSK 348


>gi|237784938|ref|YP_002905643.1| ECF-family sigma factor D [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237757850|gb|ACR17100.1| ECF-family sigma factor D [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 203

 Score = 45.2 bits (105), Expect = 0.040,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 64/195 (32%), Gaps = 19/195 (9%)

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
              GL+ AA   D     K   Y    V     R               ++    V+++ 
Sbjct: 9   AINGLVAAAASGDRDALQKVMDYIHPKVV-MYCRHRLSDDSFPGPEDTAQEICMAVLKSL 67

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            R  ++     +         +    V+   +      S       + T  + + I D  
Sbjct: 68  DRFVDRGTPFMSYV-----YGIASHKVKDGYRSMGRDRS-------QPTDEIPESIHD-- 113

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A  P + AIQ++ R    R+L  L  R   ++ +R   G  +    EE  K    T   +
Sbjct: 114 AAGPEELAIQSDGRNKLLRLLDILGERPREIIILRVLEGYTS----EETAKIIGSTPNAV 169

Query: 657 RQIEAKAIRKLKHPS 671
           R  + +AI KLK   
Sbjct: 170 RVAQFRAIAKLKKAM 184


>gi|298247626|ref|ZP_06971431.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
 gi|297550285|gb|EFH84151.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
          Length = 450

 Score = 45.2 bits (105), Expect = 0.040,   Method: Composition-based stats.
 Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 7/108 (6%)

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHL-GDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           +  VR  L         +        + L  + +E+   +       +A +R    R+L+
Sbjct: 62  MRQVRSWLYAAARTTLADYWQEQAKGAALPLETLEEHAIIPHELEQGEAQVR--VQRLLS 119

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            L  RE +VL +R+  G    +T  EVG++  +T   +R ++ +A+R+
Sbjct: 120 LLPERERQVLLLRYMQG----YTAAEVGQELGLTPGHVRVLQLRALRQ 163


>gi|240137781|ref|YP_002962253.1| hypothetical protein MexAM1_META1p1094 [Methylobacterium
          extorquens AM1]
 gi|240007750|gb|ACS38976.1| conserved hypothetical protein [Methylobacterium extorquens AM1]
          Length = 142

 Score = 45.2 bits (105), Expect = 0.042,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 30 SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
          +  ++I L R RG +T EEL A LP D +  + +   +  L   G++V
Sbjct: 8  TLDRLIALGRPRGELTAEELRAVLPVDSMDVDALVLVMLELEEAGVSV 55


>gi|47089282|gb|AAT10960.1| sigma 70 factor [Pseudomonas syringae pv. coronafaciens]
 gi|47089340|gb|AAT10989.1| sigma 70 factor [Pseudomonas syringae pv. oryzae]
 gi|47089342|gb|AAT10990.1| sigma 70 factor [Pseudomonas syringae pv. oryzae]
 gi|47089370|gb|AAT11004.1| sigma 70 factor [Pseudomonas syringae pv. syringae]
          Length = 148

 Score = 45.2 bits (105), Expect = 0.042,   Method: Composition-based stats.
 Identities = 19/194 (9%), Positives = 53/194 (27%), Gaps = 46/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAA 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +  + + ESA    ++D  +    P  A+     + +  + +   L  +    +  + 
Sbjct: 50  KAEGDDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKLGRDDKHAIA 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +                                    L +L   + L   + + LVE+
Sbjct: 110 EMV-----------------------------------ALAELFMPIKLVPKQFEGLVER 134

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 135 VRGALERLRAQERA 148


>gi|330948067|gb|EGH48327.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 110

 Score = 44.8 bits (104), Expect = 0.042,   Method: Composition-based stats.
 Identities = 17/101 (16%), Positives = 39/101 (38%), Gaps = 4/101 (3%)

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
           +    E +  P  + A      V  ++   +       +D+K ++   V    L +L   
Sbjct: 4   SDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMV---ALAELFMP 60

Query: 328 LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKR 367
           + L   + + LVE++    +R+   E  +++L      + R
Sbjct: 61  IKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPR 101


>gi|161501819|ref|NP_760693.2| RNA polymerase sigma factor [Vibrio vulnificus CMCP6]
 gi|320155548|ref|YP_004187927.1| RNA polymerase sigma-70 factor, ECF subfamily [Vibrio vulnificus
           MO6-24/O]
 gi|319930860|gb|ADV85724.1| RNA polymerase sigma-70 factor, ECF subfamily [Vibrio vulnificus
           MO6-24/O]
 gi|319999269|gb|AAO10220.2| RNA polymerase sigma-70 factor, ECF subfamily [Vibrio vulnificus
           CMCP6]
          Length = 197

 Score = 44.8 bits (104), Expect = 0.042,   Method: Composition-based stats.
 Identities = 20/104 (19%), Positives = 35/104 (33%), Gaps = 11/104 (10%)

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            + +          +  D +E         S  Q  L+E   R L  L   +  VL+  +
Sbjct: 105 DLHIHADDIWPSDYYPLDLVE-------RYSPEQDMLKEQVMRFLDCLPKAQRDVLQAVY 157

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              +      E         + R+R     A+ KL+H  ++ KL
Sbjct: 158 IEDLPHQQVAEMFDIPLGTVKSRLRL----AVEKLRHTMQADKL 197


>gi|47089310|gb|AAT10974.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089312|gb|AAT10975.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089314|gb|AAT10976.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089318|gb|AAT10978.1| sigma 70 factor [Pseudomonas syringae pv. maculicola str. M6]
 gi|47089320|gb|AAT10979.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089322|gb|AAT10980.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089326|gb|AAT10982.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089388|gb|AAT11013.1| sigma 70 factor [Pseudomonas syringae pv. tomato]
          Length = 149

 Score = 44.8 bits (104), Expect = 0.043,   Method: Composition-based stats.
 Identities = 19/194 (9%), Positives = 49/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAV 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +  + D E +A  S ++      P             D+ +          +     +
Sbjct: 50  KAEGADDDEEESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             L  +AE++                                    + L   + + LVE+
Sbjct: 110 AELVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|167765724|ref|ZP_02437777.1| hypothetical protein CLOSS21_00212 [Clostridium sp. SS2/1]
 gi|167712597|gb|EDS23176.1| hypothetical protein CLOSS21_00212 [Clostridium sp. SS2/1]
          Length = 101

 Score = 44.8 bits (104), Expect = 0.044,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 40/86 (46%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R+ +     A + ++E    +V   A+ +   G    DLIQEG IGL KA   +   
Sbjct: 11  KLLRQIQSGNDDAMECLLERYRDMVRKEARSFFLAGGDEEDLIQEGMIGLFKAVTSYQEE 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSC 517
               FST+A   V++ I  +I   + 
Sbjct: 71  KNTSFSTFAYLCVQRQIYTTITAFNR 96


>gi|325182757|emb|CCA17212.1| conserved hypothetical protein [Albugo laibachii Nc14]
 gi|325189163|emb|CCA23687.1| conserved hypothetical protein [Albugo laibachii Nc14]
          Length = 1535

 Score = 44.8 bits (104), Expect = 0.045,   Method: Composition-based stats.
 Identities = 76/606 (12%), Positives = 195/606 (32%), Gaps = 69/606 (11%)

Query: 39   RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS 98
            ++R  +T EEL   L   ++ SE++   +        N++D +    +E  + +L     
Sbjct: 851  KER--LTYEELEVHLHQFQLESERLNQELDEQKASFQNILDQEKRAHDE--KTALQEDHW 906

Query: 99   ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
                   + K KD+ D    D                      ++ + +  R    +S+ 
Sbjct: 907  RVQVHDAVVKTKDNNDALIHD----------------------LSVKAKNDRIQYRSSIS 944

Query: 159  ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
            E       ++++R++L    +   +  ++ A I  E     +         K E    + 
Sbjct: 945  EY---QSEILLYRNDLEKAESRRHD-QEMTATIRLEQLKKNYDKQLAQETTKFELEKVKL 1000

Query: 219  ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
             +D     +   E+  ++ +D    +     + E  ++   +        ++ +  +L+ 
Sbjct: 1001 AQDLTNAQQSLKEALEQIDQDHLRHLSLLSGSIETTKKEAQKAVTSVQGQVAGLNQELK- 1059

Query: 279  KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
             ++ AL +  E   +++S      +  K  K+S+K +       +    L  + S ++++
Sbjct: 1060 LLLQALTQKDEEINQVQSKTSVYHDKIKRLKASLKQQE------QETARLRRSNSTLEVI 1113

Query: 339  VEQLYDI---SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
              +  +     KR+        ++ QS  I ++         E         +     + 
Sbjct: 1114 ANEQKEALHQLKRLNTVHQSQAQMLQSQLIPKE--------NETQAVKQHMTQLHAAHQE 1165

Query: 396  KNFVACEVDSILKIRN-EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             + +A   D +  ++  +IK     + ++          + + +       +E+ +  L+
Sbjct: 1166 MSLLAQFNDRLCFVQKAKIKKYENNSRVT-------QRRIERLQVFGRSIMEEIEQLLLQ 1218

Query: 455  LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD 514
             V+  +    N+G        E    L             + +   +             
Sbjct: 1219 PVVRGSNHTRNKGSPQEVGQDERFGELTSKQRIQSKESTLRHNLQLLHR----------- 1267

Query: 515  QSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
               T +        ++    TA++   + K E   +   + +   +E   + L   K  +
Sbjct: 1268 -RWTKKWEFLTASVVNNANETAKQREQQ-KCETEVKVRDESIQSEIERQNESLLRNKMQL 1325

Query: 575  SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
              +  +  ++ S L   +  +N     +        +   + L     RE    R    +
Sbjct: 1326 HHQLQLLRKEKSQLSTTLTFQNTTLMTELNDAKKRSKILEQKLEEYHSRERNRSRESKLV 1385

Query: 635  GMNTDH 640
              N  H
Sbjct: 1386 MENESH 1391


>gi|37680783|ref|NP_935392.1| RNA polymerase sigma factor [Vibrio vulnificus YJ016]
 gi|37199532|dbj|BAC95363.1| RNA polymerase sigma-70 factor, ECF subfamily [Vibrio vulnificus
           YJ016]
          Length = 197

 Score = 44.8 bits (104), Expect = 0.046,   Method: Composition-based stats.
 Identities = 20/104 (19%), Positives = 35/104 (33%), Gaps = 11/104 (10%)

Query: 573 PISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            + +          +  D +E         S  Q  L+E   R L  L   +  VL+  +
Sbjct: 105 DLHIHADDIWPSDYYPLDLVE-------RYSPEQDMLKEQVLRFLDCLPKAQRDVLQAVY 157

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
              +      E         + R+R     A+ KL+H  ++ KL
Sbjct: 158 IEDLPHQQVAEMFNIPLGTVKSRLRL----AVEKLRHTMQADKL 197


>gi|37520799|ref|NP_924176.1| hypothetical protein glr1230 [Gloeobacter violaceus PCC 7421]
 gi|35211794|dbj|BAC89171.1| glr1230 [Gloeobacter violaceus PCC 7421]
          Length = 296

 Score = 44.8 bits (104), Expect = 0.047,   Method: Composition-based stats.
 Identities = 24/135 (17%), Positives = 53/135 (39%), Gaps = 11/135 (8%)

Query: 538 RMSNKIKREPTPEEIAKKLAM---PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
           R+   ++      E+AK   M     + + +        +SL  PI   + +     I  
Sbjct: 156 RLVQGLEDSQVRPELAKMRQMLGVGRKVILRRDPRLVPALSLNCPIRPGEGNEEYFDI-- 213

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
             A +P  + ++   R+     L  LT  E  V+   F        + +E+ ++  ++  
Sbjct: 214 --AAAPRLAGMEEACRQALHESLVHLTAGERLVVLGLFFAN----RSRKELAEEAGISTA 267

Query: 655 RIRQIEAKAIRKLKH 669
           R+ Q+  +A ++L+ 
Sbjct: 268 RVSQLLQQAYKRLRE 282


>gi|254560381|ref|YP_003067476.1| hypothetical protein METDI1916 [Methylobacterium extorquens DM4]
 gi|254267659|emb|CAX23505.1| conserved hypothetical protein [Methylobacterium extorquens DM4]
          Length = 142

 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 30 SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
          +  ++I L R RG +T EEL A LP D +  + +   +  L   G++V
Sbjct: 8  TLDRLIALGRSRGELTAEELCAVLPVDSMDVDALVLVMLELEEAGVSV 55


>gi|149917779|ref|ZP_01906274.1| DNA-binding protein AsgB [Plesiocystis pacifica SIR-1]
 gi|149821299|gb|EDM80701.1| DNA-binding protein AsgB [Plesiocystis pacifica SIR-1]
          Length = 166

 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 20/40 (50%), Positives = 26/40 (65%), Gaps = 1/40 (2%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           TLEEVG+   +TRERIRQ+E + + KLK       L S+L
Sbjct: 125 TLEEVGEILNLTRERIRQVEVRGLMKLKEAG-GDDLMSYL 163


>gi|312384947|gb|EFR29553.1| hypothetical protein AND_01358 [Anopheles darlingi]
          Length = 1096

 Score = 44.8 bits (104), Expect = 0.048,   Method: Composition-based stats.
 Identities = 49/434 (11%), Positives = 131/434 (30%), Gaps = 37/434 (8%)

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
           +T      A    + +     +PP   +   +    +             + +P      
Sbjct: 472 QTHPPAAPAGDSGEHEEKDATTPPATGDGAPKTFGHNPARRKSIFDGDTGESQPVATALD 531

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            ++  +   LR  Q                +    ++ ++  +++L Q  ID L+E    
Sbjct: 532 KKLDTLGSNLRICQ-------------ASIESFHAQIEEVRRTITLKQKYIDDLIENSET 578

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            S        +  +L   Y   +    +       D   ++  K       +     E  
Sbjct: 579 RSVAKSRFSKKKHKLEAEYEKTKKQLRKA-VVNGTDKDEINRLKSHTSHLEQRLKDLESI 637

Query: 405 SIL--KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             +  +  ++ K +      S  +   +  +++K      + ++E  E  L  V   A +
Sbjct: 638 GFIAGEAGHKKKKLQQSIKDSQKQLEVLQRLLKK-----ELDRREGFEKELEAVQKEAAR 692

Query: 463 YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               G         G   L     +       +  ++    +K+  +      +      
Sbjct: 693 TVRSG-------NAGAGTLELNESRSKIRNMNERISHIEHVLKEKSSNLKRYVNKRSAEK 745

Query: 523 VHMRDKIHKVVRTARRM-SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
             +R +I  + RT   +   + + +    E  +      +  RK+++  +   +++  I 
Sbjct: 746 ESLRCEIRNLRRTRDHLVEQRCQLDRKLREDKRP---SFDEERKLVECDEAIEAIDAAIE 802

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
            ++     + I  + ++   +S  +    +     L  L+  E R L  ++   +     
Sbjct: 803 MKN-----ELICGRRSIDTDESLQREKGEQMLMARLNKLSADEMRTLLYKYFQKVVDLKE 857

Query: 642 LEEVGKQFCVTRER 655
                +   ++ ER
Sbjct: 858 ASRKLELQFISLER 871


>gi|299473300|emb|CBN77699.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 6779

 Score = 44.8 bits (104), Expect = 0.052,   Method: Composition-based stats.
 Identities = 85/553 (15%), Positives = 167/553 (30%), Gaps = 86/553 (15%)

Query: 167  LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
            L   R    +    L++   L A  G              + + +E ++Q + +D++   
Sbjct: 5305 LAELRARHQESENFLKD--SLRAEAGARRARMRQRIAARTAERVKELTAQRRSKDEIHAE 5362

Query: 227  EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ-LRPKVMCALD 285
               I  A +  ++    V +    A            +++  ++  E + LR     A+ 
Sbjct: 5363 VAAIRDAGEAEENRFEAVLATEAEARIHAARETALAAETSLEVTQEEARDLRKNHENAMI 5422

Query: 286  EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK----------EKLVKLVGSLSLNQSRI 335
             +A    E +      V  +  EK + +   LK          ++L +L       Q ++
Sbjct: 5423 ALAAEMAEKQRRGKEGVGARLQEKKAKRLAELKKVKAKDDEVQDELARLEQEAEREQKQV 5482

Query: 336  DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            +  +EQ   I ++          LA+     R   L     R      +   +   E E 
Sbjct: 5483 EADIEQEAAILEQAEAKM-----LAKRAAEARATRLTAESSRRAGELELQKIRQAHE-EN 5536

Query: 396  KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
            +  +    +S  K+R                    +   R+ +  ASIA  E  EA  +L
Sbjct: 5537 QRILEEAQESKRKLRQR-------------TLAERLERRRQEKMNASIAALESAEAQQKL 5583

Query: 456  VISVAK-KYTNRGLQFLDLIQEGNIGLM-KAAEKFDWCLGYKFSTYAMWWVKQAITRSIA 513
              S+ K +   R     +L++E    L   A  +       + S  A   + +A  R+  
Sbjct: 5584 AASLEKERVEARAELEEELVKEACQELEVHAQRQARAEHAVRMS--AKNAIDEAEKRAKL 5641

Query: 514  DQSCTIRIPVHM------------RDKIHKVVRTARRMSNKIKREPTPEEIAKKLA--MP 559
             +         +                 ++ +  +    ++ RE    E  K+    M 
Sbjct: 5642 AREEHEESTKELDMQLAAARITQGNKLKDRLAKKRKEREKQLTRESADAEAVKEARRIME 5701

Query: 560  VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED------------------------- 594
             E  R+V +       LE  +  E      + +                           
Sbjct: 5702 EEEQREVAR-------LENHLARERERLHEENLARAKARRTREEAEERDRAIAAAQAADL 5754

Query: 595  --KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
              + AV  L    + +  +     L      E+R    +    +      +E   Q    
Sbjct: 5755 AKQEAVGCLQRLQKQHAEQ--HAALEHQMEEEKRSREAKLRDRLAKKRKAKEEEMQQAAL 5812

Query: 653  RERIRQIEAKAIR 665
             ER +QIE K + 
Sbjct: 5813 SEREKQIEQKNLE 5825


>gi|117924589|ref|YP_865206.1| sigma-70 region 4 domain-containing protein [Magnetococcus sp.
           MC-1]
 gi|117608345|gb|ABK43800.1| sigma-70 region 4 domain protein [Magnetococcus sp. MC-1]
          Length = 187

 Score = 44.8 bits (104), Expect = 0.053,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R    R +  L+ RE +V+ MR       +   E+V K   +TRER+R IEAKA +K+K
Sbjct: 122 RIMLGRAMQHLSAREAQVVNMRM-----ENLRYEDVAKVMKITRERVRIIEAKASKKIK 175


>gi|330874712|gb|EGH08861.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 81

 Score = 44.8 bits (104), Expect = 0.053,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             + L  L  R   +L  R+        TL ++ +++ V+ ERIRQ+E  A+ KLK
Sbjct: 23  LHQALDVLDERSRDILYQRWLAE--EKATLHDLAQKYNVSAERIRQLEKSAMNKLK 76


>gi|317968505|ref|ZP_07969895.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 74

 Score = 44.8 bits (104), Expect = 0.054,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 613 TTRVLASLTPREERVLRMRFGI------GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
              +L  L   + RVL+MR+ I        +   +L  +G+   ++R+R+R +E   +  
Sbjct: 1   MRGLLDQLPDLQGRVLKMRYAIPCRDVPDPDEPMSLTGIGRVLGISRDRVRNLERDGLAG 60

Query: 667 LKHPSRS 673
           L+  S++
Sbjct: 61  LRRLSQN 67


>gi|289582531|ref|YP_003480997.1| methyl-accepting chemotaxis sensory transducer [Natrialba magadii
           ATCC 43099]
 gi|289532084|gb|ADD06435.1| methyl-accepting chemotaxis sensory transducer [Natrialba magadii
           ATCC 43099]
          Length = 526

 Score = 44.8 bits (104), Expect = 0.054,   Method: Composition-based stats.
 Identities = 32/304 (10%), Positives = 96/304 (31%), Gaps = 13/304 (4%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF 105
             ++   L      S+ ++ +V  L    + V D  D   +  ++ S  +   +   +  
Sbjct: 229 YADIEDELEHRTEVSKNVQSSVTELRERSVEVSDRSDEISDLAAQQSDAMGEISGEVAGL 288

Query: 106 LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
               ++ A  +          E+ +     R  EI  A          +  +        
Sbjct: 289 SATVEEIASNA---------EEVSATS--ERAEEI--ANDTTETAEEAIDKMAVVDDAAD 335

Query: 166 ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
            +    ++L +    + EI+D+   I  ++     + +   +             ++V+ 
Sbjct: 336 EVTDDVEDLRESVQKIDEIVDVINDIADQTNLLALNASIEAATAGEAGDGFAVVANEVKS 395

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
              + +  AK  +    ++ +  E   +     +E+ +     +    D L        +
Sbjct: 396 LAEESQDEAKNIERMIDQIQADTEETVDSLETANEEIESGVGLVEETVDNLERIEESVQE 455

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
               +     +  D A + ++    +        ++   + ++     ++D LV+++   
Sbjct: 456 ASTGIQEVAMATDDQAASTEEVASMTDTAMEQSHEVATEIEAIVGQNEQVDELVDEIESE 515

Query: 346 SKRI 349
             R+
Sbjct: 516 VGRL 519


>gi|302828474|ref|XP_002945804.1| hypothetical protein VOLCADRAFT_86130 [Volvox carteri f. nagariensis]
 gi|300268619|gb|EFJ52799.1| hypothetical protein VOLCADRAFT_86130 [Volvox carteri f. nagariensis]
          Length = 2493

 Score = 44.8 bits (104), Expect = 0.054,   Method: Composition-based stats.
 Identities = 65/460 (14%), Positives = 145/460 (31%), Gaps = 39/460 (8%)

Query: 233  AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
             +  S+       +   + E  +  L +   D    +S    +++      L ++   Y 
Sbjct: 1025 PSSASQSPGEPTLASRLSLEPLKDALTKSLQDELEKVSKQVAEVKASYDKQLADVRAEYE 1084

Query: 293  ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
               +        Q  +  ++  + ++E        +       +  ++++    +R    
Sbjct: 1085 RQLAEARTVHQKQLLDVRALAERQVEEARAHHRKQMEDVHVHNERKLDEVRRRMERQAEE 1144

Query: 353  EGELL-RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV---------ACE 402
                  R+      +RD  LE  +  +      +  +     E    +         A  
Sbjct: 1145 ARAAQERVLVEARAQRDKVLEDARLAQTKALEDARGQQQRALEDTRALHERVLADTQAVH 1204

Query: 403  VDSILKIRN----EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
            V  +++++N    E++  + + G ++ + R +    R+ E EA  AK+E V         
Sbjct: 1205 VKQVVELKNLYESELRRAAHDVGRAVDDTRRVAEEARRQEAEARRAKEEAV--------- 1255

Query: 459  VAKKYTNRGLQFLDLIQEGNI-GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
             A +    GL+     ++G +        + D     + +      +K+A    +  +  
Sbjct: 1256 -ALRDRILGLEAELRARDGALREAETRFVQLDTRSKTELAETQANAIKEAALMKLEMEDA 1314

Query: 518  TIRIPVHMRD-------KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
               +    +           +V R    +  +  R    EE+ +      E +       
Sbjct: 1315 KAALSRVRQQYEEAAMAHAAEVTRYRAELDAQ--RVMAEEELQRARLATAEQIAAAEARG 1372

Query: 571  KEPISLETPIGDEDTSHLGDFIEDKNAV---SPLDSAIQANLRETTTRVLASLTPREERV 627
            +    L+  I +         I ++  V     L + + A L E    V  S   REER 
Sbjct: 1373 RRAGMLDKEIAEATIRQQMAAIAEEKEVVARHRLSAELLAQLTEKVRSVAVSSLEREERA 1432

Query: 628  LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK--AIR 665
            L        + +  L    K       R+ Q E +  A+R
Sbjct: 1433 LSALERDVADREGRLAAREKLLGEREGRVAQREREVDALR 1472


>gi|47089274|gb|AAT10956.1| sigma 70 factor [Pseudomonas syringae pv. actinidiae]
 gi|47089386|gb|AAT11012.1| sigma 70 factor [Pseudomonas syringae pv. theae]
          Length = 149

 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 19/194 (9%), Positives = 49/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAV 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +  + D E +A  S ++      P             D+ +          +     +
Sbjct: 50  KAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             L  +AE++                                    + L   + + LVE+
Sbjct: 110 AELVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|194332619|ref|NP_001123798.1| hypothetical protein LOC100170549 [Xenopus (Silurana) tropicalis]
 gi|189441913|gb|AAI67592.1| LOC100170549 protein [Xenopus (Silurana) tropicalis]
          Length = 1853

 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 66/344 (19%), Positives = 127/344 (36%), Gaps = 29/344 (8%)

Query: 47   EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD-GDDLEDEEGSEDSLDLASSASNSSVF 105
            ++ N  LP    +    ++    L NM   + D    ++D +G      + + A+ ++  
Sbjct: 1497 DDCNGALPVSAKALSTAQNITLELENMANRLKDIAQKIQDIQGIAQDAKVQTEATLANAK 1556

Query: 106  LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM-ASLCESPLTF 164
              KR+      + + +R +++++   + L+ EG  A  + IE     ++  SL  SP   
Sbjct: 1557 ESKRRIED---STEKLREFIKKIK--DFLTEEG--ADPESIELVARQVLNISLPASPGDI 1609

Query: 165  QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
            +AL+    E     +   EI+   + I   +K       E  +  +   ++    +  +Q
Sbjct: 1610 EALVNKIKESIGNLSCTDEILTNTSEILATAKNLHKEAVEAQAKAEAVSANISDAQALLQ 1669

Query: 225  ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
            E E   +SA K  K  +  +       E   + L   E      +  +   L  KV   L
Sbjct: 1670 EAEAKAKSAEKALKKAKQSIKDVKSKVEQTMQTLTGVEQKEMDIMERI-GNLSEKVDDLL 1728

Query: 285  DE------IAEVYRELRSLQDNAVNGQKDEKSSV--KCKVLKEKLVKLVGSLSLNQSRID 336
            D+      IA   +E  +L  N+    + E   V  K   LKEK+     S      RI+
Sbjct: 1729 DKTESNRQIASDAKERANLVLNSTGELRKEMDDVQRKYDDLKEKVGGYNSSSGTALDRIE 1788

Query: 337  LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
             + E+   +  +    + EL +L               +  E +
Sbjct: 1789 KIKEEAKALYDKANTAKKELAKLEAQ-----------FRANEAN 1821


>gi|47089350|gb|AAT10994.1| sigma 70 factor [Pseudomonas syringae pv. phaseolicola]
          Length = 149

 Score = 44.4 bits (103), Expect = 0.056,   Method: Composition-based stats.
 Identities = 20/194 (10%), Positives = 50/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTCVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAV 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             + T+ D E +A  S D+      P             D+ +          +     +
Sbjct: 50  KAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +AE++                                    + L   + + LVE+
Sbjct: 110 AEMVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|213621633|ref|ZP_03374416.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 79

 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E    +    E+    +PL   ++ +LR+     + SL  RE+ VL + +      +  L
Sbjct: 2   EHGDSIELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYYQ----EELNL 57

Query: 643 EEVGKQFCVTRERIRQIEAKAI 664
           +E+G    V   R+ Q+ ++AI
Sbjct: 58  KEIGAVLEVGESRVSQLHSQAI 79


>gi|47089352|gb|AAT10995.1| sigma 70 factor [Pseudomonas syringae pv. pisi]
 gi|47089354|gb|AAT10996.1| sigma 70 factor [Pseudomonas syringae pv. pisi]
 gi|47089356|gb|AAT10997.1| sigma 70 factor [Pseudomonas syringae pv. pisi]
          Length = 149

 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 22/194 (11%), Positives = 50/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L ++  L   I P+               K   +    + +
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAAKTEGADDDE 58

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +        ESA    ++D  +    P  A+     + +  + +   L            
Sbjct: 59  E--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------------ 98

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
                                  +K  +           L +L   + L   + + LVE+
Sbjct: 99  -----------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|239625074|ref|ZP_04668105.1| LOW QUALITY PROTEIN: RNA polymerase sigma-B factor [Clostridiales
           bacterium 1_7_47_FAA]
 gi|239521460|gb|EEQ61326.1| LOW QUALITY PROTEIN: RNA polymerase sigma-B factor [Clostridiales
           bacterium 1_7_47FAA]
          Length = 180

 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +      DFI D+ A    ++ + A + 
Sbjct: 63  EQYTDFYRDKERWRYLKKLDTKNSLLSLDGFTDSEGKPLDFIADE-AADIAETVVNAVMV 121

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +F +T+  + + +A+ +RKL+ 
Sbjct: 122 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARFGITQSVVNKRKARILRKLRK 176


>gi|119488697|ref|ZP_01621706.1| DNA-directed RNA polymerase ECF-type sigma factor (sigma-W)
           [Lyngbya sp. PCC 8106]
 gi|119455120|gb|EAW36261.1| DNA-directed RNA polymerase ECF-type sigma factor (sigma-W)
           [Lyngbya sp. PCC 8106]
          Length = 396

 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 27/179 (15%), Positives = 69/179 (38%), Gaps = 21/179 (11%)

Query: 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL------AMPV 560
              R    + C   +  +  +    + R   +   KIK+     +  K         + +
Sbjct: 34  EQHRDYLFRCCVKWMNGNSIEAEDVLSRAIIKAWEKIKQNTVVIDNFKAWLTKLTYNLCI 93

Query: 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASL 620
           +  R+  + TK+  SL+T    +    +          +P  SA +    +     + +L
Sbjct: 94  DIHRQHNRNTKKIESLDTVCSTQQEEWVS------QEETPFLSATRRETAQFLRNAIENL 147

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
            PR    LR  F +  + + + +E+ +   ++ + +R+  ++A + L+     ++L+ +
Sbjct: 148 PPR----LREVFVLFADQELSYQEIAQHLNISYDNVRKRISQARKTLR-----EQLQEY 197


>gi|29347317|ref|NP_810820.1| putative RNA polymerase sigma factor RpoS [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|29339216|gb|AAO77014.1| putative RNA polymerase sigma factor RpoS [Bacteroides
           thetaiotaomicron VPI-5482]
          Length = 405

 Score = 44.4 bits (103), Expect = 0.057,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK---LKH 669
           + RE+ +    +G+  N    +  +G +  ++RERIRQ++ K  +K   L+ 
Sbjct: 28  SDREQYIFSELYGLEGNEIQNMISLGDKLGLSRERIRQLKVKVFKKFGILRK 79


>gi|91070518|gb|ABE11425.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-3E5]
          Length = 109

 Score = 44.4 bits (103), Expect = 0.058,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 73  MGINVVDGD---DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           MGI +       D   E     +    S  + +S+  ++ +  + R   D +  YL  +G
Sbjct: 2   MGIPLESAKSFSDKNSEGPRLPNTAGKSRKTKASLTSKQSQKKSGRLASDSIGHYLSSIG 61

Query: 130 SIELLSREGEIAIAKRIEA 148
            + LL+   EI +A  ++ 
Sbjct: 62  RVPLLTPAEEIELAHHVQN 80


>gi|224052372|ref|XP_002192279.1| PREDICTED: discs, large homolog 5 (Drosophila) [Taeniopygia
           guttata]
          Length = 1891

 Score = 44.4 bits (103), Expect = 0.058,   Method: Composition-based stats.
 Identities = 44/381 (11%), Positives = 131/381 (34%), Gaps = 36/381 (9%)

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +  K     +  E  +    + +    +  S + ++L    M  L+ + + Y  LR   +
Sbjct: 216 EEMKRLHDEDQKEITDLRSQQQQVMKQNGSSEILNKLYDTAMDKLEGVKKDYDALRKRYN 275

Query: 300 NAVNGQKD-----EKSSVKCKVLKEKLVKLVGS----LSLNQ------SRIDLLVEQLYD 344
             +          E++  + + L++++  L+      +   Q       R + + ++L +
Sbjct: 276 EKIASHNTDLSRLEQAEEENRRLQKQIDMLMKQRDTAIHFQQQYSSSLRRFESVQQELSN 335

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            + +    + E+ RL       + + L+  +  E          +         +  E D
Sbjct: 336 ATAQNKELQREMERLQSEVTRFKTMQLKATKDAEKYKEERDSVFNE-----YRLIMSERD 390

Query: 405 SILKIRNEIK---SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            ++K  ++++    ++     + S  + + S   +   +   +    +E   + +  + K
Sbjct: 391 QVIKEVDKLQTELELAESKLKNTSSEKRVASEEMEALRQIQDSATLDIERANKEIEMLRK 450

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y     +  + +QE         E       + F        ++   R++ D       
Sbjct: 451 QYEAMSQELKEAVQEA--------EVAKCRRDWAFQERDKIVAERESIRTLCDNLR-RER 501

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG---VRKVLKITKEPISLET 578
              + D    +         K       +E+ +K+   +E     R+++  +    +++T
Sbjct: 502 DRAVSDLAEALRNLDDMRKQKNDAVRELKELKEKMENQLEKEARFRQLMAHSSHDSAIDT 561

Query: 579 PIGDEDTSHLGDFIEDKNAVS 599
               E  + + +F +D++ + 
Sbjct: 562 DS-LEWETEVVEFEKDRDDMD 581


>gi|320164484|gb|EFW41383.1| Ser-Thr protein kinase PK428 [Capsaspora owczarzaki ATCC 30864]
          Length = 1729

 Score = 44.4 bits (103), Expect = 0.061,   Method: Composition-based stats.
 Identities = 54/374 (14%), Positives = 123/374 (32%), Gaps = 22/374 (5%)

Query: 81   DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG-- 138
              L D+  +         A    V  +   +       D  R  L  + S + L  +   
Sbjct: 727  QSLTDQLAAAQQEARDVQAELEQVEQELDAERKKEKQKDRARRGLSTISSADALVAQLSA 786

Query: 139  -EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
                +    +     +     E   T + L    +EL      L    +L      ++K 
Sbjct: 787  CRTQLQDARDEHDLTIQQLEAEQ-QTVRKLRAELEELRLENQRLVSQTELLQQQLTDTKS 845

Query: 198  GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 T   +  +    + EK+  D QE    + +      +         + + N +R+
Sbjct: 846  SRETATSQITESETRLRALEKQASDAQEELSRVSAERDRLAERAEAQSQAAKESRNSQRS 905

Query: 258  LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317
              +        LS  E++ R + +  L+   + ++ELR L   A    + E+ S   +  
Sbjct: 906  AQDQASALRVELSQAEEE-RKRALSELEAERKAHKELRDL--KAQLSLEVERVSTDARKA 962

Query: 318  KEKLVKLVGSLSLNQS------RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
            + KL   +   + + +      +ID L  ++   +K     + +L  L       ++ F 
Sbjct: 963  QSKLDAEIARAARSPNPADLVSKIDSLTREIATAAKEQTKAQSDLEHLKARLSEDKEAFE 1022

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
               +  +L    V+  +   + E +       + + +++ +I      T +     + IV
Sbjct: 1023 R--EKADLTQQLVAKQRQVNQTEARQD-RQNKEDMRRLQQQI------TEMKSQLEKEIV 1073

Query: 432  SMVRKGECEASIAK 445
               +    +A + +
Sbjct: 1074 IRHQLEASQAKVQR 1087



 Score = 41.0 bits (94), Expect = 0.66,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 88/262 (33%), Gaps = 23/262 (8%)

Query: 150  RAMMMASLCESPLTFQAL-------IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
            R    + + ES    +AL             ++     L E  + ++    ES+      
Sbjct: 847  RETATSQITESETRLRALEKQASDAQEELSRVSAERDRLAERAEAQSQAAKESRNSQRSA 906

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE--NAENDERNLDE 260
             +  S  + E S  E+ER            A K  +D ++++    E  + +  +     
Sbjct: 907  QDQASALRVELSQAEEERKRALSELEAERKAHKELRDLKAQLSLEVERVSTDARKAQSKL 966

Query: 261  DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD-----NAVNGQKDEKSSVKCK 315
            D + +    S     L  K+     EIA   +E    Q       A   +  E    +  
Sbjct: 967  DAEIARAARSPNPADLVSKIDSLTREIATAAKEQTKAQSDLEHLKARLSEDKEAFEREKA 1026

Query: 316  VLKEKLVKLVGSLSLNQSRIDLLV-EQLYDISKRIMHNEGELLRL--------AQSYGIK 366
             L ++LV     ++  ++R D    E +  + ++I   + +L +         A    ++
Sbjct: 1027 DLTQQLVAKQRQVNQTEARQDRQNKEDMRRLQQQITEMKSQLEKEIVIRHQLEASQAKVQ 1086

Query: 367  RDVFLERHQGRELDPHWVSYAK 388
            R++    ++ +E    W     
Sbjct: 1087 RELDDTTYKLKETQAKWSDLLS 1108


>gi|257462509|ref|ZP_05626921.1| RNA polymerase factor sigma-70 [Fusobacterium sp. D12]
 gi|317060165|ref|ZP_07924650.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium sp.
           D12]
 gi|313685841|gb|EFS22676.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium sp.
           D12]
          Length = 197

 Score = 44.4 bits (103), Expect = 0.062,   Method: Composition-based stats.
 Identities = 27/144 (18%), Positives = 64/144 (44%), Gaps = 8/144 (5%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K +     A   ++E    ++   A  Y   G +  DL+QEG +GL+KA + +D  
Sbjct: 11  ELIEKAKNGDQEAITFIIERYQNVISMSASHYYMVGAEKQDLLQEGMLGLLKALKAYDKE 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F T+A+  +++ +  +I   +    +  H     H V++       ++  + + + 
Sbjct: 71  RS-SFRTFAILCIRRQLISAIKASNTKKNLVFH-----HAVIKNPLLGEEELMGKSSYD- 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPIS 575
             ++L +  E +++  +  +E  S
Sbjct: 124 -PEELYLSKEKIQEYYQYIQESFS 146


>gi|47089278|gb|AAT10958.1| sigma 70 factor [Pseudomonas syringae pv. aptata]
 gi|47089302|gb|AAT10970.1| sigma 70 factor [Pseudomonas syringae pv. japonica]
 gi|47089358|gb|AAT10998.1| sigma 70 factor [Pseudomonas syringae pv. pisi]
 gi|47089360|gb|AAT10999.1| sigma 70 factor [Pseudomonas syringae pv. pisi]
 gi|47089372|gb|AAT11005.1| sigma 70 factor [Pseudomonas syringae pv. syringae]
 gi|47089376|gb|AAT11007.1| sigma 70 factor [Pseudomonas syringae pv. syringae FF5]
 gi|47089378|gb|AAT11008.1| sigma 70 factor [Pseudomonas syringae pv. syringae]
          Length = 149

 Score = 44.4 bits (103), Expect = 0.062,   Method: Composition-based stats.
 Identities = 22/194 (11%), Positives = 50/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L ++  L   I P+               K   +    + +
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAAKAEGADDDE 58

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +        ESA    ++D  +    P  A+     + +  + +   L            
Sbjct: 59  E--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------------ 98

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
                                  +K  +           L +L   + L   + + LVE+
Sbjct: 99  -----------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|326790455|ref|YP_004308276.1| LuxR family transcriptional regulator [Clostridium lentocellum DSM
           5427]
 gi|326541219|gb|ADZ83078.1| transcriptional regulator, LuxR family [Clostridium lentocellum DSM
           5427]
          Length = 216

 Score = 44.4 bits (103), Expect = 0.063,   Method: Composition-based stats.
 Identities = 24/91 (26%), Positives = 41/91 (45%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++++     + A + +V+   R V +  K     G+   DLIQEG IGL KA   +D  
Sbjct: 21  ELIQRYRDGINEAIEVLVQRYKRFVRTKIKANYFIGVDKDDLIQEGMIGLFKAICDYDAH 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F ++A   V + ++ +    S    IP
Sbjct: 81  KDTSFKSFATLCVTRQVSTAFKAVSRQKHIP 111


>gi|221060010|ref|XP_002260650.1| hypothetical protein, conserved in Plasmodium species (fragment)
           [Plasmodium knowlesi strain H]
 gi|193810724|emb|CAQ42622.1| hypothetical protein, conserved in Plasmodium species (fragment)
           [Plasmodium knowlesi strain H]
          Length = 1229

 Score = 44.4 bits (103), Expect = 0.063,   Method: Composition-based stats.
 Identities = 47/318 (14%), Positives = 97/318 (30%), Gaps = 27/318 (8%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            EI  L+A    E K     G E  S +         + DD Q    + E       ++ 
Sbjct: 24  SEIKTLDAFWDAEEKQKGTVGDEEDSLKGEVAEEVSGKSDDHQREAENEEHGESTKMENE 83

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA------------- 288
            K    P+  E D+       ++      A+ D    +V   ++E+              
Sbjct: 84  EKEKDLPDQEEIDQMEEALQREEVYEQSEALYDNCNEEVGDMVNEMEVEETVMDDVVVDD 143

Query: 289 --------EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                   E   +   ++ NA +    +      +   E L     S     S       
Sbjct: 144 DPVEEEQPEERGDKVLMRKNAFSFNTYKSRKFSHEFSIESLSNFFRSFESVNSEYTDTSR 203

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
           +  +  +     +G+  R  +  G K +      Q +E++  +    K       +N   
Sbjct: 204 ECEETERENQQEKGKQQRKGKQKGAKEET-----QKKEVEGTFKRNQKHMNAQSIQNESD 258

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVS-MVRKGECEASIAKKEMVEANLRLVISV 459
            E    L ++  ++   + + +     R+     ++K          +M +     V  +
Sbjct: 259 AEEKFKLNVQTSVEVHKLYSHLQNHILRNFKRGYLKKMIKMFKKNYNKMEKDISDNVKRI 318

Query: 460 AKKYTNRGLQFLDLIQEG 477
             K+++R      +IQ G
Sbjct: 319 VHKFSSRDESLDGVIQFG 336


>gi|296213243|ref|XP_002807203.1| PREDICTED: LOW QUALITY PROTEIN: dynein heavy chain 10, axonemal-like
            [Callithrix jacchus]
          Length = 6257

 Score = 44.4 bits (103), Expect = 0.064,   Method: Composition-based stats.
 Identities = 49/368 (13%), Positives = 118/368 (32%), Gaps = 28/368 (7%)

Query: 158  CESPLTFQALIIWRDELNDGT-TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
             E   T+  L+  + + N      L   +D       +         E       +  + 
Sbjct: 4809 LEFNNTYSKLLDEKTQYNSAQCKRLEGGLDKLKEATIQLDELNQKLAEQKIVLAEKSIAC 4868

Query: 217  EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
            E   +++       E   K++++   +++   +    ++   +   ++    L A + +L
Sbjct: 4869 EALLEEIAINTTVAEEKKKLAEEKAMEIEEQNKVIAMEKAEAETTLEEVMPILEAAKLEL 4928

Query: 277  RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC--KVLKEKLVKLVGSLSLNQSR 334
            +      + EI   + +               K   +   K  K  +       SL +  
Sbjct: 4929 QKLDKSDVTEIRS-FAKPPKQVQTVCECILIMKGFKELNWKTAKGMMSDPNFLRSLMEIN 4987

Query: 335  IDLL----VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG-----RELDPHWVS 385
             D +    V+ +  + K +     E +      G+    F+E   G     RE+ P    
Sbjct: 4988 FDSITQSQVKNIKGLLKTLNATTEE-MEAVSKAGLGMLKFVEAVMGYCDVFREIKPKREK 5046

Query: 386  YAK-DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
             A+ +      K  +    + +  I+ E++++      +I E + +       E    IA
Sbjct: 5047 VARLERNFYLTKRELERIQNELAAIQKELETLGATYEAAILEKQKLQEEAEIMERR-LIA 5105

Query: 445  KKEMVEANLRLVISVAKKYTNRGLQFLDLIQE-----GNIGLMKAAEKFDWCLGYKFSTY 499
              +++        S   ++ N      +L+Q      G+  L  A   ++    ++F   
Sbjct: 5106 ADKLISGLG----SENVRWLN---DLDELMQRRVKLLGDCLLCAAFLSYEGAFTWEFRDE 5158

Query: 500  AMWWVKQA 507
             +  + Q 
Sbjct: 5159 MVHRIWQN 5166


>gi|219111015|ref|XP_002177259.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411794|gb|EEC51722.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 915

 Score = 44.4 bits (103), Expect = 0.065,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 68/191 (35%), Gaps = 6/191 (3%)

Query: 134 LSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI----IWRDELNDGTTLLREIIDLEA 189
           L+++  I I   I+  R  M     E+    Q ++       + ++     L  +     
Sbjct: 158 LTQQKLIEIQHEIDVERRRMERDHLEAAEALQLILHRNQETAELISAEQRRLDSVAQEGE 217

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I   +        +    QK +D+ +  +R+++       +  A  S        +   
Sbjct: 218 DIRARADKEKQTALKDEERQKEKDAQENAKRENLDSQRAAEKEEAVRSSKYEFIAKAKKL 277

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
            A+        +  + +  +     Q++  V   ++ ++E  +++R + +N       EK
Sbjct: 278 VAQLVLIRASVESFEKSKAVGKRRLQMKKIVNGKVNTLSENTQKIREVANNVSQAI--EK 335

Query: 310 SSVKCKVLKEK 320
           +  + K  KE+
Sbjct: 336 ARDEDKQAKEQ 346


>gi|310779951|ref|YP_003968283.1| RNA polymerase, sigma 30 subunit, SigH [Ilyobacter polytropus DSM
           2926]
 gi|309749274|gb|ADO83935.1| RNA polymerase, sigma 30 subunit, SigH [Ilyobacter polytropus DSM
           2926]
          Length = 203

 Score = 44.4 bits (103), Expect = 0.068,   Method: Composition-based stats.
 Identities = 26/95 (27%), Positives = 46/95 (48%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           V++V+  +     A  E+      LV+  +K Y   G    DL+QEG IGL+KA   +D 
Sbjct: 3   VNLVKMAQEGDQEAVTEIFNKYRGLVLMKSKNYFLNGADRDDLLQEGMIGLLKAIRAYDE 62

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                F+T+A   +K+ I  +I + +      +++
Sbjct: 63  GKNTSFNTFASLCIKRQIITAIKNSNSGKHRMLNL 97


>gi|162450150|ref|YP_001612517.1| ECF family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
 gi|161160732|emb|CAN92037.1| ECF-family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
          Length = 223

 Score = 44.4 bits (103), Expect = 0.068,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED+ +     +  + +LR      L +L P+E+    M +  G       EE+GK    +
Sbjct: 141 EDERSPLDEVTIARDDLRRAL-ETLGTLPPKEQVAFSMFYLDG----KEQEEIGKILGHS 195

Query: 653 RERIRQIEAKAIRKLK 668
           +  + ++  KA+ +L+
Sbjct: 196 KGYVCKLIQKAVAQLR 211


>gi|240142555|ref|YP_002967068.1| hypothetical protein MexAM1_META2p0912 [Methylobacterium extorquens
           AM1]
 gi|240012502|gb|ACS43727.1| hypothetical protein MexAM1_META2p0912 [Methylobacterium extorquens
           AM1]
          Length = 390

 Score = 44.4 bits (103), Expect = 0.071,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 4/99 (4%)

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T+   ++      ++   L D I D     P     + ++     R +A L P E RVL 
Sbjct: 235 TEADQAMFEFYQPDEVLMLEDLIADDGGTDPETEVDRHDIAMALHRAIADLAPVERRVLY 294

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +      D T+ E      +T   + +I   A   L+
Sbjct: 295 RMYL----EDATIAETAHLLGLTEAEVLKIAENAAETLR 329


>gi|218529463|ref|YP_002420279.1| hypothetical protein Mchl_1477 [Methylobacterium chloromethanicum
          CM4]
 gi|218521766|gb|ACK82351.1| conserved hypothetical protein [Methylobacterium chloromethanicum
          CM4]
          Length = 142

 Score = 44.1 bits (102), Expect = 0.072,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 30 SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
          +  ++I L R RG +T EEL A LP D +  + +   +  L   G++V
Sbjct: 8  TLDRLIALGRSRGELTAEELCAVLPVDSMDVDALVLVMLELEEAGVSV 55


>gi|95007259|emb|CAJ20479.1| hypothetical protein TgIb.0070c [Toxoplasma gondii RH]
          Length = 729

 Score = 44.1 bits (102), Expect = 0.072,   Method: Composition-based stats.
 Identities = 29/202 (14%), Positives = 73/202 (36%), Gaps = 5/202 (2%)

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  P   +     L+ +  +    L+  E Q   +V        E++  ++ L++ 
Sbjct: 241 DFDGAVGPGANDEKTMELEAELKELRGKLAEQERQAADRVRELEKRERELFGRVQELEEQ 300

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           +    +      +    +++L +L       Q R   LVE+  ++ +++  ++ EL +L 
Sbjct: 301 SALQAQVRDGFSELLDAQQQLQQLQREHRQLQQREQELVEKESELQRQLEQHQRELQQLH 360

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           Q         L+RH+  E+  + V  A      E +  V      +  +    + ++   
Sbjct: 361 QEVKE-----LQRHRAAEMRTNGVVEASLHEAEEQRAQVQQLERKVRDLEKLHRDVTERD 415

Query: 421 GISISEFRHIVSMVRKGECEAS 442
            + I        ++++    A+
Sbjct: 416 AMRIRALEEENKLLKRTSGAAA 437


>gi|33152994|ref|NP_874347.1| hypothetical protein HD2030 [Haemophilus ducreyi 35000HP]
 gi|33149219|gb|AAP96736.1| hypothetical protein HD_2030 [Haemophilus ducreyi 35000HP]
          Length = 705

 Score = 44.1 bits (102), Expect = 0.072,   Method: Composition-based stats.
 Identities = 27/134 (20%), Positives = 51/134 (38%), Gaps = 2/134 (1%)

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
           +   +++     + K   +    ++A    +  + V          I   + +   D   
Sbjct: 118 RTLNLIKKQPINTVKQALDFIFSDLATCKGISQKTVIHSQIEAIRHIQFYSNLSTPDFDK 177

Query: 588 L--GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
           L   D I      S +D   Q      T    +    R+ ++L  R+G+  ++  TLE +
Sbjct: 178 LIFQDVIFIAPQPSLIDHFKQVITLFFTQVYQSKHKERDRQILFRRYGLETHSIETLEHI 237

Query: 646 GKQFCVTRERIRQI 659
           G    +TRER+RQI
Sbjct: 238 GHSLGLTRERVRQI 251


>gi|253742508|gb|EES99337.1| Midasin [Giardia intestinalis ATCC 50581]
          Length = 4833

 Score = 44.1 bits (102), Expect = 0.073,   Method: Composition-based stats.
 Identities = 65/483 (13%), Positives = 156/483 (32%), Gaps = 58/483 (12%)

Query: 3    IGKKRNRDSDSEHEDSDDSLVFDFSDDSWK---------KMIKLARQRGYVTIEELNAFL 53
            +G  +    D  + + DD    ++SDD  K         ++    + +  +   E++   
Sbjct: 4126 MGSDQGEAIDERNYNKDDDTAEEYSDDQKKNTNDNKDTMELAAQEKDQNSIN-SEMSD-- 4182

Query: 54   PPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSA 113
            P  E   +Q +   +   +  +   D  DL+D+  S  S      +   +  + +  +  
Sbjct: 4183 PSGEHHEDQADTASST--DEQVQEDDYKDLDDKNLSGQSELSTPESGEENEEVNEELEEE 4240

Query: 114  DRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE 173
             +   D             +   + +    + I+                  +     +E
Sbjct: 4241 QQQVSD-------------ISDPDQDARATEEIDDKD-------------LPSSDENAEE 4274

Query: 174  LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD---DVQETEGDI 230
             ++    + ++ D EA     +           S Q++   + E ++D   D + T  + 
Sbjct: 4275 RDEHEAPV-DVDDSEASAEQSTVNDEEQDPINISAQQQMADNDEMQKDTEYDQENTTDNN 4333

Query: 231  ESAAKVSKDDRSKVDSPPEN--AENDERNLDEDEDDSAHTLSAMEDQLRPKVMC-ALDEI 287
              A +V  +D+ +     +    EN E   + ++ +++    A   +L+      +L+E 
Sbjct: 4334 PDANEVGANDQKQTQENSDQFRRENAEDQWEAEDTENSQGEGAESAELKEGNPDMSLEEF 4393

Query: 288  AEVYRELRSLQDNAVNGQKDEK------SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
              +++E  S++D      +  +       S K     +      G+L L +S+   +  Q
Sbjct: 4394 QRIWKERMSIRDRETEKDEAAEPQDMPLQSNKTVEFDDSKTGRDGALGLTESKHKNITNQ 4453

Query: 342  LYDISKRIMHNEGELLRLAQSYGIKRDVF--LERHQGRELDPHWVSYAKDFPEGEWKNFV 399
             +D          E            D     ER      D    S A D  +    + +
Sbjct: 4454 EFDNPNEERS--VEQKSSCDEASQPSDNRPPAERLDPEVSDEEEDSTASDHRDQGTLSHM 4511

Query: 400  ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                  ++    E++     T ++  E R     +            ++++       S+
Sbjct: 4512 RESSKDLINCETELQQ-GPATSLTCEEIRQAPEDMATAIARGQHLLVDLIKQTSAAAFSL 4570

Query: 460  AKK 462
            A++
Sbjct: 4571 AER 4573


>gi|121488739|emb|CAJ18253.1| sigma 70-type sigma factor [Chlorobaculum limnaeum]
          Length = 95

 Score = 44.1 bits (102), Expect = 0.075,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 1/96 (1%)

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D
Sbjct: 1   KISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLD 60

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
            +++   + P     + +L     R L+ L PRE  
Sbjct: 61  VLQNDGHM-PDHGLNRDSLTLEVERSLSVLAPREAD 95


>gi|124806675|ref|XP_001350792.1| conserved Plasmodium protein [Plasmodium falciparum 3D7]
 gi|23496920|gb|AAN36472.1| conserved Plasmodium protein [Plasmodium falciparum 3D7]
          Length = 5767

 Score = 44.1 bits (102), Expect = 0.075,   Method: Composition-based stats.
 Identities = 27/168 (16%), Positives = 73/168 (43%), Gaps = 2/168 (1%)

Query: 287  IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
            I E Y+EL +    ++N   D K+ +     ++K ++ +  L ++    D +++ L  I+
Sbjct: 3512 IKEEYKELLNEYKFSLNLLNDTKNKLDTLKREKKDMEKLKELQIHDK--DYIIQNLKGIN 3569

Query: 347  KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
            + + +N  E+ +      ++++  +E++     + +         + +  NF+      I
Sbjct: 3570 RELENNLNEIKKSFNEKILEKENIIEKNNDLINNLNEEIIMLKSIKIKNNNFIKELELQI 3629

Query: 407  LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
              + NEI +++     S  E R +   + + + E    + ++ +  L 
Sbjct: 3630 KNLNNEINTLNDMLKDSEEEIRMLNHTLEEKQNECVKLRNKLEQNYLH 3677


>gi|313901949|ref|ZP_07835366.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
 gi|313467795|gb|EFR63292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
          Length = 240

 Score = 44.1 bits (102), Expect = 0.076,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKFD 489
            ++ + +     A+ E++ A    V+ VA +   R L     + I  G +   +A ++FD
Sbjct: 10  QLIVQAKAGDEHARNELIRAYTPFVLKVASRVCGRYLHAGQDEEISIGLLAFNEAIDRFD 69

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQS 516
              G  F  +A   +K+ +      QS
Sbjct: 70  DTRGNNFIAFAETVIKRRLIDHFRKQS 96


>gi|312792353|ref|YP_004025276.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179493|gb|ADQ39663.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 311

 Score = 44.1 bits (102), Expect = 0.077,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 77/233 (33%), Gaps = 67/233 (28%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYT----NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
               ++ ++  NL+LV  +A K+         +  DLI EG  GL+ AA+ +   LG  F
Sbjct: 10  DKAQRQLLIADNLKLVYHIANKFMPCPKGYMYEVDDLISEGYFGLIVAAQNYKPELGTPF 69

Query: 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
            +YA   ++                         ++ R+  +                  
Sbjct: 70  VSYACKVIE------------------------SRIKRSLPKYK---------------- 89

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                     L  T    S  +   +EDTS +GD + D    S     I+ +  +   R 
Sbjct: 90  ----------LSSTISLDSPVSKEPEEDTSTIGDVVSD--GYSVEREVIRKDTLQKLQRY 137

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             +LT  E+  +      G N   +     K F       R+   K I K++ 
Sbjct: 138 FDTLTDEEKERVLYYISTGKNPPAS----DKVF-------RKARRKIIAKMRQ 179


>gi|225683156|gb|EEH21440.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb03]
          Length = 1423

 Score = 44.1 bits (102), Expect = 0.077,   Method: Composition-based stats.
 Identities = 41/290 (14%), Positives = 99/290 (34%), Gaps = 16/290 (5%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           +A I   D    G   LRE ID       +    F    +  +  + E  + EK   +++
Sbjct: 686 EAAINRLDSKLKGEDDLREEIDSLRDDLRDIGQSFVEAKDKVNELQTEKQALEKTIQNLE 745

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
           +   D+          R+   S    AE + ++L  + ++     +A++  L      A 
Sbjct: 746 KELVDL----------RTNSTSSSAEAEGEHKDLAAEFEELKIKATALQTDLTTTQQLAA 795

Query: 285 DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
               ++     ++Q      +     S + K  KE+L      L   + R + +  ++ +
Sbjct: 796 SRFKDLTDLRETIQKLQPELRTLRAESAELKASKEELKNKTNDLKRLERRHEDVRSEMKN 855

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDPHWVSYAKDFP---EGEWKNF 398
           +  +I   E E+  L Q    +    ++  Q     + D  +    K             
Sbjct: 856 LRGKIGEQESEIKALNQKVTQETKTRVKAEQALDVAQSDLRYSESKKQEAIETNENTTRL 915

Query: 399 VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
           ++   + +   R  ++ +  +      +  ++   ++    + + A+  M
Sbjct: 916 LSKTQEELRSSRTRLREVEEQVTQLNRDIENLRDEIQLKTAQYASAQSLM 965


>gi|157420100|gb|ABV55543.1| RpoD [Acinetobacter rhizosphaerae]
          Length = 165

 Score = 44.1 bits (102), Expect = 0.077,   Method: Composition-based stats.
 Identities = 27/202 (13%), Positives = 66/202 (32%), Gaps = 38/202 (18%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     ++   ++   G   L +I  L   + PE+        E  +  + E +     +
Sbjct: 1   PNAGXVVLKEYNDFLTGERRLADI--LSGYLDPETDAEIPEVLEEETELEEEAAPATPVK 58

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           + V+  + + +  ++   D   +    PE A+                            
Sbjct: 59  E-VKLDDDEEDEESESDDDSEGESGPDPEVAK---------------------------- 89

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               +E+   + + +++ +      K  ++S +     E L  +           D++ E
Sbjct: 90  -VRFNELEAAWTKTKAIIE------KHGRNSPEADEALEALATVFMMFKFTPRLFDIISE 142

Query: 341 QLYDISKRIMHNEGELLRLAQS 362
            +    ++I  NE E++R A  
Sbjct: 143 MIRGTHEQIRANEREVMRYAVR 164


>gi|284122043|ref|ZP_06386830.1| conserved hypothetical protein [Candidatus Poribacteria sp. WGA-A3]
 gi|283829372|gb|EFC33763.1| conserved hypothetical protein [Candidatus Poribacteria sp. WGA-A3]
          Length = 118

 Score = 44.1 bits (102), Expect = 0.078,   Method: Composition-based stats.
 Identities = 17/58 (29%), Positives = 24/58 (41%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           +  D + +      +D    AS  +              DDPVR+YL EM  + LLSR
Sbjct: 61  ESPDSQLKAEPVPPIDEIGEASPDAEKEIDLTPGTVNRIDDPVRLYLNEMAGVSLLSR 118


>gi|47089276|gb|AAT10957.1| sigma 70 factor [Pseudomonas syringae pv. aptata]
 gi|47089362|gb|AAT11000.1| sigma 70 factor [Pseudomonas syringae]
 gi|47089380|gb|AAT11009.1| sigma 70 factor [Pseudomonas syringae pv. syringae]
 gi|47089390|gb|AAT11014.1| sigma 70 factor [Pseudomonas syringae pv. tomato]
          Length = 149

 Score = 44.1 bits (102), Expect = 0.078,   Method: Composition-based stats.
 Identities = 22/194 (11%), Positives = 50/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L ++  L   I P+               K   +    + +
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDV--LSGYIDPDDGIAPPAEVPPPVDPKAVKAEGADDDE 58

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +        ESA    ++D  +    P  A+     + +  + +   L            
Sbjct: 59  E--------ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKAL------------ 98

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
                                  +K  +           L +L   + L   + + LVE+
Sbjct: 99  -----------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|332969693|gb|EGK08709.1| DNA-directed RNA polymerase sigma subunit SigI [Desmospora sp.
           8437]
          Length = 265

 Score = 44.1 bits (102), Expect = 0.079,   Method: Composition-based stats.
 Identities = 28/164 (17%), Positives = 58/164 (35%), Gaps = 9/164 (5%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQE 476
               +S+ E R + +            ++E+++ N   ++ VA K   R +    D    
Sbjct: 12  HNQKVSVLEERLLKAR------NDPAVREELIDENQTYILKVASKICIRNITRQDDEYSV 65

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
             +G  +A   +      KF ++A   +++ +T     ++        +         T 
Sbjct: 66  ALLGFNEAINSYRSDQSTKFHSFAFTVIRRRLTDYFRSETRHFNQVPLVSADSKDNEPTY 125

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580
             +  K   E    E+ +K    +E   K L+  K  ISL   +
Sbjct: 126 PEVIRKAFEEHHDRELEEKRRSDLEEFAKHLQRFK--ISLNDLV 167


>gi|94992644|ref|YP_600743.1| RNA polymerase sigma-B factor [Streptococcus pyogenes MGAS2096]
 gi|94546152|gb|ABF36199.1| RNA polymerase sigma-B factor [Streptococcus pyogenes MGAS2096]
          Length = 191

 Score = 44.1 bits (102), Expect = 0.079,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 52/119 (43%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ AV   ++ + A + 
Sbjct: 74  EQYTDFYRDKERWRYLQKLDTKNSLLSLDGFTDSEGNTLDFIADE-AVDVAETVVNAVMV 132

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVGK+  +T+  + + +A+ + KL+ 
Sbjct: 133 DRLKAALPLLSDSEQELIQAIFFNGLSE----REVGKRLGITQSVVNKRKARILIKLRK 187


>gi|295703128|ref|YP_003596203.1| RNA polymerase sigma-70factor [Bacillus megaterium DSM 319]
 gi|294800787|gb|ADF37853.1| RNA polymerase sigma factor, sigma-70 family [Bacillus megaterium
           DSM 319]
          Length = 203

 Score = 44.1 bits (102), Expect = 0.080,   Method: Composition-based stats.
 Identities = 19/191 (9%), Positives = 62/191 (32%), Gaps = 13/191 (6%)

Query: 490 WCLGYKFSTYAMWW-------VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
                 F T+           +          +     +  H   +   + +   +  ++
Sbjct: 12  HDKECTFHTFLTNHSATLQTHIMNTFLTPERYKRLQKAVVKHDTKEQRLLNKEFHQFYSE 71

Query: 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602
           ++      ++ +  +  V  V++  + +  P+ L+ P   +    + D +  ++      
Sbjct: 72  VRLLHYINKLCRHYSRDVMRVKEK-ERSYIPLRLQQPAALDGNRTVEDMLGVQDGAVWEH 130

Query: 603 SAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             +   L           LT +++ +L +            +E+   F ++++ +     
Sbjct: 131 EFLGNQLENRILHHAFRQLTAKQQCMLHLIIVERWTH----KEIAAYFSISQQAVSNHYQ 186

Query: 662 KAIRKLKHPSR 672
           +A+ KLK   +
Sbjct: 187 RALSKLKKIMK 197


>gi|170744691|ref|YP_001773346.1| hypothetical protein M446_6660 [Methylobacterium sp. 4-46]
 gi|168198965|gb|ACA20912.1| hypothetical protein M446_6660 [Methylobacterium sp. 4-46]
          Length = 142

 Score = 44.1 bits (102), Expect = 0.081,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 27/56 (48%)

Query: 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDL 83
            +  ++I   R+RG +T  +L A LP   +S + +   +  L   G+ V   +DL
Sbjct: 7  RATLDRLIARGRERGELTSADLRAALPISGMSPDAIALVLIELEEAGVPVELEEDL 62


>gi|87044984|gb|ABD17349.1| large variant extracellular factor [Streptococcus suis]
          Length = 1746

 Score = 44.1 bits (102), Expect = 0.081,   Method: Composition-based stats.
 Identities = 31/287 (10%), Positives = 92/287 (32%), Gaps = 11/287 (3%)

Query: 61   EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
            +          +    + D  +L  +E       +  +A  ++  + K         ++ 
Sbjct: 1056 DAKNKIAKEAESAKKAIDDNPNLTPDEKESAKNAVEEAAKVATAAIDKASTPDAVQVEED 1115

Query: 121  VRMYLREMGSIELLSREGEIA--IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
                 + + +I L++ + +    IA ++      +     E+     A  +  +E     
Sbjct: 1116 -----KGVAAINLITAKADAKGVIAAKLADEIKKLEDKQAEAEKAIDASTMTNEEKAIAK 1170

Query: 179  TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
              L++++D       ++     +     +  ++  +++      + +T  +   A +++K
Sbjct: 1171 KALQDVVDKGKAELEDAARVATNEIHEATTTEKAKAAELAGEKSLTDTGKEARDAVELAK 1230

Query: 239  DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            D     ++     E   + +++  +D+     A+ED           EI ++   +    
Sbjct: 1231 DKELAKEAIRTEEEEATKIVEKLAEDTRK---AIEDNPNLSDEDKQAEIKKLTDAVAKTL 1287

Query: 299  DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS-RIDLLVEQLYD 344
                +         +       L K   +  +     ID L   + D
Sbjct: 1288 ATIRDNADKRTQEAEKAQALADLEKAKETQKIADKAAIDRLTILVKD 1334


>gi|298032|emb|CAA50714.1| EF [Streptococcus suis]
          Length = 1822

 Score = 44.1 bits (102), Expect = 0.081,   Method: Composition-based stats.
 Identities = 31/287 (10%), Positives = 92/287 (32%), Gaps = 11/287 (3%)

Query: 61   EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
            +          +    + D  +L  +E       +  +A  ++  + K         ++ 
Sbjct: 1056 DAKNKIAKEAESAKKAIDDNPNLTPDEKESAKNAVEEAAKVATAAIDKASTPDAVQVEED 1115

Query: 121  VRMYLREMGSIELLSREGEIA--IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
                 + + +I L++ + +    IA ++      +     E+     A  +  +E     
Sbjct: 1116 -----KGVAAINLITAKADAKGVIAAKLADEIKKLEDKQAEAEKAIDASTMTNEEKAIAK 1170

Query: 179  TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
              L++++D       ++     +     +  ++  +++      + +T  +   A +++K
Sbjct: 1171 KALQDVVDKGKAELEDAARVATNEIHEATTTEKAKAAELAGEKSLTDTGKEARDAVELAK 1230

Query: 239  DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            D     ++     E   + +++  +D+     A+ED           EI ++   +    
Sbjct: 1231 DKELAKEAIRTEEEEATKIVEKLAEDTRK---AIEDNPNLSDEDKQAEIKKLTDAVAKTL 1287

Query: 299  DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS-RIDLLVEQLYD 344
                +         +       L K   +  +     ID L   + D
Sbjct: 1288 ATIRDNADKRTQEAEKAQALADLEKAKETQKIADKAAIDRLTILVKD 1334


>gi|327313254|ref|YP_004328691.1| RNA polymerase sigma factor, sigma-70 family [Prevotella denticola
           F0289]
 gi|326944626|gb|AEA20511.1| RNA polymerase sigma factor, sigma-70 family [Prevotella denticola
           F0289]
          Length = 208

 Score = 44.1 bits (102), Expect = 0.083,   Method: Composition-based stats.
 Identities = 15/76 (19%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
            + +D   +++++E    +L +LT R+   + +R+      + + EE+ +   ++   +R
Sbjct: 119 DTIIDEEEKSDIKEIVEDLLNTLTDRQREAIYLRY----MQNLSYEEIAELLDISPGSVR 174

Query: 658 QIEAKAIRKLKHPSRS 673
           ++  +AI  L+  SR 
Sbjct: 175 KLVYRAIMCLREESRK 190


>gi|237743869|ref|ZP_04574350.1| RNA polymerase sigma-30 factor [Fusobacterium sp. 7_1]
 gi|256027520|ref|ZP_05441354.1| RNA polymerase factor sigma-70 [Fusobacterium sp. D11]
 gi|289765480|ref|ZP_06524858.1| RNA polymerase sigma-30 factor [Fusobacterium sp. D11]
 gi|229432900|gb|EEO43112.1| RNA polymerase sigma-30 factor [Fusobacterium sp. 7_1]
 gi|289717035|gb|EFD81047.1| RNA polymerase sigma-30 factor [Fusobacterium sp. D11]
          Length = 113

 Score = 44.1 bits (102), Expect = 0.083,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 55/107 (51%), Gaps = 1/107 (0%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I ++++K +   S A   +++   +L+   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 1   MEDINAILKKAQSGDSEAINLILKEYSKLLSFNAQKYYLIGAEKEDLVQEGILGLLKAIK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533
            +D      FS++A   +++ +  +I   +    + ++   K + ++
Sbjct: 61  FYDETKS-SFSSFAFLCIRREMISAIRKANTQKNMVLNEALKTNAIL 106


>gi|153011783|ref|YP_001372996.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Ochrobactrum
           anthropi ATCC 49188]
 gi|151563671|gb|ABS17167.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Ochrobactrum anthropi ATCC 49188]
          Length = 390

 Score = 44.1 bits (102), Expect = 0.084,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 4/99 (4%)

Query: 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
           T+   ++      ++   L D I D     P     + ++     R +A L P E RVL 
Sbjct: 235 TEADQAMFEFYQPDEVLMLEDLIADDGGTDPETEVDRHDIAMALHRAIADLAPVERRVLY 294

Query: 630 MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             +      D T+ E      +T   + +I   A   L+
Sbjct: 295 RMYL----EDATIAETAHLLGLTEAEVLKIAENAAETLR 329


>gi|121488751|emb|CAJ18260.1| sigma 70-type sigma factor [Chlorobaculum parvum]
          Length = 94

 Score = 44.1 bits (102), Expect = 0.084,   Method: Composition-based stats.
 Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 1/95 (1%)

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
           K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D
Sbjct: 1   KISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLD 60

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
            +++   + P  +  + +L     R L+ L PRE 
Sbjct: 61  VLQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREA 94


>gi|227524603|ref|ZP_03954652.1| SMC structural maintenance of chromosomes partitioning protein
            [Lactobacillus hilgardii ATCC 8290]
 gi|227088278|gb|EEI23590.1| SMC structural maintenance of chromosomes partitioning protein
            [Lactobacillus hilgardii ATCC 8290]
          Length = 1183

 Score = 44.1 bits (102), Expect = 0.086,   Method: Composition-based stats.
 Identities = 64/435 (14%), Positives = 150/435 (34%), Gaps = 33/435 (7%)

Query: 46   IEELNAFLPPDEVSSEQMEDTVAMLSN--MGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
             + +  FL    + +E ++D + +         +V  D      G   +     S     
Sbjct: 614  FQAILDFLLGTTLIAETLDDAIQLSQQINHRTRIVSLDGQIVNAGGSLTGGANRSEGQGV 673

Query: 104  VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            +  +   +  + ST        +EM S++L  +E ++ IA      +  +          
Sbjct: 674  LVQKSELEKLEAST--------KEM-SVKLTEKEHQLQIA------KQELQKIQASFDRG 718

Query: 164  FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             Q +      ++   + L  +    +    + +      +  +  Q+ +DSS +      
Sbjct: 719  RQLVFQSGQMVDAQKSALDSL--RASKTSQKRELDALKLSLHNVKQQNQDSSDQNLVLKK 776

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME--DQLRPKVM 281
             + + +I+  A   + ++S +    +NAE+ E+      D    +   ++     + ++ 
Sbjct: 777  SQLDQEIKQVASAIEKNQSLLSDVKKNAESFEKQKQSLHDQIVISKEQLQHYQDDQKRLS 836

Query: 282  CALDEIAEVYRELRS----LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
               D++    ++L +    LQ +       EK +   K   +K   L  SL   +  +D 
Sbjct: 837  SQFDQLKNQRQDLETRSKNLQADLSEQIDPEKITKLIKESSDKQRALTTSLKTQKELVDR 896

Query: 338  LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY-----AKDFPE 392
              +Q   +   I + +  L          R+ F    +  +   + +S+       D   
Sbjct: 897  SDKQYDQLQNDIRNQQMNLNNATYELKNNREDFQNLQKSLDSSLNQLSHDFGILKSDLSH 956

Query: 393  GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR---KGECEASIAKKEMV 449
             EW   +      I  +R  I  I      +I EF+ +        K + + + AK  + 
Sbjct: 957  TEWNWDLETISRQIKLLRTGINEIGPVNISAIQEFQDVSDRYDFLLKQQQDLTDAKNHLT 1016

Query: 450  EANLRLVISVAKKYT 464
                 +  +++KK+ 
Sbjct: 1017 STMGEMDTTISKKFQ 1031


>gi|269125238|ref|YP_003298608.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268310196|gb|ACY96570.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 173

 Score = 44.1 bits (102), Expect = 0.088,   Method: Composition-based stats.
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 4/80 (5%)

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           E   A        +A        +L +L  R+  VL +R+      D + EE+     ++
Sbjct: 86  ELPEAGYIERGLERAEHDPRLWDLLTALPRRQRAVLVLRY----YEDMSDEEIAATLGIS 141

Query: 653 RERIRQIEAKAIRKLKHPSR 672
           R  +R   A+A+ KL+   R
Sbjct: 142 RGTVRSQAARALDKLRAQWR 161


>gi|157420102|gb|ABV55544.1| RpoD [Acinetobacter rhizosphaerae]
          Length = 160

 Score = 44.1 bits (102), Expect = 0.088,   Method: Composition-based stats.
 Identities = 25/197 (12%), Positives = 64/197 (32%), Gaps = 38/197 (19%)

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           P     ++   ++   G   L +I  L   + PE+        E  +  + E +     +
Sbjct: 1   PNAVXVVLKEYNDFLTGERRLADI--LSGYLDPETDAEIPEVLEEETELEEEAAPATPVK 58

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           + V+  + + +  ++   D   +    PE A+                            
Sbjct: 59  E-VKLDDDEEDEESESDDDSEGESGPDPEVAK---------------------------- 89

Query: 281 MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
               +E+   + + +++ +      K  ++S +     E L  +           D++ E
Sbjct: 90  -VRFNELEAAWTKTKAIIE------KHGRNSPEADEALEALATVFMMFKFTPRLFDIISE 142

Query: 341 QLYDISKRIMHNEGELL 357
            +    ++I  NE E++
Sbjct: 143 MIRGTHEQIRANEREVM 159


>gi|292492344|ref|YP_003527783.1| sigma-70 region 4 domain protein [Nitrosococcus halophilus Nc4]
 gi|291580939|gb|ADE15396.1| sigma-70 region 4 domain protein [Nitrosococcus halophilus Nc4]
          Length = 192

 Score = 44.1 bits (102), Expect = 0.090,   Method: Composition-based stats.
 Identities = 20/46 (43%), Positives = 30/46 (65%)

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R + +L  RF +    ++TLE++G  + +TRER+RQIEAK I  L
Sbjct: 131 ERNKDILCKRFNLEGEGEYTLEDIGIYYDLTRERVRQIEAKTISDL 176


>gi|331086351|ref|ZP_08335431.1| hypothetical protein HMPREF0987_01734 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406117|gb|EGG85640.1| hypothetical protein HMPREF0987_01734 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 246

 Score = 44.1 bits (102), Expect = 0.091,   Method: Composition-based stats.
 Identities = 45/222 (20%), Positives = 90/222 (40%), Gaps = 17/222 (7%)

Query: 350 MHNEGELLRLAQSYGIKRDVFLERH--QGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL 407
                E + L   Y + + V ++ +  QG  +       A++    E K ++A  ++ I 
Sbjct: 37  DGLSREQMELVCDYLLSQKVAVKGYVKQGGTVTEKTEEQAEEHYTEEEKRYLARYMEEIK 96

Query: 408 KIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG 467
            I+ E             E      +        ++A+  ++E  L  V+ VAK+  ++ 
Sbjct: 97  TIKAE-------------EAGERQKLFAASIEGDALARGRLIELYLEKVVEVAKEMYHKE 143

Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527
           +   DLIQEGN+ LM A +  +     +     M  V   +   I +Q+   R    + +
Sbjct: 144 VFLGDLIQEGNVSLMLALD--ELKSAEEAHGKIMEEVCAGMQMLIEEQTEVKRRDHTLLE 201

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
           K   +    +++  +  R+ T EE++  L M  E +  +L +
Sbjct: 202 KYTDLDDNIKKLKEETGRDVTIEEVSAFLDMTEEEINDILNL 243


>gi|254302087|ref|ZP_04969445.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148322279|gb|EDK87529.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 204

 Score = 44.1 bits (102), Expect = 0.091,   Method: Composition-based stats.
 Identities = 27/152 (17%), Positives = 69/152 (45%), Gaps = 4/152 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I ++++K +   + A   ++E   +++   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 1   MEDINAILKKAQSGDNEAINLILEEYSKILSFNAQKYYLVGAEQEDLVQEGILGLLKAIK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR---TARRMSNKI 543
            +D      F+++A   +++ +  +I   +    + ++   K + ++          + I
Sbjct: 61  FYDETKS-SFNSFAFLCIRREMISAIRKANTQKNMVLNEALKTNAILEDSTNFDDEEHNI 119

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               + E   ++  +  E + +  K ++   S
Sbjct: 120 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFS 151


>gi|206896523|ref|YP_002246663.1| RNA polymerase sigma factor for flagellar operon [Coprothermobacter
           proteolyticus DSM 5265]
 gi|206739140|gb|ACI18218.1| RNA polymerase sigma factor for flagellar operon [Coprothermobacter
           proteolyticus DSM 5265]
          Length = 199

 Score = 44.1 bits (102), Expect = 0.092,   Method: Composition-based stats.
 Identities = 36/233 (15%), Positives = 76/233 (32%), Gaps = 63/233 (27%)

Query: 441 ASIAKKEMVEANLRLVISVAKK--YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498
              A+++++ +  R++   A +  Y N  L++ DL+  G I   +  + ++      F  
Sbjct: 15  DDKAREQVLMSLQRVIERQASQLTYYNISLEWDDLLAVGLIAANECIDLYNLESEIPFEA 74

Query: 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAM 558
           +A   ++  +   +       +  V    +                              
Sbjct: 75  FASKVIRNKMVDYLRTTGTFTKSDVAKYKQGQ---------------------------- 106

Query: 559 PVEGVRKVLKITKEPISLETPIGD--EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
                   L + KE +SLE  I    E+    G  +E                       
Sbjct: 107 --------LTLNKEELSLEALIEQGIEEVGEQGIILE-------------------LEEA 139

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           L  L  R ++VL+ R+        +++EV     V+  R+ Q+  +A+  L+ 
Sbjct: 140 LNRLDLRHKQVLQFRYVDN----LSVKEVADILGVSPGRVSQLVNEALDLLRE 188


>gi|121488779|emb|CAJ18274.1| sigma 70-type sigma factor [Chlorobium luteolum DSM 273]
          Length = 93

 Score = 43.7 bits (101), Expect = 0.095,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           +K+ +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L 
Sbjct: 1   NKISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLL 60

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           D +++   + P     + +L     R L+ L PR
Sbjct: 61  DVLQNDGHL-PDHGLNRDSLTLEVERSLSVLAPR 93


>gi|332982726|ref|YP_004464167.1| RNA polymerase sigma-30 subunit SigH [Mahella australiensis 50-1
           BON]
 gi|332700404|gb|AEE97345.1| RNA polymerase, sigma 30 subunit, SigH [Mahella australiensis 50-1
           BON]
          Length = 216

 Score = 43.7 bits (101), Expect = 0.096,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 45/96 (46%), Gaps = 3/96 (3%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            R +VS  +K      +A + ++E    ++ + AK Y  +G    D+IQEG IGL KA +
Sbjct: 17  ERELVSRAKK---GDDVALECLIERYKSIIHNRAKTYFLKGSDREDIIQEGLIGLYKAIK 73

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            +       F ++A   + + I  ++   +    IP
Sbjct: 74  NYREDKAVSFRSFADMCITRQIITAVKAATRQKHIP 109


>gi|269124421|ref|YP_003297791.1| LuxR family transcriptional regulator [Thermomonospora curvata DSM
           43183]
 gi|268309379|gb|ACY95753.1| transcriptional regulator, LuxR family [Thermomonospora curvata DSM
           43183]
          Length = 197

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 23/157 (14%), Positives = 59/157 (37%), Gaps = 14/157 (8%)

Query: 520 RIPVHMRDKIHKVVRTARRMSN-KIKREPTPEEIAKKLAMPVEGVRKVLKITKEP--ISL 576
               ++ D+   ++R AR+++  + + E   +    K  +  + +     +        +
Sbjct: 8   EFHRYVADRGPVLLRAARQLTGDRTEAEDLLQVALAKTYLAWDRINDRAAVDGYVRRAMV 67

Query: 577 ETPIGDEDTSHLG----DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRF 632
            T I       L     D + D+          ++ + +  +R LA L  R+   + +R+
Sbjct: 68  NTHISWWRRRKLEIYPTDVLPDRPVDDHTR---RSEMHDALSRALARLPERQRLAVILRY 124

Query: 633 GIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
              +       E+ K   V+   ++   ++A+ KL+ 
Sbjct: 125 YEDLPEP----EIAKVLGVSVGTVKSTVSRAMAKLRE 157


>gi|326433499|gb|EGD79069.1| hypothetical protein PTSG_02037 [Salpingoeca sp. ATCC 50818]
          Length = 5390

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 106/711 (14%), Positives = 219/711 (30%), Gaps = 123/711 (17%)

Query: 44   VTIEELNAFLPPD--EVSSEQME---DTVAML-------SNMGINVVDGDDLEDEEGSED 91
            +T+ +L   L     +V +E  E        L         + + V D D  E ++   +
Sbjct: 4092 LTVRQLFDHLNDYSKKVDAELTEHDRQITDHLQKITKETEELHLMVKDMDVEELKQSLRE 4151

Query: 92   SLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151
             ++ ++S + S       + S +    D V + L+ +GS                   R 
Sbjct: 4152 MVETSASLTASQQERMAARASKESELIDRVNVLLKRLGS-------------------RV 4192

Query: 152  MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
             +  +L  +P +        D L  G                 SK G    +        
Sbjct: 4193 RVEDALAATPASVGK-QRSGDALAAGARRRSGAGAGAMLSSGSSKAGSDAASPASPTAVS 4251

Query: 212  EDSSQEK-----------------------ERDDVQETE----GDIESAAKVS------- 237
             D   +                        E +++ +T     GD+++            
Sbjct: 4252 GDEEGDDSGKQELMVSTQRLLAKREQQHVAEAEELGKTSLAGLGDLQTLDTEEGQTTLVN 4311

Query: 238  ---KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                D   ++DS  ++ +  +      +  +    + M   +R ++    D IAE   E 
Sbjct: 4312 KMLDDLEKQLDSAGDDGKEGDTAGSATDPFTPEEEAVMSAFIRSQLGDKFDTIAENSEE- 4370

Query: 295  RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                  A    ++     +            G   L+++ +D          + I+    
Sbjct: 4371 ---YQQARAAAENMIHRTRRDAATMAAEAAKGDAQLSKADVD--------TERLILMQVA 4419

Query: 355  ELLRLAQSY--GIKR-DVFLERHQGRELDPHWVSYAKDFPEGEW-KNFVACEVDSILKIR 410
            E     +    G+ R       +QG  L            +    K     + ++  + R
Sbjct: 4420 ETQTSGEESGEGMARVQAIAAHYQG--LRKAVRERMSAAAKRRKDKRCTKIDTEAAQQER 4477

Query: 411  NEIKSISVETG---ISISEFRHIVSMVRKGECEASIAKKEMVEANL---RLVISVAKKYT 464
             E++++        +S  E R     +++     +  +K +VEA       V  +A +  
Sbjct: 4478 EELEALQSTPEFKALSREERRLRQDKIKQRAKARARQRKRVVEAEEDAKEQV--LAARMV 4535

Query: 465  NRGLQFLDL--IQEGNIGLMKAAEKF--DWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
             + L   +L  +QE    +++A      D               +Q ++     Q   ++
Sbjct: 4536 KQ-LNTTELNKLQEATRAMVQATAGSEDDAEKMAAEFDERRNKARQHLSDQHKQQMNRMK 4594

Query: 521  IP--VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578
                     K   +           + E    E+A +  M +E + K  +       +E 
Sbjct: 4595 ERLAKTRLKKQEALTVAVSEAVEVSQLEVPELEVAPESVMELEAMEKNQQR------MEA 4648

Query: 579  PIGDEDTSHLGDF---------IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
             +       L +           E+K A+  L+   Q  L+E  +++ A +  R +   +
Sbjct: 4649 ELRKRHEQELKELEGKLRKEAEEEEKRALDALEERKQQVLKEKRSKLEAEVRARPDLSEQ 4708

Query: 630  MRFGIGMNTDHTLEEVGKQFCVTRERIRQIE-AKAIRKL-KHPSRSKKLRS 678
                +    +  L  +  +  V  ER RQ E  KA  KL +   + KKL+ 
Sbjct: 4709 EMNRLMKQHEQQLNTLSARMDV--ERNRQQELIKA--KLAERKQKRKKLQE 4755



 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 60/471 (12%), Positives = 144/471 (30%), Gaps = 62/471 (13%)

Query: 134  LSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID--- 186
            LSRE        I +R +A        +       + ++  R      TT L ++ +   
Sbjct: 4492 LSREERRLRQDKIKQRAKARARQRKRVVEAEEDAKEQVLAARMVKQLNTTELNKLQEATR 4551

Query: 187  --LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
              ++A  G E               K      ++ +  +   +  +       ++  +  
Sbjct: 4552 AMVQATAGSEDDAEKMAAEFDERRNKARQHLSDQHKQQMNRMKERLAKTRLKKQEALTVA 4611

Query: 245  DSPPENAENDERNLDEDEDDSAHTLSAME-------DQLRPKVMCALDEIAEVYRELRSL 297
             S        E    E   +S   L AME        +LR +    L E+    R+    
Sbjct: 4612 VSEAVEVSQLEVPELEVAPESVMELEAMEKNQQRMEAELRKRHEQELKELEGKLRKEAEE 4671

Query: 298  QDNAVNGQKDEKSSVKCKVLKEKL------------VKLVGSLSLNQSRIDLLVEQL--- 342
            ++       +E+     K  + KL             ++   +  ++ +++ L  ++   
Sbjct: 4672 EEKRALDALEERKQQVLKEKRSKLEAEVRARPDLSEQEMNRLMKQHEQQLNTLSARMDVE 4731

Query: 343  --------------YDISKRIMHNEGELLRLAQSYGIKRDVF--LERHQGRELDPHWVSY 386
                              ++ +  + + + L +    +R     L+  Q RE +   +  
Sbjct: 4732 RNRQQELIKAKLAERKQKRKKLQEQRQEVELQREIATQRQETEALKHEQVREAEREAMVT 4791

Query: 387  AKDFPEGEWKNFVA-----CEVDSILKIRNEI---KSISVETGISISEFRHIVSMVRKGE 438
            +      + +  VA          + +IR ++   + ++++   +  + RH   +  +  
Sbjct: 4792 SLQQTGKDAETVVASVLQRRHAQELQQIREQVEAEQDVALKELKATIQERHEARLDERAT 4851

Query: 439  CEASIAKKEMVE--ANLRLVISVAKKY--TNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
                     MVE  +         ++Y      L   +L  E    L +A    +  L  
Sbjct: 4852 RYEKEMADFMVESASIDPEAAEETRRYIEQAYKLDVSELESEYENELAQAETATNARLEL 4911

Query: 495  KFSTYAMWWVK---QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK 542
            K +   +   +   Q    ++ D S           +  ++ R  + +  +
Sbjct: 4912 KLTEMLLKRKEQHYQEFAEALRDLSPQSDESAQAEQRAMELERMRQELEQQ 4962


>gi|207743453|ref|YP_002259845.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
 gi|206594850|emb|CAQ61777.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
          Length = 184

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 48/74 (64%), Gaps = 3/74 (4%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           +++ +  IS++  ++ +E  H  +  + GE     A++ M+E NLRLV+S+AK Y  +G+
Sbjct: 109 VQHYLNRISIKPLLTPAEELHFSTRAKAGEF---AARQVMIERNLRLVVSIAKGYLKQGV 165

Query: 469 QFLDLIQEGNIGLM 482
           + +++I EGN G+M
Sbjct: 166 RLMEMISEGNRGVM 179



 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 43/130 (33%), Gaps = 20/130 (15%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD--------------- 118
            I VVD    E        +   S A++S+    + ++  +   +               
Sbjct: 44  DIEVVDTLTDEMPASEPADIVDTSDANDSADEPDEEEEDEEEEDEEAAPEEDFRTVLQAE 103

Query: 119 ---DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN 175
              D V+ YL  +    LL+   E+  + R +AG       + E  L     I     L 
Sbjct: 104 LAADTVQHYLNRISIKPLLTPAEELHFSTRAKAGEFAARQVMIERNLRLVVSIAKGY-LK 162

Query: 176 DGTTLLREII 185
            G   L E+I
Sbjct: 163 QG-VRLMEMI 171


>gi|225572790|ref|ZP_03781545.1| hypothetical protein RUMHYD_00981 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039847|gb|EEG50093.1| hypothetical protein RUMHYD_00981 [Blautia hydrogenotrophica DSM
           10507]
          Length = 171

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 4/80 (5%)

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           +  E    +S      Q  ++E  +  L  L+ RE ++L  ++  G        E+ ++ 
Sbjct: 85  EIYESSCEISVEKEVFQRQMKEDISWALQRLSERERKILVKKYYQG----KGAREIAEEM 140

Query: 650 CVTRERIRQIEAKAIRKLKH 669
            +T   +R I  +++ KLK 
Sbjct: 141 QITEGNVRVIAKRSLDKLKR 160


>gi|221503441|gb|EEE29139.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 1439

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 29/202 (14%), Positives = 72/202 (35%), Gaps = 5/202 (2%)

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  P   +     L+ +  +    L+  E Q   +V        E++  ++ L++ 
Sbjct: 241 DFDGAVGPGANDEKTMELEAELKELRGKLAEQERQAADRVRELEKRERELFGRVQELEEQ 300

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           +    +      +    +++L +L       Q R   LVE+  ++ +++  ++ EL +L 
Sbjct: 301 SALQAQVRDGFSELLDAQQQLQQLQREHRQLQQREQELVEKESELQRQLEQHQRELQQLH 360

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           Q         L+RH+  E+  + V  A      E +  V      +  +    +  +   
Sbjct: 361 QEVKE-----LQRHRAAEMRTNGVVEASLHEAEEQRAQVQQLERKVRDLEKLHRDATERD 415

Query: 421 GISISEFRHIVSMVRKGECEAS 442
            + I        ++++    A+
Sbjct: 416 AMRIRALEEENKLLKRTSGAAA 437


>gi|237840509|ref|XP_002369552.1| hypothetical protein TGME49_007370 [Toxoplasma gondii ME49]
 gi|211967216|gb|EEB02412.1| hypothetical protein TGME49_007370 [Toxoplasma gondii ME49]
          Length = 1439

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 29/202 (14%), Positives = 72/202 (35%), Gaps = 5/202 (2%)

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                  P   +     L+ +  +    L+  E Q   +V        E++  ++ L++ 
Sbjct: 241 DFDGAVGPGANDEKTMELEAELKELRGKLAEQERQAADRVRELEKRERELFGRVQELEEQ 300

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
           +    +      +    +++L +L       Q R   LVE+  ++ +++  ++ EL +L 
Sbjct: 301 SALQAQVRDGFSELLDAQQQLQQLQREHRQLQQREQELVEKESELQRQLEQHQRELQQLH 360

Query: 361 QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           Q         L+RH+  E+  + V  A      E +  V      +  +    +  +   
Sbjct: 361 QEVKE-----LQRHRAAEMRTNGVVEASLHEAEEQRAQVQQLERKVRDLEKLHRDATERD 415

Query: 421 GISISEFRHIVSMVRKGECEAS 442
            + I        ++++    A+
Sbjct: 416 AMRIRALEEENKLLKRTSGAAA 437


>gi|306518735|ref|ZP_07405082.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-32g58]
          Length = 205

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 36/87 (41%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +      IA + ++      V + AK Y   G    D+IQEG IGL KA   FD      
Sbjct: 25  RASEGDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAVRDFDGSKTNS 84

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP 522
           F  +A   + + I  +I   +    IP
Sbjct: 85  FKCFAEICITRQIITAIKTATRQKHIP 111


>gi|297199464|ref|ZP_06916861.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
 gi|197712993|gb|EDY57027.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
          Length = 173

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 22/110 (20%), Positives = 39/110 (35%), Gaps = 7/110 (6%)

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P   VR+ L   +        +       + D + D+ +    D A     R+     L 
Sbjct: 58  PEIYVRRALYHAQVDR---FRLLSWGRETVTDTLPDQPSAQVTDWADTVAQRQDIMAALR 114

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
            L  R+  V+ +R+      D   EE+     V +  +R    KA+  L+
Sbjct: 115 RLPKRQRAVIVLRYF----EDRPDEEIAAILGVAQGTVRSQTHKALASLR 160


>gi|182417954|ref|ZP_02949264.1| putative methyl-accepting chemotaxis protein [Clostridium butyricum
           5521]
 gi|237669427|ref|ZP_04529409.1| methyl-accepting chemotaxis protein [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182378263|gb|EDT75797.1| putative methyl-accepting chemotaxis protein [Clostridium butyricum
           5521]
 gi|237655314|gb|EEP52872.1| methyl-accepting chemotaxis protein [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 674

 Score = 43.7 bits (101), Expect = 0.10,   Method: Composition-based stats.
 Identities = 42/305 (13%), Positives = 118/305 (38%), Gaps = 15/305 (4%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           +++N  +    + +E++  ++  +S   IN          E ++ + ++     +    +
Sbjct: 383 DDVNEAIKQSLLGTEEITKSMEQISRGAIN--------QAENADKASEITGELVDEIKSV 434

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
             + +  +   +D ++M    +G+  + +    I   ++I         +L E       
Sbjct: 435 VDKCNYMNGIVNDSIKMS--TIGTERVQNAVENIKSIEKINNESIEQTLNLLEKSNEIGQ 492

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQE 225
           ++    E+ + T LL     +EA    E   GF    ++     K+ + + +K  + ++ 
Sbjct: 493 IVNVISEIAEQTNLLALNASIEAARAGEQGKGFAVVASQVGELAKQSNEAAKKIENIIRG 552

Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
            +  ++   K  K   ++V +  E  ++   N  E E     T   +E  +      +  
Sbjct: 553 IQQQVQVIDKQMKFGAAEVANGVETTKSVSENFTEIE----KTFKEIESVVLEVFHASNI 608

Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
              + +    S+++ A   +++  ++ +     E+    +  ++   S++D L+E L + 
Sbjct: 609 MEEKAHTTSNSIKEVAGVTEENSSATEEVTAANEEQSASMQQIAETTSKLDELIENLNET 668

Query: 346 SKRIM 350
            K+  
Sbjct: 669 IKKFK 673


>gi|326669833|ref|XP_003199092.1| PREDICTED: citron Rho-interacting kinase-like [Danio rerio]
          Length = 1619

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 54/333 (16%), Positives = 114/333 (34%), Gaps = 26/333 (7%)

Query: 35  IKLARQRGYVTIEELNAFLPPDEVSSE-QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           I+ A+++G V +EEL + L       + ++E+    L                      L
Sbjct: 143 IQKAKEQGKVEMEELLSKLQKTNGEQQVKIEELQEKL----------AKAVKASTEATEL 192

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM--GSIELLSREGEIAIAKRIEAGRA 151
                 +   +     +      + D +R  LRE   G   L ++   + + +R E+   
Sbjct: 193 LQNVRQAKERMERDLERLQTKEDSSDSLRRRLRETEDGKKSLENQVKRLEMVERRESKLK 252

Query: 152 MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKR 211
             + +        Q +    D++ +    LR+   +   +  + +       +     + 
Sbjct: 253 DDIQTKS------QQIQQMADKIMELEENLRDSQAMAQRMETQLEQKEKLFEDKIKVLET 306

Query: 212 EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE--DEDDSAHTL 269
           +  +   E+D ++  +   E  ++      S   +     E+   +L++   E   A+ L
Sbjct: 307 QMKADLAEKDLLESKQSTFEEESRERGKVISDQAATINAMESKMTSLEQRIAELSEANKL 366

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
           +A       K M A +E+    R     Q       +  K   +   L+E L KL     
Sbjct: 367 AANSSIYTQKNMKAQEEMISELR-----QQKFYLESQAGKLEAQNAKLEEHLEKLTQQEQ 421

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
            N+SR+  L  +L +I       + E+ R    
Sbjct: 422 TNKSRVLELEARLREIGLEHEEQKLEIKRQVSE 454


>gi|225166763|ref|YP_002650748.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253771350|ref|YP_003034243.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
 gi|225007427|dbj|BAH29523.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253721327|gb|ACT33620.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
          Length = 182

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 74/249 (29%), Gaps = 70/249 (28%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S+++K +     +   ++E     +   A KY   G  F DL+Q G + ++KA  K    
Sbjct: 3   SLIKKAKEGDRASIISIIEKYKPFIFKCAHKYNIPGYDFQDLVQHGYLSVIKAIHK---- 58

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
                                   +      ++      K +                 E
Sbjct: 59  -------------------YTLGSNSYNGYFINSISLNFKAL--------------LKGE 85

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRE 611
           I     +P + +                    D     DF  D   ++  +        E
Sbjct: 86  IKHFREVPDDKI-------------------MDKDDYYDFTLDDEIIAYDEV-------E 119

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              + L  L P E  ++   +  G     +  E+     V  +R+  ++ +   K++   
Sbjct: 120 KLYKSLNKLEPLEREIINRHYIKG----ESYSEIACSLDVKYDRVIYLKKRGFLKIR--- 172

Query: 672 RSKKLRSFL 680
           + + L SFL
Sbjct: 173 KEQFLYSFL 181


>gi|169334093|ref|ZP_02861286.1| hypothetical protein ANASTE_00486 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258810|gb|EDS72776.1| hypothetical protein ANASTE_00486 [Anaerofustis stercorihominis DSM
           17244]
          Length = 202

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 26/110 (23%), Positives = 52/110 (47%), Gaps = 7/110 (6%)

Query: 565 KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624
           K L    + +SLE     +   ++ DF+ D+ AV   ++ + A + +     L  L+  E
Sbjct: 99  KKLDTNHKLLSLE--GFTDSEGNVLDFVVDE-AVDVAETVVHAVMVDRLKAALPLLSGSE 155

Query: 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           + ++   F  G++      EVG +  VT+  + + +AK + KL+    +K
Sbjct: 156 QALINAIFFEGLSE----REVGLRLGVTQSVVNKRKAKILAKLRKIIENK 201


>gi|326476397|gb|EGE00407.1| midasin [Trichophyton tonsurans CBS 112818]
          Length = 4927

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 53/132 (40%), Gaps = 1/132 (0%)

Query: 183  EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
            +I+DL   +  + +     G++               +DD+ E   +     +    +  
Sbjct: 4277 DILDLPEDMDLDGEKKEDEGSDADDGMSEISMEDAANQDDLPEDTNEENKDTRPESPEVD 4336

Query: 243  KVDSPPENAENDERNLDE-DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
              ++P +NA+ D +  +E  E DS     A E++ + +++   DE  +      +  +  
Sbjct: 4337 MAENPDDNADEDGQREEETGEPDSEPQPEAGEEEDKDEIIPVEDEQQKADPNNTAPSEQV 4396

Query: 302  VNGQKDEKSSVK 313
              G + ++S+ K
Sbjct: 4397 SAGVQQDQSNEK 4408


>gi|83816830|ref|YP_446354.1| RNA polymerase ECF-type sigma factor, putative [Salinibacter ruber
           DSM 13855]
 gi|83758224|gb|ABC46337.1| RNA polymerase ECF-type sigma factor, putative [Salinibacter ruber
           DSM 13855]
          Length = 216

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 4/93 (4%)

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +  +  +    + D   D +  +P ++     LR    R +A L  R+   L     +  
Sbjct: 115 DEAVRRDHEQDVRDAHPDASPPAPDETLDADLLRSLLERWIAELPDRQREALT----LRR 170

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             D + +E+ +   V+   +     +A+R L+ 
Sbjct: 171 QKDLSHDEIAEIMDVSPNTVNNHIVRAMRTLRE 203


>gi|326484754|gb|EGE08764.1| midasin [Trichophyton equinum CBS 127.97]
          Length = 4927

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 53/132 (40%), Gaps = 1/132 (0%)

Query: 183  EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
            +I+DL   +  + +     G++               +DD+ E   +     +    +  
Sbjct: 4277 DILDLPEDMDLDGEKKEDEGSDADDGMSEISMEDAANQDDLPEDTNEENKDTRPESPEVD 4336

Query: 243  KVDSPPENAENDERNLDE-DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
              ++P +NA+ D +  +E  E DS     A E++ + +++   DE  +      +  +  
Sbjct: 4337 MAENPDDNADEDGQREEETGEPDSEPQPEAGEEEDKDEIIPVEDEQQKADPNNTAPSEQV 4396

Query: 302  VNGQKDEKSSVK 313
              G + ++S+ K
Sbjct: 4397 SAGVQQDQSNEK 4408


>gi|320108784|ref|YP_004184374.1| ECF subfamily RNA polymerase sigma-24 factor [Terriglobus saanensis
           SP1PR4]
 gi|319927305|gb|ADV84380.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Terriglobus
           saanensis SP1PR4]
          Length = 215

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/95 (16%), Positives = 37/95 (38%), Gaps = 6/95 (6%)

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D + L D +   +  +     +    R    +    L+ ++   L + F  G      L 
Sbjct: 123 DVTLLADTLAGND--NLEREIVSRLNRVHLQQAFEELSDKQRITLELYFFEG----LELM 176

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678
           E+ ++   + E +R    + ++KL+  S  + L+ 
Sbjct: 177 EIAERMNESSENVRHFYYRGLQKLRKNSFVQSLKE 211


>gi|313893511|ref|ZP_07827081.1| sigma-70, region 4 [Veillonella sp. oral taxon 158 str. F0412]
 gi|313441954|gb|EFR60376.1| sigma-70, region 4 [Veillonella sp. oral taxon 158 str. F0412]
          Length = 296

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
            D    G+ I D      + +  +  LR      L  L+P +  +LR  +G       +L
Sbjct: 206 MDIFASGENIADM----IMTADEEQRLRARLVWALGRLSPDQRDLLRRVYG----ECQSL 257

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
             V ++   +R+ I++   +AIRKL+ 
Sbjct: 258 VSVSEELNCSRQAIQRRHERAIRKLRR 284


>gi|257413671|ref|ZP_05591752.1| hypothetical protein ROSINTL182_07064 [Roseburia intestinalis
           L1-82]
 gi|257202743|gb|EEV01028.1| hypothetical protein ROSINTL182_07064 [Roseburia intestinalis
           L1-82]
          Length = 279

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 70/201 (34%), Gaps = 12/201 (5%)

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQA--ITRSIADQSCTIRIPVHMR-DKIHKVVRTA 536
            L+    KFD     +F  YA  +++      R I +      +  + R  +I  +   +
Sbjct: 54  MLLYCLPKFDPEQKTEFLKYAKHYIRDGLLFCRMIGEAGSFASLAEYRRVRQIGAIYNNS 113

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
            +   ++      +   K  ++  + +  + +  +  +SL     DED    G+ +   +
Sbjct: 114 GKRRAEVVSAFAAQSGYKDDSVSADELLTIAQRNRSIVSLYRTEQDEDGEETGEDVTRDD 173

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH--------TLEEVGKQ 648
           + +  +        +  T     L+ +E+  L  R  I M            T E++   
Sbjct: 174 SWNYAEILWNGIQAKAVTAAFEQLSYKEQWYLEKRNAICMTCGRVSPLSTQSTFEDLAVD 233

Query: 649 F-CVTRERIRQIEAKAIRKLK 668
           F   T     +   + + KL+
Sbjct: 234 FEGTTASGAERFYRRTLDKLR 254


>gi|317497614|ref|ZP_07955932.1| RNA polymerase sigma-H factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895173|gb|EFV17337.1| RNA polymerase sigma-H factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 200

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 26/91 (28%), Positives = 42/91 (46%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R+ +     A + ++E    +V   A+ +   G    DLIQEG IGL KA   +   
Sbjct: 11  KLLRQIQSGNDDAMECLLERYRDMVRKEARSFFLAGGDEEDLIQEGMIGLFKAVTSYQEE 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               FST+A   V++ I  +I   +    IP
Sbjct: 71  KNTSFSTFAYLCVQRQIYTTITAFNRKKHIP 101


>gi|121488720|emb|CAJ18246.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 95

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 1/96 (1%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 1   ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 60

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           +++   + P     + +L     R L+ L PRE  V
Sbjct: 61  LQNDGHL-PDHGLNRDSLTLEVERSLSVLAPREADV 95


>gi|294508291|ref|YP_003572349.1| RNA polymerase sigma-E factor [Salinibacter ruber M8]
 gi|294344619|emb|CBH25397.1| RNA polymerase sigma-E factor [Salinibacter ruber M8]
          Length = 216

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 4/93 (4%)

Query: 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGM 636
           +  +  +    + D   D +  +P ++     LR    R +A L  R+   L     +  
Sbjct: 115 DEAVRRDHEQDVRDAHPDASPPAPDETLDADLLRSLLERWIAELPDRQREALT----LRR 170

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
             D + +E+ +   V+   +     +A+R L+ 
Sbjct: 171 QKDLSHDEIAEIMDVSPNTVNNHIVRAMRTLRE 203


>gi|167747614|ref|ZP_02419741.1| hypothetical protein ANACAC_02335 [Anaerostipes caccae DSM 14662]
 gi|167652976|gb|EDR97105.1| hypothetical protein ANACAC_02335 [Anaerostipes caccae DSM 14662]
          Length = 135

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +      DFI D+ A    ++ + A + 
Sbjct: 18  EQYTDFYRDKERWRYLKKLDTKNSLLSLDGFTDSEGKPLDFIADE-AADIAETVVNAVMV 76

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +F +T+  + + +A+ +RKL+ 
Sbjct: 77  DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARFGITQSVVNKRKARILRKLRK 131


>gi|220926514|ref|YP_002501816.1| hypothetical protein Mnod_6755 [Methylobacterium nodulans ORS
          2060]
 gi|219951121|gb|ACL61513.1| conserved hypothetical protein [Methylobacterium nodulans ORS
          2060]
          Length = 141

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 21 SLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77
             FD    +  ++I   R +G +T  +L   LP D +S + +   +  L   GI V
Sbjct: 2  PPAFD--RATLDRLIARGRAQGQLTTADLRRELPIDGMSPDTIALVLIELEEAGIPV 56


>gi|227510451|ref|ZP_03940500.1| SMC structural maintenance of chromosomes partitioning protein
            [Lactobacillus brevis subsp. gravesensis ATCC 27305]
 gi|227190103|gb|EEI70170.1| SMC structural maintenance of chromosomes partitioning protein
            [Lactobacillus brevis subsp. gravesensis ATCC 27305]
          Length = 1183

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 64/435 (14%), Positives = 147/435 (33%), Gaps = 33/435 (7%)

Query: 46   IEELNAFLPPDEVSSEQMEDTVAMLSN--MGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
             + +  FL    + +E ++D V +         +V  D      G   +     S     
Sbjct: 614  FQAILDFLLGTTLIAETLDDAVQLSQQINHRTRIVSLDGQIVNAGGSLTGGANRSEGQGV 673

Query: 104  VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            +  +   +  + ST        +EM S++L  +E ++ IA      +  +          
Sbjct: 674  LVQKSELEKLEVST--------KEM-SVKLTDKEHQLQIA------KQELQKIQASFDRG 718

Query: 164  FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             Q +      ++   + L  +    +    + +      +  +  Q+ +DSS +      
Sbjct: 719  RQLVFQSGQMVDAQKSALDSL--RASKTSQKRELDALKLSLHNVKQQNQDSSDQNLALKK 776

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME--DQLRPKVM 281
             + + +I   A   + ++S +    +NAE+ E+      D    +   ++     + ++ 
Sbjct: 777  SQLDQEITQVASAIEKNQSLLSDVKKNAESFEKQKQSLHDQIVISKEQLQHYQDDQKRLS 836

Query: 282  CALDEIAEVYRELRS----LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
               D++    ++L +    LQ +       E+ +   K   +K   L  SL   +  +D 
Sbjct: 837  SQFDQLKNQRQDLETQLKNLQADLAEQIDPEEITKLIKESSDKQGALTTSLKTQKELVDR 896

Query: 338  LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG-----RELDPHWVSYAKDFPE 392
              +Q   +   I + +  L          R+ F    +       +L   +     D   
Sbjct: 897  SDKQYDQLQNDIRNQQMNLNNATYELKNNREDFQNLQKSLDGSLNQLSHDFGILKSDLSH 956

Query: 393  GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR---KGECEASIAKKEMV 449
             EW   +      I  +R  I  I      +I EF+ +        K + + + AK  + 
Sbjct: 957  TEWHWDLETISRQIKLLRTGINEIGPVNISAIQEFQDVSDRYDFLLKQQQDLTDAKNHLT 1016

Query: 450  EANLRLVISVAKKYT 464
                 +  +++KK+ 
Sbjct: 1017 STMGEMDTTISKKFQ 1031


>gi|225574360|ref|ZP_03782970.1| hypothetical protein RUMHYD_02427 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038416|gb|EEG48662.1| hypothetical protein RUMHYD_02427 [Blautia hydrogenotrophica DSM
           10507]
          Length = 202

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 31/158 (19%), Positives = 63/158 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K           ++E    LV   A+     G +  DLIQEG IGL KA   +   
Sbjct: 11  ELIEKLRDGQEDVADYLMEKYKELVRQKARAMYLIGGETDDLIQEGMIGLFKAVRDYQPD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F T+A   + + + ++I+  +     P++    + +     R++ +  ++ P    
Sbjct: 71  KAASFQTFARLCIDRQLYKAISGSNRQKHQPLNTYVSLSQETEGERQLRSLWEQNPEAIV 130

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
           IA++    +E   +    + E   LE  +  +D   + 
Sbjct: 131 IARENVEDLEKRIEECLSSFENQVLECYLRGKDYEQIA 168


>gi|320167897|gb|EFW44796.1| Cdc42-binding protein kinase beta [Capsaspora owczarzaki ATCC 30864]
          Length = 1937

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 73/541 (13%), Positives = 166/541 (30%), Gaps = 35/541 (6%)

Query: 144  KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
            K++E  +  M  +  +     QA    R+ + D    L E ++         K       
Sbjct: 545  KKLEREKKEMENATIDLNTRLQAAEKMRNMMKDSKQELDEQVEQLEGKLTAQKKDLKDAQ 604

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
                  + E  S   + +D+Q     ++   +    D   + +  + A+ D R+ ++   
Sbjct: 605  RLRQKAEAEFESLTAQVNDLQGQVARLDRTVRDKNADIDSLTAQRDAAKKDLRSSEKTRG 664

Query: 264  DSAHTLSAMEDQLRPK--VMCALDEIAEVYRE-LRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            D    L  ++ +L  +  V    ++++   +E L +L+D                VL+ +
Sbjct: 665  DLQSQLDDLQSELTRERSVRSKAEKLSHQLQEDLETLRDRVAGKASGAAGGD--TVLQAQ 722

Query: 321  LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
            + +L G L     R +     L D+   +      + R        +    E+ +  +  
Sbjct: 723  IAELEGKLEQEVKRHE---ASLRDVRNELQSEVENVRRQLNESKSSKSALEEQVEDLKSS 779

Query: 381  PHWVSYAKDFPEGEWKNFVACE-VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGEC 439
                +      + E     + E   +I  ++ ++K+       S S     V  ++    
Sbjct: 780  LAKSAKDLQAAKSEASTTASQESTKTIDALKAKLKAAEDALESSQSSLEDRVKTLQAQAD 839

Query: 440  EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
            +AS  K  + +      ++   K  +   Q    +      +  AA +       K  +Y
Sbjct: 840  KASEEKNRIAKLLAEETLAK-TKLESSNTQLRTELTAAVSTVDDAASQLSM-FQTKLESY 897

Query: 500  AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
                 +    R+   +  +                T     +    + + E +A    M 
Sbjct: 898  EQNLAELESLRAENTRLRSTAARRPSLALEQMFRTTDG--GDDNPEDGSVENLAGFPGMS 955

Query: 560  VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
              G        +     +     E  +   D              ++A  +E   +  A 
Sbjct: 956  GTGTISRRGGARGGAGADKKEWQERRTVKLD-----------KQVMRALQQEVDIQTQAK 1004

Query: 620  LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI--EAKAIRKLKHPSRSKKLR 677
            L       +   F        + E+        R R+ ++  E +A+++L+      K R
Sbjct: 1005 L------KMETEFNQIKVEKESSEQEVHIL---RARVSELDRELEALKRLRQDEIKSKWR 1055

Query: 678  S 678
             
Sbjct: 1056 D 1056


>gi|302876749|ref|YP_003845382.1| sigma-70 region 4 domain-containing protein [Clostridium
           cellulovorans 743B]
 gi|307687429|ref|ZP_07629875.1| sigma-70 region 4 domain-containing protein [Clostridium
           cellulovorans 743B]
 gi|302579606|gb|ADL53618.1| sigma-70 region 4 domain protein [Clostridium cellulovorans 743B]
          Length = 201

 Score = 43.7 bits (101), Expect = 0.11,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ AV   ++ + A + 
Sbjct: 53  EQYTDFYRDKERWRYLQKLDTKNRLLSLDGFTDSEGNPLDFITDE-AVDIAETVVNAVMV 111

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ + KL+ 
Sbjct: 112 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILIKLRK 166


>gi|237742620|ref|ZP_04573101.1| RNA polymerase sigma-H factor [Fusobacterium sp. 4_1_13]
 gi|229430268|gb|EEO40480.1| RNA polymerase sigma-H factor [Fusobacterium sp. 4_1_13]
          Length = 204

 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 29/152 (19%), Positives = 69/152 (45%), Gaps = 4/152 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I ++++K +   S A   +++   +L+   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 1   MEEINAILKKAQSGDSEAISLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR---TARRMSNKI 543
            +D      FS++A   +++ +  +I   +    + ++   K + ++          + I
Sbjct: 61  FYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSANFDDEEHNI 119

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               + E   ++  +  E + +  K ++   S
Sbjct: 120 NNYKSSESNPEEAYLLKEKIEEFKKFSENNFS 151


>gi|260886272|ref|ZP_05897535.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Selenomonas sputigena ATCC 35185]
 gi|330839743|ref|YP_004414323.1| RNA polymerase sigma factor, sigma-70 family [Selenomonas sputigena
           ATCC 35185]
 gi|260863991|gb|EEX78491.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Selenomonas sputigena ATCC 35185]
 gi|329747507|gb|AEC00864.1| RNA polymerase sigma factor, sigma-70 family [Selenomonas sputigena
           ATCC 35185]
          Length = 183

 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 7/87 (8%)

Query: 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
           E+     + +ED+ A           L++     + +L+ RE+ +L + +        +L
Sbjct: 101 EEGKSFWESVEDETASDASMHFA---LKDALFAAMRTLSEREKELLSLVYLADW----SL 153

Query: 643 EEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +E   +  ++      ++ +A++KLK 
Sbjct: 154 KEAAAKLGLSAAYAAVVKRRALQKLKK 180


>gi|71277187|gb|AAZ29803.1| RpoD [Pseudomonas savastanoi]
          Length = 153

 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           +  P  + A      V  ++   +       +D+K ++   V    L +L   + L   +
Sbjct: 71  ESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQ 127

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLA 360
            + LVE++    +R+   E  +++L 
Sbjct: 128 FEGLVERVRGALERLRAQERAIMQLC 153


>gi|238916437|ref|YP_002929954.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238871797|gb|ACR71507.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 203

 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 35/91 (38%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++         A + + E    +V   AK     G    DLIQEG IGL KA   +D  
Sbjct: 11  ELIDMYRAGNEQAIEYIFERYKYIVRKKAKAMFLAGGDSDDLIQEGMIGLYKAVRDYDKQ 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F T+A   + + I  ++   +     P
Sbjct: 71  KDASFMTFAGMCINRQILNAVTASNRKKNTP 101


>gi|291559860|emb|CBL38660.1| RNA polymerase sigma factor, sigma-70 family [butyrate-producing
           bacterium SSC/2]
          Length = 200

 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 26/91 (28%), Positives = 42/91 (46%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R+ +     A + ++E    +V   A+ +   G    DLIQEG IGL KA   +   
Sbjct: 11  KLLRQIQSGNDDAMECLLERYRDMVRKEARSFFLAGGDEEDLIQEGMIGLFKAVTSYQEE 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               FST+A   V++ I  +I   +    IP
Sbjct: 71  KNTSFSTFAYLCVQRQIYTTITAFNRKKHIP 101


>gi|210614501|ref|ZP_03290201.1| hypothetical protein CLONEX_02415 [Clostridium nexile DSM 1787]
 gi|210150685|gb|EEA81694.1| hypothetical protein CLONEX_02415 [Clostridium nexile DSM 1787]
          Length = 158

 Score = 43.7 bits (101), Expect = 0.12,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +      DFI D+ A    ++ + A + 
Sbjct: 41  EQYTDFYRDKERWRYLKKLDTKNSLLSLDGFTDSEGKPLDFIADE-AADIAETVVNAVMV 99

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +F +T+  + + +A+ +RKL+ 
Sbjct: 100 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARFGITQSVVNKRKARILRKLRK 154


>gi|121488783|emb|CAJ18276.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 93

 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A +L M  + V   LKI    +S++ P    D + L D 
Sbjct: 1   ISKAYSQLEQEYERDPNTKELANQLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 60

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++   + P     + +L     R L+ L PRE 
Sbjct: 61  LQNDGHL-PDHGLNRDSLTLEVERSLSVLAPREA 93


>gi|317121689|ref|YP_004101692.1| RNA polymerase, sigma 28 subunit, SigI [Thermaerobacter marianensis
           DSM 12885]
 gi|315591669|gb|ADU50965.1| RNA polymerase, sigma 28 subunit, SigI [Thermaerobacter marianensis
           DSM 12885]
          Length = 240

 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKFD 489
            ++   +     A+ E++ A    V+ VA +   R L     + I  G +   +A ++FD
Sbjct: 10  QLIVAAKAGDDDARNELIRAYTPFVLKVASRVCGRFLHAGQDEEISIGLLAFNEAIDRFD 69

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQS 516
              G+ F  +A   +++ +      QS
Sbjct: 70  ATRGHNFIAFAETVIRRRLIDHFRKQS 96


>gi|154335017|ref|XP_001563755.1| kinesin [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134060777|emb|CAM37792.1| putative kinesin [Leishmania braziliensis MHOM/BR/75/M2904]
          Length = 1037

 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 65/417 (15%), Positives = 144/417 (34%), Gaps = 26/417 (6%)

Query: 247 PPENAENDERNLDED-EDDSAHTLSAM--EDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
            PE A  D  +L E   D+      A+  E QL+  +   L  IA++  +LR   D+ + 
Sbjct: 493 DPEQARQDGCDLGEQWRDEYLRKKEALYAEYQLKGTIEKLLARIADLEAKLRECADDELA 552

Query: 304 GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE-LLRLAQS 362
                +     K L E   ++     +      +L ++L D++ ++   + E    +   
Sbjct: 553 LHLTTEIEGLQKALTEADYQMGLQRQILYGEFLMLEDELRDMNTKMQEMKDEHEEAMEGV 612

Query: 363 YGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
            G +   F +  +G E     +    D   G   + +A     + +++  + +   E   
Sbjct: 613 LGEEAGRFEDMKRGYEARLRALRDESDAALGASADEIAALRRLVAELQERLAAKETECAD 672

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN-IGL 481
            +     + +           A+ E+ +               R ++ L L QEG  + L
Sbjct: 673 VLDRLAALQAKYDADTSAGERARGELEDQL-------------RSMRALLLEQEGASLEL 719

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
            K  E+ D  L    +       +          +           +    ++  + +  
Sbjct: 720 RKQIEERDAQLATVETHLEETHTQATTLTEQLTAATRAAAERKEELERE--LQALQSVVE 777

Query: 542 KIKREP-TPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
           +++ +  T EE  ++    +    + L+ T   ++       E ++ L D  E     S 
Sbjct: 778 ELRTDMATTEEALQENTAKLAVTEETLQETSGKLADTEEALQETSAKLADTEETLQETSA 837

Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             +  +  L+ET+ ++  +     E  L+       +T+  L+E   +   T E + 
Sbjct: 838 KLAVTEEALQETSAKLADT-----EDTLQETSAKLADTEEALQETSAKLADTEETLS 889


>gi|67920930|ref|ZP_00514449.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
 gi|67857047|gb|EAM52287.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
          Length = 139

 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 30/137 (21%), Positives = 56/137 (40%), Gaps = 11/137 (8%)

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL--KITKEPISLETPIGD--EDTSHLGDF 591
            +    K  R+PT  EIA+ L + ++  +++      +EP+SL+  I +  E  + LG+ 
Sbjct: 2   RQEFREKFNRQPTDSEIAQVLEISLKEWQEIKLAFQNREPVSLDVKISNGGEGQTSLGEL 61

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D N  S   +           + L  L  +   +L   F      D T  E  +Q  +
Sbjct: 62  VPDINYRSFQLAQEDQI---RLQQALGQLEEKTRNILEFVFL----KDLTQRETAEQLGI 114

Query: 652 TRERIRQIEAKAIRKLK 668
           +   + +   K +  LK
Sbjct: 115 SVVTVSRRVKKGLEVLK 131


>gi|332027375|gb|EGI67458.1| Kinesin-like protein KIF21A [Acromyrmex echinatior]
          Length = 1484

 Score = 43.3 bits (100), Expect = 0.13,   Method: Composition-based stats.
 Identities = 43/318 (13%), Positives = 107/318 (33%), Gaps = 19/318 (5%)

Query: 130 SIELLSREGEIAIAKRIE--------AGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           +++ L+ +  + +A++           G   + + +       Q +   R  L +   + 
Sbjct: 430 TVDALTAKNALLLAEKAAGHWVATSGKGDDQVTSLIQGY---VQEIEELRARLLEAEAMY 486

Query: 182 REIIDLEACIG---PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE---GDIESAAK 235
           +++   +  +    P     F   +       + D  +E E     + +     I+S  +
Sbjct: 487 QQLKKRQMQVSAANPYGDSSFHSDSASVLIDAKRDVEKEIETLRTLKEQYSSNTIKSVDE 546

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
              DD           ++D+ +  ++ED+    +    + L   +      I E+    R
Sbjct: 547 GEIDDAENAQDSVSEDDSDDDSDRKEEDEEEAAMGRELEALTSDIDVKQRLIQELELSQR 606

Query: 296 SLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
            LQ        K  +   + +  +E+  K++ SL    +     V++L D  ++ + N  
Sbjct: 607 RLQTMKQHYEDKLSQLQARIRDTQEERDKVLLSLQQQPTPPTEKVKKLRDEYEKKLANMQ 666

Query: 355 ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR-NEI 413
           + +RL QS   +    L+     E     +       +      +    +   + + NE+
Sbjct: 667 KEMRLLQSAKKEHARLLKNQSQNENRLRGLRNELSEMKRAKVKLLNKMREEAQRHKENEL 726

Query: 414 KSISVETGISISEFRHIV 431
           +       +     RH  
Sbjct: 727 RRNREIAQLRKESRRHAN 744


>gi|318040245|ref|ZP_07972201.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 89

 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 40/77 (51%)

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
           +   P +      LR     +L  L   + RVL+MR+GIG+    +L  + ++  ++R+R
Sbjct: 5   DGTQPEELVDGECLRSDMRDLLDQLPELQGRVLKMRYGIGIEEPMSLSSIARELEMSRDR 64

Query: 656 IRQIEAKAIRKLKHPSR 672
            R +E +A  +++  S+
Sbjct: 65  ARSLERRAHEEMRRLSQ 81


>gi|297156256|gb|ADI05968.1| ECF subfamily RNA polymerase sigma factor [Streptomyces
           bingchenggensis BCW-1]
          Length = 182

 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 25/111 (22%), Positives = 45/111 (40%), Gaps = 9/111 (8%)

Query: 559 PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
           P   +R+VL    + +SL   +     + + +     +A    D+   A LR    R LA
Sbjct: 56  PEAYLRQVLYR--QQVSLWRLLRTRRETTVAEL---PDAAGREDTTGAAELRIQMRRALA 110

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            LT R+  +L +R+           EV +    +   +R    +A+ KL+ 
Sbjct: 111 RLTARQRSMLVLRYFEDCPEG----EVAELLGCSVGTVRSTTHRALAKLRK 157


>gi|207092362|ref|ZP_03240149.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 130

 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 20/135 (14%), Positives = 54/135 (40%), Gaps = 14/135 (10%)

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
             +  N+  +EP+   +A+ L   +E +++    +     +   +  ++  +  +     
Sbjct: 4   ITKHLNEHGKEPSDAYLAQTLGENIEKIKEAKTASD----IYALVPIDEQFNAIE----- 54

Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                        L E   + L  ++ RE+ ++++ +      +  L E+ +   +T  R
Sbjct: 55  -QDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYF----EELNLSEIKEILGITESR 109

Query: 656 IRQIEAKAIRKLKHP 670
           I QI  + I+K++  
Sbjct: 110 ISQIIKEVIKKVRKS 124


>gi|196003640|ref|XP_002111687.1| hypothetical protein TRIADDRAFT_55968 [Trichoplax adhaerens]
 gi|190585586|gb|EDV25654.1| hypothetical protein TRIADDRAFT_55968 [Trichoplax adhaerens]
          Length = 7710

 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 61/470 (12%), Positives = 148/470 (31%), Gaps = 44/470 (9%)

Query: 165  QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
            +  +    E       +R+  DLE+      +       E    QK E+S Q+K R+   
Sbjct: 6705 ETALKQEQERVLEDLRMRQKDDLESFTQRIERDS--KEDESKLAQKLENSKQKKVREMKN 6762

Query: 225  ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
            +   ++ +       D +         E  E     D+D     L+  E   + K     
Sbjct: 6763 KQAAELAARGNSMSTDETAALMASHQRELAELENKLDQDKHRQKLALKEKLRKRKKNKQQ 6822

Query: 285  DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS-------LSLNQSRIDL 337
            + + +  +EL            + +     +  K+ ++  +         L + +     
Sbjct: 6823 EFVDKQEQELEKETLEQEKELSEVRKKNVKEAEKQAMIAGIQQNGVEAGDLIVRRVLEQR 6882

Query: 338  LVEQLYDISKRIMHNEGE-----LLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
              +++  + K+      +     L  L +    +R+  L +HQ    D      A D  E
Sbjct: 6883 HADEMKALEKQFEAERKKSVDDALTVLLKKQAAEREAMLAKHQSELEDLENSDLAPDELE 6942

Query: 393  GEWKNFVACEVDSILKIRNEI----KSISVETGISISEFR---HIVSMVRKGECEASIAK 445
             +  N +  +   + K+  +     K +   T ++  E +     + +  +   E + A 
Sbjct: 6943 QQKSNLLNKQQLELSKLEQKHEDQRKRLERST-LTDLEVKFANEKLKLKEQQYKEYADAL 7001

Query: 446  KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
             ++       V     K                  L    +K +     +          
Sbjct: 7002 SQLTPEQDAAVKVEKAK-------------VAAQDLDNLRKKLEVQRQEQEEKLK----- 7043

Query: 506  QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV--EGV 563
                R+  +      +   ++D   ++ +       K+K++    +  K  A+    E  
Sbjct: 7044 --QERNAFETQAEDDLAKAIKDFDKQLEKEMDLQKQKLKQDIEELDARKTKAIEEKKEQA 7101

Query: 564  RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
            ++ L+  ++  S +  +      H  D +  +N +      ++++L+E  
Sbjct: 7102 KQELEAKQKSGSSKEELQRLTDQHEKDLLALQNKLDADRMRMESSLQEKL 7151


>gi|294146897|ref|YP_003559563.1| ECF-type sigma factor [Sphingobium japonicum UT26S]
 gi|292677314|dbj|BAI98831.1| ECF-type sigma factor [Sphingobium japonicum UT26S]
          Length = 244

 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 35/59 (59%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
             T  R++A L P E++V+R+R G+G +   TL    K   V+  RI QIE KA R+++
Sbjct: 31  HRTVERLIAMLEPHEQQVVRLRIGLGPSPALTLAATAKIVGVSPSRIGQIEDKAFRRIR 89


>gi|328554318|gb|AEB24810.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens TA208]
 gi|328912713|gb|AEB64309.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus amyloliquefaciens LL3]
          Length = 64

 Score = 43.3 bits (100), Expect = 0.14,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 24/41 (58%)

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           ++  RFG+ +  + T   + K+  ++R  + +IE +A+ K+
Sbjct: 1   MIVGRFGLDLKKEKTQRGIAKELGISRSYVSRIEKRALMKM 41


>gi|164686510|ref|ZP_02210538.1| hypothetical protein CLOBAR_00075 [Clostridium bartlettii DSM
           16795]
 gi|164604521|gb|EDQ97986.1| hypothetical protein CLOBAR_00075 [Clostridium bartlettii DSM
           16795]
          Length = 220

 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 36/87 (41%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           K      +A + ++      V + AK Y   G    D+IQEG IGL KA   FD      
Sbjct: 30  KANKGDKLALEYIISKYKNFVKAKAKSYFLVGADKEDIIQEGMIGLYKAVRDFDGTKTNS 89

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP 522
           F  +A   + + I  +I   +    IP
Sbjct: 90  FKCFAEICITRQIITAIKTATRQKHIP 116


>gi|310801373|gb|EFQ36266.1| microtubule associated protein [Glomerella graminicola M1.001]
          Length = 1541

 Score = 43.3 bits (100), Expect = 0.15,   Method: Composition-based stats.
 Identities = 63/370 (17%), Positives = 133/370 (35%), Gaps = 37/370 (10%)

Query: 126  REMGSIE--LLSREGEIA-IAKRIEAGRAMMMASLCESPLTFQALIIW-----------R 171
            RE+G+    L SR  E   + + IE    M       +P T  +L+              
Sbjct: 758  REVGAQTSMLTSRNREKERLYQEIED-LKMAQRRGGPAPSTIDSLLDRSASRAGAHRRSI 816

Query: 172  DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
              ++   T + E+ +LE     E +       +  S  K ++   ++E +          
Sbjct: 817  SRVSASRTQITEVDELER---EELENKLAETRDKISEIKLQNQELQRELEGCMADFETAV 873

Query: 232  SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV- 290
               + +++    +    +NA ND   L  + D++    + ME +       A +EI  + 
Sbjct: 874  EGKREAEEIAVALQEDLDNAMNDLVALQAERDEALREQADMETEFEALRKEAQEEIDALE 933

Query: 291  ------YRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
                    E++ LQ    +  ++ +    + + + E LV L    +    RI  L ++L 
Sbjct: 934  GEADQRNDEIQRLQHELNDRTENFDALQEEMRKMSEALVGLEDEQAAKIRRIQQLEQELA 993

Query: 344  DISKRIMHNEGELLRL---AQSYGIKRDV------FLERHQ-GRELDPHWVSYAKDFPEG 393
            D +K     E +LL     AQ   ++++       FL   Q G ++    +  A    E 
Sbjct: 994  DANKESEELENKLLESNDKAQRLSVQQESSQGEIAFLREEQEGDKIRIGDLEAALANTEQ 1053

Query: 394  EWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA-N 452
              ++      +   ++  E +   + +     E +  V+ + +    A    + + ++  
Sbjct: 1054 SLRDERDRVKELEQRLATERRQHEMVSNQEKEEVQQFVNEINREMSAAKDEARRLRKSLT 1113

Query: 453  LRLVISVAKK 462
             R V +   K
Sbjct: 1114 SREVEATEWK 1123


>gi|331088988|ref|ZP_08337895.1| hypothetical protein HMPREF1025_01478 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330406440|gb|EGG85953.1| hypothetical protein HMPREF1025_01478 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 169

 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ A    ++ + A + 
Sbjct: 52  EQYTDFYRDKERWRYLQKLDTKNSLLSLDGFTDSEGNPLDFIADE-AADIAETVVNAVMV 110

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +F +T+  + + +A+ + KL+ 
Sbjct: 111 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARFGITQSVVNKRKARILIKLRK 165


>gi|301105597|ref|XP_002901882.1| WD domain-containing protein, putative [Phytophthora infestans T30-4]
 gi|262099220|gb|EEY57272.1| WD domain-containing protein, putative [Phytophthora infestans T30-4]
          Length = 1299

 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 46/335 (13%), Positives = 116/335 (34%), Gaps = 26/335 (7%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL----LREIIDLEACIG 192
            E + A  + ++A        L  +    +  +    EL          L+   + EA + 
Sbjct: 879  EQKFAHEQELQAVCEQAKNELIATNEALKRSLEEDAELEVDELKSKYELKLSDEREATLR 938

Query: 193  PESKGGFFHG-----TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
             + + G          +    Q+ E  S E++  ++ E    +E   +  K +  + +  
Sbjct: 939  LKGENGIMKKKFSALQKDIEDQREEIRSLEEKGKELTENIRGLEKDIQGHKKEIREREET 998

Query: 248  PENAEN---DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
             ++ E    D +  +++ +     L     +L+ ++     EIA++  ++  +       
Sbjct: 999  IQDKEKRIYDLKKKNQELEKFKFVLDYKIKELKRQIEPREQEIADMKTQIEEMDAELEQY 1058

Query: 305  QK-DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
             K +    +    L+ K+  +   LSL  +++ L    +  +   ++    +LL   ++ 
Sbjct: 1059 HKSNAALDLMIGELRLKMDGMQKELSLQATQVALGKALVRQVQTDLLGC-AQLLDNKKAL 1117

Query: 364  GIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI- 422
             +      ++++     P              + ++  EV+S+ +   +  +IS      
Sbjct: 1118 KVAVMALNKKYEDGVT-PDAKEPNSQAEYNRQREYLEKEVESLKRKIMKGMAISESELHR 1176

Query: 423  ----------SISEFRHIVSMVRKGECEASIAKKE 447
                       ++E R     VR    E   AK +
Sbjct: 1177 LQRENAILTTQVNELRREFHNVRMQTQEVRDAKYK 1211


>gi|242020772|ref|XP_002430825.1| laminin A chain, putative [Pediculus humanus corporis]
 gi|212516028|gb|EEB18087.1| laminin A chain, putative [Pediculus humanus corporis]
          Length = 1616

 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 56/342 (16%), Positives = 122/342 (35%), Gaps = 55/342 (16%)

Query: 46   IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF 105
             +E+   L   E+ +E++++    L N    +    +    + +E   +L      S   
Sbjct: 1272 YQEIYD-LQLPEIKAEKLKEESEFLINSARKIKKEAEDLILDHTETWEELLKQIQESQFL 1330

Query: 106  LQKRKDSADRSTD-----DPVRMYLREMGSIELLSREGEIAIAK-----------RIEAG 149
            L++ ++  + + D     D  R   +E  +++L   E  I  A+           ++E  
Sbjct: 1331 LEQGEEQQNVANDLLANADVARNKAKE--AVKL--GEQTIKEAQDTFTILTDFEKKVEDS 1386

Query: 150  RAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
            +     +L         ++   D L    T      + EA +    K            Q
Sbjct: 1387 KDKAQEALA----MVDDIVNMID-LAANKTR-----EAEAALQGAEKNAQIARDVAKEAQ 1436

Query: 210  KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED-DSAHT 268
             +      KE  D++    + +  A   +D+   +       E+  + L+E  + D A T
Sbjct: 1437 SKYAEEASKEAHDIKREAEETKKKAGRLRDEADNLSGRVAVTESRLKKLEEKAELDEALT 1496

Query: 269  LSAMED---------QLRPKVMCALDEIAEVYRELRSLQDNAVNG------QKDEKSSVK 313
              A +          +   +V  AL ++ ++  EL+ L D   N       + DE     
Sbjct: 1497 AEAKKKVGQTKISVNEASKQVQKALADVNDILGELQDLSDVDENSLNDLERRLDEAEEEV 1556

Query: 314  CKVLKEKLVKLVGSLSLNQSR--------IDLLVEQLYDISK 347
                 +++++ +    ++QS+        +D L E++ +I K
Sbjct: 1557 LDSKLDEMMQFLKEEKMSQSQLMGQYQDEVDRLREEVANIEK 1598


>gi|34763277|ref|ZP_00144236.1| RNA polymerase sigma-H factor [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|256846014|ref|ZP_05551472.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_36A2]
 gi|294784859|ref|ZP_06750147.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_27]
 gi|27887048|gb|EAA24160.1| RNA polymerase sigma-H factor [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|256719573|gb|EEU33128.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_36A2]
 gi|294486573|gb|EFG33935.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_27]
          Length = 204

 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 29/152 (19%), Positives = 69/152 (45%), Gaps = 4/152 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I ++++K +   S A   +++   +L+   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 1   MEDINAILKKAQSGDSEAISLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR---TARRMSNKI 543
            +D      FS++A   +++ +  +I   +    + ++   K + ++          + I
Sbjct: 61  FYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSANFDDEEHNI 119

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               + E   ++  +  E + +  K ++   S
Sbjct: 120 NNYKSSESNPEEAYLLKEKIEEFKKFSENNFS 151


>gi|282857702|ref|ZP_06266911.1| RNA polymerase sigma factor [Pyramidobacter piscolens W5455]
 gi|282584372|gb|EFB89731.1| RNA polymerase sigma factor [Pyramidobacter piscolens W5455]
          Length = 168

 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 451 ANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL-GYKFSTYAMWWVKQAIT 509
             L L   +A +YT RG ++ DL+QEG I L +   ++D      + S +  + ++  + 
Sbjct: 19  RFLPLAKKIAWQYTRRGAEYEDLVQEGMIALFELVRRYDEERPPQRLSLFIWYRLRGRVR 78

Query: 510 RSIADQSC 517
            + A    
Sbjct: 79  DAAARLRR 86


>gi|118595065|ref|ZP_01552412.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
 gi|118440843|gb|EAV47470.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
          Length = 808

 Score = 43.3 bits (100), Expect = 0.16,   Method: Composition-based stats.
 Identities = 18/29 (62%), Positives = 23/29 (79%)

Query: 637 NTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +   TLEE+G++  VTRERIRQIEAK I+
Sbjct: 247 DKPKTLEEIGEKLGVTRERIRQIEAKVIK 275


>gi|121488753|emb|CAJ18261.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 94

 Score = 42.9 bits (99), Expect = 0.16,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 1   ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 60

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++   + P     + +L     R L+ L PRE 
Sbjct: 61  LQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREA 93


>gi|163785214|ref|ZP_02179892.1| RNA polymerase sigma factor for flagellar operon [Hydrogenivirga
           sp. 128-5-R1-1]
 gi|159879519|gb|EDP73345.1| RNA polymerase sigma factor for flagellar operon [Hydrogenivirga
           sp. 128-5-R1-1]
          Length = 177

 Score = 42.9 bits (99), Expect = 0.16,   Method: Composition-based stats.
 Identities = 49/198 (24%), Positives = 78/198 (39%), Gaps = 34/198 (17%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           K ++V  NL L+  VA K   R     + F +L+  G IGL+KA + ++  L  KFSTYA
Sbjct: 9   KNKVVLDNLNLIKKVASKIYYRLPKGEIDFDELVNIGVIGLLKALDNYNEDLA-KFSTYA 67

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560
              ++  I   +       R       K  K                           PV
Sbjct: 68  YIRIRGEILDYLRSLDIVPRGIRDKIKKEEK---------------------------PV 100

Query: 561 EGVRKV-LKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
           +   ++ L  +   +S+E  IG  +     D ++     SP + A +  LRE     L  
Sbjct: 101 DEQMEIPLSSSAIFLSIEKAIGGTEDLKFIDTLK-SRMESPEEYAYKVELREKIEEKLNL 159

Query: 620 LTPREERVLRMRFGIGMN 637
           LT  E++V++M F    +
Sbjct: 160 LTENEKKVIQMIFFEEKD 177


>gi|227513460|ref|ZP_03943509.1| SMC structural maintenance of chromosomes partitioning protein
            [Lactobacillus buchneri ATCC 11577]
 gi|227083333|gb|EEI18645.1| SMC structural maintenance of chromosomes partitioning protein
            [Lactobacillus buchneri ATCC 11577]
          Length = 1183

 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 63/435 (14%), Positives = 149/435 (34%), Gaps = 33/435 (7%)

Query: 46   IEELNAFLPPDEVSSEQMEDTVAMLSN--MGINVVDGDDLEDEEGSEDSLDLASSASNSS 103
             + +  FL    + +E ++D + +         +V  D      G   +     S     
Sbjct: 614  FQAILDFLLGTTLIAETLDDAIQLSQQINHRTRIVSLDGQIVNAGGSLTGGANRSEGQGV 673

Query: 104  VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLT 163
            +  +   +  + ST        +EM S++L  +E ++ IA      +  +          
Sbjct: 674  LVQKSELEKLEAST--------KEM-SVKLTEKEHQLQIA------KQELQKIQASFDRG 718

Query: 164  FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             Q +      ++   + L  +    +    + +      +  +  Q+ +DSS +      
Sbjct: 719  RQLVFQSGQMVDAQKSALDSL--RASKTSQKRELDALKLSLHNVKQQNQDSSDQNLVLKK 776

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME--DQLRPKVM 281
             + + +I+      + ++S +    +NAE+ E+      D    +   ++     + ++ 
Sbjct: 777  SQLDQEIKQVVSAIEKNQSLLSDVKKNAESFEKQKQSLHDQIVISKEQLQHYQDDQKRLS 836

Query: 282  CALDEIAEVYRELRS----LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337
               D++    ++L +    LQ +       EK +   K   +K   L  SL   +  +D 
Sbjct: 837  SQFDQLKNQRQDLETQSKNLQADLSEQIDPEKITKLIKESSDKQRALTTSLKTQKELVDR 896

Query: 338  LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY-----AKDFPE 392
              +Q   +   I + +  L          R+ F    +  +   + +S+       D   
Sbjct: 897  SDKQYDQLQNDIRNQQMNLNNATYELKNNREDFQNLQKSLDSSLNQLSHDFGILKSDLSH 956

Query: 393  GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR---KGECEASIAKKEMV 449
             EW   +      I  +R  I  I      +I EF+ +        K + + + AK  + 
Sbjct: 957  TEWNWDLETISRQIKLLRTGINEIGPVNISAIQEFQDVSDRYDFLLKQQQDLTDAKNHLT 1016

Query: 450  EANLRLVISVAKKYT 464
                 +  +++KK+ 
Sbjct: 1017 STMGEMDTTISKKFQ 1031


>gi|74319555|gb|ABA02922.1| RNA polymerase sigma factor sigma-70 [Acinetobacter calcoaceticus]
          Length = 154

 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 24/59 (40%)

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           K  ++S +     E L  +           D++ E +    ++I  NE E++R A   G
Sbjct: 93  KHGRNSPEADDALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREVMRYAVRRG 151


>gi|56961915|ref|YP_173637.1| RNA polymerase factor sigma-70 [Bacillus clausii KSM-K16]
 gi|56908149|dbj|BAD62676.1| DNA-directed RNA polymerase sigma-30 factor sigma-H [Bacillus
           clausii KSM-K16]
          Length = 220

 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 43/100 (43%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S  E     S++++     ++A + ++      V + A+ Y   G    D++QEG IGL 
Sbjct: 15  SPFEEWEDDSLIKEVRTGNTLALEHLIGKYRNFVRAKARSYFLIGADHEDIVQEGMIGLY 74

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           KA   F+      F  +A   + + I  +I   +    IP
Sbjct: 75  KAVRDFNVDKLSSFKAFAELCITRQIITAIKTATRQKHIP 114


>gi|326923519|ref|XP_003207983.1| PREDICTED: disks large homolog 5-like, partial [Meleagris
           gallopavo]
          Length = 1230

 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 44/381 (11%), Positives = 131/381 (34%), Gaps = 36/381 (9%)

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
           +  K     +  E  +    + +    +  S + ++L    M  L+ + + Y  LR   +
Sbjct: 254 EEMKRLHDEDQKEITDLRSQQQQVMKQNGSSEILNKLYDTAMDKLEGVKKDYDALRKRYN 313

Query: 300 NAVNGQKD-----EKSSVKCKVLKEKLVKLVGS----LSLNQ------SRIDLLVEQLYD 344
             +          E++  + + L++++  L+      +   Q       R + + ++L +
Sbjct: 314 EKIASHNTDLSRLEQAEEENRRLQKQIDMLMKQRDTAIHFQQQYSSSLRRFESVQQELSN 373

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            + +    + E+ RL       + + L+  +  E          +         +  E D
Sbjct: 374 ATAQNKELQREMERLQSEVTRFKTMQLKAAKDSEKYKEERDSVFNE-----YRLIMSERD 428

Query: 405 SILKIRNEIK---SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
            ++K  ++++    ++     + S  + + S   +   +   +    +E   + +  + K
Sbjct: 429 QVIKEVDKLQTELELAESKLKNTSSEKRVASEEMEALRQIQDSATLDIERANKEIEMLRK 488

Query: 462 KYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521
           +Y     +  + +QE         E       + F        ++   R++ D       
Sbjct: 489 QYEAMSQELKEAVQEA--------EVAKCRRDWAFQERDKIVAERESIRTLCDNLR-RER 539

Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG---VRKVLKITKEPISLET 578
              + D    +         K       +E+ +K+   +E     R+++  +    +++T
Sbjct: 540 DRAVSDLAEALRNLDDMRKQKNDAVRELKELKEKMENQLEKEARFRQLMAHSSHDSAIDT 599

Query: 579 PIGDEDTSHLGDFIEDKNAVS 599
               E  + + +F +D++ + 
Sbjct: 600 DS-LEWETEVVEFEKDRDDMD 619


>gi|307153998|ref|YP_003889382.1| ECF subfamily RNA polymerase sigma-24 factor [Cyanothece sp. PCC
           7822]
 gi|306984226|gb|ADN16107.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7822]
          Length = 219

 Score = 42.9 bits (99), Expect = 0.17,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 62/170 (36%), Gaps = 15/170 (8%)

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
                    R  +  ++   +V R  +R++  +K       IA    +  + +RK  +++
Sbjct: 62  YHLAPDWQDRADL-AQEVWIRVYRNIKRLNEPLKFRGWLSRIAT--NLFYDELRKRKRVS 118

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             P+SL+ P   +D     D + D    SP D        E     +A+L        R 
Sbjct: 119 N-PVSLDAPRRVDDGEIDWDIVSD--YPSPDDHLATREFYEQLRLAIANLPE----AFRT 171

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              +        EE+ +   V+   ++   A+A  KL+       L+ +L
Sbjct: 172 TIVLREIEGMAYEEIAEITGVSLGTVKSRIARARAKLQ-----SVLQPYL 216


>gi|332970731|gb|EGK09711.1| DNA-directed RNA polymerase sigma subunit SigH [Desmospora sp.
           8437]
          Length = 217

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 40/101 (39%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           ++  E      +V     +   A ++++      V + A+ Y   G    D++QEG IGL
Sbjct: 11  LTDYESMADEELVEYVRADDGAALEQLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGL 70

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            KA   F       F  +A   + + I  +I   +    IP
Sbjct: 71  FKAIRDFRGDKLASFKAFAELCITRQIITAIKTATRQKHIP 111


>gi|296328928|ref|ZP_06871436.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296153917|gb|EFG94727.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 204

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 29/152 (19%), Positives = 73/152 (48%), Gaps = 4/152 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I ++++K +   + A   +++   +L+   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 1   MEDINAILKKAQSGDNEAIDLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK---I 543
            +D      FS++A   +++ +  +I   +    + ++   K + ++  +    ++   I
Sbjct: 61  FYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNI 119

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               +PE   +++ +  E + +  K ++   S
Sbjct: 120 NNYKSPESNPEEVYLLKEEIEEFKKFSENNFS 151


>gi|289422448|ref|ZP_06424291.1| RNA polymerase sigma-H factor [Peptostreptococcus anaerobius 653-L]
 gi|289157020|gb|EFD05642.1| RNA polymerase sigma-H factor [Peptostreptococcus anaerobius 653-L]
          Length = 217

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 26/91 (28%), Positives = 39/91 (42%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V   +     A  +++E    +V + AK Y   G    D+IQEG IGL KA   +D  
Sbjct: 20  ELVDMAKQGDKYAINKLIEKYSIMVKAKAKTYFLVGADKEDIIQEGLIGLYKAIRDYDED 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   V + I  +I   +    IP
Sbjct: 80  KTCSFRYFADICVTRQIITAIKTATRQKHIP 110


>gi|261883762|ref|ZP_06007801.1| RNA polymerase factor sigma-32 [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 165

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 31/159 (19%), Positives = 60/159 (37%), Gaps = 13/159 (8%)

Query: 507 AITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAMPVE 561
           ++   I      +R       K     + R   +++         E   EI+ +L +   
Sbjct: 1   SMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTS 60

Query: 562 GVR-KVLKITKEPISLETPIGDEDT--SHLGDFIEDKNAVSPLDSAIQANLR---ETTTR 615
            V     +++    SL  P+  E+T  S   DF+ D + +    +    ++       TR
Sbjct: 61  DVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTR 120

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            L +L  RE  ++R R         TLE +G++  ++R 
Sbjct: 121 ALDTLNERELHIIRERRLDDDGV--TLEALGEKLGISRS 157


>gi|254973714|ref|ZP_05270186.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-66c26]
 gi|255091104|ref|ZP_05320582.1| RNA polymerase factor sigma-70 [Clostridium difficile CIP 107932]
 gi|255099216|ref|ZP_05328193.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-63q42]
 gi|255304999|ref|ZP_05349171.1| RNA polymerase factor sigma-70 [Clostridium difficile ATCC 43255]
 gi|255312759|ref|ZP_05354342.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-76w55]
 gi|255515519|ref|ZP_05383195.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-97b34]
 gi|255648612|ref|ZP_05395514.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-37x79]
 gi|255654145|ref|ZP_05399554.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-23m63]
          Length = 215

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 36/87 (41%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +      IA + ++      V + AK Y   G    D+IQEG IGL KA   FD      
Sbjct: 25  RASEGDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAVRDFDGSKTNS 84

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP 522
           F  +A   + + I  +I   +    IP
Sbjct: 85  FKCFAEICITRQIITAIKTATRQKHIP 111


>gi|307203097|gb|EFN82277.1| Kinesin-like protein KIF21B [Harpegnathos saltator]
          Length = 1486

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 47/358 (13%), Positives = 122/358 (34%), Gaps = 25/358 (6%)

Query: 130 SIELLSREGEIAIAKRIEA--------GRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           ++E L+ +  + +A+++          G   + + +       Q +   R  L +   + 
Sbjct: 430 TVEALTAKNALLLAEKVAGQWVTALGGGDEQVTSLVQGY---VQEIEELRARLLEAEAMY 486

Query: 182 REIIDLEACIG---PESKGGFFHGTEGHSYQKREDSSQEKE-----RDDVQETEGDIESA 233
           +++   +  +    P     F   +       ++D  +E E     ++        +++ 
Sbjct: 487 QQLKKRQMQVNAANPYGDSSFHPDSSTLLVDAKKDLEKEIETWKALKEQYSHGNTSVKTM 546

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            +   DD           ++D+ +  ++ED+    +    + L   +      I E+   
Sbjct: 547 DEGEIDDAENAQDSVSEDDSDDDSDRKEEDEEEAAMGRELEALTSDIDVKQRLIQELELS 606

Query: 294 LRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
            R LQ        K  +   + +  +E+  K++ SL    +     V++L D  ++ + N
Sbjct: 607 QRRLQTMKQHYEDKLAQLQARIRDTQEERDKVLMSLQQQPAPPTEKVKKLRDEYEKKLSN 666

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIR-N 411
             + +RL QS   +    L+     E     +       +      +    +   + + N
Sbjct: 667 MQKEMRLLQSAKKEHARLLKNQSQSENRLRGLRNELSEMKRAKVKLLNKMREEAQRHKEN 726

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           E++       +   +     + V +        K+ ++      V   A +  +RGL 
Sbjct: 727 ELRRNREIAQL--RKESRRNANVIRTLEADKRMKEVVLRRKQEEV--TALRRRDRGLS 780


>gi|78042626|ref|YP_359015.1| RNA polymerase sigma-70 factor [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77994741|gb|ABB13640.1| RNA polymerase sigma-70 factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 175

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 43/105 (40%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
            +   ++    +E++     L+   A++Y N  L   DL+QEG I ++++  +FD   G 
Sbjct: 8   WQKARKSREGMEELLNYLRPLIKKAAQRYRNPYLTEEDLMQEGMIAVIESVYRFDPERGV 67

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            F  Y    V   I   +  +       V + +   +V   A  +
Sbjct: 68  YFLKYVREMVYGRIYSLLRAEKARRGKEVPLEEYHIEVQHFAEEL 112


>gi|291546870|emb|CBL19978.1| RNA polymerase, sigma 30 subunit, SigH [Ruminococcus sp. SR1/5]
          Length = 194

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 35/91 (38%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           +++ +     S     ++E    LV   A+     G    DLIQEG IGL KA   +   
Sbjct: 11  ALIERLRAGESAIADYLMEKYKGLVRKKARAMFLIGGDTDDLIQEGMIGLFKAVRDYQPD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +     P
Sbjct: 71  RESSFQFFANICIDRQIYTAIKSSNRQKHQP 101


>gi|126697623|ref|YP_001086520.1| RNA polymerase factor sigma-70 [Clostridium difficile 630]
 gi|260681829|ref|YP_003213114.1| RNA polymerase factor sigma-70 [Clostridium difficile CD196]
 gi|260685427|ref|YP_003216560.1| RNA polymerase factor sigma-70 [Clostridium difficile R20291]
 gi|296449816|ref|ZP_06891583.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP08]
 gi|296877880|ref|ZP_06901900.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP07]
 gi|115249060|emb|CAJ66871.1| RNA polymerase factor sigma-70 [Clostridium difficile]
 gi|260207992|emb|CBA60155.1| RNA polymerase sigma-H factor [Clostridium difficile CD196]
 gi|260211443|emb|CBE01550.1| RNA polymerase sigma-H factor [Clostridium difficile R20291]
 gi|296261303|gb|EFH08131.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP08]
 gi|296431077|gb|EFH16904.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP07]
          Length = 220

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 36/87 (41%)

Query: 436 KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYK 495
           +      IA + ++      V + AK Y   G    D+IQEG IGL KA   FD      
Sbjct: 30  RASEGDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAVRDFDGSKTNS 89

Query: 496 FSTYAMWWVKQAITRSIADQSCTIRIP 522
           F  +A   + + I  +I   +    IP
Sbjct: 90  FKCFAEICITRQIITAIKTATRQKHIP 116


>gi|466858|gb|AAA85934.1| rpsB [Mycobacterium leprae]
          Length = 118

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 48/115 (41%), Gaps = 11/115 (9%)

Query: 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--T 570
             Q  ++++P  +++   ++      +S ++ R PT  E+     M    V + L    +
Sbjct: 10  RQQLWSVQVPRRLKELHLQLGTATAELSQRLDRAPTASEL----GMDRNEVVEGLVAGSS 65

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +  +S+++   D+D   + D + D +A        +   RE  + +L  L   E 
Sbjct: 66  QNTLSIDSGNDDDDVCAIADTLGDVDA-----GFERIENREALSLLLEVLPKWER 115


>gi|160332465|dbj|BAF93223.1| myosin heavy chain fast skeletal type 2 [Hypophthalmichthys molitrix]
          Length = 1935

 Score = 42.9 bits (99), Expect = 0.18,   Method: Composition-based stats.
 Identities = 53/373 (14%), Positives = 132/373 (35%), Gaps = 13/373 (3%)

Query: 7    RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
            +  + + + E SD +     +  +  ++ +  ++   +   E+ A L   E + E  E  
Sbjct: 1499 KRENKNLQQEISDLTEQLGETGKTIHEL-EKGKKTAEIEKSEIQAALEEAEATLEHEESK 1557

Query: 67   VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
            +  +      V    D +  E  E+   +  ++      +Q   D+  RS +D +R+  +
Sbjct: 1558 ILRVQLELNQVKGEIDRKLAEKDEEIEQIKRNSQRIIDSMQTTLDAEVRSRNDALRIKKK 1617

Query: 127  EMGSIELLSREGEIAI------AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
              G +     E EI +      A   +     +   L ++ L     +  ++++ +   +
Sbjct: 1618 MEGDLN----EMEIQLSHANRQAVEAQKQLRNVQGQLKDAQLHLDEALRAQEDMREQVAM 1673

Query: 181  LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
            +    +L      E +        G    ++E     +    +      + +  K  + D
Sbjct: 1674 VERRNNLMQAEIEELRVALEQTERGRKVAEQELVDASERVTLLHSQNTSLINTKKKLEAD 1733

Query: 241  RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
              ++    E+   + RN DE    +    + M ++L+ +   +     E  ++   +   
Sbjct: 1734 LVQIQGEMEDVVQESRNADEKAKKAITDAAMMAEELKKEQDTS--AHLERMKKNLDITVK 1791

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
             +  + DE  S+  K  K++L KL   +   +S ++    +  D  K +   E  +  L 
Sbjct: 1792 DLQHRLDEAESLAMKGGKKQLQKLEARVRELESEVEAEQRRSADAVKGVRKYERRVKELT 1851

Query: 361  QSYGIKRDVFLER 373
                  +   +  
Sbjct: 1852 YQTEEDKKNIIRL 1864


>gi|310829596|ref|YP_003961953.1| RNA polymerase [Eubacterium limosum KIST612]
 gi|308741330|gb|ADO38990.1| RNA polymerase [Eubacterium limosum KIST612]
          Length = 191

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 24/93 (25%), Positives = 38/93 (40%)

Query: 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490
           + +V+K +     A   +VE    +V   A+ +   G    DLIQEG I L+ A   +  
Sbjct: 5   LELVKKAQGGDKEAVVTIVEKYRCVVTQKARPFYYIGGDQEDLIQEGMIALLGAIWDYRE 64

Query: 491 CLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
             G  F T+A   V+  I   +         P+
Sbjct: 65  DRGTSFKTFAGLCVENRIKSVVTKAKRPKHSPM 97


>gi|157823761|ref|NP_001102511.1| kinesin-like protein KIF21A isoform 2 [Mus musculus]
          Length = 1628

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|121488763|emb|CAJ18266.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 93

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 1   ISKAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 60

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++   + P     + +L     R L+ L PRE 
Sbjct: 61  LQNDGHL-PDHGLNKDSLTLEVERSLSVLAPREA 93


>gi|47089364|gb|AAT11001.1| sigma 70 factor [Pseudomonas syringae]
 gi|161137668|gb|ABX57837.1| RpoD [Pseudomonas syringae]
 gi|161137670|gb|ABX57838.1| RpoD [Pseudomonas syringae]
 gi|161137672|gb|ABX57839.1| RpoD [Pseudomonas syringae]
 gi|161137674|gb|ABX57840.1| RpoD [Pseudomonas syringae]
 gi|161137676|gb|ABX57841.1| RpoD [Pseudomonas syringae]
 gi|161137678|gb|ABX57842.1| RpoD [Pseudomonas syringae]
          Length = 149

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 17/194 (8%), Positives = 49/194 (25%), Gaps = 45/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAV 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +  + + E +A  S ++      P             D+ +          +     +
Sbjct: 50  KAEGADDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 109

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
             +  +AE++                                    + L   + + LVE+
Sbjct: 110 AEMVALAELF----------------------------------MPIKLVPKQFEGLVER 135

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 136 VRGALERLRAQERA 149


>gi|121488733|emb|CAJ18250.1| sigma 70-type sigma factor [Chlorobium chlorovibrioides]
          Length = 93

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D 
Sbjct: 1   ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDV 60

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +++   + P  +  + +L     R L+ L PRE 
Sbjct: 61  LQNDGHM-PDHTLNRDSLTLEVERSLSVLAPREA 93


>gi|239934594|emb|CAR94611.1| DNA-directed RNA polymerase subunit D [uncultured Acidobacteria
           bacterium]
          Length = 231

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 86/239 (35%), Gaps = 11/239 (4%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           +REGE+ IA+RIE G+  ++ S+  +PL  + +I   D L+ G   +RE++        +
Sbjct: 1   TREGEVEIARRIERGKLSVIKSISRTPLVSRKVIQLGDALHTGDRTIRELVIFNDEEITD 60

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            +                 ++   E+   +  E    +  +  +  R             
Sbjct: 61  ERIAERSRQVQKQIDAVRKANLTAEKLQEKLNETPRGATTRDKRKYRKCRWLAMRARVEV 120

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
            + + E E   +     ++ +L  ++  A++ +  V RE+ S+        K +K     
Sbjct: 121 SQRIREIEFTES-----IKRRLIDEMKEAVENVKAVQREIESIDRLLHPKNKKQKLREDD 175

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
           K        L+  +   + ++  + + L      +      +LR        +   +E 
Sbjct: 176 KK------NLLRQIKDQRLKLKAMTDGLEQEPAELKQTLDTILRGEYQAEQAKKEMVEA 228


>gi|269798881|ref|YP_003312781.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Veillonella
           parvula DSM 2008]
 gi|269095510|gb|ACZ25501.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Veillonella
           parvula DSM 2008]
          Length = 288

 Score = 42.9 bits (99), Expect = 0.19,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A   + +  +  LR      L  L+P +  +LR  +G       +L  V ++   +R+ I
Sbjct: 208 ADMVMSADEEHRLRARLVWALGRLSPDQRDLLRRVYG----ECQSLVSVSEELNCSRQAI 263

Query: 657 RQIEAKAIRKLKH 669
           ++   +AIRKL+ 
Sbjct: 264 QRRHERAIRKLRR 276


>gi|291519564|emb|CBK74785.1| DNA-directed RNA polymerase specialized sigma subunit [Butyrivibrio
           fibrisolvens 16/4]
          Length = 59

 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 4/50 (8%)

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LT +E++V+     +    D TL+E+     V+  R+ Q+  KA++K++ 
Sbjct: 2   LTEKEKQVI----LLYYYEDMTLKEISAALEVSESRVSQLHTKALQKMRK 47


>gi|74184590|dbj|BAE27910.1| unnamed protein product [Mus musculus]
          Length = 1628

 Score = 42.9 bits (99), Expect = 0.20,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|115378971|ref|ZP_01466103.1| AsgB [Stigmatella aurantiaca DW4/3-1]
 gi|115364010|gb|EAU63113.1| AsgB [Stigmatella aurantiaca DW4/3-1]
          Length = 136

 Score = 42.9 bits (99), Expect = 0.21,   Method: Composition-based stats.
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLEEVG+   +TRERIRQ+E + + KL+  + ++
Sbjct: 95  TLEEVGEIMNLTRERIRQVETRGLMKLREATEAE 128


>gi|282849510|ref|ZP_06258894.1| sigma-70, region 4 [Veillonella parvula ATCC 17745]
 gi|282580447|gb|EFB85846.1| sigma-70, region 4 [Veillonella parvula ATCC 17745]
          Length = 288

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A   + +  +  LR      L  L+P +  +LR  +G       +L  V ++   +R+ I
Sbjct: 208 ADMVMSADEEHRLRARLVWALGRLSPDQRDLLRRVYG----ECQSLVSVSEELNCSRQAI 263

Query: 657 RQIEAKAIRKLKH 669
           ++   +AIRKL+ 
Sbjct: 264 QRRHERAIRKLRR 276


>gi|317970612|ref|ZP_07972002.1| hypothetical protein SCB02_13859 [Synechococcus sp. CB0205]
          Length = 136

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 9/102 (8%)

Query: 568 KITKEPISLETPIGDEDT-SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626
                 +SL+  I   D    + D + DK  +   D             ++  L+  E  
Sbjct: 32  HYRSNTLSLDQQIASADGAMTILDTVTDKEEIEIHDDYA------WMYSLMQHLSCPEAD 85

Query: 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           V+++R+G       +  EV +    T+++++++E KA+ KL+
Sbjct: 86  VIKLRYGAEDQP--SFAEVARTIGRTKDQVQRLERKALAKLR 125


>gi|251778808|ref|ZP_04821728.1| putative RNA polymerase sigma factor [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|243083123|gb|EES49013.1| putative RNA polymerase sigma factor [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 201

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 16/101 (15%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E++ I ++V + +     +  +++      +   A  +  +     DL+Q G I L+ A
Sbjct: 1   MEYKDIENLVMEAKNGDDESLLKLMVQFKPFIFKTANSFNIKDYDTYDLVQIGYIALINA 60

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
            +K+       FS+Y    +K      +   +   +   ++
Sbjct: 61  VDKYKNG-SNSFSSYVYTAIKN----CMRCTARNNKKHKNI 96


>gi|271964403|ref|YP_003338599.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270507578|gb|ACZ85856.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 171

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 12/76 (15%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664
              +LR      L +L PR+  V+ +R+   +       +  +    +   ++   +KA+
Sbjct: 95  TDVDLRRVLMDALRALPPRQRAVVVLRYWEDLGE----TQTAEILGCSAGTVKSQASKAL 150

Query: 665 RKLKHPSRSKKLRSFL 680
            KL+    ++ +   +
Sbjct: 151 TKLRSAIGAESVEGLI 166


>gi|207723155|ref|YP_002253554.1| alternative rna sigma factor rpos (partial sequence) protein
           [Ralstonia solanacearum MolK2]
 gi|206588349|emb|CAQ35312.1| alternative rna sigma factor rpos (partial sequence) protein
           [Ralstonia solanacearum MolK2]
          Length = 157

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 13/109 (11%)

Query: 74  GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTD-------------DP 120
            I VVD    E        +   S A++S+    + ++  + + +             D 
Sbjct: 44  DIEVVDTLTDEMPASEPADIVDTSDANDSADEPDEEEEDEEAAPEEDFRTVLQAELAADT 103

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           V+ YL  +    LL+   E+  + R +AG       + E  L     I 
Sbjct: 104 VQHYLNRISIKPLLTPAEELHFSTRAKAGEFAARQVMIERNLRLVVSIA 152


>gi|222479459|ref|YP_002565696.1| methyl-accepting chemotaxis sensory transducer [Halorubrum
           lacusprofundi ATCC 49239]
 gi|222452361|gb|ACM56626.1| methyl-accepting chemotaxis sensory transducer [Halorubrum
           lacusprofundi ATCC 49239]
          Length = 819

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 29/217 (13%), Positives = 82/217 (37%), Gaps = 2/217 (0%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
            IA         + A++ E       +    + + DGT  + E     +    E   G  
Sbjct: 421 EIADGFNDAMDELEATIAEVDAFAGEVTEKSEAVTDGTDEVAEAGRETSDAVDEISAGAE 480

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
             +   +    E        ++V  +  ++ + ++ + D   +      +A ++   ++E
Sbjct: 481 RQSRQLADVAGEMEDMSATVEEVAASADEVATTSQQASDLTERGREATGDAVDELHAIEE 540

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-NGQKDEKSSVKCKVLKE 319
             + +A T+  +E ++  +V   ++ I+E+  +   L  NA     +  ++     V+ E
Sbjct: 541 RSESAAKTVERLEAEM-EEVDEIVETISEIADQTNLLALNASIEAARAGEAGSGFAVVAE 599

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           ++  L      + + ++ L++ L + +   +     +
Sbjct: 600 EVKSLAEETQASAAEVETLIDGLRERTDDSVAEMAAI 636



 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 31/242 (12%), Positives = 81/242 (33%), Gaps = 9/242 (3%)

Query: 50  NAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           N  +   E +  +++     ++     V DG D   E G E S  +   ++ +    ++ 
Sbjct: 427 NDAMDELEATIAEVDAFAGEVTEKSEAVTDGTDEVAEAGRETSDAVDEISAGAERQSRQL 486

Query: 110 KDSADR-----STDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
            D A       +T + V     E+ +    + +    + +R        +  L       
Sbjct: 487 ADVAGEMEDMSATVEEVAASADEVAT----TSQQASDLTERGREATGDAVDELHAIEERS 542

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           ++     + L      + EI++  + I  ++     + +   +      S      ++V+
Sbjct: 543 ESAAKTVERLEAEMEEVDEIVETISEIADQTNLLALNASIEAARAGEAGSGFAVVAEEVK 602

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
               + +++A   +     +    +++  +   + E  DD   T+   E+ L        
Sbjct: 603 SLAEETQASAAEVETLIDGLRERTDDSVAEMAAIREGVDDGVDTVEEAENALEAVAERVT 662

Query: 285 DE 286
           D 
Sbjct: 663 DA 664


>gi|321467016|gb|EFX78008.1| hypothetical protein DAPPUDRAFT_105663 [Daphnia pulex]
          Length = 4511

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 59/426 (13%), Positives = 143/426 (33%), Gaps = 49/426 (11%)

Query: 6    KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMED 65
            K + + D   +++++       ++  +++ K + ++           L  +    +++  
Sbjct: 2287 KESEEKDRLQKEAEEKDRLLKEEEEKRRIQKESEEK---------DRLQKEAEEKDRL-- 2335

Query: 66   TVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYL 125
                L        + +    ++ SE+   L   A      L++ ++              
Sbjct: 2336 ----LKE------EEEKQRIQKESEEKDRLQKEAEEKDRLLKEEEEKQRIQ--------- 2376

Query: 126  REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL---NDGTTLLR 182
            +E    + L +E E       E      +    E     Q     +D L    +    ++
Sbjct: 2377 KESEEKDRLQKEAEEKDRLLKEEEEKQRIQKESEEKDRLQKEAEEKDRLLKEEEEKQRIQ 2436

Query: 183  EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER-----DDVQETEGDIESAAKVS 237
            +  + +  +  E++       E    Q+ +  S+EK+R     ++      + E   ++ 
Sbjct: 2437 KESEEKDRLQKETEEKDRLLKEKEEKQRMQKESEEKDRLQKEAEEKDRLLKEEEEKRRIQ 2496

Query: 238  KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
            K+   K     E  E D    +E+E       S  +D+L+ +       + E   + R  
Sbjct: 2497 KESEEKDRLQKETEEKDRLLKEEEEKQRMQKESEEKDRLQKEAEEKDRLLKEEEEKQRIQ 2556

Query: 298  QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            ++     +  +++  K ++LKE+  K      L +   D L ++L +  K  +  E E  
Sbjct: 2557 KELEEKNRLQKETEEKDRLLKEEEEKQRIQKELEEK--DCLQKELEE--KERLQKEAEEK 2612

Query: 358  RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
             L      ++  FL            +   K+  E E K+    E    +++   +    
Sbjct: 2613 DLLLKEAEEKQHFL-------TKTDEIEGTKEDIEAEEKDLTKNETQKEVEVTKRLLKEE 2665

Query: 418  VETGIS 423
                + 
Sbjct: 2666 ESVQLP 2671



 Score = 41.0 bits (94), Expect = 0.63,   Method: Composition-based stats.
 Identities = 46/364 (12%), Positives = 130/364 (35%), Gaps = 7/364 (1%)

Query: 6    KRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIE-ELNAFLPPDEVSSEQME 64
            K + + D   +++++       ++  +++ K + ++  +  E E    L  +E   ++++
Sbjct: 2347 KESEEKDRLQKEAEEKDRLLKEEEEKQRIQKESEEKDRLQKEAEEKDRLLKEEEEKQRIQ 2406

Query: 65   DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
                    +     + D L  EE  +  +   S   +      + KD   +  ++  RM 
Sbjct: 2407 KESEEKDRLQKEAEEKDRLLKEEEEKQRIQKESEEKDRLQKETEEKDRLLKEKEEKQRM- 2465

Query: 125  LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL---NDGTTLL 181
             +E    + L +E E       E      +    E     Q     +D L    +    +
Sbjct: 2466 QKESEEKDRLQKEAEEKDRLLKEEEEKRRIQKESEEKDRLQKETEEKDRLLKEEEEKQRM 2525

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER-DDVQETEGDIESAAKVSKDD 240
            ++  + +  +  E++       E    Q+ +   +EK R     E +  +    +  +  
Sbjct: 2526 QKESEEKDRLQKEAEEKDRLLKEEEEKQRIQKELEEKNRLQKETEEKDRLLKEEEEKQRI 2585

Query: 241  RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            + +++      +  E      ++     L   E + +   +   DEI     ++ + + +
Sbjct: 2586 QKELEEKDCLQKELEEKERLQKEAEEKDLLLKEAEEKQHFLTKTDEIEGTKEDIEAEEKD 2645

Query: 301  AVNGQKDEKSSVKCKVLK-EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                +  ++  V  ++LK E+ V+L       +S+ D   +++     +   ++  +  +
Sbjct: 2646 LTKNETQKEVEVTKRLLKEEESVQLPKESKEKESKQDQQQKEVEGSQIKNDEDKSRINEV 2705

Query: 360  AQSY 363
             +  
Sbjct: 2706 EERA 2709



 Score = 37.9 bits (86), Expect = 6.5,   Method: Composition-based stats.
 Identities = 69/513 (13%), Positives = 177/513 (34%), Gaps = 31/513 (6%)

Query: 164  FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
             + +    D+     T   E   ++  +    +            +  E+  + ++  + 
Sbjct: 2093 IENISGDGDKAERRKTEGEEKKSVQKEVNVAEQKKKEGEENDRRLEASEEKQRLQKEVEE 2152

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            ++     E   +  +++  + D   + AE +ER L E E+     + A +D+L+ +    
Sbjct: 2153 KDQFLREEVNRQRLQEEAEEKDRIQKEAEENERLLRESEEKQHLQMEAEKDRLQKEAEEK 2212

Query: 284  LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS--------RI 335
               + E   + R  +++    +  +++  K ++LKE+  K    +   +           
Sbjct: 2213 DRLLKEEDEKQRIQKESGEKDRLQKETEEKDRLLKEEEEKQRIQIESEEKDRLQKEAEEK 2272

Query: 336  DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            D L+++  +  +RI     E  RL +    K  +  E  + R +        +   E E 
Sbjct: 2273 DRLLKEEEEK-RRIQKESEEKDRLQKEAEEKDRLLKEEEEKRRIQKESEEKDRLQKEAEE 2331

Query: 396  KNFVACEVDSILKIRNE------IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV 449
            K+ +  E +   +I+ E      ++  + E    + E      + ++ E +  + K+   
Sbjct: 2332 KDRLLKEEEEKQRIQKESEEKDRLQKEAEEKDRLLKEEEEKQRIQKESEEKDRLQKE--A 2389

Query: 450  EANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509
            E   RL+    +K   +                   ++       K         KQ I 
Sbjct: 2390 EEKDRLLKEEEEKQRIQKESEEK-------------DRLQKEAEEKDRLLKEEEEKQRIQ 2436

Query: 510  RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569
            +   ++   ++     +D++ K     +RM  + + +   ++ A++    ++   +  +I
Sbjct: 2437 KESEEKDR-LQKETEEKDRLLKEKEEKQRMQKESEEKDRLQKEAEEKDRLLKEEEEKRRI 2495

Query: 570  TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629
             KE    +    + +        E++      +S  +  L++        L   EE+   
Sbjct: 2496 QKESEEKDRLQKETEEKDRLLKEEEEKQRMQKESEEKDRLQKEAEEKDRLLKEEEEKQRI 2555

Query: 630  MRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
             +     N      E   +     E  ++I+ +
Sbjct: 2556 QKELEEKNRLQKETEEKDRLLKEEEEKQRIQKE 2588


>gi|51892300|ref|YP_074991.1| putative RNA polymerase sigma factor SigI [Symbiobacterium
           thermophilum IAM 14863]
 gi|51855989|dbj|BAD40147.1| RNA polymerase sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 251

 Score = 42.5 bits (98), Expect = 0.21,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 2/87 (2%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF--LDLIQEGNIGLMKAAEKFD 489
            ++         A++E++ A   LV+ V  + T R L+    + +  G I L +A +KFD
Sbjct: 23  RLLGPARAGDKAAREELIRAYTPLVLRVGSQVTGRYLRVGRDEEVSVGLIALNEAIDKFD 82

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQS 516
              G  F  +A   +++ +       +
Sbjct: 83  PERGNAFIPFAEMVIRRRLVDFYRRNA 109


>gi|291242578|ref|XP_002741183.1| PREDICTED: CDC42 binding protein kinase alpha-like [Saccoglossus
           kowalevskii]
          Length = 1364

 Score = 42.5 bits (98), Expect = 0.22,   Method: Composition-based stats.
 Identities = 47/356 (13%), Positives = 122/356 (34%), Gaps = 20/356 (5%)

Query: 162 LTFQALIIWRDELNDGTTLL-REIIDLEACIGPESKGGFFHGTEGHSYQKREDS-SQEKE 219
           L  +A       L +  + L R++ D    +   S+            ++  +S + E E
Sbjct: 171 LAVEAYERRIKRLENEKSELTRKLQDTTRALHQTSQSNALDAAPSSPGRRISNSMATEPE 230

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              +++    ++   + S+ + + V+   + A    + L+  + D    +  ME   +  
Sbjct: 231 MRRLRDEVLLLKKKIQESQSETNHVERDLKEAIAIRKELENIDGDRNSRIKLMERDNKRL 290

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK----LVKLVGSLSLNQSRI 335
            +       E+ REL  + D   +  K+ K +   + L  +    L   +  L   + + 
Sbjct: 291 KIEK----EEMQRELEQMHDRYKSQTKELKEAQTQRKLAMQEFSDLNDRLSDLRSQKQKS 346

Query: 336 DLLV----EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
             LV    E+L    +++     +  +  +    KR +              ++  K   
Sbjct: 347 SRLVREKEEELEHAMQKVDMMRQDARKSEKMRKEKRALGRTPSTSGLNKQQELAKLKATM 406

Query: 392 EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
           E     +         +  NE K +  +   S +  + +V  ++  + +   +++  V  
Sbjct: 407 EKRDVMYEENLTKEKTRHINEEKKLREQLLDSENNVQRLVGEIKVIKEKLENSRRANVSD 466

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK--FDWCLGYKFSTYAMWWVK 505
           +   +  + +KY       + ++QE N  L    ++         + +      ++
Sbjct: 467 HEEKISDLRRKYER----EMAIVQEDNKKLQMDVDRANSQMEKMNRINRQLEEEMR 518


>gi|223934543|ref|ZP_03626464.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223897006|gb|EEF63446.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 485

 Score = 42.5 bits (98), Expect = 0.22,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 41/88 (46%), Gaps = 7/88 (7%)

Query: 592 IEDKNAVSPLDSAIQAN---LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           + ++ AV+       ++   ++E     ++ L P +   L +R+      D +L EVG++
Sbjct: 92  LREETAVTMQALDSDSDAGHIKEHLEPAMSELEPDDRDTLVLRYF----EDRSLREVGQE 147

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKKL 676
           F ++ +  R    +A+ KL+     K +
Sbjct: 148 FGISEDAARMRVNRALEKLRTIFNRKGI 175


>gi|302763681|ref|XP_002965262.1| hypothetical protein SELMODRAFT_83012 [Selaginella moellendorffii]
 gi|300167495|gb|EFJ34100.1| hypothetical protein SELMODRAFT_83012 [Selaginella moellendorffii]
          Length = 1056

 Score = 42.5 bits (98), Expect = 0.23,   Method: Composition-based stats.
 Identities = 42/206 (20%), Positives = 76/206 (36%), Gaps = 18/206 (8%)

Query: 148 AGRAMMMASLCESPLTF---QALIIWRDELNDG----TTLLRE-----------IIDLEA 189
                +   L E P        L+  R +L  G     + L E           I  L  
Sbjct: 458 QELEQLRRGLFERPFVVSNHDDLLTLRQQLEAGHLKMQSRLEEEEQAKAALMGRIQRLTK 517

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I   +K          S Q+R  S  E+E+ +      +  + +  S      VD    
Sbjct: 518 LILVSTKNTIPLSLPEKSTQRRRHSFGEEEKHESMHAVPEEHTPSGSSVSFEPPVDFKSR 577

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             ++  R  DE    +  T++   D LR ++     E+A     L+ L + AV   +D++
Sbjct: 578 RRKSFSRKPDELPPITGTTMADQMDLLREQMKMLAGEVALCSSSLKRLSEQAVTNPEDDQ 637

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRI 335
             ++ + LKE++ +    +S+ + RI
Sbjct: 638 LHMQMRKLKEEIDEKRRQMSIIEKRI 663


>gi|157823795|ref|NP_001102512.1| kinesin-like protein KIF21A isoform 4 [Mus musculus]
 gi|38173724|gb|AAH60698.1| Kif21a protein [Mus musculus]
 gi|38566228|gb|AAH62896.1| Kif21a protein [Mus musculus]
          Length = 1567

 Score = 42.5 bits (98), Expect = 0.23,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|71018515|ref|XP_759488.1| hypothetical protein UM03341.1 [Ustilago maydis 521]
 gi|46098976|gb|EAK84209.1| hypothetical protein UM03341.1 [Ustilago maydis 521]
          Length = 1828

 Score = 42.5 bits (98), Expect = 0.24,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 85/235 (36%), Gaps = 15/235 (6%)

Query: 224 QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA---MEDQLRPKV 280
           +     +E+  + ++     + +  E       N+ ++ +     L     +E Q + +V
Sbjct: 691 KADVAKLEAEKREAEARIDTLAADLELERERRLNMVDEVNQLRRDLEQSHRIEAQAKQEV 750

Query: 281 MCALDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           +   D +AE+  +   L  +     +    +S + + L  +     G L   Q+RI+ L 
Sbjct: 751 IEEADRVAELEAQAHELHVELEEAKRARIDASSRIEALLSEGSSFEGELRTAQARIEELT 810

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
           EQL +              +  +    ++  +  ++  E D             E    +
Sbjct: 811 EQLSNAHAEAAKAREAATEVETA----KERQIRSYRA-EADGDRAILE------EKVRAL 859

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
             ++D+  K+  +  SI+     S    R  + ++R     A +A +E+V+    
Sbjct: 860 KADLDAKTKLLEKQTSIATRAEQSRIPDREAIDLLRGQLRAADVAHEEIVKEMDH 914


>gi|262198088|ref|YP_003269297.1| hypothetical protein Hoch_4915 [Haliangium ochraceum DSM 14365]
 gi|262081435|gb|ACY17404.1| hypothetical protein Hoch_4915 [Haliangium ochraceum DSM 14365]
          Length = 246

 Score = 42.5 bits (98), Expect = 0.24,   Method: Composition-based stats.
 Identities = 17/28 (60%), Positives = 23/28 (82%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TLEEVG+   +TRERIRQ+E + +RKL+
Sbjct: 201 TLEEVGEIMNLTRERIRQVEVRGLRKLR 228


>gi|163816512|ref|ZP_02207876.1| hypothetical protein COPEUT_02701 [Coprococcus eutactus ATCC 27759]
 gi|158448212|gb|EDP25207.1| hypothetical protein COPEUT_02701 [Coprococcus eutactus ATCC 27759]
          Length = 196

 Score = 42.5 bits (98), Expect = 0.24,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 5/90 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S +E   ++     G  + + A + +++    LV   ++     G    DLIQEG IGL
Sbjct: 5   LSDNELLELI-----GTEKNNEAMETLIKRYGPLVTRQSRSLYIIGADEEDLIQEGMIGL 59

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
           +KA   +    G  F T+A   V++ +  +
Sbjct: 60  IKAINDYKPDRGASFKTFAFTCVRRQMLTA 89


>gi|313888184|ref|ZP_07821858.1| sigma-70, region 4 [Peptoniphilus harei ACS-146-V-Sch2b]
 gi|312845874|gb|EFR33261.1| sigma-70, region 4 [Peptoniphilus harei ACS-146-V-Sch2b]
          Length = 246

 Score = 42.5 bits (98), Expect = 0.25,   Method: Composition-based stats.
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 6/101 (5%)

Query: 576 LETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIG 635
           L     DE+   + D +     V      ++A         L SLTPR+  V+R+ F   
Sbjct: 152 LHDDAPDEEGLSIFDSL--DAGVDIESDFLEAERLGILKEALDSLTPRQALVVRLFF--- 206

Query: 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
                 L E+     ++R  +  ++  AI  L+    +  L
Sbjct: 207 -YERLGLSEIADFLGISRWTVVNLKRNAIANLRKFILNNNL 246


>gi|119585044|gb|EAW64640.1| trafficking protein, kinesin binding 1, isoform CRA_c [Homo
           sapiens]
          Length = 895

 Score = 42.5 bits (98), Expect = 0.25,   Method: Composition-based stats.
 Identities = 45/290 (15%), Positives = 101/290 (34%), Gaps = 22/290 (7%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE-- 139
           D +DEE         +      V   +R     ++ +D        + ++  L  E E  
Sbjct: 16  DCQDEERKPTHRQHDTQDLLEEVLCAERVGQMTKTYND--------IDAVTRLLEEKERD 67

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQA----LIIWRDELNDGTTLLREIIDLEACIGPES 195
           + +A RI         +L E     +     +     +L    ++  E++        ES
Sbjct: 68  LELAARIGQSLLKKNKTLTERNELLEEQVEHIREEVSQLRHELSMKDELLQFYTSAAEES 127

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +      T     +           D +Q+   D+E    V + + S++ +     E  E
Sbjct: 128 EPESVCSTPLKRNESSSSVQNYFHLDSLQKKLKDLEEENVVLRSEASQLKTETITYEEKE 187

Query: 256 RNLDED----EDDSAHTLSAMEDQLRPKVMCA---LDEIAEVYRELRSLQDNAVNG-QKD 307
           + L  D      D+   ++++ ++L  K   A    +EI  +  ++  LQ  A     ++
Sbjct: 188 QQLVNDCVKELRDANVQIASISEELAKKTEDAARQQEEITHLLSQIVDLQKKAKACAVEN 247

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           E+        K+   +L   L   + +    +E L++  + + +   + +
Sbjct: 248 EELVQHLGAAKDAQRQLTAELRELEDKYAECMEMLHEAQEELKNLRNKTM 297


>gi|317129425|ref|YP_004095707.1| phage tail tape measure protein, TP901 family [Bacillus
           cellulosilyticus DSM 2522]
 gi|315474373|gb|ADU30976.1| phage tail tape measure protein, TP901 family [Bacillus
           cellulosilyticus DSM 2522]
          Length = 1101

 Score = 42.5 bits (98), Expect = 0.25,   Method: Composition-based stats.
 Identities = 46/366 (12%), Positives = 110/366 (30%), Gaps = 60/366 (16%)

Query: 10  DSDSEHEDSDDSLVFDFSDDS---WKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
           D  SE          D +DD+    +++    ++                 VS E  +  
Sbjct: 591 DEVSESTQEAVGAFLDLNDDATFALRELAMTGKE-----------------VSEETRDAI 633

Query: 67  VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
           V     M   V +  D +             S  +   F        + + +D VR    
Sbjct: 634 VGNFREMSERVAEALDEQK----------DKSIRSMQEFFANANGIYEFNYEDTVR---- 679

Query: 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL----- 181
                  L+ + ++ I   IE G       + E+   F+ +    +        L     
Sbjct: 680 -------LTEDNQMDILSAIEEGYDN---RIAETERAFEQIQKIIETAEAENRELTAYEH 729

Query: 182 REIIDLEACIGPESKGGFFHGTEGHS---YQKREDSSQEKERDDVQETEGDIESAAKVSK 238
           R+I  L+  +                    +  E++S    R   +  +  +E    V  
Sbjct: 730 RKINQLQREMVENGIQAMSENELEQKIILERMHENASLITARQAAEVVKNSVEQKDAVVA 789

Query: 239 DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
           +   + +              +  ++ A  +    ++ R +V+   +E+  +  E    Q
Sbjct: 790 EAEEQYNRSIGEFIRLRDEAGDITEEQASAMIREAERQRDEVVSRAEEMHHLVVEEARKQ 849

Query: 299 DNAVNGQKDEKS------SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                   D ++        + K  KE +  ++ +    + + +   +++ + +++I   
Sbjct: 850 AEEHIFLIDWETGEILTKYEQYKKQKEAMTTILTTF--IKKKWNEQWDEVRETARKIRDY 907

Query: 353 EGELLR 358
             E + 
Sbjct: 908 PTEKME 913


>gi|318042874|ref|ZP_07974830.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 99

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
            A   + D VR YLR++G + LLS E EI + ++++
Sbjct: 6   DASGLSTDLVRSYLRDIGRVPLLSHEQEITLGRQVQ 41


>gi|157823695|ref|NP_057914.2| kinesin-like protein KIF21A isoform 3 [Mus musculus]
          Length = 1573

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|19704850|ref|NP_602345.1| RNA polymerase factor sigma-70 [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19712731|gb|AAL93644.1| RNA polymerase sigma-H factor [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 204

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 28/152 (18%), Positives = 71/152 (46%), Gaps = 4/152 (2%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I ++++K +   + A   +++   +L+   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 1   MEDINAILKKAQSGDNEAIDLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIK 60

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK---I 543
            +D      FS++A   +++ +  +I   +    + ++   K + ++  +    ++   I
Sbjct: 61  FYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNI 119

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575
               + E   ++  +  E + +  K ++   S
Sbjct: 120 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFS 151


>gi|326668722|ref|XP_001339206.4| PREDICTED: myosin heavy chain, fast skeletal muscle [Danio rerio]
          Length = 1935

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 51/375 (13%), Positives = 130/375 (34%), Gaps = 17/375 (4%)

Query: 7    RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
            +  + + + E +D +     +  +  ++ +  ++   +   E+ A L   E + E  E  
Sbjct: 1499 KRENKNLQQEITDLTEQLGETGKTIHEL-EKGKKTAEIEKSEIQAALEEAEATLEHEESK 1557

Query: 67   VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
            +  +      V    D +  E  E+   +  ++      +Q   D+  RS +D +R+  +
Sbjct: 1558 ILRVQLELNQVKGEIDRKLAEKDEEIEQIKRNSQRIIDSMQSTLDAEVRSRNDALRIKKK 1617

Query: 127  EMGSIELLSREGEIAI------AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
              G +     E EI +      A   +     +   L ++ L     +  ++++ +   +
Sbjct: 1618 MEGDLN----EMEIQLSHANRQAAEAQKQLRNVQGQLKDAQLHLDEALRAQEDMKEQVAM 1673

Query: 181  LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
            +    +L      E +        G    ++E     +    +      + +  K  + D
Sbjct: 1674 VERRNNLMQAEIEELRVALEQTERGRKVAEQELVDASERVTLLHSQNTSLINTKKKLEAD 1733

Query: 241  RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR--PKVMCALDEIAEVYRELRSLQ 298
              ++    E+   + RN +E    +    + M ++L+        L+ + +         
Sbjct: 1734 LVQIQGEMEDVVQEARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNLEVTVK-- 1791

Query: 299  DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
               +  + DE  S+  K  K++L KL   +   +S ++    +  D  K +   E  +  
Sbjct: 1792 --DLQHRLDEAESLAMKGGKKQLQKLEARVRELESEVEAEQRRGADAVKGVRKYERRVKE 1849

Query: 359  LAQSYGIKRDVFLER 373
            L       +   +  
Sbjct: 1850 LTYQTEEDKKNIIRL 1864


>gi|218441270|ref|YP_002379599.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7424]
 gi|218441280|ref|YP_002379609.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7424]
 gi|218173998|gb|ACK72731.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7424]
 gi|218174008|gb|ACK72741.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7424]
          Length = 281

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 68/187 (36%), Gaps = 21/187 (11%)

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL----- 556
           +W      R    + C   +  +  D    + +   +  NK ++        K       
Sbjct: 46  FWPIWESERDYFYKLCLRWMGGNSHDAEDVLNQVMLKAWNKWEKSANKIIYPKSWLSRII 105

Query: 557 -AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
               ++  RK  +  +   +++     +DT+   +         P  + +   +R     
Sbjct: 106 YNFCMDIHRKRKREAQNIDNIDELQLADDTAFRSEV------GIPETNMLNQEMRAYLGH 159

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           ++ SL  +    LR+ F +    D   ++V KQ  ++ E  RQ   KA R LK     K+
Sbjct: 160 LIESLPNK----LRVPFILSCYYDKPYQDVAKQLALSEENARQRIYKARRILK-----KQ 210

Query: 676 LRSFLDG 682
           L+ +L G
Sbjct: 211 LKKYLAG 217


>gi|133919920|emb|CAM12480.1| hypothetical protein [uncultured bacterium]
          Length = 170

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ AV   ++ + A + 
Sbjct: 53  EQYTDFYRDKERWRYLQKLDTKNRLLSLDGFTDSEGNPLDFITDE-AVDFAETVVNAVMV 111

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ + KL+ 
Sbjct: 112 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILIKLRK 166


>gi|121488789|emb|CAJ18279.1| sigma 70-type sigma factor [Chlorobium bathyomarinum]
          Length = 92

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D ++
Sbjct: 2   KAYSQLEQEYERDPNTKELANVLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQ 61

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           + +   P  S  + +L     R L+ L PRE 
Sbjct: 62  N-DGQRPDHSLTRDSLTLEVERSLSVLAPREA 92


>gi|167745714|ref|ZP_02417841.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|317472694|ref|ZP_07932009.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655026|gb|EDR99155.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|316899871|gb|EFV21870.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
          Length = 192

 Score = 42.5 bits (98), Expect = 0.26,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 37/77 (48%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           ++ + +     A   ++     LV   ++K+   G    DLIQEG IGL KA + +D   
Sbjct: 12  LLNEIKSGDDRAMDFLLNRYGGLVRRESRKFFLAGADEEDLIQEGMIGLFKAVKNYDDEK 71

Query: 493 GYKFSTYAMWWVKQAIT 509
              FST+A   VK+ I 
Sbjct: 72  NASFSTFASLCVKRQIY 88


>gi|217970371|ref|YP_002355605.1| methyl-accepting chemotaxis sensory transducer [Thauera sp. MZ1T]
 gi|217507698|gb|ACK54709.1| methyl-accepting chemotaxis sensory transducer [Thauera sp. MZ1T]
          Length = 598

 Score = 42.1 bits (97), Expect = 0.28,   Method: Composition-based stats.
 Identities = 47/333 (14%), Positives = 110/333 (33%), Gaps = 27/333 (8%)

Query: 45  TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV 104
           T +EL          + +M + +  + +M +N+   + ++ + G E+S   A    + + 
Sbjct: 126 THDELRELAASYNRFAAKMREIIGKVRSMSVNIA-REAVQVKLGVENSARDAQRQGDMTD 184

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIEL----LSRE--GEIAIAKRIEAGRAMMMASLC 158
            + +    +  +  + V +  R + +  L    ++RE  GE+   + + A    +   L 
Sbjct: 185 TVFEASTRSTEAIGE-VSVSARAIDASTLRNLEIARESLGEV---QNVAAKILAVSEKLQ 240

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
               T   L    + + +   L+REI D    +   +        E             K
Sbjct: 241 RFNHTVDELSQRSESVKEIAALIREIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRK 300

Query: 219 ERDDVQ--------------ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
             + V               E  GD  +   V  DD  +       +     ++  + + 
Sbjct: 301 LAERVNKATQEIVGNINGMLELVGDTRAENDVINDDVEQTRDVVTRSATQFEHMVGEFER 360

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEKLVK 323
           +   LS +   +   +      +     ++  L  + A   +  E+ ++      E + +
Sbjct: 361 TGGQLSQIAAGM-ASLTETNAHVHANVTDIHRLSAEVAGRMENCEQRTLALTKSTEAVQE 419

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
           LV    +     DLLV +       +     ++
Sbjct: 420 LVSRFKIGTGVFDLLVNETRGFRDGVQAELEQM 452


>gi|6561827|gb|AAF17083.1|AF202892_1 Kif21a [Mus musculus]
          Length = 1573

 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|308462135|ref|XP_003093353.1| CRE-LET-75 protein [Caenorhabditis remanei]
 gi|308250302|gb|EFO94254.1| CRE-LET-75 protein [Caenorhabditis remanei]
          Length = 2012

 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 92/255 (36%), Gaps = 14/255 (5%)

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            E     +   ++ E++   +     ++E +   + D  S+ +    + E   R   ++ +
Sbjct: 954  EALELTQGGSAAVEEKLTRLNSARQEVEKSLNDANDRLSEHEEKNADLEKQRRKAQQEVE 1013

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK--- 320
            +   ++ A++  L      +L+E A    ++RSLQD   +  +      K K L E+   
Sbjct: 1014 NLKKSIEAVDGNLN----KSLEEKAAKENQIRSLQDEMNSQDETIGKINKEKKLLEENNR 1069

Query: 321  -LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
             LV  + +    Q++ + L  +L      +        R+       +       +G + 
Sbjct: 1070 QLVDDLQAEEAKQAQANRLRTKLEQTLDEMEEAVEREKRIRAETEKSKRKVEGELKGAQE 1129

Query: 380  DPHWVSYAKDFPEGEWK------NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
                +S  K   +   K      + +   ++    + N +   S E    I E    +  
Sbjct: 1130 SIDELSAIKLEADASLKKKEADIHALGVRIEDEQALANRLTRQSKENAQRIIEIEDELEH 1189

Query: 434  VRKGECEASIAKKEM 448
             R+   +A  A+ E+
Sbjct: 1190 ERQSRSKADRARAEL 1204


>gi|302809795|ref|XP_002986590.1| hypothetical protein SELMODRAFT_124179 [Selaginella moellendorffii]
 gi|300145773|gb|EFJ12447.1| hypothetical protein SELMODRAFT_124179 [Selaginella moellendorffii]
          Length = 1056

 Score = 42.1 bits (97), Expect = 0.29,   Method: Composition-based stats.
 Identities = 42/206 (20%), Positives = 76/206 (36%), Gaps = 18/206 (8%)

Query: 148 AGRAMMMASLCESPLTF---QALIIWRDELNDG----TTLLRE-----------IIDLEA 189
                +   L E P        L+  R +L  G     + L E           I  L  
Sbjct: 458 QELEQLRRGLFERPFVVSNHDDLLTLRQQLEAGHLKMQSRLEEEEQAKAALMGRIQRLTK 517

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I   +K          S Q+R  S  E+E+ +      +  + +  S      VD    
Sbjct: 518 LILVSTKNTIPLNLPEKSTQRRRHSFGEEEKHESMHAVPEEHTPSGSSVSFEPPVDFKSR 577

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             ++  R  DE    +  T++   D LR ++     E+A     L+ L + AV   +D++
Sbjct: 578 RRKSFSRKPDELPPITGTTMADQMDLLREQMKMLAGEVALCSSSLKRLSEQAVTNPEDDQ 637

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRI 335
             ++ + LKE++ +    +S+ + RI
Sbjct: 638 LHMQMRKLKEEIDEKRRQMSIIEKRI 663


>gi|229542221|ref|ZP_04431281.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus coagulans
           36D1]
 gi|229326641|gb|EEN92316.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus coagulans
           36D1]
          Length = 216

 Score = 42.1 bits (97), Expect = 0.30,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 37/91 (40%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V +     S A   +++     V + A+ Y   G    D+IQEG IGL KA   +   
Sbjct: 20  ELVGRIHNGESEALDYLIQKYRNFVRAKARSYFIIGADREDIIQEGMIGLYKAIRDYRED 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   +    IP
Sbjct: 80  KLTSFKAFAELCINRQMITAIKTATRQKHIP 110


>gi|224004150|ref|XP_002295726.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209585758|gb|ACI64443.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 395

 Score = 42.1 bits (97), Expect = 0.30,   Method: Composition-based stats.
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 15/88 (17%)

Query: 471 LDLIQEGNIGLMKAAEKFDWC---------------LGYKFSTYAMWWVKQAITRSIADQ 515
            DL+ EG IGL +A +K+D+                 G +  TYA +W++  I R+I  +
Sbjct: 69  DDLLHEGTIGLAEALDKYDFSYSDLSVTEHTSSTAPKGARLGTYATYWIRGRILRAIQSR 128

Query: 516 SCTIRIPVHMRDKIHKVVRTARRMSNKI 543
               R P  +    H++V+ A+ +  + 
Sbjct: 129 EHAFRFPERVLQASHRLVKAAKELGLEW 156


>gi|225166748|ref|YP_002650733.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253771400|ref|YP_003034227.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
 gi|225007412|dbj|BAH29508.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253721377|gb|ACT33670.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
          Length = 146

 Score = 42.1 bits (97), Expect = 0.31,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 28/57 (49%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           S+++K +     +   ++E     +   A KY   G  F DL+Q G + ++KA  K+
Sbjct: 3   SLIKKAKEGDRASIISIIEKYKPFIFKCAHKYNIPGYDFEDLVQHGYLSVIKAIHKY 59


>gi|281210517|gb|EFA84683.1| hypothetical protein PPL_01675 [Polysphondylium pallidum PN500]
          Length = 980

 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 58/147 (39%), Gaps = 10/147 (6%)

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF---- 390
           +D  ++Q+  +  +I   + +   L + Y +K+  F    +  E +   +          
Sbjct: 701 MDDWIQQIRQLEAQINEEDRKRAELEKEYKVKKKTF-GLLENAEENFAKLQELCQQTSAS 759

Query: 391 ---PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                GEW+      ++   ++++E  + S E    +   + I ++++K       AK+E
Sbjct: 760 LIEMSGEWEKVRRPIIEKYRQLKDEKANQSDEAKSKVERIKEIRALIKKMIA-DIRAKEE 818

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLI 474
           +         ++  K TNR +    +I
Sbjct: 819 LFTQLQDTYKAMP-KDTNRSMYTRRII 844


>gi|150403005|ref|YP_001330299.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C7]
 gi|150034035|gb|ABR66148.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C7]
          Length = 730

 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 36/319 (11%), Positives = 111/319 (34%), Gaps = 13/319 (4%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           +EL   +    +  +++ED +         V +      E  S+ S  L  ++       
Sbjct: 425 KELREEVDLLNIQVQKVEDELKSAEETATQVTEAATQVAEASSDQSAKLQEASDQLETTY 484

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           +        + ++ V+    E+G    +  +  +  A     G   ++ +L +S    Q 
Sbjct: 485 E-VAKEVYGAAEETVKA-AEEIGENSEMGVKK-VENAISRMQGITNVIDNLGKS---IQE 538

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
           L     ++N+ T L+++I +    +   +        +         S  +   ++++++
Sbjct: 539 LGEDGKKINEVTDLIKDIAEQTGLLALNASIEAARAGDAGKGFAVVASEIKALAEEIKKS 598

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
             +I            +        +++        D+    L     +++  V  A  +
Sbjct: 599 VENINHTISGVHKRIGETMDLGLKGKDEVDKGVIAIDEVNDALL----RIKESVDAAGAK 654

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           I  + +  +S  DN     K+ +       + E+       ++ +   ++ ++E++  ++
Sbjct: 655 INGIKKGAQSAADNTEGALKNAQD---IASISEEFTATAEEVTASTEELNSIIEEIRGVA 711

Query: 347 KRIMHNEGELLRLAQSYGI 365
           + +      + + +  + I
Sbjct: 712 EEVTQVAERVTKKSSQFKI 730


>gi|15612678|ref|NP_240981.1| RNA polymerase factor sigma-70 [Bacillus halodurans C-125]
 gi|10172727|dbj|BAB03834.1| RNA polymerase sigma-H factor (sigma-30) [Bacillus halodurans
           C-125]
          Length = 217

 Score = 42.1 bits (97), Expect = 0.32,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 36/90 (40%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V +       A + ++      V + A+ Y   G    D++QEG IGL KA   F    
Sbjct: 22  LVNRVRNGDGAALEYLIHKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAIRDFKGDK 81

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  +I   +    IP
Sbjct: 82  LSSFKAFAELCITRQIITAIKTATRQKHIP 111


>gi|23097558|ref|NP_691024.1| RNA polymerase factor sigma-70 [Oceanobacillus iheyensis HTE831]
 gi|22775781|dbj|BAC12059.1| RNA polymerase sigma-H factor (sigma-30) [Oceanobacillus iheyensis
           HTE831]
          Length = 217

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 24/90 (26%), Positives = 39/90 (43%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +++      S A   +++  +  V + A+ Y   G    D+IQEG IGL KA   +D   
Sbjct: 22  LLQFIRQGNSHALDLLIQRYISFVRAKARTYFLVGADKEDIIQEGMIGLYKAIRDYDVDK 81

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   V + I  +I   +    IP
Sbjct: 82  LSSFKAFAELCVTRQIITAIKTATRQKHIP 111


>gi|313225620|emb|CBY07094.1| unnamed protein product [Oikopleura dioica]
          Length = 1487

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 36/222 (16%), Positives = 82/222 (36%), Gaps = 17/222 (7%)

Query: 178  TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
             + ++ + DL A +       +    + +   ++   S  +  DD +  +   E   +  
Sbjct: 1259 ESRVKTVEDLHANLENNVLMIYSEAEKANEVAQKLKDSSSQAFDDAENNKEKAEKILQGV 1318

Query: 238  KDDRSKVDSPPENAENDERNLDEDED------DSAHTLSAMEDQLRPKVMC---ALDEIA 288
            ++    V S   +++  +       +      D++ ++  M  +   KV     ALDEI 
Sbjct: 1319 QEAIEDVKSKNGDSDKIQNAFAAKTEEINTAKDNSESVFQMAKEAETKVKESETALDEIK 1378

Query: 289  EVY-----RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
            ++      R+L  +  +  N  ++E    K + ++ +L  L       +   +   +Q+ 
Sbjct: 1379 KLVNDIKSRKLPEIVTDIGNLVEEEGYKRKSQKIQSELYGLRNKFENIKKEQE---DQIS 1435

Query: 344  DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVS 385
             I  R+  +  +L  L    G          + R+L P W S
Sbjct: 1436 SIQDRLDVDGNQLESLLLKKGKLEAEVENLEKIRDLLPKWCS 1477


>gi|310777972|ref|YP_003966305.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747295|gb|ADO81957.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 203

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 31/68 (45%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           +     A +++ +     V   AK Y   G    DL+QEG IGL+KA   +D      F 
Sbjct: 15  QNGDQEAVRKVFDYYKNFVFLKAKNYFLIGADRDDLVQEGMIGLLKAIRAYDTEKAASFK 74

Query: 498 TYAMWWVK 505
           T+A   +K
Sbjct: 75  TFATICIK 82


>gi|310822428|ref|YP_003954786.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309395500|gb|ADO72959.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 163

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLEEVG+   +TRERIRQ+E + + KL+  + ++
Sbjct: 122 TLEEVGEIMNLTRERIRQVETRGLMKLREATEAE 155


>gi|20808677|ref|NP_623848.1| RNA polymerase factor sigma-70 [Thermoanaerobacter tengcongensis
           MB4]
 gi|20517313|gb|AAM25452.1| DNA-directed RNA polymerase specialized sigma subunits, sigma24
           homologs [Thermoanaerobacter tengcongensis MB4]
          Length = 219

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 27/98 (27%), Positives = 41/98 (41%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   IVS  ++      +A + ++E     V + A+ Y   G    D+IQEG IGL KA
Sbjct: 21  MEEEEIVSRAQQ---GDELALEYLIERYKNFVKAKARTYFLVGADKEDIIQEGMIGLYKA 77

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 78  IRDYKNNKLTSFKAFAELCVTRQIITAIKTATRQKHIP 115


>gi|309390163|gb|ADO78043.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 44/96 (45%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
            +    +++  +     A + ++  N+ +V + ++ +  +GL   D+IQEG +GL KA  
Sbjct: 4   EKEEAEIIQMAQAGNDFAIEYLINQNMDIVYAKSRFFFIKGLDHDDVIQEGRVGLYKAIR 63

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            F    G  F  ++   V + +  +I   +    +P
Sbjct: 64  DFRAEKGASFRGFSQLCVHRQLISAIKKANRQKHVP 99


>gi|291519019|emb|CBK74240.1| RNA polymerase sigma factor, sigma-70 family [Butyrivibrio
           fibrisolvens 16/4]
          Length = 195

 Score = 42.1 bits (97), Expect = 0.33,   Method: Composition-based stats.
 Identities = 24/93 (25%), Positives = 41/93 (44%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V+K +         + E    LV+  +KKY   G +  DLIQEG IGL  A   +D   
Sbjct: 15  LVKKYQDGDQAVLNYICEKYKPLVLKTSKKYFLVGGENEDLIQEGMIGLFGAIGDYDTDS 74

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
              F  +A   + + + ++I   +     P++ 
Sbjct: 75  EVTFFRFAQLCIDRQMIKAIEASNRKKHSPLNA 107


>gi|222099796|ref|YP_002534364.1| DNA double-strand break repair rad50 ATPase [Thermotoga neapolitana
           DSM 4359]
 gi|221572186|gb|ACM22998.1| DNA double-strand break repair rad50 ATPase [Thermotoga neapolitana
           DSM 4359]
          Length = 853

 Score = 42.1 bits (97), Expect = 0.34,   Method: Composition-based stats.
 Identities = 35/315 (11%), Positives = 105/315 (33%), Gaps = 7/315 (2%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
           L   E  +  ++ I       + S+ ++    + L    +E       +  I++ +  + 
Sbjct: 346 LEEAEEILERSRPILEKMIRTLESIRQAEEEVEKLHKDLEEKKRELLRIEGIVEEKKTVL 405

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
            E+K       + H        + +    D     G        + D   +     E  +
Sbjct: 406 EETKKSLAELKKNHLAWLVYQIASQLNDGDTCPVCGGEYHGKAKAVDFDREQFEEMEKRK 465

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
           +   +     ++    LS+  ++ +  +M    +++E+ +E   ++++       E    
Sbjct: 466 SSLESEIVILEERKKNLSSAIEETKESLMIREKDLSELRKEKEKMEEDLNRLGYREGMER 525

Query: 313 KCKVLKEKLVKLVGSLSL-------NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
             K  +  + +L     +        +++I+   +Q+ +I   +     EL         
Sbjct: 526 TLKERRRAVEELEKECRILSEKIISERTKIEQFDDQIRNIMDEMKAKRRELEDSKAELSH 585

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
            ++ F++R +   L         +      ++ +      I  +  +I+     +   + 
Sbjct: 586 LKEDFMKRLEDAGLSVEEFRTLVNEEPKNAEDRLKAVETEIRLLEEDIEKEKDLSPEILE 645

Query: 426 EFRHIVSMVRKGECE 440
           E + I+  + K + +
Sbjct: 646 EHKKILDHLEKIKEK 660


>gi|150389913|ref|YP_001319962.1| RNA polymerase subunit alpha [Alkaliphilus metalliredigens QYMF]
 gi|149949775|gb|ABR48303.1| RNA polymerase, alpha subunit domain protein [Alkaliphilus
           metalliredigens QYMF]
          Length = 912

 Score = 42.1 bits (97), Expect = 0.34,   Method: Composition-based stats.
 Identities = 29/97 (29%), Positives = 41/97 (42%), Gaps = 17/97 (17%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           SL   +   D     D + D   V+  +S                L  +E  V+  R   
Sbjct: 270 SLNDLLIRND----IDLLYDDRFVAIYNSF--------VIGAKDYLNDKEYDVIWQRI-- 315

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
                 TL +VGK   V+++RIRQIE KAI+KL + S
Sbjct: 316 ---QGKTLVDVGKTKDVSKQRIRQIEEKAIKKLNNAS 349


>gi|328770745|gb|EGF80786.1| hypothetical protein BATDEDRAFT_11069 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 646

 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 73/181 (40%), Gaps = 3/181 (1%)

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
           G +  + +  +  K + +V+  +  + ++  +  +++ ++    E    D     ++ + 
Sbjct: 377 GGAPPQLDPETIAKLQAEVEAEKRALLASKDIVIEEKERIAMELEKRAADLEKERQEREF 436

Query: 265 SAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
               L AME +L    +  +D+I E  REL   Q+      + E+        K++    
Sbjct: 437 LESKLKAMEGKLLIGGLNIVDKINEQERELLEAQNKLQEQHRRERELQLQLEQKQEAQLQ 496

Query: 325 VGSLSLN-QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ--GRELDP 381
           +     + Q  +D+  ++L  +  ++   + E+      +  +R+  L+  +   REL  
Sbjct: 497 LEESHASLQEEVDVKTKKLMKLWTKLQEVKTEISDAKDEFRNEREDLLDTIRELSRELSL 556

Query: 382 H 382
            
Sbjct: 557 K 557


>gi|148672369|gb|EDL04316.1| kinesin family member 21A, isoform CRA_b [Mus musculus]
          Length = 1535

 Score = 42.1 bits (97), Expect = 0.35,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|160939450|ref|ZP_02086800.1| hypothetical protein CLOBOL_04343 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437660|gb|EDP15422.1| hypothetical protein CLOBOL_04343 [Clostridium bolteae ATCC
           BAA-613]
          Length = 135

 Score = 41.7 bits (96), Expect = 0.37,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ A    ++ + A + 
Sbjct: 18  EQYTDFYRDKERWRYLQKLDTKNSLLSLDGFTDSEGNPLDFIADE-AADIAETVVNAVMV 76

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ ++   F  G++      EVG +F +T+  + + +A+ + KL+ 
Sbjct: 77  DRLKAALPLLSDSEQALIHAIFFDGLSE----REVGARFGITQSVVNKRKARILIKLRK 131


>gi|149748805|ref|XP_001490094.1| PREDICTED: CDC42 binding protein kinase alpha (DMPK-like) isoform 1
           [Equus caballus]
          Length = 1719

 Score = 41.7 bits (96), Expect = 0.37,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 141/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNTLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKNLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +    S ++  +E+   + + +     ++    +                   
Sbjct: 496 IEKLRKQVR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIK---------------- 538

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
                 A      +    +    + +     E+K    +  +++ EF  I   +      
Sbjct: 539 ------ALQQEREDLNKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHAQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGVCSI-EHQQEITKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     RE +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENLSVHNQQLEEEVKDLADKRESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|73960799|ref|XP_863624.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 7 [Canis familiaris]
          Length = 1781

 Score = 41.7 bits (96), Expect = 0.38,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|261402380|ref|YP_003246604.1| methyl-accepting chemotaxis sensory transducer [Methanocaldococcus
           vulcanius M7]
 gi|261369373|gb|ACX72122.1| methyl-accepting chemotaxis sensory transducer [Methanocaldococcus
           vulcanius M7]
          Length = 610

 Score = 41.7 bits (96), Expect = 0.38,   Method: Composition-based stats.
 Identities = 39/343 (11%), Positives = 120/343 (34%), Gaps = 24/343 (6%)

Query: 23  VFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
           + + + D+   MIK  +++    + E+N  +   E    +  +    +++    V     
Sbjct: 292 LINNALDNLANMIKELKEK----VSEVNKEIHNVEEELNRAREISDQVADATNQVATAAT 347

Query: 83  LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            +  +  + + +L    + +           +  T+      + E   + L     ++  
Sbjct: 348 DQSTKLQDITQELEEVTTIAKGVYDSAIGGVEAITN------VEESSQVGL----EKVEH 397

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           A       A ++  L +     Q L     ++N+ T L+++I +    +   +       
Sbjct: 398 AIETMQRIANVIDELGK---AIQELGEESKKINEITVLIKDIAEQTGLLALNASIEAARA 454

Query: 203 TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            E         S  +   +++ ++  DI       ++  +K        +++        
Sbjct: 455 GEAGRGFAVVASEIKSLAEEIGKSVDDINRTISEIQEKINKTIDLGLTGKDEVDRGVVAI 514

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
           D+  +    +    +  V  A+++I E+  + +   DN     +D +       + E+  
Sbjct: 515 DEVNNAFLKI----KEAVDKAMEKIEEIKEDAQKAVDNIQAALRDVQDVAS---ISEEFA 567

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                L+ +   ++ ++E++   ++++      L + A  + +
Sbjct: 568 ATAEELTASTEELNGVIEEIGKAAEKVAKIADNLAKSASKFKV 610


>gi|294497754|ref|YP_003561454.1| sigma-70 family RNA polymerase sigma factor [Bacillus megaterium QM
           B1551]
 gi|294347691|gb|ADE68020.1| RNA polymerase sigma factor, sigma-70 family [Bacillus megaterium
           QM B1551]
          Length = 203

 Score = 41.7 bits (96), Expect = 0.39,   Method: Composition-based stats.
 Identities = 16/142 (11%), Positives = 54/142 (38%), Gaps = 6/142 (4%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           + +   +  ++++      ++ +  +  V  V++  + +  P+ L+ P   +    + D 
Sbjct: 61  LNKEFHQFYSEVRLLHYINKLCRHYSRDVMRVKEK-ERSYIPLRLQQPAALDGNRTVEDM 119

Query: 592 IEDKNAVSPLDSAIQANLRET-TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
           +  ++        +   L           LT +++ +L +            +E+   F 
Sbjct: 120 LGVQDGAVWEHEFLGNQLENRILHHAFRQLTAKQQCMLHLIIVERWTH----KEIAAYFS 175

Query: 651 VTRERIRQIEAKAIRKLKHPSR 672
           ++++ +     +A+ KLK   +
Sbjct: 176 ISQQAVSSHYQRALSKLKKIMK 197


>gi|312621865|ref|YP_004023478.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202332|gb|ADQ45659.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 302

 Score = 41.7 bits (96), Expect = 0.39,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 442 SIAKKEMVEANLRLVISVAKKYT----NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
           S+ ++ ++  N++LV  VA K+         +  DLI EG IGL+ AA+ +D   G  FS
Sbjct: 7   SVQRQMLIADNIKLVYHVANKFMPCPKGYCYEVDDLISEGYIGLVVAAKNYDPAKG-SFS 65

Query: 498 TYAMWWVKQAITRS 511
           +YA   ++  I RS
Sbjct: 66  SYACKVIESRIKRS 79


>gi|73960793|ref|XP_863552.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 4 [Canis familiaris]
          Length = 1774

 Score = 41.7 bits (96), Expect = 0.39,   Method: Composition-based stats.
 Identities = 61/441 (13%), Positives = 146/441 (33%), Gaps = 38/441 (8%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRN------EIKSISVETGISISEFRHIVSMV 434
                  +        + +  E + +           E+K    +  +++ EF  I   +
Sbjct: 549 KRERETGRRRSRLCAGSLILTEQELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERL 608

Query: 435 ------RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
                 ++        K+E V+  ++ V S+ ++         +L          AAE  
Sbjct: 609 TELHTQKQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEAS 665

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
                 + S +    ++  +              +  + +I K+     +   + K    
Sbjct: 666 KDRKLREQSEHYSKQLENELEGLKVGNLGVESFGIEHQQEISKL-----KTDLEKKSIFY 720

Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQA 607
            EE++K+  +    + K LK        +    +++   L D +E ++          + 
Sbjct: 721 EEELSKREGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFEN 779

Query: 608 NLRETTTRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
             ++   R    LT        E   L   +      +  LEE  K     +E +   EA
Sbjct: 780 EFKQQYEREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEA 839

Query: 662 KAIRKLKHPSRSKKLRSFLDG 682
           +    ++  S  K  R +L  
Sbjct: 840 QITEIIQWVSDEKDARGYLQA 860


>gi|170749102|ref|YP_001755362.1| hypothetical protein Mrad2831_2695 [Methylobacterium radiotolerans
           JCM 2831]
 gi|170655624|gb|ACB24679.1| conserved hypothetical protein [Methylobacterium radiotolerans JCM
           2831]
          Length = 105

 Score = 41.7 bits (96), Expect = 0.40,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 28  DDSWKKMIKLARQRGY--VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGD 81
             +  +++  A  +    +T ++L   LPP +VS+E +E    +L+  GI V DG+
Sbjct: 49  RQAIDRLLAKAEAQRSRNLTYDDLEEALPPRDVSAEDLEAIFWILAEHGIEVEDGE 104


>gi|148672370|gb|EDL04317.1| kinesin family member 21A, isoform CRA_c [Mus musculus]
          Length = 1528

 Score = 41.7 bits (96), Expect = 0.40,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|147678014|ref|YP_001212229.1| putative RNA polymerase sigma factor SigI [Pelotomaculum
           thermopropionicum SI]
 gi|146274111|dbj|BAF59860.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 244

 Score = 41.7 bits (96), Expect = 0.41,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 38/98 (38%), Gaps = 5/98 (5%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF--LDLIQEGNIG 480
            + E    +  +RKG    S+A+++ +E     +  VA ++  R L +   D +    I 
Sbjct: 3   PVQEVEERLREIRKGN---SLAREDFLEDCKPFIFKVACRFCGRILDWGRDDELAVALIA 59

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
             +A ++F    G  F  YA   +   +      +   
Sbjct: 60  FNEAIDRFREDAGVPFPAYARMVINSRLADYRRKEGRN 97


>gi|163119564|ref|YP_079928.2| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus licheniformis ATCC 14580]
 gi|319644898|ref|ZP_07999131.1| RNA polymerase sporulation-specific sigma factor [Bacillus sp.
           BT1B_CT2]
 gi|145903073|gb|AAU24290.2| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus licheniformis ATCC 14580]
 gi|317392707|gb|EFV73501.1| RNA polymerase sporulation-specific sigma factor [Bacillus sp.
           BT1B_CT2]
          Length = 82

 Score = 41.7 bits (96), Expect = 0.42,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 32/59 (54%)

Query: 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
           L S T  +++ +  RF + +  + T  E+ K+  ++R  + +IE +A+ K+ H    +K
Sbjct: 8   LTSWTAEKKKFIAGRFSLDLKKEKTQREIAKELGISRSYVSRIEKRALMKVFHEFYREK 66


>gi|317130675|ref|YP_004096957.1| LPXTG-motif cell wall anchor domain protein [Bacillus
           cellulosilyticus DSM 2522]
 gi|315475623|gb|ADU32226.1| LPXTG-motif cell wall anchor domain protein [Bacillus
           cellulosilyticus DSM 2522]
          Length = 1622

 Score = 41.7 bits (96), Expect = 0.43,   Method: Composition-based stats.
 Identities = 57/321 (17%), Positives = 119/321 (37%), Gaps = 42/321 (13%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           D SDD ++++ + A++        LN  L  D    + +E     L++    + +  + +
Sbjct: 579 DASDDIFEQL-ETAKEA-------LNEALLADPADKDAIESATEALNDATKKLEEAAEQK 630

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           + E ++ +      A   +   Q R  +A     D                      I +
Sbjct: 631 ELENAKAA---GEEALEEAEKAQDRYKNAGGDATD---------------------EIYE 666

Query: 145 RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTE 204
            +EA + ++ A+    P   +A+    +E+ D TT+L + ID +     +          
Sbjct: 667 ALEAAKEVLEAAKLADPANKEAIEAATEEVTDLTTVLEKAIDAKELENAKF--------A 718

Query: 205 GHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV-DSPPENAENDERNLDEDED 263
           G    +  + +Q++  +   ET  D+  A + +K+   +V  + P   +  E   +   D
Sbjct: 719 GEKALEEAEKAQDRYENAGGETSDDLYEAVEAAKEALKEVLLADPAEKDAIEAATEALID 778

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           ++     A+E +       A +E  E   + +    NA   + DE      +  KE L  
Sbjct: 779 ETKKLEEAVEAKELANAKAAGEEALEKTEKAQDRYYNAGGEESDELYE-AVEAAKEVLNN 837

Query: 324 LVGSLSLNQSRIDLLVEQLYD 344
            + +    +  I+   E L D
Sbjct: 838 ALQATPAEKEAIEAATEALND 858


>gi|217076384|ref|YP_002334100.1| RNA polymerase factor sigma-70 [Thermosipho africanus TCF52B]
 gi|217036237|gb|ACJ74759.1| RNA polymerase sigma-H factor [Thermosipho africanus TCF52B]
          Length = 206

 Score = 41.7 bits (96), Expect = 0.43,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
           + I  +V   +     A + ++E    +VI ++ KY     +F D++Q G IGL+KA   
Sbjct: 9   KRIEKLVELAQSGLKEALELIIEKYYPMVIRISSKYYAPWAEFEDIVQNGLIGLIKAVFY 68

Query: 488 FDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
           FD      F+++A   ++  +   I   +    
Sbjct: 69  FDNEKS-SFNSFAWKSIEGEVQTFITYLNRKKN 100


>gi|2736153|gb|AAC02942.1| myotonic dystrophy kinase-related Cdc42-binding kinase MRCK-beta
           [Rattus norvegicus]
          Length = 1702

 Score = 41.7 bits (96), Expect = 0.44,   Method: Composition-based stats.
 Identities = 52/453 (11%), Positives = 135/453 (29%), Gaps = 48/453 (10%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMIQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                 ++     A  ++  L +   +++  L +   +L+              +  R+L
Sbjct: 525 TQRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKD----------AHQQRKRAL 574

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+ +   ++  +   + + +  +L      + +   +ID + + +    K     E  L 
Sbjct: 575 QEFSELNERMAELRSQKQKVSRQLRDKEEEMEVAMQKIDSMRQDIRKSEKSRKELEARLE 634

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                   +R +        +     +   K    G            I KIR+E++   
Sbjct: 635 DAVAEASKERKLREHSESFSKQMERELETLKVKQGGRGPGATLEHQQEISKIRSELEKKV 694

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
           +           +V   R    E    KKE+ E+                      +Q+ 
Sbjct: 695 LFY------EEELVRRERSHVLEVKNVKKEVHES----------------ESHQLALQKE 732

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH----KVV 533
            + L    EK       +        +K    R  A      +      +K+     K+ 
Sbjct: 733 VLMLKDKLEKSKRERHSEMEEAIGA-MKDKYERERAMLFDENKKLTAENEKLCSFVDKLT 791

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566
              R++ ++++   + +E        +  + + 
Sbjct: 792 AQNRQLEDELQDLASKKESVAHWEAQIAEIIQW 824


>gi|160901830|ref|YP_001567411.1| RNA polymerase factor sigma-70 [Petrotoga mobilis SJ95]
 gi|160359474|gb|ABX31088.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Petrotoga mobilis
           SJ95]
          Length = 212

 Score = 41.7 bits (96), Expect = 0.45,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 38/89 (42%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++   +   + A   ++E    +V S+  KY    L+F D +Q G +GL++A   F   
Sbjct: 15  KLIELAQIGDNQALGIILEKFEPMVKSIVGKYYGTWLEFEDFLQIGLVGLIQAVYNFRKD 74

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIR 520
              KFS++A   +   I   +   +    
Sbjct: 75  ANAKFSSFAYMNISSEIKSFVTYLNRNKH 103


>gi|332711579|ref|ZP_08431510.1| RNA polymerase, sigma subunit, ECF family [Lyngbya majuscula 3L]
 gi|332349557|gb|EGJ29166.1| RNA polymerase, sigma subunit, ECF family [Lyngbya majuscula 3L]
          Length = 240

 Score = 41.7 bits (96), Expect = 0.45,   Method: Composition-based stats.
 Identities = 43/265 (16%), Positives = 87/265 (32%), Gaps = 29/265 (10%)

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
               + ++E + ++  +       S++     E  L  V    +K +N  L      QEG
Sbjct: 5   QSQKLGVNERKKVLKAIPIMSQPISLSWST--EVKLPQVPVQPEKLSNYDLVLR--CQEG 60

Query: 478 NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
                 A  +                                R  +  ++   +V R  +
Sbjct: 61  MSPDRTAFAELLRRYQSHVDKIL----------YHLAPDWQDRSDL-AQEVWIRVYRNIK 109

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
           R++  +K +     IA    +  + +RK  ++   P+SL+ P   +D     D+      
Sbjct: 110 RLNEPVKFKGWLSRIAT--NLFYDELRKRKRVAH-PLSLDAPRHMDDGD--MDWEIASAE 164

Query: 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
             P +        E   + ++ L       + +R   GM  +   E  G      + RI 
Sbjct: 165 PGPEEDMTTREFYEQLHKAISELPEVFRTTIILREIEGMAYEEIAEITGASLGTVKSRI- 223

Query: 658 QIEAKAIRKLKHPSRSKKLRSFLDG 682
              A+A  +L+       L+++LD 
Sbjct: 224 ---ARARARLQ-----SHLQAYLDS 240


>gi|311029031|ref|ZP_07707121.1| RNA polymerase factor sigma-70 [Bacillus sp. m3-13]
          Length = 216

 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 26/99 (26%), Positives = 37/99 (37%)

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
           I E      MV       S A   ++      V + A+ Y   G    D++QEG IGL K
Sbjct: 12  ILELMEDEQMVELVHLGDSEALDYLINKYKNFVRAKARSYFLIGADREDIVQEGMIGLYK 71

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           A   F       F  +A   + + I  +I   +    IP
Sbjct: 72  AIRDFKEDKLTSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|148672368|gb|EDL04315.1| kinesin family member 21A, isoform CRA_a [Mus musculus]
          Length = 1564

 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 70/442 (15%), Positives = 135/442 (30%), Gaps = 42/442 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
              +   +        EIIDL A    E         +     K +++  ++E+ + +  
Sbjct: 520 SSAFSPTILSSDKETIEIIDL-AKKDLEKLKRKEKKKKKSVAGKDDNADTDQEKKEEKGV 578

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
                +   V ++         E  E DE   D+ E + +   S  E   +      L  
Sbjct: 579 SEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSESDEKANYQADLAN 638

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL---- 342
           I       + L D   N QK  ++  K    +EKL+ L   +   Q   D +++ L    
Sbjct: 639 ITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLERDQVLQNLGSVE 696

Query: 343 -----------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFP 391
                       +  K++     EL RL  +   +    L+     E     +       
Sbjct: 697 SYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEKQLKKLQQDVMEM 755

Query: 392 EGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      +    +   K R        EI  +  +      + R ++   ++ +      
Sbjct: 756 KKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLEAQKRNQEVVLRR 814

Query: 445 KKEMVEANLRLVISVAKKYTNR 466
           K E V A  R V  ++ K   +
Sbjct: 815 KTEEVTALRRQVRPMSDKVAGK 836


>gi|121488761|emb|CAJ18265.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 92

 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 1/92 (1%)

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D ++
Sbjct: 2   KAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQ 61

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   + P     + +L     R L+ L PRE 
Sbjct: 62  NDGHL-PDHGLNKDSLTLEVERSLSVLAPREA 92


>gi|302872437|ref|YP_003841073.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302575296|gb|ADL43087.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 244

 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 24/91 (26%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +VR        A +E++      V +  + Y   G    D+ QEG IGL KA   FD  
Sbjct: 50  ELVRYSREGIKEATEELLCRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVRDFDET 109

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   S    IP
Sbjct: 110 KYPSFRLFAEMCITRQMITAIKTASRQKHIP 140


>gi|326793785|ref|YP_004311605.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Marinomonas
           mediterranea MMB-1]
 gi|326544549|gb|ADZ89769.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Marinomonas
           mediterranea MMB-1]
          Length = 191

 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D   L D IED+++  P   A Q   +E     L  L   + +VL   +  G       E
Sbjct: 107 DPEFLWDDIEDESS-DPFREAQQKRDQENINSSLKQLPSDQRQVLAKVYLEGKTHKEASE 165

Query: 644 EVGKQFCVTRERIRQIEAKAIRKL 667
           E+       + R+R     A+ KL
Sbjct: 166 ELNIPLGTIKSRVRL----ALNKL 185


>gi|157104250|ref|XP_001648321.1| hypothetical protein AaeL_AAEL014260 [Aedes aegypti]
 gi|108869237|gb|EAT33462.1| hypothetical protein AaeL_AAEL014260 [Aedes aegypti]
          Length = 1885

 Score = 41.4 bits (95), Expect = 0.47,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 89/236 (37%), Gaps = 11/236 (4%)

Query: 53   LPPDEVSSEQMEDTVAMLSNMG--INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
            LP +EV   Q+E+  +  S+    I     + LE    SE       S S     L ++ 
Sbjct: 1519 LPVEEVKLGQVEEKSSDTSSQKNPIPEDSQEKLEQTPPSEVKETEEKSVSEEEPQLDQKT 1578

Query: 111  DSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW 170
               + ++ +PV     E  S E  S++G IA+   +  G     A++ ++P    +    
Sbjct: 1579 PVGEATSGEPV----NESESAEAQSKQG-IALGSDVVLGET---ATVSDAPQVETSSDKN 1630

Query: 171  RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
             +E+NDG     +     A    +   G     E       E   +E+     ++ E   
Sbjct: 1631 ENEVNDGDLA-EQSATETAPQEKDLDPGKIEPKEADVPSVDEQRDEEEPPKPSEKVETSE 1689

Query: 231  ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
            +S +K   D     + P  +A  +++   E+ ++     S  E+  + +   + D 
Sbjct: 1690 QSESKRIDDCEEPSEEPGHSAPEEKQESPENPEEPQEVPSPSEENSKDETAASEDA 1745


>gi|153810235|ref|ZP_01962903.1| hypothetical protein RUMOBE_00616 [Ruminococcus obeum ATCC 29174]
 gi|153855530|ref|ZP_01996649.1| hypothetical protein DORLON_02665 [Dorea longicatena DSM 13814]
 gi|154506117|ref|ZP_02042855.1| hypothetical protein RUMGNA_03659 [Ruminococcus gnavus ATCC 29149]
 gi|160934980|ref|ZP_02082366.1| hypothetical protein CLOLEP_03856 [Clostridium leptum DSM 753]
 gi|167751528|ref|ZP_02423655.1| hypothetical protein EUBSIR_02529 [Eubacterium siraeum DSM 15702]
 gi|167760878|ref|ZP_02433005.1| hypothetical protein CLOSCI_03266 [Clostridium scindens ATCC 35704]
 gi|210617837|ref|ZP_03291773.1| hypothetical protein CLONEX_04005 [Clostridium nexile DSM 1787]
 gi|223932196|ref|ZP_03624200.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptococcus suis 89/1591]
 gi|260589814|ref|ZP_05855727.1| RNA polymerase sigma-B factor [Blautia hansenii DSM 20583]
 gi|298346341|ref|YP_003719028.1| RNA polymerase sigma-B factor [Mobiluncus curtisii ATCC 43063]
 gi|325263030|ref|ZP_08129765.1| RNA polymerase sigma-B factor [Clostridium sp. D5]
 gi|149752052|gb|EDM61983.1| hypothetical protein DORLON_02665 [Dorea longicatena DSM 13814]
 gi|149833414|gb|EDM88495.1| hypothetical protein RUMOBE_00616 [Ruminococcus obeum ATCC 29174]
 gi|153793616|gb|EDN76036.1| hypothetical protein RUMGNA_03659 [Ruminococcus gnavus ATCC 29149]
 gi|156866433|gb|EDO59805.1| hypothetical protein CLOLEP_03856 [Clostridium leptum DSM 753]
 gi|167655336|gb|EDR99465.1| hypothetical protein EUBSIR_02529 [Eubacterium siraeum DSM 15702]
 gi|167661481|gb|EDS05611.1| hypothetical protein CLOSCI_03266 [Clostridium scindens ATCC 35704]
 gi|210149116|gb|EEA80125.1| hypothetical protein CLONEX_04005 [Clostridium nexile DSM 1787]
 gi|223899177|gb|EEF65534.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptococcus suis 89/1591]
 gi|260539817|gb|EEX20386.1| RNA polymerase sigma-B factor [Blautia hansenii DSM 20583]
 gi|291540148|emb|CBL13259.1| DNA-directed RNA polymerase specialized sigma subunit [Roseburia
           intestinalis XB6B4]
 gi|295090232|emb|CBK76339.1| DNA-directed RNA polymerase specialized sigma subunit [Clostridium
           cf. saccharolyticum K10]
 gi|298236402|gb|ADI67534.1| RNA polymerase sigma-B factor [Mobiluncus curtisii ATCC 43063]
 gi|324031423|gb|EGB92703.1| RNA polymerase sigma-B factor [Clostridium sp. D5]
          Length = 170

 Score = 41.4 bits (95), Expect = 0.48,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ AV   ++ + A + 
Sbjct: 53  EQYTDFYRDKERWRYLQKLDTKNRLLSLDGFTDSEGNPLDFITDE-AVDIAETVVNAVMV 111

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ + KL+ 
Sbjct: 112 DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILIKLRK 166


>gi|294500560|ref|YP_003564260.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
 gi|294350497|gb|ADE70826.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
          Length = 216

 Score = 41.4 bits (95), Expect = 0.48,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 37/90 (41%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V         + + ++     LV   A+KY   G +  D++QEG IGL KA   F+   
Sbjct: 21  LVEMVHSGDEKSLEYLINKYQNLVRGKARKYFLIGAEKEDIVQEGMIGLYKAIRDFNEDK 80

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  +I   +     P
Sbjct: 81  LTSFKGFAELCITRQIITAIKTATRQKHGP 110


>gi|153811788|ref|ZP_01964456.1| hypothetical protein RUMOBE_02181 [Ruminococcus obeum ATCC 29174]
 gi|149832191|gb|EDM87276.1| hypothetical protein RUMOBE_02181 [Ruminococcus obeum ATCC 29174]
          Length = 158

 Score = 41.4 bits (95), Expect = 0.49,   Method: Composition-based stats.
 Identities = 19/119 (15%), Positives = 44/119 (36%), Gaps = 4/119 (3%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           EI +      E    + + TK    L+    +         + D+   S  D  I     
Sbjct: 39  EIYRSKKWQPEDPETMTRKTKWTELLDCVFSENTDGIGVQDLPDEGQRSVEDLVILQAES 98

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
               + +A L+  E+ +++  +  G        E+ K   +++ R+ Q  +  ++K++ 
Sbjct: 99  AELHQNIAKLSEHEQFIIKSIYFEG----MKQVELAKILGISKVRMSQKVSAILKKMRK 153


>gi|302916785|ref|XP_003052203.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256733142|gb|EEU46490.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 2027

 Score = 41.4 bits (95), Expect = 0.49,   Method: Composition-based stats.
 Identities = 31/182 (17%), Positives = 70/182 (38%), Gaps = 5/182 (2%)

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
             +  D  +     S        E  S     +S  E  R +  +T+GD +   K+ +  +
Sbjct: 1822 DDESDTSSIRSFASALERSVTAENKSPDSITESQSETSRSNQAQTQGD-KELKKLEQRRK 1880

Query: 242  SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD----EIAEVYRELRSL 297
               +      E  +  L  +++  A TL+ M ++   +V    +    EI ++  +  + 
Sbjct: 1881 KLDEKVARLHERRQSKLQGEKEKDAATLAKMREKHDKEVAKQEEKYRREIKKLEEKREAE 1940

Query: 298  QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
            Q  A   ++      +   L  +L ++     L + +IDLL  Q+ ++  +      +L 
Sbjct: 1941 QRKAEERRRKALEREEKNNLSLELERVRAERDLARRQIDLLESQVGELQAQNTMLVRKLG 2000

Query: 358  RL 359
            ++
Sbjct: 2001 KM 2002


>gi|282882222|ref|ZP_06290861.1| putative sporulation sigma factor SigK [Peptoniphilus lacrimalis
           315-B]
 gi|281297987|gb|EFA90444.1| putative sporulation sigma factor SigK [Peptoniphilus lacrimalis
           315-B]
          Length = 256

 Score = 41.4 bits (95), Expect = 0.50,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 86/235 (36%), Gaps = 58/235 (24%)

Query: 445 KKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + ++V  NL LV      Y    +    + +++Q+G I L+KA E FD+ LG+KFS+YA+
Sbjct: 21  RNKIVLDNLSLVPYTINHYHLFIDGVHDYEEMLQDGYIALIKAVESFDYRLGFKFSSYAI 80

Query: 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE 561
             +                           + RT    +  +       E A+       
Sbjct: 81  KCI-------------------------LSLTRTRIDYNKDLSLNTPINEGAET------ 109

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLT 621
                                     + D IED++     D   +   RE    +  +L 
Sbjct: 110 -----------------------EIEMIDTIEDESIDIEKDIINENFYREIKKNLSFNLN 146

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676
             E ++++  +GI      + +++     +    +++I+ +A  K++  S  KKL
Sbjct: 147 DIELKIIKAIYGIDQ-EVRSYKDLSFILDLDINYLKKIKRQAENKIRKSSYFKKL 200


>gi|253580596|ref|ZP_04857860.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847967|gb|EES75933.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 1260

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 45/293 (15%), Positives = 103/293 (35%), Gaps = 18/293 (6%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL----REIIDLEACIGPESKGGF 199
           ++I A R  + A           +      L +G   L     ++  L+A        G 
Sbjct: 417 EQIAATRQDLNAKKESCNQGLAQIEQQEAGLAEGEAQLEGARSQLAALQAQYEQAQASGT 476

Query: 200 FHGTEGHSYQKREDSSQEK---ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
           +   +  +   +  + QE+   +   ++ +   I +A    +   S+V+S     +  E 
Sbjct: 477 YSEEDLAALAAQVSAYQEQVDSQAAQLEASRNQIAAARSELESGLSQVESGLAQLDAKEA 536

Query: 257 NLDEDEDDSAHTLSAMEDQLRP------KVMCALDEIAEVYRELRSLQDNAVNGQ-KDEK 309
            L++ E       + ++   +       K+  A  EI E   +L S Q+     + K   
Sbjct: 537 ELNQQEAAFPDAQAKIDAGWKEVKAQEKKLEPARKEIQEKEAQLESAQEQIDAAKAKLNS 596

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
           S  + +  + +L      +  N+ ++    +++ D  +++   E E+    Q     R  
Sbjct: 597 SQAQLEEKEAELASGEAQIRENEGKLASGEKEIADNEQKLRDGEKEISENEQKLKDSRKD 656

Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI 422
             +     E D        +  + + +  +A     I   ++EI  IS+   +
Sbjct: 657 IKKA----EKDLEEGKKEYEDGKKDAEKEIADGEKKIQDAQDEIDDISMPEWM 705


>gi|225677986|gb|EEH16270.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb03]
          Length = 1107

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 54/317 (17%), Positives = 99/317 (31%), Gaps = 31/317 (9%)

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
           +E  +    +GG   G     +   +     +  DD  +   D  +  KV +  +    +
Sbjct: 370 VEEDVEGSDEGGEDDGEIDFVHDGVDGVDGMQYEDDDPDRRSDAFALDKVLESRKETTMT 429

Query: 247 PPENAENDERNLDEDEDDSAHTLSA--------------MEDQLRPKVMCA---LDEIAE 289
           P  N       +  D +     L+               +E QL+ KV  A    DE+  
Sbjct: 430 PVGNGNGAGLGVGVDSEREKEMLAEARGQVSKLEKRVDELEAQLKEKVGEADRLRDEVRG 489

Query: 290 VYRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSL----SLNQSRIDLLVEQLYD 344
               L S +    + +KD ++   +   +K  L   +  L     LN S  D L  +  +
Sbjct: 490 NSDSLDSERQQWESMRKDWDRKREEWDKMKLHLEAKLLELQNLQHLNVSLQDQLEGERRE 549

Query: 345 ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
              R      ++ +   +    R+  LE   GRE+D        D   G WK+       
Sbjct: 550 YENREQDLRQQIQQALTAAAAARNTDLE--MGREIDRG-RGRETDIDSGVWKSRAEDSER 606

Query: 405 SILKIRNEIKSISVETGISISEFRHIVSMVR------KGECEASIAKKEMVEANLRLVIS 458
              +++ E++     T     E  + +  +R      +   E      +        V  
Sbjct: 607 ENQELKEELQKQREVTEQVRKEASNFLQEMRALSDRTQERWEREERLTQDFHRMEEEVKL 666

Query: 459 VAKKYTNRGLQFLDLIQ 475
              +Y     Q   L  
Sbjct: 667 WKNRYAKTKTQLQHLRS 683


>gi|229917375|ref|YP_002886021.1| RNA polymerase factor sigma-70 [Exiguobacterium sp. AT1b]
 gi|229468804|gb|ACQ70576.1| transcriptional regulator, LuxR family [Exiguobacterium sp. AT1b]
          Length = 213

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 22/107 (20%), Positives = 39/107 (36%), Gaps = 5/107 (4%)

Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
                 +S  E   +           S A + ++E     V + A+ Y   G    D++Q
Sbjct: 6   YEQFEKMSDEELVLLAR-----NEGDSDALEFLIERYRYFVRAKARSYFLIGADHEDIVQ 60

Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           EG IGL K    +       F ++A   + + +  +I   +    IP
Sbjct: 61  EGMIGLYKGVRDYKDERLASFKSFAEMCITRQMITAIKTATRQKHIP 107


>gi|121488767|emb|CAJ18268.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 91

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 1/92 (1%)

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +   ++  + +R+P   E+A  L M  + V   LKI    +S++ P    D + L D ++
Sbjct: 1   KAYSQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQ 60

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   + P     + +L     R L+ L PRE 
Sbjct: 61  NDGHL-PDHGLNKDSLTLEVERSLSVLAPREA 91


>gi|18311404|ref|NP_563338.1| RNA polymerase factor sigma-70 [Clostridium perfringens str. 13]
 gi|110798736|ref|YP_697111.1| RNA polymerase factor sigma-70 [Clostridium perfringens ATCC 13124]
 gi|168211256|ref|ZP_02636881.1| RNA polymerase sigma-H factor [Clostridium perfringens B str. ATCC
           3626]
 gi|18146088|dbj|BAB82128.1| RNA polymerase sigma-H factor [Clostridium perfringens str. 13]
 gi|110673383|gb|ABG82370.1| RNA polymerase sigma-H factor [Clostridium perfringens ATCC 13124]
 gi|170710792|gb|EDT22974.1| RNA polymerase sigma-H factor [Clostridium perfringens B str. ATCC
           3626]
          Length = 215

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 31/211 (14%), Positives = 68/211 (32%), Gaps = 10/211 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I +      ++  E   +           ++A++ ++    + V + +K Y   G    
Sbjct: 9   KINNYEEFKDLTDKEVVMLAK------NGDNMAQEYVISKYEQFVKAKSKSYFLIGADKE 62

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW----VKQAITRSIADQSCTIRIPVHMRD 527
           D+ QEG IGL KA   F+      F ++A       +  AI  +   +   +   + +  
Sbjct: 63  DIYQEGMIGLYKAIRDFNPDKFASFKSFAELCVTRQIITAIKTATRQKHIPLNTYISLSK 122

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I++       +   +    T  E        VE +   +      + LE      D   
Sbjct: 123 PIYEEESDRTLLDTVVGITITDPESLVIGKEEVEKIESAINSVLSELELEVLNSYLDGKS 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             +   D +  +         ++    + L 
Sbjct: 183 YQEIACDLDREAKSIDNALQRVKRKLEKCLN 213


>gi|310791225|gb|EFQ26754.1| myosin class II heavy chain [Glomerella graminicola M1.001]
          Length = 2101

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 86/651 (13%), Positives = 206/651 (31%), Gaps = 58/651 (8%)

Query: 12   DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
            +   E    S+  DF  +  + +++ A ++   T  +               E     LS
Sbjct: 1257 EEMREQFGASMRLDFRGEDLRNIVEEAVEKRMPTPSQ------QAATDRGNDEAVNNKLS 1310

Query: 72   NMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREM--G 129
             +   ++D ++    E ++   ++    +   +  +  +      T   V +  R +   
Sbjct: 1311 ELQAKIIDLEERLYVERNQTEKEVTDRRAAEDLAAELERKLQAAETRVEVEIMNRSIFDN 1370

Query: 130  SIELLS---REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
             I  L    R  E   A+    GR      L E     Q L+    E       LRE +D
Sbjct: 1371 RISDLEEKLRNQE-ERAQTELDGRRTAEDRLSE----VQRLLRIATE---EENRLREEVD 1422

Query: 187  LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
             +       +      T   +  +   ++  + + ++      ++   + +    ++  S
Sbjct: 1423 EQNHKIKALEQAASKHTMRMALMEASQTNATQAQTELTNKINIMDDDLRTANQQATRWRS 1482

Query: 247  PPENAENDERNLDEDEDDSAHTLSAMEDQL--RPKVMCALDEIAEVYR-ELRSLQDNAVN 303
              E A    R L  D + +      ++  L      +   + I E +R +  SLQ++   
Sbjct: 1483 EAERAVETARRLQIDYNGALDDNKELQKFLASLGAQLQENERIRESWRAKFVSLQEDMAQ 1542

Query: 304  GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRID-LLVEQLYDISKRIMHNEGELLRLAQS 362
              +D       +  +E+ +     +   + + +    E+L    +R+ + E + +R    
Sbjct: 1543 AARDITEENARRTKREQALLARQEVLDAKLQAEARTRERLETEIERLENGERQGMRAVNE 1602

Query: 363  YGIKRDVFLERHQGR-ELDPHWVSYAKDFPEGEWKNFVACEVDSILK----IRNEIKSIS 417
                    LE   G  + + H +  +    + E+K      ++ + +    ++ EI   +
Sbjct: 1603 CK-----RLETLLGEMKTENHKLHQSAMRYQSEFKEARESGINEVQRTRAAMQREIDEAN 1657

Query: 418  VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEG 477
                +   E    +  +R    +A++     VE        + +              E 
Sbjct: 1658 HHVNVVREELEEQIVKIRVEFDQANMD----VETAKAQSEMMME--------------EA 1699

Query: 478  NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
                 +A E+       +   +   W +Q             +   H+ +++        
Sbjct: 1700 QTSKAEAIEELKRKHQNELEDFQTRWERQLSN----AVEDGQKTEQHLLERLSLSTSKTE 1755

Query: 538  RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
             + +++       EIAK+ A       K   +     S+ T       +      +  + 
Sbjct: 1756 HLQDRVAHLEEKLEIAKEAARAAAQAAKSAGVEPPAQSVATFQPKAAATVAAAVPKAMDL 1815

Query: 598  VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
               +       LRE+   +   L  RE+R+  +   +         ++ K+
Sbjct: 1816 PEKISPQA---LRESIMVLQEQLQAREQRIEELESTVDKLDPEAPTKISKR 1863


>gi|213619184|ref|ZP_03373010.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 93

 Score = 41.4 bits (95), Expect = 0.51,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 30/78 (38%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
           + D+   E   E +L     + N     +     A +   D  ++YL E+G   LL+ E 
Sbjct: 16  EFDENGVEAFDEKALSEEEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEE 75

Query: 139 EIAIAKRIEAGRAMMMAS 156
           E+  A+R   G       
Sbjct: 76  EVYFARRALRGDVASRRR 93


>gi|325677915|ref|ZP_08157557.1| putative RNA polymerase sigma-H factor [Ruminococcus albus 8]
 gi|324110469|gb|EGC04643.1| putative RNA polymerase sigma-H factor [Ruminococcus albus 8]
          Length = 194

 Score = 41.4 bits (95), Expect = 0.52,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 1/90 (1%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
            +V +    +   +      V     +   +A K   R     DL+QEG + L+KA   +
Sbjct: 16  ELVRLAVDDKAALTALLLRYVSLTEYIAAGLAPK-AGREQMIKDLVQEGMMALLKAVNSY 74

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCT 518
               G  F+TYA   ++ ++   I   S  
Sbjct: 75  RPDRGAGFATYAGVCIRHSMLSYIMHDSRY 104


>gi|261417590|ref|YP_003251272.1| RNA polymerase factor sigma-70 [Geobacillus sp. Y412MC61]
 gi|319765248|ref|YP_004130749.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y412MC52]
 gi|261374047|gb|ACX76790.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y412MC61]
 gi|317110114|gb|ADU92606.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y412MC52]
          Length = 238

 Score = 41.4 bits (95), Expect = 0.53,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 79/251 (31%), Gaps = 61/251 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A   ++      V + A+ Y   G    D++QEG IGL KA   F   
Sbjct: 31  RLVALVHEGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGD 90

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F  +A   + + +  +I   +    IP++                           
Sbjct: 91  KLSSFKAFAELCITRQMITAIKTATRQKHIPLN--------------------------- 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLR 610
                                 +SL+ PI D++    L D +       P    +     
Sbjct: 124 --------------------SYVSLDKPIYDDESDRTLMDVLSGTQVTDPEQLIVNREEV 163

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     +A L    ER +   +  G +     EE+ +        ++ I   A++++K  
Sbjct: 164 DDIELKMAELLSDLERKVLALYLDGRSYQEISEELNR-------HVKSI-DNALQRVK-- 213

Query: 671 SRSKKLRSFLD 681
              +KL  +L+
Sbjct: 214 ---RKLEKYLE 221


>gi|295705913|ref|YP_003598988.1| RNA polymerase sigma-H factor [Bacillus megaterium DSM 319]
 gi|294803572|gb|ADF40638.1| RNA polymerase sigma-H factor [Bacillus megaterium DSM 319]
          Length = 216

 Score = 41.4 bits (95), Expect = 0.54,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 37/90 (41%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V         + + ++     LV   A+KY   G +  D++QEG IGL KA   F+   
Sbjct: 21  LVEMVHSGDEKSLEYLINKYQNLVRGKARKYFLIGAEKEDIVQEGMIGLYKAIRDFNEDK 80

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  +I   +     P
Sbjct: 81  LTSFKGFAELCITRQIITAIKTATRQKHGP 110


>gi|121488731|emb|CAJ18249.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 91

 Score = 41.4 bits (95), Expect = 0.55,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
           +   ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D ++
Sbjct: 1   KAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQ 60

Query: 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREE 625
           +   + P  +  + +L     R L+ L PRE 
Sbjct: 61  NDGHM-PDHTLNRDSLTLEVERSLSVLAPREA 91


>gi|210610578|ref|ZP_03288504.1| hypothetical protein CLONEX_00694 [Clostridium nexile DSM 1787]
 gi|210152437|gb|EEA83443.1| hypothetical protein CLONEX_00694 [Clostridium nexile DSM 1787]
          Length = 211

 Score = 41.4 bits (95), Expect = 0.55,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +ET   +L  LT R++ V+   F        +  E+ ++  V+   + +I  +AI +L+ 
Sbjct: 147 KETMRELLGLLTDRQKEVIVQYFW----EQKSQSEIAEKLGVSHAAVSKILTRAINRLRK 202


>gi|226314708|ref|YP_002774604.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
 gi|226097658|dbj|BAH46100.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
          Length = 218

 Score = 41.4 bits (95), Expect = 0.56,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 40/96 (41%), Gaps = 4/96 (4%)

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            I      HLGD ++ +      +  +    RE     + SL P+  +V+ + +      
Sbjct: 124 NIFPTMDDHLGDLMDRQANNQVEEEILNRVKREEIVTYIQSLAPKYRQVILLHY----YE 179

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           D ++ EV     V++E +R    +A ++LK     +
Sbjct: 180 DLSIAEVADILSVSQEVVRTRLHRARKQLKETMSKE 215


>gi|171676131|ref|XP_001903019.1| hypothetical protein [Podospora anserina S mat+]
 gi|170936131|emb|CAP60791.1| unnamed protein product [Podospora anserina S mat+]
          Length = 1919

 Score = 41.4 bits (95), Expect = 0.56,   Method: Composition-based stats.
 Identities = 35/239 (14%), Positives = 81/239 (33%), Gaps = 13/239 (5%)

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E     K + +  E E +  Q+    ++ +    KD+   +++        ++   E
Sbjct: 212 EREEELKESKADRARLELEAEGFQQHIKSLDESESRYKDENWNLETQIHELMASQKEAAE 271

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            E      L+A++ + +      L+E+ +   +       A+   + E  + +   +   
Sbjct: 272 REKKLTQALAALQSE-KNATQRELEEVKDSLAKQEEKHSAAIRNLEIELGTSRRSAVS-- 328

Query: 321 LVKLVGSLSLN-QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI---KRDVFLERHQG 376
                 S  L  Q R+D L  Q  +++K      G +L    + G+    R+   +R+ G
Sbjct: 329 ----FESERLTLQKRVDELTSQNQELAKAFSAQRGRMLERESTRGVSDEDRNSGSDRNTG 384

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
            E  P                       S+   +  I+++        +E   +  M++
Sbjct: 385 PEQSP--PPSPLKMTPRHSGLETETLKTSLGHAQRTIQTLRTNIHREKTEKLELKRMLQ 441


>gi|220932485|ref|YP_002509393.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halothermothrix
           orenii H 168]
 gi|219993795|gb|ACL70398.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halothermothrix
           orenii H 168]
          Length = 207

 Score = 41.4 bits (95), Expect = 0.57,   Method: Composition-based stats.
 Identities = 25/89 (28%), Positives = 45/89 (50%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +R+ +     A + ++ +N+ +V + AK +  +GL   D+IQEG +GL KA   F +  G
Sbjct: 11  IRQAQNRNRRAIEYLINSNMDIVYAKAKYFFIKGLDKDDVIQEGMVGLFKAIRDFKFEKG 70

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   V + +  +I   +    IP
Sbjct: 71  ASFRGFAQLCVHRQLVSAIKRANRQKHIP 99


>gi|256752506|ref|ZP_05493363.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256748641|gb|EEU61688.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 214

 Score = 41.4 bits (95), Expect = 0.57,   Method: Composition-based stats.
 Identities = 27/98 (27%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +V   +K      IA + ++E     V + A+ Y   G    D+IQEG IGL KA
Sbjct: 16  MEEEEVVFRAQK---GDEIALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 73  IRDYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIP 110


>gi|149278197|ref|ZP_01884335.1| hypothetical protein PBAL39_11587 [Pedobacter sp. BAL39]
 gi|149230963|gb|EDM36344.1| hypothetical protein PBAL39_11587 [Pedobacter sp. BAL39]
          Length = 1110

 Score = 41.4 bits (95), Expect = 0.58,   Method: Composition-based stats.
 Identities = 43/324 (13%), Positives = 104/324 (32%), Gaps = 19/324 (5%)

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR----EIIDLEACIGPESK 196
            +AK+++ G   +   + ++      +     +L  G TLL        D +       K
Sbjct: 499 EVAKKLDEGSQTLKQQMAKAIKLAGTVEKESKKL--GETLLDKKQLTFDDKKQVEQLLDK 556

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                       Q  +  + +K  ++    E   +        +    D      E  ++
Sbjct: 557 RKQLEAAVKEIQQLNQQQTSDKAENNTLTEELKEKQRQIDELFNHVLDDKTKALLEKLQQ 616

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
            +D++  +  H   +        +   LD I E+Y++L   Q+   N  + ++ + K + 
Sbjct: 617 MMDQNNKEQTHDELSKMQVDNKSLKKELDRILELYKQLEYEQNLQQNIDQLKELAKKQEA 676

Query: 317 LKEKLVKL----------VGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIK 366
           L +K                 L   Q       EQ+    +++     +L      + + 
Sbjct: 677 LSKKSTAAEQKTADRNAPKEELKKQQRENAAEFEQIRKELQQLKEKNEQLEH-PNDFSMP 735

Query: 367 RDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG--ISI 424
                +    +E     +         E +   A +++ + K   E++  S +    +++
Sbjct: 736 EKESADIKSQQEQSEESLEKNNLQKAAEHQKKAAGQLEQMAKKMEEMQQQSEQMENNLNV 795

Query: 425 SEFRHIVSMVRKGECEASIAKKEM 448
            E R ++  + K   E       +
Sbjct: 796 QELRQLLENLLKTSFEQEKVMLNL 819


>gi|290996993|ref|XP_002681066.1| predicted protein [Naegleria gruberi]
 gi|284094689|gb|EFC48322.1| predicted protein [Naegleria gruberi]
          Length = 1490

 Score = 41.4 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 58/515 (11%), Positives = 173/515 (33%), Gaps = 25/515 (4%)

Query: 161  PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
                ++    ++ +N  +  LR+I+++E+      +       E       E +    + 
Sbjct: 595  DGILESYKEEKENVNLESEELRQILNIESLTRKNFQKNIERLEEELVKTDEERNHLRSKV 654

Query: 221  DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ---LR 277
             ++ E   ++        ++ +      E   + +  L+E+ + S   ++ +  +   L 
Sbjct: 655  MEMSEKIQELSEQNMKLNENCTLSKVDFEKLSDQKAALEEEMEKSRKYIAQLSKENTKLN 714

Query: 278  PKVMCALDE----IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQS 333
             +V+   D+    +A+   E   +++N +  ++    +   K L++++  L   + L   
Sbjct: 715  EQVVNGRDKYISTVAKNQIEALQIENNELKLKQQGNETKAAKELQQQVESLKNEIKLKDV 774

Query: 334  RIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEG 393
                L++QL ++ +R  +  GEL +       K+++F +  +  E     V       E 
Sbjct: 775  SFSELLDQLKEMKQRNNNLSGELEK-------KQELFDQTIKENEDLRVEVEGLSSSVEA 827

Query: 394  EWKNFVACE--VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            +          +D + K+  E++ +         + + + S + + +  A     ++VE 
Sbjct: 828  KESEVEEMYQQIDQLPKLNYELQRLDRTVQQLSQQNQELQSRLEEYQSVARNEHSKLVEE 887

Query: 452  NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
                     KK +N   +     +     +++   K         +  +    +    + 
Sbjct: 888  -RNEFEQALKKLSNELEREKKEKERLREEVIQLNSKVSSSNSSNQTEISK---RDETIKM 943

Query: 512  IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571
            + +              I+ +         +  R  +         + +E   K ++   
Sbjct: 944  LKND--LELSKRSAEKTINDLKNNIGHDLEERTRMSSEIHAVSAKKLELEVDLKKIQSQF 1001

Query: 572  EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMR 631
              +  E     +    L D + +   ++   +  ++ ++   + +  +L  ++++     
Sbjct: 1002 TLLKKENEDKSKQLKTLSDEVVN---LNLDKNKSESEMKNQISTLKENLNEQQKQSELTI 1058

Query: 632  FGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
            + +          V         R  Q+E     K
Sbjct: 1059 YQLREENKSLSIRVNSLKETNNTRSSQLEEVLFAK 1093


>gi|189529448|ref|XP_001921312.1| PREDICTED: trafficking kinesin-binding protein 1 [Danio rerio]
          Length = 939

 Score = 41.4 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 84/233 (36%), Gaps = 12/233 (5%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDE----LNDGTTLLREIIDLE 188
           L  +E ++ +A RI         SL E     +  +    E    L     +  E++   
Sbjct: 90  LEEKERDLELAARIGQSLLKKNKSLTERNTFLEEQLEHIREEVSQLRHDLLMKDELLQFY 149

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                ES G     T  H              D +Q+   D+E    V + + + +++  
Sbjct: 150 TSAAEESDGESASTTPIHRNDTSFTVPNYLPLDSLQKKLKDLEEENIVLRSEANHLETET 209

Query: 249 ENAENDERNLDED----EDDSAHTLSAMEDQLRPKVMCA---LDEIAEVYRELRSLQDNA 301
            + E  E+ L  D      D+   +S + ++L  K   A    +EI  +  ++  LQ  A
Sbjct: 210 ISYEEKEQQLVNDCVKELRDANIQISTIAEELAKKTEDASRQQEEITHLLSQIVDLQKKA 269

Query: 302 VN-GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            +   ++E+ +      K+    L   L   + +    +E L++  + + +  
Sbjct: 270 KSYALENEELTQHLGAAKDAQRALTAELRELEDKYAECMEMLHEAQEELKNFR 322


>gi|118094499|ref|XP_422397.2| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 1101

 Score = 41.4 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 40/285 (14%), Positives = 102/285 (35%), Gaps = 26/285 (9%)

Query: 139  EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            ++ +++ +      M     +S    Q L++  ++  +        + +++    E    
Sbjct: 805  QLQLSELMNKHAKEMRDLESDSN---QKLLMENEKYQE--------LQVDSQRMQEEYEK 853

Query: 199  FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
              H  +G   +  E+ +   E    +++        +  +D R ++ +  E  +  E + 
Sbjct: 854  QLHNLQGSKNRTVEELTDYYEEKLNEKSLL----LEEAEEDMRQQLQAHEEIKKQIEEDE 909

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD-EKSSVKCKVL 317
            D +  D          + +   +    EI  + + L SLQ        D E   ++ + L
Sbjct: 910  DREIQDIKIKYERWLIEEKESNLQLKGEIGVMNKRLNSLQKELKERNNDIEDMKLEQQNL 969

Query: 318  KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI-----MHNEGELLRLAQSYGIKRDVFLE 372
            +  +  L   +S+  + I+     + +  K I      + E E  +    + I  + F +
Sbjct: 970  QGIIKSLEKDISMLNTNIEKRTNTIQEKEKHIYDLKKKNQELEKFKFVLDHRI--EQFKK 1027

Query: 373  RHQGRELDPHWVSYAKDFPEGEWKNFVACEVD---SILKIRNEIK 414
            + + RE D   +       E E +           +I +++ ++K
Sbjct: 1028 QIESRENDIKIMQKQIHEMERELEQLHKENTQLKLNITQLQQKLK 1072


>gi|298253791|ref|ZP_06977380.1| hypothetical protein GV51_1079 [Gardnerella vaginalis 5-1]
 gi|297532127|gb|EFH71100.1| hypothetical protein GV51_1079 [Gardnerella vaginalis 5-1]
          Length = 159

 Score = 41.4 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 584 DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 643
           D SHL + +   +    + +       E      ++LT ++ +V+R+ F  G        
Sbjct: 76  DKSHLAEALSTTDDYGFITNDYGFEWSEEMEHAFSTLTDKQRQVIRLMFIEGYTQS---- 131

Query: 644 EVGKQFCVTRERIRQIEAKAIRKLKH 669
           E+     ++   +++   KA+ KL+ 
Sbjct: 132 EIASMLGISSAGVKKHLDKALEKLRK 157


>gi|110802727|ref|YP_699680.1| RNA polymerase factor sigma-70 [Clostridium perfringens SM101]
 gi|110683228|gb|ABG86598.1| RNA polymerase sigma-H factor [Clostridium perfringens SM101]
          Length = 215

 Score = 41.4 bits (95), Expect = 0.59,   Method: Composition-based stats.
 Identities = 31/211 (14%), Positives = 68/211 (32%), Gaps = 10/211 (4%)

Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
           +I +      ++  E   +           ++A++ ++    + V + +K Y   G    
Sbjct: 9   KINNYEEFKDLTDKEVVMLAK------NGDNMAQEYVISKYEQFVKAKSKSYFLIGADKE 62

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW----VKQAITRSIADQSCTIRIPVHMRD 527
           D+ QEG IGL KA   F+      F ++A       +  AI  +   +   +   + +  
Sbjct: 63  DIYQEGMIGLYKAIRDFNPDKFASFRSFAELCVTRQIITAIKTATRQKHIPLNTYISLSK 122

Query: 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587
            I++       +   +    T  E        VE +   +      + LE      D   
Sbjct: 123 PIYEEESDRTLLDTVVGITITDPESLIIGKEEVEKIESAINSVLSELELEVLNSYLDGKS 182

Query: 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLA 618
             +   D +  +         ++    + L 
Sbjct: 183 YQEIACDLDREAKSIDNALQRVKRKLEKCLN 213


>gi|126332018|ref|XP_001365741.1| PREDICTED: similar to dynactin 1 p150 [Monodelphis domestica]
          Length = 1285

 Score = 41.4 bits (95), Expect = 0.60,   Method: Composition-based stats.
 Identities = 40/304 (13%), Positives = 110/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 251 ELEKHKIQLEQVQEWKSKMQEQQADLQRKLKEARKEAKDALEAKERYMEEMADTADAIEM 310

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  L+E   D     + +E++          +  L+E 
Sbjct: 311 ATLDKEMAEERAESLQQEVEALKERLEELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 370

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK +V+ + ++++  +L   L   +  ID L
Sbjct: 371 NARLKDALVRMRDLSASEKQEHIKLQKLMEKKNVELEAVRQQRERLQEELGQAERTIDEL 430

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 431 KEQVDAALGAEEMVETLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 489

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 490 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 545

Query: 456 VISV 459
           V   
Sbjct: 546 VERQ 549


>gi|167036784|ref|YP_001664362.1| RNA polymerase factor sigma-70 [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167039504|ref|YP_001662489.1| RNA polymerase factor sigma-70 [Thermoanaerobacter sp. X514]
 gi|300915246|ref|ZP_07132561.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X561]
 gi|307725170|ref|YP_003904921.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermoanaerobacter
           sp. X513]
 gi|320115206|ref|YP_004185365.1| RNA polymerase sigma-H factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166853744|gb|ABY92153.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X514]
 gi|166855618|gb|ABY94026.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|300888970|gb|EFK84117.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X561]
 gi|307582231|gb|ADN55630.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X513]
 gi|319928297|gb|ADV78982.1| RNA polymerase sigma-H factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 214

 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 27/98 (27%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +V   +K      IA + ++E     V + A+ Y   G    D+IQEG IGL KA
Sbjct: 16  MEEEEVVFRAQK---GDEIALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 73  IRDYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIP 110


>gi|313895843|ref|ZP_07829397.1| RNA polymerase sigma-H factor [Selenomonas sp. oral taxon 137 str.
           F0430]
 gi|312975268|gb|EFR40729.1| RNA polymerase sigma-H factor [Selenomonas sp. oral taxon 137 str.
           F0430]
          Length = 285

 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 32/138 (23%), Positives = 50/138 (36%), Gaps = 5/138 (3%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
               D  +       A E++   +  +E+   S+  G +  E      +V     E + A
Sbjct: 28  KSMLDDEQSAPDELEAGEIEEADEPESEMPENSIYEGYTDEEL-----LVHIRTHEGNEA 82

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
              +V      V S A+ Y   G    D++QEG IG  KA   F       F  +A   V
Sbjct: 83  LDYLVNKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRDFREDKLSSFRAFAELCV 142

Query: 505 KQAITRSIADQSCTIRIP 522
            + I  +I   +    IP
Sbjct: 143 TRQIITAIKTATRQKHIP 160


>gi|184154740|ref|YP_001843080.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum IFO 3956]
 gi|227514007|ref|ZP_03944056.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum ATCC 14931]
 gi|260663231|ref|ZP_05864123.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum 28-3-CHN]
 gi|183226084|dbj|BAG26600.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum IFO 3956]
 gi|227087651|gb|EEI22963.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum ATCC 14931]
 gi|260552423|gb|EEX25474.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum 28-3-CHN]
          Length = 192

 Score = 41.0 bits (94), Expect = 0.61,   Method: Composition-based stats.
 Identities = 26/197 (13%), Positives = 59/197 (29%), Gaps = 18/197 (9%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E R  ++++       +    E+ +    LV  +   Y+   L   D  QE  + L +A
Sbjct: 8   DEERVELALINGATKGDNETLGELFDRYQPLVRRLWLNYSIANLDRQDWQQEAFLVLDRA 67

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
              +      +F  Y    +   +                +  +     R   ++   + 
Sbjct: 68  VHNYRQEQRTRFCWYYRQLLTNRLRD--------------LYRQTRAEKRIPAQLVQDLN 113

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDS 603
            E     I   +  P + V   +        L     +E  ++L +    D   ++ +  
Sbjct: 114 AENDVTMIQDPVLTPEQIV---MWRASYQEFLAQCSTNEREAYLLESEGRDLTEIAQVMG 170

Query: 604 AIQANLRETTTRVLASL 620
             +  ++    R  A L
Sbjct: 171 CSERKVKNALHRARAKL 187


>gi|68492200|ref|XP_710120.1| likely vesicular transport factor Uso1p [Candida albicans SC5314]
 gi|46431250|gb|EAK90848.1| likely vesicular transport factor Uso1p [Candida albicans SC5314]
          Length = 1880

 Score = 41.0 bits (94), Expect = 0.62,   Method: Composition-based stats.
 Identities = 56/426 (13%), Positives = 156/426 (36%), Gaps = 32/426 (7%)

Query: 24   FDFSDDSWKKMI-KLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD 82
             + S++ +K+ I +L+++   +T          ++ +++Q+E+ +        +++D   
Sbjct: 909  LNKSNNEFKQKINELSKKIESLT--------EDNKFNAKQLEEKLRDTEENNEHLMD--K 958

Query: 83   LEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAI 142
            L     + + L  A S S       K +     S  D               + E E+  
Sbjct: 959  LRSASVAYNDLKKAKSESEEETVKAKEELETLTSKID---------------NLEKELKE 1003

Query: 143  AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
             +  +      + ++  +  T +      DEL       +EI    + +  + +      
Sbjct: 1004 QQSKKNELEGQLQNI--TDSTNEKFKELEDELKSIKKSNKEISSQNSELIQKLEKTEKDL 1061

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                    +  +  +   D++      ++S  K +++  S       +   + + L E+ 
Sbjct: 1062 QAKDEEIDKLKAETKSNIDNLNSEISSLQSKLKEAEESHSSTKDEHSSLSENLKKLKEEY 1121

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
            +++  ++ A       +   A DEI    + +  LQ+   + ++  +   +   +K  L 
Sbjct: 1122 ENTKTSMIAKLSAKIEEHKKATDEIETKTKHITDLQE--EHAKQKSQFESERNDIKSNLD 1179

Query: 323  KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            +    LS N+ ++  L ++  +++ ++   E ++  L  S  I  +   +  +    D  
Sbjct: 1180 EANKELSDNREKLSNLEKEKTELNNKLKTQEEKISDLETSVAIS-EDKSKSLKHDIEDLK 1238

Query: 383  WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS-VETGISISEFRHIVSMVRKGECEA 441
                  +    E +  +  + + +  + ++ K +      ++ ++ + I  ++RK E   
Sbjct: 1239 REKIKLETTLKENEETMFEKKEQLQVVNDKCKELEACLKKLTETKEKEINDLIRKLEAAK 1298

Query: 442  SIAKKE 447
            S    E
Sbjct: 1299 SDHDTE 1304


>gi|167949415|ref|ZP_02536489.1| putative transcriptional regulator, Fis family protein [Endoriftia
           persephone 'Hot96_1+Hot96_2']
          Length = 72

 Score = 41.0 bits (94), Expect = 0.63,   Method: Composition-based stats.
 Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 365 IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
           + R  F+      E +P W+    D  +  +   +    D I + +  + ++  E 
Sbjct: 1   MPRKEFIASFPDNETNPDWLQQQLDAGKS-YSEPLQEYADDIARAQKRLITLKQEC 55


>gi|321476144|gb|EFX87105.1| myosin heavy chain isoform 2 [Daphnia pulex]
          Length = 1946

 Score = 41.0 bits (94), Expect = 0.64,   Method: Composition-based stats.
 Identities = 69/418 (16%), Positives = 141/418 (33%), Gaps = 38/418 (9%)

Query: 35   IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
            I   R+R  V  EEL A L   E + EQ E+ V         V    D   +E  E+  +
Sbjct: 1525 IDKQRKRLEVEKEELQAALEEAESALEQEENKVLRAQLELSQVRQEIDRRIQEKEEEFEN 1584

Query: 95   LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA-GRAMM 153
               +   +   +Q   ++  +   + +RM        +L S   E+ IA        A  
Sbjct: 1585 TRKNHQRAIDSMQASLEAEAKGKAEALRM------KKKLESDINELEIALDHANKANAEA 1638

Query: 154  MASLCESPLTFQALIIWRDELNDGTTLLRE---IIDLEACIGP----ESKGGFFHGTEGH 206
              S+     + +      +E       LRE   I +  A        ES+          
Sbjct: 1639 QKSIKRYQQSIKETQSALEEEQRNRDDLREQYGIAERRANALQGELEESRTLLEQADRAR 1698

Query: 207  SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
               + E +   ++  D+        +A +  + +   + +  ++  N+ +N +E    + 
Sbjct: 1699 RQAETELADAHEQLHDLTAQAASSSAAKRKMESELQTLHADLDDMINETKNSEEKAKKAM 1758

Query: 267  HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               + + D+LR +   A  +  E  R+   LQ   +  + DE  +   K  K+ + KL  
Sbjct: 1759 VDAARLADELRAEQEHAQAQ--EKQRKALELQVKELQVRLDESENNALKGGKKAIQKLEE 1816

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +   ++ +D    +  D  K +  +E  +  L       R                   
Sbjct: 1817 RVRGLETELDGEQRRHADAQKNLRKSERRIKELTFQSDEDRKN----------------- 1859

Query: 387  AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     ++ V      I   + +I+       +++++FR     + + +  A +A
Sbjct: 1860 -----HERMQDLVDKLQQKIKTYKRQIEEAEEIAALNLAKFRKAQQELEEADERAELA 1912


>gi|281348092|gb|EFB23676.1| hypothetical protein PANDA_015360 [Ailuropoda melanoleuca]
          Length = 1754

 Score = 41.0 bits (94), Expect = 0.64,   Method: Composition-based stats.
 Identities = 63/440 (14%), Positives = 137/440 (31%), Gaps = 56/440 (12%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTVDGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IEKLRKQVR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIKTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECE 440
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERL-TELHT 591

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE-----------GNIGLMKAAEKFD 489
                   V      V  V +K          L QE                  AAE   
Sbjct: 592 QKQKLARHVRDKEEEVDLVMQK-------VESLRQELRRTERAKKEVSIHTEAVAAEASK 644

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
                + S +    ++  +      Q         + +   ++ +    +  K       
Sbjct: 645 DRKLREQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEITKLKTDLEKKSIFY--E 701

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQAN 608
           EE++K+  +    + K LK        +    +++   L D +E ++          +  
Sbjct: 702 EELSKREGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENE 760

Query: 609 LRETTTRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            ++   R    LT        E   L   +      +  LEE  K     +E +   EA+
Sbjct: 761 FKQQYEREKVLLTEENKKLTSELDKLTTLYENLSIRNQHLEEEVKDLADKKESVAHWEAQ 820

Query: 663 AIRKLKHPSRSKKLRSFLDG 682
               ++  S  K  R +L  
Sbjct: 821 ITEIIQWVSDEKDARGYLQA 840


>gi|321476143|gb|EFX87104.1| myosin heavy chain isoform 1 [Daphnia pulex]
          Length = 1946

 Score = 41.0 bits (94), Expect = 0.65,   Method: Composition-based stats.
 Identities = 69/418 (16%), Positives = 141/418 (33%), Gaps = 38/418 (9%)

Query: 35   IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
            I   R+R  V  EEL A L   E + EQ E+ V         V    D   +E  E+  +
Sbjct: 1525 IDKQRKRLEVEKEELQAALEEAESALEQEENKVLRAQLELSQVRQEIDRRIQEKEEEFEN 1584

Query: 95   LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA-GRAMM 153
               +   +   +Q   ++  +   + +RM        +L S   E+ IA        A  
Sbjct: 1585 TRKNHQRAIDSMQASLEAEAKGKAEALRM------KKKLESDINELEIALDHANKANAEA 1638

Query: 154  MASLCESPLTFQALIIWRDELNDGTTLLRE---IIDLEACIGP----ESKGGFFHGTEGH 206
              S+     + +      +E       LRE   I +  A        ES+          
Sbjct: 1639 QKSIKRYQQSIKETQSALEEEQRNRDDLREQYGIAERRANALQGELEESRTLLEQADRAR 1698

Query: 207  SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
               + E +   ++  D+        +A +  + +   + +  ++  N+ +N +E    + 
Sbjct: 1699 RQAETELADAHEQLHDLTAQAASSSAAKRKMESELQTLHADLDDMINETKNSEEKAKKAM 1758

Query: 267  HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               + + D+LR +   A  +  E  R+   LQ   +  + DE  +   K  K+ + KL  
Sbjct: 1759 VDAARLADELRAEQEHAQAQ--EKQRKALELQVKELQVRLDESENNALKGGKKAIQKLEE 1816

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +   ++ +D    +  D  K +  +E  +  L       R                   
Sbjct: 1817 RVRGLETELDGEQRRHADAQKNLRKSERRIKELTFQSDEDRKN----------------- 1859

Query: 387  AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     ++ V      I   + +I+       +++++FR     + + +  A +A
Sbjct: 1860 -----HERMQDLVDKLQQKIKTYKRQIEEAEEIAALNLAKFRKAQQELEEADERAELA 1912


>gi|284052359|ref|ZP_06382569.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Arthrospira platensis str. Paraca]
 gi|291567116|dbj|BAI89388.1| RNA polymerase ECF-type sigma factor [Arthrospira platensis
           NIES-39]
          Length = 282

 Score = 41.0 bits (94), Expect = 0.65,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 52/131 (39%), Gaps = 23/131 (17%)

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDK----------NAVSPLDSAIQANLRETT 613
           R  L      + L+        S   D IED           +  SP    ++  LR+  
Sbjct: 93  RAWLTRLTHNLCLDIHRERRRKSISIDNIEDSYIQAKEVILCSCESPESQILRHELRQFI 152

Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR- 672
             V+  L  R    LR+ F +  + + +  ++ ++  ++R+        A ++++     
Sbjct: 153 QSVVNQLPER----LRIPFILRYDRELSYPDIAEKLGISRD-------NAYKRIQQARDI 201

Query: 673 -SKKLRSFLDG 682
            ++K+RS+L G
Sbjct: 202 IAQKVRSYLSG 212


>gi|284033654|ref|YP_003383585.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283812947|gb|ADB34786.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 164

 Score = 41.0 bits (94), Expect = 0.65,   Method: Composition-based stats.
 Identities = 22/145 (15%), Positives = 52/145 (35%), Gaps = 10/145 (6%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
             R        + +        ++   P   VR++L  +   +   T       +   D 
Sbjct: 25  YQRAEDLAQIALMQAFRSWRKVQRADDPHTYVRRILVNSYLSM---TRRRSFTEAPAADL 81

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             D+    P    + ++      R LA+L+ RE  VL +R+   ++       +     +
Sbjct: 82  DPDRTVPDPATDIVNSD---DLWRALATLSARERVVLVLRYYQDLDD----RTIADLLGI 134

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKL 676
               +R + ++A+  L+   +S ++
Sbjct: 135 KPSSVRSVASRALASLRKARQSHRV 159


>gi|73960807|ref|XP_851425.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 2 [Canis familiaris]
          Length = 1732

 Score = 41.0 bits (94), Expect = 0.65,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|326391114|ref|ZP_08212660.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325992813|gb|EGD51259.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 214

 Score = 41.0 bits (94), Expect = 0.66,   Method: Composition-based stats.
 Identities = 26/98 (26%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +V   +K      +A + ++E     V + A+ Y   G    D+IQEG IGL KA
Sbjct: 16  MEEEEVVFRAQK---GDEVALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 73  IRDYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIP 110


>gi|301780766|ref|XP_002925800.1| PREDICTED: serine/threonine-protein kinase MRCK alpha-like isoform
           1 [Ailuropoda melanoleuca]
          Length = 1719

 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 62/435 (14%), Positives = 145/435 (33%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTVDGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IEKLRKQVR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIKTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEITKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENLSIRNQHLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|317121288|ref|YP_004101291.1| sigma-70 region 4 domain protein [Thermaerobacter marianensis DSM
           12885]
 gi|315591268|gb|ADU50564.1| sigma-70 region 4 domain protein [Thermaerobacter marianensis DSM
           12885]
          Length = 1063

 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
           +L +    ++  L  RE  VL +R+G+     H L  +  ++  TR+ + 
Sbjct: 310 DLEDWLRELVEPLADREREVLALRYGLLGAEPHDLAAIAARWQTTRQWVS 359


>gi|225870575|ref|YP_002746522.1| DNA-binding protein [Streptococcus equi subsp. equi 4047]
 gi|213033092|emb|CAP20375.1| putative DNA-binding protein [Streptococcus equi subsp. equi]
 gi|225699979|emb|CAW93959.1| putative DNA-binding protein [Streptococcus equi subsp. equi 4047]
          Length = 133

 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
            N V          L E     L SL   E +++   +      D TL EV KQ      
Sbjct: 59  DNTVDVEKIIETKMLIEDLYYALDSLNDEERKLIEALYF----DDKTLTEVAKQRDTNPM 114

Query: 655 RIRQIEAKAIRKLKH 669
           +I ++  K + KL+ 
Sbjct: 115 KISRLRNKILEKLRK 129


>gi|116619510|ref|YP_821666.1| ECF subfamily RNA polymerase sigma-24 factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116222672|gb|ABJ81381.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 182

 Score = 41.0 bits (94), Expect = 0.67,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D   +    SP  + ++   RE     L  L+PRE + L     +    D   EEV + 
Sbjct: 99  IDEAPESQIESPEQTLLRGEHREYLEDGLRLLSPRERQAL----LLRDVEDMPAEEVARV 154

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSKK 675
              ++  +R   A A  KL+     +K
Sbjct: 155 LDCSKATVRSHIANARIKLRRYMERRK 181


>gi|309389949|gb|ADO77829.1| RNA polymerase, sigma 30 subunit, SigH [Halanaerobium praevalens
           DSM 2228]
          Length = 219

 Score = 41.0 bits (94), Expect = 0.68,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 6/108 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
           S+     +S  E   +V            A++ +++     V++ ++ Y   G    D++
Sbjct: 14  SLEEYQQMSDDELVELVHQ------GDMEAQETLIKRYKNFVLAKSRSYFLVGADREDIV 67

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           QEG IGL KA   +       F  +A   + + I  +I   +     P
Sbjct: 68  QEGMIGLYKAVRDYKIERLASFRAFAELCITRQIITAIKAATRQKHQP 115


>gi|242018837|ref|XP_002429877.1| Centromeric protein E, putative [Pediculus humanus corporis]
 gi|212514911|gb|EEB17139.1| Centromeric protein E, putative [Pediculus humanus corporis]
          Length = 2086

 Score = 41.0 bits (94), Expect = 0.68,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 95/246 (38%), Gaps = 12/246 (4%)

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
              F    +     +++  ++EKE  +V+    ++E   + ++ + +       N E +  
Sbjct: 1081 ENFDKLEKDKGQLEKDLIAKEKETTEVKNKLTEVEEKLRKAEKNLTINRKKVSNLEKNVE 1140

Query: 257  NLDEDEDDSAHTLSAMEDQL------RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             ++E ++       ++E ++         +   + E+ +  ++ +++  +  N  ++E+ 
Sbjct: 1141 EIEEIKNSQMKKCQSLESEILDLKNSNTFLKTKISELEDEIKKDKTIIKDLENSIREERE 1200

Query: 311  SVKCKVLK------EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
                + LK      ++++ L   LS    ++D L ++L    K     E  + +      
Sbjct: 1201 KATDECLKAGSLEKKEIMALRDDLSKKTKQLDELTQKLETSEKERKSLEENIKKTETKAT 1260

Query: 365  IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISI 424
              +++F  +    E D +      +  +             +  ++++IK++   T ++ 
Sbjct: 1261 KDKEIFESKISSLEKDLNAEKRNGERIKITHDKEEKNREMELSALKSKIKTLEQSTNVTN 1320

Query: 425  SEFRHI 430
             +   +
Sbjct: 1321 KKMADL 1326


>gi|47230389|emb|CAF99582.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1905

 Score = 41.0 bits (94), Expect = 0.68,   Method: Composition-based stats.
 Identities = 57/435 (13%), Positives = 146/435 (33%), Gaps = 34/435 (7%)

Query: 233  AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            A   S+ +   VD   +  +  E+N + ++  S   +   + +   K +  L E+ +   
Sbjct: 1172 ATAGSQSEGKSVDFAAQVKDLQEQNAEMEKKMSELKIQIQKKEADRKTVTGLKELQQELE 1231

Query: 293  ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
               S Q+     +K  K+  + +   E+L ++       Q+ I  L +QL ++   +   
Sbjct: 1232 R--STQECKRLREKLAKTETELQTTVEELFQVKIEREQYQTEIRDLQDQLSEMHDELDTA 1289

Query: 353  EGELLRLAQSYGI---------------------KRDVFLERHQGRELDPHWVSYAKDFP 391
            +  +    ++  +                     +    L   + +E             
Sbjct: 1290 KKSVADGERTAMMAVTPSPLFDFSVWADMMHLKLELQEILLAKEEQEDVLKRRERELTAL 1349

Query: 392  EGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            +G  K  VA     + K++ + +       +S+ E +   + V + + E   AK   VE 
Sbjct: 1350 KGALKEEVAAHDQEVDKLKEQYEKEIGRLQLSLEEAKQSSAAVVREKAEVEAAKGA-VEG 1408

Query: 452  NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEK--------FDWCLGYKFSTYAMWW 503
                +    ++   R  +  + + + N  + +A  +               K    ++  
Sbjct: 1409 QAGRLTLETERLRRRAQELENEVAKLNRIIDEAKLQESRLGDRVGRLEKEKKQLEESLAE 1468

Query: 504  VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
            +++                  ++  ++++  T + +   ++ E + +E  K +   +E  
Sbjct: 1469 IREQEEEMSRANRALTVRLEDVQRNLNRLSVTHKELEEMLQEERSQKEQFKNMKNNIEDE 1528

Query: 564  RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
            R++L  T E   L+  + D   +     +E +  +       +  L E    +       
Sbjct: 1529 RRLLDRTVEK--LQREMNDIVDASQSSTLELQEQIDLYKEKNRRELTELQRLLKERGQEL 1586

Query: 624  EERVLRMRFGIGMNT 638
            E++ L  +      T
Sbjct: 1587 EKQQLTSKSLQEEGT 1601


>gi|307266358|ref|ZP_07547896.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306918594|gb|EFN48830.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 214

 Score = 41.0 bits (94), Expect = 0.68,   Method: Composition-based stats.
 Identities = 26/98 (26%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +V   +K      +A + ++E     V + A+ Y   G    D+IQEG IGL KA
Sbjct: 16  MEEEEVVFRAQK---GDEVALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 73  IRDYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIP 110


>gi|294498777|ref|YP_003562477.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium QM B1551]
 gi|294348714|gb|ADE69043.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium QM B1551]
          Length = 188

 Score = 41.0 bits (94), Expect = 0.69,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           +  + DFIED +         +   ++     ++ L+  ++++++  +  G+      EE
Sbjct: 97  SEEIFDFIEDDHPQIDEQLQWKEE-QQRVRHAVSKLSEDQKKIIQSVYFKGLTQQKVAEE 155

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
                   + R+R     A+RKLK
Sbjct: 156 QQIPLGTVKGRVRL----ALRKLK 175


>gi|301777127|ref|XP_002923979.1| PREDICTED: hypothetical protein LOC100470372 [Ailuropoda
           melanoleuca]
          Length = 648

 Score = 41.0 bits (94), Expect = 0.69,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 83/228 (36%), Gaps = 14/228 (6%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           EG    A+R+   +   +  +       + L   R EL          I++E  +     
Sbjct: 105 EGVRGAARRLREQQLEALTRVALMEQRVKELQRQRKELR---------IEMEVEVALLRG 155

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                       +++      ++ D  Q +    E   +    +R +V+   +  +  + 
Sbjct: 156 ELAGERVAARREEEQLRELLGQQGDTEQGSRKQREQEQRQLSQERDRVEGLRQRLQEAQG 215

Query: 257 NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCK 315
            LD   +D    L     ++R      LD     Y +L   Q +     +++++ S   +
Sbjct: 216 QLDSQPEDQRERLLQGVQEMR----EQLDVAQRAYEDLEFQQLEQESRREEEDRDSPGAQ 271

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            L  K+ +L  S++ ++ RI +L EQL  + +++      L R  +  
Sbjct: 272 ALDPKVRELQASVAQHRRRIQVLEEQLKSLGEQMAAESRGLSRKKEEA 319


>gi|289065413|gb|ADC80888.1| RNA polymerase sigma factor [Pseudomonas sp. KAAC10582]
 gi|289065419|gb|ADC80891.1| RNA polymerase sigma factor [Pseudomonas sp. ICMP3272]
          Length = 123

 Score = 41.0 bits (94), Expect = 0.69,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 41/124 (33%), Gaps = 3/124 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAVKAEGTDDDEEESADASDDEDEVESGPDPVIAQQRFGAVS 62

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 63  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 119

Query: 352 NEGE 355
            E  
Sbjct: 120 QERA 123


>gi|73960797|ref|XP_863599.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 6 [Canis familiaris]
          Length = 1728

 Score = 41.0 bits (94), Expect = 0.69,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|67524859|ref|XP_660491.1| hypothetical protein AN2887.2 [Aspergillus nidulans FGSC A4]
 gi|73622225|sp|Q5B993|ATG11_EMENI RecName: Full=Autophagy-related protein 11
 gi|40744282|gb|EAA63458.1| hypothetical protein AN2887.2 [Aspergillus nidulans FGSC A4]
          Length = 1371

 Score = 41.0 bits (94), Expect = 0.71,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 83/190 (43%), Gaps = 7/190 (3%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            EI+D+   I   S+G   H         +  +  +   + +++ E + E+A   S+  +
Sbjct: 750 DEIVDIIKAIDVLSEGLTIHAKTAEDNAMKAAAENKTLIEQLEKMESNYENAKSASEQYQ 809

Query: 242 SKVDSPPENAENDE---RNLDEDEDDSAHTLSAMEDQL---RPKVMCALDEIAEVYRELR 295
           +++    E  E ++   + ++ + +D   +L  +E +L           + +AE  ++L 
Sbjct: 810 TQLTQAREEVEQEQSKVKAIESELNDERASLLELESKLAAGETGAGALREHVAEEEQKLN 869

Query: 296 SL-QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
           ++ Q  A    +  +S  +    +++   L  S     +RID+   +L ++S+++     
Sbjct: 870 NMSQQLAETEARARRSEEEALQWRKRAEALSESDKQVAARIDIRTARLEELSRQLFGQVE 929

Query: 355 ELLRLAQSYG 364
           +L R+ +  G
Sbjct: 930 KLERMLEQLG 939


>gi|327305093|ref|XP_003237238.1| hypothetical protein TERG_01959 [Trichophyton rubrum CBS 118892]
 gi|326460236|gb|EGD85689.1| hypothetical protein TERG_01959 [Trichophyton rubrum CBS 118892]
          Length = 1379

 Score = 41.0 bits (94), Expect = 0.71,   Method: Composition-based stats.
 Identities = 43/292 (14%), Positives = 102/292 (34%), Gaps = 13/292 (4%)

Query: 80   GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLR-EMGSIELLSR 136
             D L + + + D L  A     S V   +++  A R     D VR+ +  E    + L+ 
Sbjct: 749  EDTLVETQKARDELLRARDELESEVDHIQKEIEAAREAHERDVVRLRMEAEKSEEKALAE 808

Query: 137  EGEI--AIAKRIEAGRAMMMASL--CESPLTFQALIIWRDELNDGTTLLREIIDLEACIG 192
            + E    + + I+     + A             L   ++EL+     L+  ++      
Sbjct: 809  QKERLEDLFQEIKNEDDRIAAEHLKAREDELLGQLAAKQEELDANEVALKSNVEELKITQ 868

Query: 193  PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
             E         E  S  +         ++D++  + + ES     +  R  ++    + E
Sbjct: 869  EELDEKKAELAEKFSELEALKEGLANTKNDLEAKQLECESRQNELELTRKDLEETKRHHE 928

Query: 253  NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
             +   L +  D   + +  ++++L   V+   ++  E +++ R   +  ++ + +E    
Sbjct: 929  EELSALRDALDIQTNNVREIKERLANMVLEHRNQ-EETWQKAREGYEAQLSEKAEELKLS 987

Query: 313  KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
              +    +   L     L       +VE++      +  +   L +   S G
Sbjct: 988  NEEKEVLEREGLAKEERL-----QSIVEEMRQTHNNLNKDRERLKKTLHSLG 1034


>gi|328875873|gb|EGG24237.1| myosin-5b [Dictyostelium fasciculatum]
          Length = 2624

 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 64/366 (17%), Positives = 138/366 (37%), Gaps = 23/366 (6%)

Query: 62   QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            +ME  +  + +   +V+   +L + +   +SL+ ++++ +  + + +++    R T    
Sbjct: 1387 KMEKQLEQIQSTHDHVL--LELSEYKSKSESLETSNTSMSDELTVLRKELEETRQT---- 1440

Query: 122  RMYLRE-MGSIELLSRE--GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGT 178
               L E +GS++ L RE        K +    A +     E+  T Q L     EL   T
Sbjct: 1441 ---LSEHVGSLKKLEREKLDSTETIKSVSEELATVKQQYEETSTTKQQLEQSLKELKSST 1497

Query: 179  TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238
            T    I DLE+ +G ++        E  S +K+ +  +E+       T G +    + S 
Sbjct: 1498 T--DHIKDLESRLGEKTMDCGVATGEVASLRKQVERLEEETA-----TVGHMRDTIQRSF 1550

Query: 239  DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            D+    ++   +     R +  DE D    + A+++    ++   L+ ++ +   +   Q
Sbjct: 1551 DELVGENASLRDEMERTRGVAGDEYD---RVVAIKESTEKELHSTLENVSTLQATVERHQ 1607

Query: 299  DNAVNGQKDEKSSVK-CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
                      KS+ +  K    +LV     L L  S+ +    QL +  K+I      + 
Sbjct: 1608 QQHAADTVSWKSTEEGMKQQINQLVNGGDELRLKLSQKEQEHVQLVEKYKKIKGKLENVE 1667

Query: 358  RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            + ++      +      Q  E +   ++      + E +           KI    +++ 
Sbjct: 1668 QDSRVASTDNEKIKMARQLLEDEKGLLNQQITSAKLEKEKLEVTNQHQKEKITQIKQTLE 1727

Query: 418  VETGIS 423
              T  S
Sbjct: 1728 QSTLES 1733



 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 36/269 (13%), Positives = 98/269 (36%), Gaps = 8/269 (2%)

Query: 409  IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVA-KKYTNRG 467
            I+N+I+S      ++  +  H   +++         +    + +  +V+  A +K ++R 
Sbjct: 1231 IQNKIRSQLARNQLAHLQRNHAAKVIQTAYRGYIKRRDYQRQKHAAVVLQSALRKMSSRH 1290

Query: 468  -LQFLDLIQEGNI---GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT-IRIP 522
             LQ    +Q        +    ++ D     +         +  + R          R  
Sbjct: 1291 ELQEKKTMQAATYLQAIIRACNDRRDTSRRLRGIVRLQAKWRGKMARKEYKDLRIEARSL 1350

Query: 523  VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              +++  +++      +  ++  E   ++  ++  + +E   + ++ T + + LE     
Sbjct: 1351 KTVQEAKNQLQAKLEEIQWRLTTEQRAKQHIEETKIKMEKQLEQIQSTHDHVLLELSEYK 1410

Query: 583  EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 642
              +  L       +    +        R+T +  + SL   E   L     I   ++  L
Sbjct: 1411 SKSESLETSNTSMSDELTVLRKELEETRQTLSEHVGSLKKLEREKLDSTETIKSVSEE-L 1469

Query: 643  EEVGKQFCVTRERIRQIEAKAIRKLKHPS 671
              V +Q+  T    +Q+E +++++LK  +
Sbjct: 1470 ATVKQQYEETSTTKQQLE-QSLKELKSST 1497


>gi|218442035|ref|YP_002380364.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 7424]
 gi|218174763|gb|ACK73496.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7424]
          Length = 219

 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 62/170 (36%), Gaps = 15/170 (8%)

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
                    R  +  ++   +V R  +R++  +K       IA    +  + +RK  +++
Sbjct: 62  YHLAPDWQDRADL-AQEVWIRVYRNIKRLNEPLKFRGWLSRIAT--NLFYDELRKRKRVS 118

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             P+SL+ P   +D     D + D    SP D+       E     +A L        R 
Sbjct: 119 N-PVSLDAPRRVDDGEIDWDIVSD--YPSPDDNLATREFYEQLRLAIADLPE----AFRT 171

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
              +        EE+ +   V+   ++   A+A  KL+       L+ +L
Sbjct: 172 TIVLREIEGMAYEEIAEITGVSLGTVKSRIARARAKLQ-----SVLQPYL 216


>gi|150392177|ref|YP_001322226.1| RNA polymerase factor sigma-70 [Alkaliphilus metalliredigens QYMF]
 gi|149952039|gb|ABR50567.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 213

 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 34/82 (41%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A + +++     V + A+ Y   G    D++QEG IGL KA   F       F  +A
Sbjct: 28  DLAALEFLIKKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKPDKLSSFRAFA 87

Query: 501 MWWVKQAITRSIADQSCTIRIP 522
              + + I  +I   +    IP
Sbjct: 88  ELCITRQIITAIKTATRQKHIP 109


>gi|224057696|ref|XP_002188681.1| PREDICTED: similar to WD repeat domain 65 [Taeniopygia guttata]
          Length = 980

 Score = 41.0 bits (94), Expect = 0.72,   Method: Composition-based stats.
 Identities = 28/232 (12%), Positives = 79/232 (34%), Gaps = 13/232 (5%)

Query: 143 AKRIEAGRAMMMASLCESPL-TFQALIIWRDE--------LNDGTTLLREIIDL-EACIG 192
           ++++E      +  L ES +     L    ++        L +    +R+ I+  E    
Sbjct: 651 SQKMEEEYEKQLHKLEESKIRAVAELKEHYEKKLKHKSVLLEEAKESIRKQIEAHEEMEK 710

Query: 193 PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
              + G     E     +++   +++    ++   G +       + +    +   E   
Sbjct: 711 QIYEDGDKEILELKDKYEKQLLEEKESNMQLKGEIGVMNKRLNSLQKELKDRNRDIEEMR 770

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
            +++ L +        + A++  ++ +    L++   VY      Q+           S 
Sbjct: 771 LEQQKLQDIIKSLEKDILALKTDVKERTETILEKEKHVYDLKMKNQELENFKFV---LSY 827

Query: 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
           + +  K+++      +   + +I  + EQL    K  +  +  + +L Q   
Sbjct: 828 RIEEFKKQIESRENDIETMKKQISEMEEQLEQFRKESVGLKLTITQLQQKQK 879


>gi|193215824|ref|YP_001997023.1| ECF subfamily RNA polymerase, sigma-24 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193089301|gb|ACF14576.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroherpeton
           thalassium ATCC 35110]
          Length = 224

 Score = 41.0 bits (94), Expect = 0.73,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 10/104 (9%)

Query: 575 SLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI 634
           S+ T +  E+       I D +  +           +     L +L+P+E+ ++R  +  
Sbjct: 121 SVSTTLIHEEKWQTLTEITDDSEKADSPKM------QLMKEALNTLSPKEQEIMRTIYQW 174

Query: 635 GMNT----DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
                    H +EE+ KQ+  T E IR+I ++A +K++   +S 
Sbjct: 175 YEPHTKLPSHIVEELTKQYNTTPENIRKIRSRARQKIEAYLKSH 218


>gi|73960805|ref|XP_537229.2| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 1 [Canis familiaris]
          Length = 1754

 Score = 41.0 bits (94), Expect = 0.73,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|320530729|ref|ZP_08031773.1| RNA polymerase sigma-H factor [Selenomonas artemidis F0399]
 gi|320137016|gb|EFW28954.1| RNA polymerase sigma-H factor [Selenomonas artemidis F0399]
          Length = 266

 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 32/138 (23%), Positives = 50/138 (36%), Gaps = 5/138 (3%)

Query: 385 SYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
               D  +       A E++   +  +E+   S+  G +  E      +V     E + A
Sbjct: 9   KSMLDDEQSAPDELEAGEIEEADEPESEMPENSIYEGYTDEEL-----LVHIRTHEGNEA 63

Query: 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
              +V      V S A+ Y   G    D++QEG IG  KA   F       F  +A   V
Sbjct: 64  LDYLVNKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRDFREDKLSSFRAFAELCV 123

Query: 505 KQAITRSIADQSCTIRIP 522
            + I  +I   +    IP
Sbjct: 124 TRQIITAIKTATRQKHIP 141


>gi|218245218|ref|YP_002370589.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 8801]
 gi|257058250|ref|YP_003136138.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 8802]
 gi|218165696|gb|ACK64433.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           8801]
 gi|256588416|gb|ACU99302.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           8802]
          Length = 217

 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 33/171 (19%), Positives = 64/171 (37%), Gaps = 15/171 (8%)

Query: 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
                    R  +  ++   +V R  +R++  +K       IA    +  + +RK  +++
Sbjct: 62  YHLAPDWQDRADL-AQEVWIRVYRNIKRLNEPVKFRGWLSRIAT--NLFYDELRKRKRVS 118

Query: 571 KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
             P+SL+ P   +D     D + D    SP D+       +     +A L        RM
Sbjct: 119 H-PVSLDAPRRVDDGEIEWDIVSD--YPSPDDNLATREFYDRLQVAIADLPE----AFRM 171

Query: 631 RFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
              +        EE+ +   V+   ++   A+A  KL+       L+ +LD
Sbjct: 172 TIVLREIEGMAYEEIAQLTGVSLGTVKSRIARARAKLQ-----SVLQQYLD 217


>gi|150015027|ref|YP_001307281.1| RNA polymerase factor sigma-70 [Clostridium beijerinckii NCIMB
           8052]
 gi|149901492|gb|ABR32325.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           beijerinckii NCIMB 8052]
          Length = 223

 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 61/189 (32%), Gaps = 4/189 (2%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V K +   S A++ ++      V S AK Y   G    D+ QEG IGL KA   F+    
Sbjct: 33  VAKAKSGNSRAQEYLISKYENFVKSKAKSYFLIGADKEDIYQEGMIGLYKAIRDFNAEKS 92

Query: 494 YKFSTYAMWW----VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
             F  +A       +  AI  +   +   +   V +   I++       +      + + 
Sbjct: 93  TSFKAFAEICVIRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLDVLAGLKISD 152

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
            E        ++ + K +      + LE      D     +   D    S         +
Sbjct: 153 PEELMISKEQMDYIEKKISKVLSDLELEVLTSYLDGKSYQEIASDLERHSKSIDNALQRV 212

Query: 610 RETTTRVLA 618
           +    + L 
Sbjct: 213 KRKLEKCLD 221


>gi|291225416|ref|XP_002732696.1| PREDICTED: RAS-associated protein RAB13-like [Saccoglossus
           kowalevskii]
          Length = 719

 Score = 41.0 bits (94), Expect = 0.74,   Method: Composition-based stats.
 Identities = 44/337 (13%), Positives = 107/337 (31%), Gaps = 21/337 (6%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG---INVVDGDDLEDEEGSEDSLDLA 96
           ++G++T  ++        ++ +Q+E     L + G   + + +  +         S D A
Sbjct: 36  EKGFITKRDMQRLGGELPLTPDQLEAVFDSLDDDGNGYLTLEEFTEGFGGFLGFGSEDPA 95

Query: 97  SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMAS 156
               +  V+  ++ +  D   D   +  L  +G+  L    G   + +            
Sbjct: 96  EEEGHRDVYEDEQGEEDDTQEDIAFQQALEGLGATSLFDDSGRGKLGRL----------- 144

Query: 157 LCESPLTFQALIIWRDELNDGT-TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSS 215
               P   Q +     ++      LL +  D    +  + +       E  S  +    +
Sbjct: 145 ---QPYDQQHIKELWKKIKSSEPELLGDFEDFIQKVSSDIRKARIDSDELESALRNRAYA 201

Query: 216 QEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQ 275
            ++E   + E       A K    +  K        E  +  L ++++         + +
Sbjct: 202 HDEEVRKLYEEMEIQIKAEKEKILNEEKGKERKIREEMSQELLRKEQEVQELLQKQKDLE 261

Query: 276 LRPKVM-CALDEIAEVYRELRSLQDNAVNGQKDEKSS--VKCKVLKEKLVKLVGSLSLNQ 332
            + + M     EIA    EL    ++  +  ++   S     + LKE   K +       
Sbjct: 262 TKLQEMNATQSEIATENEELAKYNESLQDKLENTSISLVEAKQYLKEIQEKALREKRERA 321

Query: 333 SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                + E +    + ++     L  + +     +D+
Sbjct: 322 QAALKVTEGIAQERESLVRQLDMLRDMNKKLKDDKDM 358


>gi|189191018|ref|XP_001931848.1| intracellular protein transport protein (UsoA) [Pyrenophora
           tritici-repentis Pt-1C-BFP]
 gi|187973454|gb|EDU40953.1| intracellular protein transport protein (UsoA) [Pyrenophora
           tritici-repentis Pt-1C-BFP]
          Length = 1006

 Score = 41.0 bits (94), Expect = 0.75,   Method: Composition-based stats.
 Identities = 47/307 (15%), Positives = 105/307 (34%), Gaps = 12/307 (3%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           ++ E T+  L    + +    D E  E  +       SA      L++  D      D  
Sbjct: 679 DEKEQTIQELKAQLMTLEQKIDQEQAEHRK----TQQSAEEQRSTLKRINDKLHEDLDKE 734

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           V    RE     L   E E     +I A    +  +  ++ L    +    DE   G+  
Sbjct: 735 VAKRDREFRQAML---ETENRYNLQIVALNNKVQQASKDANLAVSKVRQEYDEQLHGSNR 791

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ-----EKERDDVQETEGDIESAAK 235
            R+ ++    +  +++              ++   +     E   +     +       +
Sbjct: 792 ARDELEKRLAVSDKARQEAVATIRSLEEMLQQTRIEVATITETLSNAQSHVQNSEAQLKQ 851

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           + ++  S++    E  E   +    ++D+   T+  ++++++     A D+I +V     
Sbjct: 852 LQEEKESQIQLLREEKEAQLKQSKLEKDNLQSTIDKLKEEVQELKTKAQDQIWKVKDAEE 911

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
            L+                  L+EKL K V S     + ++ L+  L D+ ++   ++  
Sbjct: 912 KLRKAEAAAVTKSAKEKAITDLQEKLRKAVESEKEKTTELEDLILVLSDLEEKRSKDKER 971

Query: 356 LLRLAQS 362
           L  L + 
Sbjct: 972 LKALGEE 978


>gi|8250512|emb|CAB93660.1| AMI1 protein [Podospora anserina]
          Length = 1882

 Score = 41.0 bits (94), Expect = 0.75,   Method: Composition-based stats.
 Identities = 35/239 (14%), Positives = 81/239 (33%), Gaps = 13/239 (5%)

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E     K + +  E E +  Q+    ++ +    KD+   +++        ++   E
Sbjct: 212 EREEELKESKADRARLELEAEGFQQHIKSLDESESRYKDENWNLETQIHELMASQKEAAE 271

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            E      L+A++ + +      L+E+ +   +       A+   + E  + +   +   
Sbjct: 272 REKKLTQALAALQSE-KNATQRELEEVKDSLAKQEEKHSAAIRNLEIELGTSRRSAVS-- 328

Query: 321 LVKLVGSLSLN-QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI---KRDVFLERHQG 376
                 S  L  Q R+D L  Q  +++K      G +L    + G+    R+   +R+ G
Sbjct: 329 ----FESERLTLQKRVDELTSQNQELAKAFSAQRGRMLERESTRGVSDEDRNSGSDRNTG 384

Query: 377 RELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
            E  P                       S+   +  I+++        +E   +  M++
Sbjct: 385 PEQSP--PPSPLKMTPRHSGLETETLKTSLGHAQRTIQTLRTNIHREKTEKLELKRMLQ 441


>gi|163756128|ref|ZP_02163244.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein [Kordia
           algicida OT-1]
 gi|161324002|gb|EDP95335.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein [Kordia
           algicida OT-1]
          Length = 184

 Score = 41.0 bits (94), Expect = 0.76,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652
           ED +            L      VLA L P  ++ +++ +  G+      EE+G      
Sbjct: 95  EDLSVYKDEGITENQELHTELKGVLAKLEPHHQKAIQLVYFNGLTHKEAHEEMGVPLGTF 154

Query: 653 RERIRQIEAKAIRKLK 668
           +  +RQ    A+ KL+
Sbjct: 155 KSYVRQ----AVEKLR 166


>gi|145539902|ref|XP_001455641.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124423449|emb|CAK88244.1| unnamed protein product [Paramecium tetraurelia]
          Length = 445

 Score = 41.0 bits (94), Expect = 0.76,   Method: Composition-based stats.
 Identities = 33/209 (15%), Positives = 81/209 (38%), Gaps = 7/209 (3%)

Query: 284 LDEIAEVYRELRSLQDNAVNGQKD--EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            ++I ++ ++ +  Q+     +    EK       +  +L +    L L   +   LV++
Sbjct: 43  FNQIIQMLQKRQEFQEQEYRIKVASLEKRIKYLIQISSQLTQQNTQLKL---QYADLVKE 99

Query: 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
              +  RIM+ E  +      Y I  D   +    RE      +   +  +   K  +  
Sbjct: 100 YDIMKDRIMNYEANMKTKNSEYSISLDEVTKLKTEREKLLGLANKYHERSKIRKKQSIEQ 159

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
           E ++I  ++ ++  +  +  I +SE ++++   +     A+  +  +   N R +  + K
Sbjct: 160 E-NAITILQKQVNDLQKDNLILVSEKQNLLLQSQYNHQFANQQQNILQIGNCRKIQQIIK 218

Query: 462 KYTN-RGLQFLDLIQEGNIGLMKAAEKFD 489
           ++ N   +    +  E N  ++   E  D
Sbjct: 219 RFLNDYCIHLTYINNETNQLIVLLKEYHD 247


>gi|73960803|ref|XP_863666.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 9 [Canis familiaris]
          Length = 1719

 Score = 41.0 bits (94), Expect = 0.76,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|260589560|ref|ZP_05855473.1| RNA polymerase sigma-H factor [Blautia hansenii DSM 20583]
 gi|331082987|ref|ZP_08332106.1| hypothetical protein HMPREF0992_01030 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540128|gb|EEX20697.1| RNA polymerase sigma-H factor [Blautia hansenii DSM 20583]
 gi|330399724|gb|EGG79385.1| hypothetical protein HMPREF0992_01030 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 197

 Score = 41.0 bits (94), Expect = 0.77,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 6/108 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +     +   E   ++   ++G  +       ++     +V+  A      G +  DLI
Sbjct: 1   MMKEYENLKDEELFELLWQGQEGLEDY------LINKYKGMVLKKAHAMFLIGGEQEDLI 54

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           QEG IGL KA   +       FST+A   +++ + ++I         P
Sbjct: 55  QEGMIGLFKAVRGYHPDKNASFSTFANLCIERQMYKAIEISGRQKHKP 102


>gi|330936886|ref|XP_003305520.1| hypothetical protein PTT_18385 [Pyrenophora teres f. teres 0-1]
 gi|311317414|gb|EFQ86377.1| hypothetical protein PTT_18385 [Pyrenophora teres f. teres 0-1]
          Length = 1287

 Score = 41.0 bits (94), Expect = 0.78,   Method: Composition-based stats.
 Identities = 59/502 (11%), Positives = 153/502 (30%), Gaps = 25/502 (4%)

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           ++  A   PE          G   QK E    ++E +   E         +    +    
Sbjct: 175 VEKLATTAPEQLTLQVERISGSLEQKAEYDRLKEESEAATEDNAKHLHERRGINGELKTY 234

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
                 A+  E+ L E +D             +  +  A ++IA    EL+  + +    
Sbjct: 235 QDQKAEADEYEKKLAERDDAVVTKNLWKLYLYQQVMEKARNKIASHQEELKEHKRSVEKY 294

Query: 305 QKDEKSSVKCK-VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            +   +  + +  ++  L K   +    +  I+    +L  I ++I  +     +     
Sbjct: 295 HQRHDAERQAEAKIRRDLAKTDRNTKAKEKEIEDASNELAPIEEKIRLSNETRRKYESRL 354

Query: 364 ---GIKRDVFLERHQGRELDPH--------WVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
                KRD   +  +  + D          W    K   + + +     ++    ++R+E
Sbjct: 355 EELRKKRDNEKKAVEKCQKDLDLVQKAEKKWEDDFKAAAQRQGRELSEQDLQEYGRLRSE 414

Query: 413 IKSISVETGISISEFRHIVSMVR---KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +   +    + I + +  V   R   K   ++  + ++ VE     +  + ++      Q
Sbjct: 415 VTKRTHGDQMQIDKLKREVETDRDHVKNLQQSVDSHEKEVEKLNATISQLEERQQASKTQ 474

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             +L         +           +   Y    + Q + + ++    + R     ++  
Sbjct: 475 VKELETARAAKQQELDRLRSDRKQIEMQYYEKNQLLQEVLKQLSIVEGSRRESRKQQEAR 534

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
             + R   R  ++       + I  K+    + + +VL    + + ++T           
Sbjct: 535 RTIDRLKTRFGSEKVHGRYKDLITPKMQKYRKAIGRVLGHQMDTVIVDTEAT---AKSCI 591

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D+++ +       + + +   +     L  +       +        +        G   
Sbjct: 592 DYLKAERIGVMSFNPLDSIQIQAVDPQLKGMHEGMRLAIDCINYEPKHERAMTAACGNTM 651

Query: 650 CVTRE-------RIRQIEAKAI 664
               E        +R++E KA+
Sbjct: 652 ICNTEKLAKELRYVRRVEVKAV 673


>gi|194898809|ref|XP_001978956.1| GG10928 [Drosophila erecta]
 gi|190650659|gb|EDV47914.1| GG10928 [Drosophila erecta]
          Length = 1001

 Score = 41.0 bits (94), Expect = 0.79,   Method: Composition-based stats.
 Identities = 47/327 (14%), Positives = 116/327 (35%), Gaps = 18/327 (5%)

Query: 144 KRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGT 203
            R     + + AS+     T  +L    ++      ++  +I  +     ES  G     
Sbjct: 307 HRQRQCISDLKASIASFEQTVASLHERLNKTTAELDVMDSLI--QQHQADESPTGRLSQV 364

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            G         +       +++      ++ K  +++  ++D   E    + R L  +E+
Sbjct: 365 GGSQLVGSTPLNPVDRVGHIKQELYRALASLKNKREEVRRLDKLLEERNQELRVLRNNEN 424

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
            S   L  ++D              E+  +   LQ ++    +      +   LKEKL +
Sbjct: 425 KSLVQLETLKDVKMRLENKVKSMQQELEEQQHKLQQDSGLHSQLHAIEAERDALKEKLQQ 484

Query: 324 LVGSLSLNQSRIDLLVEQLYDISK---RIMHNEGELLRLAQ----SYGIKRDVFLERHQG 376
           +   L   +  ++ L +Q   + +   ++  +  +L   A        ++R   L R   
Sbjct: 485 IEEQLRNVEKDLEQLKQQHESLQRNYDQLSQDNRQLRTRATADNLRLELERHKILLRDSQ 544

Query: 377 RE---LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS------VETGISISEF 427
            E   L   +   A D    +++     E D++ ++++++++++        T +   E 
Sbjct: 545 SEVERLKKLYSDIATDKEALDYELRKLRESDTLKELQDQLQNLATVQRNLQLTEMKSEEL 604

Query: 428 RHIVSMVRKGECEASIAKKEMVEANLR 454
           + ++   +        A ++M E   R
Sbjct: 605 KKLLEAEKLSHERDLQALRQMNEREKR 631


>gi|73960791|ref|XP_863529.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 3 [Canis familiaris]
          Length = 1654

 Score = 40.6 bits (93), Expect = 0.79,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 336 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 395

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 396 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 448

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 449 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 492

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 493 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 549

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 550 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 606

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 607 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 665

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 666 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 725

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 726 QWVSDEKDARGYLQA 740


>gi|302898798|ref|XP_003047918.1| hypothetical protein NECHADRAFT_39939 [Nectria haematococca mpVI
           77-13-4]
 gi|256728850|gb|EEU42205.1| hypothetical protein NECHADRAFT_39939 [Nectria haematococca mpVI
           77-13-4]
          Length = 1393

 Score = 40.6 bits (93), Expect = 0.80,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 95/259 (36%), Gaps = 15/259 (5%)

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           +  S  K ++   ++E +   E         + +++    +     NA ND   L  + D
Sbjct: 701 DKISEVKLQNQELQRELETCMEDFETAIDGKRQAEEAALSLQEDLNNAMNDLVALQSERD 760

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLV 322
           ++    S ME++       A +EI  +  E     D     Q D +  S     L+E++ 
Sbjct: 761 EALREQSDMENEFESLRKEAQEEIDALESEADQHADEMQRLQADLQDRSENFDALQEEMR 820

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
           K+  +L   +   +  + ++  + + +  +  EL  L Q      D        +E    
Sbjct: 821 KMSEALIRLEDDQESKMRRIQQLEQELDSSNKELEELEQKLMESNDKNQRLSVQQESSQG 880

Query: 383 WVSYAKDFPEGEWKNF-------------VACEVDSILKIRNEIKSISVETGISISEFRH 429
            +++ ++  EG+                 +  E D + ++ N ++    +  I   + + 
Sbjct: 881 EIAFLREEQEGDKIRIGDLEAALANAEQSLREEKDRVKELENRLQQERHQREIVADQEKE 940

Query: 430 IVSM-VRKGECEASIAKKE 447
            V   V +   EAS AK E
Sbjct: 941 EVQQFVNELNREASAAKDE 959


>gi|296329094|ref|ZP_06871599.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153813|gb|EFG94626.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 979

 Score = 40.6 bits (93), Expect = 0.81,   Method: Composition-based stats.
 Identities = 17/28 (60%), Positives = 21/28 (75%)

Query: 640 HTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            TLEE+G+   VTRERIRQIE +  +KL
Sbjct: 387 KTLEEIGEALNVTRERIRQIETRGFKKL 414


>gi|134046570|ref|YP_001098055.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C5]
 gi|132664195|gb|ABO35841.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C5]
          Length = 731

 Score = 40.6 bits (93), Expect = 0.81,   Method: Composition-based stats.
 Identities = 42/355 (11%), Positives = 124/355 (34%), Gaps = 24/355 (6%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D + + ++     + +  +  ++IK           +L   +    V  +++ED +   
Sbjct: 401 ADEKRKRNNLQKAINTAIRNVAQLIK-----------DLREEVDLLNVQVQKVEDELKSA 449

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                 V +  +   E  S+ S  L  ++       +  K     + ++ VR    E+  
Sbjct: 450 EETATQVTEAANQVAEASSDQSAKLQEASDQLENTYEVAKTVYTDA-EETVR-SAEEISE 507

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
               +   ++  A     G   ++  L +S    Q L     ++N+ T L+++I +    
Sbjct: 508 NS-ENGVKKVENAISRMQGITNVIDDLGKS---IQELGEDGKKINEVTDLIKDIAEQTGL 563

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +   +        E         S  +   ++++++  +I            +       
Sbjct: 564 LALNASIEAARAGEAGKGFAVVASEIKALAEEIKKSVENINHTIDGVHKRIGETMDLGLK 623

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            +++        D+    L  +++ +    +  ++ I +        Q  A N +   K+
Sbjct: 624 GKDEVDKGVIAIDEVNDALLRIKESVNGAAIK-INGIKQ------GAQSAADNTEGALKN 676

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
           +     + E+       ++ +   ++ ++E++  I++ + H    + R +  + I
Sbjct: 677 AQDIASISEEFTATAEEVTASTEELNSIIEEIRGIAEEVTHVSERVTRKSGQFKI 731


>gi|47089316|gb|AAT10977.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
 gi|47089324|gb|AAT10981.1| sigma 70 factor [Pseudomonas syringae pv. maculicola]
          Length = 148

 Score = 40.6 bits (93), Expect = 0.82,   Method: Composition-based stats.
 Identities = 18/194 (9%), Positives = 51/194 (26%), Gaps = 46/194 (23%)

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
            T   ++     +      L +++            G+    +G +         + +  
Sbjct: 1   GTVDHILSEYTRVTSEGGRLSDVL-----------SGYIDPDDGIAPPAEVPPPVDPKAA 49

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
             +  + + E+A     ++  +    P  A+     + +  + +   L            
Sbjct: 50  KAEGDDEEEETAEATDDEEEVESGPDPVIAQQRFGAVSDQMEITRKAL------------ 97

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
                                  +K  +           L +L   + L   + + LVE+
Sbjct: 98  -----------------------KKFGRDDKHAIAEMVALAELFMPIKLVPKQFEGLVER 134

Query: 342 LYDISKRIMHNEGE 355
           +    +R+   E  
Sbjct: 135 VRGALERLRAQERA 148


>gi|321476145|gb|EFX87106.1| myosin heavy chain isoform 3 [Daphnia pulex]
          Length = 1947

 Score = 40.6 bits (93), Expect = 0.83,   Method: Composition-based stats.
 Identities = 69/418 (16%), Positives = 141/418 (33%), Gaps = 38/418 (9%)

Query: 35   IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94
            I   R+R  V  EEL A L   E + EQ E+ V         V    D   +E  E+  +
Sbjct: 1526 IDKQRKRLEVEKEELQAALEEAESALEQEENKVLRAQLELSQVRQEIDRRIQEKEEEFEN 1585

Query: 95   LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA-GRAMM 153
               +   +   +Q   ++  +   + +RM        +L S   E+ IA        A  
Sbjct: 1586 TRKNHQRAIDSMQASLEAEAKGKAEALRM------KKKLESDINELEIALDHANKANAEA 1639

Query: 154  MASLCESPLTFQALIIWRDELNDGTTLLRE---IIDLEACIGP----ESKGGFFHGTEGH 206
              S+     + +      +E       LRE   I +  A        ES+          
Sbjct: 1640 QKSIKRYQQSIKETQSALEEEQRNRDDLREQYGIAERRANALQGELEESRTLLEQADRAR 1699

Query: 207  SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
               + E +   ++  D+        +A +  + +   + +  ++  N+ +N +E    + 
Sbjct: 1700 RQAETELADAHEQLHDLTAQAASSSAAKRKMESELQTLHADLDDMINETKNSEEKAKKAM 1759

Query: 267  HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
               + + D+LR +   A  +  E  R+   LQ   +  + DE  +   K  K+ + KL  
Sbjct: 1760 VDAARLADELRAEQEHAQAQ--EKQRKALELQVKELQVRLDESENNALKGGKKAIQKLEE 1817

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +   ++ +D    +  D  K +  +E  +  L       R                   
Sbjct: 1818 RVRGLETELDGEQRRHADAQKNLRKSERRIKELTFQSDEDRKN----------------- 1860

Query: 387  AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
                     ++ V      I   + +I+       +++++FR     + + +  A +A
Sbjct: 1861 -----HERMQDLVDKLQQKIKTYKRQIEEAEEIAALNLAKFRKAQQELEEADERAELA 1913


>gi|259486176|tpe|CBF83808.1| TPA: Autophagy-related protein 11
           [Source:UniProtKB/Swiss-Prot;Acc:Q5B993] [Aspergillus
           nidulans FGSC A4]
          Length = 1329

 Score = 40.6 bits (93), Expect = 0.83,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 83/190 (43%), Gaps = 7/190 (3%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            EI+D+   I   S+G   H         +  +  +   + +++ E + E+A   S+  +
Sbjct: 793 DEIVDIIKAIDVLSEGLTIHAKTAEDNAMKAAAENKTLIEQLEKMESNYENAKSASEQYQ 852

Query: 242 SKVDSPPENAENDE---RNLDEDEDDSAHTLSAMEDQL---RPKVMCALDEIAEVYRELR 295
           +++    E  E ++   + ++ + +D   +L  +E +L           + +AE  ++L 
Sbjct: 853 TQLTQAREEVEQEQSKVKAIESELNDERASLLELESKLAAGETGAGALREHVAEEEQKLN 912

Query: 296 SL-QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
           ++ Q  A    +  +S  +    +++   L  S     +RID+   +L ++S+++     
Sbjct: 913 NMSQQLAETEARARRSEEEALQWRKRAEALSESDKQVAARIDIRTARLEELSRQLFGQVE 972

Query: 355 ELLRLAQSYG 364
           +L R+ +  G
Sbjct: 973 KLERMLEQLG 982


>gi|308174874|ref|YP_003921579.1| bacteriophage SPP1 receptor [Bacillus amyloliquefaciens DSM 7]
 gi|307607738|emb|CBI44109.1| bacteriophage SPP1 receptor [Bacillus amyloliquefaciens DSM 7]
 gi|328554828|gb|AEB25320.1| bacteriophage SPP1 receptor [Bacillus amyloliquefaciens TA208]
 gi|328913189|gb|AEB64785.1| bacteriophage SPP1 receptor [Bacillus amyloliquefaciens LL3]
          Length = 1040

 Score = 40.6 bits (93), Expect = 0.83,   Method: Composition-based stats.
 Identities = 28/198 (14%), Positives = 62/198 (31%), Gaps = 2/198 (1%)

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
           I   D+ N+   +  EI  +   +    K        GH          E         +
Sbjct: 402 IDLDDQRNELKRISAEINSISDGLKEPEKENPDPENPGHGDNGENSGGTEPNDGTAPGED 461

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEI 287
           G  +   K  +                 +N+    DD A   +  E     +V  A + +
Sbjct: 462 GKTDDGTKEQQSPSDNTGDQQTKTAATAKNVTPLADDPADDPNGSEGDGGTEVSKAKERL 521

Query: 288 AEVYRELRSLQDNAVNGQK--DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            +    ++ ++      Q+  +E+   +   L E++  L   ++  + R D L ++L   
Sbjct: 522 NQAAERIQQIEKELEEKQQTHNEELKKRLDALDEEIQGLKDQIAKVEKRADKLQKKLEQS 581

Query: 346 SKRIMHNEGELLRLAQSY 363
            +    +   + R+    
Sbjct: 582 EETRKQDFNTVYRMILKT 599


>gi|167751712|ref|ZP_02423839.1| hypothetical protein EUBSIR_02721 [Eubacterium siraeum DSM 15702]
 gi|167655520|gb|EDR99649.1| hypothetical protein EUBSIR_02721 [Eubacterium siraeum DSM 15702]
          Length = 73

 Score = 40.6 bits (93), Expect = 0.83,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I D N        I           +  L  RE+ +L++ F  G     T  EV ++
Sbjct: 1   MDQIGDNNDDRNRLDEI------ALKEAIIGLDYREKNILKLCFFRG----KTQVEVAQK 50

Query: 649 FCVTRERIRQIEAKAIRKLKHP 670
             +++ ++ ++E  A+RK+K  
Sbjct: 51  IGISQAQVSRLEKGALRKIKKA 72


>gi|331091960|ref|ZP_08340792.1| hypothetical protein HMPREF9477_01435 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330402859|gb|EGG82426.1| hypothetical protein HMPREF9477_01435 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 205

 Score = 40.6 bits (93), Expect = 0.86,   Method: Composition-based stats.
 Identities = 18/110 (16%), Positives = 42/110 (38%), Gaps = 12/110 (10%)

Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
            + + + L+  ++  S+      E+   LG                 A  +E    +L  
Sbjct: 99  EDRINRNLETRQQRKSISYSAVSEEWGVLGSL--------EATVLETAIRKEMIQELLGL 150

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           LT R++ V+   F        +  E+ ++  V+   + +I  +A+ +L+ 
Sbjct: 151 LTERQKEVVFEYFW----EQKSQSEIAEKLGVSHAAVSKILTRAVTRLRK 196


>gi|288554708|ref|YP_003426643.1| RNA polymerase factor sigma-70 [Bacillus pseudofirmus OF4]
 gi|288545868|gb|ADC49751.1| RNA polymerase factor sigma-70 [Bacillus pseudofirmus OF4]
          Length = 215

 Score = 40.6 bits (93), Expect = 0.86,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 37/90 (41%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V +     S A + ++      V + A+ Y   G    D++QEG IGL KA   F    
Sbjct: 20  LVEQVRMGDSGALEFLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAVRDFKGDK 79

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  +I   +    IP
Sbjct: 80  LASFKAFAELCITRQIITAIKTATRQKHIP 109


>gi|257053448|ref|YP_003131281.1| methyl-accepting chemotaxis sensory transducer [Halorhabdus
           utahensis DSM 12940]
 gi|256692211|gb|ACV12548.1| methyl-accepting chemotaxis sensory transducer [Halorhabdus
           utahensis DSM 12940]
          Length = 871

 Score = 40.6 bits (93), Expect = 0.87,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 77/209 (36%), Gaps = 13/209 (6%)

Query: 64  EDTVAMLSNMGINVVDG-DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           +     + +MG +V DG + +ED     + L      +N+ +           ++ + V 
Sbjct: 667 DHVADDMHDMGESVTDGIETVEDTVQLLEELVGQVEEANTGIQSINDATDDQAASTEEVV 726

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182
             + E+GSI     E   + A+ + A      AS+ +     Q+L     E       LR
Sbjct: 727 AMMDEVGSIS----EETASQAENVSAAAEEQTASITQVSSRIQSLAEQSTE-------LR 775

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           ++ID     G +S        +   ++   DS+ ++      E +  ++S  +       
Sbjct: 776 DVIDRFEVEG-DSDTATERNEDDTGFEFGTDSAIDETEAADGEADWSVDSGEESDNGVDL 834

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSA 271
                P+ A++D     ED      + +A
Sbjct: 835 VDGQEPDEADDDIGLGGEDGAAMDDSEAA 863


>gi|312077442|ref|XP_003141306.1| hypothetical protein LOAG_05721 [Loa loa]
 gi|307763532|gb|EFO22766.1| hypothetical protein LOAG_05721 [Loa loa]
          Length = 818

 Score = 40.6 bits (93), Expect = 0.88,   Method: Composition-based stats.
 Identities = 31/198 (15%), Positives = 76/198 (38%), Gaps = 2/198 (1%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           E  D    LREI++  A I  E K      +E        +   +++R  +++    I S
Sbjct: 364 EFQDEIARLREILEKRA-IKKEKKVYLDEKSENDDEAAPSEEYLDEQRKRLEDERQTIIS 422

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
            + +  +++ K+ +  E            +   A  + AM+ +L       LD+  E  +
Sbjct: 423 NSNIIAEEKRKILADLEERVRQLERERGAQIAVAAKIRAMQSKLLSGDGSLLDKTREQQK 482

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEK-LVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            L   +      ++ E+  ++    +E    ++  + S  +  +++   +L  +  ++  
Sbjct: 483 LLEYRRRQLAEQKRKEREILQQLEAQEDNTAEIHETFSNLRQEVEIKTRKLKKLYSKLQQ 542

Query: 352 NEGELLRLAQSYGIKRDV 369
              E+   + S+  +R  
Sbjct: 543 VRSEINDASASHSQERRD 560


>gi|212637937|ref|YP_002314457.1| RNA polymerase factor sigma-70 [Anoxybacillus flavithermus WK1]
 gi|212559417|gb|ACJ32472.1| RNA polymerase sigma-30 factor, sigH [Anoxybacillus flavithermus
           WK1]
          Length = 223

 Score = 40.6 bits (93), Expect = 0.88,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 37/100 (37%)

Query: 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLM 482
           S  E      +V       S A   ++      V + A+ Y   G    D++QEG IGL 
Sbjct: 18  SRYEQLEDEMIVELVHQGDSEALDYLIHKYKNFVRAKARSYFLVGADREDIVQEGMIGLY 77

Query: 483 KAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           KA   F       F  +A   + + +  +I   +    IP
Sbjct: 78  KAIRDFKEDKQSSFKAFAELCITRQMITAIKMATRQKHIP 117


>gi|149044096|gb|EDL97478.1| Cdc42 binding protein kinase beta, isoform CRA_c [Rattus
           norvegicus]
          Length = 1658

 Score = 40.6 bits (93), Expect = 0.88,   Method: Composition-based stats.
 Identities = 34/298 (11%), Positives = 93/298 (31%), Gaps = 21/298 (7%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 384 RGSLKSMIQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 436

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 437 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 496

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                 ++     A  ++  L +   +++  L +   +L+              +  R+L
Sbjct: 497 TQRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKD----------AHQQRKRAL 546

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+ +   ++  +   + + +  +L      + +   +ID + + +    K     E  L 
Sbjct: 547 QEFSELNERMAELRSQKQKVSRQLRDKEEEMEVAMQKIDSMRQDIRKSEKSRKELEARLE 606

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                   +R +        +     +   K    G            I KIR+E++ 
Sbjct: 607 DAVAEASKERKLREHSESFSKQMERELETLKVKQGGRGPGATLEHQQEISKIRSELEK 664


>gi|149183038|ref|ZP_01861492.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus sp. SG-1]
 gi|148849268|gb|EDL63464.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus sp. SG-1]
          Length = 191

 Score = 40.6 bits (93), Expect = 0.88,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 46/109 (42%), Gaps = 6/109 (5%)

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA--IQANLRETTTRVLASLT 621
           +  +   ++ ++L+ P+GDE+     + I D  A          ++            LT
Sbjct: 80  KTRMDRDRQLLTLDKPLGDEEEGTYKELIADTAAPDSYTEKSLEESISDARLMEAFQRLT 139

Query: 622 PREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
            R++ +L + +      + +  E+     V+++ + +   K ++KLK+ 
Sbjct: 140 HRQKFILNLAYV----EERSDTEIADVLGVSQQAVSKTHKKVLKKLKNA 184


>gi|172056123|ref|YP_001812583.1| RNA polymerase factor sigma-70 [Exiguobacterium sibiricum 255-15]
 gi|171988644|gb|ACB59566.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Exiguobacterium
           sibiricum 255-15]
          Length = 213

 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 35/81 (43%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           S A + ++E     V + A+ Y   G    D+IQEG IGL KA   +       F  +A 
Sbjct: 27  SDALEFLIERYRNFVRAKARSYFLIGADREDIIQEGMIGLYKAVRDYRTDKLASFKGFAE 86

Query: 502 WWVKQAITRSIADQSCTIRIP 522
             + + +  +I   +    IP
Sbjct: 87  LCITRQMITAIKTATRQKHIP 107


>gi|312126947|ref|YP_003991821.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311776966|gb|ADQ06452.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 244

 Score = 40.6 bits (93), Expect = 0.91,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V+        A +E++      V +  + Y   G    D+ QEG IGL KA   FD  
Sbjct: 50  ELVKYSREGVKEALEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVRDFDET 109

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   S    IP
Sbjct: 110 KYPSFRLFAEMCITRQMITAIKTASRQKHIP 140


>gi|269960387|ref|ZP_06174760.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269834814|gb|EEZ88900.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 91

 Score = 40.6 bits (93), Expect = 0.94,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 29/71 (40%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAK 144
           D   SE   +  +  S  +    + +  A   + D  ++YL E+G   LL+ E E+  A+
Sbjct: 16  DNAQSEGISNEPAKTSTGTKSAAREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYAR 75

Query: 145 RIEAGRAMMMA 155
           R   G      
Sbjct: 76  RALRGDEAARQ 86


>gi|317126839|ref|YP_004093121.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315471787|gb|ADU28390.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 217

 Score = 40.6 bits (93), Expect = 0.96,   Method: Composition-based stats.
 Identities = 24/91 (26%), Positives = 37/91 (40%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S+V       S A + ++      V + A+ Y   G    D++QEG IGL KA   F   
Sbjct: 21  SLVEYVREGDSSALEYLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAIRDFKGD 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 81  KLSSFKAFAELCITRQIITAIKTATRQKHIP 111


>gi|225166785|ref|YP_002650770.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253771351|ref|YP_003034261.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
 gi|225007354|dbj|BAH29453.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|225007371|dbj|BAH29469.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|225007386|dbj|BAH29483.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|225007449|dbj|BAH29545.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253721328|gb|ACT33621.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
          Length = 180

 Score = 40.6 bits (93), Expect = 0.96,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 28/57 (49%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
           S+++K +     +   ++E     +   A +Y   G  F DL+Q G + ++KA  K+
Sbjct: 3   SLIKKAKEGDRASIIFIIEKYKPFIFKSASRYNIPGYDFEDLVQHGYLSIIKAIHKY 59


>gi|289582294|ref|YP_003480760.1| methyl-accepting chemotaxis sensory transducer [Natrialba magadii
           ATCC 43099]
 gi|289531847|gb|ADD06198.1| methyl-accepting chemotaxis sensory transducer [Natrialba magadii
           ATCC 43099]
          Length = 864

 Score = 40.6 bits (93), Expect = 0.96,   Method: Composition-based stats.
 Identities = 40/298 (13%), Positives = 95/298 (31%), Gaps = 31/298 (10%)

Query: 55  PDEVSSEQMEDTV----AMLSNMGINVVDGDDLEDE--EGSEDSLDLASSASNSSVFLQK 108
            ++V +E + +       ML  +   +VD  +L +E  + S D          +S  + +
Sbjct: 495 DEDVDNEALAEIATSFNEMLDQLEWTIVDIQELAEEVDDVSADVTTRVEEIERASGEVSR 554

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSRE-GEI---------------AIAKRIEAGRAM 152
             +    +  D    +    G +  LS    EI                 A         
Sbjct: 555 SSEEIATAAADQSERFQNVYGEMNELSATVEEIASTADDVAHVSNQAADSATEASEATDE 614

Query: 153 MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
           + + + E      A+    ++L+     + EI+DL   I  ++     + +   +    E
Sbjct: 615 IQSEMAELERRADAITEQVEQLDAEMGEISEIVDLIDDIAGQTNLLALNASIEAAGAGNE 674

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
                   D+V+    +   A +   +  + V    E    +   +    ++ +  +   
Sbjct: 675 GDGFAVVADEVKSLAEETGEATQEVDERITSVQQSVEETVTEIERMRNRVEEGSAVV--- 731

Query: 273 EDQLRPKVMCALDEIAEVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                   + A+DEI E       S+Q       +  ++S +   + ++  ++     
Sbjct: 732 -----EDGIEAIDEITEQVETANDSIQSINDATDEQARASERVVTMVDEATEISEDTR 784


>gi|260892313|ref|YP_003238410.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ammonifex degensii
           KC4]
 gi|260864454|gb|ACX51560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ammonifex degensii
           KC4]
          Length = 215

 Score = 40.6 bits (93), Expect = 0.97,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A++ ++      V + A+ Y   G    D+IQEG IGL KA   F   
Sbjct: 21  EVVAYARKGDVRAQEYLINKYKNFVRAKARAYFLVGADREDIIQEGMIGLYKAIRDFRMD 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 81  KLSSFRAFAELCITRQIITAIKTATRQKHIP 111


>gi|187779022|ref|ZP_02995495.1| hypothetical protein CLOSPO_02617 [Clostridium sporogenes ATCC
           15579]
 gi|187772647|gb|EDU36449.1| hypothetical protein CLOSPO_02617 [Clostridium sporogenes ATCC
           15579]
          Length = 176

 Score = 40.6 bits (93), Expect = 0.97,   Method: Composition-based stats.
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++K     + A +++++  + L++  A KY  +   + DL+Q G + ++KAA  +   
Sbjct: 3   QLIKKYREGDNRALQKIIDNFIPLILKEASKYKIKCYDYEDLVQHGYLSVIKAANMYKGE 62

Query: 492 LGYKFSTYAMWWVKQAI 508
               F  Y +  +KQ  
Sbjct: 63  DKN-FKFYCIKAIKQNY 78


>gi|160914381|ref|ZP_02076596.1| hypothetical protein EUBDOL_00385 [Eubacterium dolichum DSM 3991]
 gi|158433539|gb|EDP11828.1| hypothetical protein EUBDOL_00385 [Eubacterium dolichum DSM 3991]
          Length = 135

 Score = 40.6 bits (93), Expect = 0.98,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 51/119 (42%), Gaps = 5/119 (4%)

Query: 551 EIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLR 610
           E         E  R + K+  +   L      +   +  DFI D+ AV   ++ + A + 
Sbjct: 18  EQYTDFYRDKERWRYLQKLDTKNRLLSLDGFTDSEGNPLDFITDE-AVDIAETVVNAVMV 76

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +     L  L+  E+ +++  F  G++      EVG +  +T+  + + +A+ + KL+ 
Sbjct: 77  DRLKAALPLLSDSEQELIQAIFFDGLSE----REVGARLGITQSVVNKRKARILIKLRK 131


>gi|149044094|gb|EDL97476.1| Cdc42 binding protein kinase beta, isoform CRA_a [Rattus
           norvegicus]
          Length = 1686

 Score = 40.6 bits (93), Expect = 0.98,   Method: Composition-based stats.
 Identities = 34/298 (11%), Positives = 93/298 (31%), Gaps = 21/298 (7%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMIQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                 ++     A  ++  L +   +++  L +   +L+              +  R+L
Sbjct: 525 TQRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKD----------AHQQRKRAL 574

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+ +   ++  +   + + +  +L      + +   +ID + + +    K     E  L 
Sbjct: 575 QEFSELNERMAELRSQKQKVSRQLRDKEEEMEVAMQKIDSMRQDIRKSEKSRKELEARLE 634

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                   +R +        +     +   K    G            I KIR+E++ 
Sbjct: 635 DAVAEASKERKLREHSESFSKQMERELETLKVKQGGRGPGATLEHQQEISKIRSELEK 692


>gi|311252357|ref|XP_003125069.1| PREDICTED: dynactin subunit 1-like [Sus scrofa]
          Length = 1313

 Score = 40.6 bits (93), Expect = 0.99,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 279 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 338

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 339 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 398

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 399 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 458

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 459 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 517

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 518 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 573

Query: 456 VISV 459
           V   
Sbjct: 574 VERQ 577


>gi|237755445|ref|ZP_04584070.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692409|gb|EEP61392.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 98

 Score = 40.6 bits (93), Expect = 0.99,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 5/83 (6%)

Query: 445 KKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
           KKE+VE ++ LV  VA K   R     ++F DL+Q G +GL+KA E ++   G KFSTYA
Sbjct: 8   KKEIVEEHIGLVKKVASKIFYRLPDCEIEFDDLVQTGIVGLLKALENYNEDKG-KFSTYA 66

Query: 501 MWWVKQAITRSIADQSCTIRIPV 523
              ++  I   +  Q    +   
Sbjct: 67  YIRIRGEILDFLRQQDIMPKTEK 89


>gi|190689487|gb|ACE86518.1| dynactin 1 (p150, glued homolog, Drosophila) protein [synthetic
           construct]
          Length = 1278

 Score = 40.6 bits (93), Expect = 0.99,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|297565341|ref|YP_003684313.1| ECF subfamily RNA polymerase sigma-24 subunit [Meiothermus silvanus
           DSM 9946]
 gi|296849790|gb|ADH62805.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Meiothermus
           silvanus DSM 9946]
          Length = 196

 Score = 40.6 bits (93), Expect = 0.99,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
           + D      L        R    R LA L+P E ++L   F  G +     E        
Sbjct: 111 LHDPEQELGLWQENDREGRVLVQRALAGLSPEERQLLEESFYWGYSHPELAERHNVPLGT 170

Query: 652 TRERIRQIEAKAIRKLKHPSRSKKLRS 678
            + +IR    +A+ KL+      ++R 
Sbjct: 171 VKTKIR----RALLKLREFLSGAQVRE 193


>gi|291556354|emb|CBL33471.1| hypothetical protein ES1_03080 [Eubacterium siraeum V10Sc8a]
          Length = 1072

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 32/289 (11%), Positives = 88/289 (30%), Gaps = 10/289 (3%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +          E  DS+  +  + +D + ++ +    +      EE+      +   SE
Sbjct: 343 AVKAFEEIAEQEETADSETEIDSEQNDSATEEAVSEPVEDAVKAFEEIAE--KEETADSE 400

Query: 62  QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
              +    ++   I+    D ++  E      + A S + S       +++     +D V
Sbjct: 401 TESEQNDTVTEEAISEPVEDAVKAFEEIAQQDETADSETESEQNETATEEAVSEPVEDAV 460

Query: 122 RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
           + +  E+        E E       E+ +  +      S     A+  + +      T  
Sbjct: 461 KAF-EEI-------AEQEETADSEAESKQNDIATEEVASEPVEDAVKAFEEIAEQEETAD 512

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            E    +     E            ++++  +  +  + +   E    +   +     + 
Sbjct: 513 SETESEQNDTATEEAVSEPVEDAVKAFEEIAEQEETADSEAESEQNDTVTEESVSEPVED 572

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
           +         + +  + + D++ +         +     + A +EIAE 
Sbjct: 573 AVKAFEEIAEQEETADSEIDDEQNDTATEEPVSEPVEDAVKAFEEIAEQ 621



 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 37/278 (13%), Positives = 94/278 (33%), Gaps = 8/278 (2%)

Query: 40  QRGYVTIEELNAF------LPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL 93
           ++G +T   +         +P    ++E++ED    +     ++   + +E+   + + +
Sbjct: 175 EKGIMTSAPIANAVQELAEMPSVIQNNEEIEDVRLPVDESIFDLYASEPVEEAVKAFEEI 234

Query: 94  DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMM 153
                 ++S    ++   + +    +PV   ++    I       +I      E      
Sbjct: 235 AEQEETADSEAESEQNDTATEEPVSEPVEDAVKAFEEIAEQKETADIETEIDSEQNETAT 294

Query: 154 MASLCE-SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
             ++ E      +A     ++     +      +  A   P S+             ++E
Sbjct: 295 EEAVSEPVEDAVKAFEEIAEQEETADSKTESEQNEIATEEPISEPVEDAVKAFEEIAEQE 354

Query: 213 DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
           +++  +   D ++ +   E A     +D  K        E    +  E E +   T  A+
Sbjct: 355 ETADSETEIDSEQNDSATEEAVSEPVEDAVKAFEEIAEKEETADSETESEQNDTVTEEAI 414

Query: 273 EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            + +   V  A +EIA+      S  ++  N    E++
Sbjct: 415 SEPVEDAV-KAFEEIAQQDETADSETESEQNETATEEA 451


>gi|34364922|emb|CAE45882.1| hypothetical protein [Homo sapiens]
          Length = 1278

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|73980501|ref|XP_852790.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 2 [Canis
           familiaris]
          Length = 1270

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|322712149|gb|EFZ03722.1| myosin class II heavy chain (MHC), putative [Metarhizium anisopliae
            ARSEF 23]
          Length = 2286

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 33/281 (11%), Positives = 94/281 (33%), Gaps = 16/281 (5%)

Query: 140  IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGF 199
            + +A+R+   +      + E      A      +L    T     +++E           
Sbjct: 1512 MDLAERLSNEQRKTEKEIAERRAAEDAGAELNRKLQAAETR----VEVEIINRSVFDQRV 1567

Query: 200  FHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLD 259
                E   +Q+ +   + K R   ++   +++   ++S ++  ++    +  +   ++L+
Sbjct: 1568 ADLEERLRHQEDKTEEEVKTRRAAEDRLAEVQRLLRISSEEEGRLRDLLDEKDARIKSLE 1627

Query: 260  EDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS-----LQDNAVNGQKDEKSSVKC 314
            +    +A  ++ +E   +     +  E+   +  L +      QDN     + E++    
Sbjct: 1628 QTGSKNAMRMTLLEAA-QTNSTKSQTEMTNKFNALDADLKAVRQDNHHWRLEAERADESA 1686

Query: 315  KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            +    +L   +      Q  +  L  QL +  +       + L L +  G          
Sbjct: 1687 RRTAGELAHTLNENKHLQKSLHTLTSQLEENERLRESWRSKFLSLQEDMG------KAAR 1740

Query: 375  QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
            +  E +   +   +     +       + ++  + R EI+ 
Sbjct: 1741 EVAEENARHIKRDQAMCARQEVLEARLQAEAKTRERLEIEM 1781


>gi|289065411|gb|ADC80887.1| RNA polymerase sigma factor [Pseudomonas syringae pv. actinidiae]
          Length = 123

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 41/124 (33%), Gaps = 3/124 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADSSDEEDEVESGPDPIIAQQRFGAVS 62

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 63  DQMEITRKALKKFGRDDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 119

Query: 352 NEGE 355
            E  
Sbjct: 120 QERA 123


>gi|149044097|gb|EDL97479.1| Cdc42 binding protein kinase beta, isoform CRA_d [Rattus
           norvegicus]
          Length = 1685

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 34/298 (11%), Positives = 93/298 (31%), Gaps = 21/298 (7%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 384 RGSLKSMIQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 436

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 437 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 496

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                 ++     A  ++  L +   +++  L +   +L+              +  R+L
Sbjct: 497 TQRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKD----------AHQQRKRAL 546

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+ +   ++  +   + + +  +L      + +   +ID + + +    K     E  L 
Sbjct: 547 QEFSELNERMAELRSQKQKVSRQLRDKEEEMEVAMQKIDSMRQDIRKSEKSRKELEARLE 606

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                   +R +        +     +   K    G            I KIR+E++ 
Sbjct: 607 DAVAEASKERKLREHSESFSKQMERELETLKVKQGGRGPGATLEHQQEISKIRSELEK 664


>gi|114578171|ref|XP_001156699.1| PREDICTED: dynactin 1 isoform 15 [Pan troglodytes]
          Length = 1274

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 248 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 307

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 308 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 367

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 368 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 427

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 428 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 486

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 487 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 542

Query: 456 VISV 459
           V   
Sbjct: 543 VERQ 546


>gi|47214961|emb|CAG10783.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 2124

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 43/309 (13%), Positives = 97/309 (31%), Gaps = 14/309 (4%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  +   +E  +      L E   +  A      +  +     +E   L      E  
Sbjct: 1557 DHQRQLVSNLEKKQKKFDQLLAE-EKSISARYAEERDHAEAEAREKETKTLSMARALEEA 1615

Query: 197  GGFFHGTEGHSYQ-KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  + Q + E       +DDV +   ++E + +  +    ++ +  E  E++ 
Sbjct: 1616 LDAKEELERLNKQLRAEMEDLMSSKDDVGKNVHELEKSKRTLEQQVEEMRTQLEELEDEL 1675

Query: 256  RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC- 314
            +  ++ +      + AM+ Q    +    ++  E  R L           +DE+      
Sbjct: 1676 QATEDAKLRLEVNMQAMKAQFERDLQAREEQGEEKKRALVKQVREMEAELEDERKQRALA 1735

Query: 315  ----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                K L+  L +L G         D  V+QL  +  ++   + EL          RD  
Sbjct: 1736 VAGKKKLELDLNELEGQAEAANKGRDEAVKQLRKLQAQVKDYQREL----DEARASRDEI 1791

Query: 371  LERHQGRELDPHWVS---YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
              + +  E     +          +   +           ++  EI S +      + E 
Sbjct: 1792 FTQAKDNEKKLKSLEAEVLQLQEEQAAAERARRHAEQERDELAEEISSSTSGKSSLLEEK 1851

Query: 428  RHIVSMVRK 436
            R + + + +
Sbjct: 1852 RRLEARLAQ 1860


>gi|297528465|ref|YP_003669740.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           C56-T3]
 gi|297251717|gb|ADI25163.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           C56-T3]
          Length = 227

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 79/251 (31%), Gaps = 61/251 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A   ++      V + A+ Y   G    D++QEG IGL KA   F   
Sbjct: 31  QLVALVHEGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGD 90

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F  +A   + + +  +I   +    IP++                           
Sbjct: 91  KLSSFKAFAELCITRQMITAIKTATRQKHIPLN--------------------------- 123

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLR 610
                                 +SL+ PI D++    L D +       P    +     
Sbjct: 124 --------------------SYVSLDKPIYDDESDRTLMDVLSGTQVTDPEQLIVNREEV 163

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     +A L    ER +   +  G +     EE+ +        ++ I   A++++K  
Sbjct: 164 DDIELKMAELLSDLERKVLALYLDGRSYQEISEELNR-------HVKSI-DNALQRVK-- 213

Query: 671 SRSKKLRSFLD 681
              +KL  +L+
Sbjct: 214 ---RKLEKYLE 221


>gi|222530009|ref|YP_002573891.1| RNA polymerase factor sigma-70 [Caldicellulosiruptor bescii DSM
           6725]
 gi|312621716|ref|YP_004023329.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|222456856|gb|ACM61118.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor bescii DSM 6725]
 gi|312202183|gb|ADQ45510.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 244

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V+        A +E++      V +  + Y   G    D+ QEG IGL KA   FD  
Sbjct: 50  ELVKYSREGVKEALEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVRDFDET 109

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   S    IP
Sbjct: 110 KYPSFRLFAEMCITRQMITAIKTASRQKHIP 140


>gi|308811769|ref|XP_003083192.1| unnamed protein product [Ostreococcus tauri]
 gi|116055071|emb|CAL57467.1| unnamed protein product [Ostreococcus tauri]
          Length = 1536

 Score = 40.6 bits (93), Expect = 1.0,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 149/435 (34%), Gaps = 36/435 (8%)

Query: 2   TIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIE---ELNAFLPPDEV 58
                 +    +   D+ D+   + +DD  KK+ K  +++     +   ++N      + 
Sbjct: 247 VTAVANDVKQQAAKIDNVDNKADEQADD-IKKVSKDVKEQEETNEDQSDDINKVEKTTKS 305

Query: 59  SSEQMEDTVAMLSNMG---------INVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKR 109
           + + ++D  +   + G         IN +D     D+   ++  D      N  V +  +
Sbjct: 306 TQDDVDDLSSKQQDQGKKIAQNEASINQLDAQVRADDSKIKEVTDDVEKTDNKIVDVSTK 365

Query: 110 KDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII 169
           + +  R  DD  R    ++        +GE   +K +E  +  +     +   T   L  
Sbjct: 366 QAAEVRELDDTERRLDNKI--------DGE---SKELEETQDQLKDETEKLEDTQDQLKD 414

Query: 170 WRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
              EL+D  + L++     A    + +G      +    + +E    + + ++  +   +
Sbjct: 415 ETKELDDTQSKLQDTTTKLAQASVKEQGDVNKLQDKIDGEDKELDETQSKLENESKELDE 474

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
            + A K    +  +  S  E+     ++    +D     L  + +    ++     ++  
Sbjct: 475 TQDALKDESKELDETKSKFEDETGKLKDATFKQDGEIDKLEEVTEGTNKELDETQSKLES 534

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
             +EL   Q       K +  S +    + K+      L   QS+++   ++L +   ++
Sbjct: 535 ESKELDETQ------SKLDDESKELDATESKVDSESKELDETQSKLESESKELDETQSKL 588

Query: 350 MHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF------VACEV 403
                EL         +     E     E +   +   +   + E K        V  E 
Sbjct: 589 DDESKELDATESKVDSESKELDETQSKLESESKELDETQSKLDDESKELDATESKVDSES 648

Query: 404 DSILKIRNEIKSISV 418
             + + +++++S S 
Sbjct: 649 KELDETQSKLESESK 663


>gi|108762633|ref|YP_631124.1| DNA-binding protein AsgB [Myxococcus xanthus DK 1622]
 gi|401779|gb|AAB59069.1| The asgB coding sequence was deduced from the DNA sequence. A
           putative DNA-binding helix-turn-helix is present near
           the C-terminus [Myxococcus xanthus]
 gi|108466513|gb|ABF91698.1| DNA-binding protein AsgB [Myxococcus xanthus DK 1622]
          Length = 163

 Score = 40.2 bits (92), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
           TLEEVG+   +TRERIRQ+E + + KL+  + ++
Sbjct: 122 TLEEVGEIMNLTRERIRQVETRGLMKLREATEAE 155


>gi|301780768|ref|XP_002925801.1| PREDICTED: serine/threonine-protein kinase MRCK alpha-like isoform
           2 [Ailuropoda melanoleuca]
          Length = 1638

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 70/181 (38%), Gaps = 16/181 (8%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTVDGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IEKLRKQVR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIKTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSI-LKIRNEI-----KSISVETGISISEFRHIVSMV 434
              V       E      +  + +    ++ NE+     K IS   G+   E +  ++ +
Sbjct: 549 KLEVHTEAVAAEASKDRKLREQSEHYSKQLENELEGLKQKQISYSPGLCSIEHQQEITKL 608

Query: 435 R 435
           +
Sbjct: 609 K 609


>gi|221053398|ref|XP_002258073.1| hypothetical protein in Plasmodium species [Plasmodium knowlesi
            strain H]
 gi|193807906|emb|CAQ38610.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
            knowlesi strain H]
          Length = 1886

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 46/126 (36%), Gaps = 2/126 (1%)

Query: 195  SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                     E     +     +E E D   E + +IES  ++  D+  + D   E  E  
Sbjct: 1598 ESDREVEPDEEIESDREMKPDEEMESDREVEPDEEIESDREMKPDEEMESDREVEPDEEI 1657

Query: 255  ERNLDEDEDDSAHTLSAME--DQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
            E N +   D+   +   ME  +++ P     +DE  +   E  +L+++    +    +  
Sbjct: 1658 ESNREMKPDEEMESDREMERNEEIEPDGETEVDEENKTNMEEVTLENDPPEEESVHLAQK 1717

Query: 313  KCKVLK 318
            K    K
Sbjct: 1718 KQTRNK 1723


>gi|194220584|ref|XP_001916761.1| PREDICTED: dynactin 1 (p150, glued homolog, Drosophila) [Equus
           caballus]
          Length = 1280

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|114578175|ref|XP_001156649.1| PREDICTED: dynactin 1 isoform 14 [Pan troglodytes]
          Length = 1266

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 240 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 299

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 300 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 359

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 360 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 419

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 420 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 478

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 479 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 534

Query: 456 VISV 459
           V   
Sbjct: 535 VERQ 538


>gi|160941753|ref|ZP_02089080.1| hypothetical protein CLOBOL_06649 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435250|gb|EDP13017.1| hypothetical protein CLOBOL_06649 [Clostridium bolteae ATCC
           BAA-613]
          Length = 167

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/105 (20%), Positives = 43/105 (40%), Gaps = 9/105 (8%)

Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
           R+V        SL+T     D     + + D + +S  D AI     +     L  LT  
Sbjct: 67  REVPYEILHYQSLDT-----DEMLGEELLYDDSGLSIEDKAIHNIYTDKLYPALVKLTDE 121

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           E  +L   +  G++       + KQ  +++  + + + K +++L+
Sbjct: 122 ERDLLYRLYYQGVSE----RVLAKQLGISQAAVHKRKEKILKQLR 162


>gi|257460916|ref|ZP_05626017.1| conserved hypothetical protein [Campylobacter gracilis RM3268]
 gi|257442247|gb|EEV17389.1| conserved hypothetical protein [Campylobacter gracilis RM3268]
          Length = 91

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 24/58 (41%)

Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
           ++        +  + D    E+     ++ ER+  IE  A+ KL+HP   KK     +
Sbjct: 10  DKVCAERVRMLKGDADVAYHELAAMLGISVERVAMIERTALAKLRHPKNRKKWMEIFE 67


>gi|295401937|ref|ZP_06811900.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312109244|ref|YP_003987560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294976067|gb|EFG51682.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311214345|gb|ADP72949.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 216

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 34/91 (37%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A   ++      V + A+ Y   G    D+IQEG IGL KA   F   
Sbjct: 20  QLVELVHQGDGDALDFLIHKYQNFVRAKARSYFLVGADREDIIQEGMIGLYKAVRDFKGD 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   +    IP
Sbjct: 80  KLSSFKAFAELCITRQMITAIKTATRQKHIP 110


>gi|225620328|ref|YP_002721585.1| hypothetical protein BHWA1_01407 [Brachyspira hyodysenteriae WA1]
 gi|225215147|gb|ACN83881.1| hypothetical protein BHWA1_01407 [Brachyspira hyodysenteriae WA1]
          Length = 1152

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 31/227 (13%), Positives = 71/227 (31%), Gaps = 31/227 (13%)

Query: 49  LNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQK 108
           LN  +   E + +++     +L + G  + D +D ++E   ED   L     N      +
Sbjct: 364 LNDVM-DYEDNDDEIIKLDDVLEDGGETIQDDNDEDEEIKIEDLSSLDKVLENEDNDEDE 422

Query: 109 RKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALI 168
                +    D V           L  ++ E+     I+         L + P       
Sbjct: 423 SIKLENIENLDDV-----------LDEQQDELEDVPNIDDVLDEQKDELEDIPS------ 465

Query: 169 IWRDELNDGTTLLREIIDLE-ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETE 227
                       L +I+D +      E         +    +  +  S +   +D    +
Sbjct: 466 ------------LDDIVDEDNEENNTEDVPNLDDVLDEQKDELEDIPSLDDVLNDDNTED 513

Query: 228 GDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
                     ++D  +     ++  ++E   +  ED+S  ++  M++
Sbjct: 514 VPNLDDVLDEQEDELEDVPNLDDVLDEEEKENNTEDNSNESMPEMKE 560


>gi|76257394|ref|NP_446072.2| serine/threonine-protein kinase MRCK beta [Rattus norvegicus]
 gi|81174936|sp|Q7TT49|MRCKB_RAT RecName: Full=Serine/threonine-protein kinase MRCK beta; AltName:
           Full=CDC42-binding protein kinase beta; AltName:
           Full=DMPK-like beta; AltName: Full=Myotonic dystrophy
           kinase-related CDC42-binding kinase beta; Short=MRCK
           beta; Short=Myotonic dystrophy protein kinase-like beta
 gi|30841498|gb|AAP34403.1| CDC42-binding protein kinase beta [Rattus norvegicus]
 gi|149044095|gb|EDL97477.1| Cdc42 binding protein kinase beta, isoform CRA_b [Rattus
           norvegicus]
          Length = 1713

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 34/298 (11%), Positives = 93/298 (31%), Gaps = 21/298 (7%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMIQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
                 ++     A  ++  L +   +++  L +   +L+              +  R+L
Sbjct: 525 TQRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKD----------AHQQRKRAL 574

Query: 298 QDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           Q+ +   ++  +   + + +  +L      + +   +ID + + +    K     E  L 
Sbjct: 575 QEFSELNERMAELRSQKQKVSRQLRDKEEEMEVAMQKIDSMRQDIRKSEKSRKELEARLE 634

Query: 358 RLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                   +R +        +     +   K    G            I KIR+E++ 
Sbjct: 635 DAVAEASKERKLREHSESFSKQMERELETLKVKQGGRGPGATLEHQQEISKIRSELEK 692


>gi|262066779|ref|ZP_06026391.1| RNA polymerase sigma-H factor [Fusobacterium periodonticum ATCC
           33693]
 gi|291379582|gb|EFE87100.1| RNA polymerase sigma-H factor [Fusobacterium periodonticum ATCC
           33693]
          Length = 195

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             +I ++++K +   S A   +++   +++   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 2   EENINTILKKAQTGDSEAIDWILKEYSKILSFNAQKYYLIGAEQEDLLQEGILGLLKAIK 61

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIA 513
            +D      FS++A   +++ +  +I 
Sbjct: 62  FYDETKS-SFSSFAFLCIRREMISAIR 87


>gi|237739548|ref|ZP_04570029.1| RNA polymerase sigma-H factor [Fusobacterium sp. 2_1_31]
 gi|229423156|gb|EEO38203.1| RNA polymerase sigma-H factor [Fusobacterium sp. 2_1_31]
          Length = 196

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             +I ++++K +   S A   +++   +++   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 3   EENINTILKKAQTGDSEAIDWILKEYSKILSFNAQKYYLIGAEQEDLLQEGILGLLKAIK 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIA 513
            +D      FS++A   +++ +  +I 
Sbjct: 63  FYDETKS-SFSSFAFLCIRREMISAIR 88


>gi|318040246|ref|ZP_07972202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 107

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/45 (33%), Positives = 26/45 (57%)

Query: 104 VFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEA 148
           V   +R  +A     D VR YLR++G + LL+ E EI + ++++ 
Sbjct: 6   VIRSERDAAALAGGTDLVRSYLRDIGRVPLLTHEQEITLGRQVQE 50


>gi|294792433|ref|ZP_06757580.1| RNA polymerase sigma factor rpoD1 [Veillonella sp. 6_1_27]
 gi|294456332|gb|EFG24695.1| RNA polymerase sigma factor rpoD1 [Veillonella sp. 6_1_27]
          Length = 130

 Score = 40.2 bits (92), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A   + +  +  LR      L  L+P +  +LR  +G       +L  V ++   +R+ I
Sbjct: 50  ADMVMSADEEHRLRARLAWALGRLSPDQRDLLRRVYG----ECQSLVSVSEELNCSRQAI 105

Query: 657 RQIEAKAIRKLKH 669
           ++   +AIRKL+ 
Sbjct: 106 QRRHERAIRKLRR 118


>gi|289065421|gb|ADC80892.1| RNA polymerase sigma factor [Pseudomonas sp. NCPPB3871]
 gi|289065423|gb|ADC80893.1| RNA polymerase sigma factor [Pseudomonas sp. PD2774]
          Length = 123

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 41/124 (33%), Gaps = 3/124 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E+ +  +    E +  P  + A      V 
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEESADASDEEDEVESGPDPVIAQQRFGAVS 62

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 63  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 119

Query: 352 NEGE 355
            E  
Sbjct: 120 QERA 123


>gi|125977832|ref|XP_001352949.1| GA21664 [Drosophila pseudoobscura pseudoobscura]
 gi|54641700|gb|EAL30450.1| GA21664 [Drosophila pseudoobscura pseudoobscura]
          Length = 1341

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 51/337 (15%), Positives = 116/337 (34%), Gaps = 35/337 (10%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 442 ELDEVAESIELLTLDKEMAEERMETLQMELEIAQERNDELSL------DVEILKAEQEEQ 495

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFF 200
             +RIE        ++  +P +    +     L      LRE ++ L   +  E +    
Sbjct: 496 QGQRIEKTEKQA--AVGGTPQSAGEFL----RLEQYNQRLRETVVRLRDTLAQEKQQAQR 549

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E          S+  E   ++E         +V   D  +       AE+    L  
Sbjct: 550 SHKE-----LETKHSEINELKSIKELLSRRVDHMEVQLMDLKEQVDASLGAESMVTQLAS 604

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            + +    +  +ED++    + AL++I E                  E +      L+E+
Sbjct: 605 LKLELEDRVKLLEDEVNE--LEALEQIQEQ---------------LIESNQELETDLREE 647

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + K+ G + +   +    +E LYD    IM     + +L +   ++ D  L        +
Sbjct: 648 IEKMAGQVKILDQQKHAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSSAN 707

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                 A +  + ++++  +        +  +IK++ 
Sbjct: 708 ESQQEEASNQSQNDYQHIFSVSKAYGRALEQQIKAVE 744


>gi|149636632|ref|XP_001510418.1| PREDICTED: similar to Vesicle docking protein [Ornithorhynchus
           anatinus]
          Length = 1009

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 55/413 (13%), Positives = 141/413 (34%), Gaps = 39/413 (9%)

Query: 19  DDSLVFDFSDDSWKKMIKL--ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76
           +D+ + +F  +  K++I+    ++       E   F+   E+ S+  +      S+    
Sbjct: 594 NDNTLENFMKEKLKQLIEKRLGKEN----FIEKLGFISKHELYSKAAQKPQPNFSSPDHM 649

Query: 77  VVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR 136
           + D +  +  +  E  +  A   S+     ++         D  V  Y + M       R
Sbjct: 650 IFDHEFTKLVKELEGIITKAIYKSSEEDQKEEEVKKTLEQHDSIVSHY-KNM------IR 702

Query: 137 EGEIAIAKRIEA-GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           E +I +    +            ++ +T QA  I + +       ++   D +    P  
Sbjct: 703 EQDIQLEDLKQQVSTLKCQNEQLQTAVTQQASQIQQHKDQYNLLKVQLGKDHQHHGVPGD 762

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                      + + RE+ ++ K + ++ + + + + A   S            + E  +
Sbjct: 763 GAQVNGLQPEETGRLREEINELKSQRELLQGQLEEKDALIESLRSEKTAGKTETSLEAFK 822

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV-------NGQKDE 308
               E+  +    L A+  QL+   + +L+       +   LQ +         +G+   
Sbjct: 823 AGDSENTTELQRELEALRSQLK---LQSLEMTKLQLEKQELLQKSETSNKSVPVSGENGA 879

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
            ++ K   L+ +L  L+      ++ +  L E+   +++++  +   +  L       + 
Sbjct: 880 VAAAKNTELEGRLSVLLQETKELKNEVKTLSEEQASLNRQLDSSNSTIAVLQNEKSKLQQ 939

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
             LE                   + E    +A +   I+ ++N++K +     
Sbjct: 940 EVLE---------------SKKEQDELLVLLADQDQKIIALKNKLKELGEPVE 977


>gi|323141212|ref|ZP_08076113.1| chromosome segregation protein SMC [Phascolarctobacterium sp. YIT
           12067]
 gi|322414355|gb|EFY05173.1| chromosome segregation protein SMC [Phascolarctobacterium sp. YIT
           12067]
          Length = 1189

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 45/350 (12%), Positives = 109/350 (31%), Gaps = 7/350 (2%)

Query: 149 GRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSY 208
           G+  +   L   P   ++L      +       ++ +                 +E  + 
Sbjct: 142 GQNKIDEVLNSRPEDRRSLFEEAAGIAKYRLRKKDAVRKLDDTANNLTRINDIRSEVDAQ 201

Query: 209 QKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            +    +  K +   + +E        V       ++      +  +        + A  
Sbjct: 202 VEPLAQAAAKTQQFNELSEALRRCRLSVLLRRLDALEETGNELQAKKEAAASAYSEQAAK 261

Query: 269 LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL 328
           + +M+ +   +V   LD++AE Y +L+   D        EK     KVL E++ +   + 
Sbjct: 262 VGSMQAE-AVQVQQELDKLAEAYNKLQD--DIKNRETALEKLRGDQKVLDERVSQNEKAS 318

Query: 329 SLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAK 388
                R + L +Q+ +   R+     E   + + + +           R+     +  AK
Sbjct: 319 ERLVQRNERLEQQVREQEARMQELATEFDAVEKRHAVADGAVKHLQAQRDEQSAKLEEAK 378

Query: 389 DFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
              E     F +  +  ++K+RNE+ ++  E          +   + + E     A+++ 
Sbjct: 379 RNDEQAQSQFFSG-MQELIKLRNELHNLEQEQEQRARRREALKKSIEEAEAADRQAQEQY 437

Query: 449 --VEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
             +           +    +G +       G   L +A          + 
Sbjct: 438 SSLLEQQSQCAHGMELVRKKGEELRSAYDAGQKEL-QAVRSSQQQCQRRL 486


>gi|195173274|ref|XP_002027418.1| GL20892 [Drosophila persimilis]
 gi|194113270|gb|EDW35313.1| GL20892 [Drosophila persimilis]
          Length = 1341

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 51/337 (15%), Positives = 116/337 (34%), Gaps = 35/337 (10%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 442 ELDEVAESIELLTLDKEMAEERMETLQMELEIAQERNDELSL------DVEILKAEQEEQ 495

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFF 200
             +RIE        ++  +P +    +     L      LRE ++ L   +  E +    
Sbjct: 496 QGQRIEKTEKQA--AVGGTPQSAGEFL----RLEQYNQRLRETVVRLRDTLAQEKQQAQR 549

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E          S+  E   ++E         +V   D  +       AE+    L  
Sbjct: 550 SHKE-----LETKHSEINELKSIKELLSRRVDHMEVQLMDLKEQVDASLGAESMVTQLAS 604

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            + +    +  +ED++    + AL++I E                  E +      L+E+
Sbjct: 605 LKLELEDRVKLLEDEVNE--LEALEQIQEQ---------------LIESNQELETDLREE 647

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + K+ G + +   +    +E LYD    IM     + +L +   ++ D  L        +
Sbjct: 648 IEKMAGQVKILDQQKHAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSSAN 707

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
                 A +  + ++++  +        +  +IK++ 
Sbjct: 708 ESQQEEASNQSQNDYQHIFSVSKAYGRALEQQIKAVE 744


>gi|121488791|emb|CAJ18280.1| sigma 70-type sigma factor [Chlorobaculum limnaeum]
          Length = 89

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 1/90 (1%)

Query: 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIED 594
              ++  + +R+P  +E+A  L M  + V   LKI    +S++ P    D + L D +++
Sbjct: 1   AYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQN 60

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPRE 624
              + P     + +L     R L+ L PRE
Sbjct: 61  DGHM-PDHGLNRDSLTLEVERSLSVLAPRE 89


>gi|6786|emb|CAA30854.1| myosin 1 [Caenorhabditis elegans]
          Length = 1938

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 39/255 (15%), Positives = 91/255 (35%), Gaps = 14/255 (5%)

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            E     +   ++ E++   +     ++E +   + D  S+ +    + E   R   ++ +
Sbjct: 896  EALELTQGGSAAIEEKLTRLNSARQEVEKSLNDANDRLSEHEEKNADLEKQRRKAQQEVE 955

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK--- 320
            +   ++ A++  L      +L+E A    ++ SLQD   +  +      K K L E+   
Sbjct: 956  NLKKSIEAVDGNLA----KSLEEKAAKENQIHSLQDEMNSQDETIGKINKEKKLLEENNR 1011

Query: 321  -LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
             LV  + +    Q++ + L  +L      +        R+       +       +G + 
Sbjct: 1012 QLVDDLQAEEAKQAQANRLRGKLEQTLDEMEEAVEREKRIRAETEKSKRKVEGELKGAQE 1071

Query: 380  DPHWVSYAKDFPEGEWK------NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
                +S  K   +   K      + +   ++    + N +   S E    I E    +  
Sbjct: 1072 TIDELSAIKLETDASLKKKEADIHALGVRIEDEQALANRLTRQSKENAQRIIEIEDELEH 1131

Query: 434  VRKGECEASIAKKEM 448
             R+   +A  A+ E+
Sbjct: 1132 ERQSRSKADRARAEL 1146


>gi|210623158|ref|ZP_03293612.1| hypothetical protein CLOHIR_01562 [Clostridium hiranonis DSM 13275]
 gi|210153791|gb|EEA84797.1| hypothetical protein CLOHIR_01562 [Clostridium hiranonis DSM 13275]
          Length = 216

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 42/109 (38%), Gaps = 3/109 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
           K++         E   IV           +A + ++      V   AK Y   G    D+
Sbjct: 7   KNVEQNENQQQKEEYEIVKRA---ANGDRMALEYIMAKYKNFVRVKAKSYFLIGADREDI 63

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           IQEG IGL KA   FD    + F ++A   + + I  +I   +    IP
Sbjct: 64  IQEGMIGLYKAIRDFDETKAHSFRSFAEVCITRQIITAIKTATRQKHIP 112


>gi|302390942|ref|YP_003826762.1| RNA polymerase, sigma 30 subunit, SigH [Acetohalobium arabaticum
           DSM 5501]
 gi|302203019|gb|ADL11697.1| RNA polymerase, sigma 30 subunit, SigH [Acetohalobium arabaticum
           DSM 5501]
          Length = 217

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 20/91 (21%), Positives = 39/91 (42%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V+  +    +A + +++     V + A+ Y   G    DL+QEG IGL KA   +   
Sbjct: 23  ELVQFAQDGNQLAMEYLLKKYKNFVRNRARSYFLIGAGRDDLVQEGMIGLYKAICDYKVE 82

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F ++A   + + +  +I   +     P
Sbjct: 83  RLASFQSFAELCITRQLITAIKTATRQKHQP 113


>gi|316968996|gb|EFV53166.1| putative SNF2 family N- domain protein [Trichinella spiralis]
          Length = 1667

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 26/177 (14%), Positives = 63/177 (35%), Gaps = 1/177 (0%)

Query: 143  AKRIEAGRA-MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
              RI   R   +   +CE  +    L+    +   G   + E           +    F 
Sbjct: 1376 CHRIGQTRDVHIYRLICERTIEENILLKATQKRKLGELAIDEGGFKADFFHNTNIKELFD 1435

Query: 202  GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
              E    +   D+  ++    V++    I +   V +    +     E+ EN      + 
Sbjct: 1436 MEESVFVRDVSDADIQQAMSKVEDDNDAIAARIAVDEAQAEERADEEEDDENATSGQKKS 1495

Query: 262  EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
            +       +++ +   P V+  L+E+ +V  ++  ++  A+   ++E++    + LK
Sbjct: 1496 DAVQNANDNSVAESSDPDVLRVLEEMKDVLSKMSEVERYALEYIEEERAFEFSEELK 1552


>gi|296109490|ref|YP_003616439.1| methyl-accepting chemotaxis sensory transducer [Methanocaldococcus
           infernus ME]
 gi|295434304|gb|ADG13475.1| methyl-accepting chemotaxis sensory transducer [Methanocaldococcus
           infernus ME]
          Length = 754

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 41/336 (12%), Positives = 118/336 (35%), Gaps = 23/336 (6%)

Query: 27  SDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86
            D   +K+I  A       ++ ++  +   +   +++ + +  L      V +  D   +
Sbjct: 429 RDVRIQKLINKA-------LDMISELIKKLKEDVDRLHEKLKTLEEEADRVKEVSDQVAD 481

Query: 87  EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIA--K 144
             ++ ++     ++      Q+ +D    + D     Y   +  +E +    E +    +
Sbjct: 482 AANQVAVAATDQSNKLQDITQELEDVNKLAND----AYNSALEGVEAVKSVEEASQVGVE 537

Query: 145 RIEAGRAMMMA---SLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
           ++E     M      + E     + L     ++N+ T L+++I +    +   +      
Sbjct: 538 KVENAIETMQRIANVIDELGRALEELGKKSQKINEITALIKDIAEQTGLLALNASIEAAR 597

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E         S  +   +++ ++  DI    +  ++   K        +N+  N    
Sbjct: 598 AGEAGRGFAVVASEIKGLAEEIGKSVDDINKTVEEIREAIEKTIDLGLTGKNEVDNGVVA 657

Query: 262 EDDSAHTLSAMED------QLRPKVMCALDEIAEVYRE-LRSLQDNAVNGQKDEKSSVKC 314
            D+  +    +++      +    +  A+  + E   + LR +QD A   ++   ++ + 
Sbjct: 658 IDEVNNAFLKIKEAVDKAHEKMEVIKQAVQNVTENVEKALRDVQDVASISEEFAATAEEL 717

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
               E+L   +  +      ++ +V+ +   S R  
Sbjct: 718 TASTEELNGAIEQIDNAVKELEQIVDDIKKSSDRFK 753


>gi|225682069|gb|EEH20353.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb03]
          Length = 501

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 56/154 (36%), Gaps = 4/154 (2%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
              +I I  RI      ++ SL       + +    +EL +    + EI ++   +GP  
Sbjct: 341 ATDQIDI-VRIMQASTGVLRSLHAQVGGVEMVEDAVEELREEMARVDEIGNIINEVGPAI 399

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE---NAE 252
             G           K +++ + KE +  +    ++E   K +    ++     E    A 
Sbjct: 400 DEGELDDELVEMEAKEQEARETKEAEATRWKLAELEQLGKPAAKVEAEAQRKAEQEYTAA 459

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
           +   + D D +DS   LS M  +   K +    +
Sbjct: 460 SQPVDYDSDLEDSIGKLSQMSIEDTSKTLDTTAK 493


>gi|17508449|ref|NP_492053.1| LEThal family member (let-75) [Caenorhabditis elegans]
 gi|205829470|sp|P02567|MYO1_CAEEL RecName: Full=Myosin-1; AltName: Full=Lethal protein 75; AltName:
            Full=Myosin heavy chain D; Short=MHC D
 gi|3876131|emb|CAA95806.1| C. elegans protein R06C7.10, confirmed by transcript evidence
            [Caenorhabditis elegans]
 gi|3878843|emb|CAA95848.1| C. elegans protein R06C7.10, confirmed by transcript evidence
            [Caenorhabditis elegans]
          Length = 1938

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 39/255 (15%), Positives = 91/255 (35%), Gaps = 14/255 (5%)

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            E     +   ++ E++   +     ++E +   + D  S+ +    + E   R   ++ +
Sbjct: 896  EALELTQGGSAAIEEKLTRLNSARQEVEKSLNDANDRLSEHEEKNADLEKQRRKAQQEVE 955

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK--- 320
            +   ++ A++  L      +L+E A    ++ SLQD   +  +      K K L E+   
Sbjct: 956  NLKKSIEAVDGNLA----KSLEEKAAKENQIHSLQDEMNSQDETIGKINKEKKLLEENNR 1011

Query: 321  -LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
             LV  + +    Q++ + L  +L      +        R+       +       +G + 
Sbjct: 1012 QLVDDLQAEEAKQAQANRLRGKLEQTLDEMEEAVEREKRIRAETEKSKRKVEGELKGAQE 1071

Query: 380  DPHWVSYAKDFPEGEWK------NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
                +S  K   +   K      + +   ++    + N +   S E    I E    +  
Sbjct: 1072 TIDELSAIKLETDASLKKKEADIHALGVRIEDEQALANRLTRQSKENAQRIIEIEDELEH 1131

Query: 434  VRKGECEASIAKKEM 448
             R+   +A  A+ E+
Sbjct: 1132 ERQSRSKADRARAEL 1146


>gi|302670826|ref|YP_003830786.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395299|gb|ADL34204.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 258

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 28/131 (21%), Positives = 55/131 (41%), Gaps = 1/131 (0%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW-CLGYKFSTY 499
              A+ +++E  L LV+ VA+ YT +G+   DLI EGN  L K     D      +   +
Sbjct: 110 DKEAQSKLIECFLPLVVDVARMYTEQGVYLEDLIGEGNFALTKGVTMLDAVGEPEEVEGF 169

Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
               +  A+   I            +   + +V   A  ++  ++R+ T +E+  +    
Sbjct: 170 LYKLMLDAMEAVIESNLAEDAGEQKVLKLVQEVADKASELAQDLRRKVTVKELMDETGWD 229

Query: 560 VEGVRKVLKIT 570
            + +R  +K +
Sbjct: 230 EDKIRSAIKFS 240


>gi|294794237|ref|ZP_06759373.1| RNA polymerase sigma factor SigK (Sigma-K factor) [Veillonella sp.
           3_1_44]
 gi|294454567|gb|EFG22940.1| RNA polymerase sigma factor SigK (Sigma-K factor) [Veillonella sp.
           3_1_44]
          Length = 130

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 597 AVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
           A   + +  +  LR      L  L+P +  +LR  +G       +L  V ++   +R+ I
Sbjct: 50  ADMVMSADEEHRLRARLVWALGRLSPDQRDLLRRVYG----ECQSLVSVSEELNCSRQAI 105

Query: 657 RQIEAKAIRKLKH 669
           ++   +AIRKL+ 
Sbjct: 106 QRRHERAIRKLRR 118


>gi|205277392|ref|NP_001128512.1| dynactin subunit 1 isoform 3 [Homo sapiens]
          Length = 1253

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|114578185|ref|XP_001156426.1| PREDICTED: dynactin 1 isoform 10 [Pan troglodytes]
          Length = 1199

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|42569586|ref|NP_180882.2| XID; motor/ protein binding [Arabidopsis thaliana]
 gi|330253710|gb|AEC08804.1| myosin XI D [Arabidopsis thaliana]
          Length = 1770

 Score = 40.2 bits (92), Expect = 1.2,   Method: Composition-based stats.
 Identities = 48/337 (14%), Positives = 122/337 (36%), Gaps = 25/337 (7%)

Query: 56   DEVSSEQMEDTVAMLSNMGI-----NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRK 110
            ++V ++++ED  + L++M +      V   +++   + +   + L        + +    
Sbjct: 932  EQVKTQEVEDLRSALNDMKLQLGETQVTKSEEILKLQSALQDMQLEFEELAKELEMTNDL 991

Query: 111  DSADRSTDDPVRMYLREM----GSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
             + +    D V    R++       E  S+  E  + + +      ++  L       +A
Sbjct: 992  AAENEQLKDLVSSLQRKIDESDSKYEETSKLSEERVKQEVPVIDQGVIIKLEAENQKLKA 1051

Query: 167  LIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQET 226
            L+   ++         + +D +  +   +       +    Y+   + + E ER     +
Sbjct: 1052 LVSTLEKKI-------DSLDRKHDVTSSNISDQLKESASSDYEMLSNLAAENERLKALVS 1104

Query: 227  EGDIESAAKVSKDDRSKVDSPPENAENDERNLD-EDEDDSAHTLSAMEDQLRPKV---MC 282
              + E+      D  ++    P+  + +    D   +D+  + L+A    L   V     
Sbjct: 1105 SLENENYENDGNDSPNEQKEGPQMLKEEILAEDFSIDDEMTNKLAAENKDLYDLVDLLER 1164

Query: 283  ALDEIAEVYRELRSLQDNAVNGQKD--EKSSVKCKVLKEKLVKLV-GSLSLNQ--SRIDL 337
             +DE  + Y E   L +  +    D  +K     ++ +E+L ++V     L +  + +  
Sbjct: 1165 KIDETEKKYEEASKLCEERLKQVVDTEKKYEEASRLCEERLKQVVDTETKLIELKTSMQR 1224

Query: 338  LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            L E++ D+         + LR + S  +     L+  
Sbjct: 1225 LEEKVSDMEAEDKILRQQALRNSASRKMSPQKSLDLF 1261


>gi|319411687|emb|CBQ73731.1| conserved hypothetical protein [Sporisorium reilianum]
          Length = 1848

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 38/275 (13%), Positives = 93/275 (33%), Gaps = 15/275 (5%)

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS 242
           E+   ++      +             + E  + +++ +  +     +E+  + ++    
Sbjct: 651 ELASAKSANEEAERALKADNDTRVVGLRAEIETLKRQVESGKADVCKLEAEKRDTQGHID 710

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSA---MEDQLRPKVMCALDEIAEVYRELRSLQ- 298
            + +  E       N+ ++ +     L      E + + + M   D +AE+  +   L  
Sbjct: 711 ALAADLELERERRLNMVDEVNQLRRDLEQSYRNEAEAKQEAMEEADRVAELEAQAHELHV 770

Query: 299 DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
           +          +S + + L  +     G L   Q+RID L EQL +              
Sbjct: 771 ELEEAKTARIDASKRIEALLSEGSSAEGELRTAQARIDELTEQLSNAHAEAAKAREAAAE 830

Query: 359 LAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV 418
           +  +   +    +  H+  E D             E    +  ++D+  K+  +  +I+ 
Sbjct: 831 VEAAKERQ----IRSHRA-EADGDRAILE------EKVRALKADLDAKEKLLEKQAAIAT 879

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
               S    R  + ++R     A +A +E+V+   
Sbjct: 880 RAEESRIPDREAIELLRGQLKAADVAHEEIVKEME 914


>gi|153813243|ref|ZP_01965911.1| hypothetical protein RUMOBE_03659 [Ruminococcus obeum ATCC 29174]
 gi|149830656|gb|EDM85747.1| hypothetical protein RUMOBE_03659 [Ruminococcus obeum ATCC 29174]
          Length = 197

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 37/91 (40%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ +     +     ++E     V   A+     G +  DLIQEG IGL KA + +   
Sbjct: 11  ELIVRLREGETEISDYLMEKYKEFVRKKARAMFLIGGETDDLIQEGMIGLFKAIQNYQAD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F T+A   + + +  ++ + +     P
Sbjct: 71  KETSFRTFASLCIDRQLYSAVQNSNRQKHQP 101


>gi|114578181|ref|XP_001156821.1| PREDICTED: dynactin 1 isoform 17 [Pan troglodytes]
 gi|332813454|ref|XP_001156762.2| PREDICTED: dynactin subunit 1 isoform 16 [Pan troglodytes]
          Length = 1253

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|312876809|ref|ZP_07736787.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796428|gb|EFR12779.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 211

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V+        A +E++      V +  + Y   G    D+ QEG IGL KA   FD  
Sbjct: 17  ELVKYSREGVKEATEELLSRYQNFVKAKCRMYFLIGADKEDIFQEGMIGLFKAVRDFDET 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   S    IP
Sbjct: 77  KYPSFRLFAEMCITRQMITAIKTASRQKHIP 107


>gi|159904780|ref|YP_001548442.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C6]
 gi|159886273|gb|ABX01210.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C6]
          Length = 729

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 40/358 (11%), Positives = 122/358 (34%), Gaps = 30/358 (8%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D   E+++     + +  +   +IK           EL   +    +  +++ED + + 
Sbjct: 399 ADESGENNNLEKAINIAVSNVADLIK-----------ELREEVDLLNIQIQKVEDELKLA 447

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                 V +      E  S+ S  L  ++       +  K+    + +D V+    E+G 
Sbjct: 448 EETASQVTEAASQVAEASSDQSGKLQEASDELENTYEVVKEVYSAA-EDTVKA-AEEIG- 504

Query: 131 IELLSREGEIAIAKRIEAGRAMMMA---SLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
                 E      K++E   + M +    + +     Q L     ++N+ T L+++I + 
Sbjct: 505 ------ENSENGVKKVENAISRMQSITNVIDDLGKAIQTLGEDGKKINEVTGLIKDIAEQ 558

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
              +   +        +         S  +   ++++++  DI                 
Sbjct: 559 TGLLALNASIEAARAGDAGRGFAVVASEIKALAEEIKKSVEDINHTIDGVNKRIEDTMDL 618

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
               +++        D+    L  ++  +    +  ++ I +        Q  A + +  
Sbjct: 619 GLKGKDEVDRGVIAIDEVNDALLRIKGSVNGAAVK-INGIKK------GAQSAADSTEGA 671

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
            K++     + E+       ++ +   ++ ++E++  +++ + +    +   +  + I
Sbjct: 672 LKNAQDIASISEEFAATAEEVTASTEELNSIIEEIRGVAEEVTNVAKRVTEKSGQFKI 729


>gi|1419567|emb|CAA67333.1| dynactin [Homo sapiens]
          Length = 1263

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 232 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 291

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 292 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 351

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 352 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 411

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 412 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 470

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 471 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 526

Query: 456 VISV 459
           V   
Sbjct: 527 VERQ 530


>gi|148666657|gb|EDK99073.1| dynactin 1 [Mus musculus]
          Length = 1280

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|114578169|ref|XP_001156535.1| PREDICTED: dynactin subunit 1 isoform 12 [Pan troglodytes]
          Length = 1278

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|13259510|ref|NP_004073.2| dynactin subunit 1 isoform 1 [Homo sapiens]
 gi|17375490|sp|Q14203|DCTN1_HUMAN RecName: Full=Dynactin subunit 1; AltName: Full=150 kDa
           dynein-associated polypeptide; AltName: Full=DAP-150;
           Short=DP-150; AltName: Full=p135; AltName:
           Full=p150-glued
 gi|5915904|gb|AAD55811.1| dynactin 1 p150 isoform [Homo sapiens]
          Length = 1278

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|332239086|ref|XP_003268736.1| PREDICTED: dynactin subunit 1 [Nomascus leucogenys]
          Length = 1278

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|301610455|ref|XP_002934764.1| PREDICTED: LOW QUALITY PROTEIN: myosin-9-like [Xenopus (Silurana)
            tropicalis]
          Length = 1947

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 43/308 (13%), Positives = 101/308 (32%), Gaps = 12/308 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  I   +E  +      L E           RD                A    E+ 
Sbjct: 1417 DHQRQIVSNLEKKQKKFDQLLGEEKTISAKYADERDRAEAEAREKETKALALARSLEEAL 1476

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +
Sbjct: 1477 EAKAELERLNKQLRTEMEDLVSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQ 1536

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS----- 311
              ++ +      L AM+ Q    +    ++  +  ++L           +DE+       
Sbjct: 1537 ATEDAKLRLEVNLQAMKAQFERDLQGRDEQSEDKKKQLVRQVKEMEAELEDERKQRSVAV 1596

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  L G +       +  ++QL  +  +I   + EL          RD  L
Sbjct: 1597 AARKKLEMDLKDLEGQIDSANKNREEAIKQLRKLQAQIKDYQREL----DDTRASRDDIL 1652

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFR 428
             + +  E     +       + E       +  +     ++ +EI + S +  +++ E R
Sbjct: 1653 SQSKESEKKLKSMEAEMIHMQEELAAAERGKRQAQQERDELADEIANNSGKGALALEEKR 1712

Query: 429  HIVSMVRK 436
             + S + +
Sbjct: 1713 RLESRIAQ 1720


>gi|291386502|ref|XP_002709771.1| PREDICTED: dynactin 1 [Oryctolagus cuniculus]
          Length = 1279

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEVMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|239825676|ref|YP_002948300.1| RNA polymerase factor sigma-70 [Geobacillus sp. WCH70]
 gi|239805969|gb|ACS23034.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           WCH70]
          Length = 216

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 34/91 (37%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A   ++      V + A+ Y   G    D+IQEG IGL KA   F   
Sbjct: 20  QLVELVHQGDGDALDFLIHKYQNFVRAKARSYFLVGADREDIIQEGMIGLYKAVRDFKGD 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   +    IP
Sbjct: 80  KLSSFKAFAELCITRQMITAIKTATRQKHIP 110


>gi|89096017|ref|ZP_01168910.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
 gi|89088871|gb|EAR67979.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
          Length = 216

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 21/90 (23%), Positives = 38/90 (42%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V   +    +A + +++     V + A K+   G    DL QEG IGL KA   F    
Sbjct: 21  LVVLFQNGDGMASEYLMKKYRHFVRAKASKFFLIGGDKDDLFQEGMIGLYKAIRDFKEDK 80

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  ++   +   ++P
Sbjct: 81  LASFKVFAELCITRQIITAVKTATRQKQMP 110


>gi|312144264|ref|YP_003995710.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311904915|gb|ADQ15356.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 219

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/103 (21%), Positives = 42/103 (40%), Gaps = 2/103 (1%)

Query: 422 ISISEFRHIV--SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
           IS  E++ +    +V         A++ ++      V++ ++ Y   G    D++QEG I
Sbjct: 13  ISFEEYKQMSDDELVELVHQGDMEAQETLIRRYKNFVLAKSRSYFLVGADREDIVQEGMI 72

Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           GL KA   +       F  +A   + + I  +I   +     P
Sbjct: 73  GLYKAVRDYKIERLASFRAFAELCITRQIITAIKAATRQKHQP 115


>gi|109103429|ref|XP_001108541.1| PREDICTED: dynactin subunit 1-like isoform 10 [Macaca mulatta]
          Length = 1253

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|254692972|ref|NP_001028457.1| serine/threonine-protein kinase MRCK alpha [Mus musculus]
          Length = 1732

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|73960801|ref|XP_863642.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform B
           isoform 8 [Canis familiaris]
          Length = 1691

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 60/435 (13%), Positives = 143/435 (32%), Gaps = 46/435 (10%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              V  +                + +     E+K    +  +++ EF  I   +      
Sbjct: 549 KELVQAS----------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVMQKVESLRQELRRTERAKKELE---VHTEAVAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EE++K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGLCSI-EHQQEISKLKTDLEKKSIFY--EEELSK 706

Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE-DKNAVSPLDSAIQANLRETT 613
           +  +    + K LK        +    +++   L D +E ++          +   ++  
Sbjct: 707 REGIHANEI-KNLKKELHDSEGQQLALNKEIMILKDKLEKNRRESQSEREEFENEFKQQY 765

Query: 614 TRVLASLTPR------EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            R    LT        E   L   +      +  LEE  K     +E +   EA+    +
Sbjct: 766 EREKVLLTEENKKLTSELDKLTTLYENVSMRNQQLEEEVKDLADKKESVAHWEAQITEII 825

Query: 668 KHPSRSKKLRSFLDG 682
           +  S  K  R +L  
Sbjct: 826 QWVSDEKDARGYLQA 840


>gi|317057764|ref|YP_004106231.1| LuxR family transcriptional regulator [Ruminococcus albus 7]
 gi|315450033|gb|ADU23597.1| transcriptional regulator, LuxR family [Ruminococcus albus 7]
          Length = 195

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 3/95 (3%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKF 488
             + +       A   ++   +     +A        R     DL+QEG + L++A   +
Sbjct: 15  EELARLSGSDKAALSALLFRYMGTAERIAAGIAPGAGREQTVKDLVQEGMMALLRAVNSY 74

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523
               G  F+ YA   ++ ++   I   +       
Sbjct: 75  RPDRGAGFAAYAGVCIRHSMLSYIMKDNRYSGENR 109


>gi|291538823|emb|CBL11934.1| Methyl-accepting chemotaxis protein [Roseburia intestinalis XB6B4]
          Length = 498

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 33/227 (14%), Positives = 79/227 (34%), Gaps = 11/227 (4%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI  A  + A       S+ E       +    +E ++ +  + +I         E+  
Sbjct: 232 QEITTASGMNAN------SIEEQNTMTATIQDAIEETSERSKQMVDIAMNSNDSIQENMR 285

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 +        +    +    +Q+   ++E  A +  +  S+ +    NA  +   
Sbjct: 286 VMDELKDQAEQITNTNHDVTEAMTKLQDKTKEVEEIAGMILNISSQTNLLALNASIESAR 345

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-KV 316
             E    +    + + +Q+R       +   E+ R    L  NA +     + SV+  + 
Sbjct: 346 AGE----AGRGFAVVAEQIRQLAEQTKNSTEEITRITNELNANANDVVVSVEGSVQATED 401

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            KEK++    + +L    I  LV  + +++K++        ++  + 
Sbjct: 402 QKEKILAASETFNLLNKNIGELVAHIEEVNKKVSGLSDSNNKIVVNC 448


>gi|291536305|emb|CBL09417.1| Methyl-accepting chemotaxis protein [Roseburia intestinalis M50/1]
          Length = 498

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 33/227 (14%), Positives = 79/227 (34%), Gaps = 11/227 (4%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI  A  + A       S+ E       +    +E ++ +  + +I         E+  
Sbjct: 232 QEITTASGMNAN------SIEEQNTMTATIQDAIEETSERSKQMVDIAMNSNDSIQENMR 285

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 +        +    +    +Q+   ++E  A +  +  S+ +    NA  +   
Sbjct: 286 VMDELKDQAEQITNTNHDVTEAMTKLQDKTKEVEEIAGMILNISSQTNLLALNASIESAR 345

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-KV 316
             E    +    + + +Q+R       +   E+ R    L  NA +     + SV+  + 
Sbjct: 346 AGE----AGRGFAVVAEQIRQLAEQTKNSTEEITRITNELNANANDVVVSVEGSVQATED 401

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            KEK++    + +L    I  LV  + +++K++        ++  + 
Sbjct: 402 QKEKILAASETFNLLNKNIGELVAHIEEVNKKVSGLSDSNNKIVVNC 448


>gi|114578173|ref|XP_001156479.1| PREDICTED: dynactin subunit 1 isoform 11 [Pan troglodytes]
          Length = 1271

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 240 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 299

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 300 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 359

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 360 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 419

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 420 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 478

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 479 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 534

Query: 456 VISV 459
           V   
Sbjct: 535 VERQ 538


>gi|187956888|gb|AAI58018.1| Cdc42bpa protein [Mus musculus]
          Length = 1732

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|153931605|ref|YP_001385116.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. ATCC 19397]
 gi|153936750|ref|YP_001388585.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. Hall]
 gi|152927649|gb|ABS33149.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A str. ATCC 19397]
 gi|152932664|gb|ABS38163.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A str. Hall]
          Length = 176

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++K     + A +++++  + L++  A KY  +   + DL+Q G + ++KAA  +   
Sbjct: 3   QLIKKYREGDNKALQKIIDNFIPLILKEASKYKIKCYDYEDLVQHGYLSVIKAANMYKGE 62

Query: 492 LGYKFSTYAMWWVKQAI 508
               F  Y +  +KQ  
Sbjct: 63  DKN-FKFYCIKAIKQNY 78


>gi|73960795|ref|XP_863576.1| PREDICTED: similar to CDC42-binding protein kinase alpha isoform A
           isoform 5 [Canis familiaris]
          Length = 1638

 Score = 40.2 bits (92), Expect = 1.3,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 68/181 (37%), Gaps = 16/181 (8%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ +  +G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTADGPLTASKDLEIKTLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           +  L   +    S ++  +E+   + + +     ++    +     +          EL+
Sbjct: 496 IENLRKQIR-ESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIRTLQQER------EELN 548

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSI-LKIRNEI-----KSISVETGISISEFRHIVSMV 434
              V       E      +  + +    ++ NE+     K IS   G+   E +  +S +
Sbjct: 549 KLEVHTEAVAAEASKDRKLREQSEHYSKQLENELEGLKQKQISYSPGLCSIEHQQEISKL 608

Query: 435 R 435
           +
Sbjct: 609 K 609


>gi|299890875|ref|NP_001177766.1| dynactin subunit 1 isoform 6 [Homo sapiens]
          Length = 1271

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 240 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 299

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 300 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 359

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 360 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 419

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 420 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 478

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 479 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 534

Query: 456 VISV 459
           V   
Sbjct: 535 VERQ 538


>gi|299890871|ref|NP_001177765.1| dynactin subunit 1 isoform 5 [Homo sapiens]
          Length = 1236

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|227500472|ref|ZP_03930531.1| sigma factor [Anaerococcus tetradius ATCC 35098]
 gi|227217386|gb|EEI82711.1| sigma factor [Anaerococcus tetradius ATCC 35098]
          Length = 135

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 30/122 (24%), Positives = 46/122 (37%), Gaps = 11/122 (9%)

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF------IEDKNAVSPLDSAIQA 607
           KK+ +P E  R   K       L+         H GDF      I DK+ +         
Sbjct: 15  KKIYVPDEVYRAYKKEINHEAHLKRLDIKHGVFHFGDFNTSVVDIADKS-IDVEKIIETK 73

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            L E     L +L   E  ++++ +      D TL EV KQ      +I ++  K + KL
Sbjct: 74  MLIEDLHCALNNLNEEERNLIKLLYF----DDKTLIEVAKQRNTNPMKISRLRNKILEKL 129

Query: 668 KH 669
           + 
Sbjct: 130 RK 131


>gi|114578187|ref|XP_515556.2| PREDICTED: dynactin subunit 1 isoform 18 [Pan troglodytes]
          Length = 1236

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|73980503|ref|XP_866352.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 13 [Canis
           familiaris]
          Length = 1281

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|146414948|ref|XP_001483444.1| hypothetical protein PGUG_04173 [Meyerozyma guilliermondii ATCC 6260]
          Length = 1840

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 38/313 (12%), Positives = 105/313 (33%), Gaps = 7/313 (2%)

Query: 143  AKRIEAGRAMMMASLCESPLTFQ----ALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            A  +++    M   L E   T +     L     ++ +    + E+         + +  
Sbjct: 1121 ATALQSEVDEMRKKLDEHESTLKTKEVELKEKTSQITEVQAKVEELESELLIAKTKLEEA 1180

Query: 199  FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                 +     K   S++   R  V + E +++     + D  ++++   E     E + 
Sbjct: 1181 EATSLKTTEELKETKSAENSARKQVAQLENEVKELKSKNADFAAEIEQLKEQKTALELHK 1240

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                +  A +++ +E+ +    +     +  + ++   +  +    +K  ++  + +   
Sbjct: 1241 TTSSEKHASSVAELEEAISKAKLQIKKNLDTLKKKDEEVSKSKAIAEKHVETISRHEKSI 1300

Query: 319  EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
            E     +  L    S  + L E++    K +  +  +L  L     + ++ F  + +  E
Sbjct: 1301 EDQKLKINELETRVSETNELKEKVR---KELEQSASKLQELTDELSLSKNDFRTKLEAAE 1357

Query: 379  LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGE 438
                 +  +    E E +   A    +      E      +   SISE +       K  
Sbjct: 1358 RRAKELEVSLSDKEKEIEQDRALLSANSETAVKEYSEKVTKLEASISELKKQNHEKVKEV 1417

Query: 439  CEASIAKKEMVEA 451
             + +  + ++V+ 
Sbjct: 1418 EDEAERQGQLVKE 1430


>gi|124006960|ref|ZP_01691789.1| serine/threonine kinase with GAF domain [Microscilla marina ATCC
           23134]
 gi|123987413|gb|EAY27133.1| serine/threonine kinase with GAF domain [Microscilla marina ATCC
           23134]
          Length = 1131

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 35/231 (15%), Positives = 88/231 (38%), Gaps = 3/231 (1%)

Query: 219 ERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP 278
            +D+V+     IE   K  +    +     E     E  + ++ ++   T  AM ++ R 
Sbjct: 638 AQDEVENKTAQIEEQKKQIEKSLEEKTEQTEMLLAQEEEMRQNMEELQATQEAMSEKQRE 697

Query: 279 KVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS-VKCKVLKEKLVKLVGSLSLNQSRIDL 337
            +  A  ++    + L+     A + + + K    + K  +E++ + +  L   Q  ++ 
Sbjct: 698 -LEKAKKKLEVNEQVLKKAYKKARDRELEIKQKNEELKAQEEEIRQNMEELKATQEAMER 756

Query: 338 LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
              ++   +K++  NE  L    +          ++++        +  AKD  E + K 
Sbjct: 757 KQIEIEGANKKLAANEKVLKLAYEQVKESESEIRKKNEEIVKQSQILEDAKDELERKNKK 816

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
             A E   + K   +I++       +I++ +     +R+   E    ++ +
Sbjct: 817 MAANER-VLKKAYEKIQAQEQGLKDTINQLQTTEEELRQNMEELQTTQEAL 866


>gi|119620093|gb|EAW99687.1| dynactin 1 (p150, glued homolog, Drosophila), isoform CRA_d [Homo
           sapiens]
          Length = 1265

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 234 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 293

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 294 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 353

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 354 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 413

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 414 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 472

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 473 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 528

Query: 456 VISV 459
           V   
Sbjct: 529 VERQ 532


>gi|118601017|ref|NP_031861.2| dynactin subunit 1 isoform 1 [Mus musculus]
          Length = 1281

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|301772226|ref|XP_002921526.1| PREDICTED: dynactin subunit 1-like isoform 1 [Ailuropoda
           melanoleuca]
          Length = 1281

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   L+  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELNQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|295704098|ref|YP_003597173.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium DSM 319]
 gi|294801757|gb|ADF38823.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium DSM 319]
          Length = 188

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
           +  + DFIED +         +   ++     ++ L+  ++++++  +  G+      EE
Sbjct: 97  SEEIFDFIEDDHPQIDEQLQWKEE-QQRVRHAVSKLSEDQKKIIQSVYFKGLTQQKVAEE 155

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
                   + R+R     A+RKLK
Sbjct: 156 QQIPLGTVKGRVRL----ALRKLK 175


>gi|114578179|ref|XP_001156593.1| PREDICTED: dynactin 1 isoform 13 [Pan troglodytes]
          Length = 1258

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|4139121|gb|AAD03694.1| dynactin 1 [Homo sapiens]
          Length = 1261

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 230 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 289

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 290 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 349

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 350 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 409

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 410 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 468

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 469 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 524

Query: 456 VISV 459
           V   
Sbjct: 525 VERQ 528


>gi|73980499|ref|XP_866328.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 12 [Canis
           familiaris]
          Length = 1274

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 240 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 299

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 300 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 359

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 360 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 419

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 420 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 478

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 479 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 534

Query: 456 VISV 459
           V   
Sbjct: 535 VERQ 538


>gi|297266319|ref|XP_001107877.2| PREDICTED: dynactin subunit 1-like isoform 1 [Macaca mulatta]
          Length = 1236

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|149036515|gb|EDL91133.1| dynactin 1, isoform CRA_b [Rattus norvegicus]
          Length = 1276

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|301772228|ref|XP_002921527.1| PREDICTED: dynactin subunit 1-like isoform 2 [Ailuropoda
           melanoleuca]
          Length = 1268

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 234 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 293

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 294 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 353

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   L+  +S ID L
Sbjct: 354 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELNQAESTIDEL 413

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 414 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 472

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 473 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 528

Query: 456 VISV 459
           V   
Sbjct: 529 VERQ 532


>gi|295694818|ref|YP_003588056.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus tusciae
           DSM 2912]
 gi|295410420|gb|ADG04912.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus tusciae
           DSM 2912]
          Length = 221

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 21/90 (23%), Positives = 36/90 (40%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           +V +       A + ++      V + A+ Y   G    D++QEG IGL K+   F    
Sbjct: 23  LVDRVRDGDEEALEYLIHRYKNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRNDK 82

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  +I   +    IP
Sbjct: 83  LVSFRAFAELCITRQIITAIKTATRQKHIP 112


>gi|297266317|ref|XP_001108486.2| PREDICTED: dynactin subunit 1-like isoform 9 [Macaca mulatta]
          Length = 1278

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|316963964|gb|EFV49303.1| conserved hypothetical protein [Trichinella spiralis]
          Length = 1024

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 26/177 (14%), Positives = 63/177 (35%), Gaps = 1/177 (0%)

Query: 143 AKRIEAGRA-MMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
             RI   R   +   +CE  +    L+    +   G   + E           +    F 
Sbjct: 733 CHRIGQTRDVHIYRLICERTIEENILLKATQKRKLGELAIDEGGFKADFFHNTNIKELFD 792

Query: 202 GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
             E    +   D+  ++    V++    I +   V +    +     E+ EN      + 
Sbjct: 793 MEESVFVRDVSDADIQQAMSKVEDDNDAIAARIAVDEAQAEERADEEEDDENATSGQKKS 852

Query: 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
           +       +++ +   P V+  L+E+ +V  ++  ++  A+   ++E++    + LK
Sbjct: 853 DAVQNANDNSVAESSDPDVLRVLEEMKDVLSKMSEVERYALEYIEEERAFEFSEELK 909


>gi|73980483|ref|XP_866205.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 5 [Canis
           familiaris]
          Length = 1261

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|296223520|ref|XP_002757645.1| PREDICTED: dynactin subunit 1 isoform 3 [Callithrix jacchus]
          Length = 1253

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|311893358|ref|NP_001185795.1| dynactin subunit 1 isoform 2 [Mus musculus]
          Length = 1264

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 230 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 289

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 290 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 349

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 350 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 409

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 410 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 468

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 469 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 524

Query: 456 VISV 459
           V   
Sbjct: 525 VERQ 528


>gi|296223516|ref|XP_002757643.1| PREDICTED: dynactin subunit 1 isoform 1 [Callithrix jacchus]
          Length = 1278

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|195445194|ref|XP_002070216.1| GK11152 [Drosophila willistoni]
 gi|194166301|gb|EDW81202.1| GK11152 [Drosophila willistoni]
          Length = 1237

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 90/627 (14%), Positives = 196/627 (31%), Gaps = 28/627 (4%)

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
               + VV+      +E   +    A   +     + +     +   +    +Y++    
Sbjct: 267 KQQEVKVVEQRKEAADEVLREKKKDAGKITRDLAKIDQEIREFETQMNKRRPLYIKAKEK 326

Query: 131 IE-----LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR--DELNDGTTLLRE 183
           +      L+S +  +  A+  +      +  L +     + L      D  N+     + 
Sbjct: 327 VTHCKKKLVSLQKTLETAREADNAHQQDIRKLEKQLSDIETLKKSFEDDIENESQRRGKS 386

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           +   E  +    +           Y+   DS   +++ +    +G+    A V +  +  
Sbjct: 387 VNMEEGLVQEYDRLKQEAEATATQYRSELDSVNREQKSEQDTLDGETNRRASVEESFKKL 446

Query: 244 VDSPPENAENDERNLDEDEDDSA--HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
                E  +  ++ +D  +   A     + ++D+LR  V  + ++I E  REL +++D  
Sbjct: 447 TLQREEAVKRRDKLMDHIKSSQAALEEQNRIKDELRRDVGSSKEKITEKQRELENVRDQL 506

Query: 302 VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
            +  K +K     +  K+++V+L           D ++       KR      ++L    
Sbjct: 507 GDA-KSDKHEDARRKKKQEVVELFK--KQVPGVYDRMINMCQPTHKRYNVAVTKVLGKFM 563

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
              I       RH  + L    +      P    +     E    +     ++ +     
Sbjct: 564 EAIIVDTEKTARHCIQILKEQMLEVETFLPLDYLQVKPLKERLRNISEPRNVRLVFDVLK 623

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEM-VEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
               E    V             +  M V   +      A        Q   LI  G+  
Sbjct: 624 FEPPEIERAVLFATGNALVCETPEDAMKVAYEIDRSRFDALALDGTFYQKSGLISGGSHD 683

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
           L + A+++D              + + +   +        +         ++     R+ 
Sbjct: 684 LARKAKRWD-EKHMAQLKMQKERLNEELKELVKKSRKQSELAT----VESQIKGLENRLK 738

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF------IED 594
             +    T ++   +    ++ V++ L      IS       +   H+ +       +ED
Sbjct: 739 YSMVDLETSKKSIGQYDNQLQDVQRQLDDFGPKISEIERRMQDREEHIQEIKENMNNVED 798

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGI-GMNTDHTLEEVGK-QFCVT 652
           K   +        N+R+   R L     R  +       I G+NT    E+    +  V 
Sbjct: 799 KVFAAFCRRLGVKNIRQYEERELVMQQERARKRAEYEQQIDGINTQLDFEKQKDTRKNVE 858

Query: 653 R-ERIRQIEAKAIRKLKHPSRSKKLRS 678
           R ER  Q E  A+  LK  + S+ L+ 
Sbjct: 859 RWERSVQDEEDALEGLK-TAESRYLKE 884


>gi|149036514|gb|EDL91132.1| dynactin 1, isoform CRA_a [Rattus norvegicus]
          Length = 1281

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|145551715|ref|XP_001461534.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124429369|emb|CAK94161.1| unnamed protein product [Paramecium tetraurelia]
          Length = 658

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 32/216 (14%), Positives = 72/216 (33%), Gaps = 14/216 (6%)

Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
           +LI  G   + +A +        + S +   W       ++  +               +
Sbjct: 245 NLIALGYSIVNRAPKALPPQYSTRLSQFI--WKLLEKIPALRPRVSHREFHSRFYQLHRQ 302

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
           +     +M  +  ++  P+    K         + +K T++P   +      DT ++GD 
Sbjct: 303 LDDALPQMQYQQHQQQRPQTSNPKSYAMQAQETEKMKKTRKPQQQDLISNGSDTIYMGDV 362

Query: 592 IE-DKNAVSPLDSAIQANLRETTTRVLASLT---------PREERVLRMRFGIGMNTDHT 641
           I+  +  V     +     ++        L           RE +    R          
Sbjct: 363 IDMTQKQVENEQISRAQQYQQLLKDQQEKLEKERLERERIDRERQERMDRERQERLEKEK 422

Query: 642 LEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
            E + +Q  + RE+I+++E +  R+LK      +L+
Sbjct: 423 QERLERQERLEREKIQRLEKE--RQLKEQQEQDRLK 456


>gi|73980513|ref|XP_866414.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 18 [Canis
           familiaris]
          Length = 1276

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|50949611|emb|CAH10575.1| hypothetical protein [Homo sapiens]
          Length = 890

 Score = 39.8 bits (91), Expect = 1.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|295108535|emb|CBL22488.1| RNA polymerase, sigma 30 subunit, SigH [Ruminococcus obeum A2-162]
          Length = 202

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 38/91 (41%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ +     +     ++E     V   A+     G +  DLIQEG IGL KA + +   
Sbjct: 11  ELIFRLRQGETEISDYLMEKYKEFVRKKARAMFLIGGETDDLIQEGMIGLFKAIQNYQPD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F T+A   + + +  ++ + +    +P
Sbjct: 71  REASFQTFAGLCIDRQLYSAVQNSNRQKHLP 101


>gi|154684616|ref|YP_001419777.1| RNA polymerase factor sigma-70 [Bacillus amyloliquefaciens FZB42]
 gi|126363077|emb|CAM35804.1| RNA polymerase sigma factor H [Bacillus amyloliquefaciens FZB42]
 gi|154350467|gb|ABS72546.1| SigH [Bacillus amyloliquefaciens FZB42]
          Length = 218

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 22  QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRED 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 82  KLTSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|322805057|emb|CBZ02617.1| RNA polymerase sigma factor RpoD [Clostridium botulinum H04402 065]
          Length = 179

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
           S++ K       A  E++E    L++  A ++  R  ++ DL+Q G + ++KA   F   
Sbjct: 3   SLLEKYRNGDVGALNEIIENFNPLILKEAARWRIRCYEYEDLVQHGYLSVIKAVNMFKGE 62

Query: 492 LGYKFSTYAMWWVKQAI 508
              KF  Y +  +K   
Sbjct: 63  -ESKFVPYCINAIKTNY 78


>gi|319647795|ref|ZP_08002013.1| YvrI protein [Bacillus sp. BT1B_CT2]
 gi|317390136|gb|EFV70945.1| YvrI protein [Bacillus sp. BT1B_CT2]
          Length = 193

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD ++D   +   +   +             LT ++++VL   +  G+    +++E+   
Sbjct: 103 GDLLDD--VLEQEEDLSEHLQDPMLYEAFLQLTDKQKKVLAQIYIHGV----SMQEIADS 156

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
              +R+ I +I  +A+ K++    SK
Sbjct: 157 LGESRQNISRIHKRALEKIRELLNSK 182


>gi|190690845|gb|ACE87197.1| dynactin 1 (p150, glued homolog, Drosophila) protein [synthetic
           construct]
          Length = 1278

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 111/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T    E 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADATEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLRQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQAIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|153004264|ref|YP_001378589.1| sigma-70 region 4 domain-containing protein [Anaeromyxobacter sp.
           Fw109-5]
 gi|152027837|gb|ABS25605.1| sigma-70 region 4 domain protein [Anaeromyxobacter sp. Fw109-5]
          Length = 194

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/28 (57%), Positives = 21/28 (75%)

Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           TLEEVG    +TRERIRQ+E + + KL+
Sbjct: 148 TLEEVGSIMNLTRERIRQVETRGLAKLR 175


>gi|114578183|ref|XP_001156304.1| PREDICTED: dynactin 1 isoform 8 [Pan troglodytes]
          Length = 1223

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|162447300|ref|YP_001620432.1| hypothetical protein ACL_0435 [Acholeplasma laidlawii PG-8A]
 gi|161985407|gb|ABX81056.1| conserved hypothetical protein [Acholeplasma laidlawii PG-8A]
          Length = 1088

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 39/286 (13%), Positives = 87/286 (30%), Gaps = 15/286 (5%)

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           IDL++ +            +       +    E +    +E    +E    + +     +
Sbjct: 197 IDLQSFVFEFLLDDEPIDIQSLKNNVTQLKRVEGQIRLDKEKLEKLEKIITLGESLNQNL 256

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
           D    N   D+    E  +    T     + L  KV    + +     +L     +    
Sbjct: 257 DQITTNELIDQMAFIEKRE----TFLNHSENLLDKVNAKYEVLKRQKDDLDRQITSNDET 312

Query: 305 QKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL---LVEQLYDISKRIMHNEGELLRLAQ 361
             + ++S +   +   L  L   L    ++ +    +V  L     R +    + + L  
Sbjct: 313 ILELETSRQNDDITRTLSNLKEQLHAKGNQYNEQKVIVSDLKATLNRELDLYRDFVNLNP 372

Query: 362 SYGIKRDVFLERHQGRELDPHWVSYAK-----DFPEGEWKNFVACEVDSILKIRNEIKSI 416
           +  I    FL+ + G E + + +  +            + N ++ E   + K RN I + 
Sbjct: 373 NTHIS--AFLKYYSGHEENSNILELSSYIEGAQSAASGYLNALSVEKSELEKERNNILNE 430

Query: 417 SVETGISISEFRHIVSMVRKGECEASIA-KKEMVEANLRLVISVAK 461
                  ++  +  V    +       A   E+     + V   A 
Sbjct: 431 LRIAENRLNALKRNVKTYPRNVQSLMDAINTELSNYYKKDVRVRAF 476


>gi|41945510|gb|AAH66061.1| Dctn1 protein [Mus musculus]
          Length = 1264

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 230 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 289

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 290 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 349

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 350 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 409

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 410 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 468

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 469 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 524

Query: 456 VISV 459
           V   
Sbjct: 525 VERQ 528


>gi|30268331|emb|CAD89954.1| hypothetical protein [Homo sapiens]
          Length = 1331

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 84/233 (36%), Gaps = 12/233 (5%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            E       +DDV ++  ++E + +  +    ++ +  E  E + +  ++ +      L A
Sbjct: 927  EMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEGELQATEDAKLRLEVNLQA 986

Query: 272  MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
            M+ Q    +    ++  E  ++L           +DE+     +    K L+  L  L  
Sbjct: 987  MKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAVAARKKLEMDLKDLEA 1046

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +       D  ++QL  +  ++     EL          R+  L + +  E     +  
Sbjct: 1047 HIDSANKNRDEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQAKENEKKLKSMEA 1102

Query: 387  AKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMVRK 436
                 + E       +  +     ++ +EI + S +  +++ E R + + + +
Sbjct: 1103 EMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARIAQ 1155


>gi|134034172|sp|Q3UU96|MRCKA_MOUSE RecName: Full=Serine/threonine-protein kinase MRCK alpha; AltName:
           Full=CDC42-binding protein kinase alpha
 gi|187957250|gb|AAI58096.1| Cdc42bpa protein [Mus musculus]
          Length = 1719

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|73980507|ref|XP_866381.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 15 [Canis
           familiaris]
          Length = 1269

 Score = 39.8 bits (91), Expect = 1.5,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 240 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 299

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 300 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 359

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 360 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 419

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 420 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 478

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 479 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 534

Query: 456 VISV 459
           V   
Sbjct: 535 VERQ 538


>gi|309355577|emb|CAP38650.2| CBR-LET-75 protein [Caenorhabditis briggsae AF16]
          Length = 2121

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 89/255 (34%), Gaps = 14/255 (5%)

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            E     +   ++ E++   +     ++E +   + D  S+ +    + E   R   ++ +
Sbjct: 958  EALELTQGGSAAIEEKLTRLNSARQEVEKSLNDANDRLSEHEEKNADLEKQRRKAQQEVE 1017

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ----KDEKSSVKCKVLKE 319
            +   ++ A++  L       L+E A    ++RSLQD   +      K  K     +    
Sbjct: 1018 NLKKSIEAVDGNLSRS----LEEKAAKENQIRSLQDEMNSQDETIGKINKEKKHLEENNR 1073

Query: 320  KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            +L+  + +    Q++ + L  +L      +        R+       +       +G + 
Sbjct: 1074 QLIDDLQAEEAKQAQANRLRGKLEQTLDEMEEAVEREKRIRAETEKSKRKVEGELKGAQE 1133

Query: 380  DPHWVSYAKDFPEGEWK------NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
                ++  K   +   K      + +   ++    + N +   S E    I E    +  
Sbjct: 1134 SIDELTAIKLEADASLKKKEADIHALGVRIEDEQALANRLTRQSKENAQRIIEIEDELEH 1193

Query: 434  VRKGECEASIAKKEM 448
             R+   +A  A+ E+
Sbjct: 1194 ERQSRSKADRARAEL 1208


>gi|194386386|dbj|BAG59757.1| unnamed protein product [Homo sapiens]
          Length = 1236

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 111/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L  + + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLERVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|332800097|ref|YP_004461596.1| ECF subfamily RNA polymerase sigma-24 subunit SigH
           [Tepidanaerobacter sp. Re1]
 gi|332697832|gb|AEE92289.1| RNA polymerase, sigma-24 subunit, SigH, ECF subfamily
           [Tepidanaerobacter sp. Re1]
          Length = 215

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 34/82 (41%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              A + ++      V S A+ Y   G    D+IQEG IGL KA   F+      F  +A
Sbjct: 29  DHEALEYLINKYKNFVKSKARSYFLIGADREDIIQEGMIGLYKAIRDFNPERLSSFRAFA 88

Query: 501 MWWVKQAITRSIADQSCTIRIP 522
              + + I  +I   +    IP
Sbjct: 89  ELCITRQIITAIKTATRQKHIP 110


>gi|296223518|ref|XP_002757644.1| PREDICTED: dynactin subunit 1 isoform 2 [Callithrix jacchus]
          Length = 1236

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|257126627|ref|YP_003164741.1| hypothetical protein Lebu_1885 [Leptotrichia buccalis C-1013-b]
 gi|257050566|gb|ACV39750.1| hypothetical protein Lebu_1885 [Leptotrichia buccalis C-1013-b]
          Length = 314

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 96/241 (39%), Gaps = 22/241 (9%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
              I    ++ E +     +E+++  L++ +  +  Y+  G  FLD +QE  +G++    
Sbjct: 75  LEDIREKYKELEKKNRNENEELIDRYLKIAVKESLLYSKYGFSFLDTVQEATLGIISGIS 134

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546
            FD           +  + +     + + +       ++ +   ++++   + S      
Sbjct: 135 YFDE----------ISRITKEPEFFVKNFA-----VKYILEFQKELLK-DIKSSELSYIL 178

Query: 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
               ++ K +   ++ + K + ++ E I  E      D  +  + IE+   +   D   Q
Sbjct: 179 YLKVKVDKSMGFSMDEISKQMNVSTEYI--EQLEKLFDDINPEELIENTQILEKADKITQ 236

Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
             + E   + L  L     ++L M +G+  +  +T +E+ K   +    +  ++ KA+ K
Sbjct: 237 MYILENIPKKLNYLDE---QILVMAYGLD-DRVYTEKEIAKSLNIASHNVNILKEKALNK 292

Query: 667 L 667
           L
Sbjct: 293 L 293


>gi|328551799|gb|AEB22291.1| RNA polymerase factor sigma-70 [Bacillus amyloliquefaciens TA208]
          Length = 218

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 22  QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRED 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 82  KLTSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|73980505|ref|XP_866367.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 14 [Canis
           familiaris]
          Length = 1249

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 220 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 279

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 280 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 339

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 340 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 399

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 400 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 458

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 459 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 514

Query: 456 VISV 459
           V   
Sbjct: 515 VERQ 518


>gi|291558000|emb|CBL35117.1| DNA-directed RNA polymerase specialized sigma subunit [Eubacterium
           siraeum V10Sc8a]
          Length = 73

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D I D N        I           +  L  RE+ +L++RF  G     T  EV ++
Sbjct: 1   MDQIGDNNDDRNWLDEI------ALKEAIIGLDDREKNILKLRFFRG----KTQVEVAQE 50

Query: 649 FCVTRERIRQIEAKAIRKLKHP 670
             +++ ++ ++E  A+ K+K  
Sbjct: 51  IGISQAQVSRLEKGALGKIKKA 72


>gi|197301393|ref|ZP_03166474.1| hypothetical protein RUMLAC_00124 [Ruminococcus lactaris ATCC
           29176]
 gi|197299550|gb|EDY34069.1| hypothetical protein RUMLAC_00124 [Ruminococcus lactaris ATCC
           29176]
          Length = 206

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 38/91 (41%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++            ++     +V   A+     G +  DLIQEG IGL+KA   +D  
Sbjct: 11  QLIKDFRNGDREIMDHLMMKYKAMVRKKARAMYLFGGENEDLIQEGMIGLIKAVRDYDPD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            G  F+++A   V + +  +I        IP
Sbjct: 71  QGASFASFAELCVSRQMYSAIEASKRKKHIP 101


>gi|56418624|ref|YP_145942.1| RNA polymerase factor sigma-70 [Geobacillus kaustophilus HTA426]
 gi|56378466|dbj|BAD74374.1| DNA-directed RNA polymerase sigma-30 factor (sigma-H) [Geobacillus
           kaustophilus HTA426]
          Length = 216

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 34/91 (37%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A   ++      V + A+ Y   G    D++QEG IGL KA   F   
Sbjct: 20  QLVALVHEGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGD 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   +    IP
Sbjct: 80  KLSSFKAFAELCITRQMITAIKTATRQKHIP 110


>gi|195027327|ref|XP_001986535.1| GH20475 [Drosophila grimshawi]
 gi|193902535|gb|EDW01402.1| GH20475 [Drosophila grimshawi]
          Length = 1176

 Score = 39.8 bits (91), Expect = 1.6,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 86/240 (35%), Gaps = 27/240 (11%)

Query: 144 KRIEAGRAMMMASL-CESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
           +RIE     +   +  E   T +AL        +     +  ++  A    ++  G    
Sbjct: 275 ERIEGTVKEIHHKIDSEMGGTLKAL--------ETELAAKRAVEATASGSLKAAKGTIEQ 326

Query: 203 TEGHSYQKREDSSQE-----KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
            E       ++ +++     K+++ +   +G+ ++       D    +      E   + 
Sbjct: 327 DEKKIRMASKNIAEDERTLLKKQEAMSNVQGEFQNLKDADAADTKAYEDAQRKFEAVSQG 386

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS----LQDNAVNGQKDEKSSVK 313
           L  DED  A TL       +  +  A   I     ELR     LQ      Q ++ + +K
Sbjct: 387 LSTDEDGQAVTLQEQLIAAKQHLSAAQTTIKTSEMELRHTRTLLQQKQGETQTNDAAYIK 446

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLL------VEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            K L ++L   + ++   + ++  L       EQL +  +++ +   EL R  +     R
Sbjct: 447 DKKLHDQLEGEIKNM---ERQLQGLNYEDGHFEQLKERRQQLHNQVRELKRDVERRSDPR 503


>gi|311270587|ref|XP_001929016.2| PREDICTED: CAP-Gly domain-containing linker protein 1 [Sus scrofa]
          Length = 1426

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 59/468 (12%), Positives = 156/468 (33%), Gaps = 23/468 (4%)

Query: 184  IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
            +ID        ++                 S  E  R  ++  E  I++       +  K
Sbjct: 746  VIDNFTSQLKAAEEKLSDLDALRKASSEGKSEIENLRQQLEAAEKQIKNLEIEKNAESGK 805

Query: 244  VDSPPENAENDE---RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
              S  +  +  E    NL E+  + +    A+E +L+       D   E     RS+Q+ 
Sbjct: 806  ASSITKELQGKELMLNNLQENLSEVSQVKEALEKELQILKEKFADASEEAVSVQRSMQET 865

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
                 + E+         EKL + +  +       D   EQL    +++ ++  E+++++
Sbjct: 866  VNQLHQKEEQFNALSSELEKLRENLTDMEAKFRERDEREEQLIKAKEKLENDIAEIMKMS 925

Query: 361  QSY-----GIKRDVFLERHQGRELDPHWVSYAKD-------------FPEGEWKNFVACE 402
              +      +  ++ L+     EL        ++               E   +      
Sbjct: 926  GDHSSQLTKMNDELRLKERNVEELQLKLTKANENASFLQKSIGEVTLKAEQSQQEAAKKH 985

Query: 403  VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             +   ++  ++  +  +  +S +E + + +   +   EA    +E+++   + ++   ++
Sbjct: 986  EEEKKELLQKLSDLEKKMEMSHNECQDLKARYEEASSEAKAKHEEVLQNLQKTLLDTEER 1045

Query: 463  YTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
                  +  DL+QE    L K A K       + +   M  + +  T ++A    + +  
Sbjct: 1046 LKAAQEENSDLLQE-MEELEKQAGKARAAQTAEDAMQIMEQMTKEKTETLASLEDSKQTN 1104

Query: 523  VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582
              +++++  +     +   ++ +      +  +         + LK      S +     
Sbjct: 1105 EKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETLKQAAAQKSQQLSALQ 1164

Query: 583  EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            E+   L + +            ++   R      L  +  RE ++++ 
Sbjct: 1165 EENVKLAEELGRSRDEVTSHQKLEEE-RSVLNNQLLEMKKRESKLIKD 1211



 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 58/390 (14%), Positives = 136/390 (34%), Gaps = 18/390 (4%)

Query: 45   TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV 104
            T+ +L+         S ++E     L++M     + D+ E++            A    +
Sbjct: 865  TVNQLHQKEEQFNALSSELEKLRENLTDMEAKFRERDEREEQLIKAKEKLENDIAEI--M 922

Query: 105  FLQKRKDSADRSTDDPVRMYLREMGSIEL-LSREGEIAIAKRIEAGRAMMMASLCESPLT 163
             +     S     +D +R+  R +  ++L L++  E A   +   G   + A   +    
Sbjct: 923  KMSGDHSSQLTKMNDELRLKERNVEELQLKLTKANENASFLQKSIGEVTLKAEQSQQ--- 979

Query: 164  FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
                   +    +   LL+++ DLE  +                      +  E+   ++
Sbjct: 980  ----EAAKKHEEEKKELLQKLSDLEKKMEMSHNECQDLKARYEEASSEAKAKHEEVLQNL 1035

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE--DDSAHTLSAMEDQLRPKVM 281
            Q+T  D E   K ++++ S +    E  E         +  +D+   +  M  + + + +
Sbjct: 1036 QKTLLDTEERLKAAQEENSDLLQEMEELEKQAGKARAAQTAEDAMQIMEQMTKE-KTETL 1094

Query: 282  CALDEIAEVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
             +L++  +   +L+  L     N  K+ +   K K L     + +         I+ L +
Sbjct: 1095 ASLEDSKQTNEKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFR---KEIETLKQ 1151

Query: 341  QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
                 S+++   + E ++LA+  G  RD  +  HQ  E +   ++      +      + 
Sbjct: 1152 AAAQKSQQLSALQEENVKLAEELGRSRDE-VTSHQKLEEERSVLNNQLLEMKKRESKLIK 1210

Query: 401  CEVDSILKIRNEIKSISVETGISISEFRHI 430
               +    ++  I   S       +E   +
Sbjct: 1211 DADEEKASLQKSISITSALLTEKDAELEKL 1240


>gi|146086892|ref|XP_001465676.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134069775|emb|CAM68102.1| hypothetical protein, unknown function [Leishmania infantum JPCM5]
          Length = 2064

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 64/537 (11%), Positives = 161/537 (29%), Gaps = 18/537 (3%)

Query: 136  REGEI-AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
            R+ E+  + +++            +       +   R++L +     R++         +
Sbjct: 1370 RDAEVADLREQLREAEERARDVEAQQCDRDAEVADLREQLREAEERTRDV----EAQQCD 1425

Query: 195  SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                     E     +      E ++ D      D+    + +++    V++   + + +
Sbjct: 1426 RDAELADLREQLREAEERTRDVEAQQCDRDAELADLREQLREAEERARDVEAQQCDRDAE 1485

Query: 255  ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
              +L E   ++      +E Q   +     D   ++       +D        +      
Sbjct: 1486 LADLREQLREAEERTRDVEAQQCDRDAEVADLREQLREAEERARDVEAQQCDRDAEVADL 1545

Query: 315  KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
            +    +  +    +   Q   D  V  L +  +       ++         +     E+ 
Sbjct: 1546 REQLREAEERARDVEAQQCDRDAEVADLREQLREAEERARDVEAQQCDRDAEVADLREQL 1605

Query: 375  QGRELDPHWVSYAKDFPEGEWKNFVA------CEVDSILKIRNEIKSISVETGISISEFR 428
            +  E     V   +   + E +           E +   +IR  ++    +    I E R
Sbjct: 1606 REAEERARDVEAQQCDRDAELERVKELLSSSMREAECSGEIRGALEDQLEDAAREIRELR 1665

Query: 429  HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
              +++ +    EA  A+   +   LR     A+    +       + +    L +A E+ 
Sbjct: 1666 EQLAVAQ-VRREALDAELADLREQLREAEERARDVEAQQCDRDAEVADLREQLREAEERT 1724

Query: 489  DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
                  +    A     +   R   +++    +     D+  +V     ++    +R   
Sbjct: 1725 RDVEAQQCDRDAELADLREQLREAEERTR--DVEAQQCDRDAEVADLREQLREAEERARD 1782

Query: 549  PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF---IEDKNAVSPLDSAI 605
             E         V  +R+ L+  +E          +  + + D    + +    +    A 
Sbjct: 1783 VEAQQCDRDAEVADLREQLREAEERARDVEAQQCDRDAEVADLREQLREAEERTRDVEAQ 1842

Query: 606  QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662
            Q +       +   L   EER   +      + D  L ++ +Q     ER R +EA+
Sbjct: 1843 QCDRDAELADLREQLREAEERTRDVE-AQQCDRDAELADLREQLREAEERARDVEAQ 1898


>gi|50949613|emb|CAH10572.1| hypothetical protein [Homo sapiens]
          Length = 890

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|213626935|gb|AAI70424.1| LOC398083 protein [Xenopus laevis]
          Length = 1962

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 43/308 (13%), Positives = 104/308 (33%), Gaps = 12/308 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  I   +E  +      L E           RD                A    E+ 
Sbjct: 1430 DHQRQIVSNLEKKQKKFDQLLGEEKAISAKYADERDRSEAEAREKETKALALARALEEAL 1489

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +
Sbjct: 1490 EAKAELERLNKQLRTEMEDLVSSKDDVGKSVHELEKSKRALEQQAEEMKTQLEELEDELQ 1549

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SS 311
              ++ +      L AM+ Q    +    ++  +  ++L           +DE+     + 
Sbjct: 1550 ATEDAKLRLEVNLQAMKAQFERDLQGRDEQSEDKKKQLVRQVKEMEAELEDERKQRSLAV 1609

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  L G +  +    +  ++QL  +  +I   + EL    +     RD  L
Sbjct: 1610 AARKKLEMDLKDLEGQIDSSNKNREDAIKQLRKLQAQIKDYQREL----EDTRASRDDIL 1665

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFR 428
             + +  E     +       + E       +  +     ++ +EI + S +  +++ E R
Sbjct: 1666 SQSKESEKKLKSMEAEMIHMQEELAAAERGKRQAQQERDELADEIANSSGKGALALEEKR 1725

Query: 429  HIVSMVRK 436
             + S + +
Sbjct: 1726 RLESRIAQ 1733


>gi|189202178|ref|XP_001937425.1| structural maintenance of chromosomes protein 1 [Pyrenophora
           tritici-repentis Pt-1C-BFP]
 gi|187984524|gb|EDU50012.1| structural maintenance of chromosomes protein 1 [Pyrenophora
           tritici-repentis Pt-1C-BFP]
          Length = 1295

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 58/502 (11%), Positives = 153/502 (30%), Gaps = 25/502 (4%)

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
           ++  A   PE          G   QK E    ++E +   E         +    +    
Sbjct: 183 VEKLATTAPEQLTLQVERISGSLEQKAEYDRLKEESEAATEDNAKHLHERRGINGELKTY 242

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
                 A+  E+ L E +D             +  +  A ++IA    EL+  + +    
Sbjct: 243 QDQKAEADEYEKKLAERDDAVVTKNLWKLYLYQQVMEKARNKIASHQEELKEHKRSVEKY 302

Query: 305 QKDEKSSVKCK-VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            +   +  + +  ++  L K   +    +  I+    +L  I ++I  +     +     
Sbjct: 303 HQRHDAERQAEAKIRRDLTKTDRNTKAKEKEIEDASNELAPIEEKIRLSNETRRKYESKL 362

Query: 364 ---GIKRDVFLERHQGRELDPH--------WVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
                KRD   +  +  + D          W    K   + + +     ++    ++R++
Sbjct: 363 EELRKKRDNEKKAVEKCQKDLDLVQKAEKKWEDDFKAAAQRQGRELSEQDLQEYGRLRSD 422

Query: 413 IKSISVETGISISEFRHIVSMVR---KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ 469
           +   +    + I + +  V   R   K   ++  + ++ VE     +  + ++      Q
Sbjct: 423 VTKRTHGDQMQIDKLKREVETDRDHVKNLQQSVDSHEKEVEKLNATISQLEERQQASKTQ 482

Query: 470 FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKI 529
             +L         +           +   Y    + Q + + ++    + R     ++  
Sbjct: 483 VKELETARAAKQQELDRLRSDRKQIEMQYYEKNQLLQEVLKQLSIVEGSRRESRKQQEAR 542

Query: 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589
             + R   R  ++       + I  K+    + + +VL    + + ++T           
Sbjct: 543 RTIDRLKTRFGSEKVHGRYKDLITPKMQKYRKAIGRVLGHQMDTVIVDTEAT---AKSCI 599

Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
           D+++ +       + + +   +     L  +       +        +        G   
Sbjct: 600 DYLKAERIGVMSFNPLDSIQIQAVDPQLKGMHEGMRLAIDCINYEPKHERAMTAACGNTM 659

Query: 650 CVTRE-------RIRQIEAKAI 664
               E        +R++E KA+
Sbjct: 660 ICNTEKLAKELRYVRRVEVKAV 681


>gi|160939951|ref|ZP_02087297.1| hypothetical protein CLOBOL_04841 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437095|gb|EDP14861.1| hypothetical protein CLOBOL_04841 [Clostridium bolteae ATCC
           BAA-613]
          Length = 134

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 44/119 (36%), Gaps = 4/119 (3%)

Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609
           EEI K         R   +      +      D +  +  D  +D  A    + A +A  
Sbjct: 16  EEIYKLYCKGERKERYFRESDIHNKTFYYNALDTEDFNGCDLFQDTRAKPVDEQAEEALE 75

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
           R      +  L PRE+ ++R  +      D +L ++ ++  V    +     K +RKL+
Sbjct: 76  RSLLFEAMKDLDPREKDIIRRIY----CYDQSLRQISRETGVPVTTLHYRHGKILRKLR 130


>gi|148378736|ref|YP_001253277.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153931118|ref|YP_001383122.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. ATCC 19397]
 gi|153937466|ref|YP_001386672.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. Hall]
 gi|148288220|emb|CAL82289.1| putative RNA polymerase sigma factor [Clostridium botulinum A str.
           ATCC 3502]
 gi|152927162|gb|ABS32662.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152933380|gb|ABS38879.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A str.
           Hall]
          Length = 179

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K       A  E++E    L++  A ++   G ++ DL+Q G + ++KA   F   
Sbjct: 3   KLLEKYRNGDIGALNEIIENFNPLILKEASRWRIGGYEYEDLVQHGYLSVIKAVNMFKGE 62

Query: 492 LGYKFSTYAMWWVKQAI 508
              KF  Y +  +K   
Sbjct: 63  -ESKFVPYCINAIKTNY 78


>gi|138893768|ref|YP_001124221.1| RNA polymerase factor sigma-70 [Geobacillus thermodenitrificans
           NG80-2]
 gi|196251121|ref|ZP_03149800.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           G11MC16]
 gi|134265281|gb|ABO65476.1| RNA polymerase sigma-30 factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196209362|gb|EDY04142.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           G11MC16]
          Length = 216

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 81/251 (32%), Gaps = 61/251 (24%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V         A   ++      V + A+ Y   G    D++QEG IGL KA   F   
Sbjct: 20  QLVALVHQGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGD 79

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551
               F  +A   + + +  +I   +    IP++                           
Sbjct: 80  KLSSFKAFAELCITRQMITAIKTATRQKHIPLN--------------------------- 112

Query: 552 IAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAVSPLDSAIQANLR 610
                                 +SL+ PI D++    L D +    A  P +  +     
Sbjct: 113 --------------------SYVSLDKPIYDDESDRTLMDVLSGTQATDPEELIVNREEV 152

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670
           +     +A L    ER +   +  G +     EE+ +        ++ I   A++++K  
Sbjct: 153 DDIELKMAELLSDLERKVLALYLDGRSYQEISEELNR-------HVKSI-DNALQRVK-- 202

Query: 671 SRSKKLRSFLD 681
              +KL  +L+
Sbjct: 203 ---RKLEKYLE 210


>gi|284047634|ref|YP_003397973.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283951855|gb|ADB46658.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 244

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 23/114 (20%), Positives = 46/114 (40%), Gaps = 7/114 (6%)

Query: 409 IRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468
           ++ E++ +     +S  E   ++      + +   A+  +++     +   A +Y   G 
Sbjct: 1   MQEELRKLYDT--LSDEELIQLIQ-----DRDDRQAQDYLLDKYKEFIRLKATRYFLVGA 53

Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +  D+IQEG IGL KA   +       F  +A   V + I  +I   +     P
Sbjct: 54  EKEDIIQEGMIGLFKAIRDYRPGKQASFKVFAEICVNRQIISAIKSATRQKHRP 107


>gi|253579508|ref|ZP_04856777.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849009|gb|EES76970.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 199

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 37/91 (40%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ + +   S     ++E    +V   A+     G +  DLIQEG IGL KA   +   
Sbjct: 11  ELISRFKNGESEILDYLMEKYKNMVRKKARTMFLIGGENDDLIQEGMIGLFKAVRDYQPD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F T+A   V + I  +I   +     P
Sbjct: 71  RDAAFQTFASICVDRQIYNAIQSSNRQKHQP 101


>gi|73980509|ref|XP_866394.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 16 [Canis
           familiaris]
          Length = 1263

 Score = 39.8 bits (91), Expect = 1.7,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 234 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 293

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 294 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 353

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 354 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 413

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 414 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 472

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 473 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 528

Query: 456 VISV 459
           V   
Sbjct: 529 VERQ 532


>gi|169835541|ref|ZP_02868729.1| hypothetical protein cdivTM_00208 [candidate division TM7
           single-cell isolate TM7a]
          Length = 45

 Score = 39.8 bits (91), Expect = 1.8,   Method: Composition-based stats.
 Identities = 21/36 (58%), Positives = 27/36 (75%)

Query: 634 IGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           +  N  HTL+E+G+Q  +TRER+RQIE KAI KLK 
Sbjct: 1   MYDNKIHTLKEIGEQMGITRERVRQIEKKAITKLKE 36


>gi|255030922|ref|ZP_05302873.1| RNA polymerase factor sigma-70 [Listeria monocytogenes LO28]
          Length = 117

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EELAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|148681214|gb|EDL13161.1| mCG6218 [Mus musculus]
          Length = 1678

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|6325437|ref|NP_015505.1| Hda3p [Saccharomyces cerevisiae S288c]
 gi|74676420|sp|Q06623|HDA3_YEAST RecName: Full=HDA1 complex subunit 3; AltName: Full=Histone
           deacetylase complex 1 subunit 3
 gi|786325|gb|AAB68112.1| Ypr179cp [Saccharomyces cerevisiae]
 gi|285815703|tpg|DAA11595.1| TPA: Hda3p [Saccharomyces cerevisiae S288c]
          Length = 655

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 48/130 (36%), Gaps = 7/130 (5%)

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN-----GQKD 307
           ++ ++  E E+  + +    +  +  ++  A+D I E   E   L +           K 
Sbjct: 527 DNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNGLESELKLKF 586

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EKS +  K L EK+  L   L L     + LV QL      + +    + R+    G  +
Sbjct: 587 EKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENL--TIPRVRTQNGNTK 644

Query: 368 DVFLERHQGR 377
                +  G 
Sbjct: 645 KKSRAKKPGN 654


>gi|303321544|ref|XP_003070766.1| hypothetical protein CPC735_038850 [Coccidioides posadasii C735
           delta SOWgp]
 gi|240110463|gb|EER28621.1| hypothetical protein CPC735_038850 [Coccidioides posadasii C735
           delta SOWgp]
          Length = 1252

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 31/216 (14%), Positives = 78/216 (36%), Gaps = 8/216 (3%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           + L   + E+      +  +         E +       +     + + +  +  +D++Q
Sbjct: 734 KELEEKQSEVEAKQEEINRLKSELESKIAELEDKRRELEQKQGELESKQTELQAIQDELQ 793

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
           E + ++E      +  ++ +D   E     +  LD+ ++  A  L+A+  QL  +     
Sbjct: 794 EVKAELEEKKSQLESKQADLDKKQEELTAKQAELDDVKEKHAAELAALRAQLEEQTNATK 853

Query: 285 DEIAEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           +   ++       Q      QKD        ++ + + KV  E+   L       + R+ 
Sbjct: 854 ERDEKIEAMTTEHQQKEEQWQKDRGDFEAQLQEKTEELKVALEEKEALAVDGKNREERLQ 913

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
            +VE++      +  +   L +   S G   D+ ++
Sbjct: 914 SIVEEMRQTHDNLNKDRERLKKTLHSLGEATDMKIK 949


>gi|298715638|emb|CBJ28164.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 1343

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 45/298 (15%), Positives = 96/298 (32%), Gaps = 28/298 (9%)

Query: 169  IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG 228
               D++ +    ++EI      +   S   FF        Q  E  + E    D+     
Sbjct: 1027 DCMDKVEEKNNRIQEI-----LVDLGSDETFFRPKWLDLEQPEEVFNVES---DMTVKPY 1078

Query: 229  DIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
            + E+  +  +    +     E A+         +D    TL   +D L    +   D + 
Sbjct: 1079 ESEADKEARRKAEEEKRRREEEAKGSNDKFRALDDMMHGTLEVKQDALTVDAVKKPDWMD 1138

Query: 289  EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
            EV  E  +        ++ E+   K K ++E+      +L L   +   L  ++ DI K 
Sbjct: 1139 EVAPEDMT----EDQKKEAEEYEAKLKEVQEEQATYRKALELELKK---LRTEVADIVKA 1191

Query: 349  IMHNEGELLRLAQSYGI---KRDVFLERHQ----GRELDPHWVSY------AKDFPEGEW 395
                  E+  L     +    +++ L R       RE D   +             +   
Sbjct: 1192 FDDRLKEMCELRVQVQMFIASQELLLTRLAMGIVEREDDDVTMEKLDKALGELFEKKALA 1251

Query: 396  KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453
            +  +      + + R EI+++  E  +    F+  +        + +    ++V+   
Sbjct: 1252 QERLEGYRLHVEQAREEIETLQAEDRLMERNFKKEIQEAASNPIDMAEMMAQLVQLYK 1309


>gi|312135726|ref|YP_004003064.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775777|gb|ADQ05264.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 211

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V+        A +E++      V +  + Y   G    D+ QEG IGL KA   FD  
Sbjct: 17  ELVKYSREGIKEATEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVRDFDET 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   S    IP
Sbjct: 77  KYPSFRLFAEMCITRQMITAIKTASRQKHIP 107


>gi|118347388|ref|XP_001007171.1| hypothetical protein TTHERM_00214750 [Tetrahymena thermophila]
 gi|89288938|gb|EAR86926.1| hypothetical protein TTHERM_00214750 [Tetrahymena thermophila
           SB210]
          Length = 965

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 51/349 (14%), Positives = 123/349 (35%), Gaps = 35/349 (10%)

Query: 143 AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI----IDLEACIGPESKGG 198
           A  IE           E     +A      E+N     +RE     + +E          
Sbjct: 175 AHEIEERLQRFKR---EFENRIKA------EMNAEVVRIREFEMAAVRMEEQEKYRKLMS 225

Query: 199 FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
            +       Y  R    +E+E+D +++    ++    ++ D R ++    E     E  +
Sbjct: 226 EYREELEKGYMDRLTKLREREKDTLEKCTNKMKEIESINHDHRQRILKDFELLRMREDEI 285

Query: 259 DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV------ 312
           D+    +  TL   + +L        ++I +       ++    N     K         
Sbjct: 286 DKQRILNDETLKIQKQKLENLEQELKEKIKKAEESALIIEKKYQNDLAYTKLEAHRDLEA 345

Query: 313 ------KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR-------IMHNEGELLRL 359
                 + K + ++ +  +  + + +     LV++L ++ ++       ++     +  +
Sbjct: 346 EKLEIIEKKRILDEDMYKIKQVKVGEFIFKKLVDELNELRRQKKEQEFELVQLRDNIRTV 405

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWK---NFVACEVDSILKIRNEIKSI 416
           + SY   +D      Q  ++    V++ K+  E + K    +   +VD++ K  NEI+  
Sbjct: 406 SDSYKRDQDSSRNLEQKLKIKDEEVNFFKNALEEQKKLVDQYKQSQVDNLKKFNNEIQVY 465

Query: 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN 465
             +  +   + + +  + ++ E     A+K+  E N R  +     + N
Sbjct: 466 QNQIEVLEEKIKELRKINKENEDLLDEARKQRYEMNYRQPLEFNHYHLN 514


>gi|73980481|ref|XP_866193.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 4 [Canis
           familiaris]
 gi|73980511|ref|XP_866403.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 17 [Canis
           familiaris]
          Length = 1256

 Score = 39.4 bits (90), Expect = 1.8,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|148225656|ref|NP_001081846.1| myosin, heavy chain 9, non-muscle [Xenopus laevis]
 gi|3660672|gb|AAC83556.1| nonmuscle myosin II heavy chain A [Xenopus laevis]
          Length = 1964

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 43/308 (13%), Positives = 104/308 (33%), Gaps = 12/308 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  I   +E  +      L E           RD                A    E+ 
Sbjct: 1430 DHQRQIVSNLEKKQKKFDQLLGEEKAISAKYADERDRSEAEAREKETKALALARALEEAL 1489

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +
Sbjct: 1490 EAKAELERLNKQLRTEMEDLVSSKDDVGKSVHELEKSKRALEQQAEEMKTQLEELEDELQ 1549

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SS 311
              ++ +      L AM+ Q    +    ++  +  ++L           +DE+     + 
Sbjct: 1550 ATEDAKLRLEVNLQAMKAQFERDLQGRDEQSEDKKKQLVRQVKEMEAELEDERKQRSLAV 1609

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  L G +  +    +  ++QL  +  +I   + EL    +     RD  L
Sbjct: 1610 AARKKLEMDLKDLEGQIDSSNKNREDAIKQLRKLQAQIKDYQREL----EDTRASRDDIL 1665

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFR 428
             + +  E     +       + E       +  +     ++ +EI + S +  +++ E R
Sbjct: 1666 SQSKESEKKLKSMEAEMIHMQEELAAAERGKRQAQQERDELADEIANSSGKGALALEEKR 1725

Query: 429  HIVSMVRK 436
             + S + +
Sbjct: 1726 RLESRIAQ 1733


>gi|78044583|ref|YP_361138.1| RNA polymerase factor sigma-70 [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996698|gb|ABB15597.1| RNA polymerase sigma-H factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 217

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 25/89 (28%), Positives = 34/89 (38%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V         A + ++      V S A+ Y   G    D+IQEG IGL KA   F     
Sbjct: 24  VEWARAGDEQALEYIINKYKNFVRSKARAYFLIGADREDIIQEGMIGLYKAVRDFRPDKL 83

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   V + I  +I   +    IP
Sbjct: 84  SSFRAFAELCVTRQIITAIKTATRQKHIP 112


>gi|114567859|ref|YP_755013.1| RNA polymerase factor sigma-70 [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114338794|gb|ABI69642.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 216

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 6/102 (5%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
            +   E   +  +          A + +++     V + A+ Y   G    D+IQEG IG
Sbjct: 16  EMCDEEIVDLAQL------GDQFAIEFLMDKYKNFVRAKARSYFLIGADKEDIIQEGMIG 69

Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           L KA   +       F  +A   + + I  +I   +    IP
Sbjct: 70  LFKAIRDYKMDKLTSFRAFAELCITRQIITAIKTATRQKHIP 111


>gi|251854892|gb|ACT22564.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1538

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 876  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 931

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 932  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 987

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 988  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1044

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1045 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1103

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1104 ETDILEEKKEI 1114


>gi|221312231|ref|ZP_03594036.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221321428|ref|ZP_03602722.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|296333095|ref|ZP_06875549.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305672797|ref|YP_003864468.1| RNA polymerase sigma factor H [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|321313769|ref|YP_004206056.1| RNA polymerase factor sigma-70 [Bacillus subtilis BSn5]
 gi|291482470|dbj|BAI83545.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. natto
           BEST195]
 gi|296149711|gb|EFG90606.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305411040|gb|ADM36158.1| RNA polymerase sigma factor H [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|320020043|gb|ADV95029.1| RNA polymerase factor sigma-70 [Bacillus subtilis BSn5]
          Length = 218

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 22  QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFKED 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 82  KLTSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|320040240|gb|EFW22173.1| conserved hypothetical protein [Coccidioides posadasii str.
           Silveira]
          Length = 1259

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 31/216 (14%), Positives = 78/216 (36%), Gaps = 8/216 (3%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           + L   + E+      +  +         E +       +     + + +  +  +D++Q
Sbjct: 741 KELEEKQSEVEAKQEEINRLKSELESKIAELEDKRRELEQKQGELESKQTELQAIQDELQ 800

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
           E + ++E      +  ++ +D   E     +  LD+ ++  A  L+A+  QL  +     
Sbjct: 801 EVKAELEEKKSQLESKQADLDKKQEELTAKQAELDDVKEKHAAELAALRAQLEEQTNATK 860

Query: 285 DEIAEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           +   ++       Q      QKD        ++ + + KV  E+   L       + R+ 
Sbjct: 861 ERDEKIEAMTTEHQQKEEQWQKDRGDFEAQLQEKTEELKVALEEKEALAVDGKNREERLQ 920

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
            +VE++      +  +   L +   S G   D+ ++
Sbjct: 921 SIVEEMRQTHDNLNKDRERLKKTLHSLGEATDMKIK 956


>gi|311070745|ref|YP_003975668.1| RNA polymerase factor sigma-70 [Bacillus atrophaeus 1942]
 gi|310871262|gb|ADP34737.1| RNA polymerase factor sigma-70 [Bacillus atrophaeus 1942]
          Length = 218

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 22  QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRED 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 82  KLTSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|251854860|gb|ACT22548.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1641

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 980  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 1035

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 1036 IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 1091

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 1092 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1148

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1149 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1207

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1208 ETDILEEKKEI 1218


>gi|255652588|ref|ZP_05399490.1| hypothetical protein CdifQCD_20566 [Clostridium difficile QCD-37x79]
          Length = 2032

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 55/353 (15%), Positives = 125/353 (35%), Gaps = 30/353 (8%)

Query: 125  LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
            L+E+     L+   +     + E     ++    E       +   ++ L      ++++
Sbjct: 1597 LKEIAREAALTSAQKHVTEIQNEIDLIDILMKNAEGDEKLDLIEKKKELLAKQAKEIKDV 1656

Query: 185  IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI---ESAAKVSKDDR 241
            I +      E + G        S   +  ++ E++ + ++  +      E A    K   
Sbjct: 1657 IKVYEDTAKELREGLSKEGFKFSADGKSITNYEQQLEFLKNNKDADKYKEIAENAKKYLD 1716

Query: 242  SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP--------------KVMCALDEI 287
              +   P+  +  ++N +E ED +     A +DQL+               ++   L EI
Sbjct: 1717 LLLKDLPDANKQIQQNKEEIEDLNKEIQDAYKDQLKEAQSLQEKIRDMYKKELEERLKEI 1776

Query: 288  AEVYRE----LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ-- 341
             +  +     L+  QD   + +K+ K     +  ++ +  L   +++ +     L  Q  
Sbjct: 1777 DKETKAKIDSLKKQQDAYNDSRKEAKYKDDYEEQQDVISDLEKQIAIAERD-SSLSGQKK 1835

Query: 342  LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
            L D+ K++   + +L  L Q +    D  +     +E D       K   E E K     
Sbjct: 1836 LKDLQKQLKEEQKKLQDLVQDH---VDDQVNDMYDKESDRLQEEADKLKEELEKKYSDEN 1892

Query: 402  EVDSILKIRNEIKSISVETGISISE---FRHIVSMVRKGECEASIAKKEMVEA 451
             VD I +  +  K + ++  +   +     +I           S+ K+E ++ 
Sbjct: 1893 LVDLINEAISSGKFVGLDGEVKKLQDAIIEYINKYESGMLAMGSVTKQEWLDR 1945


>gi|73980491|ref|XP_866265.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 9 [Canis
           familiaris]
          Length = 1202

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|301772230|ref|XP_002921528.1| PREDICTED: dynactin subunit 1-like isoform 3 [Ailuropoda
           melanoleuca]
          Length = 1256

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   L+  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELNQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|291544496|emb|CBL17605.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 204

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 31/65 (47%)

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506
           E++   ++L+   A    N  +   DL QEG +GLM A   FD     KFST+A   +  
Sbjct: 34  ELISRYMKLIWVKANTMANAVVDAEDLAQEGMLGLMNAIAHFDPNREIKFSTFADVCITN 93

Query: 507 AITRS 511
            +  +
Sbjct: 94  KMKSA 98


>gi|123461518|ref|XP_001316831.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121899549|gb|EAY04608.1| hypothetical protein TVAG_472950 [Trichomonas vaginalis G3]
          Length = 966

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 91/257 (35%), Gaps = 4/257 (1%)

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
             +K E  S +++   +++     E     S +   +     ENA+   R    ++    
Sbjct: 617 EDEKEEAESLKRDVKMLKKAFSRAEKQLSASNESLKESLLDCENAKAKLREQLANQRKQC 676

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
             L     +LR +    +DE+ E Y +L S Q          +S+     +  +   ++ 
Sbjct: 677 CDLVNEMAELRQQCKDEVDEVRENYDDLLS-QIEMSKLDNSNRSNTAVNTINSEKQAILK 735

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
            L+  +  I+ L ++L   +KR      E+ RL      ++  F E+    +        
Sbjct: 736 KLNEKEKAIERLTDELETQAKRNQQFSDEIERLTDKIDEQKICFDEKLSKEKEQLINDYE 795

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM---VRKGECEASI 443
           AK     +     A  V    +     +         + E    +++    RK   E + 
Sbjct: 796 AKINDYMKKSKTDAELVKKTTETLKNNEQKQQILLQKVKELERQLALSESQRKNTIECAE 855

Query: 444 AKKEMVEANLRLVISVA 460
            +K++ EA  + V+  A
Sbjct: 856 RQKKLFEAQQKSVMINA 872


>gi|2104495|gb|AAB57773.1| dynactin1 [Mus musculus]
          Length = 1281

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 247 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 306

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 307 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 366

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 367 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 426

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 427 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDX-LQENARETELEL 485

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 486 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 541

Query: 456 VISV 459
           V   
Sbjct: 542 VERQ 545


>gi|70998070|ref|XP_753767.1| myosin type II heavy chain [Aspergillus fumigatus Af293]
 gi|66851403|gb|EAL91729.1| myosin type II heavy chain, putative [Aspergillus fumigatus Af293]
          Length = 2405

 Score = 39.4 bits (90), Expect = 1.9,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 84/229 (36%), Gaps = 14/229 (6%)

Query: 132  ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI---IDLE 188
             LL   GE   A  ++     +     +            +E       +++I   ++ E
Sbjct: 923  PLL---GETRTANEVKKRDEKIKELEAKIKQGIAERQKLDEERRRTEIEIQKIQHTLESE 979

Query: 189  ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              +  + +  F            + +    +++ +++    + +A K + +  S+  +  
Sbjct: 980  RALALDKEEIFKRLQLREIELTEKLAGAIADQESLEDQLDTLIAAKKKADEQLSQRITQL 1039

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQL---RPKVMCALDEIAEVYRELRSLQ-----DN 300
            E A      L+ ++ D    L  ++ QL   R  V      + E+ +E++ LQ      +
Sbjct: 1040 EQAGEIIERLEAEKRDLQSRLDVLDRQLEEARSSVAEQEARVKELGQEIKMLQSHLSLKD 1099

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
                  + K     + L  KL +    L L++ +I  LVE+   I ++I
Sbjct: 1100 RKIQDLEAKLLKTDQDLDIKLARTSKDLELSKKQIKDLVEENRSIRQQI 1148


>gi|312792762|ref|YP_004025685.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312179902|gb|ADQ40072.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 211

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V+        A +E++      V +  + Y   G    D+ QEG IGL KA   FD  
Sbjct: 17  ELVKYSREGIKEATEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVRDFDET 76

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + +  +I   S    IP
Sbjct: 77  KYPSFRLFAEMCITRQMITAIKTASRQKHIP 107


>gi|116174728|ref|NP_001070680.1| dynactin 1a [Danio rerio]
 gi|75914611|gb|ABA29740.1| dynactin 1a [Danio rerio]
          Length = 1218

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 35/259 (13%), Positives = 94/259 (36%), Gaps = 18/259 (6%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           E+      L ++ +  + +  +         E     +    ++++  +++ +T   IE 
Sbjct: 196 EMEKYKIQLEQLQEWRSKMQEQQNDLQKQLKEAKKEAREALEAKDRYMEEMADTADAIEM 255

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E+ +  L+E   D       +E++          +  L+E 
Sbjct: 256 ATLDKEMAEERAESLQQETESLKEKLEELTMDMEILKHEIEEKGSDGAASSYHVKQLEEQ 315

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + + L+ +  KL   + L +  ID L
Sbjct: 316 NARLKEALVRMRDLSSSEKQEHVKLQKQMEKKNSELETLRSQKEKLQEEMKLAEDTIDEL 375

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 376 KEQVDAALGAEEMVETLTERNLDLEEKVRELRETVSDLESINEMNDE-LQENARETELEL 434

Query: 396 KNFVACEVDSILKIRNEIK 414
           +  +      + + +  ++
Sbjct: 435 REQLDLAGARVREAQKRVE 453


>gi|294783390|ref|ZP_06748714.1| RNA polymerase sigma-H factor [Fusobacterium sp. 1_1_41FAA]
 gi|294480268|gb|EFG28045.1| RNA polymerase sigma-H factor [Fusobacterium sp. 1_1_41FAA]
          Length = 196

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 47/87 (54%), Gaps = 1/87 (1%)

Query: 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE 486
             +I  +++K +   S A   +++   +++   A+KY   G +  DL+QEG +GL+KA +
Sbjct: 3   EENINIILKKAQTGDSEAIDWILKEYSKILSFNAQKYYLVGAEQEDLLQEGILGLLKAIK 62

Query: 487 KFDWCLGYKFSTYAMWWVKQAITRSIA 513
            +D      FS++A   +++ +  +I 
Sbjct: 63  FYDETKS-SFSSFAFLCIRREMISAIR 88


>gi|260834021|ref|XP_002612010.1| hypothetical protein BRAFLDRAFT_86969 [Branchiostoma floridae]
 gi|229297383|gb|EEN68019.1| hypothetical protein BRAFLDRAFT_86969 [Branchiostoma floridae]
          Length = 3706

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 52/388 (13%), Positives = 121/388 (31%), Gaps = 38/388 (9%)

Query: 46   IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVF 105
             E++        V SE +++    L       V+  +   E G   + +        ++ 
Sbjct: 2217 FEDIAEA----SVESETIDEVKEELEEQ----VEALEEAVESGDTAAQETIQEEIEETIQ 2268

Query: 106  LQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQ 165
                     + T                   EGE   A+ +E  +  M  +L E     +
Sbjct: 2269 EVAEVVEEVQETQ------------------EGE-EAAQEVEETQQEMTETLSEVEDVLE 2309

Query: 166  ------ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                     +  +      TL+ +I + E       +       +  + ++  +S     
Sbjct: 2310 DGTQEEKEEVVEELEETVDTLIEDIAEAEVQSETVVEAQEELQEQVAALEEAVESGDTAA 2369

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
            + ++QET  +     + + ++  +     E     E  + E  D+    L     + + +
Sbjct: 2370 QVEIQETISETVQEVEQAIEEVQETQEAVETVVRTEEEITETLDEVEEVLQEGTQEEKQE 2429

Query: 280  VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSL-NQSRIDLL 338
            V+  L+  + V   +  +++  V  +  +++  + +   E L + V S     Q  I   
Sbjct: 2430 VVDELE--SNVETLIEDIEEANVESETVDEARDQLEEQVEALQEAVESGDTAAQVAIQGT 2487

Query: 339  VEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
            +E+     +  ++    +  ++    I R+ F       E      +      E     F
Sbjct: 2488 IEETVQEVEEAVNEAAGVETVSVIESIPREAFTASSTLDEQHSSSYAVIGKTYEDGSPAF 2547

Query: 399  VACEVDSILKIRNEIKSISVETGISISE 426
             A   D   +       +   T +S  E
Sbjct: 2548 WAPGTDDTDQYLQ--IDMGQPTQLSTVE 2573


>gi|124801463|ref|XP_001349701.1| liver stage antigen 3 [Plasmodium falciparum 3D7]
 gi|3845309|gb|AAC71972.1| liver stage antigen 3 [Plasmodium falciparum 3D7]
          Length = 1558

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 892  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 947

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 948  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 1003

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 1004 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1060

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1061 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1119

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1120 ETDILEEKKEI 1130


>gi|293408384|ref|ZP_06652223.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291471562|gb|EFF14045.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 131

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/134 (17%), Positives = 53/134 (39%), Gaps = 14/134 (10%)

Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVR-KVLKITKEPISLETPIGDEDTSHLGDFIED 594
            R    K+  EP   E+A +     + +  + L+  +   SL+  +  E           
Sbjct: 5   IRETRKKLGHEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGI------- 57

Query: 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654
              ++  +   Q   ++     L+ L+ +E+ +L M +      +  L+E+     +T  
Sbjct: 58  --PLAGRELEDQFVTQQMLQYALSQLSEKEQLILSMYYQH----EMNLKEIALVLGLTEA 111

Query: 655 RIRQIEAKAIRKLK 668
           RI Q+  +  +K++
Sbjct: 112 RICQLNKQIAQKIR 125


>gi|291231779|ref|XP_002735841.1| PREDICTED: KIAA0216-like [Saccoglossus kowalevskii]
          Length = 2036

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 59/443 (13%), Positives = 152/443 (34%), Gaps = 24/443 (5%)

Query: 166  ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
             +I   D++++  T LR++         E         E  +  + ++   +++   VQ 
Sbjct: 1442 EIIHLDDKVDNLQTELRDLTSRGGKDETEKLDLKRFRRELEAKLQDQEEELDEQAGQVQM 1501

Query: 226  TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
             E          ++ + +     +  E +  ++  +       L A  D+   +   AL 
Sbjct: 1502 LEQAKLRLEMQLQNIKQEHQKELDAKEQEVEDVRTNSQKKLKHLEAQLDEEYSEKQAALK 1561

Query: 286  EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
            E  E+ R+L+  QD  V   KD +  ++  + K K +     + L   + +  V      
Sbjct: 1562 EKREIERQLKERQDVFVRSDKDTERRLRKDLKKTKALLRDAQIML-DKQKESAVN--KAS 1618

Query: 346  SKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS 405
             K++ +   E   ++Q+    R    E     +    +VS +K   E +  +      D 
Sbjct: 1619 FKQLQNELEESQFMSQAAVKSRKGIEEELADLQQQLDYVSKSKSEAEQKMISVTRERND- 1677

Query: 406  ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMV------EANLRLVISV 459
               ++ +I     +    + + R IV    + + + +    ++       E+    V  +
Sbjct: 1678 ---LQCKIDDQEEDFSELLKKHRAIVHQASQYQLQINDHLTQIAELSGEKESLQERVAEL 1734

Query: 460  AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI-------TRSI 512
              K  N     +D  Q     +    +  D     +        ++  +        +  
Sbjct: 1735 TMKVNNYIETTVDRSQV----VRFEGKCRDLDSRLELELLHKQRLEANLSKLKDSNEKLT 1790

Query: 513  ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE 572
            +++          ++   K+ R  + + ++       E+ A +  + +E   +  + ++E
Sbjct: 1791 SERDSYKSSEQQTQELNRKLQRQLKDLRDEFFELQRKEDDATRKKIELERQVEEAESSQE 1850

Query: 573  PISLETPIGDEDTSHLGDFIEDK 595
             +  +  +       L + +ED+
Sbjct: 1851 VLQSDLKLAFRRIQDLQNALEDQ 1873


>gi|256272445|gb|EEU07427.1| Hda3p [Saccharomyces cerevisiae JAY291]
          Length = 655

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 30/174 (17%), Positives = 56/174 (32%), Gaps = 10/174 (5%)

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
           II     +   +        E       + S  E    D++  +G + +  +     +  
Sbjct: 463 IIKEYETVLRTNNENLNRSHELEVENNLKFSQIETLEKDIETLKGSLMAQGETLSKLKDA 522

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN 303
                   +  E+     E+  + +    +  +  ++  A+D I E   E   L +    
Sbjct: 523 FVKTDNVQDEIEK-----EERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNG 577

Query: 304 -----GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
                  K EKS +  K L EK+  L   L L     + LV QL      + + 
Sbjct: 578 LESELKLKFEKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENL 631


>gi|123415211|ref|XP_001304644.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121886111|gb|EAX91714.1| hypothetical protein TVAG_384380 [Trichomonas vaginalis G3]
          Length = 648

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 84/260 (32%), Gaps = 19/260 (7%)

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           D       + +              R      K  + + E +  I+      +       
Sbjct: 307 DFTEDDLLKQRMDSITDQHALDILNRLRHEAIKRAETLAEEKTTIDDLKSRCRQQELDFY 366

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
                +   E +LD ++  S     A    ++ K M   DEI +   EL  LQ      Q
Sbjct: 367 KKNIESIAAEDDLDSEDSKSIKQNEAEISHMKRKNMIREDEIEDALDELNDLQKQYDLLQ 426

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
                       K++++  + +  L +  ++  +  L D ++R+ H    + +  +    
Sbjct: 427 ASSSD-------KDRIIAFLENQKLGRYEMENTIPILNDDNERLRHEYDLISKRHKKTKE 479

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWK-NFVACEVDSILKIRNEIK---------S 415
           K     ER    EL        +D  E E     +  E   + ++  ++K          
Sbjct: 480 KYKAISERLV--ELSQTLEKLKRDSQEREAAIKMIDPEKQRLEELEQKVKLMKKNNTQLK 537

Query: 416 ISVETGISISEFRHIVSMVR 435
            S+ T +S  E R ++  +R
Sbjct: 538 KSINTQLSEGELRRLIPQIR 557


>gi|16758474|ref|NP_446109.1| serine/threonine-protein kinase MRCK alpha [Rattus norvegicus]
 gi|81174934|sp|O54874|MRCKA_RAT RecName: Full=Serine/threonine-protein kinase MRCK alpha; AltName:
           Full=CDC42-binding protein kinase alpha; AltName:
           Full=Myotonic dystrophy kinase-related CDC42-binding
           kinase alpha; Short=MRCK alpha; Short=Myotonic dystrophy
           protein kinase-like alpha
 gi|2736151|gb|AAC02941.1| mytonic dystrophy kinase-related Cdc42-binding kinase [Rattus
           norvegicus]
          Length = 1732

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKAFEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|16077166|ref|NP_387979.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221307910|ref|ZP_03589757.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221317165|ref|ZP_03598459.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|133477|sp|P17869|RPSH_BACSU RecName: Full=RNA polymerase sigma-H factor; AltName:
           Full=Sigma-30; AltName: Full=Stage 0 sporulation protein
           H
 gi|143544|gb|AAA22756.1| RNA polymerase sigma-30 factor [Bacillus subtilis]
 gi|2632365|emb|CAB11874.1| RNA polymerase sigma-30 factor (sigma(H)) [Bacillus subtilis subsp.
           subtilis str. 168]
          Length = 218

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 22  QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFKED 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 82  KLTSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|260589994|ref|ZP_05855907.1| sigma-70 region 2 family protein [Blautia hansenii DSM 20583]
 gi|260539801|gb|EEX20370.1| sigma-70 region 2 family protein [Blautia hansenii DSM 20583]
          Length = 261

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 62/139 (44%), Gaps = 2/139 (1%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R          ++++ A    ++  AKK     + F DL+QEGN+GL+ A E+       
Sbjct: 124 RAFLAGNQECTEKLIRAYQDEIVKAAKKLNREDIFFGDLLQEGNMGLLTALERLSEQENP 183

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
                 +  ++  +   I +Q+   +    + +K+  + +  + ++     + + EE+A 
Sbjct: 184 DEW--IVREIESTMKLFIEEQAQQKKEDNILVEKVRDLEKKVKELTEDEDVKYSVEELAA 241

Query: 555 KLAMPVEGVRKVLKITKEP 573
            L M +E +  VL++T + 
Sbjct: 242 FLDMDLEEMESVLRLTGDD 260


>gi|158319526|ref|YP_001512033.1| RNA polymerase factor sigma-70 [Alkaliphilus oremlandii OhILAs]
 gi|158139725|gb|ABW18037.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           oremlandii OhILAs]
          Length = 213

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 37/90 (41%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           MV   +     A + +++     V + A+ Y   G    D++QEG IGL KA   F    
Sbjct: 20  MVEIAKEGDLEALEYLIKKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKPDK 79

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   + + I  +I   +    IP
Sbjct: 80  LSSFRAFAELCITRQIITAIKTATRQKHIP 109


>gi|67524045|ref|XP_660084.1| hypothetical protein AN2480.2 [Aspergillus nidulans FGSC A4]
 gi|40744642|gb|EAA63798.1| hypothetical protein AN2480.2 [Aspergillus nidulans FGSC A4]
 gi|259487901|tpe|CBF86940.1| TPA: vesicle-mediated transport protein (Imh1), putative
           (AFU_orthologue; AFUA_4G02990) [Aspergillus nidulans
           FGSC A4]
          Length = 1153

 Score = 39.4 bits (90), Expect = 2.0,   Method: Composition-based stats.
 Identities = 44/300 (14%), Positives = 94/300 (31%), Gaps = 6/300 (2%)

Query: 155 ASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDS 214
           ++L E       L     E       L   +  E  +  E +                  
Sbjct: 566 SALAELEKKIADLEQQLREKEQAIERLDSRLKGEEDLKEEIESLRDDLLNIGQEHVEAKD 625

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMED 274
             ++   +    EG I        D RS   +   ++E    +L ++ +      + +E 
Sbjct: 626 KIKELVAEKAALEGTISKLEAEITDLRSNNAAKSADSEKAHNDLKDEYESLKVKFTTIET 685

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
           +L      A     ++     S+Q      +K    S + +  K++L      L   +S+
Sbjct: 686 ELSAAQQLATTRFKDITDLRESIQKIQPELKKLRGESAELRSTKDELKSKTAELRTLESK 745

Query: 335 IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQG---RELDPHWVSYAKDFP 391
            D L  ++  +   I   E E+  L Q    + D  L+  +     + D  ++   K   
Sbjct: 746 HDDLQAEVKALKTSISDRETEVKTLNQKIKQELDSRLKAEESLTVAQSDLRYIESRKQEA 805

Query: 392 EGEWKNFVAC---EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEM 448
               +  ++      D +   R  ++    +T     E   +   ++    + S A+  M
Sbjct: 806 IEGKQKVLSELSNVQDELKTARARLREYEQQTSQLNKELEGLRDEIQLKTAQHSSAQSLM 865


>gi|325182193|emb|CCA16646.1| conserved hypothetical protein [Albugo laibachii Nc14]
          Length = 4903

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 68/445 (15%), Positives = 152/445 (34%), Gaps = 39/445 (8%)

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL-DEIAEVYRELRS-LQDNAVNGQK 306
            +  E +        D ++   +A +  L      AL  +I+ +       LQ +    ++
Sbjct: 3496 DELEKEFDGDSCSSDQNSEIRNAKDCVL--FSEEALWSKISNLESPFFEILQTHRTPQEQ 3553

Query: 307  DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL--YDISKRIMHNEGELLRLAQSYG 364
            D  SS     ++E L         N ++ + L +++    + + +      +    + Y 
Sbjct: 3554 DSGSSKAAIGVRESLEGR------NITQKEALCKEMIAEAVREALEGWNHPISHCREQYE 3607

Query: 365  IKRDVFLERHQG-RELDPHWVSYAKDFPEGEWKNFVACEVDSILK----IRNEIKS-ISV 418
                       G        +  A+D  E E           +++     +N ++  I  
Sbjct: 3608 QTIQRIQSMEDGQNSAILSKMEKARDEYESELSTLKLQMRSQLMEESRASQNSLREHIEK 3667

Query: 419  ETGISISEFRHIVSMVRKGECE--ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
               +   + +  +S     E    A   + EM +  +  V+    +  +R +   +LI  
Sbjct: 3668 MERMRNQQEKEQISETTDPERISAAQDRRPEM-QKLMDQVMEETVRAESRRIA-GELIS- 3724

Query: 477  GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
            GN+  MKA    D      F    +  + +    ++  Q   I     ++       +  
Sbjct: 3725 GNVSDMKA---SDLQASGSFVEEQLTKLAKTQKEALRIQQERIHADTLLQK-----EKLR 3776

Query: 537  RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN 596
             R+  +++     E+ A  + +  E   K L        L         + +   I D N
Sbjct: 3777 NRIQKRVQSSQMKEDEADDIDLMAEE-EKALVTANYDEFLADASSSLREA-VQQTISDVN 3834

Query: 597  AVSPLDSAIQANLRETTT-RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
                   A+  + +E     + A+ T R++ + R +      ++    +   +    +E 
Sbjct: 3835 REIRNCIAVFDSEKEDLALELRATRTERDKDLERNQVRNFDESEEGNTQESDRL---QEE 3891

Query: 656  IRQIEAKAIRKLK--HPSRSKKLRS 678
            IR+ E KA  +L+  H ++ + LR+
Sbjct: 3892 IRRDEKKAWEQLQVSHEAQLQSLRA 3916


>gi|289065415|gb|ADC80889.1| RNA polymerase sigma factor [Pseudomonas sp. NCPPB3873]
          Length = 123

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 40/124 (32%), Gaps = 3/124 (2%)

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
                              A   E   D++E  +  +    E +  P  + A      V 
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAVKAEGADDDEEKSADASDEEDEVESGPDPVIAQQRFGAVS 62

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ++   +       +D+K ++   V    L +L   + L   + + LVE++    +R+  
Sbjct: 63  DQMEITRKALKKFGRDDKHAIAEMV---ALAELFMPIKLVPKQFEGLVERVRGALERLRA 119

Query: 352 NEGE 355
            E  
Sbjct: 120 QERA 123


>gi|94310065|ref|YP_583275.1| FecI-like sigma-24 [Cupriavidus metallidurans CH34]
 gi|93353917|gb|ABF08006.1| RNA polymerase sigma I (sigma 19) factor [Cupriavidus metallidurans
           CH34]
          Length = 166

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 29/137 (21%), Positives = 58/137 (42%), Gaps = 10/137 (7%)

Query: 538 RMSNKIKREPTPEEIAK---KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL-GDFIE 593
           R+SN+ + E   +E      +  +  E  R  L  T   I+++T    +   HL  D IE
Sbjct: 25  RLSNRHEAEDLSQEAMLRVLEARVTPEQPRAYLHQTARNIAIDTFRKRDGHEHLPLDSIE 84

Query: 594 DKNAVSPLDSAIQANLR--ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
             +A S    A    ++      R LA L  +  +V   +   G     + +E+ ++  +
Sbjct: 85  SIHAPSGNPEADLHAVQVVAGLERALAELPLKCRQVFIWQRLDGC----SQQEIAERLNI 140

Query: 652 TRERIRQIEAKAIRKLK 668
           ++  + +   +A+R L+
Sbjct: 141 SKNMVEKYMIRAMRHLR 157


>gi|149040859|gb|EDL94816.1| CDC42 binding protein kinase alpha, isoform CRA_a [Rattus
           norvegicus]
          Length = 1732

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKAFEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|251854894|gb|ACT22565.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1466

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 804  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 859

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 860  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 915

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 916  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 972

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 973  EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1031

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1032 ETDILEEKKEI 1042


>gi|253580392|ref|ZP_04857658.1| RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848485|gb|EES76449.1| RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 178

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
              ET  + L  L+ RE  +L  RF        +  E+G+Q  ++   +R I+ +A+ KL
Sbjct: 114 MREETLRKSLEQLSDREREILLGRF----YYQKSSTELGRQMNLSPGNVRMIQKRALEKL 169

Query: 668 K 668
           +
Sbjct: 170 R 170


>gi|57642082|ref|YP_184560.1| methyl-accepting chemotaxis protein [Thermococcus kodakarensis
           KOD1]
 gi|57160406|dbj|BAD86336.1| methyl-accepting chemotaxis protein [Thermococcus kodakarensis
           KOD1]
          Length = 769

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 42/290 (14%), Positives = 103/290 (35%), Gaps = 11/290 (3%)

Query: 65  DTVAMLSNMGINV--VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           D    ++ +   V  V  +    +E   +  +     ++ S    +  +  + + ++ V 
Sbjct: 486 DVTEAINQVNEAVQQVSIEAQRQQENINEITEGMRLVADMSEESVRAMEEFEGAVNEVVH 545

Query: 123 MYL--REMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +    R+ G +       +I   + +       +  + E   + + +      + + T L
Sbjct: 546 IAEEGRQKGEVS----AQQIQSIQEMMGNIEAAVNRVNEMSRSIEEITNVITGIAEQTNL 601

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L     +EA    E+  GF    +       E    +K  D+++E    +    + + + 
Sbjct: 602 LALNAAIEAARAGEAGRGFAVVAQEIRNLAEE---SKKAADNIKEIINRMTEEIRDAVNA 658

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             +  S    +    R   E   + A  +S    +L       L    EV + L++L++ 
Sbjct: 659 TQRGVSVVSESSETLRETTEYLTNIAELISDTGARLGHVKEQILRTQEEVDKALKALENL 718

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           A + ++   S+ +     E+    +  L    + +  +VE+L DI  +  
Sbjct: 719 AASAEETTASAEEVSSAVEEQTAAIEELQRAATDLKAIVEKLRDIIGKFK 768


>gi|46138911|ref|XP_391146.1| hypothetical protein FG10970.1 [Gibberella zeae PH-1]
          Length = 1521

 Score = 39.4 bits (90), Expect = 2.1,   Method: Composition-based stats.
 Identities = 45/260 (17%), Positives = 93/260 (35%), Gaps = 17/260 (6%)

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            +  S  K ++   ++E +   E         + ++D    +     NA ND   L  + D
Sbjct: 830  DKISEVKLQNQELQRELEICMEDFETAVDGKRQAEDAALTLQEDLNNAMNDLVALQSERD 889

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD--------EKSSVKCK 315
            ++    S ME++       A +EI  +  E     +     Q D        +    + +
Sbjct: 890  EALREQSEMENEFESLRKEAQEEIDALEAEADQQAEEMQRVQADLQDRSENFDALQEEMR 949

Query: 316  VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL-------RLAQSYGIKRD 368
             + E L++L         RI  L ++L   +K +   E +L+       RL+      + 
Sbjct: 950  KMSEALIRLEDDQENKLRRIQQLEQELDSSNKELEDLEQKLMEANDKNQRLSVQQESSQG 1009

Query: 369  VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
                  + +E D   +    +      +  +  E + + ++ N ++    +  I   + +
Sbjct: 1010 EIAFLREEQETDKIRIGD-LEAAVASAEQSIHDEKERVKELENRLQQERHQREIVADQEK 1068

Query: 429  HIVSM-VRKGECEASIAKKE 447
              V   V +   EAS AK E
Sbjct: 1069 EEVQQFVNELNREASAAKDE 1088


>gi|259150336|emb|CAY87139.1| Hda3p [Saccharomyces cerevisiae EC1118]
          Length = 656

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 5/105 (4%)

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN-----GQKD 307
           ++ ++  E E+  + +    +  +  ++  A+D I E   E   L +           K 
Sbjct: 527 DNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNGLESELKLKF 586

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           EKS +  K L EK+  L   L L     + LV QL      + + 
Sbjct: 587 EKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENL 631


>gi|160892750|ref|ZP_02073540.1| hypothetical protein CLOL250_00281 [Clostridium sp. L2-50]
 gi|156865791|gb|EDO59222.1| hypothetical protein CLOL250_00281 [Clostridium sp. L2-50]
          Length = 357

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 32/149 (21%), Positives = 62/149 (41%), Gaps = 10/149 (6%)

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
            K       +    +KRE +  EK +   ++   D ES  +    D+   D+ P+  + D
Sbjct: 125 KKQEKAEIRKAKKQEKREQAEAEKAKKTEKQEAEDAESDQQDGLSDQMMQDADPDREDRD 184

Query: 255 E-RNLDEDEDDSAHTLSAMEDQL----RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
             R   ED  +   +   +  ++       V+   D+I  V R+L  ++D A   +K  +
Sbjct: 185 ANREFAEDHSEFQKSPETIFTRIGKKFDRFVIAVKDKIEAVVRKLHHMKDKAEQYKKFVR 244

Query: 310 S---SVKCKVLKEKLVKLVGSLSLNQSRI 335
           +       +VLK  ++ L+    LN ++I
Sbjct: 245 AGTTKQAFQVLKRNVILLLK--HLNPTKI 271


>gi|119479573|ref|XP_001259815.1| myosin type II heavy chain, putative [Neosartorya fischeri NRRL 181]
 gi|119407969|gb|EAW17918.1| myosin type II heavy chain, putative [Neosartorya fischeri NRRL 181]
          Length = 2405

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 36/229 (15%), Positives = 82/229 (35%), Gaps = 14/229 (6%)

Query: 132  ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT---LLREIIDLE 188
             LL   GE   A  ++     +     +            +E          ++ I++ E
Sbjct: 923  PLL---GETRTANEVKKRDEKIKELEAKMKQDIAERQKLDEERRRTEIEIQKIQHILESE 979

Query: 189  ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              +  + +  F            + +    +++ +++    + +A K + +  S+  +  
Sbjct: 980  RALALDKEEIFKRLQLREIELTEKLAGAIADQESLEDQLDTLIAAKKKADEQLSQRITQL 1039

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQLRP---KVMCALDEIAEVYRELRSLQ-----DN 300
            E A      L+ ++ D    L  ++ QL      V      + E+ +E++ LQ      +
Sbjct: 1040 EQAGEIIERLEAEKRDLQARLDVLDRQLEEAQSSVAEQEARVKELGQEIKMLQSHLSLKD 1099

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
                  + K     + L  KL +    L L++ +I  LVE+   I ++I
Sbjct: 1100 RKIQDLEAKLLKTDQDLDIKLARTSKDLELSKKQIKDLVEENRSIRQQI 1148


>gi|119195685|ref|XP_001248446.1| hypothetical protein CIMG_02217 [Coccidioides immitis RS]
          Length = 1260

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 30/216 (13%), Positives = 78/216 (36%), Gaps = 8/216 (3%)

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           + L   + E+      +  +         E +       +     + + +  +  +D+++
Sbjct: 742 KELEEKQSEVEAKQEEINRLKSELESKIAELEDKRRELEQKQGELESKQTELQAIQDELR 801

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
           E + ++E      +  ++ +D   E     +  LD+ ++  A  L+A+  QL  +     
Sbjct: 802 EVKAELEEKKSQLESKQADLDKKQEELTAKQAELDDVKEKHAAELAALRAQLEEQTNATK 861

Query: 285 DEIAEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRID 336
           +   ++       Q      QKD        ++ + + KV  E+   L       + R+ 
Sbjct: 862 ERDEKIEAMTTEHQQKEEQWQKDRGDFEAQLQEKTEELKVALEEKEALAVDGKNREERLQ 921

Query: 337 LLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
            +VE++      +  +   L +   S G   D+ ++
Sbjct: 922 SIVEEMRQTHDNLNKDRERLKKTLHSLGEATDMKIK 957


>gi|157823731|ref|NP_001102510.1| kinesin-like protein KIF21A isoform 1 [Mus musculus]
 gi|50401187|sp|Q9QXL2|KI21A_MOUSE RecName: Full=Kinesin-like protein KIF21A
          Length = 1672

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 70/454 (15%), Positives = 138/454 (30%), Gaps = 53/454 (11%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 407 KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 466

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 467 RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 519

Query: 167 LIIWRDELNDGTTLLREIIDL--EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
              +   +        EIIDL  +     + K            +   +      +DD  
Sbjct: 520 SSAFSPTILSSDKETIEIIDLAKKDLEKLKRKEKKKKKRLQKLEESGREERSVAGKDDNA 579

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAEND----------ERNLDEDEDDSAHTLSAMED 274
           +T+ + +    VS+ + +++D       +D          E   D+ E + +   S  E 
Sbjct: 580 DTDQEKKEEKGVSEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSES 639

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
             +      L  I       + L D   N QK  ++  K    +EKL+ L   +   Q  
Sbjct: 640 DEKANYQADLANITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLE 697

Query: 335 IDLLVEQL---------------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            D +++ L                +  K++     EL RL  +   +    L+     E 
Sbjct: 698 RDQVLQNLGSVESYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEK 756

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVS 432
               +       +      +    +   K R        EI  +  +      + R ++ 
Sbjct: 757 QLKKLQQDVMEMKKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLE 815

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             ++ +      K E V A  R V  ++ K   +
Sbjct: 816 AQKRNQEVVLRRKTEEVTALRRQVRPMSDKVAGK 849


>gi|323331384|gb|EGA72802.1| Hda3p [Saccharomyces cerevisiae AWRI796]
          Length = 641

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 5/105 (4%)

Query: 253 NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN-----GQKD 307
           ++ ++  E E+  + +    +  +  ++  A+D I E   E   L +           K 
Sbjct: 527 DNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNGLESELKLKF 586

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           EKS +  K L EK+  L   L L     + LV QL      + + 
Sbjct: 587 EKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENL 631


>gi|157690881|ref|YP_001485343.1| RNA polymerase factor sigma-70 [Bacillus pumilus SAFR-032]
 gi|194017543|ref|ZP_03056154.1| RNA polymerase sigma-H factor [Bacillus pumilus ATCC 7061]
 gi|157679639|gb|ABV60783.1| DNA-directed RNA polymerase sigma subunit SigH [Bacillus pumilus
           SAFR-032]
 gi|194010815|gb|EDW20386.1| RNA polymerase sigma-H factor [Bacillus pumilus ATCC 7061]
          Length = 218

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ +     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 22  QVIERVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRED 81

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 82  KLTSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|254573932|ref|XP_002494075.1| Formin, nucleates the formation of linear actin filaments [Pichia
           pastoris GS115]
 gi|238033874|emb|CAY71896.1| Formin, nucleates the formation of linear actin filaments [Pichia
           pastoris GS115]
 gi|328354105|emb|CCA40502.1| Cytokinesis protein sepA [Pichia pastoris CBS 7435]
          Length = 1800

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 91/251 (36%), Gaps = 7/251 (2%)

Query: 92  SLDLASSASNSSVFLQKRKDSADRSTDDPVR-MYLREMGSIELLSRE---GEIAIAKRIE 147
           + D+A  A   +    K+ + A    D+ +R M +   G ++ L +E    E+ ++K+  
Sbjct: 620 TDDVARKAIMEAREATKKAEEAIAERDELIRQMSMGSDGLVDQLKQELLEQEVILSKQRR 679

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
                +M+ L E+    + +     EL     L+      E      S        +   
Sbjct: 680 QNE-QIMSDLREA-RRLRMVEKQEQELEIRELLITLNSLKEKQALEHSNTEPVGAKDDRL 737

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
             +     ++K+ +   E+           K    +        E  E  + E  D+   
Sbjct: 738 KSRLLQQLEKKQIEYKTESRKYGGIVEPSKKLRSLRNQMEDIEREAKELEMTEFLDNDQK 797

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
             S +    RP  +  L+++ ++ ++L  LQ ++ +  K +    +  + K++ +  +  
Sbjct: 798 QGSPL-PPSRPPKLDDLEKLEQLRQKLYLLQKDSNDVMKYQADLSQKDLYKKEKMLAMER 856

Query: 328 LSLNQSRIDLL 338
           L   Q +   L
Sbjct: 857 LQTLQKQFKDL 867


>gi|126290275|ref|XP_001371930.1| PREDICTED: similar to splicing factor 3b, subunit 1 [Monodelphis
           domestica]
          Length = 1025

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 29/176 (16%), Positives = 65/176 (36%), Gaps = 7/176 (3%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            ++++++A I  E K            + +  +  EK   D+ + + + +S  +      
Sbjct: 743 DKMVEMQAKIDEERKALETKLDMEEEERNKARAELEKREKDLLKAQQEHQSLLEKLSALE 802

Query: 242 SKV---DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            KV            ++  L E+ +          +QLR ++     E  ++  +  SLQ
Sbjct: 803 KKVIVGGVDLLAKAEEQEKLLEESNMELEERRKRAEQLRRELEEKEQERLDIEEKYTSLQ 862

Query: 299 DNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
           + A    K  +K        K ++  L      +Q  I+ L+E +  +S+ +    
Sbjct: 863 EEAQGKTKKLKKVWTMLMAAKSEMADLQQE---HQREIEGLLENIRQLSRELRLQM 915


>gi|194214883|ref|XP_001496400.2| PREDICTED: similar to aspartyl (asparaginyl) beta hydroxylase
           [Equus caballus]
          Length = 775

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 30/335 (8%), Positives = 101/335 (30%), Gaps = 28/335 (8%)

Query: 47  EELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFL 106
           +++     P  +  E  E   ++L          D   +E+     L          +  
Sbjct: 146 DQILEGPGPQNIEDEIQEQIHSVLHETVYTEPGEDLQPEEDEPARELQPEEVEPARELQP 205

Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSR--EGEIAIAKRIEAGRAMMMASLCESPLTF 164
           +        + +D             L +     E   +  +E   +             
Sbjct: 206 EDDDFLMGGNAED---------RFEPLETGTFHEETEDSDYVEETASQA------YNQDM 250

Query: 165 QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
           + ++  ++  +     +  ++D    +  E+    +   +    +  E    E   + V+
Sbjct: 251 EEIVYEQENPDA----IEPVVDEVERMFHEADDVTYQEDDEQVREPLEHEGIENSDNAVE 306

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP--KVMC 282
           ++   +E       +++ ++        +D    ++ +      L+  +  ++       
Sbjct: 307 DSNVILEEVPVPPAEEQQEIPPETNRKTDDPEQKEKVKKKKPKLLNKFDKTIKAELDAAE 366

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
            L +  ++   + + ++      +  ++       ++ L +   S  + +  I+      
Sbjct: 367 KLRKRGKIEEAVNAFEELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRRAIET----- 421

Query: 343 YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
           Y     +     +L++L+     +R  FL   +G 
Sbjct: 422 YQEVAALPDVPADLMKLSLKRRSERQQFLGHMRGS 456


>gi|302390625|ref|YP_003826446.1| RNA polymerase, sigma 30 subunit, SigH [Thermosediminibacter oceani
           DSM 16646]
 gi|302201253|gb|ADL08823.1| RNA polymerase, sigma 30 subunit, SigH [Thermosediminibacter oceani
           DSM 16646]
          Length = 214

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 35/85 (41%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
              +  A + ++      V S A+ Y   G    D+IQEG IGL KA   F+      F 
Sbjct: 26  RRGSREALEYLINKYKNFVKSKARSYFLIGADKEDIIQEGMIGLYKAIRDFNPDKLSSFK 85

Query: 498 TYAMWWVKQAITRSIADQSCTIRIP 522
            +A   + + I  +I   +    IP
Sbjct: 86  AFAELCITRQIITAIKTATRQKHIP 110


>gi|251854870|gb|ACT22553.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1446

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 103/273 (37%), Gaps = 12/273 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 784  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 839

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 840  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 895

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 896  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 952

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 953  EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1011

Query: 280  VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
                L+E  E+ ++     +      KD ++ +
Sbjct: 1012 ETDILEEKKEIEKDHFEKFEEEAEEIKDLEADI 1044


>gi|75765127|ref|ZP_00744403.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|228902065|ref|ZP_04066229.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|74487384|gb|EAO51324.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|228857491|gb|EEN01987.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
          Length = 215

 Score = 39.4 bits (90), Expect = 2.2,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 86/264 (32%), Gaps = 63/264 (23%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            T   + E +  + +    +   SIA+   +                  ++  DLIQ G 
Sbjct: 1   MTPEKLFEEKEYLVIAAIKQRFGSIARARQIAE-------------RNNMELDDLIQVGR 47

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
           + L     K+D      F  Y M  +K A++  +                          
Sbjct: 48  MHLWACCVKYDAERIDTFHAYVMKGMKWAMSDELHM------------------------ 83

Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
                              MP +  RKV    +  I++ +     D   + +F     AV
Sbjct: 84  -----------------KGMPFKVSRKVSHEERNQINIHSIDWHRDEDSVNEFY----AV 122

Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
           SP++   +A L      V + L  +E+ ++     + +   +T  E+  +  + R  +  
Sbjct: 123 SPINVEEEALLSVEFEEVTSVLEEKEKLII-----LHVGEGYTEREIAVKLGMGRSTVNT 177

Query: 659 IEAKAIRKLKHPSRSKKLRSFLDG 682
            + +A  K+    +   +R+F  G
Sbjct: 178 KKNEAFLKINPDYKPLNVRTFFLG 201


>gi|238881346|gb|EEQ44984.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 2139

 Score = 39.4 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 37/284 (13%), Positives = 105/284 (36%), Gaps = 4/284 (1%)

Query: 165  QALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
            +      DEL       +EI    + +  + +              +  +  +   D++ 
Sbjct: 1021 EKFKELEDELKSIKKSNKEISSQNSELIQKLEKTEKDLQAKDEEIDKLKAETKSNIDNLN 1080

Query: 225  ETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                 ++S  K +++  S       +   + + L E+ +++  ++ A       +   A 
Sbjct: 1081 SEISSLQSKLKEAEESHSSTKDEHSSLSENLKKLKEEYENTKTSMIAKLSAKIEEHKKAT 1140

Query: 285  DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
            DEI    + +  LQ+   + ++  +   +   +K  L +    LS N+ ++  L ++  +
Sbjct: 1141 DEIETKTKHITDLQE--EHAKQKSQFESERNDIKSNLDEANKELSDNREKLSNLEKEKTE 1198

Query: 345  ISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVD 404
            ++ ++   E ++  L  S  I  +   +  +    D        +    E +  +  + +
Sbjct: 1199 LNNKLKTQEEKISDLETSVAIS-EDKSKSLKHDIEDLKREKIKLETTLKENEETMFEKKE 1257

Query: 405  SILKIRNEIKSIS-VETGISISEFRHIVSMVRKGECEASIAKKE 447
             +  + ++ K +      ++ ++ + I  ++RK E   S    E
Sbjct: 1258 QLQVVNDKCKELEACLKKLTETKEKEINDLIRKLEAAKSDHDTE 1301


>gi|114578203|ref|XP_001156090.1| PREDICTED: dynactin 1 isoform 5 [Pan troglodytes]
          Length = 1101

 Score = 39.4 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|56962504|ref|YP_174230.1| hypothetical protein ABC0730 [Bacillus clausii KSM-K16]
 gi|56908742|dbj|BAD63269.1| conserved hypothetical protein [Bacillus clausii KSM-K16]
          Length = 192

 Score = 39.4 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 23/119 (19%), Positives = 49/119 (41%), Gaps = 10/119 (8%)

Query: 557 AMPVEGVRKVLKITKEPISLETPIGDEDTSHL-----GDFIEDKNAVSPLDSAIQANLR- 610
              V+  +++ K  ++ +SL+    +  T+ L     GD I+D   V   D   +     
Sbjct: 65  GYSVDFDKRIRKNEQQLLSLDALFHNGQTTLLDMLAAGDVIKDAELVQEEDGHYEELFEN 124

Query: 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           E   +    L P +  VL   F  G    +  +++ K+  ++ +R+   + + +  LK 
Sbjct: 125 EVLQQAFQELKPLQREVLVYSFFYG----YRNKDIAKRLAISEQRVSYNKKRGLELLKQ 179


>gi|220930948|ref|YP_002507856.1| sporulation sigma factor SigH [Halothermothrix orenii H 168]
 gi|219992258|gb|ACL68861.1| sporulation sigma factor SigH [Halothermothrix orenii H 168]
          Length = 215

 Score = 39.4 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 20/91 (21%), Positives = 38/91 (41%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V        IA++ +++     V++ ++ Y   G    D++QEG IGL KA   +   
Sbjct: 21  ELVELVHKGDKIAEETLIKRYKNFVLAKSRSYFLVGADREDIVQEGMIGLYKAIRDYKVD 80

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +     P
Sbjct: 81  RLASFRAFAELCITRQIITAIKAATRQKHQP 111


>gi|308171989|ref|YP_003918694.1| RNA polymerase sigma-30 factor sigma H [Bacillus amyloliquefaciens
           DSM 7]
 gi|307604853|emb|CBI41224.1| RNA polymerase sigma-30 factor (sigma(H)) [Bacillus
           amyloliquefaciens DSM 7]
          Length = 206

 Score = 39.4 bits (90), Expect = 2.3,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 10  QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRED 69

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 70  KLTSFKAFAELCITRQIITAIKTATRQKHIP 100


>gi|320451090|ref|YP_004203186.1| ATP-dependent chaperone protein ClpB [Thermus scotoductus SA-01]
 gi|320151259|gb|ADW22637.1| ATP-dependent chaperone protein ClpB [Thermus scotoductus SA-01]
          Length = 861

 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 78/212 (36%), Gaps = 19/212 (8%)

Query: 229 DIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIA 288
            I+   + +   R  ++S PE  +  ER   + E +        +   + ++    +EIA
Sbjct: 388 AIDLIDEAAARLRMALESAPEEIDTLERKKLQLEIEREALKKEKDPDSQERLKAIEEEIA 447

Query: 289 EVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
            + +E++ L+        + +   K +  +++L ++   + L + +        YD+++ 
Sbjct: 448 HLNQEIQKLKAEWEA---EREVLKKLREAQQRLDEVRRQIELAERQ--------YDLNRA 496

Query: 349 IMHNEGELLRL-----AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEV 403
                GEL RL     A S  +K   F+      E           +        +  E 
Sbjct: 497 AELRYGELPRLEAEVEALSEKLKNARFVRLEVTEE---DIAEIVSRWTGIPVSKLLEGER 553

Query: 404 DSILKIRNEIKSISVETGISISEFRHIVSMVR 435
           + +L++ +E+    V    +I      +   R
Sbjct: 554 EKLLRLEDELHKRVVGQEEAIRAVADAIRRAR 585


>gi|311029632|ref|ZP_07707722.1| YueB [Bacillus sp. m3-13]
          Length = 953

 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 53/331 (16%), Positives = 121/331 (36%), Gaps = 34/331 (10%)

Query: 128 MGSIELLSREGEIAIAK----------RIEAGRAMMMASLCESPLTFQALIIWRD-ELND 176
           MGSI+LL+       A+           I  G   + +S+  +      L   R  E++ 
Sbjct: 265 MGSIQLLATAQPSRFAQVQEYFSQGGTEINNGLESVNSSMESNNTALNELSELRKSEVDR 324

Query: 177 GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD--DVQETEGDIESAA 234
            T  +    + +  I    K       E      +++  +E E++    ++ +    S+ 
Sbjct: 325 QTGDMEAFFEQQEQIAMSQKNADLSELETTLENLKDELEKEGEKEPGKPEDPKPVTTSSV 384

Query: 235 KVSKDDRSKVDSPPENAENDERNLD-----EDEDDSAHTLSAMEDQLRPKVMCALD---- 285
              KDD S+    PEN   +    +     +D +D   T++ + + +  +++  L+    
Sbjct: 385 SEVKDDDSEEVEVPENRSFENEIKELNAIAKDINDIQTTINGLGELVPEEILTVLNPLGE 444

Query: 286 ---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI------- 335
               I EV   L+ +++     +  E+   + + L+E++V  +  ++  +  I       
Sbjct: 445 LSSRITEVEESLKGVEEENPLLKIIEQLEAEKQALEEEIVGYLEQITELEEVIESLEGDK 504

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           + L   L  +   I   E E+L   Q     R   +E    +E++ +      ++     
Sbjct: 505 ESLSNNLQTVINEIEETEKEILDQIQD--EDRLRLIEPVFDKEINNNNTKDLLNYHASLV 562

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISE 426
           +       +    +   ++ I +   +S  E
Sbjct: 563 QYEQTLNRNVNEDVEALLEDIQIILNVSDPE 593


>gi|148686691|gb|EDL18638.1| Cdc42 binding protein kinase beta, isoform CRA_a [Mus musculus]
          Length = 1742

 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 96/304 (31%), Gaps = 33/304 (10%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMTQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP------KVMCALDEIAEVY 291
                 ++     A  ++  L +   +++  L +   +L+       + +    E+ E  
Sbjct: 525 THRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKDAHQQRKRALQEFSELNERM 584

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ELRSL+       +D++  ++  + K                ID + + L    K    
Sbjct: 585 AELRSLKQKVSRQLRDKEEEMEVAMQK----------------IDSMRQDLRKSEKSRKE 628

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E  L   A     +R +        +     +   K    G      +     I KIR+
Sbjct: 629 LEARLEDAAAEASKERKLREHSESFCKQMERELEALKVKQGGRGPGAASEHQQEISKIRS 688

Query: 412 EIKS 415
           E++ 
Sbjct: 689 ELEK 692


>gi|189499564|ref|YP_001959034.1| DNA repair protein RecN [Chlorobium phaeobacteroides BS1]
 gi|189495005|gb|ACE03553.1| DNA repair protein RecN [Chlorobium phaeobacteroides BS1]
          Length = 569

 Score = 39.1 bits (89), Expect = 2.3,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 92/234 (39%), Gaps = 13/234 (5%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELND--GTTLLREIIDLEACIGPES 195
            EI + + I + +      + ++P T Q L    D+L D  G    + ++  E  +    
Sbjct: 89  EEIILRREI-SAKGQSRCFINDTPGTLQVLKKLGDQLVDLHGQHEHQLLLHPETHLSLLD 147

Query: 196 KGGFFHG-TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD----SPPEN 250
           + G  +   E +    +    + KE + V      ++    + +    ++D       E 
Sbjct: 148 EFGQLNPLVESYQNVFKNLKKKRKELERVTTEADRLKEKQDLLEYQYKELDLLELKSGEQ 207

Query: 251 AENDERNLDEDEDDSAHTL-SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           A+ +E  +  +  ++  +L S++ +QL    + A   ++E  R+L  L     +     +
Sbjct: 208 ADIEEEIILHENAETRFSLCSSLSEQLYDDDLSAFVLLSEAVRQLDRLSGIDKSFSPHLQ 267

Query: 310 SSVKCKVLKEKLVKLVGS----LSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
            +V  K L E+L + V      +  N  ++D L E+   + + +      +  L
Sbjct: 268 DAVSAKSLIEELSRAVRDYSDGIEFNPEKLDQLRERHMQLQRAVKKYGRPIEEL 321


>gi|154495089|ref|ZP_02034094.1| hypothetical protein PARMER_04136 [Parabacteroides merdae ATCC
           43184]
 gi|154085639|gb|EDN84684.1| hypothetical protein PARMER_04136 [Parabacteroides merdae ATCC
           43184]
          Length = 192

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 21/150 (14%), Positives = 55/150 (36%), Gaps = 10/150 (6%)

Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL-GD 590
           +V+       + +   T + I       +   + +  +  + I+LET    ++  ++   
Sbjct: 42  IVQDMFAELWEKREMFTCQTIRIAYLFTIIKNKCLNHLRHKTIALETINNMQEEYNMTLR 101

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC 650
              D             ++ +   R L SL  + + +  M    G       E++  +  
Sbjct: 102 MNLDSLEAFEQHIFSDQDIEDLINRALDSLPTKCKEIFIMNKLEG----KKQEQIATELN 157

Query: 651 VTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
           ++   +R   + A +KL++     +L+ +L
Sbjct: 158 LSTNTVRNQISIAYKKLRN-----ELKDYL 182


>gi|153811849|ref|ZP_01964517.1| hypothetical protein RUMOBE_02242 [Ruminococcus obeum ATCC 29174]
 gi|149831983|gb|EDM87068.1| hypothetical protein RUMOBE_02242 [Ruminococcus obeum ATCC 29174]
          Length = 216

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
            ET   ++  LT R+ ++++  +        T +EV  +  +T   + +  ++A++K+++
Sbjct: 143 EETVRELMNLLTERQRQMIQRIYF----QQQTQKEVSHELGITVPAVSKCISQAMQKMRN 198

Query: 670 PS 671
            S
Sbjct: 199 NS 200


>gi|311893360|ref|NP_001185796.1| dynactin subunit 1 isoform 3 [Mus musculus]
          Length = 1239

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 449 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|237667676|ref|ZP_04527660.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237656024|gb|EEP53580.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 87

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 28/71 (39%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
            D +  +             +R    ++  SLT RE  +L MR+G+      T  E+   
Sbjct: 1   MDILSSEKDSVLDKVESNLQVRALYKKLGESLTSRESSILIMRYGLIDGKCKTQREIASN 60

Query: 649 FCVTRERIRQI 659
             ++R  + +I
Sbjct: 61  LGISRSYVSRI 71


>gi|307189823|gb|EFN74095.1| Sperm surface protein Sp17 [Camponotus floridanus]
          Length = 2219

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 38/270 (14%), Positives = 90/270 (33%), Gaps = 9/270 (3%)

Query: 62   QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            ++ D   +   M   V + +   D E    + D      N     + +  +      D +
Sbjct: 781  KINDVGKLADEMEETVSEIEKSTDAEKISTNKDDEEKKRNDE---EGKNTNEIEKVKDVI 837

Query: 122  RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
             + + E  ++  ++ + E  + + IE     M  +  E+  +   +    ++LN+   L 
Sbjct: 838  EISMNEKENLLNITEKSEDEVKEEIERSSNEMKNTTNEAETSVNKIEKSSNKLNETEILT 897

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES-AAKVSKDD 240
             E+      +  + +       E     + E S+ E ER   +++  D+E    K+  +D
Sbjct: 898  NEV-----EVTNQEEILTKAAEEVIKVSEDEKSTDENERSINEKSPTDVEKLTVKIQTED 952

Query: 241  RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
               ++   +N ++  +    + DD   T S  +                   E      +
Sbjct: 953  AQSINLKSQNNDDQSQAAVCETDDDNVTASNNKADNTVNEFSKTVACESAANEREISATD 1012

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSL 330
              +    + +  + K   +       SL L
Sbjct: 1013 LPDENTAKATKARKKREIDSCPTTSLSLEL 1042


>gi|290968523|ref|ZP_06560062.1| RNA polymerase sigma-H factor [Megasphaera genomosp. type_1 str.
           28L]
 gi|290781519|gb|EFD94108.1| RNA polymerase sigma-H factor [Megasphaera genomosp. type_1 str.
           28L]
          Length = 229

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 35/89 (39%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           +   +     A + +V      + S A+ Y   G    DLIQEG IGL KA   F     
Sbjct: 23  LWLQKTHDDRAMEYIVHKYKNFIKSKARTYFLVGADREDLIQEGMIGLYKATRDFRAEKK 82

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  ++   +    +P
Sbjct: 83  VAFRVFAELCIMRQIITAVKTATRQKHVP 111


>gi|240146688|ref|ZP_04745289.1| putative methyl-accepting chemotaxis protein signaling domain
           protein [Roseburia intestinalis L1-82]
 gi|257201164|gb|EEU99448.1| putative methyl-accepting chemotaxis protein signaling domain
           protein [Roseburia intestinalis L1-82]
          Length = 418

 Score = 39.1 bits (89), Expect = 2.4,   Method: Composition-based stats.
 Identities = 33/227 (14%), Positives = 79/227 (34%), Gaps = 11/227 (4%)

Query: 138 GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKG 197
            EI  A  + A       S+ E       +    +E ++ +  + +I         E+  
Sbjct: 152 QEITTASGMNAN------SIEEQNTMTATIQDAIEETSERSKQMVDIAMNSNDSIQENMR 205

Query: 198 GFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257
                 +        +    +    +Q+   ++E  A +  +  S+ +    NA  +   
Sbjct: 206 VMDELKDQAEQITNTNHDVTEAMTKLQDKTKEVEEIAGMILNISSQTNLLALNASIESAR 265

Query: 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-KV 316
             E    +    + + +Q+R       +   E+ R    L  NA +     + SV+  + 
Sbjct: 266 AGE----AGRGFAVVAEQIRQLAEQTKNSTEEITRITNELNANANDVVVSVEGSVQATED 321

Query: 317 LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
            KEK++    + +L    I  LV  + +++K++        ++  + 
Sbjct: 322 QKEKILAASETFNLLNKNIGELVAHIEEVNKKVSGLSDSNNKIVVNC 368


>gi|254517800|ref|ZP_05129856.1| predicted protein [Clostridium sp. 7_2_43FAA]
 gi|226911549|gb|EEH96750.1| predicted protein [Clostridium sp. 7_2_43FAA]
          Length = 188

 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 16/103 (15%), Positives = 41/103 (39%)

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
           +  ++ + +     + +E+++    LV   +  Y   G    D+ Q   + ++++ EKF+
Sbjct: 1   MNQLIVRAKHGDKKSMEEILKNFEPLVYKTSISYYIYGYSEEDIKQIARLTIIESVEKFN 60

Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
             L   F  Y    +K  + + I   +         R+  + +
Sbjct: 61  TDLSDSFPAYVQKCIKNKMYKEIEKATNKYYENKLNREITNSI 103


>gi|163852372|ref|YP_001640415.1| hypothetical protein Mext_2955 [Methylobacterium extorquens PA1]
 gi|188582381|ref|YP_001925826.1| hypothetical protein Mpop_3139 [Methylobacterium populi BJ001]
 gi|218531131|ref|YP_002421947.1| hypothetical protein Mchl_3181 [Methylobacterium chloromethanicum
          CM4]
 gi|240139707|ref|YP_002964184.1| hypothetical protein MexAM1_META1p3159 [Methylobacterium
          extorquens AM1]
 gi|254562119|ref|YP_003069214.1| hypothetical protein METDI3724 [Methylobacterium extorquens DM4]
 gi|163663977|gb|ABY31344.1| hypothetical protein Mext_2955 [Methylobacterium extorquens PA1]
 gi|179345879|gb|ACB81291.1| conserved hypothetical protein [Methylobacterium populi BJ001]
 gi|218523434|gb|ACK84019.1| conserved hypothetical protein [Methylobacterium chloromethanicum
          CM4]
 gi|240009681|gb|ACS40907.1| hypothetical protein MexAM1_META1p3159 [Methylobacterium
          extorquens AM1]
 gi|254269397|emb|CAX25363.1| hypothetical protein METDI3724 [Methylobacterium extorquens DM4]
          Length = 97

 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 17 DSDDSLVFDFSDDSWKKMIKLA--RQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMG 74
           S D+L  D    +  +++  A   +R  +T ++L   LPP +V+++ +E    +L+  G
Sbjct: 32 PSHDALPADI-RMTVDRLLAKADAERRRSLTYDDLEEALPPRDVTADDLEAIFWVLAEYG 90

Query: 75 INVVDGD 81
          I + +GD
Sbjct: 91 IELDEGD 97


>gi|19075870|ref|NP_588370.1| midasin (predicted) [Schizosaccharomyces pombe 972h-]
 gi|74676176|sp|O94248|MDN1_SCHPO RecName: Full=Midasin; AltName: Full=MIDAS-containing protein
 gi|4239674|emb|CAA20864.1| midasin (predicted) [Schizosaccharomyces pombe]
          Length = 4717

 Score = 39.1 bits (89), Expect = 2.5,   Method: Composition-based stats.
 Identities = 19/153 (12%), Positives = 49/153 (32%), Gaps = 14/153 (9%)

Query: 169  IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG 228
              +++ ++        ID E     +                 ED   +++  DV +   
Sbjct: 4045 DRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDHLDLPEDLKLDEKEGDVSKDSD 4104

Query: 229  DIESAAKVSKDDRSKVDSPPENAENDERNLDE-----DEDDSAHTLSAMEDQLRPKVMCA 283
              +   + + +++ + D+  +    D  +  E     DED      S + +         
Sbjct: 4105 LEDMDMEAADENKEEADAEKDEPMQDFEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDG 4164

Query: 284  LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
             +E         ++Q+N  + +   KS  + + 
Sbjct: 4165 FEE---------NVQENEESTEDGVKSDEELEQ 4188


>gi|115644354|ref|XP_001201170.1| PREDICTED: similar to E1a binding protein P400 [Strongylocentrotus
            purpuratus]
 gi|115956564|ref|XP_001178919.1| PREDICTED: similar to E1a binding protein P400 [Strongylocentrotus
            purpuratus]
          Length = 3330

 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 23/140 (16%), Positives = 52/140 (37%), Gaps = 3/140 (2%)

Query: 181  LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
            +++I D+    G                 ++    ++  + D   ++ ++E A   ++DD
Sbjct: 2158 IKDIFDVSKSAGILEDLMEVDKAAEPQEPEQPKEPEQDAKADKPLSQTELEKALARAEDD 2217

Query: 241  RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
                 +   +AE D    + DED         E +   +      E+ ++  +L  ++  
Sbjct: 2218 TDVKAASRAHAEQDAELAEFDEDIPYEG---EEGKGNDESSKLEKELTQLNNQLTPIERY 2274

Query: 301  AVNGQKDEKSSVKCKVLKEK 320
            AV   +D    +  + LKE 
Sbjct: 2275 AVVYLEDTLEPITAEQLKEA 2294


>gi|303287316|ref|XP_003062947.1| central pair protein [Micromonas pusilla CCMP1545]
 gi|226455583|gb|EEH52886.1| central pair protein [Micromonas pusilla CCMP1545]
          Length = 2105

 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 64/185 (34%), Gaps = 10/185 (5%)

Query: 81  DDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE--LLSREG 138
           D+  +   + +    A    + +            +T DPV+     +G+ E  L +   
Sbjct: 149 DEAREAVKAAEEDVAARRKESIAAAEDAVDAPPPTATSDPVKEADEALGNAEKALKAAMK 208

Query: 139 EIAIAKRIEAGRAMMMASLCESP--------LTFQALIIWRDELNDGTTLLREIIDLEAC 190
           E+A  +R+    A M  +   +P             +I    ++  G   LR +I++   
Sbjct: 209 ELARKERLMTAPAAMTRAYALAPDWSGSASGGEISEVISGLSDVVGGGLRLRSVINVARA 268

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
             P         +   +     +  +E   +  +  +    SA + SK   ++ +  PE 
Sbjct: 269 RLPPPTPPEPEDSAATTAPPASEDGEETTAEGAEGEDPAGASAEEASKPPPAEEEGEPEP 328

Query: 251 AENDE 255
            E D+
Sbjct: 329 PEVDD 333


>gi|226287006|gb|EEH42519.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb18]
          Length = 1241

 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 59/347 (17%), Positives = 109/347 (31%), Gaps = 43/347 (12%)

Query: 136  REGEIAIAKRIEAGRAMMMASLCESPLT-FQALIIWRDELNDGTTLLREIIDLEACIGPE 194
            RE E  +   IE GRA     + E      +   +  +EL      L E  +        
Sbjct: 927  REEEQRLLAEIEKGRAGKQRLVEELDALGIETAELSIEELQATKDRLEEAGE-NGDNDQV 985

Query: 195  SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP--ENAE 252
             +      T   +   R  SS+E E D       D  ++   S  D S   +       E
Sbjct: 986  KRFENVPKTSQEAIDMRIPSSKENEEDISPGDMADDGTSCSSSAMDESMGHTEDLFAEEE 1045

Query: 253  NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
              E+     E D +H+  +M       VM  L+E         S+ +   +  KD + + 
Sbjct: 1046 AQEQLEPLIEKDQSHSSESM----VHAVMTDLEEEPSQTNTQGSMTEPCPDPTKDNEDTR 1101

Query: 313  KCKVL---KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
            +           +KL  +   +    + +               G    L  S+ I    
Sbjct: 1102 RVNHYFTPYNSPLKLFRAYRYHPRFTEDI--------------NGGFRSLTYSHKIDPHN 1147

Query: 370  FLERHQGRELDPHWVSYAKDFPEGEWKNF--VACEVDSILKIRNEIKSISVETGISISEF 427
            ++  ++           + +    E+++F  +A   D IL     ++  SV  G +  E 
Sbjct: 1148 YICPYEA-------AGGSCNDRSCEYQHFRDMALSEDKIL-----VEMGSVREGKTPEEK 1195

Query: 428  RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
               V+ +++   +    K +    +   V      Y  R L     +
Sbjct: 1196 EEYVAGLKQTINDMRRDKVK----DFNTVAMEIAGYRRRFLDDPSRV 1238


>gi|134046620|ref|YP_001098105.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C5]
 gi|132664245|gb|ABO35891.1| methyl-accepting chemotaxis sensory transducer [Methanococcus
           maripaludis C5]
          Length = 543

 Score = 39.1 bits (89), Expect = 2.6,   Method: Composition-based stats.
 Identities = 42/355 (11%), Positives = 124/355 (34%), Gaps = 24/355 (6%)

Query: 11  SDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAML 70
           +D + + ++     + +  +  ++IK           +L   +    V  +++ED +   
Sbjct: 213 ADEKRKRNNLQKAINTAIRNVAQLIK-----------DLREEVDLLNVQVQKVEDELKSA 261

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGS 130
                 V +  +   E  S+ S  L  ++       +  K     + ++ VR    E+  
Sbjct: 262 EETATQVTEAANQVAEASSDQSAKLQEASDQLENTYEVAKTVYTDA-EETVR-SAEEISE 319

Query: 131 IELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
               +   ++  A     G   ++  L +S    Q L     ++N+ T L+++I +    
Sbjct: 320 NS-ENGVKKVENAISRMQGITNVIDDLGKS---IQELGEDGKKINEVTDLIKDIAEQTGL 375

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +   +        E         S  +   ++++++  +I            +       
Sbjct: 376 LALNASIEAARAGEAGKGFAVVASEIKALAEEIKKSVENINHTIDGVHKRIGETMDLGLK 435

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
            +++        D+    L  +++ +    +  ++ I +        Q  A N +   K+
Sbjct: 436 GKDEVDKGVIAIDEVNDALLRIKESVNGAAIK-INGIKQ------GAQSAADNTEGALKN 488

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGI 365
           +     + E+       ++ +   ++ ++E++  I++ + H    + R +  + I
Sbjct: 489 AQDIASISEEFTATAEEVTASTEELNSIIEEIRGIAEEVTHVSERVTRKSGQFKI 543


>gi|304383627|ref|ZP_07366086.1| conserved hypothetical protein [Prevotella marshii DSM 16973]
 gi|304335151|gb|EFM01422.1| conserved hypothetical protein [Prevotella marshii DSM 16973]
          Length = 283

 Score = 39.1 bits (89), Expect = 2.7,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 1/96 (1%)

Query: 264 DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK 323
           DS   + A +D     +M  L+EI E +RE+    ++ V   KD + + K + LKE ++ 
Sbjct: 34  DSLQRIIAQKDNEMNDMMATLNEIQEGFREINEA-EHRVAIVKDGEGTNKAQQLKENILF 92

Query: 324 LVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
           +  ++  N+  I+ L +Q    S +    +  +  L
Sbjct: 93  IAQTMKHNRELIEKLRKQARQSSVKGDQLKETIANL 128


>gi|198476492|ref|XP_001357374.2| GA17472 [Drosophila pseudoobscura pseudoobscura]
 gi|198137721|gb|EAL34443.2| GA17472 [Drosophila pseudoobscura pseudoobscura]
          Length = 1601

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 81/536 (15%), Positives = 195/536 (36%), Gaps = 55/536 (10%)

Query: 125  LREMGSIELLS--REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD-ELNDGTTLL 181
            LRE    ELL+  +  E  +  R++  +  +   L ++  +   L+     +L+D    +
Sbjct: 763  LREARMSELLTTLQRTEQQLTARLQEQQQQLNGELAQAKQSAAELMHSLSLQLSDSQCKI 822

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +++ D  A    E++  +                       ++E + +    A +S   R
Sbjct: 823  KQLEDRLAQGIEENESLY---------------------KRLRELQAEGSQVASLSNLQR 861

Query: 242  SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             K+      ++    +  +       +L+   ++LR +   A++EI  + REL+  Q+  
Sbjct: 862  HKMKRMDSLSDLTTISDIDPYCLQRDSLAEEYNELRSRFEKAVNEIRAMKRELKQSQNQ- 920

Query: 302  VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
             +  +  +++++ K+ + +L +    L L  +RI  L  +     +++   + +L +  +
Sbjct: 921  YDALELAQAALQQKLERCQL-EDGAQLQLMAARIQDLTLKYSSSERQVRALKQKLAKSER 979

Query: 362  SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
                 R + L+  +  EL    +                 E  S+  I    +S S E+ 
Sbjct: 980  R----RSLSLKGKEQLELKLSELQRETI------------ERKSVESISPPTESSSSESA 1023

Query: 422  ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
                   H++  +   E     +K+ + ++  +L    A + + R +  ++  ++G   L
Sbjct: 1024 SQSPLNAHLLQRLHSLEHVLLGSKERLEQSLTQLQQIRAGQRSRRSVSPMNDRKDGLRQL 1083

Query: 482  MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
             +A    + C+        +  V+ A  +    +    ++    +     + R+ + +  
Sbjct: 1084 ERAL--AETCVMVS-EQMELTCVQDACHKCCDLRQRVEKLSALQQQTETDLQRSEQLLEQ 1140

Query: 542  KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +     +    A +     E  +++L   +  +S E     E    L   +E    +   
Sbjct: 1141 R----ESDLAQALEKCASQEQEQELLLRQRNELSDELGKQQERCKRLEKRLE---LLERE 1193

Query: 602  DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERI 656
                   LRE        +   +E+  R R+ + +    TL E G      +  RI
Sbjct: 1194 HGKQLECLREVYHN--EHVNAADEQSFRKRYQLEIEQLRTLCEKGLSAMETSHRRI 1247


>gi|219666470|ref|YP_002456905.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense DCB-2]
 gi|219536730|gb|ACL18469.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
          Length = 217

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 35/82 (42%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + A++ ++      V + A+ Y   G    D+IQEG IGL KA   F       F  +A
Sbjct: 32  DAEAQEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRGDKLSSFRAFA 91

Query: 501 MWWVKQAITRSIADQSCTIRIP 522
              + + I  +I   +    IP
Sbjct: 92  ELCITRQIITAIKTATRQKHIP 113


>gi|332639124|ref|ZP_08417987.1| hypothetical protein WcibK1_10560 [Weissella cibaria KACC 11862]
          Length = 4328

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 49/378 (12%), Positives = 133/378 (35%), Gaps = 24/378 (6%)

Query: 45   TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV 104
            T+E++    P +   ++++ D    L+         +  +D    + +L   ++ +  + 
Sbjct: 2425 TLEQIATDNPDNTTIADKLADAKEQLAAAEDAKTTAEAAKDAVADQTTLADVANQTEVAD 2484

Query: 105  FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTF 164
                  D+A ++ D  V+              + + A ++ +   +A    ++       
Sbjct: 2485 EAVTAADTAQKTADQDVK--------------DAQAAASEDLATDQAAAKTAV---NNDI 2527

Query: 165  QALIIWRDELNDGTTLLREIIDLE-ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
              +    D++ D    L +I     A      K          +     D++ +    D 
Sbjct: 2528 ATITDNIDKITDDIATLTDIAAKNPADTEIADKLADAKAQLETAEGALTDATDQLTAIDN 2587

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
              T  ++  A +  +D      +  +N+  D  +     D +      +        +  
Sbjct: 2588 ATTPAEVADAREAGQDAADLSQTTADNSAQDVADAQAKSDQNLADAQKVATDTITDNIAT 2647

Query: 284  L-DEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ- 341
            + D I  +  ++ +LQD A     D   + K    +++L +   + +  +S +D + +Q 
Sbjct: 2648 IADNIQNITDDIATLQDLADKNPGDTTIADKLADAQQQLTEAEAAKTAAESDLDQVADQT 2707

Query: 342  -LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
             L D++  +     ++ +  ++    +    +  Q    +   ++ AKD  +      ++
Sbjct: 2708 TLADVADVVNDAADQVAQAQENENQAQTDVADAQQQSATN---LATAKDDAKEAINQNLS 2764

Query: 401  CEVDSILKIRNEIKSISV 418
               D I +I  +I ++  
Sbjct: 2765 DIDDDITQITADIDALEQ 2782



 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 47/349 (13%), Positives = 113/349 (32%), Gaps = 37/349 (10%)

Query: 14   EHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
            E+E+   + V D    S   +   A+       E +N  L   +    Q+   +  L   
Sbjct: 2728 ENENQAQTDVADAQQQSATNL-ATAKDD---AKEAINQNLSDIDDDITQITADIDALEQ- 2782

Query: 74   GINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIEL 133
             I   +  +    +   D+ +  ++A  +    Q+  D+ D  T          +  +  
Sbjct: 2783 -IATDNPTNTTIADKLADAKEQLAAAETAKDAAQQALDAIDEQTT---------LADVAT 2832

Query: 134  LSREGEIAIA----------KRIEAGRAMMMASLCE--------SPLTFQALIIWRDELN 175
              + GE A+A          + +   +      L             T +++      + 
Sbjct: 2833 QEKAGETALADADTAQQTADQDLATAQDEAAKDLVADQVAGKATVNETIKSIQDAITTIT 2892

Query: 176  DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
            D    L ++ D +     +         E  +  +   +  + +   +   +   +    
Sbjct: 2893 DDIATLTDLAD-KNPADTQIANDLADAKEQLATAETALTDAQDQLAAIDAAKVPADVDQA 2951

Query: 236  VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME---DQLRPKVMCALDEIAEVYR 292
            V+    +   +       ++   D      A+  +A E   D ++  V    D IA++  
Sbjct: 2952 VATAQTAGETATTAQTTANQDVSDAQTKHDANLAAAKETATDTIQTIVDGLADNIAQITD 3011

Query: 293  ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341
            ++ +LQ  A     D   + K    + +L     + +  Q+++D + +Q
Sbjct: 3012 DITTLQGLADKNPGDTVIADKLADAQNQLTDATAAQNDAQNQLDAIADQ 3060


>gi|83591295|ref|YP_431304.1| RNA polymerase factor sigma-70 [Moorella thermoacetica ATCC 39073]
 gi|83574209|gb|ABC20761.1| RNA polymerase, sigma 30 subunit, SigH [Moorella thermoacetica ATCC
           39073]
          Length = 217

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 38/89 (42%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V + +    +A++ ++      V + A+ Y   G    D++QEG IGL KA   F     
Sbjct: 22  VYQAQEGDEVAQEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFRGDKL 81

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  +I   +    IP
Sbjct: 82  SSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|47210509|emb|CAF95238.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1114

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 80/233 (34%), Gaps = 12/233 (5%)

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA----LIIWRDELNDGTTLLREIIDLE 188
           L  +E ++ +A RI         +L E     +     +     +L    ++  E++   
Sbjct: 166 LEEKERDLELAARIGQSLLKKNKALSERNDLLEEQVEHIREEVSQLRHDLSMKDELLQFY 225

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQ-------EKERDDVQETEGDIESAAKVSKDDR 241
                ES+G  F  T          +         +K+  D++E    + S A   + + 
Sbjct: 226 TNAAEESEGESFTSTPVRPADSNVSTPTFFPLDSLQKKLKDLEEENKSLRSEASHLETET 285

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN- 300
              +   +   +D      + +    +LS    +         +EI  +  ++  LQ   
Sbjct: 286 ISYEEKEQQLVHDCVKELRNSNLQITSLSEELARKSDDASRQQEEITHLLSQIVDLQKKV 345

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            ++  ++E+ +      K+   +L   L   + +    +E L++  + + +  
Sbjct: 346 KLHALENEELTQHLGAAKDAQRQLTAELRELEDKYAECMEMLHEAQEELKNLR 398


>gi|317970593|ref|ZP_07971983.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 68

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/68 (29%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSR 672
              +L  L   + RVL+MR+GI +    +L  + +   ++R+R R +E KA  +L+   R
Sbjct: 1   MRGLLDQLPDLQGRVLKMRYGIDVEEPMSLSSIARALEMSRDRARSLERKAHEELRR--R 58

Query: 673 SKKLRSFL 680
           S+++ ++L
Sbjct: 59  SEEMHAYL 66


>gi|238927910|ref|ZP_04659670.1| DNA-directed RNA polymerase sigma subunit SigH [Selenomonas
           flueggei ATCC 43531]
 gi|238884243|gb|EEQ47881.1| DNA-directed RNA polymerase sigma subunit SigH [Selenomonas
           flueggei ATCC 43531]
          Length = 266

 Score = 39.1 bits (89), Expect = 2.8,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 35/90 (38%)

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
           + R   C+   A   ++      V S A+ Y   G    D++QEG IG  KA   +    
Sbjct: 53  LNRIRGCDGDEALDYLINKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRDYRPDK 112

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              F  +A   V + I  +I   +    IP
Sbjct: 113 LSSFRAFAELCVTRQIITAIKTATRQKHIP 142


>gi|148686692|gb|EDL18639.1| Cdc42 binding protein kinase beta, isoform CRA_b [Mus musculus]
 gi|187953787|gb|AAI38036.1| CDC42 binding protein kinase beta [Mus musculus]
 gi|223460994|gb|AAI38038.1| CDC42 binding protein kinase beta [Mus musculus]
          Length = 1713

 Score = 39.1 bits (89), Expect = 2.9,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 96/304 (31%), Gaps = 33/304 (10%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMTQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP------KVMCALDEIAEVY 291
                 ++     A  ++  L +   +++  L +   +L+       + +    E+ E  
Sbjct: 525 THRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKDAHQQRKRALQEFSELNERM 584

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ELRSL+       +D++  ++  + K                ID + + L    K    
Sbjct: 585 AELRSLKQKVSRQLRDKEEEMEVAMQK----------------IDSMRQDLRKSEKSRKE 628

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E  L   A     +R +        +     +   K    G      +     I KIR+
Sbjct: 629 LEARLEDAAAEASKERKLREHSESFCKQMERELEALKVKQGGRGPGAASEHQQEISKIRS 688

Query: 412 EIKS 415
           E++ 
Sbjct: 689 ELEK 692


>gi|317123113|ref|YP_004103116.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter marianensis
           DSM 12885]
 gi|315593093|gb|ADU52389.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter marianensis
           DSM 12885]
          Length = 224

 Score = 39.1 bits (89), Expect = 2.9,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 3/101 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   IV + R+G  E   A + ++      V + A+ Y   G    D+IQEG IGL
Sbjct: 15  LDRMEDEEIVEIARQGNAE---ALEYLIGKYKNFVRAKARSYFLVGADREDIIQEGMIGL 71

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            KA   F       F  +A   + + I  +I   +    IP
Sbjct: 72  YKAIRDFRSDKLSSFRAFAELCITRQIITAIKTATRQKHIP 112


>gi|166031080|ref|ZP_02233909.1| hypothetical protein DORFOR_00762 [Dorea formicigenerans ATCC
           27755]
 gi|166028927|gb|EDR47684.1| hypothetical protein DORFOR_00762 [Dorea formicigenerans ATCC
           27755]
          Length = 202

 Score = 39.1 bits (89), Expect = 2.9,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 37/91 (40%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +++K     +     ++E    LV   A      G +  DLIQEG IGL KA + ++  
Sbjct: 11  QLIQKLRDGDNRIVDYIMEKYKNLVRKEANAMYLLGGENEDLIQEGMIGLFKAVQNYEPD 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F ++A   + + +  +I         P
Sbjct: 71  QNSSFFSFAKLCISRQLYSAIEASRRKKHSP 101


>gi|57640573|ref|YP_183051.1| methyl-accepting chemotaxis protein [Thermococcus kodakarensis
           KOD1]
 gi|57158897|dbj|BAD84827.1| methyl-accepting chemotaxis protein [Thermococcus kodakarensis
           KOD1]
          Length = 747

 Score = 39.1 bits (89), Expect = 2.9,   Method: Composition-based stats.
 Identities = 41/283 (14%), Positives = 100/283 (35%), Gaps = 11/283 (3%)

Query: 65  DTVAMLSNMGINV--VDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
           D    ++ +   V  V  +    +E   +  +     ++ S    +  +  + + ++ V 
Sbjct: 464 DVTEAINQVNEAVQQVSIEAQRQQENINEITEGMRLVADMSEESVRAMEEFEGAVNEVVH 523

Query: 123 MY--LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           +    R+ G +       +I   + +       +  + E   + + +      + + T L
Sbjct: 524 IADEGRQKGEVS----AQQIQSIQEMMGNIEAAVNRVNEMSRSIEEITNVITGIAEQTNL 579

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           L     +EA    E+  GF    +       E    +K  D+++E  G +    K + + 
Sbjct: 580 LALNAAIEAARAGEAGRGFAVVAQEIRNLAEE---SKKAADNIKEIIGRMTDEIKDAVNA 636

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
             +  S    +    R   E   + A  +S    +L       L    EV + L++L++ 
Sbjct: 637 TQRGVSVVSESSETLRETTEYLTNIAELISDTGARLGHVKEQILRTQEEVDKALKALENL 696

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLY 343
           A + ++   S+ +     E+    +  L      +  +V++L 
Sbjct: 697 AASAEETTASAEEVSSAVEEQTAAIEELKRAADELKKIVDELR 739


>gi|323490597|ref|ZP_08095802.1| RNA polymerase factor sigma-70 [Planococcus donghaensis MPA1U2]
 gi|323395689|gb|EGA88530.1| RNA polymerase factor sigma-70 [Planococcus donghaensis MPA1U2]
          Length = 216

 Score = 39.1 bits (89), Expect = 2.9,   Method: Composition-based stats.
 Identities = 25/108 (23%), Positives = 39/108 (36%), Gaps = 6/108 (5%)

Query: 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLI 474
            +   T ++  E   +V          + A   ++      V   A+ Y   G    D+I
Sbjct: 8   QLQRFTDMTDEELVSLV------HSGNTEALDFLITKFRPFVRMKARSYFLIGADKEDII 61

Query: 475 QEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           QEG IGL KA   F       F  +A   + + I  +I   +    IP
Sbjct: 62  QEGMIGLYKAIRDFKSDKLSSFRAFAELCIIRQIITAIKTATRQKHIP 109


>gi|256394643|ref|YP_003116207.1| hypothetical protein Caci_5507 [Catenulispora acidiphila DSM 44928]
 gi|256360869|gb|ACU74366.1| conserved hypothetical protein [Catenulispora acidiphila DSM 44928]
          Length = 1160

 Score = 39.1 bits (89), Expect = 3.0,   Method: Composition-based stats.
 Identities = 55/340 (16%), Positives = 111/340 (32%), Gaps = 18/340 (5%)

Query: 85  DEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG----EI 140
           D +   +   L  +   +   L + +   + + +D  R  L E G  EL +        +
Sbjct: 582 DAQRMAERSQLEEAVEKTEHLLSEVQKEHEVAVED--RQAL-ETGWNELWTPSDLPAPAV 638

Query: 141 AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
             A  + A   ++   + E       L   R   N   T LRE +       P       
Sbjct: 639 EAATDLLAALQILREQIDERDALLLTLDSDRAAANAHATRLREALADAGFAVPPESASLD 698

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E  S      +   K+R  +     ++ +    ++ + +++++   + +   + L  
Sbjct: 699 ELIEAASAFHATLAETAKKRSRITAAAENLRNELTDAQSEVTRLETELADWDEKWKRLLA 758

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D +    T + +   L       LDEIA ++ +    Q+ A     D + S     L + 
Sbjct: 759 D-NQLTGTPAQVAASLSE-----LDEIARLHADALRFQEQADEA--DIQVSAFTSRLDQA 810

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR-EL 379
           L            R   +V  L D   R   ++ ++ RL       R         R E 
Sbjct: 811 LADAGQPPLTTPDRRYAVVRSLKDYLDRQSASQDQITRLTDRLATLRGKLESARNNRAEA 870

Query: 380 DPHWVSYAKDFPEGEWKNFVA--CEVDSILKIRNEIKSIS 417
           D +  +   +         V      D+I  +  ++K++ 
Sbjct: 871 DQNVAAVLAEDSMHHEHELVEAIERTDAIRDLDKQLKAVE 910


>gi|297623754|ref|YP_003705188.1| integrase family protein [Truepera radiovictrix DSM 17093]
 gi|297164934|gb|ADI14645.1| integrase family protein [Truepera radiovictrix DSM 17093]
          Length = 450

 Score = 39.1 bits (89), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
            PR   VL    G+G   + TL ++  +  V+RER+R++  +A+  L
Sbjct: 51  PPRHGDVLARLLGLGGAKEATLAQLSLELGVSRERVRKMAQQALGAL 97


>gi|228937922|ref|ZP_04100549.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970803|ref|ZP_04131443.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977378|ref|ZP_04137773.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228782355|gb|EEM30538.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228788928|gb|EEM36867.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228821713|gb|EEM67714.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|326938402|gb|AEA14298.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 215

 Score = 39.1 bits (89), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/148 (14%), Positives = 51/148 (34%), Gaps = 20/148 (13%)

Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
            T   + E +  + +    +   SIA+   +                  ++  DLIQ G 
Sbjct: 1   MTPEKLFEEKEYLVIAAIKQRFGSIARARQIAEMNN-------------MELDDLIQVGR 47

Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM-RDKIHKVVRTAR 537
           + L +   K D      F  Y M  +K A++  +  +    ++   +  ++ +++     
Sbjct: 48  MHLWRCCMKCDAERIDTFHAYVMKGMKWAMSDELHMKGMPFKVSRKVSHEERNQIN---- 103

Query: 538 RMSNKIKREPTPEEIAKKLAMPVEGVRK 565
              + I      E + +  A+    V +
Sbjct: 104 --IHSIDWHRDEESVNEYYAVSPIDVEE 129


>gi|15790508|ref|NP_280332.1| Htr8 [Halobacterium sp. NRC-1]
 gi|169236245|ref|YP_001689445.1| transducer protein htrVIII [Halobacterium salinarum R1]
 gi|10581010|gb|AAG19812.1| Htr8 transducer [Halobacterium sp. NRC-1]
 gi|167727311|emb|CAP14097.1| transducer protein htrVIII [Halobacterium salinarum R1]
          Length = 643

 Score = 39.1 bits (89), Expect = 3.0,   Method: Composition-based stats.
 Identities = 37/284 (13%), Positives = 93/284 (32%), Gaps = 28/284 (9%)

Query: 45  TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSV 104
           TI E+ A       +SE  +  V  + +    V   + +++     D         +  +
Sbjct: 324 TIREIQAVASDVAAASEDADAGVVEIEDASGQV--SETVQEIAAGADEQREKLETVSGEM 381

Query: 105 FLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESP--- 161
                      ++ D V               E     A     G      ++ +S    
Sbjct: 382 TDLSAAIEEVAASADSV--------------AERSHETAAVAGDGEQTAEQAIADSRTVQ 427

Query: 162 LTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
              ++ +   + L+D    + EI+DL + +  ++     +     +   +         D
Sbjct: 428 SAVESTVQNVEALDDQLAEISEIVDLISDVAEQTNMLALNANIEAARADKSGDGFAVVAD 487

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           +V++   +  ++A   +   + +D+  +    + R  DE   D+   + A        V+
Sbjct: 488 EVKDLAEETRASAGDIEALVADIDAQMQATVTEARTADESVQDAISAVDA--------VV 539

Query: 282 CALDEIAEVYRELRS-LQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
            A   +AE   E  + +Q+ +        S+ +   +  ++  +
Sbjct: 540 DAFGTVAENAEETDTGVQEISTTTDDQAASTEEAVSMIAEVSDI 583


>gi|89893197|ref|YP_516684.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense Y51]
 gi|89332645|dbj|BAE82240.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 208

 Score = 38.7 bits (88), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 35/82 (42%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
            + A++ ++      V + A+ Y   G    D+IQEG IGL KA   F       F  +A
Sbjct: 23  DAEAQEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRGDKLSSFRAFA 82

Query: 501 MWWVKQAITRSIADQSCTIRIP 522
              + + I  +I   +    IP
Sbjct: 83  ELCITRQIITAIKTATRQKHIP 104


>gi|328910060|gb|AEB61656.1| RNA polymerase sigma-30 factor (sigma(H)) [Bacillus
           amyloliquefaciens LL3]
          Length = 201

 Score = 38.7 bits (88), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++ K     S A   ++      V + A+ Y   G    D++QEG IGL K+   F   
Sbjct: 5   QVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRED 64

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 65  KLTSFKAFAELCITRQIITAIKTATRQKHIP 95


>gi|188588004|ref|YP_001919656.1| RNA polymerase factor sigma-70 [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251778497|ref|ZP_04821417.1| RNA polymerase sigma-H factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498285|gb|ACD51421.1| RNA polymerase sigma-H factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082812|gb|EES48702.1| RNA polymerase sigma-H factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 206

 Score = 38.7 bits (88), Expect = 3.0,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 57/180 (31%), Gaps = 4/180 (2%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + A++ M+      V + AK Y   G    D+ QEG IGL KA   F       F  +A 
Sbjct: 24  TRAQEYMISKYENFVKAKAKSYFLIGADREDIYQEGMIGLYKAIRDFKADKLTSFKAFAE 83

Query: 502 WW----VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
                 +  AI  +   +   +   V +   I++       +      + +  E      
Sbjct: 84  LCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLDVLSGIKISDPEELLINK 143

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             ++ +   +      + LE      D     +   D +  S         ++    + L
Sbjct: 144 EHMDDIEAAIAKVLSDLELEVLTSYLDGKSYQEIACDLDRHSKSIDNALQRVKRKLEKCL 203


>gi|187933087|ref|YP_001884458.1| RNA polymerase factor sigma-70 [Clostridium botulinum B str. Eklund
           17B]
 gi|187721240|gb|ACD22461.1| RNA polymerase sigma-H factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 206

 Score = 38.7 bits (88), Expect = 3.0,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 58/180 (32%), Gaps = 4/180 (2%)

Query: 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501
           + A++ M+      V + AK Y   G    D+ QEG IGL KA   F       F  +A 
Sbjct: 24  TRAQEYMISKYENFVKAKAKSYFLIGADREDIYQEGMIGLYKAIRDFKADKLTSFKAFAE 83

Query: 502 WW----VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLA 557
                 +  AI  +   +   +   V +   I++       +      + +  E      
Sbjct: 84  LCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLDVLSGIKISDPEELLINK 143

Query: 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL 617
             ++ +   +      + LE  +   D     +   D +  S         ++    + L
Sbjct: 144 EHMDNIEAAIAKVLSDLELEVLMSYLDGKSYQEIACDLDRHSKSIDNALQRVKRKLEKCL 203


>gi|198431877|ref|XP_002125176.1| PREDICTED: similar to viral A-type inclusion protein, putative [Ciona
            intestinalis]
          Length = 3939

 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 34/288 (11%), Positives = 102/288 (35%), Gaps = 16/288 (5%)

Query: 144  KRIEAGRAMMMASLCESPLTFQAL-----------IIWRDELNDGTTLLREIIDLEACIG 192
            + +E  +  + + L ++    + L           +   ++  +   LL++ I+ +  + 
Sbjct: 746  RDLENAKEDVQSKLEDTETVIEELTKKMQKIQLENLEMLEKDKEEMELLKQEINEKNMML 805

Query: 193  PESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAE 252
             +++      +     ++ E S      +D Q    +   ++  ++D   +        +
Sbjct: 806  KDAEERLQDPSLKLDEEECEKSELTAALEDEQRRADEASLSSSSTQDKLLQYREQAGRYK 865

Query: 253  NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD--EKS 310
             +   L    D+  +  +   ++L  ++    +EI E  RE R   +  +  QKD  E+S
Sbjct: 866  QENHELKLKLDELENEKNVEIEELGMQIKRLTNEINEQKREQRESNEERIKEQKDEWERS 925

Query: 311  SVKCKVLKEKLVKLVGSLSLNQSRID---LLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +   K     L + +  L  N+  ++    L E++++ ++ +     +L         + 
Sbjct: 926  TEHYKTRITTLEEEIMILKDNERYLNNEIELKEKVHEENQSLRSKIVKLEDEVMKLKNRV 985

Query: 368  DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
                +     +     +S   +         +        +++ E++ 
Sbjct: 986  QDLEDHLTENDGSLDEISRRLEEQIRSKDRLLEQWEIRYEQLKTEMED 1033


>gi|306819821|ref|ZP_07453476.1| possible chromosome segregation protein Smc [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304552190|gb|EFM40126.1| possible chromosome segregation protein Smc [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 1177

 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 50/340 (14%), Positives = 130/340 (38%), Gaps = 24/340 (7%)

Query: 23  VFDFSDDSWKKM-IKLARQRGYVTIE------ELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           +++  ++  K + I+  + + Y+  +      E+N  L    +S+E+ E+ +A LS    
Sbjct: 194 IYNEIENQIKPLKIQKEKAQKYLEYKKELQSQEINKIL----LSNEEYENELANLSKDRE 249

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
            +++ D    E+  E S +LA     S    +K+++  ++ +    ++   +M  + L  
Sbjct: 250 RLLEEDVRTREDFQEISDNLAKLKEESEYIQRKKEELYEKKSSLSDKISQNKM-QVSL-- 306

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
           +   +   K +E    ++   L ++      + I  + +N+    + + I        E 
Sbjct: 307 KHENV---KSLEKNNDLIQEQLLQNKDEIAKIRIKIENINESKQKISDNISYIQKEISEK 363

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +       +    Q RE  ++E++  DV+     +    +  +++ S         E   
Sbjct: 364 EEKEQIYKDKIQVQNREVQAKEQKIKDVESEISKLTMRMEFVQNNISAF-------EEKI 416

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK 315
              DE   + +  +  +ED++  K    L +  E+ +    LQ N+   Q  ++ + +  
Sbjct: 417 GQYDEKNQEYSAKIKELEDEIGKKESQLLQKTDEISKLKEKLQYNSEQRQNLDEENSRIA 476

Query: 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
               +    +  ++     ++     +   SK +      
Sbjct: 477 KEINQTSLNLKDITAKTEMLENFENDMQGFSKNVKVLLKN 516


>gi|6688931|emb|CAB65343.1| liver stage antigen-3 [Plasmodium falciparum]
          Length = 1786

 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 1124 ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 1179

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 1180 IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 1235

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 1236 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1292

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1293 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1351

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1352 ETDILEEKKEI 1362


>gi|148262650|ref|YP_001229356.1| hypothetical protein Gura_0571 [Geobacter uraniireducens Rf4]
 gi|146396150|gb|ABQ24783.1| protein of unknown function DUF195 [Geobacter uraniireducens Rf4]
          Length = 503

 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 71/195 (36%), Gaps = 4/195 (2%)

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
           RDEL   T  L E +  +     E K     G E  S  + E  ++ ++R   +E    I
Sbjct: 32  RDELEAETATLTERLQGKDLQIGELKAQLAKGAEEISDLRCELKAEAEKRSAAEEKNSRI 91

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEV 290
                  K    ++    E     +  L            A E++L   +  A  ++++ 
Sbjct: 92  PELEMRLKTREEQMRQVFEENSALKAKLSSLATQLHEERKATEEKL-AILDAAHVKLSDA 150

Query: 291 YRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIM 350
           ++ L +    + N    + + V  +  +E      G L L Q  ID LV  + +  +++ 
Sbjct: 151 FKALSAEALKSNNQSFLDLAKVALEKFQE---GARGDLELRQKAIDELVRPMRESLEKVD 207

Query: 351 HNEGELLRLAQSYGI 365
               EL +   S  +
Sbjct: 208 TKIQELEKTRVSAYV 222


>gi|159126497|gb|EDP51613.1| myosin type II heavy chain, putative [Aspergillus fumigatus A1163]
          Length = 2405

 Score = 38.7 bits (88), Expect = 3.1,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 84/229 (36%), Gaps = 14/229 (6%)

Query: 132  ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI---IDLE 188
             LL   GE   A  ++     +     +            +E       +++I   ++ E
Sbjct: 923  PLL---GETRTANEVKKRDEKIKELEAKIKQDIAERQKLDEERRRTEIEIQKIQHTLESE 979

Query: 189  ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              +  + +  F            + +    +++ +++    + +A K + +  S+  +  
Sbjct: 980  RALALDKEEIFKRLQLREIELTEKLAGAIADQESLEDQLDTLIAAKKKADEQLSQRITQL 1039

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQL---RPKVMCALDEIAEVYRELRSLQ-----DN 300
            E A      L+ ++ D    L  ++ QL   R  V      + E+ +E++ LQ      +
Sbjct: 1040 EQAGEIIERLEAEKRDLQSRLDVLDRQLEEARSSVAEQEARVKELGQEIKMLQSHLSLKD 1099

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
                  + K     + L  KL +    L L++ +I  LVE+   I ++I
Sbjct: 1100 RKIQDLEAKLLKTDQDLDIKLARTSKDLELSKKQIKDLVEENRSIRQQI 1148


>gi|326678010|ref|XP_003200959.1| PREDICTED: myosin heavy chain, fast skeletal muscle-like [Danio
            rerio]
          Length = 1410

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 41/287 (14%), Positives = 111/287 (38%), Gaps = 13/287 (4%)

Query: 132  ELL-SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
             LL S E E  +A   E     M   L ++    + L      L      L+  +  E+ 
Sbjct: 841  PLLKSAETEKEMAAMKENFEK-MKEDLTKALAKKKELEEKMVSLLQEKNDLQLQVASESE 899

Query: 191  IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
               +++       +     + +     +  +D +E   ++ +  +  +D+ S++    ++
Sbjct: 900  NLSDAEERCEGLIKSKIQLEAKLKETTERLEDEEEINAELTAKKRKLEDECSELKKDIDD 959

Query: 251  AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             E     +++++  + + +  + +++  +     + IA++ +E ++LQ+       D   
Sbjct: 960  LELTLAKVEKEKHATENKVKNLTEEMASQD----ESIAKLTKEKKALQEAHQQTLDD--- 1012

Query: 311  SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                +  ++K+  L  S S  + ++D L   L    K  M  E    +L     + ++  
Sbjct: 1013 ---LQAEEDKVNTLTKSKSKLEQQVDDLEGSLEQEKKLRMDLERAKRKLEGDLKLAQESI 1069

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            ++    ++     +   KDF   +  + +  E     +++ +IK + 
Sbjct: 1070 MDLENDKQQSEEKIKK-KDFEISQLLSKIEDEQSLGAQLQKKIKELQ 1115


>gi|145528985|ref|XP_001450281.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124417892|emb|CAK82884.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1307

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 43/328 (13%), Positives = 116/328 (35%), Gaps = 30/328 (9%)

Query: 127  EMGSIELLSREGEIAIAKRIEAGRAM--MMASLCESPLTFQALIIWRDELNDGTTLL--- 181
            E+  ++L++R         IE        + SLC    T Q +   +++L +    L   
Sbjct: 726  EITQLDLITRGD-------IENKITNTFALNSLCLCSTTAQEI--RQEQLKELEYRLQNF 776

Query: 182  -REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
              +I D +      +        + H  +       +K +D + +T    ++     K+D
Sbjct: 777  KSDIDDAKEVQLNNNDYKLKKIRDEHVKEV------QKVQDQLSQTIQQSDAKNNKIKED 830

Query: 241  RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDN 300
            +  +      ++     ++E       ++  + D+L  K+   + +  E  R +      
Sbjct: 831  KKNL---IATSKKTIEEMNEQNSKKLLSIYDIRDKLNEKLQNIIKQQDEERRLVNQEYQQ 887

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA 360
            +++   DE    K + L  +  + + ++ L+Q +   +++Q     +       + L+  
Sbjct: 888  SISQVDDEYCQ-KYQDLFNRFSQAMSNMKLDQRKFKEVLQQSEKDYETFYKESQQSLKAK 946

Query: 361  QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDS-ILKIRNEIKSISVE 419
                  +   L       +        +     E  + +  E D  +  +R E+K    +
Sbjct: 947  LEEFNTQTEILRS----SISRFKKEIVRYQNRKEILHNLKKETDESLQSLRQELKGYEEK 1002

Query: 420  TGISISEFRHIVSMVRKGECEASIAKKE 447
              + +++ R    ++ + E +    + +
Sbjct: 1003 HKMMLADLREKEKLINQREQQIKDFRMK 1030


>gi|331084310|ref|ZP_08333415.1| hypothetical protein HMPREF0992_02339 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330401845|gb|EGG81422.1| hypothetical protein HMPREF0992_02339 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 247

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 62/139 (44%), Gaps = 2/139 (1%)

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           R          ++++ A    ++  AKK     + F DL+QEGN+GL+ A E+       
Sbjct: 110 RAFLAGNQECTEKLIRAYQDEIVKAAKKLNREDIFFGDLLQEGNMGLLTALERLSEQENP 169

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
                 +  ++  +   I +Q+   +    + +K+  + +  + ++     + + EE+A 
Sbjct: 170 DEW--IVREIESTMKLFIEEQAQQKKEDNILVEKVRDLEKKVKELTEDEDVKYSVEELAA 227

Query: 555 KLAMPVEGVRKVLKITKEP 573
            L M +E +  VL++T + 
Sbjct: 228 FLDMDLEEMESVLRLTGDD 246


>gi|323344763|ref|ZP_08084987.1| hypothetical protein HMPREF0663_11523 [Prevotella oralis ATCC
           33269]
 gi|323094033|gb|EFZ36610.1| hypothetical protein HMPREF0663_11523 [Prevotella oralis ATCC
           33269]
          Length = 284

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 24/102 (23%), Positives = 51/102 (50%), Gaps = 1/102 (0%)

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           +++DS   + A +D     ++  L+EI E +RE+    +N V   KD + + K + +KE 
Sbjct: 32  EQNDSLQKIIAQKDSEINDMLGTLNEIQEGFREINEA-ENRVTIAKDGEGTNKTQQIKEN 90

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
           +  +  ++  N+  +D L +QL + S +    +  +  L + 
Sbjct: 91  IQFISTAMKRNRQLVDKLRQQLRESSVKGGQFKTTIDNLMKQ 132


>gi|289065417|gb|ADC80890.1| RNA polymerase sigma factor [Pseudomonas sp. PD2766]
          Length = 122

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 20/123 (16%), Positives = 43/123 (34%), Gaps = 3/123 (2%)

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
                    ++V  P +         DE+E+ +  T    E +  P  + A      V  
Sbjct: 3   DPDDGIAPPAEVPPPVDPKAAKAEGDDEEEETADATDDEEEVESGPDPVIAQQRFGAVSD 62

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
           ++   +       + +K ++   V    L +L   + L   + + LVE++    +R+   
Sbjct: 63  QMEITRKALKKFGRSDKHAIAELV---ALAELFMPIKLVPKQFEGLVERVRGALERLRAQ 119

Query: 353 EGE 355
           E  
Sbjct: 120 ERA 122


>gi|126306936|ref|XP_001368382.1| PREDICTED: similar to pan-epithelial glycoprotein isoform 1
           [Monodelphis domestica]
          Length = 1718

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 60/404 (14%), Positives = 127/404 (31%), Gaps = 33/404 (8%)

Query: 17  DSDDSLVFDFSDDSWKKM---IKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM---L 70
            + D  +    D   K +   I+  R++  VT    +  L        Q+E+  +M   L
Sbjct: 475 STVDGPLTANKDLEIKNLKEEIEKLRKQ--VT---DSDHLEQ------QLEEASSMRREL 523

Query: 71  SNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY-LREMG 129
            +    +   +        E          +S     + K+  D  +   + M    EM 
Sbjct: 524 DDASRQIKASEKQIKLLKQEREDLNKELVESSERLKSQTKELKDAHSQRKLAMQEFSEM- 582

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
                  E    +  + +     +     E  L  Q +   R EL       +E+     
Sbjct: 583 ------NERLTDLHSQKQKLARQVRDKEEEMELVMQKVESLRQELRKTERAKKELEVHVE 636

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            +  E+            Y K+ ++  E  +         I S     +  + K D   +
Sbjct: 637 SVTAEASKDRKLRERSEQYSKQLENELEGLKQKQIGRSPGISSIEHQQEITKLKADLEKK 696

Query: 250 NA--ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
           +   E +    +    +    L         + +    EI  +  +L   +  + N +++
Sbjct: 697 SIFYEEELSKRNVIHTNEIKNLKKELRDAEGQQLALKKEIMILKDKLEKTRRESQNEREE 756

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            +S  K K  +EK++    +  L+        ++L  + +R+  N  +L    +    K+
Sbjct: 757 FESEFKQKYEREKILLTEENKKLSNEL-----DKLTAMFERLSINNRQLEEEMRDLADKK 811

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
           +              WVS  KD   G  +   +   + +  +RN
Sbjct: 812 ESVAHWEAQITEIIQWVSDEKD-ARGYLQALASKMTEELEALRN 854



 Score = 38.7 bits (88), Expect = 3.9,   Method: Composition-based stats.
 Identities = 38/212 (17%), Positives = 87/212 (41%), Gaps = 16/212 (7%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           + +    A E ++R      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 EDSLATEAYERRIRRLEQEKLELSRKLQESTQTVQALQYSTVDGPLTANKDLEIKNLKEE 495

Query: 321 LVKLVGSL----SLNQSRIDL--LVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
           + KL   +     L Q   +   +  +L D S++I  +E ++  L Q         +E  
Sbjct: 496 IEKLRKQVTDSDHLEQQLEEASSMRRELDDASRQIKASEKQIKLLKQEREDLNKELVESS 555

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM- 433
           +  +     +  A    +   + F     + +  + ++ + ++ +      E   +V   
Sbjct: 556 ERLKSQTKELKDAHSQRKLAMQEFSEMN-ERLTDLHSQKQKLARQV-RDKEEEMELVMQK 613

Query: 434 ---VRKGECEASIAKKEMVEANLRLVISVAKK 462
              +R+   +   AKKE+ E ++  V + A K
Sbjct: 614 VESLRQELRKTERAKKEL-EVHVESVTAEASK 644


>gi|313625371|gb|EFR95162.1| RNA polymerase sigma-H factor [Listeria innocua FSL J1-023]
          Length = 139

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EEMAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DESKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|311257710|ref|XP_003127243.1| PREDICTED: pleckstrin homology-like domain family B member 2-like
           [Sus scrofa]
          Length = 649

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 42/298 (14%), Positives = 97/298 (32%), Gaps = 26/298 (8%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD------PVRMYLREMGSIE 132
           D  D E  E + +      +   +    +  + S+  S+ D      PV+     +G+  
Sbjct: 37  DSGDQEGPEATVELPSGQGAEQQTEEEEEVGEGSSTESSRDAAEAPPPVQT----LGTPP 92

Query: 133 LLSREGE--IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
             +  GE    +A+R+ A +   +  +       + L   R EL          I++E  
Sbjct: 93  APTPSGEGVRGVARRLRAQQLEALTRVALMEQRVKELQRQRKELR---------IEMEVE 143

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +                 +++      ++ D  Q  +   E   +   ++R  V+   + 
Sbjct: 144 VALLRGELAGERVAARREEEQLRELLGQQVDAEQGGQEQREQEQRQLSEERDHVEELRQR 203

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +  LD   +D    L     +++ ++  A     ++  +    +       KD   
Sbjct: 204 LREAQGQLDSQPEDQRERLLQGVQEMKEQLDVAQRAYEDLEFQQLERESRREEEDKDSPG 263

Query: 311 SVKCKVLKEKLVKLVGSLSLNQ-----SRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           +       ++L   V    +        RI +L EQL  + +++      L +  +  
Sbjct: 264 TRALDPKVQELQGSVAQHKVRPGGAPQRRIQVLEEQLKSLGEQMAAESRGLSQKKEEA 321


>gi|297618401|ref|YP_003703560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297146238|gb|ADI02995.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 217

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 6/101 (5%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +S  E   +            +A + +V+     V + A+ Y   G    D+IQEG IGL
Sbjct: 16  LSDEEIVELAQ------EGEQLATEYLVDKYKNFVRAKARSYFLIGADKEDIIQEGMIGL 69

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            KA   +       F  +A   + + I  +I   +    IP
Sbjct: 70  FKAIRDYKGDKLTSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|254974765|ref|ZP_05271237.1| sporulation sigma factor SigK [Clostridium difficile QCD-66c26]
 gi|255092154|ref|ZP_05321632.1| sporulation sigma factor SigK [Clostridium difficile CIP 107932]
 gi|255306134|ref|ZP_05350306.1| sporulation sigma factor SigK [Clostridium difficile ATCC 43255]
 gi|255313891|ref|ZP_05355474.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
 gi|255516572|ref|ZP_05384248.1| sporulation sigma factor SigK [Clostridium difficile QCD-97b34]
 gi|255649672|ref|ZP_05396574.1| sporulation sigma factor SigK [Clostridium difficile QCD-37x79]
 gi|255655236|ref|ZP_05400645.1| sporulation sigma factor SigK [Clostridium difficile QCD-23m63]
 gi|296451220|ref|ZP_06892961.1| RNA polymerase sigma-K factor [Clostridium difficile NAP08]
 gi|296880427|ref|ZP_06904390.1| RNA polymerase sigma-K factor [Clostridium difficile NAP07]
 gi|306519787|ref|ZP_07406134.1| sporulation sigma factor SigK [Clostridium difficile QCD-32g58]
 gi|296260041|gb|EFH06895.1| RNA polymerase sigma-K factor [Clostridium difficile NAP08]
 gi|296428668|gb|EFH14552.1| RNA polymerase sigma-K factor [Clostridium difficile NAP07]
          Length = 94

 Score = 38.7 bits (88), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/80 (17%), Positives = 37/80 (46%)

Query: 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641
             +   L D +  +      +  ++  + +   ++   LTPRE  ++++R+G+      T
Sbjct: 1   MCNEISLLDILGTEANYVLDEVELKVQVGKLYEQLNKILTPREREIVQLRYGLTPYGYKT 60

Query: 642 LEEVGKQFCVTRERIRQIEA 661
             E+ ++  ++R  + +IE 
Sbjct: 61  QREIAQKLDISRSYVSRIEK 80


>gi|292622124|ref|XP_691467.4| PREDICTED: myosin-10-like [Danio rerio]
          Length = 2015

 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 47/314 (14%), Positives = 103/314 (32%), Gaps = 6/314 (1%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + E      +E  +      L E       L   RD     +          +    E+ 
Sbjct: 1461 QRERQNCTALEKRQKKFDQCLAEEKAVSARLQEERDRAEAESREKETRFLSLSRALQEAT 1520

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + E       +DDV +   ++E + +  + +   +    +  E++  
Sbjct: 1521 EQRDELERTNKQLRLEMEQLVNAQDDVGKNVHELERSRRALETEAQSLKEQTQELEDELG 1580

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-SVKCK 315
              +        TL A+  Q   ++    ++  E  R L           ++EK+   +  
Sbjct: 1581 EAENARLRLEVTLQALRAQFEREISTKEEKGEEKRRALNKQVRELETMLEEEKTQRAQAL 1640

Query: 316  VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQ 375
             +K++L   +          +   E+ +   KR+     EL+R      + RD  + + +
Sbjct: 1641 TVKKQLETELQEAEAQVEAANRGREEAFRQMKRLQTQMKELIRELDETKLARDEIVAQSK 1700

Query: 376  GRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS--ISVETGIS--ISEFRHIV 431
              E     +  A+     E  +    +     + R+E+    I+  TG S    E R + 
Sbjct: 1701 DSEKRLQTLE-AELLQLTEDLSVSERQKRQAQQERDEMADEIINNATGKSALFDEKRRLE 1759

Query: 432  SMVRKGECEASIAK 445
            + + + E E   A+
Sbjct: 1760 TRITQMEEELEEAQ 1773


>gi|226287265|gb|EEH42778.1| cell polarity protein [Paracoccidioides brasiliensis Pb18]
          Length = 1103

 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 51/322 (15%), Positives = 96/322 (29%), Gaps = 41/322 (12%)

Query: 187 LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRS---- 242
           +E  +    +GG   G   + +   +     +  DD  +   D  +  KV +  +     
Sbjct: 370 VEEDVEGSDEGGEDDGEIDYVHDGVDGVDGMQYEDDDPDRRSDAFALDKVLESRKETTMT 429

Query: 243 ----------KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA--------- 283
                      V    E  +                +  +E QL+ KV  A         
Sbjct: 430 LVGNGNGAGLGVGVDSEREKEMLAEARGQVSKLEKRVDELEAQLKEKVGEADRLRAEVRG 489

Query: 284 ----LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
               LD   + +  +R   D         KS ++ K+L+ + ++      LN S  D L 
Sbjct: 490 NSDSLDSERQQWESMRKDWDRKREEWDKMKSHLEAKLLELQNLQ-----HLNVSLQDQLE 544

Query: 340 EQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFV 399
            +  +   R      ++ +   +    R+  LE   GRE+D        D   G WK+  
Sbjct: 545 GERREYENREQDLRQQIQQALTAAAAARNTDLE--MGREIDRG-RGRETDIDSGVWKSRA 601

Query: 400 ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR------KGECEASIAKKEMVEANL 453
                   +++ E++     T     E  + +  +R      +   E      +      
Sbjct: 602 EDSERENQELKEELQKQREVTEQVRKEASNFLQEMRALSDRTQERWEREERLTQDFHRME 661

Query: 454 RLVISVAKKYTNRGLQFLDLIQ 475
             V     +Y     Q   L  
Sbjct: 662 EEVKLWKNRYAKTKTQLQHLRS 683


>gi|222625128|gb|EEE59260.1| hypothetical protein OsJ_11277 [Oryza sativa Japonica Group]
          Length = 691

 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 33/197 (16%), Positives = 68/197 (34%), Gaps = 21/197 (10%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           RE  DL   +G  +        E  S +       + + D+      ++ +        R
Sbjct: 15  RERFDLGVLVGDLALDEDVASDEDESLEGLRQELDDCKDDE------EVANILANGIKLR 68

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK---------VMCALD-EIAEVY 291
                   N    E +  +D    +  L ++ DQ+R           V+     EI  + 
Sbjct: 69  DYTKGVENNIRQIELDSIQDYIGESENLVSLHDQIRDCDNILSQMETVLTGFQTEIGSIS 128

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV--EQLYDISKRI 349
            E++ LQ+ +++     K+    +    KL K V  + +    ID++V  E   +  K +
Sbjct: 129 SEIKVLQEKSMDMGLKLKNRKAAES---KLSKFVEDIIVPPRMIDIIVDGEVNDEYMKTL 185

Query: 350 MHNEGELLRLAQSYGIK 366
                ++  +     +K
Sbjct: 186 ETLSRKIKFIEVDAMVK 202


>gi|254565449|ref|XP_002489835.1| Huge dynein-related AAA-type ATPase (midasin), forms extended pre-60S
            particle with the Rix1 complex [Pichia pastoris GS115]
 gi|238029631|emb|CAY67554.1| Huge dynein-related AAA-type ATPase (midasin), forms extended pre-60S
            particle with the Rix1 complex [Pichia pastoris GS115]
 gi|328350250|emb|CCA36650.1| Midasin [Pichia pastoris CBS 7435]
          Length = 4950

 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 56/352 (15%), Positives = 127/352 (36%), Gaps = 29/352 (8%)

Query: 3    IGKKRNRDSDSEHE-DSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE 61
            +G+ +N++ D +   DS+  L     ++  ++    A++   V   E    +  +    +
Sbjct: 4378 MGEDKNQNIDEDPALDSETELNPIKDEEEQEETNDPAKEEEAV---EGLDGVDEEGGQQD 4434

Query: 62   QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
             ++D  A+    GI+    +    EE  +      ++ + +   +++  D+    + +  
Sbjct: 4435 NIDDDAAVKQEAGISSEGAEAAASEERDDMGASGGAAETQAQDEIEENADNTQDPSSNEA 4494

Query: 122  RMYLREMGSI--ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELN---- 175
            +  L+++G    E   R  EI  A  ++        +    P  +Q L     EL     
Sbjct: 4495 KESLKQLGDSLKEYHRRRQEIKEANDVDDSTEQNTHN---QPDEYQHLNGENTELETQAL 4551

Query: 176  --DGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
                   ++ I D  A    E+        +  +  K  D++  ++ DD           
Sbjct: 4552 GAADKDQIQTIDDNMAIDDEETMTENLDTEQEQNPDKENDTASAEDIDDHAADGNQDMEG 4611

Query: 234  A---------KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCAL 284
                      K++  +  ++    +N   DE + +E E+ +   ++  +D         L
Sbjct: 4612 DNRKATIGERKINDFELGELMEFSDNETEDEADKNEIEELNVLDMANEDD----AAPRTL 4667

Query: 285  DEIAEVYRELR-SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
            DE  +++R    + QD A N  +  +  ++  V  +          LN  RI
Sbjct: 4668 DEARDLWRHSDLATQDLAANLCEQLRLILEPTVATKLRGDYKTGKRLNMKRI 4719


>gi|157364842|ref|YP_001471609.1| chromosome segregation protein SMC [Thermotoga lettingae TMO]
 gi|157315446|gb|ABV34545.1| chromosome segregation protein SMC [Thermotoga lettingae TMO]
          Length = 1175

 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 30/208 (14%), Positives = 78/208 (37%), Gaps = 14/208 (6%)

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
           +++ +T  ++    +     R       E   +    +  +  D ++ +   E++L+   
Sbjct: 732 EELNKTVEELNKEIESMDQLRRNYAIKSEGMRSRREQIISELSDLSNQIGIYEEELKKFD 791

Query: 281 MC------ALDEIAEVYRELRS-----LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
                    L+EI+  + EL++     L+       +  K   + + L E+  +L   + 
Sbjct: 792 EQLSHERNILEEISTQFSELKAELTNLLERRVHYESELRKLKDEKQKLSEESTQLNSQIK 851

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
             +  ID L + L D  + I   + E   L ++  ++R    ++    +L+       + 
Sbjct: 852 EIEGEIDRLKQILLDNQREIETIKKETENLFETMKMQRSDKDQKF--NKLNELEKKMQQM 909

Query: 390 FPEGEWKNFVACEVD-SILKIRNEIKSI 416
             + E        ++ SI + + +I  +
Sbjct: 910 KEDREKLRDYLHHLELSIQESQAKIDQL 937


>gi|15896019|ref|NP_349368.1| methyl-accepting chemotaxis protein [Clostridium acetobutylicum
           ATCC 824]
 gi|15025801|gb|AAK80708.1|AE007774_5 Membrane assosiated methyl-accepting chemotaxis protein with HAMP
           domain [Clostridium acetobutylicum ATCC 824]
 gi|325510173|gb|ADZ21809.1| Membrane assosiated methyl-accepting chemotaxis protein with HAMP
           domain [Clostridium acetobutylicum EA 2018]
          Length = 571

 Score = 38.7 bits (88), Expect = 3.3,   Method: Composition-based stats.
 Identities = 60/351 (17%), Positives = 127/351 (36%), Gaps = 60/351 (17%)

Query: 12  DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLS 71
           DS+ E    +   + + ++ K++IK+           + +       SSE++  T   L+
Sbjct: 241 DSKDEFGQSTKALNKAQENVKELIKV-----------IMSNAQELSASSEELSATSQELA 289

Query: 72  NMGINV----------VDGDDLEDEEGSE--------------DSLDLASSASNSSVFLQ 107
           +  I++          ++      EE S                +LD +++AS S     
Sbjct: 290 SKAISIDNEITKVATSIEESSAASEEISASIQEVDTSVNNLSSKALDGSNNASESKDRAL 349

Query: 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQAL 167
           K       ++ D + MY            E E +I K IE G+ +            + +
Sbjct: 350 KVSKEGKTASQDMINMY-----------SEKEKSILKAIEEGKVI---------GDIRIM 389

Query: 168 IIWRDELNDGTTLLREIIDLEACIGPESKGGF-FHGTEGHSYQKREDSSQEKERDDVQET 226
                E+ + T LL     +EA    E   GF     E     K+   + E     +++ 
Sbjct: 390 ADAIAEIANQTNLLSLNASIEAARAGEMGKGFAVVANEVKELAKQSGDAVEGINKTIEKV 449

Query: 227 EGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
               E  +K S +    +D   ++  +    + +  +  +  +S M  ++          
Sbjct: 450 NAAFEHLSKNSSEILKFMDENVKSQFSKFIQMGDQYEKDSEFVSDMSSEIASMAEELEAT 509

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSL-SLNQSRID 336
           I +V     ++Q+ A N Q++ +SS + K    ++      +  ++QS+ +
Sbjct: 510 IGQVND---AMQNMANNQQQEAESSEEVKGTISEVAASADQVSKMSQSQAE 557


>gi|167629450|ref|YP_001679949.1| RNA polymerase sigma-70 factor [Heliobacterium modesticaldum Ice1]
 gi|167592190|gb|ABZ83938.1| RNA polymerase sigma-70 factor [Heliobacterium modesticaldum Ice1]
          Length = 247

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            +V   +     A + ++      V + A+ Y   G    D+IQEG IGL KA   F   
Sbjct: 25  EVVEMAKEGDEEALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRCD 84

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 85  KLSSFRAFAELCITRQIITAIKTATRQKHIP 115


>gi|1150766|gb|AAA85186.1| myosin heavy chain [Dictyostelium discoideum]
          Length = 2245

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 35/301 (11%), Positives = 88/301 (29%), Gaps = 22/301 (7%)

Query: 252  ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
            EN   ++ +   +   + +  + QL  +       I E   E+  LQ         E S+
Sbjct: 1616 ENSFTDMKQRNQELIESSALYKQQLLQQTSTIDSTIKEKENEISKLQQQL------ETSN 1669

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
             +   LKE+L  +  S  L  +     + QL   ++++     E+ +          VF 
Sbjct: 1670 QQLHQLKEELNSMKQSNQLESTEQSKQLNQLIQENQQLKSVTNEISKQLDDA-----VFE 1724

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
             +     +    +  +K       ++    +   I ++++ I  +  +           +
Sbjct: 1725 NQKINNTIKEQEIK-SKRMSVELQQHIDEGKQQEIQQLQSTIAQLKQQQQSETDRLEKEI 1783

Query: 432  SMVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKF 488
              +++        + ++VE+       +  +   Y N          E       A  K 
Sbjct: 1784 QQMKRERET----QMKLVESTKLNYHMLEDRMELYRNVMEIIDYKETEWEKLARLAGCKE 1839

Query: 489  DWCL---GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
                    +  S         +                  +   + ++R+    + K   
Sbjct: 1840 LDTKLLSDFLLSCKLEHTSLGSQMWFHQIDYWCPYERDSSKGIFYGIIRSIVDFTIKNFD 1899

Query: 546  E 546
            +
Sbjct: 1900 D 1900


>gi|1589173|prf||2210342A myosin:SUBUNIT=heavy chain
          Length = 2241

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 35/301 (11%), Positives = 88/301 (29%), Gaps = 22/301 (7%)

Query: 252  ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
            EN   ++ +   +   + +  + QL  +       I E   E+  LQ         E S+
Sbjct: 1614 ENSFTDMKQRNQELIESSALYKQQLLQQTSTIDSTIKEKENEISKLQQQL------ETSN 1667

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
             +   LKE+L  +  S  L  +     + QL   ++++     E+ +          VF 
Sbjct: 1668 QQLHQLKEELNSMKQSNQLESTEQSKQLNQLIQENQQLKSVTNEISKQLDDA-----VFE 1722

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
             +     +    +  +K       ++    +   I ++++ I  +  +           +
Sbjct: 1723 NQKINNTIKEQEIK-SKRMSVELQQHIDEGKQQEIQQLQSTIAQLKQQQQSETDRLEKEI 1781

Query: 432  SMVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKF 488
              +++        + ++VE+       +  +   Y N          E       A  K 
Sbjct: 1782 QQMKRERET----QMKLVESTKLNYHMLEDRMELYRNVMEIIDYKETEWEKLARLAGCKE 1837

Query: 489  DWCL---GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
                    +  S         +                  +   + ++R+    + K   
Sbjct: 1838 LDTKLLSDFLLSCKLEHTSLGSQMWFHQIDYWCPYERDSSKGIFYGIIRSIVDFTIKNFD 1897

Query: 546  E 546
            +
Sbjct: 1898 D 1898


>gi|323342574|ref|ZP_08082806.1| hypothetical protein HMPREF0357_10987 [Erysipelothrix rhusiopathiae
            ATCC 19414]
 gi|322463686|gb|EFY08880.1| hypothetical protein HMPREF0357_10987 [Erysipelothrix rhusiopathiae
            ATCC 19414]
          Length = 1542

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 53/342 (15%), Positives = 124/342 (36%), Gaps = 24/342 (7%)

Query: 7    RNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDT 66
            +N  +  + ++   S +   ++D+ K++ KL      +T EE N     DE++ +  E  
Sbjct: 1176 KNTGNLDKKKEDSKSELDKKAEDAKKEIDKLP----NLTDEEKNKA--KDEINQKNQESK 1229

Query: 67   VAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLR 126
             A+  +     +D      ++G  D +D        +         A+ +         +
Sbjct: 1230 DAIDQSNDPKEIDKVIDTTDKGINDIVDDNKLLDTKNKAKDDFDKKAEDAK--------K 1281

Query: 127  EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIID 186
            E+  +  L+ E +    + IE        ++ +S    +        ++     + +I++
Sbjct: 1282 EIDKLPNLTDEEKTKAKEEIEQKNQESKDAIDQS----KDSKEIDKVIDTTEKGINDIVE 1337

Query: 187  LEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDS 246
                +  ++K       +    +K  D       D+ Q+ + DI+   +  K+   +  +
Sbjct: 1338 DNKLLDTKNKAKDDLDKKAEDAKKEIDKLPNLTDDEKQKAKDDIDQKTEEGKNAIDQGTT 1397

Query: 247  PPENAENDERNLDEDEDDSAHT-LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
            P +            +D    + L   +++ +  +    DE  +    L  L   A +  
Sbjct: 1398 PKDVENAKNTTDTAVKDIVDQSTLQDAKNKAKKDLEAKADETKKAIDALPGLSQEAKDKA 1457

Query: 306  KDEKSSVKCKVLK-----EKLVKLVGSLSLNQSRIDLLVEQL 342
            K E   V  + L       K+ K+  SL  +  ++D +V+ L
Sbjct: 1458 KAEVDKVLKEGLASIDSGSKVEKVNKSLHNSMDQMDKIVKAL 1499


>gi|218193052|gb|EEC75479.1| hypothetical protein OsI_12062 [Oryza sativa Indica Group]
          Length = 702

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 33/197 (16%), Positives = 68/197 (34%), Gaps = 21/197 (10%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           RE  DL   +G  +        E  S +       + + D+      ++ +        R
Sbjct: 15  RERFDLGVLVGDLALDEDVASDEDESLEGLRQELDDCKDDE------EVANILANGIKLR 68

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK---------VMCALD-EIAEVY 291
                   N    E +  +D    +  L ++ DQ+R           V+     EI  + 
Sbjct: 69  DYTKGVENNIRQIELDSIQDYIGESENLVSLHDQIRDCDNILSQMETVLTGFQTEIGSIS 128

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV--EQLYDISKRI 349
            E++ LQ+ +++     K+    +    KL K V  + +    ID++V  E   +  K +
Sbjct: 129 SEIKVLQEKSMDMGLKLKNRKAAES---KLSKFVEDIIVPPRMIDIIVDGEVNDEYMKTL 185

Query: 350 MHNEGELLRLAQSYGIK 366
                ++  +     +K
Sbjct: 186 ETLSRKIKFIEVDAMVK 202


>gi|325184901|emb|CCA19393.1| hypothetical protein CaO19.12161 [Albugo laibachii Nc14]
          Length = 5812

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 29/223 (13%), Positives = 69/223 (30%), Gaps = 9/223 (4%)

Query: 60   SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            S+Q+ED   +L      V +  +  +++  ED+     +    ++     +++ +    D
Sbjct: 4940 SDQIEDEEQLLGLRDDPVTNETESVEKKPPEDTGLEMENDFEGTIQDAPDQENEEEDDQD 4999

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA---LIIWRDELND 176
                  REMG I+      +  +      G           P   +          +  +
Sbjct: 5000 EGEELDREMGDID----PEDANLVDNKLWGEDSDDDDEDIDPEKEKFDENARSDGAKTME 5055

Query: 177  GTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKV 236
                 +   + +     +         E  +  +  +   E   DD    + + +   + 
Sbjct: 5056 DEIRGKN--EDQDTTDSKEDASEAQNQEPETKDEETEPFDEPNEDDAVNADWEDDYENEH 5113

Query: 237  SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             + D S+   P   A   +  L ED +         ED+ + +
Sbjct: 5114 GEFDESEPRDPDTEANKPDEELPEDMELDGGEPDRCEDEGQEE 5156


>gi|325288494|ref|YP_004264675.1| RNA polymerase, sigma 30 subunit, SigH [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324963895|gb|ADY54674.1| RNA polymerase, sigma 30 subunit, SigH [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 252

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 25/91 (27%), Positives = 39/91 (42%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            MV   +   SI+++ ++      V + A+ Y   G    D+IQEG IGL KA   F   
Sbjct: 59  EMVELAKNGDSISQEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRGD 118

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F  +A   + + I  +I   +    IP
Sbjct: 119 KLSSFRAFAELCITRQIITAIKTATRQKHIP 149


>gi|291402042|ref|XP_002717663.1| PREDICTED: CDC42 binding protein kinase alpha-like isoform 1
           [Oryctolagus cuniculus]
          Length = 1732

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 63/439 (14%), Positives = 144/439 (32%), Gaps = 54/439 (12%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTVDGPLTASKDLEIKNLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +    S ++  +E+   + + +     ++    +             Q RE  
Sbjct: 496 IEKLRKQV-TESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIK-------TLQQEREDL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              +  A                + +     E+K    +  +++ EF  I   +      
Sbjct: 548 NKELVQAS---------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVVQKVESLRQELRRTERAKKELE---VHTEALAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EEI K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGICSI-EHQQEITKLKTDLEKKSIFY--EEEITK 706

Query: 555 KLAMPVEGVR-----------KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +  +    ++           + L + KE + L+  +         +  E +N       
Sbjct: 707 REGIHANEIKNLKKELHDSEGQQLALNKEIMILKDKLEKTRRESQSEREEFENEFKQQYE 766

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  L E   ++ + L       L   +      +  LEE  K     +E +   EA+ 
Sbjct: 767 REKVLLTEENKKLTSELD-----KLTTLYENLSMRNQQLEEEVKDLADKKESVAHWEAQI 821

Query: 664 IRKLKHPSRSKKLRSFLDG 682
              ++  S  K  R +L  
Sbjct: 822 TEIIQWVSDEKDARGYLQA 840


>gi|251854862|gb|ACT22549.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1442

 Score = 38.7 bits (88), Expect = 3.4,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 780  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 835

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 836  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 891

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 892  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 948

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 949  EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1007

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1008 ETDILEEKKEI 1018


>gi|327438254|dbj|BAK14619.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 215

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 72/220 (32%), Gaps = 16/220 (7%)

Query: 411 NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470
            +++ +     ++  E    V +        + A   ++      V + A+ Y   G   
Sbjct: 5   EKLQMVLRFEHLTDEELVEQVHL------GNTDALDYLISKYRLFVKAKARSYFLIGADK 58

Query: 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIH 530
            D+IQEG IGL KA   F       F  +A   + + I  +I   +    IP        
Sbjct: 59  EDIIQEGMIGLYKAIRDFKEDKLASFRAFAELCITRQIITAIKTATRQKHIP-------- 110

Query: 531 KVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590
             + +   +   I  E +   +   +  P+    + L I +E          E  S L  
Sbjct: 111 --LNSYVSLDKPIYDEESERTLMDIITSPISDDPEYLMINREDYLYLEEKMGEVLSELEQ 168

Query: 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRM 630
            +  +       + I   L      +  +L   + ++ R 
Sbjct: 169 QVLVRYLEGQSYNEISEELDRHVKSIDNALQRVKRKLERH 208


>gi|251854896|gb|ACT22566.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1550

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 884  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 939

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 940  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 995

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 996  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1052

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1053 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1111

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1112 ETDILEEKKEI 1122


>gi|194766409|ref|XP_001965317.1| GF24515 [Drosophila ananassae]
 gi|190617927|gb|EDV33451.1| GF24515 [Drosophila ananassae]
          Length = 2196

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 11/112 (9%)

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS----- 237
           E+IDL+  +  +       GT      K E+++ +KE    +    + E  AKV      
Sbjct: 298 EVIDLDDELMTDESVIKKEGTPVKEEIKAEETADKKEAASPEPNTSEEEEPAKVESETEV 357

Query: 238 ------KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
                  +D  K   P   A   E++  E + D++ T  +   + + +V  A
Sbjct: 358 KDDAVKAEDSEKETEPEAKAGEKEKSPAEADKDASETEESKASEEKMEVEEA 409


>gi|115453543|ref|NP_001050372.1| Os03g0417900 [Oryza sativa Japonica Group]
 gi|31126698|gb|AAP44621.1| putative Vps52 / Sac2 family protein [Oryza sativa Japonica Group]
 gi|37718823|gb|AAR01694.1| ARE1-like protein [Oryza sativa Japonica Group]
 gi|108708843|gb|ABF96638.1| Vps52/Sac2 family protein, putative, expressed [Oryza sativa
           Japonica Group]
 gi|113548843|dbj|BAF12286.1| Os03g0417900 [Oryza sativa Japonica Group]
 gi|215737245|dbj|BAG96174.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 702

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 33/197 (16%), Positives = 68/197 (34%), Gaps = 21/197 (10%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
           RE  DL   +G  +        E  S +       + + D+      ++ +        R
Sbjct: 15  RERFDLGVLVGDLALDEDVASDEDESLEGLRQELDDCKDDE------EVANILANGIKLR 68

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK---------VMCALD-EIAEVY 291
                   N    E +  +D    +  L ++ DQ+R           V+     EI  + 
Sbjct: 69  DYTKGVENNIRQIELDSIQDYIGESENLVSLHDQIRDCDNILSQMETVLTGFQTEIGSIS 128

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV--EQLYDISKRI 349
            E++ LQ+ +++     K+    +    KL K V  + +    ID++V  E   +  K +
Sbjct: 129 SEIKVLQEKSMDMGLKLKNRKAAES---KLSKFVEDIIVPPRMIDIIVDGEVNDEYMKTL 185

Query: 350 MHNEGELLRLAQSYGIK 366
                ++  +     +K
Sbjct: 186 ETLSRKIKFIEVDAMVK 202


>gi|283135190|ref|NP_898837.2| serine/threonine-protein kinase MRCK beta [Mus musculus]
          Length = 1713

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 96/304 (31%), Gaps = 33/304 (10%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMTQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP------KVMCALDEIAEVY 291
                 ++     A  ++  L +   +++  L +   +L+       + +    E+ E  
Sbjct: 525 THRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKDAHQQRKRALQEFSELNERM 584

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ELRSL+       +D++  ++  + K                ID + + L    K    
Sbjct: 585 SELRSLKQKVSRQLRDKEEEMEVAMQK----------------IDSMRQDLRKSEKSRKE 628

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E  L   A     +R +        +     +   K    G      +     I KIR+
Sbjct: 629 LEARLEDAAAEASKERKLREHSESFCKQMERELEALKVKQGGRGPGAASEHQQEISKIRS 688

Query: 412 EIKS 415
           E++ 
Sbjct: 689 ELEK 692


>gi|302143890|emb|CBI22751.3| unnamed protein product [Vitis vinifera]
          Length = 930

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 49/338 (14%), Positives = 118/338 (34%), Gaps = 26/338 (7%)

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           L +    L    DL   +  + +      +E     +  +   E    ++ +  GDIE+ 
Sbjct: 357 LEEMRKELDYEKDLNRNLRLQLQKTQDSNSELIIAVRDLEEMLEPRNKEIFQLFGDIENR 416

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRE 293
            K       ++D+  E     ++  D   +   H     E ++    +   +E+ +    
Sbjct: 417 EKSDDLVEEQIDAK-EVGVLQKKMTDLHGEIEVHRKDREELEMHMAQLALDNEVLK---- 471

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
               Q+       ++    +   ++ +L   + ++   +S+++ L +++   ++++  + 
Sbjct: 472 ----QEKQNISTLEQYQKQELMKIQNELSASLATIKELESQVERLEKEIKKQAQKLSESS 527

Query: 354 GELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEI 413
             +  L            ++ QG E D   ++ AK   E                +R   
Sbjct: 528 NAVNELQMQVKSLEKELEKQAQGFEDDLEAMTRAKIEQEQRAIRAEET-------LRKTR 580

Query: 414 KSISVETGISISEFRHI-VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
            + +        EFR I V M  K +    +A K + EAN   V               +
Sbjct: 581 WNNAQSAERLQEEFRRISVEMTSKFDENEKVAMKAVTEANDLRVQKRI---------LEE 631

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510
           ++Q+ N  +    +++D    ++ S   +  ++  I R
Sbjct: 632 MLQKANEEIGLIKDQYDEGEKHEASFAEIQMLRAEIER 669


>gi|81174935|sp|Q7TT50|MRCKB_MOUSE RecName: Full=Serine/threonine-protein kinase MRCK beta; AltName:
           Full=CDC42-binding protein kinase beta; AltName:
           Full=DMPK-like beta; AltName: Full=Myotonic dystrophy
           kinase-related CDC42-binding kinase beta; Short=MRCK
           beta; Short=Myotonic dystrophy protein kinase-like beta
 gi|30841496|gb|AAP34402.1| CDC42-binding protein kinase beta [Mus musculus]
          Length = 1713

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 41/304 (13%), Positives = 96/304 (31%), Gaps = 33/304 (10%)

Query: 122 RMYLREMGSIELLSREGEI----AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
           R  L+ M     L+++ ++      + +IEA    +           Q  +    +L + 
Sbjct: 412 RGSLKSMTQSNTLTKDEDVQRDLENSLQIEAYERRIRRLE-------QEKLELSRKLQES 464

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
           T  ++ +      +G  ++            + +   +     +   E    +    + S
Sbjct: 465 TQTVQSLHGSTRALGNSNRDKEIKRLNEELERMKSKMADSNRLERQLEDTVTLRQEHEDS 524

Query: 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP------KVMCALDEIAEVY 291
                 ++     A  ++  L +   +++  L +   +L+       + +    E+ E  
Sbjct: 525 THRLKGLEKQYRLARQEKEELHKQLVEASERLKSQTKELKDAHQQRKRALQEFSELNERM 584

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            ELRSL+       +D++  ++  + K                ID + + L    K    
Sbjct: 585 SELRSLKQKVSRQLRDKEEEMEVAMQK----------------IDSMRQDLRKSEKSRKE 628

Query: 352 NEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRN 411
            E  L   A     +R +        +     +   K    G      +     I KIR+
Sbjct: 629 LEARLEDAAAEASKERKLREHSESFCKQMERELEALKVKQGGRGPGAASEHQQEISKIRS 688

Query: 412 EIKS 415
           E++ 
Sbjct: 689 ELEK 692


>gi|66823681|ref|XP_645195.1| hypothetical protein DDB_G0272112 [Dictyostelium discoideum AX4]
 gi|166204139|sp|P54697|MYOJ_DICDI RecName: Full=Myosin-J heavy chain; AltName: Full=Myosin-5b
 gi|60473262|gb|EAL71208.1| hypothetical protein DDB_G0272112 [Dictyostelium discoideum AX4]
          Length = 2245

 Score = 38.7 bits (88), Expect = 3.5,   Method: Composition-based stats.
 Identities = 35/301 (11%), Positives = 88/301 (29%), Gaps = 22/301 (7%)

Query: 252  ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
            EN   ++ +   +   + +  + QL  +       I E   E+  LQ         E S+
Sbjct: 1616 ENSFTDMKQRNQELIESSALYKQQLLQQTSTIDSTIKEKENEISKLQQQL------ETSN 1669

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
             +   LKE+L  +  S  L  +     + QL   ++++     E+ +          VF 
Sbjct: 1670 QQLHQLKEELNSMKQSNQLESTEQSKQLNQLIQENQQLKSVTNEISKQLDDA-----VFE 1724

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIV 431
             +     +    +  +K       ++    +   I ++++ I  +  +           +
Sbjct: 1725 NQKINNTIKEQEIK-SKRMSVELQQHIDEGKQQEIQQLQSTIAQLKQQQQSETDRLEKEI 1783

Query: 432  SMVRKGECEASIAKKEMVEANLRLVISVAKK---YTNRGLQFLDLIQEGNIGLMKAAEKF 488
              +++        + ++VE+       +  +   Y N          E       A  K 
Sbjct: 1784 QQMKRERET----QMKLVESTKLNYHMLEDRMELYRNVMEIIDYKETEWEKLARLAGCKE 1839

Query: 489  DWCL---GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKR 545
                    +  S         +                  +   + ++R+    + K   
Sbjct: 1840 LDTKLLSDFLLSCKLEHTSLGSQMWFHQIDYWCPYERDSSKGIFYGIIRSIVDFTIKNFD 1899

Query: 546  E 546
            +
Sbjct: 1900 D 1900


>gi|52081877|ref|YP_080668.1| YvrI [Bacillus licheniformis ATCC 14580]
 gi|52787265|ref|YP_093094.1| YvrI [Bacillus licheniformis ATCC 14580]
 gi|52005088|gb|AAU25030.1| YvrI [Bacillus licheniformis ATCC 14580]
 gi|52349767|gb|AAU42401.1| YvrI [Bacillus licheniformis ATCC 14580]
          Length = 193

 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
           GD ++D   +   +   +             LT ++++VL   +  G+    +++E+   
Sbjct: 103 GDLLDD--VLEQEEELSEHLQDPMLYEAFLQLTDKQKKVLAQIYIHGV----SMQEIADS 156

Query: 649 FCVTRERIRQIEAKAIRKLKHPSRSK 674
              +R+ I +I  +A+ K++    SK
Sbjct: 157 LGESRQNISKIHKRALEKIRELLNSK 182


>gi|71748798|ref|XP_823454.1| kinesin [Trypanosoma brucei TREU927]
 gi|70833122|gb|EAN78626.1| kinesin, putative [Trypanosoma brucei]
          Length = 1132

 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 75/536 (13%), Positives = 162/536 (30%), Gaps = 28/536 (5%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             +  +   L  +  +F+    + +   +  TL   +  L+  +  E +       E H+
Sbjct: 450 KTKERVRDLLMRNGCSFEE--AYGNLTREIETLRHRVATLQEEVNIEKQLSSLTRREKHA 507

Query: 208 YQKREDSSQE-KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
               +    E KE +  Q+  GD  +  + S  + S  +S  +    D     E +    
Sbjct: 508 PNSNDGMDHEGKEPEQPQKVNGDAATNTENSLANASGANSAEDPVIRDHVVALERQCAIF 567

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            ++    ++    +    D   E+ +EL          Q+  + +V      E L K+  
Sbjct: 568 QSVLRERERDLCSLESRGDVAEELRQELEQRVRQCDEAQQTLEEAVLEVGTSELLHKVTD 627

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +    Q + D + EQ   ++K +     E  R        R   ++  +  E     +  
Sbjct: 628 TFRWMQEQFDSMSEQKQVMAKTVEAMRSEQKRTMAELLEARKHIVQTEKSCEELRQRLER 687

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             +   G         +  + +    +           S  R           E      
Sbjct: 688 VTNENTGLTDQLEELNLKLLHEYTERVIREETVAWFKASGERAEECERLTTAFEDQRNLC 747

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW-VK 505
           +++++ L       ++        L  +Q+ +                +F +      V 
Sbjct: 748 DVLQSRLTSTEEELERGNKEHCALLQEMQKKDEAFRSIWILLTPQQKARFMSVGYGGDVV 807

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           +    +   Q             + K  +    +    +R+   E++  +  +  E +  
Sbjct: 808 ENSGSASLHQGHENVQLRSQVRTLKK--QLEDEILCSRERDYRIEDLECENRLLQERLLH 865

Query: 566 VLKITKEPISLETPIGDEDT------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                K  ++L+    DE        +HL  +IE+ N         +  LRE        
Sbjct: 866 RENEYKSLVALDQDYMDEREQMEGQIAHLYTYIEEHN---MKQRTSERQLREVQIEW-EK 921

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA-KAIRKLKHPSRSK 674
           L                N+   + E+  +    +E IR  EA K + K +H   S+
Sbjct: 922 LNE-----------EYCNSQREVAELTAKLNKAKEEIRIQEANKHVLKNRHQHESR 966


>gi|255022533|ref|ZP_05294519.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J1-208]
          Length = 191

 Score = 38.7 bits (88), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EELAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|251854882|gb|ACT22559.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1273

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 103/273 (37%), Gaps = 12/273 (4%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
           +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 612 ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 667

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
              S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 668 IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 723

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                  LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 724 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 780

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 781 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 839

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
               L+E  E+ ++     +      KD ++ +
Sbjct: 840 ETDILEEKKEIEKDHFEKFEEEAEEIKDLEADI 872


>gi|251854876|gb|ACT22556.1| liver stage antigen 3 [Plasmodium falciparum]
 gi|251854880|gb|ACT22558.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1313

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 103/273 (37%), Gaps = 12/273 (4%)

Query: 40  QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
           +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 652 ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 707

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
              S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 708 IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 763

Query: 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                  LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 764 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 820

Query: 220 RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
             D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 821 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 879

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV 312
               L+E  E+ ++     +      KD ++ +
Sbjct: 880 ETDILEEKKEIEKDHFEKFEEEAEEIKDLEADI 912


>gi|114578191|ref|XP_001156367.1| PREDICTED: dynactin 1 isoform 9 [Pan troglodytes]
          Length = 1138

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 112 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 171

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 172 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 231

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 232 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 291

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 292 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 350

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 351 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 406

Query: 456 VISV 459
           V   
Sbjct: 407 VERQ 410


>gi|255655907|ref|ZP_05401316.1| two-component sensor histidine kinase [Clostridium difficile
           QCD-23m63]
 gi|296450671|ref|ZP_06892424.1| two component sensor histidine kinase [Clostridium difficile NAP08]
 gi|296879212|ref|ZP_06903207.1| two component sensor histidine kinase [Clostridium difficile NAP07]
 gi|296260515|gb|EFH07357.1| two component sensor histidine kinase [Clostridium difficile NAP08]
 gi|296429755|gb|EFH15607.1| two component sensor histidine kinase [Clostridium difficile NAP07]
          Length = 302

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 33/189 (17%), Positives = 73/189 (38%), Gaps = 8/189 (4%)

Query: 282 CALDEIAEVYRELRSLQDNAVNGQKDEKSSV---KCKVLKEKLVKLVGSLSLNQSRIDLL 338
              DE++ +  ++   ++      KD ++S    + K +K+ +   V    L +  I  L
Sbjct: 23  KRYDELSLMLNQILEGKEVTYPDTKDTRASKISHQVKKIKDMIEIEVEQSKLEKEAIKGL 82

Query: 339 VEQLYDISKRIMHNEGELLRLAQSYGIK---RDVFLERHQGRELDPHWVSYAKDFPEGEW 395
           +  +    K  + N      L ++  I    +  FL++ +       W+  +        
Sbjct: 83  ISNMSHQLKTPLSNITIYCELLENINISTLQKKEFLQKMKNETFKIDWLLQSLFKMTKLE 142

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
              +  EV+ +L     I+SIS  T  + +E ++I   +        +  K+ +   +  
Sbjct: 143 DGVIEFEVEELLIKDTLIQSIS--TIFNKAEAKNIRVNLEPFSDIKLVHNKKWIIEAIVN 200

Query: 456 VISVAKKYT 464
           V+  A KY+
Sbjct: 201 VLENAIKYS 209


>gi|118099526|ref|XP_001231456.1| PREDICTED: similar to skeletal muscle myosin heavy chain MyHC-EO/IIL
            [Gallus gallus]
          Length = 2000

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 32/222 (14%), Positives = 90/222 (40%), Gaps = 5/222 (2%)

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
            +E  +  +       K +  ++    ++    +  ++  +++ +     E++   L +D 
Sbjct: 899  SENLADAEERCEGLIKSKIQLEARIKELNERMEDEEEMNAELTAKKRKLEDECSELKKDI 958

Query: 263  DDSAHTLSAMEDQLR---PKVMCALDEIAEVYRELRSL-QDNAVNGQKDEKSSVKCKVLK 318
            DD   TL+ +E +      KV    +E+A +   +  L ++     +  +++    +  +
Sbjct: 959  DDLELTLAKVEKEKHATENKVKNLTEEMAALDENISKLTKEKKALQEAHQQTLDDLQAEE 1018

Query: 319  EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
            +K+  L  + +  + ++D L   L    K+ M  E    +L     + +D  ++    ++
Sbjct: 1019 DKVSTLTKTKTKLEQQVDDLEGSLEQERKQRMDLERAKRKLDGDLKMSQDSIMDLENDKQ 1078

Query: 379  LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
                 +   KDF   + ++ +  E     +++ +IK +   T
Sbjct: 1079 QMDEKLKK-KDFEISQLQSKIEDEQAQSSQLQKKIKELQART 1119


>gi|327264671|ref|XP_003217135.1| PREDICTED: myosin-4-like [Anolis carolinensis]
          Length = 1938

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 45/291 (15%), Positives = 112/291 (38%), Gaps = 15/291 (5%)

Query: 132  ELL-SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
             LL S E E  +A   E         L +S    + L      L      L+  +  E  
Sbjct: 842  PLLRSAESEKEMANMKEEFEKT-KEDLAKSEAKRKELEEKMVTLVQEKNDLQLQVQSETE 900

Query: 191  IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
               +++       +     + +     +  +D +E   ++ +  +  +D+ S++    ++
Sbjct: 901  SLADAEERCEGLIKSKIQLEAKIKELTERLEDEEEMNAELTAKKRKLEDECSELKKDIDD 960

Query: 251  AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE-IAEVYRELRSLQDNAVNGQKDEK 309
             E     +++++  + + +  + ++     M ALDE I+++ +E +SLQ+       D  
Sbjct: 961  LELTLAKVEKEKHATENKVKNLTEE-----MAALDESISKLSKEKKSLQEAHQQTLDD-- 1013

Query: 310  SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDV 369
                 +  ++K+  L  + S  + ++D L   L    K  M  E    +L     + ++ 
Sbjct: 1014 ----LQAEEDKVNTLSKTKSKLEQQVDDLEGSLEQEKKLRMDLERAKRKLEGDLKMSQES 1069

Query: 370  FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
             ++    ++     +   K+F  G+ +  +  E     +++ +IK +    
Sbjct: 1070 VMDLENDKQQMDDKLKK-KEFEIGQLQGKIEDEQAQSSQLQKKIKELQARM 1119


>gi|149773554|ref|NP_001092526.1| pleckstrin homology-like domain family B member 3 [Bos taurus]
 gi|148743948|gb|AAI42057.1| PHLDB3 protein [Bos taurus]
          Length = 640

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 85/233 (36%), Gaps = 14/233 (6%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
             LS EG    A+R+ A +   +  +       + L   R EL          I++E  +
Sbjct: 94  PALSGEGVRGAARRLSAQQLEALTRVALMEQRVKELQRQRKELR---------IEMEVEV 144

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                            +++      ++ D  +  +   E   +    +R +V+   +  
Sbjct: 145 ALLRGELAGERVAARREEEQLRELLGQQVDSEKGGQEQREQEQRRLSQERDRVEGLRQRL 204

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-DNAVNGQKDEKS 310
           +  +  LD   +D    L     ++R      LD     Y +L   Q +     +++++ 
Sbjct: 205 QEAQEQLDSQPEDQHERLLQGMQEMR----EQLDVAQRAYEDLEFQQLERESRQEEEDRD 260

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           S    V   K+ +L  S++ ++ RI +L EQL  + +++      L R  +  
Sbjct: 261 SPGAGVPDPKVQELQASVAQHRRRIQVLEEQLKSLGEQMADESRGLSRKKEEA 313


>gi|205277396|ref|NP_001128513.1| dynactin subunit 1 isoform 4 [Homo sapiens]
 gi|119620090|gb|EAW99684.1| dynactin 1 (p150, glued homolog, Drosophila), isoform CRA_a [Homo
           sapiens]
          Length = 1139

 Score = 38.7 bits (88), Expect = 3.7,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 113 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 172

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 173 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 232

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 233 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 292

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 293 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 351

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 352 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 407

Query: 456 VISV 459
           V   
Sbjct: 408 VERQ 411


>gi|323705058|ref|ZP_08116634.1| RNA polymerase sigma factor, sigma-70 family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535484|gb|EGB25259.1| RNA polymerase sigma factor, sigma-70 family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 188

 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 24/144 (16%), Positives = 59/144 (40%), Gaps = 10/144 (6%)

Query: 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584
           ++D    ++    +   K  +E       +     +   RK        +SL      E+
Sbjct: 46  LQDGREVLIAAIHQFDEKKGKEFIAYSSMQLKFYFLNAYRKKKSF----LSLNVKAD-EE 100

Query: 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 644
            + + D IE  + ++P +      +R+     L  LT +++ ++ + F        TL E
Sbjct: 101 ENEIIDLIE-SDELTPEEKFFNDIMRKDLKEALNGLTGKQKNIIMLYFF----ERKTLVE 155

Query: 645 VGKQFCVTRERIRQIEAKAIRKLK 668
           + K+  V  + + +++ +A+ +L+
Sbjct: 156 ISKELGVGYQSVVKLKDRALDRLR 179


>gi|206973455|ref|ZP_03234376.1| P188 [Bacillus cereus AH1134]
 gi|206731625|gb|EDZ48826.1| P188 [Bacillus cereus AH1134]
          Length = 191

 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 27/111 (24%), Positives = 48/111 (43%), Gaps = 9/111 (8%)

Query: 562 GVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA---IQANLRETTTRVLA 618
            +RK     +  ++L+ P+ DE T+ + D + D    S L S    +         R L 
Sbjct: 84  KIRKN--NARLSLTLDKPMIDETTTTIKDNLPDPTVYSNLISNPSLLDEIEDHKLYRSLE 141

Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
           SLT ++ +V+ + +        T  E       T + +  I  KA++KLK+
Sbjct: 142 SLTEKQLQVIELLYA----KKLTNNEAAYYLNTTPQNVTNIHTKALKKLKN 188


>gi|312142838|ref|YP_003994284.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311903489|gb|ADQ13930.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 208

 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 67/180 (37%), Gaps = 11/180 (6%)

Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
           A + +++ N+ +V + A+ +  +GL   D+IQEG +GL KA   +    G  F  ++   
Sbjct: 21  AIEYLIDQNMDIVYAKARFFFIKGLDRDDVIQEGRVGLYKAIRDYREGKGASFRGFSQLC 80

Query: 504 VKQAITRSIADQSCTIRIPVHM-----------RDKIHKVVRTARRMSNKIKREPTPEEI 552
           V + +  +I   +    +P++             +               ++R+   +E 
Sbjct: 81  VHRQLVSAIKKANRQKHMPLNTSASLDKSLDYGNETGRTFNEILPDEGENLERKFICQET 140

Query: 553 AKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612
              +   +      L+     + L++    E +  L   ++  +           +LRE 
Sbjct: 141 LTTIVKELSRDLTDLEWNVFMLYLDSRSYQEISDQLDINVKTVDNALQRARKKIEDLREH 200


>gi|169158591|emb|CAQ15489.1| novel protein similar to vertebrate kinesin family member 5A
           (KIF5A) [Danio rerio]
          Length = 850

 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 53/317 (16%), Positives = 109/317 (34%), Gaps = 29/317 (9%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSAD 114
            +E S E++++ +  L  + +N  D    E E+ +++   L+   S  S  L        
Sbjct: 485 ENEASKEEVKEVLQALEELAVN-YDQKSQEVEDKTKEFEALSEELSQKSSTLASIDSELQ 543

Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174
           +         L+EM              A   +     MM+SL +        +   D  
Sbjct: 544 K---------LKEM--------------ANHQKKRVTEMMSSLLKDLTEIGIAVGNNDIK 580

Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAA 234
           ++G+ L+ E   +      + K       +     +   S   K+ D+  +     +   
Sbjct: 581 HEGSGLIDEEFTVARLYISKMKSEVKSMVKRCKQLENTQSESNKKMDESDKELAACQLRI 640

Query: 235 KVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
              +     +    +N E  +R L+ED D     L  +  Q +   M    EI       
Sbjct: 641 SQHEAKIKSLTEYLQNVEQKKRQLEEDVDSLNEELVKISAQEKVHAMEKESEIQSANEVK 700

Query: 295 RSLQDNAVNGQKDEKSSVKCKVLKEKL---VKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
            +++    + +  E    +   L+++L    KL+  L     +I L  E+L    +++  
Sbjct: 701 EAVEKQIQSHR--EAHQKQISSLRDELETKEKLITDLQDQNQKIMLEQERLRVEHEKLKS 758

Query: 352 NEGELLRLAQSYGIKRD 368
            + E  R      + +D
Sbjct: 759 TDQEKSRKLHELTMMQD 775


>gi|296477493|gb|DAA19608.1| pleckstrin homology-like domain, family B, member 3 [Bos taurus]
          Length = 629

 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 85/233 (36%), Gaps = 14/233 (6%)

Query: 132 ELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACI 191
             LS EG    A+R+ A +   +  +       + L   R EL          I++E  +
Sbjct: 94  PALSGEGVRGAARRLSAQQLEALTRVALMEQRVKELQRQRKELR---------IEMEVEV 144

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
                            +++      ++ D  +  +   E   +    +R +V+   +  
Sbjct: 145 ALLRGELAGERVAARREEEQLRELLGQQVDSEKGGQEQREQEQRRLSQERDRVEGLRQRL 204

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-DNAVNGQKDEKS 310
           +  +  LD   +D    L     ++R      LD     Y +L   Q +     +++++ 
Sbjct: 205 QEAQEQLDSQPEDQHERLLQGMQEMR----EQLDVAQRAYEDLEFQQLERESRQEEEDRD 260

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           S    V   K+ +L  S++ ++ RI +L EQL  + +++      L R  +  
Sbjct: 261 SPGAGVPDPKVQELQASVAQHRRRIQVLEEQLKSLGEQMADESRGLSRKKEEA 313


>gi|291402044|ref|XP_002717664.1| PREDICTED: CDC42 binding protein kinase alpha-like isoform 2
           [Oryctolagus cuniculus]
          Length = 1719

 Score = 38.7 bits (88), Expect = 3.8,   Method: Composition-based stats.
 Identities = 63/439 (14%), Positives = 144/439 (32%), Gaps = 54/439 (12%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELSRKLQESTQTVQALQYSTVDGPLTASKDLEIKNLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +    S ++  +E+   + + +     ++    +             Q RE  
Sbjct: 496 IEKLRKQV-TESSHLEQQLEEANSVRRELDDAFRQIKAYEKQIK-------TLQQEREDL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV------ 434
              +  A                + +     E+K    +  +++ EF  I   +      
Sbjct: 548 NKELVQAS---------------ERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQ 592

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
           ++        K+E V+  ++ V S+ ++         +L          AAE        
Sbjct: 593 KQKLARHVRDKEEEVDLVVQKVESLRQELRRTERAKKELE---VHTEALAAEASKDRKLR 649

Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
           + S +    ++  +      Q         + +   ++ +    +  K       EEI K
Sbjct: 650 EQSEHYSKQLENELEGLKQKQISYSPGICSI-EHQQEITKLKTDLEKKSIFY--EEEITK 706

Query: 555 KLAMPVEGVR-----------KVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
           +  +    ++           + L + KE + L+  +         +  E +N       
Sbjct: 707 REGIHANEIKNLKKELHDSEGQQLALNKEIMILKDKLEKTRRESQSEREEFENEFKQQYE 766

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
             +  L E   ++ + L       L   +      +  LEE  K     +E +   EA+ 
Sbjct: 767 REKVLLTEENKKLTSELD-----KLTTLYENLSMRNQQLEEEVKDLADKKESVAHWEAQI 821

Query: 664 IRKLKHPSRSKKLRSFLDG 682
              ++  S  K  R +L  
Sbjct: 822 TEIIQWVSDEKDARGYLQA 840


>gi|251854886|gb|ACT22561.1| liver stage antigen 3 [Plasmodium falciparum]
 gi|251854888|gb|ACT22562.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1426

 Score = 38.7 bits (88), Expect = 3.9,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 764  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 819

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 820  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 875

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 876  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 932

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 933  EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 991

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 992  ETDILEEKKEI 1002


>gi|170033490|ref|XP_001844610.1| kakapo [Culex quinquefasciatus]
 gi|167874458|gb|EDS37841.1| kakapo [Culex quinquefasciatus]
          Length = 7917

 Score = 38.7 bits (88), Expect = 3.9,   Method: Composition-based stats.
 Identities = 32/253 (12%), Positives = 82/253 (32%), Gaps = 19/253 (7%)

Query: 142  IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH 201
            IA RIE   A +     E      A+  + D +          +DL              
Sbjct: 5174 IADRIEDLHARLDDRCGELQSAATAVSQFNDAVKA------LGVDLNELESQIDSLSPPA 5227

Query: 202  GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
                    + ++ +    +  +  T   + S  +  +       +P      D+      
Sbjct: 5228 REIKTVLNQLDEVATILTK--IDRTAEHVASVERAGEQLVDSGFAPDTAVTRDQITSLRK 5285

Query: 262  EDDSAHTLSAMEDQLRPKVMCALDEIAEVYR-ELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
            +       +   D+   K + AL +  ++++  L  L D A   +K +  S + + ++ +
Sbjct: 5286 QLGKLDNRARDHDEALQKALKALQKFYDLHQGTLDDLNDVADQVKKLKPVSSELEQIRNQ 5345

Query: 321  LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
                       Q  ++ LVE++ ++++              ++ +++D+        +++
Sbjct: 5346 QDDFR---RFKQRYVEPLVEKIDEVNRSGQDLVRSAQGGVPTHVMEKDL-------EKIN 5395

Query: 381  PHWVSYAKDFPEG 393
              W    +   E 
Sbjct: 5396 EKWNDLKEKMNER 5408


>gi|164687209|ref|ZP_02211237.1| hypothetical protein CLOBAR_00850 [Clostridium bartlettii DSM
           16795]
 gi|164603633|gb|EDQ97098.1| hypothetical protein CLOBAR_00850 [Clostridium bartlettii DSM
           16795]
          Length = 1082

 Score = 38.7 bits (88), Expect = 3.9,   Method: Composition-based stats.
 Identities = 43/319 (13%), Positives = 108/319 (33%), Gaps = 34/319 (10%)

Query: 45  TI-EELNAFLPPDEVSSEQM--EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101
           T  +E    +       +++  +   A        V +  D  +E   +   + A +   
Sbjct: 233 TYSDEYQELIDSVVHDIDKITDDRIKARYDE---VVSEAQDKLNESKQKYEDNKAKAEKE 289

Query: 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR--------IEAGRAMM 153
                 K   S              E G +EL   E + + AKR        IE  +  +
Sbjct: 290 IDDAQTKINKSKTEL----------ERGKLEL---ESQKSNAKRKIQTGKVQIENAKKQL 336

Query: 154 MASLCESPLTFQALIIWRD----ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQ 209
            +   +     +     +     E     + ++++ +L+               +  +  
Sbjct: 337 KSGRVQYENALKEFKNQKKKAQGEFKKAESKIKDL-ELQKSELENGIAQINLLLKDENLS 395

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           + +    + E   +      ++S    +K + +      +++EN  +   +  D +   +
Sbjct: 396 EEQKLYYQNELKTMNSNLEQLKSGISSAKKELNSQKQKLQSSENKLKQTKQTLDSNKIKI 455

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
              E +L+     A +EI +  ++++S ++   N Q    +  K + ++EKL K    + 
Sbjct: 456 KQSEIELKQSEKTANNEIQKAEQKIKSGEEEIQNAQTTLDN--KKQEVQEKLSKAENEIK 513

Query: 330 LNQSRIDLLVEQLYDISKR 348
             Q  I+ + +  + +  R
Sbjct: 514 KAQREINKIEKPTWYVLDR 532


>gi|242021377|ref|XP_002431121.1| polo kinase kinase, putative [Pediculus humanus corporis]
 gi|212516370|gb|EEB18383.1| polo kinase kinase, putative [Pediculus humanus corporis]
          Length = 1307

 Score = 38.3 bits (87), Expect = 3.9,   Method: Composition-based stats.
 Identities = 46/388 (11%), Positives = 109/388 (28%), Gaps = 40/388 (10%)

Query: 262  EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSV----KCKVL 317
            ++           QL       LD +A   R+     +          S      + + L
Sbjct: 919  KEQQDKRFEQERLQLTRTYESDLDTLARQQRQQVEKAEQQQESDLRAASKKIRVEQEREL 978

Query: 318  KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            K+    L   + L +  IDL+ +      KR    +     LA  +  K   F E     
Sbjct: 979  KQFREGLKQEMRLLKQEIDLMPKD-----KRKNIFKTRKEALAAEHEQKEKQFAENL--N 1031

Query: 378  ELDPHWVSYAKDFPEGEWKNFVACEVDSILK-IRNEIKSISVETGISISEFRHIVSMVRK 436
            E     +    +    +        +    + +R    ++       I E + +    R+
Sbjct: 1032 ENHESLLRRLSETHREKIALMERQFLQQKQRLLRARESALWDLEERQIHEKQQLAK--RQ 1089

Query: 437  GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496
             +    + + +M+  + + +  + +    +    +           +A EK       + 
Sbjct: 1090 LKDIFFLQRHQMLIRHEKELEQIKRMNQRKEEDLIK---------RQAVEKRQLPKRIRS 1140

Query: 497  STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556
               A   + +   R                 K  +  +   R   +        ++ +  
Sbjct: 1141 EMKAREMMFRESMRISMSAMPDPEAERERLKKFQENEKKRYRAEQQRFELKHQRQLEELR 1200

Query: 557  AMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616
            A     ++++             + +E    L      ++  + L    +   RE     
Sbjct: 1201 ATSEATIKEL-----------EQLQNEKRKMLM-----EHETAKLKEQEEEYNRE-LKEW 1243

Query: 617  LASLTPREERVLRMRFGIGMNTDHTLEE 644
             + L PR++      + +G   D  L +
Sbjct: 1244 KSQLKPRKQVSYYYHYLLGTVNDWYLTD 1271


>gi|324501569|gb|ADY40696.1| JNK-interacting protein [Ascaris suum]
          Length = 1221

 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 57/425 (13%), Positives = 142/425 (33%), Gaps = 24/425 (5%)

Query: 16  EDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75
           E  + S+  +   +  +++I    +   +   +    L  ++   EQ+ +  + + +   
Sbjct: 84  EKEEYSVDLEMLKEDNEQLITQYEREKQLRRAQDQKCLEIEDTLMEQIRELESKIES--- 140

Query: 76  NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
             ++      E  ++++ D A+         +   D      +  +R ++  M   + L 
Sbjct: 141 --LESIMRMLELKAKNASDHAARLEEREADQKNEFDKLHERYNVLLRTHIDHMERTKYLM 198

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLE----ACI 191
              +  + + +      +   +  +       I    +L          ID+        
Sbjct: 199 GSDKFEMMQNMPLPSQQLRTKIGMATSLDAGTIRGVSDLISAHMSQSTTIDVNLANHISN 258

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
             + +  F           R+DSS   E   V++    +   A  + D           A
Sbjct: 259 EADWQEEFGQSGAEILQSPRDDSSSVIESPRVEQQPESLVEEAPPNADVNPPEAEDSLGA 318

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL-RSLQDNAVNGQKDEKS 310
           +  E  +D+D +++    ++     R +        +E    + R +++      +  ++
Sbjct: 319 DLTEEFIDDDGENTTVAAASEAAARRRQTSAFSSLASEDVEGMGREVENLIKENTELLET 378

Query: 311 SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                ++K  L+  V  LS  Q   D+L E++  +          +  L       R++ 
Sbjct: 379 KNALNIVKNDLIARVDELSSEQ---DILREEIRSLEMVRTKMSERIKELETEV---RELK 432

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS--ISVETGISISEFR 428
            +     E D       +D P  + K F   E+  +L  RN+ K   + ++  +  +E +
Sbjct: 433 EKIEAKSEED------GEDVPMAQRKRFTRLEMARVLMERNQYKERLMELQDAMKWTEMQ 486

Query: 429 HIVSM 433
               M
Sbjct: 487 RAKRM 491


>gi|313902852|ref|ZP_07836249.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466972|gb|EFR62489.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter
           subterraneus DSM 13965]
          Length = 224

 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 41/101 (40%), Gaps = 3/101 (2%)

Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
           +   E   IV + R+G      A + ++      V + A+ Y   G    D+IQEG IGL
Sbjct: 15  LDRMEDEEIVEIARQGN---PEALEYLIGKYKNFVRAKARSYFLVGADREDIIQEGMIGL 71

Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
            KA   F       F  +A   + + I  +I   +    IP
Sbjct: 72  YKAIRDFRSDKLSSFRAFAELCITRQIITAIKTATRQKHIP 112


>gi|294500964|ref|YP_003564664.1| chromosome segregation protein SMC [Bacillus megaterium QM B1551]
 gi|294350901|gb|ADE71230.1| chromosome segregation protein SMC [Bacillus megaterium QM B1551]
          Length = 1186

 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 39/285 (13%), Positives = 99/285 (34%), Gaps = 14/285 (4%)

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +N+    L++I+DL    G   +                 S + ++  +        ++ 
Sbjct: 114 INNQPCRLKDIVDLFMDSGLGREAFSIISQGKVEEVLSSKSDERRKIFEEAAGVLKYKTR 173

Query: 234 AKVSK-------DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
            + ++       ++ ++V       E     L      +   L   E+     V   + E
Sbjct: 174 KRKAELRLLETQENLNRVVDILHEIEGQLEPLQIQSSIAKDYLQKKEELEHIDVAVTVFE 233

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           + +++++   L+      ++ E+S       +E     + +L L+  +ID   EQL  + 
Sbjct: 234 VEDLHQKWEKLKAEMAQHEQLEESLATNIRTRE---GEIQTLRLHIQQID---EQLDSLH 287

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           K++++   E+ +L     + ++      Q +E     V       + E       E   +
Sbjct: 288 KKLLYVSEEVEKLEGKKEVLKERKKNAFQNKEQLERLVKEYTHKHQ-ELSKAKDSEGKDL 346

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            + + E++ I ++       FR     + +   +      E+  A
Sbjct: 347 EQSQKEVQEIRLKLTEQEQLFRQYSENLEEKLEQMKSEYFELANA 391


>gi|225380762|gb|ACN88675.1| RNA polymerase sigma factor sigma-70 [Acinetobacter genomosp. 13]
          Length = 146

 Score = 38.3 bits (87), Expect = 4.0,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 52/182 (28%), Gaps = 37/182 (20%)

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
           ++   G   L +I  L   + PE+        E     + ED S  K   +V+  + D E
Sbjct: 1   NDFLTGERRLADI--LSGYLDPETDEDIPEVLEEVEELEEEDESSTKSTKEVKLDDDDEE 58

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
             ++   D        PE A+     L+     +   +                      
Sbjct: 59  EESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIE--------------------- 97

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
                         K  ++S +     E L  +           D++ E +    ++I  
Sbjct: 98  --------------KHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRA 143

Query: 352 NE 353
           NE
Sbjct: 144 NE 145


>gi|221487518|gb|EEE25750.1| DNA topoisomerase II, putative [Toxoplasma gondii GT1]
          Length = 1688

 Score = 38.3 bits (87), Expect = 4.1,   Method: Composition-based stats.
 Identities = 27/171 (15%), Positives = 58/171 (33%), Gaps = 10/171 (5%)

Query: 281  MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
            +  + E A +  E    +        ++   +    L+  L  + G L +N  R   L+E
Sbjct: 1098 LEIIKEFAPIRLEFYHRRKAYCLAMLEKARRILSNRLRFILAVVNGELIINNKRKKALIE 1157

Query: 341  QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
            +L+      M    +         +KRDV ++     E                +   + 
Sbjct: 1158 ELFSQGYDPMKEIEDAANAGIRAALKRDVIVDDEALAEGGEEEEEIVAGCTAKHYDYLLG 1217

Query: 401  C-----EVDSILKIRNEIKSISVETGISISEFRHI-VSMVRKGECEASIAK 445
                   ++ +  +R E++       + + E RH  V  + K + +A +A 
Sbjct: 1218 MPMWSLTLEKVEDLRGEMRQKE----LELEELRHTSVQTLWKRDLDALVAA 1264


>gi|195155815|ref|XP_002018796.1| GL25755 [Drosophila persimilis]
 gi|194114949|gb|EDW36992.1| GL25755 [Drosophila persimilis]
          Length = 1588

 Score = 38.3 bits (87), Expect = 4.1,   Method: Composition-based stats.
 Identities = 80/536 (14%), Positives = 195/536 (36%), Gaps = 55/536 (10%)

Query: 125  LREMGSIELLS--REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD-ELNDGTTLL 181
            LRE    ELL+  +  E  +  R++  +  +   L ++  +   L+     +L++    +
Sbjct: 757  LREARMSELLTTLQRTEQQLTARLQEQQQQLNGELAQAKQSAAELMHSLSLQLSESQCKI 816

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            +++ D  A    E++  +                       ++E + +    A +S   R
Sbjct: 817  KQLEDRLAQGIEENESLY---------------------KRLRELQAEGSQVASLSNLQR 855

Query: 242  SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             K+      ++    +  +       +L+   ++LR +   A++EI  + REL+  Q+  
Sbjct: 856  HKMKRMDSLSDLTTISDIDPYCLQRDSLAEEYNELRSRFEKAVNEIRAMKRELKQSQNQ- 914

Query: 302  VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
             +  +  +++++ K+ + +L +    L L  +RI  L  +     +++   + +L +  +
Sbjct: 915  YDALELAQAALQQKLERCQL-EDGAQLQLMAARIQDLTLKYSSSERQVRALKQKLAKSER 973

Query: 362  SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
                 R + L+  +  EL    +                 E  S+  I    +S S E+ 
Sbjct: 974  R----RSLSLKGKEQLELKLSELQRETI------------ERKSVESISPPTESSSSESA 1017

Query: 422  ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
                   H++  +   E     +K+ + ++  +L    A + + R +  ++  ++G   L
Sbjct: 1018 SQSPLNAHLLQRLHSLEHVLLGSKERLEQSLTQLQQIRAGQRSRRSVSPMNDRKDGLRQL 1077

Query: 482  MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
             +A    + C+        +  V+ A  +    +    ++    +     + R+ + +  
Sbjct: 1078 ERAL--AETCVMVS-EQMELTCVQDACHKCCDLRQRVEKLSALQQQTETDLQRSEQLLEQ 1134

Query: 542  KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
            +     +    A +     E  +++L   +  +S E     E    L   +E    +   
Sbjct: 1135 R----ESDLAQALEKCASQEQEQELLLRQRNELSDELGKQQERCKRLEKRLE---LLERE 1187

Query: 602  DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERI 656
                   LRE        +   +E+  R R+ + +    TL E G      +  RI
Sbjct: 1188 HGKQLECLREVYHN--EHVNAADEQSFRKRYQLEIEQLRTLCEKGLSAMETSHRRI 1241


>gi|261333411|emb|CBH16406.1| kinesin, putative [Trypanosoma brucei gambiense DAL972]
          Length = 1132

 Score = 38.3 bits (87), Expect = 4.1,   Method: Composition-based stats.
 Identities = 75/536 (13%), Positives = 162/536 (30%), Gaps = 28/536 (5%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             +  +   L  +  +F+    + +   +  TL   +  L+  +  E +       E H+
Sbjct: 450 KTKERVRDLLMRNGCSFEE--AYGNLTREIETLRHRVATLQEEVNIEKQLSSLTRREKHA 507

Query: 208 YQKREDSSQE-KERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
               +    E KE +  Q+  GD  +  + S  + S  +S  +    D     E +    
Sbjct: 508 PNSNDGMDHEGKEPEQPQKVNGDAATNTENSLANASGANSAEDPVIRDHVVALERQCAIF 567

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVG 326
            ++    ++    +    D   E+ +EL          Q+  + +V      E L K+  
Sbjct: 568 QSVLRERERDLCSLESRGDVAEELRQELEQRVRQCDEAQQTLEEAVLEVGTSELLHKVTD 627

Query: 327 SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
           +    Q + D + EQ   ++K +     E  R        R   ++  +  E     +  
Sbjct: 628 TFRWMQEQFDSMSEQKQVMAKTVEAMRSEQKRTMAELLEARKHIVQTEKSCEELRQRLER 687

Query: 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
             +   G         +  + +    +           S  R           E      
Sbjct: 688 VTNENTGLTDQLEELNLKLLHEYAERVIREETVAWFKASGERAEECERLTTAFEDQRNLC 747

Query: 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW-VK 505
           +++++ L       ++        L  +Q+ +                +F +      V 
Sbjct: 748 DVLQSRLTSTEEELERGNKEHCALLQEMQKKDEAFRSIWILLTPQQKARFMSVGYGGDVV 807

Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565
           +    +   Q             + K  +    +    +R+   E++  +  +  E +  
Sbjct: 808 ENSGSASLHQGHENVQLRSQVRTLKK--QLEDEILCSRERDYRIEDLECENRLLQERLLH 865

Query: 566 VLKITKEPISLETPIGDEDT------SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
                K  ++L+    DE        +HL  +IE+ N         +  LRE        
Sbjct: 866 RENEYKSLVALDQDYMDEREQMEGQIAHLYTYIEEHN---MKQRTSERQLREVQIEW-EK 921

Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA-KAIRKLKHPSRSK 674
           L                N+   + E+  +    +E IR  EA K + K +H   S+
Sbjct: 922 LNE-----------EYCNSQREVAELTAKLNKAKEEIRIQEANKHVLKNRHQHESR 966


>gi|251854874|gb|ACT22555.1| liver stage antigen 3 [Plasmodium falciparum]
 gi|251854878|gb|ACT22557.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1481

 Score = 38.3 bits (87), Expect = 4.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 820  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 875

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 876  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 931

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 932  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 988

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 989  EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1047

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1048 ETDILEEKKEI 1058


>gi|158340452|ref|YP_001521808.1| hypothetical protein AM1_C0380 [Acaryochloris marina MBIC11017]
 gi|158310693|gb|ABW32307.1| hypothetical protein AM1_C0380 [Acaryochloris marina MBIC11017]
          Length = 752

 Score = 38.3 bits (87), Expect = 4.1,   Method: Composition-based stats.
 Identities = 47/311 (15%), Positives = 110/311 (35%), Gaps = 29/311 (9%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
           +  + N D+  +  +  ++     S D + +++  A     +T  ++  ++  D    E 
Sbjct: 417 VTTEANYDAFEQGAEVQNAPT---SQDQYAELLSKALDE-ELTYADIQEYISEDPQLQEY 472

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVR 122
            ++ V M         +         SE      S A  +     K  +S D    DP+R
Sbjct: 473 YDELVVMQGQEEGMSEEEARAVVRNSSEPERSEPSQAPEAEAPKAKTSESEDL---DPLR 529

Query: 123 MYLREMGSIELLSREGEIAIAKRIEAGRAMM------MASLCESPLTFQALIIWRDELND 176
           M   ++  +E L R  EI+  + I   + +       M     S +  +   + +D L +
Sbjct: 530 MINEDI--VEKLGRSIEISNLRVILNRQEIFRLDGDGMIDHNRSSVNLEQAQMIQDALKN 587

Query: 177 GT-------TLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGD 229
                      L     L    G      +    +    +       ++++ + +  + +
Sbjct: 588 PENFKGTLTIKLGTRTVLRIQNGIALPDRYNLAGKDLKAEADMPKDNQEQQGEAKSQKAE 647

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME-------DQLRPKVMC 282
            E+    ++D++++V+ P  +++N +   ++   +S +T S  E       D+L      
Sbjct: 648 TEAPKPKAQDEQAEVEEPKPDSQNQKSGDEKINVESKNTQSQNESPTAESQDELAGFTQE 707

Query: 283 ALDEIAEVYRE 293
             D I     +
Sbjct: 708 QKDTINRRREK 718


>gi|114578189|ref|XP_001156246.1| PREDICTED: dynactin 1 isoform 7 [Pan troglodytes]
          Length = 1143

 Score = 38.3 bits (87), Expect = 4.1,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 112 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 171

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 172 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 231

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 232 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 291

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 292 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 350

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 351 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 406

Query: 456 VISV 459
           V   
Sbjct: 407 VERQ 410


>gi|322823843|gb|EFZ29475.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 803

 Score = 38.3 bits (87), Expect = 4.2,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 81/245 (33%), Gaps = 20/245 (8%)

Query: 133 LLSREG-EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD--ELNDGTTLLREIID-LE 188
           LLSR+G E   A++I      +  +L E+P   Q  ++  D   + +     +E +D   
Sbjct: 523 LLSRDGMEEEFAEKIADLENRLKRALQENPTAAQVQLLEDDLWAVQEELRHAKEELDNFR 582

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKE------RDDVQETEGDIESAAKVSKDDRS 242
               P          E  S  + + ++ +++        +     G       +   ++S
Sbjct: 583 TANAPNYYTSSALRMEKESTPEAQLAAAQRQIEELEAALEEALEHGRQPQGQSLKAQEKS 642

Query: 243 KVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV 302
                 +  +   ++L+ +          + ++L  ++    +   ++  +   L+    
Sbjct: 643 NGKGGDDEMQGRIQSLNAELQRQRRDTEGIAERLNEELHAHKETRQKLADKEFELKVLWD 702

Query: 303 NGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
              + ++     +   ++           +  ++ L   L +  + +  +  +  RL   
Sbjct: 703 RQCEADREKESTRAALQE----------TERELERLRGHLREQKEELHASRPKEYRLESE 752

Query: 363 YGIKR 367
               R
Sbjct: 753 AKAPR 757


>gi|195114446|ref|XP_002001778.1| GI15125 [Drosophila mojavensis]
 gi|193912353|gb|EDW11220.1| GI15125 [Drosophila mojavensis]
          Length = 2881

 Score = 38.3 bits (87), Expect = 4.2,   Method: Composition-based stats.
 Identities = 30/170 (17%), Positives = 58/170 (34%), Gaps = 25/170 (14%)

Query: 166  ALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQE 225
             +I   DEL    +++++   ++A + PE         E    +   D   E+  ++   
Sbjct: 941  EIIDLDDELLTKESVIKKESPVKAEVKPEQSADKAEVEEASEEKATADKVDEENVEEKPA 1000

Query: 226  TEGDIESAAKVSKDDRSKVDSPP-------------------ENAENDERNLDEDEDDSA 266
             +   +  AK S +     +  P                   ++ E  E  +D D +  A
Sbjct: 1001 DKQTPQDEAKPSTETAEDAEELPAAKASEAEAETPAEAEAESKSKEQTEEKMDVDAEPIA 1060

Query: 267  HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
               +  E +            AE  +   SL+D A     ++KSS K + 
Sbjct: 1061 ENGNEKEAKTEDVAT------AEAEKPAESLKDEAAEKDDEKKSSDKQEE 1104


>gi|74180977|dbj|BAE27768.1| unnamed protein product [Mus musculus]
          Length = 2031

 Score = 38.3 bits (87), Expect = 4.2,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 85/233 (36%), Gaps = 12/233 (5%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +      L A
Sbjct: 1576 EMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAKLRLEVNLQA 1635

Query: 272  MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
            M+ Q    +    ++  E  ++L           +DE+     +    K L+  L  L  
Sbjct: 1636 MKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAMAARKKLEMDLKDLEA 1695

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +       +  ++QL  +  ++     EL          R+  L + +  E     +  
Sbjct: 1696 HIDTANKNREEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQAKENEKKLKSMEA 1751

Query: 387  AKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMVRK 436
                 + E       +  +     ++ +EI + S +  +++ E R + + + +
Sbjct: 1752 EMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARIAQ 1804


>gi|311257682|ref|XP_003127255.1| PREDICTED: pleckstrin homology-like domain family B member 3-like
           [Sus scrofa]
          Length = 522

 Score = 38.3 bits (87), Expect = 4.2,   Method: Composition-based stats.
 Identities = 42/298 (14%), Positives = 97/298 (32%), Gaps = 26/298 (8%)

Query: 79  DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD------PVRMYLREMGSIE 132
           D  D E  E + +      +   +    +  + S+  S+ D      PV+     +G+  
Sbjct: 37  DSGDQEGPEATVELPSGQGAEQQTEEEEEVGEGSSTESSRDAAEAPPPVQT----LGTPP 92

Query: 133 LLSREGE--IAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
             +  GE    +A+R+ A +   +  +       + L   R EL          I++E  
Sbjct: 93  APTPSGEGVRGVARRLRAQQLEALTRVALMEQRVKELQRQRKELR---------IEMEVE 143

Query: 191 IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
           +                 +++      ++ D  Q  +   E   +   ++R  V+   + 
Sbjct: 144 VALLRGELAGERVAARREEEQLRELLGQQVDAEQGGQEQREQEQRQLSEERDHVEELRQR 203

Query: 251 AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
               +  LD   +D    L     +++ ++  A     ++  +    +       KD   
Sbjct: 204 LREAQGQLDSQPEDQRERLLQGVQEMKEQLDVAQRAYEDLEFQQLERESRREEEDKDSPG 263

Query: 311 SVKCKVLKEKLVKLVGSLSLNQ-----SRIDLLVEQLYDISKRIMHNEGELLRLAQSY 363
           +       ++L   V    +        RI +L EQL  + +++      L +  +  
Sbjct: 264 TRALDPKVQELQGSVAQHKVRPGGAPQRRIQVLEEQLKSLGEQMAAESRGLSQKKEEA 321


>gi|312898324|ref|ZP_07757714.1| RNA polymerase sigma-H factor [Megasphaera micronuciformis F0359]
 gi|310620243|gb|EFQ03813.1| RNA polymerase sigma-H factor [Megasphaera micronuciformis F0359]
          Length = 216

 Score = 38.3 bits (87), Expect = 4.3,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 33/75 (44%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +++    LV S A  Y   G    DL+QEG IGL KA   F   +   FS +A   + + 
Sbjct: 32  LIQKYRNLVKSRAHAYFLVGADAEDLVQEGMIGLYKAIRDFKPHMHTIFSAFAEICITRQ 91

Query: 508 ITRSIADQSCTIRIP 522
           I  ++   +     P
Sbjct: 92  IISAVKTATRYKHAP 106


>gi|195504948|ref|XP_002099298.1| GE23444 [Drosophila yakuba]
 gi|194185399|gb|EDW99010.1| GE23444 [Drosophila yakuba]
          Length = 1238

 Score = 38.3 bits (87), Expect = 4.3,   Method: Composition-based stats.
 Identities = 45/288 (15%), Positives = 102/288 (35%), Gaps = 12/288 (4%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +    + VV+      +E   +    A   +     + +     +   +    +Y++   
Sbjct: 267 VRQQEVKVVEQRKEAADEILREKKKDAGKITRDLAKIDQEIREFETQMNKRRPLYIKAKE 326

Query: 130 SIE-----LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR-DELNDGTTLLRE 183
            +      L+S +  +  A+  +      +  L +     +AL     DE+ + +    +
Sbjct: 327 KVTHCKKKLVSLQKTLETAREADNAHQSDIRKLEKQLADVEALKKRFEDEIENESQRRGK 386

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
            +++E  +  E            +  + E  S  +E+   Q+T     +     ++   K
Sbjct: 387 SVNMEEGLVQEYDRLKQEAEATATQYRSELDSVNREQKSEQDTLDGETNRRASVEESFKK 446

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSA---MEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           +    E A      L +    S   L     ++D+LR  V  + ++IAE  REL  ++D 
Sbjct: 447 LTLQREEAVKRRDKLMDHIKSSQAALEEQNRIKDELRRDVGTSKEKIAEKQRELEDVRDQ 506

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
             +  K +K     +  K+++V+L           D ++       KR
Sbjct: 507 LGDA-KSDKHEDARRKKKQEVVELFK--KQVPGVYDRMINMCQPTHKR 551


>gi|12657350|emb|CAC27776.1| myosin heavy chain [Notothenia coriiceps]
          Length = 1929

 Score = 38.3 bits (87), Expect = 4.3,   Method: Composition-based stats.
 Identities = 41/287 (14%), Positives = 110/287 (38%), Gaps = 13/287 (4%)

Query: 132  ELL-SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
             LL S E E  +A   E     M   L  +    + L      L      L   I  E  
Sbjct: 832  PLLQSAETEKELANMKENYDK-MKTDLATALAKKKELEEKMVSLLQEKNDLSLQIASEGE 890

Query: 191  IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
               +++       +G    + +     +  +D +E   ++ +  +  +D+ S++    ++
Sbjct: 891  NLSDAEERCEGLIKGKIQMEAKLKETSERLEDEEEINAELTAKKRKLEDECSELKKDIDD 950

Query: 251  AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             E     +++++  + + +  + +++  +     + IA++ +E ++LQ++      D   
Sbjct: 951  LELTLAKVEKEKHATENKVKNLTEEMASQD----ESIAKLTKEKKALQESHQQTLDD--- 1003

Query: 311  SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                +  ++K+  L  + +  + ++D L   L    K  M  E    +L     + ++  
Sbjct: 1004 ---LQAEEDKVNTLTKAKTKLEQQVDDLEGSLEQEKKLRMDLERAKRKLEGDLKLAQESV 1060

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            ++    ++     +   KDF   +  + +  E     +++ +IK + 
Sbjct: 1061 MDLENDKQQSDEKIKK-KDFECSQLLSKIEDEQSLGAQLQKKIKELQ 1106


>gi|269925463|ref|YP_003322086.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789123|gb|ACZ41264.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 196

 Score = 38.3 bits (87), Expect = 4.3,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 64/182 (35%), Gaps = 15/182 (8%)

Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
           +  ++   A   C  R    M  +I +  + A  ++ +        + AK  +       
Sbjct: 17  RGDLSAMEALYDCYSRAVYSMILRIVQDQQVAEELTQETFF--RAWKQAKSFSNDRGKCA 74

Query: 565 KVLKITKEPISLETP---------IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR 615
             L      I+++           I  ED+S+    + D +   P +  +    R     
Sbjct: 75  SWLMSIAHNIAIDEIRRCKARPKSIRSEDSSNYLMNLPDSSLEDPDEIIMGGIRRNIVLE 134

Query: 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675
            L  L   + +VL M +  G+      ++VG+     + R+R     A++ L+     K 
Sbjct: 135 ALRELPENQRKVLEMSYFGGLTQSEIADKVGEPLGTIKTRMRL----ALQHLRRNLIEKG 190

Query: 676 LR 677
           ++
Sbjct: 191 IK 192


>gi|13259508|ref|NP_075408.1| dynactin subunit 1 isoform 2 [Homo sapiens]
 gi|5915905|gb|AAD55812.1| dynactin 1 p135 isoform [Homo sapiens]
          Length = 1144

 Score = 38.3 bits (87), Expect = 4.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 113 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 172

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 173 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 232

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 233 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 292

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 293 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 351

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 352 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 407

Query: 456 VISV 459
           V   
Sbjct: 408 VERQ 411


>gi|73980493|ref|XP_540222.2| PREDICTED: similar to dynactin 1 isoform 2 isoform 1 [Canis
           familiaris]
          Length = 1146

 Score = 38.3 bits (87), Expect = 4.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 112 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 171

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 172 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 231

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 232 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 291

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 292 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 350

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 351 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 406

Query: 456 VISV 459
           V   
Sbjct: 407 VERQ 410


>gi|326668417|ref|XP_683046.5| PREDICTED: myosin-10 [Danio rerio]
          Length = 1980

 Score = 38.3 bits (87), Expect = 4.4,   Method: Composition-based stats.
 Identities = 43/327 (13%), Positives = 99/327 (30%), Gaps = 12/327 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  I   +E  +      L E           RD                A    E+ 
Sbjct: 1444 DHQRQIVSNLEKKQKKFDQMLAEEKTISARYAEERDRAEAEAREKDTKALSMARALDEAL 1503

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + E       +DDV +   ++E + +  +    ++ +  E  E++ +
Sbjct: 1504 EAKEEFERLNKQLRAEMEDLISSKDDVGKNVHELEKSKRTLEQQVEEMRTQLEELEDELQ 1563

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SS 311
              ++ +      + AM+ Q    +    ++  E  R L           +DE+     + 
Sbjct: 1564 ATEDAKLRLEVNMQAMKAQFDRDLQARDEQNEEKKRALVKQVREMEAELEDERKQRALAV 1623

Query: 312  VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  +   +       D  ++QL  +  ++   + EL    +     RD   
Sbjct: 1624 AAKKKLEMDLKDVEAQIEAANKARDEAIKQLRKLQAQMKDYQREL----EEARTSRDEIF 1679

Query: 372  ERHQGRELDPHWVS---YAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFR 428
             + +  E     +              +           ++ +EI + +      + E R
Sbjct: 1680 TQSKENEKKLKSLEAEILQLQEDLASSERARRHAEQERDELADEISNSASGKAALLDEKR 1739

Query: 429  HIVSMVRKGECEASIAKKEMVEANLRL 455
             + + + + E E    +  M   N R 
Sbjct: 1740 RLEARIAQLEEELEEEQSNMELLNDRF 1766


>gi|218132995|ref|ZP_03461799.1| hypothetical protein BACPEC_00856 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991868|gb|EEC57872.1| hypothetical protein BACPEC_00856 [Bacteroides pectinophilus ATCC
           43243]
          Length = 306

 Score = 38.3 bits (87), Expect = 4.4,   Method: Composition-based stats.
 Identities = 31/150 (20%), Positives = 62/150 (41%), Gaps = 19/150 (12%)

Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG------ 493
           +   ++  ++      V+   K Y  +G+  +DLIQE N+ +M    + DW         
Sbjct: 146 KDVESRGVIINNYFLQVVEWVKAYAGKGVAMMDLIQEANVIVMDELGRRDWMKRLDAFDV 205

Query: 494 -------------YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
                         +   Y +  VK+ I + I +Q+        +  K++ V   A    
Sbjct: 206 MDSDDINAWTDLSERLDAYLIDRVKEGIGKLIEEQTDEKMAGNKILAKVNAVNDAAEAAH 265

Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
            +  R+ T EE+A+ + +P E V + L+++
Sbjct: 266 KEYGRKVTVEELAQFMHVPAEDVSEALRLS 295


>gi|116206612|ref|XP_001229115.1| hypothetical protein CHGG_02599 [Chaetomium globosum CBS 148.51]
 gi|88183196|gb|EAQ90664.1| hypothetical protein CHGG_02599 [Chaetomium globosum CBS 148.51]
          Length = 1219

 Score = 38.3 bits (87), Expect = 4.4,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 72/220 (32%), Gaps = 9/220 (4%)

Query: 146  IEAGRAMMMASLCE-SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFH--- 201
            ++     + AS  E S     A +  + +  +  + L+EI +LE  +   S   F     
Sbjct: 864  LQESVEEVKASHAEKSKKVADAKLDLQKKTKEIESRLKEISNLEGTVQKNSAQKFALLRR 923

Query: 202  -GTEGHSYQKREDSSQEKERDDV--QETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
               E       E S      +DV  ++    ++   +  +D+  +        E D   L
Sbjct: 924  CKLEQIQLPMSEGSLDNIPNEDVLLRKDHDAMDVDGEADEDEVLEAAMDDYGIEIDFDGL 983

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
            DED  +    L          +   L+++    R +  L+      +  E+     +   
Sbjct: 984  DEDLKNPDDDLEDKLQDKITSLTTELEKLNPNMRAMERLESVKSRLESTEQDFEDSRAAL 1043

Query: 319  EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
                     +   + R DL       I ++I H   +L R
Sbjct: 1044 RSARDAFTQVK--EKRFDLFNRAFAHIQEQITHVYKDLTR 1081


>gi|326472023|gb|EGD96032.1| hypothetical protein TESG_03493 [Trichophyton tonsurans CBS 112818]
          Length = 1377

 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 43/293 (14%), Positives = 97/293 (33%), Gaps = 15/293 (5%)

Query: 80   GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSRE 137
             D L + + + D L  A     S V   +++  A R     D VR+ +          + 
Sbjct: 757  EDTLVETQKARDDLLRARDELESEVDHIQKEIEAAREAHERDIVRLRMEA-------EKS 809

Query: 138  GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR-EIIDLEACIGPESK 196
             E A+A++ E    +      E        +  R++   G    + E +D          
Sbjct: 810  EEKALAEQKERLEDLFQEIKNEDNRLAAEHLKAREDELLGQLAAKQEELDANDAALKSKV 869

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                   E    +K E + +  E + ++E   + ++  +  + +     +  E    D  
Sbjct: 870  EELRVTQEELDEKKAELAEKFSELEALKEELVNTKNGLEAKQQECESRQNELELTRKDLE 929

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
                  ++    L    D     V    + +A +  E R+ ++     ++  ++ +  K 
Sbjct: 930  ETKRHHEEELAALRDALDIQTNNVKEIKERLANMVLEHRTQEETWQKAREGYEAQLSEKA 989

Query: 317  LKEKLVKLVGSLS-----LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
             + KL      +        + R+  +VE++      +  +   L +   S G
Sbjct: 990  EELKLSNEEKEVLEREGLAKEERLQSIVEEMRQTHNNLNKDRERLKKTLHSLG 1042


>gi|295706310|ref|YP_003599385.1| chromosome segregation protein SMC [Bacillus megaterium DSM 319]
 gi|294803969|gb|ADF41035.1| chromosome segregation protein SMC [Bacillus megaterium DSM 319]
          Length = 1186

 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 39/285 (13%), Positives = 99/285 (34%), Gaps = 14/285 (4%)

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +N+    L++I+DL    G   +                 S + ++  +        ++ 
Sbjct: 114 INNQPCRLKDIVDLFMDSGLGREAFSIISQGKVEEVLSSKSDERRKIFEEAAGVLKYKTR 173

Query: 234 AKVSK-------DDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
            + ++       ++ ++V       E     L      +   L   E+     V   + E
Sbjct: 174 KRKAELRLLETQENLNRVVDILHEIEGQLEPLQIQSSIAKDYLQKKEELEHIDVAVTVFE 233

Query: 287 IAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           + +++++   L+      ++ E+S       +E     + +L L+  +ID   EQL  + 
Sbjct: 234 VEDLHQKWGKLKAEMAQHEQLEESLATNIRTRE---GEIQTLRLHIQQID---EQLDSLH 287

Query: 347 KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSI 406
           K++++   E+ +L     + ++      Q +E     V       + E       E   +
Sbjct: 288 KKLLYVSEEVEKLEGKKEVLKERKKNAFQNKEQLERLVKEYTHKHQ-ELSKAKDSEGKDL 346

Query: 407 LKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEA 451
            + + E++ I ++       FR     + +   +      E+  A
Sbjct: 347 EQSQKEVQEIRLKLTEQEQLFRQYSENLEEKLEQMKSEYFELANA 391


>gi|251854898|gb|ACT22567.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1586

 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 924  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 979

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 980  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 1035

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 1036 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1092

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1093 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1151

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1152 ETDILEEKKEI 1162


>gi|118385159|ref|XP_001025717.1| hypothetical protein TTHERM_00929540 [Tetrahymena thermophila]
 gi|89307484|gb|EAS05472.1| hypothetical protein TTHERM_00929540 [Tetrahymena thermophila SB210]
          Length = 1316

 Score = 38.3 bits (87), Expect = 4.5,   Method: Composition-based stats.
 Identities = 22/165 (13%), Positives = 55/165 (33%), Gaps = 6/165 (3%)

Query: 253  NDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS-- 310
             +    +  ++D        ++  R       +EI  +  +    +       K  KS  
Sbjct: 912  EERSQRERVQNDIDKMQKDNDEIYRQIEQETKEEIENLNNKNLEHEAEVKERHKKAKSDA 971

Query: 311  ---SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
               + K    K+   +      L+Q ++  L E+   + K I   +  +    ++ G + 
Sbjct: 972  AITTKKIDQKKKDSEQYEEQFRLHQKQLKKLREENETLLKEIQQQKEIIQERDKTIGKQE 1031

Query: 368  DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
                ++ +  + +     +  D    E K  +    D I +++ E
Sbjct: 1032 KQIYKQKKKSQ-NLEKFKFVLDHKIKELKRDIGPREDEIARMKEE 1075


>gi|303233547|ref|ZP_07320205.1| copper amine oxidase N-terminal domain protein [Finegoldia magna
           BVS033A4]
 gi|302495291|gb|EFL55039.1| copper amine oxidase N-terminal domain protein [Finegoldia magna
           BVS033A4]
          Length = 784

 Score = 38.3 bits (87), Expect = 4.6,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 88/244 (36%), Gaps = 12/244 (4%)

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E  +    +    K       + +  ++ + S  ++ ++ ++  + + E   +     
Sbjct: 292 IDEKDNKIDDLTKNIKDLENQIKDLNDKKQEDQSKIDELKEKLESCKDNGEKLKQEKAKL 351

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL-QD 299
             ++          ++ +++ ++ +   L A   QL+ ++    DE A++  +  S   +
Sbjct: 352 EEEIRDKDNKIAQLDKEIEDIKNSNNDELIAEITQLKDELKSLQDENAKLKEDYSSTKWE 411

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
                +K +K+  K K ++EKL  L G L+     I+    ++ D+ K +   + ++  L
Sbjct: 412 LEAEKEKTDKNENKIKEMQEKLESLEGELAKKTKEIEDKDNRIKDLEKALDEKDAKIKDL 471

Query: 360 AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                             E          +  +    +      ++  ++  +IK +  +
Sbjct: 472 ESKKKET-----------ENSKSECCKKIEELQKAIDSLKESSENTKKELEEKIKRLEEK 520

Query: 420 TGIS 423
              S
Sbjct: 521 QKAS 524


>gi|167749750|ref|ZP_02421877.1| hypothetical protein EUBSIR_00717 [Eubacterium siraeum DSM 15702]
 gi|167657233|gb|EDS01363.1| hypothetical protein EUBSIR_00717 [Eubacterium siraeum DSM 15702]
          Length = 1114

 Score = 38.3 bits (87), Expect = 4.6,   Method: Composition-based stats.
 Identities = 41/322 (12%), Positives = 111/322 (34%), Gaps = 12/322 (3%)

Query: 4   GKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQM 63
             K   +   + E +D     + +D + ++ +    +      EE+       E +++  
Sbjct: 385 AVKAFEEIAEQEETADIETESEQNDTATEEPVSEPVEDAVKAFEEIAE----QEETADSK 440

Query: 64  EDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRM 123
            +  +  ++  +     + +ED   + + +      ++S    ++   +A+ +  +PV  
Sbjct: 441 TEIDSEQNDTAVEEAASEPVEDAVKALEEIAEQEETADSEAESEQNDIAAEEAVSEPVED 500

Query: 124 YLR---EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            ++   E+   E  + + E    +   A    +   + ++   F+ +    +  +  T +
Sbjct: 501 AVKAFEEIAEQE-ETADSETESKQNDTAAEEPISEPVEDAVKAFEEIAEQEETADSETEI 559

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
             E  D                      ++ E +  E   DD Q      E+ ++  +D 
Sbjct: 560 DSEQNDTATEEAASEPVEDAVKAFEEIAEQEETADSEAVIDDEQNDTATEEAVSEPVEDA 619

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR----ELRS 296
               +   E  E  +   + D + +         +     + A +EIAE       E +S
Sbjct: 620 VKAFEEIAEQEETADSETEIDSEQNDTATEEAVSEPVEDAVKAFEEIAEQEETADSEEKS 679

Query: 297 LQDNAVNGQKDEKSSVKCKVLK 318
           L++      ++E +S     ++
Sbjct: 680 LEEQFHAIMEEETASEPVSSIR 701


>gi|322491824|emb|CBZ27097.1| hypothetical protein, unknown function [Leishmania mexicana
            MHOM/GT/2001/U1103]
          Length = 3925

 Score = 38.3 bits (87), Expect = 4.6,   Method: Composition-based stats.
 Identities = 59/542 (10%), Positives = 153/542 (28%), Gaps = 24/542 (4%)

Query: 141  AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
             + +++            +       +   R++L +G    R++         +      
Sbjct: 2559 DLREQLREAEERARDVEAQQSDRDAEMADLREQLREGEERARDV----EAQQSDRDAEMA 2614

Query: 201  HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
               E     +      E ++ D      D+    + +++    V++   + + +  +L E
Sbjct: 2615 DLREQLREAEERARDVEAQQSDRDAEMADLREQLREAEERARDVEAQQSDRDAEMADLRE 2674

Query: 261  DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
               ++      +E Q   +     D   ++       +D        +      +    +
Sbjct: 2675 QLREAEERARDVEAQQSDRDAEVADLREQLREAEERARDVEAQQSDRDAEMADLREQLRE 2734

Query: 321  LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
              +    +   QS  D  V  L +  +       ++        ++     E+ +  E  
Sbjct: 2735 AEERARDVEAQQSDRDAEVADLREQLREAEERARDVEAQQSDRDVEMADLREQLREGEER 2794

Query: 381  PHWVSYAKDFPEGEWKNF-----VACEVDSILKIRNEIKSISVETGISISEFRHIVSMVR 435
               V   +   + E  +       A E    ++ +   +   V             +   
Sbjct: 2795 ARDVEAQQSDRDAEMADLREQLREAEERAMDVEAQQSDRDAEVADLREQLREAEERARDV 2854

Query: 436  KGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA----------- 484
            + +     A+ E V+  L   +  A   +         ++E  + + +            
Sbjct: 2855 EAQQSDRDAEIERVKELLSGAMREAAASSEICTALEKQVEEAALEIRELREQLAVTQVRR 2914

Query: 485  ----AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
                AE  +     +    ++   ++A+       S        +R+++ +    AR + 
Sbjct: 2915 EALDAECGELEQQLRDVQSSVLERREAVEDLSISHSAKDAEVADLREQLREAEERARDVE 2974

Query: 541  NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
             +           ++     E   + ++  +     E     E      +   D  A   
Sbjct: 2975 AQQSDRDAEMADLREQLREAEERARDVEAQQSDRDAEMADLREQLREAEERARDVEAQQS 3034

Query: 601  LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
               A  A+LRE             E   R       + D  + ++ +Q     ER R +E
Sbjct: 3035 DRDAEMADLREQLREAAEGQLREAEERARDVEAQQSDRDAEMADLREQLREGEERARDVE 3094

Query: 661  AK 662
            A+
Sbjct: 3095 AQ 3096


>gi|251823950|ref|NP_001156538.1| myosin-13 [Oryctolagus cuniculus]
 gi|12003423|gb|AAG43570.1|AF212147_1 skeletal muscle myosin heavy chain MyHC-EO/IIL [Oryctolagus
            cuniculus]
 gi|12003425|gb|AAG43571.1|AF212148_1 skeletal muscle myosin heavy chain MyHC-EO/IIL [Oryctolagus
            cuniculus]
 gi|12003427|gb|AAG43572.1|AF212149_1 skeletal muscle myosin heavy chain MyHC-EO/IIL [Oryctolagus
            cuniculus]
          Length = 1938

 Score = 38.3 bits (87), Expect = 4.7,   Method: Composition-based stats.
 Identities = 63/434 (14%), Positives = 155/434 (35%), Gaps = 19/434 (4%)

Query: 12   DSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIE--ELNAFLPPDEVSSEQMEDTVAM 69
            ++++   + + + +   ++ K + ++ + +  V  E  +L A L   E S E  E  +  
Sbjct: 1505 ENKNLQEEIADLTEQMAETGKNLQEVEKTKKQVEQEKSDLQAALEEAEGSLEHEESKILR 1564

Query: 70   LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
            +      V    D +  E  E+   L  ++  ++  LQ   D+  RS +D +R+  +  G
Sbjct: 1565 VQLELNQVKSELDRKLTEKDEEMEQLKRNSQRAAEALQSVLDAEIRSRNDALRLKKKMEG 1624

Query: 130  SIELLSREGEIAIAK------RIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183
             +     E EI +          +     +   L +S L     +   ++L +   ++  
Sbjct: 1625 DLN----EMEIQLGHASRQVAETQKHLRTVQGQLKDSQLHLDDALRSNEDLKEQLAMVER 1680

Query: 184  IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
               L      E K             ++E          +      + +  +  + D ++
Sbjct: 1681 RNGLLQEELEEMKVALEQTERTRRLSEQELLDASDRVQLLHSQNTSLINTKRKLEADLAQ 1740

Query: 244  VDSPPENAENDERNLDEDEDDSAHTLSAMEDQLR--PKVMCALDEIAEVYRELRSLQDNA 301
              +  EN+  + RN +E    +    + M ++L+        L+ + +   +        
Sbjct: 1741 CQAEVENSLQESRNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNLEQTVK----D 1796

Query: 302  VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
            +  + DE   +  K  K+++ KL   +   ++ +D   ++  +  K     E ++  +  
Sbjct: 1797 LQHRLDEAEQLALKGGKKQIQKLENRVRELETELDAEQKRGAEALKGAHKYERKVKEMTY 1856

Query: 362  SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
                 R  FL      +     V   K   E E +     ++    ++++E++       
Sbjct: 1857 QAEEDRKNFLRLQDLVDKLQAKVKSYKRQAE-EAEEQANTQLSRCRRVQHELEEAEERAD 1915

Query: 422  ISISEFRHIVSMVR 435
            I+ S+   + +  R
Sbjct: 1916 IAESQVNKLRAKSR 1929


>gi|327286849|ref|XP_003228142.1| PREDICTED: dynactin subunit 1-like [Anolis carolinensis]
          Length = 1255

 Score = 38.3 bits (87), Expect = 4.7,   Method: Composition-based stats.
 Identities = 45/344 (13%), Positives = 112/344 (32%), Gaps = 25/344 (7%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E ++   K         +  L +  +  + +  W+ ++ +    L++ +        E+ 
Sbjct: 209 EEKLETLKMKRNEDKAKLKELEKYKIQLEQVQEWKSKMQEQQADLQKRLKEAKKEAKEAM 268

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                  E  +           +++  +E    ++      K+    +    E  +++  
Sbjct: 269 EAKERYMEEMADTADAIEMATLDKEMAEERAESLQQEVDSLKEKVEYLTMDLEILKHEIE 328

Query: 257 NLDEDEDDSAHTLSAMEDQ---LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               D   S++ +  +E+Q   L+  ++   D  A   +E   LQ +       EK + +
Sbjct: 329 EKGSDGAASSYHVKQLEEQNARLKEALVRMRDLSASEKQEHVKLQKHM------EKKNTE 382

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVF 370
            + L+++  KL   L   +  +D L EQ+       + +       L L +     R+  
Sbjct: 383 LESLRQQKEKLQEELKQAERTVDELKEQVDAALGAEEMVETLTERNLDLEEKVRELRETV 442

Query: 371 LERHQGRELDPHWVSYAKDFP-------------EGEWKNFVACEVDSILKIRNEIKSIS 417
            +     E++      A++                 E +  V    +++   +  IK   
Sbjct: 443 GDLEAMNEMNDELQENARETELELREQLDMATARVREAEKRVEAAQETVADYQQTIKKYR 502

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             T       R ++S       +      EM +  ++   + A 
Sbjct: 503 ELTAHLQDVNRELMSQQEASAEKQQQPPPEMFDFKIKFAETKAH 546


>gi|268529498|ref|XP_002629875.1| C. briggsae CBR-LET-75 protein [Caenorhabditis briggsae]
          Length = 1938

 Score = 38.3 bits (87), Expect = 4.7,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 89/255 (34%), Gaps = 14/255 (5%)

Query: 204  EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
            E     +   ++ E++   +     ++E +   + D  S+ +    + E   R   ++ +
Sbjct: 896  EALELTQGGSAAIEEKLTRLNSARQEVEKSLNDANDRLSEHEEKNADLEKQRRKAQQEVE 955

Query: 264  DSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ----KDEKSSVKCKVLKE 319
            +   ++ A++  L       L+E A    ++RSLQD   +      K  K     +    
Sbjct: 956  NLKKSIEAVDGNLSRS----LEEKAAKENQIRSLQDEMNSQDETIGKINKEKKHLEENNR 1011

Query: 320  KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            +L+  + +    Q++ + L  +L      +        R+       +       +G + 
Sbjct: 1012 QLIDDLQAEEAKQAQANRLRGKLEQTLDEMEEAVEREKRIRAETEKSKRKVEGELKGAQE 1071

Query: 380  DPHWVSYAKDFPEGEWK------NFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
                ++  K   +   K      + +   ++    + N +   S E    I E    +  
Sbjct: 1072 SIDELTAIKLEADASLKKKEADIHALGVRIEDEQALANRLTRQSKENAQRIIEIEDELEH 1131

Query: 434  VRKGECEASIAKKEM 448
             R+   +A  A+ E+
Sbjct: 1132 ERQSRSKADRARAEL 1146


>gi|307184247|gb|EFN70720.1| Kinesin-like protein KIF21B [Camponotus floridanus]
          Length = 1490

 Score = 38.3 bits (87), Expect = 4.7,   Method: Composition-based stats.
 Identities = 52/375 (13%), Positives = 112/375 (29%), Gaps = 44/375 (11%)

Query: 99  ASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLC 158
           A  ++          D    + V+ Y++E+                        + A L 
Sbjct: 428 AEKAAGHWVAATSGGDEQVTNLVQGYVQEI----------------------EELRARLL 465

Query: 159 ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEK 218
           E+            +L      +           P     F   +       + D  +E 
Sbjct: 466 EAE-------AMYQQLKKRQMQVS-------AANPYGDSSFHSDSASVLIDAKRDVEKEI 511

Query: 219 ERDDVQETEGDIES--AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
           E     + +    S  A     +     ++    +E+D  +  + ED+    +    + L
Sbjct: 512 ETLKALKEQYSHSSITAKSDEGEIEDTENAQDSVSEDDSDDDSDQEDEEEAAMGRELEAL 571

Query: 277 RPKVMCALDEIAEVYRELRSLQD-NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRI 335
              +      I E+    R LQ        K  +   + +  +E+  K++ SL    +  
Sbjct: 572 TSDIDVKQRLIQELELSQRRLQTMKQHYEDKLAQLQTRIRNTQEERDKVLQSLQQQPTPP 631

Query: 336 DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
              V++L D  ++ + N  + +RL QS   +    L+     E     +       +   
Sbjct: 632 TEKVKKLRDEYEKKLSNMQKEMRLLQSAKKEHARLLKNQSQNENRLRGLRNELSEMKRAK 691

Query: 396 KNFVACEVDSILKIR-NEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454
              +    +   + + NE++       +     RH    V +        K+ ++     
Sbjct: 692 VKLLNKMREEAQRHKENELRRNREIAQLRKESRRHAN--VIRTLEADKRMKEVVLRRKQE 749

Query: 455 LVISVAKKYTNRGLQ 469
            V   A +  +RGL 
Sbjct: 750 EV--TALRKRDRGLS 762


>gi|302758734|ref|XP_002962790.1| hypothetical protein SELMODRAFT_438117 [Selaginella moellendorffii]
 gi|300169651|gb|EFJ36253.1| hypothetical protein SELMODRAFT_438117 [Selaginella moellendorffii]
          Length = 927

 Score = 38.3 bits (87), Expect = 4.7,   Method: Composition-based stats.
 Identities = 48/355 (13%), Positives = 117/355 (32%), Gaps = 12/355 (3%)

Query: 204 EGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDED 263
           E  + + +   +++K+R+D +        A    +++  +V+      E +E  L E ED
Sbjct: 26  ERDAAEFQARIAKKKQRNDKEIVAYGDNPAPSEEEEEVKQVNVVVRKNERNELLLPEIED 85

Query: 264 DSAHTLSAM-EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLV 322
             ++ L    E       +  +DEI ++   L+ LQ+       +       K  ++ + 
Sbjct: 86  LISNGLDIFPEPDDGKGGIKPVDEIGDLKARLQQLQEKERKLNAELLDYYGLKEREKGVK 145

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG------IKRDVFLERH-Q 375
           +L   L +   +I  L   +  +         ++   ++S G      +K     ++   
Sbjct: 146 ELEAQLLVKDEQITSLTASIRKLEDEKKKMADDIKAASKSRGELSEARMKIKDLQKKLSS 205

Query: 376 GRELDPHWVSYAKDFPEGEWKNFVACEVDSILK---IRNEIKSISVETGISISEFRHIVS 432
           G   +    +      + + +   A E  S+ K   I  +++++  E  I + E R    
Sbjct: 206 GTGTNAAQNAAQITMLKQQLETLKAKEQSSMKKNFEIEKKMQTL-KELEIEVVELRRTCR 264

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492
            ++  + + ++           L      +   R      +++  N  LM+  E      
Sbjct: 265 ELQHQKRDLTVKLSAAEAQVTSLSSVTETELVARANNESQILRHANDDLMRQVEGLQNNR 324

Query: 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREP 547
             +           A  R                D    +   ++  + ++  E 
Sbjct: 325 FSEVEELVYLRWVNACLRYELRNFKAADGKFTALDLNKSLSPRSQEKAKQLMLEY 379


>gi|194909986|ref|XP_001982050.1| GG11251 [Drosophila erecta]
 gi|190656688|gb|EDV53920.1| GG11251 [Drosophila erecta]
          Length = 1238

 Score = 38.3 bits (87), Expect = 4.8,   Method: Composition-based stats.
 Identities = 45/288 (15%), Positives = 102/288 (35%), Gaps = 12/288 (4%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           +    + VV+      +E   +    A   +     + +     +   +    +Y++   
Sbjct: 267 VRQQEVKVVEQRKEAADEILREKKKDAGKITRDLAKIDQEIREFETQMNKRRPLYIKAKE 326

Query: 130 SIE-----LLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR-DELNDGTTLLRE 183
            +      L+S +  +  A+  +      +  L +     +AL     DE+ + +    +
Sbjct: 327 KVTHCKKKLVSLQKTLETAREADNAHQSDIRKLEKQLADVEALKKRFEDEIENESQRRGK 386

Query: 184 IIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSK 243
            +++E  +  E            +  + E  S  +E+   Q+T     +     ++   K
Sbjct: 387 SVNMEEGLVQEYDRLKQEAEATATQYRSELDSVNREQKSEQDTLDGETNRRASVEESFKK 446

Query: 244 VDSPPENAENDERNLDEDEDDSAHTLSA---MEDQLRPKVMCALDEIAEVYRELRSLQDN 300
           +    E A      L +    S   L     ++D+LR  V  + ++IAE  REL  ++D 
Sbjct: 447 LTLQREEAVKRRDKLMDHIKSSQAALEEQNRIKDELRRDVGTSKEKIAEKQRELEDVRDQ 506

Query: 301 AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
             +  K +K     +  K+++V+L           D ++       KR
Sbjct: 507 LGDA-KSDKHEDARRKKKQEVVELFK--KQVPGVYDRMINMCQPTHKR 551


>gi|160425231|ref|NP_001104237.1| myosin-9 [Canis lupus familiaris]
 gi|122135145|sp|Q258K2|MYH9_CANFA RecName: Full=Myosin-9; AltName: Full=Myosin heavy chain 9; AltName:
            Full=Myosin heavy chain, non-muscle IIa; AltName:
            Full=Non-muscle myosin heavy chain IIa; Short=NMMHC II-a;
            Short=NMMHC-IIA
 gi|89994139|emb|CAJ31056.1| myosin, heavy polypeptide 9, non-muscle [Canis lupus familiaris]
          Length = 1960

 Score = 38.3 bits (87), Expect = 4.8,   Method: Composition-based stats.
 Identities = 42/302 (13%), Positives = 98/302 (32%), Gaps = 12/302 (3%)

Query: 143  AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
            A  +E  +      L E           RD                A    E+       
Sbjct: 1436 ASNLEKKQKKFDQLLAEEKTISAKYAEERDRAEAEAREKETKALSLARALEEAMEQKAEL 1495

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +
Sbjct: 1496 ERLNKQFRTEMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAK 1555

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVL 317
                  L AM+ Q    +    ++  E  ++L           +DEK     +    K L
Sbjct: 1556 LRLEVNLQAMKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDEKKQRSMAVAARKKL 1615

Query: 318  KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            +  L  L   +       D  ++QL  +  ++     EL          R+  L + +  
Sbjct: 1616 EMDLKDLEAHIDSANKNRDEAIKQLRKLQAQMKDCVREL----DDTRASREEILAQAKEN 1671

Query: 378  ELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMV 434
            E     +       + E       +  +     ++ +EI + S +  +++ E R + + +
Sbjct: 1672 EKKMKSMEAEMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARI 1731

Query: 435  RK 436
             +
Sbjct: 1732 AQ 1733


>gi|12667788|ref|NP_002464.1| myosin-9 [Homo sapiens]
 gi|6166599|sp|P35579|MYH9_HUMAN RecName: Full=Myosin-9; AltName: Full=Cellular myosin heavy chain,
            type A; AltName: Full=Myosin heavy chain 9; AltName:
            Full=Myosin heavy chain, non-muscle IIa; AltName:
            Full=Non-muscle myosin heavy chain A; Short=NMMHC-A;
            AltName: Full=Non-muscle myosin heavy chain IIa;
            Short=NMMHC II-a; Short=NMMHC-IIA
 gi|3169000|emb|CAB05105.1| myosin, heavy chain 9, non-muscle [Homo sapiens]
 gi|47678583|emb|CAG30412.1| MYH9 [Homo sapiens]
 gi|53791227|dbj|BAD52439.1| non-muscle myosin heavy polypeptide 9 [Homo sapiens]
 gi|109451392|emb|CAK54557.1| MYH9 [synthetic construct]
 gi|109451988|emb|CAK54856.1| MYH9 [synthetic construct]
 gi|119580500|gb|EAW60096.1| myosin, heavy polypeptide 9, non-muscle, isoform CRA_a [Homo sapiens]
 gi|119580502|gb|EAW60098.1| myosin, heavy polypeptide 9, non-muscle, isoform CRA_a [Homo sapiens]
 gi|152012654|gb|AAI50170.1| Myosin, heavy chain 9, non-muscle [synthetic construct]
 gi|152012993|gb|AAI50171.1| Myosin, heavy chain 9, non-muscle [synthetic construct]
 gi|166788562|dbj|BAG06729.1| MYH9 variant protein [Homo sapiens]
 gi|168270842|dbj|BAG10214.1| myosin-9 [synthetic construct]
          Length = 1960

 Score = 38.3 bits (87), Expect = 4.8,   Method: Composition-based stats.
 Identities = 41/306 (13%), Positives = 99/306 (32%), Gaps = 12/306 (3%)

Query: 139  EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            +   A  +E  +      L E           RD                A    E+   
Sbjct: 1432 QRQSACNLEKKQKKFDQLLAEEKTISAKYAEERDRAEAEAREKETKALSLARALEEAMEQ 1491

Query: 199  FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                   +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +  
Sbjct: 1492 KAELERLNKQFRTEMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQAT 1551

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVK 313
            ++ +      L AM+ Q    +    ++  E  ++L           +DE+     +   
Sbjct: 1552 EDAKLRLEVNLQAMKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAVAA 1611

Query: 314  CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             K L+  L  L   +       D  ++QL  +  ++     EL          R+  L +
Sbjct: 1612 RKKLEMDLKDLEAHIDSANKNRDEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQ 1667

Query: 374  HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHI 430
             +  E     +       + E       +  +     ++ +EI + S +  +++ E R +
Sbjct: 1668 AKENEKKLKSMEAEMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRL 1727

Query: 431  VSMVRK 436
             + + +
Sbjct: 1728 EARIAQ 1733


>gi|332231117|ref|XP_003264744.1| PREDICTED: myosin-9 isoform 1 [Nomascus leucogenys]
          Length = 1929

 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 41/306 (13%), Positives = 99/306 (32%), Gaps = 12/306 (3%)

Query: 139  EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            +   A  +E  +      L E           RD                A    E+   
Sbjct: 1439 QRQSACNLEKKQKKFDQLLAEEKTISAKYAEERDRAEAEAREKETKALSLARALEEAMEQ 1498

Query: 199  FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                   +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +  
Sbjct: 1499 KAELERLNKQFRTEMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQAT 1558

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVK 313
            ++ +      L AM+ Q    +    ++  E  ++L           +DE+     +   
Sbjct: 1559 EDAKLRLEVNLQAMKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAVAA 1618

Query: 314  CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             K L+  L  L   +       D  ++QL  +  ++     EL          R+  L +
Sbjct: 1619 RKKLEMDLKDLEAHIDSANKNRDEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQ 1674

Query: 374  HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHI 430
             +  E     +       + E       +  +     ++ +EI + S +  +++ E R +
Sbjct: 1675 AKENEKKLKSMEAEMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRL 1734

Query: 431  VSMVRK 436
             + + +
Sbjct: 1735 EARIAQ 1740


>gi|254495860|ref|ZP_05108771.1| chromosome segregation SMC protein [Legionella drancourtii LLAP12]
 gi|254354926|gb|EET13550.1| chromosome segregation SMC protein [Legionella drancourtii LLAP12]
          Length = 1164

 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 27/200 (13%), Positives = 69/200 (34%), Gaps = 23/200 (11%)

Query: 263 DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVN-GQKDEKSSVKCKVLKEKL 321
           +  A TL+A  ++L+  +    +E   +   L  LQ    +   + E+ + + +   + L
Sbjct: 727 EKLATTLAAECEELQMILEETAEEYLMIKERLLDLQSQCSDYEFQLEQCTQEKQECLDAL 786

Query: 322 VKLVGSLSLN--------------QSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
                 +                 +++I  LVE++    +R+   +  L  LA      +
Sbjct: 787 AGHNKQVETTRMALHRAELEDDREKNKIQQLVERINREQERLDILQERLESLAMQCLQTK 846

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
           +       G +L+           E E +  +    + + ++R E++ +         E 
Sbjct: 847 E------PGAQLNEQLDRQLLRHAEVELQ--LTMSREQVSQLRMELEDLEKHILNCDFEV 898

Query: 428 RHIVSMVRKGECEASIAKKE 447
           + I  ++ +   +       
Sbjct: 899 KRIQELIGQARMQEQALAVR 918


>gi|115453951|ref|NP_001050576.1| Os03g0587200 [Oryza sativa Japonica Group]
 gi|54633392|gb|AAV35794.1| kinesin heavy chain, putative [Oryza sativa Japonica Group]
 gi|108709567|gb|ABF97362.1| kinesin heavy chain, putative, expressed [Oryza sativa Japonica
            Group]
 gi|113549047|dbj|BAF12490.1| Os03g0587200 [Oryza sativa Japonica Group]
 gi|218193225|gb|EEC75652.1| hypothetical protein OsI_12410 [Oryza sativa Indica Group]
          Length = 1129

 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 73/197 (37%), Gaps = 7/197 (3%)

Query: 174  LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
            +ND   LL EI  L+  +  ++          H      D   E +R+  ++        
Sbjct: 835  VNDREELLSEIQRLKDQLKQQAGESTNVSLLEHLRNGSTDQEYELDRER-EKWMESESKW 893

Query: 234  AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL--RPKVMCALDEIAEVY 291
              ++++ R  ++S    AE  E  L  ++  +A    A++  +    +++    E+ E+Y
Sbjct: 894  ICLTEELRVDLESNRMLAEKTEMELSNEKKCTAELDDALQRAIYGHARIIEHYAELQEMY 953

Query: 292  RELRSLQDNAVNGQKDEKSSVKCKVLKE--KLVKLVGSLSLNQSRIDLLVE--QLYDISK 347
             +L       + G  + K +      K          +  L+  RID   E  QL + ++
Sbjct: 954  NDLLERHRRVMEGISEVKRAAAKAGRKGCGTAFAAALAAELSTVRIDREKERAQLKEQNR 1013

Query: 348  RIMHNEGELLRLAQSYG 364
            R+     +      + G
Sbjct: 1014 RLRIQLRDTAEAVHAAG 1030


>gi|291222160|ref|XP_002731086.1| PREDICTED: laminin B2-like [Saccoglossus kowalevskii]
          Length = 1629

 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 75/588 (12%), Positives = 176/588 (29%), Gaps = 70/588 (11%)

Query: 147  EAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL-----EACIGPESKGGFFH 201
            E    + +  +   P  +  +    DE       LR++ID      EA    + +     
Sbjct: 1029 ENRYNLALGCIA-CPACYDLVQDKVDEHRKKLNELRDLIDNIGSNPEAINDEDFEKRLKE 1087

Query: 202  GTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261
              +  +   +E          + E   DI+ +    +D   K+ S  + A+    +  +D
Sbjct: 1088 VNDTINQLLKEAKMAAGNDTTLLEHLDDIKDSIDGLQDQLQKIGSNVDMAQESTDSAKDD 1147

Query: 262  EDDSAHT-------LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA---------VNGQ 305
              ++          L+  E  L  K   ALD+ A+  ++L S  +              Q
Sbjct: 1148 IGNAEDAIKRAQDTLAEAERYLNEKGQEALDKAADAAKDLGSQSEKMTKLAKKAKEAAEQ 1207

Query: 306  KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL------LVEQLYDISKRIMHNEGELLRL 359
            + E++        E L     +L L Q  +D        ++ L D    I     E + +
Sbjct: 1208 QTEEAMEIDGTANEALDTSKEALKLAQDALDKQDDISDKIDMLKDKYDDIEALAQEAMAV 1267

Query: 360  AQSYGIKRDVFLER-------------------HQGRELDPHWVSYAKDFPEGEWKNFVA 400
            A     + +  L+                     +G   D   +    +  + E    +A
Sbjct: 1268 AMEAQERANELLKEATTILADANSPLPTIDVGPLKGNASD---IIRGANRIKAEADQLIA 1324

Query: 401  CEVDSILKIRNEIKSISV--ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVIS 458
               D + ++  E +      + G++  +   ++          + A     +  ++    
Sbjct: 1325 DNRDLLKEVEMESQEAKDLLQDGLAAQQEADLLLARVDAAEAIAQAAINQGDKTVKEARD 1384

Query: 459  VAKKYTNRGLQFLDLIQEGNIGLMKAAEKF-DWCLGYKFSTYAMWW----VKQAITRSIA 513
            +          F DL++E       A ++  +     + +          ++ A   +I 
Sbjct: 1385 MLDTLRG----FNDLVEESKGAAEDALDRIPEIERLIREANDTANEANDAIEGAEADAIQ 1440

Query: 514  DQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573
             +           +      +        +       + A +L M V+   + L    + 
Sbjct: 1441 ARDIANEAETTAVEASEGAGQVKEDAEETLDDATGLSDEAMQLMMDVDDTEQELDELDKQ 1500

Query: 574  ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV-------LASLTPRE-E 625
               +  +  E      +   +    S    +  +++ +    +       L  L   E +
Sbjct: 1501 ADNDAALAQEALMKANEARRNAQEASDTVQSALSDVNDLLNELAHLEPIDLERLNELEGQ 1560

Query: 626  RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673
                       + D+ LE++       ++ I   E  A+  L+   ++
Sbjct: 1561 LADTNDTLQDADLDNKLEDLKAARDQQKQWIMDYED-ALVDLRAAVQN 1607


>gi|134076038|emb|CAK39397.1| unnamed protein product [Aspergillus niger]
          Length = 2406

 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 85/234 (36%), Gaps = 14/234 (5%)

Query: 132  ELLSREGEIAIAKRIEAGRAMMMASLCESPLTF---QALIIWRDELNDGTTLLREIIDLE 188
             LL   GE   A  ++     + +   +        Q L   R         +++ ++ E
Sbjct: 924  PLL---GETRTANEVKRRDEKIKSLEAKMNQDIADRQKLEEERRRTEIEIQKIQQTLESE 980

Query: 189  ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              +  + +  F            + +    +++ +++   D+ +A K + D+     +  
Sbjct: 981  RALALDKEEIFKRLQVREVELSEKLAGAIADQESLEDQLDDLIAAKKRTDDELELRITQL 1040

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE---IAEVYRELRSLQ-----DN 300
            E A    +  + ++ +    L  +E +L      +L++   I E+ +EL+ LQ       
Sbjct: 1041 EQAGEIIQRFENEKHEMQARLEELEKKLAEAESSSLEKEAKIKELGQELKMLQSHLSLKE 1100

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                  + K     + L+ KL K    L  ++  I  L+E+   I ++I     
Sbjct: 1101 RKLQDLETKLLKTDQDLEVKLSKTSRDLEESKKHIKELIEENRVIRQQITDLSS 1154


>gi|47938109|gb|AAH71583.1| DCTN1 protein [Homo sapiens]
          Length = 1139

 Score = 38.3 bits (87), Expect = 4.9,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 113 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 172

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 173 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 232

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 233 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 292

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 293 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 351

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 352 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTANLQDVNRELTNQQEAS 407

Query: 456 VISV 459
           V   
Sbjct: 408 VERQ 411


>gi|258513623|ref|YP_003189845.1| RNA polymerase factor sigma-70 [Desulfotomaculum acetoxidans DSM
           771]
 gi|257777328|gb|ACV61222.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 214

 Score = 38.3 bits (87), Expect = 5.0,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 35/89 (39%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V        IA + ++      V + A+ Y   G    D+IQEG IGL KA   F     
Sbjct: 22  VEFAREGDDIALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRMDKL 81

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  +I   +    IP
Sbjct: 82  SSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|225568313|ref|ZP_03777338.1| hypothetical protein CLOHYLEM_04388 [Clostridium hylemonae DSM
           15053]
 gi|225162842|gb|EEG75461.1| hypothetical protein CLOHYLEM_04388 [Clostridium hylemonae DSM
           15053]
          Length = 203

 Score = 38.3 bits (87), Expect = 5.0,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 35/91 (38%)

Query: 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491
            ++R            +++    LV   A      G +  DLIQEG IGL KA E +D  
Sbjct: 11  QLIRNLRAGDKAIVDYIMDKYKNLVRKEANAMYLLGGENDDLIQEGMIGLFKAVEDYDVE 70

Query: 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
               F ++A   + + +  +I         P
Sbjct: 71  QQASFFSFARLCITRQMYSAIEASRRKKHSP 101


>gi|76800685|ref|YP_325693.1| transducer protein hemAT [Natronomonas pharaonis DSM 2160]
 gi|76556550|emb|CAI48121.1| transducer protein hemAT [Natronomonas pharaonis DSM 2160]
          Length = 492

 Score = 38.3 bits (87), Expect = 5.0,   Method: Composition-based stats.
 Identities = 44/294 (14%), Positives = 105/294 (35%), Gaps = 21/294 (7%)

Query: 60  SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
           +E+++  +  L ++   +VD  D E    ++D  + A   +N    L    +    +TDD
Sbjct: 213 TEEVQAPIEELKSVTDRIVDSSD-EIATLADDQAESAREVANEVGSLSATVEEVASTTDD 271

Query: 120 PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
                      +   S E +  +A    A     + ++       +++    + L+D   
Sbjct: 272 -----------VATQSAEAD-ELATEGRASAEEAIETMGSVTDAAESVTEDVETLHDRVG 319

Query: 180 LLREIIDLEACIGPESK----GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAK 235
            + EI+D+   I  ++                         ++ +   ++++       +
Sbjct: 320 QIDEIVDVIDDIADQTNILALNASIEAARAGEAGDGFGVVADEVKSLAEKSQEQASRIDE 379

Query: 236 VSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELR 295
           +  + +       EN +     +D+   +    L+A+ED +   V  A D I EV R   
Sbjct: 380 MVSEIQDDAAGTVENLDETNTAIDDSVTEVRDVLAALED-IEMAVEGASDGIHEVSR--- 435

Query: 296 SLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           ++ + A + ++      +     E+L   +  +S         V+ +    KR+
Sbjct: 436 AMDEQAASTEQIAGVVDELADRSERLTDELDEISAANRDQKRSVDDIVAAVKRL 489


>gi|317029425|ref|XP_001391561.2| myosin type II heavy chain [Aspergillus niger CBS 513.88]
          Length = 2405

 Score = 38.3 bits (87), Expect = 5.0,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 85/234 (36%), Gaps = 14/234 (5%)

Query: 132  ELLSREGEIAIAKRIEAGRAMMMASLCESPLTF---QALIIWRDELNDGTTLLREIIDLE 188
             LL   GE   A  ++     + +   +        Q L   R         +++ ++ E
Sbjct: 924  PLL---GETRTANEVKRRDEKIKSLEAKMNQDIADRQKLEEERRRTEIEIQKIQQTLESE 980

Query: 189  ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              +  + +  F            + +    +++ +++   D+ +A K + D+     +  
Sbjct: 981  RALALDKEEIFKRLQVREVELSEKLAGAIADQESLEDQLDDLIAAKKRTDDELELRITQL 1040

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE---IAEVYRELRSLQ-----DN 300
            E A    +  + ++ +    L  +E +L      +L++   I E+ +EL+ LQ       
Sbjct: 1041 EQAGEIIQRFENEKHEMQARLEELEKKLAEAESSSLEKEAKIKELGQELKMLQSHLSLKE 1100

Query: 301  AVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEG 354
                  + K     + L+ KL K    L  ++  I  L+E+   I ++I     
Sbjct: 1101 RKLQDLETKLLKTDQDLEVKLSKTSRDLEESKKHIKELIEENRVIRQQITDLSS 1154


>gi|251854872|gb|ACT22554.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1538

 Score = 38.3 bits (87), Expect = 5.0,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 876  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 931

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 932  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 987

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 988  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1044

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1045 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1103

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1104 ETDILEEKKEI 1114


>gi|251854868|gb|ACT22552.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1514

 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 852  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 907

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 908  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 963

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 964  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1020

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1021 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1079

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1080 ETDILEEKKEI 1090


>gi|71032947|ref|XP_766115.1| hypothetical protein [Theileria parva strain Muguga]
 gi|68353072|gb|EAN33832.1| hypothetical protein TP01_0594 [Theileria parva]
          Length = 973

 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 87/248 (35%), Gaps = 15/248 (6%)

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
              +G++V       DEE   + +D   S           +DS +  T+  V +    + 
Sbjct: 643 FEKLGMSVEVTSHNNDEEIKGEPVDTTKSDVLKDSEEDAVEDSGEEETEKEVII----IK 698

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEA 189
             E + ++ E  I  R+E     + A   E P+         + +    +   +I+ +E 
Sbjct: 699 KAESVVKDKETPIKNRVE---FDVKAE--EEPVEIVESAEPVEIVESAESDEEDIVYVE- 752

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
               E+        +  S     +      +    + +  IE+  K  K     V    E
Sbjct: 753 ----EADSSIASSEKSCSSSSVIEEIVVDTKKSKNKNKVKIETPVKKEKAKEKTVSKKKE 808

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK 309
           + E    + ++ ++ +   L  M  ++    +     + ++ ++L   +D+    +K  K
Sbjct: 809 DEEKRPESEEKVKETNIEDLIKMASKMDSSTLAQGSPVYDLLKKLYK-KDSEDVEEKKVK 867

Query: 310 SSVKCKVL 317
              K ++L
Sbjct: 868 KIGKYELL 875


>gi|251854884|gb|ACT22560.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1574

 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 916  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 971

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 972  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 1027

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 1028 INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1084

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1085 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1143

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1144 ETDILEEKKEI 1154


>gi|251854864|gb|ACT22550.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1514

 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 852  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 907

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 908  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 963

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 964  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1020

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1021 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1079

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1080 ETDILEEKKEI 1090


>gi|194746954|ref|XP_001955919.1| GF24935 [Drosophila ananassae]
 gi|190623201|gb|EDV38725.1| GF24935 [Drosophila ananassae]
          Length = 2933

 Score = 38.3 bits (87), Expect = 5.1,   Method: Composition-based stats.
 Identities = 74/530 (13%), Positives = 179/530 (33%), Gaps = 36/530 (6%)

Query: 135  SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
            +R+  + +++ IE  +  +   +       Q  +  + +       + ++I+    +  +
Sbjct: 781  TRDKLVNVSQDIERAQDEIQQRI-------QTTLSIQTKDQPSLAKIEQVINNLRMLKAK 833

Query: 195  SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
              G  +          +   +  + R ++ E     +  +  +    S            
Sbjct: 834  LDGIKYDYRTLVENILQFLENIVQLRREIDEYFASKQQPSASAPVSTSAGVDRSIAEHEK 893

Query: 255  ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
             R+L  D+  S  T S +    R +V+            +  L +N     +   S+   
Sbjct: 894  FRDLCMDKFRSLITQSELLID-RVRVLEPPGAREIDTDRILKLLENLRIYFESNSSARMS 952

Query: 315  KVLK-EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             + + EK+ +  G L      +D + +QL++I+        + L  A++  +  + F   
Sbjct: 953  SLERLEKIEQFRGDLEDIDRSLDSVSQQLHEIN----GQSVDSLAAAKTTSLAFEYFERT 1008

Query: 374  HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSM 433
             +  E         + F E   +  +    +S   +R+E++ ++ +       F+  V  
Sbjct: 1009 IELLE------KRIEKFTESTSQQLLISNPESEGYVRDELRKLNEK----WQSFKDQVKQ 1058

Query: 434  VRKGECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDW 490
             R+   +A+    E+VE        ++  YT   N+     D ++ GN  L+   EK+  
Sbjct: 1059 KRRSLNQATE-FFEVVEKIDAEYREISYFYTSVSNKVPYLRDAVEAGN--LVNDIEKYVT 1115

Query: 491  CLGYKFSTYAMWW--VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
                   +           +++  A  +  + I          +     R+  + +++  
Sbjct: 1116 SRETDLRSKLDSASQCAHDMSKVSALYNDVMNIFQSFVKLKMDINIVQERLKQEQRQKEQ 1175

Query: 549  PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
             E  A+  A   + +R+     +     +T +  +      +  + + A   L    QA 
Sbjct: 1176 RERDARDQAEREKALREAEARERLVREEQTRLESQRQQAAFEQAQRELAARELALREQAV 1235

Query: 609  LRETTT-RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
              E    + +     RE+           +   TL E+ K+     E +R
Sbjct: 1236 REEEARLQAIREQASREQLAREQAAREEEHRIQTLREIAKR----EEEVR 1281


>gi|134298076|ref|YP_001111572.1| RNA polymerase factor sigma-70 [Desulfotomaculum reducens MI-1]
 gi|134050776|gb|ABO48747.1| RNA polymerase, sigma 30 subunit, SigH [Desulfotomaculum reducens
           MI-1]
          Length = 214

 Score = 37.9 bits (86), Expect = 5.1,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V       + A + ++      V + A+ Y   G    D+IQEG IGL KA   F     
Sbjct: 22  VEFAREGDNAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRLDKL 81

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  +I   +    IP
Sbjct: 82  SSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|157868455|ref|XP_001682780.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68126236|emb|CAJ03601.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 4825

 Score = 37.9 bits (86), Expect = 5.2,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 79/247 (31%), Gaps = 19/247 (7%)

Query: 60   SEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDD 119
            ++Q+++   +++         D+    E  E   D A+         ++ +  +D   D+
Sbjct: 3984 TDQIDNEDQLMNMKDKEEQQADEQRQGEKDEGEEDTAADVETDFNGQKEHRSESDGEGDE 4043

Query: 120  PVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
                  +EMG ++      +     + +AG A  M                         
Sbjct: 4044 EGEESDKEMGDVD--DGTEKERKKTKKDAGDADDMNEDAGD--------------AAEEV 4087

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER--DDVQETEGDIESAAKVS 237
                + + +       + G F           ED S E +   DD +    +  S+   S
Sbjct: 4088 PEDNLAEGDEHREDNEETGGFDDKADEIRDADEDRSCEHDMVGDDDKSEMDEDGSSGGDS 4147

Query: 238  KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSL 297
             +         + +  D++   + +++   +  A E ++         E +E+  E    
Sbjct: 4148 VEHSDTDGEERDESVRDDKLPSDADEEPEESDVASEGRVDSDA-ATDAERSELGEEEVEQ 4206

Query: 298  QDNAVNG 304
            QDN+ + 
Sbjct: 4207 QDNSESA 4213


>gi|73980479|ref|XP_866178.1| PREDICTED: similar to dynactin 1 isoform 2 isoform 3 [Canis
           familiaris]
          Length = 1141

 Score = 37.9 bits (86), Expect = 5.3,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 112 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 171

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 172 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 231

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 232 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 291

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 292 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 350

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 351 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 406

Query: 456 VISV 459
           V   
Sbjct: 407 VERQ 410


>gi|323703773|ref|ZP_08115411.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531242|gb|EGB21143.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 199

 Score = 37.9 bits (86), Expect = 5.3,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 34/89 (38%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V         A + ++      V + A+ Y   G    D+IQEG IGL KA   F     
Sbjct: 7   VEFAREGDDAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRMDKL 66

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  +I   +    IP
Sbjct: 67  SSFRAFAELCITRQIITAIKTATRQKHIP 95


>gi|149040860|gb|EDL94817.1| CDC42 binding protein kinase alpha, isoform CRA_b [Rattus
           norvegicus]
          Length = 1535

 Score = 37.9 bits (86), Expect = 5.3,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 264 DSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
           D+     A E +++      L+   ++ E  + +++LQ + V+G       ++ K LKE+
Sbjct: 436 DNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEE 495

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL   +          V  L    +       EL    +             Q RE  
Sbjct: 496 IEKLRKQV--------AEVNHLEQQLEEANSVRRELDDAFRQIKAFEKQIKTLQQEREEL 547

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGI------------SISEFR 428
              +  A +  + + K          L ++  ++     T +               E  
Sbjct: 548 NKELVQASERLKNQSKELKDAHCQRKLAMQEFMEINERLTELHTQKQKLARHVRDKEEEV 607

Query: 429 HIVSM----VRKGECEASIAKKEM 448
            +V      +R+    A  AKKE+
Sbjct: 608 DLVMQKAESLRQELRRAERAKKEL 631


>gi|296191774|ref|XP_002743773.1| PREDICTED: myosin-9 [Callithrix jacchus]
          Length = 1960

 Score = 37.9 bits (86), Expect = 5.4,   Method: Composition-based stats.
 Identities = 41/300 (13%), Positives = 97/300 (32%), Gaps = 12/300 (4%)

Query: 143  AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
            A  +E  +      L E           RD                A    E+       
Sbjct: 1436 ACNLEKKQKKFDQLLAEEKTISAKYAEERDRAEAEAREKETKALSLARALEEAMEQKAEL 1495

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
               +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +
Sbjct: 1496 ERLNKQFRTEMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAK 1555

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVL 317
                  L AM+ Q    +    ++  E  ++L           +DE+     +    K L
Sbjct: 1556 LRLEVNLQAMKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAVAARKKL 1615

Query: 318  KEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGR 377
            +  L  L   +       D  ++QL  +  ++     EL          R+  L + +  
Sbjct: 1616 EMDLKDLEAHIDSANKNRDEAIKQLRKLQAQMKDCMREL----DDTRTSREEILAQAKEN 1671

Query: 378  ELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMV 434
            E     +       + E       +  +     ++ +EI + S +  +++ E R + + +
Sbjct: 1672 EKKLKSMEAEMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARI 1731


>gi|257388502|ref|YP_003178275.1| methyl-accepting chemotaxis sensory transducer [Halomicrobium
           mukohataei DSM 12286]
 gi|257170809|gb|ACV48568.1| methyl-accepting chemotaxis sensory transducer [Halomicrobium
           mukohataei DSM 12286]
          Length = 592

 Score = 37.9 bits (86), Expect = 5.4,   Method: Composition-based stats.
 Identities = 51/360 (14%), Positives = 122/360 (33%), Gaps = 33/360 (9%)

Query: 13  SEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSN 72
              E   D  VFD    ++  +I    Q    T+ ++  F      +S+++++       
Sbjct: 217 DADEIDGDEAVFDEVVTNYNDLISNLDQ----TVGDVTDFAASVATASDRVDE------- 265

Query: 73  MGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIE 132
             +N VD    E     ++    A+  +     + +       + +        E+ +  
Sbjct: 266 -NMNEVDRASEEIAASVDEISTGATRQTERHEDVAREMSKLSATVE--------EIAATA 316

Query: 133 LLSREGEIAIAKRIEAGRAMMMASLCESPLT---FQALIIWRDELNDGTTLLREIIDLEA 189
             + +     A+R E GR   + +L E          +     +L +    + EI+D+  
Sbjct: 317 DEAAQTARDAAERGENGREDAIEALDELDELESKIDHIATAVADLGEQIAAVEEIVDVIT 376

Query: 190 CIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPE 249
            I  ++               R D + +       E +   E     + +  + V+S  E
Sbjct: 377 EIAEQTN---MLALNASIEAARADGTGDGFAVVADEVKALAEETRASADEIATLVESVSE 433

Query: 250 NAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL-RSLQDNAVNGQKDE 308
            A+     +   ++  A + + +   LR       +E+  V  E+  S+Q+ +    +  
Sbjct: 434 EADETVTEVRAMDEQVASSTTTIAAALRD-----FEELVTVVGEVDDSMQEISDATGEQA 488

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS-YGIKR 367
           K++ +   + + L  +         +     +Q  +  + +  + G +   A    G+ R
Sbjct: 489 KTTEEVAKVVDDLTAVSEQTRDEAEQASAATQQQTETVETVSEDIGTVADRADELLGMLR 548


>gi|222625291|gb|EEE59423.1| hypothetical protein OsJ_11583 [Oryza sativa Japonica Group]
          Length = 1080

 Score = 37.9 bits (86), Expect = 5.4,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 73/197 (37%), Gaps = 7/197 (3%)

Query: 174 LNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESA 233
           +ND   LL EI  L+  +  ++          H      D   E +R+  ++        
Sbjct: 786 VNDREELLSEIQRLKDQLKQQAGESTNVSLLEHLRNGSTDQEYELDRER-EKWMESESKW 844

Query: 234 AKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL--RPKVMCALDEIAEVY 291
             ++++ R  ++S    AE  E  L  ++  +A    A++  +    +++    E+ E+Y
Sbjct: 845 ICLTEELRVDLESNRMLAEKTEMELSNEKKCTAELDDALQRAIYGHARIIEHYAELQEMY 904

Query: 292 RELRSLQDNAVNGQKDEKSSVKCKVLKE--KLVKLVGSLSLNQSRIDLLVE--QLYDISK 347
            +L       + G  + K +      K          +  L+  RID   E  QL + ++
Sbjct: 905 NDLLERHRRVMEGISEVKRAAAKAGRKGCGTAFAAALAAELSTVRIDREKERAQLKEQNR 964

Query: 348 RIMHNEGELLRLAQSYG 364
           R+     +      + G
Sbjct: 965 RLRIQLRDTAEAVHAAG 981


>gi|321444632|gb|EFX60467.1| hypothetical protein DAPPUDRAFT_343597 [Daphnia pulex]
          Length = 290

 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 15/98 (15%), Positives = 35/98 (35%), Gaps = 4/98 (4%)

Query: 25  DFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLE 84
           + S     K+  + +++G +T  +++A    ++ + E ++  +  L   GI V D    E
Sbjct: 164 EISSKLVNKLTAIYQKKGSLTFRDVDAAALDEDATPEMIQTLLGELKVRGIQVQDSAQDE 223

Query: 85  DEE----GSEDSLDLASSASNSSVFLQKRKDSADRSTD 118
             +    G+    D             +     +   D
Sbjct: 224 FNDIKVVGATKGDDDILGEDLDFAATDELSLDEEIDID 261


>gi|160893355|ref|ZP_02074142.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
 gi|156865047|gb|EDO58478.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
          Length = 200

 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 2/94 (2%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             + ++R  E   + A + +++  + +V   ++     G +  D+IQEG IGL+KA   F
Sbjct: 11  ENIRLIR--EENDNAAFEYLIKKYMGIVKKESRALYIIGAENEDIIQEGMIGLIKAIRSF 68

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D   G  FST+A   +K+ +  ++   +     P
Sbjct: 69  DGSKGASFSTFANLCIKRQLITAVKLSNRKKHSP 102


>gi|153852654|ref|ZP_01994091.1| hypothetical protein DORLON_00064 [Dorea longicatena DSM 13814]
 gi|149754296|gb|EDM64227.1| hypothetical protein DORLON_00064 [Dorea longicatena DSM 13814]
          Length = 247

 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 31/162 (19%), Positives = 70/162 (43%), Gaps = 4/162 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANL-RLVISVAKKYTNRGLQFLD 472
                +  +S  E +++   +R         ++E+  A     V+  A +  +  +   D
Sbjct: 85  AEKEEKQPLSAEEQKYVEEYLRGLGDMKEETQEEVRMAYYLPKVVEEAVRLHHPEVFIGD 144

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           +IQEGNI LM A ++             +  V+  +  S+  Q+   R    M +K+ ++
Sbjct: 145 MIQEGNIALMVALKEIPKEKD---EEEILEQVRAGMMASLESQTEVKRRDHKMVEKVTEL 201

Query: 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
               + M  +  R+ + +E+A++L +  + +  +LK+  E +
Sbjct: 202 DEAIKSMKEEYGRKVSVDEVAERLGISEDEIEDILKLAGEEV 243


>gi|307136479|gb|ADN34280.1| nuclear matrix constituent-like protein 1 [Cucumis melo subsp.
           melo]
          Length = 1205

 Score = 37.9 bits (86), Expect = 5.5,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 96/237 (40%), Gaps = 2/237 (0%)

Query: 210 KREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
           K+E     ++++ + +   D++   +  + +  ++D      E +++ L   +++    +
Sbjct: 518 KQEIEKYRQQKELLLKEAEDLKQQKETFEREWEELDEKRAQVEKEQKTLLLQKEEFEKRI 577

Query: 270 SAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLS 329
            + E++L+ +       I      L+  Q++     + EKS++  K   ++  +++    
Sbjct: 578 FSEEERLKNERSETEAYIHREQENLKLAQESFAASMEHEKSAIAEKAQSDR-SQMMHDFD 636

Query: 330 LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
           L +  ++  ++   +  +R    + +L +  +   ++   FL     RE+D   +   K 
Sbjct: 637 LQKRELESAMQNRVEEMERGFREKEKLFKEEKERELENIKFLRDVARREMDELKLERLKT 696

Query: 390 FPEGEWKNFVACEVD-SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAK 445
             E +        ++   ++IR +I+ +   +     +   +V+   +    A   +
Sbjct: 697 EKEKQEAEANKEHLERQRIEIRKDIEELLELSNKLKDQRERLVAERDRFISYADKHR 753


>gi|168058486|ref|XP_001781239.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667304|gb|EDQ53937.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 812

 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 41/230 (17%), Positives = 90/230 (39%), Gaps = 13/230 (5%)

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEG--HSYQKREDSSQEKERDDVQETEGD 229
            E+    T L++++  +     E K      T+       K E +   +  DD++     
Sbjct: 169 QEIESIKTELKDLLTEKLESEEEHKKELDKATKKWKEKVAKAEVARFSESEDDLKSANRR 228

Query: 230 IESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAE 289
           IE+  +  K+ +  +++   + + D       E +     S  E++L   +     EI  
Sbjct: 229 IEATDETCKNLKKDLEAVRLSHKEDVDAASRREKEH----SIKEEELSSIIDKQAKEIQA 284

Query: 290 VYRELRSLQDNAVNGQKDEKSSVKCKV-LKEKLVKLVGSLSLNQSRIDLLVEQLYDISKR 348
           + ++L  L++N     +    S   K  L E       ++ L +  ID L  +L   + +
Sbjct: 285 LDKQLHQLRENKDANVQAGDPSGNLKEQLIELKAHHNATVDLFKGEIDSLSNKLEGAASQ 344

Query: 349 IMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398
               EGE++R      I++++  +  + +ELD   +     + + + K  
Sbjct: 345 TRALEGEIIR------IRKELEEKAQEHKELDEKHIILYSSYHDLQKKLL 388


>gi|47216078|emb|CAG04817.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1690

 Score = 37.9 bits (86), Expect = 5.6,   Method: Composition-based stats.
 Identities = 53/387 (13%), Positives = 114/387 (29%), Gaps = 33/387 (8%)

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSS 311
           E     L++  D     L AM++          ++ A    +L  L        + +K  
Sbjct: 77  EGTSDVLNKLYDTVVEKLEAMKNDYEALRKRYNEKTAGHNADLSRLDQAEEENHRLQKQL 136

Query: 312 VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
                 ++  +      S +  R D   ++L     +    + E+ RL           L
Sbjct: 137 DMLLKQRDAAMHYQQQYSSSIRRFDNTQQELSKAVAQNKELQREMERLQSEV-----TRL 191

Query: 372 ERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE--FRH 429
           +  Q +          +          +  E D ++K  + ++     TG+ ++E   ++
Sbjct: 192 KTQQLKASKDGEKFKQERDSVISEYRLIMSERDQVIKEVDRLQ-----TGLEMAEAKLKN 246

Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVIS--VAKKYTNRGLQFLDLIQEGNIGLMKAAEK 487
             S  R    E    ++  +    + V     ++KY +          E    L +A + 
Sbjct: 247 TSSERRVANEELEALRQRWLTETGQFVTKTSCSEKYCHEVKDKA----EAQKELSQACKD 302

Query: 488 FDWCLGYK--FSTYAMWWVKQ------AITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
            +     +          + Q         ++   Q            +I  + +    +
Sbjct: 303 IEMVREERDVARKERTEAIIQRDQLLREYYQARQKQDSATLDMERANKEIDMLRKQCEAI 362

Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI-SLETPIGDEDTSHLGDF------I 592
           S ++K      E+AK         R  +   +E I +L   +  E    + D       +
Sbjct: 363 SQELKEALQEAEVAKCRRDWAFQERDKIVAERESIRTLCDNLRRERDRAVSDLADALRNL 422

Query: 593 EDKNAVSPLDSAIQANLRETTTRVLAS 619
           +D        +     LRE     L  
Sbjct: 423 DDMRKQKNDTARELKELREKMEDQLEK 449


>gi|332231119|ref|XP_003264745.1| PREDICTED: myosin-9 isoform 2 [Nomascus leucogenys]
          Length = 1922

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 41/306 (13%), Positives = 99/306 (32%), Gaps = 12/306 (3%)

Query: 139  EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            +   A  +E  +      L E           RD                A    E+   
Sbjct: 1432 QRQSACNLEKKQKKFDQLLAEEKTISAKYAEERDRAEAEAREKETKALSLARALEEAMEQ 1491

Query: 199  FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
                   +   + E       +DDV ++  ++E + +  +    ++ +  E  E++ +  
Sbjct: 1492 KAELERLNKQFRTEMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQAT 1551

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVK 313
            ++ +      L AM+ Q    +    ++  E  ++L           +DE+     +   
Sbjct: 1552 EDAKLRLEVNLQAMKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAVAA 1611

Query: 314  CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLER 373
             K L+  L  L   +       D  ++QL  +  ++     EL          R+  L +
Sbjct: 1612 RKKLEMDLKDLEAHIDSANKNRDEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQ 1667

Query: 374  HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHI 430
             +  E     +       + E       +  +     ++ +EI + S +  +++ E R +
Sbjct: 1668 AKENEKKLKSMEAEMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRL 1727

Query: 431  VSMVRK 436
             + + +
Sbjct: 1728 EARIAQ 1733


>gi|169830406|ref|YP_001716388.1| RNA polymerase factor sigma-70 [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169637250|gb|ACA58756.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 216

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 35/89 (39%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V       S A + ++      V + A+ Y   G    D+IQEG IGL KA   F     
Sbjct: 24  VEHAREGDSEALEFLINKYRHFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRLDKL 83

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  +I   +    IP
Sbjct: 84  SSFRAFAELCITRQIITAIKTATRQKHIP 112


>gi|149638210|ref|XP_001510678.1| PREDICTED: similar to Kinesin-like protein KIF3A (Microtubule plus
           end-directed kinesin motor 3A) [Ornithorhynchus
           anatinus]
          Length = 767

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 30/189 (15%), Positives = 68/189 (35%), Gaps = 7/189 (3%)

Query: 169 IWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEG 228
             RD+         ++++++A I  E K            + +  +  E+   D+ + + 
Sbjct: 431 KRRDQTGKKKVSPDKMVEMQAKIDEERKALETKLDMEEEERNKARAELERREKDLLKAQQ 490

Query: 229 DIESAAKVSKDDRSKV---DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
           + +S  +       KV            ++  L E+ +          +QLR ++     
Sbjct: 491 EHQSLLEKLSALEKKVIVGGVDLLAKAEEQEKLLEESNMELEERRKRAEQLRRELEEKEQ 550

Query: 286 EIAEVYRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYD 344
           E  ++  +  SLQ+ A    K  +K        K ++  L      +Q  I+ L+E +  
Sbjct: 551 ERLDIEEKYTSLQEEAQGKTKKLKKVWTMLMAAKSEMADLQQE---HQREIEGLLENIRQ 607

Query: 345 ISKRIMHNE 353
           +S+ +    
Sbjct: 608 LSRELRLQM 616


>gi|170717739|ref|YP_001784809.1| cysteine protease [Haemophilus somnus 2336]
 gi|190358892|sp|Q06277|IBPA_HAES2 RecName: Full=Adenosine monophosphate-protein transferase and
            cysteine protease ibpA; Short=HMW IgBP; AltName:
            Full=p120; Includes: RecName: Full=Adenosine
            monophosphate-protein transferase ibpA; AltName:
            Full=AMPylator ibpA; Includes: RecName: Full=Cysteine
            protease ibpA; Contains: RecName: Full=Protein p76 IgBP;
            AltName: Full=76 kDa antigen; Flags: Precursor
 gi|32400317|dbj|BAC78649.1| high molecular weight-immunoglobulin binding proteins [Histophilus
            somni]
 gi|168825868|gb|ACA31239.1| cysteine protease domain, YopT-type [Haemophilus somnus 2336]
          Length = 4095

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 36/156 (23%), Positives = 52/156 (33%), Gaps = 4/156 (2%)

Query: 163  TFQALIIWRDELNDGTTLLREIIDLEACIGPESKG--GFFHGTEGHSYQKREDSSQEKER 220
                L+   +   D +  L + +D    I  E +       G E     + E S   K  
Sbjct: 1008 ALSDLLSIPNLFVDNSVQLDKTVDKNIEIDEEDEFLLKPHTGEEPDLLNENELSENGKFL 1067

Query: 221  DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV 280
            D +    G+     +VS D     D P E     E  L E  D      S ++D+LR K 
Sbjct: 1068 DKLLGEIGEKTYIREVSDDWERDPDEPDEPDYKTESRL-ETRDRFDTLPSEVQDKLRQKF 1126

Query: 281  MCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
                 E A+  R+  +LQ    N Q         K 
Sbjct: 1127 NE-YKEKAQQKRQAEALQAKTKNEQLQSDLETGYKE 1161


>gi|329925600|ref|ZP_08280441.1| RNA polymerase sigma-H factor [Paenibacillus sp. HGF5]
 gi|328939729|gb|EGG36071.1| RNA polymerase sigma-H factor [Paenibacillus sp. HGF5]
          Length = 212

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 22/85 (25%), Positives = 34/85 (40%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
               S A + ++      V + A+ Y   G    D++QEG IGL KA   F       F 
Sbjct: 24  REGDSGALEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKGDKLSSFK 83

Query: 498 TYAMWWVKQAITRSIADQSCTIRIP 522
            +A   + + I  +I   +    IP
Sbjct: 84  AFAELCITRQIITAIKTATRQKHIP 108


>gi|313620925|gb|EFR92099.1| RNA polymerase sigma-H factor [Listeria innocua FSL S4-378]
          Length = 201

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EEMAMLELARSGDTDALEYFFSRYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DESKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|296131816|ref|YP_003639063.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermincola sp.
           JR]
 gi|296030394|gb|ADG81162.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermincola potens
           JR]
          Length = 214

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%)

Query: 434 VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493
           V   +     A + ++      V + A+ Y   G    D+IQEG IGL KA   F     
Sbjct: 22  VEFAKEGDDAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFKSDKL 81

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F  +A   + + I  +I   +    IP
Sbjct: 82  SSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|73955671|ref|XP_860825.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 7 [Canis familiaris]
          Length = 2006

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 50/328 (15%), Positives = 105/328 (32%), Gaps = 14/328 (4%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD         +E   L      E  
Sbjct: 1467 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEA-EAREKETKALSLARALEEA 1525

Query: 197  GGFFHGTEGHSYQKRED-SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  + Q R D       +DDV +   ++E + +  +    ++ +  E  E++ 
Sbjct: 1526 LETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDEL 1585

Query: 256  RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC- 314
            +  ++ +      + AM+ Q    +    ++  E  R L           +DE+      
Sbjct: 1586 QATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALA 1645

Query: 315  ----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                K L+  L  L   +       D +++QL  +  ++   + EL    +     RD  
Sbjct: 1646 VASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEI 1701

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEF 427
              + +  E     +       + E  +             ++ +EI + +      + E 
Sbjct: 1702 FAQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEK 1761

Query: 428  RHIVSMVRKGECEASIAKKEMVEANLRL 455
            R + + + + E E    +  M   N R 
Sbjct: 1762 RRLEARIAQLEEELEEEQSNMELLNDRF 1789


>gi|46123275|ref|XP_386191.1| hypothetical protein FG06015.1 [Gibberella zeae PH-1]
          Length = 592

 Score = 37.9 bits (86), Expect = 5.8,   Method: Composition-based stats.
 Identities = 33/222 (14%), Positives = 80/222 (36%), Gaps = 6/222 (2%)

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVM 281
           ++  +    ++    S    +           + ++LDE        ++   +QLR +  
Sbjct: 115 ELDSSPAAEKAFGDDSASRSAATAKANLPHSAEFQSLDELAGFENDNVAHYNEQLREQNC 174

Query: 282 CALDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVE 340
                I ++ R+L +L  D  +  +K +  S K   LK+++   +  + ++   +   VE
Sbjct: 175 QLDRRIQDLQRQLSTLTTDKQIAEEKSDTLSEKLNSLKQRMNSNMTEVEISSEALADKVE 234

Query: 341 QLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVA 400
            L   ++ +     +      S    R        G+E D   V   +D+ +     ++ 
Sbjct: 235 DLGKENRALREQLNDAQSHIFSLQPYRKELTSEEVGQEYDAL-VEQVQDWVQKFMDPWLD 293

Query: 401 CEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEAS 442
              + +  +     S + +  +  + F+HI+         AS
Sbjct: 294 DHQEGVDSLL----SNAKKRAVDATRFKHILYQYPDLLHGAS 331


>gi|254744604|ref|ZP_05202283.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Kruger B]
          Length = 191

 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|149642611|ref|NP_001092404.1| dynactin subunit 1 [Bos taurus]
 gi|148745416|gb|AAI42510.1| DCTN1 protein [Bos taurus]
          Length = 1239

 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 39/304 (12%), Positives = 109/304 (35%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  + AE     ++E   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEAEVLRERVEELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +  ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAERTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     ++   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVETLTDRNLDLEEKVRKLKETVGDLEAINEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      +   +  +++       ++++++  +   R+         + +       
Sbjct: 449 REQLDMAGAQVRDAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRALTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|326202358|ref|ZP_08192227.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325987476|gb|EGD48303.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 214

 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 33/85 (38%)

Query: 438 ECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497
                 A + ++      V + A+ Y   G    D+IQEG IGL KA   +       F 
Sbjct: 26  RAGDQQALEYLINKYKSFVRAKARTYFLIGADREDIIQEGMIGLFKAIRDYKGDKLSSFR 85

Query: 498 TYAMWWVKQAITRSIADQSCTIRIP 522
            +A   + + I  +I   +    IP
Sbjct: 86  AFAELCITRQIITAIKTATRQKHIP 110


>gi|255580072|ref|XP_002530869.1| Ubiquitin-protein ligase bre-1, putative [Ricinus communis]
 gi|223529558|gb|EEF31509.1| Ubiquitin-protein ligase bre-1, putative [Ricinus communis]
          Length = 945

 Score = 37.9 bits (86), Expect = 5.9,   Method: Composition-based stats.
 Identities = 38/312 (12%), Positives = 93/312 (29%), Gaps = 13/312 (4%)

Query: 148 AGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHS 207
             +  + +   E  L  ++L    ++L      L+ I+D+    G +S+           
Sbjct: 568 NEQKSLTSKCAEQMLEIKSLQTVIEKLQKDKLELQIILDMYGQEGYDSRDLLEIRESERK 627

Query: 208 YQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267
            Q + +  +    +   E      + A+ +   R             + +  E +     
Sbjct: 628 AQSQAEVLKIALDEHSLELRVKAANEAEAACQQRLCAAEAEIAELRAKLDASERDVWELT 687

Query: 268 TLSAMEDQLRPKVMCALDEIAEVYRELRS-----LQDNAVNGQKDEKSSVKCKVLKEKLV 322
                +D+     +  ++ I + Y +L++     LQ        + K   +    K+ L 
Sbjct: 688 EAIKSKDREAEAYISEIETIGQAYEDLQTQNQHLLQQVTERDDYNIKLVSESVKTKQALS 747

Query: 323 KLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPH 382
            L+        ++   V    +  K  +    E +++  +  I+      R         
Sbjct: 748 SLLSEKQALTKQLQQ-VNTSVEYLKIRISQSEEQMKVCLTEAIRSTEEDRRLAVNLETAR 806

Query: 383 WVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE-------TGISISEFRHIVSMVR 435
           W     +      K  V        +I+ ++  I  E             E + +   + 
Sbjct: 807 WELMDAEKELKWLKYAVGSSEKEYEQIQKKMDEIRTELRDERSEREKLDQELKELNDKIA 866

Query: 436 KGECEASIAKKE 447
           +   E+  A  +
Sbjct: 867 EMTSESGEAAIQ 878


>gi|251854866|gb|ACT22551.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1538

 Score = 37.9 bits (86), Expect = 6.1,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 876  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 931

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 932  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 987

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 988  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 1044

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 1045 EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1103

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1104 ETDILEEKKEI 1114


>gi|157112429|ref|XP_001657531.1| hypothetical protein AaeL_AAEL006125 [Aedes aegypti]
 gi|108878092|gb|EAT42317.1| conserved hypothetical protein [Aedes aegypti]
          Length = 717

 Score = 37.9 bits (86), Expect = 6.1,   Method: Composition-based stats.
 Identities = 37/289 (12%), Positives = 96/289 (33%), Gaps = 27/289 (9%)

Query: 135 SREGEIAIAKRIEAGRAMMM--ASLCESPLTFQALIIWRDELNDGTTLL----REIIDLE 188
           +   E  + + +E     +     L E+    + L    + L      L    R++ D+ 
Sbjct: 284 TESQEKLLQENVEIKNKNLFLEKELSETIAVVRKLQDKNEALESKVESLTSANRDVTDVH 343

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
                + +    +  +     K +     K+ D +++        ++ +   R    S  
Sbjct: 344 KNQLRDLEIRLANSKDAERSLKDQLGKLRKQSDQLKDELEAERKKSEDANKLRGDFASLK 403

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
              +N  +   +  +    +L      L+ +V   L+E  ++ +EL   + +     + +
Sbjct: 404 VKTDNLSKKFSDI-NAQNESLKEQIKDLKAQVDSHLEEKKKLIKELDVQRLSLKKYYQAQ 462

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRD 368
              V    LKE                    +QL  + +++        RL     IK+ 
Sbjct: 463 LEDVVADKLKEFQ------------------KQLTSVEEQLKSEAKRKERLIAERAIKQI 504

Query: 369 VFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
             +   Q  E +   ++   +  E  ++  +     +I +++ +++S  
Sbjct: 505 ELIN--QTNEQEIKLLNEKCNEQESLYRLQLTNSSKTIHELQEKLESYQ 551


>gi|73980489|ref|XP_866249.1| PREDICTED: similar to dynactin 1 isoform 1 isoform 8 [Canis
           familiaris]
          Length = 803

 Score = 37.9 bits (86), Expect = 6.1,   Method: Composition-based stats.
 Identities = 42/304 (13%), Positives = 112/304 (36%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 227 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 286

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  +  E  +  +DE   D     + +E++          +  L+E 
Sbjct: 287 ATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 346

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +S ID L
Sbjct: 347 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAESTIDEL 406

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 407 KEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDE-LQENARETELEL 465

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      + + +  +++       ++++++  +   R+         +E+       
Sbjct: 466 REQLDMAGARVREAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRELTNQQEAS 521

Query: 456 VISV 459
           V   
Sbjct: 522 VERQ 525


>gi|315606355|ref|ZP_07881371.1| conserved hypothetical protein [Prevotella buccae ATCC 33574]
 gi|315252046|gb|EFU32019.1| conserved hypothetical protein [Prevotella buccae ATCC 33574]
          Length = 284

 Score = 37.9 bits (86), Expect = 6.1,   Method: Composition-based stats.
 Identities = 22/114 (19%), Positives = 52/114 (45%), Gaps = 2/114 (1%)

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           EN   ++       D     +   ++++    M  L+EI E +R++    +N V+  KD 
Sbjct: 21  ENKNANQLAGMTQNDSLNKIIEQKDNEINDM-MGTLNEIQEGFRQISEA-ENRVSLMKDG 78

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
           + + + + L+E +  + G +  N+  I+ L +Q+ + S +    +  +  L + 
Sbjct: 79  EGANRAQQLRENIKFISGRMKENRELIEKLRQQMRESSMKGEQFKKTIESLMKQ 132


>gi|296482742|gb|DAA24857.1| dynactin 1 [Bos taurus]
          Length = 1239

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 39/304 (12%), Positives = 109/304 (35%), Gaps = 22/304 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 210 ELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADTADAIEM 269

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S  + AE     ++E   D     + +E++          +  L+E 
Sbjct: 270 ATLDKEMAEERAESLQQEAEVLRERVEELTTDLEILKAEIEEKGSDGAASSYQLKQLEEQ 329

Query: 288 -AEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + +V++++  +L   LS  +  ID L
Sbjct: 330 NARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAERTIDEL 389

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     ++   +     E++   +       E E 
Sbjct: 390 KEQVDAALGAEEMVETLTDRNLDLEEKVRKLKETVGDLEAINEMNDE-LQENARETELEL 448

Query: 396 KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
           +  +      +   +  +++       ++++++  +   R+         + +       
Sbjct: 449 REQLDMAGAQVRDAQKRVEAAQE----TVADYQQTIKKYRQLTAHLQDVNRALTNQQEAS 504

Query: 456 VISV 459
           V   
Sbjct: 505 VERQ 508


>gi|260890620|ref|ZP_05901883.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260859665|gb|EEX74165.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 291

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 35/220 (15%), Positives = 90/220 (40%), Gaps = 22/220 (10%)

Query: 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
           +++  L++ +  +  Y+  G  FLD +QE  +G+M     ++     + +    ++VK  
Sbjct: 73  LIDKYLKIAVKESLLYSKYGFSFLDTVQEATLGIMSGLNYYN--KIMEITKEPEFFVKNF 130

Query: 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
             + I +    +   +   +  + +     ++        + +EI+K++ +  E + ++ 
Sbjct: 131 AVKYILEFQKNLLKDIKSSELSYIL---YLKVKVDRSMGFSMDEISKQMNVSTEYIEQLE 187

Query: 568 KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
           K+              D     + I +   +   D   Q  + E   + L  L     ++
Sbjct: 188 KLF-------------DEVEPEELIGNTQILEKADKITQMYILENIPKKLNYLDE---QI 231

Query: 628 LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
           L M +G+  +  +T +E+ K   +    ++ ++ KA+ KL
Sbjct: 232 LVMAYGLD-DKVYTEKEIAKSLNIASHNVKILKEKALNKL 270


>gi|149409061|ref|XP_001508877.1| PREDICTED: hypothetical protein [Ornithorhynchus anatinus]
          Length = 1096

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 61/485 (12%), Positives = 129/485 (26%), Gaps = 92/485 (18%)

Query: 171 RDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDI 230
            D   +    L +II          +     GTE    +  +    E           D 
Sbjct: 69  GDISEELNRQLEDIIKTYGSATGLVEESPIKGTEKPEKKPEKPEKTESLDHPEDGENEDA 128

Query: 231 ESAAKVSKDDRSKVDSPPENAENDERNLDEDED-----DSAHTLSAMEDQLR---PKVMC 282
              ++       +  S  E     +      ++      + + L+  E++L     K   
Sbjct: 129 NDESEREASGTKEPGSIKEQKLEKKILKGLGKEATLLMQTLNKLNTSEEKLEVLFKKYAE 188

Query: 283 ALDEIAEVYRELRSLQDNAVNGQKDEKS----SVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            L+E     ++L+ LQ       K++        +  + + KL  L   L  +   +   
Sbjct: 189 MLEEHRAEQKKLKHLQKRQQQVTKEKDQLQSEHSRAILARSKLESLCRELQRHNKTLKEE 248

Query: 339 VEQ-------------------LYDISKRIMHNEGELLRLAQ--------------SYGI 365
             Q                   L DI  +I       ++L Q               Y +
Sbjct: 249 TLQRAREEDEKRKEITSHFQGTLSDIQAQIEQQSERNVKLCQENTELAEKLKSIIDQYEL 308

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
           + +   +  + REL    V    +  +   K            + N+     ++T +   
Sbjct: 309 REEHLDKIFKHRELQQKLVDAKLEQAQEMMKEAEERHQREKEYLLNQAAEWKLQTKMLKE 368

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLV--------------------ISVAKKYTN 465
           +   + + ++         +K + ++N                         +   ++ N
Sbjct: 369 QETLLQAQLKLYAERFEEFQKTLTKSNEVFATFKQEMDKTTKKMKKLEKDTATWKSRFEN 428

Query: 466 RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525
                LD+I+E      KA    ++                   +    ++    + V  
Sbjct: 429 CNKALLDMIEE------KALRTKEYECFV--------------MKIQRLENLCRALHVER 468

Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT-------KEPISLET 578
            +   K+     R   +       EE A   A   E + +  +           P SL  
Sbjct: 469 NELYKKIKDAKFRDEEEESAHCLEEEAATNAAGNEEMLAEEAREASTSGDAKNPPTSLTL 528

Query: 579 PIGDE 583
               E
Sbjct: 529 SHHME 533


>gi|332665930|ref|YP_004448718.1| hypothetical protein Halhy_3997 [Haliscomenobacter hydrossis DSM
           1100]
 gi|332334744|gb|AEE51845.1| hypothetical protein Halhy_3997 [Haliscomenobacter hydrossis DSM
           1100]
          Length = 1111

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 44/318 (13%), Positives = 116/318 (36%), Gaps = 37/318 (11%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           +Q+E  +     +   + +     +E  ++ + +            Q+  +    S +DP
Sbjct: 550 KQLEKLLERQKELEKQIKEAQKAFEE--NKKNQEQLGETPEELQEKQEMLEELMESLEDP 607

Query: 121 VRMYLRE-MGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTT 179
               ++E M  IE L +E E   A         MM  + +     +  +   +EL     
Sbjct: 608 E---MKELMEKIEKLMQEMEKDQAL-------EMMEQMKDQNEKRENELERMEELFK-QL 656

Query: 180 LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            L + I+  A    E        +E    +K      EK+++++ +   D+E   +  + 
Sbjct: 657 ELEQEINKAADKLDEMAKKQEELSEKTEDKKEAAEQLEKQQEELNKEFEDLEKKMEDIEK 716

Query: 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
              ++++P         +  E+ +D    +   E QL            +   +    Q 
Sbjct: 717 KNEELENP-----QKMDDPKEEMEDIKQDMQDSEKQLEQ----------KQNSKSAKSQK 761

Query: 300 NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV-------EQLYDISKRIMHN 352
           +A    K++ + ++ +    ++  +   + + +  ++ LV       + +  ++K  ++ 
Sbjct: 762 SAAQKMKNQANKMRSQQQANQMEAMQEDMKMLRQLLENLVGLSFDQEDLIKGLNKTEINT 821

Query: 353 EGELLRLAQSYGIKRDVF 370
              + ++ + + I +D F
Sbjct: 822 PRYVQQVQRQFKI-KDDF 838


>gi|288926030|ref|ZP_06419959.1| lipoprotein [Prevotella buccae D17]
 gi|288337250|gb|EFC75607.1| lipoprotein [Prevotella buccae D17]
          Length = 284

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 22/114 (19%), Positives = 52/114 (45%), Gaps = 2/114 (1%)

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           EN   ++       D     +   ++++    M  L+EI E +R++    +N V+  KD 
Sbjct: 21  ENKNANQLAGMTQNDSLNKIIEQKDNEINDM-MGTLNEIQEGFRQISEA-ENRVSLMKDG 78

Query: 309 KSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQS 362
           + + + + L+E +  + G +  N+  I+ L +Q+ + S +    +  +  L + 
Sbjct: 79  EGANRAQQLRENIKFISGRMKENRELIEKLRQQMRESSMKGEQFKKTIESLMKQ 132


>gi|218263538|ref|ZP_03477619.1| hypothetical protein PRABACTJOHN_03306 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222661|gb|EEC95311.1| hypothetical protein PRABACTJOHN_03306 [Parabacteroides johnsonii
           DSM 18315]
          Length = 95

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 9/75 (12%)

Query: 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665
           +  L+E   R L +L  R   V       G       +E+  +  ++   +      A++
Sbjct: 22  EEELQEVIRRALDTLPERCREVFIKSRIEG----LKYKEISDELGISVNTVENQMVTALK 77

Query: 666 KLKHPSRSKKLRSFL 680
           KL+       L+ +L
Sbjct: 78  KLRVA-----LKDYL 87


>gi|16799352|ref|NP_469620.1| RNA polymerase factor sigma-70 [Listeria innocua Clip11262]
 gi|16412704|emb|CAC95508.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria innocua
           Clip11262]
          Length = 201

 Score = 37.9 bits (86), Expect = 6.2,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EEMAMLELARSGDTDALEYFFSRYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DESKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|50545657|ref|XP_500367.1| YALI0B00968p [Yarrowia lipolytica]
 gi|49646233|emb|CAG82581.1| YALI0B00968p [Yarrowia lipolytica]
          Length = 497

 Score = 37.9 bits (86), Expect = 6.3,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 45/126 (35%), Gaps = 3/126 (2%)

Query: 207 SYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSA 266
              + +    +KE +   E +G  E     + D     D      E+D  + +E    SA
Sbjct: 322 DEGEMDVDLLDKELERALEDQGSDEGEEIEADDASESEDEGEGAGESDNSDEEELPRASA 381

Query: 267 HTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAV---NGQKDEKSSVKCKVLKEKLVK 323
                 + +        +D IA++   ++  QD+A    N    E+ + +   LK +L  
Sbjct: 382 GMDDDDDGEEGGHAKVLVDTIADLEATIKKQQDDADRTANAMLKERFNQRISKLKHELEV 441

Query: 324 LVGSLS 329
               L 
Sbjct: 442 KKKQLK 447


>gi|320582141|gb|EFW96359.1| putative nuclear condensin complex SMC ATPase [Pichia angusta DL-1]
          Length = 1272

 Score = 37.9 bits (86), Expect = 6.3,   Method: Composition-based stats.
 Identities = 33/261 (12%), Positives = 82/261 (31%), Gaps = 8/261 (3%)

Query: 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
           +  I  + K       E  S  + +  ++    D + E   DI   AK      S +   
Sbjct: 190 DQGIDLDHKRFLILQGEVESIAQMKPKAEGNSDDGLLEYLEDIIGTAKYKGTIESSIREI 249

Query: 248 PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            +  +   +     E            +         ++     + L        +    
Sbjct: 250 DDLNDICVQKAHRYEIVEKAKEDLEGGKENALKYLRKEKALADKKSLYLQYRLLKDKDLL 309

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
           EK +   + LKEKL K     + +   ID L +  +++S  +   E ++  L  ++    
Sbjct: 310 EKKTAALESLKEKLAKEKEQTAQHNDEIDELTKHHHELSSEVKAIEKQVASLKSAH---- 365

Query: 368 DVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427
               ++ +  ++         +  + +    +      + +    I  +      S ++ 
Sbjct: 366 ----KKIEREKISMDEKIKHNENRKKKAVKALQSSSSQVRENEANIAELERSQKESQTQL 421

Query: 428 RHIVSMVRKGECEASIAKKEM 448
             + S ++K + +    K E+
Sbjct: 422 EELNSALKKEQEQLEAIKYEL 442


>gi|195477273|ref|XP_002086313.1| GE22939 [Drosophila yakuba]
 gi|194186103|gb|EDW99714.1| GE22939 [Drosophila yakuba]
          Length = 1338

 Score = 37.9 bits (86), Expect = 6.3,   Method: Composition-based stats.
 Identities = 53/346 (15%), Positives = 125/346 (36%), Gaps = 35/346 (10%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 443 ELDEIAESIELLTLDKEMAEERMETLQMELEMAQERNDELSL------DVEILKAEQEEQ 496

Query: 142 IAKRIEAGRAMMMASLC-ESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFF 200
             +RIE     + A L  +S   F  L  +   L +    LR+ +  E  IG  +     
Sbjct: 497 QGQRIEKSDKQIGAGLTTQSSGEFLRLEQYNQRLRETVVRLRDTLAQEKQIGQRTHKELE 556

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                 +  K       +  D+++    D++     S    + V                
Sbjct: 557 TKHSEINELKSIKELLSRRVDNMEVQLMDLKEQVDASLGAEAMVT--------------- 601

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
                   L++++ +L  +V    DE+ E+   L  +Q+  +   ++ ++      L+E+
Sbjct: 602 -------QLASLKLELEDRVKLLEDEVNEL-EALEQIQEQLIESNQELET-----DLREE 648

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           + KL G + + + + +  +E LYD    IM     + +L +   ++ D  L        +
Sbjct: 649 IDKLSGQVKILEQQKNAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSSAN 708

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
                   +  + ++++  +        +  +IK++ +       E
Sbjct: 709 ESQQEDGSNQSQTDYQHIFSVSKAYGRALEQQIKTVELRLQRQHLE 754


>gi|303234595|ref|ZP_07321229.1| albumin-binding protein [Finegoldia magna BVS033A4]
 gi|302494258|gb|EFL54030.1| albumin-binding protein [Finegoldia magna BVS033A4]
          Length = 954

 Score = 37.9 bits (86), Expect = 6.4,   Method: Composition-based stats.
 Identities = 22/160 (13%), Positives = 54/160 (33%), Gaps = 2/160 (1%)

Query: 186 DLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVD 245
           D    +            E    +          + D+ +   +I    +  + ++ K  
Sbjct: 332 DFLNYLIESKGKIKASDDEDMVKKTLAKFDAALTKADLDKVVAEINKEIEAQEKEKQKAK 391

Query: 246 SPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQ 305
              E  EN ++++DE +  S       +  +       +DEI ++  +   +       +
Sbjct: 392 ELAEAKENAKKHIDELKHLSDKAKELAKKDIDEA--TTIDEIKDIVAKADVMDRKTAEKE 449

Query: 306 KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDI 345
           + EK +   K  KEK ++ +    +     + L+ +   I
Sbjct: 450 EAEKLAAALKDAKEKAIEAIRKEGVKSKLYEDLINKAKTI 489


>gi|114601610|ref|XP_001163775.1| PREDICTED: similar to Kinesin-like protein KIF3A (Microtubule plus
           end-directed kinesin motor 3A) isoform 3 [Pan
           troglodytes]
          Length = 701

 Score = 37.9 bits (86), Expect = 6.4,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 69/195 (35%), Gaps = 12/195 (6%)

Query: 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237
                ++I+++A I  E K            + +  +  EK   D+ + + + +S  +  
Sbjct: 415 KKRRDKMIEMQAKIDEERKALETKLDMEEEERNKARAELEKREKDLLKAQQEHQSLLEKL 474

Query: 238 KDDRSKV---DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYREL 294
                KV            ++  L E+ +          +QLR ++     E  ++  + 
Sbjct: 475 SALEKKVIVGGVDLLAKAEEQEKLLEESNMELEERRKRAEQLRRELEEKEQERLDIEEKY 534

Query: 295 RSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNE 353
            SLQ+ A    K  +K        K ++  L      +Q  I+ L+E +  +S+ +    
Sbjct: 535 TSLQEEAQGKTKKLKKVWTMLMAAKSEMADLQQE---HQREIEGLLENIRQLSRELRLQM 591

Query: 354 GELLRLAQSYGIKRD 368
             +        I RD
Sbjct: 592 LIIDNF-----IPRD 601


>gi|281208823|gb|EFA82998.1| hypothetical protein PPL_03778 [Polysphondylium pallidum PN500]
          Length = 1705

 Score = 37.9 bits (86), Expect = 6.6,   Method: Composition-based stats.
 Identities = 55/387 (14%), Positives = 115/387 (29%), Gaps = 52/387 (13%)

Query: 294 LRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL-VEQLYDISKRIMHN 352
           L  LQ   +   + E+  ++ + L+++         L Q RI+   +EQ     +RI + 
Sbjct: 195 LSQLQQIKLEKVRLEQERIEKERLEQE--------RLEQERIEKERLEQERLEQERIENE 246

Query: 353 EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
             E  R+A           +  Q R          +   E   +  +A E     +I  E
Sbjct: 247 RLEQERIAAE---------KLEQERIAAEKLAEEERIATEKHEQERLAAEKLEQERIAAE 297

Query: 413 IKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD 472
                      ++E   I + + + E  A+   ++   A  +L            +    
Sbjct: 298 KLEQERIAAEKLAEEERIAAEMLEQERIAAEKMEQERIAAEKLAEEER-------IAAEK 350

Query: 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532
           L QE       AAEK +          A   +           +  +       +K+ + 
Sbjct: 351 LEQE-----RIAAEKLEEER-IAAEKLAEERIAAEKMEQERIAAEKLEQERIAAEKLEQE 404

Query: 533 VRTARRMSNK-IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591
              A ++  + I  E   +E      +  E +       ++   +      E      + 
Sbjct: 405 RIAAEKLEQERIAAEKLEQERIAAEKLEQERIAAEHARLEQERIVAEEQRLEREREEMEI 464

Query: 592 IEDKNAVSPLDSAIQANLRETTT-----------------RVLASLTPREERVLRMRFGI 634
           +  +  V     A +   +E                     +LA+   +E  + + +   
Sbjct: 465 LAAEERVEQERIAAEKLEQERIAAEELAEKERKEREREEMEILAAEQEKERVLEQEQLAQ 524

Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEA 661
                   E +       +E+I Q+E 
Sbjct: 525 EREE---QERIAAIDQEQQEKIDQLEK 548


>gi|254758386|ref|ZP_05210413.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Australia
           94]
          Length = 170

 Score = 37.9 bits (86), Expect = 6.6,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|325290838|ref|YP_004267019.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324966239|gb|ADY57018.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 188

 Score = 37.5 bits (85), Expect = 6.8,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 38/99 (38%), Gaps = 5/99 (5%)

Query: 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT 638
            +       L D I D  A +P + +      E     + +L+ R+  +L  ++ + +  
Sbjct: 94  MVFMGMEDDLMDSIPDT-ANTPEEISAAKETYEELGAAIETLSERDRDLLYCKYNLELKE 152

Query: 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677
               +E+ +   +    IRQ   +A R+       + L+
Sbjct: 153 ----KEIAEVMNIPVNNIRQYLVRARRRALKTLNERGLQ 187


>gi|198414692|ref|XP_002123901.1| PREDICTED: similar to superfast myosin heavy chain, partial [Ciona
            intestinalis]
          Length = 2049

 Score = 37.5 bits (85), Expect = 6.8,   Method: Composition-based stats.
 Identities = 63/373 (16%), Positives = 134/373 (35%), Gaps = 11/373 (2%)

Query: 1    MTIGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSS 60
            + I K+ N++   E  D  D L       S  ++   AR++  +  EEL + L   E + 
Sbjct: 1481 LEIVKRENKNLSEEINDLTDQLT--TGGKSLHEL-DKARKKAELECEELRSALEEAEGAL 1537

Query: 61   EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
            E  E  V  L      V    D + +E  E+      +   +   +Q   D   +S  D 
Sbjct: 1538 ELEESRVLRLQLELTQVKADIDRKLQEKEEEFDSTRKNHQRAIESMQASLDVEIKSRTDA 1597

Query: 121  VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            VR   ++    +L   E ++  A R  A +  ++  L  +    Q  +     +++    
Sbjct: 1598 VRA--KKKLETQLNDAEMQLDHANRNLAEQIKLVRKLQVTIKEIQDQMDEDQRIHEELRE 1655

Query: 181  LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD----VQETEGDIESAAKV 236
               I +    I            E +   ++   ++  +  D    +      + SA + 
Sbjct: 1656 QYSIQERRLTITISELEETKSALESNERARKHAEAELLDISDRINTLSAQNSALSSAKRK 1715

Query: 237  SKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS 296
             + D  ++    E+A  + +  DE    +    + M ++LR +    L    E  ++   
Sbjct: 1716 LETDNEQLRGDLEDALMEAKTADERAKKATSDAARMSEELRSEQQHILS--IERVKKTLE 1773

Query: 297  LQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
            +Q + ++ + DE  +   K  ++ L +L   L   Q+ ++    +  +  K     +  L
Sbjct: 1774 VQVHEMSIKLDEAEAYALKGGRKALAQLQARLKDVQNELEAEQRRHAETLKNYRKMDRRL 1833

Query: 357  LRLAQSYGIKRDV 369
              L+      +  
Sbjct: 1834 KELSFQADEDQKN 1846


>gi|32451885|gb|AAH54565.1| LOC407638 protein [Danio rerio]
          Length = 910

 Score = 37.5 bits (85), Expect = 6.8,   Method: Composition-based stats.
 Identities = 34/259 (13%), Positives = 93/259 (35%), Gaps = 18/259 (6%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           E+      L ++ +  + +  +         E     +    ++++  +++ +T   IE 
Sbjct: 196 EMEKYKIQLEQLQEWRSKMQEQQNDLQKQLKEAKKEAREALEAKDRYMEEMADTADAIEM 255

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRP------KVMCALDE 286
           A    +    + +S  +  E+ +  L+E   D       +E++          V    ++
Sbjct: 256 ATLDKEMAEERAESLQQETESLKEKLEELTMDMEILKHEIEEKGSDGAASSYHVKQLEEQ 315

Query: 287 IAEVYRELRSLQDNAVNGQKD--------EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
            A +   L  ++D + + +++        EK + + + L+ +  KL   + L +  ID L
Sbjct: 316 NARLKEALVRMRDLSSSEKQEHVKLQKQMEKKNSELETLRSQKEKLQEEMKLAEDTIDEL 375

Query: 339 VEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
            EQ+       + +       L L +     R+   +     E++   +       E E 
Sbjct: 376 KEQVDAALGAEEMVETLTERNLDLEEKVRELRETVSDLESINEMNDE-LQENARETELEL 434

Query: 396 KNFVACEVDSILKIRNEIK 414
           +  +      + + +  ++
Sbjct: 435 REQLDLAGARVREAQKRVE 453


>gi|15790077|ref|NP_279901.1| Htr15 [Halobacterium sp. NRC-1]
 gi|169235800|ref|YP_001689000.1| transducer protein htr15 [Halobacterium salinarum R1]
 gi|10580513|gb|AAG19381.1| Htr15 transducer [Halobacterium sp. NRC-1]
 gi|167726866|emb|CAP13652.1| transducer protein htr15 [Halobacterium salinarum R1]
          Length = 636

 Score = 37.5 bits (85), Expect = 6.9,   Method: Composition-based stats.
 Identities = 26/162 (16%), Positives = 62/162 (38%), Gaps = 1/162 (0%)

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
             +G +     F+  +       +   +       +      E  A++  D     D   
Sbjct: 204 DAMGMDHASEAFYPDDRRVKTLADKVIESPRSAAAEFDIERSEEKAQLYADTSVMTDQGG 263

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
            +     +     +DD      A   + R + +   D + E+  EL +  D   +GQ  +
Sbjct: 264 TDRHIRFKASPIFDDDGELLAVAETIEDRTEDVRRADAVEELVDELSTTIDALSSGQLSK 323

Query: 309 KSSVKCK-VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRI 349
           ++S + + ++ E+LV +V +L+    + + LV Q+   ++ +
Sbjct: 324 RASFEHEGIINEQLVSVVSALNGMADQFERLVGQVDGQTQEL 365


>gi|323496527|ref|ZP_08101581.1| hypothetical protein VISI1226_11189 [Vibrio sinaloensis DSM 21326]
 gi|323318371|gb|EGA71328.1| hypothetical protein VISI1226_11189 [Vibrio sinaloensis DSM 21326]
          Length = 976

 Score = 37.5 bits (85), Expect = 6.9,   Method: Composition-based stats.
 Identities = 50/320 (15%), Positives = 101/320 (31%), Gaps = 24/320 (7%)

Query: 10  DSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAM 69
           D   E +  D S   D S ++   ++           +  +  L   E+    ++D    
Sbjct: 432 DDAGEDDGFDLSDEGDMSQEALDSLLAQ---------DGDSEDLDAGELDQSMLDDLFNE 482

Query: 70  LSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMG 129
           + +      DG D  D +   D  D    +  S   L +   ++D   DD +   +    
Sbjct: 483 VED------DGSDSLDFDNLLDEGDDFDLSDESETPLDEPSLASDSEIDD-IFAQMEAQA 535

Query: 130 SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIW-------RDELNDGTTLLR 182
            +E L        A   E            S      L+          D   +G  L  
Sbjct: 536 DLETLEANSLDETALLDEMLDEDAPTVDASSTDLLDELLADNTDALTKADVEAEGEDLFD 595

Query: 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDD-VQETEGDIESAAKVSKDDR 241
           E+I L+       +       E       E    + E D+ + ++ G+   +   S +  
Sbjct: 596 ELIGLDDAEPEIGQESTDLLDELIDDTDGESFDLDSELDELIGDSTGEESISLDDSTELL 655

Query: 242 SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
            ++    E+ +    +L ++  D    L  +E Q       AL   A+   E    ++  
Sbjct: 656 DELFDSEESGDVSNEDLGDEGTDLFEELLEIEKQNLEPSDEALSGAADTPEEAMEAEEPT 715

Query: 302 VNGQKDEKSSVKCKVLKEKL 321
            + ++D   S   + +  ++
Sbjct: 716 ESAEQDLDESAFVEEMVNEI 735


>gi|302390570|ref|YP_003826391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
 gi|302201198|gb|ADL08768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
          Length = 234

 Score = 37.5 bits (85), Expect = 6.9,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 49/132 (37%), Gaps = 3/132 (2%)

Query: 446 KEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
             ++E     + SV +KY  R ++    D +    I   +A +++D   G  F  +A   
Sbjct: 21  NRLIEEYRPFIASVVEKYLGRRVEYGIDDELSVAMIAFDEAVQRYDIKKGN-FLAFARNV 79

Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
           ++  +      +       +++                +  ++   EEI+++  + +  +
Sbjct: 80  IRSRLVDYYRRERKNRETVMYIVQNQEDEEYELDISIEESIKKHREEEISEQRRLEILEI 139

Query: 564 RKVLKITKEPIS 575
           +K L+      S
Sbjct: 140 KKELEKWGLTFS 151


>gi|256005340|ref|ZP_05430305.1| chromosome segregation protein SMC [Clostridium thermocellum DSM
            2360]
 gi|255990659|gb|EEU00776.1| chromosome segregation protein SMC [Clostridium thermocellum DSM
            2360]
          Length = 1210

 Score = 37.5 bits (85), Expect = 6.9,   Method: Composition-based stats.
 Identities = 54/321 (16%), Positives = 117/321 (36%), Gaps = 14/321 (4%)

Query: 157  LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
            L +     +  +   D L      L   I  E     E        +E       +    
Sbjct: 742  LAQIEENIKRSLARIDMLKQEKEQL---IRQEKDTCLELSKYEDELSEIERDIAEKKEVV 798

Query: 217  EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
             + ++  +E +   ++      D R  V+S  E+ E  +  L+   ++    + AME + 
Sbjct: 799  ARYQEKNKEEQSVRDALHNDITDYRISVNSILESMEGVKETLERLVNEKNSLVKAMERKK 858

Query: 277  RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-EKLVKLVGSLSLNQSRI 335
                     E A   +E+++LQ+      K  K   + K  K  ++ ++     + +   
Sbjct: 859  --------AEKARNEQEIKALQEKNEGLDKLIKKYEEEKSGKTFEIDRITEEKKIREEES 910

Query: 336  DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
              +++Q+ +I+K I+  + E  R+      K +  +E  Q R  D + ++Y       + 
Sbjct: 911  AGIIDQITEINKNILLLQEEYSRIEVK-KAKLESEMESIQNRMWDEYELTYTNALELKKD 969

Query: 396  KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
               +A     I +IRNEIK +      +I E+            + S   ++  +   ++
Sbjct: 970  IGSMAQAQKRIAEIRNEIKELGPVNVAAIDEYIKTKERFEFMSAQKSD-MEQAEKKLQKV 1028

Query: 456  VISVAKKYTNRGLQFLDLIQE 476
            +  +      + ++   LI E
Sbjct: 1029 INEMMTIMKRQFMEKFKLINE 1049


>gi|86134801|ref|ZP_01053383.1| conserved hypothetical protein [Polaribacter sp. MED152]
 gi|85821664|gb|EAQ42811.1| conserved hypothetical protein [Polaribacter sp. MED152]
          Length = 1122

 Score = 37.5 bits (85), Expect = 7.0,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 67/165 (40%), Gaps = 8/165 (4%)

Query: 254 DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
           +++   E           M  +   ++   LDE  E    L+  +D+      + K   K
Sbjct: 538 NDKKKVESFIKRQEQYKKMMQRQTDQLQENLDEKKENEPSLQEKKDDLKERINELKQLTK 597

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR---LAQSYGIKRDVF 370
            + L E++ K+     LN+   + LV++  +++++    +  L +   + + + +++   
Sbjct: 598 QQKLLEEIQKMAD--KLNK---EDLVQKAKELAQQNKQQQRSLEKTLEMVKRFYVEQKTM 652

Query: 371 LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKS 415
              ++  EL     S  K+    E +  V+ + D I K   E+K 
Sbjct: 653 QIANKIDELSKEQESLEKNENNLEKQQEVSKKFDDIQKDLEELKK 697


>gi|229826254|ref|ZP_04452323.1| hypothetical protein GCWU000182_01626 [Abiotrophia defectiva ATCC
           49176]
 gi|229789124|gb|EEP25238.1| hypothetical protein GCWU000182_01626 [Abiotrophia defectiva ATCC
           49176]
          Length = 280

 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 91/257 (35%), Gaps = 10/257 (3%)

Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
           KV +  + +    L L+ S+ D +   L       +  EG   +      ++      + 
Sbjct: 25  KVHESDIKEFFEDLELDDSQFDHIFAYLKASH---ITIEGYEAKEEIEAEVREYENAAKE 81

Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
           Q  E             +   K  +  + + +     E++ I   T       +    ++
Sbjct: 82  QLEEAAREGFDKKSGIKKKSNKKTLNFQSEFLNMYLEELRYIEKMT------VKEEEKLI 135

Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF-DWCLG 493
                    A+   +E  L  V+ +A+ +      F +LI EGN+GL+   ++  +    
Sbjct: 136 ELLLKGDEKAEASYIERKLHKVVEIARGFELTEDYFKELISEGNVGLLIGLKELKNLERD 195

Query: 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIA 553
            K   +    ++ A+   I +          M  K++ V   A++M       PT +E+A
Sbjct: 196 DKPIEFIESRIESAMQDFIEESLEMESTANAMVAKVNFVSDAAKKMKEMNGSSPTLKELA 255

Query: 554 KKLAMPVEGVRKVLKIT 570
               +    +  +++++
Sbjct: 256 SYTNLTEAELTDIIELS 272


>gi|222622169|gb|EEE56301.1| hypothetical protein OsJ_05377 [Oryza sativa Japonica Group]
          Length = 2676

 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 49/297 (16%), Positives = 95/297 (31%), Gaps = 16/297 (5%)

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
            LL  +ID       ES        E  S  K    +   ER    E +    +      +
Sbjct: 1705 LLSRLIDGYKTHLSESTVRSSAEMETLSETKISKDASTSER--GMEEKEMALNTLSGELE 1762

Query: 240  DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
                  +  E   ++     +       TL A  DQL+      ++    +  EL S+  
Sbjct: 1763 HTRNSLALVEQQRDEAVEKTQLLTIELETLRAQIDQLQGDGAEQMNRYQSLMLELESMTK 1822

Query: 300  NAVN-GQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLR 358
               +  +K  +   KC  L+EKL   V          D L + + +++  I   + E  +
Sbjct: 1823 QRDDLQEKLGQEEQKCTSLREKLNVAVRKGKGLVQHRDSLKQTMEEMNTMIEKLKVERKQ 1882

Query: 359  LAQSYGIKRDVFLERHQGRELDPHWVSY-------------AKDFPEGEWKNFVACEVDS 405
              +S   +R   + R    E   H  +                   + +    V      
Sbjct: 1883 HIESLESERSSLMGRLAENEKSLHDATQYLSRLLNSLSTVDIGREFDTDPITKVENFSKF 1942

Query: 406  ILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK 462
             L ++NE+K     T + ++E   +       + E   A+  + E+  +  +  + +
Sbjct: 1943 CLDLQNEVKKSKQATELLLAELNEVHERADNLQDELVKAEAALSESFKQNSVVESAR 1999


>gi|195485613|ref|XP_002091161.1| GE13493 [Drosophila yakuba]
 gi|194177262|gb|EDW90873.1| GE13493 [Drosophila yakuba]
          Length = 4467

 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 28/140 (20%), Positives = 53/140 (37%), Gaps = 4/140 (2%)

Query: 188  EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
            +    P  +  F       + Q  E+   + + +     EGD +S    S++D +  ++ 
Sbjct: 3769 DQDEQPTDENPFDIDAMKENMQPAEEPQADGDDEPDANEEGDPQSDGSDSEEDETGTEAK 3828

Query: 248  PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
            P  AE D+   +E   +        E Q R ++    D   E   E    ++     + +
Sbjct: 3829 P--AEEDQGEGEEASPEDEK--DEAETQKRGELEDEDDPKTEDTPEDSKEEEQKREDKPE 3884

Query: 308  EKSSVKCKVLKEKLVKLVGS 327
            E S  K K  KE+ V+ +  
Sbjct: 3885 EHSQSKDKASKEENVQSMPE 3904


>gi|170029180|ref|XP_001842471.1| myosin-2 heavy chain [Culex quinquefasciatus]
 gi|167881574|gb|EDS44957.1| myosin-2 heavy chain [Culex quinquefasciatus]
          Length = 1946

 Score = 37.5 bits (85), Expect = 7.1,   Method: Composition-based stats.
 Identities = 44/314 (14%), Positives = 112/314 (35%), Gaps = 13/314 (4%)

Query: 143  AKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHG 202
            A+ +E G+  + A L E+  T ++L      L      L   I+    +  E        
Sbjct: 1390 AEELEEGKRKLQARLAEAEETIESLTQKVIALEKTKQRLSTEIE---DLQLEVGRSTVIA 1446

Query: 203  TEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDE 262
                   +  D    + +  V +  G+++++ K  ++  +++       E  +  L+   
Sbjct: 1447 NSAEKKHRSFDKIIGEWKLKVDDLAGELDASQKECRNYSTELFRLKGAYEEGQEQLEAVR 1506

Query: 263  DDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ-DNAVNGQKDEKSSVKCKVLKEKL 321
             ++ +    ++D L  ++      I E+ +  + L+ +        E++    +  + K+
Sbjct: 1507 RENKNLADEVKD-LLDQIGEGGRNIHEIEKSRKRLEAEKDELQAALEEAEAALEQEENKV 1565

Query: 322  VKLVGSLSLNQSRID-LLVEQLYDISKRIMHNEGELLRLAQSY---GIKRDVFLERHQGR 377
            ++    LS  +  ID  + E+  +      +++  L  +  S+      +   L   +  
Sbjct: 1566 LRAQLELSQVRQEIDRRIQEKEEEFENTRKNHQRSLESVQASHEADAKGKAEALRMKKKL 1625

Query: 378  ELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKG 437
            E D + +  A D          A    +I + + E++ +   T             +   
Sbjct: 1626 EADINELEIALDHANKAN----AEAQKNIKRYQQELQDVQGITQEEQRARDEAREQLGIS 1681

Query: 438  ECEASIAKKEMVEA 451
            +  A   + E+ E+
Sbjct: 1682 KRRAHALQNELEES 1695


>gi|297295041|ref|XP_001099789.2| PREDICTED: kinesin family member 3A [Macaca mulatta]
          Length = 712

 Score = 37.5 bits (85), Expect = 7.2,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 69/191 (36%), Gaps = 12/191 (6%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            ++I+++A I  E K            + +  +  EK   D+ + + + +S  +      
Sbjct: 443 DKMIEMQAKIDEERKALETKLDMEEEERNKARAELEKREKDLLKAQQEHQSLLEKLSALE 502

Query: 242 SKV---DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            KV            ++  L E+ +          +QLR ++     E  ++  +  SLQ
Sbjct: 503 KKVIVGGVDLLAKAEEQEKLLEESNMELEERRKRAEQLRRELEEKEQERLDIEEKYTSLQ 562

Query: 299 DNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           + A    K  +K        K ++  L      +Q  I+ L+E +  +S+ +      + 
Sbjct: 563 EEAQGKTKKLKKVWTMLMAAKSEMADLQQE---HQREIEGLLENIRQLSRELRLQMLIID 619

Query: 358 RLAQSYGIKRD 368
                  I RD
Sbjct: 620 NF-----IPRD 625


>gi|297708729|ref|XP_002831109.1| PREDICTED: LOW QUALITY PROTEIN: myosin-9-like [Pongo abelii]
          Length = 1960

 Score = 37.5 bits (85), Expect = 7.3,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 85/233 (36%), Gaps = 12/233 (5%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +      L A
Sbjct: 1505 EMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAKLRLEVNLQA 1564

Query: 272  MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
            M+ Q    +    ++  E  ++L           +DE+     +    K L+  L  L  
Sbjct: 1565 MKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAVAARKKLEMDLKDLEA 1624

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +       D  ++QL  +  ++     EL          R+  L + +  E     +  
Sbjct: 1625 HIDSANKNRDEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQAKENEKKLKSMEA 1680

Query: 387  AKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMVRK 436
                 + E       +  +     ++ +EI + S +  +++ E R + + + +
Sbjct: 1681 EMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARIAQ 1733


>gi|71897355|ref|NP_001026538.1| dynactin subunit 1 [Gallus gallus]
 gi|14916981|sp|P35458|DCTN1_CHICK RecName: Full=Dynactin subunit 1; AltName: Full=150 kDa
           dynein-associated polypeptide; AltName: Full=DAP-150;
           Short=DP-150; AltName: Full=p150-glued
 gi|6065857|emb|CAA44617.2| dynactin [Gallus gallus]
          Length = 1224

 Score = 37.5 bits (85), Expect = 7.3,   Method: Composition-based stats.
 Identities = 42/344 (12%), Positives = 110/344 (31%), Gaps = 25/344 (7%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E ++   K         +  L +  +  + +  W+ ++ +    L+  +        ++ 
Sbjct: 221 EEKLETLKIKRNEDKAKLKELEKYKIQLEQVQEWKSKMQEQQADLQRRLKEAKKEAKDAL 280

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                  E  +           +++  +E    ++      K+    +    E  +++  
Sbjct: 281 EAKERYMEEMADTADAIEMATLDKEMAEERAESLQQEVDSLKEKVEYLTMDLEILKHEIE 340

Query: 257 NLDEDEDDSAHTLSAMEDQ---LRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVK 313
               D   S++ +  +E+Q   L+  ++   D  A   +E   LQ         EK + +
Sbjct: 341 EKGSDGAASSYQVKQLEEQNARLKEALVRMRDLSASEKQEHVKLQKQM------EKKNTE 394

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDIS---KRIMHNEGELLRLAQSYGIKRDVF 370
            + L+++  KL   +   +  +D L EQ+       + +       L L +     R+  
Sbjct: 395 LESLRQQREKLQEEVKQAEKTVDELKEQVDAALGAEEMVETLTERNLDLEEKVRELRETV 454

Query: 371 LERHQGRELDPHWVSYAKDFP-------------EGEWKNFVACEVDSILKIRNEIKSIS 417
            +     E++      A++                 E +  V    +++   +  IK   
Sbjct: 455 GDLEAMNEMNDELQENARETELELREQLDLAAARVREAEKRVEAAQETVADYQQTIKKYR 514

Query: 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK 461
             T       R ++S       +      E+ +  ++   + A 
Sbjct: 515 ELTAHLQDVNRELMSQQEASAEKQQQPPPEIFDFKIKFAETKAH 558


>gi|16802289|ref|NP_463774.1| RNA polymerase factor sigma-70 [Listeria monocytogenes EGD-e]
 gi|224502463|ref|ZP_03670770.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL R2-561]
 gi|254828703|ref|ZP_05233390.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL N3-165]
 gi|254831932|ref|ZP_05236587.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 10403S]
 gi|254900576|ref|ZP_05260500.1| RNA polymerase factor sigma-70 [Listeria monocytogenes J0161]
 gi|254913473|ref|ZP_05263485.1| RNA polymerase factor sigma-70 [Listeria monocytogenes J2818]
 gi|254937946|ref|ZP_05269643.1| RNA polymerase sigma-30 factor [Listeria monocytogenes F6900]
 gi|284800538|ref|YP_003412403.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5578]
 gi|284993724|ref|YP_003415492.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5923]
 gi|16409608|emb|CAD00770.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria monocytogenes
           EGD-e]
 gi|258601108|gb|EEW14433.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL N3-165]
 gi|258610555|gb|EEW23163.1| RNA polymerase sigma-30 factor [Listeria monocytogenes F6900]
 gi|284056100|gb|ADB67041.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5578]
 gi|284059191|gb|ADB70130.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5923]
 gi|293591481|gb|EFF99815.1| RNA polymerase factor sigma-70 [Listeria monocytogenes J2818]
          Length = 201

 Score = 37.5 bits (85), Expect = 7.3,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EELAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|299739060|ref|XP_001835024.2| nonmuscle myosin heavy chain b [Coprinopsis cinerea okayama7#130]
 gi|298403603|gb|EAU86790.2| nonmuscle myosin heavy chain b [Coprinopsis cinerea okayama7#130]
          Length = 2298

 Score = 37.5 bits (85), Expect = 7.4,   Method: Composition-based stats.
 Identities = 47/305 (15%), Positives = 100/305 (32%), Gaps = 5/305 (1%)

Query: 164  FQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDV 223
                    +EL  G+T L+++ +    +  + +       E      +E   + K     
Sbjct: 1016 IMEAEKEIEELRTGSTELQKVGEELKNLAMQREEDIARTKERADVMLQEMEGKLKSETQS 1075

Query: 224  QETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCA 283
            +E   D     +       +  +      N+   + + +++   +L    D +  +   A
Sbjct: 1076 RELLKDKYDGMERDARQAKEQLAEMARTANEYSAMIQKKEEQISSLEQQLDSVTLEKEAA 1135

Query: 284  LDEIAEVYRELRSLQDNAVNGQKDEKSSVKCK-VLKEKLVKLVGSLSLNQSRIDLLVEQL 342
              EI E+  ++ +LQ      Q+D  +    +  L+ ++  L   L+          E  
Sbjct: 1136 SKEILELQHDIDTLQAQLEAEQQDRATEHGLRTKLEAEIDDLRKVLAAKTDEATRRSEAQ 1195

Query: 343  YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF---PEGEWKNFV 399
                  I    G+L RL +     R   LE     +L+   ++              +  
Sbjct: 1196 KSKEAEITDLRGQLNRLQEELSESRKSSLEAQSKLKLELEVINREHKTLLSSHKSLADRD 1255

Query: 400  ACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISV 459
                D + K++  I  +        SE + + + +   E + S A     EA  R + + 
Sbjct: 1256 QASQDQLKKVQANIGELEKNKRAMESELQSLRTKLHDYETQMSEA-TRHKEALERQLATA 1314

Query: 460  AKKYT 464
              KY 
Sbjct: 1315 QAKYR 1319


>gi|251854890|gb|ACT22563.1| liver stage antigen 3 [Plasmodium falciparum]
          Length = 1482

 Score = 37.5 bits (85), Expect = 7.4,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 95/251 (37%), Gaps = 12/251 (4%)

Query: 40   QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA 99
            +   +T+EE+      + V  E  ++TV+++  M  N+VD  + E E+ ++  +D    +
Sbjct: 820  ESDVITVEEIKD----EPVQKEVEKETVSIIEEMEENIVDVLEEEKEDLTDKMIDAVEES 875

Query: 100  SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCE 159
               S   ++  +S      D V + + E+   ++   +  +     ++     +M    E
Sbjct: 876  IEISSDSKEETESIKDKEKD-VSLVVEEVQDNDM---DESVEKVLELKNMEEELMKDAVE 931

Query: 160  SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKE 219
                   LI    ELN+      ++I     +    K       E    +        +E
Sbjct: 932  INDITSKLIEETQELNEVEA---DLIKDMEKLKELEKALSEDSKEIIDAKDDTLEKVIEE 988

Query: 220  RDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK 279
              D+  T  ++     V +D   KV    +  E+  + + E ++  +  L   + +L+  
Sbjct: 989  EHDITTTLDEVVELKDVEEDKIEKVSDLKDLEEDILKEVKEIKELESEILEDYK-ELKTI 1047

Query: 280  VMCALDEIAEV 290
                L+E  E+
Sbjct: 1048 ETDILEEKKEI 1058


>gi|257387148|ref|YP_003176921.1| methyl-accepting chemotaxis sensory transducer [Halomicrobium
           mukohataei DSM 12286]
 gi|257169455|gb|ACV47214.1| methyl-accepting chemotaxis sensory transducer [Halomicrobium
           mukohataei DSM 12286]
          Length = 529

 Score = 37.5 bits (85), Expect = 7.4,   Method: Composition-based stats.
 Identities = 54/356 (15%), Positives = 114/356 (32%), Gaps = 28/356 (7%)

Query: 5   KKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQME 64
                D+     D+ +S+  D SD +  ++   A      T+E+ +  +  D    E++ 
Sbjct: 177 ADSEVDAIERIADAYESMTVDLSD-TVGEIRAFAT-----TVEQTSGAVAEDAAEVERLN 230

Query: 65  DTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMY 124
           +++A      I  +  D     E  + ++   +  S +   +    D       +     
Sbjct: 231 ESLAT----DIRELASDVSGQAERLQSAVAETNDLSATIEEVASTTDEVAGRATE----- 281

Query: 125 LREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREI 184
             E+G+    +       A         +  ++ E      AL    DE+ + T L+ EI
Sbjct: 282 AAEVGA----TGAERTEEAV---ETIEHVADAVDELDRLVAALDDRMDEVAETTGLIDEI 334

Query: 185 IDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKV 244
                 +   +     H   G           +   +  Q+   +IES    ++DD   V
Sbjct: 335 AQQTDMLALNANIEASHAGSGGDGFAVVADEVKGLAEQTQDAIDEIESIVDGARDDVDGV 394

Query: 245 DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNG 304
                       +  E   ++  TL  + + +   V  A+ EIA    +  +  +     
Sbjct: 395 TEEMALTRRRIDDGVETVTEAGETLGTLTETV-DDVDDAMAEIARATDDGAAATEEVSAA 453

Query: 305 QKDEKSSV-----KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
                 S      +   L +   +   ++   + R D L +Q  D+   +   E  
Sbjct: 454 LDQVAESAQQVATRSNELADTAEQTASTMRGVRERADDLNDQTADLMALLDSFETR 509


>gi|289582533|ref|YP_003480999.1| methyl-accepting chemotaxis sensory transducer [Natrialba magadii
           ATCC 43099]
 gi|289532086|gb|ADD06437.1| methyl-accepting chemotaxis sensory transducer [Natrialba magadii
           ATCC 43099]
          Length = 553

 Score = 37.5 bits (85), Expect = 7.4,   Method: Composition-based stats.
 Identities = 28/223 (12%), Positives = 79/223 (35%), Gaps = 9/223 (4%)

Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
           + E    IA          +  +         +    + L +    + EI+D+   I  +
Sbjct: 335 TSERAEEIATDTTETAEEAIDQIEGVEEAAVEVTDDVENLRESVQKIDEIVDVINDIADQ 394

Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
           +     + +        E ++  +  D       +++S A+ S+D+   ++   +  + D
Sbjct: 395 TNLLALNAS-------IEAATAGEAGDGFAVVANEVKSLAEESQDEAKNIERMIDQIQAD 447

Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRS-LQDNAVNGQKDEKSSVK 313
                +  + +   +S   D L  + +  L+ I E  +E  + +Q+ A        S+ +
Sbjct: 448 TEETVDSLETANERVSTGVD-LVEETVDNLERIEESVQEASTGIQEVATATDDQAASTEE 506

Query: 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
              + +  ++    ++     I+   E + ++   +  +   L
Sbjct: 507 VASMTDTAMETSQQVTNGLEAIERHAETVDELVDEVEADVRSL 549


>gi|328875844|gb|EGG24208.1| hypothetical protein DFA_06355 [Dictyostelium fasciculatum]
          Length = 573

 Score = 37.5 bits (85), Expect = 7.5,   Method: Composition-based stats.
 Identities = 59/403 (14%), Positives = 132/403 (32%), Gaps = 40/403 (9%)

Query: 52  FLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKD 111
            LPP  +  ++ +D    +    ++V       + E SE  +   SS  +   + ++++ 
Sbjct: 120 VLPPVTLQPQRADDIAPSVFEYNLSVFADTQEREREWSERGV---SSGLSPVEYAKQKQR 176

Query: 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWR 171
                 DD +R  L + G + L  R G                     + LT   +I   
Sbjct: 177 GVSSRMDDSIRSALVD-GGVGLEGRRG----------------NGGVSAGLTLDDIIGGF 219

Query: 172 DELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIE 231
                G   + E          + +            ++ E+   EK+R ++ E +  + 
Sbjct: 220 SGRAGGE-DMNEFARKMLFTTEQGEQTDSGAAVASGPKETEEERLEKQRQELDELQSSLT 278

Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVY 291
           +A     +    ++   +     E +++E  +D        + +++ K    LD   E  
Sbjct: 279 AAVDEIAETNRDMEEFMQLLRQLEADINE--EDGRRGDLEKQYKIKKKTFALLDNADENL 336

Query: 292 RELRSLQDNAVNGQKDEKSS---------VKCKVLKEKLVKLVGSLSLNQSRIDLLVEQL 342
           ++L+ L   +     +              K + L+++             R+  +   +
Sbjct: 337 KQLQMLCQQSSAALIEMAGEWERVRRPIVDKFRALRDERANQNDEAKSKLERVKEMRALI 396

Query: 343 YDISKRIMHNEGELLRLAQSYG-IKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVAC 401
             +   I   E    +L ++Y    +D     +  R LD   V   K       K  +  
Sbjct: 397 KKLIAEIRAKEELFGQLQETYKNAPKDTNRSMYTRRILDT--VKNIKKQKVDIDKILLDT 454

Query: 402 EVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIA 444
           +      ++ EI +I+     +    + I+    K +  A +A
Sbjct: 455 KT-----LQKEINTITDSAVRAFDNVKDILYADAKKDETAKLA 492


>gi|83582516|emb|CAJ45482.1| kinesin-like protein KIF3Abeta [Homo sapiens]
          Length = 725

 Score = 37.5 bits (85), Expect = 7.5,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 69/191 (36%), Gaps = 12/191 (6%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            ++I+++A I  E K            + +  +  EK   D+ + + + +S  +      
Sbjct: 443 DKMIEMQAKIDEERKALETKLDMEEEERNKARAELEKREKDLLKAQQEHQSLLEKLSALE 502

Query: 242 SKV---DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            KV            ++  L E+ +          +QLR ++     E  ++  +  SLQ
Sbjct: 503 KKVIVGGVDLLAKAEEQEKLLEESNMELEERRKRAEQLRRELEEKEQERLDIEEKYTSLQ 562

Query: 299 DNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           + A    K  +K        K ++  L      +Q  I+ L+E +  +S+ +      + 
Sbjct: 563 EEAQGKTKKLKKVWTMLMAAKSEMADLQQE---HQREIEGLLENIRQLSRELRLQMLIID 619

Query: 358 RLAQSYGIKRD 368
                  I RD
Sbjct: 620 NF-----IPRD 625


>gi|332823267|ref|XP_003311143.1| PREDICTED: desmoplakin isoform 2 [Pan troglodytes]
          Length = 2428

 Score = 37.5 bits (85), Expect = 7.5,   Method: Composition-based stats.
 Identities = 70/492 (14%), Positives = 163/492 (33%), Gaps = 36/492 (7%)

Query: 189  ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              +  E +      +E  +  K  D + +K + +  + +  + S  ++ +       S  
Sbjct: 1035 EVLEEELRLARDANSENCNKNKFLDQNLQKYQAECSQFKAKLASLEELKRQAELDGKSAK 1094

Query: 249  ENAENDERNLDEDEDDSAHTLSAMEDQLR--PKVMCALDEIAEVYRELRSLQDNAVNGQ- 305
            +N +     + E  +        +ED+ R    V    D+    Y +L+  +        
Sbjct: 1095 QNLDKCYGQIKELNEKITRLTYEIEDEKRRRKSVEDRFDQQKNDYDQLQKARQCEKENLG 1154

Query: 306  ----KDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQ 361
                + EK+  + +   E+L  L+      +   +  + ++ +     M N     +   
Sbjct: 1155 WQKLESEKAIKEKEYEIERLRVLLQEEGTRKREYENELAKVRNHYNEEMSNLRN--KYET 1212

Query: 362  SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421
               I +    E    +E D   +    D    E ++      D I+++ + I  +     
Sbjct: 1213 EINITKTTIKEISMQKEDDSKNLRNQLDRLSRENRDL----KDEIVRLNDSI--LQATEQ 1266

Query: 422  ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAK----KYTNRGLQFLDLIQEG 477
               +E     ++ +K      + KK+ +E  L+ V+        ++     +    IQ+ 
Sbjct: 1267 RRRAEE---NALQQKACGSEIMQKKQHLEIELKQVMQQRSEDNARHKQSLEEAAKTIQDK 1323

Query: 478  NIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTAR 537
            N  + +   +F      ++       + +A  R    ++   ++       + K+ +   
Sbjct: 1324 NKEIERLKAEFQEEAKRRWEYE--NELSKASNRIQESKNQCTQVVQERESLLVKI-KVLE 1380

Query: 538  RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNA 597
            +   +++R       AK        V++ L+  K+ I  +        S   + I    +
Sbjct: 1381 QDKARLQRLEDELNRAKATLEAETRVKQRLECEKQQIQNDLNQWKTQYSRKEEAIRKIES 1440

Query: 598  VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
                    + +LR    R+ A +   EER  R         + +  E   Q    R R  
Sbjct: 1441 EREKSEREKNSLRSEIERLQAEIKRIEERCRRKL-------EDSTRETQSQLETERSR-- 1491

Query: 658  QIEAKAIRKLKH 669
                + I KL+ 
Sbjct: 1492 --YQREIDKLRQ 1501


>gi|256544785|ref|ZP_05472157.1| surface protein [Anaerococcus vaginalis ATCC 51170]
 gi|256399674|gb|EEU13279.1| surface protein [Anaerococcus vaginalis ATCC 51170]
          Length = 784

 Score = 37.5 bits (85), Expect = 7.5,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 89/244 (36%), Gaps = 6/244 (2%)

Query: 189 ACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPP 248
              G +         +     K  ++  +   D  QE +  I+   +  +  +   +   
Sbjct: 286 DLTGQDIDEKDNKIDDLTKNIKDLENQIKDLNDKKQEDQSKIDELKEKLESCKDNGEKLK 345

Query: 249 ENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE 308
           +     E  + + ++  A     +ED         + EI ++  EL+ LQD     ++D 
Sbjct: 346 QEKAKLEEEIRDKDNKIAQLNKEIEDLKNSNNDELVAEITQLKDELKRLQDENEKLKEDY 405

Query: 309 KSSV-KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKR 367
            S+  + +  KE   K    +   Q +++ L  +L   +K I   +  +  L ++   ++
Sbjct: 406 SSTKWELEAEKENTDKNENKIKEMQEKLESLEGELAKKTKEIEDKDNRIKDLEKALD-EK 464

Query: 368 DVFLERHQGR--ELDPHWVSYAKDFPEGEWK--NFVACEVDSILKIRNEIKSISVETGIS 423
           D  ++  + +  E++       K   E +    +       +  ++ ++IK +  +   S
Sbjct: 465 DTKIKDLESKKKEIEKTKSECCKKIEELQKAIDSLKESSEKTKKELEDKIKELEEKQKSS 524

Query: 424 ISEF 427
             E 
Sbjct: 525 DEEI 528


>gi|224498911|ref|ZP_03667260.1| RNA polymerase factor sigma-70 [Listeria monocytogenes Finland
           1988]
          Length = 201

 Score = 37.5 bits (85), Expect = 7.6,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EELAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|114326446|ref|NP_071855.2| myosin-9 isoform 1 [Mus musculus]
 gi|205371802|sp|Q8VDD5|MYH9_MOUSE RecName: Full=Myosin-9; AltName: Full=Cellular myosin heavy chain,
            type A; AltName: Full=Myosin heavy chain 9; AltName:
            Full=Myosin heavy chain, non-muscle IIa; AltName:
            Full=Non-muscle myosin heavy chain A; Short=NMMHC-A;
            AltName: Full=Non-muscle myosin heavy chain IIa;
            Short=NMMHC II-a; Short=NMMHC-IIA
 gi|74180962|dbj|BAE27761.1| unnamed protein product [Mus musculus]
 gi|74180967|dbj|BAE27763.1| unnamed protein product [Mus musculus]
 gi|74180971|dbj|BAE27765.1| unnamed protein product [Mus musculus]
 gi|74180973|dbj|BAE27766.1| unnamed protein product [Mus musculus]
 gi|74180975|dbj|BAE27767.1| unnamed protein product [Mus musculus]
 gi|74180985|dbj|BAE27772.1| unnamed protein product [Mus musculus]
 gi|74180987|dbj|BAE27773.1| unnamed protein product [Mus musculus]
 gi|74180995|dbj|BAE27776.1| unnamed protein product [Mus musculus]
 gi|74180997|dbj|BAE27777.1| unnamed protein product [Mus musculus]
 gi|74180999|dbj|BAE27778.1| unnamed protein product [Mus musculus]
 gi|74181014|dbj|BAE27783.1| unnamed protein product [Mus musculus]
 gi|74181018|dbj|BAE27785.1| unnamed protein product [Mus musculus]
 gi|74181123|dbj|BAE27829.1| unnamed protein product [Mus musculus]
 gi|74184545|dbj|BAE27894.1| unnamed protein product [Mus musculus]
 gi|74184580|dbj|BAE27906.1| unnamed protein product [Mus musculus]
 gi|123233477|emb|CAM23428.1| myosin, heavy polypeptide 9, non-muscle [Mus musculus]
 gi|148697703|gb|EDL29650.1| myosin, heavy polypeptide 9, non-muscle [Mus musculus]
          Length = 1960

 Score = 37.5 bits (85), Expect = 7.6,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 85/233 (36%), Gaps = 12/233 (5%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +      L A
Sbjct: 1505 EMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAKLRLEVNLQA 1564

Query: 272  MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
            M+ Q    +    ++  E  ++L           +DE+     +    K L+  L  L  
Sbjct: 1565 MKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAMAARKKLEMDLKDLEA 1624

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +       +  ++QL  +  ++     EL          R+  L + +  E     +  
Sbjct: 1625 HIDTANKNREEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQAKENEKKLKSMEA 1680

Query: 387  AKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMVRK 436
                 + E       +  +     ++ +EI + S +  +++ E R + + + +
Sbjct: 1681 EMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARIAQ 1733


>gi|149066032|gb|EDM15905.1| myosin, heavy polypeptide 9, non-muscle [Rattus norvegicus]
          Length = 1960

 Score = 37.5 bits (85), Expect = 7.7,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 85/233 (36%), Gaps = 12/233 (5%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +      L A
Sbjct: 1505 EMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAKLRLEVNLQA 1564

Query: 272  MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
            M+ Q    +    ++  E  ++L           +DE+     +    K L+  L  L  
Sbjct: 1565 MKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSIAMAARKKLEMDLKDLEA 1624

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +       +  ++QL  +  ++     EL          R+  L + +  E     +  
Sbjct: 1625 HIDTANKNREEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQAKENEKKLKSMEA 1680

Query: 387  AKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMVRK 436
                 + E       +  +     ++ +EI + S +  +++ E R + + + +
Sbjct: 1681 EMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARIAQ 1733


>gi|195124487|ref|XP_002006724.1| GI21224 [Drosophila mojavensis]
 gi|193911792|gb|EDW10659.1| GI21224 [Drosophila mojavensis]
          Length = 1189

 Score = 37.5 bits (85), Expect = 7.7,   Method: Composition-based stats.
 Identities = 53/391 (13%), Positives = 117/391 (29%), Gaps = 29/391 (7%)

Query: 268  TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGS 327
            TL+  + +    V     +I E+  +    + N +N     + +   +  + +L+  +  
Sbjct: 809  TLAGEKIRRERWVRENTKKIKELTVKGLEAEINKMNCDHQREVTELKRAHQMELLDALEE 868

Query: 328  LSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYA 387
              L   +I+     + +   +   +  E  R A     +R +  E+    EL        
Sbjct: 869  ARLKHEQIEH---GIRESCAQDRESIIEKERTAIRERFERQLEEEQKIQAELRQKLADDF 925

Query: 388  KDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKE 447
                E         E D + K +   +    E   +  E +     + K E +       
Sbjct: 926  AAERERLQAELRQKEADYLAKRQEAQRDHDNELEQAKFEMQE---KMAKQEEKYQNRINT 982

Query: 448  MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507
            + +  L        +Y N+    L L ++       A  +       +     +  ++  
Sbjct: 983  VEQQYLADFELWKTEYENK--SKLALAEK-----ENAIRQHYRAERDRQLDELVVRMEAD 1035

Query: 508  ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567
              +S  +    I       +K  ++     +   +   E    E   +    V   +  +
Sbjct: 1036 ALQSSEEHEQKILRLKEKFEKDLQLAENVEKSLREKYAE--TREKLAEADAQVRNSQAEV 1093

Query: 568  KITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERV 627
            K  +  +S    +        GDFI            ++ NL       L  L  R ++ 
Sbjct: 1094 KQLQMELSHSKKMC-------GDFI-------NERDKLRDNLNADIQSELNVLNERHKQE 1139

Query: 628  LRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
            +         T    EE  +      +++RQ
Sbjct: 1140 MEQLQKRVHQTIQRQEETIEVLKADNDQLRQ 1170


>gi|126343507|ref|XP_001365825.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 1176

 Score = 37.5 bits (85), Expect = 7.9,   Method: Composition-based stats.
 Identities = 47/276 (17%), Positives = 90/276 (32%), Gaps = 23/276 (8%)

Query: 100 SNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSR-EGEIAIAKRIEAGRAMMMASLC 158
           SN    L    +      D+PV +  +EMG   L +R EGE             M     
Sbjct: 170 SNKKAELTAILEHFKIRVDNPVSILPQEMGRQLLRTRNEGERYSFFLKATELEQMRE--- 226

Query: 159 ESPLTFQALIIWRDELNDGTTLLREI----IDLEACIGPESKGGFFHGTEGHSYQKREDS 214
           E     +     + ++  G   L ++    +++E         G               S
Sbjct: 227 EYSEILERKARSQHQIEQGEEQLEDLKRQGVEIEEHFQTMVTLGKTLEDMKLEMTWAVVS 286

Query: 215 SQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA--------ENDERNLDEDEDDSA 266
             E++ DD+       +    +   +          A        EN ++  +E      
Sbjct: 287 ETERQLDDMISNINIGDQCTIILNQELEASKIIFNEALKRYTAIHENIQKLSEEASIIGP 346

Query: 267 HTLSAMEDQLRPK-----VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL--KE 319
             + A ED +R        +         Y E+  +     +  +  KS+V+   L  +E
Sbjct: 347 QCIQAKEDTIRTDRAYSLALAFYTSALNEYSEIEKVAGQHQSKLEILKSAVEMAELEKQE 406

Query: 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGE 355
           K+  L   +   + + D LVE++  + + I  ++ E
Sbjct: 407 KISTLKEKIRNFKDQEDSLVEEIKHLHQAIERDDKE 442


>gi|73955661|ref|XP_850098.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 2 [Canis familiaris]
          Length = 2007

 Score = 37.5 bits (85), Expect = 7.9,   Method: Composition-based stats.
 Identities = 50/328 (15%), Positives = 105/328 (32%), Gaps = 14/328 (4%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD         +E   L      E  
Sbjct: 1468 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEA-EAREKETKALSLARALEEA 1526

Query: 197  GGFFHGTEGHSYQKRED-SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  + Q R D       +DDV +   ++E + +  +    ++ +  E  E++ 
Sbjct: 1527 LETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDEL 1586

Query: 256  RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC- 314
            +  ++ +      + AM+ Q    +    ++  E  R L           +DE+      
Sbjct: 1587 QATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALA 1646

Query: 315  ----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                K L+  L  L   +       D +++QL  +  ++   + EL    +     RD  
Sbjct: 1647 VASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEI 1702

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEF 427
              + +  E     +       + E  +             ++ +EI + +      + E 
Sbjct: 1703 FAQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEK 1762

Query: 428  RHIVSMVRKGECEASIAKKEMVEANLRL 455
            R + + + + E E    +  M   N R 
Sbjct: 1763 RRLEARIAQLEEELEEEQSNMELLNDRF 1790


>gi|46906476|ref|YP_012865.1| RNA polymerase factor sigma-70 [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|226222872|ref|YP_002756979.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria monocytogenes
           Clip81459]
 gi|254825713|ref|ZP_05230714.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J1-194]
 gi|254853490|ref|ZP_05242838.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL R2-503]
 gi|254932462|ref|ZP_05265821.1| RNA polymerase sigma-30 factor [Listeria monocytogenes HPB2262]
 gi|254991757|ref|ZP_05273947.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J2-064]
 gi|255520313|ref|ZP_05387550.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J1-175]
 gi|300764632|ref|ZP_07074624.1| hypothetical protein LMHG_11122 [Listeria monocytogenes FSL N1-017]
 gi|46879740|gb|AAT03042.1| RNA polymerase sigma-30 factor [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|225875334|emb|CAS04031.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258606862|gb|EEW19470.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL R2-503]
 gi|293584018|gb|EFF96050.1| RNA polymerase sigma-30 factor [Listeria monocytogenes HPB2262]
 gi|293594957|gb|EFG02718.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J1-194]
 gi|300514739|gb|EFK41794.1| hypothetical protein LMHG_11122 [Listeria monocytogenes FSL N1-017]
 gi|328467852|gb|EGF38892.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 1816]
 gi|328476084|gb|EGF46793.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 220]
 gi|332310654|gb|EGJ23749.1| RNA polymerase sigma-30 factor [Listeria monocytogenes str. Scott
           A]
          Length = 201

 Score = 37.5 bits (85), Expect = 7.9,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EELAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|218288863|ref|ZP_03493114.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240952|gb|EED08129.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 253

 Score = 37.5 bits (85), Expect = 8.0,   Method: Composition-based stats.
 Identities = 19/177 (10%), Positives = 54/177 (30%), Gaps = 17/177 (9%)

Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANL----RLVISVAKKYTNRGLQFLDLIQE 476
           G S+ E   +  +++  +   + A+ E++   +    R+    AK+Y +           
Sbjct: 8   GRSLDERNELARLLQSAKAGNAHARNELIALYIPFILRIASQTAKRYIDPHADDE--YSV 65

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
                 +A +++       F T+A   +++ +                 + +    +R  
Sbjct: 66  SLAAFNEAIDRYQDERAASFLTFAETVIRRRLVDFFR-----------AQRQHRARLRPW 114

Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIE 593
                  + +     +    ++     R+   +    I        E     G+ +E
Sbjct: 115 SEFDQADEEDHVSNWVEVASSIAEHQRREEAAMRAYEIEEYARRLAEFGLSFGELVE 171


>gi|84684929|ref|ZP_01012829.1| ribonuclease, Rne/Rng family protein [Maritimibacter alkaliphilus
           HTCC2654]
 gi|84667264|gb|EAQ13734.1| ribonuclease, Rne/Rng family protein [Rhodobacterales bacterium
           HTCC2654]
          Length = 958

 Score = 37.5 bits (85), Expect = 8.0,   Method: Composition-based stats.
 Identities = 19/141 (13%), Positives = 41/141 (29%), Gaps = 3/141 (2%)

Query: 137 EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
           E E A A+ +E       +    +P   +          D      ++IDL+     +  
Sbjct: 91  EEERAYAEALEREEEGRKSR-RSAPRAEETRSDDEVVTKDAEPQGMDVIDLDEGGEADEA 149

Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQ--ETEGDIESAAKVSKDDRSKVDSPPENAEND 254
                       ++  D + E   D  +  E   + E++     D +        +    
Sbjct: 150 SSPMERVADTPVEEPSDETGEDVDDAEEGAEASDEAEASGDDDTDAKPSRSRRSRSRSRS 209

Query: 255 ERNLDEDEDDSAHTLSAMEDQ 275
                  +++ A  + A E  
Sbjct: 210 RSRSRPSDEEDAKPVDAAEKD 230


>gi|189189002|ref|XP_001930840.1| predicted protein [Pyrenophora tritici-repentis Pt-1C-BFP]
 gi|187972446|gb|EDU39945.1| predicted protein [Pyrenophora tritici-repentis Pt-1C-BFP]
          Length = 961

 Score = 37.5 bits (85), Expect = 8.1,   Method: Composition-based stats.
 Identities = 34/254 (13%), Positives = 74/254 (29%), Gaps = 11/254 (4%)

Query: 192 GPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENA 251
           G   K                 S  +        +   + S     +DD    +    + 
Sbjct: 125 GDSGKDRLSRPNTSDGQSPSAQSEPKSAPLSRPSSADPLTSVKFGHRDDAYTDEKTRIDI 184

Query: 252 ENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD---EIAEVYRELRSLQDNAVNGQKDE 308
           + ++    E  D     L A   +L+ + +  ++   E  E    L  LQ +     K+ 
Sbjct: 185 DEEQPAEKEHADPHLQDLVADIKRLQYENIALMEVQQEEEEALSRLSQLQQDKTKLVKEV 244

Query: 309 K----SSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL---AQ 361
           +    +  K + L+ ++ KL   L L       + E+L     R+     E  +L    Q
Sbjct: 245 RVLRETKAKTEELESEIDKLSSQLKLVTREKKKMNEELEGSRNRMEELSQERDQLLVNVQ 304

Query: 362 SYGIKRDVFLER-HQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVET 420
               +++ +  R                ++   E +  +    D +  ++ +  +   E 
Sbjct: 305 ELKQQKEEYWRRDLPLNASAKEVTIADLEWNNAELRQKLRERDDEVAYLQRDKATTQKEL 364

Query: 421 GISISEFRHIVSMV 434
                E        
Sbjct: 365 ETKQKELDEAYEYA 378


>gi|228919044|ref|ZP_04082423.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840569|gb|EEM85831.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 219

 Score = 37.5 bits (85), Expect = 8.2,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|217965669|ref|YP_002351347.1| RNA polymerase sigma-H factor (Sigma-30) [Listeria monocytogenes
           HCC23]
 gi|290892616|ref|ZP_06555609.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J2-071]
 gi|217334939|gb|ACK40733.1| RNA polymerase sigma-H factor (Sigma-30) [Listeria monocytogenes
           HCC23]
 gi|290557925|gb|EFD91446.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J2-071]
 gi|307569782|emb|CAR82961.1| RNA polymerase sigma-30 factor [Listeria monocytogenes L99]
          Length = 201

 Score = 37.5 bits (85), Expect = 8.3,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
             ++M+       + A +        ++   + +Y  +G +  DLIQE  IGL KA   +
Sbjct: 8   EELAMLELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIRDY 67

Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           D      F ++A   + + +  ++   S    IP
Sbjct: 68  DKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|198423886|ref|XP_002121135.1| PREDICTED: similar to CDC42-binding protein kinase alpha, partial
           [Ciona intestinalis]
          Length = 1586

 Score = 37.5 bits (85), Expect = 8.3,   Method: Composition-based stats.
 Identities = 40/322 (12%), Positives = 105/322 (32%), Gaps = 17/322 (5%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPES 195
            + E+  A  +      +   L     T + L   +DE++      R+    +     ++
Sbjct: 510 ADQELQAADVLRKDLEDVHQKLKALERTNRHLKQDKDEIHRDFVESRDRAKEQTRQLRDA 569

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  +      +  + +++ +     + E    +  +   ++       E  +
Sbjct: 570 HAQRRLAMEEFTDINDRLTEVQSQKNKLARQLREKEEEVDLIGNKLDQLRQDLRKTEKSK 629

Query: 256 RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDE------K 309
           +N +E+ +     L A + +LR  V   L +  E    LR      V+G+ +       +
Sbjct: 630 KNFEEESEKYKDDL-AKQTKLRLSVSERLKQTEEEVALLRRKDAIDVDGRVNMNNSTYNQ 688

Query: 310 SSVKCKVLKEKLVKLVGSLSLNQSRIDLL----VEQLYDISKRIMHNEGELLRLAQSYGI 365
           +  + + L+++L ++     L  S+ + L    V+ L   S+        L R       
Sbjct: 689 NEEEIERLQKELEQIEADHRLEISKRESLHITEVKNLKQESRESESQNISLQREIMILK- 747

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEW-----KNFVACEVDSILKIRNEIKSISVET 420
            +   + R   +EL        +               +  E++ +      +   +   
Sbjct: 748 DKVDKVRRESNQELQDTLKETRQKHERQTKILSDNNTALQSEIERVSAEMERLNQHNRTL 807

Query: 421 GISISEFRHIVSMVRKGECEAS 442
              + E +     +++ E + +
Sbjct: 808 EEEVREAKERKESIKQWEAQVA 829


>gi|37360516|dbj|BAC98236.1| mKIAA1708 protein [Mus musculus]
          Length = 1291

 Score = 37.5 bits (85), Expect = 8.3,   Method: Composition-based stats.
 Identities = 70/454 (15%), Positives = 138/454 (30%), Gaps = 53/454 (11%)

Query: 55  PDEVSSEQMEDTVAMLSNMGINVVDGD------DLEDEEGSEDSLDLASSASNSSVFLQK 108
              +  E +E    M     +   + +          E        +    S  +  +  
Sbjct: 26  KRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALRARITQLVSEQANQVLA 85

Query: 109 RKDSADRSTDDPVRMYLREMG--SIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQA 166
           R    +    + +  Y++E+     +LL  E     A   E  R  +  +   SP  F A
Sbjct: 86  RAGEGNEEISNMIHSYIKEIEDLRAKLLESE-----AVN-ENLRKNLTRATARSPY-FSA 138

Query: 167 LIIWRDELNDGTTLLREIIDL--EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQ 224
              +   +        EIIDL  +     + K            +   +      +DD  
Sbjct: 139 SSAFSPTILSSDKETIEIIDLAKKDLEKLKRKEKKKKKRLQKLEESGREERSVAGKDDNA 198

Query: 225 ETEGDIESAAKVSKDDRSKVDSPPENAEND----------ERNLDEDEDDSAHTLSAMED 274
           +T+ + +    VS+ + +++D       +D          E   D+ E + +   S  E 
Sbjct: 199 DTDQEKKEEKGVSEKENNELDVEENQEVSDHEDEEEEEEDEEEEDDIEGEESSDESDSES 258

Query: 275 QLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSR 334
             +      L  I       + L D   N QK  ++  K    +EKL+ L   +   Q  
Sbjct: 259 DEKANYQADLANITCEIAIKQKLIDELENSQKRLQTLKK--QYEEKLMMLQHKIRDTQLE 316

Query: 335 IDLLVEQL---------------YDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGREL 379
            D +++ L                +  K++     EL RL  +   +    L+     E 
Sbjct: 317 RDQVLQNLGSVESYSEEKAKKVKCEYEKKLHAMNKELQRLQTAQK-EHARLLKNQSQYEK 375

Query: 380 DPHWVSYAKDFPEGEWKNFVACEVDSILKIR-------NEIKSISVETGISISEFRHIVS 432
               +       +      +    +   K R        EI  +  +      + R ++ 
Sbjct: 376 QLKKLQQDVMEMKKTKVRLMKQMKEEQEKARLTESRRNREIAQLKKDQRKRDHQLR-LLE 434

Query: 433 MVRKGECEASIAKKEMVEANLRLVISVAKKYTNR 466
             ++ +      K E V A  R V  ++ K   +
Sbjct: 435 AQKRNQEVVLRRKTEEVTALRRQVRPMSDKVAGK 468


>gi|257453203|ref|ZP_05618502.1| hypothetical protein F3_09093 [Fusobacterium sp. 3_1_5R]
 gi|317059737|ref|ZP_07924222.1| predicted protein [Fusobacterium sp. 3_1_5R]
 gi|313685413|gb|EFS22248.1| predicted protein [Fusobacterium sp. 3_1_5R]
          Length = 291

 Score = 37.5 bits (85), Expect = 8.3,   Method: Composition-based stats.
 Identities = 50/304 (16%), Positives = 104/304 (34%), Gaps = 23/304 (7%)

Query: 365 IKRDVFLERHQGRE-LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423
           +K+  F E    +   D  +  Y +     + +  V  E  +I K           T + 
Sbjct: 1   MKQKEFEELLLNKRFSDDEFFEYLQKNTLKDIEFEVMDEQVAIEK--------KDFTLLE 52

Query: 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMK 483
            S   +I  +        S  ++  +   ++ V+  A  Y   G+ ++DL+QEG +GLMK
Sbjct: 53  SSVLEYIEELCSYDPDHLSEEREAHIALEVKKVLYYAFFYFKEGISYMDLVQEGIVGLMK 112

Query: 484 AAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKI 543
             ++    L         +W+ + I   +  +   ++       K  +            
Sbjct: 113 GVDRQSERLD--------FWIIREIFLFVYSEIQDLKFGFKNFLKGKREEAEHHHEHEHH 164

Query: 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603
                  E +       E         K     E     +    L   ++   A+  ++ 
Sbjct: 165 HDHEEDHECSCGHDPNEE----HECCGKHHHKEEEEEILDKNQILEKLLKSNTAIDEMEQ 220

Query: 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
            I+ +L      +   L   E  VL   FG+ +   +++ E+ ++F + +   + I   A
Sbjct: 221 IIEESL--DFHHIKNRLYAIEIEVLNYYFGLLVEKRYSIFEIEEKFQLQKNHAQNIFENA 278

Query: 664 IRKL 667
           + KL
Sbjct: 279 MYKL 282


>gi|257389184|ref|YP_003178957.1| methyl-accepting chemotaxis sensory transducer [Halomicrobium
           mukohataei DSM 12286]
 gi|257171491|gb|ACV49250.1| methyl-accepting chemotaxis sensory transducer [Halomicrobium
           mukohataei DSM 12286]
          Length = 832

 Score = 37.5 bits (85), Expect = 8.4,   Method: Composition-based stats.
 Identities = 38/316 (12%), Positives = 97/316 (30%), Gaps = 16/316 (5%)

Query: 61  EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
           ++       L  M  ++ D  D  + E        AS+    +      ++++  +T   
Sbjct: 338 DEFGSVYDSLDRMRRSLRDQIDAVETERQRVEEAKASAQEARAEAEAAHREASTLATSLE 397

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
            R   +E G    L+ +G++      +     M +         + L     E+    + 
Sbjct: 398 ARA--QEFGESMELAADGDLTQRLDTDLETEAMRSIATAFNEMIEQLEETVSEIRSFASA 455

Query: 181 LREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDD 240
           + E  D         +      +          + QE++   + ++  D+  A +   D 
Sbjct: 456 VDEASDTVDTRSAAIRQASERASVSIEDISSAAAKQEEQLSRIDDSVSDLSKAIEEIADA 515

Query: 241 RSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV--MCALDEIAEVYRELRSLQ 298
             +V      A        +  + SA T+  +E Q       +   +   E   ++ +L 
Sbjct: 516 SDEVADRSRRAAQRGDAGRDLAETSASTMRRIERQADETAADIEQFEADIERVGDITTLI 575

Query: 299 DNAVNGQKDEKSSVKCKVLK------------EKLVKLVGSLSLNQSRIDLLVEQLYDIS 346
           ++  +       +   +  +            +++ +L   +      ID +VE + D +
Sbjct: 576 EDIADRTNMLALNASIEAARAGEDGDGFGVVADEIKRLSSEVQSATHEIDEIVEDVRDSA 635

Query: 347 KRIMHNEGELLRLAQS 362
                    +    + 
Sbjct: 636 GDAATEMRTMQTTVED 651


>gi|73955673|ref|XP_860854.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 8 [Canis familiaris]
          Length = 1997

 Score = 37.5 bits (85), Expect = 8.4,   Method: Composition-based stats.
 Identities = 50/328 (15%), Positives = 105/328 (32%), Gaps = 14/328 (4%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD         +E   L      E  
Sbjct: 1458 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEA-EAREKETKALSLARALEEA 1516

Query: 197  GGFFHGTEGHSYQKRED-SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  + Q R D       +DDV +   ++E + +  +    ++ +  E  E++ 
Sbjct: 1517 LETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDEL 1576

Query: 256  RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC- 314
            +  ++ +      + AM+ Q    +    ++  E  R L           +DE+      
Sbjct: 1577 QATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALA 1636

Query: 315  ----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                K L+  L  L   +       D +++QL  +  ++   + EL    +     RD  
Sbjct: 1637 VASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEI 1692

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEF 427
              + +  E     +       + E  +             ++ +EI + +      + E 
Sbjct: 1693 FAQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEK 1752

Query: 428  RHIVSMVRKGECEASIAKKEMVEANLRL 455
            R + + + + E E    +  M   N R 
Sbjct: 1753 RRLEARIAQLEEELEEEQSNMELLNDRF 1780


>gi|326433276|gb|EGD78846.1| hypothetical protein PTSG_01822 [Salpingoeca sp. ATCC 50818]
          Length = 1300

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 35/216 (16%), Positives = 75/216 (34%), Gaps = 9/216 (4%)

Query: 163 TFQALIIWRDELNDGTTLL-REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERD 221
             + +      L +    L  ++  LE     + + G    +   S    + +   + R 
Sbjct: 393 RIREITSQSVRLEEENKHLKSKVARLETTASSKPEEGGVAVSSSSSPSPSDATESNRVRK 452

Query: 222 DVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAME--DQLRPK 279
              E E       ++     ++        E  ER   E    +A   S+ +  ++LR +
Sbjct: 453 LEDENEKLTAQLKRLHTSTSTEEADTDALKEERERQQREISKLTAELTSSEQQNEELRLR 512

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           V    +++A+    + SLQ+   + + +  S+    + K+        + L   RI  L 
Sbjct: 513 VKEQTEQLAKAQETVTSLQEQVASLKSNAASASPLSIEKKLGDVFERGVRLKDGRIKTLE 572

Query: 340 EQLYDI------SKRIMHNEGELLRLAQSYGIKRDV 369
            +L +        K+ M      + L +S   +RD 
Sbjct: 573 ARLKEATEHNEQLKQDMALAKRHIELLRSAASRRDS 608


>gi|322786872|gb|EFZ13136.1| hypothetical protein SINV_00390 [Solenopsis invicta]
          Length = 2417

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 59/425 (13%), Positives = 144/425 (33%), Gaps = 23/425 (5%)

Query: 38   ARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLA- 96
            A+++  +   +L   L   E    Q+      L+     + D   L DEE  E +  L  
Sbjct: 1734 AKKKLSIENSDLLRQLEEAESQVSQLSKIKISLTTQ---LEDTKRLADEESRERATLLGK 1790

Query: 97   -SSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE---IAIAKRIEAGRAM 152
              +  +    ++++ +       D  R   +     +L   + E   +A A+ +E  +  
Sbjct: 1791 FRNLEHDLDNIREQVEEEAEGKADLQRQLSKANAEAQLWRTKYESEGVARAEELEEAKRK 1850

Query: 153  MMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKRE 212
            + A L E+  T ++L      L      L   ++        +        +      + 
Sbjct: 1851 LQARLAEAEETIESLNQKVIALEKTKQRLSTEVEDLQIEVDRATAIANAAEKKQKAFDKI 1910

Query: 213  DSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
             S  + + DD+       +   +    +  ++    E  +     +  +  + A  +  +
Sbjct: 1911 ISEWKLKVDDLAAELDASQKECRNYSTELFRLRGAYEEGQEQLEAVRRENKNLADEVKDL 1970

Query: 273  EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
             DQ+       + EI +  + L + +D      ++ +++++ +  K     L   L L+Q
Sbjct: 1971 LDQIGEGG-RNIHEIEKARKRLEAEKDELQAALEEAEAALEQEENK----VLRSQLELSQ 2025

Query: 333  SRID---LLVEQLYDISKRIMHNEGELLRLAQSY---GIKRDVFLERHQGRELDPHWVSY 386
             R +    + E+  +      +++  L  +  S       +   L   +  E D + +  
Sbjct: 2026 VRQEIDRRIQEKEEEFENTRKNHQRALDSMQASLEAEAKGKAEALRMKKKLEADINELEI 2085

Query: 387  AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKK 446
            A D          A    +I + + ++K +                ++   E  A+  + 
Sbjct: 2086 ALDHANKAN----AEAQKNIKRYQQQLKDVQTALEEEQRARDEARELLGISERRANALQN 2141

Query: 447  EMVEA 451
            E+ E+
Sbjct: 2142 ELEES 2146


>gi|319654851|ref|ZP_08008926.1| RNA polymerase sigma-70 factor [Bacillus sp. 2_A_57_CT2]
 gi|317393414|gb|EFV74177.1| RNA polymerase sigma-70 factor [Bacillus sp. 2_A_57_CT2]
          Length = 218

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 29/97 (29%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +V KGE   S A   ++      V + A+ Y   G    D++QEG IGL KA 
Sbjct: 19  EDEEIVELVHKGE---SEALDYLIHKYRNFVRAKARSYFLIGADKEDIVQEGMIGLYKAI 75

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             F       F  +A   + + I  +I   +    IP
Sbjct: 76  RDFKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 112


>gi|289579162|ref|YP_003477789.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           italicus Ab9]
 gi|289528875|gb|ADD03227.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           italicus Ab9]
          Length = 214

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 25/98 (25%), Positives = 39/98 (39%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +V   +K       A + ++E     V + A+ Y   G    D++QEG IGL KA
Sbjct: 16  MEEEEVVFRAQK---GDEAALEYLLERYKSFVKAKARAYFLVGADREDIMQEGMIGLYKA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 73  IRDYKGDKLSSFKAFAELCVTRQIITAIKTATRQKHIP 110


>gi|304315923|ref|YP_003851068.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302777425|gb|ADL67984.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 214

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 25/109 (22%), Positives = 43/109 (39%), Gaps = 3/109 (2%)

Query: 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDL 473
             I +    S  +   IV   ++G      A + +++     V + A+ Y   G    D+
Sbjct: 5   AQIDLYNVFSSMDEGDIVEEAQRGN---QAALEFIIDKYYSFVKAKARSYFLVGADKEDI 61

Query: 474 IQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           +QEG IGL KA   F       F  +A   + + +  +I   +    IP
Sbjct: 62  VQEGMIGLYKAIRDFKSDKLSSFKAFAELCITRQMITAIKTATRQKHIP 110


>gi|17978023|emb|CAC85955.1| nonmuscle heavy chain myosin II-A [Mus musculus]
          Length = 1960

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 32/231 (13%), Positives = 84/231 (36%), Gaps = 12/231 (5%)

Query: 212  EDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSA 271
            E       +DDV ++  ++E + +  +    ++ +  E  E++ +  ++ +      L A
Sbjct: 1505 EMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQATEDAKLRLEVNLQA 1564

Query: 272  MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEK-----SSVKCKVLKEKLVKLVG 326
            M+ Q    +    ++  E  ++L           +DE+     +    K L+  L  L  
Sbjct: 1565 MKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELEDERKQRSMAMAARKKLEMDLKDLEA 1624

Query: 327  SLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSY 386
             +       +  ++QL  +  ++     EL          R+  L + +  E     +  
Sbjct: 1625 HIDTANKNREEAIKQLRKLQAQMKDCMREL----DDTRASREEILAQAKENEKKLKSMEA 1680

Query: 387  AKDFPEGEWKNFVACEVDSIL---KIRNEIKSISVETGISISEFRHIVSMV 434
                 + E       +  +     ++ +EI + S +  +++ E R + + +
Sbjct: 1681 EMIQLQEELAAAERAKRQAQQERDELADEIANSSGKGALALEEKRRLEARI 1731


>gi|239934590|emb|CAR94609.1| DNA-directed RNA polymerase subunit D [uncultured Acidobacteria
           bacterium]
          Length = 219

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 29/52 (55%)

Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187
           R+GE+++A+++E G+  M  S+  SPL     +   + +   +  L + +DL
Sbjct: 1   RDGEVSLARKMERGKLRMQKSISRSPLIQMMAVEIAENIKRASVELDDFVDL 52


>gi|24666810|ref|NP_730426.1| CG9279 [Drosophila melanogaster]
 gi|23093121|gb|AAF49148.2| CG9279 [Drosophila melanogaster]
 gi|28381015|gb|AAO41474.1| GH09006p [Drosophila melanogaster]
          Length = 1339

 Score = 37.5 bits (85), Expect = 8.6,   Method: Composition-based stats.
 Identities = 49/348 (14%), Positives = 129/348 (37%), Gaps = 39/348 (11%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 444 ELDEIAESIELLTLDKEMAEERMETLQMELEMAQERNDELSL------DVEILKAEQEEQ 497

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFF 200
             +RIE     + + +  +  +    +     L      LRE ++ L   +  E + G  
Sbjct: 498 QGQRIEKSEKQIGSGV--TNQSAGEFL----RLEQYNQRLRETVVRLRDTLAEEKQIG-- 549

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           ++   +++    +I     + +    +VD+      + +  +D 
Sbjct: 550 ----------------QRTHKELETKHSEINELKSIKELLSRRVDNMEMQLMDLKEQVDA 593

Query: 261 DEDDSAHT--LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                A    L++++ +L  +V    DE+ E+   L  +Q+  +   ++ ++      L+
Sbjct: 594 SLGAEAMVTQLASLKLELEDRVKLLEDEVNEL-EALEQIQEQLIESNQELET-----DLR 647

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           E++ KL G + + + + +  +E LYD    IM     + +L +   ++ D  L       
Sbjct: 648 EEIDKLSGHVKILEQQKNAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSS 707

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            +        +  + ++++  +        +  +IK++ +       E
Sbjct: 708 ANESQQEDGSNQSQTDYQHIFSVSKAYGRALEQQIKTVELRLQRQHLE 755


>gi|325510557|gb|ADZ22193.1| RNA polymerase factor sigma-70 [Clostridium acetobutylicum EA 2018]
          Length = 212

 Score = 37.5 bits (85), Expect = 8.7,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 58/186 (31%), Gaps = 10/186 (5%)

Query: 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
              +++ ++      V   AK Y   G    D+ QEG IGL KA   F       F  +A
Sbjct: 29  DEKSQEYLINKYSNFVKVKAKSYFLIGADKEDICQEGMIGLYKAIRDFKPSKLASFKAFA 88

Query: 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-------IKREPTPEEIA 553
              + + I  +I   +    IP++       + +      +           E +  E  
Sbjct: 89  EICITRQIITAIKTATRQKHIPLN---TYVSLNKPIYDEDSDRTLFDVVSSVEVSDPEEL 145

Query: 554 KKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613
                 V  +RK +      + +E      +     +  +D +  S         ++   
Sbjct: 146 IISKEEVAKIRKNMLKVLSSLEIEVLESYLEGKSYQEIAKDLDRCSKSIDNALQRVKRKL 205

Query: 614 TRVLAS 619
            + L  
Sbjct: 206 EKCLEK 211


>gi|73955667|ref|XP_860759.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 5 [Canis familiaris]
          Length = 1992

 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 50/328 (15%), Positives = 105/328 (32%), Gaps = 14/328 (4%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD         +E   L      E  
Sbjct: 1453 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEA-EAREKETKALSLARALEEA 1511

Query: 197  GGFFHGTEGHSYQKRED-SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  + Q R D       +DDV +   ++E + +  +    ++ +  E  E++ 
Sbjct: 1512 LETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDEL 1571

Query: 256  RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC- 314
            +  ++ +      + AM+ Q    +    ++  E  R L           +DE+      
Sbjct: 1572 QATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALA 1631

Query: 315  ----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                K L+  L  L   +       D +++QL  +  ++   + EL    +     RD  
Sbjct: 1632 VASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEI 1687

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEF 427
              + +  E     +       + E  +             ++ +EI + +      + E 
Sbjct: 1688 FAQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEK 1747

Query: 428  RHIVSMVRKGECEASIAKKEMVEANLRL 455
            R + + + + E E    +  M   N R 
Sbjct: 1748 RRLEARIAQLEEELEEEQSNMELLNDRF 1775


>gi|42779174|ref|NP_976421.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 10987]
 gi|218895229|ref|YP_002443640.1| RNA polymerase sigma-30 factor [Bacillus cereus G9842]
 gi|228898847|ref|ZP_04063129.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 4222]
 gi|228905891|ref|ZP_04069788.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 200]
 gi|228937396|ref|ZP_04100042.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228963194|ref|ZP_04124363.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228970282|ref|ZP_04130941.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228976852|ref|ZP_04137264.1| RNA polymerase sigma-H factor [Bacillus thuringiensis Bt407]
 gi|229027941|ref|ZP_04184094.1| RNA polymerase sigma-H factor [Bacillus cereus AH1271]
 gi|229074155|ref|ZP_04207201.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-18]
 gi|229094816|ref|ZP_04225821.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-29]
 gi|229100893|ref|ZP_04231697.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-28]
 gi|229113770|ref|ZP_04243205.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-3]
 gi|229159267|ref|ZP_04287291.1| RNA polymerase sigma-H factor [Bacillus cereus R309803]
 gi|229170945|ref|ZP_04298546.1| RNA polymerase sigma-H factor [Bacillus cereus MM3]
 gi|42735089|gb|AAS39029.1| RNA polymerase sigma-30 factor [Bacillus cereus ATCC 10987]
 gi|218544887|gb|ACK97281.1| RNA polymerase sigma-30 factor [Bacillus cereus G9842]
 gi|228612485|gb|EEK69706.1| RNA polymerase sigma-H factor [Bacillus cereus MM3]
 gi|228624159|gb|EEK80961.1| RNA polymerase sigma-H factor [Bacillus cereus R309803]
 gi|228669641|gb|EEL25048.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-3]
 gi|228682472|gb|EEL36545.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-28]
 gi|228688559|gb|EEL42432.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-29]
 gi|228708925|gb|EEL61052.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-18]
 gi|228733329|gb|EEL84158.1| RNA polymerase sigma-H factor [Bacillus cereus AH1271]
 gi|228782822|gb|EEM30988.1| RNA polymerase sigma-H factor [Bacillus thuringiensis Bt407]
 gi|228789391|gb|EEM37311.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228796452|gb|EEM43891.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228822229|gb|EEM68211.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228853706|gb|EEM98466.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 200]
 gi|228860747|gb|EEN05125.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 4222]
 gi|324324083|gb|ADY19343.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326937887|gb|AEA13783.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 219

 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|118349952|ref|XP_001008257.1| hypothetical protein TTHERM_00011780 [Tetrahymena thermophila]
 gi|89290024|gb|EAR88012.1| hypothetical protein TTHERM_00011780 [Tetrahymena thermophila SB210]
          Length = 1458

 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 84/202 (41%), Gaps = 11/202 (5%)

Query: 214  SSQEKERDDVQETEGDIESAAKVSKDD-RSKVDSPPENAENDERNLDEDEDDSAHTLSAM 272
              QEK  ++ +E +G +    +  K     K++   EN E+D        +D     S M
Sbjct: 809  QEQEKITNEYKEFKGRMNDTIEQEKRILEFKMNKMKENFESDMTRFKRQYEDLQSAKSQM 868

Query: 273  EDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQ 332
            E   +  ++   ++  +   EL SL +  +   ++EK   + + LKE+ +K    +    
Sbjct: 869  ESDYKQTIINLEEKHLKGVEELESLYERKL-AFENEKYFQQEQELKEERLKFEKKIKELS 927

Query: 333  SRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392
             + D  ++ L    K    N G+  ++ +S  +  +   + ++ R      +S  ++  E
Sbjct: 928  RKQDTNIDILK---KEFNLNFGKAQKVYESTKMTAEELKKVYEER------LSQQEEEHE 978

Query: 393  GEWKNFVACEVDSILKIRNEIK 414
             E +N V      + + + +++
Sbjct: 979  SEIRNMVEKNEKELERWKQKVQ 1000


>gi|73955669|ref|XP_860794.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 6 [Canis familiaris]
          Length = 1982

 Score = 37.1 bits (84), Expect = 8.8,   Method: Composition-based stats.
 Identities = 50/328 (15%), Positives = 105/328 (32%), Gaps = 14/328 (4%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD         +E   L      E  
Sbjct: 1443 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEA-EAREKETKALSLARALEEA 1501

Query: 197  GGFFHGTEGHSYQKRED-SSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
                   E  + Q R D       +DDV +   ++E + +  +    ++ +  E  E++ 
Sbjct: 1502 LETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDEL 1561

Query: 256  RNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC- 314
            +  ++ +      + AM+ Q    +    ++  E  R L           +DE+      
Sbjct: 1562 QATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALA 1621

Query: 315  ----KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                K L+  L  L   +       D +++QL  +  ++   + EL    +     RD  
Sbjct: 1622 VASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEI 1677

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEF 427
              + +  E     +       + E  +             ++ +EI + +      + E 
Sbjct: 1678 FAQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEK 1737

Query: 428  RHIVSMVRKGECEASIAKKEMVEANLRL 455
            R + + + + E E    +  M   N R 
Sbjct: 1738 RRLEARIAQLEEELEEEQSNMELLNDRF 1765


>gi|114601608|ref|XP_001163814.1| PREDICTED: kinesin family member 3A isoform 4 [Pan troglodytes]
          Length = 666

 Score = 37.1 bits (84), Expect = 8.9,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 69/191 (36%), Gaps = 12/191 (6%)

Query: 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
            ++I+++A I  E K            + +  +  EK   D+ + + + +S  +      
Sbjct: 384 DKMIEMQAKIDEERKALETKLDMEEEERNKARAELEKREKDLLKAQQEHQSLLEKLSALE 443

Query: 242 SKV---DSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQ 298
            KV            ++  L E+ +          +QLR ++     E  ++  +  SLQ
Sbjct: 444 KKVIVGGVDLLAKAEEQEKLLEESNMELEERRKRAEQLRRELEEKEQERLDIEEKYTSLQ 503

Query: 299 DNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           + A    K  +K        K ++  L      +Q  I+ L+E +  +S+ +      + 
Sbjct: 504 EEAQGKTKKLKKVWTMLMAAKSEMADLQQE---HQREIEGLLENIRQLSRELRLQMLIID 560

Query: 358 RLAQSYGIKRD 368
                  I RD
Sbjct: 561 NF-----IPRD 566


>gi|198423448|ref|XP_002121206.1| PREDICTED: similar to centrosomal protein 290kDa [Ciona intestinalis]
          Length = 1639

 Score = 37.1 bits (84), Expect = 9.0,   Method: Composition-based stats.
 Identities = 56/449 (12%), Positives = 152/449 (33%), Gaps = 14/449 (3%)

Query: 3    IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSE- 61
            +  + +   + E  +S+   + D   +  +++ K A++     +++ +  LP   +S E 
Sbjct: 599  LKVQEDHQVEWESRESELERLLDQFQNQQREVNKRAKK-----LDDFSEILPQTSLSVED 653

Query: 62   QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            Q++  +  +      + +          E      +  +       + +   +     P 
Sbjct: 654  QLKKALETIKEQRKTMTNLQAQVKNLEFESDRLKDARHALEGDITSRDRIINELRLHMPT 713

Query: 122  RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALII--WRDELNDGTT 179
             + L E  + +  S+  ++ +A          +++  +S   ++ L+    RD       
Sbjct: 714  TVVLPEPHTTDNESK-QQLDVAINTIETLKKRLSAKEQSIERYKELLEESRRDHEMMSAA 772

Query: 180  LLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
              R+++ ++  I  ++   F    +  +   +   S      D++     +     + ++
Sbjct: 773  HERDLLLMQNKIHVKTDDAFNKFKQAATSASQPPGSSAPSASDLRH----LNELEDMVRE 828

Query: 240  DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQD 299
              + + +  E   +   ++   +     T    E + + K+    D +    R   + + 
Sbjct: 829  QDAAMSALMERVRSSNADISRHKRALLDTKKQHEAE-KMKMQETHDVMLNALRMKLAKKH 887

Query: 300  NAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRL 359
              V     E S  K ++ ++K        +  ++ +  L E+L +  K+       L  L
Sbjct: 888  KQVEATTTELSVTKEELKRQKDANTRAPAASMKNLVQRLKEELAEKEKQQQQLSHALKEL 947

Query: 360  AQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVE 419
                  +    +      E D H V+   +     +K+ +    D I ++R  +K     
Sbjct: 948  RVDLVQQAQENVRAATAGEADTHNVTILVEKRTAHYKDDIEDLKDEIAQLRRNLKQSEKT 1007

Query: 420  TGISISEFRHIVSMVRKGECEASIAKKEM 448
                 SE R  +    K        K ++
Sbjct: 1008 ETTLKSELRKTLEEAEKKSQVIQRLKSDL 1036


>gi|160880198|ref|YP_001559166.1| hypothetical protein Cphy_2059 [Clostridium phytofermentans ISDg]
 gi|160428864|gb|ABX42427.1| hypothetical protein Cphy_2059 [Clostridium phytofermentans ISDg]
          Length = 254

 Score = 37.1 bits (84), Expect = 9.0,   Method: Composition-based stats.
 Identities = 34/210 (16%), Positives = 71/210 (33%), Gaps = 14/210 (6%)

Query: 366 KRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISIS 425
             +   +     E             + +   F+   ++ I  +      +         
Sbjct: 54  PVEEREKEDMSEEDSTPVEDELSKENKEKNSVFLEMYLEDIKHLPRLTAEL--------- 104

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E R  + ++      +      + +  L  V+ +AKKY    +   DLIQEGNIGL+   
Sbjct: 105 EERAYIRLINGDNSVSQS----ISDHWLSTVVELAKKYETYDVNMEDLIQEGNIGLLGGL 160

Query: 486 EKFDWC-LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
           ++        +   Y M  V +A    I +      +   +  KI  +       +    
Sbjct: 161 KQLLGSNQKIEAKEYLMESVLKAFENYIDEVIDEDDMENSILSKITLINEAITAFAEDNG 220

Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPI 574
             PT  EIA    +  + +  +L+++ + +
Sbjct: 221 VTPTVMEIADYTKISEDEIASILRLSLDTV 250


>gi|218546789|gb|ACK98994.1| white muscle myosin heavy chain [Sander vitreus]
          Length = 1929

 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 39/287 (13%), Positives = 110/287 (38%), Gaps = 13/287 (4%)

Query: 132  ELL-SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEAC 190
             LL + E E  +A   E     M   L  +    + L      L      L+  +  E+ 
Sbjct: 833  PLLKTAETEKELANMKENYDK-MKTDLAAALAKKKELEEKMVSLLQEKNDLQLQVASESE 891

Query: 191  IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPEN 250
               +++       +     + +     +  +D +E   ++ +  +  +D+ S++    ++
Sbjct: 892  NLNDAEERCEGLIKSKIQMEAKLKETTERLEDEEEINAELTAKKRKLEDECSELKKDIDD 951

Query: 251  AENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKS 310
             E     +++++  + + +  + +++  +     + IA++ +E ++LQ+       D   
Sbjct: 952  LELTLAKVEKEKHATENKVKNLTEEMASQD----ESIAKLTKEKKALQEAHQQTLDD--- 1004

Query: 311  SVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVF 370
                +  ++K+  L  + +  + ++D L   L    K  M  E    +L     + ++  
Sbjct: 1005 ---LQAEEDKVNTLTKAKTKLEQQVDDLEGSLEQEKKLRMDLERSKRKLEGDLKLAQESI 1061

Query: 371  LERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSIS 417
            ++    ++     +   KDF   +  + V  E     +++ +IK + 
Sbjct: 1062 MDLENEKQQSDEKIKK-KDFEISQLLSKVEDEQSLGAQLQKKIKELQ 1107


>gi|212224573|ref|YP_002307809.1| chromosome segregation protein [Thermococcus onnurineus NA1]
 gi|212009530|gb|ACJ16912.1| DNA double-strand break repair ATPase [Thermococcus onnurineus NA1]
          Length = 884

 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 44/296 (14%), Positives = 98/296 (33%), Gaps = 9/296 (3%)

Query: 146 IEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGP-----ESKGGFF 200
           I      +  +L         +     EL      LR++  L   I         + G  
Sbjct: 195 IGNMEKELAETLKVINELSPEIPKLIKELEGVEKRLRDLDALAEEINALQLETRKREGNV 254

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
              E    +  +   + +      E +    +  K S +   K+    +   +++ N ++
Sbjct: 255 KALEAKLQELEKRIEESRSHLRELEEKVRESNKLKGSAELYLKLVEFRKQYVDEKANGEK 314

Query: 261 DEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEK 320
             ++    +S +E++L        + I E+ ++   L+      ++  K+  + + LK  
Sbjct: 315 LAENYRAQISGIEERLAELSDMK-NRIGELEKKREELKKKLAELEESVKAYEEARALKTN 373

Query: 321 LVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELD 380
           L +L   L      I+ L  ++    KR    + EL  + +  G  ++   ER    +  
Sbjct: 374 LDRLRKRLKFEPEEIERLAAEIEAAKKRKEEIQRELEEINEKRGELKNRVSER---NKAI 430

Query: 381 PHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRK 436
                     P    +         + +   E+K +S E     S+ R +   + K
Sbjct: 431 IELKKAKGKCPVCNRELTEEHRKGLMERYLAEVKDVSKEIKELDSQERKLRRELVK 486


>gi|28317279|gb|AAO39639.1| AT19678p [Drosophila melanogaster]
          Length = 1339

 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 49/348 (14%), Positives = 129/348 (37%), Gaps = 39/348 (11%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 444 ELDEIAESIELLTLDKEMAEERMETLQMELEMAQERNDELSL------DVEILKAEQEEQ 497

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFF 200
             +RIE     + + +  +  +    +     L      LRE ++ L   +  E + G  
Sbjct: 498 QGQRIEKSEKQIGSGV--TNQSAGEFL----RLEQYNQRLRETVVRLRDTLAEEKQIG-- 549

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           ++   +++    +I     + +    +VD+      + +  +D 
Sbjct: 550 ----------------QRTHKELETKHSEINELKSIKELLSRRVDNMEMQLMDLKEQVDA 593

Query: 261 DEDDSAHT--LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                A    L++++ +L  +V    DE+ E+   L  +Q+  +   ++ ++      L+
Sbjct: 594 SLGAEAMVTQLASLKLELEDRVKLLEDEVNEL-EALEQIQEQLIESNQELET-----DLR 647

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           E++ KL G + + + + +  +E LYD    IM     + +L +   ++ D  L       
Sbjct: 648 EEIDKLSGHVKILEQQKNAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSS 707

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            +        +  + ++++  +        +  +IK++ +       E
Sbjct: 708 ANESQQEDGSNQSQTDYQHIFSVSKAYGRALEQQIKTVELRLQRQHLE 755


>gi|195378803|ref|XP_002048171.1| GJ13813 [Drosophila virilis]
 gi|194155329|gb|EDW70513.1| GJ13813 [Drosophila virilis]
          Length = 1839

 Score = 37.1 bits (84), Expect = 9.1,   Method: Composition-based stats.
 Identities = 35/295 (11%), Positives = 98/295 (33%), Gaps = 14/295 (4%)

Query: 62   QMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPV 121
            ++E  +   +   ++ + G          D L+  +      +   + +   +R      
Sbjct: 808  KLERMLERFNEQSLSPIKGHPGAANSAVGDMLERQNEKLEDKLAAVREQMIVERQAARTA 867

Query: 122  RMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181
             + L ++      +   +  +A+R+E     +  +  E     +AL   +DE       +
Sbjct: 868  NLSLWKVEKQLEEALSEKKMLARRMELTEERVKKAQNEREEAQRALKSAQDEYRQRDARI 927

Query: 182  REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDR 241
             E+    A    +         +    + +  S   +   +V   E  +    +     +
Sbjct: 928  DELKAELAASKRDVLKEHRMWEKAEEERMKCKSEVIEHLANVHRLEQQVREVRQKLHQSQ 987

Query: 242  SKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNA 301
             + D      +  +R L E+ D +A        +    +   L ++++ ++ L+      
Sbjct: 988  LRCDGLGLEQKRLQRELQEERDRNAAV-----GEGTQALQAELKQLSDNFQRLKYACSIT 1042

Query: 302  VNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
             N   + +S ++ +  +             QS++D    +L + + ++     EL
Sbjct: 1043 DNQLTEVESMLEAEQQRN---------KTQQSQLDACHVKLRERNDQVTELRKEL 1088


>gi|317497564|ref|ZP_07955882.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895123|gb|EFV17287.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 61

 Score = 37.1 bits (84), Expect = 9.2,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
                +  L  RE  +++MRF  G     T  EV  +  +++ ++ ++E  A++ +K+
Sbjct: 5   ALKEAMEHLPDREYDIIKMRFFEG----KTQTEVADEIAISQAQVSRLEKNALKHMKN 58


>gi|73955665|ref|XP_860724.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 4 [Canis familiaris]
          Length = 1986

 Score = 37.1 bits (84), Expect = 9.2,   Method: Composition-based stats.
 Identities = 45/327 (13%), Positives = 102/327 (31%), Gaps = 12/327 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD                A    E+ 
Sbjct: 1447 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEAEAREKETKALSLARALEEAL 1506

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + +       +DDV +   ++E + +  +    ++ +  E  E++ +
Sbjct: 1507 ETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDELQ 1566

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-- 314
              ++ +      + AM+ Q    +    ++  E  R L           +DE+       
Sbjct: 1567 ATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALAV 1626

Query: 315  ---KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  L   +       D +++QL  +  ++   + EL    +     RD   
Sbjct: 1627 ASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEIF 1682

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEFR 428
             + +  E     +       + E  +             ++ +EI + +      + E R
Sbjct: 1683 AQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEKR 1742

Query: 429  HIVSMVRKGECEASIAKKEMVEANLRL 455
             + + + + E E    +  M   N R 
Sbjct: 1743 RLEARIAQLEEELEEEQSNMELLNDRF 1769


>gi|229015496|ref|ZP_04172494.1| RNA polymerase sigma-H factor [Bacillus cereus AH1273]
 gi|229021705|ref|ZP_04178287.1| RNA polymerase sigma-H factor [Bacillus cereus AH1272]
 gi|228739573|gb|EEL89987.1| RNA polymerase sigma-H factor [Bacillus cereus AH1272]
 gi|228745783|gb|EEL95787.1| RNA polymerase sigma-H factor [Bacillus cereus AH1273]
          Length = 219

 Score = 37.1 bits (84), Expect = 9.3,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|297687346|ref|XP_002821184.1| PREDICTED: LOW QUALITY PROTEIN: WD repeat-containing protein
            C10orf79-like [Pongo abelii]
          Length = 1608

 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 39/298 (13%), Positives = 94/298 (31%), Gaps = 36/298 (12%)

Query: 129  GSIELLSREGEIAIAKRIEAGRAMMMASLC-ESPLTFQALIIWRDELNDGTTLLREIIDL 187
              +EL SRE +I     ++     +  +   E    ++        + +    +REII  
Sbjct: 994  SQLELHSREEKINQIILLKDIIYKVKTAFNNEFDAAYKQKEFEIARVKERNVRIREII-- 1051

Query: 188  EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSP 247
               +  E +   +                + E     E        AK       +    
Sbjct: 1052 ---LDLELEEAVWQPEFEDCETPERTLVVQDE-----EVIPQPAFMAKPDAVWTEEERKQ 1103

Query: 248  PENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKD 307
             ++ E   + L+E+ D    +L A   +L+  +  +     E  + L             
Sbjct: 1104 FKDYEKKVKELNEERDKYRKSLEAELKKLQNSIQESTQAFDEHLKRLFE----------- 1152

Query: 308  EKSSVKCKVLKEKLVKLVGSLSLNQSRI-----DLLVEQLYDISKRIMHNEGELLRLAQS 362
                   + +K ++V     L ++         + L  +   ++  ++  + E  + +++
Sbjct: 1153 -------RRVKAEMVTNQEELKISNKAFSLLLDEELSSRERFLNNYLIRKQHEKSQTSEA 1205

Query: 363  YGIKRDVFLERHQGRELDPHWVSYAKDFP-EGEWKNFVACEVDSILKIRNEIKSISVE 419
                R+  L+ ++    +        D   + E+      +VD + K+      IS +
Sbjct: 1206 VRKSRED-LDVYKEHYDNLLAEDKVMDRSFKKEFSEIPGHQVDILYKLFKRRPRISKQ 1262


>gi|183985668|gb|AAI66177.1| LOC100158525 protein [Xenopus (Silurana) tropicalis]
          Length = 1601

 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 52/360 (14%), Positives = 121/360 (33%), Gaps = 22/360 (6%)

Query: 61   EQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDP 120
            ++ME+ + +L +     +    L +E  +E +  LA     +    + +       TD  
Sbjct: 991  KKMEEDILVLEDQNSKFLKEKKLLEERIAESTSQLAEEEEKAKNLAKLKNKQEMMITDLE 1050

Query: 121  VRMYLREMGSIELLSREGEIAIAKRIEAGRA-MMMASLCESPLTFQAL----IIWRDELN 175
             R+   E           E+  AKR   G    +   + E     + L        +EL 
Sbjct: 1051 ERLKKEE-------KTRQELEKAKRKLDGETTDLQDQIAELQAQIEELKLQLAKKEEELQ 1103

Query: 176  DGTTLLREIIDLEAC---IGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
                   E +  +     +  E +       E    +K   +  EK++ D+ E    +++
Sbjct: 1104 AALARGDEEVLQKNNTLKVVRELQAQIAELQEDLESEKASRNKAEKQKRDLSEELEALKT 1163

Query: 233  AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
              + + D  +         E +   L +  ++      A   ++R +   AL+E++E   
Sbjct: 1164 ELEDTLDTTAAQQELRTKREQEVAELKKSIEEETRNHEAQIQEMRQRQATALEELSEQLE 1223

Query: 293  ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHN 352
            + +  + N    ++  +S  K      +L   V SL   ++  +   ++L    + +   
Sbjct: 1224 QAKRFKGNLEKNKQSLESDNK------ELATEVKSLQQMKAESEYKRKKLEGQVQELHTK 1277

Query: 353  EGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNE 412
              E  RL     +++   L+            +  K     +    +  ++    ++  E
Sbjct: 1278 VLEGDRLRAD-MVEKSSKLQNELENVSSLLEEAEKKGIKLAKDAASLESQLQDTQELLQE 1336


>gi|156031090|ref|XP_001584870.1| hypothetical protein SS1G_14153 [Sclerotinia sclerotiorum 1980]
 gi|154700544|gb|EDO00283.1| hypothetical protein SS1G_14153 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 1111

 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 51/359 (14%), Positives = 111/359 (30%), Gaps = 31/359 (8%)

Query: 3   IGKKRNRDSDSEHEDSDDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQ 62
              +  +  ++   +  D    + S +S K  I+  + +     E+++  L   E S E 
Sbjct: 519 TIVEEIKAKEAPAAEKVDLSNVESSIESIKAGIEEIKTKEVPAAEKVD--LSHIESSVES 576

Query: 63  MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSA--SNSSVFLQKRKDSADRSTDDP 120
           ++ +V  +    I   +  DL + E S +S+        S      +K   S   ++ + 
Sbjct: 577 IKASVEEIKTKEIPAAEKVDLSNVEASIESIKATVEEIKSKEVPTAEKVDLSNVEASIES 636

Query: 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTL 180
           ++  + E+       +  E  ++++++         L     +  ++    DE+      
Sbjct: 637 IKASIEEI-------KTKEAPVSEKVD---------LSSIEASIASVKSTVDEIKTKEAP 680

Query: 181 LREIIDLEACIGP-ESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239
           + E +DL +      S        +       E     K    ++  +  +E        
Sbjct: 681 VSEKVDLSSIEASIASVKSTVDEIKAKESPVSEPVDLSKIESSIESVKAIVEEIKAKEVP 740

Query: 240 DRSKVDSPPENAEN-------DERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYR 292
              KVD     A         DE       +  A  LS +E  +   V   +DEI     
Sbjct: 741 TSEKVDLSVIEASIASVKHTVDEIKATPAPEQHAVDLSNIESSI-AAVKATVDEIKATPA 799

Query: 293 ELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMH 351
                 D +               +K        ++ L+   I+  +  +      I  
Sbjct: 800 PAHEATDLSNIESSLAALRSTVDEIKATPAPEQKTIDLSN--IESSIAAVKATVDEIKA 856


>gi|154483308|ref|ZP_02025756.1| hypothetical protein EUBVEN_01009 [Eubacterium ventriosum ATCC
           27560]
 gi|149735818|gb|EDM51704.1| hypothetical protein EUBVEN_01009 [Eubacterium ventriosum ATCC
           27560]
          Length = 934

 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 77/201 (38%), Gaps = 12/201 (5%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           +L D    LR ++D +     +   G   G    + Q+ E     K  + ++ T   IE 
Sbjct: 188 KLGDEAKRLRRLVDDQNKSIGQYIDGIRCGDSFVARQQLEAIKNNKTENGIENTIDFIEE 247

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPK--------VMCAL 284
                +D    ++      E    ++D+   +     SA + +L  +         +  L
Sbjct: 248 LINNDQDLLKVINERIIKTEKALSDVDKKLVEVNRDNSAKKQKLNAEQFIESNKPNLEVL 307

Query: 285 DEIAEVYRELRSLQDNAVNGQKD-EKSSVKCKVLKEKLVKLVGSLSLNQSR---IDLLVE 340
           ++  E+ +E   ++       K+ E+   +   L +   + V  L L +++    + L +
Sbjct: 308 EKRVELCKEEEPVRKELEYKIKEQEQLMPRYDKLFDTEKEYVNELKLIKTKGSEFESLCK 367

Query: 341 QLYDISKRIMHNEGELLRLAQ 361
            + +++K +  N+  L +L  
Sbjct: 368 DIENLNKVLATNKENLQKLKD 388


>gi|149512366|ref|XP_001510342.1| PREDICTED: similar to Scaffold attachment factor B, partial
           [Ornithorhynchus anatinus]
          Length = 391

 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 42/228 (18%), Positives = 72/228 (31%), Gaps = 7/228 (3%)

Query: 46  IEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASS-----AS 100
           ++EL   L    +  E +E ++   S   I + D +D   E  +E  L +          
Sbjct: 79  MKELPDHLLEHALDEEGIESSLDASSPDVIVIQDFEDQPLEPENEKILGILGETCKCDPL 138

Query: 101 NSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES 160
                  +R  + D S + PV     E       S   E A     E+ RAM   +  E 
Sbjct: 139 KEEASELERPSAQDASYEGPVPKVAEEEEDELAASHSEEEAFDLDGESTRAMARKA--EK 196

Query: 161 PLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKER 220
           PL  +        L++       ++                 + G   Q+  +     E 
Sbjct: 197 PLGVERGEASEQALDEEKMDSDTLVVESPMDQGSKASENAEASSGGEAQEAVERDSSPET 256

Query: 221 DDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHT 268
            D QE     E  A       +K  S  E  + +  ++D+  D    +
Sbjct: 257 KDCQEDSKKTEDEASQEDSPATKESSTNEGGDQNMSSVDDGPDAKVAS 304


>gi|73955663|ref|XP_860692.1| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 3 [Canis familiaris]
          Length = 1983

 Score = 37.1 bits (84), Expect = 9.4,   Method: Composition-based stats.
 Identities = 45/327 (13%), Positives = 102/327 (31%), Gaps = 12/327 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD                A    E+ 
Sbjct: 1444 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEAEAREKETKALSLARALEEAL 1503

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + +       +DDV +   ++E + +  +    ++ +  E  E++ +
Sbjct: 1504 ETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDELQ 1563

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-- 314
              ++ +      + AM+ Q    +    ++  E  R L           +DE+       
Sbjct: 1564 ATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALAV 1623

Query: 315  ---KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  L   +       D +++QL  +  ++   + EL    +     RD   
Sbjct: 1624 ASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEIF 1679

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEFR 428
             + +  E     +       + E  +             ++ +EI + +      + E R
Sbjct: 1680 AQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEKR 1739

Query: 429  HIVSMVRKGECEASIAKKEMVEANLRL 455
             + + + + E E    +  M   N R 
Sbjct: 1740 RLEARIAQLEEELEEEQSNMELLNDRF 1766


>gi|297545332|ref|YP_003677634.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296843107|gb|ADH61623.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 214

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 25/98 (25%), Positives = 39/98 (39%), Gaps = 3/98 (3%)

Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
            E   +V   +K       A + ++E     V + A+ Y   G    D++QEG IGL KA
Sbjct: 16  MEEEEVVFRAQK---GDEAALEYLLERYKSFVKAKARAYFLVGADKEDIMQEGMIGLYKA 72

Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
              +       F  +A   V + I  +I   +    IP
Sbjct: 73  IRDYKSDKLSSFKAFAELCVTRQIITAIKTATRQKHIP 110


>gi|229083413|ref|ZP_04215761.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-44]
 gi|228699846|gb|EEL52483.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-44]
          Length = 219

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG      A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGNI---DALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|225569539|ref|ZP_03778564.1| hypothetical protein CLOHYLEM_05633 [Clostridium hylemonae DSM
           15053]
 gi|225161747|gb|EEG74366.1| hypothetical protein CLOHYLEM_05633 [Clostridium hylemonae DSM
           15053]
          Length = 236

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 35/119 (29%), Positives = 58/119 (48%), Gaps = 2/119 (1%)

Query: 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRS 511
            L LV   A +   + L   D+IQEGN+ LM A  +F+           M  V+  +   
Sbjct: 109 YLPLVADAALQMHRKELFIGDMIQEGNLSLMAALRRFEG--AVDSEQEIMEEVRAGLQAF 166

Query: 512 IADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570
           I  Q+ T R    M  ++ ++  T R MS  + R+ + +E+A++L+M  E V  +LK+ 
Sbjct: 167 IESQTETRRQDKKMVSQVAELDETIRHMSEDMGRKVSVDEVAQQLSMETEQVEALLKLA 225


>gi|30260284|ref|NP_842661.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Ames]
 gi|47525348|ref|YP_016697.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49183127|ref|YP_026379.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Sterne]
 gi|49476711|ref|YP_034446.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52145123|ref|YP_081705.1| RNA polymerase factor sigma-70 [Bacillus cereus E33L]
 gi|118475864|ref|YP_893015.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis str. Al
           Hakam]
 gi|167635061|ref|ZP_02393378.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0442]
 gi|170689558|ref|ZP_02880744.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0465]
 gi|170707536|ref|ZP_02897989.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0389]
 gi|177655592|ref|ZP_02936973.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0174]
 gi|217957669|ref|YP_002336213.1| RNA polymerase factor sigma-70 [Bacillus cereus AH187]
 gi|218901296|ref|YP_002449130.1| RNA polymerase sigma-30 factor [Bacillus cereus AH820]
 gi|222093864|ref|YP_002527914.1| RNA polymerase factor sigma-70 [Bacillus cereus Q1]
 gi|225862146|ref|YP_002747524.1| RNA polymerase sigma-30 factor [Bacillus cereus 03BB102]
 gi|227812767|ref|YP_002812776.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. CDC 684]
 gi|228912833|ref|ZP_04076480.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228925347|ref|ZP_04088443.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228931596|ref|ZP_04094502.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228943900|ref|ZP_04106285.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228983349|ref|ZP_04143562.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229089225|ref|ZP_04220506.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-42]
 gi|229119756|ref|ZP_04249017.1| RNA polymerase sigma-H factor [Bacillus cereus 95/8201]
 gi|229136940|ref|ZP_04265567.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST26]
 gi|229153872|ref|ZP_04282002.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 4342]
 gi|229182488|ref|ZP_04309739.1| RNA polymerase sigma-H factor [Bacillus cereus BGSC 6E1]
 gi|229194484|ref|ZP_04321287.1| RNA polymerase sigma-H factor [Bacillus cereus m1293]
 gi|229601909|ref|YP_002864745.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0248]
 gi|254684403|ref|ZP_05148263.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. CNEVA-9066]
 gi|254724234|ref|ZP_05186019.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. A1055]
 gi|254733752|ref|ZP_05191467.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254756308|ref|ZP_05208337.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Vollum]
 gi|300119596|ref|ZP_07057140.1| RNA polymerase factor sigma-70 [Bacillus cereus SJ1]
 gi|301051831|ref|YP_003790042.1| RNA polymerase sigma-70 factor [Bacillus anthracis CI]
 gi|30253605|gb|AAP24147.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. Ames]
 gi|47500496|gb|AAT29172.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49177054|gb|AAT52430.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. Sterne]
 gi|49328267|gb|AAT58913.1| RNA polymerase sigma-30 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51978592|gb|AAU20142.1| RNA polymerase sigma-30 factor [Bacillus cereus E33L]
 gi|118415089|gb|ABK83508.1| RNA polymerase, sigma 30 subunit, SigH [Bacillus thuringiensis str.
           Al Hakam]
 gi|167529535|gb|EDR92285.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0442]
 gi|170127532|gb|EDS96406.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0389]
 gi|170666471|gb|EDT17248.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0465]
 gi|172080056|gb|EDT65154.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0174]
 gi|217066749|gb|ACJ80999.1| RNA polymerase sigma-30 factor [Bacillus cereus AH187]
 gi|218535383|gb|ACK87781.1| RNA polymerase sigma-30 factor [Bacillus cereus AH820]
 gi|221237912|gb|ACM10622.1| RNA polymerase sigma-30 factor [Bacillus cereus Q1]
 gi|225786519|gb|ACO26736.1| RNA polymerase sigma-30 factor [Bacillus cereus 03BB102]
 gi|227007411|gb|ACP17154.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. CDC 684]
 gi|228588950|gb|EEK46965.1| RNA polymerase sigma-H factor [Bacillus cereus m1293]
 gi|228600943|gb|EEK58512.1| RNA polymerase sigma-H factor [Bacillus cereus BGSC 6E1]
 gi|228629553|gb|EEK86250.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 4342]
 gi|228646478|gb|EEL02685.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST26]
 gi|228663657|gb|EEL19236.1| RNA polymerase sigma-H factor [Bacillus cereus 95/8201]
 gi|228694064|gb|EEL47746.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-42]
 gi|228776339|gb|EEM24692.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228815733|gb|EEM61969.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228828024|gb|EEM73752.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228834269|gb|EEM79810.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228846769|gb|EEM91774.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229266317|gb|ACQ47954.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0248]
 gi|298723068|gb|EFI63966.1| RNA polymerase factor sigma-70 [Bacillus cereus SJ1]
 gi|300374000|gb|ADK02904.1| RNA polymerase sigma-70 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 218

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|268580447|ref|XP_002645206.1| Hypothetical protein CBG00059 [Caenorhabditis briggsae]
 gi|187039227|emb|CAP21584.1| hypothetical protein CBG_00059 [Caenorhabditis briggsae AF16]
          Length = 495

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 29/203 (14%), Positives = 70/203 (34%), Gaps = 15/203 (7%)

Query: 272 MEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVK-LVGSLSL 330
           ++ +LR K    L  + + + E     +     +++ +  +K  +  EKL++        
Sbjct: 143 LKSELRIKNDEELRILGDYFDEAVRELEKHTETKRNLEKKLKNTMFSEKLLEEARREFQE 202

Query: 331 NQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDF 390
              +I  L E L ++  +    EG+LL   ++  +   + ++ H  RE +   +      
Sbjct: 203 KNKKISSLEETLREVQSQ---KEGKLLEKMRNQKM---LLIDAHSTRETELEKLKEIIRN 256

Query: 391 PEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVE 450
              E    +  + D    IR           I   +       +R         +    E
Sbjct: 257 QNEEICQMIETKEDLTENIRR--------ARIEHKDLHQKNKALRIQYQTIRTERHRGEE 308

Query: 451 ANLRLVISVAKKYTNRGLQFLDL 473
             ++ +    + ++ R  +  +L
Sbjct: 309 IYMKHIDKSIEIHSGRIEELEEL 331


>gi|195354180|ref|XP_002043578.1| GM17993 [Drosophila sechellia]
 gi|194127746|gb|EDW49789.1| GM17993 [Drosophila sechellia]
          Length = 1317

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 50/348 (14%), Positives = 129/348 (37%), Gaps = 39/348 (11%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 444 ELDEIAESIELLTLDKEMAEERMETLQMELEMAQERNDELSL------DVEILKAEQEEQ 497

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFF 200
             +RIE     + A +  +  +    +     L      LRE ++ L   +  E + G  
Sbjct: 498 QGQRIEKSEKQIGAGV--TTQSAGEFL----RLEQYNQRLRETVVRLRDTLAQEKQIG-- 549

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           ++   +++    +I     + +    +VD+      + +  +D 
Sbjct: 550 ----------------QRTHKELETKHSEINELKSIKELLSRRVDNMEMQLMDLKEQVDA 593

Query: 261 DEDDSAHT--LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                A    L++++ +L  +V    DE+ E+   L  +Q+  +   ++ ++      L+
Sbjct: 594 SLGAEAMVTQLASLKLELEDRVKLLEDEVNEL-EALEQIQEQLIESNQELET-----DLR 647

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           E++ KL G + + + + +  +E LYD    IM     + +L +   ++ D  L       
Sbjct: 648 EEIDKLSGQVKILEQQKNAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSS 707

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            +        +  + ++++  +        +  +IK++ +       E
Sbjct: 708 ANESQQEDGSNQSQTDYQHIFSVSKAYGRALEQQIKTVELRLQRQHLE 755


>gi|194874119|ref|XP_001973346.1| GG13399 [Drosophila erecta]
 gi|190655129|gb|EDV52372.1| GG13399 [Drosophila erecta]
          Length = 1338

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 50/348 (14%), Positives = 129/348 (37%), Gaps = 39/348 (11%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIA 141
           +L++   S + L L    +   +   + +    +  +D + +       +E+L  E E  
Sbjct: 443 ELDEIAESIELLTLDKEMAEERLETLQMELEMAQERNDELSL------DVEILKAEQEEQ 496

Query: 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE-IIDLEACIGPESKGGFF 200
             +RIE     + A +  +  +    +     L      LRE ++ L   +  E + G  
Sbjct: 497 QGQRIEKSEKQIGAGV--TTQSAGEFL----RLEQYNQRLRETVVRLRDTLAQEKQIG-- 548

Query: 201 HGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDE 260
                           ++   +++    +I     + +    +VD+      + +  +D 
Sbjct: 549 ----------------QRTHKELETKHSEINELKSIKELLSRRVDNMEVQLMDLKEQVDA 592

Query: 261 DEDDSAHT--LSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                A    L++++ +L  +V    DE+ E+   L  +Q+  +   ++ ++      L+
Sbjct: 593 SLGAEAMVTQLASLKLELEDRVKLLEDEVNEL-EALEQIQEQLIESNQELET-----DLR 646

Query: 319 EKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRE 378
           E++ KL G + + + + +  +E LYD    IM     + +L +   ++ D  L       
Sbjct: 647 EEIDKLSGQVKILEQQKNAAMESLYDRDVTIMKFRDLVRQLQEQLQLRADGTLSIEDFSS 706

Query: 379 LDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISE 426
            +        +  + ++++  +        +  +IK++ +       E
Sbjct: 707 ANESQQEDGSNQSQTDYQHIFSVSKAYGRALEQQIKTVELRLQRQHLE 754


>gi|30018364|ref|NP_829995.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 14579]
 gi|206972181|ref|ZP_03233128.1| RNA polymerase sigma-30 factor [Bacillus cereus AH1134]
 gi|218231038|ref|YP_002364943.1| RNA polymerase factor sigma-70 [Bacillus cereus B4264]
 gi|228950642|ref|ZP_04112776.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228956535|ref|ZP_04118331.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229040999|ref|ZP_04189762.1| RNA polymerase sigma-H factor [Bacillus cereus AH676]
 gi|229067859|ref|ZP_04201176.1| RNA polymerase sigma-H factor [Bacillus cereus F65185]
 gi|229077389|ref|ZP_04210049.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-2]
 gi|229107780|ref|ZP_04237416.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-15]
 gi|229125611|ref|ZP_04254643.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-Cer4]
 gi|229142900|ref|ZP_04271341.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST24]
 gi|229148503|ref|ZP_04276759.1| RNA polymerase sigma-H factor [Bacillus cereus m1550]
 gi|229176694|ref|ZP_04304098.1| RNA polymerase sigma-H factor [Bacillus cereus 172560W]
 gi|229188379|ref|ZP_04315427.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 10876]
 gi|296500928|ref|YP_003662628.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
 gi|29893904|gb|AAP07196.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 14579]
 gi|206732755|gb|EDZ49930.1| RNA polymerase sigma-30 factor [Bacillus cereus AH1134]
 gi|218158995|gb|ACK58987.1| RNA polymerase sigma-30 factor [Bacillus cereus B4264]
 gi|228595053|gb|EEK52824.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 10876]
 gi|228606737|gb|EEK64154.1| RNA polymerase sigma-H factor [Bacillus cereus 172560W]
 gi|228634919|gb|EEK91492.1| RNA polymerase sigma-H factor [Bacillus cereus m1550]
 gi|228640521|gb|EEK96910.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST24]
 gi|228657803|gb|EEL13609.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-Cer4]
 gi|228675629|gb|EEL30837.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-15]
 gi|228705923|gb|EEL58249.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-2]
 gi|228715218|gb|EEL67077.1| RNA polymerase sigma-H factor [Bacillus cereus F65185]
 gi|228727296|gb|EEL78490.1| RNA polymerase sigma-H factor [Bacillus cereus AH676]
 gi|228803100|gb|EEM49922.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228808993|gb|EEM55478.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|296321980|gb|ADH04908.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
          Length = 219

 Score = 37.1 bits (84), Expect = 9.5,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG    + A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGN---TDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|89100740|ref|ZP_01173595.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
 gi|89084557|gb|EAR63703.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
          Length = 212

 Score = 37.1 bits (84), Expect = 9.6,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 5/106 (4%)

Query: 422 ISISEFRHIVSM-----VRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
           +   E ++ + +     +       S A   +++     V + A+ Y   G    D++QE
Sbjct: 1   MINEEEKNYLQLEDEEIIELVHRGESEALDYLIQKYRNFVRAKARSYFLIGADKEDIVQE 60

Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
           G IGL KA   F       F  +A   + + I  +I   +    IP
Sbjct: 61  GMIGLYKAIRDFKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 106


>gi|158295916|ref|XP_316519.4| AGAP006479-PA [Anopheles gambiae str. PEST]
 gi|157016262|gb|EAA11777.4| AGAP006479-PA [Anopheles gambiae str. PEST]
          Length = 1792

 Score = 37.1 bits (84), Expect = 9.7,   Method: Composition-based stats.
 Identities = 48/330 (14%), Positives = 101/330 (30%), Gaps = 30/330 (9%)

Query: 139  EIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGG 198
            EI    +IE  R +  A   E    +Q  +  +D L +    LR+ +     I  +S   
Sbjct: 1036 EITAVTQIEQARLVSQADTEEIHAAYQRTVKDKDVLENENVALRQEVRRLQRIAADSHEL 1095

Query: 199  FFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNL 258
              H     +     +                          D +  +SP ++        
Sbjct: 1096 KTHSRSVSNASSTNEEDYGYTSGRNTLDIRRASPHPYEDPSDSTVGESPEKDQ------- 1148

Query: 259  DEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK 318
                       +A+  ++R        +  ++ +EL  L+ ++    +D   + + +V  
Sbjct: 1149 -----------TAIILRMRKLFEEEKSKSEQLRKELARLKKSSTFSTEDSIRASELEVEN 1197

Query: 319  EKLVKLVGSLSLNQSR------IDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLE 372
            EKL +    L  +  R      +D     L +  KR       L  +            +
Sbjct: 1198 EKLRQDYNLLRNSIKRGVESREMDAQYGALQEELKRRREECISLKAVLAQQSQSLRSLGQ 1257

Query: 373  RHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVS 432
               G E         +     + +  V  +++S      E+++I+     ++ E   I+ 
Sbjct: 1258 TANGAETSLRIHDEGELMEAFQAQKLVNRQLES------ELRAITDANNETLVENNRIID 1311

Query: 433  MVRKGECEASIAKKEMVEANLRLVISVAKK 462
             +R    E     ++ VE     V     +
Sbjct: 1312 GLRTENGELQAILQQHVEQVGEEVDLETVR 1341


>gi|16198483|gb|AAH15922.1| Trafficking protein, kinesin binding 1 [Homo sapiens]
 gi|119585042|gb|EAW64638.1| trafficking protein, kinesin binding 1, isoform CRA_a [Homo
           sapiens]
 gi|167774167|gb|ABZ92518.1| trafficking protein, kinesin binding 1 [synthetic construct]
          Length = 688

 Score = 37.1 bits (84), Expect = 9.7,   Method: Composition-based stats.
 Identities = 45/290 (15%), Positives = 101/290 (34%), Gaps = 22/290 (7%)

Query: 82  DLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGE-- 139
           D +DEE         +      V   +R     ++ +D        + ++  L  E E  
Sbjct: 16  DCQDEERKPTHRQHDTQDLLEEVLCAERVGQMTKTYND--------IDAVTRLLEEKERD 67

Query: 140 IAIAKRIEAGRAMMMASLCESPLTFQA----LIIWRDELNDGTTLLREIIDLEACIGPES 195
           + +A RI         +L E     +     +     +L    ++  E++        ES
Sbjct: 68  LELAARIGQSLLKKNKTLTERNELLEEQVEHIREEVSQLRHELSMKDELLQFYTSAAEES 127

Query: 196 KGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDE 255
           +      T     +           D +Q+   D+E    V + + S++ +     E  E
Sbjct: 128 EPESVCSTPLKRNESSSSVQNYFHLDSLQKKLKDLEEENVVLRSEASQLKTETITYEEKE 187

Query: 256 RNLDED----EDDSAHTLSAMEDQLRPKVMCA---LDEIAEVYRELRSLQDNAVNGQ-KD 307
           + L  D      D+   ++++ ++L  K   A    +EI  +  ++  LQ  A     ++
Sbjct: 188 QQLVNDCVKELRDANVQIASISEELAKKTEDAARQQEEITHLLSQIVDLQKKAKACAVEN 247

Query: 308 EKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELL 357
           E+        K+   +L   L   + +    +E L++  + + +   + +
Sbjct: 248 EELVQHLGAAKDAQRQLTAELRELEDKYAECMEMLHEAQEELKNLRNKTM 297


>gi|326477112|gb|EGE01122.1| RNA polymerase Rpb1 C-terminal repeat domain-containing protein
            [Trichophyton equinum CBS 127.97]
          Length = 1387

 Score = 37.1 bits (84), Expect = 9.8,   Method: Composition-based stats.
 Identities = 43/293 (14%), Positives = 97/293 (33%), Gaps = 15/293 (5%)

Query: 80   GDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR--STDDPVRMYLREMGSIELLSRE 137
             D L + + + D L  A     S V   +++  A R     D VR+ +          + 
Sbjct: 757  EDTLVETQKARDDLLRARDELESEVDHIQKEIEAAREAHERDIVRLRMEA-------EKS 809

Query: 138  GEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLR-EIIDLEACIGPESK 196
             E A+A++ E    +      E        +  R++   G    + E +D          
Sbjct: 810  EEKALAEQKERLEDLFQEIKNEDDRLAAEHLKAREDELLGQLAAKQEELDANDAALKSKV 869

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                   E    +K E + +  E + ++E   + ++  +  + +     +  E    D  
Sbjct: 870  EELRVTQEELDEKKAELAEKFSELEALKEELVNTKNGLEAKQQECESRQNELELTRKDLE 929

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKV 316
                  ++    L    D     V    + +A +  E R+ ++     ++  ++ +  K 
Sbjct: 930  ETKRHHEEELAALRDALDIQTNNVKEIKERLANMVLEHRTQEETWQKAREGYEAQLSEKA 989

Query: 317  LKEKLVKLVGSLS-----LNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364
             + KL      +        + R+  +VE++      +  +   L +   S G
Sbjct: 990  EELKLSNEEKEVLEREGLAKEERLQSIVEEMRQTHNNLNKDRERLKKTLHSLG 1042


>gi|255536707|ref|XP_002509420.1| interferon-induced guanylate-binding protein, putative [Ricinus
           communis]
 gi|223549319|gb|EEF50807.1| interferon-induced guanylate-binding protein, putative [Ricinus
           communis]
          Length = 1065

 Score = 37.1 bits (84), Expect = 9.8,   Method: Composition-based stats.
 Identities = 66/464 (14%), Positives = 149/464 (32%), Gaps = 29/464 (6%)

Query: 223 VQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD---SAHTLSAMEDQLRPK 279
           +++    +    + S+  +S+       A N+++ L +D         +  ++ D+    
Sbjct: 518 IEDKMTLLNKQLEASEKHKSEYMQRYNEAINEKKKLADDYMKRISDMQSSRSLLDERCSS 577

Query: 280 VMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLV 339
           ++ AL+   +   + +   D  ++ QK ++     ++   K         L  +      
Sbjct: 578 LVKALESAKQEMSDWKRKHDQLLSKQKADEDQTSSEIAVLKSRSSATEARLAAAH----- 632

Query: 340 EQLYDISKRIMHNEG--ELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKN 397
           EQ     +     +   ++        +++   ++   G+E         +D    E+ +
Sbjct: 633 EQTKSAQEEAAEWKRKYDITVRETKAALEKAAIVQERTGKETQLR-----EDALREEFYS 687

Query: 398 FVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457
            +A +   I +    I+           E +   S ++  + E S  K E ++       
Sbjct: 688 QLAEKEREIKEKNGRIEHAEQCLTTLNLELKAAESKMKSFDSEISSLKLE-IKEWSEKFE 746

Query: 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517
           S   K  +   +   L QE            +   G +F  +A   V+     +  +   
Sbjct: 747 SANAKAQSYEREARILEQE--------KIHLEQKYGSEFERFA--EVQDRCHHAENECKR 796

Query: 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577
              +    R       R    +           E AK+    +E  +  L    + I + 
Sbjct: 797 ATELADKARADAASAQREKSELQKLAMERLAQIERAKRHIESLEREKNDLADEVDRIRIT 856

Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 637
                   + L   +E++     L        R +  + L  L   E +   +      +
Sbjct: 857 EMEAVSRVALLEARVEEREKEIELLLKSNNEERASNVKALKELLDAERKAHSVANKRAED 916

Query: 638 TDHTLEEVGKQFC-VTRERIR-QIEAKAI-RKLKHPSRSKKLRS 678
               LEE   +   + +E    ++   A+  KLK  S  K+LRS
Sbjct: 917 FSLQLEEARAKLDALQQEFTSVRLNESALDNKLKATSHGKRLRS 960


>gi|189526704|ref|XP_001342673.2| PREDICTED: dynactin subunit 1 [Danio rerio]
          Length = 1226

 Score = 37.1 bits (84), Expect = 9.8,   Method: Composition-based stats.
 Identities = 35/234 (14%), Positives = 80/234 (34%), Gaps = 17/234 (7%)

Query: 173 ELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIES 232
           EL      L ++ + ++ +  +         E     K    ++E+  +++ +T   IE 
Sbjct: 203 ELEKHKIQLEQLQEWKSKMQEQQNELQKQLKEAKREAKEALEAKERYMEEMADTADAIEM 262

Query: 233 AAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKV-----MCALDEI 287
           A    +    + +S    A+  +  +DE   D       +E++          +  L+E 
Sbjct: 263 ATLDKEMAEERAESLQLEADALKERVDELTMDLEILKHEIEEKGSDGAASSYHVKQLEEQ 322

Query: 288 AEVYREL---------RSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLL 338
               +E             Q++    +  EK + +   L+    KL   + + +  ID L
Sbjct: 323 NARLKEALVRMRDLSASEKQEHGKQQKLMEKKNFELDALRCHKEKLQEEMKMAEKTIDEL 382

Query: 339 VEQLY---DISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKD 389
            EQ+       + +       L L +     R+   +     E++      A++
Sbjct: 383 KEQVDASLGAEEMVEMLTERNLDLEEKVRELRETVADLEAINEMNDELQENARE 436


>gi|73955659|ref|XP_536636.2| PREDICTED: similar to myosin, heavy polypeptide 10, non-muscle
            isoform 1 [Canis familiaris]
          Length = 1976

 Score = 37.1 bits (84), Expect = 9.8,   Method: Composition-based stats.
 Identities = 45/327 (13%), Positives = 102/327 (31%), Gaps = 12/327 (3%)

Query: 137  EGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESK 196
            + +  IA  +E  +      L E           RD                A    E+ 
Sbjct: 1437 DHQRQIASNLEKKQKKFDQLLAEEKNISARYAEERDRAEAEAREKETKALSLARALEEAL 1496

Query: 197  GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDER 256
                     +   + +       +DDV +   ++E + +  +    ++ +  E  E++ +
Sbjct: 1497 ETKEEFERQNKQLRADMEDLISSKDDVGKNVHELEKSKRALEQQVEEMRTQLEELEDELQ 1556

Query: 257  NLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC-- 314
              ++ +      + AM+ Q    +    ++  E  R L           +DE+       
Sbjct: 1557 ATEDAKLRLEVNMQAMKAQFERDLQTRDEQNEEKKRLLVKQVRELEAELEDERKQRALAV 1616

Query: 315  ---KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFL 371
               K L+  L  L   +       D +++QL  +  ++   + EL    +     RD   
Sbjct: 1617 ASKKKLEIDLKDLEAQIEAANKARDEVIKQLRKLQAQMKDYQREL----EEARASRDEIF 1672

Query: 372  ERHQGRELDPHWVSYAKDFPEGEWKNFVACEV---DSILKIRNEIKSISVETGISISEFR 428
             + +  E     +       + E  +             ++ +EI + +      + E R
Sbjct: 1673 AQSKESEKKLKSLEAEILQLQEELASSERARRHAEQERDELADEIANSASGKSALLDEKR 1732

Query: 429  HIVSMVRKGECEASIAKKEMVEANLRL 455
             + + + + E E    +  M   N R 
Sbjct: 1733 RLEARIAQLEEELEEEQSNMELLNDRF 1759


>gi|228989302|ref|ZP_04149293.1| RNA polymerase sigma-H factor [Bacillus pseudomycoides DSM 12442]
 gi|228995485|ref|ZP_04155153.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock3-17]
 gi|229003108|ref|ZP_04160957.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock1-4]
 gi|228758144|gb|EEM07340.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock1-4]
 gi|228764214|gb|EEM13093.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock3-17]
 gi|228770380|gb|EEM18953.1| RNA polymerase sigma-H factor [Bacillus pseudomycoides DSM 12442]
          Length = 219

 Score = 37.1 bits (84), Expect = 9.9,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485
           E   IV +VRKG      A + ++      V + ++ Y   G    D++QEG IGL KA 
Sbjct: 17  EDEAIVELVRKGNI---DALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAI 73

Query: 486 EKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522
             +       F  +A   + + I  +I   +    IP
Sbjct: 74  RDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|125973444|ref|YP_001037354.1| condensin subunit Smc [Clostridium thermocellum ATCC 27405]
 gi|125713669|gb|ABN52161.1| condensin subunit Smc [Clostridium thermocellum ATCC 27405]
          Length = 1190

 Score = 37.1 bits (84), Expect = 9.9,   Method: Composition-based stats.
 Identities = 54/321 (16%), Positives = 117/321 (36%), Gaps = 14/321 (4%)

Query: 157  LCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ 216
            L +     +  +   D L      L   I  E     E        +E       +    
Sbjct: 742  LAQIEENIKRSLARIDMLKQEKEQL---IRQEKDTCLELSKYEDELSEIERDIAEKKEVV 798

Query: 217  EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQL 276
             + ++  +E +   ++      D R  V+S  E+ E  +  L+   ++    + AME + 
Sbjct: 799  ARYQEKNKEEQSVRDALHNDITDYRISVNSILESMEGVKETLERLVNEKNSLVKAMERKK 858

Query: 277  RPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLK-EKLVKLVGSLSLNQSRI 335
                     E A   +E+++LQ+      K  K   + K  K  ++ ++     + +   
Sbjct: 859  --------AEKARNEQEIKALQEKNEGLDKLIKKYEEEKSGKTFEIDRITEEKKIREEES 910

Query: 336  DLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEW 395
              +++Q+ +I+K I+  + E  R+      K +  +E  Q R  D + ++Y       + 
Sbjct: 911  AGIIDQITEINKNILLLQEEYSRIEVK-KAKLESEMESIQNRMWDEYELTYTNALELKKD 969

Query: 396  KNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRL 455
               +A     I +IRNEIK +      +I E+            + S   ++  +   ++
Sbjct: 970  IGSMAQAQKRIAEIRNEIKELGPVNVAAIDEYIKTKERFEFMSAQKSD-MEQAEKKLQKV 1028

Query: 456  VISVAKKYTNRGLQFLDLIQE 476
            +  +      + ++   LI E
Sbjct: 1029 INEMMTIMKRQFMEKFKLINE 1049


  Database: nr
    Posted date:  May 22, 2011 12:22 AM
  Number of letters in database: 999,999,966
  Number of sequences in database:  2,987,313
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 22, 2011 12:30 AM
  Number of letters in database: 999,999,796
  Number of sequences in database:  2,903,041
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 22, 2011 12:36 AM
  Number of letters in database: 999,999,281
  Number of sequences in database:  2,904,016
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 22, 2011 12:41 AM
  Number of letters in database: 999,999,960
  Number of sequences in database:  2,935,328
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 22, 2011 12:46 AM
  Number of letters in database: 842,794,627
  Number of sequences in database:  2,394,679
  
Lambda     K      H
   0.310    0.120    0.289 

Lambda     K      H
   0.267   0.0366    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,624,919,225
Number of Sequences: 14124377
Number of extensions: 363893278
Number of successful extensions: 1990185
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 23797
Number of HSP's successfully gapped in prelim test: 24943
Number of HSP's that attempted gapping in prelim test: 1787268
Number of HSP's gapped (non-prelim): 157711
length of query: 682
length of database: 4,842,793,630
effective HSP length: 146
effective length of query: 536
effective length of database: 2,780,634,588
effective search space: 1490420139168
effective search space used: 1490420139168
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 84 (37.1 bits)